Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001751.1 Hibiscus syriacus cultivar Beakdansim tig00003542_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: 64530
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:8007 original size:21 final size:21
Alignment explanation
Indices: 7964--8007 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
7954 TGATGAATTA
**
7964 TGGCTTTATAATAAAGCTTCT
1 TGGCTTTATAATAAAGCACCT
*
7985 TGGCTTTGTAATAAAGCACCT
1 TGGCTTTATAATAAAGCACCT
8006 TG
1 TG
8008 ATTCTTGACT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.27, C:0.16, G:0.18, T:0.39
Consensus pattern (21 bp):
TGGCTTTATAATAAAGCACCT
Found at i:13419 original size:16 final size:15
Alignment explanation
Indices: 13396--13434 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
13386 AAATAAAAGT
13396 AAAATAAAAACTTGA
1 AAAATAAAAACTTGA
13411 AAAAGTAAAAACTTG-
1 AAAA-TAAAAACTTGA
*
13426 CAAATAAAA
1 AAAATAAAA
13435 GTAAAACATT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
14 5 0.23
15 7 0.32
16 10 0.45
ACGTcount: A:0.67, C:0.08, G:0.08, T:0.18
Consensus pattern (15 bp):
AAAATAAAAACTTGA
Found at i:13576 original size:24 final size:22
Alignment explanation
Indices: 13537--13584 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
13527 TTGTCAAAAC
*
13537 CCTAAAAATTCTAAAAGATAATT
1 CCTAAAAATTCTAAAACAT-ATT
13560 CCTAATAAATTGC-AAAACATATT
1 CCTAA-AAATT-CTAAAACATATT
13583 CC
1 CC
13585 CTTAATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
23 10 0.45
24 11 0.50
25 1 0.05
ACGTcount: A:0.48, C:0.19, G:0.04, T:0.29
Consensus pattern (22 bp):
CCTAAAAATTCTAAAACATATT
Found at i:17962 original size:22 final size:22
Alignment explanation
Indices: 17934--18002 Score: 102
Period size: 22 Copynumber: 3.1 Consensus size: 22
17924 GTGAATGCAT
17934 TTTAGTATCATTGCCATGGCAC
1 TTTAGTATCATTGCCATGGCAC
*
17956 TTTAGTATCATTGCCATGGAAC
1 TTTAGTATCATTGCCATGGCAC
* * *
17978 TTTAGTATCAGTGCTAAGGCAC
1 TTTAGTATCATTGCCATGGCAC
18000 TTT
1 TTT
18003 CGATGTATGA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.19, G:0.19, T:0.38
Consensus pattern (22 bp):
TTTAGTATCATTGCCATGGCAC
Found at i:23783 original size:27 final size:27
Alignment explanation
Indices: 23752--23810 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
23742 TTACCTTTAA
23752 GGATTTCTTTACTTCCTCTTTCCTTTG
1 GGATTTCTTTACTTCCTCTTTCCTTTG
23779 GGATTTCTTTACTTCCTCTTTCCTTTG
1 GGATTTCTTTACTTCCTCTTTCCTTTG
23806 GGATT
1 GGATT
23811 GTGTGTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (27 bp):
GGATTTCTTTACTTCCTCTTTCCTTTG
Found at i:26169 original size:24 final size:23
Alignment explanation
Indices: 26131--26225 Score: 90
Period size: 23 Copynumber: 4.1 Consensus size: 23
26121 CTCATCAAAA
* *
26131 TCCTAAAAATTCTAAGAGATAAT
1 TCCTAAAAATGCTAAAAGATAAT
26154 TCCTAATAAATGCT--AAGATAAT
1 TCCTAA-AAATGCTAAAAGATAAT
**
26176 TCCCTAAAAAT-AAAAAAGATAAT
1 T-CCTAAAAATGCTAAAAGATAAT
26199 TCCTAATAAATTGC-AAAAGATAAT
1 TCCTAA-AAA-TGCTAAAAGATAAT
