Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004584.1 Hibiscus syriacus cultivar Beakdansim tig00010236_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: 59897
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:5869 original size:43 final size:47
Alignment explanation
Indices: 5821--5926 Score: 132
Period size: 49 Copynumber: 2.3 Consensus size: 47
5811 ATAACTAATG
*
5821 AATAAAATAATAACAAACT-AAA-CATGTTTTAACT-A-TAATTCCT
1 AATAAAATAATAACAAACTAAAATAATGTTTTAACTAACTAATTCCT
*
5864 AATAAAATAATAA-TAACTAAAATAATGTTTTAACTCAACCTTAATTCCT
1 AATAAAATAATAACAAACTAAAATAATGTTTTAACT-AA-C-TAATTCCT
5913 AATAAAATAATAAC
1 AATAAAATAATAAC
5927 TCTAATCCTA
Statistics
Matches: 53, Mismatches: 2, Indels: 9
0.83 0.03 0.14
Matches are distributed among these distances:
42 4 0.08
43 16 0.30
44 11 0.21
46 1 0.02
49 21 0.40
ACGTcount: A:0.53, C:0.13, G:0.02, T:0.32
Consensus pattern (47 bp):
AATAAAATAATAACAAACTAAAATAATGTTTTAACTAACTAATTCCT
Found at i:6201 original size:50 final size:50
Alignment explanation
Indices: 6126--6251 Score: 243
Period size: 50 Copynumber: 2.5 Consensus size: 50
6116 GGAAAGATAA
*
6126 GAGTGGATCATTTGGAAGAGTTATTACTTCTTCCTTTCCAAGGCTTGGAC
1 GAGTGGATCATTTGGAAGAGTTATTACTTATTCCTTTCCAAGGCTTGGAC
6176 GAGTGGATCATTTGGAAGAGTTATTACTTATTCCTTTCCAAGGCTTGGAC
1 GAGTGGATCATTTGGAAGAGTTATTACTTATTCCTTTCCAAGGCTTGGAC
6226 GAGTGGATCATTTGGAAGAGTTATTA
1 GAGTGGATCATTTGGAAGAGTTATTA
6252 ATCGATTGTA
Statistics
Matches: 75, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.25, C:0.14, G:0.25, T:0.36
Consensus pattern (50 bp):
GAGTGGATCATTTGGAAGAGTTATTACTTATTCCTTTCCAAGGCTTGGAC
Found at i:9710 original size:59 final size:59
Alignment explanation
Indices: 9618--9738 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 59
9608 AATAGATAGA
** * *
9618 TAAGTGTCCTGTCGAACCCTCCTAGTCACAATGAAAAGGCAAACTCGATAATATGGCTC
1 TAAGTGTCCAATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
**
9677 TAAGTGTCCAATCGAACCCTCCTAGTTGCAATGAAAAGGAAAACTCGATAATATGACTC
1 TAAGTGTCCAATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
9736 TAA
1 TAA
9739 CCAACCCTCC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
59 56 1.00
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.24
Consensus pattern (59 bp):
TAAGTGTCCAATCGAACCCTCCTAGTCACAATGAAAAGGAAAACTCGATAATATGACTC
Found at i:14096 original size:23 final size:22
Alignment explanation
Indices: 14061--14105 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
14051 TTATATTTTA
*
14061 AAATTAAAAAAAAAAATAAATT
1 AAATCAAAAAAAAAAATAAATT
14083 AAATCAAAACAAAAAAATAAATT
1 AAATCAAAA-AAAAAAATAAATT
14106 TTAAAACATG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 8 0.38
23 13 0.62
ACGTcount: A:0.76, C:0.04, G:0.00, T:0.20
Consensus pattern (22 bp):
AAATCAAAAAAAAAAATAAATT
