Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g00305.P3
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: 3172
ACGTcount: A:0.35, C:0.09, G:0.32, T:0.23
Found at i:446 original size:3 final size:3
Alignment explanation
Indices: 440--477 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
430 AGGAGGAGGA
* *
440 GGT GGT GGT GGT GGT AGT GGT GAT GGT GGT GGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GGT GG
478 AAGTGGTAGC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.05, C:0.00, G:0.63, T:0.32
Consensus pattern (3 bp):
GGT
Found at i:1608 original size:54 final size:54
Alignment explanation
Indices: 1494--1601 Score: 182
Period size: 54 Copynumber: 2.0 Consensus size: 54
1484 CTGGTAGGGT
*
1494 AAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATATAGACGTCAGTGGTAAAGA
1 AAAAGGACAAGGTAGAGGAGATGGTAGTGGTAATATAGACGTCAGTGGTAAAGA
*
1548 AAAAGGACAAGGTAGAGGAGATGGTAGTGGTAATATAGATG-CAAGTGGTAAAGA
1 AAAAGGACAAGGTAGAGGAGATGGTAGTGGTAATATAGACGTC-AGTGGTAAAGA
1602 TGAAGGAAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
53 1 0.02
54 50 0.98
ACGTcount: A:0.41, C:0.05, G:0.36, T:0.19
Consensus pattern (54 bp):
AAAAGGACAAGGTAGAGGAGATGGTAGTGGTAATATAGACGTCAGTGGTAAAGA
Found at i:1620 original size:54 final size:54
Alignment explanation
Indices: 1494--1620 Score: 166
Period size: 54 Copynumber: 2.4 Consensus size: 54
1484 CTGGTAGGGT
*
1494 AAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATATAGACGTCAGTGGTAAAGA
1 AAAAGGAAAAGGTGGAGGAGATGGTAGTGGTAATATAGACGTCAGTGGTAAAGA
* * *
1548 AAAAGGACAAGGTAGAGGAGATGGTAGTGGTAATATAGATG-CAAGTGGTAAAGA
1 AAAAGGAAAAGGTGGAGGAGATGGTAGTGGTAATATAGACGTC-AGTGGTAAAGA
** **
1602 TGAAGGAAAATTTGGAGGA
1 AAAAGGAAAAGGTGGAGGA
1621 CAGAGAAAGG
Statistics
Matches: 64, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
53 1 0.02
54 63 0.98
ACGTcount: A:0.41, C:0.04, G:0.36, T:0.19
Consensus pattern (54 bp):
AAAAGGAAAAGGTGGAGGAGATGGTAGTGGTAATATAGACGTCAGTGGTAAAGA
Found at i:1701 original size:186 final size:186
Alignment explanation
Indices: 1410--1792 Score: 653
Period size: 186 Copynumber: 2.1 Consensus size: 186
1400 AAACTAAAGC
* *
1410 TAAAGTTGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTAGAAGTGATAGCT
1 TAAAGATGAAGGAAAATTTGGAGGACAGAGAAAGGTCGATGGAAATAGTGGTAGAAGTGATAGCT
* *
1475 CTAGTTATTCTGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATATAGACGTCAGT
66 CTAGTTATTCTGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGACGCCAGT
*
1540 GGTAAAGAAAA-AGGACAAGGTAGAGGAGATGGTAGTGGTAATATAGATGCAAGTGG
131 GGTAAAGAAAAGA-GACAAGATAGAGGAGATGGTAGTGGTAATATAGATGCAAGTGG
*
1596 TAAAGATGAAGGAAAATTTGGAGGACAGAGAAAGGTCGATGGAAATAGTGGTGGAAGTGATAGCT
1 TAAAGATGAAGGAAAATTTGGAGGACAGAGAAAGGTCGATGGAAATAGTGGTAGAAGTGATAGCT
*
1661 CTAGTTATTCTGGT-GAGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCCAG
66 CTAGTTATTCTGGTAG-GGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGACGCCAG
* *
1725 TGGTAGAGAAAAGAGACAAGATGGAGGAGATGGTAGTGGTAATATAGATGCAAGTGG
130 TGGTAAAGAAAAGAGACAAGATAGAGGAGATGGTAGTGGTAATATAGATGCAAGTGG