26223 TCC
1 TCC
26226 CTTAGCTGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
22 17 0.28
23 23 0.38
24 20 0.33
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (23 bp):
TCCTAAAAATGCTAAAAGATAAT
Found at i:26181 original size:23 final size:22
Alignment explanation
Indices: 26147--26225 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
26137 AAATTCTAAG
*
26147 AGATAATTCCTAATAAATGCTA
1 AGATAATTCCTAATAAATGCAA
**
26169 AGATAATTCCCTAA-AAATAAAAA
1 AGATAATT-CCTAATAAAT-GCAA
26192 AGATAATTCCTAATAAATTGCAAA
1 AGATAATTCCTAATAAA-TGC-AA
26216 AGATAATTCC
1 AGATAATTCC
26226 CTTAGCTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 17 0.36
23 17 0.36
24 13 0.28
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.28
Consensus pattern (22 bp):
AGATAATTCCTAATAAATGCAA
Found at i:32012 original size:27 final size:27
Alignment explanation
Indices: 31981--32039 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
31971 TTACCTTTAA
31981 GGATTTCTTTACTTCCTCTTTCCTTTG
1 GGATTTCTTTACTTCCTCTTTCCTTTG
32008 GGATTTCTTTACTTCCTCTTTCCTTTG
1 GGATTTCTTTACTTCCTCTTTCCTTTG
32035 GGATT
1 GGATT
32040 GTGTGTCAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.08, C:0.24, G:0.14, T:0.54
Consensus pattern (27 bp):
GGATTTCTTTACTTCCTCTTTCCTTTG
Found at i:34394 original size:24 final size:23
Alignment explanation
Indices: 34356--34450 Score: 90
Period size: 23 Copynumber: 4.1 Consensus size: 23
34346 CTCATCAAAA
* *
34356 TCCTAAAAATTCTAAGAGATAAT
1 TCCTAAAAATGCTAAAAGATAAT
34379 TCCTAATAAATGCT--AAGATAAT
1 TCCTAA-AAATGCTAAAAGATAAT
**
34401 TCCCTAAAAAT-AAAAAAGATAAT
1 T-CCTAAAAATGCTAAAAGATAAT
34424 TCCTAATAAATTGC-AAAAGATAAT
1 TCCTAA-AAA-TGCTAAAAGATAAT
34448 TCC
1 TCC
34451 CTTAGTTGTT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
22 17 0.28
23 23 0.38
24 20 0.33
ACGTcount: A:0.49, C:0.15, G:0.07, T:0.28
Consensus pattern (23 bp):
TCCTAAAAATGCTAAAAGATAAT
Found at i:34406 original size:23 final size:22
Alignment explanation
Indices: 34372--34450 Score: 88
Period size: 22 Copynumber: 3.5 Consensus size: 22
34362 AAATTCTAAG
*
34372 AGATAATTCCTAATAAATGCTA
1 AGATAATTCCTAATAAATGCAA
**
34394 AGATAATTCCCTAA-AAATAAAAA
1 AGATAATT-CCTAATAAAT-GCAA
34417 AGATAATTCCTAATAAATTGCAAA
1 AGATAATTCCTAATAAA-TGC-AA
34441 AGATAATTCC
1 AGATAATTCC
34451 CTTAGTTGTT
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
22 17 0.36
23 17 0.36
24 13 0.28
ACGTcount: A:0.51, C:0.14, G:0.08, T:0.28
Consensus pattern (22 bp):
AGATAATTCCTAATAAATGCAA
Found at i:44453 original size:3 final size:3
Alignment explanation
Indices: 44439--44489 Score: 57
Period size: 3 Copynumber: 16.0 Consensus size: 3
44429 ATTTAAAAAA
* *
44439 TAT TAT TAAT TAT TAT TAT TAG TAT TAT TAT TAC TAT TAAT TAT TAAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT T-AT TAT T-AT
44487 TAT
1 TAT
44490 AACCTAAACC
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
3 32 0.78
4 9 0.22
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:44566 original size:22 final size:23
