Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009059.1 Hibiscus syriacus cultivar Beakdansim tig00112476_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 66977
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:1302 original size:23 final size:24
Alignment explanation
Indices: 1276--1326 Score: 68
Period size: 23 Copynumber: 2.2 Consensus size: 24
1266 AGACCAAAAC
1276 AATAAAATAAAATAAAAATA-ATA
1 AATAAAATAAAATAAAAATACATA
* * *
1299 AATAAAATAATATATATATACATA
1 AATAAAATAAAATAAAAATACATA
1323 AATA
1 AATA
1327 TTTTCAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (24 bp):
AATAAAATAAAATAAAAATACATA
Found at i:1351 original size:23 final size:23
Alignment explanation
Indices: 1314--1357 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
1304 AATAATATAT
1314 ATATACATAAATATTTTCAAAAAC
1 ATATACATAAATA-TTTCAAAAAC
*
1338 ATATA-ATATATATTTCAAAA
1 ATATACATAAATATTTCAAAA
1358 TGTTTTTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 6 0.32
24 5 0.26
ACGTcount: A:0.55, C:0.09, G:0.00, T:0.36
Consensus pattern (23 bp):
ATATACATAAATATTTCAAAAAC
Found at i:1448 original size:34 final size:34
Alignment explanation
Indices: 1410--1517 Score: 96
Period size: 34 Copynumber: 3.2 Consensus size: 34
1400 AAAAAAGATT
1410 ATATAAAT-TTTCCCAAAACGCTTTAAAAACTATA
1 ATATAAATGTTT-CCAAAACGCTTTAAAAACTATA
* * * *
1444 ATATAAATGTTTTCAAAAGGTTTTCAAAACTATA
1 ATATAAATGTTTCCAAAACGCTTTAAAAACTATA
* * * *
1478 ATAT-ATTGTTTTCAAAAATGTTTTCAAAAACTAT-
1 ATATAAATG-TTTCCAAAACGCTTT-AAAAACTATA
1512 ATATAA
1 ATATAA
1518 GTTTTCAAAT
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
33 3 0.05
34 46 0.75
35 12 0.20
ACGTcount: A:0.45, C:0.11, G:0.06, T:0.38
Consensus pattern (34 bp):
ATATAAATGTTTCCAAAACGCTTTAAAAACTATA
Found at i:1493 original size:33 final size:34
Alignment explanation
Indices: 1435--1526 Score: 118
Period size: 34 Copynumber: 2.7 Consensus size: 34
1425 AAACGCTTTA
*
1435 AAAACTATAATATAAATGTTTTC-AAAAGGTTTTC
1 AAAACTATAATAT-ATTGTTTTCAAAAAGGTTTTC
*
1469 AAAACTATAATATATTGTTTTCAAAAATGTTTTC
1 AAAACTATAATATATTGTTTTCAAAAAGGTTTTC
*
1503 AAAAACTAT-ATATA-AGTTTTCAAA
1 -AAAACTATAATATATTGTTTTCAAA
1527 TGATTTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
33 17 0.32
34 28 0.53
35 8 0.15
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.39
Consensus pattern (34 bp):
AAAACTATAATATATTGTTTTCAAAAAGGTTTTC
Found at i:1549 original size:34 final size:34
Alignment explanation
Indices: 1431--1612 Score: 116
Period size: 34 Copynumber: 5.4 Consensus size: 34
1421 CCCAAAACGC
* * *
1431 TTTAAAAACTATAATATA-AATGTTTTCAAAAGGT
1 TTTAAAAACTATATTATATAA-GTTTTCAAATGAT
* * *
1465 TTTCAAAACTATAATATAT-TGTTTTCAAAAATG-T
1 TTTAAAAACTATATTATATAAGTTTTC--AAATGAT
1499 TTTCAAAAAC--TA-TATATAAGTTTTCAAATGAT
1 TTT-AAAAACTATATTATATAAGTTTTCAAATGAT
* *
1531 TTTAAAAATTATATTATATATA-TTTTCTAAAATGTTTT
1 TTTAAAAACTATATTATATA-AGTTTTC--AAATG--AT
*
1569 TTTTAAAACTATATTATATAA-TTTT-AAA--AT
1 TTTAAAAACTATATTATATAAGTTTTCAAATGAT
*
1599 ATTAAAAACTATAT
1 TTTAAAAACTATAT
1613 ATTATATACG
Statistics
Matches: 122, Mismatches: 12, Indels: 32
0.73 0.07 0.19
Matches are distributed among these distances:
30 13 0.11
31 10 0.08
32 9 0.07
33 16 0.13
34 35 0.29
35 10 0.08
36 5 0.04
37 5 0.04
38 19 0.16
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (34 bp):
TTTAAAAACTATATTATATAAGTTTTCAAATGAT
Found at i:1549 original size:66 final size:70
Alignment explanation
Indices: 1434--1568 Score: 179
Period size: 66 Copynumber: 2.0 Consensus size: 70
1424 AAAACGCTTT
* * *
1434 AAAAACTATAATATAAATGTTTTCAAAAGGTTTTCAAAACTATAATATAT-TGTTTTCAAAAATG
1 AAAAACTATAATATAAATGTTTTCAAAAGATTTTAAAAACTATAATATATATATTTTCAAAAATG
1498 TTTTC
66 TTTTC
* * * *
1503 AAAAACTAT-ATAT-AA-GTTTTCAAATGATTTTAAAAATTATATTATATATATTTTCTAAAATG
1 AAAAACTATAATATAAATGTTTTCAAAAGATTTTAAAAACTATAATATATATATTTTCAAAAATG
1565 TTTT
66 TTTT
1569 TTTTAAAACT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
66 27 0.47
67 18 0.31
68 4 0.07
69 9 0.16
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.44
Consensus pattern (70 bp):
