Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010125.1 Kokia drynarioides strain JFW-HI SEQ_124918, 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: 194074
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 130 characters in sequence are not A, C, G, or T
Found at i:3617 original size:23 final size:22
Alignment explanation
Indices: 3591--3658 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 22
3581 TTTTGGACTT
*
3591 TTTAATTTTGAAATTAAATTTAA
1 TTTAAATTT-AAATTAAATTTAA
3614 TTTAAATTTAAGATT-AATTTAAA
1 TTTAAATTTAA-ATTAAATTT-AA
* *
3637 ATTAAATTTAAATCAAATTTAA
1 TTTAAATTTAAATTAAATTTAA
3659 AATAAATAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
22 11 0.28
23 28 0.72
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (22 bp):
TTTAAATTTAAATTAAATTTAA
Found at i:3620 original size:11 final size:11
Alignment explanation
Indices: 3601--3665 Score: 78
Period size: 11 Copynumber: 5.8 Consensus size: 11
3591 TTTAATTTTG
3601 AAATTAAATTT
1 AAATTAAATTT
*
3612 AATTTAAATTT
1 AAATTAAATTT
3623 AAGATT-AATTT
1 AA-ATTAAATTT
3634 AAAATTAAATTT
1 -AAATTAAATTT
*
3646 AAATCAAATTT
1 AAATTAAATTT
*
3657 AAAATAAAT
1 AAATTAAAT
3666 AAAAAAGGGC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
11 37 0.80
12 9 0.20
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (11 bp):
AAATTAAATTT
Found at i:3647 original size:17 final size:17
Alignment explanation
Indices: 3591--3647 Score: 71
Period size: 17 Copynumber: 3.3 Consensus size: 17
3581 TTTTGGACTT
*
3591 TTTAATTTTGAAATTAAA
1 TTTAA-TTTAAAATTAAA
*
3609 TTTAATTTAAATTTAAGA
1 TTTAATTTAAAATTAA-A
3627 -TTAATTTAAAATTAAA
1 TTTAATTTAAAATTAAA
3643 TTTAA
1 TTTAA
3648 ATCAAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
16 1 0.03
17 27 0.79
18 6 0.18
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (17 bp):
TTTAATTTAAAATTAAA
Found at i:3658 original size:17 final size:17
Alignment explanation
Indices: 3591--3659 Score: 70
Period size: 17 Copynumber: 4.0 Consensus size: 17
3581 TTTTGGACTT
3591 TTTAATTTTGAAA-TTAAA
1 TTTAA-TTT-AAATTTAAA
3609 TTTAATTTAAATTTAAGA
1 TTTAATTTAAATTTAA-A
*
3627 -TTAATTTAAAATTAAA
1 TTTAATTTAAATTTAAA
* *
3643 TTTAAATCAAATTTAAA
1 TTTAATTTAAATTTAAA
3660 ATAAATAAAA
Statistics
Matches: 44, Mismatches: 4, Indels: 7
0.80 0.07 0.13
Matches are distributed among these distances:
16 4 0.09
17 34 0.77
18 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.46
Consensus pattern (17 bp):
TTTAATTTAAATTTAAA
Found at i:3659 original size:23 final size:22
Alignment explanation
Indices: 3605--3665 Score: 72
Period size: 23 Copynumber: 2.8 Consensus size: 22
3595 ATTTTGAAAT
*
3605 TAAATTT-AATTTAAATTTAAGA
1 TAAATTTAAAATTAAATTTAA-A
*
3627 TTAATTTAAAATTAAATTTAAA
1 TAAATTTAAAATTAAATTTAAA
3649 TCAAATTTAAAA-TAAAT
1 T-AAATTTAAAATTAAAT
3666 AAAAAAGGGC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
22 13 0.38
23 21 0.62
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (22 bp):
TAAATTTAAAATTAAATTTAAA
Found at i:4842 original size:34 final size:34
Alignment explanation
Indices: 4794--4886 Score: 134
Period size: 34 Copynumber: 2.7 Consensus size: 34
4784 AGAATATGAA
*
4794 AAGTTAAGGAAGATGGAAGGTTAAAGAT-TAAGAG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAG-G
* * *
4828 AGGTTAAGGGAGATGGAAGGTTAAAGGTCAAAGG
1 AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
4862 AAGTTAAGGAAGATGGAAGGTTAAA
1 AAGTTAAGGAAGATGGAAGGTTAAA
4887 AGATGAAAAG
Statistics
Matches: 52, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
34 49 0.94
35 3 0.06
ACGTcount: A:0.44, C:0.01, G:0.35, T:0.19
Consensus pattern (34 bp):
AAGTTAAGGAAGATGGAAGGTTAAAGATCAAAGG
Found at i:4848 original size:17 final size:17
Alignment explanation
Indices: 4796--4885 Score: 71
Period size: 17 Copynumber: 5.3 Consensus size: 17
4786 AATATGAAAA
4796 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
* ** *
4813 GTTAAAGATTA-AGAGAG
1 GTTAAGGAAGATGGA-AG
*
4830 GTTAAGGGAGATGGAAG
1 GTTAAGGAAGATGGAAG
4847 GTTAAAGGTCAA-A-GGAA-
1 GTT-AAGG--AAGATGGAAG
4864 GTTAAGGAAGATGGAAG
1 GTTAAGGAAGATGGAAG
4881 GTTAA
1 GTTAA
4886 AAGATGAAAA
Statistics
Matches: 55, Mismatches: 10, Indels: 16
0.68 0.12 0.20
Matches are distributed among these distances:
14 2 0.04
15 1 0.02
16 10 0.18
17 30 0.55
18 10 0.18
19 1 0.02
20 1 0.02
ACGTcount: A:0.42, C:0.01, G:0.37, T:0.20
Consensus pattern (17 bp):
GTTAAGGAAGATGGAAG
Found at i:8231 original size:22 final size:22
Alignment explanation
Indices: 8203--8244 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
8193 CTCAAATATT
8203 TCAATCATCATTTTGTCTGCTC
1 TCAATCATCATTTTGTCTGCTC
*
8225 TCAATCATCGTTTTGTCTGC
1 TCAATCATCATTTTGTCTGC
8245 AGACTATGCC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.17, C:0.26, G:0.12, T:0.45
Consensus pattern (22 bp):
TCAATCATCATTTTGTCTGCTC
Found at i:11202 original size:14 final size:14
Alignment explanation
Indices: 11185--11226 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
11175 TATATGAATG
11185 AATAAATATACGAA
1 AATAAATATACGAA
* *
11199 AATAGATATAAGAAA
1 AATAAATATACG-AA
11214 AATAAA-ATACGAA
1 AATAAATATACGAA
11227 TCATGAATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
13 2 0.09
14 14 0.61
15 7 0.30
ACGTcount: A:0.67, C:0.05, G:0.10, T:0.19
Consensus pattern (14 bp):
AATAAATATACGAA
Found at i:11384 original size:30 final size:29
Alignment explanation
Indices: 11337--11676 Score: 174
Period size: 30 Copynumber: 11.5 Consensus size: 29
11327 GTTTAGGGTT
* * *
11337 AAATGTAATTTTGAAAAGTTTTAGGGGTTA
1 AAATATAATTTTTAAAAG-TTTAGGGGTCA
*
11367 AAATATCATTTTTAAAAGTTT-GGTGG-CA
1 AAATATAATTTTTAAAAGTTTAGG-GGTCA
*
11395 AAATTATAATTTTTGAAACGTTT-GAGGGT-A
1 AAA-TATAATTTTT-AAAAGTTTAG-GGGTCA
* ** * *
11425 AAATTATGATTTTTGGAAG-TTCGGGGGCAA
1 AAA-TATAATTTTTAAAAGTTTAGGGGTC-A
* *
11455 AAATATAATTTTTAGAAG-TTCGAGGG-CAA
1 AAATATAATTTTTAAAAGTTTAG-GGGTC-A
* * * * *
11484 AAATGTAATTTTTAGAAGTTCAAGGGTAA
1 AAATATAATTTTTAAAAGTTTAGGGGTCA
* ** *
11513 AAATGTAATTTTTGGAAGTTTAAGGGTCA
1 AAATATAATTTTTAAAAGTTTAGGGGTCA
* * *
11542 AAATGTGATTTTAAAAAAGTTTAGGGGTCA
1 AAATATAATTTT-TAAAAGTTTAGGGGTCA
* *
11572 AAATA-CATTTTTGGAAAAGTTTTGGGGTCA
1 AAATATAATTTTT--AAAAGTTTAGGGGTCA
* * * * * *
11602 AAATGTGATTTTAGAAAAAATTTAAGGGTTA
1 AAATATAATTTT--TAAAAGTTTAGGGGTCA
* *
11633 TAATATAATTTTGGAAAAGTTTAGGGGTCA
1 AAATATAATTTT-TAAAAGTTTAGGGGTCA
*
11663 AAATATGATTTTTA
1 AAATATAATTTTTA
11677 GACAATTTAG
Statistics
Matches: 246, Mismatches: 47, Indels: 35
0.75 0.14 0.11
Matches are distributed among these distances:
28 11 0.04
29 101 0.41
30 107 0.43
31 27 0.11
ACGTcount: A:0.38, C:0.04, G:0.22, T:0.37
Consensus pattern (29 bp):
AAATATAATTTTTAAAAGTTTAGGGGTCA
Found at i:11437 original size:59 final size:60
Alignment explanation
Indices: 11337--11526 Score: 156
Period size: 58 Copynumber: 3.2 Consensus size: 60
11327 GTTTAGGGTT
* * * *
11337 AAATGTAA-TTTTGAAAAGTTTTAGGGGTTAAAATATCATTTTTAAAAGTTTGGTGGCAA
1 AAATATAATTTTTGAAAAGTTTGAGGGGTTAAAATATCATTTTTAAAAGTTCGGGGGCAA
* * * **
11396 AATTATAATTTTTGAAACGTTTGA-GGG-TAAAATTATGATTTTTGGAAGTTCGGGGGCAA
1 AAATATAATTTTTGAAAAGTTTGAGGGGTTAAAA-TATCATTTTTAAAAGTTCGGGGGCAA
* * ** * * * ** *
11455 AAATATAATTTTT-AGAAGTTCGA-GGGCAAAAATGTAATTTTTAGAAGTTCAAGGGTAA
1 AAATATAATTTTTGAAAAGTTTGAGGGGTTAAAATATCATTTTTAAAAGTTCGGGGGCAA
*
11513 AAATGTAATTTTTG
1 AAATATAATTTTTG
11527 GAAGTTTAAG
Statistics
Matches: 106, Mismatches: 21, Indels: 8
0.79 0.16 0.06
Matches are distributed among these distances:
58 47 0.44
59 46 0.43
60 13 0.12
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (60 bp):
AAATATAATTTTTGAAAAGTTTGAGGGGTTAAAATATCATTTTTAAAAGTTCGGGGGCAA
Found at i:11465 original size:29 final size:29
Alignment explanation
Indices: 11366--11532 Score: 158
Period size: 29 Copynumber: 5.7 Consensus size: 29
11356 TTTAGGGGTT
* * *
11366 AAAATATCATTTTTAAAAGTTTG-GTGGCA
1 AAAATATAATTTTTAGAAGTTCGAG-GGCA
* * *
11395 AAATTATAATTTTT-GAAACGTTTGAGGGTA
1 AAAATATAATTTTTAG-AA-GTTCGAGGGCA
* * * *
11425 AAATTATGATTTTTGGAAGTTCGGGGGCA
1 AAAATATAATTTTTAGAAGTTCGAGGGCA
11454 AAAATATAATTTTTAGAAGTTCGAGGGCA
1 AAAATATAATTTTTAGAAGTTCGAGGGCA
* * *
11483 AAAATGTAATTTTTAGAAGTTCAAGGGTA
1 AAAATATAATTTTTAGAAGTTCGAGGGCA
* *
11512 AAAATGTAATTTTTGGAAGTT
1 AAAATATAATTTTTAGAAGTT
11533 TAAGGGTCAA
Statistics
Matches: 118, Mismatches: 16, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
29 93 0.79
30 23 0.19
31 2 0.02
ACGTcount: A:0.37, C:0.05, G:0.22, T:0.37
Consensus pattern (29 bp):
AAAATATAATTTTTAGAAGTTCGAGGGCA
Found at i:11537 original size:29 final size:29
Alignment explanation
Indices: 11401--11553 Score: 153
Period size: 29 Copynumber: 5.2 Consensus size: 29
11391 GGCAAAATTA
* * * *
11401 TAATTTTTGAAACGTTTGAGGGTAAAATTA
1 TAATTTTTGGAA-GTTCGAGGGTAAAAATG
* * * *
11431 TGATTTTTGGAAGTTCGGGGGCAAAAATA
1 TAATTTTTGGAAGTTCGAGGGTAAAAATG
* *
11460 TAATTTTTAGAAGTTCGAGGGCAAAAATG
1 TAATTTTTGGAAGTTCGAGGGTAAAAATG
* *
11489 TAATTTTTAGAAGTTCAAGGGTAAAAATG
1 TAATTTTTGGAAGTTCGAGGGTAAAAATG
** *
11518 TAATTTTTGGAAGTTTAAGGGTCAAAATG
1 TAATTTTTGGAAGTTCGAGGGTAAAAATG
*
11547 TGATTTT
1 TAATTTT
11554 AAAAAAGTTT
Statistics
Matches: 107, Mismatches: 16, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
29 97 0.91
30 10 0.09
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (29 bp):
TAATTTTTGGAAGTTCGAGGGTAAAAATG
Found at i:11545 original size:58 final size:58
Alignment explanation
Indices: 11391--11617 Score: 171
Period size: 58 Copynumber: 3.9 Consensus size: 58
11381 AAAGTTTGGT
* * * **
11391 GGCAAAATTATAATTTTTGAAACGTTTGAGGGT-AAAAT-TATGATTTTTGGAAGTTCGGG
1 GGCAAAAATATAATTTTTGGAA-GTTTGAGGGTCAAAATGTA--ATTTTTAGAAGTTCAAG
* *
