Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005248.1 Hibiscus syriacus cultivar Beakdansim tig00011871_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: 65838
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.33
Found at i:259 original size:113 final size:113
Alignment explanation
Indices: 1--361 Score: 494
Period size: 116 Copynumber: 3.2 Consensus size: 113
* * *
1 CAACTGTAAATGTTAATCCACCTCCTTCTGTGATGGAATCCAACCAAGGTTGAACAGTTGTTCTC
1 CAACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAAT-CAACCAAGGTTGAACAGTTCTTCTC
* * * * * *
66 ATTATGAACTTATTCTCCCTCGTCGAATGAGTTATTCTCATTATGAACTTT
65 ATTATGAACTTCTTCTCCCTCATTGGATAAG-T-TTCTCATTATGAACTCT
*
117 CCACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAAACCAAGGTTGAACAGTTCTTCTC
1 CAACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATC-AACCAAGGTTGAACAGTTCTTCTC
* *
182 ATTATGAATTTCTTTTCCCTCATTGGATAAG-TTCTCATTATGAACTCT
65 ATTATGAACTTCTTCTCCCTCATTGGATAAGTTTCTCATTATGAACTCT
* * *
230 CTACTGGAAATGTTGATCCACCTCATTCTGTGATGGAATCGACCAAGGTTGAACAG-TCTTCTCA
1 CAACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAACCAAGGTTGAACAGTTCTTCTCA
294 TTATGAAAACTTCTTCTCCCTCATTGGATAAGTTCTTCTCATTATGAACTCT
66 TTATG--AACTTCTTCTCCCTCATTGGATAAG-T-TTCTCATTATGAACTCT
346 CAAC-GGAAATGTTGAT
1 CAACTGGAAATGTTGAT
362 TGTCTTATCT
Statistics
Matches: 221, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
111 13 0.06
112 15 0.07
113 77 0.35
115 13 0.06
116 103 0.47
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (113 bp):
CAACTGGAAATGTTGATCCACCTCCTTCTGTGATGGAATCAACCAAGGTTGAACAGTTCTTCTCA
TTATGAACTTCTTCTCCCTCATTGGATAAGTTTCTCATTATGAACTCT
Found at i:875 original size:71 final size:72
Alignment explanation
Indices: 628--971 Score: 287
Period size: 71 Copynumber: 4.8 Consensus size: 72
618 CTCGAGTGAG
* * * * *
628 AAATTTCTTATTTAAGGGAAAC-CTCTCAAGTGA-GACAAAATGGTTTTAAGAAAAACCATCTCA
1 AAATTTCTTGTTCAAGGGAAACTGTCTCTAGTGAGGACAAACTGGTTTTAAGAAAAACCATCTCA
*
691 AGTGAGA
66 AGTAAGA
* * * * * *
698 TACTTT-TTGTTTCAAGGGAAAAACTGTCTCAAGCGA-GACAAAGTTGTTTTTAAGAAAAACCAT
1 AAATTTCTTG-TTCAAGGG--AAACTGTCTCTAGTGAGGACAAA-CTGGTTTTAAGAAAAACCAT
* *
761 CTCGAGTGAATA
62 CTCAAGT-AAGA
* * * **
773 AAATTTCTTGTTTTAAGGGAAATTGTCTCTAGTGAGGAGAAACTAATTTTAAG-AAAACCATCTC
1 AAATTTCTTG-TTCAAGGGAAACTGTCTCTAGTGAGGACAAACTGGTTTTAAGAAAAACCATCTC
837 AAGTAAGA
65 AAGTAAGA
* * *
845 AAATTTCTTGTTCAAGGGAAACTGTCTCTAGTG-GGACGAAACTTGTTTTGAGAAAAACAATCTC
1 AAATTTCTTGTTCAAGGGAAACTGTCTCTAGTGAGGAC-AAACTGGTTTTAAGAAAAACCATCTC
*
909 AAGTGAGA
65 AAGTAAGA
* * *
917 TAAATTT-GT-TTCAAGGGAAAACTAT-TCTAGTGA-GACAAA-AGTGTTTTAAGAAAAA
1 -AAATTTCTTGTTCAAGGG-AAACTGTCTCTAGTGAGGACAAACTG-GTTTTAAGAAAAA
972 TACTCTCAAG
Statistics
Matches: 224, Mismatches: 36, Indels: 28
0.78 0.12 0.10
Matches are distributed among these distances:
69 2 0.01
70 29 0.13
71 50 0.22
72 41 0.18
73 35 0.16
74 45 0.20
75 11 0.05
76 11 0.05
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.30
Consensus pattern (72 bp):
AAATTTCTTGTTCAAGGGAAACTGTCTCTAGTGAGGACAAACTGGTTTTAAGAAAAACCATCTCA
AGTAAGA
Found at i:984 original size:35 final size:34
Alignment explanation
Indices: 888--986 Score: 83
Period size: 35 Copynumber: 2.8 Consensus size: 34
878 GGACGAAACT
* * * **
888 TGTTTTGAGAAAAACAATCTCAAGTGAGATAAATT
1 TGTTTTAAGAAAAA-TATCTCAAGTGAGACAAAAG
* * *
923 TGTTTCAAGGGAAAACTAT-TCTAGTGAGACAAAAG
1 TGTTTTAA--GAAAAATATCTCAAGTGAGACAAAAG
958 TGTTTTAAGAAAAATACTCTCAAGTGAGA
1 TGTTTTAAGAAAAATA-TCTCAAGTGAGA
987 TAACTTTCTG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
33 7 0.14
34 1 0.02
35 34 0.69
36 2 0.04
37 5 0.10
ACGTcount: A:0.41, C:0.10, G:0.19, T:0.29
Consensus pattern (34 bp):
TGTTTTAAGAAAAATATCTCAAGTGAGACAAAAG
Found at i:2493 original size:5 final size:5
Alignment explanation
Indices: 2480--2584 Score: 51
Period size: 5 Copynumber: 20.8 Consensus size: 5
2470 TATTGGATAG
* * *
2480 TTTTC TTTTT TTTTC -TTTC GTCTCTC TTTTC TTTT- TTTCC TTTT- TTTTC
1 TTTTC TTTTC TTTTC TTTTC -T-TTTC TTTTC TTTTC TTTTC TTTTC TTTTC
* * *
2529 TATTTTT TTTTC TGTT- TTTTC -TTTC TTTTTC TTGTT- TTTTC TTCTC
1 --TTTTC TTTTC TTTTC TTTTC TTTTC -TTTTC TT-TTC TTTTC TTTTC
2575 TTTTCC TTTT
1 TTTT-C TTTT
