Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002360.1 Hibiscus syriacus cultivar Beakdansim tig00004816_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: 95479
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
File 1 of 2
Found at i:5749 original size:20 final size:19
Alignment explanation
Indices: 5724--5780 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
5714 GCAAAGCGCG
*
5724 TTTATTTTCGCAACGCGAAT
1 TTTATTTTCGCAACAC-AAT
*
5744 TTTATTTTCGAAACACAAT
1 TTTATTTTCGCAACACAAT
* *
5763 ATTAATTTCGCAACACAA
1 TTTATTTTCGCAACACAA
5781 ATGTAAACAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 18 0.56
20 14 0.44
ACGTcount: A:0.35, C:0.19, G:0.09, T:0.37
Consensus pattern (19 bp):
TTTATTTTCGCAACACAAT
Found at i:5882 original size:22 final size:22
Alignment explanation
Indices: 5855--5909 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
5845 TCTCTCACTC
*
5855 TATCCGGCGTCATCCGTCCCCA
1 TATCCGGCGACATCCGTCCCCA
* *
5877 TCTCCGGCAACATCCGTCCCCA
1 TATCCGGCGACATCCGTCCCCA
5899 TATCCGGCGAC
1 TATCCGGCGAC
5910 CCCCTCTATC
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.45, G:0.18, T:0.20
Consensus pattern (22 bp):
TATCCGGCGACATCCGTCCCCA
Found at i:7833 original size:42 final size:42
Alignment explanation
Indices: 7774--7872 Score: 144
Period size: 42 Copynumber: 2.4 Consensus size: 42
7764 CCCCCCACTT
* * *
7774 CGAGAGCCATCACCTGATCGAGCAGATTTTACAGCTCGACAC
1 CGAGAGCCATCACCTGATCGAGCAGATTATACACCTCCACAC
* * *
7816 CGAGAGTCATCACCTGATCGAGCCGATTATATACCTCCACAC
1 CGAGAGCCATCACCTGATCGAGCAGATTATACACCTCCACAC
7858 CGAGAGCCATCACCT
1 CGAGAGCCATCACCT
7873 ATTTCATCAC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 50 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.19
Consensus pattern (42 bp):
CGAGAGCCATCACCTGATCGAGCAGATTATACACCTCCACAC
Found at i:8246 original size:4 final size:4
Alignment explanation
Indices: 8237--8270 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
8227 TTTTTCGGCA
* *
8237 TTAT TTAT TTAT TTAT TTAT GTAT TAAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
8271 TAGCGGCCCG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (4 bp):
TTAT
Found at i:8440 original size:21 final size:21
Alignment explanation
Indices: 8414--8465 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
8404 ATTCACCTGT
**
8414 CATCGTTCAGGAGGCCCCTCC
1 CATCGTTCAAAAGGCCCCTCC
8435 CATCGTTCAAAAGGCCCCTCC
1 CATCGTTCAAAAGGCCCCTCC
*
8456 CACCGTTCAA
1 CATCGTTCAA
8466 GAGCCCGATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.21, C:0.42, G:0.17, T:0.19
Consensus pattern (21 bp):
CATCGTTCAAAAGGCCCCTCC
Found at i:12453 original size:24 final size:23
Alignment explanation
Indices: 12390--12441 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 23
12380 AACATCATCA
12390 AAATTCGAGTATTGACCAAGATC
1 AAATTCGAGTATTGACCAAGATC
* *
12413 AAAGTCTGGGTATTGACCAAGATC
1 AAATTC-GAGTATTGACCAAGATC
12437 AAATT
1 AAATT
12442 TCGAATACTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 5 0.20
24 20 0.80
ACGTcount: A:0.38, C:0.15, G:0.19, T:0.27
Consensus pattern (23 bp):
AAATTCGAGTATTGACCAAGATC
Found at i:13302 original size:27 final size:27
Alignment explanation
Indices: 13272--13333 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
13262 TGGAGATGGA
*
13272 ATGAGTTGTGATTTAGGGATTTAGGTT
1 ATGAGTTATGATTTAGGGATTTAGGTT
13299 ATGAGTTATGATTTAGGGATTTAGGTT
1 ATGAGTTATGATTTAGGGATTTAGGTT
13326 ATGAGTTA
1 ATGAGTTA
13334 CTGCTGCTGC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.26, C:0.00, G:0.31, T:0.44
Consensus pattern (27 bp):
ATGAGTTATGATTTAGGGATTTAGGTT
Found at i:13415 original size:40 final size:40
Alignment explanation
Indices: 13359--13480 Score: 133
Period size: 40 Copynumber: 3.0 Consensus size: 40
13349 TTATATACCC
13359 AAAACAAAATTTGTGTTGCGAATTCGAAAATCGAGTTGC-
1 AAAACAAAATTTGTGTTGCGAATTCGAAAATCGAGTTGCG
* * * **
13398 ACAAACAAAATTCGTGTTGCGATTTAGAAAATCTTGTTGCG
1 A-AAACAAAATTTGTGTTGCGAATTCGAAAATCGAGTTGCG
* *
13439 AAAA-AGAAATTTGCGTTGTGAATTC-AGAAATCGAGTTGCG
1 AAAACA-AAATTTGTGTTGCGAATTCGA-AAATCGAGTTGCG
13479 AA
1 AA
13481 TTTGAAATTC
Statistics
Matches: 67, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
39 3 0.04
40 63 0.94
41 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (40 bp):
AAAACAAAATTTGTGTTGCGAATTCGAAAATCGAGTTGCG
Found at i:13481 original size:20 final size:20
Alignment explanation
Indices: 13453--13543 Score: 62
Period size: 20 Copynumber: 4.5 Consensus size: 20
13443 AGAAATTTGC
*
13453 GTTGTGAATTCAGAAATCGA
1 GTTGCGAATTCAGAAATCGA
* *
13473 GTTGCGAATT-TGAAATTCCGT
1 GTTGCGAATTCAGAAA-T-CGA
** *
13494 GTTGCGAATTTGGAAATCGC
1 GTTGCGAATTCAGAAATCGA
*
13514 GTTGCG-ATTGCAGAAA-CTAA
1 GTTGCGAATT-CAGAAATC-GA
13534 GTTGCGAATT
1 GTTGCGAATT
13544 TGGAAAATGG
Statistics
Matches: 56, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
19 8 0.14
20 28 0.50
21 16 0.29
22 4 0.07
ACGTcount: A:0.29, C:0.13, G:0.26, T:0.32
Consensus pattern (20 bp):
GTTGCGAATTCAGAAATCGA
Found at i:15649 original size:3 final size:3
Alignment explanation
Indices: 15641--15669 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
15631 AAGTAATTTA
15641 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
15670 ATAGAAAACA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:17681 original size:2 final size:2
Alignment explanation
Indices: 17637--17668 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
17627 TAGTCGGTTC
17637 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
17669 TCTTTAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:17816 original size:12 final size:12
Alignment explanation
Indices: 17799--17828 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
17789 GATGAAACTT
*
17799 ATTAAAAATATA
1 ATTAAAAATACA
17811 ATTAAAAATACA
1 ATTAAAAATACA
17823 ATTAAA
1 ATTAAA
17829 GTTAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (12 bp):
ATTAAAAATACA
Found at i:17940 original size:39 final size:38
Alignment explanation
Indices: 17873--17984 Score: 107
Period size: 39 Copynumber: 2.9 Consensus size: 38
17863 GATTGCTATG
* * * *
17873 GTGAAATAATTTAGAAAATTAACAATTTAGAATGTTATA
1 GTGAAATAATTTA-AGAATTAAGAATTTAAAATATTATA
* * * *
17912 GTGTAATAGTTTAAGAAATTAGGAATTTAAAATATTATG
1 GTGAAATAATTTAAG-AATTAAGAATTTAAAATATTATA
* **
17951 GTGAAATAATTTGAGAATTAAGAATAAAAAATAT
1 GTGAAATAATTTAAGAATTAAGAATTTAAAATAT
17985 AATATAAAAT
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
38 17 0.29
39 41 0.71
ACGTcount: A:0.49, C:0.01, G:0.15, T:0.35
Consensus pattern (38 bp):
GTGAAATAATTTAAGAATTAAGAATTTAAAATATTATA
Found at i:18441 original size:39 final size:39
Alignment explanation
Indices: 18387--18464 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
18377 CGTTATCCCA
18387 TACAAAAATTTTATGTGGCTGATATGTGTGTGTGTGTGT
1 TACAAAAATTTTATGTGGCTGATATGTGTGTGTGTGTGT
18426 TACAAAAATTTTATGTGGCTGATATGTGTGTGTGTGTGT
1 TACAAAAATTTTATGTGGCTGATATGTGTGTGTGTGTGT
18465 GTGCGCGTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.23, C:0.05, G:0.28, T:0.44
Consensus pattern (39 bp):
TACAAAAATTTTATGTGGCTGATATGTGTGTGTGTGTGT
Found at i:18490 original size:22 final size:22
Alignment explanation
Indices: 18465--18511 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
18455 GTGTGTGTGT
18465 GTGCGCGTGCGTGCGTGCGTGC
1 GTGCGCGTGCGTGCGTGCGTGC
18487 GTGCGCGTGCGTGCGTGCGTGC
1 GTGCGCGTGCGTGCGTGCGTGC
18509 GTG
1 GTG
18512 TGTGTGTGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.00, C:0.26, G:0.51, T:0.23
Consensus pattern (22 bp):
GTGCGCGTGCGTGCGTGCGTGC
Found at i:18494 original size:18 final size:18
Alignment explanation
Indices: 18473--18509 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
18463 GTGTGCGCGT
18473 GCGTGCGTGCGTGCGTGC
1 GCGTGCGTGCGTGCGTGC
18491 GCGTGCGTGCGTGCGTGC
1 GCGTGCGTGCGTGCGTGC
18509 G
1 G
18510 TGTGTGTGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.00, C:0.27, G:0.51, T:0.22
Consensus pattern (18 bp):
GCGTGCGTGCGTGCGTGC
Found at i:20395 original size:19 final size:19
Alignment explanation
Indices: 20373--20417 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
20363 AAAATTAAGA
20373 GATTAGTGAATTATTAATG
1 GATTAGTGAATTATTAATG
20392 GATTAGTGAATTATTAATG
1 GATTAGTGAATTATTAATG
20411 GATTAGT
1 GATTAGT
20418 AAAATGGGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (19 bp):
GATTAGTGAATTATTAATG
Found at i:20845 original size:20 final size:20
Alignment explanation
Indices: 20800--20888 Score: 83
Period size: 20 Copynumber: 4.4 Consensus size: 20
20790 GGATGATCAA
* *
20800 TATCGATACTGATTTAAGAAG
1 TATCGATACTGATGT-GGAAG
*
20821 TATCGATACTGATGTGGAGG
1 TATCGATACTGATGTGGAAG
* *
20841 TATCGATAACAAGA-G-GAAAG
1 TATCGAT-AC-TGATGTGGAAG
*
20861 TATCGATACTGATGTGGAGG
1 TATCGATACTGATGTGGAAG
20881 TATCGATA
1 TATCGATA
20889 ACAAGAGGAA
Statistics
Matches: 55, Mismatches: 9, Indels: 9
0.75 0.12 0.12
Matches are distributed among these distances:
18 2 0.04
19 3 0.05
20 31 0.56
21 17 0.31
22 2 0.04
ACGTcount: A:0.35, C:0.10, G:0.27, T:0.28
Consensus pattern (20 bp):
TATCGATACTGATGTGGAAG
Found at i:20865 original size:40 final size:40
Alignment explanation
Indices: 20818--20908 Score: 182
Period size: 40 Copynumber: 2.3 Consensus size: 40
20808 CTGATTTAAG
20818 AAGTATCGATACTGATGTGGAGGTATCGATAACAAGAGGA
1 AAGTATCGATACTGATGTGGAGGTATCGATAACAAGAGGA
