Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001805.1 Hibiscus syriacus cultivar Beakdansim tig00003649_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: 71895
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:1675 original size:14 final size:14
Alignment explanation
Indices: 1658--1690 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
1648 ATTTCTATGT
*
1658 AGGGAATTATTTGC
1 AGGGAATTATTTAC
1672 AGGGAATTATTTAC
1 AGGGAATTATTTAC
1686 AGGGA
1 AGGGA
1691 TTACTCCCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.33, C:0.06, G:0.30, T:0.30
Consensus pattern (14 bp):
AGGGAATTATTTAC
Found at i:3464 original size:90 final size:90
Alignment explanation
Indices: 3352--3529 Score: 302
Period size: 90 Copynumber: 2.0 Consensus size: 90
3342 ATATCCCGAA
* * * *
3352 TATTTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATATGAAATAATAAAAACCCTAATATGAT
3417 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
*
3442 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATATGAAATAATAAAAACCCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAAATTTAATTAATATGAAATAATAAAAACCCTAATATGAT
*
3507 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
3530 GTATGTTAGG
Statistics
Matches: 82, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 82 1.00
ACGTcount: A:0.46, C:0.07, G:0.11, T:0.37
Consensus pattern (90 bp):
TATTAAATTCCAATTAATTAAATATAAATTTAATTAATATGAAATAATAAAAACCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:10346 original size:90 final size:90
Alignment explanation
Indices: 10223--10490 Score: 446
Period size: 90 Copynumber: 3.0 Consensus size: 90
10213 TAATCCCGAA
* * * *
10223 TATTTAATTTCAATTTATTAAATATAGATTTAATTAATTTGAAATAATAAAATTCCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
10288 TAGGGTAACTTGGATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
10313 TATTAAATTCCAATTAATTAAACATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
*
10378 TAGGGTAACTTGAATATAAAAGGAT
66 TAGGGTAACTTGGATATAAAAGGAT
* *
10403 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAT
1 TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
*
10468 TAGGGTAACTTGGCTATAAAAGG
66 TAGGGTAACTTGGATATAAAAGG
10491 GTGGGTTAGG
Statistics
Matches: 166, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 166 1.00
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.37
Consensus pattern (90 bp):
TATTAAATTACAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTAATATGAT
TAGGGTAACTTGGATATAAAAGGAT
Found at i:13618 original size:30 final size:30
Alignment explanation
Indices: 13579--13635 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
13569 GTTCCGAATG
*
13579 ACCTATCCATATGTTCCGAAGAACATATGT
1 ACCTATCCATATGTCCCGAAGAACATATGT
* *
13609 ACCTGTCCATATGTCCCGAAGGACATA
1 ACCTATCCATATGTCCCGAAGAACATA
13636 GGTAACCCTC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (30 bp):
ACCTATCCATATGTCCCGAAGAACATATGT
Found at i:14306 original size:20 final size:19
Alignment explanation
Indices: 14281--14346 Score: 59
Period size: 20 Copynumber: 3.6 Consensus size: 19
14271 TTTCAAAGAT
14281 GGTATCGATACTGTCCTTAA
1 GGTATCGATACTGTCCTT-A
*
14301 GGTATCGGTAC---CCTT-
1 GGTATCGATACTGTCCTTA
*
14316 GGTATCGATATTGTCCTTCA
1 GGTATCGATACTGTCCTT-A
*
14336 GGTATTGATAC
1 GGTATCGATAC
14347 CTCATGAATG
Statistics
Matches: 36, Mismatches: 5, Indels: 10
0.71 0.10 0.20
Matches are distributed among these distances:
15 9 0.25
17 4 0.11
18 4 0.11
20 19 0.53
ACGTcount: A:0.21, C:0.20, G:0.23, T:0.36
Consensus pattern (19 bp):
GGTATCGATACTGTCCTTA
Found at i:22998 original size:64 final size:63
Alignment explanation
Indices: 22913--23053 Score: 185
Period size: 64 Copynumber: 2.2 Consensus size: 63
22903 TTGTTTAAGG
* * * *
