Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007713.1 Hibiscus syriacus cultivar Beakdansim tig00109937_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: 584604
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:1634 original size:12 final size:12
Alignment explanation
Indices: 1617--1641 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1607 TCTTCGGGGA
1617 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1629 CTTTTTCTTCTT
1 CTTTTTCTTCTT
1641 C
1 C
1642 AGGATTATAT
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:3134 original size:14 final size:14
Alignment explanation
Indices: 3115--3151 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3105 CATCAATTAA
3115 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
3129 ACAAATCATCTTTT
1 ACAAATCAACATTT
3143 ACAAATCAA
1 ACAAATCAA
3152 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:3540 original size:20 final size:20
Alignment explanation
Indices: 3515--3570 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
3505 TTCATTTGAC
*
3515 TATCGCAATGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
3535 TATCGCAACGCGAAAATGGT
1 TATCGCAACGCGAAAATGGT
*
3555 TATCGCAACGAGAAAA
1 TATCGCAACGCGAAAA
3571 ATCGCAATGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.39, C:0.18, G:0.23, T:0.20
Consensus pattern (20 bp):
TATCGCAACGCGAAAATGGT
Found at i:3615 original size:14 final size:16
Alignment explanation
Indices: 3595--3668 Score: 66
Period size: 19 Copynumber: 4.5 Consensus size: 16
3585 TGAAAATCGC
3595 ATTGCGATTTTC-TCG
1 ATTGCGATTTTCTTCG
3610 -TTGCGATTTTCATTTCG
1 ATTGCGATTTTC--TTCG
3627 CATTGCGATTTTCATTTCG
1 -ATTGCGATTTTC--TTCG
3646 CATTGCGATTTTC-TCG
1 -ATTGCGATTTTCTTCG
3662 -TTGCGAT
1 ATTGCGAT
3669 AGCCATTTCG
Statistics
Matches: 54, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
14 18 0.33
16 3 0.06
17 3 0.06
19 30 0.56
ACGTcount: A:0.14, C:0.20, G:0.19, T:0.47
Consensus pattern (16 bp):
ATTGCGATTTTCTTCG
Found at i:3632 original size:19 final size:19
Alignment explanation
Indices: 3591--3658 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
3581 GAAATGAAAA
3591 TCGCATTGCGATTTTC---
1 TCGCATTGCGATTTTCATT
3607 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3624 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
3643 TCGCATTGCGATTTTC
1 TCGCATTGCGATTTTC
3659 TCGTTGCGAT
Statistics
Matches: 47, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
14 11 0.23
16 3 0.06
17 3 0.06
19 30 0.64
ACGTcount: A:0.13, C:0.22, G:0.18, T:0.47
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:5697 original size:19 final size:19
Alignment explanation
Indices: 5672--5789 Score: 124
Period size: 19 Copynumber: 6.5 Consensus size: 19
5662 CGAAACTTAA
5672 AATCGCAACGCGAAATGAC
1 AATCGCAACGCGAAATGAC
* *
5691 TATCGCAACGCGGAAATGGC
1 AATCGCAACGC-GAAATGAC
* * *
5711 TATCGCAATGCGAAATGAA
1 AATCGCAACGCGAAATGAC
5730 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
*
5748 AATCGCAA--CGACA--A-
1 AATCGCAACGCGAAATGAC
5762 AATCGCAACGCGAAATGA-
1 AATCGCAACGCGAAATGAC
5780 AATCGCAACG
1 AATCGCAACG
5790 ACAAAATCGC
Statistics
Matches: 85, Mismatches: 9, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
14 9 0.11
16 8 0.09
18 19 0.22
19 32 0.38
20 17 0.20
ACGTcount: A:0.42, C:0.24, G:0.22, T:0.13
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAC
Found at i:5716 original size:39 final size:38
Alignment explanation
Indices: 5673--5746 Score: 112
Period size: 39 Copynumber: 1.9 Consensus size: 38
5663 GAAACTTAAA
**
5673 ATCGCAACGCGAAATGACTATCGCAACGCGGAAATGGCT
1 ATCGCAACGCGAAATGAAAATCGCAACGC-GAAATGGCT
*
5712 ATCGCAATGCGAAATGAAAATCGCAACGCGAAATG
1 ATCGCAACGCGAAATGAAAATCGCAACGCGAAATG
5747 AAATCGCAAC
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
38 6 0.19
39 26 0.81
ACGTcount: A:0.38, C:0.23, G:0.24, T:0.15
Consensus pattern (38 bp):
ATCGCAACGCGAAATGAAAATCGCAACGCGAAATGGCT
Found at i:5766 original size:14 final size:14
Alignment explanation
Indices: 5747--5803 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
5737 ACGCGAAATG
5747 AAATCGCAACGACA
1 AAATCGCAACGACA
*
5761 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
5777 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
5793 AAATCGCAACG
1 AAATCGCAACG
5804 CGAAACACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.47, C:0.26, G:0.18, T:0.09
Consensus pattern (14 bp):
AAATCGCAACGACA
Found at i:5769 original size:32 final size:32
Alignment explanation
Indices: 5728--5808 Score: 162
Period size: 32 Copynumber: 2.5 Consensus size: 32
5718 ATGCGAAATG
5728 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
5760 AAAATCGCAACGCGAAATGAAATCGCAACGAC
1 AAAATCGCAACGCGAAATGAAATCGCAACGAC
5792 AAAATCGCAACGCGAAA
1 AAAATCGCAACGCGAAA
5809 CACAAATCGC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 49 1.00
ACGTcount: A:0.48, C:0.25, G:0.19, T:0.09
Consensus pattern (32 bp):
AAAATCGCAACGCGAAATGAAATCGCAACGAC
Found at i:5837 original size:19 final size:17
Alignment explanation
Indices: 5815--5910 Score: 78
Period size: 19 Copynumber: 5.6 Consensus size: 17
5805 GAAACACAAA
5815 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
*
5834 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
5850 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
*
5866 TCGCGTTGCGATTT--TG
1 TCGC-TTGCGATTTCATT
5882 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
5899 TCGCATTGCGAT
1 TCGC-TTGCGAT
5911 AGCCATTTCC
Statistics
Matches: 63, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
14 15 0.24
15 3 0.05
16 12 0.19
17 4 0.06
18 13 0.21
19 16 0.25
ACGTcount: A:0.11, C:0.20, G:0.23, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:5856 original size:14 final size:14
Alignment explanation
Indices: 5837--5894 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
5827 TTTCATTTCG
5837 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
5851 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
5867 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
5883 CGTTGCGATTTT
1 CGTTGCGATTTT
5895 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:5901 original size:33 final size:33
Alignment explanation
Indices: 5820--5910 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
5810 ACAAATCGCA
5820 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
5853 TTGCGA-TTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
*
5885 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCGTTGCGAT
5911 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 32 0.57
33 24 0.43
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
Found at i:5929 original size:20 final size:19
Alignment explanation
Indices: 5895--5949 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
5885 TTGCGATTTT
*
5895 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
5914 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
*
5934 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
5950 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
19 5 0.16
20 23 0.74
21 3 0.10
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:6446 original size:18 final size:18
Alignment explanation
Indices: 6420--6464 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
6410 GTCAATCAGA
*
6420 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
*
6438 TGATAGCTCTAGGCGAGG
1 TGATGGCTCTAGGCGAGG
6456 TGATGGCTC
1 TGATGGCTC
6465 CCGAAGTGGA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.18, C:0.16, G:0.40, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:7806 original size:20 final size:20
Alignment explanation
Indices: 7781--7818 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7771 AATAGTTTCT
7781 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
**
7801 GAAAATGACTATCGCAAC
1 GAAAATGAAAATCGCAAC
7819 GAGAGAATCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.21, G:0.16, T:0.13
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:8332 original size:20 final size:20
Alignment explanation
Indices: 8307--8400 Score: 89
Period size: 20 Copynumber: 4.7 Consensus size: 20
8297 GATTATGTAT
8307 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
8327 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* *** * *
8347 TATCTCGTTGCGATTTTTTAT
1 TATCGCGTTGCGA-AAGTCAG
* *
8368 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
8388 TATCGCATTGCGA
1 TATCGCGTTGCGA
8401 TTTTCTCAAT
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.78
21 13 0.22
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:8372 original size:41 final size:42
Alignment explanation
Indices: 8327--8462 Score: 118
Period size: 41 Copynumber: 3.3 Consensus size: 42
8317 CGAAAGTCAG
* * * *
8327 TATCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTT-TTAT
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
* * *
8368 TATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCTCAA
1 TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
** ** * *
8410 T-TCGCGTTGCG-ATTTACTTATTCGCATTGCGAATTTCCCAA
1 TATCGCGTTGCGAAAGTAAGTA-TCGCATTGCGATTTTCTCAA
8451 T-TCGCGTTGCGA
1 TATCGCGTTGCGA
8463 TTTACTTATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 3 0.04
41 70 0.92
42 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.38
Consensus pattern (42 bp):
TATCGCGTTGCGAAAGTAAGTATCGCATTGCGATTTTCTCAA
Found at i:8401 original size:20 final size:20
Alignment explanation
Indices: 8287--8401 Score: 88
Period size: 20 Copynumber: 5.7 Consensus size: 20
8277 CGCTTTGAAA
*
