Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005892.1 Hibiscus syriacus cultivar Beakdansim tig00013833_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: 83474
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.32
Found at i:1079 original size:60 final size:60
Alignment explanation
Indices: 1014--1140 Score: 141
Period size: 60 Copynumber: 2.1 Consensus size: 60
1004 AGTGGTCCCC
** *
1014 TGACTATA-AGATATTATTTTATTAAGTCTTTTGACTATTAAAAGTCACAAAATGGTC-CT
1 TGACTATAGAG-TATTATTTTATTAAGTCCCTCGACTATTAAAAGTCACAAAATGGTCACT
* * * * * *
1073 TCGACTATTGAGTGTTGTTTTGTTGAGTCCCTCGACTATTAAAAGTTACAAAATGGTCACT
1 T-GACTATAGAGTATTATTTTATTAAGTCCCTCGACTATTAAAAGTCACAAAATGGTCACT
1134 TGACTAT
1 TGACTAT
1141 TCATTATGTT
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
59 1 0.02
60 50 0.89
61 5 0.09
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (60 bp):
TGACTATAGAGTATTATTTTATTAAGTCCCTCGACTATTAAAAGTCACAAAATGGTCACT
Found at i:1351 original size:60 final size:60
Alignment explanation
Indices: 1205--1351 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 60
1195 AACATAATGA
**
1205 ATAGTC-AGGTGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACATTCT
1 ATAGTCAAGG-GACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCT
* * * * ** *
1265 ATAATCGAA-TGACTATTTTGTAACTTTTAATAGTCGATAGACTTAATAAAGTAATAACCT
1 ATAGTC-AAGGGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCT
*
1325 ATAGTCAAGGGACCGTTTGTGT-ACTTT
1 ATAGTCAAGGGACCATTT-TGTAACTTT
1352 ACCCTGAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
59 2 0.03
60 64 0.91
61 3 0.04
62 1 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.35
Consensus pattern (60 bp):
ATAGTCAAGGGACCATTTTGTAACTTTTAATAGTCGATAGACTTAACAAAACAACAACCT
Found at i:4229 original size:51 final size:50
Alignment explanation
Indices: 4153--4268 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 50
4143 TTAACAATAA
* * **
4153 AGCGCGCTCCTTGCACCGCGCTATAC-GATGATTTGGCGCCACGTAGGGTAT
1 AGCGCGCCCCTTGCACCGCACTATACAG-TGAACTGGCGCCACGT-GGGTAT
* * *
4204 AGCGCTCCCCTTGCACCGCACTATACAGTGAACTGGCGTCACGTGGTTAT
1 AGCGCGCCCCTTGCACCGCACTATACAGTGAACTGGCGCCACGTGGGTAT
*
4254 AGCGCGGCCCTTGCA
1 AGCGCGCCCCTTGCA
4269 TCGAGTTATA
Statistics
Matches: 55, Mismatches: 9, Indels: 3
0.82 0.13 0.04
Matches are distributed among these distances:
50 18 0.33
51 36 0.65
52 1 0.02
ACGTcount: A:0.18, C:0.32, G:0.28, T:0.22
Consensus pattern (50 bp):
AGCGCGCCCCTTGCACCGCACTATACAGTGAACTGGCGCCACGTGGGTAT
Found at i:4550 original size:13 final size:14
Alignment explanation
Indices: 4528--4574 Score: 51
Period size: 13 Copynumber: 3.3 Consensus size: 14
4518 TTATAAGGTA
*
4528 ATTTTGTTATAATT
1 ATTTTTTTATAATT
*
4542 -TTTTTTTATATTT
1 ATTTTTTTATAATT
4555 ATTGTTTATTATAATT
1 ATT-TTT-TTATAATT
4571 ATTT
1 ATTT
4575 GAAAAAAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
13 11 0.41
14 2 0.07
15 4 0.15
16 10 0.37
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (14 bp):
ATTTTTTTATAATT
Found at i:7933 original size:26 final size:26
Alignment explanation
Indices: 7904--7976 Score: 64
Period size: 26 Copynumber: 2.8 Consensus size: 26
7894 AACTTCCAAC
**
7904 AAATTTAACAAAATAAAGTAAGTATT
1 AAATTTAACAAAATAAAGTAAAAATT
*
7930 AAA-TGAGA-AATAATAAA--AAAAATT
1 AAATTTA-ACAA-AATAAAGTAAAAATT
7954 ACAATTTAACAAAATAAAGTAAA
1 A-AATTTAACAAAATAAAGTAAA
7977 TACAAATATA
Statistics
Matches: 36, Mismatches: 4, Indels: 13
0.68 0.08 0.25
Matches are distributed among these distances:
24 6 0.17
25 13 0.36
26 14 0.39
27 3 0.08
ACGTcount: A:0.64, C:0.04, G:0.07, T:0.25
Consensus pattern (26 bp):
AAATTTAACAAAATAAAGTAAAAATT
Found at i:10196 original size:110 final size:111
Alignment explanation
Indices: 10002--10222 Score: 381
Period size: 110 Copynumber: 2.0 Consensus size: 111
9992 ATTACAAAAA
* * * *
10002 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
10067 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
10113 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTACTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
10177 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
10223 ATGATTTTCA
Statistics
Matches: 104, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
110 71 0.68
111 33 0.32
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:10360 original size:12 final size:10
Alignment explanation
Indices: 10346--10386 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
10336 ACCTTAAAAA
*
10346 GAGAGTATTT
1 GAGAGAATTT
10356 GAGAGAAATTT
1 GAGAG-AATTT
10367 -AGAGAATTT
1 GAGAGAATTT
10376 GAGAGAATTT
1 GAGAGAATTT
10386 G
1 G
10387 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:10600 original size:51 final size:49
Alignment explanation
Indices: 10509--10628 Score: 132
Period size: 51 Copynumber: 2.4 Consensus size: 49
10499 AGATATACAG
* * * * **
10509 GTATAGCACGCTGCAGGGGCCGCGCTATACCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGG-TGCACTATACCCACGTGGCGCCAAATCACC
* *
10559 GTATAGCGCGGTGCAAGGGGTGCACTATATCCCATGTGGCGCCAAATCATC
1 GTATAGCGCGGTGC-AGGGGTGCACTATA-CCCACGTGGCGCCAAATCACC
*
10610 GTATAGCGTGGTGCAGGGG
1 GTATAGCGCGGTGCAGGGG
10629 CACGCTTTAC
Statistics
Matches: 59, Mismatches: 9, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
50 24 0.41
51 35 0.59
ACGTcount: A:0.20, C:0.28, G:0.33, T:0.18
Consensus pattern (49 bp):
