Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003172.1 Hibiscus syriacus cultivar Beakdansim tig00006669_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: 126992
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:15182 original size:369 final size:369
Alignment explanation
Indices: 14503--15241 Score: 1442
Period size: 369 Copynumber: 2.0 Consensus size: 369
14493 TGGATATGGT
14503 GCCACTGCCATGGGACAGCGCTTGTAACAATTTTTGTTGTTGTTGGTCAATCTTATTAGTATATT
1 GCCACTGCCATGGGACAGCGCTTGTAACAATTTTTGTTGTTGTTGGTCAATCTTATTAGTATATT
14568 ACACCATGTGCTTAGGATGTCTTAGATGACCCACATTTGTTATTGCAGCTTATTGGTTTTTGGTT
66 ACACCATGTGCTTAGGATGTCTTAGATGACCCACATTTGTTATTGCAGCTTATTGGTTTTTGGTT
*
14633 GTGTGTTAGTTATGGGTAATTATGATTTATACACACTTGAGTTTCTGAATGTATAGACTATAGAT
131 GTGTATTAGTTATGGGTAATTATGATTTATACACACTTGAGTTTCTGAATGTATAGACTATAGAT
*
14698 GATGAACTCTTATACCATATGTATTCACTCTATATTTTTTTCTATTTAATTCCATGTGCTAAGGT
196 GATGAACTCTTATACCATATGTATTCACTCTATATTTTTTTCTATTTAATTCCATATGCTAAGGT
14763 AGAATATTGGTACATATACATGTTGGGCCGCTAGCTAAGTTAAAGAATGACCAATTCATATGAAA
261 AGAATATTGGTACATATACATGTTGGGCCGCTAGCTAAGTTAAAGAATGACCAATTCATATGAAA
14828 AAAATAAAGACATTAAAATAAATGTTGTTGGTGAAGTCCAATAA
326 AAAATAAAGACATTAAAATAAATGTTGTTGGTGAAGTCCAATAA
*
14872 GCCACTGCCATGGGACAGCGCTTGTAACAATTTTTGTTGTTGTTGGTCAGTCTTATTAGTATATT
1 GCCACTGCCATGGGACAGCGCTTGTAACAATTTTTGTTGTTGTTGGTCAATCTTATTAGTATATT
14937 ACACCATGTGCTTAGGATGTCTTAGATGACCCACATTTGTTATTGCAGCTTATTGGTTTTTGGTT
66 ACACCATGTGCTTAGGATGTCTTAGATGACCCACATTTGTTATTGCAGCTTATTGGTTTTTGGTT
15002 GTGTATTAGTTATGGGTAATTATGATTTATACACACTTGAGTTTCTGAATGTATAGACTATAGAT
131 GTGTATTAGTTATGGGTAATTATGATTTATACACACTTGAGTTTCTGAATGTATAGACTATAGAT
15067 GATGAACTCTTATACCATATGTATTCACTCTATATTTTTTTCTATTTAATTCCATATGCTAAGGT
196 GATGAACTCTTATACCATATGTATTCACTCTATATTTTTTTCTATTTAATTCCATATGCTAAGGT
15132 AGAATATTGGTACATATACATGTTGGGCCGCTAGCTAAGTTAAAGAATGACCAATTCATATGAAA
261 AGAATATTGGTACATATACATGTTGGGCCGCTAGCTAAGTTAAAGAATGACCAATTCATATGAAA
*
15197 AAAATAAAGACATTAAAATGAATGTTGTTGGTGAAGTCCAATAA
326 AAAATAAAGACATTAAAATAAATGTTGTTGGTGAAGTCCAATAA
15241 G
1 G
15242 ACGTCAGGAA
Statistics
Matches: 366, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
369 366 1.00
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.38
Consensus pattern (369 bp):
GCCACTGCCATGGGACAGCGCTTGTAACAATTTTTGTTGTTGTTGGTCAATCTTATTAGTATATT
ACACCATGTGCTTAGGATGTCTTAGATGACCCACATTTGTTATTGCAGCTTATTGGTTTTTGGTT
GTGTATTAGTTATGGGTAATTATGATTTATACACACTTGAGTTTCTGAATGTATAGACTATAGAT
GATGAACTCTTATACCATATGTATTCACTCTATATTTTTTTCTATTTAATTCCATATGCTAAGGT
AGAATATTGGTACATATACATGTTGGGCCGCTAGCTAAGTTAAAGAATGACCAATTCATATGAAA
AAAATAAAGACATTAAAATAAATGTTGTTGGTGAAGTCCAATAA
Found at i:15608 original size:21 final size:21
Alignment explanation
Indices: 15579--15631 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
15569 ATTCTAACTA
15579 TCGCATTGCGATTTCCCAAAT
1 TCGCATTGCGATTTCCCAAAT
* * *
15600 TCGCGTTGCGATTTTCCTAAT
1 TCGCATTGCGATTTCCCAAAT
*
15621 TCGCAATGCGA
1 TCGCATTGCGA
15632 ATACGTAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTCCCAAAT
Found at i:15646 original size:20 final size:20
Alignment explanation
Indices: 15621--15712 Score: 121
Period size: 20 Copynumber: 4.5 Consensus size: 20
15611 TTTTCCTAAT
15621 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
15641 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
15662 TTGCAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
15682 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
15702 TCGCAATGCGA
1 TCGCAATGCGA
15713 TTTACATAGC
Statistics
Matches: 59, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
20 45 0.76
21 14 0.24
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.22
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:15916 original size:22 final size:21
Alignment explanation
Indices: 15891--15952 Score: 58
Period size: 18 Copynumber: 3.0 Consensus size: 21
15881 GGCGACATCC
15891 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCT-CGACGAAATCA
*
15913 GTCCCCA---CGACGATATCA
1 GTCCCCATCTCGACGAAATCA
* *
15931 GTCTCCATCTTCGGCGAAATCA
1 GTCCCCATC-TCGACGAAATCA
15953 TTTACGGTCA
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
18 16 0.50
22 16 0.50
ACGTcount: A:0.26, C:0.37, G:0.16, T:0.21
Consensus pattern (21 bp):
GTCCCCATCTCGACGAAATCA
Found at i:16366 original size:20 final size:20
Alignment explanation
Indices: 16343--16389 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
16333 CAAATTCGCA
16343 TTGCGATAGTCATTTTCATG
1 TTGCGATAGTCATTTTCATG
* ** *
16363 TTGCGGTTTTCATTTTCGTG
1 TTGCGATAGTCATTTTCATG
16383 TTGCGAT
1 TTGCGAT
16390 TTAAAGTTTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.13, C:0.15, G:0.23, T:0.49
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCATG
Found at i:18301 original size:20 final size:20
Alignment explanation
Indices: 18276--18387 Score: 179
Period size: 20 Copynumber: 5.6 Consensus size: 20
18266 AGAATAGTTT
*
18276 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCAAAAATG
*
18296 ACTATCGCAACGCAAAAATG
1 ACTATCGCAATGCAAAAATG
18316 ACTATCGCAATGCAAAAATG
1 ACTATCGCAATGCAAAAATG
*
18336 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCAAAAATG
**
18356 ACTATCGCAATGCAAATTTG
1 ACTATCGCAATGCAAAAATG
18376 ACTATCGCAATG
1 ACTATCGCAATG
18388 AAAGAATCGC
Statistics
Matches: 85, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.21
Consensus pattern (20 bp):
ACTATCGCAATGCAAAAATG
Found at i:18410 original size:21 final size:19
Alignment explanation
Indices: 18279--18423 Score: 68
Period size: 20 Copynumber: 7.6 Consensus size: 19
18269 ATAGTTTACT
**
18279 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCG-AAATGAAA
* * **
18299 ATCGCAACGCAAAAATGACT
1 ATCGCAATGC-GAAATGAAA
* **
18319 ATCGCAATGCAAAAATGACT
1 ATCGCAATGC-GAAATGAAA
**
18339 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCG-AAATGAAA
**
18359 ATCGCAATGC-AAATTTGACT
1 ATCGCAATGCGAAA--TGAAA
18379 ATCGCAAT--GAAA-G--A
1 ATCGCAATGCGAAATGAAA
18393 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
18412 ATCGCATTGCGA
1 ATCGCAATGCGA
18424 TTCTCTCTTT
Statistics
Matches: 109, Mismatches: 6, Indels: 21
0.80 0.04 0.15
Matches are distributed among these distances:
14 8 0.07
16 5 0.05
17 1 0.01
18 3 0.03
19 15 0.14
20 77 0.71
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:18451 original size:34 final size:34
Alignment explanation
Indices: 18413--18565 Score: 112
Period size: 34 Copynumber: 4.4 Consensus size: 34
18403 GAAATGAAAA
*
18413 TCGCATTGCGATTCTCTCTTTGCGATAGTCAAAT
1 TCGCATTGCGATTCTCTCTTTGCGATAGTCAATT
* * *
18447 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGAT--TC----TCTCTTTGCGATAGTCAATT
* * * * **
18487 TCGCGTTGCGATTTTGT-TGTTGCGAT-TTTTATT
1 TCGCATTGCGATTCTCTCT-TTGCGATAGTCAATT
* *
18520 TCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATTCTCTCTTTGCGATAGTCAATT
*
18554 TCGCGTTGCGAT
1 TCGCATTGCGAT
18566 AGTCATTTTC
Statistics
Matches: 88, Mismatches: 22, Indels: 18
0.69 0.17 0.14
Matches are distributed among these distances:
33 24 0.27
34 34 0.39
36 2 0.02
38 1 0.01
40 27 0.31
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (34 bp):
TCGCATTGCGATTCTCTCTTTGCGATAGTCAATT
Found at i:18457 original size:20 final size:20
Alignment explanation
Indices: 18432--18585 Score: 120
Period size: 20 Copynumber: 8.3 Consensus size: 20
18422 GATTCTCTCT
**
18432 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
18452 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
18472 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
18492 TTGCGAT--T--TTGTT-G--
1 TTGCGATAGTCATT-TTCGCA
** *
18506 TTGCGATTTTTA-TTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
18525 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
18539 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
18559 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
18579 TTGCGAT
