Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01014383.1 Kokia drynarioides strain JFW-HI SEQ_129421, 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: 88583
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Warning! 51 characters in sequence are not A, C, G, or T
Found at i:17939 original size:24 final size:24
Alignment explanation
Indices: 17912--17975 Score: 85
Period size: 24 Copynumber: 2.7 Consensus size: 24
17902 CCTCCGAGCA
*
17912 TCCTCTTCCTCTCTCCTTC-TGGCT
1 TCCTCTTCCTCT-TCCTTCTTAGCT
*
17936 TCCTCTTCCTCTTCCCTCTTAGCT
1 TCCTCTTCCTCTTCCTTCTTAGCT
*
17960 TCTTCTTCCTCTTCCT
1 TCCTCTTCCTCTTCCT
17976 CTCTCCTCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
23 5 0.14
24 30 0.86
ACGTcount: A:0.02, C:0.45, G:0.05, T:0.48
Consensus pattern (24 bp):
TCCTCTTCCTCTTCCTTCTTAGCT
Found at i:17948 original size:30 final size:30
Alignment explanation
Indices: 17912--18110 Score: 191
Period size: 30 Copynumber: 6.9 Consensus size: 30
17902 CCTCCGAGCA
*
17912 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
* *
17942 TCCTCTT-C-C-CT-CT--TAGCTTCTTCT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
* *
17966 TCCTCTTCCTCTCTCCTCCTAGCTTCTTCT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
* *
17996 TCCTCTTCCTCTCTCCTCCTGGCCTCCTTT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
* * *** *
18026 TCTTC-TCTTCTCTTAGCCT--CCTCCTCT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
* *
18053 TCCTCTTCCTCTCTCCTCCTAGCTTCTTCT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
*
18083 TCCTCTTCCTCTCTCCTCCTGGCCTCCT
1 TCCTCTTCCTCTCTCCTCCTGGCTTCCT
18111 TTTCTTCTCT
Statistics
Matches: 138, Mismatches: 22, Indels: 18
0.78 0.12 0.10
Matches are distributed among these distances:
24 16 0.12
25 1 0.01
26 3 0.02
27 15 0.11
28 13 0.09
29 11 0.08
30 79 0.57
ACGTcount: A:0.02, C:0.47, G:0.05, T:0.46
Consensus pattern (30 bp):
TCCTCTTCCTCTCTCCTCCTGGCTTCCTCT
Found at i:17953 original size:7 final size:6
Alignment explanation
Indices: 17934--18100 Score: 80
Period size: 6 Copynumber: 27.2 Consensus size: 6
17924 CTCCTTCTGG
** *
17934 CTTCCT CTTCCT CTTCCCT CTT-AG CTTCTT CTTCCT CTTCCT C-T-CT
1 CTTCCT CTTCCT CTT-CCT CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT
* * * *
17980 CCTCCT AGCTTCTT CTTCCT CTTCCT CTCTCCT CCTGGCCT CCTT-TT
1 CTTCCT --CTTCCT CTTCCT CTTCCT CT-TCCT -CT-TCCT -CTTCCT
* *
18027 CTT-CT CTT-CT CTTAGCCT CCTCCT CTTCCT CTTCCT C-T-CT CCTCCT
1 CTTCCT CTTCCT CTT--CCT CTTCCT CTTCCT CTTCCT CTTCCT CTTCCT
*
18073 AGCTTCTT CTTCCT CTTCCT CTCTCCT C
1 --CTTCCT CTTCCT CTTCCT CT-TCCT C
18101 CTGGCCTCCT
Statistics
