Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008730.1 Hibiscus syriacus cultivar Beakdansim tig00111799_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: 439989
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
File 1 of 2
Found at i:1890 original size:15 final size:16
Alignment explanation
Indices: 1858--1890 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1848 AAAATCTTTC
1858 TTTCCCGTTCTAGATT
1 TTTCCCGTTCTAGATT
*
1874 TTTCCCG-TCTGGATT
1 TTTCCCGTTCTAGATT
1889 TT
1 TT
1891 GATCTGCCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.09, C:0.24, G:0.15, T:0.52
Consensus pattern (16 bp):
TTTCCCGTTCTAGATT
Found at i:2659 original size:16 final size:16
Alignment explanation
Indices: 2635--2668 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
2625 TATCGCCGAC
*
2635 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
2651 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
2667 CG
1 CG
2669 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:8390 original size:17 final size:17
Alignment explanation
Indices: 8357--8390 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
8347 TGTGCAAAAG
* *
8357 TATAGTAAGTTATAATT
1 TATAGTAAATTAAAATT
8374 TATAGTAAATTAAAATT
1 TATAGTAAATTAAAATT
8391 AATCATATGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
TATAGTAAATTAAAATT
Found at i:23895 original size:23 final size:23
Alignment explanation
Indices: 23850--23896 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
23840 AACCTAACCT
*
23850 CTAAAAAAATAAAATTAAAAAAA
1 CTAAAAAAATAAAAATAAAAAAA
*
23873 CTAAAAAAATATAAAATATAAAAA
1 CTAAAAAAATA-AAAATAAAAAAA
23897 TGGTATTGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.19
Consensus pattern (23 bp):
CTAAAAAAATAAAAATAAAAAAA
Found at i:35104 original size:29 final size:29
Alignment explanation
Indices: 35069--35150 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
35059 AAACTAAATT
*
35069 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
35098 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
35127 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
35151 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:39873 original size:29 final size:29
Alignment explanation
Indices: 39838--39919 Score: 137
Period size: 29 Copynumber: 2.8 Consensus size: 29
39828 AAACTAAATT
*
39838 GATGTCATTACTTACATCATTTAATTAAA
1 GATGTCATTGCTTACATCATTTAATTAAA
*
39867 GATGTCATTGCTTACATCATTTAATTAAT
1 GATGTCATTGCTTACATCATTTAATTAAA
39896 GATGTCATTGCTTACATCAATTTA
1 GATGTCATTGCTTACATC-ATTTA
39920 GTTAGGTGAG
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 45 0.90
30 5 0.10
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.43
Consensus pattern (29 bp):
GATGTCATTGCTTACATCATTTAATTAAA
Found at i:49112 original size:31 final size:31
Alignment explanation
Indices: 49077--49135 Score: 109
Period size: 31 Copynumber: 1.9 Consensus size: 31
49067 AATTCGGTTA
49077 ATTCAATATGCCCTTCTCACTAGGAACCCCC
1 ATTCAATATGCCCTTCTCACTAGGAACCCCC
*
49108 ATTCAATATGTCCTTCTCACTAGGAACC
1 ATTCAATATGCCCTTCTCACTAGGAACC
49136 TCTTGGGTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.34, G:0.10, T:0.29
Consensus pattern (31 bp):
ATTCAATATGCCCTTCTCACTAGGAACCCCC
Found at i:55899 original size:112 final size:112
Alignment explanation
Indices: 55702--55928 Score: 445
Period size: 112 Copynumber: 2.0 Consensus size: 112
55692 AATGATTTTT
*
55702 AAAGCACTGTGCTAGACAGAAACATGACCTCTCCTCTTCAAGAGAAGAAAAGGGACCAGCACACC
1 AAAGCACTGTGCTAGACAGAAACATGACCTCTCCTCTTCAAGAGAAGAAAAGGGACCACCACACC
55767 TCCAGAAAAGAACCATTCATTTTAGCTACATGTAAAATGTAATCAAG
66 TCCAGAAAAGAACCATTCATTTTAGCTACATGTAAAATGTAATCAAG
55814 AAAGCACTGTGCTAGACAGAAACATGACCTCTCCTCTTCAAGAGAAGAAAAGGGACCACCACACC
1 AAAGCACTGTGCTAGACAGAAACATGACCTCTCCTCTTCAAGAGAAGAAAAGGGACCACCACACC
55879 TCCAGAAAAGAACCATTCATTTTAGCTACATGTAAAATGTAATCAAG
66 TCCAGAAAAGAACCATTCATTTTAGCTACATGTAAAATGTAATCAAG
55926 AAA
1 AAA
55929 CCGAAGTGTG
Statistics
Matches: 114, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
112 114 1.00
ACGTcount: A:0.41, C:0.23, G:0.16, T:0.19
Consensus pattern (112 bp):
AAAGCACTGTGCTAGACAGAAACATGACCTCTCCTCTTCAAGAGAAGAAAAGGGACCACCACACC
TCCAGAAAAGAACCATTCATTTTAGCTACATGTAAAATGTAATCAAG
Found at i:59887 original size:2 final size:2
Alignment explanation
Indices: 59875--59909 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
59865 TTTTTAATTT
*
59875 TA TA AA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59910 TTATTTATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:60813 original size:263 final size:257
Alignment explanation
Indices: 60346--60853 Score: 690
Period size: 263 Copynumber: 1.9 Consensus size: 257
60336 TTTTATTATT
* * *
60346 TCGGGTCGAGTTTCTAATTTATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCG
1 TCGGGTCGAGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGAGTCG
60411 GGTCGGTTTTTTTAAGTGTGATATTCGGGTCGGGTCGAGTTCGGGTTTAGGGTGAAAAACACCCG
66 GGTCGGTTTTTTTAAGTGTGATATT---GT--GG-CGAGTTCGGGTTTAGGGTGAAAAACACCCG
*
60476 ACCCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAACCCTCTATAT
125 ACCCGAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAACCCTCTATAT
* *
60541 ATAATTTTTTTTCAATTAAGTCACTGTTTTTATTGAATAAAAAT-ATTTTTTTATTATTTAGGGT
190 ATAA-TTTTTTTCAATTAAGTCAATATTTTTATTGAATAAAAATGATTTTTTTATTATTTAGGGT
60605 CAGG
254 CAGG
60609 TCGGGTC-AGATTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGTTCGGGTC
1 TCGGGTCGAG-TTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTA--TT-TT--GGTC
60673 GAGTCGGGTCGGGTTTTTTTAAGTGTGATATT-T-G-G-GTT-GGGTTTA-GGTGAAAAAAATCG
60 GAGTCGGGTC-GGTTTTTTTAAGTGTGATATTGTGGCGAGTTCGGGTTTAGGGTG--AAAAA-C-
* * * *
60732 GACTCGACCCGAAAAAAATATATAATTTTATCTTATATATTTAGGAATAATTATAATAATACCCC
120 -ACCCGACCCG-AAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAACCC
60797 TCTATATATAATTTTTTTCAATTAAGTCAATATTTTTATTGAATAAAAATGATTTTT
183 TCTATATATAATTTTTTTCAATTAAGTCAATATTTTTATTGAATAAAAATGATTTTT
60854 ATAATTTATT
Statistics
Matches: 221, Mismatches: 10, Indels: 28
0.85 0.04 0.11
Matches are distributed among these distances:
257 4 0.02
258 7 0.03
259 8 0.04
260 2 0.01
262 49 0.22
263 112 0.51
265 3 0.01
266 2 0.01
268 13 0.06
269 21 0.10
ACGTcount: A:0.29, C:0.11, G:0.20, T:0.40
Consensus pattern (257 bp):
TCGGGTCGAGTTTCTAATTCATATATTCGGATCGGGTCGGGTGAAACTTTATTTTGGTCGAGTCG
GGTCGGTTTTTTTAAGTGTGATATTGTGGCGAGTTCGGGTTTAGGGTGAAAAACACCCGACCCGA
AAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATAACCCTCTATATATAATT
TTTTTCAATTAAGTCAATATTTTTATTGAATAAAAATGATTTTTTTATTATTTAGGGTCAGG
Found at i:61402 original size:76 final size:76
Alignment explanation
Indices: 61215--61424 Score: 275
Period size: 75 Copynumber: 2.8 Consensus size: 76
61205 CAAAGCCAAA
* * **
61215 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCCTGAATG
1 AATTCCAGA-TGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATT-CCCCCCTAAACA
61280 GTTTGGCTCCGAG
64 GTTTGGCTCCGAG
* *
61293 ATTTCCAGAATGCTCGGAGGGAACCGATT--CCCCCATAGGAGGAACCGATTCCCCCCTAAACAT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
* *
61356 TTTTGTTCCGAG
65 TTTGGCTCCGAG
*
61368 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCCA-AGG-GGTACCGATTCCCCCCT
1 AATTCCAG-ATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCT
61425 GTTCAACGGT
Statistics
Matches: 118, Mismatches: 11, Indels: 9
0.86 0.08 0.07
Matches are distributed among these distances:
75 62 0.53
76 24 0.20
77 6 0.05
78 25 0.21
79 1 0.01
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.21
Consensus pattern (76 bp):
AATTCCAGATGCTCGGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:70012 original size:75 final size:76
Alignment explanation
Indices: 69854--70062 Score: 271
Period size: 75 Copynumber: 2.8 Consensus size: 76
69844 CAAAGCCAAA
* * * **
69854 AATTCCAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCCTGAATGG
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCTAAACAG
*
69919 TTTGGCTCTGAG
65 TTTGGCTCCGAG
* *
69931 ATTTCCAGAATGCTCGGAGGGAACCGATT-CCCCCATAGGAGGAACCGATTCCCCCCTAAACATT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
* *
69995 TTTGTTCCGAG
66 TTGGCTCCGAG
* *
70006 AATTCCAGTATGCTCGGAGGGAACCGATTCCCCCCCA-AGG-GGTACCGATTCCCCCCT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCCT
70063 GTTCAACGGT
Statistics
Matches: 117, Mismatches: 13, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
75 82 0.70
76 3 0.03
77 32 0.27
ACGTcount: A:0.23, C:0.32, G:0.23, T:0.22
Consensus pattern (76 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCCTAAACAGT
TTGGCTCCGAG
Found at i:74055 original size:8 final size:8
Alignment explanation
Indices: 74038--74075 Score: 67
Period size: 8 Copynumber: 4.8 Consensus size: 8
74028 TTCTTCTCAT
*
74038 ATACACGC
1 ATACATGC
74046 ATACATGC
1 ATACATGC
74054 ATACATGC
1 ATACATGC
74062 ATACATGC
1 ATACATGC
74070 ATACAT
1 ATACAT
74076 AAATACGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
8 29 1.00
ACGTcount: A:0.39, C:0.26, G:0.11, T:0.24
Consensus pattern (8 bp):
ATACATGC
Found at i:74081 original size:16 final size:16
Alignment explanation
Indices: 74046--74081 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
74036 ATATACACGC
**
74046 ATACATGCATACATGC
1 ATACATGCATACATAA
74062 ATACATGCATACATAA
1 ATACATGCATACATAA
74078 ATAC
1 ATAC
74082 GTATATATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.25
Consensus pattern (16 bp):
ATACATGCATACATAA
Found at i:76931 original size:6 final size:6
Alignment explanation
Indices: 76922--76985 Score: 128
Period size: 6 Copynumber: 10.7 Consensus size: 6
76912 TTATATAGAT
76922 TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG
1 TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG TGTGAG
76970 TGTGAG TGTGAG TGTG
1 TGTGAG TGTGAG TGTG
76986 GAATACATAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 58 1.00
ACGTcount: A:0.16, C:0.00, G:0.50, T:0.34
Consensus pattern (6 bp):
TGTGAG
Found at i:88088 original size:23 final size:23
Alignment explanation
Indices: 88058--88109 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
88048 GAATATCATA
88058 GTATTGTTGGTGCTCTTTTATAT
1 GTATTGTTGGTGCTCTTTTATAT
88081 GTATTGTTGGTGCTCTTTTATAT
1 GTATTGTTGGTGCTCTTTTATAT
88104 GTATTG
1 GTATTG
88110 ATTAAGCTAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.13, C:0.08, G:0.23, T:0.56
Consensus pattern (23 bp):
GTATTGTTGGTGCTCTTTTATAT
Found at i:93030 original size:2 final size:2
Alignment explanation
Indices: 93025--93057 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
93015 ATATGCTTTA
93025 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
93058 AATTTACAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:102636 original size:21 final size:21
