Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003681.1 Hibiscus syriacus cultivar Beakdansim tig00007862_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: 121594
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:332 original size:2 final size:2
Alignment explanation
Indices: 325--353 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
315 GAAAAAGCTA
325 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
354 ATATATATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:358 original size:2 final size:2
Alignment explanation
Indices: 353--383 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
343 TCTCTCTCTC
353 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 T
384 GAATAGATAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7780 original size:13 final size:13
Alignment explanation
Indices: 7764--7789 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
7754 AAATGCCCTT
7764 AAAAAAATTCTTC
1 AAAAAAATTCTTC
7777 AAAAAAATTCTTC
1 AAAAAAATTCTTC
7790 TTCTGTCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.15, G:0.00, T:0.31
Consensus pattern (13 bp):
AAAAAAATTCTTC
Found at i:10710 original size:2 final size:2
Alignment explanation
Indices: 10703--10731 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
10693 TTACCATTCC
10703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
10732 AGATAATCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:12637 original size:18 final size:20
Alignment explanation
Indices: 12613--12661 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
12603 AGTAGGGTTG
*
12613 TTTTTTTTTAAATTT-TATA
1 TTTTTTATTAAATTTATATA
*
12632 TTTTTTATTTAATTTATATA
1 TTTTTTATTAAATTTATATA
12652 TTTTTATATT
1 TTTTT-TATT
12662 GTTTATTGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 13 0.50
20 9 0.35
21 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTATTAAATTTATATA
Found at i:12642 original size:20 final size:20
Alignment explanation
Indices: 12613--12661 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
12603 AGTAGGGTTG
12613 TTTTTT-TTTAAATTT-TATA
1 TTTTTTATTT-AATTTATATA
12632 TTTTTTATTTAATTTATATA
1 TTTTTTATTTAATTTATATA
12652 TTTTTATATT
1 TTTTT-TATT
12662 GTTTATTGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
19 11 0.41
20 12 0.44
21 4 0.15
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTTATTTAATTTATATA
Found at i:13750 original size:17 final size:18
Alignment explanation
Indices: 13710--13750 Score: 66
Period size: 19 Copynumber: 2.3 Consensus size: 18
13700 AAAACATATA
13710 TATTTGTAAATATATTAT
1 TATTTGTAAATATATTAT
13728 TGATTTGTAAATATATT-T
1 T-ATTTGTAAATATATTAT
13746 TATTT
1 TATTT
13751 TATAAAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 4 0.18
18 3 0.14
19 15 0.68
ACGTcount: A:0.34, C:0.00, G:0.07, T:0.59
Consensus pattern (18 bp):
TATTTGTAAATATATTAT
Found at i:16568 original size:18 final size:17
Alignment explanation
Indices: 16541--16575 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
16531 AAAGAAAAAC
*
16541 AATAATAATAAAATAATA
1 AATAAAAAT-AAATAATA
16559 AATAAAAATAAATAATA
1 AATAAAAATAAATAATA
16576 TTAATATAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (17 bp):
AATAAAAATAAATAATA
Found at i:16574 original size:28 final size:29
Alignment explanation
Indices: 16541--16606 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
16531 AAAGAAAAAC
16541 AATAATAATAAAATAATAAATAAAAA-TA
1 AATAATAATAAAATAATAAATAAAAACTA
* * *
16569 AATAATATTAATATAATATATAAAAACTA
1 AATAATAATAAAATAATAAATAAAAACTA
16598 AA-AATAATA
1 AATAATAATA
16607 TGTTTTTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (29 bp):
AATAATAATAAAATAATAAATAAAAACTA
Found at i:16657 original size:38 final size:38
Alignment explanation
Indices: 16604--16884 Score: 308
Period size: 36 Copynumber: 7.4 Consensus size: 38
16594 ACTAAAAATA
* *
16604 ATATGTTTTTGAAAAATCT-TTTTTAAAACTATATATTAT
1 ATATG-TTTTCAAAAAT-TGTTTTCAAAACTATATATTAT
* * *
16643 ATATGCTTTCAAAAATTATTTTCAAAACTATATAATAT
1 ATATGTTTTCAAAAATTGTTTTCAAAACTATATATTAT
*
16681 ATATGTTTTCCAAAATTGTTTTTCAAAACTATATAATATAT
1 ATATGTTTTCAAAAATTG-TTTTCAAAACTATAT-AT-TAT
16722 ATAT-TTTTCAAAAATTGTTTTCAAAACTATATAATATAT
1 ATATGTTTTCAAAAATTGTTTTCAAAACTATAT-AT-TAT
* * *
16761 ATTTTTTTTCAAAAATTGTTTTCAAAAGTATATA--AT
1 ATATGTTTTCAAAAATTGTTTTCAAAACTATATATTAT
* * *
16797 ATATATTTTCGAAAATTGTTTTCGAAACTATATA--AT
1 ATATGTTTTCAAAAATTGTTTTCAAAACTATATATTAT
*
16833 ATATGTTTTCAAAAATTGTTTTTCAAAAC--CATATTAT
1 ATATGTTTTCAAAAATTG-TTTTCAAAACTATATATTAT
*
16870 ATATATTTTCAAAAA
1 ATATGTTTTCAAAAA
16885 CCAATTTTTT
Statistics
Matches: 213, Mismatches: 21, Indels: 18
0.85 0.08 0.07
Matches are distributed among these distances:
35 3 0.01
36 49 0.23
37 26 0.12
38 42 0.20
39 46 0.22
40 40 0.19
41 7 0.03
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (38 bp):
ATATGTTTTCAAAAATTGTTTTCAAAACTATATATTAT
Found at i:16706 original size:39 final size:38
Alignment explanation
Indices: 16591--16884 Score: 336
Period size: 39 Copynumber: 7.8 Consensus size: 38
16581 ATAATATATA
* * *
16591 AAAACTA-AAAATA-ATATGTTTTTGAAAAATCT-TTTTT
1 AAAACTATATAATATATATG-TTTTCAAAAAT-TGTTTTC
* * *
16628 AAAACTATATATTATATATGCTTTCAAAAATTATTTTC
1 AAAACTATATAATATATATGTTTTCAAAAATTGTTTTC
*
16666 AAAACTATATAATATATATGTTTTCCAAAATTGTTTTTC
1 AAAACTATATAATATATATGTTTTCAAAAATTG-TTTTC
*
16705 AAAACTATATAATATATATATTTTTCAAAAATTGTTTTC
1 AAAACTATATAATATATAT-GTTTTCAAAAATTGTTTTC
*
16744 AAAACTATATAATATATATTTTTTTTCAAAAATTGTTTTC
1 AAAACTATATAATATATA--TGTTTTCAAAAATTGTTTTC
* *
16784 AAAAGTATATAATATATA--TTTTCGAAAATTGTTTTC
1 AAAACTATATAATATATATGTTTTCAAAAATTGTTTTC
*
16820 GAAACTATAT-A-ATATATGTTTTCAAAAATTGTTTTTC
1 AAAACTATATAATATATATGTTTTCAAAAATTG-TTTTC
* *
16857 AAAACCATAT--TATATATATTTTCAAAAA
1 AAAACTATATAATATATATGTTTTCAAAAA
16885 CCAATTTTTT
Statistics
Matches: 227, Mismatches: 19, Indels: 22
0.85 0.07 0.08
Matches are distributed among these distances:
34 5 0.02
35 1 0.00
36 37 0.16
37 37 0.16
38 46 0.20
39 52 0.23
40 48 0.21
41 1 0.00
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.45
Consensus pattern (38 bp):
AAAACTATATAATATATATGTTTTCAAAAATTGTTTTC
Found at i:16939 original size:38 final size:38
Alignment explanation
Indices: 16591--16947 Score: 290
Period size: 38 Copynumber: 9.4 Consensus size: 38
16581 ATAATATATA
* * *
16591 AAAACTAAAAATA-ATATGTTTTTGAAAAATCT-TTTT-T
1 AAAACTATATATATATATG-TTTTCAAAAAT-TGTTTTCT
* *
16628 AAAACTATATATTATATATGCTTTCAAAAATTATTTTC-
1 AAAACTATATA-TATATATGTTTTCAAAAATTGTTTTCT
*
16666 AAAACTATATAATATATATGTTTTCCAAAATTGTTTT-T
1 AAAACTATAT-ATATATATGTTTTCAAAAATTGTTTTCT
*
16704 CAAAACTATATAATATATATATTTTTCAAAAATTGTTTTC-
1 -AAAACTATAT-ATATATAT-GTTTTCAAAAATTGTTTTCT
*
16744 AAAACTATATAATATATATTTTTTTTCAAAAATTGTTTTC-
1 AAAACTATAT-ATATATA--TGTTTTCAAAAATTGTTTTCT
* * *
