Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014604.1 Corchorus olitorius cultivar O-4 contig14637, 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: 108910
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.34
Found at i:7839 original size:19 final size:20
Alignment explanation
Indices: 7815--7857 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
7805 CAAAAGTTAC
*
7815 AATTATTAAG-CAAA-AAATT
1 AATTA-TAAGTCAAATAAAAT
7834 AATTATAAGTCAAATAAAAT
1 AATTATAAGTCAAATAAAAT
7854 AATT
1 AATT
7858 GCACGTCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 4 0.19
19 9 0.43
20 8 0.38
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (20 bp):
AATTATAAGTCAAATAAAAT
Found at i:9043 original size:19 final size:22
Alignment explanation
Indices: 8999--9041 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
8989 ATAGATTTTT
*
8999 TAATAATATCATCAAAGAAATA
1 TAATAATATAATCAAAGAAATA
*
9021 TAATAATATAAT-AAAAAAATA
1 TAATAATATAATCAAAGAAATA
9042 ATGTCAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.65, C:0.05, G:0.02, T:0.28
Consensus pattern (22 bp):
TAATAATATAATCAAAGAAATA
Found at i:17180 original size:60 final size:60
Alignment explanation
Indices: 17109--17225 Score: 182
Period size: 60 Copynumber: 1.9 Consensus size: 60
17099 GCATTTCCAT
* * * *
17109 ATACATTAGGGCTCTATTTAACCAAATTAAAAGTA-CGGGCCCTAAATTGAGTATTTTCGC
1 ATACATTAGGGCCCTATTTAACCAAATTAAAAGCATC-GGCACTAAATTAAGTATTTTCGC
17169 ATACATTAGGGCCCTATTTAACCAAATTAAAAGCATCGGCACTAAATTAAGTATTTT
1 ATACATTAGGGCCCTATTTAACCAAATTAAAAGCATCGGCACTAAATTAAGTATTTT
17226 TACATACGTT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
60 51 0.98
61 1 0.02
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (60 bp):
ATACATTAGGGCCCTATTTAACCAAATTAAAAGCATCGGCACTAAATTAAGTATTTTCGC
Found at i:17472 original size:85 final size:84
Alignment explanation
Indices: 17330--17499 Score: 313
Period size: 85 Copynumber: 2.0 Consensus size: 84
17320 CACTACGTGA
17330 GTGGTTTATGACAGTTTTTTTTTCAATAGGTAGTTTTTTTAAAATGATATAAATAAATTTAAATA
1 GTGGTTTATGACAGTTTTTTTTTCAATAGGTAGTTTTTTTAAAATGATATAAATAAATTTAAATA
*
17395 TTATATTTATTCTCTAATG
66 TTATATTTATCCTCTAATG
*
17414 GTGGTTTATGACAGTTTTTTATTTCAATAGGTTGTTTTTTTAAAATGATATAAATAAATTTAAAT
1 GTGGTTTATGACAGTTTTTT-TTTCAATAGGTAGTTTTTTTAAAATGATATAAATAAATTTAAAT
17479 ATTATATTTATCCTCTAATG
65 ATTATATTTATCCTCTAATG
17499 G
1 G
17500 GTAGTTTTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
84 20 0.24
85 63 0.76
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.49
Consensus pattern (84 bp):
GTGGTTTATGACAGTTTTTTTTTCAATAGGTAGTTTTTTTAAAATGATATAAATAAATTTAAATA
TTATATTTATCCTCTAATG
Found at i:20282 original size:31 final size:31
Alignment explanation
Indices: 20241--20306 Score: 123
Period size: 31 Copynumber: 2.1 Consensus size: 31
20231 TAACATTAGC
20241 TTTTTAATTCATACAATTTGGTCCCATCCGG
1 TTTTTAATTCATACAATTTGGTCCCATCCGG
*
20272 TTTTTGATTCATACAATTTGGTCCCATCCGG
1 TTTTTAATTCATACAATTTGGTCCCATCCGG
20303 TTTT
1 TTTT
20307 GGTAACTACG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.20, C:0.21, G:0.14, T:0.45
Consensus pattern (31 bp):
TTTTTAATTCATACAATTTGGTCCCATCCGG
Found at i:43981 original size:41 final size:41
Alignment explanation
Indices: 43924--44004 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
43914 TGGCCCATCA
*
43924 ATTCCTAGTTTAAAATGATTATTTCTAAATGAAATTATTCG
1 ATTCCTAGTTTAAAATGATTATTACTAAATGAAATTATTCG
* *
43965 ATTCCTTA-TTTAAAATGTTTGTTACTAAATGAAATTATTC
1 ATTCC-TAGTTTAAAATGATTATTACTAAATGAAATTATTC
44005 CTAGAAACAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 34 0.94
42 2 0.06
ACGTcount: A:0.36, C:0.10, G:0.09, T:0.46
Consensus pattern (41 bp):
ATTCCTAGTTTAAAATGATTATTACTAAATGAAATTATTCG
Found at i:52112 original size:31 final size:31
Alignment explanation
Indices: 52074--52135 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
52064 GAGTTTTGTA
*
52074 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
* *
52105 AAACTTTTGAATTGCCTATCGTACCCTTATT
1 AAACTTTTGAATCGCCTATCATACCCTTATT
52136 TTTCGAATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATCATACCCTTATT
Found at i:52278 original size:85 final size:85
Alignment explanation
Indices: 52171--52341 Score: 297
Period size: 85 Copynumber: 2.0 Consensus size: 85
52161 TTATTTAAAT
* *
52171 TTTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTACATCTAATATCCTTATAACTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
* *
52236 TTTTATTTTTACCATTTTAC
66 TTTTATTTTTACAATATTAC
*
52256 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTA
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
52321 TTTTATTTTTACAATATTAC
66 TTTTATTTTTACAATATTAC
52341 T
1 T
52342 AATTTAATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
85 81 1.00
ACGTcount: A:0.33, C:0.14, G:0.02, T:0.51
Consensus pattern (85 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTA
TTTTATTTTTACAATATTAC
Found at i:53065 original size:16 final size:16
Alignment explanation
Indices: 53025--53055 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
53015 TTGGCCTTAG
*
53025 GTCACTCGGGTTTTGA
1 GTCATTCGGGTTTTGA
53041 GTCATTCGGGTTTTG
1 GTCATTCGGGTTTTG
53056 GGTTTTTCGG
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:0.10, C:0.16, G:0.32, T:0.42
Consensus pattern (16 bp):
GTCATTCGGGTTTTGA
Found at i:53799 original size:31 final size:31
Alignment explanation
Indices: 53707--53806 Score: 89
Period size: 31 Copynumber: 3.3 Consensus size: 31
53697 AGAACCTAAA
* * * * *
53707 TAGTCCCTGTACTATCGAAAAAAGATCATTT
