Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold933
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: 7450
ACGTcount: A:0.31, C:0.15, G:0.23, T:0.31
Found at i:1905 original size:61 final size:61
Alignment explanation
Indices: 1806--1938 Score: 158
Period size: 61 Copynumber: 2.2 Consensus size: 61
1796 GTGACGTTAG
* * * * *
1806 AGATGAGAGGAATGATACAGGTACCAATATGCTAATTCACGACCAGCGATATTGAGCTTAA
1 AGATGAGAAGAATGATAAAGGTACCAATATACTAATTCAAGACCAGCAATATTGAGCTTAA
* * * * *
1867 AGATGAGAAGAATGATAAAGGTGCCAATATATTGATTCAAGGCCAGCAATATTGGGCTTAA
1 AGATGAGAAGAATGATAAAGGTACCAATATACTAATTCAAGACCAGCAATATTGAGCTTAA
* *
1928 AAATGCGAAGA
1 AGATGAGAAGA
1939 CTGTTAATGT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.40, C:0.14, G:0.24, T:0.23
Consensus pattern (61 bp):
AGATGAGAAGAATGATAAAGGTACCAATATACTAATTCAAGACCAGCAATATTGAGCTTAA
Found at i:2237 original size:51 final size:51
Alignment explanation
Indices: 1874--2597 Score: 251
Period size: 52 Copynumber: 14.0 Consensus size: 51
1864 TAAAGATGAG
* * ** * * *
1874 AAGAATGATAAAGGTGCCAATATATTGATTCAAGGCCAGCAATATTGGGCTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
* * ** * * * * * *
1926 AAAAATGCG-AAGACTGTTAATGTGCTAATTTACGGCCAGCGACATTAGACTT
1 AAGAATGAGAAAGA-TGCCAATATGCTGATTCA-GGCTAGCGATATTGGACTT
* * * * *
1978 GAAG-ATGAG-AAGAGTGCCAATGTGTTGATTCAAGATCAGCGACATT-GAGCTT
1 -AAGAATGAGAAAGA-TGCCAATATGCTGATTCAGGCT-AGCGATATTGGA-CTT
* * ** * * * *
2030 AGGAAAGTTAAAGATGCCGATATGCTAATTCAAGGCTAGGGATATTGGGCTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
* * * * * * * *
2082 AA-AGATGCG-AAGAATTCCAATATGCTAATTCACAGCCAACGACATTAGACTT
1 AAGA-ATGAGAAAG-ATGCCAATATGCTGATTCA-GGCTAGCGATATTGGACTT
* * * * * * * * *
2134 GAAG-GTGAGAAGGCA--CCAATGTGCTTATTCAAGATCAGCGACATCGGCCTT
1 -AAGAATGAGAAAG-ATGCCAATATGCTGATTCAGGCT-AGCGATATTGGACTT
** *
2185 AAGAATGTTAAAGATGCCAATATACTGATTCAGGCTAGCGATATT-GAGCTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTCAGGCTAGCGATATTGGA-CTT
* * * * *
2236 AA-AGATGCG-AAGAATGCCAATGTGCTGATTCACGACCAGC-ATATTAGACTT
1 AAGA-ATGAGAAAG-ATGCCAATATGCTGATTCA-GGCTAGCGATATTGGACTT
* * * * * * *
2287 GAAG-ATGAGAAAAACGCCAATGTGCTGATTCATGATCAGCGACATTGGGCTT
1 -AAGAATGAGAAAGATGCCAATATGCTGATTCAGGCT-AGCGATATTGGACTT
* ** * *
2339 AGGAATGTTAAAGATGGCAATATGCTGATTCAAGGATAGC--TATTGGACTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
* * * * *
2389 AAGGATGAGAAAGGTGCTAATATACTAATTCAAGGCTAGCGATATTGGACTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
* * * * * * * *
2441 AAGAA-GAAAAAGGTGCCAATTTGCTGATTCAAGACCAGTGACATTAGACTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
