Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008935.1 Hibiscus syriacus cultivar Beakdansim tig00112253_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: 1775090
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 9
Found at i:728 original size:23 final size:23
Alignment explanation
Indices: 700--745 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
690 CAAAATCCGT
*
700 GTATTGACCAATATCAAAGTTCG
1 GTATTGACCAAGATCAAAGTTCG
*
723 GTATTGACCAAGATCAAATTTCG
1 GTATTGACCAAGATCAAAGTTCG
746 AATACTGACT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.30
Consensus pattern (23 bp):
GTATTGACCAAGATCAAAGTTCG
Found at i:1823 original size:20 final size:20
Alignment explanation
Indices: 1788--1825 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1778 ATTCATTTGA
*
1788 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
*
1808 CTATCGCAATGAGAAAAT
1 CTATCGCAACGAGAAAAT
1826 CGCAATGCGA
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:0.39, C:0.21, G:0.21, T:0.18
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:1891 original size:19 final size:19
Alignment explanation
Indices: 1863--1910 Score: 71
Period size: 19 Copynumber: 2.6 Consensus size: 19
1853 GATTTTCTCG
1863 TTGCGA-TTTCATTTCACA
1 TTGCGATTTTCATTTCACA
*
1881 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCACA
*
1900 TTACGATTTTC
1 TTGCGATTTTC
1911 TCGTTGCGAT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
18 6 0.22
19 21 0.78
ACGTcount: A:0.19, C:0.21, G:0.12, T:0.48
Consensus pattern (19 bp):
TTGCGATTTTCATTTCACA
Found at i:3950 original size:20 final size:19
Alignment explanation
Indices: 3915--3980 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
3905 GAAACTTAAA
3915 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
3934 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* * *
3954 ATCACAATGCGAAATGA-A
1 ATCGCAACGCGAAATGACT
3972 ATCGCAACG
1 ATCGCAACG
3981 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
18 7 0.18
19 16 0.41
20 16 0.41
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:3989 original size:14 final size:14
Alignment explanation
Indices: 3970--4026 Score: 69
Period size: 14 Copynumber: 3.8 Consensus size: 14
3960 ATGCGAAATG
3970 AAATCGCAACGACA
1 AAATCGCAACGACA
*
3984 AAATCGCAACGCGAAA
1 AAATCGCAA--CGACA
4000 TGAAATCGCAACGACA
1 --AAATCGCAACGACA
4016 AAATCGCAACG
1 AAATCGCAACG
4027 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:4003 original size:32 final size:32
Alignment explanation
Indices: 3962--4031 Score: 140
Period size: 32 Copynumber: 2.2 Consensus size: 32
3952 CTATCACAAT
3962 GCGAAATGAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAATCGCAACGACAAAATCGCAAC
3994 GCGAAATGAAATCGCAACGACAAAATCGCAAC
1 GCGAAATGAAATCGCAACGACAAAATCGCAAC
4026 GCGAAA
1 GCGAAA
4032 CACAAATCGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.47, C:0.24, G:0.20, T:0.09
Consensus pattern (32 bp):
GCGAAATGAAATCGCAACGACAAAATCGCAAC
Found at i:4164 original size:20 final size:19
Alignment explanation
Indices: 4114--4167 Score: 72
Period size: 19 Copynumber: 2.8 Consensus size: 19
4104 TTGCGATTTT
*
4114 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
4133 CATTTCGCGTTGCGATAGT
1 CATTTCGCGTTGCGATAGC
*
4152 CATTTTCGTGTTGCGA
1 CA-TTTCGCGTTGCGA
4168 AAGTAAACTA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
19 19 0.61
20 12 0.39
ACGTcount: A:0.17, C:0.22, G:0.24, T:0.37
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:4674 original size:18 final size:18
Alignment explanation
Indices: 4648--4692 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
4638 GTCGATCAGA
*
4648 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
4666 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
4684 TGATGGCTC
1 TGATGGCTC
4693 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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:6032 original size:20 final size:20
Alignment explanation
Indices: 6007--6049 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
5997 AATAGTTTCT
6007 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
*
6027 GAAAATGAAAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
6047 GAA
1 GAA
6050 TTCGACTATC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.53, C:0.19, G:0.19, T:0.09
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:6341 original size:22 final size:22
Alignment explanation
Indices: 6314--6357 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
6304 GATGGAGATA
6314 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
6336 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
6358 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:6571 original size:20 final size:20
Alignment explanation
Indices: 6545--6617 Score: 119
Period size: 20 Copynumber: 3.6 Consensus size: 20
6535 GATTATGTAT
6545 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6565 AATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
6585 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
*
6605 TATCTCGTTGCGA
1 TATCGCGTTGCGA
6618 TTTTTTATTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:6648 original size:41 final size:41
Alignment explanation
Indices: 6525--6662 Score: 107
Period size: 41 Copynumber: 3.4 Consensus size: 41
6515 CGCTTTGAAA
* * * * * *
6525 ATCGCATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATTTTTTATTATCGCATTACGAAAGTAAGT
* *** * * * *
6566 ATCGCGTTGCGA-AAGTCAGTATCGCGTTGCGAAAGTAAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTACGAAAGTAAGT
* * * *
6606 ATCTCGTTGCGATTTTTTATTATCGCATTACGATAGTCAGT
1 ATCGCATTGCGATTTTTTATTATCGCATTACGAAAGTAAGT
6647 ATCGCATTGCGATTTT
1 ATCGCATTGCGATTTT
6663 CCCAATTCGC
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
40 32 0.42
41 44 0.58
ACGTcount: A:0.25, C:0.17, G:0.23, T:0.35
Consensus pattern (41 bp):
ATCGCATTGCGATTTTTTATTATCGCATTACGAAAGTAAGT
Found at i:6677 original size:21 final size:21
Alignment explanation
Indices: 6648--6740 Score: 100
Period size: 20 Copynumber: 4.5 Consensus size: 21
6638 ATAGTCAGTA
6648 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6669 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6689 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
6710 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
6730 TCGCATTGCGA
1 TCGCATTGCGA
6741 ATTGGGAAAA
Statistics
Matches: 58, Mismatches: 13, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
20 32 0.55
21 26 0.45
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:6693 original size:41 final size:41
Alignment explanation
Indices: 6648--6740 Score: 186
Period size: 41 Copynumber: 2.3 Consensus size: 41
6638 ATAGTCAGTA
6648 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
6689 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
6730 TCGCATTGCGA
1 TCGCATTGCGA
6741 ATTGGGAAAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 52 1.00
ACGTcount: A:0.17, C:0.25, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:9642 original size:124 final size:123
Alignment explanation
Indices: 9240--9651 Score: 447
Period size: 124 Copynumber: 3.3 Consensus size: 123
9230 TCAATCTTTC
* * * * *
9240 CTCTGAAAGACGCTAAGTCATAACTTGGGGTGATCCACTCATTTTGCTGAAGGATGCTGAATCTG
1 CTCTGAAGGACGCTAAGTCGTAATTTGGGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTG
* * * * *
9305 GTGAAGATCTCAC-CATTT-TCTCTGAAAGATACTGAGTGGTGGAGCGATCTTACTCATT
66 GTGAAAATCTCACTC-TTTCT-TCTGAAAGACATTGAGTCGTGGAACGATCTTACTCATT
* ** * ** * * *
9363 CATCTAAAGGATTCTAAGTCGTTATTCAGGATGATCCAATCCTTTTGCTGAAGGATGTTGAATTT
1 C-TCTGAAGGACGCTAAGTCGTAATTTGGGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCT
* *
9428 GGTGACAATCTCACTCTTTACTT-T-AAAGGACGTTGAGTCGTGGAACGATCTTACTTC-TT
65 GGTGAAAATCTCACTCTTT-CTTCTGAAA-GACATTGAGTCGTGGAACGATCTTAC-TCATT
* * * *
9487 CCTCTGAAGGATGCTAAGTTGTAATTTGGGGTGATCCACTCCTTTTGCTAAAGGATGTTGGATCT
1 -CTCTGAAGGACGCTAAGTCGTAATTTGGGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCT
* * *
9552 GGTGAAAATATCACTCTTTCTTCTGAAAGACATTGAGTCATGGAACAATCTTACTCATT
65 GGTGAAAATCTCACTCTTTCTTCTGAAAGACATTGAGTCGTGGAACGATCTTACTCATT
* *
9611 CTCTGAAGGACCCTAAGTCGTAATTTGGGGGTAATCCACTC
1 CTCTGAAGGACGCTAAGTCGTAATTT-GGGGTGATCCACTC
9652 TTGAGATGGG
Statistics
Matches: 237, Mismatches: 41, Indels: 21
0.79 0.14 0.07
Matches are distributed among these distances:
123 32 0.14
124 196 0.83
125 8 0.03
126 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.22, T:0.33
Consensus pattern (123 bp):
CTCTGAAGGACGCTAAGTCGTAATTTGGGGTGATCCACTCCTTTTGCTGAAGGATGTTGAATCTG
GTGAAAATCTCACTCTTTCTTCTGAAAGACATTGAGTCGTGGAACGATCTTACTCATT
Found at i:9782 original size:26 final size:27
Alignment explanation
Indices: 9732--9782 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
9722 TGTCCTAAAC
*
9732 ATGATCTAATGCAATTTGATATGATGA
1 ATGATCTAATGCAATTTAATATGATGA
* *
9759 ATGATC-AATGCATTTTAATGTGAT
1 ATGATCTAATGCAATTTAATATGAT
9783 TTAATCTAGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.35, C:0.08, G:0.18, T:0.39
Consensus pattern (27 bp):
ATGATCTAATGCAATTTAATATGATGA
Found at i:16911 original size:23 final size:23
Alignment explanation
Indices: 16885--16933 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
16875 ATAAAGAACC
*
16885 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
16908 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
16931 AAA
1 AAA
16934 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:22503 original size:23 final size:23
Alignment explanation
Indices: 22477--22525 Score: 64
Period size: 23 Copynumber: 2.1 Consensus size: 23
22467 ATAAAGAACC
*
22477 AAAATAAACT-TAAATATACCATT
1 AAAATAAACTCTAAACAT-CCATT
*
22500 AAAATAAAGTCTAAACATCCATT
1 AAAATAAACTCTAAACATCCATT
22523 AAA
1 AAA
22526 CAAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
23 17 0.74
24 6 0.26
ACGTcount: A:0.57, C:0.14, G:0.02, T:0.27
Consensus pattern (23 bp):
AAAATAAACTCTAAACATCCATT
Found at i:29220 original size:23 final size:23
Alignment explanation
Indices: 29184--29230 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 23
29174 CTTCTTCCTA
*
29184 TTTTCTTTTGTTTCTTCATTTTTT
1 TTTTCATTTGTTTCTT-ATTTTTT
*
29208 TTTTCATTT-TTTCTTGTTTTTT
1 TTTTCATTTGTTTCTTATTTTTT
29230 T
1 T
29231 CGATTTTTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 6 0.29
24 8 0.38
ACGTcount: A:0.04, C:0.11, G:0.04, T:0.81
Consensus pattern (23 bp):
TTTTCATTTGTTTCTTATTTTTT
Found at i:29227 original size:19 final size:19
Alignment explanation
Indices: 29205--29246 Score: 68
Period size: 19 Copynumber: 2.2 Consensus size: 19
29195 TTCTTCATTT
29205 TTTTTTTC-ATTTTTTCTTG
1 TTTTTTTCGATTTTTTC-TG
29224 TTTTTTTCGATTTTTTCTG
1 TTTTTTTCGATTTTTTCTG
29243 TTTT
1 TTTT
29247 CTCTCCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.05, C:0.10, G:0.07, T:0.79
Consensus pattern (19 bp):
TTTTTTTCGATTTTTTCTG
Found at i:29229 original size:20 final size:20
Alignment explanation
Indices: 29204--29246 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
29194 TTTCTTCATT
29204 TTTTTTTTC-ATTTTTTCT-
1 TTTTTTTTCGATTTTTTCTG
29222 TGTTTTTTTCGATTTTTTCTG
1 T-TTTTTTTCGATTTTTTCTG
29243 TTTT
1 TTTT