1 TTGCGAT
18586 TTTAAGTTTC
Statistics
Matches: 114, Mismatches: 6, Indels: 28
0.77 0.04 0.19
Matches are distributed among these distances:
14 14 0.12
16 12 0.11
17 5 0.04
18 5 0.04
19 7 0.06
20 71 0.62
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:18595 original size:20 final size:20
Alignment explanation
Indices: 18537--18595 Score: 64
Period size: 20 Copynumber: 3.0 Consensus size: 20
18527 GCGATTCTCT
* *
18537 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
* *
18557 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTAAGTTTCG
**
18577 CGTTGCGATTTTAAGTTTC
1 CGTTGCGATAGTAAGTTTC
18596 AGATTCTATT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTAAGTTTCG
Found at i:19133 original size:42 final size:42
Alignment explanation
Indices: 19070--19152 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
19060 CACCTGTCAT
* *
19070 CGTTCAAGAGGCCCCTATCATCCCTCAAGAGTTCCCTCCCAC
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
* ** *
19112 CGTTCAAGAGGCCACTGTCATCGTTGAAGAGGTCCCTCCCA
1 CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCA
19153 ATATTCTAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
CGTTCAAGAGGCCACTATCATCCCTCAAGAGGTCCCTCCCAC
Found at i:19136 original size:21 final size:20
Alignment explanation
Indices: 19062--19148 Score: 66
Period size: 21 Copynumber: 4.2 Consensus size: 20
19052 GCACGACTCA
19062 CCTGTCATCGTTCAAGAGGCC
1 CCTGTCATCGTTCAAGAGG-C
* ** *
19083 CCTATCATCCCTCAAGAGTTC
1 CCTGTCATCGTTCAAGAG-GC
** *
19104 CCTCCCACCGTTCAAGAGGC
1 CCTGTCATCGTTCAAGAGGC
*
19124 CACTGTCATCGTTGAAGAGGTC
1 C-CTGTCATCGTTCAAGAGG-C
19146 CCT
1 CCT
19149 CCCAATATTC
Statistics
Matches: 49, Mismatches: 14, Indels: 6
0.71 0.20 0.09
Matches are distributed among these distances:
20 2 0.04
21 45 0.92
22 2 0.04
ACGTcount: A:0.21, C:0.36, G:0.20, T:0.24
Consensus pattern (20 bp):
CCTGTCATCGTTCAAGAGGC
Found at i:20528 original size:14 final size:14
Alignment explanation
Indices: 20509--20544 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
20499 ATTGTTTAAT
20509 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
20523 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
20537 TGATTTGT
1 TGATTTGT
20545 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:20717 original size:33 final size:34
Alignment explanation
Indices: 20680--20743 Score: 112
Period size: 34 Copynumber: 1.9 Consensus size: 34
20670 CACAATGAGA
*
20680 GAATCGCAATGCG-AAATGAAAATCGTAACGAGT
1 GAATCGCAATGCGAAAATGAAAATCGCAACGAGT
20713 GAATCGCAATGCGAAAATGAAAATCGCAACG
1 GAATCGCAATGCGAAAATGAAAATCGCAACG
20744 TGAAGCGATT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.44, C:0.17, G:0.23, T:0.16
Consensus pattern (34 bp):
GAATCGCAATGCGAAAATGAAAATCGCAACGAGT
Found at i:20784 original size:14 final size:14
Alignment explanation
Indices: 20765--20799 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
20755 TCATTTCACA
20765 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
20779 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
20793 TTGCGAT
1 TTGCGAT
20800 AGTTATTTCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.43
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:20816 original size:20 final size:20
Alignment explanation
Indices: 20791--20879 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
20781 GCGATTCTCT
*
20791 CGTTGCGATAGTTATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
20811 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCATTTCCG
*
20831 CGTTGCAATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
20851 TGTTGCGATAATCATATT-CA
1 CGTTGCGATAGTCAT-TTCCG
20871 CGTTGCGAT
1 CGTTGCGAT
20880 TTCCGCGTTG
Statistics
Matches: 59, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
20 57 0.97
21 2 0.03
ACGTcount: A:0.20, C:0.21, G:0.22, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:20848 original size:40 final size:37
Alignment explanation
Indices: 20791--20899 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 37
20781 GCGATTCTCT
*
20791 CGTTGCGATAGTTATTTCCGCGTTGCGATAGTCAATTCCG
1 CGTTGC-ATAG-TATTTCCGCGTTGCGATAGTCAATT-CA
* *
20831 CGTTGCAATAGTCATTTCCGTGTTGCGATAATCATATTCA
1 CGTTGC-ATAGT-ATTTCCGCGTTGCGATAGTCA-ATTCA
20871 CGTTGC---G-ATTTCCGCGTTGCGATAGTCAA
1 CGTTGCATAGTATTTCCGCGTTGCGATAGTCAA
20900 ATGAATGTCT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
33 1 0.02
34 19 0.31
36 1 0.02
39 1 0.02
40 36 0.59
41 3 0.05
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (37 bp):
CGTTGCATAGTATTTCCGCGTTGCGATAGTCAATTCA
Found at i:21920 original size:20 final size:20
Alignment explanation
Indices: 21897--22013 Score: 87
Period size: 20 Copynumber: 5.8 Consensus size: 20
21887 TTGCGATAGT
* *
21897 CAGAATCTCGTTGCGATTTA
1 CAGAATCGCATTGCGATTTA
*
21917 CAGATTCGCATTGCGATTTA
1 CAGAATCGCATTGCGATTTA
* *
21937 C-GTATTCGCATTACGATTTA
1 CAG-AATCGCATTGCGATTTA
*
21957 C-GTAATCGCATTGCGATTTT
1 CAG-AATCGCATTGCGATTTA
* **
21977 CAAAATTCGTGTTGCGATTTA
1 CAGAA-TCGCATTGCGATTTA
*
21998 C-GTATTCGCATTGCGA
1 CAG-AATCGCATTGCGA
22014 ATTAGGAAAA
Statistics
Matches: 78, Mismatches: 15, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 1 0.01
20 63 0.81
21 14 0.18
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.37
Consensus pattern (20 bp):
CAGAATCGCATTGCGATTTA
Found at i:21997 original size:41 final size:40
Alignment explanation
Indices: 21905--22013 Score: 130
Period size: 41 Copynumber: 2.7 Consensus size: 40
21895 GTCAGAATCT
**
21905 CGTTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTAC-GTATTCGCATTGCGATTTACAAATTCG
* * * *
21945 CATTACGATTTACGTAATCGCATTGCGATTTTCAAAATTCG
1 CGTTGCGATTTACGTATTCGCATTGCGATTTAC-AAATTCG
*
21986 TGTTGCGATTTACGTATTCGCATTGCGA
1 CGTTGCGATTTACGTATTCGCATTGCGA
22014 ATTAGGAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
39 1 0.02
40 27 0.47
41 29 0.51
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGTATTCGCATTGCGATTTACAAATTCG
Found at i:22034 original size:21 final size:21
Alignment explanation
Indices: 22010--22055 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
22000 TATTCGCATT
22010 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
22031 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
22052 GCGA
1 GCGA
22056 TAGTCATAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:30798 original size:27 final size:27
Alignment explanation
Indices: 30760--30826 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
30750 GACAATGACT
30760 CTGAATCATTCAAAATGTACTTTGATG
1 CTGAATCATTCAAAATGTACTTTGATG
*
30787 CTGAATCATTCAGAATGTACTTTGATG
1 CTGAATCATTCAAAATGTACTTTGATG
30814 CTGAATCATTCAA
1 CTGAATCATTCAA
30827 CATTGTTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (27 bp):
CTGAATCATTCAAAATGTACTTTGATG
Found at i:35657 original size:6 final size:6
Alignment explanation
Indices: 35648--35681 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
35638 ATTTCTCAGC
35648 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGA
1 TGGAGG TGGAGG TGGAGG TGGAGG TGGAGG TGGA
35682 TTGCCTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.00, G:0.65, T:0.18
Consensus pattern (6 bp):
TGGAGG
Found at i:35969 original size:11 final size:12
Alignment explanation
Indices: 35942--35969 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
35932 ATCAAGAAAG
35942 AAAAAATACTTT
1 AAAAAATACTTT
35954 AAAAAATACTTT
1 AAAAAATACTTT
35966 AAAA
1 AAAA
35970 GCTTAACTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (12 bp):
AAAAAATACTTT
Found at i:37608 original size:3 final size:3
Alignment explanation
Indices: 37600--37630 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
37590 GCATCTGTCC
37600 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
37631 ATCTGATTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:46656 original size:5 final size:5
Alignment explanation
Indices: 46646--46671 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46636 TGACTTAGAA
