Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005666.1 Hibiscus syriacus cultivar Beakdansim tig00013248_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: 57060
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11952 original size:16 final size:16
Alignment explanation
Indices: 11931--11966 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
11921 ACATGTGTAC
11931 ACTTAAGCAACAAGGA
1 ACTTAAGCAACAAGGA
*
11947 ACTTAAGCAACGAGGA
1 ACTTAAGCAACAAGGA
11963 ACTT
1 ACTT
11967 TTGAATTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.19, T:0.17
Consensus pattern (16 bp):
ACTTAAGCAACAAGGA
Found at i:16488 original size:80 final size:80
Alignment explanation
Indices: 16355--16515 Score: 250
Period size: 80 Copynumber: 2.0 Consensus size: 80
16345 CAGTTTCCCA
* * *
16355 TAACTACATCCATAAGGACTTACCCTAGGCCCATTGGGCGTAGGTACCAACCTAAGAGAATATGT
1 TAACTACATCCATAAGAACTTACCCTAGGCCCATTGAGCGTAGGTACCAACCTAAGAGAATATCT
16420 TGGGGCTTGAGAGCC
66 TGGGGCTTGAGAGCC
* * * * *
16435 TAACTGCATCCATAAGAACTTACCTTAGGTCCATTGAGCGTAGGTGCCAACCTAAGGGAATATCT
1 TAACTACATCCATAAGAACTTACCCTAGGCCCATTGAGCGTAGGTACCAACCTAAGAGAATATCT
16500 TGGGGCTTGAGAGCC
66 TGGGGCTTGAGAGCC
16515 T
1 T
16516 TCCCAAGGGA
Statistics
Matches: 73, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.24
Consensus pattern (80 bp):
TAACTACATCCATAAGAACTTACCCTAGGCCCATTGAGCGTAGGTACCAACCTAAGAGAATATCT
TGGGGCTTGAGAGCC
Found at i:16545 original size:32 final size:32
Alignment explanation
Indices: 16509--16617 Score: 130
Period size: 32 Copynumber: 3.4 Consensus size: 32
16499 TTGGGGCTTG
* *
16509 AGAGCCTTCCCAAGGGAGTACCTTAGGGCCTA
1 AGAGCCTACCCAAGGAAGTACCTTAGGGCCTA
* * *
16541 AGAGCGTACCCAAGGAAGTACCTTGGGGCCTT
1 AGAGCCTACCCAAGGAAGTACCTTAGGGCCTA
* * *
16573 AGAGCCTACCCAAGGAAATGCCTT-GGGACCTT
1 AGAGCCTACCCAAGGAAGTACCTTAGGG-CCTA
16605 AGAGCCTACCCAA
1 AGAGCCTACCCAA
16618 TGTCATCTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
31 3 0.04
32 65 0.96
ACGTcount: A:0.28, C:0.28, G:0.27, T:0.17
Consensus pattern (32 bp):
AGAGCCTACCCAAGGAAGTACCTTAGGGCCTA
Found at i:16609 original size:64 final size:64
Alignment explanation
Indices: 16498--16617 Score: 154
Period size: 64 Copynumber: 1.9 Consensus size: 64
16488 AAGGGAATAT
* * * *
16498 CTTGGGGCTTGAGAGCCTTCCCAAGGGAGTACCTTAGGGCCTAAGAGCGTACCCAAGGAAGTAC
1 CTTGGGGCTTGAGAGCCTACCCAAGGAAATACCTTAGGGCCTAAGAGCCTACCCAAGGAAGTAC
* *
16562 CTTGGGGCCTT-AGAGCCTACCCAAGGAAATGCCTT-GGGACCTTAGAGCCTACCCAA
1 CTTGGGG-CTTGAGAGCCTACCCAAGGAAATACCTTAGGG-CCTAAGAGCCTACCCAA
16618 TGTCATCTTA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
63 3 0.06
64 42 0.88
65 3 0.06
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (64 bp):
CTTGGGGCTTGAGAGCCTACCCAAGGAAATACCTTAGGGCCTAAGAGCCTACCCAAGGAAGTAC
Found at i:17725 original size:27 final size:28
Alignment explanation
Indices: 17666--17729 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
17656 TAGGGTTTGG
* *
17666 GGGTATTTTTGGGTCATTTTACACTTTAG
1 GGGTA-TTTTGGGTCATTTTACACTTCAA
* *
17695 GGGTATTTT-GGTCATTTTATAGTTCAA
1 GGGTATTTTGGGTCATTTTACACTTCAA
17722 GGGTATTT
1 GGGTATTT
17730 CAATTCTTTC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 22 0.71
28 4 0.13
29 5 0.16
ACGTcount: A:0.19, C:0.08, G:0.25, T:0.48
Consensus pattern (28 bp):
GGGTATTTTGGGTCATTTTACACTTCAA
Found at i:17785 original size:9 final size:9
Alignment explanation
Indices: 17771--17802 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
17761 TAATTCAAAT
*
17771 TTTCATTTA
1 TTTCATTCA
17780 TTTCATTCA
1 TTTCATTCA
17789 TTTCATTCA
1 TTTCATTCA
17798 TTTCA
1 TTTCA
17803 AAGAATTCTA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.22, C:0.19, G:0.00, T:0.59
Consensus pattern (9 bp):
TTTCATTCA
Found at i:29465 original size:45 final size:43
Alignment explanation
Indices: 29384--29473 Score: 96
Period size: 45 Copynumber: 2.0 Consensus size: 43
29374 GAAAAAAAGT
*
29384 TAATATAGAGTATATATAATACAAAAAAAGATAAAAAGAAAGAAA
1 TAATATAGAGTATATATAATACAAAAAAAGA-AAAAA-AAACAAA
29429 TAATATAGAGTAGTATA-AATTA-AATAATAAAG-AAAAAAAACAAA
1 TAATATAGAGTA-TATATAA-TACAA-AA-AAAGAAAAAAAAACAAA
29473 T
1 T
29474 TAAGATGATA
Statistics
Matches: 40, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
44 7 0.17
45 21 0.52
46 8 0.20
47 4 0.10
ACGTcount: A:0.66, C:0.02, G:0.10, T:0.22
Consensus pattern (43 bp):
TAATATAGAGTATATATAATACAAAAAAAGAAAAAAAAACAAA
Found at i:30357 original size:6 final size:6
Alignment explanation