Found at i:14800 original size:15 final size:15
Alignment explanation
Indices: 14782--14811 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
14772 TAGAAAATAC
14782 CATTGAAGAAGAGGA
1 CATTGAAGAAGAGGA
14797 CATTGAAGAAGAGGA
1 CATTGAAGAAGAGGA
14812 AGGGATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.07, G:0.33, T:0.13
Consensus pattern (15 bp):
CATTGAAGAAGAGGA
Found at i:17394 original size:110 final size:110
Alignment explanation
Indices: 17201--17414 Score: 392
Period size: 110 Copynumber: 1.9 Consensus size: 110
17191 AGACCCCAAA
* *
17201 GGACAATGGTGCAATGACAGAAACAAACTAAAGGAGGAAGCATTTAATTTTTTCAAAGAAATTTG
1 GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGCAGTTAATTTTTTCAAAGAAATTTG
17266 CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCCTAATCT
66 CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCCTAATCT
*
17311 GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGTAGTTAATTTTTTCAAAGAAATTTG
1 GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGCAGTTAATTTTTTCAAAGAAATTTG
*
17376 CTCTTTTGATGTAACCTATTTTGGAGCATACCCAACTCC
66 CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCC
17415 CAATTTGTTT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
110 100 1.00
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.29
Consensus pattern (110 bp):
GGACAATGGTGCAATGACACAAACAAACTAAAGGAGGAAGCAGTTAATTTTTTCAAAGAAATTTG
CTCTTTTGATGTAACCTATTTGGGAGCATACCCAACTCCTAATCT
Found at i:20285 original size:40 final size:40
Alignment explanation
Indices: 20211--20290 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
20201 ACGGTGTATA
* * * *
20211 AGGTGGGCACGGCCCGACCTCAGCACTACGGTGCATTATT
1 AGGTGAGCAAGGCCCGACCTCAGCACAACGGTGCAATATT
* **
20251 AGGTGAGCAAGGCTCGACCTCAGCACAATTGTGCAATATT
1 AGGTGAGCAAGGCCCGACCTCAGCACAACGGTGCAATATT
20291 TGACTCCTAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.25, C:0.26, G:0.28, T:0.21
Consensus pattern (40 bp):
AGGTGAGCAAGGCCCGACCTCAGCACAACGGTGCAATATT
Found at i:20548 original size:21 final size:21
Alignment explanation
Indices: 20522--20568 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
20512 TATGTGTTGC
20522 ATTGCTTTAAATATTCGTATG
1 ATTGCTTTAAATATTCGTATG
*
20543 ATTGCTTTAAATATTTGTATG
1 ATTGCTTTAAATATTCGTATG
20564 ATTGC
1 ATTGC
20569 CTCACTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.49
Consensus pattern (21 bp):
ATTGCTTTAAATATTCGTATG
Found at i:21915 original size:15 final size:15
Alignment explanation
Indices: 21882--21935 Score: 65
Period size: 15 Copynumber: 3.6 Consensus size: 15
21872 CTATGAGTAC
*
21882 ATGTTATATGTGAGA-
1 ATGTTCTATGTGA-AT
21897 ATGTTCTATGTGAAT
1 ATGTTCTATGTGAAT
* *
21912 ATGTGCTAAGTGAAT
1 ATGTTCTATGTGAAT
21927 ATGTTCTAT
1 ATGTTCTAT
21936 TAGAATAAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
