Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006763.1 Hibiscus syriacus cultivar Beakdansim tig00017093_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: 127392
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:2067 original size:24 final size:24
Alignment explanation
Indices: 2021--2068 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
2011 CTTTGCTTTG
* *
2021 TCTTCTTTTTGAGAGCTGGAATTT
1 TCTTCTTTTGGAGAGCTGCAATTT
* *
2045 TCTTCTTTTGGAGTGCTTCAATTT
1 TCTTCTTTTGGAGAGCTGCAATTT
2069 GTTTGCTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.15, C:0.15, G:0.19, T:0.52
Consensus pattern (24 bp):
TCTTCTTTTGGAGAGCTGCAATTT
Found at i:8154 original size:32 final size:32
Alignment explanation
Indices: 8118--8190 Score: 128
Period size: 32 Copynumber: 2.3 Consensus size: 32
8108 TAATGGCCTT
*
8118 CATTTCTTCCCACGAAGTGATGGGGCGTTCAC
1 CATTTCTTCCCACGAAGTGACGGGGCGTTCAC
*
8150 CATTTCTTCCCACGTAGTGACGGGGCGTTCAC
1 CATTTCTTCCCACGAAGTGACGGGGCGTTCAC
8182 CATTTCTTC
1 CATTTCTTC
8191 TTCTTGAACT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.16, C:0.30, G:0.22, T:0.32
Consensus pattern (32 bp):
CATTTCTTCCCACGAAGTGACGGGGCGTTCAC
Found at i:8814 original size:22 final size:23
Alignment explanation
Indices: 8770--8815 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 23
8760 TTGGTGCTGG
8770 AAACAAGATAAGAAATAAGATTA
1 AAACAAGATAAGAAATAAGATTA
8793 AAACAAGATAA-AGAA-AAGATTA
1 AAACAAGATAAGA-AATAAGATTA
8815 A
1 A
8816 GGAATTGCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 9 0.41
23 13 0.59
ACGTcount: A:0.67, C:0.04, G:0.13, T:0.15
Consensus pattern (23 bp):
AAACAAGATAAGAAATAAGATTA
Found at i:12209 original size:25 final size:24
Alignment explanation
Indices: 12167--12214 Score: 60
Period size: 25 Copynumber: 2.0 Consensus size: 24
12157 TTCTTTGCTT
* *
12167 TTTTGTAGTGCTGGAATTTTCTTTC
1 TTTTGGAGTGCTGCAA-TTTCTTTC
*
12192 TTTTGGAGTGCTTCAATTTCTTT
1 TTTTGGAGTGCTGCAATTTCTTT
12215 TCTGATTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.56
Consensus pattern (24 bp):
TTTTGGAGTGCTGCAATTTCTTTC
Found at i:13000 original size:367 final size:370
Alignment explanation
Indices: 12351--13040 Score: 1120
Period size: 367 Copynumber: 1.9 Consensus size: 370
12341 GTACCTCTTC
* *
12351 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTACACAACTATATGGCTCAAAAGAGATAG
1 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTACACAACTATATGGCTCAAAACAAATAG
* * * *
12416 TTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGTTGTTTAATAAATGAGAGATGAAAGCTGTAG
66 TTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGCTGCTTAAT--ATGAGAGATGAAAGCGGAAG
12481 ATGATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTA
129 ATGATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTA
12546 AAGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTA
194 AAGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTA
*
12611 AGGGGTGATATGAAGGACTTTGACCCACTAGTTATA-AGAATTAGAAACCAAAAGTATCAAGGGG
259 AGGGGTGATATGAAGGACTTTGACCCACTAGTTATAGAGAACTAGAAACCAAAAGTATCAAGGGG
12675 AAAGGGGTTGATACCACATGATGTAAGGCTCTTCTGATGCCTTAACA
324 AAAGGGGTTGATACCACATGATGTAAGGCTCTTCTGATGCCTTAACA
* *
12722 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTGCA-AAGTGA-ATGGCTCAAAACATAAT