20858 AAGTATCGATACTGATGTGGAGGTATCGATAACAAGAGGA
1 AAGTATCGATACTGATGTGGAGGTATCGATAACAAGAGGA
20898 AAGTATCGATA
1 AAGTATCGATA
20909 TTGTAATTGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 51 1.00
ACGTcount: A:0.38, C:0.10, G:0.29, T:0.23
Consensus pattern (40 bp):
AAGTATCGATACTGATGTGGAGGTATCGATAACAAGAGGA
Found at i:20903 original size:20 final size:20
Alignment explanation
Indices: 20840--20908 Score: 79
Period size: 20 Copynumber: 3.5 Consensus size: 20
20830 TGATGTGGAG
20840 GTATCGATAACAAGAGGAAA
1 GTATCGATAACAAGAGGAAA
* * *
20860 GTATCGAT-AC-TGATGTGGAG
1 GTATCGATAACAAGA-G-GAAA
20880 GTATCGATAACAAGAGGAAA
1 GTATCGATAACAAGAGGAAA
20900 GTATCGATA
1 GTATCGATA
20909 TTGTAATTGA
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 29 0.74
21 3 0.08
22 2 0.05
ACGTcount: A:0.41, C:0.10, G:0.28, T:0.22
Consensus pattern (20 bp):
GTATCGATAACAAGAGGAAA
Found at i:21587 original size:23 final size:23
Alignment explanation
Indices: 21557--21624 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
21547 GTCGAGGGTT
21557 CTATGTGGTCCTTCGGAACAAAC
1 CTATGTGGTCCTTCGGAACAAAC
*
21580 CTATGTGGTCCTTCGGGACAAAC
1 CTATGTGGTCCTTCGGAACAAAC
* *
21603 CTATGTGGTCATTCAGAACAAA
1 CTATGTGGTCCTTCGGAACAAA
21625 TATGTCGCAC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.28, C:0.24, G:0.22, T:0.26
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGAACAAAC
Found at i:21776 original size:23 final size:23
Alignment explanation
Indices: 21750--21793 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
21740 AAAAGTATAC
21750 ATTGAATTTCTTATGAAATGTAA
1 ATTGAATTTCTTATGAAATGTAA
21773 ATTGAATTTCTTATGAAATGT
1 ATTGAATTTCTTATGAAATGT
21794 TTTCGTACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.14, T:0.45
Consensus pattern (23 bp):
ATTGAATTTCTTATGAAATGTAA
Found at i:25116 original size:102 final size:103
Alignment explanation
Indices: 24992--25196 Score: 295
Period size: 102 Copynumber: 2.0 Consensus size: 103
24982 ACTGATTGAG
* * **
24992 TTATCTCTCCCAATTGGTTGGATTAATGCATCCAAGTCGGATGAAGAATCCCCAGTATGTCTGTG
1 TTATCTCGCCCAATTGGTTGGATTAATGCATCCAAGTCAGATGAAGAATCCCCACCATGTCTGTG
* *
25057 GTGACCATCCTCC-GGAGAATCAGAGAAGTCATTATCA
66 GTGACAATCCTCCTGGAGAATCAGAGAAGCCATTATCA
** *
25094 TTATCTCGCCCAATTGGTTGGATTAATGCATCCAAGTCAGATGGTGAATTCCCACCATGTCTGTG
1 TTATCTCGCCCAATTGGTTGGATTAATGCATCCAAGTCAGATGAAGAATCCCCACCATGTCTGTG
*
25159 GTGACAATCCTCCTTTGGAGAATCAGAGATGCCATTAT
66 GTGACAATCCTCC--TGGAGAATCAGAGAAGCCATTAT
25197 TATCATTACC
Statistics
Matches: 90, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
102 70 0.78
105 20 0.22
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.30
Consensus pattern (103 bp):
TTATCTCGCCCAATTGGTTGGATTAATGCATCCAAGTCAGATGAAGAATCCCCACCATGTCTGTG
GTGACAATCCTCCTGGAGAATCAGAGAAGCCATTATCA
Found at i:30270 original size:20 final size:20
Alignment explanation
Indices: 30245--30359 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
30235 AATTGGGAAA
*
30245 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
30265 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * *
30285 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
30306 ATTGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
30326 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
30346 TTCGCAACGCGATA
1 ATCGCAACGCGATA
30360 ATACATAATC
Statistics
Matches: 79, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:30289 original size:61 final size:61
Alignment explanation
Indices: 30242--30373 Score: 174
Period size: 61 Copynumber: 2.2 Consensus size: 61
30232 GCGAATTGGG
* * * * *
30242 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
* * * *
30303 AAAATTGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
*
30364 ATAATCGCAA
1 AAAATCGCAA
30374 TGTGATTTTC
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCGCAACGCGATAATAC
Found at i:30893 original size:20 final size:20
Alignment explanation
Indices: 30834--30897 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
30824 GCGATTTTAG
*
30834 TTTCGCGTTGCGATAGTCAA
1 TTTCGCGTTGCGATAGTCAT
*
30854 ATTCGCGTTGCGATAGTCAT
1 TTTCGCGTTGCGATAGTCAT
* **
30874 TTTCGTGTTGCGATTTTCAT
1 TTTCGCGTTGCGATAGTCAT
30894 TTTC
1 TTTC
30898 AGAAACTATT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.16, C:0.19, G:0.22, T:0.44
Consensus pattern (20 bp):
TTTCGCGTTGCGATAGTCAT
Found at i:31088 original size:25 final size:24
Alignment explanation
Indices: 31034--31088 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
31024 TGTTTATTAT
* *
31034 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
31058 TAGTTTTTGGTATAT-TTAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
31084 TGTTT
1 TGTTT
31089 ATTGCTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 5 0.19
25 17 0.65
26 4 0.15
ACGTcount: A:0.20, C:0.07, G:0.18, T:0.55
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:32238 original size:18 final size:18
Alignment explanation
Indices: 32217--32261 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
32207 TCCACTTCGG
*
32217 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
32235 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
32253 GAGCCATCA
1 GAGCCATCA
32262 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:32768 original size:20 final size:20
Alignment explanation
Indices: 32743--32788 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
32733 TAGTTTACTT
*
32743 TCGCAACATGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
32763 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
32783 TCGCAA
1 TCGCAA
32789 TGCGAAATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:32797 original size:19 final size:20
Alignment explanation
Indices: 32754--32798 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
32744 CGCAACATGA
32754 AAATGACTATCGCAACGCGG
1 AAATGACTATCGCAACGCGG
* *
32774 AAATGGCTATCGCAATGC-G
1 AAATGACTATCGCAACGCGG
32793 AAATGA
1 AAATGA
32799 AAAGCGCAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (20 bp):
AAATGACTATCGCAACGCGG
Found at i:32806 original size:19 final size:19
Alignment explanation
Indices: 32782--32840 Score: 65
Period size: 19 Copynumber: 3.4 Consensus size: 19
32772 GGAAATGGCT
32782 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
32801 AGCGCAA--CG--A-CAAA
1 ATCGCAATGCGAAATGAAA
32815 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32834 ATCGCAA
1 ATCGCAA
32841 CGACAAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
14 9 0.29
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 16 0.52
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32820 original size:14 final size:14
Alignment explanation
Indices: 32798--32854 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
32788 ATGCGAAATG
*
32798 AAAAGCGCAACGAC
1 AAAATCGCAACGAC
*
32812 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
32831 AAAATCGCAACGAC
1 AAAATCGCAACGAC
32845 AAAATCGCAA
1 AAAATCGCAA
32855 TGCGAATTGC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 19 0.54
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.51, C:0.23, G:0.18, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:32824 original size:33 final size:33
Alignment explanation
Indices: 32782--32860 Score: 149
Period size: 33 Copynumber: 2.4 Consensus size: 33
32772 GGAAATGGCT
32782 ATCGCAATGCGAAATGAAAAGCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAAGCGCAACGACAAA
*
32815 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAAGCGCAACGACAAA
32848 ATCGCAATGCGAA
1 ATCGCAATGCGAA
32861 TTGCGACTTT
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAAGCGCAACGACAAA
Found at i:32884 original size:19 final size:18
Alignment explanation
Indices: 32860--33027 Score: 108
Period size: 19 Copynumber: 9.6 Consensus size: 18
32850 CGCAATGCGA
32860 ATTGCGACTTTCATTTCGC
1 ATTGCGA-TTTCATTTCGC
*
32879 ATTGCGATTT--TGTCG-
1 ATTGCGATTTCATTTCGC
32894 -TTGCGATTTTCATTTCGC
1 ATTGCGA-TTTCATTTCGC
*
32912 ATTGCGATTT--TGTCG-
1 ATTGCGATTTCATTTCGC
32927 -TTGCGATTTTCATTTCGC
1 ATTGCGA-TTTCATTTCGC
*
32945 ATTGCGATTT--TATCG-
1 ATTGCGATTTCATTTCGC
32960 -TTGCGATTTGCATTTCGC
1 ATTGCGATTT-CATTTCGC
**
32978 ATTGCGATAGCCATTTCCGC
1 ATTGCGAT-TTCATTT-CGC
* *
32998 GTTGCGATAGTCATTTTCGC
1 ATTGCGAT-TTCA-TTTCGC
*
33018 GTTGCGATTT
1 ATTGCGATTT
33028 TAAGTTTCGT
Statistics
Matches: 120, Mismatches: 11, Indels: 36
0.72 0.07 0.22
Matches are distributed among these distances:
14 21 0.17
15 6 0.05
16 12 0.10
17 12 0.10
18 9 0.08
19 32 0.27
20 25 0.21
21 3 0.03
ACGTcount: A:0.14, C:0.20, G:0.21, T:0.44
Consensus pattern (18 bp):
ATTGCGATTTCATTTCGC
Found at i:32899 original size:14 final size:14
Alignment explanation
Indices: 32880--32968 Score: 61
Period size: 14 Copynumber: 5.6 Consensus size: 14
32870 TCATTTCGCA
32880 TTGCGATTTTGTCG
1 TTGCGATTTTGTCG
*
32894 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
32911 CATTGCGATTTTGTCG
1 --TTGCGATTTTGTCG
*
32927 TTGCGATTTTCATTTCG
1 TTGCGA-TTT--TGTCG
*
32944 CATTGCGATTTTATCG
1 --TTGCGATTTTGTCG
32960 TTGCGATTT
1 TTGCGATTT
32969 GCATTTCGCA
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 21 0.34
15 6 0.10
16 8 0.13
17 8 0.13
18 6 0.10
19 12 0.20
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.49
Consensus pattern (14 bp):
TTGCGATTTTGTCG
Found at i:32905 original size:33 final size:33
Alignment explanation
