Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020284.1 Corchorus olitorius cultivar O-4 contig20317, 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: 99762
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:134 original size:9 final size:10
Alignment explanation
Indices: 102--133 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
92 AGTTTGAAGG
102 TTGAGAAAAT
1 TTGAGAAAAT
112 TTGAGAAAA-
1 TTGAGAAAAT
121 TTGA-AAAAT
1 TTGAGAAAAT
130 TTGA
1 TTGA
134 AGTTTGAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
8 4 0.19
9 8 0.38
10 9 0.43
ACGTcount: A:0.50, C:0.00, G:0.19, T:0.31
Consensus pattern (10 bp):
TTGAGAAAAT
Found at i:6121 original size:13 final size:15
Alignment explanation
Indices: 6097--6128 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
6087 AAAAGCTTGG
6097 TTTTGAAGAAGTG-T
1 TTTTGAAGAAGTGCT
6111 TTTTGAA-AAGTGCT
1 TTTTGAAGAAGTGCT
6125 TTTT
1 TTTT
6129 AAAGTTGGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 5 0.29
14 12 0.71
ACGTcount: A:0.25, C:0.03, G:0.22, T:0.50
Consensus pattern (15 bp):
TTTTGAAGAAGTGCT
Found at i:6547 original size:29 final size:30
Alignment explanation
Indices: 6487--6561 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 30
6477 GCTAAATACC
* *
6487 CAAAAAAATCCCTTATGTTTTGCTTTTGGGA
1 CAAAATAATCCCTTATGTTTT-CTTTGGGGA
6518 CAAAATAATCCCTTATGTTTT-TTTGGGGA
1 CAAAATAATCCCTTATGTTTTCTTTGGGGA
*
6547 CAAATTAATCCCTTA
1 CAAAATAATCCCTTA
6562 CATTTAAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
29 21 0.51
31 20 0.49
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (30 bp):
CAAAATAATCCCTTATGTTTTCTTTGGGGA
Found at i:6729 original size:31 final size:31
Alignment explanation
Indices: 6694--6775 Score: 137
Period size: 31 Copynumber: 2.6 Consensus size: 31
6684 GACTGATTTG
6694 TCCCAAAAGAAAAATATAAGGGATTTTCTTA
1 TCCCAAAAGAAAAATATAAGGGATTTTCTTA
* * *
6725 TCCCAAAAGAAAAACATAAGGGATTTTTTTG
1 TCCCAAAAGAAAAATATAAGGGATTTTCTTA
6756 TCCCAAAAGAAAAATATAAG
1 TCCCAAAAGAAAAATATAAG
6776 AGAATTTTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.48, C:0.13, G:0.13, T:0.26
Consensus pattern (31 bp):
TCCCAAAAGAAAAATATAAGGGATTTTCTTA
Found at i:6784 original size:31 final size:30
Alignment explanation
Indices: 6690--6785 Score: 129
Period size: 31 Copynumber: 3.1 Consensus size: 30
6680 AAGGGACTGA
*
6690 TTTGTCCCAAAAGAAAAATATAAGGGATTT
1 TTTGTCCCAAAAGAAAAATATAAGGAATTT
* * *
6720 TCTTATCCCAAAAGAAAAACATAAGGGATTTT
1 T-TTGTCCCAAAAGAAAAATATAA-GGAATTT
6752 TTTGTCCCAAAAGAAAAATATAAGAGAATTT
1 TTTGTCCCAAAAGAAAAATATAAG-GAATTT
6783 TTT
1 TTT
6786 TAGTATTTAG
Statistics
Matches: 56, Mismatches: 7, Indels: 5
0.82 0.10 0.07
Matches are distributed among these distances:
30 2 0.04
31 48 0.86
32 6 0.11
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (30 bp):
TTTGTCCCAAAAGAAAAATATAAGGAATTT
Found at i:7380 original size:18 final size:18
Alignment explanation
Indices: 7345--7383 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
7335 TACTATTTTA
**
7345 ATTAAAATTTTTTTATAT
1 ATTAAAATTTTTAAATAT
*
7363 ATTAGAATTTTTAAATAT
1 ATTAAAATTTTTAAATAT
7381 ATT
1 ATT
7384 TCCTACACTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (18 bp):
ATTAAAATTTTTAAATAT
Found at i:7559 original size:126 final size:125
Alignment explanation
Indices: 7401--7639 Score: 322
Period size: 126 Copynumber: 1.9 Consensus size: 125
7391 CTTATTTTTC
* **
7401 AAATATATTTTTTAAATACCATTTTTAAACTTTTACAATTTTACTCAATTAAAAACTCTATTTTT
1 AAATATATTTCTTAAATACCATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
*
7466 ATTTAA-TCAAA-TCTAATATATTTATAACTATTTTATTTTTACCATTTTACTATTTTAATT
66 ATTTAACT-AAATTC-AATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
* * ** *
7526 AAATATATTTCTTAAATGA-CATTATTTAAACTTTTACAGTTTTATTTTACCAAAAATTCTATTT
1 AAATATATTTCTTAAAT-ACCATT-TTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTT
* *
7590 TTATTTAACTAAATTCAATATTTTTATAACTATTTTATCTTTACCTTTTT
64 TTATTTAACTAAATTCAATATATTTATAACTATTTTATCTTTACCATTTT
7640 TTAGGGAATT
Statistics
Matches: 99, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
125 20 0.20
126 76 0.77
127 3 0.03
