Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006098.1 Hibiscus syriacus cultivar Beakdansim tig00014452_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: 65502
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Found at i:4524 original size:48 final size:49
Alignment explanation
Indices: 4372--4548 Score: 293
Period size: 49 Copynumber: 3.6 Consensus size: 49
4362 AACTGCTCTA
* * *
4372 TAATGAAAGTTAAATGCATAACTGTGGATTTCGGCATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCAC
* *
4421 TAATGAAAGTTAAATGCATAATGGTGCATTTTGACATAAAAGGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCAC
*
4470 TAATGAAAGTTAAATGCATAACGGTGCA-TTCGACATAAAATGTGCCAC
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCAC
4518 TAATGAAAGTTAAATGCATAACGGTGCATTT
1 TAATGAAAGTTAAATGCATAACGGTGCATTT
4549 TCAGCATAAA
Statistics
Matches: 119, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
48 46 0.39
49 73 0.61
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.28
Consensus pattern (49 bp):
TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCAC
Found at i:4544 original size:97 final size:99
Alignment explanation
Indices: 4372--4568 Score: 308
Period size: 97 Copynumber: 2.0 Consensus size: 99
4362 AACTGCTCTA
* * *
4372 TAATGAAAGTTAAATGCATAACTGTGGATTTCGGCATAAAAGGTGCCACTAATGAAAGTTAAATG
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGTTAAATG
* * *
4437 CATAATGGTGCATTTTGA-CATAAAAGGTGCCAC
66 CATAACGGTGCATTTTCAGCATAAAAAGTGCCAC
*
4470 TAATGAAAGTTAAATGCATAACGGTGCA-TTCGACATAAAATGTGCCACTAATGAAAGTTAAATG
1 TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGTTAAATG
*
4534 CATAACGGTGCATTTTCAGCATAAAAAGTGTCAC
66 CATAACGGTGCATTTTCAGCATAAAAAGTGCCAC
4568 T
1 T
4569 CATGGTATTC
Statistics
Matches: 90, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
97 50 0.56
98 40 0.44
ACGTcount: A:0.39, C:0.14, G:0.20, T:0.27
Consensus pattern (99 bp):
TAATGAAAGTTAAATGCATAACGGTGCATTTCGACATAAAAGGTGCCACTAATGAAAGTTAAATG
CATAACGGTGCATTTTCAGCATAAAAAGTGCCAC
Found at i:9758 original size:21 final size:20
Alignment explanation
Indices: 9713--9789 Score: 79
Period size: 20 Copynumber: 3.9 Consensus size: 20
9703 ACTGGAATCG
*
9713 AAGGGATTGATCCTTTT-CTA
1 AAGGGATCGAT-CTTTTGCTA
*
9733 AAGGGATCGATCTTTTGGTCA
1 AAGGGATCGATCTTTTGCT-A
9754 AAGGGA-CGATTCTTTTGCTA
1 AAGGGATCGA-TCTTTTGCTA
*
9774 AAGGAAT-GATCTTTTG
1 AAGGGATCGATCTTTTG
9790 AGCCAAAAAT
Statistics
Matches: 49, Mismatches: 4, Indels: 9
0.79 0.06 0.15
Matches are distributed among these distances:
19 12 0.24
20 22 0.45
21 15 0.31
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.36
Consensus pattern (20 bp):
AAGGGATCGATCTTTTGCTA
Found at i:9763 original size:20 final size:19
Alignment explanation
Indices: 9725--9789 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 19
9715 GGGATTGATC
9725 CTTTT-CTAAAGGGATCGAT
1 CTTTTGCTAAAGGGA-CGAT
*
9744 CTTTTGGTCAAAGGGACGATT
1 CTTTTGCT-AAAGGGACGA-T
* *
9765 CTTTTGCTAAAGGAATGAT
1 CTTTTGCTAAAGGGACGAT
9784 CTTTTG
1 CTTTTG
9790 AGCCAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
19 12 0.31
20 12 0.31
21 15 0.38
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (19 bp):
CTTTTGCTAAAGGGACGAT
Found at i:9888 original size:84 final size:84
Alignment explanation
Indices: 9748--9913 Score: 262
Period size: 84 Copynumber: 2.0 Consensus size: 84
9738 ATCGATCTTT
* * *
9748 TGGTCAAAGGGACGATTCTTTTGCTAAAGGAATGATCTTTTGAGCCAAAAATTCTTACAAACTCG
1 TGGTCAAAGGGACGATTCTTTTACTAAAGAAATGATCCTTTGAGCCAAAAATTCTTACAAACTCG
9813 ACTTTAAATCCC-AAAATG
66 ACTTTAAATCCCGAAAATG
* * *
9831 TGGTCAAAGGGATCGATTCTTTTACTAAAGAAATGGTCCTTTGAGCTATAAATTCTTACAAACTC
1 TGGTCAAAGGGA-CGATTCTTTTACTAAAGAAATGATCCTTTGAGCCAAAAATTCTTACAAACTC
9896 GACTTTAAATCCCGAAAA
65 GACTTTAAATCCCGAAAA
9914 ATGATTGAGT
Statistics
