Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001813.1 Hibiscus syriacus cultivar Beakdansim tig00003672_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: 114890
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6154 original size:16 final size:16
Alignment explanation
Indices: 6133--6164 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
6123 ATTACTTAAT
6133 TTATATTTTTATTCAA
1 TTATATTTTTATTCAA
*
6149 TTATATTTTTTTTCAA
1 TTATATTTTTATTCAA
6165 AATCATATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.00, T:0.66
Consensus pattern (16 bp):
TTATATTTTTATTCAA
Found at i:17283 original size:42 final size:41
Alignment explanation
Indices: 17255--17517 Score: 402
Period size: 42 Copynumber: 6.3 Consensus size: 41
17245 TCCAAGTTCG
17255 CGTTGCGATAGTCGAAGTTCGCGTTGCGATT-TTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
*
17295 CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTATTTCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
17337 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
*
17379 CGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
17421 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
* *
17463 CATTGCGATAGTCAAAGTTCGCGTTGCGATTTATTCCAAATT
1 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TTATTCCAAATT
17505 CGTTGCGATAGTC
1 CGTTGCGATAGTC
17518 CAAAATCGCA
Statistics
Matches: 206, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
40 29 0.14
41 2 0.01
42 175 0.85
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.37
Consensus pattern (41 bp):
CGTTGCGATAGTCGAAGTTCGCGTTGCGATTATTCCAAATT
Found at i:17410 original size:84 final size:84
Alignment explanation
Indices: 17255--17520 Score: 446
Period size: 84 Copynumber: 3.2 Consensus size: 84
17245 TCCAAGTTCG
* *
17255 CGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
*
17318 TTGCGATTTATTTCAAATT
66 TTGCGATTTATTCCAAATT
17337 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
*
17402 TTGTGATTTATTCCAAATT
66 TTGCGATTTATTCCAAATT
* * * *
17421 CGTTGTGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCAAAGTTCGCG
1 CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
17486 TTGCGATTTATTCCAAATT
66 TTGCGATTTATTCCAAATT
17505 CGTTGCGATAGTCCAA
1 CGTTGCGATAGTCCAA
17521 AATCGCAACG
Statistics
Matches: 171, Mismatches: 11, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
82 28 0.16
83 2 0.01
84 141 0.82
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (84 bp):
CGTTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCGTTGCGATAGTCGAAGTTCGCG
TTGCGATTTATTCCAAATT
Found at i:17435 original size:126 final size:124
Alignment explanation
Indices: 17245--17517 Score: 447
Period size: 126 Copynumber: 2.2 Consensus size: 124
17235 ATTGCGATAG
17245 TCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGA
1 TCCAAGTT--CGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGA
* * *
17310 AGTTCGCGTTGCGATTTATTTCAAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATTTAT
64 AGTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
* *
17371 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGTGATTTATTCCAAATTCGTTGTGATAGTCGA
1 TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGA-TT-TTCCAAATTCGTTGCGATAGTCGA
*
17436 AGTTCGCGTTGCGATTTATTCCAAGTTCATTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
64 AGTTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
*
17497 TCCAAATTCGTTGCGATAGTC
1 TCCAAGTTCGTTGCGATAGTC
17518 CAAAATCGCA
Statistics
Matches: 138, Mismatches: 7, Indels: 4
0.93 0.05 0.03
Matches are distributed among these distances:
124 28 0.20
125 2 0.01
126 108 0.78
ACGTcount: A:0.21, C:0.19, G:0.24, T:0.36
Consensus pattern (124 bp):
TCCAAGTTCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCGAAG
TTCGCGTTGCGATTTATTCCAAATTCATTGCGATAGTCAAAGTTCGCGTTGCGATTTAT
Found at i:18288 original size:6 final size:6
Alignment explanation
Indices: 18277--18315 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
18267 TCTCGTCTCG
18277 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