Indices: 32861--32985 Score: 223
Period size: 33 Copynumber: 3.8 Consensus size: 33
32851 GCAATGCGAA
*
32861 TTGCGACTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
32894 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
32927 TTGCGATTTTCATTTCGCATTGCGATTTTATCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
32960 TTGCGATTTGCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
32986 AGCCATTTCC
Statistics
Matches: 89, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:33004 original size:20 final size:19
Alignment explanation
Indices: 32970--33025 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 19
32960 TTGCGATTTG
*
32970 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
32989 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
33009 CATTTTCGCGTTGCGAT
1 CA-TTTCGCGTTGCGAT
33026 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
19 5 0.15
20 25 0.76
21 3 0.09
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:35584 original size:19 final size:19
Alignment explanation
Indices: 35533--35663 Score: 155
Period size: 19 Copynumber: 7.1 Consensus size: 19
35523 TCTTTTGGTT
*
35533 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
35552 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
35572 GAAATGACTATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
35591 AAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
35610 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
35627 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
35643 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
35662 GA
1 GA
35664 TTTTGGTTTC
Statistics
Matches: 95, Mismatches: 11, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 62 0.65
20 17 0.18
ACGTcount: A:0.46, C:0.20, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:35642 original size:52 final size:56
Alignment explanation
Indices: 35534--35664 Score: 171
Period size: 52 Copynumber: 2.4 Consensus size: 56
35524 CTTTTGGTTG
* *
35534 AAATGAAAATCGCAACGAGATAATGAGAATCGCAACGCGAAATGACTATCGCAACGCA
1 AAATGAAAATCGCAACGCGATAATGAAAATCGCAAC-CGAAATGAC-ATCGCAACGCA
* *
35592 AAATGAAAATCGCAACGCGA-AATGAAAATCGCAA-CGAGA-GA-ATCGCAACGCG
1 AAATGAAAATCGCAACGCGATAATGAAAATCGCAACCGAAATGACATCGCAACGCA
*
35644 AAATGAAAATCGCAATGCGAT
1 AAATGAAAATCGCAACGCGAT
35665 TTTGGTTTCG
Statistics
Matches: 67, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
52 29 0.43
54 2 0.03
55 4 0.06
57 13 0.19
58 19 0.28
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (56 bp):
AAATGAAAATCGCAACGCGATAATGAAAATCGCAACCGAAATGACATCGCAACGCA
Found at i:35681 original size:19 final size:19
Alignment explanation
Indices: 35659--35706 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
35649 AAAATCGCAA
*
35659 TGCGATTTTGGTTT-CGCGT
1 TGCGATTTT-ATTTCCGCGT
*
35678 TGCGATAGTTATTTCCGCGT
1 TGCGAT-TTTATTTCCGCGT
35698 TGCGATTTT
1 TGCGATTTT
35707 CATTCTCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 11 0.46
20 13 0.54
ACGTcount: A:0.10, C:0.17, G:0.27, T:0.46
Consensus pattern (19 bp):
TGCGATTTTATTTCCGCGT
Found at i:36278 original size:20 final size:19
Alignment explanation
Indices: 36226--36279 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
36216 GCTATGTAAA
*
36226 TCGCATTGCGATAGTAAGAT
1 TCGCATTGCGAT-TTAAGAT
*
36246 TCGCATTGCGATTTACGTAT
1 TCGCATTGCGATTTAAG-AT
36266 TCGCATTGCGATTT
1 TCGCATTGCGATTT
36280 TCCTAATCCG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 28 0.90
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.37
Consensus pattern (19 bp):
TCGCATTGCGATTTAAGAT
Found at i:36293 original size:21 final size:20
Alignment explanation
Indices: 36247--36296 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
36237 TAGTAAGATT
* *
36247 CGCATTGCGATTTACGTATT
1 CGCATTGCGATTTACCTATC
*
36267 CGCATTGCGATTTTCCTAATC
1 CGCATTGCGATTTACCT-ATC
36288 CGCATTGCG
1 CGCATTGCG
36297 GATTATGAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 15 0.58
21 11 0.42
ACGTcount: A:0.18, C:0.26, G:0.20, T:0.36
Consensus pattern (20 bp):
CGCATTGCGATTTACCTATC
Found at i:36350 original size:21 final size:20
Alignment explanation
Indices: 36293--36358 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
36283 TAATCCGCAT
* *
36293 TGCGGATTATGAAATCGCAA
1 TGCGAATTATGAAATTGCAA
* *
36313 CGCGAA-TACGTAAATTGCAA
1 TGCGAATTATG-AAATTGCAA
*
36333 TGCGAATTATGAAAATTGCAT
1 TGCGAATTATG-AAATTGCAA
36354 TGCGA
1 TGCGA
36359 TAGTCAGTAT
Statistics
Matches: 36, Mismatches: 8, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.08
20 17 0.47
21 16 0.44
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.26
Consensus pattern (20 bp):
TGCGAATTATGAAATTGCAA
Found at i:38881 original size:12 final size:13
Alignment explanation
Indices: 38842--38893 Score: 61
Period size: 14 Copynumber: 3.9 Consensus size: 13
38832 TAAATAATCA
38842 AAAAGAAATAAAAT
1 AAAA-AAATAAAAT
*
38856 AAAAAATTGAAAAT
1 AAAAAAAT-AAAAT
38870 AAAAAAAT-AAAT
1 AAAAAAATAAAAT
*
38882 AAAAATATAAAA
1 AAAAAAATAAAA
38894 CAATATAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
12 11 0.33
13 6 0.18
14 16 0.48
ACGTcount: A:0.79, C:0.00, G:0.04, T:0.17
Consensus pattern (13 bp):
AAAAAAATAAAAT
Found at i:38945 original size:36 final size:32
Alignment explanation
Indices: 38898--38992 Score: 104
Period size: 32 Copynumber: 2.9 Consensus size: 32
38888 ATAAAACAAT
*
38898 ATAAGAATCAACTAATTCAATGTACTTCACATTAAC
1 ATAAGAATCAACTAATT--ATCT--TTCACATTAAC
38934 ATAAGAATCAACTAA-TATCTTTCACATTAAC
1 ATAAGAATCAACTAATTATCTTTCACATTAAC
* *
38965 ATTAAGAATCAATTAA-TATCCTTCACAT
1 A-TAAGAATCAACTAATTATCTTTCACAT
38993 CGACAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
31 12 0.22
32 24 0.44
33 3 0.05
35 1 0.02
36 15 0.27
ACGTcount: A:0.44, C:0.19, G:0.04, T:0.33
Consensus pattern (32 bp):
ATAAGAATCAACTAATTATCTTTCACATTAAC
Found at i:38958 original size:31 final size:32
Alignment explanation
Indices: 38922--38992 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
38912 ATTCAATGTA
38922 CTTCACATTAACA-TAAGAATCAACTAATATC
1 CTTCACATTAACATTAAGAATCAACTAATATC
* *
38953 TTTCACATTAACATTAAGAATCAATTAATATC
1 CTTCACATTAACATTAAGAATCAACTAATATC
38985 CTTCACAT
1 CTTCACAT
38993 CGACAAATAA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
31 12 0.33
32 24 0.67
ACGTcount: A:0.42, C:0.21, G:0.03, T:0.34
Consensus pattern (32 bp):
CTTCACATTAACATTAAGAATCAACTAATATC
Found at i:39027 original size:51 final size:51
Alignment explanation
Indices: 38967--39083 Score: 180
Period size: 51 Copynumber: 2.3 Consensus size: 51
38957 ACATTAACAT
* * *
38967 TAAGAATCAATTAATATCCTTCACATCGACAAATAAAAACATAAAACAATA
1 TAAGAATCAACTAATATCCTTCACATCAACAAATAAAAACAGAAAACAATA
*
39018 TAAGAATCAACTAATATCCTTCACATCAACAAATAAAAACAGAAAATAATA
1 TAAGAATCAACTAATATCCTTCACATCAACAAATAAAAACAGAAAACAATA
* *
39069 TAATAATCATCTAAT
1 TAAGAATCAACTAAT
39084 TCAAAGCCCT
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.55, C:0.17, G:0.03, T:0.25
Consensus pattern (51 bp):
TAAGAATCAACTAATATCCTTCACATCAACAAATAAAAACAGAAAACAATA
Found at i:39190 original size:21 final size:22
Alignment explanation
Indices: 39156--39212 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
39146 GATTGAACTT
*
39156 ATAAAAATTAGAAAAAAATAAA
1 ATAAAAAATAGAAAAAAATAAA
* *
39178 A-AATAAATAG-AAAACATAAA
1 ATAAAAAATAGAAAAAAATAAA
39198 ATAAAAAATA-AAAAA
1 ATAAAAAATAGAAAAA
39213 CAGAAGAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
20 10 0.34
21 18 0.62
22 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.04, T:0.16
Consensus pattern (22 bp):
ATAAAAAATAGAAAAAAATAAA
Found at i:39210 original size:12 final size:12
Alignment explanation
Indices: 39170--39210 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
39160 AAATTAGAAA
39170 AAAATAAAAAAT
1 AAAATAAAAAAT
39182 -AAATAGAAAACAT
1 AAAATA-AAAA-AT
39195 AAAATAAAAAAT
1 AAAATAAAAAAT
39207 AAAA
1 AAAA
39211 AACAGAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.19
12 10 0.38
13 6 0.23
14 5 0.19
ACGTcount: A:0.80, C:0.02, G:0.02, T:0.15
Consensus pattern (12 bp):
AAAATAAAAAAT
Found at i:39213 original size:21 final size:20
Alignment explanation
Indices: 39167--39228 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 20
39157 TAAAAATTAG
*
39167 AAAAAA-ATAAAAAATAAAT
1 AAAAAACATAAAAAAAAAAT
*
39186 AGAAAACATAAAATAAAAAAT
1 AAAAAACATAAAA-AAAAAAT
*
39207 AAAAAACAGAAGAAAAAAAAT
1 AAAAAACATAA-AAAAAAAAT
39228 A
1 A
39229 TAGTGTATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 23 0.64
22 2 0.06
ACGTcount: A:0.81, C:0.03, G:0.05, T:0.11
Consensus pattern (20 bp):
AAAAAACATAAAAAAAAAAT
Found at i:39294 original size:16 final size:16
Alignment explanation
Indices: 39237--39295 Score: 55
Period size: 16 Copynumber: 3.6 Consensus size: 16
39227 TATAGTGTAT
*
39237 ACAGAAAATAAAAAGAAA
1 ACAGAAAAT-TAAA-AAA
* *
39255 ACATAAAATTAAAAAC
1 ACAGAAAATTAAAAAA
* *
39271 ATATAAAATTAAAAAA
1 ACAGAAAATTAAAAAA
39287 ACAGAAAAT
1 ACAGAAAAT
39296 AGAAAACATG
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
16 23 0.68
17 3 0.09
18 8 0.24
ACGTcount: A:0.73, C:0.07, G:0.05, T:0.15
Consensus pattern (16 bp):
ACAGAAAATTAAAAAA
Found at i:39483 original size:21 final size:21
Alignment explanation
Indices: 39442--39484 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
39432 CATTTGTAAG
* *
39442 AACATAAAATATATATAAAAA