Alignment explanation
Indices: 102610--102671 Score: 72
Period size: 21 Copynumber: 3.0 Consensus size: 21
102600 CGTAACTCAG
102610 TTTCCAAATTCGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
* *
102631 TTTCC-ATTTTGCGTTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
** *
102651 AGTCCAAATTCGCATTGCGAT
1 TTTCCAAATTCGCGTTGCGAT
102672 ATCGCAACGC
Statistics
Matches: 33, Mismatches: 7, Indels: 2
0.79 0.17 0.05
Matches are distributed among these distances:
20 16 0.48
21 17 0.52
ACGTcount: A:0.19, C:0.23, G:0.19, T:0.39
Consensus pattern (21 bp):
TTTCCAAATTCGCGTTGCGAT
Found at i:102672 original size:21 final size:21
Alignment explanation
Indices: 102612--102672 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
102602 TAACTCAGTT
**
102612 TCCAAATTCGCGTTGCGATTT
1 TCCAAATTCGCGTTGCGATAG
* *
102633 TCC-ATTTTGCGTTGCGATAG
1 TCCAAATTCGCGTTGCGATAG
*
102653 TCCAAATTCGCATTGCGATA
1 TCCAAATTCGCGTTGCGATA
102673 TCGCAACGCG
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 16 0.50
21 16 0.50
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (21 bp):
TCCAAATTCGCGTTGCGATAG
Found at i:102713 original size:20 final size:20
Alignment explanation
Indices: 102688--102735 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
102678 ACGCGATCTT
102688 AAATTCGCAACTCAGTTTCC
1 AAATTCGCAACTCAGTTTCC
102708 AAATTCGCAACTCAGTTTCC
1 AAATTCGCAACTCAGTTTCC
102728 AAATTCGC
1 AAATTCGC
102736 GTTGCGATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.31, C:0.29, G:0.10, T:0.29
Consensus pattern (20 bp):
AAATTCGCAACTCAGTTTCC
Found at i:102776 original size:41 final size:41
Alignment explanation
Indices: 102731--102952 Score: 390
Period size: 41 Copynumber: 5.4 Consensus size: 41
102721 AGTTTCCAAA
*
102731 TTCGCGTTGCGATAGTCTAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
*
102772 TTCGCGTTGCGATTGTCCAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
*
102813 TTCGCGTTGCGATAGTGCAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
* *
102854 TTCGCGTTGCGATAGTCCAAATTCGCATTGCGATTTTTCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
*
102895 TTCGCGTTACGATAGTCCAAAATCGCATTGCGATTTTCCAT
1 TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
102936 TTCGCGTTGCGATAGTC
1 TTCGCGTTGCGATAGTC
102953 TTACTCTTGC
Statistics
Matches: 170, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 170 1.00
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (41 bp):
TTCGCGTTGCGATAGTCCAAAATCGCATTGCGATTTTCCAT
Found at i:103220 original size:21 final size:21
Alignment explanation
Indices: 103190--103268 Score: 97
Period size: 21 Copynumber: 3.8 Consensus size: 21
103180 CAAATGCACG
*
103190 CGCAATGCGATTTTGGACTAT
1 CGCAACGCGATTTTGGACTAT
** **
103211 CGCAACGCGA-AATGGAAAAT
1 CGCAACGCGATTTTGGACTAT
103231 CGCAACGCGATTTTGGACTAT
1 CGCAACGCGATTTTGGACTAT
*
103252 CGCAACGCGAATTTGGA
1 CGCAACGCGATTTTGGA
103269 AACTGAGTAG
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 16 0.34
21 31 0.66
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.23
Consensus pattern (21 bp):
CGCAACGCGATTTTGGACTAT
Found at i:103241 original size:41 final size:41
Alignment explanation
Indices: 103190--103417 Score: 219
Period size: 41 Copynumber: 5.8 Consensus size: 41
103180 CAAATGCACG
*
103190 CGCAATGCGATTTTGGACTATCGCAACGCGAAATGGAAAAT
1 CGCAATGCGAATTTGGACTATCGCAACGCGAAATGGAAAAT
* * * *
103231 CGCAACGCGATTTTGGACTATCGCAACGCGAATTTGGAAACT
1 CGCAATGCGAATTTGGACTATCGCAACGCGAA-ATGGAAAAT
* * * *
103273 -G-AGTAGCGAATTT--A--A--G-ATCGCG--TTGCG-ATAT
1 CGCAAT-GCGAATTTGGACTATCGCAACGCGAAATG-GAAAAT
*
103304 CGCAATGCGAATTTGGACTATCGCAACGTGAAATGGAAAAT
1 CGCAATGCGAATTTGGACTATCGCAACGCGAAATGGAAAAT
* *
103345 CGCAATGCGAATTTCGACTATCGCAACGTGAAATGGAAAAT
1 CGCAATGCGAATTTGGACTATCGCAACGCGAAATGGAAAAT
* *
103386 CACAATGCGATTTTGGACTATCGCAACGCGAA
1 CGCAATGCGAATTTGGACTATCGCAACGCGAA
103418 TTTGGAAACT
Statistics
Matches: 153, Mismatches: 19, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
31 5 0.03
32 10 0.07
33 2 0.01
34 6 0.04
35 1 0.01
36 1 0.01
37 1 0.01
38 1 0.01
39 5 0.03
40 2 0.01
41 112 0.73
42 7 0.05
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.23
Consensus pattern (41 bp):
CGCAATGCGAATTTGGACTATCGCAACGCGAAATGGAAAAT
Found at i:103327 original size:21 final size:21
Alignment explanation
Indices: 103301--103423 Score: 106
Period size: 21 Copynumber: 6.0 Consensus size: 21
103291 CGCGTTGCGA
*
103301 TATCGCAATGCGAATTTGGAC
1 TATCGCAACGCGAATTTGGAC
* * *
103322 TATCGCAACGTGAA-ATGGAA
1 TATCGCAACGCGAATTTGGAC
* * *
103342 AATCGCAATGCGAATTTCGAC
1 TATCGCAACGCGAATTTGGAC
* * *
103363 TATCGCAACGTGAA-ATGGAA
1 TATCGCAACGCGAATTTGGAC
* * * *
103383 AATCACAATGCGATTTTGGAC
1 TATCGCAACGCGAATTTGGAC
103404 TATCGCAACGCGAATTTGGA
1 TATCGCAACGCGAATTTGGA
103424 AACTGAGTAG
Statistics
Matches: 73, Mismatches: 27, Indels: 4
0.70 0.26 0.04
Matches are distributed among these distances:
20 27 0.37
21 46 0.63
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (21 bp):
TATCGCAACGCGAATTTGGAC
Found at i:103538 original size:101 final size:102
Alignment explanation
Indices: 103323--103541 Score: 239
Period size: 101 Copynumber: 2.2 Consensus size: 102
103313 AATTTGGACT
** * *
103323 ATCGCAACGTGAAATGGAAAATCGCAATGCGAATTTCGACTATCGCAACGTGAAATGGAAAATCA
1 ATCGCAACGTG-AATTTAAAATCGCAATGCGAATTTCGACTATAGCAACGCGAAATGGAAAATCA
* * * * *
103388 CAATGCGATTTTGGACTATCGCAACGCGAATTTGGAAA
65 CAATGCAAATTTCGACTATCGCAACGCGAATATGAAAA
* * * *
103426 CT-G-AGTA-GTGAATTTAAGATCGCAATGCGAATTTGGACTATATCAACGCGAAATGGAAAATC
1 ATCGCA--ACGTGAATTTAAAATCGCAATGCGAATTTCGACTATAGCAACGCGAAATGGAAAATC
** *
103488 GTAATGCAAATTTCGACTATCGCAGCGCGAA-ATGAAAA
64 ACAATGCAAATTTCGACTATCGCAACGCGAATATGAAAA
103526 ATCGCAACGTGAATTT
1 ATCGCAACGTGAATTT
103542 GGAAACTGAG
Statistics
Matches: 94, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
100 7 0.07
101 80 0.85
102 5 0.05
103 2 0.02
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (102 bp):
ATCGCAACGTGAATTTAAAATCGCAATGCGAATTTCGACTATAGCAACGCGAAATGGAAAATCAC
AATGCAAATTTCGACTATCGCAACGCGAATATGAAAA
Found at i:103560 original size:121 final size:121
Alignment explanation
Indices: 103405--103632 Score: 375
Period size: 121 Copynumber: 1.9 Consensus size: 121
103395 ATTTTGGACT
*
103405 ATCGCAACGCGAATTTGGAAACTGAGTAGTGAATTTAAGATCGCAATGCGAATTTGGACTATATC
1 ATCGCAACGCGAATTTGGAAACTGAGTAGCGAATTTAAGATCGCAATGCGAATTTGGACTATATC
* * * *
103470 AACGCGAAATGGAAAATCGTAATGCAAATTTCGACTATCGCAGCGCGAAATGAAAA
66 AACGCAAAAAGGAAAATCGCAACGCAAATTTCGACTATCGCAGCGCGAAATGAAAA
* *
103526 ATCGCAACGTGAATTTGGAAACTGAGTTGCGAATTTAAGATCGCAATGCGAATTTGGACTATATC
1 ATCGCAACGCGAATTTGGAAACTGAGTAGCGAATTTAAGATCGCAATGCGAATTTGGACTATATC
* *
103591 AACGCAAAAAGGAAAATCGCAACGCGAATTTGGACTATCGCA
66 AACGCAAAAAGGAAAATCGCAACGCAAATTTCGACTATCGCA
103633 ATGCGAATTT
Statistics
Matches: 98, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
121 98 1.00
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.23
Consensus pattern (121 bp):
ATCGCAACGCGAATTTGGAAACTGAGTAGCGAATTTAAGATCGCAATGCGAATTTGGACTATATC
AACGCAAAAAGGAAAATCGCAACGCAAATTTCGACTATCGCAGCGCGAAATGAAAA
Found at i:103632 original size:21 final size:21
Alignment explanation
Indices: 103565--103643 Score: 70
Period size: 21 Copynumber: 3.8 Consensus size: 21
103555 CGAATTTAAG
*
103565 ATCGCAATGCGAATTTGGACT
1 ATCGCAACGCGAATTTGGACT
** *** **
103586 ATATCAACGC-AAAAAGGAAA
1 ATCGCAACGCGAATTTGGACT
103606 ATCGCAACGCGAATTTGGACT
1 ATCGCAACGCGAATTTGGACT
*
103627 ATCGCAATGCGAATTTG
1 ATCGCAACGCGAATTTG
103644 AAAACTGAGT
Statistics
Matches: 41, Mismatches: 16, Indels: 2
0.69 0.27 0.03
Matches are distributed among these distances:
20 13 0.32
21 28 0.68
ACGTcount: A:0.37, C:0.19, G:0.22, T:0.23
Consensus pattern (21 bp):
ATCGCAACGCGAATTTGGACT
Found at i:103647 original size:41 final size:41
Alignment explanation
Indices: 103301--103647 Score: 140
Period size: 41 Copynumber: 8.5 Consensus size: 41
103291 CGCGTTGCGA
** * * *
103301 TATCGCAATGCGAATTTGGACTATCGCAACGTGAA-ATGGAA
1 TATCGCAATGCGAATTT-GAAAATCGCAACGCGAATTTGGAC
* ** * * *
103342 AATCGCAATGCGAATTTCGACTATCGCAACGTGAA-ATGGAA
1 TATCGCAATGCGAATTT-GAAAATCGCAACGCGAATTTGGAC
* * * **
103383 AATCACAATGCGATTTTGGACTATCGCAACGCGAATTTGGA-
1 TATCGCAATGCGAATTT-GAAAATCGCAACGCGAATTTGGAC
* * * * *
103424 -AACTG-AGTAGTGAATTT-AAGATCGCAATGCGAATTTGGAC
1 TATC-GCAAT-GCGAATTTGAAAATCGCAACGCGAATTTGGAC
** * * * * * * *
103464 TATATCAACGCGAAATGGAAAATCGTAATGCAAATTTCGAC
1 TATCGCAATGCGAATTTGAAAATCGCAACGCGAATTTGGAC
** * *
103505 TATCGCAGCGCGAA-ATGAAAAATCGCAACGTGAATTTGGA-
1 TATCGCAATGCGAATTTG-AAAATCGCAACGCGAATTTGGAC
* * * *
103545 -AACTG-AGTTGCGAATTT-AAGATCGCAATGCGAATTTGGAC
1 TATC-GCA-ATGCGAATTTGAAAATCGCAACGCGAATTTGGAC
** * * ***
103585 TATATCAACGCAAAAAGGAAAATCGCAACGCGAATTTGGAC
1 TATCGCAATGCGAATTTGAAAATCGCAACGCGAATTTGGAC
103626 TATCGCAATGCGAATTTGAAAA
1 TATCGCAATGCGAATTTGAAAA
103648 CTGAGTTGCG
Statistics
Matches: 229, Mismatches: 62, Indels: 30
0.71 0.19 0.09
Matches are distributed among these distances:
39 41 0.18
40 20 0.09
41 164 0.72
42 4 0.02
ACGTcount: A:0.37, C:0.17, G:0.22, T:0.24
Consensus pattern (41 bp):
TATCGCAATGCGAATTTGAAAATCGCAACGCGAATTTGGAC
Found at i:103893 original size:16 final size:17
Alignment explanation
Indices: 103872--103904 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
103862 ATTTTATAAA
*
103872 TATTA-TTGGATTGTTT
1 TATTATTTGGAATGTTT
103888 TATTATTTGGAATGTTT
1 TATTATTTGGAATGTTT
103905 CATTCTCTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.21, C:0.00, G:0.18, T:0.61
Consensus pattern (17 bp):
TATTATTTGGAATGTTT
Found at i:115891 original size:25 final size:25
Alignment explanation
Indices: 115858--115909 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
115848 ATATAGGAAG
115858 GGGACAATGAAAAGTTAGTAATTTA
1 GGGACAATGAAAAGTTAGTAATTTA
115883 GGGACAATGAAAAGTTAGTAATTTA
1 GGGACAATGAAAAGTTAGTAATTTA
115908 GG
1 GG
115910 AGAACTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.04, G:0.27, T:0.27
Consensus pattern (25 bp):
GGGACAATGAAAAGTTAGTAATTTA
Found at i:126515 original size:14 final size:14
Alignment explanation
Indices: 126496--126536 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 14
126486 CCGAATCGAA
126496 CCGAACCGAAAAAC
1 CCGAACCGAAAAAC
126510 CCGAACCGTTAAAAAAC
1 CCGAACCG---AAAAAC
126527 CCGAACCGAA
1 CCGAACCGAA
126537 CCGAAAAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 10 0.42
17 14 0.58
ACGTcount: A:0.46, C:0.34, G:0.15, T:0.05
Consensus pattern (14 bp):
CCGAACCGAAAAAC
Found at i:148251 original size:3 final size:3
Alignment explanation
Indices: 148243--148302 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
148233 ATAATGAGTA
148243 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
