Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009211.1 Hibiscus syriacus cultivar Beakdansim tig00112798_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: 71413
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:3312 original size:17 final size:17
Alignment explanation
Indices: 3291--3329 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
3281 GCTCAGCCTA
3291 TTTTCCT-TCATTTCCC
1 TTTTCCTCTCATTTCCC
*
3307 TCTTTCCTCTCTTTTCCC
1 T-TTTCCTCTCATTTCCC
3325 TTTTC
1 TTTTC
3330 AGTGTGAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
16 1 0.05
17 10 0.50
18 9 0.45
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (17 bp):
TTTTCCTCTCATTTCCC
Found at i:6247 original size:42 final size:42
Alignment explanation
Indices: 6200--6283 Score: 134
Period size: 43 Copynumber: 2.0 Consensus size: 42
6190 GAAGATTTCA
6200 AGGGTA-CTTTCACATAACAGAAAGAACATTTTGGGGGCTTTT
1 AGGGTATCTTTCACATAACAGAAAGAACATTTT-GGGGCTTTT
* *
6242 AGGGTATTTTTCACATAATAGAAAGAACATTTTGGGGCTTTT
1 AGGGTATCTTTCACATAACAGAAAGAACATTTTGGGGCTTTT
6284 CATAAAAGTT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
42 15 0.38
43 24 0.62
ACGTcount: A:0.31, C:0.12, G:0.23, T:0.35
Consensus pattern (42 bp):
AGGGTATCTTTCACATAACAGAAAGAACATTTTGGGGCTTTT
Found at i:12435 original size:31 final size:32
Alignment explanation
Indices: 12375--12436 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 32
12365 TTAATTATAT
* *
12375 TATTTTTATAATATTTTTAAATAATAAAAATA
1 TATTTTTATAATATATTTAAATAACAAAAATA
*
12407 TATTTTTATAA-ATATTTAATTAACAAAAAT
1 TATTTTTATAATATATTTAAATAACAAAAAT
12437 TTATAAATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 16 0.59
32 11 0.41
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (32 bp):
TATTTTTATAATATATTTAAATAACAAAAATA
Found at i:12459 original size:25 final size:25
Alignment explanation
Indices: 12411--12459 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
12401 AAAATATATT
* *
12411 TTTATAAATATTTAATTAACAAAAA
1 TTTATAAATATTTAATAAAAAAAAA
**
12436 TTTATAAATATTTTCTAAAAAAAA
1 TTTATAAATATTTAATAAAAAAAA
12460 GAATATTCTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.41
Consensus pattern (25 bp):
TTTATAAATATTTAATAAAAAAAAA
Found at i:17313 original size:50 final size:50
Alignment explanation
Indices: 17206--17314 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
17196 TAACGTGACG
* * * *
17206 AGTTTCAATAAAATATATTTTTTAATTAAATTTTATCACCTCGAAGATAA
1 AGTTTTAAAAAAATATATTTTTTAATTAAAATTTATCACATCGAAGATAA
** * *
17256 AAATTTAAAAAAATATATTTTTT-ATTAAAATTTATCACATCGATGTTACA
1 AGTTTTAAAAAAATATATTTTTTAATTAAAATTTATCACATCGAAGATA-A
17306 AGTTTTAAA
1 AGTTTTAAA
17315 TCACTATAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
49 21 0.44
50 27 0.56
ACGTcount: A:0.44, C:0.08, G:0.06, T:0.42
Consensus pattern (50 bp):
AGTTTTAAAAAAATATATTTTTTAATTAAAATTTATCACATCGAAGATAA
Found at i:18882 original size:51 final size:51
Alignment explanation
Indices: 18820--18920 Score: 152
Period size: 51 Copynumber: 2.0 Consensus size: 51
18810 ATCAACTTAT
*
18820 CTCAGTGGTTAAAGGAACCA-TGATTATTCTTAAAGGTCACGA-GTTCAAACC
1 CTCAGTGGTTAAAAGAACCATTG-TTATTCTTAAAGGTCAC-ATGTTCAAACC
*
18871 CTCAGTGGTTAAAAGAATCATTGTTATTCTTAAAGGTCACATGTTCAAAC
1 CTCAGTGGTTAAAAGAACCATTGTTATTCTTAAAGGTCACATGTTCAAAC
18921 ATTAACGACT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
50 1 0.02
51 43 0.93
52 2 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (51 bp):
CTCAGTGGTTAAAAGAACCATTGTTATTCTTAAAGGTCACATGTTCAAACC