Alignment explanation
Indices: 44531--44573 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
44521 CCCACTATCC
*
44531 ACCACTAAAACCCACT-AAAACA
1 ACCACCAAAACCCACTCAAAACA
*
44553 ACCACCAAATCCCACTCAAAA
1 ACCACCAAAACCCACTCAAAA
44574 TACCTACTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.51, C:0.40, G:0.00, T:0.09
Consensus pattern (23 bp):
ACCACCAAAACCCACTCAAAACA
Found at i:45263 original size:29 final size:29
Alignment explanation
Indices: 45177--45270 Score: 93
Period size: 30 Copynumber: 3.2 Consensus size: 29
45167 TTATAATTAT
*
45177 TATTTTAGTCCCTTAAATGTTTGTTTTTAC
1 TATTTTAGTCCTTTAAAT-TTTGTTTTTAC
* *
45207 TATTTTAGTCATTTAAGTTTT-TCATTTTA-
1 TATTTTAGTCCTTTAAATTTTGT--TTTTAC
* *
45236 TATTTTAGTCCTTTAAATTCCTGTTTTTGC
1 TATTTTAGTCCTTTAAATT-TTGTTTTTAC
45266 TATTT
1 TATTT
45271 AATCCATTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
28 1 0.02
29 24 0.46
30 26 0.50
31 1 0.02
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.60
Consensus pattern (29 bp):
TATTTTAGTCCTTTAAATTTTGTTTTTAC
Found at i:47371 original size:14 final size:15
Alignment explanation
Indices: 47345--47373 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
47335 GAACATTTCA
47345 TGCATTATTGCATTT
1 TGCATTATTGCATTT
47360 TGCATT-TTGCATTT
1 TGCATTATTGCATTT
47374 ACATATCATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.17, C:0.14, G:0.14, T:0.55
Consensus pattern (15 bp):
TGCATTATTGCATTT
Found at i:48577 original size:10 final size:10
Alignment explanation
Indices: 48564--48588 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
48554 AAAGAAGCAA
48564 AAAAACAAAG
1 AAAAACAAAG
48574 AAAAACAAAG
1 AAAAACAAAG
48584 AAAAA
1 AAAAA
48589 AGCAAAGAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.08, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAACAAAG
Found at i:48587 original size:22 final size:20
Alignment explanation
Indices: 48562--48623 Score: 61
Period size: 22 Copynumber: 2.9 Consensus size: 20
48552 GAAAAGAAGC
48562 AAAAAAACAAAGAAAAACAAA
1 AAAAAAACAAAGAAAAA-AAA
*
48583 GAAAAAAGCAAAGAGAAAAAAA
1 -AAAAAAACAAAGA-AAAAAAA
*
48605 AACAAAAATAAAGGAAAAA
1 AA-AAAAACAAA-GAAAAA
48624 GTGAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.06
22 26 0.76
23 6 0.18
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.02
Consensus pattern (20 bp):
AAAAAAACAAAGAAAAAAAA
Found at i:49677 original size:32 final size:32
Alignment explanation
Indices: 49631--49703 Score: 103
Period size: 32 Copynumber: 2.3 Consensus size: 32
49621 TGAGGAACAA
*
49631 TTGGGGCATATTTGAAGATTTAACA-TCAAATG
1 TTGGGGCATATTTGAAGATTCAA-AGTCAAATG
* *
49663 TTGGGTCATCTTTGAAGATTCAAAGTCAAATG
1 TTGGGGCATATTTGAAGATTCAAAGTCAAATG
49695 TTGGGGCAT
1 TTGGGGCAT
49704 TTTTTGTGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 1 0.03
32 35 0.97
ACGTcount: A:0.30, C:0.11, G:0.25, T:0.34
Consensus pattern (32 bp):
TTGGGGCATATTTGAAGATTCAAAGTCAAATG
Found at i:49715 original size:32 final size:32
