Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014295.1 Kokia drynarioides strain JFW-HI SEQ_129330, 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: 86187
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Warning! 82 characters in sequence are not A, C, G, or T
Found at i:27 original size:18 final size:18
Alignment explanation
Indices: 4--47 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
1 AAT
*
4 AAATTTAAATTTTTAAAC
1 AAATTTAAATTTTAAAAC
*
22 AAATTT-AATTTTAAAAT
1 AAATTTAAATTTTAAAAC
39 AAATTTAAA
1 AAATTTAAA
48 GGGAATTTGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
17 15 0.65
18 8 0.35
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (18 bp):
AAATTTAAATTTTAAAAC
Found at i:175 original size:34 final size:34
Alignment explanation
Indices: 137--283 Score: 78
Period size: 34 Copynumber: 4.1 Consensus size: 34
127 AGTTTATCTA
137 ACTAGTGCTGGGCACACTTTTGTTGGCTTATCCG
1 ACTAGTGCTGGGCACACTTTTGTTGGCTTATCCG
** * * * * * *
171 ACTAGCACTAGGCGCAATATTGTTGGTTTATCCA
1 ACTAGTGCTGGGCACACTTTTGTTGGCTTATCCG
* * * * * * *
205 ACTAGAGCTGGACTCATTAGTAATATCATTAGCTTATCTG
1 ACTAGTGCTGGGCACACT--T--T-T-GTTGGCTTATCCG
* * *
245 ACTAGTGATGGGCACACTTTTGTCGGTTTATCCG
1 ACTAGTGCTGGGCACACTTTTGTTGGCTTATCCG
279 ACTAG
1 ACTAG
284 CGTTGGGCGC
Statistics
Matches: 77, Mismatches: 30, Indels: 12
0.65 0.25 0.10
Matches are distributed among these distances:
34 51 0.66
35 1 0.01
36 1 0.01
38 2 0.03
39 1 0.01
40 21 0.27
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.34
Consensus pattern (34 bp):
ACTAGTGCTGGGCACACTTTTGTTGGCTTATCCG
Found at i:350 original size:108 final size:107
Alignment explanation
Indices: 84--356 Score: 341
Period size: 108 Copynumber: 2.5 Consensus size: 107
74 GGCTTCAACA
* * ** * *
84 GTTGGTTTATCAAACTAAAGCTGGGCTCATTAATAATATTGTCAGTTTATCTAACTAGTGCTGGG
1 GTTGGTTTATCCAACTAGAGCTGGGCTCATT-ATAATATCATCAGTTTATCTGACTAGTGATGGG
* *
149 CACACTTTTGTTGGCTTATCCGACTAGCACTAGGCGCAATATT
65 CACACTTTTGTCGGCTTATCCGACTAGCACTAGGCGCAATATC
* * *
192 GTTGGTTTATCCAACTAGAGCTGGACTCATTAGTAATATCATTAGCTTATCTGACTAGTGATGGG
1 GTTGGTTTATCCAACTAGAGCTGGGCTCATTA-TAATATCATCAGTTTATCTGACTAGTGATGGG
* ** *
257 CACACTTTTGTCGGTTTATCCGACTAGCGTTGGGCGCAATATC
65 CACACTTTTGTCGGCTTATCCGACTAGCACTAGGCGCAATATC
* * *
300 GTTGGTTTGTCCAACTAGAGCTGGGCTCACATT-TAATATCATCGGTTTATCCGACTA
1 GTTGGTTTATCCAACTAGAGCTGGGCT--CATTATAATATCATCAGTTTATCTGACTA
357 TCGTTAGGCG
Statistics
Matches: 141, Mismatches: 21, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
107 1 0.01
108 136 0.96
110 4 0.03
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (107 bp):
GTTGGTTTATCCAACTAGAGCTGGGCTCATTATAATATCATCAGTTTATCTGACTAGTGATGGGC
ACACTTTTGTCGGCTTATCCGACTAGCACTAGGCGCAATATC
Found at i:3892 original size:22 final size:23
Alignment explanation
Indices: 3840--3892 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 23
3830 TTTAAAATTT
*
3840 AATTTTATATTTTTATTTTTAAG
1 AATTTTAAATTTTTATTTTTAAG
*
3863 AA-TATAAATTTTT-TATTTTAA-
1 AATTTTAAATTTTTAT-TTTTAAG
3884 AATTTTAAA
1 AATTTTAAA
3893 ATTTAAATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 3 0.12
22 20 0.80
23 2 0.08
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AATTTTAAATTTTTATTTTTAAG
Found at i:7143 original size:19 final size:19
Alignment explanation
Indices: 7098--7144 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
7088 AAATTTATAT
7098 TTTTTAAAAATTCTAAAAA
1 TTTTTAAAAATTCTAAAAA
* *
7117 ATATTAAAAATT-TAAAAA
1 TTTTTAAAAATTCTAAAAA
7135 TTTTCTAAAA
1 TTTT-TAAAA
7145 TAATAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.40
Consensus pattern (19 bp):
TTTTTAAAAATTCTAAAAA
Found at i:10270 original size:33 final size:33
Alignment explanation
Indices: 10223--10288 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 33
10213 ATCTTTATGC
**
10223 CTTAAATTGGAAATGAT-TTTTA-TATAGGGGGAG
1 CTTAAATTCAAAATG-TCTTTTATTA-AGGGGGAG
10256 CTTAAATTCAAAATGTCTTTTATTAAGGGGGAG
1 CTTAAATTCAAAATGTCTTTTATTAAGGGGGAG
10289 TAATCTATTC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 1 0.03
33 26 0.90
34 2 0.07
ACGTcount: A:0.33, C:0.06, G:0.24, T:0.36
Consensus pattern (33 bp):
CTTAAATTCAAAATGTCTTTTATTAAGGGGGAG
Found at i:14306 original size:26 final size:26
Alignment explanation
Indices: 14268--14322 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
