Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167966.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_225, 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: 46882
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.20
File 2 of 2
Found at i:27204 original size:23 final size:24
Alignment explanation
Indices: 27178--27222 Score: 74
Period size: 23 Copynumber: 1.9 Consensus size: 24
27168 GGACAAATAA
27178 TCAATAAAAAATA-AAATAAAAAG
1 TCAATAAAAAATATAAATAAAAAG
*
27201 TCAATACAAAATATAAATAAAA
1 TCAATAAAAAATATAAATAAAA
27223 GCAAAAGGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 12 0.60
24 8 0.40
ACGTcount: A:0.71, C:0.07, G:0.02, T:0.20
Consensus pattern (24 bp):
TCAATAAAAAATATAAATAAAAAG
Found at i:27342 original size:14 final size:14
Alignment explanation
Indices: 27323--27374 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
27313 AAAGCAAGAA
27323 AAAATAAAAAAATT
1 AAAATAAAAAAATT
*
27337 AAAATACAAAACA-T
1 AAAATA-AAAAAATT
*
27351 ATAA-AAAAAAATT
1 AAAATAAAAAAATT
*
27364 AAAACAAAAAA
1 AAAATAAAAAA
27375 GAGAAAGCAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
12 5 0.16
13 5 0.16
14 16 0.52
15 5 0.16
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAATAAAAAAATT
Found at i:27668 original size:22 final size:21
Alignment explanation
Indices: 27619--27670 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
27609 AAGCAAAAGG
* * *
27619 AAAAAGATAAAATAAGTAATAA
1 AAAAAGA-AAAAAAAATAAAAA
27641 AAAAAGAAAAAAAAATAAAAA
1 AAAAAGAAAAAAAAATAAAAA
27662 AATAAAGAA
1 AA-AAAGAA
27671 GTAAGGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
21 13 0.50
22 13 0.50
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (21 bp):
AAAAAGAAAAAAAAATAAAAA
Found at i:28159 original size:19 final size:18
Alignment explanation
Indices: 28121--28160 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
28111 AGAAAATTTT
* *
28121 AAAACAAAGAAAAAAGTG
1 AAAACAAAAAAAAAAATG
28139 AAAACAAAAAAAAAATATG
1 AAAACAAAAAAAAAA-ATG
28158 AAA
1 AAA
28161 GCACATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAACAAAAAAAAAAATG
Found at i:28298 original size:8 final size:8
Alignment explanation
Indices: 28256--28414 Score: 54
Period size: 8 Copynumber: 19.0 Consensus size: 8
28246 CAACAATGAT
28256 AAATAAAA
1 AAATAAAA
*
28264 AAAGAAAA
1 AAATAAAA
*
28272 GAA-AAAA
1 AAATAAAA
* *
28279 AGATAGAA
1 AAATAAAA
28287 AAATAAAA
1 AAATAAAA
28295 AAATCCAAAA
1 AAAT--AAAA
*
28305 CATTATAAAA
1 -A-AATAAAA
* *
28315 ATTTATGAAA
1 A--AATAAAA
* *
28325 ATATAAAT
1 AAATAAAA
* *
28333 AAAGAAAG
1 AAATAAAA
*
28341 AAAT-TAA
1 AAATAAAA
28348 AAATAAAA
1 AAATAAAA
*
28356 ATAAGAAAA
1 A-AATAAAA
**
28365 AAAT-ATT
1 AAATAAAA
*
28372 AAAGAAAA
1 AAATAAAA
28380 AAATAAAA
1 AAATAAAA
*
28388 TAAAAAAAA
1 -AAATAAAA
28397 ACAATAAAA
1 A-AATAAAA
28406 AATATAAAA
1 AA-ATAAAA
28415 GTAAGAAAAA
Statistics
Matches: 111, Mismatches: 28, Indels: 23
0.69 0.17 0.14
Matches are distributed among these distances:
7 14 0.13
8 50 0.45
9 28 0.25
10 16 0.14
11 1 0.01
12 2 0.02
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:28357 original size:25 final size:27
Alignment explanation
Indices: 28322--28395 Score: 75
Period size: 25 Copynumber: 2.8 Consensus size: 27
28312 AAAATTTATG
* *
28322 AAAATATAAATAAAG-AAAGAA-ATTA
1 AAAATAAAAATAAAGAAAAAAATATTA
28347 AAAATAAAAAT-AAGAAAAAAATATTA
1 AAAATAAAAATAAAGAAAAAAATATTA
*
28373 AAGAA-AAAAATAAAATAAAAAAA
1 AA-AATAAAAAT-AAAGAAAAAAA
28396 AACAATAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
24 3 0.07
25 15 0.37
26 12 0.29
27 2 0.05
28 9 0.22
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAATAAAAATAAAGAAAAAAATATTA
Found at i:28381 original size:26 final size:27
Alignment explanation
Indices: 28322--28394 Score: 73
Period size: 26 Copynumber: 2.8 Consensus size: 27
28312 AAAATTTATG
* * *
28322 AAAATATAAAT-AAAGAAAGAA-ATTA
1 AAAATAAAAATAAAATAAAAAATATTA
*
28347 AAAATAAAAATAAGA-AAAAAATATTA
1 AAAATAAAAATAAAATAAAAAATATTA
28373 AAGAA-AAAAATAAAATAAAAAA
1 AA-AATAAAAATAAAATAAAAAA
28395 AAACAATAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
25 15 0.38
26 17 0.43
27 8 0.20
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (27 bp):
AAAATAAAAATAAAATAAAAAATATTA
Found at i:28381 original size:31 final size:29
Alignment explanation
Indices: 28346--28426 Score: 92
Period size: 30 Copynumber: 2.8 Consensus size: 29
28336 GAAAGAAATT
* *
28346 AAAAATAAAAATAAGAAAAAAATATTAAA
1 AAAAATAAAAATAAGAAAAAAACAATAAA
*
28375 GAAAAAAATAAAATAA-AAAAAAACAATAAA
1 -AAAAATA-AAAATAAGAAAAAAACAATAAA
* *
28405 AAATATAAAAGTAAGAAAAAAA
1 AAAAATAAAAATAAGAAAAAAA
28427 AAGGCAAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.14
29 12 0.28
30 18 0.42
31 7 0.16
ACGTcount: A:0.80, C:0.01, G:0.05, T:0.14
Consensus pattern (29 bp):
AAAAATAAAAATAAGAAAAAAACAATAAA
Found at i:28406 original size:39 final size:39
Alignment explanation
Indices: 28332--28428 Score: 92
Period size: 40 Copynumber: 2.5 Consensus size: 39
28322 AAAATATAAA
* * *
28332 TAAAGAAAGAAATTAAAAATAAAAATAA-GAAAAAAATAT
1 TAAAGAAA-AAAATAAAAATAAAAAAAACAAAAAAAATAT
28371 TAAAGAAAAAAAT-AAAATAAAAAAAAACAATAAAAAATAT
1 TAAAGAAAAAAATAAAAAT-AAAAAAAACAA-AAAAAATAT
* *
28411 AAAAGTAAGAAAA-AAAAA