* * * * * *
2492 AA-AGATAACAAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTAGACTT
1 AAGA-ATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
* * * * * * *
2544 AAGAAAGAAAAAGGTGCCAATGTGTTGATTCAAGGCTAGCGACATTGGGCTT
1 AAGAATGAGAAAGATGCCAATATGCTGATTC-AGGCTAGCGATATTGGACTT
2596 AA
1 AA
2598 AGATGGTTTG
Statistics
Matches: 496, Mismatches: 140, Indels: 72
0.70 0.20 0.10
Matches are distributed among these distances:
50 50 0.10
51 150 0.30
52 276 0.56
53 20 0.04
ACGTcount: A:0.35, C:0.15, G:0.24, T:0.25
Consensus pattern (51 bp):
AAGAATGAGAAAGATGCCAATATGCTGATTCAGGCTAGCGATATTGGACTT
Found at i:2267 original size:154 final size:153
Alignment explanation
Indices: 1874--2537 Score: 606
Period size: 154 Copynumber: 4.3 Consensus size: 153
1864 TAAAGATGAG
* * * * * *
1874 AAGAATGATAAAGGTGCCAATATATTGATTCAAGGCCAGCAATATTGGGCTTAAAAATGCGAAGA
1 AAGAATGTTAAAGATGCCAATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGCGAAGA
* ** * *
1939 CTGTTAATGTGCTAATTTACGGCCAGCGACATTAGACTTGAAGATGAGAAGAGTGCCAATGTG-T
66 ATGCCAATGTGCTAATTCAC-GCCAGCGACATTAGACTTGAAGATGAGAAG-GCGCCAATGTGCT
2003 TGATTCAAGATCAGCGACATTGAGCTT
129 T-ATTCAAGATCAGCGACATTG-GCTT
* * * * * *
2030 AGGAAAGTTAAAGATGCCGATATGCTAATTCAAGGCTAGGGATATTGGGCTTAAAGATGCGAAGA
1 AAGAATGTTAAAGATGCCAATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGCGAAGA
* * * * *
2095 ATTCCAATATGCTAATTCACAGCCAACGACATTAGACTTGAAGGTGAGAAGGCACCAATGTGCTT
66 ATGCCAATGTGCTAATTCAC-GCCAGCGACATTAGACTTGAAGATGAGAAGGCGCCAATGTGCTT
*
2160 ATTCAAGATCAGCGACATCGGCCTT
130 ATTCAAGATCAGCGACATTGG-CTT
*
2185 AAGAATGTTAAAGATGCCAATATACTGATTC-AGGCTAGCGATATTGAGCTTAAAGATGCGAAGA
1 AAGAATGTTAAAGATGCCAATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGCGAAGA
* * **
2249 ATGCCAATGTGCTGATTCACGACCAGC-ATATTAGACTTGAAGATGAGAAAAACGCCAATGTGCT
66 ATGCCAATGTGCTAATTCACG-CCAGCGACATTAGACTTGAAGATGAG-AAGGCGCCAATGTGCT
* *
2313 GATTCATGATCAGCGACATTGGGCTT
129 TATTCAAGATCAGCGACATT-GGCTT
* * * * * * *
2339 AGGAATGTTAAAGATGGCAATATGCTGATTCAAGGATAGC--TATTGGACTTAAGGATGAGAA-A
1 AAGAATGTTAAAGATGCCAATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGCGAAGA
* * * * * * * * * * * *
2401 GGTGCTAATATACTAATTCAAGGCTAGCGATATTGGACTT-AAGAAGAAAAAGGTGCCAATTTGC
66 -ATGCCAATGTGCTAATTC-ACGCCAGCGACATTAGACTTGAAGATG-AGAAGGCGCCAATGTGC
* * * *
2465 TGATTCAAGACCAGTGACATTAGACTT
128 TTATTCAAGATCAGCGACATT-GGCTT
*** * * * *
2492 AA-AGATAACAAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATT
1 AAGA-ATGTTAAAGATGCCAATATACTGATTCAAGGCTAGCGATATT
2538 AGACTTAAGA
Statistics
Matches: 416, Mismatches: 79, Indels: 27