1782 TAAAGATGAAG
1 TAAAGATGAAG
1793 CTAAAGCTAA
Statistics
Matches: 186, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
185 1 0.01
186 184 0.99
187 1 0.01
ACGTcount: A:0.37, C:0.05, G:0.36, T:0.21
Consensus pattern (186 bp):
TAAAGATGAAGGAAAATTTGGAGGACAGAGAAAGGTCGATGGAAATAGTGGTAGAAGTGATAGCT
CTAGTTATTCTGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGACGCCAGT
GGTAAAGAAAAGAGACAAGATAGAGGAGATGGTAGTGGTAATATAGATGCAAGTGG
Found at i:1761 original size:54 final size:53
Alignment explanation
Indices: 1680--1783 Score: 172
Period size: 54 Copynumber: 1.9 Consensus size: 53
1670 CTGGTGAGGT
* *
1680 AAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCCAGTGGTAGAG
1 AAAAGGACAAGATGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAGAG
*
1733 AAAAGAGACAAGATGGAGGAGATGGTAGTGGTAATATAGATGCAAGTGGTA
1 AAAAG-GACAAGATGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTA
1784 AAGATGAAGC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
53 5 0.11
54 42 0.89
ACGTcount: A:0.38, C:0.06, G:0.38, T:0.18
Consensus pattern (53 bp):
AAAAGGACAAGATGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAGAG
Found at i:1964 original size:54 final size:54
Alignment explanation
Indices: 1890--1995 Score: 176
Period size: 54 Copynumber: 2.0 Consensus size: 54
1880 CTGGTGGGGT
* * * *
1890 AAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAAAAA
1 AAAAGGACAAGGTGAAGGAGATGGTAATGGTAATACAAATGCAAGAGGTAAAAA
1944 AAAAGGACAAGGTGAAGGAGATGGTAATGGTAATACAAATGCAAGAGGTAAA
1 AAAAGGACAAGGTGAAGGAGATGGTAATGGTAATACAAATGCAAGAGGTAAA
1996 GATGAAGCTA
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 48 1.00
ACGTcount: A:0.45, C:0.06, G:0.33, T:0.16
Consensus pattern (54 bp):
AAAAGGACAAGGTGAAGGAGATGGTAATGGTAATACAAATGCAAGAGGTAAAAA
Found at i:2159 original size:54 final size:54
Alignment explanation
Indices: 2100--2207 Score: 171
Period size: 54 Copynumber: 2.0 Consensus size: 54
2090 CCGGTGGGGT
* * * *
2100 AAAAGGACAAGGTGGAGGAGATGGTAGTGGTGACACAGATGCAAGTGGTAAAGA
1 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAACACAAATGCAAGTGGTAAAGA
*
2154 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGA
1 AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAACACAAATGCAAGTGGTAAAGA
2208 TGAAGCTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 49 1.00
ACGTcount: A:0.42, C:0.07, G:0.35, T:0.16
Consensus pattern (54 bp):
AAAAGGACAAGGTCGAGGAGATAGTAGTGGTAACACAAATGCAAGTGGTAAAGA
Found at i:2362 original size:210 final size:209
Alignment explanation
Indices: 1602--2363 Score: 1161
Period size: 210 Copynumber: 3.6 Consensus size: 209
1592 GTGGTAAAGA
* * * *
1602 TGAAGGAAAATTTGGAGGACAGAGAAAGGTCGATGGAAATAGTGGTGGAAGTGATAGCTCTAGTT
1 TGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGTGACAGCTCTAATG
* * * *
1667 ATTCTGGTGAGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCCAGTGGTAGA
66 ATTCCGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAAA
* * *
1732 G-AAAAGAGACAAGATGGAGGAGATGGTAGTGGTAATATAGATGCAAGTGGTAAAGATGAAGCTA