22913 TGCATCGATGCACATGCAGTGCATCGATGCAT-GAATTTAAATAGAAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCATCCAA-TTAAATA-AAAACATCGAATAAGATTTA
* * *
22977 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATACAAACATCGAATAAGATTTA
1 TGCATCGATGCATAAGCAGTGCATCGATGCAT-CCAATTAAATAAAAACATCGAATAAGATTTA
23041 TGCATCGATGCAT
1 TGCATCGATGCAT
23054 GGTGTGGTGC
Statistics
Matches: 68, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
64 60 0.88
65 7 0.10
66 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.26
Consensus pattern (63 bp):
TGCATCGATGCATAAGCAGTGCATCGATGCATCCAATTAAATAAAAACATCGAATAAGATTTA
Found at i:23425 original size:18 final size:18
Alignment explanation
Indices: 23391--23425 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
23381 AAATGGGTAT
* *
23391 ATATGTTATATGTATTGC
1 ATATGTTACATGAATTGC
23409 ATATGTTACATGAATTG
1 ATATGTTACATGAATTG
23426 AATGAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
ATATGTTACATGAATTGC
Found at i:24678 original size:149 final size:147
Alignment explanation
Indices: 24410--24711 Score: 568
Period size: 149 Copynumber: 2.0 Consensus size: 147
24400 GAGTCGAGGG
24410 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
1 TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
*
24475 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTAGTCCTTATGGACATTATTAT
66 CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGAGTCCTTATGGACATTATTAT
24540 ATGGCACTACGGTGCAA
131 ATGGCACTACGGTGCAA
24557 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGG--ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
24622 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATTATT
64 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGAGTCCTTATGGACATTATT
24687 ATATGGCACTACGGTGCAA
129 ATATGGCACTACGGTGCAA
24706 TTCTAC
1 TTCTAC
24712 ATGGCACTTC
Statistics
Matches: 151, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
147 19 0.13
149 132 0.87
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (147 bp):
TTCTACGCGGTCCTTCGGGATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACATA
CTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGAGTCCTTATGGACATTATTAT
ATGGCACTACGGTGCAA
Found at i:28470 original size:18 final size:18
Alignment explanation
Indices: 28436--28470 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28426 AAATGGGTAT
* *
28436 ATATGTTATATGTATTGC
1 ATATGTTACATGAATTGC
28454 ATATGTTACATGAATTG
1 ATATGTTACATGAATTG
28471 AATGAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
ATATGTTACATGAATTGC
Found at i:29770 original size:147 final size:148
Alignment explanation
Indices: 29457--29759 Score: 581
Period size: 147 Copynumber: 2.0 Consensus size: 148
29447 GAGTCGAGGG
29457 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGGA-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
29522 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
65 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATTATT
29587 ATATGGCACTACGGTGCAA
130 ATATGGCACTACGGTGCAA
29606 TTCTACGCGGTCCTTCGGG-ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TTCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
29670 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATTATTA
29735 TATGGCACTACGGTGCAA
131 TATGGCACTACGGTGCAA
29753 TTCTACG
1 TTCTACG
29760 TGGCACTTCG
Statistics
Matches: 153, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 134 0.88
149 19 0.12
ACGTcount: A:0.28, C:0.16, G:0.21, T:0.35
Consensus pattern (148 bp):
TTCTACGCGGTCCTTCGGGAATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATTATTA
TATGGCACTACGGTGCAA
Found at i:29771 original size:23 final size:23
Alignment explanation
Indices: 29737--29782 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
29727 CATTATTATA
*
