Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005657.1 Hibiscus syriacus cultivar Beakdansim tig00013227_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: 60438
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Found at i:2065 original size:16 final size:16
Alignment explanation
Indices: 2046--2098 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2036 CCATAACCCC
2046 TATCACACATATATCA
1 TATCACACATATATCA
** * *
2062 TATCATGCACACATCA
1 TATCACACATATATCA
2078 TATCACACATCATATACA
1 TATCACACAT-ATAT-CA
2096 TAT
1 TAT
2099 ATCACATACA
Statistics
Matches: 27, Mismatches: 8, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
16 19 0.70
17 3 0.11
18 5 0.19
ACGTcount: A:0.42, C:0.26, G:0.02, T:0.30
Consensus pattern (16 bp):
TATCACACATATATCA
Found at i:2451 original size:23 final size:23
Alignment explanation
Indices: 2425--2493 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2415 CACCACAGCT
*
2425 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* * *
2448 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
2471 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
2494 TATAATAATG
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.26, C:0.25, G:0.28, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:2680 original size:103 final size:103
Alignment explanation
Indices: 2509--2720 Score: 379
Period size: 103 Copynumber: 2.1 Consensus size: 103
2499 TAATGTCCAT
* * * *
2509 AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTCACCA
1 AAGGACAACATATCATTCCTTAAGAATCATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
2574 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
*
2612 AAGGACAACATATCATTCCTTAAGAATCATATAAATATGCCAAGGATCAAGTATGTGTCTCACCA
1 AAGGACAACATATCATTCCTTAAGAATCATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
2677 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
66 GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
2715 AAGGAC
1 AAGGAC
2721 CCCGTAGACC
Statistics
Matches: 104, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
103 104 1.00
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AAGGACAACATATCATTCCTTAAGAATCATATAAATATACCAAGGATCAAGTATGTGTCTCACCA
GACTTCACACATGTTCCAAAGAATACATATATGTCCCG
Found at i:5679 original size:64 final size:64
Alignment explanation
Indices: 5528--5681 Score: 166
Period size: 64 Copynumber: 2.4 Consensus size: 64
5518 TCTTTAACGG
* * **
5528 TGCATCGATGCACTACTTGTGTATCGGTGCATAAAATACATTCGATGTTTCAATATTAAGGTGA
1 TGCATCGATGCACTACTTGTGCATCGATGCATAAAATACATTCGATGTTTCAATATTAAGAAGA
* ** * * * * * *
5592 TGCATCGATACACGCCTTATGCATCGATGCATTAATTGCATTTGATGTTTCTATTATTAAGAAG-
1 TGCATCGATGCACTACTTGTGCATCGATGCATAAAATACATTCGATGTTTC-AATATTAAGAAGA
*
5656 TTCATCGATGCACTACTTGTGCATCG
1 TGCATCGATGCACTACTTGTGCATCG
5682 GTACACCTTC
Statistics
Matches: 71, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
64 62 0.87
65 9 0.13
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (64 bp):
TGCATCGATGCACTACTTGTGCATCGATGCATAAAATACATTCGATGTTTCAATATTAAGAAGA
Found at i:9423 original size:18 final size:18
Alignment explanation
Indices: 9396--9430 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9386 TTCAGTATTC
*
9396 GTCCCGAAGGACCACTAT
1 GTCCCAAAGGACCACTAT
9414 GTCCCAAAGGACCACTA
1 GTCCCAAAGGACCACTA
9431 GATATGTCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.34, G:0.20, T:0.14
Consensus pattern (18 bp):
GTCCCAAAGGACCACTAT
Found at i:9439 original size:22 final size:22
Alignment explanation
Indices: 9395--9517 Score: 155
Period size: 22 Copynumber: 5.8 Consensus size: 22
9385 ATTCAGTATT