1 TAAAG-AAAAAAATAAAAA
28429 GGCAAAAATT
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
37 5 0.10
38 11 0.23
39 9 0.19
40 13 0.27
41 10 0.21
ACGTcount: A:0.78, C:0.01, G:0.06, T:0.14
Consensus pattern (39 bp):
TAAAGAAAAAAATAAAAATAAAAAAAACAAAAAAAATAT
Found at i:28407 original size:13 final size:13
Alignment explanation
Indices: 28322--28428 Score: 65
Period size: 13 Copynumber: 7.7 Consensus size: 13
28312 AAAATTTATG
28322 AAAATATAAATAAA
1 AAAATA-AAATAAA
* * *
28336 GAAAGAAATTAAA
1 AAAATAAAATAAA
* *
28349 AATAAAAATAAGAAA
1 AA-AATAA-AATAAA
*
28364 AAAATATTAAAGAAA
1 AAAATA--AAATAAA
28379 AAAATAAAATAAA
1 AAAATAAAATAAA
28392 AAAA-AACAATAAA
1 AAAATAA-AATAAA
28405 AAATATAAAAGTAAGA
1 AAA-ATAAAA-TAA-A
28421 AAAA-AAAA
1 AAAATAAAA
28429 GGCAAAAATT
Statistics
Matches: 75, Mismatches: 9, Indels: 18
0.74 0.09 0.18
Matches are distributed among these distances:
12 2 0.03
13 26 0.35
14 18 0.24
15 24 0.32
16 5 0.07
ACGTcount: A:0.79, C:0.01, G:0.06, T:0.15
Consensus pattern (13 bp):
AAAATAAAATAAA
Found at i:28926 original size:23 final size:22
Alignment explanation
Indices: 28900--29028 Score: 73
Period size: 23 Copynumber: 5.5 Consensus size: 22
28890 ATAATTAATC
28900 AAAAATAAAAAATTGAAAAAAAA
1 AAAAATAAAAAATT-AAAAAAAA
* * *
28923 AAAAAAAAATAAAATAAAATACTAA
1 AAAAATAAA-AAATTAAAA-A-AAA
*
28948 AAAAAT-AACAATTAAAAATAAA
1 AAAAATAAAAAATTAAAAA-AAA
* *
28970 CAAAAA-CAAAAAGTAAAAAAGTAA
1 -AAAAATAAAAAATTAAAAAA--AA
* * *
28994 GAAAATAAAAAATTAGAGAATAA
1 AAAAATAAAAAATTA-AAAAAAA
*
29017 AAAAATATAAAA
1 AAAAATAAAAAA
29029 CGATAAAATG
Statistics
Matches: 80, Mismatches: 17, Indels: 18
0.70 0.15 0.16
Matches are distributed among these distances:
22 4 0.05
23 50 0.62
24 16 0.20
25 10 0.12
ACGTcount: A:0.78, C:0.03, G:0.05, T:0.15
Consensus pattern (22 bp):
AAAAATAAAAAATTAAAAAAAA
Found at i:29015 original size:15 final size:16
Alignment explanation
Indices: 28978--29020 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
28968 AACAAAAACA
28978 AAAAGTAAAAAAGTAAG
1 AAAA-TAAAAAAGTAAG
*
28995 AAAATAAAAAA-TTAG
1 AAAATAAAAAAGTAAG
*
29010 AGAATAAAAAA
1 AAAATAAAAAA
29021 ATATAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (16 bp):
AAAATAAAAAAGTAAG
Found at i:29162 original size:24 final size:23
Alignment explanation
Indices: 29135--29190 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
29125 AAAGACATAA
29135 AAAATCAAAGACAAAAAATAAAAT
1 AAAATCAAAGACAAAAAAT-AAAT
* *
29159 AAAAGTC-AATACAAAATATAAAT
1 AAAA-TCAAAGACAAAAAATAAAT
29182 AAAATCAAA
1 AAAATCAAA
29191 AGGAAGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 10 0.36
24 14 0.50
25 2 0.07
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAATCAAAGACAAAAAATAAAT
Found at i:30576 original size:22 final size:23
Alignment explanation
Indices: 30538--30600 Score: 74
Period size: 23 Copynumber: 2.7 Consensus size: 23
30528 CAAATTTTAT
*
30538 TAAATAAAAGATAAATTACACGA
1 TAAATAAAAGATAAATTACAAGA
*
30561 TAAATAAAA-ATAAATTTCAAGA
1 TAAATAAAAGATAAATTACAAGA
* *
30583 TAAAATACAAGATGAATT
1 T-AAATAAAAGATAAATT
30601 TAATTAGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
22 12 0.35
23 16 0.47
24 6 0.18
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.25
Consensus pattern (23 bp):
TAAATAAAAGATAAATTACAAGA
Found at i:30745 original size:14 final size:14
Alignment explanation
Indices: 30707--30765 Score: 50
Period size: 14 Copynumber: 4.1 Consensus size: 14
30697 TAAAATTTTT
**
30707 ATAAAAAAACAAAA
1 ATAAAAAATTAAAA
30721 ATAACAAAAATTAAAA
1 AT-A-AAAAATTAAAA
30737 ATAAAAAA-TAAAA
1 ATAAAAAATTAAAA
30750 GGA-AAAAAATTAAAA
1 --ATAAAAAATTAAAA
30765 A
1 A
30766 GAGCACAAAA
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
13 6 0.16
14 13 0.34
15 8 0.21
16 11 0.29
ACGTcount: A:0.80, C:0.03, G:0.03, T:0.14
Consensus pattern (14 bp):
ATAAAAAATTAAAA
Found at i:31495 original size:19 final size:19
Alignment explanation
Indices: 31473--31518 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
31463 ATGAAAATAT
*
31473 AAATAAAGA-AAGAAATAAA
1 AAATAAAAATAAGAAA-AAA
31492 AAATAAAAATAAGAAAAAA
1 AAATAAAAATAAGAAAAAA
*
31511 ATATAAAA
1 AAATAAAA
31519 TGTAAATAAG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.75
20 6 0.25
ACGTcount: A:0.80, C:0.00, G:0.07, T:0.13
Consensus pattern (19 bp):
AAATAAAAATAAGAAAAAA
Found at i:31497 original size:7 final size:7
Alignment explanation
Indices: 31466--31598 Score: 67
Period size: 7 Copynumber: 18.9 Consensus size: 7
31456 AAAATTTATG
*
31466 AAAATAT
1 AAAAAAT
*
31473 AAATAAAG
1 AAA-AAAT
31481 AAAGAAAT
1 AAA-AAAT
31489 AAAAAAT
1 AAAAAAT
31496 -AAAAAT
1 AAAAAAT
*
31502 AAGAAA-
1 AAAAAAT
*
31508 AAAATAT
1 AAAAAAT
**
31515 AAAATGT
1 AAAAAAT
* *
31522 AAATAAG
1 AAAAAAT
*
31529 CAAAAAT
1 AAAAAAT
*
31536 --ACAAT
1 AAAAAAT
31541 AAAAAAT
1 AAAAAAT
31548 ATAAAAAGT
1 A-AAAAA-T
31557 AAGAAAAT
1 AA-AAAAT
31565 AAAAAAT
1 AAAAAAT
**
31572 AATGAAT
1 AAAAAAT
* *
31579 CAAAAAC
1 AAAAAAT
31586 AAAAAAT
1 AAAAAAT
31593 AAAAAA
1 AAAAAA
31599 AGACAAAAAT
Statistics
Matches: 93, Mismatches: 25, Indels: 16
0.69 0.19 0.12
Matches are distributed among these distances:
5 4 0.04
6 10 0.11
7 53 0.57
8 20 0.22
9 6 0.06