GTATAGCGCGGTGCAGGGGTGCACTATACCCACGTGGCGCCAAATCACC
Found at i:12338 original size:42 final size:42
Alignment explanation
Indices: 12291--12391 Score: 202
Period size: 42 Copynumber: 2.4 Consensus size: 42
12281 ATCAGTCATC
12291 TTAAATATATTATTTAACAGTAAAATAAAGGTGTTAATTTAT
1 TTAAATATATTATTTAACAGTAAAATAAAGGTGTTAATTTAT
12333 TTAAATATATTATTTAACAGTAAAATAAAGGTGTTAATTTAT
1 TTAAATATATTATTTAACAGTAAAATAAAGGTGTTAATTTAT
12375 TTAAATATATTATTTAA
1 TTAAATATATTATTTAA
12392 ATTGGCTTAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.45
Consensus pattern (42 bp):
TTAAATATATTATTTAACAGTAAAATAAAGGTGTTAATTTAT
Found at i:14749 original size:20 final size:20
Alignment explanation
Indices: 14717--14772 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
14707 ACGCGATTTT
*
14717 AAATTCGCTACACGAACTCC
1 AAATTCGCAACACGAACTCC
* **
14737 AATTTCGCAACAC-AGTTTCC
1 AAATTCGCAACACGA-ACTCC
14757 AAATTCGCAACACGAA
1 AAATTCGCAACACGAA
14773 TTTAACAATT
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.21
Consensus pattern (20 bp):
AAATTCGCAACACGAACTCC
Found at i:15509 original size:20 final size:20
Alignment explanation
Indices: 15463--15520 Score: 89
Period size: 20 Copynumber: 2.9 Consensus size: 20
15453 CTTGAAACTT
* *
15463 AAATTCACAACACGAAAATG
1 AAATTCGCAACGCGAAAATG
15483 AAATTCGCAACGCGAAAATG
1 AAATTCGCAACGCGAAAATG
*
15503 AAATTCGCAATGCGAAAA
1 AAATTCGCAACGCGAAAA
15521 CAAAAATCGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.50, C:0.19, G:0.16, T:0.16
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:15530 original size:20 final size:20
Alignment explanation
Indices: 15487--15540 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
15477 AAAATGAAAT
** *
15487 TCGCAACGCGAAAATGAAAT
1 TCGCAACGCGAAAACAAAAA
*
15507 TCGCAATGCGAAAACAAAAA
1 TCGCAACGCGAAAACAAAAA
* *
15527 TCGCCACACGAAAA
1 TCGCAACGCGAAAA
15541 ATAAATTCGA
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (20 bp):
TCGCAACGCGAAAACAAAAA
Found at i:15566 original size:20 final size:20
Alignment explanation
Indices: 15543--15580 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
15533 CACGAAAAAT
15543 AAATTCG-AGTTGCGAATTCA
1 AAATTCGTA-TTGCGAATTCA
15563 AAATTCGTATTGCGAATT
1 AAATTCGTATTGCGAATT
15581 TCATTTTCGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 16 0.94
21 1 0.06
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.34
Consensus pattern (20 bp):
AAATTCGTATTGCGAATTCA
Found at i:15589 original size:20 final size:20
Alignment explanation
Indices: 15566--15656 Score: 61
Period size: 20 Copynumber: 4.8 Consensus size: 20
15556 GAATTCAAAA
15566 TTCGTATTGCGAATTTCATT
1 TTCGTATTGCGAATTTCATT
15586 TTCG-AGTTGCG------ATT
1 TTCGTA-TTGCGAATTTCATT
* *
15600 TTCGTTTTACGAATTTCATT
1 TTCGTATTGCGAATTTCATT
* * *
15620 TTCATGTTGTGAATTTCATT
1 TTCGTATTGCGAATTTCATT
* *
15640 TTCGTGTTGCGATTTTC
1 TTCGTATTGCGAATTTC
15657 GTGTTGCGAA
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
14 11 0.20
19 1 0.02
20 42 0.78
ACGTcount: A:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTCGTATTGCGAATTTCATT
Found at i:15654 original size:14 final size:14
Alignment explanation
Indices: 15637--15665 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
15627 TGTGAATTTC
15637 ATTTTCGTGTTGCG
1 ATTTTCGTGTTGCG
15651 ATTTTCGTGTTGCG
1 ATTTTCGTGTTGCG
15665 A
1 A
15666 ATTTAAGTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.14, G:0.28, T:0.48
Consensus pattern (14 bp):
ATTTTCGTGTTGCG
Found at i:17242 original size:42 final size:42
Alignment explanation
Indices: 17196--17298 Score: 115
Period size: 39 Copynumber: 2.5 Consensus size: 42
17186 ATTCTCTACT
*
17196 TCGACA-TCGAGATCCATCACCTGATCGAGCCGATTATACACC
1 TCGACACT-GAGATCCATCACCTGATCGAGCCGACTATACACC
* * * * *
17238 TCGACACTGAGAGCCATCA---GCTCTAGCCGACTCTATACC
1 TCGACACTGAGATCCATCACCTGATCGAGCCGACTATACACC
17277 TCGACACTGAGATCCATCACCT
1 TCGACACTGAGATCCATCACCT
17299 ATTCTATCAT
Statistics
Matches: 50, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
39 33 0.66
42 16 0.32
43 1 0.02
ACGTcount: A:0.27, C:0.35, G:0.17, T:0.21
Consensus pattern (42 bp):
TCGACACTGAGATCCATCACCTGATCGAGCCGACTATACACC
Found at i:17424 original size:21 final size:21
Alignment explanation
Indices: 17398--17567 Score: 112
Period size: 21 Copynumber: 8.1 Consensus size: 21
17388 ACCTCCACGA
*
17398 GATGAGTTAGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
17419 GATGAGGTCA-ATACTTTACGT
1 GATGAGGT-AGGTGCTTTACGT
*
17440 GATGAGGTCGGTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
*** * **
17461 GAT-AACAATGGTGCATGGCGT
1 GATGAGGTA-GGTGCTTTACGT
**
17482 GATGAGGTAGG-GTCTTTAATT
1 GATGAGGTAGGTG-CTTTACGT
* * *
17503 GGTGATGTAGCTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* * *
17524 GGTGAAGTAGCTGCTTTACGT
1 GATGAGGTAGGTGCTTTACGT
* *
17545 GATGAGGTCGGTGCTCTACGT
1 GATGAGGTAGGTGCTTTACGT
17566 GA
1 GA
17568 GATTGTTTCA
Statistics
Matches: 111, Mismatches: 32, Indels: 12
0.72 0.21 0.08
Matches are distributed among these distances:
20 2 0.02
21 105 0.95
22 4 0.04
ACGTcount: A:0.21, C:0.13, G:0.34, T:0.33
Consensus pattern (21 bp):
GATGAGGTAGGTGCTTTACGT
Found at i:17876 original size:21 final size:20
Alignment explanation
Indices: 17850--17961 Score: 100
Period size: 21 Copynumber: 5.3 Consensus size: 20
17840 GAAGAAGCTT
*
17850 GATCCACCTACCATTGTTCAG
