Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000126.1 Hibiscus syriacus cultivar Beakdansim tig00000226_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: 91585
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4762 original size:22 final size:22
Alignment explanation
Indices: 4690--4764 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
4680 TTTTTTTTTA
* *
4690 ACTATCACAACAACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
* *
4712 ACTATCGCAACG--AA-TTTGG
1 ACTATCGCAACGACAACTGTAG
**
4731 AAAATCGCAACGACAACTGTAG
1 ACTATCGCAACGACAACTGTAG
4753 ACTATCGCAACG
1 ACTATCGCAACG
4765 CGAAATGAAA
Statistics
Matches: 40, Mismatches: 10, Indels: 6
0.71 0.18 0.11
Matches are distributed among these distances:
19 13 0.32
20 2 0.05
21 2 0.05
22 23 0.57
ACGTcount: A:0.40, C:0.25, G:0.16, T:0.19
Consensus pattern (22 bp):
ACTATCGCAACGACAACTGTAG
Found at i:4775 original size:41 final size:42
Alignment explanation
Indices: 4697--4780 Score: 111
Period size: 41 Copynumber: 2.0 Consensus size: 42
4687 TTAACTATCA
*
4697 CAACAACAACTGTAGACTATCGCAACGAATTTGG-AAAATCG
1 CAACAACAACTGTAGACTATCGCAACGAATATGGAAAAATCG
*
4738 CAACGACAACTGTAGACTATCGCAACGCGAA-AT-GAAAAATCG
1 CAACAACAACTGTAGACTATCGCAA--CGAATATGGAAAAATCG
4780 C
1 C
4781 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
41 25 0.66
42 9 0.24
43 4 0.11
ACGTcount: A:0.42, C:0.24, G:0.18, T:0.17
Consensus pattern (42 bp):
CAACAACAACTGTAGACTATCGCAACGAATATGGAAAAATCG
Found at i:4822 original size:20 final size:20
Alignment explanation
Indices: 4797--4889 Score: 78
Period size: 20 Copynumber: 4.6 Consensus size: 20
4787 ATTTTCAACT
* *
4797 ATCGCAACGCGCAATGGAAA
1 ATCGCAACGCGAAATAGAAA
4817 ATCGCAACGCGAAATAGAAA
1 ATCGCAACGCGAAATAGAAA
*** ** ** *
4837 ATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGAAATAGAA-A
*
4858 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAA
4878 ATCGCAACGCGA
1 ATCGCAACGCGA
4890 TTTTCAACTA
Statistics
Matches: 54, Mismatches: 18, Indels: 2
0.73 0.24 0.03
Matches are distributed among these distances:
20 42 0.78
21 12 0.22
ACGTcount: A:0.38, C:0.24, G:0.23, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAATAGAAA
Found at i:4822 original size:61 final size:61
Alignment explanation
Indices: 4756--4889 Score: 243
Period size: 61 Copynumber: 2.2 Consensus size: 61
4746 ACTGTAGACT
*
4756 ATCGCAACGCGAAAT-GAAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGCAATGGAAA
1 ATCGCAACGCGAAATAG-AAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGGAAA
4817 ATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGGAAA
4878 ATCGCAACGCGA
1 ATCGCAACGCGA
4890 TTTTCAACTA
Statistics
Matches: 71, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
61 70 0.99
62 1 0.01
ACGTcount: A:0.37, C:0.23, G:0.22, T:0.19
Consensus pattern (61 bp):
ATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCAACTATCGCAACGCGAAATGGAAA
Found at i:4869 original size:21 final size:21
Alignment explanation
Indices: 4845--4905 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 21
4835 AAATCGCGTT
4845 GCGATTTTCAACTATCGCAAC
1 GCGATTTTCAACTATCGCAAC
** ** *
4866 GCGAAATGGAA-AATCGCAAC
1 GCGATTTTCAACTATCGCAAC
4886 GCGATTTTCAACTATCGCAA
1 GCGATTTTCAACTATCGCAA
4906 TACGAAATGC
Statistics
Matches: 29, Mismatches: 10, Indels: 2
0.71 0.24 0.05
Matches are distributed among these distances:
20 15 0.52
21 14 0.48
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (21 bp):
GCGATTTTCAACTATCGCAAC
Found at i:4912 original size:41 final size:41
Alignment explanation
Indices: 4817--4914 Score: 142
Period size: 41 Copynumber: 2.4 Consensus size: 41
4807 GCAATGGAAA
* ***
4817 ATCGCAACGCGAAATAGAAAATCGCGTTGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
4858 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
**
4899 ATCGCAATACGAAATG
1 ATCGCAACGCGAAATG
4915 CAACGCGAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (41 bp):
ATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACT
Found at i:7158 original size:19 final size:20
Alignment explanation
Indices: 7104--7151 Score: 96
Period size: 20 Copynumber: 2.4 Consensus size: 20
7094 TAATAATAAT
7104 AAAATATTATAATATTTAGA
1 AAAATATTATAATATTTAGA
7124 AAAATATTATAATATTTAGA
1 AAAATATTATAATATTTAGA
7144 AAAATATT
1 AAAATATT
7152 GAATATTACT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (20 bp):
AAAATATTATAATATTTAGA
Found at i:8526 original size:29 final size:28
Alignment explanation
Indices: 8493--8594 Score: 78
Period size: 29 Copynumber: 3.4 Consensus size: 28
8483 GAGTAAGGTT
8493 GTGTTTGTGTTCGTTTGTTTTTTTTGAAG
1 GTGTTTGTGTTCGTTT-TTTTTTTTGAAG
* * * * *
8522 GTGTTTATGTTTGTTTAATTTTTTTAACATC
1 GTGTTTGTGTTCGTTT-TTTTTTTTGA-A-G
*
8553 GTGTTTGTGTTCACTTATTTTTTTTGTGAAG
1 GTGTTTGTGTTC-GTT-TTTTTTTT-TGAAG
*
8584 GTATTTGTGTT
1 GTGTTTGTGTT
8595 TGTTCATTTA
Statistics
Matches: 55, Mismatches: 13, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
29 22 0.40
30 1 0.02
31 20 0.36
32 9 0.16
33 3 0.05
ACGTcount: A:0.13, C:0.05, G:0.22, T:0.61
Consensus pattern (28 bp):
GTGTTTGTGTTCGTTTTTTTTTTTGAAG
Found at i:18217 original size:12 final size:12
Alignment explanation
Indices: 18200--18233 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
18190 AAGTCTTAAT
18200 TAGGTTTGAGAA
1 TAGGTTTGAGAA
18212 TAGGTTTGAGAA
1 TAGGTTTGAGAA
*
18224 TAAGTTTGAG
1 TAGGTTTGAG
18234 TTATGTACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (12 bp):
TAGGTTTGAGAA
Found at i:18792 original size:6 final size:6
Alignment explanation
Indices: 18783--18807 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
18773 GGGATGATAA
18783 ACGGGG ACGGGG ACGGGG ACGGGG A
1 ACGGGG ACGGGG ACGGGG ACGGGG A
18808 AAACCCATTT
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:0.20, C:0.16, G:0.64, T:0.00
Consensus pattern (6 bp):
ACGGGG
Found at i:18970 original size:23 final size:23
Alignment explanation
Indices: 18940--18986 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
18930 ATATTAATAA
18940 ATTTAATTTAAATAAAAATATAT
1 ATTTAATTTAAATAAAAATATAT
* *
18963 ATTTAATTTAAATATATATATAT
1 ATTTAATTTAAATAAAAATATAT
18986 A
1 A
18987 CCCGGCCCGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