14258 CTTCCTAAAA
14268 TTTAGCTCATACGAGCCCAGAAAGAG
1 TTTAGCTCATACGAGCCCAGAAAGAG
** *
14294 TTTAGCTTTTACGAGCCCAGATAGAG
1 TTTAGCTCATACGAGCCCAGAAAGAG
14320 TTT
1 TTT
14323 TTACTAGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (26 bp):
TTTAGCTCATACGAGCCCAGAAAGAG
Found at i:14471 original size:81 final size:81
Alignment explanation
Indices: 14336--14550 Score: 299
Period size: 81 Copynumber: 2.7 Consensus size: 81
14326 CTAGTTTACG
* * *
14336 ATGCTACTCACACAAGCTGATGAGAATCCGCAACATATGCAAGACCTCAGCCATCACTACGGTCT
1 ATGCTGCTCACATAAGCTGATGAGAATCCGCAACATATGCAAGATCTCAGCCATCACTACGGTCT
***
14401 AAATCACTTGCTCACA
66 AAATCACCCACTCACA
* * *
14417 ATGCTGCTCACATAAGCTGATGAGAATCCGCAACATATGAAATATCTCAGCCATCATTACGGTCT
1 ATGCTGCTCACATAAGCTGATGAGAATCCGCAACATATGCAAGATCTCAGCCATCACTACGGTCT
* *
14482 ATATCACCCACTCACG
66 AAATCACCCACTCACA
* *
14498 ATGTTGCTCACAT--GTTGATGAGAATCCGCAACATATGCAAGATCTCAGCCATC
1 ATGCTGCTCACATAAGCTGATGAGAATCCGCAACATATGCAAGATCTCAGCCATC
14551 GTAAAGGTCC
Statistics
Matches: 119, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
79 37 0.31
81 82 0.69
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (81 bp):
ATGCTGCTCACATAAGCTGATGAGAATCCGCAACATATGCAAGATCTCAGCCATCACTACGGTCT
AAATCACCCACTCACA
Found at i:14965 original size:18 final size:19
Alignment explanation
Indices: 14928--14965 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
14918 TTCAAATCAA
*
14928 TATGAAATTCAAGTCATTT
1 TATGAAAATCAAGTCATTT
*
14947 TATGAAAAT-AAGTCCTTT
1 TATGAAAATCAAGTCATTT
14965 T
1 T
14966 GGTATTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 9 0.53
19 8 0.47
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TATGAAAATCAAGTCATTT
Found at i:16807 original size:43 final size:43
Alignment explanation
Indices: 16733--16835 Score: 147
Period size: 43 Copynumber: 2.4 Consensus size: 43
16723 TCTTGTCGAA
*
16733 ACATAAGTCTTCC-TTTATAAATAATCTTATGCTCCT-CCCGAG
1 ACATAAGTCTTCCATTTATAAATAATCTTATGC-CCTACCAGAG
* *
16775 TCATAAGTCTTCCATTTATAAATATTCTTATGCCCTACCAGAG
1 ACATAAGTCTTCCATTTATAAATAATCTTATGCCCTACCAGAG
*
16818 ACAAAAGTCTTCCATTTA
1 ACATAAGTCTTCCATTTA
16836 ATACTCTTCG
Statistics
Matches: 54, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
42 15 0.28
43 39 0.72
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (43 bp):
ACATAAGTCTTCCATTTATAAATAATCTTATGCCCTACCAGAG
Found at i:20001 original size:16 final size:16
Alignment explanation
Indices: 19980--20015 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
19970 AAATAATCTC
*
19980 AAAATTACAAGTTTCA
1 AAAATTAAAAGTTTCA
19996 AAAATTAAAAGTTTCA
1 AAAATTAAAAGTTTCA
20012 AAAA
1 AAAA
20016 CACTTTATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.58, C:0.08, G:0.06, T:0.28
Consensus pattern (16 bp):
AAAATTAAAAGTTTCA
Found at i:26042 original size:49 final size:49
Alignment explanation
Indices: 25953--26047 Score: 127
Period size: 49 Copynumber: 1.9 Consensus size: 49
25943 CTATTTAAAT
* * *** *
25953 GTTGAAAGACCTTATATTAATCAATGTCAAATGGATGAAGTGTAGTAAG
1 GTTGAAAAACCTTATATTAATCAACGTCAAAAAAAAGAAGTGTAGTAAG
*
26002 GTTGAAAAACCTTATTTTAATCAACGTCAAAAAAAAGAAGTGTAGT
1 GTTGAAAAACCTTATATTAATCAACGTCAAAAAAAAGAAGTGTAGT
26048 TCTATATGGA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
49 39 1.00
ACGTcount: A:0.42, C:0.09, G:0.19, T:0.29
Consensus pattern (49 bp):
GTTGAAAAACCTTATATTAATCAACGTCAAAAAAAAGAAGTGTAGTAAG
Found at i:26992 original size:17 final size:17
Alignment explanation
Indices: 26967--27002 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
26957 AGCAAATATG
26967 AGCTCATTGATTGTCTA
1 AGCTCATTGATTGTCTA
*
26984 AGCTTATTGATTGTCTA
1 AGCTCATTGATTGTCTA
27001 AG
1 AG
27003 TTCAAACTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.25, C:0.14, G:0.19, T:0.42
Consensus pattern (17 bp):
AGCTCATTGATTGTCTA
Found at i:33157 original size:9 final size:9
Alignment explanation
Indices: 33143--33173 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
33133 ACCCAAAAAA
*
33143 CTTCATCAC
1 CTTCATCAT
33152 CTTCATCAT
1 CTTCATCAT
33161 CTTCATCAT
1 CTTCATCAT
33170 CTTC
1 CTTC
33174 TCCAAACGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.19, C:0.39, G:0.00, T:0.42
Consensus pattern (9 bp):
CTTCATCAT
Found at i:36188 original size:32 final size:31
