Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004604.1 Hibiscus syriacus cultivar Beakdansim tig00010290_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: 54341
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5103 original size:2 final size:2
Alignment explanation
Indices: 5096--5132 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5086 TACTATGTTA
*
5096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5133 AAAGTAGAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:6441 original size:75 final size:75
Alignment explanation
Indices: 6352--6532 Score: 197
Period size: 76 Copynumber: 2.4 Consensus size: 75
6342 TAAACTCAAG
* * * * * * *
6352 TTTAGGATAATATTTTAAACATTATATTTTATCTT-TGTATTTTAGTTTAAATAGGTTTTGGTAT
1 TTTAGGATATTATTTTAAATATTATATTTTAT-TTAGGTATTTTAGTTTAAAAAGATTTTAGTAC
*
6416 TTTAATTAAGT
65 TTTAATTAAGA
* *
6427 TTTAGGATATTATTTTTATATTTTATATTTGT-TTTAGGTATTTTAGTTTAAAAAGATTTTAGTA
1 TTTAGGATATTA-TTTTAAATATTATATTT-TATTTAGGTATTTTAGTTTAAAAAGATTTTAGTA
* *
6491 CTTTAGTTAGGA
64 CTTTAATTAAGA
*
6503 TTTAGAATATTATTTTAAATATTAT-TTTTA
1 TTTAGGATATTATTTTAAATATTATATTTTA
6533 GGTATTTTTT
Statistics
Matches: 87, Mismatches: 15, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
73 1 0.01
74 3 0.03
75 24 0.28
76 58 0.67
77 1 0.01
ACGTcount: A:0.31, C:0.02, G:0.12, T:0.56
Consensus pattern (75 bp):
TTTAGGATATTATTTTAAATATTATATTTTATTTAGGTATTTTAGTTTAAAAAGATTTTAGTACT
TTAATTAAGA
Found at i:7198 original size:18 final size:19
Alignment explanation
Indices: 7159--7202 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
7149 CTTTAATTTG
* *
7159 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTATCT
7178 TTTATTTAATT-CTTATCT
1 TTTATTTAATTACTTATCT
7196 TTTATTT
1 TTTATTT
7203 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTATCT
Found at i:7251 original size:16 final size:15
Alignment explanation
Indices: 7225--7255 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
7215 TTAAAATCCC
7225 CTATTATATTTATTA
1 CTATTATATTTATTA
7240 CTATTAATATTTATTA
1 CTATT-ATATTTATTA
7256 TTTTATTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (15 bp):
CTATTATATTTATTA
Found at i:12585 original size:5 final size:5
Alignment explanation
Indices: 12572--12632 Score: 77
Period size: 5 Copynumber: 11.8 Consensus size: 5
12562 GTTATATATT
* **
12572 TTTTA TTTTGT TTTTA TTTTA TTTTA TTTTA TTTTA TTTCG TTTTA TTTTTA
1 TTTTA TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA
12624 TTTTA TTTT
1 TTTTA TTTT
12633 TTAACGAACT
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
5 39 0.81
6 9 0.19
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:12610 original size:31 final size:31
Alignment explanation
Indices: 12572--12632 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
12562 GTTATATATT
*
12572 TTTTATTTTGTTTT-TATTTTATTTTATTTTA
1 TTTTATTTCGTTTTAT-TTTTATTTTATTTTA
12603 TTTTATTTCGTTTTATTTTTATTTTATTTT
1 TTTTATTTCGTTTTATTTTTATTTTATTTT
12633 TTAACGAACT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
31 27 0.96
32 1 0.04
ACGTcount: A:0.15, C:0.02, G:0.03, T:0.80
Consensus pattern (31 bp):
TTTTATTTCGTTTTATTTTTATTTTATTTTA
Found at i:13488 original size:70 final size:74
Alignment explanation
Indices: 13307--13493 Score: 224
Period size: 74 Copynumber: 2.6 Consensus size: 74
13297 TTTTATCTTT
* * * * * * * *
13307 GTATTTTAGTTTAAATAGGTCTTGGTATTTTAATTAAGTTTTAGGATATTATTTTTATATTTTAT
1 GTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATTTTTATAATATAT
13372 ATTTTTTAG
66 ATTTTTTAG
* *