ATTTAATTTAAATAAAAATATAT
Found at i:19038 original size:12 final size:12
Alignment explanation
Indices: 18984--19038 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
18974 ATATATATAT
* *
18984 ATACCCGGCCCG
1 ATACCCGACCCA
*
18996 ATTCCCGACCCA
1 ATACCCGACCCA
*
19008 ATACCCAACCCA
1 ATACCCGACCCA
*
19020 ATACCCGGCCCA
1 ATACCCGACCCA
19032 ATACCCG
1 ATACCCG
19039 TTTAAATAAC
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 36 1.00
ACGTcount: A:0.27, C:0.49, G:0.13, T:0.11
Consensus pattern (12 bp):
ATACCCGACCCA
Found at i:22032 original size:22 final size:21
Alignment explanation
Indices: 21990--22029 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
21980 AAGACTATTT
21990 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
22011 TCATTTTTGT-ATTTTGAAA
1 TCATTTTT-TAATTTTGAAA
22030 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.30, C:0.05, G:0.07, T:0.57
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:24687 original size:15 final size:14
Alignment explanation
Indices: 24653--24690 Score: 58
Period size: 15 Copynumber: 2.6 Consensus size: 14
24643 AACATATAAG
24653 CATCCAAATTCAAA
1 CATCCAAATTCAAA
24667 CAATCCATAATTCAAA
1 C-ATCCA-AATTCAAA
24683 CATCCAAA
1 CATCCAAA
24691 ATGTTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.50, C:0.29, G:0.00, T:0.21
Consensus pattern (14 bp):
CATCCAAATTCAAA
Found at i:26394 original size:21 final size:21
Alignment explanation
Indices: 26368--26412 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
26358 GATTTCTGGG
* *
26368 CAAGGGGAATCGGTACCCATT
1 CAAGGGGAACCGATACCCATT
*
26389 CAAGGGGAACCGATACCCCTT
1 CAAGGGGAACCGATACCCATT
26410 CAA
1 CAA
26413 ACGACAAAAT
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:0.31, C:0.29, G:0.24, T:0.16
Consensus pattern (21 bp):
CAAGGGGAACCGATACCCATT
Found at i:27010 original size:18 final size:18
Alignment explanation
Indices: 26987--27021 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
26977 CTAGGAGATT
26987 TGAACATA-AATGATAAGA
1 TGAACATATAA-GATAAGA
27005 TGAACATATAAGATAAG
1 TGAACATATAAGATAAG
27022 CTAGATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.54, C:0.06, G:0.17, T:0.23
Consensus pattern (18 bp):
TGAACATATAAGATAAGA
Found at i:27107 original size:21 final size:22
Alignment explanation
Indices: 27078--27121 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
27068 GTTGTATGAT
27078 AGAAAATTAT-GAAGTTATATG
1 AGAAAATTATAGAAGTTATATG
* *
27099 AGAAGATTATAGGAGTTATATG
1 AGAAAATTATAGAAGTTATATG
27121 A
1 A
27122 AATTGAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 9 0.45
22 11 0.55
ACGTcount: A:0.45, C:0.00, G:0.23, T:0.32
Consensus pattern (22 bp):
AGAAAATTATAGAAGTTATATG
Found at i:28186 original size:149 final size:149
Alignment explanation
Indices: 28005--28306 Score: 595
Period size: 149 Copynumber: 2.0 Consensus size: 149
27995 GTCGAGGGTA
28005 TACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
1 TACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
28070 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
28135 TGGCACTACGGTGCAATTC
131 TGGCACTACGGTGCAATTC
*
28154 TACGCGGTTCTTCGGGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
1 TACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
28219 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
28284 TGGCACTACGGTGCAATTC
131 TGGCACTACGGTGCAATTC
28303 TACG
1 TACG
28307 GGGCACTTCG
Statistics
Matches: 152, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (149 bp):
TACGCGGTTCTTCGAGACATATGTATATTCTTTGGAACATGTGTGAAGTCTAGAAAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATTCTATGTGGTCCTTATGGACATTATTATA
TGGCACTACGGTGCAATTC
Found at i:28329 original size:23 final size:23
Alignment explanation
Indices: 28285--28329 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
28275 ATTATTATAT
*
28285 GGCACTACGGTGCAATTCTACGG
1 GGCACTACGGTGCAATTATACGG
* *
28308 GGCACTTCGGTGCATTTATACG
1 GGCACTACGGTGCAATTATACG
28330 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.29, T:0.27
Consensus pattern (23 bp):
GGCACTACGGTGCAATTATACGG
Found at i:29958 original size:22 final size:23
Alignment explanation
Indices: 29912--29979 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
29902 ATTCCCCTGT
*
29912 GGGGGAATCAATTCCCCTTCAAA
1 GGGGGAATCAATTCCCCTGCAAA
* *
29935 GGGGGAATCAGTTCCCCTGCAAG
1 GGGGGAATCAATTCCCCTGCAAA
* *
29958 GGGGGTATCGATTCCCTCTGCA
1 GGGGGAATCAATTCCC-CTGCA
29980 CCAAAATACT
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 33 0.87
24 5 0.13
ACGTcount: A:0.22, C:0.26, G:0.29, T:0.22
Consensus pattern (23 bp):
GGGGGAATCAATTCCCCTGCAAA
Found at i:36637 original size:23 final size:22
Alignment explanation
Indices: 36607--36682 Score: 82
Period size: 23 Copynumber: 3.5 Consensus size: 22
36597 GCATGGCCTT
36607 GTGCATCGATGCACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
* * *
36629 CGTGCATCGGTGCACCTTC-ATG
1 -GTGCATCGATGCACATTCAAGG
* *
36651 GTGTATCGATACACATTCAAGG
1 GTGCATCGATGCACATTCAAGG
*
36673 ATGCATCGAT
1 GTGCATCGAT
36683 CCACTGTTAG
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
21 14 0.33
22 12 0.29
23 16 0.38
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAAGG
Found at i:43236 original size:22 final size:21
Alignment explanation
Indices: 43194--43233 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
43184 AAGACTATTT
43194 TCATTTTTTAATTTTGAAATA
1 TCATTTTTTAATTTTGAAATA
*
43215 TCATTTTTTTATTTTGAAA
1 TCATTTTTTAATTTTGAAA
43234 ATAAAGTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.60
Consensus pattern (21 bp):
TCATTTTTTAATTTTGAAATA
Found at i:44944 original size:10 final size:10
Alignment explanation
Indices: 44929--44953 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
44919 CTCTTGATTC
44929 TTGTTTCTTG
1 TTGTTTCTTG
44939 TTGTTTCTTG
1 TTGTTTCTTG
44949 TTGTT
1 TTGTT
44954 GATCAATGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.20, T:0.72
Consensus pattern (10 bp):
TTGTTTCTTG
Found at i:50009 original size:39 final size:37
Alignment explanation
Indices: 49919--50218 Score: 176
Period size: 35 Copynumber: 8.5 Consensus size: 37
49909 ACATATAATA
* *
