Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009224.1 Hibiscus syriacus cultivar Beakdansim tig00112825_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: 67613
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:3299 original size:22 final size:22
Alignment explanation
Indices: 3274--3322 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
3264 CCACCATATG
3274 CACTAGGTATCATTTAGAGCTA
1 CACTAGGTATCATTTAGAGCTA
* * *
3296 CACTTGGTATCTTTTAGTGCTA
1 CACTAGGTATCATTTAGAGCTA
*
3318 AACTA
1 CACTA
3323 ATATGCAGCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (22 bp):
CACTAGGTATCATTTAGAGCTA
Found at i:15722 original size:30 final size:32
Alignment explanation
Indices: 15679--15764 Score: 117
Period size: 32 Copynumber: 2.8 Consensus size: 32
15669 GGACCTATCT
15679 ATATGT-TCTGAAGAACATAGGTAAT-TGTCC
1 ATATGTCTCTGAAGAACATAGGTAATATGTCC
15709 ATATGTCTC-GAAGAACATAGGTAATCATGTCC
1 ATATGTCTCTGAAGAACATAGGTAAT-ATGTCC
* *
15741 CTATGTC-CTGAAGGACATAGGTAA
1 ATATGTCTCTGAAGAACATAGGTAA
15765 CCCTCGACTC
Statistics
Matches: 50, Mismatches: 2, Indels: 6
0.86 0.03 0.10
Matches are distributed among these distances:
30 22 0.44
31 3 0.06
32 25 0.50
ACGTcount: A:0.34, C:0.16, G:0.21, T:0.29
Consensus pattern (32 bp):
ATATGTCTCTGAAGAACATAGGTAATATGTCC
Found at i:24021 original size:67 final size:67
Alignment explanation
Indices: 23937--24104 Score: 210
Period size: 67 Copynumber: 2.5 Consensus size: 67
23927 CCACCTTATT
* * ** * * * *
23937 CACTAAATGTTCTTACACACTACAGTGATATCCTGAATATGAAACATAAAGTCTTGCCCACCACC
1 CACTAAGTGTTCTTACACACTATAGTGATATCCCAAATATGAAACATAAAGACGTACCCACAACC
24002 TG
66 TG
* * *
24004 CACTAAGTGTTCTTACACACTATAGTGTTATCCCAAATATGACACATAAGGACGTACCCACAACC
1 CACTAAGTGTTCTTACACACTATAGTGATATCCCAAATATGAAACATAAAGACGTACCCACAACC
24069 TG
66 TG
* * *
24071 CACTAAGTGTCCTTAGACACTATAGTGCTATCCC
1 CACTAAGTGTTCTTACACACTATAGTGATATCCC
24105 TAGTATACAA
Statistics
Matches: 87, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
67 87 1.00
ACGTcount: A:0.33, C:0.27, G:0.13, T:0.27
Consensus pattern (67 bp):
CACTAAGTGTTCTTACACACTATAGTGATATCCCAAATATGAAACATAAAGACGTACCCACAACC
TG
Found at i:26252 original size:23 final size:23
Alignment explanation
Indices: 26222--26268 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
26212 GCTTGAAGAC
26222 AATTTCATGAA-ATTTCTACATTT
1 AATTTCATGAACATTTCT-CATTT
*
26245 AATTTCATGAACATTTGTCATTT
1 AATTTCATGAACATTTCTCATTT
26268 A
1 A
26269 TTTAACTTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 17 0.77
24 5 0.23
ACGTcount: A:0.34, C:0.13, G:0.06, T:0.47
Consensus pattern (23 bp):
AATTTCATGAACATTTCTCATTT
Found at i:29742 original size:7 final size:8
Alignment explanation
Indices: 29721--29746 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
29711 ATAATTTATC
29721 ATAAAAAT
1 ATAAAAAT
29729 ATAAAAAT
1 ATAAAAAT
29737 ATAAAAAT
1 ATAAAAAT
29745 AT
1 AT
29747 CTTGACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (8 bp):
ATAAAAAT
Found at i:39135 original size:112 final size:112
Alignment explanation
Indices: 38972--39192 Score: 376
Period size: 112 Copynumber: 2.0 Consensus size: 112
38962 ATTTTCTTAG
38972 CACAAGTTGATTCAGGATCTTAATATGGGTAAATTTCTTTCTTCCATACATGAACAAAACCTAGT
1 CACAAGTTGATTCAGGATCTTAATATGGGTAAATTTCTTTCTTCCATACATGAACAAAACCTAGT
*
39037 TGAACTC-TACGGTGGTTTGCGGTAATTAATGGTGGTTTGTGACATTTAA
66 TAAACTCTTAC-GTGG-TTGCGGTAATTAATGGTGG-TTGTGACATTTAA
*
39086 CACAAG-TGATTCAGGATCTTAATATGGG-AAATTTCTTTCTTCCATACATGAATAAAACCTAGT
1 CACAAGTTGATTCAGGATCTTAATATGGGTAAATTTCTTTCTTCCATACATGAACAAAACCTAGT
39149 TAAACTCTTACGTGGTTGCGGTAATTAATGGTGGTTGTGACATT
66 TAAACTCTTACGTGGTTGCGGTAATTAATGGTGGTTGTGACATT
39193 AATGTGGTAC
Statistics
Matches: 104, Mismatches: 2, Indels: 6
0.93 0.02 0.05
Matches are distributed among these distances:
110 10 0.10
111 19 0.18
112 44 0.42
113 25 0.24
114 6 0.06
ACGTcount: A:0.29, C:0.15, G:0.20, T:0.36