46646 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
46672 AATAATAATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:46835 original size:5 final size:5
Alignment explanation
Indices: 46825--46850 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
46815 TTCACGCTAA
46825 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
46851 ACAGTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:50726 original size:21 final size:21
Alignment explanation
Indices: 50700--50758 Score: 118
Period size: 21 Copynumber: 2.8 Consensus size: 21
50690 TGGGAGCGTG
50700 GGTGTATCGGTACACTCTCTA
1 GGTGTATCGGTACACTCTCTA
50721 GGTGTATCGGTACACTCTCTA
1 GGTGTATCGGTACACTCTCTA
50742 GGTGTATCGGTACACTC
1 GGTGTATCGGTACACTC
50759 AGTGTAAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.19, C:0.24, G:0.25, T:0.32
Consensus pattern (21 bp):
GGTGTATCGGTACACTCTCTA
Found at i:52922 original size:13 final size:12
Alignment explanation
Indices: 52906--52940 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
52896 TAATGGGCAA
52906 TTTTGAAAACTAT
1 TTTTGAAAAC-AT
52919 TTTTGAAAACAT
1 TTTTGAAAACAT
52931 TGTTTGAAAA
1 T-TTTGAAAA
52941 ATCATAATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 3 0.14
13 18 0.86
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (12 bp):
TTTTGAAAACAT
Found at i:53001 original size:20 final size:21
Alignment explanation
Indices: 52965--53009 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
52955 AGTTTTCATG
52965 AAAAACAACATAATTAAA-TC
1 AAAAACAACATAATTAAAGTC
*
52985 AAAAACAACA-ATTTTAAAGTC
1 AAAAACAACATA-ATTAAAGTC
53006 AAAA
1 AAAA
53010 CTTTTTTTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 1 0.05
20 15 0.68
21 6 0.27
ACGTcount: A:0.64, C:0.13, G:0.02, T:0.20
Consensus pattern (21 bp):
AAAAACAACATAATTAAAGTC
Found at i:53480 original size:21 final size:23
Alignment explanation
Indices: 53427--53486 Score: 79
Period size: 23 Copynumber: 2.7 Consensus size: 23
53417 GGTACACTAT
53427 TGAGTGTATCGATACACATTCAA
1 TGAGTGTATCGATACACATTCAA
* * *
53450 TGAATGTATCGGTACACTTTC-A
1 TGAGTGTATCGATACACATTCAA
53472 T-AGTGTATCGATACA
1 TGAGTGTATCGATACA
53487 TAGTGAGGAT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
21 12 0.38
22 2 0.06
23 18 0.56
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (23 bp):
TGAGTGTATCGATACACATTCAA
Found at i:56128 original size:11 final size:10
Alignment explanation
Indices: 56114--56159 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 10
56104 GAACCGGAAG
56114 AACCGGCTGAA
1 AACCGGC-GAA
56125 AACCGG-GAA
1 AACCGGCGAA
56134 AACCGGCTGAA
1 AACCGGC-GAA
*
56145 AACTGGC-AA
1 AACCGGCGAA
56154 AACCGG
1 AACCGG
56160 TTTGAACCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 16 0.52
11 15 0.48
ACGTcount: A:0.39, C:0.26, G:0.28, T:0.07
Consensus pattern (10 bp):
AACCGGCGAA
Found at i:56128 original size:20 final size:21
Alignment explanation
Indices: 56092--56147 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
56082 GGATTAGCAC
*
56092 AGAACCGG-TAAAGAACC-GGA
1 AGAACCGGCTGAA-AACCGGGA
56112 AGAACCGGCTGAAAACCGGGA
1 AGAACCGGCTGAAAACCGGGA
56133 A-AACCGGCTGAAAAC
1 AGAACCGGCTGAAAAC
56148 TGGCAAAACC
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
20 26 0.79
21 7 0.21
ACGTcount: A:0.43, C:0.23, G:0.29, T:0.05
Consensus pattern (21 bp):
AGAACCGGCTGAAAACCGGGA
Found at i:56155 original size:20 final size:20
Alignment explanation
Indices: 56105--56159 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
56095 ACCGGTAAAG
56105 AACCGG-AAGAACCGGCTGAA
1 AACCGGCAA-AACCGGCTGAA
*
56125 AACCGGGAAAACCGGCTGAA
1 AACCGGCAAAACCGGCTGAA
*
56145 AACTGGCAAAACCGG
1 AACCGGCAAAACCGG
56160 TTTGAACCGC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.94
21 2 0.06
ACGTcount: A:0.40, C:0.25, G:0.29, T:0.05
Consensus pattern (20 bp):
AACCGGCAAAACCGGCTGAA
Found at i:56424 original size:24 final size:24
Alignment explanation
Indices: 56394--56449 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
56384 TAGAAGTTCG
56394 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
56418 ATTGAAGCCTAAAATTTGAGCTCA
1 ATTGAAGCCTAAAATTTGAGCTCA
56442 ATTGAAGC
1 ATTGAAGC
56450 GAAAGAATAG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (24 bp):
ATTGAAGCCTAAAATTTGAGCTCA
Found at i:61344 original size:2 final size:2
Alignment explanation
Indices: 61333--61378 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
61323 TCCCTATTTT
61333 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61374 TA TA T
1 TA TA T
61379 CGGGTCATGT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:62428 original size:2 final size:2
Alignment explanation
Indices: 62421--62530 Score: 220
Period size: 2 Copynumber: 55.0 Consensus size: 2
62411 GTGTTTTCTT
62421 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
62463 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
62505 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
62531 TATATATATA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 108 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:62535 original size:2 final size:2
Alignment explanation
Indices: 62530--62561 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
62520 ACACACACAC
62530 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
62562 TTTAATTTTT
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:62711 original size:29 final size:30
Alignment explanation
Indices: 62666--62726 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 30
62656 CTAAATGAGT
*
62666 AACGAAATGAAACATTAAACACCAAATTAA
1 AACGAAATGAAACATTAAACACCAAACTAA
*
62696 AACGAAAT-AAACATTAAACACTAAACTAA
1 AACGAAATGAAACATTAAACACCAAACTAA
62725 AA
1 AA
62727 AAACAAATCT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.62, C:0.16, G:0.05, T:0.16
Consensus pattern (30 bp):
AACGAAATGAAACATTAAACACCAAACTAA
Found at i:62898 original size:20 final size:20
Alignment explanation
Indices: 62875--62926 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
62865 AACGCGATCC
62875 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
62895 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
62915 CCAAAATCGCAA
1 CCAGAATCGCAA
62927 CGCGATTCTT
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:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:63007 original size:20 final size:20
Alignment explanation
Indices: 62982--63175 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
62972 GATTTTCCAT
* *
62982 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
63002 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
63022 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
63042 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
63062 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
63082 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
63102 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
63122 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
63143 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
63163 AATCGCAACGCGA
1 AATCGCAACGCGA
63176 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:63027 original size:40 final size:39
Alignment explanation
Indices: 62978--63175 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
62968 TTGCGATTTT
* ** *
62978 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
63016 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
63057 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
63097 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
63136 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
63176 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:63065 original size:60 final size:60
Alignment explanation
Indices: 62982--63174 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
62972 GATTTTCCAT
* ** * *
62982 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