49919 ATAT-ATATATAATTTTGAAAACGGTTTTT-GAAA-AT
1 ATATAATATATATTTTTGAAAAC-ATTTTTGGAAACAT
* *
49954 ATATATTATATAATTTTTGGAAAACTTTTTTGGAAACAT
1 ATATAATATAT-ATTTTT-GAAAACATTTTTGGAAACAT
** * *
49993 ATATAATATATGATTTTTGAAAACATTTTAATATATATAT
1 ATATAATATAT-ATTTTTGAAAACATTTT--TGGAAACAT
*
50033 ATATATTATATAATTTTTGAAAACA-TTTT-GAAA-AT
1 ATATAATATAT-ATTTTTGAAAACATTTTTGGAAACAT
* * *
50068 ATATATTATATAGTTTTGAAATCATTTTT----A-A-
1 ATATAATATATATTTTTGAAAACATTTTTGGAAACAT
**** *
50099 ATATAATATATATTAAAAAAAACATTTTT-GAAA-AC
1 ATATAATATATATTTTTGAAAACATTTTTGGAAACAT
* *
50134 ATGTAATATATAATTTT-AAAACATTTTT-GAAA-ATT
1 ATATAATATATATTTTTGAAAACATTTTTGGAAACA-T
* *
50169 ATATAATATA-ATTTTGGAAAATATTTTT---AA-AT
1 ATATAATATATATTTTTGAAAACATTTTTGGAAACAT
50201 ATATAATATATAGTTTTT
1 ATATAATATATA-TTTTT
50219 AATATTTTTT
Statistics
Matches: 215, Mismatches: 34, Indels: 33
0.76 0.12 0.12
Matches are distributed among these distances:
31 22 0.10
32 13 0.06
33 4 0.02
34 37 0.17
35 52 0.24
36 7 0.03
37 11 0.05
38 20 0.09
39 21 0.10
40 28 0.13
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (37 bp):
ATATAATATATATTTTTGAAAACATTTTTGGAAACAT
Found at i:50024 original size:25 final size:26
Alignment explanation
Indices: 49980--50028 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
49970 TTGGAAAACT
*
49980 TTTTTGGAAACATATATAATATATGA
1 TTTTTGAAAACATATATAATATATGA
*
50006 TTTTTGAAAACAT-TTTAATATAT
1 TTTTTGAAAACATATATAATATAT
50029 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATGA
Found at i:50040 original size:79 final size:73
Alignment explanation
Indices: 49919--50246 Score: 252
Period size: 66 Copynumber: 4.7 Consensus size: 73
49909 ACATATAATA
* * *
49919 ATAT-ATATATAATTTTGAAAACGGTTTTT-GA-A-AATATATATTATATAATTTTTGGAAAACT
1 ATATAATATATAGTTTTGAAAAC-ATTTTTAAATATAATATATATTATATAATTTTT-GAAAAC-
*
49980 TTTTTGGAAACAT
63 ATTTT-GAAA-AT
*
49993 ATATAATATATGATTTTTGAAAACA-TTTTAATATATATATATATATTATATAATTTTTGAAAAC
1 ATATAATATAT-AGTTTTGAAAACATTTTTAA-ATATA-ATATATATTATATAATTTTTGAAAAC
50057 ATTTTGAAAAT
63 ATTTTGAAAAT
* *
50068 ATATATTATATAGTTTTGAAATCATTTTTAAATATAATATATATTA-A-AA------AAAACATT
1 ATATAATATATAGTTTTGAAAACATTTTTAAATATAATATATATTATATAATTTTTGAAAACA-T
*
50125 TTTGAAAAC
65 TTTGAAAAT
* * * *
50134 ATGTAATATATAATTTT-AAAACATTTTTGAAA-AT--TATATA--ATATAATTTTGGAAAATAT
1 ATATAATATATAGTTTTGAAAACATTTTT-AAATATAATATATATTATATAATTTTTGAAAACAT
*
50193 TTT-TAAAT
65 TTTGAAAAT
* * * *
50201 ATATAATATATAGTTTT--TAATATTTTT-TATATATTATATATTATAT
1 ATATAATATATAGTTTTGAAAACATTTTTAAATATAATATATATTATAT
50247 TTTATTATTA
Statistics
Matches: 211, Mismatches: 20, Indels: 51
0.75 0.07 0.18
Matches are distributed among these distances:
61 1 0.00
62 1 0.00
63 8 0.04
64 1 0.00
65 20 0.09
66 34 0.16
67 24 0.11
68 4 0.02
69 9 0.04
71 2 0.01
72 1 0.00
73 10 0.05
74 24 0.11
75 24 0.11
76 16 0.08
77 5 0.02
78 7 0.03
79 20 0.09
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (73 bp):
ATATAATATATAGTTTTGAAAACATTTTTAAATATAATATATATTATATAATTTTTGAAAACATT
TTGAAAAT
Found at i:50070 original size:35 final size:35
Alignment explanation
Indices: 49919--50218 Score: 217
Period size: 34 Copynumber: 8.5 Consensus size: 35
49909 ACATATAATA
*
49919 ATATA-TATATAA-TTTTGAAAACGGTTTTTGAAAAT
1 ATATATTATATAATTTTTGAAAAC--ATTTTGAAAAT
*
49954 ATATATTATATAATTTTTGGAAAACTTTTTTGGAAACAT
1 ATATATTATATAATTTTT-GAAAAC-ATTTT-GAAA-AT
* * *
49993 ATATAATATATGATTTTTGAAAACATTTTAATATATATAT
1 ATATATTATATAATTTTTGAAAACATTTT--GA-A-A-AT
50033 ATATATTATATAATTTTTGAAAACATTTTGAAAAT
1 ATATATTATATAATTTTTGAAAACATTTTGAAAAT
* * *
50068 ATATATTATAT-AGTTTTGAAATCATTTT-TAAAT
1 ATATATTATATAATTTTTGAAAACATTTTGAAAAT
**** *
50101 ATA-A-TATAT-ATTAAAAAAAACATTTTTGAAAAC
1 ATATATTATATAATTTTTGAAAACA-TTTTGAAAAT
* *
50134 ATGTAATATATAA-TTTT-AAAACATTTTTGAAAAT
1 ATATATTATATAATTTTTGAAAACA-TTTTGAAAAT
* * * *
50168 -TATATAATATAATTTTGGAAAATATTTT-TAAAT
1 ATATATTATATAATTTTTGAAAACATTTTGAAAAT
* *
50201 ATATAATATATAGTTTTT
1 ATATATTATATAATTTTT
50219 AATATTTTTT
Statistics
Matches: 213, Mismatches: 36, Indels: 33
0.76 0.13 0.12
Matches are distributed among these distances:
31 12 0.06
32 5 0.02
33 25 0.12
34 52 0.24
35 29 0.14
36 9 0.04
37 14 0.07
38 18 0.08
39 19 0.09
40 30 0.14
ACGTcount: A:0.45, C:0.03, G:0.07, T:0.46
Consensus pattern (35 bp):
ATATATTATATAATTTTTGAAAACATTTTGAAAAT
Found at i:50079 original size:77 final size:75
Alignment explanation
Indices: 49919--50113 Score: 215
Period size: 77 Copynumber: 2.6 Consensus size: 75
49909 ACATATAATA
* * *
49919 ATATAT-ATATAATTTTGAAAACGGTTTTT-GA-A-AATATATATTATATAATTTTTGGAAAACT
1 ATATATAATATAGTTTTGAAAAC-ATTTTTAAATATAATATATATTATATAATTTTTGGAAAACT
* *
49980 TTTTTGGAAAC
65 ATTTTGAAAAC
49991 ATATATAATATATGATTTTTGAAAACA-TTTTAATATATATATATATATTATATAATTTTT-GAA
1 ATATATAATATA-G--TTTTGAAAACATTTTTAA-ATATA-ATATATATTATATAATTTTTGGAA
*
50054 AAC-ATTTTGAAAAT
61 AACTATTTTGAAAAC
* *
50068 ATATATTATATAGTTTTGAAATCATTTTTAAATATAATATATATTA
1 ATATATAATATAGTTTTGAAAACATTTTTAAATATAATATATATTA
50114 AAAAAAACAT
Statistics
Matches: 105, Mismatches: 8, Indels: 19
0.80 0.06 0.14
Matches are distributed among these distances:
72 6 0.06
73 15 0.14
74 19 0.18
75 6 0.06
76 12 0.11
77 20 0.19
78 7 0.07
79 20 0.19
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (75 bp):
ATATATAATATAGTTTTGAAAACATTTTTAAATATAATATATATTATATAATTTTTGGAAAACTA
TTTTGAAAAC
Found at i:50110 original size:40 final size:39
Alignment explanation
Indices: 49911--50111 Score: 158
Period size: 40 Copynumber: 5.3 Consensus size: 39
49901 TTTGAAATAC
*
49911 ATATAATA-ATATA-TATATAA-TTTTGAAAACGGTTTT-
1 ATATAATATATATATTATATAATTTTTGAAAAC-ATTTTA
* *
49947 -TGA-AA-ATATATATTATATAATTTTTGGAAAACTTTTTT
1 AT-ATAATATATATATTATATAATTTTT-GAAAACATTTTA
** * * *
49985 GGA-AACATATATAATATATGATTTTTGAAAACATTTTA
1 ATATAATATATATATTATATAATTTTTGAAAACATTTTA
50023 ATATATATATATATATTATATAATTTTTGAAAACATTTT-
1 ATATA-ATATATATATTATATAATTTTTGAAAACATTTTA
* * *
50062 -GA-AA-ATATATATTATAT-AGTTTTGAAATCATTTTTAA
1 ATATAATATATATATTATATAATTTTTGAAAACA-TTTT-A
50099 ATATAATATATAT
1 ATATAATATATAT
50112 TAAAAAAAAC
Statistics
Matches: 134, Mismatches: 15, Indels: 28
0.76 0.08 0.16
Matches are distributed among these distances:
34 12 0.09
35 25 0.19
36 9 0.07