16784 AAAAGTATATA-ATATATATTTTCGAAAATTGTTTTC-
1 AAAACTATATATATATATGTTTTCAAAAATTGTTTTCT
*
16820 GAAACTATATA-ATATATGTTTTCAAAAATTGTTTT-T
1 AAAACTATATATATATATGTTTTCAAAAATTGTTTTCT
* * *** *
16856 CAAAACCATAT-TATATATATTTTCAAAAACCAATTTTTT
1 -AAAACTATATATATATATGTTTTCAAAAA-TTGTTTTCT
** **
16895 AAAAAAAGTATATATAATATGTTTTCAAAAACCGTTTTCT
1 AAAACTA-TATATAT-ATATGTTTTCAAAAATTGTTTTCT
*
16935 AAAAAT-TATATAT
1 AAAACTATATATAT
16948 TGTATTTTTT
Statistics
Matches: 272, Mismatches: 29, Indels: 37
0.80 0.09 0.11
Matches are distributed among these distances:
36 49 0.18
37 34 0.12
38 68 0.25
39 48 0.18
40 58 0.21
41 15 0.06
ACGTcount: A:0.43, C:0.08, G:0.04, T:0.44
Consensus pattern (38 bp):
AAAACTATATATATATATGTTTTCAAAAATTGTTTTCT
Found at i:25008 original size:3 final size:3
Alignment explanation
Indices: 25000--25038 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
24990 AAATATTTAA
*
25000 AAT AAT AAT AAT AAT AAC AAT AAT AAT AA- AAT AAAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT
25039 TTAAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (3 bp):
AAT
Found at i:26324 original size:18 final size:17
Alignment explanation
Indices: 26301--26334 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
26291 AGAAAAGAAA
*
26301 AAATAATAATAATATAAC
1 AAATAAAAATAA-ATAAC
26319 AAATAAAAATAAATAA
1 AAATAAAAATAAATAA
26335 TACTAATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (17 bp):
AAATAAAAATAAATAAC
Found at i:26341 original size:28 final size:29
Alignment explanation
Indices: 26301--26366 Score: 91
Period size: 28 Copynumber: 2.3 Consensus size: 29
26291 AGAAAAGAAA
26301 AAATAATAATAATATAACAAATAAAAA-T
1 AAATAATAATAATATAACAAATAAAAACT
* * *
26329 AAATAATACTAATATAATATATAAAAACT
1 AAATAATAATAATATAACAAATAAAAACT
26358 AAA-AATAAT
1 AAATAATAAT
26367 TTGTTTTCGA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
28 29 0.88
29 4 0.12
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (29 bp):
AAATAATAATAATATAACAAATAAAAACT
Found at i:26426 original size:38 final size:36
Alignment explanation
Indices: 26376--26664 Score: 227
Period size: 38 Copynumber: 7.6 Consensus size: 36
26366 TTTGTTTTCG
* * *
26376 AAAAATTCATTTTTAAAACTATATATTATTTATGCTTTT
1 AAAAATT-GTTTTCAAAACTATATATTATATAT--TTTT
* *
26415 AAAAATTATTTTCAAAACTATATAATATATATGTTTT
1 AAAAATTGTTTTCAAAACTATATATTATATAT-TTTT
26452 CAAAAATTGTTTTTCAAAACTATATAATGTATATATTTTT
1 -AAAAATTG-TTTTCAAAACTATAT-AT-TATATATTTTT
* *
26492 AGAAATTGTTTTCAAAACTATAAATTATATATTTTT
1 AAAAATTGTTTTCAAAACTATATATTATATATTTTT
* * * * *
26528 TAAAATTGTTTTCGAAACTATATAATATATGTTTTC
1 AAAAATTGTTTTCAAAACTATATATTATATATTTTT
* * * * *
26564 AAAAATCGATTTTTTAAAAAAGTATATATTATATGTTTTC
1 AAAAAT---TGTTTT-CAAAACTATATATTATATATTTTT
** * *
26604 AAAAACCGTTTTCTAAAAACTATATATTGTATGTTTTT
1 AAAAATTGTTTTC--AAAACTATATATTATATATTTTT
* * *
26642 CAAAAGTATTTTCAAAAACTATA
1 AAAAATTGTTTTC-AAAACTATA
26665 CTATATTATC
Statistics
Matches: 208, Mismatches: 32, Indels: 22
0.79 0.12 0.08
Matches are distributed among these distances:
36 45 0.22
37 20 0.10
38 72 0.35
39 34 0.16
40 30 0.14
41 7 0.03
ACGTcount: A:0.41, C:0.08, G:0.06, T:0.46
Consensus pattern (36 bp):
AAAAATTGTTTTCAAAACTATATATTATATATTTTT
Found at i:26492 original size:77 final size:75
Alignment explanation
Indices: 26352--26664 Score: 257
Period size: 77 Copynumber: 4.1 Consensus size: 75
26342 ATAATATATA
* * * *
26352 AAAACTA-AAAATA-ATTTGTTTTCGAAAAATTCATTTTT-AAAACTATATATTATTTATGCTTT
1 AAAACTATATAATATATATGTTTTC-AAAAATT-GTTTTTCAAAACTATATATTATATAT--TTT
26414 TAAAAATTATTTTC
62 TAAAAATTATTTTC
26428 AAAACTATATAATATATATGTTTTCAAAAATTGTTTTTCAAAACTATATAATGTATATATTTTTA
1 AAAACTATATAATATATATGTTTTCAAAAATTGTTTTTCAAAACTATAT-AT-TATATATTTTTA
* *
26493 GAAATTGTTTTC
64 AAAATTATTTTC
* * * * *
26505 AAAACTATA-AATTATATAT-TTTT-TAAAATTG-TTTTCGAAACTATATAATATATGTTTTCAA
1 AAAACTATATAA-TATATATGTTTTCAAAAATTGTTTTTCAAAACTATATATTATATATTTTTAA
* *
26566 AAATCGATTTTTT
65 AAAT-TA-TTTTC
* ** * * *
26579 AAAA-AAGTAT-ATATTATATGTTTTCAAAAACCGTTTTCTAAAAACTATATATTGTATGTTTTT
1 AAAACTA-TATAATA-TATATGTTTTCAAAAATTGTTTT-TCAAAACTATATATTATATATTTTT
* *
26642 CAAAAGTATTTTC
63 AAAAATTATTTTC
26655 AAAAACTATA
1 -AAAACTATA
26665 CTATATTATC
Statistics
Matches: 191, Mismatches: 29, Indels: 33
0.75 0.11 0.13
Matches are distributed among these distances:
72 14 0.07
73 4 0.02
74 30 0.16
75 11 0.06
76 27 0.14
77 63 0.33
78 36 0.19
79 6 0.03
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.45
Consensus pattern (75 bp):
AAAACTATATAATATATATGTTTTCAAAAATTGTTTTTCAAAACTATATATTATATATTTTTAAA
AATTATTTTC
Found at i:28058 original size:31 final size:31
Alignment explanation
Indices: 28007--28073 Score: 100
Period size: 31 Copynumber: 2.2 Consensus size: 31
27997 TTAATGTATA
* *
28007 TATTTTATTATGTTATAAATATTTTTA-TTT
1 TATTTTATTATGATATAAATATCTTTAGTTT
28037 TATTTTATTAATGATATAAATATCTTTAGTTT
1 TATTTTATT-ATGATATAAATATCTTTAGTTT
28069 TATTT
1 TATTT
28074 CATCTCGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 9 0.27
31 16 0.48
32 8 0.24
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (31 bp):
TATTTTATTATGATATAAATATCTTTAGTTT
Found at i:28894 original size:19 final size:19
Alignment explanation
Indices: 28870--28911 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
28860 GATGACGCGG
28870 TGGCCGGTGCTACAGTCAA
1 TGGCCGGTGCTACAGTCAA
*
28889 TGGCCGGTGCTACAGTCAG
1 TGGCCGGTGCTACAGTCAA
28908 TGGC
1 TGGC
28912 GGCTCTCATC
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:0.17, C:0.26, G:0.36, T:0.21
Consensus pattern (19 bp):
TGGCCGGTGCTACAGTCAA
Found at i:29510 original size:51 final size:50
Alignment explanation
Indices: 29449--29590 Score: 185
Period size: 50 Copynumber: 2.8 Consensus size: 50
29439 TTGTGTTGTA
* * *
29449 TTTTAATTTATGCATCTTAGTCACTGTTTATTTCTGATTTGGCCACTATTC
1 TTTTAATTTATGCATTTTAGTCACT-ATTATTTCTGATTTGGCCACTATCC
* *
29500 TTTTATTTTATGCATTTTAGTCACTATTATTTCTGATTTGGCTACTATCC
1 TTTTAATTTATGCATTTTAGTCACTATTATTTCTGATTTGGCCACTATCC
* * * *
29550 TTTCAATTTACGCATTTTGGTCACTACTTATTTCTCATTTG
1 TTTTAATTTATGCATTTTAGTCACTA-TTATTTCTGATTTG
29591 ATCAACTATT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
50 44 0.55
51 36 0.45
ACGTcount: A:0.20, C:0.18, G:0.11, T:0.52
Consensus pattern (50 bp):
TTTTAATTTATGCATTTTAGTCACTATTATTTCTGATTTGGCCACTATCC
Found at i:29708 original size:2 final size:2
Alignment explanation
Indices: 29701--29732 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
29691 AGTCCCATGA
29701 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29733 GCATGTTTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:30849 original size:20 final size:20
Alignment explanation
Indices: 30821--30992 Score: 107
Period size: 20 Copynumber: 8.5 Consensus size: 20
30811 GATTTTCCAG
* *
