Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006154.1 Hibiscus syriacus cultivar Beakdansim tig00014623_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: 160070
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:183 original size:14 final size:14
Alignment explanation
Indices: 164--200 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
154 CATCAATTAA
164 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
178 ACAAATCACCTTTT
1 ACAAATCAACTTTT
192 ACAAATCAA
1 ACAAATCAA
201 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:1596 original size:21 final size:21
Alignment explanation
Indices: 1530--1596 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
1520 GTGAATCGGG
*
1530 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
1550 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
1572 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
1593 CTCT
1 CTCT
1597 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:1615 original size:42 final size:41
Alignment explanation
Indices: 1530--1652 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
1520 GTGAATCGGG
* * * *
1530 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
1572 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
1614 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
1653 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:3676 original size:20 final size:19
Alignment explanation
Indices: 3631--3785 Score: 63
Period size: 19 Copynumber: 8.8 Consensus size: 19
3621 TCTTTTGGTT
3631 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3650 GATAATGAGAATCGCAATGCG-
1 GA-AATGAAAATCGCAA--CGA
**
3671 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
*
3690 G--A-G--AATCGCAACGC
1 GAAATGAAAATCGCAACGA
** *
3704 GAAATGACTATCGCGACGA
1 GAAATGAAAATCGCAACGA
*
3723 G--A-G--AATCGCGACGA
1 GAAATGAAAATCGCAACGA
* *
3737 G--A-G--AATCGCAATGC
1 GAAATGAAAATCGCAACGA
* *
3751 GAAATAAAAATCGCAACGC
1 GAAATGAAAATCGCAACGA
3770 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
3786 TGCGATTTTT
Statistics
Matches: 107, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
14 32 0.30
16 4 0.04
17 3 0.03
18 2 0.02
19 37 0.35
20 25 0.23
21 2 0.02
22 2 0.02
ACGTcount: A:0.43, C:0.19, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:3699 original size:14 final size:14
Alignment explanation
Indices: 3680--3747 Score: 64
Period size: 14 Copynumber: 4.5 Consensus size: 14
3670 GGAAATGACT
3680 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
*
3694 ATCGCAACGCGAAATGA
1 ATCGCAA--CGAGA-GA
*
3711 CTATCGCGACGAGAGA
1 --ATCGCAACGAGAGA
*
3727 ATCGCGACGAGAGA
1 ATCGCAACGAGAGA
3741 ATCGCAA
1 ATCGCAA
3748 TGCGAAATAA
Statistics
Matches: 45, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
14 27 0.60
16 6 0.13
17 6 0.13
19 6 0.13
ACGTcount: A:0.38, C:0.24, G:0.28, T:0.10
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:3713 original size:33 final size:34
Alignment explanation
Indices: 3656--3731 Score: 127
Period size: 33 Copynumber: 2.3 Consensus size: 34
3646 ACGAGATAAT
*
3656 GAGAATCGCAATGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
*
3690 GAGAATCGCAACGC-GAAATGACTATCGCGACGA
1 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
3723 GAGAATCGC
1 GAGAATCGC
3732 GACGAGAGAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 27 0.68
34 13 0.32
ACGTcount: A:0.37, C:0.22, G:0.28, T:0.13
Consensus pattern (34 bp):
GAGAATCGCAACGCGGAAATGACTATCGCAACGA
Found at i:3762 original size:19 final size:19
Alignment explanation
Indices: 3740--3790 Score: 84
Period size: 19 Copynumber: 2.7 Consensus size: 19
3730 GCGACGAGAG
3740 AATCGCAATGCGAAATAAA
1 AATCGCAATGCGAAATAAA
* *
3759 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATAAA
3778 AATCGCAATGCGA
1 AATCGCAATGCGA
3791 TTTTTGTTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATAAA
Found at i:3822 original size:19 final size:19
Alignment explanation
Indices: 3786--3830 Score: 72
Period size: 19 Copynumber: 2.4 Consensus size: 19
3776 AAAATCGCAA
*
3786 TGCGATTTTTGTTTCGCGT
1 TGCGATTTTTATTTCGCGT
*
3805 TGCGTTTTTTATTTCGCGT
1 TGCGATTTTTATTTCGCGT
3824 TGCGATT
1 TGCGATT
3831 CTCTCGTTGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.07, C:0.16, G:0.24, T:0.53
Consensus pattern (19 bp):
TGCGATTTTTATTTCGCGT
Found at i:4430 original size:20 final size:20
Alignment explanation
Indices: 4380--4432 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
4370 GCGCTATGTA
*
4380 AATCGCGTTGAGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
4400 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
4420 TATCTCGTTGCGA
1 AATCGCGTTGCGA
4433 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.28, C:0.19, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:4466 original size:20 final size:20
Alignment explanation
Indices: 4441--4494 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
4431 GATTTTGTAT
4441 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
4461 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
4481 TATCGCATTGCGAT
1 TATCGCATTGCGAT
4495 TTTTCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:4513 original size:61 final size:61
Alignment explanation
Indices: 4376--4515 Score: 151
Period size: 61 Copynumber: 2.3 Consensus size: 61
4366 AATGGCGCTA
* * * * * *
4376 TGTAA-ATCGCGTTGAGAAAGTCAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
* * * *
4436 TGTATTATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTT
1 TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
4497 T-TCCAAT-TCGCGTTGCGAT
1 TGT--AATATCGCGTTGCGAT
4516 TTACTTATTC
Statistics
Matches: 65, Mismatches: 12, Indels: 5
0.79 0.15 0.06
Matches are distributed among these distances:
60 5 0.08
61 58 0.89
62 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.24, T:0.34
Consensus pattern (61 bp):
TGTAATATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTT
Found at i:11167 original size:653 final size:657
Alignment explanation
Indices: 9894--11538 Score: 2960
Period size: 653 Copynumber: 2.5 Consensus size: 657
9884 ATTGAGATTG
*
9894 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
1 TATTACAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
*
9959 GGCAAATCACGTTGGAGTCCAAGTTTAGATGATTCTAGTTGATATCCTGTGCACAACATGTAT-G
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
*
10023 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACATAAACTATCCA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
*
10088 ATTGCATCCGTTATCACGTTGGACATAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
10153 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
261 TGGACTGAACTGAATTA-GAATATTGTAATTCTTAATTGACATAATTG-TTCTTCTTTAGATGTG
* *
10218 AACTCTATTACATAAATTAACATTGCAATAGGTATATGGGAACTTGCTCTGACCAAGGGCATGAT
324 AACTCTATTACAGAAATCAACATTGCAATAGGTATATGGGAACTTGCTCTGACCAAGGGCATGAT
*
10283 AGTTTGGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCATGTGCACAACATG
389 AGTTTGGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTAATATCATGTGCACAACATG
10348 TATGGGGACTGTTGTATTTGTTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTA
454 TATGGGGACTGTTGTATTTGTTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTA
* *
10413 TCCAATTGCATCCTTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCG
519 TCCAATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGCAGATCGATCG
*
10478 ACTCTGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGA
584 ACTCTGGACTGAACTGAATTACGAATATTATAATTCTTAATTGACATAATTGTTTCTTCTTTAGA
10543 TGTGAACTC
649 TGTGAACTC
* *
10552 TATTATAGAAATCAACATTGCAATAGGTATATGGGAGCTTACTCTGACCAAGGGCATGATAGTTT
1 TATTACAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
10617 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
* *
10682 GGACTGTTGTATTTTATTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTATCCA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
*
10747 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATAATTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
10812 TGGACTGAACTGAA-T-GAATATTGTAATTCTTAATTGACATAATTG-T-TTC-TTAGATGTGAA
261 TGGACTGAACTGAATTAGAATATTGTAATTCTTAATTGACATAATTGTTCTTCTTTAGATGTGAA
* *
10872 CTCTATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAG
326 CTCTATTACAGAAATCAACATTGCAATAGGTATATGGGAACTTGCTCTGACCAAGGGCATGATAG
*
10937 TTTGGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTAATATCATGTGCACAATATGTA
391 TTTGGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTAATATCATGTGCACAACATGTA
*
11002 TGGGGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTAT
456 TGGGGACTGTTGTA-TTTGTTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTAT
*
11067 CCAATTGCATCCGTTATCACGTTGGACACAGTAACAAACATACTTTTTGGTGGCAGATCGATCGA
520 CCAATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGCAGATCGATCGA
11132 CTCTGGACTGAACTGAATTACGAATATTATAATTCTTAATTGACATAATTGTTTCTTCTTTAGAT
585 CTCTGGACTGAACTGAATTACGAATATTATAATTCTTAATTGACATAATTGTTTCTTCTTTAGAT
11197 GTGAACTC
650 GTGAACTC
*
11205 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
1 TATTACAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
* *
11270 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCATAACATGCATGG
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
* * *
11335 GGACTGTTGTATTTTGTTAGTTCCTTTATATCAGTATTCTTCTTCTTTGAAATACAAACTATCTA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
11400 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
*
11465 TGGACTAAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
261 TGGACTGAACTGAATTA-GAATATTGTAATTCTTAATTGACATAATTG-TTCTTCTTTAGATGTG
11530 AACTCTATT
324 AACTCTATT
11539 CCACGATATA
Statistics
Matches: 946, Mismatches: 32, Indels: 16
0.95 0.03 0.02
Matches are distributed among these distances:
652 149 0.16
653 448 0.47
654 2 0.00