Found at i:26132 original size:31 final size:31
Alignment explanation
Indices: 26094--26159 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
26084 TTAAAAAATA
26094 TAAGATATGATCAATTTTGTTTCTATTTAAT
1 TAAGATATGATCAATTTTGTTTCTATTTAAT
* * *
26125 TAAGATATGGTTAATTTTGTTTTTATTTAAT
1 TAAGATATGATCAATTTTGTTTCTATTTAAT
26156 TAAG
1 TAAG
26160 TTGTGGTCAC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.03, G:0.12, T:0.53
Consensus pattern (31 bp):
TAAGATATGATCAATTTTGTTTCTATTTAAT
Found at i:26953 original size:25 final size:27
Alignment explanation
Indices: 26895--26963 Score: 79
Period size: 27 Copynumber: 2.6 Consensus size: 27
26885 TATAATATAA
* * *
26895 ATATATATATTAATTTAAAAATATTTT
1 ATATTTATTTTAATTTAAAAATATTAT
* *
26922 ATTTTTATTTTCATTTAAAAATA-TAT
1 ATATTTATTTTAATTTAAAAATATTAT
26948 A-ATTTATTTTAATTTA
1 ATATTTATTTTAATTTA
26964 TTAAAAGTAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
25 13 0.37
26 3 0.09
27 19 0.54
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (27 bp):
ATATTTATTTTAATTTAAAAATATTAT
Found at i:35430 original size:20 final size:20
Alignment explanation
Indices: 35405--35455 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
35395 GGTTTTGGCT
35405 TTGGCCTTTGAAAGGGTGAG
1 TTGGCCTTTGAAAGGGTGAG
35425 TTGGCCTTTGAAAGGGTGAG
1 TTGGCCTTTGAAAGGGTGAG
35445 TTGGCCTTTGA
1 TTGGCCTTTGA
35456 TTGTTTTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.18, C:0.12, G:0.37, T:0.33
Consensus pattern (20 bp):
TTGGCCTTTGAAAGGGTGAG
Found at i:36484 original size:23 final size:23
Alignment explanation
Indices: 36458--36508 Score: 84
Period size: 23 Copynumber: 2.2 Consensus size: 23
36448 TAAGCTACCA
36458 AAAGACAGAGAAAAACATATCAC
1 AAAGACAGAGAAAAACATATCAC
* *
36481 AAAGACAGAGATAAACATGTCAC
1 AAAGACAGAGAAAAACATATCAC
36504 AAAGA
1 AAAGA
36509 TATAATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.59, C:0.16, G:0.16, T:0.10
Consensus pattern (23 bp):
AAAGACAGAGAAAAACATATCAC
Found at i:37634 original size:18 final size:18
Alignment explanation
Indices: 37611--37649 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
37601 GTCATTTAAC
37611 ATTTTAAAAGTAT-TATAT
1 ATTTT-AAAGTATATATAT
*
37629 ATTTTAAATTATATATAT
1 ATTTTAAAGTATATATAT
37647 ATT
1 ATT
37650 CAATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
ATTTTAAAGTATATATAT
Found at i:41583 original size:116 final size:117
Alignment explanation
Indices: 41461--41677 Score: 312
Period size: 116 Copynumber: 1.9 Consensus size: 117
41451 TAGTTAGGGC
** * *
41461 TCCTAATTATTATAATTTCATAAAATTTTTAGTTTTTGATCCTCTTTTTCCATTTATGTTATTAA
1 TCCTAATTATTATAATTTCATAAAACGTTTAGTTTTTGACCCTCTTTTTCCATTTATCTTATTAA
* *
41526 TTCA-TCTAATTTTGAATTAAAATTAACCA-TTTTTTATATTTATAATTAGAT
66 TTCATTC-AATCTTAAATTAAAATTAACCACTTTTTTATATTTATAATTAGAT
* * *
41577 TCCTAATTTTTATAATTTCATAAAACGTTTAGTTTTTGACCCTCTTTTTCCATTTCTCTTATTTA
1 TCCTAATTATTATAATTTCATAAAACGTTTAGTTTTTGACCCTCTTTTTCCATTTATCTTATTAA
* *
41642 TTCATTCAATCTTAAATTAAATTTAATCACTTTTTT
66 TTCATTCAATCTTAAATTAAAATTAACCACTTTTTT
41678 CAAATATTAC
Statistics
Matches: 88, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
116 80 0.91
117 8 0.09
ACGTcount: A:0.29, C:0.13, G:0.04, T:0.53
Consensus pattern (117 bp):
TCCTAATTATTATAATTTCATAAAACGTTTAGTTTTTGACCCTCTTTTTCCATTTATCTTATTAA
TTCATTCAATCTTAAATTAAAATTAACCACTTTTTTATATTTATAATTAGAT
Found at i:43636 original size:21 final size:21
Alignment explanation
Indices: 43612--43660 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