148291 AAT AAT AAT AAT
1 AAT AAT AAT AAT
148303 GGAGCTTGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:152963 original size:24 final size:24
Alignment explanation
Indices: 152936--152981 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
152926 AGAGTCATAT
152936 TAACGAGTCGTAGTCATTTTTCCG
1 TAACGAGTCGTAGTCATTTTTCCG
*
152960 TAACTAGTCGTAGTCATTTTTC
1 TAACGAGTCGTAGTCATTTTTC
152982 AATCTGTGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.22, C:0.20, G:0.17, T:0.41
Consensus pattern (24 bp):
TAACGAGTCGTAGTCATTTTTCCG
Found at i:155200 original size:30 final size:29
Alignment explanation
Indices: 155166--155225 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
155156 TCAAACTCTT
155166 AATTCTA-ACAAACTAAAAATCCTAAATAAA
1 AATTCTATACAAACT-AAAATCCT-AATAAA
* *
155196 AATTCTATGCAAACTAAATTCCTAATAAA
1 AATTCTATACAAACTAAAATCCTAATAAA
155225 A
1 A
155226 TAATAAAATC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 7 0.26
30 14 0.52
31 6 0.22
ACGTcount: A:0.55, C:0.17, G:0.02, T:0.27
Consensus pattern (29 bp):
AATTCTATACAAACTAAAATCCTAATAAA
Found at i:158059 original size:23 final size:23
Alignment explanation
Indices: 158016--158080 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
158006 TAATTATTAA
* *
158016 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
158037 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
158060 -ATATTTTTTAATATTATAATA
1 AATA-TTTATAATAATATAATA
158081 AAATAATCAA
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
21 11 0.30
22 7 0.19
23 19 0.51
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:158061 original size:26 final size:24
Alignment explanation
Indices: 157999--158061 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
157989 CATTTTAATC
157999 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
158023 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
158046 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
158062 ATTTTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:158080 original size:31 final size:33
Alignment explanation
Indices: 158027--158097 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 33
158017 ATATTTAAAA
*
158027 TATATTTATTAATATTTATAATAATATAAT-AT
1 TATATTTATTAATATTTATAATAAAATAATAAT
*
158059 TATATTTTTTAATA-TTATAATAAAATAATCAAT
1 TATATTTATTAATATTTATAATAAAATAAT-AAT
158092 TATATT
1 TATATT
158098 ATAAAAATGT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 14 0.40
32 13 0.37
33 8 0.23
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (33 bp):
TATATTTATTAATATTTATAATAAAATAATAAT
Found at i:158192 original size:27 final size:27
Alignment explanation
Indices: 158156--158246 Score: 89
Period size: 27 Copynumber: 3.3 Consensus size: 27
158146 TATTAATAAA
*
158156 AAATTATATTATTTATTAATTTAATAT
1 AAATAATATTATTTATTAATTTAATAT
*
158183 AAATAATATTATTAAATT-A-TTAATAAT
1 AAATAATATTATT-TATTAATTTAAT-AT
*
158210 GAATAATATTATTTA-TATATTTAATATT
1 AAATAATATTATTTATTA-ATTTAATA-T
158238 AATATAATA
1 AA-ATAATA
158247 ATCTAATAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
25 1 0.02
26 6 0.12
27 29 0.56
28 10 0.19
29 6 0.12
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.49
Consensus pattern (27 bp):
AAATAATATTATTTATTAATTTAATAT
Found at i:158199 original size:54 final size:56
Alignment explanation
Indices: 158046--158255 Score: 168
Period size: 54 Copynumber: 3.8 Consensus size: 56
158036 TAATATTTAT
* * * *
158046 AATAATATAATATTATATTTTTTAATATTATAATAA-A-ATAATCAATTATATTATAAAA
1 AATAATATTAT-TTATA-TATTTAATATTA-AATAATATATAATAAATTAT-TAATAAAA
* * * *
158104 ATGTAAGA-TA-TTATAT-TTTTAT-TTTAATAATATATAATAAATTATTAATAAAA
1 A-ATAATATTATTTATATATTTAATATTAAATAATATATAATAAATTATTAATAAAA
* * **
158157 AATTATATTATTTAT-TAATTTAATA-TAAATAATAT-TATTAAATTATTAATAATG
1 AATAATATTATTTATAT-ATTTAATATTAAATAATATATAATAAATTATTAATAAAA
*
158211 AATAATATTATTTATATATTTAATATTAATATAATAATCTAATAA
1 AATAATATTATTTATATATTTAATATTAA-ATAAT-ATATAATAA
158256 TAATTTAATA
Statistics
Matches: 122, Mismatches: 17, Indels: 26
0.74 0.10 0.16
Matches are distributed among these distances:
52 8 0.07
53 14 0.11
54 58 0.48
55 19 0.16
56 10 0.08
57 2 0.02
58 7 0.06
59 4 0.03
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (56 bp):
AATAATATTATTTATATATTTAATATTAAATAATATATAATAAATTATTAATAAAA
Found at i:158273 original size:54 final size:52
Alignment explanation
Indices: 158129--158273 Score: 134
Period size: 54 Copynumber: 2.7 Consensus size: 52
158119 TTTTTATTTT
* *
158129 AATAATATATAATAAATTATTAATAAAAAATTATATTATTTATTAATTTAATATA
1 AATAATAT-TAATAAATAATT-ATAATAAA-TATATTATTTATTAATTTAATATA
* * *
158184 AATAATATTATTAAATTATTAATAATGAATAATATTATTTA-TATATTTAATATTA
1 AATAATATTAATAAATAATT-ATAATAAAT-ATATTATTTATTA-ATTTAATA-TA
158239 ATATAATAATCTAAT-AATAATT-TAATAAATATATT
1 A-ATAAT-AT-TAATAAATAATTATAATAAATATATT
158274 TAAAACATAC
Statistics
Matches: 78, Mismatches: 6, Indels: 13
0.80 0.06 0.13
Matches are distributed among these distances:
53 3 0.04
54 41 0.53
55 18 0.23
56 5 0.06
57 8 0.10
58 3 0.04
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (52 bp):
AATAATATTAATAAATAATTATAATAAATATATTATTTATTAATTTAATATA
Found at i:158401 original size:20 final size:20
Alignment explanation
Indices: 158361--158417 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
158351 TTTTTATTTC
* * *
158361 AATAAAATATATCAATTATA
1 AATAAAATATTTTAATAATA
158381 AA-AATAATATTTTAATAATA
1 AATAA-AATATTTTAATAATA
*
158401 AATAAATTATTTTAATA
1 AATAAAATATTTTAATA
158418 TTTTAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.06
20 27 0.87
21 2 0.06
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (20 bp):
AATAAAATATTTTAATAATA
Found at i:158407 original size:22 final size:23
Alignment explanation
Indices: 158380--158435 Score: 64
Period size: 22 Copynumber: 2.5 Consensus size: 23
158370 TATCAATTAT
158380 AAAAATAATATTTTAATA-ATAA
1 AAAAATAATATTTTAATATATAA
* *
158402 ATAAAT--TATTTTAATATTTTAA
1 AAAAATAATATTTTAATA-TATAA
158424 AAAAATAATATT
1 AAAAATAATATT
158436 AAGTTTTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
20 10 0.37
22 13 0.48
24 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAATAATATTTTAATATATAA
Found at i:166765 original size:24 final size:24
Alignment explanation
Indices: 166738--166785 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
166728 GGCTCGATTT
*
166738 TCTTCCAACAGTCAGACCTTTTAA
1 TCTTCCAACAGTCAAACCTTTTAA
166762 TCTTCCAACAGTCAAACCTTTTAA
1 TCTTCCAACAGTCAAACCTTTTAA
166786 ATTCCAATTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.31, C:0.29, G:0.06, T:0.33
Consensus pattern (24 bp):
TCTTCCAACAGTCAAACCTTTTAA
Found at i:167154 original size:24 final size:26
Alignment explanation
Indices: 167127--167184 Score: 66
Period size: 29 Copynumber: 2.2 Consensus size: 26
167117 CTCCTACAGG
*
167127 TAATTT-A-CTTCACTGTAATTTGTT
1 TAATTTCATCTTCAATGTAATTTGTT
167151 TAATTGCTTCATCTTCAATGTAATTTGTT
1 TAA-T--TTCATCTTCAATGTAATTTGTT
167180 TAATT
1 TAATT
167185 GTTTATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 8
0.76 0.03 0.22
Matches are distributed among these distances:
24 3 0.11
25 1 0.04
26 1 0.04
27 2 0.07
28 2 0.07
29 19 0.68
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (26 bp):
TAATTTCATCTTCAATGTAATTTGTT
Found at i:171352 original size:23 final size:24
Alignment explanation
Indices: 171302--171352 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 24
171292 TTTTTTTATT
* * *
171302 TAAAATTAATATAAAAATTGTTAT
1 TAAAAATAATATAAAAATTGATAA
*
171326 TAAAAATAATAT-TAAATTGATAA
1 TAAAAATAATATAAAAATTGATAA
171349 TAAA
1 TAAA
171353 TGTGGATTTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 12 0.52
24 11 0.48
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (24 bp):
TAAAAATAATATAAAAATTGATAA
Found at i:189157 original size:3 final size:3
Alignment explanation
Indices: 189143--189187 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
189133 CAAAATGTAT
* *
189143 TAA TAA -AA TAA TAA TAA TAA TAC TAA TTA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
189188 TACAATTAGA
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
2 2 0.05
3 35 0.95
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:189468 original size:40 final size:40
Alignment explanation
Indices: 189348--189469 Score: 111
Period size: 40 Copynumber: 3.0 Consensus size: 40
189338 TTGGTTGTTG
*
189348 GGGACGACACTGCTCATACATGATGAAGAGTTCTGGTCGTATAA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTC----AA
* ** * * * **
189392 AGG-TGACAAGGTTCCTACATGATGAGGAAATCTGGTCAA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCAA
*
189431 GGGATGACACTGCTCATACATGATGAAGAGTTATGGTCA
1 GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCA
189470 TCTTTAGGAG
Statistics
Matches: 59, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
39 4 0.07
40 27 0.46
43 26 0.44
44 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (40 bp):
GGGATGACACTGCTCATACATGATGAAGAGTTCTGGTCAA
Found at i:189560 original size:42 final size:40
Alignment explanation
Indices: 189524--189986 Score: 117
Period size: 40 Copynumber: 10.7 Consensus size: 40
189514 CTGGTTATTT
189524 AGGATGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAG
1 AGGATGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAG
* * * *
189564 GGGATGACACTGCTCATACGTGATGAAGAGTTATGGCCATCTTTAGG
1 AGGATGACACGGCTCCTACGTGATGAAGAGTTCTGG---TC---A-G
* * * * * * * *
189611 TAGGGCGATAATACGGTTCCTACATGATGAGGACG-GCTGGTTATCT
1 -A--G-GATGACACGGCTCCTACGTGATGAAGA-GTTCTGGTCA--G
* * * **
189657 ATGGTTGACACGGCTCCTACATGATGAGGAAATCTGGTCAG
1 A-GGATGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAG
* * * *
189698 GGGATGACATGACTCATACGTGATGAAGAGTTCTGGCCATCTTTAGG
1 AGGATGACACGGCTCCTACGTGATGAAGAGTTCTGG---TC---A-G
* * * * *
189745 AAGGGCGATAACACGGTTCCTACGTGATGAGGACG-GCTGGTTAACTG
1 -A--G-GATGACACGGCTCCTACGTGATGAAGA-GTTCTGG-T--CAG
* * *
189792 TGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTC-G
1 AGGATGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAG
* * *
189831 GGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAA
1 AGG-ATGACACGGCTCCTACGTGATGAAGAGTTCTGG---TC-AG
* * * * * * *
189876 AGGTGATAACACGGTTCCTACATGATGAGGACG-GCTGGTTATCT
1 A-G-GATGACACGGCTCCTACGTGATGAAGA-GTTCTGGTCA--G
* *
189920 ATGGTTGACACGGCTCCTACGTGATGAAGAGATCTGGTC-G
1 A-GGATGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAG
* * *
189960 GGGAATGACACGGTTCCTACATGATGA
1 AGG-ATGACACGGCTCCTACGTGATGA
189987 GGACGGCTGG
Statistics
Matches: 303, Mismatches: 78, Indels: 84
0.65 0.17 0.18
Matches are distributed among these distances:
39 5 0.02
40 110 0.36
42 4 0.01
43 90 0.30
44 4 0.01
45 2 0.01
46 28 0.09
47 5 0.02
48 1 0.00
49 1 0.00
50 2 0.01
51 49 0.16
52 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (40 bp):
AGGATGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAG
Found at i:189728 original size:134 final size:132
Alignment explanation
Indices: 189395--190139 Score: 906
Period size: 134 Copynumber: 5.6 Consensus size: 132
189385 CGTATAAAGG
* * * * * * *
189395 TGACAAGGTTCCTACATGATGAGGAAATCTGGTCAAGGG-ATGACACTGCTCATACATGATGAAG
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGAATGACA-TGCTCATACGTGATGAAG
* * * * * *
189459 AGTTATGGTCATCTTTAGGAGGAGTGATAACCCGATTCCTACGTGATGAGGACGGCTGGTTATTT
64 AGTTCTGGCCATCTTTAGGAGG-GTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCT
*
189524 A-GGA
128 ATGGT
*
189528 TGACACGGCTCCTACGTGATGAAGAGTTCTGGTCAGGGG-ATGACACTGCTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGAATGACA-TGCTCATACGTGATGAAG
* * *
189592 AGTTATGGCCATCTTTAGGTAGGGCGATAATACGGTTCCTACATGATGAGGACGGCTGGTTATCT
64 AGTTCTGGCCATCTTTAGG-AGGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCT
189657 ATGGT
128 ATGGT
* * *
189662 TGACACGGCTCCTACATGATGAGGAAATCTGGTCAGGGG-ATGACATGACTCATACGTGATGAAG
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTC-GGGGAATGACATG-CTCATACGTGATGAAG
* * *
189726 AGTTCTGGCCATCTTTAGGAAGGGCGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTAACT
64 AGTTCTGGCCATCTTTAGG-AGGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCT
*
189791 GTGGT
128 ATGGT
*
189796 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACA-TGCTCATACGTGATGAAGA
*
189861 GTTCTGGCCATC--TA--AAGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTAT
65 GTTCTGGCCATCTTTAGGAGGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTAT
189922 GGT
130 GGT
* * * * *
189925 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACA-TGCTCATACGTGATGAAGA
*
189990 CG-GCTGGCCATC-TTA--A-GGTGATAACAACGGTTCCTACATGATGAGGACGGCTGGTTATCT
65 -GTTCTGGCCATCTTTAGGAGGGTGATAAC-ACGGTTCCTACATGATGAGGACGGCTGGTTATCT
190050 ATGGT
128 ATGGT
* * * * *
190055 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACA-TGCTCATACGTGATGAAGA
*
190120 CG-GCTGGCCATCTTTAGGAG
65 -GTTCTGGCCATCTTTAGGAG
190140 TTATGGTTTC
Statistics
Matches: 560, Mismatches: 40, Indels: 23
0.90 0.06 0.04
Matches are distributed among these distances:
129 124 0.22
130 120 0.21
131 3 0.01
132 2 0.00
133 118 0.21
134 192 0.34
135 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (132 bp):
TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACATGCTCATACGTGATGAAGAG
TTCTGGCCATCTTTAGGAGGGTGATAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATG
GT
Found at i:189948 original size:89 final size:83
Alignment explanation
Indices: 189836--189996 Score: 216
Period size: 83 Copynumber: 1.9 Consensus size: 83
189826 GGTCGGGGAA
* *
189836 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTG-ATAACACGGTTCCTACATG
1 TGACACGGCTCATACGTGATGAAGAGATCTGG---TC----GGGGAATAACACGGTTCCTACATG
189900 ATGAGGACGGCTGGTTATCTATGGT
59 ATGAGGACGGCTGGTTATCTATGGT
* *
189925 TGACACGGCTCCTACGTGATGAAGAGATCTGGTCGGGGAATGACACGGTTCCTACATGATGAGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATAACACGGTTCCTACATGATGAGGA
189990 CGGCTGG
66 CGGCTGG
189997 CCATCTTAAG
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
82 3 0.04
83 32 0.48
86 2 0.03
89 30 0.45
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (83 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGTCGGGGAATAACACGGTTCCTACATGATGAGGA
CGGCTGGTTATCTATGGT
Found at i:189985 original size:40 final size:40
Alignment explanation
Indices: 189796--190116 Score: 136
Period size: 40 Copynumber: 7.5 Consensus size: 40
189786 TAACTGTGGT
*
189796 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACATGATGAAGAG-TCTGGATCAGGGG-A
* * *
189836 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCCTACATGATGAAGAG-TCTGG--ATC---AGGGGA
* * * * * *
189882 TAACACGGTTCCTACATGATGAGGACGGCTGGTTATCTA-TGGT
1 TGACACGGCTCCTACATGATGAAGA-GTCTGG--ATC-AGGGGA
*
189925 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACATGATGAAGAG-TCTGGATCAGGGG-A
* * * *
189965 TGACACGGTTCCTACATGATGAGGACGGCTGGCCATCTTAAGGTGA
1 TGACACGGCTCCTACATGATGAAGA-GTCTGG--ATC---AGGGGA
* * * * * *
190011 TAACAACGGTTCCTACATGATGAGGACGGCTGGTTATCTA-TGGT
1 TGAC-ACGGCTCCTACATGATGAAGA-GTCTGG--ATC-AGGGGA
*
190055 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCCTACATGATGAAGAG-TCTGGATCAGGGG-A
*
190095 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACATGATGA
190117 GGACGGCTGG
Statistics
Matches: 215, Mismatches: 43, Indels: 46
0.71 0.14 0.15
Matches are distributed among these distances:
39 4 0.02
40 80 0.37
41 1 0.00
42 2 0.01
43 52 0.24
44 5 0.02
45 1 0.00
46 32 0.15
47 38 0.18
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (40 bp):
TGACACGGCTCCTACATGATGAAGAGTCTGGATCAGGGGA
Found at i:190087 original size:43 final size:43
Alignment explanation
Indices: 189755--190079 Score: 186
Period size: 43 Copynumber: 7.5 Consensus size: 43
189745 AAGGGCGATA
* * * *
189755 ACACGGTTCCTACGTGATGAGGACGGCTGGTTAACTGTGGTTG
1 ACACGGCTCCTACGTGATGAAGACGGCTGGTTATCTATGGTTG
* ** *
189798 ACACGGCTCCTACGTGATGAAGA-GATCTGG---TC-GGGGAATG
1 ACACGGCTCCTACGTGATGAAGACG-GCTGGTTATCTATGG-TTG
* * ** * *
189838 ACACGGCTCATACGTGATGAAGA-GTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGACG-GCTGGTTATCT-ATGGT--TG
* * *
189884 ACACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAAGACGGCTGGTTATCTATGGTTG
* ** *
189927 ACACGGCTCCTACGTGATGAAGA-GATCTGG---TC-GGGGAATG
1 ACACGGCTCCTACGTGATGAAGACG-GCTGGTTATCTATGG-TTG
* * * ** * *
189967 ACACGGTTCCTACATGATGAGGACGGCTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAAGACGGCTGGTTATC-TATGGT--TG
* * *
190013 ACAACGGTTCCTACATGATGAGGACGGCTGGTTATCTATGGTTG
1 AC-ACGGCTCCTACGTGATGAAGACGGCTGGTTATCTATGGTTG
190057 ACACGGCTCCTACGTGATGAAGA
1 ACACGGCTCCTACGTGATGAAGA
190080 GATCTGGTCG
Statistics
Matches: 218, Mismatches: 43, Indels: 42
0.72 0.14 0.14
Matches are distributed among these distances:
39 5 0.02
40 59 0.27
41 1 0.00
42 2 0.01
43 72 0.33
44 3 0.01
45 8 0.04
46 36 0.17
47 32 0.15
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.25
Consensus pattern (43 bp):
ACACGGCTCCTACGTGATGAAGACGGCTGGTTATCTATGGTTG
Found at i:190185 original size:28 final size:28
Alignment explanation
Indices: 190165--190226 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
190155 AAACCAAATT
190165 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
190193 AAAGATTTGTTTCAAGAA-AAATAAACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
190221 AAAGAT
1 AAAGAT
190227 GATATTTTTA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 29 0.94
29 2 0.06
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.24
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:191167 original size:66 final size:66
Alignment explanation
Indices: 191091--191314 Score: 308
Period size: 67 Copynumber: 3.4 Consensus size: 66
191081 AGAGATTTAC
*** * * *
191091 TTCAAAAGAAACGGTCTCAAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTT
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAATT-TTGTTTCAA-AGAAACAGACTCAAAGATTTT
*
191154 CGT
64 TGT
*
191157 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAGACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAATTTTGTTT-CAAAGAAACAGACTCAAAGATTTTT
191222 GT
65 GT
* *
191224 TTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTT
1 TTCAAAAGAAATTATCTCAAGAGAGACAAAATTTTGTTT-CAAAGAAACAGACTCAAAGATTTTT
191289 GT
65 GT
191291 TTCAAAAGAAATTATCTCAAGAGA
1 TTCAAAAGAAATTATCTCAAGAGA
191315 TTTTTTTTTC
Statistics
Matches: 145, Mismatches: 10, Indels: 5
0.91 0.06 0.03
Matches are distributed among these distances:
65 1 0.01
66 31 0.21
67 111 0.77
68 2 0.01
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.29
Consensus pattern (66 bp):
TTCAAAAGAAATTATCTCAAGAGAGACAAAATTTTGTTTCAAAGAAACAGACTCAAAGATTTTTG
T
Found at i:191202 original size:37 final size:38
Alignment explanation
Indices: 191144--191271 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 38
191134 GAAACAGATT
191144 CAAAGATTTTCGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGATTTT-GTTTCAAAAGAAATTATCTTAAGAGAGA
* **
191183 CAAA-ATTTTGTTTCCAAAG-AA--A-C-----AGACT
1 CAAAGATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
191211 CAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
1 CAAAGA-TTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
*
191250 CAAA-ATTTTGTTTCCAAAGAAA
1 CAAAGATTTTGTTTCAAAAGAAA
191272 CAAACTCAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 24
0.70 0.07 0.24
Matches are distributed among these distances:
28 7 0.10
29 1 0.01
30 13 0.18
31 2 0.03
33 2 0.03
34 2 0.03
36 2 0.03
37 25 0.35
38 6 0.08
39 11 0.15
ACGTcount: A:0.44, C:0.12, G:0.13, T:0.31
Consensus pattern (38 bp):
CAAAGATTTTGTTTCAAAAGAAATTATCTTAAGAGAGA
Found at i:191226 original size:67 final size:67
Alignment explanation
Indices: 191133--191314 Score: 328
Period size: 67 Copynumber: 2.7 Consensus size: 67
191123 TCATTTTAAG
* *
191133 AGAAACAGATTCAAAGATTTTCGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
191198 AA
66 AA
191200 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
191265 AA
66 AA
* *
191267 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCTCAAGAGA
1 AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGA
191315 TTTTTTTTTC
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 111 1.00
ACGTcount: A:0.45, C:0.12, G:0.13, T:0.30
Consensus pattern (67 bp):
AGAAACAGACTCAAAGATTTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAATTTTGTTTCC
AA
Found at i:191310 original size:30 final size:31
Alignment explanation
Indices: 191188--191324 Score: 98
Period size: 30 Copynumber: 4.3 Consensus size: 31
191178 AGAGACAAAA
* *
191188 TTTTGTTTCCAAAGAAACAGACTCAA-AGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAGAGAT
** * * *
191218 TTTTGTTTCAAAAGAAATTATCTTAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACAAAC-TCA-AGAG----AT
*
191255 TTTTGTTTCCAAAGAAACAAACTCAA-AGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAGAGAT
** *
191285 TTTTGTTTCAAAAGAAATTATCTCAAGAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAGAGAT
*
191316 TTTTTTTTC
1 TTTTGTTTC
191325 CGCAAAATTG
Statistics
Matches: 81, Mismatches: 18, Indels: 15
0.71 0.16 0.13
Matches are distributed among these distances:
30 40 0.49
31 14 0.17
32 1 0.01
33 2 0.02
34 2 0.02
35 1 0.01
36 2 0.02
37 19 0.23
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.36
Consensus pattern (31 bp):
TTTTGTTTCAAAAGAAACAAACTCAAGAGAT
Found at i:191487 original size:29 final size:29
Alignment explanation
Indices: 191420--191583 Score: 255
Period size: 29 Copynumber: 5.8 Consensus size: 29
191410 TTCAAAATAG
*
191420 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