1 TAGTCCCTCTACTATTGGAAAACGATCAATT
* *
53738 TAGTCCCTCTATTA-T-GAAATCTG-TCAATT
1 TAGTCCCTCTACTATTGGAAAAC-GATCAATT
*
53767 TAGTCCCTTTACTATTGGAAAACGATCAATT
1 TAGTCCCTCTACTATTGGAAAACGATCAATT
*
53798 TAATCCCTC
1 TAGTCCCTC
53807 CGTTTAATTG
Statistics
Matches: 53, Mismatches: 12, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
29 20 0.38
30 3 0.06
31 30 0.57
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (31 bp):
TAGTCCCTCTACTATTGGAAAACGATCAATT
Found at i:54937 original size:22 final size:22
Alignment explanation
Indices: 54886--54943 Score: 62
Period size: 22 Copynumber: 2.5 Consensus size: 22
54876 ACTAAAAAAA
54886 TTAAAAATTAAAAAATCAGATTTC
1 TTAAAAA--AAAAAATCAGATTTC
** *
54910 CGAAAAAAAAAAATCAGATTTT
1 TTAAAAAAAAAAATCAGATTTC
*
54932 TTAAAATAAAAA
1 TTAAAAAAAAAA
54944 TTAATTTACA
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
22 23 0.82
24 5 0.18
ACGTcount: A:0.60, C:0.07, G:0.05, T:0.28
Consensus pattern (22 bp):
TTAAAAAAAAAAATCAGATTTC
Found at i:55084 original size:31 final size:30
Alignment explanation
Indices: 55049--55145 Score: 99
Period size: 31 Copynumber: 3.2 Consensus size: 30
55039 TTAAACAGAT
55049 GGACTAAATTGATCATTTTCCAATAGTAGAG
1 GGACTAAATTGATCATTTT-CAATAGTAGAG
* * *
55080 GGACTAAATTGA-CAGATTTC-ATAATGGAG
1 GGACTAAATTGATCA-TTTTCAATAGTAGAG
* * *
55109 GGACTAAAATGATCTTTTTTCAATAGTACAG
1 GGACTAAATTGATC-ATTTTCAATAGTAGAG
55140 GGACTA
1 GGACTA
55146 TTTAGGTTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 8
0.76 0.13 0.11
Matches are distributed among these distances:
29 18 0.34
30 8 0.15
31 27 0.51
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (30 bp):
GGACTAAATTGATCATTTTCAATAGTAGAG
Found at i:55439 original size:20 final size:19
Alignment explanation
Indices: 55416--55460 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
55406 AACTTGAGCT
*
55416 TTCAAGCTTTGTCTTGTCAC
1 TTCAAGCTTTGT-TTATCAC
*
55436 TTCAAATCTTTGTTTATCAC
1 TTC-AAGCTTTGTTTATCAC
55456 TTCAA
1 TTCAA
55461 TCGTAGGCCT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 2 0.09
20 12 0.55
21 8 0.36
ACGTcount: A:0.22, C:0.22, G:0.09, T:0.47
Consensus pattern (19 bp):
TTCAAGCTTTGTTTATCAC
Found at i:57886 original size:26 final size:28
Alignment explanation
Indices: 57841--57895 Score: 69
Period size: 26 Copynumber: 2.0 Consensus size: 28
57831 TTTTAGCGGT
*
57841 CATCTTTTTTCTTTAGAGAGTA-AAATC
1 CATCTTTTTTCTTTAGAGAGCACAAATC
**
57868 CATC-TTTTTCTTTTTAGAGCACAAATC
1 CATCTTTTTTCTTTAGAGAGCACAAATC
57895 C
1 C
57896 CACATGGCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
26 14 0.58
27 10 0.42
ACGTcount: A:0.27, C:0.20, G:0.09, T:0.44
Consensus pattern (28 bp):
CATCTTTTTTCTTTAGAGAGCACAAATC
Found at i:60971 original size:98 final size:98
Alignment explanation
Indices: 60797--60992 Score: 347
Period size: 98 Copynumber: 2.0 Consensus size: 98
60787 GGTTCGGGCT
*
60797 CTTCCTGCACTCTACCTAGATTTGAAATTCCGCTCATCGTTATCTTTCATTTAGTAGGTAATCTG
1 CTTCCTGCACTCTACCTAGATTTGAAATTCCGCTCATCGCTATCTTTCATTTAGTAGGTAATCTG
60862 TAAATTATGAAAAACTCACAAGTGAAAGTCCAA
66 TAAATTATGAAAAACTCACAAGTGAAAGTCCAA
* * *
60895 CTTCCTGCACTCTACTTAGATTTGAAATTCCGCTTATCGCTATCTTTCATTTGGTAGGTAATCTG
1 CTTCCTGCACTCTACCTAGATTTGAAATTCCGCTCATCGCTATCTTTCATTTAGTAGGTAATCTG
*
60960 TAAATTCTGAAAAACTCACAAGTGAAAGTCCAA
66 TAAATTATGAAAAACTCACAAGTGAAAGTCCAA
60993 TGGATCTGTA
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 93 1.00
ACGTcount: A:0.31, C:0.21, G:0.14, T:0.34
Consensus pattern (98 bp):
CTTCCTGCACTCTACCTAGATTTGAAATTCCGCTCATCGCTATCTTTCATTTAGTAGGTAATCTG
TAAATTATGAAAAACTCACAAGTGAAAGTCCAA
Found at i:65179 original size:19 final size:19
Alignment explanation
Indices: 65147--65192 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
65137 CATTAGAAAG
65147 AAATTG-GA-GTGCTTTAA
1 AAATTGCGATGTGCTTTAA
*
65164 AAATTGCGATGTGCTTTTA
1 AAATTGCGATGTGCTTTAA
65183 AAATTGCGAT
1 AAATTGCGAT
65193 AAGTTTTTGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 6 0.23
18 2 0.08
19 18 0.69
ACGTcount: A:0.33, C:0.09, G:0.22, T:0.37
Consensus pattern (19 bp):
AAATTGCGATGTGCTTTAA
Found at i:65200 original size:19 final size:19
Alignment explanation
Indices: 65157--65199 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
65147 AAATTGGAGT
* **
65157 GCTTTAAAAATTGCGATGT
1 GCTTTTAAAATTGCGATAA
65176 GCTTTTAAAATTGCGATAA
1 GCTTTTAAAATTGCGATAA
65195 G-TTTT
1 GCTTTT
65200 TGTTTGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
18 4 0.19
19 17 0.81
ACGTcount: A:0.30, C:0.09, G:0.19, T:0.42
Consensus pattern (19 bp):
GCTTTTAAAATTGCGATAA
Found at i:67180 original size:20 final size:19
Alignment explanation
Indices: 67147--67185 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
67137 TCAAGCTTCT
67147 CTTGTCACTCCAATTCTTTG
1 CTTGTCACTCCAA-TCTTTG
* *
67167 CTTGTTACTTCAATCTTTG
1 CTTGTCACTCCAATCTTTG
67186 GCCTCATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.15, C:0.26, G:0.10, T:0.49
Consensus pattern (19 bp):
CTTGTCACTCCAATCTTTG
Found at i:75010 original size:109 final size:109
Alignment explanation
Indices: 74819--75098 Score: 560
Period size: 109 Copynumber: 2.6 Consensus size: 109
74809 TAGACCTAAC
74819 CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAATTG
1 CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAATTG
74884 AGCATGAAAAAATGGAAGGAAATTAAGGGAAAAAGAACAAAAAA
66 AGCATGAAAAAATGGAAGGAAATTAAGGGAAAAAGAACAAAAAA
74928 CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAATTG
1 CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAATTG
74993 AGCATGAAAAAATGGAAGGAAATTAAGGGAAAAAGAACAAAAAA
66 AGCATGAAAAAATGGAAGGAAATTAAGGGAAAAAGAACAAAAAA
75037 CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAA
1 CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAA
75099 ACAAAAAAAA
Statistics
Matches: 171, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
109 171 1.00
ACGTcount: A:0.52, C:0.16, G:0.19, T:0.13
Consensus pattern (109 bp):
CCAGAAAGACACTCCAAAATGCATGCTGAACTGAGCAAAAAAACATGAACATGGACATCAAATTG
AGCATGAAAAAATGGAAGGAAATTAAGGGAAAAAGAACAAAAAA
Found at i:77906 original size:6 final size:6
Alignment explanation
Indices: 77895--77923 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
77885 TCCCTTTAAC
77895 AATGGA AATGGA AATGGA AATGGA AATGG
1 AATGGA AATGGA AATGGA AATGGA AATGG
77924 GGATGGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.34, T:0.17
Consensus pattern (6 bp):
AATGGA
Found at i:84337 original size:30 final size:29
Alignment explanation
Indices: 84271--84339 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
84261 CTGGTAGGAT
84271 GTTTTGCCCCATGAACTTCAATCTCGGAC
1 GTTTTGCCCCATGAACTTCAATCTCGGAC
* * * *
84300 ATTTTGCCCCATGAACTTGAATTTTGGAAC
1 GTTTTGCCCCATGAACTTCAATCTCGG-AC
84330 GTTTTGCCCC
1 GTTTTGCCCC
84340 CTCAACCTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 23 0.68
30 11 0.32
ACGTcount: A:0.20, C:0.28, G:0.17, T:0.35
Consensus pattern (29 bp):
GTTTTGCCCCATGAACTTCAATCTCGGAC
Found at i:87432 original size:28 final size:29
Alignment explanation
Indices: 87372--87435 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
87362 AAACCATCTT
*
87372 GAGGGTCAGAGACCAAGCCTGAGGGATTTC
1 GAGGGTCAGAGACCAAGCCAGAGGGA-TTC
*
87402 GAGGGTGAGAGACCAAGCCAGAGGGA-TC
1 GAGGGTCAGAGACCAAGCCAGAGGGATTC
87430 GAGGGT
1 GAGGGT
87436 TTAGAGAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 8 0.25
30 24 0.75
ACGTcount: A:0.28, C:0.17, G:0.42, T:0.12
Consensus pattern (29 bp):
GAGGGTCAGAGACCAAGCCAGAGGGATTC
Found at i:91612 original size:21 final size:21
Alignment explanation
Indices: 91586--91625 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
91576 CGCTGCTGTA
*
91586 ATAATCTCATCTATACAGTAT
1 ATAATCTAATCTATACAGTAT
*
91607 ATAATCTAATCTGTACAGT
1 ATAATCTAATCTATACAGT
91626 GTAATCTCAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.38, C:0.17, G:0.07, T:0.38
Consensus pattern (21 bp):
ATAATCTAATCTATACAGTAT
Found at i:91632 original size:19 final size:19
Alignment explanation
Indices: 91608--91644 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
91598 ATACAGTATA
*
91608 TAATCTAATCTGTACAGTG
1 TAATCTAATATGTACAGTG
*
91627 TAATCTCATATGTACAGT
1 TAATCTAATATGTACAGT
91645 TGTCAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (19 bp):
TAATCTAATATGTACAGTG
Found at i:97794 original size:29 final size:29
Alignment explanation
Indices: 97726--97810 Score: 116
Period size: 29 Copynumber: 2.9 Consensus size: 29
97716 ACGGCATCCG
*
97726 ATATGGCACGCCATGTGTACCAAAAAGGAC
1 ATATGGCACGCCACGTGTA-CAAAAAGGAC
**
97756 ACGTGGGCACGCCACGTGTACAAAAAGGAC
1 ATAT-GGCACGCCACGTGTACAAAAAGGAC
*
97786 ATATGGCACGTCACGTGTACAAAAA
1 ATATGGCACGCCACGTGTACAAAAA
97811 TGCCACATGC
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 20 0.42
30 14 0.29
31 14 0.29
ACGTcount: A:0.36, C:0.24, G:0.25, T:0.15
Consensus pattern (29 bp):
ATATGGCACGCCACGTGTACAAAAAGGAC
Found at i:100011 original size:36 final size:36
Alignment explanation
Indices: 99964--100035 Score: 135
Period size: 36 Copynumber: 2.0 Consensus size: 36
99954 GTGGAATGCC
99964 CTCCAATGTTTTTGACGTTCAATTATATATTTTTAT
1 CTCCAATGTTTTTGACGTTCAATTATATATTTTTAT
*
100000 CTCCAATGTTTTTGGCGTTCAATTATATATTTTTAT
1 CTCCAATGTTTTTGACGTTCAATTATATATTTTTAT
100036 GAGAATTTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.24, C:0.14, G:0.10, T:0.53
Consensus pattern (36 bp):
CTCCAATGTTTTTGACGTTCAATTATATATTTTTAT
Found at i:101267 original size:662 final size:654
Alignment explanation
Indices: 100151--102908 Score: 2636
Period size: 662 Copynumber: 4.2 Consensus size: 654
100141 ACGCGTCCGC
* * *
100151 CTCAATTTTGCATGATTTTTGGCTG-CGAGACTACTTGAAATATCTACATTGATCTAATCAAATC
1 CTCAATTTTGCATGATTTTTGGC-GCCAAGACTCCTTGAAATATCTACATTCATCTAATCAAATC
*
100215 TCAGCCACATTGGATTT-AAGAATTTGTTTTTACGAGCATCTGAAA-CTTGTTTCCATTTAATTA
65 TCAGCCACATTGGATTTAAAG-ATTTGTTTTTACGAGCATCT-AAATCTTGTTTCGATTTAATTA
* * * *
100278 AAAATTAATTCAG-AAAAATAGGAAAAATGATATTAGAAA-CGTCAAAAGCCCTTTAATCTTTTT
128 GAAATTAATTCAGAAAAAATAGGAAAAACGATATTA-AAAGCGTTAAAAGCCCTTCAATCTTTTT
* * * *
100341 GGCGTTGAATTATATA-TTTTTATGAGTATTTTAGTCAAAACTTGAGGAAATATCTTTCGAGTCA
192 GGCGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCA
* * * * * * *
100405 ATTTTTACAAAATTTTAGTCGAAATCATGTAATAATCATCACAGTTTTTGGCTAAAAAAGCATTC
257 ATTTTTGCAAAA-TTTAGCCGAAATCGTGTACTAA-CATCACGGTTTTTGGCTAAAAACGCGTTC
* ** ** * * ** * ** * *
100470 CGGGGTCTTGACTCAGTTTTGCATGATTTTTGGT-GCCAAGACTTATTGAGATATCCATATACTT
320 CGGGGCCACGACTTTGTTTTGCATGATTTTT-GTCACCGAGACTCCTTGAAATATCTTTATTCAT
* * * *
100534 CTAATCAAATCTCAGCCACATTGGATTTAAAAATTTGTTTTTACGAGAATCTGAATCTTATTTCG
384 CTAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGTGCATCTGAATCTTGTTTCG
* * ** * * * * * *
100599 ATTTAATTAAAAAATAATTCAGAAAAAATATGAAAAACGATACTATAAGCGT-AAAAAGTCCTCC
449 ATTTAATTAGAAATTAATTTGGAAAAAATATGAAAAACGATATTAGAAGTGTGAAAAAGACTTTC
* * *
100663 GATCTTTTGGGCGTTAAATTGTATATATATTTTATGAGTATTTTATCCAAAAATTGA-GAAAATA
514 -ATCTTTTTGGCGTTGAATTATATAT-TATTTTATGAGTATTTT-TCCAAAAATTGAGGAAAA-A
* * * *
100727 TTTTTCGGGTCATTTTTTACAAAATTTTAGCCAAAATCGTGT-A-CACGGTTTTGGACTAAAAAC
