Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008223.1 Hibiscus syriacus cultivar Beakdansim tig00110855_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: 138744
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:21516 original size:21 final size:21
Alignment explanation
Indices: 21471--21517 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
21461 AGTGCCCAAC
*
21471 AATAACAAAACCGGTAAAAAA
1 AATAACAAAACCAGTAAAAAA
* * *
21492 AATAACAAAATCAGTATAAAT
1 AATAACAAAACCAGTAAAAAA
21513 AATAA
1 AATAA
21518 TTTTTCCGAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.66, C:0.11, G:0.06, T:0.17
Consensus pattern (21 bp):
AATAACAAAACCAGTAAAAAA
Found at i:23866 original size:17 final size:16
Alignment explanation
Indices: 23839--23870 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
23829 ACATCTCCAC
23839 TTAATAATTTTTATCA
1 TTAATAATTTTTATCA
23855 TTAATCAATTTTTATC
1 TTAAT-AATTTTTATC
23871 TCCACAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.56
Consensus pattern (16 bp):
TTAATAATTTTTATCA
Found at i:30335 original size:61 final size:61
Alignment explanation
Indices: 30222--30341 Score: 186
Period size: 61 Copynumber: 2.0 Consensus size: 61
30212 CTGCAATTAT
*
30222 TTGTGGCCATGTGCCATACATTGGACCAGGAGAATATGCTATTATGGTCTTTAAATTTGAG
1 TTGTGGCCATGTGCCATACATTGGACCAGGAGAATATGCTATTATGGCCTTTAAATTTGAG
* * * * *
30283 TTGTGGCCATGTGCTATACATTGGACTAGGAGAATATGCTATTGTTGCCTTTACATTTG
1 TTGTGGCCATGTGCCATACATTGGACCAGGAGAATATGCTATTATGGCCTTTAAATTTG
30342 TGTTAATATT
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.37
Consensus pattern (61 bp):
TTGTGGCCATGTGCCATACATTGGACCAGGAGAATATGCTATTATGGCCTTTAAATTTGAG
Found at i:31198 original size:31 final size:31
Alignment explanation
Indices: 31163--31232 Score: 104
Period size: 31 Copynumber: 2.3 Consensus size: 31
31153 ATTATTCATG
* *
31163 AGTTAAATTAATATTTTATTTAAAGTTCAAA
1 AGTTAAATTAATATTTTATCTAAAATTCAAA
*
31194 AGTTAAATTAATATTTTATCTAAAATTTAAA
1 AGTTAAATTAATATTTTATCTAAAATTCAAA
*
31225 AGATAAAT
1 AGTTAAAT
31233 AAGTGTTTTA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.06, T:0.43
Consensus pattern (31 bp):
AGTTAAATTAATATTTTATCTAAAATTCAAA
Found at i:31410 original size:31 final size:31
Alignment explanation
Indices: 31336--31416 Score: 92
Period size: 31 Copynumber: 2.6 Consensus size: 31
31326 TTACAAATTG
* * *
31336 ATAAATTAAAGGATCAAAACCTTATAAATCG
1 ATAAAGTAAATGATCAAAACCTTATAAATCA
* *
31367 ATAAAGTGAATGATCAAATCCTTATAAATCA
1 ATAAAGTAAATGATCAAAACCTTATAAATCA
*
31398 ATAACA-TAAATGATTAAAA
1 ATAA-AGTAAATGATCAAAA
31417 TATTATTTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
31 40 0.98
32 1 0.02
ACGTcount: A:0.53, C:0.11, G:0.09, T:0.27
Consensus pattern (31 bp):
ATAAAGTAAATGATCAAAACCTTATAAATCA
Found at i:37777 original size:20 final size:20
Alignment explanation
Indices: 37755--38011 Score: 146
Period size: 20 Copynumber: 12.7 Consensus size: 20
37745 TTTTCACAAT
* *
37755 TCGCAATGCGAATAAATAAT
1 TCGCAATGCGAATAAGTAAA
*
37775 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
37795 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
** *
37815 TCGCAATGCGAATTTGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
* *
37836 TCGCAATGCG-AT-ACTGACTA
1 TCGCAATGCGAATAAGT-A-AA
*** *
37856 TCGCAATGC-AATTTTCCTAAT
1 TCGCAATGCGAA--TAAGTAAA
* * * * *
37877 TCGCATTACGATTTACGT-AT
1 TCGCAATGCGA-ATAAGTAAA
** * * *
37897 TCGCGTTGCGATTTTCA-TAAT
1 TCGCAATGCGA--ATAAGTAAA
*
37918 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
37938 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
37958 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
37979 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
37999 TCGCAATGCGAAT
1 TCGCAATGCGAAT
38012 CTGACTATCG
Statistics
Matches: 186, Mismatches: 38, Indels: 26
0.74 0.15 0.10
Matches are distributed among these distances:
19 3 0.02
20 121 0.65
21 57 0.31
22 3 0.02
23 2 0.01
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.26
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:37870 original size:143 final size:143
Alignment explanation
Indices: 37693--37989 Score: 379
Period size: 143 Copynumber: 2.1 Consensus size: 143
37683 GTTTCCAGAT
* * * *
37693 TCGCAACGCGATTATGACTATCGCAATGCGATTTTCC-AATTTCGCGTTGC-ATTTTTCAC-AAT
1 TCGCAATGCGATTATGACTATCGCAATGCAATTTTCCTAA-TTCGCATTACGA--TTT-ACGAAT
*
37755 TCGCAATGCGA-ATAAATAATTCGCAATGCAAATAAGTAAATCGCAATGCGAATAAGTAAATCGC
62 TCGCAATGCGATATAAATAATTCGCAATGCAAATAAGTAAATCGCAACGCGAATAAGTAAATCGC
*
37819 AATGCGAATTTGGAAAA
127 AATGCGAATTAGGAAAA
*
37836 TCGCAATGCGA-TACTGACTATCGCAATGCAATTTTCCTAATTCGCATTACGATTTACGTATTCG
1 TCGCAATGCGATTA-TGACTATCGCAATGCAATTTTCCTAATTCGCATTACGATTTACGAATTCG
** * ** * * *
37900 CGTTGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAATCGCAAT
65 CAATGCGATATAAATAATTCGCAATGCAAATAAGTAAATCGCAACGCGAATAAGTAAATCGCAAT
37965 GCGAATTAGGAAAA
130 GCGAATTAGGAAAA
37979 TCGCAATGCGA
1 TCGCAATGCGA
37990 ATACGTAAAT
Statistics
Matches: 134, Mismatches: 15, Indels: 10
0.84 0.09 0.06
Matches are distributed among these distances:
141 2 0.01
142 16 0.12
143 113 0.84
144 3 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (143 bp):
TCGCAATGCGATTATGACTATCGCAATGCAATTTTCCTAATTCGCATTACGATTTACGAATTCGC
AATGCGATATAAATAATTCGCAATGCAAATAAGTAAATCGCAACGCGAATAAGTAAATCGCAATG
CGAATTAGGAAAA
Found at i:37922 original size:163 final size:163
Alignment explanation
Indices: 37733--38032 Score: 435
Period size: 163 Copynumber: 1.8 Consensus size: 163
37723 ATTTTCCAAT
* *
37733 TTCGCGTTGCATTTTTCACAATTCGCAATGCGAATAAATAATTCGCAATGCAAATAAGTAAATCG
1 TTCGCGTTGCATTTTTCACAATTCGCAATGCGAATAAATAAATCGCAACGCAAATAAGTAAATCG
* **
37798 CAATGCGAA-TAAGTAAATCGCAATGCGAATTTGGAAAATCGCAATGCG-ATACTGACTATCGCA
66 CAATGCGAATTAAGAAAATCGCAATGCGAA-TACGAAAATCGCAATGCGAAT-CTGACTATCGCA
37861 ATGCAATTTTCCTAATTCGCATTACGATTTACGTA
129 ATGCAATTTTCCTAATTCGCATTACGATTTACGTA
* ** * *
37896 TTCGCGTTGCGA-TTTTCATAATTCGCAATGCGAATACGTAAATCGCAACGCGATTAAGTAAATC
