Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001882.1 Hibiscus syriacus cultivar Beakdansim tig00003822_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: 81714
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:15565 original size:68 final size:68
Alignment explanation
Indices: 15464--15590 Score: 166
Period size: 67 Copynumber: 1.9 Consensus size: 68
15454 TACGGTTTAT
* * ** *
15464 TTTTTATCACAAATTCTTCGACTGAGTTGATATTTTTTATATCAACTCAGAACGAAGTTTAGAAA
1 TTTTCATCACAAATTCTTCGACCGAGTTGATA-TTTAGATATCAACTCAGAACAAAGTTTAGAAA
15529 TAAA
65 TAAA
* * *
15533 TTTTCATCGCAAATTCTT-TACCGAGTTGATATTTAGATATCAACTCGGAACAAAGTTT
1 TTTTCATCACAAATTCTTCGACCGAGTTGATATTTAGATATCAACTCAGAACAAAGTTT
15591 CAGTATTAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
67 23 0.46
68 11 0.22
69 16 0.32
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.39
Consensus pattern (68 bp):
TTTTCATCACAAATTCTTCGACCGAGTTGATATTTAGATATCAACTCAGAACAAAGTTTAGAAAT
AAA
Found at i:19036 original size:2 final size:2
Alignment explanation
Indices: 19025--19058 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
19015 TGAGGCGTTT
19025 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19059 TTTGTACTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:21003 original size:14 final size:14
Alignment explanation
Indices: 20980--21009 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
20970 ATGAGAACAA
20980 GATATCATCTATGT
1 GATATCATCTATGT
*
20994 GATATGATCTATGT
1 GATATCATCTATGT
21008 GA
1 GA
21010 CCATATGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (14 bp):
GATATCATCTATGT
Found at i:21266 original size:32 final size:31
Alignment explanation
Indices: 21230--21408 Score: 236
Period size: 31 Copynumber: 5.7 Consensus size: 31
21220 ACCTGTGTTC
* *
21230 TTCGGAACATATGAACAAGATTACCTATGTCT
1 TTCGGGACATATGGAC-AGATTACCTATGTCT
*
21262 TTCGGGATATATGGACATGATTACCTATGTCT
1 TTCGGGACATATGGACA-GATTACCTATGTCT
*
21294 TTCGGGACATATGGACATATTACCTATGTCT
1 TTCGGGACATATGGACAGATTACCTATGTCT
* **
21325 TTCGAGACATATGGACATTTTACCTATGT-T
1 TTCGGGACATATGGACAGATTACCTATGTCT
*
21355 CTTCGGGACATATGGACAGTTTACCTATGT-T
1 -TTCGGGACATATGGACAGATTACCTATGTCT
21386 ATTCGGGACATATGGACAGATTA
1 -TTCGGGACATATGGACAGATTA
21409 TTATACGAGC
Statistics
Matches: 134, Mismatches: 11, Indels: 5
0.89 0.07 0.03
Matches are distributed among these distances:
30 1 0.01
31 90 0.67
32 43 0.32
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (31 bp):
TTCGGGACATATGGACAGATTACCTATGTCT
Found at i:24795 original size:3 final size:3
Alignment explanation
Indices: 24787--24816 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
24777 CCTAAAAATC
*
24787 ATA ATA ATA ATA CTA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
24817 TAACAGTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25255 original size:28 final size:27
Alignment explanation
Indices: 25177--25255 Score: 77
Period size: 29 Copynumber: 2.8 Consensus size: 27
25167 TGGGGAATGA
*
25177 AATTAGAATATTTAAAAATTTAGGGATT
1 AATTAGAATA-TTAAAAATTTAGGGATG
* * * *
25205 AGATTAGAAATAGTCATAATTTAGGGGTG
1 A-ATTAG-AATATTAAAAATTTAGGGATG
25234 AATTAGAATATTAAAAAGTTTA
1 AATTAGAATATTAAAAA-TTTA
25256 ATGACTAATT
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
27 8 0.20
28 10 0.25
29 18 0.45
30 4 0.10
ACGTcount: A:0.46, C:0.01, G:0.18, T:0.35
Consensus pattern (27 bp):
AATTAGAATATTAAAAATTTAGGGATG
Found at i:26422 original size:3 final size:3