575 TCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCACGGTTTTGG-CTAAAAAC
* *
100790 GCGTTTCGGGGCCCCCA
639 GCGTTTCGAGG-CCCGA
* * * *
100807 CTCAATTTTGCATGATTTTTGGCGCCGAGACTCCTTCAAATATCTATATTCATCTAATAAAATCT
1 CTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTACATTCATCTAATCAAATCT
* * * * * *
100872 TATCCGCATTGCATTTAAAGATTTTTTTTTACGAGCATCTAAATTTTGTTTCGATTTAATTAGAA
66 CAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
* * * * *
100937 ATTATTTCAGAAAAAATTATGAAAAACGATATTAAAAGCATGAAAAGCACTTCAATCTTTTTGGC
131 ATTAATTCAGAAAAAA-TAGGAAAAACGATATTAAAAGCGTTAAAAGCCCTTCAATCTTTTTGGC
** * * * *
101002 GTTAAATTATATATTCTTTATGAGTATTGTGGCTAAAAATTGAGGAAATATCTTTCGGGTCAATT
195 GTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAA--
*
101067 TTTTTGCAAAATTTCAACCGAAATCGTGTACTAACATTCACGGTTTTTTGGCTAAAAACGCGTTC
258 TTTTTGCAAAATTT-AGCCGAAATCGTGTACTAACA-TCACGG-TTTTTGGCTAAAAACGCGTTC
** * *
101132 CAAGGCCACGGCTTTGTTTTGCAAGATTTTTGTCACCGAGACTCCTTGAAATATCTTTATTCATC
320 CGGGGCCACGACTTTGTTTTGCATGATTTTTGTCACCGAGACTCCTTGAAATATCTTTATTCATC
* * * * * * *
101197 TAATTAGATCTCAGCCACGTTGGATTTAAGGATTTGTTTTTACGTGCATTTGAATTTTGTTTCCA
385 TAATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGTGCATCTGAATCTTGTTTCGA
* * * *
101262 TTTAATCAGTAATTAATTTGGAAATAAAATAGGAAAAACG-TATTAGAAGTGTGAAAAAGGCTTT
450 TTTAATTAGAAATTAATTTGG-AA-AAAATATGAAAAACGATATTAGAAGTGTGAAAAAGACTTT
* * *
101326 CAACTTTTTTGGCGTTGAATTATATATTA-TTTATGAGTATTTTTGCTAGAAATTGAGGAAAAAT
513 CATC-TTTTTGGCGTTGAATTATATATTATTTTATGAGTATTTTT-CCAAAAATTGAGGAAAAAT
* * *
101390 CTTTCGGGTCAATTTTTGCAAACTTTAAGCCGAAATTGTGTACTAACCATCACGGTTTTTGGCTA
576 CTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG---TAA-C--CACGG-TTTTGGCTA
* * *
101455 AAAATGCGTTCCGTGGCCCGA
634 AAAACGCGTTTCGAGGCCCGA
* * * * *
101476 CAT-AGTTTTGCATGATTTTTGGTGTCAAGTCTCCTTGAAATATCT---TTACATCTAACCAAAT
1 C-TCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTACATT-CATCTAATCAAAT
* * * * *
101537 CTCAGACATATTGGATTTAAGGATTTGTTTTTACGAGTATCTAAATCTTGTTTCGATTTATTTAG
64 CTCAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAG
* *
101602 AAATTAATTCAGATAAAAATAGGAAAAAC-AGTATTAGAAGCGTTAAAAGTCCTTCAATCTTTTT
129 AAATTAATTCAGA-AAAAATAGGAAAAACGA-TATTAAAAGCGTTAAAAGCCCTTCAATCTTTTT
** * * *
101666 GATGTCGAATTAAATATTTTTTATGAGTATTTTAGCCAAAAATTAAGGAAATGTCTTTCGGGTCA
192 GGCGTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCA
* * *
101731 ATTTTTGCAAAAATTTAGCCGAAATCGTATACT-CCATCATGGTTTTTGGCTAAAAACGCGTTCC
257 ATTTTTGC-AAAATTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTCC
* * * * *
101795 GGGGCCACAACATTGTTTTGCATGATTTTTGACACGGAGACTCCTTGAAATATCTTTCTTCATCT
321 GGGGCCACGACTTTGTTTTGCATGATTTTTGTCACCGAGACTCCTTGAAATATCTTTATTCATCT
* * *
101860 AACCAAATCTCAGTCACATTGGATTTAAGTATTTGTTTTTACGTGCATCTGAATCTTGTTTCGAT
386 AATCAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGTGCATCTGAATCTTGTTTCGAT
* *
101925 TTAATTAGCAATTAATTTGGAAATATAAT-TGGATAAACGATATTAGAAGTGTGAAAAAGACTTT
451 TTAATTAGAAATTAATTTGGAAA-A-AATAT-GAAAAACGATATTAGAAGTGTGAAAAAGACTTT
* ** * * * * * *
101989 CATTTTTTTCACATTGAATTATATGTTTTTTTATGAGTATTGTTTACATAAACTGAGGAAAAATC
513 CATCTTTTTGGCGTTGAATTATATATTATTTTATGAGTATT-TTTCCAAAAATTGAGGAAAAATC
* *
102054 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCATGTACTAACCATCATGGTTTCGGCTAAA
577 TTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATC--GT-GTAACCA-C--GGTTTTGGCTAAA
*
102119 AACGCG-TTCTGAGGCCCGG
636 AACGCGTTTC-GAGGCCCGA
* ** *
102138 CTCAGTTTTGCATGA-TTTTGGTTCCAAGACTCTTTGAAATATCTACATTCATCTAATCAAATCT
1 CTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTACATTCATCTAATCAAATCT
* * * * * * *
102202 CAACCACATTAGATTTAATGATTTGTTTTTACGAGTATCAAAATCTTATTTTGATTTAATTAGAA
66 CAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
* * ** * * *
102267 ATTAAATCAGAAAAAATAGCAAAAATAATATTAGAAGCGTTAAAAGCCCTTCAATATTTTTGATC
131 ATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTTAAAAGCCCTTCAATCTTTTTG-GC
102332 -TCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAA--
195 GTCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATT
* **
102394 -TT------TTT----G----C----A--AA-ATCACGGTTTTTGGCTAAAACCGCGTTCCAAGG
260 TTTGCAAAATTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTCCGGGG
* * * * * * ** *
102437 TCATGGCTCTGTTTTGCATGATTTTTAG-CGCCGATACTAATTAAAATATCTTTATTCATCTAAT
325 CCACGACTTTGTTTTGCATGATTTTT-GTCACCGAGACTCCTTGAAATATCTTTATTCATCTAAT
* * * * *
102501 CAGATCTCAGCCACATTGGATTTAAGGATTTTTTTTTACGTGTATATGAATCTTGTTTCGATTTA
389 CAAATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTA
* * * * * * *
102566 ATCAGCAATTAAATTGGAAATAAAATAGGAAAAATGATATTAGAAGCGTGAAAAAGGCTTTCAAT
454 ATTAGAAATTAATTTGG-AA-AAAATATGAAAAACGATATTAGAAGTGTGAAAAAGACTTTC-AT
* * * * *
102631 -TTGTTTGGCATTGAATTATATATT-TTTTGTGAGTATTTTTGCTAGAAATTGAGAAAAAATCTT
516 CTT-TTTGGCGTTGAATTATATATTATTTTATGAGTATTTTT-CCAAAAATTGAGGAAAAATCTT
* * ** *
102694 TTGGGTCAATTTTTAG-AAAATTTTAGCCGAAATTGTGTACTAACCATCACACTTTCT-GCAAAA
579 TCGGGTCAATTTTT-GCAAAATTTTAGCCGAAATCGTG---TAA-C--CACGGTTT-TGGCTAAA
* * *
102757 AACGCGTTCCGAGACCCAA
636 AACGCGTTTCGAGGCCCGA
* * * * * * * * *
102776 CTCAGTTTTGCATGATTTTTTGTGCCAAGTCTCCTTGAATTATATA-A-ACATCTAACCAAATAT
1 CTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTACATTCATCTAATCAAATCT
* * * * ** * * *
102839 CAGCCATATTGGACTTAAGGATTTGTTTTTTCGAATATCTGAATCTTGATTCGATTTAATAAGAA
66 CAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
102904 ATTAA
131 ATTAA
102909 GGATTTTGGT
Statistics
Matches: 1755, Mismatches: 277, Indels: 159