Alignment explanation
Indices: 49647--49752 Score: 99
Period size: 32 Copynumber: 3.3 Consensus size: 32
49637 CATATTTGAA
* * * *
49647 GATTTAACATCAAATGTTGGGTCA-TCTTTGAA
1 GATTCAACATCAAATGTTGGGGCATTTTTTG-T
49679 GATTCAA-AGTCAAATGTTGGGGCATTTTTTGT
1 GATTCAACA-TCAAATGTTGGGGCATTTTTTGT
* * * * *
49711 GATTCAACATCGAATATTGGAGCATCTTTGGT
1 GATTCAACATCAAATGTTGGGGCATTTTTTGT
49743 GATTCAACAT
1 GATTCAACAT
49753 TCTGATGCGA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
31 1 0.02
32 55 0.89
33 6 0.10
ACGTcount: A:0.29, C:0.13, G:0.21, T:0.37
Consensus pattern (32 bp):
GATTCAACATCAAATGTTGGGGCATTTTTTGT
Found at i:50228 original size:61 final size:61
Alignment explanation
Indices: 50133--50541 Score: 540
Period size: 61 Copynumber: 6.7 Consensus size: 61
50123 TAAAGTTTTT
* * *
50133 AAGATTGGATTTCAACTTTACAACGAAGGATATCCAACTCAAAGACAATTTGGTGAAGCAG
1 AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAC
*** *
50194 AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGTTGATTTTGTGAAGCAC
1 AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAC
* * *
50255 AAGATTAGATTTCAACTTCACAACGAATGG-TATCCAACTCAAAACCAATTTGGTGAAACTTACA
1 AAGATTGGATTTCAACTTCACAACGAA-GGATATCCAACTCAAAGCCAATTTGGTG-AA---GCA
50319 C
61 C
* * * *
50320 AAGCTTGGATTTCAACTTCACCACGAAGGATATCCAACTCAAAGCCGATTTGGTAAAGCA-
1 AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAC
* *
50380 ATA-CTTGGATTTCAACTTCACAACGAAGGATATCCAACTTAAAGCCAATTTGGTGAA--AC
1 A-AGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAC
* *
50439 AAGATTGGATTTCAACTTCACAACAAAGGATATCCAACTCAAAGCCGATTTGGTGAAGCAC
1 AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAC
* * *
50500 AAGATTGGATTTCCACTTCACAACGAAGGATGTCCAATTCAA
1 AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAA
50542 CGCTCAACTT
Statistics
Matches: 305, Mismatches: 32, Indels: 22
0.85 0.09 0.06
Matches are distributed among these distances:
58 2 0.01
59 51 0.17
60 51 0.17
61 144 0.47
62 4 0.01
64 4 0.01
65 49 0.16
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.25
Consensus pattern (61 bp):
AAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAGCCAATTTGGTGAAGCAC
Found at i:50853 original size:231 final size:230
Alignment explanation
Indices: 50498--51067 Score: 716
Period size: 230 Copynumber: 2.5 Consensus size: 230
50488 TTGGTGAAGC
* * ** * * *
50498 ACAAGATTGGATTTCCACTTCACAACGAAGGATGTCCAATTCAACGCTCAACTTCACAGCGAATG
1 ACAAGATTGGATTTCAACTTCACAACGAAGAACATCCAATTCAAAGCTCAACTGCACAGCGAAGG
* * *
50563 AGCCATCCACGATTTCAACTTCACGATAAAGGATATCGTGCCCAAAAGATTGACCCAACTTCACG
66 AGCCATCCACGATTTCAACTTCACAACAAAGGATATCGTACCCAAAAGATTGACCCAACTTCACG
* *
50628 ATGAATGAGTCATCTGTGACACAACAATGAAAAACCAGTTTCATTCAGAGTCAATTTCAACTTCA
131 AAGAATGAGTCATCTGTGACACAACAATG-AAAACCAATTTCATTCAGAGTCAATTTCAACTTCA
* *
50693 CAACGAAAGATATTGAACTCAAAAGTGATTCAATTT
195 CAACGAAAGATATTGAACTCAAAAGAGATACAATTT
* * **
50729 ACAAGATTGGATTTTAACTTCACAACGAATAACATTTAATTCAAAGCTCAACTGCACAGCGAAGG
1 ACAAGATTGGATTTCAACTTCACAACGAAGAACATCCAATTCAAAGCTCAACTGCACAGCGAAGG