13381 GTATTTTAGTTTAAATAGGTTTTAGTAG-TTTAGTTAGGGTTTAGAATATTA-TTTTA-AATAT-
1 GTATTTTAGTTTAAATAGGTTTTAGT-GTTTTAATTAGGATTTAGAATATTATTTTTATAATATA
13442 TA-TTTTTAG
65 TATTTTTTAG
13451 GTATTTTAGTTTAAATA-GTTTTAAGTGTTTTAATTAGGATTTA
1 GTATTTTAGTTTAAATAGGTTTT-AGTGTTTTAATTAGGATTTA
13494 AGATGTTTTA
Statistics
Matches: 99, Mismatches: 11, Indels: 10
0.82 0.09 0.08
Matches are distributed among these distances:
69 6 0.06
70 40 0.40
71 2 0.02
72 3 0.03
73 5 0.05
74 43 0.43
ACGTcount: A:0.29, C:0.01, G:0.16, T:0.55
Consensus pattern (74 bp):
GTATTTTAGTTTAAATAGGTTTTAGTGTTTTAATTAGGATTTAGAATATTATTTTTATAATATAT
ATTTTTTAG
Found at i:14122 original size:18 final size:19
Alignment explanation
Indices: 14083--14126 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 19
14073 CTTTAATTTG
* *
14083 TTTATTTAATTATTTTTCT
1 TTTATTTAATTACTTATCT
14102 TTTATTTAATT-CTTATCT
1 TTTATTTAATTACTTATCT
14120 TTTATTT
1 TTTATTT
14127 TTTAAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 12 0.52
19 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTATTTAATTACTTATCT
Found at i:14188 original size:8 final size:8
Alignment explanation
Indices: 14175--14201 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
14165 ACTATTACTA
14175 TTTATTAT
1 TTTATTAT
14183 TTTATTAT
1 TTTATTAT
14191 TTTATTAT
1 TTTATTAT
14199 TTT
1 TTT
14202 TTCTCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTATTAT
Found at i:14199 original size:23 final size:24
Alignment explanation
Indices: 14154--14231 Score: 63
Period size: 23 Copynumber: 3.3 Consensus size: 24
14144 AAATCCCCTT
* *
14154 TTATATTTATTACTATTACTATTTA
1 TTATATTTATTA-TTTTATTATTTA
*
14179 TTAT-TTTATTATTTTATTATTTT
1 TTATATTTATTATTTTATTATTTA
* *
14202 TTCTCTTT-TT-TTTTAATTATTTA
1 TTATATTTATTATTTT-ATTATTTA
*
14225 TTTTATT
1 TTATATT
14232 ATATCTTTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
22 4 0.09
23 26 0.59
24 10 0.23
25 4 0.09
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (24 bp):
TTATATTTATTATTTTATTATTTA
Found at i:15448 original size:11 final size:11
Alignment explanation
Indices: 15432--15463 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
15422 TTAGATTTTG
15432 GATTTTGAAAT
1 GATTTTGAAAT
15443 GATTTTGAAAT
1 GATTTTGAAAT
15454 GATTTTGAAA
1 GATTTTGAAA
15464 ACTATTGGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
GATTTTGAAAT
Found at i:19004 original size:2 final size:2
Alignment explanation
Indices: 18997--19027 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
18987 TACTATGTTA
18997 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
19028 AAAGTATAGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26253 original size:2 final size:2
Alignment explanation
Indices: 26246--26299 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
26236 TCCTATATGC
26246 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
26288 AT AT AT AT AT AT
1 AT AT AT AT AT AT
26300 CTTCTCGTTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:34151 original size:2 final size:2
Alignment explanation
Indices: 34146--34170 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
34136 TATATGTAGG
34146 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 T
34171 GTTTTCTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35076 original size:21 final size:21
Alignment explanation
Indices: 35052--35104 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
35042 ATTCTGACTA
35052 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTCCAAAT
*
35073 TCGCATTGCGATTTTCCTAAT
1 TCGCATTGCGATTTTCCAAAT