656 60 0.06
658 126 0.13
659 143 0.15
660 18 0.02
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (657 bp):
TATTACAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
TGGACTGAACTGAATTAGAATATTGTAATTCTTAATTGACATAATTGTTCTTCTTTAGATGTGAA
CTCTATTACAGAAATCAACATTGCAATAGGTATATGGGAACTTGCTCTGACCAAGGGCATGATAG
TTTGGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTAATATCATGTGCACAACATGTA
TGGGGACTGTTGTATTTGTTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTATC
CAATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGCAGATCGATCGAC
TCTGGACTGAACTGAATTACGAATATTATAATTCTTAATTGACATAATTGTTTCTTCTTTAGATG
TGAACTC
Found at i:11342 original size:330 final size:330
Alignment explanation
Indices: 9894--11538 Score: 2975
Period size: 330 Copynumber: 5.0 Consensus size: 330
9884 ATTGAGATTG
9894 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
1 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
*
9959 GGCAAATCACGTTGGAGTCCAAGTTTAGATGATTCTAGTTGATATCCTGTGCACAACATGTAT-G
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
*
10023 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACATAAACTATCCA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
*
10088 ATTGCATCCGTTATCACGTTGGACATAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
10153 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
261 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
10218 AACTC
326 AACTC
* * * *
10223 TATTACATAAATTAACATTGCAATAGGTATATGGGAACTTGCTCTGACCAAGGGCATGATAGTTT
1 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
*
10288 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCATGTGCACAACATGTATGG
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
*
10353 GGACTGTTGTA-TTTGTTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTATCCA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
*
10417 ATTGCATCCTTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
10482 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
261 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
10547 AACTC
326 AACTC
** *
10552 TATTATAGAAATCAACATTGCAATAGGTATATGGGAGCTTACTCTGACCAAGGGCATGATAGTTT
1 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
10617 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
* *
10682 GGACTGTTGTATTTTATTAGTTCCTATATATCAATATTCTTCTTCTTTGAAACACAAACTATCCA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
*
10747 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATAATTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
10812 TGGACTGAACTGAA-T--GAATATTGTAATTCTTAATTGACATAATTG--T-TTC-TTAGATGTG
261 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
10870 AACTC
326 AACTC
10875 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
1 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
* * *
10940 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTAATATCATGTGCACAATATGTATGG
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
11005 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
* *
11070 ATTGCATCCGTTATCACGTTGGACACAGTAACAAACATACTTTTTGGTGGCAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
*
11135 TGGACTGAACTGAATTACGAATATTATAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
261 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
11200 AACTC
326 AACTC
11205 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
1 TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
* *
11270 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCATAACATGCATGG
66 GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
* * *
11335 GGACTGTTGTATTTTGTTAGTTCCTTTATATCAGTATTCTTCTTCTTTGAAATACAAACTATCTA
131 GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
11400 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
196 ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
*
11465 TGGACTAAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
261 TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
11530 AACTC
326 AACTC
11535 TATT
1 TATT
11539 CCACGATATA
Statistics
Matches: 1264, Mismatches: 43, Indels: 17
0.95 0.03 0.01
Matches are distributed among these distances:
323 277 0.22
324 4 0.00
325 1 0.00
326 29 0.02
327 30 0.02
328 1 0.00
329 445 0.35
330 477 0.38
ACGTcount: A:0.29, C:0.16, G:0.19, T:0.36
Consensus pattern (330 bp):
TATTGCAGAAATCAACATTGCAATAGGTATATGGGAGCTTGCTCTGACCAAGGGCATGATAGTTT
GGCAAATCACGTTGGAGTCCAAGTTTAGATGGTTCTAGTTGATATCCTGTGCACAACATGTATGG
GGACTGTTGTATTTTGTTAGTTCCTATATATCAGTATTCTTCTTCTTTGAAACACAAACTATCCA
ATTGCATCCGTTATCACGTTGGACACAATAACAAACATACTTTTTGGTGGTAGATCGATCGACTC
TGGACTGAACTGAATTACGAATATTGTAATTCTTAATTGACATAATTGTTTCTTCTTTAGATGTG
AACTC
Found at i:12785 original size:57 final size:56
Alignment explanation
Indices: 12667--12775 Score: 132
Period size: 57 Copynumber: 1.9 Consensus size: 56
12657 AGTGCATCGA
* * * *
12667 TGCATGAAATGTATTCGATGTTTCAAAATAGTCAGAGTGCATCGATGCATGGCTGG
1 TGCATCAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATAGCTGG
*
12723 TGCATCAAATGCATTCGATGTTTTCATAAA-ACTCTA-AGTGCATTGATGCATAG
1 TGCATCAAATGCATTCGATG-TTTCA-AAATACTC-AGAGTGCATCGATGCATAG
12776 TATGTGCATC
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
56 18 0.40
57 23 0.51
58 4 0.09
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (56 bp):
TGCATCAAATGCATTCGATGTTTCAAAATACTCAGAGTGCATCGATGCATAGCTGG
Found at i:15598 original size:23 final size:21
Alignment explanation
Indices: 15568--15628 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
15558 TGGCCTTGTG
15568 CATCGATGCACATTCAAGGCGTT
1 CATCGATGCACATTCAA-GCG-T
* *
15591 CATCGATGCACCTTCATAGTGT
1 CATCGATGCACATTCA-AGCGT
15613 -ATCGATGCACATTCAA
1 CATCGATGCACATTCAA
15629 AGGGATGTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 1 0.03
21 14 0.41
22 1 0.03
23 17 0.50
24 1 0.03
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
CATCGATGCACATTCAAGCGT
Found at i:15618 original size:21 final size:23
Alignment explanation
Indices: 15592--15645 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
15582 CAAGGCGTTC
* *
15592 ATCGATGCACCTTCATA-G-TGT
1 ATCGATGCACATTCAAAGGATGT
15613 ATCGATGCACATTCAAAGGGATGT
1 ATCGATGCACATTCAAA-GGATGT
15637 ATCGATGCA
1 ATCGATGCA
15646 ATGTTAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 15 0.54
23 1 0.04
24 12 0.43
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (23 bp):
ATCGATGCACATTCAAAGGATGT
Found at i:21175 original size:7 final size:7
Alignment explanation
Indices: 21163--21188 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
21153 TTTGATTCTC
21163 TCTTGAT
1 TCTTGAT
21170 TCTTGAT
1 TCTTGAT
21177 TCTTGAT
1 TCTTGAT
21184 TCTTG
1 TCTTG
21189 TGTTTTCTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.15, G:0.15, T:0.58
Consensus pattern (7 bp):
TCTTGAT
Found at i:21627 original size:65 final size:63
Alignment explanation
Indices: 21429--21636 Score: 190
Period size: 65 Copynumber: 3.2 Consensus size: 63
21419 TTCACTAAGA
* * * * *
21429 GTGCATCGATGCATGAAATGAATTCGATGTTTCAAAATAGCCA-GAGTGCATCGATGCATGGCTG
1 GTGCATCGATGCATGAAATGCATTTGATGTTT--AATTAACCATGAGTGCATCGATGCATGGTTG
* * * * *
21493 GTGCATCGATGCATCAAATGCATGTGATGTTTTCATAAAACTC-TGAGTGCATCGATGCATAGTA
1 GTGCATCGATGCATGAAATGCATTTGATG-TTTAAT-TAAC-CATGAGTGCATCGATGCATGGT-
21557 T-
62 TG
* *
21558 GTGCATTGATGCATGAAATGCATTTGATGTTTAATTTATTCCATG-GTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTTGATGTTTAA-TTA-ACCATGAGTGCATCGATGCATGG-TT
21622 G
63 G
*
21623 GTGCATCGGTGCAT
1 GTGCATCGATGCAT
21637 CACTTTGAAA
Statistics
Matches: 115, Mismatches: 19, Indels: 19
0.75 0.12 0.12
Matches are distributed among these distances:
63 1 0.01
64 49 0.43
65 64 0.56
66 1 0.01
ACGTcount: A:0.27, C:0.16, G:0.25, T:0.32
Consensus pattern (63 bp):
GTGCATCGATGCATGAAATGCATTTGATGTTTAATTAACCATGAGTGCATCGATGCATGGTTG
Found at i:22830 original size:34 final size:32
Alignment explanation
Indices: 22777--22846 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
22767 CCTTACAAAC
* *
22777 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACATT
*
22809 TCCCTAGCTTTTACACGGGCTAAGCTAGAACATT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACATT
22843 TCCC
1 TCCC
22847 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.30, G:0.16, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACATT
Found at i:23124 original size:21 final size:21
Alignment explanation
Indices: 23098--23139 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
23088 CCAGAATGGG
*
23098 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
23119 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
23140 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:23370 original size:29 final size:30
Alignment explanation
Indices: 23338--23396 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
23328 AAATTTTGAA
23338 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAGTCCAAA-ACCATTTTG
23367 TAAATTCAATTCAAGTCCAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAACCATTTTG
23397 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 12 0.43
30 16 0.57
ACGTcount: A:0.41, C:0.17, G:0.07, T:0.36
Consensus pattern (30 bp):
TAAATTCAATTCAAGTCCAAAACCATTTTG
Found at i:23681 original size:83 final size:83
Alignment explanation
Indices: 23504--23766 Score: 321
Period size: 83 Copynumber: 3.2 Consensus size: 83
23494 GTAATGGAAC
* ** * * *
23504 AAGCACCTTTCATTTCAGATATGATGAAATACTATGACATGACAAAGATTCT-TTAATAATAATG
1 AAGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
* *
23568 GAAAATGCTTCCCTTGGA
66 GAAAACGCTTCCCCTGGA
* * * * *
23586 AAGCTCTTTTCATTTTGGATGGGATGAAACATTATGAAATGACAGAGATTCTCTGAATAATAATG
1 AAGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
23651 GAAAACGCTTCCCCTGGA
66 GAAAACGCTTCCCCTGGA
* * * **
23669 ATGCACCTTTCATTTCGGATGGGGTGGAACACTATGACATGGTAGAGATTCTCTGAATAATAATG