2585 TTCTTTTTTT
Statistics
Matches: 75, Mismatches: 12, Indels: 25
0.67 0.11 0.22
Matches are distributed among these distances:
4 20 0.27
5 36 0.48
6 12 0.16
7 7 0.09
ACGTcount: A:0.01, C:0.18, G:0.03, T:0.78
Consensus pattern (5 bp):
TTTTC
Found at i:2495 original size:10 final size:10
Alignment explanation
Indices: 2480--2594 Score: 67
Period size: 10 Copynumber: 11.2 Consensus size: 10
2470 TATTGGATAG
2480 TTTTCTTTTT
1 TTTTCTTTTT
2490 TTTTCTTTCGTCT
1 TTTTCTTT--T-T
*
2503 CTCTTT-TCTTT
1 -T-TTTCTTTTT
*
2514 TTTTCCTTTT
1 TTTTCTTTTT
2524 TTTTCTATTTT
1 TTTTCT-TTTT
*
2535 TTTT-TCTGTT
1 TTTTCT-TTTT
*
2545 TTTTCTTTCT
1 TTTTCTTTTT
*
2555 TTTTCTTGTT
1 TTTTCTTTTT
* *
2565 TTTTCTTCTC
1 TTTTCTTTTT
*
2575 TTTTC--CTT
1 TTTTCTTTTT
2583 TTTTCTTTTT
1 TTTTCTTTTT
2593 TT
1 TT
2595 CTCTATTTTA
Statistics
Matches: 81, Mismatches: 14, Indels: 20
0.70 0.12 0.17
Matches are distributed among these distances:
8 7 0.09
9 3 0.04
10 52 0.64
11 10 0.12
12 2 0.02
13 1 0.01
14 3 0.04
15 3 0.04
ACGTcount: A:0.01, C:0.17, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTTCTTTTT
Found at i:2535 original size:12 final size:11
Alignment explanation
Indices: 2511--2594 Score: 64
Period size: 12 Copynumber: 7.4 Consensus size: 11
2501 CTCTCTTTTC
*
2511 TTTTTTTC-CT
1 TTTTTTTCTTT
2521 TTTTTTTCTATT
1 TTTTTTTCT-TT
2533 TTTTTTTCTGTT
1 TTTTTTTCT-TT
2545 TTTTCTTTCTTT
1 TTTT-TTTCTTT
* *
2557 TTCTTGT-TTT
1 TTTTTTTCTTT
* *
2567 TTCTTCTCTTT
1 TTTTTTTCTTT
2578 TCCTTTTTTCTTT
1 T--TTTTTTCTTT
2591 TTTT
1 TTTT
2595 CTCTATTTTA
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
10 17 0.28
11 9 0.15
12 21 0.34
13 14 0.23
ACGTcount: A:0.01, C:0.15, G:0.02, T:0.81
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:2537 original size:21 final size:20
Alignment explanation
Indices: 2511--2594 Score: 84
Period size: 20 Copynumber: 4.2 Consensus size: 20
2501 CTCTCTTTTC
2511 TTTTTTTCCTTTTTTTTCTAT
1 TTTTTTTCCTTTTTTTTCT-T
* *
2532 TTTTTTTTCTGTTTTTTCTT
1 TTTTTTTCCTTTTTTTTCTT
*
2552 TCTTTTT-CTTGTTTTTTCTT
1 TTTTTTTCCTT-TTTTTTCTT
* *
2572 CTCTTTTCC--TTTTTTCTT
1 TTTTTTTCCTTTTTTTTCTT
2590 TTTTT
1 TTTTT
2595 CTCTATTTTA
Statistics
Matches: 52, Mismatches: 9, Indels: 7
0.76 0.13 0.10
Matches are distributed among these distances:
18 12 0.23
19 2 0.04
20 20 0.38
21 18 0.35
ACGTcount: A:0.01, C:0.15, G:0.02, T:0.81
Consensus pattern (20 bp):
TTTTTTTCCTTTTTTTTCTT
Found at i:2603 original size:19 final size:19
Alignment explanation
Indices: 2506--2629 Score: 78
Period size: 20 Copynumber: 6.4 Consensus size: 19
2496 TTCGTCTCTC
*
2506 TTTTCTTTTTTTC-CTTTT
1 TTTTCTTTTTTTCTCTATT
* *
2524 TTTTCTATTTTTTTTTCTGTT
1 TTTTC--TTTTTTTCTCTATT
*
2545 TTTTCTTTCTTTT-TCTTGTT
1 TTTTCTTT-TTTTCTC-TATT
2565 TTTTCTTCTCTTTTC-C--TT
1 TTTTCTT-T-TTTTCTCTATT
2583 TTTTCTTTTTTTCTCTATT
1 TTTTCTTTTTTTCTCTATT
* * *
2602 TTATGTTTTTTTCGCTATAT
1 TTTTCTTTTTTTCTCTAT-T
2622 CTTTTCTT
1 -TTTTCTT
2630 CTTTCTCTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 21
0.76 0.06 0.18
Matches are distributed among these distances:
16 5 0.06
17 2 0.02
18 14 0.16
19 22 0.25
20 23 0.26
21 21 0.24
ACGTcount: A:0.04, C:0.16, G:0.03, T:0.77
Consensus pattern (19 bp):
TTTTCTTTTTTTCTCTATT
Found at i:6606 original size:26 final size:25
Alignment explanation
Indices: 6559--6620 Score: 65
Period size: 26 Copynumber: 2.4 Consensus size: 25
6549 AAATTGCATA
*
6559 AAATCTAATAATAGTGAATAAATGCA-
1 AAAT-TAAAAATAGTGAATAAAT-CAG
6585 ATAATTAAAAATAGT-AACTAAATCAG
1 A-AATTAAAAATAGTGAA-TAAATCAG
6611 AAATTAAAAA
1 AAATTAAAAA
6621 GTGACTAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
25 13 0.41
26 16 0.50
27 3 0.09
ACGTcount: A:0.60, C:0.06, G:0.08, T:0.26
Consensus pattern (25 bp):
AAATTAAAAATAGTGAATAAATCAG
Found at i:9019 original size:35 final size:34
Alignment explanation
Indices: 8973--9158 Score: 264
Period size: 35 Copynumber: 5.3 Consensus size: 34
8963 AAAGTTTGCA
*
8973 TCGATTCAAGTCGAACGGAAGAAAGCATCACACTT
1 TCGATTCAAGTCGAACGGAAG-AAGCATCGCACTT
* *
9008 TCGATTCAAGTCGAACGGAAGGAAGCGTTGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
*
9043 TCGATTCAAGTAGAACGGAATGAAGCATCGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