131 GAAAAAG-GACAAGGT-GAGGAGATGGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAGCTA
* *
1796 AAGCTAAAGCTGAAGC
194 AAGATAAAGCTGAAGT
* * * * *
1812 TGGAGGAAATTTTGAAGGACAGGGAAAGGTCGATGGAAATATTGGTGGAAGTGACAGCTCTAGTG
1 TGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGTGACAGCTCTAATG
*
1877 ATTCTGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAAA
66 ATTCCGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAAA
* * *
1942 AAAAAAGGACAAGGTGAAGGAGATGGTAATGGTAATACAAATGCAAGAGGTAAAGATGAAGCTAA
131 GAAAAAGGACAAGGTG-AGGAGATGGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAGCTAA
2007 AGATAAAGCTGAAGT
195 AGATAAAGCTGAAGT
* * * * *
2022 TGAAGGAAAATTTGGAGGGA-AGGGAAAGGTTGATGAAAATAATGGTGGAAATAACAGCTCTAAT
1 TGAAGGAAAATTTGGA-GGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGTGACAGCTCTAAT
* *
2086 GATTCCGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTGACACAGATGCAAGTGGTAA
65 GATTCCGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAA
*
2151 AGAAAAAGGACAAGGTCGAGGAGATAGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAGCTA
130 AGAAAAAGGACAAGGT-GAGGAGATGGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAGCTA
2216 AAGATAAAGCTGAAGT
194 AAGATAAAGCTGAAGT
*
2232 TGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGTGACGGCTCTAATG
1 TGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGTGACAGCTCTAATG
*
2297 ATTCCGGTAGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACA-AGTGCAAGTGGTAA
66 ATTCCGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGA-TGCAAGTGGTAA
2361 AGA
130 AGA
2364 TGAAGCTAAA
Statistics
Matches: 503, Mismatches: 43, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
209 5 0.01
210 489 0.97
211 9 0.02
ACGTcount: A:0.38, C:0.07, G:0.35, T:0.20
Consensus pattern (209 bp):
TGAAGGAAAATTTGGAGGACAGGGAAAGGTCGATGGAAATAGTGGTGGAAGTGACAGCTCTAATG
ATTCCGGTGGGGTAAAAGGACAAGGTGGAGGAGATGGTAGTGGTAATACAGATGCAAGTGGTAAA
GAAAAAGGACAAGGTGAGGAGATGGTAGTGGTAATACAAATGCAAGTGGTAAAGATGAAGCTAAA
GATAAAGCTGAAGT
Found at i:2375 original size:6 final size:6
Alignment explanation
Indices: 2366--2562 Score: 119
Period size: 6 Copynumber: 32.8 Consensus size: 6
2356 GGTAAAGATG
* * * ** * *
2366 AAGCTA AAGCTG AAGCTG AAGCTC AAGCTA AAGCTA AAAATG AAGTTA
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
* * * * * * * *
2414 AAGCTG AAGATG AAGCTC AAGCTA AAGTTA AAGATG AAGCTA AAGCTG
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
* * * * * *
2462 AATCTG AAGCTA AAGCTA AATCTA AAG-AA GAAGCTA AAGTTG AAGCTA
1 AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA -AAGCTA AAGCTA AAGCTA
* * ** * *
2510 AAGCTA AAGCTG AAGCTAA AAG-TG AAGCCG AAGATG AAGCTA AAGCTA
1 AAGCTA AAGCTA AAGCT-A AAGCTA AAGCTA AAGCTA AAGCTA AAGCTA
2558 AAGCT
1 AAGCT
2563 GAAGGAAAGG
Statistics
Matches: 147, Mismatches: 40, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
5 4 0.03
6 139 0.95
7 4 0.03
ACGTcount: A:0.46, C:0.14, G:0.22, T:0.18
Consensus pattern (6 bp):
AAGCTA
Found at i:2379 original size:12 final size:12
Alignment explanation