11450 GGCAAAAATATAATTTTTAGAAGTTCGAGGG-CAAAAATGTAATTTTTAGAAGTTCAAG
1 GGCAAAAATATAATTTTTGGAAGTTTGAGGGTC-AAAATGTAATTTTTAGAAGTTCAAG
* * * * * * * *
11508 GGTAAAAATGTAATTTTTGGAAGTTTAAGGGTCAAAATGTGATTTTAAAAAAGTTTAGG
1 GGCAAAAATATAATTTTTGGAAGTTTGAGGGTCAAAATGTAATTTT-TAGAAGTTCAAG
* *
11567 GGTC-AAAATA-CATTTTTGGAAAAGTTTTG-GGGTCAAAATGTGA-TTTTAGAA
1 GG-CAAAAATATAATTTTTGG--AAG-TTTGAGGGTCAAAATGTAATTTTTAGAA
11618 AAAATTTAAG
Statistics
Matches: 136, Mismatches: 23, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
58 71 0.52
59 43 0.32
60 19 0.14
61 3 0.02
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (58 bp):
GGCAAAAATATAATTTTTGGAAGTTTGAGGGTCAAAATGTAATTTTTAGAAGTTCAAG
Found at i:11654 original size:61 final size:60
Alignment explanation
Indices: 11528--11674 Score: 204
Period size: 61 Copynumber: 2.4 Consensus size: 60
11518 TAATTTTTGG
* * * *
11528 AAGTTTAAGGGTCAAAATGTGATTTTAAAAAAGTTTAGGGGTCAAAATACATTTTTGGAA
1 AAGTTTAGGGGTCAAAATGTGATTTTAAAAAAATTTAAGGGTCAAAATACAATTTTGGAA
* * * *
11588 AAGTTTTGGGGTCAAAATGTGATTTTAGAAAAAATTTAAGGGTTATAATATAATTTTGGAA
1 AAGTTTAGGGGTCAAAATGTGATTTTA-AAAAAATTTAAGGGTCAAAATACAATTTTGGAA
*
11649 AAGTTTAGGGGTCAAAATATGATTTT
1 AAGTTTAGGGGTCAAAATGTGATTTT
11675 TAGACAATTT
Statistics
Matches: 76, Mismatches: 10, Indels: 1
0.87 0.11 0.01
Matches are distributed among these distances:
60 25 0.33
61 51 0.67
ACGTcount: A:0.39, C:0.03, G:0.22, T:0.36
Consensus pattern (60 bp):
AAGTTTAGGGGTCAAAATGTGATTTTAAAAAAATTTAAGGGTCAAAATACAATTTTGGAA
Found at i:13163 original size:17 final size:17
Alignment explanation
Indices: 13136--13220 Score: 84
Period size: 17 Copynumber: 5.1 Consensus size: 17
13126 AACTTAATTT
13136 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
13152 TAAATTTAAATTTAAAA
1 TAAATTTAAATTTAAAA
* ** *
13169 TAAATTCAAGCTCAAAA
1 TAAATTTAAATTTAAAA
* *
13186 TAAGTTTTAAACTT-AAA
1 TAA-ATTTAAATTTAAAA
*
13203 TAAATTAAAATTTAAAA
1 TAAATTTAAATTTAAAA
13220 T
1 T
13221 TTAAAATTGG
Statistics
Matches: 55, Mismatches: 11, Indels: 5
0.77 0.15 0.07
Matches are distributed among these distances:
16 14 0.25
17 35 0.64
18 6 0.11
ACGTcount: A:0.55, C:0.05, G:0.02, T:0.38
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:14538 original size:117 final size:114
Alignment explanation
Indices: 14323--14559 Score: 420
Period size: 117 Copynumber: 2.1 Consensus size: 114
14313 TGACCACCCA
*
14323 TTCAGGGTAGAGGAGTAGCAACAACAGCTAGACAAGCACTCCTGGCAAGCCCTCCTCCTTGATAA
1 TTCAAGGTAGAGGAGTAGCAACAACAGCTAGACAAGCACTCCTGGCAAGCCCTCCTCCTTGATAA
*
14388 TGAAATGAACACTCACTTCTAAAGCATCCAATTTTAGGTGTGATCACTC
66 TGAAATGAACACTCACTTCTAAAGCATCCAATTTTACGTGTGATCACTC
*
14437 TTCAAGGTAGAGGAGTAGCAACAACAGCTAGACAAGCACTCCTGGCAGGCCCTCCTTCTCCTTGA
1 TTCAAGGTAGAGGAGTAGCAACAACAGCTAGACAAGCACTCCTGGCAAGCCCT-C--CTCCTTGA
14502 TAATGAAATGAACACTCACTTCTAAAGCATCCAATTTTACGTGTGATCACTC
63 TAATGAAATGAACACTCACTTCTAAAGCATCCAATTTTACGTGTGATCACTC
14554 TTCAAG
1 TTCAAG
14560 CGTTTATTTT
Statistics
Matches: 117, Mismatches: 3, Indels: 3
0.95 0.02 0.02
Matches are distributed among these distances:
114 51 0.44
115 1 0.01
117 65 0.56
ACGTcount: A:0.31, C:0.26, G:0.19, T:0.24
Consensus pattern (114 bp):
TTCAAGGTAGAGGAGTAGCAACAACAGCTAGACAAGCACTCCTGGCAAGCCCTCCTCCTTGATAA
TGAAATGAACACTCACTTCTAAAGCATCCAATTTTACGTGTGATCACTC
Found at i:19337 original size:17 final size:17
Alignment explanation
Indices: 19287--19372 Score: 100
Period size: 17 Copynumber: 5.1 Consensus size: 17
19277 CCCAGTTTTC
* * *
19287 ATTTATTATAAGTTTGA
1 ATTTATTTTAAATTTAA
* * *
19304 ATTTAGTATAAACTTAA
1 ATTTATTTTAAATTTAA
*
19321 ATTTATTTTGAATTTAA
1 ATTTATTTTAAATTTAA
*
19338 ATTCATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
19355 ATTTATTTTAAATTTAA
1 ATTTATTTTAAATTTAA
19372 A
1 A
19373 ATTAATTAAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.52
Consensus pattern (17 bp):
ATTTATTTTAAATTTAA
Found at i:19355 original size:34 final size:35
Alignment explanation
Indices: 19310--19390 Score: 110
Period size: 34 Copynumber: 2.3 Consensus size: 35
19300 TTGAATTTAG
* * *
19310 TATAAACTTAAATTTATTTTGAATTT-AAATTCAT
1 TATAAATTTAAATTTATTTTAAATTTAAAATTAAT
*
19344 TTTAAATTTAAATTTATTTTAAATTTAAAATTAAT
1 TATAAATTTAAATTTATTTTAAATTTAAAATTAAT
*
19379 TAAAAATTTAAA
1 TATAAATTTAAA
19391 AAAAGTCCAA
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
34 23 0.57
35 17 0.43
ACGTcount: A:0.47, C:0.02, G:0.01, T:0.49
Consensus pattern (35 bp):
TATAAATTTAAATTTATTTTAAATTTAAAATTAAT
Found at i:19955 original size:9 final size:9
Alignment explanation
Indices: 19941--19974 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19931 TGAATCCTTT
19941 TATATTCTA
1 TATATTCTA
19950 TATATTCTA
1 TATATTCTA
*
19959 TATATACTAA
1 TATATTCT-A
19969 TATATT
1 TATATT
19975 ATTTATTACA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (9 bp):
TATATTCTA
Found at i:26314 original size:8 final size:8
Alignment explanation
Indices: 26294--26343 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
26284 AATAATAAAG
26294 AGAGAAAA
1 AGAGAAAA
26302 A-AGAAAA
1 AGAGAAAA
26309 AGAGAAAA
1 AGAGAAAA
26317 AGAGAAAA
1 AGAGAAAA
*
26325 TAGA-AAAT
1 -AGAGAAAA
*
26333 CGAGAAAA
1 AGAGAAAA
26341 AGA
1 AGA
26344 AAATGAGAGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
7 9 0.26
8 23 0.66
9 3 0.09
ACGTcount: A:0.72, C:0.02, G:0.22, T:0.04
Consensus pattern (8 bp):
AGAGAAAA
Found at i:26340 original size:9 final size:8
Alignment explanation
Indices: 26303--26351 Score: 50
Period size: 8 Copynumber: 6.4 Consensus size: 8
26293 GAGAGAAAAA
*
26303 AGAAAAAG
1 AGAAAATG
*
26311 AGAAAAAG
1 AGAAAATG
26319 AGAAAAT-
1 AGAAAATG
26326 AGAAAATCG
1 AGAAAAT-G
26335 AGAAAA--
1 AGAAAATG
26341 AGAAAATG
1 AGAAAATG
26349 AGA
1 AGA
26352 GGTCGAGGTG
Statistics
Matches: 36, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
6 6 0.17
7 7 0.19
8 17 0.47
9 6 0.17
ACGTcount: A:0.69, C:0.02, G:0.22, T:0.06
Consensus pattern (8 bp):
AGAAAATG
Found at i:26344 original size:15 final size:14
Alignment explanation
Indices: 26306--26351 Score: 56
Period size: 15 Copynumber: 3.1 Consensus size: 14
26296 AGAAAAAAGA
*
26306 AAAAGAGAAAAAGAG
1 AAAA-AGAAAATGAG
26321 AAAATAGAAAATCGAG
1 AAAA-AGAAAAT-GAG
26337 AAAAAGAAAATGAG
1 AAAAAGAAAATGAG
26351 A
1 A
26352 GGTCGAGGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 4 0.14
15 17 0.61
16 7 0.25
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.07
Consensus pattern (14 bp):
AAAAAGAAAATGAG
Found at i:27861 original size:37 final size:39
Alignment explanation
Indices: 27774--27917 Score: 130
Period size: 39 Copynumber: 3.6 Consensus size: 39
27764 ACTGAAGATT
* * * *
27774 CGATCTCTTACCCCAAGGCTTGAGGCAGATCACCATCAGCCACC
1 CGATCTCTTACCTCGA-GCATGAGGCAGAT---CA-CAGCCATC
27818 CGATCTCTTACCTCGA-CATG-GGCAGATCACAGCCATC
1 CGATCTCTTACCTCGAGCATGAGGCAGATCACAGCCATC
* * * * * *
27855 CAATCTCTTACCACGAGCTTGAGGCAGATTATAGTCATC
1 CGATCTCTTACCTCGAGCATGAGGCAGATCACAGCCATC
*
27894 CGATCTCTTACCTCGAGCCTGAGG
1 CGATCTCTTACCTCGAGCATGAGG
27918 TAAATCACCA
Statistics
Matches: 85, Mismatches: 13, Indels: 9
0.79 0.12 0.08
Matches are distributed among these distances:
37 21 0.25
38 5 0.06
39 35 0.41
41 7 0.08
42 3 0.04
44 14 0.16
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.23
Consensus pattern (39 bp):
CGATCTCTTACCTCGAGCATGAGGCAGATCACAGCCATC
Found at i:27950 original size:43 final size:43
Alignment explanation
Indices: 27890--28063 Score: 208
Period size: 43 Copynumber: 4.0 Consensus size: 43
27880 AGATTATAGT
* *
27890 CATCCGATCTCTTACCTCGAGCCTGAGGTAAATCACCATCAAC
1 CATCCGATCTCTTACCTCGAGCCTGGGGTAAATCACCATCAGC
* * * * *
27933 CATCTGATTTCTTACCTCGAGCTTGGGATAGATCACCATCAGC
1 CATCCGATCTCTTACCTCGAGCCTGGGGTAAATCACCATCAGC
*
27976 CA-CACGATCTCTTACC-CTAAGCCTGGGGTAAATCACCATCAGC
1 CATC-CGATCTCTTACCTC-GAGCCTGGGGTAAATCACCATCAGC
* * * *
28019 CATCCGATATCTTACCTTGAGCTTGGGGTAGATCACCATCAGC
1 CATCCGATCTCTTACCTCGAGCCTGGGGTAAATCACCATCAGC
28062 CA
1 CA
28064 ATCTTTTACC
Statistics
Matches: 109, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
42 2 0.02
43 106 0.97
44 1 0.01
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.25
Consensus pattern (43 bp):
CATCCGATCTCTTACCTCGAGCCTGGGGTAAATCACCATCAGC
Found at i:28006 original size:86 final size:86
Alignment explanation
Indices: 27894--28063 Score: 261
Period size: 86 Copynumber: 2.0 Consensus size: 86
27884 TATAGTCATC
* * *
27894 CGATCTCTTACCTCGAGCCTGAGGTAAATCACCATCAACCATCTGATTTCTTACCTCGAGCTTGG
1 CGATCTCTTACCTCAAGCCTGAGGTAAATCACCATCAACCATCCGATATCTTACCTCGAGCTTGG
27959 GATAGATCACCATCAGCCACA
66 GATAGATCACCATCAGCCACA
* * *
27980 CGATCTCTTACC-CTAAGCCTGGGGTAAATCACCATCAGCCATCCGATATCTTACCTTGAGCTTG
1 CGATCTCTTACCTC-AAGCCTGAGGTAAATCACCATCAACCATCCGATATCTTACCTCGAGCTTG
*
28044 GGGTAGATCACCATCAGCCA
65 GGATAGATCACCATCAGCCA
28064 ATCTTTTACC
Statistics
Matches: 76, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
85 1 0.01
86 75 0.99
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (86 bp):
CGATCTCTTACCTCAAGCCTGAGGTAAATCACCATCAACCATCCGATATCTTACCTCGAGCTTGG
GATAGATCACCATCAGCCACA
Found at i:28084 original size:39 final size:39
Alignment explanation
Indices: 28037--28168 Score: 135
Period size: 39 Copynumber: 3.4 Consensus size: 39
28027 ATCTTACCTT
*
28037 GAGCTTGGGGTAGATCACCATCAGCCAATCTTTTACCCC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTTTTACCCC
* * *
28076 GAGTTTGGGGCAAATAGCAGCCATCTG---ATCTTTTACCCC
1 GAGCTTGGGGCAGAT--CA-CCATCAGCCAATCTTTTACCCC
* * * * *
28115 GAGCTTAGGGTAGACCACCATCATCCAATCTCTTACCCC
1 GAGCTTGGGGCAGATCACCATCAGCCAATCTTTTACCCC
28154 GAGCTTGGGGCAGAT
1 GAGCTTGGGGCAGAT
28169 TGCCACCTCG
Statistics
