Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009309.1 Hibiscus syriacus cultivar Beakdansim tig00113046_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: 78360
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:318 original size:24 final size:24
Alignment explanation
Indices: 291--378 Score: 104
Period size: 24 Copynumber: 3.7 Consensus size: 24
281 ATATATCAAA
* *
291 ATCAAAACATAATTCAGGTCAAGT
1 ATCAAATCAAAATTCAGGTCAAGT
* * *
315 ATCAAATCAGACTCCAGGTCAAGT
1 ATCAAATCAAAATTCAGGTCAAGT
*
339 ATCAGATCAAAATTCAGGTCAAGT
1 ATCAAATCAAAATTCAGGTCAAGT
* *
363 ATCAGATCAGAATTCA
1 ATCAAATCAAAATTCA
379 TGTCGAAAAT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 55 1.00
ACGTcount: A:0.42, C:0.19, G:0.15, T:0.24
Consensus pattern (24 bp):
ATCAAATCAAAATTCAGGTCAAGT
Found at i:390 original size:24 final size:24
Alignment explanation
Indices: 301--398 Score: 92
Period size: 24 Copynumber: 4.1 Consensus size: 24
291 ATCAAAACAT
* * *
301 AATTCAGGTCAAGTATCAAATCAG
1 AATTCAGGTCAAGAATCAGATCAA
* * *
325 ACTCCAGGTCAAGTATCAGATCAA
1 AATTCAGGTCAAGAATCAGATCAA
* *
349 AATTCAGGTCAAGTATCAGATCAG
1 AATTCAGGTCAAGAATCAGATCAA
*
373 AATTCATGTCGAA-AATCAGAT-AA
1 AATTCAGGTC-AAGAATCAGATCAA
396 AAT
1 AAT
399 ATTCATGTGA
Statistics
Matches: 63, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.06
24 57 0.90
25 2 0.03
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.24
Consensus pattern (24 bp):
AATTCAGGTCAAGAATCAGATCAA
Found at i:391 original size:48 final size:47
Alignment explanation
Indices: 301--398 Score: 126
Period size: 48 Copynumber: 2.1 Consensus size: 47
291 ATCAAAACAT
* *
301 AATTCAGGTCAAGTATCAAATCAGACTCCAGGTCAAGTATCAGATCAA
1 AATTCAGGTCAAGTATCAAATCAGAATCCAGGTCAAGAATCAGAT-AA
* * *
349 AATTCAGGTCAAGTATCAGATCAGAATTCATGTCGAA-AATCAGATAA
1 AATTCAGGTCAAGTATCAAATCAGAATCCAGGTC-AAGAATCAGATAA
396 AAT
1 AAT
399 ATTCATGTGA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
47 5 0.11
48 37 0.84
49 2 0.05
ACGTcount: A:0.42, C:0.17, G:0.16, T:0.24
Consensus pattern (47 bp):
AATTCAGGTCAAGTATCAAATCAGAATCCAGGTCAAGAATCAGATAA
Found at i:2607 original size:22 final size:19
Alignment explanation
Indices: 2582--2630 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 19
2572 ATCAACGCCC
*
2582 GGTCAAAGTTCTGGTCAACGGT
1 GGTCAAAG-TC-GGTCAAC-GA
*
2604 GGTCAACGTCGGTCAACGA
1 GGTCAAAGTCGGTCAACGA
2623 GGTCAAAG
1 GGTCAAAG
2631 GTCAACAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 8 0.33
20 7 0.29
21 2 0.08
22 7 0.29
ACGTcount: A:0.27, C:0.20, G:0.33, T:0.20
Consensus pattern (19 bp):
GGTCAAAGTCGGTCAACGA
Found at i:4759 original size:24 final size:24
Alignment explanation
Indices: 4732--4798 Score: 86
Period size: 21 Copynumber: 2.9 Consensus size: 24
4722 AACATAATTA
4732 AGGTCAAGTATCAAATCAGAATCC
