Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004901.1 Hibiscus syriacus cultivar Beakdansim tig00011028_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: 63145
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:746 original size:33 final size:33
Alignment explanation
Indices: 709--802 Score: 109
Period size: 33 Copynumber: 2.8 Consensus size: 33
699 TTTTCTAACT
* *
709 TACTAACATCCTAACTTTTATTTTATTTGTTCA
1 TACTAACATACTAACTTTTATTTTATTTATTCA
* *
742 TACTAACATACTTACTTTTATTTT-TATTATTCT
1 TACTAACATACTAACTTTTATTTTAT-TTATTCA
* *
775 TACTAACTTGCTAACATTTTATTTTATT
1 TACTAACATACTAAC-TTTTATTTTATT
803 GTATAAATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
32 1 0.02
33 39 0.76
34 10 0.20
35 1 0.02
ACGTcount: A:0.28, C:0.16, G:0.02, T:0.54
Consensus pattern (33 bp):
TACTAACATACTAACTTTTATTTTATTTATTCA
Found at i:966 original size:34 final size:32
Alignment explanation
Indices: 919--1004 Score: 104
Period size: 34 Copynumber: 2.6 Consensus size: 32
909 AAACAACCTC
919 CTAACTTTTATTTTATT-TTTTCATACTAACATT-
1 CTAACTTTTATTTTATTGTTTT--TACTAAC-TTA
952 CTAACTTTTTATTTTTATTGTTTTTACTAACTTA
1 CTAAC-TTTTA-TTTTATTGTTTTTACTAACTTA
986 CTAACATTTTATTTTATTG
1 CTAAC-TTTTATTTTATTG
1005 CACAACTAAC
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
33 15 0.31
34 22 0.46
35 7 0.15
36 4 0.08
ACGTcount: A:0.26, C:0.13, G:0.02, T:0.59
Consensus pattern (32 bp):
CTAACTTTTATTTTATTGTTTTTACTAACTTA
Found at i:1075 original size:201 final size:199
Alignment explanation
Indices: 717--1129 Score: 603
Period size: 201 Copynumber: 2.1 Consensus size: 199
707 CTTACTAACA
*
717 TCCTAACTTTTATTTTATTTGTTCATACTAACATACTTACTTTTATTTTTATTATTCTTACTAAC
1 TCCTAACTTTTATTTTATTTGTTCATACTAACATACTAACTTTTATTTTTATTATTCTTACTAAC
* * *
782 TTGCTAACATTTTATTTTATTGTATAAATTAACCGCTAATATTCTAACATTCGAATATTCAACGA
66 TTACTAACATTTTATTTTATTGCATAAACTAACCGCTAATATTCTAACATTCGAATATTCAACGA
* * *
847 CCTTGCGGTGACCTGCCCTGGGGGACGATCCGCATTATTTATGATCCGGGTTAAACGATTAAAAA
131 CCTTACGGTGACCCGCCCTGGGGGACGATCCACATTATTTATGATCCGGGTTAAACGATTAAAAA
912 CAACC
196 CAA-C
* * * *
917 TCCTAACTTTTATTTTATTTTTTCATACTAACATTCTAACTTTTTATTTTTATTGTTTTTACTAA
1 TCCTAACTTTTATTTTATTTGTTCATACTAACATACTAAC-TTTTATTTTTATTATTCTTACTAA
* * *
982 CTTACTAACATTTTATTTTATTGCA-CAACTAACCCGCTAATTTTCTAACATTCGAATATTTAAC
65 CTTACTAACATTTTATTTTATTGCATAAACTAA-CCGCTAATATTCTAACATTCGAATATTCAAC
* * * * * *
1046 GACCTTATGGTGACCCGTCTTGTGGGACGATCCACATTATTTATGGTCCGGGTTAAACGGTTAAA
129 GACCTTACGGTGACCCGCCCTGGGGGACGATCCACATTATTTATGATCCGGGTTAAACGATTAAA
1111 AACAAC
194 AACAAC
1117 TGCCTAACTTTTA
1 T-CCTAACTTTTA
1130 AATTTATGCA
Statistics
Matches: 190, Mismatches: 20, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
200 44 0.23
201 146 0.77
ACGTcount: A:0.28, C:0.19, G:0.11, T:0.41
Consensus pattern (199 bp):
TCCTAACTTTTATTTTATTTGTTCATACTAACATACTAACTTTTATTTTTATTATTCTTACTAAC
TTACTAACATTTTATTTTATTGCATAAACTAACCGCTAATATTCTAACATTCGAATATTCAACGA
CCTTACGGTGACCCGCCCTGGGGGACGATCCACATTATTTATGATCCGGGTTAAACGATTAAAAA
CAAC
Found at i:2271 original size:2 final size:2
Alignment explanation
Indices: 2264--2302 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2254 GATCGTAATT
2264 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2303 TTGTAATTTC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2682 original size:85 final size:84
Alignment explanation
Indices: 2530--2698 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 84
2520 ACTTACTTTA
2530 AAGATTGAGGTTGACTCTAAAATCAAATTATTTAAACTTAATTTAATCATCTTTCTCTGAATTAA
1 AAGATTGAGGTTGACTCTAAAATCAAATTATTTAAACTTAATTTAATCATCTTTCTCTGAATTAA
2595 TTTTTGTATAACAAACCCT
66 TTTTTGTATAACAAACCCT
2614 AAGATTGAGGTTGACTCT-AAATCAAATTATTTCAAACTTAAATTTAATCATCTTTCTCTGAATT
1 AAGATTGAGGTTGACTCTAAAATCAAATTATTT-AAACTT-AATTTAATCATCTTTCTCTGAATT
2678 AATTTTTGTATAACAAACCCT
64 AATTTTTGTATAACAAACCCT
2699 TGAGGGACGT
Statistics
Matches: 83, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
83 14 0.17
84 24 0.29
85 45 0.54
ACGTcount: A:0.37, C:0.15, G:0.08, T:0.40
Consensus pattern (84 bp):
AAGATTGAGGTTGACTCTAAAATCAAATTATTTAAACTTAATTTAATCATCTTTCTCTGAATTAA
TTTTTGTATAACAAACCCT
Found at i:6946 original size:22 final size:22
Alignment explanation
Indices: 6921--6962 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
6911 TTCGGTTTTA
6921 ATCGAATTAA-CTGAATTAACCG
1 ATCGAATTAATC-GAATTAACCG
6943 ATCGAATTAATCGAATTAAC
1 ATCGAATTAATCGAATTAAC
6963 TAAAAATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 18 0.95
23 1 0.05
ACGTcount: A:0.43, C:0.17, G:0.12, T:0.29
Consensus pattern (22 bp):
ATCGAATTAATCGAATTAACCG
Found at i:13590 original size:27 final size:26
Alignment explanation
Indices: 13543--13606 Score: 67
Period size: 27 Copynumber: 2.4 Consensus size: 26
13533 AATATGATTT
* *
13543 AAAACAAATAATAGTTGGATGACTAAA
