Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001583.1 Hibiscus syriacus cultivar Beakdansim tig00003155_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: 74790
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:2176 original size:38 final size:40
Alignment explanation
Indices: 2123--2201 Score: 108
Period size: 38 Copynumber: 2.0 Consensus size: 40
2113 TTTGAAAATA
* *
2123 TTTTTTAAAAAATATAATATATAGATTTT-AGAAAA-CGG
1 TTTTTGAAAAAATATAATATATACATTTTAAGAAAATCGG
* *
2161 TTTTTGAAAACATATAATATATACTTTTTAAGAAAATCGG
1 TTTTTGAAAAAATATAATATATACATTTTAAGAAAATCGG
2201 T
1 T
2202 ATAGTTTTGA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
38 25 0.71
39 6 0.17
40 4 0.11
ACGTcount: A:0.44, C:0.05, G:0.10, T:0.41
Consensus pattern (40 bp):
TTTTTGAAAAAATATAATATATACATTTTAAGAAAATCGG
Found at i:2240 original size:35 final size:35
Alignment explanation
Indices: 2201--2473 Score: 268
Period size: 34 Copynumber: 7.9 Consensus size: 35
2191 AGAAAATCGG
2201 TATAGTTTTGAAAACAATTTTTGAAAAATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAAATATATTA
**
2236 TATAGTTTTG-AAACGGTTTTTGAAAATATATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAA-ATATATTA
2271 TATAGTTTT-AAAACAA-TTTTG-AAAATATATATA
1 TATAGTTTTGAAAACAATTTTTGAAAAATATAT-TA
** *
2304 TATTAGTTTTGAAAATGATTTTTGAATATATATATT-
1 TA-TAGTTTTGAAAACAATTTTTGAA-AAATATATTA
* *
2340 TATAGTTTTTG--AATAATTTTTGAAATATATATTA
1 TATAG-TTTTGAAAACAATTTTTGAAAAATATATTA
*
2374 TATAGTTTTGAAAAC-GTTTTT-AAAAA-ATATTA
1 TATAGTTTTGAAAACAATTTTTGAAAAATATATTA
* *
2406 TATAG-TTTGAAAATCAGCTTTTGGAAACAATATA-T-
1 TATAGTTTTGAAAA-CA-ATTTTTGAAA-AATATATTA
*
2441 TATA-TTTTGAAAAATAATTTTTGAAAAATATAT
1 TATAGTTTTG-AAAACAATTTTTGAAAAATATAT
2474 ATAGTTTTTA
Statistics
Matches: 201, Mismatches: 16, Indels: 43
0.77 0.06 0.17
Matches are distributed among these distances:
31 8 0.04
32 18 0.09
33 31 0.15
34 60 0.30
35 53 0.26
36 19 0.09
37 5 0.02
38 7 0.03
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (35 bp):
TATAGTTTTGAAAACAATTTTTGAAAAATATATTA
Found at i:2301 original size:69 final size:70
Alignment explanation
Indices: 2201--2445 Score: 290
Period size: 69 Copynumber: 3.5 Consensus size: 70
2191 AGAAAATCGG
2201 TATAGTTTTGAAAACAATTTTTGAAAAATATATTATATAGTTTTG-AAACGGTTTTTGAAAATAT
1 TATAGTTTT-AAAACAATTTTTGAAAAATATATTATATAGTTTTGAAAACGGTTTTTGAAAATAT
2265 ATATTA
65 ATATTA
* * *
2271 TATAGTTTTAAAACAA-TTTTG-AAAATATATATATATTAGTTTTGAAAATGATTTTTGAATATA
1 TATAGTTTTAAAACAATTTTTGAAAAATATAT-TATA-TAGTTTTGAAAACGGTTTTTGAAAATA
2334 TATATT-
64 TATATTA
** * *
2340 TATAGTTTTTGAATAATTTTTGAAATATATATTATATAGTTTTGAAAAC-GTTTTT-AAAA-A-A
1 TATAGTTTTAAAACAATTTTTGAAAAATATATTATATAGTTTTGAAAACGGTTTTTGAAAATATA
2401 TATTA
66 TATTA
* * *
2406 TATAGTTTGAAAATCAGCTTTTGGAAACAATATATTATAT
1 TATAGTTTTAAAA-CA-ATTTTTGAAA-AATATATTATAT
2446 TTTGAAAAAT
Statistics
Matches: 149, Mismatches: 17, Indels: 19
0.81 0.09 0.10
Matches are distributed among these distances:
65 5 0.03
66 11 0.07
67 13 0.09
68 22 0.15
69 51 0.34
70 39 0.26
71 8 0.05
ACGTcount: A:0.41, C:0.03, G:0.10, T:0.46
Consensus pattern (70 bp):
TATAGTTTTAAAACAATTTTTGAAAAATATATTATATAGTTTTGAAAACGGTTTTTGAAAATATA
TATTA
Found at i:3775 original size:5 final size:5
Alignment explanation
Indices: 3765--3804 Score: 53
Period size: 5 Copynumber: 7.6 Consensus size: 5
3755 TTATTCTCTT
*
3765 TTTTA TTTTA TTTTA TTTTA TTTCA TTTTCA TTATTA TTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT-A TT-TTA TTT
3805 CACATTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 23 0.74
6 6 0.19
7 2 0.06
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:3802 original size:27 final size:27
Alignment explanation
Indices: 3732--3804 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 27
3722 TAATCCTTTA
* **
3732 ATTCTAATTTTC-TTTTAAATT-TTTT
1 ATTCTCATTTTCATTTTATTTTATTTT
* *
3757 ATTCTCTTTTTTATTTTATTTTATTTT
1 ATTCTCATTTTCATTTTATTTTATTTT
3784 ATT-TCATTTTCATTATTATTT
1 ATTCTCATTTTCATT-TTATTT
3805 CACATTAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
25 9 0.24
26 16 0.42
27 13 0.34
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.71
Consensus pattern (27 bp):
ATTCTCATTTTCATTTTATTTTATTTT
Found at i:3957 original size:5 final size:5
Alignment explanation
Indices: 3947--3972 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
3937 TCTTTGTTTG
3947 TTTTA TTTTA TTTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA TTTTA TTTTA T
3973 CATTTAACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTTA
Found at i:9914 original size:32 final size:34
Alignment explanation
Indices: 9877--9946 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
9867 CCTTACAAAC
*
9877 TCCCTAG-TTTTTC-CGGGCTAACCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAACCTAGAACCTT
*
9909 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAACCTAGAACCTT
9943 TCCC
1 TCCC
9947 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.20, C:0.33, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAACCTAGAACCTT
Found at i:12278 original size:28 final size:28
Alignment explanation
Indices: 12226--12282 Score: 80
Period size: 28 Copynumber: 2.0 Consensus size: 28
12216 CCGCTGTTGC
* *
12226 TTTCAAGCATTGACTCTATGGCATAATG
1 TTTCAAGCATTGACTCAATGACATAATG
12254 TTTCAAGCACTTG-CTCAATGACATAATG
1 TTTCAAGCA-TTGACTCAATGACATAATG
12282 T
1 T
12283 AAATGGAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
28 23 0.88
29 3 0.12
ACGTcount: A:0.30, C:0.19, G:0.16, T:0.35
Consensus pattern (28 bp):
TTTCAAGCATTGACTCAATGACATAATG
Found at i:12644 original size:31 final size:31
Alignment explanation
Indices: 12609--12683 Score: 132
Period size: 31 Copynumber: 2.4 Consensus size: 31
12599 AAATTACACA
*
12609 TTTAGTACCTAAAATATCAATTTTGATCCAT
1 TTTAGTACCTAAAATATCAATTCTGATCCAT
*
12640 TTTAGTACCTAAAATATCAATTCTGGTCCAT
1 TTTAGTACCTAAAATATCAATTCTGATCCAT
12671 TTTAGTACCTAAA
1 TTTAGTACCTAAA
12684 CTTTAACTTT
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.35, C:0.17, G:0.08, T:0.40
Consensus pattern (31 bp):
TTTAGTACCTAAAATATCAATTCTGATCCAT
Found at i:13537 original size:36 final size:35
Alignment explanation
Indices: 13460--13557 Score: 106
Period size: 36 Copynumber: 2.8 Consensus size: 35
13450 AACACAGTCA
* * **
13460 TCAATTATATTCTAAACCCCAAATTCTAAAATGTT
1 TCAATTACATTCTAAACCCCAAATTCAAAAATAAT
* *
13495 TTAATTACATTCTAAACCTCAAATTCCAAAAATAAT
1 TCAATTACATTCTAAACCCCAAATT-CAAAAATAAT
