Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009285.1 Hibiscus syriacus cultivar Beakdansim tig00112973_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: 80278
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4113 original size:18 final size:19
Alignment explanation
Indices: 4090--4151 Score: 62
Period size: 18 Copynumber: 3.5 Consensus size: 19
4080 ACCCGACCCG
4090 AAATATATATTT-ATTAAA
1 AAATATATATTTAATTAAA
* *
4108 AAATATTTTTTTCAA-T-AA
1 AAATATATATTT-AATTAAA
4126 AAATATAT-TTTAATTAAA
1 AAATATATATTTAATTAAA
4144 AAA-ATATA
1 AAATATATA
4152 GAGAGATGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 2 0.06
17 8 0.22
18 24 0.67
19 1 0.03
20 1 0.03
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AAATATATATTTAATTAAA
Found at i:6565 original size:16 final size:16
Alignment explanation
Indices: 6546--6580 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
6536 AGGTTTTTTT
6546 TATTAATATAGAGTA-A
1 TATTAATATA-AGTATA
6562 TATTAATATAAGTATA
1 TATTAATATAAGTATA
6578 TAT
1 TAT
6581 ATATGTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 14 0.78
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (16 bp):
TATTAATATAAGTATA
Found at i:14284 original size:124 final size:124
Alignment explanation
Indices: 14064--14312 Score: 498
Period size: 124 Copynumber: 2.0 Consensus size: 124
14054 TAAGAGTTTG
14064 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
1 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
14129 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
66 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
14188 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
1 GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
14253 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
66 AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
14312 G
1 G
14313 GGAGACAATA
Statistics
Matches: 125, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
124 125 1.00
ACGTcount: A:0.31, C:0.11, G:0.20, T:0.39
Consensus pattern (124 bp):
GAATACTCGTTTGTAGTTGACTTTTTGTTAAAGGCAAATTGTCCTTGATATGGATAGATTTAGAA
AGAAGTGCCCTTTAATTATCCTTAAATGTTAATATCTGTGACGTTGAAAGATTTGTCAA
Found at i:18515 original size:17 final size:17
Alignment explanation
Indices: 18493--18525 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
18483 CAATTGTAGT
18493 TAAAATATC-AAATTAAA
1 TAAAATA-CAAAATTAAA
18510 TAAAATACAAAATTAA
1 TAAAATACAAAATTAA
18526 GGGATTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 1 0.07
17 14 0.93
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TAAAATACAAAATTAAA
Found at i:20749 original size:21 final size:21
Alignment explanation
Indices: 20713--20762 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 21
20703 TTGGGATGGA
20713 TGGGTGTTGGAATTTAAGGATT
1 TGGGT-TTGGAATTTAAGGATT
20735 TAGGGTTTGG-ATTTAAGGATT
1 T-GGGTTTGGAATTTAAGGATT
20756 TGGGTTT
1 TGGGTTT
20763 AGAGATTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.22
21 12 0.44
22 5 0.19
23 4 0.15
ACGTcount: A:0.20, C:0.00, G:0.36, T:0.44
Consensus pattern (21 bp):
TGGGTTTGGAATTTAAGGATT
Found at i:22512 original size:6 final size:6
Alignment explanation
Indices: 22501--22563 Score: 56
Period size: 6 Copynumber: 10.5 Consensus size: 6
22491 TCTTTATGGC
* * * *
22501 CTTATT CTTATT CTTATG CTTATG CTTATT CTTGTT CTT-TT GCTTCTT
1 CTTATT CTTATT CTTATT CTTATT CTTATT CTTATT CTTATT -CTTATT
* *
22549 CATATC CTTATT CTT
1 CTTATT CTTATT CTT
22564 CTTTTTCTCC
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
5 2 0.04
6 43 0.91
7 2 0.04
ACGTcount: A:0.13, C:0.21, G:0.06, T:0.60
Consensus pattern (6 bp):
CTTATT
Found at i:22530 original size:24 final size:24
Alignment explanation
Indices: 22501--22563 Score: 72
Period size: 24 Copynumber: 2.6 Consensus size: 24
22491 TCTTTATGGC
22501 CTTATTCTTATTCTTATGCTTATG
1 CTTATTCTTATTCTTATGCTTATG
* * * *
22525 CTTATTCTTGTTCTTTTGCTTCTT
1 CTTATTCTTATTCTTATGCTTATG
* *
22549 CATATCCTTATTCTT
1 CTTATTCTTATTCTT
22564 CTTTTTCTCC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.13, C:0.21, G:0.06, T:0.60
Consensus pattern (24 bp):
CTTATTCTTATTCTTATGCTTATG