AAAAACTATAATATAAATGTTTTCAAAAGATTTTAAAAACTATAATATATATATTTTCAAAAATG
TTTTC
Found at i:2380 original size:84 final size:82
Alignment explanation
Indices: 2278--3213 Score: 845
Period size: 84 Copynumber: 11.5 Consensus size: 82
2268 CTCGGGAGTC
* *
2278 TTTGGCAGATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
2343 TCGAACTCGAAGGTCTT
66 TCGAACTCGAAGGTCTT
* * * *** * *
2360 TGATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGCCCCTCGAAGCTGAGCGT
1 T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGT
* *
2425 AATCGAACTCG-GGGTC--
64 AGTCGAACTCGAAGGTCTT
* *
2441 -TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
*
2505 TCGAACTCAAAGGTCTT
66 TCGAACTCGAAGGTCTT
* ** * * * * * * * * *
2522 TGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGT
1 T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGT
* *
2587 AATCGAACTCG-GGAGTC--
64 AGTCGAACTCGAAG-GTCTT
* *
2604 TTTGGCAGATGGCCCTTCTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
*
2669 TCAAACTCGAAGGTCTT
66 TCGAACTCGAAGGTCTT
* * * * * *
2686 TGATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATACGCCCTCGAAGCTGAGCG
1 T--TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCG
* *
2751 TAATCGAACTCG-GGGTC--
63 TAGTCGAACTCGAAGGTCTT
*
2768 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGC-AA--A-ATGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
*
2829 TCGAACTCAAAGGTCTT
66 TCGAACTCGAAGGTCTT
* ** * * * * * * * * *
2846 TGCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGT
1 T-TTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGT
* *
2911 AATCGAACT-TAAGGGTC--
64 AGTCGAACTCGAA-GGTCTT
* * *
2928 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
*
2993 TCGAACTCAAAGGTCTT
66 TCGAACTCGAAGGTCTT
** * * * * * * * * *
3010 TTCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGTGT
1 TT-TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATG-CCTTGGAGCTGAGCGT
* *
3075 AATCGAACT-TAAGGGTC--
64 AGTCGAACTCGAA-GGTCTT
* * *
3092 TTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGC-AATGATGTGCCTTGGAGCTGAGCGTAG
1 TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
3156 TCGAACTCGAAGGTCTT
66 TCGAACTCGAAGGTCTT
** * * * *
3173 GGTGGCAGGTAGCCCTTCT-GTCCTTGAGCTAAGCTGCAAAT
1 TTTGGCAGATAGCCCTTCTCG-ACTTAAGCTATGCTGCAAAT
3214 AGTTTGTTTA
Statistics
Matches: 673, Mismatches: 145, Indels: 72
0.76 0.16 0.08
Matches are distributed among these distances:
75 23 0.03
76 6 0.01
77 1 0.00
78 64 0.10
79 58 0.09
80 96 0.14
81 123 0.18
82 12 0.02
83 79 0.12
84 188 0.28
85 23 0.03
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (82 bp):
TTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAG
TCGAACTCGAAGGTCTT
Found at i:2437 original size:164 final size:162
Alignment explanation
Indices: 2231--3172 Score: 1324
Period size: 164 Copynumber: 5.8 Consensus size: 162
2221 CATGAGCTAT
* * *
2231 TGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
1 TGTAAATG-TATGCCCTCGAAGCTGAGTGTAATCGAACTCGGG-GTCTTTGGCAGATAGCCCTTC
* * *
2296 TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
64 TCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
** * * *
2361 GATTGGCAGATAACCCTTCTTGACTTAAGTTATGC
129 G-TTAACAGATAACCCTTCTAGCCTTGAGTTATGC
* *
2396 TGCAAATG-ATGCCCCTCGAAGCTGAGCGTAATCGAACTCGGGGTC-TTGGCAGATAGCCCTTCT
1 TGTAAATGTATG-CCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCT
* *
2459 CGACTTAAGCTATTCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG
65 CGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG
*
2524 CTAACAGATAACCCTTCTAGCCTTGAGTTATGC
130 TTAACAGATAACCCTTCTAGCCTTGAGTTATGC
* *
2557 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
1 TGTAAATG-TATGCCCTCGAAGCTGAGTGTAATCGAACTCGGG-GTCTTTGGCAGATAGCCCTTC
* * * *
2622 TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
64 TCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
** * * *
2687 GATTGGCAGATAACCCTTCTTGACTTAAGTTATGC
129 G-TTAACAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
2722 TGCAAATGATACGCCCTCGAAGCTGAGCGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCT
1 TGTAAATG-TATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCT
*
2787 CGACTTAAGCTATTCTGC-AA--A-ATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG
65 CGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTG
*
2848 CTAACAGATAACCCTTCTAGCCTTGAGTTATGC
130 TTAACAGATAACCCTTCTAGCCTTGAGTTATGC
* ** *
2881 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTC
1 TGTAAATG-TATGCCCTCGAAGCTGAGTGTAATCGAAC-TCGGGGTCTTTGGCAGATAGCCCTTC
*
2946 TCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
64 TCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTT
3011 -TCTAACAGATAACCCTTCTAGCCTTGAGTTATGC
129 GT-TAACAGATAACCCTTCTAGCCTTGAGTTATGC
* ** *
3045 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTC
1 TGTAAATG-TATGCCCTCGAAGCTGAGTGTAATCGAAC-TCGGGGTCTTTGGCAGATAGCCCTTC
* *
3110 TCGACTTAAGCTATACTGC-AATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
64 TCGACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
3173 GGTGGCAGGT
Statistics
Matches: 707, Mismatches: 58, Indels: 26
0.89 0.07 0.03
Matches are distributed among these distances:
159 60 0.08
160 79 0.11
161 37 0.05
162 106 0.15
163 58 0.08
164 295 0.42
165 72 0.10
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (162 bp):
TGTAAATGTATGCCCTCGAAGCTGAGTGTAATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTC
GACTTAAGCTATACTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGT
TAACAGATAACCCTTCTAGCCTTGAGTTATGC
Found at i:2979 original size:324 final size:325
Alignment explanation
Indices: 2231--3172 Score: 1500
Period size: 324 Copynumber: 2.9 Consensus size: 325
2221 CATGAGCTAT
* * * *
2231 TGTAAATGATATGACCTCGAAGTTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
1 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
2296 TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
66 TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
*
2361 GATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATGC-CCCTCGAAGCTGAGCGT
131 GATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATACGCCCTCGAAGCTGAGCGT
2425 AATCGAACTCGGGGTC-TTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCC
196 AATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAAT-A--TGCC
2489 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTA
258 TTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTA
2554 TGC
323 TGC
2557 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
1 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
*
2622 TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCAAACTCGAAGGTCTTT
66 TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
2687 GATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATACGCCCTCGAAGCTGAGCGT
131 GATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATACGCCCTCGAAGCTGAGCGT
2752 AATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAA-ATGCCTTG
196 AATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATATGCCTTG
2816 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGC
261 GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGC
** * *
2881 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTTAAGG-GTCTTTGGCAGATAGCTCTT
1 TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAAC-TCGGGAGTCTTTGGCAGATGGCCCTT
* * * *
2945 CTCGACTTAAGCTATACTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
65 CTTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
** * * * * * * * *
3010 T--TCTAACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTATGCCCTTGAAGCTGAGT
130 TGAT-TGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATACGCCCTCGAAGCTGAGC
** * * *
3073 GTAATCGAACTTAAGGGTCTTTGGCAGATAGCTCTTCTCGACTTAAGCTATACTGCAATGATGTG
194 GTAATCGAAC-TCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAA--ATATG
*
3138 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
256 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
3173 GGTGGCAGGT
Statistics
Matches: 577, Mismatches: 31, Indels: 15
0.93 0.05 0.02
Matches are distributed among these distances:
322 1 0.00
323 60 0.10
324 232 0.40
325 3 0.01