14 1 0.03
15 32 0.97
ACGTcount: A:0.30, C:0.06, G:0.22, T:0.43
Consensus pattern (15 bp):
ATGTTCTATGTGAAT
Found at i:22181 original size:24 final size:24
Alignment explanation
Indices: 22154--22205 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
22144 ACAAATATAT
* * *
22154 GTGGGACTTCGGTGCATATTCTAC
1 GTGGCACTTCGATGCAAATTCTAC
*
22178 GTGGCACTTCGATGCAAATTCTAT
1 GTGGCACTTCGATGCAAATTCTAC
22202 GTGG
1 GTGG
22206 TAGTGGTGAT
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:0.19, C:0.19, G:0.29, T:0.33
Consensus pattern (24 bp):
GTGGCACTTCGATGCAAATTCTAC
Found at i:23814 original size:37 final size:37
Alignment explanation
Indices: 23773--23843 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
23763 AGCATAATGT
23773 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATACGA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATACGA
*
23810 TAGAGTTTTACTATGATTCAAACTCCTAAAAATA
1 TAGAGTTTTACTAGGATTCAAACTCCTAAAAATA
23844 GGATCCACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.41, C:0.15, G:0.11, T:0.32
Consensus pattern (37 bp):
TAGAGTTTTACTAGGATTCAAACTCCTAAAAATACGA
Found at i:24525 original size:34 final size:32
Alignment explanation
Indices: 24486--24609 Score: 101
Period size: 33 Copynumber: 3.7 Consensus size: 32
24476 TATATACATA
*
24486 TATTTTATTTATTATTCTTATACCCTT-CTATTTT
1 TATTTTATTTATTACTCTT-TA--CTTACTATTTT
24520 TATTTTATTTTATTACTCTTTACTTACTATTTT
1 TATTTTA-TTTATTACTCTTTACTTACTATTTT
* *
24553 TATTATTATTAGTATTACT-ATTA-TTATTATTATT
1 TATT-TTATT--TATTACTCTTTACTTACTATT-TT
* *
24587 CTATTTTATTTATTTCTATTTAC
1 -TATTTTATTTATTACTCTTTAC
24610 CCTTTTTATT
Statistics
Matches: 76, Mismatches: 5, Indels: 18
0.77 0.05 0.18
Matches are distributed among these distances:
32 9 0.12
33 23 0.30
34 22 0.29
35 22 0.29
ACGTcount: A:0.24, C:0.10, G:0.01, T:0.65
Consensus pattern (32 bp):
TATTTTATTTATTACTCTTTACTTACTATTTT
Found at i:24560 original size:3 final size:3
Alignment explanation
Indices: 24547--24586 Score: 53
Period size: 3 Copynumber: 13.3 Consensus size: 3
24537 CTTTACTTAC
* * *
24547 TAT TTT TAT TAT TAT TAG TAT TAC TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
24587 CTATTTTATT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:24724 original size:30 final size:30
Alignment explanation
Indices: 24634--24730 Score: 92
Period size: 30 Copynumber: 3.1 Consensus size: 30
24624 TCCTCCATTC
*
24634 ATTTTTATTTTTATTCCTTATCTTTA-TTATTT
1 ATTTTTA-TTTTCTT-CTTAT-TTTATTTATTT
* *
24666 ATTTTTTATCTTCTT-TACATTTGT-TTTATTT
1 A-TTTTTATTTTCTTCT-TATTT-TATTTATTT
24697 ATTTTTATTTTCTTCTTATTTTATTTATTT
1 ATTTTTATTTTCTTCTTATTTTATTTATTT
24727 ATTT
1 ATTT
24731 GTTTATTATG
Statistics
Matches: 54, Mismatches: 5, Indels: 14
0.74 0.07 0.19
Matches are distributed among these distances:
