Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004580.1 Hibiscus syriacus cultivar Beakdansim tig00010218_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: 65104
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:8887 original size:16 final size:17
Alignment explanation
Indices: 8857--8907 Score: 77
Period size: 16 Copynumber: 3.1 Consensus size: 17
8847 CAAAGTTTTT
*
8857 GTCAACGGTGGTCAACG
1 GTCAACGCTGGTCAACG
*
8874 GTCAACGC-GGTCAACA
1 GTCAACGCTGGTCAACG
8890 GTCAACGCTGGTCAACG
1 GTCAACGCTGGTCAACG
8907 G
1 G
8908 GTCGGGTCGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
16 15 0.50
17 15 0.50
ACGTcount: A:0.25, C:0.27, G:0.31, T:0.16
Consensus pattern (17 bp):
GTCAACGCTGGTCAACG
Found at i:8948 original size:20 final size:20
Alignment explanation
Indices: 8907--8963 Score: 66
Period size: 20 Copynumber: 3.0 Consensus size: 20
8897 CTGGTCAACG
* *
8907 GGTCGGGTCGG-TC-AGTCG
1 GGTCGGGTCGGACCGAGTCA
8925 GGTCGGGTCGGACCGAGTCA
1 GGTCGGGTCGGACCGAGTCA
*
8945 GGTCAGGTCGGACCG-GTCA
1 GGTCGGGTCGGACCGAGTCA
8964 AACTAGTTTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 11 0.32
19 5 0.15
20 18 0.53
ACGTcount: A:0.12, C:0.25, G:0.46, T:0.18
Consensus pattern (20 bp):
GGTCGGGTCGGACCGAGTCA
Found at i:10834 original size:13 final size:13
Alignment explanation
Indices: 10816--10847 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
10806 TATCCCACTG
*
10816 TATTTGATTGATA
1 TATTTGATTGAAA
10829 TATTTGATTGAAA
1 TATTTGATTGAAA
10842 TATTTG
1 TATTTG
10848 GTTACACAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.16, T:0.53
Consensus pattern (13 bp):
TATTTGATTGAAA
Found at i:20877 original size:20 final size:21
Alignment explanation
Indices: 20852--20944 Score: 100
Period size: 21 Copynumber: 4.5 Consensus size: 21
20842 TTTTCCCAAT
*
20852 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
20872 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
*
20893 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
20913 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
20934 TCGCAATGCGA
1 TCGCAATGCGA
20945 TACTAACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:20897 original size:41 final size:41
Alignment explanation
Indices: 20852--20944 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
20842 TTTTCCCAAT
20852 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
20893 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
20934 TCGCAATGCGA
1 TCGCAATGCGA
20945 TACTAACTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:20957 original size:41 final size:41
Alignment explanation
Indices: 20871--21005 Score: 141
Period size: 41 Copynumber: 3.3 Consensus size: 41
20861 GAATAAGTAA
*
20871 ATCGCAACGCGAATTGGGAAAATCGCAATGCGA-A-TAAGT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTAACT
20910 AAATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTAACT
1 --ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTAACT
* * ** * * *
20953 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTAACT
*
20994 TTCGCAACGCGA
1 ATCGCAACGCGA
21006 TACTGACTTT
Statistics
Matches: 81, Mismatches: 10, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
41 74 0.91
42 3 0.04
43 4 0.05
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTAACT
Found at i:20958 original size:20 final size:20
Alignment explanation
Indices: 20933--21026 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
20923 AATTGGGAAA
20933 ATCGCAATGCGATACTAACT
1 ATCGCAATGCGATACTAACT
* **
20953 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATACT-AACT
* * *
20974 ATCGCAACGAGATACTTACT
1 ATCGCAATGCGATACTAACT
* * *
20994 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATACTAACT
*
21014 TTCGCAATGCGAT
1 ATCGCAATGCGAT
21027 TTTCAAAGCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 45 0.75
21 15 0.25
ACGTcount: A:0.35, C:0.23, G:0.17, T:0.24
Consensus pattern (20 bp):
ATCGCAATGCGATACTAACT
Found at i:21222 original size:22 final size:22
Alignment explanation
Indices: 21194--21237 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
21184 CACTCTCTCA
21194 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
* *
21216 CCCATCTCTGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
21238 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.20, C:0.43, G:0.16, T:0.20
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:21526 original size:20 final size:20