18316 AATACGTGTC
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:0.00, C:0.15, G:0.51, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:18470 original size:42 final size:42
Alignment explanation
Indices: 18408--18512 Score: 201
Period size: 42 Copynumber: 2.5 Consensus size: 42
18398 TGCGATTTTG
*
18408 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
18450 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
18492 GACTATCGCAACGAACTTGGA
1 GACTATCGCAACGAACTTGGA
18513 CTATCACAAC
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:18516 original size:61 final size:61
Alignment explanation
Indices: 18433--18573 Score: 210
Period size: 61 Copynumber: 2.3 Consensus size: 61
18423 TTTGGAATAA
* * *
18433 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTGGACTATCACAACGAACTTGGAATAAATCGCAACGCAAACTTCGACT
* *
18496 ATCGCAACGAACTTGGACTATCACAACGAATTTGGAATAAATCGCAACGCAAACTTGGACT
1 ATCGCAACGAACTTGGACTATCACAACGAACTTGGAATAAATCGCAACGCAAACTTCGACT
*
18557 ATCGCAACGAATTTGGA
1 ATCGCAACGAACTTGGA
18574 AAATCGCATT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
61 65 0.90
63 7 0.10
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (61 bp):
ATCGCAACGAACTTGGACTATCACAACGAACTTGGAATAAATCGCAACGCAAACTTCGACT
Found at i:18551 original size:42 final size:38
Alignment explanation
Indices: 18496--18581 Score: 127
Period size: 42 Copynumber: 2.2 Consensus size: 38
18486 AACTTCGACT
18496 ATCGCAACGAACTTGGACTATCACAACGAATTTGGAATAA
1 ATCGCAACGAACTTGGACTATCACAACGAATTTGG-A-AA
*
18536 ATCGCAACGCAAACTTGGACTATCGCAACGAATTTGGAAA
1 ATCGCAACG--AACTTGGACTATCACAACGAATTTGGAAA
18576 ATCGCA
1 ATCGCA
18582 TTGCGATAGT
Statistics
Matches: 43, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
40 17 0.40
41 1 0.02
42 25 0.58
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (38 bp):
ATCGCAACGAACTTGGACTATCACAACGAATTTGGAAA
Found at i:23918 original size:37 final size:37
Alignment explanation
Indices: 23858--23954 Score: 131
Period size: 37 Copynumber: 2.6 Consensus size: 37
23848 ACTTTTCGTC
* *
23858 CTACTAGGATTCAAACTCTTAAAAATATGATAGAATT
1 CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
* * * *
23895 TTGCTAGGATTTAAATTCCTAAAAATATGATAGAGTT
1 CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
*
23932 CTACTATGATTTAAACTCCTAAA
1 CTACTAGGATTTAAACTCCTAAA
23955 GATAGGATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.40, C:0.13, G:0.11, T:0.35
Consensus pattern (37 bp):
CTACTAGGATTTAAACTCCTAAAAATATGATAGAATT
Found at i:24620 original size:22 final size:26
Alignment explanation
Indices: 24570--24619 Score: 79
Period size: 23 Copynumber: 2.0 Consensus size: 26
24560 TTTATTCTAC
24570 TTATTTATATTATATATGTATATTTT
1 TTATTTATATTATATATGTATATTTT
24596 TTATTT-TATTAT-TAT-TATATTTT
1 TTATTTATATTATATATGTATATTTT
24619 T
1 T
24620 ACTTTCTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
23 9 0.38
24 3 0.12
25 6 0.25
26 6 0.25
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (26 bp):
TTATTTATATTATATATGTATATTTT
Found at i:24658 original size:12 final size:11
Alignment explanation
Indices: 24636--24675 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
24626 TCTTTCTTTT
24636 TATTATTCTTG
1 TATTATTCTTG
24647 TATTATTACTTG
1 TATTATT-CTTG
* *
24659 TATTATTTTTA
1 TATTATTCTTG
24670 TATTAT
1 TATTAT
24676 CTATTTTGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
11 15 0.58
12 11 0.42
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:29573 original size:8 final size:8
Alignment explanation
Indices: 29568--29617 Score: 59
Period size: 8 Copynumber: 6.2 Consensus size: 8
29558 GGGCAAAAAC
29568 AAAAAAGA
1 AAAAAAGA
*
29576 AAAGAAGA
1 AAAAAAGA
29584 AAAAAAGA
1 AAAAAAGA
29592 AGAAAAA-A
1 A-AAAAAGA
29600 AAGAAAA-A
1 AA-AAAAGA
29608 AAAAAAGA
1 AAAAAAGA
29616 AA
1 AA
29618 GAACAAAACT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
7 5 0.14
8 27 0.73
9 5 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (8 bp):
AAAAAAGA
Found at i:29599 original size:28 final size:28