1 AAAATAAATAATAGTTAGATGA-TAAA
13570 AAAATAAATAATAAG-TAGATGATAAA
1 AAAATAAATAAT-AGTTAGATGATAAA
* *
13596 TAAGTAAATAA
1 AAAATAAATAA
13607 GCATAGATGG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
26 13 0.41
27 17 0.53
28 2 0.06
ACGTcount: A:0.61, C:0.03, G:0.12, T:0.23
Consensus pattern (26 bp):
AAAATAAATAATAGTTAGATGATAAA
Found at i:14039 original size:20 final size:21
Alignment explanation
Indices: 14014--14065 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
14004 TTTTCTCAAT
*
14014 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
14034 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
14055 TCGCAATGCGA
1 TCGCAATGCGA
14066 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:14079 original size:20 final size:20
Alignment explanation
Indices: 14054--14147 Score: 100
Period size: 20 Copynumber: 4.7 Consensus size: 20
14044 AATTGGGAAA
14054 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATACTGACT
*
14074 ATCGCAATGCGATACTTACT
1 ATCGCAATGCGATACTGACT
* *
14094 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAATGCGATACTGAC--T
* *
14115 ATCGCAACGAGATACTGACT
1 ATCGCAATGCGATACTGACT
* *
14135 TTCGCAACGCGAT
1 ATCGCAATGCGAT
14148 TTACATAGCG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
19 2 0.03
20 45 0.73
21 13 0.21
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAATGCGATACTGACT
Found at i:14694 original size:19 final size:19
Alignment explanation
Indices: 14656--14722 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
14646 TTCGAGAATG
14656 AAAATCGCAACGCGGAAATA
1 AAAATCGCAACGC-GAAATA
**
14676 ACTATCGCAACGCGAAATA
1 AAAATCGCAACGCGAAATA
**
14695 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAATA
14714 AAAATCGCA
1 AAAATCGCA
14723 TTGCGATTTT
Statistics
Matches: 41, Mismatches: 6, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
19 30 0.73
20 11 0.27
ACGTcount: A:0.48, C:0.25, G:0.16, T:0.10
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATA
Found at i:14740 original size:19 final size:19
Alignment explanation
Indices: 14718--14848 Score: 112
Period size: 19 Copynumber: 7.1 Consensus size: 19
14708 GAAACCAAAA
*
14718 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
14737 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
14756 TCGCGTTACGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
14770 TC-TGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
**
14788 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
14807 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
14827 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
14847 TC
1 TC
14849 AACCAAAAGA
Statistics
Matches: 94, Mismatches: 10, Indels: 16
0.78 0.08 0.13
Matches are distributed among these distances:
13 6 0.06
14 2 0.02
15 2 0.02
17 3 0.03
18 2 0.02
19 46 0.49
20 32 0.34
21 1 0.01
ACGTcount: A:0.15, C:0.23, G:0.19, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:14799 original size:51 final size:52
Alignment explanation
Indices: 14723--14823 Score: 141
Period size: 51 Copynumber: 2.0 Consensus size: 52
14713 CAAAATCGCA
** **
14723 TTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCGTTACGATTCTCTG
1 TTGCGATAGTCATTTCGCATTGCGATAGTCATTTCCGCGTTACGATTCTCTG
* *
14774 TTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 TTGCGATAGTCATTTCGCATTGCGATAGTCATTTCCGCGTTACGATTCTC
14824 ATTATCTCGT
Statistics
Matches: 43, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
51 29 0.67
52 14 0.33
ACGTcount: A:0.14, C:0.23, G:0.21, T:0.43
Consensus pattern (52 bp):
TTGCGATAGTCATTTCGCATTGCGATAGTCATTTCCGCGTTACGATTCTCTG
Found at i:14814 original size:20 final size:19
Alignment explanation
Indices: 14773--14839 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 19
14763 ACGATTCTCT
14773 GTTGCGATAGTCATTTCGC
1 GTTGCGATAGTCATTTCGC
14792 GTTGCGATAGTCATTTCCGC
1 GTTGCGATAGTCATTT-CGC
** *
14812 GTTGCGATTCTCATTATCTC
1 GTTGCGATAGTCATT-TCGC
14832 GTTGCGAT
1 GTTGCGAT
14840 TTTCATTTCA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 16 0.37
20 26 0.60
21 1 0.02
ACGTcount: A:0.15, C:0.22, G:0.24, T:0.39
Consensus pattern (19 bp):
GTTGCGATAGTCATTTCGC
Found at i:14846 original size:40 final size:39
Alignment explanation
Indices: 14773--14848 Score: 98
Period size: 40 Copynumber: 1.9 Consensus size: 39
14763 ACGATTCTCT
*
14773 GTTGCGATAGTCATTTCGCGTTGCGATAGTCATTTCCGC
1 GTTGCGATACTCATTTCGCGTTGCGATAGTCATTTCCGC
* * **
14812 GTTGCGATTCTCATTATCTCGTTGCGATTTTCATTTC
1 GTTGCGATACTCATT-TCGCGTTGCGATAGTCATTTC
14849 AACCAAAAGA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
39 13 0.42
40 18 0.58
ACGTcount: A:0.14, C:0.22, G:0.21, T:0.42
Consensus pattern (39 bp):
GTTGCGATACTCATTTCGCGTTGCGATAGTCATTTCCGC
Found at i:17006 original size:21 final size:20
Alignment explanation