ACGTcount: A:0.36, C:0.11, G:0.01, T:0.52
Consensus pattern (125 bp):
AAATATATTTCTTAAATACCATTTTTAAACTTTTACAATTTTACTCAACCAAAAACTCTATTTTT
ATTTAACTAAATTCAATATATTTATAACTATTTTATCTTTACCATTTTACTATTTTAATT
Found at i:7881 original size:32 final size:31
Alignment explanation
Indices: 7798--7880 Score: 139
Period size: 31 Copynumber: 2.7 Consensus size: 31
7788 ACTAAATACT
*
7798 AAAAAAATCCCTAATGTTTTTCTTTTGAGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGAGAC
*
7829 AAAAAAATCCCTTATGTTTTTCTTTTGGGAC
1 AAAAAAATCCCTTATGTTTTTCTTTTGAGAC
*
7860 AAAAAAATCTCTTATGTTTTT
1 AAAAAAATCCCTTATGTTTTT
7881 TTTAGACAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 49 1.00
ACGTcount: A:0.34, C:0.14, G:0.10, T:0.42
Consensus pattern (31 bp):
AAAAAAATCCCTTATGTTTTTCTTTTGAGAC
Found at i:8085 original size:29 final size:30
Alignment explanation
Indices: 8043--8107 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 30
8033 GTAACGTAAG
8043 GGATTAATTTGTCCCAAAA-AAAACATAAA
1 GGATTAATTTGTCCCAAAACAAAACATAAA
* *
8072 GGATTATTTTGTCCCAAAAGCAAAACATAAG
1 GGATTAATTTGTCCCAAAA-CAAAACATAAA
8103 GGATT
1 GGATT
8108 TTTCTGGGTA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 18 0.56
31 14 0.44
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (30 bp):
GGATTAATTTGTCCCAAAACAAAACATAAA
Found at i:12600 original size:22 final size:22
Alignment explanation
Indices: 12515--12730 Score: 125
Period size: 22 Copynumber: 10.2 Consensus size: 22
12505 TATAATTTTT
12515 TTTTGATAACCTC-CTTATGAAA
1 TTTTGATAACCTCAC-TATGAAA
*
12537 TCTTGATAA-CT-AC----AAA
1 TTTTGATAACCTCACTATGAAA
* * **
12553 TTTTGATAACTTCCCTATGATT
1 TTTTGATAACCTCACTATGAAA
*
12575 TTTTGATAACCTCATTATGAAA
1 TTTTGATAACCTCACTATGAAA
* ** *
12597 TTTTGTTATTCTCCCTATGAAA
1 TTTTGATAACCTCACTATGAAA
* *
12619 TTTTGATCTACAT-ACTATGAAA
1 TTTTGAT-AACCTCACTATGAAA
* *
12641 TTTTAATAACCCTC-TTATGAAA
1 TTTTGATAA-CCTCACTATGAAA
* *
12663 TTTTGA-AAACTAAACTATGAAA
1 TTTTGATAACCT-CACTATGAAA
* *
12685 TTTTGATCATCTTCA-TATGAAA
1 TTTTGAT-AACCTCACTATGAAA
*
12707 TTTTGATATCCTC-CT-TGAAA
1 TTTTGATAACCTCACTATGAAA
12727 TTTT
1 TTTT
12731 AATTACTCCA
Statistics
Matches: 144, Mismatches: 35, Indels: 32
0.68 0.17 0.15
Matches are distributed among these distances:
16 11 0.08
17 1 0.01
18 1 0.01
20 11 0.08
21 12 0.08
22 104 0.72
23 2 0.01
24 2 0.01
ACGTcount: A:0.33, C:0.16, G:0.08, T:0.43
Consensus pattern (22 bp):
TTTTGATAACCTCACTATGAAA
Found at i:12797 original size:22 final size:22
Alignment explanation
Indices: 12611--12798 Score: 85
Period size: 22 Copynumber: 8.9 Consensus size: 22
12601 GTTATTCTCC
*
12611 CTATGAAATTTTGATCTA-CATA
1 CTATGAAATTTTGAT-AACCATA
* *
12633 CTATGAAATTTTAATAACCCT-
1 CTATGAAATTTTGATAACCATA
* * *
12654 CTTATGAAATTTTGAAAACTAAA
1 C-TATGAAATTTTGATAACCATA
* * *
12677 CTATGAAATTTTGATCATC-TT
1 CTATGAAATTTTGATAACCATA
* *
12698 CATATGAAATTTTGATATCC-TC
1 C-TATGAAATTTTGATAACCATA
* *
12720 CT-TGAAATTTTAATTACTCCATA
1 CTATGAAATTTTGA-TA-ACCATA
* * *
12743 --ATAAAAGTTTAATAACCA-A
1 CTATGAAATTTTGATAACCATA
* *
12762 C-CT--AA-TTTGGTAACCATA
1 CTATGAAATTTTGATAACCATA
12780 CTATGAAATTTTGATAACC
1 CTATGAAATTTTGATAACC
12799 TCTTCAGAAA
Statistics
Matches: 124, Mismatches: 28, Indels: 28
0.69 0.16 0.16
Matches are distributed among these distances:
17 9 0.07
18 4 0.03
19 2 0.02
20 14 0.11
21 10 0.08
22 83 0.67
23 2 0.02
ACGTcount: A:0.38, C:0.15, G:0.08, T:0.38
Consensus pattern (22 bp):
CTATGAAATTTTGATAACCATA
Found at i:13313 original size:131 final size:131
Alignment explanation
Indices: 13074--13314 Score: 428
Period size: 131 Copynumber: 1.8 Consensus size: 131
13064 AGCTTTGGAA
* **
13074 AAACTATTGATTTTGTCTCATTTCGGCCAAATAGGCCCATTAGACTCGTTTGAGTCCATAAAGTC
1 AAACTATTGATTTTGTCTAATTTCAACCAAATAGGCCCATTAGACTCGTTTGAGTCCATAAAGTC
*
13139 CAAATTGCCAAGTCAGATGTCTTGAAGTCTCAATCTGAAATTCTTGCTCGTTTGAGTCCATGAGA
66 CAAATTGCCAAGCCAGATGTCTTGAAGTCTCAATCTGAAATTCTTGCTCGTTTGAGTCCATGAGA
13204 C
131 C
*
13205 AAACTATTGATTTTGTCTAATTTCAACCAAATAGGCCCATTAGACTCGTTTGAGTCCATGAAGTC
1 AAACTATTGATTTTGTCTAATTTCAACCAAATAGGCCCATTAGACTCGTTTGAGTCCATAAAGTC
*
13270 CAAATTGCCAAGCCAGATGTCTTGAAGTCTCAATCTGATATTCTT