* **
13531 TCAATTACATGCCCAACCCCAAATTCA
1 TCAATTACATTCTAAACCCCAAATTCA
13558 TAAACCATTC
Statistics
Matches: 51, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
35 24 0.47
36 27 0.53
ACGTcount: A:0.42, C:0.24, G:0.02, T:0.32
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAATTCAAAAATAAT
Found at i:14475 original size:17 final size:17
Alignment explanation
Indices: 14453--14488 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
14443 TGTAATTAAA
14453 GTATTTTGGAATTTGAG
1 GTATTTTGGAATTTGAG
14470 GTATTTTGGAATTTGAG
1 GTATTTTGGAATTTGAG
14487 GT
1 GT
14489 TTAGAATGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (17 bp):
GTATTTTGGAATTTGAG
Found at i:17595 original size:19 final size:19
Alignment explanation
Indices: 17571--17610 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
17561 CTCGCGACCC
*
17571 GTCCGACGATGGATCCGAA
1 GTCCGACGATGGATCCAAA
*
17590 GTCCGACTATGGATCCAAA
1 GTCCGACGATGGATCCAAA
17609 GT
1 GT
17611 ATATCGTATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.28, C:0.25, G:0.28, T:0.20
Consensus pattern (19 bp):
GTCCGACGATGGATCCAAA
Found at i:18667 original size:31 final size:31
Alignment explanation
Indices: 18629--18698 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
18619 CTTTTAAAAC
18629 TTGCAATACAATCCC-CTAACATTTAGTCCAT
1 TTGCAATACAATCCCTC-AACATTTAGTCCAT
***
18660 TTGCAATATGGTCCCTCAACATTTAGTCCAT
1 TTGCAATACAATCCCTCAACATTTAGTCCAT
18691 TTGCAATA
1 TTGCAATA
18699 TGGTCCCCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
31 34 0.97
32 1 0.03
ACGTcount: A:0.30, C:0.26, G:0.10, T:0.34
Consensus pattern (31 bp):
TTGCAATACAATCCCTCAACATTTAGTCCAT
Found at i:18699 original size:31 final size:30
Alignment explanation
Indices: 18642--18705 Score: 119
Period size: 31 Copynumber: 2.1 Consensus size: 30
18632 CAATACAATC
18642 CCCTAACATTTAGTCCATTTGCAATATGGT
1 CCCTAACATTTAGTCCATTTGCAATATGGT
18672 CCCTCAACATTTAGTCCATTTGCAATATGGT
1 CCCT-AACATTTAGTCCATTTGCAATATGGT
18703 CCC
1 CCC
18706 CGATGTAACT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 4 0.12
31 29 0.88
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.34
Consensus pattern (30 bp):
CCCTAACATTTAGTCCATTTGCAATATGGT
Found at i:20708 original size:31 final size:31
Alignment explanation
Indices: 20670--20735 Score: 105
Period size: 31 Copynumber: 2.1 Consensus size: 31
20660 AGTTACATCG
20670 GGGACCATATTGCAAATGAACTAAATATTGA
1 GGGACCATATTGCAAATGAACTAAATATTGA
* * *
20701 GGGACCATATTGTAAATGGACTAAATGTTGA
1 GGGACCATATTGCAAATGAACTAAATATTGA
20732 GGGA
1 GGGA
20736 TTGTATTATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.38, C:0.11, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGCAAATGAACTAAATATTGA
Found at i:25541 original size:28 final size:29
Alignment explanation
Indices: 25510--25665 Score: 104
Period size: 29 Copynumber: 5.4 Consensus size: 29
25500 TAACTTTGGG
*
25510 TTTTTATTGTAAATTGTAAAAAG-TATGT
1 TTTTTATTGTAAATTGTAAAAAGTTATGC
*
25538 TTTTTATTAT-AATTGTAAAAAAGTATAT--
1 TTTTTATTGTAAATTGT-AAAAAGT-TATGC
* * * * *
25566 TTCATTCTTGTAATTTGTAAGAAGTTTTGC
1 TT-TTTATTGTAAATTGTAAAAAGTTATGC
** * *
25596 TTTTTATTGTATTTTGTAAGAAGTTTTGC
1 TTTTTATTGTAAATTGTAAAAAGTTATGC
** * * *
25625 TTTTTATTGTATTTTGTAAGAAGTTTTGG
1 TTTTTATTGTAAATTGTAAAAAGTTATGC
*
25654 TCTTTATTGTAA
1 TTTTTATTGTAA
25666 TTTATAAGAA
Statistics
Matches: 108, Mismatches: 13, Indels: 13
0.81 0.10 0.10
Matches are distributed among these distances:
27 6 0.06
28 19 0.18
29 73 0.68
30 10 0.09
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (29 bp):
TTTTTATTGTAAATTGTAAAAAGTTATGC
Found at i:25605 original size:29 final size:29
Alignment explanation
Indices: 25573--25681 Score: 173
Period size: 29 Copynumber: 3.8 Consensus size: 29
25563 TATTTCATTC
25573 TTGTAATTTGTAAGAAGTTTTGCTTTTTA
1 TTGTAATTTGTAAGAAGTTTTGCTTTTTA
*
25602 TTGTATTTTGTAAGAAGTTTTGCTTTTTA
1 TTGTAATTTGTAAGAAGTTTTGCTTTTTA
* * *
25631 TTGTATTTTGTAAGAAGTTTTGGTCTTTA
1 TTGTAATTTGTAAGAAGTTTTGCTTTTTA
*
25660 TTGTAATTTATAAGAAGTTTTG
1 TTGTAATTTGTAAGAAGTTTTG
25682 GTCTTAACTA
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 75 1.00
ACGTcount: A:0.24, C:0.03, G:0.18, T:0.55
Consensus pattern (29 bp):
TTGTAATTTGTAAGAAGTTTTGCTTTTTA
Found at i:25695 original size:29 final size:29
Alignment explanation
Indices: 25641--25708 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
25631 TTGTATTTTG
* * *
25641 TAAGAAGTTTTGGTCTTTATTGTAATTTA
1 TAAGAAGTTTTGGTCTTAACTATAATTTA
25670 TAAGAAGTTTTGGTCTTAACTATAATTTA
1 TAAGAAGTTTTGGTCTTAACTATAATTTA
*
25699 TAAAAAGTTT
1 TAAGAAGTTT
25709 GTCCTCGGTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.34, C:0.04, G:0.15, T:0.47
Consensus pattern (29 bp):
TAAGAAGTTTTGGTCTTAACTATAATTTA
Found at i:25707 original size:58 final size:58
Alignment explanation
Indices: 25576--25708 Score: 158
Period size: 58 Copynumber: 2.3 Consensus size: 58
25566 TTCATTCTTG
* * * * * * *
25576 TAATTTGTAAGAAGTTTTGCTTTTTATTGTATTTTGTAAGAAGTTTTGCTTTTTATTG
1 TAATTTGTAAGAAGTTTTGCTCTTTATTGTAATTTATAAGAAGTTTTGCTCTTAACTA
* * *
25634 TATTTTGTAAGAAGTTTTGGTCTTTATTGTAATTTATAAGAAGTTTTGGTCTTAACTA
1 TAATTTGTAAGAAGTTTTGCTCTTTATTGTAATTTATAAGAAGTTTTGCTCTTAACTA
* *
25692 TAATTTATAAAAAGTTT
1 TAATTTGTAAGAAGTTT
25709 GTCCTCGGTT
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
58 62 1.00
ACGTcount: A:0.28, C:0.04, G:0.16, T:0.53
Consensus pattern (58 bp):
TAATTTGTAAGAAGTTTTGCTCTTTATTGTAATTTATAAGAAGTTTTGCTCTTAACTA
Found at i:25812 original size:28 final size:29
Alignment explanation
Indices: 25742--25831 Score: 155
Period size: 29 Copynumber: 3.1 Consensus size: 29
25732 TAATTTGTTA
*
25742 TTTATTATCATTTATAAAAACTTTAGACT
1 TTTATTATAATTTATAAAAACTTTAGACT
25771 TTTATTATAATTTATAAAAACTTTAGACT
1 TTTATTATAATTTATAAAAACTTTAGACT
*
25800 TTTATTAT-ATTTATAAAAACTTTAGACA
1 TTTATTATAATTTATAAAAACTTTAGACT
25828 TTTA
1 TTTA
25832 ATTTAATGTA
Statistics
Matches: 59, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
28 23 0.39
29 36 0.61
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (29 bp):
TTTATTATAATTTATAAAAACTTTAGACT
Found at i:27114 original size:3 final size:3
Alignment explanation
Indices: 27106--27198 Score: 165
Period size: 3 Copynumber: 32.0 Consensus size: 3
27096 ACTTATTACT
27106 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27153 TAA T-A TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
27199 CATACAATGT