8287 ATCGCATTGCGATTATGT-ATT
1 ATCGCATTGCGA-TA-GTCAGT
* *
8308 ATCGCGTTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * *
8328 ATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
8348 ATCTCGTTGCGATTTTTTATT
1 ATCGCATTGCGA-TAGTCAGT
8369 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
8389 ATCGCATTGCGAT
1 ATCGCATTGCGAT
8402 TTTCTCAATT
Statistics
Matches: 76, Mismatches: 16, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
19 2 0.03
20 50 0.66
21 24 0.32
ACGTcount: A:0.23, C:0.17, G:0.23, T:0.36
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:8434 original size:20 final size:20
Alignment explanation
Indices: 8390--8482 Score: 105
Period size: 21 Copynumber: 4.5 Consensus size: 20
8380 ATAGTCAGTA
*
8390 TCGCATTGCGATTTTCTCAAT
1 TCGCATTGCGATTTACT-AAT
* *
8411 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
* *
8431 TCGCATTGCGAATTTCCCAAT
1 TCGCATTGCG-ATTTACTAAT
* *
8452 TCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTACTAAT
8472 TCGCATTGCGA
1 TCGCATTGCGA
8483 ATTGGGAAAA
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
TCGCATTGCGATTTACTAAT
Found at i:8463 original size:41 final size:41
Alignment explanation
Indices: 8390--8485 Score: 174
Period size: 41 Copynumber: 2.3 Consensus size: 41
8380 ATAGTCAGTA
* *
8390 TCGCATTGCGATTTTCTCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
8431 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
8472 TCGCATTGCGAATT
1 TCGCATTGCGAATT
8486 GGGAAAATCG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.41
Consensus pattern (41 bp):
TCGCATTGCGAATTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:8902 original size:31 final size:36
Alignment explanation
Indices: 8835--8902 Score: 83
Period size: 35 Copynumber: 2.0 Consensus size: 36
8825 ATAAAGTTTC
* *
8835 ACCCGACCCGACCCGACCTGAATATATGAATTAAAA
1 ACCCGACCCGACCCGACCTCAATATATGAATAAAAA
8871 ACCCGA-CCGACCCGA-CTCAA-A-AT-AATAAAAA
1 ACCCGACCCGACCCGACCTCAATATATGAATAAAAA
8902 A
1 A
8903 TTATTTTTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
31 8 0.27
32 2 0.07
33 1 0.03
34 4 0.13
35 9 0.30
36 6 0.20
ACGTcount: A:0.44, C:0.31, G:0.12, T:0.13
Consensus pattern (36 bp):
ACCCGACCCGACCCGACCTCAATATATGAATAAAAA
Found at i:9194 original size:32 final size:33
Alignment explanation
Indices: 9135--9218 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
9125 ACCCGACCCG
* * *
9135 ACCCGACCTGACCTGAATATTACACTTAAAAAA
1 ACCCGACCTGACCCGAATATCAAACTTAAAAAA
*
9168 ACCCGACC-GACCCGAATATCAAACTTAAAATA
1 ACCCGACCTGACCCGAATATCAAACTTAAAAAA
*
9200 ACCCGATCTGAACCCGAAT
1 ACCCGACCTG-ACCCGAAT
9219 TTTTTTTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 3
0.85 0.10 0.06
Matches are distributed among these distances:
32 27 0.61
33 9 0.20
34 8 0.18
ACGTcount: A:0.40, C:0.31, G:0.11, T:0.18
Consensus pattern (33 bp):
ACCCGACCTGACCCGAATATCAAACTTAAAAAA
Found at i:20851 original size:27 final size:27
Alignment explanation
Indices: 20809--20903 Score: 158
Period size: 27 Copynumber: 3.6 Consensus size: 27
20799 CTATAGGAAT
20809 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
20834 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
**
20861 TATAGAGATATGATTTGTTACCATTTT
1 TATAGAGATATGATTTGTTACCATTCC
20888 TATAGAGATATGATTT
1 TATAGAGATATGATTT
20904 TGTAAATAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 7 0.11
27 59 0.89
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.43
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:24642 original size:27 final size:27
Alignment explanation
Indices: 24600--24694 Score: 167
Period size: 27 Copynumber: 3.6 Consensus size: 27
24590 GTGTAGGAAT
24600 TATAGAG--ATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
*
24625 TATAGAGATATGATTTGTTATCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
24652 TATAGAGATATGATTTGTTACCATTCC
1 TATAGAGATATGATTTGTTACCATTCC
24679 TATAGAGATATGATTT
1 TATAGAGATATGATTT
24695 TGTAAATAGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
25 7 0.11
27 59 0.89
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.42
Consensus pattern (27 bp):
TATAGAGATATGATTTGTTACCATTCC
Found at i:30590 original size:45 final size:45
Alignment explanation
Indices: 30450--30633 Score: 282
Period size: 45 Copynumber: 4.1 Consensus size: 45
30440 GTAGCCATGC
*
30450 AAATAAGCTTACGAGCTTATGGAAT-AATGGCAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
* *
30494 AAATAAGCTTACGAGCTTATGGGATTAAATGGTAAGTATTTTGGTA
1 AAATAAGCTTACGAGCTTAT-GGAATAAATGGTAAGTATATTGGTA
* * *
30540 AAATAAGCTTACAAGCTTATGGAACAAATGGTAAGTATATTGTTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
*
30585 GAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATA-TGGTA
1 AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
30629 AAATA
1 AAATA
30634 TTGGATATGC
Statistics
Matches: 125, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
44 28 0.22
45 61 0.49
46 36 0.29
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.31
Consensus pattern (45 bp):
AAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATTGGTA
Found at i:37206 original size:18 final size:18
Alignment explanation
Indices: 37183--37218 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
37173 AGGGATTTAC
37183 AGTGGTCCTTCAGGACAT
1 AGTGGTCCTTCAGGACAT
*
37201 AGTGGTCCTTCGGGACAT
1 AGTGGTCCTTCAGGACAT
37219 TTCATAGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.31, T:0.28
Consensus pattern (18 bp):
AGTGGTCCTTCAGGACAT
Found at i:37235 original size:23 final size:23
Alignment explanation
Indices: 37198--37319 Score: 172
Period size: 23 Copynumber: 5.2 Consensus size: 23
37188 TCCTTCAGGA
*
37198 CATAGTGGTCCTTCGGGACATTT
1 CATAGTGGTCATTCGGGACATTT
*
37221 CATAGTAGTCATTCGGGACATTT
1 CATAGTGGTCATTCGGGACATTT
*
37244 CATAGTGGTCATTCGGGATATTT
1 CATAGTGGTCATTCGGGACATTT
* * *
37267 CATAGTCGTCCTTTGGGACATTT
1 CATAGTGGTCATTCGGGACATTT
37290 CATAGTGGTCATTCGGGACAAATTT
1 CATAGTGGTCATTCGGGAC--ATTT
37315 CATAG
1 CATAG
37320 CCTCTAGTGG
Statistics
Matches: 86, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
23 77 0.90
25 9 0.10
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (23 bp):
CATAGTGGTCATTCGGGACATTT
Found at i:44977 original size:182 final size:181
Alignment explanation
Indices: 44745--45073 Score: 516
Period size: 182 Copynumber: 1.8 Consensus size: 181
44735 GATCCAAATT
* * * **
44745 AAAAATATGTCGATCCAAAACGATATAACAGGTAAAACTATGACAAAACCGGTATTGAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGATATCAAAATGATA
* *
44810 AAACCGG-AAAAGCGCTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACACTT
66 AAACCGGTAAAA-CGCTACCGGATACATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACTT
44874 CGTGAATTTAAAAGAGAAGCAATTTTAAATCCTATAAAGTGTTGATACTTTTA
129 CGTGAATTTAAAAGAGAAGCAATTTTAAATCCTATAAAGTGTTGATACTTTTA
* * *
44927 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGATATCAAAATGATA
1 AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGATATCAAAATGATA
* * *
44992 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTTG
66 AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
45057 TGAATTTAAAAGAGAAG
131 TGAATTTAAAAGAGAAG
45074 TAGTTTTAGC
Statistics
Matches: 133, Mismatches: 13, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
181 36 0.27
182 93 0.70
183 4 0.03
ACGTcount: A:0.43, C:0.14, G:0.17, T:0.26
Consensus pattern (181 bp):
AAAAATATATCGATCCAAAACGATATAACAGGTAAAAATATGACAAAACCGATATCAAAATGATA
AAACCGGTAAAACGCTACCGGATACATTGAAAGTGTCGATACTTTATATAAGGATCGACACTTCG
TGAATTTAAAAGAGAAGCAATTTTAAATCCTATAAAGTGTTGATACTTTTA
Found at i:47889 original size:21 final size:21
Alignment explanation
Indices: 47863--47925 Score: 94
Period size: 21 Copynumber: 3.1 Consensus size: 21
47853 AAGATAATCA
47863 AGAGTCGAAGAGAAACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
47884 AGAGTCGAAGAGAAACTTG--
1 AGAGTCGAAGAGAAACTTGAT
* *
47903 AGAGTCGAAGATACACTTGAT
1 AGAGTCGAAGAGAAACTTGAT
47924 AG
1 AG
47926 GCATAAGGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.45
21 21 0.55
ACGTcount: A:0.41, C:0.11, G:0.29, T:0.19
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAT
Found at i:47998 original size:33 final size:33
Alignment explanation
Indices: 47956--48020 Score: 103
Period size: 33 Copynumber: 2.0 Consensus size: 33
47946 AAAAATAGAG
*
47956 GTGGTGAAAGAAGTAGAGGTGTTGAGGGGTGAA
1 GTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGAA
* *
47989 GTGGTGAAAGAAGTTGGGGTGTTAAGGGGTGA
1 GTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGA
48021 TATTAATGGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.49, T:0.23
Consensus pattern (33 bp):
GTGGTGAAAGAAGTAGAGGTGTTAAGGGGTGAA
Found at i:49826 original size:19 final size:19
Alignment explanation
Indices: 49802--49869 Score: 127
Period size: 19 Copynumber: 3.6 Consensus size: 19
49792 AATGTAGGGT
49802 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
49821 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
49840 TAATTTTGTATATGATTTA
1 TAATTTTGTATAAGATTTA
49859 TAATTTTGTAT
1 TAATTTTGTAT
49870 GTGAATATAA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:50831 original size:200 final size:200
Alignment explanation
Indices: 50125--51272 Score: 1868
Period size: 200 Copynumber: 5.8 Consensus size: 200
50115 GTGCAACCAT
*
50125 AAAGTGTCGATCCCATAAACATTGAAACCCAAAAGTATAATGTAATAGGT-ATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
*
50189 TCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAA-GTA-CGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
