Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000914.1 Hibiscus syriacus cultivar Beakdansim tig00001825_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1342319
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
File 1 of 6
Found at i:1608 original size:19 final size:20
Alignment explanation
Indices: 1581--1622 Score: 52
Period size: 19 Copynumber: 2.1 Consensus size: 20
1571 TAACTTTTTC
1581 TTTTATC-TTCATTATTAA-T
1 TTTTATCTTTCATT-TTAACT
*
1600 TTTTCTCTTTCATTTTAACT
1 TTTTATCTTTCATTTTAACT
1620 TTT
1 TTT
1623 ACCTTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 10 0.50
20 10 0.50
ACGTcount: A:0.19, C:0.14, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTTATCTTTCATTTTAACT
Found at i:1628 original size:19 final size:20
Alignment explanation
Indices: 1588--1628 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
1578 TTCTTTTATC
*
1588 TTCATTATTAATTTTTCTCT
1 TTCATTATTAATTTTACTCT
1608 TTCATT-TTAACTTTTAC-CT
1 TTCATTATTAA-TTTTACTCT
1627 TT
1 TT
1629 TTTCTTCTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.20, C:0.17, G:0.00, T:0.63
Consensus pattern (20 bp):
TTCATTATTAATTTTACTCT
Found at i:5383 original size:16 final size:15
Alignment explanation
Indices: 5354--5387 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
5344 CACGTGAGGA
5354 TATTTTCTTCTTATT
1 TATTTTCTTCTTATT
*
5369 TATTTATCTTTTTATT
1 TATTT-TCTTCTTATT
5385 TAT
1 TAT
5388 GTTTTTACCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.74
Consensus pattern (15 bp):
TATTTTCTTCTTATT
Found at i:9293 original size:16 final size:16
Alignment explanation
Indices: 9269--9326 Score: 57
Period size: 16 Copynumber: 3.6 Consensus size: 16
9259 TATATCTGCA
*
9269 AAAAAATTAATTAAAT
1 AAAATATTAATTAAAT
*
9285 AAAATATTAAATAAAT
1 AAAATATTAATTAAAT
*
9301 TAAATA--AATTAAAT
1 AAAATATTAATTAAAT
9315 ACAAAATATTAA
1 --AAAATATTAA
9327 AAATATAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 6
0.75 0.11 0.14
Matches are distributed among these distances:
14 7 0.21
16 24 0.73
18 2 0.06
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAATATTAATTAAAT
Found at i:9302 original size:9 final size:9
Alignment explanation
Indices: 9272--9315 Score: 56
Period size: 9 Copynumber: 5.1 Consensus size: 9
9262 ATCTGCAAAA
*
9272 AAATTAATT
1 AAATTAAAT
9281 AAA-TAAA-
1 AAATTAAAT
*
9288 ATATTAAAT
1 AAATTAAAT
9297 AAATTAAAT
1 AAATTAAAT
9306 AAATTAAAT
1 AAATTAAAT
9315 A
1 A
9316 CAAAATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
7 2 0.07
8 7 0.23
9 21 0.70
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:9321 original size:25 final size:25
Alignment explanation
Indices: 9267--9322 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 25
9257 TTTATATCTG
*
9267 CAAAA-AAATTAATTAAATAAAATA
1 CAAAATAAATTAAATAAATAAAATA
** *
9291 TTAAATAAATTAAATAAATTAAATA
1 CAAAATAAATTAAATAAATAAAATA
9316 CAAAATA
1 CAAAATA
9323 TTAAAAATAT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
24 3 0.12
25 22 0.88
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.29
Consensus pattern (25 bp):
CAAAATAAATTAAATAAATAAAATA
Found at i:20728 original size:14 final size:15
Alignment explanation
Indices: 20694--20731 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20684 AGAGTCAATG
* *
20694 AGTTGACTCTATTCG
1 AGTTGACTCGATTCA
20709 AGTTGACTCGA-TCA
1 AGTTGACTCGATTCA
20723 AGTTGACTC
1 AGTTGACTC
20732 AGTTCGACCC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.24, C:0.21, G:0.21, T:0.34
Consensus pattern (15 bp):
AGTTGACTCGATTCA
Found at i:26678 original size:21 final size:20
Alignment explanation
Indices: 26592--26749 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
26582 AAATGACCAA
**
26592 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
26611 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
26631 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
26651 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
26672 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
26693 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
26713 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
26734 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
26750 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:26765 original size:40 final size:40
Alignment explanation
Indices: 26716--26870 Score: 186
Period size: 40 Copynumber: 3.9 Consensus size: 40
26706 CGATTTTCCA
* ** *
26716 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
* * *
26756 AAATCGCAACGCGTATCCGTAAATCGCAACGTGTATC-CGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCG-AACACAT
* ** *
26796 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
26836 AAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
26871 TATTTAAAGC
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
39 1 0.01
40 62 0.65
41 33 0.34
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.18
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAACACAT
Found at i:26778 original size:20 final size:20
Alignment explanation
Indices: 26716--26869 Score: 168
Period size: 20 Copynumber: 7.7 Consensus size: 20
26706 CGATTTTCCA
* ** *
26716 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
26736 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
26756 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26776 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
26796 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
26816 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
26836 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
26857 AAATCGCAACGCG
1 AAATCGCAACGCG
26870 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 17, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
19 2 0.02
20 92 0.82
21 17 0.15
22 1 0.01
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:27291 original size:33 final size:33
Alignment explanation
Indices: 27252--27322 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
27242 TTCACTTAGA
* *
27252 TTTCATTTCGCGTTACGATTCTGTCGTTGCAAT
1 TTTCATTTCGCATTACGATTCTCTCGTTGCAAT
* * *
27285 TTTCATTTCGCATTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCATTACGATTCTCTCGTTGCAAT
27318 TTTCA
1 TTTCA
27323 AGTTAGTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.23, G:0.15, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCATTACGATTCTCTCGTTGCAAT
Found at i:27459 original size:41 final size:41
Alignment explanation
Indices: 27401--27478 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
27391 TTGCAGAAGA
*
27401 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
27442 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
27479 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:27475 original size:21 final size:21
Alignment explanation
Indices: 27402--27477 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
27392 TGCAGAAGAG
*
27402 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
27423 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
27443 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
27464 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
27478 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:27481 original size:14 final size:14
Alignment explanation
Indices: 27462--27518 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
27452 GAGAAATGAA
27462 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
27476 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
*
27495 AATCGCAACTAGAG
1 AATCGCAACGAGAG
27509 AATCGCAACG
1 AATCGCAACG
27519 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
15 1 0.03
16 2 0.06
17 1 0.03
18 1 0.03
19 10 0.29
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:27494 original size:33 final size:33
Alignment explanation
Indices: 27454--27534 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
27444 CGCAACGAGA
27454 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
27487 GAAATGAAAATCGCAACTAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
**
27520 GAAACCAAAATCGCA
1 GAAATGAAAATCGCA
27535 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:27552 original size:19 final size:19
Alignment explanation
Indices: 27530--27627 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
27520 GAAACCAAAA
*
27530 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27549 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
27563 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27582 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
**
27596 TCTAGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
27615 TCGCGTTGCGATT
1 TCGCGTTGCGATT
27628 CTCTCGTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
16 6 0.10
17 6 0.10
19 31 0.50
ACGTcount: A:0.11, C:0.22, G:0.21, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:27571 original size:14 final size:14
Alignment explanation
Indices: 27552--27641 Score: 63
Period size: 14 Copynumber: 5.7 Consensus size: 14
27542 TTTCATTTCG
27552 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
27566 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
27585 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
27599 AGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
27618 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
27632 CGTTGCGATT
1 CGTTGCGATT
27642 TTCATTTCAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 29 0.48
16 6 0.10
17 6 0.10
19 19 0.32
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:27577 original size:33 final size:33
Alignment explanation
Indices: 27535--27649 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
27525 CAAAATCGCA
27535 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
27568 TTGCGATTTTCATTTCGCGTTGCGATTCTCTAG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
27601 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
27634 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
27650 AACCAAAAGA
Statistics
Matches: 80, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 80 1.00
ACGTcount: A:0.10, C:0.23, G:0.20, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:29501 original size:93 final size:93
Alignment explanation
Indices: 29341--29903 Score: 1101
Period size: 93 Copynumber: 6.1 Consensus size: 93
29331 TAGATTGCTT
*
29341 AGTAAATTTATTCGGTTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
1 AGTAAATTTGTTCGG-TTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGT
29406 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
65 ATTTGTCTTTGTTTTGTCTTTTGGTTGAA
29435 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29500 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29528 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29593 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29621 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29686 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29714 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29779 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29807 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
29872 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
29899 AGTAA
1 AGTAA
29904 TGCAATCCAT
Statistics
Matches: 468, Mismatches: 1, Indels: 2
0.99 0.00 0.00
Matches are distributed among these distances:
92 6 0.01
93 448 0.96
94 14 0.03
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:29991 original size:19 final size:19
Alignment explanation
Indices: 29951--30079 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
29941 TAGTTTACTT
* *
29951 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
29971 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
29990 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
30009 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
30023 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
30042 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
30056 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
30075 TCGCA
1 TCGCA
30080 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:30030 original size:33 final size:32
Alignment explanation
Indices: 29987--30079 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
29977 CGCGAAACCA
**
29987 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
30019 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
30052 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
30080 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:30077 original size:52 final size:52
Alignment explanation
Indices: 29951--30079 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
29941 TAGTTTACTT
**
29951 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
30003 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
30056 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
30080 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:30097 original size:19 final size:19
Alignment explanation
Indices: 30075--30209 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
30065 GAAACCAAAA
*
30075 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
30094 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
30110 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
30127 TCGCATTGCGA--TT-ATG
1 TCGCGTTGCGATTTTCATT
30143 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
30160 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
30179 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
30199 TCGTGTTGCGA
1 TCGCGTTGCGA
30210 AAGTAAACTA
Statistics
Matches: 95, Mismatches: 10, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 46 0.48
20 12 0.13
ACGTcount: A:0.12, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:30116 original size:14 final size:14
Alignment explanation
Indices: 30097--30153 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
30087 TTTCATTTCG
30097 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
30111 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
* *
30128 CGCATTGCGATTATGT
1 CG--TTGCGATTCTTT
30144 CGTTGCGATT
1 CGTTGCGATT
30154 TTCATTTCGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 16 0.44
16 7 0.19
17 7 0.19
19 6 0.17
ACGTcount: A:0.12, C:0.19, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:30122 original size:33 final size:33
Alignment explanation
Indices: 30080--30172 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
30070 CAAAATCGCA
* *
30080 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
*
30113 TTGCGATTTTCATTTCGCATTGCGATTATGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
30146 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
30173 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 56 1.00
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTATGTCG
Found at i:32150 original size:14 final size:14
Alignment explanation
Indices: 32131--32166 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
32121 ATTGTTTAAT
32131 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
32145 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
32159 TGATTTGT
1 TGATTTGT
32167 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:32297 original size:19 final size:19
Alignment explanation
Indices: 32273--32388 Score: 179
Period size: 19 Copynumber: 6.4 Consensus size: 19
32263 AAAATTGACT
32273 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32292 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
32311 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32330 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
32344 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
32363 ATCGCAATGCGGAATGAAA
1 ATCGCAATGCGAAATGAAA
32382 ATCGCAA
1 ATCGCAA
32389 CGGGAGAATC
Statistics
Matches: 89, Mismatches: 3, Indels: 10
0.87 0.03 0.10
Matches are distributed among these distances:
14 10 0.11
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 73 0.82
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:32420 original size:52 final size:52
Alignment explanation
Indices: 32291--32407 Score: 216
Period size: 52 Copynumber: 2.2 Consensus size: 52
32281 GCGAAATGAA
32291 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
* *
32343 AATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCGCAACGGGAG
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
32395 AATCGCAATGCGA
1 AATCGCAATGCGA
32408 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 63 1.00
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:32420 original size:71 final size:68
Alignment explanation
Indices: 32273--32402 Score: 192
Period size: 71 Copynumber: 1.9 Consensus size: 68
32263 AAAATTGACT
*
32273 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAC
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--AGGAAAATCGCAAC
32338 GAGAGA
63 GAGAGA
* *
32344 ATCGCAATGCGAAATGAAAATCGCAATGCGGAATGAAAATCGCAA-CG-GGAGAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGGAAAATCGCAA
32403 TGCGATTTTA
Statistics
Matches: 56, Mismatches: 3, Indels: 5
0.88 0.05 0.08
Matches are distributed among these distances:
66 10 0.18
69 2 0.04
71 44 0.79
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.14
Consensus pattern (68 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGGAAAATCGCAACGAG
AGA
Found at i:32425 original size:19 final size:19
Alignment explanation
Indices: 32397--32585 Score: 219
Period size: 19 Copynumber: 10.7 Consensus size: 19
32387 AACGGGAGAA
* *
32397 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
32416 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
32432 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32449 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
32468 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
32484 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32501 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32520 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
32539 TCCGCATTGCGATTTTCA--
1 T-CGCATTGCGATTTTCATT
*
32557 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
32573 TCGCATTGCGATT
1 TCGCATTGCGATT
32586 CTCTCGTTGC
Statistics
Matches: 146, Mismatches: 8, Indels: 32
0.78 0.04 0.17
Matches are distributed among these distances:
14 23 0.16
16 16 0.11
17 14 0.10
18 1 0.01
19 76 0.52
20 16 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:32453 original size:52 final size:52
Alignment explanation
Indices: 32397--32599 Score: 281
Period size: 52 Copynumber: 3.9 Consensus size: 52
32387 AACGGGAGAA
* *
32397 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
32449 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
*
32501 TCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCA--
1 TCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCT-CG--TTGCGATTTTCATT
*
32557 T-G--TTGGGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATT
32600 GTAATTTCCG
Statistics
Matches: 140, Mismatches: 5, Indels: 17
0.86 0.03 0.10
Matches are distributed among these distances:
47 8 0.06
49 2 0.01
50 2 0.01
51 3 0.02
52 80 0.57
53 24 0.17
54 3 0.02
55 3 0.02
56 3 0.02
58 12 0.09
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:32607 original size:33 final size:33
Alignment explanation
Indices: 32454--32599 Score: 195
Period size: 33 Copynumber: 4.2 Consensus size: 33
32444 TCATTTCGCA
32454 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
32487 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG
*
32523 CATTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 --TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
32559 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
32592 TTGCGATT
1 TTGCGATT
32600 GTAATTTCCG
Statistics
Matches: 99, Mismatches: 6, Indels: 16
0.82 0.05 0.13
Matches are distributed among these distances:
32 1 0.01
33 47 0.47
34 14 0.14
35 3 0.03
36 6 0.06
37 3 0.03
38 15 0.15
39 10 0.10
ACGTcount: A:0.14, C:0.21, G:0.18, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:35061 original size:24 final size:24
Alignment explanation
Indices: 35026--35073 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
35016 TCTGAAACAT
35026 TATCAAAATCCGTG-TATTGACCAA
1 TATCAAAATCCG-GATATTGACCAA
*
35050 TATCAAAGTCCGGATATTGACCAA
1 TATCAAAATCCGGATATTGACCAA
35074 GACCAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 21 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.27
Consensus pattern (24 bp):
TATCAAAATCCGGATATTGACCAA
Found at i:35784 original size:20 final size:20
Alignment explanation
Indices: 35756--35985 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
35746 AAATTTCAGT
* * *