29247 CTCTCCCATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 1 0.05
19 8 0.36
20 12 0.55
21 1 0.05
ACGTcount: A:0.05, C:0.09, G:0.07, T:0.79
Consensus pattern (20 bp):
TTTTTTTTCGATTTTTTCTG
Found at i:34577 original size:23 final size:23
Alignment explanation
Indices: 34547--34628 Score: 85
Period size: 23 Copynumber: 3.6 Consensus size: 23
34537 TCATAAAATG
* *
34547 CACCGAAGTGCTACGTAGATTTA
1 CACCGAAGTGCCACATAGATTTA
*
34570 CACCGAAGTGCCACATAGATTTG
1 CACCGAAGTGCCACATAGATTTA
* * *
34593 CACCAAAGTGCCGCATAGAAATT-
1 CACCGAAGTGCCACATAG-ATTTA
*
34616 CACCGGAGTGCCA
1 CACCGAAGTGCCA
34629 TATAAGATGT
Statistics
Matches: 49, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 46 0.94
24 3 0.06
ACGTcount: A:0.32, C:0.27, G:0.22, T:0.20
Consensus pattern (23 bp):
CACCGAAGTGCCACATAGATTTA
Found at i:35433 original size:99 final size:99
Alignment explanation
Indices: 35308--35512 Score: 356
Period size: 99 Copynumber: 2.1 Consensus size: 99
35298 TCTGTGTACT
* *
35308 GATACACGGGTATCAATACACCCCTGAATGTATCGATACACTATGTAGATATTCTTCAAAATTTG
1 GATACACGGGTATCAATACACACCTGAATGCATCGATACACTATGTAGATATTCTTCAAAATTTG
*
35373 GTCTTAGTGTATCGGTACCTATTCATAGTATACC
66 GTCTTAGTGTATCGGTACCTATTCATAATATACC
* *
35407 GATACACGGGTATCGATACACACCTGAATGCATCGATACACTATGTAGCTATTCTTCAAAATTTG
1 GATACACGGGTATCAATACACACCTGAATGCATCGATACACTATGTAGATATTCTTCAAAATTTG
*
35472 GTCTTAGTGTATCGGTACCTATTCATAATGTACC
66 GTCTTAGTGTATCGGTACCTATTCATAATATACC
35506 GATACAC
1 GATACAC
35513 CCTGCCCAAA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 100 1.00
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.32
Consensus pattern (99 bp):
GATACACGGGTATCAATACACACCTGAATGCATCGATACACTATGTAGATATTCTTCAAAATTTG
GTCTTAGTGTATCGGTACCTATTCATAATATACC
Found at i:51524 original size:29 final size:29
Alignment explanation
Indices: 51482--51556 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
51472 AACCCAACCA
**
51482 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
51511 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
51540 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
51557 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:51562 original size:29 final size:29
Alignment explanation
Indices: 51483--51570 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
51473 ACCCAACCAT
* * ****
51483 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
51512 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
51541 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
51570 A
1 A
51571 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:51812 original size:29 final size:29
Alignment explanation
Indices: 51777--51863 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
51767 GTTGGCTGGT
*
51777 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
51806 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
51835 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
51864 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:52683 original size:29 final size:29
Alignment explanation
Indices: 52641--52715 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
52631 AACCCAACCA
**
52641 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
52670 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
52699 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
52716 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:52721 original size:29 final size:29
Alignment explanation
Indices: 52642--52729 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
52632 ACCCAACCAT
* * ****
52642 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
52671 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
52700 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
52729 A
1 A
52730 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:52959 original size:10 final size:10
Alignment explanation
Indices: 52946--53003 Score: 55
Period size: 10 Copynumber: 5.6 Consensus size: 10
52936 CAGGGCATGG
52946 ATGGGCGTGC
1 ATGGGCGTGC
52956 ATGGGCGTGCTCC
1 ATGGGCGTG---C
* * *
52969 TTTGGCGAG-
1 ATGGGCGTGC
52978 ATGGGCGTGC
1 ATGGGCGTGC
52988 ATGGGCGTGC
1 ATGGGCGTGC
52998 ATGGGC
1 ATGGGC
53004 ATGGAGGTCG
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
9 6 0.16
10 25 0.66
13 7 0.18
ACGTcount: A:0.10, C:0.21, G:0.47, T:0.22
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:53058 original size:29 final size:29
Alignment explanation
Indices: 53023--53109 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
53013 GTTGGCTGGT
*
53023 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
53052 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
53081 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
53110 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:54481 original size:18 final size:16
Alignment explanation
Indices: 54440--54495 Score: 85
Period size: 16 Copynumber: 3.4 Consensus size: 16
54430 ATGTTTCAGA
54440 TTCAGATTTCAATTCC
1 TTCAGATTTCAATTCC
54456 TTCAGATTTCAATTCC
1 TTCAGATTTCAATTCC
54472 TTCACAGATTTCAATTCC
1 TT--CAGATTTCAATTCC
*
54490 ATCAGA
1 TTCAGA
54496 AACATTCCAA
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
16 22 0.59
18 15 0.41
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.39
Consensus pattern (16 bp):
TTCAGATTTCAATTCC
Found at i:64685 original size:22 final size:20
Alignment explanation
Indices: 64634--64704 Score: 63
Period size: 19 Copynumber: 3.5 Consensus size: 20
64624 TGCAAAAATG
* *
64634 GTATTGATACCATAATAGG-
1 GTATCGATACCATAGTAGGA
* *
64653 GTATAGGTACCATAGTATGGTA
1 GTATCGATACCATAGTA-GG-A
* *
64675 GTATCGATACCATGGTAGGG
1 GTATCGATACCATAGTAGGA
64695 GTATCGATAC
1 GTATCGATAC
64705 TGAGGAGCCA
Statistics
Matches: 42, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
19 14 0.33
20 12 0.29
21 2 0.05
22 14 0.33
ACGTcount: A:0.31, C:0.13, G:0.27, T:0.30
Consensus pattern (20 bp):
GTATCGATACCATAGTAGGA
Found at i:65163 original size:45 final size:45
Alignment explanation
Indices: 65108--65422 Score: 486
Period size: 45 Copynumber: 7.0 Consensus size: 45
65098 AATGAATAAA
*
65108 CAAAATAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* *
65153 CAAAAGAATAATTCATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
** * *
65198 CAAAAGAATAATGCATATATGTGCATTATGGGCATAAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* *
65243 CAAAAGAATAATGTATATGGGTGCATTATCGGCATGAAAGGATGC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
*
65288 CAAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGA
1 C-AAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* *
65334 CAAAAGAATAATGTATATGGGTGCATTATTGGCATGAAAGGATTC
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
* * *
65379 TAAAAGAATAATGCATATAGGTGCATTATTGGTATGAAAGGATG
1 CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATG
65423 TCATAGCTGA
Statistics
Matches: 245, Mismatches: 24, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
45 203 0.83
46 42 0.17
ACGTcount: A:0.39, C:0.10, G:0.25, T:0.26
Consensus pattern (45 bp):
CAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGC
Found at i:83149 original size:20 final size:19
Alignment explanation
Indices: 83121--83170 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
83111 TGATTCAATC
* *
83121 AGTAGCGATACTAAAGGGA
1 AGTATCGATACCAAAGGGA
*
83140 GAGTATCGATACCGAAGGGA
1 -AGTATCGATACCAAAGGGA
83160 AGGTATCGATA
1 A-GTATCGATA
83171 ACAGTCAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 1 0.04
20 25 0.96
ACGTcount: A:0.38, C:0.12, G:0.32, T:0.18
Consensus pattern (19 bp):
AGTATCGATACCAAAGGGA
Found at i:83247 original size:22 final size:19
Alignment explanation
Indices: 83195--83265 Score: 81
Period size: 19 Copynumber: 3.6 Consensus size: 19
83185 ATGCAAAAAT
*
83195 GGTATCGATACCATAATAG
1 GGTATCGATACCATAGTAG
83214 GGTATC-AGTACCATAGTATG
1 GGTATCGA-TACCATAGTA-G
*
83234 GTAGTATCGATACCATGGTAG
1 G--GTATCGATACCATAGTAG
83255 GGTATCGATAC
1 GGTATCGATAC
83266 TGAGGAGCCA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 1 0.02
19 25 0.56
20 2 0.04
21 2 0.04
22 14 0.31
23 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.28
Consensus pattern (19 bp):
GGTATCGATACCATAGTAG
Found at i:83758 original size:45 final size:45
Alignment explanation
Indices: 83694--83909 Score: 328
Period size: 45 Copynumber: 4.8 Consensus size: 45
83684 GCATATGGGT
* * *
83694 AAAGGATGCCAAAAGAATAATGCATATGGGTGTATTATAGACATG
1 AAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
83739 AAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
1 AAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
*
83784 AAAAGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
1 AAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
* *
83829 AAAGGATGCCAAAAGAATAATGCACATGGGTGCATTATTGGCATG
1 AAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
* *
83874 AAAGGATGCC-ATAG-CTGAAATGCATATGGGTGCATT
1 AAAGGATGCCAAAAGAAT--AATGCATATGGGTGCATT
83910 TTAAGCATAA
Statistics
Matches: 159, Mismatches: 10, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
43 1 0.01
44 3 0.02
45 155 0.97
ACGTcount: A:0.38, C:0.12, G:0.26, T:0.23
Consensus pattern (45 bp):
AAAGGATGCCAAAAGAATAATGCATATGGGTGCATTATCGGCATG
Found at i:101231 original size:20 final size:20
Alignment explanation
Indices: 101202--101239 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
101192 CCCCTTCAAA
*
101202 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
101222 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
101240 TGTACCAAAA
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:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:117060 original size:22 final size:21
Alignment explanation
Indices: 117018--117057 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
117008 GAGCTTATTT
*
117018 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
117039 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
117058 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:119912 original size:69 final size:70
Alignment explanation
Indices: 119801--119939 Score: 271
Period size: 69 Copynumber: 2.0 Consensus size: 70
119791 GGTCTTATTG
119801 TCATTCTATAAAATTTTCCCTTAAGTTTTAGAGGCACCTTCTTGTCACACAAAACTCCAGTA-AA
1 TCATTCTATAAAATTTTCCCTTAAGTTTTAGAGGCACCTTCTTGTCACACAAAACTCCAGTAGAA
119865 GCCAT
66 GCCAT
119870 TCATTCTATAAAATTTTCCCTTAAGTTTTAGAGGCACCTTCTTGTCACACAAAACTCCAGTAGAA
1 TCATTCTATAAAATTTTCCCTTAAGTTTTAGAGGCACCTTCTTGTCACACAAAACTCCAGTAGAA
119935 GCCAT
66 GCCAT
119940 CCACTTTAGC
Statistics
Matches: 69, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
69 62 0.90
70 7 0.10
ACGTcount: A:0.32, C:0.24, G:0.11, T:0.33
Consensus pattern (70 bp):
TCATTCTATAAAATTTTCCCTTAAGTTTTAGAGGCACCTTCTTGTCACACAAAACTCCAGTAGAA
GCCAT
Found at i:124591 original size:342 final size:342
Alignment explanation
Indices: 123951--124632 Score: 928
Period size: 342 Copynumber: 2.0 Consensus size: 342
123941 ATTGAAAAAT
* **
123951 ATATTTCACATGAATTTAAAATAAAGAATTATAACTATAATAGTATTAAATATGTACTTATATTT
1 ATATTTCACATAAATTTAAAATAAAGAATTATAACTATAATAGTATTAAATATAAACTTATATTT
* **
124016 AACACCCCTTTAAAATTTAAGCCATAAGAATATTAAGTTATTTTCTTCTATTTAAGCGAAAAATC