ACGTcount: A:0.75, C:0.03, G:0.06, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:31505 original size:24 final size:24
Alignment explanation
Indices: 31466--31572 Score: 99
Period size: 24 Copynumber: 4.2 Consensus size: 24
31456 AAAATTTATG
31466 AAAATATAAATAAAGAAAGAAATAA
1 AAAATATAAAT-AAGAAAGAAATAA
* * *
31491 AAAATAAAAATAAGAAAAAAATAT
1 AAAATATAAATAAGAAAGAAATAA
* *
31515 AAAATGTAAATAAGCAAAAATACAATAA
1 AAAATATAAATAAG---AAAGA-AATAA
*
31543 AAAATATAAA-AAGTAAGAAAATAA
1 AAAATATAAATAAGAAAG-AAATAA
31567 AAAATA
1 AAAATA
31573 ATGAATCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 11
0.76 0.11 0.12
Matches are distributed among these distances:
24 36 0.54
25 11 0.16
27 7 0.10
28 13 0.19
ACGTcount: A:0.75, C:0.02, G:0.07, T:0.17
Consensus pattern (24 bp):
AAAATATAAATAAGAAAGAAATAA
Found at i:31569 original size:35 final size:33
Alignment explanation
Indices: 31488--31569 Score: 94
Period size: 35 Copynumber: 2.4 Consensus size: 33
31478 AAGAAAGAAA
*
31488 TAAAAAATAAAAATAAGAAAAAAATATAAAATG
1 TAAAAAATAAAAATAAGAAAAAAATATAAAAAG
**
31521 TAAATAAGCAAAAATACA-ATAAAAAATATAAAAAG
1 TAAA-AAATAAAAATA-AGA-AAAAAATATAAAAAG
31556 TAAGAAAATAAAAA
1 TAA-AAAATAAAAA
31570 ATAATGAATC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
33 4 0.10
34 10 0.25
35 25 0.62
36 1 0.03
ACGTcount: A:0.74, C:0.02, G:0.06, T:0.17
Consensus pattern (33 bp):
TAAAAAATAAAAATAAGAAAAAAATATAAAAAG
Found at i:31929 original size:463 final size:466
Alignment explanation
Indices: 31436--32307 Score: 1170
Period size: 473 Copynumber: 1.9 Consensus size: 466
31426 TAAAAAGATA
31436 AAAAAATCAAAAACATTATAAAAATTTATGAAAATATAAATAAAGAAAGAAATAAAAAAT-AA-A
1 AAAAAATCAAAAACATTATAAAAATTTATGAAAATATAAATAAAGAAAGAAATAAAAAATAAACA
* * * * *
31499 AATAAGAAA-AAAATATA-AAATGTAA-A-T-AAGC-AAA-AATACAATAAAAAATATA-AAAAG
66 AATAA-AAATAAAATA-AGAAAAG-AATATTAAAGCAAAACAAAAAAAT-AAAAATAAACAAAAA
*
31556 T-AA-GAAAATA-AAAAATAATGAATCAA-AAACAAA-AAATAA-AAAAAGACAAAAATTGAATA
127 TAAATAAAAATATAAAAATAA-GAA--AATAAA-AAATAAATAACAAAAAGACAAAAATTGAATA
*
31615 AAAATTTCA-AAAATG-AAAGGAAATGACAAAATAGAAAAAAAATA-TTTTAAAAAATACAAAAA
188 AAAATTT-AGAAAATGAAAAAG-AATGACAAAATA-AAAAAAAATAGTTTT-AAAAATACAAAAA
* * *
31677 ATTGAAAAACATATAAGAAATAATAAGAAAACAATATAAAAAATCAAAGACAAAAGATTAAAAAA
249 ATTGAAAAACATATAAGAAATAACAAGAAAACAATAGAAAAAATCAAAGACAAAAAATTAAAAAA
*
31742 GAGAAAAGTTAATGCAAAATAAAAATGAAAACCAAAGAAGAAAATGCAACAAAAAAACTATAAGA
314 GAG--AAGTTAATGCAAAATAAAAATGAAAACCAAAGAAGAAAATG-AA-AAAAAAACTACAAGA
* *
31807 ATTTGAAAATGAAAATAAGAAATAAAAAGAAATTTGTGAAAAAATTAAGAAAATAATAAAAATGA
375 ATTTAAAAACGAAAATAAGAAATAAAAAGAAATTTGTGAAAAAATTAAGAAAATAATAAAAATGA
31872 AAAGACAAAAGATGATTTATGAAAAAT
440 AAAGACAAAAGATGATTTATGAAAAAT
* * * *
31899 AAAAAATCCAAAACATTCTAAACATTTATGAAAATTTAAATAAAGAAAGAAATAAAAAATAAACC
1 AAAAAATCAAAAACATTATAAAAATTTATGAAAATATAAATAAAGAAAGAAATAAAAAATAAA-C
*
31964 AAATAAAAATAAAATAAGAAAAGAATATTAAAGTAAAACAAAAAAATAAAAATAAACAAAAATAC
65 AAATAAAAATAAAATAAGAAAAGAATATTAAAGCAAAACAAAAAAATAAAAATAAACAAAAATA-
* * *
32029 AATAAAAATATAAAAGTAAGAAAATAAAAAATAATTAATCAAAAATACAAAAATTGAATAAAAAT
129 AATAAAAATATAAAAATAAGAAAATAAAAAATAAATAA-CAAAAAGACAAAAATTGAATAAAAAT
*
32094 TTAGAAAGTGAAAAAGAATGACAAAATAAAAAAAAATAGTTTTAAAAATACAAAAAATTGAAAAA
193 TTAGAAAATGAAAAAGAATGACAAAATAAAAAAAAATAGTTTTAAAAATACAAAAAATTGAAAAA
**
32159 CATATAAGAAATAACAAGAAAACAATAGAAAAGGTCAAAGACAAAAAATTAAAAAAGAGAAGTTA
258 CATATAAGAAATAACAAGAAAACAATAGAAAAAATCAAAGACAAAAAATTAAAAAAGAGAAGTTA
* * * * * *
32224 TTGCAAAATAAAAATGAAAACCAAAGGAGAAATTGAAAAAAAAAGTACGAGAATTTAAAAACGCA
323 ATGCAAAATAAAAATGAAAACCAAAGAAGAAAATGAAAAAAAAACTACAAGAATTTAAAAACGAA
32289 AATAAGAAATAAAAAGAAA
388 AATAAGAAATAAAAAGAAA
32308 AGCAAGAATA
Statistics
Matches: 357, Mismatches: 30, Indels: 38
0.84 0.07 0.09
Matches are distributed among these distances:
463 56 0.16
464 2 0.01
465 6 0.02
466 17 0.05
467 1 0.00
468 3 0.01
469 52 0.15
470 13 0.04
471 43 0.12
472 10 0.03
473 96 0.27
474 54 0.15
475 4 0.01
ACGTcount: A:0.68, C:0.05, G:0.09, T:0.18
Consensus pattern (466 bp):
AAAAAATCAAAAACATTATAAAAATTTATGAAAATATAAATAAAGAAAGAAATAAAAAATAAACA
AATAAAAATAAAATAAGAAAAGAATATTAAAGCAAAACAAAAAAATAAAAATAAACAAAAATAAA
TAAAAATATAAAAATAAGAAAATAAAAAATAAATAACAAAAAGACAAAAATTGAATAAAAATTTA
GAAAATGAAAAAGAATGACAAAATAAAAAAAAATAGTTTTAAAAATACAAAAAATTGAAAAACAT
ATAAGAAATAACAAGAAAACAATAGAAAAAATCAAAGACAAAAAATTAAAAAAGAGAAGTTAATG
CAAAATAAAAATGAAAACCAAAGAAGAAAATGAAAAAAAAACTACAAGAATTTAAAAACGAAAAT
AAGAAATAAAAAGAAATTTGTGAAAAAATTAAGAAAATAATAAAAATGAAAAGACAAAAGATGAT
TTATGAAAAAT
Found at i:31996 original size:53 final size:50
Alignment explanation
Indices: 31939--32062 Score: 114
Period size: 48 Copynumber: 2.4 Consensus size: 50
31929 AAAATTTAAA
31939 TAAAGAAAGAAATAAAAAATAAACCAAATAAAAATAAAATA-AGA-AAAGAATAT
1 TAAAGAAAGAAATAAAAAATAAA--AAATAAAAA-AAAATACA-ATAAA-AATAT
* *
31992 TAAAGTAAA-ACA-AAAAAAT-AAAAATAAACAAAAATACAATAAAAATAT
1 TAAAG-AAAGAAATAAAAAATAAAAAATAAAAAAAAATACAATAAAAATAT
* *
32040 AAAAGTAAGAAAATAAAAAATAA
1 TAAAGAAAG-AAATAAAAAATAA
32063 TTAATCAAAA
Statistics
Matches: 59, Mismatches: 5, Indels: 16
0.74 0.06 0.20
Matches are distributed among these distances:
47 2 0.03
48 16 0.27
49 14 0.24
50 7 0.12
51 3 0.05
52 7 0.12
53 7 0.12
54 3 0.05