1 GATCCACCT-CCATCGTTCAG
*
17871 GATCCACCTCCTATTGTTCAG
1 GATCCACCTCC-ATCGTTCAG
* *
17892 GATTCACCTCTCATCGTTCAA
1 GATCCACCTC-CATCGTTCAG
* *
17913 GATGCC-CCTCCTATCATTTAG
1 GAT-CCACCTCC-ATCGTTCAG
*
17934 GATCCACCTCCCATCGTTCAA
1 GATCCACCT-CCATCGTTCAG
17955 GATCCAC
1 GATCCAC
17962 ATTCCATACC
Statistics
Matches: 75, Mismatches: 10, Indels: 12
0.77 0.10 0.12
Matches are distributed among these distances:
20 5 0.07
21 66 0.88
22 4 0.05
ACGTcount: A:0.22, C:0.36, G:0.12, T:0.29
Consensus pattern (20 bp):
GATCCACCTCCATCGTTCAG
Found at i:17923 original size:42 final size:42
Alignment explanation
Indices: 17850--17957 Score: 128
Period size: 42 Copynumber: 2.6 Consensus size: 42
17840 GAAGAAGCTT
* * * **
17850 GATCCACCTACCATTGTTCAGGAT-CCACCTCCTATTGTTCAG
1 GATCCACCTCCCATCGTTCAAGATGCC-CCTCCTATCATTCAG
* * *
17892 GATTCACCTCTCATCGTTCAAGATGCCCCTCCTATCATTTAG
1 GATCCACCTCCCATCGTTCAAGATGCCCCTCCTATCATTCAG
17934 GATCCACCTCCCATCGTTCAAGAT
1 GATCCACCTCCCATCGTTCAAGAT
17958 CCACATTCCA
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 53 0.96
43 2 0.04
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (42 bp):
GATCCACCTCCCATCGTTCAAGATGCCCCTCCTATCATTCAG
Found at i:20234 original size:12 final size:12
Alignment explanation
Indices: 20213--20246 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
20203 AGTTGTGGAT
*
20213 TTTGAGATTGTG
1 TTTGATATTGTG
20225 TTTGATATTGTG
1 TTTGATATTGTG
*
20237 TTTGGTATTG
1 TTTGATATTG
20247 GAAATGTGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.29, T:0.56
Consensus pattern (12 bp):
TTTGATATTGTG
Found at i:21157 original size:39 final size:40
Alignment explanation
Indices: 21051--21178 Score: 120
Period size: 39 Copynumber: 3.2 Consensus size: 40
21041 CAAAAATCGA
** ** * *
21051 GTTGCGAAAAATAAAATTCGCGTTGCGAAATTGAAACGTGCT
1 GTTGCGAATTATAAAATT-GCGTTGCGAAAAAGAATCTTG-T
* *
21093 -TTGCGAATTATAAAATCT-TGTTGCGAAAACGAATCTTGT
1 GTTGCGAATTATAAAAT-TGCGTTGCGAAAAAGAATCTTGT
21132 GTTGCGAATT-TAAAATTGCGTTGCGAAAAAGAAAT-TTGT
1 GTTGCGAATTATAAAATTGCGTTGCGAAAAAG-AATCTTGT
21171 GTTGCGAA
1 GTTGCGAA
21179 ATTGTCAAAT
Statistics
Matches: 73, Mismatches: 9, Indels: 11
0.78 0.10 0.12
Matches are distributed among these distances:
38 1 0.01
39 30 0.41
40 27 0.37
41 14 0.19
42 1 0.01
ACGTcount: A:0.34, C:0.12, G:0.23, T:0.31
Consensus pattern (40 bp):
GTTGCGAATTATAAAATTGCGTTGCGAAAAAGAATCTTGT
Found at i:21176 original size:20 final size:20
Alignment explanation
Indices: 21111--21179 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
21101 TATAAAATCT
*
21111 TGTTGCGAAAACG-AATCTTG
1 TGTTGCGAAAAAGAAAT-TTG
**
21131 TGTTGCGAATTTA-AAA-TTG
1 TGTTGCGAA-AAAGAAATTTG
*
21150 CGTTGCGAAAAAGAAATTTG
1 TGTTGCGAAAAAGAAATTTG
21170 TGTTGCGAAA
1 TGTTGCGAAA
21180 TTGTCAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 1 0.03
19 14 0.37
20 21 0.55
21 2 0.05
ACGTcount: A:0.33, C:0.10, G:0.25, T:0.32
Consensus pattern (20 bp):
TGTTGCGAAAAAGAAATTTG
Found at i:25383 original size:21 final size:21
Alignment explanation
Indices: 25357--25431 Score: 114
Period size: 21 Copynumber: 3.6 Consensus size: 21
25347 GTTTCCAGAT
**
25357 TCGCAATGCGATTTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
25378 TCGCAATGTGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
25399 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTGGACTA
*
25420 TCGTAATGCGAA
1 TCGCAATGCGAA
25432 TATGTAAATC
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.28, C:0.20, G:0.24, T:0.28
Consensus pattern (21 bp):
TCGCAATGCGAACTTGGACTA
Found at i:25481 original size:21 final size:21
Alignment explanation
Indices: 25455--25496 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
25445 ATGCGATAGT
25455 TTGCGATAGTCCAAAATCGCA
1 TTGCGATAGTCCAAAATCGCA
25476 TTGCGATAGTCCAAAATCGCA
1 TTGCGATAGTCCAAAATCGCA
25497 ACGACTGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.19, T:0.24
Consensus pattern (21 bp):
TTGCGATAGTCCAAAATCGCA
Found at i:26090 original size:15 final size:15
Alignment explanation
Indices: 26070--26102 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
26060 GCCGTCCGTC
26070 TCGGGTCGGGTCGTG
1 TCGGGTCGGGTCGTG
26085 TCGGGTCGGGTCGTG
1 TCGGGTCGGGTCGTG
26100 TCG
1 TCG
26103 TGGTAATACG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.00, C:0.21, G:0.52, T:0.27
Consensus pattern (15 bp):
TCGGGTCGGGTCGTG
Found at i:26572 original size:19 final size:19
Alignment explanation
Indices: 26548--26592 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
26538 TATAAAATAT
*
26548 TTTAAAACTTAAGAAC-TAA
1 TTTAAAA-TAAAGAACATAA
*
26567 TTTAAAATAAAGATCATAA
1 TTTAAAATAAAGAACATAA
26586 TTTAAAA
1 TTTAAAA
26593 ACATAGTACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.56, C:0.07, G:0.04, T:0.33
Consensus pattern (19 bp):
TTTAAAATAAAGAACATAA
Found at i:27745 original size:18 final size:18
Alignment explanation
Indices: 27695--27745 Score: 52
Period size: 18 Copynumber: 2.9 Consensus size: 18
27685 TATGAAATTG
* *
27695 GATTCCAATTCC-TGACA
1 GATTTCAATTCCTTCACA
*
27712 GA-TTCTAATTCATTCACA
1 GATTTC-AATTCCTTCACA
27730 GATTTCAATTCCTTCA
1 GATTTCAATTCCTTCA
27746 GAAATATTCC
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
16 2 0.07
17 7 0.26
18 15 0.56
19 3 0.11
ACGTcount: A:0.29, C:0.25, G:0.08, T:0.37
Consensus pattern (18 bp):
GATTTCAATTCCTTCACA
