Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008029.1 Hibiscus syriacus cultivar Beakdansim tig00110505_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: 3983240
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 18
Found at i:828016 original size:24 final size:24
Alignment explanation
Indices: 827949--828016 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
827939 TTGAAAAATC
* * *
827949 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
827973 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
827997 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
828017 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:828705 original size:21 final size:21
Alignment explanation
Indices: 828681--828726 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
828671 TAATCGCGTT
828681 GCGAATTAGGAAAATCGCAAC
1 GCGAATTAGGAAAATCGCAAC
* * *
828702 GCGAATTTGGGAAATCGCAAT
1 GCGAATTAGGAAAATCGCAAC
828723 GCGA
1 GCGA
828727 TAGTCAGAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.17, G:0.28, T:0.17
Consensus pattern (21 bp):
GCGAATTAGGAAAATCGCAAC
Found at i:833119 original size:23 final size:24
Alignment explanation
Indices: 833045--833130 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 24
833035 TCATATAAAT
* *
833045 TTGCACCGAAGTGCCACATAGAAT
1 TTGCACCGAAGTGCCACGTAGAAG
* *
833069 TTGTACCGAAG-GACCGCGTA-AAG
1 TTGCACCGAAGTG-CCACGTAGAAG
* *
833092 ATGCACTGAAGTGCCACGTAGAA-
1 TTGCACCGAAGTGCCACGTAGAAG
*
833115 TTGCACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
833131 TATAATATGT
Statistics
Matches: 48, Mismatches: 11, Indels: 7
0.73 0.17 0.11
Matches are distributed among these distances:
23 30 0.62
24 18 0.38
ACGTcount: A:0.30, C:0.24, G:0.26, T:0.20
Consensus pattern (24 bp):
TTGCACCGAAGTGCCACGTAGAAG
Found at i:833852 original size:19 final size:20
Alignment explanation
Indices: 833812--833865 Score: 83
Period size: 19 Copynumber: 2.8 Consensus size: 20
833802 TTTCCTTTAG
* *
833812 GGGGAATCGATTCCCACCCA
1 GGGGTATCGGTTCCCACCCA
833832 GGGGTATCGGTTCCC-CCCA
1 GGGGTATCGGTTCCCACCCA
833851 GGGGTATCGGTTCCC
1 GGGGTATCGGTTCCC
833866 TCTGTAAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 19 0.59
20 13 0.41
ACGTcount: A:0.15, C:0.33, G:0.31, T:0.20
Consensus pattern (20 bp):
GGGGTATCGGTTCCCACCCA
Found at i:836721 original size:13 final size:13
Alignment explanation
Indices: 836703--836730 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
836693 CATTTATGCG
836703 TACTTATGGCTTA
1 TACTTATGGCTTA
836716 TACTTATGGCTTA
1 TACTTATGGCTTA
836729 TA
1 TA
836731 TAATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.25, C:0.14, G:0.14, T:0.46
Consensus pattern (13 bp):
TACTTATGGCTTA
Found at i:836834 original size:25 final size:25
Alignment explanation
Indices: 836786--836834 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
836776 AAAAGTTGTA
*
836786 TTTTTGGTCAAAATAGATATCTAAT
1 TTTTTGGTCAAAATAGATACCTAAT
* *
836811 TTTTTTGTCAAAATAGGTACCTAA
1 TTTTTGGTCAAAATAGATACCTAA
836835 AGTATTTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.35, C:0.10, G:0.12, T:0.43
Consensus pattern (25 bp):
TTTTTGGTCAAAATAGATACCTAAT
Found at i:841028 original size:18 final size:19
Alignment explanation
Indices: 841005--841041 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
840995 TGAGTAATAA
841005 ATTTAATT-TTTATATTTT
1 ATTTAATTGTTTATATTTT
*
841023 ATTTAATTGTTTTTATTTT
1 ATTTAATTGTTTATATTTT
841042 TCATATTTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (19 bp):
ATTTAATTGTTTATATTTT
Found at i:841460 original size:19 final size:19
Alignment explanation
Indices: 841438--841519 Score: 56
Period size: 19 Copynumber: 4.0 Consensus size: 19
841428 TTAATAACTT
841438 ATTTTAATTTTAATTATTA
1 ATTTTAATTTTAATTATTA
* *
841457 ATTTCAATAAATTATATTATATA
1 ATTTTAAT--TTTA-ATTAT-TA
* * *
841480 ATTTAATATTTATAATGATTG
1 ATTTTA-ATTT-TAATTATTA
*
841501 ATTTTAATTATAATTATTA
1 ATTTTAATTTTAATTATTA
841520 GTCAAATTTA
Statistics
Matches: 47, Mismatches: 10, Indels: 12
0.68 0.14 0.17
Matches are distributed among these distances:
19 14 0.30
20 3 0.06
21 9 0.19
22 10 0.21
23 9 0.19
24 2 0.04
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.55
Consensus pattern (19 bp):
ATTTTAATTTTAATTATTA
Found at i:843330 original size:21 final size:21
Alignment explanation
Indices: 843304--843357 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
843294 GCGTTGCATT
843304 TCGCGTTGCGATAATTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
843325 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAATTGAAAA
*
843346 TCGCGTTTCGAT
1 TCGCGTTGCGAT
843358 TTTGCAGTTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.31
Consensus pattern (21 bp):
TCGCGTTGCGATAATTGAAAA
Found at i:844215 original size:41 final size:41
Alignment explanation
Indices: 844170--844299 Score: 167
Period size: 41 Copynumber: 3.2 Consensus size: 41
844160 CTGTAGACTT
* *
844170 TCGCAACAACAACTGTAGACTATCGCAACGAATTTGGAAAA
1 TCGCAACGACAATTGTAGACTATCGCAACGAATTTGGAAAA
*
844211 TCGCAACGATAATTGTAGACTATCGCAACGAATTT-GAAAA
1 TCGCAACGACAATTGTAGACTATCGCAACGAATTTGGAAAA
* * *
844251 TCGCAATGAC-ATTGTAGATTATCGCAACGCGAA-ATGGAAAA
1 TCGCAACGACAATTGTAGACTATCGCAA--CGAATTTGGAAAA
844292 TCGCAACG
1 TCGCAACG
844300 CGAAATGGAA
Statistics
Matches: 78, Mismatches: 8, Indels: 6
0.85 0.09 0.07
Matches are distributed among these distances:
39 16 0.21
40 14 0.18
41 48 0.62
ACGTcount: A:0.39, C:0.20, G:0.19, T:0.22
Consensus pattern (41 bp):
TCGCAACGACAATTGTAGACTATCGCAACGAATTTGGAAAA
Found at i:844238 original size:22 final size:22
Alignment explanation
Indices: 844147--844241 Score: 88
Period size: 22 Copynumber: 4.5 Consensus size: 22
844137 AATTTGGAAA
*
844147 ATCGTAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* *
844169 TTCGCAACAACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
* * **
844191 ATCGCAACG--AA-TTTGGAAA
1 ATCGCAACGACAACTGTAGACT
* *
844210 ATCGCAACGATAATTGTAGACT
1 ATCGCAACGACAACTGTAGACT
844232 ATCGCAACGA
1 ATCGCAACGA
844242 ATTTGAAAAT
Statistics
Matches: 57, Mismatches: 13, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
19 13 0.23
20 2 0.04
21 2 0.04
22 40 0.70
ACGTcount: A:0.38, C:0.22, G:0.18, T:0.22
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:844296 original size:20 final size:20
Alignment explanation
Indices: 844271--844322 Score: 104
Period size: 20 Copynumber: 2.6 Consensus size: 20
844261 ATTGTAGATT
844271 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
844291 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
844311 ATCGCAACGCGA
1 ATCGCAACGCGA
844323 TTCTCAACGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.42, C:0.23, G:0.25, T:0.10
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:844351 original size:21 final size:21
Alignment explanation
Indices: 844327--844376 Score: 100
Period size: 21 Copynumber: 2.4 Consensus size: 21
844317 ACGCGATTCT
844327 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
844348 CAACGCGATTTTCAACTATCG
1 CAACGCGATTTTCAACTATCG
844369 CAACGCGA
1 CAACGCGA
844377 AATGCAACGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.24
Consensus pattern (21 bp):
CAACGCGATTTTCAACTATCG
Found at i:844384 original size:21 final size:21
Alignment explanation
Indices: 844339--844384 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
844329 ACGCGATTTT
** *
844339 CAACTATCGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
844360 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
844381 CAAC
1 CAAC
844385 GCGAATTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.35, C:0.30, G:0.15, T:0.20
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:844586 original size:23 final size:24
Alignment explanation
Indices: 844537--844586 Score: 66
Period size: 23 Copynumber: 2.1 Consensus size: 24
844527 TAATAAAACT
*
844537 TAATTATATTTTATAATAATTTAA
1 TAATTATATTTTATAATAATGTAA
* *
844561 TAATTAT-TTTTATAATGATGTGA
1 TAATTATATTTTATAATAATGTAA
844584 TAA
1 TAA
844587 AATAAAATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (24 bp):
TAATTATATTTTATAATAATGTAA
Found at i:854424 original size:21 final size:22
Alignment explanation
Indices: 854400--854444 Score: 56
Period size: 25 Copynumber: 2.0 Consensus size: 22
854390 ATAATGATAA
854400 AAAC-ATCAATTAATATATCCT
1 AAACAATCAATTAATATATCCT
854421 AAACTTAAATCAATTAATATATCC
1 AAAC---AATCAATTAATATATCC
854445 ATAACTGCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 4 0.20
25 16 0.80
ACGTcount: A:0.49, C:0.18, G:0.00, T:0.33
Consensus pattern (22 bp):
AAACAATCAATTAATATATCCT
Found at i:854733 original size:2 final size:2
Alignment explanation
Indices: 854728--854754 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
854718 TATGTGTGAC
854728 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 T
854755 CACTGTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:856314 original size:3 final size:3
Alignment explanation
Indices: 856294--856358 Score: 60
Period size: 3 Copynumber: 21.3 Consensus size: 3
856284 TGCAAAAAAA
* * * *
856294 AAT ATT AAT AGT ATT AAT AAT -AT AAT AAT AAT AATT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT AAT
*
856339 AATT ATT AAT AAT AAT AAT A
1 AA-T AAT AAT AAT AAT AAT A
856359 TATATATATA
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
2 2 0.04
3 44 0.88
4 4 0.08
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (3 bp):
AAT
Found at i:856337 original size:13 final size:13
Alignment explanation