0.80 0.13 0.07
Matches are distributed among these distances:
636 2 0.00
637 73 0.04
638 284 0.16
639 52 0.03
640 3 0.00
641 2 0.00
644 1 0.00
648 1 0.00
652 3 0.00
655 4 0.00
656 116 0.07
657 11 0.01
658 50 0.03
659 44 0.03
660 8 0.00
661 65 0.04
662 511 0.29
663 197 0.11
664 49 0.03
665 25 0.01
666 11 0.01
667 169 0.10
668 5 0.00
669 41 0.02
670 22 0.01
671 6 0.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (654 bp):
CTCAATTTTGCATGATTTTTGGCGCCAAGACTCCTTGAAATATCTACATTCATCTAATCAAATCT
CAGCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAGAA
ATTAATTCAGAAAAAATAGGAAAAACGATATTAAAAGCGTTAAAAGCCCTTCAATCTTTTTGGCG
TCGAATTATATATTTTTTATGAGTATTTTAGCCAAAAATTGAGGAAATATCTTTCGGGTCAATTT
TTGCAAAATTTAGCCGAAATCGTGTACTAACATCACGGTTTTTGGCTAAAAACGCGTTCCGGGGC
CACGACTTTGTTTTGCATGATTTTTGTCACCGAGACTCCTTGAAATATCTTTATTCATCTAATCA
AATCTCAGCCACATTGGATTTAAGAATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAAT
TAGAAATTAATTTGGAAAAAATATGAAAAACGATATTAGAAGTGTGAAAAAGACTTTCATCTTTT
TGGCGTTGAATTATATATTATTTTATGAGTATTTTTCCAAAAATTGAGGAAAAATCTTTCGGGTC
AATTTTTGCAAAATTTTAGCCGAAATCGTGTAACCACGGTTTTGGCTAAAAACGCGTTTCGAGGC
CCGA
Found at i:104696 original size:333 final size:331
Alignment explanation
Indices: 103450--105219 Score: 1935
Period size: 333 Copynumber: 5.3 Consensus size: 331
103440 TCTTCATGGC
* * *
103450 GTTGAATTATATATTTTTTATGAGTATTTTTGCTAGAAATTGAGGAAAAATCTTTCGGATCAATT
1 GTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATT
* * * *
103515 TTTGCAAAAGTTTAGTCGAAATCGTGTACCAACCATCATGGTTTTCGGCTAAAAAAGCGTTCCGA
66 TTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGG
* * * * * *
103580 GGCCCGGCTCAGTTTTGCATGATTTTTGGTGCCAATACTCTTTGAAATATCTATATTCATCTAAG
131 GGCCCGACTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTTTATTCATCTAAC
* * *
103645 CAAATCTCAGCCACATTAGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTA
196 CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
* * * *
103710 ATTAGAAATTAATTCAGATAAAAATAGCAAAAACAATATTAGAATCGTTAAAAGCCCTTCAATAT
261 ATTAGAAATTAATTCAGAT-AAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCTTTCAATTT
103775 TTTTGAT
325 TTTTGAT
*
103782 -TTCGAATTATATATTTTTTTATGAGTATTTTAGCCAAAAATTGA-GAAAATATCTTTCGGGTCA
1 GTT-GAATTATATA-TTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAA-ATCTTTCGGGTCA
* ** * * * * *
103845 ATTTTTGCAAAAGTTTAACCGAAGTCGTGTACAAACAATCACGGTTTTGGGCTAAAAACGCGTTT
63 ATTTTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCACGGTTTTCGGCTAAAAACGCGTTC
* * * * * *
103910 CAGGGCCACGGCTCTA-TTTTACATGACTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCAT
128 CGGGGCC-CGACT-TAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTTTATTCAT
* * * * ** *
103974 CTAATCAGATCTCAACCACATCGGATTTAAGGATTTGGCTTTACGTGCATCTGAATCTTGTTTCG
191 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* * * * ** * *
104039 ATTTAATTAGCAATTAATTTGGAAATAAAATAGGAAAACCGCTATTAGAAGCGTGAAAAAGGCTT
256 ATTTAATTAGAAATTAA-TT-CAGATAAAATAGGAAAAACAATATTAGAAGCGT-TAAAAGCCTT
**
104104 TCAATTTTTTTGCC
318 TCAATTTTTTTGAT
* * * *
104118 GTTGAATTATATATTTTTTATGAATATTTTTGCTTTAAAATTGAGGAAAAATCTTTCGGATCAAT
1 GTTGAATTATATATTTTTTATGAGTATTTTAGC-TAAAAATTGAGGAAAAATCTTTCGGGTCAAT
* * *
104183 TTTTGCAAAATTTTAGCCGAAAT--TGTAACTAACCATCACGGTTTTC-GCTAAAAACGCGTTAC
65 TTTTGCAAAATTTTAGTCGAAATCGTGT-ACCAACCATCACGGTTTTCGGCTAAAAACGCGTTCC
* ** * * * * * *
104245 GAGGG-CCG-GTTCAGGGTCGTATGATTTTTGGTTCCAA-ATATCATTGAAATATC--TATACAT
129 G-GGGCCCGACTT-AGTTTTGCATGATTTTTGGTGCCAAGA-CTCCTTGAAATATCTTTATTCAT
* * * * * *
104305 CAAACTAAATCTCAGCCATATTGGATATAAGGATTTGTTCTTACGAGTATCTGAATCTTGTTTCG
191 CTAACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCG
* *
104370 ATTTATTTAGAAATTAATTCAGATAAAAGTAGGAAAAACAATATTAGAAGCATTAAAAGCCTTTC
256 ATTTAATTAGAAATTAATTCAGATAAAA-TAGGAAAAACAATATTAGAAGCGTTAAAAGCCTTTC
*
104435 AATCTTTTTGAT
320 AATTTTTTTGAT
* * * * *
104447 GTTGAATTAAATATTTTTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCTTTTGGGTCAATT
1 GTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATT
* * * * * * *
104512 TTTACAAAAATTAAGTCGAAATCATGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGG
66 TTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGG
* * * ** ** * * *
104577 GGCCACGACTTTGTTTTGCATGATCTTCGACGCGGAGGCTCCTTAAAATATCTTTCTTCATCTAA
131 GGCC-CGACTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTTTATTCATCTAA
*
104642 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTT
195 CCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTT
* * * * ** * * *
104707 AATCAGCAATTAATTTGGAAATAAAATAGG-AAAATGATATTAGAAGCGTGAAAATGGCTTTCAT
260 AATTAGAAATTAA-TT-CAGATAAAATAGGAAAAACAATATTAGAAGCGTTAAAA-GCCTTTCAA
104771 TTTTTTTGGA-
322 TTTTTTT-GAT
* *** * *
104781 ATTGAATTATATATTTTTTATGAGTATTTTTTATATAAATTGAGGAAAAATCTTTCGGTTCAATT
1 GTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATT
* * *
104846 TTTGCAAAAGTTTAGTCGAAATCGTGTACCAACCATCATGGTTTTCGGCTAAAAACGCGTTCCGA
66 TTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGG
*
104911 GGCCCGA-TTCAGTTTTGCATGATTTTTGGTGCCAAGACTCTTTGAAATAT-TTATATTCATCTA
131 GGCCCGACTT-AGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTT-TATTCATCTA
* * * * * * * *
104974 AGCAAATCTCAG-C-C---GCA-TTAAGGATTAGTTTTTACGAACATCAGAAACTTATTTTGATT
194 ACCAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATT
* * * *
105033 TAATTAGAAATTAATTCAGATGAAAATAGCAAAAACAATATTAGAAGCGTTTAAATCCCTTCAAT
259 TAATTAGAAATTAATTCAGAT-AAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCTTTCAA-
*
105098 GTTTTTTTTAT
322 -TTTTTTTGAT
