Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005983.1 Hibiscus syriacus cultivar Beakdansim tig00014064_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: 781742
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 5
Found at i:386624 original size:19 final size:19
Alignment explanation
Indices: 386600--386647 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
386590 AACTAAATCG
386600 CAATGCGATCGATAATTCA
1 CAATGCGATCGATAATTCA
*
386619 CAATGCGATCGATAATTCG
1 CAATGCGATCGATAATTCA
*
386638 CAACGCGATC
1 CAATGCGATC
386648 TTCGGTATCG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.33, C:0.25, G:0.19, T:0.23
Consensus pattern (19 bp):
CAATGCGATCGATAATTCA
Found at i:386700 original size:21 final size:21
Alignment explanation
Indices: 386675--386722 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
386665 GTTTTCAGAT
* *
386675 TCGCAACGCGAATTTCGACTA
1 TCGCAACGCGAACTTAGACTA
* *
386696 TCGCAATGTGAACTTAGACTA
1 TCGCAACGCGAACTTAGACTA
386717 TCGCAA
1 TCGCAA
386723 TGCAAATATG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.25, G:0.19, T:0.25
Consensus pattern (21 bp):
TCGCAACGCGAACTTAGACTA
Found at i:386740 original size:41 final size:39
Alignment explanation
Indices: 386695--386919 Score: 164
Period size: 41 Copynumber: 5.3 Consensus size: 39
386685 AATTTCGACT
* *
386695 ATCGCAATGTGAACTTAGACTATCGCAATGCAAATATGTAA
1 ATCGCAATGCGAA--TAGACTATCGCAATGCGAATATGTAA
*
386736 ATCGCAATGCGAATATGTA-AATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATA-G-ACTATCGCAATGCGAATATGTAA
* *
386776 ATCGCAATACGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-A-TAGACTATCGCAATGCGAATATGTAA
* * * *
386817 ATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGATGCGAATATGTAA
1 ATCGCAATGCGA-A-T---AG-AC-TA-T-CG-CA-ATGCGAATATGTAA
* *
386867 ATCGTAATGCGATAGTCGACTATCGCAATGCGAATATGTAA
1 ATCGCAATGCGA-A-TAGACTATCGCAATGCGAATATGTAA
*
386908 ATCGCATTGCGA
1 ATCGCAATGCGA
386920 TAGTCGAAGT
Statistics
Matches: 150, Mismatches: 20, Indels: 28
0.76 0.10 0.14
Matches are distributed among these distances:
39 2 0.01
40 32 0.21
41 73 0.49
42 2 0.01
43 2 0.01
44 2 0.01
45 2 0.01
46 2 0.01
47 2 0.01
48 2 0.01
49 1 0.01
50 28 0.19
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.26
Consensus pattern (39 bp):
ATCGCAATGCGAATAGACTATCGCAATGCGAATATGTAA
Found at i:386741 original size:20 final size:20
Alignment explanation
Indices: 386716--386828 Score: 149
Period size: 20 Copynumber: 5.6 Consensus size: 20
386706 AACTTAGACT
*
386716 ATCGCAATGCAAATATGTAA
1 ATCGCAATGCGAATATGTAA
386736 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
386756 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
* *
386776 ATCGCAATACG-ATA-GTCGACT
1 ATCGCAATGCGAATATGT--A-A
386797 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
386817 ATCGCATTGCGA
1 ATCGCAATGCGA
386829 TAGTCGAAGT
Statistics
Matches: 82, Mismatches: 6, Indels: 10
0.84 0.06 0.10
Matches are distributed among these distances:
18 2 0.02
19 3 0.04
20 61 0.74
21 11 0.13
22 3 0.04
23 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:386843 original size:21 final size:21
Alignment explanation
Indices: 386818--386962 Score: 91
Period size: 21 Copynumber: 6.6 Consensus size: 21
386808 AATATGTAAA
386818 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
386839 TCGCATTGCGATAGATGCGAATATGT
1 TCGCATTGCGATAG-T-CG-A-A-GT
* * *
386865 AAATCGTAATGCGATAGTCG-ACT
1 ---TCGCATTGCGATAGTCGAAGT
* *
386888 ATCGCAATGCGAATA-T-GTAA-A
1 -TCGCATTGCG-ATAGTCG-AAGT
386909 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCGAAGT
* *
386930 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCGAAGT
*
386951 TCGCGTTGCGAT
1 TCGCATTGCGAT
386963 TTATTCAAAA
Statistics
Matches: 101, Mismatches: 9, Indels: 28
0.73 0.07 0.20
Matches are distributed among these distances:
19 3 0.03
20 13 0.13
21 57 0.56
22 5 0.05
23 3 0.03
24 2 0.02
25 1 0.01
26 2 0.02
27 2 0.02
28 1 0.01
29 12 0.12
ACGTcount: A:0.27, C:0.19, G:0.26, T:0.28
Consensus pattern (21 bp):
TCGCATTGCGATAGTCGAAGT
Found at i:386878 original size:50 final size:50
Alignment explanation
Indices: 386803--386943 Score: 174
Period size: 41 Copynumber: 3.0 Consensus size: 50
386793 GACTATCGCA
386803 ATGCGAATATGTAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAG
1 ATGCGAATATGTAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAG
* * * *
386853 ATGCGAATATGTAAATCGTAATGCGATAGTCG-A---C-TA-T-CG-CA-
1 ATGCGAATATGTAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAG
*
386894 ATGCGAATATGTAAATCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAG
1 ATGCGAATATGTAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAG
386944 TCCAAGTTCG
Statistics
Matches: 73, Mismatches: 9, Indels: 18
0.73 0.09 0.18
Matches are distributed among these distances:
41 30 0.41
42 2 0.03
43 2 0.03
44 1 0.01
45 2 0.03
46 1 0.01
47 1 0.01
48 2 0.03
49 2 0.03
50 30 0.41
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (50 bp):
ATGCGAATATGTAAATCGCATTGCGATAGTCGAAGTTCGCATTGCGATAG
Found at i:386913 original size:20 final size:20
Alignment explanation
Indices: 386853--386919 Score: 66
Period size: 20 Copynumber: 3.3 Consensus size: 20
386843 ATTGCGATAG
*
386853 ATGCGAATATGTAAATCGTA
1 ATGCGAATATGTAAATCGCA
*
386873 ATGCG-ATA-GTCGACTATCGCA
1 ATGCGAATATGT--A-AATCGCA
386894 ATGCGAATATGTAAATCGCA
1 ATGCGAATATGTAAATCGCA
*
386914 TTGCGA
1 ATGCGA
386920 TAGTCGAAGT
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
18 2 0.05
19 3 0.08
20 17 0.45
21 11 0.29
22 3 0.08
23 2 0.05
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (20 bp):
ATGCGAATATGTAAATCGCA
Found at i:386917 original size:91 final size:91
Alignment explanation
Indices: 386762--386943 Score: 337
Period size: 91 Copynumber: 2.0 Consensus size: 91
386752 GTAAATCGCA
386762 ATGCGAATATGTAAATCGCAATACGATAGTCGACTATCGCAATGCGAATATGTAAATCGCATTGC
1 ATGCGAATATGTAAATCGCAATACGATAGTCGACTATCGCAATGCGAATATGTAAATCGCATTGC
386827 GATAGTCGAAGTTCGCATTGCGATAG
66 GATAGTCGAAGTTCGCATTGCGATAG
* *
386853 ATGCGAATATGTAAATCGTAATGCGATAGTCGACTATCGCAATGCGAATATGTAAATCGCATTGC
1 ATGCGAATATGTAAATCGCAATACGATAGTCGACTATCGCAATGCGAATATGTAAATCGCATTGC
*
386918 GATAGTCGAAGTTCGCGTTGCGATAG
66 GATAGTCGAAGTTCGCATTGCGATAG
386944 TCCAAGTTCG
Statistics
Matches: 88, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
91 88 1.00
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (91 bp):
ATGCGAATATGTAAATCGCAATACGATAGTCGACTATCGCAATGCGAATATGTAAATCGCATTGC
GATAGTCGAAGTTCGCATTGCGATAG
Found at i:388812 original size:22 final size:21
Alignment explanation
Indices: 388779--388820 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
388769 AACTTATAAC
*
388779 TTATTTTAAAATACATTAATT
1 TTATGTTAAAATACATTAATT
*
388800 TTATGTTATAAATATATTAAT
1 TTATGTTA-AAATACATTAAT
388821 ATAGGAATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.52
Consensus pattern (21 bp):
TTATGTTAAAATACATTAATT
Found at i:414568 original size:177 final size:178
Alignment explanation
Indices: 414272--414627 Score: 696
Period size: 177 Copynumber: 2.0 Consensus size: 178
414262 TAGGTTCCGG
414272 ATGGTAGTGAGAGTTGCAGGTAAAGTCCCCGTCAATGCATTATCGGAGAGGTTAAGGAATCGGAG
1 ATGGTAGTGAGAGTTGCAGGTAAAGTCCCCGTCAATGCATTATCGGAGAGGTTAAGGAATCGGAG
414337 ATTTCTCAACCGTCCTATTGTTTCCGGTATAAACCCAGAAATGGAATTGTTAGACAAATCAA-CG
66 ATTTCTCAACCGTCCTATTGTTTCCGGTATAAACCCAGAAATGGAATTGTTAGACAAATCAAGCG
414401 ACCGAAGCTGTGTTGCATTGAAAAATGAAAGAGGAAGAGACCCGTTGA
131 ACCGAAGCTGTGTTGCATTGAAAAATGAAAGAGGAAGAGACCCGTTGA
414449 ATGGTAGTGAGAGTTGCAGGTAAAGTCCCCGTCAATGCATTATCGGAGAGGTTAAGGAATCGGAG
1 ATGGTAGTGAGAGTTGCAGGTAAAGTCCCCGTCAATGCATTATCGGAGAGGTTAAGGAATCGGAG
414514 ATTTCTCAACCGTCCTATTGTTTCCGGTATAAACCCAGAAATGGAATTGTTAGACAAATCAAGCG
66 ATTTCTCAACCGTCCTATTGTTTCCGGTATAAACCCAGAAATGGAATTGTTAGACAAATCAAGCG
*
414579 ACCGAAGCTGTGTTGCATTGAAAATTGAAAGAGGAAGAGACCCGTTGA
131 ACCGAAGCTGTGTTGCATTGAAAAATGAAAGAGGAAGAGACCCGTTGA
414627 A
1 A
414628 GGAATTATTG
Statistics
Matches: 177, Mismatches: 1, Indels: 1
0.99 0.01 0.01
Matches are distributed among these distances:
177 127 0.72
178 50 0.28
ACGTcount: A:0.33, C:0.17, G:0.26, T:0.24
Consensus pattern (178 bp):
ATGGTAGTGAGAGTTGCAGGTAAAGTCCCCGTCAATGCATTATCGGAGAGGTTAAGGAATCGGAG
ATTTCTCAACCGTCCTATTGTTTCCGGTATAAACCCAGAAATGGAATTGTTAGACAAATCAAGCG
ACCGAAGCTGTGTTGCATTGAAAAATGAAAGAGGAAGAGACCCGTTGA
Found at i:446733 original size:22 final size:22
Alignment explanation
Indices: 446708--446766 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
446698 TAATAAAATT
446708 ACATTTATAATTATAATAATAA
1 ACATTTATAATTATAATAATAA
* * *
446730 ACATGTATATTTGTAATAATAA
1 ACATTTATAATTATAATAATAA
*
446752 ACATGTAATAATTAT
1 ACAT-TTATAATTAT
446767 TCAATTTTAC
Statistics
Matches: 29, Mismatches: 7, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
22 23 0.79
23 6 0.21
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (22 bp):
ACATTTATAATTATAATAATAA
Found at i:447082 original size:23 final size:22
Alignment explanation
Indices: 447051--447112 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
447041 CAAACAATCG
*
447051 AAAACGTGACATAAATGTA-AAAA
1 AAAATGTGACATAAA-G-ACAAAA
*
447074 AAAATGTGATATAAAGACAAAA
1 AAAATGTGACATAAAGACAAAA
*
447096 AAAATGTGTCATGAAAG
1 AAAATGTGACAT-AAAG
447113 CATAGCTGTT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 1 0.03
22 15 0.45
23 17 0.52
ACGTcount: A:0.58, C:0.06, G:0.16, T:0.19