Alignment explanation
Indices: 29568--29625 Score: 82
Period size: 28 Copynumber: 2.1 Consensus size: 28
29558 GGGCAAAAAC
* *
29568 AAAAAAGAAAAGAAGAAAA-AAAGAAGAA
1 AAAAAAGAAAA-AAAAAAAGAAAGAACAA
29596 AAAAAAGAAAAAAAAAAAGAAAGAACAA
1 AAAAAAGAAAAAAAAAAAGAAAGAACAA
29624 AA
1 AA
29626 CTCAAAAAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (28 bp):
AAAAAAGAAAAAAAAAAAGAAAGAACAA
Found at i:29617 original size:12 final size:12
Alignment explanation
Indices: 29562--29617 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 12
29552 AAAAAAGGGC
*
29562 AAAAACAAAAAA
1 AAAAAGAAAAAA
* *
29574 GAAAAG-AAGAA
1 AAAAAGAAAAAA
*
29585 AAAAAGAAGAAA
1 AAAAAGAAAAAA
29597 AAAAAGAAAAAA
1 AAAAAGAAAAAA
29609 AAAAAGAAA
1 AAAAAGAAA
29618 GAACAAAACT
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
11 9 0.25
12 27 0.75
ACGTcount: A:0.86, C:0.02, G:0.12, T:0.00
Consensus pattern (12 bp):
AAAAAGAAAAAA
Found at i:29625 original size:12 final size:11
Alignment explanation
Indices: 29575--29617 Score: 63
Period size: 10 Copynumber: 4.0 Consensus size: 11
29565 AACAAAAAAG
29575 AAAAGAAGAAA
1 AAAAGAAGAAA
29586 AAAAGAAGAAAA
1 AAAAGAAG-AAA
29598 AAAAGAA-AAA
1 AAAAGAAGAAA
29608 AAAA-AAGAAA
1 AAAAGAAGAAA
29618 GAACAAAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
9 2 0.07
10 10 0.33
11 8 0.27
12 10 0.33
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAAA
Found at i:29625 original size:16 final size:15
Alignment explanation
Indices: 29562--29639 Score: 54
Period size: 16 Copynumber: 5.2 Consensus size: 15
29552 AAAAAAGGGC
*
29562 AAAAACAAAAAAGAA
1 AAAAAAAAAAAAGAA
*
29577 AAGAAGAAAAAAAG--
1 AA-AAAAAAAAAAGAA
*
29591 -AAGAAAAAAAAGAA
1 AAAAAAAAAAAAGAA
29605 AAAAAAAAAGAAAGAA
1 AAAAAAAAA-AAAGAA
***
29621 CAAAACTCAAAAAGAA
1 -AAAAAAAAAAAAGAA
29637 AAA
1 AAA
29640 GGGACAAAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 12
0.71 0.12 0.17
Matches are distributed among these distances:
12 9 0.18
13 1 0.02
15 12 0.24
16 21 0.43
17 6 0.12
ACGTcount: A:0.82, C:0.05, G:0.12, T:0.01
Consensus pattern (15 bp):
AAAAAAAAAAAAGAA
Found at i:30272 original size:22 final size:22
Alignment explanation
Indices: 30244--30298 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
30234 GCTACCCCAT
30244 CAAACCTTTGAGCATCAAATGC
1 CAAACCTTTGAGCATCAAATGC
*
30266 CAAACCTTTGAGCATGAAATGC
1 CAAACCTTTGAGCATCAAATGC
30288 CAAACCTTTGA
1 CAAACCTTTGA
30299 CCAAACATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGC
Found at i:31338 original size:106 final size:106
Alignment explanation
Indices: 31121--32600 Score: 2117
Period size: 106 Copynumber: 14.0 Consensus size: 106
31111 ATATCGTGCC
* * * * * * *
31121 ACTCAAGACAACACATGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AACAATTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
31185 AATTTCTGAGCCAATTTTAACTTCACAGTGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
31226 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
31291 AATTTCAGATCCAATTTCAACTTCACAGCGAAGGATAATT-G
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGAT-ATTGG
* * * *
31332 AATCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAACTTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
31397 AATTTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
31438 ACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
**
31503 AATTTCAGAGCCAATTTCAACTTCACAATGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
31544 ACTTCATACAACGCAAGTTCAACTTCACGACGAAGGGACCGTTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
31609 AATTT-AGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * **
31649 ACTCCAGACAACGCAAGTTCAACTTCACAACGAAGGGACCGCTGGTTATCAACAAACAACTTATC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* *
31714 AATTTTAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
31755 ACTCCAGACAACGCAGGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
31820 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
31861 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