Statistics
Matches: 87, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
2 6 0.07
3 81 0.93
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:27456 original size:80 final size:80
Alignment explanation
Indices: 27343--27598 Score: 311
Period size: 82 Copynumber: 3.1 Consensus size: 80
27333 CCATTTTTCT
* * *
27343 TTCAGGGGAAATCAGACCTGATTTCTTCCTC-TTTTGGGTAGTCAAATCAATTTTTGAAGACGTG
1 TTCAGGGGAGATCAGACTTGATTT-GTCCTCTTTTTGGGTAGTCAAATCAATTTTTGAAGACGTG
** *
27407 TCTTTTCCACTATTCA
65 TCTGCTCTACTATTCA
* *
27423 TTAAGGGGAGATCAGACTTGATTTGTCCATCTTTTTTGGGTAGTCATATCAA-TTTTGAAAGACG
1 TTCAGGGGAGATCAGACTTGATTTGTCC-TC-TTTTTGGGTAGTCAAATCAATTTTTG-AAGACG
*
27487 TGTCTGCTCTACTATTTA
63 TGTCTGCTCTACTATTCA
* * * *
27505 TTCAGGGGAGATAAGACTTGATCAATG-CCTCTTTTTTGGGTAGTCAGATCAATTTTGGAAGACG
1 TTCAGGGGAGATCAGACTTGAT--TTGTCCTC-TTTTTGGGTAGTCAAATCAATTTTTGAAGACG
27569 TGTCTGCTCTACTATTCA
63 TGTCTGCTCTACTATTCA
27587 TTCAGGGGAGAT
1 TTCAGGGGAGAT
27599 AAAACTTTAG
Statistics
Matches: 154, Mismatches: 15, Indels: 12
0.85 0.08 0.07
Matches are distributed among these distances:
79 3 0.02
80 23 0.15
81 5 0.03
82 115 0.75
83 6 0.04
84 2 0.01
ACGTcount: A:0.24, C:0.17, G:0.21, T:0.38
Consensus pattern (80 bp):
TTCAGGGGAGATCAGACTTGATTTGTCCTCTTTTTGGGTAGTCAAATCAATTTTTGAAGACGTGT
CTGCTCTACTATTCA
Found at i:27485 original size:82 final size:80
Alignment explanation
Indices: 27374--27605 Score: 313
Period size: 82 Copynumber: 2.8 Consensus size: 80
27364 TTTCTTCCTC
** * * *
27374 TTTTGGGTAGTCAAATCAATTTTTGAAGACGTGTCTTTTCCACTATTCATTAAGGGGAGATCAGA
1 TTTTGGGTAGTCAAATCAA-TTTTGAAGACGTGTCTGCTCTACTATTCATTCAGGGGAGATAAGA
*
27439 CTTGAT-TTGTCCATCTT
65 CTTGATAATG-CC-TCTT
* *
27456 TTTTGGGTAGTCATATCAATTTTGAAAGACGTGTCTGCTCTACTATTTATTCAGGGGAGATAAGA
1 TTTTGGGTAGTCAAATCAATTTTG-AAGACGTGTCTGCTCTACTATTCATTCAGGGGAGATAAGA
27521 CTTGATCAATGCCTCTT
65 CTTGAT-AATGCCTCTT
* *
27538 TTTTGGGTAGTCAGATCAATTTTGGAAGACGTGTCTGCTCTACTATTCATTCAGGGGAGATAAAA
1 TTTTGGGTAGTCAAATCAATTTT-GAAGACGTGTCTGCTCTACTATTCATTCAGGGGAGATAAGA
27603 CTT
65 CTT
27606 TAGAAATTTT
Statistics
Matches: 135, Mismatches: 11, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
81 5 0.04
82 125 0.93
83 3 0.02
84 2 0.01
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (80 bp):
TTTTGGGTAGTCAAATCAATTTTGAAGACGTGTCTGCTCTACTATTCATTCAGGGGAGATAAGAC
TTGATAATGCCTCTT
Found at i:27869 original size:88 final size:88
Alignment explanation
Indices: 27687--27938 Score: 314
Period size: 88 Copynumber: 2.8 Consensus size: 88
27677 ATGGGTCTGC
* * * * * *
27687 CGGGAAGACCAAATCT-AAA-ATTAGAAGAATCTGCTCCATTACTCTTCTCTGATGATCAGACTT
1 CGGGAAGACCAAATCTGAAATATT-G-AGAATTTGTTCCACTACTCTTCTGTGGTGAT-AGACTC
*
27750 GAGATTGATTTGTTTCACTACTCTTT
63 GAGATTGATTTGTCTCACTACTCTTT
* *
27776 CGGGAAGACCAAATATGAAATATTGAGAATTTGTTCCACTACTCTTCTGTGGTGATAAACTCGAG
1 CGGGAAGACCAAATCTGAAATATTGAGAATTTGTTCCACTACTCTTCTGTGGTGATAGACTCGAG
*
27841 ATTGATTTGTCTCGCTACTCTTT
66 ATTGATTTGTCTCACTACTCTTT
* *
27864 CGGGAAGACCAAATCTGAAATATAGAGAATCTT-TTCCACTACACTT-TCGTGGTGATTAGACTC
1 CGGGAAGACCAAATCTGAAATATTGAGAAT-TTGTTCCACTACTCTTCT-GTGGTGA-TAGACTC
27927 GAGATTGATTTG
63 GAGATTGATTTG
27939 CCTTGAAGAC
Statistics
Matches: 144, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
87 1 0.01
88 75 0.52
89 61 0.42
90 4 0.03
91 3 0.02
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.34
Consensus pattern (88 bp):
CGGGAAGACCAAATCTGAAATATTGAGAATTTGTTCCACTACTCTTCTGTGGTGATAGACTCGAG
ATTGATTTGTCTCACTACTCTTT
Found at i:27993 original size:76 final size:76
Alignment explanation
Indices: 27867--28015 Score: 201
Period size: 76 Copynumber: 2.0 Consensus size: 76
27857 ACTCTTTCGG
** * * *
27867 GAAGACCAAATCTGAAATATAGAGAATCTTTTCCACTACACTTTCGTGGTGATTAGACTCGAGAT
1 GAAGACCAAATCTGAAATATAGAGAATCTGCTCCACTACACTTCCGTGGTGATCAGACTCGAAAT
27932 TGATTTGCCTT
66 TGATTTGCCTT
* * * *
27943 GAAGACCAAATCTGACATA-AGAAGAATCTGCTCTACTACTCTTCCGTGGTGATCAGACTTGAAA
1 GAAGACCAAATCTGAAATATAG-AGAATCTGCTCCACTACACTTCCGTGGTGATCAGACTCGAAA
28007 TTGATTTGC
65 TTGATTTGC
28016 TTCGCTACTC
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
75 2 0.03
76 61 0.97
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (76 bp):
GAAGACCAAATCTGAAATATAGAGAATCTGCTCCACTACACTTCCGTGGTGATCAGACTCGAAAT
TGATTTGCCTT
Found at i:28445 original size:42 final size:42
Alignment explanation
Indices: 28367--28469 Score: 131
Period size: 42 Copynumber: 2.5 Consensus size: 42
28357 ACCCGAAGGT
* * *
28367 CTTACGGATAGCCCGAAAGACTT-ATCATCTTGCTCGAAAGA
1 CTTACAGATAGCCCGAAGGATTTAATCATCTTGCTCGAAAGA
28408 CTTACAGAT-GACCCGAAGGATTTAATCATCATT-CTCGAAAGA
1 CTTACAGATAG-CCCGAAGGATTTAATCATC-TTGCTCGAAAGA
*
28450 CTTACTGATAGCCCGAAGGA
1 CTTACAGATAGCCCGAAGGA
28470 CTTACAAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 1 0.02
41 18 0.33
42 32 0.59
43 3 0.06
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.24
Consensus pattern (42 bp):
CTTACAGATAGCCCGAAGGATTTAATCATCTTGCTCGAAAGA
Found at i:28678 original size:41 final size:42
Alignment explanation
Indices: 28618--28717 Score: 139
Period size: 42 Copynumber: 2.4 Consensus size: 42
28608 ACACAAAATT
* * *
28618 CTTACGGATGACCCTAAGGATTCAA-TATCTTGCTCGAAAGA
1 CTTACAGATGACCCGAAGGATTCAATTATCATGCTCGAAAGA
*
28659 CTTACAGATGACCCGAAGGATTTAATTATCATGCTCGAAAGA
1 CTTACAGATGACCCGAAGGATTCAATTATCATGCTCGAAAGA
* *
28701 CTTACTGATGGCCCGAA
1 CTTACAGATGACCCGAA
28718 TGACTTACAA
Statistics
Matches: 52, Mismatches: 6, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 22 0.42
42 30 0.58
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.26
Consensus pattern (42 bp):
CTTACAGATGACCCGAAGGATTCAATTATCATGCTCGAAAGA
Found at i:29237 original size:42 final size:41
Alignment explanation
Indices: 29136--29242 Score: 124
Period size: 42 Copynumber: 2.6 Consensus size: 41
29126 ACCCGAAGGT
* * * * *
29136 CTTACAGATGGCCCTAAAGACTTATCATCTTGCTCGAAATA
1 CTTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
* ** *
29177 CTTACAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGA
1 CTTACAGATGGCCCGAAGGACTT-AGCATCATGCTCGAAAGA
29219 CTTACAGATGGCCCGAAGGACTTA
1 CTTACAGATGGCCCGAAGGACTTA
29243 CAAATTTTGG
Statistics
Matches: 52, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
41 18 0.35
42 34 0.65
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (41 bp):
CTTACAGATGGCCCGAAGGACTTAGCATCATGCTCGAAAGA
Found at i:29305 original size:259 final size:253
Alignment explanation