ACGTcount: A:0.75, C:0.04, G:0.06, T:0.15
Consensus pattern (50 bp):
TAAAGAAAGAAATAAAAAATAAAAAATAAAAAAAAATACAATAAAAATAT
Found at i:32045 original size:48 final size:48
Alignment explanation
Indices: 31987--32078 Score: 116
Period size: 48 Copynumber: 1.9 Consensus size: 48
31977 ATAAGAAAAG
*
31987 AATATTAAAGTAA-AACAA-AAAAATAAAAATAAACAAAAATACAATAAA
1 AATATAAAAGTAAGAA-AATAAAAA-AAAAATAAACAAAAATACAATAAA
* * *
32035 AATATAAAAGTAAGAAAATAAAAAATAATTAATCAAAAATACAA
1 AATATAAAAGTAAGAAAATAAAAAAAAAATAAACAAAAATACAA
32079 AAATTGAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
48 31 0.82
49 7 0.18
ACGTcount: A:0.73, C:0.05, G:0.03, T:0.18
Consensus pattern (48 bp):
AATATAAAAGTAAGAAAATAAAAAAAAAATAAACAAAAATACAATAAA
Found at i:32394 original size:22 final size:20
Alignment explanation
Indices: 32344--32395 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
32334 ACAAAAGATT
*
32344 TGAAATAAAAAAGAAAACGA
1 TGAAATAAAAAAGAAAACAA
*
32364 -GAAAGTAAAAATATTAAAACAA
1 TGAAA-TAAAAA-A-GAAAACAA
32386 TGAAATAAAA
1 TGAAATAAAA
32396 TAAAAATGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 4 0.15
20 6 0.23
21 1 0.04
22 11 0.42
23 4 0.15
ACGTcount: A:0.69, C:0.04, G:0.12, T:0.15
Consensus pattern (20 bp):
TGAAATAAAAAAGAAAACAA
Found at i:32516 original size:8 final size:7
Alignment explanation
Indices: 32505--32632 Score: 62
Period size: 7 Copynumber: 16.7 Consensus size: 7
32495 AAAAAAAGAC
32505 AAAATAA
1 AAAATAA
32512 GAAAATGAA
1 -AAAAT-AA
32521 AAAATAAA
1 AAAAT-AA
32529 AAAGATTCAA
1 AAA-A-T-AA
32539 AAAAT-A
1 AAAATAA
32545 AAAATAA
1 AAAATAA
32552 AAAATAA
1 AAAATAA
* *
32559 ATTAATAT
1 A-AAATAA
*
32567 AAAATATT
1 AAAATA-A
*
32575 AATATAA
1 AAAATAA
32582 AAGAA-AA
1 AA-AATAA
*
32589 AAATAAACA
1 AAA-ATA-A
*
32598 AAAACAA
1 AAAATAA
32605 AAAATAA
1 AAAATAA
*
32612 AAAAGGAA
1 AAAA-TAA
32620 GAAAATAA
1 -AAAATAA
32628 AAAAT
1 AAAAT
32633 TAGCTAATAA
Statistics
Matches: 96, Mismatches: 12, Indels: 25
0.72 0.09 0.19
Matches are distributed among these distances:
6 7 0.07
7 36 0.38
8 35 0.36
9 12 0.12
10 6 0.06
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:32565 original size:15 final size:13
Alignment explanation
Indices: 32537--32614 Score: 59
Period size: 13 Copynumber: 5.9 Consensus size: 13
32527 AAAAAGATTC
32537 AAAAAATAAAAAT
1 AAAAAATAAAAAT
32550 AAAAAATAAATTAAT
1 AAAAAATAAA--AAT
* **
32565 ATAAAATATTAAT
1 AAAAAATAAAAAT
* *
32578 ATAAAAGAAAAA-
1 AAAAAATAAAAAT
* * *
32590 AATAAACAAAAAC
1 AAAAAATAAAAAT
32603 AAAAAATAAAAA
1 AAAAAATAAAAA
32615 AGGAAGAAAA
Statistics
Matches: 51, Mismatches: 11, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
12 9 0.18
13 32 0.63
15 10 0.20
ACGTcount: A:0.78, C:0.03, G:0.01, T:0.18
Consensus pattern (13 bp):
AAAAAATAAAAAT
Found at i:32901 original size:26 final size:26
Alignment explanation
Indices: 32882--32934 Score: 67
Period size: 26 Copynumber: 2.2 Consensus size: 26
32872 AAAAAGCAAG
32882 AAAAAAT-AAAAAAATTAAAATACAA
1 AAAAAATAAAAAAAATTAAAATACAA
* *
32907 AACATATAAAAAAAATT-AAA-ACAA
1 AAAAAATAAAAAAAATTAAAATACAA
32931 AAAA
1 AAAA
32935 GAGAAAGCAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
24 7 0.29
25 8 0.33
26 9 0.38
ACGTcount: A:0.79, C:0.06, G:0.00, T:0.15
Consensus pattern (26 bp):
AAAAAATAAAAAAAATTAAAATACAA
Found at i:33719 original size:19 final size:18
Alignment explanation
Indices: 33681--33720 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
33671 AGAAAATTTT
* *
33681 AAAACAAAGAAAAAAGTG
1 AAAACAAAAAAAAAAATG
33699 AAAACAAAAAAAAAATATG
1 AAAACAAAAAAAAAA-ATG
33718 AAA
1 AAA
33721 GCACATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAACAAAAAAAAAAATG
Found at i:33916 original size:13 final size:11
Alignment explanation
Indices: 33888--33974 Score: 57
Period size: 12 Copynumber: 7.2 Consensus size: 11
33878 ATGAAAATAT
33888 AAATAAAGAAAGA
1 AAATAAA-AAA-A
*
33901 AATTAAAAATAA
1 AAATAAAAA-AA
33913 AAATAAGAAAAA
1 AAATAA-AAAAA
*
33925 ATATTAAAGAAAA
1 A-AATAAA-AAAA
33938 AAATAAAATAAA
1 AAATAAAA-AAA
*
33950 AAATATAAAAAG
1 AAATA-AAAAAA
* *
33962 TAAGAAAAAAA
1 AAATAAAAAAA
33973 AA
1 AA
33975 GGCAAAAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
11 7 0.12
12 30 0.51
13 22 0.37
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:33916 original size:25 final size:26
Alignment explanation
Indices: 33881--33960 Score: 87
Period size: 25 Copynumber: 3.2 Consensus size: 26
33871 AAAATTTATG
* *
33881 AAAATATAAATAAAGAAAGAA-ATTA
1 AAAATAAAAATAAAGAAAAAATATTA
33906 AAAATAAAAAT-AAGAAAAAATATTA
1 AAAATAAAAATAAAGAAAAAATATTA
*
33931 AAGAA-AAAAATAAAATAAAAAATA-TA
1 AA-AATAAAAAT-AAAGAAAAAATATTA
33957 AAAA
1 AAAA
33961 GTAAGAAAAA
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
24 8 0.17
25 24 0.50
26 6 0.12
27 10 0.21
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (26 bp):
AAAATAAAAATAAAGAAAAAATATTA
Found at i:33934 original size:14 final size:14
Alignment explanation
Indices: 33917--33959 Score: 61
Period size: 14 Copynumber: 3.1 Consensus size: 14
33907 AAATAAAAAT
*
33917 AAGAAAAAATATTA
1 AAGAAAAAATATAA
33931 AAGAAAAAA-ATAA
1 AAGAAAAAATATAA
*
33944 AATAAAAAATATAA
1 AAGAAAAAATATAA
33958 AA
1 AA