66 AACACCCCTTTAAAATTTAAGCCATAAGAATATTAAGTTATTTCCTTCTATTTAAGAAAAAAATC
* * *
124081 CAAAGCATGGGCAAACCTAGATTTTCTTTTTTTCTTTAATTTTATTTACATTAGCAAAAAACTCC
131 CAAAGCAAGGGCAAACCTAGATTTTC-TCTTTTCTTTAATTTTATTTACATTAGCAAAAAACACC
*
124146 TATAATAATTTATTTCTAGGAGGACAACAAGCACTAGTGGTCTAGTGGTAGAATAGTACCCTGCC
195 TATAATAATTTATTTCTAGGAGGACAACAAGCACCAGTGGTCTAGTGGTAGAATAGTACCCTGCC
*
124211 ATGATATAGACCCAAGTTTGATTCCCGATTGATGCACCTTTCAAGCAATGAT-GAAAGTTGTATT
260 ATGATACAGACCCAAGTTTGATTCCCGATTGATGCACCTTTCAAGCAATGATAG-AAGTTGTATT
124275 ATAGAAGAATAGGGTTATG
324 ATAGAAGAATAGGGTTATG
* * * *
124294 ATATTTCACATAAATTTAAAATAAA-AATTTTTACTATAATCGTATTAAATCTAAACTTATATTT
1 ATATTTCACATAAATTTAAAATAAAGAATTATAACTATAATAGTATTAAATATAAACTTATATTT
* * * * * * **
124358 AACACTCTCTTTAAATTTTATGTCATATGAATATTTAGTTATTTCCTTCTATTTATTAAAATAAA
66 AACAC-CCCTTTAAAATTTAAGCCATAAGAATATTAAGTTATTTCCTTCTATTTAAGAAAA-AAA
**
124423 TCCAATA-CAAGGGCATTTCCTAGATTTTC-CTTTT-TTTAATTTTATTTACATTAGCAAAAAGA
129 TCCAA-AGCAAGGGCA-AACCTAGATTTTCTCTTTTCTTTAATTTTATTTACATTAGCAAAAA-A
*
124485 -ACCTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGGTCTAGTGGTAGAATAGTACCC
191 CACCTATAATAATTTATTTCTAGGAGGACAACAAGCACCAGTGGTCTAGTGGTAGAATAGTACCC
** *** * *
124549 TGCCATGATACAGACCCGGGTTTGATTTTTG-TCTGGTGCACCTTTGAAGCAATGATAGAAGTTG
256 TGCCATGATACAGACCCAAGTTTGATTCCCGAT-TGATGCACCTTTCAAGCAATGATAGAAGTTG
* *
124613 TATTATAGAATAATGGGGTT
320 TATTATAGAAGAATAGGGTT
124633 GTTCTTCAAA
Statistics
Matches: 297, Mismatches: 35, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
341 1 0.00
342 195 0.66
343 74 0.25
344 15 0.05
345 12 0.04
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.37
Consensus pattern (342 bp):
ATATTTCACATAAATTTAAAATAAAGAATTATAACTATAATAGTATTAAATATAAACTTATATTT
AACACCCCTTTAAAATTTAAGCCATAAGAATATTAAGTTATTTCCTTCTATTTAAGAAAAAAATC
CAAAGCAAGGGCAAACCTAGATTTTCTCTTTTCTTTAATTTTATTTACATTAGCAAAAAACACCT
ATAATAATTTATTTCTAGGAGGACAACAAGCACCAGTGGTCTAGTGGTAGAATAGTACCCTGCCA
TGATACAGACCCAAGTTTGATTCCCGATTGATGCACCTTTCAAGCAATGATAGAAGTTGTATTAT
AGAAGAATAGGGTTATG
Found at i:128672 original size:549 final size:548
Alignment explanation
Indices: 127215--130136 Score: 3285
Period size: 543 Copynumber: 5.3 Consensus size: 548
127205 ACTCGAGTTT
* * * * *
127215 GATTCTTGACTGGTGCACCTTTGAAGCAATGACGAAAGTTGTATTATAGAAGAATAAGGTTCTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATAGGGTTCTTC
* * * * *
127280 ---TTC-AAAATCTAGATGGCAATCAACGA-TTTTACTGAGTTTCAAT-TTTAC-TTTTTTTTGT
66 AAAATCTAAAATCTATATGACAATCAACGACGTTT-CTGAGTTTC-ATGTTTACTTTTTTTTTGG
* * * *
127338 TTCAATGAACTTTTATGTAAAGTTTCATGAAAAGCAATTCAATGCAATTTTCAACCTAATTTAAA
129 TTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTAACCT-ATTTCAA
* ** *
127403 AAATCATCAAGAGTTTAGTATAAATAATAATTTAGTGCAACTTTAGACCATCAAAATTTTTAATA
193 AAACCATCAAGAGTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCATCAAAATTTTTAATA
* *
127468 TTATTGAAAAAGATATTTCACATGAAATTAAAAATAAAAA-TTATAACTATAATCGTATTAAATA
258 TTATTGAAAAATATATTTCACATGATATT-AAAATAAAAATTTATAACTATAATCGTATTAAATA
* * *
127532 CGTACTTATATTTAACACTCACTTT-AAATTTAAGTCATATGAATATTAAGTTACTTCCTTCTTC
322 TGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATAAATATTAAGTTA------T-TTC
** * *
127596 TTCTTCTTATTTTTTTTGAAAAATCCAATGCAAGGGCATTTCCTAGA-TAT-TTTTTT-CTTTAA
380 --CTTC-TA-TTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAA
* * *
127658 TTTTATTTACATTAGCAAAATAACATATAATAATTTATTTCTAGGATGACAACAAGCACTAGTGG
441 TTTTATTTATATTAGCAAAA-AACCTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGG
** *
127723 TCTAGTGGTAGAATAGTA-CCTTCCCATGGTAAAGAGTCAGGTTT
505 TCTAGTGGTAGAATAGTACCCTT-CCATGGTAAAGACCCAGGTTC
* * * ** *
127767 AATTCCCGGCTGGTGCACCTTTGAAGCAATGATGGGAGTTGTATTATAGAAGAATGGGGTTCTCC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATAGGG-T-T-C
* *
127832 TTCAAAATCTAAAATCTATATTACAATCAACGACGTTTCTGAGTTT-ATGTGTACTTAATTATTT
63 TTCAAAATCTAAAATCTATATGACAATCAACGACGTTTCTGAGTTTCA--TGT--TTACTT-TTT
* * *
127896 TTTTGGTTCAATGAACTTTGATGTAAATTTTCGTGAAAAGCAAATCAATGCATTTTTTCAACCTA
123 TTTTGGTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTT-AACCT-
* * * *
127961 ATTTCAAAAACCTTCATGAGTTTAGTATAAATAATAATTTACTGTGACTATGGACCATCAAAATT
186 ATTTCAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCATCAAAATT
*
128026 TTTAATATTATTGAAAAATATATTTCACATGA-ATCTAAAATAAAAATTTATAACTATAATCTTA
251 TTTAATATTATTGAAAAATATATTTCACATGATAT-TAAAATAAAAATTTATAACTATAATCGTA
* ** * *
128090 TTAAATATGAACTTGTATTTAACACGGACTTTAAAATTTATGTCATAAAAATATTAAGTTATTTC
315 TTAAATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATAAATATTAAGTTATTTC
* * *
128155 CGTCTAATAATTC-AAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTAAATTTT
380 CTTCTATTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTT
* * *
128219 ATTTACATTAGCAAAAGAACTTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTTGTCTA
445 ATTTATATTAGCAAAA-AACCTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGGTCTA
* * * ** *
128284 GTGATAGAATAATACCTTTCCATGGTAAAGAGACAGGTTT
509 GTGGTAGAATAGTACCCTTCCATGGTAAAGACCCAGGTTC
* *
128324 GATTCCCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTTTTATAGAAGAATAGGGTTCTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATAGGGTTCTTC
* * *
128389 AAAATCTAAAAT-TGATATGACAATCAATGACTTTTCTGAGCTTCATGTTTACTTTTTTTTTGGT
66 AAAATCTAAAATCT-ATATGACAATCAACGACGTTTCTGAGTTTCATGTTTACTTTTTTTTTGGT
* ** * *
128453 TCAATGAACTTTGATGTAAAGTTTTATGAAAATTAGATCAATGCAATTTTTGACCTGATTTCAAA
130 TCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTAACCT-ATTTCAAA
* * *
128518 AACCATCAAGAGTTTAGTATAAATAATACTTTAGTGTGACTATGGACCATCAAAATTTCTAATAT
194 AACCATCAAGAGTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCATCAAAATTTTTAATAT
* * *
128583 TATTGAAACATATATTTCACATGATCTTAAAATAAAAATTTATAACTATAATTGTATTAAATATG
259 TATTGAAAAATATATTTCACATGATATTAAAATAAAAATTTATAACTATAATCGTATTAAATATG
* * * *
128648 AACTTATATTTATCACTCACTTTAAAATTTAAATCATATAAATATTAAATTATTTCCTTTTATTA
324 AACTTATATTTAACACTCACTTTAAAATTTAAGTCATATAAATATTAAGTTATTTCCTTCTATTA
* *
128713 TTTCGAAAAATCCAATGCAAGGGTATTTCC----TTTT-TTTTTTGCTTTAATTTTATTTATATT
389 ATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTTATTTATATT
* * *
128773 AG--GAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCATCAGTAGTCTAGTGGT--AAT
454 AGCAAAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGGTCTAGTGGTAGAAT
* * *
128834 AATACCCTGCCATGGTACAA-ACCCGGGTTC
519 AGTACCCTTCCATGGTA-AAGACCCAGGTTC
* * * * * * * * *
128864 GATTTTTGACTGGTGAACCTTTGAAGAAAAGATGGAAGTTGTATAATATAAGAATGGGGTTCTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATAGGG---TTC
* * * * * *
128929 TTCAAAATCTAAAATCTAGATGATAGTCAACAACGTTTCTGA--CTCAAGTTTA-TTTAATCTTT
63 TTCAAAATCTAAAATCTATATGACAATCAACGACGTTTCTGAGTTTCATGTTTACTTT--T-TTT
* * *
128991 TTGGTTCAATGAACTTTGATGTAACGTTTCATGAAAAGCAAATCAATGCAATTTTCCATCCTAGT
125 TTGGTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTT-TAACCTA-T
* * * * * * * *
129056 TTAAAAAAACCATGAGGATTTTAGTATAAATAATAATTTAATTTGAATTTGGACCATC-AATTTT
188 TT-CAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCATCAAAATTT
* * * **
129120 TTACTATTATTGAAAAATAT-TTTTACATGAAATTAAAAT-AAAATTTATAACTATAATAATATT
252 TTAATATTATTGAAAAATATATTTCACATGATATTAAAATAAAAATTTATAACTATAATCGTATT
* * * * *
129183 AAATATCAACTTATATTTAGCACTCACTTTTAAATTTAAGTCATCT-AATATTAAATTATTTCCT
317 AAATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATAAATATTAAGTTATTTCCT
* * * * *
129247 TTTATTAATTCGAAATATCCAACGTAAGGGTATTTCCTA-ATTTTTCTTTTTTGCTTTAA-TTTA
382 TCTATTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGA-TTTTCTTTTTTGCTTTAATTTTA
* * * *
129310 TTTATATTAGGAAAAAACCTATTATAATTTATTTCTAGGATGACAACAAGCATC-GTGGTTTAGT
446 TTTATATTAGCAAAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGGTCTAGT
* * * *
129374 GGTAGAAGAGTACCCTACCATGGTACAA-ACTCGGGTTC
511 GGTAGAATAGTACCCTTCCATGGTA-AAGACCCAGGTTC
* * * * * *
129412 GATTATTGGCTGGTGCACCTTTGGAGTAATGATGAAAGTTGTTTTATAGAAAAAT-GTGGTTCTT
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATAG-GGTTC-T
* *
129476 CCTCAAAATCTAAAATCT-TGATGACAATCAATGACG---CTGAGTTTCAAGTTTACTTATCTTT
64 --TCAAAATCTAAAATCTAT-ATGACAATCAACGACGTTTCTGAGTTTCATGTTTACTT-T-TTT
129537 TTT--TT-AATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAG
124 TTTGGTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTT-AACCTA-
* * *
129599 TTTCAAAAACCATCAAGATTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCACCAAAAATT
187 TTTCAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCATCAAAATTT
* *
129664 TTAATATTATTGATAAATATATTTCACAATAAT-TTAAAATAAAAA-TTATAACTATAATCG-A-
252 TTAATATTATTGAAAAATATATTTCAC-ATGATATTAAAATAAAAATTTATAACTATAATCGTAT
* **
129725 -AAATATGTACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGGATATTAAGTTATTTCC
316 TAAATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATAAATATTAAGTTATTTCC
*
129789 TTCTATTTATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTC-TTTTTGCTTTAATTTTA
381 TTCTATTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTTA
* *
129853 TTTATATTAG-AAAAAACAACTATAATAATTTATTTCTAGGATGACAACAAGCACTAGTGGTCGA
446 TTTATATTAGCAAAAAAC--CTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGGTCTA
*** *
129917 GCAATAGAATAGTACCCTT-CATGGTATAGACCC-GAGTTC
509 GTGGTAGAATAGTACCCTTCCATGGTAAAGACCCAG-GTTC
* * * * *
129956 GATTCTCAGTTGGTGCACCATTGAAGGAATGATGAAAGTTGTATTATAGAAGAATAAGGTTTTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAAT-AGG--GTTC
* *
130021 TTCAAAATCTAAAA-C-ATAGTTGACATTCAACGACGTTTCTAAGTTTCATGTTTACTTAATTTT
63 TTCAAAATCTAAAATCTATA--TGACAATCAACGACGTTTCTGAGTTTCATGTTTAC----TTTT
* *
130084 TTTTTGGTTCAATGAACTTTGATGTAAAGTTTCGTGAAAATCAAATCAATGCA
122 TTTTTGGTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCA
130137 GAATGATGAA
Statistics
Matches: 2033, Mismatches: 251, Indels: 172
0.83 0.10 0.07
Matches are distributed among these distances:
540 75 0.04
541 61 0.03
542 174 0.09
543 229 0.11
544 228 0.11
545 145 0.07
546 38 0.02
547 73 0.04
548 106 0.05
549 195 0.10
550 80 0.04
551 9 0.00
552 91 0.04
553 5 0.00
554 71 0.03
555 11 0.01
556 9 0.00
557 159 0.08
558 5 0.00
559 32 0.02
560 5 0.00
562 3 0.00
563 1 0.00
564 66 0.03
565 137 0.07
566 25 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (548 bp):
GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATAGGGTTCTTC
AAAATCTAAAATCTATATGACAATCAACGACGTTTCTGAGTTTCATGTTTACTTTTTTTTTGGTT
CAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTAACCTATTTCAAAAA
CCATCAAGAGTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCATCAAAATTTTTAATATTA
TTGAAAAATATATTTCACATGATATTAAAATAAAAATTTATAACTATAATCGTATTAAATATGAA
CTTATATTTAACACTCACTTTAAAATTTAAGTCATATAAATATTAAGTTATTTCCTTCTATTAAT
TCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTTATTTATATTAG
CAAAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTGGTCTAGTGGTAGAATAG
TACCCTTCCATGGTAAAGACCCAGGTTC
Found at i:129600 original size:544 final size:548
Alignment explanation
Indices: 127215--130136 Score: 3184
Period size: 544 Copynumber: 5.3 Consensus size: 548
127205 ACTCGAGTTT
* * * * **
127215 GATTCTTGACTGGTGCACCTTTGAAGCAATGACGAAAGTTGTATTATAGAAGAATAAGGTTCTT-
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
* * ** *
