Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 91 of 171
Found at i:29686078 original size:338 final size:328
Alignment explanation
Indices: 29685265--29686025 Score: 876
Period size: 338 Copynumber: 2.2 Consensus size: 328
29685255 CTGCAGGTCT
* * * * **
29685265 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTGAAGTAA
1 CAACATCATCCCCTTGAAATTGAAGTAAAGTGGATAACAAGCCTTCACCTCTGAAATTGAAGTAA
* * * * *
29685330 GAGCAGCGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAG
66 GAG-AACGTCA----C---AAATTG-A--AGAG-GCACAACACATCTTTATCTCTGAAATTGAAG
29685395 TAAGAGCAACGTCATCCCTTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTG
119 TAAGAGCAACGTCATCCCTTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTG
* * *
29685460 AAGTAAGAGCAGCGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATATCTTCATCTCTGAAA
184 AAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAA
*
29685525 TTGAAGTAAGAGCAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG
249 TTGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTG
* *
29685590 AAATTGAAGTAAGGG
314 AAATTGAAATAAGAG
* * * * *
29685605 CAACGTCATCCCCTTGAAATTGAAGTAGAGTGGATAACATGTCTTCATCTCTGAAATTGAAGTAA
1 CAACATCATCCCCTTGAAATTGAAGTAAAGTGGATAACAAGCCTTCACCTCTGAAATTGAAGTAA
* *
29685670 GAGCAACGTCATCCCTCGAAATTGAAGTGGAGTGGATAACACATCTTTATCTCTGAAATTGAAGT
66 GAG-AACGTCA-----C-AAATTGAA---GAG-GCACAACACATCTTTATCTCTGAAATTGAAGT
* * *
29685735 AAGAGCAACGTCATCCC-TCGAAATTGAAGTAGAGTGGATAACATGTCTTTATCTCTGAAATTGA
120 AAGAGCAACGTCATCCCTTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTGA
*
29685799 AGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTTATCTCTGAAAT
185 AGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAAT
* * * *
29685864 TGAAGTAAGCGCAACGTCATCCCCTCGGAATTGAAGTAGAGTGGATAGCACGTCTTTATCTCTGA
250 TGAAGTAAGAGCAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGA
29685929 AATTGTTGAAATAAGAG
315 AA---TTGAAATAAGAG
* *
29685946 CGACATCATTTTCCTATCTTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGCCCCTCTGA
1 CAACATCA---TCC---C--CTTGAAATTGAAGTAAAG-TGGATAACAAGCCTT--CACCTCTGA
29686011 AATTGAAGTAAGAGA
55 AATTGAAGTAAGAGA
29686026 GTAAGATAAA
Statistics
Matches: 375, Mismatches: 28, Indels: 25
0.88 0.07 0.06
Matches are distributed among these distances:
336 1 0.00
338 168 0.45
339 58 0.15
340 73 0.19
341 19 0.05
344 3 0.01
347 1 0.00
349 17 0.05
350 13 0.03
351 1 0.00
352 21 0.06
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.27
Consensus pattern (328 bp):
CAACATCATCCCCTTGAAATTGAAGTAAAGTGGATAACAAGCCTTCACCTCTGAAATTGAAGTAA
GAGAACGTCACAAATTGAAGAGGCACAACACATCTTTATCTCTGAAATTGAAGTAAGAGCAACGT
CATCCCTTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATATCTGAAATTGAAGTAAGAGCAA
CGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACATCTTCATCTCTGAAATTGAAGTAAGAG
CAACGTCATCCCCTCGAAATTGAAGTAGAGTGGATAACACGTCTTCATCTCTGAAATTGAAATAA
GAG
Found at i:29686451 original size:22 final size:22
Alignment explanation
Indices: 29686438--29686492 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
29686428 TATTTTAATC
29686438 TTAAATTTACTTTAAATTCAAT
1 TTAAATTTACTTTAAATTCAAT
* * *
29686460 TTAAATTTAAATTTGAATTTAAT
1 TTAAATTT-ACTTTAAATTCAAT
29686483 TTAAAATTTA
1 TT-AAATTTA
29686493 ATATTATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 8 0.29
23 14 0.50
24 6 0.21
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (22 bp):
TTAAATTTACTTTAAATTCAAT
Found at i:29686468 original size:6 final size:6
Alignment explanation
Indices: 29686421--29686493 Score: 57
Period size: 6 Copynumber: 12.7 Consensus size: 6
29686411 CATTTGAAAA
* * *
29686421 TTAAAT TT--AT TTTAAT CTTAAAT TT-ACT TTAAA- TTCAAT TTAAAT
1 TTAAAT TTAAAT TTAAAT -TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
*
29686466 TTAAAT TTGAAT TT-AAT TTAAAAT TTAA
1 TTAAAT TTAAAT TTAAAT TT-AAAT TTAA
29686494 TATTATTATA
Statistics
Matches: 54, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
4 4 0.07
5 13 0.24
6 27 0.50
7 10 0.19
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (6 bp):
TTAAAT
Found at i:29686468 original size:17 final size:17
Alignment explanation
Indices: 29686441--29686508 Score: 61
Period size: 17 Copynumber: 3.9 Consensus size: 17
29686431 TTTAATCTTA
*
29686441 AATTTACTTTAAA-TTC
1 AATTTAATTTAAATTTC
*
29686457 AATTTAAATTTAAATTTG
1 AATTT-AATTTAAATTTC
29686475 AATTTAATTTAAAATTT-
1 AATTTAATTT-AAATTTC
29686492 AATATT-ATTATAAATTT
1 AAT-TTAATT-TAAATTT
29686509 AAAAAGAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
16 5 0.11
17 24 0.53
18 16 0.36
ACGTcount: A:0.44, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
AATTTAATTTAAATTTC
Found at i:29686478 original size:12 final size:12
Alignment explanation
Indices: 29686421--29686493 Score: 57
Period size: 11 Copynumber: 6.3 Consensus size: 12
29686411 CATTTGAAAA
29686421 TTAAATTT--AT
1 TTAAATTTAAAT
*
29686431 TTTAATCTTAAAT
1 TTAAAT-TTAAAT
*
29686444 TT-ACTTTAAA-
1 TTAAATTTAAAT
*
29686454 TTCAATTTAAAT
1 TTAAATTTAAAT
*
29686466 TTAAATTTGAAT
1 TTAAATTTAAAT
29686478 TT-AATTTAAAAT
1 TTAAATTT-AAAT
29686490 TTAA
1 TTAA
29686494 TATTATTATA
Statistics
Matches: 50, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
10 7 0.14
11 19 0.38
12 19 0.38
13 5 0.10
ACGTcount: A:0.42, C:0.04, G:0.01, T:0.52
Consensus pattern (12 bp):
TTAAATTTAAAT
Found at i:29686494 original size:12 final size:11
Alignment explanation
Indices: 29686418--29686494 Score: 75
Period size: 12 Copynumber: 6.8 Consensus size: 11
29686408 AACCATTTGA
*
29686418 AAATTAAATTT
1 AAATTTAATTT
*
29686429 -ATTTTAATCTT
1 AAATTTAAT-TT
*
29686440 AAATTTACTTT
1 AAATTTAATTT
*
29686451 AAATTCAATTT
1 AAATTTAATTT
29686462 AAATTTAAATTT
1 AAATTT-AATTT
*
29686474 GAATTTAATTT
1 AAATTTAATTT
29686485 AAAATTTAAT
1 -AAATTTAAT
29686495 ATTATTATAA
Statistics
Matches: 53, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
10 6 0.11
11 23 0.43
12 24 0.45
ACGTcount: A:0.44, C:0.04, G:0.01, T:0.51
Consensus pattern (11 bp):
AAATTTAATTT
Found at i:29686613 original size:12 final size:14
Alignment explanation
Indices: 29686585--29686628 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
29686575 ATTTTTCGGT
29686585 CCAATTACAATGGC
1 CCAATTACAATGGC
29686599 CCAATTA-AA-GGC
1 CCAATTACAATGGC
*
29686611 CCAATTACAATGGG
1 CCAATTACAATGGC
29686625 CCAA
1 CCAA
29686629 ATAGGCCAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
12 10 0.37
13 4 0.15
14 13 0.48
ACGTcount: A:0.39, C:0.27, G:0.16, T:0.18
Consensus pattern (14 bp):
CCAATTACAATGGC
Found at i:29688582 original size:30 final size:30
Alignment explanation
Indices: 29688338--29688580 Score: 360
Period size: 30 Copynumber: 8.1 Consensus size: 30
29688328 ATAGGTCCCT
29688338 AAACTTTTCCAAAATTACATTTTAACCCCA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
* *** *
29688368 AAACTTTTCCAAAATTATATTCCGACCCTA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
*
29688398 AAACTTTTCCAAAATTACATTTTGACCCCA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
*
29688428 AAACTTTTCCAAAATTATATTTTAACCCCA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
* *
29688458 AAACTTTTCCAAAATTATATTTTGACCCCA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
* *
29688488 AAACTTTTCCAAAAATACATTTTAACCCCT
1 AAACTTTTCCAAAATTACATTTTAACCCCA
*
29688518 AAACTTTTCCAAAATTACATTTTGACCCCA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
* *
29688548 AAAATTTTCCAAAATTACATTTTAACCCAA
1 AAACTTTTCCAAAATTACATTTTAACCCCA
29688578 AAA
1 AAA
29688581 ATCTCCTAAA
Statistics
Matches: 191, Mismatches: 22, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 191 1.00
ACGTcount: A:0.40, C:0.25, G:0.02, T:0.34
Consensus pattern (30 bp):
AAACTTTTCCAAAATTACATTTTAACCCCA
Found at i:29688686 original size:30 final size:30
Alignment explanation
Indices: 29688593--29688688 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
29688583 CTCCTAAATC
* *
29688593 CCATTTTTAACCACGATTTCACCAAAATTTA
1 CCATTTTTAACCCCGATATCACCAAAA-TTA
* * * ***
29688624 CCA-TTTTACCCCCGAAACCTTTAAAATT-
1 CCATTTTTAACCCCGATATCACCAAAATTA
29688652 CCATTTTTAACCCCGATATCACCAAAATTA
1 CCATTTTTAACCCCGATATCACCAAAATTA
29688682 CCATTTT
1 CCATTTT
29688689 ACCCTCGGGT
Statistics
Matches: 49, Mismatches: 14, Indels: 5
0.72 0.21 0.07
Matches are distributed among these distances:
28 3 0.06
29 21 0.43
30 22 0.45
31 3 0.06
ACGTcount: A:0.33, C:0.29, G:0.03, T:0.34
Consensus pattern (30 bp):
CCATTTTTAACCCCGATATCACCAAAATTA
Found at i:29688689 original size:29 final size:29
Alignment explanation
Indices: 29688597--29688689 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 29
29688587 TAAATCCCAT
* *
29688597 TTTTAACCACGATTTCACCAAAATTTACCA
1 TTTTAACCCCGATATCACCAAAA-TTACCA
* * * ***
29688627 TTTTACCCCCGAAACCTTTAAAATT-CCA
1 TTTTAACCCCGATATCACCAAAATTACCA
29688655 TTTTTAACCCCGATATCACCAAAATTACCA
1 -TTTTAACCCCGATATCACCAAAATTACCA
29688685 TTTTA
1 TTTTA
29688690 CCCTCGGGTA
Statistics
Matches: 47, Mismatches: 14, Indels: 5
0.71 0.21 0.08
Matches are distributed among these distances:
28 3 0.06
29 26 0.55
30 18 0.38
ACGTcount: A:0.34, C:0.28, G:0.03, T:0.34
Consensus pattern (29 bp):
TTTTAACCCCGATATCACCAAAATTACCA
Found at i:29692151 original size:24 final size:24
Alignment explanation
Indices: 29692122--29692167 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
29692112 TTTAGATCAA
29692122 ATTTAGTTTT-AAATATAAATTTTG
1 ATTTAGTTTTAAAAT-TAAATTTTG
29692146 ATTTAGTTTTAAAATTAAATTT
1 ATTTAGTTTTAAAATTAAATTT
29692168 AATTTACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (24 bp):
ATTTAGTTTTAAAATTAAATTTTG
Found at i:29697377 original size:16 final size:17
Alignment explanation
Indices: 29697341--29697377 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
29697331 TATTTTATTT
*
29697341 TAATAATAAATTTTAAA
1 TAATAATAAATATTAAA
29697358 -AATAAT-AATATTAAA
1 TAATAATAAATATTAAA
29697373 TAATA
1 TAATA
29697378 TTCTTCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAATAATAAATATTAAA
Found at i:29699422 original size:21 final size:21
Alignment explanation
Indices: 29699392--29699490 Score: 69
Period size: 21 Copynumber: 4.5 Consensus size: 21
29699382 AAAAATGCAT
29699392 AAAAATAACATCCAAAATAAC
1 AAAAATAACATCCAAAATAAC
*
29699413 AAAAACAACAAT-CAAAATAGTAGC
1 AAAAATAAC-ATCCAAAATA--A-C
* *
29699437 AAAAATAACA-ACAAAATAAT
1 AAAAATAACATCCAAAATAAC
*
29699457 AACAAA-AACAACCAAAATAGCAGC
1 AA-AAATAACATCCAAAATA--A-C
29699481 AAAAATAACA
1 AAAAATAACA
29699491 ATAAAAATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
20 6 0.10
21 26 0.42
22 2 0.03
23 13 0.21
24 15 0.24
ACGTcount: A:0.68, C:0.17, G:0.04, T:0.11
Consensus pattern (21 bp):
AAAAATAACATCCAAAATAAC
Found at i:29699451 original size:12 final size:12
Alignment explanation
Indices: 29699436--29699508 Score: 64
Period size: 12 Copynumber: 6.4 Consensus size: 12
29699426 AAAATAGTAG
29699436 CAAAAATAACAA
1 CAAAAATAACAA
*
29699448 C-AAAATAATAA
1 CAAAAATAACAA
29699459 C--AAA-AACAA
1 CAAAAATAACAA
* * *
29699468 CCAAAATAGCAG
1 CAAAAATAACAA
29699480 CAAAAATAACAA
1 CAAAAATAACAA
* *
29699492 TAAAAATAATAA
1 CAAAAATAACAA
29699504 CAAAA
1 CAAAA
29699509 GTAGCATCAA
Statistics
Matches: 48, Mismatches: 10, Indels: 6
0.75 0.16 0.09
