Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006055.1 Hibiscus syriacus cultivar Beakdansim tig00014327_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: 105793
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:587 original size:23 final size:24
Alignment explanation
Indices: 552--596 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
542 ATGTGCCCCT
* *
552 CCACTACCTCCGCCTCC-CCACCA
1 CCACCACCACCGCCTCCTCCACCA
575 CCACCACCACCGCCTCCTCCAC
1 CCACCACCACCGCCTCCTCCAC
597 TCCGGAACCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.18, C:0.67, G:0.04, T:0.11
Consensus pattern (24 bp):
CCACCACCACCGCCTCCTCCACCA
Found at i:5221 original size:20 final size:21
Alignment explanation
Indices: 5198--5239 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
5188 ATTCAAAAGT
5198 TTAATAAATA-AATTAA-AAAA
1 TTAA-AAATACAATTAATAAAA
5218 TTAAAAATACAATTAATAAAA
1 TTAAAAATACAATTAATAAAA
5239 T
1 T
5240 CGAGAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 10 0.50
21 5 0.25
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (21 bp):
TTAAAAATACAATTAATAAAA
Found at i:9881 original size:84 final size:84
Alignment explanation
Indices: 9781--9947 Score: 307
Period size: 84 Copynumber: 2.0 Consensus size: 84
9771 TTTTCTCCTT
*
9781 TTGCTTCTGTTCCTTGCCATTGCTGTTTTAGTTATTGATGCAACTCAACCTGGTTAAACTCTGCT
1 TTGCTTCTGCTCCTTGCCATTGCTGTTTTAGTTATTGATGCAACTCAACCTGGTTAAACTCTGCT
9846 AGACTGTTTCTTCTTCTGG
66 AGACTGTTTCTTCTTCTGG
* *
9865 TTGCTTCTGCTCCTTGCCATTGCTGTTTTAGTTATTGTTGCAACTCAACCTGGTTAAACTCTGTT
1 TTGCTTCTGCTCCTTGCCATTGCTGTTTTAGTTATTGATGCAACTCAACCTGGTTAAACTCTGCT
9930 AGACTGTTTCTTCTTCTG
66 AGACTGTTTCTTCTTCTG
9948 CTTGAATTTG
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 80 1.00
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (84 bp):
TTGCTTCTGCTCCTTGCCATTGCTGTTTTAGTTATTGATGCAACTCAACCTGGTTAAACTCTGCT
AGACTGTTTCTTCTTCTGG
Found at i:11377 original size:20 final size:22
Alignment explanation
Indices: 11352--11402 Score: 70
Period size: 20 Copynumber: 2.4 Consensus size: 22
11342 AATTATAAAA
11352 TAATTATTATAAT-ATTA-TAT
1 TAATTATTATAATGATTATTAT
*
11372 TAATTATGATAATGATTATTTAT
1 TAATTATTATAATGATTA-TTAT
11395 TAATTATT
1 TAATTATT
11403 TGATAAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 12 0.46
21 4 0.15
23 10 0.38
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (22 bp):
TAATTATTATAATGATTATTAT
Found at i:11419 original size:21 final size:22
Alignment explanation
Indices: 11389--11488 Score: 64
Period size: 21 Copynumber: 4.7 Consensus size: 22
11379 GATAATGATT
* *
11389 ATTTATTAATTATTTGATAA-A
1 ATTTAATAATTATTTAATAACA
* * *
11410 ATTTAATAATCATTTTATAACT
1 ATTTAATAATTATTTAATAACA
* *
11432 ATTCAATAA-AATTTAATAATC-
1 ATTTAATAATTATTTAATAA-CA
* * *
11453 ATTTTATAACTATTCAATAA-A
1 ATTTAATAATTATTTAATAACA
*
11474 ATTTAATGATTATTT
1 ATTTAATAATTATTT
11489 TATACTAATA
Statistics
Matches: 60, Mismatches: 15, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
21 43 0.72
22 17 0.28
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTTAATAATTATTTAATAACA
Found at i:11429 original size:11 final size:10
Alignment explanation
Indices: 11400--11480 Score: 54
Period size: 11 Copynumber: 7.7 Consensus size: 10
11390 TTTATTAATT
* *
11400 ATTTGATAAA
1 ATTTAATAAC
11410 ATTTAATAATC
1 ATTTAATAA-C
*
11421 ATTTTATAAC
1 ATTTAATAAC
* *
11431 TATTCAATAAA
1 -ATTTAATAAC
11442 ATTTAATAATC
1 ATTTAATAA-C
*
11453 ATTTTATAAC
1 ATTTAATAAC
* *
11463 TATTCAATAAA
1 -ATTTAATAAC
11474 ATTTAAT
1 ATTTAAT
11481 GATTATTTTA
Statistics
Matches: 54, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
10 24 0.44
11 30 0.56
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.44
Consensus pattern (10 bp):
ATTTAATAAC
Found at i:11441 original size:32 final size:32
Alignment explanation
Indices: 11405--11492 Score: 158
Period size: 32 Copynumber: 2.8 Consensus size: 32
11395 TAATTATTTG
11405 ATAAAATTTAATAATCATTTTATAACTATTCA
1 ATAAAATTTAATAATCATTTTATAACTATTCA
11437 ATAAAATTTAATAATCATTTTATAACTATTCA
1 ATAAAATTTAATAATCATTTTATAACTATTCA
* *
11469 ATAAAATTTAATGATTATTTTATA
1 ATAAAATTTAATAATCATTTTATA
11493 CTAATAAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 54 1.00
ACGTcount: A:0.47, C:0.07, G:0.01, T:0.45
Consensus pattern (32 bp):
ATAAAATTTAATAATCATTTTATAACTATTCA
Found at i:12210 original size:38 final size:38
Alignment explanation
Indices: 12159--12234 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
12149 TGTTTTTAGT
12159 CAAATAAAAAGATTAGGATCCGAGCAAACTGAGTTGTC
1 CAAATAAAAAGATTAGGATCCGAGCAAACTGAGTTGTC
12197 CAAATAAAAAGATTAGGATCCGAGCAAACTGAGTTGTC
1 CAAATAAAAAGATTAGGATCCGAGCAAACTGAGTTGTC
12235 GCCTGATACC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (38 bp):
CAAATAAAAAGATTAGGATCCGAGCAAACTGAGTTGTC
Found at i:12360 original size:29 final size:28
Alignment explanation
Indices: 12312--12370 Score: 109
Period size: 29 Copynumber: 2.1 Consensus size: 28
12302 AAATAAACTG
12312 ACTGTAAGTTATTTAATTTTGATATCCC
1 ACTGTAAGTTATTTAATTTTGATATCCC
12340 ACTGTAAGTTGATTTAATTTTGATATCCC
1 ACTGTAAGTT-ATTTAATTTTGATATCCC
12369 AC
1 AC
12371 AACAGTGCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 10 0.33
29 20 0.67
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (28 bp):
ACTGTAAGTTATTTAATTTTGATATCCC
Found at i:19700 original size:2 final size:2
Alignment explanation
Indices: 19693--19721 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
19683 ACAAATCAAC
19693 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 A
19722 GTTTCCTTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20832 original size:2 final size:2
Alignment explanation
Indices: 20825--20860 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
20815 TAAATGTAGA
20825 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
20861 GAAAATATGT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28179 original size:67 final size:67
Alignment explanation
Indices: 27977--28181 Score: 252
Period size: 69 Copynumber: 3.0 Consensus size: 67
27967 AGTACATATT
27977 AATAAAATTGTTGCGGTTTTATTTAAAAAAGGCCACTATAGATGGACCTATTGTGACGTTTTTCA