Alignment explanation
Indices: 26411--26447 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
26401 TTTTTTATCG
26411 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
26448 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:26459 original size:13 final size:13
Alignment explanation
Indices: 26412--26455 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
26402 TTTTTATCGT
26412 TATT-TTATTAT-
1 TATTATTATTATG
*
26423 TATTATTATTATT
1 TATTATTATTATG
26436 TATTATTATTATG
1 TATTATTATTATG
26449 T-TTATTA
1 TATTATTA
26456 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:26459 original size:19 final size:19
Alignment explanation
Indices: 26418--26459 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
26408 TCGTTATTTT
*
26418 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
26437 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
26456 ATTA
1 ATTA
26460 CATATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:28870 original size:17 final size:18
Alignment explanation
Indices: 28848--28881 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
28838 AAGTCGAGTA
*
28848 TATTTTACTAAT-TAATT
1 TATTTTAATAATGTAATT
28865 TATTTTAATAATGTAAT
1 TATTTTAATAATGTAAT
28882 GTGTGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTAATAATGTAATT
Found at i:32682 original size:26 final size:25
Alignment explanation
Indices: 32653--32731 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 25
32643 AATTTTTGAC
32653 ATTCTATTTCTTTGAGACCTTGAAAT
1 ATTCT-TTTCTTTGAGACCTTGAAAT
*
32679 ATTCTTTTC-----GACCTTGAAAC
1 ATTCTTTTCTTTGAGACCTTGAAAT
* *
32699 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTTTCTTTGAGACCTTGAAAT
32725 ATTCTTT
1 ATTCTTT
32732 CCACCTTGAA
Statistics
Matches: 41, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 13 0.32
21 4 0.10
25 6 0.15
26 18 0.44
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (25 bp):
ATTCTTTTCTTTGAGACCTTGAAAT
Found at i:32685 original size:20 final size:20
Alignment explanation
Indices: 32660--32731 Score: 63
Period size: 20 Copynumber: 3.3 Consensus size: 20
32650 GACATTCTAT
32660 TTCTTTGAGACCTTGAAATA
1 TTCTTTGAGACCTTGAAATA
** *
32680 TTCTTTTCGACCTTGAAACATTCCC
1 TTCTTTGAGACCTTG-AA-A-T--A
32705 TCTCTTTGAGACCTTGAAATA
1 T-TCTTTGAGACCTTGAAATA
32726 TTCTTT
1 TTCTTT
32732 CCACCTTGAA
Statistics
Matches: 40, Mismatches: 6, Indels: 12
0.69 0.10 0.21
Matches are distributed among these distances:
20 18 0.45
21 3 0.08
22 1 0.03
23 2 0.05
24 1 0.03
25 3 0.08
26 12 0.30
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (20 bp):
TTCTTTGAGACCTTGAAATA
Found at i:33374 original size:11 final size:11
Alignment explanation
Indices: 33346--33383 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
33336 AAGAGCAAAG
33346 AGAAAAATCAA
1 AGAAAAATCAA
33357 AGCAAAAATCAA
1 AG-AAAAATCAA
*
33369 AGAAAAAGCAA
1 AGAAAAATCAA
33380 AGAA
1 AGAA
33384 CAAAAGAGGA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:34566 original size:4 final size:4
Alignment explanation
Indices: 34557--34592 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
34547 AGAAAAGTAT
34557 ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
34593 CCATGATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:35200 original size:105 final size:101
Alignment explanation
Indices: 35059--35296 Score: 264
Period size: 105 Copynumber: 2.3 Consensus size: 101
35049 TGAGATTTTT