Matches are distributed among these distances:
9 5 0.10
10 3 0.06
11 13 0.27
12 27 0.56
ACGTcount: A:0.71, C:0.15, G:0.03, T:0.11
Consensus pattern (12 bp):
CAAAAATAACAA
Found at i:29699467 original size:44 final size:44
Alignment explanation
Indices: 29699392--29699508 Score: 155
Period size: 44 Copynumber: 2.6 Consensus size: 44
29699382 AAAAATGCAT
* * * *
29699392 AAAAATAACATCCAAAATAACAA-AAACAACAATCAAAATAGTAGC
1 AAAAATAACA-ACAAAATAATAACAAA-AACAACCAAAATAGCAGC
29699437 AAAAATAACAACAAAATAATAACAAAAACAACCAAAATAGCAGC
1 AAAAATAACAACAAAATAATAACAAAAACAACCAAAATAGCAGC
*
29699481 AAAAATAACAATAAAAATAATAACAAAA
1 AAAAATAACAA-CAAAATAATAACAAAA
29699509 GTAGCATCAA
Statistics
Matches: 65, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
44 37 0.57
45 28 0.43
ACGTcount: A:0.69, C:0.15, G:0.03, T:0.12
Consensus pattern (44 bp):
AAAAATAACAACAAAATAATAACAAAAACAACCAAAATAGCAGC
Found at i:29699538 original size:12 final size:12
Alignment explanation
Indices: 29699469--29699538 Score: 56
Period size: 12 Copynumber: 5.9 Consensus size: 12
29699459 CAAAAACAAC
*
29699469 CAAAATAGC-AG
1 CAAAATAGCAAT
*
29699480 CAAAAATAACAAT
1 C-AAAATAGCAAT
* **
29699493 AAAAATAATAA-
1 CAAAATAGCAAT
29699504 CAAAAGTAGC-AT
1 CAAAA-TAGCAAT
29699516 CAAAATAGCAAT
1 CAAAATAGCAAT
29699528 CAAAATAGCAA
1 CAAAATAGCAA
29699539 AAAGCAACAC
Statistics
Matches: 47, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
11 10 0.21
12 36 0.77
13 1 0.02
ACGTcount: A:0.63, C:0.14, G:0.09, T:0.14
Consensus pattern (12 bp):
CAAAATAGCAAT
Found at i:29699614 original size:22 final size:22
Alignment explanation
Indices: 29699544--29699617 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
29699534 AGCAAAAAGC
*
29699544 AACACCAAAACA--ATAAAAA-
1 AACACCAAAACAGTAAAAAAAT
*
29699563 AA-ACTAAAACAGTAAAAAAAT
1 AACACCAAAACAGTAAAAAAAT
** *
29699584 AGTATCAAAACAGTAAAAAAAT
1 AACACCAAAACAGTAAAAAAAT
29699606 AACACCAAAACA
1 AACACCAAAACA
29699618 ACAATATAAT
Statistics
Matches: 43, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
18 8 0.19
19 2 0.05
20 6 0.14
21 1 0.02
22 26 0.60
ACGTcount: A:0.69, C:0.16, G:0.04, T:0.11
Consensus pattern (22 bp):
AACACCAAAACAGTAAAAAAAT
Found at i:29702472 original size:22 final size:22
Alignment explanation
Indices: 29702446--29702489 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
29702436 GACCTAATTG
** *
29702446 ATATAATTTTAATAGTTTAAAT
1 ATATAATTAGAATAATTTAAAT
29702468 ATATAATTAGAATAATTTAAAT
1 ATATAATTAGAATAATTTAAAT
29702490 TAAAGAATCA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (22 bp):
ATATAATTAGAATAATTTAAAT
Found at i:29702504 original size:18 final size:17
Alignment explanation
Indices: 29702476--29702511 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
29702466 ATATATAATT
*
29702476 AGAATAATTTAAATTAA
1 AGAATAATTTAAAATAA
29702493 AGAATCAATTTAAAATAA
1 AGAAT-AATTTAAAATAA
29702511 A
1 A
29702512 CATAACAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.31
Consensus pattern (17 bp):
AGAATAATTTAAAATAA
Found at i:29704053 original size:2 final size:2
Alignment explanation
Indices: 29704046--29704113 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
29704036 CGACCCTCAA
29704046 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29704088 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29704114 TTTCGACTCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29705715 original size:15 final size:15
Alignment explanation
Indices: 29705670--29705717 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 15
29705660 TATTAATAAT
29705670 TTAATAATAAATATTTA
1 TTAATAATAAATA--TA
*
29705687 TTACAATTATAAATATA
1 TT--AATAATAAATATA
29705704 TTAATAATAAATAT
1 TTAATAATAAATAT
29705718 TTTGTAGTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 11 0.41
17 6 0.22
19 10 0.37
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
TTAATAATAAATATA
Found at i:29707543 original size:23 final size:24
Alignment explanation
Indices: 29707500--29707544 Score: 58
Period size: 23 Copynumber: 1.9 Consensus size: 24
29707490 TAACAGAAAA
*
29707500 GAACAATTTACTCTTTAATCTAAT
1 GAACAATTTACTATTTAATCTAAT
29707524 GAACAA-TTACTAATTT-ATCTA
1 GAACAATTTACT-ATTTAATCTA
29707545 TTTTTTAAGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (24 bp):
GAACAATTTACTATTTAATCTAAT
Found at i:29719288 original size:21 final size:21
Alignment explanation
Indices: 29719246--29719294 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
29719236 CTCGCCTTCA
*
29719246 TCTTTGCTTCTCTTTTTCTTG
1 TCTTTGCTTCTCTCTTTCTTG
*
29719267 TCTTTGCTCTTTCTCTTT-TTG
1 TCTTTGCT-TCTCTCTTTCTTG
29719288 TCCTTTG
1 T-CTTTG
29719295 AATCAACCGG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 12 0.50
22 12 0.50
ACGTcount: A:0.00, C:0.24, G:0.10, T:0.65
Consensus pattern (21 bp):
TCTTTGCTTCTCTCTTTCTTG
Found at i:29727347 original size:2 final size:2
Alignment explanation
Indices: 29727340--29727377 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
29727330 CATTAATAAC
29727340 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
29727378 ACAATAATAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29727856 original size:2 final size:2
Alignment explanation
Indices: 29727849--29727894 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
29727839 TTAACCTTAA
29727849 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29727891 AT AT
1 AT AT
29727895 TTAAAATTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29732950 original size:20 final size:18
Alignment explanation
Indices: 29732925--29732967 Score: 50
Period size: 20 Copynumber: 2.3 Consensus size: 18
29732915 ATAAAATTTT
*
29732925 AAAATTCATATTATTATATA
1 AAAATTCAAATT-TT-TATA
*
29732945 AAAATTGAAATTTTTATA
1 AAAATTCAAATTTTTATA
29732963 AAAAT
1 AAAAT
29732968 AAAAAAAGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 2 0.10
20 10 0.48
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATTCAAATTTTTATA
Found at i:29733021 original size:2 final size:2
Alignment explanation
Indices: 29733016--29733041 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29733006 ATTAAAATTA
29733016 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29733042 TCTAGAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29734542 original size:23 final size:22
Alignment explanation
Indices: 29734516--29734596 Score: 108
Period size: 23 Copynumber: 3.5 Consensus size: 22
29734506 TATTATTTGT
29734516 TATTAATATTAAGTAATTAATAA
1 TATT-ATATTAAGTAATTAATAA
*
29734539 TATTCATATTAAGTACTTAATAA
1 TATT-ATATTAAGTAATTAATAA
*
29734562 TATTTATATTAAATAATTAATAA
1 TA-TTATATTAAGTAATTAATAA
29734585 TATCTATATTAA
1 TAT-TATATTAA
29734597 TATATTTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
22 1 0.02
23 49 0.94
24 2 0.04
ACGTcount: A:0.48, C:0.04, G:0.02, T:0.46
Consensus pattern (22 bp):
TATTATATTAAGTAATTAATAA
Found at i:29734656 original size:15 final size:14
Alignment explanation
Indices: 29734623--29734679 Score: 57
Period size: 15 Copynumber: 4.1 Consensus size: 14
29734613 AATCTATATT
29734623 TCTA-TATTATTTA
1 TCTATTATTATTTA
29734636 T-T-TTATTATTCTA
1 TCTATTATTATT-TA
29734649 TCTATTATTATATTA
1 TCTATTATTAT-TTA
*
29734664 TCTACTATTATATTA
1 TCTATTATTAT-TTA
29734679 T
1 T
29734680 TCTTATAATA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
12 8 0.21
13 4 0.11
14 1 0.03
15 24 0.63
16 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.00, T:0.61
Consensus pattern (14 bp):
TCTATTATTATTTA
Found at i:29734656 original size:20 final size:18
Alignment explanation
Indices: 29734633--29734680 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
29734623 TCTATATTAT
29734633 TTATTTTATTATTCTATCTA
1 TTATTTTATTA-TCTA-CTA
*
29734653 TTATTATATTATCTACTA
1 TTATTTTATTATCTACTA
*
29734671 TTATATTATT
1 TTATTTTATT
29734681 CTTATAATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 11 0.44
19 4 0.16
20 10 0.40
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.62
Consensus pattern (18 bp):
TTATTTTATTATCTACTA
Found at i:29739506 original size:14 final size:14
Alignment explanation
Indices: 29739473--29739506 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
29739463 AATTCCTCAC
29739473 AACAAAGGAGTTAT
1 AACAAAGGAGTTAT
*
29739487 AGACAAGGGAGTTAT
1 A-ACAAAGGAGTTAT
29739502 AACAA
1 AACAA
29739507 TAATCAGCAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.50, C:0.09, G:0.24, T:0.18
Consensus pattern (14 bp):
AACAAAGGAGTTAT
Found at i:29745249 original size:5 final size:5
Alignment explanation
Indices: 29745239--29745278 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
29745229 TATAGTAATA
*
29745239 TTTCT TTTCT TTT-T TTTCT TTT-T TCT-T TTTCT TTTCT TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
29745279 GCTCATTCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
4 10 0.32
5 21 0.68
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (5 bp):
TTTCT
Found at i:29756217 original size:20 final size:20
Alignment explanation
Indices: 29756189--29756236 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
29756179 CTTTGTTGTT
*
29756189 TTTACTCTTACTCTCT-CAAG
1 TTTATTCTT-CTCTCTACAAG
*
29756209 TTTATTCTTTTCTCTACAAG
1 TTTATTCTTCTCTCTACAAG
*
29756229 TTTCTTCT
1 TTTATTCT
29756237 AACCTTTTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 5 0.21
20 19 0.79
ACGTcount: A:0.17, C:0.25, G:0.04, T:0.54
Consensus pattern (20 bp):
TTTATTCTTCTCTCTACAAG
Found at i:29770851 original size:11 final size:11
Alignment explanation
Indices: 29770816--29770856 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
29770806 AAATAGTGAG
29770816 AAAAAGAAAGA
1 AAAAAGAAAGA
29770827 AAAGAA-AAAG-
1 AAA-AAGAAAGA
*
29770837 AAAAAGAATGA
1 AAAAAGAAAGA
29770848 AAAAAGAAA
1 AAAAAGAAA
29770857 TAATTTGCTG
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 2 0.08
10 6 0.24
11 15 0.60
12 2 0.08
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAAAGAAAGA
Found at i:29777101 original size:18 final size:17
Alignment explanation
Indices: 29777075--29777110 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
29777065 CGAGGTAACA
29777075 TCTTCTTTTTCTTCCTTC
1 TCTTCTTTTTCTT-CTTC
*
29777093 TCTTTTTTTTCTTCTTC
1 TCTTCTTTTTCTTCTTC
29777110 T
1 T
29777111 TTTGCCTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTCTTTTTCTTCTTC
Found at i:29777106 original size:14 final size:16
Alignment explanation
Indices: 29777075--29777113 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
29777065 CGAGGTAACA
29777075 TCTTCTTTTTCTTCCT
1 TCTTCTTTTTCTTCCT
*
29777091 TC-TCTTTTT-TTTCT
1 TCTTCTTTTTCTTCCT
29777105 TCTTCTTTT
1 TCTTCTTTT
29777114 GCCTTAATAC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 6 0.29
15 13 0.62
16 2 0.10
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (16 bp):
TCTTCTTTTTCTTCCT
Found at i:29780829 original size:24 final size:24
Alignment explanation
Indices: 29780781--29780827 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
29780771 AAGAGTTAAT
29780781 TTGTCAATGCAAATATAAAATAAA
1 TTGTCAATGCAAATATAAAATAAA
*
29780805 TTGTCAGA-GCAAAT-TAAGATAAA
1 TTGTCA-ATGCAAATATAAAATAAA
29780828 ATGAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
23 8 0.38
24 12 0.57
25 1 0.05
ACGTcount: A:0.51, C:0.09, G:0.13, T:0.28