Matches: 127, Mismatches: 18, Indels: 31
0.72 0.10 0.18
Matches are distributed among these distances:
4 6 0.05
5 19 0.15
6 67 0.53
7 15 0.12
8 20 0.16
ACGTcount: A:0.02, C:0.47, G:0.04, T:0.47
Consensus pattern (6 bp):
CTTCCT
Found at i:18071 original size:87 final size:85
Alignment explanation
Indices: 17912--18191 Score: 344
Period size: 87 Copynumber: 3.3 Consensus size: 85
17902 CCTCCGAGCA
* * * *
17912 TCCTCTTCCTCTCTCCTTCTGGCTTCCTCTTC--CTCTTCCCTCTTAG-CTTCTTCTTCCTCTTC
1 TCCTCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTT--CTCTTAGCCTTCCTCTTCCTCTTC
17974 CTCTCTCCTCCTAGCTTCTTCT
64 CTCTCTCCTCCTAGCTTCTTCT
17996 TCCTCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTTCTCTTAGCCTCCTCCTCTTCCTCTTC
1 TCCTCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTTCTCTTAGCCT--TCCTCTTCCTCTTC
18061 CTCTCTCCTCCTAGCTTCTTCT
64 CTCTCTCCTCCTAGCTTCTTCT
18083 TCCTCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTTCTCTTAG-C-T--TCTTCCT-TCTCC
1 TCCTCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTTCTCTTAGCCTTCCTCTTCCTCT-TCC
* ** *
18143 TCTCTTCTTTTAGCTTCTTCC
65 TCTCTCCTCCTAGCTTCTTCT
* * *
18164 TCCTCCT-CTCTCCTCTTTCTGGCCTCCT
1 TCCTCTTCCTCT-CTCCTCCTGGCCTCCT
18192 CTTCCTCCTT
Statistics
Matches: 178, Mismatches: 11, Indels: 17
0.86 0.05 0.08
Matches are distributed among these distances:
80 5 0.03
81 47 0.26
83 1 0.01
84 36 0.20
85 2 0.01
86 6 0.03
87 81 0.46
ACGTcount: A:0.02, C:0.45, G:0.05, T:0.47
Consensus pattern (85 bp):
TCCTCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTTCTCTTAGCCTTCCTCTTCCTCTTCCT
CTCTCCTCCTAGCTTCTTCT
Found at i:18137 original size:27 final size:27
Alignment explanation
Indices: 18020--18164 Score: 91
Period size: 27 Copynumber: 5.1 Consensus size: 27
18010 CCTCCTGGCC
* *
18020 TCCTTTTCTTCTCTTCTCTTAGCCTCC
1 TCCTTTTCTTCTCTTCTCTTAGCTTCT
*
18047 TCCTCTTCCTCTTCCTCTCTCCTCCTAGCTTCT
1 TCCT-TT--TCTT-CTCT-T-CTCTTAGCTTCT
* * *
18080 T-CTTCCTCTTCCTCTCTCCTCCTGGC--C-
1 TCCTT-TTCTT-CTCT-T-CTCTTAGCTTCT
18107 TCCTTTTCTTCTCTTCTCTTAGCTTCT
1 TCCTTTTCTTCTCTTCTCTTAGCTTCT
* * *
18134 TCCTTCTCCTCTCTTCTTTTAGCTTCT
1 TCCTTTTCTTCTCTTCTCTTAGCTTCT
18161 TCCT
1 TCCT
18165 CCTCCTCTCT
Statistics
Matches: 96, Mismatches: 11, Indels: 22
0.74 0.09 0.17
Matches are distributed among these distances:
24 6 0.06
25 1 0.01
26 5 0.05
27 37 0.39
28 6 0.06
30 23 0.24
31 5 0.05
32 3 0.03
33 10 0.10
ACGTcount: A:0.03, C:0.43, G:0.04, T:0.50
Consensus pattern (27 bp):
TCCTTTTCTTCTCTTCTCTTAGCTTCT
Found at i:18165 original size:117 final size:116
Alignment explanation
Indices: 17934--18180 Score: 290
Period size: 117 Copynumber: 2.1 Consensus size: 116