Indices: 30341--30398 Score: 57
Period size: 6 Copynumber: 9.3 Consensus size: 6
30331 AACAGACCTG
*
30341 AAAAT- AAAATA AAAATAA AATTAATA AAAGATA AAAA-A TAAATA AAAATA
1 AAAATA AAAATA AAAAT-A AA--AATA AAA-ATA AAAATA AAAATA AAAATA
30391 AAAATA AA
1 AAAATA AA
30399 TAACAACGAT
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
5 9 0.20
6 21 0.47
7 9 0.20
8 3 0.07
9 3 0.07
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (6 bp):
AAAATA
Found at i:30395 original size:34 final size:36
Alignment explanation
Indices: 30341--30419 Score: 101
Period size: 34 Copynumber: 2.2 Consensus size: 36
30331 AACAGACCTG
*
30341 AAAATAAAATAAAAATAAAATTAATAA-AA-GATAA-
1 AAAAT-AAATAAAAATAAAATAAATAACAACGATAAT
30375 AAAATAAATAAAAATAAAAATAAATAACAACGATAAT
1 AAAATAAATAAAAAT-AAAATAAATAACAACGATAAT
30412 AACAATAA
1 AA-AATAA
30420 TATTATTACA
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
33 10 0.26
34 15 0.38
35 2 0.05
36 5 0.13
37 2 0.05
38 5 0.13
ACGTcount: A:0.75, C:0.04, G:0.03, T:0.19
Consensus pattern (36 bp):
AAAATAAATAAAAATAAAATAAATAACAACGATAAT
Found at i:30505 original size:36 final size:35
Alignment explanation
Indices: 30458--30863 Score: 323
Period size: 36 Copynumber: 11.4 Consensus size: 35
30448 TCCAAAAACC
* *
30458 TATATAATATATATTTTCAAAAGTATTTTAAAATTA
1 TATATTATATATATTTTCAAAA-TATTTTAAAACTA
* * *
30494 TATATTATATAT-TTTTAAAAAAATGTTT---TC-A
1 TATATTATATATATTTTCAAAATAT-TTTAAAACTA
* * *
30525 -AAATTATATA-GTTTTCAAAAATGTTTTTAAAACTA
1 TATATTATATATATTTTC-AAAAT-ATTTTAAAACTA
*
30560 TATATTATATA-AGTTTTCAAAATGATTTCAAAACTA
1 TATATTATATATA-TTTTCAAAAT-ATTTTAAAACTA
* * * *
30596 TATAATATATATGTTTTCAAAATGATTTAAAAATTA
1 TATATTATATATATTTTCAAAAT-ATTTTAAAACTA
*
30632 TATAATATATATATTTTCAAAA-ATGTTTCAAAAACTA
1 TATATTATATATATTTTCAAAATAT-TTT--AAAACTA
* *
30669 TATATTATATTTATTTTCAAAATGTTTTAAAAACTA
1 TATATTATATATATTTTCAAAATATTTT-AAAACTA
*
30705 TATA--ATATATATTTTCAAAATGTTTTAAAAACTA
1 TATATTATATATATTTTCAAAATATTTT-AAAACTA
* *
30739 TATATTATATTTATTTTCAAAATGTTTTAGAAACTA
1 TATATTATATATATTTTCAAAATATTTTA-AAACTA
* *
30775 TATAATATATAAATATTTTCAAACATGTTTTCAAAACTA
1 TAT-AT-TATATATATTTTCAAA-ATATTTT-AAAACTA
* * * * *
30814 TAT-TATATATATATATTAAAAATGTTTTCAAGCTA
1 TATAT-TATATATATTTTCAAAATATTTTAAAACTA
30849 TATATATATATATAT
1 TATAT-TATATATAT
30864 ATATATAATT
Statistics
Matches: 314, Mismatches: 33, Indels: 46
0.80 0.08 0.12
Matches are distributed among these distances:
30 13 0.04
31 8 0.03
32 1 0.00
34 38 0.12
35 23 0.07
36 148 0.47
37 51 0.16
38 15 0.05
39 16 0.05
40 1 0.00
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
TATATTATATATATTTTCAAAATATTTTAAAACTA
Found at i:30531 original size:30 final size:29
Alignment explanation
Indices: 30497--30565 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 29
30487 AAAATTATAT
30497 ATTATATATTTTTAAAAAAATGTTTTCAAA
1 ATTATATATTTTT-AAAAAATGTTTTCAAA
* * *
30527 ATTATATAGTTTTCAAAAATGTTTTTAAA
1 ATTATATATTTTTAAAAAATGTTTTCAAA
*
30556 ACTATATATT
1 ATTATATATT
30566 ATATAAGTTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
29 22 0.65
30 12 0.35
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.48
Consensus pattern (29 bp):
ATTATATATTTTTAAAAAATGTTTTCAAA
Found at i:30666 original size:109 final size:107
Alignment explanation
Indices: 30529--30863 Score: 406
Period size: 109 Copynumber: 3.1 Consensus size: 107
30519 TTTTCAAAAT
* *
30529 TATATAGTTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTTTTCAAAATGATTTCAAAAC
1 TATATA-TTTTCAAAAATGTTTTAAAAACTATATATTATATAA-TTTTCAAAATGTTTTCAAAAC
*
30594 TATATAATATATATGTTTTCAAAATGATTTAAAAATTATATAATA
64 TATATAATATATAT-TTTTCAAAATGATTTAAAAACTATATAATA
* * *
30639 TATATATTTTCAAAAATGTTTCAAAAACTATATATTATATTTATTTTCAAAATGTTTTAAAAACT
1 TATATATTTTCAAAAATGTTTTAAAAACTATATATTATA-TAATTTTCAAAATGTTTTCAAAACT
* *
30704 ATATAATATATA-TTTTCAAAATGTTTTAAAAACTATATATTA
65 ATATAATATATATTTTTCAAAATGATTTAAAAACTATATAATA
* * *
30746 TATTTATTTTC-AAAATGTTTTAGAAACTATATAATATATAAATATTTTCAAACATGTTTTCAAA
1 TATATATTTTCAAAAATGTTTTAAAAACTATAT-AT-TATATA-ATTTTCAAA-ATGTTTTCAAA
* * * ** *
30810 ACTATATTATATATATATATTAAAAATG-TTTTCAAGCTATATATATA
62 ACTATATAATATATAT-TTTTCAAAATGATTTAAAAACTATATA-ATA
30857 TATATAT
1 TATATAT
30864 ATATATAATT
Statistics
Matches: 195, Mismatches: 22, Indels: 15
0.84 0.09 0.06
Matches are distributed among these distances:
106 19 0.10
107 39 0.20
108 13 0.07
109 87 0.45
110 20 0.10
111 17 0.09
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (107 bp):