29 1 0.02
30 30 0.56
31 11 0.20
32 6 0.11
33 6 0.11
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.73
Consensus pattern (30 bp):
ATTTTTATTTTCTTCTTATTTTATTTATTT
Found at i:29224 original size:15 final size:15
Alignment explanation
Indices: 29206--29245 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
29196 ATATGAGTAC
29206 ATGTTATATGTGAAA
1 ATGTTATATGTGAAA
* *
29221 ATGTTAAATGTGAAT
1 ATGTTATATGTGAAA
*
29236 ATGTTCTATG
1 ATGTTATATG
29246 GGAATAAATG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.35, C:0.03, G:0.20, T:0.42
Consensus pattern (15 bp):
ATGTTATATGTGAAA
Found at i:29445 original size:24 final size:24
Alignment explanation
Indices: 29413--29562 Score: 107
Period size: 24 Copynumber: 6.3 Consensus size: 24
29403 TCGAGGGTTT
* *
29413 TACGCGGTCCTTCAGGACAAATTC
1 TACGTGGTCCTTCGGGACAAATTC
*
29437 TACGTGGTCCTTTGGGACAAATTC
1 TACGTGGTCCTTCGGGACAAATTC
*
29461 TACGCT-GTCCTACGGGACAAA-TC
1 TACG-TGGTCCTTCGGGACAAATTC
* * *
29484 TATGAGG-CACTTCGGTG-CATATTC
1 TACGTGGTC-CTTCGG-GACAAATTC
* *
29508 TACGTGG-CACTTCGGTACATATTC
1 TACGTGGTC-CTTCGGGACAAATTC
*
29532 TATGTGG-CACTTCGGTG-CAAATTC
1 TACGTGGTC-CTTCGG-GACAAATTC
29556 TACGTGG
1 TACGTGG
29563 CAGTGGTGAC
Statistics
Matches: 103, Mismatches: 16, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
22 1 0.01
23 14 0.14
24 87 0.84
25 1 0.01
ACGTcount: A:0.22, C:0.24, G:0.24, T:0.30
Consensus pattern (24 bp):
TACGTGGTCCTTCGGGACAAATTC
Found at i:29563 original size:24 final size:24
Alignment explanation
Indices: 29430--29564 Score: 118
Period size: 24 Copynumber: 5.7 Consensus size: 24
29420 TCCTTCAGGA
*
29430 CAAATTCTACGTGGTC-CTTTGG-G
1 CAAATTCTACGTGG-CACTTCGGTG
* *
29453 ACAAATTCTACGCTGTC-CTACGG-G
1 -CAAATTCTACG-TGGCACTTCGGTG
* *
29477 ACAAA-TCTATGAGGCACTTCGGTG
1 -CAAATTCTACGTGGCACTTCGGTG
* *
29501 CATATTCTACGTGGCACTTCGGTA
1 CAAATTCTACGTGGCACTTCGGTG
* *
29525 CATATTCTATGTGGCACTTCGGTG
1 CAAATTCTACGTGGCACTTCGGTG
29549 CAAATTCTACGTGGCA
1 CAAATTCTACGTGGCA
29565 GTGGTGACTG
Statistics
Matches: 92, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
22 2 0.02
23 13 0.14
24 75 0.82
25 2 0.02
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (24 bp):
CAAATTCTACGTGGCACTTCGGTG
Found at i:31058 original size:19 final size:19
Alignment explanation
Indices: 31030--31068 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
31020 GTGAGTGAGC
31030 TGTTGAAGTCTATTATGAA
1 TGTTGAAGTCTATTATGAA
* *
31049 TGTTGGAGTCTGTTATGAA
1 TGTTGAAGTCTATTATGAA
31068 T
1 T
31069 CTGTTATAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.05, G:0.26, T:0.44
Consensus pattern (19 bp):
TGTTGAAGTCTATTATGAA
Found at i:40328 original size:19 final size:20
Alignment explanation
Indices: 40291--40328 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