17924 CTCCTTCTGG
* *
17934 CTTCCTCTTCCTCTTCCCTCTTAGCTTCTTCTTCCTCTTCCTCTCTCCTCCTAGCTTCTTCTTCC
1 CTTCCTCTTCCTCTTCCCTCCTAGCTTCTTCTTCCTCTTCCTCTCTCCTCCTAGC-TCTCCTTCC
* * *
17999 TCTTCCTCTCTCCTCCTGGCCTCCTTTTCTTCTCTTCTCTTAGCCTCCTCCT
65 TCTTCCTCTCTCCTCCTAGCCTCCTTCTCCTCTCTTCTCTTAGCCTCCTCCT
* *
18051 CTTCCTCTTCCTC-TCTCCTCCTAGCTTCTTCTTCCTCTTCCTCTCTCCTCCTGGC-CTCCTT-T
1 CTTCCTCTTCCTCTTC-CCTCCTAGCTTCTTCTTCCTCTTCCTCTCTCCTCCTAGCTCTCCTTCC
* * * *
18113 TCTT-CTCT-T-CTCTTAGCTTCTTCCTTCTCCTCTCTTCTTTTAGCTTCTTCCT
65 TCTTCCTCTCTCCTCCTAGC--C-TCCTTCTCCTCTCTTCTCTTAGCCTCCTCCT
*
18165 CCTCCTCTCTCCTCTT
1 CTTCCTCT-TCCTCTT
18181 TCTGGCCTCC
Statistics
Matches: 112, Mismatches: 12, Indels: 13
0.82 0.09 0.09
Matches are distributed among these distances:
111 6 0.05
112 1 0.01
113 5 0.04
114 37 0.33
115 10 0.09
116 3 0.03
117 50 0.45
ACGTcount: A:0.02, C:0.45, G:0.04, T:0.48
Consensus pattern (116 bp):
CTTCCTCTTCCTCTTCCCTCCTAGCTTCTTCTTCCTCTTCCTCTCTCCTCCTAGCTCTCCTTCCT
CTTCCTCTCTCCTCCTAGCCTCCTTCTCCTCTCTTCTCTTAGCCTCCTCCT
Found at i:18169 original size:27 final size:27
Alignment explanation
Indices: 18116--18180 Score: 103
Period size: 27 Copynumber: 2.4 Consensus size: 27
18106 CTCCTTTTCT
*
18116 TCTCTTCTCTTAGCTTCTTCCTTCTCC
1 TCTCTTCTCTTAGCTTCTTCCTCCTCC
*
18143 TCTCTTCTTTTAGCTTCTTCCTCCTCC
1 TCTCTTCTCTTAGCTTCTTCCTCCTCC
*
18170 TCTCTCCTCTT
1 TCTCTTCTCTT
18181 TCTGGCCTCC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.03, C:0.42, G:0.03, T:0.52
Consensus pattern (27 bp):
TCTCTTCTCTTAGCTTCTTCCTCCTCC
Found at i:28041 original size:111 final size:111
Alignment explanation
Indices: 27843--28171 Score: 514
Period size: 111 Copynumber: 2.9 Consensus size: 111
27833 AATTAATCAT
27843 AATCGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGGTTCCACTGCAGTCC
1 AATCGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGGTTCCACTGCAGTCC
*
27908 ACATACACGTGGCGCAAACATCTAAATGTAATTAGAATCAATCGCA
66 ACATACACGTGGCGCTAACATCTAAATGTAATTAGAATCAATCGCA
* * * * *
27954 AATTGATTGGACGATGAGTCCCTTAACCGTCAACTATGCTATTAACAAAGGCTCCGCTGCAGTCC
1 AATCGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGGTTCCACTGCAGTCC
*
28019 ACATACACGTGGCGCTAACATCTAAATGTAATTAGAATCGATCGCA
66 ACATACACGTGGCGCTAACATCTAAATGTAATTAGAATCAATCGCA
* * * *
28065 AATCGATTGGATGATGAGTCCTTTAACTGTCAACTATGCTATTAACAAAGATTCAACTGCAGTCG
1 AATCGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGGTTCCACTGCAGTCC
* *
28130 ACATACACGCGGCGCTAACAACATCTAAATGTAATTACAATC
66 ACATACACGTGGCGCT---AACATCTAAATGTAATTAGAATC
28172 GACCTCAAAA
Statistics
Matches: 197, Mismatches: 18, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
111 175 0.89
