Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003291.1 Hibiscus syriacus cultivar Beakdansim tig00006921_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: 134134
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1000 original size:83 final size:85
Alignment explanation
Indices: 857--1107 Score: 328
Period size: 83 Copynumber: 3.0 Consensus size: 85
847 TACCATGCGG
* * * * * * *
857 TTGATATGTCATTGAGCTGAATGGAATCGAAC-CGATAGTTTTTTGTTGACAGATAACCCTTATC
1 TTGATATGCCCTTGAGCTGAATGTAATCAAACTCGA-AGGTCTTTGTTGACAGATAACCCTTCTC
921 GCCTTGAGCTATGCTGTAAAT
65 GCCTTGAGCTATGCTGTAAAT
** * *
942 TTGATATGCCCTTGAGCTGAATGTAATTGAACTCG-AGG-GTTTGTTGACAGATAACCCTTCTCA
1 TTGATATGCCCTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
*
1005 CCTTGAGTTATGCTGTAAAT
66 CCTTGAGCTATGCTGTAAAT
* * * *
1025 TTGGTATGCCTTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAGCCCTTCTTG
1 TTGATATGCCCTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
1090 CCTTGAGCTATGCTGTAA
66 CCTTGAGCTATGCTGTAA
1108 TAGGCTGGAG
Statistics
Matches: 145, Mismatches: 18, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
83 72 0.50
84 5 0.03
85 66 0.46
86 2 0.01
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.35
Consensus pattern (85 bp):
TTGATATGCCCTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAACCCTTCTCG
CCTTGAGCTATGCTGTAAAT
Found at i:1373 original size:64 final size:64
Alignment explanation
Indices: 1299--1551 Score: 381
Period size: 64 Copynumber: 4.0 Consensus size: 64
1289 GCGTTGTTTC
* * * * *
1299 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTGACTCTAAATAAAACTAGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1363 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
*
1427 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAA---G-TTGTT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
* * * *
1487 GAGTCCAATATCC-TCGCTGCGAAGTTGAAATTAACTCTGAATGAAACTGGACAGTTGTTTATT
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
1550 GA
1 GA
1552 CAGACAACTT
Statistics
Matches: 174, Mismatches: 11, Indels: 9
0.90 0.06 0.05
Matches are distributed among these distances:
59 36 0.21
60 18 0.10
61 1 0.01
62 1 0.01
63 6 0.03
64 112 0.64
ACGTcount: A:0.31, C:0.14, G:0.22, T:0.34
Consensus pattern (64 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGGAAAGTTGTTTGTT
Found at i:2208 original size:32 final size:32
Alignment explanation
Indices: 2126--2209 Score: 89
Period size: 32 Copynumber: 2.6 Consensus size: 32
2116 CGCATCAGGA
* * *
2126 TTGAATTCCCAAATATGCCCCAATATTCGATG
1 TTGAATTCTCAAAAATGCCCCAACATTCGATG
* *
2158 TTGAA-TCTCAAAAAATGCCCTAACATTTGATG
1 TTGAATTCTC-AAAAATGCCCCAACATTCGATG
* *
2190 TTGAATTTTCAAAGATGCCC
1 TTGAATTCTCAAAAATGCCC
2210 ATTGTTCCTC
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
31 3 0.07
32 37 0.86
33 3 0.07
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.32
Consensus pattern (32 bp):
TTGAATTCTCAAAAATGCCCCAACATTCGATG
Found at i:3264 original size:13 final size:13
Alignment explanation
Indices: 3248--3272 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3238 TTTTTGTTTA
3248 TCTTTTTATTTTC
1 TCTTTTTATTTTC
3261 TCTTTTTATTTT
1 TCTTTTTATTTT
3273 TTTTTCTCTT
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:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (13 bp):
TCTTTTTATTTTC
Found at i:3286 original size:19 final size:19
Alignment explanation
Indices: 3250--3285 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
3240 TTTGTTTATC
3250 TTTTTATTTTCTCTTTTTA
1 TTTTTATTTTCTCTTTTTA
3269 TTTTT-TTTTCTCTTTTT
1 TTTTTATTTTCTCTTTTT
3286 TCTTTTTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.06, C:0.11, G:0.00, T:0.83
Consensus pattern (19 bp):
TTTTTATTTTCTCTTTTTA
Found at i:3297 original size:18 final size:18
Alignment explanation
Indices: 3258--3297 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
3248 TCTTTTTATT
*
3258 TTCTCTTTTTATTTTTTT
1 TTCTCTTTTTATTTTTTG
3276 TTCTCTTTTT-TCTTTTTG
1 TTCTCTTTTTAT-TTTTTG
3294 TTCT
1 TTCT
3298 GATTGGATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (18 bp):
TTCTCTTTTTATTTTTTG
Found at i:6158 original size:16 final size:16