TATATATTTTCAAAAATGTTTTAAAAACTATATATTATATAATTTTCAAAATGTTTTCAAAACTA
TATAATATATATTTTTCAAAATGATTTAAAAACTATATAATA
Found at i:30804 original size:145 final size:142
Alignment explanation
Indices: 30529--30861 Score: 418
Period size: 145 Copynumber: 2.3 Consensus size: 142
30519 TTTTCAAAAT
* *
30529 TATATAGTTTTCAAAAATGTTTTTAAAACTATATATTATATAAGTTTTCAAAATGATTTCAAAAC
1 TATATA-TTTTC-AAAATG-TTTTAAAACTATATAATATAT-A-TTTTCAAAATGATTTAAAAAC
* *
30594 TATATAATATATATGTTTTCAAAATGATTTAAAAATTATATAATATATATATTTTCAAAAATG-T
61 TATATAATATATATATTTTCAAAATGATTTAAAAACTATATAATATATATATTTTCAAAAATGTT
30658 TTCAAAAACTATA-TATTA
126 TTC-AAAACTATATTA-TA
* *
30676 TATTTATTTTCAAAATGTTTTAAAAACTATATAATATATATTTTCAAAATGTTTTAAAAACTATA
1 TATATATTTTCAAAATGTTTT-AAAACTATATAATATATATTTTCAAAATGATTTAAAAACTATA
* * * * *
30741 TATTATATTTATTTTCAAAATGTTTTAGAAACTATATAATATATAAATATTTTCAAACATGTTTT
65 TAATATATATATTTTCAAAATGATTTAAAAACTATATAATATAT--ATATTTTCAAAAATGTTTT
30806 CAAAACTATATTATA
128 CAAAACTATATTATA
* * * *
30821 TATATATATTAAAAATGTTTTCAAGCTATATATATATATAT
1 TATATATTTTCAAAATGTTTTAAAACTATATA-ATATATAT
30862 ATATATATAA
Statistics
Matches: 164, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
143 61 0.37
144 14 0.09
145 73 0.45
146 11 0.07
147 5 0.03
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (142 bp):
TATATATTTTCAAAATGTTTTAAAACTATATAATATATATTTTCAAAATGATTTAAAAACTATAT
AATATATATATTTTCAAAATGATTTAAAAACTATATAATATATATATTTTCAAAAATGTTTTCAA
AACTATATTATA
Found at i:30865 original size:36 final size:36
Alignment explanation
Indices: 30529--30863 Score: 366
Period size: 36 Copynumber: 9.2 Consensus size: 36
30519 TTTTCAAAAT
30529 TATATAGTTTTCAAAAATGTTTTTAAAACTATATAT-TA
1 TATATA-TTTTC-AAAATG-TTTTAAAACTATATATATA
*
30567 TATA-AGTTTTCAAAATGATTTCAAAACTATATA-ATA
1 TATATA-TTTTCAAAATG-TTTTAAAACTATATATATA
* * *
30603 TATATGTTTTCAAAATGATTTAAAAAT-TATATAATA
1 TATATATTTTCAAAATGTTTTAAAACTATATAT-ATA
*
30639 TATATATTTTCAAAAATGTTTCAAAAACTATATAT-TA
1 TATATATTTTC-AAAATGTTT-TAAAACTATATATATA
*
30676 TATTTATTTTCAAAATGTTTTAAAA--ACTATATA-A
1 TATATATTTTCAAAATGTTTTAAAACTA-TATATATA
30710 TATATATTTTCAAAATGTTTTAAAAACTATATAT-TA
1 TATATATTTTCAAAATGTTTT-AAAACTATATATATA
*
30746 TATTTATTTTCAAAATGTTTTAGAAACTATATAATATA
1 TATATATTTTCAAAATGTTTTA-AAACTATAT-ATATA
*
30784 TAAATATTTTCAAACATGTTTTCAAAACTATAT-TATA
1 TATATATTTTCAAA-ATGTTTT-AAAACTATATATATA
* * * *
30821 TATATATATTAAAAATGTTTTCAAGCTATATATATA
1 TATATATTTTCAAAATGTTTTAAAACTATATATATA
30857 TATATAT
1 TATATAT
30864 ATATATAATT
Statistics
Matches: 257, Mismatches: 21, Indels: 40
0.81 0.07 0.13
Matches are distributed among these distances:
33 1 0.00
34 30 0.12
35 24 0.09
36 112 0.44
37 45 0.18
38 23 0.09
39 21 0.08
40 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.45
Consensus pattern (36 bp):
TATATATTTTCAAAATGTTTTAAAACTATATATATA
Found at i:30876 original size:143 final size:142
Alignment explanation
Indices: 30541--30879 Score: 364
Period size: 143 Copynumber: 2.4 Consensus size: 142
30531 TATAGTTTTC
* * * * *
30541 AAAAATGTTTTTAAAACTATATATTATATAAGTTTTCAAAATGATTTCAAAACTATATAATATAT
1 AAAAATGTTTTAAAAACTATATAATATAT-A-TTAT-AAAATGAATTAAAAACTATATAATATAT
* *
30606 ATGTTTTCAAAATGATTTAAAAATTATATAATATATATATTTTCAAAAATGTTTCAAAAACTATA
63 ATATTTTCAAAATGATTTAAAAACTATATAATATATATATTTTCAAAAATGTTTCAAAAACTATA
* *
30671 TATTATATTTATTTT
128 TATTATATATATATT
* * ** * *
30686 CAAAATGTTTTAAAAACTATATAATATATATTTTCAAAATGTTTTAAAAACTATATATTATATTT
1 AAAAATGTTTTAAAAACTATATAATATATATTAT-AAAATGAATTAAAAACTATATAATATATAT
* * *
30751 ATTTTCAAAATGTTTTAGAAACTATATAATATATAAATATTTTCAAACATGTTTTC-AAAACTAT
65 ATTTTCAAAATGATTTAAAAACTATATAATATAT--ATATTTTCAAAAATG-TTTCAAAAACTAT
30815 AT-TATATATATATATT
127 ATAT-TATATATATATT
* * *
30831 AAAAATGTTTT-CAAGCTATAT-ATATATATATATATATAT-AATTAAAAAC
1 AAAAATGTTTTAAAAACTATATAATATATAT-TATA-AAATGAATTAAAAAC
30880 AAAGACGAAA
Statistics
Matches: 167, Mismatches: 21, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
143 78 0.47
144 15 0.09
145 70 0.42
146 4 0.02
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (142 bp):
AAAAATGTTTTAAAAACTATATAATATATATTATAAAATGAATTAAAAACTATATAATATATATA
TTTTCAAAATGATTTAAAAACTATATAATATATATATTTTCAAAAATGTTTCAAAAACTATATAT
TATATATATATT
Found at i:31696 original size:84 final size:84
Alignment explanation
Indices: 31468--32489 Score: 1021
Period size: 84 Copynumber: 12.3 Consensus size: 84
31458 TTTGCCTCTA
* * * * * * * *