127279 CT-----TC-AAAATCTAGATGGCAATCAACGATTTTACTGAGTTTCAATTTTAC-T--TTTTTT
66 CTCAAAATCTAAAATCTTGATGACAATCAACGA-CGT-CTGAGTTTCAAGTTTACTTAATTTTTT
* * *
127335 TGTTTCAATGAACTTTTATGTAAAGTTTCATGAAAAGCAATTCAATGCAA-TTTTCAACCTAATT
129 TG-TTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAGTT
* * * ** *
127399 TAAAAAATCATCAAGAGTTTAGTATAAATAATAATTTAGTGCAACTTTAGACCATCAAAATTTTT
193 TCAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAATGTGACTTTGGACCATCAAAATTTTT
* *
127464 AATATTATTGAAAAAGATATTTCACATGAAATTAAAAATAAAAATTATAACTATAATCGTATTAA
258 AATATTATTGAAAAATATATTTCACATGAAATT-AAAATAAAATTTATAACTATAATCGTATTAA
* * *
127529 ATACGTACTTATATTTAACACTCACTTT-AAATTTAAGTCATATGAATATTAAGTTACTTCCTTC
322 ATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGAATATTAA---A-TT--AT-
** * *
127593 TTCTTCTTCTTATTTTTTTTGAAAAATCCAATGCAAGGGCATTTCCTAGA-TAT-TTTTTT-CTT
380 TTC--CTT-TTA-TTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTT
* * * *
127655 TAATTTTATTTACATTAGCAAAATAACATATAATAATTTATTTCTAGGATGACAACAAGCACTAG
441 TAATTTTATTTATATTAGGAAAA-AACCTATAATAATTTATTTCTAGGATGACAACAAGCA-TCG
* ** * *
127720 TGGTCTAGTGGTAGAATAGTACCTTCCCATGGTAAAGAGTCAGGTTT
504 TGGTCTAGTGGTAGAATAGTACCCT-CCATGGTAAA-ACCCGGGTTC
* * * **
127767 AATTCCCGGCTGGTGCACCTTTGAAGCAATGATGGGAGTTGTATTATAGAAGAATGGGGTTC-TC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
* * *
127831 CTTCAAAATCTAAAATCTAT-ATTACAATCAACGACGTTTCTGAGTTT-ATGTGTACTTAATTAT
66 C-TCAAAATCTAAAATCT-TGATGACAATCAACGACG--TCTGAGTTTCAAGTTTACTT-A--AT
* * *
127894 TTTTTTGGTTCAATGAACTTTGATGTAAATTTTCGTGAAAAGCAAATCAATGCATTTTTTCAACC
124 TTTTTT-GTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACC
* * * * *
127959 TAATTTCAAAAACCTTCATGAGTTTAGTATAAATAATAATTTACTGTGACTATGGACCATCAAAA
188 TAGTTTCAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAATGTGACTTTGGACCATCAAAA
*
128024 TTTTTAATATTATTGAAAAATATATTTCACATG-AATCTAAAATAAAAATTTATAACTATAATCT
253 TTTTTAATATTATTGAAAAATATATTTCACATGAAAT-TAAAAT-AAAATTTATAACTATAATCG
* ** * ** *
128088 TATTAAATATGAACTTGTATTTAACACGGACTTTAAAATTTATGTCATAAAAATATTAAGTTATT
316 TATTAAATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGAATATTAAATTATT
* * * *
128153 TCCGTCTAATAATTC-AAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTAAATT
381 TCCTTTTATTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATT
* * * * *
128217 TTATTTACATTAGCAAAAGAACTTATAATAATTTATTTCTAGGATGACAACAAGCACCAGTTGTC
446 TTATTTATATTAGGAAAA-AACCTATAATAATTTATTTCTAGGATGACAACAAGCATC-GTGGTC
* * * ** * *
128282 TAGTGATAGAATAATACCTTTCCATGGTAAAGAGACAGGTTT
509 TAGTGGTAGAATAGTACC-CTCCATGGTAAA-ACCCGGGTTC
* * *
128324 GATTCCCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTTTTATAGAAGAATAGGGTTC-T-
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
* * * *
128387 -TCAAAATCTAAAA--TTGATATGACAATCAATGACTTTTCTGAGCTTCATGTTTACTT--TTTT
66 CTCAAAATCTAAAATCTTG--ATGACAATCAACGAC--GTCTGAGTTTCAAGTTTACTTAATTTT
* ** * *
128447 TTTGGTTCAATGAACTTTGATGTAAAGTTTTATGAAAATTAGATCAATGCAATTTTT-GACCT-G
127 TTT-GTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAG
* * *
128510 ATTTCAAAAACCATCAAGAGTTTAGTATAAATAATACTTTAGTGTGACTATGGACCATCAAAATT
191 -TTTCAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAATGTGACTTTGGACCATCAAAATT
* * ** *
128575 TCTAATATTATTGAAACATATATTTCACATGATCTTAAAATAAAAATTTATAACTATAATTGTAT
255 TTTAATATTATTGAAAAATATATTTCACATGAAATTAAAAT-AAAATTTATAACTATAATCGTAT
* * *
128640 TAAATATGAACTTATATTTATCACTCACTTTAAAATTTAAATCATATAAATATTAAATTATTTCC
319 TAAATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGAATATTAAATTATTTCC
* *
128705 TTTTATTATTTCGAAAAATCCAATGCAAGGGTATTTCC----TTTT-TTTTTTGCTTTAATTTTA
384 TTTTATTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTTA
*
128765 TTTATATTAGG--AAAACCTATAATAATTTATTTCTAGGATGACAACAAGCATCAGTAGTCTAGT
449 TTTATATTAGGAAAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCATC-GTGGTCTAGT
*
128828 GGT--AATAATACCCTGCCATGGTACAAACCCGGGTTC
513 GGTAGAATAGTACCCT-CCATGGTA-AAACCCGGGTTC
* * * * * * * *
128864 GATTTTTGACTGGTGAACCTTTGAAGAAAAGATGGAAGTTGTATAATATAAGAATGGGGTTCTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
* * * * * * *
128929 TTCAAAATCTAAAATCTAGATGATAGTCAACAACGTTTCTGA--CTCAAGTTTATTTAATCTTTT
66 CTCAAAATCTAAAATCTTGATGACAATCAACGACG--TCTGAGTTTCAAGTTTACTTAAT-TTTT
* * * *
128992 TGGTTCAATGAACTTTGATGTAACGTTTCATGAAAAGCAAATCAATGCAATTTTCCATCCTAGTT
128 TTGTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAGTT
* * * * * * *
129057 TAAAAAAACCATGAGGATTTTAGTATAAATAATAATTTAATTTGAATTTGGACCATC-AATTTTT
193 T-CAAAAACCATCAAGAGTTTAGTATAAATAATAATTTAATGTGACTTTGGACCATCAAAATTTT
* * **
129121 TACTATTATTGAAAAATAT-TTTTACATGAAATTAAAATAAAATTTATAACTATAATAATATTAA
257 TAATATTATTGAAAAATATATTTCACATGAAATTAAAATAAAATTTATAACTATAATCGTATTAA
* * * *
129185 ATATCAACTTATATTTAGCACTCACTTTTAAATTTAAGTCATCT-AATATTAAATTATTTCCTTT
322 ATATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGAATATTAAATTATTTCCTTT
* * * *
129249 TATTAATTCGAAATATCCAACGTAAGGGTATTTCCTA-ATTTTTCTTTTTTGCTTTAA-TTTATT
387 TATTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGA-TTTTCTTTTTTGCTTTAATTTTATT
* *
129312 TATATTAGGAAAAAACCTATTATAATTTATTTCTAGGATGACAACAAGCATCGTGGTTTAGTGGT
451 TATATTAGGAAAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCATCGTGGTCTAGTGGT
* *
129377 AGAAGAGTACCCTACCATGGTACAAACTCGGGTTC
516 AGAATAGTACCCT-CCATGGTA-AAACCCGGGTTC
* * * * * * *
129412 GATTATTGGCTGGTGCACCTTTGGAGTAATGATGAAAGTTGTTTTATAGAAAAATGTGGTTCTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
*
129477 CTCAAAATCTAAAATCTTGATGACAATCAATGACG-CTGAGTTTCAAGTTTACTT-ATCTTTTTT
66 CTCAAAATCTAAAATCTTGATGACAATCAACGACGTCTGAGTTTCAAGTTTACTTAAT-TTTTTT
129540 -TT-AATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAGTTTC
130 GTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAGTTTC
* * * *
129603 AAAAACCATCAAGATTTTAGTATAAATAATAATTTAGTGTGACTTTGGACCACCAAAAATTTTAA
195 AAAAACCATCAAGAGTTTAGTATAAATAATAATTTAATGTGACTTTGGACCATCAAAATTTTTAA
* * *
129668 TATTATTGATAAATATATTTCACAAT-AATTTAAAATAAAAATTATAACTATAATCG-A--AAAT
260 TATTATTGAAAAATATATTTCAC-ATGAAATTAAAATAAAATTTATAACTATAATCGTATTAAAT
* * * *
129729 ATGTACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGGATATTAAGTTATTTCCTTCTA
324 ATGAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGAATATTAAATTATTTCCTTTTA
*
129794 TTTATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTC-TTTTTGCTTTAATTTTATTTAT
389 TTAATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTTATTTAT
* * ***
129858 ATTA-GAAAAAACAACTATAATAATTTATTTCTAGGATGACAACAAGCACTAGTGGTCGAGCAAT
454 ATTAGGAAAAAAC--CTATAATAATTTATTTCTAGGATGACAACAAGCA-TCGTGGTCTAGTGGT
* * *
129922 AGAATAGTACCCTTCATGGTATAGACCCGAGTTC
516 AGAATAGTACCCTCCATGGTA-AAACCCGGGTTC
* * * * ** *
129956 GATTCTCAGTTGGTGCACCATTGAAGGAATGATGAAAGTTGTATTATAGAAGAATAAGGTTTTTC
1 GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
* * * * * *
130021 TTCAAAATCTAAAA-CATAGTTGACATTCAACGACGTTTCTAAGTTTCATGTTTACTTAATTTTT
66 CTCAAAATCTAAAATC-TTGATGACAATCAACGACG--TCTGAGTTTCAAGTTTACTTAA--TTT
* *
130085 TTTTGGTTCAATGAACTTTGATGTAAAGTTTCGTGAAAATCAAATCAATGCA
126 TTTT-GTTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCA
130137 GAATGATGAA
Statistics
Matches: 2024, Mismatches: 265, Indels: 162
0.83 0.11 0.07
Matches are distributed among these distances:
539 1 0.00
540 74 0.04
541 64 0.03
542 173 0.09
543 211 0.10
544 244 0.12
545 152 0.08
546 38 0.02
547 68 0.03
548 112 0.06
549 192 0.09
550 80 0.04
551 4 0.00
552 96 0.05
553 1 0.00
554 63 0.03
555 14 0.01
556 8 0.00
557 161 0.08
558 9 0.00
559 31 0.02
560 2 0.00
562 2 0.00
564 57 0.03
565 146 0.07
566 21 0.01
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (548 bp):
GATTCTCGGCTGGTGCACCTTTGAAGAAATGATGAAAGTTGTATTATAGAAGAATGGGGTTCTTC
CTCAAAATCTAAAATCTTGATGACAATCAACGACGTCTGAGTTTCAAGTTTACTTAATTTTTTTG
TTCAATGAACTTTGATGTAAAGTTTCATGAAAAGCAAATCAATGCAATTTTTCAACCTAGTTTCA
AAAACCATCAAGAGTTTAGTATAAATAATAATTTAATGTGACTTTGGACCATCAAAATTTTTAAT
ATTATTGAAAAATATATTTCACATGAAATTAAAATAAAATTTATAACTATAATCGTATTAAATAT
GAACTTATATTTAACACTCACTTTAAAATTTAAGTCATATGAATATTAAATTATTTCCTTTTATT
AATTCGAAAAATCCAATGCAAGGGCATTTCCTAGATTTTCTTTTTTGCTTTAATTTTATTTATAT
TAGGAAAAAACCTATAATAATTTATTTCTAGGATGACAACAAGCATCGTGGTCTAGTGGTAGAAT
AGTACCCTCCATGGTAAAACCCGGGTTC
Found at i:135592 original size:78 final size:79
Alignment explanation
Indices: 135449--135608 Score: 313
Period size: 78 Copynumber: 2.0 Consensus size: 79
135439 GAATTTGTAT
135449 AAAAGGCTATAAAACAGAAAAGTTCGATAAAAATTTGGATAATCAATCGAATAAAAAATTCTAAA
1 AAAAGGCTATAAAACAGAAAAGTTCGATAAAAATTTGGATAATCAATCGAATAAAAAATTCTAAA
135514 AATTTTGATGAATG
66 AATTTTGATGAATG
135528 AAAAGGCTATAAAACAGAAAAGTTCGAT-AAAATTTGGATAATCAATCGAATAAAAAATTCTAAA
1 AAAAGGCTATAAAACAGAAAAGTTCGATAAAAATTTGGATAATCAATCGAATAAAAAATTCTAAA
135592 AATTTTGATGAATG
66 AATTTTGATGAATG
135606 AAA
1 AAA
135609 TGTTTTCGTA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 53 0.65
79 28 0.35
ACGTcount: A:0.53, C:0.07, G:0.14, T:0.26
Consensus pattern (79 bp):
AAAAGGCTATAAAACAGAAAAGTTCGATAAAAATTTGGATAATCAATCGAATAAAAAATTCTAAA
AATTTTGATGAATG
Found at i:138593 original size:12 final size:12
Alignment explanation
Indices: 138576--138600 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
138566 CCTAATACAT
138576 TTTTATATGATA
1 TTTTATATGATA
138588 TTTTATATGATA
1 TTTTATATGATA
138600 T
1 T
138601 ATAATATATG
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:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTTATATGATA
Found at i:138618 original size:22 final size:22
Alignment explanation
Indices: 138590--138637 Score: 96
Period size: 22 Copynumber: 2.2 Consensus size: 22
138580 ATATGATATT
138590 TTATATGATATATAATATATGG
1 TTATATGATATATAATATATGG
138612 TTATATGATATATAATATATGG
1 TTATATGATATATAATATATGG
138634 TTAT
1 TTAT
138638 GGATGATTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (22 bp):
TTATATGATATATAATATATGG
Found at i:138938 original size:27 final size:28
Alignment explanation
Indices: 138908--138968 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 28
138898 GGCACTTCCA
* *
138908 AGTGCGATTACTA-ATGAAACACTTTCG
1 AGTGCGATTAATATATGAAACACTTGCG
* **
138935 AGTGTGATTAATATATGAGGCACTTGCG
1 AGTGCGATTAATATATGAAACACTTGCG
138963 AGTGCG
1 AGTGCG
138969 TATTGCACAC
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 11 0.41
28 16 0.59
ACGTcount: A:0.30, C:0.15, G:0.26, T:0.30
Consensus pattern (28 bp):
AGTGCGATTAATATATGAAACACTTGCG
Found at i:138959 original size:28 final size:28
Alignment explanation
Indices: 138891--138968 Score: 86
Period size: 27 Copynumber: 2.8 Consensus size: 28
138881 TGGTGCAAGT
* *
138891 TATATGAGGCACTTCCAAGTGCGATTAC
1 TATATGAGGCACTTCCGAGTGCGATTAA
** * *
138919 TA-ATGAAACACTTTCGAGTGTGATTAA
1 TATATGAGGCACTTCCGAGTGCGATTAA
*
138946 TATATGAGGCACTTGCGAGTGCG
1 TATATGAGGCACTTCCGAGTGCG
138969 TATTGCACAC
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.29, C:0.17, G:0.24, T:0.29
Consensus pattern (28 bp):
TATATGAGGCACTTCCGAGTGCGATTAA
Found at i:146155 original size:32 final size:32
Alignment explanation
Indices: 146119--146220 Score: 159
Period size: 32 Copynumber: 3.1 Consensus size: 32
146109 TCCAAACATT
* *
146119 TATACATACAATATTGATTGGACATATATATGTA