Matches: 72, Mismatches: 15, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
36 5 0.07
37 2 0.03
39 57 0.79
41 2 0.03
42 6 0.08
ACGTcount: A:0.23, C:0.29, G:0.23, T:0.25
Consensus pattern (39 bp):
GAGCTTGGGGCAGATCACCATCAGCCAATCTTTTACCCC
Found at i:28210 original size:24 final size:24
Alignment explanation
Indices: 28149--28216 Score: 100
Period size: 24 Copynumber: 2.8 Consensus size: 24
28139 CCAATCTCTT
28149 ACCCCGAGCTTGGGGCAGATTGCC
1 ACCCCGAGCTTGGGGCAGATTGCC
*
28173 ACCTCGAGCTTGGGGCAGATTGCC
1 ACCCCGAGCTTGGGGCAGATTGCC
* * *
28197 ACCCCAAGCCTGGGGTAGAT
1 ACCCCGAGCTTGGGGCAGAT
28217 CACCATCAGC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.19, C:0.31, G:0.32, T:0.18
Consensus pattern (24 bp):
ACCCCGAGCTTGGGGCAGATTGCC
Found at i:28734 original size:209 final size:208
Alignment explanation
Indices: 28309--28803 Score: 663
Period size: 208 Copynumber: 2.4 Consensus size: 208
28299 TAGTTATCTA
* * * * * * *
28309 AAGCAATAAAGCGGTAGTCTTCTTGATGAGATATAGAGAAGCGGATCAAATTCGTCTTCTTGATA
1 AAGCAATAAATCGGTCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATG
* * * * *
28374 AGATACAGAGGAA-TGAATTAAAATAAGTAATGCGATCATCTTCCTGATGAGGTACTAAGAACTA
66 AGATACAGA-GAAGCGAATCAAAACAAGTAATGCGATCATCTTCCTAATGAGATACTAAGAACTA
* * *
28438 GACCAAATCAATGAAACAAAGCTTGATGTAAGTAAAACTTCGACCCCAACTTCCTGATGAGATAC
130 GACCAAATCAATGAAACAAAACTTGATGTAAGCAAAACTTCGAACCCAACTTCCTGATGAGATAC
*
28503 TGAGAAGTAAGTCG
195 TGAGAAGCAAGTCG
* * * *
28517 AAGCAATAAATCGATCGTCTTCCTGATAAGATACAGAGAAATGGACCAAATCCGTCTTCTTGATG
1 AAGCAATAAATCGGTCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATG
* * * * *
28582 AGATACAGAGAAGCGAATCAAAACAAGTGATGCGGTCATCTTGCTAATGAGATACTGAGAAGTAG
66 AGATACAGAGAAGCGAATCAAAACAAGTAATGCGATCATCTTCCTAATGAGATACTAAGAACTAG
* * * *
28647 ACCAAATCAATGAAACCAAAACTTGATGTGAGCAAAACTTCTAACCCAGCTTCTTGATGAGATAC
131 ACCAAATCAATGAAA-CAAAACTTGATGTAAGCAAAACTTCGAACCCAACTTCCTGATGAGATAC
28712 TGAGAAGCAAGTCG
195 TGAGAAGCAAGTCG
28726 AAGCAATAAAAT-GGTCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGTCTT-TCTGA
1 AAGCAAT-AAATCGGTCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCT-TGA
*
28789 TGAGATACTGAGAAG
64 TGAGATACAGAGAAG
28804 TAGACCAAAT
Statistics
Matches: 249, Mismatches: 34, Indels: 7
0.86 0.12 0.02
Matches are distributed among these distances:
207 3 0.01
208 121 0.49
209 121 0.49
210 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.24
Consensus pattern (208 bp):
AAGCAATAAATCGGTCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCGTCTTCTTGATG
AGATACAGAGAAGCGAATCAAAACAAGTAATGCGATCATCTTCCTAATGAGATACTAAGAACTAG
ACCAAATCAATGAAACAAAACTTGATGTAAGCAAAACTTCGAACCCAACTTCCTGATGAGATACT
GAGAAGCAAGTCG
Found at i:28782 original size:37 final size:37
Alignment explanation
Indices: 28741--28814 Score: 114
Period size: 37 Copynumber: 2.0 Consensus size: 37
28731 ATAAAATGGT
*
28741 CGTC-TTCTTGATGAGATACAGAGAAGTGGACCAAATC
1 CGTCTTTC-TGATGAGATACAGAGAAGTAGACCAAATC
*
28778 CGTCTTTCTGATGAGATACTGAGAAGTAGACCAAATC
1 CGTCTTTCTGATGAGATACAGAGAAGTAGACCAAATC
28815 AATGAAACTA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
37 31 0.91
38 3 0.09
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (37 bp):
CGTCTTTCTGATGAGATACAGAGAAGTAGACCAAATC
Found at i:28892 original size:160 final size:160
Alignment explanation
Indices: 28628--28963 Score: 555
Period size: 160 Copynumber: 2.1 Consensus size: 160
28618 CATCTTGCTA
* *
28628 ATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAACTTGATGTGAGCAAAACTTCTAACC
1 ATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAACTCGATGTGAGCAAAACTTCGAACC
* * *
28693 CAGCTTCTTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCGTCTTCTTGATGAGAT
66 CAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCATCTTCCTGATGAGAT
28758 ACAGAGAAGTGGACCAAATCCGTCTTTCTG
131 ACAGAGAAGTGGACCAAATCCGTCTTTCTG
* * *
28788 ATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAAAGCTCGATGTGAGCAAAGCTTCGAACC
1 ATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAACTCGATGTGAGCAAAACTTCGAACC
* *
28853 TAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCATCTTCCTGATGAGAT
66 CAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCATCTTCCTGATGAGAT
*
28918 ACAGAGAAGTGGACCAAATCTGTCTTTCTG
131 ACAGAGAAGTGGACCAAATCCGTCTTTCTG
* *
28948 ATGAGATGCAGAGAAG
1 ATGAGATACTGAGAAG
28964 CGGATTAAAA
Statistics
Matches: 163, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
160 163 1.00
ACGTcount: A:0.37, C:0.18, G:0.23, T:0.23
Consensus pattern (160 bp):
ATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAACTCGATGTGAGCAAAACTTCGAACC
CAGCTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAAATGGTCATCTTCCTGATGAGAT
ACAGAGAAGTGGACCAAATCCGTCTTTCTG
Found at i:29013 original size:369 final size:368
Alignment explanation
Indices: 28412--29173 Score: 1030
Period size: 369 Copynumber: 2.1 Consensus size: 368
28402 AATGCGATCA
* * * * *
28412 TCTTCCTGATGAGGTACTAAGAACTAGACCAAATCAATGAAACAAAGCTTGATGTAAGTAAAACT
1 TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAAGCTCGATGTAAGCAAAACT
* * *
28477 TCGACCCCAACTTCCTGATGAGATACTGAGAAGTAAGTCGAAGCAATAAATCGATCGTCTTCCTG
66 TCGAACCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAATCGATCATCTTCCTG
28542 ATAAGATACAGAGAAATGGACCAAATCCGTCTTCTTGATGAGATACAGAGAAGCGAATCAAAACA
131 ATAAGATACAGAGAAATGGACCAAATCCGTCTTCTTGATGAGATACAGAGAAGCGAATCAAAACA
* * **
28607 AGTGATGCGGTCATCTTGCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACCAAAACTTG
196 AGTGAAGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAA-CAAAACTCA
* * * * *
28672 ATGTGAGCAAAACTTCTAACC-CAGCTTCTTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAA
260 ATATGAGCAAAACTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAACAATAAA
** * * *
28736 ATGGTCGTCTTCTTGATGAGATACAGAGAAGTGGACCAAATCCG
325 ATGGTCACCTTCCTAATGAGATACAAAGAAGTGGACCAAATCCG
* * *
28780 TCTTTCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACTAAAGCTCGATGTGAGCAAAGC
1 TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAAC-AAAGCTCGATGTAAGCAAAAC
* * * *
28845 TTCGAACCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAAT-GGTCATCTTCC
65 TTCGAACCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAAT-AAATCGATCATCTTCC
* * * * * *
28909 TGATGAGATACAGAGAAGTGGACCAAATCTGTCTT-TCTGATGAGATGCAGAGAAGCGGATTAAA
129 TGATAAGATACAGAGAAATGGACCAAATCCGTCTTCT-TGATGAGATACAGAGAAGCGAATCAAA
* * *
28973 ACAAGTGAAGCGGTCATCTTCCTGATGAGATA-TAGAGAAGTATACCAAATCAATGAAACAAAGC
193 ACAAGTGAAGCGGTCATCTTCCTAATGAGATACT-GAGAAGTAGACCAAATCAATGAAACAAAAC
** * **
29037 TCAATATGAGTGAAACTTCGAACCACAGCTTCCTGATGAGATATTGAGAAGCGGGTCAAAACAAT
257 TCAATATGAGCAAAACTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAACAAT
*
29102 AAAATGGTCACCTTCCTAATGAGATACAAAGAAGTGGACCAAATCTG
322 AAAATGGTCACCTTCCTAATGAGATACAAAGAAGTGGACCAAATCCG
*
29149 TCTTCCTGATTAGATA-TAGAGAAGT
1 TCTTCCTGATGAGATACT-GAGAAGT
29174 GGAAATAAAT
Statistics
Matches: 342, Mismatches: 46, Indels: 11
0.86 0.12 0.03
Matches are distributed among these distances:
368 65 0.19
369 273 0.80
370 4 0.01
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.23
Consensus pattern (368 bp):
TCTTCCTGATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAAGCTCGATGTAAGCAAAACT
TCGAACCCAACTTCCTGATGAGATACTGAGAAGCAAGTCGAAGCAATAAATCGATCATCTTCCTG
ATAAGATACAGAGAAATGGACCAAATCCGTCTTCTTGATGAGATACAGAGAAGCGAATCAAAACA
AGTGAAGCGGTCATCTTCCTAATGAGATACTGAGAAGTAGACCAAATCAATGAAACAAAACTCAA
TATGAGCAAAACTTCGAACCACAGCTTCCTGATGAGATACTGAGAAGCAAGTCAAAACAATAAAA
TGGTCACCTTCCTAATGAGATACAAAGAAGTGGACCAAATCCG
Found at i:29069 original size:209 final size:204
Alignment explanation
Indices: 28780--29344 Score: 659
Period size: 209 Copynumber: 2.7 Consensus size: 204
28770 ACCAAATCCG
* * *
28780 TCTTTCTGATGAGATACT-GAGAAGTAGACCAAATCAATGAAACTAAAGCTCGATGTGAG-CAAA
1 TCTTCCTGATGAGATA-TAGAGAAGTAGACCAAATCAATGAAAC-AAAGCTCAATGTGAGTGAAA
*
28843 GCTTCGAACCTAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCATCTTC
64 -CTTCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCATCTTC
* * *
28908 CTGATGAGATACAGAGAAGTGGACCAAATCTGTCTTTCTGATGAGATGCAGAGAAGCGGATTAAA
128 CTGATGAGATACAAAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGCGGA--AAA
**
28973 ACAAGTGAA-GCGGTCA
191 A-AA-T-AAGGCAATCA
* *
28989 TCTTCCTGATGAGATATAGAGAAGTATACCAAATCAATGAAACAAAGCTCAATATGAGTGAAACT
1 TCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGTGAGTGAAACT
* * * * *
29054 TCGAACCACAGCTTCCTGATGAGATATTGAGAAGCGGGTCAAAACAATAAAATGGTCACCTTCCT
66 TCGAACC-CAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCATCTTCCT
* * * * *
29119 AATGAGATACAAAGAAGTGGACCAAATCTGTCTTCCTGATTAGATATAGAGAAGTGGAAATAAAT
130 GATGAGATACAAAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGCGGAAAAAAAT
29184 AAGGCAATCA
195 AAGGCAATCA
* ** * * *
29194 TCTTCCTGATGAGATACAGAGAAGTAGACCAAATCAAGTGAAGGAAAGTTCAGATGCGAGTGAAG
1 TCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAA-TGAAACAAAGCTCA-ATGTGAGTGAAA
* * ** * * **
29259 CTTCAAACCCTTATCTTCCTGATGAGATACAAAAAAGTAGGTCGAAGCAATAAAGCGGTCATCTT
64 CTTCGAACCC--AGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCATCTT
* *
29324 CCTGATGAGATATAAGGAAGT
127 CCTGATGAGATACAAAGAAGT
29345 AGACTAAGAG
Statistics
Matches: 303, Mismatches: 45, Indels: 17
0.83 0.12 0.05
Matches are distributed among these distances:
204 2 0.01
205 41 0.14
206 14 0.05
207 20 0.07
208 82 0.27
209 144 0.48
ACGTcount: A:0.38, C:0.17, G:0.22, T:0.23
Consensus pattern (204 bp):
TCTTCCTGATGAGATATAGAGAAGTAGACCAAATCAATGAAACAAAGCTCAATGTGAGTGAAACT
TCGAACCCAGCTTCCTGATGAGATACTGAGAAGCAGGTCGAAGCAATAAAATGGTCATCTTCCTG
ATGAGATACAAAGAAGTGGACCAAATCTGTCTTCCTGATGAGATACAGAGAAGCGGAAAAAAATA
AGGCAATCA
Found at i:29751 original size:17 final size:17