326 173 0.30
327 69 0.12
328 39 0.07
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (325 bp):
TGTAAATGTTATGCCCTTGAAGCTGAGTGTAATCGAACTCGGGAGTCTTTGGCAGATGGCCCTTC
TTGACTTAAGCTATGCTGCAAATGATATGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT
GATTGGCAGATAACCCTTCTTGACTTAAGTTATGCTGCAAATGATACGCCCTCGAAGCTGAGCGT
AATCGAACTCGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATATGCCTTG
GAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGTTATGC
Found at i:9439 original size:9 final size:10
Alignment explanation
Indices: 9411--9446 Score: 51
Period size: 9 Copynumber: 3.9 Consensus size: 10
9401 AGACCAAAAC
9411 AATAA-ATAA
1 AATAATATAA
9420 AATAA-ATAA
1 AATAATATAA
9429 AATAATA-AA
1 AATAATATAA
9438 AATAATATA
1 AATAATATA
9447 TATATACATA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 23 0.92
10 2 0.08
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (10 bp):
AATAATATAA
Found at i:9587 original size:36 final size:37
Alignment explanation
Indices: 9547--9697 Score: 116
Period size: 36 Copynumber: 4.1 Consensus size: 37
9537 AAAAAAGATT
*
9547 ATATAAAT-TTTCCCAAAACGCTTTAAAAACTATATA
1 ATATAAATGTTTCCCAAAACGTTTTAAAAACTATATA
* * *
9583 ATATAAATGTTT-TCAAAAGGTTTTCAAAAC--TATA
1 ATATAAATGTTTCCCAAAACGTTTTAAAAACTATATA
* * * *
9617 ATATATATGTTTTCAAAAATGTTTTCAAAAACTATATA
1 ATATAAATGTTTCCCAAAACGTTTT-AAAAACTATATA
* * *
9655 TATATATAA-GTTT-TCAAAATGATTTTAAAAATTATATA
1 -ATATA-AATGTTTCCCAAAACG-TTTTAAAAACTATATA
*
9693 TTATA
1 ATATA
9698 TATATTTTCT
Statistics
Matches: 93, Mismatches: 14, Indels: 15
0.76 0.11 0.12
Matches are distributed among these distances:
34 15 0.16
35 9 0.10
36 27 0.29
37 7 0.08
38 21 0.23
39 13 0.14
40 1 0.01
ACGTcount: A:0.46, C:0.09, G:0.05, T:0.40
Consensus pattern (37 bp):
ATATAAATGTTTCCCAAAACGTTTTAAAAACTATATA
Found at i:9606 original size:72 final size:73
Alignment explanation
Indices: 9499--9673 Score: 194
Period size: 72 Copynumber: 2.4 Consensus size: 73
9489 AAATGTTTTT
* * * * *
9499 AAACTATATAATATATGAATTTTTTCAACATGTTTTCAAAAAAAGATTATATAAATTTTCCCAAA
1 AAACTATATAATATAT-AATGTTTTCAAAAGGTTTTCAAAAAAAGAATATATAAATTTT-CAAAA
9564 ACGCTTT-AA
64 ACGCTTTCAA
** * ** *
9573 AAACTATATAATATA-AATGTTTTCAAAAGGTTTTCAAAACTATAATATATATGTTTTCAAAAAT
1 AAACTATATAATATATAATGTTTTCAAAAGGTTTTCAAAAAAAGAATATATAAATTTTCAAAAAC
*
9637 GTTTTCAA
66 GCTTTCAA
9645 AAACTATATATATATATAA-GTTTTCAAAA
1 AAACTATATA-ATATATAATGTTTTCAAAA
9674 TGATTTTAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
71 9 0.10
72 45 0.52
73 15 0.17
74 17 0.20
ACGTcount: A:0.46, C:0.10, G:0.06, T:0.39
Consensus pattern (73 bp):
AAACTATATAATATATAATGTTTTCAAAAGGTTTTCAAAAAAAGAATATATAAATTTTCAAAAAC
GCTTTCAA
Found at i:9640 original size:12 final size:12
Alignment explanation
Indices: 9623--9647 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
9613 TATAATATAT
9623 ATGTTTTCAAAA
1 ATGTTTTCAAAA
9635 ATGTTTTCAAAA
1 ATGTTTTCAAAA
9647 A
1 A
9648 CTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.40
Consensus pattern (12 bp):
ATGTTTTCAAAA
Found at i:9685 original size:38 final size:37
Alignment explanation
Indices: 9568--9769 Score: 176
Period size: 38 Copynumber: 5.5 Consensus size: 37
9558 CCCAAAACGC
* *
9568 TTTAAAAACTATATAATATA-AATGTTTTCAAAA-GGT
1 TTTAAAAACTATATATTATATAA-GTTTTCAAAATGAT
* *
9604 TTTCAAAACTATA-A-TATATATGTTTTCAAAAATG-T
1 TTTAAAAACTATATATTATATAAGTTTTC-AAAATGAT
9639 TTTCAAAAACTATATATATATATAAGTTTTCAAAATGAT
1 TTT-AAAAACTATATAT-TATATAAGTTTTCAAAATGAT
* *
9678 TTTAAAAATTATATATTATATATA-TTTTCTAAAATGTTTT
1 TTTAAAAACTATATATTATATA-AGTTTTC-AAAATG--AT
*
9718 TTTTAAAACTATATATTATAT-A-TTTT-AAAACT-A-
1 TTTAAAAACTATATATTATATAAGTTTTCAAAA-TGAT
9751 -TTAAAAACTATATATTATA
1 TTTAAAAACTATATATTATA
9770 CGTAGTTTCA
Statistics
Matches: 143, Mismatches: 10, Indels: 30
0.78 0.05 0.16
Matches are distributed among these distances:
32 18 0.13
34 10 0.07
35 10 0.07
36 26 0.18
37 13 0.09
38 30 0.21
39 16 0.11
40 20 0.14
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (37 bp):
TTTAAAAACTATATATTATATAAGTTTTCAAAATGAT
Found at i:19754 original size:26 final size:26