1 TATACACACAATATTGATTGG--ATATATATATA
*
146153 TACACACACAATATTGATTGGATATATATATA
1 TATACACACAATATTGATTGGATATATATATA
146185 TATACACACAATATTGATTGGATATATATATA
1 TATACACACAATATTGATTGGATATATATATA
146217 TATA
1 TATA
146221 TATATATATA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
32 45 0.70
34 19 0.30
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.37
Consensus pattern (32 bp):
TATACACACAATATTGATTGGATATATATATA
Found at i:146211 original size:2 final size:2
Alignment explanation
Indices: 146206--146230 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
146196 TATTGATTGG
146206 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 A
146231 CACACACAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:146221 original size:34 final size:33
Alignment explanation
Indices: 146119--146222 Score: 156
Period size: 34 Copynumber: 3.1 Consensus size: 33
146109 TCCAAACATT
* *
146119 TATACATACAATATTGATTGGACATATATATGTA
1 TATACACACAATATTGATTGGA-ATATATATATA
*
146153 TACACACACAATATTGATTGG-ATATATATATA
1 TATACACACAATATTGATTGGAATATATATATA
146185 TATACACACAATATTGATTGGATATATATATATA
1 TATACACACAATATTGATTGGA-ATATATATATA
146219 TATA
1 TATA
146223 TATATATACA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
32 30 0.47
34 34 0.53
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (33 bp):
TATACACACAATATTGATTGGAATATATATATA
Found at i:149783 original size:41 final size:41
Alignment explanation
Indices: 149732--149820 Score: 151
Period size: 41 Copynumber: 2.2 Consensus size: 41
149722 AATTTATATA
*
149732 TATTTGTAATAAAATTTGTATACAAATAACTTAATAATTTT
1 TATTTTTAATAAAATTTGTATACAAATAACTTAATAATTTT
* *
149773 TATTTTTAATAAATTTTGTATACAAATAACTTAATATTTTT
1 TATTTTTAATAAAATTTGTATACAAATAACTTAATAATTTT
149814 TATTTTT
1 TATTTTT
149821 TAATTCATTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.39, C:0.04, G:0.03, T:0.53
Consensus pattern (41 bp):
TATTTTTAATAAAATTTGTATACAAATAACTTAATAATTTT
Found at i:156568 original size:24 final size:24
Alignment explanation
Indices: 156541--156591 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 24
156531 AACGTGGCCT
* *
156541 AGGTAGAGGTAGAGGCCATGGACG
1 AGGTAGAAGTAGACGCCATGGACG
* * *
156565 AGGTGGAAGTCGACGTCATGGACG
1 AGGTAGAAGTAGACGCCATGGACG
156589 AGG
1 AGG
156592 CTGGAATTAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.27, C:0.14, G:0.45, T:0.14
Consensus pattern (24 bp):
AGGTAGAAGTAGACGCCATGGACG
Found at i:156619 original size:15 final size:15
Alignment explanation
Indices: 156596--156625 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
156586 ACGAGGCTGG
156596 AATTACAACAACAAC
1 AATTACAACAACAAC
*
156611 AATTCCAACAACAAC
1 AATTACAACAACAAC
156626 TATGAGAAAG
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:0.57, C:0.30, G:0.00, T:0.13
Consensus pattern (15 bp):
AATTACAACAACAAC
Found at i:167014 original size:14 final size:13
Alignment explanation
Indices: 166991--167040 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
166981 TGAAAATATA
166991 AATGCAAATGCAT
1 AATGCAAATGCAT
167004 AATGCATAATGCAGT
1 AATGCA-AATGCA-T
* * *
167019 GATGAAAATTCAT
1 AATGCAAATGCAT
167032 AATGCAAAT
1 AATGCAAAT
167041 ATTCAAATGC
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 14 0.47
14 11 0.37
15 5 0.17
ACGTcount: A:0.46, C:0.12, G:0.16, T:0.26
Consensus pattern (13 bp):
AATGCAAATGCAT
Found at i:168506 original size:2 final size:2
Alignment explanation
Indices: 168499--168551 Score: 97
Period size: 2 Copynumber: 26.0 Consensus size: 2
168489 TAATCCAAAG
168499 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT ACT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT
168542 AT AT AT AT AT
1 AT AT AT AT AT
168552 GGGTAAATTT
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 48 0.96
3 2 0.04
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:169828 original size:98 final size:101
Alignment explanation
Indices: 169720--169903 Score: 257
Period size: 104 Copynumber: 1.8 Consensus size: 101
169710 AATTGTGATG
* * *
169720 AATTTTTTTGACACTAAAA-ATATTTTGTGACAATCAATATTGTCAC-ACAA-TTTTTATTGACC
1 AATTTATTTGACACTAAAAGATATTTTGTGACAACCAATATTGTCACAACAAGTTTTTAGTGACC
*
169782 AAATGTTTGATACTATTATTAATAGAAATCGTGAAA
66 AAATGTTTGACACTATTATTAATAGAAATCGTGAAA
* * *
169818 AATTTATTTGACACTAAAAGTATATTTTGTGACCACCAATGTTGTCACAATAAGTGTTTTTAGTG
1 AATTTATTTGACACTAAAAG-ATATTTTGTGACAACCAATATTGTCACAACAA--GTTTTTAGTG
169883 ACCAAATGTTTGACACTATTA
63 ACCAAATGTTTGACACTATTA
169904 ACAATAACTT
Statistics
Matches: 73, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
98 18 0.25
100 24 0.33
101 3 0.04
104 28 0.38
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (101 bp):
AATTTATTTGACACTAAAAGATATTTTGTGACAACCAATATTGTCACAACAAGTTTTTAGTGACC
AAATGTTTGACACTATTATTAATAGAAATCGTGAAA
Found at i:170948 original size:3 final size:3
Alignment explanation
Indices: 170940--170970 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
170930 TTATCCGGGA
170940 TAT TAT TAT TAT TAT TAT TAT T-T TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
170971 ATAATGTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:173526 original size:19 final size:19
Alignment explanation
Indices: 173502--173541 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
173492 AAGTCGTAAC
173502 CGTTTTGAAACTAAATAAT
1 CGTTTTGAAACTAAATAAT
173521 CGTTTTGAAACTAAATAAT
1 CGTTTTGAAACTAAATAAT
173540 CG
1 CG
173542 GTTTCGCATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (19 bp):
CGTTTTGAAACTAAATAAT
Found at i:181997 original size:10 final size:9
Alignment explanation
Indices: 181983--182023 Score: 55
Period size: 10 Copynumber: 4.3 Consensus size: 9
181973 AAAAATATAT
*
181983 GAAAAAAAG
1 GAAAAAAAA
181992 GAAAAAAAA
1 GAAAAAAAA
182001 GAACAAAAAA
1 GAA-AAAAAA
182011 GAAAGAAAAA
1 GAAA-AAAAA
182021 GAA
1 GAA
182024 GGGTTCAAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
9 12 0.41
10 17 0.59
ACGTcount: A:0.80, C:0.02, G:0.17, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:182008 original size:20 final size:20
Alignment explanation
Indices: 181985--182023 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
181975 AAATATATGA
181985 AAAAAAGGAAA-AAAAAGAAC
1 AAAAAA-GAAAGAAAAAGAAC
182005 AAAAAAGAAAGAAAAAGAA
1 AAAAAAGAAAGAAAAAGAA
182024 GGGTTCAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.82, C:0.03, G:0.15, T:0.00
Consensus pattern (20 bp):
AAAAAAGAAAGAAAAAGAAC
Found at i:183469 original size:248 final size:247
Alignment explanation
Indices: 182984--183479 Score: 885
Period size: 249 Copynumber: 2.0 Consensus size: 247
182974 ATGATAGTTG
*
182984 AAGATTGAAGATTGCAGCATGAAGATGAGGAGACTAGTTTGGTGATCTTGAAAAGATTGACGACG
1 AAGATTGAAGATTGCAGCATGAAGATGAGAAGACTAGTTTGGTGATCTTGAAAAGATTGACGACG
183049 ATTTGAGCCAGAATAGATTCTCGTATCTAAGGGTTCTTAAACAATTTCAAGATGAGACAAATTTT
66 ATTTGAGCCAGAATAGATTCTCGTATCTAAGGGTTCTTAAACAATTTCAAGATGAGACAAATTTT
183114 CAAAAATTTTCTTGAACTCTGAATTGTTGAGTATAATATTTTGAAGCATACATTAATGAGTGATA
131 CAAAAATTTTCTTGAACTCTGAATTGTTGAGTATAATATTTTGAAGCATACATTAATGAGTGATA
183179 ACGTTTGATTTTCAGGTTTAACCTTCGAAGAAAATCAACTTAAGCCTTCACA
196 ACGTTTGATTTTCAGGTTTAACCTTCGAAGAAAATCAACTTAAGCCTTCACA
183231 AAGATTGAAGATATTGCAGCATGAAGATGAGAAGACTAG-TTGGTGATCTTGAAAAGATGATGAC
1 AAGATTGAAG--ATTGCAGCATGAAGATGAGAAGACTAGTTTGGTGATCTTGAAAAGAT--TGAC
*
183295 GACGA-TTGAGCCAGAATAGATTCTCGTATCTAAGGGTTCTTAAATAA-TTCAAGATGAAGACAA
62 GACGATTTGAGCCAGAATAGATTCTCGTATCTAAGGGTTCTTAAACAATTTCAAGATG-AGACAA
183358 ATTTTCAAAAATTTTCTTGAACTCTGAATTGTTGAGTATAATA-TTTGAAGCATACATTAATGAG
126 ATTTTCAAAAATTTTCTTGAACTCTGAATTGTTGAGTATAATATTTTGAAGCATACATTAATGAG
183422 TGATAACGTTTGATTTTCAGGTTTAACCTTCGAAG-AAATCAAACTTAAGCCTTCACA
191 TGATAACGTTTGATTTTCAGGTTTAACCTTCGAAGAAAATC-AACTTAAGCCTTCACA
183479 A
1 A
183480 GAAAGTAGTG
Statistics
Matches: 241, Mismatches: 2, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
247 15 0.06
248 101 0.42
249 116 0.48
250 9 0.04
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (247 bp):
AAGATTGAAGATTGCAGCATGAAGATGAGAAGACTAGTTTGGTGATCTTGAAAAGATTGACGACG
ATTTGAGCCAGAATAGATTCTCGTATCTAAGGGTTCTTAAACAATTTCAAGATGAGACAAATTTT
CAAAAATTTTCTTGAACTCTGAATTGTTGAGTATAATATTTTGAAGCATACATTAATGAGTGATA
ACGTTTGATTTTCAGGTTTAACCTTCGAAGAAAATCAACTTAAGCCTTCACA
Found at i:183710 original size:104 final size:104
Alignment explanation
Indices: 183500--183902 Score: 558
Period size: 104 Copynumber: 3.9 Consensus size: 104
183490 AAGCAGAAGG
*
183500 AGATGTCTGAGTTCTATACTCCCT-GA-AAAGAGGGAGCGAACCGTTTGAAGAAGATATCCGAGT
1 AGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCGTTTGAAGAAGATATCCGAGT
183563 TCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGA
66 TCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGA
183602 AGATGTCCGAGTTCTATACTCCCT-GAAGAAAGAGGGAAGCGAACCCGTTTGAAGAAGATATCC-
1 AGATGTCCGAGTTCTATACTCCCTAG-AGAAAGAGGG-AGCGAA-CCGTTTGAAGAAGATATCCG
183665 AGTTCCATACTCCTTAAAGAAAG-AGGAGCGAACCCGTTTGA
63 AGTTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGA
* *
183706 AGATGTTCGAGTTCTATA-TCCCTAGAGAAAGAGGGAGCGAACCCG-TTGAAGAATATATCCGAG
1 AGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAA-CCGTTTGAAGAAGATATCCGAG
* *
183769 TTCCATACTCCTTAAAAAAAGAAGGAGCGAACCCGTGTGA
65 TTCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGA
* * * * *
183809 AGATGTTCGAGTTCCATACCCCCTAGAGAAAGAGGGAGCGAACCG--TG-TGAAGATATTCGAGT
1 AGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCGTTTGAAGAAGATATCCGAGT
** * *
183871 TATATACTTCC-TGAAGAAAGAGGGAGCGAACC
66 TCCATAC-TCCTTAAAGAAAGAAGGAGCGAACC
183903 GTAAGAAGAA
Statistics
Matches: 277, Mismatches: 15, Indels: 19
0.89 0.05 0.06
Matches are distributed among these distances:
101 49 0.18
102 61 0.22
103 53 0.19
104 66 0.24
105 29 0.10
106 19 0.07
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.21
Consensus pattern (104 bp):
AGATGTCCGAGTTCTATACTCCCTAGAGAAAGAGGGAGCGAACCGTTTGAAGAAGATATCCGAGT
TCCATACTCCTTAAAGAAAGAAGGAGCGAACCCGTTTGA
Found at i:183903 original size:50 final size:51
Alignment explanation
Indices: 183508--183952 Score: 355
Period size: 51 Copynumber: 8.7 Consensus size: 51
183498 GGAGATGTCT
* * * *
183508 GAGTTCTATACTCCCTG-A-AAAGAGGGAGCGAA-CCGTTTGAAGAAGATATCC
1 GAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACCCG--TG-TGAAGATATTC
* * * * *
183559 GAGTTCCATAC-TCCTTAAAGAAAGAAGGAGCGAACCCGTTTGAAGATGTCC
1 GAGTTCCATACTTCC-TGAAGAAAGAGGGAGCGAACCCGTGTGAAGATATTC
* * * *
183610 GAGTTCTATACTCCCTGAAGAAAGAGGGAAGCGAACCCGTTTGAAGAAGATATC
1 GAGTTCCATACTTCCTGAAGAAAGAGGG-AGCGAACCCGTGTGAAG-ATAT-TC
* * * *
183664 CAGTTCCATAC-TCCTTAAAGAAAGA-GGAGCGAACCCGTTTGAAGATGTTC
1 GAGTTCCATACTTCC-TGAAGAAAGAGGGAGCGAACCCGTGTGAAGATATTC
* *
183714 GAGTTCTATA-TCCCT-AGAGAAAGAGGGAGCGAACCCGT-TGAAGAATATATCC
1 GAGTTCCATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTGTGAAG-ATAT-T-C
* * * *
183766 GAGTTCCATAC-TCCTTAAAAAAAGAAGGAGCGAACCCGTGTGAAGATGTTC
1 GAGTTCCATACTTCC-TGAAGAAAGAGGGAGCGAACCCGTGTGAAGATATTC
**
183817 GAGTTCCATACCCCCT-AGAGAAAGAGGGAGCGAA-CCGTGTGAAGATATTC
1 GAGTTCCATACTTCCTGA-AGAAAGAGGGAGCGAACCCGTGTGAAGATATTC
** * *
183867 GAGTTATATACTTCCTGAAGAAAGAGGGAGCGAA-CCGTAAGAAGAAGAT-TTT
1 GAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACCCGT--G-TGAAGATATTC
*
