Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007728.1 Hibiscus syriacus cultivar Beakdansim tig00109979_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: 71199
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.32
Found at i:65 original size:21 final size:21
Alignment explanation
Indices: 38--94 Score: 60
Period size: 21 Copynumber: 2.7 Consensus size: 21
28 ATAAATGTAA
38 TCCTTTGGAACATATATGCGG
1 TCCTTTGGAACATATATGCGG
* * * **
59 TTCTTTGGGACACATATTTGG
1 TCCTTTGGAACATATATGCGG
*
80 TCCTTTGGAATATAT
1 TCCTTTGGAACATAT
95 GTGATCTTAA
Statistics
Matches: 27, Mismatches: 9, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.21, T:0.40
Consensus pattern (21 bp):
TCCTTTGGAACATATATGCGG
Found at i:1339 original size:91 final size:91
Alignment explanation
Indices: 1175--1701 Score: 769
Period size: 91 Copynumber: 5.8 Consensus size: 91
1165 GATGGTTTCA
* * * *
1175 CCAAGGTTGAACAAGTTTTTCTCATTATGAACTT-TTCTCCCTCGTTGAATGAGTTATTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
* * *
1239 ATGAACTCTCCTCTAGAAATGTTAAT
66 ATGAACTCTCCACTGGAAATGTTGAT
1265 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
* *
1330 ATAAACTCTCCACTGGAAATGTTGAG
66 ATGAACTCTCCACTGGAAATGTTGAT
* *
1356 CCAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTT-G-TCGAGTTCTTCTCAT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGAT-GAGTTCTTCTCAT
1419 TATGAACTCTCCACTGGAAATGTTGAT
65 TATGAACTCTCCACTGGAAATGTTGAT
* * * *
1446 CCATGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCTCTCTCATTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
* *
1511 ATGAACTCTCTACTGGAAACGTTGAT
66 ATGAACTCTCCACTGGAAATGTTGAT
** *
1537 TAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
*
1602 ATGAACTCTCCACTGGAAATGTTGAG
66 ATGAACTCTCCACTGGAAATGTTGAT
* * * * *
1628 CCAAGATTGAACAAGTTC-T-T-ATTATGAACTTTTTCTCCCTCGTTGAATGAGTTCTTATCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
1690 ATGAACTCTCCA
66 ATGAACTCTCCA
1702 TAAAAAATGT
Statistics
Matches: 397, Mismatches: 36, Indels: 10
0.90 0.08 0.02
Matches are distributed among these distances:
88 50 0.13
89 2 0.01
90 114 0.29
91 230 0.58
92 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (91 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCATTGGATGAGTTCTTCTCATT
ATGAACTCTCCACTGGAAATGTTGAT
Found at i:1493 original size:181 final size:180
Alignment explanation
Indices: 1175--1701 Score: 774
Period size: 181 Copynumber: 2.9 Consensus size: 180
1165 GATGGTTTCA
* *
1175 CCAAGGTTGAACAAGTTTTTCTCATTATGAACTTTTCTCCCTCGTTGAATGAGTTATTCTCATTA
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTCCCTCGTTG-ATGAGTTCTTCTCATTA
* * *
1240 TGAACTCTCCTCTAGAAATGTTAATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTC
65 TGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTC
* *
1305 CCTCATTGGATGAGTTCTTCTCATTATAAACTCTCCACTGGAAATGTTGAG
130 CCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACGTTGAG
*
1356 CCAAGATTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTG-TCGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTCCCTCGTTGAT-GAGTTCTTCTCATT
* * *
1420 ATGAACTCTCCACTGGAAATGTTGATCCATGGTTGAACAAGTTCTTCTCATTATAAACTTCTTCT
64 ATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCT
* * *
1485 CTCTCATTGGATGAGTTCTTCTCATTATGAACTCTCTACTGGAAACGTTGAT
129 CCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACGTTGAG
** *
1537 TAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATTGGATGAGTTCTTCTCATT
1 CCAAGGTTGAACAAGTTCTTCTCATTATGAACTT-TTCTCCCTCGTT-GATGAGTTCTTCTCATT
* * *
1602 ATGAACTCTCCACTGGAAATGTTGAGCCAAGATTGAACAAGTTC-T-T-ATTATGAACTTTTTCT
64 ATGAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCT
* * *
1664 CCCTCGTTGAATGAGTTCTTATCATTATGAACTCTCCA
129 CCCTCATTGGATGAGTTCTTCTCATTATGAACTCTCCA
1702 TAAAAAATGT
Statistics
Matches: 313, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
179 47 0.15
180 2 0.01
181 194 0.62
182 69 0.22
183 1 0.00
ACGTcount: A:0.26, C:0.22, G:0.14, T:0.38
Consensus pattern (180 bp):
CCAAGGTTGAACAAGTTCTTCTCATTATGAACTTTTCTCCCTCGTTGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCC
CTCATTGGATGAGTTCTTCTCATTATGAACTCTCCACTGGAAACGTTGAG
Found at i:2807 original size:58 final size:55
Alignment explanation
Indices: 2744--2887 Score: 154
Period size: 58 Copynumber: 2.6 Consensus size: 55
2734 TTCTTAGTTG
* * *
2744 TCATCAAGGAACCCCTAAAAATTAGCCTTAGCTTCCTTTAAAAATTC-TTTGAAAATCA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTT-CTCTAAAAA-TCATTTGAAAA--A
* * *
2802 TCATCAAGAAAACCCTAAAAATCAGGCTTAG-TT-TCTAAAAATCATTTGCAAAA
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTCTAAAAATCATTTGAAAAA
*
2855 --ATCAAGAAACCCCTAAAAATTAGGCTTAACTTC
1 TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTC
2888 ATTAAAATCT
Statistics
Matches: 74, Mismatches: 9, Indels: 11