31468 AGCTGAGTGTAATCGAGCTCGAAGGTCTTCGGTTGGTAGATAACCCTTCTCGACTTGAGCTATGT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
31533 TGTAAATGA--TGCCTTGG
66 TGCAAATGATGTGCCTTGG
* * *
31550 AGTTGAGCGTAGTCAAACTC-AAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGCTT-T
1 AGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAG-TTAT
*
31609 GCTGCAAATGATGTACCTTGG
64 GCTGCAAATGATGTGCCTTGG
* * * *
31630 AGCTGAGCGTAGACAAATTCGAAGGTCTTTGGTTGGCATATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
31695 TGTAAATGATATGCCTTGG
66 TGCAAATGATGTGCCTTGG
* * * * * *
31714 AGCTGAGCATAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATA
1 AGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* ***
31778 CTGTAAATGATGTGCCCTCAA
65 CTGCAAATGATGTG-CCTTGG
* * * * * *
31799 AGTTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAGCCCTTCTCGACTTAAGTTATGT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
31860 TGCAAATGATGTGCCTTCG
66 TGCAAATGATGTGCCTTGG
* * * *
31879 AGCTGAGCATAGTCAAACTCGAAGGTCTTTGGTTGGTAGATAACCCTTCTCGACTTAAGTTAAGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
31944 TACAAATGATATGCCTTGG
66 TGCAAATGATGTGCCTTGG
* * * ** * * *
31963 AGATGAGCGTAGTCGAAGTCGAAGGTTTTTTGG-TGATAGATAACCCTTCTAGCCTTGAGTTATG
1 AGCTGAGCGTAGTCGAACTCGAAGG-TCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATG
* * * *
32027 CTGTAAATTATGTGCCCTCGA
65 CTGCAAATGATGTG-CCTTGG
* * * ** *
32048 AGCTGAGTGTAATCGAACTCGAGGGTC--T--TTGGCAGATAACCCTTCTCGACTTAAACTATAC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
*
32109 TGCAAATGATGTGCCTTGA
66 TGCAAATGATGTGCCTTGG
* * *
32128 AGCTGAGCATAGTCGAACTCGAAGGTATTTAGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* * *
32193 TACAAATGATATGCCTTAG
66 TGCAAATGATGTGCCTTGG
* * * * *
32212 AGCTGAGCGTAG-CTGAACTTGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTAT
1 AGCTGAGCGTAGTC-GAACTCGAAGGTC-TTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTAT
* * *
32275 GTTGTAAATGATGTGCCCTTGA
64 GCTGCAAATGATGTG-CCTTGG
* * * * *
32297 AGCTGAGTGTAATCGAACTCGATGG--TTT--TTGGAAGATAACCCTTCTCGACTTAAGCTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
32358 TGCAAATGATGTGCCTTGG
66 TGCAAATGATGTGCCTTGG
*
32377 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATATCCCTTCTCGACTTAAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
* *
32442 TACAAATGATATGCCTTGG
66 TGCAAATGATGTGCCTTGG
* * *
32461 AGCCGAGCGTAGTCTAACTCAAAGGTCTT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
32490 GGCTGACACA
Statistics
Matches: 760, Mismatches: 147, Indels: 64
0.78 0.15 0.07
Matches are distributed among these distances:
78 34 0.04
79 1 0.00
80 106 0.14
81 113 0.15
82 30 0.04
83 3 0.00
84 385 0.51
85 87 0.11
86 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (84 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGC
TGCAAATGATGTGCCTTGG
Found at i:31868 original size:249 final size:249
Alignment explanation
Indices: 31468--32489 Score: 1451
Period size: 249 Copynumber: 4.1 Consensus size: 249
31458 TTTGCCTCTA
* * * * ** * * *
31468 AGCTGAGTGTAATCGAGCTCGAAGGTC-TTCGGTTGGTAGATAACCCTTCTCGACTTGAGCTATG
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGG-TGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * * * * * *
31532 TTGTAAATGA--TG-CCTTGGAGTTGAGCGTAGTCAAACTCAAGGGTCTTTGGCAGATAGCCCTT
65 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTT
* * * * *
31594 CTCGACTTAAGCTTTGCTGCAAATGATGTACCTTGGAGCTGAGCGTAGACAAATTCGAAGGTCTT
130 CTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTT
* **
31659 TGGTTGGCATATAACCCTTCTCGACTTAAGTTATGCTGTAAATGATATGCCTTGG
195 TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
* *
31714 AGCTGAGCATAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATAC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
* * *
31779 TGTAAATGATGTGCCCTCAAAGTTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTC
66 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
* * *
31844 TCGACTTAAGTTATGTTGCAAATGATGTGCCTTCGAGCTGAGCATAGTCAAACTCGAAGGTCTTT
131 TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTT
* *
31909 GGTTGGTAGATAACCCTTCTCGACTTAAGTTAAGCTACAAATGATATGCCTTGG
196 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
* * * *
31963 AGATGAGCGTAGTCGAAGTCGAAGGTTTTTTGGTGATAGATAACCCTTCTAGCCTTGAGTTATGC
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
*
32028 TGTAAATTATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
66 TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