114 22 0.11
ACGTcount: A:0.34, C:0.23, G:0.17, T:0.26
Consensus pattern (111 bp):
AATCGATTGGATGATGAGTCCTTTAACCGTCAACTATGCTATTAACAAAGGTTCCACTGCAGTCC
ACATACACGTGGCGCTAACATCTAAATGTAATTAGAATCAATCGCA
Found at i:35602 original size:19 final size:19
Alignment explanation
Indices: 35578--35615 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
35568 TTTAAAAAAA
*
35578 TTAAAAACTGCAAAATTAT
1 TTAAAAACTACAAAATTAT
*
35597 TTAAAAACTATAAAATTAT
1 TTAAAAACTACAAAATTAT
35616 AAAGATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (19 bp):
TTAAAAACTACAAAATTAT
Found at i:36569 original size:8 final size:8
Alignment explanation
Indices: 36556--36585 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
36546 AATAACCTAT
*
36556 AAATTTTG
1 AAATTTTA
36564 AAATTTTA
1 AAATTTTA
36572 AAATTTTA
1 AAATTTTA
36580 AAATTT
1 AAATTT
36586 CAACACATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (8 bp):
AAATTTTA
Found at i:37537 original size:18 final size:18
Alignment explanation
Indices: 37510--37564 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
37500 AGAATCCATA
*
37510 AATAACAACGACAATAAT
1 AATAACAACGAAAATAAT
* *
37528 CATAAGAACGAAAATAAT
1 AATAACAACGAAAATAAT
* *
37546 AATAATAACAAAAATAAT
1 AATAACAACGAAAATAAT
37564 A
1 A
37565 GCAATCTTTA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.65, C:0.11, G:0.05, T:0.18
Consensus pattern (18 bp):
AATAACAACGAAAATAAT
Found at i:40063 original size:26 final size:26
Alignment explanation
Indices: 40028--40080 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
40018 TTATTTTAAA
*
40028 ATTAAGTTTATAATAAATTTAAATTT
1 ATTAAATTTATAATAAATTTAAATTT
*
40054 ATTAAATTTATTATAAATTTAAATTT
1 ATTAAATTTATAATAAATTTAAATTT
40080 A
1 A
40081 AAATATCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (26 bp):
ATTAAATTTATAATAAATTTAAATTT
Found at i:40080 original size:17 final size:17
Alignment explanation
Indices: 40008--40057 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 17
39998 GGGCCTATTG
* *
40008 AAATTTGAATTTATTTT
1 AAATTTAAATTTATTAT
* * *
40025 AAAATTAAGTTTATAAT
1 AAATTTAAATTTATTAT
40042 AAATTTAAATTTATTA
1 AAATTTAAATTTATTA
40058 AATTTATTAT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
AAATTTAAATTTATTAT
Found at i:41934 original size:30 final size:29
Alignment explanation
Indices: 41869--42315 Score: 330
Period size: 30 Copynumber: 15.1 Consensus size: 29
41859 CCCTAAATTG
*
41869 TCCAAAAATTTCATTTTTACCTCC-AAACT
1 TCCAAAAATCTCATTTTTACC-CCAAAACT
* *
41898 TCCAAAAATCTCATTTTTGACCCCGAAACA
1 TCCAAAAATCTCATTTTT-ACCCCAAAACT
*
41928 TCCAAAAA-CTCCATTTTTACCCCCAAACT
1 TCCAAAAATCT-CATTTTTACCCCAAAACT