Indices: 28096--29361 Score: 1672
Period size: 251 Copynumber: 5.0 Consensus size: 253
28086 TAACAAAAAT
* * *
28096 TGAAAACATCCTACCCGAAGGTCTTATGGATGGCCC-AAAGGACTTATCATCTTGCTCAAAATAC
1 TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAA-GACTTATCATCTTGCTCGAAAGAC
* * * * *
28160 TAACATATGTCCCGAATGATTTAATCATCATGCTCGAAAGAATTACTGATGGCCCGAAGGACTTA
65 TTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTA
* *
28225 CAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATTGCTTTCTTACTTTTCAAGAATT
130 CAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAATT
** * * * *
28290 TCATTTT-TTTAAATATTAAATAAGAAACTTTAGAAATCGCTTTCTCA---TTTTCATG
195 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTTTCATG
* * *
28345 TGAAAATATCATACCCGAAGGTCTTACGGATAGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
1 TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
* *
28410 TACAGATGACCCGAAGGATTTAATCATCATTCTCGAAAGACTTACTGATAGCCCGAAGGACTTAC
66 TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
* *
28475 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCACTTTCTTACTTTTTCAAGAATT
131 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCGCTTTCTTAC-TTTTCAATAATT
* * *
28540 TTATTTTCTGAAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCA---TTTTCATG
195 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTTTCATG
* * ** * * *
28596 TGAAAACATCCTACACAAAATTCTTACGGATGACCCTAAGGA-TTCAAT-ATCTTGCTCGAAAGA
1 TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAAGACTT--ATCATCTTGCTCGAAAGA
* *
28659 CTTACAGATGACCCGAAGGATTTAATTATCATGCTCGAAAGACTTACTGATGGCCCGAATGACTT
64 CTTACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* *
28724 ACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTAGTAACCGCTTTCTTACTTTTCAATAAT
129 ACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAAT
*
28789 TTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATGGCTTTCTCAGTTTTTTTAAAATCAT
194 TTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCA--TTTTTT----TCAT
*
28854 A
253 G
* * * * *
28855 TGGAAACATTCTACCCGAAGGTCTTACAGATGGCCCGAAGGACTTATCATCTTACTCGAAAAGAC
1 TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAAGACTTATCATCTTGCTCG-AAAGAC
* ** * * *
28920 TTATAGATGAATCAAAGGATTTAAGT-ATCATGCTCAAAAGACTTACTGATGGCCCGAAGAACTT
65 TTACAGATGACCCGAAGGATTTAA-TCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTT
* ***
28984 ACAAATTTTGGAAATAATATACTCATTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAAT
129 ACAAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAAT
*
29049 TTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATTGCTTTCTCATTTTTTGAAAATCATG
194 TTCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTT-----TCATG
* * * *
29114 TGGAAACATCCTACCCGAAGGTCTTACAGATGGCCCTAAAGACTTATCATCTTGCTCGAAATACT
1 TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
** * *
29179 TACAGATGACTTGAAGGATTTAAGCATCATGCTCGAAAGACTTACAGATGGCCCGAAGGACTTAC
66 TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
* * ** *
29244 AAATTTTGGAAATAATTTACTAGGTAAGAAACTTTGTTAATCATTTTTTTTACTTTTCAATAATT
131 AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATC-GCTTTCTTACTTTTCAATAATT
*
29309 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCACTTTCTCATTTTT
195 TCATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTT
29362 AAAATAACTT
Statistics
Matches: 902, Mismatches: 94, Indels: 32
0.88 0.09 0.03
Matches are distributed among these distances:
249 163 0.18
250 78 0.09
251 200 0.22
252 2 0.00
255 3 0.00
258 107 0.12
259 178 0.20
260 170 0.19
261 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.15, T:0.34
Consensus pattern (253 bp):
TGAAAACATCCTACCCGAAGGTCTTACGGATGGCCCGAAAGACTTATCATCTTGCTCGAAAGACT
TACAGATGACCCGAAGGATTTAATCATCATGCTCGAAAGACTTACTGATGGCCCGAAGGACTTAC
AAATTTTGGAAATAATTTACTGGGTAAGAAACTTTGGTAATCGCTTTCTTACTTTTCAATAATTT
CATTTTCTAAAAACATTAAATGAGAAACTTTGGTAATCGCTTTCTCATTTTTTTCATG
Found at i:31678 original size:2 final size:2
Alignment explanation
Indices: 31671--31707 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31661 TCAATTTTAT
31671 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
31708 CTTTATCAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31811 original size:97 final size:96
Alignment explanation
Indices: 31691--31898 Score: 276
Period size: 97 Copynumber: 2.1 Consensus size: 96
31681 TATATATATA
* * *
31691 TATATATATATATATATCTTTATCA-GACTAGCTGAATCTTATCCATAAAGCTGGGGCATTTAAC
1 TATATAT-TATA-ATACCTTTATCACG-CTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAAC
*
31755 CAATTGCTCTAGAGGGACAACTCAAGCTTAATTG
63 CAATTACTCTAGAGGGACAACTCAAGCTTAATTG
* *
31789 TATATATTATAATCACCTTTATCACGCTAGTTGAATCTTATCTATAAAGCCGGAGCATTTAACCA
1 TATATATTATAAT-ACCTTTATCACGCTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAACCA
** *
31854 ATTACTCTAGAGGGACAGTTCAAGCTTTATTG
65 ATTACTCTAGAGGGACAACTCAAGCTTAATTG
*
31886 TATACA-TATAATA
1 TATATATTATAATA
31899 TTATCTGGGT
Statistics
Matches: 98, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
95 1 0.01
96 8 0.08
97 81 0.83
98 8 0.08
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.35
Consensus pattern (96 bp):
TATATATTATAATACCTTTATCACGCTAGCTGAATCTTATCCATAAAGCCGGAGCATTTAACCAA
TTACTCTAGAGGGACAACTCAAGCTTAATTG
Found at i:36588 original size:17 final size:16
Alignment explanation
Indices: 36547--36588 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 16
36537 AAATATATTT
36547 TAAAATAATTTTAAGA
1 TAAAATAATTTTAAGA
36563 -AAAATAATTTTAAAAGA
1 TAAAATAATTTT--AAGA
36580 TAAAA-AATT
1 TAAAATAATT
36589 GATCTGTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
15 11 0.48
17 8 0.35
18 4 0.17
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (16 bp):
TAAAATAATTTTAAGA
Found at i:38441 original size:3 final size:3
Alignment explanation
Indices: 38435--38502 Score: 136
Period size: 3 Copynumber: 22.7 Consensus size: 3
38425 TATTTATTAT
38435 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38483 TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TA
38503 TACAATGTAG
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 65 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:40867 original size:19 final size:20
Alignment explanation
Indices: 40843--40893 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
40833 AATGACCAAT
*
40843 AAAATCGCAATGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