33960 AGTAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.79, C:0.00, G:0.05, T:0.16
Consensus pattern (14 bp):
AAGAAAAAATATAA
Found at i:33944 original size:12 final size:12
Alignment explanation
Indices: 33888--33954 Score: 59
Period size: 12 Copynumber: 5.4 Consensus size: 12
33878 ATGAAAATAT
33888 AAATAAAGAAAGA
1 AAATAAAGAAA-A
*
33901 AATTAAA-AATAA
1 AAATAAAGAA-AA
33913 AAAT-AAGAAAA
1 AAATAAAGAAAA
33924 AATATTAAAGAAAA
1 AA-A-TAAAGAAAA
33938 AAATAAA-ATAAA
1 AAATAAAGA-AAA
33950 AAATA
1 AAATA
33955 TAAAAAGTAA
Statistics
Matches: 46, Mismatches: 2, Indels: 13
0.75 0.03 0.21
Matches are distributed among these distances:
11 7 0.15
12 21 0.46
13 9 0.20
14 9 0.20
ACGTcount: A:0.78, C:0.00, G:0.06, T:0.16
Consensus pattern (12 bp):
AAATAAAGAAAA
Found at i:33972 original size:27 final size:26
Alignment explanation
Indices: 33906--33975 Score: 68
Period size: 27 Copynumber: 2.5 Consensus size: 26
33896 AAAGAAATTA
*
33906 AAAATAAAAATAAGAAAAAATATTAAAG
1 AAAA-AAAAA-AAGAAAAAATATAAAAG
*
33934 AAAAAAATAAAATAAAAAATATAAAAAG
1 AAAAAAA-AAAAGAAAAAATAT-AAAAG
33962 TAAGAAAAAAAAAG
1 -AA-AAAAAAAAAG
33976 GCAAAAATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
27 14 0.40
28 10 0.29
29 6 0.17
30 5 0.14
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (26 bp):
AAAAAAAAAAAGAAAAAATATAAAAG
Found at i:34513 original size:46 final size:46
Alignment explanation
Indices: 34462--34558 Score: 108
Period size: 46 Copynumber: 2.1 Consensus size: 46
34452 AAAAAAATTG
* * *
34462 AAAAAAA-ATAAAATAAAATACTAAAAAAATAACAATTA-AAAATA
1 AAAAAAACAAAAAATAAAAAACTAAAAAAATAAAAATTAGAAAATA
* * * *
34506 AACAAAAACAAAAAGTAAAAAAGTAAGAAAATAAAAATTAGAGAATA
1 AA-AAAAACAAAAAATAAAAAACTAAAAAAATAAAAATTAGAAAATA
34553 AAAAAA
1 AAAAAA
34559 TATAAAACGA
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
44 2 0.05
45 5 0.12
46 29 0.67
47 7 0.16
ACGTcount: A:0.76, C:0.04, G:0.05, T:0.14
Consensus pattern (46 bp):
AAAAAAACAAAAAATAAAAAACTAAAAAAATAAAAATTAGAAAATA
Found at i:34699 original size:24 final size:23
Alignment explanation
Indices: 34672--34727 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 23
34662 AAAGACATAA
34672 AAAATCAAAGACAAAAAATAAAAT
1 AAAATCAAAGACAAAAAAT-AAAT
* *
34696 AAAAGTC-AATACAAAATATAAAT
1 AAAA-TCAAAGACAAAAAATAAAT
34719 AAAATCAAA
1 AAAATCAAA
34728 AGGAAGTTCA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
22 2 0.07
23 10 0.36
24 14 0.50
25 2 0.07
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAATCAAAGACAAAAAATAAAT
Found at i:36847 original size:19 final size:18
Alignment explanation
Indices: 36809--36848 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
36799 AGAAAATTTT
* *
36809 AAAACAAAGAAAAAAGTG
1 AAAACAAAAAAAAAAATG
36827 AAAACAAAAAAAAAATATG
1 AAAACAAAAAAAAAA-ATG
36846 AAA
1 AAA
36849 GCACATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAACAAAAAAAAAAATG
Found at i:37042 original size:7 final size:7
Alignment explanation
Indices: 37011--37142 Score: 70
Period size: 7 Copynumber: 17.9 Consensus size: 7
37001 AAAATTTATG
*
37011 AAAATAT
1 AAAAAAT
*
37018 AAATAAAG
1 AAA-AAAT
37026 AAAGAAAT
1 AAA-AAAT
37034 AAAAAAT
1 AAAAAAT
*
37041 AAAAATAAG
1 -AAAA-AAT
37050 AAAAAAT
1 AAAAAAT
*
37057 ATAAAAT
1 AAAAAAT
**
37064 -GTAAAT
1 AAAAAAT
37070 AAACAAA-
1 AAA-AAAT
*
37077 AATACAAT
1 AA-AAAAT
37085 AAAAAAT
1 AAAAAAT
37092 ATAAAAAGT
1 A-AAAAA-T
37101 AAGAAAAT
1 AA-AAAAT
37109 AAAAAAT
1 AAAAAAT
**
37116 AATGAAT
1 AAAAAAT
* *
37123 CAAAAAC
1 AAAAAAT
37130 AAAAAAT
1 AAAAAAT
37137 AAAAAA
1 AAAAAA
37143 GACAAAAATT
Statistics
Matches: 94, Mismatches: 21, Indels: 20
0.70 0.16 0.15
Matches are distributed among these distances:
6 4 0.04
7 48 0.51
8 34 0.36
9 8 0.09
ACGTcount: A:0.76, C:0.03, G:0.05, T:0.16
Consensus pattern (7 bp):
AAAAAAT
Found at i:37050 original size:24 final size:23
Alignment explanation
Indices: 37011--37117 Score: 81
Period size: 24 Copynumber: 4.4 Consensus size: 23
37001 AAAATTTATG
* *
37011 AAAATATAAATAAAGAAAGAAAT
1 AAAAAATAAAAAAAGAAAGAAAT
37034 AAAAAATAAAAATAAGAAA-AAAT
1 AAAAAATAAAAA-AAGAAAGAAAT
* * *
37057 ATAAAATGTAAATAAACAAAAATACAAT
1 A-AAAA-ATAAA-AAA-AGAAAGA-AAT
* *
37085 AAAAAATATAAAAAGTAAGAAAAT
1 AAAAAATAAAAAAAGAAAG-AAAT
37109 AAAAAATAA
1 AAAAAATAA
37118 TGAATCAAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 15
0.73 0.11 0.16
Matches are distributed among these distances:
23 15 0.23
24 24 0.36
25 9 0.14
26 9 0.14
27 5 0.08
28 4 0.06
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.17
Consensus pattern (23 bp):
AAAAAATAAAAAAAGAAAGAAAT
Found at i:37057 original size:35 final size:37
Alignment explanation
Indices: 37018--37144 Score: 86
Period size: 39 Copynumber: 3.4 Consensus size: 37
37008 ATGAAAATAT
37018 AAATAAAGAAAG-AAATAAAAAATAA-A-AATAAGAAA
1 AAATAAAGAAAGAAAATAAAAAATAATACAATAA-AAA
* *
37053 AAATATAA-AATGTAAATAAACAAA-AATACAATAAAAA
1 AAATA-AAGAAAGAAAATAAA-AAATAATACAATAAAAA
* * *
37090 ATATAAAAAGTAAGAAAATAAAAAATAATGAATCAAAAACAAA
1 A-A-ATAAAGAAAGAAAATAAAAAATAAT--A-CAATAA-AAA
37133 AAATAAA-AAAGA
1 AAATAAAGAAAGA
37145 CAAAAATTGA
Statistics
Matches: 71, Mismatches: 8, Indels: 21
0.71 0.08 0.21
Matches are distributed among these distances:
35 8 0.11
36 11 0.15
37 8 0.11
38 11 0.15
39 14 0.20