41957 TCCAAAAATC-CTATTTTTGACCCCAAAACT
1 TCCAAAAATCTC-ATTTTT-ACCCCAAAACT
* *
41987 TCCAAAAATCCCATTTTTGACCTCAAAACT
1 TCCAAAAATCTCATTTTT-ACCCCAAAACT
* *
42017 TCCAAAACT-TCCATTTTTACCCTC-GAACT
1 TCCAAAAATCT-CATTTTTACCC-CAAAACT
* * *
42046 TCCAAAAAT-TCCATTTTTGATCTCGAAACT
1 TCCAAAAATCT-CATTTTT-ACCCCAAAACT
*
42076 TCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATCTCATTTTT-ACCCCAAAACT
** *
42106 TTAAAAAATCCCATTTTTAAACCCCAAAACT
1 TCCAAAAATCTCATTTTT--ACCCCAAAACT
*
42137 TCCAAAAAATC-CAATTTTTTCCCCAAAACT
1 TCC-AAAAATCTC-ATTTTTACCCCAAAACT
* * * *
42167 TTCAAAAATTTCATTTTTAGCCTC-GAACT
1 TCCAAAAATCTCATTTTTA-CCCCAAAACT
* *
42196 TCCAAAAAT-T-ACCTTTTACCCTC-GAACT
1 TCCAAAAATCTCA-TTTTTACCC-CAAAACT
**
42224 TCCAAAAAATC-CATTTTTGACCCTTAAACT
1 TCC-AAAAATCTCATTTTT-ACCCCAAAACT
* *
42254 TCCAAAAAT-TACATTTCTACCCCTAAAC-
1 TCCAAAAATCT-CATTTTTACCCCAAAACT
* *
42282 CCCAAAAAT-TCCATTTTTAGCCCCAAAAAT
1 TCCAAAAATCT-CATTTTTA-CCCCAAAACT
42312 TCCA
1 TCCA
42316 TTTTTACCCC
Statistics
Matches: 347, Mismatches: 43, Indels: 55
0.78 0.10 0.12
Matches are distributed among these distances:
27 3 0.01
28 32 0.09
29 125 0.36
30 159 0.46
31 15 0.04
32 13 0.04
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (29 bp):
TCCAAAAATCTCATTTTTACCCCAAAACT
Found at i:41961 original size:59 final size:59
Alignment explanation
Indices: 41869--42308 Score: 375
Period size: 59 Copynumber: 7.5 Consensus size: 59
41859 CCCTAAATTG
* * * *
41869 TCCAAAAATTTCATTTTT-ACCTCCAAACTTCCAAAAATCTCATTTTTGACCCCGAAACA
1 TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCTCATTTTT-ACCCCAAAACT
*
41928 TCCAAAAACTCCATTTTT-ACCCCCAAACTTCCAAAAATC-CTATTTTTGACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCTC-ATTTTT-ACCCCAAAACT
* * * * *
41987 TCCAAAAATCCCATTTTTGACCTCAAAACTTCCAAAACT-TCCATTTTTACCCTC-GAACT
1 TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCT-CATTTTTACCC-CAAAACT
* * * *
42046 TCCAAAAATTCCATTTTTGATCTCGAAACTTCCAAAAATCCCATTTTTAACCCCAAAACT
1 TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCTCATTTTT-ACCCCAAAACT
** * * * *
42106 TTAAAAAATCCCATTTTTAAACCCCAAAACTTCCAAAAAATC-CAATTTTTTCCCCAAAACT
1 TCCAAAAATTCCATTTTT-GACCCCCAAACTTCC-AAAAATCTC-ATTTTTACCCCAAAACT
* * * * * * *
42167 TTCAAAAATTTCATTTTT-AGCCTCGAACTTCCAAAAAT-T-ACCTTTTACCCTC-GAACT
1 TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCTCA-TTTTTACCC-CAAAACT
* ** * *
42224 TCCAAAAAATCCATTTTTGACCCTTAAACTTCCAAAAAT-TACATTTCTACCCCTAAAC-
1 TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCT-CATTTTTACCCCAAAACT
* *
42282 CCCAAAAATTCCATTTTT-AGCCCCAAA
1 TCCAAAAATTCCATTTTTGACCCCCAAA
42309 AATTCCATTT
Statistics
Matches: 314, Mismatches: 49, Indels: 38