* * * *
35059 AAAACAAATTGTGTTTCGCTTGAGACATTTTTCCTTTGAGATACAAATTTTGAATTTGATTCAC-
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
** *
35123 TAAAAACAAAATTAATCTCACCTTAGATTGTTGTTTCTTTC-
66 T-AAAACAAAATTAATCTCA-CTT-GA-AATCGTTTC--TCA
* * * *
35164 AAAACAAATTTTGTCTCGCTTGAGACCTTTTCCCTTTGAGATCCAAATTTCGGATTTGTTTCACA
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
* * *
35229 TTAAACAAAGTTGATCTCACTTGAAATCGTTTCTCA
66 TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
* *
35265 AAAACAAACTTTGTCTCGCTTGAGACAATTTC
1 AAAACAAATTTTGTCTCGCTTGAGACATTTTC
35297 TCTAAAAACA
Statistics
Matches: 114, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
100 2 0.02
101 29 0.25
102 6 0.05
103 2 0.02
104 3 0.03
105 71 0.62
106 1 0.01
ACGTcount: A:0.31, C:0.18, G:0.12, T:0.38
Consensus pattern (101 bp):
AAAACAAATTTTGTCTCGCTTGAGACATTTTCCCTTTGAGATACAAATTTCGAATTTGATTCACA
TAAAACAAAATTAATCTCACTTGAAATCGTTTCTCA
Found at i:35287 original size:35 final size:36
Alignment explanation
Indices: 35243--35323 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
35233 ACAAAGTTGA
*
35243 TCTCACTTGAAATC-GTTTCTC-AAAAACAAACTTTG
1 TCTCACTTGAAA-CAATTTCTCTAAAAACAAACTTTG
* * *
35278 TCTCGCTTGAGACAATTTCTCTAAAAACAAATTTTG
1 TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
*
35314 TCTCATTTGA
1 TCTCACTTGA
35324 GACTATATCT
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
34 1 0.03
35 16 0.42
36 21 0.55
ACGTcount: A:0.32, C:0.21, G:0.10, T:0.37
Consensus pattern (36 bp):
TCTCACTTGAAACAATTTCTCTAAAAACAAACTTTG
Found at i:35314 original size:36 final size:36
Alignment explanation
Indices: 35258--35361 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
35248 CTTGAAATCG
*
35258 TTTCTC-AAAAACAAACTTTGTCTCGCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
** *
35293 TTTCTCTAAAAACAAATTTTGTCTCATTTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
* * *
35329 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACA
35362 TCATAATACA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 29 0.50
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCGCTTGAGACAA
Found at i:35698 original size:27 final size:28
Alignment explanation
Indices: 35596--35786 Score: 233
Period size: 30 Copynumber: 6.7 Consensus size: 28
35586 ACAATTTCTT
* *
35596 TTGAAAAAAATCTTTGGGTTTGTTTCTC
1 TTGAAAAAAATCTTTGAGTTTGTTCCTC
35624 TTGAAAAAAAAATCTTTGAGTTTGTTCCTC
1 TTG--AAAAAAATCTTTGAGTTTGTTCCTC
35654 TTGAAAAAAAAATCTTTGAGTTTGTTCCTC
1 TTG--AAAAAAATCTTTGAGTTTGTTCCTC
* *
35684 TTG-AAAAAATCTTTGAGTTTGCTCCTT
1 TTGAAAAAAATCTTTGAGTTTGTTCCTC
* *
35711 TTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTC
* *
35740 TTGAATAAAAATCTTTGAG-TTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTC
*
35768 TTGAAAAATATCTTTGAGT
1 TTGAAAAAAATCTTTGAGT
35787 CTATTTATTT
Statistics
Matches: 149, Mismatches: 9, Indels: 10
0.89 0.05 0.06
Matches are distributed among these distances:
27 37 0.25
28 17 0.11
29 39 0.26
30 56 0.38
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.44
Consensus pattern (28 bp):
TTGAAAAAAATCTTTGAGTTTGTTCCTC
Found at i:35799 original size:56 final size:56
Alignment explanation
Indices: 35593--35786 Score: 248
Period size: 57 Copynumber: 3.4 Consensus size: 56
35583 AAGACAATTT
* *
35593 CTTTTGAAAAAAATCTTTGGGTTTGTTTCTCTTGAAAAAAAAATCTTTGAGTTTGTTC
1 CTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTTG--AAAAAAATCTTTGAGTTTGTTC
* *
