Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001924.1 Hibiscus syriacus cultivar Beakdansim tig00003892_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: 39788
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.32
Found at i:766 original size:21 final size:20
Alignment explanation
Indices: 715--773 Score: 66
Period size: 20 Copynumber: 2.8 Consensus size: 20
705 GATAATTTTC
715 ATTTATTTATTCATTTAGAATA
1 ATTTA-TTATT-ATTTAGAATA
737 ATTTATTATTATTTCA-AATA
1 ATTTATTATTATTT-AGAATA
757 ATTTACTTATTAATTTA
1 ATTTA-TTATT-ATTTA
774 TTTTAAATAA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
20 13 0.38
21 12 0.35
22 9 0.26
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (20 bp):
ATTTATTATTATTTAGAATA
Found at i:776 original size:26 final size:27
Alignment explanation
Indices: 745--800 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
735 TAATTTATTA
745 TTATTTCAAATAATTTACTTA-TTAAT
1 TTATTTCAAATAATTTACTTATTTAAT
* *
771 TTATTTTAAATAATTTATTTATTTAAT
1 TTATTTCAAATAATTTACTTATTTAAT
798 TTA
1 TTA
801 AGGGGTATGA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 19 0.70
27 8 0.30
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATTTCAAATAATTTACTTATTTAAT
Found at i:786 original size:14 final size:14
Alignment explanation
Indices: 745--790 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
735 TAATTTATTA
*
745 TTATTTCAAATAAT
1 TTATTTTAAATAAT
* *
759 TTA-CTT-ATTAAT
1 TTATTTTAAATAAT
771 TTATTTTAAATAAT
1 TTATTTTAAATAAT
785 TTATTT
1 TTATTT
791 ATTTAATTTA
Statistics
Matches: 25, Mismatches: 5, Indels: 4
0.74 0.15 0.12
Matches are distributed among these distances:
12 8 0.32
13 3 0.12
14 14 0.56
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTTAAATAAT
Found at i:788 original size:22 final size:22
Alignment explanation
Indices: 715--801 Score: 81
Period size: 26 Copynumber: 3.9 Consensus size: 22
705 GATAATTTTC
*
715 ATTTATTTATTCA-TTTAGAATA
1 ATTTATTTATTTATTTTA-AATA
*
737 ATTTA-TTA-TTATTTCAAATA
1 ATTTATTTATTTATTTTAAATA
757 ATTTACTTATTAATTTATTTTAAATA
1 ATTTA--T-TT-ATTTATTTTAAATA
*
783 ATTTATTTATTTAATTTAA
1 ATTTATTTATTTATTTTAA
802 GGGGTATGAA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
20 11 0.20
21 6 0.11
22 15 0.28
23 2 0.04
24 3 0.06
25 1 0.02
26 16 0.30
ACGTcount: A:0.38, C:0.03, G:0.01, T:0.57
Consensus pattern (22 bp):
ATTTATTTATTTATTTTAAATA
Found at i:1722 original size:20 final size:20
Alignment explanation
Indices: 1697--1748 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
1687 TATGCAAGCA
1697 GTATCGATACCAAGA-GAGGG
1 GTATCGATACCAAGAGGA-GG
* * *
1717 GTATCGATACTATGAGGATG
1 GTATCGATACCAAGAGGAGG
1737 GTATCGATACCA
1 GTATCGATACCA
1749 TTATTAACAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 25 0.93
21 2 0.07
ACGTcount: A:0.33, C:0.15, G:0.29, T:0.23
Consensus pattern (20 bp):
GTATCGATACCAAGAGGAGG
Found at i:2467 original size:47 final size:47
Alignment explanation
Indices: 2264--2874 Score: 767
Period size: 47 Copynumber: 13.1 Consensus size: 47
2254 TGCATATGGG
* * * *
2264 TGCATTATAGGCATGAAAGGATGCCA-AAATAATAATGCAT--ATGGG
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* ** * *
2309 TGCATTATAGGCATGAAAGGATGCCA-AAATATTAATGCAT--ATGGG
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* * * **
2354 TGCATTATAGGCATGAAAGGATGCTA-AAATAATAATGCAT-ATTGG-
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
*
2399 TGTATTATAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
1 TGCATTA-AGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* * *