* *
9078 TCGATTTAAGTCGAATGGAATGAAGCATCGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
*
9113 TCGATTCATGTCGAACGGAAGGAAGCATCGCACTT
1 TCGATTCAAGTCGAACGGAA-GAAGCATCGCACTT
9148 TCGATTCAAGT
1 TCGATTCAAGT
9159 GTTCATCTTT
Statistics
Matches: 135, Mismatches: 15, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
35 134 0.99
36 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (34 bp):
TCGATTCAAGTCGAACGGAAGAAGCATCGCACTT
Found at i:10752 original size:51 final size:50
Alignment explanation
Indices: 10661--10765 Score: 129
Period size: 51 Copynumber: 2.1 Consensus size: 50
10651 AGCAGTAAAG
** * ** *
10661 CGCGCCCCCTGCACTGCGTTATACGATGATTTGGCGCCACGTGGGGTATAA
1 CGCGCCCCCTGCACCACGCTATACGATGAGCTGGCACCACGT-GGGTATAA
* *
10712 CGCGCCCCCTGCACCACGCTATACGGTGAGCTGGCACCACGTGGGTATAG
1 CGCGCCCCCTGCACCACGCTATACGATGAGCTGGCACCACGTGGGTATAA
10762 CGCG
1 CGCG
10766 TCCGTATAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 1
0.84 0.15 0.02
Matches are distributed among these distances:
50 11 0.24
51 35 0.76
ACGTcount: A:0.17, C:0.33, G:0.30, T:0.19
Consensus pattern (50 bp):
CGCGCCCCCTGCACCACGCTATACGATGAGCTGGCACCACGTGGGTATAA
Found at i:10889 original size:49 final size:51
Alignment explanation
Indices: 10811--10933 Score: 189
Period size: 49 Copynumber: 2.5 Consensus size: 51
10801 CACGTAGGGG
**
10811 TATAGCGCGGATCAGGTACCGCGCTATACCTTTACTCCT-A-ATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTA
*
10860 TATAGTGCGGGGCAGGTACCGCGAC-ATACCTTTACTCCTGACATAATTTTA
1 TATAGCGCGGGGCAGGTACCGCG-CTATACCTTTACTCCTGACATAATTTTA
10911 TATAGCGCGGGGCAGGTACCGCG
1 TATAGCGCGGGGCAGGTACCGCG
10934 TTTTGTATAA
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
49 34 0.51
50 2 0.03
51 31 0.46
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (51 bp):
TATAGCGCGGGGCAGGTACCGCGCTATACCTTTACTCCTGACATAATTTTA
Found at i:16305 original size:110 final size:111
Alignment explanation
Indices: 16111--16331 Score: 372
Period size: 110 Copynumber: 2.0 Consensus size: 111
16101 ATTACAAAAA
* * * *
16111 TTAATTCTTAATCTAATAATCATGCATTAAATGAATCAACTAATTATTAATAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
16176 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTCGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
*
16222 TTAATTATTAATATAATAATCATGCATTAAATAAAT-AACTAAATATTATTAATAATTTAAATTA
1 TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
*
16286 AATTAAAACGTTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
66 AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
16332 ATGATTTCCA
Statistics
Matches: 103, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
110 70 0.68
111 33 0.32
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.36
Consensus pattern (111 bp):
TTAATTATTAATATAATAATCATGCATTAAATAAATCAACTAAATATTAATAATAATTTAAATTA
AATTAAAACATTAAAATGTTACCGTATCAGCAAAGTGTAGAGATAT
Found at i:16470 original size:10 final size:10
Alignment explanation
Indices: 16455--16486 Score: 64
Period size: 10 Copynumber: 3.2 Consensus size: 10
16445 ACCTTAAAAA
16455 GAGAGAATTT
1 GAGAGAATTT
16465 GAGAGAATTT
1 GAGAGAATTT
16475 GAGAGAATTT
1 GAGAGAATTT
16485 GA
1 GA
16487 TGTGATAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:19339 original size:6 final size:6
Alignment explanation
Indices: 19318--19351 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
19308 GCTCGGCTCG
19318 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
19352 ACGTGTCTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.36
6 18 0.64
ACGTcount: A:0.00, C:0.18, G:0.53, T:0.29
Consensus pattern (6 bp):
GGTCGT
Found at i:22502 original size:67 final size:66
Alignment explanation
Indices: 22429--22638 Score: 204
Period size: 67 Copynumber: 3.0 Consensus size: 66
22419 GATAATTATC
* * * ** *
22429 GATACTTTTAAATATTGATAAAGTTGATAAAAAAAATCAAAATTTAAAATATCGATACTTATGTG
1 GATACTTTTAAATATTGAAAAAATTGAT-AAAAAGATTGAAATTTAAAATATCAATACTTATGTG
22494 AT
65 AT
** * * * * *
22496 GATACTTTTGTATATTGAAAAAATTAATGAAGATGATTGATAGTTAAAATATCAATACTTATGCG
1 GATACTTTTAAATATTGAAAAAATTGAT-AAAAAGATTGAAATTTAAAATATCAATACTTAT---
22561 GTAATGATT
62 G---TGA-T
* *
22570 GATACTTTTAAATATTGAAAAAATTGATAAAAAGATTGAAATTTAAAATATCAATTCTTATGCGA