43602 AGTACTGTGG
43612 ACAATCATGTCAGCACCGTAA
1 ACAATCATGTCAGCACCGTAA
* *
43633 ACAATCATGTCAGTACCGTGA
1 ACAATCATGTCAGCACCGTAA
*
43654 ACTATCA
1 ACAATCA
43661 CATCAACACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.37, C:0.27, G:0.14, T:0.22
Consensus pattern (21 bp):
ACAATCATGTCAGCACCGTAA
Found at i:45568 original size:37 final size:37
Alignment explanation
Indices: 45482--45579 Score: 110
Period size: 37 Copynumber: 2.6 Consensus size: 37
45472 ATTCGATTTT
* * *
45482 AAAAATATATACCCTCCACCCGAATATGACCCGATCTG
1 AAAAATATATATCCT-CACCCGAATACGACCCGATCTA
* * *
45520 AAAAATATATATCCTTCACCCGACT-CGACCTGTTCTA
1 AAAAATATATATCC-TCACCCGAATACGACCCGATCTA
45557 AAAAATATATATCC-CACCCGAAT
1 AAAAATATATATCCTCACCCGAAT
45580 CTAATCCAAG
Statistics
Matches: 52, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
35 8 0.15
37 22 0.42
38 21 0.40
39 1 0.02
ACGTcount: A:0.38, C:0.30, G:0.08, T:0.24
Consensus pattern (37 bp):
AAAAATATATATCCTCACCCGAATACGACCCGATCTA
Found at i:46012 original size:31 final size:31
Alignment explanation
Indices: 45954--46017 Score: 83
Period size: 31 Copynumber: 2.1 Consensus size: 31
45944 ACATCAACAC
* * * * *
45954 TTTAAATACATAATATTTGTTATATTATCAT
1 TTTAAACACATAATATGTATAACATTATCAT
45985 TTTAAACACATAATATGTATAACATTATCAT
1 TTTAAACACATAATATGTATAACATTATCAT
46016 TT
1 TT
46018 ACTATAATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.41, C:0.09, G:0.03, T:0.47
Consensus pattern (31 bp):
TTTAAACACATAATATGTATAACATTATCAT
Found at i:47079 original size:2 final size:2
Alignment explanation
Indices: 47072--47135 Score: 57
Period size: 2 Copynumber: 34.5 Consensus size: 2
47062 ACTTGAATTC
* * *
47072 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TC T- TA TA TA GA GA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
47112 -A TA -A GA -A TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
47136 TCTTATTTTT
Statistics
Matches: 56, Mismatches: 1, Indels: 10
0.84 0.01 0.15
Matches are distributed among these distances:
1 5 0.09
2 51 0.91
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (2 bp):
TA
Found at i:50215 original size:25 final size:25
Alignment explanation
Indices: 50177--50300 Score: 216
Period size: 25 Copynumber: 5.0 Consensus size: 25
50167 AGTTAGGGGA
*
50177 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
50201 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
50226 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
50251 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
50276 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
50301 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:50425 original size:3 final size:3
Alignment explanation
Indices: 50417--50477 Score: 65
Period size: 3 Copynumber: 21.0 Consensus size: 3
50407 TGCAAAATTG
* **
50417 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
50461 TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA
50478 CGGAAAAAAC
Statistics
Matches: 48, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
2 5 0.10
3 40 0.83
4 3 0.06
ACGTcount: A:0.67, C:0.02, G:0.03, T:0.28
Consensus pattern (3 bp):
TAA
Found at i:50613 original size:1 final size:1
Alignment explanation
Indices: 50574--50598 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
50564 AGAAAACACG
50574 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
50599 GGTTCTCCTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:50724 original size:43 final size:43