40862 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
40882 AAAATCGCAACG
1 AAAATCGCAACG
40894 TTAAAAAGAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.18
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:40887 original size:20 final size:20
Alignment explanation
Indices: 40843--41180 Score: 160
Period size: 20 Copynumber: 16.6 Consensus size: 20
40833 AATGACCAAT
* * *
40843 AAAATCGCAATGCGATAT-C
1 AAAATCGCAACGCGATTTAG
40862 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
40882 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
40902 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
40922 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
40943 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
40966 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* ** *
40986 AGAATCGCAATACGATTTAT
1 AAAATCGCAACGCGATTTAG
* ** *
41006 AGAATCGCAATACGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
41026 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
41046 AGAGTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
41069 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
41089 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
41109 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
41129 AGAATTGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
41149 AGAATTGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
41169 AAAATCGCAACG
1 AAAATCGCAACG
41181 TTAAAAAGAA
Statistics
Matches: 257, Mismatches: 50, Indels: 23
0.78 0.15 0.07
Matches are distributed among these distances:
19 16 0.06
20 198 0.77
21 14 0.05
23 29 0.11
ACGTcount: A:0.39, C:0.18, G:0.22, T:0.20
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:41022 original size:40 final size:40
Alignment explanation
Indices: 40947--41178 Score: 230
Period size: 40 Copynumber: 5.7 Consensus size: 40
40937 GCTTCCAAGT
* *
40947 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAATGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * * * *
40990 TCGCAATACGATTTATAGAATCGCAATACGATTTATAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * * *
41030 TCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGA-TT-G-AGAGAA
* * *
41073 TCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * *
41113 TCGCAATGCGATTTATAGAATTGCAACGCGATTGAGAGAA
1 TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* * *
41153 TTGCAACGCGATTTAGAAAATCGCAA
1 TCGCAATGCGATTTAGAGAATCGCAA
41179 CGTTAAAAAG
Statistics
Matches: 156, Mismatches: 30, Indels: 9
0.80 0.15 0.05
Matches are distributed among these distances:
40 105 0.67
41 3 0.02
42 3 0.02
43 45 0.29
ACGTcount: A:0.38, C:0.17, G:0.24, T:0.22
Consensus pattern (40 bp):
TCGCAATGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:41075 original size:83 final size:83
Alignment explanation
Indices: 40988--41145 Score: 208
Period size: 83 Copynumber: 1.9 Consensus size: 83
40978 CGATTGATAG
* * * * * * *
40988 AATCGCAATACGATTTATAGAATCGCAATACGATTTATAGAATCGCAATGCGATTGAGAGAGTCG
1 AATCGCAATACGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
41053 CAACGCGATTTAGAAGAA
66 CAACGCGATTTAGAAGAA
* * * * *
41071 AATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAATTG
1 AATCGCAATACGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
41136 CAACGCGATT
66 CAACGCGATT
41146 GAGAGAATTG
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
83 63 1.00
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (83 bp):
AATCGCAATACGACTGAGAGAATCGCAATACGACTGAGAGAATCGCAATGCGATTGAGAGAATCG
CAACGCGATTTAGAAGAA
Found at i:41079 original size:103 final size:103
Alignment explanation
Indices: 40947--41170 Score: 349
Period size: 103 Copynumber: 2.2 Consensus size: 103
40937 GCTTCCAAGT
* * * * *
40947 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATACGATTTATAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
* *
41012 GCAATACGATTTATAGAATCGCAATGCGATTGAGAGAG
66 GCAATACGATTTATAGAATCGCAACGCGATTGAGAGAA
*
41050 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAATC
1 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
* *
41115 GCAATGCGATTTATAGAATTGCAACGCGATTGAGAGAA
66 GCAATACGATTTATAGAATCGCAACGCGATTGAGAGAA
*
41153 TTGCAACGCGATTTAGAA
1 TCGCAACGCGATTTAGAA
41171 AATCGCAACG
Statistics
Matches: 110, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
103 110 1.00
ACGTcount: A:0.37, C:0.17, G:0.24, T:0.22
Consensus pattern (103 bp):
TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATACGACTGAGAGAATC
GCAATACGATTTATAGAATCGCAACGCGATTGAGAGAA
Found at i:41190 original size:20 final size:20
Alignment explanation
Indices: 41167--41210 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
41157 AACGCGATTT
*
41167 AGAAAATCGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
41187 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
41207 AGAA
1 AGAA
41211 TAGTTAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.55, C:0.16, G:0.18, T:0.11
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:41199 original size:60 final size:61
Alignment explanation
Indices: 41026--41200 Score: 151
Period size: 60 Copynumber: 2.9 Consensus size: 61
41016 TACGATTTAT
* * * * * *
41026 AGAATCGCAATGCGATTGAGAGAGTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAG
1 AGAATCGCAACGCGACTGAGAAAATCGCAA-GCGA-TTAAAAGAAAATCGCAACGCGACTGAG
* * * * * *
41089 AGAATCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAG--AATTGCAACGCGATTGAG
1 AGAATCGCAACGCGACTGAGAAAATCGCAA-GCGATTAAAAGAAAATCGCAACGCGACTGAG
* * *
41149 AGAATTGCAACGCGATTTAGAAAATCGCAA-CG-TTAAAAAGAAAATCGCAACG
1 AGAATCGCAACGCGACTGAGAAAATCGCAAGCGATT-AAAAGAAAATCGCAACG
41201 GTCAAAAGAA
Statistics
Matches: 92, Mismatches: 17, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
57 2 0.02
58 5 0.05
60 49 0.53
62 4 0.04
63 32 0.35
ACGTcount: A:0.39, C:0.17, G:0.25, T:0.19
Consensus pattern (61 bp):
AGAATCGCAACGCGACTGAGAAAATCGCAAGCGATTAAAAGAAAATCGCAACGCGACTGAG
Found at i:41299 original size:6 final size:6
Alignment explanation
Indices: 41288--41331 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
41278 GACACGTATT
41288 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
41332 CGAGACGAGA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.13
6 33 0.87
ACGTcount: A:0.32, C:0.52, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:42033 original size:6 final size:6
Alignment explanation