1 GATACTTTTAAATATTGAAAAAATTGATAAAAAGATTGAAATTTAAAATATCAATACTTATGTGA
22635 T
66 T
22636 GAT
1 GAT
22639 GATCGATACT
Statistics
Matches: 113, Mismatches: 23, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
66 4 0.04
67 50 0.44
70 2 0.02
73 31 0.27
74 26 0.23
ACGTcount: A:0.45, C:0.06, G:0.13, T:0.37
Consensus pattern (66 bp):
GATACTTTTAAATATTGAAAAAATTGATAAAAAGATTGAAATTTAAAATATCAATACTTATGTGA
T
Found at i:22547 original size:141 final size:139
Alignment explanation
Indices: 22279--22672 Score: 436
Period size: 141 Copynumber: 2.7 Consensus size: 139
22269 TTAATATATG
* * *
22279 ATTATCAATAC-TTTAAATGTTGAAAAGATT-A-ACAAAAAGATCAAAATTTAAAATATCGATAT
1 ATTATCGATACTTTTAAATATTGAAAAG-TTGATA-AAAAAGATCAAAATTTAAAATATCGATAC
** *
22341 TTATGTGATGATGATCGATAGTTTTATATTGAAAAAATTGCTGAAGGTGATTGATAGTTAAAATA
64 TTATGTGATGAT-A-C--T--TTTTATATTGAAAAAATTAATGAAGATGATTGATAGTTAAAATA
**
22406 TTGATACTTATGCGATA
123 TCAATACTTATGCGATA
*
22423 ATTATCGATACTTTTAAATATTGATAAAGTTGATAAAAAAAATCAAAATTTAAAATATCGATACT
1 ATTATCGATACTTTTAAATATTGA-AAAGTTGATAAAAAAGATCAAAATTTAAAATATCGATACT
22488 TATGTGATGATACTTTTGTATATTGAAAAAATTAATGAAGATGATTGATAGTTAAAATATCAATA
65 TATGTGATGATACTTTT-TATATTGAAAAAATTAATGAAGATGATTGATAGTTAAAATATCAATA
*
22553 CTTATGCGGTA
129 CTTATGCGATA
* * * ** * *
22564 ATGATTGATACTTTTAAATATTGAAAAAATTGAT-AAAAAGATTGAAATTTAAAATATCAATTCT
1 ATTATCGATACTTTTAAATATTG-AAAAGTTGATAAAAAAGATCAAAATTTAAAATATCGATAC-
22628 TATGCGATGATGATCGATACTTTTATATATTGAAAAAATTAATGA
64 T-T---ATG-TGAT-GATACTTTT-TATATTGAAAAAATTAATGA
22673 GAATGTTTTT
Statistics
Matches: 218, Mismatches: 19, Indels: 23
0.84 0.07 0.09
Matches are distributed among these distances:
140 27 0.12
141 82 0.38
142 3 0.01
144 11 0.05
145 17 0.08
146 48 0.22
147 30 0.14
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (139 bp):
ATTATCGATACTTTTAAATATTGAAAAGTTGATAAAAAAGATCAAAATTTAAAATATCGATACTT
ATGTGATGATACTTTTTATATTGAAAAAATTAATGAAGATGATTGATAGTTAAAATATCAATACT
TATGCGATA
Found at i:22624 original size:73 final size:74
Alignment explanation
Indices: 22286--22672 Score: 339
Period size: 73 Copynumber: 5.4 Consensus size: 74
22276 ATGATTATCA
* * ** ** * *
22286 ATAC-TTTAAATGTTGAAAAGATT-AACAAAAAGATCAAAATTTAAAATATCGATATTTATGTGA
1 ATACTTTTAAATATTGAAAAAATTGATGAAAAAGATTGAAATTTAAAATATCGATACTTATGCGA
*
22349 TGATGATCG
66 TAATGATCG
* * *** * * *
22358 ATAGTTTT--ATATTGAAAAAATTGCTGAAGGTGATTGATAGTTAAAATATTGATACTTATGCGA
1 ATACTTTTAAATATTGAAAAAATTGATGAAAAAGATTGAAATTTAAAATATCGATACTTATGCGA
*
22421 TAATTATCG
66 TAATGATCG
* * * * **
22430 ATACTTTTAAATATTGATAAAGTTGATAAAAAAAATCAAAATTTAAAATATCGATACTTAT--G-
1 ATACTTTTAAATATTGAAAAAATTGATGAAAAAGATTGAAATTTAAAATATCGATACTTATGCGA
22492 ---TGAT-G
66 TAATGATCG
** * * * * * * *
22497 ATACTTTTGTATATTGAAAAAATTAATGAAGATGATTGATAGTTAAAATATCAATACTTATGCGG
1 ATACTTTTAAATATTGAAAAAATTGATGAAAAAGATTGAAATTTAAAATATCGATACTTATGCGA
*
22562 TAATGATTG
66 TAATGATCG
* *
22571 ATACTTTTAAATATTGAAAAAATTGAT-AAAAAGATTGAAATTTAAAATATCAATTCTTATGCGA
1 ATACTTTTAAATATTGAAAAAATTGATGAAAAAGATTGAAATTTAAAATATCGATACTTATGCGA
*
22635 TGATGATCG
66 TAATGATCG
* *
22644 ATACTTTTATATATTGAAAAAATTAATGA
1 ATACTTTTAAATATTGAAAAAATTGATGA
22673 GAATGTTTTT
Statistics
Matches: 243, Mismatches: 60, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
67 48 0.20
68 3 0.01
69 1 0.00
71 12 0.05
72 45 0.19
73 70 0.29
74 64 0.26
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (74 bp):
ATACTTTTAAATATTGAAAAAATTGATGAAAAAGATTGAAATTTAAAATATCGATACTTATGCGA
TAATGATCG
Found at i:23180 original size:73 final size:72
Alignment explanation
Indices: 22960--23182 Score: 202
Period size: 72 Copynumber: 3.1 Consensus size: 72
22950 CATAATATAT
* * * * *
22960 GTATCAATATTTTAACTATCGAACATCTTCATCAACTTTTTCAATATATAAAAGTA-CTGATCAT
1 GTATCAATATTTTAACTTTAGATC-T-TTCTTCAACTTTTTCAATATTTAAAAGTATC-GATCAT
* *
23024 CGTCGCATAA
63 CATCACATAA
** * * ** * * *
23034 GTATTGATATTTTAAATTTTGATCTTT-TTACAATCAATTT-AGTATTTAAAATTATCGATCATT
1 GTATCAATATTTTAACTTTAGATCTTTCTT-CAA-CTTTTTCAATATTTAAAAGTATCGATCATC
*
23097 GTCACATAA
64 ATCACATAA
23106 GTATCAATATTTTAACTTTAGATCTTATCTTCAACTTTTTCAATATTTAAAAGTATCGATCATCA
1 GTATCAATATTTTAACTTTAGATCTT-TCTTCAACTTTTTCAATATTTAAAAGTATCGATCATCA