1 AGGTCAAGTATCAAATCAGAATCC
* *
4756 AGGTC-A--ATCAGATCAAAATCC
1 AGGTCAAGTATCAAATCAGAATCC
*
4777 AGGTCAAGTATCATATCAGAAT
1 AGGTCAAGTATCAAATCAGAAT
4799 TCATATCGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 18 0.50
22 1 0.03
23 1 0.03
24 16 0.44
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.22
Consensus pattern (24 bp):
AGGTCAAGTATCAAATCAGAATCC
Found at i:19363 original size:20 final size:22
Alignment explanation
Indices: 19338--19396 Score: 95
Period size: 22 Copynumber: 2.8 Consensus size: 22
19328 TTTGGTGCAT
*
19338 AGGGAATCGATTCCCCC-TTG-
1 AGGGAACCGATTCCCCCTTTGA
19358 AGGGAACCGATTCCCCCTTTGA
1 AGGGAACCGATTCCCCCTTTGA
19380 AGGGAACCGATTCCCCC
1 AGGGAACCGATTCCCCC
19397 ACAGGGGAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
20 16 0.44
21 3 0.08
22 17 0.47
ACGTcount: A:0.22, C:0.34, G:0.24, T:0.20
Consensus pattern (22 bp):
AGGGAACCGATTCCCCCTTTGA
Found at i:28476 original size:208 final size:201
Alignment explanation
Indices: 28074--28486 Score: 763
Period size: 208 Copynumber: 2.0 Consensus size: 201
28064 AGAGAAGTAG
28074 AGGAAAAGACAATCCTTGAATCTCTAAGACTCGATGAATACAACGCTTTGTACCATGACCCTACA
1 AGGAAAAGACAATCCTTGAATCTCTAAGACTCGATGAATACAACGCTTTGTACCATGACCCTACA
28139 ATCGAGATGTACAGACAAGACATTTTTGGCTCAGGCAAATTATTTCAGAAGACGATTCTGAAAAT
66 ATCGAGATGTACAGACAAGACATTTTTGGCTCAGGCAAATTATTTCAGAAGACGATTCTGAAAAT
28204 TATGGACAATGGAAAACTGAACAATGAACGCCCTGAAAATGACACAAATGCAGGATACGAAGGGA
131 TATGGACAATGGAAAACTGAACAATGAACGCCCTGAAAATGACACAAATGCAGGATACGAAGGGA
28269 ATACAA
196 ATACAA
28275 AGGAAAAGACAATCCTTGAATCTCTAAGACTCGATGAATACAACGCTTTGTACCATGACCCCTAC
1 AGGAAAAGACAATCCTTGAATCTCTAAGACTCGATGAATACAACGCTTTGTACCATGA-CCCTAC
28340 AATCGAGATGTACAGACAAGACATTTTTGGCTCAGGCAAATTATTTTCAGAAGACGATTCTGAAA
65 AATCGAGATGTACAGACAAGACATTTTTGGCTCAGGCAAATTA-TTTCAGAAGACGATTCTGAAA
28405 ATTATGGCCCTGACAATGGAAAACTGAACAATGAACGCCCTGAAAATGACACAAATGCAGGATAC
129 ATTAT-G----GACAATGGAAAACTGAACAATGAACGCCCTGAAAATGACACAAATGCAGGATAC
28470 GAAGGGAATACAA
189 GAAGGGAATACAA
28483 AGGA
1 AGGA
28487 TCAACCAAGG
Statistics
Matches: 205, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
201 58 0.28
202 49 0.24
203 26 0.13
204 1 0.00
208 71 0.35
ACGTcount: A:0.40, C:0.19, G:0.20, T:0.21
Consensus pattern (201 bp):
AGGAAAAGACAATCCTTGAATCTCTAAGACTCGATGAATACAACGCTTTGTACCATGACCCTACA
ATCGAGATGTACAGACAAGACATTTTTGGCTCAGGCAAATTATTTCAGAAGACGATTCTGAAAAT
TATGGACAATGGAAAACTGAACAATGAACGCCCTGAAAATGACACAAATGCAGGATACGAAGGGA
ATACAA
Found at i:33406 original size:4 final size:4
Alignment explanation
Indices: 33351--33393 Score: 77
Period size: 4 Copynumber: 10.8 Consensus size: 4
33341 CCCCTATGAA
*
33351 AAAT AAAT AAAT AAAT TAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
33394 AGTTGATAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