37 9 0.07
38 22 0.16
39 21 0.16
40 36 0.27
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (39 bp):
ATATAATATATATATTATATAATTTTTGAAAACATTTTA
Found at i:50135 original size:77 final size:77
Alignment explanation
Indices: 49952--50118 Score: 200
Period size: 79 Copynumber: 2.2 Consensus size: 77
49942 GTTTTTGAAA
* * * *
49952 ATATATATTATATAATTTTTGGAAAACTTTTTTGGAAACATATATAATATATGATTTTTGAAAAC
1 ATATATATTAAAAAATTTTT-GAAAAC-ATTTTGGAAACATATATAATATATGAGTTTTGAAAAC
50017 ATTTTAATATATAT
64 ATTTTAATATATAT
* * * *
50031 ATATATATTATATAATTTTTGAAAACATTTT-GAAA-ATATATATTATAT-AGTTTTGAAATCAT
1 ATATATATTAAAAAATTTTTGAAAACATTTTGGAAACATATATAATATATGAGTTTTGAAAACA-
50093 TTTTAA-ATATA-
65 TTTTAATATATAT
50104 ATATATATTAAAAAA
1 ATATATATTAAAAAA
50119 AACATTTTTG
Statistics
Matches: 81, Mismatches: 6, Indels: 8
0.85 0.06 0.08
Matches are distributed among these distances:
73 13 0.16
74 16 0.20
75 18 0.22
76 4 0.05
77 4 0.05
78 6 0.07
79 20 0.25
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (77 bp):
ATATATATTAAAAAATTTTTGAAAACATTTTGGAAACATATATAATATATGAGTTTTGAAAACAT
TTTAATATATAT
Found at i:50239 original size:7 final size:7
Alignment explanation
Indices: 50227--50263 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
50217 TTAATATTTT
50227 TTATATA
1 TTATATA
50234 TTATATA
1 TTATATA
*
50241 TTATATT
1 TTATATA
50248 TTAT-TA
1 TTATATA
50254 TTAT-TA
1 TTATATA
50260 TTAT
1 TTAT
50264 TCTTTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATATA
Found at i:50246 original size:14 final size:13
Alignment explanation
Indices: 50227--50279 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
50217 TTAATATTTT
50227 TTATATATTATATA
1 TTATATATTAT-TA
*
50241 TTATATTTTATTA
1 TTATATATTATTA
*
50254 TTAT-TATTATTC
1 TTATATATTATTA
*
50266 TTTTA-ATTATTA
1 TTATATATTATTA
50278 TT
1 TT
50280 TTTTCTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 17 0.52
13 6 0.18
14 10 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:50281 original size:12 final size:11
Alignment explanation
Indices: 50215--50290 Score: 56
Period size: 10 Copynumber: 7.3 Consensus size: 11
50205 AATATATAGT
*
50215 TTTTAATATT-
1 TTTTATTATTA
50225 TTTTATATATTA
1 TTTTAT-TATTA
*
50237 -TATATTA-TA
1 TTTTATTATTA
50246 TTTTATTATTA
1 TTTTATTATTA
*
50257 --TTATTATTC
1 TTTTATTATTA
50266 TTTTAATTATTA
1 TTTT-ATTATTA
*
50278 TTTT-TTCTTA
1 TTTTATTATTA
50288 TTT
1 TTT
50291 ATTTATTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 10 0.19
10 21 0.40
11 12 0.23
12 10 0.19
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:50291 original size:21 final size:22
Alignment explanation
Indices: 50227--50297 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
50217 TTAATATTTT
* *
50227 TTATATATTATATATTATATTTTA
1 TTAT-TATTAT-TATTCTATTTAA
50251 TTATTATTATTATTCT-TTTAA
1 TTATTATTATTATTCTATTTAA
*
50272 TTATTATT-TT-TTCTTATTTAT
1 TTATTATTATTATTC-TATTTAA
50293 TTATT
1 TTATT
50298 TCTTTTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 21 0.50
22 5 0.12
23 6 0.14
24 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATTATTATTATTCTATTTAA
Found at i:50301 original size:34 final size:31
Alignment explanation
Indices: 50240--50303 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
50230 TATATTATAT
50240 ATTATATTTTATTATTATTATTATTCTTTTA
1 ATTATATTTTATTATTATTATTATTCTTTTA
*
50271 ATTATTATTTT-TTCTTATTTATTTATTTCTTTT
1 ATTA-TATTTTATTATTA-TTA-TTA-TTCTTTT
50304 TGTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 9 0.32
32 9 0.32
33 3 0.11
34 7 0.25
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (31 bp):
ATTATATTTTATTATTATTATTATTCTTTTA
Found at i:51025 original size:13 final size:13
Alignment explanation
Indices: 51007--51037 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
50997 CGGCCACCGG
51007 CGCCGCCGTGCGA
1 CGCCGCCGTGCGA
51020 CGCCGCCGTGCGA
1 CGCCGCCGTGCGA
51033 CGCCG
1 CGCCG
51038 TAGCTCCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.48, G:0.39, T:0.06
Consensus pattern (13 bp):
CGCCGCCGTGCGA
Found at i:51678 original size:15 final size:16
Alignment explanation
Indices: 51658--51687 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
51648 TAATTATCAT
51658 TTTTTTTG-ATATTTC
1 TTTTTTTGAATATTTC
51673 TTTTTTTGAATATTT
1 TTTTTTTGAATATTT
51688 TTAGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTTTGAATATTTC
Found at i:52742 original size:17 final size:16
Alignment explanation
Indices: 52720--52759 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
52710 TCTCACTAAC
*
52720 TTTTTTTCTCCTTT-CA
1 TTTTTTT-TCTTTTGCA
52736 TTTTTTTTCTTTTGCA
1 TTTTTTTTCTTTTGCA
52752 TTTTTTTT
1 TTTTTTTT
52760 ATCATTCACA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.05, C:0.15, G:0.03, T:0.78
Consensus pattern (16 bp):
TTTTTTTTCTTTTGCA
Found at i:53407 original size:19 final size:19
Alignment explanation
Indices: 53373--53417 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
53363 ATTTAGACAT
53373 TTTGCA-TTTCTTATTTTC
1 TTTGCATTTTCTTATTTTC
*
53391 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTCTTATTTTC
53410 TTTGCATT
1 TTTGCATT
53418 CACATTAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 6 0.24
19 19 0.76
ACGTcount: A:0.11, C:0.13, G:0.09, T:0.67
Consensus pattern (19 bp):
TTTGCATTTTCTTATTTTC
Found at i:57047 original size:84 final size:83
Alignment explanation
Indices: 56768--57548 Score: 908
Period size: 84 Copynumber: 9.5 Consensus size: 83
56758 TTTAAAACAA
* * * * ** *
56768 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCA-CAAAAGACCTTCGAGTTCGACT
*
56833 ACGCTCAGCTCCAAGGCAC
65 ACGCTCAGCTCTAAGGCAC
* * * *
56852 ATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTG-C-C-AAAGACCTTCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTA
* * *
56914 CACTCAGCTCTGAGGGCAT
66 CGCTCAGCTCT-AAGGCAC
* * *
56933 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACT
56998 ACGCTCAGCTCTAAGGCAC
65 ACGCTCAGCTCTAAGGCAC
* * * *
57017 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-C-AAAGACC-CCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTA
* * * *
57078 CACTCAGCTTCGAGGGCAT
66 CGCTCAGC-TCTAAGGCAC
* * *
57097 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACT
57162 ACGCTCAGCTCTAAGGCAC
65 ACGCTCAGCTCTAAGGCAC
* * * * *
57181 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-C-AAAGACC-CCGAGTTTGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTA
* * *
57242 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCTAAGGCAC
* * *
57261 ATCATTTGTAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACT
57326 ACGCTCAGCTCTAAGGCAC
65 ACGCTCAGCTCTAAGGCAC
* * * *
57345 ATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-C-AAAGACC-CCGAGTTCGATTA
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTA
* * *
57406 CACTCAGCTTCGAGGGCAC
66 CGCTCAGC-TCTAAGGCAC
* *
57425 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCC-ACAAAAGACCTTCGAGTTCGACT
*
57490 ACGCTCAGCTCCAAGGCAC
65 ACGCTCAGCTCTAAGGCAC
* *
57509 ATCATTTGCAGCATAGCTTAAGTCGAGAGGGGTTATCTGC
1 ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGC
57549 TAAAGACCTT
Statistics
Matches: 583, Mismatches: 91, Indels: 46
0.81 0.13 0.06
Matches are distributed among these distances:
79 53 0.09
80 175 0.30
81 45 0.08
82 1 0.00
83 6 0.01
84 220 0.38
85 83 0.14
ACGTcount: A:0.29, C:0.25, G:0.22, T:0.24
Consensus pattern (83 bp):
ATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCTGCCACAAAAGACCTTCGAGTTCGACTA
CGCTCAGCTCTAAGGCAC
Found at i:57151 original size:164 final size:164
Alignment explanation
Indices: 56768--57570 Score: 1320
Period size: 164 Copynumber: 4.9 Consensus size: 164
56758 TTTAAAACAA
* * * ** * *
56768 ATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTGACCAAAAGACCTTTGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* *
56833 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGGAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
* *
56898 CCTTCGAGTTCGATTACACTCAGC-TCTGAGGGCAT
131 CC-CCGAGTTCGATTACACTCAGCTTC-GAGGGCAC
* *
56933 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
56998 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
57063 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAT
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
57097 ATCATTTGCAGCACAACTTAAGTCTAGAAGGGTTGTCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
57162 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
*
57227 CCCCGAGTTTGATTACACTCAGCTTCGAGGGCAC
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* * *
57261 ATCATTTGTAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
57326 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
66 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
57391 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
131 CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
* *
57425 ATCATTTGCAGTATAACTTAAGTCAAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
1 ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
* * * *
57490 ACGCTCAGCTCCAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAGGGGTTATCTGCTAAAGA
66 ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
**
57555 CCTTTGAGTTCGATTA
131 CC-CCGAGTTCGATTA
57571 TATTCAACTT
Statistics
Matches: 609, Mismatches: 27, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
164 475 0.78
165 134 0.22
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (164 bp):
ATCATTTGCAGCATAACTTAAGTCTAGAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACT
ACGCTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGA
CCCCGAGTTCGATTACACTCAGCTTCGAGGGCAC
Found at i:58256 original size:42 final size:39
Alignment explanation
Indices: 58204--58383 Score: 137
Period size: 37 Copynumber: 4.6 Consensus size: 39
58194 TTTGCGAATG
58204 TTTTTG-AAATACATATAATATATATATAATTTTGAAAAC
1 TTTTTGAAAATACATAT-ATATATATATAATTTTGAAAAC
*
58243 GGTTTTTGAAAAT--ATATAT-TATATA-ATTTTTGGAAAAC
1 --TTTTTGAAAATACATATATATATATATAATTTT-GAAAAC
* *
58281 TTTTTTG-GAA-ACATATATA-ATATATGATTTTTGAAAAC
1 -TTTTTGAAAATACATATATATATATAT-AATTTTGAAAAC
* *
58319 ATTTT-AATATATATATATATATATTATATAATTTTTGAAAAC
1 TTTTTGAA-A-ATACATATATATA-TATATAA-TTTTGAAAAC
* *
58361 ATTTTGAAAATATATAT-TATATA
1 TTTTTGAAAATACATATATATATA
58384 GTTTTGAAAT
Statistics
Matches: 117, Mismatches: 7, Indels: 32
0.75 0.04 0.21
Matches are distributed among these distances:
36 2 0.02
37 26 0.22
38 19 0.16
39 11 0.09
40 16 0.14
41 16 0.14
42 25 0.21
43 2 0.02
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.46
Consensus pattern (39 bp):
TTTTTGAAAATACATATATATATATATAATTTTGAAAAC
Found at i:58260 original size:35 final size:34
Alignment explanation
Indices: 58221--58513 Score: 190
Period size: 35 Copynumber: 8.3 Consensus size: 34
58211 AATACATATA
*
58221 ATATATATATAATTTTGAAAACGGTTTTTGAAAAT
1 ATATATATATAATTTTGAAAAC-ATTTTTGAAAAT
*
58256 ATATATTATATAATTTTTGGAAAACTTTTTTGGAAACAT
1 ATATA-TATATAA-TTTT-GAAAACATTTTT-GAAA-AT
* *
58295 ATATAATATATGATTTTTGAAAACATTTTAATATATATATAT
1 ATAT-ATATAT-AATTTTGAAAACATTTT--T-GA-A-A-AT
** *
58337 ATATATTATATAATTTTTGAAA-ACATTTTGAAAAT
1 ATATA-TATATAATTTTGAAAACA-TTTTTGAAAAT
* *
58372 ATATATTATATAGTTTTGAAATCATTTTT--AAAT
1 ATATA-TATATAATTTTGAAAACATTTTTGAAAAT
*** *
58405 ATA-ATATAT-ATTAAAAAAAACATTTTTGAAAAC
1 ATATATATATAATT-TTGAAAACATTTTTGAAAAT
*
58438 ATGTAATATATAATTTT-AAAACATTTTTGAAAAT
1 ATAT-ATATATAATTTTGAAAACATTTTTGAAAAT
*
58472 -TATATAATATAATTTTGGAAAATATTTTT--AAAT
1 ATATAT-ATATAATTTT-GAAAACATTTTTGAAAAT
*
58505 ATAAATATA
1 ATATATATA
58514 GTTTTTAATA
Statistics
Matches: 205, Mismatches: 29, Indels: 50
0.72 0.10 0.18
Matches are distributed among these distances:
30 2 0.01
31 15 0.07
32 3 0.01
33 31 0.15
34 20 0.10
35 45 0.22
36 12 0.06
37 10 0.05
38 21 0.10
39 16 0.08
40 5 0.02
41 13 0.06
42 12 0.06
ACGTcount: A:0.46, C:0.03, G:0.06, T:0.45
Consensus pattern (34 bp):
ATATATATATAATTTTGAAAACATTTTTGAAAAT
Found at i:58326 original size:25 final size:26
Alignment explanation
Indices: 58282--58330 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
58272 TTGGAAAACT
*
58282 TTTTTGGAAACATATATAATATATGA
1 TTTTTGAAAACATATATAATATATGA
*
58308 TTTTTGAAAACAT-TTTAATATAT
1 TTTTTGAAAACATATATAATATAT
58331 ATATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 9 0.43
26 12 0.57
ACGTcount: A:0.41, C:0.04, G:0.08, T:0.47
Consensus pattern (26 bp):
TTTTTGAAAACATATATAATATATGA