Indices: 856305--856354 Score: 77
Period size: 13 Copynumber: 4.0 Consensus size: 13
856295 ATATTAATAG
856305 TATTAATAAT-A-
1 TATTAATAATAAT
*
856316 TAATAATAATAAT
1 TATTAATAATAAT
856329 TATTAATAATAAT
1 TATTAATAATAAT
856342 TATTAATAATAAT
1 TATTAATAATAAT
856355 AATATATATA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
11 9 0.26
12 1 0.03
13 25 0.71
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
TATTAATAATAAT
Found at i:866958 original size:12 final size:13
Alignment explanation
Indices: 866928--866953 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
866918 AATGAAAATT
866928 AAGTAAAGGAAAA
1 AAGTAAAGGAAAA
866941 AAGTAAAGGAAAA
1 AAGTAAAGGAAAA
866954 GGTAATTAAG
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:0.69, C:0.00, G:0.23, T:0.08
Consensus pattern (13 bp):
AAGTAAAGGAAAA
Found at i:867244 original size:47 final size:46
Alignment explanation
Indices: 867156--867244 Score: 117
Period size: 46 Copynumber: 1.9 Consensus size: 46
867146 TTCGGTAGAG
* * *
867156 TACTGCTTAAAATGTTATTTTTTTTACAAGAAATGTTAATATCGGA
1 TACTGCCTAAAATATTATTTTTTTTACAAGAAATGTAAATATCGGA
*
867202 TACTGCCTAAAATATTATTTTTTTCTAC-CGAAAATGTAAATAT
1 TACTGCCTAAAATATTATTTTTTT-TACAAG-AAATGTAAATAT
867245 AGAAAATATT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
46 23 0.62
47 14 0.38
ACGTcount: A:0.36, C:0.11, G:0.10, T:0.43
Consensus pattern (46 bp):
TACTGCCTAAAATATTATTTTTTTTACAAGAAATGTAAATATCGGA
Found at i:872490 original size:55 final size:55
Alignment explanation
Indices: 872421--872751 Score: 239
Period size: 55 Copynumber: 6.1 Consensus size: 55
872411 GGGATAAATG
* * *
872421 AGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGTATA
1 AGACTCGAACAATCTTCAAATAACGAGCCTGCTCCCTATTCCTTCAGAG-AGTATA
* * ** * *
872476 AGACTCGAACAATCTTCATAA-AATGTGTATGCTCTCTATTCATTCAGAGAGTATA
1 AGACTCGAACAATCTTCA-AATAACGAGCCTGCTCCCTATTCCTTCAGAGAGTATA
* * * *
872531 AGACTTGAACAATCTTCAATAAAACGAGTCTGCTCTCTATTCCTTCAGAGAGTAT-
1 AGACTCGAACAATCTTCAA-ATAACGAGCCTGCTCCCTATTCCTTCAGAGAGTATA
872586 AGAACTCGGAA-AATCTTC-AATAAAC-AGGTCC-GCTCCCTATTCCTTCAGAGAGTATA
1 AG-ACTC-GAACAATCTTCAAAT-AACGA-G-CCTGCTCCCTATTCCTTCAGAGAGTATA
* ** * *
872642 AGACT----CAATCTTTAACA-AACTTGTCTGCTCCCTATTCCTTTAGAGAGTATA
1 AGACTCGAACAATCTTCAA-ATAACGAGCCTGCTCCCTATTCCTTCAGAGAGTATA
* * *
872693 AGACTCG----ATCTTCATAA-AATGTGTCC-GCTCCCTATTCCTTCATAGAGTATA
1 AGACTCGAACAATCTTCA-AATAACGAG-CCTGCTCCCTATTCCTTCAGAGAGTATA
*
872744 TGACTCGA
1 AGACTCGA
872752 TTTTCATAAA
Statistics
Matches: 227, Mismatches: 29, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
50 1 0.00
51 79 0.35
52 3 0.01
53 1 0.00
54 3 0.01
55 92 0.41
56 45 0.20
57 3 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (55 bp):
AGACTCGAACAATCTTCAAATAACGAGCCTGCTCCCTATTCCTTCAGAGAGTATA
Found at i:872578 original size:111 final size:109
Alignment explanation
Indices: 872421--872748 Score: 372
Period size: 111 Copynumber: 3.0 Consensus size: 109
872411 GGGATAAATG
* ** *
872421 AGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAA
1 AGACTTGAACAATCTTCAAAAAACGAGTCTGCTCCCTATTCCTTCAGAG-AGTATAAGACTCGAA
** * *
872485 CAATCTTCATAAAATGTGTATGCTCTCTATTCATTCAGAGAGTATA
65 -AATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATA
*
872531 AGACTTGAACAATCTTCAATAAAACGAGTCTGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGG
1 AGACTTGAACAATCTTCAA-AAAACGAGTCTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTC-G
872595 AAAATCTTCAATAAACA-G-GTCCGCTCCCTATTCCTTCAGAGAGTATA
63 AAAATCTTC-ATAAA-ATGTGTCCGCTCCCTATTCCTTCAGAGAGTATA
* * ** *
872642 AGAC-T---CAATCTTTAACAAACTTGTCTGCTCCCTATTCCTTTAGAGAGTATAAGACTCG---
1 AGACTTGAACAATCTTCAAAAAACGAGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAA
*
872700 ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCATAGAGTATA
66 ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATA
*
872744 TGACT
1 AGACT
872749 CGATTTTCAT
Statistics
Matches: 191, Mismatches: 17, Indels: 27
0.81 0.07 0.11
Matches are distributed among these distances:
100 1 0.01
101 6 0.03
102 37 0.19
105 1 0.01
106 34 0.18
107 11 0.06
110 21 0.11
111 69 0.36
112 10 0.05
113 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.31
Consensus pattern (109 bp):
AGACTTGAACAATCTTCAAAAAACGAGTCTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAAA
ATCTTCATAAAATGTGTCCGCTCCCTATTCCTTCAGAGAGTATA
Found at i:872750 original size:51 final size:51
Alignment explanation
Indices: 872449--872764 Score: 284
Period size: 51 Copynumber: 5.9 Consensus size: 51
872439 AATGACGAGC
872449 CTGCTCCCTATTCCTTCAG-GAAGTATAAGACTCGAACAATCTTCATAAAATGTGT
1 CTGCTCCCTATTCCTTCAGAG-AGTATAAGACTCG----ATCTTCATAAAATGTGT
* * * * * *
872504 ATGCTCTCTATTCATTCAGAGAGTATAAGACTTGAACAATCTTCAATAAAACGAGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGAC-T---CGATCTTC-ATAAAATGTGT
*
872560 CTGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCGGAAAATCTTCAATAAACA-G-GT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAG-ACTC-G---ATCTTC-ATAAA-ATGTGT
* * *
872615 CCGCTCCCTATTCCTTCAGAGAGTATAAGACTCAATCTTTA-ACAAACT-TGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCATA-AAA-TGTGT
*
872666 CTGCTCCCTATTCCTTTAGAGAGTATAAGACTCGATCTTCATAAAATGTGT
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCATAAAATGTGT
* * * *
872717 CCGCTCCCTATTCCTTCATAGAGTATATGACTCGATTTTCATAAAATG
1 CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCATAAAATG
872765 AGTTTTGCTT
Statistics
Matches: 220, Mismatches: 22, Indels: 42
0.77 0.08 0.15
Matches are distributed among these distances:
49 2 0.01
50 4 0.02
51 93 0.42
52 2 0.01
55 65 0.30
56 52 0.24
57 1 0.00
59 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
CTGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCATAAAATGTGT
Found at i:872822 original size:37 final size:36
Alignment explanation
Indices: 872768--872838 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 36
872758 TAAAATGAGT
872768 TTTGCTTCACTAATCTTCCGTGAAGGCTTACAGATGG
1 TTTGCTTCACTAATCTTCCGTGAAGGCTTA-AGATGG
* *
872805 TTTGCTTTACTACTCTTCCGTGAAGGCTTAAGAT
1 TTTGCTTCACTAATCTTCCGTGAAGGCTTAAGAT
872839 TGACCTGTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 28 0.88
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (36 bp):
TTTGCTTCACTAATCTTCCGTGAAGGCTTAAGATGG
Found at i:874127 original size:7 final size:7
Alignment explanation
Indices: 874104--874263 Score: 77
Period size: 7 Copynumber: 23.1 Consensus size: 7
874094 CCTCCTTTTA
874104 TTTCTTCT
1 TTTCTT-T
874112 TTT-TTT
1 TTTCTTT
874118 TTTCTTT
1 TTTCTTT
874125 TTTC-TT
1 TTTCTTT
**
874131 TTTCCAT
1 TTTCTTT
**
874138 TTTC-CA
1 TTTCTTT
*
874144 TTTCATT
1 TTTCTTT
*
874151 TTTCATT
1 TTTCTTT
*
874158 TTTC-AT
1 TTTCTTT
*
874164 TTTCATT
1 TTTCTTT
*
874171 TTTCATT
1 TTTCTTT
874178 TTTCATTTT
1 TTTC--TTT
*
874187 TTTCCTT
1 TTTCTTT
*
874194 TTTC--C
1 TTTCTTT
*
874199 TTTCCTT
1 TTTCTTT
874206 TTTCTTT
1 TTTCTTT
874213 TTTCTTT
1 TTTCTTT
874220 TTTCTTT
1 TTTCTTT
874227 TTT-TATT
1 TTTCT-TT
874234 TTT-TATT
1 TTTCT-TT
*
874241 TATCTTT
1 TTTCTTT
874248 TTT-TTT
1 TTTCTTT
874254 CATTTCTTT
1 --TTTCTTT
874263 T
1 T
874264 CAGGCGAAAT
Statistics
Matches: 125, Mismatches: 14, Indels: 27
0.75 0.08 0.16
Matches are distributed among these distances:
5 4 0.03
6 23 0.18
7 82 0.66
8 7 0.06
9 9 0.07
ACGTcount: A:0.07, C:0.16, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTCTTT
Found at i:874127 original size:13 final size:13
Alignment explanation
Indices: 874099--874263 Score: 71
Period size: 13 Copynumber: 12.0 Consensus size: 13
874089 TGAACCCTCC
*
874099 TTTTATTTCTTCTT
1 TTTTTTTTCTT-TT
874113 TTTTTTTTCTTTT
1 TTTTTTTTCTTTT
* **
874126 TTCTTTTTCCATT
1 TTTTTTTTCTTTT
***
874139 TTCCATTTCATTTT
1 TTTTTTTTC-TTTT
** *
874153 TCATTTTTCATTT
1 TTTTTTTTCTTTT
**
874166 TCATTTTTCATTTT
1 TTTTTTTTC-TTTT
*
874180 TCATTTTTTTCCTTT
1 T--TTTTTTTCTTTT
** *
874195 TTCCTTTCCTTTT
1 TTTTTTTTCTTTT
*
874208 TCTTTTTTCTTTT
1 TTTTTTTTCTTTT
874221 TTCTTTTTT-TATTT
1 TT-TTTTTTCT-TTT
*
874235 TTTATTTATCTTTT
1 TTT-TTTTTCTTTT
874249 TTTTTCATTTCTTTT
1 TTTTT--TTTCTTTT
874264 CAGGCGAAAT
Statistics
Matches: 113, Mismatches: 28, Indels: 19
0.71 0.17 0.12
Matches are distributed among these distances:
13 53 0.47
14 42 0.37
15 12 0.11
16 6 0.05
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (13 bp):
TTTTTTTTCTTTT
Found at i:874152 original size:20 final size:19
Alignment explanation
Indices: 874125--874209 Score: 72
Period size: 20 Copynumber: 4.5 Consensus size: 19
874115 TTTTTTCTTT
874125 TTTCTTTTTCCATTTTCCA
1 TTTCTTTTTCCATTTTCCA
*
874144 TTTCATTTTT-CATTTTTCA
1 TTTC-TTTTTCCATTTTCCA
*
874163 TTTTCATTTTT-CATTTTTCA
1 -TTTC-TTTTTCCATTTTCCA
*
874183 -TT-TTTTTCCTTTTTCC-
1 TTTCTTTTTCCATTTTCCA
874199 TTTCCTTTTTC
1 TTT-CTTTTTC
874210 TTTTTTCTTT
Statistics
Matches: 57, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
16 5 0.09
17 8 0.14
18 2 0.04
19 18 0.32
20 24 0.42
ACGTcount: A:0.09, C:0.21, G:0.00, T:0.69
Consensus pattern (19 bp):
TTTCTTTTTCCATTTTCCA
Found at i:874208 original size:35 final size:35
Alignment explanation
Indices: 874149--874222 Score: 96
Period size: 35 Copynumber: 2.1 Consensus size: 35
874139 TTCCATTTCA
*
874149 TTTTTCATTTTTCATTTTCATTTTTCATTTTTCATT
1 TTTTTCATTTTTCACTTTCATTTTTCATTTTTC-TT
* * *
874185 TTTTTCCTTTTTC-CTTTCCTTTTTCTTTTTTCTT
1 TTTTTCATTTTTCACTTTCATTTTTCATTTTTCTT
874219 TTTT
1 TTTT
874223 CTTTTTTTAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
34 6 0.18
35 16 0.47
36 12 0.35
ACGTcount: A:0.07, C:0.18, G:0.00, T:0.76