* * * * *
32093 TCGACTTAAACTATACTGCAAATGATGTGCCTTGAAGCTGAGCATAGTCGAACTCGAAGGTATTT
131 TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTT
* *
32158 AGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTAG
196 GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
*
32212 AGCTGAGCGTAG-CTGAACTTGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
1 AGCTGAGCGTAGTC-GAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATG
* * * * *
32276 TTGTAAATGATGTGCCCTTGAAGCTGAGTGTAATCGAACTCGATGGTTTTTGGAAGATAACCCTT
65 CTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTT
* *
32341 CTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
130 CTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTT
*
32406 TGGTTGGCAGATATCCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
195 TGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
* * *
32461 AGCCGAGCGTAGTCTAACTCAAAGGTCTT
1 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
32490 GGCTGACACA
Statistics
Matches: 693, Mismatches: 77, Indels: 9
0.89 0.10 0.01
Matches are distributed among these distances:
246 57 0.08
247 4 0.01
248 3 0.00
249 628 0.91
250 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.31
Consensus pattern (249 bp):
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGC
TGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTCTTTGGCAGATAACCCTTC
TCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCATAGTCAAACTCGAAGGTCTTT
GGTTGGCAGATAACCCTTCTCGACTTAAGTTATGCTACAAATGATATGCCTTGG
Found at i:33836 original size:95 final size:95
Alignment explanation
Indices: 33673--33852 Score: 310
Period size: 95 Copynumber: 1.9 Consensus size: 95
33663 AATATGTAAA
*
33673 CACCTTTATCAGGTTAGCTGAATCTTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGG
1 CACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGG
*
33738 GACAGCTCAAGCTTTATTGTATAGTATAAT
66 GACAACTCAAGCTTTATTGTATAGTATAAT
33768 CACCTTTATCA-GTCTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTG-CTCTAGA
1 CACCTTTATCAGGT-TAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCT-TAGA
33831 GGGACAACTCAAGCTTTATTGT
64 GGGACAACTCAAGCTTTATTGT
33853 TGATATATAT
Statistics
Matches: 81, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
94 4 0.05
95 77 0.95
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (95 bp):
CACCTTTATCAGGTTAGCTGAATATTATCCATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGG
GACAACTCAAGCTTTATTGTATAGTATAAT
Found at i:37313 original size:12 final size:13
Alignment explanation
Indices: 37288--37316 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
37278 TAATTGCGAA
37288 AAATTAGAAATTT
1 AAATTAGAAATTT
37301 AAATTAG-AATTT
1 AAATTAGAAATTT
37313 AAAT
1 AAAT
37317 ACTCGATTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.38
Consensus pattern (13 bp):
AAATTAGAAATTT
Found at i:38567 original size:33 final size:33
Alignment explanation
Indices: 38494--38561 Score: 84
Period size: 33 Copynumber: 2.0 Consensus size: 33
38484 AACGGACCTG
* *
38494 AAAATAAAATGAAAATAAAATTAATAAAAGATAA
1 AAAAT-AAATAAAAATAAAATAAATAAAAGATAA
38528 AAAATAAATAAAAAT-AAATAAATAACAACGATAA
1 AAAATAAATAAAAATAAAATAAATAA-AA-GATAA
38562 TAATAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 9 0.30
33 11 0.37
34 10 0.33
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.19
Consensus pattern (33 bp):
AAAATAAATAAAAATAAAATAAATAAAAGATAA
Found at i:38679 original size:30 final size:28
Alignment explanation
Indices: 38645--38713 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 28
38635 AAAATTATAT
38645 ATTATATATTTTAAAAAAAATGTTTTCAAA
1 ATTATATATTTT--AAAAAATGTTTTCAAA
* *
38675 ATTATATAGTTTTCAAAAATGTTTTTAAA
1 ATTATATA-TTTTAAAAAATGTTTTCAAA
*
38704 ACTATATATT
1 ATTATATATT
38714 ATATAAGTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.06
29 21 0.60
30 8 0.23
31 4 0.11
ACGTcount: A:0.45, C:0.04, G:0.04, T:0.46
Consensus pattern (28 bp):
ATTATATATTTTAAAAAATGTTTTCAAA
Found at i:38730 original size:36 final size:35
Alignment explanation
Indices: 38675--38913 Score: 185
Period size: 36 Copynumber: 6.2 Consensus size: 35
38665 TGTTTTCAAA
* *
38675 ATTATATAGTTTTCAAAAATGTTTTTAAAACTATAT
1 ATTATATAATTTTC-AAAATGTTTTAAAAACTATAT
* *
38711 ATTATATAAGTTTTCAAAATGATTTCAAAACTATACAAT
1 ATTATATAA-TTTTCAAAATGTTTTAAAAACTAT---AT
38750 ATATATATATATATATAT-ATGTTTTCAAAATGTTTTAAAAACTATAT
1 AT-TATATA-AT-T-T-TCA-------A-AATGTTTTAAAAACTATAT
* *
38797 AATATAT-ATATTCAAAATGTTTTAAAAACTATAT