* * * *
50794 AGTCATTCACGATTTCAACTTCACAACGAATGATATCGTACCCAAAAGATTGACCCAACTTCACG
66 AGCCATCCACGATTTCAACTTCACAACAAAGGATATCGTACCCAAAAGATTGACCCAACTTCACG
**
50859 AAGAATGAGTCATCTGTGGTACAACAATGAAAACCAATTTCATTCAGAGTCAATTTCAACTTCAC
131 AAGAATGAGTCATCTGTGACACAACAATGAAAACCAATTTCATTCAGAGTCAATTTCAACTTCAC
*
50924 AGCGAAAGATATTGAACTCAAAAGAGATACAATTT
196 AACGAAAGATATTGAACTCAAAAGAGATACAATTT
** * * * * *** *
50959 ACAAGCGTGGATTTCAACTTCACGAC-AAAAGATATCCAACTCAAAGAAAAACTTCAC-GACGAA
1 ACAAGATTGGATTTCAACTTCACAACGAAGA-ACATCCAATTCAAAGCTCAACTGCACAG-CGAA
* * * *
51022 GGAGCTA-CACATGATTTCAACTTCACGAA-GAAGGATATCGTGCCCA
64 GGAGCCATC-CACGATTTCAACTTCAC-AACAAAGGATATCGTACCCA
51068 GTGGATCGAC
Statistics
Matches: 291, Mismatches: 44, Indels: 9
0.85 0.13 0.03
Matches are distributed among these distances:
229 4 0.01
230 147 0.51
231 140 0.48
ACGTcount: A:0.38, C:0.22, G:0.15, T:0.24
Consensus pattern (230 bp):
ACAAGATTGGATTTCAACTTCACAACGAAGAACATCCAATTCAAAGCTCAACTGCACAGCGAAGG
AGCCATCCACGATTTCAACTTCACAACAAAGGATATCGTACCCAAAAGATTGACCCAACTTCACG
AAGAATGAGTCATCTGTGACACAACAATGAAAACCAATTTCATTCAGAGTCAATTTCAACTTCAC
AACGAAAGATATTGAACTCAAAAGAGATACAATTT
Found at i:51624 original size:22 final size:22
Alignment explanation
Indices: 51599--51642 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
51589 TACCCACTAT
51599 CCACCACTAAAACCCACTCAAA
1 CCACCACTAAAACCCACTCAAA
*
51621 CCACCACTAAATCCCACTCAAA
1 CCACCACTAAAACCCACTCAAA
51643 ATACTTACTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.43, C:0.45, G:0.00, T:0.11
Consensus pattern (22 bp):
CCACCACTAAAACCCACTCAAA
Found at i:52359 original size:29 final size:30
Alignment explanation
Indices: 52267--52358 Score: 93
Period size: 29 Copynumber: 3.2 Consensus size: 30
52257 TTATAATGAT
*
52267 TATTTTAGTCCCTTAAATGT--T-TTTTTGC
1 TATTTTAGTCCTTTAAAT-TCCTGTTTTTGC
* * * * *
52295 TATTTTAGTCATTTAAGTTTCTGATTTT-A
1 TATTTTAGTCCTTTAAATTCCTGTTTTTGC
52324 TATTTTAGTCCTTTAAATTCCTGTTTTTGC
1 TATTTTAGTCCTTTAAATTCCTGTTTTTGC
52354 TATTT
1 TATTT
52359 AATCCATTAA
Statistics
Matches: 50, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
27 1 0.02
28 15 0.30
29 25 0.50
30 9 0.18
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.59
Consensus pattern (30 bp):
TATTTTAGTCCTTTAAATTCCTGTTTTTGC
Found at i:52379 original size:57 final size:57
Alignment explanation
Indices: 52267--52379 Score: 135
Period size: 57 Copynumber: 2.0 Consensus size: 57
52257 TTATAATGAT
* *
52267 TATTTTAGTCCCTTAAATGTTTTTTTGCTATTTTAGTCATTTAAGTTTCTGATTTTA
1 TATTTTAGTCCCTTAAATGTTTTTTTGCTATTTTAATCATTTAAGTTTCTCATTTTA
*
52324 TATTTTAGTCCTTTAAAT-TCCTGTTTTTGCTA-TTTAATCCA-TTAAGTTTC-CATTTT
1 TATTTTAGTCCCTTAAATGT--T-TTTTTGCTATTTTAAT-CATTTAAGTTTCTCATTTT
52380 GGTCTTTTAA
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
56 1 0.02
57 22 0.45
58 15 0.31
59 11 0.22
ACGTcount: A:0.21, C:0.13, G:0.09, T:0.57
Consensus pattern (57 bp):
TATTTTAGTCCCTTAAATGTTTTTTTGCTATTTTAATCATTTAAGTTTCTCATTTTA