1 AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTACACAACT-ATATGGCTCAAAACA-AAT
* * * *
12785 GGTTAAGGGTGGTAAACGTATGGGTGATTAGGTGGGCTGCTTAAT-TGAGAGATGGAAGCGGAAG
64 AGTTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGCTGCTTAATATGAGAGATGAAAGCGGAAG
* * *
12849 ATGTTTGATATGGCTAT-GGTTATGGTTTATGAAACAAAGGGATGGTTGTGAGGATAGTATCTTA
129 ATGATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTA
*
12913 AAGAAGACTCAAAGAAGAACCAATGCTATATAGAGCAAAGACCCAGACTTTATATTGCTTCTTTA
194 AAGAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTA
* * * *
12978 AGGGGTGGTATGAAGTACTTTGACCCACTAGTTATAGAGAACTAGGAACCAGAAGTATCAAGG
259 AGGGGTGATATGAAGGACTTTGACCCACTAGTTATAGAGAACTAGAAACCAAAAGTATCAAGG
13041 TAAAAAGAGA
Statistics
Matches: 295, Mismatches: 21, Indels: 9
0.91 0.06 0.03
Matches are distributed among these distances:
367 143 0.48
368 55 0.19
370 15 0.05
371 82 0.28
ACGTcount: A:0.36, C:0.12, G:0.27, T:0.26
Consensus pattern (370 bp):
AATTGATTGTGGATCTAGGAAGGAAGCAAAACAACCTACACAACTATATGGCTCAAAACAAATAG
TTAAGGGTGGTAAACGTAAGGGTGAATAGGTGGGCTGCTTAATATGAGAGATGAAAGCGGAAGAT
GATTGATATGGCTATGGGTTATGGTTAATGAAACAAAGGGATGGTTGTAAGGATAGTATCTTAAA
GAAGACTCAAAGAAGAACCAATGCTATAGAGAGCAAAGACCCAGACTTTATATTGCTTCTTTAAG
GGGTGATATGAAGGACTTTGACCCACTAGTTATAGAGAACTAGAAACCAAAAGTATCAAGGGGAA
AGGGGTTGATACCACATGATGTAAGGCTCTTCTGATGCCTTAACA
Found at i:16382 original size:19 final size:20
Alignment explanation
Indices: 16341--16391 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
16331 GAAACCCCTT
*
16341 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
16361 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
16380 TGAAGATACATG
1 TGAAAATACATG
16392 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:17325 original size:30 final size:30
Alignment explanation
Indices: 17290--17346 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
17280 CTGCCATGAT
**
17290 ATCTAAATGAAATGAAAACATAATAAATTA
1 ATCTAAAACAAATGAAAACATAATAAATTA
* *
17320 ATCTAAAACATATGTAAACATAATAAA
1 ATCTAAAACAAATGAAAACATAATAAA
17347 AAGATGTGAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (30 bp):
ATCTAAAACAAATGAAAACATAATAAATTA
Found at i:20510 original size:19 final size:20
Alignment explanation
Indices: 20469--20519 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
20459 GAAACCCCTT
*
20469 TGAAAATACATGATTTTTGA
1 TGAAAATACATGATTTTTAA
20489 TGAAAATACATGA-TTTTAA
1 TGAAAATACATGATTTTTAA
*
20508 TGAAGATACATG
1 TGAAAATACATG
20520 CTCTTGGCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:38960 original size:24 final size:24
Alignment explanation
Indices: 38911--38961 Score: 68
Period size: 24 Copynumber: 2.1 Consensus size: 24
38901 ATTCTTTGTT
* *
38911 TTTTCTTCTTTTTGAGTGTTGTAA
1 TTTTCTTCTTTTGGAGTGTTGCAA
38935 TTTTCTTCTTTTGGAGTGCTT-CAA
1 TTTTCTTCTTTTGGAGTG-TTGCAA
38959 TTT
1 TTT
38962 GTTTGCTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 22 0.92
25 2 0.08
ACGTcount: A:0.12, C:0.12, G:0.16, T:0.61
Consensus pattern (24 bp):
TTTTCTTCTTTTGGAGTGTTGCAA
Found at i:42800 original size:17 final size:17
Alignment explanation
Indices: 42772--42828 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
42762 AATTGGACTG
42772 CAAAAAGAAAAGAAAAGA
1 CAAAAAGAAAAGAAAA-A