Consensus pattern (22 bp):
AAAATGTGACATAAAGACAAAA
Found at i:448409 original size:17 final size:17
Alignment explanation
Indices: 448387--448420 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
448377 GAATAATCAC
448387 ATTGTATTTGAAACAAG
1 ATTGTATTTGAAACAAG
448404 ATTGTATTTGAAACAAG
1 ATTGTATTTGAAACAAG
448421 TGTTGGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.06, G:0.18, T:0.35
Consensus pattern (17 bp):
ATTGTATTTGAAACAAG
Found at i:448578 original size:6 final size:6
Alignment explanation
Indices: 448559--448596 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
448549 GTCCGTCTCG
*
448559 GGTCG- GGTCAT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
448597 AATACGTGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
5 4 0.13
6 26 0.87
ACGTcount: A:0.03, C:0.16, G:0.50, T:0.32
Consensus pattern (6 bp):
GGTCGT
Found at i:448737 original size:22 final size:22
Alignment explanation
Indices: 448709--448761 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
448699 AATTTGGAAA
448709 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
448731 ATCGCAACGACAACTGTAGACT
1 ATCGCAACGACAACTGTAGACT
*
448753 TTCGCAACG
1 ATCGCAACG
448762 CGAAATGGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (22 bp):
ATCGCAACGACAACTGTAGACT
Found at i:448813 original size:21 final size:21
Alignment explanation
Indices: 448754--448813 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
448744 CTGTAGACTT
*
448754 TCGCAACGCGAAATGGAA-AA
1 TCGCAACGCGAAATGCAACAA
** * *
448774 TCGCAACGCGATTTTCAACTA
1 TCGCAACGCGAAATGCAACAA
*
448795 TCGCAATGCGAAATGCAAC
1 TCGCAACGCGAAATGCAAC
448814 GCGAATTTAC
Statistics
Matches: 30, Mismatches: 9, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
20 14 0.47
21 16 0.53
ACGTcount: A:0.37, C:0.25, G:0.20, T:0.18
Consensus pattern (21 bp):
TCGCAACGCGAAATGCAACAA
Found at i:450328 original size:3 final size:3
Alignment explanation
Indices: 450320--450356 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
450310 TATATATAGA
450320 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
450357 TTAAACCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:454541 original size:37 final size:38
Alignment explanation
Indices: 454475--454577 Score: 145
Period size: 37 Copynumber: 2.7 Consensus size: 38
454465 GTTATTTTCG
* **
454475 AATTCATATTCGATTAAAATATGAATATATTATTGATA
1 AATTCATATTCAATTAAAATACAAATATATTATTGATA
* *
454513 AATTCATATTTAATT-AAATACAAATATATTATTTATA
1 AATTCATATTCAATTAAAATACAAATATATTATTGATA
*
454550 AATTTATATTCAATTAAAATACAAATAT
1 AATTCATATTCAATTAAAATACAAATAT
454578 GCAATTACGA
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
37 32 0.56
38 25 0.44
ACGTcount: A:0.49, C:0.06, G:0.03, T:0.43
Consensus pattern (38 bp):
AATTCATATTCAATTAAAATACAAATATATTATTGATA
Found at i:464897 original size:43 final size:43
Alignment explanation
Indices: 464852--465172 Score: 463
Period size: 43 Copynumber: 7.5 Consensus size: 43
464842 GCACATAACA
* *
464852 AAAGAG-CCTGGGGAAACTGTAAGGCTTACCCTTGCACACATC
1 AAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
* *
464894 AAA-AGAACCT-GGGAAACTGTAAGGCTTACCCTTGCACACAAC
1 AAAGAG-ACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
* *
464936 AAAGAAACCTGGGGGAACTGTAAGGCTTACCCTTGCACATAGC
1 AAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
*
464979 AAAGTGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
1 AAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
*
465022 AAAGGGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
1 AAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
* * *
465065 AAAGGGACCTGGGGG-ACTGTAAGGGTTACCCTTGCACACAAC
1 AAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
* *
465107 AAACG-GACCTGGGGAAACTGTAAGGCCTACCCTTGCACACAGC
1 AAA-GAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
*
465150 AAAGGGACCTGGGGGAACTGTAA
1 AAAGAGACCTGGGGGAACTGTAA
465173 CGGTAATTAA
Statistics
Matches: 256, Mismatches: 16, Indels: 13
0.90 0.06 0.05
Matches are distributed among these distances:
41 2 0.01
42 79 0.31
43 175 0.68
ACGTcount: A:0.31, C:0.25, G:0.27, T:0.17
Consensus pattern (43 bp):
AAAGAGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGC
Found at i:464990 original size:128 final size:127
Alignment explanation
Indices: 464839--465172 Score: 508
Period size: 128 Copynumber: 2.6 Consensus size: 127
464829 AGGTCTTATA
* * * *
464839 CTTGCACATAACAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAAGAACCT
1 CTTGCACATAACAAAGGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
*
464904 -GGGAAACTGTAAGGCTTACCCTTGCACACAACAAAGAAACCTGGGGGAACTGTAAGGCTTACC
65 GGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGAAACCTGGGGG-ACTGTAAGGCTTACC
* *
464967 CTTGCACATAGCAAAGTGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACATAACAAAG-GACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
* ** *
465032 GGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGACTGTAAGGGTTACC
65 GGGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGAAACCTGGGGGACTGTAAGGCTTACC
* *
465095 CTTGCACACAACAAACGGACCTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACATAACAAA-GGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
465160 GGGGGAACTGTAA
65 GGGGGAACTGTAA
465173 CGGTAATTAA
Statistics
Matches: 188, Mismatches: 15, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
128 142 0.76
129 46 0.24
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.17
Consensus pattern (127 bp):
CTTGCACATAACAAAGGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
GGGGAACTGTAAGGCTTACCCTTGCACACAACAAAGAAACCTGGGGGACTGTAAGGCTTACC
Found at i:465128 original size:171 final size:171
Alignment explanation
Indices: 464858--465172 Score: 506
Period size: 171 Copynumber: 1.8 Consensus size: 171
464848 AACAAAAGAG
*
464858 CCTGGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAAGAACCTGGGAAACTGTAAGGCTTAC
1 CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGAAACTGTAAGGCTTAC
* * * *
464923 CCTTGCACACAACAAAGAAACCTGGGGGAACTGTAAGGCTTACCCTTGCACATAGCAAAGTGACC
66 CCTTGCACACAACAAAGAAACCTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGACC
464988 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
131 TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
* * * ** *
465029 CCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTGGGGGACTGTAAGGGTTAC
1 CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGAAACTGTAAGGCTTAC
*
465094 CCTTGCACACAACAAACG-GACCTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGAC
66 CCTTGCACACAACAAA-GAAACCTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGAC
465158 CTGGGGGAACTGTAA
130 CTGGGGGAACTGTAA
465173 CGGTAATTAA
Statistics
Matches: 131, Mismatches: 12, Indels: 2
0.90 0.08 0.01
Matches are distributed among these distances:
171 130 0.99
172 1 0.01
ACGTcount: A:0.30, C:0.25, G:0.27, T:0.17
Consensus pattern (171 bp):
CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGAACCTGGGAAACTGTAAGGCTTAC
CCTTGCACACAACAAAGAAACCTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGACC
TGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGA
Found at i:468010 original size:18 final size:18
Alignment explanation
Indices: 467987--468045 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
467977 ACGGGTCAAT
467987 GGGTTGGGACAACGGGTC
1 GGGTTGGGACAACGGGTC
*
468005 GGGTTGGGTCAACGGGTC
1 GGGTTGGGACAACGGGTC
* *
468023 AGGTCGGGTA-AACGGGTC
1 GGGTTGGG-ACAACGGGTC
468041 GGGTT
1 GGGTT
468046 ATGATCGGTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.15, C:0.15, G:0.49, T:0.20
Consensus pattern (18 bp):
GGGTTGGGACAACGGGTC
Found at i:470008 original size:43 final size:43
Alignment explanation
Indices: 469950--470283 Score: 464
Period size: 43 Copynumber: 7.8 Consensus size: 43
469940 AGGTCTTATA
* *
469950 CTTGCACATAGCAAA-AGAGCCTGGGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGA-CCTGGGGGAACTGTAAGGCTTACC
* *
469993 CTTGCACACATCAAA-AGAACCT-GGGAAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAG-ACCTGGGGGAACTGTAAGGCTTACC
*
470035 CTTGCACACAACTAAAGA-ACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGC-AAAGAGACCTGGGGGAACTGTAAGGCTTACC
* *
470078 CTTGCACATAGCAAAGTGACCTGGGGGAACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
* *
470121 CTTGCACACAGCAAAGGGACCTGGGGGAACTATAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
*
470164 CTTGCACACAGCAAAGGGACCTGGGGG-ACTGTAAGGCTTACC
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
* * *
470206 CTTGCACACAGCAAATG-GACTTGGGGAAACTGTAAGGCCTACC
1 CTTGCACACAGCAAA-GAGACCTGGGGGAACTGTAAGGCTTACC
*
470249 CTTGCACACAGCAAAGGGACCTGGGGGAACTGTAA
1 CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAA
470284 CGGTAATTAA
Statistics
Matches: 267, Mismatches: 16, Indels: 16
0.89 0.05 0.05
Matches are distributed among these distances:
42 77 0.29
43 188 0.70
44 2 0.01
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (43 bp):
CTTGCACACAGCAAAGAGACCTGGGGGAACTGTAAGGCTTACC
Found at i:470042 original size:85 final size:87
Alignment explanation
Indices: 469950--470283 Score: 466
Period size: 85 Copynumber: 3.9 Consensus size: 87
469940 AGGTCTTATA
* * *
469950 CTTGCACATAGCAAAAGAG-CCTGGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAAGAACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGGACC
*
470014 T-GGGAAACTGTAAGGCTTACC
66 TGGGGGAACTGTAAGGCTTACC
* * * *