Alignment explanation
Indices: 6137--6168 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
6127 ATTAGCACCC
6137 TTGTACTGCCCTTTCA
1 TTGTACTGCCCTTTCA
6153 TTGTACTGCCCTTTCA
1 TTGTACTGCCCTTTCA
6169 GTGCCAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.31, G:0.12, T:0.44
Consensus pattern (16 bp):
TTGTACTGCCCTTTCA
Found at i:27976 original size:14 final size:14
Alignment explanation
Indices: 27957--27986 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
27947 TGTTTCTCCC
27957 ACCGGCAACTTTCT
1 ACCGGCAACTTTCT
27971 ACCGGCAACTTTCT
1 ACCGGCAACTTTCT
27985 AC
1 AC
27987 AGCAAAGTAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.23, C:0.37, G:0.13, T:0.27
Consensus pattern (14 bp):
ACCGGCAACTTTCT
Found at i:32084 original size:21 final size:21
Alignment explanation
Indices: 32060--32162 Score: 84
Period size: 21 Copynumber: 5.0 Consensus size: 21
32050 GCAAATTCGC
32060 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* ** ***
32081 GTTGAAAATCGCAACGCGAT-
1 GTTGCATTTCGCGTTGCGATA
*
32101 TTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
32122 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
32142 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
32163 ATCTACAGTT
Statistics
Matches: 58, Mismatches: 22, Indels: 4
0.69 0.26 0.05
Matches are distributed among these distances:
20 28 0.48
21 30 0.52
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.35
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:32106 original size:41 final size:41
Alignment explanation
Indices: 32061--32162 Score: 168
Period size: 41 Copynumber: 2.5 Consensus size: 41
32051 CAAATTCGCG
32061 TTGCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATT
1 TTGCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATT
***
32102 TTGCATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATT
1 TTGCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATT
*
32143 TTCCATTTCGCGTTGCGATA
1 TTGCATTTCGCGTTGCGATA
32163 ATCTACAGTT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 57 1.00
ACGTcount: A:0.21, C:0.20, G:0.25, T:0.35
Consensus pattern (41 bp):
TTGCATTTCGCGTTGCGATAGTTGAAAATCGCAACGCGATT
Found at i:32119 original size:20 final size:20
Alignment explanation
Indices: 32096--32161 Score: 78
Period size: 20 Copynumber: 3.2 Consensus size: 20
32086 AAATCGCAAC
32096 GCGATTTTGCATTTCGCGTT
1 GCGATTTTGCATTTCGCGTT
* * **
32116 GCGATAGTTGAAAATCGCGTT
1 GCGAT-TTTGCATTTCGCGTT
*
32137 GCGATTTTCCATTTCGCGTT
1 GCGATTTTGCATTTCGCGTT
32157 GCGAT
1 GCGAT
32162 AATCTACAGT
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 20 0.56
21 16 0.44
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.38
Consensus pattern (20 bp):
GCGATTTTGCATTTCGCGTT
Found at i:33096 original size:24 final size:24
Alignment explanation
Indices: 33069--33159 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
33059 CATAATTCAA
*
33069 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
33093 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
33117 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
33140 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
33160 TCAAATTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:33139 original size:47 final size:48
Alignment explanation
Indices: 33069--33159 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
33059 CATAATTCAA
* * *
33069 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
33117 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
33160 TCAAATTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:35661 original size:18 final size:18
Alignment explanation
Indices: 35638--35672 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
35628 GTCAACGATC
35638 AACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTA
35656 AACGGGTCGGGTCGGGT
1 AACGGGTCGGGTCGGGT
35673 CGGGTTATGA
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:0.14, C:0.17, G:0.51, T:0.17
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTA
Found at i:37781 original size:24 final size:24
Alignment explanation
Indices: 37754--37844 Score: 121
Period size: 24 Copynumber: 3.8 Consensus size: 24
37744 CATAATTCAA