Consensus pattern (35 bp):
TTTTTCATTTTTCACTTTCATTTTTCATTTTTCTT
Found at i:887892 original size:20 final size:20
Alignment explanation
Indices: 887867--887980 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
887857 AATTGGGAAA
*
887867 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
887887 ATCGCAATGCGATACTTACT
1 ATCGCAACGCGATACTGACT
* * * *
887907 ATCGCAATGCAATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
*
887928 ATCGCAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
887948 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
887968 TTCGCAACGCGAT
1 ATCGCAACGCGAT
887981 TTACTTAGCA
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
19 2 0.03
20 63 0.80
21 12 0.15
22 2 0.03
ACGTcount: A:0.32, C:0.25, G:0.18, T:0.25
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:887911 original size:61 final size:61
Alignment explanation
Indices: 887846--887979 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
887836 GAATAAGTAA
** * * * *
887846 ATCGCAACGCGAAT-TGGGAAAATCGCAATGCGATACTGACTATCGCAATGCGATACTTACT
1 ATCGCAACGCGAATAT-ACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
* * *
887907 ATCGCAATGC-AATAATACAAAATCGCAACGAGATACTGACTTTCGCAACGCGATTCTGACT
1 ATCGCAACGCGAAT-ATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
*
887968 TTCGCAACGCGA
1 ATCGCAACGCGA
887980 TTTACTTAGC
Statistics
Matches: 59, Mismatches: 11, Indels: 5
0.79 0.15 0.07
Matches are distributed among these distances:
60 3 0.05
61 54 0.92
62 2 0.03
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (61 bp):
ATCGCAACGCGAATATACAAAATCGCAACGAGATACTGACTATCGCAACGCGATACTGACT
Found at i:888562 original size:19 final size:19
Alignment explanation
Indices: 888514--888555 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
888504 ACGAGATAAT
*
888514 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
888533 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
888552 CGCA
1 CGCA
888556 TTGCGAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:888628 original size:39 final size:38
Alignment explanation
Indices: 888551--888640 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
888541 GAAACAAAAA
* *
888551 TCGCATTGCGAATTTTATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
888589 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTTATTTCGC-GTTGCGATTTTCATT
888628 TCGCGTTGCGATT
1 TCGCGTTGCGATT
888641 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTTATTTCGCGTTGCGATTTTCATT
Found at i:888639 original size:19 final size:19
Alignment explanation
Indices: 888551--888735 Score: 158
Period size: 19 Copynumber: 10.1 Consensus size: 19
888541 GAAACAAAAA
*
888551 TCGCATTGCGAATTTT-ATT
1 TCGCGTTGCG-ATTTTCATT
888570 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
888589 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
888608 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
*
888628 TCGCGTTGCGATTGTC---
1 TCGCGTTGCGATTTTCATT
* **
888644 T-G-GTCGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
888661 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
888675 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
*
888694 TCCGCGTTGCGATTCTCATT
1 T-CGCGTTGCGATTTTCATT
*
888714 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
888734 TC
1 TC
888736 AACCAAAAGA
Statistics
Matches: 137, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
14 20 0.15
15 1 0.01
16 3 0.02
17 3 0.02
18 6 0.04
19 54 0.39
20 49 0.36
21 1 0.01
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:888651 original size:39 final size:39
Alignment explanation
Indices: 888570--888651 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
888560 GAATTTTATT
* **
888570 TCGC-GTTGCGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
888608 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GG
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGG
888647 TCGCG
1 TCGCG
888652 ATAGTCATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 4 0.10
39 33 0.85
40 2 0.05
ACGTcount: A:0.09, C:0.21, G:0.27, T:0.44
Consensus pattern (39 bp):
TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
Found at i:888660 original size:33 final size:33
Alignment explanation
Indices: 888623--888710 Score: 140
Period size: 33 Copynumber: 2.6 Consensus size: 33
888613 GTTGCGATTT
* *
888623 TCATTTCGCGTTGCGATTGTCTGGTCGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
*
888656 TCATTTCGCGTTGCGATTCTCTCGTTGCGATAG
1 TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
888689 TCATTTCCGCGTTGCGATTCTC
1 TCATTT-CGCGTTGCGATTCTC
888711 ATTATCTCGT
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
33 36 0.71
34 15 0.29
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (33 bp):
TCATTTCGCGTTGCGATTCTCTCGTCGCGATAG
Found at i:888712 original size:20 final size:20
Alignment explanation
Indices: 888678--888735 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
888668 GCGATTCTCT
**
888678 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
888698 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
888718 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
888736 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:889309 original size:14 final size:14
Alignment explanation
Indices: 889290--889325 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
889280 ATTGTTTAAT
889290 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
*
889304 TGATTTGTAAAAGT
1 TGATTTGTAAAAGG
889318 TGATTTGT
1 TGATTTGT
889326 TTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:889526 original size:19 final size:19
Alignment explanation
Indices: 889504--889653 Score: 69
Period size: 19 Copynumber: 8.7 Consensus size: 19
889494 CGAAATTAAA
889504 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
889523 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* * *
889538 -CCTCGTTGCAATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* *
889556 TTCGCATTGCGA-----AA
1 TTCGCGTTGCGATTTTCAT
*
889570 TTAGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
889589 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
889604 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
889622 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
*
889641 TCCGCGTTGCGAT
1 TTCGCGTTGCGAT
889654 AGACATTAAG
Statistics
Matches: 92, Mismatches: 24, Indels: 30
0.63 0.16 0.21
Matches are distributed among these distances:
14 27 0.29
16 6 0.07
17 6 0.07
19 53 0.58
ACGTcount: A:0.16, C:0.23, G:0.20, T:0.41
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:889552 original size:33 final size:32
Alignment explanation
Indices: 889508--889634 Score: 184
Period size: 33 Copynumber: 3.9 Consensus size: 32
889498 ATTAAATTCG
889508 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
889541 CGTTGCAATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
889574 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
889607 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
889635 AGTAATTCCG
Statistics
Matches: 84, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
31 3 0.04
33 78 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.23, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:889597 original size:66 final size:66
Alignment explanation
Indices: 889501--889633 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
889491 ACACGAAATT
*
889501 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
889566 G
66 G
* *
889567 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
889632 G
66 G
889633 A
1 A
889634 TAGTAATTCC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.17, C:0.23, G:0.19, T:0.41
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCGTTGCAATTTTCATTTCGCATTGC
G
Found at i:891936 original size:12 final size:12
Alignment explanation
Indices: 891919--891943 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
891909 TTCTTCGGGA
891919 CTTTTTCTTCTT
1 CTTTTTCTTCTT
891931 CTTTTTCTTCTT
1 CTTTTTCTTCTT
891943 C
1 C
891944 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:892152 original size:24 final size:24
Alignment explanation
Indices: 892118--892171 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
892108 CTGAAACATC
* *
892118 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
892142 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
892166 ATCAAA
1 ATCAAA
892172 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:893250 original size:20 final size:20
Alignment explanation
Indices: 893225--893275 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
893215 ATTCATTTGA
893225 CTATCGCAACGCAAAAATGG
1 CTATCGCAACGCAAAAATGG
*
893245 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCAAAAATGG
893265 CTATCGCAACG
1 CTATCGCAACG
893276 AGAAAATCGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.22, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGCAAAAATGG
Found at i:893280 original size:20 final size:20
Alignment explanation
Indices: 893225--893282 Score: 91
Period size: 20 Copynumber: 2.9 Consensus size: 20
893215 ATTCATTTGA
893225 CTATCGCAACGCA-AAAATGG
1 CTATCGCAACG-AGAAAATGG
*
893245 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGAGAAAATGG
893265 CTATCGCAACGAGAAAAT
1 CTATCGCAACGAGAAAAT
893283 CGCAATGCGA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.40, C:0.24, G:0.21, T:0.16
Consensus pattern (20 bp):
CTATCGCAACGAGAAAATGG
Found at i:893340 original size:19 final size:19
Alignment explanation