35756 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
35776 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
35796 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
35816 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
35836 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
35856 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
35876 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
35896 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
35916 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
35936 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
35956 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
35976 GTTGCGATTT
1 GTTGCGATTT
35986 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:36002 original size:21 final size:21
Alignment explanation
Indices: 35972--36054 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
35962 ATTTTCATAT
*
35972 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
35993 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
36014 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
36035 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
36055 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:36045 original size:42 final size:43
Alignment explanation
Indices: 35952--36050 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
35942 ATTTATGTGT
* *
35952 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
35993 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
36035 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
36051 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:41719 original size:31 final size:31
Alignment explanation
Indices: 41683--41741 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
41673 AACTTAAAAG
* *
41683 AGTTTTGCAATACTGAGATTTAAATAATTTT
1 AGTTTTACAATACTGAAATTTAAATAATTTT
41714 AGTTTTACAATACTGAAATTTAAATAAT
1 AGTTTTACAATACTGAAATTTAAATAAT
41742 CCATACAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.41, C:0.07, G:0.10, T:0.42
Consensus pattern (31 bp):
AGTTTTACAATACTGAAATTTAAATAATTTT
Found at i:41825 original size:54 final size:54
Alignment explanation
Indices: 41756--42208 Score: 243
Period size: 54 Copynumber: 8.4 Consensus size: 54
41746 ACAACTACAA
*
41756 TAATAAATTATTTAAAATAAAACAATCCATATTTTAAAATAAATCAATCTATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
* * ** *
41810 TAATAAATTATTTAAAATAAATCAATCGATACAACTACAATAATAAATCAATCCATAC
1 TAATAAATTATTTAAAATAAATCAATCCAT---ATTTTAA-AATAAATCAATCTATAC
* * *** * * *
41868 AAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT-AATAAATCAAT-C
1 TAATAAATTATTTAAAATAAATCAATCCATA-TTTTAAAATAAATCAATCTATAC
* * * * * * *
41921 -CAT--A-T-TTTAAAATAAACCAATCCATA--CT--AATAAAT-TATTTAAAA
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
* * * * * *
41965 TAAATCAATCCATATTTTAAAATAAATCAATCCATA--CT--AATAAAT-TATTTAAAA
1 T-AATAAAT---TA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
* * *
42019 TAAATCAATCCTATTTTAAAATAATCAATCTATACTAATAATTATTTAAAATAAATCAATCTATA
1 T-AATAAAT--TA-TTTAAAAT-A--AATCAAT-C-CAT-A-T-TTTAAAATAAATCAATCTATA
42084 C
54 C
*
42085 -AACTACA--A--T--AATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
1 TAA-TAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
*
42133 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATAC
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
42187 TAATAAATTATTTAAAATAAAT
1 TAATAAATTATTTAAAATAAAT
42209 TATTTTAAAA
Statistics
Matches: 322, Mismatches: 39, Indels: 76
0.74 0.09 0.17
Matches are distributed among these distances:
43 6 0.02
44 3 0.01
45 2 0.01
46 2 0.01
48 45 0.14
49 4 0.01
50 3 0.01
51 2 0.01
52 5 0.02
53 19 0.06
54 145 0.45
55 5 0.02
56 10 0.03
57 5 0.02
58 47 0.15
59 1 0.00
61 1 0.00
63 1 0.00
64 2 0.01
65 9 0.03
66 5 0.02
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (54 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
Found at i:41826 original size:32 final size:31
Alignment explanation
Indices: 41788--41901 Score: 132
Period size: 32 Copynumber: 3.8 Consensus size: 31
41778 CAATCCATAT
41788 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATAC-AATAAATTA
* *
41820 TTTAAAATAAATCAATCGATACAACTACA--A
1 TTTAAAATAAATCAATCTATACAA-TAAATTA
*
41850 --T--AATAAATCAATCCATACAAATAAATTA
1 TTTAAAATAAATCAATCTATAC-AATAAATTA
41878 TTTAAAATAAATCAATCTATACAA
1 TTTAAAATAAATCAATCTATACAA
41902 CTACAATAAT
Statistics
Matches: 69, Mismatches: 5, Indels: 17
0.76 0.05 0.19
Matches are distributed among these distances:
26 19 0.28
27 2 0.03
28 2 0.03
30 2 0.03
31 4 0.06
32 40 0.58
ACGTcount: A:0.54, C:0.13, G:0.01, T:0.32
Consensus pattern (31 bp):
TTTAAAATAAATCAATCTATACAATAAATTA
Found at i:41855 original size:26 final size:26
Alignment explanation
Indices: 41825--41924 Score: 110
Period size: 26 Copynumber: 3.6 Consensus size: 26
41815 AATTATTTAA
*
41825 AATAAATCAATCGATACAACTACAAT
1 AATAAATCAATCCATACAACTACAAT
* *
41851 AATAAATCAATCCATACAAATAAATTATTT
1 AATAAATCAATCCATACAACTACA--A--T
*
41881 AAAATAAATCAATCTATACAACTACAAT
1 --AATAAATCAATCCATACAACTACAAT
41909 AATAAATCAATCCATA
1 AATAAATCAATCCATA
41925 TTTTAAAATA
Statistics
Matches: 61, Mismatches: 7, Indels: 12
0.76 0.09 0.15
Matches are distributed among these distances:
26 36 0.59
28 2 0.03
30 2 0.03
32 21 0.34
ACGTcount: A:0.55, C:0.17, G:0.01, T:0.27
Consensus pattern (26 bp):
AATAAATCAATCCATACAACTACAAT
Found at i:41882 original size:58 final size:58
Alignment explanation
Indices: 41793--41924 Score: 237
Period size: 58 Copynumber: 2.3 Consensus size: 58
41783 CATATTTTAA
* *
41793 AATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAATCGATACAACTACAAT
1 AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACAACTACAAT
*
41851 AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACAACTACAAT
1 AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACAACTACAAT
41909 AATAAATCAATCCATA
1 AATAAATCAATCCATA
41925 TTTTAAAATA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
58 71 1.00
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.30
Consensus pattern (58 bp):
AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCGATACAACTACAAT
Found at i:41931 original size:138 final size:134
Alignment explanation
Indices: 41771--42028 Score: 408
Period size: 138 Copynumber: 1.9 Consensus size: 134
41761 AATTATTTAA
* *
41771 AATAAAACAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAAACAATCCATATTTTAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
41836 CGATACAACTACAATAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACA
66 CCAT---ACTACAA-AATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACA
41901 ACTACAAT
127 ACTACAAT
*
41909 AATAAATCAATCCATATTTTAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAAACAATCCATATTTTAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAAT
* ** *
41974 CCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAATC
66 CCATACTACAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATC
42029 CTATTTTAAA
Statistics
Matches: 112, Mismatches: 8, Indels: 4
0.90 0.06 0.03
Matches are distributed among these distances:
134 43 0.38
135 4 0.04
138 65 0.58
ACGTcount: A:0.53, C:0.14, G:0.00, T:0.32
Consensus pattern (134 bp):
AATAAAACAATCCATATTTTAAAATAAACCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATACTACAAAATAAATCAATCCATACAAATAAATTATTTAAAATAAATCAATCTATACAACTA
CAAT
Found at i:41965 original size:32 final size:32
Alignment explanation
Indices: 41926--42029 Score: 129
Period size: 32 Copynumber: 3.6 Consensus size: 32
41916 CAATCCATAT
*
41926 TTTAAAATAAACCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
41958 TTTAAAATAAATCAAT-C---C--AT--A-T-
1 TTTAAAATAAATCAATCCATACTAATAAATTA
41980 TTTAAAATAAATCAATCCATACTAATAAATTA
1 TTTAAAATAAATCAATCCATACTAATAAATTA
42012 TTTAAAATAAATCAATCC
1 TTTAAAATAAATCAATCC
42030 TATTTTAAAA
Statistics
Matches: 61, Mismatches: 1, Indels: 20
0.74 0.01 0.24
Matches are distributed among these distances:
22 16 0.26
23 2 0.03
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 2 0.03
32 33 0.54
ACGTcount: A:0.52, C:0.14, G:0.00, T:0.34
Consensus pattern (32 bp):
TTTAAAATAAATCAATCCATACTAATAAATTA
Found at i:41984 original size:22 final size:22
Alignment explanation
Indices: 41958--42000 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
41948 TAATAAATTA
41958 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATCCATAT
41980 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
42001 CTAATAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.51, C:0.14, G:0.00, T:0.35
Consensus pattern (22 bp):
TTTAAAATAAATCAATCCATAT
Found at i:42009 original size:22 final size:22
Alignment explanation
Indices: 41960--42008 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
41950 ATAAATTATT
**
41960 TAAAATAAATCAATCCATATTT
1 TAAAATAAATCAATCCATATAA
41982 TAAAATAAATCAATCCATACTAA
1 TAAAATAAATCAATCCATA-TAA
42005 TAAA
1 TAAA
42009 TTATTTAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAAATAAATCAATCCATATAA
Found at i:42135 original size:131 final size:134
Alignment explanation
Indices: 41963--42208 Score: 453
Period size: 131 Copynumber: 1.9 Consensus size: 134
41953 AATTATTTAA
41963 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
*
42028 CC-TATTTTAAAAT-AATCAATCTATACTAAT-AATTATTTAAAATAAATCAATCTATACAACTA
66 CCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
42090 CAAT
131 CAAT
*
42094 AATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTATTTAAAATAAATCAAT
1 AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
42159 CCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAAT
66 CCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAAT
42209 TATTTTAAAA
Statistics
Matches: 110, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
131 66 0.60
132 11 0.10
133 16 0.15
134 17 0.15
ACGTcount: A:0.52, C:0.12, G:0.00, T:0.36
Consensus pattern (134 bp):
AATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTATTTAAAATAAATCAAT
CCATATTTTAAAATAAATCAATATATACTAATAAATTATTTAAAATAAATCAATCTATACAACTA
CAAT
Found at i:42140 original size:22 final size:23
Alignment explanation
Indices: 42065--42139 Score: 73
Period size: 22 Copynumber: 3.2 Consensus size: 23
42055 AATAATTATT
42065 TAAAATAAATCAATCTATAC-AA
1 TAAAATAAATCAATCTATACTAA
* **