1 AACATAAAACATATAAAAAAA
*
39463 AACATAAAACATA-AAACAAA
1 AACATAAAACATATAAAAAAA
39483 AA
1 AA
39485 GCAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.74, C:0.09, G:0.00, T:0.16
Consensus pattern (21 bp):
AACATAAAACATATAAAAAAA
Found at i:40065 original size:19 final size:19
Alignment explanation
Indices: 40038--40078 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
40028 TTACAAATGA
*
40038 ATAATACAAAAAA-AATAAC
1 ATAAAACAAAAAACAA-AAC
40057 ATAAAACAAAAAACAAAAC
1 ATAAAACAAAAAACAAAAC
40076 ATA
1 ATA
40079 CTACTAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.76, C:0.12, G:0.00, T:0.12
Consensus pattern (19 bp):
ATAAAACAAAAAACAAAAC
Found at i:40088 original size:26 final size:26
Alignment explanation
Indices: 40045--40120 Score: 64
Period size: 26 Copynumber: 2.9 Consensus size: 26
40035 TGAATAATAC
* *
40045 AAAAAAAATAACATAAAACAAAAAAC-
1 AAAACAAATAATA-AAAACAAAAAACG
* * * *
40071 AAAACATACTACTAAAAATAGAAAACG
1 AAAACA-AATAATAAAAACAAAAAACG
*
40098 AAAAGAAATAATAAAAACAAAAA
1 AAAACAAATAATAAAAACAAAAA
40121 GTAAATAAAG
Statistics
Matches: 37, Mismatches: 11, Indels: 4
0.71 0.21 0.08
Matches are distributed among these distances:
26 28 0.76
27 9 0.24
ACGTcount: A:0.75, C:0.11, G:0.04, T:0.11
Consensus pattern (26 bp):
AAAACAAATAATAAAAACAAAAAACG
Found at i:40126 original size:20 final size:21
Alignment explanation
Indices: 40083--40128 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
40073 AACATACTAC
*
40083 TAAA-AATAGAAAACGAAAAG
1 TAAATAATAGAAAACAAAAAG
40103 -AAATAATA-AAAACAAAAAG
1 TAAATAATAGAAAACAAAAAG
40122 TAAATAA
1 TAAATAA
40129 AGTAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 13 0.57
20 10 0.43
ACGTcount: A:0.74, C:0.04, G:0.09, T:0.13
Consensus pattern (21 bp):
TAAATAATAGAAAACAAAAAG
Found at i:40200 original size:2 final size:2
Alignment explanation
Indices: 40195--40233 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
40185 AAACAAAAAC
40195 AT AT AT 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 AT AT AT A
40234 AAAGAAAATT
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:40728 original size:28 final size:28
Alignment explanation
Indices: 40697--40872 Score: 95
Period size: 28 Copynumber: 5.9 Consensus size: 28
40687 TAGTTTATAA
40697 ACTATATATAAATATAAACTATATATCT
1 ACTATATATAAATATAAACTATATATCT
* * *
40725 ACTATGTATAAGTATAAACTATATAGTTT
1 ACTATATATAAATATAAACTATATA-TCT
* * * *
40754 GCATATAGTTTATATTAATAAACTATATAATTTAT
1 AC-TATA-TATA-AAT-ATAAACTATAT-A--TCT
* * * *
40789 ACATAGTATATATAATTTATAATTATACATAGT
1 AC-TA-TATATA-AATATA-AACTATATAT-CT
40822 A-TATATATAAATATAAACTATATATCT
1 ACTATATATAAATATAAACTATATATCT
* * *
40849 ACTATGTATAAGTATATAC-ATATA
1 ACTATATATAAATATAAACTATATA
40873 AATTATAGAA
Statistics
Matches: 114, Mismatches: 23, Indels: 23
0.71 0.14 0.14
Matches are distributed among these distances:
27 7 0.06
28 45 0.39
29 8 0.07
30 9 0.08
31 5 0.04
32 3 0.03
33 13 0.11
34 4 0.04
35 18 0.16
36 2 0.02
ACGTcount: A:0.46, C:0.07, G:0.05, T:0.41
Consensus pattern (28 bp):
ACTATATATAAATATAAACTATATATCT
Found at i:40795 original size:33 final size:33
Alignment explanation
Indices: 40738--40801 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
40728 ATGTATAAGT
* * * *
40738 ATAAACTATATAGTTTGCATATAGTTTATATTA
1 ATAAACTATATAATTTACACATAGTATATATTA
*
40771 ATAAACTATATAATTTATACATAGTATATAT
1 ATAAACTATATAATTTACACATAGTATATAT
40802 AATTTATAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (33 bp):
ATAAACTATATAATTTACACATAGTATATATTA
Found at i:41619 original size:15 final size:14
Alignment explanation
Indices: 41583--41770 Score: 137
Period size: 13 Copynumber: 13.8 Consensus size: 14
41573 TACTTATAAG
*
41583 TATAATGTATACTTA
1 TATAATATATA-TTA
41598 TAT--TATATATGTA
1 TATAATATATAT-TA
41611 TAT-A-ATATA-TA
1 TATAATATATATTA
41622 TAT-ATATATATTA
1 TATAATATATATTA
* *
41635 TATACTTTATACTTA
1 TATAATATATA-TTA
*
41650 TATATTATATATTA
1 TATAATATATATTA
* * *
41664 TGTACT-TATA-AA
1 TATAATATATATTA
*
41676 TATAATGTATACTTA
1 TATAATATATA-TTA
*
41691 TATTATATATA-TA
1 TATAATATATATTA
*
41704 TATACT-TATATTA
1 TATAATATATATTA
41717 TAT-ATATATATTA
1 TATAATATATATTA
*
41730 TATAAATATAAATTA
1 TAT-AATATATATTA
*
41745 TATTATATTATATTA
1 TATAATA-TATATTA
41760 TATAATATATA
1 TATAATATATA
41771 AATATATATA
Statistics
Matches: 139, Mismatches: 20, Indels: 29
0.74 0.11 0.15
Matches are distributed among these distances:
11 6 0.04
12 16 0.12
13 49 0.35
14 19 0.14
15 49 0.35
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.51
Consensus pattern (14 bp):
TATAATATATATTA
Found at i:41687 original size:93 final size:94
Alignment explanation
Indices: 41556--41733 Score: 290
Period size: 93 Copynumber: 1.9 Consensus size: 94
41546 GTTCTACACA
* *
41556 TATATACTTTATATATGTACTTATAAGTATAATGTATACTTATATTATATATGTATATA-ATATA
1 TATATACTTTATATATGTACTTATAAATATAATGTATACTTATATTATATATATATATACATATA
41620 -TATATATATATATTATATACTTTATACT
66 TTATATATATATATTATATACTTTATACT
*
41648 TATATA-TTATATATTATGTACTTATAAATATAATGTATACTTATATTATATATATATATACTTA
1 TATATACTT-TATA-TATGTACTTATAAATATAATGTATACTTATATTATATATATATATACATA
41712 TATTATATATATATATTATATA
64 TATTATATATATATATTATATA
41734 AATATAAATT
Statistics
Matches: 79, Mismatches: 3, Indels: 5
0.91 0.03 0.06
Matches are distributed among these distances:
91 2 0.03
92 10 0.13
93 44 0.56
94 4 0.05
95 19 0.24
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (94 bp):
TATATACTTTATATATGTACTTATAAATATAATGTATACTTATATTATATATATATATACATATA
TTATATATATATATTATATACTTTATACT
Found at i:41692 original size:6 final size:5
Alignment explanation
Indices: 41683--41767 Score: 79
Period size: 5 Copynumber: 17.0 Consensus size: 5
41673 AAATATAATG
41683 TATACT TATAT TATA- TATAT ATATACT TATAT TATA- TATA- TATAT
1 TATA-T TATAT TATAT TATAT -TATA-T TATAT TATAT TATAT TATAT
* * *
41728 TATA- TAAAT ATAAAT TATAT TATAT TATAT TATAT AATAT
1 TATAT TATAT -TATAT TATAT TATAT TATAT TATAT TATAT
41768 ATAAATATAT
Statistics
Matches: 70, Mismatches: 3, Indels: 13
0.81 0.03 0.15
Matches are distributed among these distances:
4 15 0.21
5 37 0.53
6 17 0.24
7 1 0.01
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (5 bp):
TATAT
Found at i:41747 original size:93 final size:92
Alignment explanation
Indices: 41555--41757 Score: 277
Period size: 93 Copynumber: 2.2 Consensus size: 92
41545 AGTTCTACAC
* *
41555 ATATATACTT-TATATATGTACTTATAAGTATAATGTATACTTATATTATATATGTATATAATAT
1 ATATATA-TTATATATATGTACTTATAAATATAATGTATACTTATATTATATATATATATAATAT
** *
41619 ATATATATATATATTATATACTTTATAC
65 ATATATATATATATTATATACAATATAA
* *
41647 TTATATATTATATATTATGTACTTATAAATATAATGTATACTTATATTATATATATATATACTTA
1 ATATATATTATATA-TATGTACTTATAAATATAATGTATACTTATATTATATATATATATA-ATA
41712 TATTATATATATATATTATATA-AATATAA
64 TA-TATATATATATATTATATACAATATAA
41741 AT-TATATTATATTATAT
1 ATATATATTATA-TATAT
41758 TATATAATAT
Statistics
Matches: 98, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
91 2 0.02
92 10 0.10
93 56 0.57
94 11 0.11
95 19 0.19
ACGTcount: A:0.43, C:0.04, G:0.03, T:0.50
Consensus pattern (92 bp):
ATATATATTATATATATGTACTTATAAATATAATGTATACTTATATTATATATATATATAATATA
TATATATATATATTATATACAATATAA
Found at i:41861 original size:13 final size:13
Alignment explanation
Indices: 41596--41865 Score: 130
Period size: 13 Copynumber: 20.5 Consensus size: 13
41586 AATGTATACT
* *
41596 TATATTATATATG
1 TATATAATATATA
41609 TATATAATATATA
1 TATATAATATATA
41622 TATAT-ATATAT-
1 TATATAATATATA
* *
41633 TATATACTTTATA
1 TATATAATATATA
*
41646 CTTATATATTATATA
1 --TATATAATATATA
* *
41661 TTATGTACT-TATA
1 -TATATAATATATA
* *
41674 AATATAATGTATA
1 TATATAATATATA
*
41687 CTTATATTATATATA
1 --TATATAATATATA
*
41702 TATATACT-TATA
1 TATATAATATATA
41714 T-TATATATATATA
1 TATATA-ATATATA
41727 TTATATAA-ATATA
1 -TATATAATATATA
* *
41740 AATTATATTATAT-
1 TA-TATAATATATA
*
41753 TATATTATATA-A
1 TATATAATATATA
41765 TATATAAATATATA
1 TATAT-AATATATA
* *
41779 TATCTACATATAAA
1 TATATA-ATATATA
41793 TATA-AACTATAGTA
1 TATATAA-TATA-TA
* *
41807 TATAGT-TTTTATA
1 TATA-TAATATATA
** *
41820 TATATCTTATATG
1 TATATAATATATA
*
41833 TAAACT-ATATAGTA
1 TATA-TAATATA-TA
41847 TATATAATATATA
1 TATATAATATATA
41860 TATATA
1 TATATA
41866 TAGTTTACAT
Statistics
Matches: 197, Mismatches: 35, Indels: 50
0.70 0.12 0.18
Matches are distributed among these distances:
11 9 0.05
12 36 0.18
13 82 0.42
14 45 0.23
15 25 0.13
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (13 bp):
TATATAATATATA
Found at i:41865 original size:15 final size:15
Alignment explanation
Indices: 41596--41867 Score: 135
Period size: 15 Copynumber: 17.3 Consensus size: 15
41586 AATGTATACT
* *
41596 TATATTATATATGTA
1 TATAATATATATATA
41611 TATAATATATATATA
1 TATAATATATATATA
*
41626 TAT-ATATTATATACTT
1 TATAATA-TATATA-TA
*
41642 TATACTTATATATTATA
1 TATA-ATATATA-TATA
* * *
41659 TATTATGTACTTATAAA
1 TATAATATA--TATATA
*
41676 TATAATGTATACT-TA
1 TATAATATATA-TATA
*
41691 TATTATATATATATA
1 TATAATATATATATA
*
41706 TACTTATATTATATATA
1 TA-TAATA-TATATATA
* *
41723 TATATTATATAAATA
1 TATAATATATATATA
41738 TA-AAT-TATAT-TA
1 TATAATATATATATA
*
41750 TATTATATTATATAATA
1 TATAATA-TATAT-ATA
41767 TATAA-ATATATATA
1 TATAATATATATATA
* *
41781 TCTACATATAAATATA
1 TATA-ATATATATATA
* *
41797 AACT-ATAGTATATAGTT
1 TA-TAATA-TATATA-TA
* *
41814 TTTATATATATCTTATA
1 TATA-ATATAT-ATATA
*
41831 TGTAAACTATATAGTATA