30821 AATCACAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
30841 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* *
30861 AATCGCAACGCG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
30881 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * * *
30902 AATCGCAACGTGTATTCGTA
1 AATCGCAACGCGAATACGAA
30922 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
30943 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
30963 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
30983 AATCGCAACG
1 AATCGCAACG
30993 AGATTCTGAC
Statistics
Matches: 119, Mismatches: 25, Indels: 16
0.74 0.16 0.10
Matches are distributed among these distances:
19 2 0.02
20 82 0.69
21 35 0.29
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:30908 original size:21 final size:20
Alignment explanation
Indices: 30882--30994 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
30872 GATTCTGACT
*
30882 ATCGCAACGAGTATCCGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
30903 ATCGCAACGTGTATTCGTAA
1 ATCGCAACGAGTATACGTAA
**
30923 ATCGCAACGACAATACGTAAA
1 ATCGCAACGAGTATACGT-AA
* *
30944 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATACGTAA
*
30964 ATCGCAACGAGAATACGTAA
1 ATCGCAACGAGTATACGTAA
30984 ATCGCAACGAG
1 ATCGCAACGAG
30995 ATTCTGACTA
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
20 46 0.59
21 32 0.41
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (20 bp):
ATCGCAACGAGTATACGTAA
Found at i:30908 original size:61 final size:60
Alignment explanation
Indices: 30839--31010 Score: 177
Period size: 61 Copynumber: 2.8 Consensus size: 60
30829 CGCGAATATG
* *
30839 AAAATCGCAACGCGAACATATAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGT
1 AAAATCGCAACGAGAA-ATGTAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGT
* * * * * ** *
30900 AAAATCGCAACGTGTATTCGTAAATCGCAACGACAATAC-GTAAAATCGCAACGCGTATCCGT
1 AAAATCGCAACGAGAAAT-GTAAATCGCAACG-CGATTCTG-ACTATCGCAACGAGTATCCGT
* *
30962 -AAATCGCAACGAGAATACGTAAATCGCAACGAGATTCTGACTATCGCAA
1 AAAATCGCAACGAGAA-ATGTAAATCGCAACGCGATTCTGACTATCGCAA
31011 TACTGAATTT
Statistics
Matches: 88, Mismatches: 18, Indels: 11
0.75 0.15 0.09
Matches are distributed among these distances:
60 12 0.14
61 54 0.61
62 22 0.25
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.20
Consensus pattern (60 bp):
AAAATCGCAACGAGAAATGTAAATCGCAACGCGATTCTGACTATCGCAACGAGTATCCGT
Found at i:30927 original size:41 final size:41
Alignment explanation
Indices: 30882--30992 Score: 170
Period size: 41 Copynumber: 2.7 Consensus size: 41
30872 GATTCTGACT
* * * *
30882 ATCGCAACGAGTATCCGTAAAATCGCAACGTGTATTCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
30923 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
30964 ATCGCAACGAGAATACGT-AAATCGCAACG
1 ATCGCAACGAGAATACGTAAAATCGCAACG
30993 AGATTCTGAC
Statistics
Matches: 64, Mismatches: 6, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
40 11 0.17
41 53 0.83
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:31879 original size:24 final size:24
Alignment explanation
Indices: 31852--31905 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
31842 GTATTCGAAA
31852 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
31876 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
31900 TTTGAT
1 TTTGAT
31906 GATTTTTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:34373 original size:33 final size:33
Alignment explanation
Indices: 34326--34492 Score: 172
Period size: 33 Copynumber: 4.8 Consensus size: 33
34316 CTTAATGTCT
*
34326 ATCGTAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
34359 ATCGCAATGCGAAATGAAAATCACAACGTGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * * *
34392 ATCGCAACGCGAATATGAATATCGTAACGCGGAAATGA
1 ATCGCAATGCGAA-ATGAAAATCGCAA--C-GAGA-GA
34430 CTATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 --ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* * *
34465 ATCGCAAAGCAAAATGAAAATTGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
34493 CGAATTTAGT
Statistics
Matches: 109, Mismatches: 18, Indels: 14
0.77 0.13 0.10
Matches are distributed among these distances:
33 66 0.61
34 10 0.09
35 2 0.02
36 4 0.04
37 3 0.03
38 1 0.01
39 11 0.10
40 12 0.11
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.16
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:34410 original size:20 final size:19
Alignment explanation
Indices: 34334--34496 Score: 95
Period size: 19 Copynumber: 9.3 Consensus size: 19
34324 CTATCGTAAT
34334 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
* *
34352 -CG--A-GAGAATCGCAAT
1 GCGAAATGAAAATCGCAAC
*
34367 GCGAAATGAAAATCACAA-
1 GCGAAATGAAAATCGCAAC
34385 -CG---TGAAAATCGCAAC
1 GCGAAATGAAAATCGCAAC
* *
34400 GCGAATATGAATATCGTAAC
1 GCGAA-ATGAAAATCGCAAC
** *
34420 GCGGAAATGACTATCGCAAT
1 GC-GAAATGAAAATCGCAAC
34440 GCGAAATGAAAATCGCAA-
1 GCGAAATGAAAATCGCAAC
* *
34458 -CG--A-GAGAATCGCAAA
1 GCGAAATGAAAATCGCAAC
* *
34473 GCAAAATGAAAATTGCAAC
1 GCGAAATGAAAATCGCAAC
34492 GCGAA
1 GCGAA
34497 TTTAGTTTTG
Statistics
Matches: 111, Mismatches: 17, Indels: 33
0.69 0.11 0.20
Matches are distributed among these distances:
14 31 0.28
15 2 0.02
16 5 0.05
17 6 0.05
18 2 0.02
19 36 0.32
20 26 0.23
21 3 0.03
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
GCGAAATGAAAATCGCAAC
Found at i:34524 original size:18 final size:20
Alignment explanation
Indices: 34492--34537 Score: 69
Period size: 19 Copynumber: 2.4 Consensus size: 20
34482 AAATTGCAAC
*
34492 GCGAATTTAGTTTTG-CGTT
1 GCGATTTTAGTTTTGTCGTT
34511 GCGATTTTAG-TTTGTCGTT
1 GCGATTTTAGTTTTGTCGTT
34530 GCGATTTT
1 GCGATTTT
34538 CATTTCGCAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 4 0.16
19 21 0.84
ACGTcount: A:0.13, C:0.11, G:0.26, T:0.50
Consensus pattern (20 bp):
GCGATTTTAGTTTTGTCGTT
Found at i:36134 original size:21 final size:21
Alignment explanation
Indices: 36068--36134 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
36058 GTGAATCGGG
*
36068 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
36088 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
36110 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
36131 CTCT
1 CTCT
36135 CGAAGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:36153 original size:42 final size:41
Alignment explanation
Indices: 36068--36190 Score: 115
Period size: 42 Copynumber: 2.9 Consensus size: 41
36058 GTGAATCGGG
* * *
36068 CTCTTGAATGGTGGGA-GGGACCTCTTC-AACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAA-GATGATAGGGGC
36110 CTCTTGAACGGTGGGAGGGGACTCTCGAAGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAAG-ATGATAGGGGC
* * * * *
36152 CTCTTCAACGATAGGAGTGGACTCTTGAAGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGAA-GATGATAGG
36191 CGAGTCGGGC
Statistics
Matches: 69, Mismatches: 8, Indels: 8