Found at i:32529 original size:20 final size:21
Alignment explanation
Indices: 32496--32534 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
32486 TAATTCGGGG
32496 TAAACTACATA-TTTAGTAAA
1 TAAACTACATATTTTAGTAAA
32516 TAAACTATCA-ATTTTAGTA
1 TAAACTA-CATATTTTAGTA
32535 CTTAAACTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.38
Consensus pattern (21 bp):
TAAACTACATATTTTAGTAAA
Found at i:42914 original size:16 final size:16
Alignment explanation
Indices: 42889--42929 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
42879 ATAAAACATC
* *
42889 TGAATTATTCAGTATT
1 TGAATCATTCAATATT
42905 TGAATCATTCAATATT
1 TGAATCATTCAATATT
*
42921 TAAATCATT
1 TGAATCATT
42930 TAACGCTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.37, C:0.10, G:0.07, T:0.46
Consensus pattern (16 bp):
TGAATCATTCAATATT
Found at i:43343 original size:19 final size:18
Alignment explanation
Indices: 43319--43354 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
43309 AAATAATGTT
*
43319 TTTGTTTGTTTTGATTTTA
1 TTTGTTT-TTTTAATTTTA
43338 TTTGTTTTTTTAATTTT
1 TTTGTTTTTTTAATTTT
43355 CTGAACTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (18 bp):
TTTGTTTTTTTAATTTTA
Found at i:48798 original size:21 final size:20
Alignment explanation
Indices: 48712--48869 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
48702 AAATGACCAA
**
48712 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
48731 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
48751 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
48771 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
48792 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
48813 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
48833 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
48854 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
48870 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:48860 original size:20 final size:20
Alignment explanation
Indices: 48836--49105 Score: 276
Period size: 20 Copynumber: 13.5 Consensus size: 20
48826 CGATTTTCCA
* ** *
48836 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
48856 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
48876 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
48896 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
48916 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
**
48936 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
48956 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
48976 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
48996 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
49016 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
49036 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
49056 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
49076 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
49096 AAATCACAAC
1 AAATCGCAAC
49106 ACTGAAATTT
Statistics
Matches: 213, Mismatches: 31, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 1 0.00
20 210 0.99
21 2 0.01
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:49826 original size:24 final size:24
Alignment explanation
Indices: 49787--49833 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
49777 AAATTTGGTC
49787 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
49811 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
49834 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:50025 original size:12 final size:12
Alignment explanation
Indices: 50008--50032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
49998 ATATAATCCT
50008 GAAGAAGAAAAA
1 GAAGAAGAAAAA
50020 GAAGAAGAAAAA
1 GAAGAAGAAAAA
50032 G
1 G
50033 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:52407 original size:19 final size:19
Alignment explanation
Indices: 52367--52464 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
52357 GATTCTCTCG
52367 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
52387 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
52406 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
52420 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52439 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
52458 TTGCGAT
1 TTGCGAT
52465 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:52461 original size:52 final size:53
Alignment explanation
Indices: 52348--52464 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
52338 GAAATGAAAA
52348 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
52401 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
52453 TCGCATTGCGAT
1 TCGCATTGCGAT
52465 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:52590 original size:14 final size:14
Alignment explanation
Indices: 52571--52607 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
52561 CATCAATTAC
52571 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
52585 ACAAATCATCTTTT
1 ACAAATCAACTTTT
52599 ACAAATCAA
1 ACAAATCAA
52608 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:54576 original size:14 final size:14
Alignment explanation
Indices: 54557--54613 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54547 GCGAAATGAA
*
54557 AATCGCAACGACAG
1 AATCGCAACGAAAG
54571 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
54588 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