Consensus pattern (24 bp):
TTGTCAATGCAAATATAAAATAAA
Found at i:29783006 original size:17 final size:17
Alignment explanation
Indices: 29782986--29783028 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
29782976 AAATGAATTA
*
29782986 ACAAGTAAAATGCAACG
1 ACAACTAAAATGCAACG
*
29783003 ACAACTAAAATGCAATG
1 ACAACTAAAATGCAACG
*
29783020 ACAATTAAA
1 ACAACTAAA
29783029 TGAGATGCAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (17 bp):
ACAACTAAAATGCAACG
Found at i:29787757 original size:27 final size:27
Alignment explanation
Indices: 29787719--29787793 Score: 105
Period size: 27 Copynumber: 2.7 Consensus size: 27
29787709 AGGAGTAATT
* *
29787719 TGATTCTAGCTCGAAAGAGCGTTATTC
1 TGATTCTGGCTCGAAAGAGCATTATTC
*
29787746 TGATTCTGGCTCGAAAAAGCATTATTC
1 TGATTCTGGCTCGAAAGAGCATTATTC
*
29787773 TGATTCTGGGCTCGTAAGAGC
1 TGATTCT-GGCTCGAAAGAGC
29787794 TAACCATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
27 31 0.74
28 11 0.26
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (27 bp):
TGATTCTGGCTCGAAAGAGCATTATTC
Found at i:29787813 original size:24 final size:24
Alignment explanation
Indices: 29787775--29787833 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
29787765 CATTATTCTG
29787775 ATTCTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
* *
29787799 ATTTTGGGCTTGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCTAACC
29787823 ATTCTGGGCTC
1 ATTCTGGGCTC
29787834 ATGTGATCTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.22, C:0.22, G:0.25, T:0.31
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCTAACC
Found at i:29791686 original size:8 final size:8
Alignment explanation
Indices: 29791673--29791701 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
29791663 TAAATTCAAT
29791673 TTCTTTTC
1 TTCTTTTC
29791681 TTCTTTTC
1 TTCTTTTC
29791689 TTCTTTTC
1 TTCTTTTC
29791697 TTCTT
1 TTCTT
29791702 CTTCAAGCCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (8 bp):
TTCTTTTC
Found at i:29792439 original size:27 final size:27
Alignment explanation
Indices: 29792401--29792470 Score: 95
Period size: 27 Copynumber: 2.6 Consensus size: 27
29792391 TGAGGAGTAA
* * *
29792401 TCTGATTTTGGCTCGAAAAAGCTTTAT
1 TCTGATTCTGGCTCGAAAAAACATTAT
*
29792428 TCTGATTCTGGCTTGAAAAAACATTAT
1 TCTGATTCTGGCTCGAAAAAACATTAT
29792455 TCTGATTCTGGGCTCG
1 TCTGATTCT-GGCTCG
29792471 TAAGAGCAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (27 bp):
TCTGATTCTGGCTCGAAAAAACATTAT
Found at i:29792519 original size:24 final size:24
Alignment explanation
Indices: 29792459--29792511 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
29792449 CATTATTCTG
29792459 ATTCTGGGCTCGTAAGAGCAAACC
1 ATTCTGGGCTCGTAAGAGCAAACC
* *
29792483 ATTTTGGGCTCGTAAGAGCTAACC
1 ATTCTGGGCTCGTAAGAGCAAACC
29792507 ATTCT
1 ATTCT
29792512 AGGTTCGTGT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (24 bp):
ATTCTGGGCTCGTAAGAGCAAACC
Found at i:29808429 original size:25 final size:23
Alignment explanation
Indices: 29808400--29808446 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
29808390 AGTTGGATCC
*
29808400 AAATTAAACTCTAAAAAGATAATTA
1 AAATTAAA-TATAAAAA-ATAATTA
29808425 AAATTAAATATAAAAAATAATT
1 AAATTAAATATAAAAAATAATT
29808447 TCCTAATTGG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.29
24 7 0.33
25 8 0.38
ACGTcount: A:0.64, C:0.04, G:0.02, T:0.30
Consensus pattern (23 bp):
AAATTAAATATAAAAAATAATTA
Found at i:29811092 original size:18 final size:18
Alignment explanation
Indices: 29811055--29811114 Score: 63
Period size: 17 Copynumber: 3.4 Consensus size: 18
29811045 GAGCTCGCAA
* *
29811055 GTGAGCTCTC-ATGCTTG
1 GTGAGCTCACAATGTTTG
29811072 GTGAGCTCACAATGTTTG
1 GTGAGCTCACAATGTTTG
*
29811090 GTGAGCTCGCACA--TTTG
1 GTGAGCTCACA-ATGTTTG
29811107 GTGAGCTC
1 GTGAGCTC
29811115 GCCATGATTA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
17 21 0.55
18 16 0.42
19 1 0.03
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.32
Consensus pattern (18 bp):
GTGAGCTCACAATGTTTG
Found at i:29813190 original size:2 final size:2
Alignment explanation
Indices: 29813183--29813208 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
29813173 TAAACAAATA
29813183 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
29813209 TGTTTTTAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:29818710 original size:17 final size:17
Alignment explanation
Indices: 29818685--29818723 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
29818675 AGAAATATAT
29818685 AAATAAAGAATAGAAAA
1 AAATAAAGAATAGAAAA
*
29818702 AAATCAAGAATAGAAAA
1 AAATAAAGAATAGAAAA
29818719 AAATA
1 AAATA
29818724 TATATGTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (17 bp):
AAATAAAGAATAGAAAA
Found at i:29820228 original size:4 final size:5
Alignment explanation
Indices: 29820211--29820254 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
29820201 TGCAACAAGA
* *
29820211 TTTAT TTTAC TTTA- TTTAT TTTAT TTTCAT TTTAT TTTAG TTTA
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT-AT TTTAT TTTAT TTTA
29820255 ACATTTTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.11
5 26 0.74
6 5 0.14
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (5 bp):
TTTAT
Found at i:29821509 original size:12 final size:12
Alignment explanation
Indices: 29821494--29821519 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
29821484 TTTTTTTTAC
29821494 TTGTTATTTTTG
1 TTGTTATTTTTG
29821506 TTGTTATTTTTG
1 TTGTTATTTTTG
29821518 TT
1 TT
29821520 ATTCTTTTAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.15, T:0.77
Consensus pattern (12 bp):
TTGTTATTTTTG
Found at i:29822080 original size:21 final size:21
Alignment explanation
Indices: 29822056--29822100 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
29822046 CTAACGGTAG
29822056 AACTGAGGCTTCTACCGATAC
1 AACTGAGGCTTCTACCGATAC
** * *
29822077 AACTTTGGGTTTTACCGATAC
1 AACTGAGGCTTCTACCGATAC
29822098 AAC
1 AAC
29822101 CCAAACTTCT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (21 bp):
AACTGAGGCTTCTACCGATAC
Found at i:29833014 original size:28 final size:27
Alignment explanation
Indices: 29832958--29833014 Score: 62
Period size: 28 Copynumber: 2.0 Consensus size: 27
29832948 TTAGCCTAAA
* *
29832958 TTCTCTTTTTTTAGTTTAGTTTAGTTTT
1 TTCTCTTTTATTAGTTTAATTTAG-TTT
29832986 TTCTCTTTTATTAGGCTTTAATTTA-TTT
1 TTCTCTTTTATTA-G-TTTAATTTAGTTT
29833014 T
1 T
29833015 GTTCTTTGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
28 16 0.64
29 1 0.04
30 8 0.32
ACGTcount: A:0.14, C:0.09, G:0.09, T:0.68
Consensus pattern (27 bp):
TTCTCTTTTATTAGTTTAATTTAGTTT
Found at i:29838880 original size:7 final size:7
Alignment explanation
Indices: 29838870--29838927 Score: 53
Period size: 7 Copynumber: 8.0 Consensus size: 7
29838860 AATAAAAAAT
29838870 ATATAAA
1 ATATAAA
*
29838877 ATATTAA
1 ATATAAA
*
29838884 ATATTAA
1 ATATAAA
*
29838891 ATATTAA
1 ATATAAA
*
29838898 ATATTAA
1 ATATAAA
29838905 ATATTAAA
1 ATA-TAAA
*
29838913 ATAATATA
1 AT-ATAAA
29838921 ATATAAA
1 ATATAAA
29838928 TATCTAAAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
7 34 0.76
8 10 0.22
9 1 0.02
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (7 bp):
ATATAAA
Found at i:29838892 original size:14 final size:14
Alignment explanation
Indices: 29838870--29838935 Score: 80
Period size: 14 Copynumber: 4.6 Consensus size: 14
29838860 AATAAAAAAT
*
29838870 ATATAAAATATTAA
1 ATATTAAATATTAA
29838884 ATATTAAATATTAA
1 ATATTAAATATTAA
29838898 ATATTAAATATTAAA
1 ATATTAAATATT-AA
*
29838913 ATAATATAATA-TAA
1 ATATTA-AATATTAA
29838927 ATATCTAAA
1 ATAT-TAAA
29838936 AAAGTGAAAA
Statistics
Matches: 46, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
14 32 0.70
15 10 0.22
16 4 0.09
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (14 bp):
ATATTAAATATTAA
Found at i:29838899 original size:21 final size:21
Alignment explanation
Indices: 29838870--29838935 Score: 80
Period size: 21 Copynumber: 3.0 Consensus size: 21
29838860 AATAAAAAAT
*
29838870 ATATAAAATATTAAATATTAA
1 ATATTAAATATTAAATATTAA
29838891 ATATTAAATATTAAATATTAAA
1 ATATTAAATATTAAATATT-AA
*
29838913 ATAATATAATA-TAAATATCTAA
1 ATATTA-AATATTAAATAT-TAA
29838935 A
1 A
29838936 AAAGTGAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
21 18 0.45
22 17 0.43
23 5 0.12
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (21 bp):
ATATTAAATATTAAATATTAA
Found at i:29838899 original size:37 final size:37
Alignment explanation
Indices: 29838858--29838935 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 37
29838848 AAAAATTCCA
*
29838858 TAAATAAAAAATATATAAAATATTA-AATATTAAATAT-
1 TAAATAAAAAATAT-TAAAATAATATAATA-TAAATATC
**
29838895 TAAATATTAAATATTAAAATAATATAATATAAATATC
1 TAAATAAAAAATATTAAAATAATATAATATAAATATC
29838932 TAAA
1 TAAA
29838936 AAAGTGAAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
36 16 0.44
37 20 0.56
ACGTcount: A:0.63, C:0.01, G:0.00, T:0.36
Consensus pattern (37 bp):
TAAATAAAAAATATTAAAATAATATAATATAAATATC
Found at i:29863799 original size:44 final size:44
Alignment explanation
Indices: 29863751--29863839 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
29863741 AGATTTTTAA
29863751 TACTTAAAAATCAAGTTTCAATCACCATTTACACTAATACAAAC
1 TACTTAAAAATCAAGTTTCAATCACCATTTACACTAATACAAAC
29863795 TACTTAAAAATCAAGTTTCAATCACCATTTACACTAATACAAAC
1 TACTTAAAAATCAAGTTTCAATCACCATTTACACTAATACAAAC
29863839 T
1 T
29863840 CAACTAAACA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.45, C:0.22, G:0.02, T:0.30
Consensus pattern (44 bp):
TACTTAAAAATCAAGTTTCAATCACCATTTACACTAATACAAAC
Found at i:29866934 original size:10 final size:10
Alignment explanation
Indices: 29866902--29866969 Score: 73
Period size: 10 Copynumber: 6.8 Consensus size: 10
29866892 TATCATAAAT
*
29866902 TGTGATTAAA
1 TGTGATTATA
* *
29866912 AGTGATTAAA
1 TGTGATTATA
29866922 TGTGATTATA
1 TGTGATTATA
* *
29866932 TGTCATTATT
1 TGTGATTATA
*
29866942 TGTGACTATA
1 TGTGATTATA
*
29866952 TGTGGTTATA
1 TGTGATTATA
29866962 TGTGATTA
1 TGTGATTA
29866970 ACATGTGATG
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
10 47 1.00
ACGTcount: A:0.31, C:0.03, G:0.21, T:0.46
Consensus pattern (10 bp):
TGTGATTATA
Found at i:29866939 original size:20 final size:20
Alignment explanation
Indices: 29866902--29866978 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
29866892 TATCATAAAT
* *
29866902 TGTGATTAAAAGTGATTAAA
1 TGTGATTAAATGTGATTATA
* * *
29866922 TGTGATTATATGTCATTATT
1 TGTGATTAAATGTGATTATA
* * *
29866942 TGTGACTATATGTGGTTATA
1 TGTGATTAAATGTGATTATA
29866962 TGTGATTAACATGTGAT
1 TGTGATTAA-ATGTGAT
29866979 GGAATATATG
Statistics
Matches: 44, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
20 38 0.86
21 6 0.14
ACGTcount: A:0.31, C:0.04, G:0.21, T:0.44
Consensus pattern (20 bp):
TGTGATTAAATGTGATTATA
Found at i:29869665 original size:37 final size:37
Alignment explanation
Indices: 29869592--29869702 Score: 125
Period size: 37 Copynumber: 3.0 Consensus size: 37
29869582 GTTCTTGGAT
* * * * *
29869592 CACCGGCAC-AAAGCCTGCTAGACACATATCCCGAATA
1 CACCGGCACGAAA-CCTACTAGGCACACAGCCTGAATA
*
29869629 CACTGGCACGAAACCTACTAGGCACACAGCCTGAATA
1 CACCGGCACGAAACCTACTAGGCACACAGCCTGAATA
** *
29869666 CACCGGCACGAAGTCTGCTAGGCACACAGCCTGAATA