2447 TGCGTTAAGGCATTAAAGGATGTCATAACTAAAAATGCATGAATA-GA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAA-AGGA
2494 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
*
2541 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAACGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
2588 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* * *
2635 TGCATTAAGGCAAGAAAGGATGCCATAACTAAAAATGCATGAACGAA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* *
2682 TGCATTAAGGCATTAAAGGATGCCATAACTAAAACTGCATGAAAGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* *
2729 TGCATTAAGGCATGAAAGGATTCCATAACT-AAAATGCATGAACGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* * * * * *
2775 TGTATTAAGGCATTAAAGAATGTCATAACTAAGAATGCATGATAGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
* * * *
2822 TGCATTATGGCAAGAAAGGATGACATAACTAAAAATGCATAAAAGGA
1 TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
2869 TTGCAT
1 -TGCAT
2875 AACTAAAATG
Statistics
Matches: 510, Mismatches: 48, Indels: 13
0.89 0.08 0.02
Matches are distributed among these distances:
45 106 0.21
46 55 0.11
47 338 0.66
48 11 0.02
ACGTcount: A:0.43, C:0.12, G:0.22, T:0.23
Consensus pattern (47 bp):
TGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGGA
Found at i:2541 original size:27 final size:27
Alignment explanation
Indices: 2503--2677 Score: 158
Period size: 27 Copynumber: 7.3 Consensus size: 27
2493 ATGCATTAAG
2503 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCCATAACTAAAAAT
*
2530 GCATGAAAGGATG-CAT---T---AAG
1 GCATGAAAGGATGCCATAACTAAAAAT
2550 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCCATAACTAAAAAT
* *
2577 GCATGAACGGATG-CAT---T---AAG
1 GCATGAAAGGATGCCATAACTAAAAAT
2597 GCATGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCCATAACTAAAAAT
*
2624 GCATGAAAGGATG-CAT---T---AAG
1 GCATGAAAGGATGCCATAACTAAAAAT
*
2644 GCAAGAAAGGATGCCATAACTAAAAAT
1 GCATGAAAGGATGCCATAACTAAAAAT
2671 GCATGAA
1 GCATGAA
2678 CGAATGCATT
Statistics
Matches: 117, Mismatches: 10, Indels: 42
0.69 0.06 0.25
Matches are distributed among these distances:
20 43 0.37
21 9 0.08
23 3 0.03
24 3 0.03
26 9 0.08
27 50 0.43
ACGTcount: A:0.45, C:0.14, G:0.23, T:0.18
Consensus pattern (27 bp):
GCATGAAAGGATGCCATAACTAAAAAT
Found at i:2895 original size:26 final size:26
Alignment explanation
Indices: 2836--2899 Score: 85
Period size: 26 Copynumber: 2.4 Consensus size: 26
2826 TTATGGCAAG
2836 AAAGGATGACATAACTAAAAATGCATA
1 AAAGGATG-CATAACTAAAAATGCATA
*
2863 AAAGGATTGCATAACT-AAAATGCATG
1 AAAGGA-TGCATAACTAAAAATGCATA
*
2889 AAGGGATGCAT
1 AAAGGATGCAT
2900 TAAGGCATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
25 5 0.15
26 14 0.41
27 13 0.38
28 2 0.06
ACGTcount: A:0.48, C:0.11, G:0.20, T:0.20
Consensus pattern (26 bp):
AAAGGATGCATAACTAAAAATGCATA
Found at i:7475 original size:36 final size:36
Alignment explanation
Indices: 7408--7477 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
7398 GATCTTCAAA
*
7408 GGGTATCGATACCTAAAGAATAGTATTGATACCAAG
1 GGGTATCGATACCTAAAGAATAGTATCGATACCAAG
* * *
7444 GGGTATCGATACTTTAAGGAA-GGTATCGATACCA
1 GGGTATCGATAC-CTAAAGAATAGTATCGATACCA
7478 TCTTGAACTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 23 0.79
37 6 0.21
ACGTcount: A:0.36, C:0.14, G:0.24, T:0.26
Consensus pattern (36 bp):
GGGTATCGATACCTAAAGAATAGTATCGATACCAAG
Found at i:7573 original size:22 final size:22
Alignment explanation
Indices: 7508--7573 Score: 55
