Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009212.1 Hibiscus syriacus cultivar Beakdansim tig00112799_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: 55421
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:10590 original size:25 final size:25
Alignment explanation
Indices: 10552--10675 Score: 216
Period size: 25 Copynumber: 5.0 Consensus size: 25
10542 AGTTAGGGGA
*
10552 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
10576 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
10601 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
10626 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
10651 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
10676 GGGTTGGTTC
Statistics
Matches: 97, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
24 9 0.09
25 88 0.91
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:10802 original size:3 final size:3
Alignment explanation
Indices: 10794--10860 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
10784 GCAAAAATTG
* **
10794 TAA TAA TAAA TAA TAA TAA -AA TAA TAA -GA TAA CGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
10838 TAA TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA
10861 CGGACAAAAC
Statistics
Matches: 54, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 5 0.09
3 46 0.85
4 3 0.06
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:10852 original size:35 final size:35
Alignment explanation
Indices: 10794--10862 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
10784 GCAAAAATTG
*
10794 TAATAATAAATAATAATAAAATAATAAGATAACGA
1 TAATAATAAATAATAATAAAATAATAAAATAACGA
10829 TAATAAT-AATAATAATAATAATAATAAAATAACG
1 TAATAATAAATAATAATAA-AATAATAAAATAACG
10863 GACAAAACCC
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
34 11 0.34
35 21 0.66
ACGTcount: A:0.65, C:0.03, G:0.04, T:0.28
Consensus pattern (35 bp):
TAATAATAAATAATAATAAAATAATAAAATAACGA
Found at i:11866 original size:31 final size:31
Alignment explanation
Indices: 11831--11942 Score: 197
Period size: 31 Copynumber: 3.6 Consensus size: 31
11821 TCCGTAGATT
* *
11831 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
11862 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
11893 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
11924 CCAAAGAACATAGGTAAAC
1 CCGAAGAACATAGGTAAAC
11943 CCTCAACCCT
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.39, C:0.23, G:0.19, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:12886 original size:21 final size:21
Alignment explanation
Indices: 12835--12886 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
12825 AGGGGTATCG
* *
12835 ATTCCCCATTGAATGTGTACCT
1 ATTCCCC-TTGAATGGGTACCC
12857 ATT-CCCTTGAATGGGTACCC
1 ATTCCCCTTGAATGGGTACCC
12877 ATTCCCCTTG
1 ATTCCCCTTG
12887 CCCAGAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 15 0.56
21 9 0.33
22 3 0.11
ACGTcount: A:0.19, C:0.31, G:0.15, T:0.35
Consensus pattern (21 bp):
ATTCCCCTTGAATGGGTACCC
Found at i:13785 original size:11 final size:11
Alignment explanation
Indices: 13751--13786 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
13741 CATGAATTCA
13751 GCTGCATTATT
1 GCTGCATTATT
*
13762 GCAGCACTTATT
1 GCTGCA-TTATT
13774 GCTGCATTATT
1 GCTGCATTATT
13785 GC
1 GC
13787 ATCCCGTGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
11 12 0.55
12 10 0.45
ACGTcount: A:0.19, C:0.22, G:0.19, T:0.39
Consensus pattern (11 bp):
GCTGCATTATT
Found at i:14014 original size:8 final size:9
Alignment explanation
Indices: 13984--14021 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
13974 GAGGTAAGTT
13984 TTTTAATTA
1 TTTTAATTA
13993 TTTTAATTA
1 TTTTAATTA
*
14002 GTTT-ATTA
1 TTTTAATTA
14010 TTTTAAATTA
1 TTTT-AATTA
14020 TT
1 TT
14022 AGTTTGTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 12 0.48
10 6 0.24
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (9 bp):
TTTTAATTA
Found at i:14142 original size:28 final size:27
Alignment explanation
Indices: 14103--14155 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
14093 TATATTAAAA
14103 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
14131 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
14156 TAAATAGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.32, C:0.02, G:0.17, T:0.49
Consensus pattern (27 bp):
AATAATTAATTAGTGTGTAGTTAGTCT
Found at i:14161 original size:27 final size:29
Alignment explanation
Indices: 14102--14166 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
14092 ATATATTAAA