Alignment explanation
Indices: 21501--21538 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
21491 CGATTCTCTC
21501 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
21521 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
21539 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:22878 original size:18 final size:18
Alignment explanation
Indices: 22857--22901 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
22847 TCCACTTCGG
* *
22857 GAGCCATCACCTCGCCTA
1 GAGCCATCACCTCACCCA
*
22875 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
22893 GAGCCATCA
1 GAGCCATCA
22902 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:23434 original size:19 final size:20
Alignment explanation
Indices: 23380--23446 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
23370 TAGTTTACTT
* *
23380 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
23400 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
23420 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
23439 TCGCAACG
1 TCGCAACG
23447 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:23454 original size:14 final size:14
Alignment explanation
Indices: 23435--23492 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
23425 ATGCGAAATG
23435 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
23449 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
23465 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
23481 AAAATCGTAACG
1 AAAATCGCAACG
23493 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:23477 original size:32 final size:33
Alignment explanation
Indices: 23419--23509 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
23409 GGAAATGGCT
*
23419 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
23452 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
23484 ATCGTAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
23510 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 31 0.56
33 24 0.44
ACGTcount: A:0.47, C:0.22, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:23514 original size:19 final size:18
Alignment explanation
Indices: 23419--23514 Score: 66
Period size: 19 Copynumber: 5.6 Consensus size: 18
23409 GGAAATGGCT
23419 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
*
23438 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
23452 ATCGCAACGCGAAATG-AA
1 ATCGCAA-GCGAAATGAAA
*
23470 ATCGCAA-CG--A-CAAA
1 ATCGCAAGCGAAATGAAA
*
23484 ATCGTAACGCGAAATGAAA
1 ATCGCAA-GCGAAATGAAA
23503 ATCGCAATGCGA
1 ATCGCAA-GCGA
23515 TTTGTGTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 22
0.67 0.08 0.25
Matches are distributed among these distances:
14 19 0.32
15 1 0.02
16 6 0.10
17 2 0.03
18 11 0.19
19 20 0.34
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (18 bp):
ATCGCAAGCGAAATGAAA
Found at i:23555 original size:19 final size:18
Alignment explanation
Indices: 23533--23640 Score: 80
Period size: 19 Copynumber: 5.9 Consensus size: 18
23523 TCGCGTTGCG
23533 ATTTTGTCGTTGCGATTTC
1 ATTTTG-CGTTGCGATTTC
23552 ATTTTGCGTTGCGA-TT-
1 ATTTTGCGTTGCGATTTC
*
23568 -TTGT-CGTTGCGATTTTC
1 ATTTTGCGTTGCGA-TTTC
* **
23585 ATTTTGCATTGCGATAGCC
1 ATTTTGCGTTGCGAT-TTC
* *
23604 ATTTCCGCGTTGCGATAGTC
1 ATTT-TGCGTTGCGAT-TTC
*
23624 ATTTCGCGTTGCGATTT
1 ATTTTGCGTTGCGATTT
23641 TAAGTTTCGT
Statistics
Matches: 73, Mismatches: 9, Indels: 15
0.75 0.09 0.15
Matches are distributed among these distances:
14 8 0.11
15 3 0.04
16 2 0.03
17 2 0.03
18 13 0.18
19 29 0.40
20 16 0.22
ACGTcount: A:0.13, C:0.19, G:0.23, T:0.45
Consensus pattern (18 bp):
ATTTTGCGTTGCGATTTC
Found at i:23564 original size:32 final size:33
Alignment explanation
Indices: 23525--23599 Score: 134
Period size: 32 Copynumber: 2.3 Consensus size: 33
23515 TTTGTGTTTC
23525 GCGTTGCGATTTTGTCGTTGCGA-TTTCATTTT
1 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTT
23557 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTT
1 GCGTTGCGATTTTGTCGTTGCGATTTTCATTTT
*
23590 GCATTGCGAT
1 GCGTTGCGAT
23600 AGCCATTTCC
Statistics
Matches: 41, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
32 23 0.56
33 18 0.44
ACGTcount: A:0.11, C:0.16, G:0.25, T:0.48
Consensus pattern (33 bp):
GCGTTGCGATTTTGTCGTTGCGATTTTCATTTT
Found at i:23568 original size:13 final size:14
Alignment explanation
Indices: 23526--23583 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
23516 TTGTGTTTCG
23526 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