470035 CTTGCACACAACTAAAGA-ACCTGGGGGAACTGTAAGGCTTACCCTTGCACATAGC-AAAGTGAC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAG-GAC
470098 CTGGGGGAACTGTAAGGCTTACC
65 CTGGGGGAACTGTAAGGCTTACC
* * * *
470121 CTTGCACACAGC-AAAGGGACCTGGGGGAACTATAAGGCTTACCCTTGCACACAGCAAAGGGACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGGACC
470185 TGGGGG-ACTGTAAGGCTTACC
66 TGGGGGAACTGTAAGGCTTACC
* * * *
470206 CTTGCACACAGCAAATG-GACTTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGACC
1 CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGGACC
470270 TGGGGGAACTGTAA
66 TGGGGGAACTGTAA
470284 CGGTAATTAA
Statistics
Matches: 224, Mismatches: 18, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
84 4 0.02
85 132 0.59
86 85 0.38
87 3 0.01
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (87 bp):
CTTGCACACAGCAAAAGAGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAAGGACC
TGGGGGAACTGTAAGGCTTACC
Found at i:470195 original size:128 final size:128
Alignment explanation
Indices: 469950--470279 Score: 495
Period size: 128 Copynumber: 2.6 Consensus size: 128
469940 AGGTCTTATA
* * * *
469950 CTTGCACATAGCAAAAGAGCCTGGGGAAACTGTAAGGCTTACCCTTGCACACATCAAAAGAACCT
1 CTTGCACATAGCAAATGA-CCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
* *
470015 -GGGAAACTGTAAGGCTTACCCTTGCACACAACTAAAGAACCTGGGGGAACTGTAAGGCTTACC
65 GGGGGAACTATAAGGCTTACCCTTGCACACAACTAAAGAACCTGGGGGAACTGTAAGGCTTACC
*
470078 CTTGCACATAGCAAAGTGACCTGGGGGAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACATAGCAAA-TGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
* *
470143 GGGGGAACTATAAGGCTTACCCTTGCACACAGC-AAAGGGACCTGGGGG-ACTGTAAGGCTTACC
65 GGGGGAACTATAAGGCTTACCCTTGCACACAACTAAA-GAACCTGGGGGAACTGTAAGGCTTACC
* * *
470206 CTTGCACACAGCAAATGGACTTGGGGAAACTGTAAGGCCTACCCTTGCACACAGCAAAGGGACCT
1 CTTGCACATAGCAAAT-GACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCT
470271 GGGGGAACT
65 GGGGGAACT
470280 GTAACGGTAA
Statistics
Matches: 185, Mismatches: 13, Indels: 8
0.90 0.06 0.04
Matches are distributed among these distances:
127 1 0.01
128 143 0.77
129 41 0.22
ACGTcount: A:0.31, C:0.25, G:0.26, T:0.18
Consensus pattern (128 bp):
CTTGCACATAGCAAATGACCTGGGGAAACTGTAAGGCTTACCCTTGCACACAGCAAAGGGACCTG
GGGGAACTATAAGGCTTACCCTTGCACACAACTAAAGAACCTGGGGGAACTGTAAGGCTTACC
Found at i:473505 original size:20 final size:20
Alignment explanation
Indices: 473480--473527 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
473470 ACTGAAATTA
*
473480 ATGACGAACGGCGACGATTC
1 ATGACGAACGACGACGATTC
* *
473500 ATGACGAACGACGATGATTT
1 ATGACGAACGACGACGATTC
473520 ATGACGAA
1 ATGACGAA
473528 AGGTTTGATG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (20 bp):
ATGACGAACGACGACGATTC
Found at i:486976 original size:38 final size:38
Alignment explanation
Indices: 486924--486998 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
486914 TCTATAGTGA
*
486924 ATTCTTGAGTTTTAGACAAGGATGAGCACTCCATGGAC
1 ATTCTTGAGCTTTAGACAAGGATGAGCACTCCATGGAC
* *
486962 ATTCTTGAGCTTTAGATAAGGATGAGCACTCGATGGA
1 ATTCTTGAGCTTTAGACAAGGATGAGCACTCCATGGA
486999 GTCGAGTTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.29
Consensus pattern (38 bp):
ATTCTTGAGCTTTAGACAAGGATGAGCACTCCATGGAC
Found at i:487315 original size:91 final size:91
Alignment explanation
Indices: 487160--487342 Score: 357
Period size: 91 Copynumber: 2.0 Consensus size: 91
487150 GAGACAAATA
*
487160 ATAAATTAGATGAGCTTGGTTTGCTATGGTGATTCACATGCACCCTACAATTCTATATCCCTTGT
1 ATAAATTAGATGAGCTTGGCTTGCTATGGTGATTCACATGCACCCTACAATTCTATATCCCTTGT
487225 AACAGTTGTCTCCTCAATTATATTAT
66 AACAGTTGTCTCCTCAATTATATTAT
487251 ATAAATTAGATGAGCTTGGCTTGCTATGGTGATTCACATGCACCCTACAATTCTATATCCCTTGT
1 ATAAATTAGATGAGCTTGGCTTGCTATGGTGATTCACATGCACCCTACAATTCTATATCCCTTGT
487316 AACAGTTGTCTCCTCAATTATATTAT
66 AACAGTTGTCTCCTCAATTATATTAT
487342 A
1 A
487343 CACATTATTC
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
91 91 1.00
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.38
Consensus pattern (91 bp):
ATAAATTAGATGAGCTTGGCTTGCTATGGTGATTCACATGCACCCTACAATTCTATATCCCTTGT
AACAGTTGTCTCCTCAATTATATTAT
Found at i:490148 original size:22 final size:24
Alignment explanation
Indices: 490087--490148 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 24
490077 AAAACTTTTT
490087 TTATA-AAATTTAAAAAATAAAAA
1 TTATATAAATTTAAAAAATAAAAA
** * *
490110 TTATATATTTTTTAAAAA-GAAAA
1 TTATATAAATTTAAAAAATAAAAA
*
490133 -TATATAAATTTCAAAA
1 TTATATAAATTTAAAAA
490149 TATCCTCAAA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
22 13 0.42
23 9 0.29
24 9 0.29
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (24 bp):
TTATATAAATTTAAAAAATAAAAA
Found at i:491567 original size:13 final size:13
Alignment explanation
Indices: 491549--491575 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
491539 GTCCATTTGC
491549 TATTTTTTATTTT
1 TATTTTTTATTTT
491562 TATTTTTTATTTT
1 TATTTTTTATTTT
491575 T
1 T
491576 TTAAGAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TATTTTTTATTTT
Found at i:492609 original size:119 final size:119
Alignment explanation
Indices: 492393--492637 Score: 472
Period size: 119 Copynumber: 2.0 Consensus size: 119
492383 GCTTGTTTCA
492393 TTCCTCCCTGATGAGGTAAACAAGTGCATTCCATGTCATTTTAAGAATAAGCACAACGAGCGACT
1 TTCC-CCCTGATGAGGTAAACAAGTGCATTCCATGTCATTTTAAGAATAAGCACAACGAGCGACT
492458 TACCTTTGAGAACGTTAACCGTGTAAGAAAGCTCTTGCACCCATGAACACACACG
65 TACCTTTGAGAACGTTAACCGTGTAAGAAAGCTCTTGCACCCATGAACACACACG
492513 TTCCCCCTGATGAGGTAAACAAGTGCATTCCATGTCATTTTAAGAATAAGCACAACGAGCGACTT
1 TTCCCCCTGATGAGGTAAACAAGTGCATTCCATGTCATTTTAAGAATAAGCACAACGAGCGACTT
492578 ACCTTTGAGAACGTTAACCGTGTAAGAAAGCTCTTGCACCCATGAACACACACG
66 ACCTTTGAGAACGTTAACCGTGTAAGAAAGCTCTTGCACCCATGAACACACACG
492632 TCTCCC
1 T-TCCC
492638 ACAATTATAA
Statistics
Matches: 124, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
119 116 0.94
120 8 0.06
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (119 bp):
TTCCCCCTGATGAGGTAAACAAGTGCATTCCATGTCATTTTAAGAATAAGCACAACGAGCGACTT
ACCTTTGAGAACGTTAACCGTGTAAGAAAGCTCTTGCACCCATGAACACACACG
Found at i:495855 original size:30 final size:31
Alignment explanation
Indices: 495819--495885 Score: 84
Period size: 30 Copynumber: 2.2 Consensus size: 31
495809 AGTGAACCAG
* *
495819 CGGTTCAAAC-CGGTTTTGCTGGTTTTCAAA
1 CGGTTCAAACTCGGTTTTACCGGTTTTCAAA
* *
495849 CGGTTC-ACCTCGGTTTTACCGGTTTTCAAC
1 CGGTTCAAACTCGGTTTTACCGGTTTTCAAA
495879 CGGTTCA
1 CGGTTCA
495886 TTACCAATCC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.16, C:0.25, G:0.22, T:0.36
Consensus pattern (31 bp):
CGGTTCAAACTCGGTTTTACCGGTTTTCAAA
Found at i:496842 original size:22 final size:22
Alignment explanation
Indices: 496793--496861 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
496783 AGTAGTATTA
* *
496793 AATAAATAATTATAATATTTTTAA
1 AATAAATAA-TATTAT-TTTTTAT
496817 AATAAATAATATTATTTTTTAT
1 AATAAATAATATTATTTTTTAT
* * *
496839 AATACATAATTTTATTTATTAT
1 AATAAATAATATTATTTTTTAT
496861 A
1 A
496862 TTTTATATTT
Statistics
Matches: 40, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
22 26 0.65
23 5 0.12
24 9 0.22
ACGTcount: A:0.48, C:0.01, G:0.00, T:0.51
Consensus pattern (22 bp):
AATAAATAATATTATTTTTTAT
Found at i:498545 original size:51 final size:51
Alignment explanation
Indices: 498457--498572 Score: 135
Period size: 51 Copynumber: 2.3 Consensus size: 51
498447 AGAATTAGAT
* * * * *
498457 TTATTATTTTTATTAGGAATTAAGATCGAGTTAAAACATTAT-TCTTAGTTTA
1 TTATTA-TTTTATTAAGAATTAAGATAGAATCAAAACATTATCT-TTAATTTA
* *
498509 TTATTATTTTATTAAGAATTATGATAGAATCGAAACATTATCTTTAATTTA
1 TTATTATTTTATTAAGAATTAAGATAGAATCAAAACATTATCTTTAATTTA
*
498560 TAATTATTTTATT
1 TTATTATTTTATT
498573 CATTAGTCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
51 48 0.87
52 7 0.13
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (51 bp):
TTATTATTTTATTAAGAATTAAGATAGAATCAAAACATTATCTTTAATTTA
Found at i:500010 original size:44 final size:44
Alignment explanation
Indices: 499947--500034 Score: 176
Period size: 44 Copynumber: 2.0 Consensus size: 44
499937 CATTCAATGA
499947 CGGAAATCGTTGATTAAATGACCACATTATATTTGCTTTTTAAG
1 CGGAAATCGTTGATTAAATGACCACATTATATTTGCTTTTTAAG
499991 CGGAAATCGTTGATTAAATGACCACATTATATTTGCTTTTTAAG
1 CGGAAATCGTTGATTAAATGACCACATTATATTTGCTTTTTAAG
500035 TTGAAGGACG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (44 bp):
CGGAAATCGTTGATTAAATGACCACATTATATTTGCTTTTTAAG
Found at i:504015 original size:29 final size:28
Alignment explanation
Indices: 503961--504015 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 28
503951 ATAATTGATC
503961 ATTTTATATTTTTATTAGTTAAATAAGT
1 ATTTTATATTTTTATTAGTTAAATAAGT
503989 ATTTTATAATATTTTATTA-TTAAATAA
1 ATTTTAT-AT-TTTTATTAGTTAAATAA
504016 CTTAAATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
28 7 0.28
29 10 0.40
30 8 0.32
ACGTcount: A:0.40, C:0.00, G:0.04, T:0.56
Consensus pattern (28 bp):
ATTTTATATTTTTATTAGTTAAATAAGT
Found at i:510457 original size:21 final size:21
Alignment explanation
Indices: 510433--510477 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
510423 GATTTTTGGG
**
510433 CAAGGGGAATTGATACCCATT
1 CAAGGGGAACCGATACCCATT
*
510454 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
510475 CAA
1 CAA
510478 ACGAACAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.27, G:0.22, T:0.18
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:511813 original size:65 final size:65
Alignment explanation
Indices: 511653--511813 Score: 204