*
37754 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
37778 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
37802 GTCAA-TATCAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
37825 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
37845 TCAATTTTGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
23 21 0.36
24 37 0.64
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:37824 original size:47 final size:48
Alignment explanation
Indices: 37754--37844 Score: 139
Period size: 47 Copynumber: 1.9 Consensus size: 48
37744 CATAATTCAA
* * *
37754 GTCAAGTATCATATCAGAATCCAGGTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
*
37802 GTCAA-TATCAGATCAGAATCCAGGTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAAT
37845 TCAATTTTGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
47 34 0.87
48 5 0.13
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (48 bp):
GTCAAGTATCAGATCAGAATCCAGGTCAGGTATCAGAACAGAATCCAT
Found at i:41272 original size:30 final size:30
Alignment explanation
Indices: 41216--41369 Score: 256
Period size: 30 Copynumber: 5.1 Consensus size: 30
41206 GAAGGACCTA
* * *
41216 TCCAGAGGTCACAAAGA-CCCCGGTAACTA
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
*
41245 TCCAGAGGTCACAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
41275 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
41305 TCCAGAGGTCATAAAGATCCTCGGTAACTG
1 TCCAGAGGTCATAAAGATCCTCGGTAACTG
41335 TCCAGAGGTCATAAAGATCCTCGGTAAACTG
1 TCCAGAGGTCATAAAGATCCTCGGT-AACTG
41366 TCCA
1 TCCA
41370 TATGTCTCAA
Statistics
Matches: 120, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
29 17 0.14
30 94 0.78
31 9 0.08
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.21
Consensus pattern (30 bp):
TCCAGAGGTCATAAAGATCCTCGGTAACTG
Found at i:42904 original size:21 final size:21
Alignment explanation
Indices: 42874--42918 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
42864 ATTCTGTCAT
* *
42874 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
42895 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
42916 TTG
1 TTG
42919 CCCAGAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:45873 original size:30 final size:30
Alignment explanation
Indices: 45814--45962 Score: 237
Period size: 30 Copynumber: 5.0 Consensus size: 30
45804 CCCGAAGGAC
* *
45814 CTATCCAGAGGTCACAAAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
45843 CTATCCAGAGGTCACAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
45873 CTGTCCAGAGGTCATAAAGATCCTCCGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
45903 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
45933 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
45963 ACTGTCCATA
Statistics
Matches: 112, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
29 20 0.18
30 92 0.82
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:47402 original size:14 final size:14
Alignment explanation
Indices: 47378--47411 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
47368 TACTAGCAAC
47378 TTAAA-CGAACTTA
1 TTAAACCGAACTTA
47391 TTAAACCGAACTTA
1 TTAAACCGAACTTA
47405 TTAAACC
1 TTAAACC
47412 AATATTCGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.44, C:0.21, G:0.06, T:0.29
Consensus pattern (14 bp):
TTAAACCGAACTTA
Found at i:47525 original size:21 final size:21
Alignment explanation
Indices: 47495--47539 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
47485 ATTCTGTCGT
* *
47495 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
47516 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
47537 TTG
1 TTG
47540 CCCAGAACTC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:48584 original size:6 final size:6
Alignment explanation
Indices: 48573--48611 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
48563 GGGTGTTACA
48573 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
48612 CGGCGGCGGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.51, G:0.15, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:49136 original size:6 final size:6
Alignment explanation
Indices: 49105--49180 Score: 117
Period size: 6 Copynumber: 13.5 Consensus size: 6