9395 CGTCCCGAAGGACCACT--AT-
1 CGTCCCGAAGGACCACTGGATA
* *
9414 -GTCCCAAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTGGATA
* *
9435 TGTCCCGAATGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
9457 CGTCCCGAAAGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
9479 CGTCCCGAATGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
9501 CGCCCCGAAGGACCACT
1 CGTCCCGAAGGACCACT
9518 ATGTCCCGAA
Statistics
Matches: 91, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
18 15 0.16
20 2 0.02
22 74 0.81
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.15
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTGGATA
Found at i:9484 original size:44 final size:43
Alignment explanation
Indices: 9395--9531 Score: 155
Period size: 44 Copynumber: 3.3 Consensus size: 43
9385 ATTCAGTATT
*
9395 CGTCCCGAAGGACCACT--AT--GTCCC-AAAGGACCACTAGATA
1 CGTCCCGAATGACCACTGGATACGTCCCGAAA-GACCACT-GATA
*
9435 TGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACTGGATA
1 CGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACT-GATA
* *
9479 CGTCCCGAATGACCACTGGATACGCCCCGAAGGACCACT-AT-
1 CGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACTGATA
9520 -GTCCCGAATGAC
1 CGTCCCGAATGAC
9532 TAATATACCC
Statistics
Matches: 86, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
40 27 0.31
42 4 0.05
44 52 0.60
45 3 0.03
ACGTcount: A:0.29, C:0.33, G:0.22, T:0.16
Consensus pattern (43 bp):
CGTCCCGAATGACCACTGGATACGTCCCGAAAGACCACTGATA
Found at i:9666 original size:28 final size:27
Alignment explanation
Indices: 9615--9667 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
9605 TATTTTATCA
*
9615 CACTTTCACATATTCACATGTACATGT
1 CACTTTCACATATTCACATATACATGT
* *
9642 CACTTTCATATGATTCATATATACAT
1 CACTTTCACAT-ATTCACATATACAT
9668 CACATAGCAC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.40
Consensus pattern (27 bp):
CACTTTCACATATTCACATATACATGT
Found at i:18109 original size:3 final size:3
Alignment explanation
Indices: 18101--18128 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
18091 TTGAAAGTCG
18101 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
18129 AAAAGATGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:19993 original size:51 final size:50
Alignment explanation
Indices: 19938--20128 Score: 134
Period size: 54 Copynumber: 3.6 Consensus size: 50
19928 ATGCTCTGAC
* *
19938 CAGCATAGTTCTCATTCTTACCTGCATTCTCATTGTTGGTGTTGATTTGAA
1 CAGCATAGTTCTCATTCTGACCTGCATTCTCATTGTTGGTG-TAATTTGAA
* * ** * *
19989 CAGCATTATTATTCTCATTCTGACTTGCATTCTCACCGTTGTTGTAATTCTGGGA
1 CAGCA-TA--GTTCTCATTCTGACCTGCATTCTCATTGTTGGTGTAATT-T-GAA
* ** * *
20044 -GGCATTCTTCTCATTCAT-ACCTGCTTTCTCATTGTTGGTGCCAATTTGAA
1 CAGCATAGTTCTCATTC-TGACCTGCATTCTCATTGTTGGTG-TAATTTGAA
* *
20094 CAGCATTGTTATTCTCATTCTGACTTGCATTCTCA
1 CAGCATAG---TTCTCATTCTGACCTGCATTCTCA
20129 CTGATATTGT
Statistics
Matches: 106, Mismatches: 22, Indels: 21
0.71 0.15 0.14
Matches are distributed among these distances:
50 2 0.02
51 37 0.35
52 7 0.07
53 6 0.06
54 52 0.49
55 2 0.02
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (50 bp):
CAGCATAGTTCTCATTCTGACCTGCATTCTCATTGTTGGTGTAATTTGAA
Found at i:20193 original size:111 final size:105
Alignment explanation
Indices: 19946--20170 Score: 306
Period size: 105 Copynumber: 2.1 Consensus size: 105
19936 ACCAGCATAG
* * ***
19946 TTCTCATTCTTACCTGCATTCTCATTGTTGGTGTTGATTTGAACAGCATTATTATTCTCATTCTG
1 TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTATTATTCTCATTCTG
* *
20011 ACTTGCATTCTCACCGTTGTTGTAATTCTGGGAGGCATTC
66 ACTTGCATTCTCACCGTTGTTGTAATTCTGGGAAGCATTA
*
20051 TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTGTTATTCTCATTCTG
1 TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTATTATTCTCATTCTG
* *
20116 ACTTGCATTCTCACTGATATTGTTGTTGTAGTTCTGGGAAGCATTA
66 ACTTGCATTCTCAC------CGTTGTTGTAATTCTGGGAAGCATTA
20162 TTCTCATTC
1 TTCTCATTC
20171 TGACTGGCTT
Statistics
Matches: 104, Mismatches: 10, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
105 73 0.70
111 31 0.30
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (105 bp):
TTCTCATTCATACCTGCTTTCTCATTGTTGGTGCCAATTTGAACAGCATTATTATTCTCATTCTG
ACTTGCATTCTCACCGTTGTTGTAATTCTGGGAAGCATTA
Found at i:20334 original size:57 final size:57
Alignment explanation
Indices: 20208--20464 Score: 267
Period size: 57 Copynumber: 4.6 Consensus size: 57
20198 CCCTGAGCAG
* * * * * * * * *
20208 CATTGTTCTCATTCTCACTCGCGTTCTCATGGTTGTTAGTGTTGATCTGAACAGAAGT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAA-T
* * * * *
20266 -TTTATTTTCATTCTGACTTGCATTCTCATTGTTGCTGGTATTGATCTGAACGGCAT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
* * *
20322 CATTGTTCTCATTCTGATTTGCATTATCATTGTTGCCGGTATTGATCTGAACGAAAT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
* * *
20379 CATTGTTCTCATTCTGACCTGCATTATCATTGTTG-T--TGTTGCTCTG---GGAAT
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
*
20430 CATTATTCTCATTCTGACTTGCATTATCATTGTTG
1 CATTGTTCTCATTCTGACTTGCATTATCATTGTTG
20465 TTGTTGCTCT
Statistics
Matches: 170, Mismatches: 28, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
51 37 0.22
54 8 0.05
56 1 0.01
57 124 0.73
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.44
Consensus pattern (57 bp):
CATTGTTCTCATTCTGACTTGCATTATCATTGTTGCTGGTATTGATCTGAACGGAAT
Found at i:20453 original size:51 final size:52
Alignment explanation
Indices: 20267--20496 Score: 230
Period size: 57 Copynumber: 4.3 Consensus size: 52
20257 AACAGAAGTT
* * *
20267 TTATTTTCATTCTGACTTGCATTCTCATTGTTGCTGGTATTGATCTGAACGGCATCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTTG-T--TATTGATCTG-A-GGAATCA
* * * *
20324 TTGTTCTCATTCTGATTTGCATTATCATTGTTGCCGGTATTGATCTGAACGAAATCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTT---GTTATTGATCTG-A-GGAATCA
* * * *
20381 TTGTTCTCATTCTGACCTGCATTATCATTGTTGTTGTTGCTCTG-GGAATCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTTGTTATTGATCTGAGGAATCA
* * *
20432 TTATTCTCATTCTGACTTGCATTATCATTGTTGTTGTTGCTCTG-GGAAGCA
1 TTATTCTCATTCTGACTTGCATTATCATTGTTGTTATTGATCTGAGGAATCA
20483 TTATTCTCATTCTG
1 TTATTCTCATTCTG
20497 TTCAGCATTC
Statistics
Matches: 154, Mismatches: 16, Indels: 12
0.85 0.09 0.07
Matches are distributed among these distances:
51 68 0.44
54 9 0.06
57 76 0.49
60 1 0.01
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.45
Consensus pattern (52 bp):
TTATTCTCATTCTGACTTGCATTATCATTGTTGTTATTGATCTGAGGAATCA
Found at i:20469 original size:57 final size:49
Alignment explanation
Indices: 20300--20496 Score: 110
Period size: 51 Copynumber: 3.7 Consensus size: 49
20290 CTCATTGTTG
* * *
20300 CTGGTATTGATCTGAACGGCATCATTGTTCTCATTCTGATTTGCATTATCA
1 CTGGTATTGATCTG-A-GGAATCATTATTCTCATTCTGACTTGCATTATCA
* * * *
20351 TTGTTGCCGGTATTGATCTGAACGAAATCATTGTTCTCATTCTGACCTGCATTATCA
1 ------CTGGTATTGATCTG-A-GGAATCATTATTCTCATTCTGACTTGCATTATCA
* * *
20408 TTGTTGTTGTTGCTCTG-GGAATCATTATTCTCATTCTGACTTGCATTATCA
1 CTG--G-TATTGATCTGAGGAATCATTATTCTCATTCTGACTTGCATTATCA
* * * *
20459 TTGTTGTTGTTGCTCTG-GGAAGCATTATTCTCATTCTG
1 CTG--G-TATTGATCTGAGGAATCATTATTCTCATTCTG
20497 TTCAGCATTC
Statistics
Matches: 124, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
51 69 0.56
53 1 0.01
54 8 0.06
57 46 0.37
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.43