Found at i:55455 original size:28 final size:28
Alignment explanation
Indices: 55390--55448 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
55380 TTTGTTCGGG
*
55390 TCGGGTCAGG-TTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
55417 TCGGGTCGGGTTTTTTTAAGTGTGATAT
1 TCGGGTCGGGTTTTTTTAAGTGTGATAT
55445 TCGG
1 TCGG
55449 TTTGGGTCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 9 0.30
28 21 0.70
ACGTcount: A:0.15, C:0.08, G:0.32, T:0.44
Consensus pattern (28 bp):
TCGGGTCGGGTTTTTTTAAGTGTGATAT
Found at i:56094 original size:18 final size:17
Alignment explanation
Indices: 56040--56103 Score: 101
Period size: 17 Copynumber: 3.7 Consensus size: 17
56030 TATGGAATTG
*
56040 GATTCCAATTCCTAACA
1 GATTTCAATTCCTAACA
56057 GATTTCAATTCCTAACA
1 GATTTCAATTCCTAACA
*
56074 GATTTCAATTCCTTCACA
1 GATTTCAATTCC-TAACA
56092 GATTTCAATTCC
1 GATTTCAATTCC
56104 CTCATAAACA
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
17 28 0.64
18 16 0.36
ACGTcount: A:0.31, C:0.27, G:0.06, T:0.36
Consensus pattern (17 bp):
GATTTCAATTCCTAACA
Found at i:60846 original size:25 final size:22
Alignment explanation
Indices: 60815--60879 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 22
60805 AATAATATTA
* *
60815 TTTATATATATTTATAATAAAT
1 TTTAAATATATATATAATAAAT
60837 ATTTAAATATATATAT-ATAAAT
1 -TTTAAATATATATATAATAAAT
60859 TTTAAATA-ATAACTATAATAA
1 TTTAAATATAT-A-TATAATAA
60880 TAAAAGTAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
20 2 0.05
21 9 0.24
22 9 0.24
23 17 0.46
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (22 bp):
TTTAAATATATATATAATAAAT
Found at i:60876 original size:20 final size:22
Alignment explanation
Indices: 60813--60866 Score: 74
Period size: 23 Copynumber: 2.5 Consensus size: 22
60803 TAAATAATAT
* *
60813 TATTTATATATATTTATAATAAA
1 TATTTAAATATATATAT-ATAAA
60836 TATTTAAATATATATATATAAA
1 TATTTAAATATATATATATAAA
60858 T-TTTAAATA
1 TATTTAAATA
60867 ATAACTATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 8 0.28
22 6 0.21
23 15 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTAAATATATATATATAAA
Found at i:62895 original size:115 final size:117
Alignment explanation
Indices: 62621--62907 Score: 365
Period size: 115 Copynumber: 2.5 Consensus size: 117
62611 GTTGAACAAG
* * * * * *
62621 TTCTT-CTCTTCAGATGAGTTCTTATCATTATGAACTTCTTCTGGAAATGATGGTGCTGATCTAT
1 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAAC--CTTCTAGAAA--ATGTTGATGATATAT
*
62685 CTCCTTATGTGATAGAATCATACAAAAAGTTGAACAAGTCTTCTCATTTGAACTTC
62 CTCCTTATGTGATAGAATCATACAAAAAGTTGAACAAGTCTTCTCATTCGAACTTC
62741 TTCTTCCTC-TCAGATAAGTTCTTCTCATTATGAACCTTCT-GAAAATGTTGATGATATATCTCC
1 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACCTTCTAGAAAATGTTGATGATATATCTCC
* * *
62804 TT-TGTGATAGAATCGA-GC-AAAGGTTGAACAAATTCTTCTCATTACGAACTTC
66 TTATGTGATAGAATC-ATACAAAAAGTTGAAC-AAGTCTTCTCATT-CGAACTTC
62856 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAA-CTTCTAGAAAA-GTTGAT