Period size: 64 Copynumber: 2.5 Consensus size: 65
511643 TTGTTTAAGG
* * * **
511653 TGCATCGATGCACATGCAGTGCATCGATGCAT--GAATTTAAATAGAAAACATCGAATAGGATTT
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCA-TTAAATAGAAAACATCGAATAGGATTT
511716 A
65 A
*
511717 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATA-CAAACATCGAATAGGATTTA
1 TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
*
511781 TGCATCGATGCAT-GGTGTAGTGCATCGATGCAT
1 TGCATCGATGCATAAG-G-AGTGCATCGATGCAT
511814 ACCTTCATTA
Statistics
Matches: 86, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
63 1 0.01
64 62 0.72
65 22 0.26
66 1 0.01
ACGTcount: A:0.34, C:0.18, G:0.22, T:0.27
Consensus pattern (65 bp):
TGCATCGATGCATAAGGAGTGCATCGATGCATCCCCATTAAATAGAAAACATCGAATAGGATTTA
Found at i:512165 original size:18 final size:18
Alignment explanation
Indices: 512131--512165 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
512121 AAATGGGTAT
* *
512131 ATATGTTATATGTATTGC
1 ATATGTTACATGAATTGC
512149 ATATGTTACATGAATTG
1 ATATGTTACATGAATTG
512166 AATGAATATA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.06, G:0.17, T:0.46
Consensus pattern (18 bp):
ATATGTTACATGAATTGC
Found at i:513615 original size:23 final size:23
Alignment explanation
Indices: 513581--513626 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
513571 CATTATTATA
* *
513581 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTACAATTATACG
*
513604 TGGCACTTCGGTACAATTATACG
1 TGGCACTACGGTACAATTATACG
513627 AGTTGTGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (23 bp):
TGGCACTACGGTACAATTATACG
Found at i:513634 original size:149 final size:149
Alignment explanation
Indices: 513152--513603 Score: 872
Period size: 149 Copynumber: 3.0 Consensus size: 149
513142 GAGTCGAGGG
513152 TTCTACGCGGTCCTTCGGG--ATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
513215 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
513280 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
513299 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
513364 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGATATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
513429 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
513448 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
1 TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
*
513513 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGGGGTCCTTATGGACATTATT
66 TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
513578 ATATGGCACTACGGTGCAA
131 ATATGGCACTACGGTGCAA
513597 TTCTACG
1 TTCTACG
513604 TGGCACTTCG
Statistics
Matches: 300, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
147 19 0.06
149 281 0.94
ACGTcount: A:0.28, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TTCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATGTGTGAAGTCTTGTAAGACACA
TACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATAATATGTGGTCCTTATGGACATTATT
ATATGGCACTACGGTGCAA
Found at i:515530 original size:103 final size:103
Alignment explanation
Indices: 515351--515571 Score: 381
Period size: 103 Copynumber: 2.1 Consensus size: 103
515341 GGGTCTACGC
*
515351 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
1 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
* *
515416 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
515454 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
*
515519 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
515557 GGTCCTT-ATGGACAT
1 GGTCCTTCA-GGACAT
515572 TATTATATGG
Statistics
Matches: 112, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
102 1 0.01
103 111 0.99
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GGTCCTTCAGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAAACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:515613 original size:23 final size:23
Alignment explanation
Indices: 515587--515647 Score: 95
Period size: 23 Copynumber: 2.7 Consensus size: 23
515577 TATGGCATTA
515587 CGGTGCAATTCTACGCGGCACTC
1 CGGTGCAATTCTACGCGGCACTC
* *
515610 CGGTGCAATTCTACGTGGCACTT
1 CGGTGCAATTCTACGCGGCACTC
*
515633 CGGTGCAATTATACG
1 CGGTGCAATTCTACG
515648 AGCTGTGGTG
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.20, C:0.28, G:0.26, T:0.26
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGGCACTC
Found at i:515695 original size:16 final size:17
Alignment explanation
Indices: 515676--515709 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
515666 GTGCACAACC
515676 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
515692 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
515709 T
1 T
515710 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:520523 original size:103 final size:103
Alignment explanation
Indices: 520339--520551 Score: 372
Period size: 103 Copynumber: 2.1 Consensus size: 103
520329 GGGTCTACGC
* *
520339 GGTCCTTCGGGATATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGATACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
* *
520404 CCTTGGCATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
*
520442 GGTCTTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
1 GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
*
520507 CCCTAGTATATGTATATGATTCTTAAGGAATGATATGT
66 CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
520545 GGTCCTT
1 GGTCCTT
520552 ATGGACATTA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 103 1.00
ACGTcount: A:0.26, C:0.13, G:0.24, T:0.38
Consensus pattern (103 bp):
GGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGAT
CCCTAGCATATGTATATGATTCTTAAGGAATGATATGT
Found at i:520601 original size:23 final size:23
Alignment explanation
Indices: 520568--520630 Score: 99
Period size: 23 Copynumber: 2.7 Consensus size: 23
520558 ATTATTATAT
520568 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
520591 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
*
520614 GGCACTTCGGTGCAATT
1 GGCACTACGGTGCAATT
520631 ATACAAGCTG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
23 37 1.00
ACGTcount: A:0.19, C:0.29, G:0.27, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:520683 original size:16 final size:17
Alignment explanation
Indices: 520664--520697 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
520654 GTGCACAACC
520664 TCTATAG-ACTCACATA
1 TCTATAGTACTCACATA
*
520680 TCTATAGTTCTCACATA
1 TCTATAGTACTCACATA
520697 T
1 T
520698 GTACATGGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.32, C:0.24, G:0.06, T:0.38
Consensus pattern (17 bp):
TCTATAGTACTCACATA
Found at i:524808 original size:35 final size:35
Alignment explanation
Indices: 524735--524809 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
524725 CGTCACTAAC
**
524735 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
524770 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
524805 AGTAA
1 AGTAA
524810 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:524967 original size:23 final size:23
Alignment explanation
Indices: 524891--524976 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
524881 ATTCAAGTCA
524891 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* * *
524914 ATGTATCAGATCATAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
*
524938 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
524961 AGGATCATAACAGAAT
1 AGTATCATATCAGAAT
524977 TCAAGTCGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 32 0.62
24 20 0.38
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:526142 original size:18 final size:18
Alignment explanation
Indices: 526121--526156 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
526111 CTTCCATCCG
*
526121 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
526139 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
526157 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:527509 original size:13 final size:13
Alignment explanation
Indices: 527491--527559 Score: 84
Period size: 13 Copynumber: 4.9 Consensus size: 13
527481 CGAGTCAACA
527491 GTCAACGGGTCGG
1 GTCAACGGGTCGG
527504 GTCAACGGGTCGGGTCGG
1 GTCAA-----CGGGTCGG
527522 GTCAACGGGTCGG
1 GTCAACGGGTCGG
527535 GTCAACGGGTCGG
1 GTCAACGGGTCGG
*
527548 GTAAACGGGTCG
1 GTCAACGGGTCG
527560 AGTCGGGTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
13 37 0.74
18 13 0.26
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:527529 original size:31 final size:31
Alignment explanation
Indices: 527491--527549 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
527481 CGAGTCAACA
527491 GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
527522 GTCAACGGGTCGGGTCAACGGGTCGGGT
1 GTCAACGGGTCGGGTCAACGGGTCGGGT
527550 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.17
Consensus pattern (31 bp):
GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
Found at i:527549 original size:18 final size:18
Alignment explanation
Indices: 527496--527537 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
527486 CAACAGTCAA
527496 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
527514 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
527532 CGGGTC
1 CGGGTC
527538 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:527565 original size:31 final size:29
Alignment explanation
Indices: 527499--527567 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 29
527489 CAGTCAACGG
*
527499 GTCGGGTCAACGGGTCGGGTCGGGTCAACGG