49095 TCTCGTCTCG
49105 GGTCG- GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCG- GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
49148 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
49181 AATACGTGTC
Statistics
Matches: 69, Mismatches: 0, Indels: 3
0.96 0.00 0.04
Matches are distributed among these distances:
5 25 0.36
6 44 0.64
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:49180 original size:18 final size:17
Alignment explanation
Indices: 49105--49176 Score: 121
Period size: 17 Copynumber: 4.3 Consensus size: 17
49095 TCTCGTCTCG
49105 GGTCGGGTCG-GGTCG-
1 GGTCGGGTCGTGGTCGT
49120 GGTCGGGTCGTGGTCGT
1 GGTCGGGTCGTGGTCGT
49137 GGTCGGGTCGTGGTCGT
1 GGTCGGGTCGTGGTCGT
49154 GGTCGTGGTCGTGGTCGT
1 GGTCG-GGTCGTGGTCGT
49172 GGTCG
1 GGTCG
49177 TGGTAATACG
Statistics
Matches: 54, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
15 10 0.19
16 5 0.09
17 22 0.41
18 17 0.31
ACGTcount: A:0.00, C:0.18, G:0.54, T:0.28
Consensus pattern (17 bp):
GGTCGGGTCGTGGTCGT
Found at i:49339 original size:20 final size:20
Alignment explanation
Indices: 49314--49430 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
49304 ACTGTAGACT
49314 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
49334 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
*
49355 ATCGCAACGCGAACTGGAAA
1 ATCGCAACGCGAAATGGAAA
49375 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
49395 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
49415 ATCGCAACGCGAAATG
1 ATCGCAACGCGAAATG
49431 CAACGCGAAT
Statistics
Matches: 85, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
20 70 0.82
21 15 0.18
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:58323 original size:35 final size:34
Alignment explanation
Indices: 58238--58325 Score: 99
Period size: 35 Copynumber: 2.5 Consensus size: 34
58228 ATTTGATATT
*
58238 TAAATACAACAAACTTACAATAAGAATTAAATGG
1 TAAATACAACAAAATTACAATAAGAATTAAATGG
* *
58272 TAAATGATAACCAAATTACAATAACTGATATTAAATGG
1 TAAAT-ACAACAAAATTACAATAA--GA-ATTAAATGG
58310 T-AATA-AACAAAATTAC
1 TAAATACAACAAAATTAC
58326 TAAAATATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
34 5 0.11
35 25 0.54
36 1 0.02
37 5 0.11
38 10 0.22
ACGTcount: A:0.55, C:0.11, G:0.08, T:0.26
Consensus pattern (34 bp):
TAAATACAACAAAATTACAATAAGAATTAAATGG
Found at i:58944 original size:18 final size:18
Alignment explanation
Indices: 58921--58955 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
58911 CGATGACGGT
58921 ATCATATATGGTTGCGGC
1 ATCATATATGGTTGCGGC
58939 ATCATATATGGTTGCGG
1 ATCATATATGGTTGCGG
58956 TGGCTGCTGG
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:0.23, C:0.14, G:0.29, T:0.34
Consensus pattern (18 bp):
ATCATATATGGTTGCGGC
Found at i:60599 original size:111 final size:111
Alignment explanation
Indices: 60462--60683 Score: 390
Period size: 111 Copynumber: 2.0 Consensus size: 111
60452 ATTACAAAAA
* * *
60462 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
*
60527 AATTAAAACATTAAAATGTTATCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
60573 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
1 TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
* *
60638 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTGGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
60684 ATGATTTCCA
Statistics
Matches: 105, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
111 105 1.00
ACGTcount: A:0.45, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTCTTAATCTAATAATCATGCATTAAATAAATAAACTAAATATTACTAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
Found at i:60832 original size:10 final size:11
Alignment explanation
Indices: 60814--60868 Score: 66
Period size: 10 Copynumber: 5.5 Consensus size: 11
60804 AAAAAAGAGT
60814 ATTTGAGAGAA
1 ATTTGAGAGAA
*
60825 ATTT-AGAG-T
1 ATTTGAGAGAA
60834 ATTTGAGAGAA
1 ATTTGAGAGAA
60845 ATTT-AGAG-A
1 ATTTGAGAGAA
60854 ATTTGAGAG-A
1 ATTTGAGAGAA
60864 ATTTG
1 ATTTG
60869 GTGTGATAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
9 9 0.23
10 22 0.56
11 8 0.21
ACGTcount: A:0.40, C:0.00, G:0.25, T:0.35
Consensus pattern (11 bp):
ATTTGAGAGAA
Found at i:60834 original size:20 final size:20