1 TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACCTTCTAGAAAATGTTGAT
62908 CCATCGAGTG
Statistics
Matches: 152, Mismatches: 9, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
113 10 0.07
114 25 0.16
115 46 0.30
116 30 0.20
117 4 0.03
118 5 0.03
120 29 0.19
121 3 0.02
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (117 bp):
TTCTTCCTCTTCAGATAAGTTCTTCTCATTATGAACCTTCTAGAAAATGTTGATGATATATCTCC
TTATGTGATAGAATCATACAAAAAGTTGAACAAGTCTTCTCATTCGAACTTC
Found at i:63450 original size:19 final size:19
Alignment explanation
Indices: 63421--63478 Score: 80
Period size: 19 Copynumber: 2.9 Consensus size: 19
63411 TTTACAAAAT
63421 AAAAGAATAAATTGAATTTC
1 AAAA-AATAAATTGAATTTC
* *
63441 AAAAAATAAATTAAATCTC
1 AAAAAATAAATTGAATTTC
63460 AAAAATATAAATTGAATTT
1 AAAAA-ATAAATTGAATTT
63479 AGAGAAAATA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.59, C:0.05, G:0.05, T:0.31
Consensus pattern (19 bp):
AAAAAATAAATTGAATTTC
Found at i:63489 original size:20 final size:18
Alignment explanation
Indices: 63420--63490 Score: 70
Period size: 20 Copynumber: 3.6 Consensus size: 18
63410 ATTTACAAAA
63420 TAAAAGAATAAATTGAATT
1 TAAAA-AATAAATTGAATT
*
63439 TCAAAAAATAAATTAAATCT
1 T-AAAAAATAAATTGAAT-T
*
63459 CAAAAATATAAATTGAATT
1 TAAAAA-ATAAATTGAATT
63478 TAGAGAAAATAAA
1 TA-A-AAAATAAA
63491 ACTTAGAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
19 19 0.44
20 21 0.49
21 3 0.07
ACGTcount: A:0.61, C:0.04, G:0.07, T:0.28
Consensus pattern (18 bp):
TAAAAAATAAATTGAATT
Found at i:63835 original size:15 final size:15
Alignment explanation
Indices: 63806--63839 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
63796 CTCTTTTGTA
63806 TTTTCTTCTTTTTTC
1 TTTTCTTCTTTTTTC
63821 TTTTCTT-TTTCTTTC
1 TTTTCTTCTTT-TTTC
63836 TTTT
1 TTTT
63840 TTCATTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 3 0.17
15 15 0.83
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (15 bp):
TTTTCTTCTTTTTTC
Found at i:63836 original size:22 final size:22
Alignment explanation
Indices: 63797--63859 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
63787 CATCTTGACC
*
63797 TCTTTTGTATTTTC-TTCTTTTT
1 TCTTTTCT-TTTTCTTTCTTTTT
63819 TCTTTTCTTTTTCTTTCTTTTT
1 TCTTTTCTTTTTCTTTCTTTTT
*
63841 TCATTTCATTTTTTCTTTC
1 TCTTTTC--TTTTTCTTTC
63860 AAGCATAATA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.14
22 21 0.58
24 10 0.28
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (22 bp):
TCTTTTCTTTTTCTTTCTTTTT
Found at i:63860 original size:12 final size:11
Alignment explanation
Indices: 63806--63859 Score: 67
Period size: 11 Copynumber: 4.8 Consensus size: 11
63796 CTCTTTTGTA
63806 TTTTC-TTCTT
1 TTTTCTTTCTT
63816 TTTTCTTT-TCT
1 TTTTCTTTCT-T
63827 TTTTCTTTCTT
1 TTTTCTTTCTT
63838 TTTTCATTTCATT
1 TTTTC-TTTC-TT
63851 TTTTCTTTC
1 TTTTCTTTC
63860 AAGCATAATA
Statistics
Matches: 39, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
10 6 0.15
11 17 0.44
12 9 0.23
13 7 0.18
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTCTTTCTT
Done.