Indices: 16982--17051 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
16972 TCATTCCTCG
16982 AGAGTCCCCTCCCACCGTTCA
1 AGAG-CCCCTCCCACCGTTCA
* ** * *
17003 AGAGGCCACTGTCATCGTTGA
1 AGA-GCCCCTCCCACCGTTCA
*
17024 AGAGCTCCCTCCCACCATTCA
1 AGAGC-CCCTCCCACCGTTCA
17045 AGAGCCC
1 AGAGCCC
17052 GATTCATATG
Statistics
Matches: 36, Mismatches: 11, Indels: 5
0.69 0.21 0.10
Matches are distributed among these distances:
20 4 0.11
21 31 0.86
22 1 0.03
ACGTcount: A:0.23, C:0.40, G:0.19, T:0.19
Consensus pattern (20 bp):
AGAGCCCCTCCCACCGTTCA
Found at i:18372 original size:14 final size:14
Alignment explanation
Indices: 18353--18388 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
18343 ATTGTTTAAT
18353 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
18367 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
18381 TGATTTGT
1 TGATTTGT
18389 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:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:18539 original size:33 final size:33
Alignment explanation
Indices: 18494--18557 Score: 119
Period size: 33 Copynumber: 1.9 Consensus size: 33
18484 CAAAAGTACT
*
18494 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
18527 ATCGCAACGCGAAATGAAAATCGCAACGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGA
18558 AATTAAATTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.45, C:0.20, G:0.23, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:18553 original size:19 final size:19
Alignment explanation
Indices: 18494--18560 Score: 72
Period size: 19 Copynumber: 3.8 Consensus size: 19
18484 CAAAAGTACT
*
18494 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
18513 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
18527 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
18546 ATCGCAACGAGAAAT
1 ATCGCAACGCGAAAT
18561 TAAATTCGTT
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.25
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 24 0.60
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:18671 original size:34 final size:33
Alignment explanation
Indices: 18574--18694 Score: 181
Period size: 33 Copynumber: 3.6 Consensus size: 33
18564 ATTCGTTGTA
*
18574 ATTTTCATTTCGCATTGCGATTCCCTCGTTGCG
1 ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
* *
18607 ATTTTCATTTCGCATTGCGAAAT-TCGCGTTGCG
1 ATTTTCATTTCGCATTGCG-ATTCTCTCGTTGCG
*
18640 ATTTTCATTTTTGCATTGCGATTCTCTCGTTGCG
1 ATTTTCA-TTTCGCATTGCGATTCTCTCGTTGCG
18674 ATTTTCATTTCGCATTGCGAT
1 ATTTTCATTTCGCATTGCGAT
18695 AGTAATTTCC
Statistics
Matches: 78, Mismatches: 7, Indels: 6
0.86 0.08 0.07
Matches are distributed among these distances:
33 49 0.63
34 29 0.37
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (33 bp):
ATTTTCATTTCGCATTGCGATTCTCTCGTTGCG
Found at i:21002 original size:12 final size:12
Alignment explanation
Indices: 20985--21009 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
20975 TCTTCGAGGA
20985 CTTTTTCTTCTT
1 CTTTTTCTTCTT
20997 CTTTTTCTTCTT
1 CTTTTTCTTCTT
21009 C
1 C
21010 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:21218 original size:24 final size:24
Alignment explanation
Indices: 21184--21237 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
21174 CTGAAACATC
*
21184 ATCAAAATCCGAGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
* *
21208 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
21232 ATCAAA
1 ATCAAA
21238 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:22035 original size:20 final size:21
Alignment explanation
Indices: 22010--22061 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
22000 TTTTCCTAAT
*
22010 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
**
22030 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAATTAAGAAAA
22051 TCGCAATGCGA
1 TCGCAATGCGA
22062 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:22093 original size:20 final size:20
Alignment explanation
Indices: 22046--22096 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
22036 TGCGAATTTG
* *
22046 GAAAATCGCAATGCGATACT
1 GAAAATCGCAACGAGATACT
** *
22066 GACTATCGCAACGAGATTCT
1 GAAAATCGCAACGAGATACT
22086 GAAAATCGCAA
1 GAAAATCGCAA
22097 TCATCTTCAA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.39, C:0.22, G:0.20, T:0.20
Consensus pattern (20 bp):
GAAAATCGCAACGAGATACT
Found at i:22385 original size:20 final size:20
Alignment explanation
Indices: 22310--22377 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 20
22300 CAACGGGGAA
22310 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
** ***
22330 ATCGCAATTCG-AAATGAAAA
1 ATCGCAACGCGAAAATG-GCT
22350 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
22370 ATCGCAAC
1 ATCGCAAC
22378 TAGAAAATCG
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Found at i:22389 original size:34 final size:34