191446 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
191475 ACTCCAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
191504 ACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
191533 ACTCAAAGATTTTT-TTCAAGAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
**
191561 ACTCAAAGATTTTTCCTCAAAAG
1 ACTCAAAGATTTTTATTCAAAAG
191584 AAATTGTCTT
Statistics
Matches: 128, Mismatches: 6, Indels: 5
0.92 0.04 0.04
Matches are distributed among these distances:
26 9 0.07
27 4 0.03
28 38 0.30
29 77 0.60
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:191515 original size:58 final size:57
Alignment explanation
Indices: 191420--191583 Score: 260
Period size: 57 Copynumber: 2.9 Consensus size: 57
191410 TTCAAAATAG
*
191420 ACTCAAAGA-TTTTTTCAAAAGAAAC-AACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTTTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
*
191475 ACTCCAAGATTTTTATTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTT-TTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
* **
191533 ACTCAAAGATTTTTTTCAAGAGGAACAAACTCAAAGATTTTTCCTCAAAAG
1 ACTCAAAGATTTTTTTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAG
191584 AAATTGTCTT
Statistics
Matches: 100, Mismatches: 6, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
55 8 0.08
56 4 0.04
57 45 0.45
58 43 0.43
ACGTcount: A:0.46, C:0.16, G:0.10, T:0.28
Consensus pattern (57 bp):
ACTCAAAGATTTTTTTCAAAAGGAACAAACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:191910 original size:36 final size:36
Alignment explanation
Indices: 191826--191929 Score: 133
Period size: 36 Copynumber: 3.0 Consensus size: 36
191816 GAGAAAATGA
* *
191826 TGTCTCAAGCGAGACAAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
191860 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
191896 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
191930 ACGATCTCAA
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
34 20 0.34
35 10 0.17
36 29 0.49
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:191957 original size:36 final size:36
Alignment explanation
Indices: 191827--191945 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
191817 AGAAAATGAT
* * *
191827 GTCTCAAGCGAGACAAAATTTG-CTTTA-AGATATA-
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGA-AAAC
* **
191861 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
191897 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
191932 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
191946 TCAACTTTGT
Statistics
Matches: 70, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
34 20 0.29
35 12 0.17
36 38 0.54
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:192076 original size:105 final size:101
Alignment explanation
Indices: 191897--192129 Score: 276
Period size: 105 Copynumber: 2.3 Consensus size: 101
191887 TAGAGAAATT
*
191897 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* * *
191961 GTGAAACAAATTCGAAATTTAG-ATCTCAAAGGGATAAG
64 GTGAAACAAATTCAAAATTT-GTATCTCAAAGGAAAAAG
* *
191999 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* *
192063 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
*
192104 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
192130 AAAATTCTCA
Statistics
Matches: 114, Mismatches: 9, Indels: 13
0.84 0.07 0.10
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 5 0.04
105 76 0.67
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.19, T:0.31
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGTATCTCAAAGGAAAAAG
Found at i:196190 original size:210 final size:210
Alignment explanation
Indices: 195795--196194 Score: 476
Period size: 210 Copynumber: 1.9 Consensus size: 210
195785 AAATGGATCG
* * * *
195795 CTGCTTCGTCTCAGATCTTCGTCCTTGAAAATAATGCCCCTCAATGATCTGTAATCTGACACCAT
1 CTGCTTCGTCTCAGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCAT
* * * * *
195860 TAATGCCCCGGCGGTACTGAAGTCCGTGCGTCGCTCCTTGATGGATAGCGATGAAATAATTATAG
66 TAATACCCCGGCGATACTGAAGTCCGTGCGTCACTCCCTGATGGATAACGATGAAATAATTATAG
* * * * * * *
195925 ATGAGAATCTACTGTTGGATTACTCTTTGGCTCAATGGATCATCGTTTTAGTCTCGAATGTTGCA
131 ATGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATCATCATATCAGTCTCGAATGTTGCA
195990 CAATCTTTGAGCTCA
196 CAATCTTTGAGCTCA
* * * * * * *
196005 CTGCTTCGTCTCGGATCTTTGTACTTGGAACCGATGCCCCTCAATGCTCTGTAAACTAACTCCAT
1 CTGCTTCGTCTCAGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCAT
* * * ** * * * * *
196070 TAATACCTCGGCTATGCTGAAGTTTGTGCTTCACTCCCTGATGGTTAACGATGGAATAATTGTGG
66 TAATACCCCGGCGATACTGAAGTCCGTGCGTCACTCCCTGATGGATAACGATGAAATAATTATAG
* * *
196135 ATGATAATCTACTGCTGGATTACTCCTTAGATCAGTGGATTATCATATCAGTCTCGAATG
131 ATGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATCATCATATCAGTCTCGAATG
196195 ATACACGATC
Statistics
Matches: 154, Mismatches: 36, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
210 154 1.00
ACGTcount: A:0.24, C:0.23, G:0.20, T:0.33
Consensus pattern (210 bp):
CTGCTTCGTCTCAGATCTTCGTACTTGAAAACAATGCCCCTCAATGATCTGTAAACTAACACCAT
TAATACCCCGGCGATACTGAAGTCCGTGCGTCACTCCCTGATGGATAACGATGAAATAATTATAG
ATGAGAATCTACTGCTGGATTACTCCTTAGATCAATGGATCATCATATCAGTCTCGAATGTTGCA
CAATCTTTGAGCTCA
Found at i:200256 original size:3 final size:3
Alignment explanation
Indices: 200248--200285 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
200238 TATTAATAAG
* *
200248 ATA ATA ATA ATA ATA CTA ATT ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
200286 TACAATTAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:200274 original size:18 final size:18
Alignment explanation
Indices: 200251--200287 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
200241 TAATAAGATA
*
200251 ATAATAATAATACTAATT
1 ATAATAATAATAATAATT
200269 ATAATAATAATAATAATT
1 ATAATAATAATAATAATT
200287 A
1 A
200288 CAATTAGATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (18 bp):
ATAATAATAATAATAATT
Found at i:201152 original size:17 final size:17
Alignment explanation
Indices: 201130--201163 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
201120 AACCTTCTTG
201130 ATTTTGCATGCTAAGTA
1 ATTTTGCATGCTAAGTA
201147 ATTTTGCATGCTAAGTA
1 ATTTTGCATGCTAAGTA
201164 TGGCAAGGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.12, G:0.18, T:0.41
Consensus pattern (17 bp):
ATTTTGCATGCTAAGTA
Found at i:210542 original size:2 final size:2
Alignment explanation
Indices: 210535--210563 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
210525 CAATCTAACA
210535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
210564 CTTATTCTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:213722 original size:20 final size:20
Alignment explanation
Indices: 213678--213925 Score: 181
Period size: 20 Copynumber: 12.2 Consensus size: 20
213668 AATGACCAAC
*
213678 AAAATCGCAACGCGAAAT-A-
1 AAAATCGCAACGCG-ATTCAG
*
213697 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTCAG
* **
213717 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
* **
213737 AAAATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCAG
213757 AAAATCGCAACGCGATATTCCA-
1 AAAATCGCAACGCG--ATT-CAG
* * *
213779 AGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCGATTCAG
* *
213799 AGAATCGCAACGCGATCTTTTCTG
1 AAAATCGCAACGCGA----TTCAG
*
213823 --AATCGCAATGCGATTCAG
1 AAAATCGCAACGCGATTCAG
213841 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
213861 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
213881 AAAATCGCAACGCGATTCCA-
1 AAAATCGCAACGCGATT-CAG
*
213901 AGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCAG
213921 AAAAT
1 AAAAT
213926 GAGTAAATTC
Statistics
Matches: 191, Mismatches: 20, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
18 6 0.03
19 21 0.11
20 129 0.68
21 7 0.04
22 24 0.13
23 1 0.01
24 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATTCAG
Found at i:213877 original size:40 final size:40
Alignment explanation
Indices: 213678--213925 Score: 236
Period size: 40 Copynumber: 6.1 Consensus size: 40
213668 AATGACCAAC
* * *
213678 AAAATCGCAACGCGAAAT--AAAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCG-ATTCCAAGAATCGCAACGCGATTCAG
* **** * **
213717 AAAATCGCAACGTTGAAAAGAA-AATCGCAACGTTGA-AAAG
1 AAAATCGCAACG-CGATTCCAAGAATCGCAACG-CGATTCAG
* *
213757 AAAATCGCAACGCGATATTCCAAGAATCGCAATGCGATTAAG
1 AAAATCGCAACGCG--ATTCCAAGAATCGCAACGCGATTCAG
* * * *
213799 AGAATCGCAACGCGATCTTTTC-TGAATCGCAATGCGATTCAG
1 AAAATCGCAACGCGA---TTCCAAGAATCGCAACGCGATTCAG
213841 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
213881 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
1 AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
213921 AAAAT
1 AAAAT
213926 GAGTAAATTC
Statistics
Matches: 176, Mismatches: 21, Indels: 23
0.80 0.10 0.10
Matches are distributed among these distances:
39 18 0.10
40 89 0.51
41 9 0.05
42 57 0.32
43 3 0.02
ACGTcount: A:0.41, C:0.22, G:0.19, T:0.18
Consensus pattern (40 bp):
AAAATCGCAACGCGATTCCAAGAATCGCAACGCGATTCAG
Found at i:214031 original size:6 final size:6
Alignment explanation
Indices: 214020--214117 Score: 182
Period size: 6 Copynumber: 16.7 Consensus size: 6
214010 AGACACGTAT
214020 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
214068 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACC-C GACC-C
1 GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC GACCAC
214114 GACC
1 GACC
214118 CGAGACGAGA
Statistics
Matches: 92, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 10 0.11
6 82 0.89
ACGTcount: A:0.32, C:0.51, G:0.17, T:0.00
Consensus pattern (6 bp):
GACCAC
Found at i:214640 original size:6 final size:6
Alignment explanation
Indices: 214614--214691 Score: 135
Period size: 6 Copynumber: 13.5 Consensus size: 6
214604 TCTCGTCTCG
214614 GGTCG- GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
214659 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
214692 AATACGTGTC
Statistics
Matches: 72, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 15 0.21
6 57 0.79
ACGTcount: A:0.00, C:0.17, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:214945 original size:20 final size:20
Alignment explanation
Indices: 214787--214972 Score: 139
Period size: 20 Copynumber: 9.2 Consensus size: 20
214777 GAATTTACTC
*
214787 ATTTTCTGAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
214807 ATTCTT-GGAATCGCGTTGCG
1 ATT-TTCTAAATCGCGTTGCG
*
214827 ATTTTCTAAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
* * *
214847 ATTCTCTTAATCGCATTGCG
1 ATTTTCTAAATCGCGTTGCG
**
214867 ATTCTTGGAATATCGCGTTGCG
1 ATT-TTCTAA-ATCGCGTTGCG
* *
214889 ATTTTCT--TTTGACCGTTGCG
1 ATTTTCTAAATCG--CGTTGCG
** *
214909 ATTTTCT-TTTCAACGTTGCG
1 ATTTTCTAAATC-GCGTTGCG
214929 ATTTTCTAAATCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
**
214949 ATTTT-TATTTCGCGTTGCG