42087 CTACAATAATAAATCAATCCATA-TTT
1 -T--AA-AATAAATCAATCTATACTAA
42113 TAAAATAAATCAATCTATACTAA
1 TAAAATAAATCAATCTATACTAA
42136 TAAA
1 TAAA
42140 TTATTTAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
22 15 0.37
23 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.55, C:0.15, G:0.00, T:0.31
Consensus pattern (23 bp):
TAAAATAAATCAATCTATACTAA
Found at i:42143 original size:185 final size:189
Alignment explanation
Indices: 41756--42208 Score: 752
Period size: 185 Copynumber: 2.4 Consensus size: 189
41746 ACAACTACAA
*
41756 TAATAAATTATTTAAAATAAAACAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
41821 TTAAAATAAATCAATCGATACAACTACAATAATAAATCAATCCATACAAATAAATTATTTAAAAT
66 TTAAAATAAATCAATC---ACAACTACAATAATAAATCAATCCATACAAATAAATTATTTAAAAT
41886 AAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAACCAATCCATAC
128 AAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAACCAATCCATAC
*
41948 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCCATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
* * ** * *
42013 TTAAAATAAATCAATC-CTATTTTAA-AAT-AATCAATCTATACTAAT-AATTATTTAAAATAAA
66 TTAAAATAAATCAATCACAACTACAATAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
* *
42074 TCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATCTATAC
131 TCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAACCAATCCATAC
*
42133 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTAT
1 TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
42198 TTAAAATAAAT
66 TTAAAATAAAT
42209 TATTTTAAAA
Statistics
Matches: 249, Mismatches: 12, Indels: 7
0.93 0.04 0.03
Matches are distributed among these distances:
185 147 0.59
186 15 0.06
187 3 0.01
188 5 0.02
192 79 0.32
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.34
Consensus pattern (189 bp):
TAATAAATTATTTAAAATAAATCAATCCATATTTTAAAATAAATCAATCTATACTAATAAATTAT
TTAAAATAAATCAATCACAACTACAATAATAAATCAATCCATACAAATAAATTATTTAAAATAAA
TCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAACCAATCCATAC
Found at i:42150 original size:32 final size:32
Alignment explanation
Indices: 42111--42208 Score: 117
Period size: 32 Copynumber: 3.4 Consensus size: 32
42101 CAATCCATAT
42111 TTTAAAATAAATCAATCTATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
42143 TTTAAAATAAATCAATC----C--AT--A-T-
1 TTTAAAATAAATCAATCTATACTAATAAATTA
*
42165 TTTAAAATAAATCAATATATACTAATAAATTA
1 TTTAAAATAAATCAATCTATACTAATAAATTA
42197 TTTAAAATAAAT
1 TTTAAAATAAAT
42209 TATTTTAAAA
Statistics
Matches: 55, Mismatches: 1, Indels: 20
0.72 0.01 0.26
Matches are distributed among these distances:
22 16 0.29
23 1 0.02
24 1 0.02
26 3 0.05
28 3 0.05
30 1 0.02
31 1 0.02
32 29 0.53
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (32 bp):
TTTAAAATAAATCAATCTATACTAATAAATTA
Found at i:42169 original size:22 final size:22
Alignment explanation
Indices: 42143--42243 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
42133 TAATAAATTA
*
42143 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
*
42165 TTTAAAATAAATCAATATATACT
1 TTTAAAATAAATCAATACATA-T
** * ** * *
42188 AATAAATTATTTAAAATAAATTAT
1 TTTAAAATAAAT-CAATACA-TAT
*
42212 TTTAAAATAAATCAATCCATAT
1 TTTAAAATAAATCAATACATAT
*
42234 TTTATAATAA
1 TTTAAAATAA
42244 TTTATTTTAA
Statistics
Matches: 58, Mismatches: 18, Indels: 6
0.71 0.22 0.07
Matches are distributed among these distances:
22 31 0.53
23 12 0.21
24 13 0.22
25 2 0.03
ACGTcount: A:0.52, C:0.08, G:0.00, T:0.40
Consensus pattern (22 bp):
TTTAAAATAAATCAATACATAT
Found at i:42174 original size:79 final size:77
Alignment explanation
Indices: 41980--42163 Score: 253
Period size: 80 Copynumber: 2.3 Consensus size: 77
41970 CAATCCATAT
41980 TTTAAAATAAATCAATCCATACTAA-TAAATTATTTAAAATAAATCAATCCTATTTTAAAATAAT
1 TTTAAAATAAATCAATCCATAC-AACTAAA--A--T--AATAAATCAATCCTATTTTAAAATAAT
42044 CAATCTATACTAATAATTA
59 CAATCTATACTAATAATTA
* *
42063 TTTAAAATAAATCAATCTATACAACTACAATAATAAATCAATCCATATTTTAAAATAAATCAATC
1 TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCC-TATTTTAAAAT-AATCAATC
42128 TATACTAATAAATTA
64 TATACTAAT-AATTA
42143 TTTAAAATAAATCAATCCATA
1 TTTAAAATAAATCAATCCATA
42164 TTTTAAAATA
Statistics
Matches: 94, Mismatches: 3, Indels: 11
0.87 0.03 0.10
Matches are distributed among these distances:
77 13 0.14
78 11 0.12
79 18 0.19
80 25 0.27
81 1 0.01
82 2 0.02
83 24 0.26
ACGTcount: A:0.52, C:0.13, G:0.00, T:0.35
Consensus pattern (77 bp):
TTTAAAATAAATCAATCCATACAACTAAAATAATAAATCAATCCTATTTTAAAATAATCAATCTA
TACTAATAATTA
Found at i:42217 original size:15 final size:15
Alignment explanation
Indices: 42188--42335 Score: 172
Period size: 15 Copynumber: 9.5 Consensus size: 15
42178 AATATATACT
42188 AATAAATTA-TTTAA
1 AATAAATTATTTTAA
42202 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
42217 AATAAATCAATCCATATTTTAT
1 AAT--A--AAT---TATTTTAA
*
42239 AATAATTTATTTTAA
1 AATAAATTATTTTAA
*
42254 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
42269 AATAAATTATTTTAT
1 AATAAATTATTTTAA
*
42284 AATAAATTATTTTAT
1 AATAAATTATTTTAA
42299 AATAAATTATTTTAA
1 AATAAATTATTTTAA
*
42314 AATAAACTATTTTAA
1 AATAAATTATTTTAA
42329 AATAAAT
1 AATAAAT
42336 AACCTTATTA
Statistics
Matches: 118, Mismatches: 8, Indels: 15
0.84 0.06 0.11
Matches are distributed among these distances:
14 9 0.08
15 92 0.78
17 1 0.01
18 2 0.02
19 3 0.03
20 1 0.01
22 10 0.08
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATAAATTATTTTAA
Found at i:42230 original size:69 final size:67
Alignment explanation
Indices: 42134--42290 Score: 210
Period size: 69 Copynumber: 2.3 Consensus size: 67
42124 AATCTATACT
*
42134 AATAAATTA-TTTAAAATAAATCAATCCATATTTTAAAATAAATCAATATATACTAATAAATTA-
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAAT-AATCAAT-TATA-AAATAAATTAT
42197 TTTAA
63 TTTAA
* ** *
42202 AATAAATTATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAATTATTTT
1 AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTT
*
42267 AT
66 AA
*
42269 AATAAATTATTTTATAATAAAT
1 AATAAATTATTTTAAAATAAAT
42291 TATTTTATAA
Statistics
Matches: 80, Mismatches: 7, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
66 9 0.11
67 28 0.35
68 14 0.17
69 29 0.36
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (67 bp):
AATAAATTATTTTAAAATAAATCAATCCATATTTTAAAATAATCAATTATAAAATAAATTATTTT
AA
Found at i:42247 original size:47 final size:50
Alignment explanation
Indices: 42108--42319 Score: 171
Period size: 54 Copynumber: 4.3 Consensus size: 50
42098 AATCAATCCA
*
42108 TATTTTAAAATAAATCAATCTATACTAATAAAT--TA-TTTAAAATAAATCAAT
1 TATTTTAAAATAAATCAATATATACTAATAAATAATATTTTAAAAT--A--AAT
42159 CCATATTTTAAAATAAATCAATATATACTAATAAAT--TA-TTTAAAATAAAT
1 ---TATTTTAAAATAAATCAATATATACTAATAAATAATATTTTAAAATAAAT
* *
42209 TATTTTAAAATAAATCAATCCATAT-TTTAT-AATAATTTATTTTAAAATAAAT
1 TATTTTAAAATAAATCAAT--ATATACTAATAAATAA--TATTTTAAAATAAAT
* * * *
42261 TATTTTATAATAAAT-TAT-TTTA-TAATAAAT--TATTTTATAATAAAT
1 TATTTTAAAATAAATCAATATATACTAATAAATAATATTTTAAAATAAAT
42306 TATTTTAAAATAAA
1 TATTTTAAAATAAA
42320 CTATTTTAAA
Statistics
Matches: 140, Mismatches: 9, Indels: 27
0.80 0.05 0.15
Matches are distributed among these distances:
45 27 0.19
47 22 0.16
48 8 0.06
49 7 0.05
50 3 0.02
51 4 0.03
52 27 0.19
54 42 0.30
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (50 bp):
TATTTTAAAATAAATCAATATATACTAATAAATAATATTTTAAAATAAAT
Found at i:42249 original size:37 final size:34
Alignment explanation
Indices: 42108--42319 Score: 144
Period size: 30 Copynumber: 6.4 Consensus size: 34
42098 AATCAATCCA
*
42108 TATTTTAAAATAAATCAATCTA--TACTAATAAAT
1 TATTTTAAAATAAATCAATCTATTTA-AAATAAAT
42141 TA-TTTAAAATAAATCAATCCATATTTTAAAATAAAT
1 TATTTTAAAATAAATCAAT-C-TA-TTTAAAATAAAT
* * * * * *
42177 CAATATATACT-AATAAAT-TATTTAAAATAAAT
1 TATTTTAAAATAAATCAATCTATTTAAAATAAAT
* *
42209 TATTTTAAAATAAATCAATCCATATTTTATAATAATT
1 TATTTTAAAATAAATCAAT-C-TA-TTTAAAATAAAT
* *
42246 TATTTTAAAATAAAT---TAT-TTTATAATAAAT
1 TATTTTAAAATAAATCAATCTATTTAAAATAAAT
* * *
42276 TATTTTATAATAAAT---TAT-TTTATAATAAAT
1 TATTTTAAAATAAATCAATCTATTTAAAATAAAT
42306 TATTTTAAAATAAA
1 TATTTTAAAATAAA
42320 CTATTTTAAA
Statistics
Matches: 150, Mismatches: 18, Indels: 25
0.78 0.09 0.13
Matches are distributed among these distances:
30 53 0.35
32 35 0.23
33 11 0.07
34 3 0.02
36 16 0.11
37 32 0.21
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (34 bp):
TATTTTAAAATAAATCAATCTATTTAAAATAAAT
Found at i:42282 original size:45 final size:45
Alignment explanation
Indices: 42162--42335 Score: 188
Period size: 45 Copynumber: 3.7 Consensus size: 45
42152 AATCAATCCA
* *
42162 TATTTTAAAATAAATCAATATATACTAATAAATTA-TTTAAAATAAAT
1 TATTTTAAAATAAA-CTAT-TTTA-TAATAAATTATTTTAAAATAAAT
*
42209 TATTTTAAAATAAATCAATCCATATTTTATAATAATTTATTTTAAAATAAAT
1 TATTTTAAAAT--A--AA--C-TATTTTATAATAAATTATTTTAAAATAAAT
* * *
42261 TATTTTATAATAAATTATTTTATAATAAATTATTTTATAATAAAT
1 TATTTTAAAATAAACTATTTTATAATAAATTATTTTAAAATAAAT
*
42306 TATTTTAAAATAAACTATTTTAAAATAAAT
1 TATTTTAAAATAAACTATTTTATAATAAAT
42336 AACCTTATTA
Statistics
Matches: 109, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
45 55 0.50
47 11 0.10
48 2 0.02
49 1 0.01
50 1 0.01
51 11 0.10
52 26 0.24
53 2 0.02
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (45 bp):
TATTTTAAAATAAACTATTTTATAATAAATTATTTTAAAATAAAT
Found at i:43324 original size:21 final size:22
Alignment explanation
Indices: 43300--43351 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 22
43290 ATATTATTAT
43300 TATAATATTACATA-TTT-AAAA
1 TATAATATT-CATATTTTCAAAA
* *
43321 TATATTTATTGATATTTTCAAAA
1 TATA-ATATTCATATTTTCAAAA
43344 TATAATAT
1 TATAATAT
43352 AAGGTTCGTA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 7 0.28
22 10 0.40
23 8 0.32
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (22 bp):
TATAATATTCATATTTTCAAAA
Found at i:43382 original size:15 final size:15
Alignment explanation
Indices: 43362--43391 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
43352 AAGGTTCGTA
43362 TTTTAATATTATAAT
1 TTTTAATATTATAAT
43377 TTTTAATATTATAAT
1 TTTTAATATTATAAT
43392 AATATTATCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TTTTAATATTATAAT
Found at i:43414 original size:23 final size:25
Alignment explanation
Indices: 43365--43414 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
43355 GTTCGTATTT
43365 TAATATTATAATTTTTAATATTATAA
1 TAATATTATAATTTTTAATA-TATAA