Indices: 893318--893366 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
893308 CGATTTCTCG
893318 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
893337 TTGCAATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
893356 TTGTGATTTTC
1 TTGCGATTTTC
893367 TCGTTGCGAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.16, C:0.18, G:0.14, T:0.51
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:893512 original size:14 final size:13
Alignment explanation
Indices: 893483--893517 Score: 52
Period size: 14 Copynumber: 2.6 Consensus size: 13
893473 CATCAATTAA
893483 ACAAATCACATTT
1 ACAAATCACATTT
*
893496 ACAAATCATCTTTT
1 ACAAATCA-CATTT
893510 ACAAATCA
1 ACAAATCA
893518 ATTAAACAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.46, C:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
ACAAATCACATTT
Found at i:895413 original size:20 final size:19
Alignment explanation
Indices: 895378--895444 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
895368 GAAACTTAAA
895378 ATCGCAACGCGAAATGACT
1 ATCGCAACGCGAAATGACT
*
895397 ATCGCAACGCGGAAATGGCT
1 ATCGCAACGC-GAAATGACT
* **
895417 ATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
895436 ATCGCAACG
1 ATCGCAACG
895445 ACAAAATCGC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.37, C:0.24, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:895452 original size:14 final size:14
Alignment explanation
Indices: 895433--895490 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
895423 ATGCGAAATG
895433 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
895447 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
895463 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
895479 AAAATCGCAACG
1 AAAATCGCAACG
895491 CGAAACACAA
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.48, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:895475 original size:32 final size:33
Alignment explanation
Indices: 895417--895495 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
895407 GGAAATGGCT
*
895417 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
895450 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
895482 ATCGCAACGCGAAA
1 ATCGCAACGCGAAA
895496 CACAAATCGC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 30 0.67
33 15 0.33
ACGTcount: A:0.47, C:0.24, G:0.19, T:0.10
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:895543 original size:14 final size:14
Alignment explanation
Indices: 895524--895581 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
895514 TTTCATTTCG
895524 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
895538 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
895554 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
895570 CGTTGCGATTTT
1 CGTTGCGATTTT
895582 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:895588 original size:33 final size:33
Alignment explanation
Indices: 895507--895597 Score: 166
Period size: 32 Copynumber: 2.8 Consensus size: 33
895497 ACAAATCGCA
*
895507 TTGCGATTTTCATTTCGCGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
895540 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
895572 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
895598 AGCCATTTCC
Statistics
Matches: 56, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
32 31 0.55
33 25 0.45
ACGTcount: A:0.12, C:0.19, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:895632 original size:19 final size:19
Alignment explanation
Indices: 895582--895624 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
895572 TTGCGATTTT
*
895582 CATTT-CGCATTGCGATAGC
1 CATTTCCGCGTTG-GATAGC
*
895601 CATTTCCGCGTTGGATAGT
1 CATTTCCGCGTTGGATAGC
895620 CATTT
1 CATTT
895625 TCGTGTTGCG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 15 0.71
20 6 0.29
ACGTcount: A:0.19, C:0.23, G:0.21, T:0.37
Consensus pattern (19 bp):
CATTTCCGCGTTGGATAGC
Found at i:896136 original size:18 final size:18
Alignment explanation
Indices: 896110--896154 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
896100 GTCGATCAGA
*
896110 TGATGGCTCTAGGTGAGG
1 TGATGGCTCTAGGCGAGG
* *
896128 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTAGGCGAGG
896146 TGATGGCTC
1 TGATGGCTC
896155 CCGAAGTGGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.16, C:0.16, G:0.42, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTAGGCGAGG
Found at i:897781 original size:22 final size:22
Alignment explanation
Indices: 897754--897797 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
897744 GATGGAGATA
897754 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
897776 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
897798 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:898038 original size:20 final size:20
Alignment explanation
Indices: 897985--898057 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
897975 GATTATGTAT
*
897985 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAATCAG
* *
898005 AATTGCGTTGCGAAAATCAG
1 TATCGCGTTGCGAAAATCAG
* *
898025 TATCGCGGTT-CGAAAGTAAG
1 TATCGC-GTTGCGAAAATCAG
*
898045 TATCTCGTTGCGA
1 TATCGCGTTGCGA
898058 TTTTTTATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
19 3 0.07
20 37 0.86
21 3 0.07
ACGTcount: A:0.27, C:0.18, G:0.27, T:0.27
Consensus pattern (20 bp):
TATCGCGTTGCGAAAATCAG
Found at i:898076 original size:21 final size:21
Alignment explanation
Indices: 898043--898143 Score: 59
Period size: 20 Copynumber: 4.9 Consensus size: 21
898033 TTCGAAAGTA
* * *
898043 AGTATCTCGTTGCGATTTTTT
1 AGTATCGCATTGCGATTTTTC
* **
898064 ATTATCGCATTGCGA-TAGTC
1 AGTATCGCATTGCGATTTTTC
*
898084 AGTATCGCATTGCGATTTTCCC
1 AGTATCGCATTGCGATTTT-TC
* *
898106 AAT-TCGCGTTGCGATTTACTT-
1 AGTATCGCATTGCGATTT--TTC
898127 A-T-TCGCATTGCGATTTT
1 AGTATCGCATTGCGATTTT
898144 CCCAATTCGC
Statistics
Matches: 62, Mismatches: 14, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
18 1 0.02
20 30 0.48
21 27 0.44
22 3 0.05
23 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.19, T:0.43
Consensus pattern (21 bp):
AGTATCGCATTGCGATTTTTC
Found at i:898153 original size:21 final size:21
Alignment explanation
Indices: 898088--898163 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
898078 ATAGTCAGTA
898088 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
* * **
898109 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTCCCAAT
898129 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTCCCAAT
*
898150 TCGCGTTGCGATTT
1 TCGCATTGCGATTT
898164 ACGCGTTGCG
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.16, C:0.25, G:0.18, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCCCAAT
Found at i:898163 original size:41 final size:41
Alignment explanation
Indices: 898088--898165 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
898078 ATAGTCAGTA
898088 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
898129 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAC
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTAC
898166 GCGTTGCGAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.17, C:0.26, G:0.18, T:0.40
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:898170 original size:14 final size:14
Alignment explanation
Indices: 898151--898179 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
898141 TTTCCCAATT
898151 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
898165 CGCGTTGCGATTTA
1 CGCGTTGCGATTTA
898179 C
1 C
898180 TTATTCGCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.24, G:0.28, T:0.34
Consensus pattern (14 bp):
CGCGTTGCGATTTA
Found at i:899289 original size:17 final size:17
Alignment explanation
Indices: 899267--899328 Score: 90
Period size: 17 Copynumber: 3.5 Consensus size: 17
899257 TATGTTAAGG
899267 TTTTATAATATATTATA
1 TTTTATAATATATTATA
899284 TTTTATAATATATTATA
1 TTTTATAATATATTATA
899301 TTTTATAATA-ATTAATA
1 TTTTATAATATATT-ATA
899318 TCATTTATAAT
1 T--TTTATAAT
899329 TTAAACTTAT
Statistics
Matches: 42, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
16 3 0.07
17 31 0.74
19 8 0.19
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTATAATATATTATA
Found at i:900599 original size:23 final size:23
Alignment explanation
Indices: 900552--900601 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
900542 AATAACATAT
* **
900552 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
900575 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
900598 TAGG
1 TAGG
900602 CATTTAACCG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.08, G:0.20, T:0.32
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:901276 original size:196 final size:198
Alignment explanation
Indices: 900607--901286 Score: 730
Period size: 197 Copynumber: 3.4 Consensus size: 198
900597 ATAGGCATTT
* * * * *
900607 AACCGGTATATTTATACCGG-TAGTATTGCAAATTTACCTATTGCATTATAATTATTAGTTTCGT
1 AACCGGTATATTTATACTGGTTA-CATTGTAAATTTACCTATTACATTATAATTATTAGTTTCGA
* ** *
900671 TGTTTTTTGGATCGATACAATTTTAAATGTATCGACACTTTATGCTTGCACCTCGCTGGGCATTC
65 TGTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCTTGCACCTCG-TTTG---TG
* * * * *
900736 CTAATTCATTCTGGAAAAAAGTATCGACACAAAC-TATAAAGGTGTCGATACATTATTTAGACTT
126 CT--TTCATTATGGAAAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTATTT-GACAT
900800 ATTTTCTCATA
188 ATTTTCTCATA
* * * * *
900811 AAACGGTATATTTATA-TCGGGTACATTGTAAATTTACCTATAACATTGTAATT-TTCGTTTCGA
1 AACCGGTATATTTATACT-GGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTTTCGA
* * * *