Alignment explanation
Indices: 22294--22397 Score: 109
Period size: 40 Copynumber: 2.9 Consensus size: 34
22284 ATTCATTTGA
** *
22294 CTATCGCAACGGGGAAATCGCAACGCGAAAATGG
1 CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
22328 CTATCGCAATTCGAAATGAAAAATCGCAACGCGAAAATGG
1 CTATCGCAA--C--AA-G-AAAATCGCAACGCGAAAATGG
* *
22368 CTATCGCAACTAGAAAATCGCAATGCGAAA
1 CTATCGCAACAAGAAAATCGCAACGCGAAA
22398 TGAAAATCGC
Statistics
Matches: 59, Mismatches: 5, Indels: 12
0.78 0.07 0.16
Matches are distributed among these distances:
34 25 0.42
35 1 0.02
36 2 0.03
38 1 0.02
39 1 0.02
40 29 0.49
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (34 bp):
CTATCGCAACAAGAAAATCGCAACGCGAAAATGG
Found at i:22428 original size:14 final size:16
Alignment explanation
Indices: 22408--22481 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
22398 TGAAAATCGC
22408 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
22423 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
22440 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
22459 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
22475 -TTGCGAT
1 ATTGCGAT
22482 AGTCAGTTTC
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:22445 original size:19 final size:19
Alignment explanation
Indices: 22404--22471 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
22394 GAAATGAAAA
22404 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
22420 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
22437 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
22456 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
22472 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:24108 original size:21 final size:20
Alignment explanation
Indices: 24084--24143 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
24074 AACGGTGGGG
24084 GGGGACTCTTGAGGGA-GGATA
1 GGGGACTCTTGAGGGATGG--A
* **
24105 GGGGCCTCTTGAACGATTGGA
1 GGGGACTCTTGAGGGA-TGGA
24126 GGGGACTCTTGAGGGATG
1 GGGGACTCTTGAGGGATG
24144 ACAGGTGAGT
Statistics
Matches: 31, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
20 2 0.06
21 27 0.87
23 2 0.06
ACGTcount: A:0.20, C:0.13, G:0.45, T:0.22
Consensus pattern (20 bp):
GGGGACTCTTGAGGGATGGA
Found at i:24575 original size:19 final size:19
Alignment explanation
Indices: 24507--24640 Score: 83
Period size: 20 Copynumber: 7.5 Consensus size: 19
24497 CAAAAAACTT
*
24507 AAAATCGCAACGCGAAAATG
1 AAAATCGCAATGCG-AAATG
** *
24527 ACTATCGCAACGCGGAAATG
1 AAAATCGCAATGC-GAAATG
***
24547 GCTATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
* *
24566 AAAATTGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
24580 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
*
24599 AAAATCGCAA--CG--A-C
1 AAAATCGCAATGCGAAATG
24613 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATG
24632 -AAATCGCAA
1 AAAATCGCAA
24641 CGACAAAATA
Statistics
Matches: 90, Mismatches: 13, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 11 0.12
19 22 0.24
20 27 0.30
21 1 0.01
ACGTcount: A:0.45, C:0.21, G:0.20, T:0.14
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATG
Found at i:24589 original size:14 final size:14
Alignment explanation
Indices: 24566--24656 Score: 65
Period size: 14 Copynumber: 5.9 Consensus size: 14
24556 ATGCGAAATG
*
24566 AAAATTGCAACGAC
1 AAAATCGCAACGAC
*
24580 AAAATCGCAATGCGAAATG
1 AAAATCGCAA--CG--A-C
24599 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
24613 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
24629 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
24645 AAAATAGCAACG
1 AAAATCGCAACG
24657 CGAAACACAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
14 29 0.47
15 1 0.02
16 10 0.16
17 2 0.03
18 10 0.16
19 10 0.16
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:24641 original size:32 final size:33
Alignment explanation
Indices: 24550--24661 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
24540 GGAAATGGCT
*
24550 ATCGCAATGCGAAATGAAAATTGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
24583 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
24616 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* *
24648 ATAGCAACGCGAAA
1 ATCGCAATGCGAAA
24662 CACAAATCGC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 28 0.37
33 48 0.63
ACGTcount: A:0.48, C:0.21, G:0.19, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:24669 original size:65 final size:66
Alignment explanation
Indices: 24550--24672 Score: 187
Period size: 65 Copynumber: 1.9 Consensus size: 66
24540 GGAAATGGCT
* * * *
24550 ATCGCAATGCGAAATGAAAATTGCAACGACAAAATCGCAATGCGAAATGAAAATCGCAACGACAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATAGCAACGCGAAATCAAAATCGCAACGACAA
24615 A
66 A