40281 ATCAGTTTTG
* *
40291 ATTCGTTTTATTTTTAAAAC
1 ATTCATTTTATTTTCAAAAC
40311 ATTCATTTT-TTTTCAAAA
1 ATTCATTTTATTTTCAAAA
40329 TCATACTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.32, C:0.11, G:0.03, T:0.55
Consensus pattern (20 bp):
ATTCATTTTATTTTCAAAAC
Found at i:44539 original size:53 final size:53
Alignment explanation
Indices: 44413--44540 Score: 222
Period size: 53 Copynumber: 2.4 Consensus size: 53
44403 GCTAGGATTC
44413 TTCTTAGGAAATGGGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
1 TTCTTAGGAAATGGGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
* *
44466 TTCTTAGGAAATGAGG-TTTTATTTCAAGGAAGTAGAATCAGTGGTGAATGGCG
1 TTCTTAGGAAATG-GGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
44519 TTCTTAGGAAATGGGTTTTTAT
1 TTCTTAGGAAATGGGTTTTTAT
44541 GAAGCAAGAG
Statistics
Matches: 71, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
52 2 0.03
53 67 0.94
54 2 0.03
ACGTcount: A:0.29, C:0.08, G:0.29, T:0.34
Consensus pattern (53 bp):
TTCTTAGGAAATGGGTTTTTATTTCAAGGAAGCAGAATCAGTGGAGAATGGCG
Found at i:45056 original size:82 final size:82
Alignment explanation
Indices: 44940--45205 Score: 273
Period size: 82 Copynumber: 3.2 Consensus size: 82
44930 CATGCGATTA
* * * * * *** *
44940 TAGCGACGTTTGTTACACAAACACCACTATATATCGGGCTATCGCGGTGGTTTTTACATAAACAC
1 TAGCGACATTT-TCACAAAAACGCCACTATATATCTGGCTATCGCGGCATTTTTTACATAAACGC
* *
45005 CACTAAAGTATGCATTTG
65 CACTAAAGTACGCGTTTG
* * * * * *
45023 TAGCGGCGTTTTCACAAAAACGCCACTAAATATCTAGCTATCACGACATTTTTTACATAAACGCC
1 TAGCGACATTTTCACAAAAACGCCACTATATATCTGGCTATCGCGGCATTTTTTACATAAACGCC
* *
45088 ACTAAAGTACGTGTTTT
66 ACTAAAGTACGCGTTTG
* * * * *
45105 TAG-TAGCATTTTCATAAAAATGCCACTATATATTTGGCTATCGTGGCATTTTTTACATAAACGC
1 TAGCGA-CATTTTCACAAAAACGCCACTATATATCTGGCTATCGCGGCATTTTTTACATAAACGC
*
45169 CGCTAAAGTACGCGTTTG
65 CACTAAAGTACGCGTTTG
*
45187 TAGCGACATTTTCCCAAAA
1 TAGCGACATTTTCACAAAA
45206 CACCATATAT
Statistics
Matches: 147, Mismatches: 34, Indels: 5
0.79 0.18 0.03
Matches are distributed among these distances:
82 136 0.93
83 11 0.07
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Consensus pattern (82 bp):
TAGCGACATTTTCACAAAAACGCCACTATATATCTGGCTATCGCGGCATTTTTTACATAAACGCC
ACTAAAGTACGCGTTTG
Found at i:47445 original size:17 final size:17
Alignment explanation
Indices: 47420--47475 Score: 60
Period size: 17 Copynumber: 3.3 Consensus size: 17
47410 CTTTATCTCA
47420 ATTTATTTATTTTATTT
1 ATTTATTTATTTTATTT
*
47437 ATTTGTTTATTTTA-TT
1 ATTTATTTATTTTATTT
* *
47453 CTTTATATCATTTTATTT
1 ATTTAT-TTATTTTATTT
*
47471 CTTTA
1 ATTTA
47476 AACAATTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
16 6 0.18
17 20 0.61
18 7 0.21
ACGTcount: A:0.21, C:0.05, G:0.02, T:0.71
Consensus pattern (17 bp):
ATTTATTTATTTTATTT