*
35094 TCGCAATGCGA
1 TCGCATTGCGA
35105 ATACGTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.36
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCAAAT
Found at i:35119 original size:20 final size:20
Alignment explanation
Indices: 35094--35146 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
35084 TTTTCCTAAT
35094 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
35114 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
*
35134 TCGCAATGTGAAT
1 TCGCAATGCGAAT
35147 CTGACTATAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.38, C:0.19, G:0.21, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:35369 original size:22 final size:21
Alignment explanation
Indices: 35344--35408 Score: 67
Period size: 22 Copynumber: 3.0 Consensus size: 21
35334 GCGACATCCA
* *
35344 TCCCTATCTCCAACGAAATCAG
1 TCCC-ATCTCCGACGAAATCAC
* *
35366 TCCCCATCTCCGATGATATCAC
1 T-CCCATCTCCGACGAAATCAC
35388 TCTCCATCTCCGACGAAATCA
1 TC-CCATCTCCGACGAAATCA
35409 TTCACGGTCA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 1 0.03
22 31 0.89
23 3 0.09
ACGTcount: A:0.28, C:0.38, G:0.09, T:0.25
Consensus pattern (21 bp):
TCCCATCTCCGACGAAATCAC
Found at i:35816 original size:20 final size:20
Alignment explanation
Indices: 35776--35845 Score: 59
Period size: 20 Copynumber: 3.5 Consensus size: 20
35766 TGCGATTATT
* **
35776 GCGTTGCGATAGTCAAATTC
1 GCGTTACGATAGTCATTTTC
35796 GCGTTACGATAGTCATTTTC
1 GCGTTACGATAGTCATTTTC
* * * **
35816 GTGTTGCAATTTTCATTTTC
1 GCGTTACGATAGTCATTTTC
*
35836 GTGTTACGAT
1 GCGTTACGAT
35846 TTAAAGTTTC
Statistics
Matches: 40, Mismatches: 10, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.20, C:0.17, G:0.21, T:0.41
Consensus pattern (20 bp):
GCGTTACGATAGTCATTTTC
Found at i:35847 original size:20 final size:20
Alignment explanation
Indices: 35793--35847 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
35783 GATAGTCAAA
* **
35793 TTCGCGTTACGATAGTCATT
1 TTCGTGTTACGATTTTCATT
* *
35813 TTCGTGTTGCAATTTTCATT
1 TTCGTGTTACGATTTTCATT
35833 TTCGTGTTACGATTT
1 TTCGTGTTACGATTT
35848 AAAGTTTCAA
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.16, C:0.16, G:0.18, T:0.49
Consensus pattern (20 bp):
TTCGTGTTACGATTTTCATT
Found at i:37747 original size:20 final size:20
Alignment explanation
Indices: 37722--37811 Score: 135
Period size: 20 Copynumber: 4.5 Consensus size: 20
37712 AGAATAGTTT
* * *
37722 ACTATCACATTGCAAAAATG
1 ACTATCGCAATGCGAAAATG
*
37742 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
37762 ACCATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
37782 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
37802 ACTATCGCAA
1 ACTATCGCAA
37812 CGAAAGAATC
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 63 1.00
ACGTcount: A:0.41, C:0.23, G:0.17, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:37823 original size:34 final size:38
Alignment explanation
Indices: 37736--37832 Score: 121
Period size: 40 Copynumber: 2.6 Consensus size: 38
37726 TCACATTGCA
*
37736 AAAATGACTATCGCAACGCGAAAATGACCATCGCAATGCG
1 AAAATGAC-ATCGCAATGCGAAAATGACCATCGCAA-GCG
*
37776 AAAATGACTATCGCAATGCGAAAATGACTATCGCAA-CG
1 AAAATGAC-ATCGCAATGCGAAAATGACCATCGCAAGCG
37814 -AAA-GA-ATCGCAATGCGAAA
1 AAAATGACATCGCAATGCGAAA
37833 TGAAAATCAC
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
34 14 0.25
36 2 0.04
37 3 0.05
38 2 0.04
40 34 0.62
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (38 bp):
AAAATGACATCGCAATGCGAAAATGACCATCGCAAGCG
Found at i:37910 original size:20 final size:20