1 TAT-AA-TATATA-TATA
41849 TATAATATATATATA
1 TATAATATATATATA
41864 TATA
1 TATA
41868 GTTTACATAT
Statistics
Matches: 197, Mismatches: 33, Indels: 54
0.69 0.12 0.19
Matches are distributed among these distances:
12 4 0.02
13 6 0.03
14 12 0.06
15 69 0.35
16 37 0.19
17 46 0.23
18 23 0.12
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.49
Consensus pattern (15 bp):
TATAATATATATATA
Found at i:41894 original size:11 final size:11
Alignment explanation
Indices: 41838--42163 Score: 97
Period size: 11 Copynumber: 30.4 Consensus size: 11
41828 ATATGTAAAC
41838 TATATAGTATATA
1 TATATAGT-T-TA
*
41851 TAATATA-TATA
1 T-ATATAGTTTA
41862 TATATAGTTTA
1 TATATAGTTTA
*
41873 CATATAG--TA
1 TATATAGTTTA
*
41882 TATATGGTTTA
1 TATATAGTTTA
41893 TATATAGTTTA
1 TATATAGTTTA
* **
41904 TAT-TAATAAA
1 TATATAGTTTA
*
41914 CTATATA-ATT-
1 -TATATAGTTTA
41924 TATA-A--TTA
1 TATATAGTTTA
**
41932 TATATAGCATA
1 TATATAGTTTA
* **
41943 TAAATA-TAAA
1 TATATAGTTTA
*
41953 CTATACAGTTTA
1 -TATATAGTTTA
*
41965 TATATAGTTCA
1 TATATAGTTTA
41976 TATATAG-TT-
1 TATATAGTTTA
41985 TATATAGTTTA
1 TATATAGTTTA
*
41996 TATATA-ATT-
1 TATATAGTTTA
42005 TATATAG-TT-
1 TATATAGTTTA
42014 TAT-TAGTTTATA
1 TATATAG-TT-TA
**
42026 TATATAGTTCG
1 TATATAGTTTA
* ***
42037 TATGTAAACTA
1 TATATAGTTTA
42048 TATA-A-TTTA
1 TATATAGTTTA
42057 T-T-TAGTTTATA
1 TATATAG-TT-TA
42068 TATATAGTTTA
1 TATATAGTTTA
42079 TATATAG--TA
1 TATATAGTTTA
*
42088 TATATGGTTTA
1 TATATAGTTTA
*
42099 TATATAATTATA
1 TATATAGTT-TA
*
42111 TATTAATATGTATAAA
1 TA-T-ATA-GT-T-TA
42127 CTATATAGTTTA
1 -TATATAGTTTA
***
42139 TATATAAACTA
1 TATATAGTTTA
42150 TATATAG-TTA
1 TATATAGTTTA
42160 TATA
1 TATA
42164 AATTAAACCT
Statistics
Matches: 233, Mismatches: 46, Indels: 71
0.67 0.13 0.20
Matches are distributed among these distances:
7 2 0.01
8 10 0.04
9 41 0.18
10 26 0.11
11 107 0.46
12 17 0.07
13 10 0.04
14 10 0.04
15 4 0.02
16 4 0.02
17 2 0.01
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.48
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:41978 original size:9 final size:9
Alignment explanation
Indices: 41965--42027 Score: 74
Period size: 9 Copynumber: 6.7 Consensus size: 9
41955 ATACAGTTTA
41965 TATATAGTT
1 TATATAGTT
41974 CATATATAGTT
1 --TATATAGTT
41985 TATATAGTTT
1 TATATAG-TT
*
41995 ATATATAATT
1 -TATATAGTT
42005 TATATAGTT
1 TATATAGTT
42014 TAT-TAGTT
1 TATATAGTT
42022 TATATA
1 TATATA
42028 TATAGTTCGT
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 8 0.17
9 20 0.43
10 4 0.09
11 15 0.32
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.54
Consensus pattern (9 bp):
TATATAGTT
Found at i:42144 original size:13 final size:13
Alignment explanation
Indices: 41985--42084 Score: 62
Period size: 13 Copynumber: 7.3 Consensus size: 13
41975 ATATATAGTT
41985 TATATAGTTTATA
1 TATATAGTTTATA
41998 TATA-A-TTTATA
1 TATATAGTTTATA
42009 TAGTTTATTAGTTTATA
1 TA---TA-TAGTTTATA
*
42026 TATATAGTTCGTATG
1 TATATAGTT--TATA
* * *
42041 TAAACTA-TATAATT
1 TATA-TAGT-TTATA
*
42055 TATTTAGTTTATA
1 TATATAGTTTATA
42068 TATATAGTTTATA
1 TATATAGTTTATA
42081 TATA
1 TATA
42085 GTATATATGG
Statistics
Matches: 67, Mismatches: 9, Indels: 22
0.68 0.09 0.22
Matches are distributed among these distances:
11 8 0.12
12 1 0.01
13 30 0.45
14 9 0.13
15 7 0.10
16 4 0.06
17 8 0.12
ACGTcount: A:0.37, C:0.02, G:0.08, T:0.53
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:42328 original size:13 final size:11
Alignment explanation
Indices: 42303--42338 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
42293 AAATATAAAC
42303 TATATAGTTTA
1 TATATAGTTTA
*
42314 TATATAGTTTG
1 TATATAGTTTA
*
42325 TATATAGTCTA
1 TATATAGTTTA
42336 TAT
1 TAT
42339 TAATAAACTA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.33, C:0.03, G:0.11, T:0.53
Consensus pattern (11 bp):
TATATAGTTTA
Found at i:42362 original size:107 final size:108
Alignment explanation
Indices: 42202--42422 Score: 274
Period size: 107 Copynumber: 2.1 Consensus size: 108
42192 GTATAAACTA
*
42202 TATATATAGTTTATACATAGTAGTATATAAACATAAACTATATAATTTATACAT-AGTAAATATA
1 TATATATAGTTTATACATAGTACTATATAAACATAAACTATATAATTTATACATAAGT--ATATA
* *
42266 ATTTATAATTATA-A-ATAGTATTTTTATAAATATAAACTATATAGTT
64 ATTTATAATTATATATATA-TATATATATAAATATAAACTATATA--T
* * *
42312 TATATATAGTTTGTATATAGT-CTATAT-TA-ATAAACTATATAATTTATACATAAGTATATAAT
1 TATATATAGTTTATACATAGTACTATATAAACATAAACTATATAATTTATACATAAGTATATAAT
* * *
42374 TTATATTTATATATATATATATATATATATATAAATTATATAT
66 TTATAATTATATATATATATATATATAAATATAAACTATATAT
42417 TATATA
1 TATATA
42423 CTTATGTATA
Statistics
Matches: 99, Mismatches: 9, Indels: 11
0.83 0.08 0.09
Matches are distributed among these distances:
105 7 0.07
106 17 0.17
107 44 0.44
108 7 0.07
109 5 0.05
110 19 0.19
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.46
Consensus pattern (108 bp):
TATATATAGTTTATACATAGTACTATATAAACATAAACTATATAATTTATACATAAGTATATAAT
TTATAATTATATATATATATATATATAAATATAAACTATATAT
Found at i:42420 original size:26 final size:27
Alignment explanation
Indices: 42383--42441 Score: 86
Period size: 26 Copynumber: 2.2 Consensus size: 27
42373 TTTATATTTA
42383 TATATATATATATA-TATATATATAAAT
1 TATATATATATATACT-TATATATAAAT
*
42410 TATATAT-TATATACTTATGTATAAAT
1 TATATATATATATACTTATATATAAAT
42436 TATATA
1 TATATA
42442 GTTTATTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 22 0.73
27 8 0.27
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (27 bp):
TATATATATATATACTTATATATAAAT
Found at i:42441 original size:2 final size:2
Alignment explanation
Indices: 41596--42422 Score: 164
Period size: 2 Copynumber: 412.0 Consensus size: 2
41586 AATGTATACT
*
41596 TA TA T- TA TA TA TG TA TA TA -A TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
41635 TA TA CTT TA TA CT- TA TA TA T- TA TA TA T- TA TG TA CT- TA TA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
41674 AA TA TA -A TG TA TA CT- TA TA T- TA TA TA TA TA TA TA CT- TA TA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* *
41714 T- TA TA TA TA TA TA T- TA TA TA AA TA TA AA T- TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * *
41752 T- TA TA T- TA TA TA -A TA TA TA AA TA TA TA TA TC TA CA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
41791 AA TA TA AA CTA TA GTA TA TA GTT TT TA TA TA TA TC T- TA TA TG
1 TA TA TA TA -TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA
* * *
41833 TA AA CTA TA TA GTA TA TA TA -A TA TA TA TA TA TA TA GTT TA CA
1 TA TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * *
41875 TA TA GTA TA TA TGG TT TA TA TA TA GTT TA TA T- TA -A TA AA CTA
1 TA TA -TA TA TA T-A TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* * * *
41917 TA TA -A TT TA TA -A T- TA TA TA TA GCA TA TA AA TA TA AA CTA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA -TA TA
* * * *
41958 CA GTT TA TA TA TA GT- TCA TA TA TA GTT TA TA TA GTT TA TA TA TA
1 TA -TA TA TA TA TA -TA T-A TA TA TA -TA TA TA TA -TA TA TA TA TA
* * * * *
42002 -A TT TA TA TA GTT TA T- TA GTT TA TA TA TA TA GT- TCG TA TG TA
1 TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA -TA T-A TA TA TA
* * * * *
42043 AA CTA TA TA -A TT TA TT TA GTT TA TA TA TA TA GTT 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
* * *
42085 GTA TA TA TGG TT TA TA TA TA -A T- TA TA TA T- TA -A TA TG TA TA
1 -TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
42125 AA CTA TA TA GTT TA TA TA TA AA CTA TA TA TA GT- TA TA TA AA T-
1 TA -TA TA TA -TA TA TA TA TA TA -TA TA TA TA -TA TA TA TA TA TA
* ** * * * *
42167 TA AA CC TA AA CCA TA TA TA CTA TA TG TA TA AA CTA 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
* * * * * *
42210 GTT TA TA CA TA GTA GTA TA TA AA CA TA AA CTA TA TA -A TT TA TA
1 -TA TA TA TA TA -TA -TA TA TA TA TA TA TA -TA TA TA TA TA TA TA
* * * * * *
42253 CA TA GTA AA TA TA -A TT TA TA -A T- TA TA AA TA GTA TT TT TA TA
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
* * * * * *
42294 AA TA TA AA CTA TA TA GTT TA TA TA TA GTT TG TA TA TA GTC TA TA
1 TA TA TA TA -TA TA TA -TA TA TA TA TA -TA TA TA TA TA -TA TA TA
* * * *
42338 T- TA -A TA AA CTA TA TA -A TT TA TA CA TA -A GTA TA TA -A TT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
* *
42377 TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA AA T- TA TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42417 TA TA TA
1 TA TA TA
42423 CTTATGTATA
Statistics
Matches: 583, Mismatches: 146, Indels: 192
0.63 0.16 0.21
Matches are distributed among these distances:
1 47 0.08
2 477 0.82
3 59 0.10
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.47
Consensus pattern (2 bp):
TA
Found at i:43859 original size:57 final size:56
Alignment explanation
Indices: 43797--43915 Score: 145
Period size: 57 Copynumber: 2.1 Consensus size: 56
43787 TTCATGCATC
*
43797 GATGCA-CATACCATGCATCGATGAACTA-AG-TATTTTATGAAAACATCGAATGCATTT
1 GATGCACCA-ACCATGCATCGATGAACTATAGTTA-TTT-TG-AAACATCGAATGCACTT
* * *
43854 GATGCACCAGCCATGCATCGATGCACTATGGTTATTTTGAAACATCGAATGCACTT
1 GATGCACCAACCATGCATCGATGAACTATAGTTATTTTGAAACATCGAATGCACTT
43910 GATGCA
1 GATGCA
43916 TCGATGCACT
Statistics
Matches: 55, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
56 22 0.40
57 25 0.45
58 6 0.11
59 2 0.04
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.29
Consensus pattern (56 bp):