0.80 0.15 0.05
Matches are distributed among these distances:
152 2 0.00
153 120 0.29
154 127 0.31
155 70 0.17
156 97 0.23
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (153 bp):
AAGAATGTTAAAGATGCCAATATACTGATTCAAGGCTAGCGATATTGGGCTTAAAGATGCGAAGA
ATGCCAATGTGCTAATTCACGCCAGCGACATTAGACTTGAAGATGAGAAGGCGCCAATGTGCTTA
TTCAAGATCAGCGACATTGGCTT
Found at i:2508 original size:103 final size:104
Alignment explanation
Indices: 2384--2601 Score: 285
Period size: 103 Copynumber: 2.1 Consensus size: 104
2374 ATAGCTATTG
* * * * * * *
2384 GACTTAAGGATGAGAAAGGTGCTAATATACTAATTCAAGGCTAGCGATATTGGACTTAAG-AAGA
1 GACTTAAAGATAACAAAGGTGCCAATATACTAATTCAAAGCCAGCGATATTAGACTTAAGAAAGA
* *
2448 AAAAGGTGCCAATTTGCTGATTCAAGACCAGTGACATTA
66 AAAAGGTGCCAATGTGCTGATTCAAGACCAGCGACATTA
* *
2487 GACTTAAAGATAACAAAGGTGCCAATATGCTGATTCAAAGCCAGCGATATTAGACTTAAGAAAGA
1 GACTTAAAGATAACAAAGGTGCCAATATACTAATTCAAAGCCAGCGATATTAGACTTAAGAAAGA
* * * *
2552 AAAAGGTGCCAATGTGTTGATTCAAGGCTAGCGACATTG
66 AAAAGGTGCCAATGTGCTGATTCAAGACCAGCGACATTA
*
2591 GGCTTAAAGAT
1 GACTTAAAGAT
2602 GGTTTGACAA
Statistics
Matches: 98, Mismatches: 16, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
103 51 0.52
104 47 0.48
ACGTcount: A:0.38, C:0.14, G:0.23, T:0.24
Consensus pattern (104 bp):
GACTTAAAGATAACAAAGGTGCCAATATACTAATTCAAAGCCAGCGATATTAGACTTAAGAAAGA
AAAAGGTGCCAATGTGCTGATTCAAGACCAGCGACATTA
Found at i:2721 original size:31 final size:32
Alignment explanation
Indices: 2657--2785 Score: 142
Period size: 31 Copynumber: 4.1 Consensus size: 32
2647 GCTTAGAAGA
* *
2657 TGCCACCGACTTGTGTGAGCTTTTGAA-AGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGA-GGT
*
2689 TGCCATCGACTT-TGTGGGCTTTAAGAA-AGGT
1 TGCCACCGACTTGTGTGGGCTTT-AGAAGAGGT
*
2720 TGCCA-CTAGCTTGTGTGGGCTTTAGAAGAGGT
1 TGCCACCGA-CTTGTGTGGGCTTTAGAAGAGGT
* *
2752 TGCCACCGACTT-AGTGGGATTTAGAAGAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGAGGT
2783 TGC
1 TGC
2786 AATCAACTTA
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
30 2 0.02
31 44 0.52
32 37 0.44
33 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.32, T:0.30
Consensus pattern (32 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGAGGT
Found at i:2742 original size:63 final size:63
Alignment explanation
Indices: 2666--2785 Score: 163
Period size: 63 Copynumber: 1.9 Consensus size: 63
2656 ATGCCACCGA
* * * *
2666 CTTGTGTGAGCTTTTGAA-AGGGTTGCCATCGACTTTGTGGGCTTTAAGAA-AGGTTGCCACTAG
1 CTTGTGTGAGCTTTAGAAGA-GGTTGCCACCGACTTAGTGGGATTT-AGAAGAGGTTGCCACTAG
*
2729 CTTGTGTGGGCTTTAGAAGAGGTTGCCACCGACTTAGTGGGATTTAGAAGAGGTTGC