54604 AATCGCAACG
1 AATCGCAACG
54614 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:54584 original size:33 final size:33
Alignment explanation
Indices: 54538--54629 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
54528 GCGAAACCAA
*
54538 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
54571 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
54604 AATCGCAACGCGAAATG-AAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
54630 TGCGATTTTG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 9 0.16
33 47 0.84
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:54595 original size:19 final size:19
Alignment explanation
Indices: 54501--54634 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
54491 TAGTTTACTT
* *
54501 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
54521 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
54540 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
54559 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
54573 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
54592 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
54606 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
54624 TCGCAATGCGA
1 TCGCAACGCGA
54635 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 20
0.78 0.06 0.16
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
18 12 0.12
19 35 0.36
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:54652 original size:19 final size:19
Alignment explanation
Indices: 54630--54758 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
54620 GAAATCGCAA
54630 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
54649 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
54663 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
54682 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
54696 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
54715 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
54734 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
54754 TGCGA
1 TGCGA
54759 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:54672 original size:33 final size:33
Alignment explanation
Indices: 54630--54721 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
54620 GAAATCGCAA
54630 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
54663 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
54696 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
54722 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:54961 original size:93 final size:93
Alignment explanation
Indices: 54802--55182 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
54792 TTGAATGGAT
54802 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
54867 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
54895 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
54960 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
54988 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55053 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55081 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
* *
55146 AGTTTAGCAGAATTGGCAGCAACTGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55174 AAATTTACT
1 AAATTTACT
55183 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:56908 original size:14 final size:14
Alignment explanation
Indices: 56889--56978 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
56879 TTGAAATGAA
56889 AATCGCAACGAGAG
1 AATCGCAACGAGAG
56903 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
56920 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
56936 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
56955 AATCGCAACGAGAG
1 AATCGCAACGAGAG
56969 AATCGCAACG
1 AATCGCAACG
56979 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:56926 original size:33 final size:33
Alignment explanation
Indices: 56881--56995 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
56871 TCTTTTGGTT
56881 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
56914 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
56947 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
56980 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
56996 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:56927 original size:19 final size:18
Alignment explanation
Indices: 56888--57000 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
56878 GTTGAAATGA
56888 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
56903 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
56920 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
56936 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
56953 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
56969 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
56986 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
57001 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:57031 original size:14 final size:14
Alignment explanation
Indices: 57012--57065 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
57002 TTTGGTTTCG
57012 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57026 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57045 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57059 CGTTGCG
1 CGTTGCG