4 37 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:38239 original size:22 final size:22
Alignment explanation
Indices: 38210--38259 Score: 73
Period size: 22 Copynumber: 2.3 Consensus size: 22
38200 TTTAACTTTT
38210 AGTCAAAGTCAACGATGGCCAA
1 AGTCAAAGTCAACGATGGCCAA
* * *
38232 GGTCAAAGTCAACTATGGTCAA
1 AGTCAAAGTCAACGATGGCCAA
38254 AGTCAA
1 AGTCAA
38260 CGACCAAGTC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.40, C:0.20, G:0.22, T:0.18
Consensus pattern (22 bp):
AGTCAAAGTCAACGATGGCCAA
Found at i:40582 original size:38 final size:35
Alignment explanation
Indices: 40531--40725 Score: 135
Period size: 36 Copynumber: 5.4 Consensus size: 35
40521 TATATCTATA
* * *
40531 TATATATTATATAGTTTGCAAATGATTTTTGAGACATG
1 TATATAATATATAGTTTGAAAATCA-TTTTGA-A-ATG
*
40569 TATATAATATATAGTTTTTAAAATCATTTTGAAATG
1 TATATAATATATAG-TTTGAAAATCATTTTGAAATG
* * * **
40605 TATATAACATATAGTTTTTAAAA-CGCTTTTGAAAAC
1 TATATAATATATAG-TTTGAAAATC-ATTTTGAAATG
* * * **
40641 TAGATAATATATAGTTTTTAAAA-CATTTTAAAAAA
1 TATATAATATATAG-TTTGAAAATCATTTTGAAATG
* *
40676 TATATAATATATGGTTTTTAAAATCATTTTGAAAACT-
1 TATATAATATATAG-TTTGAAAATCATTTTG-AAA-TG
40713 TATATAATATATA
1 TATATAATATATA
40726 ATTTTTTGAA
Statistics
Matches: 134, Mismatches: 18, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
35 30 0.22
36 61 0.46
37 16 0.12
38 19 0.14
39 8 0.06
ACGTcount: A:0.43, C:0.05, G:0.09, T:0.44
Consensus pattern (35 bp):
TATATAATATATAGTTTGAAAATCATTTTGAAATG
Found at i:40606 original size:36 final size:34
Alignment explanation
Indices: 40569--40797 Score: 208
Period size: 36 Copynumber: 6.2 Consensus size: 34
40559 TTGAGACATG
40569 TATATAATATATAGTTTTTAAAATCATTTTGAAAT
1 TATATAATATATAGTTTTTAAAA-CATTTTGAAAT
* * *
40604 GTATATAACATATAGTTTTTAAAACGCTTTTGAAAAC
1 -TATATAATATATAGTTTTTAAAAC-ATTTTG-AAAT
* * *
40641 TAGATAATATATAGTTTTTAAAACATTTTAAAAAA
1 TATATAATATATAGTTTTTAAAACATTTT-GAAAT
*
40676 TATATAATATATGGTTTTTAAAATCATTTTGAAAACT
1 TATATAATATATAGTTTTTAAAA-CATTTTG-AAA-T
*
40713 TATATAATATATAATTTTTTGAAAACATTTTTGAAAACTT
1 TATATAATATAT-AGTTTTT-AAAACA-TTTTG-AAA--T
*
40753 ATATATAATATATA-TTTTTGAAAACTTTTTTGGAAAT
1 -TATATAATATATAGTTTTT-AAAAC-ATTTT-GAAAT
40790 TATATAAT
1 TATATAAT
40798 TTTTAAAACT
Statistics
Matches: 164, Mismatches: 16, Indels: 26
0.80 0.08 0.13
Matches are distributed among these distances:
35 29 0.18
36 66 0.40
37 16 0.10
38 7 0.04
39 31 0.19
40 3 0.02
41 12 0.07
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (34 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAT
Found at i:40663 original size:72 final size:72
Alignment explanation
Indices: 40572--40776 Score: 227
Period size: 71 Copynumber: 2.8 Consensus size: 72
40562 AGACATGTAT
** *
40572 ATAATATATAGTTTTTAAAATCATTTTGAAATGTATATAACATATAGTTTTTAAAA-CGCTTTTG