1 GTCGGGTCAACGGGTCGGGTCGGGT--ACGA
527530 GTCGGGTCAACGGGTCGGGTAAACGGGT-CGA
1 GTCGGGTCAACGGGTCGGGT---CGGGTACGA
527561 GTCGGGT
1 GTCGGGT
527568 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 29 0.85
34 5 0.15
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.17
Consensus pattern (29 bp):
GTCGGGTCAACGGGTCGGGTCGGGTACGA
Found at i:529610 original size:35 final size:35
Alignment explanation
Indices: 529537--529611 Score: 123
Period size: 35 Copynumber: 2.1 Consensus size: 35
529527 CGTCACTAAC
**
529537 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
529572 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
529607 AGTAA
1 AGTAA
529612 TCTTCCTCCA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.33, C:0.29, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:529769 original size:23 final size:23
Alignment explanation
Indices: 529693--529778 Score: 109
Period size: 23 Copynumber: 3.7 Consensus size: 23
529683 ATTCAAGTCA
529693 AGTATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* * *
529716 ATGTATCAGATCATAATCCATGTC
1 A-GTATCATATCAGAATCCAGGTC
*
529740 AATATCATATCAGAATCCAGGTC
1 AGTATCATATCAGAATCCAGGTC
* *
529763 AGGATCATAACAGAAT
1 AGTATCATATCAGAAT
529779 TCAAGTCGGA
Statistics
Matches: 52, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
23 32 0.62
24 20 0.38
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (23 bp):
AGTATCATATCAGAATCCAGGTC
Found at i:530944 original size:18 final size:18
Alignment explanation
Indices: 530923--530958 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
530913 CTTCCATCCG
*
530923 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
530941 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
530959 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:532290 original size:15 final size:15
Alignment explanation
Indices: 532270--532316 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
532260 GGTCAACTCC
532270 GGTCAACGGTCAACG
1 GGTCAACGGTCAACG
*
532285 GGTCAACAGTCAACG
1 GGTCAACGGTCAACG
*
532300 GGTC--GGGTCAACG
1 GGTCAACGGTCAACG
532313 GGTC
1 GGTC
532317 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
13 11 0.38
15 18 0.62
ACGTcount: A:0.23, C:0.26, G:0.36, T:0.15
Consensus pattern (15 bp):
GGTCAACGGTCAACG
Found at i:532311 original size:13 final size:13
Alignment explanation
Indices: 532293--532361 Score: 84
Period size: 13 Copynumber: 4.9 Consensus size: 13
532283 CGGGTCAACA
532293 GTCAACGGGTCGG
1 GTCAACGGGTCGG
532306 GTCAACGGGTCGGGTCGG
1 GTCAA-----CGGGTCGG
532324 GTCAACGGGTCGG
1 GTCAACGGGTCGG
532337 GTCAACGGGTCGG
1 GTCAACGGGTCGG
*
532350 GTAAACGGGTCG
1 GTCAACGGGTCG
532362 AGTCGGGTTG
Statistics
Matches: 50, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
13 37 0.74
18 13 0.26
ACGTcount: A:0.16, C:0.22, G:0.46, T:0.16
Consensus pattern (13 bp):
GTCAACGGGTCGG
Found at i:532331 original size:31 final size:31
Alignment explanation
Indices: 532293--532351 Score: 118
Period size: 31 Copynumber: 1.9 Consensus size: 31
532283 CGGGTCAACA
532293 GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
1 GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
532324 GTCAACGGGTCGGGTCAACGGGTCGGGT
1 GTCAACGGGTCGGGTCAACGGGTCGGGT
532352 AAACGGGTCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.14, C:0.22, G:0.47, T:0.17
Consensus pattern (31 bp):
GTCAACGGGTCGGGTCAACGGGTCGGGTCGG
Found at i:532351 original size:18 final size:18
Alignment explanation
Indices: 532298--532339 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
532288 CAACAGTCAA
532298 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
532316 CGGGTCGGGTCAACGGGT
1 CGGGTCGGGTCAACGGGT
532334 CGGGTC
1 CGGGTC
532340 AACGGGTCGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.10, C:0.24, G:0.50, T:0.17
Consensus pattern (18 bp):
CGGGTCGGGTCAACGGGT
Found at i:532367 original size:31 final size:29
Alignment explanation
Indices: 532301--532369 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 29
532291 CAGTCAACGG
*
532301 GTCGGGTCAACGGGTCGGGTCGGGTCAACGG
1 GTCGGGTCAACGGGTCGGGTCGGGT--ACGA
532332 GTCGGGTCAACGGGTCGGGTAAACGGGT-CGA
1 GTCGGGTCAACGGGTCGGGT---CGGGTACGA
532363 GTCGGGT
1 GTCGGGT
532370 TGTGACCGGT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
31 29 0.85
34 5 0.15
ACGTcount: A:0.14, C:0.20, G:0.48, T:0.17
Consensus pattern (29 bp):
GTCGGGTCAACGGGTCGGGTCGGGTACGA
Found at i:535071 original size:23 final size:23
Alignment explanation
Indices: 535045--535088 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
535035 ATAGTGAATT
* *
535045 TTTAATATAAAGAATAAAAATGA
1 TTTAATAAAAAAAATAAAAATGA
*
535068 TTTAATAAAAAAAATTAAAAT
1 TTTAATAAAAAAAATAAAAAT
535089 AATGAGTTTG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.05, T:0.32
Consensus pattern (23 bp):
TTTAATAAAAAAAATAAAAATGA
Found at i:538489 original size:7 final size:7
Alignment explanation
Indices: 538477--538507 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
538467 GTCAAAGAAA
538477 GTCAACG
1 GTCAACG
538484 GTCAACG
1 GTCAACG
538491 GTCAACG
1 GTCAACG
538498 GTCAACG
1 GTCAACG
538505 GTC
1 GTC
538508 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:538514 original size:5 final size:5
Alignment explanation
Indices: 538504--538561 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
538494 AACGGTCAAC
* *
538504 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
538553 GGTCG GGTC
1 GGTCG GGTC
538562 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:538525 original size:22 final size:22
Alignment explanation
Indices: 538497--538561 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
538487 AACGGTCAAC
538497 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
538519 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
538541 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
538562 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:538581 original size:19 final size:18
Alignment explanation
Indices: 538558--538636 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
538548 GGTCGGGTCG
538558 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
538576 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
538595 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
538615 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
538634 GGT
1 GGT
538637 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:538615 original size:29 final size:31
Alignment explanation
Indices: 538583--538657 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
538573 ACCGAGTCAG
538583 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
538612 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
538642 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
538658 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:538657 original size:9 final size:9
Alignment explanation
Indices: 538558--538656 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
538548 GGTCGGGTCG
*
538558 GGTCAGACC
1 GGTCAAACC
538567 GGTCAAACC
1 GGTCAAACC
*
538576 GAGTCAGACC
1 G-GTCAAACC
538586 GGTCAAACC
1 GGTCAAACC
*
538595 GGTTCGAACC
1 GG-TCAAACC
*
538605 GGTTGAAACC
1 GG-TCAAACC
538615 GGTCAAACC
1 GGTCAAACC
538624 GGTCAGAACC
1 GGTCA-AACC
*
538634 GGTTGAAAACC
1 GG-T-CAAACC
*
538645 GGTTAAACC
1 GGTCAAACC
538654 GGT
1 GGT
538657 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:545829 original size:7 final size:7
Alignment explanation
Indices: 545817--545847 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
545807 GTCAAAGAAA
545817 GTCAACG
1 GTCAACG
545824 GTCAACG
1 GTCAACG
545831 GTCAACG
1 GTCAACG
545838 GTCAACG
1 GTCAACG
545845 GTC
1 GTC
545848 GGGTCGGGTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:545854 original size:5 final size:5
Alignment explanation
Indices: 545844--545901 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
545834 AACGGTCAAC
* *
545844 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
545893 GGTCG GGTC
1 GGTCG GGTC
545902 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:545865 original size:22 final size:22
Alignment explanation
Indices: 545837--545901 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
545827 AACGGTCAAC
545837 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
545859 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
545881 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
545902 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:545921 original size:19 final size:18
Alignment explanation
Indices: 545898--545976 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
545888 GGTCGGGTCG
545898 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
545916 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
545935 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
545955 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
545974 GGT
1 GGT
545977 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:545955 original size:29 final size:31
Alignment explanation
Indices: 545923--545997 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
545913 ACCGAGTCAG
545923 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
545952 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
545982 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
545998 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:545997 original size:9 final size:9