900874 TGTTTTTGGGATCGATACAATTTTAAATGTATCGACACGTTATTCTTGCACCTCG-TTGGGCATT
65 TGTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCTTGCACCTCGTTTGTGCTTT
* * * *
900938 CATTATAGACAAAATGTATCGACACAAA-TTACACAAGTGTCGATACTTTATTCTGACCTATTTT
130 CATTATGGA-AAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTATT-TGACATATTTT
901002 CTCATAA
193 CTCAT-A
* * * * * *
901009 AACCGGTAAATTTAAACCGGTTACATTGTAAATTGACCTATTATATTATAATTATCAGTTTCGAT
1 AACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTTTCGAT
* * * *
901074 GTTTTTGTGATCGATAAAATTTTAAATGTATCGACACTTTATGCGTGAACCT-GTTTGTGCTTTC
66 GTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCTTGCACCTCGTTTGTGCTTTC
* * * *
901138 -TTTTGGAAAAAAGTATCGACACAAACTTA-AAAAGTGTCGATGCTTTATGTTGACATGTTTTAT
131 ATTATGGAAAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTAT-TTGACATATTTTCT
* *
901201 AATT
195 CATA
* * * ** *
901205 AACCGGTATATGTATACTGATTACATTGTTAATTTAAATATTACATTATAATTATTTGTTTCGAT
1 AACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTTTCGAT
*
901270 GTTTTTGGGGTCGATAC
66 GTTTTTGGGATCGATAC
901287 TTTTTGAAAA
Statistics
Matches: 396, Mismatches: 69, Indels: 30
0.80 0.14 0.06
Matches are distributed among these distances:
196 76 0.19
197 96 0.24
198 56 0.14
199 63 0.16
201 1 0.00
203 60 0.15
204 42 0.11
205 2 0.01
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.40
Consensus pattern (198 bp):
AACCGGTATATTTATACTGGTTACATTGTAAATTTACCTATTACATTATAATTATTAGTTTCGAT
GTTTTTGGGATCGATACAATTTTAAATGTATCGACACTTTATGCTTGCACCTCGTTTGTGCTTTC
ATTATGGAAAAAAGTATCGACACAAACTTACAAAAGTGTCGATACTTTATTTGACATATTTTCTC
ATA
Found at i:904733 original size:21 final size:21
Alignment explanation
Indices: 904707--904751 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
904697 GATTTCTGGG
*
904707 CAAGGGGAATCGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
904728 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
904749 CAA
1 CAA
904752 AAGAATAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:906062 original size:31 final size:31
Alignment explanation
Indices: 905941--906068 Score: 143
Period size: 31 Copynumber: 4.1 Consensus size: 31
905931 AGAGTCGAGG
905941 GTTTACCTATGTTCTACGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
905972 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* * *
906004 ATATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * *
906035 GTTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
906066 GTT
1 GTT
906069 ACCGAGGATC
Statistics
Matches: 80, Mismatches: 12, Indels: 10
0.78 0.12 0.10
Matches are distributed among these distances:
31 53 0.66
32 27 0.34
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:906088 original size:30 final size:30
Alignment explanation
Indices: 906027--906123 Score: 113
Period size: 30 Copynumber: 3.2 Consensus size: 30
906017 CTAAGGAACA
* * ***
906027 TATGGACAGTTTACCTAGGTTCTTCGGGACC
1 TATGGACAG-TTACCGAGGATCTTTATGACC
906058 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
906088 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
906118 TCTGGA
1 TATGGA
906124 TAGGTCATTC
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
30 50 0.85
31 9 0.15
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:906124 original size:30 final size:30
Alignment explanation
Indices: 906054--906126 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
906044 GGTTCTTCGG
* *
906054 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
906084 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
906114 GACCTCTGGATAG
1 GACCTCTGGATAG
906127 GTCATTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:910454 original size:32 final size:31
Alignment explanation
Indices: 910412--910539 Score: 125
Period size: 31 Copynumber: 4.1 Consensus size: 31
910402 AGAGTCGAGG
* *
910412 GTTTACCTATGTTCTACGGAATATATAGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
*
910443 GTTTTACCTATG-TCTTTC-GAGACATATGGACA
1 G-TTTACCTATGTTC-TACGGA-ACATATGGACA
* *
910475 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
* * * * *
910506 ATTTACCTAGGTTCTTCGGGACCTATGGACA
1 GTTTACCTATGTTCTACGGAACATATGGACA
910537 GTT
1 GTT
910540 ACCGAGGATC
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
31 52 0.67
32 26 0.33
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTACGGAACATATGGACA
Found at i:910533 original size:62 final size:62
Alignment explanation
Indices: 910414--910542 Score: 163
Period size: 62 Copynumber: 2.1 Consensus size: 62
910404 AGTCGAGGGT
* * * *
910414 TTACCTATGTTCTACGGAATATATAGACAGTTTTACCTATGTCTTTCGAGACATATGGACAG
1 TTACCTATGTTCTAAGGAACATATAGACAGATTTACCTAGGTCTTTCGAGACATATGGACAG
* * *
910476 TATACCTATGTTCTAAGGAACATATGGACA-ATTTACCTAGGT-TCTTCGGGACCTATGGACAG
1 T-TACCTATGTTCTAAGGAACATATAGACAGATTTACCTAGGTCT-TTCGAGACATATGGACAG
910538 TTACC
1 TTACC
910543 GAGGATCTTT
Statistics
Matches: 58, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
61 5 0.09
62 28 0.48
63 25 0.43
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (62 bp):
TTACCTATGTTCTAAGGAACATATAGACAGATTTACCTAGGTCTTTCGAGACATATGGACAG
Found at i:910595 original size:30 final size:30
Alignment explanation
Indices: 910525--910597 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
910515 GGTTCTTCGG
* *
910525 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
910555 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
910585 GACCTCTGGATAG
1 GACCTCTGGATAG
910598 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:914468 original size:182 final size:182
Alignment explanation
Indices: 914157--914671 Score: 646
Period size: 182 Copynumber: 2.8 Consensus size: 182
914147 TTGGGGTGTT
* * * * *
914157 ACACTTTTTAAGCGCAATAACTTTTTATCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
1 ACACTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
* * * * *
914222 TATCGACACTTTTAACATATCCGGTAACTTTTTCCGGTTTTGTCATTTTTGAGACCTGTTTTATC
66 TATCGACACTTTCAACATATCCGATAACTTTTTACAGTTTTGTCATTTTTGAGACATGTTTTATC
*
914287 ATATTTTTACCTGTTATATTGGTAAGGATCGATATAT-TTTCATAAAGTGTAG
131 ATATTTTTACCTGTTATATTGGTAAGGATCGATAT-TGTTTCATAAAGTATAG
* * *
914339 ACACTTTGTAGGCGCTATAACTTATTCTCTTTTAAATTCATAAAGTGTCGATACTAATATTAAAT
1 ACACTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
*
914404 TATCGACACTTTCAATATATCCGATAACTTTTTACAGTTTTGTCATTTTTGAGATCAT-TTTTAT
66 TATCGACACTTTCAACATATCCGATAACTTTTTACAGTTTTGTCATTTTTGAGA-CATGTTTTAT
* *** ** *
914468 CATATTTTTACCTGTTATATTGTTGTTGATCGATATTGTTTTTTAAAGTATCG
130 CATATTTTTACCTGTTATATTGGTAAGGATCGATATTGTTTCATAAAGTATAG
* *
914521 ACACTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAATTTCGATACTTATATTAAAT
1 ACACTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
* * * *
914586 TATCGACAC--TCGACACATATCCGGTAGCGTTTTACCGGTTTTGTCA-TTTTGAGAC-TGGTTT
66 TATCGACACTTTC-A-ACATATCCGATAACTTTTTA-CAGTTTTGTCATTTTTGAGACAT-GTTT
* * * *
914647 TGTCATATTTGTAGCTGTAATATTG
127 TATCATATTTTTACCTGTTATATTG
914672 CTATAGAGCG
Statistics
Matches: 291, Mismatches: 35, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
180 3 0.01
181 3 0.01
182 273 0.94
183 12 0.04
ACGTcount: A:0.28, C:0.15, G:0.13, T:0.44
Consensus pattern (182 bp):
ACACTTTATAGGCGCTATAACTTATTCTCTTTTAAATTCAGAAAGTGTCGATACTTATATTAAAT
TATCGACACTTTCAACATATCCGATAACTTTTTACAGTTTTGTCATTTTTGAGACATGTTTTATC
ATATTTTTACCTGTTATATTGGTAAGGATCGATATTGTTTCATAAAGTATAG
Found at i:920338 original size:15 final size:15
Alignment explanation
Indices: 920318--920363 Score: 65
Period size: 15 Copynumber: 3.1 Consensus size: 15
920308 AAATAATTAT
* *
920318 AAAGGAAAAGAGAGG
1 AAAGGAAAAGAAAAG
920333 AAAGGAAAAGAAAAG
1 AAAGGAAAAGAAAAG
*
920348 AAAGGAAAGGAAAAG
1 AAAGGAAAAGAAAAG
920363 A
1 A
920364 TAATTTTTGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGGAAAAGAAAAG
Found at i:920340 original size:5 final size:5
Alignment explanation
Indices: 920318--920360 Score: 50
Period size: 5 Copynumber: 8.6 Consensus size: 5
920308 AAATAATTAT
* * * *
920318 AAAGG AAAAG AGAGG AAAGG AAAAG AAAAG AAAGG AAAGG AAA
1 AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAAGG AAA
920361 AGATAATTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (5 bp):
AAAGG
Found at i:920347 original size:20 final size:20
Alignment explanation
Indices: 920322--920363 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
920312 AATTATAAAG
*
920322 GAAAAGAGAGGAAAGGAAAA
1 GAAAAGAAAGGAAAGGAAAA
920342 GAAAAGAAAGGAAAGGAAAA
1 GAAAAGAAAGGAAAGGAAAA
920362 GA
1 GA
920364 TAATTTTTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (20 bp):
GAAAAGAAAGGAAAGGAAAA
Found at i:922297 original size:25 final size:20
Alignment explanation
Indices: 922239--922290 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
922229 ACGAGAAGGT
*
922239 TTGTTCAACCT-TTTTAGTA
1 TTGTTCAACATGTTTTAGTA
922258 TTGTTCAACATGTTTTAGTA
1 TTGTTCAACATGTTTTAGTA
922278 TTGTTCAACATGT
1 TTGTTCAACATGT
922291 CAGGTTTCAT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 10 0.32
20 21 0.68
ACGTcount: A:0.23, C:0.13, G:0.13, T:0.50
Consensus pattern (20 bp):
TTGTTCAACATGTTTTAGTA
Found at i:945704 original size:23 final size:24
Alignment explanation
Indices: 945678--945727 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 24
945668 CTACTAGGGG
945678 CTATGA-AATTTGTCCCGAAGGAC
1 CTATGACAATTTGTCCCGAAGGAC
*
945701 CTATGACTGTATTTGTCCCGAAGGAC
1 CTATGAC--AATTTGTCCCGAAGGAC
945727 C
1 C
945728 ACTCCTTAAG
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 6 0.26
26 17 0.74
ACGTcount: A:0.26, C:0.24, G:0.22, T:0.28
Consensus pattern (24 bp):