1 AAGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
* *
23734 GAAAACACTTCTCCTGGA
66 GAAAACGCTTCCCCTGGA
* *
23752 ACGCTCCTTTCATTT
1 AAGCACCTTTCATTT
23767 TTAGATGGGT
Statistics
Matches: 153, Mismatches: 27, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
82 42 0.27
83 111 0.73
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Consensus pattern (83 bp):
AAGCACCTTTCATTTCGGATGGGATGAAACACTATGACATGACAGAGATTCTCTGAATAATAATG
GAAAACGCTTCCCCTGGA
Found at i:23888 original size:138 final size:138
Alignment explanation
Indices: 23639--23890 Score: 335
Period size: 138 Copynumber: 1.8 Consensus size: 138
23629 AGAGATTCTC
* * *
23639 TGAATAATAATGGAAAACGCTTCCCCTGGAATGCACCTTTCATTTCGGATGGGGTGGAACACTAT
1 TGAATAATAATGGAAAACGCTTCCCCTGGAACGCACCTTTCATTTCGGATGGGATGAAACACTAT
** * * *
23704 GACATGGTAGAGATTCTCTGAATAATAATGGAAAACACTTCTCCTGGAACGCTCCTTTCATTTTT
66 GACATGACAGAGATCCTCTCAATAATAATGGAAAACACTTCCCCTGGAACGCTCCTTTCATTTTT
23769 AGATGGGT
131 AGATGGGT
* * *
23777 TGAATAATAATGGAAAACG-TTTCCCTTGAACCGTACCTTTCATTTCGGATGGGATGAAACACTA
1 TGAATAATAATGGAAAACGCTTCCCCTGGAA-CGCACCTTTCATTTCGGATGGGATGAAACACTA
* * * * **
23841 TGATATGACATATATCCTTTCAATAATAATGGAAAACGTTTCCCCTGGAA
65 TGACATGACAGAGATCCTCTCAATAATAATGGAAAACACTTCCCCTGGAA
23891 TGTGCATTTC
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
137 9 0.09
138 87 0.91
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (138 bp):
TGAATAATAATGGAAAACGCTTCCCCTGGAACGCACCTTTCATTTCGGATGGGATGAAACACTAT
GACATGACAGAGATCCTCTCAATAATAATGGAAAACACTTCCCCTGGAACGCTCCTTTCATTTTT
AGATGGGT
Found at i:23947 original size:221 final size:221
Alignment explanation
Indices: 23558--23959 Score: 585
Period size: 221 Copynumber: 1.8 Consensus size: 221
23548 AAGATTCTTT
* * * *
23558 AATAATAATGGAAAATGCTTCCCTTGGAAAGCTCTTTTCATTTTGGATGGGATGAAACATTATGA
1 AATAATAATGGAAAACGCTTCCCTTGGAAAGCTCCTTTCATTTCGGATGGGATGAAACACTATGA
* * *
23623 AATGACAGAGATTCTCTGAATAATAATGGAAAACGCTTCCCCTGGAATGCACCTTTCATTTCGGA
66 AATGACAGAGATCCTCTCAATAATAATGGAAAACGCTTCCCCTGGAATGCACATTTCATTTCGGA
* * *
23688 TGGGGTGGAACACTATGACATGGTAGAGATTCTCTGAATAATAATGGAAAACACTTCTCCTGGAA
131 TGGGATGGAACACTATGACATGGTAGAGATTATCTGAATAATAAAGGAAAACACTTCTCCTGGAA
23753 CGCTCCTTTCATTTTTAGATGGGTTG
196 CGCTCCTTTCATTTTTAGATGGGTTG
* *
23779 AATAATAATGGAAAACGTTTCCCTT-G-AACCGTACCTTTCATTTCGGATGGGATGAAACACTAT
1 AATAATAATGGAAAACGCTTCCCTTGGAAAGC-T-CCTTTCATTTCGGATGGGATGAAACACTAT
* * * * * **
23842 GATATGACATATATCCTTTCAATAATAATGGAAAACGTTTCCCCTGGAATGTGCATTTCATTTCG
64 GAAATGACAGAGATCCTCTCAATAATAATGGAAAACGCTTCCCCTGGAATGCACATTTCATTTCG
23907 GATGGGATGGAACACTATGACAT-GTAAGAGATTATCTGAATAATAAAGGAAAA
129 GATGGGATGGAACACTATGACATGGT-AGAGATTATCTGAATAATAAAGGAAAA
23960 TGTTTCCCTA
Statistics
Matches: 159, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
219 3 0.02
220 4 0.03
221 152 0.96
ACGTcount: A:0.33, C:0.16, G:0.20, T:0.31
Consensus pattern (221 bp):
AATAATAATGGAAAACGCTTCCCTTGGAAAGCTCCTTTCATTTCGGATGGGATGAAACACTATGA
AATGACAGAGATCCTCTCAATAATAATGGAAAACGCTTCCCCTGGAATGCACATTTCATTTCGGA
TGGGATGGAACACTATGACATGGTAGAGATTATCTGAATAATAAAGGAAAACACTTCTCCTGGAA
CGCTCCTTTCATTTTTAGATGGGTTG
Found at i:24009 original size:82 final size:80
Alignment explanation
Indices: 23777--24042 Score: 284
Period size: 83 Copynumber: 3.2 Consensus size: 80
23767 TTAGATGGGT
*
23777 TGAATAATAATGGAAAACGTTTCCCTTGAA-CCGTACCTTTCATTTCGGATGGGATGAAACACTA
1 TGAATAATAATGGAAAACGTTTCCCTT-AATGCGT--CTTTCATTTCGGATGGGATGAAACACTA
* * * * *
23841 TGATATGACATATATCCTT
63 TGACATGA-AGAGATTCTC
* * * *
23860 TCAATAATAATGGAAAACGTTTCCCCTGGAATGTG-CATTTCATTTCGGATGGGATGGAACACTA
1 TGAATAATAATGGAAAACGTTT-CCCT-TAATGCGTC-TTTCATTTCGGATGGGATGAAACACTA
*
23924 TGACATGTAAGAGATTATC
63 TGACATG-AAGAGATTCTC
* *
23943 TGAATAATAAAGGAAAATGTTTCCCTATAATGCGTCTTTCATTTCGGATGGGATGAAACACTATG
1 TGAATAATAATGGAAAACGTTTCCCT-TAATGCGTCTTTCATTTCGGATGGGATGAAACACTATG
*
24008 ACATGGCAGAGATTCTC
65 ACAT-GAAGAGATTCTC
* *
24025 TAAATAATAATAGAAAAC
1 TGAATAATAATGGAAAAC
24043 ACTATGATAT
Statistics
Matches: 152, Mismatches: 24, Indels: 15
0.80 0.13 0.08
Matches are distributed among these distances:
82 65 0.43
83 79 0.52
84 7 0.05
85 1 0.01
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (80 bp):
TGAATAATAATGGAAAACGTTTCCCTTAATGCGTCTTTCATTTCGGATGGGATGAAACACTATGA
CATGAAGAGATTCTC
Found at i:24954 original size:26 final size:27
Alignment explanation
Indices: 24918--24970 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 27
24908 ATGTGAACTA
*
24918 TAAAAAACAAACCA-TAAACATTACAT
1 TAAAAAACAAACCACTAAACATGACAT
* *
24944 TAAACAACAAACTACTAAACATGACAT
1 TAAAAAACAAACCACTAAACATGACAT
24971 GAAGCATACC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.58, C:0.21, G:0.02, T:0.19
Consensus pattern (27 bp):
TAAAAAACAAACCACTAAACATGACAT
Found at i:25058 original size:31 final size:32
Alignment explanation
Indices: 25018--25082 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 32
25008 TATTTAACAA
*
25018 ACCTTAAACAATAAATAAAA-CATACACATAC
1 ACCTAAAACAATAAATAAAAGCATACACATAC
*
25049 ACCTAAAACAGTAAATAAAAGCATACACATAC
1 ACCTAAAACAATAAATAAAAGCATACACATAC
25081 AC
1 AC
25083 ACACCTAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
31 18 0.58
32 13 0.42
ACGTcount: A:0.57, C:0.23, G:0.03, T:0.17
Consensus pattern (32 bp):
ACCTAAAACAATAAATAAAAGCATACACATAC
Found at i:25479 original size:18 final size:17
Alignment explanation
Indices: 25458--25491 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
25448 AAATAAGAGG
*
25458 AAAATACATAATAAATAC
1 AAAATAAATAA-AAATAC
25476 AAAATAAATAAAAATA
1 AAAATAAATAAAAATA
25492 TTGACATAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.21
Consensus pattern (17 bp):
AAAATAAATAAAAATAC
Found at i:25491 original size:10 final size:11
Alignment explanation
Indices: 25459--25491 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
25449 AATAAGAGGA
*
25459 AAATACATAAT
1 AAATACAAAAT
25470 AAATACAAAAT
1 AAATACAAAAT
25481 AAATA-AAAAT
1 AAATACAAAAT
25491 A
1 A
25492 TTGACATAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
10 6 0.29
11 15 0.71
ACGTcount: A:0.73, C:0.06, G:0.00, T:0.21
Consensus pattern (11 bp):
AAATACAAAAT
Found at i:25606 original size:21 final size:21
Alignment explanation
Indices: 25580--25652 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
25570 GTCGTCTTCC
*
25580 TCATCATCCTCCTCATCGTTA
1 TCATCATCCTCCTCATCGTCA
* * *
25601 TCATCATCGTCGTCGTCGTCA
1 TCATCATCCTCCTCATCGTCA
* *
25622 TCATCGTCCTCCTCCTCGTCA
1 TCATCATCCTCCTCATCGTCA
25643 TGTCATCATC
1 --TCATCATC
25653 ACTCTCAATA
Statistics
Matches: 41, Mismatches: 9, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
21 34 0.83
23 7 0.17
ACGTcount: A:0.15, C:0.38, G:0.11, T:0.36
Consensus pattern (21 bp):
TCATCATCCTCCTCATCGTCA
Found at i:25616 original size:18 final size:18
Alignment explanation
Indices: 25580--25629 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
25570 GTCGTCTTCC
* * *
25580 TCATCATCCTCCTCATCG
1 TCATCATCATCGTCGTCG
*
25598 TTATCATCATCGTCGTCG
1 TCATCATCATCGTCGTCG
*
25616 TCGTCATCATCGTC
1 TCATCATCATCGTC
25630 CTCCTCCTCG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.36, G:0.12, T:0.36
Consensus pattern (18 bp):
TCATCATCATCGTCGTCG
Found at i:26387 original size:16 final size:16
Alignment explanation
Indices: 26368--26400 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
26358 ACTATTCAAA
26368 TCGGTCTGATTTGAGC
1 TCGGTCTGATTTGAGC
*
26384 TCGGTTTGATTTGAGC
1 TCGGTCTGATTTGAGC
26400 T
1 T
26401 TCTTCAAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.15, G:0.30, T:0.42
Consensus pattern (16 bp):
TCGGTCTGATTTGAGC
Found at i:26790 original size:23 final size:23
Alignment explanation
Indices: 26763--26827 Score: 78
Period size: 23 Copynumber: 2.8 Consensus size: 23
26753 ACCAAAGTCT
26763 CTGAAAGACCACATAGAATTGA-C
1 CTGAAAGACCACATAGAATT-ATC
* * *
26786 GTGAAGGACTACATAGAATTATC
1 CTGAAAGACCACATAGAATTATC
*
26809 CCGAAAGACCACATAGAAT
1 CTGAAAGACCACATAGAAT
26828 CCCTCAACTC
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (23 bp):
CTGAAAGACCACATAGAATTATC
Found at i:28920 original size:26 final size:29
Alignment explanation
Indices: 28854--28925 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 29
28844 TTTTTTTATC
*
28854 AAAATTAAAATGAAATTCAAATTATATAAAT
1 AAAATTAAAATGAAA-T-AAATTAAATAAAT
*
28885 GAAATT-AAAT-AAA-AAATTAAATAAA-
1 AAAATTAAAATGAAATAAATTAAATAAAT
28910 AAAATTAAAATTGAAA
1 AAAATTAAAA-TGAAA
28926 AATGTACCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
25 5 0.14
26 14 0.40
27 1 0.03
28 3 0.09
29 3 0.09
30 4 0.11
31 5 0.14
ACGTcount: A:0.67, C:0.01, G:0.04, T:0.28
Consensus pattern (29 bp):
AAAATTAAAATGAAATAAATTAAATAAAT
Found at i:28928 original size:14 final size:13
Alignment explanation
Indices: 28872--28918 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
28862 AATGAAATTC
* *
28872 AAATTATATAAATG
1 AAATTAAATAAA-A
28886 AAATTAAAT-AAA
1 AAATTAAATAAAA
28898 AAATTAAATAAAA
1 AAATTAAATAAAA
28911 AAATTAAA
1 AAATTAAA
28919 ATTGAAAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
12 9 0.30
13 13 0.43
14 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (13 bp):
AAATTAAATAAAA
Found at i:29871 original size:14 final size:14
Alignment explanation
Indices: 29852--29903 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
29842 CAAAAATATT
*
29852 TAAATAAATTCAAA
1 TAAATAAATTAAAA
29866 TAAATAAATTAAAA
1 TAAATAAATTAAAA
* *
29880 T-AATAAAATAATA
1 TAAATAAATTAAAA
29893 TATAATAAATT
1 TA-AATAAATT
29904 TTATAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
13 11 0.34
14 14 0.44
15 7 0.22
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (14 bp):
TAAATAAATTAAAA
Found at i:29923 original size:17 final size:19
Alignment explanation
Indices: 29887--29922 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
29877 AAATAATAAA