50252 TGTGTCGATA-TTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
50316 TAT-A
196 TATAA
* *
50320 AAAGTGTTGATCCGAT-AACATCG-AACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* **
50383 TCGGTACAAGTATACCGGTTTTAAAAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
* * *
50448 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACATGGTGTAACAATAAAGTGTCGACCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
50513 TAT-A
196 TATAA
* *
50517 AAAGTGTCGATCCGATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAGTCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* * *
50582 TCGGTACAAGTATACTGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGAT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
50647 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
50712 TATAA
196 TATAA
* * *
50717 AAAGTGACGATCCGATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* *
50782 CCGGTACAAGTATATCAGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
*
50847 TGTGTCGATATTTTTTGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
50912 TATAA
196 TATAA
* *
50917 AAAGTGTCGATCCCATAAACATCGAAACCCATATGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
*
50982 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTGTCGACACTTTTGTAGTT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
*
51047 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAATAGGGTGCAACAATAAAGTGTCGATCCATA
131 TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
51112 TATAA
196 TATAA
*
51117 AAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATGTAATAGGTAATTTTTCAATCTAA
1 AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
* * * * ** * *
51182 CCGGTATAAATATACCGATTTTATGAGCGAATAGGTCTACAA-CCTATATCGACACTTTT-TAAT
66 CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTA-AATAATGTATCGACACTTTTGTAGT
* *
51245 ATTGTGTCGGTACTTTAT-GTCCAGAATG
130 -TTGTGTCGATA-TTTTTGGTCCAGAATG
51273 GAAGAAAAAT
Statistics
Matches: 897, Mismatches: 46, Indels: 15
0.94 0.05 0.02
Matches are distributed among these distances:
193 25 0.03
194 62 0.07
195 17 0.02
196 26 0.03
197 70 0.08
198 7 0.01
199 168 0.19
200 516 0.58
201 6 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.31
Consensus pattern (200 bp):
AAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATGTAATAGGTAATTTTTCAATCTAA
CCGGTACAAGTATACCGGTTTTATGAGAGAATAGGTCTAAATAATGTATCGACACTTTTGTAGTT
TGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCAACAATAAAGTGTCGATCCATA
TATAA
Found at i:54845 original size:80 final size:78
Alignment explanation
Indices: 54747--54894 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 78
54737 AGGTCAATAT
54747 AAGCGCTACCTATTACATTATAT-AGCGCTATC-TAATATGTTATTGTACTTG-TAATATTTTCC
1 AAGCGCTACCTATTACATTATATAAGCGCTA-CATAATATG---TTGTACTTGATAATA-TTTCC
*
54809 TGTTAAATTTTTATTATA
61 GGTTAAATTTTTATTATA
* *
54827 AAGCGCTATCTATTACATTATATAAGCGTTACATAATATGTTGTACTTGATAATATTTCCGGTTA
1 AAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTGTACTTGATAATATTTCCGGTTA
54892 AAT
66 AAT
54895 AATATAATAT
Statistics
Matches: 62, Mismatches: 3, Indels: 8
0.85 0.04 0.11
Matches are distributed among these distances:
78 21 0.34
79 5 0.08
80 23 0.37
81 13 0.21
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (78 bp):
AAGCGCTACCTATTACATTATATAAGCGCTACATAATATGTTGTACTTGATAATATTTCCGGTTA
AATTTTTATTATA
Found at i:58404 original size:15 final size:15
Alignment explanation
Indices: 58366--58396 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
58356 ATCCGGTCCG
*
58366 ATCCAAATAACACAT
1 ATCCCAATAACACAT
58381 ATCCCAATAACACAT
1 ATCCCAATAACACAT
58396 A
1 A
58397 CTCGAATATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.29, G:0.00, T:0.19
Consensus pattern (15 bp):
ATCCCAATAACACAT
Found at i:68988 original size:16 final size:17
Alignment explanation
Indices: 68955--68988 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
68945 CCTTCTGTTT
*
68955 TTATTTTATATTTTAAA
1 TTATTTTATATATTAAA
68972 TTATTTT-TATATTAAA
1 TTATTTTATATATTAAA
68988 T
1 T
68989 AATAAAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTTTATATATTAAA
Found at i:69446 original size:12 final size:13
Alignment explanation
Indices: 69405--69434 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
69395 AATATTATTT
69405 TAAAAAAAATTA-
1 TAAAAAAAATTAC
69417 TAAAAAAAATTAC
1 TAAAAAAAATTAC
69430 TAAAA
1 TAAAA
69435 TTATAAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.71
13 5 0.29
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAAAATTAC
Found at i:69455 original size:21 final size:22
Alignment explanation
Indices: 69409--69455 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
69399 TTATTTTAAA
*
69409 AAAAATTATAAAAAAAATTACT
1 AAAAATTATAAAAAAAATCACT
*
69431 -AAAATTATAAAAAAAA-CCCT
1 AAAAATTATAAAAAAAATCACT
69451 AAAAA
1 AAAAA
69456 ATTAAAATTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (22 bp):
AAAAATTATAAAAAAAATCACT
Found at i:73918 original size:26 final size:26
Alignment explanation
Indices: 73888--73940 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
73878 AAAAATAAAT
73888 GCAATGTTAATGAATTATCACCAATG
1 GCAATGTTAATGAATTATCACCAATG
73914 GCAATGTTAATGAATTATCACCAATG
1 GCAATGTTAATGAATTATCACCAATG
73940 G
1 G
73941 AGGCAAGAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (26 bp):
GCAATGTTAATGAATTATCACCAATG
Found at i:81343 original size:19 final size:20
Alignment explanation
Indices: 81319--81360 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
81309 AGAACCACCA
*
81319 GTTCAC-ACCGGTTTTACCG
1 GTTCACAACCAGTTTTACCG
81338 GTTCACAACCAGTTTTACCG
1 GTTCACAACCAGTTTTACCG
81358 GTT
1 GTT
81361 TCTACTGGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.19, C:0.29, G:0.19, T:0.33
Consensus pattern (20 bp):
GTTCACAACCAGTTTTACCG
Found at i:84514 original size:33 final size:33
Alignment explanation
Indices: 84472--84536 Score: 112
Period size: 33 Copynumber: 2.0 Consensus size: 33
84462 TCTGCAAACA
*
84472 AGGATGAAAAATTGAAATATTGTAGAACTACCG
1 AGGATGAAAAATTGAAATATTATAGAACTACCG
*
84505 AGGATGAAAAATTGAAATGTTATAGAACTACC
1 AGGATGAAAAATTGAAATATTATAGAACTACC
84537 AGACAAGACA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.46, C:0.09, G:0.20, T:0.25
Consensus pattern (33 bp):
AGGATGAAAAATTGAAATATTATAGAACTACCG
Found at i:93268 original size:18 final size:18
Alignment explanation
Indices: 93232--93276 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 18
93222 TAATATTTTA
*
93232 ATTTTTAAGTAAAATAAT
1 ATTTTTAAATAAAATAAT
93250 ATTTATTAAATAAAA-AAT
1 ATTT-TTAAATAAAATAAT
93268 ATTTGTTAA
1 ATTT-TTAA
93277 CTTGACATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 15 0.62
19 9 0.38
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.44
Consensus pattern (18 bp):
ATTTTTAAATAAAATAAT
Found at i:94574 original size:28 final size:30
Alignment explanation
Indices: 94537--94602 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 30
94527 TTAACTTATT
*
94537 AAATATATTT-TATTTTTAACTTAATTTTA
1 AAATATATTTATATTTTTAACTTAATTTAA
* **
94566 AAATA-ATTTATTTTTTTATTTTAATTTAA
1 AAATATATTTATATTTTTAACTTAATTTAA
94595 AAATATAT
1 AAATATAT
94603 ATTTTATTCA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
28 4 0.13
29 25 0.81
30 2 0.06
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (30 bp):
AAATATATTTATATTTTTAACTTAATTTAA
Found at i:94631 original size:33 final size:30
Alignment explanation
Indices: 94594--94673 Score: 97
Period size: 33 Copynumber: 2.5 Consensus size: 30
94584 TTTTAATTTA
94594 AAAATATATATTTTATTCATATCTAAACTTTC
1 AAAATATATATTTTATT-AT-TCTAAACTTTC
* * *
94626 TAAAATATATTTTATTATTATTTTAAATTTTC
1 -AAAATATATATT-TTATTATTCTAAACTTTC
94658 AAAATATATATTTTAT
1 AAAATATATATTTTAT
94674 CTTAATTTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 4 0.10
31 11 0.26
32 9 0.21
33 13 0.31
34 5 0.12
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (30 bp):
AAAATATATATTTTATTATTCTAAACTTTC
Found at i:94637 original size:31 final size:33
Alignment explanation
Indices: 94594--94673 Score: 103
Period size: 32 Copynumber: 2.5 Consensus size: 33
94584 TTTTAATTTA
94594 AAAATATATATTTTATTCA-TA-TCTAAACTTTC
1 AAAATATATATTTTATT-ATTATTCTAAACTTTC
* * *
94626 TAAA-ATATATTTTATTATTATTTTAAATTTTC
1 AAAATATATATTTTATTATTATTCTAAACTTTC
94658 AAAATATATATTTTAT
1 AAAATATATATTTTAT
94674 CTTAATTTAT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
30 1 0.02
31 14 0.34
32 15 0.37
33 11 0.27
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (33 bp):
AAAATATATATTTTATTATTATTCTAAACTTTC
Found at i:94673 original size:64 final size:60
Alignment explanation
Indices: 94539--94673 Score: 155
Period size: 64 Copynumber: 2.2 Consensus size: 60
94529 AACTTATTAA
** * * *
94539 ATATATTTTATTTTTAACTTAATTTTAAAATAATTTATTTTTTTATTTTAATTTAAAAAT
1 ATATATTTTATTCATAACTAAATTTTAAAATAATTTATATTATTATTTTAATTTAAAAAT
* *
94599 ATATATTTTATTCATATCTAAACTTTCTAAAATATATTT-TATTATTATTTTAAATTTTCAAAAT
1 ATATATTTTATTCATAACTAAA-TTT-TAAAATA-ATTTATATTATTATTTT-AA-TTTAAAAAT
94663 ATATATTTTAT
1 ATATATTTTAT
94674 CTTAATTTAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
60 18 0.29
61 3 0.05
62 17 0.27
63 6 0.10
64 19 0.30
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (60 bp):
ATATATTTTATTCATAACTAAATTTTAAAATAATTTATATTATTATTTTAATTTAAAAAT
Found at i:95846 original size:8 final size:8
Alignment explanation
Indices: 95833--95858 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
95823 TGACGTTATT
95833 GGTGGGTA
1 GGTGGGTA
95841 GGTGGGTA
1 GGTGGGTA
95849 GGTGGGTA
1 GGTGGGTA
95857 GG
1 GG