31926 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
31967 ACTCAAGACAACGCAAGTTCAACTTCACGATGAAGGGACGGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
*
32032 AATTTCAGAGCCAATTTCAACTTCACAGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
32073 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACCAACAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
32138 AATTTTAGAGCCAATTTCAACTTCACAACGAAGAATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
32179 ACTCAAGACAACGC-AGATTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCC
1 ACTCCAGACAACGCAAG-TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCC
*
32243 CAATTTCAGAGCCAATTTCAACTTCACAGCGTAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
32285 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
* * *
32350 AATTTCAGAGCCAATTTCAACTTCTCAGCGAAGGATCTTGA
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * **
32391 AC-CCAAGGCAACACAAGCTCAACTTCACGACGAAGAGG-CGGCTAATTGTCAAC-AA-AA-TT-
1 ACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG-GGACCGCTGGTTGTCAACAAACAACTTC
* * *
32450 TC-A-TTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
64 CCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
32491 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCG-CTGGTTGTCAACAAACAACTTCC
** *
32555 CGGTTCCAGAGCCAATTTCAACTTCACGAAG-G-AGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCAC--AGCGAAGGATATTGG
32597 ACTC
1 ACTC
32601 AGAAAAATGC
Statistics
Matches: 1242, Mismatches: 114, Indels: 37
0.89 0.08 0.03
Matches are distributed among these distances:
99 3 0.00
100 72 0.06
101 4 0.00
102 3 0.00
103 4 0.00
104 3 0.00
105 149 0.12
106 995 0.80
107 8 0.01
108 1 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAACTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:33695 original size:2 final size:2
Alignment explanation
Indices: 33688--33755 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
33678 CTTAATTAGT
33688 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
33730 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
33756 CATACTTGCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:33937 original size:21 final size:21
Alignment explanation
Indices: 33912--33956 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
33902 ATTCTACTTA
33912 TTTATATTATA-TATGTATATT
1 TTTATATTATATTAT-TATATT
*
33933 TTTATATTTTATTATTATATT
1 TTTATATTATATTATTATATT
33954 TTT
1 TTT
33957 TACTTTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 19 0.86
22 3 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (21 bp):
TTTATATTATATTATTATATT
Found at i:33996 original size:12 final size:11
Alignment explanation
Indices: 33974--34014 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
33964 TCTTTCTTTT
33974 TATTATTCTTG
1 TATTATTCTTG
33985 TATTATTACTTG
1 TATTATT-CTTG
* *
33997 TATTATTTTTA
1 TATTATTCTTG
34008 TATTATT
1 TATTATT
34015 TATTTTGTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.24, C:0.05, G:0.05, T:0.66
Consensus pattern (11 bp):
TATTATTCTTG
Found at i:34030 original size:2 final size:2
Alignment explanation
Indices: 34023--34047 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34013 TTTATTTTGT
34023 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
34048 GCGTATGTTC
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:44372 original size:21 final size:22
Alignment explanation
Indices: 44337--44458 Score: 128
Period size: 21 Copynumber: 5.7 Consensus size: 22
44327 TTGGTGCAGA
*
44337 GGGAATCGA-TCCCCCCATGA-
1 GGGAACCGATTCCCCCCATGAG
**
44357 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCCCATG-AG
* *
44380 GGGAACCGATTCCTCCCA-CAG
1 GGGAACCGATTCCCCCCATGAG
*
44401 GGGAACCGATTCCCCCCA-CAG
1 GGGAACCGATTCCCCCCATGAG
44422 GGGAACCGATTCCCCCCAT-AG
1 GGGAACCGATTCCCCCCATGAG
* *
44443 GGGAATCGATACCCCC
1 GGGAACCGATTCCCCC
44459 TGGGGTTCTG
Statistics
Matches: 88, Mismatches: 10, Indels: 7
0.84 0.10 0.07
Matches are distributed among these distances:
20 8 0.09
21 64 0.73
22 1 0.01