0.79 0.10 0.12
Matches are distributed among these distances:
51 26 0.35
52 2 0.03
53 1 0.01
54 2 0.03
55 14 0.19
57 2 0.03
58 27 0.36
ACGTcount: A:0.42, C:0.22, G:0.09, T:0.28
Consensus pattern (55 bp):
TCATCAAGAAACCCCTAAAAATTAGGCTTAGCTTCTCTAAAAATCATTTGAAAAA
Found at i:4878 original size:7 final size:7
Alignment explanation
Indices: 4854--4912 Score: 75
Period size: 7 Copynumber: 8.1 Consensus size: 7
4844 GATCTGTTTA
4854 TTTTCTT
1 TTTTCTT
4861 CTTTTCGTT
1 -TTTTC-TT
4870 TTTTCTT
1 TTTTCTT
*
4877 TTTTATT
1 TTTTCTT
4884 TTTTCTT
1 TTTTCTT
4891 TTTTC-T
1 TTTTCTT
4897 TTTTCATT
1 TTTTC-TT
4905 TTTTCTT
1 TTTTCTT
4912 T
1 T
4913 CTTTTCTATC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
6 6 0.13
7 22 0.48
8 16 0.35
9 2 0.04
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTCTT
Found at i:4900 original size:21 final size:21
Alignment explanation
Indices: 4854--4912 Score: 84
Period size: 21 Copynumber: 2.8 Consensus size: 21
4844 GATCTGTTTA
4854 TTTTC-TTCTTTTCGTTTTTTCT
1 TTTTCATT-TTTTC-TTTTTTCT
*
4876 TTTTTATTTTTTCTTTTTTCT
1 TTTTCATTTTTTCTTTTTTCT
4897 TTTTCATTTTTTCTTT
1 TTTTCATTTTTTCTTT
4913 CTTTTCTATC
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 23 0.68
22 9 0.26
23 2 0.06
ACGTcount: A:0.03, C:0.14, G:0.02, T:0.81
Consensus pattern (21 bp):
TTTTCATTTTTTCTTTTTTCT
Found at i:4927 original size:21 final size:21
Alignment explanation
Indices: 4854--4955 Score: 56
Period size: 21 Copynumber: 4.9 Consensus size: 21
4844 GATCTGTTTA
4854 TTTTCT-TCTTTTCGTTT-TTTC
1 TTTTCTATCTTTT--TTTCTTTC
* *
4875 TTTTTTAT-TTTTTCTTTTTTC
1 TTTTCTATCTTTTT-TTCTTTC
*
4896 -TTT-T-TCATTTTTTCTTTC
1 TTTTCTATCTTTTTTTCTTTC
4914 TTTTCTATCTTTTTATGTCTTT-
1 TTTTCTATCTTTTT-T-TCTTTC
*
4936 TTCTTGCTATATTTTTTTCT
1 TT-TT-CTATCTTTTTTTCT
4956 CTCTGTGTCG
Statistics
Matches: 65, Mismatches: 5, Indels: 21
0.71 0.05 0.23
Matches are distributed among these distances:
18 7 0.11
19 9 0.14
20 6 0.09
21 19 0.29
22 7 0.11
23 8 0.12
24 9 0.14
ACGTcount: A:0.06, C:0.15, G:0.03, T:0.76
Consensus pattern (21 bp):
TTTTCTATCTTTTTTTCTTTC
Found at i:8453 original size:42 final size:42
Alignment explanation
Indices: 8394--8486 Score: 123
Period size: 42 Copynumber: 2.2 Consensus size: 42
8384 TTATAGATGG
* *
8394 CCCGAAAGAATTAATCATCATGCTCGTAAGACTTACTAATGA
1 CCCGAAGGAATTAATCATCATGCTCGAAAGACTTACTAATGA
* * * * *
8436 CCCGAAGGATTTAATCATTATGCTCGAAAGACTTATTGATGG
1 CCCGAAGGAATTAATCATCATGCTCGAAAGACTTACTAATGA
8478 CCCGAAGGA
1 CCCGAAGGA
8487 CTTACTAATC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.34, C:0.20, G:0.19, T:0.26
Consensus pattern (42 bp):
CCCGAAGGAATTAATCATCATGCTCGAAAGACTTACTAATGA
Found at i:8657 original size:58 final size:59
Alignment explanation
Indices: 8565--8719 Score: 224
Period size: 59 Copynumber: 2.6 Consensus size: 59
8555 TTGAGTAATC
* * *
8565 GTCAAGAAACCTCTAAAAATCAGACTTAGCTTCTTTAAAAT-TCATTTAAAAACATCAT
1 GTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAATAACATTTAAAAACATCAT
* *
8623 GTCAAGAAACCTCTGAAAATCAGACCTAGTTTCTTTAAAATAACATTTGAAAACATCAT
1 GTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAATAACATTTAAAAACATCAT
* *
8682 GTCAAGAAACCAT-TGAAAATAAAACTTAGTTTCTTTAA
1 GTCAAGAAACC-TCTGAAAATCAGACTTAGTTTCTTTAA
8720 TGATATCATA
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
58 38 0.44
59 48 0.55
60 1 0.01
ACGTcount: A:0.43, C:0.17, G:0.09, T:0.30
Consensus pattern (59 bp):
GTCAAGAAACCTCTGAAAATCAGACTTAGTTTCTTTAAAATAACATTTAAAAACATCAT
Found at i:11071 original size:33 final size:31
Alignment explanation
Indices: 11029--11092 Score: 92
Period size: 33 Copynumber: 2.0 Consensus size: 31
11019 AAAATAAACT
11029 AACAAATAATAAAAATAAAAATAAACAGTAAAA
1 AACAAATAATAAAAAT-AAAATAAACA-TAAAA
* *
11062 AACATATAATAAAAATGAAATAAACATAAAA
1 AACAAATAATAAAAATAAAATAAACATAAAA
11093 TAAGGACCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 5 0.17
32 9 0.31
33 15 0.52
ACGTcount: A:0.73, C:0.06, G:0.03, T:0.17
Consensus pattern (31 bp):
AACAAATAATAAAAATAAAATAAACATAAAA
Found at i:11382 original size:38 final size:40
Alignment explanation
Indices: 11339--11415 Score: 104
Period size: 38 Copynumber: 2.0 Consensus size: 40
11329 GACTAAATTC
* * * *
11339 AAATAAATCAGAATAATAATAGTG-ACTAAATTA-AAATA
1 AAATAAAACAAAATAATAAAAGTGCAATAAATTAGAAATA
11377 AAATAAAACAAAATAATAAAAGTGCAATAAATTAGAAAT
1 AAATAAAACAAAATAATAAAAGTGCAATAAATTAGAAAT
11416 GAAAGGTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 21 0.64
39 8 0.24
40 4 0.12
ACGTcount: A:0.64, C:0.05, G:0.08, T:0.23
Consensus pattern (40 bp):
AAATAAAACAAAATAATAAAAGTGCAATAAATTAGAAATA
Found at i:13077 original size:2 final size:2
Alignment explanation
Indices: 13070--13103 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
13060 TGGTTGAATT
13070 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