Alignment explanation
Indices: 60809--60864 Score: 103
Period size: 20 Copynumber: 2.8 Consensus size: 20
60799 ACTTAAAAAA
60809 AGAGTATTTGAGAGAAATTT
1 AGAGTATTTGAGAGAAATTT
60829 AGAGTATTTGAGAGAAATTT
1 AGAGTATTTGAGAGAAATTT
*
60849 AGAGAATTTGAGAGAA
1 AGAGTATTTGAGAGAA
60865 TTTGGTGTGA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.43, C:0.00, G:0.27, T:0.30
Consensus pattern (20 bp):
AGAGTATTTGAGAGAAATTT
Found at i:61045 original size:50 final size:50
Alignment explanation
Indices: 60991--61116 Score: 150
Period size: 50 Copynumber: 2.5 Consensus size: 50
60981 AGATATCCAG
* *
60991 GTATAGCGCGGATCAGGGGGCGCGTTATACCCACGTGGCGCCAGATCACC
1 GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
*
61041 GTATATAGCG-GGA-CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCAGC
1 G--TATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
* * *
61091 ATATAACGCGG-TGCAGGGGGTGCGCT
1 GTATAGCGCGGAT-CAGGGGGCGCGCT
61117 TTCCTGCTAA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
48 6 0.09
49 2 0.03
50 47 0.72
51 3 0.05
52 7 0.11
ACGTcount: A:0.21, C:0.27, G:0.36, T:0.16
Consensus pattern (50 bp):
GTATAGCGCGGATCAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACC
Found at i:61050 original size:52 final size:50
Alignment explanation
Indices: 60992--61088 Score: 158
Period size: 50 Copynumber: 1.9 Consensus size: 50
60982 GATATCCAGG
* *
60992 TATAGCGCGGATCAGGGGGCGCGTTATACCCACGTGGCGCCAGATCACCGTA
1 TATAGCG-GGA-CAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTA
61044 TATAGCGGGACAGGGGGCGCGCTATACCCACGTGGCGCCAAATCA
1 TATAGCGGGACAGGGGGCGCGCTATACCCACGTGGCGCCAAATCA
61089 GCATATAACG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
50 33 0.77
51 3 0.07
52 7 0.16
ACGTcount: A:0.23, C:0.29, G:0.33, T:0.15
Consensus pattern (50 bp):
TATAGCGGGACAGGGGGCGCGCTATACCCACGTGGCGCCAAATCACCGTA
Found at i:70437 original size:29 final size:28
Alignment explanation
Indices: 70405--70473 Score: 70
Period size: 29 Copynumber: 2.4 Consensus size: 28
70395 TAGCAGTTCG
70405 AAAAAAAACTATTCGAAAG-AAAAA-GGAAA
1 AAAAAAAAC-A-T-GAAAGAAAAAATGGAAA
*
70434 AAAAAAGACATGAAAGAAAAAAATGGAAA
1 AAAAAAAACATGAAAG-AAAAAATGGAAA
70463 ACAAAAAAACA
1 A-AAAAAAACA
70474 AAAGTGTGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 5 0.15
27 1 0.03
28 6 0.18
29 14 0.41
30 8 0.24
ACGTcount: A:0.72, C:0.07, G:0.13, T:0.07
Consensus pattern (28 bp):
AAAAAAAACATGAAAGAAAAAATGGAAA
Found at i:82939 original size:16 final size:17
Alignment explanation
Indices: 82907--82939 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
82897 GACTTTGACC
82907 CAAAAAGTCAAATTTTT
1 CAAAAAGTCAAATTTTT
*
82924 CAAAAAGTCATATTTT
1 CAAAAAGTCAAATTTT
82940 AGGTTTTTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
CAAAAAGTCAAATTTTT
Found at i:83464 original size:3 final size:3
Alignment explanation
Indices: 83456--83493 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
83446 GAGACTATCA
83456 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
83494 AAATAAATTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:84652 original size:118 final size:119
Alignment explanation
Indices: 84529--84742 Score: 256
Period size: 118 Copynumber: 1.8 Consensus size: 119
84519 ATATTTTATA
* * * *
84529 ATATTTTGAATTAAGACCATTAATT-TATATATTTTTACAA-TTTAATCAC-TGAGGTTTAATAT
1 ATATTTAGAATTAAGACCATTAATTGT-GATA-TTTTACAATTTTAATC-CTTGAGCTTTAAAAT
** *
84591 TTTAATTTTAAATAATA-TTTTAGGATTATTTACACTAATAATACCTAGATTTCATG
63 AATAATTTTAAATAATATTTTTAGAATTATTTACACTAATAATACCTAGATTTCATG
* *** *
84647 ATATTTAGAATTAGGATTTTTAATTGTGATATTTTACAATTTTAATCCTTTAGCTTTAAAATAAT
1 ATATTTAGAATTAAGACCATTAATTGTGATATTTTACAATTTTAATCCTTGAGCTTTAAAATAAT
*
84712 AATTTTAAATATTATTTTTAGAATTATTTAC
66 AATTTTAAATAATATTTTTAGAATTATTTAC
84743 TATTATAGTA
Statistics
Matches: 79, Mismatches: 13, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
117 9 0.11
118 54 0.68
119 16 0.20
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (119 bp):
ATATTTAGAATTAAGACCATTAATTGTGATATTTTACAATTTTAATCCTTGAGCTTTAAAATAAT
AATTTTAAATAATATTTTTAGAATTATTTACACTAATAATACCTAGATTTCATG
Found at i:86393 original size:20 final size:20