0.78 0.12 0.09
Matches are distributed among these distances:
56 1 0.00
57 32 0.10
58 43 0.14
59 139 0.44
60 48 0.15
61 38 0.12
62 13 0.04
ACGTcount: A:0.36, C:0.30, G:0.03, T:0.31
Consensus pattern (59 bp):
TCCAAAAATTCCATTTTTGACCCCCAAACTTCCAAAAATCTCATTTTTACCCCAAAACT
Found at i:42202 original size:28 final size:28
Alignment explanation
Indices: 42163--42275 Score: 102
Period size: 29 Copynumber: 3.9 Consensus size: 28
42153 TTTTCCCCAA
* * * *
42163 AACTTTCAAAAATTTCATTTTTAGCCTCG
1 AACTTCCAAAAATTAC-CTTTTACCCTCG
42192 AACTTCCAAAAATTACCTTTTACCCTCG
1 AACTTCCAAAAATTACCTTTTACCCTCG
* **
42220 AACTTCCAAAAAAT-CCATTTTTGACCCTTA
1 AACTTCCAAAAATTACC--TTTT-ACCCTCG
*
42250 AACTTCCAAAAATTACATTTCTACCC
1 AACTTCCAAAAATTACCTTT-TACCC
42276 CTAAACCCCA
Statistics
Matches: 70, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
27 2 0.03
28 23 0.33
29 25 0.36
30 19 0.27
31 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.35
Consensus pattern (28 bp):
AACTTCCAAAAATTACCTTTTACCCTCG
Found at i:42319 original size:20 final size:21
Alignment explanation
Indices: 42281--42326 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
42271 TACCCCTAAA
42281 CCCCAAAAATTCCATTTTTAG
1 CCCCAAAAATTCCATTTTTAG
*
42302 CCCCAAAAATTCCATTTTTAC
1 CCCCAAAAATTCCATTTTTAG
42323 CCCC
1 CCCC
42327 GAACTTTCAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.30, C:0.37, G:0.02, T:0.30
Consensus pattern (21 bp):
CCCCAAAAATTCCATTTTTAG
Found at i:42338 original size:108 final size:108
Alignment explanation
Indices: 42197--42408 Score: 254
Period size: 108 Copynumber: 2.0 Consensus size: 108
42187 CCTCGAACTT
* *
42197 CCAAAAATTACCTTTTACCCTCGAACTTCCAAAAAAT-CCATTTTTGA-CCCTTAAACTTCCAAA
1 CCAAAAATTACCTTTTACCCCCGAACTTCC-AAAAATGCCATTTTTGATCCC-GAAACTTCCAAA
42260 AATTACA-TTTCTACCC-CTAAACCCCAAAAATTCCATTTTTAGCC
64 AATTACATTTTC-ACCCTCTAAACCCCAAAAATTCCATTTTTAGCC
* * *
42304 CCAAAAATT-CCATTTTTACCCCCGAACTTTCAAAAATGCCATTTTTGATCCCGAAATTTCTAAA
1 CCAAAAATTACC--TTTTACCCCCGAACTTCCAAAAATGCCATTTTTGATCCCGAAACTTCCAAA
* *** *
42368 AATTCCATTTTCACCCTCTAATGTCTAAAAATTCCATTTTT
64 AATTACATTTTCACCCTCTAAACCCCAAAAATTCCATTTTT
42409 GAACCTCGAA
Statistics
Matches: 89, Mismatches: 10, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
106 2 0.02
107 15 0.17
108 45 0.51
109 27 0.30
ACGTcount: A:0.34, C:0.28, G:0.04, T:0.34
Consensus pattern (108 bp):
CCAAAAATTACCTTTTACCCCCGAACTTCCAAAAATGCCATTTTTGATCCCGAAACTTCCAAAAA
TTACATTTTCACCCTCTAAACCCCAAAAATTCCATTTTTAGCC
Found at i:42376 original size:30 final size:29
Alignment explanation
Indices: 42306--42439 Score: 105
Period size: 29 Copynumber: 4.5 Consensus size: 29
