Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010467.1 Kokia drynarioides strain JFW-HI SEQ_125365, 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: 75571
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1029 original size:17 final size:17
Alignment explanation
Indices: 1009--1095 Score: 93
Period size: 17 Copynumber: 5.1 Consensus size: 17
999 CCAATTTTAA
*
1009 ATTTTAAATTTTAATTT
1 ATTTTAAATTTAAATTT
**
1026 ATTTTAAGCTTAAATTT
1 ATTTTAAATTTAAATTT
* *
1043 ATTTTAAATTTATACTT
1 ATTTTAAATTTAAATTT
* *
1060 ATTTTTGAGTTTAAATTT
1 A-TTTTAAATTTAAATTT
*
1078 ATTTTGAATTTAAATTT
1 ATTTTAAATTTAAATTT
1095 A
1 A
1096 AAATTTAATT
Statistics
Matches: 57, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
17 44 0.77
18 13 0.23
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (17 bp):
ATTTTAAATTTAAATTT
Found at i:1708 original size:15 final size:15
Alignment explanation
Indices: 1690--1724 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1680 ATTTATTTCG
*
1690 AAATTAATATTAAAT
1 AAATAAATATTAAAT
1705 AAATAAATATTAAAT
1 AAATAAATATTAAAT
1720 AAATA
1 AAATA
1725 CTTAATAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATAAATATTAAAT
Found at i:1718 original size:11 final size:12
Alignment explanation
Indices: 1704--1735 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
1694 TAATATTAAA
1704 TAAATAAATA-T
1 TAAATAAATACT
1715 TAAATAAATACT
1 TAAATAAATACT
1727 T-AATAAATA
1 TAAATAAATA
1736 AAATAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 18 0.90
12 2 0.10
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.34
Consensus pattern (12 bp):
TAAATAAATACT
Found at i:1733 original size:15 final size:15
Alignment explanation
Indices: 1690--1742 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
1680 ATTTATTTCG
* *
1690 AAATTAATATTAAAT
1 AAATAAATAATAAAT
*
1705 AAATAAATATTAAAT
1 AAATAAATAATAAAT
**
1720 AAATACTTAATAAAT
1 AAATAAATAATAAAT
1735 AAAATAAA
1 -AAATAAA
1743 AAAGGAAGTT
Statistics
Matches: 31, Mismatches: 6, Indels: 1
0.82 0.16 0.03
Matches are distributed among these distances:
15 26 0.84
16 5 0.16
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (15 bp):
AAATAAATAATAAAT
Found at i:2795 original size:30 final size:29
Alignment explanation
Indices: 2759--3060 Score: 129
Period size: 30 Copynumber: 10.2 Consensus size: 29
2749 TATTTTATTT
*
2759 AAAAATTACATTTTAACCCTCAAGCTTCAC
1 AAAAATTACATTTTAACCCTCAA-CTTCTC
*
2789 AAAAATTACATTTTGACCCTCGAACTTCTC
1 AAAAATTACATTTTAACCCTC-AACTTCTC
* * *
2819 AAAAATCACATTATAACCCTCGATCTTCTTC
1 AAAAATTACATTTTAACCCTC-AACTTC-TC
* *
2850 -ATAATTACATTTTAACCCTCAAACTTTTC
1 AAAAATTACATTTTAACCCTC-AACTTCTC
* * * * * * * *
2879 CAAAATCAAAATTTCATCCC-AAAATTTTC
1 AAAAAT-TACATTTTAACCCTCAACTTCTC
* * * * *
2908 -CAAATTGCATTTTTGATCCC-GAACATC-C
1 AAAAATTACA-TTTT-AACCCTCAACTTCTC
* *
2936 AAAAATTACCATTTTGA-CCTCAAACTTTTC
1 AAAAATTA-CATTTTAACCCTC-AACTTCTC
* *
2966 CAAAATTACATTTTTACCCTCGAACATTC-C
1 AAAAATTACATTTTAACCCTC-AAC-TTCTC
* * * *
2996 AAAAATTACCATTTTCACTCTAAACATC-C
1 AAAAATTA-CATTTTAACCCTCAACTTCTC
* *
3025 AAAAATTACCATTTTGA-CCTCGAACATC-C
1 AAAAATTA-CATTTTAACCCTC-AACTTCTC
3054 AAAAATT
1 AAAAATT
3061 CCCATTTGCC
Statistics
Matches: 210, Mismatches: 47, Indels: 31
0.73 0.16 0.11
Matches are distributed among these distances:
27 3 0.01
28 10 0.05
29 70 0.33
30 102 0.49
31 25 0.12
ACGTcount: A:0.37, C:0.26, G:0.04, T:0.33
Consensus pattern (29 bp):
AAAAATTACATTTTAACCCTCAACTTCTC
Found at i:2836 original size:60 final size:60
Alignment explanation
Indices: 2759--2886 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
2749 TATTTTATTT
* * * *
2759 AAAAATTACATTTTAACCCTCAAGCTTC-ACAAAAATTACATTTTGACCCTCGAACTTCTC
1 AAAAATCACATTATAACCCTCAAGCTTCTAC-AAAATTACATTTTAACCCTCAAACTTCTC
* * * * *
2819 AAAAATCACATTATAACCCTCGATCTTCTTCATAATTACATTTTAACCCTCAAACTTTTC