Alignment explanation
Indices: 86354--86410 Score: 55
Period size: 20 Copynumber: 3.0 Consensus size: 20
86344 TTTCATTTTA
*
86354 CATTCACATCTTTGCATTTG
1 CATTCACATCTTTACATTTG
* *
86374 CATTCGCATCTTTACGTTTG
1 CATTCACATCTTTACATTTG
* *
86394 TATTTACAT-TTT-CATTT
1 CATTCACATCTTTACATTT
86411 TTTACATTTG
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
18 4 0.13
19 3 0.10
20 23 0.77
ACGTcount: A:0.19, C:0.21, G:0.09, T:0.51
Consensus pattern (20 bp):
CATTCACATCTTTACATTTG
Found at i:90743 original size:64 final size:63
Alignment explanation
Indices: 90593--90755 Score: 219
Period size: 58 Copynumber: 2.6 Consensus size: 63
90583 TGAGACTTTT
* *
90593 AGAGTCAATTTTAACTTCACAGCGAAGGATATTGGACTCAACAAATAACTTTTCAATTTCATTC
1 AGAGTCAATTTCAA-TTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAATTTCATTC
* *
90657 AGAGTCAA---C--TTCACAGCGAAGGATATTGGGCTCAACAAACAACTTTTCAGTTTCATTC
1 AGAGTCAATTTCAATTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAATTTCATTC
* *
90715 AGAGTCAATTTCAAATTTACAGCGAAGGATATTGAACTCAA
1 AGAGTCAATTTC-AATTCACAGCGAAGGATATTGGACTCAA
90756 ATCAATACAA
Statistics
Matches: 86, Mismatches: 7, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
58 54 0.63
61 1 0.01
64 31 0.36
ACGTcount: A:0.36, C:0.19, G:0.15, T:0.29
Consensus pattern (63 bp):
AGAGTCAATTTCAATTCACAGCGAAGGATATTGGACTCAACAAACAACTTTTCAATTTCATTC
Found at i:90888 original size:103 final size:103
Alignment explanation
Indices: 90709--90905 Score: 313
Period size: 103 Copynumber: 1.9 Consensus size: 103
90699 CTTTTCAGTT
* * *
90709 TCATTCAGAGTCAATTTCAAATTTACAGCGAAGGATATTGAACTCAAATCAATACAACCAAAGAT
1 TCATTCAGAGTCAATTTAAAATTCACAGCGAAGGATATTGAACTCAAAGCAATACAACCAAAGAT
*
90774 TGGATTTCAACTTCACAATGAAGGATATCAAATTCAAA
66 TGGATTTCAACTTCACAACGAAGGATATCAAATTCAAA
* * **
90812 TCATTTAGAGTCAATTTAAAATTCACAGTGAAGGATATTGAACTCAAAGCAATACAATGAAAGAT
1 TCATTCAGAGTCAATTTAAAATTCACAGCGAAGGATATTGAACTCAAAGCAATACAACCAAAGAT
*
90877 TGGATTTCAACTTCACGACGAAGGATATC
66 TGGATTTCAACTTCACAACGAAGGATATC
90906 GTGTCCACCA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
103 85 1.00
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (103 bp):
TCATTCAGAGTCAATTTAAAATTCACAGCGAAGGATATTGAACTCAAAGCAATACAACCAAAGAT
TGGATTTCAACTTCACAACGAAGGATATCAAATTCAAA
Found at i:91485 original size:137 final size:137
Alignment explanation
Indices: 91287--91850 Score: 914
Period size: 137 Copynumber: 4.1 Consensus size: 137
91277 GTCCACCAAC
*
91287 AACAATGTCATCCACCGATCAGAACTCCTCATCACGAATGAGCAACATCATTCTTAGATAGCCAG
1 AACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAGCCAG
* * *
91352 ATGTCCTCATCACGAAAGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTTATC
66 ACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATC
91417 ACGAAGG
131 ACGAAGG
* *
91424 AACAATGTCATCCACCGATCAGAATTCCTCATCATGAAGGAGCAACATCATTCTTAGATAGCCAG
1 AACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAGCCAG
*
91489 ACGTTCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATC
66 ACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATC
91554 ACGAAGG
131 ACGAAGG
* *
91561 AACAATGTCATCCACCGATCAGAATTCCTCATCACGAATGAGCAACATCATTCTTAGATAGCCAG
1 AACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAGCCAG
*
91626 ACGTCCTCATTACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATC
66 ACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATC
91691 ACGAAGG
131 ACGAAGG
* * * * * *
91698 AACAAAGTCATCCACTGATCAGAACTCCTCATCACGTAGGAGTAGA-GTTATTCTTAGATAGCCA
1 AACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCA-ACATCATTCTTAGATAGCCA
* * *
91762 GATGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTCAAAGATGGCCAGACTTCCTCAT
65 GACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCAT
*
91827 CATGAAGG
130 CACGAAGG
* *
91835 AACAATATCATACACC
1 AACAATGTCATCCACC
91851 AGTTGGATCT
Statistics
Matches: 398, Mismatches: 28, Indels: 2
0.93 0.07 0.00
Matches are distributed among these distances:
137 397 1.00
138 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (137 bp):
AACAATGTCATCCACCGATCAGAACTCCTCATCACGAAGGAGCAACATCATTCTTAGATAGCCAG
ACGTCCTCATCACGAAGGAACCGTGTTATCTCAAATATCTTTAAAGATGGCCAGACGTCCTCATC
ACGAAGG