Alignment explanation
Indices: 36145--36207 Score: 85
Period size: 30 Copynumber: 2.0 Consensus size: 31
36135 TTATAATTTA
36145 TAAAATATATAACAAAA-TTGTATTTTAATTTTT
1 TAAAATATATAA-AAAATTTG-A-TTTAATTTTT
36178 TAAAAT-TATAAAAAATTTGATTTAATTTTT
1 TAAAATATATAAAAAATTTGATTTAATTTTT
36208 ATCCAAAACA
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
30 10 0.34
31 5 0.17
32 8 0.28
33 6 0.21
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (31 bp):
TAAAATATATAAAAAATTTGATTTAATTTTT
Found at i:36488 original size:20 final size:21
Alignment explanation
Indices: 36454--36493 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
36444 TTAATCAAAG
*
36454 TGTAATATACTAATACATTTA
1 TGTAATATACAAATACATTTA
*
36475 TGTAA-ATACAAATATATTT
1 TGTAATATACAAATACATTT
36494 TTTGGTGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.42
Consensus pattern (21 bp):
TGTAATATACAAATACATTTA
Found at i:40590 original size:13 final size:14
Alignment explanation
Indices: 40574--40615 Score: 50
Period size: 13 Copynumber: 2.9 Consensus size: 14
40564 TGTCAATTTT
40574 ATTTTAATAATA-A
1 ATTTTAATAATATA
*
40587 ATTTTAAAAATGATA
1 ATTTTAATAAT-ATA
40602 ATTTTAAATAATAT
1 ATTTT-AATAATAT
40616 TCTTCACATA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
13 10 0.42
14 1 0.04
15 8 0.33
16 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (14 bp):
ATTTTAATAATATA
Found at i:40664 original size:15 final size:15
Alignment explanation
Indices: 40644--40700 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
40634 AATATTTATT
40644 AATATTTTAATAATA
1 AATATTTTAATAATA
*
40659 AATATTTATTACAATTATA
1 AATA-TT-TT--AATAATA
* *
40678 AATATATTAATAACA
1 AATATTTTAATAATA
40693 AATATTTT
1 AATATTTT
40701 GTAGTATAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
15 16 0.48
16 2 0.06
17 4 0.12
18 1 0.03
19 10 0.30
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTTTAATAATA
Found at i:42122 original size:6 final size:6
Alignment explanation
Indices: 42100--42177 Score: 56
Period size: 6 Copynumber: 13.5 Consensus size: 6
42090 ATTTAAGCTG
* * *
42100 ATTTAA ATTTAT TTTTAA ATTTAA ATTT-- ATCTTAA ATTTAA ATTT-G
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT-TTAA ATTTAA ATTTAA
* * **
42146 CTTGAA ATTTAA ATTT-A ATCAAA ATTTAA ATT
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATT
42178 GATATTAAAT
Statistics
Matches: 53, Mismatches: 14, Indels: 10
0.69 0.18 0.13
Matches are distributed among these distances:
4 2 0.04
5 7 0.13
6 42 0.79
7 2 0.04
ACGTcount: A:0.42, C:0.04, G:0.03, T:0.51
Consensus pattern (6 bp):
ATTTAA
Found at i:42136 original size:17 final size:17
Alignment explanation
Indices: 42100--42188 Score: 92
Period size: 17 Copynumber: 5.2 Consensus size: 17
42090 ATTTAAGCTG
*
42100 ATTTAAATTTATTTTTAA
1 ATTTAAATTTA-TCTTAA
42118 ATTTAAATTTATCTTAA
1 ATTTAAATTTATCTTAA
*
42135 ATTTAAATTT-GCTTGAA
1 ATTTAAATTTATCTT-AA
*
42152 ATTTAAATTTAATC-AAA
1 ATTTAAATTT-ATCTTAA
* *
42169 ATTTAAATTGATATTAA
1 ATTTAAATTTATCTTAA
42186 ATT
1 ATT
42189 AAAAACCGAA
Statistics
Matches: 60, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
16 5 0.08
17 43 0.72
18 11 0.18
19 1 0.02
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTATCTTAA
Found at i:44007 original size:29 final size:29
Alignment explanation
Indices: 43955--44262 Score: 334
Period size: 30 Copynumber: 10.4 Consensus size: 29
43945 AAACTGTTCG
* *
43955 AAAATTCCATTTTCAACCTCCAAACTTCCA
1 AAAATTCCATTTT-TACCCCCAAACTTCCA
43985 AAAATTCCATTTTTACCCCCAAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
**
44014 AAAATTCCATTTTTAACCCTAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCCAAACTTCCA
** *
44044 AAAATTCCATTTTTA-CCCTTAACTTTCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* *
44072 AAAATTCCATTTTTAACTCCGAAACTTCCA
1 AAAATTCCATTTTT-ACCCCCAAACTTCCA
*
44102 AAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTACCCCCAAACTTCCA
* * * *
44131 AAAATTCCATTTTCAACCTCGAAACATCCA
1 AAAATTCCATTTT-TACCCCCAAACTTCCA
*
44161 AAAATTCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTT-ACCCCCAAACTTCCA
* *
44191 AAAATTCCATTTTTACCCTCGAAACTTTCAA
1 AAAATTCCATTTTTACCC-CCAAAC-TTCCA
* **
44222 AAAATACCATTTTT-CCCCTGAA-TGTCCA
1 AAAATTCCATTTTTACCCCCAAACT-TCCA
*
44250 AAAACTCCATTTT
1 AAAATTCCATTTT
44263 CGACCTCAAA
Statistics