0.81 0.09 0.09
Matches are distributed among these distances:
41 3 0.04
42 61 0.88
43 5 0.07
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAAGATGATAGGGGC
Found at i:36627 original size:19 final size:19
Alignment explanation
Indices: 36587--36705 Score: 96
Period size: 19 Copynumber: 6.7 Consensus size: 19
36577 TCTGGAACTT
*
36587 AAAATCGCAACGTGAAAAATG
1 AAAATCGCAACGCG--AAATG
**
36608 ACTATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
36627 AAAATCGCAA--CG--AT-
1 AAAATCGCAACGCGAAATG
*
36641 AGAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
36660 AAAATCGCAA--CG--A-G
1 AAAATCGCAACGCGAAATG
* *
36674 AGAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
36693 AAAATCGCAACGC
1 AAAATCGCAACGC
36706 AATTATAGTT
Statistics
Matches: 78, Mismatches: 10, Indels: 22
0.71 0.09 0.20
Matches are distributed among these distances:
14 19 0.24
15 3 0.04
16 4 0.05
17 4 0.05
18 3 0.04
19 34 0.44
21 11 0.14
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:36653 original size:33 final size:33
Alignment explanation
Indices: 36611--36704 Score: 170
Period size: 33 Copynumber: 2.8 Consensus size: 33
36601 AAAAATGACT
*
36611 ATCGCAACGCGAAATGAAAATCGCAACGATAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
36644 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
36677 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAACGCGAAATGAAAATCGCAACG
36705 CAATTATAGT
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 59 1.00
ACGTcount: A:0.45, C:0.21, G:0.22, T:0.12
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:36735 original size:19 final size:19
Alignment explanation
Indices: 36713--36750 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
36703 CGCAATTATA
36713 GTTTCGCGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
*
36732 GTTTCGTGTTGCGATTTTG
1 GTTTCGCGTTGCGATTTTG
36751 TCGTTGCGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.05, C:0.13, G:0.32, T:0.50
Consensus pattern (19 bp):
GTTTCGCGTTGCGATTTTG
Found at i:37013 original size:94 final size:93
Alignment explanation
Indices: 36867--37152 Score: 491
Period size: 94 Copynumber: 3.1 Consensus size: 93
36857 ATGGATTGCA
* * *
36867 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAATT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
*
36932 TAGCAGAATTGGCAGCAACCGAAAAAAT
66 TAGCAGAATTGGCAGCAACCGAATAAAT
36960 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
37025 TTAGAAGAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
*
37054 TTACTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAACAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
37119 TTAGCAGTATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAATAAAT
37148 TTACT
1 TTACT
37153 AAGCAATCTA
Statistics
Matches: 183, Mismatches: 8, Indels: 3
0.94 0.04 0.02
Matches are distributed among these distances:
93 23 0.13
94 160 0.87
ACGTcount: A:0.48, C:0.18, G:0.12, T:0.21
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAATAAAT
Found at i:37024 original size:17 final size:17
Alignment explanation
Indices: 37002--37034 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
36992 ATACTAACTT
37002 CACAGTGTTA-AAGAATA
1 CACAGT-TTAGAAGAATA
37019 CACAGTTTAGAAGAAT
1 CACAGTTTAGAAGAAT
37035 TGGCAGCAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.45, C:0.12, G:0.18, T:0.24
Consensus pattern (17 bp):
CACAGTTTAGAAGAATA
Found at i:38902 original size:40 final size:39
Alignment explanation
Indices: 38856--38963 Score: 102
Period size: 33 Copynumber: 2.9 Consensus size: 39
38846 TCTTTTGGTT
**
38856 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAAAGCG
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAAAGCG
** *
38896 GAAATGACTATCGCAACGCGAAATGAAAATCGC-AA-C-
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAAAGCG
* *
38932 G--A-GAGAATCGCAACGCGAAATGAAAATCGCAA
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAA
38964 TGCGATTTTG
Statistics
Matches: 60, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
33 26 0.43
34 2 0.03
36 1 0.02
37 1 0.02
38 2 0.03
39 10 0.17
40 18 0.30
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.12
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAAAGCG
Found at i:38920 original size:19 final size:19
Alignment explanation
Indices: 38856--38968 Score: 101
Period size: 19 Copynumber: 6.1 Consensus size: 19
38846 TCTTTTGGTT
*
38856 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
38875 GAGAATGACTATCGCAAAGC
1 GA-AATGAAAATCGCAACGC
**
38895 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
38915 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
38932 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
38948 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
38967 GA
1 GA
38969 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 30 0.39
20 29 0.38
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:38999 original size:14 final size:14
Alignment explanation
Indices: 38980--39036 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
38970 TTTGGTTTCG
38980 CGTTGCGATTATCT
1 CGTTGCGATTATCT
*
38994 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TT-A--TCT
*
39013 CGTTGCGATTCTCT
1 CGTTGCGATTATCT
39027 CGTTGCGATT
1 CGTTGCGATT
39037 TTCATTTCTC
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 2 0.06
17 3 0.09
19 10 0.29
ACGTcount: A:0.11, C:0.23, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTATCT
Found at i:39012 original size:33 final size:33
Alignment explanation
Indices: 38964--39044 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
38954 AAAATCGCAA
**
38964 TGCGATTTTGGTTTCGCGTTGCGATTATCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
*
38997 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
39030 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
39045 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.10, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTATCTCGT
Found at i:39047 original size:21 final size:20
Alignment explanation
Indices: 39028--39099 Score: 92
Period size: 20 Copynumber: 3.5 Consensus size: 20
39018 CGATTCTCTC
39028 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
39048 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
39069 GTTGCGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
39089 GTTGCGATTTT
1 GTTGCGATTTT
39100 AAGTTTAGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
20 30 0.67
21 15 0.33
ACGTcount: A:0.12, C:0.17, G:0.19, T:0.51
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:39691 original size:20 final size:20
Alignment explanation
Indices: 39656--39848 Score: 130
Period size: 20 Copynumber: 9.5 Consensus size: 20
39646 TTTAAAAATC
* *
39656 TCGTTGCGATTTTACGTATTG
1 TCGTTGCGA-TTTACGGATCG