23171 T-ACATTAA
65 TCACA-TAA
23179 GTAT
1 GTAT
23183 TGATATTTAA
Statistics
Matches: 118, Mismatches: 24, Indels: 15
0.75 0.15 0.10
Matches are distributed among these distances:
71 1 0.01
72 59 0.50
73 38 0.32
74 20 0.17
ACGTcount: A:0.35, C:0.14, G:0.08, T:0.43
Consensus pattern (72 bp):
GTATCAATATTTTAACTTTAGATCTTTCTTCAACTTTTTCAATATTTAAAAGTATCGATCATCAT
CACATAA
Found at i:23189 original size:73 final size:71
Alignment explanation
Indices: 22991--23197 Score: 222
Period size: 72 Copynumber: 2.9 Consensus size: 71
22981 AACATCTTCA
* * *
22991 TCAACTTTTTCAATATATAAAAGTA-CTGATCATCGTCGCATAAGTATTGATATTTTAAATTTTG
1 TCAACTTTTTCAATATTTAAAAGTATC-GATCATCGTCACATAAGTATTGATATTTTAAATTTAG
23055 ATCTTTT
65 ATCTTTT
** * * * ** *
23062 TACAATCAATTT-AGTATTTAAAATTATCGATCATTGTCACATAAGTATCAATATTTTAACTTTA
1 T-CAA-CTTTTTCAATATTTAAAAGTATCGATCATCGTCACATAAGTATTGATATTTTAAATTTA
23126 GATCTTATCT
64 GATCTT-T-T
* *
23136 TCAACTTTTTCAATATTTAAAAGTATCGATCATCAT-ACATTAAGTATTGATATTTAAAATTT
1 TCAACTTTTTCAATATTTAAAAGTATCGATCATCGTCACA-TAAGTATTGATATTTTAAATTT
23198 TGAAATGCTT
Statistics
Matches: 108, Mismatches: 21, Indels: 12
0.77 0.15 0.09
Matches are distributed among these distances:
71 1 0.01
72 57 0.53
73 48 0.44
74 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.44
Consensus pattern (71 bp):
TCAACTTTTTCAATATTTAAAAGTATCGATCATCGTCACATAAGTATTGATATTTTAAATTTAGA
TCTTTT
Found at i:27210 original size:11 final size:12
Alignment explanation
Indices: 27194--27233 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
27184 TAAAAGTTGA
27194 AAATAA-AAATT
1 AAATAATAAATT
27205 AAATAATAAATT
1 AAATAATAAATT
*
27217 -AATAGTAAA-T
1 AAATAATAAATT
27227 AAATAAT
1 AAATAAT
27234 TTACCCTAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
10 1 0.04
11 19 0.76
12 5 0.20
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (12 bp):
AAATAATAAATT
Found at i:27915 original size:30 final size:30
Alignment explanation
Indices: 27879--27937 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
27869 AGTTTTTTTG
27879 AAAAATATTTTACATAAAATAAATTATCTA
1 AAAAATATTTTACATAAAATAAATTATCTA
** *
27909 AAAAATATTTTATGTAAAATGAATTATCT
1 AAAAATATTTTACATAAAATAAATTATCT
27938 CGAAGTTATT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (30 bp):
AAAAATATTTTACATAAAATAAATTATCTA
Found at i:31466 original size:51 final size:52
Alignment explanation
Indices: 31136--31816 Score: 761
Period size: 55 Copynumber: 12.8 Consensus size: 52
31126 TAACGAGTTT
* * * * * *
31136 GCTCCCTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAGC-AAATGTGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACGAACT-TGTCC
* * * * ** *
31191 GCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCT
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCA-ACGAACTTGTCC
* * * *
31246 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACGAACTTGTCC
* * * **
31301 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTC-ATGAAACGGGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACG-AACTTGTCC
* * *
31356 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACGAACTTGTCC
*
31411 GCTCCCTATTCATTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACGAACTTGTCC
* ** *
31462 GCTCCCTATTCCTTCAGAGAGTATAGGACTCGAGCAATCTTCATA-AAACGGGTTC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT--A-CAATCTTCA-ACGAACTTGTCC
* *
31517 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACT---ACAATCTTCAACGAACTTGTCC
31572 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACGAACTTGTCC
*
31623 GCTCCCTATTCATTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACGAACTTGTCC
31674 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACGAACTTGTCC
31725 GCTCCCTATTCCTTCAGAGAGTATAGGACT-CAATCTTCAACGAACTTGTCC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACGAACTTGTCC
*
31776 GCTCCCTATTCTTTCAGAGAGTATAGGACT-CAATCTTCAAC
1 GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAAC
31817 AAACGAATTT
Statistics
Matches: 573, Mismatches: 41, Indels: 28
0.89 0.06 0.04
Matches are distributed among these distances:
51 261 0.46
54 3 0.01
55 304 0.53
56 5 0.01
ACGTcount: A:0.28, C:0.27, G:0.16, T:0.29
