Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001737.1 Hibiscus syriacus cultivar Beakdansim tig00003510_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: 55922
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:456 original size:26 final size:25
Alignment explanation
Indices: 417--493 Score: 93
Period size: 26 Copynumber: 3.0 Consensus size: 25
407 GGAAGAAATG
*
417 TTTTTGGGTCGTTAAACGAACGATAT
1 TTTTTAGGTCGTT-AACGAACGATAT
*
443 TTTTTAGGTGGTT-ACGAACGATATAT
1 TTTTTAGGTCGTTAACGAACG--ATAT
469 TTTTTAGGTCGTTATACGAACGATA
1 TTTTTAGGTCGTTA-ACGAACGATA
494 AATTTGTGAT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
24 7 0.16
26 30 0.68
28 7 0.16
ACGTcount: A:0.27, C:0.10, G:0.22, T:0.40
Consensus pattern (25 bp):
TTTTTAGGTCGTTAACGAACGATAT
Found at i:473 original size:28 final size:28
Alignment explanation
Indices: 412--498 Score: 92
Period size: 26 Copynumber: 3.2 Consensus size: 28
402 TAGTTGGAAG
* * *
412 AAATGTTTTTGGGTCGTTAAACGAACGAT
1 AAAT-TTTTTAGGTCGGTATACGAACGAT
441 --ATTTTTTAGGT-GGT-TACGAACGAT
1 AAATTTTTTAGGTCGGTATACGAACGAT
* *
465 ATATTTTTTAGGTCGTTATACGAACGAT
1 AAATTTTTTAGGTCGGTATACGAACGAT
493 AAATTT
1 AAATTT
499 GTGATTTCAT
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 9 0.18
25 2 0.04
26 19 0.39
27 4 0.08
28 15 0.31
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (28 bp):
AAATTTTTTAGGTCGGTATACGAACGAT
Found at i:2714 original size:7 final size:7
Alignment explanation
Indices: 2699--2729 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
2689 TGTCCGTACT
*
2699 TCGTGTC
1 TCGTTTC
2706 TCGTTTC
1 TCGTTTC
2713 TCGTTTC
1 TCGTTTC
2720 TCGTTTC
1 TCGTTTC
2727 TCG
1 TCG
2730 GTCACCTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.00, C:0.29, G:0.19, T:0.52
Consensus pattern (7 bp):
TCGTTTC
Found at i:4035 original size:462 final size:467
Alignment explanation
Indices: 3139--4068 Score: 1699
Period size: 462 Copynumber: 2.0 Consensus size: 467
3129 GTCTACGTCC
*
3139 ACTACCTTAGCTATCAACACTAAGGATTTTCTAACAAATTCACTAATTTGTTCTTTCTTTTAAAG
1 ACTACCTTAGCTATCAACACTAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTAAAG
*
3204 ACAAAGAGTAACCTTACAACTTTCTCAAGAATTATACCTCAAATTCTTGAGAACACTCTCTCCCA
66 ACAAAGAGTAACCTTACAACTTTCTCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCA
3269 AAGAGAAATACAAAAATTTGCTAACTTACAAAAAAACCTCACAAGGTAAGATGTTTTCACAATTC
131 AAGAGAAATACAAAAATTTGCTAACTTACAAAAAAACCTCACAAGGTAAGA-GTTTTCACAATTC
3334 TAGAACAAAGAAAGAACACTAAAAAATAAATACAATTGAGCACAATAAGTGTTCTTGAAAGAAAA
195 TAGAACAAAGAAAGAACACTAAAAAATAAATACAATTGAGCACAATAAGTGTTCTTGAAAGAAAA
3399 ATGAATATTGAATGAAAAATAGGTTTGAAATGCTCAAACTTGAGGTTTGATGCTTTCACTTTGAT
260 ATGAATATTGAATGAAAAATAGGTTTGAAATGCTCAAACTTGAGGTTTGATGCTTTCACTTTGAT
* * *