Found at i:51802 original size:45 final size:45
Alignment explanation
Indices: 51737--52171 Score: 468
Period size: 45 Copynumber: 9.6 Consensus size: 45
51727 TTTTATACCA
* *
51737 ATAATGCACTGTTATACATTTTCATTTATGGAACCTTTTATGCTG
1 ATAATGCACCGTTATGCATTTTCATTTATGGAACCTTTTATGCTG
* * *
51782 ATAATGTACCCTTATGCATTTTTATTTATGGAACCTTTTATG-TCG
1 ATAATGCACCGTTATGCATTTTCATTTATGGAACCTTTTATGCT-G
** * *
51827 ATAATGCACCGTTATTTATTTTCATTTATGGCACCTTTTATGCTA
1 ATAATGCACCGTTATGCATTTTCATTTATGGAACCTTTTATGCTG
* * *
51872 ATAATGCACTGTTATGCATTTTCATTTAT-AACACCTTTTATGCTA
1 ATAATGCACCGTTATGCATTTTCATTTATGGA-ACCTTTTATGCTG
* * *
51917 ATAATGCACCGTTATACATTTTCATTTATGGCACCTTTTATGCCG
1 ATAATGCACCGTTATGCATTTTCATTTATGGAACCTTTTATGCTG
* *
51962 ATAATGCACCGTTATGCATTTTCATTTAT-GACACCTTTAATGCCG
1 ATAATGCACCGTTATGCATTTTCATTTATGGA-ACCTTTTATGCTG
* * * * * **
52007 ATAATGCACTGTTATGAATTTTCATTTA-AGACACTTTTTTATTCCA
1 ATAATGCACCGTTATGCATTTTCATTTATGGA-AC-CTTTTATGCTG
* * * * *
52053 ATAATGCATCGTTATTCATTTTCATTTATGGCACATTTTATGTTG
1 ATAATGCACCGTTATGCATTTTCATTTATGGAACCTTTTATGCTG
* *
52098 ATAATGCACCGTTATGCATTTTTATTTAT-GATATCTTTTATG-TCG
1 ATAATGCACCGTTATGCATTTTCATTTATGGA-ACCTTTTATGCT-G
* *
52143 ATAATGCACCATTATGCATTTTCTTTTAT
1 ATAATGCACCGTTATGCATTTTCATTTAT
52172 TTTGATAACA
Statistics
Matches: 328, Mismatches: 52, Indels: 20
0.82 0.13 0.05
Matches are distributed among these distances:
44 4 0.01
45 289 0.88
46 34 0.10
47 1 0.00
ACGTcount: A:0.26, C:0.17, G:0.12, T:0.45
Consensus pattern (45 bp):
ATAATGCACCGTTATGCATTTTCATTTATGGAACCTTTTATGCTG
Found at i:51964 original size:135 final size:135
Alignment explanation
Indices: 51723--52171 Score: 569
Period size: 135 Copynumber: 3.3 Consensus size: 135
51713 CCATGAGTGG
* * * *
51723 CACCTTTTATACCAATAATGCACTGTTATACATTTTCATTTATGGA-ACCTTTTATGCTGATAAT
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTAT-AACACCTTTTATGCTAATAAT
* * * * * **
51787 GTACCCTTATGCATTTTTATTTATGGAACCTTTTATGTCGATAATGCACCGTTATTTATTTTCAT
65 GCACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCAT
*
51852 TTATGG
130 TTATGA
*
51858 CACCTTTTATGCTAATAATGCACTGTTATGCATTTTCATTTATAACACCTTTTATGCTAATAATG
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATAACACCTTTTATGCTAATAATG
*
51923 CACCGTTATACATTTTCATTTATGGCACCTTTTATGCCGATAATGCACCGTTATGCATTTTCATT
66 CACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATT
51988 TATGA
131 TATGA
* * * * * *
51993 CACCTTTAATGCCGATAATGCACTGTTATGAATTTTCATTTA-AGACACTTTTTTATTCCAATAA
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATA-ACAC-CTTTTATGCTAATAA
* * * * *
52057 TGCATCGTTATTCATTTTCATTTATGGCACATTTTATGTTGATAATGCACCGTTATGCATTTTTA
64 TGCACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCA
52122 TTTATGA
129 TTTATGA
* * * * ** *
52129 TATCTTTTATGTCGATAATGCACCATTATGCATTTTCTTTTAT