24616 ATCGCAATGCGAAATG-AAATCGCAACGACAAAATAGCAACGCGAAA-CACAAATCGCA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAAATAGCAACGCGAAATCA-AAATCGCA
24673 TTGCGATTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
64 1 0.02
65 35 0.67
66 16 0.31
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (66 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAAATAGCAACGCGAAATCAAAATCGCAACGACAA
A
Found at i:24690 original size:19 final size:18
Alignment explanation
Indices: 24668--24763 Score: 73
Period size: 19 Copynumber: 5.7 Consensus size: 18
24658 GAAACACAAA
24668 TCGCATTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
* *
24687 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
*
24703 T--CTTTGCGATTTCATT
1 TCGCATTGCGATTTCATT
* *
24719 TCGCATTACGATTT--TG
1 TCGCATTGCGATTTCATT
24735 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
24752 TCGCATTGCGAT
1 TCGCATTGCGAT
24764 AGCAATTTCC
Statistics
Matches: 59, Mismatches: 9, Indels: 19
0.68 0.10 0.22
Matches are distributed among these distances:
14 15 0.25
15 3 0.05
16 8 0.14
17 4 0.07
18 13 0.22
19 16 0.27
ACGTcount: A:0.14, C:0.20, G:0.20, T:0.47
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:24746 original size:14 final size:14
Alignment explanation
Indices: 24690--24747 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 14
24680 TTTCATTTCG
24690 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
* *
24704 CTTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
*
24720 CGCATTACGATTTTGT
1 CG--TTGCGATTTTGT
24736 CGTTGCGATTTT
1 CGTTGCGATTTT
24748 CATTTCGCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
14 19 0.56
16 7 0.21
18 8 0.24
ACGTcount: A:0.12, C:0.17, G:0.21, T:0.50
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:24754 original size:33 final size:33
Alignment explanation
Indices: 24673--24763 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
24663 ACAAATCGCA
* *
24673 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCT
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
*
24706 TTGCGA-TTTCATTTCGCATTACGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
24738 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
24764 AGCAATTTCC
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
32 29 0.55
33 24 0.45
ACGTcount: A:0.13, C:0.19, G:0.20, T:0.48
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:24791 original size:20 final size:19
Alignment explanation
Indices: 24736--24791 Score: 60
Period size: 20 Copynumber: 2.9 Consensus size: 19
24726 ACGATTTTGT
**
24736 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
*
24755 CATTGCGATAG-CAATTTCCG
1 CGTTGCGATAGTC-ATTT-CG
24775 CGTTGCGATAGTCATTT
1 CGTTGCGATAGTCATTT
24792 TCATGTTGCG
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
18 1 0.03
19 12 0.40
20 16 0.53
21 1 0.03
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.39
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:25310 original size:18 final size:18
Alignment explanation
Indices: 25284--25328 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
25274 GTCGATCAGA
25284 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
*
25302 TGATAGCTCTGGGTGAGG
1 TGATGGCTCTGGGTGAGG
25320 TGATGGCTC
1 TGATGGCTC
25329 CCGAAGTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.13, C:0.13, G:0.44, T:0.29
Consensus pattern (18 bp):
TGATGGCTCTGGGTGAGG
Found at i:26673 original size:20 final size:20
Alignment explanation
Indices: 26648--26721 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 20
26638 AATAGTTTCT
*
26648 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACGC
**
26668 GAAAATGACTATCGCAACGC
1 GAAAATGAAAATCGCAACGC
** *
26688 GAATTTGACAATCGCAACGC
1 GAAAATGAAAATCGCAACGC
*
26708 GAAACT-AAAATCGC
1 GAAAATGAAAATCGC
26722 GTTGCGATTT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 7 0.16
20 38 0.84
ACGTcount: A:0.45, C:0.23, G:0.18, T:0.15
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACGC
Found at i:26982 original size:22 final size:22
Alignment explanation
Indices: 26955--26998 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
26945 GATGGAGATA
26955 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
26977 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
26999 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:27272 original size:20 final size:20
Alignment explanation
Indices: 27166--27300 Score: 121
Period size: 20 Copynumber: 6.7 Consensus size: 20
27156 CGCTTTGAAA
*
27166 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* * *
27187 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
* *
27207 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * * *
27227 ATCTCGTTGCGATTTTGT-ATT
1 ATCGCATTGCGA--TAGTCAGT
*
27248 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
