Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006515.1 Hibiscus syriacus cultivar Beakdansim tig00015870_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: 112678
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4643 original size:19 final size:20
Alignment explanation
Indices: 4604--4642 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4594 CCAGAATGCT
*
4604 AGGGGGGAATCGATACCCCC
1 AGGGGGGAAACGATACCCCC
*
4624 AGGGGGGAAACGATTCCCC
1 AGGGGGGAAACGATACCCC
4643 ATAATAAAAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.28, G:0.36, T:0.10
Consensus pattern (20 bp):
AGGGGGGAAACGATACCCCC
Found at i:5304 original size:102 final size:101
Alignment explanation
Indices: 5107--5321 Score: 387
Period size: 102 Copynumber: 2.1 Consensus size: 101
5097 GTAGAGGGTC
*
5107 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAATATGTGTGAGGTCTGGTGAGACATACTT
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATACTT
5172 GATCCTTGGTATATGTATATGATTCTTAAGGAATGA
66 GATCCTTGGTATATGTATATGATTCTTAAGGAATGA
*
5208 TATGTGGTCCTTCGGGAC-TATATTTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAG--ACATAC
5272 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
64 TTGATCCTTGGTATATGTATATGATTCTTAAGGAATGA
5310 TATGTGGTCCTT
1 TATGTGGTCCTT
5322 ATGGACATTA
Statistics
Matches: 110, Mismatches: 2, Indels: 3
0.96 0.02 0.03
Matches are distributed among these distances:
100 36 0.33
101 18 0.16
102 56 0.51
ACGTcount: A:0.24, C:0.12, G:0.25, T:0.39
Consensus pattern (101 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAGGTCTGGTGAGACATACTT
GATCCTTGGTATATGTATATGATTCTTAAGGAATGA
Found at i:5399 original size:23 final size:22
Alignment explanation
Indices: 5337--5400 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 22
5327 CATTATTACA
5337 TGGCACTACGGTGCAATTCTACG
1 TGGCACTA-GGTGCAATTCTACG
* * *
5360 CGGCACTCGTGTACAATTCTACG
1 TGGCACTAG-GTGCAATTCTACG
5383 TGGCACTTAGGTGCAATT
1 TGGCAC-TAGGTGCAATT
5401 ATATGAGCTG
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
22 1 0.03
23 30 0.91
24 2 0.06
ACGTcount: A:0.22, C:0.25, G:0.25, T:0.28
Consensus pattern (22 bp):
TGGCACTAGGTGCAATTCTACG
Found at i:7643 original size:30 final size:30
Alignment explanation
Indices: 7607--7701 Score: 190
Period size: 30 Copynumber: 3.2 Consensus size: 30
7597 TAATCATGTG
7607 TTTAGTACCTAAATTATCAGATTTGGTTGT
1 TTTAGTACCTAAATTATCAGATTTGGTTGT
7637 TTTAGTACCTAAATTATCAGATTTGGTTGT
1 TTTAGTACCTAAATTATCAGATTTGGTTGT
7667 TTTAGTACCTAAATTATCAGATTTGGTTGT
1 TTTAGTACCTAAATTATCAGATTTGGTTGT
7697 TTTAG
1 TTTAG
7702 CAATTTATTC
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 65 1.00
ACGTcount: A:0.26, C:0.09, G:0.17, T:0.47
Consensus pattern (30 bp):
TTTAGTACCTAAATTATCAGATTTGGTTGT
Found at i:12017 original size:28 final size:28
Alignment explanation
Indices: 11976--12032 Score: 82
Period size: 28 Copynumber: 2.0 Consensus size: 28
11966 AACCCTAAAA
11976 TATGGATTTAGGGTTTAGAT-TTTATGAAT
1 TATGGATTTAGGGTTTA-ATGTTTAT-AAT
12005 TATGG-TTTAGGGTTTAATGTTTATAAT
1 TATGGATTTAGGGTTTAATGTTTATAAT
12032 T
1 T
12033 TAGGGTTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
27 6 0.22
28 16 0.59
29 5 0.19
ACGTcount: A:0.26, C:0.00, G:0.23, T:0.51
Consensus pattern (28 bp):
TATGGATTTAGGGTTTAATGTTTATAAT
Found at i:12039 original size:28 final size:28
Alignment explanation
Indices: 11982--12040 Score: 77
Period size: 28 Copynumber: 2.1 Consensus size: 28
11972 AAAATATGGA
*
11982 TTTAGGGTTTAGATTTTATGAATTATGG
1 TTTAGGGTTTAGATTTTATGAATTAGGG
12010 TTTAGGGTTTA-ATGTTTAT-AATTTAGGG
1 TTTAGGGTTTAGAT-TTTATGAA-TTAGGG
12038 TTT
1 TTT
12041 TAAGTTAGGG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
27 4 0.14
28 24 0.86
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.53
Consensus pattern (28 bp):
TTTAGGGTTTAGATTTTATGAATTAGGG
Found at i:12463 original size:2 final size:2
Alignment explanation
Indices: 12456--12494 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12446 GAGATGAGTT
12456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12495 TTAAGCCAGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:23112 original size:5 final size:5
Alignment explanation
Indices: 23102--23126 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
23092 GCAAGATGCT
23102 TTTTA TTTTA TTTTA TTTTA TTTTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA
23127 AATTTTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTTA
Found at i:33070 original size:19 final size:19
Alignment explanation
Indices: 32974--33082 Score: 83
Period size: 19 Copynumber: 5.4 Consensus size: 19
32964 AACGCGATTT
*
32974 TGAAAAATGTGTTGTGATAG
1 TGAAAAA-GTGTTGCGATAG
* * *
32994 TTAAAATGTGTTGCAATAG
1 TGAAAAAGTGTTGCGATAG
* * **
33013 TTAAAATGTGTTGCGAGCG
1 TGAAAAAGTGTTGCGATAG
33032 TTTGAAAAACGTTTTGTTGCGATAG
1 --TGAAAAA-G---TGTTGCGATAG
33057 TGAAAAAGTGTTGCGATAG
1 TGAAAAAGTGTTGCGATAG
33076 TGAAAAA
1 TGAAAAA
33083 TCCAAAATAA
Statistics
Matches: 72, Mismatches: 11, Indels: 13
0.75 0.11 0.14
Matches are distributed among these distances:
19 44 0.61
20 5 0.07
21 5 0.07
22 2 0.03
23 7 0.10
25 9 0.12
ACGTcount: A:0.35, C:0.06, G:0.27, T:0.33
Consensus pattern (19 bp):
TGAAAAAGTGTTGCGATAG
Found at i:33606 original size:20 final size:20
Alignment explanation
Indices: 33577--33650 Score: 78
Period size: 20 Copynumber: 3.6 Consensus size: 20
33567 ATTTTGTATT
*
33577 ATCGCATTGCGATAGTCAGA
1 ATCGCGTTGCGATAGTCAGA
* * *
33597 ATCGCGTTGCGAT-TTTATA
1 ATCGCGTTGCGATAGTCAGA
33616 TTATCGCGTTGCGATAGTCAGA
1 --ATCGCGTTGCGATAGTCAGA
*
33638 ATCGCGTTACGAT
1 ATCGCGTTGCGAT
33651 TTACATATTC
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
19 3 0.07
20 24 0.56
21 13 0.30
22 3 0.07
ACGTcount: A:0.24, C:0.19, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCGTTGCGATAGTCAGA
Found at i:33612 original size:41 final size:41
Alignment explanation
Indices: 33555--33670 Score: 155
Period size: 41 Copynumber: 2.9 Consensus size: 41
33545 AAATTTGAAA
* * *
33555 AATCGCATTGTGATTTTGTATTATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATTTTATATTATCGCATTGCGATAGTCAG
*
33596 AATCGCGTTGCGATTTTATATTATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATTTTATATTATCGCATTGCGATAGTCAG
* *
33637 AATCGCGTTACGA-TTTACA-TATTCGCATTGCGAT
1 AATCGCGTTGCGATTTTATATTA-TCGCATTGCGAT
33671 TTTCTAAAAT
Statistics
Matches: 67, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
39 2 0.03
40 16 0.24
41 49 0.73
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.37
Consensus pattern (41 bp):
AATCGCGTTGCGATTTTATATTATCGCATTGCGATAGTCAG
Found at i:33690 original size:21 final size:21
Alignment explanation
Indices: 33666--33712 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
33656 TATTCGCATT
*
33666 GCGATTTTCTAAAATCGCAAC
1 GCGATTTTCAAAAATCGCAAC
* * *
33687 GCGAATTTGAAAAATCGCAAT
1 GCGATTTTCAAAAATCGCAAC
33708 GCGAT
1 GCGAT
33713 AGTCTAAATT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.19, G:0.19, T:0.26
Consensus pattern (21 bp):
GCGATTTTCAAAAATCGCAAC
Found at i:38064 original size:53 final size:53
Alignment explanation
Indices: 37949--38067 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 53
37939 TATAATATAG
* * * * * *
37949 TAAAACAATAATTAAAGTAATGATTGAAAATATATTAAAATAATAAAAATTAAGT
1 TAAAAC-ATAACTAAA-CAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
**
38004 TAAAACATAACTAAACAATGATTAAAAATA-AATAAAATAATAAATGTAAAAT
1 TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
*
38056 TATGAACATAAC
1 TA-AAACATAAC
38068 CTGAATCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 19 0.35
53 21 0.39
54 8 0.15
55 6 0.11
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (53 bp):
TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
Found at i:38929 original size:14 final size:15
Alignment explanation
Indices: 38907--38938 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
38897 CTTTTCCTCC
38907 TCTGTTTTTTTTCGT
1 TCTGTTTTTTTTCGT
38922 TCTGTTTTTTTT-GT
1 TCTGTTTTTTTTCGT
38936 TCT
1 TCT
38939 CTGCCGTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (15 bp):
TCTGTTTTTTTTCGT
Found at i:39364 original size:3 final size:3
Alignment explanation
Indices: 39356--39454 Score: 139
Period size: 3 Copynumber: 33.0 Consensus size: 3
39346 TTATTTATTA
*
39356 AAT AAT AAT AAT ATAT AAT AAT AAT -AT AAT ATT AAT AAT AAT AAT
1 AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* *
39401 AAT AAT AAAT AAT TAT AAT TAT AAT AAT AAT AAT -AT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
39446 AAT AAT AAT
1 AAT AAT AAT
39455 TTTAAATGAA
Statistics
Matches: 86, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
2 4 0.05
3 76 0.88
4 6 0.07
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:39977 original size:75 final size:76
Alignment explanation
Indices: 39578--40217 Score: 1198
Period size: 76 Copynumber: 8.5 Consensus size: 76
39568 GATGGAAATG
* *
39578 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGTTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39643 CCCGAAGGCTT
66 CCCGAAGGCTT
*
39654 TTTGAAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATC-AAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39717 CCCGAAGGCTT
66 CCCGAAGGCTT
39728 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39793 CCCGAAGGCTT
66 CCCGAAGGCTT
39804 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39869 CCCGAAGGCTT
66 CCCGAAGGCTT
39880 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
39944 CCCGAAGGCTT
66 CCCGAAGGCTT
39955 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAAGC
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATC-AAAAAGC
*
40020 TCCCGAATGCTT
65 TCCCGAAGGCTT
40032 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTG-AAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
40096 CCCGAAGGCTT
66 CCCGAAGGCTT
40107 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
*
40172 CCCGAATGCTT
66 CCCGAAGGCTT
40183 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
1 TTTGGAAACATCATGCACTGAAGGACTTACAGATG
40218 TGGGAAATAG
Statistics
Matches: 554, Mismatches: 5, Indels: 10
0.97 0.01 0.02
Matches are distributed among these distances:
74 66 0.12
75 156 0.28
76 265 0.48
77 67 0.12
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (76 bp):
TTTGGAAACATCATGCACTGAAGGACTTACAGATGACCCGAAGGCTTTGAAAACATCAAAAAGCT
CCCGAAGGCTT
Found at i:40911 original size:22 final size:22
Alignment explanation
Indices: 40886--40937 Score: 95
Period size: 22 Copynumber: 2.4 Consensus size: 22
40876 CACAAAGCTT
*
40886 TCATCTTTAAAAAGAGAATCTG
1 TCATCTTTAAAAAGAGAATCTA
40908 TCATCTTTAAAAAGAGAATCTA
1 TCATCTTTAAAAAGAGAATCTA
40930 TCATCTTT
1 TCATCTTT
40938 GAAGAGTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.38, C:0.15, G:0.10, T:0.37
Consensus pattern (22 bp):
TCATCTTTAAAAAGAGAATCTA
Found at i:43601 original size:115 final size:114
Alignment explanation
Indices: 43288--43627 Score: 547
Period size: 114 Copynumber: 3.0 Consensus size: 114
43278 GATCATGCAG
* * * * * * *
43288 TTCATCTTTCAATTCCAATGATCGG-TTCTGGGTTCCTACCGAATCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
* * *
43352 ACACTTTCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
* *
43401 TTCATCTTTTAAATCCAATGATTGGTTTTGGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
1 TTCATCTTTAAAATCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
43466 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
43515 TTCATCTTTAAAATCCAATGATTGGTTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
1 TTCATCTTTAAAATCCAATGATTGG-TTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAG
*
43580 AACACTTCCAGAAGATGCTATTAAGTCTTCTTATTTCTACTATGAGCA