13104 GTTACTTGTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14494 original size:36 final size:36
Alignment explanation
Indices: 14454--14567 Score: 158
Period size: 36 Copynumber: 3.2 Consensus size: 36
14444 AAGTCTCTGC
14454 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
1 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
* *
14490 AGGTTTAGCTCTGATCAAGCTGGTAATTCCTTATAC
1 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
* * * * *
14526 AGGTTCAGCACCGATC-GGTTCGTAATTCCTTATAT
1 AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
14561 AGGTTCA
1 AGGTTCA
14568 ATATTGATCA
Statistics
Matches: 69, Mismatches: 9, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
35 22 0.32
36 47 0.68
ACGTcount: A:0.25, C:0.20, G:0.20, T:0.35
Consensus pattern (36 bp):
AGGTTCAGCTCTGATCAAGCTGGTAATTCCTTATAT
Found at i:14586 original size:35 final size:36
Alignment explanation
Indices: 14464--14593 Score: 122
Period size: 35 Copynumber: 3.7 Consensus size: 36
14454 AGGTTCAGCT
* *
14464 CTGATCAAGCTGGTAATTCCTTATATAGGTTTAGCT-
1 CTGATCAAGCTGGTAATTCCTTATATAGGTTCA-ATA
* **
14500 CTGATCAAGCTGGTAATTCCTTATACAGGTTCAGCA
1 CTGATCAAGCTGGTAATTCCTTATATAGGTTCAATA
* * * *
14536 CCGATC-GGTTCGTAATTCCTTATATAGGTTCAATA
1 CTGATCAAGCTGGTAATTCCTTATATAGGTTCAATA
* * *
14571 TTGATC-AGCTAGTAATTCGTTAT
1 CTGATCAAGCTGGTAATTCCTTAT
14594 GGATCTAAGG
Statistics
Matches: 76, Mismatches: 17, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
35 40 0.53
36 36 0.47
ACGTcount: A:0.26, C:0.18, G:0.18, T:0.37
Consensus pattern (36 bp):
CTGATCAAGCTGGTAATTCCTTATATAGGTTCAATA
Found at i:20412 original size:37 final size:38
Alignment explanation
Indices: 20365--20437 Score: 139
Period size: 38 Copynumber: 1.9 Consensus size: 38
20355 TTTTGTTCGG
20365 GTCGGGTCGGG-TTTTTTAAGTGTGATATTCGGGTCGA
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
20402 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
1 GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTC
20438 TGGTTCGGGT
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 11 0.31
38 24 0.69
ACGTcount: A:0.12, C:0.11, G:0.37, T:0.40
Consensus pattern (38 bp):
GTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGA
Found at i:21047 original size:18 final size:16
Alignment explanation
Indices: 21011--21056 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
21001 TATGAAATTG
21011 GATTCCAATTCCTACA
1 GATTCCAATTCCTACA
*
21027 GATTCCAATTCATTCACA
1 GATTCCAATTC-CT-ACA
21045 GATTCCAATTCC
1 GATTCCAATTCC
21057 CTCATAAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
16 11 0.42
17 1 0.04
18 14 0.54
ACGTcount: A:0.30, C:0.30, G:0.07, T:0.33
Consensus pattern (16 bp):
GATTCCAATTCCTACA
Found at i:21413 original size:16 final size:16
Alignment explanation
Indices: 21392--21423 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
21382 CGTTGCGATT
21392 TTCCAAATTTACGTTA
1 TTCCAAATTTACGTTA
21408 TTCCAAATTTACGTTA
1 TTCCAAATTTACGTTA
21424 GTCTAAATTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.06, T:0.44
Consensus pattern (16 bp):
TTCCAAATTTACGTTA
Found at i:21431 original size:16 final size:16
Alignment explanation
Indices: 21393--21432 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
21383 GTTGCGATTT
*
21393 TCCAAATTTACGTTAT
1 TCCAAATTTACGTTAG
21409 TCCAAATTTACGTTAG
1 TCCAAATTTACGTTAG
*
21425 TCTAAATT
1 TCCAAATT
21433 CGTTGCGATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.33, C:0.17, G:0.07, T:0.42
Consensus pattern (16 bp):
TCCAAATTTACGTTAG
Found at i:21458 original size:21 final size:21
Alignment explanation
Indices: 21433--21638 Score: 186
Period size: 21 Copynumber: 10.4 Consensus size: 21
21423 AGTCTAAATT
*
21433 CGTTGCGATAGTCCAAGTTCA
1 CGTTGCGATAGTCCAAGTTCG
*
21454 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
** *
21475 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCG
*
21494 CGTTGCGATAGTCTAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
*
21515 CGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
* * **
21536 CATTGTGATTTTCCAAGTT--
1 CGTTGCGATAGTCCAAGTTCG
*
21555 TGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
** *
21576 CGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAGTTCG
21595 CGTTGCGATA----AA-TT--
1 CGTTGCGATAGTCCAAGTTCG
21609 CGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAGTTCG
21630 CGTTGCGAT
1 CGTTGCGAT
21639 TTTCCAAATT
Statistics
Matches: 148, Mismatches: 26, Indels: 22
0.76 0.13 0.11
Matches are distributed among these distances:
14 12 0.08
15 2 0.01
18 2 0.01
19 40 0.27
21 92 0.62
ACGTcount: A:0.20, C:0.20, G:0.25, T:0.34
Consensus pattern (21 bp):
CGTTGCGATAGTCCAAGTTCG
Found at i:21498 original size:40 final size:40
Alignment explanation
Indices: 21433--21657 Score: 180
Period size: 40 Copynumber: 5.7 Consensus size: 40