1 ATAATATATAGTTTTTAAAA-CATTTTGAAAAATATATAACATATAGTTTTTAAAATC-ATTTTG
40636 AAAAC-TAG
64 AAAACTTAG
* * *
40644 ATAATATATAGTTTTTAAAACATTTTAAAAAATATATAATATATGGTTTTTAAAATCATTTTGAA
1 ATAATATATAGTTTTTAAAACATTTTGAAAAATATATAACATATAGTTTTTAAAATCATTTTGAA
*
40709 AACTTAT
66 AACTTAG
* *
40716 ATAATATATAATTTTTTGAAAACATTTTTGAAAACTTATATATAATATATA-TTTTTGAAAA
1 ATAATATAT-AGTTTTT-AAAACA-TTTTGAAAA---ATATATAACATATAGTTTTT-AAAA
40777 CTTTTTTGGA
Statistics
Matches: 114, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
71 40 0.35
72 32 0.28
73 6 0.05
74 6 0.05
75 8 0.07
77 5 0.04
78 17 0.15
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (72 bp):
ATAATATATAGTTTTTAAAACATTTTGAAAAATATATAACATATAGTTTTTAAAATCATTTTGAA
AACTTAG
Found at i:40805 original size:29 final size:30
Alignment explanation
Indices: 40760--40884 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 30
40750 CTTATATATA
* *
40760 ATATATATTTTTGAAAACTTTTTTGGAAATT
1 ATATAGATTTTT-AAAACTTTTTTGAAAATT
40791 ATATA-ATTTTTAAAACTTTTTTGAAAATT
1 ATATAGATTTTTAAAACTTTTTTGAAAATT
40820 ATAT--A-TTTTAAAACTTTTTTGAAAATT
1 ATATAGATTTTTAAAACTTTTTTGAAAATT
* *
40847 ATATAGTTTTTTAAAAAACATTTTTGAAAATTT
1 ATATAGATTTTT--AAAACTTTTTTGAAAA-TT
40880 ATATA
1 ATATA
40885 TAATATATAG
Statistics
Matches: 85, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
27 26 0.31
28 1 0.01
29 21 0.25
30 10 0.12
31 5 0.06
32 15 0.18
33 7 0.08
ACGTcount: A:0.41, C:0.03, G:0.06, T:0.50
Consensus pattern (30 bp):
ATATAGATTTTTAAAACTTTTTTGAAAATT
Found at i:40808 original size:56 final size:57
Alignment explanation
Indices: 40739--40862 Score: 155
Period size: 56 Copynumber: 2.2 Consensus size: 57
40729 TTTTGAAAAC
* *
40739 ATTTTTGAAAACTTATAT-ATAA-TATATATTTTTGAAAACTTTTTTGGAAATTATATA-
1 ATTTTT-AAAACTTATATGAAAATTATATA-TTTT-AAAACTTTTTTGAAAATTATATAG
* *
40796 ATTTTTAAAACTTTTTTGAAAATTATATATTTTAAAACTTTTTTGAAAATTATATAG
1 ATTTTTAAAACTTATATGAAAATTATATATTTTAAAACTTTTTTGAAAATTATATAG
*
40853 TTTTTTAAAA
1 ATTTTTAAAA
40863 AACATTTTTG
Statistics
Matches: 59, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
56 31 0.53
57 22 0.37
58 6 0.10
ACGTcount: A:0.40, C:0.03, G:0.06, T:0.51
Consensus pattern (57 bp):
ATTTTTAAAACTTATATGAAAATTATATATTTTAAAACTTTTTTGAAAATTATATAG
Found at i:40933 original size:41 final size:42
Alignment explanation
Indices: 40844--40945 Score: 122
Period size: 42 Copynumber: 2.5 Consensus size: 42
40834 TTTTTTGAAA
* *
40844 ATTATATAGTTTTTTAAAAAACATTTTTGAAAATTTATATAT
1 ATTATATAGTTTTTAAAAAAACATTTTTAAAAATTTATATAT
* *
40886 AATATATAGTTTTTAAAAGAAATATTTTTTAAAAATTT-T-T-T
1 ATTATATAGTTTTTAAAA-AAACA-TTTTTAAAAATTTATATAT
40927 ATTATATAG-TTTTAAAAAA
1 ATTATATAGTTTTTAAAAAA
40946 TATATACTTT
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
39 2 0.04
40 8 0.15
41 9 0.17
42 17 0.32
43 5 0.09