* * * *
105109 CTCGAATTATATATTTTTTATGAGTATTTTAGCAAAAAATTGAGGAAATATCTTTCGGGTCAATT
1 GTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATT
*
105174 TTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCATGGTTTTC
66 TTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCACGGTTTTC
105220 ATTATAAAAC
Statistics
Matches: 1184, Mismatches: 217, Indels: 78
0.80 0.15 0.05
Matches are distributed among these distances:
325 3 0.00
326 14 0.01
327 68 0.06
328 154 0.13
329 76 0.06
330 42 0.04
331 103 0.09
332 25 0.02
333 278 0.23
334 269 0.23
335 72 0.06
336 73 0.06
337 7 0.01
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (331 bp):
GTTGAATTATATATTTTTTATGAGTATTTTAGCTAAAAATTGAGGAAAAATCTTTCGGGTCAATT
TTTGCAAAATTTTAGTCGAAATCGTGTACCAACCATCACGGTTTTCGGCTAAAAACGCGTTCCGG
GGCCCGACTTAGTTTTGCATGATTTTTGGTGCCAAGACTCCTTGAAATATCTTTATTCATCTAAC
CAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCAGATAAAATAGGAAAAACAATATTAGAAGCGTTAAAAGCCTTTCAATTTT
TTTGAT
Found at i:104935 original size:664 final size:663
Alignment explanation
Indices: 102912--105211 Score: 2939
Period size: 664 Copynumber: 3.4 Consensus size: 663
102902 AAATTAAGGA
* * *
102912 TTTTGGTGCCAAGA-CTCTTTGAAATATCTATATTCATCTACGCAAATCTCAGCCACATTTGATT
1 TTTTGGTGCCAA-ATATCTTTGAAATATCTATA-TCATCTAAGCAAATCTCAGCCACATTGGATT
* * *
102976 TAAGGATTTATTTTTACAAGCATCTGAATCTTATTTTGATTTAATTAAAAATTAATTCAGATAAA
64 TAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGATAAA
*
103041 AATAGCAAAAACAATATTAAAAGCGTTAAAAGCCCTTCAATCTTTTTGATCTCGAATTATATATT
129 AATAGCAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATCTCGAATTATATATT
* *
103106 TTTTATGAGTATTTTAGCCAAAAATTGAGAAAATACCTTTCGGGTCAATTTTTGCAAAATTTTAG
194 TTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTAAG
*
103171 CCGAAGTCGTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCAGGGCCACGGCTCTGTT
259 CCGAAATCGTGTACTAACCATCACG-TTTTTGGCTAAAAACGCGTTCCAGGGCCACGGCTCTGTT
* * *
103236 TTGCATAACTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATGAGATCTCAGACAC
323 TTGCATGACTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAGATCTCAGCCAC
* * *
103301 ATTGGATTTAAGGATTTGTTTTTATGTCCATCTGAATCTTGTTTCGATTTAATCGGCAATTAATT
388 ATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATCAGCAATTAATT
* * ** * *
103366 TGGAAGA-AGGAAT-CGAAGAAGGGATTTGCATTTA-AGGCGATTCCTTCTCCGGGGAAGAGCGC
453 TGGAA-ATA-AAATAGGAA-AACCGA--T--A-TTAGAAGCG--------T-----GAAAAG-GC
** * ** **
103428 TAGGGACGCGATTCTTCATGGCGTTGAATTATATATTTTTTATGAGTATTTTTGCTAGAAATTGA
496 T-----TTC-ATTTTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTTTTTATA-AAATTGA
103493 GGAAAAATCTTTCGGATCAATTTTTGCAAAAGTTTAGTCGAAATCGTGTACCAACCATCATGGTT
554 GGAAAAATCTTTCGGATCAATTTTTGCAAAAGTTTAGTCGAAATCGTGTACCAACCATCATGGTT
* *
103558 TTCGGCTAAAAAAGCGTTCCGAGGCCCGGCTCAGTTTTGCATGAT
619 TTCGGCTAAAAACGCGTTCCGAGGCCCGGTTCAGTTTTGCATGAT
*
103603 TTTTGGTGCC-AATACTCTTTGAAATATCTATATTCATCTAAGCAAATCTCAGCCACATTAGATT
1 TTTTGGTGCCAAATA-TCTTTGAAATATCTATA-TCATCTAAGCAAATCTCAGCCACATTGGATT
103667 TAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGATAAA
64 TAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGATAAA
* * *
103732 AATAGCAAAAACAATATTAGAATCGTTAAAAGCCCTTCAATATTTTTGATTTCGAATTATATATT
129 AATAGCAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATCTCGAATTATATA-T
103797 TTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAAGTTTA
193 TTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAA-TTTA
* * * * * *
103862 A-CCGAAGTCGTGTACAAACAATCACGGTTTTGGGCTAAAAACGCGTTTCAGGGCCACGGCTCTA
257 AGCCGAAATCGTGTACTAACCATCAC-GTTTTTGGCTAAAAACGCGTTCCAGGGCCACGGCTCTG
* *
103926 TTTTACATGACTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAGATCTCAACC
321 TTTTGCATGACTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAGATCTCAGCC
* ** *
103991 ACATCGGATTTAAGGATTTGGCTTTACGTGCATCTGAATCTTGTTTCGATTTAATTAGCAATTAA
386 ACATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATCAGCAATTAA
* * *
104056 TTTGGAAATAAAATAGGAAAACCGCTATTAGAAGCGTGAAAAAGGCTTTCAATTTTTTTGCCGTT
451 TTTGGAAATAAAATAGGAAAACCGATATTAGAAGCGTG-AAAAGGCTTTCATTTTTTTTGGCGTT
* *
104121 GAATTATATATTTTTTATGAATATTTTTGCTTTAAAATTGAGGAAAAATCTTTCGGATCAATTTT
515 GAATTATATATTTTTTATGAGTATTTTT--TATAAAATTGAGGAAAAATCTTTCGGATCAATTTT
* * * * *
104186 TGCAAAATTTTAGCCGAAAT--TGTAACTAACCATCACGGTTTTC-GCTAAAAACGCGTTACGAG
578 TGCAAAAGTTTAGTCGAAATCGTGT-ACCAACCATCATGGTTTTCGGCTAAAAACGCGTTCCGAG
* ** * *
104248 GGCCGGTTCAGGGTCGTATGAT
642 GCCCGGTTCAGTTTTGCATGAT
* * * * *
104270 TTTTGGTTCCAAATATCATTGAAATATCTATA-CATC-AAACTAAATCTCAGCCATATTGGATAT
1 TTTTGGTGCCAAATATCTTTGAAATATCTATATCATCTAAGC-AAATCTCAGCCACATTGGATTT
* * * * *
104333 AAGGATTTGTTCTTACGAGTATCTGAATCTTGTTTCGATTTATTTAGAAATTAATTCAGATAAAA
65 AAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGATAAAA
* * * * * * *
104398 GTAGGAAAAACAATATTAGAAGCATTAAAAGCCTTTCAATCTTTTTGATGTTGAATTAAATATTT
130 ATAGCAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATCTCGAATTATATATTT
* * * * * *
104463 TTTATGAGTATTTTAGCCAAAAATTAAGGAAATATCTTTTGGGTCAATTTTTACAAAAATTAAGT
195 TTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTAAGC
* * * *
104528 CGAAATCATGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCCACGACTTTGTTT
260 CGAAATCGTGTACTAACCATCAC-GTTTTTGGCTAAAAACGCGTTCCAGGGCCACGGCTCTGTTT
* * * * * * * *
104593 TGCATGA-TCTTCGACGCGGAGGCTCCTTAAAATATCTTTCTTCATCTAACCAAATCTCAGCCAC
324 TGCATGACT-TTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAGATCTCAGCCAC
104657 ATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATCAGCAATTAATT
388 ATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATCAGCAATTAATT
* **
104722 TGGAAATAAAATAGGAAAA-TGATATTAGAAGCGTGAAAATGGCTTTCATTTTTTTTGGAATTGA
453 TGGAAATAAAATAGGAAAACCGATATTAGAAGCGTGAAAA-GGCTTTCATTTTTTTTGGCGTTGA
*
104786 ATTATATATTTTTTATGAGTATTTTTTATATAAATTGAGGAAAAATCTTTCGGTTCAATTTTTGC
517 ATTATATATTTTTTATGAGTATTTTTTATA-AAATTGAGGAAAAATCTTTCGGATCAATTTTTGC
104851 AAAAGTTTAGTCGAAATCGTGTACCAACCATCATGGTTTTCGGCTAAAAACGCGTTCCGAGGCCC
581 AAAAGTTTAGTCGAAATCGTGTACCAACCATCATGGTTTTCGGCTAAAAACGCGTTCCGAGGCCC
*
104916 GATTCAGTTTTGCATGAT
646 GGTTCAGTTTTGCATGAT
* * *
104934 TTTTGGTGCCAAGA-CTCTTTGAAATATTTATATTCATCTAAGCAAATCTCAG-C-C---GCA-T
1 TTTTGGTGCCAA-ATATCTTTGAAATATCTATA-TCATCTAAGCAAATCTCAGCCACATTGGATT
* * * * *
104992 TAAGGATTAGTTTTTACGAACATCAGAAACTTATTTTGATTTAATTAGAAATTAATTCAGATGAA
64 TAAGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGATAAA
* * * *
105057 AATAGCAAAAACAATATTAGAAGCGTTTAAATCCCTTCAATGTTTTTTTTATCTCGAATTATATA
129 AATAGCAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAA--TCTTTTTGATCTCGAATTATATA
* * *
105122 TTTTTTATGAGTATTTTAGCAAAAAATTGAGGAAATATCTTTCGGGTCAATTTTTGCAAAATTTT
192 TTTTTTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTA
* *
105187 AGTCGAAATCGTGTACCAACCATCA
257 AGCCGAAATCGTGTACTAACCATCA
105212 TGGTTTTCAT
Statistics
Matches: 1416, Mismatches: 166, Indels: 83
0.85 0.10 0.05
Matches are distributed among these distances:
660 89 0.06
661 5 0.00
662 152 0.11
663 81 0.06
664 309 0.22
665 138 0.10
666 13 0.01
667 64 0.05
668 58 0.04
669 50 0.04
670 2 0.00
674 4 0.00
675 4 0.00
679 1 0.00
686 3 0.00
687 5 0.00
689 2 0.00
690 1 0.00
691 185 0.13
692 245 0.17
693 5 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.36
Consensus pattern (663 bp):
TTTTGGTGCCAAATATCTTTGAAATATCTATATCATCTAAGCAAATCTCAGCCACATTGGATTTA
AGGATTTGTTTTTACGAGCATCTGAATCTTATTTTGATTTAATTAGAAATTAATTCAGATAAAAA
TAGCAAAAACAATATTAGAAGCGTTAAAAGCCCTTCAATCTTTTTGATCTCGAATTATATATTTT
TTATGAGTATTTTAGCCAAAAATTGAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTTAAGCC
GAAATCGTGTACTAACCATCACGTTTTTGGCTAAAAACGCGTTCCAGGGCCACGGCTCTGTTTTG
CATGACTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAGATCTCAGCCACATT
GGATTTAAGGATTTGTTTTTACGTGCATCTGAATCTTGTTTCGATTTAATCAGCAATTAATTTGG
AAATAAAATAGGAAAACCGATATTAGAAGCGTGAAAAGGCTTTCATTTTTTTTGGCGTTGAATTA
TATATTTTTTATGAGTATTTTTTATAAAATTGAGGAAAAATCTTTCGGATCAATTTTTGCAAAAG
TTTAGTCGAAATCGTGTACCAACCATCATGGTTTTCGGCTAAAAACGCGTTCCGAGGCCCGGTTC
AGTTTTGCATGAT
Found at i:106564 original size:41 final size:41
Alignment explanation
Indices: 106519--106605 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 41
106509 AAAATTGAAG
*
106519 AAAAATAAAACATTTTAGTAGACCATTTTCCCAAATTTGTC
1 AAAAAAAAAACATTTTAGTAGACCATTTTCCCAAATTTGTC
* * *** * *
106560 AAAAAAAAAAGATTTTGGTAGATGGTTTTTCCAAATTTGTT
1 AAAAAAAAAACATTTTAGTAGACCATTTTCCCAAATTTGTC
106601 AAAAA
1 AAAAA
106606 GAGATTTTCA
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
41 38 1.00
ACGTcount: A:0.44, C:0.10, G:0.11, T:0.34
Consensus pattern (41 bp):
AAAAAAAAAACATTTTAGTAGACCATTTTCCCAAATTTGTC
Found at i:106905 original size:42 final size:41
Alignment explanation
Indices: 106848--106937 Score: 101
Period size: 42 Copynumber: 2.2 Consensus size: 41
106838 AAAATTGGAG
* *
106848 AAAAATAAAACATTTTAGTAG-GCTGTTTTCCCAAATTTGTCA
1 AAAAAAAAAACATTTTAGTAGATC-GTTTTCCCAAATTTG-CA
* * * *
106890 AAAAAAAAAAGATTTTTGTAGATCGTTTTCCTAAATTTGCT
1 AAAAAAAAAACATTTTAGTAGATCGTTTTCCCAAATTTGCA
106931 AAAAAAA
1 AAAAAAA
106938 TTTTCAAACC
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 8 0.20
42 32 0.78
43 1 0.02
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.34
Consensus pattern (41 bp):
AAAAAAAAAACATTTTAGTAGATCGTTTTCCCAAATTTGCA
Found at i:107022 original size:23 final size:24
Alignment explanation
Indices: 106951--107022 Score: 74
Period size: 27 Copynumber: 2.9 Consensus size: 24
106941 TCAAACCAAT
*
106951 ACTTTTTTTAAATTAAAATTCACA
1 ACTTCTTTTAAATTAAAATTCACA
**
106975 ACTTCTTTACCTAAAAAAAAATTCACA
1 ACTTCTTT---TAAATTAAAATTCACA
*
107002 ACTTC-TTTAAATTAAATTTCA
1 ACTTCTTTTAAATTAAAATTCA
107023 AGTTTTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 7
0.75 0.12 0.13
Matches are distributed among these distances:
23 11 0.28
24 7 0.18
26 2 0.05
27 19 0.49
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (24 bp):
ACTTCTTTTAAATTAAAATTCACA
Found at i:107685 original size:325 final size:320
Alignment explanation
Indices: 106991--108132 Score: 1325
Period size: 325 Copynumber: 3.7 Consensus size: 320
106981 TTACCTAAAA
*
106991 AAAAATTCACAACTTCTTTAAATTAAATTTCAAGTTTTATTTATTTTTGAATTTAAGGCCCAAAC
1 AAAAATTCACAACTTCTTTAAATTAAATTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAAC
* * *
107056 TGA-T-TA-TAT-TATATAGTATAATCTCATTTCAAGCCCACAAGCATCA-TTTTTTATATGAAA
66 TTATTATATTATATATATAGTATAACCTCATTTCAAGCCCACACGCATCATTTTTTTATATGAAA
* * * *
107116 ATTTGATGCGTGTGACCGG--CT--TATT--TTT-GTGGTTAAATATTTACATAATTTCTTTA-G
131 ATCTGATTCGTGTGACCGGCCCTCCTCTTACTTTGGTGGTTAAATAATTACATAATTT-TTTATG
* *
107173 TTTAAAATAAAATTGGAGAGAAAAAAATTATAGTGGATCGTTTTCCCAAATTTGCCAAAAAAAAA
195 ATTAAAATAAAATTGGAGGGAAAAAAATTATAGTGGATCGTTTTCCCAAATTTG-CAAAAAAAAA
* **
107238 AGATTTTGGTAGATTGTTTTCCCAAATTTGTTAAATTTTTTTAACAAATAATTTTTTTAATT
259 AGATTTTGGTAGATCGTTTTCCCAAATTTGTTAAATTTTTCAAACAAATAATTTTTTTAATT
* * *
107300 AAAAAATCACAACTTCTTTAAATTAAATTTCAAATTTTATTAGTTTTTGAATTTAAGGCCCAAAC
1 AAAAATTCACAACTTCTTTAAATTAAATTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAAC
*