Found at i:58341 original size:44 final size:42
Alignment explanation
Indices: 58255--58383 Score: 144
Period size: 42 Copynumber: 3.1 Consensus size: 42
58245 TTTTTGAAAA
* * *
58255 TATATATTATATAATTTTTGGAAAACTTTTTTG-GAA-ACATA-
1 TATATATTATATAATTTTT-GAAAAC-ATTTTGAAAATATATAT
* *
58296 TATA-A-TATATGATTTTTGAAAACATTTT-AATATATATAT
1 TATATATTATATAATTTTTGAAAACATTTTGAAAATATATAT
58335 ATATATATTATATAATTTTTGAAAACATTTTGAAAATATATAT
1 -TATATATTATATAATTTTTGAAAACATTTTGAAAATATATAT
58378 TATATA
1 TATATA
58384 GTTTTGAAAT
Statistics
Matches: 74, Mismatches: 7, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
37 5 0.07
38 10 0.14
39 11 0.15
40 5 0.07
41 5 0.07
42 28 0.38
43 10 0.14
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.47
Consensus pattern (42 bp):
TATATATTATATAATTTTTGAAAACATTTTGAAAATATATAT
Found at i:58405 original size:33 final size:35
Alignment explanation
Indices: 58335--58507 Score: 125
Period size: 34 Copynumber: 5.1 Consensus size: 35
58325 ATATATATAT
*
58335 ATATATATTATATAATTTTTGAAAACATTTTGAAA
1 ATATATATTATATAAGTTTTGAAAACATTTTGAAA
* *
58370 ATATATATTATAT-AGTTTTGAAATCATTTT-TAA
1 ATATATATTATATAAGTTTTGAAAACATTTTGAAA
***
58403 ATATA-A-TATAT-A-TTAAAAAAAACATTTTTGAAA
1 ATATATATTATATAAGTT-TTGAAAACA-TTTTGAAA
* * *
58436 ACATGTAATATATAA-TTTT-AAAACATTTTTGAAA
1 ATATATATTATATAAGTTTTGAAAACA-TTTTGAAA
* * *
58470 AT-TATATAATATAA-TTTTGGAAAATATTTT-TAA
1 ATATATATTATATAAGTTTT-GAAAACATTTTGAAA
58503 ATATA
1 ATATA
58508 AATATAGTTT
Statistics
Matches: 111, Mismatches: 18, Indels: 19
0.75 0.12 0.13
Matches are distributed among these distances:
30 2 0.02
31 11 0.10
32 5 0.05
33 29 0.26
34 38 0.34
35 23 0.21
36 3 0.03
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (35 bp):
ATATATATTATATAAGTTTTGAAAACATTTTGAAA
Found at i:58415 original size:81 final size:81
Alignment explanation
Indices: 58254--58415 Score: 230
Period size: 81 Copynumber: 2.1 Consensus size: 81
58244 GTTTTTGAAA
* *
58254 ATATATATTATATAATTTTTGGAAAACTTTTTTGGAAACATATATAATATATGATTTTTGAAAAC
1 ATATATATTATATAATTTTTGGAAAACTATTTTGGAAACATATATAATATATGAGTTTTGAAAAC
58319 ATTTTAATATATATAT
66 ATTTTAATATATATAT
* *
58335 ATATATATTATATAATTTTT-GAAAAC-ATTTT-GAAA-ATATATATTATAT-AGTTTTGAAATC
1 ATATATATTATATAATTTTTGGAAAACTATTTTGGAAACATATATAATATATGAGTTTTGAAAAC
58395 ATTTTTAA-ATATA-AT
66 A-TTTTAATATATATAT
58410 ATATAT
1 ATATAT
58416 TAAAAAAAAC
Statistics
Matches: 76, Mismatches: 4, Indels: 8
0.86 0.05 0.09
Matches are distributed among these distances:
75 8 0.11
76 16 0.21
77 18 0.24
78 4 0.05
79 4 0.05
80 6 0.08
81 20 0.26
ACGTcount: A:0.43, C:0.03, G:0.06, T:0.48
Consensus pattern (81 bp):
ATATATATTATATAATTTTTGGAAAACTATTTTGGAAACATATATAATATATGAGTTTTGAAAAC
ATTTTAATATATATAT
Found at i:58430 original size:77 final size:79
Alignment explanation
Indices: 58267--58439 Score: 194
Period size: 77 Copynumber: 2.2 Consensus size: 79
58257 TATATTATAT
* *
58267 AATTTTTGGAAAACTTTTTTGGAAACATATATAATATATGATTTTTGAAAACATTTTAATATATA
1 AATTTTT-GAAAACATTT-TGGAAACATATATAATATATGAGTTTTGAAAACATTTTAATATATA
** * *
58332 TATATATATATTATAT
64 TATATATATAAAAAAA
* *
58348 AATTTTTGAAAACATTTT-GAAA-ATATATATTATAT-AGTTTTGAAATCATTTTTAA-ATATA-
1 AATTTTTGAAAACATTTTGGAAACATATATAATATATGAGTTTTGAAAACA-TTTTAATATATAT
58408 ATATATATTAAAAAAA
65 ATATATA-TAAAAAAA
58424 ACATTTTTGAAAACAT
1 A-ATTTTTGAAAACAT
58440 GTAATATATA
Statistics
Matches: 81, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
75 7 0.09
76 21 0.26
77 32 0.40
78 4 0.05
79 1 0.01
80 9 0.11
81 7 0.09
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (79 bp):
AATTTTTGAAAACATTTTGGAAACATATATAATATATGAGTTTTGAAAACATTTTAATATATATA
TATATATAAAAAAA
Found at i:58540 original size:7 final size:7
Alignment explanation
Indices: 58528--58564 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
58518 TTAATATTTT
58528 TTATATA
1 TTATATA
58535 TTATATA
1 TTATATA
*
58542 TTATATT
1 TTATATA
58549 TTAT-TA
1 TTATATA
58555 TTAT-TA
1 TTATATA
58561 TTAT
1 TTAT
58565 TCTTTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
6 11 0.39
7 17 0.61
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (7 bp):
TTATATA
Found at i:58547 original size:14 final size:13
Alignment explanation
Indices: 58528--58580 Score: 56
Period size: 12 Copynumber: 4.2 Consensus size: 13
58518 TTAATATTTT
58528 TTATATATTATATA
1 TTATATATTAT-TA
*
58542 TTATATTTTATTA
1 TTATATATTATTA
*
58555 TTAT-TATTATTC
1 TTATATATTATTA
*
58567 TTTTA-ATTATTA
1 TTATATATTATTA
58579 TT
1 TT
58581 TTTTCTTATT
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
12 17 0.52
13 6 0.18
14 10 0.30
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (13 bp):
TTATATATTATTA
Found at i:58582 original size:12 final size:11
Alignment explanation
Indices: 58516--58591 Score: 56
Period size: 10 Copynumber: 7.3 Consensus size: 11
58506 TAAATATAGT
*
58516 TTTTAATATT-
1 TTTTATTATTA
58526 TTTTATATATTA
1 TTTTAT-TATTA
*
58538 -TATATTA-TA
1 TTTTATTATTA
58547 TTTTATTATTA
1 TTTTATTATTA
*
58558 --TTATTATTC
1 TTTTATTATTA
58567 TTTTAATTATTA
1 TTTT-ATTATTA
*
58579 TTTT-TTCTTA
1 TTTTATTATTA
58589 TTT
1 TTT
58592 ATTTATTTCT
Statistics
Matches: 53, Mismatches: 6, Indels: 14
0.73 0.08 0.19
Matches are distributed among these distances:
9 10 0.19
10 21 0.40
11 12 0.23
12 10 0.19
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.70
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:58592 original size:21 final size:22
Alignment explanation
Indices: 58528--58598 Score: 67
Period size: 21 Copynumber: 3.2 Consensus size: 22
58518 TTAATATTTT
* *
58528 TTATATATTATATATTATATTTTA
1 TTAT-TATTAT-TATTCTATTTAA
58552 TTATTATTATTATTCT-TTTAA
1 TTATTATTATTATTCTATTTAA
*
58573 TTATTATT-TT-TTCTTATTTAT
1 TTATTATTATTATTC-TATTTAA
58594 TTATT
1 TTATT
58599 TCTTTTTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
19 3 0.07
20 3 0.07
21 21 0.50
22 5 0.12
23 6 0.14
24 4 0.10
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (22 bp):
TTATTATTATTATTCTATTTAA
Found at i:58602 original size:34 final size:31
Alignment explanation
Indices: 58541--58604 Score: 76
Period size: 31 Copynumber: 2.0 Consensus size: 31
58531 TATATTATAT
58541 ATTATATTTTATTATTATTATTATTCTTTTA