1 CACCGGCACGAAACCTACTAGGCACACAGCCTGAATA
29869703 TTATGCAAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
37 60 0.95
38 3 0.05
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.14
Consensus pattern (37 bp):
CACCGGCACGAAACCTACTAGGCACACAGCCTGAATA
Found at i:29878569 original size:25 final size:25
Alignment explanation
Indices: 29878475--29878571 Score: 88
Period size: 25 Copynumber: 3.8 Consensus size: 25
29878465 TTGGGTCTTT
*
29878475 CAGAAT-TTAGCTCATACGAGCCCAGA
1 CAGAATATT-GCTCTTACGAG-CCAGA
* * * * *
29878501 AAGACTATTGCACTTACAAGCTAGA
1 CAGAATATTGCTCTTACGAGCCAGA
* *
29878526 CAGAATATCGCTCTGACGAGCCAGA
1 CAGAATATTGCTCTTACGAGCCAGA
*
29878551 CAGAATATTTCTCTTACGAGC
1 CAGAATATTGCTCTTACGAGC
29878572 TGAAGTTCAG
Statistics
Matches: 54, Mismatches: 16, Indels: 3
0.74 0.22 0.04
Matches are distributed among these distances:
25 40 0.74
26 12 0.22
27 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.23
Consensus pattern (25 bp):
CAGAATATTGCTCTTACGAGCCAGA
Found at i:29878625 original size:28 final size:28
Alignment explanation
Indices: 29878594--29878775 Score: 141
Period size: 28 Copynumber: 6.5 Consensus size: 28
29878584 AATTTCTCCA
* * *
29878594 CCGAGCCAGAATTAGAACATCGCTCTTT
1 CCGAGCCAAAATCAGAACATCGCTCTTC
** *
29878622 CCGAGTTAAAATCAGAACTTCGCTCTTC
1 CCGAGCCAAAATCAGAACATCGCTCTTC
* * * *
29878650 CCAAGCCAAAATCAGAACTTCGTTATTC
1 CCGAGCCAAAATCAGAACATCGCTCTTC
* * * *
29878678 CCGACCCAGAATCTGAACACCGCTCTTC
1 CCGAGCCAAAATCAGAACATCGCTCTTC
* * *
29878706 CCGAGCCAAAATCAAAACTTCACTCTTC
1 CCGAGCCAAAATCAGAACATCGCTCTTC
* * * *
29878734 TCGAGCCACAATCTA-AACACCGCTCTTT
1 CCGAGCCAAAATC-AGAACATCGCTCTTC
* *
29878762 CTGAGCCAGAATCA
1 CCGAGCCAAAATCA
29878776 AAGTAGTTAT
Statistics
Matches: 118, Mismatches: 35, Indels: 3
0.76 0.22 0.02
Matches are distributed among these distances:
27 1 0.01
28 116 0.98
29 1 0.01
ACGTcount: A:0.31, C:0.33, G:0.13, T:0.23
Consensus pattern (28 bp):
CCGAGCCAAAATCAGAACATCGCTCTTC
Found at i:29878768 original size:56 final size:56
Alignment explanation
Indices: 29878642--29878777 Score: 164
Period size: 56 Copynumber: 2.4 Consensus size: 56
29878632 ATCAGAACTT
* * ** * *
29878642 CGCTCTTCCCAAGCCAAAATCAGAACTTCGTTATTCCCGACCCAGAATCTGAACAC
1 CGCTCTTCCCGAGCCAAAATCAAAACTTCACTATTCCCGACCCACAATCTAAACAC
* * *
29878698 CGCTCTTCCCGAGCCAAAATCAAAACTTCACTCTTCTCGAGCCACAATCTAAACAC
1 CGCTCTTCCCGAGCCAAAATCAAAACTTCACTATTCCCGACCCACAATCTAAACAC
* * *
29878754 CGCTCTTTCTGAGCCAGAATCAAA
1 CGCTCTTCCCGAGCCAAAATCAAA
29878778 GTAGTTATTA
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
56 68 1.00
ACGTcount: A:0.31, C:0.35, G:0.12, T:0.22
Consensus pattern (56 bp):
CGCTCTTCCCGAGCCAAAATCAAAACTTCACTATTCCCGACCCACAATCTAAACAC
Found at i:29879214 original size:15 final size:15
Alignment explanation
Indices: 29879194--29879233 Score: 62
Period size: 15 Copynumber: 2.6 Consensus size: 15
29879184 TCAATACAAT
29879194 TTCATTCCAATTTTA
1 TTCATTCCAATTTTA
*
29879209 TTCATTTCAATTTTA
1 TTCATTCCAATTTTA
29879224 TTCAATTCCA
1 TTC-ATTCCA
29879234 CAAATTTAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.28, C:0.20, G:0.00, T:0.53
Consensus pattern (15 bp):
TTCATTCCAATTTTA
Found at i:29879866 original size:84 final size:84
Alignment explanation
Indices: 29879725--29879896 Score: 317
Period size: 84 Copynumber: 2.0 Consensus size: 84
29879715 AAATTATCCT
29879725 ATTTAACAACCAAAATTAAAAATTCATCATAAAGTTCCAAGAATATACAAAAATCAACAATGCCA
1 ATTTAACAACCAAAATTAAAAATTCATCATAAAGTTCCAAGAATATACAAAAATCAACAATGCCA
*
29879790 TAACCCACAATATTTAACA
66 TAACCCACAACATTTAACA
* *
29879809 ATTTAACAACCAAAATTAAAAATTCATTATAAAGTTCCAAGAATATACAAAAATCAACAATGGCA
1 ATTTAACAACCAAAATTAAAAATTCATCATAAAGTTCCAAGAATATACAAAAATCAACAATGCCA
29879874 TAACCCACAACATTTAACA
66 TAACCCACAACATTTAACA
29879893 ATTT
1 ATTT
29879897 TACGAATTAG
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
84 85 1.00
ACGTcount: A:0.52, C:0.19, G:0.04, T:0.25
Consensus pattern (84 bp):
ATTTAACAACCAAAATTAAAAATTCATCATAAAGTTCCAAGAATATACAAAAATCAACAATGCCA
TAACCCACAACATTTAACA
Found at i:29883269 original size:19 final size:20
Alignment explanation
Indices: 29883247--29883289 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 20
29883237 TGCAAAAAAT
*
29883247 AAAAAATAA-AAAAATTTTA
1 AAAAAATAATAAAAATTATA
29883266 AAAAAATAATTAAAAATTATA
1 AAAAAATAA-TAAAAATTATA
29883287 AAA
1 AAA
29883290 GAAAAAAATG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 9 0.43
21 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (20 bp):
AAAAAATAATAAAAATTATA
Found at i:29883271 original size:21 final size:20
Alignment explanation
Indices: 29883247--29883295 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
29883237 TGCAAAAAAT
*
29883247 AAAAAATAAAAAAATTTTAAA
1 AAAAAAT-AAAAAATTATAAA
*
29883268 AAAATAATTAAAAATTATAAA
1 AAAA-AATAAAAAATTATAAA
29883289 AGAAAAA
1 A-AAAAA
29883296 AATGTTTGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 18 0.75
22 6 0.25
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (20 bp):
AAAAAATAAAAAATTATAAA
Found at i:29885480 original size:22 final size:22
Alignment explanation
Indices: 29885455--29885498 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
29885445 AACTGTTGCC
29885455 ATGAAGTAATTGGGGATAGACA
1 ATGAAGTAATTGGGGATAGACA
29885477 ATGAAGTAATTGGGGATAGACA
1 ATGAAGTAATTGGGGATAGACA
29885499 GTAGTACCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.41, C:0.05, G:0.32, T:0.23
Consensus pattern (22 bp):
ATGAAGTAATTGGGGATAGACA
Found at i:29900763 original size:17 final size:18
Alignment explanation
Indices: 29900731--29900764 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
29900721 AGTATACAAA
29900731 AGTGTATGTGTGAGAAAT
1 AGTGTATGTGTGAGAAAT
*
29900749 AGTGT-TGTGTTAGAAA
1 AGTGTATGTGTGAGAAA
29900765 GTTTAAAATG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (18 bp):
AGTGTATGTGTGAGAAAT
Found at i:29904982 original size:68 final size:68
Alignment explanation
Indices: 29904783--29905207 Score: 376
Period size: 68 Copynumber: 6.2 Consensus size: 68
29904773 TCATAATTAA
** * * *
29904783 GTAGAGTGAGGCTCGCCTTGAAGATAAAGCGTAGATCTCG-AATCCTTAAAATCACACTCACATT
1 GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAAT-CTTAAAATCACACTCACCTT
* *
29904847 AAAA
65 GAAG
* * * * * ** * * * * * * *
29904851 GAAAAGCGAGGCTCACCTTGTAGGCCAAA-CATATATCTC-AAACCTGAGAATCGA-ACTCACTT
1 GTAGAGTGAGGCTCGCCTTGAAGG-CAAAGTGTAGATATCGTAATCTTAAAATC-ACACTCACCT
29904913 TGAAG
64 TGAAG
* * *
29904918 GTAGAGTAAGGCTTGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAATCACACTCACTTTG
1 GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAATCACACTCACCTTG
29904983 AAG
66 AAG
29904986 GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAATTACACTCACCCAC
1 GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTT--AA--A-A-TCA--CAC
*
29905051 TCACCTTGACG
58 TCACCTTGAAG
* * * * * *
29905062 GAAGAGTGAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAATCAAACTCACCTTA
1 GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAATCACACTCACCTTG
29905127 AAG
66 AAG
* * * * *
29905130 GTAGAGTGAGGCTTGCTTTGAAGGCAAAGTGTAGATCTTG-AATCCTTAAAATCACAC-CCCCTT
1 GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAAT-CTTAAAATCACACTCACCTT
29905193 GAAG
65 GAAG
29905197 GTAGAGTGAGG
1 GTAGAGTGAGG
29905208 TTTGACTTGT
Statistics
Matches: 290, Mismatches: 52, Indels: 31
0.78 0.14 0.08
Matches are distributed among these distances:
66 4 0.01
67 63 0.22
68 151 0.52
69 3 0.01
70 5 0.02
71 1 0.00
72 2 0.01
73 1 0.00
74 5 0.02
76 55 0.19
ACGTcount: A:0.34, C:0.20, G:0.22, T:0.24
Consensus pattern (68 bp):
GTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAATCACACTCACCTTG
AAG
Found at i:29905098 original size:76 final size:76
Alignment explanation
Indices: 29904972--29905123 Score: 232
Period size: 76 Copynumber: 2.0 Consensus size: 76
29904962 CTTAAAATCA
* * * * *
29904972 CACTCACTTTGAAGGTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAA
1 CACTCACCTTGAAGGAAGAGTGAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAA
* *
29905037 TTACACTCACC
66 TCAAACTCACC
*
29905048 CACTCACCTTGACGGAAGAGTGAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAA
1 CACTCACCTTGAAGGAAGAGTGAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAA
29905113 TCAAACTCACC
66 TCAAACTCACC
29905124 TTAAAGGTAG
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
76 68 1.00
ACGTcount: A:0.34, C:0.23, G:0.20, T:0.24
Consensus pattern (76 bp):
CACTCACCTTGAAGGAAGAGTGAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAA
TCAAACTCACC
Found at i:29905165 original size:144 final size:144
Alignment explanation
Indices: 29904905--29905165 Score: 405
Period size: 144 Copynumber: 1.8 Consensus size: 144
29904895 TGAGAATCGA
* * * * * *
29904905 ACTCACTTTGAAGGTAGAGTAAGGCTTGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAAAAT
1 ACTCACCTTGAAGGAAGAGTAAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAAT
* * *
29904970 CACACTCACTTTGAAGGTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAA
66 CAAACTCACCTTAAAGGTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAA
29905035 AATTACACTCACCC
131 AATTACACTCACCC
* *
29905049 ACTCACCTTGACGGAAGAGTGAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAAT
1 ACTCACCTTGAAGGAAGAGTAAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAAT
* *
29905114 CAAACTCACCTTAAAGGTAGAGTGAGGCTTGCTTTGAAGGCAAAGTGTAGAT
66 CAAACTCACCTTAAAGGTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGAT
29905166 CTTGAATCCT
Statistics
Matches: 104, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
144 104 1.00
ACGTcount: A:0.33, C:0.18, G:0.23, T:0.26
Consensus pattern (144 bp):
ACTCACCTTGAAGGAAGAGTAAGACTCGCCTTAAAGGCAAAGCGTAGATATCGTAATCTTAAAAT
CAAACTCACCTTAAAGGTAGAGTGAGGCTCGCCTTGAAGGCAAAGTGTAGATATCGTAATCTTAA
AATTACACTCACCC
Found at i:29911136 original size:57 final size:57
Alignment explanation
Indices: 29911041--29911153 Score: 165
Period size: 57 Copynumber: 2.0 Consensus size: 57
29911031 AAAGGATCAA
* * * *
29911041 AAGTGTTCATATTATGTGGTTGTTCGAGATTGCCAAGGCATTCAACATATTCACACC
1 AAGTGTTCACATTACGTGGCTGTTAGAGATTGCCAAGGCATTCAACATATTCACACC
*
29911098 AAGTGTTCACATTACGTGGCTGTTTAG-GATTGCTAAGGCATTCAACATATTCACAC
1 AAGTGTTCACATTACGTGGCTG-TTAGAGATTGCCAAGGCATTCAACATATTCACAC
29911154 AATGTGGCTG
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
57 47 0.94
58 3 0.06
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.33
Consensus pattern (57 bp):
AAGTGTTCACATTACGTGGCTGTTAGAGATTGCCAAGGCATTCAACATATTCACACC
Found at i:29914437 original size:15 final size:15
Alignment explanation
Indices: 29914417--29914446 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
29914407 TGTTATTGCG
*
29914417 GTTAGTTTTTAGTTT
1 GTTAGTTGTTAGTTT
29914432 GTTAGTTGTTAGTTT
1 GTTAGTTGTTAGTTT
29914447 ATTTAGTTAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.00, G:0.23, T:0.63
Consensus pattern (15 bp):
GTTAGTTGTTAGTTT
Found at i:29915833 original size:23 final size:25
Alignment explanation
Indices: 29915789--29915838 Score: 59
Period size: 23 Copynumber: 2.1 Consensus size: 25
29915779 ATGAATCTAC
** *
29915789 TTTATTCAAAATATCCTTTAA-TGG
1 TTTATTCAAAATAAACTCTAATTGG
29915813 TTTA-TCAAAATAAACTCTAATTGG