3464 TCTCTAGCTTCTCTTCTTAATGGTTGTTAATCAATGGCTCCTAAGCTTTTTTAAATACTCCTTTG
325 TCTCTAGCTTCTCTTCTTAATGGTTGTTAATCAATGGCTCCTAAGCTTGTTTAAATACTCATTGG
3529 ATCACTTCTGAACGTTGAGGATCATTAGTGGAGTCAATAGAGTCGTTATTGTGTGAAAACAATTA
390 ATCACTTCTGAACGTTGAGGATCATTAGTGGAGTCAATAGAGTCGTTATTGTGTGAAAACAATTA
3594 ATAAAACAATTGA
455 ATAAAACAATTGA
* * *
3607 ACTATCTTAGCTATCCACACTAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTAAGG
1 ACTACCTTAGCTATCAACACTAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTAAAG
*
3672 ACAAAGAGTGACCTTACAACTTTCTCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCA
66 ACAAAGAGTAACCTTACAACTTTCTCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCA
* *
3737 AAGAGAAATACACAAATTTGCTAACTTAC-AAGAAACCTCACAAGGTAAGA-TTTT-ACAATTCT
131 AAGAGAAATACAAAAATTTGCTAACTTACAAAAAAACCTCACAAGGTAAGAGTTTTCACAATTCT
*
3799 AGAACAAAGAAAGAATACTAAAAAATAAATACAATTGAGCACAATAAGTGTTCTTGAAAG-AAAA
196 AGAACAAAGAAAGAACACTAAAAAATAAATACAATTGAGCACAATAAGTGTTCTTGAAAGAAAAA
3863 TGAATATTGAATG-AAAATAGGTTTGAAATGCTCAAACTTGAGGTTTGATGCTTTCACTTTGATT
261 TGAATATTGAATGAAAAATAGGTTTGAAATGCTCAAACTTGAGGTTTGATGCTTTCACTTTGATT
3927 CTCTAGCTTCTCTTCTTAATGGTTGTTAATCAATGGCTCCTAAGCTTGTTTAAATACTCATTGGA
326 CTCTAGCTTCTCTTCTTAATGGTTGTTAATCAATGGCTCCTAAGCTTGTTTAAATACTCATTGGA
*
3992 TCTCTTCTGAACGTTGAGGATCATTAGTGGAGTCAATAGAGTCGTTATTGTGTGAAAACAATTAA
391 TCACTTCTGAACGTTGAGGATCATTAGTGGAGTCAATAGAGTCGTTATTGTGTGAAAACAATTAA
4057 TAAAACAATTGA
456 TAAAACAATTGA
4069 GAGCGTATGG
Statistics
Matches: 449, Mismatches: 13, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
462 189 0.42
463 17 0.04
464 67 0.15
465 4 0.01
467 20 0.04
468 152 0.34
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (467 bp):
ACTACCTTAGCTATCAACACTAAGGATTTTCCAACAAATTCACTAATTTGTTCTTTCTTTTAAAG
ACAAAGAGTAACCTTACAACTTTCTCAAGAATTATACCCCAAATTCTTGAGAACACTCTCTCCCA
AAGAGAAATACAAAAATTTGCTAACTTACAAAAAAACCTCACAAGGTAAGAGTTTTCACAATTCT
AGAACAAAGAAAGAACACTAAAAAATAAATACAATTGAGCACAATAAGTGTTCTTGAAAGAAAAA
TGAATATTGAATGAAAAATAGGTTTGAAATGCTCAAACTTGAGGTTTGATGCTTTCACTTTGATT
CTCTAGCTTCTCTTCTTAATGGTTGTTAATCAATGGCTCCTAAGCTTGTTTAAATACTCATTGGA
TCACTTCTGAACGTTGAGGATCATTAGTGGAGTCAATAGAGTCGTTATTGTGTGAAAACAATTAA
TAAAACAATTGA
Found at i:13015 original size:64 final size:65
Alignment explanation
Indices: 12880--13035 Score: 228
Period size: 64 Copynumber: 2.4 Consensus size: 65
12870 TACACTAGGA
* * * *
12880 GTGCATCAGTACACTAATTACATTCGATGTTTCAAAGAAGCCTGGAGTGCATCGATGCATGGTCT
1 GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAGAACCCTGGAGTGCATCGATGCATGGTCT
12945 GTGCATCGGTACA-TAAAATGCATTCGATGTTTCAATA-AACCCT-GAGTGCATCGATGCATGGT
1 GTGCATCGGTACACT-AAATGCATTCGATGTTTCAA-AGAACCCTGGAGTGCATCGATGCATGGT
*
13007 GT
64 CT
13009 GTGCATCGGTACACTAAATGCATTCGA
1 GTGCATCGGTACACTAAATGCATTCGA
13036 AATGGGGTGT