GATGCACCAACCATGCATCGATGAACTATAGTTATTTTGAAACATCGAATGCACTT
Found at i:43924 original size:17 final size:19
Alignment explanation
Indices: 43896--43944 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
43886 TATTTTGAAA
43896 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
43914 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
43933 CACCGATGCACT
1 CATCGATGCACT
43945 AAGGGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:48267 original size:16 final size:17
Alignment explanation
Indices: 48248--48280 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
48238 TGATATATAA
48248 TTTAAATTTTT-ATATT
1 TTTAAATTTTTAATATT
*
48264 TTTATATTTTTAATATT
1 TTTAAATTTTTAATATT
48281 AATATATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTAAATTTTTAATATT
Found at i:48890 original size:20 final size:20
Alignment explanation
Indices: 48796--49164 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
48786 GATTTTCCAT
* ** *
48796 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
48816 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
48836 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48856 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
48876 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
48896 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
48916 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
48936 AATTGCAACGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
* *
48956 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
48976 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
48996 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
49016 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
49036 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
49056 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
49076 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
49096 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
49116 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
49136 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
49156 AATCACAAC
1 AATCGCAAC
49165 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:49886 original size:24 final size:24
Alignment explanation
Indices: 49847--49893 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
49837 AAATTTGGTC
49847 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
49871 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
49894 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:52386 original size:19 final size:19
Alignment explanation
Indices: 52364--52580 Score: 240
Period size: 19 Copynumber: 12.4 Consensus size: 19
52354 CGGAAAATAC
*
52364 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
52383 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
52397 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
52417 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
52431 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52450 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
52469 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
52483 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52502 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
52521 AATCGCAA--CGACA-G--
1 AATCGCAATGCGAAATGAA
52535 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52554 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
52573 AATCGCAA
1 AATCGCAA
52581 CGAGATAATC
Statistics
Matches: 169, Mismatches: 8, Indels: 42
0.77 0.04 0.19
Matches are distributed among these distances:
14 40 0.24
15 2 0.01
16 10 0.06
17 9 0.05
18 3 0.02
19 92 0.54
20 13 0.08
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:52451 original size:33 final size:33
Alignment explanation
Indices: 52364--52561 Score: 192
Period size: 33 Copynumber: 5.8 Consensus size: 33
52354 CGGAAAATAC
* *
52364 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
52397 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
52431 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
*
52469 AATCGCAA--CG--A-GAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAA
* *
52502 AATCGCAATGCGAAATGAAAATCGCAACGACAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
52535 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
52562 TGCGAAATGA
Statistics
Matches: 145, Mismatches: 8, Indels: 24
0.82 0.05 0.14
Matches are distributed among these distances:
33 83 0.57
34 31 0.21
35 5 0.03
36 4 0.03
37 2 0.01
38 20 0.14
ACGTcount: A:0.46, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:52591 original size:33 final size:32
Alignment explanation
Indices: 52449--52602 Score: 150
Period size: 33 Copynumber: 4.5 Consensus size: 32
52439 TGCGAAATGA
52449 AAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AAATCGCAATGCGAAATGAAAATCGCAACGAG
* *
52481 AGAATCGCAATGCGAAATGAAAATCGCAATGCG
1 A-AATCGCAATGCGAAATGAAAATCGCAACGAG
* * *
52514 AAAT-GAAAAT-CGCAACGACAGAATCGCAATGCGAAATG
1 AAATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-G
52552 AAAATCGCAATGCGAAATGAAAATCGCAACGAG
1 -AAATCGCAATGCGAAATGAAAATCGCAACGAG
52585 ATAATCGCAATGCGAAAT
1 A-AATCGCAATGCGAAAT
52603 TATAAACGCA
Statistics
Matches: 99, Mismatches: 10, Indels: 25
0.74 0.07 0.19
Matches are distributed among these distances:
31 7 0.07
32 9 0.09
33 55 0.56
34 1 0.01
35 1 0.01
36 2 0.02
38 9 0.09
39 8 0.08
40 7 0.07
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.14
Consensus pattern (32 bp):
AAATCGCAATGCGAAATGAAAATCGCAACGAG
Found at i:52618 original size:52 final size:52
Alignment explanation
Indices: 52392--52602 Score: 395
Period size: 52 Copynumber: 4.0 Consensus size: 52
52382 AAATCCCAAC
52392 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
52445 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
52497 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
52549 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
52601 AT
1 AT
52603 TATAAACGCA
Statistics
Matches: 155, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 139 0.90
53 16 0.10
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:52718 original size:19 final size:19
Alignment explanation
Indices: 52609--52710 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
52599 AAATTATAAA
52609 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
52628 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
52648 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
52664 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
52681 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
52700 CGCATTGCGAT
1 CGCATTGCGAT
52711 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:52834 original size:14 final size:14
Alignment explanation
Indices: 52815--52851 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
52805 CATCAATTAC
52815 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
52829 ACAAATCATCTTTT
1 ACAAATCAACTTTT
52843 ACAAATCAA
1 ACAAATCAA
52852 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:54824 original size:14 final size:14
Alignment explanation
Indices: 54805--54861 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
54795 GCGAAATGAA
*
54805 AATCGCAACGACAG
1 AATCGCAACGAAAG
54819 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
54836 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
54852 AATCGCAACG
1 AATCGCAACG
54862 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:54832 original size:33 final size:33
Alignment explanation
Indices: 54786--54878 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
54776 GCGAAACCAA
*
54786 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
54819 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
54852 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
54879 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:54843 original size:19 final size:19
Alignment explanation
Indices: 54749--54883 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
54739 TAGTTTACTT
* *
54749 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
54769 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
54788 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
54807 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
54821 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
54840 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
54854 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
54873 TCGCAATGCGA
1 TCGCAACGCGA
54884 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
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:54901 original size:19 final size:19
Alignment explanation
Indices: 54879--55007 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
54869 AAAATCGCAA
54879 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
54898 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
54912 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
54931 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
54945 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
54964 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
54983 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
55003 TGCGA
1 TGCGA
55008 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:54921 original size:33 final size:33
Alignment explanation