39677 TCGTTGCGATTTACGGATACG
1 TCGTTGCGATTTACGGAT-CG
* * *
39698 -CATTGTGATTTACGTATTC-
1 TCGTTGCGATTTACGGA-TCG
*
39717 TCGTTGCGATTTACAGATACG
1 TCGTTGCGATTTACGGAT-CG
* * *
39738 -CGTTGTGATTCACGTATTC-
1 TCGTTGCGATTTACGGA-TCG
*
39757 TCGTTACGATTTACGGATACG
1 TCGTTGCGATTTACGGAT-CG
* * *
39778 -CGTTGCGATTTTATGTATTG
1 TCGTTGCGA-TTTACGGATCG
39798 TCGTTGCGATTTACGGATACG
1 TCGTTGCGATTTACGGAT-CG
39819 -CGTTGCGATTTTACGGATAC-
1 TCGTTGCGA-TTTACGGAT-CG
39839 TCGTTGCGAT
1 TCGTTGCGAT
39849 AGTCAGAATC
Statistics
Matches: 134, Mismatches: 24, Indels: 29
0.72 0.13 0.16
Matches are distributed among these distances:
19 2 0.01
20 85 0.63
21 47 0.35
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (20 bp):
TCGTTGCGATTTACGGATCG
Found at i:39808 original size:41 final size:41
Alignment explanation
Indices: 39657--39848 Score: 271
Period size: 40 Copynumber: 4.7 Consensus size: 41
39647 TTAAAAATCT
*
39657 CGTTGCGATTTTACGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
39698 CATTGTGA-TTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* * *
39738 CGTTGTGA-TTCACGTATTCTCGTTACGATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* *
39778 CGTTGCGATTTTATGTATTGTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
* *
39819 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGATTTTACGTATTCTCGTTGCGAT
39849 AGTCAGAATC
Statistics
Matches: 133, Mismatches: 17, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 73 0.55
41 60 0.45
ACGTcount: A:0.19, C:0.18, G:0.24, T:0.39
Consensus pattern (41 bp):
CGTTGCGATTTTACGTATTCTCGTTGCGATTTACGGATACG
Found at i:39912 original size:21 final size:20
Alignment explanation
Indices: 39857--39930 Score: 130
Period size: 20 Copynumber: 3.6 Consensus size: 20
39847 ATAGTCAGAA
39857 TCGCGTTGCGATTTTTATGT
1 TCGCGTTGCGATTTTTATGT
39877 TCGCGTTGCGATTTTTATGT
1 TCGCGTTGCGATTTTTATGT
*
39897 TCGCGTTGCGATTTTTCATAT
1 TCGCGTTGCGATTTTT-ATGT
39918 TCGCGTTGCGATT
1 TCGCGTTGCGATT
39931 CTGAAAAATC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
20 36 0.69
21 16 0.31
ACGTcount: A:0.11, C:0.18, G:0.24, T:0.47
Consensus pattern (20 bp):
TCGCGTTGCGATTTTTATGT
Found at i:39942 original size:21 final size:21
Alignment explanation
Indices: 39897--40017 Score: 102
Period size: 21 Copynumber: 5.8 Consensus size: 21
39887 ATTTTTATGT
* * *
39897 TCGCGTTGCGATTTTTCATAT
1 TCGCGTTGCGATTCTGCATAA
* *
39918 TCGCGTTGCGATTCTGAAAAA
1 TCGCGTTGCGATTCTGCATAA
** * *
39939 TCGCAATGCTAATT-TGTACT-A
1 TCGCGTTGC-GATTCTGCA-TAA
* *
39960 TCGCATTGCGATTCTTCATAA
1 TCGCGTTGCGATTCTGCATAA
*
39981 TCGCGTTGCGATTCTTCATAA
1 TCGCGTTGCGATTCTGCATAA
40002 TCGCGTTGCGATTCTG
1 TCGCGTTGCGATTCTG
40018 GGAACTGATT
Statistics
Matches: 80, Mismatches: 16, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
20 4 0.05
21 73 0.91
22 3 0.04
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (21 bp):
TCGCGTTGCGATTCTGCATAA
Found at i:40005 original size:42 final size:41
Alignment explanation
Indices: 39855--40016 Score: 132
Period size: 42 Copynumber: 3.9 Consensus size: 41
39845 CGATAGTCAG
* ** *
39855 AATCGCGTTGCGATTTTTATGTTCGCGTTGCGATT-TTTAT
1 AATCGCGTTGCGATTTTCATAATCGCGTTGCGATTCTTAAT
** * * *
39895 GTTCGCGTTGCGATTTTTCATATTCGCGTTGCGATTCTGAAA
1 AATCGCGTTGCGA-TTTTCATAATCGCGTTGCGATTCTTAAT
** * * *
39937 AATCGCAATGCTAATTTGT-ACT-ATCGCATTGCGATTCTTCAT
1 AATCGCGTTGC-GATTT-TCA-TAATCGCGTTGCGATTCTTAAT
39979 AATCGCGTTGCGATTCTTCATAATCGCGTTGCGATTCT
1 AATCGCGTTGCGATT-TTCATAATCGCGTTGCGATTCT
40017 GGGAACTGAT
Statistics
Matches: 93, Mismatches: 21, Indels: 14
0.73 0.16 0.11
Matches are distributed among these distances:
40 11 0.12
41 25 0.27
42 54 0.58
43 3 0.03
ACGTcount: A:0.19, C:0.20, G:0.20, T:0.41
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTCATAATCGCGTTGCGATTCTTAAT
Found at i:40050 original size:20 final size:20
Alignment explanation
Indices: 39980--40054 Score: 71
Period size: 20 Copynumber: 3.7 Consensus size: 20
39970 ATTCTTCATA
** *
39980 ATCGCGTTGCGATTCTTCATA
1 ATCGCGTTGCGATTCTGGA-G
40001 ATCGCGTTGCGATTCTGG-G
1 ATCGCGTTGCGATTCTGGAG
* **
40020 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCTGGAG
40041 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
40055 TTTATTTCGC
Statistics
Matches: 43, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
19 2 0.05
20 22 0.51
21 19 0.44
ACGTcount: A:0.17, C:0.20, G:0.28, T:0.35
Consensus pattern (20 bp):
ATCGCGTTGCGATTCTGGAG
Found at i:45320 original size:15 final size:15
Alignment explanation
Indices: 45300--45329 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
45290 GATTATTATT
45300 AATTTAATTTATAAA
1 AATTTAATTTATAAA
*
45315 AATTTAATTTCTAAA
1 AATTTAATTTATAAA
45330 CAACTCAACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (15 bp):
AATTTAATTTATAAA
Found at i:47903 original size:20 final size:20
Alignment explanation
Indices: 47880--47921 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
47870 GGACAGATCT
47880 GAACCG-GCCTAACCCGACCC
1 GAACCGAGCC-AACCCGACCC
47900 GAACCGAGCCAACCCGACCC
1 GAACCGAGCCAACCCGACCC
47920 GA
1 GA
47922 CCTGTTGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 18 0.86
21 3 0.14
ACGTcount: A:0.29, C:0.48, G:0.21, T:0.02
Consensus pattern (20 bp):
GAACCGAGCCAACCCGACCC
Found at i:51148 original size:19 final size:19
Alignment explanation
Indices: 51124--51212 Score: 79
Period size: 19 Copynumber: 4.7 Consensus size: 19
51114 AAATAGAGTT
* * *
51124 ATCAGAAATCAGAGCAGAG
1 ATCAGAGATCAGAACAGAA
*
51143 ATCAGAGATCATAACAGAA
1 ATCAGAGATCAGAACAGAA
* *
51162 ATCAGAGATCAGAATAGAT
1 ATCAGAGATCAGAACAGAA
* * *
51181 ATCAAAGTTCAGGACAGAA
1 ATCAGAGATCAGAACAGAA
* *
51200 ATTAGAGGTCAGA
1 ATCAGAGATCAGA
51213 CTGTTTTTTA
Statistics
Matches: 54, Mismatches: 16, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
19 54 1.00
ACGTcount: A:0.47, C:0.13, G:0.22, T:0.17
Consensus pattern (19 bp):
ATCAGAGATCAGAACAGAA
Found at i:61164 original size:16 final size:15
Alignment explanation
Indices: 61129--61204 Score: 62
Period size: 16 Copynumber: 4.7 Consensus size: 15
61119 TGTTAGAGGG
*
61129 AAAAAATGAATAAATGA
1 AAAAAAT-AA-AAATAA
61146 AAAAAATAAAGAATAA
1 AAAAAATAAA-AATAA
*
61162 AAATAAGTAAAAATAA
1 AAA-AAATAAAAATAA
**
61178 ATAAAAATAAAAGGAA
1 A-AAAAATAAAAATAA
61194 AAATAAATAAA
1 AAA-AAATAAA
61205 TAAATGAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
15 3 0.06
16 32 0.64
17 15 0.30
ACGTcount: A:0.76, C:0.00, G:0.08, T:0.16
Consensus pattern (15 bp):
AAAAAATAAAAATAA
Found at i:61166 original size:26 final size:26
Alignment explanation
Indices: 61137--61208 Score: 76
Period size: 26 Copynumber: 2.8 Consensus size: 26
61127 GGAAAAAATG
*
61137 AATAAATGAAAA-AAATAAAGAATAAA
1 AATAAATAAAAATAAATAAA-AATAAA
*
61163 AATAAGTAAAAATAAATAAAAATAAA
1 AATAAATAAAAATAAATAAAAATAAA