Period size: 22 Copynumber: 3.0 Consensus size: 22
7498 AATGTAATAT
* **
7508 GGGTATCGATACCTCAGTTAAA
1 GGGTACCGATACCTCCTTTAAA
* *
7530 GGATGTACCAATA-CT-CTATAAA
1 GG--GTACCGATACCTCCTTTAAA
7552 GGGTACCGATACCTCCTTTAAA
1 GGGTACCGATACCTCCTTTAAA
7574 TAAGAAATGA
Statistics
Matches: 33, Mismatches: 7, Indels: 8
0.69 0.15 0.17
Matches are distributed among these distances:
20 8 0.24
21 2 0.06
22 14 0.42
23 2 0.06
24 7 0.21
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.27
Consensus pattern (22 bp):
GGGTACCGATACCTCCTTTAAA
Found at i:8173 original size:22 final size:23
Alignment explanation
Indices: 8144--8195 Score: 79
Period size: 22 Copynumber: 2.3 Consensus size: 23
8134 GAGTCAAGAG
* *
8144 TTTCATAGGTCCTTCGGGACATA
1 TTTCATAGGTCCTTAGGGACAAA
8167 -TTCATAGGTCCTTAGGGACAAA
1 TTTCATAGGTCCTTAGGGACAAA
8189 TTTCATA
1 TTTCATA
8196 TGCCACTCAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
22 20 0.77
23 6 0.23
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (23 bp):
TTTCATAGGTCCTTAGGGACAAA
Found at i:15101 original size:21 final size:23
Alignment explanation
Indices: 15074--15124 Score: 70
Period size: 22 Copynumber: 2.3 Consensus size: 23
15064 GAGTTGAGGG
* *
15074 TTTCATAGGT-CTTCGGGACATA
1 TTTCATAGGTACTTAGGGACAAA
15096 -TTCATAGGTACTTAGGGACAAA
1 TTTCATAGGTACTTAGGGACAAA
15118 TTTCATA
1 TTTCATA
15125 TGCTACTCAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 9 0.36
22 10 0.40
23 6 0.24
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (23 bp):
TTTCATAGGTACTTAGGGACAAA
Found at i:16973 original size:45 final size:45
Alignment explanation
Indices: 16924--17053 Score: 233
Period size: 45 Copynumber: 2.9 Consensus size: 45
16914 AACGAATGAA
*
16924 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAATGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
16969 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
* *
17014 CAAAATAATAATGTATATGGGTGCATTATAAGCATGAAAG
1 CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAG
17054 AATACCATAA
Statistics
Matches: 82, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 82 1.00
ACGTcount: A:0.42, C:0.10, G:0.22, T:0.26
Consensus pattern (45 bp):
CAAAATAATAATGCATATGGGTGCATTATAGGCATGAAAGGATGC
Found at i:17152 original size:47 final size:46
Alignment explanation
Indices: 17073--17333 Score: 342
Period size: 47 Copynumber: 5.6 Consensus size: 46
17063 ACTAAAAATA
* *
17073 CATTAAGGCATGAAATGATGCCATAACTAAAAATCCATGAACAGATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAA-AGATG
* * *
17120 CATTGAGGCATGAAATGATGCCATAACAAAAAATGCATGAAAGGATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAA-GATG
* **
17167 CATTAAGGCATGAAATGATTTCATAACTAAAAATGCATGAAAGGATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAA-GATG
* * *
17214 CATTAAGGCATGAAAGGAAGACATAACTAAAAATGCATGAACGAATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAG-ATG
* *
17261 CATTAAGGCATGAAAGGATGTCATAACTAAAAATGCATGAAGGGATG
1 CATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAA-AGATG
**
17308 CATTAAGGTGTGAAAGGATGCCATAA
1 CATTAAGGCATGAAAGGATGCCATAA
17334 ATGAAATTAA
Statistics
Matches: 193, Mismatches: 18, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
46 2 0.01
47 190 0.98
48 1 0.01
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (46 bp):
CATTAAGGCATGAAAGGATGCCATAACTAAAAATGCATGAAAGATG
Found at i:17179 original size:20 final size:20
Alignment explanation
Indices: 17154--17231 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 20
17144 AACAAAAAAT