23 15 0.17
ACGTcount: A:0.24, C:0.37, G:0.25, T:0.15
Consensus pattern (22 bp):
GGGAACCGATTCCCCCCATGAG
Found at i:60075 original size:2 final size:2
Alignment explanation
Indices: 60070--60108 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
60060 CTTGTCTTTT
60070 TA TA TA TA TA TA TA 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 TA TA TA TA TA TA TA T
60109 GCATTTTAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:60120 original size:8 final size:8
Alignment explanation
Indices: 60109--60140 Score: 64
Period size: 8 Copynumber: 4.0 Consensus size: 8
60099 ATATATATAT
60109 GCATTTTA
1 GCATTTTA
60117 GCATTTTA
1 GCATTTTA
60125 GCATTTTA
1 GCATTTTA
60133 GCATTTTA
1 GCATTTTA
60141 ATTTAATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 24 1.00
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.50
Consensus pattern (8 bp):
GCATTTTA
Found at i:61471 original size:20 final size:20
Alignment explanation
Indices: 61435--61472 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
61425 ATCCTATTCC
**
61435 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
61455 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
61473 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:63917 original size:30 final size:30
Alignment explanation
Indices: 63883--63971 Score: 160
Period size: 30 Copynumber: 3.0 Consensus size: 30
63873 ACTTTGACTG
*
63883 ACCGTTGACTTTGACCAGAGTTGACCGTTA
1 ACCGTTAACTTTGACCAGAGTTGACCGTTA
*
63913 ACCGTTAACTTTGACCAGAGTTGACTGTTA
1 ACCGTTAACTTTGACCAGAGTTGACCGTTA
63943 ACCGTTAACTTTGACCAGAGTTGACCGTT
1 ACCGTTAACTTTGACCAGAGTTGACCGTT
63972 GACCATTGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 56 1.00
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (30 bp):
ACCGTTAACTTTGACCAGAGTTGACCGTTA
Found at i:67738 original size:18 final size:18
Alignment explanation
Indices: 67712--67755 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
67702 TAAATCAGGG
* *
67712 TCAGTAGGCTCTTTTGCT
1 TCAGCAGGCTCTTCTGCT
67730 TCAGCAGGCTCTTCTGCT
1 TCAGCAGGCTCTTCTGCT
67748 TCAGCAGG
1 TCAGCAGG
67756 ATGGGGACGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.14, C:0.27, G:0.25, T:0.34
Consensus pattern (18 bp):
TCAGCAGGCTCTTCTGCT
Found at i:80406 original size:31 final size:31
Alignment explanation
Indices: 80368--80432 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
80358 AAGAGTCGAG
*
80368 GGTTACCTATGTCATTTGGGACATATGGACA
1 GGTTACCTATGTCAGTTGGGACATATGGACA
* *
80399 GGTTACCTATGTCCGTTGGGACATATGGATA
1 GGTTACCTATGTCAGTTGGGACATATGGACA
80430 GGT
1 GGT
80433 CCTTCGGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.15, G:0.29, T:0.32
Consensus pattern (31 bp):
GGTTACCTATGTCAGTTGGGACATATGGACA
Found at i:90530 original size:20 final size:20
Alignment explanation
Indices: 90506--90559 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
90496 AACATTAAGA
90506 AATAAAATAAATAAAA-ATTT
1 AATAAAATAAATAAAACA-TT
* *
90526 CAT-AATTAAATAAAACATT
1 AATAAAATAAATAAAACATT
*
90545 AAGAAAATAAATAAA
1 AATAAAATAAATAAA
90560 TAAAACAAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.26
Consensus pattern (20 bp):
AATAAAATAAATAAAACATT
Found at i:94518 original size:76 final size:76
Alignment explanation
Indices: 94408--94603 Score: 351
Period size: 76 Copynumber: 2.6 Consensus size: 76
94398 ATTTTAAATA
*
94408 TTATATTTTATCTTT-TTTTATGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
*
94472 GGATATTATTT
66 AGATATTATTT
94483 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
94548 AGATATTATTT
66 AGATATTATTT
*
94559 TTATATTTTATCTTTGTTTTAGATATTTTAGTTTAAATA-GTTTTA
1 TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTA
94604 AGTGTTTAAT
Statistics
Matches: 117, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
75 21 0.18
76 96 0.82
ACGTcount: A:0.27, C:0.02, G:0.10, T:0.62
Consensus pattern (76 bp):
TTATATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATATGTTTTAGTATTTTAATTAAGTTTTA
AGATATTATTT
Found at i:98036 original size:5 final size:5
Alignment explanation