65 AACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCA
43628 CATGGAACTT
Statistics
Matches: 211, Mismatches: 14, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
113 22 0.10
114 104 0.49
115 85 0.40
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (114 bp):
TTCATCTTTAAAATCCAATGATTGGTTTTTGGGTTCATACCAAACCAGATCAGATAACTCAAAGA
ACACTTCCAGAAGATGCTATTGAGTCTTCTTATTTCTACTATGAGCAAA
Found at i:51136 original size:53 final size:53
Alignment explanation
Indices: 51021--51139 Score: 123
Period size: 53 Copynumber: 2.2 Consensus size: 53
51011 TATAATATAG
* * * * * *
51021 TAAAACAATAATTAAAGTAATGATTGAAAATATATTAAAATAATAAAAATTAAGT
1 TAAAAC-ATAACTAAA-CAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
**
51076 TAAAACATAACTAAACAATGATTAAAAATA-AATAAAATAATAAATGTAAAAT
1 TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
*
51128 TATGAACATAAC
1 TA-AAACATAAC
51140 CTGAATCATC
Statistics
Matches: 54, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
52 19 0.35
53 21 0.39
54 8 0.15
55 6 0.11
ACGTcount: A:0.61, C:0.05, G:0.06, T:0.28
Consensus pattern (53 bp):
TAAAACATAACTAAACAATGATTAAAAATATAATAAAATAATAAAAATAAAAT
Found at i:52000 original size:14 final size:15
Alignment explanation
Indices: 51978--52009 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
51968 CTTTTCCTCC
51978 TCTGTTTTTTTTCGT
1 TCTGTTTTTTTTCGT
51993 TCTGTTTTTTTT-GT
1 TCTGTTTTTTTTCGT
52007 TCT
1 TCT
52010 CTGCCGTCTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.00, C:0.12, G:0.12, T:0.75
Consensus pattern (15 bp):
TCTGTTTTTTTTCGT
Found at i:52435 original size:3 final size:3
Alignment explanation
Indices: 52427--52528 Score: 141
Period size: 3 Copynumber: 33.0 Consensus size: 3
52417 TTATTTATTA
*
52427 AAT AAT AAT ATAT AAT AAT AAT ATAT AAT ATT AAT AAT AAT AAT AAT
1 AAT AAT AAT A-AT AAT AAT AAT A-AT AAT AAT AAT AAT AAT AAT AAT
* * *
52474 AAT AAAT AAT TAT AAT TAT AAT AAT AAT AAT AAT ACT AAT AAT AAT
1 AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
52520 AAT AAT AAT
1 AAT AAT AAT
52529 TTTAAATGAA
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
3 79 0.90
4 9 0.10
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (3 bp):
AAT
Found at i:54749 original size:46 final size:46
Alignment explanation
Indices: 54683--54775 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
54673 AATAGTTAAT
54683 GAAAGAAACTATACCATCACAGATGTGTCTAAATGCCAAAGCAGCA
1 GAAAGAAACTATACCATCACAGATGTGTCTAAATGCCAAAGCAGCA
54729 GAAAGAAACTATACCATCACAGATGTGTCTAAATGCCAAAGCAGCA
1 GAAAGAAACTATACCATCACAGATGTGTCTAAATGCCAAAGCAGCA
54775 G
1 G
54776 CTGCAGCGGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.43, C:0.22, G:0.18, T:0.17
Consensus pattern (46 bp):
GAAAGAAACTATACCATCACAGATGTGTCTAAATGCCAAAGCAGCA
Found at i:55203 original size:22 final size:22
Alignment explanation
Indices: 55175--55218 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
55165 AACCAATCAC
55175 GAACAATGTGTATTCTATGGAT
1 GAACAATGTGTATTCTATGGAT
55197 GAACAATGTGTATTCTATGGAT
1 GAACAATGTGTATTCTATGGAT
55219 TATTAACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.32, C:0.09, G:0.23, T:0.36
Consensus pattern (22 bp):
GAACAATGTGTATTCTATGGAT
Found at i:66331 original size:33 final size:34
Alignment explanation
Indices: 66289--66352 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 34
66279 AAATTATCCT
* *
66289 TATTATATATTTATTTTTTTAACAAGTTAAAAAA
1 TATTATATATATATTTTTTTAAAAAGTTAAAAAA
*
66323 TATT-TATATATATTTTTTTAAAAATTTAAA
1 TATTATATATATATTTTTTTAAAAAGTTAAA
66353 TTCATAAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
33 23 0.85
34 4 0.15
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (34 bp):
TATTATATATATATTTTTTTAAAAAGTTAAAAAA
Found at i:66397 original size:37 final size:37
Alignment explanation
Indices: 66324--66398 Score: 100
Period size: 37 Copynumber: 2.0 Consensus size: 37
66314 GTTAAAAAAT
* *
66324 ATTTATATATATTTTTTTAAAAATTTAAATTCATAAA
1 ATTTATATATATTTTTTTAAAAATTAAAAATCATAAA
66361 ATTTATATA-ATTTTTTTTACAAAATTAAAAAT-ATAAA
1 ATTTATATATA-TTTTTTTA-AAAATTAAAAATCATAAA
66398 A
1 A
66399 AGGTTTAATA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 1 0.03
37 23 0.68
38 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTTATATATATTTTTTTAAAAATTAAAAATCATAAA
Found at i:69973 original size:20 final size:20
Alignment explanation
Indices: 69937--69988 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
69927 TTAAAACGAA
*
69937 ATTC-ATAATTTTATAATT-
1 ATTCAATAAATTTATAATTC
69955 ATTCAATAAATTTAGTAATTC
1 ATTCAATAAATTTA-TAATTC
* *
69976 TTTTAATAAATTT
1 ATTCAATAAATTT
69989 TGAAATTTAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 4 0.14
19 8 0.29
20 5 0.18
21 11 0.39
ACGTcount: A:0.40, C:0.06, G:0.02, T:0.52
Consensus pattern (20 bp):
ATTCAATAAATTTATAATTC
Found at i:76659 original size:14 final size:14
Alignment explanation
Indices: 76640--76668 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
76630 TCTTTTATTC
76640 TTTTTATTTATTTA
1 TTTTTATTTATTTA
76654 TTTTTATTTATTTA
1 TTTTTATTTATTTA
76668 T
1 T
76669 ATATGTATAT
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (14 bp):
TTTTTATTTATTTA
Found at i:76945 original size:65 final size:66
Alignment explanation
Indices: 76822--76945 Score: 155
Period size: 65 Copynumber: 1.9 Consensus size: 66
76812 TTCATTATTA
* *
76822 TTTTTTATCTCTCTTTGTTTGTTTTATTATTATTATATTGTTATTTTTTATCTCATATTTTTTCC
1 TTTTTTATCTCTCTTTGTTTGATTTATTATTATTATATTGTTATTTTTTATCTAATATTTTTTCC
76887 T
66 T
* * * *
76888 TTTTTTCTCTTTCTTT-TTTGATTTATTATT-TTGGTATT-TTATTTATTTATTTAATATT
1 TTTTTTATCTCTCTTTGTTTGATTTATTATTATT-ATATTGTTATTT-TTTATCTAATATT
76946 ATCATTTTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
64 8 0.16
65 28 0.56
66 14 0.28
ACGTcount: A:0.16, C:0.08, G:0.05, T:0.71
Consensus pattern (66 bp):