183919 GAGTT-CATACTTCCTGAAGAAA-AGAGAGCGAACC
1 GAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACC
183953 TGTTTGTTGA
Statistics
Matches: 327, Mismatches: 41, Indels: 52
0.78 0.10 0.12
Matches are distributed among these distances:
48 1 0.00
49 13 0.04
50 87 0.27
51 89 0.27
52 61 0.19
53 48 0.15
54 28 0.09
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (51 bp):
GAGTTCCATACTTCCTGAAGAAAGAGGGAGCGAACCCGTGTGAAGATATTC
Found at i:183965 original size:51 final size:51
Alignment explanation
Indices: 183835--183992 Score: 148
Period size: 50 Copynumber: 3.1 Consensus size: 51
183825 TACCCCCTAG
* * *
183835 AGAAAGAGGGAGCGAACCGT--G-TGAAGATATTCGAGTTATATACTTCCTGA
1 AGAAAGAGAGAGCGAACCGTAAGATGAAGAT-TTTGAGTT-CATACTTCCTGA
* *
183885 AGAAAGAGGGAGCGAACCGTAAGAAGAAGATTTTGAGTTCATACTTCCTGA
1 AGAAAGAGAGAGCGAACCGTAAGATGAAGATTTTGAGTTCATACTTCCTGA
** *
183936 AGAAA-AGAGAGCGAACCTGTTTGTTGAAGATTGTTCGAGTCTCATAC-T-CTGA
1 AGAAAGAGAGAGCGAACC-GTAAGATGAAGATT-TT-GAGT-TCATACTTCCTGA
183988 AGAAA
1 AGAAA
183993 TATGGAGCAG
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
50 31 0.33
51 26 0.28
52 19 0.20
53 11 0.12
54 6 0.06
ACGTcount: A:0.35, C:0.14, G:0.27, T:0.24
Consensus pattern (51 bp):
AGAAAGAGAGAGCGAACCGTAAGATGAAGATTTTGAGTTCATACTTCCTGA
Found at i:184131 original size:111 final size:109
Alignment explanation
Indices: 183959--184165 Score: 308
Period size: 111 Copynumber: 1.9 Consensus size: 109
183949 AACCTGTTTG
* *
183959 TTGAAGATTGTTCGAGTCTCATACTCTGAAGAAATATGGAGCAGACACGATTATTAAAGATTGTT
1 TTGAAGATTGTTCAAGTCTCATACTCTGAAGAAATAGGGAGCAGACACGATTATTAAAGATTGTT
184024 -CGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
66 CCG-GTCTCATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
* * * * * *
184068 TTGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCATATACGTTTATTGAAGATTG
1 TTGAAGATTGTTCAAGTCTCATA--CTCTGAAGAAATAGGGAGCAGACACGATTATTAAAGATTG
184133 TTCCGGTCTCATACTCTCTGAAGGAATAGGGAG
64 TTCCGGTCTCATACTCTCTGAAGGAATAGGGAG
184166 TGAACATGTT
Statistics
Matches: 87, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
109 21 0.24
111 64 0.74
112 2 0.02
ACGTcount: A:0.30, C:0.15, G:0.24, T:0.30
Consensus pattern (109 bp):
TTGAAGATTGTTCAAGTCTCATACTCTGAAGAAATAGGGAGCAGACACGATTATTAAAGATTGTT
CCGGTCTCATACTCTCTGAAGGAATAGGGAGCAGACACGATTGT
Found at i:184152 original size:55 final size:55
Alignment explanation
Indices: 183954--184165 Score: 288
Period size: 55 Copynumber: 3.9 Consensus size: 55
183944 GAGCGAACCT
* * *
183954 GTTTGTTGAAGATTGTTCGAGTCTCATA--CTCTGAAGAAATATGGAGCAGACAC
1 GTTTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACAC
* *
184007 GATTATTAAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACAC
1 GTTTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACAC
* * * *
184062 GATTGT-TTGAAGATTGTTCAAGTCTTATACTCTCTGAAGGAATAGGGAGCATATAC
1 G-TT-TATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACAC
184118 GTTTATTGAAGATTGTTCCG-GTCTCATACTCTCTGAAGGAATAGGGAG
1 GTTTATTGAAGATTGTT-CGAGTCTCATACTCTCTGAAGGAATAGGGAG
184166 TGAACATGTT
Statistics
Matches: 140, Mismatches: 13, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
53 25 0.18
54 1 0.01
55 65 0.46
56 48 0.34
57 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.25, T:0.31
Consensus pattern (55 bp):
GTTTATTGAAGATTGTTCGAGTCTCATACTCTCTGAAGGAATAGGGAGCAGACAC
Found at i:184377 original size:16 final size:16
Alignment explanation
Indices: 184352--184386 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
184342 TTTGTCCGGG
*
184352 ATATTATTATTATTAT
1 ATATTATTATTATAAT
*
184368 ATATTTTTATTATAAT
1 ATATTATTATTATAAT
184384 ATA
1 ATA
184387 ATGTTAACGT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
ATATTATTATTATAAT
Found at i:192121 original size:17 final size:16
Alignment explanation
Indices: 192080--192140 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 16
192070 CTCAGATGTT
**
192080 TCGGGTACCC-GATAA
1 TCGGGTACCCGGATTG
* *
192095 TCGAGTACCCGGATTT
1 TCGGGTACCCGGATTG
*
192111 TGCGGGTACCCGTA-TG
1 T-CGGGTACCCGGATTG
192127 TCGGGTACCCGGAT
1 TCGGGTACCCGGAT
192141 ACCTAGATTT
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
15 20 0.56
16 6 0.17
17 10 0.28
ACGTcount: A:0.18, C:0.26, G:0.31, T:0.25
Consensus pattern (16 bp):
TCGGGTACCCGGATTG
Found at i:192225 original size:26 final size:26
Alignment explanation
Indices: 192189--192266 Score: 129
Period size: 26 Copynumber: 3.0 Consensus size: 26
192179 ACAAATCTGA
* *
192189 GTTAGGTTGTTTAGGAGTAGCAATTT
1 GTTAGCTTGTTTAGCAGTAGCAATTT
*
192215 GTTAGCTTGTTTAGCAATAGCAATTT
1 GTTAGCTTGTTTAGCAGTAGCAATTT
192241 GTTAGCTTGTTTAGCAGTAGCAATTT
1 GTTAGCTTGTTTAGCAGTAGCAATTT
192267 ATAAAAAGTG
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.24, C:0.09, G:0.24, T:0.42
Consensus pattern (26 bp):
GTTAGCTTGTTTAGCAGTAGCAATTT
Found at i:194460 original size:48 final size:48
Alignment explanation
Indices: 194408--194628 Score: 298
Period size: 48 Copynumber: 4.6 Consensus size: 48
194398 CATAAGTAAT
* * * * *
194408 GTCAGATGTGCTAATCATCATCAATAGGAGCACAATCATCACACAGAC
1 GTCAGACGTGCTAATCATCATCAATAGTAGCACCACCGTCACACAGAC
* * *
194456 GTCAGACGTGCTAATCATCATCAATAGTAGAACCACCGTCACACATAT
1 GTCAGACGTGCTAATCATCATCAATAGTAGCACCACCGTCACACAGAC
* * * *
194504 ATCAAACGTGTTAATCATCATCAATAGTAGCACCACCGTCACATAGAC
1 GTCAGACGTGCTAATCATCATCAATAGTAGCACCACCGTCACACAGAC
* * *
194552 GTCAGATGTGCTAATCATCATCAATAGTAGCACCACCGTCAAATAGAC
1 GTCAGACGTGCTAATCATCATCAATAGTAGCACCACCGTCACACAGAC
*
194600 GTCAGACGTGTTAATCATCATCAATAGTA
1 GTCAGACGTGCTAATCATCATCAATAGTA
194629 TTCATAAATA
Statistics
Matches: 151, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
48 151 1.00
ACGTcount: A:0.36, C:0.25, G:0.15, T:0.24
Consensus pattern (48 bp):
GTCAGACGTGCTAATCATCATCAATAGTAGCACCACCGTCACACAGAC
Found at i:195476 original size:21 final size:22
Alignment explanation
Indices: 195428--195527 Score: 78
Period size: 21 Copynumber: 4.5 Consensus size: 22
195418 ATAAAATGCA
* *
195428 CCGAAGTG-CCACATAGAATGTT
1 CCGAAG-GACCACATAGAATATC
195450 CCGAAGGACCACATAG-ATATC
1 CCGAAGGACCACATAGAATATC
* * *
195471 CCGAAGGACCGCGTAGAAATTGTC
1 CCGAAGGACCACATAG-AA-TATC
* *
195495 CCAAAGGACCACGTAGAATTATC
1 CCGAAGGACCACATAGAA-TATC
*
195518 CTGAAGGACC
1 CCGAAGGACC
195528 GCGTAGAACC
Statistics
Matches: 64, Mismatches: 10, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
21 18 0.28
22 14 0.22
23 15 0.23
24 17 0.27
ACGTcount: A:0.34, C:0.26, G:0.23, T:0.17
Consensus pattern (22 bp):
CCGAAGGACCACATAGAATATC
Found at i:195524 original size:23 final size:23
Alignment explanation
Indices: 195450--195535 Score: 95
Period size: 23 Copynumber: 3.8 Consensus size: 23
195440 ATAGAATGTT
*
195450 CCGAAGGACCACATAG-A-TATC
1 CCGAAGGACCACGTAGAATTATC
* *
195471 CCGAAGGACCGCGTAGAAATTGTC
1 CCGAAGGACCACGTAG-AATTATC
*
195495 CCAAAGGACCACGTAGAATTATC
1 CCGAAGGACCACGTAGAATTATC
* *
195518 CTGAAGGACCGCGTAGAA
1 CCGAAGGACCACGTAGAA
195536 CCCTCGACTC
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
21 14 0.26
23 22 0.42
24 17 0.32
ACGTcount: A:0.35, C:0.26, G:0.24, T:0.15
Consensus pattern (23 bp):
CCGAAGGACCACGTAGAATTATC
Found at i:195665 original size:14 final size:14
Alignment explanation
Indices: 195646--195674 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
195636 AGTAATCAAG
195646 TAGGTTATGTCACA
1 TAGGTTATGTCACA
195660 TAGGTTATGTCACA
1 TAGGTTATGTCACA
195674 T
1 T
195675 TTCTTATATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.14, G:0.21, T:0.38
Consensus pattern (14 bp):
TAGGTTATGTCACA
Found at i:195746 original size:44 final size:44
Alignment explanation
Indices: 195655--195755 Score: 114
Period size: 44 Copynumber: 2.3 Consensus size: 44
195645 GTAGGTTATG
* * * *
195655 TCACATAGGTTATGTCACATTTCTTATATCCTATATTCATGTAT
1 TCACATAGATCATGTCACATATCTTATATCCTATATTCATATAT
* * * *
195699 TCACGTAGATCATGTCACATATCTTATATCTTGT-TCTCATATGT
1 TCACATAGATCATGTCACATATCTTATATCCTATAT-TCATATAT
195743 TCACATAGATCAT
1 TCACATAGATCAT
195756 ATAGCACATA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
43 1 0.02
44 46 0.98
ACGTcount: A:0.28, C:0.20, G:0.10, T:0.43
Consensus pattern (44 bp):
TCACATAGATCATGTCACATATCTTATATCCTATATTCATATAT
Found at i:203988 original size:2 final size:2
Alignment explanation
Indices: 203983--204007 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
203973 ATTTTTATTG
203983 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 A
204008 AACTATATGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:204606 original size:23 final size:23
Alignment explanation
Indices: 204539--204607 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
204529 ACATTTTATA
* *
204539 TGGCACTACGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTATACG
** * *
204562 CAGCACTTCGGTGCAATCATACG
1 TGGCACTTCGGTGCATTTATACG
*
204585 TGGCACTTTGGTGCATTTATACG
1 TGGCACTTCGGTGCATTTATACG
204608 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 11, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTATACG
Found at i:205366 original size:38 final size:38
Alignment explanation
Indices: 205312--205419 Score: 110
Period size: 42 Copynumber: 2.8 Consensus size: 38
205302 CAATAGTGAT
* * * *
205312 AAAAAAA-ATTTGTCGTCACAAATCACCAAGACTAGTG
1 AAAAAAACATTTATCGTCAGAAATCACCAAGACTAATA
*
205349 ACAAAAACATTTATCGTCAGAAATCATCAACTAAGACTAATA
1 AAAAAAACATTTATCGTCAGAAATCA-C--C-AAGACTAATA
* *
205391 AAAAAAACAATTATTGTCAGAAATCACCA
1 AAAAAAACATTTATCGTCAGAAATCACCA
205420 TCAAAGACTG
Statistics
Matches: 58, Mismatches: 8, Indels: 9
0.77 0.11 0.12
Matches are distributed among these distances:
37 6 0.10
38 17 0.29
39 2 0.03
41 2 0.03
42 31 0.53
ACGTcount: A:0.50, C:0.19, G:0.09, T:0.22
Consensus pattern (38 bp):
AAAAAAACATTTATCGTCAGAAATCACCAAGACTAATA
Found at i:208443 original size:13 final size:13
Alignment explanation
Indices: 208425--208449 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
208415 GAGCATAGAT
208425 GTATGAAGAAGAA
1 GTATGAAGAAGAA
208438 GTATGAAGAAGA
1 GTATGAAGAAGA
208450 TGAACAATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.32, T:0.16
Consensus pattern (13 bp):
GTATGAAGAAGAA
Found at i:208676 original size:29 final size:31
Alignment explanation
Indices: 208620--208691 Score: 94
Period size: 29 Copynumber: 2.4 Consensus size: 31
208610 TTCAACGTCC
*
208620 AAGTGACCAAAACTTAATAAAACGATAA-GT
1 AAGTGACCAAAACTTAAAAAAACGATAACGT
* **
208650 AA-TTACCAAAACTTAAAAAAATTATAACGT
1 AAGTGACCAAAACTTAAAAAAACGATAACGT
208680 AAGTGACCAAAA
1 AAGTGACCAAAA
208692 GTGTACAAAT
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 21 0.60
30 6 0.17
31 8 0.23
ACGTcount: A:0.56, C:0.14, G:0.10, T:0.21
Consensus pattern (31 bp):
AAGTGACCAAAACTTAAAAAAACGATAACGT
Found at i:208870 original size:31 final size:31
Alignment explanation
Indices: 208843--208902 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
208833 ACATCTTTAT
*
208843 TAAAACGAAATGAAAGTGACTAAATCTTAAC
1 TAAAACGAAACGAAAGTGACTAAATCTTAAC
*
208874 TAAAACGAAACGAAAATGA-TCAAATCTTA
1 TAAAACGAAACGAAAGTGACT-AAATCTTA
208903 TGTTTTTTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 1 0.04
31 25 0.96
ACGTcount: A:0.53, C:0.13, G:0.12, T:0.22
Consensus pattern (31 bp):
TAAAACGAAACGAAAGTGACTAAATCTTAAC