Indices: 54879--54970 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
54869 AAAATCGCAA
54879 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
54912 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
54945 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
54971 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:55341 original size:92 final size:93
Alignment explanation
Indices: 55051--55707 Score: 1284
Period size: 93 Copynumber: 7.1 Consensus size: 93
55041 TTGAATGGAT
55051 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55116 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55144 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55209 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55237 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55301 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55329 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55394 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55422 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55486 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55514 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55578 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55606 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
55671 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
55699 AAATTTACT
1 AAATTTACT
55708 AAGCAATCTA
Statistics
Matches: 560, Mismatches: 1, Indels: 6
0.99 0.00 0.01
Matches are distributed among these distances:
92 276 0.49
93 284 0.51
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:55364 original size:185 final size:186
Alignment explanation
Indices: 55051--55707 Score: 1284
Period size: 185 Copynumber: 3.5 Consensus size: 186
55041 TTGAATGGAT
55051 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55116 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
55181 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55237 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55301 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
55366 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55422 AAATTTACTTTCAACC-AAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
55486 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
55551 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
55606 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
55671 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
55708 AAGCAATCTA
Statistics
Matches: 468, Mismatches: 1, Indels: 5
0.99 0.00 0.01
Matches are distributed among these distances:
184 91 0.19
185 338 0.72
186 39 0.08
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:57427 original size:14 final size:14
Alignment explanation
Indices: 57408--57497 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
57398 TTGAAATGAA
57408 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57422 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
57439 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
57455 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
57474 AATCGCAACGAGAG
1 AATCGCAACGAGAG
57488 AATCGCAACG
1 AATCGCAACG
57498 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:57445 original size:33 final size:33
Alignment explanation
Indices: 57400--57514 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
57390 TCTTTTGGTT
57400 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
57433 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57466 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
57499 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
57515 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:57446 original size:19 final size:18
Alignment explanation
Indices: 57407--57519 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
57397 GTTGAAATGA
57407 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
57422 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
57439 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
57455 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
57472 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
57488 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
57505 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
57520 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:57550 original size:14 final size:14
Alignment explanation
Indices: 57531--57585 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
57521 TTTGGTTTCG
57531 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
57545 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
57564 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
57578 CGTTGCGA
1 CGTTGCGA
57586 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:57563 original size:33 final size:33
Alignment explanation
Indices: 57515--57585 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
57505 AAAATCGCAA
**
57515 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
57548 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
57581 TGCGA
1 TGCGA
57586 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:57593 original size:33 final size:33
Alignment explanation
Indices: 57526--57607 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
57516 GCGATTTTGG
***
57526 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
57559 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
57592 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
57608 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:57612 original size:20 final size:20
Alignment explanation
Indices: 57538--57626 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
57528 TCGCGTTGCG
57538 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
57558 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
57571 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
57591 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
57611 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
57627 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:57748 original size:33 final size:33
Alignment explanation
Indices: 57706--57776 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
57696 AATACTAACT
*
57706 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
57739 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
57772 TGAAA
1 TGAAA
57777 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:58010 original size:22 final size:22
Alignment explanation
Indices: 57958--58012 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
57948 TGGTTGTGAG
**
57958 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
57980 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
58002 GGATTTCTTCG
1 GGATTTCTTCG
58013 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:58184 original size:20 final size:20
Alignment explanation
Indices: 58159--58371 Score: 259
Period size: 20 Copynumber: 10.6 Consensus size: 20
58149 CTTTAAATAT
58159 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
58179 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58199 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
58221 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58240 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
58260 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
58280 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
58300 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
58320 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
58340 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
58360 CGCGTTGCGATT
1 CGCGTTGCGATT
58372 ATGGAAAATC
Statistics
Matches: 166, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
19 2 0.01
20 147 0.89
21 15 0.09
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:58344 original size:60 final size:60
Alignment explanation
Indices: 58158--58371 Score: 293
Period size: 60 Copynumber: 3.5 Consensus size: 60
58148 GCTTTAAATA
58158 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTAT
** * * ***
58219 TATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGCATTGCGATTTACCCAT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
* * *
58279 ACGCGTTGCGATTTACGGATACACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
* ** *
58339 TCGCGTTGCGATTTTCATATTCGCGTTGCGATT
1 TCGCGTTGCGATTTACGGATACGCGTTGCGATT
58372 ATGGAAAATC
Statistics
Matches: 130, Mismatches: 23, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
60 83 0.64
61 47 0.36
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
TCGCGTTGCGATTTACGGATACGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTAT
Found at i:58452 original size:20 final size:20
Alignment explanation
Indices: 58427--58478 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
58417 AAGAATCGCG
*
58427 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
58447 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
58467 TTGCGATTCTGG
1 TTGCGATTCTGG
58479 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:59735 original size:21 final size:21
Alignment explanation
Indices: 59692--59735 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
59682 ATTCCTCCAA
*
59692 AACATTTTAATAGGAATATTT
1 AACATTTTAATAGGAATACTT
*
59713 AACATTTTATATAGTAAT-CTT
1 AACATTTTA-ATAGGAATACTT