1 TTCGCGTTGC-ATTTTTCACAATTCGCAATGCGAATAAATAAATCGCAACGCAAATAAGTAAATC
* *
37960 GCAATGCGAATTAGGAAAATCGCAATGCGAATACGTAAATCGCAATGCGAATCTGACTATCGCAA
65 GCAATGCGAATTAAGAAAATCGCAATGCGAATACGAAAATCGCAATGCGAATCTGACTATCGCAA
*
38025 TGCGATTT
130 TGCAATTT
38033 ACATAGCGCC
Statistics
Matches: 121, Mismatches: 13, Indels: 6
0.86 0.09 0.04
Matches are distributed among these distances:
163 100 0.83
164 21 0.17
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.28
Consensus pattern (163 bp):
TTCGCGTTGCATTTTTCACAATTCGCAATGCGAATAAATAAATCGCAACGCAAATAAGTAAATCG
CAATGCGAATTAAGAAAATCGCAATGCGAATACGAAAATCGCAATGCGAATCTGACTATCGCAAT
GCAATTTTCCTAATTCGCATTACGATTTACGTA
Found at i:37927 original size:21 final size:21
Alignment explanation
Indices: 37856--37928 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
37846 ATACTGACTA
* *
37856 TCGCAATGCAATTTTCCTAAT
1 TCGCAATGCGATTTTCATAAT
* * * *
37877 TCGCATTACGATTTACGT-AT
1 TCGCAATGCGATTTTCATAAT
**
37897 TCGCGTTGCGATTTTCATAAT
1 TCGCAATGCGATTTTCATAAT
37918 TCGCAATGCGA
1 TCGCAATGCGA
37929 ATACGTAAAT
Statistics
Matches: 40, Mismatches: 11, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 16 0.40
21 24 0.60
ACGTcount: A:0.25, C:0.22, G:0.16, T:0.37
Consensus pattern (21 bp):
TCGCAATGCGATTTTCATAAT
Found at i:37949 original size:41 final size:41
Alignment explanation
Indices: 37791--38037 Score: 152
Period size: 41 Copynumber: 6.0 Consensus size: 41
37781 TGCAAATAAG
* **
37791 TAAATCGCAATGCGAATAAGTAAATCGCAATGCGAATTTGGA
1 TAAATCGCAATGCGAATACGTAAATCGCAATGCG-ATTTTCA
* * *
37833 -AAATCGCAATGCG-ATAC-TGACTATCGCAATGCAATTTTCC
1 TAAATCGCAATGCGAATACGT-A-AATCGCAATGCGATTTTCA
* * * * * **
37873 TAATTCGCATTACGATTTACGT-ATTCGCGTTGCGATTTTCA
1 TAAATCGCAATGCGA-ATACGTAAATCGCAATGCGATTTTCA
* * *
37914 TAATTCGCAATGCGAATACGTAAATCGCAACGCGA--TTAA
1 TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTTTCA
* * * * *
37953 GTAAATCGCAATGCGAATTAGGAAAATCGCAATGCGA-ATACG
1 -TAAATCGCAATGCGAA-TACGTAAATCGCAATGCGATTTTCA
* *
37995 TAAATCGCAATGCGAAT-C-TGACTATCGCAATGCGATTTACA
1 TAAATCGCAATGCGAATACGT-A-AATCGCAATGCGATTTTCA
38036 TA
1 TA
38038 GCGCCATTCG
Statistics
Matches: 156, Mismatches: 36, Indels: 27
0.71 0.16 0.12
Matches are distributed among these distances:
39 5 0.03
40 41 0.26
41 105 0.67
42 1 0.01
43 3 0.02
44 1 0.01
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.27
Consensus pattern (41 bp):
TAAATCGCAATGCGAATACGTAAATCGCAATGCGATTTTCA
Found at i:38597 original size:19 final size:19
Alignment explanation
Indices: 38573--38712 Score: 84
Period size: 19 Copynumber: 7.8 Consensus size: 19
38563 CAACGAGAAA
**
38573 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTCATTTCGCGT
38592 TGCGATTTTCATTTCGCGT
1 TGCGATTTTCATTTCGCGT
*
38611 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
* ** *
38625 TACGATAGTCATTTCGCAT
1 TGCGATTTTCATTTCGCGT
*
38644 TGCGA--TTC---TCTCGT
1 TGCGATTTTCATTTCGCGT
**
38658 TGCGATAGTCATTTCCGCGT
1 TGCGATTTTCATTT-CGCGT
* *
38678 TGCGATTTTCATTATCTCCT
1 TGCGATTTTCATT-TCGCGT
38698 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
38713 AACCAAAAGA
Statistics
Matches: 92, Mismatches: 17, Indels: 24
0.69 0.13 0.18
Matches are distributed among these distances:
14 18 0.20
16 4 0.04
17 5 0.05
19 33 0.36
20 31 0.34
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TGCGATTTTCATTTCGCGT
Found at i:38647 original size:33 final size:33
Alignment explanation
Indices: 38600--38684 Score: 143
Period size: 33 Copynumber: 2.5 Consensus size: 33
38590 GTTGCGATTT
38600 TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
* *
38633 TCATTTCGCATTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
38666 TCATTTCCGCGTTGCGATT
1 TCATTT-CGCGTTGCGATT
38685 TTCATTATCT
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 37 0.77
34 11 0.23
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTTACGATAG
Found at i:38689 original size:20 final size:20
Alignment explanation
Indices: 38649--38712 Score: 69
Period size: 20 Copynumber: 3.1 Consensus size: 20
38639 CGCATTGCGA
**
38649 TTCTCTCGTTGCGATAGTCAT
1 TTCTC-CGTTGCGATTTTCAT
38670 TTC-CGCGTTGCGATTTTCAT
1 TTCTC-CGTTGCGATTTTCAT
38690 TATCTCC-TTGCGATTTTCAT
1 T-TCTCCGTTGCGATTTTCAT
38710 TTC
1 TTC
38713 AACCAAAAGA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
19 2 0.05
20 29 0.76
21 6 0.16
22 1 0.03
ACGTcount: A:0.12, C:0.25, G:0.16, T:0.47
Consensus pattern (20 bp):
TTCTCCGTTGCGATTTTCAT
Found at i:40596 original size:94 final size:93
Alignment explanation
Indices: 40404--40779 Score: 598
Period size: 94 Copynumber: 4.1 Consensus size: 93
40394 TAGATTGCTT
* * *
40404 AGTAAATTTATTCGGTTGCTGCCAATACTGCTAAAC--TGT-TT-ATTAACATTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
40465 ATTTGTCTTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTC-TTTGTTTTGTCTTTTGGTTGA
40494 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
40559 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* *
40588 AGTAAATTTGTTCGGTTGCTGTCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
* *
40653 ATTTGCCTTTGTTTTATCTTTTGGTTGAA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTG-A
* * * *
40682 AGTAAATTTGTTCGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAATACTCTGAAGTTAGT
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
40747 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
66 ATTTGTCTTTGTTTTGTCTTTTGGTTGA
40775 AGTAA
1 AGTAA
40780 TGCAATCCAT
Statistics
Matches: 268, Mismatches: 13, Indels: 7
0.93 0.05 0.02
Matches are distributed among these distances:
90 35 0.13
92 3 0.01
93 28 0.10
94 202 0.75
ACGTcount: A:0.22, C:0.12, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAGTTAGT
ATTTGTCTTTGTTTTGTCTTTTGGTTGA
Found at i:40868 original size:12 final size:12
Alignment explanation
Indices: 40851--40876 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
40841 TTAGTAACAC
40851 TGTTTTGTCTTT
1 TGTTTTGTCTTT
40863 TGTTTTGTCTTT