Matches: 75, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
83 12 0.16
84 59 0.79
85 4 0.05
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Consensus pattern (84 bp):
TGGTCAAAGGGACGATTCTTTTACTAAAGAAATGATCCTTTGAGCCAAAAATTCTTACAAACTCG
ACTTTAAATCCCGAAAATG
Found at i:13211 original size:20 final size:20
Alignment explanation
Indices: 13165--13212 Score: 82
Period size: 19 Copynumber: 2.5 Consensus size: 20
13155 TCTAAATCAT
13165 TTTTC-AAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
13184 -TTTCAAAATTTCATTTTGA
1 TTTTCAAAATTTCATTTTGA
13203 TTTTCAAAAT
1 TTTTCAAAAT
13213 CAAAAGTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 4 0.15
19 14 0.52
20 9 0.33
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTTCAAAATTTCATTTTGA
Found at i:14276 original size:16 final size:16
Alignment explanation
Indices: 14255--14303 Score: 89
Period size: 16 Copynumber: 3.0 Consensus size: 16
14245 ATTGCCCTTT
14255 TATTTAATCTCTTTAC
1 TATTTAATCTCTTTAC
14271 TATTTAATCTCTTTAC
1 TATTTAATCTCTTTAC
14287 TATTTAATCTCATTTAC
1 TATTTAATCTC-TTTAC
14304 CAAAACCCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
16 27 0.84
17 5 0.16
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (16 bp):
TATTTAATCTCTTTAC
Found at i:24236 original size:44 final size:44
Alignment explanation
Indices: 24173--24261 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
24163 TTGAGAGCCG
24173 AAGGTTAAAGTTATCTTTTGCAGTTGATTGTGGAAGTTGGTAGA
1 AAGGTTAAAGTTATCTTTTGCAGTTGATTGTGGAAGTTGGTAGA
24217 AAGGTTAAAGTTATCTTTTGCAGTTGATTGTGGAAGTTGGTAGA
1 AAGGTTAAAGTTATCTTTTGCAGTTGATTGTGGAAGTTGGTAGA
24261 A
1 A
24262 CTCTCTTAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.28, C:0.04, G:0.29, T:0.38
Consensus pattern (44 bp):
AAGGTTAAAGTTATCTTTTGCAGTTGATTGTGGAAGTTGGTAGA
Found at i:29587 original size:3 final size:3
Alignment explanation
Indices: 29579--29649 Score: 106
Period size: 3 Copynumber: 23.3 Consensus size: 3
29569 TTTAAAATTT
* *
29579 TTA TTA TTA TTA TAA TTTA TTA TTA TTA TTA TTA TTA TAA TTA TTA
1 TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
29625 TTA TTA TAA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
29650 GAAATAAAAA
Statistics
Matches: 61, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 59 0.97
4 2 0.03
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:31256 original size:22 final size:23
Alignment explanation
Indices: 31210--31261 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
31200 TCTATTCTGG
*
31210 TATTTTAAATAAATAAATATTTT
1 TATTTTAAATAAATAAATATATT
* *
31233 TATTTTAAA-AATTATATATATT
1 TATTTTAAATAAATAAATATATT
*
31255 TAATTTA
1 TATTTTA
31262 GTTTTTATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
22 16 0.64
23 9 0.36
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
TATTTTAAATAAATAAATATATT
Found at i:31411 original size:2 final size:2
Alignment explanation
Indices: 31404--31490 Score: 174
Period size: 2 Copynumber: 43.5 Consensus size: 2
31394 TACAAAACCC
31404 TA TA TA TA TA TA 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
31446 TA TA TA TA TA TA 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
31488 TA T
1 TA T
31491 TTAATTTTTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 85 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:33482 original size:13 final size:14
Alignment explanation
Indices: 33456--33485 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
33446 GCATTTGTAT
33456 TTTTCATCTTTGCA
1 TTTTCATCTTTGCA
33470 TTTTCAT-TTTGCA
1 TTTTCATCTTTGCA
33483 TTT
1 TTT
33486 GTTGTTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.13, C:0.17, G:0.07, T:0.63
Consensus pattern (14 bp):
TTTTCATCTTTGCA
Found at i:33917 original size:42 final size:42
Alignment explanation
Indices: 33857--33939 Score: 112