95859 ACAGATCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.65, T:0.23
Consensus pattern (8 bp):
GGTGGGTA
Found at i:98712 original size:20 final size:20
Alignment explanation
Indices: 98676--98713 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
98666 ATCCTATTCC
**
98676 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
98696 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
98714 GTTAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:100476 original size:23 final size:23
Alignment explanation
Indices: 100446--100491 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
100436 TGTTGACGTG
100446 ACAGATGGGCTAAATTTAGTTTT
1 ACAGATGGGCTAAATTTAGTTTT
100469 ACAGATGGGCTAAATTTAGTTTT
1 ACAGATGGGCTAAATTTAGTTTT
100492 TAGTCTTGTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.09, G:0.22, T:0.39
Consensus pattern (23 bp):
ACAGATGGGCTAAATTTAGTTTT
Found at i:100741 original size:2 final size:2
Alignment explanation
Indices: 100736--100791 Score: 96
Period size: 2 Copynumber: 28.5 Consensus size: 2
100726 ATGTGTGTGC
100736 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
100778 AT AT GT A- AT AT AT A
1 AT AT AT AT AT AT AT A
100792 ATAATAGCAT
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (2 bp):
AT
Found at i:109625 original size:21 final size:22
Alignment explanation
Indices: 109601--109646 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
109591 TGATAAAATA
109601 TTATTAAAAATATT-ATTATTT
1 TTATTAAAAATATTAATTATTT
* *
109622 TTATTTAAAATATTAATTTTTT
1 TTATTAAAAATATTAATTATTT
109644 TTA
1 TTA
109647 ATAATTTTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
TTATTAAAAATATTAATTATTT
Found at i:110035 original size:30 final size:30
Alignment explanation
Indices: 110000--110064 Score: 96
Period size: 30 Copynumber: 2.2 Consensus size: 30
109990 AGAACCGGAA
*
110000 GAACCGACTGAGAA-CAGACAAAACCGGGGT
1 GAACCGACTGAAAATC-GACAAAACCGGGGT
*
110030 GAACCGACTGAAAATCGACAAAACCGGTGT
1 GAACCGACTGAAAATCGACAAAACCGGGGT
110060 GAACC
1 GAACC
110065 TCCAGTTCTC
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
30 31 0.97
31 1 0.03
ACGTcount: A:0.40, C:0.25, G:0.26, T:0.09
Consensus pattern (30 bp):
GAACCGACTGAAAATCGACAAAACCGGGGT
Found at i:110320 original size:24 final size:27
Alignment explanation
Indices: 110283--110331 Score: 68
Period size: 25 Copynumber: 1.9 Consensus size: 27
110273 CGAACTCAAA
*
110283 AAAATTTAGAAGCTCGA-TTGAAGCCT
1 AAAATTTAGAAGCTCAATTTGAAGCCT
110309 AAAATTT-G-AGCTCAATTTGAAGC
1 AAAATTTAGAAGCTCAATTTGAAGC
110332 AAATAATAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 8 0.38
26 7 0.33
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (27 bp):
AAAATTTAGAAGCTCAATTTGAAGCCT
Found at i:111498 original size:34 final size:30
Alignment explanation
Indices: 111468--111528 Score: 97
Period size: 30 Copynumber: 2.0 Consensus size: 30
111458 ACAATTTAAG
111468 ACAAAATGATTTTTGGACTTGAATTGAATTT-
1 ACAAAATG-TTTTTGGACTT-AATTGAATTTA
111499 ACAAAATGTTTTTGGACTTAATTGAATTTA
1 ACAAAATGTTTTTGGACTTAATTGAATTTA
111529 TTCAAAGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
29 10 0.34
30 11 0.38
31 8 0.28
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
ACAAAATGTTTTTGGACTTAATTGAATTTA
Found at i:111526 original size:29 final size:31
Alignment explanation
Indices: 111468--111528 Score: 108
Period size: 29 Copynumber: 2.0 Consensus size: 31
111458 ACAATTTAAG
111468 ACAAAATGATTTTTGGACTTGAATTGAATTT
1 ACAAAATGATTTTTGGACTTGAATTGAATTT
111499 ACAAAATG-TTTTTGGACTT-AATTGAATTT
1 ACAAAATGATTTTTGGACTTGAATTGAATTT
111528 A
1 A
111529 TTCAAAGTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.37
30 11 0.37
31 8 0.27
ACGTcount: A:0.36, C:0.07, G:0.15, T:0.43
Consensus pattern (31 bp):
ACAAAATGATTTTTGGACTTGAATTGAATTT
Found at i:111634 original size:21 final size:21
Alignment explanation
Indices: 111608--111702 Score: 124
Period size: 21 Copynumber: 4.5 Consensus size: 21
111598 AGGGTGTCAA
*
111608 AGTGCATCCATGCACCCCTGT
1 AGTGCATCCATGCACCCCTGC
111629 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
111650 AGTGCATCCATGCA--CCTGCAC
1 AGTGCATCCATGCACCCCTG--C
*
111671 TAGTGCATCCATGCA-CCATGC
1 -AGTGCATCCATGCACCCCTGC
111692 AGTGCATCCAT
1 AGTGCATCCAT
111703 ACACTCAAAC
Statistics
Matches: 68, Mismatches: 2, Indels: 9
0.86 0.03 0.11
Matches are distributed among these distances:
19 4 0.06
20 11 0.16
21 36 0.53
22 14 0.21
23 3 0.04
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:111693 original size:42 final size:42
Alignment explanation
Indices: 111608--111702 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
111598 AGGGTGTCAA
** *
111608 AGTGCATCCATGCACCCCTGTAGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCACTAGTGCATCCATGCACCCATGC
*
111650 AGTGCATCCATGCACCTGCACTAGTGCATCCATGCA-CCATGC
1 AGTGCATCCATGCACC-CCACTAGTGCATCCATGCACCCATGC
111692 AGTGCATCCAT
1 AGTGCATCCAT
111703 ACACTCAAAC
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
42 32 0.67
43 16 0.33
ACGTcount: A:0.22, C:0.37, G:0.19, T:0.22
Consensus pattern (42 bp):
AGTGCATCCATGCACCCCACTAGTGCATCCATGCACCCATGC
Found at i:111779 original size:21 final size:21
Alignment explanation
Indices: 111748--111809 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
111738 CATCCTTCTA
*
111748 TGCATCAATGCATCAAGGCTG
1 TGCATCCATGCATCAAGGCTG
** **
111769 TGCATTGATGCATC-CTGCTG
1 TGCATCCATGCATCAAGGCTG
*
111789 TGCATCCATGCATGAAGGCTG
1 TGCATCCATGCATCAAGGCTG
111810 CAACGGCTAG
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.48
21 16 0.52
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.27
Consensus pattern (21 bp):
TGCATCCATGCATCAAGGCTG
Found at i:111799 original size:20 final size:20
Alignment explanation
Indices: 111727--111801 Score: 78
Period size: 20 Copynumber: 3.7 Consensus size: 20
111717 AATGCAATTA
*
111727 GTGCATCCATGCATCCTTCT
1 GTGCATCCATGCATCCTGCT
* * **
111747 ATGCATCAATGCATCAAGGCT
1 GTGCATCCATGCATC-CTGCT
**
111768 GTGCATTGATGCATCCTGCT
1 GTGCATCCATGCATCCTGCT
111788 GTGCATCCATGCAT
1 GTGCATCCATGCAT
111802 GAAGGCTGCA
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 28 0.67
21 14 0.33
ACGTcount: A:0.21, C:0.28, G:0.20, T:0.31
Consensus pattern (20 bp):
GTGCATCCATGCATCCTGCT
Found at i:114598 original size:29 final size:30
Alignment explanation
Indices: 114528--114587 Score: 95
Period size: 29 Copynumber: 2.0 Consensus size: 30
114518 CAATTTAAGG
114528 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAAT-GTTTTTGGACTTGAATTGAATTTA
*
114559 CAAAATATTTTTGGACTT-AATTGAATTTA
1 CAAAATGTTTTTGGACTTGAATTGAATTTA
114588 TTCAAAGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.15, T:0.43
Consensus pattern (30 bp):
CAAAATGTTTTTGGACTTGAATTGAATTTA
Found at i:114789 original size:20 final size:20
Alignment explanation
Indices: 114727--114817 Score: 101
Period size: 20 Copynumber: 4.5 Consensus size: 20
114717 GCAATTAGTT
*
114727 CATCCATGCATCCTTCTGTG
1 CATCCATGCATCCTGCTGTG
** * **
114747 CATAGATACATCAAGGCTGTG
1 CATCCATGCATC-CTGCTGTG
* *
114768 CATCGATGCATCCTGTTGTG
1 CATCCATGCATCCTGCTGTG
114788 CATCCATGCATCCTGCTGTG
1 CATCCATGCATCCTGCTGTG
114808 CATCCATGCA
1 CATCCATGCA
114818 CGAAGGCTGC
Statistics
Matches: 57, Mismatches: 13, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
20 42 0.74
21 15 0.26
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.30
Consensus pattern (20 bp):
CATCCATGCATCCTGCTGTG
Found at i:116926 original size:15 final size:15
Alignment explanation
Indices: 116894--116923 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
116884 TTTTCTATCA
116894 ATTTTATTATTATTT
1 ATTTTATTATTATTT
116909 ATTTTATCTATTATT
1 ATTTTAT-TATTATT
116924 ATTAAGATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (15 bp):
ATTTTATTATTATTT
Found at i:118232 original size:16 final size:16
Alignment explanation
Indices: 118185--118224 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
118175 TCCGTATCCG
*
118185 ATCCGAAAAATCGGAT
1 ATCCGAAAAGTCGGAT
118201 ATCCGAAAAGTCGGAT
1 ATCCGAAAAGTCGGAT
118217 ATCC-AAAA
1 ATCCGAAAA
118225 TTTCGGATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 4 0.17
16 19 0.83
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.17
Consensus pattern (16 bp):
ATCCGAAAAGTCGGAT
Found at i:119978 original size:22 final size:23
Alignment explanation
Indices: 119925--119979 Score: 58
Period size: 27 Copynumber: 2.3 Consensus size: 23
119915 CCGAGTACAT
119925 AGATTTTAGATACAGTTGGGTTG
1 AGATTTTAGATACAGTTGGGTTG
*
119948 AATTAGATTTTAGATATAGTTGGGTTG
1 ----AGATTTTAGATACAGTTGGGTTG
119975 -GATTT
1 AGATTT
119980 GAAGCATGAG
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 5 0.19
27 22 0.81
ACGTcount: A:0.27, C:0.02, G:0.27, T:0.44
Consensus pattern (23 bp):
AGATTTTAGATACAGTTGGGTTG
Found at i:120620 original size:24 final size:23
Alignment explanation
Indices: 120580--120624 Score: 63
Period size: 24 Copynumber: 1.9 Consensus size: 23
120570 TAAATTCAAT
120580 TTATTTTAATCAATTTAATAATGA
1 TTATTTTAATCAATTT-ATAATGA
* *
120604 TTATTTTAATTATTTTATAAT
1 TTATTTTAATCAATTTATAAT
120625 TATCAATATG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 5 0.26
24 14 0.74
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (23 bp):
TTATTTTAATCAATTTATAATGA
Found at i:132222 original size:19 final size:20
Alignment explanation
Indices: 132174--132222 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
132164 TAATTTGTTT
132174 TTGTTTTGATATTAAAATTG
1 TTGTTTTGATATTAAAATTG
*
132194 TTGTTTTTGAT-TT-AATTATG
1 TTG-TTTTGATATTAAAAT-TG
132214 TTGTTTTGA
1 TTGTTTTGA