44 12 0.23
ACGTcount: A:0.45, C:0.01, G:0.05, T:0.49
Consensus pattern (42 bp):
ATTATATAGTTTTTAAAAAAACATTTTTAAAAATTTATATAT
Found at i:40934 original size:43 final size:42
Alignment explanation
Indices: 40644--40945 Score: 119
Period size: 39 Copynumber: 7.5 Consensus size: 42
40634 TGAAAACTAG
40644 ATAATATATAGTTTTT---AAAACA-TTTTAAAAA---ATAT
1 ATAATATATAGTTTTTAAAAAAACATTTTTAAAAATTTATAT
* * * *
40679 ATAATATATGGTTTTT--AAAATCA-TTTTGAAAA-CT-TAT
1 ATAATATATAGTTTTTAAAAAAACATTTTTAAAAATTTATAT
* ** * *
40716 ATAATATATAATTTTT-TGAAAACATTTTTGAAAACTTATAT
1 ATAATATATAGTTTTTAAAAAAACATTTTTAAAAATTTATAT
* * **
40757 ATAATATATA-TTTTT--GAAAACTTTTTTGGAAA-TTATAT
1 ATAATATATAGTTTTTAAAAAAACATTTTTAAAAATTTATAT
* * * * ** * * *
40795 A-ATTTTTAAAACTTTTTTGAAAATTATATATTTTAAAACTTT-TTT
1 ATA-ATAT-ATA-GTTTTT-AAAAAAACAT-TTTTAAAAATTTATAT
* * *
40840 GAAAATTATATAGTTTTTTAAAAAACATTTTTGAAAATTTATAT
1 -ATAA-TATATAGTTTTTAAAAAAACATTTTTAAAAATTTATAT
*
40884 ATAATATATAGTTTTTAAAAGAAATATTTTTTAAAAATTT-T-T
1 ATAATATATAGTTTTTAAAA-AAACA-TTTTTAAAAATTTATAT
*
40926 -TATTATATAG-TTTTAAAAAA
1 ATAATATATAGTTTTTAAAAAA
40946 TATATACTTT
Statistics
Matches: 207, Mismatches: 38, Indels: 40
0.73 0.13 0.14
Matches are distributed among these distances:
35 15 0.07
36 13 0.06
37 18 0.09
38 14 0.07
39 28 0.14
40 14 0.07
41 27 0.13
42 16 0.08
43 18 0.09
44 23 0.11
45 13 0.06
46 5 0.02
47 3 0.01
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (42 bp):
ATAATATATAGTTTTTAAAAAAACATTTTTAAAAATTTATAT
Found at i:40977 original size:3 final size:3
Alignment explanation
Indices: 40962--41010 Score: 71
Period size: 3 Copynumber: 15.7 Consensus size: 3
40952 CTTTTCATAT
*
40962 TTA TTA TTG TTA TTA TTTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA
41009 TT
1 TT
41011 TATTTCTTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
3 36 0.86
4 6 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:40980 original size:16 final size:16
Alignment explanation
Indices: 40959--41014 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
40949 ATACTTTTCA
*
40959 TATTTATTATTGTTAT
1 TATTTATTATTATTAT
40975 TATTTATTATTATTAT
1 TATTTATTATTATTAT
40991 TA-TTATTATTATTTAT
1 TATTTATTATTA-TTAT
41007 TATTTATT
1 TATTTATT
41015 TCTTTTTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
15 9 0.24
16 23 0.62
17 5 0.14
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.70
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:41025 original size:25 final size:25
Alignment explanation
Indices: 40962--41010 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
40952 CTTTTCATAT
*
40962 TTATTATTGTTATTATTTATTATTA
1 TTATTATTATTATTATTTATTATTA
40987 TTATTATTATTATTATTTATTATT
1 TTATTATTATTATTATTTATTATT
41011 TATTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (25 bp):