66 CAAATTGCCAAGCCAGATGTCTTGAAGTCTCAATCTGAAATTCTT
13315 AGGCCCAATT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
131 104 1.00
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Consensus pattern (131 bp):
AAACTATTGATTTTGTCTAATTTCAACCAAATAGGCCCATTAGACTCGTTTGAGTCCATAAAGTC
CAAATTGCCAAGCCAGATGTCTTGAAGTCTCAATCTGAAATTCTTGCTCGTTTGAGTCCATGAGA
C
Found at i:14292 original size:178 final size:177
Alignment explanation
Indices: 13935--14305 Score: 446
Period size: 178 Copynumber: 2.1 Consensus size: 177
13925 ACAAATTATG
* * * * * *
13935 TAATATTAAGTAGACCGTGTATTTCGTTGACCGAAACAACTAATTCTTTGGAATCATTTTTTATA
1 TAATATTAAGTAGACCGTCTATTCCGTTAACCGAAACAACTAAATCTTTGGAAGCATTTTTGATA
* * *
14000 CCTTGAACATTAAATTTAGTTTTCGAGTCCTTCATAAAAGTTGTAGATCATGGAACAACCTTTCA
66 CCTTGAACATTAAATTTAGTTTTCGAGTCATTCATAAAAGTTGTAGATAATGAAACAACCTTTCA
* * * * *
14065 AGAGACACTTGAATCATCTCAATCAGACATCTGGAGCAAAAGTTATA
131 AGAGACACTTAAATCACCTCAATCAGACAACCGGAGCAAAAGCTATA
*
14112 TAATATTAAGTGGACCGTCTATTCCCGTTAACCGAAACAAC-AAATCTTTCGGAAGCATTTTTGA
1 TAATATTAAGTAGACCGTCTATT-CCGTTAACCGAAACAACTAAATCTTT-GGAAGCATTTTTGA
* *
14176 TA-CTTGAAACATTAAATTTAGTTTTCGAGTCATTCATGAAAGTTGTAGATAATGAAACAATCTT
64 TACCTTG-AACATTAAATTTAGTTTTCGAGTCATTCATAAAAGTTGTAGATAATGAAACAACCTT
* * * *
14240 TTAATAGACACTTAAATCACC-CTAATCGGATAACCGAAGAG-AAAA-CTATA
128 TCAAGAGACACTTAAATCACCTC-AATCAGACAACCG--GAGCAAAAGCTATA
* *
14290 TAATGTTAAATAGACC
1 TAATATTAAGTAGACC
14306 ATTTAGCCAA
Statistics
Matches: 164, Mismatches: 24, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
177 33 0.20
178 124 0.76
179 4 0.02
180 3 0.02
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (177 bp):
TAATATTAAGTAGACCGTCTATTCCGTTAACCGAAACAACTAAATCTTTGGAAGCATTTTTGATA
CCTTGAACATTAAATTTAGTTTTCGAGTCATTCATAAAAGTTGTAGATAATGAAACAACCTTTCA
AGAGACACTTAAATCACCTCAATCAGACAACCGGAGCAAAAGCTATA
Found at i:14758 original size:21 final size:20
Alignment explanation
Indices: 14734--14780 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 20
14724 CAAGAAATTG
*
14734 TAGGGAGATTAACAAAAATCA
1 TAGGAAGATT-ACAAAAATCA
* *
14755 TAGGAAGGTTACAAAATTCA
1 TAGGAAGATTACAAAAATCA
14775 TAGGAA
1 TAGGAA
14781 AGTTTATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 15 0.65
21 8 0.35
ACGTcount: A:0.49, C:0.09, G:0.21, T:0.21
Consensus pattern (20 bp):
TAGGAAGATTACAAAAATCA
Found at i:14867 original size:43 final size:44
Alignment explanation
Indices: 14806--14908 Score: 118
Period size: 43 Copynumber: 2.4 Consensus size: 44
14796 CATAATTAGG
* * * * *
14806 TTATCAAAGTTTCTTATGGAGTTTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
* * *
14849 TTATCAAAATTTCATATGGTGGTTATTAAAATTTAATAGGGTGA
1 TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
*
14893 TTATCGAAATTTCATA
1 TTATCAAAATTTCATA
14909 AAAATATTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
43 31 0.62
44 19 0.38
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (44 bp):
TTATCAAAATTTCATATGGAGGTTATCAAAATTTAATAGGGTAA
Found at i:14879 original size:22 final size:22
Alignment explanation
Indices: 14806--14908 Score: 91
Period size: 22 Copynumber: 4.7 Consensus size: 22
14796 CATAATTAGG
* * * *
14806 TTATCAAAGTTTCTTATGGAGT
1 TTATCAAAATTTCATATGGTGA
* * *
14828 TTATCACAATTTTATA-GGTAA
1 TTATCAAAATTTCATATGGTGA
*
14849 TTATCAAAATTTCATATGGTGG
1 TTATCAAAATTTCATATGGTGA
* * *
14871 TTATTAAAATTTAATAGGGTGA
1 TTATCAAAATTTCATATGGTGA
*
14893 TTATCGAAATTTCATA
1 TTATCAAAATTTCATA
14909 AAAATATTTA
Statistics
Matches: 62, Mismatches: 18, Indels: 2
0.76 0.22 0.02
Matches are distributed among these distances:
21 16 0.26
22 46 0.74
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGTGA
Found at i:17784 original size:13 final size:13
Alignment explanation
Indices: 17751--17803 Score: 60
Period size: 12 Copynumber: 4.4 Consensus size: 13
17741 GCACCCAAAA
*
17751 CATTTAT-TAAAA
1 CATTTATATAAAG
17763 CATTT-TATAAAG
1 CATTTATATAAAG
17775 CATTTATATAAAG
1 CATTTATATAAAG
*
17788 CAGTTATA-AAA-
1 CATTTATATAAAG
17799 CATTT
1 CATTT
17804 CCTCAACGGG
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
11 5 0.14
12 17 0.47