57066 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57044 original size:33 final size:33
Alignment explanation
Indices: 56996--57076 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
56986 AAAATCGCAA
**
56996 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
57029 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
57062 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
57077 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:57112 original size:41 final size:41
Alignment explanation
Indices: 57052--57129 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
57042 TCGCGTTGCG
* *
57052 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
57093 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
57130 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:57128 original size:21 final size:21
Alignment explanation
Indices: 57053--57128 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
57043 CGCGTTGCGA
*
57053 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
57074 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
57094 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
57115 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
57129 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:57255 original size:33 final size:33
Alignment explanation
Indices: 57208--57278 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
57198 AATACTAACT
* *
57208 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
57241 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
57274 TGAAA
1 TGAAA
57279 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:57512 original size:22 final size:22
Alignment explanation
Indices: 57460--57514 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
57450 TGGTTGTGAG
**
57460 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
57482 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
57504 GGATTTCTTCG
1 GGATTTCTTCG
57515 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:57685 original size:20 final size:20
Alignment explanation
Indices: 57660--57853 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
57650 CTTTAAATAT
57660 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
57680 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
57702 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
57721 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
57741 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
57761 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
57781 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
57801 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
57821 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
57841 CGCGTTGCGATTT
1 CGCGTTGCGATTT
57854 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:57847 original size:60 final size:60
Alignment explanation
Indices: 57660--57853 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
57650 CTTTAAATAT
**
57660 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
57721 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
57781 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
57841 CGCGTTGCGATTT
1 CGCGTTGCGATTT
57854 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:57870 original size:21 final size:21
Alignment explanation
Indices: 57840--57922 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
57830 ATTTTCATAT
*
57840 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
57861 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
57882 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
57903 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
57923 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:57913 original size:42 final size:43
Alignment explanation
Indices: 57820--57918 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
57810 ATTTATGTGT
* *
57820 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
57861 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
57903 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
57919 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:62526 original size:1 final size:1
Alignment explanation
Indices: 62520--62559 Score: 53
Period size: 1 Copynumber: 40.0 Consensus size: 1
62510 GTATGAGTAC
** *
62520 TTTTTTTTTGGTTTTTTGTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
62560 GAATATGAAG
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.07, T:0.93
Consensus pattern (1 bp):
T
Found at i:63096 original size:17 final size:17
Alignment explanation
Indices: 63074--63110 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
63064 GAGAAACAAT
*
63074 GAATGAAGATTCCATTA
1 GAATGAAGATTCCACTA
63091 GAATGAAGATTCCACTA
1 GAATGAAGATTCCACTA
63108 GAA
1 GAA
63111 GTAATCCTGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.14, G:0.19, T:0.24
Consensus pattern (17 bp):
GAATGAAGATTCCACTA
Found at i:63723 original size:32 final size:34
Alignment explanation
Indices: 63687--63789 Score: 115
Period size: 32 Copynumber: 3.1 Consensus size: 34
63677 AAAATAATTT
* *
63687 TAAATAATTTAATAAGG-TT-ATTTATTTTAAAA
1 TAAATTATTTAATATGGATTGATTTATTTTAAAA
63719 TAAATTATTATAAAATATGGATTGATTTATTTT-AAA
1 TAAATTATT-T--AATATGGATTGATTTATTTTAAAA
* *
63755 TAATTTA-TTAGTATGGATTGATTTATTTTAAAA
1 TAAATTATTTAATATGGATTGATTTATTTTAAAA