Consensus pattern (112 bp):
CACAAGTTGATTCAGGATCTTAATATGGGTAAATTTCTTTCTTCCATACATGAACAAAACCTAGT
TAAACTCTTACGTGGTTGCGGTAATTAATGGTGGTTGTGACATTTAA
Found at i:39825 original size:30 final size:32
Alignment explanation
Indices: 39765--39825 Score: 90
Period size: 30 Copynumber: 2.0 Consensus size: 32
39755 GAGTATAGTT
* *
39765 TAATGACTCCTGGTGTAAGTTACCCTTTTTCC
1 TAATGACTCATGGTGTAAGTTACACTTTTTCC
39797 TAATGAC-CATGGTGTAA-TTACACTTTTTC
1 TAATGACTCATGGTGTAAGTTACACTTTTTC
39826 TTTCTTCTCC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 11 0.41
31 9 0.33
32 7 0.26
ACGTcount: A:0.23, C:0.21, G:0.15, T:0.41
Consensus pattern (32 bp):
TAATGACTCATGGTGTAAGTTACACTTTTTCC
Found at i:41395 original size:317 final size:320
Alignment explanation
Indices: 40973--41563 Score: 1043
Period size: 321 Copynumber: 1.9 Consensus size: 320
40963 CTATCAAAGT
40973 CACTTGGCTCGGGCAAATACATGTTTGAATTATCTTATTTGTTTTTTTCGGTTTTACGCTAATCA
1 CACTTGGCTCGGGCAAATACATGTTTGAATTATCTTATTTGTTTTTTTCGGTTTTACGCTAATCA
*
41038 TATTCATTTGTTCCCCCGTCAGAGGAGGAGGATTAAATACATATTTTTTCTTAAAATTATCTAC-
66 TATTCATTTGTTCCCCCGTCAGAGGAGGAGGATTAAATACATATTTTATCTTAAAATTATCTACT
41102 TTTATTATTTTTAAAT-ATA-TTTATCTTAATTGTTTTTTTAGGTTTTACACTAATCATATTCGT
131 TTTATTATTTTTAAATAATATTTTATCTTAATTGTTTTTTTAGGTTTTACACTAATCATATTCGT
*
41165 TTTTATTGTTGTTATTG-TTATTA-TTTTTAAGGTTAGATTTGACATCAT-CCATCGATCAAGAT
196 TTTTATTGTTGTTATTGTTTATCATTTTTTAAGGTTAGATTTGACATCATACCATCGATCAAGAT
41227 GATAT-TATTATCATGAGATCACAACAGAAAAAACTCACTTTACTATCGAAGTCACTTGG
261 GATATATATTATCATGAGATCACAACAGAAAAAACTCACTTTACTATCGAAGTCACTTGG
*
41286 CACTTGGCTCGGGCAAAATACATGTTTGAATTATCTTATTTGTTTTTTTTTTGGTTTTACGCTAA
1 CACTTGGCTCGGGC-AAATACATGTTTGAATTATCTTATTTG--TTTTTTTCGGTTTTACGCTAA
41351 TCATATTCATTTTGTTCCCCCGTCAGAGGAGGAGGATTAAATACATATTTTATCTTAAAATTATC
63 TCATATTCA-TTTGTTCCCCCGTCAGAGGAGGAGGATTAAATACATATTTTATCTTAAAATTATC
41416 TACTTTTATTATTTTTAAATACATATTTTATCTTAATTGTTTTTTTAGGTTTTACACTAATCATA
127 TACTTTTATTATTTTTAAATA-ATATTTTATCTTAATTGTTTTTTTAGGTTTTACACTAATCATA
41481 TTCGTTTTTATTGTTGTTATTGTTTATCATTTTTTAAGGTTAGATTTGACATCATCACCATCGAT
191 TTCGTTTTTATTGTTGTTATTGTTTATCATTTTTTAAGGTTAGATTTGACATCAT-ACCATCGAT
*
41546 CAAGATGATGTATATTAT
255 CAAGATGATATATATTAT
41564 TATCATGCTT
Statistics
Matches: 261, Mismatches: 4, Indels: 13
0.94 0.01 0.05
Matches are distributed among these distances:
313 14 0.05
314 27 0.10
316 29 0.11
317 57 0.22
318 16 0.06
320 3 0.01
321 61 0.23
322 5 0.02
323 25 0.10
325 18 0.07
326 6 0.02
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.46
Consensus pattern (320 bp):
CACTTGGCTCGGGCAAATACATGTTTGAATTATCTTATTTGTTTTTTTCGGTTTTACGCTAATCA
TATTCATTTGTTCCCCCGTCAGAGGAGGAGGATTAAATACATATTTTATCTTAAAATTATCTACT
TTTATTATTTTTAAATAATATTTTATCTTAATTGTTTTTTTAGGTTTTACACTAATCATATTCGT
TTTTATTGTTGTTATTGTTTATCATTTTTTAAGGTTAGATTTGACATCATACCATCGATCAAGAT
GATATATATTATCATGAGATCACAACAGAAAAAACTCACTTTACTATCGAAGTCACTTGG
Found at i:42212 original size:20 final size:20
Alignment explanation
Indices: 42187--42279 Score: 96
Period size: 21 Copynumber: 4.5 Consensus size: 20
42177 TTTTCCCAAT
42187 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
42207 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGTAAA
42227 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGTAAA
* ** *
42248 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
42269 TCGCAATGCGA
1 TCGCAATGCGA
42280 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 27 0.47
21 31 0.53
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:42229 original size:41 final size:41
Alignment explanation
Indices: 42184--42279 Score: 183
Period size: 41 Copynumber: 2.3 Consensus size: 41
42174 CGATTTTCCC
42184 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
42225 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
1 AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
*
42266 AAATCGCAATGCGA
1 AATTCGCAATGCGA