29737 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
*
29760 TGGCACTTCGGTGCAATTATACG
1 TGGCACTACGGTGCAATTATACG
29783 AGCTGTGGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:30909 original size:8 final size:7
Alignment explanation
Indices: 30888--30912 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30878 TATTTTATTT
30888 ATTAAAA
1 ATTAAAA
30895 ATTAAAA
1 ATTAAAA
30902 ATTAAAA
1 ATTAAAA
30909 ATTA
1 ATTA
30913 TATTTTTGTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTAAAA
Found at i:34891 original size:23 final size:25
Alignment explanation
Indices: 34839--34892 Score: 69
Period size: 23 Copynumber: 2.2 Consensus size: 25
34829 TTAGTTGAAA
34839 CATTTTCTTTAGGAATTATCTTTTG
1 CATTTTCTTTAGGAATTATCTTTTG
*
34864 TATTTTC-TTA-GAATTAT-TTTTAG
1 CATTTTCTTTAGGAATTATCTTTT-G
34887 CATTTT
1 CATTTT
34893 TAGGGGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
22 4 0.15
23 13 0.50
24 3 0.12
25 6 0.23
ACGTcount: A:0.22, C:0.09, G:0.09, T:0.59
Consensus pattern (25 bp):
CATTTTCTTTAGGAATTATCTTTTG
Found at i:39531 original size:2 final size:2
Alignment explanation
Indices: 39524--39551 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
39514 AAACAAAAAT
39524 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
39552 GACTAAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40068 original size:20 final size:21
Alignment explanation
Indices: 40030--40084 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 21
40020 CCCATTCAAG
*
40030 TAGTATCGGTACTGCATGA-A
1 TAGTATCGATACTGCATGAGA
*
40050 TAGTATCGATACT-CGATGAGT
1 TAGTATCGATACTGC-ATGAGA
40071 TCAGTATCGATACT
1 T-AGTATCGATACT
40085 AGGCTAGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 1 0.03
20 16 0.53
21 1 0.03
22 12 0.40
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (21 bp):
TAGTATCGATACTGCATGAGA
Found at i:48439 original size:18 final size:19
Alignment explanation
Indices: 48404--48441 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
48394 CTCTCTTATT
*
48404 TTTATTTAAATTGCTTTTA
1 TTTATTTAAATCGCTTTTA
48423 TTTATTT-AATCGCTTTTA
1 TTTATTTAAATCGCTTTTA
48441 T
1 T
48442 CACTTAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.24, C:0.08, G:0.05, T:0.63
Consensus pattern (19 bp):
TTTATTTAAATCGCTTTTA
Found at i:59438 original size:21 final size:20
Alignment explanation
Indices: 59414--59488 Score: 71
Period size: 21 Copynumber: 3.5 Consensus size: 20
59404 GCCATAGCAT
59414 ACAAAGTACTACTACATGTAC
1 ACAAAGTACTACT-CATGTAC
59435 ACAAAGTACT-CTTGTCATAGTAC
1 ACAAAGTACTAC---TCAT-GTAC
* *
59458 ACAAAGTACTACTCTAAGTAT
1 ACAAAGTACTACTC-ATGTAC
59479 ACAAAGTACT
1 ACAAAGTACT
59489 CTTACAAAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
20 1 0.02
21 25 0.54
22 4 0.09
23 15 0.33
24 1 0.02
ACGTcount: A:0.41, C:0.21, G:0.11, T:0.27
Consensus pattern (20 bp):
ACAAAGTACTACTCATGTAC
Found at i:60621 original size:17 final size:17
Alignment explanation
Indices: 60598--60641 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
60588 ACAAAGAATC
60598 AAAAAAGAAAAACAA-AA
1 AAAAAAGAAAAA-AAGAA
*
60615 GAAAAAGAAAAAAAGAA
1 AAAAAAGAAAAAAAGAA
60632 AAAAAAGAAA
1 AAAAAAGAAA
60642 GAGAACCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 2 0.08
17 22 0.92
ACGTcount: A:0.86, C:0.02, G:0.11, T:0.00
Consensus pattern (17 bp):
AAAAAAGAAAAAAAGAA
Found at i:60625 original size:23 final size:23
Alignment explanation
Indices: 60598--60646 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 23
60588 ACAAAGAATC
60598 AAAAAAGAAAAACAAAAGAAAAAGA
1 AAAAAAG-AAAA-AAAAGAAAAAGA
*
60623 AAAAAAGAAAAAAAAGAAAGAGA
1 AAAAAAGAAAAAAAAGAAAAAGA
60646 A
1 A
60647 CCAAATTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
24 4 0.17
25 7 0.30
ACGTcount: A:0.84, C:0.02, G:0.14, T:0.00
Consensus pattern (23 bp):