Alignment explanation
Indices: 545898--545996 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
545888 GGTCGGGTCG
*
545898 GGTCAGACC
1 GGTCAAACC
545907 GGTCAAACC
1 GGTCAAACC
*
545916 GAGTCAGACC
1 G-GTCAAACC
545926 GGTCAAACC
1 GGTCAAACC
*
545935 GGTTCGAACC
1 GG-TCAAACC
*
545945 GGTTGAAACC
1 GG-TCAAACC
545955 GGTCAAACC
1 GGTCAAACC
545964 GGTCAGAACC
1 GGTCA-AACC
*
545974 GGTTGAAAACC
1 GG-T-CAAACC
*
545985 GGTTAAACC
1 GGTCAAACC
545994 GGT
1 GGT
545997 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:547120 original size:32 final size:32
Alignment explanation
Indices: 547060--547120 Score: 86
Period size: 32 Copynumber: 1.9 Consensus size: 32
547050 TATTTTTTTG
*
547060 ACGTCTTGCTTGGGATCTCCCGGCGTCTTCAA
1 ACGTCTTGCTTGGAATCTCCCGGCGTCTTCAA
* * *
547092 ACGTCTTGTTTGGAATCTTCCGGTGTCTT
1 ACGTCTTGCTTGGAATCTCCCGGCGTCTT
547121 GAGAGTGTTG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
32 25 1.00
ACGTcount: A:0.11, C:0.26, G:0.25, T:0.38
Consensus pattern (32 bp):
ACGTCTTGCTTGGAATCTCCCGGCGTCTTCAA
Found at i:547304 original size:22 final size:22
Alignment explanation
Indices: 547261--547305 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
547251 CGAATCTAAC
*
547261 AAATTTTTAAATACTTTCTATA
1 AAATTTTTAAATACTTTATATA
*
547283 AAATTTTTATAA-ATTTTATATA
1 AAATTTTTA-AATACTTTATATA
547305 A
1 A
547306 GTTTACGCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.51
Consensus pattern (22 bp):
AAATTTTTAAATACTTTATATA
Found at i:554215 original size:18 final size:18
Alignment explanation
Indices: 554184--554218 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
554174 GCTGAATATT
* *
554184 TGTCCTGAATGACCACTA
1 TGTCCCGAAGGACCACTA
554202 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
554219 GATAATCCCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.31, G:0.20, T:0.23
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:558491 original size:12 final size:12
Alignment explanation
Indices: 558459--558498 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
558449 TTCAAAGAAA
558459 TTAAAA-TTA-T
1 TTAAAATTTATT
*
558469 TT-AAATCTATT
1 TTAAAATTTATT
558480 TTAAAATTTATT
1 TTAAAATTTATT
558492 TTAAAAT
1 TTAAAAT
558499 ATGGATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:558549 original size:22 final size:22
Alignment explanation
Indices: 558485--558541 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
558475 CTATTTTAAA
** *
558485 ATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAAATATATATTG
558507 ATTTATTTTAAAATATATATTG
1 ATTTATTTTAAAATATATATTG
558529 ATTTATTTTAAAA
1 ATTTATTTTAAAA
558542 AAATTATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.54
Consensus pattern (22 bp):
ATTTATTTTAAAATATATATTG
Found at i:558622 original size:31 final size:31
Alignment explanation
Indices: 558565--558623 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
558555 AGTTGTATGG
* *
558565 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
*
558596 ATTATTTAAATTTCAGTATTGCAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
558624 CTTTTAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:566348 original size:18 final size:19
Alignment explanation
Indices: 566323--566406 Score: 68
Period size: 19 Copynumber: 4.5 Consensus size: 19
566313 AAATTTAGTT
566323 TTTATATTAATTATAATT-
1 TTTATATTAATTATAATTC
* *
566341 TGTATATTATAAATT-TGATT-
1 T-T-TA-TATTAATTATAATTC
**
566361 TTTATATTAATTCCAATTC
1 TTTATATTAATTATAATTC
*
566380 TTTATATTATTTATAATTC
1 TTTATATTAATTATAATTC
566399 -TTATATTA
1 TTTATATTA
566407 TAAATTTTAT
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.13
18 14 0.26
19 18 0.34
20 7 0.13
21 7 0.13
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTATATTAATTATAATTC
Found at i:566420 original size:13 final size:14
Alignment explanation
Indices: 566386--566422 Score: 51
Period size: 13 Copynumber: 2.7 Consensus size: 14
566376 ATTCTTTATA
566386 TTATTTAT-AATTC
1 TTATTTATAAATTC
566399 TTATATTATAAATT-
1 TTAT-TTATAAATTC
566413 TTATTTATAA
1 TTATTTATAA
566423 TCACTAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 10 0.45
14 8 0.36
15 4 0.18
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (14 bp):
TTATTTATAAATTC
Found at i:569376 original size:20 final size:20
Alignment explanation
Indices: 569351--569427 Score: 57
Period size: 22 Copynumber: 3.6 Consensus size: 20
569341 TAAATTATAC
569351 TATATAGTATATATAGTTTT
1 TATATAGTATATATAGTTTT
* * *
569371 TATATATATAATATATAGTGTA
1 TATATA-GT-ATATATAGTTTT
* *
569393 TAAATA-TAAACTATAGTTTAT
1 TATATAGTATA-TATAGTTT-T
569414 ATATATAGTATATA
1 -TATATAGTATATA
569428 CTATATAAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 10
0.69 0.15 0.16
Matches are distributed among these distances:
19 2 0.05
20 14 0.33
21 1 0.02
22 22 0.52
23 3 0.07
ACGTcount: A:0.44, C:0.01, G:0.08, T:0.47
Consensus pattern (20 bp):
TATATAGTATATATAGTTTT
Found at i:569384 original size:22 final size:20
Alignment explanation
Indices: 569345--569427 Score: 78
Period size: 20 Copynumber: 3.9 Consensus size: 20
569335 CATATGTAAA
569345 TTATACTATATAGTATATATAGTTT
1 TTATA-TATATA--ATATATAG--T
569370 TTATATATATAATATATAGT
1 TTATATATATAATATATAGT
* *
569390 GTATAAATATAA-ACTATAGT
1 TTATATATATAATA-TATAGT
*
569410 TTATATATATAGTATATA
1 TTATATATATAATATATA
569428 CTATATAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
19 1 0.02
20 30 0.59
21 1 0.02
22 8 0.16
24 6 0.12
25 5 0.10
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.47
Consensus pattern (20 bp):
TTATATATATAATATATAGT
Found at i:569432 original size:18 final size:18
Alignment explanation
Indices: 569411--569445 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
569401 AACTATAGTT
*
569411 TATATATATAGTATATAC
1 TATATAAATAGTATATAC
*
569429 TATATAAATAGTGTATA
1 TATATAAATAGTATATA
569446 TAGTTCACCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (18 bp):
TATATAAATAGTATATAC
Found at i:569434 original size:20 final size:20
Alignment explanation
Indices: 569371--569449 Score: 63
Period size: 20 Copynumber: 4.0 Consensus size: 20
569361 ATATAGTTTT
* * *
569371 TATATATATAATATATAGTG
1 TATAAATATAGTATATAGTA
* *
569391 TATAAATATA-AACTATAGTT
1 TATAAATATAGTA-TATAGTA
* *
569411 TATATATATAGTATATACTA
1 TATAAATATAGTATATAGTA
569431 TATAAATAGT-GTATATAGT
1 TATAAATA-TAGTATATAGT
569450 TCACCAATGA
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
19 1 0.02
20 44 0.94
21 2 0.04
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.43
Consensus pattern (20 bp):
TATAAATATAGTATATAGTA
Found at i:569448 original size:40 final size:40
Alignment explanation
Indices: 569354--569450 Score: 115
Period size: 40 Copynumber: 2.4 Consensus size: 40
569344 ATTATACTAT
* *
569354 ATAGTATATATAGTTTTTATATATATAATATATAGTGTATAA
1 ATAGTATATATAG--TTTATATATATAATATATACTATATAA
* *
569396 ATA-TAAACTATAGTTTATATATATAGTATATACTATATAA
1 ATAGTATA-TATAGTTTATATATATAATATATACTATATAA
*
569436 ATAGTGTATATAGTT
1 ATAGTATATATAGTT
569451 CACCAATGAA
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
40 34 0.72
41 5 0.11
42 8 0.17
ACGTcount: A:0.43, C:0.02, G:0.09, T:0.45
Consensus pattern (40 bp):
ATAGTATATATAGTTTATATATATAATATATACTATATAA
Found at i:569523 original size:31 final size:32
Alignment explanation
Indices: 569462--569530 Score: 113
Period size: 33 Copynumber: 2.2 Consensus size: 32
569452 ACCAATGAAC
569462 TATATATATAGTTCATATGTAAACTATATAGTT
1 TATATATATAGTTCATATGTAAAC-ATATAGTT
569495 TATATATATAGTTCATATGTAAAC-TATAGTT
1 TATATATATAGTTCATATGTAAACATATAGTT
*
569526 CATAT
1 TATAT
569531 GTAAATATCA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
31 11 0.31
33 24 0.69
ACGTcount: A:0.39, C:0.07, G:0.09, T:0.45
Consensus pattern (32 bp):
TATATATATAGTTCATATGTAAACATATAGTT
Found at i:569524 original size:18 final size:18
Alignment explanation
Indices: 569468--569535 Score: 74
Period size: 18 Copynumber: 3.9 Consensus size: 18
569458 GAACTATATA
569468 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
*
569486 TATATAGTT--TA--TATA-
1 --TATAGTTCATATGTAAAC
569501 TATAGTTCATATGTAAAC
1 TATAGTTCATATGTAAAC
569519 TATAGTTCATATGTAAA
1 TATAGTTCATATGTAAA
569536 TATCAACCTT
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
13 7 0.17
15 2 0.05
16 3 0.07
17 3 0.07
18 19 0.46
20 7 0.17
ACGTcount: A:0.40, C:0.07, G:0.10, T:0.43
Consensus pattern (18 bp):
TATAGTTCATATGTAAAC
Found at i:569565 original size:38 final size:38
Alignment explanation
Indices: 569514--569591 Score: 147
Period size: 38 Copynumber: 2.1 Consensus size: 38
569504 AGTTCATATG
*
569514 TAAACTATAGTTCATATGTAAATATCAACCTTAGTATA
1 TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
569552 TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
1 TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
569590 TA
1 TA
569592 TATTTATATA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (38 bp):
TAAACTATAGTTCATATATAAATATCAACCTTAGTATA
Found at i:569571 original size:18 final size:18
Alignment explanation
Indices: 569468--569573 Score: 73
Period size: 18 Copynumber: 5.9 Consensus size: 18
569458 GAACTATATA
*
569468 TATAGTTCATATGTAAAC
1 TATAGTTCATATATAAAC
569486 TATATAGTT--TATAT--A-
1 --TATAGTTCATATATAAAC
*
569501 TATAGTTCATATGTAAAC
1 TATAGTTCATATATAAAC
*
569519 TATAGTTCATATGTAAA-
1 TATAGTTCATATATAAAC
*
569536 TATCAACCTT-AGTATATAAAC
1 TAT--A-GTTCA-TATATAAAC
569557 TATAGTTCATATATAAA
1 TATAGTTCATATATAAA
569574 TATCAACCTT