21423 AGTCTAAATT
* *
21433 CGTTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCG
1 CGTTGCGATAGTCCAAATT--CGTTGCGATAGTCCAAGTTCG
** *
21475 CGTTGCGATTTTCCAAATTCGTTGCGATAGTCTAAGTTCG
1 CGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAAGTTCG
* * * **
21515 CGTTGCGATAGTCGAAGTTCGCATTGTGATTTTCCAAGTT--
1 CGTTGCGATAGTCCAAATTCG--TTGCGATAGTCCAAGTTCG
* * ** *
21555 TGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--
1 CGTTGCGATAGTCCAAATT--CGTTGCGATAGTCCAAGTTCG
21595 CGTTGCG--A-T--AAATTCGTTGCGATAGTCCAAGTTCG
1 CGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAAGTTCG
**
21630 CGTTGCGATTTTCCAAATTCGTTGCGAT
1 CGTTGCGATAGTCCAAATTCGTTGCGAT
21658 TTTATCGCAA
Statistics
Matches: 150, Mismatches: 22, Indels: 24
0.77 0.11 0.12
Matches are distributed among these distances:
33 16 0.11
35 11 0.07
37 1 0.01
38 2 0.01
40 89 0.59
42 31 0.21
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (40 bp):
CGTTGCGATAGTCCAAATTCGTTGCGATAGTCCAAGTTCG
Found at i:21523 original size:61 final size:61
Alignment explanation
Indices: 21428--21638 Score: 283
Period size: 61 Copynumber: 3.6 Consensus size: 61
21418 ACGTTAGTCT
*
21428 AAATTCGTTGCGATAGTCCAAGTTCACGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCC
1 AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCC
* * *
21489 AAATTCGTTGCGATAGTCTAAGTTCGCGTTGCGATAGTCGAAGTTCGCATTGTGATTTTCC
1 AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCC
* * ** * *
21550 AAGTTTGTTGCGATAGTCCAAGTTCGCGTTGCGATTTTCCAAATT--CGTTGCGA---T--
1 AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCC
21604 AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGAT
1 AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGAT
21639 TTTCCAAATT
Statistics
Matches: 135, Mismatches: 15, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
54 33 0.24
56 1 0.01
59 6 0.04
61 95 0.70
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (61 bp):
AAATTCGTTGCGATAGTCCAAGTTCGCGTTGCGATAGTCGAAGTTCGCGTTGCGATTTTCC
Found at i:21609 original size:14 final size:14
Alignment explanation
Indices: 21590--21618 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
21580 GCGATTTTCC
21590 AAATTCGTTGCGAT
1 AAATTCGTTGCGAT
21604 AAATTCGTTGCGAT
1 AAATTCGTTGCGAT
21618 A
1 A
21619 GTCCAAGTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.14, G:0.21, T:0.34
Consensus pattern (14 bp):
AAATTCGTTGCGAT
Found at i:21644 original size:21 final size:19
Alignment explanation
Indices: 21475--21660 Score: 112
Period size: 21 Copynumber: 9.6 Consensus size: 19
21465 TCGAAGTTCG
21475 CGTTGCGATTTTCCAAATT
1 CGTTGCGATTTTCCAAATT
** * *
21494 CGTTGCGATAGTCTAAGTT
1 CGTTGCGATTTTCCAAATT
** * *
21513 CGCGTTGCGATAGTCGAAGTT
1 --CGTTGCGATTTTCCAAATT
* *
21534 CGCATTGTGATTTTCCAAGTT
1 CG--TTGCGATTTTCCAAATT
* ** *
21555 TGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
21574 CGCGTTGCGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
21595 CGTTGCGA---T--AAATT
1 CGTTGCGATTTTCCAAATT
** *
21609 CGTTGCGATAGTCCAAGTT
1 CGTTGCGATTTTCCAAATT
21628 CGCGTTGCGATTTTCCAAATT
1 --CGTTGCGATTTTCCAAATT
21649 CGTTGCGATTTT
1 CGTTGCGATTTT
21661 ATCGCAACGA
Statistics
Matches: 133, Mismatches: 21, Indels: 26
0.74 0.12 0.14
Matches are distributed among these distances:
14 13 0.10
16 1 0.01
17 1 0.01
19 55 0.41
21 63 0.47
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (19 bp):
CGTTGCGATTTTCCAAATT
Found at i:22084 original size:19 final size:20
Alignment explanation
Indices: 22059--22149 Score: 105
Period size: 19 Copynumber: 4.4 Consensus size: 20
22049 CTTATTTTGG
22059 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
22079 -TTTTTCACTATCGCAACAAC
1 ATTTTTCACTATCGCAAC-AC
22099 ACGTTTTTCAAACTATCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
* *
22123 A-TTTTAACTATCACAACAC
1 ATTTTTCACTATCGCAACAC
22142 ATTTTTCA
1 ATTTTTCA
22150 AAATCGCGTT
Statistics
Matches: 61, Mismatches: 3, Indels: 14
0.78 0.04 0.18
Matches are distributed among these distances:
19 30 0.49
20 7 0.11
21 4 0.07
23 6 0.10
24 3 0.05
25 11 0.18
ACGTcount: A:0.33, C:0.27, G:0.04, T:0.35
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:22121 original size:44 final size:41
Alignment explanation
Indices: 22059--22151 Score: 118
Period size: 44 Copynumber: 2.2 Consensus size: 41
22049 CTTATTTTGG
* *
22059 ATTTTTC--ACTATCGCAACACTTTTTCACTATCGCAACAACAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTAT--C-ACAACAC
*
22101 GTTTTTCAAACTATCGCAACACATTTTAACTATCACAACAC
1 ATTTTTCAAACTATCGCAACACATTTTAACTATCACAACAC
22142 ATTTTTCAAA
1 ATTTTTCAAA
22152 ATCGCGTTGC
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
41 16 0.36
42 7 0.16
44 22 0.49
ACGTcount: A:0.34, C:0.27, G:0.04, T:0.34
Consensus pattern (41 bp):
ATTTTTCAAACTATCGCAACACATTTTAACTATCACAACAC