23540 CGTTGCGATTTCATTTT
1 CGTTGCGA-TT--TTGT
23557 GCGTTGCGATTTTGT
1 -CGTTGCGATTTTGT
23572 CGTTGCGATTTT
1 CGTTGCGATTTT
23584 CATTTTGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.53
15 5 0.13
17 5 0.13
18 8 0.21
ACGTcount: A:0.09, C:0.16, G:0.26, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:23618 original size:20 final size:19
Alignment explanation
Indices: 23593--23638 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 19
23583 TCATTTTGCA
23593 TTGCGATAGCCATTTCCGCG
1 TTGCGATAGCCATTT-CGCG
*
23613 TTGCGATAGTCATTTCGCG
1 TTGCGATAGCCATTTCGCG
23632 TTGCGAT
1 TTGCGAT
23639 TTTAAGTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 11 0.44
20 14 0.56
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (19 bp):
TTGCGATAGCCATTTCGCG
Found at i:25530 original size:14 final size:14
Alignment explanation
Indices: 25511--25546 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
25501 ATTGTTTAAT
25511 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
25525 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
25539 TGATTTGT
1 TGATTTGT
25547 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:25685 original size:19 final size:19
Alignment explanation
Indices: 25663--25711 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
25653 ATCGCAACGA
25663 GAAAATCGTAATGCGAAAT
1 GAAAATCGTAATGCGAAAT
*
25682 GAAAATCGCAATGCGAAAT
1 GAAAATCGTAATGCGAAAT
25701 GAAAATCGTAA
1 GAAAATCGTAA
25712 GGAGAATCGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.18
Consensus pattern (19 bp):
GAAAATCGTAATGCGAAAT
Found at i:25769 original size:20 final size:20
Alignment explanation
Indices: 25719--25769 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
25709 TAAGGAGAAT
*
25719 CGTTGCGATAACCATTTTCG
1 CGTTGCGATAGCCATTTTCG
25739 CGTTGCGATAGCCATTTTCG
1 CGTTGCGATAGCCATTTTCG
25759 CGTTGCGATAG
1 CGTTGCGATAG
25770 TCAAATGAGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.18, C:0.24, G:0.25, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGCCATTTTCG
Found at i:26154 original size:14 final size:14
Alignment explanation
Indices: 26135--26170 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26125 ATTGTTTAAT
26135 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26149 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26163 TGATTTGT
1 TGATTTGT
26171 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26309 original size:19 final size:19
Alignment explanation
Indices: 26287--26354 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
26277 ATCGCAACGA
26287 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
26306 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
26325 GAAAATCGCAA-G-G--A-
1 GAAAATCGCAATGCGAAAT
26339 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
26355 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 2 0.04
16 1 0.02
17 1 0.02
18 1 0.02
19 30 0.65
ACGTcount: A:0.47, C:0.16, G:0.24, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:26430 original size:20 final size:20
Alignment explanation
Indices: 26373--26430 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
26363 TCGCATTGCG
* *
26373 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
26393 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
26413 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
26431 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:26816 original size:14 final size:14
Alignment explanation
Indices: 26797--26832 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
26787 ATTGTTTAAT
26797 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
26811 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
26825 TGATTTGT
1 TGATTTGT
26833 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:26940 original size:19 final size:19
Alignment explanation
Indices: 26916--26969 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
26906 GCAAAACAGA
26916 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
26935 CTATCGCAACGCGAAATGG
1 CTATCGCAACGCGAAATGG
*
26954 CTATCGCAACGAGAAA
1 CTATCGCAACGCGAAA
26970 ATCGCAATGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (19 bp):
CTATCGCAACGCGAAATGG
Found at i:26988 original size:19 final size:19
Alignment explanation
Indices: 26966--27033 Score: 92
Period size: 19 Copynumber: 3.8 Consensus size: 19
26956 ATCGCAACGA
*
26966 GAAAATCGCAATGTGAAAT
1 GAAAATCGCAATGCGAAAT