Period size: 42 Copynumber: 2.0 Consensus size: 42
33847 GATATGATTT
* * * *
33857 ATCAAGTAAAAAAGTTCCAGGGTGATTCAAATGAACAAATGG
1 ATCAAGCAAAAAAGTTCCAAGATGATTCAAAAGAACAAATGG
* *
33899 ATCAAGCAAAAAATTTCCAAGATGATTCAAAAGAGCAAATG
1 ATCAAGCAAAAAAGTTCCAAGATGATTCAAAAGAACAAATG
33940 ACAAAACTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.48, C:0.13, G:0.18, T:0.20
Consensus pattern (42 bp):
ATCAAGCAAAAAAGTTCCAAGATGATTCAAAAGAACAAATGG
Found at i:36333 original size:21 final size:21
Alignment explanation
Indices: 36307--36352 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
36297 GAGTTGCGAA
36307 ACACCTGTTATAGTCAACTTC
1 ACACCTGTTATAGTCAACTTC
36328 ACACCTGTTATAGTCAACTTC
1 ACACCTGTTATAGTCAACTTC
36349 ACAC
1 ACAC
36353 AAGCACTCAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.30
Consensus pattern (21 bp):
ACACCTGTTATAGTCAACTTC
Found at i:38437 original size:75 final size:75
Alignment explanation
Indices: 38331--38576 Score: 370
Period size: 75 Copynumber: 3.3 Consensus size: 75
38321 CTCACATCAA
* * * *
38331 CAAATGATGGGGCAAGCTGAAAGCCCATTTCATTCAGAAATTGGAATATTGGCGCATTTTGAACG
1 CAAATGATAGGGCATGCTGAAAGCCCTTTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
38396 TCTGTATTAG
66 TCTGTATTAG
* * *
38406 CAAATGCTGGGGCATGCTGAAAGCCCTTTTCAATCAAAAATTGGAATATTGGCGCATTTTGAACG
1 CAAATGATAGGGCATGCTGAAAGCCCTTTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
38471 TCTGTATTAG
66 TCTGTATTAG
38481 CAAATGATAGGGCATGCTGAAAGCCCATTTT-AATCAGAAATTGGAATATTGGCGCATTTTGAAC
1 CAAATGATAGGGCATGCTGAAAGCCC-TTTTCAATCAGAAATTGGAATATTGGCGCATTTTGAAC
*
38545 GT-TCATATTAG
65 GTCT-GTATTAG
* *
38556 CAAATGCTAGGACATGCTGAA
1 CAAATGATAGGGCATGCTGAA
38577 GGCCTACATC
Statistics
Matches: 158, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
74 1 0.01
75 153 0.97
76 4 0.03
ACGTcount: A:0.32, C:0.16, G:0.23, T:0.29
Consensus pattern (75 bp):
CAAATGATAGGGCATGCTGAAAGCCCTTTTCAATCAGAAATTGGAATATTGGCGCATTTTGAACG
TCTGTATTAG
Found at i:39143 original size:27 final size:27
Alignment explanation
Indices: 39106--39165 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
39096 TGAACTGAGT
* *
39106 TTTCATCTATTTTGTTTATCATGTGTG
1 TTTCATATATTTTATTTATCATGTGTG
39133 TTTCATATATTTTATTTATCATGTGTG
1 TTTCATATATTTTATTTATCATGTGTG
39160 TTTCAT
1 TTTCAT
39166 CTACAACAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.18, C:0.10, G:0.12, T:0.60
Consensus pattern (27 bp):
TTTCATATATTTTATTTATCATGTGTG
Found at i:39538 original size:54 final size:55
Alignment explanation
Indices: 39475--39693 Score: 250
Period size: 54 Copynumber: 4.1 Consensus size: 55
39465 TTCACTGGCA
* *
39475 AACATCTGTGCAA-AAGCCACAGGAAAGGATGAATATGTTGTCAAATGTTTTACG
1 AACATCTGTGCAAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACG
* *
39529 AACATCTGTG-AAGAAACCACAGGAAATGATGAATGTGTTGTCAAATGATTTACG
1 AACATCTGTGCAAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACG
* * * * *
39583 AACATATG-GGAAGAAGCCAC-GGTAAAGAATGAATGTGTTGTCAAATATTTTACG
1 AACATCTGTGCAAGAAACCACAGG-AAAGGATGAATGTGTTGTCAAATGTTTTACG
* * * * * * *
39637 AGCATCTGAGCAA-AAACCATATGAGATGATGAATGTGTTGTCAAATGTTTTAGG
1 AACATCTGTGCAAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACG
39691 AAC
1 AAC
39694 CAGTTATTCT
Statistics
Matches: 138, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
53 5 0.04
54 129 0.93
55 4 0.03
ACGTcount: A:0.38, C:0.13, G:0.23, T:0.26
Consensus pattern (55 bp):
AACATCTGTGCAAGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACG
Found at i:39666 original size:108 final size:108
Alignment explanation
Indices: 39488--39693 Score: 290
Period size: 108 Copynumber: 1.9 Consensus size: 108
39478 ATCTGTGCAA
* * *
39488 AAGCCACAGGAAAGGATGAATATGTTGTCAAATGTTTTACGAACATCTGTGAAGAAACCACAGGA
1 AAGCCACAGGAAAGAATGAATATGTTGTCAAATATTTTACGAACATCTGAGAAGAAACCACAGGA