Indices: 98028--98101 Score: 53
Period size: 5 Copynumber: 14.8 Consensus size: 5
98018 ATATTTTTGT
* ** * * *
98028 TTTTA TTTTC TTTTA TTTTCA TTGAA CTTTA TTTAA TTCTA -TTTA TTTTA
1 TTTTA TTTTA TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA
*
98078 TTTTGA -ATTA TTTTA TTTTA TTTT
1 TTTT-A TTTTA TTTTA TTTTA TTTT
98102 TCTCTGAACA
Statistics
Matches: 51, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
4 4 0.08
5 43 0.84
6 4 0.08
ACGTcount: A:0.22, C:0.05, G:0.03, T:0.70
Consensus pattern (5 bp):
TTTTA
Found at i:100099 original size:44 final size:43
Alignment explanation
Indices: 100049--100175 Score: 123
Period size: 44 Copynumber: 3.2 Consensus size: 43
100039 TTAAATATTT
100049 TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
1 TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
* **
100092 GTATTTTAATTAAGTTTTAGG-A---TA--TT--AT---TTTTA
1 -TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
*
100125 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAA
1 TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-A
100169 TATTTTA
1 TATTTTA
100176 ATTAAGTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 24
0.67 0.07 0.25
Matches are distributed among these distances:
32 16 0.25
33 6 0.09
36 4 0.06
38 4 0.06
40 4 0.06
43 5 0.08
44 25 0.39
ACGTcount: A:0.26, C:0.01, G:0.13, T:0.61
Consensus pattern (43 bp):
TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTA
Found at i:100157 original size:76 final size:76
Alignment explanation
Indices: 100049--100250 Score: 345
Period size: 76 Copynumber: 2.7 Consensus size: 76
100039 TTAAATATTT
*
100049 TATTTTATTTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGA
*
100114 TATTATTTTTA
66 AATTATTTTTA
*
100125 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAATATTTTAATTAAGTTTTAGGA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGA
100190 AATTATTTTTA
66 AATTATTTTTA
*
100201 TATTTTATCTTTGTTTTAGGTA-TTTAGTTTAAATA-GTTTTAAGTGTTTTA
1 TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTT-AGTATTTTA
100251 GGATTTAAGA
Statistics
Matches: 120, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
74 5 0.04
75 20 0.17
76 95 0.79
ACGTcount: A:0.27, C:0.01, G:0.13, T:0.59
Consensus pattern (76 bp):
TATTTTATCTTTGTTTTAGGTATTTTAGTTTAAATAGGTTTTAGTATTTTAATTAAGTTTTAGGA
AATTATTTTTA
Found at i:100942 original size:19 final size:19
Alignment explanation
Indices: 100918--100966 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 19
100908 TTAATATTTA
*
100918 TTATTTATTATT-TCTCTTT
1 TTATTTATTATTATCT-ATT
100937 TTATTTATTATTATCTATT
1 TTATTTATTATTATCTATT
100956 TTATTTTATTA
1 TTA-TTTATTA
100967 AATCTTTTCA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.22, C:0.06, G:0.00, T:0.71
Consensus pattern (19 bp):
TTATTTATTATTATCTATT
Found at i:100963 original size:20 final size:21
Alignment explanation
Indices: 100894--100966 Score: 75
Period size: 20 Copynumber: 3.7 Consensus size: 21
100884 TAAAACCCCC
* *
100894 TTTTATCTTTATTATTA-ATA
1 TTTTATATTTATTATTATCTA
*
100914 -TTTATTATTTATTATT-TCTC
1 TTTTA-TATTTATTATTATCTA
100934 TTTT-TATTTATTATTATCTA
1 TTTTATATTTATTATTATCTA
100954 TTTTAT-TTTATTA
1 TTTTATATTTATTA
100967 AATCTTTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
19 15 0.34
20 25 0.57
21 4 0.09
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (21 bp):
TTTTATATTTATTATTATCTA
Found at i:104948 original size:44 final size:45
Alignment explanation
Indices: 104898--104987 Score: 155
Period size: 45 Copynumber: 2.0 Consensus size: 45
104888 AACACTCTAC
*
104898 CATTAAATCCATTAGATT-ATCCCCATCAGTTGATTTTTTATCAT
1 CATTAAATCCATTAGATTCATCCCCATCAGTTGATTTTCTATCAT
*
104942 CATTAAATCCATTAGATTCATCCCCATCGGTTGATTTTCTATCAT
1 CATTAAATCCATTAGATTCATCCCCATCAGTTGATTTTCTATCAT
104987 C
1 C
104988 GATGACAAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
44 18 0.42
45 25 0.58
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (45 bp):
CATTAAATCCATTAGATTCATCCCCATCAGTTGATTTTCTATCAT
Found at i:106278 original size:11 final size:11