Statistics
Matches: 70, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
13 7 0.10
15 4 0.06
16 1 0.01
17 4 0.06
18 31 0.44
19 4 0.06
20 16 0.23
21 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.41
Consensus pattern (18 bp):
TATAGTTCATATATAAAC
Found at i:569589 original size:20 final size:20
Alignment explanation
Indices: 569532--569591 Score: 65
Period size: 20 Copynumber: 3.1 Consensus size: 20
569522 AGTTCATATG
569532 TAAATATCAACCTTAGTATA
1 TAAATATCAACCTTAGTATA
*
569552 TAAACTAT--A-GTTCA-TATA
1 TAAA-TATCAACCTT-AGTATA
569570 TAAATATCAACCTTAGTATA
1 TAAATATCAACCTTAGTATA
569590 TA
1 TA
569592 TATTTATATA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
17 3 0.09
18 10 0.31
19 4 0.12
20 12 0.38
21 3 0.09
ACGTcount: A:0.45, C:0.13, G:0.05, T:0.37
Consensus pattern (20 bp):
TAAATATCAACCTTAGTATA
Found at i:569663 original size:20 final size:21
Alignment explanation
Indices: 569639--569737 Score: 62
Period size: 20 Copynumber: 4.6 Consensus size: 21
569629 TATATATAAT
* *
569639 ATATAAATATAAACTATAGTTT
1 ATATAAATATAAAATATAG-TA
569661 ATATAAATCGTATAAAATATAGT-
1 ATATAAA---TATAAAATATAGTA
*
569684 ATATAAATATAAATTATAGT-
1 ATATAAATATAAAATATAGTA
* **
569704 ATGTAGTTTATATAAATATA--A
1 ATATA-AATATA-AAATATAGTA
569725 ATATAAATATAAA
1 ATATAAATATAAA
569738 CCCTAAACCA
Statistics
Matches: 62, Mismatches: 9, Indels: 15
0.72 0.10 0.17
Matches are distributed among these distances:
19 2 0.03
20 20 0.32
21 8 0.13
22 13 0.21
23 7 0.11
24 1 0.02
25 11 0.18
ACGTcount: A:0.54, C:0.02, G:0.06, T:0.38
Consensus pattern (21 bp):
ATATAAATATAAAATATAGTA
Found at i:569690 original size:23 final size:24
Alignment explanation
Indices: 569646--569691 Score: 67
Period size: 25 Copynumber: 1.9 Consensus size: 24
569636 AATATATAAA
*
569646 TATAAACTATAGTTTATATAAATCG
1 TATAAAATATAG-TTATATAAATCG
569671 TATAAAATATAG-TATATAAAT
1 TATAAAATATAGTTATATAAAT
569692 ATAAATTATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 9 0.45
25 11 0.55
ACGTcount: A:0.50, C:0.04, G:0.07, T:0.39
Consensus pattern (24 bp):
TATAAAATATAGTTATATAAATCG
Found at i:569724 original size:6 final size:6
Alignment explanation
Indices: 569713--569737 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
569703 TATGTAGTTT
569713 ATATAA ATATAA ATATAA ATATAA A
1 ATATAA ATATAA ATATAA ATATAA A
569738 CCCTAAACCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (6 bp):
ATATAA
Found at i:569786 original size:9 final size:9
Alignment explanation
Indices: 569747--569849 Score: 54
Period size: 9 Copynumber: 11.3 Consensus size: 9
569737 ACCCTAAACC
*
569747 ATATATACT
1 ATATATAAT
569756 ATATAT-AT
1 ATATATAAT
569764 ATATATAA-
1 ATATATAAT
569772 ACTATATAAT
1 A-TATATAAT
*
569782 TTATATTAAT
1 ATATA-TAAT
569792 AAACTATATAAT
1 --A-TATATAAT
* *
569804 TTATACAA-
1 ATATATAAT
*
569812 A-ATATATT
1 ATATATAAT
*
569820 ATTTATAATT
1 ATATATAA-T
*
569830 ATACATAAT
1 ATATATAAT
569839 ATATA-AAT
1 ATATATAAT
569847 ATA
1 ATA
569850 AATTGTATAG
Statistics
Matches: 71, Mismatches: 13, Indels: 21
0.68 0.12 0.20
Matches are distributed among these distances:
7 4 0.06
8 15 0.21
9 33 0.46
10 11 0.15
12 4 0.06
13 4 0.06
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (9 bp):
ATATATAAT
Found at i:569793 original size:22 final size:24
Alignment explanation
Indices: 569759--569891 Score: 87
Period size: 26 Copynumber: 5.3 Consensus size: 24
569749 ATATACTATA
569759 TATATATATATAAACTATATAATT
1 TATATATATATAAACTATATAATT
569783 TATAT-TA-ATAAACTATATAATT
1 TATATATATATAAACTATATAATT
* * * *
569805 TATACAAAATATATTA-TTTATAATT
1 TATA-TATATATA-AACTATATAATT
*
569830 ATACATAATATATAAA-TATA-AATT
1 -TATAT-ATATATAAACTATATAATT
*
569854 GTATAGTTTATATATAATTCATATATAATT
1 -TATA---TATATATAA-AC-TATATAATT
569884 TATATATA
1 TATATATA
569892 AACTATGTAG
Statistics
Matches: 84, Mismatches: 12, Indels: 24
0.70 0.10 0.20
Matches are distributed among these distances:
22 19 0.23
23 2 0.02
24 13 0.15
25 15 0.18
26 22 0.26
27 1 0.01
29 8 0.10
30 4 0.05
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.46
Consensus pattern (24 bp):
TATATATATATAAACTATATAATT
Found at i:569870 original size:20 final size:20
Alignment explanation
Indices: 569763--570058 Score: 119
Period size: 20 Copynumber: 14.4 Consensus size: 20
569753 ACTATATATA
* *
569763 TATATATAAACTATATAATT
1 TATATATAAATTATATAGTT
* *
569783 TATATTAATAAACTATATAATT
1 TATA-T-ATAAATTATATAGTT
*
569805 TATACA-AAA-TATATTA-TT
1 TATATATAAATTATA-TAGTT
* *
569823 TATAATTATACA-TA-ATA-TA
1 TAT-A-TATAAATTATATAGTT
* *
569842 TAAATATAAATTGTATAGTT
1 TATATATAAATTATATAGTT
* *
569862 TATATATAATTCATATATAATT
1 TATATATAAAT--TATATAGTT
* *
569884 TATATATAAACTATGTAGTT
1 TATATATAAATTATATAGTT
*
569904 TCTATAT-AATTCA-ATAGTT
1 TATATATAAATT-ATATAGTT
* *
569923 CATATATAAACTATATAGTAT
1 TATATATAAATTATATAGT-T
*
569944 TATAGTTTATACATGGAATATATAGTT
1 TATA---TATA-A---ATTATATAGTT
* * * *
569971 TATACT-T-TA-TACATAATA
1 TATA-TATAAATTATATAGTT
*
569989 TATATATAAACTATATAGTT
1 TATATATAAATTATATAGTT
* *
570009 TATATATATAATACATATACTT
1 TATATATA-AAT-TATATAGTT
*
570031 TATATATAAACTATATAGTT
1 TATATATAAATTATATAGTT
570051 TATATATA
1 TATATATA
570059 TATATTAGTT
Statistics
Matches: 210, Mismatches: 39, Indels: 54
0.69 0.13 0.18
Matches are distributed among these distances:
17 6 0.03
18 22 0.10
19 30 0.14
20 68 0.32
21 13 0.06
22 50 0.24
24 5 0.02
25 2 0.01
27 5 0.02
28 9 0.04
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.45
Consensus pattern (20 bp):
TATATATAAATTATATAGTT
Found at i:569890 original size:13 final size:11
Alignment explanation
Indices: 569855--569892 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
569845 ATATAAATTG
*
569855 TATAGTTTATA
1 TATAATTTATA
*
569866 TATAATTCATA
1 TATAATTTATA
569877 TATAATTTATA
1 TATAATTTATA
569888 TATAA
1 TATAA
569893 ACTATGTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (11 bp):
TATAATTTATA
Found at i:569979 original size:27 final size:26
Alignment explanation
Indices: 569934--569992 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
569924 ATATATAAAC
*
569934 TATATAGTATTATAGTTTATACATGGAA
1 TATATAGTATTATACTTTATACAT--AA
569962 TATATAGT-TTATACTTTATACATAA
1 TATATAGTATTATACTTTATACATAA
569987 TATATA
1 TATATA
569993 TATAAACTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 8 0.27
27 14 0.47
28 8 0.27
ACGTcount: A:0.41, C:0.05, G:0.08, T:0.46
Consensus pattern (26 bp):
TATATAGTATTATACTTTATACATAA
Found at i:569993 original size:2 final size:2
Alignment explanation
Indices: 569986--570063 Score: 50
Period size: 2 Copynumber: 37.0 Consensus size: 2
569976 TTTATACATA
* * *
569986 AT AT AT AT AT AA ACT AT AT AGT TT AT AT AT AT A- AT AC AT AT ACT
1 AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT AT AT A-T
* * *
570030 TT AT AT AT AA ACT AT AT AGT TT AT AT AT AT AT AT
1 AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT
570064 TAGTTGTTTT
Statistics
Matches: 58, Mismatches: 12, Indels: 12
0.71 0.15 0.15
Matches are distributed among these distances:
1 1 0.02
2 52 0.90
3 5 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:570003 original size:22 final size:20
Alignment explanation
Indices: 569987--570060 Score: 62
Period size: 22 Copynumber: 3.5 Consensus size: 20
569977 TTATACATAA
*
569987 TATATATATAAACTATATAGTT
1 TATATATATAAACTATACA--T
570009 TATATATATAATACATATAC-T
1 TATATATATAA-AC-TATACAT
*
570030 T-TATATATAAACTATATAGTT
1 TATATATATAAACTATACA--T
570051 TATATATATA
1 TATATATATA
570061 TATTAGTTGT
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
18 4 0.09
19 2 0.05
20 9 0.20
21 4 0.09
22 19 0.43
23 2 0.05
24 4 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (20 bp):
TATATATATAAACTATACAT
Found at i:570075 original size:42 final size:42
Alignment explanation
Indices: 569962--570060 Score: 145
Period size: 42 Copynumber: 2.5 Consensus size: 42
569952 ATACATGGAA
*
569962 TATATAGTTTATACT-T-T-ATACATA-A-TATATATATAAAC
1 TATATAGTTTATA-TATATAATACATATACTTTATATATAAAC
570000 TATATAGTTTATATATATAATACATATACTTTATATATAAAC
1 TATATAGTTTATATATATAATACATATACTTTATATATAAAC
570042 TATATAGTTTATATATATA
1 TATATAGTTTATATATATA
570061 TATTAGTTGT
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
37 1 0.02
38 14 0.25
39 1 0.02
40 7 0.13
41 1 0.02
42 31 0.56
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.46
Consensus pattern (42 bp):
TATATAGTTTATATATATAATACATATACTTTATATATAAAC
Found at i:570475 original size:216 final size:216
Alignment explanation
Indices: 570088--570480 Score: 696
Period size: 216 Copynumber: 1.8 Consensus size: 216
570078 TTTTCTCAAC
* *
570088 TTATTTCTTATTTCTATTTATTAATTGGCCCATAACTTTTTAAATAAGTATAATTTAGTACTTTT
1 TTATTACTTAATTCTATTTATTAATTGGCCCATAACTTTTTAAATAAGTATAATTTAGTACTTTT
* *
570153 TTGTATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCGTCAATGTGTGTTGT
66 TTATATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGT
*
570218 ATAATTTATTTAAATTTTTATTTGTAATTTCATATTTGTTCAATTTAGTCCTCCAAATTTTATTT
131 ATAATTTATTTAAATTTTTATTTGTAATTTCATACTTGTTCAATTTAGTCCTCCAAATTTTATTT
570283 GCATATGAAATTGATCCATTA
196 GCATATGAAATTGATCCATTA
* **
570304 TTATTACTTAATTCTATTTTTTAATTGGCCCATAACTTTTTAAATGGGTATAATTTAGTACTTTT
1 TTATTACTTAATTCTATTTATTAATTGGCCCATAACTTTTTAAATAAGTATAATTTAGTACTTTT
*
570369 TTATATTAATTTCAACCTCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGT
66 TTATATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGT
*