Found at i:23927 original size:90 final size:90
Alignment explanation
Indices: 23788--24314 Score: 770
Period size: 90 Copynumber: 5.9 Consensus size: 90
23778 AAGTAGCAGG
* *
23788 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCAGAATGTCCGAGAACAGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
* * *
23853 TCCATCTTCATCTTGGAGTAATCGA
66 TCTATCATCATCTTGGAGTAACCGA
* *
23878 CGGCGATTCCATGCTTCATTCTTTTCTCTAAACGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
* *
23943 TCCATCATCATCTTGTAGTAACCGA
66 TCTATCATCATCTTGGAGTAACCGA
*
23968 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGACGTCCAATCGGAATGTCCGAGAACCGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
*
24033 TCTATCATCATCTTGTAGTAACCGA
66 TCTATCATCATCTTGGAGTAACCGA
*
24058 CGACGATTCCATGC-TCTATTCTTTTCTCTAAAGGAAGTCCAATCGGAATGTCCGAGAACCGGAA
1 CGACGATTCCATGCTTC-ATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAA
* ** * *
24122 GTTTATCATCATCTTGGAACAATCGG
65 GTCTATCATCATCTTGGAGTAACCGA
* * * *
24148 CGGCGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGACCTAGAACGGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
* *
24213 -CATATCCTCATCTTGCAGTAACCGA
66 TC-TATCATCATCTTGGAGTAACCGA
* * * * *
24238 CGACGATTCCATGCTTCATTCTTCTCTCTAAAAGAAGTCCAATCAGAATGGCCTAGAACCGGAAG
1 CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
24303 TCTATCATCATC
66 TCTATCATCATC
24315 ATCTTGAAGT
Statistics
Matches: 395, Mismatches: 38, Indels: 8
0.90 0.09 0.02
Matches are distributed among these distances:
89 2 0.01
90 390 0.99
91 3 0.01
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (90 bp):
CGACGATTCCATGCTTCATTCTTTTCTCTAAATGAAGTCCAATCGGAATGTCCGAGAACCGGAAG
TCTATCATCATCTTGGAGTAACCGA
Found at i:36085 original size:15 final size:15
Alignment explanation
Indices: 36065--36106 Score: 84
Period size: 15 Copynumber: 2.8 Consensus size: 15
36055 GGTTCAGTCC
36065 TTTTAAATCTTTTAA
1 TTTTAAATCTTTTAA
36080 TTTTAAATCTTTTAA
1 TTTTAAATCTTTTAA
36095 TTTTAAATCTTT
1 TTTTAAATCTTT
36107 AAGAGGTTGT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (15 bp):
TTTTAAATCTTTTAA
Found at i:36251 original size:31 final size:31
Alignment explanation
Indices: 36203--36272 Score: 95
Period size: 31 Copynumber: 2.3 Consensus size: 31
36193 TTTTTTTTGG
* * *
36203 CTCAAGCGCGCGATTTCAATCCGAAAGTTCT
1 CTCAATCGCACGATTTCAATCCAAAAGTTCT
* *
36234 CTCGATCGCACGATTTCAATCCAAAATTTCT
1 CTCAATCGCACGATTTCAATCCAAAAGTTCT
36265 CTCAATCG
1 CTCAATCG
36273 TGCGATCCCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (31 bp):
CTCAATCGCACGATTTCAATCCAAAAGTTCT
Found at i:41209 original size:133 final size:130
Alignment explanation
Indices: 40955--41343 Score: 428
Period size: 133 Copynumber: 2.9 Consensus size: 130
40945 AAGCAATGGA
* * *
40955 GACTCCTCTCTTTGCGAGTCAAGTCT-AGTTTTACATGACTTCTATTCGTGGGTTAAGTCAAGTT
1 GACTCCTCTC-TTGCGAGTTAAGT-TGAGTTTTAGATGACTTC-ATT-GTTGGTTAAGTCAAGTT
* ** * ** * *
41019 GAAATTAGCTCCTTTTTGCGAGTTGAGCTAGTTGAGATTGGTGTCTCCTTGCAAGTTGAGTCGAG
62 GAAATTAGCTCC-TTTTGCAAGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAGCCAAG
41084 TTGTG
126 TTGTG
41089 GACTCCTCCTCATTGCGAGTTAAGTTGAGTTTTAGATGACTTCATTGTTGGTTAAGTCAAGTTGA
1 GACTCCT-CTC-TTGCGAGTTAAGTTGAGTTTTAGATGACTTCATTGTTGGTTAAGTCAAGTTGA
* *
41154 AATTAGCTCCTCTTTGCAAGTTGAGCTAGTTGAAATTGACGCCTCCTTGTGAGTTGGGCCAAGTT
64 AATTAGCTCCT-TTTGCAAGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAGCCAAGTT
41219 GTG
128 GTG
* * * *
41222 GACTCCTC-CTTGCGAGTTAAGTCGAGTTTTGGATGACTCCCCTT-TGTGGTTTAAGTCAAG-TG
1 GACTCCTCTCTTGCGAGTTAAGTTGAGTTTTAGATGACT-TCATTGT-TGG-TTAAGTCAAGTTG
* * * *
41284 AGAATTAGCTCCTTAT-CACGAGTTAAGCTAGTTGAGATTGACTCCTCTTTGTGAGTTGAG
63 A-AATTAGCTCCTTTTGCA--AGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAG
41344 ACATGCCGTG
Statistics
Matches: 222, Mismatches: 24, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
130 30 0.14
131 12 0.05
132 58 0.26
133 81 0.36
134 11 0.05
135 30 0.14
ACGTcount: A:0.21, C:0.18, G:0.25, T:0.37
Consensus pattern (130 bp):
GACTCCTCTCTTGCGAGTTAAGTTGAGTTTTAGATGACTTCATTGTTGGTTAAGTCAAGTTGAAA
TTAGCTCCTTTTGCAAGTTGAGCTAGTTGAGATTGACGCCTCCTTGTGAGTTGAGCCAAGTTGTG