*
42790 CAAAAAG-AAAGAAAAT
1 CAAAAAGAAAAGAAAAA
42806 CAGAAAAGAAAAGAAAAA
1 CA-AAAAGAAAAGAAAAA
*
42824 GAAAA
1 CAAAA
42829 TTAAAAAGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 2 0.06
17 16 0.47
18 16 0.47
ACGTcount: A:0.77, C:0.05, G:0.16, T:0.02
Consensus pattern (17 bp):
CAAAAAGAAAAGAAAAA
Found at i:42814 original size:25 final size:23
Alignment explanation
Indices: 42782--42842 Score: 70
Period size: 24 Copynumber: 2.6 Consensus size: 23
42772 CAAAAAGAAA
42782 AGAAAAGACAAAAAGAAAGAAAATC
1 AGAAAAGA-AAAAA-AAAGAAAATC
*
42807 AGAAAAGAAAAGAAAAAGAAAATT
1 AGAAAAGAAAA-AAAAAGAAAATC
*
42831 A-AAAAGAGAAAA
1 AGAAAAGAAAAAA
42843 CAAGCCAAGG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
22 2 0.06
23 8 0.24
24 13 0.39
25 10 0.30
ACGTcount: A:0.75, C:0.03, G:0.16, T:0.05
Consensus pattern (23 bp):
AGAAAAGAAAAAAAAAGAAAATC
Found at i:42834 original size:11 final size:11
Alignment explanation
Indices: 42773--42828 Score: 53
Period size: 11 Copynumber: 4.9 Consensus size: 11
42763 ATTGGACTGC
42773 AAAAAGAAAAG
1 AAAAAGAAAAG
42784 -AAAAGACAAA-
1 AAAAAGA-AAAG
*
42794 AAGAAAGAAAATC
1 AA-AAAGAAAA-G
42807 AGAAAAGAAAAG
1 A-AAAAGAAAAG
42819 AAAAAGAAAA
1 AAAAAGAAAA
42829 TTAAAAAGAG
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
10 6 0.16
11 16 0.42
12 6 0.16
13 9 0.24
14 1 0.03
ACGTcount: A:0.79, C:0.04, G:0.16, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:42842 original size:30 final size:29
Alignment explanation
Indices: 42773--42827 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
42763 ATTGGACTGC
42773 AAAAAGAAAAGAAAAGACAAAAAGAAAGA
1 AAAAAGAAAAGAAAAGACAAAAAGAAAGA
*
42802 AAATCAGAAAAGAAAAG--AAAAAGAAA
1 AAA-AAGAAAAGAAAAGACAAAAAGAAA
42828 ATTAAAAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 9 0.38
29 3 0.12
30 12 0.50
ACGTcount: A:0.78, C:0.04, G:0.16, T:0.02
Consensus pattern (29 bp):
AAAAAGAAAAGAAAAGACAAAAAGAAAGA
Found at i:44697 original size:18 final size:18
Alignment explanation
Indices: 44674--44709 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
44664 CCAAATTGAT
44674 CAAATCAAGATAAAACAA
1 CAAATCAAGATAAAACAA
44692 CAAATCAAGATAAAACAA
1 CAAATCAAGATAAAACAA
44710 AGTGTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.11
Consensus pattern (18 bp):
CAAATCAAGATAAAACAA
Found at i:50029 original size:19 final size:20
Alignment explanation
Indices: 50005--50044 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
49995 TATCCTTTCT
*
50005 TTATTTCTTTTCATT-CTTA
1 TTATTTATTTTCATTACTTA
*
50024 TTATTTATTTTTATTACTTA
1 TTATTTATTTTCATTACTTA
50044 T
1 T
50045 ATTATTATCC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:51363 original size:9 final size:9
Alignment explanation
Indices: 51349--51401 Score: 54
Period size: 9 Copynumber: 5.7 Consensus size: 9
51339 TTTATTTTTC
51349 AAAAAAACA
1 AAAAAAACA
51358 AAAAAAACA
1 AAAAAAACA
**
51367 AAAAAGGCA
1 AAAAAAACA
51376 AAAAAAA-A
1 AAAAAAACA
51384 GGCAAAAAAACA
1 ---AAAAAAACA
51396 AAAAAA
1 AAAAAA
51402 GAGCCAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
8 1 0.03
9 27 0.75
11 7 0.19
12 1 0.03
ACGTcount: A:0.83, C:0.09, G:0.08, T:0.00
Consensus pattern (9 bp):
AAAAAAACA
Found at i:51381 original size:12 final size:12
Alignment explanation