1 CTTGTGTGAGCTTTAGAAGAGGTTGCCACCGACTTAGTGGGATTTAGAAGAGGTTGC
2786 AATCAACTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
62 4 0.08
63 45 0.90
64 1 0.02
ACGTcount: A:0.21, C:0.15, G:0.33, T:0.32
Consensus pattern (63 bp):
CTTGTGTGAGCTTTAGAAGAGGTTGCCACCGACTTAGTGGGATTTAGAAGAGGTTGCCACTAG
Found at i:2795 original size:31 final size:31
Alignment explanation
Indices: 2734--2795 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
2724 ACTAGCTTGT
* * *
2734 GTGGGCTTTAGAAGAGGTTGCCACCGACTTA
1 GTGGGATTTAGAAGAGGTTGCAACCAACTTA
*
2765 GTGGGATTTAGAAGAGGTTGCAATCAACTTA
1 GTGGGATTTAGAAGAGGTTGCAACCAACTTA
2796 TATGGCTTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (31 bp):
GTGGGATTTAGAAGAGGTTGCAACCAACTTA
Found at i:2810 original size:63 final size:63
Alignment explanation
Indices: 2678--2811 Score: 143
Period size: 63 Copynumber: 2.2 Consensus size: 63
2668 TGTGTGAGCT
* * * * * * *
2678 TTTGA-AAGGGTTGCCATCGACTTTGTGGGCTTTAAGAAAGGTTGCCACTAGCTTGTGTGGGC
1 TTTGAGAAGGGTTGCCACCGACTTAGTGGGATTTAAGAAAGGTTGCAACTAACTTATATGGGC
2740 TTT-AGAAGAGGTTGCCACCGACTTAGTGGGATTT-AGAAGAGGTTGCAA-TCAACTTATAT-GG
1 TTTGAGAAG-GGTTGCCACCGACTTAGTGGGATTTAAGAA-AGGTTGCAACT-AACTTATATGGG
2801 C
63 C
2802 TTTGAGAAGG
1 TTTGAGAAGG
2812 AAAATGTGCC
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
61 1 0.02
62 18 0.30
63 41 0.68
ACGTcount: A:0.25, C:0.14, G:0.31, T:0.31
Consensus pattern (63 bp):
TTTGAGAAGGGTTGCCACCGACTTAGTGGGATTTAAGAAAGGTTGCAACTAACTTATATGGGC
Found at i:2897 original size:33 final size:33
Alignment explanation
Indices: 2850--3230 Score: 266
Period size: 34 Copynumber: 11.8 Consensus size: 33
2840 AAGGAAAAGG
* *
2850 GGTGCTACGGAGTTGTGGGCTTTGAAAAGAAATA
1 GGTGCCAC-GAGTTGTGGGCTTTGAAAAGAAAAA
* *
2884 GTTGCCACGAGTTGTGGAC-TT-AAAAGGAAAAA
1 GGTGCCACGAGTTGTGGGCTTTGAAAA-GAAAAA
* * *
2916 GGATGCCATGGAGTTGTAGGCTTTGAAAAAAAAAA
1 GG-TGCCA-CGAGTTGTGGGCTTTGAAAAGAAAAA
* *
2951 GGTGCCATGGAGTTGTGGAC-TT-AAAAG-----
1 GGTGCCA-CGAGTTGTGGGCTTTGAAAAGAAAAA
*
2978 GGTGCCATGGAGTTGTGGGCTTTGAAAAGAAAAA
1 GGTGCCA-CGAGTTGTGGGCTTTGAAAAGAAAAA
* * *
3012 AGTGCCATGGAGTTATGGGC-TTGAAAAGAAAAA
1 GGTGCCA-CGAGTTGTGGGCTTTGAAAAGAAAAA
* * *
3045 GGTGCCAAGAGTTGTAGGCTTTG-AATGAAAAA
1 GGTGCCACGAGTTGTGGGCTTTGAAAAGAAAAA
* * *
3077 GGTGCCACAAAGTTGTTGG-ATT-AAAAG-----
1 GGTGCCAC-GAGTTGTGGGCTTTGAAAAGAAAAA
* * *
3104 GGTGCCATGAATTGT-GG-ATT-AAAAGAAAAAA
1 GGTGCCACGAGTTGTGGGCTTTGAAAAG-AAAAA
*
3135 GGTGCCACGGAGTTGTGGGTTTTGAAAAGAAAAA
1 GGTGCCAC-GAGTTGTGGGCTTTGAAAAGAAAAA
* *
3169 GGTGCCACGGAGTTATGGGTTTTGAAAAGAAAAA
1 GGTGCCAC-GAGTTGTGGGCTTTGAAAAGAAAAA
*
3203 GGTGCCACGAAGTTGTGGAC-TTGAAAAG