CTATGACAATTTGTCCCGAAGGAC
Found at i:951073 original size:2 final size:2
Alignment explanation
Indices: 951068--951109 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
951058 ATATTCATTC
951068 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
951110 CAAATACACA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:952370 original size:64 final size:64
Alignment explanation
Indices: 952296--952455 Score: 171
Period size: 64 Copynumber: 2.5 Consensus size: 64
952286 TTCCTTTGAA
* *
952296 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACCTTCGATGTTT-TCATTTTAAGGG
1 GTGCATCGATGCACT-CCTCATGCATCGATACACAAATCACATTCGATGTTTCCCATTTTAA-GG
952359 G
64 G
* * * ** * *
952360 GTGCATCGATGCACTCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCCTTTTTAATGG
1 GTGCATCGATGCACTCCTCATGCATCGATACACAAATCACATTCGATGTTTCCCATTTTAAGGG
* * **
952424 GTGCATCGATGCAGTTCTTGTGCATCGATACA
1 GTGCATCGATGCACTCCTCATGCATCGATACA
952456 TACTGAACAA
Statistics
Matches: 81, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
63 2 0.02
64 72 0.89
65 7 0.09
ACGTcount: A:0.23, C:0.24, G:0.20, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTCCTCATGCATCGATACACAAATCACATTCGATGTTTCCCATTTTAAGGG
Found at i:955319 original size:2 final size:2
Alignment explanation
Indices: 955312--955349 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
955302 AAATGAATGA
955312 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
955350 TTACATCTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:956836 original size:24 final size:24
Alignment explanation
Indices: 956809--956861 Score: 106
Period size: 24 Copynumber: 2.2 Consensus size: 24
956799 AGCATAGAGA
956809 AAAAATTGGGGATAATAGTCGCAT
1 AAAAATTGGGGATAATAGTCGCAT
956833 AAAAATTGGGGATAATAGTCGCAT
1 AAAAATTGGGGATAATAGTCGCAT
956857 AAAAA
1 AAAAA
956862 CCTCATAATA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.47, C:0.08, G:0.23, T:0.23
Consensus pattern (24 bp):
AAAAATTGGGGATAATAGTCGCAT
Found at i:957271 original size:23 final size:25
Alignment explanation
Indices: 957218--957277 Score: 70
Period size: 23 Copynumber: 2.4 Consensus size: 25
957208 AAGGAACGTA
*
957218 TCACTAGAACAGAGAAAAAACATGTC
1 TCACAAGAACAGAG-AAAAACATGTC
* *
957244 ACACAAGAACAGAG-AAAA-ATGTG
1 TCACAAGAACAGAGAAAAACATGTC
957267 TCACAAGAACA
1 TCACAAGAACA
957278 TAAATTCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
23 14 0.47
24 4 0.13
26 12 0.40
ACGTcount: A:0.53, C:0.18, G:0.17, T:0.12
Consensus pattern (25 bp):
TCACAAGAACAGAGAAAAACATGTC
Found at i:957503 original size:2 final size:2
Alignment explanation
Indices: 957496--957543 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
957486 ATGAGTATTA
957496 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
957538 AT AT AT
1 AT AT AT
957544 GATCGAAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:959110 original size:2 final size:2
Alignment explanation
Indices: 959103--959136 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
959093 ATGAGTCATA
959103 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
959137 CACAAGACAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:966359 original size:2 final size:2
Alignment explanation
Indices: 966354--966402 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
966344 AGATCACAAC
966354 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
966396 TA TA TA T
1 TA TA TA T
966403 GTAAAATTAA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:967667 original size:66 final size:68
Alignment explanation
Indices: 967579--967711 Score: 182
Period size: 66 Copynumber: 2.0 Consensus size: 68
967569 TAATCATGTA
* *
967579 TAATTATTTTTTTCCTTCAATGGCTACATTATTCAATGCGTCCTTTTCTTT-ATAACATGCTAAA
1 TAATTATTTTTTCCCTTCAATGGCTACATTATTCAATGCGTCCTTTTCTTTAAT-ACATGATAAA
967643 AGAT
65 AGAT
* ** *
967647 TAATTA-TTTTTCCCTT-AATGGCTACATTATTCGATGTTTCTTTTTCTTTAATACATGATAAAA
1 TAATTATTTTTTCCCTTCAATGGCTACATTATTCAATGCGTCCTTTTCTTTAATACATGATAAAA
967710 GA
66 GA
967712 GAAAAACAAC
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
66 41 0.71
67 11 0.19
68 6 0.10
ACGTcount: A:0.29, C:0.16, G:0.09, T:0.47
Consensus pattern (68 bp):
TAATTATTTTTTCCCTTCAATGGCTACATTATTCAATGCGTCCTTTTCTTTAATACATGATAAAA
GAT
Found at i:969013 original size:40 final size:40
Alignment explanation
Indices: 968958--969079 Score: 244
Period size: 40 Copynumber: 3.0 Consensus size: 40
968948 CGACTAGCAG
968958 TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
1 TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
968998 TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
1 TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
969038 TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
1 TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
969078 TA
1 TA
969080 TCTCCTTGGT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 82 1.00
ACGTcount: A:0.33, C:0.10, G:0.27, T:0.30
Consensus pattern (40 bp):
TAGTAGTATGAAAGTGTACAACGTACTTTGTTAGGGGAAC
Found at i:971185 original size:20 final size:21
Alignment explanation
Indices: 971145--971186 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
971135 AACAGAATGT
971145 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
*
971166 CCAGGGGGTACCGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
971187 TGTTTAACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.17, C:0.40, G:0.29, T:0.14
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:983148 original size:2 final size:2
Alignment explanation
Indices: 983141--983182 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
983131 ACTCATAGTC
983141 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
983183 GTGTGTAGAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:983341 original size:40 final size:40
Alignment explanation
Indices: 983231--983356 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
983221 ATATATAGTA
* *
983231 ATATAATATA-TTTTTT-GAAAATGATTTTGAAAA-ATAT
1 ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAATATAT
** * **
983268 A-AT-ATATAGTTTTCAAAAAAACGGTTTCCGAAAATATAT
1 ATATAATATAGTTTTTTAAAAAA-TGTTTTTGAAAATATAT
983307 ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAACT-TAT
1 ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAA-TATAT
*
983347 ATACAATATA
1 ATATAATATA
983357 CAAGTTTTAA
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
35 5 0.07
36 6 0.09
37 5 0.07
38 8 0.12
39 5 0.07
40 23 0.33
41 17 0.25
ACGTcount: A:0.46, C:0.05, G:0.08, T:0.41
Consensus pattern (40 bp):
ATATAATATAGTTTTTTAAAAAATGTTTTTGAAAATATAT
Found at i:983457 original size:73 final size:68
Alignment explanation
Indices: 983361--983569 Score: 230
Period size: 73 Copynumber: 3.0 Consensus size: 68
983351 AATATACAAG
* * *
983361 TTTT-AAAACA-TTTTGAAAGTTATATAATATATGGTTTTGAAATCATTTTGAAAATATAATGTA
1 TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAAATATAAT-TA
983424 TAGT
65 TAGT
*
983428 TTTTAAAAAAACATTTTTGAAAAATTTATATAATATATAGTTTTAAAAACATTTTGAAAA-ACTT
1 TTTT--AAAAACATTTTTG-AAAA-TTATATAATATATAGTTTTGAAAACATTTTGAAAATA--T
983492 ATATTATA-T
60 A-ATTATAGT
* * * *
983501 TTTTAAAATCATTTTTGAAAACTATATAATATATAGTTTTGAAAACATTTT-TAAGTATAATATA
1 TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAAATATAAT-TA
983565 TAGT
65 TAGT
983569 T
1 T
983570 CAAAAAATAT
Statistics
Matches: 121, Mismatches: 9, Indels: 23
0.79 0.06 0.15
Matches are distributed among these distances:
66 2 0.02
67 10 0.08
68 4 0.03
69 29 0.24
70 10 0.08
71 17 0.14
72 4 0.03
73 37 0.31
74 6 0.05
75 2 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.45
Consensus pattern (68 bp):
TTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTGAAAACATTTTGAAAATATAATTAT
AGT
Found at i:983486 original size:108 final size:109
Alignment explanation
Indices: 983297--983545 Score: 276
Period size: 110 Copynumber: 2.3 Consensus size: 109
983287 AACGGTTTCC
* * ** *
983297 GAAAATATATATATAATATAGTTTTTTAAAAAATGTTTTTGAAAACTTATATACAATATACAAGT
1 GAAAACATATA-AT-ATATAGTTTTTAAAAAAACATTTTTGAAAAATTATATACAATATACAAGT
* *
983362 TTTAAAACATTTTG-AAAGTTATATAATATATGGTTTTGAAATCA-TTTT
64 TTTAAAACATTTTGAAAACTTATAT--TATAT--TTTTAAAATCATTTTT
* * *
983410 G-AAA-ATATAATGTATAGTTTTTAAAAAAACATTTTTGAAAAATT-TATATAATATA-TAGTTT
1 GAAAACATATAATATATAGTTTTTAAAAAAACATTTTTGAAAAATTATATACAATATACAAGTTT
983471 TAAAAACATTTTGAAAAACTTATATTATATTTTTAAAATCATTTTT
66 T-AAAACATTTTG-AAAACTTATATTATATTTTTAAAATCATTTTT
*
983517 GAAAACTATATAATATATAGTTTTGAAAA
1 GAAAAC-ATATAATATATAGTTTTTAAAA
983546 CATTTTTAAG
Statistics
Matches: 118, Mismatches: 11, Indels: 17
0.81 0.08 0.12
Matches are distributed among these distances:
106 10 0.08
107 11 0.09
108 29 0.25
109 28 0.24
110 31 0.26
111 5 0.04
112 3 0.03
113 1 0.01
ACGTcount: A:0.45, C:0.04, G:0.08, T:0.43
Consensus pattern (109 bp):
GAAAACATATAATATATAGTTTTTAAAAAAACATTTTTGAAAAATTATATACAATATACAAGTTT
TAAAACATTTTGAAAACTTATATTATATTTTTAAAATCATTTTT
Found at i:983582 original size:31 final size:31
Alignment explanation
Indices: 983525--983583 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
983515 TTGAAAACTA
***
983525 TATAATATATAGTTTTGAAAACATTTTTAAG
1 TATAATATATAGTTCAAAAAACATTTTTAAG
*
983556 TATAATATATAGTTCAAAAAATATTTTT
1 TATAATATATAGTTCAAAAAACATTTTT
983584 TTATATATTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (31 bp):
TATAATATATAGTTCAAAAAACATTTTTAAG
Found at i:1000479 original size:31 final size:30
Alignment explanation
Indices: 1000441--1000500 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 30