Indices: 42012--42048 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
42002 TCTCGTCTCG
42012 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
42049 AATACGTGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 10 0.32
6 21 0.68
ACGTcount: A:0.00, C:0.16, G:0.54, T:0.30
Consensus pattern (6 bp):
GGTCGT
Found at i:42151 original size:20 final size:20
Alignment explanation
Indices: 42126--42169 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
42116 TTTTTAACTA
*
42126 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
42146 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
42166 TTCT
1 TTCT
42170 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:42179 original size:20 final size:20
Alignment explanation
Indices: 42156--42493 Score: 151
Period size: 20 Copynumber: 16.6 Consensus size: 20
42146 TTCTTTTTAA
42156 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
42176 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
42196 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
42216 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * * *
42236 CATTACGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
* * * *
42256 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
42276 CATTGCGATTCTCTTCTAAATCG
1 CGTTGCGA-T-T-TTCTAAATCG
* * *
42299 CGTTGCGACTCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
42319 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* *** *
42339 CATTGCGATTCAATCAATCG
1 CGTTGCGATTTTCTAAATCG
* *
42359 CATTGCGATTTTCTTCTAAATTG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
42382 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
* *
42403 CGTTGCGATTTTCT--TTTG
1 CGTTGCGATTTTCTAAATCG
* *** **
42421 ACCGTTGCGCTTTTCTTTTTAA
1 --CGTTGCGATTTTCTAAATCG
42443 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
42463 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
42482 CGTTGCGATTTT
1 CGTTGCGATTTT
42494 ATTGGTCATT
Statistics
Matches: 255, Mismatches: 52, Indels: 23
0.77 0.16 0.07
Matches are distributed among these distances:
18 2 0.01
19 17 0.07
20 191 0.75
21 14 0.05
22 5 0.02
23 26 0.10
ACGTcount: A:0.19, C:0.24, G:0.19, T:0.38
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:42202 original size:40 final size:40
Alignment explanation
Indices: 42158--42368 Score: 278
Period size: 40 Copynumber: 5.2 Consensus size: 40
42148 CTTTTTAACG
* *
42158 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
42198 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * * *
42238 TTACGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
42278 TTGCGATTCTCTTCTAAATCGCGTTGCGACTCTCTCAATCGCA
1 TTGCGA-T-TC-TCTAAATCGCATTGCGATTCTCTCAATCGCA
* **
42321 TTGCGATTCTATAAATCGCATTGCGATTCAATCAATCGCA
1 TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
42361 TTGCGATT
1 TTGCGATT
42369 TTCTTCTAAA
Statistics
Matches: 149, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
40 111 0.74
41 3 0.02
42 3 0.02
43 32 0.21
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:42483 original size:19 final size:20
Alignment explanation
Indices: 42443--42493 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
42433 TTCTTTTTAA
*
42443 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCGAAATCG
*
42463 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCGAAATCG
42482 CGTTGCGATTTT
1 CGTTGCGATTTT
42494 ATTGGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.16, C:0.18, G:0.24, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTTTCGAAATCG
Found at i:44382 original size:407 final size:407
Alignment explanation
Indices: 43627--44446 Score: 1631
Period size: 407 Copynumber: 2.0 Consensus size: 407
43617 TACTTTCATC
43627 CCTATATTGGCGTCAAGATGCCACCACCCATATTTCGAATTTTCCCGAAATATGTTTGACTACCT
1 CCTATATTGGCGTCAAGATGCCACCACCCATATTTCGAATTTTCCCGAAATATGTTTGACTACCT
43692 CCTCGTTCCTCTAGGGAGAAGTCTTTGAGTCAGCTACACGTACACAAAACCTTTAGATAAGACTT
66 CCTCGTTCCTCTAGGGAGAAGTCTTTGAGTCAGCTACACGTACACAAAACCTTTAGATAAGACTT
43757 CTAATACACCCACATAACCTACTAGAATAAAATCCAAGATTTGACTATCATATCTATCTAATATG
131 CTAATACACCCACATAACCTACTAGAATAAAATCCAAGATTTGACTATCATATCTATCTAATATG
43822 CTGACCTAAATATAATCATAATAATCTTATATATGGTGCTATCAGCTTAAGACCATTATACAACT
196 CTGACCTAAATATAATCATAATAATCTTATATATGGTGCTATCAGCTTAAGACCATTATACAACT
43887 GAGGAGGGGGCTGGAACATCATCAACACCCAATCTCATTCTTTTTTACCGACTCTGACTAAAAAC
261 GAGGAGGGGGCTGGAACATCATCAACACCCAATCTCATTCTTTTTTACCGACTCTGACTAAAAAC
43952 ATTGTTGAACGACCACAACTCTTCATCCTAACCAAAGAGGATGAACCGTTAACGGCCAATCAAAT
326 ATTGTTGAACGACCACAACTCTTCATCCTAACCAAAGAGGATGAACCGTTAACGGCCAATCAAAT
44017 CAATTTGTTCTATTCAA
391 CAATTTGTTCTATTCAA
44034 CCTATATTGGCGTCAAGATGCCACCACCCATATTTCGAATTTTCCCGAAATATGTTTGACTACCT
1 CCTATATTGGCGTCAAGATGCCACCACCCATATTTCGAATTTTCCCGAAATATGTTTGACTACCT
44099 CCTCGTTCCTCTAGGGAGAAGTCTTTGAGTCAGCTACACGTACACAAAACCTTTAGATAAGACTT
66 CCTCGTTCCTCTAGGGAGAAGTCTTTGAGTCAGCTACACGTACACAAAACCTTTAGATAAGACTT
44164 CTAATACACCCACATAACCTACTAGAATAAAATCCAAGATTTGACTATCATATCTATCTAATATG
131 CTAATACACCCACATAACCTACTAGAATAAAATCCAAGATTTGACTATCATATCTATCTAATATG
*
44229 CTGACCTACATATAATCATAATAATCTTATATATGGTGCTATCAGCTTAAGACCATTATACAACT
196 CTGACCTAAATATAATCATAATAATCTTATATATGGTGCTATCAGCTTAAGACCATTATACAACT
44294 GAGGAGGGGGCTGGAACATCATCAACACCCAATCTCATTCTTTTTTACCGACTCTGACTAAAAAC
261 GAGGAGGGGGCTGGAACATCATCAACACCCAATCTCATTCTTTTTTACCGACTCTGACTAAAAAC
44359 ATTGTTGAACGACCACAACTCTTCATCCTAACCAAAGAGGATGAACCGTTAACGGCCAATCAAAT
326 ATTGTTGAACGACCACAACTCTTCATCCTAACCAAAGAGGATGAACCGTTAACGGCCAATCAAAT
44424 CAATTTGTTCTATTCAA
391 CAATTTGTTCTATTCAA
44441 CCTATA
1 CCTATA
44447 GTAATTAAGT
Statistics
Matches: 412, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
407 412 1.00
ACGTcount: A:0.34, C:0.24, G:0.13, T:0.29
Consensus pattern (407 bp):
CCTATATTGGCGTCAAGATGCCACCACCCATATTTCGAATTTTCCCGAAATATGTTTGACTACCT
CCTCGTTCCTCTAGGGAGAAGTCTTTGAGTCAGCTACACGTACACAAAACCTTTAGATAAGACTT
CTAATACACCCACATAACCTACTAGAATAAAATCCAAGATTTGACTATCATATCTATCTAATATG
CTGACCTAAATATAATCATAATAATCTTATATATGGTGCTATCAGCTTAAGACCATTATACAACT
GAGGAGGGGGCTGGAACATCATCAACACCCAATCTCATTCTTTTTTACCGACTCTGACTAAAAAC
ATTGTTGAACGACCACAACTCTTCATCCTAACCAAAGAGGATGAACCGTTAACGGCCAATCAAAT
CAATTTGTTCTATTCAA
Found at i:54061 original size:136 final size:136
Alignment explanation
Indices: 53817--54089 Score: 528
Period size: 136 Copynumber: 2.0 Consensus size: 136
53807 TCGCACAAAC