40 4 0.06
41 5 0.07
42 6 0.08
43 4 0.06
ACGTcount: A:0.76, C:0.03, G:0.06, T:0.15
Consensus pattern (37 bp):
AAATAAAGAAAGAAAATAAAAAATAATACAATAAAAA
Found at i:37142 original size:8 final size:8
Alignment explanation
Indices: 36945--37114 Score: 60
Period size: 8 Copynumber: 20.2 Consensus size: 8
36935 CAACAACGAT
36945 AAATAAAA
1 AAATAAAA
*
36953 AAA-GAAA
1 AAATAAAA
*
36960 AGATAAAA
1 AAATAAAA
*
36968 AGATAAAA
1 AAATAAAA
36976 AAATAAAA
1 AAATAAAA
36984 AAATCCAAAA
1 AAAT--AAAA
*
36994 CATTATAAAA
1 -A-AATAAAA
* *
37004 ATTTATGAAA
1 A--AATAAAA
* *
37014 ATATAAAT
1 AAATAAAA
* *
37022 AAAGAAAG
1 AAATAAAA
37030 AAAT-AAA
1 AAATAAAA
37037 AAATAAAA
1 AAATAAAA
*
37045 ATAAGAAAA
1 A-AATAAAA
37054 AATATAAAA
1 AA-ATAAAA
*
37063 TGTAAATAAAC
1 ---AAATAAAA
*
37074 AAA-AATA
1 AAATAAAA
*
37081 CAAT-AAA
1 AAATAAAA
37088 AAATATAAA
1 AAATA-AAA
* *
37097 AAGTAAGA
1 AAATAAAA
37105 AAATAAAA
1 AAATAAAA
37113 AA
1 AA
37115 TAATGAATCA
Statistics
Matches: 122, Mismatches: 25, Indels: 30
0.69 0.14 0.17
Matches are distributed among these distances:
7 20 0.16
8 56 0.46
9 20 0.16
10 16 0.13
11 6 0.05
12 4 0.03
ACGTcount: A:0.74, C:0.03, G:0.06, T:0.17
Consensus pattern (8 bp):
AAATAAAA
Found at i:38044 original size:8 final size:7
Alignment explanation
Indices: 38033--38160 Score: 57
Period size: 8 Copynumber: 16.7 Consensus size: 7
38023 AAAAAAAGAC
38033 AAAATAA
1 AAAATAA
38040 GAAAATGAA
1 -AAAAT-AA
38049 AAAATAAA
1 AAAAT-AA
38057 AAAGATTCAA
1 AAA-A-T-AA
38067 AAAAT-A
1 AAAATAA
38073 AAAATAA
1 AAAATAA
38080 AAAA-AA
1 AAAATAA
38086 ATAAATTAATA
1 A-AAA-T-A-A
*
38097 AAAATATT
1 AAAATA-A
*
38105 AATATAA
1 AAAATAA
*
38112 AAGA-AA
1 AAAATAA
38118 AAAATAA
1 AAAATAA
38125 ACAAA-ACA
1 A-AAATA-A
38133 AAAATAA
1 AAAATAA
*
38140 AAAAGGAA
1 AAAA-TAA
38148 GAAAATAA
1 -AAAATAA
38156 AAAAT
1 AAAAT
38161 TAGCTAATAA
Statistics
Matches: 96, Mismatches: 9, Indels: 31
0.71 0.07 0.23
Matches are distributed among these distances:
6 14 0.15
7 28 0.29
8 33 0.34
9 9 0.09
10 10 0.10
11 2 0.02
ACGTcount: A:0.77, C:0.02, G:0.05, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:38082 original size:30 final size:28
Alignment explanation
Indices: 38048--38143 Score: 86
Period size: 30 Copynumber: 3.2 Consensus size: 28
38038 AAGAAAATGA
*
38048 AAAAATAAAAAAGATTCAAAAAATAAAAAT
1 AAAAA-AAAAAA-ATTAAAAAAATAAAAAT
*
38078 AAAAAAAAATAAATTAATAAAAATATTAATAT
1 AAAAAAAAA-AAATTAA-AAAAATA--AAAAT
* *
38110 AAAAGAAAAAAA-TAAACAAAACAAAAAT
1 AAAAAAAAAAAATTAAA-AAAATAAAAAT
38138 AAAAAA
1 AAAAAA
38144 GGAAGAAAAT
Statistics
Matches: 55, Mismatches: 6, Indels: 12
0.75 0.08 0.16
Matches are distributed among these distances:
28 9 0.16
29 9 0.16
30 22 0.40
31 3 0.05
32 12 0.22
ACGTcount: A:0.78, C:0.03, G:0.02, T:0.17
Consensus pattern (28 bp):
AAAAAAAAAAAATTAAAAAAATAAAAAT
Found at i:39237 original size:19 final size:18
Alignment explanation
Indices: 39199--39238 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
39189 AGAAAATTTT
* *
39199 AAAACAAAGAAAAAAGTG
1 AAAACAAAAAAAAAAATG
39217 AAAACAAAAAAAAAATATG
1 AAAACAAAAAAAAAA-ATG
39236 AAA
1 AAA
39239 GCACATGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.78, C:0.05, G:0.10, T:0.07
Consensus pattern (18 bp):
AAAACAAAAAAAAAAATG
Found at i:39427 original size:17 final size:16
Alignment explanation
Indices: 39405--39450 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
39395 TATAAATAAG
39405 AAAGAAAAAATAAAATT
1 AAAGAAAAAA-AAAATT
*
39422 AAAGAAAAAAAAAATA
1 AAAGAAAAAAAAAATT
*
39438 AAATAAACAAAAA
1 AAAGAAA-AAAAA
39451 TACATAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 15 0.58
ACGTcount: A:0.83, C:0.02, G:0.04, T:0.11
Consensus pattern (16 bp):
AAAGAAAAAAAAAATT
Found at i:39444 original size:20 final size:20
Alignment explanation
Indices: 39391--39450 Score: 77
Period size: 21 Copynumber: 3.0 Consensus size: 20
39381 AAAATTTATG
*
39391 AAAATATAAAT-AAGAAAGAA
1 AAAATA-AAATAAAGAAAAAA
39411 AAAATAAAATTAAAGAAAAAA
1 AAAATAAAA-TAAAGAAAAAA
*
39432 AAAATAAAATAAACAAAAA
1 AAAATAAAATAAAGAAAAA
39451 TACATAAAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 3 0.08
20 16 0.44
21 17 0.47
ACGTcount: A:0.80, C:0.02, G:0.05, T:0.13
Consensus pattern (20 bp):
AAAATAAAATAAAGAAAAAA
Found at i:39898 original size:17 final size:19
Alignment explanation
Indices: 39876--39913 Score: 62
Period size: 17 Copynumber: 2.1 Consensus size: 19
39866 ATATTAAAGT
39876 AAAACAAAAA-A-AATAAA
1 AAAACAAAAATACAATAAA
39893 AAAACAAAAATACAATAAA
1 AAAACAAAAATACAATAAA
39912 AA
1 AA
39914 TATAAAAGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 10 0.53
18 1 0.05
19 8 0.42
ACGTcount: A:0.84, C:0.08, G:0.00, T:0.08
Consensus pattern (19 bp):
AAAACAAAAATACAATAAA
Found at i:39912 original size:33 final size:34
Alignment explanation
Indices: 39847--39912 Score: 82
Period size: 33 Copynumber: 2.0 Consensus size: 34
39837 AACCAAAATA
* * *
39847 AAAATAAAATAAGAAAACAATATTAAAGTAAAAC
1 AAAATAAAATAAAAAAACAAAAATAAAGTAAAAC
39881 AAAA-AAAATAAAAAAACAAAAATACAA-TAAAA
1 AAAATAAAATAAAAAAACAAAAATA-AAGTAAAA
39913 ATATAAAAGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
33 22 0.79
34 6 0.21
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (34 bp):