1 TTTATTCAAAATAAACTCTAATTGG
29915837 TT
1 TT
29915839 GGGCCTTGAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.36, C:0.12, G:0.08, T:0.44
Consensus pattern (25 bp):
TTTATTCAAAATAAACTCTAATTGG
Found at i:29917610 original size:16 final size:16
Alignment explanation
Indices: 29917591--29917624 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29917581 ATTATATAAT
29917591 ATATAAAAATA-ACATA
1 ATATAAAAA-AGACATA
29917607 ATATAAAAAAGACATA
1 ATATAAAAAAGACATA
29917623 AT
1 AT
29917625 GACTGTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 1 0.06
16 16 0.94
ACGTcount: A:0.68, C:0.06, G:0.03, T:0.24
Consensus pattern (16 bp):
ATATAAAAAAGACATA
Found at i:29918245 original size:27 final size:26
Alignment explanation
Indices: 29918190--29918247 Score: 64
Period size: 27 Copynumber: 2.2 Consensus size: 26
29918180 CCATTAATTT
*
29918190 TTTTTATATTTTTAATAACTTAATGA
1 TTTTTATATTTTTAATAACTTAATAA
* *
29918216 TTTTTA-ATTTTTAAAATAATTTTATAA
1 TTTTTATATTTTT--AATAACTTAATAA
29918243 TTTTT
1 TTTTT
29918248 TTAAATTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
25 6 0.22
26 6 0.22
27 15 0.56
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTTTATATTTTTAATAACTTAATAA
Found at i:29921888 original size:27 final size:27
Alignment explanation
Indices: 29921813--29921877 Score: 114
Period size: 27 Copynumber: 2.4 Consensus size: 27
29921803 AAATTTTAAA
*
29921813 TTTAAATTTAAAATGTCCAAATACATT
1 TTTAAATTTAAAATATCCAAATACATT
29921840 TTTAAATTTAAAATATCCAAATACA-T
1 TTTAAATTTAAAATATCCAAATACATT
29921866 TTTAAATTTAAA
1 TTTAAATTTAAA
29921878 TTTGCTTAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
26 13 0.35
27 24 0.65
ACGTcount: A:0.48, C:0.09, G:0.02, T:0.42
Consensus pattern (27 bp):
TTTAAATTTAAAATATCCAAATACATT
Found at i:29922327 original size:2 final size:2
Alignment explanation
Indices: 29922322--29922350 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
29922312 CTATACACGA
29922322 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29922351 CAGATACATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:29923078 original size:31 final size:30
Alignment explanation
Indices: 29923000--29923145 Score: 179
Period size: 30 Copynumber: 4.9 Consensus size: 30
29922990 CTCAGTAGGT
*
29923000 CCCTAAACTTTT-CAAAATTACATTGTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
29923029 CCCTAAACTTCTCCAAAATTTCATTTTAAC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
** *
29923059 CTTTAAACTTTTTCCAAAATTTCATTTTAAC
1 CCCTAAAC-TTTTCCAAAATTACATTTTAAC
* *
29923090 CCCTAATCTTTTCCAAAATTACATTTTAGC
1 CCCTAAACTTTTCCAAAATTACATTTTAAC
* *
29923120 CCTTAAAC-TTTCAAAAATTACATTTT
1 CCCTAAACTTTTCCAAAATTACATTTT
29923146 TGCCCTCGAA
Statistics
Matches: 101, Mismatches: 14, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
29 28 0.28
30 47 0.47
31 26 0.26
ACGTcount: A:0.34, C:0.24, G:0.01, T:0.40
Consensus pattern (30 bp):
CCCTAAACTTTTCCAAAATTACATTTTAAC
Found at i:29923105 original size:61 final size:60
Alignment explanation
Indices: 29923003--29923143 Score: 180
Period size: 61 Copynumber: 2.4 Consensus size: 60
29922993 AGTAGGTCCC
* *
29923003 TAAAC-TTTTCAAAATTACATTGTAACCCCTAAACTTCTCCAAAATTTCATTTTAACCTT
1 TAAACTTTTTCAAAATTACATTGTAACCCCTAAACTTCTCCAAAATTACATTTTAACCCT
* * * * *
29923062 TAAACTTTTTCCAAAATTTCATTTTAACCCCTAATCTTTTCCAAAATTACATTTTAGCCCT
1 TAAACTTTTT-CAAAATTACATTGTAACCCCTAAACTTCTCCAAAATTACATTTTAACCCT
29923123 TAAAC--TTTCAAAAATTACATT
1 TAAACTTTTTC-AAAATTACATT
29923144 TTTGCCCTCG
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
58 1 0.01
59 18 0.25
60 4 0.06
61 48 0.68
ACGTcount: A:0.35, C:0.23, G:0.01, T:0.40
Consensus pattern (60 bp):
TAAACTTTTTCAAAATTACATTGTAACCCCTAAACTTCTCCAAAATTACATTTTAACCCT
Found at i:29923165 original size:29 final size:28
Alignment explanation
Indices: 29923100--29923203 Score: 100
Period size: 29 Copynumber: 3.6 Consensus size: 28
29923090 CCCTAATCTT
* **
29923100 TTCCAAAATTACATTTTAGCCCTTAAAC
1 TTCCAAAATTACATTTTTGCCCTCGAAC
*
29923128 TTTCAAAAATTACATTTTTGCCCTCGAATC
1 -TTCCAAAATTACATTTTTGCCCTCGAA-C
* * * *
29923158 TTCCAAAAATGCAATTTTACCCTCGAAC
1 TTCCAAAATTACATTTTTGCCCTCGAAC
*
29923186 TTCCAAAAATCACATTTT
1 TTCC-AAAATTACATTTT
29923204 ACCCCCGAAC
Statistics
Matches: 60, Mismatches: 13, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
28 5 0.08
29 54 0.90
30 1 0.02
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.36
Consensus pattern (28 bp):
TTCCAAAATTACATTTTTGCCCTCGAAC
Found at i:29923202 original size:28 final size:28
Alignment explanation
Indices: 29923100--29923223 Score: 117
Period size: 28 Copynumber: 4.3 Consensus size: 28
29923090 CCCTAATCTT
* **
29923100 TTCC-AAAATTACATTTTAGCCCTTAAAC
1 TTCCAAAAATCACATTTTA-CCCTCGAAC
* * *
29923128 TTTCAAAAATTACATTTTTGCCCTCGAATC
1 TTCCAAAAATCACA-TTTTACCCTCGAA-C
29923158 TTCCAAAAATGCA-ATTTTACCCTCGAAC
1 TTCCAAAAAT-CACATTTTACCCTCGAAC
*
29923186 TTCCAAAAATCACATTTTACCCCCGAAC
1 TTCCAAAAATCACATTTTACCCTCGAAC
29923214 AGTTCCAAAA
1 --TTCCAAAA
29923224 GTTTGATTTT
Statistics
Matches: 81, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
27 2 0.02
28 28 0.35
29 27 0.33
30 23 0.28
31 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.06, T:0.31
Consensus pattern (28 bp):
TTCCAAAAATCACATTTTACCCTCGAAC
Found at i:29931962 original size:49 final size:49
Alignment explanation
Indices: 29931902--29932156 Score: 152
Period size: 49 Copynumber: 5.2 Consensus size: 49
29931892 TATAACGGCG
29931902 AACCCGATACCATGAAGATTT-AAAGGGAAAGGTTGAGC-CTGCAACGACA
1 AACCCGATACCATGAAGATTTGAAA-GGAAAGGTTGAGCTC-GCAACGACA
* * *
29931951 AACCCGGTACCATGAAGATTTGAAAGGAAAGGTTGAGGTCGCAATGACA
1 AACCCGATACCATGAAGATTTGAAAGGAAAGGTTGAGCTCGCAACGACA
* * * * * *
29932000 AACCCGACACCTTAAAAGATGTG--ATGAGAAGGATTGAGGC-CGCAACGACG
1 AACCCGATACCAT-GAAGATTTGAAAGGA-AAGG-TTGA-GCTCGCAACGACA
* * * ** *
29932050 AATCCG-TACCATGAA-ATATG-ATGAGAAAGGTTGAGGCT-GCAATAACG
1 AACCCGATACCATGAAGATTTGAAAG-GAAAGGTTGA-GCTCGCAACGACA
** * * * * *
29932097 AACTAGGTACCATAAAGATTTGAAGGGGAAGGTTGAGGC-CGCAACGGCA
1 AACCCGATACCATGAAGATTTGAAAGGAAAGGTTGA-GCTCGCAACGACA
*
29932146 AACTCGATACC
1 AACCCGATACC
29932157 TTAGGAAAAT
Statistics
Matches: 159, Mismatches: 34, Indels: 26
0.73 0.16 0.12
Matches are distributed among these distances:
47 21 0.13
48 17 0.11
49 90 0.57
50 30 0.19
51 1 0.01
ACGTcount: A:0.37, C:0.19, G:0.27, T:0.17
Consensus pattern (49 bp):
AACCCGATACCATGAAGATTTGAAAGGAAAGGTTGAGCTCGCAACGACA
Found at i:29932743 original size:235 final size:233
Alignment explanation
Indices: 29932308--29932744 Score: 529
Period size: 235 Copynumber: 1.9 Consensus size: 233
29932298 GAAGATTCCG
* *
29932308 ATCTCTTATCCCGAGCATGAGGTAGATTGCAGCCATCCGATCTTTTACCCGAGCTTAGGGCAGAT
1 ATCTCTTACCCCGAGCATGAGGTAGATTGAAGCCATCCGATCTTTTACCCGAGCTTAGGGCAGAT
* * * * * * *
29932373 CACCATCAGCCAATCTTTTACCCCGAGCTTGGGGCAGATTGCAGCCATGAAATCTTTTACCCCGA
66 CACCAACAACCAATCTCTTACCCCGAGCCTGGGACAGATTGAAGCCATCAAATCTTTTACCCCGA
* * * * * * **
29932438 GTCTAAAGCAGATCACCATCAGCCAATCTCTTACCCCAAGCTTGAGACAAATTGTAGCTATCTGA
131 GTCTAAAGCAAATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGACAAATTGCAACCATCCAA
29932503 TCTCTTACCCCGAGCCTAAAGCAGATCATCATCAGCTA
196 TCTCTTACCCCGAGCCTAAAGCAGATCATCATCAGCTA
* * * *
29932541 ATCTCTTACCCCGAGCTTGGGGTAGATTGAAGTCATCCGGTCTTTTACCCTCGAGCTT-GAGGCA
1 ATCTCTTACCCCGAGCATGAGGTAGATTGAAGCCATCCGATCTTTTA-CC-CGAGCTTAG-GGCA
* * * *
29932605 GATCACCAACAATCAATCTCTTACCTCGAGCCTGGGACAGATTGAAGCCATCCAATCTTTTACCT
63 GATCACCAACAACCAATCTCTTACCCCGAGCCTGGGACAGATTGAAGCCATCAAATCTTTTACCC
** * * * *
29932670 CGAG-CTTAGGGCAAATCACTATCAGCCAATCTCTTACCTCGAA-CCTAAGATAGATTGCAACCA
128 CGAGTC-TAAAGCAAATCACCATCAGCCAATCTCTTACC-CCAAGCCTAAGACAAATTGCAACCA
29932733 TCCAATCTCTTA
191 TCCAATCTCTTA
29932745 TCCAGATCAT
Statistics
Matches: 168, Mismatches: 31, Indels: 8
0.81 0.15 0.04
Matches are distributed among these distances:
233 41 0.24
234 4 0.02
235 120 0.71
236 3 0.02
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (233 bp):
ATCTCTTACCCCGAGCATGAGGTAGATTGAAGCCATCCGATCTTTTACCCGAGCTTAGGGCAGAT
CACCAACAACCAATCTCTTACCCCGAGCCTGGGACAGATTGAAGCCATCAAATCTTTTACCCCGA
GTCTAAAGCAAATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGACAAATTGCAACCATCCAA
TCTCTTACCCCGAGCCTAAAGCAGATCATCATCAGCTA
Found at i:29932764 original size:235 final size:233
Alignment explanation
Indices: 29932308--29932802 Score: 521
Period size: 235 Copynumber: 2.1 Consensus size: 233
29932298 GAAGATTCCG
* * *
29932308 ATCTCTTATCCCGAGCATGAGGTAGATTGCAGCCATCCGATCTTTTACCCGAGCTTAGGGCAGAT
1 ATCTCTTACCCCGAGCTTGAGGTAGATTGAAGCCATCCGATCTTTTACCCGAGCTTAGGGCAGAT
* * * * * * *
29932373 CACCATCAGCCAATCTTTTACCCCGAGCTTGGGGCAGATTGCAGCCATGAAATCTTTTACCCCGA
66 CACCAACAACCAATCTCTTACCCCGAGCCTGGGACAGATTGAAGCCATCAAATCTTTTACCCCGA
* * * * * * **
29932438 GTCTAAAGCAGATCACCATCAGCCAATCTCTTACCCCAAGCTTGAGACAAATTGTAGCTATCTGA
131 GTCTAAAGCAAATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGACAAATTGCAACCATCCAA
* * *
29932503 TCTCTTACCCCGAGCCTAAAGCAGATCATCA-TCAGCTA
196 TCTCTTACCCAGAGCATAAAGCAGATCA-CAGTCAGCCA
* * *
29932541 ATCTCTTACCCCGAGCTTGGGGTAGATTGAAGTCATCCGGTCTTTTACCCTCGAGCTT-GAGGCA
1 ATCTCTTACCCCGAGCTTGAGGTAGATTGAAGCCATCCGATCTTTTA-CC-CGAGCTTAG-GGCA
* * * *
29932605 GATCACCAACAATCAATCTCTTACCTCGAGCCTGGGACAGATTGAAGCCATCCAATCTTTTACCT
63 GATCACCAACAACCAATCTCTTACCCCGAGCCTGGGACAGATTGAAGCCATCAAATCTTTTACCC
** * * * *
29932670 CGAG-CTTAGGGCAAATCACTATCAGCCAATCTCTTACCTCGAA-CCTAAGATAGATTGCAACCA
128 CGAGTC-TAAAGCAAATCACCATCAGCCAATCTCTTACC-CCAAGCCTAAGACAAATTGCAACCA
* * *** * *
29932733 TCCAATCTCTTATCCAGATCATGGGGCAGATCACAGTCATCCG
191 TCCAATCTCTTACCCAGAGCATAAAGCAGATCACAGTCAGCCA
* *
29932776 ATCTTTTACCCCGAGCTTGAGGCAGAT
1 ATCTCTTACCCCGAGCTTGAGGTAGAT
29932803 CACCAAAAGC
Statistics
Matches: 212, Mismatches: 44, Indels: 10
0.80 0.17 0.04
Matches are distributed among these distances:
233 41 0.19
234 6 0.03
235 162 0.76
236 3 0.01
ACGTcount: A:0.27, C:0.29, G:0.18, T:0.26
Consensus pattern (233 bp):
ATCTCTTACCCCGAGCTTGAGGTAGATTGAAGCCATCCGATCTTTTACCCGAGCTTAGGGCAGAT
CACCAACAACCAATCTCTTACCCCGAGCCTGGGACAGATTGAAGCCATCAAATCTTTTACCCCGA
GTCTAAAGCAAATCACCATCAGCCAATCTCTTACCCCAAGCCTAAGACAAATTGCAACCATCCAA
TCTCTTACCCAGAGCATAAAGCAGATCACAGTCAGCCA
Found at i:29933417 original size:78 final size:78
Alignment explanation
Indices: 29933318--29933855 Score: 517
Period size: 78 Copynumber: 6.9 Consensus size: 78
29933308 TCATAGTCAA
** ** * * *
29933318 TCGATCTTTTACCCTAAGCTTGGGGCAGATCACCAAAAACGAATCTCTTACCCCGAGCTTGGGGT
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
29933383 AGATTGAAGCCAT
66 AGATTGAAGCCAT
* * * * *
29933396 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACTATCAGTCTATCTCTTACCCCGAGCCTGGGGT
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
**
29933461 AGATAAAAGCCAT
66 AGATTGAAGCCAT
* * * * * * *
29933474 TCGATCTTTTACCCTGAGCTTAGGGCAAATCACCATCAGCCAATCTCTTACTCCAATCATGGGGC
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
* *
29933539 AGA-TCACAGTCAT
66 AGATTGA-AGCCAT
* * * * *
29933552 CCAATCTTTTACCCCTAGCTTGAGGCAGATCACCATCAGCCAATCTCTTACCTCGAGCTT-GGGC
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
29933616 AGATTGAAGCCAT
66 AGATTGAAGCCAT