29887 ATAATATATAATAAATTTT
1 ATAATATATAATAAATTTT
*
29906 ATAATAT-TCATAAATTT
1 ATAATATATAATAAATTT
29923 AAAAAAGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (19 bp):
ATAATATATAATAAATTTT
Found at i:33889 original size:14 final size:14
Alignment explanation
Indices: 33870--33897 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
33860 TAACAGACTT
33870 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
33884 GTCTGTTTTCTACA
1 GTCTGTTTTCTACA
33898 TTTTGCATAG
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:0.14, C:0.21, G:0.14, T:0.50
Consensus pattern (14 bp):
GTCTGTTTTCTACA
Found at i:38993 original size:18 final size:18
Alignment explanation
Indices: 38966--39005 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
38956 TACATCTAAA
*
38966 AAAATCAAAATAAGATCC
1 AAAATAAAAATAAGATCC
* *
38984 AAAATAAAAATTATATCC
1 AAAATAAAAATAAGATCC
39002 AAAA
1 AAAA
39006 AAATCAATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.65, C:0.12, G:0.03, T:0.20
Consensus pattern (18 bp):
AAAATAAAAATAAGATCC
Found at i:42305 original size:2 final size:2
Alignment explanation
Indices: 42300--42338 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
42290 TAAATTTTAC
42300 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
42339 CTATTTCATT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42434 original size:20 final size:20
Alignment explanation
Indices: 42409--42446 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
42399 TTTAATTCAT
*
42409 AAAATTATAATTTTTTAAAC
1 AAAATTATAATTTATTAAAC
42429 AAAATTATAATTTATTAA
1 AAAATTATAATTTATTAA
42447 TTCACAAATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTATAATTTATTAAAC
Found at i:42640 original size:13 final size:13
Alignment explanation
Indices: 42622--42647 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
42612 ATATATTTAT
42622 AATTTTAAAAATA
1 AATTTTAAAAATA
42635 AATTTTAAAAATA
1 AATTTTAAAAATA
42648 CGTTTATTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
AATTTTAAAAATA
Found at i:44941 original size:16 final size:15
Alignment explanation
Indices: 44914--44959 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 15
44904 TTACGTTGTC
44914 GTTTTATTAAGTTTT
1 GTTTTATTAAGTTTT
44929 -TTTTCACTTAAGTTATT
1 GTTTT-A-TTAAGTT-TT
44946 GTTTTATTAAGTTT
1 GTTTTATTAAGTTT
44960 AGGTCACTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
14 4 0.15
15 2 0.07
16 14 0.52
17 3 0.11
18 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.11, T:0.63
Consensus pattern (15 bp):
GTTTTATTAAGTTTT
Found at i:45503 original size:23 final size:24
Alignment explanation
Indices: 45472--45516 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
45462 CCTCCAATAA
45472 TAAGTATC-AGAAAAAATTAAATTG
1 TAAGTATCAAGAAAAAA-TAAATTG
45496 TAAG-ATCAAGAAAAAATAAAT
1 TAAGTATCAAGAAAAAATAAAT
45517 AAATTTGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.60, C:0.04, G:0.11, T:0.24
Consensus pattern (24 bp):
TAAGTATCAAGAAAAAATAAATTG
Found at i:45770 original size:43 final size:41
Alignment explanation
Indices: 45715--45994 Score: 211
Period size: 43 Copynumber: 6.7 Consensus size: 41
45705 GAGCTTAAAC
* *
45715 TATAAAAGTAAAAAGTATGATTGGAAAAATTAGGGACTTCAAT
1 TATAAAGGTAAAAAGTA-GATTGGAAAAATTAGGG-CCTCAAT
*
45758 TATGAAGGTAAAAAGTGAGATT---AAAATTAGGGCCTCAAT
1 TATAAAGGTAAAAAGT-AGATTGGAAAAATTAGGGCCTCAAT
* *
45797 T-TTAAGGT-AAAAGTTGAGATTGGAAAAATTAGGGCCTAAAT
1 TATAAAGGTAAAAAG-T-AGATTGGAAAAATTAGGGCCTCAAT
* * *
45838 TATATAAGTTAAAAATGT-GATTGAAAAAAATTAGGGGTCTCAAT
1 TATA-AAGGTAAAAA-GTAGATTG-GAAAAATTA-GGGCCTCAAT
45882 TAT-AAGGTAAAAAGTGAGATT-GAAAAATTTAGGAG-CTCAAT
1 TATAAAGGTAAAAAGT-AGATTGGAAAAA-TTAGG-GCCTCAAT
* * ** *
45923 TATAAATGTACAAAGTGAGATT-GAAAAACTTAGTATCATCAAT
1 TATAAAGGTAAAAAGT-AGATTGGAAAAA-TTAG-GGCCTCAAT
* *
45966 TATAAATGTACAAAGTAAGATTGGAAAAA
1 TATAAAGGTAAAAAGT-AGATTGGAAAAA
45995 AATGGGAGGC
Statistics
Matches: 199, Mismatches: 19, Indels: 37
0.78 0.07 0.15
Matches are distributed among these distances:
37 5 0.03
38 13 0.07
39 7 0.04
40 10 0.05
41 35 0.18
42 45 0.23
43 60 0.30
44 23 0.12
45 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (41 bp):
TATAAAGGTAAAAAGTAGATTGGAAAAATTAGGGCCTCAAT
Found at i:45864 original size:41 final size:42
Alignment explanation
Indices: 45722--45955 Score: 213
Period size: 42 Copynumber: 5.6 Consensus size: 42
45712 AACTATAAAA
* *
45722 GTAAAAAGT-ATGATTGGAAAAATTAGGGACTTCAATTAT-GAAG
1 GTAAAAAGTGA-GATT-GAAAAATTAGGG-CCTCAATTATATAAG
45765 GTAAAAAGTGAGATT--AAAATTAGGGCCTCAATT-T-TAAG
1 GTAAAAAGTGAGATTGAAAAATTAGGGCCTCAATTATATAAG
*
45803 GT-AAAAGTTGAGATTGGAAAAATTAGGGCCTAAATTATATAAG
1 GTAAAAAG-TGAGATT-GAAAAATTAGGGCCTCAATTATATAAG
* * *
45846 TTAAAAA-TGTGATTGAAAAAAATTAGGGGTCTCAA-T-TATAAG
1 GTAAAAAGTGAGATTG--AAAAATTA-GGGCCTCAATTATATAAG
*
45888 GTAAAAAGTGAGATTGAAAAATTTAGGAG-CTCAATTATA-AAT
1 GTAAAAAGTGAGATTGAAAAA-TTAGG-GCCTCAATTATATAAG
*
45930 GTACAAAGTGAGATTGAAAAACTTAG
1 GTAAAAAGTGAGATTGAAAAA-TTAG
45956 TATCATCAAT
Statistics
Matches: 163, Mismatches: 12, Indels: 33
0.78 0.06 0.16
Matches are distributed among these distances:
37 5 0.03
38 13 0.08
39 7 0.04
40 10 0.06
41 30 0.18
42 50 0.31
43 36 0.22
44 12 0.07
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (42 bp):
GTAAAAAGTGAGATTGAAAAATTAGGGCCTCAATTATATAAG
Found at i:45945 original size:85 final size:82
Alignment explanation
Indices: 45722--45994 Score: 231
Period size: 85 Copynumber: 3.3 Consensus size: 82
45712 AACTATAAAA
*
45722 GTAAAAAGT-ATGATTGGAAAAATTAGGGACTTCAATTATGAAGGTAAAAAGTGAGATT----AA
1 GTAAAAAGTGA-GATTGGAAAAATTAGGGAC-TCAATTAT-AAAGT-AAAAGTGAGATTGAAAAA
*
45782 AATTAGGGCCTCAATTTTAAG
62 AATTAGGGCCTCAATTATAAG
* * * *
45803 GT-AAAAGTTGAGATTGGAAAAATTAGGGCCTAAATTATATAAGTTAAAAATGTGATTGAAAAAA
1 GTAAAAAG-TGAGATTGGAAAAATTAGGGACTCAATTATA-AAG-TAAAAGTGAGATTGAAAAAA
*
45867 ATTAGGGGTCTCAATTATAAG
63 ATTA-GGGCCTCAATTATAAG
45888 GTAAAAAGTGAGATT-GAAAAATTTA-GGAGCTCAATTATAAATGTACAAAGTGAGATTG-AAAA
1 GTAAAAAGTGAGATTGGAAAAA-TTAGGGA-CTCAATTATAAA-GTA-AAAGTGAGATTGAAAAA
* ** * *
45950 ACTTAGTATCATCAATTATAAAT
62 AATTAG-GGCCTCAATTAT-AAG
* *
45973 GTACAAAGTAAGATTGGAAAAA
1 GTAAAAAGTGAGATTGGAAAAA
45995 AATGGGAGGC
Statistics
Matches: 156, Mismatches: 19, Indels: 29
0.76 0.09 0.14
Matches are distributed among these distances:
79 1 0.01
80 24 0.15
81 22 0.14
82 1 0.01
83 1 0.01
84 35 0.22
85 61 0.39
86 11 0.07
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (82 bp):
GTAAAAAGTGAGATTGGAAAAATTAGGGACTCAATTATAAAGTAAAAGTGAGATTGAAAAAAATT
AGGGCCTCAATTATAAG
Found at i:46491 original size:2 final size:2
Alignment explanation
Indices: 46484--46522 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
46474 ATTATGAAAC
46484 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
46523 ATTTAGCTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49616 original size:23 final size:24
Alignment explanation
Indices: 49580--49628 Score: 91
Period size: 23 Copynumber: 2.1 Consensus size: 24
49570 GGTATAAAAG
49580 AAAGATTTTTATTTTAGGGTTTCA
1 AAAGATTTTTATTTTAGGGTTTCA
49604 AAAGA-TTTTATTTTAGGGTTTCA
1 AAAGATTTTTATTTTAGGGTTTCA
49627 AA
1 AA
49629 TCCCTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.80
24 5 0.20
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (24 bp):
AAAGATTTTTATTTTAGGGTTTCA
Found at i:54718 original size:14 final size:13
Alignment explanation
Indices: 54678--54726 Score: 62
Period size: 13 Copynumber: 3.6 Consensus size: 13
54668 ATTAAAAATA
*
54678 ATTAAATACAAAT
1 ATTAAATACAAAC
54691 ATTAAATACAAAC
1 ATTAAATACAAAC
*
54704 ATTACAATTCAAAC
1 ATTA-AATACAAAC
54718 AATTAAATA
1 -ATTAAATA
54727 ATAACAACAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
13 16 0.52
14 11 0.35
15 4 0.13
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
ATTAAATACAAAC
Found at i:56214 original size:26 final size:26
Alignment explanation
Indices: 56185--56234 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
56175 ATATTAGTAA
56185 ATTAAATCATAATTAA-ATAATAAACT
1 ATTAAATCATAA-TAATATAATAAACT
* *
56211 ATTAAATGATTATAATATAATAAA
1 ATTAAATCATAATAATATAATAAA
56235 AAAATTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 3 0.14
26 18 0.86
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (26 bp):
ATTAAATCATAATAATATAATAAACT
Found at i:56935 original size:20 final size:20
Alignment explanation
Indices: 56907--56966 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
56897 TTTCTGTGAT
56907 GTATGTATAGTAATCATCAA
1 GTATGTATAGTAATCATCAA
* *
56927 GTATTTATAGTAATAATCAA
1 GTATGTATAGTAATCATCAA
*
56947 GTATGTATGGTAATCATCAA
1 GTATGTATAGTAATCATCAA
56967 CTGTCATTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (20 bp):
GTATGTATAGTAATCATCAA
Found at i:64396 original size:15 final size:15
Alignment explanation
Indices: 64372--64401 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
64362 TGTTTCTCCT
*
64372 CTTCATTCTCTTCCC
1 CTTCACTCTCTTCCC
64387 CTTCACTCTCTTCCC
1 CTTCACTCTCTTCCC
64402 ATGCAATCGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.07, C:0.50, G:0.00, T:0.43
Consensus pattern (15 bp):
CTTCACTCTCTTCCC
Found at i:65273 original size:15 final size:15
Alignment explanation
Indices: 65253--65341 Score: 57
Period size: 15 Copynumber: 6.3 Consensus size: 15
65243 GAGATATTGC
*
65253 AGAGTGACGGAGAAG
1 AGAGTGAAGGAGAAG
*
65268 AGAGTGAAGG-GGA-
1 AGAGTGAAGGAGAAG
*
65281 AGAG-GAAGAAGAAG
1 AGAGTGAAGGAGAAG
* *
65295 AGAGGGAAGG-GGA-
1 AGAGTGAAGGAGAAG
*
65308 AGAG-GAAGAAGAAG
1 AGAGTGAAGGAGAAG
*
65322 AGAGGGAAAGG-GAAG
1 AGAGTG-AAGGAGAAG
65337 AGAGT
1 AGAGT
65342 AAATTAATTA
Statistics
Matches: 57, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
12 8 0.14
13 12 0.21
14 12 0.21
15 22 0.39
16 3 0.05
ACGTcount: A:0.46, C:0.01, G:0.49, T:0.03
Consensus pattern (15 bp):
AGAGTGAAGGAGAAG
Found at i:65295 original size:27 final size:27