26985 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
27004 GAAAATCGCAA-G-G--A-
1 GAAAATCGCAATGCGAAAT
27018 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
27034 TTTTCATTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 11 0.24
15 2 0.04
16 1 0.02
17 1 0.02
18 1 0.02
19 29 0.64
ACGTcount: A:0.47, C:0.15, G:0.24, T:0.15
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:27109 original size:20 final size:20
Alignment explanation
Indices: 27052--27109 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
27042 TCGCATTGCG
* *
27052 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
27072 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
27092 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
27110 TCAAATGAAT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:27161 original size:679 final size:660
Alignment explanation
Indices: 25718--27296 Score: 2892
Period size: 679 Copynumber: 2.4 Consensus size: 660
25708 GTAAGGAGAA
*
25718 TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAGTGTC
1 TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTC
25783 TAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTA
66 TAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTA
25848 ACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
131 ACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
25913 CTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAG
196 CTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAG
25978 ATGTGTAGGAAGTCTTGTTTGAGCAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGCGT
261 ATGTGTAGGAAGTCTTGTTTGAGCAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGCGT
26043 GAAATGGATGTACGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGA
326 GAAATGGATGTACGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGA
26108 ATTATTATTATTTTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTT
391 ATTATTATTATTTTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTT
*
26173 AATTGATGTGTACATAATTTGTGTTGAAATGTAATTGTTGATTTGTTGATTTTCAATCTGCTTTA
456 AATTGA-GTGTACATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTA
26238 TGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGA
520 TGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGA
26303 AATGAAAATCGCAATGCGAAATGAAAATCGCAAGGAGAAAATCGCAATGCGATTTTCATTTCGCA
585 AATGAAAATCGCAATGCGAAATGAAAATCGCAAGGAGAAAATCGCAATGCGATTTTCATTTCGCA
26368 TTGCGATTTTC
650 TTGCGATTTTC
26379 TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTC
1 TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTC
26444 TAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTA
66 TAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTA
*
26509 ACTGAAAATGTTAAAAGTGCACATATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
131 ACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
26574 CTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAG
196 CTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAG
*
26639 ATGTGTAGGAAGTCTTGTTTGAGCAAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTTAGCTGCG
261 ATGTGTAGGAAGTCTTGTTTGAGC-AATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGCG
26704 TGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAG
325 TGAAATGGATGTACGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAG
26769 AATTATTATTATTTTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTT
390 AATTATTATTATTTTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTT
26834 TAATTGA-TGTACATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTA
455 TAATTGAGTGTACATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTA
26898 TGTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTATCGCAACGCGAAATGGCTATCGCAA
520 TGTTGAAGGC---A-A-A--A---C-A---G--A---CTATCGCAACGCGAAATGGCTATCGCAA
*
26963 CGAGAAAATCGCAATGTGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGGAGAAAATCGCA
566 CGAGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGGAGAAAATCGCA
27028 ATGCGATTTTCATTTCGCATTGCGATTTTC
631 ATGCGATTTTCATTTCGCATTGCGATTTTC
27058 TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTC
1 TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTC
* *
27123 TAATAAGTGATGACAACTAAACAGATCATAGTAATGTTCAAACTCAAGTTACTAATACATGCCTA
66 TAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTA
27188 ACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
131 ACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