1 TGTTTTGTCTTT
40875 TG
1 TG
40877 GTTTCGCGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.08, G:0.19, T:0.73
Consensus pattern (12 bp):
TGTTTTGTCTTT
Found at i:42839 original size:14 final size:14
Alignment explanation
Indices: 42819--42855 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
42809 GATTATTTAA
42819 TTGATTTGTAAAA-
1 TTGATTTGTAAAAG
42832 TATGATTTGTAAAAG
1 T-TGATTTGTAAAAG
42847 TTGATTTGT
1 TTGATTTGT
42856 TTAATTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 1 0.05
14 20 0.91
15 1 0.05
ACGTcount: A:0.32, C:0.00, G:0.19, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:43010 original size:33 final size:33
Alignment explanation
Indices: 42962--43055 Score: 152
Period size: 33 Copynumber: 2.8 Consensus size: 33
42952 AAAAATGACT
* *
42962 ATCGCAATGCAAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
42995 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* *
43028 ATTGTAACGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
43056 CGAAACTAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:43070 original size:19 final size:19
Alignment explanation
Indices: 42962--43060 Score: 74
Period size: 19 Copynumber: 5.7 Consensus size: 19
42952 AAAAATGACT
* *
42962 ATCGCAATGCAAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
42981 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
42995 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
*
43014 ATCGCAA--CG--A-GAGA
1 ATCGCAACGCGAAATGAAA
* *
43028 ATTGTAACGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
43047 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
43061 CTAAATTCGC
Statistics
Matches: 61, Mismatches: 9, Indels: 20
0.68 0.10 0.22
Matches are distributed among these distances:
14 18 0.30
15 2 0.03
16 4 0.07
17 3 0.05
18 2 0.03
19 32 0.52
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.12
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:43088 original size:19 final size:19
Alignment explanation
Indices: 43066--43216 Score: 98
Period size: 19 Copynumber: 8.7 Consensus size: 19
43056 CGAAACTAAA
*
43066 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* *
43085 TTCGCTTTGCGA--TTC-C
1 TTCGCATTGCGATTTTCAT
*
43101 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
43118 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
43134 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
43151 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
*
43166 -TCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
* **
43184 TTCGCATTACGATAGTCAT
1 TTCGCATTGCGATTTTCAT
*
43203 TTCCGCGTTGCGAT
1 TT-CGCATTGCGAT
43217 AGACATTAAG
Statistics
Matches: 102, Mismatches: 14, Indels: 31
0.69 0.10 0.21
Matches are distributed among these distances:
14 22 0.22
16 16 0.16
17 16 0.16
19 39 0.38
20 9 0.09
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:43112 original size:33 final size:33
Alignment explanation
Indices: 43070--43196 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
43060 ACTAAATTCG
* *
43070 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
43103 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
43136 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
43169 CATTGCGATTTTCATTTCGCATTACGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
43197 AGTCATTTCC
Statistics
Matches: 90, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 90 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:43143 original size:14 final size:14
Alignment explanation
Indices: 43091--43178 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
43081 TCATTTCGCT
*
43091 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
43105 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
43122 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
43138 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
43155 CATTGCGATTCTCTCA
1 --TTGCGATTCTCTCG
43171 TTGCGATT
1 TTGCGATT
43179 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 13 0.22
17 13 0.22
19 12 0.21
ACGTcount: A:0.12, C:0.25, G:0.18, T:0.44
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:43218 original size:20 final size:20
Alignment explanation
Indices: 43180--43262 Score: 55
Period size: 20 Copynumber: 4.2 Consensus size: 20
43170 ATTGCGATTT
* *
43180 TCATTT-CGCATTACGATAG
1 TCATTTCCGCGTTGCGATAG
43199 TCATTTCCGCGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
* ** *
43219 ACA-TTAAGATGATTGCGA-ACG
1 TCATTTCCG-CG-TTGCGATA-G
*
43240 TCATTTCCGTGTTGCGATAG
1 TCATTTCCGCGTTGCGATAG
43260 TCA
1 TCA
43263 AATGATTGCC
Statistics
Matches: 49, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
19 9 0.18
20 25 0.51
21 12 0.24
22 3 0.06
ACGTcount: A:0.24, C:0.20, G:0.22, T:0.34
Consensus pattern (20 bp):
TCATTTCCGCGTTGCGATAG
Found at i:45542 original size:12 final size:12
Alignment explanation
Indices: 45525--45549 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45515 TCTTCGGGGA
45525 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45537 CTTTTTCTTCTT
1 CTTTTTCTTCTT
45549 C
1 C
45550 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:46545 original size:20 final size:20
Alignment explanation
Indices: 46524--46611 Score: 140
Period size: 20 Copynumber: 4.4 Consensus size: 20
46514 TGTATTATCT
* *
46524 CGTTGCGATAGTCAGAATCT
1 CGTTGCGAAAGTCAGAATCG
*
46544 CGTTGCGAAAGTCAAAATCG
1 CGTTGCGAAAGTCAGAATCG
46564 CGTTGCGAAAGTCAGAATCG
1 CGTTGCGAAAGTCAGAATCG
*
46584 CGTTGCGAAAGTCAGTATCG
1 CGTTGCGAAAGTCAGAATCG
46604 CGTTGCGA
1 CGTTGCGA
46612 TTTTGTATTA
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.27, C:0.20, G:0.28, T:0.24
Consensus pattern (20 bp):
CGTTGCGAAAGTCAGAATCG
Found at i:46645 original size:20 final size:20
Alignment explanation
Indices: 46519--46653 Score: 137
Period size: 20 Copynumber: 6.7 Consensus size: 20
46509 GATTCTGTAT
*
46519 TATCTCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
* * * *
46539 AATCTCGTTGCGAAAGTCAA
