Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167943.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_204, 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: 51768
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.35
Found at i:1326 original size:32 final size:32
Alignment explanation
Indices: 1290--1386 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 32
1280 ATTTTTTTGA
1290 AACTTTGATTTTCAAGAAAAATTGATACTTTC
1 AACTTTGATTTTCAAGAAAAATTGATACTTTC
* * * ** *
1322 AAC--T--TTTCCCA-AAAAA-TGTTTTTTTGA
1 AACTTTGATTTTCAAGAAAAATTGATACTTT-C
*
1349 AACTTTGATTTTCAAGGAAAATTGATACTTTC
1 AACTTTGATTTTCAAGAAAAATTGATACTTTC
1381 AACTTT
1 AACTTT
1387 TCTCCAAAAT
Statistics
Matches: 45, Mismatches: 13, Indels: 14
0.62 0.18 0.19
Matches are distributed among these distances:
26 6 0.13
27 8 0.18
28 5 0.11
29 1 0.02
30 1 0.02
31 5 0.11
32 13 0.29
33 6 0.13
ACGTcount: A:0.35, C:0.13, G:0.09, T:0.42
Consensus pattern (32 bp):
AACTTTGATTTTCAAGAAAAATTGATACTTTC
Found at i:1403 original size:59 final size:58
Alignment explanation
Indices: 1069--1405 Score: 453
Period size: 59 Copynumber: 5.7 Consensus size: 58
1059 TTTTGTGCAA
* * * *
1069 GAAAATTGATACTTTCAACTTTTTCCAAAAAAATATTCTTTTGAAACTTTAATTTCGAG
1 GAAAATTGATACTTTCAAC-TTTTCCCAAAAAATATTTTTTTGAAACTTTATTTTCAAG
* ** * *
1128 GAAAATTGATACTTTCAACTTTTTCTCAAAAGTTTATTTTTTTGAAAATTTATTTTTAAG
1 GAAAATTGATACTTTCAAC-TTTTCCCAAAA-AATATTTTTTTGAAACTTTATTTTCAAG
* *
1188 GAAAATTGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTGAAATTTTATTTTTAAG
1 GAAAATTGATACTTTCAACTTTTCC-CAAAAAATATTTTTTTGAAACTTTATTTTCAAG
*
1246 GAAAGTTGATACTTTCAACTTTTCCCAAAAAAATATTTTTTTGAAACTTTGATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCC-AAAAAATATTTTTTTGAAACTTT-ATTTTCAAG
* *
1306 AAAAATTGATACTTTCAACTTTTCCCAAAAAATGTTTTTTTGAAACTTTGATTTTCAAG
1 GAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTGAAACTTT-ATTTTCAAG
*
1365 GAAAATTGATACTTTCAACTTTTCTCC-AAAATTATTTTTTT
1 GAAAATTGATACTTTCAACTTTTC-CCAAAAAATATTTTTTT
1406 TTATTTTTAT
Statistics
Matches: 250, Mismatches: 22, Indels: 12
0.88 0.08 0.04
Matches are distributed among these distances:
57 1 0.00
58 49 0.20
59 125 0.50
60 75 0.30
ACGTcount: A:0.35, C:0.12, G:0.08, T:0.45
Consensus pattern (58 bp):
GAAAATTGATACTTTCAACTTTTCCCAAAAAATATTTTTTTGAAACTTTATTTTCAAG
Found at i:1440 original size:13 final size:12
Alignment explanation
Indices: 1422--1492 Score: 60
Period size: 13 Copynumber: 6.1 Consensus size: 12
1412 TTATTTAAAG
*
1422 AAAATAGAATAA
1 AAAATAAAATAA
1434 TAAAATAAAATAA
1 -AAAATAAAATAA
*
1447 AAAAT--GATAA
1 AAAATAAAATAA
*
1457 AAAAGAAAAGTAA
1 AAAATAAAA-TAA
*
1470 AACA-AAAAT-A
1 AAAATAAAATAA
1480 AAAATAAAATAA
1 AAAATAAAATAA
1492 A
1 A
1493 GATAAAAAGA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
10 12 0.26
11 6 0.13
12 12 0.26
13 17 0.36
ACGTcount: A:0.77, C:0.01, G:0.06, T:0.15
Consensus pattern (12 bp):
AAAATAAAATAA
Found at i:1497 original size:17 final size:17
Alignment explanation
Indices: 1432--1500 Score: 56
Period size: 17 Copynumber: 4.1 Consensus size: 17
1422 AAAATAGAAT
1432 AATAAAATAAA-ATAAAA
1 AATAAAATAAAGAT-AAA
1449 AATGATAAA-AAAG--AAA
1 AAT-A-AAATAAAGATAAA
* * *
1465 AGTAAAACAAAAATAAA
1 AATAAAATAAAGATAAA
1482 AATAAAATAAAGATAAA
1 AATAAAATAAAGATAAA
1499 AA
1 AA
1501 GAATATTAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 12
0.71 0.09 0.21
Matches are distributed among these distances:
14 3 0.07
15 4 0.10
16 5 0.12
17 22 0.54
18 4 0.10
19 3 0.07
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (17 bp):
AATAAAATAAAGATAAA
Found at i:1542 original size:4 final size:4
Alignment explanation
Indices: 1535--1560 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1525 TAAATAAATA
1535 AATT AATT AATT AATT AATT AATT AA
1 AATT AATT AATT AATT AATT AATT AA
1561 AAAAAAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (4 bp):