Alignment explanation
Indices: 106262--106286 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
106252 CTTTCTTCCC
106262 TTTTTTCAATT
1 TTTTTTCAATT
106273 TTTTTTCAATT
1 TTTTTTCAATT
106284 TTT
1 TTT
106287 CTGTTTTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.16, C:0.08, G:0.00, T:0.76
Consensus pattern (11 bp):
TTTTTTCAATT
Found at i:112031 original size:10 final size:10
Alignment explanation
Indices: 112016--112043 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
112006 TGAACTATGT
112016 TGCATGCTCG
1 TGCATGCTCG
112026 TGCATGCTCG
1 TGCATGCTCG
112036 TGCATGCT
1 TGCATGCT
112044 ATACTCTATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.11, C:0.29, G:0.29, T:0.32
Consensus pattern (10 bp):
TGCATGCTCG
Found at i:112798 original size:18 final size:17
Alignment explanation
Indices: 112744--112792 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
112734 GTGGACTCCT
* *
112744 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TGA
112762 GAGTGCATCGATGCATGA
1 -AGTGCATCGATGCATGA
112780 AGTGCATTCGATG
1 AGTGCA-TCGATG
112793 TTTGAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.18, G:0.31, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATGA
Found at i:112828 original size:45 final size:45
Alignment explanation
Indices: 112764--112868 Score: 210
Period size: 45 Copynumber: 2.3 Consensus size: 45
112754 TGCACTAAGA
112764 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTG
1 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTG
112809 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTG
1 GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTG
112854 GTGCATCGATGCATG
1 GTGCATCGATGCATG
112869 GATTGTGCAT
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 60 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.29
Consensus pattern (45 bp):
GTGCATCGATGCATGAAGTGCATTCGATGTTTGAAAAATAGCCTG
Found at i:112929 original size:63 final size:64
Alignment explanation
Indices: 112854--113015 Score: 202
Period size: 63 Copynumber: 2.5 Consensus size: 64
112844 AAATAGCCTG
* * *
112854 GTGCATCGATGCATGGATTGTGCATCGATGCATCAAATGCATTGATGTTTTAATTAAATCA-GA
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCATGTTTCAATTAAATCATGA
** ** * *
112917 GTGCATCGATGCATGGAGAGTGCATCGGTGCATGGAATGCATTCATGTTTCAATTTATTCATTGA
1 GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCATGTTTCAATTAAATCA-TGA
112982 -TGCATCGATGCATGGTATTGATGCATCGGTGCAT
1 GTGCATCGATGCATGG-ATTG-TGCATCGGTGCAT
113016 GCCTTTGAAA
Statistics
Matches: 84, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
63 52 0.62
64 15 0.18
65 4 0.05
66 13 0.15
ACGTcount: A:0.26, C:0.15, G:0.25, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCATGGATTGTGCATCGGTGCATCAAATGCATTCATGTTTCAATTAAATCATGA
Found at i:112938 original size:19 final size:19
Alignment explanation
Indices: 112914--112952 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
112904 TAATTAAATC
112914 AGAGTGCATCGATGCATGG
1 AGAGTGCATCGATGCATGG
*
112933 AGAGTGCATCGGTGCATGG
1 AGAGTGCATCGATGCATGG
112952 A
1 A
112953 ATGCATTCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.38, T:0.21
Consensus pattern (19 bp):
AGAGTGCATCGATGCATGG
Found at i:113003 original size:21 final size:21
Alignment explanation
Indices: 112977--113016 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
112967 CAATTTATTC
112977 ATTGATGCATCGATGCATGGT
1 ATTGATGCATCGATGCATGGT
*
112998 ATTGATGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
113017 CCTTTGAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.15, G:0.30, T:0.33
Consensus pattern (21 bp):
ATTGATGCATCGATGCATGGT
Found at i:113350 original size:15 final size:15
Alignment explanation
Indices: 113332--113361 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
113322 AAATCAGCTT
113332 TTGAAAAATTACTCC
1 TTGAAAAATTACTCC
113347 TTGAAAAATTACTCC
1 TTGAAAAATTACTCC
113362 CCTTACTATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.07, T:0.33
Consensus pattern (15 bp):
TTGAAAAATTACTCC
Done.