1 ATTATATAATTTTCAAAATGTTTTAAAAACTATAT
*
38831 ATTATATTTATTTTCAAAATGTTTTAAAAACTATAT
1 ATTATA-TAATTTTCAAAATGTTTTAAAAACTATAT
*
38867 ATTATATAAATATTTTCAAACATGTTTTCAAAACTATAT
1 ATTATAT--A-ATTTTCAAA-ATGTTTTAAAAACTATAT
38906 ATTATATA
1 ATTATATA
38914 TATATTTTTT
Statistics
Matches: 168, Mismatches: 11, Indels: 47
0.74 0.05 0.21
Matches are distributed among these distances:
34 24 0.14
35 3 0.02
36 57 0.34
37 6 0.04
38 9 0.05
39 28 0.17
40 7 0.04
41 3 0.02
42 4 0.02
43 1 0.01
44 2 0.01
46 5 0.03
47 3 0.02
49 1 0.01
50 15 0.09
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.45
Consensus pattern (35 bp):
ATTATATAATTTTCAAAATGTTTTAAAAACTATAT
Found at i:38777 original size:50 final size:49
Alignment explanation
Indices: 38706--38807 Score: 159
Period size: 50 Copynumber: 2.1 Consensus size: 49
38696 TTTTTAAAAC
*
38706 TATATATTATATAAGTTTTCAAAATGATTTCAAAACTATACAATATATA
1 TATATATTATATAAGTTTTCAAAATGATTTAAAAACTATACAATATATA
* * *
38755 TATATATATATATATGTTTTCAAAATGTTTTAAAAACTATATAATATATA
1 TATATAT-TATATAAGTTTTCAAAATGATTTAAAAACTATACAATATATA
38805 TAT
1 TAT
38808 TCAAAATGTT
Statistics
Matches: 48, Mismatches: 4, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
49 7 0.15
50 41 0.85
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (49 bp):
TATATATTATATAAGTTTTCAAAATGATTTAAAAACTATACAATATATA
Found at i:38796 original size:39 final size:39
Alignment explanation
Indices: 38753--38959 Score: 254
Period size: 36 Copynumber: 5.5 Consensus size: 39
38743 ATACAATATA
*
38753 TATATATATATATATATGTTTTCAAAATGTTTTAAAAAC
1 TATATATATATATATATATTTTCAAAATGTTTTAAAAAC
38792 --TATATA-ATATATATA--TTCAAAATGTTTTAAAAAC
1 TATATATATATATATATATTTTCAAAATGTTTTAAAAAC
38826 TATATAT-TATAT-T-TATTTTCAAAATGTTTTAAAAAC
1 TATATATATATATATATATTTTCAAAATGTTTTAAAAAC
* *
38862 TATATAT-TATATAAATATTTTCAAACATGTTTTCAAAAC
1 TATATATATATATATATATTTTCAAA-ATGTTTTAAAAAC
* * * *
38901 TATATATTATATATATATTTTTTAAAAATATTTT-CAAAC
1 TATATA-TATATATATATATTTTCAAAATGTTTTAAAAAC
38940 TATATAATATATATATATAT
1 TATAT-ATATATATATATAT
38960 ATATATAATA
Statistics
Matches: 148, Mismatches: 9, Indels: 22
0.83 0.05 0.12
Matches are distributed among these distances:
34 21 0.14
35 1 0.01
36 48 0.32
37 6 0.04
38 10 0.07
39 39 0.26
40 8 0.05
41 15 0.10
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (39 bp):
TATATATATATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:39699 original size:17 final size:17
Alignment explanation
Indices: 39628--39703 Score: 57
Period size: 16 Copynumber: 4.5 Consensus size: 17
39618 ATGTAATTAA
39628 TAAAAAT-TAAAGATAT
1 TAAAAATATAAAGATAT
* * *
39644 TAAAATTTTAGA-ATAT
1 TAAAAATATAAAGATAT
* * *
39660 TATAAATATAAAAAAATT
1 TAAAAATATAAAGATA-T
*
39678 ATAAAAATATAGAGATAT
1 -TAAAAATATAAAGATAT
39696 TAAAAATA
1 TAAAAATA
39704 AACATTAATA
Statistics
Matches: 45, Mismatches: 11, Indels: 7
0.71 0.17 0.11
Matches are distributed among these distances:
16 18 0.40
17 13 0.29
18 2 0.04
19 12 0.27
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TAAAAATATAAAGATAT
Found at i:39700 original size:25 final size:25
Alignment explanation
Indices: 39622--39700 Score: 70
Period size: 25 Copynumber: 3.1 Consensus size: 25
39612 TTTTTTATGT
39622 AATTAATAAAAAT-TAAAGATATTAA
1 AATT-ATAAAAATATAAAGATATTAA
* * * **
39647 AATTTTAGAATATTATAAATATAAAAA
1 AATTATA-AA-AATATAAAGATATTAA
*
39674 AATTATAAAAATATAGAGATATTAA
1 AATTATAAAAATATAAAGATATTAA
39699 AA
1 AA
39701 ATAAACATTA
Statistics
Matches: 40, Mismatches: 11, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
24 2 0.05
25 19 0.47
26 4 0.10
27 15 0.38
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (25 bp):
AATTATAAAAATATAAAGATATTAA
Found at i:39944 original size:22 final size:22
Alignment explanation
Indices: 39887--39945 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
39877 ACACGATTCT
39887 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
39909 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
39930 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
39946 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:39959 original size:20 final size:20
Alignment explanation
Indices: 39934--40005 Score: 110
Period size: 20 Copynumber: 3.6 Consensus size: 20
39924 TTTTCCGACT
39934 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
39954 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
39974 ATCGCAATGCGATTATG-ACT
1 ATCGCAATGCGAATATGTA-A
39994 ATCGCAATGCGA