AATT
Found at i:2133 original size:25 final size:23
Alignment explanation
Indices: 2093--2143 Score: 66
Period size: 25 Copynumber: 2.1 Consensus size: 23
2083 TCGAAATCTG
* *
2093 AAAATTTTCCAGAAATTTCTAAA
1 AAAATTTTCCAAAAATCTCTAAA
2116 AAAAGTTTTGCCAAAAATCTCTAAA
1 AAAA-TTTT-CCAAAAATCTCTAAA
2141 AAA
1 AAA
2144 TTATTTTCGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 16 0.67
ACGTcount: A:0.51, C:0.14, G:0.06, T:0.29
Consensus pattern (23 bp):
AAAATTTTCCAAAAATCTCTAAA
Found at i:2515 original size:24 final size:21
Alignment explanation
Indices: 2431--2617 Score: 102
Period size: 22 Copynumber: 8.6 Consensus size: 21
2421 CCAGCCTTTC
* *
2431 AAAATAAAAATCAGATAAAATA
1 AAAATAATAATAAGAT-AAATA
*
2453 AAAA-AATTTAAT-AGATAATTAGA
1 AAAATAA--TAATAAGATAA--ATA
2476 AAAATAATAATAAGATAAATCA
1 AAAATAATAATAAGATAAAT-A
*
2498 ACAATAATATTATAAGATAAATA
1 AAAATAATA--ATAAGATAAATA
*
2521 AAAATAATAATAACAT--ATA
1 AAAATAATAATAAGATAAATA
*
2540 AATAATTATATAATTAGATAAATA
1 AA-AA-TA-ATAATAAGATAAATA
*
2564 AAAATACAT-ATAAAATAAAATGA
1 AAAATA-ATAATAAGAT-AAAT-A
* * *
2587 AAAAGAA-AATAA-AAAAAGA
1 AAAATAATAATAAGATAAATA
2606 AAAATAA-AATAA
1 AAAATAATAATAA
2618 AAAATATATT
Statistics
Matches: 133, Mismatches: 15, Indels: 37
0.72 0.08 0.20
Matches are distributed among these distances:
19 17 0.13
20 5 0.04
21 19 0.14
22 42 0.32
23 32 0.24
24 18 0.14
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (21 bp):
AAAATAATAATAAGATAAATA
Found at i:2540 original size:23 final size:22
Alignment explanation
Indices: 2475--2654 Score: 99
Period size: 23 Copynumber: 8.1 Consensus size: 22
2465 AGATAATTAG
2475 AAAAATAATAAT-AAGATAAAT
1 AAAAATAATAATAAAGATAAAT
* *
2496 CAACAATAATATTATAAGATAAAT
1 -AAAAATAATAATA-AAGATAAAT
*
2520 AAAAATAATAATAACATATAAAT
1 AAAAATAATAATAA-AGATAAAT
** *
2543 AATTAT-ATAAT-TAGATAAAT
1 AAAAATAATAATAAAGATAAAT
2563 AAAAATACAT-ATAAA-ATAAAAT
1 AAAAATA-ATAATAAAGAT-AAAT
* *
2585 GAAAAAGAA-AATAAA-A-AAAG
1 -AAAAATAATAATAAAGATAAAT
* *
2605 AAAAATAA-AATAAAAAATATATT
1 AAAAATAATAAT-AAAGATA-AAT
* *
2628 AATAAATAGTAATAATAAATAAAT
1 AA-AAATAATAATAA-AGATAAAT
2652 AAA
1 AAA
2655 TACATAGGAT
Statistics
Matches: 123, Mismatches: 19, Indels: 31
0.71 0.11 0.18
Matches are distributed among these distances:
19 10 0.08
20 17 0.14
21 5 0.04
22 31 0.25
23 32 0.26
24 20 0.16
25 8 0.07
ACGTcount: A:0.69, C:0.02, G:0.04, T:0.25
Consensus pattern (22 bp):
AAAAATAATAATAAAGATAAAT
Found at i:2568 original size:43 final size:44
Alignment explanation
Indices: 2475--2569 Score: 120
Period size: 43 Copynumber: 2.2 Consensus size: 44
2465 AGATAATTAG
* * *
2475 AAAAATAATAATAAGATAAATCAACAATAATATTATAAGATAAAT
1 AAAAATAATAATAACAT-AATAAACAATAATATAATAAGATAAAT
* * *
2520 AAAAATAATAATAACAT-ATAAATAATTATATAATTAGATAAAT
1 AAAAATAATAATAACATAATAAACAATAATATAATAAGATAAAT
2563 AAAAATA
1 AAAAATA
2570 CATATAAAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
43 28 0.64
45 16 0.36
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.28
Consensus pattern (44 bp):
AAAAATAATAATAACATAATAAACAATAATATAATAAGATAAAT
Found at i:2607 original size:19 final size:19
Alignment explanation
Indices: 2580--2621 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
2570 CATATAAAAT
*
2580 AAAATGAAAAAGAAAATAA
1 AAAAAGAAAAAGAAAATAA
*
2599 AAAAAGAAAAATAAAATAA
1 AAAAAGAAAAAGAAAATAA
2618 AAAA
1 AAAA
2622 TATATTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.83, C:0.00, G:0.07, T:0.10
Consensus pattern (19 bp):
AAAAAGAAAAAGAAAATAA
Found at i:2609 original size:14 final size:13
Alignment explanation
Indices: 2586--2623 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
2576 AAATAAAATG
2586 AAAAAGAAAATAA
1 AAAAAGAAAATAA
2599 AAAAAGAAAAATAA
1 AAAAAG-AAAATAA
*
2613 AATAA-AAAATA
1 AAAAAGAAAATA
2624 TATTAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
12 6 0.26
13 6 0.26
14 11 0.48