Alignment explanation
Indices: 50667--50903 Score: 167
Period size: 43 Copynumber: 5.4 Consensus size: 43
50657 CTCATATGCA
* *
50667 ATGAAGAGGTCTGGTCGTCTAAGGGTGACACGGCTCCTACGTG
1 ATGAAGAGATCTGGTCATCTAAGGGTGACACGGCTCCTACGTG
* * * * * *
50710 ATGAGGAGATCTGGTTATCTTTAGGGATGATAACTCGGTTCCTACGTA
1 ATGAAGAGATCTGGTCATC-TAAGGG-TG---ACACGGCTCCTACGTG
* * * *
50758 ATGAGGACGA-CTGGTTATC--AGGTTGACACGGCTCTTACGTG
1 ATGAAGA-GATCTGGTCATCTAAGGGTGACACGGCTCCTACGTG
* * *
50799 ATGAAGAGATCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTG
1 ATGAAGAGATCTGGTCATCT-AAGG-G-TGACACGGCTCCTACGTG
* * * * * *
50845 ATGAGGACG-GCTGGTTATCTATGGTTGACACGGCTCATACGTG
1 ATGAAGA-GATCTGGTCATCTAAGGGTGACACGGCTCCTACGTG
50888 ATGAAGAGATCTGGTC
1 ATGAAGAGATCTGGTC
50904 CGGGGGATGA
Statistics
Matches: 148, Mismatches: 32, Indels: 28
0.71 0.15 0.13
Matches are distributed among these distances:
40 2 0.01
41 25 0.17
42 1 0.01
43 41 0.28
44 10 0.07
45 8 0.05
46 29 0.20
47 1 0.01
48 29 0.20
49 2 0.01
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.27
Consensus pattern (43 bp):
ATGAAGAGATCTGGTCATCTAAGGGTGACACGGCTCCTACGTG
Found at i:50859 original size:87 final size:91
Alignment explanation
Indices: 50692--50901 Score: 302
Period size: 89 Copynumber: 2.4 Consensus size: 91
50682 CGTCTAAGGG
* * ** * * *
50692 TGACACGGCTCCTACGTGATGAGGAGATCTGGTTATCTTTAGGGATGATAACTCGGTTCCTACGT
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAAAGGATGATAACACGGTTCCTACGT
50757 AATGAGGACGACTGGTTATC-A-GGT
66 AATGAGGACGACTGGTTATCTATGGT
*
50781 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TAAAGG-TGATAACACGGTTCCTACGT
1 TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAAAGGATGATAACACGGTTCCTACGT
* *
50844 GATGAGGACGGCTGGTTATCTATGGT
66 AATGAGGACGACTGGTTATCTATGGT
50870 TGACACGGCTCATACGTGATGAAGAGATCTGG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG
50902 TCCGGGGGAT
Statistics
Matches: 109, Mismatches: 10, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
87 37 0.34
88 5 0.05
89 67 0.61
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.27
Consensus pattern (91 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGCCATCTTAAAGGATGATAACACGGTTCCTACGT
AATGAGGACGACTGGTTATCTATGGT
Found at i:50944 original size:130 final size:134
Alignment explanation
Indices: 50781--51027 Score: 353
Period size: 135 Copynumber: 1.9 Consensus size: 134
50771 GTTATCAGGT
* * *
50781 TGACACGGCTCTTACGTGATGAAGAGATCTGGCCATC-TA-AA-GGTGATAACACGGTTCCTACG
1 TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
*
50843 TGATGAGGACGGCTGGTTAT-CT-ATGGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCG
66 TGATGAGGACGACTGGTTATCCTAAT-GTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCG
50906 GGGGA
130 GGGGA
* *
50911 TGACACGGTTCATACATGATGAA-AAACTCTGGCCATCTTTAGGAAGGGTGATAACTCGGTTCCT
1 TGACACGGCTCATACATGATGAAGAAA-TCTGGCCATC-TTA-GAAGGGTGATAACACGGTTCCT
*
50975 ACGTGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCCTACGTGATGA
63 ACGTGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCATACGTGATGA
51028 GGAAGTCCGG
Statistics
Matches: 102, Mismatches: 7, Indels: 10
0.86 0.06 0.08
Matches are distributed among these distances:
129 2 0.02
130 30 0.29
132 2 0.02
134 2 0.02
135 39 0.38
136 25 0.25
137 2 0.02
ACGTcount: A:0.26, C:0.20, G:0.29, T:0.26
Consensus pattern (134 bp):
TGACACGGCTCATACATGATGAAGAAATCTGGCCATCTTAGAAGGGTGATAACACGGTTCCTACG
TGATGAGGACGACTGGTTATCCTAATGTTGACACGGCTCATACGTGATGAAGAGATCTGGTCCGG