17154 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
* * *
17174 GCATGAAATGATTTCATAACTAAAAAT
1 GCATGAAAGGA-TGCAT---T---AAG
17201 GCATGAAAGGATGCATTAAG
1 GCATGAAAGGATGCATTAAG
17221 GCATGAAAGGA
1 GCATGAAAGGA
17232 AGACATAACT
Statistics
Matches: 45, Mismatches: 6, Indels: 14
0.69 0.09 0.22
Matches are distributed among these distances:
20 23 0.51
21 4 0.09
23 1 0.02
24 1 0.02
26 4 0.09
27 12 0.27
ACGTcount: A:0.44, C:0.10, G:0.24, T:0.22
Consensus pattern (20 bp):
GCATGAAAGGATGCATTAAG
Found at i:17333 original size:94 final size:94
Alignment explanation
Indices: 17073--17333 Score: 380
Period size: 94 Copynumber: 2.8 Consensus size: 94
17063 ACTAAAAATA
* * * *
17073 CATTAAGGCATGAAATGATGCCATAACTAAAAATCCATGAACA-GATGCATTGAGGCATGAAATG
1 CATTAAGGCATGAAATGATGTCATAACTAAAAATGCATGAA-AGGATGCATTAAGGCATGAAAGG
*
17137 ATGCCATAACAAAAAATGCATGAAAGGATG
65 ATGCCATAACAAAAAATGCATGAAAGAATG
*
17167 CATTAAGGCATGAAATGATTTCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
1 CATTAAGGCATGAAATGATGTCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
* * * *
17232 AGACATAACTAAAAATGCATGAACGAATG
66 TGCCATAACAAAAAATGCATGAAAGAATG
* * **
17261 CATTAAGGCATGAAAGGATGTCATAACTAAAAATGCATGAAGGGATGCATTAAGGTGTGAAAGGA
1 CATTAAGGCATGAAATGATGTCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
17326 TGCCATAA
66 TGCCATAA
17334 ATGAAATTAA
Statistics
Matches: 149, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
93 1 0.01
94 148 0.99
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (94 bp):
CATTAAGGCATGAAATGATGTCATAACTAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGA
TGCCATAACAAAAAATGCATGAAAGAATG
Found at i:17333 original size:141 final size:141
Alignment explanation
Indices: 17073--17333 Score: 380
Period size: 141 Copynumber: 1.9 Consensus size: 141
17063 ACTAAAAATA
* * * * *
17073 CATTAAGGCATGAAATGATGCCATAACTAAAAATCCATGAACAGATGCATTGAGGCATGAAATGA
1 CATTAAGGCATGAAAGGAAGACATAACTAAAAATCCATGAACAGATGCATTAAGGCATGAAAGGA
* **
17138 TGCCATAACAAAAAATGCATGAAAGGATGCATTAAGGCATGAAATGATTTCATAACTAAAAATGC
66 TGCCATAACAAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGC
17203 ATGAAAGGATG
131 ATGAAAGGATG
*
17214 CATTAAGGCATGAAAGGAAGACATAACTAAAAATGCATGAAC-GAATGCATTAAGGCATGAAAGG
1 CATTAAGGCATGAAAGGAAGACATAACTAAAAATCCATGAACAG-ATGCATTAAGGCATGAAAGG
* * * **
17278 ATGTCATAACTAAAAATGCATGAAGGGATGCATTAAGGTGTGAAAGGATGCCATAA
65 ATGCCATAACAAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAA
17334 ATGAAATTAA
Statistics
Matches: 105, Mismatches: 14, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
140 1 0.01
141 104 0.99
ACGTcount: A:0.44, C:0.13, G:0.22, T:0.21
Consensus pattern (141 bp):
CATTAAGGCATGAAAGGAAGACATAACTAAAAATCCATGAACAGATGCATTAAGGCATGAAAGGA
TGCCATAACAAAAAATGCATGAAAGGATGCATTAAGGCATGAAAGGATGCCATAACTAAAAATGC
ATGAAAGGATG
Found at i:27984 original size:103 final size:103
Alignment explanation
Indices: 27800--28003 Score: 336
Period size: 103 Copynumber: 2.0 Consensus size: 103
27790 TGCTCTTCAG
*
27800 GGAAGATTGAATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATTTGAAAGAAGAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATCTGAAAGAAGAAG
*
27865 AATTTGCTCCAATACTCTTTAGGGGAGATAAGACTCTA
66 AATATGCTCCAATACTCTTTAGGGGAGATAAGACTCTA
* * *
27903 GGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGACCAAATCTGAAAGAATAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATCTGAAAGAAGAAG
** *
27968 AATATGCTCCTCTACTCTTTAGGGGAGATCAGACTC
66 AATATGCTCCAATACTCTTTAGGGGAGATAAGACTC