27253 C-TTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAAT
196 CTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAAT
27297 AATTGTTAAA
Statistics
Matches: 890, Mismatches: 8, Indels: 23
0.97 0.01 0.02
Matches are distributed among these distances:
660 66 0.07
661 282 0.32
662 176 0.20
663 1 0.00
664 1 0.00
665 1 0.00
667 1 0.00
670 1 0.00
671 1 0.00
674 1 0.00
676 1 0.00
678 43 0.05
679 315 0.35
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.34
Consensus pattern (660 bp):
TCGTTGCGATAACCATTTTCGCGTTGCGATAGCCATTTTCGCGTTGCGATAGTCAAATGAATGTC
TAATAAGTGATGACAACTGAACAGATCATAGCAATGTTCAAACTCAAGTTACTAATACATGCCTA
ACTGAAAATGTTAAAAGTGCACACATAAAATACACATAATGCAAGTTTTGTTAACATATATACTC
CTTTTGGTTTGAAAATGTTTGGTTAAGTACCTAGAATTCAATAATTTGCTGTTTGTAGGTTTTAG
ATGTGTAGGAAGTCTTGTTTGAGCAATGTTTGGTTTCTGCAGGTTAATCCTTAAGTGAGCTGCGT
GAAATGGATGTACGGGGTCACAAAGTTGTTGATTCATTGATTCAATAATTGATGAAGAAATAAGA
ATTATTATTATTTTTTGATTGTTTAATTGATTTGTAAAAGATGATTTGTAAATGTTGATTTGTTT
AATTGAGTGTACATAATTTGTGTTGAAATGTAATAGTTGATTTGTTGATTTTCAATCTGCTTTAT
GTTGAAGGCAAAACAGACTATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAA
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGGAGAAAATCGCAATGCGATTTTCATTTCGCAT
TGCGATTTTC
Found at i:28218 original size:24 final size:24
Alignment explanation
Indices: 28162--28220 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
28152 AGTCAGTATT
* *
28162 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
28186 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
28210 CGAATTTTGAT
1 CGAAATTTGAT
28221 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:29402 original size:19 final size:19
Alignment explanation
Indices: 29380--29510 Score: 94
Period size: 19 Copynumber: 7.7 Consensus size: 19
29370 GGAAATTACT
29380 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29399 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
29413 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
29432 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
29446 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
29465 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
29479 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
29498 ATCGCAACGCGAA
1 ATCGCAATGCGAA
29511 TTTAATTTCG
Statistics
Matches: 84, Mismatches: 13, Indels: 30
0.66 0.10 0.24
Matches are distributed among these distances:
14 27 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 39 0.46
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:29422 original size:33 final size:33
Alignment explanation
Indices: 29380--29506 Score: 202
Period size: 33 Copynumber: 3.8 Consensus size: 33
29370 GGAAATTACT
29380 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
29413 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
29445 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
29479 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
29507 CGAATTTAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
32 1 0.01
33 83 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.20, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:29487 original size:66 final size:66
Alignment explanation
Indices: 29381--29513 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
29371 GAAATTACTA
*
29381 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
29446 T
66 T
*
29447 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
29512 T
66 T
29513 T
1 T
29514 AATTTCGCGT
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.41, C:0.20, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:29528 original size:19 final size:20
Alignment explanation
Indices: 29506--29548 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
29496 AAATCGCAAC
29506 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
29525 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
29545 GCGA
1 GCGA
29549 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:29533 original size:14 final size:14
Alignment explanation
Indices: 29534--29567 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
29524 TGCGATTTTC
29534 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
29548 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
29562 ATTTTC
1 ATTTTC
29568 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:29708 original size:14 final size:14
Alignment explanation
Indices: 29689--29725 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