GGGA
Found at i:65511 original size:25 final size:25
Alignment explanation
Indices: 65473--65595 Score: 207
Period size: 25 Copynumber: 5.0 Consensus size: 25
65463 AGTTAGGGGA
*
65473 TTAGGG-TTGAAACCCTAAAT-TGTT
1 TTAGGGTTTGAAACCCT-AATCTGAT
65497 TTAGGGTTTGAAACCCTAATCTGA-
1 TTAGGGTTTGAAACCCTAATCTGAT
65521 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
65546 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
65571 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAATCTGAT
65596 GGGTTGGTTC
Statistics
Matches: 95, Mismatches: 1, Indels: 5
0.94 0.01 0.05
Matches are distributed among these distances:
24 33 0.35
25 62 0.65
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.36
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGAT
Found at i:65549 original size:49 final size:49
Alignment explanation
Indices: 65471--65595 Score: 209
Period size: 49 Copynumber: 2.6 Consensus size: 49
65461 GTAGTTAGGG
*
65471 GATTAGGG-TTGAAACCCTAAAT-TGTTTTAGGGTTTGAAACCCTAATCT
1 GATTAGGGTTTGAAACCCT-AATCTGATTTAGGGTTTGAAACCCTAATCT
65519 GATTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAATCT
1 GATTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAATCT
65568 GATTTAGGGTTTGAAACCCTAATCTGAT
1 GA-TTAGGGTTTGAAACCCTAATCTGAT
65596 GGGTTGGTTC
Statistics
Matches: 73, Mismatches: 1, Indels: 4
0.94 0.01 0.05
Matches are distributed among these distances:
48 11 0.15
49 37 0.51
50 25 0.34
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (49 bp):
GATTAGGGTTTGAAACCCTAATCTGATTTAGGGTTTGAAACCCTAATCT
Found at i:65719 original size:3 final size:3
Alignment explanation
Indices: 65711--65768 Score: 59
Period size: 3 Copynumber: 20.0 Consensus size: 3
65701 GCAAAAATTG
* **
65711 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
65755 TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA
65769 ATAACGGACA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
2 5 0.11
3 37 0.82
4 3 0.07
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (3 bp):
TAA
Found at i:65766 original size:11 final size:11
Alignment explanation
Indices: 65711--65772 Score: 60
Period size: 11 Copynumber: 6.0 Consensus size: 11
65701 GCAAAAATTG
65711 TAATAATA-AA
1 TAATAATATAA
*
65721 TAATAATAAAA
1 TAATAATATAA
*
65732 TAATAAGATAA
1 TAATAATATAA
**
65743 CGAT-A-ATAA
1 TAATAATATAA
65752 TAATAATATAA
1 TAATAATATAA
65763 TAATAA-ATAA
1 TAATAATATAA
65773 CGGACAAAAC
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
9 6 0.14
10 14 0.33
11 23 0.53
ACGTcount: A:0.66, C:0.02, G:0.03, T:0.29
Consensus pattern (11 bp):
TAATAATATAA
Found at i:66808 original size:30 final size:31
Alignment explanation
Indices: 66732--66835 Score: 174
Period size: 31 Copynumber: 3.4 Consensus size: 31
66722 TCCGTAGATT
* *
66732 CCGAAGAACCTAGGTAATCAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
66763 CCGAAGAACATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
66794 CCGAAGAA-ATAGGTAAACAGTCCATATGTC
1 CCGAAGAACATAGGTAAACAGTCCATATGTC
*
66824 CCAAAGAACATA
1 CCGAAGAACATA
66836 AAACCCTCAA
Statistics
Matches: 69, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
30 29 0.42
31 40 0.58
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (31 bp):
CCGAAGAACATAGGTAAACAGTCCATATGTC
Found at i:67777 original size:20 final size:21
Alignment explanation
Indices: 67729--67779 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
67719 GAGGGGATCG
*
67729 ATTCCCCATTGAATGTGTACCT
1 ATTCCCC-TTGAATGGGTACCT