1 ATTTTCTAAATCGCGTTGCG
214968 ATTTT
1 ATTTT
214973 GTTGGTCATT
Statistics
Matches: 135, Mismatches: 22, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
18 2 0.01
19 19 0.14
20 91 0.67
21 10 0.07
22 13 0.10
ACGTcount: A:0.17, C:0.19, G:0.20, T:0.44
Consensus pattern (20 bp):
ATTTTCTAAATCGCGTTGCG
Found at i:215453 original size:30 final size:30
Alignment explanation
Indices: 215417--215490 Score: 114
Period size: 30 Copynumber: 2.5 Consensus size: 30
215407 AAAATTGAAT
*
215417 TAAACGGGGACGGAGAAAAA-TCGTTTATGC
1 TAAACGGGGACGG-GAAAAACCCGTTTATGC
*
215447 TAAACGGGGACGGGAAAAACCCGTTTATGT
1 TAAACGGGGACGGGAAAAACCCGTTTATGC
215477 TAAACGGGGACGGG
1 TAAACGGGGACGGG
215491 GACGGGTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
29 6 0.15
30 35 0.85
ACGTcount: A:0.34, C:0.15, G:0.34, T:0.18
Consensus pattern (30 bp):
TAAACGGGGACGGGAAAAACCCGTTTATGC
Found at i:215535 original size:12 final size:12
Alignment explanation
Indices: 215507--215555 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
215497 TTTAGTAATC
*
215507 CCCGCTCCGATTA
1 CCCGCCCCGA-TA
215520 CCCGCCCCGATA
1 CCCGCCCCGATA
*
215532 CCCGGCCCGATA
1 CCCGCCCCGATA
* *
215544 CCTGACCCGATA
1 CCCGCCCCGATA
215556 AATATTAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 23 0.72
13 9 0.28
ACGTcount: A:0.18, C:0.49, G:0.18, T:0.14
Consensus pattern (12 bp):
CCCGCCCCGATA
Found at i:215668 original size:12 final size:12
Alignment explanation
Indices: 215651--215681 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
215641 TTAAATATAT
215651 ATACCCGACCCG
1 ATACCCGACCCG
*
215663 ATACCCGGCCCG
1 ATACCCGACCCG
215675 ATACCCG
1 ATACCCG
215682 TTTAAATAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.48, G:0.19, T:0.10
Consensus pattern (12 bp):
ATACCCGACCCG
Found at i:215919 original size:25 final size:25
Alignment explanation
Indices: 215885--215943 Score: 109
Period size: 25 Copynumber: 2.4 Consensus size: 25
215875 GCAATCTCTG
215885 AAATTTTAAGAGGAGTATAATTATA
1 AAATTTTAAGAGGAGTATAATTATA
*
215910 AAATTTTAAGAGGAGTATATTTATA
1 AAATTTTAAGAGGAGTATAATTATA
215935 AAATTTTAA
1 AAATTTTAA
215944 TAAAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.47, C:0.00, G:0.14, T:0.39
Consensus pattern (25 bp):
AAATTTTAAGAGGAGTATAATTATA
Found at i:220250 original size:108 final size:108
Alignment explanation
Indices: 220058--220254 Score: 274
Period size: 108 Copynumber: 1.8 Consensus size: 108
220048 GTTCACGAGA
* * * * *
220058 ATAATGATGATAATGGCTTCTCTTATTCTCTAGAGGAAGGTGGTCACCGCATACATGTTGGGGGA
1 ATAATGATGATAACGGCTTCTCTTATTCTCCAGAGGAAGGTGGTCACAGCAGACATGCTGGGGGA
* **
220123 TCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGGCAGG
66 TCTCCATCTGACTCAGATGCATTAGTTCAACCAATTGGGCAGG
220166 ATAATGATGATAACGGCTTCT-TTAATTCTCCAGA-GAAGGATGGTCACAGCAGACATGCT-GGG
1 ATAATGATGATAACGGCTTCTCTT-ATTCTCCAGAGGAAGG-TGGTCACAGCAGACATGCTGGGG
220228 GATTCTCCATCTGACTCAGATGCATTA
64 GA-TCTCCATCTGACTCAGATGCATTA
220255 ATCCAATCAA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
107 12 0.15
108 66 0.85
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.30
Consensus pattern (108 bp):
ATAATGATGATAACGGCTTCTCTTATTCTCCAGAGGAAGGTGGTCACAGCAGACATGCTGGGGGA
TCTCCATCTGACTCAGATGCATTAGTTCAACCAATTGGGCAGG
Found at i:220277 original size:108 final size:108
Alignment explanation
Indices: 220053--220277 Score: 269
Period size: 108 Copynumber: 2.1 Consensus size: 108
220043 AGGATGTTCA
* * * * *
220053 CGAGAATAATGATGATAATGGCTTCTCTTATTCTCTAGAGGAAGGTGGTCACCGCATACATGTTG
1 CGAG-ATAATGATGATAACGGCTTCTCTTATTCTCCAGAGGAAGGTGGTCACAGCAGACATGCTG
* ** * * *
220118 GGGGATCTTCATCTGACTTGGATGCATTAGTTCAACCAATTGGG
65 GGGGATCTCCATCTGACTCAGATGCATTAATCCAACCAATAGGG
220162 C-AGGATAATGATGATAACGGCTTCT-TTAATTCTCCAGA-GAAGGATGGTCACAGCAGACATGC
1 CGA-GATAATGATGATAACGGCTTCTCTT-ATTCTCCAGAGGAAGG-TGGTCACAGCAGACATGC
*
220224 T-GGGGATTCTCCATCTGACTCAGATGCATTAATCCAATCAATAGGG
63 TGGGGGA-TCTCCATCTGACTCAGATGCATTAATCCAACCAATAGGG
220270 CGAGATAA
1 CGAGATAA
220278 CTCCATCAGT
Statistics
Matches: 99, Mismatches: 12, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
107 12 0.12
108 84 0.85
109 3 0.03
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (108 bp):
CGAGATAATGATGATAACGGCTTCTCTTATTCTCCAGAGGAAGGTGGTCACAGCAGACATGCTGG
GGGATCTCCATCTGACTCAGATGCATTAATCCAACCAATAGGG
Found at i:224833 original size:35 final size:35
Alignment explanation
Indices: 224787--224862 Score: 125
Period size: 35 Copynumber: 2.2 Consensus size: 35
224777 AAAATAGTCC
* *
224787 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
*
224822 TCAATTTCATTCTAAACCCTAAATTCCAAAATAAT
1 TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
224857 TCAATT
1 TCAATT
224863 AAATTCAATT
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 38 1.00
ACGTcount: A:0.39, C:0.24, G:0.01, T:0.36
Consensus pattern (35 bp):
TCAATTTCATTCTAAACCCCAAATTCCAAAATAAT
Found at i:225405 original size:130 final size:130
Alignment explanation
Indices: 225259--225506 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
225249 TATTTATATA
* **
225259 ATCAATTTGGTCCTAAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* *
225324 TTAGCACATGATCATGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
225389 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
1 ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
* * *
225454 TTAACACATGATCATGATATATGTTATTGGTGACACATGTCACCACCTAATTA
66 TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTA
225507 GAAGAAAATT
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.35
Consensus pattern (130 bp):
ATCAATTTGGTCCTAAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTG
TTAACACATGATCATGACACATGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCT
Found at i:225537 original size:130 final size:129
Alignment explanation
Indices: 225273--225537 Score: 309
Period size: 130 Copynumber: 2.0 Consensus size: 129
225263 ATTTGGTCCT
* ** *
225273 AAATTAAATAGAATTTAATAAATTAATCATTTAATTAGGATCTGACATGTGTTAGCACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* *** * * **** *
225338 TGACACGTGTCATTGGTGACACATGTCACCACCTAATTATTTATATATGCTATCAATTTGGTCCT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGT-CA
225403 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
1 AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
* * * *
225468 TGATATATGTTATTGGTGACACATGTCACCACCTAATTAGAAGAAAATTAAGTTA-CAAAGAAGT
66 TGACACATGTCATTGGTGACACATGTCACCACCTAATT--AAGAAAA-TAAGCTATCAAAGAAGT
225532 -A
128 CA
225533 AAATT
1 AAATT
225538 TGGGTCTTGG
Statistics
Matches: 113, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
130 100 0.88
132 8 0.07
133 5 0.04
ACGTcount: A:0.40, C:0.14, G:0.13, T:0.34
Consensus pattern (129 bp):
AAATTAAATAAAATTTAATAAATTAATCATTTAACCAGGATCTGACATGTGTTAACACATGATCA
TGACACATGTCATTGGTGACACATGTCACCACCTAATTAAGAAAATAAGCTATCAAAGAAGTCA
Found at i:225861 original size:28 final size:27
Alignment explanation
Indices: 225830--225892 Score: 63
Period size: 28 Copynumber: 2.3 Consensus size: 27
225820 AGTTGATACA
*
225830 ATATTTTAAAAGAATAAATTTAAGATTT
1 ATATTTTAAAA-AATAAATTTAAGAATT
** * *
225858 ATATATTTTTAAACTAAATTTAATAATT
1 ATAT-TTTAAAAAATAAATTTAAGAATT
225886 ATATTTT
1 ATATTTT
225893 TCATATTTAT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
27 3 0.10
28 21 0.72
29 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (27 bp):
ATATTTTAAAAAATAAATTTAAGAATT
Found at i:225993 original size:16 final size:17
Alignment explanation
Indices: 225972--226004 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
225962 ATTTCTTATT
225972 AAAAATAAAAT-ATTCA
1 AAAAATAAAATGATTCA
*
225988 AAAAATATAATGATTCA
1 AAAAATAAAATGATTCA
226005 TACATTAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.64, C:0.06, G:0.03, T:0.27
Consensus pattern (17 bp):
AAAAATAAAATGATTCA
Found at i:239893 original size:35 final size:35
Alignment explanation
Indices: 239836--239902 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 35
239826 TGGAGTATGG
*
239836 AGGTTCAGCTCGGTCAAACTGGTAATTCCTTATAT
1 AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
* * *
239871 AGGTTCAGCTTGATCGATCTGGTAATTCCTTA
1 AGGTTCAGCTCGATCAAACTGGTAATTCCTTA
239903 CGGACCTAAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 28 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (35 bp):
AGGTTCAGCTCGATCAAACTGGTAATTCCTTATAT
Found at i:240072 original size:24 final size:22
Alignment explanation
Indices: 240037--240081 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
240027 ATTTATGTGA
240037 TTTAAATAACTACAT-GATCATT
1 TTTAAATAACTAC-TCGATCATT
240059 TTTACAATATACTACTCGATCAT
1 TTTA-AATA-ACTACTCGATCAT
240082 GATTTTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 4 0.20
23 5 0.25
24 11 0.55
ACGTcount: A:0.38, C:0.18, G:0.04, T:0.40
Consensus pattern (22 bp):
TTTAAATAACTACTCGATCATT
Found at i:244727 original size:36 final size:34
Alignment explanation
Indices: 244651--244754 Score: 84
Period size: 34 Copynumber: 3.0 Consensus size: 34
244641 AAAAGTGAAA
* * *
244651 TAAAATAATATATACAAATGTAAAATAATAAGAG
1 TAAAATAAAATATACAAATGTAAAATAAAAAAAG
* * *
244685 TTAAATAAAATATACATATGTATATATAAAAAAATG
1 TAAAATAAAATATACAAATGTA-AAATAAAAAAA-G
***
244721 TAAAATAATAGCGTACAAA-GTAAAATAAATAAAA
1 TAAAATAA-AATATACAAATGTAAAATAAA-AAAA
244755 TTAATAAGAA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
34 19 0.35
35 14 0.26
36 15 0.28
37 6 0.11
ACGTcount: A:0.62, C:0.04, G:0.08, T:0.27
Consensus pattern (34 bp):
TAAAATAAAATATACAAATGTAAAATAAAAAAAG
Found at i:244860 original size:137 final size:139
Alignment explanation
Indices: 244712--244990 Score: 490
Period size: 137 Copynumber: 2.0 Consensus size: 139
244702 ATGTATATAT
*
244712 AAAAAAATGTAAAATAATAGCGTACAAAGTAAAATAAATAAAATTAATAAGAACATATAATAATA
1 AAAAAAATGTAAAATAATAGCGTACAAAGTAAAATAAATAAAATTAATAAAAACATATAATAATA
*
244777 TCAATACC-ATATATATATAATAGCTAAATATGAGAGGGAGG-AAAAATATGTATAATAATAATA
66 TCAATACCAATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATAATAATAATA
244840 GAAAAACTA
131 GAAAAACTA
* *
244849 AAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAATAAAAACATATAATAATA
1 AAAAAAATGTAAAATAATAGCGTACAAAGTAAAATAAATAAAATTAATAAAAACATATAATAATA
*
244914 TTAATACCATATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATAATAATAAT
66 TCAATACCA-ATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATAATAATAAT
244979 AGAAAAACTA
130 AGAAAAACTA
244989 AA
1 AA
244991 TAATGAAAAT
Statistics
Matches: 134, Mismatches: 5, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
137 69 0.51
139 33 0.25
140 32 0.24
ACGTcount: A:0.59, C:0.05, G:0.10, T:0.25
Consensus pattern (139 bp):
AAAAAAATGTAAAATAATAGCGTACAAAGTAAAATAAATAAAATTAATAAAAACATATAATAATA
TCAATACCAATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATAATAATAATA
GAAAAACTA
Found at i:245077 original size:139 final size:136
Alignment explanation
Indices: 244711--245045 Score: 389
Period size: 137 Copynumber: 2.4 Consensus size: 136
244701 TATGTATATA
* * * * *
244711 TAAAAAAATGTAAAATAATAGCGTACAAAGTAAAATAAATAAA-ATTAATAAGAACATATAATAA
1 TAAAAAAATGTAAAATAATA--GTATAAAATAAAATAAATAAAGA-TAATAAAAAAATACAATAA
* *
244775 TATCAATACC--ATATATATATAATAGCTAAATATGAGAGGGAGGAAAAATATGTATAATAATAA
63 TATTAATACCATATATATATATAATAGCTAAATATGAGAGGGAGGAAAAATATATATAATAATAA
244838 TAGAAAAAC
128 TAGAAAAAC
* * * *
244847 TAAAAAAAATGTAAAATAATAGCGTATAAAGTAAAATAAATAAAGTTAATAAAAACATATAATAA
1 T-AAAAAAATGTAAAATAATA--GTATAAAATAAAATAAATAAAGATAATAAAAAAATACAATAA
244912 TATTAATACCATATATATATATAATAGCTAAATATGAGAGGGAGGAAAAAATATATATAATAATA
63 TATTAATACCATATATATATATAATAGCTAAATATGAGAGGGAGG-AAAAATATATATAATAATA
244977 ATAGAAAAAC
127 ATAGAAAAAC
* *
244987 T-AAATAATG-AAAATAA-A-TATAATAATAAAA-AAGTAAAGAAATAATAAGATAAAATACAA
1 TAAAAAAATGTAAAATAATAGTATAA-AATAAAATAAATAAAG--ATAATAA-A-AAAATACAA
245046 AATGTATACA
Statistics
Matches: 178, Mismatches: 11, Indels: 19
0.86 0.05 0.09
Matches are distributed among these distances:
133 12 0.07
134 6 0.03
135 6 0.03
136 3 0.02
137 82 0.46
138 7 0.04
139 33 0.19
140 29 0.16
ACGTcount: A:0.61, C:0.04, G:0.10, T:0.25
Consensus pattern (136 bp):
TAAAAAAATGTAAAATAATAGTATAAAATAAAATAAATAAAGATAATAAAAAAATACAATAATAT
TAATACCATATATATATATAATAGCTAAATATGAGAGGGAGGAAAAATATATATAATAATAATAG
AAAAAC
Found at i:245120 original size:9 final size:9
Alignment explanation
Indices: 245108--245141 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
245098 TGAAAACGAA
245108 AAAAATAAT
1 AAAAATAAT
245117 AAAAATAAT
1 AAAAATAAT
*
245126 AAATAATAAG
1 AAA-AATAAT
245136 AAAAAT
1 AAAAAT
245142 GTAATTAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (9 bp):
AAAAATAAT
Found at i:246224 original size:12 final size:12
Alignment explanation
Indices: 246204--246248 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
246194 AAATATGTAA
*
246204 ATATTATATA-T
1 ATATAATATATT
246215 ATATGAATATATT
1 ATAT-AATATATT
246228 ATATAATATATT
1 ATATAATATATT
246240 ATATAATAT
1 ATATAATAT
246249 GATAACGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
11 4 0.13
12 22 0.71
13 5 0.16
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (12 bp):
ATATAATATATT
Found at i:246850 original size:28 final size:28
Alignment explanation
Indices: 246813--246875 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
246803 ATTGAATTAC
* * * *
246813 ATAATAAAATGTTAGACATTAAATTAAA
1 ATAAAAAAATATTAAACACTAAATTAAA
246841 ATAAAAAAATATTAAACACTAAATTAAA
1 ATAAAAAAATATTAAACACTAAATTAAA
246869 ACTAAAA
1 A-TAAAA
246876 CATACGTTGG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 25 0.83
29 5 0.17
ACGTcount: A:0.63, C:0.06, G:0.03, T:0.27
Consensus pattern (28 bp):
ATAAAAAAATATTAAACACTAAATTAAA
Found at i:249330 original size:2 final size:2
Alignment explanation
Indices: 249323--249350 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
249313 TAATGCTTTC
249323 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
249351 TTAATTACAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:250059 original size:34 final size:34
Alignment explanation
Indices: 250014--250109 Score: 117
Period size: 34 Copynumber: 2.8 Consensus size: 34
250004 AATGTATTTG
*
250014 TTATCTTTTTAAATTTAAATATTAAAAGGATCA-TA
1 TTATCTATTTAAATTTAAATATTAAAA-GAT-ATTA
250049 -TATCTATTTAATAATTTAAAT-TTAAAAGATATTA
1 TTATCTATTT-A-AATTTAAATATTAAAAGATATTA
*
250083 TTATCTATTTAAATTTAGATATTAAAA
1 TTATCTATTTAAATTTAAATATTAAAA
250110 TATGTTTAGT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
33 9 0.17
34 20 0.37
35 16 0.30
36 9 0.17
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.47
Consensus pattern (34 bp):
TTATCTATTTAAATTTAAATATTAAAAGATATTA
Found at i:250088 original size:35 final size:36
Alignment explanation
Indices: 250025--250109 Score: 108
Period size: 35 Copynumber: 2.4 Consensus size: 36
250015 TATCTTTTTA
250025 AATTTAAATATTAAAAGGATCATATATCTATTTAAT
1 AATTTAAATATTAAAAGGATCATATATCTATTTAAT
250061 AATTTAAAT-TTAAAA-GAT-ATTATTATCTATTT-A-
1 AATTTAAATATTAAAAGGATCA-TA-TATCTATTTAAT
*
250094 AATTTAGATATTAAAA
1 AATTTAAATATTAAAA
250110 TATGTTTAGT
Statistics
Matches: 45, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
33 9 0.20
34 12 0.27
35 15 0.33
36 9 0.20
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.44
Consensus pattern (36 bp):
AATTTAAATATTAAAAGGATCATATATCTATTTAAT
Found at i:250289 original size:83 final size:83
Alignment explanation
Indices: 250055--250300 Score: 343
Period size: 83 Copynumber: 3.0 Consensus size: 83
250045 CATATATCTA
* *
250055 TTTAATAATTTAAATTTAAAAGATATTATTATCTATTTAAATTTAGATATTAAAATATGTTTAGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAATATGTTTAGT
* * * *
250120 TAGAGTAAAACTTTTAGT
66 TGGAGTAAAACTCTCACT
* * * *
250138 TTTGATATTTTTAATGTAAAATATATTATTATCTGTTTAAATTTAGATATTAAAATATGTTTAGT
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAATATGTTTAGT
250203 TGGAGTAAAACTCTCACT
66 TGGAGTAAAACTCTCACT
* *
250221 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAAATATT-AATTGA-GATTTA
1 TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAAT-ATG-TTTA
*
250284 ATTGGAGTAAAACTCTC
64 GTTGGAGTAAAACTCTC
250301 TCAAAATTCA
Statistics
Matches: 144, Mismatches: 17, Indels: 4
0.87 0.10 0.02
Matches are distributed among these distances:
82 4 0.03
83 140 0.97
ACGTcount: A:0.39, C:0.04, G:0.09, T:0.47
Consensus pattern (83 bp):
TTTAATATTTTAAATTTAAAAGATATTATTATCTGTTTAAATTTAGATATTAAAATATGTTTAGT
TGGAGTAAAACTCTCACT
Found at i:262926 original size:93 final size:93
Alignment explanation
Indices: 262819--262987 Score: 266
Period size: 93 Copynumber: 1.8 Consensus size: 93
262809 TGATTGTGTA
* * *
262819 AACATTACCTGACTGTTTAATTGGTTGTGTTGAGCAAATGCTCTGATCGATTCTATGAAGTTATT
1 AACATCACCCGACTGTTTAATTGGTTGTGTTGAACAAATGCTCTGATCGATTCTATGAAGTTATT
262884 GTTTCATAATCCATTTTGGTGGTTCTGT
66 GTTTCATAATCCATTTTGGTGGTTCTGT
* * * *
262912 AACATCACCCGACTGTTTAATTGGTTGTGTTGAACAAGTGTTGTGATTGATTCTATGAAGTTATT
1 AACATCACCCGACTGTTTAATTGGTTGTGTTGAACAAATGCTCTGATCGATTCTATGAAGTTATT
*
262977 GTTTCTTAATC
66 GTTTCATAATC
262988 GCTGTAACAT
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
93 68 1.00
ACGTcount: A:0.24, C:0.14, G:0.20, T:0.43
Consensus pattern (93 bp):
AACATCACCCGACTGTTTAATTGGTTGTGTTGAACAAATGCTCTGATCGATTCTATGAAGTTATT
GTTTCATAATCCATTTTGGTGGTTCTGT
Found at i:263198 original size:28 final size:28
Alignment explanation
Indices: 263157--263210 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
263147 TGTTTTATAG
* *
263157 AAAAACTTGTAGAGTTGTGATATTGTAA
1 AAAAACTAGAAGAGTTGTGATATTGTAA
263185 AAAAACTAGAAGAGTTGTGATATTGT
1 AAAAACTAGAAGAGTTGTGATATTGT
263211 TCTCGAAAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (28 bp):
AAAAACTAGAAGAGTTGTGATATTGTAA
Found at i:264906 original size:28 final size:28
Alignment explanation
Indices: 264875--264933 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
264865 AAAATTTTAC
* **
264875 CCCCTAAAATTTTATAAGTTCAGTTTCG
1 CCCCTAAAATTTTATAAATTCAAATTCG
264903 CCCCTAAAATTTTATAAATTCAAATTCG
1 CCCCTAAAATTTTATAAATTCAAATTCG
264931 CCC
1 CCC
264934 TGTAACATAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.32, C:0.25, G:0.07, T:0.36
Consensus pattern (28 bp):
CCCCTAAAATTTTATAAATTCAAATTCG
Found at i:273847 original size:27 final size:27
Alignment explanation
Indices: 273816--273880 Score: 130
Period size: 27 Copynumber: 2.4 Consensus size: 27
273806 TTGCAGGTTT
273816 CAACTTCTATTGCTTGCAAGGATGAGG
1 CAACTTCTATTGCTTGCAAGGATGAGG
273843 CAACTTCTATTGCTTGCAAGGATGAGG
1 CAACTTCTATTGCTTGCAAGGATGAGG
273870 CAACTTCTATT
1 CAACTTCTATT
273881 ACAATTGACA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.26, C:0.20, G:0.22, T:0.32
Consensus pattern (27 bp):
CAACTTCTATTGCTTGCAAGGATGAGG
Found at i:293849 original size:13 final size:13
Alignment explanation
Indices: 293831--293866 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
293821 CAATCCAGGC
*
293831 GACATACGGGGGT
1 GACATACGAGGGT
293844 GACATACGAGGGT
1 GACATACGAGGGT
293857 GACATACGAG
1 GACATACGAG
293867 CCATATACGA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.31, C:0.17, G:0.39, T:0.14
Consensus pattern (13 bp):
GACATACGAGGGT
Found at i:294038 original size:93 final size:92
Alignment explanation
Indices: 293880--294087 Score: 348
Period size: 93 Copynumber: 2.3 Consensus size: 92
293870 TATACGAGTC
* * *
293880 ATACGAGCCAATGGGGAGGATGCAACGAGCCATACGAGGCAATGGGGAGCATGCAGGAATAGAGA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAACGGGGAGCATGCAGGAATAGAGA
293945 GCCAATGGGGAGCATGCAACGAGCCAT
66 GCCAATGGGGAGCATGCAACGAGCCAT
*
293972 ATACGAGCC-ATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 ATACGAGCCAATGGGGAGCATGCAACGAGCC--ATACGAGCCAACGGGGAGCATGCAGGAATAGA
294036 GAGCCAATGGGGAGCATGCAACGAGCCAT
64 GAGCCAATGGGGAGCATGCAACGAGCCAT
294065 ATACGAGCCAAT-GGGAGCATGCA
1 ATACGAGCCAATGGGGAGCATGCA
294088 GGAATAGAGA
Statistics
Matches: 109, Mismatches: 4, Indels: 5
0.92 0.03 0.04
Matches are distributed among these distances:
91 20 0.18
92 9 0.08
93 78 0.72
94 2 0.02
ACGTcount: A:0.33, C:0.22, G:0.34, T:0.11
Consensus pattern (92 bp):
ATACGAGCCAATGGGGAGCATGCAACGAGCCATACGAGCCAACGGGGAGCATGCAGGAATAGAGA
GCCAATGGGGAGCATGCAACGAGCCAT
Found at i:294134 original size:60 final size:60
Alignment explanation
Indices: 293976--294134 Score: 284
Period size: 60 Copynumber: 2.6 Consensus size: 60
293966 AGCCATATAC
*
293976 GAGCC-ATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAG-CCAAGGGGAGCATGCAGGAATAGA
*
294036 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAATGGGAGCATGCAGGAATAGA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAAGGGGAGCATGCAGGAATAGA
294096 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCA
1 GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCA
294135 TGCAGGAATA
Statistics
Matches: 96, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
60 66 0.69
61 30 0.31
ACGTcount: A:0.33, C:0.23, G:0.33, T:0.11
Consensus pattern (60 bp):
GAGCCAATGGGGAGCATGCAACGAGCCATATACGAGCCAAGGGGAGCATGCAGGAATAGA
Found at i:294134 original size:93 final size:93
Alignment explanation
Indices: 293880--294115 Score: 326
Period size: 93 Copynumber: 2.6 Consensus size: 93
293870 TATACGAGTC
* * * *
293880 ATACGAGCCAATGGGGAGGATGCAACGAGCCAT--ACGAGGCAATGGGGAGCATGCAGGAATAGA
1 ATACGAGCC-ATGGGGAGCATGCAACGAGCAATAGACGAGCCAACGGGGAGCATGCAGGAATAGA
293943 GAGCCAATGGGGAGCATGCAACGAGCCAT
65 GAGCCAATGGGGAGCATGCAACGAGCCAT
* * *
293972 ATACGAGCCATGGGGAGCATGCAACGAGCCATATACGAGCCCACGGGGAGCATGCAGGAATAGAG
1 ATACGAGCCATGGGGAGCATGCAACGAGCAATAGACGAGCCAACGGGGAGCATGCAGGAATAGAG