107365 TTATTATATTATATATATAGTATAACCTCATTTCAAGTCCACACGCATCATTTTTTTATATGAAA
66 TTATTATATTATATATATAGTATAACCTCATTTCAAGCCCACACGCATCATTTTTTTATATGAAA
107430 ATCTGATTCGTGTGACCGGCCCTCCTCTTACTTTGGTGGTTAAATAATTACATAATTTTTTATGA
131 ATCTGATTCGTGTGACCGGCCCTCCTCTTACTTTGGTGGTTAAATAATTACATAATTTTTTATGA
* * * *
107495 TTAAAGTAAAATTGGAGGGGGAAAATATTATAGTGGATCGTTTCCCCAAATTTAGC-AAAAAAAA
196 TTAAAATAAAATTGGA-GGGAAAAAAATTATAGTGGATCGTTTTCCCAAATTT-GCAAAAAAAAA
*
107559 TGATTTTGGTAGATCGTTTTCCCAAATTTGTTAAAAAATATTTTCAAACAAATAATTTTTTTAAT
259 AGATTTTGGTAGATCGTTTTCCCAAATTTGTT---AAAT-TTTTCAAACAAATAATTTTTTTAAT
107624 T
320 T
*
107625 AGAAATTCACAACTTCTTTAAATTAAATTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAAC
1 AAAAATTCACAACTTCTTTAAATTAAATTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAAC
*
107690 TTATTAT-TT-TATAT-TA-TATAACCTCATTTCAAGCCCACACGCATTATTTTTTTTATATGAA
66 TTATTATATTATATATATAGTATAACCTCATTTCAAGCCCACACGCATCA-TTTTTTTATATGAA
* * * * *
107751 AGTCTGATTTGTGTGATCGGCCCTCCCCTTACTTTGGTGGTAATTAAATAATTACATAATTTCTT
130 AATCTGATTCGTGTGACCGGCCCTCCTCTTACTTTGGTGG---TTAAATAATTACATAATTTTTT
* * * * *
107816 ATGATTAAAATAAAATTGGAGGAAAAAAAATTATAGTAGATCATTTTACCAAATTTTCAAAAAAA
192 ATGATTAAAATAAAATTGGAGGGAAAAAAATTATAGTGGATCGTTTTCCCAAATTTGCAAAAAAA
* *
107881 AAAGATTTTGGTAGATCGTTTTGCC-----------A-----C---C-AATTATTTTTTTAATT
257 AAAGATTTTGGTAGATCGTTTTCCCAAATTTGTTAAATTTTTCAAACAAATAATTTTTTTAATT
* *
107925 AAAAATTTACAA---CTTTAAATTAAATTTTCAAGTTTTATTTGCTTTTGAATTTAAGG-CCAAA
1 AAAAATTCACAACTTCTTTAAATTAAA-TTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAA
* * * * * * *
107986 CTGA-T-CA-TAT-TGTATAGGATAAGCTCATTTCAAACCCACACGTATCATTTTTTTTATATGA
65 CTTATTATATTATATATATAGTATAACCTCATTTCAAGCCCACACGCATCA-TTTTTTTATATGA
* * * * * *
108047 AAATCTGATGCGTGTGACCAGCCCTCCTATTTACTTTTGATGGTTAAACAATTACATAATTTCTT
129 AAATCTGATTCGTGTGACCGGCCCTCCT-CTTAC-TTTGGTGGTTAAATAATTACATAATTTTTT
* *
108112 AAG-TTGATAATAAAATTGGAG
192 ATGATT-AAAATAAAATTGGAG
108133 AAAAATAAAA
Statistics
Matches: 734, Mismatches: 67, Indels: 77
0.84 0.08 0.09
Matches are distributed among these distances:
295 5 0.01
296 41 0.06
297 81 0.11
298 34 0.05
299 7 0.01
300 25 0.03
301 1 0.00
304 1 0.00
309 63 0.09
310 2 0.00
311 2 0.00
312 3 0.00
313 34 0.05
314 31 0.04
316 2 0.00
318 3 0.00
320 7 0.01
321 104 0.14
322 85 0.12
323 7 0.01
324 64 0.09
325 132 0.18
ACGTcount: A:0.35, C:0.13, G:0.12, T:0.40
Consensus pattern (320 bp):
AAAAATTCACAACTTCTTTAAATTAAATTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAAC
TTATTATATTATATATATAGTATAACCTCATTTCAAGCCCACACGCATCATTTTTTTATATGAAA
ATCTGATTCGTGTGACCGGCCCTCCTCTTACTTTGGTGGTTAAATAATTACATAATTTTTTATGA
TTAAAATAAAATTGGAGGGAAAAAAATTATAGTGGATCGTTTTCCCAAATTTGCAAAAAAAAAAG
ATTTTGGTAGATCGTTTTCCCAAATTTGTTAAATTTTTCAAACAAATAATTTTTTTAATT
Found at i:108180 original size:297 final size:282
Alignment explanation
Indices: 107591--108330 Score: 789
Period size: 297 Copynumber: 2.5 Consensus size: 282
107581 CAAATTTGTT
*
107591 AAAAAATATTTTCAAA--CA-AATAATTTTTTTAATTAGAAATTCACAACTTCTTTAAATTAAAT
1 AAAAAAT-TTTTCAAACCCACAAT-ATTTTTTTAATTAAAAATTCACAA---CTTTAAATTAAAT
* *
107653 TTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAACTTATTATTTTATATTA-TATAACCTCAT
61 TTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAACTGATTATATTATA-TAGTATAACCTCAT
* * ** * * *
107717 TTCAAGCCCACACGCATTATTTTTTTTATATGAAAGTCTGATTTGTGTGATCGGCCCTCCCCTTA
125 TTCAAGCCCACACGCATCATTTTTTTTATATGAAAATCTGATGCGTGTGACCAGCCCTCCACTTA
* * * *
107782 CTTTGGTGGTAATTAAATAATTACATAATTTCTTATGATTAAAATAAAATTGGAGGAAAAAAAAT
190 CTTTGATGG--ATTAAACAATTACATAATTTCTTAAGATTAAAATAAAATTGGAGAAAAAAAAAT
*
107847 TATAGTAGATCATTTTACCAAATTTTCAAAAA
253 TATAGTAGATCAGTTTACCAAA-TTTC-AAAA
* *
107879 AAAAAGATTTTGGT-AGATCGTTTTGCCACCAATTATTTTTTTAATTAAAAATTTACAACTTTAA
1 AAAAA-ATTTT--TCA-AAC------CCA-CAA-TATTTTTTTAATTAAAAATTCACAACTTTAA
* * * *
107943 ATTAAATTTTCAAGTTTTATTTGCTTTTGAATTTAAGG-CCAAACTGATCATATTGTATAGGATA
54 ATTAAA-TTTCAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAACTGATTATATTATATAGTATA
* * *
108007 AGCTCATTTCAAACCCACACGTATCATTTTTTTTATATGAAAATCTGATGCGTGTGACCAGCCCT
118 ACCTCATTTCAAGCCCACACGCATCATTTTTTTTATATGAAAATCTGATGCGTGTGACCAGCCCT
* *
108072 CCTATTTACTTTTGATGG-TTAAACAATTACATAATTTCTTAAG-TTGATAATAAAATTGGAGAA
183 CC-ACTTAC-TTTGATGGATTAAACAATTACATAATTTCTTAAGATT-AAAATAAAATTGGAG-A
* * ***
108135 AAATAAAACATTTTAGTAGATCAGTTTGCCAAA-TTCGTTA
244 AAA-AAAA-ATTATAGTAGATCAGTTTACCAAATTTCAAAA
* *
108175 AAAAAATTTTTCAAACCGATAAT-TTTTTTTAATTAAAAATTCACAACTTCTATAAATTAAATTT
1 AAAAAATTTTTCAAACCCACAATATTTTTTTAATTAAAAATTCACAAC-T-T-TAAATTAAATTT
108239 CAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAACTGATTATATTATATATAGTATAACCTCATT
63 CAAGTTTTATTTGTTTTTGAATTTAAGGCCCAAACTGATTATA-T-TATATAGTATAACCTCATT
*
108304 TCAAGCCCACACACATCATATTTTTTT
126 TCAAGCCCACACGCATCAT-TTTTTTT
108331 TCTTTTATGA
Statistics
Matches: 378, Mismatches: 43, Indels: 60
0.79 0.09 0.12
Matches are distributed among these distances:
284 23 0.06
285 2 0.01
286 33 0.09
287 24 0.06
288 9 0.02
289 35 0.09
290 9 0.02
293 3 0.01
294 1 0.00
295 7 0.02
296 45 0.12
297 94 0.25
298 40 0.11
299 28 0.07
300 24 0.06
301 1 0.00
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (282 bp):
AAAAAATTTTTCAAACCCACAATATTTTTTTAATTAAAAATTCACAACTTTAAATTAAATTTCAA
GTTTTATTTGTTTTTGAATTTAAGGCCCAAACTGATTATATTATATAGTATAACCTCATTTCAAG
CCCACACGCATCATTTTTTTTATATGAAAATCTGATGCGTGTGACCAGCCCTCCACTTACTTTGA
TGGATTAAACAATTACATAATTTCTTAAGATTAAAATAAAATTGGAGAAAAAAAAATTATAGTAG
ATCAGTTTACCAAATTTCAAAA
Done.