Consensus pattern (52 bp):
GCTCCCTATTCCTTCAGAGAGTATAGGACTACAATCTTCAACGAACTTGTCC
Found at i:33180 original size:16 final size:15
Alignment explanation
Indices: 33144--33182 Score: 60
Period size: 16 Copynumber: 2.5 Consensus size: 15
33134 TTATTTCTTT
33144 TTTTTTTCATTTTTC
1 TTTTTTTCATTTTTC
33159 TCTTTTTTCATTTTTC
1 T-TTTTTTCATTTTTC
*
33175 ATTTTTTC
1 TTTTTTTC
33183 TTCCCTTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (15 bp):
TTTTTTTCATTTTTC
Found at i:33252 original size:19 final size:18
Alignment explanation
Indices: 33230--33265 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
33220 GTTTTTTCCA
33230 TCATTTTTTTCTCATTTTT
1 TCATTTTTTTCTC-TTTTT
33249 TCATTTTTTTCTCTTTT
1 TCATTTTTTTCTCTTTT
33266 ATTTCTTCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.08, C:0.17, G:0.00, T:0.75
Consensus pattern (18 bp):
TCATTTTTTTCTCTTTTT
Found at i:54464 original size:26 final size:26
Alignment explanation
Indices: 54434--54484 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 26
54424 TCTCCAAATA
*
54434 ATAA-TAATATATTTTTACTTTTTAAT
1 ATAATTAATATATTATTA-TTTTTAAT
*
54460 ATAATTTATATATTATTATTTTTAA
1 ATAATTAATATATTATTATTTTTAA
54485 AAAATAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
26 11 0.50
27 11 0.50
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (26 bp):
ATAATTAATATATTATTATTTTTAAT
Found at i:54932 original size:22 final size:22
Alignment explanation
Indices: 54881--54939 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
54871 ACGCGATTCT
54881 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * * *
54903 AAAT-TCGCGTTGCGATTTTTC
1 GACTATCGCATTGCGATTTTCC
*
54924 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
54940 ATATGTAAAT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
21 17 0.61
22 11 0.39
ACGTcount: A:0.22, C:0.24, G:0.20, T:0.34
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:55000 original size:20 final size:20
Alignment explanation
Indices: 54924--55054 Score: 131
Period size: 20 Copynumber: 6.5 Consensus size: 20
54914 GCGATTTTTC
*
54924 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
54944 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
*
54964 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
54984 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
** *
55004 GACTATCGCAACACGATTCT
1 GACTATCGCAATGCGATTAT
* *
55024 GACTATCGCAACGCGATTCT
1 GACTATCGCAATGCGATTAT
*
55044 GACTGTCGCAA
1 GACTATCGCAA
55055 CACTGAATTT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
19 1 0.01
20 99 0.98
21 1 0.01
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.26
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:55012 original size:40 final size:40
Alignment explanation
Indices: 54866--55054 Score: 141
Period size: 40 Copynumber: 4.7 Consensus size: 40
54856 GTTTCCAGAT
* * **
54866 TCGCAACGCGATTCTGACTATCGCATTGCGATT-TTCCAAA
1 TCGCAATGCGATTCTGACTATCGCAATGCGATTATGAC-AA
** * *
54906 TTCGCGTTGCGATTTTTCGACTATCGCAATGCGAATATGTA-AA
1 -TCGCAATGCGA-TTCT-GACTATCGCAATGCGATTATG-ACAA
* * * *
54949 TCGCAATGCGAATATGTA-AATCGCAATGCGATTATGACTA
1 TCGCAATGCGATTCTG-ACTATCGCAATGCGATTATGACAA
** * *
54989 TCGCAATGCGATTCTGACTATCGCAACACGATTCTGACTA
1 TCGCAATGCGATTCTGACTATCGCAATGCGATTATGACAA
* *
55029 TCGCAACGCGATTCTGACTGTCGCAA
1 TCGCAATGCGATTCTGACTATCGCAA
55055 CACTGAATTT
Statistics
Matches: 118, Mismatches: 23, Indels: 15
0.76 0.15 0.10
Matches are distributed among these distances:
39 2 0.02
40 74 0.63
41 11 0.09
42 12 0.10
43 18 0.15
44 1 0.01
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.29
Consensus pattern (40 bp):
TCGCAATGCGATTCTGACTATCGCAATGCGATTATGACAA
Found at i:55922 original size:24 final size:24
Alignment explanation
Indices: 55867--55929 Score: 81
Period size: 24 Copynumber: 2.6 Consensus size: 24
55857 TACTAGTCGG
*
55867 TATTCGAAATTTGATCTTGGTCAA
1 TATTCGGAATTTGATCTTGGTCAA
** *
55891 TACCCGGACTTTGATCTTGGTCAA
1 TATTCGGAATTTGATCTTGGTCAA
*
55915 TATTCGGATTTTGAT
1 TATTCGGAATTTGAT
55930 GATGTTTCAG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.24, C:0.16, G:0.19, T:0.41
Consensus pattern (24 bp):
TATTCGGAATTTGATCTTGGTCAA
Found at i:58214 original size:18 final size:18