TTATTATTATTATTATTTATTATTA
Found at i:42275 original size:15 final size:15
Alignment explanation
Indices: 42264--42292 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
42254 TTGATTTCTT
42264 TTTTATTTATTTTAA
1 TTTTATTTATTTTAA
42279 TTTTATTTATTTTA
1 TTTTATTTATTTTA
42293 TTCTTTTCCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (15 bp):
TTTTATTTATTTTAA
Found at i:42356 original size:12 final size:12
Alignment explanation
Indices: 42332--42380 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
42322 ATTTTTTTGC
*
42332 TTTATTTAATTT
1 TTTATTTATTTT
*
42344 TTTACTTATTTT
1 TTTATTTATTTT
42356 TTTATTTATTTGT
1 TTTATTTATTT-T
42369 TTTATTTATTTT
1 TTTATTTATTTT
42381 CATTGTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
12 21 0.64
13 12 0.36
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.78
Consensus pattern (12 bp):
TTTATTTATTTT
Found at i:43819 original size:27 final size:27
Alignment explanation
Indices: 43784--43844 Score: 113
Period size: 27 Copynumber: 2.3 Consensus size: 27
43774 ATAATGATGT
*
43784 TTTTATGGATTTTCATCCTTATGAATA
1 TTTTGTGGATTTTCATCCTTATGAATA
43811 TTTTGTGGATTTTCATCCTTATGAATA
1 TTTTGTGGATTTTCATCCTTATGAATA
43838 TTTTGTG
1 TTTTGTG
43845 AAGGATGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 33 1.00
ACGTcount: A:0.21, C:0.10, G:0.15, T:0.54
Consensus pattern (27 bp):
TTTTGTGGATTTTCATCCTTATGAATA
Found at i:48187 original size:18 final size:18
Alignment explanation
Indices: 48164--48198 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
48154 AACTTAAGTA
48164 TGGTTTAGGTA-CTAAACC
1 TGGTTTA-GTACCTAAACC
48182 TGGTTTAGTACCTAAAC
1 TGGTTTAGTACCTAAAC
48199 TTTCAATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 3 0.19
18 13 0.81
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (18 bp):
TGGTTTAGTACCTAAACC
Found at i:50509 original size:17 final size:17
Alignment explanation
Indices: 50487--50520 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
50477 GACAGTCGCA
50487 TTCTATAAATTTCAAAT
1 TTCTATAAATTTCAAAT
* *
50504 TTCTATATATTTTAAAT
1 TTCTATAAATTTCAAAT
50521 ATTTCCTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTCTATAAATTTCAAAT
Found at i:54958 original size:15 final size:15
Alignment explanation
Indices: 54938--54971 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
54928 AATTGACCCG
54938 TATTTTA-ATTATGTT
1 TATTTTACATTAT-TT
54953 TATTTTACATTATTT
1 TATTTTACATTATTT
54968 TATT
1 TATT
54972 AGTCTAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 13 0.72
16 5 0.28
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (15 bp):
TATTTTACATTATTT
Found at i:55282 original size:177 final size:173
Alignment explanation
Indices: 55044--55363 Score: 471
Period size: 177 Copynumber: 1.8 Consensus size: 173
55034 CCTACACCTA
* * * *