**
61189 AGGAAA-AATAAATAAATAAA
1 AATAAATAA-AAATAAATAAA
61209 TGAAATATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
25 2 0.05
26 30 0.77
27 7 0.18
ACGTcount: A:0.76, C:0.00, G:0.07, T:0.17
Consensus pattern (26 bp):
AATAAATAAAAATAAATAAAAATAAA
Found at i:61174 original size:10 final size:10
Alignment explanation
Indices: 61157--61204 Score: 60
Period size: 10 Copynumber: 4.6 Consensus size: 10
61147 AAAAATAAAG
61157 AATAAAAATA
1 AATAAAAATA
*
61167 AGTAAAAATA
1 AATAAAAATA
61177 AATAAAAATAA
1 AATAAAAAT-A
*
61188 AAGGAAAAATA
1 AA-TAAAAATA
61199 AATAAA
1 AATAAA
61205 TAAATGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
10 20 0.62
11 6 0.19
12 6 0.19
ACGTcount: A:0.77, C:0.00, G:0.06, T:0.17
Consensus pattern (10 bp):
AATAAAAATA
Found at i:61198 original size:22 final size:22
Alignment explanation
Indices: 61147--61209 Score: 74
Period size: 22 Copynumber: 2.8 Consensus size: 22
61137 AATAAATGAA
* *
61147 AAAAATAAAGAATAAAAATAAGT
1 AAAAATAAATAA-AAAAATAAGG
61170 AAAAATAAATAAAAATAA-AAGG
1 AAAAATAAATAAAAA-AATAAGG
*
61192 AAAAATAAATAAATAAAT
1 AAAAATAAATAAAAAAAT
61210 GAAATATTAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 20 0.57
23 13 0.37
ACGTcount: A:0.76, C:0.00, G:0.06, T:0.17
Consensus pattern (22 bp):
AAAAATAAATAAAAAAATAAGG
Found at i:62877 original size:21 final size:21
Alignment explanation
Indices: 62853--62901 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
62843 GTATATATAT
62853 ATATATATAAATA-AATAAAAA
1 ATATATATAAATATAAT-AAAA
* * *
62874 ATATATGTATATATAATAATA
1 ATATATATAAATATAATAAAA
62895 ATATATA
1 ATATATA
62902 GTGTAAACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
ATATATATAAATATAATAAAA
Found at i:62884 original size:23 final size:23
Alignment explanation
Indices: 62851--62906 Score: 60
Period size: 23 Copynumber: 2.4 Consensus size: 23
62841 GTGTATATAT
*
62851 ATATATATATAAATAAATAA-AAA
1 ATATATGTATAAAT-AATAATAAA
* *
62874 ATATATGTATATATAATAATAAT
1 ATATATGTATAAATAATAATAAA
62897 ATATAGTGTA
1 ATATA-TGTA
62907 AACAAATTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.18
23 19 0.68
24 4 0.14
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (23 bp):
ATATATGTATAAATAATAATAAA
Found at i:63725 original size:12 final size:12
Alignment explanation
Indices: 63708--63749 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
63698 AGTGAAAAAA
63708 ATTTTAAACATT
1 ATTTTAAACATT
63720 ATTTTAAA-ATAT
1 ATTTTAAACAT-T
*
63732 AATTTAAACACTT
1 ATTTTAAACA-TT
63745 ATTTT
1 ATTTT
63750 TATATTAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
11 2 0.08
12 16 0.64
13 6 0.24
14 1 0.04
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (12 bp):
ATTTTAAACATT
Found at i:64863 original size:64 final size:64
Alignment explanation
Indices: 64734--64879 Score: 168
Period size: 64 Copynumber: 2.3 Consensus size: 64
64724 CCATTGGGAG
* * *
64734 TAAGAGCCAACCTAAGGGAATATCTTGGGGGCCTGAGAGCCTACCCAAGACAGTACCTTAAGGCC
1 TAAGAGCCTACCTAA-GGAATACCTTGGGGGCCTGAGAGCCTACCCAAGACAATACCTTAAGGCC
* ** * **
64799 TAAGAGCCTACCTAAGGAAGTACCTT-GGGGCCTTAGAGCCTACCCAAGGGAATGCCTTGGGGCC
1 TAAGAGCCTACCTAAGGAA-TACCTTGGGGGCCTGAGAGCCTACCCAAGACAATACCTTAAGGCC
* *
64863 TCAGAGCCTACCCAAGG
1 TAAGAGCCTACCTAAGG
64880 TCACCTTAGG
Statistics
Matches: 69, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
64 50 0.72
65 19 0.28
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (64 bp):
TAAGAGCCTACCTAAGGAATACCTTGGGGGCCTGAGAGCCTACCCAAGACAATACCTTAAGGCC
Found at i:64879 original size:32 final size:32
Alignment explanation
Indices: 64734--64879 Score: 150
Period size: 32 Copynumber: 4.5 Consensus size: 32
64724 CCATTGGGAG
* * *
64734 TAAGAGCCAACCTAAGGGAATATCTTGGGGGCC
1 TAAGAGCCTACCCAAGGGAATACCTT-GGGGCC
* ** * **
64767 TGAGAGCCTACCCAAGACAGTACCTTAAGGCC
1 TAAGAGCCTACCCAAGGGAATACCTTGGGGCC
*
64799 TAAGAGCCTACCTAA-GGAAGTACCTTGGGGCC
1 TAAGAGCCTACCCAAGGGAA-TACCTTGGGGCC
* *
64831 TTAGAGCCTACCCAAGGGAATGCCTTGGGGCC
1 TAAGAGCCTACCCAAGGGAATACCTTGGGGCC
*
64863 TCAGAGCCTACCCAAGG
1 TAAGAGCCTACCCAAGG
64880 TCACCTTAGG
Statistics
Matches: 91, Mismatches: 20, Indels: 5
0.78 0.17 0.04
Matches are distributed among these distances:
31 1 0.01
32 67 0.74
33 23 0.25
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.17
Consensus pattern (32 bp):
TAAGAGCCTACCCAAGGGAATACCTTGGGGCC
Found at i:66015 original size:28 final size:28
Alignment explanation
Indices: 65957--66020 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
65947 TCCAGGGCTT
*
65957 GGGGTATTTTAGGTTATTTCATACTTCA
1 GGGGTATTTTAGGTCATTTCATACTTCA
* *
65985 GGGGTATTTT-GGTCATTTTATAGTTCA
1 GGGGTATTTTAGGTCATTTCATACTTCA
*
66012 AGGGTATTT
1 GGGGTATTT
66021 CAATCCTTTC
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 22 0.69
28 10 0.31
ACGTcount: A:0.20, C:0.08, G:0.25, T:0.47
Consensus pattern (28 bp):
GGGGTATTTTAGGTCATTTCATACTTCA
Found at i:72395 original size:32 final size:32
Alignment explanation
Indices: 72336--72397 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
72326 GATTATGTGT
* * *
72336 CATGTGTCACATTACCTAAAGTGATGACATAA
1 CATGTGTCACATCACCTAAAATAATGACATAA
72368 CATGTGTCACATCATCC-AAAATAATGACAT
1 CATGTGTCACATCA-CCTAAAATAATGACAT
72398 GGCATATGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 24 0.92
33 2 0.08
ACGTcount: A:0.39, C:0.21, G:0.13, T:0.27
Consensus pattern (32 bp):
CATGTGTCACATCACCTAAAATAATGACATAA
Found at i:74432 original size:20 final size:21
Alignment explanation
Indices: 74407--74457 Score: 79
Period size: 20 Copynumber: 2.5 Consensus size: 21
74397 TTGAAGAGAT
*
74407 TATCGATACTACAT-GGTTGG
1 TATCGATACTACATAGGGTGG
74427 TATCGATACT-CATAGGGTGG
1 TATCGATACTACATAGGGTGG
74447 TATCGATACTA
1 TATCGATACTA
74458 GAAAACATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 3 0.11
20 25 0.89
ACGTcount: A:0.27, C:0.16, G:0.24, T:0.33
Consensus pattern (21 bp):
TATCGATACTACATAGGGTGG
Found at i:77056 original size:31 final size:31
Alignment explanation
Indices: 77018--77088 Score: 124
Period size: 31 Copynumber: 2.3 Consensus size: 31
77008 TTTATGATCC
* *
77018 GATCTCAGGATGATGATGATGCAGCTAATGT
1 GATCTCAGGAGGAGGATGATGCAGCTAATGT
77049 GATCTCAGGAGGAGGATGATGCAGCTAATGT
1 GATCTCAGGAGGAGGATGATGCAGCTAATGT
77080 GATCTCAGG
1 GATCTCAGG
77089 TACCCTTACC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.28, C:0.14, G:0.32, T:0.25
Consensus pattern (31 bp):
GATCTCAGGAGGAGGATGATGCAGCTAATGT
Found at i:82639 original size:14 final size:14
Alignment explanation
Indices: 82616--82649 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
82606 AAACAATTAT
82616 ATTA-ATAATAATA
1 ATTATATAATAATA
82629 ATTATATAATAATA
1 ATTATATAATAATA
*
82643 ATAATAT
1 ATTATAT
82650 TCAGGATGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
ATTATATAATAATA
Found at i:82648 original size:20 final size:18