ACGTcount: A:0.84, C:0.00, G:0.05, T:0.11
Consensus pattern (13 bp):
AAAAAGAAAATAA
Found at i:2645 original size:13 final size:12
Alignment explanation
Indices: 2517--2653 Score: 52
Period size: 12 Copynumber: 11.2 Consensus size: 12
2507 TTATAAGATA
*
2517 AATAAAAATAAT
1 AATAAATATAAT
2529 AATAACATATAAAT
1 AATAA-ATAT-AAT
*
2543 AAT-TATATAATT
1 AATAAATATAA-T
2555 AGATAAATA-AA-
1 A-ATAAATATAAT
*
2566 AATACATATAA-
1 AATAAATATAAT
*
2577 AATAAA-ATGAAA
1 AATAAATAT-AAT
* * *
2589 AAGAAAATAAAAAA
1 AA-TAAAT-ATAAT
* *
2603 AGAAAAATAAAAT
1 A-ATAAATATAAT
* *
2616 AAAAAATATATT
1 AATAAATATAAT
2628 AATAAATAGTAAT
1 AATAAATA-TAAT
2641 AATAAATA-AAT
1 AATAAATATAAT
2652 AA
1 AA
2654 ATACATAGGA
Statistics
Matches: 100, Mismatches: 12, Indels: 27
0.72 0.09 0.19
Matches are distributed among these distances:
10 8 0.08
11 17 0.17
12 29 0.29
13 26 0.26
14 18 0.18
15 2 0.02
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.25
Consensus pattern (12 bp):
AATAAATATAAT
Found at i:2656 original size:25 final size:25
Alignment explanation
Indices: 2613--2661 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
2603 AGAAAAATAA
* *
2613 AATAAAAAATATATTAATAAATAGT
1 AATAAAAAATAAATAAATAAATAGT
* *
2638 AATAATAAATAAATAAATACATAG
1 AATAAAAAATAAATAAATAAATAG
2662 GATATAAAGG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.65, C:0.02, G:0.04, T:0.29
Consensus pattern (25 bp):
AATAAAAAATAAATAAATAAATAGT
Found at i:5343 original size:16 final size:16
Alignment explanation
Indices: 5318--5350 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5308 TTTTATCTTT
5318 TATGTGAATTTTAATA
1 TATGTGAATTTTAATA
*
5334 TATGTTAATTTTAATA
1 TATGTGAATTTTAATA
5350 T
1 T
5351 TAATTGAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (16 bp):
TATGTGAATTTTAATA
Found at i:6281 original size:19 final size:19
Alignment explanation
Indices: 6247--6326 Score: 99
Period size: 19 Copynumber: 4.2 Consensus size: 19
6237 CTTCTTAATT
* *
6247 TAAACTAAATCTTAAACCC
1 TAAACCAAATCCTAAACCC
* *
6266 TAAATCAAA-CTCTAAACCT
1 TAAACCAAATC-CTAAACCC
*
6285 TAAACCAAATCCTAAATCC
1 TAAACCAAATCCTAAACCC
6304 TAAACCAAATCCTAAACCC
1 TAAACCAAATCCTAAACCC
6323 TAAA
1 TAAA
6327 TTATCTCTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
18 1 0.02
19 49 0.96
20 1 0.02
ACGTcount: A:0.49, C:0.29, G:0.00, T:0.23
Consensus pattern (19 bp):
TAAACCAAATCCTAAACCC
Found at i:7645 original size:31 final size:31
Alignment explanation
Indices: 7607--7668 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
7597 GTCCATAGAG
7607 ATTTTTCAATTCAAGAATTTCTAAACTAATT
1 ATTTTTCAATTCAAGAATTTCTAAACTAATT
7638 ATTTTTCAATTCAAGAATTTCTAAACTAATT
1 ATTTTTCAATTCAAGAATTTCTAAACTAATT
7669 CTTTATTGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.13, G:0.03, T:0.45
Consensus pattern (31 bp):
ATTTTTCAATTCAAGAATTTCTAAACTAATT
Found at i:9307 original size:30 final size:30
Alignment explanation
Indices: 9271--9345 Score: 141
Period size: 30 Copynumber: 2.5 Consensus size: 30
9261 TGATTAATTA
9271 TAACTTAAAATAATTTCACTTTAGTCTTTG
1 TAACTTAAAATAATTTCACTTTAGTCTTTG
*
9301 TAACTTAAAATAATTTCATTTTAGTCTTTG
1 TAACTTAAAATAATTTCACTTTAGTCTTTG
9331 TAACTTAAAATAATT
1 TAACTTAAAATAATT
9346 GATATTTATA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.37, C:0.11, G:0.05, T:0.47
Consensus pattern (30 bp):
TAACTTAAAATAATTTCACTTTAGTCTTTG
Found at i:14202 original size:36 final size:37
Alignment explanation
Indices: 14162--14231 Score: 133
Period size: 36 Copynumber: 1.9 Consensus size: 37
14152 TAAATATGCC
14162 ACTTGATCTATTTAAAAGAGAAATGCA-GAAAAAGCT
1 ACTTGATCTATTTAAAAGAGAAATGCAGGAAAAAGCT
14198 ACTTGATCTATTTAAAAGAGAAATGCAGGAAAAA
1 ACTTGATCTATTTAAAAGAGAAATGCAGGAAAAA
14232 CTAGATTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 27 0.82
37 6 0.18
ACGTcount: A:0.49, C:0.10, G:0.17, T:0.24
Consensus pattern (37 bp):