1 ATCGCAATGCGA
40006 TTCTGACTAT
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
19 1 0.02
20 48 0.98
ACGTcount: A:0.36, C:0.18, G:0.21, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:40006 original size:20 final size:20
Alignment explanation
Indices: 39930--40040 Score: 109
Period size: 20 Copynumber: 5.5 Consensus size: 20
39920 GCGATTTTCC
*
39930 GACTATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTAT
* *
39950 GTA-AATCGCAATGCGAATAT
1 G-ACTATCGCAATGCGATTAT
*
39970 GTA-AATCGCAATGCGATTAT
1 G-ACTATCGCAATGCGATTAT
*
39990 GACTATCGCAATGCGATTCT
1 GACTATCGCAATGCGATTAT
* * *
40010 GACTATCGCAACGAGATTCT
1 GACTATCGCAATGCGATTAT
*
40030 TACTATCGCAA
1 GACTATCGCAA
40041 CTCAATTCTG
Statistics
Matches: 82, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 80 0.98
21 1 0.01
ACGTcount: A:0.33, C:0.21, G:0.19, T:0.27
Consensus pattern (20 bp):
GACTATCGCAATGCGATTAT
Found at i:40018 original size:40 final size:40
Alignment explanation
Indices: 39930--40060 Score: 115
Period size: 40 Copynumber: 3.3 Consensus size: 40
39920 GCGATTTTCC
* * * *
39930 GACTATCGCAATGCGAATATGTA-AATCGCAATGCGAATAT
1 GACTATCGCAATGCGATTATG-ACTATCGCAATGCGATTCT
*
39970 GTA-AATCGCAATGCGATTATGACTATCGCAATGCGATTCT
1 G-ACTATCGCAATGCGATTATGACTATCGCAATGCGATTCT
* * * * *
40010 GACTATCGCAACGAGATTCTTACTATCGCAACT-CAATTCT
1 GACTATCGCAATGCGATTATGACTATCGCAA-TGCGATTCT
*
40050 GACTGTCGCAA
1 GACTATCGCAA
40061 CACTGAATTT
Statistics
Matches: 75, Mismatches: 12, Indels: 8
0.79 0.13 0.08
Matches are distributed among these distances:
39 2 0.03
40 71 0.95
41 2 0.03
ACGTcount: A:0.32, C:0.22, G:0.18, T:0.27
Consensus pattern (40 bp):
GACTATCGCAATGCGATTATGACTATCGCAATGCGATTCT
Found at i:40041 original size:20 final size:20
Alignment explanation
Indices: 39974--40061 Score: 88
Period size: 20 Copynumber: 4.4 Consensus size: 20
39964 GAATATGTAA
* * *
39974 ATCGCAATGCGATTATGACT
1 ATCGCAACGAGATTCTGACT
* *
39994 ATCGCAATGCGATTCTGACT
1 ATCGCAACGAGATTCTGACT
*
40014 ATCGCAACGAGATTCTTACT
1 ATCGCAACGAGATTCTGACT
*
40034 ATCGCAACTCA-ATTCTGACT
1 ATCGCAAC-GAGATTCTGACT
*
40054 GTCGCAAC
1 ATCGCAAC
40062 ACTGAATTTC
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
20 59 0.98
21 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.17, T:0.28
Consensus pattern (20 bp):
ATCGCAACGAGATTCTGACT
Found at i:41073 original size:18 final size:18
Alignment explanation
Indices: 41040--41074 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41030 AGAAAAAGGC
**
41040 AATCAAAATCGTAATCAA
1 AATCAAAATCCCAATCAA
41058 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
41075 CAACCGGCTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.23, G:0.03, T:0.20
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:41794 original size:18 final size:18
Alignment explanation
Indices: 41771--41836 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
41761 GAAACTTAAA
41771 ATCGCAACACG-AATGACT
1 ATCGCAAC-CGAAATGACT
*
41789 ATCGCAACCTGAAAATGAAT
1 ATCGCAACC-G-AAATGACT
*
41809 ATCGCAACGTGAAAATGACT
1 ATCGCAAC-CG-AAATGACT
41829 ATCGCAAC
1 ATCGCAAC
41837 GAGAGAATCG
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
17 1 0.02
18 9 0.22
20 31 0.76
ACGTcount: A:0.41, C:0.24, G:0.17, T:0.18
Consensus pattern (18 bp):
ATCGCAACCGAAATGACT
Found at i:41837 original size:20 final size:20
Alignment explanation
Indices: 41782--41837 Score: 94
Period size: 20 Copynumber: 2.8 Consensus size: 20
41772 TCGCAACACG
*
41782 AATGACTATCGCAACCTGAA
1 AATGACTATCGCAACGTGAA
*
41802 AATGAATATCGCAACGTGAA
1 AATGACTATCGCAACGTGAA
41822 AATGACTATCGCAACG
1 AATGACTATCGCAACG
41838 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGTGAA
Found at i:41909 original size:20 final size:20
Alignment explanation
Indices: 41880--41947 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
41870 GCGATTCTTT
* **
41880 CGTTGTGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
41900 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
*
41920 CGTTGCGATAGTCATTTTCA
1 CGTTGCGATAGTCATTTTCG
41940 CGTTGCGA
1 CGTTGCGA
41948 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.19, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:42118 original size:18 final size:18
Alignment explanation
Indices: 42095--42162 Score: 136
Period size: 18 Copynumber: 3.8 Consensus size: 18
42085 TTTACTAAGC
42095 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
42113 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