TTTTTTATCTCTCTTTGTTTGATTTATTATTATTATATTGTTATTTTTTATCTAATATTTTTTCC
T
Found at i:81957 original size:84 final size:84
Alignment explanation
Indices: 81660--82598 Score: 860
Period size: 84 Copynumber: 11.4 Consensus size: 84
81650 TTAAAGACAA
* * * * * * *
81660 CATTTGCAGCATAACTCAAGACTATAAGGGTTATCTGCCA-ACAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
81724 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * * *
81743 CATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCT----GCCAAAGACCCTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* * * *
81804 ACTCAGCTTCGAGGGAACAT
66 GCTCAGC-TCCAAGGCACAT
* * * *** * * * *
81824 CATTTACAACATAACTCAAGGATAGAATGGTTATCTGTCA-CCGAAAGACCTTCGAGTTCAACTA
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCC-AAAGACCTTCGAGTTCGACTA
* *
81888 TGCTCAGCTCAAAGGCACAT
65 CGCTCAGCTCCAAGGCACAT
* * * ** * *
81908 CATTTCCAGTATAGCTTAAGTCGAGAAGAACTATCTGCCAGCCAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* *
81973 ACTCAGCTTCAAGGGCACAT
66 GCTCAGCTCCAA-GGCACAT
* * * *
81993 CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCT----GCCAAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* * *
82054 ACTCAGCTTCGAGGGCACAT
66 GCTCAGC-TCCAAGGCACAT
* * * * * * * * *
82074 CATTTACAGCATAACTCAAGGCTA-AGAGGGTTATATGTCAAG-AAAAGATCTTCGAGTTCGACT
1 CATTTGCAGCATAACTTAAGTCGAGA-AGGGCTATCTG-CCAGCCAAAGACCTTCGAGTTCGACT
* *
82137 ATGCTCAGCTCCAAGGCATAT
64 ACGCTCAGCTCCAAGGCACAT
* * * *
82158 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* *
82223 GCTCATCTCTAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * * * * *
82242 CATTTGTAACATAGCTTAAGTTGAGAAGGGCTATCT----GCCAAAGACCCTCGAGTTTGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
*
82303 GCTCAGCTCCAAGGCATAT
66 GCTCAGCTCCAAGGCACAT
* * * *
82322 CATTTGCAGCATAACTTAAGTCGAAAAGGGTTATCTGCAAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
82387 GCTCAGCTCCAAGGCACAT
66 GCTCAGCTCCAAGGCACAT
* * * *
82406 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----GCCAAAGACC-CCGAGTTCGATTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* * *
82466 ACTCAGCTTCGAGGGCACAT
66 GCTCAGC-TCCAAGGCACAT
* * * * * * ** * *
82486 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCA-ACAAAGACCTGCGAGTTCGACTAC
1 CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
*
82550 GCTCAGCTCCAAGGTACAT
66 GCTCAGCTCCAAGGCACAT
82569 CATTTGCAGCATAACTTAAGTCGAGAAGGG
1 CATTTGCAGCATAACTTAAGTCGAGAAGGG
82599 AAATCTGCTA
Statistics
Matches: 690, Mismatches: 138, Indels: 56
0.78 0.16 0.06
Matches are distributed among these distances:
79 18 0.03
80 142 0.21
81 104 0.15
82 2 0.00
83 73 0.11
84 263 0.38
85 87 0.13
86 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (84 bp):
CATTTGCAGCATAACTTAAGTCGAGAAGGGCTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACAT
Found at i:82178 original size:250 final size:248
Alignment explanation
Indices: 81660--82584 Score: 1021
Period size: 250 Copynumber: 3.7 Consensus size: 248
81650 TTAAAGACAA
* * * * * * *
81660 CATTTGCAGCATAACTCAAGACTATAAGGGTTATCTGCCA-ACAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* * * * * * * *
81724 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAAGACC
66 ACTCAGCTTCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGACC
* * * * * * *
81789 CTCGAGTTCGATTACACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGGAT-AGAATG
131 CTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAAG-AGG
* * *
81853 GTTATCTGTCACCG-AAAGACCTTCGAGTTCAACTATGCTCAGCTCAAAGGCACAT
194 GTTATCTGTCA-AGAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACAT
* * *** * *
81908 CATTTCCAGTATAGCTTAAGTCGAGAAGAACTATCTGCCAGCCAAAGACCTTTGAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
*
81973 ACTCAGCTTCAAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGAC
66 ACTCAGCTTCAA-GGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGAC
* * * *
82038 CTTCGAGTTCGATTACACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTAAGAGG
130 CCTCGAGTTCGACTACACTCAGC-TCCAAGGCACATCATTTACAGCATAACTCAAGGCTAAGAGG
* * *
82103 GTTATATGTCAAGAAAAGATCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATAT
194 GTTATCTGTCAAGAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACAT
* * * *
82158 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* * * * * *
82223 GCTCATC-TCTAAGGCACATCATTTGTAACATAGCTTAA-GTTGAGAAGGGCTATCTGCCAAAGA
66 ACTCAGCTTC-AAGGCACATCATTTGCAACATAACTCAAGGCT-AGAAGGGCTATCTGCCAAAGA
* * * * * * * *
82286 CCCTCGAGTTTGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCATAACTTAAGTCGAAAAGG
129 CCCTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAAGAGG
*
82351 GTTATCTG-CAA-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACAT
194 GTTATCTGTCAAGA--AAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACAT
* *
82406 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCT----GCCAAAGACC-CCGAGTTCGATTAC
1 CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
* * * *
82466 ACTCAGCTTCGAGGGCACATCATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCAACAAA
66 ACTCAGCTTC-AAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTATCT-GC--CAAA
* * *
82531 GA-CCTGCGAGTTCGACTACGCTCAGCTCCAAGGTACATCATTTGCAGCATAACT
127 GACCCT-CGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACT
82585 TAAGTCGAGA
Statistics
Matches: 577, Mismatches: 86, Indels: 29
0.83 0.12 0.04
Matches are distributed among these distances:
243 16 0.03
244 45 0.08
245 3 0.01
246 4 0.01
247 54 0.09
248 145 0.25
249 96 0.17
250 212 0.37
251 2 0.00
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.25
Consensus pattern (248 bp):
CATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAGCCAAAGACCTTCGAGTTCGACTAC
ACTCAGCTTCAAGGCACATCATTTGCAACATAACTCAAGGCTAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGACTACACTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGCTAAGAGGGT
TATCTGTCAAGAAAAGACCTTCGAGTTCGACTATGCTCAGCTCCAAGGCACAT
Found at i:82330 original size:164 final size:164
Alignment explanation
Indices: 81660--82684 Score: 1089
Period size: 164 Copynumber: 6.2 Consensus size: 164
81650 TTAAAGACAA
* * *
81660 CATTTGCAGCATAACTCAAGACTATAAGGGTTATCTGCCAA-CAAAGACCTTCAAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
81724 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * *
81789 CTCGAGTTCGATTACACTCAGCTTCGAGGGAACAT
131 CTCGAGTTCGATTACACTCAGC-TCCAAGGCACAT
* * * * * *
81824 CATTTACAACATAACTCAAGGATAGAATGGTTATCTGTC-ACCGAAAGACCTTCGAGTTCAACTA
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACC-AAAGACCTTCGAGTTCGACTA
* * * * **
81888 TGCTCAGCTCAAAGGCACATCATTTCCAGTATAGCTTAAGTCGAGAAGAACTATCTGCCAGCCAA
65 CGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT----GCCAA
* * *
81953 AGACCTTTGAGTTCGATTACACTCAGCTTCAAGGGCACAT
126 AGACCCTCGAGTTCGATTACACTCAGCTCCAA-GGCACAT
* *
81993 CATTTGCAGCATAACTCAAGGCTAGAAGGGCTATCTG----CCAAAGACCTTCGAGTTCGATTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * * * * * * * *
82054 ACTCAGCTTCGAGGGCACATCATTTACAGCATAACTCAAGGCTA-AGAGGGTTATATGTCAAGAA
66 GCTCAGC-TCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGA-AGGGCTATCTG-C---CA
* * * ** *
82118 AAGATCTTCGAGTTCGACTATGCTCAGCTCCAAGGCATAT
125 AAGACCCTCGAGTTCGATTACACTCAGCTCCAAGGCACAT
* * * * *
82158 CATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAATACCTTCGAGTTCGACTAT
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * * * *
82223 GCTCATCTCTAAGGCACATCATTTGTAACATAGCTTAAGTTGAGAAGGGCTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * *
82288 CTCGAGTTTGACTACGCTCAGCTCCAAGGCATAT
131 CTCGAGTTCGATTACACTCAGCTCCAAGGCACAT
* * * * *
82322 CATTTGCAGCATAACTTAAGTCGAAAAGGGTTATCTGCAAACCAAAGACCTTCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
*
82387 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGTTATCTGCCAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* *
82452 C-CGAGTTCGATTACACTCAGCTTCGAGGGCACAT
131 CTCGAGTTCGATTACACTCAGC-TCCAAGGCACAT
* * ** *
82486 CATTTACAACATAACTCAAGGCTAGAAGGGTTATCTATCAA-CAAAGACCTGCGAGTTCGACTAC
1 CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
* * ** *
82550 GCTCAGCTCCAAGGTACATCATTTGCAGCATAACTTAAGTCGAGAAGGGAAATCTGCTAAAGACC
66 GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
* * * * *
82615 TTCGAGTTCGATTATATTCAACT-CAGAGGCAAAT
131 CTCGAGTTCGATTACACTCAGCTCCA-AGGCACAT
* * * *
82649 CAAGCTTACAGCATAGCTCAAGGCAAGAAGGGTTAT
1 C-A-TTTGCAGCATAACTCAAGGCTAGAAGGGTTAT
82685 TTGTCAATAA
Statistics
Matches: 719, Mismatches: 119, Indels: 45
0.81 0.13 0.05
Matches are distributed among these distances:
162 2 0.00
163 109 0.15
164 250 0.35
165 161 0.22
166 64 0.09
167 1 0.00
168 37 0.05
169 95 0.13
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.24
Consensus pattern (164 bp):
CATTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACCAAAGACCTTCGAGTTCGACTAC
GCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACC
CTCGAGTTCGATTACACTCAGCTCCAAGGCACAT
Found at i:84296 original size:4 final size:4
Alignment explanation
Indices: 84287--84314 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
84277 TTTATTATTA
84287 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT
84315 ATATGTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:84325 original size:2 final size:2
Alignment explanation
Indices: 84312--84344 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
84302 TTTATTTATT
*
84312 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
84345 TTCGTATTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:86525 original size:34 final size:34
Alignment explanation
Indices: 86487--86585 Score: 108
Period size: 34 Copynumber: 2.9 Consensus size: 34
86477 AAAAATAGAA
* *
86487 GCAAGCACATAGGTACACGGTGCAAAAGAGAAAT
1 GCAAGCACATACGTACACAGTGCAAAAGAGAAAT
* *
86521 GCAAGCATATACGTACACAGTGCAAAAGTGAAAT
1 GCAAGCACATACGTACACAGTGCAAAAGAGAAAT
* ** * * *
86555 GAAAGCGTATAAGTACATAGTGCATAAGAGA
1 GCAAGCACATACGTACACAGTGCAAAAGAGA
86586 TGCAAAATCC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 55 1.00
ACGTcount: A:0.44, C:0.15, G:0.24, T:0.16
Consensus pattern (34 bp):
GCAAGCACATACGTACACAGTGCAAAAGAGAAAT
Found at i:87912 original size:13 final size:13
Alignment explanation
Indices: 87874--87917 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
87864 AACGAAAGCT
*
87874 ACAACAAAGCAAA
1 ACAAAAAAGCAAA
* *
87887 ATAAAAAA-AAAA
1 ACAAAAAAGCAAA
87899 ACAAAAAAGCAAA
1 ACAAAAAAGCAAA
87912 ACAAAA
1 ACAAAA
87918 TCAATTTTCA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.80, C:0.14, G:0.05, T:0.02
Consensus pattern (13 bp):
ACAAAAAAGCAAA
Found at i:87978 original size:8 final size:8
Alignment explanation
Indices: 87965--87992 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
87955 TCACTTCATC
87965 AAAAGAAA
1 AAAAGAAA
87973 AAAAGAAA
1 AAAAGAAA
87981 AAAAGAAA
1 AAAAGAAA
87989 AAAA
1 AAAA
87993 TCAAACGGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (8 bp):
AAAAGAAA
Found at i:89551 original size:13 final size:13
Alignment explanation
Indices: 89533--89558 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
89523 TGGTCACTCC
89533 ATCATTAAATAGT
1 ATCATTAAATAGT
89546 ATCATTAAATAGT
1 ATCATTAAATAGT
89559 TAACGGCGTT
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:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
ATCATTAAATAGT
Found at i:94988 original size:15 final size:15
Alignment explanation
Indices: 94968--95049 Score: 121
Period size: 15 Copynumber: 5.5 Consensus size: 15
94958 TTCCAGAAAA
94968 TGAATTACTGGAATT
1 TGAATTACTGGAATT
94983 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
94998 TGAATTACTGGAAAA
1 TGAATTACTGGAATT