13 14 0.39
ACGTcount: A:0.45, C:0.09, G:0.06, T:0.40
Consensus pattern (13 bp):
CATTTATATAAAG
Found at i:19013 original size:24 final size:26
Alignment explanation
Indices: 18986--19068 Score: 82
Period size: 25 Copynumber: 3.2 Consensus size: 26
18976 CCTTATCCGG
*
18986 TTTTCCCTTTTTTTTCTTT-CTTTT-
1 TTTTCCTTTTTTTTTCTTTCCTTTTC
19010 TTTTCCTTTTCTTTTTCCTTTTCCTTTTC
1 TTTTCCTTTT-TTTTT-C-TTTCCTTTTC
* * *
19039 CTTTCCTTTTTTTTTCTCTCC-TCTC
1 TTTTCCTTTTTTTTTCTTTCCTTTTC
19064 TTTTC
1 TTTTC
19069 TTGGCTTGGG
Statistics
Matches: 49, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
24 9 0.18
25 12 0.24
26 5 0.10
27 4 0.08
28 10 0.20
29 9 0.18
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTCCTTTTTTTTTCTTTCCTTTTC
Found at i:19024 original size:12 final size:12
Alignment explanation
Indices: 18986--19049 Score: 67
Period size: 12 Copynumber: 5.3 Consensus size: 12
18976 CCTTATCCGG
*
18986 TTTTCCCTTT-T
1 TTTTCCTTTTCT
* *
18997 TTTTCTTTCTTTT
1 TTTTCCTT-TTCT
19010 TTTTCCTTTTCT
1 TTTTCCTTTTCT
*
19022 TTTTCCTTTTCC
1 TTTTCCTTTTCT
*
19034 TTTTCCTTTCCT
1 TTTTCCTTTTCT
19046 TTTT
1 TTTT
19050 TTTTCTCTCC
Statistics
Matches: 44, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
11 6 0.14
12 30 0.68
13 8 0.18
ACGTcount: A:0.00, C:0.25, G:0.00, T:0.75
Consensus pattern (12 bp):
TTTTCCTTTTCT
Found at i:19043 original size:5 final size:6
Alignment explanation
Indices: 19010--19048 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
19000 TCTTTCTTTT
*
19010 TTTTCC TTTTCT TTTTCC TTTTCC TTTTCC -TTTCC TTTT
1 TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTTCC TTTT
19049 TTTTTCTCTC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 25 0.83
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (6 bp):
TTTTCC
Found at i:19049 original size:18 final size:19
Alignment explanation
Indices: 19009--19057 Score: 61
Period size: 18 Copynumber: 2.8 Consensus size: 19
18999 TTCTTTCTTT
*
19009 TTTTTCCTTTTCTTTTTCC
1 TTTTTCCTTTTCTCTTTCC
19028 -TTTTCCTTTTC-CTTTCC
1 TTTTTCCTTTTCTCTTTCC
19045 TTTTT--TTTTCTCT
1 TTTTTCCTTTTCTCT
19058 CCTCTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
16 5 0.19
17 7 0.26
18 15 0.56
ACGTcount: A:0.00, C:0.27, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTTCCTTTTCTCTTTCC
Found at i:21040 original size:22 final size:21
Alignment explanation
Indices: 20981--21068 Score: 72
Period size: 22 Copynumber: 4.1 Consensus size: 21
20971 TTTTATGAAA
*
20981 TTTGATAATCAT-TATAAAAT
1 TTTGATAATTATCTATAAAAT
*
21001 TTTGATAACCT-TCATATAAAAT
1 TTTGATAA-TTATC-TATAAAAT
*
21023 TTTGATAATTATACTATAAAGT
1 TTTGATAATTAT-CTATAAAAT
* * *
21045 TTTTATGATTATACTATAGAAT
1 TTTGATAATTAT-CTATAAAAT
21067 TT
1 TT
21069 CGAGAACCTC
Statistics
Matches: 55, Mismatches: 8, Indels: 8
0.77 0.11 0.11
Matches are distributed among these distances:
20 9 0.16
21 1 0.02
22 44 0.80
23 1 0.02
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.47
Consensus pattern (21 bp):
TTTGATAATTATCTATAAAAT
Found at i:21212 original size:46 final size:44
Alignment explanation
Indices: 21157--21259 Score: 125
Period size: 46 Copynumber: 2.3 Consensus size: 44
21147 ACCACCCATA
* *
21157 AAATTTTGATAACATCCCAATGAAATGTTGGTAAGCGCACATTATG
1 AAATTTTGATAACATCCCAATAAAATATTGGTAA--GCACATTATG
* * * * *
21203 ATATTTTGATAACCTTCCGATAAAATATTGGTAATCACATTATG
1 AAATTTTGATAACATCCCAATAAAATATTGGTAAGCACATTATG
21247 AAATTTTGATAAC
1 AAATTTTGATAAC
21260 CATACCATAA
Statistics
Matches: 49, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 21 0.43
46 28 0.57
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (44 bp):
AAATTTTGATAACATCCCAATAAAATATTGGTAAGCACATTATG
Found at i:21330 original size:22 final size:22
Alignment explanation
Indices: 21136--22251 Score: 200
Period size: 22 Copynumber: 50.3 Consensus size: 22
21126 CCACTTAATG
*
21136 AAATTTTGATAACCACCC-ATA
1 AAATTTTGATAACCTCCCTATA
* * *
21157 AAATTTTGATAACATCCCAATG
1 AAATTTTGATAACCTCCCTATA
* * * ** *
21179 AAATGTTGGTAAGCGCACATTATG
1 AAATTTTGATAA-C-CTCCCTATA
* * *
21203 ATATTTTGATAACCTTCCGATA
1 AAATTTTGATAACCTCCCTATA
* * * * ** *