ACTTGATCTATTTAAAAGAGAAATGCAGGAAAAAGCT
Found at i:15201 original size:26 final size:25
Alignment explanation
Indices: 15162--15221 Score: 75
Period size: 26 Copynumber: 2.4 Consensus size: 25
15152 ATATATAAAC
* **
15162 AAATATAAATATATTTTTTAAAAAT
1 AAATATAAAAATATTTAGTAAAAAT
*
15187 AAATAATAAAAATATTTAGTAAATAT
1 AAAT-ATAAAAATATTTAGTAAAAAT
15213 AAATATAAA
1 AAATATAAA
15222 TTAAAGGCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 9 0.30
26 21 0.70
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (25 bp):
AAATATAAAAATATTTAGTAAAAAT
Found at i:15862 original size:16 final size:16
Alignment explanation
Indices: 15814--15910 Score: 53
Period size: 15 Copynumber: 6.1 Consensus size: 16
15804 TGATTTATTT
15814 ATTTTTATATAAATTATA
1 ATTTTTAT-TAAA-TATA
*
15832 ATTTAATTATAAAATATA
1 ATTT--TTATTAAATATA
*
15850 GTTTTTATTAAAT-TA
1 ATTTTTATTAAATATA
** *
15865 A--AATATCAAATA-A
1 ATTTTTATTAAATATA
15878 TATTTTTATT-AATATA
1 -ATTTTTATTAAATATA
*
15894 ATATTTA-TAAATATA
1 ATTTTTATTAAATATA
15909 AT
1 AT
15911 AAATAATAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 19
0.67 0.12 0.21
Matches are distributed among these distances:
13 8 0.13
14 2 0.03
15 20 0.33
16 12 0.20
18 11 0.18
19 3 0.05
20 4 0.07
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (16 bp):
ATTTTTATTAAATATA
Found at i:16216 original size:14 final size:15
Alignment explanation
Indices: 16190--16218 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
16180 TGTATTGAAT
16190 TAAAATATTAAATAA
1 TAAAATATTAAATAA
16205 TAAAAT-TTAAATAA
1 TAAAATATTAAATAA
16219 ATTATATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAAAATATTAAATAA
Found at i:16235 original size:28 final size:27
Alignment explanation
Indices: 16194--16247 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
16184 TTGAATTAAA
*
16194 ATATTAAATAATAAAATTTAAATAAATT
1 ATATTAAATAATAAAA-GTAAATAAATT
16222 ATATATAAAT-ATAAAAGTAAATAAAT
1 ATAT-TAAATAATAAAAGTAAATAAAT
16248 AAATAATTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 9 0.38
28 10 0.42
29 5 0.21
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (27 bp):
ATATTAAATAATAAAAGTAAATAAATT
Found at i:16416 original size:14 final size:16
Alignment explanation
Indices: 16399--16430 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
16389 AAGATATAAA
16399 TTATTTT-ATT-ATTT
1 TTATTTTAATTGATTT
16413 TTATTTTAATTGATTT
1 TTATTTTAATTGATTT
16429 TT
1 TT
16431 TATTATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.22, C:0.00, G:0.03, T:0.75
Consensus pattern (16 bp):
TTATTTTAATTGATTT
Found at i:16477 original size:25 final size:24
Alignment explanation
Indices: 16449--16519 Score: 63
Period size: 25 Copynumber: 2.8 Consensus size: 24
16439 AATTATATAA
*
16449 AAAAAGTAAAAATAAAATAATTTTT
1 AAAAAGTAAAAATAAAA-AATTTTG
16474 AAAAA-TCCAAAAAATAAAAAATTTTG
1 AAAAAGT---AAAAATAAAAAATTTTG
* *
16500 AAAAGGAAATAAATAAAAAA
1 AAAAAGTAA-AAATAAAAAA
16520 ACAAAAGTAA
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
24 3 0.08
25 15 0.39
26 10 0.26
27 10 0.26
ACGTcount: A:0.69, C:0.03, G:0.06, T:0.23
Consensus pattern (24 bp):
AAAAAGTAAAAATAAAAAATTTTG
Found at i:17636 original size:22 final size:22
Alignment explanation
Indices: 17605--17659 Score: 56
Period size: 24 Copynumber: 2.4 Consensus size: 22
17595 ATGATAGTTT
*
17605 ATTAAAATATTAAAAATATCAA
1 ATTAATATATTAAAAATATCAA
***
17627 ATTAATATATATTTTTAATATCAA
1 ATT-A-ATATATTAAAAATATCAA
17651 ATTAATATA
1 ATTAATATA
17660 AATTATATTA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 8 0.30
23 2 0.07
24 17 0.63
ACGTcount: A:0.55, C:0.04, G:0.00, T:0.42
Consensus pattern (22 bp):
ATTAATATATTAAAAATATCAA
Found at i:17715 original size:19 final size:18
Alignment explanation
Indices: 17682--17719 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
17672 ATATTACTTA
*
17682 TAAAAAAATTTTATAATT
1 TAAAAAAATTATATAATT