63042 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
63102 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
63163 AATCGCAACGCG
1 AATCGCAACGCG
63175 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:63595 original size:33 final size:33
Alignment explanation
Indices: 63556--63626 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
63546 TTCACTTAGA
*
63556 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
63589 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
63622 TTTCA
1 TTTCA
63627 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:63766 original size:14 final size:14
Alignment explanation
Indices: 63747--63801 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
63737 AGAATGACTG
63747 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
63761 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
63780 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
63794 TCGCAACG
1 TCGCAACG
63802 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:63784 original size:33 final size:33
Alignment explanation
Indices: 63747--63817 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
63737 AGAATGACTG
**
63747 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
63780 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
63813 TCGCA
1 TCGCA
63818 TTGCGATTTT
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:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:63835 original size:19 final size:19
Alignment explanation
Indices: 63813--63910 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
63803 GAAACCAAAA
*
63813 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63832 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
63846 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
63865 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
63879 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
63898 TCGCGTTGCGATT
1 TCGCGTTGCGATT
63911 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:63854 original size:14 final size:14
Alignment explanation
Indices: 63835--63924 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
63825 TTTCATTTCG
63835 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
63849 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
63868 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
63882 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
63899 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
63915 CGTTGCGATT
1 CGTTGCGATT
63925 TTCATTTCAA
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:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:63860 original size:33 final size:33
Alignment explanation
Indices: 63818--63932 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
63808 CAAAATCGCA
63818 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
63851 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
63884 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
63917 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
63933 AACCAAAAGA
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:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:65859 original size:185 final size:185
Alignment explanation
Indices: 65629--66100 Score: 926
Period size: 185 Copynumber: 2.6 Consensus size: 185
65619 TAGATTGCTT
*
65629 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65694 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
65759 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65814 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65879 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
*
65944 GTGTATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65999 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
66064 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66101 ATCCATTCAA
Statistics
Matches: 285, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
185 285 1.00
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (185 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTATATTCTTTAACACTGTGAAATATATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:65943 original size:93 final size:93
Alignment explanation
Indices: 65629--66100 Score: 912
Period size: 93 Copynumber: 5.1 Consensus size: 93
65619 TAGATTGCTT
*
65629 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65694 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
65722 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTATATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65786 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65814 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65879 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65907 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
65971 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
65999 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
66064 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66092 AGTAAATTT
1 AGTAAATTT
66101 ATCCATTCAA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 183 0.49
93 191 0.51
ACGTcount: A:0.22, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:66184 original size:19 final size:19
Alignment explanation
Indices: 66144--66272 Score: 116
Period size: 19 Copynumber: 7.3 Consensus size: 19
66134 TAGTTTACTT
* *
66144 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
66164 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
66183 TCGCAACGCGAAATTAAAA
1 TCGCAACGCGAAACCAAAA
*
66202 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
*
66216 TCGCAACGCAAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
66235 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
66249 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
66268 TCGCA
1 TCGCA
66273 TTGCGATTTT
Statistics
Matches: 88, Mismatches: 11, Indels: 21
0.73 0.09 0.17
Matches are distributed among these distances:
14 19 0.22
15 2 0.02
16 3 0.03
17 3 0.03
18 2 0.02
19 46 0.52
20 13 0.15
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:66223 original size:33 final size:32
Alignment explanation
Indices: 66180--66272 Score: 141
Period size: 33 Copynumber: 2.8 Consensus size: 32
66170 CGCGAAACCA
**
66180 AAATCGCAACGCGAAATTAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
*
66212 AGAATCGCAACGCAAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
66245 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
66273 TTGCGATTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
32 2 0.04
33 53 0.96
ACGTcount: A:0.47, C:0.28, G:0.16, T:0.09
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:66270 original size:52 final size:52
Alignment explanation
Indices: 66144--66272 Score: 122
Period size: 52 Copynumber: 2.5 Consensus size: 52
66134 TAGTTTACTT
* ** *
66144 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACGCGAAACACAAAATCGCAACGCAAAACCAAAATCGCAACGCGAAA
*** *
66196 TTAAAATCGC--AACGACAGAATCGCAACGCAAAACCAAAATCGCAACGAC-AAGA
1 TCGCAA-CGCGAAAC-ACAAAATCGCAACGCAAAACCAAAATCGCAACG-CGAA-A
66249 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACGCGAAACACAAAATCGCA
66273 TTGCGATTTT
Statistics
Matches: 59, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
51 3 0.05
52 46 0.78
53 7 0.12
54 3 0.05
ACGTcount: A:0.47, C:0.29, G:0.16, T:0.09
Consensus pattern (52 bp):
TCGCAACGCGAAACACAAAATCGCAACGCAAAACCAAAATCGCAACGCGAAA
Found at i:66290 original size:19 final size:19
Alignment explanation
Indices: 66268--66402 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
66258 GAAACCAAAA
*
66268 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
66287 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
66303 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
66320 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
66336 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