1 ATTATATTTTATTATTATTATTATTCTTTTA
*
58572 ATTATTATTTT-TTCTTATTTATTTATTTCTTTT
1 ATTA-TATTTTATTATTA-TTA-TTA-TTCTTTT
58605 TGTTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
31 9 0.32
32 9 0.32
33 3 0.11
34 7 0.25
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (31 bp):
ATTATATTTTATTATTATTATTATTCTTTTA
Found at i:59325 original size:13 final size:13
Alignment explanation
Indices: 59307--59337 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
59297 CGGCCACCGG
59307 CGCCGCCGTGCGA
1 CGCCGCCGTGCGA
59320 CGCCGCCGTGCGA
1 CGCCGCCGTGCGA
59333 CGCCG
1 CGCCG
59338 TAGCTCCGCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.06, C:0.48, G:0.39, T:0.06
Consensus pattern (13 bp):
CGCCGCCGTGCGA
Found at i:59985 original size:15 final size:16
Alignment explanation
Indices: 59965--59994 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
59955 TAATTATCAT
59965 TTTTTTTG-ATATTTC
1 TTTTTTTGAATATTTC
59980 TTTTTTTGAATATTT
1 TTTTTTTGAATATTT
59995 TTAGTAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.17, C:0.03, G:0.07, T:0.73
Consensus pattern (16 bp):
TTTTTTTGAATATTTC
Found at i:63700 original size:23 final size:22
Alignment explanation
Indices: 63658--63702 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
63648 TTTGGGTGGA
63658 GGTTTTCTTGGGTTGATTGTTTC
1 GGTTTTCTTGGGTT-ATTGTTTC
63681 GGTTGTTCTTGGTGTT-TTGTTT
1 GGTT-TTCTTGG-GTTATTGTTT
63703 AATTGTAGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 10 0.50
24 7 0.35
25 3 0.15
ACGTcount: A:0.02, C:0.07, G:0.31, T:0.60
Consensus pattern (22 bp):
GGTTTTCTTGGGTTATTGTTTC
Found at i:64965 original size:15 final size:17
Alignment explanation
Indices: 64929--64965 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
64919 GGGAACGTTT
64929 AGAGAAACAGATTCATG
1 AGAGAAACAGATTCATG
*
64946 AGAGAAACAGATTCAGG
1 AGAGAAACAGATTCATG
64963 AGA
1 AGA
64966 CTGAGAGGAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.14
Consensus pattern (17 bp):
AGAGAAACAGATTCATG
Found at i:65243 original size:32 final size:31
Alignment explanation
Indices: 65154--65244 Score: 85
Period size: 32 Copynumber: 2.9 Consensus size: 31
65144 CCAACCTAAG
* * * *
65154 GGAATATCTTGGGGCCTGAGAGCCTACCCGAT
1 GGAATACCTTGGGGCCTCAAAGCCTA-CCGAA
* * *
65186 GGAGTACCTT-GAGCCTTAAAGCCTACCGAA
1 GGAATACCTTGGGGCCTCAAAGCCTACCGAA
*
65216 GGAAATACCTTGGGGCCTCATAGCCTACC
1 GG-AATACCTTGGGGCCTCAAAGCCTACC
65245 CAAGTGTCAC
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
30 6 0.13
31 19 0.40
32 22 0.47
ACGTcount: A:0.25, C:0.27, G:0.26, T:0.21
Consensus pattern (31 bp):
GGAATACCTTGGGGCCTCAAAGCCTACCGAA
Found at i:68758 original size:3 final size:3
Alignment explanation
Indices: 68750--68811 Score: 65
Period size: 3 Copynumber: 20.7 Consensus size: 3
68740 AAAATGATAT
* * *
68750 TAA TAA TAA TAC TAA TAA TAA TAA TCA TAA TCA TAA T-A TAA TATA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A
68795 TAA TAA T-A TATA TAA TA
1 TAA TAA TAA TA-A TAA TA
68812 TTTTTTTAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
2 4 0.08
3 39 0.80
4 6 0.12
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:69300 original size:136 final size:136
Alignment explanation
Indices: 69057--69406 Score: 521
Period size: 136 Copynumber: 2.6 Consensus size: 136
69047 TGTTGAGCTA
* * *
69057 AGGTTGAACAAGTTCTTCTCATTATGAACTTC-T-T-CCTCTA-GA-ATGAGTTTTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
* * * *
69117 GAACTCTCCATTAGAGATGTCAATCCCTCAAGCGAGACATCATTGATTCAAAATGTCGTGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGACATCACTGATTCAAAATGTCATGAATCG
69182 AGTGAT
131 AGTGAT
*
69188 AGGTTGAACAAGCTCTTATCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
** * *
69253 GAACTCTTAATTGGAAATGTCAATCCCTCAAGCGAGGCGTCACTGATTCAAAATGTCATGAATCG
66 GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGACATCACTGATTCAAAATGTCATGAATCG
69318 AGTGAT
131 AGTGAT
** * *
69324 AGGCCGAACAAGCTCTTCTCATTATTAACTTATTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
1 AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
69389 GAACTCTCCATTGGAAAT
66 GAACTCTCCATTGGAAAT
69407 ATTGATCAGT
Statistics
Matches: 195, Mismatches: 19, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
131 30 0.15
132 1 0.01
133 1 0.01
134 6 0.03
135 1 0.01
136 156 0.80
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (136 bp):
AGGTTGAACAAGCTCTTCTCATTATGAACTTCTTCTCCCTCTATCAGATGAGTTCTTCTCATTAT
GAACTCTCCATTGGAAATGTCAATCCCTCAAGCGAGACATCACTGATTCAAAATGTCATGAATCG
AGTGAT
Found at i:69677 original size:21 final size:19
Alignment explanation
Indices: 69608--69701 Score: 51
Period size: 21 Copynumber: 5.2 Consensus size: 19
69598 GTTTCAAGGG
69608 AAACTGTCTCAAGAGAGAC
1 AAACTGTCTCAAGAGAGAC
* *
69627 AAAATTTGTTTCAAG-G-G--
1 -AAA-CTGTCTCAAGAGAGAC
69644 AAACTGTCTCAAGAGAGACC
1 AAACTGTCTCAAGAGAGA-C
*
69664 AAACTTGTTTCAAG-G-G--
1 AAAC-TGTCTCAAGAGAGAC
* *
69680 AAACTATCTCAAGCGAGAC
1 AAACTGTCTCAAGAGAGAC
69699 AAA
1 AAA
69702 ATCTTCTGTT
Statistics
Matches: 56, Mismatches: 7, Indels: 23
0.65 0.08 0.27
Matches are distributed among these distances:
15 15 0.27
16 9 0.16
17 2 0.04
19 5 0.09
20 9 0.16
21 16 0.29
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (19 bp):
AAACTGTCTCAAGAGAGAC
Found at i:69723 original size:39 final size:38
Alignment explanation
Indices: 69595--69784 Score: 228
Period size: 36 Copynumber: 5.1 Consensus size: 38
69585 AGATACAGTT
*
69595 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA--
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATC
* *
69631 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACCAAA-C
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATC
*
69668 -TTGTTTCAAGGGAAACTATCTCAAGCGAGACAAAATC
1 TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATC
* * *
69705 TTCTGTTTCGAGAGAAACTATCTCAAGTA-AGATAAAATC
1 TT-TGTTTCAAGGGAAACTATCTCAAG-AGAGACAAAATC
* * *
69744 TTTTGTTTCGAGGGAAACTATCTCAAGGGAGATAAAATC
1 -TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATC
69783 TT
1 TT
69785 CTTTAAAAAC
Statistics
Matches: 137, Mismatches: 10, Indels: 12
0.86 0.06 0.08
Matches are distributed among these distances:
36 67 0.49
37 1 0.01
38 3 0.02