Found at i:23436 original size:20 final size:20
Alignment explanation
Indices: 23411--23470 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
23401 TAAAACTGAT
23411 AGTACAAATATCAAAATTTA
1 AGTACAAATATCAAAATTTA
*
23431 AGTACAAAT-TCTAGAATTTTA
1 AGTACAAATATC-A-AAATTTA
* *
23452 A-TATAAATATAAAAATTTA
1 AGTACAAATATCAAAATTTA
23471 TTATTAAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
19 8 0.24
20 17 0.52
21 8 0.24
ACGTcount: A:0.53, C:0.07, G:0.05, T:0.35
Consensus pattern (20 bp):
AGTACAAATATCAAAATTTA
Found at i:24040 original size:2 final size:2
Alignment explanation
Indices: 24033--24062 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
24023 ATGATGAATA
24033 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
24063 ACTCATCTAG
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:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:24590 original size:6 final size:6
Alignment explanation
Indices: 24579--24651 Score: 119
Period size: 6 Copynumber: 12.2 Consensus size: 6
24569 ACGGCTCGGC
* * *
24579 TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG TCGTGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
24627 TCGTGG TCGTGG TCGTGG TCGTGG T
1 TCGTGG TCGTGG TCGTGG TCGTGG T
24652 AATACGTGTC
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 65 1.00
ACGTcount: A:0.04, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:24951 original size:22 final size:22
Alignment explanation
Indices: 24926--24980 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
24916 TCAGGAGTTA
* *
24926 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
24948 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
24970 CGGGAGTTATA
1 CAGGAGTTATA
24981 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:30527 original size:5 final size:5
Alignment explanation
Indices: 30513--30561 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
30503 GTCCGTCCGT
* * * *
30513 CTCGT CTCGG CTCGG CACGG CACGG CACGG CTCGG CTCGG CTCGG CTCG
1 CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCGG CTCG
30562 TGGTCGTGGT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 41 1.00
ACGTcount: A:0.06, C:0.41, G:0.37, T:0.16
Consensus pattern (5 bp):
CTCGG
Found at i:30570 original size:6 final size:6
Alignment explanation
Indices: 30559--30619 Score: 95
Period size: 6 Copynumber: 10.2 Consensus size: 6
30549 TCGGCTCGGC
* * *
30559 TCGTGG TCGTGG TCGTGG TCGTGG TCGAGG TCGAGG TCGAGG TCGTGG
1 TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG TCGTGG
30607 TCGTGG TCGTGG T
1 TCGTGG TCGTGG T
30620 AATACGTGTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.05, C:0.16, G:0.49, T:0.30
Consensus pattern (6 bp):
TCGTGG
Found at i:30919 original size:22 final size:22
Alignment explanation
Indices: 30894--30948 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
30884 TCAGGAGTTA
* *
30894 CAGGAGTTATTTGATTTAATTC
1 CAGGAGTTATATGATATAATTC
* * *
30916 CAGGGGTTACATGATATAATTT
1 CAGGAGTTATATGATATAATTC
*
30938 CGGGAGTTATA
1 CAGGAGTTATA
30949 ACAGCTGAAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.29, C:0.09, G:0.24, T:0.38
Consensus pattern (22 bp):
CAGGAGTTATATGATATAATTC
Found at i:35888 original size:18 final size:19
Alignment explanation
Indices: 35865--35908 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
35855 TCAGTAATCC
*
35865 TATTCC-CTGGTAATCTTT
1 TATTCCACTGGTAATCTTA
35883 TATTCCCACTGGTAATCTTA
1 TATT-CCACTGGTAATCTTA
35903 TATTCC
1 TATTCC
35909 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 4 0.17
19 4 0.17
20 15 0.65
ACGTcount: A:0.20, C:0.25, G:0.09, T:0.45
Consensus pattern (19 bp):
TATTCCACTGGTAATCTTA
Found at i:35896 original size:20 final size:20
Alignment explanation
Indices: 35871--35908 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
35861 ATCCTATTCC
*
35871 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTATATTCCCA
35891 CTGGTAATCTTATATTCC
1 CTGGTAATCTTATATTCC
35909 GTGAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.21, C:0.24, G:0.11, T:0.45
Consensus pattern (20 bp):
CTGGTAATCTTATATTCCCA
Found at i:39740 original size:42 final size:41
Alignment explanation
Indices: 39602--39810 Score: 355
Period size: 42 Copynumber: 5.0 Consensus size: 41
39592 CTAGGAAAAT
39602 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAAAC
1 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAAAC
* *
39643 TGTAAGGCTTACCCTTGCACACAACAAAGGAACCTGGGAAC
1 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAAAC
39684 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGTAAAC
1 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGG-AAAC
* *
39726 TGTAAGGCTTACCCTTGCACACAACAAAGAAACCTGGGAAAC
1 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGAAAC
39768 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAAC
1 TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGAAAC
39810 T
1 T
39811 TCCTTCAATC
Statistics
Matches: 158, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
41 75 0.47
42 81 0.51
43 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.22, T:0.18
Consensus pattern (41 bp):
TGTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAAAC
Found at i:40717 original size:13 final size:14
Alignment explanation
Indices: 40699--40733 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
40689 AACAGTCAAT
40699 GGTCAACGGA-TCA
1 GGTCAACGGAGTCA
40712 GGTCAAC-GAGTCA
1 GGTCAACGGAGTCA
40725 GGTCAACGG
1 GGTCAACGG
40734 GTCGGGTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 2 0.10
13 17 0.85
14 1 0.05
ACGTcount: A:0.29, C:0.23, G:0.34, T:0.14
Consensus pattern (14 bp):
GGTCAACGGAGTCA
Found at i:47302 original size:543 final size:541
Alignment explanation
Indices: 46402--48054 Score: 2354
Period size: 543 Copynumber: 3.0 Consensus size: 541
46392 AGACCCGGCT
* * *
46402 TGAACGCTAGGCCTAAACCTAAGCAGTCACATATCCCATTCAGAGATTCTTTTTATATTTAAAAC
1 TGAACGCTAGGCCCAAACCTAAGCAGTCACATATCACATTCAAAGATTCTTTTTATATTTAAAAC
*
46467 AATGTTGAAATCCATGTTTCATTAATATATATATGAAATTTATCCCTAATAAAGATTTATATAAT
66 AACGTTGAAATCCATGTTTCATTAATATATATATGAAATTTATCCCTAATAAAGATTTATATAAT
* * *
46532 AAACATATATGA-ACA-CATTTTAGAAAACCATATAAAACATTTACAGAACAAAATATCAGTAAT
131 AAACTTATATGACACATAATTTTAGAAAACCATATAAAACATTTACGGAACAAAATATCAGTAAT
* *
46595 ACGAATATATCCAATACGATAGCAAAATGCATGTCACCAAATACAAATGAAAACATATAAGAATA
196 ACGAATATATCCAATACGATAGCAAAATACATGTCACCAAATACAACTGAAAACATATAAGAATA
* *
46660 TACTTTCGTACAAAGTAAAAGTAGTTGATCTCCCCTGATGCCAAATCTGCTAGCTTACGGTCTGT
261 TACGTTCGTACAAAGTAAAAGTAGTTGATCTCCCCTGATGCCAAATCTGCTAGCTTACGGTCTGC
* * * *
46725 TGTTATCTGAAAAGGGTAAAATGTACATAATGAGCTAAAAAGGCCAGTATGCTCTTGTGGTGTAT
326 TGTTATCTGAAAAAGGTAAAATTTACAAAATGAGCTAAAAAGCCCAGTATGCTCTTGTGGTGTAT
* *
46790 AAAAGCATACAAATCAAAGTAATTCAGAAGAAAACTCAATTTATCAAAACATGTTTTAAAAACAA
391 AAAA-CATACAGATCAAAGTAATTCAGAAGAAAACTCAATTTATCAAAACATGTTTTAAAAACAT
*
46855 GAACACTACCCCCATCCAATCACCAGAATGTGTAGGTTCACCCGAACCATACACCCACCTGTATA
455 GAACACTACCCCCATCCAATCACCAGAATGTGTAGGTTCACCCGAACCATACACCCACCTGTACA
*
46920 CCGGTAAGGCTTAACATGTGCC
520 CCGGTAAGGCTTAACCTGTGCC
* * * *
46942 TGAACGCTAGCCCCAAACCTAAGCAGTAACATATCACATTCATAGATTCTTTTTATATTTAAAAG
1 TGAACGCTAGGCCCAAACCTAAGCAGTCACATATCACATTCAAAGATTCTTTTTATATTTAAAAC
*
47007 AACGTTGAAATCCATGTTTCATTAATATATATATGAAATTTATCCCTAATAAAGATTTATATGAT
66 AACGTTGAAATCCATGTTTCATTAATATATATATGAAATTTATCCCTAATAAAGATTTATATAAT
*
47072 AAACTTATATGAGCACATAATTTTAGAAAACCATATAAAACATTTACGGGACAAAATATCAGTAA
131 AAACTTATATGA-CACATAATTTTAGAAAACCATATAAAACATTTACGGAACAAAATATCAGTAA
47137 TACGAATATATCCAATACGATAGCAAAATACATGTCACCAAATACAACTGAAAACATATAAGAAT
195 TACGAATATATCCAATACGATAGCAAAATACATGTCACCAAATACAACTGAAAACATATAAGAAT
* **
47202 ATACGTTCGTACAAAGTAAAAGTAGTTGATCTCCCCTGATGCCAAATCTACTAGCTTACAATCTG
260 ATACGTTCGTACAAAGTAAAAGTAGTTGATCTCCCCTGATGCCAAATCTGCTAGCTTACGGTCTG
* * *
47267 CTATTATCTGAAAAAGGTAAAATTTACAGAATGAGCTAAAAAGCCCAATATGCTCTTGTGGTGTA
325 CTGTTATCTGAAAAAGGTAAAATTTACAAAATGAGCTAAAAAGCCCAGTATGCTCTTGTGGTGTA
*
47332 TAAAAACATACAGATCAAAGTAATTTAGAAGAAAACTCAATTTATCAAAACATGTTTTAAAAACA
390 T-AAAACATACAGATCAAAGTAATTCAGAAGAAAACTCAATTTATCAAAACATGTTTTAAAAACA
* *
47397 TGAACACTACCCCCATCCAATCACCAGAATGTGTAGGTTGACCCGAACCATACACCCACTTGTAC
454 TGAACACTACCCCCATCCAATCACCAGAATGTGTAGGTTCACCCGAACCATACACCCACCTGTAC
*
47462 ACCGGTAAGGCTTAACCTGTGCT
519 ACCGGTAAGGCTTAACCTGTGCC
*
47485 TGAACGCTAGGCCCAAACCTAAGCAGTCACATAT-ACCATTCAAATATTCTTTTTATATTTAAAA
1 TGAACGCTAGGCCCAAACCTAAGCAGTCACATATCA-CATTCAAAGATTCTTTTTATATTTAAAA
* * * ***
47549 CAACGTTGAAATCTATGTCATTAATATATATATATATATATATATATATATATATATATATATAT
65 CAACGTTGAAATCCATG---TT--T-CAT-TA-ATATATATAT-GA-A-AT-T-TATCCCTA-AT
* *
47614 ATATATGAAATTTATCCCTAATAAAGATTTATATGATAAACATATGAACACATAATTTTAGAAAA
116 A-A-A-G--ATTTAT--ATAAT-AA-A-CT-TAT-AT--------G-ACACATAATTTTAGAAAA
47679 CCATATAAAACATTTACGGAAC-AAA-ATCAGTAATACGAATATATCCAATACGATAGCAAAATA
160 CCATATAAAACATTTACGGAACAAAATATCAGTAATACGAATATATCCAATACGATAGCAAAATA
* *
47742 CATGTCACCAAATACAACAG-AAACATAT---AATACACGTTCGTACAAAGTAAAAGTAGTTGAT
225 CATGTCACCAAATACAACTGAAAACATATAAGAATATACGTTCGTACAAAGTAAAAGTAGTTGAT
* * *
47803 CTCCCTTGATACCAAATATGCTAGCTTACGGTCTGCTGTTATCT-AAAAAGGGTAAAATTTACAA
290 CTCCCCTGATGCCAAATCTGCTAGCTTACGGTCTGCTGTTATCTGAAAAA-GGTAAAATTTACAA
* * *
47867 AATGAGATAAAAAGTCCAGTGTGCTCTTGTGGTGTATACAAACATACAGATCAAAGTAATTCAGA
354 AATGAGCTAAAAAGCCCAGTATGCTCTTGTGGTGTATA-AAACATACAGATCAAAGTAATTCAGA
*
47932 AGAAAACTCAATTTATCAAAACATATTTTAAAAACATGAACACTACCCCCATCCAATCACCAGAA
418 AGAAAACTCAATTTATCAAAACATGTTTTAAAAACATGAACACTACCCCCATCCAATCACCAGAA
* * * *
47997 TGTTTAGGTTTACCCGAACAATACACCCACCTGTACACCGGTAAGGCTTCACCTGTGC