Indices: 2358--2639 Score: 146
Period size: 12 Copynumber: 23.5 Consensus size: 12
2348 GTGCAAGTGG
*
2358 TAAAGATGAAGC
1 TAAAGCTGAAGC
2370 TAAAGCTGAAGC
1 TAAAGCTGAAGC
* *
2382 TGAAGCTCAAGC
1 TAAAGCTGAAGC
* **
2394 TAAAGCTAAAAA
1 TAAAGCTGAAGC
* * *
2406 TGAAGTTAAAGC
1 TAAAGCTGAAGC
* *
2418 TGAAGATGAAGC
1 TAAAGCTGAAGC
* * *
2430 TCAAGCTAAAGT
1 TAAAGCTGAAGC
*
2442 TAAAGATGAAGC
1 TAAAGCTGAAGC
*
2454 TAAAGCTGAATC
1 TAAAGCTGAAGC
* *
2466 TGAAGCTAAAGC
1 TAAAGCTGAAGC
* *
2478 TAAATCTAAAG-
1 TAAAGCTGAAGC
* * *
2489 AAGAAGCTAAAGT
1 TA-AAGCTGAAGC
* *
2502 TGAAGCTAAAGC
1 TAAAGCTGAAGC
2514 TAAAGCTGAAGC
1 TAAAGCTGAAGC
2526 TAAAAG-TGAAGC
1 T-AAAGCTGAAGC
** *
2538 CGAAGATGAAGC
1 TAAAGCTGAAGC
*
2550 TAAAGCTAAAGC
1 TAAAGCTGAAGC
*
2562 TGAAG--GAAAGGC
1 TAAAGCTG-AA-GC
*
2574 TGAAGCTGAAGC
1 TAAAGCTGAAGC
2586 TGAAA-CTGAAGC
1 T-AAAGCTGAAGC
*
2598 AAAAGCTGAAGC
1 TAAAGCTGAAGC
2610 -AAAGGCTGAAGC
1 TAAA-GCTGAAGC
*
2622 -AAACACTGAAGC
1 TAAA-GCTGAAGC
*
2634 AAAAGC
1 TAAAGC
2640 AAAAGCTGAA
Statistics
Matches: 210, Mismatches: 48, Indels: 24
0.74 0.17 0.09
Matches are distributed among these distances:
11 12 0.06
12 186 0.89
13 11 0.05
14 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (12 bp):
TAAAGCTGAAGC
Found at i:2387 original size:18 final size:18
Alignment explanation
Indices: 2364--2597 Score: 150
Period size: 18 Copynumber: 13.0 Consensus size: 18
2354 GTGGTAAAGA
2364 TGAAGCTAAAGCTGAAGC
1 TGAAGCTAAAGCTGAAGC
* *
2382 TGAAGCTCAAGCTAAAGC
1 TGAAGCTAAAGCTGAAGC
* ** * * *
2400 TAAAAATGAAGTTAAAGC
1 TGAAGCTAAAGCTGAAGC
* * *
2418 TGAAGATGAAGCTCAAGC
1 TGAAGCTAAAGCTGAAGC
* * *
2436 TAAAGTTAAAGATGAAGC
1 TGAAGCTAAAGCTGAAGC
* * *
2454 TAAAGCTGAATCTGAAGC
1 TGAAGCTAAAGCTGAAGC
* * * *
2472 TAAAGCTAAATCTAAAGA
1 TGAAGCTAAAGCTGAAGC
* *
2490 AGAAGCTAAAGTTGAAGC
1 TGAAGCTAAAGCTGAAGC
*
2508 TAAAGCTAAAGCTGAAGC
1 TGAAGCTAAAGCTGAAGC
* * * *
2526 TAAAAG-TGAAGCCGAAGA
1 T-GAAGCTAAAGCTGAAGC
*
2544 TGAAGCTAAAGCTAAAGC
1 TGAAGCTAAAGCTGAAGC
*
2562 TGAAG-GAAAGGCTGAAGC
1 TGAAGCTAAA-GCTGAAGC
2580 TGAAGCTGAAA-CTGAAGC
1 TGAAGCT-AAAGCTGAAGC
2598 AAAAGCTGAA
Statistics
Matches: 168, Mismatches: 43, Indels: 10
0.76 0.19 0.05
Matches are distributed among these distances:
17 6 0.04
18 155 0.92
19 4 0.02
20 3 0.02
ACGTcount: A:0.44, C:0.14, G:0.24, T:0.18
Consensus pattern (18 bp):
TGAAGCTAAAGCTGAAGC
Found at i:2422 original size:42 final size:42
Alignment explanation
Indices: 2358--2609 Score: 247
Period size: 42 Copynumber: 6.0 Consensus size: 42
2348 GTGCAAGTGG
* *
2358 TAAAGATGAAGCTAAAGCTGAAGCTGAAGCTCAAGCTAAAGC
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* * * *
2400 TAAAAATGAAGTTAAAGCTGAAGATGAAGCTCAAGCTAAAGT
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* * *
2442 TAAAGATGAAGCTAAAGCTGAATCTGAAGCTAAAGCTAAATC
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* * *
2484 TAAAGAA-GAAGCTAAAGTTGAAGCTAAAGCTAAAGCTGAAGC
1 TAAA-AATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* ** * * *
2526 TAAAAGTGAAGCCGAAGATGAAGCTAAAGCTAAAGCTGAAG-
1 TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