Indices: 51366--51393 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
51356 CAAAAAAAAC
51366 AAAAAAGGCAAA
1 AAAAAAGGCAAA
51378 AAAAAAGGCAAA
1 AAAAAAGGCAAA
51390 AAAA
1 AAAA
51394 CAAAAAAAGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.79, C:0.07, G:0.14, T:0.00
Consensus pattern (12 bp):
AAAAAAGGCAAA
Found at i:51382 original size:20 final size:20
Alignment explanation
Indices: 51348--51413 Score: 66
Period size: 20 Copynumber: 3.4 Consensus size: 20
51338 ATTTATTTTT
51348 CAAAAAAAC--AAAAAAA-A
1 CAAAAAAACAAAAAAAAAGA
* *
51365 CAAAAAAGGCAAAAAAAAAGG
1 CAAAAAA-ACAAAAAAAAAGA
* *
51386 CAAAAAAACAAAAAAAGAGC
1 CAAAAAAACAAAAAAAAAGA
51406 CAAAAAAA
1 CAAAAAAA
51414 GCCAAAATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
17 7 0.17
18 1 0.03
20 25 0.62
21 7 0.17
ACGTcount: A:0.79, C:0.12, G:0.09, T:0.00
Consensus pattern (20 bp):
CAAAAAAACAAAAAAAAAGA
Found at i:51391 original size:13 final size:13
Alignment explanation
Indices: 51361--51393 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
51351 AAAAACAAAA
51361 AAAACAAAAAAGGC
1 AAAA-AAAAAAGGC
51375 -AAAAAAAAAGGC
1 AAAAAAAAAAGGC
51387 AAAAAAA
1 AAAAAAA
51394 CAAAAAAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.79, C:0.09, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAGGC
Found at i:51410 original size:10 final size:10
Alignment explanation
Indices: 51348--51420 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 10
51338 ATTTATTTTT
51348 CAAAAAAA--
1 CAAAAAAAGC
*
51356 CAAAAAAA-A
1 CAAAAAAAGC
*
51365 CAAAAAAGGC
1 CAAAAAAAGC
* *
51375 AAAAAAAAAGG
1 -CAAAAAAAGC
51386 CAAAAAAA-C
1 CAAAAAAAGC
*
51395 AAAAAAAGAGC
1 CAAAAAA-AGC
51406 CAAAAAAAGC
1 CAAAAAAAGC
51416 CAAAA
1 CAAAA
51421 TTTCAAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
8 8 0.16
9 13 0.25
10 16 0.31
11 14 0.27
ACGTcount: A:0.77, C:0.14, G:0.10, T:0.00
Consensus pattern (10 bp):
CAAAAAAAGC
Found at i:51414 original size:30 final size:29
Alignment explanation
Indices: 51349--51420 Score: 85
Period size: 30 Copynumber: 2.5 Consensus size: 29
51339 TTTATTTTTC
*
51349 AAAAAAA-CAAAAAAAACAAAAAAGGCAA
1 AAAAAAAGCCAAAAAAACAAAAAAGGCAA
* *
51377 AAAAAAAGGCAAAAAAACAAAAAAAGAGC-C
1 AAAAAAAGCCAAAAAAAC-AAAAAAG-GCAA
51407 AAAAAAAGCCAAAA
1 AAAAAAAGCCAAAA
51421 TTTCAAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 7 0.19
29 8 0.22
30 20 0.54
31 2 0.05
ACGTcount: A:0.78, C:0.12, G:0.10, T:0.00
Consensus pattern (29 bp):
AAAAAAAGCCAAAAAAACAAAAAAGGCAA
Found at i:60356 original size:12 final size:11
Alignment explanation
Indices: 60329--60369 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
60319 TTTATTTTTT
*
60329 CAAAAATAAAA
1 CAAAAAAAAAA
*
60340 TAAAAAAAAAGA
1 CAAAAAAAAA-A
60352 CAAAAAAAAAA
1 CAAAAAAAAAA
60363 CAAAAAA
1 CAAAAAA
60370 GCCAAAATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.85, C:0.07, G:0.02, T:0.05
Consensus pattern (11 bp):
CAAAAAAAAAA
Found at i:75151 original size:15 final size:17
Alignment explanation
Indices: 75133--75194 Score: 78
Period size: 16 Copynumber: 3.9 Consensus size: 17
75123 AAATTACTAT
75133 TATAATA-AT-TATAGA
1 TATAATATATATATAGA
*
75148 TATAATATATATATATA
1 TATAATATATATATAGA
*
75165 TAT-ATATATATATATA
1 TATAATATATATATAGA