55044 CATATGTGGTGTTCGAACTCGAAAATTCTAGGAATAACAACAATTCTTTAATTACTAAGGTCGCT
1 CATATGTGGTGTTAGAACTCGAAAATTCAAGGAATAACAACAATTATTTAATCACTAAGGTCGCT
*
55109 TAGTTCGTTCTTTTATTTTTTTTTATATTATTTAAATAGTTTGGAGTGAATATAAT-GTAATATA
66 TAGTTCGTTATTTTA----TTTTTATATTATTTAAATAGTTTGGAGTGAATAT-ATGGTAATATA
55173 TGTTCAAAGATTCTCAATTATATGACACTGAACGCTCATAAACTCCTG
126 TGTTCAAAGATTCTCAATTATATGACACTGAACGCTCATAAACTCCTG
* * * * *
55221 CATATGTGGTGTTAGAACTCGGAACTTCAATGAATAACAATAATTATTTAATCATTAAGGTCGCT
1 CATATGTGGTGTTAGAACTCGAAAATTCAAGGAATAACAACAATTATTTAATCACTAAGGTCGCT
* * *
55286 TAGTTCGTTATTTTATTTTTATATTATTTTATTAGTTTGGGGTGAATATATGGTAATATATGTTC
66 TAGTTCGTTATTTTATTTTTATATTATTTAAATAGTTTGGAGTGAATATATGGTAATATATGTTC
55351 AAAGATTCTCAAT
131 AAAGATTCTCAAT
55364 CATTTAACAT
Statistics
Matches: 129, Mismatches: 13, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
172 2 0.02
173 57 0.44
177 70 0.54
ACGTcount: A:0.32, C:0.12, G:0.15, T:0.42
Consensus pattern (173 bp):
CATATGTGGTGTTAGAACTCGAAAATTCAAGGAATAACAACAATTATTTAATCACTAAGGTCGCT
TAGTTCGTTATTTTATTTTTATATTATTTAAATAGTTTGGAGTGAATATATGGTAATATATGTTC
AAAGATTCTCAATTATATGACACTGAACGCTCATAAACTCCTG
Found at i:55432 original size:173 final size:172
Alignment explanation
Indices: 54946--55475 Score: 497
Period size: 173 Copynumber: 3.1 Consensus size: 172
54936 CGTATTTTAA
* * * * **
54946 TTATGTTTA-TTTTACATTATTTTATTAGTCT-AGATGAATATAAAATAATATATGTTCAAAGAT
1 TTAT-TTTATTTTTATATTATTTTATTAGTTTGGGGTGAATAT-ATGTAATATATGTTCAAAGAT
* * * * * ** *
55009 TTTTAATCATTTAATATTGAACGTTCCTACA--CCTACATATGTGGTGTTCGAACT-CGAAAATT
64 TCTCAATCATTTAACATTGAACGCTCATACACTCCTACATATGTGGTGTTTAAACTCCG-AACTT
* * *
55071 CT-AGGAATAACAACAATTCTTTAATTACTAAGGTCGCTTAGTTCG
128 -TAAAGAATAACAACAATTATTTAATCACTAAGGTCGCTTAGTTCG
* * * *
55116 TTCTTTTATTTTTTTTTATATTATTTAAATAGTTTGGAGTGAATATAATGTAATATATGTTCAAA
1 TTATTTTA----TTTTTATATTATTTTATTAGTTTGGGGTGAATAT-ATGTAATATATGTTCAAA
* * * * * * *
55181 GATTCTCAATTATATGACACTGAACGCTCATAAACTCCTGCATATGTGGTG-TTAGAACTCGGAA
61 GATTCTCAATCATTTAACATTGAACGCTCATACACTCCTACATATGTGGTGTTTA-AACTCCGAA
* * * *
55245 CTTCAATGAATAACAATAATTATTTAATCATTAAGGTCGCTTAGTTCG
125 CTTTAAAGAATAACAACAATTATTTAATCACTAAGGTCGCTTAGTTCG
55293 TTATTTTATTTTTATATTATTTTATTAGTTTGGGGTGAATATATGGTAATATATGTTCAAAGATT
1 TTATTTTATTTTTATATTATTTTATTAGTTTGGGGTGAATATAT-GTAATATATGTTCAAAGATT
* * * *
55358 CTCAATCATTTAACATTGAATGCTCGTACACTCCTACATACGTGATGTTTAAACTCCGAACTTTA
65 CTCAATCATTTAACATTGAACGCTCATACACTCCTACATATGTGGTGTTTAAACTCCGAACTTTA
* * * * *
55423 AAAAATAACAAC---TCTTTAATTACTAAGGTCACTTAATAT-G
130 AAGAATAACAACAATTATTTAATCACTAAGGTCGCTTAGT-TCG
*
55463 TTCTTTTATTTTT
1 TTATTTTATTTTT
55476 TACATTTGAA
Statistics
Matches: 290, Mismatches: 56, Indels: 28
0.78 0.15 0.07
Matches are distributed among these distances:
169 4 0.01
170 36 0.12
171 1 0.00