Found at i:212719 original size:19 final size:20
Alignment explanation
Indices: 212692--212729 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
212682 TTGGGAAAAG
212692 TCGG-TTTTTTTTAACCGGA
1 TCGGATTTTTTTTAACCGGA
212711 TCGGATTTTTTTTAACCGG
1 TCGGATTTTTTTTAACCGG
212730 TTATTTTAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 4 0.22
20 14 0.78
ACGTcount: A:0.16, C:0.16, G:0.21, T:0.47
Consensus pattern (20 bp):
TCGGATTTTTTTTAACCGGA
Found at i:212738 original size:13 final size:13
Alignment explanation
Indices: 212720--212744 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
212710 ATCGGATTTT
212720 TTTTAACCGGTTA
1 TTTTAACCGGTTA
212733 TTTTAACCGGTT
1 TTTTAACCGGTT
212745 TGGAAAAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.20, C:0.16, G:0.16, T:0.48
Consensus pattern (13 bp):
TTTTAACCGGTTA
Found at i:214939 original size:46 final size:46
Alignment explanation
Indices: 214872--214971 Score: 191
Period size: 46 Copynumber: 2.2 Consensus size: 46
214862 GGAGCGGCTC
*
214872 GGAAGCAACATATCACCACCCTAGAATATGCAATTGATGCCGATTT
1 GGAAGCAACATATCACCACCCTAGAAGATGCAATTGATGCCGATTT
214918 GGAAGCAACATATCACCACCCTAGAAGATGCAATTGATGCCGATTT
1 GGAAGCAACATATCACCACCCTAGAAGATGCAATTGATGCCGATTT
214964 GGAAGCAA
1 GGAAGCAA
214972 ACTTACACAT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
46 53 1.00
ACGTcount: A:0.36, C:0.23, G:0.20, T:0.21
Consensus pattern (46 bp):
GGAAGCAACATATCACCACCCTAGAAGATGCAATTGATGCCGATTT
Found at i:215087 original size:21 final size:21
Alignment explanation
Indices: 215063--215104 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
215053 AGTTTATTTT
215063 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
215084 TAAACTTTATTTCAATTATCG
1 TAAACTTTATTTCAATTATCG
215105 AACTTGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.05, T:0.48
Consensus pattern (21 bp):
TAAACTTTATTTCAATTATCG
Found at i:215136 original size:33 final size:33
Alignment explanation
Indices: 215091--215198 Score: 164
Period size: 33 Copynumber: 3.3 Consensus size: 33
215081 TCGTAAACTT
215091 TATTTCAA-TTATCGAACTTGGAAGTTTTTAAG
1 TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
* *
215123 TATTTGAATTTATCGAACTTGGAAATTTTTAAG
1 TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
* * *
215156 TATTTGAATTTATCGATCTTGGAAGTATTTAAG
1 TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
215189 TATTTCAATT
1 TATTTCAATT
215199 ATCATAAACT
Statistics
Matches: 69, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
32 7 0.10
33 62 0.90
ACGTcount: A:0.31, C:0.07, G:0.15, T:0.46
Consensus pattern (33 bp):
TATTTCAATTTATCGAACTTGGAAGTTTTTAAG
Found at i:218318 original size:30 final size:30
Alignment explanation
Indices: 218252--218318 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 30
218242 GAGTAACGAG
*
218252 TTTAACGAGCATGAGTCGAGCAATAATTTT
1 TTTAACGAGCATGAGTCAAGCAATAATTTT
218282 TATTAACGAGCATGAGTCAAGCAA-AATTTT
1 T-TTAACGAGCATGAGTCAAGCAATAATTTT
218312 ATTTAAC
1 -TTTAAC
218319 TTAACGAGCA
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
30 12 0.35
31 22 0.65
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.33
Consensus pattern (30 bp):
TTTAACGAGCATGAGTCAAGCAATAATTTT
Found at i:232064 original size:11 final size:12
Alignment explanation
Indices: 232048--232076 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
232038 TTGTATTAGC
232048 TAAATAATATA-
1 TAAATAATATAT
232059 TAAATAATATAT
1 TAAATAATATAT
232071 TAAATA
1 TAAATA
232077 TTTAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TAAATAATATAT
Found at i:234506 original size:19 final size:18
Alignment explanation
Indices: 234465--234500 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
234455 ATTACGTACA
*
234465 AAACAAAAAAAATGTAAC
1 AAACAAAAAAAATGCAAC
234483 AAACAAAAAAATATGCAA
1 AAACAAAAAAA-ATGCAA
234501 TTAACACCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.72, C:0.11, G:0.06, T:0.11
Consensus pattern (18 bp):
AAACAAAAAAAATGCAAC
Found at i:235146 original size:28 final size:29
Alignment explanation
Indices: 235100--235178 Score: 97
Period size: 28 Copynumber: 2.7 Consensus size: 29
235090 TTTTACTAAT
* * *
235100 ATTTTTTAACATTTATTATTAAGGG-TCC
1 ATTTTTTAATATTTGTTATTAAGGGCTCA
* *
235128 ATTTTTTAATACTTGTTATTAGGGGCTCA
1 ATTTTTTAATATTTGTTATTAAGGGCTCA
235157 ATTATTTTAATATTTGTTATTA
1 ATT-TTTTAATATTTGTTATTA
235179 GTAGTACTTT
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
28 21 0.49
29 5 0.12
30 17 0.40
ACGTcount: A:0.28, C:0.08, G:0.11, T:0.53
Consensus pattern (29 bp):
ATTTTTTAATATTTGTTATTAAGGGCTCA
Found at i:235226 original size:19 final size:18
Alignment explanation
Indices: 235185--235227 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
235175 ATTAGTAGTA
235185 CTTTTTAAAATTTAGTTT
1 CTTTTTAAAATTTAGTTT
235203 CTTTTCTAAAATTTA-TTT
1 CTTTT-TAAAATTTAGTTT
*
235221 GTTTTTA
1 CTTTTTA
235228 TTACGAGTCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 2 0.09
18 12 0.52
19 9 0.39
ACGTcount: A:0.26, C:0.07, G:0.05, T:0.63
Consensus pattern (18 bp):
CTTTTTAAAATTTAGTTT
Found at i:235256 original size:30 final size:27
Alignment explanation
Indices: 235222--235288 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 27
235212 AATTTATTTG
235222 TTTTTATTACG-AGTCTAATTGTTTTAATA
1 TTTTTATTA-GAAGT-TAATT-TTTTAATA
*
235251 CTTTTTATTAGAAGTTCATTTTTTAATA
1 -TTTTTATTAGAAGTTAATTTTTTAATA
235279 TTTATTATTA
1 TTT-TTATTA
235289 TGAACATACT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
27 3 0.09
28 14 0.41
29 5 0.15
30 12 0.35
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTTATTAGAAGTTAATTTTTTAATA
Found at i:236582 original size:32 final size:33
Alignment explanation
Indices: 236531--236606 Score: 93
Period size: 33 Copynumber: 2.3 Consensus size: 33
236521 ATTTGCAACA
* * *
236531 AAGTTACGAT-AATTGAAATAC-TAAATACTTTC
1 AAGTT-CGATAAATTCAAATACTTAAAAACTTCC
236563 AAGTTCGATAAATTCAAATACTTAAAAACTTCC
1 AAGTTCGATAAATTCAAATACTTAAAAACTTCC
*
236596 AAGTTTGATAA
1 AAGTTCGATAA
236607 TTGAAACAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 4 0.11
32 15 0.39
33 19 0.50
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (33 bp):
AAGTTCGATAAATTCAAATACTTAAAAACTTCC
Found at i:241208 original size:14 final size:14
Alignment explanation
Indices: 241189--241215 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
241179 TTGTAAGAAT
241189 TAATAATAATATAA
1 TAATAATAATATAA
241203 TAATAATAATATA
1 TAATAATAATATA
241216 TTATTATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
TAATAATAATATAA
Found at i:241533 original size:43 final size:43
Alignment explanation
Indices: 241486--241639 Score: 141
Period size: 43 Copynumber: 3.5 Consensus size: 43
241476 GAATCTGTTT
* *
241486 CACTACTTTTCCCTGAAGATCAGATTCAAGGTTGATTTGCTTC
1 CACTACTCTTCCGTGAAGATCAGATTCAAGGTTGATTTGCTTC
* ** ** ** * *
241529 CACTACTCTTCCGTGGAGATTGGATTGACTTGGAAAGAATCTG-TTT
1 CACTACTCTTCCGTGAAGATCAGATT--CAAGG-TTG-ATTTGCTTC
*
241575 CACTACTCTTCCGTGCAGATCAGATT-AGAGGTTGATTTGCTTC
1 CACTACTCTTCCGTGAAGATCAGATTCA-AGGTTGATTTGCTTC
241618 CACTACTCTTCCGTGAAGATCA
1 CACTACTCTTCCGTGAAGATCA
241640 AATCTGCAAC
Statistics
Matches: 84, Mismatches: 21, Indels: 12
0.72 0.18 0.10
Matches are distributed among these distances:
42 4 0.05
43 45 0.54
44 2 0.02
45 3 0.04
46 26 0.31
47 4 0.05
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.34
Consensus pattern (43 bp):
CACTACTCTTCCGTGAAGATCAGATTCAAGGTTGATTTGCTTC
Found at i:241595 original size:89 final size:89
Alignment explanation
Indices: 241435--241637 Score: 288
Period size: 89 Copynumber: 2.3 Consensus size: 89
241425 CTTGATTGCA
** * * *
241435 TTGCTT-CACTACTCTTTTGTGAATACTT-GATT-ACATGGAAAGAATCTGTTTCACTACTTTTC
1 TTGCTTCCACTACTCTTCCGTGAAGA-TTGGATTGACTTGGAAAGAATCTGTTTCACTACTCTTC
241497 CCTGAAGATCAGATTCA-AGGTTGAT
65 CCTGAAGATCAGATT-AGAGGTTGAT
*
241522 TTGCTTCCACTACTCTTCCGTGGAGATTGGATTGACTTGGAAAGAATCTGTTTCACTACTCTTCC
1 TTGCTTCCACTACTCTTCCGTGAAGATTGGATTGACTTGGAAAGAATCTGTTTCACTACTCTTCC
* *
241587 GTGCAGATCAGATTAGAGGTTGAT
66 CTGAAGATCAGATTAGAGGTTGAT
241611 TTGCTTCCACTACTCTTCCGTGAAGAT
1 TTGCTTCCACTACTCTTCCGTGAAGAT
241638 CAAATCTGCA
Statistics
Matches: 103, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
87 8 0.08
88 20 0.19
89 75 0.73
ACGTcount: A:0.24, C:0.21, G:0.19, T:0.37
Consensus pattern (89 bp):
TTGCTTCCACTACTCTTCCGTGAAGATTGGATTGACTTGGAAAGAATCTGTTTCACTACTCTTCC
CTGAAGATCAGATTAGAGGTTGAT
Found at i:249261 original size:20 final size:20
Alignment explanation
Indices: 249233--249271 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
249223 CAAGAAATTA
249233 ATTGATGCATCGATGCATGG
1 ATTGATGCATCGATGCATGG
* *
249253 ATTGGTGCATCGGTGCATG
1 ATTGATGCATCGATGCATG
249272 CCCTTGAAAA
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:0.21, C:0.15, G:0.33, T:0.31
Consensus pattern (20 bp):
ATTGATGCATCGATGCATGG
Found at i:250013 original size:145 final size:147
Alignment explanation
Indices: 249733--250025 Score: 540
Period size: 145 Copynumber: 2.0 Consensus size: 147
249723 ATTTAGAAAC
249733 TTAAAGATTAAGCTGCTAAGATCAAAGATCAAAAGAGAGATTAGCCATTAGTTTCATAATCAATA
1 TTAAAGATTAAGCTGCTAAGATCAAAGATCAAAAGAGAGATTAGCCATTAGTTTCATAATCAATA
249798 TTCATAATAAATTGTGAAATGGCATAATTGGTCATATGCAACTAATATGTAAATGATGCAAGAAT
66 TTCATAATAAATTGTGAAATGGCATAATTGGTCATATGCAACTAATATGTAAATGATGCAAGAAT
249863 TAACCAAACCAAATATT
131 TAACCAAACCAAATATT
249880 TTAAAGATTAAGCTGCTAAGATCAAAGATC-AAA-AGAGATTAGCCATTAGTTTCATAATCAATA
1 TTAAAGATTAAGCTGCTAAGATCAAAGATCAAAAGAGAGATTAGCCATTAGTTTCATAATCAATA
249943 TTCATAATAAATTGTGAAATGGCATAATTGGTCATAATGCAACT-A-ATGTAAATGATGCAAGAA
66 TTCATAATAAATTGTGAAATGGCATAATTGGTCAT-ATGCAACTAATATGTAAATGATGCAAGAA
250006 TTAAACCAAACCAAATATT
130 TT-AACCAAACCAAATATT
250025 T
1 T
250026 ATAATAAGTT
Statistics
Matches: 144, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
144 20 0.14
145 83 0.58
146 11 0.08
147 30 0.21
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.29
Consensus pattern (147 bp):
TTAAAGATTAAGCTGCTAAGATCAAAGATCAAAAGAGAGATTAGCCATTAGTTTCATAATCAATA
TTCATAATAAATTGTGAAATGGCATAATTGGTCATATGCAACTAATATGTAAATGATGCAAGAAT
TAACCAAACCAAATATT
Found at i:252094 original size:44 final size:44
Alignment explanation
Indices: 252011--252112 Score: 127
Period size: 44 Copynumber: 2.3 Consensus size: 44
252001 AAACCCGACA
* * *
252011 GATGCATCGATGCATGACCATATGCATCGATGCACATTC-AAGG
1 GATGCATCGATGCATCAACATATGAATCGATGCACATTCAAAGG
* *
252054 CG-TGCATCGGTGCATCAACATGATGAATTGATGCACATTCAAAGG
1 -GATGCATCGATGCATCAACAT-ATGAATCGATGCACATTCAAAGG
252099 GATGCATCGATGCA
1 GATGCATCGATGCA
252113 CTGTTAAGTG
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
43 16 0.33
44 18 0.37
45 15 0.31
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.24
Consensus pattern (44 bp):
GATGCATCGATGCATCAACATATGAATCGATGCACATTCAAAGG
Found at i:255940 original size:22 final size:21
Alignment explanation
Indices: 255898--255937 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
255888 GAGTTTGTTT
*
255898 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
255919 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
255938 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:264004 original size:7 final size:7