AAAAAAGAAAAAAAAGAAAAAGA
Found at i:60630 original size:14 final size:13
Alignment explanation
Indices: 60605--60643 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
60595 ATCAAAAAAG
*
60605 AAAAACAAAAGAA
1 AAAAAAAAAAGAA
60618 AAAGAAAAAAAGAA
1 AAA-AAAAAAAGAA
*
60632 AAAAAAGAAAGA
1 AAAAAAAAAAGA
60644 GAACCAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.85, C:0.03, G:0.13, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGAA
Found at i:64245 original size:137 final size:135
Alignment explanation
Indices: 63945--64286 Score: 316
Period size: 137 Copynumber: 2.5 Consensus size: 135
63935 TACAAACCAG
* * * * * *
63945 ATCTCCTCAATATGAAGGATCAGTCTCATCATCAGACAATCAGACTTCCTC-A-TGAAGGAACAG
1 ATCTCCACAATACGAAGAAGCAGTGTCATCATCAGACAATCAGACTTCCTCAAGAGAAGGAACA-
* * * * *
64008 TGATTGCCTCCAAATTATCCAAATACGTCTAGACTTCCTCAATGCGAAGGAAGAATGTCATCCAC
65 TG-TTGCCTCCAAATTATCCAAATACGTATAAACGTCCTCAATGCGAAGAAAGAATGTCATACAC
64073 TGAACAA
129 TGAACAA
* ** * * * * *
64080 ATCTCCTCAATGTGAAGGAGTAGAGTCATCATCAGACAATCAAAATTCCTCAACGAGAAGGAACG
1 ATCTCCACAATACGAAGAAGCAGTGTCATCATCAGACAATCAGACTTCCTCAA-GAGAAGGAAC-
* * * * **
64145 ATGTTGTCTCCAAATT-TCCTAAATACTTATAAACGTCCTGAATGCGAAGAAATAATGTTGTACA
64 ATGTTGCCTCCAAATTATCC-AAATACGTATAAACGTCCTCAATGCGAAGAAAGAATGTCATACA
64209 CTG-ACAA
128 CTGAACAA
* * *
64216 GATTTCCACAATACGAAGAAGCAGTGTCAT-ACTCAGACAAGCAGACTTCCTCAATGCGAAGGAA
1 -ATCTCCACAATACGAAGAAGCAGTGTCATCA-TCAGACAATCAGACTTCCTCAA-GAGAAGGAA
64280 CTATGTT
63 C-ATGTT
64287 ATCTTTAAAC
Statistics
Matches: 168, Mismatches: 32, Indels: 12
0.79 0.15 0.06
Matches are distributed among these distances:
135 44 0.26
136 9 0.05
137 104 0.62
138 10 0.06
139 1 0.01
ACGTcount: A:0.36, C:0.23, G:0.17, T:0.25
Consensus pattern (135 bp):
ATCTCCACAATACGAAGAAGCAGTGTCATCATCAGACAATCAGACTTCCTCAAGAGAAGGAACAT
GTTGCCTCCAAATTATCCAAATACGTATAAACGTCCTCAATGCGAAGAAAGAATGTCATACACTG
AACAA
Found at i:64651 original size:20 final size:23
Alignment explanation
Indices: 64626--64674 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
64616 CTGAGTTTTA
64626 ATTTTATT-AT-A-ATTATTATT
1 ATTTTATTAATAATATTATTATT
*
64646 ATTTTATTAATAATATTTTTATT
1 ATTTTATTAATAATATTATTATT
64669 ATTTTA
1 ATTTTA
64675 CAGACAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
20 8 0.32
21 2 0.08
22 1 0.04
23 14 0.56
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (23 bp):
ATTTTATTAATAATATTATTATT
Found at i:71454 original size:3 final size:3
Alignment explanation
Indices: 71446--71477 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
71436 GTTGATCTTG
71446 TAA TAA TAA TAA -AA TAA TAA TAA T-A TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
71478 CAACACAACA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:71463 original size:11 final size:11
Alignment explanation
Indices: 71447--71477 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
71437 TTGATCTTGT
71447 AATAATAATAA
1 AATAATAATAA
71458 AATAATAATAA
1 AATAATAATAA
*
71469 TATAATAAT
1 AATAATAAT
71478 CAACACAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AATAATAATAA
Found at i:71465 original size:14 final size:14
Alignment explanation
Indices: 71446--71477 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
71436 GTTGATCTTG
71446 TAATAATAATAAAA
1 TAATAATAATAAAA
*
71460 TAATAATAATATAA
1 TAATAATAATAAAA
71474 TAAT
1 TAAT
71478 CAACACAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (14 bp):
TAATAATAATAAAA
Found at i:71721 original size:13 final size:13
Alignment explanation
Indices: 71703--71728 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71693 CTGTAAGGGT
71703 AAATAATCCCTGC
1 AAATAATCCCTGC
71716 AAATAATCCCTGC
1 AAATAATCCCTGC
71729 GTAAAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
AAATAATCCCTGC
Done.