Alignment explanation
Indices: 58191--58226 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
58181 AAGAAAAAGG
*
58191 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
58209 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
58227 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:58542 original size:140 final size:140
Alignment explanation
Indices: 58287--58552 Score: 514
Period size: 140 Copynumber: 1.9 Consensus size: 140
58277 AAACGTTGTA
58287 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
58352 TGATCTGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATTGCAACGCGAATTTGACTAT
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
58417 TATGTGTATT
131 TATGTGTATT
58427 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
58492 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
66 TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGA
58553 TTATCGCAAC
Statistics
Matches: 124, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
140 124 1.00
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATGTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:58552 original size:20 final size:20
Alignment explanation
Indices: 58527--58711 Score: 151
Period size: 20 Copynumber: 9.8 Consensus size: 20
58517 TTACACATTC
*
58527 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
58547 ATTTGATTATCGCAACTC-A
1 ATTTGACTATCGCAACGCGA
* *
58566 A----A-AATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
* *
58581 ATTCGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
58601 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
58620 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
58635 ATTTGTCTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
58655 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * * *
58675 ATTTGATTATCGCGATGAGT
1 ATTTGACTATCGCAACGCGA
58695 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
58712 AGAAAATCGC
Statistics
Matches: 131, Mismatches: 22, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
14 19 0.15
15 6 0.05
19 5 0.04
20 101 0.77
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:58616 original size:54 final size:54
Alignment explanation
Indices: 58534--58672 Score: 215
Period size: 54 Copynumber: 2.6 Consensus size: 54
58524 TTCATTTGAA
* *
58534 TATCGCAACGCGAATTTGATTATCGCAACTCAAAAATCGCAACGCAAATTCGAC
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCAAATTCGAC
* * * * *
58588 TATCGCAACACGAATATGACTATCGCAACGCAAAAATCGCAACGCGAATTTGTC
1 TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCAAATTCGAC
58642 TATCGCAACGCGAATTTGACTATCGCAACGC
1 TATCGCAACGCGAATTTGACTATCGCAACGC
58673 GAATTTGATT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 76 1.00
ACGTcount: A:0.35, C:0.27, G:0.17, T:0.22
Consensus pattern (54 bp):
TATCGCAACGCGAATTTGACTATCGCAACGCAAAAATCGCAACGCAAATTCGAC
Found at i:58779 original size:20 final size:20
Alignment explanation
Indices: 58754--58792 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
58744 CACGAATTGA
*
58754 CTTTCGCGTTGCGATTTTGG
1 CTTTCGCATTGCGATTTTGG
58774 CTTTCGCATTGCGATTTTG
1 CTTTCGCATTGCGATTTTG
58793 AGTTTAGCGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.08, C:0.21, G:0.26, T:0.46
Consensus pattern (20 bp):
CTTTCGCATTGCGATTTTGG
Found at i:58948 original size:14 final size:14
Alignment explanation
Indices: 58929--58965 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
58919 TCAATATTAA
58929 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
58943 ACAAATCAATTTTT
1 ACAAATCAACTTTT
*
58957 ATAAATCAA
1 ACAAATCAA
58966 ATTAAACAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.35
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:60465 original size:42 final size:42
Alignment explanation
Indices: 60386--60467 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
60376 CCTCTTCAAC
* * *
60386 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* *
60428 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGA
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGA
60468 ACAATGACAG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 31 0.91
43 3 0.09