AAAATAAAATAAAAAAACAAAAATAAAGTAAAAC
Found at i:40063 original size:16 final size:15
Alignment explanation
Indices: 40037--40079 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
40027 AACAAAAACA
40037 AAAAGTAAAAAAGTAAG
1 AAAA-TAAAAAA-TAAG
*
40054 AAAATAAAAAATTAG
1 AAAATAAAAAATAAG
*
40069 AGAATAAAAAA
1 AAAATAAAAAA
40080 ATATAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (15 bp):
AAAATAAAAAATAAG
Found at i:40222 original size:24 final size:23
Alignment explanation
Indices: 40195--40249 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 23
40185 AAAGACATAA
40195 AAAATCAAAGACAAAAAATAAAAT
1 AAAATCAAAGACAAAAAAT-AAAT
* *
40219 AAAAGTC-AATACAAAATATAAAT
1 AAAA-TCAAAGACAAAAAATAAAT
40242 AAAATCAA
1 AAAATCAA
40250 CAGGAAGTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
22 2 0.07
23 9 0.33
24 14 0.52
25 2 0.07
ACGTcount: A:0.71, C:0.09, G:0.04, T:0.16
Consensus pattern (23 bp):
AAAATCAAAGACAAAAAATAAAT
Found at i:42409 original size:18 final size:18
Alignment explanation
Indices: 42372--42410 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
42362 AGAAAATTTT
*
42372 AAAACAAAGAAAAAAGTG
1 AAAACAAAGAAAAAAATG
42390 AAAACAAA-AAAAAATATG
1 AAAACAAAGAAAAAA-ATG
42408 AAA
1 AAA
42411 GCACATGAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 13 0.68
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (18 bp):
AAAACAAAGAAAAAAATG
Found at i:42534 original size:8 final size:8
Alignment explanation
Indices: 42494--42692 Score: 50
Period size: 8 Copynumber: 23.4 Consensus size: 8
42484 CAACAACGAT
42494 AAATAAAA
1 AAATAAAA
*
42502 AAA-GAAA
1 AAATAAAA
*
42509 AGATAAAA
1 AAATAAAA
*
42517 AGATAAAA
1 AAATAAAA
42525 AAAT-AAA
1 AAATAAAA
42532 AAATCCAAAA
1 AAAT--AAAA
*
42542 CATTATAAAA
1 -A-AATAAAA
* *
42552 ATTTATGAAA
1 A--AATAAAA
* *
42562 ATATAAAT
1 AAATAAAA
* *
42570 AAAGAAAG
1 AAATAAAA
42578 AAAT-AAA
1 AAATAAAA
42585 AAATAAAA
1 AAATAAAA
*
42593 ATAAGAAAA
1 A-AATAAAA
42602 AAATATAAA
1 AAATA-AAA
**
42611 ATGTAAATA
1 AAATAAA-A
42620 AACA-AAAA
1 AA-ATAAAA
42628 TACAAT-AAA
1 -A-AATAAAA
42637 AAATATAAA
1 AAATA-AAA
* *
42646 AAGTAAGA
1 AAATAAAA
42654 AAATCAAAA
1 AAAT-AAAA
42663 ATAATGAATCAA
1 A-AAT-AA--AA
*
42675 AAA-CAAA
1 AAATAAAA
42682 AAATAAAA
1 AAATAAAA
42690 AAA
1 AAA
42693 GACAAAAATT
Statistics
Matches: 143, Mismatches: 26, Indels: 44
0.67 0.12 0.21
Matches are distributed among these distances:
7 26 0.18
8 52 0.36
9 36 0.25
10 21 0.15
11 3 0.02
12 5 0.03
ACGTcount: A:0.74, C:0.04, G:0.06, T:0.17
Consensus pattern (8 bp):
AAATAAAA
Found at i:42588 original size:19 final size:19
Alignment explanation
Indices: 42566--42700 Score: 61
Period size: 20 Copynumber: 7.0 Consensus size: 19
42556 ATGAAAATAT
*
42566 AAATAAAGA-AAGAAATAAA
1 AAATAAAAATAAGAAA-AAA
42585 AAATAAAAATAAGAAAAAA
1 AAATAAAAATAAGAAAAAA
* * *
42604 ATAT-AAAAT--G-TAAAT
1 AAATAAAAATAAGAAAAAA
*
42619 AAACAAAAATACA-ATAAAAA
1 AAATAAAAATA-AGA-AAAAA
*
42639 ATATAAAAAGTAAGAAAATCAA
1 AAATAAAAA-TAAGAAAA--AA
*
42661 AAATAATGAATCAA-AAACAAA
1 AAATAA-AAAT-AAGAAA-AAA
42682 AAATAAAAA-AAGACAAAAA
1 AAATAAAAATAAGA-AAAAA
42701 TTGAATAAAA
Statistics
Matches: 87, Mismatches: 13, Indels: 32
0.66 0.10 0.24
Matches are distributed among these distances:
15 5 0.06
16 6 0.07
18 7 0.08
19 18 0.21
20 24 0.28
21 11 0.13
22 11 0.13
23 5 0.06
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.14
Consensus pattern (19 bp):
AAATAAAAATAAGAAAAAA
Found at i:42594 original size:25 final size:25
Alignment explanation
Indices: 42559--42691 Score: 101
Period size: 24 Copynumber: 5.2 Consensus size: 25
42549 AAAATTTATG
*
42559 AAAATATAAATAAAGAAAGAAATAA
1 AAAATATAAATAAAGAAAAAAATAA
* *
42584 AAAATAAAAAT-AAGAAAAAAATAT
1 AAAATATAAATAAAGAAAAAAATAA
* *
42608 AAAATGTAAATAAACAAAAATACAATAA
1 AAAATATAAATAAA-GAAAA-A-AATAA
* *
42636 AAAATAT-AA-AAAGTAAGAAAATCA
1 AAAATATAAATAAAG-AAAAAAATAA
* *
42660 AAAATAATGAATCAAAAACAAAAAATAA
1 AAAAT-ATAAAT-AAAGA-AAAAAATAA
42688 AAAA
1 AAAA
42692 AGACAAAAAT
Statistics
Matches: 84, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
24 29 0.35
25 15 0.18
26 12 0.14
27 4 0.05
28 24 0.29
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (25 bp):
AAAATATAAATAAAGAAAAAAATAA
Found at i:43396 original size:24 final size:24
Alignment explanation
Indices: 43369--43442 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 24
43359 AACGCAAATA
43369 AGAAATAAAAAGAAAAGCAAGAAT
1 AGAAATAAAAAGAAAAGCAAGAAT
*
43393 AG-AATAAAAATGAAAAGACAAAAGATT
1 AGAAATAAAAA-GAAAAG-C--AAGAAT
*
43420 TGAAATAAAAAAGAAAA-CAAGAA
1 AGAAAT-AAAAAGAAAAGCAAGAA
43443 AGTAAAAATA
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
23 8 0.20
24 12 0.29
25 1 0.02
26 1 0.02
27 6 0.15
28 8 0.20
29 5 0.12
ACGTcount: A:0.70, C:0.04, G:0.15, T:0.11
Consensus pattern (24 bp):
AGAAATAAAAAGAAAAGCAAGAAT
Found at i:43590 original size:8 final size:7
Alignment explanation
Indices: 43579--43713 Score: 65
Period size: 8 Copynumber: 17.6 Consensus size: 7
43569 AAAAAAAGAC
43579 AAAATAA
1 AAAATAA
43586 GAAAATGAA
1 -AAAAT-AA
43595 AAAATAAA
1 AAAAT-AA
43603 AAAGATTCAA
1 AAA-A-T-AA
43613 AAAATAA
1 AAAATAA
*
43620 AAATAAAA
1 AAA-ATAA
*
43628 ATAAATGA
1 A-AAATAA
43636 AAAATAA