35651 CTCTTGAAAAAAAAATCTTTGAGTTTGTTCCTCTTG-AAAAAATCTTTGAGTTTGCTC
1 CTTTTG--AAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTC
* * *
35708 CTTTTGAATAAAAATCTTGGAGTTTGTTCCTTTTGAATAAAAATCTTTGAG-TTGTTT
1 CTTTTGAA-AAAAATCTTTGAGTTTGTTCCTCTTGAA-AAAAATCTTTGAGTTTGTTC
*
35765 CTTTTGAAAAATATCTTTGAGT
1 CTTTTGAAAAAAATCTTTGAGT
35787 CTATTTATTT
Statistics
Matches: 120, Mismatches: 11, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
55 2 0.02
56 36 0.30
57 38 0.32
58 18 0.15
60 26 0.22
ACGTcount: A:0.29, C:0.11, G:0.15, T:0.44
Consensus pattern (56 bp):
CTTTTGAAAAAAATCTTTGAGTTTGTTCCTCTTGAAAAAAATCTTTGAGTTTGTTC
Found at i:35855 original size:51 final size:53
Alignment explanation
Indices: 35797--35899 Score: 174
Period size: 52 Copynumber: 2.0 Consensus size: 53
35787 CTATTTATTT
35797 TGAAACAAAG-TTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
35848 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
35900 ATTGTTTCTT
Statistics
Matches: 48, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
51 10 0.21
52 25 0.52
54 13 0.27
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:35923 original size:27 final size:27
Alignment explanation
Indices: 35886--35951 Score: 91
Period size: 27 Copynumber: 2.4 Consensus size: 27
35876 AATTTTGTGA
*
35886 AAAAAATCTTTGAGATT-GTTTCTTTTG
1 AAAAAATCTTTGAG-TTGGTTTCTTTGG
35913 AAAAAATCTTTGAGTTGGTTTCTTTGG
1 AAAAAATCTTTGAGTTGGTTTCTTTGG
35940 AAATAAAT-TTTG
1 AAA-AAATCTTTG
35952 TCTCTCTTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 2 0.06
27 30 0.83
28 4 0.11
ACGTcount: A:0.32, C:0.06, G:0.17, T:0.45
Consensus pattern (27 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGG
Found at i:35991 original size:66 final size:67
Alignment explanation
Indices: 35913--36051 Score: 235
Period size: 67 Copynumber: 2.1 Consensus size: 67
35903 GTTTCTTTTG
* *
35913 AAAAAATCTTTGAGTTGGTTTCTTTGGAAA-TAAATTTTGTCTCTCTTAAGATAATTTCTTTTGA
1 AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTAA
35977 AA
66 AA
* *
35979 CAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTAA
1 AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTAA
36044 AA
66 AA
36046 AAAAAA
1 AAAAAA
36052 AAAAAAAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
66 28 0.42
67 39 0.58
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (67 bp):
AAAAAATCTTTGAGTTGGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATAATTTCTTTTAA
AA
Found at i:36402 original size:63 final size:62
Alignment explanation
Indices: 36300--36422 Score: 174
Period size: 63 Copynumber: 2.0 Consensus size: 62
36290 GATGTAATCC
* * *
36300 ATCTTTGAGTATGTTTCTTTTAAAACAAAATTTTATCTCTTAACGACAATTTCTTTTGAAAAA
1 ATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTATCTCTCAA-GACAACTTCTTTTGAAAAA
* * * *
36363 ATCTTTGAGTCTGTTTCTTTGGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAA
1 ATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAA
36423 CCACCCACAT
Statistics
Matches: 53, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
62 16 0.30
63 37 0.70
ACGTcount: A:0.31, C:0.15, G:0.11, T:0.43
Consensus pattern (62 bp):
ATCTTTGAGTATGTTTCTTTGAAAACAAAATTTTATCTCTCAAGACAACTTCTTTTGAAAAA
Found at i:36919 original size:35 final size:36
Alignment explanation
Indices: 36853--36927 Score: 100
Period size: 35 Copynumber: 2.1 Consensus size: 36
36843 TATTTCTTTG
* *
36853 GAAACAAAATTCACCATCTTTGAATCGGTTTCCCTT