*
43391 TAATATTATCA-TTTTAATA-ATAA
1 TAATATTATAATTTTTAATATATAA
43414 T
1 T
43415 TAATGTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 5 0.22
25 8 0.35
26 10 0.43
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (25 bp):
TAATATTATAATTTTTAATATATAA
Found at i:43446 original size:18 final size:18
Alignment explanation
Indices: 43372--43455 Score: 73
Period size: 18 Copynumber: 4.6 Consensus size: 18
43362 TTTTAATATT
* * *
43372 ATAATTTTTAATATTATA
1 ATAATATTTATTATTTTA
*
43390 ATAATA-TTATCATTTTA
1 ATAATATTTATTATTTTA
* *
43407 ATAATAATTAATGTA-ATTA
1 ATAAT-ATTTAT-TATTTTA
43426 ATAATATTTATTATTTTA
1 ATAATATTTATTATTTTA
43444 ATAATATATTAT
1 ATAATAT-TTAT
43456 AATATACTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
17 15 0.29
18 21 0.40
19 15 0.29
20 1 0.02
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
ATAATATTTATTATTTTA
Found at i:43493 original size:27 final size:26
Alignment explanation
Indices: 43434--43496 Score: 67
Period size: 27 Copynumber: 2.3 Consensus size: 26
43424 TAATAATATT
*
43434 TATTATTTTAATAATATATTATAATA
1 TATTATTTTAATAATAAATTATAATA
43460 TACTTATTTTAATAA-ACAATTA-AATTTA
1 TA-TTATTTTAATAATA-AATTATAA--TA
43488 TATTATTTT
1 TATTATTTT
43497 TATTTTAGTA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 5 0.16
27 23 0.72
28 4 0.12
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (26 bp):
TATTATTTTAATAATAAATTATAATA
Found at i:44116 original size:2 final size:2
Alignment explanation
Indices: 44109--44138 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
44099 GCCCAAAGAA
44109 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
44139 GGGTCTAGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46493 original size:14 final size:14
Alignment explanation
Indices: 46471--46522 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 14
46461 ATTGGACCTG
*
46471 GAAAAAAATAAAAT
1 GAAATAAATAAAAT
46485 GAAATAAAT--AA-
1 GAAATAAATAAAAT
46496 -AAATAAATAAAAT
1 GAAATAAATAAAAT
46509 G-AATAAAATAAAAT
1 GAAAT-AAATAAAAT
46523 AAAAATATAC
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
10 8 0.25
12 4 0.12
13 3 0.09
14 17 0.53
ACGTcount: A:0.75, C:0.00, G:0.06, T:0.19
Consensus pattern (14 bp):
GAAATAAATAAAAT
Found at i:46504 original size:24 final size:23
Alignment explanation
Indices: 46472--46525 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 23
46462 TTGGACCTGG
46472 AAAA-AAATAAAATGAA-ATAAAT
1 AAAATAAATAAAATGAATA-AAAT
46494 AAAAATAAATAAAATGAATAAAAT
1 -AAAATAAATAAAATGAATAAAAT
46518 AAAATAAA
1 AAAATAAA
46526 AATATACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
23 12 0.41
24 16 0.55
25 1 0.03
ACGTcount: A:0.78, C:0.00, G:0.04, T:0.19
Consensus pattern (23 bp):
AAAATAAATAAAATGAATAAAAT
Found at i:46518 original size:5 final size:5
Alignment explanation
Indices: 46475--46526 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
46465 GACCTGGAAA
* *
46475 AAAAT AAAAT GAAAT -AAAT AAAA- ATAAAT AAAAT -GAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT
46523 AAAA
1 AAAA
46527 ATATACTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
4 8 0.20
5 31 0.77
6 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:46522 original size:19 final size:19
Alignment explanation
Indices: 46475--46526 Score: 70
Period size: 19 Copynumber: 2.7 Consensus size: 19
46465 GACCTGGAAA
*
46475 AAAATAAAATGAAATAAAT
1 AAAATAAAATAAAATAAAT
*
46494 AAAA-ATAAATAAAATGAAT
1 AAAATA-AAATAAAATAAAT
46513 AAAATAAAATAAAA
1 AAAATAAAATAAAA
46527 ATATACTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 1 0.03
19 27 0.93
20 1 0.03
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (19 bp):
AAAATAAAATAAAATAAAT
Found at i:46681 original size:31 final size:30
Alignment explanation
Indices: 46622--46682 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 30
46612 TATGTTACAT
*
46622 AGTTTTCAAAATGTTTTAAAATATTATATA
1 AGTTTTCAAAATGTTTTAAAATACTATATA
*
46652 AGTTTTCAAAAATTGTTTTTAAA-ACTATATA
1 AGTTTTC-AAAA-TGTTTTAAAATACTATATA
46683 TTATATATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 7 0.26
31 11 0.41
32 9 0.33
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.46
Consensus pattern (30 bp):
AGTTTTCAAAATGTTTTAAAATACTATATA
Found at i:46801 original size:37 final size:37
Alignment explanation
Indices: 46544--46956 Score: 341
Period size: 37 Copynumber: 11.5 Consensus size: 37
46534 AAATATAATT
* * * *
46544 TATATAATATAT-ATATTTCAAAAATATTTTTTAAAC
1 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
*
46580 TATATA-T-TAT-ATTTTT-AAAAA-GTTTTCAAAAC
1 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
* * *
46612 --TATGTTACAT-AGTTTTC-AAAATG-TTTT--AA-
1 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
*
46641 -A-ATATTATATAAGTTTTCAAAAATTGTTTTTAAAAC
1 TATATATTATATAATTTTTCAAAAA-TGTTTTTAAAAC
*
46677 TATATATTATATATATTTTTAAAAAAAATGTTTTTAAAAC
1 TATATATTATATA-ATTTTT--CAAAAATGTTTTTAAAAC
* *
46717 TATATATTATATAATTTTTTAAAAAATGTTTTTTAAAAT
1 TATATATTATATAA-TTTTTCAAAAATG-TTTTTAAAAC
* *
46756 TATTTATTATATAATTTTTCAAAAATGTTTTTAGAAC
1 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
* *
46793 TATATATTATATAATTTTTCAAAAATATTTTAAAAAC
1 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
* * *
46830 TATATACTATATAAGTTTTC-AAAATGTTTTAAAAAC
1 TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
* * * *
46866 TATACAATATATAAATGTTTTC-AAAATGTTTTCAACAC
1 TATATATTATAT-AAT-TTTTCAAAAATGTTTTTAAAAC
* *
46904 TATATATTATAT-A---TT-AAAAATATTTTCAAAAAC
1 TATATATTATATAATTTTTCAAAAATGTTTT-TAAAAC
* *
46937 TATATAATATATAAATTTTC
1 TATATATTATATAATTTTTC
46957 GGAAAATCGT
Statistics
Matches: 314, Mismatches: 35, Indels: 54
0.78 0.09 0.13
Matches are distributed among these distances:
29 7 0.02
30 12 0.04
31 5 0.02
32 35 0.11
33 25 0.08
34 9 0.03
35 3 0.01
36 32 0.10
37 64 0.20
38 59 0.19
39 28 0.09
40 30 0.10
41 5 0.02
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATATTATATAATTTTTCAAAAATGTTTTTAAAAC
Found at i:46939 original size:33 final size:32
Alignment explanation
Indices: 46888--46949 Score: 88
Period size: 33 Copynumber: 1.9 Consensus size: 32
46878 AAATGTTTTC
* * *
46888 AAAATGTTTTCAACACTATATATTATATATTA
1 AAAATATTTTCAAAACTATATAATATATATTA
46920 AAAATATTTTCAAAAACTATATAATATATA
1 AAAATATTTTC-AAAACTATATAATATATA
46950 AATTTTCGGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 10 0.38
33 16 0.62
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (32 bp):
AAAATATTTTCAAAACTATATAATATATATTA
Found at i:47029 original size:2 final size:2
Alignment explanation
Indices: 47022--47068 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
47012 ACTATATTAC
*
47022 TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA -A AA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47061 TA TA TA TA
1 TA TA TA TA
47069 AAAACAAAAT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
1 3 0.07
2 38 0.93
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:47079 original size:21 final size:21
Alignment explanation
Indices: 47035--47079 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 21
47025 ATATATATAT
*
47035 ATATATATATATAATAAAATA
1 ATATATATATATAATAAAAAA
47056 ATATATATATATAA-AAACAAA
1 ATATATATATATAATAAA-AAA
47077 ATA
1 ATA
47080 ACTCCGGACG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.33
Consensus pattern (21 bp):
ATATATATATATAATAAAAAA
Found at i:48140 original size:84 final size:84
Alignment explanation
Indices: 47700--48132 Score: 503
Period size: 84 Copynumber: 5.2 Consensus size: 84
47690 CTTAGTGTAA
* * * *
47700 TCAAACTCAAAGGTCTTCGGTTGGCAAATAGA-CCTTATCGACTTAAGCTATGCTGCAAATGATG
1 TCAAACTCGAAGGTCTTCGGTTGGCAGATA-ACCCTTCTCGACTTAAGTTATGCTGCAAATGATG
* *
47764 TGCCTTGGAGATGAGCGTAA
65 TGCCTTGGAGCTGAGCGTAG
* * *
47784 TCGAACTCGAAGGTCTTCCGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATAT
1 TCAAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
*
47849 GCCTTGGAGCTGAGCTTAG
66 GCCTTGGAGCTGAGCGTAG
* * * * * * * * * *
47868 TCTAACTCGAAGGTTTTTTGG-TGACATG-TAACACTTCTAGCCTTGAGTTATGTTGTAAATGAT
1 TCAAACTCGAAGG-TCTTCGGTTGGCA-GATAACCCTTCTCGACTTAAGTTATGCTGCAAATGAT
* * ** *
47931 GTGCCTCGAAGCTGAGTATAA
64 GTGCCTTGGAGCTGAGCGTAG
* * * * *
47952 TCGAACTCGAGGGTATTCGGTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGATAT
1 TCAAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
* *
48017 GTCTTGGAGCTGAGTGTAG
66 GCCTTGGAGCTGAGCGTAG
* * *
48036 TCAAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGAATTAAGTTATACTGCAAATGATGT
1 TCAAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
48101 GCCTTGGAGCTGAGCGTAG
66 GCCTTGGAGCTGAGCGTAG
48120 TCAAACTCGAAGG
1 TCAAACTCGAAGG
48133 CCTTTGGTGG
Statistics
Matches: 289, Mismatches: 55, Indels: 10
0.82 0.16 0.03
Matches are distributed among these distances:
83 7 0.02
84 277 0.96
85 5 0.02
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (84 bp):
TCAAACTCGAAGGTCTTCGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCGTAG
Found at i:48465 original size:110 final size:110
Alignment explanation
Indices: 48247--49012 Score: 1175
Period size: 110 Copynumber: 7.0 Consensus size: 110
48237 ATCCAAAAAT
* * * * *
48247 TTGTGTTATTTCGAGGCCAATATCCTTCGTTGTGAAGTTGAAATTAACTCTG-A--AAA-TGGAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
48308 AGTTGTTTGTTGACAG-CTAGCCTCCCCTTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTC-AGTCGCCCCTTCGCTGTGAAGTTGAGC
*
48353 TTGTGTTGTCTCGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
*
48418 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGATGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * *
48463 TTGTGTTGTCTTGAGTCCAATATCCTT-TTCTATGAAGTTGAAATTGACTCTGAATGAAACTGAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGT-TGTGAAGTTGAAATTGACTCTGAATGAAACTGAA
*
48527 AAGTTGTTTGTTGACAGTCAGTCGCCCCTTTGCTGTGAAGTTGAGC
65 AAGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * *
48573 TTGTGTTGTCTCGAGTCCAATATCATTCGCTCTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
48638 AGTTGTTTGTTGACAGTCAGTCGTCCCTTCGCTGTGAAGTTTAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
*
48683 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTTAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* *
48748 AGTTGTTTGTTGACAATCAGTCGCCCATTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* * *