Alignment explanation
Indices: 19725--19776 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
19715 TTTTGTTTTC
19725 TTCG-TCTCTAAAATTTTATAAATTTA
1 TTCGTTCT-TAAAATTTTATAAATTTA
*
19751 TTCGTTCTTAGAATTTTATAAATTTA
1 TTCGTTCTTAAAATTTTATAAATTTA
19777 CCTCTCTAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 21 0.88
27 3 0.12
ACGTcount: A:0.33, C:0.10, G:0.06, T:0.52
Consensus pattern (26 bp):
TTCGTTCTTAAAATTTTATAAATTTA
Found at i:22477 original size:18 final size:18
Alignment explanation
Indices: 22454--22488 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
22444 CTTTGACCCC
22454 TGTTGATGA-GGTTTTCTT
1 TGTTGA-GATGGTTTTCTT
22472 TGTTGAGATGGTTTTCT
1 TGTTGAGATGGTTTTCT
22489 AACGTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 14 0.88
ACGTcount: A:0.11, C:0.06, G:0.29, T:0.54
Consensus pattern (18 bp):
TGTTGAGATGGTTTTCTT
Found at i:25472 original size:18 final size:19
Alignment explanation
Indices: 25451--25499 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
25441 ATTTTTTATA
25451 AAATTTTA-TATTTTAAAG
1 AAATTTTATTATTTTAAAG
*
25469 AAA-TTTATTATTTTAAAT
1 AAATTTTATTATTTTAAAG
*
25487 AAATTTTCTTATT
1 AAATTTTATTATT
25500 CCAATAGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 4 0.15
18 15 0.56
19 8 0.30
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (19 bp):
AAATTTTATTATTTTAAAG
Found at i:25774 original size:14 final size:14
Alignment explanation
Indices: 25755--25782 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
25745 CAACCTTTTG
25755 AAATGATAACATAC
1 AAATGATAACATAC
25769 AAATGATAACATAC
1 AAATGATAACATAC
25783 CATGTTATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.21
Consensus pattern (14 bp):
AAATGATAACATAC
Found at i:27674 original size:7 final size:7
Alignment explanation
Indices: 27658--27695 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
27648 GTCAAAGAAA
*
27658 GTCAATG
1 GTCAACG
27665 GTCAACG
1 GTCAACG
27672 GTCAACG
1 GTCAACG
27679 GTCAACG
1 GTCAACG
27686 GTCAACG
1 GTCAACG
27693 GTC
1 GTC
27696 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:27702 original size:5 final size:5
Alignment explanation
Indices: 27692--27754 Score: 72
Period size: 5 Copynumber: 11.8 Consensus size: 5
27682 AACGGTCAAC
* *
27692 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
27741 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
27755 AACGGTCGAG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
5 42 0.84
7 8 0.16
ACGTcount: A:0.06, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:27713 original size:22 final size:22
Alignment explanation
Indices: 27685--27771 Score: 165
Period size: 22 Copynumber: 4.0 Consensus size: 22
27675 AACGGTCAAC
27685 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
27707 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
27729 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
27751 GGTCAACGGTCGAGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
27772 AGACCGGTCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 64 1.00
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:27792 original size:19 final size:18
Alignment explanation
Indices: 27770--27856 Score: 77
Period size: 19 Copynumber: 4.6 Consensus size: 18
27760 TCGAGTCGGG
27770 TCAGACCGGTCAAACCGAT
1 TCAGACCGGTCAAACCG-T
27789 TCAGACCGGTCAAACCGGT
1 TCAGACCGGTCAAACC-GT
* *
27808 TC-GAACCGGTTGAAACCGG
1 TCAG-ACCGG-TCAAACCGT
* *
27827 TCAAACCGGTCAGAACCGG
1 TCAGACCGGTCA-AACCGT
27846 TCAGAACCGGT
1 TCAG-ACCGGT
27857 TGAAAACCGG
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
18 3 0.05
19 41 0.72
20 13 0.23
ACGTcount: A:0.29, C:0.30, G:0.26, T:0.15
Consensus pattern (18 bp):
TCAGACCGGTCAAACCGT
Found at i:27825 original size:20 final size:19
Alignment explanation
Indices: 27800--27877 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 19
27790 CAGACCGGTC
*
27800 AAACCGGTTCGAACCGGTTG
1 AAACCGG-TCAAACCGGTTG
*
27820 AAACCGGTCAAACCGG-TC
1 AAACCGGTCAAACCGGTTG
27838 AGAACCGGTCAGAACCGGTTG
1 A-AACCGGTCA-AACCGGTTG
*
27859 AAAACCGGTTAAACCGGTT