1 AATAAAATTGTTGCGGTTTTATTTAAAAAAGGCCACTATAGATGGACCTATTGTGACGTTTTTCA
28042 AA
66 AA
** * ** * **
28044 AATAAAAAACG--CCACTATTATTAATAAAAAATGGGTACTATAGATGGACCTATTGTGACGTTT
1 AAT-AAAATTGTTGCGGTTTTATT--TAAAAAA-GGCCACTATAGATGGACCTATTGTGACGTTT
28107 TTCAAA
62 TTCAAA
* * * *
28113 AATAAAATTGTTGCGGTTTTATTTAAAAAAGGCCACTATAGATGGATCTATTGCGGCGTTTGTCA
1 AATAAAATTGTTGCGGTTTTATTTAAAAAAGGCCACTATAGATGGACCTATTGTGACGTTTTTCA
28178 AA
66 AA
28180 AA
1 AA
28182 ACGCCACTAT
Statistics
Matches: 112, Mismatches: 20, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
66 7 0.06
67 36 0.32
68 24 0.21
69 38 0.34
70 7 0.06
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (67 bp):
AATAAAATTGTTGCGGTTTTATTTAAAAAAGGCCACTATAGATGGACCTATTGTGACGTTTTTCA
AA
Found at i:29844 original size:21 final size:21
Alignment explanation
Indices: 29818--29860 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
29808 AACTTAAAAT
*
29818 CCTAAATTATAGACCT-TAAAC
1 CCTAAATCATA-ACCTCTAAAC
29839 CCTAAATCATAACCTCTAAAC
1 CCTAAATCATAACCTCTAAAC
29860 C
1 C
29861 ATAATGTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.42, C:0.30, G:0.02, T:0.26
Consensus pattern (21 bp):
CCTAAATCATAACCTCTAAAC
Found at i:35159 original size:23 final size:23
Alignment explanation
Indices: 35129--35176 Score: 69
Period size: 23 Copynumber: 2.1 Consensus size: 23
35119 TCCATCTTTA
* *
35129 TGGCACATTTTTATCTATTTTTG
1 TGGCACATTTTCATCTATTGTTG
*
35152 TGGCACATTTTCATCTGTTGTTG
1 TGGCACATTTTCATCTATTGTTG
35175 TG
1 TG
35177 ACACGCTTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.52
Consensus pattern (23 bp):
TGGCACATTTTCATCTATTGTTG
Found at i:35615 original size:19 final size:19
Alignment explanation
Indices: 35593--35632 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35583 GTTTAATTTA
35593 TTATTATAATTATAA-ATAT
1 TTATTAT-ATTATAAGATAT
*
35612 TTATTATATTTTAAGATAT
1 TTATTATATTATAAGATAT
35631 TT
1 TT
35633 TATATTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TTATTATATTATAAGATAT
Found at i:40017 original size:24 final size:24
Alignment explanation
Indices: 39972--40017 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
39962 GAGTTTAGTA
**
39972 TTTTAAATTATCACTTTTAATTAT
1 TTTTAAATTATCACTTAAAATTAT
39996 TTTTAAAATTAT-ACTTAAAATT
1 TTTT-AAATTATCACTTAAAATT
40018 TAATTTTTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.54
Consensus pattern (24 bp):
TTTTAAATTATCACTTAAAATTAT
Found at i:40024 original size:25 final size:24
Alignment explanation
Indices: 39971--40024 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
39961 CGAGTTTAGT
**
39971 ATTTTAAATTATCACTTTTAATTA
1 ATTTTAAATTATCACTTAAAATTA
*
39995 TTTTTAAAATTAT-ACTTAAAATTTA
1 ATTTT-AAATTATCACTTAAAA-TTA
40020 ATTTT
1 ATTTT
40025 TGTTTTATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 10 0.42
25 14 0.58
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.56
Consensus pattern (24 bp):
ATTTTAAATTATCACTTAAAATTA
Found at i:40055 original size:19 final size:19
Alignment explanation
Indices: 40010--40060 Score: 70