14102 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
14131 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
14157 AAATAGTTAA
1 AAATAATTAA
14167 ATTATATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
26 1 0.03
27 16 0.50
28 15 0.47
ACGTcount: A:0.37, C:0.02, G:0.15, T:0.46
Consensus pattern (29 bp):
AAATAATTAATTAGTGTGTTAGTTAGTCT
Found at i:14384 original size:21 final size:21
Alignment explanation
Indices: 14359--14398 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
14349 GTTAATTAGT
14359 TTGTTAGTTTAAGTTATATTA
1 TTGTTAGTTTAAGTTATATTA
14380 TTGTTAGTTTAAGTTATAT
1 TTGTTAGTTTAAGTTATAT
14399 CATATAGAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (21 bp):
TTGTTAGTTTAAGTTATATTA
Found at i:14601 original size:29 final size:29
Alignment explanation
Indices: 14546--14602 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
14536 GCAGAGACTT
**
14546 CAAGCTCGCCCGGATGCCATGGTGACCTC
1 CAAGCTCGCCCGGATGCCATGACGACCTC
* *
14575 CAAGGTCGCCCGGATGGCATGACGACCT
1 CAAGCTCGCCCGGATGCCATGACGACCT
14603 ACGGCAACAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.19, C:0.35, G:0.30, T:0.16
Consensus pattern (29 bp):
CAAGCTCGCCCGGATGCCATGACGACCTC
Found at i:23080 original size:27 final size:27
Alignment explanation
Indices: 23050--23110 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 27
23040 TCGGTTAATC
* * *
23050 AACCGATTTTGAAATAAATTAACCGTT
1 AACCGATTATAAAAAAAATTAACCGTT
23077 AACCGAATTATAAAAAAAATTAACCGTT
1 AACCG-ATTATAAAAAAAATTAACCGTT
23105 AACCGA
1 AACCGA
23111 CCGAATTAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 6 0.20
28 24 0.80
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.26
Consensus pattern (27 bp):
AACCGATTATAAAAAAAATTAACCGTT
Found at i:23304 original size:21 final size:23
Alignment explanation
Indices: 23257--23301 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
23247 TTTGAAAATT
* *
23257 TTATCTGAATAATATTTTTTTACA
1 TTATCTAAATAATATCTTTTTA-A
23281 TTATCTAAATAATA-CTTTTTA
1 TTATCTAAATAATATCTTTTTA
23302 TTAAAATAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 6 0.32
24 13 0.68
ACGTcount: A:0.36, C:0.09, G:0.02, T:0.53
Consensus pattern (23 bp):
TTATCTAAATAATATCTTTTTAA
Found at i:25097 original size:26 final size:24
Alignment explanation
Indices: 25066--25143 Score: 68
Period size: 27 Copynumber: 3.0 Consensus size: 24
25056 TTAATATTTC
25066 TAATAATAAATATTATATTTTTAA
1 TAATAATAAATATTATATTTTTAA
*
25090 TATTATAATAAAATAATCAATTATTTTATAA
1 TA--ATAAT-AAAT-AT-TA-TATTTT-TAA
25121 TAAT-ATAAGATATTATATTTTTA
1 TAATAATAA-ATATTATATTTTTA
25144 TTTTAATAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 16
0.71 0.03 0.26
Matches are distributed among these distances:
24 4 0.09
25 6 0.14
26 6 0.14
27 8 0.18
28 6 0.14
29 3 0.07
30 6 0.14
31 5 0.11
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (24 bp):
TAATAATAAATATTATATTTTTAA
Found at i:25623 original size:14 final size:14
Alignment explanation
Indices: 25586--25624 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
25576 CAAACATCGT
*
25586 AAAACGTTTTCCTG
1 AAAACGTTTTCCGG
**
25600 AAAATATTTTCCGG
1 AAAACGTTTTCCGG
25614 AAAACGTTTTC
1 AAAACGTTTTC
25625 AGTAACAAAC
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (14 bp):
AAAACGTTTTCCGG
Found at i:28184 original size:20 final size:21
Alignment explanation
Indices: 28159--28210 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
28149 TTTTCCCAAT
*
28159 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
28179 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
28200 TCGCAATGCGA
1 TCGCAATGCGA
28211 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:28224 original size:20 final size:20
Alignment explanation
Indices: 28199--28312 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
28189 AATTGGGAAA
*
28199 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
28219 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
28239 ATCACAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
28260 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
28280 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
28300 TTCGCAACGCGAT
1 ATCGCAACGCGAT
28313 TTACATAGCG
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:28312 original size:61 final size:61
Alignment explanation
Indices: 28196--28312 Score: 153
Period size: 61 Copynumber: 1.9 Consensus size: 61
28186 GCGAATTGGG
* * * * *
28196 AAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACTATCACAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
* * * *