1 AAAAATCACATTATAACCCTCAAGCTTCTACAAAATTACATTTTAACCCTCAAACTTCTC
*
2879 CAAAATCA
1 AAAAATCA
2887 AAATTTCATC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 56 0.98
61 1 0.02
ACGTcount: A:0.38, C:0.27, G:0.03, T:0.33
Consensus pattern (60 bp):
AAAAATCACATTATAACCCTCAAGCTTCTACAAAATTACATTTTAACCCTCAAACTTCTC
Found at i:2978 original size:59 final size:59
Alignment explanation
Indices: 2898--3077 Score: 196
Period size: 59 Copynumber: 3.1 Consensus size: 59
2888 AATTTCATCC
* *
2898 CAAAATTTTCC-AAATTGCATTTTTGATCC-CGAACATCCAAAAATTACCATTTTGACCT
1 CAAACTTTTCCAAAATTACATTTTTGA-CCTCGAACATCCAAAAATTACCATTTTGACCT
*
2956 CAAACTTTTCCAAAATTACATTTTT-ACCCTCGAACATTCCAAAAATTACCATTTTCA-CT
1 CAAACTTTTCCAAAATTACATTTTTGA-CCTCGAACA-TCCAAAAATTACCATTTTGACCT
* * *
3015 CTAAAC--ATCCAAAAATTACCA-TTTTGACCTCGAACATCCAAAAATTCCCA-TTTGCCCT
1 C-AAACTTTTCC-AAAATTA-CATTTTTGACCTCGAACATCCAAAAATTACCATTTTGACCT
3073 CAAAC
1 CAAAC
3078 ATCCAAAAAT
Statistics
Matches: 106, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
57 7 0.07
58 32 0.30
59 41 0.39
60 26 0.25
ACGTcount: A:0.36, C:0.28, G:0.04, T:0.32
Consensus pattern (59 bp):
CAAACTTTTCCAAAATTACATTTTTGACCTCGAACATCCAAAAATTACCATTTTGACCT
Found at i:3117 original size:58 final size:58
Alignment explanation
Indices: 2992--3234 Score: 185
Period size: 58 Copynumber: 4.2 Consensus size: 58
2982 CCCTCGAACA
* * * * * *
2992 TTCCAAAAATTACCATTTTCACTCTAAACATCCAAAAATTACCATTTTGACCTCGAA-C
1 TTCC-AAAATTACCATTTGCCCTCTAAACATCCAAAAATTACGATTTTGACCCCAAATT
* * *
3050 ATCCAAAAATTCCCATTTGCCCTC-AAACATCCAAAAATTATGATTTTGACCCCAAACTT
1 TTCC-AAAATTACCATTTGCCCTCTAAACATCCAAAAATTACGATTTTGACCCCAAA-TT
* * * *
3109 TTCCAAAATTACCATTTTGCCC-CTAAGCATCCAAAAATTACTATTTTG-CCCTAAAAT
1 TTCCAAAATTACCA-TTTGCCCTCTAAACATCCAAAAATTACGATTTTGACCCCAAATT
* * * * * * *
3166 TTCCATAAGT-CACATTTCGACCTC-AAATATTCCAAAAGTT-CGATTTTAATCCCAAATT
1 TTCCAAAATTAC-CATTT-GCCCTCTAAACA-TCCAAAAATTACGATTTTGACCCCAAATT
3224 TTCCAACAATT
1 TTCCAA-AATT
3235 TTGATTTTGA
Statistics
Matches: 146, Mismatches: 29, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
56 4 0.03
57 51 0.35
58 57 0.39
59 34 0.23
ACGTcount: A:0.36, C:0.27, G:0.05, T:0.32
Consensus pattern (58 bp):
TTCCAAAATTACCATTTGCCCTCTAAACATCCAAAAATTACGATTTTGACCCCAAATT
Found at i:3161 original size:28 final size:29
Alignment explanation
Indices: 2929--3163 Score: 207
Period size: 29 Copynumber: 8.1 Consensus size: 29
2919 TTTGATCCCG
2929 AACATCCAAAAATTACCATTTTGA-CCTCA
1 AACATCCAAAAATTACCATTTTGACCCT-A
* * *
2958 AACTTTTCC-AAAATTA-CATTTTTACCCTCG
1 AAC--ATCCAAAAATTACCATTTTGACCCT-A
* *
2988 AACATTCCAAAAATTACCATTTTCACTCTA
1 AACA-TCCAAAAATTACCATTTTGACCCTA
*
3018 AACATCCAAAAATTACCATTTTGA-CCTCG
1 AACATCCAAAAATTACCATTTTGACCCT-A
*
3047 AACATCCAAAAATTCCCA-TTTG-CCCTCA
1 AACATCCAAAAATTACCATTTTGACCCT-A
** *
3075 AACATCCAAAAATTATGATTTTGACCCCA
1 AACATCCAAAAATTACCATTTTGACCCTA
* *
3104 AACTTTTCC-AAAATTACCATTTTGCCCCTA
1 AAC--ATCCAAAAATTACCATTTTGACCCTA
* *
3134 AGCATCCAAAAATTACTATTTTG-CCCTA
1 AACATCCAAAAATTACCATTTTGACCCTA
3162 AA
1 AA
3164 ATTTCCATAA
Statistics
Matches: 168, Mismatches: 25, Indels: 27
0.76 0.11 0.12
Matches are distributed among these distances:
28 34 0.20
29 71 0.42
30 47 0.28
31 16 0.10
ACGTcount: A:0.37, C:0.28, G:0.04, T:0.31
Consensus pattern (29 bp):
AACATCCAAAAATTACCATTTTGACCCTA
Found at i:3190 original size:116 final size:115
Alignment explanation
Indices: 2929--3234 Score: 264
Period size: 116 Copynumber: 2.6 Consensus size: 115
2919 TTTGATCCCG
* * * * *
2929 AACATCCAAAAA-TTACCATTTTGACCTCAAACTTTTCC-AAAATTAC-ATTTTTACCCTCGAAC
1 AACATCCAAAAAGTCA-CA-TTTGACCTCAAAC-ATTCCAAAAATT-CGATTTTAACCC-CAAAT
* * **
2991 ATTCCAAAAATTACCATTTTCACTCTAAACATCCAAAAATTACCATTTTGACCTCG
61 TTTCC-AAAATTACCATTTTCACCCTAAACATCCAAAAATTACCATTTTGACCTAA
* * * * *
3047 AACATCCAAAAATTCCCATTTGCCCTCAAACA-TCCAAAAATTATGATTTTGACCCCAAACTTTT