1 CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTAT
52172 TTTGATAACA
Statistics
Matches: 275, Mismatches: 35, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
134 2 0.01
135 161 0.59
136 112 0.41
ACGTcount: A:0.26, C:0.18, G:0.11, T:0.45
Consensus pattern (135 bp):
CACCTTTTATGCCAATAATGCACTGTTATGCATTTTCATTTATAACACCTTTTATGCTAATAATG
CACCGTTATACATTTTCATTTATGGCACCTTTTATGTCGATAATGCACCGTTATGCATTTTCATT
TATGA
Found at i:55125 original size:27 final size:26
Alignment explanation
Indices: 55095--55147 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 26
55085 TTAATTATAT
* *
55095 TTTTTTTTTGAATTATAAAATATTTAA
1 TTTTTTTATAAATTATAAAAT-TTTAA
55122 TTTTTTTATAAATTATAAAATTTTAA
1 TTTTTTTATAAATTATAAAATTTTAA
55148 AAATATTCTG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (26 bp):
TTTTTTTATAAATTATAAAATTTTAA
Found at i:59757 original size:44 final size:45
Alignment explanation
Indices: 59707--59897 Score: 232
Period size: 44 Copynumber: 4.3 Consensus size: 45
59697 CCAAGAGGGG
*
59707 CACCTTTTATGCCAATAATGCACCTTTATGCA-TTTCA-TTAGTGA
1 CACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTA-TGA
* * * *
59751 CACCTTTTATGTCGATAAGGTACCGTTT-TGCATTTTCATTTATGG
1 CACCTTTTATGCCGATAATGCACC-TTTATGCATTTTCATTTATGA
59796 CACCTTTTATGCCGATAATGCA-CTATTATGCA-TTTCATTTATGA
1 CACCTTTTATGCCGATAATGCACCT-TTATGCATTTTCATTTATGA
* * *
59840 CACCTTTAATG-CGATAATGCACTTTTATGCATTTTCATTTATGG
1 CACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTATGA
*
59884 CACTTTTTATGCCG
1 CACCTTTTATGCCG
Statistics
Matches: 125, Mismatches: 14, Indels: 15
0.81 0.09 0.10
Matches are distributed among these distances:
43 18 0.14
44 69 0.55
45 35 0.28
46 3 0.02
ACGTcount: A:0.24, C:0.20, G:0.14, T:0.42
Consensus pattern (45 bp):
CACCTTTTATGCCGATAATGCACCTTTATGCATTTTCATTTATGA
Found at i:59897 original size:88 final size:89
Alignment explanation
Indices: 59705--59897 Score: 277
Period size: 89 Copynumber: 2.2 Consensus size: 89
59695 GACCAAGAGG
* *
59705 GGCACCTTTTATGCCAATAATGCACCTTTATGCATTTCATTAGTGACACCTTTTATGTCGATAAG
1 GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTCATTAGTGACACCTTTAATGTCGATAAG
*
59770 GTACCGTTTTGCATTTTCATTTAT
66 GCACCGTTTTGCATTTTCATTTAT
59794 GGCACCTTTTATGCCGATAATGCA-CTATTATGCATTTCATTTA-TGACACCTTTAATG-CGATA
1 GGCACCTTTTATGCCGATAATGCACCT-TTATGCATTTCA-TTAGTGACACCTTTAATGTCGATA
* *
59856 ATGCA-CTTTTATGCATTTTCATTTAT
64 AGGCACCGTTT-TGCATTTTCATTTAT
*
59882 GGCACTTTTTATGCCG
1 GGCACCTTTTATGCCG
Statistics
Matches: 95, Mismatches: 6, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
87 4 0.04
88 40 0.42
89 48 0.51
90 3 0.03
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (89 bp):
GGCACCTTTTATGCCGATAATGCACCTTTATGCATTTCATTAGTGACACCTTTAATGTCGATAAG
GCACCGTTTTGCATTTTCATTTAT
Done.