Found at i:42349 original size:10 final size:10
Alignment explanation
Indices: 42330--42401 Score: 51
Period size: 9 Copynumber: 7.2 Consensus size: 10
42320 TAAAATGTTA
42330 TCTTTCTTCT
1 TCTTTCTTCT
*
42340 TCTTTTTTCT
1 TCTTTCTTCT
*
42350 TAATTT-TATCT
1 T-CTTTCT-TCT
**
42361 TCCTCCCTTCT
1 T-CTTTCTTCT
*
42372 TTTTTCTTCT
1 TCTTTCTTCT
42382 TC-TTCTTCT
1 TCTTTCTTCT
42391 TC-TTCTTCT
1 TCTTTCTTCT
42400 TC
1 TC
42402 CCCTCCCATT
Statistics
Matches: 49, Mismatches: 10, Indels: 7
0.74 0.15 0.11
Matches are distributed among these distances:
9 18 0.37
10 18 0.37
11 12 0.24
12 1 0.02
ACGTcount: A:0.04, C:0.29, G:0.00, T:0.67
Consensus pattern (10 bp):
TCTTTCTTCT
Found at i:42383 original size:3 final size:3
Alignment explanation
Indices: 42367--42401 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
42357 ATCTTCCTCC
42367 CTT CTT -TT -TT CTT CTT CTT CTT CTT CTT CTT CTT C
1 CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT CTT C
42402 CCCTCCCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 4 0.13
3 27 0.87
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
CTT
Found at i:43569 original size:15 final size:15
Alignment explanation
Indices: 43549--43591 Score: 86
Period size: 15 Copynumber: 2.9 Consensus size: 15
43539 TTTTAAAATA
43549 AATATTAATTTATCT
1 AATATTAATTTATCT
43564 AATATTAATTTATCT
1 AATATTAATTTATCT
43579 AATATTAATTTAT
1 AATATTAATTTAT
43592 AGAGATTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (15 bp):
AATATTAATTTATCT
Found at i:51112 original size:16 final size:16
Alignment explanation
Indices: 51093--51130 Score: 67
Period size: 16 Copynumber: 2.4 Consensus size: 16
51083 TTTAATGGTT
*
51093 CTCATCGTTAACGGTG
1 CTCATCGATAACGGTG
51109 CTCATCGATAACGGTG
1 CTCATCGATAACGGTG
51125 CTCATC
1 CTCATC
51131 TATACTATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.21, C:0.29, G:0.21, T:0.29
Consensus pattern (16 bp):
CTCATCGATAACGGTG
Found at i:52384 original size:18 final size:18
Alignment explanation
Indices: 52357--52397 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
52347 AATTGATAGA
52357 ATTT-TTAAA-TATTATTG
1 ATTTATTAAATTATT-TTG
52374 ATTTATTAAATTATTTTG
1 ATTTATTAAATTATTTTG
*
52392 AATTAT
1 ATTTAT
52398 GACAAATTTG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
17 4 0.19
18 13 0.62
19 4 0.19
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (18 bp):
ATTTATTAAATTATTTTG
Found at i:52497 original size:21 final size:20
Alignment explanation
Indices: 52473--52538 Score: 78
Period size: 21 Copynumber: 3.2 Consensus size: 20
52463 TTTTCGTTAC
52473 GCGAATTGGGAAATTCGCAAT
1 GCGAATTGGGAAA-TCGCAAT
** * *
52494 GCGAATAAGTAAATCGCAAC
1 GCGAATTGGGAAATCGCAAT
52514 GCGAATTGGGAAAATCGCAAT
1 GCGAATTGGG-AAATCGCAAT
52535 GCGA
1 GCGA
52539 TACTGACTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 13 0.36
21 23 0.64
ACGTcount: A:0.38, C:0.17, G:0.27, T:0.18
Consensus pattern (20 bp):
GCGAATTGGGAAATCGCAAT
Found at i:52569 original size:41 final size:41
Alignment explanation
Indices: 52524--52601 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
52514 GCGAATTGGG
* * * *
52524 AAAATCGCAATGCGATACTGACTATCGTAATGCGATAATAA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
* *
52565 AAAATCGCAACGAGATACTTACTTTCGCAACGCGATA
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATA
52602 CTGACTTTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAA
Found at i:52594 original size:20 final size:20
Alignment explanation
Indices: 52569--52621 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
52559 TAATAAAAAA
* *
52569 TCGCAACGAGATACTTACTT
1 TCGCAACGCGATACTGACTT
52589 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATACTGACTT
52609 TCGCAACGCGATA
1 TCGCAACGCGATA
52622 ATACATAATC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (20 bp):
TCGCAACGCGATACTGACTT
Found at i:52837 original size:22 final size:22
Alignment explanation
Indices: 52809--52852 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
52799 CACTCTCTCA
52809 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
52831 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