29679 CATCAATTAA
29689 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
29703 ACAAATCACCTTTT
1 ACAAATCAACTTTT
29717 ACAAATCAA
1 ACAAATCAA
29726 TTAAACAAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:31202 original size:42 final size:42
Alignment explanation
Indices: 31120--31203 Score: 96
Period size: 42 Copynumber: 2.0 Consensus size: 42
31110 CGATGACAGT
* * * *
31120 GGCCTCTTGAACGGTGGGAGGGGACTATCGAGGAATGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTATCGAGGAACGATAGG
* * * *
31162 GGCCTCTTCAACGATAGGAGTGGACTCTTGAGGGACGATAGG
1 GGCCTCTTCAACGATAGGAGGGGACTATCGAGGAACGATAGG
31204 CGAGTCGGGC
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.24, C:0.17, G:0.39, T:0.20
Consensus pattern (42 bp):
GGCCTCTTCAACGATAGGAGGGGACTATCGAGGAACGATAGG
Found at i:33286 original size:33 final size:33
Alignment explanation
Indices: 33229--33326 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 33
33219 ACGAGATAAT
*
33229 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
33263 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* * **
33296 AACAATCGCAACGCGAAATGAAAATCGCAAC
1 GAGAATCGCAACGCGAAATGACTATCGCAAC
33327 TGCGAAATAA
Statistics
Matches: 57, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 43 0.75
34 14 0.25
ACGTcount: A:0.41, C:0.26, G:0.22, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:33321 original size:19 final size:19
Alignment explanation
Indices: 33204--33407 Score: 212
Period size: 19 Copynumber: 11.1 Consensus size: 19
33194 TCTTTTGGTT
*
33204 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
33223 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
33243 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
33261 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
33277 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
33295 --AA--ACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
33310 GAAATGAAAATCGCAACTGC
1 GAAATGAAAATCGCAAC-GC
*
33330 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
33349 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
33368 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
33387 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
33406 GA
1 GA
33408 TTTTGGTTTC
Statistics
Matches: 157, Mismatches: 15, Indels: 26
0.79 0.08 0.13
Matches are distributed among these distances:
14 18 0.11
15 2 0.01
16 4 0.03
17 3 0.02
18 3 0.02
19 80 0.51
20 45 0.29
21 2 0.01
ACGTcount: A:0.45, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:33425 original size:19 final size:19
Alignment explanation
Indices: 33403--33448 Score: 65
Period size: 20 Copynumber: 2.4 Consensus size: 19
33393 AAAATCGCAA
*
33403 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
33422 TGCGAATTTTTATTTCGCGT
1 TGCG-ATTTTGATTTCGCGT
33442 TGCGATT
1 TGCGATT
33449 ATCTCGTTCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.11, C:0.15, G:0.26, T:0.48
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:33427 original size:57 final size:58
Alignment explanation
Indices: 33299--33407 Score: 193
Period size: 58 Copynumber: 1.9 Consensus size: 58
33289 GCGACCAAAC
33299 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAAAATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAAAATCGCAACGCGAAATGAA
* *
33357 AATCGCAACGCGAAATGAAAATCGCAAC-GCGAAATGAAAATCGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAAAATCGCAACGCGA
33408 TTTTGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 21 0.43
58 28 0.57
ACGTcount: A:0.47, C:0.21, G:0.20, T:0.12
Consensus pattern (58 bp):
AATCGCAACGCGAAATGAAAATCGCAACTGCGAAATAAAAATCGCAACGCGAAATGAA
Found at i:34025 original size:20 final size:20
Alignment explanation
Indices: 34000--34052 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
33990 GCGCTATGTA
34000 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
34020 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
34040 TATCTCGTTGCGA
1 AATCGCGTTGCGA
34053 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:34086 original size:20 final size:20
Alignment explanation
Indices: 34061--34110 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
34051 GATTTTGTAT
34061 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
34081 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
34101 TATCGCATTG
1 TATCGCATTG
34111 TGATTTTCCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:34116 original size:61 final size:61