28004 GAGAAAATTT
Statistics
Matches: 93, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 93 1.00
ACGTcount: A:0.34, C:0.18, G:0.21, T:0.27
Consensus pattern (103 bp):
GGAAGATTGAATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATCTGAAAGAAGAAG
AATATGCTCCAATACTCTTTAGGGGAGATAAGACTCTA
Found at i:28098 original size:237 final size:237
Alignment explanation
Indices: 27680--28128 Score: 659
Period size: 237 Copynumber: 1.9 Consensus size: 237
27670 TGATTCAAAT
* * * * *
27680 GAATCGATTTGCTTCACTGCTCTTGAGAAATACCAAATTTGAAAGAAGAAGCACCTAGTGCACTA
1 GAATCGATTTGCTTCACTGCTCTTCAGAAAGACCAAATCTGAAAGAAGAAGCACATAGTCCACTA
* * *
27745 CTCTTTAGAGGAGATCAAACTCGTGAAAATTTTGATCCACTTCAATGCTCTTCAGGGAAGATTGA
66 CTCTTTAGAGGAGATCAAACTCGAGAAAATTTTGATCAACTTCAATGCTCTTCAGGGAAGATTAA
* *
27810 ATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATTTGAAAGAAGAAGAATTTGCTCC
131 ATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATTTGCTCC
*
27875 AATACTCTTTAGGGGAGATAAGACTCTAGGAAGATTGAATCA
196 AATACTCTTTAGAGGAGATAAGACTCTAGGAAGATTGAATCA
* * * *
27917 GAATCGATTTGCTTCACTTCTCTTCAGGAAGACCAAATCTGAAAGAATAAG-A-ATATGCTCCTC
1 GAATCGATTTGCTTCACTGCTCTTCAGAAAGACCAAATCTGAAAGAAGAAGCACATA-G-TCCAC
* * * *
27980 TACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCAATTTCATTGCTCTTCAGGGAAGATT
64 TACTCTTTAGAGGAGATCAAACTCGAGAAAATTTTGATCAACTTCAATGCTCTTCAGGGAAGATT
* * *
28045 AAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAATAATTTGTT
129 AAATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATTTGCT
*
28110 CCACTACTCTTTAGAGGAG
194 CCAATACTCTTTAGAGGAG
28129 GTTTGACTCG
Statistics
Matches: 187, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
235 2 0.01
236 2 0.01
237 183 0.98
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (237 bp):
GAATCGATTTGCTTCACTGCTCTTCAGAAAGACCAAATCTGAAAGAAGAAGCACATAGTCCACTA
CTCTTTAGAGGAGATCAAACTCGAGAAAATTTTGATCAACTTCAATGCTCTTCAGGGAAGATTAA
ATCAGAATCGATTTGCTTCACTGCGCTTCAGGAAGACCAAATCTAAAAGAAGAAGAATTTGCTCC
AATACTCTTTAGAGGAGATAAGACTCTAGGAAGATTGAATCA
Found at i:28143 original size:134 final size:134
Alignment explanation
Indices: 27903--28269 Score: 495
Period size: 134 Copynumber: 2.7 Consensus size: 134
27893 TAAGACTCTA
* *
27903 GGAAGATTGAATCAGAATCGATTTGCTTCACTTCTCTTCAGGAAGACCAAATCTGAAAGAATAAG
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * * * *
27968 AATATGCTCCTCTACTCTTTAGGGGAGATCAGACTCGAGAAAATTTTGATCAATTTCATTGCTCT
66 AATATGTTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAATTTTGATCAACTTCACTGCTCT
28033 TCAG
131 TCAG
* * *
28037 GGAAGATTAAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTAAAAGAAGAAT
1 GGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
* * ** * *
28102 AATTTGTTCCACTACTCTTTAGAGGAGGTTTGACTCGAGAAAATTTTGATCCACTTCGCTGCTCT
66 AATATGTTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAATTTTGATCAACTTCACTGCTCT
28167 TCAG
131 TCAG
** * * *
28171 GGAAGGCTGAATC-GAACTTGATTTGCTTCGCTGCTCTTCAGGAAGACGAAATCTGAAAGAAGAA
1 GGAAGATTGAATCAGAA-TCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAA
* *
28235 GAATATGCTT-CACTACTCTTTAGGGGAAATCAGAC
65 GAATATG-TTCCACTACTCTTTAGAGGAGATCAGAC
28270 CTTTTAAAGA
Statistics
Matches: 201, Mismatches: 30, Indels: 4
0.86 0.13 0.02
Matches are distributed among these distances:
133 3 0.01
134 196 0.98
135 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.29
Consensus pattern (134 bp):
GGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATCTGAAAGAAGAAG
AATATGTTCCACTACTCTTTAGAGGAGATCAGACTCGAGAAAATTTTGATCAACTTCACTGCTCT