Statistics
Matches: 83, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
64 46 0.55
65 36 0.43
66 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.29
Consensus pattern (65 bp):
GTGCATCGGTACACTAAATGCATTCGATGTTTCAAAGAACCCTGGAGTGCATCGATGCATGGTCT
Found at i:18701 original size:16 final size:16
Alignment explanation
Indices: 18677--18709 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
18667 AAATATTTTT
18677 AAATGAAAAAATGAAAA
1 AAATGAAAAAAT-AAAA
18694 AAAT-AAAAAATAAAA
1 AAATGAAAAAATAAAA
18709 A
1 A
18710 TGTGATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.31
16 7 0.44
17 4 0.25
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AAATGAAAAAATAAAA
Found at i:24167 original size:15 final size:14
Alignment explanation
Indices: 24142--24257 Score: 94
Period size: 14 Copynumber: 8.1 Consensus size: 14
24132 GAGAGAGAAG
*
24142 AAGATAAAAAAAGA
1 AAGAAAAAAAAAGA
24156 AAGAAAAAAAAAGA
1 AAGAAAAAAAAAGA
24170 AA-AAAAAGAAAAGA
1 AAGAAAAA-AAAAGA
* *
24184 TAGAAAAAAGAAGA
1 AAGAAAAAAAAAGA
* * *
24198 ACG-GAAAAAGAGAA
1 AAGAAAAAAAAAG-A
* *
24212 AAGAAAAATATAG-
1 AAGAAAAAAAAAGA
24225 AAGAAGAAAAGAAAGA
1 AAGAA-AAAA-AAAGA
24241 AAGAGAAAAAAAAGA
1 AAGA-AAAAAAAAGA
24256 AA
1 AA
24258 AAACAAATCA
Statistics
Matches: 80, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
13 16 0.20
14 34 0.43
15 21 0.26
16 8 0.10
17 1 0.01
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (14 bp):
AAGAAAAAAAAAGA
Found at i:24184 original size:38 final size:39
Alignment explanation
Indices: 24137--24260 Score: 126
Period size: 46 Copynumber: 3.0 Consensus size: 39
24127 AAAAGGAGAG
24137 AGAAGAAGATAAAAAAAGAAAGAAAAAAAAAGAAAAAAA
1 AGAAGAAGATAAAAAAAGAAAGAAAAAAAAAGAAAAAAA
*
24176 AGAA-AAGATAGAAAAAAGAAGAACGGAAAAAGAGAAAAGAAAAATAT
1 AGAAGAAGATA-AAAAAAG-A-AA--G-AAAA-A-AAAAGAAAAA-AA
*
24223 AGAAGAAGA-AAAGAAAGAAAGAGAAAAAAAAGAAAAAA
1 AGAAGAAGATAAAAAAAGAAAGA-AAAAAAAAGAAAAAA
24261 CAAATCAAGT
Statistics
Matches: 72, Mismatches: 2, Indels: 22
0.75 0.02 0.23
Matches are distributed among these distances:
38 6 0.08
39 12 0.17
40 11 0.15
41 4 0.06
42 4 0.06
43 1 0.01
44 6 0.08
45 2 0.03
46 16 0.22
47 6 0.08
48 4 0.06
ACGTcount: A:0.77, C:0.01, G:0.19, T:0.03
Consensus pattern (39 bp):
AGAAGAAGATAAAAAAAGAAAGAAAAAAAAAGAAAAAAA
Found at i:25530 original size:32 final size:31
Alignment explanation
Indices: 25467--25530 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 31
25457 TTATTTCGTC
* *
25467 ACTAAATATTTTTTATAACTTTTTTACTGTG
1 ACTAAATATTTTTTACAACTTTGTTACTGTG
*
25498 ACTAAATAATTTTGTTACAA-TTTGTTATTGTG
1 ACTAAAT-ATTTT-TTACAACTTTGTTACTGTG
25530 A
1 A
25531 AAGAATATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
31 7 0.25
32 16 0.57
33 5 0.18
ACGTcount: A:0.31, C:0.08, G:0.09, T:0.52