17700 TAAAATAAATTATATAATT
1 TAAAA-AAATTATATAATT
17719 T
1 T
17720 TAATTATCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAAAAAAATTATATAATT
Found at i:19900 original size:23 final size:22
Alignment explanation
Indices: 19851--19922 Score: 72
Period size: 22 Copynumber: 3.1 Consensus size: 22
19841 TAATTTTAAT
* *
19851 TTTTAAAATACTATAATGTTAAAA
1 TTTTAAAATA-TAT-TTTTTAAAA
** *
19875 TTTTAATGTATTATTTTTTAATA
1 TTTTAAAATA-TATTTTTTAAAA
19898 TTTTAAAATATATTTTTTAAAA
1 TTTTAAAATATATTTTTTAAAA
19920 TTT
1 TTT
19923 CGAGCCTCCC
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
22 14 0.36
23 14 0.36
24 11 0.28
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (22 bp):
TTTTAAAATATATTTTTTAAAA
Found at i:20895 original size:21 final size:21
Alignment explanation
Indices: 20813--20897 Score: 62
Period size: 21 Copynumber: 4.0 Consensus size: 21
20803 TAGTATGAGT
* * *
20813 CATAGTGATGGGTCATCGTAC
1 CATAGTAATGAGTCATTGTAC
* * * *
20834 CATAAGTGATAAGTCACTATAC
1 CAT-AGTAATGAGTCATTGTAC
* ** *
20856 CATAATAATGAACCTTTGTAC
1 CATAGTAATGAGTCATTGTAC
20877 CATAGTAATGAGTCATTGTAC
1 CATAGTAATGAGTCATTGTAC
20898 TTTAGTTATG
Statistics
Matches: 46, Mismatches: 17, Indels: 2
0.71 0.26 0.03
Matches are distributed among these distances:
21 30 0.65
22 16 0.35
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.31
Consensus pattern (21 bp):
CATAGTAATGAGTCATTGTAC
Found at i:20903 original size:21 final size:21
Alignment explanation
Indices: 20879--20924 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
20869 CTTTGTACCA
* *
20879 TAGTAATGAGTCATTGTACTT
1 TAGTAATGACTCACTGTACTT
* *
20900 TAGTTATGACTCACTGTCCTT
1 TAGTAATGACTCACTGTACTT
20921 TAGT
1 TAGT
20925 CTTATCCTAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.43
Consensus pattern (21 bp):
TAGTAATGACTCACTGTACTT
Found at i:29285 original size:20 final size:21
Alignment explanation
Indices: 29230--29279 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
29220 TGTTTGATTC
29230 AAAATAATTTAATTTCGAAGA
1 AAAATAATTTAATTTCGAAGA
29251 AAAATAATTTAATTTCGAAGA
1 AAAATAATTTAATTTCGAAGA
29272 AAAATAAT
1 AAAATAAT
29280 AAATTTTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.56, C:0.04, G:0.08, T:0.32
Consensus pattern (21 bp):
AAAATAATTTAATTTCGAAGA
Found at i:29287 original size:21 final size:21
Alignment explanation
Indices: 29230--29285 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
29220 TGTTTGATTC
*
29230 AAAATAATTTAATTTCGAAGA
1 AAAATAATTAAATTTCGAAGA
*
29251 AAAATAATTTAATTTCGAAGA
1 AAAATAATTAAATTTCGAAGA
29272 AAAATAA-TAAATTT
1 AAAATAATTAAATTT
29286 TCAATAGTAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
20 6 0.18
21 28 0.82
ACGTcount: A:0.55, C:0.04, G:0.07, T:0.34
Consensus pattern (21 bp):
AAAATAATTAAATTTCGAAGA
Found at i:30028 original size:62 final size:62
Alignment explanation
Indices: 29955--30180 Score: 199
Period size: 62 Copynumber: 3.6 Consensus size: 62
29945 TCAAATGATC
* *
29955 ATTTAAG-CATTTTTGGACTAAAAATGTCTTAAATAATCCCTTGATACATTTTAAGAGGATT
1 ATTTAAGACATTTTTGGACCAAAAATATCTTAAATAATCCCTTGATACATTTTAAGAGGATT
* * * * **
30016 ATTTAAGACATTTTT-TATCCAAAAATACCTTAAATAATCTCTTTATATTTTTTAA-AGGACATT
1 ATTTAAGACATTTTTGGA-CCAAAAATATCTTAAATAATCCCTTGATACATTTTAAGAGG--ATT
* * ** * *
30079 GTTTAAGGCATTTTTGGATAAAAAATATATCTTAAATAATTCCC-CGATACATTTTAAAGGGGAT
1 ATTTAAGACATTTTTGGA-CCAAAA-ATATCTTAAATAA-TCCCTTGATACATTTT-AAGAGGAT
30143 T
62 T
* * * *
30144 ATTTAATATATTTTTGAACCAAAAACATCTTAAATAA
1 ATTTAAGACATTTTTGGACCAAAAATATCTTAAATAA
30181 ATGTCATTTA
Statistics
Matches: 128, Mismatches: 28, Indels: 16
0.74 0.16 0.09
Matches are distributed among these distances:
61 11 0.09
62 37 0.29
63 28 0.22
64 10 0.08
65 35 0.27
66 5 0.04
67 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.40
Consensus pattern (62 bp):
ATTTAAGACATTTTTGGACCAAAAATATCTTAAATAATCCCTTGATACATTTTAAGAGGATT