52853 TATCTAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:53141 original size:20 final size:20
Alignment explanation
Indices: 53116--53153 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53106 CGATTCTCTC
53116 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
53136 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
53154 AGAAACTATT
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:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:54493 original size:18 final size:18
Alignment explanation
Indices: 54472--54516 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
54462 TCCACTTCGG
*
54472 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
54490 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
54508 GAGCCATCA
1 GAGCCATCA
54517 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:55008 original size:20 final size:19
Alignment explanation
Indices: 54983--55048 Score: 69
Period size: 20 Copynumber: 3.4 Consensus size: 19
54973 TAGTTTACTT
54983 TCGCAACACGAAAATGACTA
1 TCGCAACACG-AAATGACTA
* *
55003 TCGCAACGCGGAAATGGCTA
1 TCGCAACAC-GAAATGACTA
* **
55023 TCGCAATACGAAATGAAAA
1 TCGCAACACGAAATGACTA
55042 TCGCAAC
1 TCGCAAC
55049 GACAAAATCG
Statistics
Matches: 37, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 13 0.35
20 23 0.62
21 1 0.03
ACGTcount: A:0.41, C:0.24, G:0.20, T:0.15
Consensus pattern (19 bp):
TCGCAACACGAAATGACTA
Found at i:55057 original size:14 final size:14
Alignment explanation
Indices: 55038--55101 Score: 76
Period size: 14 Copynumber: 4.4 Consensus size: 14
55028 ATACGAAATG
55038 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
55052 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
55068 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
55084 AAAATCGCAACG-C
1 AAAATCGCAACGAC
55097 AAAAT
1 AAAAT
55102 GAAAATCGCA
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.14
14 21 0.48
16 8 0.18
18 9 0.20
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:55080 original size:32 final size:33
Alignment explanation
Indices: 55022--55112 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
55012 GGAAATGGCT
**
55022 ATCGCAATACGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
55055 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
55087 ATCGCAACGCAAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
55113 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 31 0.57
33 23 0.43
ACGTcount: A:0.49, C:0.23, G:0.16, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:55106 original size:19 final size:18
Alignment explanation
Indices: 55033--55112 Score: 61
Period size: 14 Copynumber: 4.8 Consensus size: 18
55023 TCGCAATACG
55033 AAATGAAAATCGCAACG-
1 AAATGAAAATCGCAACGC
*
55050 --A-CAAAATCGCAACGC
1 AAATGAAAATCGCAACGC
55065 GAAATG-AAATCGCAACG-
1 -AAATGAAAATCGCAACGC
*
55082 --A-CAAAATCGCAACGC
1 AAATGAAAATCGCAACGC
55097 AAAATGAAAATCGCAA
1 -AAATGAAAATCGCAA
55113 TGCGATTTGT
Statistics
Matches: 48, Mismatches: 4, Indels: 20
0.67 0.06 0.28
Matches are distributed among these distances:
14 24 0.50
15 1 0.02
18 13 0.27
19 10 0.21
ACGTcount: A:0.51, C:0.23, G:0.16, T:0.10
Consensus pattern (18 bp):
AAATGAAAATCGCAACGC
Found at i:55148 original size:14 final size:14
Alignment explanation
Indices: 55129--55186 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
55119 TTGTGTTTCG
55129 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
55143 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
55159 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
*
55175 CGTTGCAATTTT
1 CGTTGCGATTTT
55187 CATTTCGCTT
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 22 0.59
16 4 0.11
18 11 0.30
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:55163 original size:32 final size:33
Alignment explanation
Indices: 55124--55202 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
55114 GCGATTTGTG
*
55124 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
55156 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
*
55189 TTTCGCTTTGCGAT
1 TTTCGCGTTGCGAT
55203 AGCCATTTCC
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