27268 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
27288 ATCGCATTGCGAT
1 ATCGCATTGCGAT
27301 TTTCCCAATT
Statistics
Matches: 96, Mismatches: 14, Indels: 9
0.81 0.12 0.08
Matches are distributed among these distances:
19 5 0.05
20 66 0.69
21 23 0.24
22 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.33
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:27272 original size:61 final size:61
Alignment explanation
Indices: 27166--27303 Score: 195
Period size: 61 Copynumber: 2.3 Consensus size: 61
27156 CGCTTTGAAA
* * * *
27166 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
* * * * *
27227 ATCTCGTTGCGATTTTGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
27288 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
27304 CCCAATTCGC
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 66 1.00
ACGTcount: A:0.24, C:0.17, G:0.24, T:0.35
Consensus pattern (61 bp):
ATCGCATTGCGATTTTGTATTATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGT
Found at i:27343 original size:21 final size:21
Alignment explanation
Indices: 27289--27343 Score: 58
Period size: 20 Copynumber: 2.7 Consensus size: 21
27279 ATAGTCAGTA
* *
27289 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGAATTTACCAAT
* **
27310 TCGCGTTGC-AATTTACTTAT
1 TCGCATTGCGAATTTACCAAT
27330 TCGCATTGCGAATT
1 TCGCATTGCGAATT
27344 GGGAAAATCG
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
20 15 0.56
21 12 0.44
ACGTcount: A:0.20, C:0.24, G:0.16, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGAATTTACCAAT
Found at i:27703 original size:31 final size:31
Alignment explanation
Indices: 27646--27709 Score: 92
Period size: 31 Copynumber: 2.1 Consensus size: 31
27636 TTTTATATTA
* **
27646 AATTTGATCTTCAATCTTTTTGAAATAATTG
1 AATTTGATCTTAAATCTTTTAAAAATAATTG
*
27677 AATTTGATCTTAAATCTTTTAAAAATAGTTG
1 AATTTGATCTTAAATCTTTTAAAAATAATTG
27708 AA
1 AA
27710 AAGGTAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.45
Consensus pattern (31 bp):
AATTTGATCTTAAATCTTTTAAAAATAATTG
Found at i:27726 original size:2 final size:2
Alignment explanation
Indices: 27719--27772 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
27709 AAAGGTAAAT
27719 TA TA TA 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
27761 TA TA TA TA TA TA
1 TA TA TA TA TA TA
27773 GACCGAAACA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28611 original size:2 final size:2
Alignment explanation
Indices: 28604--28635 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
28594 AAAGTAGTTA
28604 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
28636 AACTTATTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29766 original size:115 final size:116
Alignment explanation
Indices: 29632--29870 Score: 329
Period size: 116 Copynumber: 2.1 Consensus size: 116
29622 AGGATCCCCA
* ** * * *
29632 ATTTTTTATATTTATAATTAGGGCCCCTAA-TTTTATAATTTCATAATTTTTTTAGTTTTGAGCA
1 ATTTTTTATACTTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAATGTTTAATTTTGACCA
29696 TC-TTTTTCTATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAACC
66 TCTTTTTTC-ATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAACC
* * *
29747 ATTTTTTATACTTATAATTAGGGCCCCTAATTTTTATATTTTCATAAAATGTTTAATTTTTACCC
1 ATTTTTTATACTTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAATGTTTAATTTTGACCA
* * * *
29812 TCTTTTTTCGTTTCTCTTCTTTATTCATTCAATTTTGAATTAAATTTAATC
66 TCTTTTTTCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAACC
29863 ATGTTTTT
1 AT-TTTTT
29871 CTTATTCTTT
Statistics
Matches: 108, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
115 29 0.27
116 68 0.63
117 11 0.10
ACGTcount: A:0.26, C:0.13, G:0.06, T:0.55
Consensus pattern (116 bp):
ATTTTTTATACTTATAATTAGGGCCCCTAATTTTTATAATTTCATAAAATGTTTAATTTTGACCA
TCTTTTTTCATTTCTCTTATTAATTCATTCAATTTTGAATTAAATTTAACC
Found at i:33731 original size:18 final size:19
Alignment explanation
Indices: 33708--33744 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
33698 TCATTTCAAA
33708 GTTGGTTAT-GTTGTTAAG
1 GTTGGTTATGGTTGTTAAG
*
33726 GTTGGTTTTGGTTGTTAAG
1 GTTGGTTATGGTTGTTAAG
33745 CCTGATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.14, C:0.00, G:0.35, T:0.51
Consensus pattern (19 bp):
GTTGGTTATGGTTGTTAAG
Found at i:36787 original size:44 final size:44
Alignment explanation
Indices: 36723--36806 Score: 150
Period size: 44 Copynumber: 1.9 Consensus size: 44
36713 CTTTAATGGC
* *
36723 GTTTGTTTTCTAAAATGCCTCTACATGTTATGATATTTAGCGGT
1 GTTTATTTTCTAAAACGCCTCTACATGTTATGATATTTAGCGGT
36767 GTTTATTTTCTAAAACGCCTCTACATGTTATGATATTTAG
1 GTTTATTTTCTAAAACGCCTCTACATGTTATGATATTTAG
36807 TGGCATTTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.45
Consensus pattern (44 bp):
GTTTATTTTCTAAAACGCCTCTACATGTTATGATATTTAGCGGT
Found at i:39802 original size:8 final size:8
Alignment explanation