294037 AGCCAATGGGGAGCATGCAACGAGCCAT
66 AGCCAATGGGGAGCATGCAACGAGCCAT
*
294065 ATACGAGCCAAT-GGGAGCATGC-A-G-G-AATAGA-GAGCCAATGGGGAGCATGCA
1 ATACGAGCC-ATGGGGAGCATGCAACGAGCAATAGACGAGCCAACGGGGAGCATGCA
294116 ACGAGCCATA
Statistics
Matches: 133, Mismatches: 8, Indels: 10
0.88 0.05 0.07
Matches are distributed among these distances:
88 18 0.14
89 4 0.03
90 1 0.01
91 23 0.17
92 10 0.08
93 75 0.56
94 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.35, T:0.11
Consensus pattern (93 bp):
ATACGAGCCATGGGGAGCATGCAACGAGCAATAGACGAGCCAACGGGGAGCATGCAGGAATAGAG
AGCCAATGGGGAGCATGCAACGAGCCAT
Found at i:294192 original size:29 final size:29
Alignment explanation
Indices: 294148--294256 Score: 200
Period size: 29 Copynumber: 3.8 Consensus size: 29
294138 AGGAATAGAG
* *
294148 AGGTCGCCATGCAGTCCCGGTGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
294177 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
294206 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
294235 AGGTCGCCATGTAGTCCCGGCG
1 AGGTCGCCATGTAGTCCCGGCG
294257 CCATTCCCAT
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
29 78 1.00
ACGTcount: A:0.14, C:0.31, G:0.32, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:294375 original size:36 final size:37
Alignment explanation
Indices: 294307--294380 Score: 141
Period size: 37 Copynumber: 2.0 Consensus size: 37
294297 CATAGATTCC
294307 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
294344 TTCACGTGCTCCCCGCTGCA-TGCCTACACCTCCCAA
1 TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
294380 T
1 T
294381 GCATGCATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 17 0.46
37 20 0.54
ACGTcount: A:0.16, C:0.46, G:0.14, T:0.24
Consensus pattern (37 bp):
TTCACGTGCTCCCCGCTGCATTGCCTACACCTCCCAA
Found at i:294408 original size:18 final size:18
Alignment explanation
Indices: 294385--294419 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
294375 CCCAATGCAT
294385 GCATGTGAACCATTTGAG
1 GCATGTGAACCATTTGAG
294403 GCATGTGAACCATTTGA
1 GCATGTGAACCATTTGA
294420 TTATTGGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.29, C:0.17, G:0.26, T:0.29
Consensus pattern (18 bp):
GCATGTGAACCATTTGAG
Found at i:294550 original size:23 final size:23
Alignment explanation
Indices: 294522--294567 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
294512 TAAAGAAAGA
294522 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
294545 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGGGAGAAGAGATTGCAG
294568 CCGAGAAAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.48, C:0.04, G:0.39, T:0.09
Consensus pattern (23 bp):
AAGAAAGGGAGAAGAGATTGCAG
Found at i:294582 original size:25 final size:23
Alignment explanation
Indices: 294522--294582 Score: 59
Period size: 23 Copynumber: 2.6 Consensus size: 23
294512 TAAAGAAAGA
**
294522 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
**
294545 AAGAAAGGGAGAAGAGATTGCAG
1 AAGAAAGAAAGAAGAGATTGCAG
*
294568 CCGAGAAAGAAAGAA
1 --AAGAAAGAAAGAA
294583 AGAAGGGAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
23 23 0.70
25 10 0.30
ACGTcount: A:0.51, C:0.07, G:0.36, T:0.07
Consensus pattern (23 bp):
AAGAAAGAAAGAAGAGATTGCAG
Found at i:294618 original size:24 final size:26
Alignment explanation
Indices: 294591--294643 Score: 65
Period size: 27 Copynumber: 2.0 Consensus size: 26
294581 AAAGAAGGGA
294591 GAAAG-GAAAAAGAAAGGGAGA-AAG
1 GAAAGAGAAAAAGAAAGGGAGATAAG
*
294615 GAAAGTAAGAAGAAGAAAGGGAGATAAG
1 GAAAG--AGAAAAAGAAAGGGAGATAAG
294643 G
1 G
294644 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.21
27 15 0.62
28 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (26 bp):
GAAAGAGAAAAAGAAAGGGAGATAAG
Found at i:294634 original size:19 final size:19
Alignment explanation
Indices: 294570--294626 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 19
294560 GATTGCAGCC
294570 GAGAAA-GAAAGAAAGAAGG
1 GAGAAAGGAAAG-AAGAAGG
294589 GAGAAAGGAAA-AAGAAAGG
1 GAGAAAGGAAAGAAG-AAGG
294608 GAGAAAGGAAAGTAAGAAG
1 GAGAAAGGAAAG-AAGAAG
294627 AAGAAAGGGA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
18 3 0.09
19 21 0.62
20 7 0.21
21 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.37, T:0.02
Consensus pattern (19 bp):
GAGAAAGGAAAGAAGAAGG
Found at i:294890 original size:46 final size:48
Alignment explanation
Indices: 294827--294918 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
294817 TTATATAGTT
294827 AAAAAATAATTAATTAGTTTGTATT-GTT-AATAGTT-AGTTATATAA
1 AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
* *
294872 AAAAAATTATTTAATTAGTTTGTGTTAGTTAAATAGTTAAGTTATAT
1 AAAAAA-TAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATAT
294919 TTGTTTGTTG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
45 6 0.15
46 17 0.41
47 3 0.07
48 7 0.17
49 8 0.20
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (48 bp):
AAAAAATAATTAATTAGTTTGTATTAGTTAAATAGTTAAGTTATATAA
Found at i:295116 original size:15 final size:14
Alignment explanation
Indices: 295098--295128 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
295088 GTTTATTAGT
295098 TTATTATATTATAAG
1 TTATTATATTA-AAG
295113 TTATTATATTAAAG
1 TTATTATATTAAAG
295127 TT
1 TT
295129 TAGTGTTGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (14 bp):
TTATTATATTAAAG
Found at i:297295 original size:17 final size:17
Alignment explanation
Indices: 297273--297305 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
297263 CAATGATTTT
*
297273 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
297290 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
297306 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:297450 original size:26 final size:26
Alignment explanation
Indices: 297400--297699 Score: 254
Period size: 26 Copynumber: 12.1 Consensus size: 26
297390 CATTTGTTAG
*
297400 TATTA-AATCATTATTAT-AAATCAT
1 TATTATAATGATTATTATCAAATCAT
297424 TATTATAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATCAAATCAT
* * * * * * *
297450 TACTA-AATCATCA-AATC-ATTAAA
1 TATTATAATGATTATTATCAAATCAT
* *
297473 TATT-TAA--ATCATTATTAAATCAT
1 TATTATAATGATTATTATCAAATCAT
* *
297496 TTTTATAATGATTATTA-CTAAATTAT
1 TATTATAATGATTATTATC-AAATCAT
297522 TATTATAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATCAAATCAT
*
297548 TACTATAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATCAAATCAT
* * * * * * *
297574 TACTA-AATCATCA-AATC-ATTAAA
1 TATTATAATGATTATTATCAAATCAT
* *
297597 TATT-TAA--ATCATTATTAAATCAT
1 TATTATAATGATTATTATCAAATCAT
*
297620 TTTTATAATGATTATTA-CTAAATCAT
1 TATTATAATGATTATTATC-AAATCAT
297646 TATTATAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATCAAATCAT
*
297672 TACTATAATGATTATTATCAAATCAT
1 TATTATAATGATTATTATCAAATCAT
297698 TA
1 TA
297700 CTAAATCATC
Statistics
Matches: 220, Mismatches: 38, Indels: 34
0.75 0.13 0.12
Matches are distributed among these distances:
21 8 0.04
22 4 0.02
23 28 0.13
24 17 0.08
25 23 0.10
26 138 0.63
27 2 0.01
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
TATTATAATGATTATTATCAAATCAT
Found at i:297547 original size:124 final size:124
Alignment explanation
Indices: 297400--297757 Score: 666
Period size: 124 Copynumber: 2.9 Consensus size: 124
297390 CATTTGTTAG
* *
297400 TATTA-AATCATTATTAT-AAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATCA
1 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
*
297463 AATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATTAT
66 AATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCAT
297522 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
1 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
297587 AATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCAT
66 AATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCAT
297646 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
1 TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
*
297711 AATCATTAAATATTTAAATAATTATTAAATCATTTTTATAATGATTA
66 AATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTA
297758 ATAAATACAT
Statistics
Matches: 230, Mismatches: 4, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
122 5 0.02
123 11 0.05
124 214 0.93
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
TATTATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCA
AATCATTAAATATTTAAATCATTATTAAATCATTTTTATAATGATTATTACTAAATCAT
Found at i:297751 original size:20 final size:19
Alignment explanation
Indices: 297715--297758 Score: 52
Period size: 20 Copynumber: 2.3 Consensus size: 19
297705 TCATCAAATC
*
297715 ATTAAATATTTAAATAATT
1 ATTAAATATTTAAATAATG
**
297734 ATTAAATCATTTTTATAATG
1 ATTAAAT-ATTTAAATAATG
297754 ATTAA
1 ATTAA
297759 TAAATACATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (19 bp):
ATTAAATATTTAAATAATG
Found at i:300637 original size:26 final size:24
Alignment explanation
Indices: 300579--300637 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
300569 CTAATAAACC
*
300579 TAATAATGATTTGATAATTACTAT
1 TAATAATGATTTGATAATTAATAT
*
300603 TAATCTAATGATTTGATATTTAATGATT
1 TAA--TAATGATTTGATAATTAAT-A-T
300631 TAATAAT
1 TAATAAT
300638 AATATGATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 3 0.10
26 21 0.72
27 1 0.03
28 4 0.14
ACGTcount: A:0.41, C:0.03, G:0.08, T:0.47
Consensus pattern (24 bp):
TAATAATGATTTGATAATTAATAT
Found at i:301503 original size:28 final size:28
Alignment explanation
Indices: 301437--301496 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
301427 ATTTTTTATA
*
301437 TAATAT-ATATAACTTAAACTAATAAAC
1 TAATATAATATAACTTAAACTAACAAAC
301464 TAATATAATATAACTTAAACTAACAAAC
1 TAATATAATATAACTTAAACTAACAAAC
301492 TAATA
1 TAATA
301497 ATTTATACTA
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.19
28 25 0.81
ACGTcount: A:0.57, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
TAATATAATATAACTTAAACTAACAAAC
Found at i:301506 original size:21 final size:21
Alignment explanation
Indices: 301473--301521 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
301463 CTAATATAAT
301473 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
301494 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
301515 ATTAACT
1 A-TAACT
301522 AGATTTTAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:302060 original size:25 final size:25
Alignment explanation
Indices: 302006--302063 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 25
301996 GTTCCCACGT
* *
302006 CCCATGCACAGCATGCATCTGCATG
1 CCCATGCACAGCATGCATCTCCATC
* *
302031 ACCATGCACAGCATGCATC-CCCTCC
1 CCCATGCACAGCATGCATCTCCAT-C
302056 CCCATGCA
1 CCCATGCA
302064 TTCCCACGGC
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
24 2 0.07
25 25 0.93
ACGTcount: A:0.24, C:0.43, G:0.16, T:0.17
Consensus pattern (25 bp):
CCCATGCACAGCATGCATCTCCATC
Done.