* * * * ** **
29933629 CCGATCTTTTACCCCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCTTAGCTTGAAGC
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
29933694 AGATT-ATAGCCAT
66 AGATTGA-AGCCAT
* * * * * *
29933707 CCGATCTTTTACCTCGAACATGGGGCAGATTACCATCAACCAATCTCTTACCCCGAGCTTGGGGC
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
*
29933772 AGATTGCAA-TCAT
66 AGATTG-AAGCCAT
** * * * * * * * * * * *
29933785 TCGATCTTTTTTCCCAATCATGGGGCAAATCATCGTCAGCCAATCTTTTATCCCGCGATAGGGGC
1 TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
29933850 AGATTG
66 AGATTG
29933856 TAACCATACA
Statistics
Matches: 377, Mismatches: 77, Indels: 12
0.81 0.17 0.03
Matches are distributed among these distances:
77 67 0.18
78 308 0.82
79 1 0.00
80 1 0.00
ACGTcount: A:0.25, C:0.29, G:0.19, T:0.27
Consensus pattern (78 bp):
TCGATCTTTTACCCCGAGCTTGGGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGC
AGATTGAAGCCAT
Found at i:29933628 original size:233 final size:234
Alignment explanation
Indices: 29933280--29933775 Score: 606
Period size: 233 Copynumber: 2.1 Consensus size: 234
29933270 TTACAACTAT
* * * *
29933280 CCAATCTCTTACCCCGATCAT-GGGCAAATCATAGTCAATCGATCTTTTACCCTAAGCTTGGGGC
1 CCAATCTCTTACCCCGATCATGGGGCAGATCACAGTCAATCAATCTTTTACCCTAAGCTTGAGGC
* * *
29933344 AGATCACCAAAAACGAATCTCTTACCCCGAGCTTGGGGTAGATTGAAGCCATTCGATCTTTTACC
66 AGATCACCAAAAACCAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATCCGATCTTTTACC
* * * * * * ** *
29933409 CCGAGCTTGGGGCAGATCACTATCAGTCTATCTCTTACCCCGAGCCTGGGGTAGATAAAAGCCAT
131 CCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAAGCAGATAAAAGCCAT
* * * *
29933474 TCGATCTTTTACC-CTGAGCTTAGGGCAAATCACCATCAG
196 CCGATCTTTTACCTC-GAACATAGGGCAAATCACCATCAA
* *
29933513 CCAATCTCTTACTCCAATCATGGGGCAGATCACAGTC-ATCCAATCTTTTACCCCT-AGCTTGAG
1 CCAATCTCTTACCCCGATCATGGGGCAGATCACAGTCAAT-CAATCTTTTA-CCCTAAGCTTGAG
** * *
29933576 GCAGATCACCATCAGCCAATCTCTTACCTCGAGCTT-GGGCAGATTGAAGCCATCCGATCTTTTA
64 GCAGATCACCAAAAACCAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATCCGATCTTTTA
** * * *
29933640 CCCCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCTTAGCTTGAAGCAGATTATAGCC
129 CCCCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAAGCAGATAAAAGCC
* * *
29933705 ATCCGATCTTTTACCTCGAACATGGGGCAGATTACCATCAA
194 ATCCGATCTTTTACCTCGAACATAGGGCAAATCACCATCAA
* *
29933746 CCAATCTCTTACCCCGAGCTTGGGGCAGAT
1 CCAATCTCTTACCCCGATCATGGGGCAGAT
29933776 TGCAATCATT
Statistics
Matches: 221, Mismatches: 38, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
233 156 0.71
234 61 0.28
235 4 0.02
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.26
Consensus pattern (234 bp):
CCAATCTCTTACCCCGATCATGGGGCAGATCACAGTCAATCAATCTTTTACCCTAAGCTTGAGGC
AGATCACCAAAAACCAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATCCGATCTTTTACC
CCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAAGCAGATAAAAGCCAT
CCGATCTTTTACCTCGAACATAGGGCAAATCACCATCAA
Found at i:29933776 original size:39 final size:39
Alignment explanation
Indices: 29932341--29933775 Score: 537
Period size: 39 Copynumber: 36.8 Consensus size: 39
29932331 AGATTGCAGC
* * *
29932341 CATCCGATCTTTTA-CCCGAGCTTAGGGCAGATCACCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* *
29932379 CAGCCAATCTTTTACCCCGAGCTTGGGGCAGATTGCAGCCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCAT
* * ***
29932421 GA---AATCTTTTACCCCGAG-TCTAAAGCAGATCACCAT
1 CATCCAATCTCTTACCCCGAGCT-TGGGGCAGATCACCAT
* * * * * * *
29932457 CAGCCAATCTCTTACCCCAAGCTTGAGACAAATTGTAGC-T
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-T-CACCAT
** * *** *
29932497 -ATCTGATCTCTTACCCCGAGCCTAAAGCAGATCATCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * *
29932535 CAGCTAATCTCTTACCCCGAGCTTGGGGTAGATTGA--AGT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-TCACCA-T
** * * *
29932574 CATCCGGTCTTTTACCCTCGAGCTTGAGGCAGATCACCAA
1 CATCCAATCTCTTACCC-CGAGCTTGGGGCAGATCACCAT
* * * * *
29932614 CAAT-CAATCTCTTACCTCGAGCCTGGGACAGATTGA--AGC
1 C-ATCCAATCTCTTACCCCGAGCTTGGGGCAGA-TCACCA-T
* * * * *
29932653 CATCCAATCTTTTACCTCGAGCTTAGGGCAAATCACTAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * ** ** ** * *
29932692 CAGCCAATCTCTTACCTCGAACCTAAGATAGATTGCAAC
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * *
29932731 CATCCAATCTCTTATCCAGATCATGGGGCAGATCA-CAGT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCA-T
* * * *
29932770 CATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCAA
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * * *
29932809 AAGCCAATCTTTTACCCTGAGCTTGGGGCAGATTGA--AGC
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-TCACCA-T
* * * * * *
29932848 CATCCGATCTTTTACCTCGAGCTTGGGACAGATCATCAA
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* ** * * *
29932887 CAAT-CAATGTCTTACCTTGAGCTTGGGGCAGATTACAAC
1 C-ATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * *
29932926 CATCCGATCTTTTACCCCGAGCTTGAGGCAGATCACCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * * * * * * *
29932965 TAGCCAATCTCTTGCCCTGAGCCTAGGACAGATTACAAC
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * *
29933004 CATCCGATCTCTTACCCCGATCATGGGGTAGATCA-CAGT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCA-T
* * * * * *
29933043 CATTCGATCTTTTACCCCGAGCTTGAGGCAAATCATCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * *
29933082 CACCCAATCTCTTACCCCGAGCTTGGGGCAAATTGA-AAC
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-TCACCAT
** * * ** ** * *
29933121 CATCTGATCTTTTACCCCGAGCCTAAGATAAATCACCAA
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * * * * *
29933160 CAGCCAATCCCTTACCTCGA-ATCGGAGGCAAATTGA--AGC
1 CATCCAATCTCTTACCCCGAGCTTGG-GGCAGA-TCACCA-T
* * * *
29933199 CATCCGATCTTTTACCCCGAGCTTAGGGCAGATCACTAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * *** * *
29933238 TAACCAATCTCTTACCCCGAGCTTGAAACAGATTA-CAA
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * *
29933276 CTATCCAATCTCTTACCCCGATCAT-GGGCAAATCA-TAGT
1 C-ATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCA-T
* * ** *
29933315 CAAT-CGATCTTTTACCCTAAGCTTGGGGCAGATCACCAA
1 C-ATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * *
29933354 AAACGAATCTCTTACCCCGAGCTTGGGGTAGATTGAAGCCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-T-CA-CCAT
* * *
29933396 --T-CGATCTTTTACCCCGAGCTTGGGGCAGATCACTAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * ** *
29933432 CAGT-CTATCTCTTACCCCGAGCCTGGGGTAGAT-AAAAGC
1 CA-TCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCA-T
* * * * * *
29933471 CATTCGATCTTTTACCCTGAGCTTAGGGCAAATCACCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * * *
29933510 CAGCCAATCTCTTACTCCAATCATGGGGCAGATCA-CAGT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCA-T
* * *
29933549 CATCCAATCTTTTACCCCTAGCTTGAGGCAGATCACCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* * * *
29933588 CAGCCAATCTCTTACCTCGAGCTT-GGGCAGATTGA--AGC
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGA-TCACCA-T
* * * * *
29933626 CATCCGATCTTTTACCCCGAGCCTGAGCCAGATCACCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
* ** ** * * *
29933665 CAGCCAATCTCTTACCCTTAGCTTGAAGCAGATTA-TAGC
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCA-T
* * * * * *
29933704 CATCCGATCTTTTACCTCGAACATGGGGCAGATTACCAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
*
29933743 CAACCAATCTCTTACCCCGAGCTTGGGGCAGAT
1 CATCCAATCTCTTACCCCGAGCTTGGGGCAGAT
29933776 TGCAATCATT
Statistics
Matches: 997, Mismatches: 335, Indels: 129
0.68 0.23 0.09
Matches are distributed among these distances:
36 8 0.01
37 6 0.01
38 90 0.09
39 821 0.82
40 56 0.06
41 8 0.01
42 8 0.01
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.26
Consensus pattern (39 bp):
CATCCAATCTCTTACCCCGAGCTTGGGGCAGATCACCAT
Found at i:29933826 original size:233 final size:234
Alignment explanation
Indices: 29933280--29933855 Score: 557
Period size: 233 Copynumber: 2.5 Consensus size: 234
29933270 TTACAACTAT
* * * * * * * * *
29933280 CCAATCTCTTACCCCGATCAT-GGGCAAATCATAGTCAAT-CGATCTTTTACCCTAAGCTTGGGG
1 CCAATCTCTTACCCCAAGCATGGGGCAGATCACAATC-ATCCAATCTTTTACCCCAAGCATGAGG
* ** * * * *
29933343 CAGATCACCAAAAACGAATCTCTTACCCCGAGCTTGGGGTAGATTGAAGCCATTCGATCTTTTAC
65 CAAATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATCCGATCTTTTAC
* * * * * * ** *
29933408 CCCGAGCTTGGGGCAGATCACTATCAGTCTATCTCTTACCCCGAGCCTGGGGTAGATAAAAGCCA
130 CCCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAAGCAGATAAAAGCCA
* * * *
29933473 TTCGATCTTTTACCCTGAGCTTAGGGCAAATCACCATCAG
195 TCCGATCTTTTACCCTGAACATAGGGCAAATCACCATCAA
* * * * *
29933513 CCAATCTCTTACTCCAATCATGGGGCAGATCACAGTCATCCAATCTTTTACCCCTAGCTTGAGGC
1 CCAATCTCTTACCCCAAGCATGGGGCAGATCACAATCATCCAATCTTTTACCCCAAGCATGAGGC
* *
29933578 AGATCACCATCAGCCAATCTCTTACCTCGAGCTT-GGGCAGATTGAAGCCATCCGATCTTTTACC
66 AAATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATCCGATCTTTTACC
** * * *
29933642 CCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCTTAGCTTGAAGCAGATTATAGCCAT
131 CCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAAGCAGATAAAAGCCAT
* * *
29933707 CCGATCTTTTA-CCTCGAACATGGGGCAGATTACCATCAA
196 CCGATCTTTTACCCT-GAACATAGGGCAAATCACCATCAA
* * ** * * ** * *
29933746 CCAATCTCTTACCCCGAGCTTGGGGCAGATTGCAATCATTCGATCTTTTTTCCCAATCATGGGGC
1 CCAATCTCTTACCCCAAGCATGGGGCAGATCACAATCATCCAATCTTTTACCCCAAGCATGAGGC
* * * * * * *
29933811 AAATCATCGTCAGCCAATCTTTTATCCCGCGATAGGGGCAGATTG
66 AAATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTG
29933856 TAACCATACA
Statistics
Matches: 279, Mismatches: 60, Indels: 7
0.81 0.17 0.02
Matches are distributed among these distances:
232 3 0.01
233 203 0.73
234 73 0.26
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.27
Consensus pattern (234 bp):
CCAATCTCTTACCCCAAGCATGGGGCAGATCACAATCATCCAATCTTTTACCCCAAGCATGAGGC
AAATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGCAGATTGAAGCCATCCGATCTTTTACC
CCGAGCCTGAGCCAGATCACCATCAGCCAATCTCTTACCCCGAGCCTGAAGCAGATAAAAGCCAT
CCGATCTTTTACCCTGAACATAGGGCAAATCACCATCAA
Found at i:29935852 original size:30 final size:30
Alignment explanation
Indices: 29935820--29935966 Score: 152
Period size: 30 Copynumber: 4.9 Consensus size: 30
29935810 TCATATGTTG
* * *
29935820 ACCTCTAAACTTCTCTAAAATTACATTATG
1 ACCTCTAAACTTTTCTAAAATTACATTTTA
* * * *
29935850 ACCTTTACACTTTTTTAAAATTTCATTTTA
1 ACCTCTAAACTTTTCTAAAATTACATTTTA
*
29935880 ACCTCCTAAACTTTTCCAAAATTACATTTTA
1 ACCT-CTAAACTTTTCTAAAATTACATTTTA
* *
29935911 ACC-CTAAACTTTTTTAGAATTACATTTTA
1 ACCTCTAAACTTTTCTAAAATTACATTTTA
* * *
29935940 ACCCCTAAAATTTTACAAAAATTACAT
1 ACCTCTAAACTTTT-CTAAAATTACAT
29935967 GTTGGTCAAT
Statistics
Matches: 95, Mismatches: 19, Indels: 5
0.80 0.16 0.04
Matches are distributed among these distances:
29 26 0.27
30 36 0.38
31 33 0.35
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (30 bp):
ACCTCTAAACTTTTCTAAAATTACATTTTA
Found at i:29935901 original size:31 final size:30
Alignment explanation
Indices: 29935866--29935966 Score: 123
Period size: 29 Copynumber: 3.3 Consensus size: 30
29935856 ACACTTTTTT
* *
29935866 AAAATTTCATTTTAACCTCCTAAACTTTTCC
1 AAAATTACATTTTAACC-CCTAAACTTTTAC
**
29935897 AAAATTACATTTTAA-CCCTAAACTTTTTT
1 AAAATTACATTTTAACCCCTAAACTTTTAC