Indices: 39791--39846 Score: 85
Period size: 8 Copynumber: 7.0 Consensus size: 8
39781 CACACACGCA
*
39791 CATGCATG
1 CATGTATG
39799 CATGTATG
1 CATGTATG
39807 CATGTATG
1 CATGTATG
*
39815 AATGTATG
1 CATGTATG
*
39823 AATGTATG
1 CATGTATG
39831 CATGTATG
1 CATGTATG
39839 CATGTATG
1 CATGTATG
39847 TATTGGTGCA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
8 45 1.00
ACGTcount: A:0.29, C:0.11, G:0.25, T:0.36
Consensus pattern (8 bp):
CATGTATG
Found at i:39849 original size:4 final size:4
Alignment explanation
Indices: 39800--39849 Score: 55
Period size: 4 Copynumber: 12.5 Consensus size: 4
39790 ACATGCATGC
* * * * *
39800 ATGT ATGC ATGT ATGA ATGT ATGA ATGT ATGC ATGT ATGC ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
39848 AT
1 AT
39850 TGGTGCATCC
Statistics
Matches: 36, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.30, C:0.06, G:0.24, T:0.40
Consensus pattern (4 bp):
ATGT
Found at i:40434 original size:21 final size:21
Alignment explanation
Indices: 40410--40501 Score: 175
Period size: 21 Copynumber: 4.4 Consensus size: 21
40400 TCTTTTAGCT
40410 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
40431 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
40452 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
40473 AATGAAACCATAACGCTTCAA
1 AATGAAACCATAACGCTTCAA
*
40494 AAAGAAAC
1 AATGAAAC
40502 ATCTATTCTT
Statistics
Matches: 70, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
21 70 1.00
ACGTcount: A:0.50, C:0.23, G:0.10, T:0.17
Consensus pattern (21 bp):
AATGAAACCATAACGCTTCAA
Found at i:41407 original size:35 final size:35
Alignment explanation
Indices: 41338--41407 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
41328 AACAGTAACA
* * * *
41338 AACGTCACTAAAGTATGAGTTTTTAGCGGTGTTTG
1 AACGCCACTAAAGTATGAATCTTTAGCGGCGTTTG
**
41373 AACGCCACTAAAGTATGAATCTTTAGTTGCGTTTG
1 AACGCCACTAAAGTATGAATCTTTAGCGGCGTTTG
41408 TAAATACAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (35 bp):
AACGCCACTAAAGTATGAATCTTTAGCGGCGTTTG
Found at i:41439 original size:43 final size:43
Alignment explanation
Indices: 41373--41597 Score: 192
Period size: 43 Copynumber: 5.3 Consensus size: 43
41363 GCGGTGTTTG
* * ** *
41373 AACGCCACTAAAGTATGAATCTTTAGTTGCGTTTGTAAATACA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAAA
* * * **
41416 AACGCCACTAAAGTAAGAGTCTTTAGCTGCATTTGTAAACACG
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAAA
* * *
41459 AACGCCACTACAGTACGAGTCTTTAGCGGCG-TT-TATATAAA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAAA
* * * *
41500 AGCGCCACTAAAGTACGAGTCTATAGCAGCGTTTGT--ATAAA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAAA
** * *
41541 AATACCACTAAAGTAAGAGTCTATAGTGGTC-TTTGTAAA-AAA
1 AACGCCACTAAAGTAAGAGTCTTTAGCGG-CGTTTGTAAATAAA
* *
41583 AATGCCGCTAAAGTA
1 AACGCCACTAAAGTA
41598 CTACTCTATT
Statistics
Matches: 151, Mismatches: 26, Indels: 11
0.80 0.14 0.06
Matches are distributed among these distances:
41 64 0.42
42 21 0.14
43 66 0.44
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (43 bp):
AACGCCACTAAAGTAAGAGTCTTTAGCGGCGTTTGTAAATAAA
Found at i:41535 original size:84 final size:86
Alignment explanation
Indices: 41372--41536 Score: 210
Period size: 84 Copynumber: 1.9 Consensus size: 86
41362 AGCGGTGTTT
* **
41372 GAACGCCACTAAAGTATGAATCTTTAGTTGCGTTTGTAAATACAAACGCCACTAAAGTAAGAGTC
1 GAACGCCACTAAAGTACGAATCTTTAGCGGCGTTTGTAAATACAAACGCCACTAAAGTAAGAGTC
* *
41437 TTTAGCTGCATTTGTAAACAC
66 TATAGCAGCATTTGTAAACAC
* * * *
41458 GAACGCCACTACAGTACGAGTCTTTAGCGGCG-TT-TATATA-AAAGCGCCACTAAAGTACGAGT
1 GAACGCCACTAAAGTACGAATCTTTAGCGGCGTTTGTAAATACAAA-CGCCACTAAAGTAAGAGT
*
41520 CTATAGCAGCGTTTGTA
65 CTATAGCAGCATTTGTA
41537 TAAAAATACC
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
83 3 0.04
84 36 0.53
85 2 0.03
86 27 0.40
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (86 bp):
GAACGCCACTAAAGTACGAATCTTTAGCGGCGTTTGTAAATACAAACGCCACTAAAGTAAGAGTC
TATAGCAGCATTTGTAAACAC
Found at i:41576 original size:41 final size:42
Alignment explanation
Indices: 41377--41597 Score: 124
Period size: 41 Copynumber: 5.3 Consensus size: 42
41367 TGTTTGAACG
* * * ** * **
41377 CCACTAAAGTATGAATCTTTAGTTGCGTTTGTAAATACAAACG
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAA-AAAAATA
* * * ** **
41420 CCACTAAAGTAAGAGTCTTTAGCTGCATTTGTAAACACGAACG
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAA-AAAAATA
* * * * * * ***
41463 CCACTACAGTACGAGTCTTTAGCGGCGTTTAT-ATAAAAGCG
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAAAAAAATA
* *
41504 CCACTAAAGTACGAGTCTATAGCAGCGTTTGT-ATAAAAATA
1 CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAAAAAAATA
** *
41545 CCACTAAAGTAAGAGTCTATAGTGGTC-TTTGTAAAAAAAATG
1 CCACTAAAGTAAGAGTCTATAGCAG-CGTTTGTAAAAAAAATA
*
41587 CCGCTAAAGTA
1 CCACTAAAGTA