75181 TAT-ATATATATATA
1 TATAATATATATATA
75195 TGAAAATAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 3
0.92 0.02 0.06
Matches are distributed among these distances:
15 7 0.16
16 29 0.66
17 8 0.18
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (17 bp):
TATAATATATATATAGA
Found at i:75209 original size:2 final size:2
Alignment explanation
Indices: 75142--75195 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
75132 TTATAATAAT
*
75142 TA TA GA TA TA -A 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 TA TA
75183 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
75196 GAAAATAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
TA
Found at i:81150 original size:73 final size:72
Alignment explanation
Indices: 81030--81170 Score: 169
Period size: 73 Copynumber: 1.9 Consensus size: 72
81020 GAACACATCA
* * * * * *
81030 TTTGGCCGAATTCATCCCACCTTGTGTGAACTTGTTGATTTGTCTTCTATGGATGAATGTTCATG
1 TTTGGCCGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCT-TGCATGAATATGCATG
81095 AATGTATT
65 AATGTATT
* *
81103 TTTGGCTGAAATTCTTCCC-CCTTGTGTGAACATGACT-ATTTGGCTTCTTGCATGAATATGCAT
1 TTTGGCCG-AATTCATCCCACCTTGTGTGAACATG-CTGATTTGGCTTCTTGCATGAATATGCAT
81166 GAATG
64 GAATG
81171 GATGAATTTA
Statistics
Matches: 58, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
72 17 0.29
73 31 0.53
74 10 0.17
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (72 bp):
TTTGGCCGAATTCATCCCACCTTGTGTGAACATGCTGATTTGGCTTCTTGCATGAATATGCATGA
ATGTATT
Found at i:84305 original size:24 final size:26
Alignment explanation
Indices: 84259--84306 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 26
84249 CTATAGATAT
*
84259 AATATATATATATATATACGAAATTA
1 AATATATATATATACATACGAAATTA
*
84285 AATATAT-TATA-ACATATGAAAT
1 AATATATATATATACATACGAAAT
84307 AAGCATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 9 0.45
25 4 0.20
26 7 0.35
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.38
Consensus pattern (26 bp):
AATATATATATATACATACGAAATTA
Found at i:88641 original size:11 final size:11
Alignment explanation
Indices: 88625--88654 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
88615 TGCCATGATA
88625 TTTGTGAGCTG
1 TTTGTGAGCTG
88636 TTTGTGAGCTG
1 TTTGTGAGCTG
88647 TTTGTGAG
1 TTTGTGAG
88655 TTGTATATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.10, C:0.07, G:0.37, T:0.47
Consensus pattern (11 bp):
TTTGTGAGCTG
Found at i:90591 original size:91 final size:91
Alignment explanation
Indices: 90432--90614 Score: 258
Period size: 91 Copynumber: 2.0 Consensus size: 91
90422 CCTAGAACAC
* * **
90432 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCTGAGAAG
1 CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATGTGGATCATTTAGGAGCCAAGAAG
* *
90497 AAGAGTTCTCTCCCTATTCGGCCAAG
66 AAGAATTCTCTCCCTATTCAGCCAAG
** * * * *
90523 CCATGTGTTTTGCATGTGATCAGCCCCCATATGCCTTGCATGTGGTTCATTTAGGAGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATGTGGATCATTTAGGAGCCAAGAAG
90588 AAGAATTCTCTCCCTATTCAGCCAAG
66 AAGAATTCTCTCCCTATTCAGCCAAG
90614 C
1 C
90615 ATCATGATGC
Statistics
Matches: 80, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.22, C:0.27, G:0.22, T:0.28
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATATGCCTTGCATGTGGATCATTTAGGAGCCAAGAAG