Found at i:30149 original size:65 final size:61
Alignment explanation
Indices: 29955--30149 Score: 171
Period size: 65 Copynumber: 3.1 Consensus size: 61
29945 TCAAATGATC
* *
29955 ATTTAA-GCATTTTTGGACTAAAAATGTCTTAAATAATCCCTTGATACATTTT-AAGAGGATT
1 ATTTAAGGCATTTTTGGA-TAAAAATATCTTAAATAATCCC-TGATACATTTTAAAGGGGATT
* * * * * ** **
30016 ATTTAAGACATTTTT-TATCCAAAAATACCTTAAATAATCTCTTTATATTTTTTAAAGGACATT
1 ATTTAAGGCATTTTTGGAT--AAAAATATCTTAAATAATC-CCTGATACATTTTAAAGGGGATT
* *
30079 GTTTAAGGCATTTTTGGATAAAAAATATATCTTAAATAATTCCCCGATACATTTTAAAGGGGATT
1 ATTTAAGGCATTTTTGGAT--AAAA-ATATCTTAAATAA-TCCCTGATACATTTTAAAGGGGATT
30144 ATTTAA
1 ATTTAA
30150 TATATTTTTG
Statistics
Matches: 101, Mismatches: 25, Indels: 12
0.73 0.18 0.09
Matches are distributed among these distances:
60 1 0.01
61 7 0.07
62 32 0.32
63 20 0.20
64 6 0.06
65 33 0.33
66 2 0.02
ACGTcount: A:0.37, C:0.11, G:0.11, T:0.41
Consensus pattern (61 bp):
ATTTAAGGCATTTTTGGATAAAAATATCTTAAATAATCCCTGATACATTTTAAAGGGGATT
Found at i:32426 original size:17 final size:16
Alignment explanation
Indices: 32406--32449 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
32396 ATTTTATAGG
32406 GATTTTTATTTGAAAAA
1 GATTTTT-TTTGAAAAA
* *
32423 GATTTTTTTATTAAAAG
1 GATTTTTTT-TGAAAAA
32440 GATTTTTTTT
1 GATTTTTTTT
32450 TGTTTTTATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
16 3 0.12
17 21 0.88
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (16 bp):
GATTTTTTTTGAAAAA
Found at i:32517 original size:41 final size:44
Alignment explanation
Indices: 32433--32520 Score: 119
Period size: 44 Copynumber: 2.1 Consensus size: 44
32423 GATTTTTTTA
*
32433 TTAAAAGGATTTTTTTTTGTTTTTATAAATATATTTTTTAAAAC
1 TTAAAAGGATTTTTTTTTGTTTTTATAAATATATTTTTGAAAAC
** *
32477 TTAAAAGTTTTTTTTTTTGTTTTTAT-TAT-TA-TTTTGAAAAC
1 TTAAAAGGATTTTTTTTTGTTTTTATAAATATATTTTTGAAAAC
32518 TTA
1 TTA
32521 TTTGAATTTT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
41 12 0.30
42 2 0.05
43 2 0.05
44 24 0.60
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (44 bp):
TTAAAAGGATTTTTTTTTGTTTTTATAAATATATTTTTGAAAAC
Found at i:32531 original size:41 final size:44
Alignment explanation
Indices: 32433--32540 Score: 116
Period size: 44 Copynumber: 2.5 Consensus size: 44
32423 GATTTTTTTA
* *
32433 TTAAAAGGATTTTTTTTTGTTTTTATAAATATATTTTTTAAAAC
1 TTAAAAGAATTTTTTTTTGTTTTTATAAATATATTTTTGAAAAC
** *
32477 TTAAAAGTTTTTTTTTTTGTTTTTAT-TAT-TA-TTTTGAAAAC
1 TTAAAAGAATTTTTTTTTGTTTTTATAAATATATTTTTGAAAAC
***
32518 TTATTTGAA-TTTTTTTTGTTTTT
1 TTAAAAGAATTTTTTTTTGTTTTT
32541 TGTTTTTTTT
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
40 14 0.25
41 13 0.24
42 2 0.04
43 2 0.04
44 24 0.44
ACGTcount: A:0.27, C:0.02, G:0.07, T:0.64
Consensus pattern (44 bp):
TTAAAAGAATTTTTTTTTGTTTTTATAAATATATTTTTGAAAAC
Found at i:32686 original size:6 final size:6
Alignment explanation
Indices: 32677--32746 Score: 70
Period size: 6 Copynumber: 10.7 Consensus size: 6
32667 AAAACCATAA
32677 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAATGAGCT AAAAA- ATAAAAT
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA--A--T AAAAAT A-AAAAT
32729 CAAAAAAT AAAAAT AAAA
1 --AAAAAT AAAAAT AAAA
32747 TGAAAAAAAG
Statistics
Matches: 56, Mismatches: 0, Indels: 16
0.78 0.00 0.22
Matches are distributed among these distances:
5 1 0.02
6 42 0.75
8 7 0.12
9 1 0.02
10 5 0.09
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:33658 original size:3 final size:3
Alignment explanation
Indices: 33626--33712 Score: 67
Period size: 3 Copynumber: 30.3 Consensus size: 3
33616 AGGAAGAAAA
* * * ** *
33626 AAT AAA AAT AAT AAA AAT AAT GAT GGT AAT AAT AAT -AT AAT AAG AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
33673 AAT AGA- AAT -AT AAT AGT AAT AAT AAT AA- AAT AAT -AT AAT A
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33713 CTATACAATA
Statistics