1 GAAACAAAATTAAACATCTTTGAATCGGTTTCCCTT
*
36889 GAAACAAAA-TAAACATCTTTGAGATC-GTTTCTCTT
1 GAAACAAAATTAAACATCTTTGA-ATCGGTTTCCCTT
36924 GAAA
1 GAAA
36928 TGAATTTTGT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
35 23 0.66
36 12 0.34
ACGTcount: A:0.36, C:0.20, G:0.12, T:0.32
Consensus pattern (36 bp):
GAAACAAAATTAAACATCTTTGAATCGGTTTCCCTT
Found at i:37254 original size:28 final size:28
Alignment explanation
Indices: 37204--37257 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
37194 TCAAAATCCA
* *
37204 ATCTTTGAGTTTGTTTCTATTGAAACAC
1 ATCTTTGAGTTGGTTCCTATTGAAACAC
37232 ATCTTTGAGTTGGTCTCCT-TTGAAAC
1 ATCTTTGAGTTGGT-TCCTATTGAAAC
37258 CATTATCCTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 20 0.87
29 3 0.13
ACGTcount: A:0.22, C:0.17, G:0.17, T:0.44
Consensus pattern (28 bp):
ATCTTTGAGTTGGTTCCTATTGAAACAC
Found at i:37393 original size:43 final size:43
Alignment explanation
Indices: 37267--37523 Score: 193
Period size: 43 Copynumber: 5.9 Consensus size: 43
37257 CCATTATCCT
*
37267 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 ATAGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCA--ACC
* * * * * *
37312 TTTAAATAGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCAACC
1 -ATAGATAACC-AGACCTCCTCATCACGTAGGAACCGTGTCAACC
*
37357 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGTTATCACC
1 ATAGATAACCAGACC-TCCTCATCACGTAGGAACCGTGTCA--ACC
* ** * * * * * *
37402 TTTAGATGGCCAGAACTCTTCATCGCGTATGAGCCGTGTCATCC
1 -ATAGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACC
** * *
37446 CCAG---ACCAGATCTCCTCATCACGTAGGAGCCGTGTCAACC
1 ATAGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACC
37486 ATAGATAACCAG-CCGTCCTCATCACGTAGGAACCGTGT
1 ATAGATAACCAGACC-TCCTCATCACGTAGGAACCGTGT
37524 TATCACCTTT
Statistics
Matches: 164, Mismatches: 36, Indels: 25
0.73 0.16 0.11
Matches are distributed among these distances:
40 32 0.20
42 2 0.01
43 53 0.32
44 9 0.05
45 6 0.04
46 36 0.22
47 25 0.15
48 1 0.01
ACGTcount: A:0.27, C:0.30, G:0.19, T:0.23
Consensus pattern (43 bp):
ATAGATAACCAGACCTCCTCATCACGTAGGAACCGTGTCAACC
Found at i:37505 original size:129 final size:130
Alignment explanation
Indices: 37332--37572 Score: 439
Period size: 129 Copynumber: 1.9 Consensus size: 130
37322 CAAGAACTCT
37332 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
* * * *
37397 TCACCTTTAGATGGCC-AGAACTCTTCATCGCGTATGAGCCGTGTCATCCCCAGACCAGATCTCC
66 TCACCTTTAAATAGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCC
37461 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
1 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
37526 TCACCTTTAAATAGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
66 TCACCTTTAAATAGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCA
37573 CCTTTAGACG
Statistics
Matches: 107, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
129 79 0.74
130 28 0.26
ACGTcount: A:0.27, C:0.30, G:0.20, T:0.23
Consensus pattern (130 bp):
TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTA
TCACCTTTAAATAGCCAAGAACTCTTCATCACGTAGGAGCCGTGTCATCCCCAGACCAGATCTCC
Found at i:37784 original size:3 final size:3
Alignment explanation
Indices: 37773--37809 Score: 58
Period size: 3 Copynumber: 12.3 Consensus size: 3
37763 TTTTTTATCG
37773 TTA TT- TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T
37810 GTTTATTAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TTA
Found at i:37821 original size:13 final size:13