132223 GAACTACATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 9 0.35
20 10 0.38
21 7 0.27
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.61
Consensus pattern (20 bp):
TTGTTTTGATATTAAAATTG
Found at i:133630 original size:17 final size:17
Alignment explanation
Indices: 133608--133646 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
133598 TAGGATTTAT
133608 TGTTTTAACATTTTGGA
1 TGTTTTAACATTTTGGA
***
133625 TGTTTTTGGATTTTGGA
1 TGTTTTAACATTTTGGA
133642 TGTTT
1 TGTTT
133647 GAATTGTTTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.15, C:0.03, G:0.23, T:0.59
Consensus pattern (17 bp):
TGTTTTAACATTTTGGA
Found at i:137456 original size:9 final size:9
Alignment explanation
Indices: 137442--137470 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
137432 ATAAAAAAAT
137442 CCGACCCGA
1 CCGACCCGA
137451 CCGACCCGA
1 CCGACCCGA
137460 CCGACCCGA
1 CCGACCCGA
137469 CC
1 CC
137471 AGTCACATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.21, C:0.59, G:0.21, T:0.00
Consensus pattern (9 bp):
CCGACCCGA
Found at i:143139 original size:20 final size:20
Alignment explanation
Indices: 143111--143148 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
143101 TTAAAATATA
*
143111 TTTCGCATATTATTTGTTAG
1 TTTCACATATTATTTGTTAG
143131 TTTCACATATTATTTGTT
1 TTTCACATATTATTTGTT
143149 TGCATATAGT
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:0.21, C:0.11, G:0.11, T:0.58
Consensus pattern (20 bp):
TTTCACATATTATTTGTTAG
Found at i:144139 original size:59 final size:59
Alignment explanation
Indices: 144039--144166 Score: 150
Period size: 59 Copynumber: 2.2 Consensus size: 59
144029 ATTAAAATAA
** * * *
144039 AAATAGAAAGATAAAAACGTTCAAGTACAAAATGTTTAAACATATATATACAA-ACGTTC
1 AAATAGAAAGATAAAAACGTTCAAGTACAAAACATTCAAACAGACATATACAATA-GTTC
* * * *
144098 AAATAGACATATATAAACGTTCAAGTGCAAAACATTCAAACAGACATATACAATAGTTC
1 AAATAGAAAGATAAAAACGTTCAAGTACAAAACATTCAAACAGACATATACAATAGTTC
144157 AAATATGAAA
1 AAATA-GAAA
144167 TCATTGAGGC
Statistics
Matches: 57, Mismatches: 10, Indels: 3
0.81 0.14 0.04
Matches are distributed among these distances:
59 53 0.93
60 4 0.07
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.24
Consensus pattern (59 bp):
AAATAGAAAGATAAAAACGTTCAAGTACAAAACATTCAAACAGACATATACAATAGTTC
Found at i:147423 original size:21 final size:21
Alignment explanation
Indices: 147377--147426 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
147367 CAAAATAGAG
*
147377 AAGGGATCGATCATTTCTGTC
1 AAGGGATCGATCATTTCTGCC
* *
147398 GAGGGATTGATCATTTTCT-CC
1 AAGGGATCGATCA-TTTCTGCC
147419 AAGGGATC
1 AAGGGATC
147427 AATCCTTATG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
21 18 0.78
22 5 0.22
ACGTcount: A:0.24, C:0.18, G:0.26, T:0.32
Consensus pattern (21 bp):
AAGGGATCGATCATTTCTGCC
Found at i:149274 original size:15 final size:15
Alignment explanation
Indices: 149242--149282 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
149232 AAGGAATAAG
149242 GAAGAATGAAGAAAAA
1 GAAGAATG-AGAAAAA
*
149258 GAAGAATGAGAAGAA
1 GAAGAATGAGAAAAA
149273 GAAGAATGAG
1 GAAGAATGAG
149283 GGGTTTAACG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 16 0.67
16 8 0.33
ACGTcount: A:0.61, C:0.00, G:0.32, T:0.07
Consensus pattern (15 bp):
GAAGAATGAGAAAAA
Found at i:151144 original size:20 final size:20
Alignment explanation
Indices: 151088--151137 Score: 91
Period size: 20 Copynumber: 2.5 Consensus size: 20
151078 TCCTATTGCA
151088 TGGTAATCTTTTATTCCCAC
1 TGGTAATCTTTTATTCCCAC
*
151108 TGGTAATCTTTTATTCCCAT
1 TGGTAATCTTTTATTCCCAC
151128 TGGTAATCTT
1 TGGTAATCTT
151138 ACATTCCGTG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.20, C:0.20, G:0.12, T:0.48
Consensus pattern (20 bp):
TGGTAATCTTTTATTCCCAC
Found at i:152466 original size:6 final size:6
Alignment explanation
Indices: 152455--152480 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
152445 GATTAATGGG
152455 GACGAA GACGAA GACGAA GACGAA GA
1 GACGAA GACGAA GACGAA GACGAA GA
152481 ATGGGATGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.15, G:0.35, T:0.00
Consensus pattern (6 bp):
GACGAA
Found at i:153007 original size:54 final size:54
Alignment explanation
Indices: 152925--153039 Score: 151
Period size: 54 Copynumber: 2.1 Consensus size: 54
152915 TCAATTAAAT
* * *
152925 TTTAATTTTAATTTAGTTTAAAAAATTAA-CTCTACTACATGTTAACATGTTAGA
1 TTTAATTATAATTTAATTTAAAAAATTAACCT-TACTACATGTCAACATGTTAGA
* ** *
152979 TTTAATTATAGTTTAATTTAAAAAATTAACCTTGTTATATGTCAACATGTTAGA
1 TTTAATTATAATTTAATTTAAAAAATTAACCTTACTACATGTCAACATGTTAGA
153033 TTTAATT
1 TTTAATT
153040 TAAAAAATTA
Statistics
Matches: 53, Mismatches: 7, Indels: 2
0.85 0.11 0.03
Matches are distributed among these distances:
54 51 0.96
55 2 0.04
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (54 bp):
TTTAATTATAATTTAATTTAAAAAATTAACCTTACTACATGTCAACATGTTAGA
Found at i:153915 original size:11 final size:12
Alignment explanation
Indices: 153899--153927 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
153889 TGTGACTTTG
153899 AATTTTCTA-AT
1 AATTTTCTATAT
153910 AATTTTCTATAT
1 AATTTTCTATAT
153922 AATTTT
1 AATTTT
153928 AATTTTTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (12 bp):
AATTTTCTATAT
Found at i:154022 original size:2 final size:2
Alignment explanation
Indices: 154017--154051 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
154007 TTTCATTAAC
154017 TA TA TA TA TA 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 TA TA TA TA TA T
154052 GAAAGAATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:156714 original size:6 final size:6
Alignment explanation
Indices: 156698--156733 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
156688 TCTAAAGATG
*
156698 CATATA TATATA CATATA CATATA CATATA CATATA
1 CATATA CATATA CATATA CATATA CATATA CATATA
156734 AGGACGTGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (6 bp):
CATATA
Found at i:161290 original size:365 final size:365
Alignment explanation
Indices: 160618--161351 Score: 1333
Period size: 365 Copynumber: 2.0 Consensus size: 365
160608 AAGCTAGACT
160618 ACTCCACCTCCAATGGAAACTCCTTGGGCTCCTTGATGCTTTATTCTTCAATGAGACTCTCATAA
1 ACTCCACCTCCAATGGAAACTCCTTGGGCTCCTTGATGCTTTATTCTTCAATGAGACTCTCATAA
160683 TTTGCCAGCTGTATGAAATTGTTGTGGCAAAATTGATCAACTTCCCCTTCTATCAATGAATCCAC
66 TTTGCCAGCTGTATGAAATTGTTGTGGCAAAATTGATCAACTTCCCCTTCTATCAATGAATCCAC
* *
160748 TTCAATAATGCTCTGGCATTCTTTCAAGTCATCAAAAAATTTGAAAGTATTAATTACATTCACAG
131 TTCAACAATGCTCTGGCATTCTTTCAAGTCATCAAAAAATTTGAAAGTATTAATGACATTCACAG
160813 TCACACATTGGTCGACCACTCTCATGGTGAGTTCACCCTTTTCACGGATGCGACCAATGACTAGG
196 TCACACATTGGTCGACCACTCTCATGGTGAGTTCACCCTTTTCACGGATGCGACCAATGACTAGG
* * *
160878 AAAAGCCTCCCAAAAATTATGAGTACGTTAGTATCAACCTTGCAATCAAGTATAAGGAAGTCCAC
261 AAAAACCTCCCAAAAATTATGAGTACATTAGTATCAACCTCGCAATCAAGTATAAGGAAGTCCAC
* *
160943 TGGGAACACAAATTTGTTCACCCACACAATGGCATCTTTG
326 TGGGAACACAAATTTGTTCACCCACAAAATGGCATCTTCG
** *
160983 ACTCCACCTCCAATGGAATTTCCTTGGGCTCCTTGATGCTTTATTCTTTAATGAGACTCTCATAA
1 ACTCCACCTCCAATGGAAACTCCTTGGGCTCCTTGATGCTTTATTCTTCAATGAGACTCTCATAA
*
161048 TTTGCCATCTGTATGAAATTGTTGTGGCAAAATTGATCAACTTCCCCTTCTATCAATGAATCCAC
66 TTTGCCAGCTGTATGAAATTGTTGTGGCAAAATTGATCAACTTCCCCTTCTATCAATGAATCCAC
* *
161113 TTCAACAATGCTCTGGCATTCTTTCGAGTCATCAAAAAATTTGAGAGTATTAATGACATTCACAG
131 TTCAACAATGCTCTGGCATTCTTTCAAGTCATCAAAAAATTTGAAAGTATTAATGACATTCACAG
* *
161178 TCACACATTGGTCGACCATTCTCATGGTGAGTTCACCTTTTTCACGGATGCGACCAATGACTAGG
196 TCACACATTGGTCGACCACTCTCATGGTGAGTTCACCCTTTTCACGGATGCGACCAATGACTAGG
161243 AAAAACCTCCCAAAAATTATGAGTACATTAGTATCAACCTCGCAATCAAGTATAAGGAAGTCCAC
261 AAAAACCTCCCAAAAATTATGAGTACATTAGTATCAACCTCGCAATCAAGTATAAGGAAGTCCAC
161308 TGGGAACACAAATTTGTTCACCCACAAAATGGCATCTTCG
326 TGGGAACACAAATTTGTTCACCCACAAAATGGCATCTTCG
161348 ACTC
1 ACTC
161352 TTCCTTTGGG
Statistics
Matches: 354, Mismatches: 15, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
365 354 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.30
Consensus pattern (365 bp):
ACTCCACCTCCAATGGAAACTCCTTGGGCTCCTTGATGCTTTATTCTTCAATGAGACTCTCATAA
TTTGCCAGCTGTATGAAATTGTTGTGGCAAAATTGATCAACTTCCCCTTCTATCAATGAATCCAC
TTCAACAATGCTCTGGCATTCTTTCAAGTCATCAAAAAATTTGAAAGTATTAATGACATTCACAG
TCACACATTGGTCGACCACTCTCATGGTGAGTTCACCCTTTTCACGGATGCGACCAATGACTAGG
AAAAACCTCCCAAAAATTATGAGTACATTAGTATCAACCTCGCAATCAAGTATAAGGAAGTCCAC
TGGGAACACAAATTTGTTCACCCACAAAATGGCATCTTCG
Found at i:164264 original size:103 final size:103
Alignment explanation
Indices: 164085--164412 Score: 611
Period size: 103 Copynumber: 3.2 Consensus size: 103
164075 CATATAAAGT
* *
164085 TGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGAGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
164150 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
*
164188 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAATATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
*
164253 CTCAACAGACCTCACACATGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
*
164291 TATCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
164356 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
164394 TGTCCCGAAGGACCACATA
1 TGTCCCGAAGGACCACATA
164413 GACCCTCTAC
Statistics
Matches: 217, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 217 1.00
ACGTcount: A:0.38, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
Found at i:166247 original size:20 final size:20
Alignment explanation
Indices: 166222--166263 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
166212 TTAAAGCCGC
166222 AACACGACTAAATTGAATAG