Consensus pattern (31 bp):
ACTAAATATTTTTTACAACTTTGTTACTGTG
Found at i:25784 original size:17 final size:17
Alignment explanation
Indices: 25764--25801 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
25754 TTATGATGAG
25764 AAATTAATA-TTTGATAT
1 AAATTAATATTTTGAT-T
*
25781 AAATTATTATTTTGATT
1 AAATTAATATTTTGATT
25798 AAAT
1 AAAT
25802 AAATTTGTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (17 bp):
AAATTAATATTTTGATT
Found at i:25853 original size:18 final size:18
Alignment explanation
Indices: 25813--25849 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
25803 AATTTGTCAG
*
25813 AATTTTTTATTTTGACAT
1 AATTTTCTATTTTGACAT
25831 AATTTTCTATTTTGA-AT
1 AATTTTCTATTTTGACAT
25848 AA
1 AA
25850 ATTTATTACG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
AATTTTCTATTTTGACAT
Found at i:27772 original size:3 final size:3
Alignment explanation
Indices: 27764--27801 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
27754 TTTTCTTAAG
27764 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
27802 TAAAGCATAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:31696 original size:45 final size:45
Alignment explanation
Indices: 31647--31732 Score: 154
Period size: 45 Copynumber: 1.9 Consensus size: 45
31637 TAAAAAGAAG
* *
31647 TCAATCTTTCAGTACTATCTTTCTTGACTCCCTCGTGAAGAAAAA
1 TCAATCTTTCAGTACTATATTTCTTGACACCCTCGTGAAGAAAAA
31692 TCAATCTTTCAGTACTATATTTCTTGACACCCTCGTGAAGA
1 TCAATCTTTCAGTACTATATTTCTTGACACCCTCGTGAAGA
31733 GGATCGATCA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.28, C:0.24, G:0.12, T:0.36
Consensus pattern (45 bp):
TCAATCTTTCAGTACTATATTTCTTGACACCCTCGTGAAGAAAAA
Found at i:31812 original size:36 final size:38
Alignment explanation
Indices: 31712--32136 Score: 519
Period size: 38 Copynumber: 11.3 Consensus size: 38
31702 AGTACTATAT
** * *
31712 TTCTTGACACCCTCGTGAAGAGGATCGATCAATCTTTGTTG
1 TTCTTGACTTCCTCGTGAAGA-GA-AG-TCAATCTTTGTTA
*
31753 TTCTTAACTTCCTC-TGAAGAGAAGTCAATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
*
31790 -TCTTGACTT-CTCGTGAATAGAAGTCAATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
* * *
31826 CTCTTGACTTTCTCATGAAGAGAA-TC-ATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
* * *
31862 TTCTTTACTTTCTCATGAAGAGAAGTC-ATC-TT-TTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
*
31897 TTCTTGACTTCCTTGTGAAGA-AAGTCAATCTTT-TTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
* * *
31933 TTCTTGACTTCCTCATGAAGAAAAGTCGATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
* * *
31971 TTCTTGACTTCCTCATGAAGAAAAGTCGATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
*
32009 TTCTTGACTTCCTCGTAAAGAGAAGTCAATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