1 AACATCCAAAAAGTCACATTTGACCTCAAACATTCCAAAAATT-CGATTTTAACCCCAAA-TTTT
* * *
3111 CCAAAATTACCATTTTGC-CCCTAAGCATCCAAAAATTACTATTTTGCCCTAA
64 CCAAAATTACCATTTT-CACCCTAAACATCCAAAAATTACCATTTTGACCTAA
** * * * *
3163 AATTTCC-ATAAGTCACATTTCGACCTCAAATATTCCAAAAGTTCGATTTTAATCCCAAATTTTC
1 AACATCCAAAAAGTCACATTT-GACCTCAAACATTCCAAAAATTCGATTTTAACCCCAAATTTTC
3227 CAACAATT
65 CAA-AATT
3235 TTGATTTTGA
Statistics
Matches: 154, Mismatches: 26, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
115 21 0.14
116 83 0.54
117 35 0.23
118 14 0.09
119 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.05, T:0.32
Consensus pattern (115 bp):
AACATCCAAAAAGTCACATTTGACCTCAAACATTCCAAAAATTCGATTTTAACCCCAAATTTTCC
AAAATTACCATTTTCACCCTAAACATCCAAAAATTACCATTTTGACCTAA
Found at i:3248 original size:30 final size:30
Alignment explanation
Indices: 3189--3254 Score: 80
Period size: 30 Copynumber: 2.2 Consensus size: 30
3179 ATTTCGACCT
*
3189 CAAATATTCCAAAAGTTCGATTTTAAT-CC
1 CAAATTTTCCAAAAGTTCGATTTTAATCCC
* * *
3218 CAAATTTTCCAACAATTTTGATTTTGATCCC
1 CAAATTTTCCAA-AAGTTCGATTTTAATCCC
3249 CAAATT
1 CAAATT
3255 CCTCGAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 11 0.35
30 12 0.39
31 8 0.26
ACGTcount: A:0.35, C:0.21, G:0.06, T:0.38
Consensus pattern (30 bp):
CAAATTTTCCAAAAGTTCGATTTTAATCCC
Found at i:6008 original size:6 final size:6
Alignment explanation
Indices: 5992--6025 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
5982 ATATTGTGAT
*
5992 TTATA- TTATAC TTATAC TTATAA TTATAC TTATA
1 TTATAC TTATAC TTATAC TTATAC TTATAC TTATA
6026 AAGTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (6 bp):
TTATAC
Found at i:6019 original size:18 final size:17
Alignment explanation
Indices: 5992--6025 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
5982 ATATTGTGAT
5992 TTATATTATACTTATAC
1 TTATATTATACTTATAC
6009 TTATAATTATACTTATA
1 TTAT-ATTATACTTATA
6026 AAGTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATATTATACTTATAC
Found at i:7439 original size:27 final size:28
Alignment explanation
Indices: 7369--7469 Score: 132
Period size: 27 Copynumber: 3.5 Consensus size: 28
7359 TTGAATAAAT
*
7369 AAAAATAAAATAAAAAGGATTAAAATTTTTA
1 AAAAATAAAAT-AAAAGGATT-AAA-TTTAA
*
7400 AAAAATAAGATAAAAGGATTAAA-TTAA
1 AAAAATAAAATAAAAGGATTAAATTTAA
7427 AAAAATAAAATAAAAGGATTAAATTTTAA
1 AAAAATAAAATAAAAGGATTAAA-TTTAA
*
7456 AAAAATAGAATAAA
1 AAAAATAAAATAAA
7470 GCGGCCAATA
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
27 25 0.39
29 20 0.31
30 9 0.14
31 10 0.16
ACGTcount: A:0.67, C:0.00, G:0.08, T:0.25
Consensus pattern (28 bp):
AAAAATAAAATAAAAGGATTAAATTTAA
Found at i:7487 original size:56 final size:58
Alignment explanation
Indices: 7367--7493 Score: 147
Period size: 56 Copynumber: 2.2 Consensus size: 58
7357 TATTGAATAA
* **
7367 ATAAAAATAAAATAAAAAGGATTAAAATTTTTAAAAAATAAGATAAAAGGATTAAATT
1 ATAAAAATAAAATAAAAAGGATTAAAATTTTAAAAAAATAAGATAAAAGGACCAAATT
* *
7425 AAAAAAATAAAAT-AAAAGGATT-AAATTTTAAAAAAAT-AGA-ATAAAGCGGCCAATATT
1 ATAAAAATAAAATAAAAAGGATTAAAATTTTAAAAAAATAAGATA-AAAG-GACCAA-ATT
7482 -TAAAAATAAAAT
1 ATAAAAATAAAAT
7494 GATGAAGGGA
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
54 1 0.02
55 7 0.12
56 28 0.47
57 12 0.20
58 12 0.20
ACGTcount: A:0.64, C:0.02, G:0.09, T:0.25
Consensus pattern (58 bp):
ATAAAAATAAAATAAAAAGGATTAAAATTTTAAAAAAATAAGATAAAAGGACCAAATT
Found at i:9692 original size:49 final size:49
Alignment explanation
Indices: 9219--9698 Score: 468
Period size: 49 Copynumber: 9.8 Consensus size: 49
9209 TACCTTTCTT
* * *** ** **
9219 CATCTTTAGGGTATAAGATTCACTTTTGCAACTTCAATC-GACCCTTCTT
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCC-TCCA
* ** **
9268 CATCTTTAGGGTATAAGATTCGCCTTTGCGGCTTCAATCTGCCCCTCTT
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
* * * ** * * * *