* ** * * * *
2567 GAAAGGCTGAAGCTGAAGCTGAAACTGAAGCAAAAGCTGAAGC
1 TAAA-AATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
2610 AAAGGCTGAA
Statistics
Matches: 177, Mismatches: 29, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
41 4 0.02
42 172 0.97
43 1 0.01
ACGTcount: A:0.45, C:0.13, G:0.24, T:0.17
Consensus pattern (42 bp):
TAAAAATGAAGCTAAAGCTGAAGCTGAAGCTAAAGCTAAAGC
Found at i:2614 original size:42 final size:43
Alignment explanation
Indices: 2364--2649 Score: 235
Period size: 42 Copynumber: 6.8 Consensus size: 43
2354 GTGGTAAAGA
* * * **
2364 TGAAGCTAAAGCTGAAGCTGAAGCTCAAGCTAAAGCTAAA-AA
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * * * * * *
2406 TGAAGTTAAAGCTGAAGATGAAGCTCAAGCTAAAGTTAAA-GA
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * * * *
2448 TGAAGCTAAAGCTGAATCTGAAGCTAAAGCTAAATCTAAA-GA
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * *
2490 AGAAGCTAAAGTTGAAGCTAAAGCTAAAGCTGAAGCTAAAAG-
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
** * *
2532 TGAAGCCGAAGATGAAGCTAAAGCTAAAGCTGAAG-GAAAGGC
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * * *
2574 TGAAGCTGAAGCTGAAACTGAAGCAAAAGCTGAAGC-AAAGGC
1 TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
* * *
2616 TGAAGC-AAACACTGAAGCAAAAGCAAAAGCTGAA
1 TGAAGCTAAA-GCTGAAGCTAAAGCTAAAGCTGAA
2650 ATAGGAGGAC
Statistics
Matches: 208, Mismatches: 32, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
41 6 0.03
42 201 0.97
43 1 0.00
ACGTcount: A:0.46, C:0.14, G:0.24, T:0.16
Consensus pattern (43 bp):
TGAAGCTAAAGCTGAAGCTAAAGCTAAAGCTGAAGCTAAAGGC
Found at i:2645 original size:24 final size:24
Alignment explanation
Indices: 2594--2645 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
2584 GCTGAAACTG
* **
2594 AAGCAAAAGCTGAAGCAAAGGCTG
1 AAGCAAAAGCTGAAGCAAAAGCAA
2618 AAGCAAACA-CTGAAGCAAAAGCAA
1 AAGCAAA-AGCTGAAGCAAAAGCAA
2642 AAGC
1 AAGC
2646 TGAAATAGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 23 0.96
25 1 0.04
ACGTcount: A:0.52, C:0.19, G:0.23, T:0.06
Consensus pattern (24 bp):
AAGCAAAAGCTGAAGCAAAAGCAA
Found at i:2709 original size:6 final size:6
Alignment explanation
Indices: 2691--2816 Score: 94
Period size: 6 Copynumber: 21.0 Consensus size: 6
2681 GTGGTGGTGG
* * * *
2691 TGAAGC CGAAGC TGAAGC TAAAGC TAAAGC TGAAG- -GAAAGGC TAAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TG-AA-GC TGAAGC
** * ** *
2739 TGAAGC TGAAGC CAAAGC TGAAGC GGAAGC AAAAGC CGAAGC TGAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC
** * *
2787 TGAAGC AAAAGC CGAAGC TGAAGC CGAAGC
1 TGAAGC TGAAGC TGAAGC TGAAGC TGAAGC
2817 AAACACCGAA
Statistics
Matches: 94, Mismatches: 22, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
4 1 0.01
5 2 0.02
6 89 0.95
7 2 0.02
ACGTcount: A:0.40, C:0.20, G:0.30, T:0.10
Consensus pattern (6 bp):
TGAAGC
Found at i:2720 original size:18 final size:18
Alignment explanation
Indices: 2699--2816 Score: 105
Period size: 18 Copynumber: 6.6 Consensus size: 18
2689 GGTGAAGCCG
*