Alignment explanation
Indices: 65263--65338 Score: 134
Period size: 27 Copynumber: 2.8 Consensus size: 27
65253 AGAGTGACGG
*
65263 AGAAGAGAGTGAAGGGGAAGAGGAAGA
1 AGAAGAGAGGGAAGGGGAAGAGGAAGA
65290 AGAAGAGAGGGAAGGGGAAGAGGAAGA
1 AGAAGAGAGGGAAGGGGAAGAGGAAGA
*
65317 AGAAGAGAGGGAAAGGGAAGAG
1 AGAAGAGAGGGAAGGGGAAGAG
65339 AGTAAATTAA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.50, T:0.01
Consensus pattern (27 bp):
AGAAGAGAGGGAAGGGGAAGAGGAAGA
Found at i:65329 original size:21 final size:21
Alignment explanation
Indices: 65277--65316 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
65267 GAGAGTGAAG
65277 GGGAAGAGGAAGAAGAAGAGA
1 GGGAAGAGGAAGAAGAAGAGA
* *
65298 GGGAAGGGGAAGAGGAAGA
1 GGGAAGAGGAAGAAGAAGA
65317 AGAAGAGAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (21 bp):
GGGAAGAGGAAGAAGAAGAGA
Found at i:66662 original size:13 final size:13
Alignment explanation
Indices: 66644--66691 Score: 69
Period size: 13 Copynumber: 3.7 Consensus size: 13
66634 TGCGTCATAA
66644 ATTTATGACGCGC
1 ATTTATGACGCGC
**
66657 ATTTATGACAAGC
1 ATTTATGACGCGC
*
66670 ATTTATGACGCGT
1 ATTTATGACGCGC
66683 ATTTATGAC
1 ATTTATGAC
66692 TCTCATTGCG
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (13 bp):
ATTTATGACGCGC
Found at i:66862 original size:2 final size:2
Alignment explanation
Indices: 66855--66879 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
66845 TGTCGTAAAT
66855 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
66880 TGTAGATTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:71983 original size:19 final size:20
Alignment explanation
Indices: 71959--72005 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
71949 GATACACTTA
71959 TTAAATTATATAAT-T-TCAT
1 TTAAATTATATAATATAT-AT
*
71978 TTAAA-TATTTAATATATAT
1 TTAAATTATATAATATATAT
71997 TTAAATTAT
1 TTAAATTAT
72006 TATCATATTC
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 7 0.29
19 13 0.54
20 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TTAAATTATATAATATATAT
Found at i:79110 original size:17 final size:17
Alignment explanation
Indices: 79083--79124 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 17
79073 TTTTCTCTCT
79083 TTTTCTTTCGAA-TAGCTC
1 TTTT-TTTCGAACT-GCTC
*
79101 TTTTTTTCGAACTGCTG
1 TTTTTTTCGAACTGCTC
79118 TTTTTTT
1 TTTTTTT
79125 TCTTCTTTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.12, C:0.17, G:0.12, T:0.60
Consensus pattern (17 bp):
TTTTTTTCGAACTGCTC
Found at i:84636 original size:14 final size:14
Alignment explanation
Indices: 84617--84657 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
84607 TAATATGTTT
*
84617 GTTTATGTTCATTC
1 GTTTATGCTCATTC
84631 GTTTATGCTCATTC
1 GTTTATGCTCATTC
84645 GTTTATGCTCATT
1 GTTTATGCTCATT
84658 TATGTTCTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (14 bp):
GTTTATGCTCATTC
Found at i:87970 original size:27 final size:27
Alignment explanation
Indices: 87887--87972 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
87877 AATTCATAAT
*
87887 TTTTATATATATTAACTTA---AAATTA
1 TTTTAT-TATATTAACTTATTTAAAATA
* *
87912 TTTTTTTATATTAACTTATTTAATATA
1 TTTTATTATATTAACTTATTTAAAATA
87939 TTTTATTAT-TT-ACTTAATTTTAAAATA
1 TTTTATTATATTAACTT-A-TTTAAAATA
87966 TTTTATT
1 TTTTATT
87973 TTCATTTTCA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 12 0.24
25 9 0.18
26 3 0.06
27 27 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (27 bp):
TTTTATTATATTAACTTATTTAAAATA
Found at i:88169 original size:31 final size:31
Alignment explanation
Indices: 88127--88201 Score: 123
Period size: 31 Copynumber: 2.4 Consensus size: 31
88117 TAACCTGTGA
*
88127 TGATCACATCTTAATTAAATAAAAACAAAAG
1 TGATCATATCTTAATTAAATAAAAACAAAAG
*
88158 TGATCATATCTTAATTAAATAAAAACGAAAG
1 TGATCATATCTTAATTAAATAAAAACAAAAG
*
88189 TGACCATATCTTA
1 TGATCATATCTTA
88202 TATTTTTAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 41 1.00
ACGTcount: A:0.49, C:0.13, G:0.08, T:0.29
Consensus pattern (31 bp):
TGATCATATCTTAATTAAATAAAAACAAAAG
Found at i:95991 original size:51 final size:51
Alignment explanation
Indices: 95882--95978 Score: 158
Period size: 51 Copynumber: 1.9 Consensus size: 51
95872 AGGCAGGGGT
* *
95882 CGCGCCTTACCTTTAATTCTGACACAATTATGTAAGGCGCGGTGCAAGAAC
1 CGCGCCTTACCTTTAACTCTGACACAATTATGTAAGGCACGGTGCAAGAAC
* *
95933 CGCGCCTTAGCTTTAACTCTGATACAATTATGTAAGGCACGGTGCA
1 CGCGCCTTACCTTTAACTCTGACACAATTATGTAAGGCACGGTGCA
95979 TGTACTGCGC
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
51 42 1.00
ACGTcount: A:0.27, C:0.25, G:0.22, T:0.27
Consensus pattern (51 bp):
CGCGCCTTACCTTTAACTCTGACACAATTATGTAAGGCACGGTGCAAGAAC
Found at i:96186 original size:16 final size:16
Alignment explanation
Indices: 96155--96195 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
96145 TGTAATTTTG
96155 TTATAATT-TT-TTTA
1 TTATAATTATTGTTTA
*
96169 TTATACTTATTGTTTA
1 TTATAATTATTGTTTA
96185 TTATAATTATT
1 TTATAATTATT
96196 TGAAAAAGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
14 7 0.30
15 2 0.09
16 14 0.61
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.66
Consensus pattern (16 bp):
TTATAATTATTGTTTA
Found at i:99329 original size:23 final size:23
Alignment explanation
Indices: 99295--99381 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
99285 ACATATTATA
99295 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTCTACG
* * *
99318 TGGCACTTCGGTGTATTTCTACG
1 TGGCACTACGGTGCAATTCTACG
* *
99341 CGGTC-CTTCGG-GACAAAATTCTACG
1 TGG-CACTACGGTG-C--AATTCTACG
99366 TGGCACTACGGTGCAA
1 TGGCACTACGGTGCAA
99382 ATTTATATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
22 1 0.02
23 30 0.60
24 2 0.04
25 16 0.32
26 1 0.02
ACGTcount: A:0.21, C:0.25, G:0.26, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTCTACG
Found at i:102429 original size:35 final size:34
Alignment explanation
Indices: 102390--102477 Score: 92
Period size: 33 Copynumber: 2.6 Consensus size: 34
102380 AATGGTAATA
* *
102390 AACAAAATTAACCTAAAA-ATATTAACAAAAAGTCC
1 AACAAAATTAACC-AAAATAAATTAA-AAAAAATCC
* *
102425 AACAATATTAA-CAAAATAAATTAAAAAAAATCT
1 AACAAAATTAACCAAAATAAATTAAAAAAAATCC
*
102458 AACCAAATTAA-CAAAATAAA
1 AACAAAATTAACCAAAATAAA
102478 ATAAGTATTA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
33 29 0.63
34 7 0.15
35 10 0.22
ACGTcount: A:0.65, C:0.14, G:0.01, T:0.20
Consensus pattern (34 bp):
AACAAAATTAACCAAAATAAATTAAAAAAAATCC
Found at i:105363 original size:46 final size:46
Alignment explanation
Indices: 105311--105404 Score: 179
Period size: 46 Copynumber: 2.0 Consensus size: 46
105301 AAAAAAATCA
105311 AACCCGTCAACATATTTCAAGGTTTGATATAAAATTGGGTTGATTT
1 AACCCGTCAACATATTTCAAGGTTTGATATAAAATTGGGTTGATTT
*
105357 AACCCGTCGACATATTTCAAGGTTTGATATAAAATTGGGTTGATTT
1 AACCCGTCAACATATTTCAAGGTTTGATATAAAATTGGGTTGATTT
105403 AA
1 AA
105405 TTGACAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (46 bp):
AACCCGTCAACATATTTCAAGGTTTGATATAAAATTGGGTTGATTT
Found at i:117843 original size:21 final size:20
Alignment explanation
Indices: 117816--117914 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
117806 AATCAGTTTC
117816 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
117837 GAAAATCGCAATGCGATAATA
1 CAAAATCGCAACGCGAT-TTT
* **
117858 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
117878 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
117899 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
117915 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 16 0.26
21 45 0.74
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:117943 original size:20 final size:20
Alignment explanation
Indices: 117881--118110 Score: 205
Period size: 20 Copynumber: 11.5 Consensus size: 20
117871 CGATTTTCCA
* ** *
117881 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
117901 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
*
117921 AAATCGCAACTCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
117941 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
117961 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
* *
117981 AAATCGAAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
118001 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
118021 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
* * *
118041 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
* *
118061 AAATCGCAACG-ATAATCCAT
1 AAATCGCAACGCGT-ATCCGT
* * *
118081 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGTATCCGT
*
118101 AAATCACAAC
1 AAATCGCAAC
118111 ACTGAAATTT
Statistics
Matches: 170, Mismatches: 34, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
19 2 0.01
20 166 0.98
21 2 0.01
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:118832 original size:24 final size:24
Alignment explanation
Indices: 118793--118839 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
118783 AAATTTGGTC
118793 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
118817 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
118840 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:119031 original size:12 final size:12
Alignment explanation
Indices: 119014--119038 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
119004 ATATAATCCT
119014 GAAGAAGAAAAA
1 GAAGAAGAAAAA
119026 GAAGAAGAAAAA
1 GAAGAAGAAAAA
119038 G
1 G
119039 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:121387 original size:20 final size:19
Alignment explanation
Indices: 121364--121519 Score: 144
Period size: 19 Copynumber: 8.9 Consensus size: 19
121354 AAATCCCAAC
*
121364 ATGAAAATCGCAATGAGGAA
1 ATGAAAATCGCAATG-CGAA
121384 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
121399 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
121417 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
121436 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