Period size: 18 Copynumber: 2.8 Consensus size: 19
40000 AAAATTATAC
40010 TTAAAATTTAAT-TTTTGT
1 TTAAAATTTAATATTTTGT
* *
40028 TT-TATTTTAATATTTTGT
1 TTAAAATTTAATATTTTGT
40046 TTAAAATTTAATATT
1 TTAAAATTTAATATT
40061 AAATTTTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
17 7 0.26
18 10 0.37
19 10 0.37
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (19 bp):
TTAAAATTTAATATTTTGT
Found at i:55695 original size:128 final size:128
Alignment explanation
Indices: 55467--55722 Score: 512
Period size: 128 Copynumber: 2.0 Consensus size: 128
55457 CTAAATATGA
55467 ATTAAATTCAAAGATAATTTTCAATCTATACGCGGAAGGAATTACCCAAAAGGGTAAATTATATA
1 ATTAAATTCAAAGATAATTTTCAATCTATACGCGGAAGGAATTACCCAAAAGGGTAAATTATATA
55532 TTTTTTTTCATTGAATTTTACTATTTCTCTTATTTTGTTCATTATATTTTTAGATATTTCAAT
66 TTTTTTTTCATTGAATTTTACTATTTCTCTTATTTTGTTCATTATATTTTTAGATATTTCAAT
55595 ATTAAATTCAAAGATAATTTTCAATCTATACGCGGAAGGAATTACCCAAAAGGGTAAATTATATA
1 ATTAAATTCAAAGATAATTTTCAATCTATACGCGGAAGGAATTACCCAAAAGGGTAAATTATATA
55660 TTTTTTTTCATTGAATTTTACTATTTCTCTTATTTTGTTCATTATATTTTTAGATATTTCAAT
66 TTTTTTTTCATTGAATTTTACTATTTCTCTTATTTTGTTCATTATATTTTTAGATATTTCAAT
55723 CTACTTACTA
Statistics
Matches: 128, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.34, C:0.11, G:0.09, T:0.46
Consensus pattern (128 bp):
ATTAAATTCAAAGATAATTTTCAATCTATACGCGGAAGGAATTACCCAAAAGGGTAAATTATATA
TTTTTTTTCATTGAATTTTACTATTTCTCTTATTTTGTTCATTATATTTTTAGATATTTCAAT
Found at i:56966 original size:23 final size:24
Alignment explanation
Indices: 56923--56967 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56913 CCCCCCAACT
56923 ATACTCATCAACTTTTCTTTTCCG
1 ATACTCATCAACTTTTCTTTTCCG
* *
56947 ATACTCGTCAA-TTTTTTTTTC
1 ATACTCATCAACTTTTCTTTTC
56968 TTTATCAAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 9 0.47
24 10 0.53
ACGTcount: A:0.20, C:0.24, G:0.04, T:0.51
Consensus pattern (24 bp):
ATACTCATCAACTTTTCTTTTCCG
Found at i:59424 original size:21 final size:21
Alignment explanation
Indices: 59400--59440 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
59390 TATTGCAATG
59400 TCAAAATTAGGTACAATAATA
1 TCAAAATTAGGTACAATAATA
*
59421 TCAAAATTAGGTGCAATAAT
1 TCAAAATTAGGTACAATAAT
59441 GTTTGAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.49, C:0.10, G:0.12, T:0.29
Consensus pattern (21 bp):
TCAAAATTAGGTACAATAATA
Found at i:63987 original size:21 final size:21
Alignment explanation
Indices: 63962--64009 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
63952 CCTAATATTG
63962 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
63983 CAATGTCAAAATTAGGTGCAA
1 CAATGTCAAAATTAGGTGCAA
*
64004 TAATGT
1 CAATGT
64010 TTGAAAATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.42, C:0.12, G:0.19, T:0.27
Consensus pattern (21 bp):
CAATGTCAAAATTAGGTGCAA
Found at i:71366 original size:24 final size:24
Alignment explanation
Indices: 71330--71375 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 24
71320 AATTGAACCT
* *
71330 AAAATGTTTTATTCTTAATAATCG
1 AAAATATTATATTCTTAATAATCG
* *