28257 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGAT
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGAT
28313 TTACATAGCG
Statistics
Matches: 47, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 47 1.00
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.24
Consensus pattern (61 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACTATCACAACGCGATAATAC
Found at i:28902 original size:18 final size:19
Alignment explanation
Indices: 28864--28907 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
28854 GCAACGAGAG
*
28864 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAACAAA
*
28883 AA-CGCAACGCGAAACCAA
1 AATCGCAACGCGAAACAAA
28901 AATCGCA
1 AATCGCA
28908 TTGCGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.50, C:0.27, G:0.16, T:0.07
Consensus pattern (19 bp):
AATCGCAACGCGAAACAAA
Found at i:28944 original size:19 final size:19
Alignment explanation
Indices: 28903--29013 Score: 99
Period size: 19 Copynumber: 6.1 Consensus size: 19
28893 GAAACCAAAA
*
28903 TCGCATTGCGATTTTCA-T
1 TCGCGTTGCGATTTTCATT
28921 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
28940 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
28954 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
* *
28973 TCGCATTGCGATTCTCATT
1 TCGCGTTGCGATTTTCATT
* *
28992 ATCTCGTTGCGATTTTTATT
1 -TCGCGTTGCGATTTTCATT
29012 TC
1 TC
29014 AACCAAAAGA
Statistics
Matches: 75, Mismatches: 11, Indels: 13
0.76 0.11 0.13
Matches are distributed among these distances:
14 10 0.13
16 2 0.03
17 3 0.04
18 16 0.21
19 29 0.39
20 15 0.20
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:29013 original size:39 final size:36
Alignment explanation
Indices: 28903--29013 Score: 120
Period size: 33 Copynumber: 3.1 Consensus size: 36
28893 GAAACCAAAA
*
28903 TCGCATTGCGATTTTCATTCGCGTTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATTCTCGTTGCGATTTTCATT
* **
28940 TCGCGTTGCGA-TTC--TCTCGTTGCGATAGTCATT
1 TCGCATTGCGATTTCATTCTCGTTGCGATTTTCATT
*
28973 TCGCATTGCGATTCTCATTATCTCGTTGCGATTTTTATT
1 TCGCATTGCGATT-TCA-T-TCTCGTTGCGATTTTCATT
29012 TC
1 TC
29014 AACCAAAAGA
Statistics
Matches: 60, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
33 26 0.43
34 1 0.02
35 5 0.08
37 10 0.17
39 18 0.30
ACGTcount: A:0.14, C:0.23, G:0.19, T:0.45
Consensus pattern (36 bp):
TCGCATTGCGATTTCATTCTCGTTGCGATTTTCATT
Found at i:31063 original size:42 final size:42
Alignment explanation
Indices: 31001--31123 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 42
30991 GCCCGACTCG
* * *
31001 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * * *
31043 CCTATCATTCCTCGATAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
* * ** * *
31085 ACTGTCATCGTTGAAGAGGTCC-CTCCCACCATTCAAGAG
1 CCTATCATCCCTCAAGA-GTCCACTCCCACCGTTCAAGAG
31124 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
42 60 0.94
43 4 0.06
ACGTcount: A:0.23, C:0.37, G:0.17, T:0.24
Consensus pattern (42 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
Found at i:31122 original size:21 final size:20
Alignment explanation
Indices: 31063--31123 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
31053 CTCGATAGTC
31063 CCCTCCCACCGTTCAAGAGG
1 CCCTCCCACCGTTCAAGAGG
** * *
31083 CCACTGTCATCGTTGAAGAGG
1 CC-CTCCCACCGTTCAAGAGG
*
31104 TCCCTCCCACCATTCAAGAG
1 -CCCTCCCACCGTTCAAGAG
31124 CCCGATTCAC
Statistics
Matches: 30, Mismatches: 9, Indels: 3
0.71 0.21 0.07
Matches are distributed among these distances:
20 2 0.07
21 26 0.87
22 2 0.07
ACGTcount: A:0.23, C:0.38, G:0.20, T:0.20
Consensus pattern (20 bp):
CCCTCCCACCGTTCAAGAGG
Found at i:32520 original size:14 final size:14
Alignment explanation
Indices: 32478--32514 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
32468 TATTGTTTAA
*
32478 TTGATTTGTAAAAG
1 TTGATTTGTAAAAT
*
32492 GTGATTTGTAAAAT
1 TTGATTTGTAAAAT
32506 TTGATTTGT
1 TTGATTTGT
32515 TTAATTGATG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.49
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:32715 original size:19 final size:19
Alignment explanation
Indices: 32693--32843 Score: 71
Period size: 19 Copynumber: 8.7 Consensus size: 19
32683 CGAAATTAAA
32693 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32712 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
32727 -CCCCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
32745 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
32759 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
32778 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