21225 AAATATTGGTAATCACATTATG
1 AAATTTTGATAACCTCCCTATA
*
21247 AAATTTTGATAACCATACC-ATA
1 AAATTTTGATAACC-TCCCTATA
* ** * *
21269 AAAATGCGAT-ACCTCACTATG
1 AAATTTTGATAACCTCCCTATA
21290 AAATTTTGTATAAACCTCCCTATA
1 AAATTTTG-AT-AACCTCCCTATA
* * *
21314 AAATTTTGATAACCTCCATTTG
1 AAATTTTGATAACCTCCCTATA
21336 AAATTTTGATAACCT--C-A-A
1 AAATTTTGATAACCTCCCTATA
* * *
21354 GAAATTTTGAAAACC-ACCTCATG
1 -AAATTTTGATAACCTCCCT-ATA
* * *
21377 CAATTTTGATAACCAT-CTTATG
1 AAATTTTGATAACC-TCCCTATA
*
21399 AAATTTTGATAACATCCCTATA
1 AAATTTTGATAACCTCCCTATA
* * *
21421 AATTTTTTTATAACCTCCTTATA
1 AA-ATTTTGATAACCTCCCTATA
*
21444 AAATTTTGTTAACCT-CCTACT-
1 AAATTTTGATAACCTCCCTA-TA
*** * * *
21465 AAATTTTGATAAGAACACAATT
1 AAATTTTGATAACCTCCCTATA
* * *
21487 ACATTTTGATAA-C-CCCAATG
1 AAATTTTGATAACCTCCCTATA
**
21507 AAATTTTGATAATTAATTACACC-AT-
1 AAATTTTGAT-A--ACCT-C-CCTATA
* * * *
21532 AAATTTACGATAACTTACCTATG
1 AAATTT-TGATAACCTCCCTATA
* *
21555 AAATTTTGTTAATCTCCCTATA
1 AAATTTTGATAACCTCCCTATA
* * * *
21577 AAATTTTGAGAACCACACTATC
1 AAATTTTGATAACCTCCCTATA
* * *
21599 AAATTTTGTTAATCTCACTAT-
1 AAATTTTGATAACCTCCCTATA
* **
21620 AAATTTTGATAAACTCATTATA
1 AAATTTTGATAACCTCCCTATA
* * * * *
21642 AAATTTTAACTGCCACAGTCCACACAATG
1 AAATTTTGA-T---A-A--CCTCCCTATA
* *
21671 AAAATTTGATAACCTCTCCCTCT-
1 AAATTTTGATAA-C-CTCCCTATA
* * **
21694 GAA-----AT-ACCACATTATA
1 AAATTTTGATAACCTCCCTATA
* *
21710 AAATTTTGATAACCACAC--T-
1 AAATTTTGATAACCTCCCTATA
** *
21729 AAATTTTGATAATATCCCCTCTA
1 AAATTTTGATAACCT-CCCTATA
* * *
21752 AAATTTCGATAACCTCCCCATG
1 AAATTTTGATAACCTCCCTATA
* * *
21774 AAATGTTGTTAACCT--CTATG
1 AAATTTTGATAACCTCCCTATA
* * * *
21794 AAATTGTGATTA-TTACACTATGA
1 AAATTTTGATAACCT-CCCTAT-A
* ** * *
21817 AAA-TTTGGTAACAACACT-TG
1 AAATTTTGATAACCTCCCTATA
*
21837 AAATTTTGATAAGCTCACTCTATCTCA
1 AAATTTTGATAACCTC-C-CTA--T-A
* * * * *
21864 CTAGTAATCTTTATAAGCACACTATA
1 --A--AATTTTGATAACCTCCCTATA
* *
21890 AAATTTTGATAATCTTCCTATA
1 AAATTTTGATAACCTCCCTATA
* *
21912 AAATTTTAATAACCTCCATATA
1 AAATTTTGATAACCTCCCTATA
* * * * *
21934 AGATTTCGATAATCGCCCTATG
1 AAATTTTGATAACCTCCCTATA
* ****
21956 AAATTTTGATAAGCAGAGTATA
1 AAATTTTGATAACCTCCCTATA
* *
21978 AAATTTT-AGTAACCTCCCTGTG
1 AAATTTTGA-TAACCTCCCTATA
*
22000 AAATTTTGACAACCTTCCC-AT-
1 AAATTTTGATAACC-TCCCTATA
* * * *
22021 GAATTTCGATAACCTCCTTATG
1 AAATTTTGATAACCTCCCTATA
* * *
22043 AAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATA
* * * *
22065 GAATTTTGATAACCTTCATATG
1 AAATTTTGATAACCTCCCTATA
*
22087 AAATTTTGATAACAT-CCTAATGA
1 AAATTTTGATAACCTCCCT-AT-A
* * * *
22110 AATTTTATTTTAATAACCTGCTTATG
1 AA----ATTTTGATAACCTCCCTATA
* *
22136 AAATTTTGATAACATCCC-ATG
1 AAATTTTGATAACCTCCCTATA
* *
22157 AAATTGTGATAA-CTACACTATA
1 AAATTTTGATAACCT-CCCTATA
* * * * *
22179 AAATTTTAACATCCTACCTATG
1 AAATTTTGATAACCTCCCTATA
* * *
22201 AAATTTTGGTAACCACACTATA
1 AAATTTTGATAACCTCCCTATA
* *
22223 AAATTTTGATAACCACACTATA
1 AAATTTTGATAACCTCCCTATA
22245 AAATTTT
1 AAATTTT
22252 AGTAACCACA
Statistics
Matches: 777, Mismatches: 236, Indels: 163
0.66 0.20 0.14
Matches are distributed among these distances:
15 4 0.01
16 3 0.00
17 1 0.00
18 2 0.00
19 26 0.03
20 39 0.05
21 106 0.14
22 429 0.55
23 64 0.08
24 36 0.05
25 8 0.01
26 11 0.01
27 17 0.02
28 3 0.00
29 16 0.02
31 12 0.02
ACGTcount: A:0.37, C:0.18, G:0.09, T:0.36
Consensus pattern (22 bp):
AAATTTTGATAACCTCCCTATA
Found at i:21360 original size:41 final size:43
Alignment explanation
Indices: 21314--21411 Score: 112
Period size: 41 Copynumber: 2.3 Consensus size: 43
21304 CCTCCCTATA
* *
21314 AAATTTTGATAACCTCCAT-TTGAAATTTTGATAACC-TC-AAG
1 AAATTTTGATAACCACC-TCATGAAATTTTGATAACCATCTAAG
* * *
21355 AAATTTTGAAAACCACCTCATGCAATTTTGATAACCATCTTATG
1 AAATTTTGATAACCACCTCATGAAATTTTGATAACCATC-TAAG
21399 AAATTTTGATAAC
1 AAATTTTGATAAC
21412 ATCCCTATAA
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
40 1 0.02
41 30 0.64
42 2 0.04
44 14 0.30
ACGTcount: A:0.38, C:0.17, G:0.09, T:0.36
Consensus pattern (43 bp):
AAATTTTGATAACCACCTCATGAAATTTTGATAACCATCTAAG
Found at i:21433 original size:23 final size:23
Alignment explanation
Indices: 21402--21471 Score: 72