9317 TATCTTTAGAGTATAAGACTCGCCTTTGCAGCTCCAATC-TGCGTCTCCT
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTC-CCTCCA
* * * **
9366 CATCTTCAGGGTATAAGATTCGCCTTTGTGGCTTTAAT-TTTTCCTTTA
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
* * * *
9414 CATCTCTAGGGTATAAGATTCGCCGTAGCGG-TATCAATCTTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCT-TCAATCTTTCCCTCCA
* * *
9463 CATCTTTAGGATATAAGATTCGCCTTTGCGACTTCAATCTTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
* * *
9512 CATCTTTAGGGTATAAGATTCGTCGTTGTGACTTCAATCTTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
* * *
9561 CATCTTTAGGGTATAAGATTTGCCTTTGTAGCTTTAATCTTTCCCTCCA
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
* * * *
9610 TATCTCTAGGGTATAAGATTCGCCTTTGCGGCTTCAATCTTTCCCTCTA
1 CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
9659 CAT-TTCTAGGGTATAAGATTCG-CTATTGTGGCTTCAATCT
1 CATCTT-TAGGGTATAAGATTCGCCT-TTGTGGCTTCAATCT
9699 ACATAAAAAA
Statistics
Matches: 361, Mismatches: 62, Indels: 16
0.82 0.14 0.04
Matches are distributed among these distances:
47 1 0.00
48 36 0.10
49 319 0.88
50 5 0.01
ACGTcount: A:0.21, C:0.25, G:0.16, T:0.38
Consensus pattern (49 bp):
CATCTTTAGGGTATAAGATTCGCCTTTGTGGCTTCAATCTTTCCCTCCA
Found at i:13927 original size:12 final size:12
Alignment explanation
Indices: 13910--13950 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
13900 TGTAGAAGGC
13910 ATAAAATAAAAG
1 ATAAAATAAAAG
*
13922 ATAAAATAAAAT
1 ATAAAATAAAAG
13934 AGT-AAATAAAAG
1 A-TAAAATAAAAG
13946 A-AAAA
1 ATAAAA
13951 GCTTGAGTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 3 0.12
12 21 0.84
13 1 0.04
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (12 bp):
ATAAAATAAAAG
Found at i:22099 original size:23 final size:22
Alignment explanation
Indices: 22050--22119 Score: 61
Period size: 23 Copynumber: 2.9 Consensus size: 22
22040 ATATACTTTC
22050 TTACTCATGGTTTTCCTCTTTTGTTT
1 TTACTCAT--TTTT-CT-TTTTGTTT
22076 TTACTCATTTTTCTTTTTGATTT
1 TTACTCATTTTTCTTTTTG-TTT
22099 TTCAC-CATTTCTCTCTTTTTG
1 TT-ACTCATTT-T-TCTTTTTG
22120 GCTAAAGTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
22 5 0.12
23 12 0.30
24 7 0.17
25 8 0.20
26 8 0.20
ACGTcount: A:0.10, C:0.20, G:0.07, T:0.63
Consensus pattern (22 bp):
TTACTCATTTTTCTTTTTGTTT
Found at i:24751 original size:25 final size:24
Alignment explanation
Indices: 24694--24752 Score: 59
Period size: 23 Copynumber: 2.4 Consensus size: 24
24684 AAACTTGATT
* *
24694 AAAATTAATAAAATAAACGAATAAT
1 AAAATTAA-ATAATAAACGAATAAA
24719 AAAA-TAAATAATAAA-GAACTAACA
1 AAAATTAAATAATAAACGAA-TAA-A
24743 AAAATTAAAT
1 AAAATTAAAT
24753 TAGGGAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 3 0.10
23 10 0.34
24 7 0.24
25 9 0.31
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.22
Consensus pattern (24 bp):
AAAATTAAATAATAAACGAATAAA
Found at i:29110 original size:22 final size:22
Alignment explanation
Indices: 29063--29127 Score: 69
Period size: 22 Copynumber: 3.0 Consensus size: 22
29053 CTTTGTTTAT
* *
29063 TAGCACGTTTAGTGC-TTCCGTT
1 TAGCACGTTT-GTGCTTTCTGTC
29085 TAGCACGTTTGTGCTTTCTGTC
1 TAGCACGTTTGTGCTTTCTGTC
* * *
29107 TAGCACCTTTGTTCTCTCTGT
1 TAGCACGTTTGTGCTTTCTGT
29128 TCATTAGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 4 0.11
22 33 0.89
ACGTcount: A:0.11, C:0.25, G:0.20, T:0.45
Consensus pattern (22 bp):
TAGCACGTTTGTGCTTTCTGTC
Found at i:31500 original size:18 final size:18
Alignment explanation
Indices: 31479--31513 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
31469 GAGAGGAAGA
*
31479 GAAGAAAAGAAAAGAAAG
1 GAAGAAAAAAAAAGAAAG
31497 GAAGAAAAAAAAAGAAA
1 GAAGAAAAAAAAAGAAA
31514 AAAAAATGTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (18 bp):
GAAGAAAAAAAAAGAAAG
Found at i:31563 original size:16 final size:16
Alignment explanation
Indices: 31544--31596 Score: 53