32793 -TCTCGTTGTGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
32811 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
32830 TTCTGCGTTGCGAT
1 TTC-GCGTTGCGAT
32844 AGACATTAAG
Statistics
Matches: 93, Mismatches: 23, Indels: 31
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.06
17 6 0.06
19 45 0.48
20 9 0.10
ACGTcount: A:0.15, C:0.22, G:0.21, T:0.42
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:32739 original size:33 final size:32
Alignment explanation
Indices: 32697--32823 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
32687 ATTAAATTCG
32697 CGTTGCGATTTTCATTTCGCATTGCGATTCCCC
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCC
**
32730 CGTTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCC
*
32763 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CC
*
32796 CGTTGTGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
32824 AGTAATTTCT
Statistics
Matches: 85, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
31 3 0.04
33 79 0.93
35 3 0.04
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCC
Found at i:32786 original size:66 final size:66
Alignment explanation
Indices: 32690--32822 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
32680 ACGCGAAATT
*
32690 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCCCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCCCGTTGCGATTTTCATTTCGCATTGC
32755 G
66 G
* * *
32756 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGTGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCCCGTTGCGATTTTCATTTCGCATTGC
32821 G
66 G
32822 A
1 A
32823 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.23, G:0.20, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCCCGTTGCGATTTTCATTTCGCATTGC
G
Found at i:35132 original size:12 final size:12
Alignment explanation
Indices: 35115--35139 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
35105 TCTTCGGGGA
35115 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35127 CTTTTTCTTCTT
1 CTTTTTCTTCTT
35139 C
1 C
35140 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:35348 original size:24 final size:24
Alignment explanation
Indices: 35314--35367 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
35304 CTGAAACATC
* *
35314 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
35338 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
35362 ATCAAA
1 ATCAAA
35368 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:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:36449 original size:20 final size:20
Alignment explanation
Indices: 36424--36481 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
36414 ATTCATTTGA
36424 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
36444 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
*
36464 CTATCGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
36482 CGCAATGCGA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:36541 original size:19 final size:19
Alignment explanation
Indices: 36500--36567 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
36490 GAAATGAAAA
36500 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
36516 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36533 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
36552 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
36568 TCATTGTGAT
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:36573 original size:33 final size:33
Alignment explanation
Indices: 36531--36596 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
36521 GCGATTTTCA
***
36531 TTTCGCATTGCGATTTTCATTTCGCATTGCGAT
1 TTTCGCATTGCGATAGCCATTTCGCATTGCGAT
* * *
36564 TTTCTCATTGTGATAGCCATTTCGCGTTGCGAT
1 TTTCGCATTGCGATAGCCATTTCGCATTGCGAT
36597 AGTCTGTTTT
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.15, C:0.21, G:0.20, T:0.44
Consensus pattern (33 bp):
TTTCGCATTGCGATAGCCATTTCGCATTGCGAT
Found at i:36703 original size:14 final size:14
Alignment explanation
Indices: 36684--36720 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
36674 CATCAATTAA
36684 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
36698 ACAAATCATCTTTT
1 ACAAATCAACATTT
36712 ACAAATCAA
1 ACAAATCAA
36721 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:38611 original size:19 final size:19
Alignment explanation
Indices: 38586--38671 Score: 111
Period size: 19 Copynumber: 4.5 Consensus size: 19
38576 CGAAACTTAA
38586 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
38605 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