1 -AAACCGGTCAAACCGGTT
27878 TCCAGCAGCC
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
18 2 0.04
19 17 0.34
20 21 0.42
21 9 0.18
22 1 0.02
ACGTcount: A:0.31, C:0.26, G:0.27, T:0.17
Consensus pattern (19 bp):
AAACCGGTCAAACCGGTTG
Found at i:27853 original size:29 final size:28
Alignment explanation
Indices: 27769--27876 Score: 94
Period size: 29 Copynumber: 3.7 Consensus size: 28
27759 GTCGAGTCGG
* *
27769 GTCAGACCGGTCAAACCGATTCAG-ACCG
1 GTCAAACCGGTCAAACCG-GTCAGAACCG
* *
27797 GTCAAACCGGTTCGAACCGGT-TGAAACCG
1 GTCAAACCGG-TCAAACCGGTCAG-AACCG
27826 GTCAAACCGGTCAGAACCGGTCAGAACCG
1 GTCAAACCGGTCA-AACCGGTCAGAACCG
* *
27855 GTTGAAAACCGGTTAAACCGGT
1 G-T-CAAACCGGTCAAACCGGT
27877 TTCCAGCAGC
Statistics
Matches: 65, Mismatches: 8, Indels: 12
0.76 0.09 0.14
Matches are distributed among these distances:
27 1 0.02
28 12 0.18
29 34 0.52
30 9 0.14
31 9 0.14
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.16
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTCAGAACCG
Found at i:27866 original size:11 final size:9
Alignment explanation
Indices: 27774--27877 Score: 73
Period size: 10 Copynumber: 10.8 Consensus size: 9
27764 GTCGGGTCAG
*
27774 ACCGGTCAA
1 ACCGGTTAA
* *
27783 ACCGATTCAG
1 ACCGGTT-AA
*
27793 ACCGGTCAA
1 ACCGGTTAA
*
27802 ACCGGTTCGA
1 ACCGGTT-AA
27812 ACCGGTTGAA
1 ACCGGTT-AA
*
27822 ACCGGTCAA
1 ACCGGTTAA
*
27831 ACCGGTCAGA
1 ACCGGTTA-A
*
27841 ACCGGTCAGA
1 ACCGGTTA-A
27851 ACCGGTTGAAA
1 ACCGGTT--AA
27862 ACCGGTTAA
1 ACCGGTTAA
27871 ACCGGTT
1 ACCGGTT
27878 TCCAGCAGCC
Statistics
Matches: 78, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
9 31 0.40
10 38 0.49
11 8 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.26, T:0.16
Consensus pattern (9 bp):
ACCGGTTAA
Found at i:35037 original size:7 final size:7
Alignment explanation
Indices: 35021--35058 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
35011 GTCAAAGAAA
*
35021 GTCAATG
1 GTCAACG
35028 GTCAACG
1 GTCAACG
35035 GTCAACG
1 GTCAACG
35042 GTCAACG
1 GTCAACG
35049 GTCAACG
1 GTCAACG
35056 GTC
1 GTC
35059 GGGTCGGGTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.26, C:0.26, G:0.29, T:0.18
Consensus pattern (7 bp):
GTCAACG
Found at i:35065 original size:5 final size:5
Alignment explanation
Indices: 35055--35116 Score: 63
Period size: 5 Copynumber: 11.8 Consensus size: 5
35045 AACGGTCAAC
* *
35055 GGTCG GGTCG GGTC- GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
35103 GGTCG GGTCG GGTC
1 GGTCG GGTCG GGTC
35117 AACGGTCGAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
4 4 0.08
5 37 0.76
7 8 0.16
ACGTcount: A:0.06, C:0.23, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:35097 original size:22 final size:22
Alignment explanation
Indices: 35048--35133 Score: 156
Period size: 22 Copynumber: 4.0 Consensus size: 22
35038 AACGGTCAAC
35048 GGTCAACGGTCGGGTCGGGTC-
1 GGTCAACGGTCGGGTCGGGTCG
35069 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
35091 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
35113 GGTCAACGGTCGAGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
35134 AGACCGGTCA
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
21 21 0.33
22 42 0.67
ACGTcount: A:0.10, C:0.23, G:0.48, T:0.19
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:35148 original size:9 final size:9
Alignment explanation
Indices: 35130--35228 Score: 81
Period size: 9 Copynumber: 10.3 Consensus size: 9
35120 GGTCGAGTCG
*
35130 GGTCAGACC
1 GGTCAAACC
35139 GGTCAAACC
1 GGTCAAACC
* *
35148 GATTCAGACC
1 G-GTCAAACC
35158 GGTCAAACC
1 GGTCAAACC
*
35167 GGTTCGAACC
1 GG-TCAAACC
*
35177 GGTTGAAACC
1 GG-TCAAACC
35187 GGTCAAACC
1 GGTCAAACC
35196 GGTCAGAACC
1 GGTCA-AACC
*
35206 GGTTGAAAACC
1 GG-T-CAAACC
*
35217 GGTTAAACC
1 GGTCAAACC
35226 GGT
1 GGT
35229 TTCCAGCAGC
Statistics
Matches: 74, Mismatches: 11, Indels: 10
0.78 0.12 0.11
Matches are distributed among these distances:
9 36 0.49
10 30 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (9 bp):
GGTCAAACC
Found at i:35187 original size:29 final size:31