Alignment explanation
Indices: 29729--29815 Score: 111
Period size: 17 Copynumber: 5.1 Consensus size: 17
29719 ACCCATTTTT
* *
29729 AATTTATTTTAAGTTTG
1 AATTTATTTTAAATTTA
* * *
29746 AATTTAGTATAAACTTA
1 AATTTATTTTAAATTTA
*
29763 AATTTATTTTGAATTTA
1 AATTTATTTTAAATTTA
*
29780 AATTCATTTTAAATTTA
1 AATTTATTTTAAATTTA
29797 AATTTATTTTAAATTTA
1 AATTTATTTTAAATTTA
29814 AA
1 AA
29816 ATTAATTAAA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 58 1.00
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (17 bp):
AATTTATTTTAAATTTA
Found at i:29832 original size:34 final size:33
Alignment explanation
Indices: 29729--29832 Score: 100
Period size: 34 Copynumber: 3.1 Consensus size: 33
29719 ACCCATTTTT
* * * * *
29729 AATTTATTTTAAGTTTGAATTTAGTATAAACTTA
1 AATTTATTTTAAATTTAAATTAATTA-AAAATTA
* * * *
29763 AATTTATTTTGAATTTAAATTCATTTTAAATTTA
1 AATTTATTTTAAATTTAAATT-AATTAAAAATTA
29797 AATTTATTTTAAATTTAAAATTAATTAAAAATTA
1 AATTTATTTTAAATTT-AAATTAATTAAAAATTA
29831 AA
1 AA
29833 AAGAAAGTCC
Statistics
Matches: 56, Mismatches: 12, Indels: 4
0.78 0.17 0.06
Matches are distributed among these distances:
34 50 0.89
35 6 0.11
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (33 bp):
AATTTATTTTAAATTTAAATTAATTAAAAATTA
Found at i:32720 original size:24 final size:25
Alignment explanation
Indices: 32675--32723 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
32665 TGGCGACTCT
*
32675 CATTTTTTTCGATCATTTAAAATATC
1 CATTTTTTTCGAT-ATTAAAAATATC
32701 CATTTTTTTCGAT-TTAAAAATAT
1 CATTTTTTTCGATATTAAAAATAT
32724 TATTCAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 9 0.41
26 13 0.59
ACGTcount: A:0.33, C:0.12, G:0.04, T:0.51
Consensus pattern (25 bp):
CATTTTTTTCGATATTAAAAATATC
Found at i:37494 original size:13 final size:13
Alignment explanation
Indices: 37473--37525 Score: 54
Period size: 13 Copynumber: 4.1 Consensus size: 13
37463 CAAACATGGG
37473 ACATAAGAAATTA
1 ACATAAGAAATTA
*
37486 ACATCAG-AATATA
1 ACATAAGAAAT-TA
*
37499 AAATAAGAAATTA
1 ACATAAGAAATTA
* *
37512 ACATTAGAATTTA
1 ACATAAGAAATTA
37525 A
1 A
37526 AACAAAAAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 3 0.09
13 26 0.81
14 3 0.09
ACGTcount: A:0.58, C:0.08, G:0.08, T:0.26
Consensus pattern (13 bp):
ACATAAGAAATTA
Found at i:37511 original size:26 final size:26
Alignment explanation
Indices: 37475--37527 Score: 88
Period size: 26 Copynumber: 2.0 Consensus size: 26
37465 AACATGGGAC
37475 ATAAGAAATTAACATCAGAATATAAA
1 ATAAGAAATTAACATCAGAATATAAA
* *
37501 ATAAGAAATTAACATTAGAATTTAAA
1 ATAAGAAATTAACATCAGAATATAAA
37527 A
1 A
37528 CAAAAAAAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (26 bp):
ATAAGAAATTAACATCAGAATATAAA
Found at i:39293 original size:5 final size:5
Alignment explanation
Indices: 39283--39327 Score: 81
Period size: 5 Copynumber: 9.0 Consensus size: 5
39273 GGTTCGAACC
*
39283 AGAAA AGAAA AGAAA AGAAA GGAAA AGAAA AGAAA AGAAA AGAAA
1 AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA AGAAA
39328 TATCCTCACA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
5 38 1.00
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (5 bp):
AGAAA
Found at i:43257 original size:5 final size:6
Alignment explanation
Indices: 43239--43263 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
43229 CAAAATTAAT
43239 AATAAA AATAAA AATAAA AATAAA A
1 AATAAA AATAAA AATAAA AATAAA A
43264 GGGACAAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (6 bp):
AATAAA
Found at i:50529 original size:39 final size:38
Alignment explanation
Indices: 50485--51219 Score: 279
Period size: 39 Copynumber: 18.9 Consensus size: 38
50475 ACCCCTATCG
*
50485 CGGGGTAAAAGACTGGCTGATGGTGATCTGCCTCAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTGCC-CAAGCT
** *
50524 CGGGGTAAAAGA-T--CAAATGGTTGCAATCTGCCCTAGGCT
1 CGGGGTAAAAGATTGGCTGATGG-TG--ATCTGCCC-AAGCT
* * *
50563 CGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTGCCC-AAGCT
* *
50602 CGGGGTAAAAGATT-G--AATGGCTGCAATTTGCTCCAAGCT
1 CGGGGTAAAAGATTGGCTGATGG-TG--ATCTGC-CCAAGCT
* * *
50641 CGGGGTAAGAGATTGGCTGATGGTGATCTATCCCAGGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCT-GCCCAAGCT
* * ** * **** *
50680 CGAGGTAAAAGATCGAATGGTTACAATTTGCCCCAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTG-CCCAAGCT
* ** * * *
50719 CGGGGTAAGAGATTGATTGATGGTGTTCTTCCCTAGGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTGCCC-AAGCT
* * * * * *
50758 CAGGGTAAAAGATCGGATGGTTGTAATCTGTCCCAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTG-CCCAAGCT
** ** *
50797 CGGGGTAAGGGATTGGCTGATGACGATTTGCCCCAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTG-CCCAAGCT
** ** * * * *
50836 CAAGGTAAAAGATTGAATGACT-ATAATTTGCCCCAGGCT
1 CGGGGTAAAAGATTGGCTGA-TGGTGATCTG-CCCAAGCT
* * ** *
50875 CAGGGTAAGAGATTGATTGATGGTGATCTGCCCTTAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTGCCC-AAGCT
* ** * * *
50914 CGGGGTAAAAGATCGAATTGCT-GTAATCTGCCCTAGACT
1 CGGGGTAAAAGATTG-GCTGATGGTGATCTGCCCAAG-CT
*
50953 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTG-CCCAAGCT
* * ** * * ** * * *
50992 CGAGGTAAAAGATCGAATGGTTGCAATCTGTCCTAGGTT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTG-CCCAAGCT
* *
51031 CGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTGCC-CAAGCT
** * ** ** * *
51070 CAAGGTAAAAGATCGAATGACT-GCAATCTGCCCTAGGTT
1 CGGGGTAAAAGATTGGCTGA-TGGTGATCTGCCC-AAGCT
* * * *
51109 TGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCT
1 CGGGGTAAAAGATTGGCTGATGGTGATCTG-CCCAAGCT
* * * * * *
51148 CGGGATAAATGA-T--CAGATGGCTACAATATGCCCCAGGCT
1 CGGGGTAAAAGATTGGCTGATGG-T--GATCTG-CCCAAGCT
* *
51187 CGAGGTAAGAGATTGGCTGATGGTGATCTGCCC
1 CGGGGTAAAAGATTGGCTGATGGTGATCTGCCC
51220 CTCTTTAAGG
Statistics
Matches: 508, Mismatches: 152, Indels: 73
0.69 0.21 0.10
Matches are distributed among these distances:
36 15 0.03
37 5 0.01
38 24 0.05
39 421 0.83
40 24 0.05
41 5 0.01
42 14 0.03
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (38 bp):
CGGGGTAAAAGATTGGCTGATGGTGATCTGCCCAAGCT
Found at i:50591 original size:78 final size:77
Alignment explanation
Indices: 50485--51219 Score: 765
Period size: 78 Copynumber: 9.4 Consensus size: 77
50475 ACCCCTATCG
* * * *
50485 CGGGGTAAAAGACTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCAAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
50550 TCTGCCCTAGGCT
65 TCTGCCCTAGGCT
* * *
50563 CGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGATTGAATGGCTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCGGGGTAAAAGATCGAATGGCTGCAA
* *
50628 TTTGCTCC-AAGCT
65 TCTGC-CCTAGGCT
* * * * *
50641 CGGGGTAAGAGATTGGCTGATGGTGATCTATCCCAGGCTCGAGGTAAAAGATCGAATGGTTACAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCT-GCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
* * *
50706 TTTGCCCCAAGCT
65 TCTGCCCTAGGCT
** * * * * * * *
50719 CGGGGTAAGAGATTGATTGATGGTGTTCTTCCCTAGGCTCAGGGTAAAAGATCGGATGGTTGTAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCGGGGTAAAAGATCGAATGGCTGCAA
*
50784 TCTGTCCC-AAGCT
65 TCTG-CCCTAGGCT
* ** * ** * * **
50797 CGGGGTAAGGGATTGGCTGATGACGATTTGCCCCAAGCTCAAGGTAAAAGATTGAATGACTATAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
* *
50862 TTTGCCCCAGGCT
65 TCTGCCCTAGGCT
* ** * * *
50875 CAGGGTAAGAGATTGATTGATGGTGATCTGCCCTTAGCTCGGGGTAAAAGATCGAATTGCTGTAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCC-AAGCTCGGGGTAAAAGATCGAATGGCTGCAA
*
50940 TCTGCCCTAGACT
65 TCTGCCCTAGGCT
* *
50953 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
* *
51018 TCTGTCCTAGGTT
65 TCTGCCCTAGGCT
* ** *
51031 CGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCAAGGTAAAAGATCGAATGACTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCC-CAAGCTCGGGGTAAAAGATCGAATGGCTGCAA
*
51096 TCTGCCCTAGGTT
65 TCTGCCCTAGGCT
* * * * * *
51109 TGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCGGGATAAATGATC-AGATGGCTACA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTG-CCCAAGCTCGGGGTAAAAGATCGA-ATGGCTGCA
* *
51173 ATATGCCCCAGGCT
64 ATCTGCCCTAGGCT
*
51187 CGAGGTAAGAGATTGGCTGATGGTGATCTGCCC
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCC
51220 CTCTTTAAGG
Statistics
Matches: 552, Mismatches: 92, Indels: 27
0.82 0.14 0.04
Matches are distributed among these distances:
77 19 0.03
78 517 0.94
79 16 0.03
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (77 bp):
CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCAAGCTCGGGGTAAAAGATCGAATGGCTGCAAT
CTGCCCTAGGCT
Found at i:50739 original size:156 final size:155
Alignment explanation
Indices: 50485--51219 Score: 875
Period size: 156 Copynumber: 4.7 Consensus size: 155
50475 ACCCCTATCG
* * * * * *
50485 CGGGGTAAAAGACTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCAAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTACAA
* *
50550 TCTGCCCTAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGAT
66 TCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCAGGGTAAAAGAT
* *
50615 TGAATGGCTGCAATTTGCTCCAAGCT
131 CGAATGGCTGCAATCTGC-CCAAGCT
** *
50641 CGGGGTAAGAGATTGGCTGATGGTGATCTATCCCAGGCTCGAGGTAAAAGATCGAATGGTTACAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTACAA
* * * * * * *
50706 TTTGCCCCAAGCTCGGGGTAAGAGATTGATTGATGGTGTTCTTCCCTAGGCTCAGGGTAAAAGAT
66 TCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCAGGGTAAAAGAT
* * *
50771 CGGATGGTTGTAATCTGTCCCAAGCT
131 CGAATGGCTGCAATCTG-CCCAAGCT
* ** * * * ** *
50797 CGGGGTAAGGGATTGGCTGATGACGATTTGCCCCAAGCTCAAGGTAAAAGATTGAATGACTATAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTACAA
* * * *
50862 TTTGCCCCAGGCTC-AGGGTAAGAGATTGATTGATGGTGATCTGCCCTTAGCTCGGGGTAAAAGA
66 TCTGCCCCAGGCTCGA-GGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCAGGGTAAAAGA
* * *
50926 TCGAATTGCTGTAATCTGCCCTAGACT
130 TCGAATGGCTGCAATCTGCCCAAG-CT
*
50953 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTACAA
* * * * *
51018 TCTGTCCTAGGTTCGAGGTAAGAGATTGGCTGATGGTGATCTG-CCTCAAGCTCAAGGTAAAAGA
66 TCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCT-AAGCTCAGGGTAAAAGA
* * *
51082 TCGAATGACTGCAATCTGCCCTAGGTT
130 TCGAATGGCTGCAATCTGCCC-AAGCT
* * * * *
51109 TGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCTCG-GGATAAATGATC-AGATGGCTAC
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGG-TAAAAGATCGA-ATGGTTAC
* *
51172 AATATGCCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCC
64 AATCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCC
51220 CTCTTTAAGG
Statistics
Matches: 489, Mismatches: 81, Indels: 17
0.83 0.14 0.03
Matches are distributed among these distances:
155 11 0.02
156 473 0.97
157 5 0.01
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (155 bp):
CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTACAA
TCTGCCCCAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCAGGGTAAAAGAT
CGAATGGCTGCAATCTGCCCAAGCT
Found at i:50898 original size:234 final size:231
Alignment explanation
Indices: 50485--51220 Score: 877
Period size: 234 Copynumber: 3.1 Consensus size: 231
50475 ACCCCTATCG
* * * *
50485 CGGGGTAAAAGACTGGCTGATGGTGATCTGCCTCAAGCTCGGGGTAAAAGATCAAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGTTGCAA
* * **
50550 TCTG-CCCTAGGCTCGAGGTAAGAGATTGGTTGATGGTGATCTGCCCTAAGCTCGGGGTAAAAGA
65 TCTGTCCC-AGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAAGGTAAAAGA
* * * * *
50614 TTGAATGGCTGCAATTTGCTCCAAGCTCGGGGTAAGAGATTGGCTGATGGTGATCTATCCCAGGC
129 TTGAATGACTGCAATTTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-CCCCAGGC
* *
50679 TCGAGGTAAAAGATCGAATGGTTACAATTTGCCCCAAGCT
193 TCG-GGTAAAAGATCGAATGGCTACAATATGCCCCAAGCT
** * * * * * *
50719 CGGGGTAAGAGATTGATTGATGGTGTTCTTCCCTAGGCTCAGGGTAAAAGATCGGATGGTTGTAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTC-GGGTAAAAGATCGAATGGTTGCAA
* * * ** *
50784 TCTGTCCCAAGCTCGGGGTAAGGGATTGGCTGATGACGATTTGCCCCAAGCTCAAGGTAAAAGAT
65 TCTGTCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAAGGTAAAAGAT
** * * *
50849 TGAATGACTATAATTTGCCCCAGGCTCAGGGTAAGAGATTGATTGATGGTGATCTGCCCTTA-GC
130 TGAATGACTGCAATTTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-CCC-CAGGC
* ** * *
50913 TCGGGGTAAAAGATCGAATTGCTGTAATCTG-CCCTAGACT
193 TC-GGGTAAAAGATCGAATGGCTACAATATGCCCCAAG-CT
50953 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGAGGTAAAAGATCGAATGGTTGCAA
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCG-GGTAAAAGATCGAATGGTTGCAA
* * *
51018 TCTGTCCTAGGTTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCTCAAGCTCAAGGTAAAAGAT
65 TCTGTCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAAGGTAAAAGAT
* * * * *
51083 CGAATGACTGCAATCTGCCCTAGGTTTGGGGTAAGAGATTGACTGATGGTGATCTGCCCCAGGCT
130 TGAATGACTGCAATTTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCT-CCCCAGGCT
* *
51148 CGGGATAAATGATC-AGATGGCTACAATATGCCCCAGGCT
194 CGGG-TAAAAGATCGA-ATGGCTACAATATGCCCCAAGCT
*
51187 CGAGGTAAGAGATTGGCTGATGGTGATCTGCCCC
1 CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCC
51221 TCTTTAAGGG
Statistics
Matches: 418, Mismatches: 75, Indels: 18
0.82 0.15 0.04
Matches are distributed among these distances:
233 11 0.03
234 398 0.95
235 9 0.02
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (231 bp):
CGGGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCGGGTAAAAGATCGAATGGTTGCAAT
CTGTCCCAGGCTCGAGGTAAGAGATTGGCTGATGGTGATCTGCCCCAAGCTCAAGGTAAAAGATT
GAATGACTGCAATTTGCCCCAGGCTCGGGGTAAGAGATTGACTGATGGTGATCTCCCCAGGCTCG
GGTAAAAGATCGAATGGCTACAATATGCCCCAAGCT
Found at i:51594 original size:48 final size:47
Alignment explanation
Indices: 51549--51824 Score: 162
Period size: 48 Copynumber: 5.7 Consensus size: 47
51539 GTCATTACAG
*
51549 CCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTGCTATTACGA
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGTTT-CTATTACGA
* *** * * * *
51597 CCTCAATCC-TTCTCATCTCGTCTTCTAAGGTACCGGGTTCGTCGTTGCGA
1 CCTCAA-CCTTTCCCATCAAATCTTC-ATGGTACCGGTTTC-T-ATTACGA
** * * * * *
51647 CCTCAACCTTTCCTTTTAAATCTTCATGGTACCGGGTTCGCCATTGCGG
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACC-GGTT-TCTATTACGA
* * * ** *
51696 CCTCAACCTTTCTCATCACAT-TTCATGGTACCGAATTTACCGTTGCGA
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACCG-GTTT-CTATTACGA
* * * * *
51744 CCTCAATCTTTCCCATCACATCTTCTAAGGTACCAGG-TTCATAGTTATGG
1 CCTCAACCTTTCCCATCAAATCTTC-ATGGTACC-GGTTTC-TA-TTACGA
*
51794 CCTCAACCTTTCCCTTCAAATCTTCATGGTA
1 CCTCAACCTTTCCCATCAAATCTTCATGGTA
51825 TCGAGTTTAC
Statistics
Matches: 170, Mismatches: 44, Indels: 27
0.71 0.18 0.11
Matches are distributed among these distances:
47 1 0.01
48 58 0.34
49 54 0.32
50 55 0.32
51 2 0.01
ACGTcount: A:0.20, C:0.31, G:0.14, T:0.34
Consensus pattern (47 bp):
CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGTTTCTATTACGA
Found at i:51599 original size:97 final size:97
Alignment explanation
Indices: 51440--51728 Score: 273
Period size: 98 Copynumber: 3.0 Consensus size: 97
51430 GGTATAAGAC
* * * * * * *
51440 TCGTCGTTACGGCCTCAACCTTTCCCATCATAT-TTCATGGTATCGAATTTACCGTTATGACCTT
1 TCGTCGTTAC-GCCTCAACCTTTCCCTTCAAATCTTCATGGTACCG-GTTTACCATTACGACCTC
* * **
51504 AATCCTTTTCATC-CATCTTTTAAGGTGTCGGGT
64 AATCCTTCTCATCTCATCTTCTAAGGTACCGGGT
* * *
51537 TCGTCATTACAGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTGCTATTACGACCTCA
1 TCGTCGTTAC-GCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTACCATTACGACCTCA
*
51602 ATCCTTCTCATCTCGTCTTCTAAGGTACCGGGT
65 ATCCTTCTCATCTCATCTTCTAAGGTACCGGGT
* * * ** * *
51635 TCGTCGTTGCGACCTCAACCTTTCCTTTTAAATCTTCATGGTACCGGGTTCGCCATTGCGGCCTC
1 TCGTCGTTACG-CCTCAACCTTTCCCTTCAAATCTTCATGGTACC-GGTTTACCATTACGACCTC
* *
51700 AA-CCTTTCTCATCACAT-TTC-ATGGTACCG
64 AATCC-TTCTCATCTCATCTTCTAAGGTACCG
51729 AATTTACCGT
Statistics
Matches: 160, Mismatches: 27, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
97 62 0.39
98 71 0.44
99 27 0.17
ACGTcount: A:0.19, C:0.30, G:0.16, T:0.36
Consensus pattern (97 bp):
TCGTCGTTACGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTACCATTACGACCTCAA
TCCTTCTCATCTCATCTTCTAAGGTACCGGGT
Found at i:51653 original size:98 final size:98
Alignment explanation
Indices: 51440--51782 Score: 277
Period size: 97 Copynumber: 3.5 Consensus size: 98
51430 GGTATAAGAC
* * * * * * *
51440 TCGTCGTTACGGCCTCAACCTTTCCCATCATAT-TTCATGGTATC-GAATTTACCGTTATGACCT
1 TCGTCGTTACGACCTCAACCTTTCCCATCAAATCTTCATGGTACCAG-GTTTGCCATTACGACCT
* * * **
51503 TAATCCTTTTCATCCATCTTTTAAGGTGTCGGGT
65 CAATCCTTCTCATCCATCTTCTAAGGTACCGGGT
* * *
51537 TCGTCATTAC-AGCCTCAACCTTTCCCTTCAAATCTTCATGGTACC-GGTTTGCTATTACGACCT
1 TCGTCGTTACGA-CCTCAACCTTTCCCATCAAATCTTCATGGTACCAGGTTTGCCATTACGACCT
*
51600 CAATCCTTCTCATCTCGTCTTCTAAGGTACCGGGT
65 CAATCCTTCTCATC-CATCTTCTAAGGTACCGGGT
* ** * * * * *
51635 TCGTCGTTGCGACCTCAACCTTTCCTTTTAAATCTTCATGGTACCGGGTTCGCCATTGCGGCCTC
1 TCGTCGTTACGACCTCAACCTTTCCCATCAAATCTTCATGGTACCAGGTTTGCCATTACGACCTC
* **
51700 AA-CCTTTCTCATCACAT-TTC-ATGGTACCGAAT
66 AATCC-TTCTCATC-CATCTTCTAAGGTACCGGGT
*** * * * *
51732 TTACCGTTGCGACCTCAATCTTTCCCATCACATCTTCTAAGGTACCAGGTT
1 TCGTCGTTACGACCTCAACCTTTCCCATCAAATCTTC-ATGGTACCAGGTT
51783 CATAGTTATG
Statistics
Matches: 200, Mismatches: 39, Indels: 13
0.79 0.15 0.05
Matches are distributed among these distances:
97 90 0.45
98 82 0.41
99 28 0.14
ACGTcount: A:0.20, C:0.30, G:0.15, T:0.36
Consensus pattern (98 bp):
TCGTCGTTACGACCTCAACCTTTCCCATCAAATCTTCATGGTACCAGGTTTGCCATTACGACCTC
AATCCTTCTCATCCATCTTCTAAGGTACCGGGT
Found at i:51679 original size:49 final size:49
Alignment explanation
Indices: 51549--51920 Score: 219
Period size: 50 Copynumber: 7.6 Consensus size: 49
51539 GTCATTACAG
* ** ** *
51549 CCTCAACCTTTCCCTTCAAATCTTCATGGTACC-GGTTTGCTATTACGA
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGGTTCACCGTTGCGA
* *** * **
51597 CCTCAATCC-TTCTCATCTCGTCTTCTAAGGTACCGGGTTCGTCGTTGCGA
1 CCTCAA-CCTTTCCCATCAAATCTTC-ATGGTACCGGGTTCACCGTTGCGA
** * * * *
51647 CCTCAACCTTTCCTTTTAAATCTTCATGGTACCGGGTTCGCCATTGCGG
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGGTTCACCGTTGCGA
* * ** *
51696 CCTCAACCTTTCTCATCACAT-TTCATGGTACCGAATTTACCGTTGCGA
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGGTTCACCGTTGCGA
* * * * ** ** *
51744 CCTCAATCTTTCCCATCACATCTTCTAAGGTACCAGGTTCATAGTTATGG
1 CCTCAACCTTTCCCATCAAATCTTC-ATGGTACCGGGTTCACCGTTGCGA
* * * * * *
51794 CCTCAACCTTTCCCTTCAAATCTTCATGGTATCGAGTTTACCGTTACGG
1 CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGGTTCACCGTTGCGA
* * ** * * ** * *
51843 CCTCAATCTTTCTCATCTCATCTTTTAAGGTATTGGGTTCGCCGTTGCGG
1 CCTCAACCTTTCCCATCAAATC-TTCATGGTACCGGGTTCACCGTTGCGA
* * *
51893 TCTCAACCTTTCCCTTTAAATCTTCATG
1 CCTCAACCTTTCCCATCAAATCTTCATG
51921 TTTCCTTGGT
Statistics
Matches: 240, Mismatches: 77, Indels: 13
0.73 0.23 0.04
Matches are distributed among these distances:
48 57 0.24
49 87 0.36
50 96 0.40
ACGTcount: A:0.19, C:0.30, G:0.15, T:0.36
Consensus pattern (49 bp):
CCTCAACCTTTCCCATCAAATCTTCATGGTACCGGGTTCACCGTTGCGA
Found at i:51768 original size:147 final size:147
Alignment explanation
Indices: 51532--51859 Score: 379
Period size: 147 Copynumber: 2.2 Consensus size: 147
51522 TTTAAGGTGT
* * * * * * *
51532 CGGGTTCGTCATTACAGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGGTTTGCTATTACGA
1 CGGGTTCGCCATTACGGCCTCAACCTTTCTCATCAAATCTTCATGGTACCGATTTACCATTACGA
* * * * * * * *
51597 CCTCAATCCTTCTCATCTCGTCTTCTAAGGTACCGGGTTCGTCGTTGCGACCTCAACCTTTCCTT
66 CCTCAATCCTTCCCATCACATCTTCTAAGGTACCAGGTTCATAGTTACGACCTCAACCTTTCCCT