38625 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
38644 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
38662 AATCGCAACG
1 AATCGCAACG
38672 ACAAAATCGC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
18 10 0.17
19 32 0.54
20 17 0.29
ACGTcount: A:0.40, C:0.23, G:0.23, T:0.14
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:38630 original size:39 final size:38
Alignment explanation
Indices: 38587--38660 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
38577 GAAACTTAAA
**
38587 ATCGCAACGCGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
38626 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
38661 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:38719 original size:19 final size:18
Alignment explanation
Indices: 38697--38792 Score: 91
Period size: 19 Copynumber: 5.7 Consensus size: 18
38687 GAAACACAAA
38697 TCGCATTGCGATTTCCATT
1 TCGCATTGCGATTT-CATT
* *
38716 TCGCGTTGCGATTT--TG
1 TCGCATTGCGATTTCATT
38732 TCG--TTGCGATTTCATT
1 TCGCATTGCGATTTCATT
*
38748 TCGCATTGCGATTT--TG
1 TCGCATTGCGATTTCATT
38764 TCG--TTGCGATTTTCATT
1 TCGCATTGCGA-TTTCATT
38781 TCGCATTGCGAT
1 TCGCATTGCGAT
38793 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 10 0.16
19 19 0.30
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (18 bp):
TCGCATTGCGATTTCATT
Found at i:38738 original size:14 final size:14
Alignment explanation
Indices: 38719--38776 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
38709 TTCCATTTCG
38719 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
38733 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
38749 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
38765 CGTTGCGATTTT
1 CGTTGCGATTTT
38777 CATTTCGCAT
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:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:38757 original size:32 final size:32
Alignment explanation
Indices: 38702--38792 Score: 155
Period size: 32 Copynumber: 2.8 Consensus size: 32
38692 ACAAATCGCA
*
38702 TTGCGATTTCCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTT-CATTTCGCATTGCGATTTTGTCG
38735 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTCATTTCGCATTGCGATTTTGTCG
38767 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGA-TTTCATTTCGCATTGCGAT
38793 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 28 0.50
33 28 0.50
ACGTcount: A:0.12, C:0.20, G:0.22, T:0.46
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCATTGCGATTTTGTCG
Found at i:38811 original size:20 final size:19
Alignment explanation
Indices: 38777--38831 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
38767 TTGCGATTTT
*
38777 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
38796 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
38816 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
38832 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:39339 original size:18 final size:18
Alignment explanation
Indices: 39310--39357 Score: 78
Period size: 18 Copynumber: 2.7 Consensus size: 18
39300 CGGGTCGATC
39310 AGATGATGGCTCTGGGTG
1 AGATGATGGCTCTGGGTG
* *
39328 AGGTGATAGCTCTGGGTG
1 AGATGATGGCTCTGGGTG
39346 AGATGATGGCTC
1 AGATGATGGCTC
39358 CCGAAGTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.19, C:0.12, G:0.42, T:0.27
Consensus pattern (18 bp):
AGATGATGGCTCTGGGTG
Found at i:40717 original size:20 final size:20
Alignment explanation
Indices: 40675--40717 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
40665 AATAGTTTCT
*
40675 GAAAATGAAAATCGTAACAC
1 GAAAATGAAAATCGCAACAC
*
40695 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
40715 GAA
1 GAA
40718 TTCGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.53, C:0.16, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:41252 original size:20 final size:20
Alignment explanation
Indices: 41226--41339 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
41216 GATTATGTAT
41226 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41246 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41266 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
41286 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
41307 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
41327 TATCGCATTGCGA
1 TATCGCGTTGCGA
41340 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 15, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 65 0.83
21 13 0.17
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:41343 original size:41 final size:41
Alignment explanation