Consensus pattern (49 bp):
CTGGTATTGATCTGAGGAATCATTATTCTCATTCTGACTTGCATTATCA
Found at i:20505 original size:51 final size:51
Alignment explanation
Indices: 20379--20575 Score: 214
Period size: 51 Copynumber: 3.9 Consensus size: 51
20369 TGAACGAAAT
* * *
20379 CATTGTTCTCATTCTGACCTGCATTATCATTGTTGTTGTTGCTCTGGGAAT
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
**
20430 CATTATTCTCATTCTGACTTGCATTATCATTGTTGTTGTTGCTCTGGGAAG
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
** * ** * **** * *
20481 CATTATTCTCATTCTGTTCAGCATTCTGGTTGTTGGTAACACTCTGAGCAG
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
* * *
20532 CATTTTTCTCATTTTGACCAGCATTCTCATTGTTGTTGTTGCTC
1 CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTC
20576 AGAACAGTAT
Statistics
Matches: 118, Mismatches: 28, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
51 118 1.00
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (51 bp):
CATTATTCTCATTCTGACCAGCATTATCATTGTTGTTGTTGCTCTGGGAAG
Found at i:25402 original size:34 final size:33
Alignment explanation
Indices: 25326--25432 Score: 85
Period size: 34 Copynumber: 3.1 Consensus size: 33
25316 GTGGTAAGAA
* *
25326 ATTTATTTTTATGTTAGTAT-TTT-TTTAAATAGTT
1 ATTT-TTTTTAT-TTAATATATTTATATAAATA-TT
*
25360 ATTATTTTTTATATTAATATATTTATCTAAATATT
1 ATT-TTTTTTAT-TTAATATATTTATATAAATATT
* *
25395 A-TTTTTTTATTAAATTAATATTTATATAATTATT
1 ATTTTTTTTATTTAA-T-ATATTTATATAAATATT
25429 ATTT
1 ATTT
25433 ATTTAGAATT
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
32 3 0.05
33 9 0.15
34 33 0.54
35 9 0.15
36 7 0.11
ACGTcount: A:0.34, C:0.01, G:0.03, T:0.63
Consensus pattern (33 bp):
ATTTTTTTTATTTAATATATTTATATAAATATT
Found at i:25406 original size:31 final size:34
Alignment explanation
Indices: 25359--25437 Score: 101
Period size: 34 Copynumber: 2.4 Consensus size: 34
25349 TTTAAATAGT
*
25359 TATTATTTTTTATATT-AA-T-ATATTTATCTAAA
1 TATTATTTTTT-TATTAAATTAATATTTATATAAA
*
25391 TATTATTTTTTTATTAAATTAATATTTATATAAT
1 TATTATTTTTTTATTAAATTAATATTTATATAAA
*
25425 TATTATTTATTTA
1 TATTATTTTTTTA
25438 GAATTATTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
31 4 0.10
32 13 0.32
33 1 0.02
34 23 0.56
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.62
Consensus pattern (34 bp):
TATTATTTTTTTATTAAATTAATATTTATATAAA
Found at i:25600 original size:17 final size:17
Alignment explanation
Indices: 25578--25631 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
25568 AATGTTAATA
25578 TTTAAATTTATTTTTAT
1 TTTAAATTTATTTTTAT
* * * *
25595 TTTAAAGTTATTATGAA
1 TTTAAATTTATTTTTAT
* *
25612 TTTATATTAATTTTTAT
1 TTTAAATTTATTTTTAT
25629 TTT
1 TTT
25632 TATAATGTAT
Statistics
Matches: 27, Mismatches: 10, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (17 bp):
TTTAAATTTATTTTTAT
Found at i:27191 original size:21 final size:21
Alignment explanation
Indices: 27161--27208 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
27151 GCAGGGGTAC
* *
27161 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
27182 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
27203 ATGCCA
1 ATGCCA
27209 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:27238 original size:21 final size:21
Alignment explanation
Indices: 27212--27305 Score: 113
Period size: 21 Copynumber: 4.5 Consensus size: 21
27202 TATGCCATCT
*
27212 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATTCCTAGC
27233 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATTCCTAGC
27254 CCGCCA-GGTTACATGT-CTAGC
1 CCG-CAGGGTTACAT-TCCTAGC
* *
27275 CTGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATTCCTAGC
27296 CCGCAGGGTT