32047 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
* *
32085 TTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTTAGTGTTA
1 TTCTTGACTTCCTCGTGAAGAGAAGTCAATC--TT--TGTTA
32127 TTCTTGACTT
1 TTCTTGACTT
32137 TATCATGAAG
Statistics
Matches: 346, Mismatches: 26, Indels: 23
0.88 0.07 0.06
Matches are distributed among these distances:
34 5 0.01
35 26 0.08
36 88 0.25
37 39 0.11
38 153 0.44
39 2 0.01
40 8 0.02
41 11 0.03
42 14 0.04
ACGTcount: A:0.24, C:0.19, G:0.16, T:0.41
Consensus pattern (38 bp):
TTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTA
Found at i:32117 original size:114 final size:114
Alignment explanation
Indices: 31740--32136 Score: 535
Period size: 109 Copynumber: 3.5 Consensus size: 114
31730 AGAGGATCGA
* *
31740 TCAATCTTTGTTGTTCTTAACTTCCTC-TGAAGAGAAGTCAATCTTTGTTA-TCTTGACTT-CTC
1 TCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
* * *
31802 GTGAATAGAAGTCAATCTTTGTTACTCTTGACTTTCTCATGAAGAGAA-
66 GTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
* * *
31850 TC-ATCTTTGTTATTCTTTACTTTCTCATGAAGAGAAGTC-ATC-TT-TTATTCTTGACTTCCTT
1 TCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
*
31911 GTGAAGA-AAGTCAATCTTT-TTATTCTTGACTTCCTCATGAAGAAAAG
66 GTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
* * *
31958 TCGATCTTTGTTATTCTTGACTTCCTCATGAAGAAAAGTCGATCTTTGTTATTCTTGACTTCCTC
1 TCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
* *
32023 GTAAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCGTGAAGAGAAG
66 GTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
* * *
32072 TCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGAGTCAATCTTTTAGTGTTATTCTTGACTT
1 TCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATC--TT--TGTTATTCTTGACTT
32137 TATCATGAAG
Statistics
Matches: 252, Mismatches: 21, Indels: 20
0.86 0.07 0.07
Matches are distributed among these distances:
107 27 0.11
108 25 0.10
109 66 0.26
110 17 0.07
111 2 0.01
112 22 0.09
113 12 0.05
114 64 0.25
116 2 0.01
118 15 0.06
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (114 bp):
TCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTC
GTGAAGAGAAGTCAATCTTTGTTATTCTTGACTTCCTCATGAAGAGAAG
Found at i:32192 original size:85 final size:80
Alignment explanation
Indices: 31894--32210 Score: 321
Period size: 76 Copynumber: 4.0 Consensus size: 80
31884 AAGTCATCTT
* ** * * **
31894 TTATTCTTGACTTCCTTGTGAAG-AAAGTCAATCTTT-TTATTCTTGACTTCCTCATGAAGAAAA
1 TTATTCTTGACTTCATCATGAAGAAAAGTCAATCTTTGTTATTCTTGACTTCCTCGTAAAGAGGA
*
31957 GTCGATC--TT--TG
66 GTCAATCTTTTAGTG
* * *
31968 TTATTCTTGACTTCCTCATGAAGAAAAGTCGATCTTTGTTATTCTTGACTTCCTCGTAAAGAGAA
1 TTATTCTTGACTTCATCATGAAGAAAAGTCAATCTTTGTTATTCTTGACTTCCTCGTAAAGAGGA
32033 GTCAATC--TT--TG
66 GTCAATCTTTTAGTG
* * * * *