32 26 0.59
33 18 0.41
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCAATTTTCA
Found at i:55221 original size:20 final size:19
Alignment explanation
Indices: 55187--55241 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
55177 TTGCAATTTT
*
55187 CATTTCGCTTTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
55206 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
55226 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
55242 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.15, C:0.25, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:57270 original size:14 final size:15
Alignment explanation
Indices: 57251--57327 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
57241 CGAAATGGCT
57251 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
57265 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
57283 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
57302 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
57316 ATCGCAATGCGA
1 ATCGCAA-GCGA
57328 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:57283 original size:19 final size:19
Alignment explanation
Indices: 57261--57327 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
57251 ATCGCAACGA
57261 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
57280 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
57298 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
57312 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
57328 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:57403 original size:20 final size:20
Alignment explanation
Indices: 57353--57403 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
57343 GCGATATTCT
* *
57353 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCA
57373 CGTTGCGATAGCCATTTTCA
1 CGTTGCGATAGCCATTTTCA
57393 CGTTGCGATAG
1 CGTTGCGATAG
57404 TCAAATGAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCA
Found at i:58516 original size:24 final size:24
Alignment explanation
Indices: 58460--58518 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
58450 AGTCAGTATT
* *
58460 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
58484 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
58508 CGAATTTTGAT
1 CGAAATTTGAT
58519 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:58710 original size:12 final size:12
Alignment explanation
Indices: 58693--58717 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
58683 ATATAATCCT
58693 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58705 GAAGAAGAAAAA
1 GAAGAAGAAAAA
58717 G
1 G
58718 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:61039 original size:19 final size:19
Alignment explanation
Indices: 61017--61111 Score: 84
Period size: 19 Copynumber: 5.5 Consensus size: 19
61007 AATTACTATT
61017 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
61036 GCAA--CG--A-GAGAATC
1 GCAATGCGAAATGAAAATC
61050 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
**
61069 GCAA--CG--A-GGGAATC
1 GCAATGCGAAATGAAAATC
61083 GCAATGCGAAATGAAAATC
1 GCAATGCGAAATGAAAATC
*
61102 GCAACGCGAA
1 GCAATGCGAA
61112 TTTAATTTCG
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (19 bp):
GCAATGCGAAATGAAAATC
Found at i:61059 original size:33 final size:33
Alignment explanation
Indices: 61017--61107 Score: 173
Period size: 33 Copynumber: 2.8 Consensus size: 33
61007 AATTACTATT
61017 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
*
61050 GCAATGCGAAATGAAAATCGCAACGAGGGAATC
1 GCAATGCGAAATGAAAATCGCAACGAGAGAATC
61083 GCAATGCGAAATGAAAATCGCAACG
1 GCAATGCGAAATGAAAATCGCAACG
61108 CGAATTTAAT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.44, C:0.19, G:0.25, T:0.12
Consensus pattern (33 bp):
GCAATGCGAAATGAAAATCGCAACGAGAGAATC
Found at i:61129 original size:19 final size:20
Alignment explanation
Indices: 61107--61149 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
61097 AAATCGCAAC
61107 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
61126 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
61146 GCGA
1 GCGA
61150 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:61134 original size:14 final size:14