1000431 TTATATAAGC
1000441 TATGTGATAAA-GTGATGGAACATGATATGTT
1 TATGTGATAAAGGT-ATGGAA-ATGATATGTT
*
1000472 TATGTGATAAAGGTATGGAAATTATATGT
1 TATGTGATAAAGGTATGGAAATGATATGT
1000501 CTATACAATA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
30 8 0.30
31 17 0.63
32 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.25, T:0.37
Consensus pattern (30 bp):
TATGTGATAAAGGTATGGAAATGATATGTT
Found at i:1005103 original size:60 final size:60
Alignment explanation
Indices: 1005039--1005188 Score: 237
Period size: 60 Copynumber: 2.5 Consensus size: 60
1005029 AACCACTGTA
* *
1005039 TAACTTTTAATAGCCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCGTTATG
1 TAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCATTATG
* * *
1005099 TAACTTTTAATAGTCGAGAGAGTCAACGAAACAACTCCCTATAGTCGGGAGACCATTATG
1 TAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCATTATG
**
1005159 TAACTTTTAATAGTCGAGGGGTTCAACAAA
1 TAACTTTTAATAGTCGAGGGACTCAACAAA
1005189 GCAATATCTT
Statistics
Matches: 81, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
60 81 1.00
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (60 bp):
TAACTTTTAATAGTCGAGGGACTCAACAAAACAACTCCCTATAGTCGGGAGACCATTATG
Found at i:1005605 original size:2 final size:2
Alignment explanation
Indices: 1005598--1005622 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1005588 CCAAGACACT
1005598 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 T
1005623 TTATATCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1012155 original size:22 final size:22
Alignment explanation
Indices: 1012125--1012168 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
1012115 TAAACACCCG
* *
1012125 AAATGCCACTAAAATACCATTA
1 AAATCCCACTAAAACACCATTA
*
1012147 AAATCCCACTCAAACACCATTA
1 AAATCCCACTAAAACACCATTA
1012169 TTCGGGCACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.30, G:0.02, T:0.20
Consensus pattern (22 bp):
AAATCCCACTAAAACACCATTA
Found at i:1018693 original size:14 final size:13
Alignment explanation
Indices: 1018653--1018693 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1018643 ATGGGAAAAT
*
1018653 TTTGAAAACTATG
1 TTTGAAAACAATG
1018666 TTTGAAAACAATG
1 TTTGAAAACAATG
1018679 TTTGAAAATCAATG
1 TTTGAAAA-CAATG
1018693 T
1 T
1018694 GTAGTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1018742 original size:21 final size:20
Alignment explanation
Indices: 1018716--1018755 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
1018706 CAATATAATT
*
1018716 AAATCAAAAACAACAAATTTA
1 AAATC-AAAACAAAAAATTTA
1018737 AAATCAAAACAAAAAATTT
1 AAATCAAAACAAAAAATTT
1018756 TTATTTTGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.20
Consensus pattern (20 bp):
AAATCAAAACAAAAAATTTA
Found at i:1019210 original size:23 final size:23
Alignment explanation
Indices: 1019149--1019210 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
1019139 CAGAACCCGT
*
1019149 GGAGGGTATCGATACCCATTCAA
1 GGAGGGTATCGATACCCATGCAA
* *
1019172 GGATGGTAATTG-TACCCATGCAAA
1 GGAGGGT-ATCGATACCCATGC-AA
1019196 GG-GGGTATCGATACC
1 GGAGGGTATCGATACC
1019211 TAGCACGTAG
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
22 3 0.10
23 21 0.68
24 7 0.23
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.23
Consensus pattern (23 bp):
GGAGGGTATCGATACCCATGCAA
Found at i:1020821 original size:19 final size:19
Alignment explanation
Indices: 1020797--1020842 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
1020787 CTTCTTAGTA
1020797 TAGCCTTGAGCAACAAATC
1 TAGCCTTGAGCAACAAATC
*
1020816 TAGCCTTGAGCAACAAGTC
1 TAGCCTTGAGCAACAAATC
1020835 TAGCCTTG
1 TAGCCTTG
1020843 TTTTTCACTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.24
Consensus pattern (19 bp):
TAGCCTTGAGCAACAAATC
Found at i:1027731 original size:19 final size:19
Alignment explanation
Indices: 1027668--1027726 Score: 64
Period size: 23 Copynumber: 2.8 Consensus size: 19
1027658 ACCCTCATGA
1027668 GGGAACCGATTCCCCCTTTGAAG
1 GGGAACCGATTCCCCC--T--AG
1027691 GGGAACCGATTCCCCCTAG
1 GGGAACCGATTCCCCCTAG
*
1027710 GGGAATCGATATCCCCC
1 GGGAACCGAT-TCCCCC
1027727 CGGGGTTCTG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
19 11 0.32
20 6 0.18
21 1 0.03
23 16 0.47
ACGTcount: A:0.22, C:0.34, G:0.25, T:0.19
Consensus pattern (19 bp):
GGGAACCGATTCCCCCTAG
Found at i:1029195 original size:28 final size:28
Alignment explanation
Indices: 1029158--1029220 Score: 117
Period size: 28 Copynumber: 2.2 Consensus size: 28
1029148 CTAGATGCCG
*
1029158 TCTTTCCTCTAAAGAAACAAATTAATCT
1 TCTTTCCTCTAAAGAAACAAATTAAGCT
1029186 TCTTTCCTCTAAAGAAACAAATTAAGCT
1 TCTTTCCTCTAAAGAAACAAATTAAGCT
1029214 TCTTTCC
1 TCTTTCC
1029221 ACCAGAAGCT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.35, C:0.24, G:0.05, T:0.37
Consensus pattern (28 bp):
TCTTTCCTCTAAAGAAACAAATTAAGCT
Found at i:1031277 original size:22 final size:21
Alignment explanation
Indices: 1031235--1031274 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1031225 AAGACTATTT
1031235 TCATTTTTCAATTTTGAAATA
1 TCATTTTTCAATTTTGAAATA
**
1031256 TCATTTTTGTATTTTGAAA
1 TCATTTTTCAATTTTGAAA
1031275 ATAAAGTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (21 bp):
TCATTTTTCAATTTTGAAATA
Found at i:1035439 original size:14 final size:13
Alignment explanation
Indices: 1035399--1035439 Score: 64
Period size: 13 Copynumber: 3.1 Consensus size: 13
1035389 ATGGGAAAAT
*
1035399 TTTGAAAACTATG
1 TTTGAAAACAATG
1035412 TTTGAAAACAATG
1 TTTGAAAACAATG
1035425 TTTGAAAATCAATG
1 TTTGAAAA-CAATG
1035439 T
1 T
1035440 GTAGTTTTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
13 20 0.77
14 6 0.23
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (13 bp):
TTTGAAAACAATG
Found at i:1036271 original size:15 final size:15
Alignment explanation
Indices: 1036253--1036283 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1036243 TATATATTTC
*
1036253 ATATTCATTAATAAA
1 ATATACATTAATAAA
1036268 ATATACATTAATAAA
1 ATATACATTAATAAA
1036283 A
1 A
1036284 GAAAGGTGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.35
Consensus pattern (15 bp):
ATATACATTAATAAA
Found at i:1039524 original size:19 final size:20
Alignment explanation
Indices: 1039500--1039550 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
1039490 AATGACCAAT
1039500 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATATAC
* *
1039519 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATATAC
1039539 AAAATCGCAACG
1 AAAATCGCAACG
1039551 TTAAAAAGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.43, C:0.24, G:0.18, T:0.16
Consensus pattern (20 bp):
AAAATCGCAACGCGATATAC
Found at i:1039544 original size:20 final size:20
Alignment explanation
Indices: 1039500--1039837 Score: 214
Period size: 20 Copynumber: 16.6 Consensus size: 20
1039490 AATGACCAAT
* *
1039500 AAAATCGCAACGCGATAT-C
1 AAAATCGCAACGCGATTTAG
1039519 AAAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
** ***
1039539 AAAATCGCAACGTTAAAAAG
1 AAAATCGCAACGCGATTTAG
**
1039559 AAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGAT--TTAG
* **
1039579 AAAATCGCAACGCGAGCTTCC
1 AAAATCGCAACGCGA-TTTAG
**
1039600 AAGTTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1039623 AAAATCGCAATGCGATTGAT
1 AAAATCGCAACGCGATTTAG
* * *
1039643 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* * *
1039663 AGAATCGCAATGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1039683 AGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTT---AG
* * *
1039706 AAAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * * *
1039726 AGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTTAG
* * *
1039746 AGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTTAG
* *
1039766 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
* *
1039786 AGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTTAG
*
1039806 AGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTTAG
1039826 AAAATCGCAACG
1 AAAATCGCAACG
1039838 TTAAGTTAAA
Statistics
Matches: 262, Mismatches: 45, Indels: 23
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.06
20 202 0.77
21 14 0.05
23 29 0.11
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.19
Consensus pattern (20 bp):
AAAATCGCAACGCGATTTAG
Found at i:1039678 original size:40 final size:40
Alignment explanation
Indices: 1039604--1039835 Score: 293
Period size: 40 Copynumber: 5.7 Consensus size: 40
1039594 GCTTCCAAGT
*
1039604 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * *
1039647 TCGCAATGCGATTTATAGAATCGCAATGCGATTGAGAGAT
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
1039687 TCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAA
1 TCGCAACGCGATTTAG-AG--AATCGCAATGCGATTGAGAGAA
* * * * *
1039730 TCGCAATGCGACTGAGAGAATCGCAATGCGATTTATAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
* *
1039770 TCGCAACGCGATTGAGAGAATCGCAACGCGATTGAGAGAA
1 TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
*
1039810 TCGCAACGCGATTTAGAAAATCGCAA
1 TCGCAACGCGATTTAGAGAATCGCAA
1039836 CGTTAAGTTA
Statistics
Matches: 165, Mismatches: 21, Indels: 9
0.85 0.11 0.05
Matches are distributed among these distances:
40 112 0.68
41 2 0.01
42 4 0.02
43 47 0.28
ACGTcount: A:0.37, C:0.18, G:0.25, T:0.20
Consensus pattern (40 bp):
TCGCAACGCGATTTAGAGAATCGCAATGCGATTGAGAGAA
Found at i:1039713 original size:83 final size:83
Alignment explanation
Indices: 1039603--1039835 Score: 337
Period size: 83 Copynumber: 2.8 Consensus size: 83
1039593 AGCTTCCAAG
* *
1039603 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTATAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