Alignment explanation
Indices: 37858--37924 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
37848 GATTCTCTCG
** *
37858 TTGCGATAGTCAAATTAGCA
1 TTGCGATAGTCATTTTCGCA
37878 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
37898 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
37918 TTGCGAT
1 TTGCGAT
37925 TTTAAGTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.18, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:38499 original size:21 final size:21
Alignment explanation
Indices: 38408--38511 Score: 75
Period size: 21 Copynumber: 5.0 Consensus size: 21
38398 GACTCACCTG
* **
38408 TCATCGTTCAAGAGTCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTA
38430 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
** * * *
38450 TCATCCCTCAATAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* * *
38471 CCACCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGGCCCCTA
* *
38492 TCATCGTTGAAGAGGTCCCT
1 TCATCGTTCAAGAGGCCCCT
38512 CCCAACATTC
Statistics
Matches: 60, Mismatches: 21, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
20 3 0.05
21 56 0.93
22 1 0.02
ACGTcount: A:0.22, C:0.37, G:0.16, T:0.25
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:38512 original size:42 final size:41
Alignment explanation
Indices: 38408--38515 Score: 119
Period size: 42 Copynumber: 2.6 Consensus size: 41
38398 GACTCACCTG
* *
38408 TCATCGTTCAAGAGT-CCTCCCCTATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGTCCCT-CCC-ACCGTTCAAGAGGCCACTA
** *
38450 TCATCCCTCAATAGTCCCCTCCCACCGTTCAAGAGGCCACTA
1 TCATCGTTCAAGAGT-CCCTCCCACCGTTCAAGAGGCCACTA
*
38492 TCATCGTTGAAGAGGTCCCTCCCA
1 TCATCGTTCAAGA-GTCCCTCCCA
38516 ACATTCTAGA
Statistics
Matches: 54, Mismatches: 9, Indels: 6
0.78 0.13 0.09
Matches are distributed among these distances:
42 46 0.85
43 5 0.09
44 3 0.06
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (41 bp):
TCATCGTTCAAGAGTCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:39917 original size:14 final size:14
Alignment explanation
Indices: 39898--39933 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
39888 ATTGTTTAAT
39898 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
39912 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
39926 TGATTTGT
1 TGATTTGT
39934 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:40096 original size:33 final size:34
Alignment explanation
Indices: 40050--40134 Score: 118
Period size: 33 Copynumber: 2.5 Consensus size: 34
40040 TCGCAACACG
** *
40050 GAAATGACTATCGCAGCGAGAGAATCACAATGC-
1 GAAATGAAAATCGCAACGAGAGAATCACAATGCA
*
40083 GAAATGAAAATCGCAACGAGAGAATCGCAATGCA
1 GAAATGAAAATCGCAACGAGAGAATCACAATGCA
*
40117 AAAATGAAAATCGCAACG
1 GAAATGAAAATCGCAACG
40135 CGAAACTAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
33 29 0.63
34 17 0.37
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (34 bp):
GAAATGAAAATCGCAACGAGAGAATCACAATGCA
Found at i:40174 original size:20 final size:19
Alignment explanation
Indices: 40145--40211 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
40135 CGAAACTAAA
*
40145 TTCGCGTTGCGATTTTCATT
1 TTCGCATTGCGATTTTCA-T
40165 TTCGCATTGCGA--TTCA-
1 TTCGCATTGCGATTTTCAT
*
40181 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
40198 TTCGCATTGCGATT
1 TTCGCATTGCGATT
40212 CTCTCGTTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 11
0.74 0.06 0.21
Matches are distributed among these distances:
14 6 0.15
16 7 0.18
17 3 0.08
18 4 0.10
19 8 0.21
20 11 0.28
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.45