Alignment explanation
Indices: 61135--61168 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
61125 TGCGATTTTC
61135 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
61149 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
61163 ATTTTC
1 ATTTTC
61169 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:61309 original size:14 final size:14
Alignment explanation
Indices: 61290--61326 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
61280 CATCAATTAA
61290 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
61304 ACAAATCACCTTTT
1 ACAAATCAACTTTT
61318 ACAAATCAA
1 ACAAATCAA
61327 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:62751 original size:21 final size:21
Alignment explanation
Indices: 62685--62751 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
62675 GTGAATCGGG
*
62685 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
62705 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
62727 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
62748 CTCT
1 CTCT
62752 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:62770 original size:42 final size:41
Alignment explanation
Indices: 62685--62807 Score: 106
Period size: 42 Copynumber: 2.9 Consensus size: 41
62675 GTGAATCGGG
* * * * *
62685 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
62727 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * *
62769 CTCTTCG-ACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTT-GAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
62808 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 9, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
41 4 0.06
42 57 0.84
43 7 0.10
ACGTcount: A:0.22, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:64840 original size:20 final size:20
Alignment explanation
Indices: 64817--64871 Score: 67
Period size: 20 Copynumber: 2.7 Consensus size: 20
64807 TGAAATGAAA
64817 ATCGCAAC-AAGATAATGACT
1 ATCGCAACGAAGA-AATGACT
**
64837 ATCGCAACGCGGAAATGACT
1 ATCGCAACGAAGAAATGACT
64857 ATCGCAACGAGAGAA
1 ATCGCAACGA-AGAA
64872 TCGCAACGCG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 24 0.83
21 5 0.17
ACGTcount: A:0.42, C:0.22, G:0.22, T:0.15
Consensus pattern (20 bp):
ATCGCAACGAAGAAATGACT
Found at i:64890 original size:33 final size:33
Alignment explanation
Indices: 64837--64931 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
64827 GATAATGACT
* *
64837 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAACGC-GAAATGACTATCGCAACCAGACA
*
64871 ATCGCAACGCGAAATGACTATCGCGACCAGACA
1 ATCGCAACGCGAAATGACTATCGCAACCAGACA
**
64904 ATCGCAACGCGAAATGAAAATCGCAACC
1 ATCGCAACGCGAAATGACTATCGCAACC
64932 GTGAAATTAA
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
33 45 0.82
34 10 0.18
ACGTcount: A:0.39, C:0.27, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGACTATCGCAACCAGACA
Found at i:64943 original size:20 final size:20
Alignment explanation
Indices: 64903--64950 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
64893 GCGACCAGAC
64903 AATCGCAA-CGCGAAATGAA
1 AATCGCAACCGCGAAATGAA
* *
64922 AATCGCAACCGTGAAATTAA
1 AATCGCAACCGCGAAATGAA
64942 AATCGCAAC
1 AATCGCAAC
64951 GCAAATGCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 8 0.31
20 18 0.69
ACGTcount: A:0.46, C:0.23, G:0.17, T:0.15
Consensus pattern (20 bp):
AATCGCAACCGCGAAATGAA
Found at i:64980 original size:19 final size:19
Alignment explanation
Indices: 64956--65000 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
64946 GCAACGCAAA
*
64956 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
64975 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
64994 TGCGATT
1 TGCGATT
65001 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:65638 original size:20 final size:20
Alignment explanation
Indices: 65553--65646 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
65543 CGCTATGTAA
*
65553 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
65573 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
65593 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