32044 TTATTCTTGACTTCCTCGTGAAGAGAAGTCAATCTTTGTTATTCTTGACTCCCTCGTGAAGAGGA
1 TTATTCTTGACTTCATCATGAAGAAAAGTCAATCTTTGTTATTCTTGACTTCCTCGTAAAGAGGA
32109 GTCAATCTTTTAGTG
66 GTCAATCTTTTAGTG
* * * * *
32124 TTATTCTTGACTTTATCATGAAGAAAATTCACTCTTAGTATTGTCATTCTTGACTTTCTCGTAAA
1 TTATTCTTGACTTCATCATGAAGAAAAGTCAATC----T-TTGTTATTCTTGACTTCCTCGTAAA
*
32189 GAGGAGTCAATATTTTAGTG
61 GAGGAGTCAATCTTTTAGTG
32209 TT
1 TT
32211 GTCCTTCTTG
Statistics
Matches: 208, Mismatches: 24, Indels: 11
0.86 0.10 0.05
Matches are distributed among these distances:
74 21 0.10
75 12 0.06
76 100 0.48
78 2 0.01
80 30 0.14
84 1 0.00
85 42 0.20
ACGTcount: A:0.26, C:0.17, G:0.16, T:0.41
Consensus pattern (80 bp):
TTATTCTTGACTTCATCATGAAGAAAAGTCAATCTTTGTTATTCTTGACTTCCTCGTAAAGAGGA
GTCAATCTTTTAGTG
Found at i:32219 original size:45 final size:45
Alignment explanation
Indices: 32102--32565 Score: 347
Period size: 45 Copynumber: 10.4 Consensus size: 45
32092 CTCCCTCGTG
* * *
32102 AAGAGGAGTCAATCTTTTAGTG-T-T-ATTCTTGACTTTATCATG
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
** * * * * *
32144 AAGAAAATTC-A-CTCTTAGTATTGTCATTCTTGACTTTCTCGTA
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
* * ****
32187 AAGAGGAGTCAATATTTTAGTGTTGTCCTTCTTGACTTTATTGCG
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
* ** **
32232 AAGAGGAGTCAAT-ATCCAGTGTTGTCCTTCTTGACTTTCTCACG
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
** * * * *
32276 AAGAGGAGTCAATCTTTCGGTGTTTTCTTTTTTGACTTTCTCGTTA
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTC-ATA
* * **
32322 AA-AGGAGTAAATCTTTTAGTGTTGCCCTTCTTGACTTTCTCGCGA
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTC-ATA
* * *
32367 AA-AGGAGTCAATCTTTTAGTGTTATCTTTCTTGACTTTCTCACA
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
* * * * *
32411 AATAGGAGTCAATATTTT-GATGTTAT-CTTCCTTGACTTTCTAATG
1 AAGAGGAGTCAATCTTTTAG-TGTTGTCCTT-CTTGACTTTCTCATA
* * *
32456 AATAGGAGTTAATCTTTTAGTGTTGT-CTTCCTTGACTTTCTCATG
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTT-CTTGACTTTCTCATA
* * * * * *
32501 AATAGGAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTTAGA
1 AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
* **
32546 AAGAGAAGTTGATCTTTTAG
1 AAGAGGAGTCAATCTTTTAG
32566 AGATGTCATT
Statistics
Matches: 340, Mismatches: 70, Indels: 21
0.79 0.16 0.05
Matches are distributed among these distances:
40 7 0.02
41 2 0.01
42 8 0.02
43 22 0.06
44 45 0.13
45 251 0.74
46 5 0.01
ACGTcount: A:0.24, C:0.16, G:0.18, T:0.42
Consensus pattern (45 bp):
AAGAGGAGTCAATCTTTTAGTGTTGTCCTTCTTGACTTTCTCATA
Found at i:32463 original size:135 final size:134
Alignment explanation
Indices: 32172--32550 Score: 427
Period size: 135 Copynumber: 2.8 Consensus size: 134
32162 TATTGTCATT
* * * * * *