Period size: 23 Copynumber: 3.1 Consensus size: 23
21392 TCTTATGAAA
* *
21402 TTTTGATAACATCCCTATAAATT
1 TTTTTATAACCTCCCTATAAATT
* *
21425 TTTTTATAACCTCCTTATAAAAT
1 TTTTTATAACCTCCCTATAAATT
*
21448 TTTGT-TAACCT-CCTACTAAATT
1 TTTTTATAACCTCCCTA-TAAATT
21470 TT
1 TT
21472 GATAAGAACA
Statistics
Matches: 39, Mismatches: 7, Indels: 3
0.80 0.14 0.06
Matches are distributed among these distances:
21 3 0.08
22 13 0.33
23 23 0.59
ACGTcount: A:0.31, C:0.19, G:0.03, T:0.47
Consensus pattern (23 bp):
TTTTTATAACCTCCCTATAAATT
Found at i:21442 original size:45 final size:45
Alignment explanation
Indices: 21380--21471 Score: 116
Period size: 45 Copynumber: 2.0 Consensus size: 45
21370 CCTCATGCAA
*
21380 TTTTGATAACCATCTTATGAAATTTTGATAACATCCCTA-TAAATT
1 TTTTGATAACCATCTTATAAAATTTTGATAACAT-CCTACTAAATT
* * *
21425 TTTTTATAACC-TCCTTATAAAATTTTGTTAACCTCCTACTAAATT
1 TTTTGATAACCAT-CTTATAAAATTTTGATAACATCCTACTAAATT
21470 TT
1 TT
21472 GATAAGAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
44 5 0.12
45 36 0.88
ACGTcount: A:0.33, C:0.17, G:0.04, T:0.46
Consensus pattern (45 bp):
TTTTGATAACCATCTTATAAAATTTTGATAACATCCTACTAAATT
Found at i:22035 original size:43 final size:44
Alignment explanation
Indices: 21987--22095 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 44
21977 AAAATTTTAG
* * *
21987 TAACCTCCCTGTGAAATTTTGACAACCTTCCCAT-GAATTTCGA
1 TAACCTCCATATGAAATTTTGACAACCTTCACATGGAATTTCGA
* * * *
22030 TAACCTCCTTATGAAATTTTGATAACCTTCATATGGAATTTTGA
1 TAACCTCCATATGAAATTTTGACAACCTTCACATGGAATTTCGA
*
22074 TAACCTTCATATGAAATTTTGA
1 TAACCTCCATATGAAATTTTGA
22096 TAACATCCTA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
43 29 0.51
44 28 0.49
ACGTcount: A:0.31, C:0.20, G:0.11, T:0.38
Consensus pattern (44 bp):
TAACCTCCATATGAAATTTTGACAACCTTCACATGGAATTTCGA
Found at i:22139 original size:49 final size:48
Alignment explanation
Indices: 22067--22161 Score: 145
Period size: 49 Copynumber: 2.0 Consensus size: 48
22057 TTCATATGGA
* *
22067 ATTTTGATAACCTTCATATGAAATTTTGATAACATCCTAATGAAATTTT
1 ATTTTAATAACCTGCATATGAAATTTTGATAACATCC-AATGAAATTTT
* *
22116 ATTTTAATAACCTGCTTATGAAATTTTGATAACATCCCATGAAATT
1 ATTTTAATAACCTGCATATGAAATTTTGATAACATCCAATGAAATT
22162 GTGATAACTA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
48 8 0.19
49 34 0.81
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (48 bp):
ATTTTAATAACCTGCATATGAAATTTTGATAACATCCAATGAAATTTT
Found at i:22257 original size:22 final size:22
Alignment explanation
Indices: 22166--22262 Score: 108
Period size: 22 Copynumber: 4.4 Consensus size: 22
22156 GAAATTGTGA
* *
22166 TAACTACACTATAAAATTTTAA
1 TAACCACACTATAAAATTTTAG
* * * *
22188 CATCCTAC-CTATGAAATTTTGG
1 TAACC-ACACTATAAAATTTTAG
22210 TAACCACACTATAAAATTTT-G
1 TAACCACACTATAAAATTTTAG
22231 ATAACCACACTATAAAATTTTAG
1 -TAACCACACTATAAAATTTTAG
22254 TAACCACAC
1 TAACCACAC
22263 AATGAATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
21 3 0.05
22 56 0.90
23 3 0.05
ACGTcount: A:0.42, C:0.21, G:0.05, T:0.32
Consensus pattern (22 bp):
TAACCACACTATAAAATTTTAG
Found at i:22272 original size:21 final size:22
Alignment explanation
Indices: 22196--22278 Score: 114
Period size: 22 Copynumber: 3.8 Consensus size: 22
22186 AACATCCTAC
*
22196 CTATGAAATTTTGGTAACCACA
1 CTATAAAATTTTGGTAACCACA
*
22218 CTATAAAATTTTGATAACCACA
1 CTATAAAATTTTGGTAACCACA
*
22240 CTATAAAATTTTAGTAACCACA
1 CTATAAAATTTTGGTAACCACA
* *
22262 CAAT-GAATTTTGGTAAC
1 CTATAAAATTTTGGTAAC
22279 TTCCAAAATT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
21 11 0.20
22 43 0.80
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.33
Consensus pattern (22 bp):
CTATAAAATTTTGGTAACCACA
Found at i:23487 original size:14 final size:14
Alignment explanation
Indices: 23465--23503 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 14
23455 TATATATAGT
23465 ATAGATATAGATAA
1 ATAGATATAGATAA
*
23479 ATAGGTATAGATAGA
1 ATAGATATAGATA-A
23494 TATAGATATA
1 -ATAGATATA
23504 TTTCTGAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 1 0.05
16 8 0.38
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (14 bp):
ATAGATATAGATAA