Matches: 66, Mismatches: 12, Indels: 12
0.73 0.13 0.13
Matches are distributed among these distances:
2 9 0.14
3 56 0.85
4 1 0.02
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:33675 original size:20 final size:21
Alignment explanation
Indices: 33652--33707 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
33642 ATAATGATGG
33652 TAATAATAATATAATAAG-AA
1 TAATAATAATATAATAAGTAA
33672 TAATAGA-AATATAAT-AGTAA
1 TAATA-ATAATATAATAAGTAA
*
33692 TAATAATAAAATAATA
1 TAATAATAATATAATA
33708 TAATACTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
19 3 0.10
20 27 0.87
21 1 0.03
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.30
Consensus pattern (21 bp):
TAATAATAATATAATAAGTAA
Found at i:33780 original size:21 final size:21
Alignment explanation
Indices: 33754--33798 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
33744 AATAATGAAT
33754 CACGGTCCAG-TTGACCTCGGA
1 CACGGT-CAGATTGACCTCGGA
*
33775 CACGGTCTGATTGACCTCGGA
1 CACGGTCAGATTGACCTCGGA
33796 CAC
1 CAC
33799 AAATGAGTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.20, C:0.33, G:0.27, T:0.20
Consensus pattern (21 bp):
CACGGTCAGATTGACCTCGGA
Found at i:34437 original size:16 final size:17
Alignment explanation
Indices: 34416--34453 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
34406 AAGCCTTAGA
* *
34416 TTTATTTTATAGTTT-T
1 TTTATTATAGAGTTTCT
34432 TTTATTATAGAGTTTCT
1 TTTATTATAGAGTTTCT
34449 TTTAT
1 TTTAT
34454 CTTACAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 13 0.68
17 6 0.32
ACGTcount: A:0.21, C:0.03, G:0.08, T:0.68
Consensus pattern (17 bp):
TTTATTATAGAGTTTCT
Found at i:35025 original size:16 final size:16
Alignment explanation
Indices: 35004--35036 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
34994 GTCTTGCTTT
35004 GTATAACCTCCTAAAG
1 GTATAACCTCCTAAAG
35020 GTATAACCTCCTAAAG
1 GTATAACCTCCTAAAG
35036 G
1 G
35037 GAAAAGGAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.15, T:0.24
Consensus pattern (16 bp):
GTATAACCTCCTAAAG
Found at i:35948 original size:27 final size:26
Alignment explanation
Indices: 35903--35954 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
35893 GTCAAATTTA
*
35903 AAAAAATTTCTCACCTAAAGATTTTTT
1 AAAAAATTTATCACCTAAA-ATTTTTT
**
35930 AAAAAATTTATCATTTAAAATTTTT
1 AAAAAATTTATCACCTAAAATTTTT
35955 AAGAAGCTCA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 6 0.27
27 16 0.73
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (26 bp):
AAAAAATTTATCACCTAAAATTTTTT
Found at i:36024 original size:3 final size:3
Alignment explanation
Indices: 36011--36048 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
36001 TTAACCTCAT
36011 TTA TGTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
36049 AAAATTTTCT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:36156 original size:24 final size:25
Alignment explanation
Indices: 36121--36177 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 25
36111 AAAAATAATT
* *
36121 AAATAAACAAATAAACAAAACT-AA
1 AAATAAATAAATAAACAAAAATGAA
*
36145 AAATAAATAAATAAATAAAAATGAA
1 AAATAAATAAATAAACAAAAATGAA
36170 AAA-AAATA
1 AAATAAATA
36178 CAAAAAAAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
24 24 0.83
25 5 0.17
ACGTcount: A:0.77, C:0.05, G:0.02, T:0.16
Consensus pattern (25 bp):
AAATAAATAAATAAACAAAAATGAA
Found at i:37453 original size:28 final size:28
Alignment explanation
Indices: 37413--37470 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
37403 AATGTGGAGT
*
37413 TTGACTCATTGAAAAATACATATGAGGA
1 TTGACTCATTGAAAAATACATACGAGGA
37441 TTGACTCATTGAAAAATACATACGAGGA
1 TTGACTCATTGAAAAATACATACGAGGA
37469 TT
1 TT
37471 CCAAGGTGGT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.29
Consensus pattern (28 bp):
TTGACTCATTGAAAAATACATACGAGGA
Found at i:38509 original size:10 final size:10
Alignment explanation
Indices: 38494--38531 Score: 67