Alignment explanation
Indices: 263988--264047 Score: 66
Period size: 7 Copynumber: 8.6 Consensus size: 7
263978 GTAAGTATAA
*
263988 TTTAGTG
1 TTTAGGG
263995 TTTAGGG
1 TTTAGGG
264002 TTTAGGG
1 TTTAGGG
*
264009 TTTAGAG
1 TTTAGGG
*
264016 TTTATGG
1 TTTAGGG
*
264023 TTTAGGA
1 TTTAGGG
*
264030 TTTAAGG
1 TTTAGGG
*
264037 TTTAGAG
1 TTTAGGG
264044 TTTA
1 TTTA
264048 TTGCAATGAC
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
7 43 1.00
ACGTcount: A:0.22, C:0.00, G:0.30, T:0.48
Consensus pattern (7 bp):
TTTAGGG
Found at i:264028 original size:28 final size:28
Alignment explanation
Indices: 263994--264048 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
263984 ATAATTTAGT
* *
263994 GTTTAGGGTTTAGGGTTTAGAGTTTATG
1 GTTTAGGATTTAAGGTTTAGAGTTTATG
264022 GTTTAGGATTTAAGGTTTAGAGTTTAT
1 GTTTAGGATTTAAGGTTTAGAGTTTAT
264049 TGCAATGACA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (28 bp):
GTTTAGGATTTAAGGTTTAGAGTTTATG
Found at i:264107 original size:11 final size:11
Alignment explanation
Indices: 264091--264153 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
264081 GTATTATAGA
264091 ATTTTTAATAT
1 ATTTTTAATAT
264102 ATTTTTAA-A-
1 ATTTTTAATAT
264111 ATTTTATAAT-T
1 ATTTT-TAATAT
*** * *
264122 ATCAATAGTGT
1 ATTTTTAATAT
264133 ATTTTTAATAT
1 ATTTTTAATAT
264144 ATTTTTAATA
1 ATTTTTAATA
264154 ATGTAATTTT
Statistics
Matches: 39, Mismatches: 9, Indels: 8
0.70 0.16 0.14
Matches are distributed among these distances:
9 5 0.13
10 7 0.18
11 27 0.69
ACGTcount: A:0.38, C:0.02, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTTTTAATAT
Found at i:269290 original size:36 final size:36
Alignment explanation
Indices: 269250--269358 Score: 97
Period size: 36 Copynumber: 3.2 Consensus size: 36
269240 GTAGCGAGAT
269250 GAGCAAAAGTTTAATGAGCTTAACGAGCAACAAGTC
1 GAGCAAAAGTTTAATGAGCTTAACGAGCAACAAGTC
269286 GAGCAAAAAAG-TT--T---CTTAACGAGC-ACAAGTC
1 GAGC--AAAAGTTTAATGAGCTTAACGAGCAACAAGTC
* * * * *
269317 AAGTAAAATTTTAACGAGCTTAACGAGCAACGAGTC
1 GAGCAAAAGTTTAATGAGCTTAACGAGCAACAAGTC
*
269353 TAGCAA
1 GAGCAA
269359 CAAATTTTCT
Statistics
Matches: 57, Mismatches: 7, Indels: 18
0.70 0.09 0.22
Matches are distributed among these distances:
29 4 0.07
30 2 0.04
31 9 0.16
32 10 0.18
35 11 0.19
36 14 0.25
37 2 0.04
38 5 0.09
ACGTcount: A:0.42, C:0.17, G:0.20, T:0.20
Consensus pattern (36 bp):
GAGCAAAAGTTTAATGAGCTTAACGAGCAACAAGTC
Found at i:269341 original size:67 final size:67
Alignment explanation
Indices: 269253--269402 Score: 212
Period size: 67 Copynumber: 2.2 Consensus size: 67
269243 GCGAGATGAG
* *
269253 CAAAAGTTTAATGAGCTTAACGAGCAACAAGTCGAGCAAAAAAGTTTCTTAACGAGCACAAGTC-
1 CAAAATTTTAACGAGCTTAACGAGCAACAAGTCGAGCAAAAAAGTTTCTTAACGAGCACAAGTCG
269317 AA
66 AA
* * * * * *
269319 GTAAAATTTTAACGAGCTTAACGAGCAACGAGTCTAGCAACAAATTTTCTTAACGAGCACGAGTC
1 -CAAAATTTTAACGAGCTTAACGAGCAACAAGTCGAGCAAAAAAGTTTCTTAACGAGCACAAGTC
269384 GAA
65 GAA
269387 CAAAATTTTAACGAGC
1 CAAAATTTTAACGAGC
269403 AATGAGTCGA
Statistics
Matches: 73, Mismatches: 9, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
67 71 0.97
68 2 0.03
ACGTcount: A:0.41, C:0.19, G:0.18, T:0.22
Consensus pattern (67 bp):
CAAAATTTTAACGAGCTTAACGAGCAACAAGTCGAGCAAAAAAGTTTCTTAACGAGCACAAGTCG
AA
Found at i:269400 original size:26 final size:29
Alignment explanation
Indices: 269335--269412 Score: 90
Period size: 27 Copynumber: 2.7 Consensus size: 29
269325 TTTTAACGAG
*
269335 CTTAACGAGCAACGAGTCTAGCAACAAATTTT
1 CTTAACGAGCAACGAGTC--G-AACAAATATT
269367 CTTAACGAGC-ACGAGTCGAACAAA-ATT
1 CTTAACGAGCAACGAGTCGAACAAATATT
*
269394 -TTAACGAGCAATGAGTCGA
1 CTTAACGAGCAACGAGTCGA
269413 GTTGAGAAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
26 9 0.21
27 10 0.23
28 6 0.14
29 1 0.02
31 7 0.16
32 10 0.23
ACGTcount: A:0.38, C:0.21, G:0.19, T:0.22
Consensus pattern (29 bp):
CTTAACGAGCAACGAGTCGAACAAATATT
Found at i:270881 original size:13 final size:13
Alignment explanation
Indices: 270863--270892 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
270853 AGAGCACATT
270863 ATCACTATACTAA
1 ATCACTATACTAA
270876 ATCACTATACTAA
1 ATCACTATACTAA
270889 ATCA
1 ATCA
270893 AAATCAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.47, C:0.23, G:0.00, T:0.30
Consensus pattern (13 bp):
ATCACTATACTAA
Found at i:271660 original size:21 final size:21
Alignment explanation
Indices: 271618--271660 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
271608 TATTAAGCCG
***
271618 AAATTGTAAATTTTAGTGATT
1 AAATTGTAAATTTTAAAAATT
*
271639 AAATTGTAATTTTTAAAAATT
1 AAATTGTAAATTTTAAAAATT
271660 A
1 A
271661 TAAAGGGAAA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (21 bp):
AAATTGTAAATTTTAAAAATT
Found at i:273755 original size:13 final size:13
Alignment explanation
Indices: 273737--273770 Score: 59
Period size: 13 Copynumber: 2.6 Consensus size: 13
273727 TTAAAACGGA
273737 TTTGGAGCTCGGG
1 TTTGGAGCTCGGG
273750 TTTGGAGCTCGGG
1 TTTGGAGCTCGGG
*
273763 TTTAGAGC
1 TTTGGAGC
273771 CTTAGATGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.12, C:0.15, G:0.41, T:0.32
Consensus pattern (13 bp):
TTTGGAGCTCGGG
Found at i:274791 original size:2 final size:2
Alignment explanation
Indices: 274784--274828 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
274774 ATCAAAGTAA
274784 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
274826 AT A
1 AT A
274829 CATAAAGTAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:275381 original size:35 final size:35
Alignment explanation
Indices: 275342--275413 Score: 117
Period size: 35 Copynumber: 2.1 Consensus size: 35
275332 CTAAAAAAAC
* * *
275342 CTATTTTAGACTAGTATTTGAGTCCTAATCCAACT
1 CTATTCTAAACTAGTATTTGAGTCATAATCCAACT
275377 CTATTCTAAACTAGTATTTGAGTCATAATCCAACT
1 CTATTCTAAACTAGTATTTGAGTCATAATCCAACT
275412 CT
1 CT
275414 TCTTTATTGG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.39
Consensus pattern (35 bp):
CTATTCTAAACTAGTATTTGAGTCATAATCCAACT
Found at i:290740 original size:24 final size:23
Alignment explanation
Indices: 290713--290761 Score: 62
Period size: 24 Copynumber: 2.1 Consensus size: 23
290703 AGTTTATTTT
*
290713 AATATATAAAATTATCAATAAATA
1 AATACATAAAATTAT-AATAAATA
* *
290737 AATACATAATATTATAATATATA
1 AATACATAAAATTATAATAAATA
290760 AA
1 AA
290762 AAAATAAATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
23 9 0.41
24 13 0.59
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (23 bp):
AATACATAAAATTATAATAAATA
Found at i:296808 original size:2 final size:2
Alignment explanation
Indices: 296801--296829 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
296791 AGCTCTGCCC
296801 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
296830 AATTTAATGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:301689 original size:2 final size:2
Alignment explanation
Indices: 301684--301713 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
301674 TATAAATTTG
301684 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
301714 CACTTAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301840 original size:2 final size:2
Alignment explanation
Indices: 301833--301858 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
301823 AGTTAATTCG
301833 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
301859 CACTTAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:301866 original size:145 final size:145
Alignment explanation
Indices: 301688--301983 Score: 556
Period size: 145 Copynumber: 2.0 Consensus size: 145
301678 AATTTGATAT
* *
301688 ATATATATATATATATATATATATATCACTTAATTGCCGAATTTAACATGTATTAGAATCAAAAT
1 ATATATATATATATATATATATATATCACTTAATTGCCGAATTTAAAAGGTATTAGAATCAAAAT
301753 ATCTAAAAATATAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACA
66 ATCTAAAAATATAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACA
301818 TTTAAAGTTAATTCG
131 TTTAAAGTTAATTCG
301833 ATATATATATATATATATATATATATCACTTAATTGCCGAATTTAAAAGGTATTAGAATCAAAAT
1 ATATATATATATATATATATATATATCACTTAATTGCCGAATTTAAAAGGTATTAGAATCAAAAT
*
301898 ATCTAAAAGTATAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACA
66 ATCTAAAAATATAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACA
301963 TTTAAAGTTAATTCG
131 TTTAAAGTTAATTCG
301978 AGTATA
1 A-TATA
301984 GTTTAGATAA
Statistics
Matches: 147, Mismatches: 3, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
145 143 0.97
146 4 0.03
ACGTcount: A:0.46, C:0.09, G:0.06, T:0.38
Consensus pattern (145 bp):
ATATATATATATATATATATATATATCACTTAATTGCCGAATTTAAAAGGTATTAGAATCAAAAT
ATCTAAAAATATAATTATAATGTTAGAAATATCACATATTCTTTAAACAAAAAATTCATTATACA
TTTAAAGTTAATTCG
Found at i:302192 original size:13 final size:14
Alignment explanation
Indices: 302165--302191 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
302155 CCTGATAATT
302165 TAAAAAAATTAAAA
1 TAAAAAAATTAAAA
302179 TAAAAAAATTAAA
1 TAAAAAAATTAAA
302192 TTATATATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAAAAAATTAAAA
Found at i:302198 original size:2 final size:2
Alignment explanation
Indices: 302193--302247 Score: 110
Period size: 2 Copynumber: 27.5 Consensus size: 2
302183 AAAATTAAAT
302193 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
302235 TA TA TA TA TA TA T
1 TA TA TA TA TA TA T
302248 TGAAAAGAAA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 53 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:302980 original size:19 final size:19
Alignment explanation
Indices: 302952--302988 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
302942 TTTTCATTCC
*
302952 ATATCAATTTGTTTAATTT
1 ATATCAATTTATTTAATTT
*
302971 ATATCCATTTATTTAATT
1 ATATCAATTTATTTAATT
302989 AGCCCAATAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.32, C:0.08, G:0.03, T:0.57
Consensus pattern (19 bp):
ATATCAATTTATTTAATTT
Found at i:303164 original size:23 final size:22
Alignment explanation
Indices: 303064--303180 Score: 96
Period size: 23 Copynumber: 5.2 Consensus size: 22
303054 CACCACTGCT
303064 CACATAATTTG-CACCGAAGTG-C
1 CACATAATTTGTC-CCGAAG-GAC
* *
303086 CACAT-ATTTGTCCCAAAGGAT
1 CACATAATTTGTCCCGAAGGAC
* * *
303107 CATATAGATTTGTCCTGAATGAC
1 CACATA-ATTTGTCCCGAAGGAC
**
303130 CACATGGGTTTGTCCCGAAGGAC
1 CACAT-AATTTGTCCCGAAGGAC
*
303153 CACATAATTTTGTCTCGAAGGAC
1 CACATAA-TTTGTCCCGAAGGAC
303176 CACAT
1 CACAT
303181 TGAACCCTCG
Statistics
Matches: 74, Mismatches: 15, Indels: 11
0.74 0.15 0.11
Matches are distributed among these distances:
20 1 0.01
21 14 0.19
22 6 0.08
23 53 0.72
ACGTcount: A:0.30, C:0.24, G:0.19, T:0.27
Consensus pattern (22 bp):
CACATAATTTGTCCCGAAGGAC
Found at i:303165 original size:46 final size:46
Alignment explanation
Indices: 303092--303180 Score: 110
Period size: 46 Copynumber: 1.9 Consensus size: 46
303082 GTGCCACATA
* * *
303092 TTTGTCCCAAAGGATCATATAGATTTGTC-CTGAATGACCACATGGG
1 TTTGTCCCAAAGGACCACATAGATTTGTCTC-GAAGGACCACATGGG
*
303138 TTTGTCCCGAAGGACCACATA-ATTTTGTCTCGAAGGACCACAT
1 TTTGTCCCAAAGGACCACATAGA-TTTGTCTCGAAGGACCACAT
303181 TGAACCCTCG
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
45 1 0.03
46 35 0.95
47 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.29
Consensus pattern (46 bp):
TTTGTCCCAAAGGACCACATAGATTTGTCTCGAAGGACCACATGGG
Done.