67751 ATT-CCCTTGAATGGGTACC-
1 ATTCCCCTTGAATGGGTACCT
67770 ATTCCCCTTG
1 ATTCCCCTTG
67780 CCCAGAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 3 0.11
20 18 0.67
21 3 0.11
22 3 0.11
ACGTcount: A:0.20, C:0.29, G:0.16, T:0.35
Consensus pattern (21 bp):
ATTCCCCTTGAATGGGTACCT
Found at i:69001 original size:28 final size:27
Alignment explanation
Indices: 68965--69017 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
68955 ATTATTAAAA
68965 AATAATTAATTAGTGTGTTAGTTAGTCT
1 AATAATTAATTAGTGTG-TAGTTAGTCT
* *
68993 AATATTTAATTAGTTTGTAGTTAGT
1 AATAATTAATTAGTGTGTAGTTAGT
69018 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:69023 original size:27 final size:29
Alignment explanation
Indices: 68964--69028 Score: 82
Period size: 27 Copynumber: 2.3 Consensus size: 29
68954 TATTATTAAA
68964 AAATAATTAATTAGTGTGTTAGTTAGTCT
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
* *
68993 -AATATTTAATTAGTTTG-TAGTTAGT-T
1 AAATAATTAATTAGTGTGTTAGTTAGTCT
*
69019 AAATAGTTAA
1 AAATAATTAA
69029 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:69118 original size:36 final size:38
Alignment explanation
Indices: 69049--69124 Score: 104
Period size: 39 Copynumber: 2.0 Consensus size: 38
69039 GGTTGTTGAA
*
69049 TTTTATATATATAAAAATTAGTTTATTAGTAGTTTAAGT
1 TTTTATATATATAAAAAATAGTTTATTA-TAGTTTAAGT
69088 TTTTAT-TATAATAAAAAATAGTTTA-T-TAGTTTAAGT
1 TTTTATATAT-ATAAAAAATAGTTTATTATAGTTTAAGT
69124 T
1 T
69125 ATATAAAAGA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
36 11 0.31
38 4 0.11
39 20 0.57
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.51
Consensus pattern (38 bp):
TTTTATATATATAAAAAATAGTTTATTATAGTTTAAGT
Found at i:69120 original size:28 final size:28
Alignment explanation
Indices: 69089--69192 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 28
69079 AGTTTAAGTT
*
69089 TTTATTATAATAAAAAATAGTTTATTAG
1 TTTATTATTATAAAAAATAGTTTATTAG
*
69117 TTTAAGTTA-TATAAAAGAATAATTATTTAATTAG
1 TTT-A-TTATTATAAAA-AAT-A--GTTT-ATTAG
* * *
69151 -TTATTGTTATAAATTATTAGTTTATTAG
1 TTTATTATTATAAA-AAATAGTTTATTAG
69179 TTTATTATTATAAA
1 TTTATTATTATAAA
69193 TTAGGGTAAA
Statistics
Matches: 59, Mismatches: 7, Indels: 19
0.69 0.08 0.22
Matches are distributed among these distances:
28 8 0.14
29 22 0.37
30 6 0.10
31 4 0.07
32 9 0.15
33 5 0.08
34 5 0.08
ACGTcount: A:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (28 bp):
TTTATTATTATAAAAAATAGTTTATTAG
Found at i:69184 original size:29 final size:28
Alignment explanation
Indices: 69138--69195 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 28
69128 TAAAAGAATA
*
69138 ATTATTTAATTAGTTATTGTTATAAATT
1 ATTATTTAATTAGTTATTATTATAAATT
69166 ATTAGTTT-ATTAGTTTATTATTATAAATT
1 ATTA-TTTAATTAG-TTATTATTATAAATT
69195 A
1 A
69196 GGGTAAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 9 0.33
29 18 0.67
ACGTcount: A:0.36, C:0.00, G:0.07, T:0.57
Consensus pattern (28 bp):
ATTATTTAATTAGTTATTATTATAAATT
Found at i:69413 original size:28 final size:29
Alignment explanation
Indices: 69380--69438 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
69370 GCCATGCACA
*
69380 GCCATGCAGA-CTTCAAGCTCGCCCGGAT
1 GCCATGCAGACCTCCAAGCTCGCCCGGAT
** *
69408 GCCATGGTGACCTCCAAGGTCGCCCGGAT
1 GCCATGCAGACCTCCAAGCTCGCCCGGAT
69437 GC
1 GC
69439 ATGACGACCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 8 0.31
29 18 0.69
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.17
Consensus pattern (29 bp):
GCCATGCAGACCTCCAAGCTCGCCCGGAT
Done.