Found at i:24272 original size:26 final size:26
Alignment explanation
Indices: 24220--24278 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
24210 AAATTTCCAT
24220 TATTTTAATAATGGAATAATTAAAATA
1 TATTTTAATAATGGAAT-ATTAAAATA
* *
24247 TTTTTTAATAATGGCAAT-TTAGAATA
1 TATTTTAATAATGG-AATATTAAAATA
24273 TATTTT
1 TATTTT
24279 GAAAAAAGGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 12 0.43
27 13 0.46
28 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (26 bp):
TATTTTAATAATGGAATATTAAAATA
Found at i:24278 original size:27 final size:26
Alignment explanation
Indices: 24222--24278 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
24212 ATTTCCATTA
24222 TTTTAATAATGGAATAATTAAAATATT
1 TTTTAATAATGGAAT-ATTAAAATATT
* *
24249 TTTTAATAATGGCAAT-TTAGAATATA
1 TTTTAATAATGG-AATATTAAAATATT
24275 TTTT
1 TTTT
24279 GAAAAAAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
26 12 0.44
27 12 0.44
28 3 0.11
ACGTcount: A:0.42, C:0.02, G:0.09, T:0.47
Consensus pattern (26 bp):
TTTTAATAATGGAATATTAAAATATT
Found at i:24348 original size:6 final size:6
Alignment explanation
Indices: 24331--24362 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
24321 GTATTTTTAT
24331 ATATAG -TATAG ATATAG ATATAG ATATAG ATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATA
24363 GCTTTGGAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.50, C:0.00, G:0.16, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:27863 original size:17 final size:17
Alignment explanation
Indices: 27841--27873 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
27831 ATACATAGGG
27841 CTATCTAGTGTAACAAA
1 CTATCTAGTGTAACAAA
*
27858 CTATCTGGTGTAACAA
1 CTATCTAGTGTAACAA
27874 CTTTACAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.30
Consensus pattern (17 bp):
CTATCTAGTGTAACAAA
Found at i:35379 original size:31 final size:31
Alignment explanation
Indices: 35338--35513 Score: 156
Period size: 31 Copynumber: 5.7 Consensus size: 31
35328 GTGTTCGACA
* * *
35338 TGGCATGCCACGTGTATCAAAAAGCGAAATG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
*
35369 CGGCACGCCACGTGTACCAAAAAGCGACATG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
** ** *
35400 TGATACGCCATATGTACCAAAAAGTGACATG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* * *
35431 TGGCACGCCATGTGTACCAAAAAGTGACACG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
* * * ** * * *
35462 TGGTATGCCATGTGTTTCAAAAAGTGGCACG
1 TGGCACGCCACGTGTACCAAAAAGCGACATG
*
35493 TGGCATGCCACGTGTA-CAAAA
1 TGGCACGCCACGTGTACCAAAA
35514 GGATACGTGC
Statistics
Matches: 123, Mismatches: 22, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
30 5 0.04
31 118 0.96
ACGTcount: A:0.33, C:0.23, G:0.25, T:0.19
Consensus pattern (31 bp):
TGGCACGCCACGTGTACCAAAAAGCGACATG
Found at i:35437 original size:62 final size:62
Alignment explanation
Indices: 35350--35513 Score: 195
Period size: 62 Copynumber: 2.7 Consensus size: 62
35340 GCATGCCACG
* * * *
35350 TGTATCAAAAAGCGAAATGCGGCACGCCACGTGTACCAAAAAGCGACATGTGATACGCCATA
1 TGTATCAAAAAGTGACATGTGGCACGCCACGTGTACCAAAAAGCGACACGTGATACGCCATA
* * * * * *
35412 TGTACCAAAAAGTGACATGTGGCACGCCATGTGTACCAAAAAGTGACACGTGGTATGCCATG
1 TGTATCAAAAAGTGACATGTGGCACGCCACGTGTACCAAAAAGCGACACGTGATACGCCATA
* * * *
35474 TGTTTCAAAAAGTGGCACGTGGCATGCCACGTGTA-CAAAA
1 TGTATCAAAAAGTGACATGTGGCACGCCACGTGTACCAAAA
35514 GGATACGTGC
Statistics
Matches: 86, Mismatches: 16, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
61 5 0.06
62 81 0.94
ACGTcount: A:0.34, C:0.22, G:0.24, T:0.20
Consensus pattern (62 bp):
TGTATCAAAAAGTGACATGTGGCACGCCACGTGTACCAAAAAGCGACACGTGATACGCCATA
Found at i:40745 original size:22 final size:22
Alignment explanation
Indices: 40720--40796 Score: 95
Period size: 22 Copynumber: 3.5 Consensus size: 22
40710 TATTTTTATG
*
40720 AAATTTTGATAACTATCCTATT
1 AAATTTTGATAACTATCCTATA
*
40742 AAATTTTGATAACTA-CCATATG
1 AAATTTTGATAACTATCC-TATA
*
40764 AAATTTTGATAATTAT-CTATA
1 AAATTTTGATAACTATCCTATA
*
40785 AAATTGTGATAA
1 AAATTTTGATAA
40797 ATTCCATAAA
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
21 16 0.33
22 33 0.67
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (22 bp):