1 CCGCAGGGTT
27306 TTATACCATA
Statistics
Matches: 65, Mismatches: 4, Indels: 8
0.84 0.05 0.10
Matches are distributed among these distances:
20 2 0.03
21 60 0.92
22 3 0.05
ACGTcount: A:0.18, C:0.33, G:0.27, T:0.22
Consensus pattern (21 bp):
CCGCAGGGTTACATTCCTAGC
Found at i:27964 original size:14 final size:14
Alignment explanation
Indices: 27945--27974 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
27935 TTTTATCATT
*
27945 AACATATATATTAA
1 AACATATACATTAA
27959 AACATATACATTAA
1 AACATATACATTAA
27973 AA
1 AA
27975 TCAACTTATG
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:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (14 bp):
AACATATACATTAA
Found at i:28458 original size:128 final size:128
Alignment explanation
Indices: 28230--28985 Score: 1248
Period size: 128 Copynumber: 5.9 Consensus size: 128
28220 TTACCTGATT
28230 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
28295 TGATGAAATAATAGAAGGCGCGCCCCCGAGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
28358 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
28423 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTCCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGT-GAATAGTGAAATAATAGG
* *
28486 TAATGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGCTAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
28551 TGATGAAATAATGGAAGGCGCACCCCCGGGAACGCGTCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
28614 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATATGGCAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*** *
28679 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTTCCCT-GAGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATG-TGAATAGTGAAATAATAGG
* * *
28742 TAATGATATATCTAGTGTCCCCGAGGGATATGAGTGACATAATAGGGAAATGATAACATATTCTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
* * *
28807 TGATGAAATAATGGAAGGCACG-CCCCGGGTACGCGCCTTCATGTGAATAGTGAAATAATAGG
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
*
28869 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTTTC
1 TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
*
28934 TGACAAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
66 TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGT
28986 ACTCCGATTA
Statistics
Matches: 578, Mismatches: 45, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
126 2 0.00
127 113 0.20
128 460 0.80
129 3 0.01
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.24
Consensus pattern (128 bp):
TACTGATATATCTAGTGTCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAACATATTCTC
TGACGAAATAATGGAAGGCGCGCCCCCGGGAACGCGCCTTCATGTGAATAGTGAAATAATAGG
Found at i:29069 original size:8 final size:8
Alignment explanation
Indices: 29056--29095 Score: 55
Period size: 8 Copynumber: 5.1 Consensus size: 8
29046 TCACAATCTT
29056 TCAAATTC
1 TCAAATTC
29064 TCAAATTC
1 TCAAATTC
* *
29072 CCAAACTC
1 TCAAATTC
29080 T-AAATTC
1 TCAAATTC
29087 TCAAATTC
1 TCAAATTC
29095 T
1 T
29096 TTGAAAATGA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.35
Consensus pattern (8 bp):
TCAAATTC
Found at i:32119 original size:18 final size:18
Alignment explanation
Indices: 32098--32147 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
32088 TAAATATATT
32098 TAATATATTATAATATAA
1 TAATATATTATAATATAA
*
32116 TAATATATTATTAGT-TAA
1 TAATATATTA-TAATATAA
*
32134 TAAT-TAATATAATA
1 TAATATATTATAATA
32148 AATTCCACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 5
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.11
17 4 0.15
18 17 0.63
19 3 0.11
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