AAGAATTCTCTCCCTATTCAGCCAAG
Found at i:98178 original size:30 final size:31
Alignment explanation
Indices: 98126--98185 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
98116 CTTAGCTTTA
**
98126 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
98156 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
98186 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:98377 original size:20 final size:21
Alignment explanation
Indices: 98352--98390 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
98342 ACGTCCTATG
98352 CATGTTATC-TAGCTTATATA
1 CATGTTATCTTAGCTTATATA
98372 CATGTTATCTTAGCTTATA
1 CATGTTATCTTAGCTTATA
98391 GATGATCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.28, C:0.15, G:0.10, T:0.46
Consensus pattern (21 bp):
CATGTTATCTTAGCTTATATA
Found at i:99098 original size:19 final size:20
Alignment explanation
Indices: 99074--99124 Score: 77
Period size: 20 Copynumber: 2.6 Consensus size: 20
99064 CGGCCAAGAG
* *
99074 CATGTATCTTCAT-TAAAAT
1 CATGTATTTTCATCAAAAAT
99093 CATGTATTTTCATCAAAAAT
1 CATGTATTTTCATCAAAAAT
99113 CATGTATTTTCA
1 CATGTATTTTCA
99125 AATGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 12 0.41
20 17 0.59
ACGTcount: A:0.35, C:0.16, G:0.06, T:0.43
Consensus pattern (20 bp):
CATGTATTTTCATCAAAAAT
Found at i:99561 original size:19 final size:20
Alignment explanation
Indices: 99537--99576 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
99527 TATCCTTTCT
99537 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
99556 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
99576 T
1 T
99577 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:106360 original size:30 final size:31
Alignment explanation
Indices: 106308--106367 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
106298 CTTAGCTTTA
**
106308 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
* *
106338 TATTATGTTTGCATTTCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
106368 GGCAGCATGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.27, C:0.08, G:0.10, T:0.55
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:107301 original size:19 final size:20
Alignment explanation
Indices: 107277--107322 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
107267 CATCCAACAG
*
107277 CATGTATCATCAT-TAAAAT
1 CATGTATCATCATCAAAAAT
**
107296 CATGTATTTTCATCAAAAAT
1 CATGTATCATCATCAAAAAT
107316 CATGTAT
1 CATGTAT
107323 TTTCAAAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 11 0.48
20 12 0.52
ACGTcount: A:0.39, C:0.15, G:0.07, T:0.39
Consensus pattern (20 bp):
CATGTATCATCATCAAAAAT
Found at i:107764 original size:19 final size:20
Alignment explanation
Indices: 107740--107779 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
107730 TATCCTTTAT
107740 TTATTTCATTTCATT-CTTA
1 TTATTTCATTTCATTACTTA
*
107759 TTATTTCTTTTCATTACTTA
1 TTATTTCATTTCATTACTTA
107779 T
1 T
107780 ATTATTATTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.20, C:0.15, G:0.00, T:0.65
Consensus pattern (20 bp):
TTATTTCATTTCATTACTTA
Found at i:109525 original size:91 final size:91
Alignment explanation
Indices: 109377--109551 Score: 287
Period size: 91 Copynumber: 1.9 Consensus size: 91
109367 CCCATGTGCC
*