Period size: 10 Copynumber: 3.8 Consensus size: 10
38484 AAAGGATCGA
*
38494 AAATAACTTC
1 AAATAATTTC
38504 AAATAATTTC
1 AAATAATTTC
38514 AAATAATTTC
1 AAATAATTTC
38524 AAATAATT
1 AAATAATT
38532 CAATAAGCAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 27 1.00
ACGTcount: A:0.53, C:0.11, G:0.00, T:0.37
Consensus pattern (10 bp):
AAATAATTTC
Found at i:40017 original size:170 final size:170
Alignment explanation
Indices: 39735--40079 Score: 539
Period size: 170 Copynumber: 2.0 Consensus size: 170
39725 GGCCTCAAGC
* * *
39735 CATTTGGTAAAATAGTCAATAGTAATTAGCACAAATCTTTTGTGTCGAGTGGCTGATGTGAATAA
1 CATTTGGTAAAATAGTCAATAGTAACTAGCACAAATCTTCTGTGTCAAGTGGCTGATGTGAATAA
** * * *
39800 ATTGAGTACATCCATCCTTTTTTGCATGAAGGGCCATGGGCTTATTATGAGAGTTAGCTCAGTCG
66 ATTGAGTACATCCATCCTCATTTGCATAAAGGGCCATGGGCTTATTATGAGAGTCAACTCAGTCG
* *
39865 ATGGAAGATGCTACAATGATCAAATCTTTGGCATTTATCA
131 AGGGAAGATGCTACAATGATAAAATCTTTGGCATTTATCA
39905 CATTTGGTAAAATAGTCAATAGTAACTAGCACAAATCTTCTGTG-CTAAGTGGCTGATGTGAATA
1 CATTTGGTAAAATAGTCAATAGTAACTAGCACAAATCTTCTGTGTC-AAGTGGCTGATGTGAATA
* * *
39969 GATTGAGTACATCCATCCTCATTTGCATAAAGGGCCATTGGCTTATTATGAGAGTCAACTTAGTC
65 AATTGAGTACATCCATCCTCATTTGCATAAAGGGCCATGGGCTTATTATGAGAGTCAACTCAGTC
* *
40034 GAGGGAAGATGCTGCAATGATAAAATCTTTTGCATTTATCA
130 GAGGGAAGATGCTACAATGATAAAATCTTTGGCATTTATCA
40075 CATTT
1 CATTT
40080 CTTCTCTAGG
Statistics
Matches: 159, Mismatches: 15, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
169 1 0.01
170 158 0.99
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (170 bp):
CATTTGGTAAAATAGTCAATAGTAACTAGCACAAATCTTCTGTGTCAAGTGGCTGATGTGAATAA
ATTGAGTACATCCATCCTCATTTGCATAAAGGGCCATGGGCTTATTATGAGAGTCAACTCAGTCG
AGGGAAGATGCTACAATGATAAAATCTTTGGCATTTATCA
Found at i:44008 original size:15 final size:15
Alignment explanation
Indices: 43988--44019 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
43978 TGACCATAAA
*
43988 GGCAGAAGAAATTAG
1 GGCAGAAGAAATCAG
44003 GGCAGAAGAAATCAG
1 GGCAGAAGAAATCAG
44018 GG
1 GG
44020 AAAGGAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.44, C:0.09, G:0.38, T:0.09
Consensus pattern (15 bp):
GGCAGAAGAAATCAG
Found at i:44680 original size:23 final size:23
Alignment explanation
Indices: 44651--44696 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
44641 CATGCAATTG
44651 TTGTCATTATTACAAGTTTATGA
1 TTGTCATTATTACAAGTTTATGA
*
44674 TTGTCATTATTATAAGTTTATGA
1 TTGTCATTATTACAAGTTTATGA
44697 CCACTTTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.30, C:0.07, G:0.13, T:0.50
Consensus pattern (23 bp):
TTGTCATTATTACAAGTTTATGA
Found at i:48330 original size:13 final size:14
Alignment explanation
Indices: 48296--48333 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
48286 ATGATTGATG
48296 ATAAATT-ATCATT
1 ATAAATTAATCATT
48309 ATGAAATTAAT-ATT
1 AT-AAATTAATCATT
48323 ATAAATTAATC
1 ATAAATTAATC
48334 TACTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 10 0.45
14 10 0.45
15 2 0.09
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (14 bp):
ATAAATTAATCATT
Found at i:48785 original size:17 final size:19
Alignment explanation
Indices: 48748--48786 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
48738 AATTACAAAT
*
48748 AATATAATTAAGATATCAA
1 AATATAATTAAAATATCAA
48767 AATATAA-TAAAAT-TCAA
1 AATATAATTAAAATATCAA
48784 AAT
1 AAT
48787 TTTAATTCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 7 0.37
18 5 0.26
19 7 0.37
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
AATATAATTAAAATATCAA
Found at i:48803 original size:8 final size:8
Alignment explanation
Indices: 48790--48814 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
48780 TCAAAATTTT
48790 AATTCAAA
1 AATTCAAA
48798 AATTCAAA
1 AATTCAAA
48806 AATTCAAA
1 AATTCAAA
48814 A
1 A
48815 CATATAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.64, C:0.12, G:0.00, T:0.24
Consensus pattern (8 bp):
AATTCAAA
Done.