32172 CTTGACTTTCTCGTAAAGAGGAGTCAATATTTTAGTGTTGTCCTTCTTGACTTTATTGCGAAGAG
1 CTTGACTTTCTCGTAAAAAGGAGTAAATCTTTTAGTGTTG-CCTTCTTGACTTTCTCGCGAAAAG
* * * * * * *
32237 GAGTCAAT-ATCCAGTGTTGTCCTTCTTGACTTTCTCACGAAGAGGAGTCAATCTTTCGGTGTTT
65 GAGTCAATCTTTCAGTGTTGTCATTCTTGACTTTCTCACAAAGAGGAGTCAATATTTCGATGTTA
*
32301 TCTTT
130 TCTTC
* *
32306 TTTGACTTTCTCGTTAAAAGGAGTAAATCTTTTAGTGTTGCCCTTCTTGACTTTCTCGCGAAAAG
1 CTTGACTTTCTCGTAAAAAGGAGTAAATCTTTTAGTGTTG-CCTTCTTGACTTTCTCGCGAAAAG
* * * * *
32371 GAGTCAATCTTTTAGTGTTATCTTTCTTGACTTTCTCACAAATAGGAGTCAATATTTTGATGTTA
65 GAGTCAATCTTTCAGTGTTGTCATTCTTGACTTTCTCACAAAGAGGAGTCAATATTTCGATGTTA
32436 TCTTC
130 TCTTC
** * * * * ** *
32441 CTTGACTTTCTAATGAATAGGAGTTAATCTTTTAGTGTTGTCTTCCTTGACTTTCTCATGAATAG
1 CTTGACTTTCTCGTAAAAAGGAGTAAATCTTTTAGTGTTGCCTT-CTTGACTTTCTCGCGAAAAG
* * *
32506 GAGTCAATCTTTCAGTATTGTCATTCTTGACTTTCTTAGAAAGAG
65 GAGTCAATCTTTCAGTGTTGTCATTCTTGACTTTCTCACAAAGAG
32551 AAGTTGATCT
Statistics
Matches: 205, Mismatches: 38, Indels: 3
0.83 0.15 0.01
Matches are distributed among these distances:
134 67 0.33
135 138 0.67
ACGTcount: A:0.23, C:0.17, G:0.18, T:0.42
Consensus pattern (134 bp):
CTTGACTTTCTCGTAAAAAGGAGTAAATCTTTTAGTGTTGCCTTCTTGACTTTCTCGCGAAAAGG
AGTCAATCTTTCAGTGTTGTCATTCTTGACTTTCTCACAAAGAGGAGTCAATATTTCGATGTTAT
CTTC
Found at i:33544 original size:134 final size:133
Alignment explanation
Indices: 33174--33544 Score: 528
Period size: 134 Copynumber: 2.8 Consensus size: 133
33164 TTGATTTTCA
* * * *
33174 GATTAAATATTCCCTGAAGATCACTGAAGTGGATCAAAGATTTCTCGAGTTTGATCTCCCCTAAA
1 GATTCAATATT-CCTGAAGAGCAGTGAAGTGGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAA
* * * * *
33239 GAGTAGTAGAGTATATTCTTCTTCTTTAAGATTTGGTATTCCTGAAGAGTAGGGAAGCAAATCAA
65 GAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGTAGGGAAGCAAATCAA
33304 GTTC
130 GTTC
* *
33308 GATTCAATATTCCTTGAAGAGAAGTGAAGTGGATCAAAGTTTTCTCGAGTCTGATCTCCCCTAAA
1 GATTCAATATTCC-TGAAGAGCAGTGAAGTGGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAA
* * **
33373 GAGTAGTGGAGCATATTCTTCTTTTTTCAGATTTGGTCTTCCTAAAGAGTAGTGAAGCAAATTGA
65 GAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGTAGGGAAGCAAATCAA
33438 -TTC
130 GTTC
* * *
33441 TGATTCAATCTTTCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTCTCGATTTTGATATCCCCTAA
1 -GATTCAAT-ATTCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAA
*
33506 AGAGTAGTGGAGCATATTTTTCTTCTTTCAGATTTGGTC
64 AGAGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTC
33545 ATCTGATAAA
Statistics
Matches: 212, Mismatches: 22, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
133 5 0.02
134 203 0.96
135 4 0.02
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (133 bp):
GATTCAATATTCCTGAAGAGCAGTGAAGTGGATCAAAGTTTTCTCGAGTTTGATCTCCCCTAAAG