121451 A-GATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
121469 ATGAAAATCGCAA--CG--
1 ATGAAAATCGCAATGCGAA
*
121484 A-GAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
* *
121502 ATTAAAATCGCATTGCGA
1 ATGAAAATCGCAATGCGA
121520 TTCTCCCGTT
Statistics
Matches: 112, Mismatches: 9, Indels: 31
0.74 0.06 0.20
Matches are distributed among these distances:
14 30 0.27
15 3 0.03
16 6 0.05
17 5 0.04
18 3 0.03
19 52 0.46
20 13 0.12
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:121426 original size:33 final size:33
Alignment explanation
Indices: 121322--121429 Score: 164
Period size: 33 Copynumber: 3.2 Consensus size: 33
121312 CGGAAATTAC
121322 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
* * *
121355 AATCCCAAC-ATGAAAATCGCAATGAGGAAATGAA
1 AATCGCAACGA-GAGAATCGCAATG-CGAAATGAA
121389 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCGCAATGCGAAATGAA
121422 AATCGCAA
1 AATCGCAA
121430 TGCGAAATGA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
32 1 0.02
33 36 0.55
34 28 0.42
35 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:121449 original size:52 final size:53
Alignment explanation
Indices: 121364--121481 Score: 211
Period size: 52 Copynumber: 2.2 Consensus size: 53
121354 AAATCCCAAC
*
121364 ATGAAAATCGCAATGAGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
121417 ATGAAAATCGCAATG-CGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
121469 ATGAAAATCGCAA
1 ATGAAAATCGCAA
121482 CGAGAGAATC
Statistics
Matches: 63, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
52 48 0.76
53 15 0.24
ACGTcount: A:0.47, C:0.16, G:0.22, T:0.14
Consensus pattern (53 bp):
ATGAAAATCGCAATGACGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:121459 original size:33 final size:33
Alignment explanation
Indices: 121422--121513 Score: 166
Period size: 33 Copynumber: 2.8 Consensus size: 33
121412 GCGAAATGAA
*
121422 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
121455 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
*
121488 AATCGCAATGCGAAATTAAAATCGCA
1 AATCGCAATGCGAAATGAAAATCGCA
121514 TTGCGATTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAG
Found at i:121498 original size:85 final size:86
Alignment explanation
Indices: 121336--121519 Score: 300
Period size: 85 Copynumber: 2.2 Consensus size: 86
121326 GCAACGAGAG
*
121336 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGAGGAAATGAAAATCGCAACGAG
1 AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGACGAAATGAAAATCGCAACGAG
121401 AGAATCGCAATGCGAAATGAA
66 AGAATCGCAATGCGAAATGAA
* *
121422 AATCGCAATGCGAAATGAAAATCGCAACGA-GATAATCGCAATG-CGAAATGAAAATCGCAACGA
1 AATCGCAATGCGAAATGAAAATCCCAAC-ATGAAAATCGCAATGACGAAATGAAAATCGCAACGA
*
121485 GAGAATCGCAATGCGAAATTAA
65 GAGAATCGCAATGCGAAATGAA
*
121507 AATCGCATTGCGA
1 AATCGCAATGCGA
121520 TTCTCCCGTT
Statistics
Matches: 92, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
85 52 0.57
86 39 0.42
87 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (86 bp):
AATCGCAATGCGAAATGAAAATCCCAACATGAAAATCGCAATGACGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAA
Found at i:121511 original size:52 final size:51
Alignment explanation
Indices: 121322--121519 Score: 144
Period size: 52 Copynumber: 3.9 Consensus size: 51
121312 CGGAAATTAC
*
121322 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGAGAATCGCAAT-CGAAATGAAAATCGCAATGCGAAATGAA
* * * *
121369 AATCGCAATGAG-GAAAT-GAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAG-AATCG-CAATCGAAATGA-A-AATCGCAATGCGAAATGAA
* * * * *
121422 AATCGCAATGCGA-AAT-GAAAATCGCAACGAGATAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAGAATCG-CAATCGAAATGA-A-AATCGCAATGCGAAATGAA
* *
121474 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGAGAATCGCAAT-CGAAATGAAAATCGCAATGCGA
121520 TTCTCCCGTT
Statistics
Matches: 124, Mismatches: 14, Indels: 21
0.78 0.09 0.13
Matches are distributed among these distances:
46 8 0.06
47 18 0.15
48 7 0.06
50 1 0.01
52 61 0.49
53 23 0.19
54 6 0.05
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (51 bp):
AATCGCAACGAGAGAATCGCAATCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:121622 original size:52 final size:53
Alignment explanation
Indices: 121509--121625 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
121499 GAAATTAAAA
121509 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
*
121562 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
121614 TCGCATTGCGAT
1 TCGCATTGCGAT
121626 AGTCATTTTT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 30 0.48
53 33 0.52
ACGTcount: A:0.14, C:0.25, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:121633 original size:19 final size:19
Alignment explanation
Indices: 121528--121625 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
121518 GATTCTCCCG
121528 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
121548 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
121567 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
121581 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
121600 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
121619 TTGCGAT
1 TTGCGAT
121626 AGTCATTTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:121751 original size:14 final size:14
Alignment explanation
Indices: 121732--121768 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
121722 CATCAATTAC
121732 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
121746 ACAAATCATCTTTT
1 ACAAATCAACTTTT
121760 ACAAATCAA
1 ACAAATCAA
121769 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:123733 original size:19 final size:19
Alignment explanation
Indices: 123691--123830 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
123681 TAGTTTACTT
* *
123691 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
123711 TCGCAACGCGAAATGATAA
1 TCGCAACGCGAAATGAAAA
* **
123730 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
123749 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
123768 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
123787 TCGCAA--CG--A-GAGAA
1 TCGCAACGCGAAATGAAAA
*
123801 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
123820 TCGCAATGCGA
1 TCGCAACGCGA
123831 TTTTGGTTTC
Statistics
Matches: 103, Mismatches: 12, Indels: 11
0.82 0.10 0.09
Matches are distributed among these distances:
14 10 0.10
15 1 0.01
16 2 0.02
17 2 0.02
18 1 0.01
19 75 0.73
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:123848 original size:19 final size:19
Alignment explanation
Indices: 123826--123954 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
123816 AAAATCGCAA
123826 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
123845 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
123859 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
123878 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
123892 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
123911 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
123930 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
123950 TGCGA
1 TGCGA
123955 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:123868 original size:33 final size:33
Alignment explanation
Indices: 123826--123917 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
123816 AAAATCGCAA
123826 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
123859 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
123892 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
123918 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:124118 original size:93 final size:93
Alignment explanation
Indices: 124002--124191 Score: 364
Period size: 93 Copynumber: 2.1 Consensus size: 93
123992 ATGGATTGCA
124002 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
124066 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
124094 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
124159 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
124187 TTACT
1 TTACT
124192 AAGCAATCTA
Statistics
Matches: 96, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
92 4 0.04
93 92 0.96
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:125889 original size:14 final size:14
Alignment explanation
Indices: 125870--125959 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
125860 TTGAAATGAA
125870 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
125884 AATCGCAACGCGAAATGAC
1 AATCGCAA--CG--A-GAG
125903 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
125917 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
125936 AATCGCAACGAGAG
1 AATCGCAACGAGAG
125950 AATCGCAACG
1 AATCGCAACG
125960 CGAAATGAAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:125907 original size:33 final size:33
Alignment explanation
Indices: 125862--125976 Score: 221
Period size: 33 Copynumber: 3.5 Consensus size: 33
125852 TCTTTTGGTT
125862 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
*
125895 GAAATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
125928 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
125961 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
125977 TGTGATTTTG
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:0.46, C:0.21, G:0.23, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:125908 original size:19 final size:19
Alignment explanation
Indices: 125884--125976 Score: 89
Period size: 19 Copynumber: 5.4 Consensus size: 19
125874 GCAACGAGAG
*
125884 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAA
*
125903 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
125917 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
125936 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
125950 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
125969 AATCGCAA