59734 AA
1 AA
59736 AAGGTATTGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 13 0.65
22 7 0.35
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (21 bp):
AACATTTTAATAGGAATACTT
Found at i:63679 original size:2 final size:2
Alignment explanation
Indices: 63672--63697 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63662 TGCTATTTTA
63672 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
63698 CGTTATCTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:75861 original size:18 final size:18
Alignment explanation
Indices: 75838--75876 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
75828 GGAGCAGCAC
*
75838 GAGGAACAAGCTCCTCCA
1 GAGGAACAACCTCCTCCA
*
75856 GAGGAACAACCTCGTCCA
1 GAGGAACAACCTCCTCCA
75874 GAG
1 GAG
75877 TATCAAATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.33, C:0.31, G:0.26, T:0.10
Consensus pattern (18 bp):
GAGGAACAACCTCCTCCA
Found at i:76170 original size:17 final size:16
Alignment explanation
Indices: 76141--76206 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
76131 CATTTTAGAT
*
76141 ATTTTGGAATGTTTGA
1 ATTTTGGATTGTTTGA
76157 ATTTGTGGATTGTTTG-
1 ATTT-TGGATTGTTTGA
* *
76173 ACTTTGAATTTGTTTGA
1 ATTTTGGA-TTGTTTGA
76190 ATTTATGGA-TGTTTGA
1 ATTT-TGGATTGTTTGA
76206 A
1 A
76207 CTTATATTTC
Statistics
Matches: 41, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
15 3 0.07
16 22 0.54
17 13 0.32
18 3 0.07
ACGTcount: A:0.23, C:0.02, G:0.24, T:0.52
Consensus pattern (16 bp):
ATTTTGGATTGTTTGA
Found at i:76482 original size:25 final size:25
Alignment explanation
Indices: 76451--76531 Score: 79
Period size: 25 Copynumber: 3.6 Consensus size: 25
76441 TAACAAAAAG
76451 GGGGAGAAATGTTAAAGTGTTTAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
* *
76476 GGGGAGAAGTGTT--AGAG--T-AA
1 GGGGAGAAATGTTAAAGTGTTTAAA
76496 GGGG-G--ATGTTAAAGTGTTTAAA
1 GGGGAGAAATGTTAAAGTGTTTAAA
*
76518 GGGGAGAAGTGTTA
1 GGGGAGAAATGTTA
76532 GAGTAAGGGG
Statistics
Matches: 43, Mismatches: 5, Indels: 16
0.67 0.08 0.25
Matches are distributed among these distances:
17 4 0.09
19 4 0.09
20 6 0.14
21 2 0.05
22 6 0.14
23 4 0.09
25 17 0.40
ACGTcount: A:0.35, C:0.00, G:0.40, T:0.26
Consensus pattern (25 bp):
GGGGAGAAATGTTAAAGTGTTTAAA
Found at i:76485 original size:17 final size:17
Alignment explanation
Indices: 76465--76530 Score: 51
Period size: 21 Copynumber: 3.4 Consensus size: 17
76455 AGAAATGTTA
76465 AAGTGTTTAAAGGGGAG
1 AAGTGTTTAAAGGGGAG
*
76482 AAGTGTTAGAGTAAGGGGGATG
1 AAGTGTT----TAAAGGGGA-G
76504 TTAAAGTGTTTAAAGGGGAG
1 ---AAGTGTTTAAAGGGGAG
76524 AAGTGTT
1 AAGTGTT
76531 AGAGTAAGGG
Statistics
Matches: 39, Mismatches: 2, Indels: 16
0.68 0.04 0.28
Matches are distributed among these distances:
17 14 0.36
20 1 0.03
21 16 0.41
22 1 0.03
25 7 0.18
ACGTcount: A:0.33, C:0.00, G:0.39, T:0.27
Consensus pattern (17 bp):
AAGTGTTTAAAGGGGAG
Found at i:76511 original size:42 final size:42
Alignment explanation
Indices: 76459--76543 Score: 170
Period size: 42 Copynumber: 2.0 Consensus size: 42
76449 AGGGGGAGAA
76459 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
76501 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
1 ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
76543 A
1 A
76544 GTAATTTCAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.34, C:0.00, G:0.40, T:0.26
Consensus pattern (42 bp):
ATGTTAAAGTGTTTAAAGGGGAGAAGTGTTAGAGTAAGGGGG
Found at i:76521 original size:21 final size:21
Alignment explanation
Indices: 76459--76522 Score: 55
Period size: 21 Copynumber: 3.0 Consensus size: 21
76449 AGGGGGAGAA
76459 ATGTTAAAGTGTTTAAAGGGG
1 ATGTTAAAGTGTTTAAAGGGG
*
76480 A-G---AAGTGTTAGAGTAAGGGGG
1 ATGTTAAAGTGTT----TAAAGGGG
76501 ATGTTAAAGTGTTTAAAGGGG
1 ATGTTAAAGTGTTTAAAGGGG
76522 A
1 A
76523 GAAGTGTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 16
0.65 0.04 0.31
Matches are distributed among these distances:
17 7 0.21
20 1 0.03
21 17 0.52
22 1 0.03
25 7 0.21
ACGTcount: A:0.34, C:0.00, G:0.38, T:0.28
Consensus pattern (21 bp):
ATGTTAAAGTGTTTAAAGGGG
Found at i:76542 original size:21 final size:21
Alignment explanation
Indices: 76476--76544 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 21
76466 AGTGTTTAAA
76476 GGGGAGAAGTGTTAGAGTAAG
1 GGGGAGAAGTGTTAGAGTAAG
*
76497 GGGGATGTTAAAGTGTT----TAAA
1 GGGGA-G---AAGTGTTAGAGTAAG
76518 GGGGAGAAGTGTTAGAGTAAG
1 GGGGAGAAGTGTTAGAGTAAG
76539 GGGGAG
1 GGGGAG
76545 TAATTTCAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 16
0.68 0.04 0.29
Matches are distributed among these distances:
17 7 0.18
20 1 0.03
21 22 0.58
22 1 0.03
25 7 0.18
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.22
Consensus pattern (21 bp):
GGGGAGAAGTGTTAGAGTAAG
Found at i:80274 original size:18 final size:19
Alignment explanation
Indices: 80233--80274 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
80223 CCTTTTTTAT
**
80233 ATATTATTTTATTTCTCTA
1 ATATTATTTTATCCCTCTA
*
80252 TTATTATTTT-TCCCTCTA
1 ATATTATTTTATCCCTCTA
80270 ATATT
1 ATATT
80275 TAATTATATA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.24, C:0.14, G:0.00, T:0.62
Consensus pattern (19 bp):
ATATTATTTTATCCCTCTA
Found at i:80428 original size:3 final size:3
Alignment explanation
Indices: 80389--80452 Score: 76
Period size: 3 Copynumber: 21.3 Consensus size: 3
80379 TCCTCTTTAT
* * * *
80389 TTA TTT TTA TTA ATA TTA ATA TTA GTA -TA TATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA
80434 TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA T
80453 GGTTTTGTTT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:89146 original size:22 final size:22
Alignment explanation
Indices: 89110--89155 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
89100 AGTTTCTAGA
*
89110 GAATGCATTTCGATAGTG-CATC
1 GAATGCATTACGATA-TGACATC
*
89132 GAATGCATTAGGATATGACATC
1 GAATGCATTACGATATGACATC
89154 GA
1 GA
89156 GGCAATCCCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 2 0.10
22 19 0.90
ACGTcount: A:0.33, C:0.15, G:0.24, T:0.28
Consensus pattern (22 bp):
GAATGCATTACGATATGACATC
Found at i:90851 original size:14 final size:14
Alignment explanation
Indices: 90832--90877 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
90822 TCTTAAGTCA
90832 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
90846 AAAAAAAAGAAAAG
1 AAAAAAAAGAAAAG
* *
90860 AACAAAAA-AAGAG
1 AAAAAAAAGAAAAG
90873 AAAAA
1 AAAAA
90878 CGTTTAGGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAAAAGAAAAG
Found at i:90867 original size:18 final size:19
Alignment explanation
Indices: 90831--90876 Score: 60
Period size: 18 Copynumber: 2.5 Consensus size: 19
90821 GTCTTAAGTC
90831 AAAAA-AAAAGAAAAGAAA
1 AAAAAGAAAAGAAAAGAAA
*
90849 AAAAAGAAAAGAACA-AAA
1 AAAAAGAAAAGAAAAGAAA
*
90867 AAAGAGAAAA
1 AAAAAGAAAA
90877 ACGTTTAGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 17 0.68
19 8 0.32
ACGTcount: A:0.85, C:0.02, G:0.13, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAGAAA
Found at i:93804 original size:13 final size:13
Alignment explanation
Indices: 93784--93823 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
93774 CATATATTTT
*
93784 TATATTTTTATTC
1 TATATTTTTATTA
* *
93797 TTTATTTTTACTA
1 TATATTTTTATTA
93810 TATATTTTTATTA
1 TATATTTTTATTA
93823 T
1 T
93824 TTTTATTACT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.25, C:0.05, G:0.00, T:0.70
Consensus pattern (13 bp):
TATATTTTTATTA
Found at i:93839 original size:28 final size:26
Alignment explanation
Indices: 93784--93858 Score: 82
Period size: 26 Copynumber: 2.8 Consensus size: 26
93774 CATATATTTT
*
93784 TATATTTTTATTCTTTATTTTTACTA
1 TATATTTTTATTATTTATTTTTACTA
*
93810 TATATTTTTATTATTT-TTATTACTA
1 TATATTTTTATTATTTATTTTTACTA
93835 TTATATCCTTTT-TTATATTATTTT
1 -TATAT--TTTTATTAT-TTATTTT
93859 ATTTCTCTAT
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
25 8 0.20
26 20 0.49
27 4 0.10
28 6 0.15
29 3 0.07
ACGTcount: A:0.24, C:0.07, G:0.00, T:0.69
Consensus pattern (26 bp):
TATATTTTTATTATTTATTTTTACTA
Found at i:93937 original size:25 final size:25
Alignment explanation
Indices: 93893--93941 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
93883 AATATTTAAT
* *
93893 TATATATGTATCTATACATTTATTA
1 TATATATATATATATACATTTATTA
*
93918 TATATATATATATATTCATTTATT
1 TATATATATATATATACATTTATT
93942 CATTTTATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (25 bp):
TATATATATATATATACATTTATTA
Found at i:94036 original size:3 final size:3
Alignment explanation
Indices: 94000--94051 Score: 52
Period size: 3 Copynumber: 17.3 Consensus size: 3
93990 TCCTCTTTAT
* * * *
94000 TTA TTT TTA TTA ATA -TA ATA TTA GTA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
94045 TTA TTA T
1 TTA TTA T
94052 GGTTTTGTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
2 2 0.05
3 36 0.88
4 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:94079 original size:17 final size:17
Alignment explanation
Indices: 94054--94100 Score: 51
Period size: 17 Copynumber: 2.7 Consensus size: 17
94044 ATTATTATGG
94054 TTTTGTTTTCTTTATAT-
1 TTTT-TTTTCTTTATATA
* *
94071 TTATTTTTTATTTATCTA
1 TT-TTTTTTCTTTATATA
94089 TTTTTTTTCTTT
1 TTTTTTTTCTTT
94101 GCTTTATTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 21 0.84
18 4 0.16
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (17 bp):
TTTTTTTTCTTTATATA
Done.