Found at i:93115 original size:118 final size:118
Alignment explanation
Indices: 92990--93243 Score: 257
Period size: 118 Copynumber: 2.1 Consensus size: 118
92980 TAGGGTTAAA
* *
92990 TTACACTATTAGTACTTATATTTTATAATATTTTA-AATTAAGACCATTAATTTAT-ATATTTTT
1 TTACACTA-TAGTACTTAGATTTCATAATA-TTTAGAATTAAGACCATTAATTT-TGATA-TTTT
* ** *
93053 ACAA-TTTAATCAC-TGAGGTTTAATATTTTAATTTTAAATAATA-TTTTAGGATTAT
62 ACAATTTTAATC-CTTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
* * * * ***
93108 TTACACTAATAATACCTAGATTTCATGATATTTAGAATTAGGATTTTTAATTTTGATATTTTACA
1 TTACACT-ATAGTACTTAGATTTCATAATATTTAGAATTAAGACCATTAATTTTGATATTTTACA
* * *
93173 ATTTTAATCCTTTAGTTTTAAAATAATAATTTTAAATATTATTTTTAGAATTAT
65 ATTTTAATCCTTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
*
93227 TTACTATTATAGTACTT
1 TTAC-ACTATAGTACTT
93244 TGCATATTAA
Statistics
Matches: 110, Mismatches: 19, Indels: 13
0.77 0.13 0.09
Matches are distributed among these distances:
117 14 0.13
118 71 0.65
119 23 0.21
120 2 0.02
ACGTcount: A:0.37, C:0.07, G:0.06, T:0.50
Consensus pattern (118 bp):
TTACACTATAGTACTTAGATTTCATAATATTTAGAATTAAGACCATTAATTTTGATATTTTACAA
TTTTAATCCTTGAGGTTTAAAATAATAATTTTAAATAATATTTTTAGAATTAT
Found at i:99394 original size:13 final size:13
Alignment explanation
Indices: 99378--99416 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
99368 AAACCAGTCC
*
99378 GACCCTACCCGTT
1 GACCCAACCCGTT
* *
99391 GACCCGACCTGTT
1 GACCCAACCCGTT
99404 GACCCAACCCGTT
1 GACCCAACCCGTT
99417 TACCGTTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.44, G:0.18, T:0.21
Consensus pattern (13 bp):
GACCCAACCCGTT
Found at i:112550 original size:60 final size:61
Alignment explanation
Indices: 112427--112553 Score: 143
Period size: 60 Copynumber: 2.1 Consensus size: 61
112417 GAACATATGA
* * **
112427 ATAGTC-AAGTGACTATTTTGTAACTTTTAATAGTCGAATGACTCAACAAAGCAACGTCAT
1 ATAGTCGAAGTGACTATTTTGTAACTTGTAATAGTCGAATGACTCAACAAAACAACACCAT
* * * * *
112487 ATAGTCGAA-TGATTATTTTGTAACTTGTAATAGTCGGGA-GACTCAACAAAATAGCACCCT
1 ATAGTCGAAGTGACTATTTTGTAACTTGTAATAGTC-GAATGACTCAACAAAACAACACCAT
112547 ATAGTCG
1 ATAGTCG
112554 GGGACTATTT
Statistics
Matches: 56, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
60 52 0.93
61 4 0.07
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (61 bp):
ATAGTCGAAGTGACTATTTTGTAACTTGTAATAGTCGAATGACTCAACAAAACAACACCAT
Found at i:116420 original size:41 final size:40
Alignment explanation
Indices: 116375--116453 Score: 104
Period size: 41 Copynumber: 1.9 Consensus size: 40
116365 AATCTTTTAG
** *
116375 ATTTAAAATTTTTAGTTTGATTATTTTATTATTAATTTTTT
1 ATTTAAAAGCTTTAATTTGATTATTTTATTATT-ATTTTTT
**
116416 ATTTAGGAGCTTTAATTTGATTATTTTATTATTATTTT
1 ATTTAAAAGCTTTAATTTGATTATTTTATTATTATTTT
116454 AGTTAAGAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
40 5 0.15
41 28 0.85
ACGTcount: A:0.28, C:0.01, G:0.08, T:0.63
Consensus pattern (40 bp):
ATTTAAAAGCTTTAATTTGATTATTTTATTATTATTTTTT
Found at i:119367 original size:29 final size:29
Alignment explanation
Indices: 119325--119383 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
119315 ATTTTCACCT
119325 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
119354 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
119383 A
1 A
119384 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:124038 original size:29 final size:29
Alignment explanation
Indices: 123996--124054 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
123986 ATTTTCACCT
123996 AACTAAATTGATGTAACCAATGACATCAA
1 AACTAAATTGATGTAACCAATGACATCAA
*
124025 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAACCAATGACATCAA
124054 A
1 A
124055 TTAATTTAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAACCAATGACATCAA
Found at i:124108 original size:2 final size:2
Alignment explanation
Indices: 124101--124157 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
124091 ATTTTCAACA
124101 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
124143 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
124158 GTTCTAGAAG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:124313 original size:12 final size:13
Alignment explanation
Indices: 124294--124326 Score: 59