AGTAGTGGAGCATATTCTTCTTCTTTCAGATTTGGTCTTCCTAAAGAGTAGGGAAGCAAATCAAG
TTC
Found at i:38532 original size:17 final size:19
Alignment explanation
Indices: 38510--38552 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
38500 AAAAACTCGA
*
38510 ATGCACT-TGA-TGCATCG
1 ATGCACTCTGAGTGCACCG
*
38527 ATGCACTCTTAGTGCACCG
1 ATGCACTCTGAGTGCACCG
38546 ATGCACT
1 ATGCACT
38553 AAGGTTCCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 2 0.09
19 13 0.59
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.28
Consensus pattern (19 bp):
ATGCACTCTGAGTGCACCG
Found at i:47955 original size:21 final size:21
Alignment explanation
Indices: 47913--47956 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
47903 ACTCCGGGAG
* * *
47913 CTAGTTCCTCTCGAGCTGCTC
1 CTAGCTCCTCTCGAGATCCTC
*
47934 CTAGCTCCTCTCGTGATCCTC
1 CTAGCTCCTCTCGAGATCCTC
47955 CT
1 CT
47957 CCTCCTCCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.41, G:0.16, T:0.34
Consensus pattern (21 bp):
CTAGCTCCTCTCGAGATCCTC
Found at i:48671 original size:19 final size:19
Alignment explanation
Indices: 48647--48684 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
48637 AAAGGGGGAG
48647 AAATGTTAAGTGTTGAAAT
1 AAATGTTAAGTGTTGAAAT
*
48666 AAATGTTAAGTGTTTAAAT
1 AAATGTTAAGTGTTGAAAT
48685 GTTTTTTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.18, T:0.39
Consensus pattern (19 bp):
AAATGTTAAGTGTTGAAAT
Found at i:49134 original size:17 final size:17
Alignment explanation
Indices: 49114--49146 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
49104 CAAATGCATT
*
49114 CCATGCATCGATGCACA
1 CCATGCACCGATGCACA
49131 CCATGCACCGATGCAC
1 CCATGCACCGATGCAC
49147 TGAGGATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.27, C:0.39, G:0.18, T:0.15
Consensus pattern (17 bp):
CCATGCACCGATGCACA
Found at i:49176 original size:63 final size:64
Alignment explanation
Indices: 49049--49252 Score: 206
Period size: 65 Copynumber: 3.2 Consensus size: 64
49039 TTTTTCAGAG
* * * * *
49049 TGATGCATCGATGCACCAATCCATGCATCGATGCAC-CATGA-A-TTAAATTGAACATCAAATGC
1 TGATGCATCGATGCACC-AGCCATGCACCGATGCACTCAGGATATTTTAA--GAACATCGAATGC
49111 AT
63 AT
* *
49113 TCCATGCATCGATGCA-CA-CCATGCACCGATGCACTGAGGAT-TTTATAAGAACATCGAATGCA
1 T-GATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTT-TAAGAACATCGAATGCA
49175 TT
64 -T
* * *
49177 TGATGCATCGATGCACCAGCCATGCATCGATGCACTCTGGCTATTTTAA-AACATCGAATGCACT
1 TGATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTAAGAACATCGAATGCA-T
49241 TGATGCATCGAT
1 TGATGCATCGAT
49253 CCAATCTTAG
Statistics
Matches: 119, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
62 15 0.13
63 30 0.25
64 34 0.29
65 37 0.31
66 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAGCCATGCACCGATGCACTCAGGATATTTTAAGAACATCGAATGCAT
Done.