1 AACACGACTAAATTGAATAG
166242 AACACGACTAAATTGAATAG
1 AACACGACTAAATTGAATAG
166262 AA
1 AA
166264 TTAAAATAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.52, C:0.14, G:0.14, T:0.19
Consensus pattern (20 bp):
AACACGACTAAATTGAATAG
Found at i:172379 original size:23 final size:23
Alignment explanation
Indices: 172353--172421 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
172343 CACCACAGCT
*
172353 CGTATAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
* * *
172376 CGTAGAATTGCACCGTAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
*
172399 CATAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
172422 TATAAAGTTG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.32, C:0.26, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:172674 original size:100 final size:103
Alignment explanation
Indices: 172430--172750 Score: 576
Period size: 103 Copynumber: 3.1 Consensus size: 103
172420 CATATAAAGT
* *
172430 TGTCCCTAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCATAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
* *
172495 CTCAACAAACCTCACACCTGTTCCAAAGAATATATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
*
172533 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCAAATACATATGCCAAAGATCAA-TATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
172597 CTCAACAGACCTCACACCTGTT-CAAAGAA-ACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
172633 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
1 TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
172698 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
66 CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
172736 TGTCCCGAAGGACCA
1 TGTCCCGAAGGACCA
172751 TATAGACCCT
Statistics
Matches: 209, Mismatches: 6, Indels: 6
0.95 0.03 0.03
Matches are distributed among these distances:
100 62 0.30
101 36 0.17
102 35 0.17
103 76 0.36
ACGTcount: A:0.37, C:0.25, G:0.12, T:0.25
Consensus pattern (103 bp):
TGTCCCGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAAGATCAAGTATGTGT
CTCAACAGACCTCACACCTGTTCCAAAGAATACATATA
Found at i:175787 original size:21 final size:21
Alignment explanation
Indices: 175762--175813 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 21
175752 TACTCAGGAA
*
175762 AGTATCGATACCTC-ATACAGG
1 AGTATCGATACCTCGA-ACAAG
*
175783 AGTATCAATA-CTCGAACAAG
1 AGTATCGATACCTCGAACAAG
175803 AGTATCGATAC
1 AGTATCGATAC
175814 AAATTATTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.38, C:0.21, G:0.17, T:0.23
Consensus pattern (21 bp):
AGTATCGATACCTCGAACAAG
Found at i:178536 original size:31 final size:31
Alignment explanation
Indices: 178501--178567 Score: 91
Period size: 31 Copynumber: 2.2 Consensus size: 31
178491 AGCTGCTCAT
*
178501 GAGCTTCAGTTC-AGGATTTCGAGTTCGAGTC
1 GAGCTTCAGTTCAAAGATTTCGAG-TCGAGTC
* *
178532 GAGCTTCATTTCAAAGTTTTCGAGTCGAGTC
1 GAGCTTCAGTTCAAAGATTTCGAGTCGAGTC
178563 GAGCT
1 GAGCT
178568 CAGCAATACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 23 0.72
32 9 0.28
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (31 bp):
GAGCTTCAGTTCAAAGATTTCGAGTCGAGTC
Found at i:179117 original size:20 final size:20
Alignment explanation
Indices: 179092--179130 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
179082 TCAGAAAACT
*
179092 AAAAATAAATACTATTTCTA
1 AAAAATAAAAACTATTTCTA
*
179112 AAAAATAAAAATTATTTCT
1 AAAAATAAAAACTATTTCT
179131 GGAATCATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATAAAAACTATTTCTA
Found at i:189165 original size:17 final size:18
Alignment explanation
Indices: 189139--189178 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
189129 ATTATATGGA
189139 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
189155 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
189173 TATTAT
1 TATTAT
189179 GTATGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:189451 original size:19 final size:19
Alignment explanation
Indices: 189429--189471 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
189419 TATCTTATAA
189429 TTTTATA-TATTTATATTAT
1 TTTTATATTATTTATATT-T
*
189448 TTTT-TATTATTTTTATTT
1 TTTTATATTATTTATATTT
189466 TTTTAT
1 TTTTAT
189472 TCATTATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
18 7 0.33
19 14 0.67
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTATATTATTTATATTT
Found at i:189460 original size:8 final size:8
Alignment explanation
Indices: 189409--189495 Score: 57
Period size: 9 Copynumber: 9.9 Consensus size: 8
189399 ATTTATTTGT
*
189409 TTATTTAA
1 TTATTTTA
*
189417 TATATCTTA
1 T-TATTTTA
*
189426 TAATTTTA
1 TTATTTTA
189434 TATATTTATA
1 T-TATTT-TA
189444 TTATTTTTTA
1 TTA--TTTTA
189454 TTATTTTTA
1 TTA-TTTTA
*
189463 TTTTTTTA
1 TTATTTTA
189471 TTCATTATTA
1 TT-ATT-TTA
*
189481 TTATATTA
1 TTATTTTA
189489 TTATTTT
1 TTATTTT
189496 TTTAAAAAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 14
0.73 0.10 0.16
Matches are distributed among these distances:
8 23 0.37
9 24 0.38
10 13 0.21
11 3 0.05
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (8 bp):
TTATTTTA
Found at i:189462 original size:21 final size:21
Alignment explanation
Indices: 189429--189495 Score: 68
Period size: 21 Copynumber: 3.2 Consensus size: 21
189419 TATCTTATAA
*
189429 TTTTA-TATATTTATATTATT
1 TTTTATTATTTTTATATTATT
189449 TTTTATTATTTTTAT-TT-TT
1 TTTTATTATTTTTATATTATT
*
189468 TTATTCATTATTATTATATTATT
1 TT-TT-ATTATTTTTATATTATT
189491 ATTTT
1 -TTTT
189496 TTTAAAAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
19 4 0.10
20 9 0.23
21 18 0.46
22 2 0.05
23 4 0.10
24 2 0.05
ACGTcount: A:0.25, C:0.01, G:0.00, T:0.73
Consensus pattern (21 bp):
TTTTATTATTTTTATATTATT
Found at i:190896 original size:5 final size:5
Alignment explanation
Indices: 190886--190913 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
190876 TCTTTTCATC
190886 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
190914 CATCACTTGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:193477 original size:8 final size:8
Alignment explanation
Indices: 193466--193535 Score: 61
Period size: 8 Copynumber: 8.5 Consensus size: 8
193456 CAAAAAGGGC
193466 AAAAAGAA
1 AAAAAGAA
193474 AAAAAGAA
1 AAAAAGAA
*
193482 AAAAAGCA
1 AAAAAGAA
*
193490 AAAAAGGA
1 AAAAAGAA
*
193498 AAAAACAA
1 AAAAAGAA
193506 GAACAAA-AA
1 -AA-AAAGAA
*
193515 AGAAAGAA
1 AAAAAGAA
*
193523 CAAAAATAA
1 -AAAAAGAA
193532 AAAA
1 AAAA
193536 GGGAACAAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
7 3 0.06
8 35 0.69
9 10 0.20
10 3 0.06
ACGTcount: A:0.81, C:0.06, G:0.11, T:0.01
Consensus pattern (8 bp):
AAAAAGAA
Found at i:193514 original size:21 final size:21
Alignment explanation
Indices: 193482--193537 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
193472 AAAAAAAGAA
193482 AAAAAGCAAAAAAGGAAAAAAC
1 AAAAA-CAAAAAAGGAAAAAAC
* *
193504 AAGAACAAAAAA-GAAAGAAC
1 AAAAACAAAAAAGGAAAAAAC
*
193524 AAAAATAAAAAAGG
1 AAAAACAAAAAAGG
193538 GAACAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
20 17 0.59
21 8 0.28
22 4 0.14
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (21 bp):
AAAAACAAAAAAGGAAAAAAC
Found at i:193519 original size:20 final size:20
Alignment explanation
Indices: 193473--193536 Score: 64
Period size: 20 Copynumber: 3.4 Consensus size: 20
193463 GGCAAAAAGA
193473 AAAAAAG-AAAAA-AAG--C
1 AAAAAAGAAAAAACAAGAAC
193489 AAAAAAGGAAAAAACAAGAAC
1 AAAAAA-GAAAAAACAAGAAC
* * *
193510 AAAAAAGAAAGAACAAAAAT
1 AAAAAAGAAAAAACAAGAAC
193530 AAAAAAG
1 AAAAAAG
193537 GGAACAAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
16 6 0.15
17 1 0.03
18 5 0.12
19 3 0.08
20 18 0.45
21 7 0.17
ACGTcount: A:0.80, C:0.06, G:0.12, T:0.02
Consensus pattern (20 bp):
AAAAAAGAAAAAACAAGAAC
Found at i:195081 original size:36 final size:36
Alignment explanation
Indices: 195034--195138 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
195024 GTGCTCACCA
195034 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
195070 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
195107 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
195139 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:195128 original size:37 final size:37
Alignment explanation
Indices: 195034--195143 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
195024 GTGCTCACCA
195034 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
195070 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
195107 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
195144 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:195228 original size:102 final size:102
Alignment explanation
Indices: 195052--195443 Score: 635
Period size: 102 Copynumber: 3.9 Consensus size: 102
195042 CTTGAGACAG
** * *
195052 TTTCCCTTGAAACAAACTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCC
1 TTTCCCTTGAAATGAA-TTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCC
195116 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
65 TTGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* * *
195154 TTTCCCTTGAAATGAGTTTGGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
195219 TGAGACAGTTTCTCTTGAAACATAAACATTGGAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
*
195256 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
*
195321 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACA
66 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
* *
195358 TTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCT
1 TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
**
195422 TGAGACAACTTCTCTTGAAACA