71354 AAAATATTATATTTTTCATAAT
1 AAAATATTATATTCTTAATAAT
71376 ATTTTAGGTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.04, T:0.48
Consensus pattern (24 bp):
AAAATATTATATTCTTAATAATCG
Found at i:75508 original size:2 final size:2
Alignment explanation
Indices: 75501--75525 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
75491 TCTACTTGTC
75501 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 A
75526 AATTAAAAGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:79904 original size:33 final size:31
Alignment explanation
Indices: 79857--79926 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 31
79847 TTAAATTTTT
* *
79857 TTAAAAAAATATATA-AATATTTTACAATTTG
1 TTAAAAAAATATATATAATA-ATGACAATTTG
79888 TTAAAAAAATAAATATATAATAATGACAATTTG
1 TTAAAAAAAT--ATATATAATAATGACAATTTG
*
79921 ATAAAA
1 TTAAAA
79927 TATATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 10 0.30
33 19 0.58
34 4 0.12
ACGTcount: A:0.57, C:0.03, G:0.04, T:0.36
Consensus pattern (31 bp):
TTAAAAAAATATATATAATAATGACAATTTG
Found at i:80075 original size:18 final size:18
Alignment explanation
Indices: 80025--80077 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
80015 TAAATAATTC
*
80025 TATTCTCTGATAATCTTT
1 TATTCTCTGATAATCTTA
*
80043 TATTCCTACTTATAATCTTA
1 TATT-CT-CTGATAATCTTA
80063 TATTCTCTGATAATC
1 TATTCTCTGATAATC
80078 ATACGCATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 12 0.40
19 4 0.13
20 14 0.47
ACGTcount: A:0.26, C:0.19, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTCTCTGATAATCTTA
Found at i:83811 original size:19 final size:19
Alignment explanation
Indices: 83789--83835 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
83779 AAATAGACCC
83789 TAAAATAAAAATTAAAT-T
1 TAAAATAAAAATTAAATAT
* **
83807 TTAAATATAATTTTAAATAT
1 TAAAATA-AAAATTAAATAT
83827 TAAAATAAA
1 TAAAATAAA
83836 CTAAAAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 6 0.26
19 10 0.43
20 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (19 bp):
TAAAATAAAAATTAAATAT
Found at i:101557 original size:38 final size:38
Alignment explanation
Indices: 101514--101588 Score: 105
Period size: 38 Copynumber: 2.0 Consensus size: 38
101504 TCAAAAAAAT
* * *
101514 GGGTCAAGTTCGAGTCGGATGAAGGGTATATAATTTTC
1 GGGTCAAGTTCAAATCGAATGAAGGGTATATAATTTTC
* *
101552 GGGTCAAGTTCAAATCGAATGGAGGGTGTATAATTTT
1 GGGTCAAGTTCAAATCGAATGAAGGGTATATAATTTT
101589 TGAATCGATT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.28, C:0.09, G:0.31, T:0.32
Consensus pattern (38 bp):
GGGTCAAGTTCAAATCGAATGAAGGGTATATAATTTTC
Found at i:102558 original size:4 final size:4
Alignment explanation
Indices: 102549--102611 Score: 126
Period size: 4 Copynumber: 15.8 Consensus size: 4
102539 AATTTGAAAT
102549 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
1 ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA ATAA
102597 ATAA ATAA ATAA ATA
1 ATAA ATAA ATAA ATA
102612 GTAGATTAGT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 59 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAA
Done.