39 64 0.47
40 2 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (38 bp):
TTTGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATC
Found at i:69765 original size:78 final size:78
Alignment explanation
Indices: 69560--69786 Score: 245
Period size: 78 Copynumber: 3.0 Consensus size: 78
69550 TGTCAAATTA
* * * * * * *
69560 GTTTTAAGAAAAACCATCTCAAGTGAGATACAGT-TTTTGTTTCAAGGGAAACTGTCTCAAGAGA
1 GTTTCAAGAGAAACTATCTCAAGTAAGATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGAGA
69624 GACAAAA--TT-T
66 GACAAAATCTTCT
* * ** *
69634 GTTTCAAGGGAAACTGTCTCAAG-AGAGACCAAA-C--TTGTTTCAAGGGAAACTATCTCAAGCG
1 GTTTCAAGAGAAACTATCTCAAGTA-AGATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGAG
69695 AGACAAAATCTTCT
65 AGACAAAATCTTCT
* * *
69709 GTTTCGAGAGAAACTATCTCAAGTAAGATAAAATCTTTTGTTTCGAGGGAAACTATCTCAAGGGA
1 GTTTCAAGAGAAACTATCTCAAGTAAGATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGAGA
*
69774 GATAAAATCTTCT
66 GACAAAATCTTCT
69787 TTAAAAACAA
Statistics
Matches: 124, Mismatches: 20, Indels: 14
0.78 0.13 0.09
Matches are distributed among these distances:
72 33 0.27
74 24 0.19
75 27 0.22
76 2 0.02
78 38 0.31
ACGTcount: A:0.37, C:0.16, G:0.19, T:0.28
Consensus pattern (78 bp):
GTTTCAAGAGAAACTATCTCAAGTAAGATAAAATCTTTTGTTTCAAGGGAAACTATCTCAAGAGA
GACAAAATCTTCT
Found at i:70013 original size:75 final size:77
Alignment explanation
Indices: 69789--70026 Score: 290
Period size: 76 Copynumber: 3.1 Consensus size: 77
69779 AATCTTCTTT
* * * * *
69789 AAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTCGAGTAAAA-ATCGTCTCATGCGATATAAA
1 AAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTTGAGTAAAACAT-GTCTCAAGTGAGACAAA
*
69853 -TCTTACTTTAAG
65 GTCTTATTTTAAG
* * * * *
69865 AAAAA-AAACATGTAGTGAAATGAAATGTCTTGTTTTGAATAAAACATGTCTCAAGTGAGACAAA
1 AAAAACAATCTTG-AGTAAAATGAAATGTCTTCTTTTGAGTAAAACATGTCTCAAGTGAGACAAA
*
69929 G-CTTGTTTTAAG
65 GTCTTATTTTAAG
* *
69941 AAAAACAATCTTGAGTCAAATGAAATGTCTTTTTTTGAGTAAAACA-GTCTCAAGTGAGACAAAG
1 AAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTTGAGTAAAACATGTCTCAAGTGAGACAAAG
70005 TC-TATTTTAAG
66 TCTTATTTTAAG
70016 AAAAACAATCT
1 AAAAACAATCT
70027 CCAGTGAGAT
Statistics
Matches: 139, Mismatches: 18, Indels: 11
0.83 0.11 0.07
Matches are distributed among these distances:
75 42 0.30
76 90 0.65
77 7 0.05
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (77 bp):
AAAAACAATCTTGAGTAAAATGAAATGTCTTCTTTTGAGTAAAACATGTCTCAAGTGAGACAAAG
TCTTATTTTAAG
Found at i:70022 original size:36 final size:37
Alignment explanation
Indices: 69913--70035 Score: 115
Period size: 36 Copynumber: 3.3 Consensus size: 37
69903 ATAAAACATG
*
69913 TCTCAAGTGAGACAAAG-CTTGTTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAAGTCTTATTTTAAGAAAAACAA
** * * * * * * *
69949 TCTTGAGTCAAATGAAATGTCTTTTTTTGAGTAAAACAG
1 TCTCAAGTGAGA-CAAA-GTCTTATTTTAAGAAAAACAA
69988 TCTCAAGTGAGACAAAGTC-TATTTTAAGAAAAACAA
1 TCTCAAGTGAGACAAAGTCTTATTTTAAGAAAAACAA
*
70024 TCTCCAGTGAGA
1 TCTCAAGTGAGA
70036 TAAATCCTCC
Statistics
Matches: 65, Mismatches: 19, Indels: 6
0.72 0.21 0.07
Matches are distributed among these distances:
36 32 0.49
37 6 0.09
38 4 0.06
39 23 0.35
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (37 bp):
TCTCAAGTGAGACAAAGTCTTATTTTAAGAAAAACAA
Found at i:83201 original size:19 final size:18
Alignment explanation
Indices: 83152--83222 Score: 56
Period size: 19 Copynumber: 3.9 Consensus size: 18
83142 GATGAAGTTG
* *
83152 AAAAT-ATATATTAAAAT
1 AAAATAATATAATAAAAA
83169 AAAATAA-ATAAATAAAAGA
1 AAAATAATAT-AATAAAA-A
*
83188 AAAATAATATAATAATAA
1 AAAATAATATAATAAAAA
* *
83206 ATATTAATAGTAATAAA
1 AAAATAATA-TAATAAA
83223 TATAAAAAGG
Statistics
Matches: 43, Mismatches: 6, Indels: 8
0.75 0.11 0.14
Matches are distributed among these distances:
17 7 0.16
18 15 0.35
19 19 0.44
20 2 0.05
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (18 bp):
AAAATAATATAATAAAAA
Found at i:83293 original size:21 final size:22
Alignment explanation
Indices: 83260--83300 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
83250 GGTTAAAATA
83260 AAAAATAAGAATTAAATAAAAG
1 AAAAATAAGAATTAAATAAAAG
*
83282 AAAAA-AATAATTAAATAAA
1 AAAAATAAGAATTAAATAAA
83301 CAAATTAAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (22 bp):
AAAAATAAGAATTAAATAAAAG
Found at i:83984 original size:19 final size:19
Alignment explanation
Indices: 83928--83990 Score: 54
Period size: 19 Copynumber: 3.2 Consensus size: 19
83918 CTATTTAAAC
**
83928 TAAAATACCTAAAAATTAAT
1 TAAAATA-CTAAAACCTAAT
* * *
83948 ATAATATTCTAAATCCTAAT
1 -TAAAATACTAAAACCTAAT
*
83968 TAAAATACTAAAACCTATT
1 TAAAATACTAAAACCTAAT
83987 TAAA
1 TAAA
83991 CTAAAATACA
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
19 19 0.58
20 9 0.27
21 5 0.15
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATACTAAAACCTAAT
Found at i:85865 original size:7 final size:8
Alignment explanation
Indices: 85851--85876 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
85841 TAAAGTTCAC
85851 TAAAAAAA
1 TAAAAAAA
85859 TAAAAAAA
1 TAAAAAAA
85867 TAAAAAAA
1 TAAAAAAA
85875 TA
1 TA
85877 TAATTAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
TAAAAAAA
Found at i:91432 original size:7 final size:7
Alignment explanation
Indices: 91400--91450 Score: 52
Period size: 7 Copynumber: 7.4 Consensus size: 7
91390 TATTAAAATA
*
91400 AAATAAA
1 AAATAAT
91407 AAATAA-
1 AAATAAT
91413 AAATAAT
1 AAATAAT
91420 ATAATAAT
1 A-AATAAT
*
91428 AAATATT
1 AAATAAT
*
91435 AAGTAAT
1 AAATAAT
91442 AAAT-AT
1 AAATAAT
91448 AAA
1 AAA
91451 AGGGGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 5
0.81 0.09 0.11
Matches are distributed among these distances:
6 11 0.29
7 20 0.53
8 7 0.18
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (7 bp):
AAATAAT
Found at i:91517 original size:17 final size:18
Alignment explanation
Indices: 91474--91514 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
91464 ACAATTATGG
*
91474 TTAAAATAAAAAATAGAA
1 TTAAAATAAAAAAAAGAA
*
91492 TTAAAATAAAAAAAATAA
1 TTAAAATAAAAAAAAGAA
91510 TTAAA
1 TTAAA
91515 TAACAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.02, T:0.24
Consensus pattern (18 bp):
TTAAAATAAAAAAAAGAA
Done.