Alignment explanation
Indices: 37774--37817 Score: 58
Period size: 12 Copynumber: 3.6 Consensus size: 13
37764 TTTTTATCGT
37774 TATT-TTATTAT-
1 TATTATTATTATG
*
37785 TATTATTATTATT
1 TATTATTATTATG
37798 TATTATTATTATG
1 TATTATTATTATG
37811 T-TTATTA
1 TATTATTA
37818 ATTACATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 13 0.43
13 13 0.43
ACGTcount: A:0.30, C:0.00, G:0.02, T:0.68
Consensus pattern (13 bp):
TATTATTATTATG
Found at i:37821 original size:19 final size:19
Alignment explanation
Indices: 37780--37821 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
37770 TCGTTATTTT
*
37780 ATTATTATTATTATTATTT
1 ATTATTATTATTATTATTA
37799 ATTATTATTATGT-TTATTA
1 ATTATTATTAT-TATTATTA
37818 ATTA
1 ATTA
37822 CATATTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 20 0.95
20 1 0.05
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (19 bp):
ATTATTATTATTATTATTA
Found at i:39854 original size:28 final size:27
Alignment explanation
Indices: 39822--39877 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 27
39812 GTTTTTGCTG
*
39822 TTTAGCCTCCTAAGT-TTGTTTATATTAT
1 TTTAGCC-CCTAAATGTT-TTTATATTAT
*
39850 TTTAGCCCTTAAATGTTTTTATATTAT
1 TTTAGCCCCTAAATGTTTTTATATTAT
39877 T
1 T
39878 GGTTTGTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 16 0.64
28 9 0.36
ACGTcount: A:0.23, C:0.12, G:0.09, T:0.55
Consensus pattern (27 bp):
TTTAGCCCCTAAATGTTTTTATATTAT
Found at i:40187 original size:17 final size:18
Alignment explanation
Indices: 40165--40198 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
40155 AAGTCGAGTA
*
40165 TATTTTACTAAT-TAATT
1 TATTTTAATAATGTAATT
40182 TATTTTAATAATGTAAT
1 TATTTTAATAATGTAAT
40199 GTGTGTTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (18 bp):
TATTTTAATAATGTAATT
Found at i:41162 original size:208 final size:206
Alignment explanation
Indices: 40807--41220 Score: 785
Period size: 208 Copynumber: 2.0 Consensus size: 206
40797 CAGCGCCGAT
*
40807 TTGGCTCCAACTCACCCGATCCGGCTCGGATTGGCACTCAATTCTGTTTTCTACTACGAGCTTCA
1 TTGGCTCCAACTCACCCGATCCGGCTCGGATTGGCACTCAATTCTGTTTTCTACTACGAGATTCA
40872 ACTCTCCTGATCGCGCTTGCAATCTTGCAAAACAGGCTGGTTACAATTACCTTCTTTTTTCTCTC
66 ACTCTCCTGATCGCGCTTGCAATCTTGCAAAACAGGCTGGTTACAATTACCTTCTTTTTTCTCTC
40937 CCTGAAATAAATATAATATG-CGATACATCTAGAGTAGCTAATGTGCTGCCTTGTGATCGTGGCA
131 CCTGAAATAAATATAATATGCCGATACATCTAGAGTAGCTAATGTGCTGCCTTGTGATCGTGGCA
41001 GGCATTGATGA
196 GGCATTGATGA
41012 TTGGCTCCAACTCACCCGATCCGGCTCGGATTGGCACTCAATTCTCTGTTTTCTACTACGAGATC
1 TTGGCTCCAACTCACCCGATCCGGCTCGGATTGGCACTCAA-T-TCTGTTTTCTACTACGAGAT-
41077 TCAACTCTCCTGATCGCGCTTGCAATCTTGCAAAACAGGCTGGTTACAATTACCTTCTTTTTTCT
63 TCAACTCTCCTGATCGCGCTTGCAATCTTGCAAAACAGGCTGGTTACAATTACCTTCTTTTTTCT
41142 CTCCCTGAAATAAATATAATATGCCGATACATCTAGAGTAGCTAATGTGCTGCCTTGTGATCGTG
128 CTCCCTGAAATAAATATAATATGCCGATACATCTAGAGTAGCTAATGTGCTGCCTTGTGATCGTG
41207 GCAGGCATTGATGA
193 GCAGGCATTGATGA
41221 AGCAATCGCG
Statistics
Matches: 204, Mismatches: 1, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
205 41 0.20
206 1 0.00
207 19 0.09
208 88 0.43
209 55 0.27
ACGTcount: A:0.23, C:0.26, G:0.19, T:0.32
Consensus pattern (206 bp):
TTGGCTCCAACTCACCCGATCCGGCTCGGATTGGCACTCAATTCTGTTTTCTACTACGAGATTCA
ACTCTCCTGATCGCGCTTGCAATCTTGCAAAACAGGCTGGTTACAATTACCTTCTTTTTTCTCTC
CCTGAAATAAATATAATATGCCGATACATCTAGAGTAGCTAATGTGCTGCCTTGTGATCGTGGCA
GGCATTGATGA
Found at i:41837 original size:15 final size:15