1 TATCGCGTTGCGATAGTCAG
* *
46559 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
46579 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGATAGTCAG
* *
46599 TATCGCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--TAGTCAG
46620 TATCGCGTTGCGATAGTCAG
1 TATCGCGTTGCGATAGTCAG
*
46640 TATCGCATTGCGAT
1 TATCGCGTTGCGAT
46654 TTTCCAAATT
Statistics
Matches: 100, Mismatches: 12, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.03
20 81 0.81
21 14 0.14
22 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.30
Consensus pattern (20 bp):
TATCGCGTTGCGATAGTCAG
Found at i:46672 original size:41 final size:41
Alignment explanation
Indices: 46580--46674 Score: 120
Period size: 41 Copynumber: 2.3 Consensus size: 41
46570 GAAAGTCAGA
* * ** *
46580 ATCGCGTTGCGAAAGTCAGTATCGCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
46621 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCCAAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTT-CAAAT
*
46663 -TCGCATTGCGAT
1 ATCGCGTTGCGAT
46675 TTACTTATTC
Statistics
Matches: 47, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 45 0.96
42 2 0.04
ACGTcount: A:0.21, C:0.20, G:0.24, T:0.35
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCGATTTTCAAAT
Found at i:46686 original size:20 final size:21
Alignment explanation
Indices: 46642--46690 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
46632 ATAGTCAGTA
*
46642 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
46663 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
46683 TCGCATTG
1 TCGCATTG
46691 TGAATTGGGA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:46722 original size:21 final size:22
Alignment explanation
Indices: 46693--46735 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
46683 TCGCATTGTG
46693 AATTGGGAAAATCGCAATGCGA
1 AATTGGGAAAATCGCAATGCGA
*
46715 AATT-GGAAAATCGCATTGCGA
1 AATTGGGAAAATCGCAATGCGA
46736 TAGTCATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 16 0.80
22 4 0.20
ACGTcount: A:0.40, C:0.14, G:0.26, T:0.21
Consensus pattern (22 bp):
AATTGGGAAAATCGCAATGCGA
Found at i:51908 original size:17 final size:18
Alignment explanation
Indices: 51888--51921 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
51878 AATGATATTT
51888 AAATTAAATT-ATAATTC
1 AAATTAAATTCATAATTC
*
51905 AAATTAATTTCATAATT
1 AAATTAAATTCATAATT
51922 TAGATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
AAATTAAATTCATAATTC
Found at i:54390 original size:16 final size:17
Alignment explanation
Indices: 54371--54408 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
54361 TTATCAATAA
54371 AAAATATAAAA-AAATT
1 AAAATATAAAAGAAATT
*
54387 AAAATATAAAAGAATTT
1 AAAATATAAAAGAAATT
54404 AAAAT
1 AAAAT
54409 TTTTAGGTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (17 bp):
AAAATATAAAAGAAATT
Found at i:68448 original size:18 final size:19
Alignment explanation
Indices: 68427--68467 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
68417 ACTTTTCATA
68427 AAAAAATATAT-AAATTTT
1 AAAAAATATATAAAATTTT
*
68445 AAAAAATTTATGAAAATTTT
1 AAAAAATATAT-AAAATTTT
68465 AAA
1 AAA
68468 TTTTTAGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
AAAAAATATATAAAATTTT
Found at i:68624 original size:2 final size:2
Alignment explanation
Indices: 68617--68650 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
68607 GTGGGAAATG
* *
68617 AT AT AT AT AT AT AT AT AT AT AT AT TT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
68651 TTTTTAGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:73081 original size:20 final size:20
Alignment explanation
Indices: 73056--73108 Score: 79
Period size: 21 Copynumber: 2.6 Consensus size: 20
73046 ATCAATAATT
*
73056 TTTTTTTTTAATTTAATTAC
1 TTTTTTTTTAATTTAATTAA
73076 TTTTTTTTTAAATTTAATTAA
1 TTTTTTTTT-AATTTAATTAA
*
73097 TTTTTATTTAAT
1 TTTTTTTTTAAT
73109 ATTAGTTTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.40
21 18 0.60
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTTTTAATTTAATTAA
Found at i:74616 original size:33 final size:33
Alignment explanation
Indices: 74578--74644 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
74568 AAATAATGTA
*
74578 TAAAGAAACAGAAAA-TTAAACCTTAATTATTCT
1 TAAAGAAACA-AAAAGTAAAACCTTAATTATTCT
* * *
74611 TAAAGAAATAAAAAGTAAAACCTTAGTTGTTCT
1 TAAAGAAACAAAAAGTAAAACCTTAATTATTCT
74644 T
1 T
74645 TTTGTCACAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
32 4 0.14
33 25 0.86
ACGTcount: A:0.49, C:0.10, G:0.09, T:0.31
Consensus pattern (33 bp):
TAAAGAAACAAAAAGTAAAACCTTAATTATTCT
Found at i:74976 original size:2 final size:2
Alignment explanation
Indices: 74969--75000 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
74959 ACCCTAACAA
74969 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
75001 CCATACTGAA
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:76619 original size:2 final size:2
Alignment explanation
Indices: 76612--76646 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
76602 ATCTTTTTAA
76612 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
76647 CCCCCATCCG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:76912 original size:24 final size:24
Alignment explanation
Indices: 76805--76913 Score: 78
Period size: 24 Copynumber: 4.5 Consensus size: 24
76795 AAACGGAGAT
*
76805 ATCAGAAATCAAAACATAATTCAA
1 ATCAGAAATCAAAACAGAATTCAA
* * *
76829 ATCAGATATCAGAACAGAA-TCTAG
1 ATCAGAAATCAAAACAGAATTC-AA
* * * * *
76853 GTTA-AGAATCATAACAGATTTCAG
1 ATCAGA-AATCAAAACAGAATTCAA
* **
76877 ATAAGATGTCAAAACAGAATTCAA
1 ATCAGAAATCAAAACAGAATTCAA
76901 ATCAGAAATCAAA
1 ATCAGAAATCAAA
76914 TAAAATATTC
Statistics
Matches: 62, Mismatches: 19, Indels: 8
0.70 0.21 0.09
Matches are distributed among these distances:
23 3 0.05
24 56 0.90
25 3 0.05
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (24 bp):
ATCAGAAATCAAAACAGAATTCAA
Found at i:81270 original size:30 final size:30
Alignment explanation
Indices: 81227--81297 Score: 124