172 2 0.01
173 109 0.38
174 21 0.07
175 48 0.17
176 1 0.00
177 67 0.23
178 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.12, T:0.42
Consensus pattern (172 bp):
TTATTTTATTTTTATATTATTTTATTAGTTTGGGGTGAATATATGTAATATATGTTCAAAGATTC
TCAATCATTTAACATTGAACGCTCATACACTCCTACATATGTGGTGTTTAAACTCCGAACTTTAA
AGAATAACAACAATTATTTAATCACTAAGGTCGCTTAGTTCG
Found at i:59462 original size:26 final size:26
Alignment explanation
Indices: 59432--59494 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
59422 GGTGAAATTC
*
59432 TTGGTCATTTGCATACTAGAGGTATT
1 TTGGTCATTTCCATACTAGAGGTATT
*
59458 TTGGTCATTTCCATACTAGGGGTATT
1 TTGGTCATTTCCATACTAGAGGTATT
59484 TTGGTCATTTC
1 TTGGTCATTTC
59495 ACAGATCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (26 bp):
TTGGTCATTTCCATACTAGAGGTATT
Found at i:64736 original size:26 final size:26
Alignment explanation
Indices: 64706--64768 Score: 108
Period size: 26 Copynumber: 2.4 Consensus size: 26
64696 GGTGAAATTC
*
64706 TTGGTCATTTGCATACTAGAGGTATT
1 TTGGTCATTTCCATACTAGAGGTATT
*
64732 TTGGTCATTTCCATACTAGGGGTATT
1 TTGGTCATTTCCATACTAGAGGTATT
64758 TTGGTCATTTC
1 TTGGTCATTTC
64769 ACAGATCCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 35 1.00
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.44
Consensus pattern (26 bp):
TTGGTCATTTCCATACTAGAGGTATT
Found at i:70001 original size:26 final size:25
Alignment explanation
Indices: 69971--70036 Score: 105
Period size: 26 Copynumber: 2.6 Consensus size: 25
69961 GGTGAAATTC
69971 TTGGTCATTTGCATACTAGAGGTATT
1 TTGGTCATTT-CATACTAGAGGTATT
*
69997 TTGGTCATTTCCATACTAGGGGTATT
1 TTGGTCATTT-CATACTAGAGGTATT
70023 TTGGTCATTTCATA
1 TTGGTCATTTCATA
70037 GATCCATTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
25 4 0.11
26 34 0.89
ACGTcount: A:0.21, C:0.14, G:0.21, T:0.44
Consensus pattern (25 bp):
TTGGTCATTTCATACTAGAGGTATT
Found at i:73502 original size:20 final size:20
Alignment explanation
Indices: 73452--73502 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 20
73442 CCAAAGTTCC
*
73452 GAAACTTTAAGGTAAGTTTT
1 GAAACTTTGAGGTAAGTTTT
73472 GAAACTTTTGAGG-AAGTTTT
1 GAAAC-TTTGAGGTAAGTTTT
73492 GAAACTATTGA
1 GAAACT-TTGA
73503 AAAGCATCGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 1 0.04
20 21 0.75
21 6 0.21
ACGTcount: A:0.35, C:0.06, G:0.22, T:0.37
Consensus pattern (20 bp):
GAAACTTTGAGGTAAGTTTT
Found at i:74764 original size:21 final size:22
Alignment explanation
Indices: 74722--74764 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
74712 GATAATTTTC
* *
74722 TATATAAAATAGTATGCATAAT
1 TATAGAAAATAGTATACATAAT
74744 TATAGAAAATA-TATACATAAT
1 TATAGAAAATAGTATACATAAT
74765 GTGAGAAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.53, C:0.05, G:0.07, T:0.35
Consensus pattern (22 bp):
TATAGAAAATAGTATACATAAT
Done.