Alignment explanation
Indices: 41803--41831 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
41793 CTCTGTTTTA
41803 GCTAATGAATATTGT
1 GCTAATGAATATTGT
41818 GCTAATGAATATTG
1 GCTAATGAATATTG
41832 GTCTAAGATA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.07, G:0.21, T:0.38
Consensus pattern (15 bp):
GCTAATGAATATTGT
Found at i:52243 original size:60 final size:61
Alignment explanation
Indices: 52142--52257 Score: 225
Period size: 60 Copynumber: 1.9 Consensus size: 61
52132 TGAAAATCTA
52142 ATTAAAGTAAGTTTTTTTTTTTAAATTTTTTATTAAACAGATACATTACATTAACAGATAC
1 ATTAAAGTAAGTTTTTTTTTTTAAATTTTTTATTAAACAGATACATTACATTAACAGATAC
52203 ATTAAAGTAAGTTTTTTTTTTT-AATTTTTTATTAAACAGATACATTACATTAACA
1 ATTAAAGTAAGTTTTTTTTTTTAAATTTTTTATTAAACAGATACATTACATTAACA
52258 AGGAAAATCT
Statistics
Matches: 55, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
60 33 0.60
61 22 0.40
ACGTcount: A:0.39, C:0.08, G:0.06, T:0.47
Consensus pattern (61 bp):
ATTAAAGTAAGTTTTTTTTTTTAAATTTTTTATTAAACAGATACATTACATTAACAGATAC
Found at i:52646 original size:16 final size:16
Alignment explanation
Indices: 52625--52656 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
52615 TTAATAGAAG
52625 TTCAAAAATTTATTTA
1 TTCAAAAATTTATTTA
*
52641 TTCAAAAATTTGTTTA
1 TTCAAAAATTTATTTA
52657 GGGTTCAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.03, T:0.50
Consensus pattern (16 bp):
TTCAAAAATTTATTTA
Found at i:55484 original size:31 final size:31
Alignment explanation
Indices: 55418--55497 Score: 99
Period size: 31 Copynumber: 2.6 Consensus size: 31
55408 TGAAATTTAG
** *
55418 ATAAAATATTAATTTAATTTATAAATTTTAG
1 ATAAAATATTAATTTAATTTATAAACATTAA
55449 ATAAAATATTAATTTAATTCT-TAAACATTAA
1 ATAAAATATTAATTTAATT-TATAAACATTAA
* *
55480 ATAAAATATCAATCTAAT
1 ATAAAATATTAATTTAAT
55498 CATTAAATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
31 42 0.98
32 1 0.02
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.42
Consensus pattern (31 bp):
ATAAAATATTAATTTAATTTATAAACATTAA
Found at i:64630 original size:3 final size:3
Alignment explanation
Indices: 64613--64685 Score: 101
Period size: 3 Copynumber: 24.3 Consensus size: 3
64603 GATGTATCCT
* * *
64613 ATG ATG ACG AGG ATG ATG ATG ATG ATG ATG ATG ATG ATG GTG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
* *
64661 ATG ATG ATG GTG ACG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
64686 AGAATCAGGC
Statistics
Matches: 61, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.32, C:0.03, G:0.37, T:0.29
Consensus pattern (3 bp):
ATG
Found at i:67941 original size:60 final size:60
Alignment explanation
Indices: 67803--67945 Score: 175
Period size: 59 Copynumber: 2.4 Consensus size: 60
67793 TGAGTACTCT
* **
67803 GACTATTAAAAGTTACAAAAT-AATCCCTCGAGTATAAGGCGTCCCTTTGTTGAGTCCTT
1 GACTATTAAAAGTTACAAAATGATTCCCTCGAGTATAAGGCGTCCCTTTGTTGAGTCCCC
* * * **
67862 AATTATTAAAAGTTACAAAATGATTCCC-CG-GTTATAGGGCGTCGTTTTGTTGAGTCTCCC
1 GACTATTAAAAGTTACAAAATGATTCCCTCGAG-TATAAGGCGTCCCTTTGTTGAGTC-CCC
67922 GACTATTAAAAGTTACAAAATGAT
1 GACTATTAAAAGTTACAAAATGAT
67946 CACTCGACCA
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
58 1 0.01
59 42 0.59
60 28 0.39
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (60 bp):
GACTATTAAAAGTTACAAAATGATTCCCTCGAGTATAAGGCGTCCCTTTGTTGAGTCCCC
Found at i:74832 original size:19 final size:20
Alignment explanation
Indices: 74808--74857 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