41598 CTACTCTATT
Statistics
Matches: 148, Mismatches: 28, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
41 65 0.44
42 19 0.13
43 64 0.43
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.28
Consensus pattern (42 bp):
CCACTAAAGTAAGAGTCTATAGCAGCGTTTGTAAAAAAAATA
Found at i:41753 original size:80 final size:80
Alignment explanation
Indices: 41580--41850 Score: 319
Period size: 80 Copynumber: 3.3 Consensus size: 80
41570 TCTTTGTAAA
* * * *
41580 AAAAATGCCGCTAAAGTACTACTCTATTACGGCGTTTATTGAAAAAAAATCCACTATAGATAAAT
1 AAAAACGCCGCTAAAGTACTACTATGTTA-GGCGTTTATTG--AAAAAAGCCACTATAGATAAA-
*
41645 CCTATTGCGTCGTTTGTAT
62 CCTATTGCGGCGTTTGTAT
* * * * *
41664 AAAAACGCCGCTAAAGTACTACTATGTTATGGCTTTTGTTG-AAAACGCCACTATAGATGACCCT
1 AAAAACGCCGCTAAAGTACTACTATGTTA-GGCGTTTATTGAAAAAAGCCACTATAGATAAACCT
*
41728 CTTGCGGCGTTTGTAT
65 ATTGCGGCGTTTGTAT
* *
41744 AAAAACGCCGCTAAAGTACCACTATGTTGAGGCGTTTATTGAAAAAATGCCACTATGGATAAACC
1 AAAAACGCCGCTAAAGTACTACTATGTT-AGGCGTTTATTGAAAAAA-GCCACTATAGATAAACC
* *
41809 TATTGCAGCATTTGTAT
64 TATTGCGGCGTTTGTAT
* *
41826 AAAAACGCCGTTGAAGTACTACTAT
1 AAAAACGCCGCTAAAGTACTACTAT
41851 ATTGCGGTGT
Statistics
Matches: 159, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
80 53 0.33
81 21 0.13
82 50 0.31
84 35 0.22
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (80 bp):
AAAAACGCCGCTAAAGTACTACTATGTTAGGCGTTTATTGAAAAAAGCCACTATAGATAAACCTA
TTGCGGCGTTTGTAT
Found at i:41789 original size:41 final size:41
Alignment explanation
Indices: 41655--41789 Score: 113
Period size: 40 Copynumber: 3.3 Consensus size: 41
41645 CCTATTGCGT
*
41655 CGTTTGTAT-AAAAACGCCGCTAAAGTACTACTATGTT-ATGG
1 CGTTTGT-TGAAAAACGCCGCTAAAGTACCACTATGTTGA-GG
* * * * *
41696 CTTTTGTTG-AAAACGCCACTATAGATGACC-C--TCTTGCGG
1 CGTTTGTTGAAAAACGCCGCTAAAG-T-ACCACTATGTTGAGG
41735 CGTTTGTAT-AAAAACGCCGCTAAAGTACCACTATGTTGAGG
1 CGTTTGT-TGAAAAACGCCGCTAAAGTACCACTATGTTGAGG
*
41776 CGTTTATTGAAAAA
1 CGTTTGTTGAAAAA
41790 ATGCCACTAT
Statistics
Matches: 72, Mismatches: 12, Indels: 20
0.69 0.12 0.19
Matches are distributed among these distances:
38 3 0.04
39 13 0.18
40 29 0.40
41 25 0.35
42 2 0.03
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.30
Consensus pattern (41 bp):
CGTTTGTTGAAAAACGCCGCTAAAGTACCACTATGTTGAGG
Found at i:49119 original size:23 final size:22
Alignment explanation
Indices: 49093--49165 Score: 76
Period size: 23 Copynumber: 3.2 Consensus size: 22
49083 ATAAAAAAAA
*
49093 GTGCCACAAAGGTAAAGATAAAC
1 GTGCGACAAA-GTAAAGATAAAC
* *
49116 GTGCGACAAAGACAAAGATAAAT
1 GTGCGACAAAG-TAAAGATAAAC
49139 GTGCGACACAA-TAAGAGATAAAC
1 GTGCGACA-AAGTAA-AGATAAAC
49162 GTGC
1 GTGC
49166 AACACAGACA
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
22 3 0.07
23 37 0.88
24 2 0.05
ACGTcount: A:0.47, C:0.16, G:0.23, T:0.14
Consensus pattern (22 bp):
GTGCGACAAAGTAAAGATAAAC
Found at i:49170 original size:23 final size:24
Alignment explanation
Indices: 49106--49175 Score: 83
Period size: 23 Copynumber: 3.0 Consensus size: 24
49096 CCACAAAGGT
49106 AAAGATAAACGTGCGACA-AAGAC
1 AAAGATAAACGTGCGACACAAGAC
* *
49129 AAAGATAAATGTGCGACACAATA-
1 AAAGATAAACGTGCGACACAAGAC
* *
49152 AGAGATAAACGTGCAACAC-AGAC
1 AAAGATAAACGTGCGACACAAGAC
49175 A
1 A
49176 TAATTATTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 2 0.05
23 34 0.87
24 3 0.08
ACGTcount: A:0.51, C:0.17, G:0.20, T:0.11
Consensus pattern (24 bp):
AAAGATAAACGTGCGACACAAGAC
Found at i:57194 original size:18 final size:18
Alignment explanation
Indices: 57156--57196 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
57146 AGAACAGCAC
* * *
57156 GAGGAACAAGCTCCACTA
1 GAGGAACAAGCACAACCA
57174 GAGGAACAAGCACAACCA
1 GAGGAACAAGCACAACCA
57192 GAGGA
1 GAGGA
57197 TCAAATGCCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.44, C:0.24, G:0.27, T:0.05
Consensus pattern (18 bp):
GAGGAACAAGCACAACCA
Found at i:60091 original size:28 final size:29
Alignment explanation
Indices: 60049--60115 Score: 84
Period size: 28 Copynumber: 2.3 Consensus size: 29
60039 AAATACTGAC
* *
60049 AAATAAAATAAATAA-CGAATAAAAAAAAT
1 AAAT-AAATACATAACCAAATAAAAAAAAT
*
60078 AAATAAATACATAACCAAATAAAATAAAT
1 AAATAAATACATAACCAAATAAAAAAAAT
60107 -AATAAATAC
1 AAATAAATAC
60116 TTCTGGATTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
28 18 0.53
29 16 0.47
ACGTcount: A:0.72, C:0.07, G:0.01, T:0.19
Consensus pattern (29 bp):
AAATAAATACATAACCAAATAAAAAAAAT
Found at i:60097 original size:20 final size:20
Alignment explanation
Indices: 60074--60111 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
60064 CGAATAAAAA
60074 AAAT-AAATAAATACATAACC
1 AAATAAAATAAATA-ATAACC
60094 AAATAAAATAAATAATAA
1 AAATAAAATAAATAATAA
60112 ATACTTCTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.71, C:0.08, G:0.00, T:0.21
Consensus pattern (20 bp):
AAATAAAATAAATAATAACC
Done.