1 AATCGCAA
125977 TGTGATTTTG
Statistics
Matches: 60, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
14 20 0.33
15 2 0.03
16 4 0.07
17 4 0.07
18 2 0.03
19 28 0.47
ACGTcount: A:0.45, C:0.23, G:0.23, T:0.10
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:126012 original size:14 final size:14
Alignment explanation
Indices: 125993--126049 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
125983 TTTGGTTTCG
125993 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
126007 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
126026 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
126040 CGTTGCGATT
1 CGTTGCGATT
126050 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:126025 original size:33 final size:33
Alignment explanation
Indices: 125988--126057 Score: 140
Period size: 33 Copynumber: 2.1 Consensus size: 33
125978 GTGATTTTGG
125988 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
126021 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
126054 TTTC
1 TTTC
126058 TCTCGTTGCG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 37 1.00
ACGTcount: A:0.09, C:0.24, G:0.20, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
Found at i:126060 original size:21 final size:21
Alignment explanation
Indices: 126034--126109 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
126024 CGCGTTGCGA
126034 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
126055 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
126075 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
126096 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
126110 CTCTTCTGCA
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:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:126090 original size:41 final size:41
Alignment explanation
Indices: 126033--126110 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
126023 TCGCGTTGCG
*
126033 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
126074 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
126111 TCTTCTGCAA
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:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:126231 original size:33 final size:33
Alignment explanation
Indices: 126189--126259 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
126179 AATACTAACT
126189 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
* *
126222 TGAAAATCGCAACGAGAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
126255 TGAAA
1 TGAAA
126260 TCTAAGTGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
Found at i:126493 original size:22 final size:22
Alignment explanation
Indices: 126441--126495 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
126431 TGGTTGTGAG
**
126441 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
126463 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
126485 GGATTTCTTCG
1 GGATTTCTTCG
126496 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:126667 original size:20 final size:20
Alignment explanation
Indices: 126642--126794 Score: 200
Period size: 20 Copynumber: 7.7 Consensus size: 20
126632 CTTTAAATAT
126642 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
126662 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
126682 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
126702 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
126722 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
126742 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
126762 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
126782 CGCGTTGCGATTT
1 CGCGTTGCGATTT
126795 TGGAAAATCG
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
20 118 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.20, G:0.27, T:0.34
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:126811 original size:21 final size:21
Alignment explanation
Indices: 126781--126863 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
126771 ATTTTCATAT
*
126781 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
126802 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
126823 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
126844 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
126864 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:126854 original size:42 final size:43
Alignment explanation
Indices: 126761--126859 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
126751 ATTTATGTGT
* *
126761 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
126802 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
126844 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
126860 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:127888 original size:21 final size:21
Alignment explanation
Indices: 127840--127896 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
127830 ACGTATATTG
127840 ATTTTTTTAGTAATTTAATTAT
1 ATTTTTTTAGT-ATTTAATTAT
* **
127862 -TATTTTTAGTATTTTTTTAT
1 ATTTTTTTAGTATTTAATTAT
*
127882 ATTTTTTTAATATTT
1 ATTTTTTTAGTATTT
127897 GGATAATTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
20 8 0.28
21 21 0.72
ACGTcount: A:0.26, C:0.00, G:0.04, T:0.70
Consensus pattern (21 bp):
ATTTTTTTAGTATTTAATTAT
Found at i:131214 original size:18 final size:18
Alignment explanation
Indices: 131191--131225 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
131181 CCACTATGAA
*
131191 ATGTCCCGAATGACCACT
1 ATGTCCCGAAGGACCACT
131209 ATGTCCCGAAGGACCAC
1 ATGTCCCGAAGGACCAC
131226 GTAGAACCCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.29, C:0.34, G:0.20, T:0.17
Consensus pattern (18 bp):
ATGTCCCGAAGGACCACT
Found at i:133936 original size:12 final size:11
Alignment explanation
Indices: 133919--133978 Score: 54
Period size: 12 Copynumber: 5.5 Consensus size: 11
133909 GTTAGATAAG
133919 AAATAATAAAAA
1 AAATAA-AAAAA
133931 AAAT--AAAAA
1 AAATAAAAAAA
*
133940 AAATAAAAAATC
1 AAATAAAAAA-A
133952 AAATAAAAAAGA
1 AAATAAAAAA-A
*
133964 AAA-AAGAAAA
1 AAATAAAAAAA
133974 AAATA
1 AAATA
133979 TATTAAATAA
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
9 9 0.22
10 4 0.10
11 10 0.25
12 17 0.43
ACGTcount: A:0.83, C:0.02, G:0.03, T:0.12
Consensus pattern (11 bp):
AAATAAAAAAA
Found at i:133937 original size:9 final size:9
Alignment explanation
Indices: 133923--133949 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
133913 GATAAGAAAT
133923 AATAAAAAA
1 AATAAAAAA
133932 AATAAAAAA
1 AATAAAAAA
133941 AATAAAAAA
1 AATAAAAAA
133950 TCAAATAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AATAAAAAA
Found at i:133950 original size:28 final size:27
Alignment explanation
Indices: 133914--133978 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 27
133904 AAAATGTTAG
* *
133914 ATAAGAAATAATAAAAAAAATAAAAAAA
1 ATAAAAAATAA-AAAAAAAAGAAAAAAA
* *
133942 ATAAAAAATCAAATAAAAAAGAAAAAAG
1 ATAAAAAAT-AAAAAAAAAAGAAAAAAA
133970 A-AAAAAATA
1 ATAAAAAATA
133979 TATTAAATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 1 0.03
27 7 0.22
28 22 0.69
29 2 0.06
ACGTcount: A:0.82, C:0.02, G:0.05, T:0.12
Consensus pattern (27 bp):
ATAAAAAATAAAAAAAAAAGAAAAAAA
Found at i:134049 original size:5 final size:5
Alignment explanation
Indices: 134039--134099 Score: 61
Period size: 5 Copynumber: 11.4 Consensus size: 5
134029 TTTTAAAAGT
*
134039 AATAA AATAA AA-AT AATAA GAAGTAAA AATAA AATAA AATAAAA AATAA
1 AATAA AATAA AATAA AATAA -AA-T-AA AATAA AATAA AAT--AA AATAA
134088 AATAA AATAA AA
1 AATAA AATAA AA
134100 GCATACTAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
4 3 0.06
5 32 0.67
6 3 0.06
7 8 0.17
8 2 0.04
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (5 bp):
AATAA
Found at i:134070 original size:22 final size:22
Alignment explanation
Indices: 134039--134099 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
134029 TTTTAAAAGT
* *
134039 AATAAAATAAAA-ATAATAAGA
1 AATAAAATAAAATAAAATAAAA
*
134060 AGTAAAAATAAAATAAAATAAAA
1 AAT-AAAATAAAATAAAATAAAA
134083 AATAAAATAAAATAAAA
1 AATAAAATAAAATAAAA
134100 GCATACTAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.06
22 23 0.68
23 9 0.26
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (22 bp):
AATAAAATAAAATAAAATAAAA
Found at i:134083 original size:17 final size:16
Alignment explanation
Indices: 134039--134099 Score: 81
Period size: 17 Copynumber: 3.8 Consensus size: 16
134029 TTTTAAAAGT
134039 AATAAAATAAAAAT--
1 AATAAAATAAAAATAA
134053 AATAAGAAGTAAAAATAA
1 AATAA-AA-TAAAAATAA
134071 AATAAAATAAAAAATAA
1 AATAAAAT-AAAAATAA
134088 AATAAAATAAAA
1 AATAAAATAAAA
134100 GCATACTAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
14 5 0.12
15 2 0.05
16 12 0.29
17 18 0.43
18 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (16 bp):
AATAAAATAAAAATAA
Found at i:135376 original size:20 final size:20
Alignment explanation
Indices: 135348--135387 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
135338 TATTATATAT
* *
135348 TTTCTAAAACGTTTTCAAAA
1 TTTCAAAAACATTTTCAAAA
135368 TTTCAAAAACATTTTCAAAA
1 TTTCAAAAACATTTTCAAAA
135388 CTTATTTATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.38
Consensus pattern (20 bp):
TTTCAAAAACATTTTCAAAA
Found at i:135454 original size:42 final size:44
Alignment explanation
Indices: 135397--135480 Score: 120
Period size: 42 Copynumber: 2.0 Consensus size: 44
135387 ACTTATTTAT
*
135397 TATATATGTTTAAAAATGTTTT-AAAAATATATA-TATATATTA
1 TATATATGTTTAAAAATATTTTCAAAAATATATATTATATATTA
*
135439 TATATAT-TTTCAAAAATATTTTCAAAACTATATATTATATAT
1 TATATATGTTT-AAAAATATTTTCAAAAATATATATTATATAT
135481 GTTTTCAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
41 3 0.08
42 17 0.46
43 10 0.27
44 7 0.19
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (44 bp):
TATATATGTTTAAAAATATTTTCAAAAATATATATTATATATTA
Found at i:135476 original size:37 final size:37