95013 TGAATTACTGGAATT
1 TGAATTACTGGAATT
**
95028 TGAATT-CTGGAAAA
1 TGAATTACTGGAATT
95042 TGAATTAC
1 TGAATTAC
95050 ATTTCTGTAA
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
14 12 0.20
15 48 0.80
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (15 bp):
TGAATTACTGGAATT
Found at i:95002 original size:30 final size:30
Alignment explanation
Indices: 94968--95049 Score: 139
Period size: 30 Copynumber: 2.8 Consensus size: 30
94958 TTCCAGAAAA
**
94968 TGAATTACTGGAATTTGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
94998 TGAATTACTGGAAAATGAATTACTGGAATT
1 TGAATTACTGGAAAATGAATTACTGGAATT
95028 TGAATT-CTGGAAAATGAATTAC
1 TGAATTACTGGAAAATGAATTAC
95050 ATTTCTGTAA
Statistics
Matches: 50, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
29 16 0.32
30 34 0.68
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.35
Consensus pattern (30 bp):
TGAATTACTGGAAAATGAATTACTGGAATT
Found at i:95027 original size:45 final size:44
Alignment explanation
Indices: 94963--95049 Score: 147
Period size: 45 Copynumber: 2.0 Consensus size: 44
94953 TGGTTTTCCA
**
94963 GAAAATGAATTACTGGAATTTGAATTACTGGAATTTGAATTACTG
1 GAAAATGAATTACTGGAATTTGAATT-CTGGAAAATGAATTACTG
95008 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
1 GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTAC
95050 ATTTCTGTAA
Statistics
Matches: 40, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
44 14 0.35
45 26 0.65
ACGTcount: A:0.40, C:0.07, G:0.20, T:0.33
Consensus pattern (44 bp):
GAAAATGAATTACTGGAATTTGAATTCTGGAAAATGAATTACTG
Found at i:95055 original size:20 final size:20
Alignment explanation
Indices: 95032--95101 Score: 131
Period size: 20 Copynumber: 3.5 Consensus size: 20
95022 GGAATTTGAA
95032 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
*
95052 TTCTGTAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
95072 TTCTGGAAAATGAATTACAT
1 TTCTGGAAAATGAATTACAT
95092 TTCTGGAAAA
1 TTCTGGAAAA
95102 CATCTGGAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.40, C:0.10, G:0.14, T:0.36
Consensus pattern (20 bp):
TTCTGGAAAATGAATTACAT
Found at i:95324 original size:29 final size:27
Alignment explanation
Indices: 95268--95333 Score: 78
Period size: 28 Copynumber: 2.3 Consensus size: 27
95258 TTTACTAAAA
* *
95268 TATTATTGAAATATATAAATAATATTAT
1 TATTATT-AAATATATAAAAAAAATTAT
95296 TCATTATTAAATATATAAAAAAAATTTAT
1 T-ATTATTAAATATATAAAAAAAA-TTAT
95325 TATATATTA
1 TAT-TATTA
95334 TTATAATAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
28 17 0.52
29 16 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (27 bp):
TATTATTAAATATATAAAAAAAATTAT
Found at i:95342 original size:29 final size:29
Alignment explanation
Indices: 95327--95420 Score: 94
Period size: 29 Copynumber: 3.4 Consensus size: 29
95317 AAATTTATTA
95327 TATATTATTATAATAAAAATATAATATCT
1 TATATTATTATAATAAAAATATAATATCT
* *
95356 TATATTATTATAAT-ATAAT-TGATTAT-T
1 TATATTATTATAATAAAAATAT-AATATCT
* *
95383 T-TA-TATAATATTAAAAATATAATA--T
1 TATATTATTATAATAAAAATATAATATCT
95408 TATATTATTATAA
1 TATATTATTATAA
95421 ATATTAATAA
Statistics
Matches: 52, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
25 9 0.17
26 11 0.21
27 10 0.19
28 8 0.15
29 14 0.27
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.49
Consensus pattern (29 bp):
TATATTATTATAATAAAAATATAATATCT
Found at i:95411 original size:22 final size:23
Alignment explanation
Indices: 95386--95429 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
95376 GATTATTTTA
95386 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
95408 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
95430 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:95434 original size:22 final size:22
Alignment explanation
Indices: 95390--95446 Score: 64
Period size: 21 Copynumber: 2.6 Consensus size: 22
95380 ATTTTATATA
* *
95390 ATATTAAAAATA-TAATATTAT
1 ATATTATAAATATTAATATAAT
95411 ATTATTATAAATATTAATA-AAT
1 A-TATTATAAATATTAATATAAT
*
95433 ATATTTTAAATATT
1 ATATTATAAATATT
95447 TTAATAATTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 13 0.42
23 5 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (22 bp):
ATATTATAAATATTAATATAAT
Found at i:95644 original size:19 final size:19
Alignment explanation
Indices: 95620--95671 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
95610 TCTGTTACTA
*
95620 GGAAAATGAATTACATTCC
1 GGAAAACGAATTACATTCC
95639 GGAAAACGAATTACATTCC
1 GGAAAACGAATTACATTCC
95658 GGAAAACGAATTAC
1 GGAAAACGAATTAC
95672 GTGAAACAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.44, C:0.17, G:0.17, T:0.21
Consensus pattern (19 bp):
GGAAAACGAATTACATTCC
Found at i:98885 original size:2 final size:2
Alignment explanation
Indices: 98878--98905 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
98868 AATGAAATTC
98878 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA
98906 TTACCTTGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:99842 original size:196 final size:194
Alignment explanation
Indices: 99455--99917 Score: 795
Period size: 195 Copynumber: 2.4 Consensus size: 194
99445 TGTTTGGGTC
* * *
99455 AATTTACTTTAAATATTTATGAATAATTATAATAATATCACTCTATATATATATATATTTTTTTT
1 AATTTACCTTAAATATTTATGAATAATTACAATAATATCACTC--TATATATATATATTATTTTT
* * * *
99520 TTAAAATTAAGGGTCGGATTTTTATAAAAAAAATCAGGTTCGGGTCAGTTTTTTTTAATGTGATG
64 TTAAAATTAAGGGTCGGATTTTTATAAAAAAAATCAAGTCCGAGTCAGTTTTTTTTAATGTGATA
* *
99585 TTCGGGTCAGGTCGGTTCAGGTTTATGGTGAAAAATACCTGACCGACCTGACTCGAAAAAAAATG
129 TTCGGGTCAGGTCGGTTCAGGTTTAGGGTGAAAAATACCTGACCGACCTGACCCGAAAAAAAATG
99650 T
194 T
*
99651 AATTTACCTTAAATATTTATGAATAATTACAATAATACCACTCTATATATATATATTATTTTTTT
1 AATTTACCTTAAATATTTATGAATAATTACAATAATATCACTCTATATATATATATTATTTTTTT
99716 AAAATTAAGGGTCGGATTTTTATAAAAAAAATCAAGTCCGAGTCAGGTTTTTTTTAATGTGATAT