*
51662 TTAAATCTTCATGGTAC
131 TCAAATCTTCATGGTAC
* * * *
51679 CGGGTTCGCCATTGCGGCCTCAACCTTTCTCATCACAT-TTCATGGTACCGAATTTACCGTTGCG
1 CGGGTTCGCCATTACGGCCTCAACCTTTCTCATCAAATCTTCATGGTACCG-ATTTACCATTACG
* * *
51743 ACCTCAATCTTTCCCATCACATCTTCTAAGGTACCAGGTTCATAGTTATGGCCTCAACCTTTCCC
65 ACCTCAATCCTTCCCATCACATCTTCTAAGGTACCAGGTTCATAGTTACGACCTCAACCTTTCCC
*
51808 TTCAAATCTTCATGGTAT
130 TTCAAATCTTCATGGTAC
* ** * *
51826 CGAGTTTACCGTTACGGCCTCAATCTTTCTCATC
1 CGGGTTCGCCATTACGGCCTCAACCTTTCTCATC
51860 TCATCTTTTA
Statistics
Matches: 150, Mismatches: 30, Indels: 2
0.82 0.16 0.01
Matches are distributed among these distances:
146 12 0.08
147 138 0.92
ACGTcount: A:0.20, C:0.31, G:0.15, T:0.34
Consensus pattern (147 bp):
CGGGTTCGCCATTACGGCCTCAACCTTTCTCATCAAATCTTCATGGTACCGATTTACCATTACGA
CCTCAATCCTTCCCATCACATCTTCTAAGGTACCAGGTTCATAGTTACGACCTCAACCTTTCCCT
TCAAATCTTCATGGTAC
Found at i:51849 original size:99 final size:99
Alignment explanation
Indices: 51693--51920 Score: 269
Period size: 99 Copynumber: 2.3 Consensus size: 99
51683 TTCGCCATTG
* * * *
51693 CGGCCTCAACCTTTCTCATCACAT-TTCATGGTACCGAATTTACCGTTGCGACCTCAATCTTTCC
1 CGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGAATTTACCGTTACGACCTCAATCTTTCC
*
51757 CATCACATCTTCTAAGGTACCAGGTTCATAGTTA
66 CATCACATCTTCTAAGGTACCAGGTTCACAGTTA
* * * * *
51791 TGGCCTCAACCTTTCCCTTCAAATCTTCATGGTATCGAGTTTACCGTTACGGCCTCAATCTTTCT
1 CGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGAATTTACCGTTACGACCTCAATCTTTCC
* * *** * * *
51856 CATCTCATCTTTTAAGGTATTGGGTTCGCCGTTG
66 CATCACATCTTCTAAGGTACCAGGTTCACAGTTA
* *
51890 CGGTCTCAACCTTTCCCTTTAAATCTTCATG
1 CGGCCTCAACCTTTCCCTTCAAATCTTCATG
51921 TTTCCTTGGT
Statistics
Matches: 108, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
98 20 0.19
99 88 0.81
ACGTcount: A:0.20, C:0.29, G:0.14, T:0.36
Consensus pattern (99 bp):
CGGCCTCAACCTTTCCCTTCAAATCTTCATGGTACCGAATTTACCGTTACGACCTCAATCTTTCC
CATCACATCTTCTAAGGTACCAGGTTCACAGTTA
Found at i:52915 original size:67 final size:67
Alignment explanation
Indices: 52780--52905 Score: 216
Period size: 67 Copynumber: 1.9 Consensus size: 67
52770 CCTTTTCAAG
*
52780 TTTTCAACTCAAATCTCCTTAGGTTTCGAGATGCCCTTTACGAGTTTTCAACTCGACCTCTCTTT
1 TTTTCAACTCAAATCTCCTTAGGTTTCGAGATGCCCTTTACGAGTTTTCAACTCAACCTCTCTTT
52845 TT
66 TT
* * *
52847 TTTTCAACTCAAATCTCCTTAGGTTTCGAGATGCCCTTTACGGGTTTTCACCTTAACCT
1 TTTTCAACTCAAATCTCCTTAGGTTTCGAGATGCCCTTTACGAGTTTTCAACTCAACCT
52906 TTTATTTTTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (67 bp):
TTTTCAACTCAAATCTCCTTAGGTTTCGAGATGCCCTTTACGAGTTTTCAACTCAACCTCTCTTT
TT
Found at i:57824 original size:247 final size:249
Alignment explanation
Indices: 57386--57883 Score: 829
Period size: 247 Copynumber: 2.0 Consensus size: 249
57376 CTCATACGTG
* * * * * * *
57386 TTTGAAGGAAAGATGATGACATTCTTTATTGCATCTGGGCACACTATGTCTTGTGGGTTTTTCAA
1 TTTGAAGCAAAGATAACGACATTATTTATTGCATCTAGGCACACTATGTCTTGCGGGTTTTCCAA
57451 AGTAATGTACTTGTTATCCCCTTTTTCCTTGATCAGGGCTGTAACCCAATGCTCGCTCATTCAGA
66 AGTAATGTACTTGTTATCCCCTTTTTCCTTGATCAGGGCTGTAACCCAATGCTCGCTCATTCAGA
57516 ATAGGTCTTATGATTTTTAAATCCTCGGGCAACGTAACGTATTCCTCTTCCTTACGTTCATGTTT
131 ATAGGTCTTATGATTTTTAAATCCTCGGGCAACGTAACGTATTCCTCTTCCTTACGTTCATGTTT
*
57581 CTGAAAGTGAAGTAACT-AGCTTGAGTGTGTAAGGCAAATCAAAATATTCGAAT
196 CTGAAAGTGAAGCAACTAAGCTTGAGTGTGTAAGGCAAATCAAAATATTCGAAT
* *
57634 TTTGAAGCAAAGATAACGACATTATTTCTTGCATCTAGGTACACTATGTCTTGCGGGTTTTCCAA
1 TTTGAAGCAAAGATAACGACATTATTTATTGCATCTAGGCACACTATGTCTTGCGGGTTTTCCAA
* *
57699 AGTAATGTATTTGTTATCCCC-TTTTCCTTGATTAGGGCTGTAACCCAATGCTCGCTCATTCAGA
66 AGTAATGTACTTGTTATCCCCTTTTTCCTTGATCAGGGCTGTAACCCAATGCTCGCTCATTCAGA
* * *
57763 ATAGGTCTTATGATTTTTGAATCCTCGGGTAACGTAACGTATTCCTCTTCCTTATGTTCATGTTT
131 ATAGGTCTTATGATTTTTAAATCCTCGGGCAACGTAACGTATTCCTCTTCCTTACGTTCATGTTT
* *
57828 TTGAAAGTGAAGCAACTAAGCTTGAGTGTGTAAGGCAAATCAACATATTCGAAT
196 CTGAAAGTGAAGCAACTAAGCTTGAGTGTGTAAGGCAAATCAAAATATTCGAAT
57882 TT
1 TT
57884 GAACTTTTGC
Statistics
Matches: 232, Mismatches: 17, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
247 119 0.51
248 113 0.49
ACGTcount: A:0.26, C:0.18, G:0.19, T:0.36
Consensus pattern (249 bp):
TTTGAAGCAAAGATAACGACATTATTTATTGCATCTAGGCACACTATGTCTTGCGGGTTTTCCAA
AGTAATGTACTTGTTATCCCCTTTTTCCTTGATCAGGGCTGTAACCCAATGCTCGCTCATTCAGA
ATAGGTCTTATGATTTTTAAATCCTCGGGCAACGTAACGTATTCCTCTTCCTTACGTTCATGTTT
CTGAAAGTGAAGCAACTAAGCTTGAGTGTGTAAGGCAAATCAAAATATTCGAAT
Found at i:60810 original size:30 final size:30
Alignment explanation
Indices: 60764--60828 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 30
60754 ATTTTTGAGG
* *
60764 AATTTGGGGGTTAAAATTAAAATTTTTGGAA
1 AATTTGGGGATTAAAA-TAAAACTTTTGGAA
**
60795 AATTT-GGGATTAAAATCGAACTTTTGGAA
1 AATTTGGGGATTAAAATAAAACTTTTGGAA
60824 AATTT
1 AATTT
60829 AAGGTTGAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.53
30 9 0.30
31 5 0.17
ACGTcount: A:0.38, C:0.03, G:0.20, T:0.38
Consensus pattern (30 bp):
AATTTGGGGATTAAAATAAAACTTTTGGAA
Found at i:60893 original size:29 final size:29
Alignment explanation
Indices: 60861--60932 Score: 90
Period size: 29 Copynumber: 2.5 Consensus size: 29
60851 ATTTAGGGGC
* * **
60861 AAAATGGTAATTTTTGGATGTTTGAGGGT
1 AAAATGGTAATTTTTGAATATTCAAGGGT
60890 AAAATGGTAATTTTTGAATATTCAAGGGT
1 AAAATGGTAATTTTTGAATATTCAAGGGT
**
60919 AAAATCATAATTTT
1 AAAATGGTAATTTT
60933 GGAGAAGTTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.36, C:0.03, G:0.21, T:0.40
Consensus pattern (29 bp):
AAAATGGTAATTTTTGAATATTCAAGGGT
Found at i:60991 original size:30 final size:29
Alignment explanation
Indices: 60926--61092 Score: 192
Period size: 30 Copynumber: 5.6 Consensus size: 29
60916 GGTAAAATCA
*
60926 TAATTTTGGAGAAGTTTAAGGTCAAAACT-
1 TAATTTTGGAAAAGTTTAAGGTCAAAA-TG
*
60955 TAATTTTGGAAAAGTTTGAAGGTTAAAATG
1 TAATTTTGGAAAAGTTT-AAGGTCAAAATG
* *
60985 TGATTTTGGAAAAGTTTAGGGGTCAAAATG
1 TAATTTTGGAAAAGTTTA-AGGTCAAAATG
*
61015 TAATTTTGAAAAAGTTTAAGGATCAAAATG
1 TAATTTTGGAAAAGTTTAAGG-TCAAAATG
* *
61045 TAATTTTGGAAAAGTTTAAGGGTTAAAATA
1 TAATTTTGGAAAAGTTTAA-GGTCAAAATG
* * *
61075 TGATTTTTGAAAAATTTA
1 TAATTTTGGAAAAGTTTA
61093 GGGACCTTTT
Statistics
Matches: 119, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
29 20 0.17
30 97 0.82
31 2 0.02
ACGTcount: A:0.40, C:0.02, G:0.21, T:0.37
Consensus pattern (29 bp):
TAATTTTGGAAAAGTTTAAGGTCAAAATG
Found at i:61058 original size:90 final size:89
Alignment explanation
Indices: 60926--61095 Score: 254
Period size: 90 Copynumber: 1.9 Consensus size: 89
60916 GGTAAAATCA
* * *
60926 TAATTTTGGAGAAGTTTAAGGTCAAAACTTAATTTTGGAAAAGTTTGAA-GGTTAAAATGTGATT
1 TAATTTTGAAAAAGTTTAAGGTCAAAACTTAATTTTGGAAAAGTTT-AAGGGTTAAAATATGATT
*
60990 TTGGAAAAGTTTAGGGGTCAAAATG
65 TTGGAAAAATTTAGGGGTCAAAATG
61015 TAATTTTGAAAAAGTTTAAGGATCAAAA-TGTAATTTTGGAAAAGTTTAAGGGTTAAAATATGAT
1 TAATTTTGAAAAAGTTTAAGG-TCAAAACT-TAATTTTGGAAAAGTTTAAGGGTTAAAATATGAT
*
61079 TTTTGAAAAATTTAGGG
64 TTTGGAAAAATTTAGGG
61096 ACCTTTTAGG
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
89 22 0.30
90 51 0.70
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (89 bp):
TAATTTTGAAAAAGTTTAAGGTCAAAACTTAATTTTGGAAAAGTTTAAGGGTTAAAATATGATTT
TGGAAAAATTTAGGGGTCAAAATG
Found at i:68989 original size:28 final size:29
Alignment explanation
Indices: 68957--69016 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
68947 GGATTTAGAC
* * *
68957 AATTTTTAAA-AAAAAATTGGGAATTGAA
1 AATTTTAAAATAAAAAATTGAGAAATGAA
68985 AA-TTTAAAATAAAAAATTGAGAAATGAA
1 AATTTTAAAATAAAAAATTGAGAAATGAA
69013 AATT
1 AATT
69017 GAGAATAAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 6 0.22
28 20 0.74
29 1 0.04
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.30
Consensus pattern (29 bp):
AATTTTAAAATAAAAAATTGAGAAATGAA
Found at i:69014 original size:14 final size:14
Alignment explanation
Indices: 68969--69021 Score: 54
Period size: 14 Copynumber: 3.8 Consensus size: 14
68959 TTTTTAAAAA
* *
68969 AAAATTGGGAATTG
1 AAAATTGAGAAATG
* *
68983 AAAATTTA-AAATAA
1 AAAATTGAGAAAT-G
68997 AAAATTGAGAAATG
1 AAAATTGAGAAATG
69011 AAAATTGAGAA
1 AAAATTGAGAA
69022 TAAGAAATTG
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
13 3 0.10
14 24 0.77
15 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.17, T:0.25
Consensus pattern (14 bp):
AAAATTGAGAAATG
Found at i:69023 original size:28 final size:28
Alignment explanation
Indices: 68967--69036 Score: 86
Period size: 28 Copynumber: 2.5 Consensus size: 28
68957 AATTTTTAAA
* * *
68967 AAAAAATTGGGAATTGAAAATTTAAAAT
1 AAAAAATTGAGAAATGAAAATTGAAAAT
*
68995 AAAAAATTGAGAAATGAAAATTGAGAAT
1 AAAAAATTGAGAAATGAAAATTGAAAAT
* *
69023 AAGAAATTGTGAAA
1 AAAAAATTGAGAAA
69037 AATAAACCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.59, C:0.00, G:0.17, T:0.24
Consensus pattern (28 bp):
AAAAAATTGAGAAATGAAAATTGAAAAT
Found at i:79808 original size:27 final size:28
Alignment explanation
Indices: 79778--79844 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 28
79768 TTTCGGGTAA
* *
79778 AATTAAATTAATTCGGTTAA-TCGATCG
1 AATTAAATTAATTCGGTCAATTCAATCG
** *
79805 AATTTGATTAA-TCGGTCAATTTAATCG
1 AATTAAATTAATTCGGTCAATTCAATCG
*
79832 AATTAATTTAATT
1 AATTAAATTAATT
79845 AGAGTCGGTT
Statistics
Matches: 30, Mismatches: 8, Indels: 3
0.73 0.20 0.07
Matches are distributed among these distances:
26 7 0.23
27 22 0.73
28 1 0.03
ACGTcount: A:0.37, C:0.09, G:0.12, T:0.42
Consensus pattern (28 bp):
AATTAAATTAATTCGGTCAATTCAATCG
Found at i:84262 original size:317 final size:317
Alignment explanation
Indices: 83687--84321 Score: 1153
Period size: 317 Copynumber: 2.0 Consensus size: 317
83677 CTGAATTGAG
* *
83687 TGAGGCGTCTAAAATACTCACACTCCTCAACACTTGTTTGGCAATGAACACTCCCAAAATAGATG