66353 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
66372 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
66392 TCGTGTTGCGA
1 TCGCGTTGCGA
66403 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:66309 original size:14 final size:14
Alignment explanation
Indices: 66290--66346 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
66280 TTTCATTTCG
66290 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
66304 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
66321 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
66337 CGTTGCGATT
1 CGTTGCGATT
66347 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:66315 original size:33 final size:33
Alignment explanation
Indices: 66273--66365 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
66263 CAAAATCGCA
*
66273 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
66306 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
66339 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
66366 TTGGTTTCGC
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:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:68322 original size:14 final size:14
Alignment explanation
Indices: 68303--68338 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
68293 ATTGTTTAAT
68303 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
68317 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
68331 TGATTTGT
1 TGATTTGT
68339 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:68461 original size:19 final size:19
Alignment explanation
Indices: 68445--68546 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
68435 AAAAATGACT
68445 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
68464 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
68483 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
68497 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
68516 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
68536 ATCGCAATGCG
1 ATCGCAATGCG
68547 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:68599 original size:19 final size:19
Alignment explanation
Indices: 68575--68990 Score: 541
Period size: 19 Copynumber: 23.4 Consensus size: 19
68565 GATTATCTCG
68575 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68594 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68613 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
68627 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68646 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68665 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
68684 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
68703 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
68717 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68736 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68755 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
68769 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68788 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68807 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68826 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
68845 TTGCGATTTTAATTTTGCA
1 TTGCGATTTTCATTTCGCA
*
68864 TTGCGA--TTC-TGTCG--
1 TTGCGATTTTCATTTCGCA
68878 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
68897 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
68916 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
68930 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
68950 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
68964 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
68983 TTGCGATT
1 TTGCGATT
68991 GTATTTTCCG
Statistics
Matches: 352, Mismatches: 14, Indels: 62
0.82 0.03 0.14
Matches are distributed among these distances:
14 41 0.12
16 38 0.11
17 34 0.10
18 3 0.01
19 224 0.64
20 12 0.03
ACGTcount: A:0.14, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:68725 original size:142 final size:142
Alignment explanation
Indices: 68537--68962 Score: 593
Period size: 142 Copynumber: 3.0 Consensus size: 142
68527 GAAATGAAAA
* *
68537 TCGCAATGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGAT
1 TCGCATTGCGATTT-TAATTTCGCATTGCGATTATATCGTTGCGATTTTCATTTCGCATTGCGAT
68601 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
65 TTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
68666 TGCGATTTTCATT
130 TGCGATTTTCATT
* *
68679 TCGCATTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCATTGCGATT
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTATATCGTTGCGATTTTCATTTCGCATTGCGATT
68744 TTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
66 TTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
68809 GCGATTTTCATT
131 GCGATTTTCATT
* * * * *
68821 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTAAT-TTTGC-A-TTGCGA-TTCTGTCGTTGC
1 TCGCATTGCGATTTTAATTTCGCATTGCGATTAT-ATCGTTGCGATTTTC-ATTTC-G-CATTGC
*
68882 GATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCA
62 GATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTCA
68942 TTTCCGCATTGCGATTTTCAT
122 TTT-CGCATTGCGATTTTCAT
68963 GTTGGGATTT
Statistics
Matches: 263, Mismatches: 10, Indels: 21
0.89 0.03 0.07
Matches are distributed among these distances:
140 6 0.02
141 3 0.01
142 212 0.81
143 21 0.08
144 7 0.03
145 8 0.03
147 6 0.02
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (142 bp):
TCGCATTGCGATTTTAATTTCGCATTGCGATTATATCGTTGCGATTTTCATTTCGCATTGCGATT
TTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATT
GCGATTTTCATT
Found at i:68924 original size:52 final size:52
Alignment explanation
Indices: 68575--68962 Score: 543
Period size: 52 Copynumber: 7.2 Consensus size: 52
68565 GATTATCTCG
68575 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
68627 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
* *
68684 TTGCGATTTTAATTTCGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
68736 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
68788 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCA
* * *
68845 TTGCGATTTTAATTTTGCATTGCGATTCTGTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
*
68897 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTT-CGCA
68950 TTGCGATTTTCAT
1 TTGCGATTTTCAT
68963 GTTGGGATTT
Statistics
Matches: 315, Mismatches: 10, Indels: 21
0.91 0.03 0.06
Matches are distributed among these distances:
52 202 0.64
53 17 0.05
54 14 0.04
55 16 0.05
57 66 0.21
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCA
Found at i:71287 original size:12 final size:12
Alignment explanation
Indices: 71270--71294 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
71260 TCTTCGGGGA
71270 CTTTTTCTTCTT
1 CTTTTTCTTCTT
71282 CTTTTTCTTCTT
1 CTTTTTCTTCTT
71294 C
1 C
71295 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:71503 original size:24 final size:24
Alignment explanation
Indices: 71469--71515 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
71459 CTGAAACATC
71469 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
71493 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
71516 GACCAAATTT
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:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:72224 original size:20 final size:20
Alignment explanation
Indices: 72196--72564 Score: 451
Period size: 20 Copynumber: 18.4 Consensus size: 20
72186 AAATTTAAGT
* * * *
72196 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
72216 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
72236 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
72256 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
72276 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72296 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
72316 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