ACGTcount: A:0.21, C:0.17, G:0.40, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:60987 original size:18 final size:18
Alignment explanation
Indices: 60964--61030 Score: 80
Period size: 20 Copynumber: 3.5 Consensus size: 18
60954 GAAACTTAAA
**
60964 ATCGCAACATGAATGACT
1 ATCGCAACGCGAATGACT
60982 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCG--AATGACT
61002 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAA--TGACT
61022 ATCGCAACG
1 ATCGCAACG
61031 AGAGAATCGC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
18 11 0.26
20 32 0.74
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.19
Consensus pattern (18 bp):
ATCGCAACGCGAATGACT
Found at i:61000 original size:20 final size:20
Alignment explanation
Indices: 60975--61030 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
60965 TCGCAACATG
60975 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
60995 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
61015 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
61031 AGAGAATCGC
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:61113 original size:20 final size:21
Alignment explanation
Indices: 61073--61121 Score: 91
Period size: 20 Copynumber: 2.4 Consensus size: 21
61063 GCGATTCTTT
61073 CGTTGCGATAGTCATTTTTCG
1 CGTTGCGATAGTCATTTTTCG
61094 CGTTGCGATAGTCA-TTTTCG
1 CGTTGCGATAGTCATTTTTCG
61114 CGTTGCGA
1 CGTTGCGA
61122 AAGTAAACTA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 14 0.50
21 14 0.50
ACGTcount: A:0.14, C:0.20, G:0.27, T:0.39
Consensus pattern (21 bp):
CGTTGCGATAGTCATTTTTCG
Found at i:63041 original size:20 final size:20
Alignment explanation
Indices: 63018--63085 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
63008 TCTGAAACTT
63018 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
63038 AAAATCGCAACACGAAAATG
1 AAAATCGCAACACGAAAATG
** * *
63058 ACTATCGCAACGCGAAACT-
1 AAAATCGCAACACGAAAATG
63077 AAAATCGCA
1 AAAATCGCA
63086 TTGCGATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
19 7 0.17
20 35 0.83
ACGTcount: A:0.50, C:0.24, G:0.15, T:0.12
Consensus pattern (20 bp):
AAAATCGCAACACGAAAATG
Found at i:63485 original size:20 final size:21
Alignment explanation
Indices: 63460--63508 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
63450 TCTGAGAGAT
63460 GGAGAT-AGAC-GAATTTCGTC
1 GGAGATGAGACTG-ATTTCGTC
*
63480 GGAGATGGGGACTGATTTCGTC
1 GGAGAT-GAGACTGATTTCGTC
63502 GGAGATG
1 GGAGATG
63509 GGGACGGATG
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 6 0.24
21 1 0.04
22 17 0.68
23 1 0.04
ACGTcount: A:0.24, C:0.12, G:0.39, T:0.24
Consensus pattern (21 bp):
GGAGATGAGACTGATTTCGTC
Found at i:63499 original size:22 final size:22
Alignment explanation
Indices: 63472--63513 Score: 84
Period size: 22 Copynumber: 1.9 Consensus size: 22
63462 AGATAGACGA
63472 ATTTCGTCGGAGATGGGGACTG
1 ATTTCGTCGGAGATGGGGACTG
63494 ATTTCGTCGGAGATGGGGAC
1 ATTTCGTCGGAGATGGGGAC
63514 GGATGTCGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.19, C:0.14, G:0.40, T:0.26
Consensus pattern (22 bp):
ATTTCGTCGGAGATGGGGACTG
Found at i:63713 original size:20 final size:20
Alignment explanation
Indices: 63688--63802 Score: 106
Period size: 20 Copynumber: 5.7 Consensus size: 20
63678 GCGCTTTGAA
63688 AATCGCATTGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
* *
63708 AATCGCGTTGCGATAGTCAT
1 AATCGCATTGCGATAGTCAG
* *
63728 AATCGCATTGCGAT-TTACAT
1 AATCGCATTGCGATAGT-CAG
* * *
63748 ATTCACATTGCGATAGTCGGAA
1 AATCGCATTGCGATAGTC--AG
* *
63770 AATCGTAATGCGATAGTCAG
1 AATCGCATTGCGATAGTCAG
*
63790 AATCGCGTTGCGA
1 AATCGCATTGCGA
63803 ATCTGGAAAC
Statistics
Matches: 75, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
19 1 0.01
20 58 0.77
21 1 0.01
22 15 0.20
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (20 bp):
AATCGCATTGCGATAGTCAG
Found at i:65568 original size:2 final size:2
Alignment explanation
Indices: 65561--65604 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
65551 ATTCAAAATT
65561 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- 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
65602 TA T
1 TA T
65605 TACAAAATTG
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.