Period size: 30 Copynumber: 2.3 Consensus size: 30
81217 AGTTCCATTT
*
81227 GGACCATCATCACGCGCAGTGGCGGCGCGTG
1 GGACC-TCCTCACGCGCAGTGGCGGCGCGTG
81258 GGACCTCCTCACGCGCAGTGGCGGCGCGTG
1 GGACCTCCTCACGCGCAGTGGCGGCGCGTG
81288 GGACCTCCTC
1 GGACCTCCTC
81298 CGGTGTCTTG
Statistics
Matches: 39, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
30 34 0.87
31 5 0.13
ACGTcount: A:0.13, C:0.37, G:0.37, T:0.14
Consensus pattern (30 bp):
GGACCTCCTCACGCGCAGTGGCGGCGCGTG
Found at i:95528 original size:13 final size:13
Alignment explanation
Indices: 95510--95540 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
95500 TAATTATTTT
95510 TTATTTACTTTAA
1 TTATTTACTTTAA
*
95523 TTATTTATTTTAA
1 TTATTTACTTTAA
95536 TTATT
1 TTATT
95541 CATTTAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTACTTTAA
Found at i:101840 original size:31 final size:31
Alignment explanation
Indices: 101800--101872 Score: 130
Period size: 30 Copynumber: 2.4 Consensus size: 31
101790 TAAAGTTAAT
101800 TTATTAAAAAAATAAAACTTTT-AATTGAAA
1 TTATTAAAAAAATAAAACTTTTAAATTGAAA
*
101830 TTATTAAAAAATTAAAACTTTTAAATTGAAA
1 TTATTAAAAAAATAAAACTTTTAAATTGAAA
101861 TTATTAAAAAAA
1 TTATTAAAAAAA
101873 CTTTAAAGAC
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
30 21 0.52
31 19 0.47
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (31 bp):
TTATTAAAAAAATAAAACTTTTAAATTGAAA
Found at i:104646 original size:21 final size:20
Alignment explanation
Indices: 104560--104717 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
104550 AAATGACCAA
**
104560 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
104579 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
104599 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
104619 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
104640 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
104661 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
104681 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
104702 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
104718 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:104746 original size:20 final size:20
Alignment explanation
Indices: 104684--104877 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
104674 CGATTTTCCA
* ** *
104684 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
104704 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
104724 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
104744 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
104764 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
104784 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
104804 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* ***
104824 AAATCGCAACG-ATAATAAAT
1 AAATCGCAACGCGT-ATCCGT
104844 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
104865 AAATCGCAACGCG
1 AAATCGCAACGCG
104878 ATATTTAAAG
Statistics
Matches: 144, Mismatches: 25, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
19 2 0.01
20 125 0.87
21 16 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:104768 original size:60 final size:60
Alignment explanation
Indices: 104684--104877 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
104674 CGATTTTCCA
* ** * * *
104684 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* * *** *
104744 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
* **
104804 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATAAATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAAT-AAATCGCAACGCGTATCCGT
104865 AAATCGCAACGCG
1 AAATCGCAACGCG
104878 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATAAATAAATCGCAACGCGTATCCGT
Found at i:105276 original size:33 final size:33
Alignment explanation
Indices: 105237--105307 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
105227 TTCACTTAGA
*
105237 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
105270 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
105303 TTTCA
1 TTTCA
105308 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:105431 original size:20 final size:19
Alignment explanation
Indices: 105387--105462 Score: 89
Period size: 20 Copynumber: 3.8 Consensus size: 19
105377 TGCAGAAGAG
*
105387 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-GAATG-AAA
**
105408 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAGAATGA-AA
105428 TCGCAACGAGAGAAATGAAA
1 TCGCAACGAGAG-AATGAAA
105448 TCGCAACGAGAGAAT
1 TCGCAACGAGAGAAT
105463 CGCAACGCGA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
19 4 0.08
20 28 0.58
21 16 0.33
ACGTcount: A:0.45, C:0.17, G:0.25, T:0.13
Consensus pattern (19 bp):
TCGCAACGAGAGAATGAAA
Found at i:105460 original size:40 final size:41
Alignment explanation
Indices: 105386--105462 Score: 138
Period size: 40 Copynumber: 1.9 Consensus size: 41
105376 TTGCAGAAGA
*
105386 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
105427 GTCGCAACGAGAGAAATG-AAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
105463 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 18 0.51
41 17 0.49
ACGTcount: A:0.44, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:105503 original size:19 final size:19
Alignment explanation
Indices: 105481--105578 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
105471 GAAACCAAAA
*
105481 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
105500 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
105514 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
105533 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* *
105547 TCTCGTTGCGATTGTCATT
1 TCGCGTTGCGATTTTCATT
105566 TCGCGTTGCGATT
1 TCGCGTTGCGATT
105579 CTCTCGTTAC
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:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:105522 original size:14 final size:14
Alignment explanation
Indices: 105503--105592 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
105493 TTTCATTTCG