42280 TACTGACTAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 54 1.00
ACGTcount: A:0.40, C:0.18, G:0.24, T:0.19
Consensus pattern (41 bp):
AATTCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGA
Found at i:42233 original size:21 final size:20
Alignment explanation
Indices: 42187--42279 Score: 96
Period size: 20 Copynumber: 4.5 Consensus size: 20
42177 TTTTCCCAAT
*
42187 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGGAAA
* **
42207 TCGCAACGCGAATTGGGAAA
1 TCGCAATGCGAATAAGGAAA
*
42227 TTCGCAATGCGAATAAGTAAA
1 -TCGCAATGCGAATAAGGAAA
* **
42248 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGG-AAA
42269 TCGCAATGCGA
1 TCGCAATGCGA
42280 TACTGACTAT
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 29 0.50
21 29 0.50
ACGTcount: A:0.39, C:0.18, G:0.25, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGGAAA
Found at i:42293 original size:20 final size:19
Alignment explanation
Indices: 42268--42378 Score: 66
Period size: 20 Copynumber: 5.7 Consensus size: 19
42258 AATTGGGAAA
*
42268 ATCGCAATGCGATACTGACT
1 ATCGCAATGCGATAAT-ACT
**
42288 ATCGCAATGCGATAATAAAAA
1 ATCGCAATGCGATAAT--ACT
*
42309 ATCGCAA--CGA-GATACT
1 ATCGCAATGCGATAATACT
* * *
42325 TTCGCAACGCGATACTGACT
1 ATCGCAATGCGATAAT-ACT
* *
42345 TTCGCAACGCGATAATACAT
1 ATCGCAATGCGATAATAC-T
42365 AATCGCAATGCGAT
1 -ATCGCAATGCGAT
42379 TTTCAAAGCG
Statistics
Matches: 71, Mismatches: 13, Indels: 13
0.73 0.13 0.13
Matches are distributed among these distances:
16 7 0.10
18 5 0.07
19 6 0.08
20 34 0.48
21 19 0.27
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.23
Consensus pattern (19 bp):
ATCGCAATGCGATAATACT
Found at i:42331 original size:16 final size:16
Alignment explanation
Indices: 42310--42340 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
42300 TAATAAAAAA
42310 TCGCAACGAGATACTT
1 TCGCAACGAGATACTT
*
42326 TCGCAACGCGATACT
1 TCGCAACGAGATACT
42341 GACTTTCGCA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (16 bp):
TCGCAACGAGATACTT
Found at i:42574 original size:22 final size:22
Alignment explanation
Indices: 42546--42589 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
42536 CACTCTCTCA
42546 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
42568 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
42590 TATCTAAATC
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:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:42858 original size:20 final size:20
Alignment explanation
Indices: 42833--42870 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42823 CGATTCTCTC
42833 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
42853 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
42871 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:44198 original size:18 final size:18
Alignment explanation
Indices: 44177--44221 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
44167 TCCACTTCGG
*
44177 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
44195 GAGCTATCACCTCACCTA
1 GAGCCATCACCTCACCCA
44213 GAGCCATCA
1 GAGCCATCA
44222 TCTGATCGAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.27, C:0.42, G:0.16, T:0.16
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:44741 original size:19 final size:20
Alignment explanation
Indices: 44687--44753 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
44677 TAGTTTACTT
* *
44687 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
44707 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
44727 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
44746 TCGCAACG
1 TCGCAACG
44754 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:44761 original size:14 final size:14
Alignment explanation
Indices: 44742--44799 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
44732 ATGCGAAATG
44742 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
44756 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