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:40206 original size:33 final size:33
Alignment explanation
Indices: 40149--40233 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
40139 ACTAAATTCG
40149 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
40183 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
40216 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
40234 CGCGTTGAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:40245 original size:20 final size:20
Alignment explanation
Indices: 40216--40300 Score: 118
Period size: 20 Copynumber: 4.2 Consensus size: 20
40206 GCGATTCTCT
40216 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
* * *
40236 CGTTGAGATAGTCAATTCCA
1 CGTTGCGATAGTCATTTCCG
40256 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCATTTCCG
*
40276 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCAT-TTCCG
40296 CGTTG
1 CGTTG
40301 TGATTTCCGC
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
20 54 0.96
21 2 0.04
ACGTcount: A:0.19, C:0.21, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTCCG
Found at i:40271 original size:40 final size:41
Alignment explanation
Indices: 40216--40294 Score: 133
Period size: 40 Copynumber: 2.0 Consensus size: 41
40206 GCGATTCTCT
40216 CGTTGCGATAGTCATTTCCGCGTTGAGATAGTCA-ATTCCA
1 CGTTGCGATAGTCATTTCCGCGTTGAGATAGTCATATTCCA
* *
40256 CGTTGCGATAGTCATTTCCGTGTTGCGATAGTCATATTC
1 CGTTGCGATAGTCATTTCCGCGTTGAGATAGTCATATTC
40295 GCGTTGTGAT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
40 32 0.89
41 4 0.11
ACGTcount: A:0.20, C:0.22, G:0.23, T:0.35
Consensus pattern (41 bp):
CGTTGCGATAGTCATTTCCGCGTTGAGATAGTCATATTCCA
Found at i:41972 original size:24 final size:24
Alignment explanation
Indices: 41945--41991 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
41935 CAAAATCTGA
41945 GTATTGACCAAGATCAAAGTTCGG
1 GTATTGACCAAGATCAAAGTTCGG
*
41969 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
41992 AATACTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (24 bp):
GTATTGACCAAGATCAAAGTTCGG
Found at i:42000 original size:24 final size:24
Alignment explanation
Indices: 41949--42000 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
41939 ATCTGAGTAT
** *
41949 TGACCAAGATCAAAGTTCGGGTAT
1 TGACCAAGATCAAAGTTCGAATAC
*
41973 TGACCAAGATCAAATTTCGAATAC
1 TGACCAAGATCAAAGTTCGAATAC
41997 TGAC
1 TGAC
42001 TAGTACTCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (24 bp):
TGACCAAGATCAAAGTTCGAATAC
Found at i:42853 original size:20 final size:20
Alignment explanation
Indices: 42828--42874 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
42818 AAATTCAGTA
*
42828 TTGCGATAGTCAGAATCTCG
1 TTGCGATAGTCAGAATCGCG
*
42848 TTGCGATAGTCAGATTCGCG
1 TTGCGATAGTCAGAATCGCG
42868 TTGCGAT
1 TTGCGAT
42875 TTACATATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.21, C:0.19, G:0.28, T:0.32
Consensus pattern (20 bp):
TTGCGATAGTCAGAATCGCG
Found at i:42884 original size:20 final size:20
Alignment explanation
Indices: 42861--42974 Score: 147
Period size: 20 Copynumber: 5.7 Consensus size: 20
42851 CGATAGTCAG
* *
42861 ATTCGCGTTGCGATTTACAT
1 ATTCGCATTGCGATTTACGT
*
42881 ATTCGCATTGGGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
42901 ATTTGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* **
42921 ATTCGCATTGCGATTTTCCAA
1 ATTCGCATTGCGA-TTTACGT
*
42942 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
42962 ATTCGCATTGCGA
1 ATTCGCATTGCGA
42975 ATTAGGAAAA
Statistics