TCAG
Found at i:29138 original size:45 final size:45
Alignment explanation
Indices: 29017--29785 Score: 364
Period size: 45 Copynumber: 18.2 Consensus size: 45
29007 AGTCAAGTTG
* * * *
29017 AGAATGACATCACTAAAAGGTTAACTTCTCTTTC-CAAGAAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTC-TTCACGAGAAAGTCA
* * * * * * *
29062 AGAATAACACCGCTACAAGATTGGCTCCTCTTCGCAAGAAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * * *
29107 GGAATAACATCACTAAAAGGTTGAATTCTCTTCACGAGAAAGTTA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * * * *** *
29152 AGAACAACATTACAAAAATATTGACTTCTCTTCGTAACAAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * * *
29197 AGAA-AGGCAACACTAAAAGATTGACTCCTCCTCACGAGAAAGTCA
1 AGAATA-ACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * * * *** *
29242 AGAATAACAAT-ACTGAAATATTAACTTCTTTTTGTGAGAAAATCGA
1 AGAATAAC-ATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTC-A
* * *
29288 GGAA-AGA-AACACTAAAAGATTGA-ATCATCTTCACGAGAAAGTCA
1 AGAATA-ACATCACTAAAAGATTGACTTC-TCTTCACGAGAAAGTCA
* * *
29332 AGAATGACAAT-ACTAAAAGATTGACTTCTTTTCGCGAGAAAGTCGA
1 AGAATAAC-ATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTC-A
* * * *
29378 TGAATGAA-A-CACTAAAATATTGACTCCTCTTCACAAGAAAGTCA
1 AGAAT-AACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* *
29422 AGAAT---A--AC--AAAGATTGATTTCTCTTCACGAGGAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
*
29460 AGAAT-A-A-CA-T---AGATTGACTTCTCTTCACGAGGAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * * **
29498 AGAATAACAT---TGAAAGATTGACTACTCTTTACGAGGGAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * *
29540 AG-A-AA-A--AC--AAAGATTTATTTCTCTTCACGAGGAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * *
29578 AGAAT---A--AC--AAAGATCGGCTTCTCTTCATGAGGAAA-TCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGA-GAAAGTCA
* **
29616 AGAATAACAT---TAAATA-ATTGACTCCTCTTCACGAGGGAGTCA
1 AGAATAACATCACTAAA-AGATTGACTTCTCTTCACGAGAAAGTCA
* * *
29658 AGAAT--GA--A--AAAAGATTGACTTCTATTCACGAGGAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
* * ** **
29697 AGAATAACAT---TGAAAGATTGACTCCTCTTCAATAGGGAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
*
29739 AGAAT---A--A-T-AAAGATTGACTTCTCTTCACGAGGAAGTCA
1 AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
29777 AGAATAACA
1 AGAATAACA
29786 GAGATCGACT
Statistics
Matches: 557, Mismatches: 120, Indels: 98
0.72 0.15 0.13
Matches are distributed among these distances:
38 149 0.27
39 41 0.07
40 7 0.01
41 7 0.01
42 81 0.15
43 1 0.00
44 17 0.03
45 238 0.43
46 15 0.03
47 1 0.00
ACGTcount: A:0.41, C:0.18, G:0.17, T:0.25
Consensus pattern (45 bp):
AGAATAACATCACTAAAAGATTGACTTCTCTTCACGAGAAAGTCA
Found at i:29447 original size:38 final size:38
Alignment explanation
Indices: 29396--30104 Score: 846
Period size: 38 Copynumber: 18.2 Consensus size: 38
29386 ACACTAAAAT
* * *
29396 ATTGACTCCTCTTCACAAGAAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
29434 ATTGATTTCTCTTCACGAGGAAGTCAAGAATAACATAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
29472 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* * * *
29514 ATTGACTACTCTTTACGAGGGAGTCAAGAAAAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
29552 ATTTATTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* * * * *
29590 ATCGGCTTCTCTTCATGAGGAAATCAAGAATAACATTAAATA
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC---AAA-G
* * *