Alignment explanation
Indices: 82610--82647 Score: 69
Period size: 17 Copynumber: 2.2 Consensus size: 18
82600 TGTAAAAAAC
82610 AATTATATTAATAATAAT
1 AATTATATTAATAATAAT
82628 AATTATA-TAATAATAAT
1 AATTATATTAATAATAAT
82645 AAT
1 AAT
82648 ATTCAGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 13 0.65
18 7 0.35
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (18 bp):
AATTATATTAATAATAAT
Found at i:103964 original size:18 final size:19
Alignment explanation
Indices: 103943--103980 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
103933 ATTTTTTATA
103943 TTTTTATTA-ATAATTTGT
1 TTTTTATTATATAATTTGT
* *
103961 TTTTTCTTATTTAATTTGT
1 TTTTTATTATATAATTTGT
103980 T
1 T
103981 CTCTAATATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (19 bp):
TTTTTATTATATAATTTGT
Found at i:105987 original size:21 final size:21
Alignment explanation
Indices: 105963--106016 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 21
105953 CACTGAAAAC
105963 TTTATAAATATTAAAAATATA
1 TTTATAAATATTAAAAATATA
*
105984 TTTA-AAA-A-T-AATATATA
1 TTTATAAATATTAAAAATATA
* *
106001 TATATATATATTAAAA
1 TTTATAAATATTAAAA
106017 TACAGAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
17 10 0.40
18 3 0.12
19 2 0.08
20 4 0.16
21 6 0.24
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (21 bp):
TTTATAAATATTAAAAATATA
Found at i:106254 original size:29 final size:29
Alignment explanation
Indices: 106197--106254 Score: 66
Period size: 30 Copynumber: 2.0 Consensus size: 29
106187 TGGTAAAAAT
* *
106197 TAAAAAAAAAATAATAAAAAATTAGGGAC
1 TAAAAAAAAAATAATAAAAAATCAAGGAC
106226 TAAAATAAAACAA-AATAAAAAA-CAAGGAC
1 TAAAA-AAAA-AATAATAAAAAATCAAGGAC
106255 AAATCAGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
29 10 0.40
30 13 0.52
31 2 0.08
ACGTcount: A:0.71, C:0.07, G:0.09, T:0.14
Consensus pattern (29 bp):
TAAAAAAAAAATAATAAAAAATCAAGGAC
Found at i:109291 original size:55 final size:55
Alignment explanation
Indices: 109186--109686 Score: 539
Period size: 55 Copynumber: 9.1 Consensus size: 55
109176 AATTGAAAAG
* * ** * *
109186 AATCTTCTGCAAACGGGTTCGCTCCCAATTCCTTCAGGGAGTATAAAACTCAAAC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTCGAAC
* *** * *
109241 AATCCTCTGAAAATAAGTTTGCTCCCTATTGTTTCAGGGAGTATAGAACTCAAAC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTCGAAC
* * * *
109296 AATATTATGAAAACGGGTTCGC-CCCTATTCCTTTTAGGGAGTATAGAACTCGAAC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATT-GTTTCAGGGAGTATAGAACTCGAAC
* * * *
109351 AATCTTCTGCAAATGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAAC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTCGAAC
* * *
109406 AATCTTCTGAAAATGGGTTCGC-CCTCTATTGCTTCAAGGAGTATAGAACTCGAAC
1 AATCTTCTGAAAACGGGTTCGCTCC-CTATTGTTTCAGGGAGTATAGAACTCGAAC
*
109461 AATCTTCT-ACAAACGGGTTCGCTCCCTATTGCTTCAGAGG-GTATAGAACTCGAAC
1 AATCTTCTGA-AAACGGGTTCGCTCCCTATTGTTTCAG-GGAGTATAGAACTCGAAC
* *
109516 AATCTTCTGAAAACGGGTTCG-TCCCTATTCCTTTCAGGGAGTATAGAACTTGAAC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATT-GTTTCAGGGAGTATAGAACTCGAAC
* * *
109571 AATCTTCTGCAAACGGGTTCGCTCCCTATTACTTT-AGGGAGTATGGAACTCTG-AC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATT-GTTTCAGGGAGTATAGAACTC-GAAC
** ** * * ** * *
109626 AATCTTCTGCCAACATGTTCGCTCCCTCTTGCTTCATAGAATATGGAACTCGAAC
1 AATCTTCTGAAAACGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTCGAAC
109681 AATCTT
1 AATCTT
109687 GATTTGCTTC
Statistics
Matches: 384, Mismatches: 49, Indels: 26
0.84 0.11 0.06
Matches are distributed among these distances:
54 23 0.06
55 336 0.88
56 25 0.07
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (55 bp):
AATCTTCTGAAAACGGGTTCGCTCCCTATTGTTTCAGGGAGTATAGAACTCGAAC
Found at i:109389 original size:110 final size:109
Alignment explanation
Indices: 109186--109686 Score: 608
Period size: 110 Copynumber: 4.6 Consensus size: 109
109176 AATTGAAAAG
* * * * * *
109186 AATCTTCTGCAAACGGGTTCGCTCCCAATTCCTTCAGGGAGTATAAAACTCAAACAATCCTCTGA
1 AATCTTCTGAAAACGGGTTCGC-CCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCTGC
*** * *
109251 AAATAAGTTTGCTCCCTATTGTTTCAGGGAGTATAGAACTCAAAC
65 AAACGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAAC
* * *
109296 AATATTATGAAAACGGGTTCGCCCCTATTCCTTTTAGGGAGTATAGAACTCGAACAATCTTCTGC
1 AATCTTCTGAAAACGGGTTCGCCCCTATTCC-TTCAGGGAGTATAGAACTCGAACAATCTTCTGC
*
109361 AAATGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAAC
65 AAACGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAAC
* * * *
109406 AATCTTCTGAAAATGGGTTCGCCCTCTATTGCTTCAAGGAGTATAGAACTCGAACAATCTTCTAC
1 AATCTTCTGAAAACGGGTTCGCCC-CTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCTGC
*
109471 AAACGGGTTCGCTCCCTATTGCTTCAGAGG-GTATAGAACTCGAAC
65 AAACGGGTTCGCTCCCTATTGCTTCAG-GGAGTATAGAACTCAAAC
* *
109516 AATCTTCTGAAAACGGGTTCGTCCCTATTCCTTTCAGGGAGTATAGAACTTGAACAATCTTCTGC
1 AATCTTCTGAAAACGGGTTCGCCCCTATTCC-TTCAGGGAGTATAGAACTCGAACAATCTTCTGC
* * * **
109581 AAACGGGTTCGCTCCCTATTACTTTAGGGAGTATGGAACTCTGAC
65 AAACGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAAC
** ** * * ** * *
109626 AATCTTCTGCCAACATGTTCGCTCCCTCTTGCTTCATAGAATATGGAACTCGAACAATCTT
1 AATCTTCTGAAAACGGGTTCGC-CCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTT
109687 GATTTGCTTC
Statistics
Matches: 340, Mismatches: 45, Indels: 12
0.86 0.11 0.03
Matches are distributed among these distances:
109 16 0.05
110 309 0.91
111 15 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (109 bp):
AATCTTCTGAAAACGGGTTCGCCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCTGCA
AACGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAAC
Found at i:109477 original size:165 final size:165
Alignment explanation
Indices: 109186--109686 Score: 609
Period size: 165 Copynumber: 3.0 Consensus size: 165
109176 AATTGAAAAG
* * *
109186 AATCTTCTGCAAACGGGTTCGCTCCCAATTCCTTCAGGGAGTATAAAACTCAAACAATCCTCTGA
1 AATCTTCTGCAAACGGGTTCGCTCCCTATTCCTTCAGGGAGTATAGAACTCAAACAATCTTCTGA
** * * * * *
109251 AAATAAGTTTGCTCCCTATTGTTTCAGGGAGTATAGAACTCAAACAATATTATGAAAACGGGTTC
66 AAATGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTC
*
109316 GC-CCCTATTCCTTTTAG-GGAGTATAGAACTCGAAC
131 GCTCCCTATTCC-TTCAGAGG-GTATAGAACTCGAAC
* *
109351 AATCTTCTGCAAATGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCAAACAATCTTCTGA
1 AATCTTCTGCAAACGGGTTCGCTCCCTATTCCTTCAGGGAGTATAGAACTCAAACAATCTTCTGA
*
109416 AAATGGGTTCGC-CCTCTATTGCTTCAAGGAGTATAGAACTCGAACAATCTTCT-ACAAACGGGT
66 AAATGGGTTCGCTCC-CTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGA-AAACGGGT
*
109479 TCGCTCCCTATTGCTTCAGAGGGTATAGAACTCGAAC
129 TCGCTCCCTATTCCTTCAGAGGGTATAGAACTCGAAC
* **
109516 AATCTTCTGAAAACGGGTTCG-TCCCTATTCCTTTCAGGGAGTATAGAACTTGAACAATCTTCTG
1 AATCTTCTGCAAACGGGTTCGCTCCCTATTCC-TTCAGGGAGTATAGAACTCAAACAATCTTCTG
* * * * * ** **