42131 AATCTAAGTGAAATGGTT
1 AATCTAAGTGAAATGGTT
42149 AATCTAAGTGAAAT
1 AATCTAAGTGAAAT
42163 TACGAGTAAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 50 1.00
ACGTcount: A:0.41, C:0.06, G:0.21, T:0.32
Consensus pattern (18 bp):
AATCTAAGTGAAATGGTT
Found at i:43948 original size:20 final size:20
Alignment explanation
Indices: 43890--43963 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 20
43880 GAAACTTAAA
* **
43890 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
43910 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
43930 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
*
43950 ATCACAACGCGAAA
1 ATCGCAACGCGAAA
43964 CTAAAATCGC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.45, C:0.24, G:0.16, T:0.15
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:44387 original size:22 final size:22
Alignment explanation
Indices: 44360--44420 Score: 104
Period size: 22 Copynumber: 2.8 Consensus size: 22
44350 GAGATAGGCG
*
44360 GATTTCGCCGGAGATGGGGACT
1 GATTTCGTCGGAGATGGGGACT
*
44382 GATTTCGTCAGAGATGGGGACT
1 GATTTCGTCGGAGATGGGGACT
44404 GATTTCGTCGGAGATGG
1 GATTTCGTCGGAGATGG
44421 AGACGGATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.20, C:0.15, G:0.39, T:0.26
Consensus pattern (22 bp):
GATTTCGTCGGAGATGGGGACT
Found at i:44631 original size:20 final size:20
Alignment explanation
Indices: 44601--44738 Score: 186
Period size: 20 Copynumber: 6.9 Consensus size: 20
44591 GCGCTTTGAA
*
44601 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
44621 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
44641 AATCTCGTTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
44661 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
44681 AATCTCGTTACGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
44701 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
44721 AATCGCATTGCGATAGTC
1 AATCGCGTTGCGATAGTC
44739 GGAAAATCGC
Statistics
Matches: 105, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 105 1.00
ACGTcount: A:0.26, C:0.21, G:0.25, T:0.28
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:45396 original size:16 final size:16
Alignment explanation
Indices: 45375--45408 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
45365 CTTATAACTT
45375 CCTTAAGAATTATACC
1 CCTTAAGAATTATACC
45391 CCTTAAGAATTATACC
1 CCTTAAGAATTATACC
45407 CC
1 CC
45409 AAATTCTTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.29, G:0.06, T:0.29
Consensus pattern (16 bp):
CCTTAAGAATTATACC
Found at i:48738 original size:20 final size:19
Alignment explanation
Indices: 48713--48785 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 19
48703 CGATGAGAGC
*
48713 AGTATCGATACTAGGCTAGT
1 AGTATCGATACTA-GCAAGT
48733 AGTATCGATACCTAGCAAGAAT
1 AGTATCGATA-CTAGCAAG--T
* *
48755 AATATCGATACTATGCGAGT
1 AGTATCGATACTA-GCAAGT
48775 AGTATCGATAC
1 AGTATCGATAC
48786 CAAGTGCACA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
20 25 0.56
21 6 0.13
22 14 0.31
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (19 bp):
AGTATCGATACTAGCAAGT
Found at i:54584 original size:24 final size:24
Alignment explanation
Indices: 54556--54628 Score: 91
Period size: 24 Copynumber: 3.2 Consensus size: 24
54546 TGATGGAGTG
54556 TCGATACTACTATGTATAGTAGTA
1 TCGATACTACTATGTATAGTAGTA
** *
54580 TCGATAC--C-ATCCA-AGGAGTA
1 TCGATACTACTATGTATAGTAGTA
54600 TCGATACTACTATGTATAGTAGTA
1 TCGATACTACTATGTATAGTAGTA
54624 TCGAT
1 TCGAT
54629 GCCTAAACAT
Statistics
Matches: 39, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
20 13 0.33
21 3 0.08
22 2 0.05
23 3 0.08
24 18 0.46
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (24 bp):
TCGATACTACTATGTATAGTAGTA
Found at i:55592 original size:12 final size:12
Alignment explanation
Indices: 55575--55602 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
55565 AAATATATTA
55575 AATTATAAATTT
1 AATTATAAATTT
55587 AATTATAAATTT
1 AATTATAAATTT
55599 AATT
1 AATT
55603 TCTTAACTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (12 bp):
AATTATAAATTT
Found at i:55833 original size:18 final size:19
Alignment explanation
Indices: 55797--55835 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
55787 ACTCCCTTAA
*
55797 TTTTAATACTTTATGTAATT
1 TTTTAATAATTTA-GTAATT
55817 TTTTAATAATTTA-TAATT
1 TTTTAATAATTTAGTAATT
55835 T
1 T
55836 ATCATATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.62
Consensus pattern (19 bp):
TTTTAATAATTTAGTAATT
Done.