44772 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
44788 AAAATCGCAACG
1 AAAATCGCAACG
44800 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:44784 original size:32 final size:33
Alignment explanation
Indices: 44726--44816 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
44716 GGAAATGGCT
*
44726 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
44759 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
44791 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
44817 TGCGATTTGT
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:44810 original size:19 final size:19
Alignment explanation
Indices: 44687--44821 Score: 85
Period size: 19 Copynumber: 7.6 Consensus size: 19
44677 TAGTTTACTT
* **
44687 TCGCAACACGAAAATGACTA
1 TCGCAACGCG-AAATGAAAA
***
44707 TCGCAACGCGGAAATGGCTA
1 TCGCAACGC-GAAATGAAAA
*
44727 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
44746 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
44760 TCGCAACGCGAAATG-AAA
1 TCGCAACGCGAAATGAAAA
*
44778 TCGCAA--CG--A-CAAAA
1 TCGCAACGCGAAATGAAAA
44792 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
44811 TCGCAATGCGA
1 TCGCAACGCGA
44822 TTTGTGTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
14 20 0.22
15 1 0.01
16 6 0.07
17 2 0.02
18 11 0.12
19 27 0.29
20 24 0.26
21 1 0.01
ACGTcount: A:0.43, C:0.24, G:0.21, T:0.13
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:44891 original size:19 final size:19
Alignment explanation
Indices: 44828--44950 Score: 96
Period size: 20 Copynumber: 6.7 Consensus size: 19
44818 GCGATTTGTG
44828 TTTCGCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTCA
44846 TTTCGCGTTGCGA-TTT--
1 TTTCGCGTTGCGATTTTCA
*
44862 TGT--CGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTCA
* ***
44879 TTTCGCATTGCGATAGCCA
1 TTTCGCGTTGCGATTTTCA
**
44898 TTTCCGCGTTGCGATAGTCA
1 TTT-CGCGTTGCGATTTTCA
* *
44918 TTTCGCATTGCGATTTTAA
1 TTTCGCGTTGCGATTTTCA
*
44937 GTTTCGTGTTGCGA
1 -TTTCGCGTTGCGA
44951 AAGTAAACTA
Statistics
Matches: 84, Mismatches: 14, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 16 0.19
19 25 0.30
20 28 0.33
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.42
Consensus pattern (19 bp):
TTTCGCGTTGCGATTTTCA
Found at i:44948 original size:39 final size:36
Alignment explanation
Indices: 44811--44950 Score: 117
Period size: 39 Copynumber: 3.8 Consensus size: 36
44801 GAAATGAAAA
*
44811 TCGCAATGCGATTTGTGTTTCGCGTTGCGATTTCATT
1 TCGCATTGCGATTT-TGTTTCGCGTTGCGATTTCATT
*
44848 TCGCGTTGCGATTTTG--T--CGTTGCGATTTTCATT
1 TCGCATTGCGATTTTGTTTCGCGTTGCGA-TTTCATT
**** *
44881 TCGCATTGCGATAGCCATTTCCGCGTTGCGATAGTCATT
1 TCGCATTGCGAT-TTTGTTT-CGCGTTGCGAT-TTCATT
*
44920 TCGCATTGCGATTTTAAGTTTCGTGTTGCGA
1 TCGCATTGCGATTTT--GTTTCGCGTTGCGA
44951 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 13, Indels: 18
0.72 0.12 0.16
Matches are distributed among these distances:
32 8 0.10
33 18 0.22
34 1 0.01
36 3 0.04
37 12 0.15
38 1 0.01
39 34 0.43
40 3 0.04
ACGTcount: A:0.14, C:0.20, G:0.24, T:0.41
Consensus pattern (36 bp):
TCGCATTGCGATTTTGTTTCGCGTTGCGATTTCATT
Found at i:46805 original size:14 final size:14
Alignment explanation
Indices: 46786--46821 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
46776 ATTGTTTAAT
46786 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
46800 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
46814 TGATTTGT
1 TGATTTGT
46822 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:46947 original size:14 final size:15
Alignment explanation
Indices: 46928--47004 Score: 59
Period size: 14 Copynumber: 4.7 Consensus size: 15
46918 CGAAATGGCT
46928 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
*
46942 ATCGCAATGCGAAATGAA
1 ATCGCAA-GCGAGA--AA
46960 ATCGCAATGCGAAATGAAA
1 ATCGCAA-GCG--A-GAAA
46979 ATCGCAA-CGAGAAA
1 ATCGCAAGCGAGAAA
46993 ATCGCAATGCGA
1 ATCGCAA-GCGA
47005 TTTTCATTTC