72336 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72356 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72376 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
72396 GTTGC-AGTTTACGGATACGC
1 GTTGCGA-TTTACGGATACGC
72416 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
72436 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
72456 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
72476 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
72496 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
72516 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
72536 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
72556 GTTGCGATT
1 GTTGCGATT
72565 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 30, Indels: 20
0.86 0.08 0.06
Matches are distributed among these distances:
19 6 0.02
20 297 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:82263 original size:16 final size:17
Alignment explanation
Indices: 82242--82274 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
82232 TTACAAATAT
*
82242 GTATATCCAA-GATACA
1 GTATATACAATGATACA
82258 GTATATACAATGATACA
1 GTATATACAATGATACA
82275 AATCCATAAG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.27
Consensus pattern (17 bp):
GTATATACAATGATACA
Found at i:87892 original size:21 final size:21
Alignment explanation
Indices: 87812--87893 Score: 78
Period size: 21 Copynumber: 3.9 Consensus size: 21
87802 CGCAAATCAA
*
87812 TTTCCAGATTCGCAACGCGATT
1 TTTCCA-ATTCGCAATGCGATT
* * *
87834 ATTACTA-TCGCAATGCGA-T
1 TTTCCAATTCGCAATGCGATT
**
87853 TTTCCAAATTCGCGTTGCGATT
1 TTTCC-AATTCGCAATGCGATT
87875 TTTCCAATTCGCAATGCGA
1 TTTCCAATTCGCAATGCGA
87894 ATAAGTAAAT
Statistics
Matches: 46, Mismatches: 11, Indels: 7
0.72 0.17 0.11
Matches are distributed among these distances:
19 4 0.09
20 11 0.24
21 22 0.48
22 9 0.20
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.34
Consensus pattern (21 bp):
TTTCCAATTCGCAATGCGATT
Found at i:87908 original size:20 final size:21
Alignment explanation
Indices: 87883--87934 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
87873 TTTTTCCAAT
*
87883 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
87903 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
87924 TCGCAATGCGA
1 TCGCAATGCGA
87935 TACTGACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 12 0.43
21 16 0.57
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:87913 original size:41 final size:41
Alignment explanation
Indices: 87868--88079 Score: 121
Period size: 41 Copynumber: 5.2 Consensus size: 41
87858 AAATTCGCGT
*
87868 TGCGATTTTTCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGAATTTTCCAATTCGCAATGCGAATAAGTAAATCGCAA
*** * * *
87909 TGCGAATTTGGAAAATCGCAATGCG-AT-ACTGACTATCGCAA
1 TGCGAATTTTCCAATTCGCAATGCGAATAAGT-A-AATCGCAA
* * * * **
87950 TGC-AATTTTCCTAATTCGCATTGCGATTTACGT-ATTCGCGT
1 TGCGAATTTTCC-AATTCGCAATGCGA-ATAAGTAAATCGCAA
* *
87991 TGCG-ATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGAATTTTC-CAATTCGCAATGCGAATAAGTAAATCGCAA
* **** * * *
88032 CGCG-ATTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGAATTTTCCAATTCGCAATGCGAA-TAAGTAAATCGCAA
88073 TGCGAAT
1 TGCGAAT
88080 ACGTAAATCG
Statistics
Matches: 127, Mismatches: 33, Indels: 21
0.70 0.18 0.12
Matches are distributed among these distances:
39 2 0.02
40 28 0.22
41 93 0.73
42 2 0.02
43 1 0.01
44 1 0.01
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (41 bp):
TGCGAATTTTCCAATTCGCAATGCGAATAAGTAAATCGCAA
Found at i:87978 original size:21 final size:21
Alignment explanation
Indices: 87944--88016 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
87934 ATACTGACTA
* *
87944 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * *
87965 TCGCATTGCGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
87985 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
88006 TCGCAATGCGA
1 TCGCAATGCGA
88017 ATACGTAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 17 0.40
21 25 0.60
ACGTcount: A:0.23, C:0.22, G:0.18, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:88031 original size:20 final size:20
Alignment explanation
Indices: 88006--88099 Score: 134
Period size: 20 Copynumber: 4.7 Consensus size: 20
87996 TTTTCATAAT
88006 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
88026 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
88046 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
88067 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
88087 TCGCAATGCGAAT
1 TCGCAATGCGAAT
88100 CTGACTATCG
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 46 0.72
21 18 0.28
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:88086 original size:41 final size:41
Alignment explanation
Indices: 88006--88099 Score: 136
Period size: 41 Copynumber: 2.3 Consensus size: 41
87996 TTTTCATAAT
* *
88006 TCGCAATGCGAA-TACGTAAATCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
* * *
88046 TCGCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
88087 TCGCAATGCGAAT
1 TCGCAATGCGAAT
88100 CTGACTATCG
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 12 0.25
41 36 0.75
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (41 bp):
TCGCAATGCGAATTACGAAAATCGCAACGCGAATAAGTAAA
Found at i:88685 original size:19 final size:19
Alignment explanation
Indices: 88621--88705 Score: 81
Period size: 19 Copynumber: 4.7 Consensus size: 19
88611 TAGTTTCGAG
88621 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGC-GA
**
88641 AATGACTATCGCAA--CG-
1 AATGAAAATCGCAACGCGA
*
88657 -A-GAGAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
88674 AATGAAAATCGCAACGCGA
1 AATGAAAATCGCAACGCGA
**
88693 AACCAAAATCGCA
1 AATGAAAATCGCA
88706 TTGCGATTTT
Statistics
Matches: 53, Mismatches: 7, Indels: 11
0.75 0.10 0.15
Matches are distributed among these distances:
14 9 0.17
15 1 0.02
16 2 0.04
17 1 0.02
18 2 0.04
19 26 0.49
20 12 0.23
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.11
Consensus pattern (19 bp):
AATGAAAATCGCAACGCGA
Found at i:88748 original size:33 final size:33
Alignment explanation
Indices: 88706--88827 Score: 145
Period size: 33 Copynumber: 3.5 Consensus size: 33
88696 CAAAATCGCA
*
88706 TTGCGATTTTCATTTCGCGTTGTGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
88739 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
** *
88772 TTGCGATAGTAATTTCCGCGTTGCGATTTTCATTCTCTCG
1 TTGCGATTTTCATTT-CGCGTTGCG------ATTCTCTCG
88812 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
88828 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 44 0.59
34 9 0.12
39 1 0.01
40 21 0.28
ACGTcount: A:0.11, C:0.22, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:88813 original size:20 final size:20
Alignment explanation
Indices: 88730--88825 Score: 82
Period size: 20 Copynumber: 5.2 Consensus size: 20
88720 TCGCGTTGTG
88730 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
88750 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
** *
88763 ATTCTCTCGTTGCGATAGTA
1 ATTCTCTCGTTGCGATTTTC
*
88783 ATT-TCCGCGTTGCGATTTTC
1 ATTCT-CTCGTTGCGATTTTC
88803 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
88823 ATT
1 ATT
88826 TCAACCAAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 18
0.71 0.08 0.21
Matches are distributed among these distances:
13 3 0.05
14 9 0.15
19 10 0.17
20 37 0.62
21 1 0.02
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.46
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:90706 original size:94 final size:94
Alignment explanation
Indices: 90519--90823 Score: 485
Period size: 94 Copynumber: 3.3 Consensus size: 94
90509 TATATTGCTT
* * *
90519 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--AGT-TT-ATTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
90580 ATTTGTCTTTTGTTTTGTCTTTTGGTTG-A
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGAA
*
90609 AGTAAATTTATTCGGTTGCTGCCAATTTTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