483 TGTGTAGGTTCACCCGAACCATACACCCACCTGTACACCGGTAAGGCTTAACCTGTGC
48055 ACAAAGCAGA
Statistics
Matches: 1002, Mismatches: 69, Indels: 53
0.89 0.06 0.05
Matches are distributed among these distances:
540 133 0.13
542 4 0.00
543 439 0.44
544 4 0.00
546 2 0.00
548 1 0.00
549 2 0.00
550 2 0.00
551 10 0.01
552 1 0.00
553 1 0.00
554 2 0.00
555 1 0.00
556 5 0.00
557 3 0.00
558 1 0.00
559 1 0.00
560 1 0.00
562 6 0.01
564 3 0.00
565 2 0.00
566 1 0.00
567 1 0.00
568 3 0.00
569 2 0.00
570 6 0.01
571 257 0.26
574 8 0.01
575 57 0.06
576 3 0.00
577 39 0.04
578 1 0.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (541 bp):
TGAACGCTAGGCCCAAACCTAAGCAGTCACATATCACATTCAAAGATTCTTTTTATATTTAAAAC
AACGTTGAAATCCATGTTTCATTAATATATATATGAAATTTATCCCTAATAAAGATTTATATAAT
AAACTTATATGACACATAATTTTAGAAAACCATATAAAACATTTACGGAACAAAATATCAGTAAT
ACGAATATATCCAATACGATAGCAAAATACATGTCACCAAATACAACTGAAAACATATAAGAATA
TACGTTCGTACAAAGTAAAAGTAGTTGATCTCCCCTGATGCCAAATCTGCTAGCTTACGGTCTGC
TGTTATCTGAAAAAGGTAAAATTTACAAAATGAGCTAAAAAGCCCAGTATGCTCTTGTGGTGTAT
AAAACATACAGATCAAAGTAATTCAGAAGAAAACTCAATTTATCAAAACATGTTTTAAAAACATG
AACACTACCCCCATCCAATCACCAGAATGTGTAGGTTCACCCGAACCATACACCCACCTGTACAC
CGGTAAGGCTTAACCTGTGCC
Found at i:47579 original size:2 final size:2
Alignment explanation
Indices: 47572--47619 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
47562 TATGTCATTA
47572 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47614 AT AT AT
1 AT AT AT
47620 GAAATTTATC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:48132 original size:42 final size:41
Alignment explanation
Indices: 48037--48290 Score: 321
Period size: 42 Copynumber: 6.0 Consensus size: 41
48027 CTGTACACCG
* * *
48037 GTAAGGCTT-CACCTGTGCACAAAGCAGAGGAGCCTAGGAAAACT
1 GTAAGGCTTAC-CCT-TGCACACAGCAAAGGAACCT-GG-AAACT
*
48081 GTAAGGCTTACCCTTGCACACAGCAAATGAACCTAGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGAAACT
48123 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGAGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG-GAAACT
* * *
48165 GTAAGACTTACCCTTGTACACAACAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGAAACT
* * *
48207 GTAAGGCTTACCCGTGCACATAACAAAGGAACCTGTGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTG-GAAACT
*
48249 ATAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGGAAACT
1 GTAAGGCTTACCCTTGCACACAGCAAAGGAACCT-GGAAACT
48291 TCCTTCAATG
Statistics
Matches: 189, Mismatches: 16, Indels: 12
0.87 0.07 0.06
Matches are distributed among these distances:
41 2 0.01
42 153 0.81
43 21 0.11
44 12 0.06
45 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.18
Consensus pattern (41 bp):
GTAAGGCTTACCCTTGCACACAGCAAAGGAACCTGGAAACT
Found at i:51290 original size:18 final size:18
Alignment explanation
Indices: 51267--51311 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
51257 TTTCAAGACA
51267 AGACACCCAAATTAAATG
1 AGACACCCAAATTAAATG
51285 AGACACCCAAATTAAATG
1 AGACACCCAAATTAAATG
51303 AGACACCCA
1 AGACACCCA
51312 GACTTAACAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.49, C:0.27, G:0.11, T:0.13
Consensus pattern (18 bp):
AGACACCCAAATTAAATG
Found at i:54806 original size:62 final size:62
Alignment explanation
Indices: 54729--54858 Score: 235
Period size: 62 Copynumber: 2.1 Consensus size: 62
54719 TAATTTTATA
*
54729 TTTTC-TATCTCATGTATGTTGAAAATATGTTATGATGAATATTTTCTAAAGTTTTAATGAT
1 TTTTCATATCTCATGTATGTTGAAAATATGTTATGACGAATATTTTCTAAAGTTTTAATGAT
*
54790 TTTTCATATCTCATGTATGTTGAAAATATGTTATGACGAATATTTTCTAAAGTTTTAATTAT
1 TTTTCATATCTCATGTATGTTGAAAATATGTTATGACGAATATTTTCTAAAGTTTTAATGAT
54852 TTTTCAT
1 TTTTCAT
54859 GAATGTTTGT
Statistics
Matches: 66, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
61 5 0.08
62 61 0.92
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.50
Consensus pattern (62 bp):
TTTTCATATCTCATGTATGTTGAAAATATGTTATGACGAATATTTTCTAAAGTTTTAATGAT
Found at i:55139 original size:11 final size:11
Alignment explanation
Indices: 55123--55185 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
55113 AAAATTACAT
55123 TATTAAAAATA
1 TATTAAAAATA
55134 TATTAAAAATA
1 TATTAAAAATA
* * ***
55145 CACTATTGATA
1 TATTAAAAATA
55156 -ATTATAAAAT-
1 TATTA-AAAATA
55166 T-TTAAAAATA
1 TATTAAAAATA
55176 TATTAAAAAT
1 TATTAAAAAT
55186 TCTTCAATAC
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.57, C:0.03, G:0.02, T:0.38
Consensus pattern (11 bp):
TATTAAAAATA
Found at i:55248 original size:7 final size:7
Alignment explanation
Indices: 55232--55261 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
55222 CTTTATAATG
55232 AACCCTA
1 AACCCTA
*
55239 AACTCTA
1 AACCCTA
55246 AACCCTA
1 AACCCTA
55253 AACCCTA
1 AACCCTA
55260 AA
1 AA
55262 TTGTACTTAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.47, C:0.37, G:0.00, T:0.17
Consensus pattern (7 bp):
AACCCTA
Found at i:55345 original size:14 final size:14