1 TGAGGCGTCTAAAATACTCACACTCCTAAACACTTGTTTGGCAATGAACACTCCCAAAACAGATG
* *
83752 CCTCATAGATTCTTCTGATGATTAACACAACGGGTAGTAGTTGTGAACTGCCAGATTTTTCATCT
66 CCTCACAGATTCTTCTGATGATTAACACAACGGGCAGTAGTTGTGAACTGCCAGATTTTTCATCT
*
83817 GTAAATTACTGAAAGTAAGGACATAATTGTTAGTAATTTTCCAAAAAAGTGATTTTAATTTTGCT
131 GTAAATTACTGAAAGTAAGGACATAATTGTTAGCAATTTTCCAAAAAAGTGATTTTAATTTTGCT
83882 GGCAAGTTGTAGGCTCCAAATTTTGTTGTAGAATTCAGTAAGAGATGCTTGCTGTGTAATAACTA
196 GGCAAGTTGTAGGCTCCAAATTTTGTTGTAGAATTCAGTAAGAGATGCTTGCTGTGTAATAACTA
* *
83947 TCTAATTTTTTATTTTTGTATTCATTAGCCATTTGTAACCACTCTTAGTGGAATATA
261 TCTAATTTTTTATTTCTGTATTCATTAGCCATTTGTAACCACTCTTAATGGAATATA
*
84004 TGAGGCGTCTAGAATACTCACACTCCTAAACACTTGTTTGGCAATGAACACTCCCAAAACAGATG
1 TGAGGCGTCTAAAATACTCACACTCCTAAACACTTGTTTGGCAATGAACACTCCCAAAACAGATG
* * * *
84069 CCTCACAGATTCTTTTGATGATTTACACAACGGGCAGTAGTTGTGAACTGTCAGATTTTTCTTCT
66 CCTCACAGATTCTTCTGATGATTAACACAACGGGCAGTAGTTGTGAACTGCCAGATTTTTCATCT
84134 GTAAATTACTGAAAGTAAGGACATAATTGTTAGCAATTTTCCAAAAAAGTGATTTTAATTTTGCT
131 GTAAATTACTGAAAGTAAGGACATAATTGTTAGCAATTTTCCAAAAAAGTGATTTTAATTTTGCT
84199 GGCAAGTTGTAGGCTCCAAATTTTGTTGTAGAATTCAGTAAGAGATGCTTGCTGTGTAATAACTA
196 GGCAAGTTGTAGGCTCCAAATTTTGTTGTAGAATTCAGTAAGAGATGCTTGCTGTGTAATAACTA
*
84264 TCTGATTTTTTATTTCTGTATTCATTAGCCATTTGTAACCACTCTTAATGGAATATA
261 TCTAATTTTTTATTTCTGTATTCATTAGCCATTTGTAACCACTCTTAATGGAATATA
84321 T
1 T
84322 CCCTGTATTA
Statistics
Matches: 305, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
317 305 1.00
ACGTcount: A:0.31, C:0.16, G:0.17, T:0.36
Consensus pattern (317 bp):
TGAGGCGTCTAAAATACTCACACTCCTAAACACTTGTTTGGCAATGAACACTCCCAAAACAGATG
CCTCACAGATTCTTCTGATGATTAACACAACGGGCAGTAGTTGTGAACTGCCAGATTTTTCATCT
GTAAATTACTGAAAGTAAGGACATAATTGTTAGCAATTTTCCAAAAAAGTGATTTTAATTTTGCT
GGCAAGTTGTAGGCTCCAAATTTTGTTGTAGAATTCAGTAAGAGATGCTTGCTGTGTAATAACTA
TCTAATTTTTTATTTCTGTATTCATTAGCCATTTGTAACCACTCTTAATGGAATATA
Found at i:87259 original size:26 final size:26
Alignment explanation
Indices: 87206--87259 Score: 65
Period size: 26 Copynumber: 2.1 Consensus size: 26
87196 ATTTTGGGCG
**
87206 CAATTCTAGACACGTTCATGCAGTGA
1 CAATTCTAGACACGTTCATGCAACGA
*
87232 CAATTCT-GTACATGTTCATGCAACGA
1 CAATTCTAG-ACACGTTCATGCAACGA
87258 CA
1 CA
87260 TTCCTGGGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.31, C:0.24, G:0.17, T:0.28
Consensus pattern (26 bp):
CAATTCTAGACACGTTCATGCAACGA
Found at i:87290 original size:37 final size:38
Alignment explanation
Indices: 87249--87346 Score: 110
Period size: 38 Copynumber: 2.6 Consensus size: 38
87239 GTACATGTTC
87249 ATGCAACGACATTCCTGGGTGCAA-TTGAAGAATACTT
1 ATGCAACGACATTCCTGGGTGCAATTTGAAGAATACTT
* * * *
87286 ATGCAACGATAGTT-CTAGATGCAATTTGAAGAATATTT
1 ATGCAACGACA-TTCCTGGGTGCAATTTGAAGAATACTT
* * *
87324 ATGCAATGACAGTCTTGGGTGCA
1 ATGCAACGACATTCCTGGGTGCA
87347 TTTAGGAAAT
Statistics
Matches: 48, Mismatches: 10, Indels: 5
0.76 0.16 0.08
Matches are distributed among these distances:
37 19 0.40
38 29 0.60
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (38 bp):
ATGCAACGACATTCCTGGGTGCAATTTGAAGAATACTT
Found at i:87408 original size:37 final size:37
Alignment explanation
Indices: 87366--87445 Score: 106
Period size: 37 Copynumber: 2.2 Consensus size: 37
87356 TATTCCTACG
* * * **
87366 ACGACAGTTTTGGGTGCAATCTGGAAGTGCTCATGCA
1 ACGACAATTTTAGGCGCAATCTAAAAGTGCTCATGCA
*
87403 GCGACAATTTTAGGCGCAATCTAAAAGTGCTCATGCA
1 ACGACAATTTTAGGCGCAATCTAAAAGTGCTCATGCA
87440 ACGACA
1 ACGACA
87446 TTAGTAGTAA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (37 bp):
ACGACAATTTTAGGCGCAATCTAAAAGTGCTCATGCA
Found at i:92023 original size:19 final size:19
Alignment explanation
Indices: 91985--92023 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
91975 ATTATGAACT
* *
91985 GACCACGTAATACTGCTCA
1 GACCACGTAATACCGATCA
92004 GACCACGTAATACCGATCA
1 GACCACGTAATACCGATCA
92023 G
1 G
92024 TATTAGTTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.33, C:0.31, G:0.18, T:0.18
Consensus pattern (19 bp):
GACCACGTAATACCGATCA
Found at i:92234 original size:21 final size:21
Alignment explanation
Indices: 92210--92256 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
92200 TTTTTATCAT
92210 ATTATTAA-ATTCACATTTAAA
1 ATTATTAATATTCA-ATTTAAA
* * *
92231 ATTAATAATATTTAATTTAGA
1 ATTATTAATATTCAATTTAAA
92252 ATTAT
1 ATTAT
92257 AAGTTAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (21 bp):
ATTATTAATATTCAATTTAAA
Found at i:92322 original size:17 final size:17
Alignment explanation
Indices: 92282--92314 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
92272 AAATAAAATG
92282 AAAATTATATATTTAAA
1 AAAATTATATATTTAAA
92299 AATAATTATA-ATTTAA
1 AA-AATTATATATTTAA
92315 TAGAAATTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AAAATTATATATTTAAA
Found at i:95767 original size:22 final size:22
Alignment explanation
Indices: 95739--95782 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
95729 AATACATTAA
95739 ACCCAAACCAATAAGCCCAAAT
1 ACCCAAACCAATAAGCCCAAAT
* *
95761 ACCCAAATCAATAAGCTCAAAT
1 ACCCAAACCAATAAGCCCAAAT
95783 TAATCCAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.50, C:0.32, G:0.05, T:0.14
Consensus pattern (22 bp):
ACCCAAACCAATAAGCCCAAAT
Found at i:98087 original size:21 final size:21
Alignment explanation
Indices: 98063--98113 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
98053 GACTTCTACT
**
98063 GATACAAGTGACAATTTTACC
1 GATACAAGTGACAATTCGACC
* **
98084 GATATAAGTGACTCTTCGACC
1 GATACAAGTGACAATTCGACC
98105 GATACAAGT
1 GATACAAGT
98114 CTTACTTTTA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (21 bp):
GATACAAGTGACAATTCGACC
Found at i:102521 original size:52 final size:52
Alignment explanation
Indices: 102443--102679 Score: 314
Period size: 52 Copynumber: 4.5 Consensus size: 52
102433 AAATGAAAAG
* *
102443 GGTCCGATGATTAAGTGTCATTGTGAGTAAATGAATCCTTTACGGATTATGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * *
102495 GGTCCAATGACTAAGTGTCATCGTGAGTAAATGAGTCCTTTACGGATTATAA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * *
102547 GGTCCGATGGCTAAGTGTCATCGTGAGTATATGAATCCTTTACGGATTGTGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
* * * *
102599 GGTCCGATGACTAAGTGTCATCGTGAGTACATGAATTCTTTTACGGAATAGGA
1 GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCTTTACGGATTATGA
* * *
102652 GGTCTGACGACTATA-TGTCATTGTGAGT
1 GGTCCGATGACTA-AGTGTCATCGTGAGT
102680 TTTAAATGAA
Statistics
Matches: 163, Mismatches: 20, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
52 126 0.77
53 36 0.22
54 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.26, T:0.32
Consensus pattern (52 bp):
GGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATTATGA
Found at i:110331 original size:21 final size:22
Alignment explanation
Indices: 110263--110339 Score: 79
Period size: 21 Copynumber: 3.5 Consensus size: 22
110253 TGACTTGAGT
*
110263 TGTATCGGTAG-TTGGATTGCA
1 TGTATCGGTAGTTTGTATTGCA
*
110284 AGTATCGGTAGTTATGTGTATTG-A
1 TGTATCGGTAG-T-T-TGTATTGCA
110308 TGTATCGGTAGTTTGTA-TGCA
1 TGTATCGGTAGTTTGTATTGCA
*
110329 TGTATCAGTAG
1 TGTATCGGTAG
110340 AAGTTGCAGG
Statistics
Matches: 47, Mismatches: 4, Indels: 10
0.77 0.07 0.16
Matches are distributed among these distances:
20 2 0.04
21 25 0.53
22 1 0.02
23 1 0.02
24 12 0.26
25 6 0.13
ACGTcount: A:0.22, C:0.08, G:0.30, T:0.40
Consensus pattern (22 bp):
TGTATCGGTAGTTTGTATTGCA
Found at i:116783 original size:13 final size:13
Alignment explanation
Indices: 116765--116789 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
116755 CACCGTAAGG
116765 TGAATAGAATTCA
1 TGAATAGAATTCA
116778 TGAATAGAATTC
1 TGAATAGAATTC
116790 GTTGCGTTTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.08, G:0.16, T:0.32
Consensus pattern (13 bp):
TGAATAGAATTCA
Found at i:124519 original size:21 final size:21
Alignment explanation
Indices: 124492--124568 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 21
124482 TAACTTGAGT
124492 TGTATCGGTAGTTGGATTGCA
1 TGTATCGGTAGTTGGATTGCA
* *
124513 AGTATCGATAGTTATGTGTATTG-A
1 TGTATCGGTAG-T-TG-G-ATTGCA
*
124537 TGTATCGGTAGTTTG-TATGCA
1 TGTATCGGTAGTTGGAT-TGCA
124558 TGTATCGGTAG
1 TGTATCGGTAG
124569 AAGTTGCAGA
Statistics
Matches: 45, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
19 1 0.02
20 2 0.04
21 22 0.49
22 2 0.04
23 3 0.07
24 11 0.24
25 4 0.09
ACGTcount: A:0.22, C:0.08, G:0.30, T:0.40
Consensus pattern (21 bp):
TGTATCGGTAGTTGGATTGCA
Found at i:128584 original size:14 final size:14
Alignment explanation
Indices: 128565--128591 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
128555 ATTTTTAAAA
128565 AAAATTTAATTTAT
1 AAAATTTAATTTAT
128579 AAAATTTAATTTA
1 AAAATTTAATTTA
128592 ATAATTATCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
AAAATTTAATTTAT
Found at i:128636 original size:48 final size:49
Alignment explanation
Indices: 128580--128679 Score: 150
Period size: 48 Copynumber: 2.1 Consensus size: 49
128570 TTAATTTATA
* * *
128580 AAATTTAATTTAATAAT-TATCTTAATAA-TATTTTATTAATTTAATATT
1 AAATTTAATCTAAT-ATGTACCTTAATAAGTATTATATTAATTTAATATT
128628 AAATTTAATCTAATATGTACCTTAATAAGTATTATATTAATTTAATATT
1 AAATTTAATCTAATATGTACCTTAATAAGTATTATATTAATTTAATATT
128677 AAA
1 AAA
128680 GTGATTAAAT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
47 2 0.04
48 23 0.49
49 22 0.47
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (49 bp):
AAATTTAATCTAATATGTACCTTAATAAGTATTATATTAATTTAATATT
Found at i:132510 original size:21 final size:19
Alignment explanation
Indices: 132472--132511 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 19
132462 TTGGTACTCG
*
132472 AATTTGATATATATTTTTT
1 AATTTGATATAAATTTTTT
132491 AATTTGATATTTAAATTTTTT