1 GGTGCCACG-AGTTGTGGGCTTTGAAAAG
3231 GTGCCGCGAC
Statistics
Matches: 286, Mismatches: 35, Indels: 53
0.76 0.09 0.14
Matches are distributed among these distances:
25 10 0.03
26 5 0.02
27 26 0.09
28 2 0.01
29 5 0.02
31 11 0.04
32 47 0.16
33 58 0.20
34 104 0.36
35 14 0.05
36 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.24
Consensus pattern (33 bp):
GGTGCCACGAGTTGTGGGCTTTGAAAAGAAAAA
Found at i:2908 original size:67 final size:68
Alignment explanation
Indices: 2812--3231 Score: 270
Period size: 67 Copynumber: 6.5 Consensus size: 68
2802 TTTGAGAAGG
* * * * * * *
2812 AAAATGTGCCATAGAGTTATGGACTTAAAAGGAAAAGGGGTGCTACGGAGTTGTGGGCTTTGAAA
1 AAAAGGTGCCATCGAGTTGTGGACTTAAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTGAAA
*
2877 AGA
66 AAA
* * *
2880 AATAGTTGCCA-CGAGTTGTGGACTTAAAAGGAAAAAGGATGCCATGGAGTTGTAGGCTTTGAAA
1 AAAAGGTGCCATCGAGTTGTGGACTTAAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTGAAA
2944 AAA
66 AAA
* * *
2947 AAAAGGTGCCATGGAGTTGTGGACTTAAAA-G-----GG-TGCCATGGAGTTGTGGGCTTTGAAA
1 AAAAGGTGCCATCGAGTTGTGGACTTAAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTGAAA
3005 AGAA
66 A-AA
* * * *
3009 AAAA-GTGCCATGGAGTTATGGGCTTGAAAA-GAAAAAGG-TGCCA-AGAGTTGTAGGCTTTG-A
1 AAAAGGTGCCATCGAGTTGTGGACTT-AAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTGAA
**
3069 ATGA
65 AAAA
* * * *
3073 AAAAGGTGCCA-CAAAGTTGTTGGA-TTAAAA-G-----GG-TGCCA-TGAATTGT-GG-ATT-A
1 AAAAGGTGCCATC-GAGTTG-TGGACTTAAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTGA
3125 AAAGAA
64 AAA-AA
** * * *
3131 AAAAGGTGCCA-CGGAGTTGTGGGTTTTGAAAA-GAAAAAGG-TGCCACGGAGTTATGGGTTTTG
1 AAAAGGTGCCATC-GAGTTGT-GGACTT-AAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTG
*
3193 AAAAGA
63 AAAAAA
3199 AAAAGGTGCCA-CGAAGTTGTGGACTTGAAAAGG
1 AAAAGGTGCCATCG-AGTTGTGGACTT-AAAAGG
3232 TGCCGCGACA
Statistics
Matches: 285, Mismatches: 40, Indels: 54
0.75 0.11 0.14
Matches are distributed among these distances:
57 5 0.02
58 22 0.08
59 15 0.05
60 5 0.02
61 44 0.15
62 13 0.05
64 10 0.04
65 21 0.07
66 22 0.08
67 77 0.27
68 47 0.16
69 4 0.01
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.23
Consensus pattern (68 bp):
AAAAGGTGCCATCGAGTTGTGGACTTAAAAGGAAAAAGGATGCCACGGAGTTGTAGGCTTTGAAA
AAA
Found at i:3011 original size:61 final size:62
Alignment explanation
Indices: 2843--3235 Score: 295
Period size: 61 Copynumber: 6.2 Consensus size: 62
2833 GACTTAAAAG
* * * * *
2843 GAAAAGGGGTGCTACGGAGTTGTGGGCTTTGAAAAGAAATAGTTGCCAC-GAGTTGTGGACTT
1 GAAAA-GGGTGCCATGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* * *