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 18 0.35
15 1 0.02
16 7 0.13
17 2 0.04
18 13 0.25
19 9 0.17
20 1 0.02
21 1 0.02
ACGTcount: A:0.45, C:0.19, G:0.22, T:0.13
Consensus pattern (15 bp):
ATCGCAAGCGAGAAA
Found at i:46960 original size:19 final size:19
Alignment explanation
Indices: 46938--47004 Score: 92
Period size: 18 Copynumber: 3.8 Consensus size: 19
46928 ATCGCAACGA
46938 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
46957 G-AAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
46975 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
46989 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
47005 TTTTCATTTC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
14 11 0.25
15 1 0.02
16 2 0.05
17 2 0.05
18 18 0.41
19 10 0.23
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:47043 original size:19 final size:19
Alignment explanation
Indices: 46994--47035 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
46984 AACGAGAAAA
46994 TCGCAATGCGATTTTCATT
1 TCGCAATGCGATTTTCATT
47013 TCGCAATGCGATTTTCATT
1 TCGCAATGCGATTTTCATT
47032 TCGC
1 TCGC
47036 GTTGCGATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.19, C:0.24, G:0.17, T:0.40
Consensus pattern (19 bp):
TCGCAATGCGATTTTCATT
Found at i:47071 original size:15 final size:15
Alignment explanation
Indices: 47051--47081 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
47041 GATATTCTCG
47051 TTGCGATAACCATTT
1 TTGCGATAACCATTT
*
47066 TTGCGATAGCCATTT
1 TTGCGATAACCATTT
47081 T
1 T
47082 CACATTGCGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (15 bp):
TTGCGATAACCATTT
Found at i:47469 original size:14 final size:14
Alignment explanation
Indices: 47450--47485 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
47440 ATTGTTTAAT
47450 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
47464 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
47478 TGATTTGT
1 TGATTTGT
47486 TAATTGATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:48775 original size:24 final size:24
Alignment explanation
Indices: 48719--48777 Score: 73
Period size: 24 Copynumber: 2.5 Consensus size: 24
48709 AGTCAGTATT
* *
48719 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATATTGGTCAATACA
* *
48743 CGGACTTTGATATTGGTCAATACA
1 CGAAATTTGATATTGGTCAATACA
*
48767 CGAATTTTGAT
1 CGAAATTTGAT
48778 GATGTTTCAG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (24 bp):
CGAAATTTGATATTGGTCAATACA
Found at i:48968 original size:12 final size:12
Alignment explanation
Indices: 48951--48975 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
48941 ATATAATCCT
48951 GAAGAAGAAAAA
1 GAAGAAGAAAAA
48963 GAAGAAGAAAAA
1 GAAGAAGAAAAA
48975 G
1 G
48976 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:51311 original size:33 final size:33
Alignment explanation
Indices: 51264--51357 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
51254 GGAAATTACT
51264 ATCGCAATGAGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGAGAAATGAAAATCGCAACGAGAGA
* *
51297 ATCGCAATGTGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGAGAAATGAAAATCGCAACGAGAGA
*
51330 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGAGAAATGAAAATCGCAACG
51358 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGAGAAATGAAAATCGCAACGAGAGA
Found at i:51360 original size:19 final size:19
Alignment explanation
Indices: 51264--51361 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
51254 GGAAATTACT
*
51264 ATCGCAATGAGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
51283 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
*
51297 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
51316 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
51330 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
51349 ATCGCAACGCGAA
1 ATCGCAATGCGAA
51362 TTTAATTTCG
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