2699 AAGCTGAAGCTAAAGCTA
1 AAGCTGAAGCTGAAGCTA
2717 AAGCTGAAG--GAAAGGCTA
1 AAGCTGAAGCTG-AA-GCTA
*
2735 AAGCTGAAGCTGAAGCCA
1 AAGCTGAAGCTGAAGCTA
* *
2753 AAGCTGAAGCGGAAGCAA
1 AAGCTGAAGCTGAAGCTA
* *
2771 AAGCCGAAGCTGAAGCTG
1 AAGCTGAAGCTGAAGCTA
** * *
2789 AAGCAAAAGCCGAAGCTG
1 AAGCTGAAGCTGAAGCTA
*
2807 AAGCCGAAGC
1 AAGCTGAAGC
2817 AAACACCGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
17 2 0.02
18 78 0.94
19 2 0.02
20 1 0.01
ACGTcount: A:0.42, C:0.19, G:0.30, T:0.09
Consensus pattern (18 bp):
AAGCTGAAGCTGAAGCTA
Found at i:2804 original size:36 final size:36
Alignment explanation
Indices: 2693--2874 Score: 128
Period size: 36 Copynumber: 5.2 Consensus size: 36
2683 GGTGGTGGTG
* * *
2693 AAGCCGAAGCTGAAGCTAAAGCTAAAGCTGAAGGAA
1 AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
* ** *
2729 AGGCTAAAGCTGAAGCTGAAGCCAAAGCTGAAGC--
1 AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
** * **
2763 --G--GAAGCAAAAGCCGAAGCTGAAGCTGAAGCAA
1 AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
* *
2795 AAGCCGAAGCTGAAGCCGAAGCAAACA-CCGAAGCAA
1 AAGCCGAAGCTGAAGCTGAAGCAAA-AGCTGAAGCAA
* * * *
2831 AAGCCAAAGC-AAAGGCTGAAGCAAAGGCCGAAGCAA
1 AAGCCGAAGCTGAA-GCTGAAGCAAAAGCTGAAGCAA
2867 AAGCCGAA
1 AAGCCGAA
2875 ATAGGAGGAC
Statistics
Matches: 115, Mismatches: 22, Indels: 18
0.74 0.14 0.12
Matches are distributed among these distances:
30 23 0.20
32 1 0.01
34 1 0.01
35 2 0.02
36 87 0.76
37 1 0.01
ACGTcount: A:0.44, C:0.21, G:0.28, T:0.07
Consensus pattern (36 bp):
AAGCCGAAGCTGAAGCTGAAGCAAAAGCTGAAGCAA
Found at i:2817 original size:24 final size:24
Alignment explanation
Indices: 2747--2874 Score: 143
Period size: 24 Copynumber: 5.3 Consensus size: 24
2737 GCTGAAGCTG
* *
2747 AAGCCAAAGCTGAAGCGGAAGCAA
1 AAGCCGAAGCTGAAGCCGAAGCAA
*
2771 AAGCCGAAGCTGAAGCTGAAGCAA
1 AAGCCGAAGCTGAAGCCGAAGCAA
2795 AAGCCGAAGCTGAAGCCGAAGCAA
1 AAGCCGAAGCTGAAGCCGAAGCAA
** *
2819 ACA-CCGAAGCAAAAGCCAAAGCAA
1 A-AGCCGAAGCTGAAGCCGAAGCAA
* * *
2843 AGGCTGAAGC-AAAGGCCGAAGCAA
1 AAGCCGAAGCTGAA-GCCGAAGCAA
2867 AAGCCGAA
1 AAGCCGAA
2875 ATAGGAGGAC
Statistics
Matches: 90, Mismatches: 11, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
23 3 0.03
24 86 0.96
25 1 0.01
ACGTcount: A:0.45, C:0.23, G:0.27, T:0.04
Consensus pattern (24 bp):
AAGCCGAAGCTGAAGCCGAAGCAA
Found at i:2872 original size:12 final size:12
Alignment explanation
Indices: 2759--2874 Score: 126
Period size: 12 Copynumber: 9.7 Consensus size: 12
2749 GCCAAAGCTG
*
2759 AAGCGGAAGCAA
1 AAGCCGAAGCAA
**
2771 AAGCCGAAGCTG
1 AAGCCGAAGCAA
*
2783 AAGCTGAAGCAA
1 AAGCCGAAGCAA
**
2795 AAGCCGAAGCTG
1 AAGCCGAAGCAA
2807 AAGCCGAAGCAA
1 AAGCCGAAGCAA
2819 ACA-CCGAAGCAA
1 A-AGCCGAAGCAA
*
2831 AAGCCAAAGCAA
1 AAGCCGAAGCAA
* *
2843 AGGCTGAAGCAA
1 AAGCCGAAGCAA
*
2855 AGGCCGAAGCAA
1 AAGCCGAAGCAA
2867 AAGCCGAA
1 AAGCCGAA
2875 ATAGGAGGAC
Statistics
Matches: 85, Mismatches: 17, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
11 1 0.01
12 83 0.98
13 1 0.01
ACGTcount: A:0.46, C:0.23, G:0.28, T:0.03
Consensus pattern (12 bp):
AAGCCGAAGCAA
Done.