Period size: 14 Copynumber: 3.6 Consensus size: 16
31534 TTTATTTTTT
31544 TATATTTAAAATATTA
1 TATATTTAAAATATTA
*
31560 TATATTT--ATTATTA
1 TATATTTAAAATATTA
*
31574 TAT-TTTGAAATA--A
1 TATATTTAAAATATTA
31587 TATATTTAAA
1 TATATTTAAA
31597 GGGATTAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
13 7 0.23
14 14 0.45
15 3 0.10
16 7 0.23
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (16 bp):
TATATTTAAAATATTA
Found at i:31590 original size:29 final size:26
Alignment explanation
Indices: 31536--31591 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 26
31526 TTTATGTTTT
*
31536 TATTTTTTTATATTTAAAATATTATA
1 TATTTTTTTATATTTAAAATAATATA
*
31562 TATTTATTATTATATTTTGAAATAATATA
1 TATTT-TT-TTATA-TTTAAAATAATATA
31591 T
1 T
31592 TTAAAGGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.20
27 2 0.08
28 5 0.20
29 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (26 bp):
TATTTTTTTATATTTAAAATAATATA
Found at i:32764 original size:20 final size:19
Alignment explanation
Indices: 32716--32772 Score: 62
Period size: 18 Copynumber: 2.9 Consensus size: 19
32706 AAATTTTAGA
* *
32716 AATTTTATAAA-TATTTTG
1 AATTTTAAAAATTATTTTC
32734 AATTTTAAAAATTATTTTC
1 AATTTTAAAAATTATTTTC
*
32753 AATTTTTGAAAATTAATTTT
1 AA-TTTTAAAAATT-ATTTT
32773 TTTTTGTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 10 0.30
19 8 0.24
20 10 0.30
21 5 0.15
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (19 bp):
AATTTTAAAAATTATTTTC
Found at i:32952 original size:9 final size:9
Alignment explanation
Indices: 32938--32972 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
32928 TCAAGTTGAC
32938 TCGAATAAT
1 TCGAATAAT
**
32947 TCGAATACC
1 TCGAATAAT
32956 TCGAATAAT
1 TCGAATAAT
32965 TCGAATAA
1 TCGAATAA
32973 CTCAATTCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (9 bp):
TCGAATAAT
Found at i:32960 original size:18 final size:18
Alignment explanation
Indices: 32937--32971 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
32927 TTCAAGTTGA
32937 CTCGAATAATTCGAATAC
1 CTCGAATAATTCGAATAC
32955 CTCGAATAATTCGAATA
1 CTCGAATAATTCGAATA
32972 ACTCAATTCG
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:0.40, C:0.20, G:0.11, T:0.29
Consensus pattern (18 bp):
CTCGAATAATTCGAATAC
Found at i:40667 original size:91 final size:90
Alignment explanation
Indices: 40512--40690 Score: 281
Period size: 91 Copynumber: 2.0 Consensus size: 90
40502 ACATCTTTTA
*
40512 TCAATTTGGTTCTTATTGTTTTTAGTTAAGTTTCATCATTTACCTTTTAGAAAGAGTTAATTTTT
1 TCAATTTGATTCTTATTGTTTTTAGTTAAGTTTCATCATTTACCTTTTAGAAAGAGTTAA-TTTT
40577 TTTCTAAATAGAAA-TGCTGATTAATT
65 TTTCTAAATA-AAACTGCTGATTAATT
* *
40603 TCAATTTGATTCTTATTTTTTTTAGTTAAGTTTCATCATTTA-CTTTTTGAAAAGAGTTAATTTT
1 TCAATTTGATTCTTATTGTTTTTAGTTAAGTTTCATCATTTACCTTTTAG-AAAGAGTTAATTTT
*
40667 TTTCTATATAAAACTGCTGATTAA
65 TTTCTAAATAAAACTGCTGATTAA
40691 AACATTATTA
Statistics
Matches: 82, Mismatches: 4, Indels: 5
0.90 0.04 0.05
Matches are distributed among these distances:
89 3 0.04
90 29 0.35
91 50 0.61
ACGTcount: A:0.29, C:0.09, G:0.11, T:0.51
Consensus pattern (90 bp):
TCAATTTGATTCTTATTGTTTTTAGTTAAGTTTCATCATTTACCTTTTAGAAAGAGTTAATTTTT
TTCTAAATAAAACTGCTGATTAATT
Found at i:41026 original size:2 final size:2
Alignment explanation
Indices: 41019--41044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
41009 TTTATTTATG
41019 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
41045 GGTGCACCCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41742 original size:36 final size:31
Alignment explanation
Indices: 41668--41735 Score: 136
Period size: 31 Copynumber: 2.2 Consensus size: 31
41658 GGCTTAATTA
41668 TATTTTTTAAATTATGGGTTTAATTTTATTT
1 TATTTTTTAAATTATGGGTTTAATTTTATTT
41699 TATTTTTTAAATTATGGGTTTAATTTTATTT
1 TATTTTTTAAATTATGGGTTTAATTTTATTT
41730 TATTTT
1 TATTTT
41736 ATTTTTTTAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.25, C:0.00, G:0.09, T:0.66