14 19 0.32
15 2 0.03
16 3 0.05
17 2 0.03
18 2 0.03
19 31 0.53
ACGTcount: A:0.45, C:0.17, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:51379 original size:19 final size:19
Alignment explanation
Indices: 51357--51419 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 19
51347 AAATCGCAAC
*
51357 GCGAATTTAATTTCGCGTT
1 GCGATTTTAATTTCGCGTT
*
51376 GCGATTTTCATTTTCGCGTT
1 GCGATTTT-AATTTCGCGTT
* *
51396 GCGATTTTCATTTCGCATT
1 GCGATTTTAATTTCGCGTT
51415 GCGAT
1 GCGAT
51420 AGTACTTTTT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
19 20 0.53
20 18 0.47
ACGTcount: A:0.16, C:0.19, G:0.21, T:0.44
Consensus pattern (19 bp):
GCGATTTTAATTTCGCGTT
Found at i:51392 original size:20 final size:19
Alignment explanation
Indices: 51366--51419 Score: 90
Period size: 20 Copynumber: 2.8 Consensus size: 19
51356 CGCGAATTTA
51366 ATTTCGCGTTGCGATTTTC
1 ATTTCGCGTTGCGATTTTC
51385 ATTTTCGCGTTGCGATTTTC
1 A-TTTCGCGTTGCGATTTTC
*
51405 ATTTCGCATTGCGAT
1 ATTTCGCGTTGCGAT
51420 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 14 0.42
20 19 0.58
ACGTcount: A:0.13, C:0.20, G:0.20, T:0.46
Consensus pattern (19 bp):
ATTTCGCGTTGCGATTTTC
Found at i:51545 original size:14 final size:14
Alignment explanation
Indices: 51526--51562 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
51516 CATCAATTAA
51526 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
51540 ACAAATCACCTTTT
1 ACAAATCAACTTTT
51554 ACAAATCAA
1 ACAAATCAA
51563 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:52981 original size:21 final size:21
Alignment explanation
Indices: 52915--52981 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
52905 GTGAATCGGG
*
52915 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
52935 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
52957 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
52978 CTCT
1 CTCT
52982 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:53000 original size:42 final size:41
Alignment explanation
Indices: 52915--53037 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
52905 GTGAATCGGG
* * * * *
52915 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
52957 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
52999 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
53038 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:55145 original size:19 final size:19
Alignment explanation
Indices: 55028--55212 Score: 174
Period size: 19 Copynumber: 10.1 Consensus size: 19
55018 GTCTTTGGTT
*
55028 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
55047 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
55067 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
55085 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
55101 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
55119 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
55134 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
*
55154 GAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
55173 GAAATGAAAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
55192 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
55211 GA
1 GA
55213 TTTTGGTTTC
Statistics
Matches: 138, Mismatches: 15, Indels: 26
0.77 0.08 0.15
Matches are distributed among these distances:
14 19 0.14
15 3 0.02
16 2 0.01
17 1 0.01
18 4 0.03
19 62 0.45
20 45 0.33
21 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:55166 original size:39 final size:38
Alignment explanation
Indices: 55028--55212 Score: 174
Period size: 33 Copynumber: 5.1 Consensus size: 38
55018 GTCTTTGGTT
* *
55028 GAAATGAAAATCGCAACGAGATAATGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGCGA-AATGAAAATCGCAACGC
** *
55067 GGAAATGACTATCGCAA--CG--A-GAGAATCGCAACGC
1 -GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
** * *
55101 GAAATGACTATCGCGAC-C---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