66 AAAATTAAGGGTCGGATTTTTATAAAAAAAATCAAGTCCGAGTCA-GTTTTTTTTAATGTGATAT
99781 TCGGGTCAGGTCGGTTCAGGTTTAGGGTGAAAAATACCTGACCGACCTGACCCGAAAAAAAATGT
130 TCGGGTCAGGTCGGTTCAGGTTTAGGGTGAAAAATACCTGACCGACCTGACCCGAAAAAAAATGT
99846 AATTTACCTTAAATATTTATGAATAATTACAATAATATCACTC--TATATATATATTATTTTTTT
1 AATTTACCTTAAATATTTATGAATAATTACAATAATATCACTCTATATATATATATTATTTTTTT
99909 AAAATTAAG
66 AAAATTAAG
99918 TCATTGTTTT
Statistics
Matches: 255, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
193 29 0.11
194 63 0.25
195 123 0.48
196 40 0.16
ACGTcount: A:0.36, C:0.11, G:0.14, T:0.39
Consensus pattern (194 bp):
AATTTACCTTAAATATTTATGAATAATTACAATAATATCACTCTATATATATATATTATTTTTTT
AAAATTAAGGGTCGGATTTTTATAAAAAAAATCAAGTCCGAGTCAGTTTTTTTTAATGTGATATT
CGGGTCAGGTCGGTTCAGGTTTAGGGTGAAAAATACCTGACCGACCTGACCCGAAAAAAAATGT
Found at i:101290 original size:19 final size:19
Alignment explanation
Indices: 101266--101312 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
101256 AAAATTAAAA
*
101266 AAAAATTGATTTAATTTAT
1 AAAAATTGATTTAATCTAT
101285 AAAAATTGATTTAATCTAT
1 AAAAATTGATTTAATCTAT
101304 AAAAATTGA
1 AAAAATTGA
101313 CACAAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.40
Consensus pattern (19 bp):
AAAAATTGATTTAATCTAT
Found at i:103884 original size:30 final size:30
Alignment explanation
Indices: 103578--103874 Score: 540
Period size: 30 Copynumber: 9.9 Consensus size: 30
103568 GGTTGAGTTG
103578 GGTTGAATCTCATATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
*
103608 GGTTGAATCTCGTATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
* *
103638 GGTTGAATCTCATATGGATTGCTGGAACTA
1 GGTTGAATCTCATATGGATAGCTGGAACTC
*
103668 GGTTGAACCTCATATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
103698 GGTTGAATCTCATATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
103728 GGTTGAATCTCATATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
103758 GGTTGAATCTCATATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
*
103788 GGTTGAATCTCATATGGATTGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
103818 GGTTGAATCTCATATGGATAGCTGGAACTC
1 GGTTGAATCTCATATGGATAGCTGGAACTC
*
103848 GGTTGAATCTCATATGGATTGCTGGAA
1 GGTTGAATCTCATATGGATAGCTGGAA
103875 TGGGGTTGAA
Statistics
Matches: 256, Mismatches: 11, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 256 1.00
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (30 bp):
GGTTGAATCTCATATGGATAGCTGGAACTC
Found at i:104959 original size:32 final size:32
Alignment explanation
Indices: 104923--104992 Score: 77
Period size: 32 Copynumber: 2.2 Consensus size: 32
104913 TATGATCAAT
104923 TGATGACGTGGTATATGGCATATCACCCAAAG
1 TGATGACGTGGTATATGGCATATCACCCAAAG
** * * * *
104955 TGATGGTGTGGTATGTGTCATGTCACTCAAAG
1 TGATGACGTGGTATATGGCATATCACCCAAAG
*
104987 TAATGA
1 TGATGA
104993 TGTTATATGT
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.29, C:0.14, G:0.27, T:0.30
Consensus pattern (32 bp):
TGATGACGTGGTATATGGCATATCACCCAAAG
Found at i:105360 original size:2 final size:2
Alignment explanation
Indices: 105353--105395 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
105343 CATTATGCCT
105353 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
105395 T
1 T
105396 GGATATGACC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:108793 original size:20 final size:20
Alignment explanation
Indices: 108768--108858 Score: 87
Period size: 20 Copynumber: 4.5 Consensus size: 20
108758 TGGGAAAATT
*
108768 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* * *
108788 GCAATGCGATAAT-ACAAAATC
1 GCAACGCGATACTGAC--TATC
* *
108809 GCAACGAGATACTGACTTTC
1 GCAACGCGATACTGACTATC
*
108829 GCAACGCGATTCTGACT-TC
1 GCAACGCGATACTGACTATC
108848 GCAACGCGATA
1 GCAACGCGATA
108859 ATACATAATC
Statistics
Matches: 58, Mismatches: 10, Indels: 7
0.77 0.13 0.09
Matches are distributed among these distances:
19 14 0.24
20 29 0.50
21 13 0.22
22 2 0.03
ACGTcount: A:0.33, C:0.25, G:0.20, T:0.22
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:108872 original size:21 final size:20
Alignment explanation
Indices: 108768--108878 Score: 75
Period size: 20 Copynumber: 5.5 Consensus size: 20
108758 TGGGAAAATT
* *
108768 GCAATGCGATACTGACTATC
1 GCAACGCGATAATGACTATC
* *
108788 GCAATGCGATAAT-ACAAAATC
1 GCAACGCGATAATGAC--TATC
* * *
108809 GCAACGAGATACTGACTTTC
1 GCAACGCGATAATGACTATC
**
108829 GCAACGCGATTCTGACT-TC
1 GCAACGCGATAATGACTATC
108848 GCAACGCGATAAT-ACATAATC
1 GCAACGCGATAATGAC-T-ATC
*
108869 GCAATGCGAT
1 GCAACGCGAT
108879 TTTCAAAGCG
Statistics
Matches: 73, Mismatches: 12, Indels: 11
0.76 0.12 0.11
Matches are distributed among these distances:
18 2 0.03
19 16 0.22
20 29 0.40
21 24 0.33
22 2 0.03
ACGTcount: A:0.34, C:0.24, G:0.19, T:0.23
Consensus pattern (20 bp):
GCAACGCGATAATGACTATC
Found at i:109074 original size:22 final size:22
Alignment explanation
Indices: 109046--109089 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
109036 CACTCTCTCA
*
109046 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
*
109068 CCCATCTCCGGCAAAATCCGTC
1 CCCATCTCCGACAAAATCCGTC
109090 TATCTCCATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.23, C:0.45, G:0.14, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACAAAATCCGTC
Found at i:109404 original size:20 final size:20
Alignment explanation
Indices: 109350--109408 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
109340 GCGATTCTCT
**
109350 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
109370 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
109390 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
109409 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:110741 original size:18 final size:18
Alignment explanation
Indices: 110720--110764 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
110710 TCCACTTCGG
*
110720 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