63788 TA
1 TA
63790 TTGATTGATT
Statistics
Matches: 61, Mismatches: 4, Indels: 11
0.80 0.05 0.14
Matches are distributed among these distances:
32 27 0.44
33 6 0.10
34 1 0.02
35 7 0.11
36 11 0.18
37 9 0.15
ACGTcount: A:0.43, C:0.00, G:0.09, T:0.49
Consensus pattern (34 bp):
TAAATTATTTAATATGGATTGATTTATTTTAAAA
Found at i:63763 original size:36 final size:32
Alignment explanation
Indices: 63683--63840 Score: 112
Period size: 32 Copynumber: 5.2 Consensus size: 32
63673 TATTAAAATA
*
63683 ATTTTAAAT-AA-T-TTAATAAGG-TT-ATTT
1 ATTTTAAATAAATTATTAATATGGATTGATTT
63710 ATTTTAAAATAAATTATTATAAAATATGGATTGATTT
1 ATTTT-AAATAAATTA-T-T--AATATGGATTGATTT
* *
63747 ATTTTAAATAATTTATTAGTATGGATTGATTT
1 ATTTTAAATAAATTATTAATATGGATTGATTT
63779 A-TTT---TAAA--A-T-AT-T-GATTGATTT
1 ATTTTAAATAAATTATTAATATGGATTGATTT
* * *
63801 ATTTTAAATAATTTATTAGTATAGATTGATTT
1 ATTTTAAATAAATTATTAATATGGATTGATTT
63833 ATTTTAAA
1 ATTTTAAA
63841 ATATAGATTG
Statistics
Matches: 104, Mismatches: 7, Indels: 35
0.71 0.05 0.24
Matches are distributed among these distances:
22 10 0.10
23 4 0.04
24 1 0.01
25 1 0.01
26 4 0.04
27 5 0.05
28 8 0.08
29 3 0.03
30 2 0.02
31 4 0.04
32 33 0.32
33 1 0.01
34 1 0.01
35 7 0.07
36 11 0.11
37 9 0.09
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (32 bp):
ATTTTAAATAAATTATTAATATGGATTGATTT
Found at i:63787 original size:54 final size:54
Alignment explanation
Indices: 63723--63911 Score: 333
Period size: 54 Copynumber: 3.5 Consensus size: 54
63713 TTAAAATAAA
*
63723 TTATTATAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *
63777 TTATTTTAAAATATTGATTGATTTATTTTAAATAATTTATTAGTATAGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
* *
63831 TTATTTTAAAATATAGATTGATTTATTTTAAATAATTTATTCGTATGGATTGAT
1 TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
63885 TTATTTTAAAATATGGATTGATTTATT
1 TTATTTTAAAATATGGATTGATTTATT
63912 ATTGTAGTTG
Statistics
Matches: 128, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 128 1.00
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (54 bp):
TTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
Found at i:63833 original size:32 final size:32
Alignment explanation
Indices: 63792--63894 Score: 118
Period size: 32 Copynumber: 3.5 Consensus size: 32
63782 TTAAAATATT
63792 GATTGATTTATTTTAAATAATTTATTAGTATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
63824 GATTGATTTA-TTT---TAA---A--A-TATA
1 GATTGATTTATTTTAAATAATTTATTAGTATA
* *
63846 GATTGATTTATTTTAAATAATTTATTCGTATG
1 GATTGATTTATTTTAAATAATTTATTAGTATA
63878 GATTGATTTATTTTAAA
1 GATTGATTTATTTTAAA
63895 ATATGGATTG
Statistics
Matches: 59, Mismatches: 2, Indels: 20
0.73 0.02 0.25
Matches are distributed among these distances:
22 14 0.24
23 4 0.07
25 1 0.02
26 3 0.05
28 3 0.05
29 1 0.02
31 3 0.05
32 30 0.51
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.52
Consensus pattern (32 bp):
GATTGATTTATTTTAAATAATTTATTAGTATA
Found at i:63845 original size:22 final size:22
Alignment explanation
Indices: 63820--63862 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
63810 AATTTATTAG
63820 TATAGATTGATTTATTTTAAAA
1 TATAGATTGATTTATTTTAAAA
63842 TATAGATTGATTTATTTTAAA
1 TATAGATTGATTTATTTTAAA
63863 TAATTTATTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.09, T:0.51
Consensus pattern (22 bp):
TATAGATTGATTTATTTTAAAA
Found at i:63943 original size:80 final size:80
Alignment explanation
Indices: 63842--63991 Score: 264
Period size: 80 Copynumber: 1.9 Consensus size: 80
63832 TATTTTAAAA
* * * *
63842 TATAGATTGATTTATTTTAAATAATTTATTCGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATAAATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTGAT
63907 TTATTATTGTAGTTG
66 TTATTATTGTAGTTG
63922 TATAAATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTGAT
1 TATAAATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTGAT
63987 TTATT
66 TTATT
63992 TTAAAAAATT
Statistics
Matches: 66, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
80 66 1.00
ACGTcount: A:0.35, C:0.01, G:0.12, T:0.53
Consensus pattern (80 bp):
TATAAATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTGAT
TTATTATTGTAGTTG
Found at i:63952 original size:134 final size:134
Alignment explanation
Indices: 63793--64045 Score: 461
Period size: 134 Copynumber: 1.9 Consensus size: 134
63783 TAAAATATTG
*
63793 ATTGATTTATTTTAAATAATTTATTAGTATAGATTGATTTATTTTAAAATATAGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAGATTGATTTATT
* * *
63858 TTAAATAATTTATTCGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGT
66 TTAAAAAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGT
63923 ATAA
131 ATAA
*
63927 ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGGATTGATTTATT
1 ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAGATTGATTTATT
63992 TTAAAAAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATT
66 TTAAAAAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATT
64046 TTAAATAATT
Statistics
Matches: 114, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
134 114 1.00
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.52
Consensus pattern (134 bp):
ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATAGATTGATTTATT
TTAAAAAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGTTGT
ATAA
Found at i:63967 original size:32 final size:31
Alignment explanation