105503 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
105517 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
105536 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
105550 CGTTGCGATTGTCATTTCG
1 CGTTGCGA-T-TC---TCT
105569 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
105583 CGTTACGATT
1 CGTTGCGATT
105593 TTCATTTCAA
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 29 0.48
15 1 0.02
16 5 0.08
17 5 0.08
18 1 0.02
19 20 0.33
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:105528 original size:33 final size:33
Alignment explanation
Indices: 105486--105600 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
105476 CAAAATCGCA
105486 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
105519 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
105552 TTGCGATTGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
105585 TTACGATTTTCATTTC
1 TTGCGATTTTCATTTC
105601 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:107458 original size:93 final size:93
Alignment explanation
Indices: 107299--107767 Score: 913
Period size: 93 Copynumber: 5.1 Consensus size: 93
107289 TAGATTGCTT
*
107299 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
107364 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
107392 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
107457 TTTGTCTTTATTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
107485 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
107550 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
107578 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
107643 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
107671 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
107736 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
107763 AGTAA
1 AGTAA
107768 TGCAATCCAT
Statistics
Matches: 373, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 367 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:107855 original size:19 final size:19
Alignment explanation
Indices: 107815--107943 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
107805 TAGTTTACTT
* *
107815 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
107835 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
107854 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
107873 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
107887 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
107906 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
107920 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
107939 TCGCA
1 TCGCA
107944 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:107894 original size:33 final size:32
Alignment explanation
Indices: 107851--107943 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
107841 CGCGAAACCA
**
107851 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
107883 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
107916 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
107944 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:107941 original size:52 final size:52
Alignment explanation
Indices: 107815--107943 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
107805 TAGTTTACTT
**
107815 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
107867 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
107920 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
107944 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:107961 original size:19 final size:19
Alignment explanation
Indices: 107939--108073 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
107929 GAAACCAAAA
*
107939 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
107958 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
107974 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
107991 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
108007 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
108024 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
108043 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
108063 TCGTGTTGCGA
1 TCGCGTTGCGA
108074 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:107980 original size:14 final size:14
Alignment explanation
Indices: 107961--108017 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
107951 TTTCATTTCG
107961 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
107975 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
107992 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
108008 CGTTGCGATT
1 CGTTGCGATT
108018 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:107986 original size:33 final size:33
Alignment explanation
Indices: 107944--108036 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
107934 CAAAATCGCA
*
107944 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
107977 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
108010 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
108037 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:110014 original size:14 final size:14
Alignment explanation
Indices: 109995--110030 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
109985 ATTGTTTAAT
109995 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
110009 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
110023 TGATTTGT
1 TGATTTGT
110031 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:110153 original size:19 final size:19
Alignment explanation
Indices: 110137--110234 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
110127 AAAAATGACT
110137 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
110156 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
110175 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
110189 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
110208 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
110228 ATCGCAA
1 ATCGCAA