110738 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
110756 GAGCCATCA
1 GAGCCATCA
110765 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:111332 original size:20 final size:20
Alignment explanation
Indices: 111307--111349 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
111297 TAGTTTACTT
111307 TCGCAACACGAAAATGACTA
1 TCGCAACACGAAAATGACTA
* * *
111327 TCGCAACGCGGAAATGGCTA
1 TCGCAACACGAAAATGACTA
111347 TCG
1 TCG
111350 GAATGAGAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.26, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACACGAAAATGACTA
Found at i:111397 original size:19 final size:18
Alignment explanation
Indices: 111375--111474 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
111365 ATCGCACGAC
111375 AAAATCGCAATGCGAAATA
1 AAAATCGCAA-GCGAAATA
*
111394 AAAATCGCAA-CG--A-C
1 AAAATCGCAAGCGAAATA
111408 AAAATCGCAACGCGAAATA
1 AAAATCGCAA-GCGAAATA
*
111427 AAAATCGCAA-CG--A-C
1 AAAATCGCAAGCGAAATA
*
111441 AAAATCGCAACGCGAAATG
1 AAAATCGCAA-GCGAAATA
111460 AAAATCGCAATGCGA
1 AAAATCGCAA-GCGA
111475 TTTGTGTTTC
Statistics
Matches: 66, Mismatches: 5, Indels: 20
0.73 0.05 0.22
Matches are distributed among these distances:
14 20 0.30
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 34 0.52
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.11
Consensus pattern (18 bp):
AAAATCGCAAGCGAAATA
Found at i:111412 original size:33 final size:33
Alignment explanation
Indices: 111356--111469 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
111346 ATCGGAATGA
* *
111356 GAAATGAAAATCGC-ACGACAAAATCGCAATGC
1 GAAATAAAAATCGCAACGACAAAATCGCAACGC
111388 GAAATAAAAATCGCAACGACAAAATCGCAACGC
1 GAAATAAAAATCGCAACGACAAAATCGCAACGC
111421 GAAATAAAAATCGCAACGACAAAATCGCAACGC
1 GAAATAAAAATCGCAACGACAAAATCGCAACGC
*
111454 GAAATGAAAATCGCAA
1 GAAATAAAAATCGCAA
111470 TGCGATTTGT
Statistics
Matches: 78, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 13 0.17
33 65 0.83
ACGTcount: A:0.51, C:0.22, G:0.17, T:0.11
Consensus pattern (33 bp):
GAAATAAAAATCGCAACGACAAAATCGCAACGC
Found at i:111413 original size:14 final size:14
Alignment explanation
Indices: 111362--111452 Score: 67
Period size: 14 Copynumber: 5.9 Consensus size: 14
111352 ATGAGAAATG
111362 AAAATCGC-ACGAC
1 AAAATCGCAACGAC
*
111375 AAAATCGCAATGCGAAATA
1 AAAATCGCAA--CG--A-C
111394 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
111408 AAAATCGCAACGCGAAATA
1 AAAATCGCAA--CG--A-C
111427 AAAATCGCAACGAC
1 AAAATCGCAACGAC
111441 AAAATCGCAACG
1 AAAATCGCAACG
111453 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 21
0.72 0.05 0.24
Matches are distributed among these distances:
13 8 0.13
14 23 0.37
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 20 0.32
ACGTcount: A:0.51, C:0.24, G:0.15, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:111504 original size:13 final size:13
Alignment explanation
Indices: 111486--111543 Score: 53
Period size: 14 Copynumber: 3.9 Consensus size: 13
111476 TTGTGTTTCG
111486 CGTTGCGATTTTT
1 CGTTGCGATTTTT
111499 CGTTGCGATTTTCATTT
1 CGTTGCGA--TT--TTT
111516 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTT-T
111532 CGTTGCGATTTT
1 CGTTGCGATTTT
111544 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
13 8 0.21
14 12 0.32
15 4 0.11
16 1 0.03
17 5 0.13
19 8 0.21
ACGTcount: A:0.09, C:0.17, G:0.24, T:0.50
Consensus pattern (13 bp):
CGTTGCGATTTTT
Found at i:111515 original size:19 final size:19
Alignment explanation
Indices: 111499--111616 Score: 79
Period size: 20 Copynumber: 6.4 Consensus size: 19
111489 TGCGATTTTT
111499 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
111518 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
111532 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
111551 CATTGCGATAGCCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
**
111571 CG-T-CGATAGTCATTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
111589 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
111609 TGTTGCGA
1 CGTTGCGA
111617 AAGTAAACTA
Statistics
Matches: 78, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.03
17 2 0.03
18 19 0.24
19 20 0.26
20 24 0.31
ACGTcount: A:0.14, C:0.19, G:0.24, T:0.43
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:111540 original size:33 final size:32
Alignment explanation
Indices: 111481--111559 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 32
111471 GCGATTTGTG
111481 TTTCGCGTTGCGATTTTTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTTCGTTGCGATTTTCA
111513 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTT-TCGTTGCGATTTTCA
*
111546 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
111560 AGCCATTTTC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 17 0.38
33 28 0.62
ACGTcount: A:0.10, C:0.19, G:0.23, T:0.48
Consensus pattern (32 bp):
TTTCGCGTTGCGATTTTTCGTTGCGATTTTCA
Found at i:111571 original size:20 final size:19
Alignment explanation
Indices: 111546--111597 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
111536 GCGATTTTCA
111546 TTTCGCATTGCGATAGCCAT
1 TTTCGC-TTGCGATAGCCAT
* *
111566 TTTCGCGT-CGATAGTCAT
1 TTTCGCTTGCGATAGCCAT
111584 TTTCGCGTTGCGAT
1 TTTCGC-TTGCGAT
111598 TTTAAGTTTC
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 15 0.56
19 2 0.07
20 10 0.37
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (19 bp):
TTTCGCTTGCGATAGCCAT
Found at i:111579 original size:18 final size:18
Alignment explanation
Indices: 111556--111591 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
111546 TTTCGCATTG
111556 CGATAGCCATTTTCGCGT
1 CGATAGCCATTTTCGCGT
*
111574 CGATAGTCATTTTCGCGT
1 CGATAGCCATTTTCGCGT
111592 TGCGATTTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.17, C:0.25, G:0.22, T:0.36
Consensus pattern (18 bp):
CGATAGCCATTTTCGCGT
Done.