53817 AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTAAGCTTGTCATG
1 AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTAAGCTTGTCATG
53882 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
66 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
53947 CATCTG
131 CATCTG
* *
53953 AAGGATGCATCAACTCTTGACTCCTCAAACCCTAATTCCAACAGACACCCTTTGAGCTTGTCATG
1 AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTAAGCTTGTCATG
54018 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
66 CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
54083 CATCTG
131 CATCTG
54089 A
1 A
54090 GGCATATTCT
Statistics
Matches: 135, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.29, C:0.27, G:0.19, T:0.25
Consensus pattern (136 bp):
AAGGATGCATCAACTCTCGACTCCTCAAACCCTAATTCCAACAGACACCCTTTAAGCTTGTCATG
CCAGTTTTGCGGTGCCTGTCGAAGACCATACAATGCCTTTTGAAGTTTGCAAACCAGAGGAGAAC
CATCTG
Found at i:54310 original size:19 final size:19
Alignment explanation
Indices: 54286--54327 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
54276 ACTTGAGAGA
54286 AGCCATTAGTCACAAGCCT
1 AGCCATTAGTCACAAGCCT
*
54305 AGCCATTAGTCACAAGTCT
1 AGCCATTAGTCACAAGCCT
54324 AGCC
1 AGCC
54328 TTGTAACAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (19 bp):
AGCCATTAGTCACAAGCCT
Found at i:61874 original size:13 final size:13
Alignment explanation
Indices: 61841--61874 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
61831 TTGAAAAAGG
*
61841 AAGAAAAGGAAAT
1 AAGAAAAGGAAAC
61854 AAGAAAAGGAAAC
1 AAGAAAAGGAAAC
*
61867 AAGCAAAG
1 AAGAAAAG
61875 ACATGAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.24, T:0.03
Consensus pattern (13 bp):
AAGAAAAGGAAAC
Found at i:62292 original size:14 final size:15
Alignment explanation
Indices: 62268--62296 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
62258 GTATTTAACT
62268 TGTTCTAATTGATGA
1 TGTTCTAATTGATGA
62283 TGTT-TAATTGATGA
1 TGTTCTAATTGATGA
62297 ATGAATGAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.48
Consensus pattern (15 bp):
TGTTCTAATTGATGA
Found at i:62911 original size:23 final size:22
Alignment explanation
Indices: 62885--62941 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
62875 AAGAATTACC
62885 TTTAGGATTTATTTGTTATT-TAT
1 TTTAGGATTTATTT-TTATTGT-T
*
62908 TTTAGGAATTATATTTTTCTTGTT
1 TTTAGG-ATT-TATTTTTATTGTT
62932 TTTAGGATTT
1 TTTAGGATTT
62942 TGAAGGCTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.03
23 9 0.30
24 14 0.47
25 6 0.20
ACGTcount: A:0.21, C:0.02, G:0.14, T:0.63
Consensus pattern (22 bp):
TTTAGGATTTATTTTTATTGTT
Found at i:65552 original size:11 final size:12
Alignment explanation
Indices: 65513--65555 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 12
65503 ACAACTTTTC
65513 AACCA-CTAGCT
1 AACCATCTAGCT
* *
65524 AATCGTCTAGCT
1 AACCATCTAGCT
65536 AACCATCTAGC-
1 AACCATCTAGCT
65547 AACCATCTA
1 AACCATCTA
65556 ACTATAAGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
11 12 0.44
12 15 0.56
ACGTcount: A:0.35, C:0.33, G:0.09, T:0.23
Consensus pattern (12 bp):
AACCATCTAGCT
Found at i:68253 original size:43 final size:43
Alignment explanation
Indices: 68192--68315 Score: 212
Period size: 43 Copynumber: 2.9 Consensus size: 43
68182 TTTAACGGCG
* **
68192 TTTTTCTTTACAAACGCCGCTATTGTCTGTGTATTTAGCGGTA
1 TTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGACA
*
68235 TTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGACG
1 TTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGACA
68278 TTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAG
1 TTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAG
68316 TGGCATTTGT
Statistics
Matches: 77, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 77 1.00
ACGTcount: A:0.20, C:0.19, G:0.18, T:0.43
Consensus pattern (43 bp):
TTTTTCTTTACAAACGCCGCTATTGACTGTGTATTTAGCGACA
Found at i:68437 original size:15 final size:15
Alignment explanation
Indices: 68417--68445 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
68407 GCATAAAACA
68417 AAACTATACACATTG
1 AAACTATACACATTG
68432 AAACTATACACATT
1 AAACTATACACATT
68446 AGTTCACCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.21, G:0.03, T:0.28
Consensus pattern (15 bp):
AAACTATACACATTG
Found at i:69730 original size:21 final size:21
Alignment explanation
Indices: 69704--69745 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
69694 AAGCTTAAAT
69704 GTGTTATAGCCGGCAGCACCG
1 GTGTTATAGCCGGCAGCACCG
69725 GTGTTATAGCCGGCAGCACCG
1 GTGTTATAGCCGGCAGCACCG
69746 AGCCTTGTTC
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:0.19, C:0.29, G:0.33, T:0.19
Consensus pattern (21 bp):
GTGTTATAGCCGGCAGCACCG
Found at i:71666 original size:123 final size:123
Alignment explanation
Indices: 71507--71944 Score: 595
Period size: 123 Copynumber: 3.6 Consensus size: 123
71497 TTGTAAACTT
* ** *
71507 GCGGCATTTGTA-AACAAACGCCACTAAAACACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
1 GCGGCGTTTGTATAA-AAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCA
* *
71571 CTAAATCATGAGTCTATAGCGACGTTTG-TAAAAAATGCCACTAAATCACGAGTCTATA
65 CTAAATCATGAGTCTATAGCGGCGTTTGATAAAAAACGCCACTAAATCACGAGTCTATA
* *
71629 GCGGCGTTTGTA-ACAAACACGCCACTAAAGTATGAGTCTTTAGCGGCGATTGTATAAAAACGCC
1 GCGGCGTTTGTATA-AAA-ACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCC
* * *
71693 ACTAAAGT-ACGAGTCT-TAGTGGCGTTTGTATAAAAAACGCCACTAAATCATGAGTCTATA
64 ACTAAA-TCATGAGTCTATAGCGGCGTTTG-ATAAAAAACGCCACTAAATCACGAGTCTATA
*
71753 GCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC-GCGTTTGTATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
*
71817 TAAATCATGAGTCTATAGCGGCGTTTGTATAAAAAACGCCACTAAAGT-ACAAGTCTATA
66 TAAATCATGAGTCTATAGCGGCGTTTG-ATAAAAAACGCCACTAAA-TCACGAGTCTATA
* ** * *
71876 GCGTCGTTTGTATAAAAATACCACTAAATTAC-AGACTTTAGCGGCGTTTGTATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
71940 TAAAT
66 TAAAT
71945 TACATTCTTT
Statistics
Matches: 283, Mismatches: 23, Indels: 19
0.87 0.07 0.06
Matches are distributed among these distances:
121 1 0.00
122 64 0.23
123 173 0.61
124 44 0.16
125 1 0.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.26
Consensus pattern (123 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGCGGCGTTTGTATAAAAACGCCAC
TAAATCATGAGTCTATAGCGGCGTTTGATAAAAAACGCCACTAAATCACGAGTCTATA
Found at i:71673 original size:82 final size:82
Alignment explanation
Indices: 71507--71977 Score: 618
Period size: 82 Copynumber: 5.8 Consensus size: 82