Matches: 238, Mismatches: 32, Indels: 18
0.83 0.11 0.06
Matches are distributed among these distances:
27 1 0.00
28 37 0.16
29 62 0.26
30 121 0.51
31 17 0.07
ACGTcount: A:0.36, C:0.29, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCCAAACTTCCA
Found at i:44047 original size:59 final size:60
Alignment explanation
Indices: 43955--44351 Score: 390
Period size: 59 Copynumber: 6.7 Consensus size: 60
43945 AAACTGTTCG
* * *
43955 AAAATTCCATTTTCAA-CCTCCAAACTTCCAAAAATTCCATTTTTACCCCCAAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
** *
44014 AAAATTCCATTTTTAACCCT-AAAACTTCCAAAAATTCCATTTTTA-CCCTTAACTTTCA
1 AAAATTCCATTTTTAACCCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
* *
44072 AAAATTCCATTTTTAACTC-CGAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
* * * **
44131 AAAATTCCATTTTCAA-CCTCGAAACATCCAAAAATTCCATTTTTGACCCCAAAACTTCCA
1 AAAATTCCATTTTTAACCCTCAAAACTTCCAAAAATTCCATTTTT-ACCCCCGAACTTCCA
* * * *
44191 AAAATTCCATTTTT-ACCCTCGAAACTTTCAAAAAATACCATTTTT-CCCCTGAA-TGTCCA
1 AAAATTCCATTTTTAACCCTCAAAAC-TTCCAAAAATTCCATTTTTACCCCCGAACT-TCCA
* ** * * * *
44250 AAAACTCCATTTTCGA-CCTCAAAAC-TCTC-GAAATTACC-CTTTTACCCTCGAA-TGTCTA
1 AAAATTCCATTTTTAACCCTCAAAACTTC-CAAAAATT-CCATTTTTACCCCCGAACT-TCCA
** *
44308 AAAATTCCATTTTTAACCCT-AAATTTTCCCAAAATTACCATTTT
1 AAAATTCCATTTTTAACCCTCAAAACTTCCAAAAATT-CCATTTT
44352 GCCCCGAGAA
Statistics
Matches: 284, Mismatches: 38, Indels: 31
0.80 0.11 0.09
Matches are distributed among these distances:
57 10 0.04
58 84 0.30
59 132 0.46
60 42 0.15
61 16 0.06
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.33
Consensus pattern (60 bp):
AAAATTCCATTTTTAACCCTCAAAACTTCCAAAAATTCCATTTTTACCCCCGAACTTCCA
Found at i:44368 original size:27 final size:28
Alignment explanation
Indices: 44336--44396 Score: 106
Period size: 27 Copynumber: 2.2 Consensus size: 28
44326 CTAAATTTTC
44336 CCAAAATTACCATTTTG-CCCCGAGAAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
*
44363 CCAAAATTACCATTTTGCCCCCGAGTAT
1 CCAAAATTACCATTTTGCCCCCGAGAAT
44391 CCAAAA
1 CCAAAA
44397 GTCTCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 17 0.53
28 15 0.47
ACGTcount: A:0.34, C:0.31, G:0.10, T:0.25
Consensus pattern (28 bp):
CCAAAATTACCATTTTGCCCCCGAGAAT
Found at i:44404 original size:28 final size:27
Alignment explanation
Indices: 44336--44406 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 27
44326 CTAAATTTTC
*
44336 CCAAAATTACCATTTTGCCCCGAGAAT
1 CCAAAAGTACCATTTTGCCCCGAGAAT
* *
44363 CCAAAATTACCATTTTGCCCCCGAGTAT
1 CCAAAAGTACCATTTTG-CCCCGAGAAT
44391 CCAAAAGT-CTCATTTT
1 CCAAAAGTAC-CATTTT
44407 CAACTTCGAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
27 18 0.45
28 22 0.55
ACGTcount: A:0.31, C:0.30, G:0.10, T:0.30
Consensus pattern (27 bp):
CCAAAAGTACCATTTTGCCCCGAGAAT
Found at i:58034 original size:29 final size:29
Alignment explanation
Indices: 57993--58250 Score: 204
Period size: 30 Copynumber: 8.8 Consensus size: 29
57983 TTTTTAGCCC
*
57993 AAACTTCTAAAAATTCCATTTTCGACCTCG
1 AAACTTCCAAAAATTCCATTTT-GACCTCG
* *
58023 AAACTTCC-AAAATTCCAGTTTTTACCCCG
1 AAACTTCCAAAAATTCCA-TTTTGACCTCG
* *
58052 AAACTTCCAAAAATTCCATTTTTGACCCCA
1 AAACTTCCAAAAATTCCA-TTTTGACCTCG
* *
58082 AAACTTCCAAAAAATCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGA-CCTCG
* * *
58112 -AACTTCCAAAAAATCCATTTTCAACCTCA
1 AAACTTCCAAAAATTCCATTTT-GACCTCG
*
58141 AAACTTCCAAAAATTCCATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTGA-CCTCG
* * * * *
58171 -AACCTCCAAGATTTCCATTTTTAACC-CTA
1 AAACTTCCAAAAATTCCA-TTTTGACCTC-G
** *
58200 AAACTTTTAAAAATTACCATTTTGCCCTCG
1 AAACTTCCAAAAATT-CCATTTTGACCTCG
*
58230 -AA-TGTCCAAAAACTCCATTTT
1 AAACT-TCCAAAAATTCCATTTT
58251 CATCCTTGAA
Statistics
Matches: 185, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
28 9 0.05
29 78 0.42
30 94 0.51
31 4 0.02
ACGTcount: A:0.35, C:0.29, G:0.04, T:0.32
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTGACCTCG
Found at i:58057 original size:59 final size:60
Alignment explanation
Indices: 57981--58251 Score: 283
Period size: 59 Copynumber: 4.6 Consensus size: 60
57971 TCGAAATTTA
* * *
57981 CATTTTTAGCC-C-AAACTTCTAAAAATTCCATTTTCGACCTCGAAACTTCC-AAAATTC
1 CATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTC
* * *
58038 CAGTTTTTACCC-CGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAATC
1 CA-TTTTTACCCTCGAAACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTC
* *
58098 CATTTTTACCCTCG-AACTTCCAAAAAATCCATTTTCAACCTCAAAACTTCCAAAAATTC
1 CATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTC
* * * ** **
58157 CATTTTTACCCTCG-AACCTCCAAGATTTCCATTTTTAACC-CTAAAACTTTTAAAAATTAC
1 CATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTCGACCTC-AAAACTTCCAAAAATT-C
* *
58217 CA-TTTTGCCCTCG-AA-TGTCCAAAAACTCCATTTTC
1 CATTTTTACCCTCGAAACT-TCCAAAAATTCCATTTTC
58252 ATCCTTGAAA
Statistics
Matches: 183, Mismatches: 24, Indels: 12
0.84 0.11 0.05
Matches are distributed among these distances:
57 2 0.01
58 10 0.05
59 158 0.86
60 13 0.07
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (60 bp):
CATTTTTACCCTCGAAACTTCCAAAAATTCCATTTTCGACCTCAAAACTTCCAAAAATTC
Found at i:58179 original size:118 final size:119
Alignment explanation
Indices: 57981--58252 Score: 331
Period size: 118 Copynumber: 2.3 Consensus size: 119
57971 TCGAAATTTA
* * * * * *
57981 CATTTTTAGCC-CAAACTTCTAAAAATTCCATTTTCGACCTCGAAACTTCCAAAATTCCAGTTTT
1 CATTTTTACCCTCGAACTTCCAAAAAATCCATTTTCAACCTCAAAACTTCCAAAATTCCAGTTTT
* *
58045 TACCCCGAAACTTCCAAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAAT-C
66 TACCCCGAAACCTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAATAC
58098 CATTTTTACCCTCGAACTTCCAAAAAATCCATTTTCAACCTCAAAACTTCCAAAAATTCCA-TTT
1 CATTTTTACCCTCGAACTTCCAAAAAATCCATTTTCAACCTCAAAACTTCC-AAAATTCCAGTTT
* * * ** *
58162 TTACCCTCG-AACCTCCAAGATTTCCATTTTTAACCCTAAAACTTTTAAAAATTAC
65 TTACCC-CGAAACCTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAATAC
* *
58217 CA-TTTTGCCCTCGAA-TGTCCAAAAACTCCATTTTCA
1 CATTTTTACCCTCGAACT-TCCAAAAAATCCATTTTCA
58253 TCCTTGAAAC
Statistics
Matches: 134, Mismatches: 16, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
117 11 0.08
118 109 0.81
119 14 0.10
ACGTcount: A:0.34, C:0.29, G:0.04, T:0.32
Consensus pattern (119 bp):
CATTTTTACCCTCGAACTTCCAAAAAATCCATTTTCAACCTCAAAACTTCCAAAATTCCAGTTTT
TACCCCGAAACCTCCAAAAATTCCATTTTTAACCCCAAAACTTCCAAAAAATAC
Found at i:58263 original size:59 final size:59
Alignment explanation
Indices: 58001--58347 Score: 253
Period size: 59 Copynumber: 5.9 Consensus size: 59
57991 CCAAACTTCT
* * *
58001 AAAAATTCCATTTTCGACCTCGAAACTTC-CAAAATT-CCAGTTTTTACCC-CGAAACT-TCC
1 AAAAATTCCATTTTCAACCTCAAAACTTCTAAAAATTACCA--TTTTACCCTCG-AA-TGTCC
** * * *
58060 AAAAATTCCATTTTTGACCCCAAAACTTCCAAAAAAT-CCATTTTTACCCTCGAACT-TCC
1 AAAAATTCCATTTTCAACCTCAAAACTTCTAAAAATTACCA-TTTTACCCTCGAA-TGTCC
* * **
58119 AAAAAATCCATTTTCAACCTCAAAACTTCCAAAAATT-CCATTTTTACCCTCGAACCTCC
1 AAAAATTCCATTTTCAACCTCAAAACTTCTAAAAATTACCA-TTTTACCCTCGAATGTCC
* * * * *
58178 AAGATTTCCATTTTTAACC-CTAAAACTTTTAAAAATTACCATTTTGCCCTCGAATGTCC
1 AAAAATTCCATTTTCAACCTC-AAAACTTCTAAAAATTACCATTTTACCCTCGAATGTCC
* * ** ** * * **
58237 AAAAACTCCATTTTCATCCTTGAAAC-TCTCGAATTTACCCTTTTACCCTCGAATGTTT
1 AAAAATTCCATTTTCAACCTCAAAACTTCTAAAAATTACCATTTTACCCTCGAATGTCC
* * ** ** *
58295 AAAAATTCCATTTTTAACCCCAAATTTTCCCAAAATTACCATTTTGCCCTCGA
1 AAAAATTCCATTTTCAACCTCAAAACTTCTAAAAATTACCATTTTACCCTCGA
58348 GAATCTAAAA
Statistics
Matches: 233, Mismatches: 48, Indels: 14
0.79 0.16 0.05
Matches are distributed among these distances:
58 43 0.18
59 177 0.76
60 13 0.06
ACGTcount: A:0.33, C:0.29, G:0.05, T:0.33
Consensus pattern (59 bp):
AAAAATTCCATTTTCAACCTCAAAACTTCTAAAAATTACCATTTTACCCTCGAATGTCC
Found at i:58385 original size:28 final size:28
Alignment explanation
Indices: 58324--58385 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
58314 CCAAATTTTC
* *
58324 CCAAAATTACCATTTTGCCCTCGAGAAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
* * *
58352 CTAAAATTACCATTTTACCCCCGGGTAT
1 CCAAAATTACCATTTTACCCCCGAGAAT
58380 CCAAAA
1 CCAAAA
58386 AGTCTCATTT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.34, C:0.29, G:0.10, T:0.27
Consensus pattern (28 bp):
CCAAAATTACCATTTTACCCCCGAGAAT
Found at i:59360 original size:21 final size:20
Alignment explanation
Indices: 59331--59405 Score: 73
Period size: 21 Copynumber: 3.6 Consensus size: 20
59321 GGAGTTTTTA
*
59331 GTATTGGTAGAAGTAAGACTT
1 GTATCGGTAGAA-TAAGACTT
59352 GTATCGGTAGAA-AAGTCACTT
1 GTATCGGTAGAATAAG--ACTT
*
59373 GTATCGGTAGAACTATCG-CTT
1 GTATCGGTAGAA-TA-AGACTT
59394 GTATCGGTAGAA