39553 AATGATGAATGTGTTGTCAAATGATTTACGAACATATGGGAAG
66 AATGATGAATGTGTTGTCAAATGATTTACGAACATATGGGAAG
* * * *
39596 AAGCCAC-GGTAAAGAATGAATGTGTTGTCAAATATTTTACGAGCATCTGAGCAA-AAACCATAT
1 AAGCCACAGG-AAAGAATGAATATGTTGTCAAATATTTTACGAACATCTGAG-AAGAAACCACAG
* * *
39659 GAGATGATGAATGTGTTGTCAAATGTTTTAGGAAC
64 GAAATGATGAATGTGTTGTCAAATGATTTACGAAC
39694 CAGTTATTCT
Statistics
Matches: 86, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
107 2 0.02
108 82 0.95
109 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (108 bp):
AAGCCACAGGAAAGAATGAATATGTTGTCAAATATTTTACGAACATCTGAGAAGAAACCACAGGA
AATGATGAATGTGTTGTCAAATGATTTACGAACATATGGGAAG
Found at i:40088 original size:22 final size:22
Alignment explanation
Indices: 40060--40248 Score: 297
Period size: 22 Copynumber: 8.6 Consensus size: 22
40050 ACATCTACAT
*
40060 TCTTCAAAGATGATAGATTATC
1 TCTTCAAAGATGATAGATTCTC
40082 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
40104 TCTCCAAAGATGATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
40126 TCTTCAAAGATGATATATTCTA
1 TCTTCAAAGATGATAGATTCTC
40148 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
40170 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
40192 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
40214 TCTTCAAAGATAATATATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
40236 TTTTTAAAGATGA
1 TCTTCAAAGATGA
40249 AAGCTTTATT
Statistics
Matches: 155, Mismatches: 12, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 155 1.00
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:40952 original size:45 final size:45
Alignment explanation
Indices: 40901--41561 Score: 1060
Period size: 45 Copynumber: 14.7 Consensus size: 45
40891 GGGATCTTTT
*
40901 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
40946 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
40991 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
41036 TGATGTTTTCAAAGCCTTTCGGGTCATCTGTAAGCCCTTCAGTGTA
1 TGATGTTTTCAAAGCC-TTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
41082 TGA--TTTTCAAAGCCTTCGGGTCATCTTTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
41125 TGATGTTTTCAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
41170 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTTAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
41215 TGATGTTTTCAAAACCTTCGGGTCATCTGTAAGCCCCTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
41260 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
41305 TGATGTTTTCATAA-CCTTTGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCA-AAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
41350 TGATGTTTTCAAAGCCTTCGGGTAATCTGTAAGCCCTTCAATGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * * *
41395 TGATGTTTTCAAAACCTTCGGCTCATCTATAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
41440 TGATGTTTTCAAAACCTTCGGGTCAT-TCATAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCT-GTAAGCCCTTCAGTGCA
* * * *
41485 TGATGTTTTCAAAACCTTAGGGTCATTTGTAAGACCTTCAGTGCA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
41530 TGATGTTTTCAAAGCCTCCGGGTCATCTGTAA
1 TGATGTTTTCAAAGCCTTCGGGTCATCTGTAA
41562 ACCTTCTGAG
Statistics
Matches: 579, Mismatches: 30, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
43 30 0.05
44 14 0.02
45 501 0.87
46 34 0.06
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATGTTTTCAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:41501 original size:25 final size:25
Alignment explanation
Indices: 41473--41542 Score: 69
Period size: 20 Copynumber: 3.0 Consensus size: 25
41463 CATTCATAAG
41473 ACCTTCAGTGCATGATGTTTTCAAA
1 ACCTTCAGTGCATGATGTTTTCAAA
* * * *
41498 ACCTT-AG-G-GTCAT-TTGT-AAG
1 ACCTTCAGTGCATGATGTTTTCAAA
41518 ACCTTCAGTGCATGATGTTTTCAAA
1 ACCTTCAGTGCATGATGTTTTCAAA
41543 GCCTCCGGGT
Statistics