*
55134 GAAATGAAAATCGCAACCGCGAAATTAAAATCGCAACGC
1 GAAATGAAAATCGCAA-CGCGAAATGAAAATCGCAACGC
*
55173 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
55211 GA
1 GA
55213 TTTTGGTTTC
Statistics
Matches: 126, Mismatches: 12, Indels: 16
0.82 0.08 0.10
Matches are distributed among these distances:
33 42 0.33
34 16 0.13
35 2 0.02
38 24 0.19
39 28 0.22
40 14 0.11
ACGTcount: A:0.43, C:0.22, G:0.22, T:0.12
Consensus pattern (38 bp):
GAAATGAAAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:55241 original size:19 final size:19
Alignment explanation
Indices: 55208--55252 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
55198 AAAATCGCAA
*
55208 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGATTTCGCGT
*
55227 TGCGATTTTTATTTCGCGT
1 TGCGATTTTGATTTCGCGT
55246 TGCGATT
1 TGCGATT
55253 ATCTCGTTGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.09, C:0.16, G:0.27, T:0.49
Consensus pattern (19 bp):
TGCGATTTTGATTTCGCGT
Found at i:55886 original size:20 final size:20
Alignment explanation
Indices: 55801--55894 Score: 80
Period size: 20 Copynumber: 4.7 Consensus size: 20
55791 CGCTAAGTAA
*
55801 ATCGCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
* * *
55821 ATCGTGTTGCGAAAGTAAGT
1 ATCGCGTTGCGATAGTCAGT
* ** * *
55841 ATCTCGTTGCGATTTTTTATT
1 ATCGCGTTGCGA-TAGTCAGT
*
55862 ATCGCATTGCGATAGTCAGT
1 ATCGCGTTGCGATAGTCAGT
*
55882 ATCGCATTGCGAT
1 ATCGCGTTGCGAT
55895 TTTCCCAATT
Statistics
Matches: 58, Mismatches: 15, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
20 45 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.17, G:0.24, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGT
Found at i:55912 original size:21 final size:21
Alignment explanation
Indices: 55883--55957 Score: 89
Period size: 21 Copynumber: 3.6 Consensus size: 21
55873 ATAGTCAGTA
55883 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
55904 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
*
55924 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
55945 TCGCGTTGCGATT
1 TCGCATTGCGATT
55958 ACTTATTCGC
Statistics
Matches: 43, Mismatches: 10, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
20 16 0.37
21 27 0.63
ACGTcount: A:0.17, C:0.25, G:0.19, T:0.39
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:55971 original size:40 final size:41
Alignment explanation
Indices: 55883--55977 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
55873 ATAGTCAGTA
*
55883 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
55924 TCGCATTGCGAATTTCCCAATTCGCGTTGCGA-TTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
55964 TCGCATTGCGAATT
1 TCGCATTGCGAATT
55978 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
40 22 0.42
41 31 0.58
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.39
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:59585 original size:5 final size:5
Alignment explanation
Indices: 59575--59601 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
59565 TACTTATGAA
59575 AGAAG AGAAG AGAAG AGAAG AGAAG AG
1 AGAAG AGAAG AGAAG AGAAG AGAAG AG
59602 GCAAAGAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (5 bp):
AGAAG
Found at i:66910 original size:3 final size:3
Alignment explanation
Indices: 66892--66929 Score: 60
Period size: 3 Copynumber: 12.7 Consensus size: 3
66882 TTTACAAAAA
66892 TAT TAT TAAT TA- TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
66930 AAAAAATGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 28 0.85
4 3 0.09
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:67286 original size:3 final size:3
Alignment explanation
Indices: 67239--67271 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
67229 TTATATTAAA
*
67239 ATT A-T ATT ATT ATT ATT ATT AAT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
67272 ATGTTACATA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Done.