Period size: 12 Copynumber: 2.6 Consensus size: 13
124284 TAAATCTTTG
124294 TATATTTTAATTA
1 TATATTTTAATTA
124307 T-TATTTTAATTA
1 TATATTTTAATTA
124319 TATATTTT
1 TATATTTT
124327 TGATTTGATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 12 0.63
13 7 0.37
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TATATTTTAATTA
Found at i:125108 original size:39 final size:39
Alignment explanation
Indices: 125065--125143 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
125055 ATTGATTTTA
125065 GATCTACGGCGTTTTGAAACTCAGATTTGAATTTCTGTT
1 GATCTACGGCGTTTTGAAACTCAGATTTGAATTTCTGTT
125104 GATCTACGGCGTTTTGAAACTCAGATTTGAATTTCTGTT
1 GATCTACGGCGTTTTGAAACTCAGATTTGAATTTCTGTT
125143 G
1 G
125144 TTGTTACAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.23, C:0.15, G:0.22, T:0.41
Consensus pattern (39 bp):
GATCTACGGCGTTTTGAAACTCAGATTTGAATTTCTGTT
Found at i:129583 original size:32 final size:35
Alignment explanation
Indices: 129547--129624 Score: 92
Period size: 35 Copynumber: 2.3 Consensus size: 35
129537 TTTTTAGAAA
* *
129547 ATAAAAAAA-TATTTA-A-ATTTAAAATATAAAAT
1 ATAAAAAAATTATTAAGATATTTAAAAAATAAAAT
*
129579 ATAAAAAAATTATTAAGATATTTAAAAAATTAAAT
1 ATAAAAAAATTATTAAGATATTTAAAAAATAAAAT
*
129614 A-AAAAATATTA
1 ATAAAAAAATTA
129625 CGAATTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
32 9 0.23
33 5 0.13
34 10 0.26
35 15 0.38
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.33
Consensus pattern (35 bp):
ATAAAAAAATTATTAAGATATTTAAAAAATAAAAT
Found at i:129641 original size:30 final size:31
Alignment explanation
Indices: 129582--129645 Score: 78
Period size: 30 Copynumber: 2.1 Consensus size: 31
129572 ATAAAATATA
129582 AAAAAATTATTAAGATATTTAAAAAATTAAAT
1 AAAAAATTATTAAGATATTTAAAAAATT-AAT
* **
129614 AAAAAA-TATTACGA-ATTTAAATTATTAAT
1 AAAAAATTATTAAGATATTTAAAAAATTAAT
129643 AAA
1 AAA
129646 GTTTAATTTA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
29 6 0.21
30 10 0.34
31 7 0.24
32 6 0.21
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.34
Consensus pattern (31 bp):
AAAAAATTATTAAGATATTTAAAAAATTAAT
Found at i:132740 original size:63 final size:63
Alignment explanation
Indices: 132665--132886 Score: 347
Period size: 63 Copynumber: 3.5 Consensus size: 63
132655 CCTATGTAAA
* *
132665 CTGTTCATATGTTCCTTAGAACATAGGTATATTGTCCATATGTCCAGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCCAGAAAGACATAGGTAATT
* * *
132728 CTGTCCATATGTTCCGTT-GAACATAGGTATACTGTCTATATATCCTGAAAGACATAGGTAATT
1 CTGTCCATATGTTCC-TTAGAACATAGGTATACTGTCCATATGTCCAGAAAGACATAGGTAATT
* * *
132791 ATGTCCATATGTTCCGTAGAACATAGGTATACTGTCCATATGTCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCCAGAAAGACATAGGTAATT
*
132854 CTATCCATATGTTCCTTAGAACATAGGTATACT
1 CTGTCCATATGTTCCTTAGAACATAGGTATACT
132887 CCTCGACTCT
Statistics
Matches: 144, Mismatches: 13, Indels: 4
0.89 0.08 0.02
Matches are distributed among these distances:
62 1 0.01
63 141 0.98
64 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (63 bp):
CTGTCCATATGTTCCTTAGAACATAGGTATACTGTCCATATGTCCAGAAAGACATAGGTAATT
Found at i:132878 original size:32 final size:32
Alignment explanation
Indices: 132665--132882 Score: 191
Period size: 32 Copynumber: 6.9 Consensus size: 32
132655 CCTATGTAAA
*
132665 CTGTTCATATGTTCCTTAGAACATAGGT-ATAT
1 CTGTCCATATGTTCCTTAGAACATAGGTAAT-T
** *
132697 -TGTCCATATG-TCCAGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCTTAGA-ACATAGGTAATT
*
132728 CTGTCCATATGTTCCGTT-GAACATAGGT-ATA
1 CTGTCCATATGTTCC-TTAGAACATAGGTAATT
* * * *
132759 CTGTCTATAT-ATCCTGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCTTAGA-ACATAGGTAATT
* * *
132791 ATGTCCATATGTTCCGTAGAACATAGGT-ATA
1 CTGTCCATATGTTCCTTAGAACATAGGTAATT
** *
132822 CTGTCCATATG-TCCCGAAAGACATAGGTAATT
1 CTGTCCATATGTTCCTTAGA-ACATAGGTAATT
*
132854 CTATCCATATGTTCCTTAGAACATAGGTA
1 CTGTCCATATGTTCCTTAGAACATAGGTA
132883 TACTCCTCGA
Statistics
Matches: 145, Mismatches: 29, Indels: 24
0.73 0.15 0.12
Matches are distributed among these distances:
29 1 0.01
30 14 0.10
31 57 0.39
32 59 0.41
33 14 0.10
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.33
Consensus pattern (32 bp):
CTGTCCATATGTTCCTTAGAACATAGGTAATT
Done.