Alignment explanation
Indices: 135368--135527 Score: 155
Period size: 37 Copynumber: 4.2 Consensus size: 37
135358 GTTTTCAAAA
*
135368 TTTCAAAAACATTTTCAAAACT-TAT-TTATTATATAT
1 TTTCAAAAATATTTTCAAAACTATATATTA-TATATAT
* * *
135404 GTTT-AAAAATGTTTTAAAAATATATATATATATTATATATAT
1 -TTTCAAAAATATTTT--CAA-A-A-CTATATATTATATATAT
*
135446 TTTCAAAAATATTTTCAAAACTATATATTATATATGT
1 TTTCAAAAATATTTTCAAAACTATATATTATATATAT
* ** *
135483 TTTCAAAAAAAAATTCAAAACTATATAATATATATAT
1 TTTCAAAAATATTTTCAAAACTATATATTATATATAT
135520 TTTCAAAA
1 TTTCAAAA
135528 CTATATAATA
Statistics
Matches: 102, Mismatches: 13, Indels: 16
0.78 0.10 0.12
Matches are distributed among these distances:
36 9 0.09
37 58 0.57
38 3 0.03
39 2 0.02
40 3 0.03
41 4 0.04
42 20 0.20
43 3 0.03
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (37 bp):
TTTCAAAAATATTTTCAAAACTATATATTATATATAT
Found at i:135508 original size:78 final size:74
Alignment explanation
Indices: 135368--135527 Score: 180
Period size: 78 Copynumber: 2.1 Consensus size: 74
135358 GTTTTCAAAA
* ****
135368 TTTCAAAAACATTTTCAAAACTTATTTATTATATATGTTTAAAAATGTTTTAAAAATATATATAT
1 TTTCAAAAACATTTTCAAAACTTATATATTATATATGTTTAAAAAAAAATT-AAAA-ATATATAT
135433 ATATTATATATAT
64 A-A-TATATATAT
* * *
135446 TTTCAAAAATATTTTCAAAAC-TATATATTATATATGTTTTCAAAAAAAAATTCAAAA-CTATAT
1 TTTCAAAAACATTTTCAAAACTTATATATTATATATG-TTT-AAAAAAAAATTAAAAATATATAT
135509 AATATATATAT
64 AATATATATAT
135520 TTTCAAAA
1 TTTCAAAA
135528 CTATATAATA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
74 17 0.24
75 1 0.01
76 6 0.08
77 15 0.21
78 26 0.36
79 7 0.10
ACGTcount: A:0.47, C:0.07, G:0.02, T:0.44
Consensus pattern (74 bp):
TTTCAAAAACATTTTCAAAACTTATATATTATATATGTTTAAAAAAAAATTAAAAATATATATAA
TATATATAT
Found at i:135528 original size:62 final size:60
Alignment explanation
Indices: 135454--135649 Score: 252
Period size: 62 Copynumber: 3.2 Consensus size: 60
135444 ATTTTCAAAA
135454 ATATTTTCAAAACTATATATTATATATGTTTTCAAAAAAAAATTCAAAACTATATAATATAT
1 ATATTTTCAAAACTATATATTATATAT-TTTTC-AAAAAAAATTCAAAACTATATAATATAT
* *
135516 ATATTTTCAAAACTATATAATATATATTTTTTC-AAAAAAATTCAAAAC-ATATAGTATAT
1 ATATTTTCAAAACTATATATTATATA-TTTTTCAAAAAAAATTCAAAACTATATAATATAT
* ****
135575 ATATTTTTCAAAATTATATACTATATATATTTTTCAAAATGTTTTCAAAACTATATAATATAT
1 ATA-TTTTCAAAACTATATA-T-TATATATTTTTCAAAAAAAATTCAAAACTATATAATATAT
*
135638 ATTTTTTCAAAA
1 ATATTTTCAAAA
135650 TGTTTTCAAA
Statistics
Matches: 118, Mismatches: 10, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
59 13 0.11
60 30 0.25
61 6 0.05
62 56 0.47
63 13 0.11
ACGTcount: A:0.47, C:0.08, G:0.02, T:0.43
Consensus pattern (60 bp):
ATATTTTCAAAACTATATATTATATATTTTTCAAAAAAAATTCAAAACTATATAATATAT
Found at i:135538 original size:23 final size:25
Alignment explanation
Indices: 135496--135552 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
135486 CAAAAAAAAA
135496 TTCAAAACTATATAATATATATATT
1 TTCAAAACTATATAATATATATATT
*
135521 TTCAAAACTATATAATATATATTTT
1 TTCAAAACTATATAATATATATATT
135546 TTCAAAA
1 TTCAAAA
135553 AAATTCAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (25 bp):
TTCAAAACTATATAATATATATATT
Found at i:135568 original size:34 final size:36
Alignment explanation
Indices: 135521--135649 Score: 113
Period size: 26 Copynumber: 3.9 Consensus size: 36
135511 TATATATATT
135521 TTCAAAACTATATAATATATAT-TTTTTCAAAAAAA
1 TTCAAAACTATATAATATATATATTTTTCAAAAAAA
*
135556 TTCAAAAC-ATATAGTATATATATTTTTC---AAAA
1 TTCAAAACTATATAATATATATATTTTTCAAAAAAA
* ***
135588 -T------TATATACTATATATATTTTTCAAAATGTT
1 TTCAAAACTATATAATATATATATTTTTCAAAA-AAA
135618 TTCAAAACTATATAATATATAT-TTTTTCAAAA
1 TTCAAAACTATATAATATATATATTTTTCAAAA
135650 TGTTTTCAAA
Statistics
Matches: 75, Mismatches: 6, Indels: 25
0.71 0.06 0.24
Matches are distributed among these distances:
26 19 0.25
29 1 0.01
31 2 0.03
32 4 0.05
34 12 0.16
35 14 0.19
36 10 0.13
37 13 0.17
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (36 bp):
TTCAAAACTATATAATATATATATTTTTCAAAAAAA
Found at i:135582 original size:36 final size:34
Alignment explanation
Indices: 135521--135649 Score: 107
Period size: 35 Copynumber: 3.9 Consensus size: 34
135511 TATATATATT
135521 TTCAAAACTATATAATATATATTTTTTCAAAAAAA
1 TTCAAAACTATATAATATATA-TTTTTCAAAAAAA
135556 TTCAAAAC-ATATAGTATATATATTTTTC---AAAA
1 TTCAAAACTATATA--ATATATATTTTTCAAAAAAA
***
135588 TT----A-TATACT-ATATATATTTTTCAAAATGTT
1 TTCAAAACTATA-TAATATATATTTTTCAAAA-AAA
135618 TTCAAAACTATATAATATATATTTTTTCAAAA
1 TTCAAAACTATATAATATATA-TTTTTCAAAA
135650 TGTTTTCAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 29
0.70 0.03 0.27
Matches are distributed among these distances:
26 13 0.17
28 4 0.05
29 2 0.03
30 2 0.03
32 6 0.08
34 7 0.09
35 25 0.33
36 17 0.22
ACGTcount: A:0.46, C:0.09, G:0.02, T:0.44
Consensus pattern (34 bp):
TTCAAAACTATATAATATATATTTTTCAAAAAAA
Found at i:135651 original size:36 final size:37
Alignment explanation
Indices: 135579--135660 Score: 139
Period size: 37 Copynumber: 2.2 Consensus size: 37
135569 GTATATATAT
* *
135579 TTTTCAAAATTATATACTATATATATTTTTCAAAATG
1 TTTTCAAAACTATATAATATATATATTTTTCAAAATG
135616 TTTTCAAAACTATATAATATATAT-TTTTTCAAAATG
1 TTTTCAAAACTATATAATATATATATTTTTCAAAATG
135652 TTTTCAAAA
1 TTTTCAAAA
135661 TGTTTTCAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
36 21 0.49
37 22 0.51
ACGTcount: A:0.41, C:0.09, G:0.02, T:0.48
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATATATTTTTCAAAATG
Found at i:135657 original size:11 final size:11
Alignment explanation
Indices: 135641--135671 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
135631 AATATATATT
135641 TTTTCAAAATG
1 TTTTCAAAATG
135652 TTTTCAAAATG
1 TTTTCAAAATG
135663 TTTTCAAAA
1 TTTTCAAAA
135672 CTATATAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.06, T:0.45
Consensus pattern (11 bp):
TTTTCAAAATG
Found at i:135658 original size:47 final size:47
Alignment explanation
Indices: 135605--135696 Score: 175
Period size: 47 Copynumber: 2.0 Consensus size: 47
135595 CTATATATAT
*
135605 TTTTCAAAATGTTTTCAAAACTATATAATATATATTTTTTCAAAATG
1 TTTTCAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAATG
135652 TTTTCAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAA
1 TTTTCAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAA
135697 ATTATATATT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 44 1.00
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (47 bp):
TTTTCAAAATGTTTTCAAAACTATATAATATATATATTTTCAAAATG
Found at i:137142 original size:59 final size:60
Alignment explanation
Indices: 137073--137201 Score: 172
Period size: 60 Copynumber: 2.1 Consensus size: 60
137063 ATCGGGTGAC
*
137073 CATTTTGTAACTTTTAATA-ACAATGGACTCAATAAAGCAATACTCTATAGTCGAA-GGAT
1 CATTTTGTAACTTTTAATAGACAATGAACTCAATAAAGCAATACTCTATAGT-GAATGGAT
*** * *
137132 CATTTTGTAACTTTTAATAGTTGATGAACTTAATAAAGCAATACTCTATAGTGAATGGTT
1 CATTTTGTAACTTTTAATAGACAATGAACTCAATAAAGCAATACTCTATAGTGAATGGAT
137192 CATTTGTGTA
1 CATTT-TGTA
137202 CTTAACTCAT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 22 0.36
60 35 0.57
61 4 0.07
ACGTcount: A:0.36, C:0.12, G:0.15, T:0.37
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAGACAATGAACTCAATAAAGCAATACTCTATAGTGAATGGAT
Found at i:137559 original size:36 final size:36
Alignment explanation
Indices: 137379--137682 Score: 251
Period size: 38 Copynumber: 8.1 Consensus size: 36
137369 TGCAAATGGT
*
137379 TTTTGAAAATATATATAATATATAGTTTTGAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTGAAAACA
*
137415 TGTTTGAAAACATTTATATATTATATAGTTTTTTTTGAAAACA
1 T-TTTGAAAACA--TATATAATATATAG----TTTTGAAAACA
* * *
137458 TTTTGAAAATACGTATATAATATATAATTTTGAAAATA
1 TTTTG-AAA-ACATATATAATATATAGTTTTGAAAACA
* * * *
137496 TTTTGAAAACGTTTAAATATTATATAGTTTTTAAAACA
1 TTTTGAAAAC--ATATATAATATATAGTTTTGAAAACA
* *
137534 TTTTGAAAACATATATATTATATAGTTTTAAAAACA
1 TTTTGAAAACATATATAATATATAGTTTTGAAAACA
* *
137570 TTTTTTGTAAAA-TTATATAATATATAGTTTTAAAAACA
1 --TTTTG-AAAACATATATAATATATAGTTTTGAAAACA
*
137608 TTTTTTTTGAAAACTTATATAATAT-T--TTTT-AAAACA
1 ----TTTTGAAAACATATATAATATATAGTTTTGAAAACA
* * *
137644 TTTTGGAAAC-TATGTAATATATAGTTTTGAAAACT
1 TTTTGAAAACATATATAATATATAGTTTTGAAAACA
137679 TTTT
1 TTTT
137683 TAAAGTATAT
Statistics
Matches: 227, Mismatches: 20, Indels: 43
0.78 0.07 0.15
Matches are distributed among these distances:
31 9 0.04
32 10 0.04
34 4 0.02
35 9 0.04
36 32 0.14
37 16 0.07
38 74 0.33
39 22 0.10
40 18 0.08
42 16 0.07
43 15 0.07
44 2 0.01
ACGTcount: A:0.42, C:0.04, G:0.08, T:0.46
Consensus pattern (36 bp):
TTTTGAAAACATATATAATATATAGTTTTGAAAACA
Found at i:139091 original size:12 final size:11
Alignment explanation
Indices: 139067--139159 Score: 57
Period size: 11 Copynumber: 8.5 Consensus size: 11
139057 ACTTTACTAC
139067 ATTTTTTTATT
1 ATTTTTTTATT
*
139078 ATTTTTATTCTT
1 ATTTTT-TTATT
* *
139090 ATTTATTT-GT
1 ATTTTTTTATT
* *
139100 -TTTTTTAACT
1 ATTTTTTTATT
* *
139110 AATCTTTTATT
1 ATTTTTTTATT
139121 ATTGTTTTTTATT
1 A-T-TTTTTTATT
*
139134 ATTTTATT-TT
1 ATTTTTTTATT
*
139144 ATTATTTTATT
1 ATTTTTTTATT
139155 ATTTT
1 ATTTT
139160 CTTTTTCCTT
Statistics
Matches: 60, Mismatches: 16, Indels: 12
0.68 0.18 0.14
Matches are distributed among these distances:
9 5 0.08
10 10 0.17
11 26 0.43
12 10 0.17
13 9 0.15
ACGTcount: A:0.20, C:0.03, G:0.02, T:0.74
Consensus pattern (11 bp):
ATTTTTTTATT
Found at i:139130 original size:13 final size:13
Alignment explanation
Indices: 139114--139154 Score: 66
Period size: 13 Copynumber: 3.2 Consensus size: 13
139104 TTAACTAATC
139114 TTTTATTATTGTT-
1 TTTTATTATT-TTA
139127 TTTTATTATTTTA
1 TTTTATTATTTTA
139140 TTTTATTATTTTA
1 TTTTATTATTTTA
139153 TT
1 TT
139155 ATTTTCTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
12 2 0.07
13 25 0.93
ACGTcount: A:0.20, C:0.00, G:0.02, T:0.78
Consensus pattern (13 bp):
TTTTATTATTTTA
Done.