65614 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
65634 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
65647 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:65664 original size:21 final size:20
Alignment explanation
Indices: 65635--65710 Score: 80
Period size: 21 Copynumber: 3.7 Consensus size: 20
65625 ATAGTCAGTA
65635 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTT-CCAAT
* * **
65656 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCAAT
65676 TCGCATTGCGAATTTTCCAAT
1 TCGCATTGCG-ATTTTCCAAT
**
65697 TCGTGTTGCGATTT
1 TCGCATTGCGATTT
65711 ACTTATTCGC
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 16 0.36
21 28 0.64
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.42
Consensus pattern (20 bp):
TCGCATTGCGATTTTCCAAT
Found at i:65665 original size:41 final size:41
Alignment explanation
Indices: 65635--65730 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
65625 ATAGTCAGTA
* *
65635 TCGCATTGCG-ATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTT-CCAATTCGCGTTGCGATTCACGTAT
* * *
65676 TCGCATTGCGAATTTTCCAATTCGTGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTTCCAATTCGCGTTGCGATTCACGTAT
*
65717 TCGCATTACGAATT
1 TCGCATTGCGAATT
65731 GGGAAAATCG
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
41 47 0.90
42 5 0.10
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGAATTTTCCAATTCGCGTTGCGATTCACGTAT
Found at i:65679 original size:20 final size:20
Alignment explanation
Indices: 65654--65720 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
65644 GATTTTCCCA
65654 ATTCGCGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
* * **
65674 ATTCGCATTGCGAATTTTCCA
1 ATTCGCGTTGCG-ATTTACTT
*
65695 ATTCGTGTTGCGATTTACTT
1 ATTCGCGTTGCGATTTACTT
65715 ATTCGC
1 ATTCGC
65721 ATTACGAATT
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.18, C:0.21, G:0.18, T:0.43
Consensus pattern (20 bp):
ATTCGCGTTGCGATTTACTT
Found at i:66674 original size:2 final size:2
Alignment explanation
Indices: 66667--66693 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
66657 TTTATGGGGT
66667 TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG T
66694 TTTTGCAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:73008 original size:48 final size:48
Alignment explanation
Indices: 72953--73049 Score: 167
Period size: 48 Copynumber: 2.0 Consensus size: 48
72943 CATAGTTTGT
72953 GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
1 GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
* * *
73001 GTATGATGATTATCGATCGATTTTGTTTAATGCATATGTTGCATTTTC
1 GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
73049 G
1 G
73050 CATCAGTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
48 46 1.00
ACGTcount: A:0.25, C:0.11, G:0.19, T:0.45
Consensus pattern (48 bp):
GTATGATGACTATCGATCGATTTTATTTAATGCATAAGTTGCATTTTC
Found at i:75054 original size:26 final size:24
Alignment explanation
Indices: 75025--75072 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
75015 ACCATTGTTC
75025 ATTTATAAATCTAAATAAATAAGATT
1 ATTT-TAAATCTAAA-AAATAAGATT
* *
75051 ATTTTACATCTAAAATATAAGA
1 ATTTTAAATCTAAAAAATAAGA
75073 AATATGTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 9 0.45
26 4 0.20
ACGTcount: A:0.52, C:0.06, G:0.04, T:0.38
Consensus pattern (24 bp):
ATTTTAAATCTAAAAAATAAGATT
Found at i:77451 original size:26 final size:26
Alignment explanation
Indices: 77412--77474 Score: 110
Period size: 26 Copynumber: 2.4 Consensus size: 26
77402 GACTAAAACA
77412 GAAATAAAAA-ATAACGTTAGTATTTT
1 GAAA-AAAAATATAACGTTAGTATTTT
77438 GAAAAAAAATATAACGTTAGTATTTT
1 GAAAAAAAATATAACGTTAGTATTTT
77464 GAAAAAAAATA
1 GAAAAAAAATA
77475 ATTGTACAAC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
25 5 0.14
26 31 0.86
ACGTcount: A:0.56, C:0.03, G:0.11, T:0.30
Consensus pattern (26 bp):
GAAAAAAAATATAACGTTAGTATTTT
Found at i:78226 original size:2 final size:2
Alignment explanation
Indices: 78219--78251 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
78209 TGTTCATTTA
78219 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78252 ACATATTATC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.