TAATATATTATAATATAA
Found at i:38901 original size:31 final size:31
Alignment explanation
Indices: 38866--38933 Score: 82
Period size: 31 Copynumber: 2.2 Consensus size: 31
38856 ATATAATAAA
* *
38866 TTATAAAAAATGAAAAAATTTATTGATTATT
1 TTATAAAAAATGAAAAAATTTAATGACTATT
* * * *
38897 TTATAATAATTTAACAAATTTAATGACTATT
1 TTATAAAAAATGAAAAAATTTAATGACTATT
38928 TTATAA
1 TTATAA
38934 TATTTTAATA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.44
Consensus pattern (31 bp):
TTATAAAAAATGAAAAAATTTAATGACTATT
Found at i:38934 original size:31 final size:29
Alignment explanation
Indices: 38879--38984 Score: 113
Period size: 31 Copynumber: 3.5 Consensus size: 29
38869 TAAAAAATGA
* *
38879 AAAAATTTATTGATTATTTTATAATAATTT
1 AAAAATTTAATGA-TATTTTATAATATTTT
38909 AACAAATTTAATGACTATTTTATAATATTTT
1 AA-AAATTTAATGA-TATTTTATAATATTTT
* * *
38940 AATAAAATTAAAGATATTTTCATAACATTTT
1 AA-AAATTTAATGATATTTT-ATAATATTTT
*
38971 AAAATTTTAATGAT
1 AAAAATTTAATGAT
38985 TAAAATGACC
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
30 17 0.27
31 47 0.73
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (29 bp):
AAAAATTTAATGATATTTTATAATATTTT
Found at i:43119 original size:18 final size:18
Alignment explanation
Indices: 43076--43120 Score: 56
Period size: 18 Copynumber: 2.5 Consensus size: 18
43066 ATACTCGATT
*
43076 TAATAATTTTTAATTAGA
1 TAATAATTATTAATTAGA
*
43094 TAAAAATTATTAATTA-A
1 TAATAATTATTAATTAGA
43111 CTAATAATTA
1 -TAATAATTA
43121 ATGATATTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
17 1 0.04
18 22 0.96
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (18 bp):
TAATAATTATTAATTAGA
Found at i:44009 original size:2 final size:2
Alignment explanation
Indices: 44002--44052 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
43992 AACTTTTTAA
44002 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
44044 AT AT AT AT A
1 AT AT AT AT A
44053 CTAATCTATT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:44914 original size:15 final size:15
Alignment explanation
Indices: 44894--44923 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
44884 TACTTCTAAC
44894 CAAACCAAACCAAAT
1 CAAACCAAACCAAAT
*
44909 CAAACCAAACTAAAT
1 CAAACCAAACCAAAT
44924 TTTAAATTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.60, C:0.30, G:0.00, T:0.10
Consensus pattern (15 bp):
CAAACCAAACCAAAT
Found at i:47663 original size:2 final size:2
Alignment explanation
Indices: 47656--47693 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47646 GTAATGTACT
47656 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47694 ATTGCCTTAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51147 original size:35 final size:36
Alignment explanation
Indices: 51087--51155 Score: 113
Period size: 35 Copynumber: 1.9 Consensus size: 36
51077 AAGTCTTTGC
*
51087 AGGTTCAGATCTGATCAAACTGGTAATTCCTTATAT
1 AGGTTCAGATCCGATCAAACTGGTAATTCCTTATAT
*
51123 AGGTTCAGA-CCGATCGAACTGGTAATTCCTTAT
1 AGGTTCAGATCCGATCAAACTGGTAATTCCTTAT
51156 GGACCTAAGG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 22 0.71
36 9 0.29
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (36 bp):
AGGTTCAGATCCGATCAAACTGGTAATTCCTTATAT
Found at i:56612 original size:22 final size:22
Alignment explanation
Indices: 56584--56632 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
56574 AGTCAACTCA
56584 TTGACTTTGACCA-TAGTTGACT
1 TTGACTTTGACCAGT-GTTGACT
**
56606 TTGACTTTGATTAGTGTTGACT
1 TTGACTTTGACCAGTGTTGACT
56628 TTGAC
1 TTGAC
56633 AAAAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.45
Consensus pattern (22 bp):
TTGACTTTGACCAGTGTTGACT
Done.