74798 AAAATGTTTT
*
74808 TATGAATAGTAT-TATACTG
1 TATGAATAGTATCGATACTG
74827 TATGAATAGTATCGATACTG
1 TATGAATAGTATCGATACTG
*
74847 TGTGAATAGTA
1 TATGAATAGTA
74858 ATGAACATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
19 12 0.43
20 16 0.57
ACGTcount: A:0.36, C:0.06, G:0.20, T:0.38
Consensus pattern (20 bp):
TATGAATAGTATCGATACTG
Found at i:75907 original size:25 final size:24
Alignment explanation
Indices: 75863--75913 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 24
75853 CATAATGCAT
75863 ATAATATGAATTCATGTCATGTATC
1 ATAATATGAATTCA-GTCATGTATC
75888 ATAATATGGAATGTCA-TCATGTATC
1 ATAATAT-GAAT-TCAGTCATGTATC
75913 A
1 A
75914 ATATATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
25 17 0.71
26 4 0.17
27 3 0.12
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (24 bp):
ATAATATGAATTCAGTCATGTATC
Found at i:79226 original size:52 final size:52
Alignment explanation
Indices: 79168--79272 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
79158 CCAAAGCGCC
79168 CCCACACACCTCCTAATACTCTGAGCGAACCAGACTTCTAATAATTGACTAA
1 CCCACACACCTCCTAATACTCTGAGCGAACCAGACTTCTAATAATTGACTAA
79220 CCCACACACCTCCTAATACTCTGAGCGAACCAGACTTCTAATAATTGACTAA
1 CCCACACACCTCCTAATACTCTGAGCGAACCAGACTTCTAATAATTGACTAA
79272 C
1 C
79273 ATTTTTGGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.34, C:0.33, G:0.10, T:0.23
Consensus pattern (52 bp):
CCCACACACCTCCTAATACTCTGAGCGAACCAGACTTCTAATAATTGACTAA
Found at i:79262 original size:25 final size:25
Alignment explanation
Indices: 79180--79262 Score: 80
Period size: 25 Copynumber: 3.2 Consensus size: 25
79170 CACACACCTC
79180 CTAATACTCTGAGCGAACCAGACTT
1 CTAATACTCTGAGCGAACCAGACTT
* * * *
79205 CTAATAAT-TGA-CTAACCCACACACCTC
1 CTAATACTCTGAGCGAA--C-CAGA-CTT
79232 CTAATACTCTGAGCGAACCAGACTT
1 CTAATACTCTGAGCGAACCAGACTT
79257 CTAATA
1 CTAATA
79263 ATTGACTAAC
Statistics
Matches: 44, Mismatches: 8, Indels: 12
0.69 0.12 0.19
Matches are distributed among these distances:
23 3 0.07
24 3 0.07
25 16 0.36
26 6 0.14
27 10 0.23
28 3 0.07
29 3 0.07
ACGTcount: A:0.35, C:0.30, G:0.11, T:0.24
Consensus pattern (25 bp):
CTAATACTCTGAGCGAACCAGACTT
Found at i:80092 original size:2 final size:2
Alignment explanation
Indices: 80085--80117 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
80075 TTTGGACCCA
*
80085 TC TC TC TC TC TC TC TC TC TC TC TA TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
80118 GTACTTTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.03, C:0.45, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:81200 original size:5 final size:5
Alignment explanation
Indices: 81190--81231 Score: 77
Period size: 5 Copynumber: 8.6 Consensus size: 5
81180 ATGAAGCTAC
81190 TTTGG TTTGG TTTGG TTTGG -TTGG TTTGG TTTGG TTTGG TTT
1 TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTTGG TTT
81232 TGACATATTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
4 4 0.11
5 32 0.89
ACGTcount: A:0.00, C:0.00, G:0.38, T:0.62
Consensus pattern (5 bp):
TTTGG
Found at i:81215 original size:19 final size:19
Alignment explanation
Indices: 81191--81230 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
81181 TGAAGCTACT
81191 TTGGTTTGGTTTGGTTTGG
1 TTGGTTTGGTTTGGTTTGG
81210 TTGGTTTGGTTTGGTTTGG
1 TTGGTTTGGTTTGGTTTGG
81229 TT
1 TT
81231 TTGACATATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.40, T:0.60
Consensus pattern (19 bp):
TTGGTTTGGTTTGGTTTGG
Done.