90674 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
90703 AGTAAATTTGTTCGGTTGCTGCCAATTCTACTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
*
90768 ATTTGTCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
* *
90797 AGTAAATTTGTTCGTTTGCTGCCAATT
1 AGTAAATTTATTCGGTTGCTGCCAATT
90824 GAAACTATTC
Statistics
Matches: 201, Mismatches: 9, Indels: 6
0.93 0.04 0.03
Matches are distributed among these distances:
90 34 0.17
92 2 0.01
93 22 0.11
94 143 0.71
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (94 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:90852 original size:24 final size:24
Alignment explanation
Indices: 90820--90877 Score: 116
Period size: 24 Copynumber: 2.4 Consensus size: 24
90810 GTTTGCTGCC
90820 AATTGAAACTATTCTTCTTATGCA
1 AATTGAAACTATTCTTCTTATGCA
90844 AATTGAAACTATTCTTCTTATGCA
1 AATTGAAACTATTCTTCTTATGCA
90868 AATTGAAACT
1 AATTGAAACT
90878 TGAATGAATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.36, C:0.16, G:0.09, T:0.40
Consensus pattern (24 bp):
AATTGAAACTATTCTTCTTATGCA
Found at i:91316 original size:21 final size:21
Alignment explanation
Indices: 91292--91358 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
91282 TCATTCCTCG
91292 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
91313 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
91334 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
91355 AGAG
1 AGAG
91359 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:91316 original size:42 final size:42
Alignment explanation
Indices: 91240--91358 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
91230 GACTCGCCTG
* * * * * * *
91240 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
91282 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
91324 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
91359 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.23, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:92728 original size:14 final size:14
Alignment explanation
Indices: 92709--92744 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
92699 ATTGTTTAAT
92709 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
92723 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
92737 TGATTTGT
1 TGATTTGT
92745 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:92867 original size:19 final size:17
Alignment explanation
Indices: 92851--92901 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
92841 AAAAATGACT
92851 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATG--A
*
92870 ATCGCAA--CGAGA-GA
1 ATCGCAATGCGAAATGA
92884 ATCGCAATGCGAAATGA
1 ATCGCAATGCGAAATGA
92901 A
1 A
92902 AATCGTAACG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
14 8 0.30
16 5 0.19
17 7 0.26
19 7 0.26
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (17 bp):
ATCGCAATGCGAAATGA
Found at i:92893 original size:33 final size:33
Alignment explanation
Indices: 92851--92944 Score: 136
Period size: 33 Copynumber: 2.8 Consensus size: 33
92841 AAAAATGACT
* *
92851 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
92884 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
92917 ATCGCAACGCGAAACT-AAAATCGCAACG
1 ATCGCAATGCGAAA-TGAAAATCGCAACG
92945 CGAAACTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.46, C:0.21, G:0.20, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:92966 original size:19 final size:19
Alignment explanation
Indices: 92914--92959 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
92904 TCGTAACGAC
92914 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
92933 AAAATCGCAACGCGAAACT
1 AAAATCGCAACGCGAAACT
*
92952 AAATTCGC
1 AAAATCGC
92960 GTTGCGATTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.46, C:0.26, G:0.15, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACT
Found at i:93001 original size:33 final size:33
Alignment explanation
Indices: 92959--93118 Score: 293
Period size: 33 Copynumber: 4.8 Consensus size: 33
92949 ACTAAATTCG
* *
92959 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
92992 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
93025 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
*
93058 CGTTGCGGTTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
93091 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
93119 AGTCATTAAG
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 123 1.00
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:93032 original size:14 final size:14
Alignment explanation
Indices: 92980--93100 Score: 62
Period size: 14 Copynumber: 7.6 Consensus size: 14
92970 TCATTTCGCT
*
92980 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
92994 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
93011 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
93027 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
93044 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
* *
93060 TTGCGGTTTTCATTTCG
1 TTGC-G-ATTC-TCTCG
93077 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
93093 TTGCGATT
1 TTGCGATT
93101 TTCATTTCGC
Statistics
Matches: 83, Mismatches: 9, Indels: 30
0.68 0.07 0.25
Matches are distributed among these distances:
14 24 0.29
15 1 0.01
16 21 0.25
17 20 0.24
18 1 0.01
19 16 0.19
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:93125 original size:19 final size:17
Alignment explanation
Indices: 92955--93118 Score: 82
Period size: 19 Copynumber: 9.8 Consensus size: 17
92945 CGAAACTAAA
*
92955 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGA--TTCAT
* *
92974 TTCGCTTTGCGATTC-C
1 TTCGCATTGCGATTCAT
*
92990 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGA--TTCAT
93007 TTCGCATTGCGATTC-T
1 TTCGCATTGCGATTCAT
*
93023 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGA--TTCAT
93040 TTCGCATTGCGATTC-T
1 TTCGCATTGCGATTCAT
* *
93056 CTCG--TTGCGGTTTTCAT
1 TTCGCATTGC-G-ATTCAT
93073 TTCGCATTGCGATTC-T
1 TTCGCATTGCGATTCAT
*
93089 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGA--TTCAT
93106 TTCGCATTGCGAT
1 TTCGCATTGCGAT
93119 AGTCATTAAG
Statistics
Matches: 112, Mismatches: 13, Indels: 42
0.67 0.08 0.25
Matches are distributed among these distances:
14 22 0.20
15 1 0.01
16 27 0.24
17 28 0.25
18 1 0.01
19 33 0.29
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (17 bp):
TTCGCATTGCGATTCAT
Found at i:96549 original size:20 final size:21
Alignment explanation
Indices: 96505--96556 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
96495 ATAGTCAGTA
*
96505 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
96526 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
96546 TCGCATTGCGA
1 TCGCATTGCGA
96557 ATTGGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.21, C:0.23, G:0.17, T:0.38
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:105696 original size:42 final size:43
Alignment explanation
Indices: 105592--105739 Score: 173
Period size: 42 Copynumber: 3.5 Consensus size: 43
105582 TAGGGGCATA
* *
105592 AATTAT-AAAGTAAAAAGT-ATAATTGAAAACATTAG-GAACCTC
1 AATTATAAAAGTAAAAAGTGA-GATTGAAAAAATTAGAG-ACCTC
* *
105634 AATTATAAAGGTAAAAAGTGAGATT-AAAAAGATTAGATACCTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAA-ATTAGAGACCTC
* *
105677 -ATTTTGAAAGTAAAAAGTGAGATTGAAAAAATTAGAGACCTC
1 AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGAGACCTC
105719 AATTATAAAAGT-AAAAGTGAG
1 AATTATAAAAGTAAAAAGTGAG
105740 TGTTAGAATT
Statistics
Matches: 90, Mismatches: 10, Indels: 12
0.80 0.09 0.11
Matches are distributed among these distances:
42 51 0.57
43 38 0.42
44 1 0.01
ACGTcount: A:0.51, C:0.07, G:0.16, T:0.26
Consensus pattern (43 bp):
AATTATAAAAGTAAAAAGTGAGATTGAAAAAATTAGAGACCTC
Found at i:106174 original size:42 final size:43
Alignment explanation
Indices: 106091--106275 Score: 203
Period size: 43 Copynumber: 4.3 Consensus size: 43
106081 ATTGTAACAG