Indices: 41206--41341 Score: 148
Period size: 41 Copynumber: 3.3 Consensus size: 41
41196 CGCTTTGAAA
* *
41206 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * * *
41247 ATCGCGTTGCGA-AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
* * * * *
41287 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
41328 ATCGCATTGCGATT
1 ATCGCATTGCGATT
41342 TTCCCAATTC
Statistics
Matches: 75, Mismatches: 19, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.43
41 43 0.57
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTATTTATTATCGCGTTGCGAAAGTCAGT
Found at i:41359 original size:41 final size:41
Alignment explanation
Indices: 41206--41361 Score: 109
Period size: 41 Copynumber: 3.8 Consensus size: 41
41196 CGCTTTGAAA
* ** * * * *
41206 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* *** * *
41247 ATCGCGTTGCGAAAGT-CAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
* * ** * * *
41287 ATCTCGTTGCGATTTTTTATTATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
41328 ATCGCATTGCGATTTTCCCAAT-TCGCGTTGCGAT
1 ATCGCATTGCGATTTT-CCAATATCGCGTTGCGAT
41362 TTACTTATTC
Statistics
Matches: 90, Mismatches: 23, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
40 32 0.36
41 56 0.62
42 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.34
Consensus pattern (41 bp):
ATCGCATTGCGATTTTCCAATATCGCGTTGCGATAGTAAGT
Found at i:46310 original size:18 final size:18
Alignment explanation
Indices: 46287--46326 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
46277 TGACCGGTCC
*
46287 GACCCGACCTGACCCGTT
1 GACCCGACCCGACCCGTT
*
46305 GACCCGACCCGACCTGTT
1 GACCCGACCCGACCCGTT
46323 GACC
1 GACC
46327 GTTGACCACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.45, G:0.23, T:0.15
Consensus pattern (18 bp):
GACCCGACCCGACCCGTT
Found at i:47437 original size:117 final size:117
Alignment explanation
Indices: 47231--47524 Score: 516
Period size: 117 Copynumber: 2.5 Consensus size: 117
47221 GAAGTATTTA
* *
47231 AGGCTCCTCGACTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTTTGGG
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGG
47296 AAACCTACACATTTTGGTGATTGGAGTGATTGGATGAGAAAGTTATTACCGC
66 AAACCTACACATTTTGGTGATTGGAGTGATTGGATGAGAAAGTTATTACCGC
* *
47348 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCATTACTGGTGTGCATGTGGGTGTATGGTTATGGG
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGG
* *
47413 GAACCTACACATTTTGGTGATTGGAGTGATTGGATGGGAAAGTTATTACCGC
66 AAACCTACACATTTTGGTGATTGGAGTGATTGGATGAGAAAGTTATTACCGC
* *
47465 AGGCTCCTCGGCTTTATGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGTGTGTATGGTT
1 AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTT
47525 CTGGAAAATA
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
117 167 1.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.33
Consensus pattern (117 bp):
AGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTATGGG
AAACCTACACATTTTGGTGATTGGAGTGATTGGATGAGAAAGTTATTACCGC
Found at i:53654 original size:12 final size:13
Alignment explanation
Indices: 53629--53657 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
53619 CAATTAACCC
53629 GACCCGACCCGTT
1 GACCCGACCCGTT
53642 GACCCGA-CCGTT
1 GACCCGACCCGTT
53654 GACC
1 GACC
53658 ACATTTGACC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.17, C:0.45, G:0.24, T:0.14
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:54767 original size:117 final size:117
Alignment explanation
Indices: 54554--54849 Score: 493
Period size: 117 Copynumber: 2.5 Consensus size: 117
54544 GGAAGTATTT
* * *
54554 CAGGCTCCACGACTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGAGTGTATGGTTCTGG
1 CAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
54619 GGAACCTACACATTTTGGTGATTAGAGTGATTGGATGGGAAAGTTAGTACTG
66 GGAACCTACACATTTTGGTGATTAGAATGATTGGATGGGAAAGTTAGTACCG
* *
54671 CAGGCTCCTCGGCTTTGTGCTTAGGGTAAGTCTTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
1 CAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
* *
54736 GGAACCTACACATTTTGGTGATTGGAATGATTGGATGGGAAAGTTATTACCG
66 GGAACCTACACATTTTGGTGATTAGAATGATTGGATGGGAAAGTTAGTACCG
* *
54788 CAGGCTCCTCGGCTTTATGCTCAGGGTAAGTCCTTATTGGTGTGCAGGTGGGTGTATGGTTC
1 CAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTC
54850 CGGAAAATAT
Statistics
Matches: 166, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
117 166 1.00
ACGTcount: A:0.19, C:0.16, G:0.33, T:0.32
Consensus pattern (117 bp):
CAGGCTCCTCGGCTTTGTGCTCAGGGTAAGTCCTTACTGGTGTGCAGGTGGGTGTATGGTTCTGG
GGAACCTACACATTTTGGTGATTAGAATGATTGGATGGGAAAGTTAGTACCG
Done.