Alignment explanation
Indices: 55328--55381 Score: 81
Period size: 14 Copynumber: 3.9 Consensus size: 14
55318 CTCTAATCCC
55328 TAAACCCTAAACTA
1 TAAACCCTAAACTA
55342 TAAACCCTAAACTA
1 TAAACCCTAAACTA
* * *
55356 TGAACTCTAAATTA
1 TAAACCCTAAACTA
55370 TAAACCCTAAAC
1 TAAACCCTAAAC
55382 CCGATTATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 34 1.00
ACGTcount: A:0.48, C:0.26, G:0.02, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACTA
Found at i:55361 original size:21 final size:21
Alignment explanation
Indices: 55313--55366 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
55303 TGTCTTTATA
*
55313 ATGAACTCTAATCCCTAAACC
1 ATGAACTCTAAACCCTAAACC
* * * *
55334 CTAAACTATAAACCCTAAACT
1 ATGAACTCTAAACCCTAAACC
55355 ATGAACTCTAAA
1 ATGAACTCTAAA
55367 TTATAAACCC
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.44, C:0.28, G:0.04, T:0.24
Consensus pattern (21 bp):
ATGAACTCTAAACCCTAAACC
Found at i:57844 original size:18 final size:17
Alignment explanation
Indices: 57816--57856 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
57806 TGGTTGATAG
57816 TTTTTTGGTCTTTT-TT
1 TTTTTTGGTCTTTTCTT
57832 TTCTTTTGTGTCTTTTCTT
1 TT-TTTTG-GTCTTTTCTT
57851 TTTTTT
1 TTTTTT
57857 TTTTGTGATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 2 0.09
17 5 0.23
18 11 0.50
19 4 0.18
ACGTcount: A:0.00, C:0.10, G:0.10, T:0.80
Consensus pattern (17 bp):
TTTTTTGGTCTTTTCTT
Found at i:60347 original size:2 final size:2
Alignment explanation
Indices: 60340--60371 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60330 ATGTACATCC
60340 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
60372 TGGATACTGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60742 original size:22 final size:21
Alignment explanation
Indices: 60714--60792 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
60704 GTTCTTAAGG
60714 AGTGGTCCTTCGGGACATATA
1 AGTGGTCCTTCGGGACATATA
60735 CAGTGGTCCTTCGGGAC--AT-
1 -AGTGGTCCTTCGGGACATATA
* *
60754 AGTAGTCCTTCGGGACATACA
1 AGTGGTCCTTCGGGACATATA
* *
60775 TAGTGGTCTTTCAGGACA
1 -AGTGGTCCTTCGGGACA
60793 AATATTCAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
18 15 0.31
20 3 0.06
22 30 0.62
ACGTcount: A:0.23, C:0.22, G:0.28, T:0.28
Consensus pattern (21 bp):
AGTGGTCCTTCGGGACATATA
Found at i:63600 original size:17 final size:17
Alignment explanation
Indices: 63580--63613 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
63570 ATAAAATAGT
63580 AATATA-AATATTATAAC
1 AATATAGAAT-TTATAAC
63597 AATATAGAATTTATAAC
1 AATATAGAATTTATAAC
63614 TTTCTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (17 bp):
AATATAGAATTTATAAC
Found at i:64185 original size:93 final size:95
Alignment explanation
Indices: 63992--64202 Score: 270
Period size: 97 Copynumber: 2.2 Consensus size: 95
63982 GGAACCTAAA
*
63992 AAAT-AACAAT-ATATTTTAACTACCGAAAACGTTTGTTTCGTGTAATAAAGATTAAATGTTTAT
1 AAATCAACAATAATATTTTAACTACCGAAAACGTTTATTTCGTGTAATAAAGA-T--ATGTTTAT
* * *
64055 CCTTTTGGGCTATTCTTTTTTATTTGGTGTGAT
63 CCTTTTGGGCTATTATTATTTATTTAGTGTGAT
* * *
64088 AAATCGACAATAAT-TTTTAACTACTGAAAATGTTTATTTCGTGTAATAAAG-T-TGTTTATCCT
1 AAATCAACAATAATATTTTAACTACCGAAAACGTTTATTTCGTGTAATAAAGATATGTTTATCC-
*
64150 TTTTGGGCTATTATTATTTATTTATTGTGAT
65 TTTTGGGCTATTATTATTTATTTAGTGTGAT
64181 AAATCAACAATAAATATTTTAA
1 AAATCAACAAT-AATATTTTAA
64203 AAAATATCTA
Statistics
Matches: 101, Mismatches: 9, Indels: 11
0.83 0.07 0.09
Matches are distributed among these distances:
92 9 0.09
93 37 0.37
94 3 0.03
95 7 0.07
96 4 0.04
97 39 0.39
98 2 0.02
ACGTcount: A:0.33, C:0.09, G:0.12, T:0.45
Consensus pattern (95 bp):
AAATCAACAATAATATTTTAACTACCGAAAACGTTTATTTCGTGTAATAAAGATATGTTTATCCT
TTTGGGCTATTATTATTTATTTAGTGTGAT
Found at i:65138 original size:2 final size:2
Alignment explanation
Indices: 65131--65181 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
65121 AATTACTCAA
65131 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
65173 AT AT AT AT A
1 AT AT AT AT A
65182 CTAAGTCCAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:65221 original size:2 final size:2
Alignment explanation
Indices: 65214--65253 Score: 66
Period size: 2 Copynumber: 21.0 Consensus size: 2
65204 AGACTTAAAT
65214 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65254 ATTTCCCAGT
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.06
2 34 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:68104 original size:16 final size:16
Alignment explanation
Indices: 68079--68109 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
68069 ACCTTATTCT
68079 ATGGTATCTACCCAAC
1 ATGGTATCTACCCAAC
*
68095 ATGGTGTCTACCCAA
1 ATGGTATCTACCCAA
68110 TCATACTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.29, C:0.29, G:0.16, T:0.26
Consensus pattern (16 bp):
ATGGTATCTACCCAAC
Done.