1039668 CGCAATGCGATTGAGAGA
66 CGCAATGCGATTGAGAGA
* * *
1039686 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAGAGAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
* *
1039751 CGCAATGCGATTTATAGA
66 CGCAATGCGATTGAGAGA
* * * * *
1039769 ATCGCAACGCGA-TT-G-AGAGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAGAAAAT
1 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
1039831 CGCAA
66 CGCAA
1039836 CGTTAAGTTA
Statistics
Matches: 135, Mismatches: 15, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
80 45 0.33
81 1 0.01
82 2 0.01
83 87 0.64
ACGTcount: A:0.36, C:0.18, G:0.25, T:0.21
Consensus pattern (83 bp):
TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGAGAGAATCGCAATGCGATTTAGAGAAT
CGCAATGCGATTGAGAGA
Found at i:1039836 original size:40 final size:40
Alignment explanation
Indices: 1039500--1039837 Score: 265
Period size: 40 Copynumber: 8.3 Consensus size: 40
1039490 AATGACCAAT
*
1039500 AAAATCGCAACGCGATATCA-A-AATCGCAACGCGATTTAG
1 AAAATCGCAACGCGAT-TGAGAGAATCGCAACGCGATTTAG
** *** * **
1039539 AAAATCGCAACGTTAAAAAGAAAATCGCAACG-G-TCAAAAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGAT--TTAG
* *
1039579 AAAATCGCAACGCGAGCTTCCA-AG-TTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGA--TT-GAGAGAATCGCAACGCGATTT---AG
* * * *
1039623 AAAATCGCAATGCGATTGATAGAATCGCAATGCGATTTAT
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* * *
1039663 AGAATCGCAATGCGATTGAGAGATTCGCAACGCGATTTAGAAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTT---AG
* * * * *
1039706 AAAATCGCAATGCGACTGAGAGAATCGCAATGCGACTGAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
* * * * *
1039746 AGAATCGCAATGCGATTTATAGAATCGCAACGCGATTGAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
*
1039786 AGAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
1 AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
1039826 AAAATCGCAACG
1 AAAATCGCAACG
1039838 TTAAGTTAAA
Statistics
Matches: 239, Mismatches: 43, Indels: 33
0.76 0.14 0.10
Matches are distributed among these distances:
38 2 0.01
39 15 0.06
40 143 0.60
41 9 0.04
42 6 0.03
43 48 0.20
44 16 0.07
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.19
Consensus pattern (40 bp):
AAAATCGCAACGCGATTGAGAGAATCGCAACGCGATTTAG
Found at i:1039928 original size:6 final size:6
Alignment explanation
Indices: 1039917--1039973 Score: 114
Period size: 6 Copynumber: 9.5 Consensus size: 6
1039907 GACACGTATT
1039917 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1039965 ACCACG ACC
1 ACCACG ACC
1039974 CGAGACGAGA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 51 1.00
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1040684 original size:6 final size:6
Alignment explanation
Indices: 1040668--1040723 Score: 105
Period size: 6 Copynumber: 9.5 Consensus size: 6
1040658 TCTCGTCTCG
1040668 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1040715 GGTCGT GGT
1 GGTCGT GGT
1040724 AATACGTGTC
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
5 5 0.10
6 45 0.90
ACGTcount: A:0.00, C:0.16, G:0.52, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:1040826 original size:20 final size:20
Alignment explanation
Indices: 1040801--1040844 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
1040791 TTTTTAACTA
*
1040801 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
1040821 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
1040841 TTCT
1 TTCT
1040845 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:1040854 original size:20 final size:20
Alignment explanation
Indices: 1040831--1041084 Score: 292
Period size: 20 Copynumber: 12.4 Consensus size: 20
1040821 TTCTTTTTAA
* *
1040831 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTCTCTCAATCG
1040851 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
* * *
1040871 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTCAATCG
1040891 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
1040911 CGTTGCGATTCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
*
1040931 CGTTGCGATTCTCTCAGTCG
1 CGTTGCGATTCTCTCAATCG
* *
1040951 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTCAATCG
*
1040974 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTCTCTCAATCG
* * *
1040994 CATTGCGATTCTATAAATCG
1 CGTTGCGATTCTCTCAATCG
* *
1041014 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
1041034 CATTGCGATTCTATCAATCG
1 CGTTGCGATTCTCTCAATCG
* *
1041054 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TTC-TCTCAATCG
1041077 CGTTGCGA
1 CGTTGCGA
1041085 ACTTGGAAGC
Statistics
Matches: 205, Mismatches: 23, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
20 169 0.82
21 2 0.01
22 6 0.03
23 28 0.14
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (20 bp):
CGTTGCGATTCTCTCAATCG
Found at i:1040877 original size:40 final size:40
Alignment explanation
Indices: 1040833--1041063 Score: 327
Period size: 40 Copynumber: 5.7 Consensus size: 40
1040823 CTTTTTAACG
* *
1040833 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCA
*
1040873 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCG
1 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCA
* * *
1040913 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCA
* *
1040953 TTGCGATTTTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
1 TTGCGA--TTC-TATAAATCGCGTTGCGATTCTCTCAATCGCA
* *
1040996 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCA
* *
1041036 TTGCGATTCTATCAATCGCATTGCGATT
1 TTGCGATTCTATAAATCGCGTTGCGATT
1041064 TTCTTCTAAA
Statistics
Matches: 173, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
40 133 0.77
41 3 0.02
42 3 0.02
43 34 0.20
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (40 bp):
TTGCGATTCTATAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:1041005 original size:103 final size:103
Alignment explanation
Indices: 1040831--1041085 Score: 345
Period size: 103 Copynumber: 2.5 Consensus size: 103
1040821 TTCTTTTTAA
* * * * * * *
1040831 CGTTGCGATTTTCTAAATCGCGTTGCGA--TTC-TCTCAATCGCATTGCGATTCTATAAATCGCG
1 CGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTATAAATCGCA
* * * *
1040893 TTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAATCG
66 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
* * *
1040931 CGTTGCGATTCTCTCAGTCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
1 CGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTATAAATCGCA
1040996 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
66 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
* *
1041034 CATTGCGATTCTATCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAA
1 CGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAA
1041086 CTTGGAAGCT
Statistics
Matches: 135, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
100 24 0.18
102 3 0.02
103 108 0.80
ACGTcount: A:0.21, C:0.25, G:0.18, T:0.36
Consensus pattern (103 bp):
CGTTGCGATTCTCTCAATCGCATTGCGATTTTCTTCTAAATCGCGTTGCGAATCTATAAATCGCA
TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCG
Found at i:1041031 original size:123 final size:123
Alignment explanation
Indices: 1040841--1041063 Score: 392
Period size: 123 Copynumber: 1.8 Consensus size: 123
1040831 CGTTGCGATT
* * *
1040841 TTCTAAATCGCGTTGCGATTCTCTCAATCGCATTGCGATTCTATAAATCGCGTTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
* * *
1040906 AATCGCGTTGCGATTCTCTCAATCGCGTTGCGATTCTCTCAGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
1040964 TTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1041029 AATCGCATTGCGATTCTATCAATCGCATTGCGATT
66 AATCGCATTGCGATTCTATCAATCGCATTGCGATT
1041064 TTCTTCTAAA
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
123 94 1.00
ACGTcount: A:0.21, C:0.26, G:0.17, T:0.36
Consensus pattern (123 bp):
TTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTCTATCAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTTTC
Found at i:1041123 original size:20 final size:20
Alignment explanation
Indices: 1041098--1041171 Score: 123
Period size: 20 Copynumber: 3.7 Consensus size: 20
1041088 TGGAAGCTCG
1041098 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
1041118 CGTTGCGATTTTCTTTTGAC
1 CGTTGCGATTTTCTTTTGAC
*
1041138 CGTTGCGATTTTCTTTTTTA-
1 CGTTGCGATTTTC-TTTTGAC
1041158 CGTTGCGATTTTCT
1 CGTTGCGATTTTCT
1041172 AAATCGCAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
19 1 0.02
20 46 0.88
21 5 0.10
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
CGTTGCGATTTTCTTTTGAC
Found at i:1043102 original size:21 final size:21
Alignment explanation
Indices: 1043048--1043120 Score: 78
Period size: 21 Copynumber: 3.5 Consensus size: 21
1043038 ACCCGATTTG
1043048 AAATAATATATTTATTAA-AA
1 AAATAATATATTTATTAATAA
* *
1043068 AAATATTATTTTTATTTAATAA
1 AAATAATATATTTA-TTAATAA
*
1043090 AAATAATA-ATTTAATAAATAA
1 AAATAATATATTT-ATTAATAA
*
1043111 TAATAATATA
1 AAATAATATA
1043121 GAGAGAGACA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
20 12 0.28
21 20 0.47
22 11 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (21 bp):
AAATAATATATTTATTAATAA
Found at i:1043114 original size:18 final size:17
Alignment explanation
Indices: 1043081--1043117 Score: 65
Period size: 17 Copynumber: 2.1 Consensus size: 17
1043071 TATTATTTTT
1043081 ATTTAATAAAAATAATA
1 ATTTAATAAAAATAATA
1043098 ATTTAATAAATAATAATA
1 ATTTAATAAA-AATAATA
1043116 AT
1 AT
1043118 ATAGAGAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATTTAATAAAAATAATA
Done.