Consensus pattern (31 bp):
TATTTTTTAAATTATGGGTTTAATTTTATTT
Found at i:41792 original size:31 final size:30
Alignment explanation
Indices: 41746--41871 Score: 100
Period size: 31 Copynumber: 4.1 Consensus size: 30
41736 ATTTTTTTAC
41746 TTTT-AGAGGGCTTAATAAGAA-TTTCTAAAAA
1 TTTTAAGA-GGCTTAATAA-AATTTTC-AAAAA
41777 TTTTGAA-AGGCTTAATTAAAATTTTCAAAAA
1 TTTT-AAGAGGCTTAA-TAAAATTTTCAAAAA
* *
41808 TTTTAAGAGGCTTAATGATAATTTAC-AAAA
1 TTTTAAGAGGCTTAAT-AAAATTTTCAAAAA
* * *
41838 TTTTCAG-GGCCTAATTAAAATCTTCATAAAA
1 TTTTAAGAGGCTTAA-TAAAATTTTCA-AAAA
41869 TTT
1 TTT
41872 AAAGGACATT
Statistics
Matches: 79, Mismatches: 7, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
29 12 0.15
30 14 0.18
31 44 0.56
32 8 0.10
33 1 0.01
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (30 bp):
TTTTAAGAGGCTTAATAAAATTTTCAAAAA
Found at i:41820 original size:62 final size:61
Alignment explanation
Indices: 41746--41871 Score: 141
Period size: 62 Copynumber: 2.0 Consensus size: 61
41736 ATTTTTTTAC
* *
41746 TTTTAGAGGGCTTAATAAGAATTT-CTAAAAATTTTGAAAGGCTTAATTAAAATTTTCA-AAAA
1 TTTTAGAGGGCTTAATAAGAATTTAC--AAAATTTT-AAAGGCCTAATTAAAATCTTCATAAAA
* * * *
41808 TTTTA-AGAGGCTTAATGATAATTTACAAAATTTTCAGGGCCTAATTAAAATCTTCATAAAA
1 TTTTAGAG-GGCTTAATAAGAATTTACAAAATTTTAAAGGCCTAATTAAAATCTTCATAAAA
41869 TTT
1 TTT
41872 AAAGGACATT
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
60 18 0.33
61 17 0.31
62 19 0.35
63 1 0.02
ACGTcount: A:0.41, C:0.09, G:0.12, T:0.38
Consensus pattern (61 bp):
TTTTAGAGGGCTTAATAAGAATTTACAAAATTTTAAAGGCCTAATTAAAATCTTCATAAAA
Found at i:45852 original size:21 final size:21
Alignment explanation
Indices: 45809--45855 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
45799 CTTATGACAG
* * *
45809 TTCTACCGATACAAGTGAAGC
1 TTCTACCGAAACAAATCAAGC
*
45830 TTCTACCGAAACAAATCATGC
1 TTCTACCGAAACAAATCAAGC
45851 TTCTA
1 TTCTA
45856 TTGGTACTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (21 bp):
TTCTACCGAAACAAATCAAGC
Found at i:56773 original size:19 final size:19
Alignment explanation
Indices: 56749--56787 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
56739 TTCATTCACA
56749 CTTAATTTATGCAAATAAT
1 CTTAATTTATGCAAATAAT
56768 CTTAATTTATGCAAATAAT
1 CTTAATTTATGCAAATAAT
56787 C
1 C
56788 ATCCTTGAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.41, C:0.13, G:0.05, T:0.41
Consensus pattern (19 bp):
CTTAATTTATGCAAATAAT
Found at i:58031 original size:43 final size:43
Alignment explanation
Indices: 57970--58052 Score: 166
Period size: 43 Copynumber: 1.9 Consensus size: 43
57960 CTCGGAAGAC
57970 TGAATTATATTGCTCGATTTATCTCACAGTTAACTGAGAATAT
1 TGAATTATATTGCTCGATTTATCTCACAGTTAACTGAGAATAT
58013 TGAATTATATTGCTCGATTTATCTCACAGTTAACTGAGAA
1 TGAATTATATTGCTCGATTTATCTCACAGTTAACTGAGAA
58053 ATGTGATCCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 40 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.39
Consensus pattern (43 bp):
TGAATTATATTGCTCGATTTATCTCACAGTTAACTGAGAATAT
Found at i:61232 original size:49 final size:49
Alignment explanation
Indices: 61097--61955 Score: 513
Period size: 49 Copynumber: 17.5 Consensus size: 49
61087 CAGGTTTCAT
* * * * * *
61097 TACCATGAAGACATGAAGGGAAAGATTTAAG-CTGCGATGGTGAATCCAA
1 TACCATGAAGATATGAAGGGAAAGATTTAAGTC-GCAACGGCGAATCTAG
* * *
61146 TACCACGACA-ATAATGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAG
1 TACCATGA-AGAT-ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * * *
61196 TACCATGAAGATTTGAAGGGAAGGGTTTAAGTCGCAACGACAAACCTTG
1 TACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * *
61245 TACC-TCGGAAGA-ATAAAGGGAAAGATTTAAGCCGCAATGGCGAATCCAG
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * * *
61294 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAGTGAACCTTG
1 TACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * *
61343 TACC-TCGGAAGA-ATTAAGGGAAAGATTTAAGCCGCGATGGCGAATCCAG
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * * *
61392 TACCACGAAAATAATGAAGGGAAGGGTTTAAGTCGCAACGACGAACCTTG
1 TACCATGAAGAT-ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * *
61442 TACC-TCGGAAGA-ATAAAGGAAAAGATTTAAG-CTACAACGGCAAATAC-AG
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTC-GCAACGGCGAAT-CTAG
** * * *
61491 TACCACAAATATATGGAA-GGAAAGGTTTAAGTCGCAACGGCGAA-CTTG
1 TACCATGAAGATAT-GAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * *
61539 TACC-TCAGAAGA-ATGAAGGGAAAAATTTAAG-CTGCGATGGCGAATCCAG
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTC-GCAACGGCGAATCTAG
* ** * * * * *
61588 TACCATGAAAATAATGAAATGAAAGATTTAAGCCACAATGGTGAATCCAG
1 TACCATGAAGAT-ATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * * * *
61638 TACTAGGAAGATTTGAAGGGAAGGGTTTAAGTCGCAACGACGAACCTTG
1 TACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * *
61687 TACC-TCAGAAGA-ATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAA
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* * * * * * *
61736 TACCACGAAGATATGGAGGGAAAGGTTTAAGTCGAAACGACGAACCTTG
1 TACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
*
61785 TACC-TCGGAAGA-ATGAAGGGAAAGATTTAAG-CTGCAACGGTGAATCTAG
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTC-GCAACGGCGAATCTAG
* * * * * *
61834 TACCACGAAGATATGGAGGGAAATG-TTTAAGTCGTAATGGCGAACCTTG
1 TACCATGAAGATATGAAGGGAAA-GATTTAAGTCGCAACGGCGAATCTAG
* * *
61883 TACC-TCAGAAG-CATGAAGGGAAAGATTTAAGCCACAACGGCGAATCTAG
1 TACCAT--GAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
* *
61932 TACCACGAAGATATGGAGGGAAAG
1 TACCATGAAGATATGAAGGGAAAG
61956 GTTACGACCG
Statistics
Matches: 597, Mismatches: 166, Indels: 94
0.70 0.19 0.11
Matches are distributed among these distances:
47 5 0.01
48 61 0.10
49 386 0.65
50 139 0.23
51 6 0.01
ACGTcount: A:0.38, C:0.17, G:0.26, T:0.19
Consensus pattern (49 bp):
TACCATGAAGATATGAAGGGAAAGATTTAAGTCGCAACGGCGAATCTAG
Found at i:61297 original size:98 final size:99
Alignment explanation
Indices: 61162--61619 Score: 570
Period size: 98 Copynumber: 4.7 Consensus size: 99
61152 GACAATAATG
* * * * * *
61162 AAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTACCATGAAGAT-TTGAAGGGAAGGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATAATGAAGGGAAAGGTTTAA
*
61226 GTCGCAACGACAAACCTTGTACCTCGGAAGAATA
66 GTCGCAACGACGAACCTTGTACCTCGGAAGAATA
*
61260 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGAT-ATGGAGGGAAAGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATAATGAAGGGAAAGGTTTAA
* *
61324 GTCGCAAC-AGTGAACCTTGTACCTCGGAAGAATT
66 GTCGCAACGA-CGAACCTTGTACCTCGGAAGAATA
* * *
61358 AAGGGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCACGAAAATAATGAAGGGAAGGGTTTAA
1 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATAATGAAGGGAAAGGTTTAA
61423 GTCGCAACGACGAACCTTGTACCTCGGAAGAATA
66 GTCGCAACGACGAACCTTGTACCTCGGAAGAATA
* ** * * *
61457 AAGGAAAAGATTTAAGCTACAACGGCAAATACAGTACCAC-AA-ATATATGGAA-GGAAAGGTTT
1 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATA-AT-GAAGGGAAAGGTTT
* * *
61519 AAGTCGCAACGGCGAA-CTTGTACCTCAGAAGAATG
64 AAGTCGCAACGACGAACCTTGTACCTCGGAAGAATA
* * * * * ** *
61554 AAGGGAAAAATTTAAGCTGCGATGGCGAATCCAGTACCATGAAAATAATGAAATGAAAGATTTAA
1 AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATAATGAAGGGAAAGGTTTAA
61619 G
66 G
61620 CCACAATGGT
Statistics
Matches: 315, Mismatches: 37, Indels: 16
0.86 0.10 0.04
Matches are distributed among these distances:
97 56 0.18
98 173 0.55
99 85 0.27
100 1 0.00
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.19
Consensus pattern (99 bp):
AAGGGAAAGATTTAAGCCGCAATGGCGAATCCAGTACCACGAAGATAATGAAGGGAAAGGTTTAA
GTCGCAACGACGAACCTTGTACCTCGGAAGAATA
Found at i:61448 original size:197 final size:196
Alignment explanation