66 TGAGACAGTTTCTCTTGAAACA
195444 CAAAACCTTT
Statistics
Matches: 273, Mismatches: 16, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
101 37 0.14
102 236 0.86
ACGTcount: A:0.30, C:0.21, G:0.12, T:0.36
Consensus pattern (102 bp):
TTTCCCTTGAAATGAATTTCGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACA
Found at i:195323 original size:37 final size:37
Alignment explanation
Indices: 195256--195342 Score: 115
Period size: 37 Copynumber: 2.4 Consensus size: 37
195246 ATTGGAAACA
** * *
195256 TTTCCCTTGAAA-TGAATTTTGTCTCTCTTGAGATAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
195292 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
1 TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
195329 TTTCTCC-TGAAACA
1 TTTC-CCTTGAAACA
195343 TAAACATTGA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
36 12 0.27
37 31 0.69
38 2 0.04
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (37 bp):
TTTCCCTTGAAACAAAATTTTGTCTCCCTTGAGACAG
Found at i:195402 original size:204 final size:203
Alignment explanation
Indices: 195052--195510 Score: 675
Period size: 204 Copynumber: 2.2 Consensus size: 203
195042 CTTGAGACAG
*
195052 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTTTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
* * * *
195117 TGAGACAGTTTCTCTTGAAACATAAACATTGAAAACATTTCCCTTGAAATGAGTTTGGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
* * **
195182 TGAGATAGTTTCCCTTGAAACAAAATTTTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAACA
131 TGAGATAATTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACATAAACA
195247 TTGGAAACA
195 TTGGAAACA
** * *
195256 TTTCCCTTGAAATGAATTTTGTCTCTCTTGAGATAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
195321 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
66 TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
* *
195386 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAAACC
131 TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACA-TAAACA
* ***
195451 TTTGAGATTG
195 TTGGA-AACA
* * * * *
195461 TTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACA
1 TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
195511 CAAAATCTTT
Statistics
Matches: 227, Mismatches: 26, Indels: 3
0.89 0.10 0.01
Matches are distributed among these distances:
203 34 0.15
204 149 0.66
205 44 0.19
ACGTcount: A:0.30, C:0.22, G:0.13, T:0.36
Consensus pattern (203 bp):
TTTCCCTTGAAACAAACTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATTTTGTCTCCCT
TGAGACAGTTTCTCCTGAAACATAAACATTGAAAACATTTCCCTAGAAATGAATTTCGTCTCTCT
TGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACATAAACAT
TGGAAACA
Found at i:195412 original size:36 final size:36
Alignment explanation
Indices: 195357--195443 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 36
195347 CATTGAAAAC
* ** * *
195357 ATTTCCCTAGAAATGAATTTCGTCTCTCTTGAGATA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
*
195393 ATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACA
1 ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
* *
195429 ACTTCTCTTGAAACA
1 ATTTCCCTTGAAACA
195444 CAAAACCTTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
36 43 1.00
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (36 bp):
ATTTCCCTTGAAACAAATTTCGTCTCCCTTGAGACA
Found at i:195534 original size:67 final size:67
Alignment explanation
Indices: 195385--195543 Score: 214
Period size: 67 Copynumber: 2.4 Consensus size: 67
195375 TTCGTCTCTC
** *
195385 TTGAGATAATTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAACTTCTCTTGAAACACAAAAC
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
195450 CT
66 CT
* ** *
195452 TTGAGATTGTTTCCCTCGAAACAAATTTTGTCTCCCATGAGACAGTTTCTCTTGAAACACAAAAT
1 TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
195517 CT
66 CT
*
195519 TTGA-ATT-TATCTCCCTTAAAACAAA
1 TTGAGATTGT-T-TCCCTTGAAACAAA
195544 ATTTCGTTTC
Statistics
Matches: 81, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
65 1 0.01
66 4 0.05
67 76 0.94
ACGTcount: A:0.33, C:0.23, G:0.11, T:0.34
Consensus pattern (67 bp):
TTGAGATTGTTTCCCTTGAAACAAATTTTGTCTCCCATGAGACAACTTCTCTTGAAACACAAAAC
CT
Found at i:196748 original size:105 final size:105
Alignment explanation
Indices: 196376--197348 Score: 1419
Period size: 105 Copynumber: 9.3 Consensus size: 105
196366 GCCATCCGCG
* * * * * *
196376 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* * *
196441 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCTCAGAGCCA
196485 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * *
196550 ACCGCTGGTTGTCAATAAACAATTTTTCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAA-CAACAA-CTTCCCAATCTCAGAGCCA
*
196592 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
196657 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
196697 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
196762 ACCGCTGGTTGTCAACAACAACTTCCCAACCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
196802 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
196867 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
196907 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
196972 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* *
197007 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
197072 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* **
197112 ATTTCAACTTCACAATGAAATATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * **
197177 ACCGCTGCTTGTCAACAA-AA-TT-TC-AT-TCAGATTCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
* * *
197212 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
197277 ACGGCTGGTTGTCAACAAATAATTTCCCGGT-TCCAGAGCCA
66 ACCGCTGGTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCA
* *
197318 ATTTCAACTTCACGACGGAGGATATTGGACT
1 ATTTCAACTTCACAACGAAGGATATTGGACT
197349 TAGAACAATG
Statistics
Matches: 796, Mismatches: 55, Indels: 29
0.90 0.06 0.03
Matches are distributed among these distances:
100 168 0.21
101 8 0.01
102 6 0.01
103 7 0.01
104 7 0.01
105 387 0.49
106 93 0.12
107 98 0.12
109 22 0.03
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
Found at i:197110 original size:205 final size:209
Alignment explanation
Indices: 196376--197348 Score: 1426
Period size: 205 Copynumber: 4.7 Consensus size: 209
196366 GCCATCCGCG
* * * * *
196376 ATTTCAACTCCAC-GACGGAGGATATCGTGGCACTCAAGACAACACAAGTTCAACTTCACAACGA
1 ATTTCAACTTCACAG-CGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGA
* * *
196440 AGGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAG
62 AGGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAG
* *
196505 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAAC
126 GATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAA-CAAC
*
196570 AATTTTTCCAATTTCAGAGCCA
190 AA-TTTT-CAACTTCAGAGCCA
196592 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
196657 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
* *
196722 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAACAACTTC
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAA-TTT
* *
196787 CCAACCTCAGAGCCA
195 TCAACTTCAGAGCCA
* * *
196802 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCATGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
196867 ACCGCTGCTTGTCAACAACAACTTTCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
196932 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTT
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTT
196995 C-A-TTCAGAGCCA
196 CAACTTCAGAGCCA
*
197007 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * **
197072 ACCGCTGTTTGTCAACAACAACTTCCCAATCCCAGAGCCAATTTCAACTTCACAATGAAATATAT
66 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
197137 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAA-AA-TTT
131 TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTT
**
197200 C-A-TTCAGATTCA
196 CAACTTCAGAGCCA
* * * *
197212 ATTTCAACTTCACAACGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGG
1 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* * * ** * *
197277 ACGGCTGGTTGTCAACAAATAATTTCCCGGT-TCCAGAGCCAATTTCAACTTCACGACGGAGGAT
66 ACCGCTGGTTGTCAAC-AACAACTTCCCAATCT-CAGAGCCAATTTCAACTTCACAACGAAGGAT
197341 ATTGGACT
129 ATTGGACT
197349 TAGAACAATG
Statistics
Matches: 704, Mismatches: 50, Indels: 16
0.91 0.06 0.02
Matches are distributed among these distances:
205 278 0.39
206 45 0.06
207 2 0.00
209 2 0.00
210 194 0.28
211 7 0.01
212 102 0.14
213 49 0.07
214 3 0.00
216 21 0.03
217 1 0.00
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.22
Consensus pattern (209 bp):
ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGATAT
TGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGCTTGTCAACAACAATTTT
CAACTTCAGAGCCA
Found at i:198384 original size:18 final size:17
Alignment explanation
Indices: 198345--198387 Score: 61
Period size: 18 Copynumber: 2.5 Consensus size: 17
198335 ATTATATGGA
198345 TATT-TTATTCATTTAT
1 TATTATTATTCATTTAT
*
198361 TTTTATTATTCATGTTAT
1 TATTATTATTCAT-TTAT
198379 TATTATTAT
1 TATTATTAT
198388 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 3 0.13
17 8 0.35
18 12 0.52
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (17 bp):
TATTATTATTCATTTAT
Found at i:198713 original size:21 final size:21
Alignment explanation
Indices: 198660--198714 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
198650 TTTTATATAT
* * *
198660 TTATATTATTTTTTATTATTT
1 TTATATTATTATTCATTATTA
* * *
198681 TTGTTTTTTTATTCATTATTA
1 TTATATTATTATTCATTATTA
198702 TTATATTATTATT
1 TTATATTATTATT