48793 TTATGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTAAAATTGACTATGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * *
48858 AGTTGTTTGTTGACAATCAGTCGCCTCTTTGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
* *
48903 TTGTGTTGTCTCGAGTCCAATATCCTTCATTGTGAAGTTAAAATTGACTCTGAATGAAACTGAAA
1 TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
* * * *
48968 AGTTATTTGTTGACCGTTAATCGCCCCTTCGCTGTGAAGTTGAGC
66 AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
49013 AACCACCATC
Statistics
Matches: 606, Mismatches: 47, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
106 47 0.08
107 1 0.00
109 3 0.00
110 554 0.91
111 1 0.00
ACGTcount: A:0.24, C:0.17, G:0.23, T:0.36
Consensus pattern (110 bp):
TTGTGTTGTCTCGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAA
AGTTGTTTGTTGACAGTCAGTCGCCCCTTCGCTGTGAAGTTGAGC
Found at i:54114 original size:45 final size:45
Alignment explanation
Indices: 54063--54216 Score: 220
Period size: 45 Copynumber: 3.4 Consensus size: 45
54053 TATAAAATCT
* *
54063 CTTACCATGTATCCCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
54108 CTTACCATTTAATACCATAAGCTCGTAAGCTTATTTTACCAATATA
1 CTTACCATTT-ATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
* * * *
54154 CTTACTATTTGTTCCATAAGCTCATAAGCTTATTTTACCAATACA
1 CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
*
54199 CTTGCCA-TTATTCCATAA
1 CTTACCATTTATTCCATAA
54217 CCATATACCA
Statistics
Matches: 98, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
44 10 0.10
45 45 0.46
46 43 0.44
ACGTcount: A:0.32, C:0.23, G:0.07, T:0.38
Consensus pattern (45 bp):
CTTACCATTTATTCCATAAGCTCGTAAGCTTATTTTACCAATATA
Found at i:54238 original size:20 final size:20
Alignment explanation
Indices: 54213--54255 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
54203 CCATTATTCC
* * *
54213 ATAACCATATACCATAGGCA
1 ATAACCATAAACAATAGACA
54233 ATAACCATAAACAATAGACA
1 ATAACCATAAACAATAGACA
54253 ATA
1 ATA
54256 GCCCAATATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.53, C:0.21, G:0.07, T:0.19
Consensus pattern (20 bp):
ATAACCATAAACAATAGACA
Found at i:55028 original size:237 final size:237
Alignment explanation
Indices: 54613--55098 Score: 945
Period size: 237 Copynumber: 2.1 Consensus size: 237
54603 AAATCATATA
54613 TGTTCATGATAACATCATATGCAAAAATCAGTGATCAATGCATTTTATTTTCAACCTTTGACATA
1 TGTTCATGATAACATCATATGCAAAAATCAGTGATCAATGCATTTTATTTTCAACCTTTGACATA
54678 TTTAGAATATATCAAATATATGATAAATGACATAAATATCATGTCAACATAAACAAGGTCGACTT
66 TTTAGAATATATCAAATATATGATAAATGACATAAATATCATGTCAACATAAACAAGGTCGACTT
*
54743 ATCGCAAGTCTTCCTGATGATGTATAAAACATTCATGTATAATGTCATGCATGTATTGCACTCAC
131 ATCGCAAGTATTCCTGATGATGTATAAAACATTCATGTATAATGTCATGCATGTATTGCACTCAC
54808 CTTGACACTTTATAATTTTTCCAAATATATGTGCCTCACTAT
196 CTTGACACTTTATAATTTTTCCAAATATATGTGCCTCACTAT
54850 TGTTCATGATAACATCATATGCAAAAATCAGTGATCAATGCATTTTATTTTCAACCTTTGACATA
1 TGTTCATGATAACATCATATGCAAAAATCAGTGATCAATGCATTTTATTTTCAACCTTTGACATA
54915 TTTAGAATATATCAAATATATGATAAATGACATAAATATCATGTCAACATAAACAAGGTCGACTT
66 TTTAGAATATATCAAATATATGATAAATGACATAAATATCATGTCAACATAAACAAGGTCGACTT
54980 ATCGCAAGTATTCCTGATGATGTATAAAACATTCATGTATAATGTCATGCATGTATTGCACTCAC
131 ATCGCAAGTATTCCTGATGATGTATAAAACATTCATGTATAATGTCATGCATGTATTGCACTCAC
55045 CTTGACACTTTATAATTTTTCCAAATATATGTGCCTCACTAT
196 CTTGACACTTTATAATTTTTCCAAATATATGTGCCTCACTAT
* *
55087 TGTCCATAATAA
1 TGTTCATGATAA
55099 GCCCTTTTAT
Statistics
Matches: 246, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
237 246 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (237 bp):
TGTTCATGATAACATCATATGCAAAAATCAGTGATCAATGCATTTTATTTTCAACCTTTGACATA
TTTAGAATATATCAAATATATGATAAATGACATAAATATCATGTCAACATAAACAAGGTCGACTT
ATCGCAAGTATTCCTGATGATGTATAAAACATTCATGTATAATGTCATGCATGTATTGCACTCAC
CTTGACACTTTATAATTTTTCCAAATATATGTGCCTCACTAT
Found at i:55588 original size:14 final size:14
Alignment explanation
Indices: 55569--55604 Score: 72
Period size: 14 Copynumber: 2.6 Consensus size: 14
55559 TGATCAACAA
55569 AATCTGTTTTGCAG
1 AATCTGTTTTGCAG
55583 AATCTGTTTTGCAG
1 AATCTGTTTTGCAG
55597 AATCTGTT
1 AATCTGTT
55605 GTCAGATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.44
Consensus pattern (14 bp):
AATCTGTTTTGCAG
Found at i:61997 original size:20 final size:21
Alignment explanation
Indices: 61974--62052 Score: 72
Period size: 20 Copynumber: 3.8 Consensus size: 21
61964 TTGATGCAGA
*
61974 GGGAATCGATCCCCCCATGA-
1 GGGAACCGATCCCCCCATGAG
**
61994 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGA-TCCCCCCATG-AG
*
62017 GGGAACCGATCCCCCCA-CAG
1 GGGAACCGATCCCCCCATGAG
* *
62037 GGGAATCGATACCCCC
1 GGGAACCGATCCCCCC
62053 TGGGGTTCTG
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
20 24 0.50
21 8 0.17
22 7 0.15
23 9 0.19
ACGTcount: A:0.24, C:0.37, G:0.25, T:0.14
Consensus pattern (21 bp):
GGGAACCGATCCCCCCATGAG
Found at i:64285 original size:11 final size:11
Alignment explanation
Indices: 64269--64301 Score: 66
Period size: 11 Copynumber: 3.0 Consensus size: 11
64259 AAAGGGGGAG
64269 AAGTGTGTTTT
1 AAGTGTGTTTT
64280 AAGTGTGTTTT
1 AAGTGTGTTTT
64291 AAGTGTGTTTT
1 AAGTGTGTTTT
64302 TAAAATAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.18, C:0.00, G:0.27, T:0.55
Consensus pattern (11 bp):
AAGTGTGTTTT
Found at i:64360 original size:21 final size:20
Alignment explanation
Indices: 64315--64357 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
64305 AATAATAAAT
64315 GGGAGAAGTGTTAAAGTAAG
1 GGGAGAAGTGTTAAAGTAAG
64335 GGGAGAAGTGTTAAAGTAAG
1 GGGAGAAGTGTTAAAGTAAG
64355 GGG
1 GGG
64358 GAGTAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.44, T:0.19
Consensus pattern (20 bp):
GGGAGAAGTGTTAAAGTAAG
Found at i:66514 original size:5 final size:5
Alignment explanation
Indices: 66506--66566 Score: 63
Period size: 5 Copynumber: 12.2 Consensus size: 5
66496 CTGGAAAAGA
* * *
66506 AAAAT AAAAT GAAAT AAATT AAAAT -GAAT AAAAT AAAAT AAAAT -AAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
66554 AATAAT AATAAT A
1 AA-AAT AA-AAT A
66567 TACTAAATAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
4 7 0.15
5 30 0.64
6 10 0.21
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (5 bp):
AAAAT
Found at i:66541 original size:19 final size:19
Alignment explanation
Indices: 66506--66566 Score: 68
Period size: 19 Copynumber: 3.1 Consensus size: 19
66496 CTGGAAAAGA
* *
66506 AAAATAAAATGAAATAAATT
1 AAAAT-AAATAAAATAAAAT
*
66526 AAAATGAATAAAATAAAAT
1 AAAATAAATAAAATAAAAT
66545 AAAATAAATAATAATAATAAT
1 AAAATAAATAA-AATAA-AAT
66566 A
1 A
66567 TACTAAATAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 21 0.60
20 10 0.29
21 4 0.11
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (19 bp):
AAAATAAATAAAATAAAAT
Found at i:66560 original size:15 final size:14
Alignment explanation
Indices: 66506--66561 Score: 60
Period size: 14 Copynumber: 3.9 Consensus size: 14
66496 CTGGAAAAGA
66506 AAAATAAAATGAAAT
1 AAAATAAAAT-AAAT
* *
66521 AAATTAAAATGAAT
1 AAAATAAAATAAAT
66535 AAAATAAAATAAA-
1 AAAATAAAATAAAT
66548 ATAAATAATAATAA
1 A-AAATAA-AATAA
66562 TAATATACTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
13 1 0.03
14 20 0.57
15 14 0.40
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (14 bp):
AAAATAAAATAAAT
Found at i:66622 original size:31 final size:32
Alignment explanation
Indices: 66587--66660 Score: 89
Period size: 32 Copynumber: 2.3 Consensus size: 32
66577 AATTTATATA
**
66587 ATATA-TATATTTCAAAAATA-TTTTTTAAACT
1 ATATATTATATTTCAAAAA-AGTTTTCAAAACT
*
66618 ATATATTATATTTTAAAAAAGTTTTCAAAACT
1 ATATATTATATTTCAAAAAAGTTTTCAAAACT
*
66650 ATATGTTATAT
1 ATATATTATAT
66661 AGTTTTCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 6 0.16
32 31 0.84
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (32 bp):
ATATATTATATTTCAAAAAAGTTTTCAAAACT
Found at i:66790 original size:76 final size:72
Alignment explanation
Indices: 66581--67020 Score: 365
Period size: 76 Copynumber: 6.2 Consensus size: 72
66571 AAATATAATT
* * * ** *
66581 TATATAATATAT-ATATTTCAAAAATATTTTTTAAACTATAT-AT-TAT-A-TTTTAAAAAAGTT
1 TATATATTATATAAT-TTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTTAAAAATGTT
*
66641 TTCAAAAC
65 TTTAAAAC
* * * * * * *
66649 TATATGTTATAT-AGTTTTCAAAATGTTTT-AAAA-T-TAT--TATAAAAGTTTTCAAAGT-TTT
1 TATATATTATATAATTTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTTAAAAATGTTT
66707 TTAAAAC
66 TTAAAAC
* *
66714 TATATATTATATAATTTTTTAAAAATGTTTTTAAAACTATATATTATATAATTTTTAAAAAAATG
1 TATATATTATATAA-TTTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTT--AAAAATG
*
66779 TTTTTTTAAAC
63 -TTTTTAAAAC
* * *
66790 TATATATTATATAATTTTTTAAAAATGTTTTTAAAACTATATATTATATAATATTTCAAAAATG-
1 TATATATTATATAA-TTTTTAAAAATGTTTTAAAAACTATATAATATATAAT-TTTTAAAAATGT
66854 TTTTAAAAC
64 TTTTAAAAC
* * * * *
66863 TATATACTATATAAGTTTTCAAAATGTTTTAAAAACTATACAATATATAAATGTTTTCAAAATGT
1 TATATATTATATAATTTTTAAAAATGTTTTAAAAACTATATAATATAT-AAT-TTTTAAAAATGT
66928 TTTTAAAAC
64 TTTTAAAAC
* ** **
66937 TATATA-T-TAT-A-TTTTAAAAATATTTTCAAAAACTATATAATATATAAATTTTCGAAAATCA
1 TATATATTATATAATTTTTAAAAATGTTTT-AAAAACTATATAATATAT-AATTTTTAAAAATGT
*
66998 TTTTAGACAAT
64 TTTTA-A-AAC
67009 TATATATTATAT
1 TATATATTATAT
67021 TTTGTCAAAA
Statistics
Matches: 311, Mismatches: 39, Indels: 38
0.80 0.10 0.10
Matches are distributed among these distances:
63 1 0.00
64 5 0.02
65 22 0.07
66 11 0.04
67 26 0.08
68 15 0.05
69 1 0.00
70 29 0.09
71 23 0.07
72 50 0.16
73 35 0.11
74 22 0.07
75 7 0.02
76 61 0.20
77 3 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (72 bp):
TATATATTATATAATTTTTAAAAATGTTTTAAAAACTATATAATATATAATTTTTAAAAATGTTT
TTAAAAC
Found at i:66995 original size:38 final size:37
Alignment explanation
Indices: 66581--67020 Score: 372
Period size: 37 Copynumber: 12.3 Consensus size: 37
66571 AAATATAATT
* * * *
66581 TATATAATATATATA-TTTCAAAAATATTTTTTAAAC
1 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
* *
66617 TATATA-T-TAT--ATTTT-AAAAAAGTTTTCAAAAC
1 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
* *
66649 TATATGTTATAT-AGTTTTC-AAAATG-TTTT-AAA-
1 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
*
66681 -AT-TATTATA-AAAGTTTTC-AAAGT-TTTTTAAAAC
1 TATATATTATATAAA-TTTTCAAAAATGTTTTTAAAAC
* *
66714 TATATATTATATAATTTTTTAAAAATGTTTTTAAAAC
1 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
* * *
66751 TATATATTATATAATTTTTAAAAAAATGTTTTTTTAAAC