71497 TTGTAAACTT
* **
71507 GCGGCATTTGTA-AACAAACGCCACTAAAACACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
1 GCGGCGTTTGTATAA-AAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
71571 CTAAATCATGAGTCTATA
65 CTAAATCATGAGTCTATA
* *
71589 GCGACGTTTGTA-AAAAATGCCACTAAA-TCACGAGTCTATAGCGGCGTTTGTA-ACAAACACGC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGT-ACGAGTCTATAGCGGCGTTTGTATA-AAA-ACGC
*
71651 CACTAAAGT-ATGAGTCTTTA
63 CACTAAA-TCATGAGTCTATA
* *
71671 GCGGCGATTGTATAAAAACGCCACTAAAGTACGAGTCT-TAGTGGCGTTTGTATAAAAAACGCCA
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTAT-AAAAACGCCA
71735 CTAAATCATGAGTCTATA
65 CTAAATCATGAGTCTATA
* *
71753 GCGACGTTTGTATAAAAACGCCACTAAAGTACGAGTCTTTAGC-GCGTTTGTATAAAAACGCCAC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
71817 TAAATCATGAGTCTATA
66 TAAATCATGAGTCTATA
* * **
71834 GCGGCGTTTGTATAAAAAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATAAAAATACCA
1 GCGGCGTTTGTAT-AAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
* * * *
71899 CTAAATTA-CAGACTTTA
65 CTAAATCATGAGTCTATA
* * * *
71916 GCGGCGTTTGTATAAAAACGCCACTAAATTAC-ATTCTTTAGCGGCATTTGTATAAAAACGCC
1 GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCC
71978 GCTATAGTAG
Statistics
Matches: 347, Mismatches: 30, Indels: 26
0.86 0.07 0.06
Matches are distributed among these distances:
80 25 0.07
81 97 0.28
82 170 0.49
83 53 0.15
84 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.26
Consensus pattern (82 bp):
GCGGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
TAAATCATGAGTCTATA
Found at i:71889 original size:205 final size:203
Alignment explanation
Indices: 71507--72005 Score: 634
Period size: 205 Copynumber: 2.5 Consensus size: 203
71497 TTGTAAACTT
* * *
71507 GCGGCATTTGTA-AACAAACGCCACTAAAACACGAGTCTATAGCGGCGTTTGTATAAAAACGCCA
1 GCGGCGTTTGTATAAAAAACGCCACTAAATCA-GAGTCTATAGCGGCGTTTGTATAAAAACGCCA
* * *
71571 CTAAA-TCATGAGTCTATAGCGACGTTTGTAAAAAATGCCACTAAATCACGAGTCTATAGCGGCG
65 CTAAAGT-ACGAGTCTTTAGCG-CGTTTGTAAAAAACGCCACTAAATCACGAGTCTATAGCGGCG
* ** * *
71635 TTTGTAACAAACACGCCACTAAAGTATGAGTCTTTAGCGGCGATTGTATAAAAACGCCACTAAAG
128 TTTGTAACAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGATTGTATAAAAACACCACTAAAG
*
71700 TAC-GAGTCTTA
193 TACAGACT-TTA
* *
71711 GTGGCGTTTGTATAAAAAACGCCACTAAATCATGAGTCTATAGCGACGTTTGTATAAAAACGCCA
1 GCGGCGTTTGTATAAAAAACGCCACTAAATCA-GAGTCTATAGCGGCGTTTGTATAAAAACGCCA
*
71776 CTAAAGTACGAGTCTTTAGCGCGTTTGTATAAAAACGCCACTAAATCATGAGTCTATAGCGGCGT
65 CTAAAGTACGAGTCTTTAGCGCGTTTGTA-AAAAACGCCACTAAATCACGAGTCTATAGCGGCGT
* * * *
71841 TTGTATA-AAAAACGCCACTAAAGTACAAGTCTATAGCGTCGTTTGTATAAAAATACCACTAAAT
129 TTGTA-ACAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGATTGTATAAAAACACCACTAAAG
71905 TACAGACTTTA
193 TACAGACTTTA
* * * * * *
71916 GCGGCGTTTGTAT-AAAAACGCCACTAAATTACATTCTTTAGCGGCATTTGTATAAAAACGCCGC
1 GCGGCGTTTGTATAAAAAACGCCACTAAATCAGAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
* *
71980 TATAGTAGGAG--TTTAGCAGCGTTTGT
66 TAAAGTACGAGTCTTTAGC-GCGTTTGT
72006 TCTAAAACGC
Statistics
Matches: 259, Mismatches: 30, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
201 6 0.02
202 8 0.03
203 36 0.14
204 35 0.14
205 169 0.65
206 5 0.02
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.27
Consensus pattern (203 bp):
GCGGCGTTTGTATAAAAAACGCCACTAAATCAGAGTCTATAGCGGCGTTTGTATAAAAACGCCAC
TAAAGTACGAGTCTTTAGCGCGTTTGTAAAAAACGCCACTAAATCACGAGTCTATAGCGGCGTTT
GTAACAAAAACGCCACTAAAGTACAAGTCTATAGCGGCGATTGTATAAAAACACCACTAAAGTAC
AGACTTTA
Found at i:72770 original size:29 final size:29
Alignment explanation
Indices: 72725--72857 Score: 119
Period size: 29 Copynumber: 4.6 Consensus size: 29
72715 TTGTTTTAGT
* * *
72725 CCTTTTAG-TTTTATTTTTATTGTTTATC
1 CCTTTAAGATTTTGTTTTTACTGTTTATC
* * *
72753 CCTTTAAGATTATGTTTTTACTATTTAGC
1 CCTTTAAGATTTTGTTTTTACTGTTTATC
** * *
72782 CCTTTAAGATTTTGTAATTAATATTTTAGT-
1 CCTTTAAGATTTTGTTTTTACT-GTTTA-TC
* *
72812 CCTTTTAGTTTTTGTTTTTACTGTTTATC
1 CCTTTAAGATTTTGTTTTTACTGTTTATC
72841 CCTTTAAGA-TTTGTTTT
1 CCTTTAAGATTTTGTTTT
72858 ACTATTTTAG
Statistics
Matches: 81, Mismatches: 20, Indels: 8
0.74 0.18 0.07
Matches are distributed among these distances:
28 16 0.20
29 44 0.54
30 21 0.26
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.59
Consensus pattern (29 bp):
CCTTTAAGATTTTGTTTTTACTGTTTATC
Found at i:72885 original size:57 final size:59
Alignment explanation
Indices: 72753--72894 Score: 189
Period size: 57 Copynumber: 2.4 Consensus size: 59
72743 ATTGTTTATC
*
72753 CCTTTAAGATTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
1 CCTTTAAGTTTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
* * * * * *
72812 CCTTTTAGTTTTTGTTTTTACTGTTTATCCCTTTAAGA-TTTGT-TTTACTATTTTAGT
1 CCTTTAAGTTTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
* *
72869 CCTTTGAGTTTATGTTTTTTCTATTT
1 CCTTTAAGTTTATGTTTTTACTATTT
72895 TGGTCGTTGT
Statistics
Matches: 72, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
57 34 0.47
58 5 0.07
59 33 0.46
ACGTcount: A:0.20, C:0.11, G:0.11, T:0.58
Consensus pattern (59 bp):
CCTTTAAGTTTATGTTTTTACTATTTAGCCCTTTAAGATTTTGTAATTAATATTTTAGT
Found at i:72895 original size:87 final size:87
Alignment explanation
Indices: 72705--72873 Score: 261
Period size: 87 Copynumber: 1.9 Consensus size: 87
72695 CTCTGGTTTA
* * *
72705 TTTGTAATTATTGTTTTAGTCCTTTTAGTTTTATTTTTATTGTTTATCCCTTTAAGATTATGTTT
1 TTTGTAATTAATATTTTAGTCCTTTTAGTTTTATTTTTACTGTTTATCCCTTTAAGATTATGTTT
72770 TTACTATTTAGCCCTTTAAGAT
66 TTACTATTTAGCCCTTTAAGAT
*
72792 TTTGTAATTAATATTTTAGTCCTTTTAGTTTTTGTTTTTACTGTTTATCCCTTTAAGATT-TG-T
1 TTTGTAATTAATATTTTAGTCCTTTTAG-TTTTATTTTTACTGTTTATCCCTTTAAGATTATGTT
*
72855 TTTACTATTTTAGTCCTTT
65 TTTACTA-TTTAGCCCTTT
72874 GAGTTTATGT
Statistics
Matches: 75, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
86 8 0.11
87 38 0.51
88 29 0.39
ACGTcount: A:0.20, C:0.11, G:0.10, T:0.60
Consensus pattern (87 bp):
TTTGTAATTAATATTTTAGTCCTTTTAGTTTTATTTTTACTGTTTATCCCTTTAAGATTATGTTT
TTACTATTTAGCCCTTTAAGAT
Found at i:73925 original size:15 final size:15
Alignment explanation
Indices: 73905--73935 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
73895 TATGAGCAAT
73905 TCAAAAGTTAAGTAA
1 TCAAAAGTTAAGTAA
73920 TCAAAAGTTAAGTAA
1 TCAAAAGTTAAGTAA
73935 T
1 T
73936 TAAATTTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.13, T:0.29
Consensus pattern (15 bp):
TCAAAAGTTAAGTAA
Done.