2905 AAAAGGAAAAAGGATGCCATGGAGTTGTAGGCTTTGAAAAAAAAAAGGTGCCATGGAGTTGTGGA
1 -----G-AAAAGGGTGCCATGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGA
2970 CTT
60 CTT
* * * * *
2973 -AAAAGGGTGCCATGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTATGGGCTT
1 GAAAAGGGTGCCATGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
* * **
3034 GAAAAGAAAAAGGTGCCA-AGAGTTGTAGGCTTTG-AATGAAAAAGGTGCCACAAAGTTGTTGGA
1 GAAAAG-----GGTGCCATGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTG-TGGA
3097 -TT
60 CTT
* * **
3099 -AAAAGGGTGCCAT-GAATTGT-GG-ATT-AAAAGAAAAAAGGTGCCACGGAGTTGTGGGTTTT
1 GAAAAGGGTGCCATGGAGTTGTAGGCTTTGAAAAG-AAAAAGGTGCCACGGAGTTGT-GGACTT
* * * * *
3158 GAAAAGAAAAAGGTGCCACGGAGTTATGGGTTTTGAAAAGAAAAAGGTGCCACGAAGTTGTGGAC
1 GAAAAG-----GGTGCCATGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGAC
3223 TT
61 TT
3225 GAAAA-GGTGCC
1 GAAAAGGGTGCC
3236 GCGACATTAT
Statistics
Matches: 266, Mismatches: 36, Indels: 54
0.75 0.10 0.15
Matches are distributed among these distances:
57 6 0.02
58 22 0.08
59 15 0.06
60 5 0.02
61 61 0.23
62 5 0.02
64 5 0.02
65 27 0.10
66 22 0.08
67 54 0.20
68 39 0.15
69 5 0.02
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.23
Consensus pattern (62 bp):
GAAAAGGGTGCCATGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGGAGTTGTGGACTT
Found at i:3110 original size:27 final size:25
Alignment explanation
Indices: 3072--3128 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 25
3062 GCTTTGAATG
*
3072 AAAAAGGTGCCACAAAGTTGTTGGATT
1 AAAAGGGTGCCACAAA-TTG-TGGATT
**
3099 AAAAGGGTGCCATGAATTGTGGATT
1 AAAAGGGTGCCACAAATTGTGGATT
3124 AAAAG
1 AAAAG
3129 AAAAAAGGTG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 11 0.41
26 3 0.11
27 13 0.48
ACGTcount: A:0.39, C:0.09, G:0.28, T:0.25
Consensus pattern (25 bp):
AAAAGGGTGCCACAAATTGTGGATT
Found at i:3201 original size:126 final size:127
Alignment explanation
Indices: 2844--3235 Score: 435
Period size: 126 Copynumber: 3.1 Consensus size: 127
2834 ACTTAAAAGG
* * * * * * *
2844 AAAAGGGGTGCTACGGAGTTGTGGGCTTTGAAAAG-AAATAGTTGCCAC-GAGTTGTGGACTT-A
1 AAAA-GGGTGCCATGGAATTGTGGGCATTGAAAAGAAAAAAG-TGCCACGGAGTTATGGGCTTGA
* * *
2906 AAAGGAAAAAGGATGCCATGGAGTTGTAGGCTTTGAAAAAAAAAAGGTGCCATGGAGTTGTGGAC
64 AAA-GAAAAAGG-TGCCA-GGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGAAGTTGTGGAC
2971 TT
126 TT
* * *
2973 AAAAGGGTGCCATGGAGTTGTGGGCTTTGAAAAGAAAAAAGTGCCATGGAGTTATGGGCTTGAAA
1 AAAAGGGTGCCATGGAATTGTGGGCATTGAAAAGAAAAAAGTGCCACGGAGTTATGGGCTTGAAA
* * *
3038 AGAAAAAGGTGCCAAGAGTTGTAGGCTTTG-AATGAAAAAGGTGCCACAAAGTTGTTGGA-TT
66 AGAAAAAGGTGCCAGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGAAGTTG-TGGACTT
* *
3099 AAAAGGGTGCCAT-GAATTGT-GG-ATT-AAAAGAAAAAAGGTGCCACGGAGTTGTGGGTTTTGA
1 AAAAGGGTGCCATGGAATTGTGGGCATTGAAAAGAAAAAA-GTGCCACGGAGTTATGGG-CTTGA
* * *
3160 AAAGAAAAAGGTGCCACGGAGTTATGGGTTTTGAAAAGAAAAAGGTGCCACGAAGTTGTGGACTT
64 AAAGAAAAAGGTGCCA-GGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGAAGTTGTGGACTT
3225 GAAAA-GGTGCC
1 -AAAAGGGTGCC
3236 GCGACATTAT
Statistics
Matches: 230, Mismatches: 23, Indels: 23
0.83 0.08 0.08
Matches are distributed among these distances:
122 11 0.05
123 18 0.08
124 22 0.10
125 22 0.10
126 64 0.28
127 23 0.10
128 38 0.17
129 28 0.12
130 4 0.02
ACGTcount: A:0.35, C:0.10, G:0.32, T:0.23
Consensus pattern (127 bp):
AAAAGGGTGCCATGGAATTGTGGGCATTGAAAAGAAAAAAGTGCCACGGAGTTATGGGCTTGAAA
AGAAAAAGGTGCCAGGAGTTGTAGGCTTTGAAAAGAAAAAGGTGCCACGAAGTTGTGGACTT
Found at i:3248 original size:27 final size:27
Alignment explanation
Indices: 3199--3261 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 27
3189 TTTGAAAAGA
*
3199 AAAAGGTGCCACGAAGTTGTGGA-CTT
1 AAAAGGTGCCACGAAGTTATGGAGCTT
* *
3225 GAAAAGGTGCCGCGACA-TTATGGAGGTT
1 -AAAAGGTGCCACGA-AGTTATGGAGCTT
3253 AAAAGGTGC
1 AAAAGGTGC
3262 GACAGAGTTG
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
27 28 0.90
28 3 0.10
ACGTcount: A:0.32, C:0.14, G:0.33, T:0.21
Consensus pattern (27 bp):
AAAAGGTGCCACGAAGTTATGGAGCTT
Found at i:3332 original size:29 final size:30
Alignment explanation
Indices: 3289--3431 Score: 109
Period size: 29 Copynumber: 4.8 Consensus size: 30
3279 AAAGAAAAAA
*
3289 AGGTGCCAC-AGAGTTGTGGGCTTTAGGAAG
1 AGGTGCCACGA-AGTCGTGGGCTTTAGGAAG
* *
3319 -GGTGCCACGAAGTTGTGGGCTTTTGGAAG
1 AGGTGCCACGAAGTCGTGGGCTTTAGGAAG
* *
3348 AAAGGTGCCACTAAGTCGTGGAC-TTA-GAGAG
1 --AGGTGCCACGAAGTCGTGGGCTTTAGGA-AG
* * * *
3379 AGATGCCACTG-AGTCATAGACTTTAGGAAG
1 AGGTGCCAC-GAAGTCGTGGGCTTTAGGAAG
*
3409 -GGTGCCACGGAGTCGTGGGCTTT
1 AGGTGCCACGAAGTCGTGGGCTTT
3432 TAGAAAAATA
Statistics
Matches: 91, Mismatches: 13, Indels: 19
0.74 0.11 0.15
Matches are distributed among these distances:
28 1 0.01
29 59 0.65
30 8 0.09
31 6 0.07
32 17 0.19
ACGTcount: A:0.24, C:0.16, G:0.36, T:0.24
Consensus pattern (30 bp):
AGGTGCCACGAAGTCGTGGGCTTTAGGAAG
Found at i:4644 original size:10 final size:10
Alignment explanation
Indices: 4614--4644 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
4604 TTTTTTTCGA
4614 TTTTTCTTTT
1 TTTTTCTTTT
*
4624 CTTTTCTTTT
1 TTTTTCTTTT
4634 TTTTTCTTTT
1 TTTTTCTTTT
4644 T
1 T
4645 CGTGCTTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (10 bp):
TTTTTCTTTT
Done.