42296 TTTTAGCCCC
*
42306 AAAAATTCCATTTTT-ACCCCCGAACTTTC-
1 AAAAATTCCATTTTTGA--CCCGAAATTTCT
*
42335 AAAAATGCCATTTTTGATCCCGAAATTTCT
1 AAAAATTCCATTTTTGA-CCCGAAATTTCT
* ** *
42365 AAAAATTCCA-TTTTCACCCTCTAATGTCT
1 AAAAATTCCATTTTTGACCC-GAAATTTCT
*
42394 AAAAATTCCATTTTTGAACCTCGAATTTTCCT
1 AAAAATTCCATTTTTG-ACC-CGAAATTT-CT
42426 -AAAATTACCATTTT
1 AAAAATT-CCATTTT
42440 GCCCCCGGGT
Statistics
Matches: 84, Mismatches: 13, Indels: 13
0.76 0.12 0.12
Matches are distributed among these distances:
28 3 0.04
29 45 0.54
30 14 0.17
31 12 0.14
32 10 0.12
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (29 bp):
AAAAATTCCATTTTTGACCCGAAATTTCT
Found at i:42398 original size:59 final size:61
Alignment explanation
Indices: 42306--42439 Score: 159
Period size: 59 Copynumber: 2.2 Consensus size: 61
42296 TTTTAGCCCC
* * *
42306 AAAAATTCCATTTTTACCCCCGAACTTTCAAAAATGCCATTTTTGATCC-CGAAATTT-CT
1 AAAAATTCCATTTTCACCCCCGAACTGTCAAAAATGCCATTTTTGAACCTCGAAATTTCCT
* * * *
42365 AAAAATTCCATTTTCACCCTCTAA-TGTCTAAAAATTCCATTTTTGAACCTCGAATTTTCCT
1 AAAAATTCCATTTTCACCCCCGAACTGTC-AAAAATGCCATTTTTGAACCTCGAAATTTCCT
42426 -AAAATTACCATTTT
1 AAAAATT-CCATTTT
42440 GCCCCCGGGT
Statistics
Matches: 64, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
58 3 0.05
59 39 0.61
60 13 0.20
61 9 0.14
ACGTcount: A:0.33, C:0.24, G:0.05, T:0.38
Consensus pattern (61 bp):
AAAAATTCCATTTTCACCCCCGAACTGTCAAAAATGCCATTTTTGAACCTCGAAATTTCCT
Found at i:45790 original size:19 final size:18
Alignment explanation
Indices: 45753--45814 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 18
45743 AAACAGGAGG
45753 AAGCAAAAAAGAAAAAGA
1 AAGCAAAAAAGAAAAAGA
45771 AAGCAGAAAAAGCAAGAGAAG-
1 AAGCA-AAAAAG-AA-A-AAGA
45792 AAGCAAAAAGAGAAGAAA-A
1 AAGCAAAAA-AGAA-AAAGA
45811 AAGC
1 AAGC
45815 CTTGGCAAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
18 5 0.13
19 12 0.32
20 10 0.26
21 8 0.21
22 3 0.08
ACGTcount: A:0.69, C:0.08, G:0.23, T:0.00
Consensus pattern (18 bp):
AAGCAAAAAAGAAAAAGA
Found at i:45808 original size:18 final size:17
Alignment explanation
Indices: 45752--45808 Score: 51
Period size: 18 Copynumber: 3.0 Consensus size: 17
45742 GAAACAGGAG
*
45752 GAAGCAAAAAAGAAAAA
1 GAAGCAAAAAAGAAGAA
45769 GAAAGCAGAAAAAGCAAGAGAA
1 G-AAGCA-AAAAAG--A-AGAA
45791 GAAGCAAAAAGAGAAGAA
1 GAAGCAAAAA-AGAAGAA
45809 AAAAGCCTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 11
0.73 0.02 0.24
Matches are distributed among these distances:
17 1 0.03
18 9 0.27
19 7 0.21
20 4 0.12
21 8 0.24
22 4 0.12
ACGTcount: A:0.68, C:0.07, G:0.25, T:0.00
Consensus pattern (17 bp):
GAAGCAAAAAAGAAGAA
Found at i:51256 original size:15 final size:15