109580 CAAACGGGTTCGCTCCCTATTACTTTAGGGAGTATGGAACTCTG-ACAATCTTCTGCCAACATGT
65 AAAATGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTC-GAACAATCTTCTGAAAACGGGT
* * * ** *
109644 TCGCTCCCTCTTGCTTCATAGAATATGGAACTCGAAC
129 TCGCTCCCTATTCCTTCAGAGGGTATAGAACTCGAAC
109681 AATCTT
1 AATCTT
109687 GATTTGCTTC
Statistics
Matches: 293, Mismatches: 35, Indels: 16
0.85 0.10 0.05
Matches are distributed among these distances:
164 12 0.04
165 268 0.91
166 13 0.04
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.30
Consensus pattern (165 bp):
AATCTTCTGCAAACGGGTTCGCTCCCTATTCCTTCAGGGAGTATAGAACTCAAACAATCTTCTGA
AAATGGGTTCGCTCCCTATTGCTTCAGGGAGTATAGAACTCGAACAATCTTCTGAAAACGGGTTC
GCTCCCTATTCCTTCAGAGGGTATAGAACTCGAAC
Found at i:113095 original size:59 final size:59
Alignment explanation
Indices: 113028--113253 Score: 269
Period size: 59 Copynumber: 3.8 Consensus size: 59
113018 CTATATGTTT
* * *
113028 TAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATAAAGTATTGAGTGTGC
1 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCATTGAGTGTGC
* * * * *
113087 GAAAATGATAAGGAAATCCTACTAAGTGTACTGG-TTTCCATATGAAGCATTGAGTGTGC
1 TAAAATGATAAGGAAATCATACTGAGTGTA-TGGATTTCCAGATAAAGCATTGAGTGTGC
* * ** *
113146 TAAAATGATAAGGAAATCATATTGAAG-ATATGGATTTCCAGATAGGGCATT-ATATGTGC
1 TAAAATGATAAGGAAATCATACTG-AGTGTATGGATTTCCAGATAAAGCATTGA-GTGTGC
* *
113205 TAAAATGATAAGGGAATCATACTGAGTTTATGGATTTCCAGATAAAGCA
1 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCA
113254 CTAAGGGTTC
Statistics
Matches: 141, Mismatches: 21, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
58 6 0.04
59 131 0.93
60 4 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (59 bp):
TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCATTGAGTGTGC
Found at i:113243 original size:118 final size:118
Alignment explanation
Indices: 113028--113347 Score: 299
Period size: 118 Copynumber: 2.7 Consensus size: 118
113018 CTATATGTTT
* * ** * * *
113028 TAAAATGATAAGGAAATCATACTG-AGTGTATGAATTTCCATATAAAGTATTGA-GTGTGCGAAA
1 TAAAATGATAAGGAAATCATACTGAAG-GTATGGATTTCCACATAGGGCATT-ATATGTGCTAAA
* * * * * *
113091 ATGATAAGGAAATCCTACTAAGTGTACTGGTTTCCATATGAAGCATTGAGTGTGC
64 ATGATAAGGAAATCATACTAAGTGTACTGGTTTCCAGATAAAGCACTAAGGGTGC
* * *
113146 TAAAATGATAAGGAAATCATATTGAAGATATGGATTTCCAGATAGGGCATTATATGTGCTAAAAT
1 TAAAATGATAAGGAAATCATACTGAAGGTATGGATTTCCACATAGGGCATTATATGTGCTAAAAT
* * * *
113211 GATAAGGGAATCATACTGAGTTTA-TGGATTTCCAGATAAAGCACTAAGGGTTC
66 GATAAGGAAATCATACTAAGTGTACTGG-TTTCCAGATAAAGCACTAAGGGTGC
* * * * *
113264 TACAAGGATAAGAAAATAATACT-AATGGTATGGATTTTCACATAGGGCATT-TCATGTGCTAAA
1 TAAAATGATAAGGAAATCATACTGAA-GGTATGGATTTCCACATAGGGCATTAT-ATGTGCTAAA
* ** *
113327 ATGGTAACAAAATCCTACTAA
64 ATGATAAGGAAATCATACTAA
113348 TGGTACGGAT
Statistics
Matches: 164, Mismatches: 33, Indels: 10
0.79 0.16 0.05
Matches are distributed among these distances:
117 7 0.04
118 155 0.95
119 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.21, T:0.30
Consensus pattern (118 bp):
TAAAATGATAAGGAAATCATACTGAAGGTATGGATTTCCACATAGGGCATTATATGTGCTAAAAT
GATAAGGAAATCATACTAAGTGTACTGGTTTCCAGATAAAGCACTAAGGGTGC
Found at i:113274 original size:59 final size:59
Alignment explanation
Indices: 113028--113300 Score: 266
Period size: 59 Copynumber: 4.6 Consensus size: 59
113018 CTATATGTTT
* * * *
113028 TAAAATGATAAGGAAATCATACTGAGTGTATGAATTTCCATATAAAGTATTGAGTGTGC
1 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCATTAAGTGTGC
* * * * * *
113087 GAAAATGATAAGGAAATCCTACTAAGTGTACTGG-TTTCCATATGAAGCATTGAGTGTGC
1 TAAAATGATAAGGAAATCATACTGAGTGTA-TGGATTTCCAGATAAAGCATTAAGTGTGC
* * **
113146 TAAAATGATAAGGAAATCATATTGAAG-ATATGGATTTCCAGATAGGGCATTATA-TGTGC
1 TAAAATGATAAGGAAATCATACTG-AGTGTATGGATTTCCAGATAAAGCATTA-AGTGTGC
* * * * *
113205 TAAAATGATAAGGGAATCATACTGAGTTTATGGATTTCCAGATAAAGCACTAAGGGTTC
1 TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCATTAAGTGTGC
* * * * *
113264 TACAAGGATAAGAAAATAATACT-AATGGTATGGATTT
1 TAAAATGATAAGGAAATCATACTGAGT-GTATGGATTT
113301 TCACATAGGG
Statistics
Matches: 176, Mismatches: 31, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
58 8 0.05
59 163 0.93
60 5 0.03
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.30
Consensus pattern (59 bp):
TAAAATGATAAGGAAATCATACTGAGTGTATGGATTTCCAGATAAAGCATTAAGTGTGC
Found at i:113339 original size:59 final size:59
Alignment explanation
Indices: 113276--113388 Score: 140
Period size: 59 Copynumber: 1.9 Consensus size: 59
113266 CAAGGATAAG
* *
113276 AAAATAATACTAATGGTATGGATTTTC-ACATAGGGCA-TTTCATGTGCTAAAATGGTAAC
1 AAAATAATACTAATGGTACGGATATTCGA-ATAGGGCACTTT-ATGTGCTAAAATGGTAAC
** * *
113335 AAAATCCTACTAATGGTACGGATATTCGAATAGGGTACTTTGTGTGCTAAAATG
1 AAAATAATACTAATGGTACGGATATTCGAATAGGGCACTTTATGTGCTAAAATG
113389 AAAGAGGAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
59 42 0.91
60 4 0.09
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.32
Consensus pattern (59 bp):
AAAATAATACTAATGGTACGGATATTCGAATAGGGCACTTTATGTGCTAAAATGGTAAC
Found at i:116168 original size:186 final size:186
Alignment explanation
Indices: 115847--116195 Score: 599
Period size: 186 Copynumber: 1.9 Consensus size: 186
115837 ATTTTAAATT
*
115847 TTAAATATATTATATCTAACATATGGGCTCAGCACAAACCATTTAAAACCCAATTAATAATTTAA
1 TTAAATATATTATATATAACATATGGGCTCAGCACAAACCATTTAAAACCCAATTAATAATTTAA
* * * *
115912 GATCCAATAACTTTTAAACCTAAATTAATATTAATTAATTAAAAAATTTATATACATTTTTTAGT
66 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTAGT
*
115977 TTATAATTATATATTATTTAAATTAATTGTAAATTGTTTTTCTGAATAAAAGAATA
131 TTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTCTGAATAAAAGAATA
* * * *
116033 TTAAATATATTATATATAACATATGGGTTCAGCCCAAACCATTTAAAATCCAATTATTAATTTAA
1 TTAAATATATTATATATAACATATGGGCTCAGCACAAACCATTTAAAACCCAATTAATAATTTAA
*
116098 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTATT
66 GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTAGT
116163 TTATAATTATATATTATTTAAATTAATTATAAA
131 TTATAATTATATATTATTTAAATTAATTATAAA
116196 CTATTTTTTT
Statistics
Matches: 152, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
186 152 1.00
ACGTcount: A:0.45, C:0.09, G:0.04, T:0.41
Consensus pattern (186 bp):
TTAAATATATTATATATAACATATGGGCTCAGCACAAACCATTTAAAACCCAATTAATAATTTAA
GATCCAATAACTTTTAAACCTAAATCAATATTAATTAATTAAAAAAATTATATAAAATTTTTAGT
TTATAATTATATATTATTTAAATTAATTATAAATTGTTTTTCTGAATAAAAGAATA
Found at i:116200 original size:20 final size:20
Alignment explanation
Indices: 116166--116222 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 20
116156 TTTTATTTTA
* *
116166 TAATTATATATTATTTAAAT
1 TAATTATAAAATATTTAAAT
* **
116186 TAATTATAAACTATTT-TTT
1 TAATTATAAAATATTTAAAT
116205 TAATTATAAAATATTTAA
1 TAATTATAAAATATTTAA
116223 TTTTTATATA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
TAATTATAAAATATTTAAAT
Done.