1 AAAATAA
*
43643 ATTAATAA
1 A-AAATAA
43651 AAAAT-A
1 AAAATAA
** *
43657 TTAATAT
1 AAAATAA
*
43664 AAAAGAA
1 AAAATAA
43671 AAAATAAA
1 AAAAT-AA
*
43679 CAAAACAA
1 -AAAATAA
43687 AAAATAA
1 AAAATAA
*
43694 AAAAGGAA
1 AAAA-TAA
43702 GAAAATAA
1 -AAAATAA
43710 AAAA
1 AAAA
43714 ATTAGCTAAT
Statistics
Matches: 96, Mismatches: 20, Indels: 23
0.69 0.14 0.17
Matches are distributed among these distances:
6 4 0.04
7 35 0.36
8 37 0.39
9 14 0.15
10 6 0.06
ACGTcount: A:0.76, C:0.02, G:0.06, T:0.16
Consensus pattern (7 bp):
AAAATAA
Found at i:43896 original size:29 final size:27
Alignment explanation
Indices: 43821--43897 Score: 68
Period size: 29 Copynumber: 2.8 Consensus size: 27
43811 AAAATATAAC
*
43821 AAATATAAA-AAAAGGACAAA-TAATCA
1 AAATATAAATAAAA-GAAAAAGTAATCA
* *
43847 AAGATAAAAATAAAATAAAAAGTCAATACA
1 AA-ATATAAATAAAAGAAAAAGT-AAT-CA
*
43877 AAATATAAATAAAAGCAAAAG
1 AAATATAAATAAAAGAAAAAG
43898 GAAGTACACA
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
26 2 0.05
27 10 0.25
28 5 0.12
29 19 0.47
30 4 0.10
ACGTcount: A:0.70, C:0.06, G:0.08, T:0.16
Consensus pattern (27 bp):
AAATATAAATAAAAGAAAAAGTAATCA
Found at i:44009 original size:15 final size:17
Alignment explanation
Indices: 43989--44025 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
43979 AAAAGCAAGA
43989 AAAAATA-AAAAAAT-T
1 AAAAATACAAAAAATAT
*
44004 AAAAATACAAAACATAT
1 AAAAATACAAAAAATAT
44021 AAAAA
1 AAAAA
44026 AAATTAAAAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 7 0.37
16 6 0.32
17 6 0.32
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.16
Consensus pattern (17 bp):
AAAAATACAAAAAATAT
Found at i:44563 original size:27 final size:24
Alignment explanation
Indices: 44524--44581 Score: 62
Period size: 26 Copynumber: 2.3 Consensus size: 24
44514 GAGAAAGTAG
* *
44524 AAAAAAAATTAATTTAGAAAATACA
1 AAAAAAAATTAA-TAAGAAAAAACA
*
44549 AAAAAATAATGTAATAAGAAAAAATA
1 AAAAAA-AAT-TAATAAGAAAAAACA
44575 AAAAAAA
1 AAAAAAA
44582 TCAAAGATAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
25 7 0.25
26 18 0.64
27 3 0.11
ACGTcount: A:0.74, C:0.02, G:0.05, T:0.19
Consensus pattern (24 bp):
AAAAAAAATTAATAAGAAAAAACA
Found at i:44798 original size:19 final size:18
Alignment explanation
Indices: 44761--44799 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
44751 AGAAAATTTT
* *
44761 AAACAAAGAAAAAAGTGA
1 AAACAAAAAAAAAAATGA
44779 AAACAAAAAAAAAATATGA
1 AAACAAAAAAAAAA-ATGA
44798 AA
1 AA
44800 GCACAATGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.77, C:0.05, G:0.10, T:0.08
Consensus pattern (18 bp):
AAACAAAAAAAAAAATGA
Found at i:44999 original size:24 final size:25
Alignment explanation
Indices: 44960--45006 Score: 69
Period size: 24 Copynumber: 1.9 Consensus size: 25
44950 AAAATTTATG
* *
44960 AAAATATAAATAAAGAAAGAAATTA
1 AAAATAAAAATAAAGAAAAAAATTA
44985 AAAATAAAAAT-AAGAAAAAAAT
1 AAAATAAAAATAAAGAAAAAAAT
45007 ATTAAAGCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 10 0.50
25 10 0.50
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (25 bp):
AAAATAAAAATAAAGAAAAAAATTA
Found at i:45052 original size:21 final size:21
Alignment explanation
Indices: 45009--45049 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
44999 AAAAAAATAT
45009 TAAAGCAAAAAAAAAATAAAA
1 TAAAGCAAAAAAAAAATAAAA
* *
45030 TAAA-CAAAAATACAATAAAA
1 TAAAGCAAAAAAAAAATAAAA
45050 ATATAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.78, C:0.07, G:0.02, T:0.12
Consensus pattern (21 bp):
TAAAGCAAAAAAAAAATAAAA
Found at i:45442 original size:19 final size:19
Alignment explanation
Indices: 45420--45490 Score: 53
Period size: 19 Copynumber: 3.8 Consensus size: 19
45410 AAATAATACC
45420 AAAAATATAATAAAATAAGA
1 AAAAATATAATAAAATAA-A
*
45440 AAACAATAT--TAAAGTAACA
1 AAA-AATATAATAAAATAA-A
45459 AAAAA-ATAA-AAAA-AACA
1 AAAAATATAATAAAATAA-A
*
45476 AAAAATACAATAAAA
1 AAAAATATAATAAAA
45491 ATATAAAAGG
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
17 11 0.26
18 8 0.19
19 15 0.36
20 3 0.07
21 5 0.12
ACGTcount: A:0.76, C:0.06, G:0.03, T:0.15
Consensus pattern (19 bp):
AAAAATATAATAAAATAAA
Found at i:45640 original size:16 final size:15
Alignment explanation
Indices: 45614--45656 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
45604 AACAAAAACA
45614 AAAAGTAAAAAAGTAAG
1 AAAA-TAAAAAA-TAAG
*
45631 AAAATAAAAAATTAG
1 AAAATAAAAAATAAG
*
45646 AGAATAAAAAA
1 AAAATAAAAAA
45657 ATATAAAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 13 0.54
16 7 0.29
17 4 0.17
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (15 bp):
AAAATAAAAAATAAG
Found at i:46411 original size:34 final size:31
Alignment explanation
Indices: 46373--46463 Score: 83
Period size: 34 Copynumber: 2.7 Consensus size: 31
46363 CAAACGAAAA
46373 ATAAAAAATATAACAAATAATAAGAAATAAAGAT
1 ATAAAAAATATAACAAA-AA-AAGAAA-AAAGAT
** *
46407 ATAAAAAATCAATGATTAAAAAAAGAAAAAAGTT
1 ATAAAAAAT--AT-AACAAAAAAAGAAAAAAGAT
* *
46441 ATAAAAAATAAAACAAAGAAAGA
1 ATAAAAAATATAACAAAAAAAGA
46464 GTGTGGATAA
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
31 9 0.19
32 1 0.02
34 23 0.49
35 6 0.13
36 4 0.09
37 4 0.09
ACGTcount: A:0.71, C:0.03, G:0.08, T:0.18
Consensus pattern (31 bp):
ATAAAAAATATAACAAAAAAAGAAAAAAGAT
Done.