198715 TTTAAAAAAA
Statistics
Matches: 25, Mismatches: 9, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.02, G:0.02, T:0.73
Consensus pattern (21 bp):
TTATATTATTATTCATTATTA
Found at i:206425 original size:17 final size:17
Alignment explanation
Indices: 206393--206426 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
206383 TAATTTTAAC
* *
206393 TTATTATTATTTAAAAT
1 TTATTATTAATAAAAAT
206410 TTATTATTAATAAAAAT
1 TTATTATTAATAAAAAT
206427 ATGAAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TTATTATTAATAAAAAT
Found at i:209747 original size:31 final size:31
Alignment explanation
Indices: 209703--209773 Score: 115
Period size: 31 Copynumber: 2.3 Consensus size: 31
209693 TAAAAAAACA
209703 TAAGATATGGTCACTTTCGTTTTTATTAAAT
1 TAAGATATGGTCACTTTCGTTTTTATTAAAT
* * *
209734 TAATATATTGTCACTTTCGTTTTTATTTAAT
1 TAAGATATGGTCACTTTCGTTTTTATTAAAT
209765 TAAGATATG
1 TAAGATATG
209774 ATCATCACAT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.30, C:0.08, G:0.11, T:0.51
Consensus pattern (31 bp):
TAAGATATGGTCACTTTCGTTTTTATTAAAT
Found at i:209946 original size:21 final size:23
Alignment explanation
Indices: 209895--209946 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
209885 TAAATAAATT
209895 TTAACATAAAATATATATTTTAAA
1 TTAA-ATAAAATATATATTTTAAA
*
209919 TGAAAATAAAA-ATAT-TTTTAAA
1 T-TAAATAAAATATATATTTTAAA
209941 TTAAAT
1 TTAAAT
209947 TATTAATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
21 4 0.16
22 8 0.32
23 4 0.16
24 7 0.28
25 2 0.08
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (23 bp):
TTAAATAAAATATATATTTTAAA
Found at i:209982 original size:25 final size:25
Alignment explanation
Indices: 209902--209982 Score: 69
Period size: 27 Copynumber: 3.2 Consensus size: 25
209892 ATTTTAACAT
* *
209902 AAAATATATATTT--TAAATGAA-A
1 AAAAAATATATTTAATAAATTAATA
* *
209924 ATAAAAATATTTTTAAATTAAATTATTA
1 A-AAAAATATATTT-AA-TAAATTAATA
*
209952 ATAAAATATATTTAATAAATTAATA
1 AAAAAATATATTTAATAAATTAATA
209977 AAAAAA
1 AAAAAA
209983 ATCTTAAACC
Statistics
Matches: 45, Mismatches: 8, Indels: 9
0.73 0.13 0.15
Matches are distributed among these distances:
22 1 0.02
23 10 0.22
25 14 0.31
26 2 0.04
27 16 0.36
28 2 0.04
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.38
Consensus pattern (25 bp):
AAAAAATATATTTAATAAATTAATA
Found at i:212332 original size:49 final size:50
Alignment explanation
Indices: 212255--212366 Score: 156
Period size: 49 Copynumber: 2.3 Consensus size: 50
212245 TTTTTAAGAT
* **
212255 ATAATAA-ATATTAAATATTAAATTTAAATTTAATTATAT-TATTTTATC
1 ATAATAACATAATAAATATTAAATTTAAATCCAATTATATATATTTTATC
* * *
212303 ATAATAACATAATAAATTTTAATTTTAAATCCAATTATATATTTTTTATC
1 ATAATAACATAATAAATATTAAATTTAAATCCAATTATATATATTTTATC
212353 ATAATAACATAATA
1 ATAATAACATAATA
212367 GTTTGAAGGT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
48 7 0.12
49 27 0.48
50 22 0.39
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.46
Consensus pattern (50 bp):
ATAATAACATAATAAATATTAAATTTAAATCCAATTATATATATTTTATC
Found at i:214824 original size:39 final size:40
Alignment explanation
Indices: 214770--214850 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
214760 TTCTACCCAA
214770 TGTATATTTATGAGAATGC-AGACACATGAGTCAGACGAG
1 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
214809 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
1 TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
214849 TG
1 TG
214851 AGCACAATAA
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
39 19 0.46
40 22 0.54
ACGTcount: A:0.36, C:0.12, G:0.26, T:0.26
Consensus pattern (40 bp):
TGTATATTTATGAGAATGCAAGACACATGAGTCAGACGAG
Found at i:216471 original size:19 final size:20
Alignment explanation
Indices: 216447--216491 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
216437 AAAATAATTA
* *
216447 AATTTC-ACATTCTAACATC
1 AATTTCAACACTCAAACATC
*
216466 AATTTCAACACTCAAACATT
1 AATTTCAACACTCAAACATC
216486 AATTTC
1 AATTTC
216492 CAAAATAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (20 bp):
AATTTCAACACTCAAACATC
Found at i:222622 original size:15 final size:15
Alignment explanation
Indices: 222604--222633 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
222594 ACTAAAAAAA
*
222604 GTAAAAAGCTACTTT
1 GTAAAAAGATACTTT
222619 GTAAAAAGATACTTT
1 GTAAAAAGATACTTT
222634 AATATGTTTC
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:0.43, C:0.10, G:0.13, T:0.33
Consensus pattern (15 bp):
GTAAAAAGATACTTT
Found at i:223852 original size:17 final size:19
Alignment explanation
Indices: 223830--223870 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
223820 TATTTTATTT
223830 ATTTAAA-A-ATAAATATA
1 ATTTAAATATATAAATATA
*
223847 ATTTAAATATATTAATATA
1 ATTTAAATATATAAATATA
223866 ATTTA
1 ATTTA
223871 TTACTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 1 0.05
19 13 0.62
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTTAAATATATAAATATA
Found at i:223883 original size:15 final size:14
Alignment explanation
Indices: 223863--223972 Score: 83
Period size: 15 Copynumber: 8.1 Consensus size: 14
223853 ATATATTAAT
223863 ATAATTTATTACTTA
1 ATAATTTATTA-TTA
*
223878 ATAATTTAATATTA
1 ATAATTTATTATTA
* * *
223892 A-CA-TCATTA-AA
1 ATAATTTATTATTA
223903 ATAATTTATTATTTA
1 ATAATTTATTA-TTA
*
223918 CTAATTTATT-TTA
1 ATAATTTATTATTA
223931 ATAA-TTATT-TTA
1 ATAATTTATTATTA
223943 A-ATATTTATTACTTA
1 ATA-ATTTATTA-TTA
223958 ATAATTTATT-TTA
1 ATAATTTATTATTA
223971 AT
1 AT
223973 TTATTATAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
11 3 0.04
12 15 0.20
13 22 0.29
14 4 0.05
15 31 0.41
16 1 0.01
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.54
Consensus pattern (14 bp):
ATAATTTATTATTA
Found at i:223938 original size:12 final size:12
Alignment explanation
Indices: 223910--223972 Score: 56
Period size: 13 Copynumber: 4.9 Consensus size: 12
223900 AAAATAATTT
*
223910 ATTA-TTTACTA
1 ATTATTTTAATA
223921 ATTTATTTTAATA
1 A-TTATTTTAATA
223934 ATTATTTTAAATA
1 ATTATTTT-AATA
*
223947 TTTATTACTTAATA
1 ATTATT--TTAATA
223961 ATTTATTTTAAT
1 A-TTATTTTAAT
223973 TTATTATAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
11 1 0.02
12 10 0.23
13 21 0.49
14 4 0.09
15 7 0.16
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (12 bp):
ATTATTTTAATA
Found at i:223972 original size:40 final size:40
Alignment explanation
Indices: 223857--223972 Score: 137
Period size: 40 Copynumber: 2.9 Consensus size: 40
223847 ATTTAAATAT
* * *
223857 ATTAATATAATTTATTACTTAATAATTTAATATTAA-CATC
1 ATTAAAATAATTTATTACTTAATAATTT-ATTTTAATAATC
* * *
223897 ATTAAAATAATTTATTATTTACTAATTTATTTTAATAATT
1 ATTAAAATAATTTATTACTTAATAATTTATTTTAATAATC
*
223937 ATTTTAAAT-ATTTATTACTTAATAATTTATTTTAAT
1 A-TTAAAATAATTTATTACTTAATAATTTATTTTAAT
223973 TTATTATAAT
Statistics
Matches: 65, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
39 6 0.09
40 53 0.82
41 6 0.09
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.53
Consensus pattern (40 bp):
ATTAAAATAATTTATTACTTAATAATTTATTTTAATAATC
Found at i:223974 original size:25 final size:23
Alignment explanation
Indices: 223910--223979 Score: 70
Period size: 25 Copynumber: 2.8 Consensus size: 23
223900 AAAATAATTT
223910 ATTATTTACTAATTTATT-TTAATA
1 ATTATTT--TAATTTATTATTAATA
223934 ATTATTTTAAATATTTATTACTTAATA
1 ATTATTTT--A-ATTTATTA-TTAATA
223961 ATTTATTTTAATTTATTAT
1 A-TTATTTTAATTTATTAT
223980 AATTTAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 12
0.77 0.00 0.23
Matches are distributed among these distances:
22 1 0.03
24 9 0.22
25 15 0.38
26 1 0.03
27 7 0.17
28 7 0.17
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTATTTTAATTTATTATTAATA
Found at i:223986 original size:28 final size:27
Alignment explanation
Indices: 223927--223986 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
223917 ACTAATTTAT
*
223927 TTTAATAATTATTTTAAATATTTATTA
1 TTTAATAATTATTTTAAATATTTATAA
* *
223954 CTTAATAATTTATTTT-AATTTATTATAA
1 TTTAATAA-TTATTTTAAATAT-TTATAA
223982 TTTAA
1 TTTAA
223987 ATGATATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTAATAATTATTTTAAATATTTATAA
Found at i:224614 original size:29 final size:29
Alignment explanation
Indices: 224565--224620 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
224555 TGATACTAAA
*
224565 TGAAATAAAAACTAAACTTTAGGTATTTT
1 TGAAATAAAAACTAAACTTTAGATATTTT
* *
224594 TGAAA-AAAAATTAAAAGTTTAGATATT
1 TGAAATAAAAACT-AAACTTTAGATATT
224621 AAAACCAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
28 6 0.26
29 17 0.74
ACGTcount: A:0.50, C:0.04, G:0.11, T:0.36
Consensus pattern (29 bp):
TGAAATAAAAACTAAACTTTAGATATTTT
Found at i:225311 original size:81 final size:80
Alignment explanation
Indices: 225142--225311 Score: 200
Period size: 81 Copynumber: 2.1 Consensus size: 80
225132 AATTTGAAAC
* ** * *
225142 ATATTTAATAGTTATATAACTCAACAAAATGTCACACTATACTCAAGAGACTATTTATATACTTT
1 ATATTTAATAATTATATAACTCAACAAAACCTCACAATATACTCAAGAGACTATTTATATACTTC
225207 ACGCTAAAATTTTGT
66 ACGCTAAAATTTTGT
* * * **
225222 AAATTTTAATAATTGATA-GACTCAACAAAACCTCACAATATAGTCAAGAGGTTATTTATATACT
1 ATA-TTTAATAATT-ATATAACTCAACAAAACCTCACAATATACTCAAGAGACTATTTATATACT
225286 TCAC-CTAAAATTTATTGT
64 TCACGCTAAAA-TT-TTGT
225304 ATATTTAA
1 ATATTTAA
225312 ATGTTTTAAT
Statistics
Matches: 75, Mismatches: 11, Indels: 7
0.81 0.12 0.08
Matches are distributed among these distances:
80 8 0.11
81 58 0.77
82 9 0.12
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.37
Consensus pattern (80 bp):
ATATTTAATAATTATATAACTCAACAAAACCTCACAATATACTCAAGAGACTATTTATATACTTC
ACGCTAAAATTTTGT
Done.