Alignment explanation
Indices: 51236--51265 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
51226 GTTGAAAAGA
51236 ATGAAATTTGACTAT
1 ATGAAATTTGACTAT
51251 ATGAAATTTGACTAT
1 ATGAAATTTGACTAT
51266 CTATGCTGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (15 bp):
ATGAAATTTGACTAT
Found at i:52208 original size:23 final size:23
Alignment explanation
Indices: 52164--52209 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
52154 TTCTCCCTCC
*
52164 AAAAACAACATAATTAATGAATT
1 AAAAACAACATAAATAATGAATT
*
52187 AAAAA-AACATAAATGATCGAATT
1 AAAAACAACATAAATAAT-GAATT
52210 TAATTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 10 0.50
23 10 0.50
ACGTcount: A:0.61, C:0.09, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAAACAACATAAATAATGAATT
Found at i:52671 original size:15 final size:17
Alignment explanation
Indices: 52638--52671 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
52628 CTATTTTTTA
52638 TATAAAAGATATAAATT
1 TATAAAAGATATAAATT
52655 TATAAAA-ATAT-AATT
1 TATAAAAGATATAAATT
52670 TA
1 TA
52672 CTTTATAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.35
16 4 0.24
17 7 0.41
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TATAAAAGATATAAATT
Found at i:57530 original size:24 final size:23
Alignment explanation
Indices: 57490--57547 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
57480 TATATATTCT
*
57490 AATTAA-ATTTTATAAATAATTAA
1 AATTAATA-TTTAGAAATAATTAA
* *
57513 TATTAATTATTTAGAAATATTTAA
1 AATTAA-TATTTAGAAATAATTAA
57537 AATTAATATTT
1 AATTAATATTT
57548 CACATATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.34
24 18 0.62
25 1 0.03
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
AATTAATATTTAGAAATAATTAA
Found at i:57666 original size:18 final size:19
Alignment explanation
Indices: 57629--57667 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
57619 ATTAATTTAA
*
57629 TATTATTTAAGTATATATT
1 TATTATTTAAGTACATATT
*
57648 TATTATTTTA-TACATATT
1 TATTATTTAAGTACATATT
57666 TA
1 TA
57668 AAATAAACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (19 bp):
TATTATTTAAGTACATATT
Found at i:72826 original size:29 final size:29
Alignment explanation
Indices: 72793--72849 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
72783 CGTGTGTCAT
*
72793 TTTATTCTTTATAAATTT-AGAATTTAATC
1 TTTATGCTTT-TAAATTTAAGAATTTAATC
**
72822 TTTATGCTTTTATTTTTAAGAATTTAAT
1 TTTATGCTTTTAAATTTAAGAATTTAAT
72850 TCATTTACTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 5 0.21
29 19 0.79
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.58
Consensus pattern (29 bp):
TTTATGCTTTTAAATTTAAGAATTTAATC
Done.