110235 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:110266 original size:53 final size:53
Alignment explanation
Indices: 110137--110252 Score: 225
Period size: 53 Copynumber: 2.2 Consensus size: 53
110127 AAAAATGACT
110137 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
110189 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
110242 ATCGCAATGCG
1 ATCGCAATGCG
110253 TTTATAATTT
Statistics
Matches: 63, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:110305 original size:19 final size:19
Alignment explanation
Indices: 110281--110478 Score: 193
Period size: 19 Copynumber: 11.4 Consensus size: 19
110271 GATTCTCTCG
110281 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
110300 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
110319 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
*
110333 TTGTGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
110352 TTGCGATTTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
110371 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
110385 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
110404 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
110418 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
110438 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
*
110452 TTGGGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
110471 TTGCGATT
1 TTGCGATT
110479 CTCTCGTTGC
Statistics
Matches: 147, Mismatches: 11, Indels: 42
0.74 0.05 0.21
Matches are distributed among these distances:
14 28 0.19
16 23 0.16
17 20 0.14
18 3 0.02
19 61 0.41
20 12 0.08
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:110316 original size:52 final size:52
Alignment explanation
Indices: 110259--110492 Score: 306
Period size: 52 Copynumber: 4.6 Consensus size: 52
110249 TGCGTTTATA
110259 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
110311 ATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
*
110363 ATTTCGTATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATT-T-TC
* * * *
110417 GTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCA--T-G--TTGGGATTTTC
1 ATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
110463 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
110493 GTAATTTCCG
Statistics
Matches: 163, Mismatches: 10, Indels: 23
0.83 0.05 0.12
Matches are distributed among these distances:
46 9 0.06
47 13 0.08
48 9 0.06
49 2 0.01
50 1 0.01
51 3 0.02
52 100 0.61
53 17 0.10
54 9 0.06
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:110359 original size:85 final size:84
Alignment explanation
Indices: 110259--110478 Score: 293
Period size: 85 Copynumber: 2.6 Consensus size: 84
110249 TGCGTTTATA
110259 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
1 ATTTCGCATTGCGATT-TCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCG
*
110324 ATTCTCTCGTTGTGATTTTC
65 ATTCTCTCGTTGCGATTTTC
* * * * *
110344 ATTTCGCATTGCGATTT-TCATTTCG-TATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTG
1 ATTTCGCATTGCGATTTCTCGTTGCGAT-TTTC-ATT-TCGCATTGCGATTTTCATTTCGCATTG
110407 CGATTCTCTCGTTGCGATTTTC
63 CGATTCTCTCGTTGCGATTTTC
*
110429 ATTTCCGCATTGCGATTT-TCATGTTGGGATTTTCATTTCGCATTGCGATT
1 ATTT-CGCATTGCGATTTCTC--GTTGCGATTTTCATTTCGCATTGCGATT
110479 CTCTCGTTGC
Statistics
Matches: 116, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
82 1 0.01
83 9 0.08
84 4 0.03
85 66 0.57
86 26 0.22
87 3 0.03
88 6 0.05
89 1 0.01
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (84 bp):
ATTTCGCATTGCGATTTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA
TTCTCTCGTTGCGATTTTC
Found at i:110390 original size:14 final size:14
Alignment explanation
Indices: 110371--110425 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
110361 TCATTTCGTA
110371 TTGCGATTCTCTCG
1 TTGCGATTCTCTCG
*
110385 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
110402 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
110418 TTGCGATT
1 TTGCGATT
110426 TTCATTTCCG
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 14 0.41
16 7 0.21
17 7 0.21
19 6 0.18
ACGTcount: A:0.11, C:0.24, G:0.20, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:110500 original size:33 final size:33
Alignment explanation
Indices: 110259--110492 Score: 262
Period size: 33 Copynumber: 6.9 Consensus size: 33
110249 TGCGTTTATA
110259 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
*
110292 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTC
1 ATTTCGCATTGCGA--TTC-TCTCG--TTGCGATT-T-TC
* * * *
110332 GTTGT-G-ATTTTC-ATT-TCGCATTGCGATTTTC
1 ATT-TCGCA-TTGCGATTCTCTCGTTGCGATTTTC
*
110363 ATTTCGTATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
110396 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
1 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
* *
110429 ATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTC
1 ATTT-CGCATTGCGATTCTC-TCGTTGCGATTTTC
110463 ATTTCGCATTGCGATTCTCTCGTTGCGATT
1 ATTTCGCATTGCGATTCTCTCGTTGCGATT
110493 GTAATTTCCG
Statistics
Matches: 170, Mismatches: 15, Indels: 32
0.78 0.07 0.15
Matches are distributed among these distances:
30 1 0.01
31 8 0.05
32 6 0.04
33 94 0.55
34 29 0.17
35 6 0.04
36 4 0.02
37 2 0.01
38 8 0.05
39 3 0.02
40 8 0.05
41 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (33 bp):
ATTTCGCATTGCGATTCTCTCGTTGCGATTTTC
Found at i:111794 original size:20 final size:20
Alignment explanation
Indices: 111766--111975 Score: 228
Period size: 20 Copynumber: 10.5 Consensus size: 20
111756 AATTTTCAGT
* * * *
111766 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
111786 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
111806 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
111826 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
111846 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
111866 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
111886 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