Alignment explanation
Indices: 34001--34117 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
33991 CGCTATGTAA
* * * * *
34001 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * * *
34062 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGTGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
34118 CCCAATTCGC
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:34133 original size:61 final size:61
Alignment explanation
Indices: 34001--34135 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
33991 CGCTATGTAA
* * * * * ** *
34001 ATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * * *
34062 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGTGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
34124 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
34136 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:38692 original size:75 final size:75
Alignment explanation
Indices: 38613--38755 Score: 180
Period size: 75 Copynumber: 1.9 Consensus size: 75
38603 TCATAGCATA
* * * *
38613 AGTATCCATATTTCAAATTTCGATCTAATTTTCAGTAAAAAA-TTTTGAACCTAAAGTATCAAAC
1 AGTATCCAAATTTCAAATTTCAATATAATTTTCAG-AAAAAACTTTTAAACCTAAAGTATCAAAC
38677 CACAGAGCACG
65 CACAGAGCACG
* * * * **
38688 AGTATCGAAATTTCAAATTTCAATATATTTTTTAGAAAAAACTTTTAAATCTAAAGTATTGAACC
1 AGTATCCAAATTTCAAATTTCAATATAATTTTCAGAAAAAACTTTTAAACCTAAAGTATCAAACC
38753 ACA
66 ACA
38756 TAGTAGGAGT
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
74 6 0.11
75 51 0.89
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.34
Consensus pattern (75 bp):
AGTATCCAAATTTCAAATTTCAATATAATTTTCAGAAAAAACTTTTAAACCTAAAGTATCAAACC
ACAGAGCACG
Found at i:44978 original size:187 final size:185
Alignment explanation
Indices: 44661--45010 Score: 443
Period size: 187 Copynumber: 1.9 Consensus size: 185
44651 CCCTTTCAAC
* *
44661 TTGTTTTGTTACCGTGGATATTTTTTGACCCATTTGCTAAATTTCAATAACAATTCCCGTCAAAA
1 TTGTTTTGTTACCGTGGATATTTTTTGACCCATTCGCTAAATCTCAATAACAATTCCCGTCAAAA
* * * * * *
44726 TCGGGTTTATTTAAGAACCTTTTAACATTCCCGATCTCAACCTATTTTCATAGTGACGGGTAACA
66 TCGGATTTATTCAAGAACCTTTTAACATTCCCGATCTCAACATAATTTCATAGAGACAGGTAACA
* * *
44791 TTCTTGGGTACAACCAGATTTGTCATAGTCATTAATAACATTTTCGTCTTTTAAT
131 TTCTTAGGCACAACCAGATTTGTCATAGCCATTAATAACATTTTCGTCTTTTAAT
* * *
44846 TTGTTTTGTTATCGTGGATATTTTCTTTGACCCATTCGCTAAA-CTCTGATAACAATT-TCGATC
1 TTGTTTTGTTACCGTGGATA-TTT-TTTGACCCATTCGCTAAATCTC-AATAACAATTCCCG-TC
**** * *
44909 AAAATCGGATTTATTCAAGAACCTTTTAACATTTTTTATCTCAACATAATTTCTTAGAGACATGT
62 AAAATCGGATTTATTCAAGAACCTTTTAACATTCCCGATCTCAACATAATTTCATAGAGACAGGT
** *
44974 AACATTCTTAGGCACAACTGGATTTGTTATAGCCATT
127 AACATTCTTAGGCACAACCAGATTTGTCATAGCCATT
45011 CATTTTTGTC
Statistics
Matches: 138, Mismatches: 23, Indels: 6
0.83 0.14 0.04
Matches are distributed among these distances:
185 19 0.14
186 7 0.05
187 112 0.81
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (185 bp):
TTGTTTTGTTACCGTGGATATTTTTTGACCCATTCGCTAAATCTCAATAACAATTCCCGTCAAAA
TCGGATTTATTCAAGAACCTTTTAACATTCCCGATCTCAACATAATTTCATAGAGACAGGTAACA
TTCTTAGGCACAACCAGATTTGTCATAGCCATTAATAACATTTTCGTCTTTTAAT
Found at i:45484 original size:31 final size:31
Alignment explanation
Indices: 45443--45501 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
45433 CTGTAACCAT
45443 TATAACCGGTCTCGTCATTTATTAGCCTTAA
1 TATAACCGGTCTCGTCATTTATTAGCCTTAA
*
45474 TATAATCGGTCTCGTCATTTATTAGCCT
1 TATAACCGGTCTCGTCATTTATTAGCCT
45502 CCCTTAGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.24, C:0.22, G:0.14, T:0.41
Consensus pattern (31 bp):
TATAACCGGTCTCGTCATTTATTAGCCTTAA
Found at i:54561 original size:23 final size:23
Alignment explanation
Indices: 54531--54574 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
54521 ATTACAATAA
54531 AAAGCTTGAACAAATTGATGACG
1 AAAGCTTGAACAAATTGATGACG
54554 AAAGCTTGAACAAATTGATGA
1 AAAGCTTGAACAAATTGATGA
54575 TGAATGGAGG
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:0.45, C:0.11, G:0.20, T:0.23
Consensus pattern (23 bp):
AAAGCTTGAACAAATTGATGACG
Found at i:61710 original size:21 final size:21
Alignment explanation
Indices: 61666--61712 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
61656 ACTTTGGAAT
* *
61666 TTTTCCTAGGATGCAACTAGC
1 TTTTCCTAGGATGCAACCAAC
* *
61687 TTTTCCTGGGATGTAACCAAC
1 TTTTCCTAGGATGCAACCAAC
61708 TTTTC
1 TTTTC
61713 TTGTGAAATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TTTTCCTAGGATGCAACCAAC
Done.