1 AATTTGATA--TAAATTTTTT
132512 TGACTTAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
21 9 0.50
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (19 bp):
AATTTGATATAAATTTTTT
Found at i:132589 original size:31 final size:31
Alignment explanation
Indices: 132460--132589 Score: 101
Period size: 31 Copynumber: 4.3 Consensus size: 31
132450 TTAATATAAT
**
132460 ATTTGGTACTCGAATTTGATATATATTTT-TTA
1 ATTTGGTACTTAAATTTGATAT-T-TTTTCTTA
* * **
132492 ATTTGATATTTAAA-TT--T-TTTTGACTTA
1 ATTTGGTACTTAAATTTGATATTTTTTCTTA
* * * *
132519 ATTTGGTAAC-TGAACTTGACACTTTTTCTTA
1 ATTTGGT-ACTTAAATTTGATATTTTTTCTTA
132550 ATTTGGTACTTAAATTTGATATTTTTTCTTA
1 ATTTGGTACTTAAATTTGATATTTTTTCTTA
132581 ATTTGGTAC
1 ATTTGGTAC
132590 CTAAGCTTTT
Statistics
Matches: 74, Mismatches: 17, Indels: 15
0.70 0.16 0.14
Matches are distributed among these distances:
26 2 0.03
27 13 0.18
28 4 0.05
29 1 0.01
30 2 0.03
31 42 0.57
32 10 0.14
ACGTcount: A:0.27, C:0.08, G:0.12, T:0.53
Consensus pattern (31 bp):
ATTTGGTACTTAAATTTGATATTTTTTCTTA
Found at i:132904 original size:31 final size:31
Alignment explanation
Indices: 132826--132906 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
132816 GGACCCAAAA
* *
132826 AAGTTTCAGTACCAATTTAAAAAAAAAGTGTC
1 AAGTTT-AGTACCAAATTAAAAAAAAAGTCTC
* *
132858 AAGTTTAGGTTCCAAATT-AGAAAAAAGTCTC
1 AAGTTTA-GTACCAAATTAAAAAAAAAGTCTC
132889 AAGTTTGAGTACCAAATT
1 AAGTTT-AGTACCAAATT
132907 GGACCAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
31 27 0.64
32 15 0.36
ACGTcount: A:0.43, C:0.12, G:0.15, T:0.30
Consensus pattern (31 bp):
AAGTTTAGTACCAAATTAAAAAAAAAGTCTC
Found at i:132914 original size:90 final size:91
Alignment explanation
Indices: 132772--132965 Score: 243
Period size: 91 Copynumber: 2.1 Consensus size: 91
132762 TAAAAAAAGA
* *
132772 TTAGGTACCAAATTAAGAAAAAAGTCAAGTCCAAGTACTAAATTGGACCCAAAAAAGTTTCA-GT
1 TTAGGTACCAAATTAAGAAAAAAGTCAAGTCCAAGTACCAAATTGGACCCAAAAAAATTT-AGGT
* ***
132836 ACCAATTTAA-AAAAAAAGTGTCAAGT
65 ACCAAATTAAGAAAAAAAACATCAAGT
* ***
132862 TTAGGTTCCAAATT-AGAAAAAAGTCTCAAGTTTGAGTACCAAATTGGA-CCAAAAAAATTTAGG
1 TTAGGTACCAAATTAAGAAAAAAG--TCAAGTCCAAGTACCAAATTGGACCCAAAAAAATTTAGG
132925 TACCAAATTAAGAAAAAAAACATCAAGT
64 TACCAAATTAAGAAAAAAAACATCAAGT
132953 TTAGGTACCAAAT
1 TTAGGTACCAAAT
132966 GTTATATTAA
Statistics
Matches: 89, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
89 10 0.11
90 35 0.39
91 44 0.49
ACGTcount: A:0.47, C:0.14, G:0.14, T:0.24
Consensus pattern (91 bp):
TTAGGTACCAAATTAAGAAAAAAGTCAAGTCCAAGTACCAAATTGGACCCAAAAAAATTTAGGTA
CCAAATTAAGAAAAAAAACATCAAGT
Found at i:132956 original size:33 final size:32
Alignment explanation
Indices: 132826--132965 Score: 100
Period size: 33 Copynumber: 4.5 Consensus size: 32
132816 GGACCCAAAA
* **
132826 AAGTTTCA-GTACCAATTTA-AAAAAAAAGTGTC
1 AAGTTT-AGGTACCAAATTAGAAAAAAAA-CATC
* **
132858 AAGTTTAGGTTCCAAATTAGAAAAAAGTC-TC
1 AAGTTTAGGTACCAAATTAGAAAAAAAACATC
* **
132889 AAGTTT-GAGTACCAAATT-GGACCAAAA-A--
1 AAGTTTAG-GTACCAAATTAGAAAAAAAACATC
132917 AA-TTTAGGTACCAAATTAAGAAAAAAAACATC
1 AAGTTTAGGTACCAAATT-AGAAAAAAAACATC
132949 AAGTTTAGGTACCAAAT
1 AAGTTTAGGTACCAAAT
132966 GTTATATTAA
Statistics
Matches: 83, Mismatches: 14, Indels: 21
0.70 0.12 0.18
Matches are distributed among these distances:
27 13 0.16
28 3 0.04
29 6 0.07
30 6 0.07
31 18 0.22
32 17 0.20
33 20 0.24
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (32 bp):
AAGTTTAGGTACCAAATTAGAAAAAAAACATC
Found at i:134983 original size:11 final size:12
Alignment explanation
Indices: 134964--135028 Score: 61
Period size: 11 Copynumber: 5.8 Consensus size: 12
134954 GTGATTAAAA
134964 GAGAAAGAAATG
1 GAGAAAGAAATG
134976 GA-AAAGAAA-G
1 GAGAAAGAAATG
134986 GAGAAAGAAAT-
1 GAGAAAGAAATG
* *
134997 AAGAAAGGAAT-
1 GAGAAAGAAATG
135008 GAGAGAA-AAAT-
1 GAGA-AAGAAATG
135019 GAGAAAGAAA
1 GAGAAAGAAA
135029 GTGAGAGGCT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
10 5 0.11
11 36 0.80
12 4 0.09
ACGTcount: A:0.65, C:0.00, G:0.29, T:0.06
Consensus pattern (12 bp):
GAGAAAGAAATG
Found at i:135003 original size:33 final size:33
Alignment explanation
Indices: 134965--135028 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
134955 TGATTAAAAG
134965 AGAAAGAAATG-GAAAAGAAAGGAGAAAGAAATA
1 AGAAAGAAATGAGAAAA-AAAGGAGAAAGAAATA
* * *
134998 AGAAAGGAATGAGAGAAAAATGAGAAAGAAA
1 AGAAAGAAATGAGAAAAAAAGGAGAAAGAAA
135029 GTGAGAGGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.66, C:0.00, G:0.28, T:0.06
Consensus pattern (33 bp):
AGAAAGAAATGAGAAAAAAAGGAGAAAGAAATA
Found at i:141579 original size:13 final size:13
Alignment explanation
Indices: 141561--141585 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
141551 TTTCAAAAAT
141561 GTCAACGGTCAAA
1 GTCAACGGTCAAA
141574 GTCAACGGTCAA
1 GTCAACGGTCAA
141586 CGGTCGGTCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (13 bp):
GTCAACGGTCAAA
Found at i:142166 original size:11 final size:11
Alignment explanation
Indices: 142134--142204 Score: 58
Period size: 11 Copynumber: 6.5 Consensus size: 11
142124 ATGAGTGATT
142134 AAAAGAGAAAG
1 AAAAGAGAAAG
*
142145 AAATG-GAAAAG
1 AAAAGAG-AAAG
142156 AAAAGAGAAAG
1 AAAAGAGAAAG
142167 AAATA-AGAAAG
1 AAA-AGAGAAAG
* *
142178 GAATGAGAGAA-
1 AAAAGAGA-AAG
*
142189 AAATGAGAAAG
1 AAAAGAGAAAG
142200 AAAAG
1 AAAAG
142205 TGAGAGGCTT
Statistics
Matches: 48, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
10 3 0.06
11 41 0.85
12 4 0.08
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.06
Consensus pattern (11 bp):
AAAAGAGAAAG
Found at i:142177 original size:22 final size:21
Alignment explanation
Indices: 142134--142204 Score: 72
Period size: 22 Copynumber: 3.2 Consensus size: 21
142124 ATGAGTGATT
*
142134 AAAAGAGAAAGAAATGGAAAAG
1 AAAAGAGAAAGAAATAG-AAAG
142156 AAAAGAGAAAGAAATAAGAAAG
1 AAAAGAGAAAGAAAT-AGAAAG
* *
142178 GAATGAGAGAA-AAATGAGAAAG
1 AAAAGAGA-AAGAAAT-AGAAAG
142200 AAAAG
1 AAAAG
142205 TGAGAGGCTT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
22 38 0.93
23 3 0.07
ACGTcount: A:0.68, C:0.00, G:0.27, T:0.06
Consensus pattern (21 bp):
AAAAGAGAAAGAAATAGAAAG
Found at i:142177 original size:33 final size:33
Alignment explanation
Indices: 142139--142202 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
142129 TGATTAAAAG
142139 AGAAAGAAATG-GAAAAGAAAAGAGAAAGAAATA
1 AGAAAGAAATGAGAAAA-AAAAGAGAAAGAAATA
* * *
142172 AGAAAGGAATGAGAGAAAAATGAGAAAGAAA
1 AGAAAGAAATGAGAAAAAAAAGAGAAAGAAA
142203 AGTGAGAGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.67, C:0.00, G:0.27, T:0.06
Consensus pattern (33 bp):
AGAAAGAAATGAGAAAAAAAAGAGAAAGAAATA
Found at i:144070 original size:17 final size:18
Alignment explanation
Indices: 144048--144108 Score: 61
Period size: 20 Copynumber: 3.3 Consensus size: 18
144038 TCATTGATAC
144048 ATATATATAAACTAT-TA
1 ATATATATAAACTATATA
* *
144065 ATATATTATATACTATATT
1 ATATA-TATAAACTATATA
*
144084 ATATGATATAACATTATATA
1 ATAT-ATATAA-ACTATATA
144104 ATATA
1 ATATA
144109 GTAGGCGGAC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
17 5 0.14
18 9 0.26
19 10 0.29
20 11 0.31
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (18 bp):
ATATATATAAACTATATA
Found at i:174711 original size:8 final size:7
Alignment explanation
Indices: 174690--174723 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
174680 ACCATTGTAC
174690 TAGTTTT
1 TAGTTTT
174697 TAGTTTT
1 TAGTTTT
174704 TAGTTTT
1 TAGTTTT
*
174711 TAATTTT
1 TAGTTTT
174718 TA-TTTT
1 TAGTTTT
174724 GTATTTTCGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
6 4 0.15
7 22 0.85
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (7 bp):
TAGTTTT
Found at i:180908 original size:20 final size:20
Alignment explanation
Indices: 180853--180910 Score: 84
Period size: 18 Copynumber: 3.0 Consensus size: 20
180843 ATACTGAACA
180853 AATTACTAAGTTAAAAATGC
1 AATTACTAAGTTAAAAATGC
* *
180873 AGTTACTTAG--AAAAATGC
1 AATTACTAAGTTAAAAATGC
180891 AATTACTAAGTTAAAAATGC
1 AATTACTAAGTTAAAAATGC
180911 TAAAAATGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
18 16 0.50
20 16 0.50
ACGTcount: A:0.48, C:0.10, G:0.12, T:0.29
Consensus pattern (20 bp):
AATTACTAAGTTAAAAATGC
Found at i:187105 original size:16 final size:15
Alignment explanation
Indices: 187056--187107 Score: 61
Period size: 16 Copynumber: 3.3 Consensus size: 15
187046 TGAGCCTCTG
187056 TTCTTTCTTCTTTTGT
1 TTCTTT-TTCTTTTGT
187072 TTCTGTTTT-TTTTGT
1 TTCT-TTTTCTTTTGT
*
187087 TTCTTTATTCTTTTAT
1 TTCTTT-TTCTTTTGT
187103 TTCTT
1 TTCTT
187108 ATATATATAT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.06
15 12 0.38
16 16 0.50
17 2 0.06
ACGTcount: A:0.04, C:0.13, G:0.06, T:0.77
Consensus pattern (15 bp):
TTCTTTTTCTTTTGT
Found at i:187109 original size:15 final size:15
Alignment explanation
Indices: 187063--187109 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
187053 CTGTTCTTTC
187063 TTCTTTTGTTTCTGT-
1 TTCTTTTGTTTCT-TA
*
187078 TTTTTTTGTTTCTTTA
1 TTCTTTTGTTTC-TTA
*
187094 TTCTTTTATTTCTTA
1 TTCTTTTGTTTCTTA
187109 T
1 T
187110 ATATATATAT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.06, C:0.11, G:0.06, T:0.77
Consensus pattern (15 bp):
TTCTTTTGTTTCTTA
Found at i:193390 original size:6 final size:6
Alignment explanation
Indices: 193379--193423 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
193369 TAATAGGGAC
* *
193379 TTTCAA TTTCAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAA TTTCA
1 TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCA
193424 CATATTAAAT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 1 0.03
5 5 0.15
6 27 0.82
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (6 bp):
TTTCAA
Done.