111906 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
111926 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
111946 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
111966 GTTGCGATTT
1 GTTGCGATTT
111976 TGGAAAATCG
Statistics
Matches: 165, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
19 3 0.02
20 159 0.96
21 3 0.02
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:111992 original size:21 final size:21
Alignment explanation
Indices: 111962--112044 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
111952 ATTTATGTGT
*
111962 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
111983 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
112004 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
112025 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
112045 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:119621 original size:37 final size:38
Alignment explanation
Indices: 119566--119649 Score: 120
Period size: 37 Copynumber: 2.3 Consensus size: 38
119556 TGGTAACCAA
119566 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
* *
119603 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
*
119640 -GTTGAAAAAT
1 CTTTGAAAAAT
119650 GATAATGGGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 9 0.21
37 33 0.77
38 1 0.02
ACGTcount: A:0.33, C:0.05, G:0.19, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTGGTAAATGTTT
Found at i:124209 original size:37 final size:38
Alignment explanation
Indices: 124154--124237 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 38
124144 TGGTAACCAA
*
124154 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
* *
124191 CTTTGAAAAATA-GTTTTTCAAAGTTTAGTAGATGTTT
1 CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
*
124228 -GTTGAAAAAT
1 CTTTGAAAAAT
124238 GATAATGGGA
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
36 9 0.21
37 32 0.76
38 1 0.02
ACGTcount: A:0.35, C:0.05, G:0.18, T:0.43
Consensus pattern (38 bp):
CTTTGAAAAATATGGTTTTCAAAGTTTAGTAAATGTTT
Found at i:124966 original size:412 final size:412
Alignment explanation
Indices: 124202--125027 Score: 1598
Period size: 412 Copynumber: 2.0 Consensus size: 412
124192 TTTGAAAAAT
124202 AGTTTTTCAAAGTTTAGTAGATGTTTGTTGAAAAATGATAATGGGATAATCACAATTAATCCCTA
1 AGTTTTTCAAAGTTTAGTAGATGTTTGTTGAAAAATGATAATGGGATAATCACAATTAATCCCTA
*
124267 GACTTTAGGGTATTTACAAGATTAAGTCCTTAAGTTTCAACTATAAATACCCTAGCTCATTTAGT
66 GACTTTAGGGTATTTACAAGATTAAGTCCTTAAGTTTCAACTATAAATACCCTAGCTCATTTAGC
124332 TTCAAAACCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGTTTTCTTGTGAGTAGTGAG
131 TTCAAAACCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGTTTTCTTGTGAGTAGTGAG
*
124397 TATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCTGCAGCAGTCCGGAGACGTAAG
196 TATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCTGCAGCAATCCGGAGACGTAAG
124462 CACAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCTGCTTTTATTTCGTATTCTCA
261 CACAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCTGCTTTTATTTCGTATTCTCA
*
124527 CTAATCTGACTATAGGGAAATTACTTGTTACTCGTTTATTTCCTAACAGGAATATATAGCAAAAA
326 CTAATATGACTATAGGGAAATTACTTGTTACTCGTTTATTTCCTAACAGGAATATATAGCAAAAA
124592 GATGCCTTCTGGACACTCAAGA
391 GATGCCTTCTGGACACTCAAGA
*
124614 AGTTTTTCAAAGTTTGGTAGATGTTTGTTGAAAAATGATAATGGGATAATCACAATTAATCCCTA
1 AGTTTTTCAAAGTTTAGTAGATGTTTGTTGAAAAATGATAATGGGATAATCACAATTAATCCCTA
*
124679 GACTTTAGGGTATTTACAAGATTAAGTCCTTAAGTTTCAACTATAAATACCCTATCTCATTTAGC
66 GACTTTAGGGTATTTACAAGATTAAGTCCTTAAGTTTCAACTATAAATACCCTAGCTCATTTAGC
124744 TTCAAAACCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGTTTTCTTGTGAGTAGTGAG
131 TTCAAAACCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGTTTTCTTGTGAGTAGTGAG
*
124809 TGTTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCTGCAGCAATCCGGAGACGTAAG
196 TATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCTGCAGCAATCCGGAGACGTAAG
124874 CACAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCTGCTTTTATTTCGTATTCTCA
261 CACAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCTGCTTTTATTTCGTATTCTCA
124939 CTAATATGACTATAGGGAAATTACTTGTTACTCGTTTATTTCCTAACAGGAATATATAGCAAAAA
326 CTAATATGACTATAGGGAAATTACTTGTTACTCGTTTATTTCCTAACAGGAATATATAGCAAAAA
125004 GATGCCTTCTGGACACTCAAGA
391 GATGCCTTCTGGACACTCAAGA
125026 AG
1 AG
125028 ACCGGATGCA
Statistics
Matches: 408, Mismatches: 6, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
412 408 1.00
ACGTcount: A:0.31, C:0.17, G:0.16, T:0.36
Consensus pattern (412 bp):
AGTTTTTCAAAGTTTAGTAGATGTTTGTTGAAAAATGATAATGGGATAATCACAATTAATCCCTA
GACTTTAGGGTATTTACAAGATTAAGTCCTTAAGTTTCAACTATAAATACCCTAGCTCATTTAGC
TTCAAAACCATCCCAAAAATCATTTCTTTCTCCCAATACTAGAGAGTTTTCTTGTGAGTAGTGAG
TATTTTGTAAACACCTGTAAATTTTCTCTCTTAGTAAAAGATCTGCAGCAATCCGGAGACGTAAG
CACAATTGGCTGAACTCCGTTATCAATTTCGGGTATTATTTTTCTGCTTTTATTTCGTATTCTCA
CTAATATGACTATAGGGAAATTACTTGTTACTCGTTTATTTCCTAACAGGAATATATAGCAAAAA
GATGCCTTCTGGACACTCAAGA
Found at i:127722 original size:28 final size:27
Alignment explanation
Indices: 127657--127723 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
127647 CGTCTTGGTG
* *
127657 TAATTATTAATATTTTTTAATTTCATT
1 TAATTATTAATATTTTTTAATTTAAAT
*
127684 TCAATTTTTAATATTTTTATAA-TTAAAT
1 T-AATTATTAATATTTTT-TAATTTAAAT
127712 TAATTAATTAAT
1 TAATT-ATTAAT
127724 TTATATCGAG
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 5 0.15
28 25 0.76
29 3 0.09
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (27 bp):
TAATTATTAATATTTTTTAATTTAAAT
Found at i:137402 original size:19 final size:19
Alignment explanation
Indices: 137357--137403 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
137347 CCAAAATATG
137357 GTAAAAAT-AAAATTATTA
1 GTAAAAATAAAAATTATTA
*
137375 GTTATAAATAAAAATT-TTAA
1 G-TAAAAATAAAAATTATT-A
137395 GTAAAAATA
1 GTAAAAATA
137404 TAACAGAAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 1 0.04
19 15 0.62
20 8 0.33
ACGTcount: A:0.60, C:0.00, G:0.06, T:0.34
Consensus pattern (19 bp):
GTAAAAATAAAAATTATTA
Done.