570434 TTAATTTATTTAAATTTTTATTTGTAATTTCATACTTGTTCAATTTA
131 ATAATTTATTTAAATTTTTATTTGTAATTTCATACTTGTTCAATTTA
570481 ATTTTTAAAT
Statistics
Matches: 167, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
216 167 1.00
ACGTcount: A:0.29, C:0.12, G:0.08, T:0.51
Consensus pattern (216 bp):
TTATTACTTAATTCTATTTATTAATTGGCCCATAACTTTTTAAATAAGTATAATTTAGTACTTTT
TTATATTAATTTCAACATCACAATTTAAAATTATTTCGATTTGATCCCTCATCAATGTGTGTTGT
ATAATTTATTTAAATTTTTATTTGTAATTTCATACTTGTTCAATTTAGTCCTCCAAATTTTATTT
GCATATGAAATTGATCCATTA
Found at i:574222 original size:22 final size:22
Alignment explanation
Indices: 574195--574263 Score: 84
Period size: 26 Copynumber: 3.0 Consensus size: 22
574185 CAACAGTTTG
574195 AAAAATTGATCCTTAATATTTA
1 AAAAATTGATCCTTAATATTTA
* *
574217 AAAAATTTATCGTCTCTTAATGTTTA
1 AAAAATTGA---TC-CTTAATATTTA
574243 AAAAATTGATCCTTAATATTT
1 AAAAATTGATCCTTAATATTT
574264 GAACTTTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
22 17 0.44
23 2 0.05
25 2 0.05
26 18 0.46
ACGTcount: A:0.41, C:0.10, G:0.06, T:0.43
Consensus pattern (22 bp):
AAAAATTGATCCTTAATATTTA
Found at i:578786 original size:80 final size:79
Alignment explanation
Indices: 578654--578848 Score: 266
Period size: 80 Copynumber: 2.4 Consensus size: 79
578644 TGTAAGTCCT
* ** * ** *
578654 TACGGACCTAAGGATATCTTGGGTAAGCCCAAGATATATCCTTAGGTTGGTTCCATTTGCTGTGT
1 TACGGATCTAAGGATGCCTTGGGTAGGCCCAAGGCATATCCTTAGATTGGTTCCATTTGCTGTGT
578719 GCATGAA-GTAACCC
66 GC-TGAAGGTAACCC
*
578733 TACGGATCTAAGGATGCCATTGGGTAGGCCCAAGGCATATCCTTAGATTGGTTCCTTTTGCTGTG
1 TACGGATCTAAGGATGCC-TTGGGTAGGCCCAAGGCATATCCTTAGATTGGTTCCATTTGCTGTG
*
578798 TGCTTAAGGTAACCC
65 TGCTGAAGGTAACCC
*
578813 TACGGATCTAAGGATGTCCTTGGGTAGACCCAAGGC
1 TACGGATCTAAGGATG-CCTTGGGTAGGCCCAAGGC
578849 CCCAAGGTAT
Statistics
Matches: 103, Mismatches: 10, Indels: 5
0.87 0.08 0.04
Matches are distributed among these distances:
79 18 0.17
80 83 0.81
81 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (79 bp):
TACGGATCTAAGGATGCCTTGGGTAGGCCCAAGGCATATCCTTAGATTGGTTCCATTTGCTGTGT
GCTGAAGGTAACCC
Found at i:580662 original size:21 final size:21
Alignment explanation
Indices: 580636--580682 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
580626 GAAATGCCAT
580636 CAGCAAGCTCAGTTACTTGCA
1 CAGCAAGCTCAGTTACTTGCA
580657 CAGCAAGCTCAGTTACTTGCA
1 CAGCAAGCTCAGTTACTTGCA
580678 CAGCA
1 CAGCA
580683 TGTAACAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (21 bp):
CAGCAAGCTCAGTTACTTGCA
Found at i:581508 original size:18 final size:17
Alignment explanation
Indices: 581471--581539 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
581461 GACCGGTCAC
**
581471 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
581488 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
581506 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
581519 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
581536 GACC
1 GACC
581540 GTTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
15 1 0.02
16 1 0.02
17 21 0.47
18 10 0.22
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:581511 original size:13 final size:13
Alignment explanation
Indices: 581493--581529 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
581483 TAGTTGACCC
581493 GACCCGACCCGTT
1 GACCCGACCCGTT
581506 GACCCGACCCGTT
1 GACCCGACCCGTT
581519 GACCCGACCCG
1 GACCCGACCCG
581530 ACCGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:581589 original size:29 final size:29
Alignment explanation
Indices: 581547--581626 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
581537 ACCGTTGACC
* *
581547 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
581576 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
581605 GGTGCTATTCTGGTAAATAATT
1 GGTGCTATTCTGGTAAATAATT
581627 AGAAAAAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:588772 original size:18 final size:17
Alignment explanation
Indices: 588735--588803 Score: 83
Period size: 17 Copynumber: 4.2 Consensus size: 17
588725 GACCGGTCAC
**
588735 GACCCGACCCGATAGTT
1 GACCCGACCCGACCGTT
588752 GACCCGACCCGACCCGTT
1 GACCCGACCCGA-CCGTT
588770 GACCCGA--C--CCGTT
1 GACCCGACCCGACCGTT
588783 GACCCGACCCGACCGTT
1 GACCCGACCCGACCGTT
588800 GACC
1 GACC
588804 GTTGACCGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
13 12 0.27
15 1 0.02
16 1 0.02
17 21 0.47
18 10 0.22
ACGTcount: A:0.19, C:0.45, G:0.23, T:0.13
Consensus pattern (17 bp):
GACCCGACCCGACCGTT
Found at i:588775 original size:13 final size:13
Alignment explanation
Indices: 588757--588793 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
588747 TAGTTGACCC
588757 GACCCGACCCGTT
1 GACCCGACCCGTT
588770 GACCCGACCCGTT
1 GACCCGACCCGTT
588783 GACCCGACCCG
1 GACCCGACCCG
588794 ACCGTTGACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.16, C:0.49, G:0.24, T:0.11
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:588853 original size:29 final size:29
Alignment explanation
Indices: 588811--588890 Score: 142
Period size: 29 Copynumber: 2.8 Consensus size: 29
588801 ACCGTTGACC
* *
588811 GGTGCTATTTTGGTAAATAATTCGGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
588840 GGTGCTATTCTGGTAAATAATTCAGTTTT
1 GGTGCTATTCTGGTAAATAATTCAGTTTT
588869 GGTGCTATTCTGGTAAATAATT
1 GGTGCTATTCTGGTAAATAATT
588891 AGAAAAAGGG
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.24, C:0.09, G:0.23, T:0.45
Consensus pattern (29 bp):
GGTGCTATTCTGGTAAATAATTCAGTTTT
Found at i:593434 original size:92 final size:90
Alignment explanation
Indices: 593288--593463 Score: 291
Period size: 92 Copynumber: 1.9 Consensus size: 90
593278 CCATGATCCC
*
593288 AATGAAAGACCAGCAATTGTACCGCCACTAAAAATCAATAAAAGAATTGTCACTCAGCACTGCTT
1 AATGAAAGACCAGCAATTGTACCGCCACTAAAAATCAATAAAAGAATTGTCACTCAACACTGC--
593353 TTGTCTACGATCTGGAGCCAAACATAA
64 TTGTCTACGATCTGGAGCCAAACATAA
* *
593380 AATGTAAAGACCAGCAATTGTACCGCCACT-AAAATCAATAAAAGAGTTGTCACTCAACATTGCT
1 AATG-AAAGACCAGCAATTGTACCGCCACTAAAAATCAATAAAAGAATTGTCACTCAACACTGCT
593444 TGTCTACGATCTGGAGCCAA
65 TGTCTACGATCTGGAGCCAA
593464 GCCCAAATGA
Statistics
Matches: 80, Mismatches: 3, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
90 21 0.26
92 34 0.43
93 25 0.31
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (90 bp):
AATGAAAGACCAGCAATTGTACCGCCACTAAAAATCAATAAAAGAATTGTCACTCAACACTGCTT
GTCTACGATCTGGAGCCAAACATAA
Found at i:595704 original size:6 final size:7
Alignment explanation
Indices: 595687--595725 Score: 62
Period size: 7 Copynumber: 5.7 Consensus size: 7
595677 ATTTCAAATC
595687 AAAAAGG
1 AAAAAGG
595694 AAAAAGG
1 AAAAAGG
595701 AAAAAGG
1 AAAAAGG
595708 AAAAA-G
1 AAAAAGG
*
595714 AAAAAAG
1 AAAAAGG
595721 AAAAA
1 AAAAA
595726 TTTACCTTCA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.19
7 25 0.81
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (7 bp):
AAAAAGG
Found at i:595706 original size:14 final size:13
Alignment explanation
Indices: 595687--595725 Score: 60
Period size: 13 Copynumber: 2.9 Consensus size: 13
595677 ATTTCAAATC
595687 AAAAAGGAAAAAGG
1 AAAAAGGAAAAA-G
595701 AAAAAGGAAAAAG
1 AAAAAGGAAAAAG
*
595714 AAAAAAGAAAAA
1 AAAAAGGAAAAA
595726 TTTACCTTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (13 bp):
AAAAAGGAAAAAG
Found at i:595711 original size:21 final size:20
Alignment explanation
Indices: 595687--595725 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
595677 ATTTCAAATC
*
595687 AAAAAGGAAAAAGGAAAAAGG
1 AAAAA-GAAAAAAGAAAAAGG
595708 AAAAAGAAAAAAGAAAAA
1 AAAAAGAAAAAAGAAAAA
595726 TTTACCTTCA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (20 bp):
AAAAAGAAAAAAGAAAAAGG
Found at i:596547 original size:18 final size:17
Alignment explanation
Indices: 596513--596550 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
596503 TTATGGAAAA
596513 ATTTATTTAATAAATAT
1 ATTTATTTAATAAATAT
596530 ATTTATTTGAAT--ATAT
1 ATTTATTT-AATAAATAT
596546 ATTTA
1 ATTTA
596551 AATAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 8 0.40
18 3 0.15
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
ATTTATTTAATAAATAT
Found at i:599330 original size:184 final size:184
Alignment explanation
Indices: 599021--599389 Score: 738
Period size: 184 Copynumber: 2.0 Consensus size: 184
599011 TACTTCATAT
599021 AGTTTAAAAAATTATTATTTTTTATATTATTTGAATAATATATTTTTATTTATAGAATATATGAA
1 AGTTTAAAAAATTATTATTTTTTATATTATTTGAATAATATATTTTTATTTATAGAATATATGAA
599086 TTATCGATGATTAAGAAAAAATATAAATAGATACAATCTTATAATCACTTTAATCTATTAAAAAT
66 TTATCGATGATTAAGAAAAAATATAAATAGATACAATCTTATAATCACTTTAATCTATTAAAAAT
599151 ATCTTTATTAAATATAATTATTATCTATACTATATTAAGATTTTTAAATTGTAA
131 ATCTTTATTAAATATAATTATTATCTATACTATATTAAGATTTTTAAATTGTAA
599205 AGTTTAAAAAATTATTATTTTTTATATTATTTGAATAATATATTTTTATTTATAGAATATATGAA
1 AGTTTAAAAAATTATTATTTTTTATATTATTTGAATAATATATTTTTATTTATAGAATATATGAA
599270 TTATCGATGATTAAGAAAAAATATAAATAGATACAATCTTATAATCACTTTAATCTATTAAAAAT
66 TTATCGATGATTAAGAAAAAATATAAATAGATACAATCTTATAATCACTTTAATCTATTAAAAAT
599335 ATCTTTATTAAATATAATTATTATCTATACTATATTAAGATTTTTAAATTGTAA
131 ATCTTTATTAAATATAATTATTATCTATACTATATTAAGATTTTTAAATTGTAA
599389 A
1 A
599390 TGAATTGTTA
Statistics
Matches: 185, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
184 185 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (184 bp):
AGTTTAAAAAATTATTATTTTTTATATTATTTGAATAATATATTTTTATTTATAGAATATATGAA
TTATCGATGATTAAGAAAAAATATAAATAGATACAATCTTATAATCACTTTAATCTATTAAAAAT
ATCTTTATTAAATATAATTATTATCTATACTATATTAAGATTTTTAAATTGTAA
Done.