Matches: 79, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
20 63 0.80
21 16 0.20
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:42964 original size:41 final size:40
Alignment explanation
Indices: 42861--42974 Score: 156
Period size: 41 Copynumber: 2.8 Consensus size: 40
42851 CGATAGTCAG
* * **
42861 ATTCGCGTTGCGATTTACATATTCGCATTGGGATTTACGT
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACAA
* * *
42901 ATTTGCATTGCGATTTACGTATTCGCATTGCGATTTTCCAA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA-TTTACAA
42942 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA
1 ATTCGCGTTGCGATTTACGTATTCGCATTGCGA
42975 ATTAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
40 29 0.45
41 35 0.55
ACGTcount: A:0.20, C:0.19, G:0.21, T:0.39
Consensus pattern (40 bp):
ATTCGCGTTGCGATTTACGTATTCGCATTGCGATTTACAA
Found at i:42995 original size:21 final size:21
Alignment explanation
Indices: 42971--43016 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
42961 TATTCGCATT
42971 GCGAATTAGGAAAATCGCAAA
1 GCGAATTAGGAAAATCGCAAA
* *
42992 GCGAATTTGGAAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAA
43013 GCGA
1 GCGA
43017 TAGTCAGAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.41, C:0.15, G:0.26, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAA
Found at i:45117 original size:12 final size:12
Alignment explanation
Indices: 45095--45141 Score: 69
Period size: 12 Copynumber: 3.8 Consensus size: 12
45085 ATACTATTTT
45095 TTATCTTTTAAAA
1 TTAT-TTTTAAAA
45108 TTATTTTTAAAA
1 TTATTTTTAAAA
45120 TTA-TTTTAAAA
1 TTATTTTTAAAA
45131 TTTATTTTTAA
1 -TTATTTTTAA
45142 GGTGTTCGAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.25
12 14 0.44
13 10 0.31
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTTTTAAAA
Found at i:46444 original size:16 final size:17
Alignment explanation
Indices: 46423--46457 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
46413 CTCCCCCTTA
46423 CTTT-AACACTTCTCCC
1 CTTTAAACACTTCTCCC
46439 CTTTAAAACACTTCTCCC
1 CTTT-AAACACTTCTCCC
46457 C
1 C
46458 CTTTTTGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
18 13 0.76
ACGTcount: A:0.23, C:0.43, G:0.00, T:0.34
Consensus pattern (17 bp):
CTTTAAACACTTCTCCC
Found at i:48285 original size:21 final size:21
Alignment explanation
Indices: 48250--48332 Score: 87
Period size: 21 Copynumber: 3.8 Consensus size: 21
48240 ATAACCCATT
*
48250 GGGGGTATCGATTCCC-TCAA
1 GGGGGAATCGATTCCCTTCAA
*
48270 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCC-TTC-AA
*
48294 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATT-CCCTTCAA
*
48316 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
48333 CTGCCCTATA
Statistics
Matches: 54, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
20 2 0.04
21 16 0.30
22 13 0.24
23 16 0.30
24 7 0.13
ACGTcount: A:0.20, C:0.24, G:0.31, T:0.24
Consensus pattern (21 bp):
GGGGGAATCGATTCCCTTCAA
Found at i:48320 original size:22 final size:22
Alignment explanation
Indices: 48250--48331 Score: 87
Period size: 23 Copynumber: 3.7 Consensus size: 22
48240 ATAACCCATT
*
48250 GGGGGTATCGATT-CCC-TCAA
1 GGGGGAATCGATTCCCCTTCAA
* *
48270 GGAGGGAATCGGTTCCCATTCAAA
1 GG-GGGAATCGATTCCCCTTC-AA
*
48294 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGAATCGATTCCCCTTCAA
*
48316 GGGGGTATCGATTCCC
1 GGGGGAATCGATTCCC
48332 TCTGCCCTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
20 2 0.04
21 9 0.17
22 18 0.35
23 19 0.37
24 4 0.08
ACGTcount: A:0.21, C:0.24, G:0.32, T:0.23
Consensus pattern (22 bp):
GGGGGAATCGATTCCCCTTCAA
Done.