Indices: 63921--64029 Score: 110
Period size: 32 Copynumber: 3.7 Consensus size: 31
63911 TATTGTAGTT
*
63921 GTATAAATTGATTTATTTTAAATAATTTATTA
1 GTATAGATTGATTTATTTTAAA-AATTTATTA
*
63953 GTATAGATTAATTTATTTT-AAAA--TA-T-
1 GTATAGATTGATTTATTTTAAAAATTTATTA
63979 G----GATTGATTTATTTTAAAAAATTTATTA
1 GTATAGATTGATTTATTTT-AAAAATTTATTA
*
64007 GTATGGATTGATTTATTTTAAAA
1 GTATAGATTGATTTATTTTAAAA
64030 TATGGATTAA
Statistics
Matches: 64, Mismatches: 3, Indels: 21
0.73 0.03 0.24
Matches are distributed among these distances:
22 13 0.20
24 4 0.06
26 3 0.05
27 2 0.03
28 3 0.05
30 2 0.03
31 6 0.09
32 31 0.48
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.50
Consensus pattern (31 bp):
GTATAGATTGATTTATTTTAAAAATTTATTA
Found at i:63991 original size:54 final size:54
Alignment explanation
Indices: 63927--64066 Score: 235
Period size: 54 Copynumber: 2.6 Consensus size: 54
63917 AGTTGTATAA
63927 ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGG
1 ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGG
* * *
63981 ATTGATTTATTTTAAAAAATTTATTAGTATGGATTGATTTATTTTAAAATATGG
1 ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGG
* *
64035 ATTAATTTATTTTAAATAATTTATTATTATAG
1 ATTGATTTATTTTAAATAATTTATTAGTATAG
64067 TTGTATGGAT
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (54 bp):
ATTGATTTATTTTAAATAATTTATTAGTATAGATTAATTTATTTTAAAATATGG
Found at i:64060 original size:22 final size:22
Alignment explanation
Indices: 64008--64050 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
63998 AATTTATTAG
*
64008 TATGGATTGATTTATTTTAAAA
1 TATGGATTAATTTATTTTAAAA
64030 TATGGATTAATTTATTTTAAA
1 TATGGATTAATTTATTTTAAA
64051 TAATTTATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTAATTTATTTTAAAA
Found at i:64132 original size:31 final size:31
Alignment explanation
Indices: 64075--64133 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
64065 AGTTGTATGG
* **
64075 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATATCAGTATTACAAAACTAAA
64106 ATTATTTAAATATCAGTATTACAAAACT
1 ATTATTTAAATATCAGTATTACAAAACT
64134 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATATCAGTATTACAAAACTAAA
Found at i:67040 original size:2 final size:2
Alignment explanation
Indices: 67033--67072 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
67023 TCTTTGATGG
67033 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
67073 GAGAATTCGA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:68116 original size:21 final size:21
Alignment explanation
Indices: 68087--68128 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
68077 ATTTTGAAAT
*
68087 TTATTTTTA-AAAAAAATATTA
1 TTATATTTATAAAAAAA-ATTA
68108 TTATATTTATAAAAAAAATTA
1 TTATATTTATAAAAAAAATTA
68129 ATTTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATATTTATAAAAAAAATTA
Found at i:76659 original size:6 final size:6
Alignment explanation
Indices: 76648--76687 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
76638 TATAGACAAA
* *
76648 AAAATT AAAATT AAAATT AAAATT AAAATG AAATTT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAATT AAAATT AAAA
76688 GTTCACGCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (6 bp):
AAAATT
Found at i:79827 original size:6 final size:6
Alignment explanation
Indices: 79816--79850 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
79806 CGTGGAGTCC
*
79816 GGATTT GGATTT GGATTT GGATTT AGATTT GGATT
1 GGATTT GGATTT GGATTT GGATTT GGATTT GGATT
79851 AGGCACGTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.20, C:0.00, G:0.31, T:0.49
Consensus pattern (6 bp):
GGATTT
Found at i:81228 original size:2 final size:2
Alignment explanation
Indices: 81221--81251 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
81211 CTCCAAAACA
81221 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 A
81252 GTGAATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:81780 original size:2 final size:2
Alignment explanation
Indices: 81773--81818 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
81763 CACCTGAGAA
81773 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
81815 AT AT
1 AT AT
81819 TGTTAAACAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82138 original size:135 final size:134
Alignment explanation
Indices: 81885--82144 Score: 299
Period size: 135 Copynumber: 1.9 Consensus size: 134
81875 TTCACATGGG
* * * * * * * *
81885 CATGCAGATCCTCATAGCTAATAGACTTGAAAATTTACTCACCCCTCTCCCTTGCTTTTTTAGGT
1 CATGCAGACCCTCATAACTAAAAGACCTGAAAATTCACTCACCCCTCTCCATTGCTTGTTTAGAT
* * * ***
81950 TTTCTTTCCGTTTTCGCAGATTCAGCTTGAGCTGCCGTGTCAAGGAAATAACAAATTATTAGCCA
66 TTTCTTTCCATTTTCGCAGAGTCAGATTGAGCTGCCACATCAAGGAAATAACAAATTATTAGCCA
82015 AAAT
131 AAAT
* *
82019 CATGCAGGACCCTCATAACTAAAAGACCTGAAAATTCACTTACCCTTCTCCATTGCTTGTTTAGA
1 CATGCA-GACCCTCATAACTAAAAGACCTGAAAATTCACTCACCCCTCTCCATTGCTTGTTTAGA
* * * *
82084 TTTTGTTTCCAATTTT-GTAGAGTCAGATTGAGCTGCCACATCAGGGGAAA-AACAATTTATT
65 TTTTCTTTCC-ATTTTCGCAGAGTCAGATTGAGCTGCCACATCA-AGGAAATAACAAATTATT
82145 CAAGCAGTGA
Statistics
Matches: 103, Mismatches: 20, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
134 6 0.06
135 88 0.85
136 9 0.09
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (134 bp):
CATGCAGACCCTCATAACTAAAAGACCTGAAAATTCACTCACCCCTCTCCATTGCTTGTTTAGAT
TTTCTTTCCATTTTCGCAGAGTCAGATTGAGCTGCCACATCAAGGAAATAACAAATTATTAGCCA
AAAT
Done.