109377 TTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGTTCT
*
109442 CTCCCTATTCGGCCAAGCAATGTGTT
66 ATCCCTATTCGGCCAAGCAATGTGTT
* * * * *
109468 TTGCATGTGATCAGCCCCCATGTTCCTTGCATGTGGTTCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGTTCT
109533 ATCCCTATTCGGCCAAGCA
66 ATCCCTATTCGGCCAAGCA
109552 TCAACTACCA
Statistics
Matches: 77, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 77 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCACCAAGATGAAGAGTTCT
ATCCCTATTCGGCCAAGCAATGTGTT
Found at i:110353 original size:23 final size:24
Alignment explanation
Indices: 110327--110380 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 24
110317 AAATCCAGCA
110327 AAGAAAATCAAAGCACT-AAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
* *
110350 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATCAAAGCACTCAAAAAG
110374 AAGAAAA
1 AAGAAAA
110381 AGAAAGAAAG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 15 0.56
24 12 0.44
ACGTcount: A:0.65, C:0.11, G:0.15, T:0.09
Consensus pattern (24 bp):
AAGAAAATCAAAGCACTCAAAAAG
Found at i:110385 original size:24 final size:23
Alignment explanation
Indices: 110327--110386 Score: 84
Period size: 24 Copynumber: 2.6 Consensus size: 23
110317 AAATCCAGCA
*
110327 AAGAAAATCAAAGCACTAAAAAG
1 AAGAAAATGAAAGCACTAAAAAG
*
110350 AAGAAATTGAAAGCACTCAAAAAG
1 AAGAAAATGAAAGCACT-AAAAAG
*
110374 AAGAAAAAGAAAG
1 AAGAAAATGAAAG
110387 AAAGAAAAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 15 0.47
24 17 0.53
ACGTcount: A:0.65, C:0.10, G:0.17, T:0.08
Consensus pattern (23 bp):
AAGAAAATGAAAGCACTAAAAAG
Found at i:111635 original size:24 final size:21
Alignment explanation
Indices: 111601--111643 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
111591 TCCACAAGAT
*
111601 ATGTCCTTTGACATTTCAAAGG
1 ATGTCCTTTGA-AATTCAAAGG
111623 ATGTACCTCTTGAAATTCAAA
1 ATGT-CCT-TTGAAATTCAAA
111644 ATAATGAGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 10 0.56
24 4 0.22
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.35
Consensus pattern (21 bp):
ATGTCCTTTGAAATTCAAAGG
Found at i:113502 original size:91 final size:91
Alignment explanation
Indices: 113347--113527 Score: 272
Period size: 91 Copynumber: 2.0 Consensus size: 91
113337 CCTAGAACAC
* *
113347 CCATGTGCCTTGCATATGACCAGCCTCCATGTGCCTTGCATGTGGATCATTTAGGTGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
113412 AAGAGTTCTCTCCCTATTCGGCCAAT
66 AAGAGTTCTCTCCCTATTCGACCAAT
** * * * *
113438 CCATGTGTTTTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTGATTTAGGCGCCAAGATG
1 CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
*
113503 AAGAGTTCTCTCCTTATTCGACCAA
66 AAGAGTTCTCTCCCTATTCGACCAA
113528 GCATCAACTA
Statistics
Matches: 80, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
91 80 1.00
ACGTcount: A:0.20, C:0.26, G:0.23, T:0.31
Consensus pattern (91 bp):
CCATGTGCCTTGCATATGACCAGCCCCCATGTGCCTTGCATGTGGATCATTTAGGCGCCAAGATG
AAGAGTTCTCTCCCTATTCGACCAAT
Found at i:115085 original size:2 final size:2
Alignment explanation
Indices: 115078--115107 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
115068 ATTTATTTTC
115078 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
115108 CCTATAGTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.