1 GTATCGGTAGAA
59406 ATCTACATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 10
0.80 0.03 0.17
Matches are distributed among these distances:
19 3 0.06
21 42 0.89
23 1 0.02
24 1 0.02
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (20 bp):
GTATCGGTAGAATAAGACTT
Found at i:59769 original size:17 final size:17
Alignment explanation
Indices: 59747--59780 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
59737 TAGTACATGT
*
59747 CATATGAACTTGTGATA
1 CATATGAACCTGTGATA
59764 CATATGAACCTGTGATA
1 CATATGAACCTGTGATA
59781 GTGTGACACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (17 bp):
CATATGAACCTGTGATA
Found at i:59805 original size:32 final size:32
Alignment explanation
Indices: 59764--59826 Score: 126
Period size: 32 Copynumber: 2.0 Consensus size: 32
59754 ACTTGTGATA
59764 CATATGAACCTGTGATAGTGTGACACAGATGT
1 CATATGAACCTGTGATAGTGTGACACAGATGT
59796 CATATGAACCTGTGATAGTGTGACACAGATG
1 CATATGAACCTGTGATAGTGTGACACAGATG
59827 AATCTGATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (32 bp):
CATATGAACCTGTGATAGTGTGACACAGATGT
Found at i:65889 original size:188 final size:191
Alignment explanation
Indices: 65565--65987 Score: 629
Period size: 188 Copynumber: 2.2 Consensus size: 191
65555 ATGGCTGGGA
* * **
65565 TATCGCATATGTTGCGAGTCCTCGACAGCTCATGTGAGTAGCATCGTGATTCGGAAAAGAGATAT
1 TATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGATTCCAAAAAGAGATAT
* * * * * *
65630 GAATCCTAAATGCATTATAGGCCCTTCGATGGCTGGGACTTATGTTTTATGCATACTCTCGACAG
66 GAATCCTAAATGAATTATAGGCCCTTCGATGGCTAGGACTTATGCTTTATGCATACTCCCAACAA
* * **
65695 CTCGTGTGAACAGCATCGTTAGGGAACAGTTTACAGACGGACATCGTA-TCGATAG-TTGGG
131 CTCGTGTGAACAGCATCGTTAGGGAACAGTTTACAGACAGACACCGTACT-GATAGCTAAGG
65755 TA-C-CATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGATTCCAAAAAGAGATAT
1 TATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGATTCCAAAAAGAGATAT
65818 GAATCCTAAATGAATTATAGGCCCTTCGATGGCTAGGACTTATGCTTTATGCATACTCCCAACAA
66 GAATCCTAAATGAATTATAGGCCCTTCGATGGCTAGGACTTATGCTTTATGCATACTCCCAACAA
* *
65883 CTCGTGTGAGCAGCATCGTTAGGGAACAGTTTACAGACAGACACCGTACTGATGGCTAAGG
131 CTCGTGTGAACAGCATCGTTAGGGAACAGTTTACAGACAGACACCGTACTGATAGCTAAGG
* * * *
65944 TATCGTATATGTTGCGAATCCTTGATAGCTCGTGTGAGCAGCAT
1 TATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCAT
65988 TGAGTACTGG
Statistics
Matches: 209, Mismatches: 20, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
188 164 0.78
189 7 0.03
190 3 0.01
191 35 0.17
ACGTcount: A:0.27, C:0.21, G:0.25, T:0.28
Consensus pattern (191 bp):
TATCGCATATGTTGCGAGTCCTCGACAGCTCGTGTGAGCAGCATCGTGATTCCAAAAAGAGATAT
GAATCCTAAATGAATTATAGGCCCTTCGATGGCTAGGACTTATGCTTTATGCATACTCCCAACAA
CTCGTGTGAACAGCATCGTTAGGGAACAGTTTACAGACAGACACCGTACTGATAGCTAAGG
Found at i:66729 original size:21 final size:20
Alignment explanation
Indices: 66688--66741 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
66678 GGAGTTTTTA
66688 GTATCGGTAGAAGTAAGACTT
1 GTATCGGTAGAAG-AAGACTT
66709 GTATCGGTAGAAG-AGTCACTT
1 GTATCGGTAGAAGAAG--ACTT
*
66730 GTATCGATAGAA
1 GTATCGGTAGAA
66742 CTGCCGCTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 2 0.07
21 28 0.93
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (20 bp):
GTATCGGTAGAAGAAGACTT
Found at i:69479 original size:22 final size:22
Alignment explanation
Indices: 69420--69466 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
69410 CGATCTAAGG
69420 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
69441 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
69463 AAAA
1 AAAA
69467 GTTATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:71891 original size:25 final size:25
Alignment explanation
Indices: 71852--71911 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
71842 GGACAAAAAT
*
71852 AAATAAATAAAT-AAAATAAGATAGAA
1 AAATAAA-AAATAAAAATAA-AAAGAA
*
71878 AAATAAAAAATAAAAATAAAAATAA
1 AAATAAAAAATAAAAATAAAAAGAA
71903 AAATAAAAA
1 AAATAAAAA
71912 TAATTGGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
25 17 0.55
26 14 0.45
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (25 bp):
AAATAAAAAATAAAAATAAAAAGAA
Found at i:71892 original size:6 final size:6
Alignment explanation
Indices: 71846--71914 Score: 70
Period size: 6 Copynumber: 11.3 Consensus size: 6
71836 TTTCCTGGAC
* * *