Indices: 61158--61605 Score: 673
Period size: 197 Copynumber: 2.3 Consensus size: 196
61148 CCACGACAAT
* * * * * *
61158 AATGAAGGAAAAGATTTAAGCCGCAACGGCGAATCTAGTACCATGAAGAT-TTGAAGGGAAGGGT
1 AATGAAGGGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCATGAAAATAATGAAGGGAAGGGT
* * * *
61222 TTAAGTCGCAACGACAAACCTTGTACCTCGGAAGAATAAAGGGAAAGATTTAAGCCGCAATGGCG
66 TTAAGTCGCAACGACAAACCTTGTACCTCGGAAGAATAAAGGAAAAGATTTAAGCCACAACGGCA
* * * * *
61287 AATCCAGTACCACGAAGATATGGAGGGAAAGGTTTAAGTCGCAACAGTGAACCTTGTACCTCGGA
131 AATACAGTACCACAAAGATATGGAAGGAAAGGTTTAAGTCGCAACAGCGAA-CTTGTACCTCAGA
61352 AG
195 AG
* *
61354 AATTAAGGGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCACGAAAATAATGAAGGGAAGGGT
1 AATGAAGGGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCATGAAAATAATGAAGGGAAGGGT
* *
61419 TTAAGTCGCAACGACGAACCTTGTACCTCGGAAGAATAAAGGAAAAGATTTAAGCTACAACGGCA
66 TTAAGTCGCAACGACAAACCTTGTACCTCGGAAGAATAAAGGAAAAGATTTAAGCCACAACGGCA
* *
61484 AATACAGTACCACAAATATATGGAAGGAAAGGTTTAAGTCGCAACGGCGAACTTGTACCTCAGAA
131 AATACAGTACCACAAAGATATGGAAGGAAAGGTTTAAGTCGCAACAGCGAACTTGTACCTCAGAA
61549 G
196 G
* *
61550 AATGAAGGGAAAAATTTAAGCTGCGATGGCGAATCCAGTACCATGAAAATAATGAA
1 AATGAAGGGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCATGAAAATAATGAA
61606 ATGAAAGATT
Statistics
Matches: 226, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
196 109 0.48
197 117 0.52
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (196 bp):
AATGAAGGGAAAGATTTAAGCCGCGATGGCGAATCCAGTACCATGAAAATAATGAAGGGAAGGGT
TTAAGTCGCAACGACAAACCTTGTACCTCGGAAGAATAAAGGAAAAGATTTAAGCCACAACGGCA
AATACAGTACCACAAAGATATGGAAGGAAAGGTTTAAGTCGCAACAGCGAACTTGTACCTCAGAA
G
Found at i:62024 original size:196 final size:195
Alignment explanation
Indices: 61627--62012 Score: 452
Period size: 196 Copynumber: 2.0 Consensus size: 195
61617 AAGCCACAAT
* * * *
61627 GGTGAATCCAGTACTAGGAAGATTTGAAGGGAAGGGTTTAAGTCGCAACGACGAACCTTGTACCT
1 GGTGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCT
*
61692 CAGAAGAATGAAGGGAAAGATTTAAGCCGCAACAGCGAATCCAATACCACGAAGATATGGAGGGA
66 CAGAAGAATGAAGGGAAAGATTTAAGCCACAACAGCGAATCCAATACCACGAAGATATGGAGGGA
* ** * * * ** *
61757 AAGGTTTAAGTCGAAACGACGAACCTTGTACCTCGGAAGAATGAAGGGAAAGATTTAAGCTGCAA
131 AAGGTTTAAGCCGAAACGACGAACCCAGTACCTCAGAAGAAAGAAGAGAAAGATCGAACCTG-AA
61822 C
195 C
* * * * * *
61823 GGTGAATCTAGTACCACGAAGATATGGAGGGAAATGTTTAAGTCGTAATGGCGAACCTTGTACCT
1 GGTGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCT
* * * *
61888 CAGAAGCATGAAGGGAAAGATTTAAGCCACAACGGCGAATCTAGTACCACGAAGATATGGAGGGA
66 CAGAAGAATGAAGGGAAAGATTTAAGCCACAACAGCGAATCCAATACCACGAAGATATGGAGGGA
* * * * * * *
61953 AAGG-TTACGACCGTAACGGCGATCCCAGTACCTTATAA-ACAAGACGAGAAAGATCGAACC
131 AAGGTTTAAG-CCGAAACGACGAACCCAGTACCTCAGAAGA-AAGAAGAGAAAGATCGAACC
62013 CATGACGGTG
Statistics
Matches: 157, Mismatches: 31, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
195 5 0.03
196 152 0.97
ACGTcount: A:0.37, C:0.18, G:0.27, T:0.18
Consensus pattern (195 bp):
GGTGAATCCAGTACCACGAAGATATGAAGGGAAAGGTTTAAGTCGCAACGACGAACCTTGTACCT
CAGAAGAATGAAGGGAAAGATTTAAGCCACAACAGCGAATCCAATACCACGAAGATATGGAGGGA
AAGGTTTAAGCCGAAACGACGAACCCAGTACCTCAGAAGAAAGAAGAGAAAGATCGAACCTGAAC
Found at i:72908 original size:19 final size:19
Alignment explanation
Indices: 72860--72899 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
72850 GGGTTCCTCA
72860 GAAAAAGTCAACAATCAAC
1 GAAAAAGTCAACAATCAAC
*
72879 GAAAAAGTCAACGATCAAC
1 GAAAAAGTCAACAATCAAC
72898 GA
1 GA
72900 TCAAGTCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.55, C:0.20, G:0.15, T:0.10
Consensus pattern (19 bp):
GAAAAAGTCAACAATCAAC
Found at i:75549 original size:2 final size:2
Alignment explanation
Indices: 75542--75571 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
75532 TACTAAAATA
75542 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.