106091 TGAGATT-AAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
1 TGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
106133 TGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
1 TGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
* ** * * * *
106176 TGAGATTAAAAAAATTAGAAG-TTCAATTATAAAGATACAAAG
1 TGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
* * * * * ** *
106218 TGGGATTGAAAAACTTAGGGTCATCAATTGTAAATGTAAAAAGT
1 TGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAA-A
*
106262 TGATATTGAAAAAA
1 TGAGATTGAAAAAA
106276 ATTAAAAGTC
Statistics
Matches: 118, Mismatches: 22, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
42 39 0.33
43 68 0.58
44 11 0.09
ACGTcount: A:0.51, C:0.06, G:0.17, T:0.26
Consensus pattern (43 bp):
TGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
Found at i:106236 original size:85 final size:84
Alignment explanation
Indices: 106091--106390 Score: 234
Period size: 85 Copynumber: 3.5 Consensus size: 84
106081 ATTGTAACAG
*** * * * *
106091 TGAGATT-AAAAAATTAGGGGCCTCAATTATAAAAATAAAAAATGAGATTGAAAAAATTAGGGGC
1 TGAGATTAAAAAAATTAAAAGCTTCAATTATAAAAAT-AAAAGTGGGATTG-AAAAATTAGGGAC
*
106155 CTCAATTATAAAAATAAAAAA
64 ATCAATTATAAAAATAAAAAA
* * *
106176 TGAGATTAAAAAAATTAGAAG-TTCAATTATAAAGATACAAAGTGGGATTGAAAAACTTAGGGTC
1 TGAGATTAAAAAAATTAAAAGCTTCAATTATAAAAATA-AAAGTGGGATTGAAAAA-TTAGGGAC
* ** *
106240 ATCAATTGTAAATGTAAAAAGT
64 ATCAATTATAAAAATAAAAA-A
* * * *
106262 TGATATTGAAAAAAATTAAAAG-TCTCAATTACAAATATAAAATGTAGGATT-ATGAAAATTAGG
1 TGAGATT-AAAAAAATTAAAAGCT-TCAATTATAAAAATAAAA-GTGGGATTGA--AAAATTAGG
* *
106325 AACTTCAATTAT-AAAATAATAAAA
61 GACATCAATTATAAAAATAA-AAAA
* *
106349 TTAAAATTAAAAAAATTAAAAGACTT-AATTATAAAAATAAAA
1 -TGAGATTAAAAAAATTAAAAG-CTTCAATTATAAAAATAAAA
106391 AATGCTGTAA
Statistics
Matches: 174, Mismatches: 28, Indels: 24
0.77 0.12 0.11
Matches are distributed among these distances:
84 6 0.03
85 53 0.30
86 17 0.10
87 51 0.29
88 42 0.24
89 5 0.03
ACGTcount: A:0.54, C:0.06, G:0.13, T:0.27
Consensus pattern (84 bp):
TGAGATTAAAAAAATTAAAAGCTTCAATTATAAAAATAAAAGTGGGATTGAAAAATTAGGGACAT
CAATTATAAAAATAAAAAA
Found at i:106324 original size:88 final size:83
Alignment explanation
Indices: 106112--106390 Score: 240
Period size: 87 Copynumber: 3.2 Consensus size: 83
106102 AATTAGGGGC
* * * *
106112 CTCAATTATAAAAATAAAA-AATGAGATTGAAAAAATTAGGGGCCTCAATTATAAAAATAAAAAA
1 CTCAATTATAAAAATAAAAGTA-G-GATTG-AAAAATTAGGGACATCAATTAT-AAAATAAAAAT
* *
106176 TGAGATTAAAAAAATTAGAAGT
62 TGAAATTAAAAAAATTAAAAGT
* * * * *
106198 -TCAATTATAAAGATACAAAGTGGGATTGAAAAACTTAGGGTCATCAATTGTAAATGTAAAAAGT
1 CTCAATTATAAAAATA-AAAGTAGGATTGAAAAA-TTAGGGACATCAATTATAAA-ATAAAAA-T
*
106262 TGATATTGAAAAAAATTAAAAGT
62 TGAAATT-AAAAAAATTAAAAGT
* * * *
106285 CTCAATTACAAATATAAAATGTAGGATT-ATGAAAATTAGGAACTTCAATTATAAAATAATAAAA
1 CTCAATTATAAAAATAAAA-GTAGGATTGA--AAAATTAGGGACATCAATTATAAAAT-A-AAAA
* *
106349 TTAAAATTAAAAAAATTAAAAGA
61 TTGAAATTAAAAAAATTAAAAGT
*
106372 CTTAATTATAAAAATAAAA
1 CTCAATTATAAAAATAAAA
106391 AATGCTGTAA
Statistics
Matches: 157, Mismatches: 24, Indels: 23
0.77 0.12 0.11
Matches are distributed among these distances:
84 8 0.05
85 39 0.25
86 10 0.06
87 49 0.31
88 43 0.27
89 8 0.05
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.28
Consensus pattern (83 bp):
CTCAATTATAAAAATAAAAGTAGGATTGAAAAATTAGGGACATCAATTATAAAATAAAAATTGAA
ATTAAAAAAATTAAAAGT
Found at i:106365 original size:15 final size:14
Alignment explanation
Indices: 106336--106369 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
106326 ACTTCAATTA
*
106336 TAAAATAATAAAAT
1 TAAAATAAAAAAAT
106350 TAAAATTAAAAAAAT
1 TAAAA-TAAAAAAAT
106365 TAAAA
1 TAAAA
106370 GACTTAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAAATAAAAAAAT
Found at i:108074 original size:114 final size:115
Alignment explanation
Indices: 107956--108162 Score: 292
Period size: 114 Copynumber: 1.8 Consensus size: 115
107946 TCAAAATTAA
* * *
107956 ATGAATAAATAAGAGAAAT-GAAAAAGAAAGTCAAAAAGTAAATATTTTATGAAATTATAAAAAT
1 ATGAATAAATAACACAAATAGAAAAAGAAAGT-AAAAAGTAAAAATTTTATGAAATTATAAAAAT
*
108020 T-AGGGTCGTAATTATAAATATAAAAAATGGTAAATTTGATTCAATATCGG
65 TAAGGATCGTAATTATAAATATAAAAAATGGTAAATTTGATTCAATATCGG
* * * * * *
108070 ATGAATTAATAACACAAATAGTAAAATAGAGTTAAAATTAAAAATTTTATGAAATTATAAAAATT
1 ATGAATAAATAACACAAATAGAAAAAGAAAGTAAAAAGTAAAAATTTTATGAAATTATAAAAATT
*
108135 AAGGATCTTAATTATAAATATAAAAAAT
66 AAGGATCGTAATTATAAATATAAAAAAT
108163 TAAAAGTCCT
Statistics
Matches: 80, Mismatches: 11, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
114 46 0.57
115 34 0.43
ACGTcount: A:0.55, C:0.03, G:0.12, T:0.30
Consensus pattern (115 bp):
ATGAATAAATAACACAAATAGAAAAAGAAAGTAAAAAGTAAAAATTTTATGAAATTATAAAAATT
AAGGATCGTAATTATAAATATAAAAAATGGTAAATTTGATTCAATATCGG
Found at i:108886 original size:30 final size:30
Alignment explanation
Indices: 108815--108926 Score: 149
Period size: 30 Copynumber: 3.8 Consensus size: 30
108805 ATTAAATTAA
* * *
108815 TTAAAAA-GTATTTTATTTTTATTT-TA-T
1 TTAAAAATATATTTTATTCTTATTTAAAGT
*
108842 TTAAAAGGTATATTTTATTCTTATTTAAAGT
1 TTAAAA-ATATATTTTATTCTTATTTAAAGT
108873 TTAAAAATATATTTTATTCTTATTTAAAGT
1 TTAAAAATATATTTTATTCTTATTTAAAGT
*
108903 TTAAAAATATATTTTATTATTATT
1 TTAAAAATATATTTTATTCTTATT
108927 GCTTTAACTT
Statistics
Matches: 75, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
27 6 0.08
29 15 0.20
30 47 0.63
31 7 0.09
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (30 bp):
TTAAAAATATATTTTATTCTTATTTAAAGT
Found at i:109005 original size:19 final size:18
Alignment explanation
Indices: 108977--109023 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 18
108967 ATATTATTAC
108977 TTTAAATTATTAAATATAT
1 TTTAAATTATTAAA-ATAT
*
108996 TTTAATTTATTAAAATAT
1 TTTAAATTATTAAAATAT
*
109014 AATTAAATTA
1 -TTTAAATTA
109024 AGATAATATA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
TTTAAATTATTAAAATAT
Found at i:109022 original size:20 final size:19
Alignment explanation
Indices: 108978--109022 Score: 56
Period size: 20 Copynumber: 2.4 Consensus size: 19
108968 TATTATTACT
*
108978 TTAAA-TTATTAAATATAT
1 TTAAATTTATTAAATATAA
*
108996 TTTAATTTATTAAAATATAA
1 TTAAATTTATT-AAATATAA
109016 TTAAATT
1 TTAAATT
109023 AAGATAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 4 0.18
19 5 0.23
20 13 0.59
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
TTAAATTTATTAAATATAA
Found at i:114971 original size:119 final size:120
Alignment explanation
Indices: 114817--115058 Score: 389
Period size: 119 Copynumber: 2.0 Consensus size: 120
114807 ATGACATCAA
* *
114817 ATTAATTAAATATATTTAACAATACAGACATATTTTTATTGTTAACTATTCATATTATATAAATT
1 ATTAATTAAATATATTTAACAACACAGACATATTTTTATTGTTAACTATCCATATTATATAAATT
*
114882 CTAATATGTTTTTGTA-TTGTTTTACGTTAATATTACTTTTAAA-CTATATTATC
66 CTAATATGTTTTTCTATTTGTTTTACGTTAATATTACTTTTAAATCTATATTATC
*
114935 ATTAATTAAATATATTATAACAACAGAGACATATTTTTATTGTTAACTATCCATATTATATAAAT
1 ATTAATTAAATATATT-TAACAACACAGACATATTTTTATTGTTAACTATCCATATTATATAAAT
* * *
115000 TCTAATCTGTTTTTCTATTTGTTTTATGTTAATATTACTTTTAAATTTTATATTATC
65 TCTAATATGTTTTTCTATTTGTTTTACGTTAATATTACTTTTAAA-TCTATATTATC
115057 AT
1 AT
115059 ATTTGAGTAT
Statistics
Matches: 113, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
118 16 0.14
119 60 0.53
120 26 0.23
122 11 0.10
ACGTcount: A:0.36, C:0.09, G:0.05, T:0.50
Consensus pattern (120 bp):
ATTAATTAAATATATTTAACAACACAGACATATTTTTATTGTTAACTATCCATATTATATAAATT
CTAATATGTTTTTCTATTTGTTTTACGTTAATATTACTTTTAAATCTATATTATC
Found at i:121106 original size:13 final size:12
Alignment explanation
Indices: 121075--121109 Score: 52
Period size: 13 Copynumber: 2.8 Consensus size: 12
121065 TATGCATATG
121075 TAATTAAGTATT
1 TAATTAAGTATT
*
121087 TATTTAAGTGATT
1 TAATTAAGT-ATT
121100 TAATTAAGTA
1 TAATTAAGTA
121110 CGTCTAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.40, C:0.00, G:0.11, T:0.49
Consensus pattern (12 bp):
TAATTAAGTATT
Done.