71846 AAAAAT AAATAA- ATAAAT -AAAAT AAGATAG AAAAAT AAAAAAT AAAAAT
1 AAAAAT AAA-AAT AAAAAT AAAAAT AA-AAAT AAAAAT -AAAAAT AAAAAT
71895 AAAAAT AAAAAT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AA
71915 TTGGGTTGCC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 6 0.12
6 34 0.65
7 12 0.23
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:71892 original size:12 final size:12
Alignment explanation
Indices: 71846--71911 Score: 57
Period size: 13 Copynumber: 5.3 Consensus size: 12
71836 TTTCCTGGAC
71846 AAAAAT-AAATA
1 AAAAATAAAATA
71857 AATAAATAAAATA
1 AA-AAATAAAATA
*
71870 AGATAGA-AAAATA
1 A-A-AAATAAAATA
71883 AAAAATAAAA-A
1 AAAAATAAAATA
71894 TAAAAATAAAAATA
1 -AAAAAT-AAAATA
71908 AAAA
1 AAAA
71912 TAATTGGGTT
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
11 5 0.11
12 15 0.33
13 21 0.46
14 5 0.11
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:78267 original size:20 final size:21
Alignment explanation
Indices: 78225--78268 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
78215 TATATGTAAA
*
78225 AATAATATAAAATATAAATTC
1 AATAATATAAAATATAAACTC
78246 AATAGATAT-AAA-ATAAACTC
1 AATA-ATATAAAATATAAACTC
78266 AAT
1 AAT
78269 TAAACAATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 10 0.48
21 7 0.33
22 4 0.19
ACGTcount: A:0.61, C:0.07, G:0.02, T:0.30
Consensus pattern (21 bp):
AATAATATAAAATATAAACTC
Found at i:80285 original size:15 final size:16
Alignment explanation
Indices: 80260--80289 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
80250 GAATTAAAAA
80260 TAAAAGAAAATAGAAT
1 TAAAAGAAAATAGAAT
80276 TAAAAG-AAATAGAA
1 TAAAAGAAAATAGAA
80290 AACAGGGCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (16 bp):
TAAAAGAAAATAGAAT
Found at i:80291 original size:22 final size:22
Alignment explanation
Indices: 80234--80280 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
80224 CGATCTAAGG
80234 AAAAATAAAAG-AAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
80255 AAAAATAAAAGAAAATAGAATT
1 AAAAATAAAAGAAAATAGAATT
80277 AAAA
1 AAAA
80281 GAAATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.74, C:0.00, G:0.09, T:0.17
Consensus pattern (22 bp):
AAAAATAAAAGAAAATAGAATT
Found at i:82274 original size:16 final size:18
Alignment explanation
Indices: 82235--82268 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
82225 TAAGTTTATA
82235 ATATTT-TATATTATGTT
1 ATATTTATATATTATGTT
*
82252 ATTTTTATATATTATGT
1 ATATTTATATATTATGT
82269 AATTTAATAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTATATATTATGTT
Found at i:82627 original size:6 final size:6
Alignment explanation
Indices: 82607--82688 Score: 62
Period size: 6 Copynumber: 14.2 Consensus size: 6
82597 TCGAACTCCC
* * * *
82607 TTTAAA TTT-AT TTTAAA TTTAAA TTT-AT TTTTAA TTTAAG TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA
** * * *
82653 TTTATT TTTAAA TTTAAA ATT-AC TATAAA TTTAAA T
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA T
82689 AAAGTTAAAA
Statistics
Matches: 56, Mismatches: 17, Indels: 6
0.71 0.22 0.08
Matches are distributed among these distances:
5 10 0.18
6 46 0.82
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:82629 original size:17 final size:18
Alignment explanation
Indices: 82607--82688 Score: 78
Period size: 17 Copynumber: 4.4 Consensus size: 18
82597 TCGAACTCCC
82607 TTTAAATTTA-TTTTAAA
1 TTTAAATTTATTTTTAAA
82624 TTTAAATTTATTTTTAATTTAA
1 TTTAAATTTATTTTT-A---AA
82646 GTTTAAATTTATTTTTAAA
1 -TTTAAATTTATTTTTAAA
* * *
82665 TTTAAAATTA-CTATAAA
1 TTTAAATTTATTTTTAAA
82682 TTTAAAT
1 TTTAAAT
82689 AAAGTTAAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
17 21 0.38
18 13 0.24
19 3 0.05
22 3 0.05
23 15 0.27
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.56
Consensus pattern (18 bp):
TTTAAATTTATTTTTAAA
Found at i:82639 original size:23 final size:23
Alignment explanation
Indices: 82613--82670 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
82603 TCCCTTTAAA
*
82613 TTTATTTTAAATTTAAATTTATT
1 TTTAATTTAAATTTAAATTTATT
*
82636 TTTAATTTAAGTTTAAATTTATT
1 TTTAATTTAAATTTAAATTTATT
82659 TTTAAATTTAAA
1 TTT-AATTTAAA
82671 ATTACTATAA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 24 0.77
24 7 0.23
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTAATTTAAATTTAAATTTATT
Found at i:83421 original size:3 final size:3
Alignment explanation
Indices: 83402--83439 Score: 58
Period size: 3 Copynumber: 12.0 Consensus size: 3
83392 AATATTGTCC
83402 TAA TAAA TAA TTAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA
83440 GGAAACGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 27 0.82
4 6 0.18
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:84506 original size:30 final size:29
Alignment explanation
Indices: 84436--84812 Score: 334
Period size: 29 Copynumber: 12.8 Consensus size: 29
84426 GGAGGTCCCT
*
84436 AAACTGTCCAAAAATTCCATTTTTACCCTCG
1 AAACT-TCCAAAAATTCCATTTTTAACC-CG
*
84467 -AACTTCCAAAAATCCCATTTTCTAACCCG
1 AAACTTCCAAAAATTCCATTTT-TAACCCG
* * *
84496 AAATTTCCAAAAATTCTATTTTTACCCTCG
1 AAACTTCCAAAAATTCCATTTTTAACC-CG
84526 -AACTTCC-AAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTAA-CCCG
* * *
84554 AAACTTCTAAAAATTACCA-TTTTACCCCT
1 AAACTTCCAAAAATT-CCATTTTTAACCCG
* *
84583 AAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATTCCATTTTTAACC-CG
* * * *
84613 AAACTTCTAAAAATTACCA-TTATACCCCT
1 AAACTTCCAAAAATT-CCATTTTTAACCCG
* * *
84642 AAACTTCCAAAAATCCCATTTTTTATCCCT
1 AAACTTCCAAAAATTCCA-TTTTTAACCCG
* * * * *
84672 TAACTTCTAAAAATCCCATTTTTGACCCT
1 AAACTTCCAAAAATTCCATTTTTAACCCG
*
84701 AGAACTTCC-AAAATTCCATTTTTAACCTTG
1 A-AACTTCCAAAAATTCCATTTTTAACC-CG
* * *
84731 AAACTTCTAAAAATTCCATTTTTAGCCCC
1 AAACTTCCAAAAATTCCATTTTTAACCCG
* *
84760 AAACTTCCCAAAATTCCATTTTTGACTCCG
1 AAACTTCCAAAAATTCCATTTTTAAC-CCG
*
84790 AAACTTCCTAAAATTACCATTTT
1 AAACTTCCAAAAATT-CCATTTT
84813 ACCCCCGGAT
Statistics
Matches: 284, Mismatches: 45, Indels: 34
0.78 0.12 0.09
Matches are distributed among these distances:
28 22 0.08
29 126 0.44
30 123 0.43
31 13 0.05
ACGTcount: A:0.35, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCCAAAAATTCCATTTTTAACCCG
Found at i:84517 original size:59 final size:57
Alignment explanation
Indices: 84436--84817 Score: 369
Period size: 59 Copynumber: 6.5 Consensus size: 57
84426 GGAGGTCCCT
84436 AAACTGTCCAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATCCCATTTTCTAACCCG
1 AAACT-TCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTT-TAACCCG
* * *
84496 AAATTTCCAAAAATTCTATTTTTACCCTCGAACTTCC-AAAATTCCATTTTTAACCCCG
1 AAACTTCCAAAAATTCCATTTTTACCC-CGAACTTCCAAAAATCCCATTTTTAA-CCCG
* * *
84554 AAACTTCTAAAAATTACCA-TTTTACCCCTAAACTTCCAAAAATCCCATTTTTAACCTCA
1 AAACTTCCAAAAATT-CCATTTTTACCCC-GAACTTCCAAAAATCCCATTTTTAACC-CG
* * * * *
84613 AAACTTCTAAAAATTACCA-TTATACCCCTAAACTTCCAAAAATCCCATTTTTTATCCCT
1 AAACTTCCAAAAATT-CCATTTTTACCCC-GAACTTCCAAAAATCCCA-TTTTTAACCCG
* * * * * *
84672 TAACTTCTAAAAATCCCATTTTTGACCCTAGAACTTCC-AAAATTCCATTTTTAACCTTG
1 AAACTTCCAAAAATTCCATTTTT-ACCC-CGAACTTCCAAAAATCCCATTTTTAACC-CG
* * * * *
84731 AAACTTCTAAAAATTCCATTTTTAGCCCCAAACTTCCCAAAATTCCATTTTTGACTCCG
1 AAACTTCCAAAAATTCCATTTTTA-CCCCGAACTTCCAAAAATCCCATTTTTAAC-CCG
*
84790 AAACTTCCTAAAATTACCA-TTTTACCCC
1 AAACTTCCAAAAATT-CCATTTTTACCCC
84818 CGGATGTCCA
Statistics
Matches: 279, Mismatches: 29, Indels: 30
0.83 0.09 0.09
Matches are distributed among these distances:
57 4 0.01
58 69 0.25
59 179 0.64
60 27 0.10
ACGTcount: A:0.35, C:0.29, G:0.03, T:0.34
Consensus pattern (57 bp):
AAACTTCCAAAAATTCCATTTTTACCCCGAACTTCCAAAAATCCCATTTTTAACCCG
Found at i:84890 original size:29 final size:29
Alignment explanation
Indices: 84856--84919 Score: 94
Period size: 29 Copynumber: 2.2 Consensus size: 29
84846 CCGAATTTTC
*
84856 CCAAAATTATC-GTTTTGCCCCTCGAGAAT
1 CCAAAATTATCAGTTTTACCCC-CGAGAAT
*
84885 CCAAAATTATCATTTTTACCCCCGAGAAT
1 CCAAAATTATCAGTTTTACCCCCGAGAAT
84914 CCAAAA
1 CCAAAA
84920 AGTCTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 24 0.75
30 8 0.25
ACGTcount: A:0.34, C:0.28, G:0.09, T:0.28
Consensus pattern (29 bp):
CCAAAATTATCAGTTTTACCCCCGAGAAT
Found at i:84930 original size:30 final size:30
Alignment explanation
Indices: 84868--84930 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
84858 AAAATTATCG
* *
84868 TTTTGCCCCTCGAGAATCCAAAATTATCAT
1 TTTTACCCCTCGAGAATCCAAAAGTATCAT
*
84898 TTTTACCCC-CGAGAATCCAAAAAGTCTCAT
1 TTTTACCCCTCGAGAATCC-AAAAGTATCAT
84928 TTT
1 TTT
84931 GAACTCCGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.30, C:0.27, G:0.10, T:0.33
Consensus pattern (30 bp):
TTTTACCCCTCGAGAATCCAAAAGTATCAT
Done.