29632 ATTGACTCCTCTTCACGAGGGAGTCAAGAATGAAAAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAAT-AACAAAG
*
29671 ATTGACTTCTATTCACGAGGAAGTCAAGAATAACATTGAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC----AAAG
* ** * *
29713 ATTGACTCCTCTTCAATAGGGAGTCAAGAATAATAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
29751 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAGAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
29789 ATCGACTTCTCTTCACGAGGAAGTCTAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
** * *
29827 AACGACTTCTCTTCATGAGGAAGTCTATG-ATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTC-AAGAATAACAAAG
* * *
29865 ATTAACTTCTCTTCACGAGGAACTCAATAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
29903 ATTGACTT-TCCTTCAAGAGGAAGTCAAGAATAACACTGAAAG
1 ATTGACTTCT-CTTCACGAGGAAGTCAAGAAT-A-AC--AAAG
* * * *
29945 ATAGACTCCTCTTCACGAGGGAGTCAAGAATGACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
*
29983 ATTGACTTCTCTTCATGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
* *
30021 ATTGACTTCTCTTCACGAGAAAGTCTAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
30059 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
1 ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
30097 ATTGACTT
1 ATTGACTT
30105 TTTGTCACAC
Statistics
Matches: 569, Mismatches: 81, Indels: 42
0.82 0.12 0.06
Matches are distributed among these distances:
37 2 0.00
38 405 0.71
39 30 0.05
40 7 0.01
41 3 0.01
42 119 0.21
43 3 0.01
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.25
Consensus pattern (38 bp):
ATTGACTTCTCTTCACGAGGAAGTCAAGAATAACAAAG
Found at i:29560 original size:118 final size:116
Alignment explanation
Indices: 29347--30104 Score: 843
Period size: 118 Copynumber: 6.4 Consensus size: 116
29337 GACAATACTA
* * * * * *
29347 AAAGATTGACTTCTTTTCGCGAGAAAGTCGATGAATGAAACACTAAAATATTGACTCCTCTTCAC
1 AAAGATTGACTTCTCTTCACGAGGAAGTC-AAGAAT--AACA-T-AAAGATTGACTTCTCTTCAC
* * *
29412 AAGAAAGTCAAGAATAACAAAGATTGATTTCTCTTCACGAGGAAGTCAAGAATAAC
61 GAGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * *
29468 ATAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATTGAAAGATTGACTACTCTTTACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA-T-AAAGATTGACTTCTCTTCACGAG
* * * *
29533 GGAGTCAAGAAAAACAAAGATTTATTTCTCTTCACGAGGAAGTCAAGAATAAC
64 GAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* * * * * *
29586 AAAGATCGGCTTCTCTTCATGAGGAAATCAAGAATAACATTAAATAATTGACTCCTCTTCACGAG
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACA-TAAA-GATTGACTTCTCTTCACGAG
* * *
29651 GGAGTCAAGAATGAAAAAAGATTGACTTCTATTCACGAGGAAGTCAAGAATAAC
64 GAAGTCAAGAAT-AACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
* ** *
29705 ATTGAAAGATTGACTCCTCTTCAATAGGGAGTCAAGAAT-A-ATAAAGATTGACTTCTCTTCACG
1 ----AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATAAAGATTGACTTCTCTTCACG
* * *
29768 AGGAAGTCAAGAATAACAGAGATCGACTTCTCTTCACGAGGAAGTCTAGAATAAC
62 AGGAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
** * * *
29823 AAAGAACGACTTCTCTTCATGAGGAAGTCTATG-ATAAC--AAAGATTAACTTCTCTTCACGAGG
1 AAAGATTGACTTCTCTTCACGAGGAAGTC-AAGAATAACATAAAGATTGACTTCTCTTCACGAGG
* * *
29885 AACTCAATAATAACAAAGATTGACTT-TCCTTCAAGAGGAAGTCAAGAATAACAC
65 AAGTCAAGAATAACAAAGATTGACTTCT-CTTCACGAGGAAGTCAAGAAT-A-AC
* * * * *
29939 TGAAAGATAGACTCCTCTTCACGAGGGAGTCAAGAATGAC--AAAGATTGACTTCTCTTCATGAG
1 --AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATAAAGATTGACTTCTCTTCACGAG
* *
30002 GAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGAAAGTCTAGAATAAC
64 GAAGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
30055 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC--AAAGATTGACTT
1 AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATAAAGATTGACTT
30105 TTTGTCACAC
Statistics
Matches: 546, Mismatches: 75, Indels: 39
0.83 0.11 0.06
Matches are distributed among these distances:
113 1 0.00
114 135 0.25
115 4 0.01
116 4 0.01
117 6 0.01
118 265 0.49
119 67 0.12
120 9 0.02
121 26 0.05
122 1 0.00
123 28 0.05
ACGTcount: A:0.39, C:0.17, G:0.18, T:0.25
Consensus pattern (116 bp):
AAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAACATAAAGATTGACTTCTCTTCACGAGGA
AGTCAAGAATAACAAAGATTGACTTCTCTTCACGAGGAAGTCAAGAATAAC
Found at i:30759 original size:37 final size:37
Alignment explanation
Indices: 30704--30783 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
30694 AGGGAGTAAT
* * *
30704 CGGCCAATCAAAATAACCCTTTTCGTTACCGCACGTG
1 CGGCCAATCAAAACAACCCTTTTCATTACCGCACATG
30741 CGGCCAATCAAAACAACCCTTTTCATTACCGCACATG
1 CGGCCAATCAAAACAACCCTTTTCATTACCGCACATG
*
30778 CCGCCA
1 CGGCCA
30784 CACACTGATA
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (37 bp):
CGGCCAATCAAAACAACCCTTTTCATTACCGCACATG
Found at i:35540 original size:14 final size:14
Alignment explanation
Indices: 35490--35540 Score: 68
Period size: 14 Copynumber: 3.7 Consensus size: 14
35480 CCAACCCGGA
35490 CTGAGTCAACTCAT
1 CTGAGTCAACTCAT
*
35504 CTGAG-CAACTCGT
1 CTGAGTCAACTCAT
* *
35517 CCGAGCCAACTCAT
1 CTGAGTCAACTCAT
35531 CTGAGTCAAC
1 CTGAGTCAAC
35541 CTGTTGACTT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 11 0.35
14 20 0.65
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.22
Consensus pattern (14 bp):
CTGAGTCAACTCAT
Found at i:35559 original size:13 final size:13
Alignment explanation
Indices: 35541--35574 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
35531 CTGAGTCAAC
35541 CTGTTGACTTTGA
1 CTGTTGACTTTGA
35554 CTGTTGATCTTTGA
1 CTGTTGA-CTTTGA
35568 CT-TTGAC
1 CTGTTGAC
35575 CCAAAAAGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.05
13 11 0.55
14 8 0.40
ACGTcount: A:0.15, C:0.18, G:0.21, T:0.47
Consensus pattern (13 bp):
CTGTTGACTTTGA
Found at i:36977 original size:16 final size:18
Alignment explanation
Indices: 36938--36978 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
36928 GTGTATTGGA
*
36938 GTTTAAGAGTATGAAAGG
1 GTTTAAGAGCATGAAAGG
*
36956 GATTAAGA-CATG-AAGG
1 GTTTAAGAGCATGAAAGG
36972 GTTTAAG
1 GTTTAAG
36979 TTGATATTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
16 10 0.50
17 3 0.15
18 7 0.35
ACGTcount: A:0.39, C:0.02, G:0.32, T:0.27
Consensus pattern (18 bp):
GTTTAAGAGCATGAAAGG
Found at i:37901 original size:21 final size:21
Alignment explanation
Indices: 37877--37939 Score: 99
Period size: 21 Copynumber: 3.0 Consensus size: 21
37867 AGTCGAGGGT
*
37877 TATACAAGGTCCTTTGGGACA
1 TATACGAGGTCCTTTGGGACA
37898 TATACGAGGTCCTTTGGGACA
1 TATACGAGGTCCTTTGGGACA
* *
37919 TATATGATGTCCTTTGGGACA
1 TATACGAGGTCCTTTGGGACA
37940 AATTTTATAT
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.32
Consensus pattern (21 bp):
TATACGAGGTCCTTTGGGACA
Found at i:39184 original size:14 final size:15
Alignment explanation
Indices: 39167--39203 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
39157 AGCAAGAATT
*
39167 TTGAATCTG-AGCAA
1 TTGAATCAGAAGCAA
39181 TTGAATCAGAAGCAA
1 TTGAATCAGAAGCAA
39196 TTGAATCA
1 TTGAATCA
39204 CACTGTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.27
Consensus pattern (15 bp):
TTGAATCAGAAGCAA
Done.