1 TATATATTATATAAATTTT-CAAAAATG-TTTTTAAAAC
* *
66790 TATATATTATATAATTTTTTAAAAATGTTTTTAAAAC
1 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
66827 TATATATTATAT-AATATTTCAAAAATG-TTTTAAAAC
1 TATATATTATATAAAT-TTTCAAAAATGTTTTTAAAAC
* * *
66863 TATATACTATATAAGTTTTC-AAAATGTTTTAAAAAC
1 TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
* *
66899 TATACAATATATAAATGTTTTC-AAAATGTTTTTAAAAC
1 TATATATTATATAAA--TTTTCAAAAATGTTTTTAAAAC
* *
66937 TATATA-T-TAT--ATTTT-AAAAATATTTTCAAAAAC
1 TATATATTATATAAATTTTCAAAAATGTTTT-TAAAAC
* * ** *
66970 TATATAATATATAAATTTTCGAAAATCATTTTAGACAAT
1 TATATATTATATAAATTTTCAAAAATGTTTTTA-A-AAC
67009 TATATATTATAT
1 TATATATTATAT
67021 TTTGTCAAAA
Statistics
Matches: 337, Mismatches: 36, Indels: 59
0.78 0.08 0.14
Matches are distributed among these distances:
30 7 0.02
31 15 0.04
32 35 0.10
33 18 0.05
34 13 0.04
35 30 0.09
36 61 0.18
37 69 0.20
38 48 0.14
39 41 0.12
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.47
Consensus pattern (37 bp):
TATATATTATATAAATTTTCAAAAATGTTTTTAAAAC
Found at i:67104 original size:19 final size:19
Alignment explanation
Indices: 67067--67104 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
67057 TACATATATT
*
67067 TATATATAATAAAATAATA
1 TATATATAATAAAAAAATA
67086 TATATATAA-AAATAAAATA
1 TATATATAATAAA-AAAATA
67105 ACTCCGGGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
TATATATAATAAAAAAATA
Found at i:68031 original size:3 final size:3
Alignment explanation
Indices: 68023--68078 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
68013 CGGGTCTTTT
68023 TTA TTA TTA TTA TTTA TATA TTTA TTA TTA TTA TT- TTA TTA TT- TTA
1 TTA TTA TTA TTA -TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
68069 TTA ATA TTA T
1 TTA TTA TTA T
68079 ATTTTTACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
2 4 0.09
3 34 0.74
4 7 0.15
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:68048 original size:21 final size:22
Alignment explanation
Indices: 68021--68078 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
68011 TCCGGGTCTT
68021 TTTTATTATTATTA-TTTA-TA
1 TTTTATTATTATTATTTTATTA
68041 TATTTATTATTATTATTTTATTA
1 T-TTTATTATTATTATTTTATTA
*
68064 TTTTATTAATATTAT
1 TTTTATTATTATTAT
68079 ATTTTTACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 17 0.50
23 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTATTATTATTTTATTA
Found at i:68061 original size:8 final size:8
Alignment explanation
Indices: 68019--68071 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
68009 TGTCCGGGTC
68019 TTTT-TTA
1 TTTTATTA
68026 TTATTATTA
1 TT-TTATTA
68035 -TTTA-TA
1 TTTTATTA
68041 TATTTATTA
1 T-TTTATTA
68050 --TTATTA
1 TTTTATTA
68056 TTTTATTA
1 TTTTATTA
68064 TTTTATTA
1 TTTTATTA
68072 ATATTATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
6 8 0.21
7 5 0.13
8 21 0.54
9 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTATTA
Found at i:69675 original size:30 final size:30
Alignment explanation
Indices: 69614--69675 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
69604 GTAATTACTG
*
69614 TTTAGTCCTTTAAATTTATGTTTTTCTTAT
1 TTTAGTCCTTTAAATTTATGTTTTGCTTAT
*
69644 TTTAGTCCTTTAAGTTTATGTTTGTGC-TAT
1 TTTAGTCCTTTAAATTTATGTTT-TGCTTAT
69674 TT
1 TT
69676 ACATCCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.18, C:0.10, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTATGTTTTGCTTAT
Found at i:69921 original size:19 final size:19
Alignment explanation
Indices: 69880--69922 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
69870 ATTCCTTTTG
* **
69880 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
69899 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
69918 TATGT
1 TATGT
69923 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:71769 original size:30 final size:31
Alignment explanation
Indices: 71733--71792 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
71723 TCTTGCTTGC
71733 ACTAACTC-GTTTCTCT-ATTTTGTTTGTGTT
1 ACTAACTCAGTTTCTCTCA-TTTGTTTGTGTT
* *
71763 ACTAACTCATTTTTTCTCATTTGTTTGTGT
1 ACTAACTCAGTTTCTCTCATTTGTTTGTGT
71793 CATTTTTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 8 0.31
31 17 0.65
32 1 0.04
ACGTcount: A:0.15, C:0.17, G:0.12, T:0.57
Consensus pattern (31 bp):
ACTAACTCAGTTTCTCTCATTTGTTTGTGTT
Found at i:75357 original size:4 final size:4
Alignment explanation
Indices: 75348--75431 Score: 84
Period size: 4 Copynumber: 21.0 Consensus size: 4
75338 TCACAAATCA
* *
75348 ACAT ACAT ACAT -CAAT ACAA ACAT ATAT -CAAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT AC-AT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT ACAT
* *
75396 ACAT GCAT ACAT ACAT ACAT -CAAC ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT AC-AT ACAT ACAT ACAT
75432 GTTATATAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
3 2 0.03
4 61 0.92
5 3 0.05
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (4 bp):
ACAT
Found at i:75372 original size:20 final size:20
Alignment explanation
Indices: 75348--75431 Score: 97
Period size: 20 Copynumber: 4.4 Consensus size: 20
75338 TCACAAATCA
75348 ACATACATACATCAATAC--
1 ACATACATACATCAATACAT
*
75366 A-A-ACATATATCAATACAT
1 ACATACATACATCAATACAT
*
75384 ACATACATACAT-ACATGCAT
1 ACATACATACATCA-ATACAT
*
75404 ACATACATACATCAACACAT
1 ACATACATACATCAATACAT
75424 ACATACAT
1 ACATACAT
75432 GTTATATAAG
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
16 13 0.24
17 1 0.02
18 2 0.04
19 2 0.04
20 36 0.65
21 1 0.02
ACGTcount: A:0.50, C:0.25, G:0.01, T:0.24
Consensus pattern (20 bp):
ACATACATACATCAATACAT
Found at i:76548 original size:28 final size:28
Alignment explanation
Indices: 76430--76533 Score: 165
Period size: 29 Copynumber: 3.7 Consensus size: 28
76420 ACAGTTTCTC
76430 TTGAAAAAAATCTTTGAGTTTGTTCCTT
1 TTGAAAAAAATCTTTGAGTTTGTTCCTT
*
76458 TTGAACAAAAATCTTGGAGTTTGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
*
76487 TTGAATAAAAATCTTTGAG-TTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTTGTTCCTT
76515 TTGAAAAAAATCTTTGAGT
1 TTGAAAAAAATCTTTGAGT
76534 CTATTTATTT
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
27 13 0.19
28 18 0.26
29 39 0.56
ACGTcount: A:0.31, C:0.10, G:0.15, T:0.44
Consensus pattern (28 bp):
TTGAAAAAAATCTTTGAGTTTGTTCCTT
Found at i:76558 original size:28 final size:27
Alignment explanation
Indices: 76430--76548 Score: 116
Period size: 29 Copynumber: 4.2 Consensus size: 27
76420 ACAGTTTCTC
*
76430 TTGAAAAAAATCTTTGAGTT-TGTTCCTT
1 TTGAAAAAAATCTTTGAGTTAT-TT-ATT
* *
76458 TTGAACAAAAATCTTGGAGTT-TGTTCCTT
1 TTGAA-AAAAATCTTTGAGTTAT-TT-ATT
* *
76487 TTGAATAAAAATCTTTGAGTTGTTTCTT
1 TTGAA-AAAAATCTTTGAGTTATTTATT
76515 TTGAAAAAAATCTTTGAGTCTATTTATT
1 TTGAAAAAAATCTTTGAGT-TATTTATT
76543 TTGAAA
1 TTGAAA
76549 CAAAGTTTTG
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
27 14 0.17
28 25 0.30
29 43 0.52
30 1 0.01
ACGTcount: A:0.31, C:0.09, G:0.14, T:0.45
Consensus pattern (27 bp):
TTGAAAAAAATCTTTGAGTTATTTATT
Found at i:76622 original size:52 final size:53
Alignment explanation
Indices: 76544--76646 Score: 190
Period size: 52 Copynumber: 2.0 Consensus size: 53
76534 CTATTTATTT
76544 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
76596 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAG
76647 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 36 0.73
53 13 0.27
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:76698 original size:29 final size:30
Alignment explanation
Indices: 76634--76697 Score: 110
Period size: 30 Copynumber: 2.1 Consensus size: 30
76624 AATTTTGTGA
*
76634 AAAAATCTTTGAGATTGTTTCTTTTGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
*
76664 AAAAATCTTTGAGTTTGTTTCTTTGGAAAC
1 AAAAATCTTTGAGATTGTTTCTTTGGAAAC
76694 AAAA
1 AAAA
76698 TTTTGTCTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (30 bp):
AAAAATCTTTGAGATTGTTTCTTTGGAAAC
Found at i:76789 original size:67 final size:66
Alignment explanation
Indices: 76650--76789 Score: 176
Period size: 67 Copynumber: 2.1 Consensus size: 66
76640 CTTTGAGATT
* *
76650 GTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGA
1 GTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTT-GAAACAAAATTTTGTCTCTCTTAAGA
*
76715 TA
65 CA
* * *
76717 ATTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTCTT-AAA-ATGATTTTTGTCTCTCTTAAA
1 GTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCT-TTGAAACA-AAATTTTGTCTCTCTT-AA
76780 GACA
63 GACA
76784 GTTTCT
1 GTTTCT
76790 CTCGAAGTAA
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
65 1 0.02
66 17 0.27
67 43 0.68
68 2 0.03
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (66 bp):
GTTTCTTTTGAAACAAAAATCTTTGAATCTGTTTCTTTGAAACAAAATTTTGTCTCTCTTAAGAC
A
Found at i:77754 original size:28 final size:28
Alignment explanation
Indices: 77708--77784 Score: 95
Period size: 28 Copynumber: 2.6 Consensus size: 28
77698 GAGACAGTTG
77708 CTTTTGAAACACATTATCTTTGAG-CTTGTTT
1 CTTTTGAAACA-A--ATCTTTGAGTC-TGTTT
77739 -TTCTTGAAACAAATCTTTGAGTCTGTTT
1 CTT-TTGAAACAAATCTTTGAGTCTGTTT
77767 CTTTTGAAACAAATCTTT
1 CTTTTGAAACAAATCTTT
77785 AATTTGGTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 9
0.83 0.00 0.17
Matches are distributed among these distances:
28 29 0.67
29 3 0.07
30 3 0.07
31 8 0.19
ACGTcount: A:0.26, C:0.16, G:0.12, T:0.47
Consensus pattern (28 bp):
CTTTTGAAACAAATCTTTGAGTCTGTTT
Found at i:77794 original size:28 final size:28
Alignment explanation
Indices: 77734--77804 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
77724 TCTTTGAGCT
* *
77734 TGTTTTTCTTGAAACAAATCTTTGAGTC
1 TGTTTCTCTTGAAACAAATCTTTGAATC
* *
77762 TGTTTCTTTTGAAACAAATCTTT-AATT
1 TGTTTCTCTTGAAACAAATCTTTGAATC
77789 TGGTTTCTCTTGAAAC
1 T-GTTTCTCTTGAAAC
77805 CATAACTCCT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 3 0.08
28 34 0.92
ACGTcount: A:0.25, C:0.14, G:0.13, T:0.48
Consensus pattern (28 bp):
TGTTTCTCTTGAAACAAATCTTTGAATC
Found at i:77891 original size:40 final size:40
Alignment explanation
Indices: 77833--78064 Score: 146
Period size: 43 Copynumber: 5.5 Consensus size: 40
77823 TCAGCCGTCT
*
77833 TCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* * ** *
77873 TCATCACGTAGGAGCCGTGTCAACCATAGATAACCAG-CCGTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGATC-TCC
* * * *
77916 TCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCCAGAACTCT
1 TCATCACGTAGGAACCGTGTCATC-CC--CAGA---CCAGATCTCC
* * * * *
77962 TCATCACGTATGAGCTGTGTCATCCCCTGACCAGATTTCC
1 TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
* * *
78002 TCATCACGTAGGAACCGGGTCA-CCCTTAGATAACCAG-TAGTCC
1 TCATCACGTAGGAACCGTGTCATCCC-CAG---ACCAGAT-CTCC
78045 TCATCACGTAGGAACCGTGT
1 TCATCACGTAGGAACCGTGT
78065 TATCACCTTG
Statistics
Matches: 147, Mismatches: 29, Indels: 29
0.72 0.14 0.14
Matches are distributed among these distances:
39 3 0.02
40 50 0.34
42 2 0.01
43 59 0.40
44 1 0.01
45 2 0.01
46 29 0.20
47 1 0.01
ACGTcount: A:0.25, C:0.31, G:0.20, T:0.24
Consensus pattern (40 bp):
TCATCACGTAGGAACCGTGTCATCCCCAGACCAGATCTCC
Found at i:78047 original size:129 final size:130
Alignment explanation
Indices: 77830--78160 Score: 461
Period size: 129 Copynumber: 2.6 Consensus size: 130
77820 TGGTCAGCCG
* * * * * *
77830 TCTTCATCATGTAGGAACCGTGTCATCCCCAGACCAGATCTCCTCATCACGTAGGAGCCGTGTCA
1 TCTTCATCATGTATGAGCTGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAACCGAGTCA
* * * *
77895 ACCATAGATAACCAGCCGTCCTCATCACGTAGGAACCGTGTTATCACCTTTAGATGGCC-AGAAC
66 CCCTTAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTGAGATGGCCAAGAAC
* * *
77959 TCTTCATCACGTATGAGCTGTGTCATCCCCTGACCAGATTTCCTCATCACGTAGGAACCGGGTCA
1 TCTTCATCATGTATGAGCTGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAACCGAGTCA
*
78024 CCCTTAGATAACCAGTAGTCCTCATCACGTAGGAACCGTGTTATCACCTTGAGATGGCCAAGAAC
66 CCCTTAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTGAGATGGCCAAGAAC
* * * *
78089 TCTTCATCATGTATGAG-TAGTGTCAT-CCTTCGACCAGATGTCTTCATCATGTAGGAACCGAGT
1 TCTTCATCATGTATGAGCT-GTGTCATCCCCT-GACCAGATCTCCTCATCACGTAGGAACCGAGT
78152 CACCCTTAG
64 CACCCTTAG
78161 TCGACCCGAA
Statistics
Matches: 180, Mismatches: 19, Indels: 5
0.88 0.09 0.02
Matches are distributed among these distances:
129 115 0.64
130 65 0.36
ACGTcount: A:0.25, C:0.29, G:0.20, T:0.26
Consensus pattern (130 bp):
TCTTCATCATGTATGAGCTGTGTCATCCCCTGACCAGATCTCCTCATCACGTAGGAACCGAGTCA
CCCTTAGATAACCAGCAGTCCTCATCACGTAGGAACCGTGTTATCACCTTGAGATGGCCAAGAAC
Found at i:78356 original size:3 final size:3
Alignment explanation
Indices: 78348--78403 Score: 62
Period size: 3 Copynumber: 18.3 Consensus size: 3
78338 CGGGTCTTTT
78348 TTA TTA TTA TTA TTTA TATA TTTA TTA TTA TTA TT- TTA TTA TT- TTA
1 TTA TTA TTA TTA -TTA T-TA -TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
78394 TTA ATA TTA T
1 TTA TTA TTA T
78404 ATTTTTACAT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
2 4 0.09
3 34 0.74
4 7 0.15
5 1 0.02
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:78373 original size:21 final size:22
Alignment explanation
Indices: 78346--78403 Score: 84
Period size: 22 Copynumber: 2.7 Consensus size: 22
78336 TCCGGGTCTT
78346 TTTTATTATTATTA-TTTA-TA
1 TTTTATTATTATTATTTTATTA
78366 TATTTATTATTATTATTTTATTA
1 T-TTTATTATTATTATTTTATTA
*
78389 TTTTATTAATATTAT
1 TTTTATTATTATTAT
78404 ATTTTTACAT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
20 1 0.03
21 13 0.38
22 17 0.50
23 3 0.09
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TTTTATTATTATTATTTTATTA
Found at i:78386 original size:8 final size:8
Alignment explanation
Indices: 78344--78396 Score: 53
Period size: 8 Copynumber: 7.0 Consensus size: 8
78334 TGTCCGGGTC
78344 TTTT-TTA
1 TTTTATTA
78351 TTATTATTA
1 TT-TTATTA
78360 -TTTA-TA
1 TTTTATTA
78366 TATTTATTA
1 T-TTTATTA
78375 --TTATTA
1 TTTTATTA
78381 TTTTATTA
1 TTTTATTA
78389 TTTTATTA
1 TTTTATTA
78397 ATATTATATT
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
6 8 0.21
7 5 0.13
8 21 0.54
9 5 0.13
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (8 bp):
TTTTATTA
Found at i:80004 original size:30 final size:30
Alignment explanation
Indices: 79943--80004 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
79933 GTAATTACTG
*
79943 TTTAGTCCTTTAAATTTATGTTTTTCTTAT
1 TTTAGTCCTTTAAATTTATGTTTTGCTTAT
*
79973 TTTAGTCCTTTAAGTTTATGTTTGTGC-TAT
1 TTTAGTCCTTTAAATTTATGTTT-TGCTTAT
80003 TT
1 TT
80005 ACATCCCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 27 0.93
31 2 0.07
ACGTcount: A:0.18, C:0.10, G:0.11, T:0.61
Consensus pattern (30 bp):
TTTAGTCCTTTAAATTTATGTTTTGCTTAT
Found at i:80251 original size:19 final size:19
Alignment explanation
Indices: 80210--80252 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
80200 ATTCCTTTTG
* **
80210 TATGTACTTATTTTTATGT
1 TATGTACTTATTTATATCA
*
80229 TATGTATTTATTTATATCA
1 TATGTACTTATTTATATCA
80248 TATGT
1 TATGT
80253 GAATTAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.05, G:0.09, T:0.60
Consensus pattern (19 bp):
TATGTACTTATTTATATCA
Found at i:84619 original size:15 final size:14
Alignment explanation
Indices: 84578--84620 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
84568 TTAAAATATT
*
84578 TTAAAGATTTTTTA
1 TTAAATATTTTTTA
* *
84592 TAAAATATATTTTGA
1 TTAAATAT-TTTTTA
84607 TTAAATATTTTTTA
1 TTAAATATTTTTTA
84621 CATTTTAATT
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
14 11 0.48
15 12 0.52
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (14 bp):
TTAAATATTTTTTA
Found at i:95219 original size:16 final size:16
Alignment explanation
Indices: 95198--95231 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
95188 TTACTATTCA
*
95198 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
95214 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
95230 CG
1 CG
95232 GTCGGCGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:106155 original size:32 final size:33
Alignment explanation
Indices: 106101--106176 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
106091 GCTATAAAGG
* *
106101 GTCA-TTAATTTCTATCATATTATTATAAAAT-
1 GTCATTTAATTTCTAACAAATTATTATAAAATA
106132 GATCATTTAATTT-TAACAAATTATTATAAAATA
1 G-TCATTTAATTTCTAACAAATTATTATAAAATA
*
106165 GTCATTAAATTT
1 GTCATTTAATTT
106177 AGTTAGTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
31 1 0.03
32 30 0.77
33 8 0.21
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (33 bp):
GTCATTTAATTTCTAACAAATTATTATAAAATA
Found at i:107407 original size:5 final size:5
Alignment explanation
Indices: 107397--107432 Score: 72
Period size: 5 Copynumber: 7.2 Consensus size: 5
107387 TTCCCGCCCC
107397 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT C
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT C
107433 TATTGCGTGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 31 1.00
ACGTcount: A:0.00, C:0.61, G:0.00, T:0.39
Consensus pattern (5 bp):
CCCTT
Found at i:108512 original size:42 final size:42
Alignment explanation
Indices: 108465--108563 Score: 117
Period size: 42 Copynumber: 2.4 Consensus size: 42
108455 GGTTATGTTC
* ** *
108465 TTTAGCGGCGTTTTTTTATAAACGCTGCTGCATGTAATGATA
1 TTTAGCGGCGTTTTTTTACAAACGCTGCTAAAAGTAATGATA
* ** *
108507 TTTAGCAGTATTTTTTTACAAACGCTGTTAAAAGTAATGATA
1 TTTAGCGGCGTTTTTTTACAAACGCTGCTAAAAGTAATGATA
*
108549 TTTAGTGGCGTTTTT
1 TTTAGCGGCGTTTTT
108564 CCAAACGTCG
Statistics
Matches: 45, Mismatches: 12, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.26, C:0.11, G:0.19, T:0.43
Consensus pattern (42 bp):
TTTAGCGGCGTTTTTTTACAAACGCTGCTAAAAGTAATGATA
Found at i:111750 original size:31 final size:31
Alignment explanation
Indices: 111715--111773 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
111705 GCAGTTCAAA
* *
111715 CCGGTTTTGCCGATTTTCAGCCGGTTCACCC
1 CCGGTTTTACCAATTTTCAGCCGGTTCACCC
111746 CCGGTTTTACCAATTTTCAGCCGGTTCA
1 CCGGTTTTACCAATTTTCAGCCGGTTCA
111774 TTGCCAGCCC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.14, C:0.32, G:0.20, T:0.34
Consensus pattern (31 bp):
CCGGTTTTACCAATTTTCAGCCGGTTCACCC
Found at i:113555 original size:21 final size:21
Alignment explanation
Indices: 113529--113573 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
113519 GATTTCTGGG
* *
113529 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
113550 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
113571 CAA
1 CAA
113574 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:115079 original size:14 final size:14
Alignment explanation
Indices: 115060--115087 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
115050 GAAAAGAAGC
115060 TATGTGATACGTGA
1 TATGTGATACGTGA
115074 TATGTGATACGTGA
1 TATGTGATACGTGA
115088 ATTACAAGTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.07, G:0.29, T:0.36
Consensus pattern (14 bp):
TATGTGATACGTGA
Found at i:115458 original size:149 final size:149
Alignment explanation
Indices: 115188--115502 Score: 560
Period size: 149 Copynumber: 2.1 Consensus size: 149
115178 GAGTCGAGGG
* * *
115188 TCTACGCGGTCCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
115253 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
*
115318 TATGGCACTACGGTGCAAT
131 TATGGCACTACGATGCAAT
*
115337 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
1 TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
*
115402 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTGTTA
66 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
115467 TATGGCACTACGATGCAAT
131 TATGGCACTACGATGCAAT
115486 TCTACGCGG-CACTTCGG
1 TCTACGCGGTC-CTTCGG
115503 TGCAATTATA
Statistics
Matches: 159, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
148 1 0.01
149 158 0.99
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGACATATATATATTCTGTGGAACATGTATGAAGTCTTGAAAGACACAT
ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATTA
TATGGCACTACGATGCAAT
Found at i:115506 original size:23 final size:23
Alignment explanation
Indices: 115470--115514 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
115460 ATTGTTATAT
*
115470 GGCACTACGATGCAATTCTACGC
1 GGCACTACGATGCAATTATACGC
* *
115493 GGCACTTCGGTGCAATTATACG
1 GGCACTACGATGCAATTATACG
115515 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.24, C:0.27, G:0.24, T:0.24
Consensus pattern (23 bp):
GGCACTACGATGCAATTATACGC
Found at i:116664 original size:21 final size:20
Alignment explanation
Indices: 116640--116682 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
116630 TTTGATATGA
* *
116640 GTATTTGTGATATATGTTATT
1 GTATATGTGATATA-ATTATT
*
116661 GTATATGTTATATAATTATT
1 GTATATGTGATATAATTATT
116681 GT
1 GT
116683 GAATACATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.28, C:0.00, G:0.16, T:0.56
Consensus pattern (20 bp):
GTATATGTGATATAATTATT
Done.