Alignment explanation
Indices: 35155--35229 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
35145 ACCGATTCAG
35155 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
35184 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
35214 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
35230 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:35207 original size:19 final size:19
Alignment explanation
Indices: 35130--35228 Score: 80
Period size: 19 Copynumber: 5.2 Consensus size: 19
35120 GGTCGAGTCG
35130 GGTCAG-ACCGGTCAAACC
1 GGTCAGAACCGGTCAAACC
*
35148 GATTCAG-ACCGGTCAAACC
1 G-GTCAGAACCGGTCAAACC
*
35167 GGTTC-GAACCGGTTGAAACC
1 GG-TCAGAACCGG-TCAAACC
35187 GGTCA-AACCGGTCAGAACC
1 GGTCAGAACCGGTCA-AACC
* * *
35206 GGTTGAAAACCGGTTAAACC
1 GG-TCAGAACCGGTCAAACC
35226 GGT
1 GGT
35229 TTCCAGCAGC
Statistics
Matches: 67, Mismatches: 6, Indels: 15
0.76 0.07 0.17
Matches are distributed among these distances:
18 4 0.06
19 39 0.58
20 16 0.24
21 8 0.12
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.16
Consensus pattern (19 bp):
GGTCAGAACCGGTCAAACC
Found at i:38376 original size:99 final size:97
Alignment explanation
Indices: 38196--38379 Score: 296
Period size: 99 Copynumber: 1.9 Consensus size: 97
38186 TCTTTCTTTG
* * * *
38196 GTGTTTCTTTTACAGTAATTTCCTGAGAGTTGAGTTGATATTTTAATGTTAAAATGATATTCATT
1 GTGTTTCTTTTACAGTAATTGCCTGAGAGTTGAGTTGATATTTCAATATTAAAATGAGATTCATT
*
38261 ACTTGTAGTACTATGAGTCTGACAGCAATTTC
66 ACTTCTAGTACTATGAGTCTGACAGCAATTTC
*
38293 GTGTTTCTTTTACAGTAATTGCCTGAGAGTTTTAGTTGATATTTCAATATTAAAAATGAGATTCA
1 GTGTTTCTTTTACAGTAATTGCCTGAGAG-TTGAGTTGATATTTCAATATT-AAAATGAGATTCA
38358 TTACTTCTAGTACTATGAGTCT
64 TTACTTCTAGTACTATGAGTCT
38380 ATGACAGTTA
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
97 28 0.35
98 18 0.23
99 33 0.42
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.43
Consensus pattern (97 bp):
GTGTTTCTTTTACAGTAATTGCCTGAGAGTTGAGTTGATATTTCAATATTAAAATGAGATTCATT
ACTTCTAGTACTATGAGTCTGACAGCAATTTC
Found at i:44435 original size:34 final size:35
Alignment explanation
Indices: 44397--44507 Score: 147
Period size: 34 Copynumber: 3.2 Consensus size: 35
44387 CCAACTTGAA
44397 AAAATGGTTTTCAAAGTTT-GTAAATGTTTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
44431 AAAATGGTTTTCAAAGTTTGGTAAATG-TTCTTTG
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
44465 AAAAATAGTTTTTCAAAGTTTTGGTAGATGTTT-GTTG
1 -AAAAT-GGTTTTCAAAG-TTTGGTAAATGTTTCTTTG
44502 AAAATG
1 AAAATG
44508 ATAATGAGAT
Statistics
Matches: 69, Mismatches: 3, Indels: 9
0.85 0.04 0.11
Matches are distributed among these distances:
34 26 0.38
35 13 0.19
36 15 0.22
37 13 0.19
38 2 0.03
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.44
Consensus pattern (35 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:48373 original size:21 final size:21
Alignment explanation
Indices: 48331--48373 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
48321 TTTCTGGGTT
* * *
48331 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
48352 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
48373 A
1 A
48374 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:48433 original size:65 final size:66
Alignment explanation
Indices: 48331--48499 Score: 207
Period size: 65 Copynumber: 2.5 Consensus size: 66
48321 TTTCTGGGTT
* * *
48331 AGGGGAATCGGTACCCATTCAAGGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGC
1 AGGGGAATCGGTACCC--CCAGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGC
48395 TAG
64 TAG
* * * *
48398 AGGGGAATCGGTACCCCCAGGGGGAACCGATA-CCCCTCATCGTATATGAAATTCCAGATTGCTT
1 AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTA
48462 G
66 G
* * *
48463 AGAGGAATCGATACCCCCAGGGGGGAACCGATTCCCC
1 AGGGGAATCGGTACCCCCA-GGGGGAACCGATACCCC
48500 ATGAGAAAAA
Statistics
Matches: 89, Mismatches: 10, Indels: 6
0.85 0.10 0.06
Matches are distributed among these distances:
64 9 0.10
65 49 0.55
66 12 0.13
67 19 0.21
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.18
Consensus pattern (66 bp):
AGGGGAATCGGTACCCCCAGGGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGAATGCTA
G
Found at i:48900 original size:30 final size:30
Alignment explanation
Indices: 48864--48921 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
48854 GTTGTATGAG
* *
48864 CTATGTGATAAAGATATGTAAATGATATTT
1 CTATGTGATAAAGATATGGAAATAATATTT
*
48894 CTATGTGATAAAGGTATGGAAATAATAT
1 CTATGTGATAAAGATATGGAAATAATAT
48922 GACTACGCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.19, T:0.36
Consensus pattern (30 bp):
CTATGTGATAAAGATATGGAAATAATATTT
Found at i:49164 original size:22 final size:22
Alignment explanation
Indices: 49136--49199 Score: 119
Period size: 22 Copynumber: 2.9 Consensus size: 22
49126 TTAGGGACAT
49136 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
49158 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
49180 AATTCTACGGGGCACTTCGG
1 AATTCTAC-GGGCACTTCGG
49200 GCATTTATAC
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.73
23 11 0.27
ACGTcount: A:0.19, C:0.27, G:0.28, T:0.27
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:55190 original size:21 final size:21
Alignment explanation
Indices: 55148--55190 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
55138 TTTCTGGGTT
* * *
55148 AGGGGAATCGGTACCCATTCA
1 AGGGGAACCGATACCCACTCA
*
55169 AGGGGAACCGATACCCCCTCA
1 AGGGGAACCGATACCCACTCA
55190 A
1 A
55191 CGAAATGAAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.30, G:0.26, T:0.14
Consensus pattern (21 bp):
AGGGGAACCGATACCCACTCA
Found at i:55251 original size:65 final size:63
Alignment explanation
Indices: 55170--55314 Score: 177
Period size: 65 Copynumber: 2.3 Consensus size: 63
55160 ACCCATTCAA
* * *
55170 GGGGAACCGATACCCCCTCAACG-AAATGAATTTCCAGAATGCTAGAGGGGAATCGGTA-CCCAG
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAG-AT--T-GAGAGGAATCGATACCCCAG
55233 GG
62 GG
* *
55235 GGGGAACCGATACCCCCTCATCGTATATGAAATTCCAGATTGAGAGGAATCGATACCCCCAGGG
1 GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGATTGAGAGGAATCGATA-CCCCAGGG
*
55299 GGGGAACCGATTCCCC
1 GGGGAACCGATACCCC
55315 ATGAGAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
62 12 0.17
63 1 0.01
64 22 0.31
65 24 0.34
66 12 0.17
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.17
Consensus pattern (63 bp):
GGGGAACCGATACCCCCTCAACGTAAATGAAATTCCAGATTGAGAGGAATCGATACCCCAGGG
Found at i:55711 original size:31 final size:31
Alignment explanation
Indices: 55673--55731 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
55663 GTTGTATGAG
* *
55673 CTATGTGATAAAGGTATGTAAATGATATTTT
1 CTATGTGATAAAGGTATGGAAATAATATTTT
55704 CTATGTGATAAAGGTATGGAAATAATAT
1 CTATGTGATAAAGGTATGGAAATAATAT
55732 GACTACGCGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.37
Consensus pattern (31 bp):
CTATGTGATAAAGGTATGGAAATAATATTTT
Found at i:55999 original size:23 final size:22
Alignment explanation
Indices: 55939--56006 Score: 127
Period size: 22 Copynumber: 3.0 Consensus size: 22
55929 TTAGGGACAT
55939 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
55961 AATTCTACGGGCACTTCGGTGC
1 AATTCTACGGGCACTTCGGTGC
55983 AATTCTACGGGGCACTTCGGTGC
1 AATTCTAC-GGGCACTTCGGTGC
56006 A
1 A
56007 TTTATACGAG
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
22 30 0.67
23 15 0.33
ACGTcount: A:0.19, C:0.26, G:0.28, T:0.26
Consensus pattern (22 bp):
AATTCTACGGGCACTTCGGTGC
Found at i:57980 original size:37 final size:37
Alignment explanation
Indices: 57882--57999 Score: 149
Period size: 34 Copynumber: 3.3 Consensus size: 37
57872 GGGTAACCAA
57882 CTTTGAAAAA-ATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GGTTTTCAAAGTTTGGTAAATGTTT
57919 CTTTG--AAAT-GGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
* *
57953 CTTTGAAAAATAGTTTTTC-AAGTTTTGGTAGATGTTT
1 CTTTGAAAAATAGGTTTTCAAAG-TTTGGTAAATGTTT
*
57990 -GTTGAAAAAT
1 CTTTGAAAAAT
58000 GATAATGGGA
Statistics
Matches: 73, Mismatches: 3, Indels: 11
0.84 0.03 0.13
Matches are distributed among these distances:
34 30 0.41
35 3 0.04
36 16 0.22
37 24 0.33
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (37 bp):
CTTTGAAAAATAGGTTTTCAAAGTTTGGTAAATGTTT
Done.