Matches: 32, Mismatches: 8, Indels: 10
0.64 0.16 0.20
Matches are distributed among these distances:
20 7 0.22
21 5 0.16
22 4 0.12
23 4 0.12
24 5 0.16
25 7 0.22
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.36
Consensus pattern (25 bp):
ACCTTCAGTGCATGATGTTTTCAAA
Found at i:41759 original size:3 final size:3
Alignment explanation
Indices: 41751--41783 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
41741 CTATTTTAAA
41751 ATT ATT ATT ATT ATT ATT ATTT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT A-TT ATT ATT ATT AT
41784 GAAATAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:47019 original size:13 final size:12
Alignment explanation
Indices: 47001--47047 Score: 58
Period size: 13 Copynumber: 3.7 Consensus size: 12
46991 TGTTTAGTAT
47001 ATATTATTATTA
1 ATATTATTATTA
47013 CATATTATTATATA
1 -ATATTATTAT-TA
47027 ATATTTATTATTA
1 ATA-TTATTATTA
*
47040 TTATTATT
1 ATATTATT
47048 GTTGTTGTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
12 5 0.16
13 17 0.55
14 9 0.29
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
ATATTATTATTA
Found at i:47024 original size:23 final size:23
Alignment explanation
Indices: 46998--47046 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
46988 AAATGTTTAG
*
46998 TATATATTA-TTATTACATATTAT
1 TATATAATATTTATTA-ATATTAT
*
47021 TATATAATATTTATTATTATTAT
1 TATATAATATTTATTAATATTAT
47044 TAT
1 TAT
47047 TGTTGTTGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
TATATAATATTTATTAATATTAT
Found at i:57856 original size:16 final size:16
Alignment explanation
Indices: 57823--57877 Score: 56
Period size: 16 Copynumber: 3.2 Consensus size: 16
57813 AATAGCTTTT
*
57823 ATATTTATACTATATA
1 ATATTTATAATATATA
*
57839 ATATTTATAATATGTA
1 ATATTTATAATATATA
*
57855 ATGTGTCTATATATATATA
1 ATAT-T-TATA-ATATATA
57874 ATAT
1 ATAT
57878 AGTTGTTGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
16 17 0.55
17 1 0.03
18 4 0.13
19 9 0.29
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (16 bp):
ATATTTATAATATATA
Found at i:58077 original size:3 final size:3
Alignment explanation
Indices: 58069--58140 Score: 58
Period size: 3 Copynumber: 23.7 Consensus size: 3
58059 GTTTAGTATA
* * * * *
58069 TAT TAT TAT TACT TAT TAT TAT ATAA TATT TAT TGT TGT TGT TGT TAT
1 TAT TAT TAT TA-T TAT TAT TAT -TAT TA-T TAT TAT TAT TAT TAT TAT
58117 TAT TA- TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
58141 ATTTAGTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 10
0.81 0.05 0.14
Matches are distributed among these distances:
2 4 0.07
3 49 0.82
4 7 0.12
ACGTcount: A:0.29, C:0.01, G:0.06, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:62468 original size:15 final size:15
Alignment explanation
Indices: 62448--62509 Score: 74
Period size: 15 Copynumber: 4.2 Consensus size: 15
62438 TGTCCCATGT
62448 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
62463 TTATTTTTATTTTTA
1 TTATTTTTATTTTTA
*
62478 TT-TATTTATTTATTA
1 TTATTTTTATTT-TTA
* *
62493 -TATTATTATTATTA
1 TTATTTTTATTTTTA
62507 TTA
1 TTA
62510 ATACTTCCGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
14 12 0.30
15 28 0.70
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (15 bp):
TTATTTTTATTTTTA
Found at i:62499 original size:3 final size:3
Alignment explanation
Indices: 62448--62509 Score: 54
Period size: 3 Copynumber: 20.0 Consensus size: 3
62438 TGTCCCATGT
* * * *
62448 TTA TTT TTA TTT TTA TTA TTT TTA TTT TTA TTTA TTTA TTTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA -TTA -TTA TTA TTA
62495 TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
62510 ATACTTCCGG
Statistics
Matches: 49, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
2 2 0.04
3 36 0.73
4 11 0.22
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (3 bp):
TTA
Done.