* *
29935926 AGAATTACATTTTAACCCCTAAAATTTTAC
1 AAAATTACATTTTAACCCCTAAACTTTTAC
29935956 AAAAATTACAT
1 -AAAATTACAT
29935967 GTTGGTCAAT
Statistics
Matches: 60, Mismatches: 8, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
29 25 0.42
30 12 0.20
31 23 0.38
ACGTcount: A:0.40, C:0.20, G:0.01, T:0.40
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTTAC
Found at i:29935937 original size:60 final size:61
Alignment explanation
Indices: 29935820--29935966 Score: 174
Period size: 60 Copynumber: 2.4 Consensus size: 61
29935810 TCATATGTTG
* * * * * *
29935820 ACCT-CTAAACTTCTCTAAAATTACATTATGACCTTTACACTTTTTTAAAATTTCATTTTA
1 ACCTCCTAAACTTTTCAAAAATTACATTATAACCTCTAAACTTTTTTAAAATTACATTTTA
* * *
29935880 ACCTCCTAAACTTTTCCAAAATTACATTTTAACC-CTAAACTTTTTTAGAATTACATTTTA
1 ACCTCCTAAACTTTTCAAAAATTACATTATAACCTCTAAACTTTTTTAAAATTACATTTTA
*
29935940 ACC-CCTAAAATTTTACAAAAATTACAT
1 ACCTCCTAAACTTTT-CAAAAATTACAT
29935967 GTTGGTCAAT
Statistics
Matches: 75, Mismatches: 10, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
59 10 0.13
60 40 0.53
61 25 0.33
ACGTcount: A:0.37, C:0.21, G:0.01, T:0.41
Consensus pattern (61 bp):
ACCTCCTAAACTTTTCAAAAATTACATTATAACCTCTAAACTTTTTTAAAATTACATTTTA
Found at i:29938651 original size:12 final size:12
Alignment explanation
Indices: 29938610--29938654 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
29938600 GTTCACGAAC
*
29938610 AAGCTCGTTTAA
1 AAGCTCGTTTAT
*
29938622 AAACTCGTTTAT
1 AAGCTCGTTTAT
**
29938634 TGGCTCGTTTAT
1 AAGCTCGTTTAT
29938646 AAGCTCGTT
1 AAGCTCGTT
29938655 ATTTATTAAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.40
Consensus pattern (12 bp):
AAGCTCGTTTAT
Found at i:29938850 original size:23 final size:23
Alignment explanation
Indices: 29938760--29938858 Score: 92
Period size: 23 Copynumber: 4.3 Consensus size: 23
29938750 TTCGTGAATG
* *
29938760 TGTTCAATTATATGTTCATGAACA
1 TGTTCGATTA-ATGTTAATGAACA
**** *
29938784 TGTTCGATTAATGTTCGCAAATA
1 TGTTCGATTAATGTTAATGAACA
**
29938807 TGTTCGATTAATGTTTGTGAACA
1 TGTTCGATTAATGTTAATGAACA
29938830 TGTTCGATTAA-GTTAAATGAACA
1 TGTTCGATTAATGTT-AATGAACA
29938853 TGTTCG
1 TGTTCG
29938859 TGAACATTAA
Statistics
Matches: 63, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
22 3 0.05
23 51 0.81
24 9 0.14
ACGTcount: A:0.30, C:0.11, G:0.18, T:0.40
Consensus pattern (23 bp):
TGTTCGATTAATGTTAATGAACA
Found at i:29938868 original size:23 final size:23
Alignment explanation
Indices: 29938824--29938869 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
29938814 TTAATGTTTG
* *
29938824 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
29938847 TGAACATGTTCG-TGAACATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
29938870 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:29946665 original size:69 final size:69
Alignment explanation
Indices: 29946533--29947012 Score: 369
Period size: 69 Copynumber: 7.0 Consensus size: 69
29946523 TTTGTTGACT
* * * * * * * *
29946533 AAGGCTTGCCAGTTTAAGATCACAGTCTCCAAAACAACTCGCGGACTTATGCTCTCA-CTTGATA
1 AAGGCTCGCCAGTTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACGTTCCCAGC-TGATA
29946597 TTCTA
65 TTCTA
* * *
29946602 AAGGCTCGCCAGTTTAAGATCACAGCCTCCAAAACAACTTGTGGATCTACGTTCCCAGCTGATAT
1 AAGGCTCGCCAGTTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACGTTCCCAGCTGATAT
*
29946667 TCAA
66 TCTA
* ** * * * * * *
29946671 AAAGCTCATCAGTTTAAGATTGC-GACCTTCAAAATAGCTCT-CGGACCTATGTTCCCAGCTAAT
1 AAGGCTCGCCAGTTTAAGATCGCAG-CCTCCAAAACAACT-TGCGGACCTACGTTCCCAGCTGAT
29946734 ATTCTA
64 ATTCTA
* * * * * * * *
29946740 AAAGCTTGCCAGTTTAAGATCGCAGCCTCCAAAA-TAGTTCGCAGAGCTACGTT-CCTGACTAAT
1 AAGGCTCGCCAGTTTAAGATCGCAGCCTCCAAAACAACTT-GCGGACCTACGTTCCCAG-CTGAT
29946803 ATTCTA
64 ATTCTA
** * **
29946809 AAGGCTCATC-GATTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACATTCCCAATTGATA
1 AAGGCTCGCCAG-TTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACGTTCCCAGCTGATA
*
29946873 TTCTC
65 TTCTA
* * * ** * ** *
29946878 AAGGCTTGCCGGTTTAAGATCGCAACCTGTAAAACAACTCGCAAACCTACGTTCCTAGCTGATAT
1 AAGGCTCGCCAGTTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACGTTCCCAGCTGATAT
29946943 TCTA
66 TCTA
**** * * *** * *
29946947 AAGGCTCATTGGTTTAAAATCGCAACCTCCAAAACAACTCATGGACCTACATTCCCAACTGATAT
1 AAGGCTCGCCAGTTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACGTTCCCAGCTGATAT
29947012 T
66 T
29947013 ATTAAAGTTC
Statistics
Matches: 323, Mismatches: 77, Indels: 22
0.77 0.18 0.05
Matches are distributed among these distances:
67 1 0.00
68 6 0.02
69 307 0.95
70 9 0.03
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (69 bp):
AAGGCTCGCCAGTTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACGTTCCCAGCTGATAT
TCTA
Found at i:29946978 original size:207 final size:207
Alignment explanation
Indices: 29946594--29946980 Score: 445
Period size: 207 Copynumber: 1.9 Consensus size: 207
29946584 CTCTCACTTG
* * *
29946594 ATATTCTAAAGGCTCGCCAGTTTAAGATCACAGCCTCCAAAACAACTTGTGGATCTACGTTCCCA
1 ATATTCTAAAGGCTCGCCAGTTTAAGATCACAGCCTCCAAAACAACTTGCGGACCTACATTCCCA
* * * * * * * ** *
29946659 GCTGATATTCAAAAAGCTCATCAGTTTAAGATTGCGACCTTCAAAATAGCTCTCGGACCTATGTT
66 ACTGATATTCAAAAAGCTCACCAGTTTAAGATCGCAACCTTCAAAACAACTCGCAAACCTACGTT
** * *
29946724 CCCAGCTAATATTCTAAAAGCTTGCCAGTTTAAGATCGCAGCCTCCAAAATAGTTCGCAGAGCTA
131 CCCAGCTAATATTCTAAAAGCTCACCAGTTTAAAATCGCAACCTCCAAAATAGTTCGCAGAGCTA
29946789 CGTTCCTGACTA
196 CGTTCCTGACTA
** *
29946801 ATATTCTAAAGGCTCATC-GATTTAAGATCGCAGCCTCCAAAACAACTTGCGGACCTACATTCCC
1 ATATTCTAAAGGCTCGCCAG-TTTAAGATCACAGCCTCCAAAACAACTTGCGGACCTACATTCCC
* ** * ** *
29946865 AATTGATATTCTCAAGGCTTGCCGGTTTAAGATCGCAACCTGT-AAAACAACTCGCAAACCTACG
65 AACTGATATTCAAAAAGCTCACCAGTTTAAGATCGCAACCT-TCAAAACAACTCGCAAACCTACG
* * * ***
29946929 TTCCTAGCTGATATTCTAAAGGCTCATTGGTTTAAAATCGCAACCTCCAAAA
129 TTCCCAGCTAATATTCTAAAAGCTCACCAGTTTAAAATCGCAACCTCCAAAA
29946981 CAACTCATGG
Statistics
Matches: 145, Mismatches: 33, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
206 1 0.01
207 143 0.99
208 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (207 bp):
ATATTCTAAAGGCTCGCCAGTTTAAGATCACAGCCTCCAAAACAACTTGCGGACCTACATTCCCA
ACTGATATTCAAAAAGCTCACCAGTTTAAGATCGCAACCTTCAAAACAACTCGCAAACCTACGTT
CCCAGCTAATATTCTAAAAGCTCACCAGTTTAAAATCGCAACCTCCAAAATAGTTCGCAGAGCTA
CGTTCCTGACTA
Found at i:29955341 original size:29 final size:29
Alignment explanation
Indices: 29955308--29955366 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 29
29955298 TTAGCCCTCA
*
29955308 AAATTCATAA-TTAACTCAA-TTAAGTCCCT
1 AAATTCACAAGTT-ACTCAATTTAA-TCCCT
29955337 AAATTCACAAGTTACTCAATTTAATCCCT
1 AAATTCACAAGTTACTCAATTTAATCCCT
29955366 A
1 A
29955367 TTTTAAAATT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
29 21 0.78
30 6 0.22
ACGTcount: A:0.41, C:0.22, G:0.03, T:0.34
Consensus pattern (29 bp):
AAATTCACAAGTTACTCAATTTAATCCCT
Found at i:29955544 original size:19 final size:19
Alignment explanation
Indices: 29955516--29955559 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
29955506 TTAGATTTTA
* *
29955516 AAATTTAATTACATTTAGT
1 AAATTAAATTACATTGAGT
**
29955535 AAATTAAATTTTATTGAGT
1 AAATTAAATTACATTGAGT
29955554 AAATTA
1 AAATTA
29955560 CACTCATAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.45, C:0.02, G:0.07, T:0.45
Consensus pattern (19 bp):
AAATTAAATTACATTGAGT
Found at i:29955688 original size:3 final size:3
Alignment explanation
Indices: 29955680--29955744 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
29955670 TTTATAAAGG
29955680 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
29955728 TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TT
29955745 TATAAGTTAG
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:29956459 original size:16 final size:16
Alignment explanation
Indices: 29956440--29956504 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 16
29956430 ATACAAATTC
29956440 AGGCTTTGTGCCTAGT
1 AGGCTTTGTGCCTAGT
29956456 AGGCTTTGTGCC-AGTGTTAT
1 AGGCTTTGTGCCTA--G---T
29956476 CAGGCTTTGTGCCTAGT
1 -AGGCTTTGTGCCTAGT
*
29956493 AGGTTTTGTGCC
1 AGGCTTTGTGCC
29956505 AGTGTTATCA
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
15 1 0.02
16 23 0.56
17 2 0.05
20 2 0.05
21 12 0.29
22 1 0.02
ACGTcount: A:0.12, C:0.18, G:0.31, T:0.38
Consensus pattern (16 bp):
AGGCTTTGTGCCTAGT
Found at i:29956482 original size:21 final size:21
Alignment explanation
Indices: 29956456--29956525 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
29956446 TGTGCCTAGT
29956456 AGGCTTTGTGCCAGTGTTATC
1 AGGCTTTGTGCCAGTGTTATC
29956477 AGGCTTTGTGCC-----TAGT-
1 AGGCTTTGTGCCAGTGTTA-TC
*
29956493 AGGTTTTGTGCCAGTGTTATC
1 AGGCTTTGTGCCAGTGTTATC
*
29956514 AAGCTTTGTGCC
1 AGGCTTTGTGCC
29956526 TAATAGGCTT
Statistics
Matches: 39, Mismatches: 3, Indels: 14
0.70 0.05 0.25
Matches are distributed among these distances:
16 13 0.33
17 1 0.03
20 1 0.03
21 24 0.62
ACGTcount: A:0.14, C:0.19, G:0.29, T:0.39
Consensus pattern (21 bp):
AGGCTTTGTGCCAGTGTTATC
Found at i:29956488 original size:37 final size:37
Alignment explanation
Indices: 29956438--29956545 Score: 180
Period size: 37 Copynumber: 2.9 Consensus size: 37
29956428 TTATACAAAT
29956438 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTGTTA
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTGTTA
*
29956475 TCAGGCTTTGTGCCTAGTAGGTTTTGTGCCAGTGTTA
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTGTTA
* * *
29956512 TCAAGCTTTGTGCCTAATAGGCTTTATGCCAGTG
1 TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTG
29956546 ATCTAACAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 66 1.00
ACGTcount: A:0.16, C:0.19, G:0.28, T:0.38
Consensus pattern (37 bp):
TCAGGCTTTGTGCCTAGTAGGCTTTGTGCCAGTGTTA
Found at i:29957743 original size:29 final size:29
Alignment explanation
Indices: 29957711--29957859 Score: 112
Period size: 29 Copynumber: 5.1 Consensus size: 29
29957701 AAAACGGGAG
*
29957711 TTTTGGAAAGTTCGGGGGTGAAATGGTAA
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAA
* *
29957740 TTTTGGTGAAA--TC-GAGATCGAAAATGG-AA
1 TTTT-G-GAAAGTTCGGGGGT--AAAATGGTAA
* *
29957769 TGTTGAAAAGTTCGGGGGTAAAATGGTAA
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAA
* * *
29957798 TTTTAGTGAAA-ATCGAGGTTAAAATGG-AA
1 TTTT-G-GAAAGTTCGGGGGTAAAATGGTAA
* *
29957827 TTTTGGAAAGTTTGAGGGTAAAATGGTAA
1 TTTTGGAAAGTTCGGGGGTAAAATGGTAA
29957856 TTTT
1 TTTT
29957860 TGGTGAAATC
Statistics
Matches: 93, Mismatches: 15, Indels: 24
0.70 0.11 0.18
Matches are distributed among these distances:
27 7 0.08
28 25 0.27
29 30 0.32
30 24 0.26
31 7 0.08
ACGTcount: A:0.34, C:0.03, G:0.30, T:0.32
Consensus pattern (29 bp):
TTTTGGAAAGTTCGGGGGTAAAATGGTAA
Found at i:29957746 original size:58 final size:57
Alignment explanation
Indices: 29957667--29957955 Score: 285
Period size: 58 Copynumber: 5.0 Consensus size: 57
29957657 TGGATACTTA
* * * * *
29957667 GGGGCAAAATGGTAATCTTGGTTGAAATTG-GGTCAAAACGGGAGTTTTGGAAAGTTCG
1 GGGGTAAAATGGTAATTTTGG-TGAAATCGAGGTCAAAA-TGGAATTTTGGAAAGTTCG
* * * *
29957725 GGGGTGAAATGGTAATTTTGGTGAAATCGAGATCGAAAATGGAATGTTGAAAAGTTCG
1 GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTC-AAAATGGAATTTTGGAAAGTTCG
* * *
29957783 GGGGTAAAATGGTAATTTTAGTGAAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTG
1 GGGGTAAAATGGTAATTTTGGTG-AAATCGAGGTCAAAATGGAATTTTGGAAAGTTCG
* * * * **
29957841 AGGGTAAAATGGTAATTTTTGGTGAAATC-AGGGCTAAAAATGGATTTTTGGAAAATTTA
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGA-GG-TCAAAATGGAATTTTGGAAAGTTCG
* * * * *
29957900 AGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGAAATTTTGTAAAGTT
1 GGGGTAAAATGGTAA-TTTTGGTGAAATCGAGGTCAAAATGGAATTTTGGAAAGTT
29957956 TAAAGGTTAA
Statistics
Matches: 196, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
57 8 0.04
58 116 0.59
59 72 0.37
ACGTcount: A:0.35, C:0.04, G:0.30, T:0.31
Consensus pattern (57 bp):
GGGGTAAAATGGTAATTTTGGTGAAATCGAGGTCAAAATGGAATTTTGGAAAGTTCG
Found at i:29957822 original size:30 final size:30
Alignment explanation
Indices: 29957731--29957948 Score: 106
Period size: 28 Copynumber: 7.5 Consensus size: 30
29957721 TTCGGGGGTG
* *
29957731 AAATGGTAATTTTGGTG-AAATCGAGATCGA
1 AAATGGTAATTTTGGTGAAAATCGAGGT-TA
* * *
29957761 AAATGG-AA---TGTTGAAAAGTTCGGGGGTA
1 AAATGGTAATTTTGGTGAAAA--TCGAGGTTA
*
29957789 AAATGGTAATTTTAGTGAAAATCGAGGTTA
1 AAATGGTAATTTTGGTGAAAATCGAGGTTA
* * *
29957819 AAATGG-AATTTT-G-GAAAGTTTGAGGGTA
1 AAATGGTAATTTTGGTGAAA-ATCGAGGTTA
*
29957847 AAATGGTAATTTTTGGTG-AAATC-AGGGCTAA
1 AAATGGTAA-TTTTGGTGAAAATCGA-GG-TTA
* ** *
29957878 AAATGG--ATTTTTG-GAAAATTTAAGGGTA
1 AAATGGTAATTTTGGTGAAAA-TCGAGGTTA
*
29957906 AAATGGTAATTTTTGGTG-AAATCGGGGTTA
1 AAATGGTAA-TTTTGGTGAAAATCGAGGTTA
*
29957936 AAAT-GAAATTTTG
1 AAATGGTAATTTTG
29957949 TAAAGTTTAA
Statistics
Matches: 141, Mismatches: 26, Indels: 44
0.67 0.12 0.21
Matches are distributed among these distances:
26 4 0.03
27 8 0.06
28 41 0.29
29 24 0.17
30 37 0.26
31 18 0.13
32 9 0.06
ACGTcount: A:0.37, C:0.03, G:0.28, T:0.33
Consensus pattern (30 bp):
AAATGGTAATTTTGGTGAAAATCGAGGTTA
Found at i:29957916 original size:117 final size:116
Alignment explanation
Indices: 29957711--29957956 Score: 300
Period size: 117 Copynumber: 2.1 Consensus size: 116
29957701 AAAACGGGAG
* * * *
29957711 TTTTGGAAAGTTCGGGGGTGAAATGGTAATTTTGGTGAAATCGAGATCGAAAATGGAATGTTGAA
1 TTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTGGTGAAATCGAGATCAAAAATGGAATGTTGAA
** *
29957776 AAGTTCGGGGGTAAAATGGTAA-TTTTAGTGAAAATCGAGGTTAAAATGGAA
66 AAGTTCAAGGGTAAAATGGTAATTTTTAGTG-AAATCGAGGTTAAAATGAAA
** * *
29957827 TTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTGAAATC-AGGGCTAAAAATGGATTTTTG
1 TTTTGGAAAGTTTGAGGGTAAAATGGTAA-TTTTGGTGAAATCGAGATC-AAAAATGGAATGTT-
* * *
29957891 GAAAA-TTTAAGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAATGAAA
63 GAAAAGTTCAAGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAATGAAA
*
29957944 TTTTGTAAAGTTT
1 TTTTGGAAAGTTT
29957957 AAAGGTTAAA
Statistics
Matches: 111, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
116 29 0.26
117 70 0.63
118 12 0.11
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.33
Consensus pattern (116 bp):
TTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTGGTGAAATCGAGATCAAAAATGGAATGTTGAA
AAGTTCAAGGGTAAAATGGTAATTTTTAGTGAAATCGAGGTTAAAATGAAA
Found at i:29957999 original size:30 final size:30
Alignment explanation
Indices: 29957964--29958036 Score: 121
Period size: 30 Copynumber: 2.4 Consensus size: 30
29957954 TTTAAAGGTT
29957964 AAAATATAATTTTCAGAAAA-TTTTGGGGTC
1 AAAATATAATTTT-AGAAAAGTTTTGGGGTC
*
29957994 AAAATATAATTTTAGAAAAGTTTTGGGGTT
1 AAAATATAATTTTAGAAAAGTTTTGGGGTC
29958024 AAAATATAATTTT
1 AAAATATAATTTT
29958037 TAGATAGTTC
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
29 6 0.15
30 35 0.85
ACGTcount: A:0.42, C:0.03, G:0.15, T:0.40
Consensus pattern (30 bp):
AAAATATAATTTTAGAAAAGTTTTGGGGTC
Found at i:29958012 original size:117 final size:117
Alignment explanation
Indices: 29957784--29958012 Score: 248
Period size: 117 Copynumber: 2.0 Consensus size: 117
29957774 AAAAGTTCGG
* *
29957784 GGGTAAAATGGTAATTTTAGTGAAAATCGAGGTTAAAATGGAATTTTGGAAAGTTTGAGGGTAAA
1 GGGTAAAATGGTAATTTTAGTGAAAATCGAGGTTAAAATGAAATTTTGGAAAGTTTAAGGGTAAA
* ** * * * *
29957849 ATGGTAATTTTTGGTGAAATCAGGGCTAAAAATGGATTTTTGGAAAATTTAA
66 ATGATAATTTTCAGTAAAATCAGGGCTAAAAATAGAATTTTAGAAAATTTAA
* * * *
29957901 GGGTAAAATGGTAATTTTTGGTG-AAATCGGGGTTAAAATGAAATTTTGTAAAGTTTAAAGGTTA
1 GGGTAAAATGGTAA-TTTTAGTGAAAATCGAGGTTAAAATGAAATTTTGGAAAGTTT-AAGGGTA
** * * *
29957965 AAAT-ATAATTTTCAG-AAAATTTTGGGGTCAAAATATAATTTTAGAAAA
64 AAATGATAATTTTCAGTAAAA-TCAGGGCTAAAAATAGAATTTTAGAAAA
29958013 GTTTTGGGGT
Statistics
Matches: 91, Mismatches: 18, Indels: 6
0.79 0.16 0.05
Matches are distributed among these distances:
116 3 0.03
117 72 0.79
118 16 0.18
ACGTcount: A:0.39, C:0.03, G:0.24, T:0.34
Consensus pattern (117 bp):
GGGTAAAATGGTAATTTTAGTGAAAATCGAGGTTAAAATGAAATTTTGGAAAGTTTAAGGGTAAA
ATGATAATTTTCAGTAAAATCAGGGCTAAAAATAGAATTTTAGAAAATTTAA
Found at i:29958555 original size:23 final size:24
Alignment explanation
Indices: 29958522--29958569 Score: 80
Period size: 23 Copynumber: 2.0 Consensus size: 24
29958512 ACCCCCCTTT
*
29958522 CTTTCTCTCCTCTCTTTCATCTCA
1 CTTTCTCTCCTCTCTCTCATCTCA
29958546 CTTT-TCTCCTCTCTCTCATCTCA
1 CTTTCTCTCCTCTCTCTCATCTCA
29958569 C
1 C
29958570 CATGTCCGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 19 0.83
24 4 0.17
ACGTcount: A:0.08, C:0.44, G:0.00, T:0.48
Consensus pattern (24 bp):
CTTTCTCTCCTCTCTCTCATCTCA
Found at i:29959930 original size:17 final size:17
Alignment explanation
Indices: 29959908--29959948 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
29959898 TAATGATTTT
29959908 AATTTAAATTAAATCCA
1 AATTTAAATTAAATCCA
**
29959925 AATTTAAATTAAATTTA
1 AATTTAAATTAAATCCA
29959942 AATTTAA
1 AATTTAA
29959949 TAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (17 bp):
AATTTAAATTAAATCCA
Found at i:29959958 original size:6 final size:6
Alignment explanation
Indices: 29959903--29959948 Score: 51
Period size: 6 Copynumber: 8.0 Consensus size: 6
29959893 ATTTATAATG
* **
29959903 ATTTTA ATTTAA A-TTAA ATCCAA ATTTAA A-TTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
29959949 TAAATTTAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
5 10 0.30
6 23 0.70
ACGTcount: A:0.50, C:0.04, G:0.00, T:0.46
Consensus pattern (6 bp):
ATTTAA
Found at i:29960369 original size:92 final size:92
Alignment explanation
Indices: 29960212--29960480 Score: 425
Period size: 92 Copynumber: 2.9 Consensus size: 92
29960202 TGACGTCTAG
* *
29960212 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGA-TT-CATTATCCAACTTTACTATAA
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGACAAAGACTTGC--TATCCAACTTTACTACAA
29960275 CTTCAAGAGGATAAGAATTGACGTTTAAT
64 CTTCAAGAGGATAAGAATTGACGTTTAAT
*
29960304 GCTTCATCTTGCTCTTACTATAACTTCAGAGAGACAAAGACTTGCTATCCAACTTTACTACAACT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGACAAAGACTTGCTATCCAACTTTACTACAACT
* * *
29960369 TCAAGAGGATAGGAATTGATGTTTGAT
66 TCAAGAGGATAAGAATTGACGTTTAAT
*
29960396 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGACAAAGACTTGCTATCCATCTTTTACTACAAC
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGACAAAGACTTGCTATCCAAC-TTTACTACAAC
*
29960461 TTCAAGAGGATACGAATTGA
65 TTCAAGAGGATAAGAATTGA
29960481 TGTTATTTTG
Statistics
Matches: 165, Mismatches: 9, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
92 132 0.80
93 32 0.19
94 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.32
Consensus pattern (92 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGACAAAGACTTGCTATCCAACTTTACTACAACT
TCAAGAGGATAAGAATTGACGTTTAAT
Found at i:29968970 original size:81 final size:81
Alignment explanation
Indices: 29968875--29969046 Score: 222
Period size: 81 Copynumber: 2.1 Consensus size: 81
29968865 TTAGTAGAGA
* *
29968875 TAAAA-TTATACTTTGACCT-CCTAAAAATGATAAAATTTTGATTTAATCTTTTAAAAATTACAT
1 TAAAATTTA-ACTTTG-CCTCCCTAAAAATAATAAAATTTTGATTTAATCCTTTAAAAATTACAT
29968938 CTTTACTATCACAAAAAT
64 CTTTACTATCACAAAAAT
* * * ** *
29968956 TAAAATTTAACTTTGTCTCCCTAAAATTAATAAGATTTTGATTTAATCCTTTAAAAATTGTATTT
1 TAAAATTTAACTTTGCCTCCCTAAAAATAATAAAATTTTGATTTAATCCTTTAAAAATTACATCT
*
29969021 TTACTATCATAAAAAT
66 TTACTATCACAAAAAT
*
29969037 TACAATTTAA
1 TAAAATTTAA
29969047 TTTATTTTAA
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
80 2 0.03
81 74 0.94
82 3 0.04
ACGTcount: A:0.42, C:0.12, G:0.04, T:0.42
Consensus pattern (81 bp):
TAAAATTTAACTTTGCCTCCCTAAAAATAATAAAATTTTGATTTAATCCTTTAAAAATTACATCT
TTACTATCACAAAAAT
Found at i:29969188 original size:40 final size:38
Alignment explanation
Indices: 29969138--29969213 Score: 100
Period size: 38 Copynumber: 1.9 Consensus size: 38
29969128 TTAAAAATAT
29969138 TTATACTAAAAAAACTACAAA-AAATACAATAAATATTTGA
1 TTATACT--AAAAACT-CAAATAAATACAATAAATATTTGA
* *
29969178 TTATATTAAAAACTCAAATAAATATAATAAATATTT
1 TTATACTAAAAACTCAAATAAATACAATAAATATTT
29969214 ATTGTGTTAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
37 4 0.12
38 23 0.70
40 6 0.18
ACGTcount: A:0.58, C:0.08, G:0.01, T:0.33
Consensus pattern (38 bp):
TTATACTAAAAACTCAAATAAATACAATAAATATTTGA
Found at i:29971439 original size:16 final size:15
Alignment explanation
Indices: 29971408--29971451 Score: 52
Period size: 16 Copynumber: 2.9 Consensus size: 15
29971398 AAAGAATTAG
*
29971408 AAAATTTGAAAAAAT
1 AAAATTAGAAAAAAT
*
29971423 AAATATTAGAAATAAT
1 AAA-ATTAGAAAAAAT
*
29971439 AAAATTATAAAAA
1 AAAATTAGAAAAA
29971452 GAAATGGATT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (15 bp):
AAAATTAGAAAAAAT
Found at i:29972671 original size:18 final size:18
Alignment explanation
Indices: 29972650--29972688 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
29972640 AGAAATTATA
29972650 AAAATTCAAAAAATAAAT
1 AAAATTCAAAAAATAAAT
* *
29972668 AAAATTCAAAAGATTAAT
1 AAAATTCAAAAAATAAAT
29972686 AAA
1 AAA
29972689 CGATTTCTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (18 bp):
AAAATTCAAAAAATAAAT
Found at i:29975258 original size:23 final size:23
Alignment explanation
Indices: 29975232--29975298 Score: 134
Period size: 23 Copynumber: 2.9 Consensus size: 23
29975222 TTTTTTCTAC
29975232 ATTTTTCTTTAATAATAATATAA
1 ATTTTTCTTTAATAATAATATAA
29975255 ATTTTTCTTTAATAATAATATAA
1 ATTTTTCTTTAATAATAATATAA
29975278 ATTTTTCTTTAATAATAATAT
1 ATTTTTCTTTAATAATAATAT
29975299 GCTAAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.54
Consensus pattern (23 bp):
ATTTTTCTTTAATAATAATATAA
Found at i:29978857 original size:4 final size:4
Alignment explanation
Indices: 29978825--29978878 Score: 58
Period size: 4 Copynumber: 13.8 Consensus size: 4
29978815 AACGAAATTT
* * *
29978825 GAAA GAAA -AAA GAAA AAAA TAAGA GAAA GAAA GAAA GAAA GAGA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAA-A GAAA GAAA GAAA GAAA GAAA GAAA
29978872 GAAA GAA
1 GAAA GAA
29978879 GAAGGGGAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 6
0.79 0.09 0.11
Matches are distributed among these distances:
3 5 0.12
4 34 0.81
5 3 0.07
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:29979089 original size:12 final size:12
Alignment explanation
Indices: 29979072--29979096 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
29979062 TTAAGTTTGG
29979072 TTAATTTTAAAA
1 TTAATTTTAAAA
29979084 TTAATTTTAAAA
1 TTAATTTTAAAA
29979096 T
1 T
29979097 ATTTTAATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TTAATTTTAAAA
Done.