AAATTTTGATAACTATCCTATA
Found at i:40804 original size:43 final size:44
Alignment explanation
Indices: 40716--40804 Score: 126
Period size: 43 Copynumber: 2.0 Consensus size: 44
40706 TGAATATTTT
* * *
40716 TATGAAATTTTGATAACTATCCTATTAAATTTTGATAACTACCA
1 TATGAAATTTTGATAACTATCCTATAAAATTGTGATAAATACCA
* *
40760 TATGAAATTTTGATAATTAT-CTATAAAATTGTGATAAATTCCA
1 TATGAAATTTTGATAACTATCCTATAAAATTGTGATAAATACCA
40803 TA
1 TA
40805 AAAAACTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
43 21 0.52
44 19 0.47
ACGTcount: A:0.40, C:0.10, G:0.08, T:0.42
Consensus pattern (44 bp):
TATGAAATTTTGATAACTATCCTATAAAATTGTGATAAATACCA
Found at i:43419 original size:27 final size:26
Alignment explanation
Indices: 43365--43425 Score: 72
Period size: 27 Copynumber: 2.3 Consensus size: 26
43355 CTAAATTTTC
43365 ATTATTTTAATAATGGAATAATTAAAAT
1 ATTA-TTTAATAATGGAAT-ATTAAAAT
43393 ATTATTTAATAATGGCAAT-TTAGAAAT
1 ATTATTTAATAATGG-AATATTA-AAAT
43420 A-TATTT
1 ATTATTT
43426 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 8 0.26
27 16 0.52
28 7 0.23
ACGTcount: A:0.46, C:0.02, G:0.08, T:0.44
Consensus pattern (26 bp):
ATTATTTAATAATGGAATATTAAAAT
Found at i:57896 original size:76 final size:75
Alignment explanation
Indices: 57760--57910 Score: 180
Period size: 76 Copynumber: 2.0 Consensus size: 75
57750 ACAAGGACCC
** * *
57760 CGACTCCACCTGGGGCCCACATGGTTGCCTTGAGCACCCATGTGGTTTGCTTGAGAACCCAGGTG
1 CGACTCCACCTGGGGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGAACCCAGATG
57825 GGCAGTGTCA
66 GGCAGTGTCA
* * **
57835 CGACTCCAGCTGGGTGCCCACATGGTTTGTCTAAAG-ACCCATGT-GTTTCGCCTGATCACCCAG
1 CGACTCCACCTGGG-GCCCACATGG-TTGCCTAAAGCACCCATGTGGTTT-GCCTGAGAACCCAG
*
57898 ATGGGCTGTGTCA
63 ATGGGCAGTGTCA
57911 TAGCTCATCA
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
75 17 0.27
76 40 0.62
77 7 0.11
ACGTcount: A:0.18, C:0.29, G:0.28, T:0.25
Consensus pattern (75 bp):
CGACTCCACCTGGGGCCCACATGGTTGCCTAAAGCACCCATGTGGTTTGCCTGAGAACCCAGATG
GGCAGTGTCA
Found at i:58847 original size:20 final size:21
Alignment explanation
Indices: 58807--58847 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
58797 TTAATTATGT
* *
58807 GTGTGTTAAGTGTGTTTTAGA
1 GTGTGTTAAGTGTGATGTAGA
58828 GTGT-TTAAGTGTGATGTAGA
1 GTGTGTTAAGTGTGATGTAGA
58848 CTTATGCAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
GTGTGTTAAGTGTGATGTAGA
Found at i:59321 original size:79 final size:77
Alignment explanation
Indices: 59179--59332 Score: 245
Period size: 79 Copynumber: 2.0 Consensus size: 77
59169 CTACGCCTAG
* *
59179 TATGCAATGACAGGAGTCATATGCTCTGCAGTTGCCACCCTCGGTGGATCCTCTGCATCAGAAAC
1 TATGCAATGACAGGAGTAATATGCTCTGCAGTTGCCACCCTCAGTGGATCCTCTGCATCAGAAAC
59244 TCCCTACATTGT
66 TCCCTACATTGT
* * *
59256 TATGCAATGAACATGAGTAATATGTTTTGCAGTTGCCACCCTCAAGTGGATCCTCTGCATCAGAA
1 TATGCAATG-ACAGGAGTAATATGCTCTGCAGTTGCCACCCTC-AGTGGATCCTCTGCATCAGAA
59321 ACTCCCTACATT
64 ACTCCCTACATT
59333 ATTGTTATAC
Statistics
Matches: 70, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
77 9 0.13
78 29 0.41
79 32 0.46
ACGTcount: A:0.26, C:0.27, G:0.19, T:0.29
Consensus pattern (77 bp):
TATGCAATGACAGGAGTAATATGCTCTGCAGTTGCCACCCTCAGTGGATCCTCTGCATCAGAAAC
TCCCTACATTGT
Found at i:63298 original size:19 final size:19
Alignment explanation
Indices: 63274--63319 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
63264 TGAATGCAGT
63274 ATTGCAGGTAAGAGGGAGA
1 ATTGCAGGTAAGAGGGAGA
63293 ATTGCAGGTAAGAGGGAGA
1 ATTGCAGGTAAGAGGGAGA
63312 ATTGCAGG
1 ATTGCAGG
63320 AGAAAAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.35, C:0.07, G:0.41, T:0.17
Consensus pattern (19 bp):
ATTGCAGGTAAGAGGGAGA
Found at i:63333 original size:20 final size:19
Alignment explanation
Indices: 63274--63337 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 19
63264 TGAATGCAGT
* * *
63274 ATTGCAGGTAAGAGGGAGA
1 ATTGCAGGGAAAAGAGAGA
* * *
63293 ATTGCAGGTAAGAGGGAGA
1 ATTGCAGGGAAAAGAGAGA
63312 ATTGCAGGAGAAAAGAGAGA
1 ATTGCAGG-GAAAAGAGAGA
63332 ATTGCA
1 ATTGCA
63338 AAAGAAAGGG
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 27 0.66
20 14 0.34
ACGTcount: A:0.41, C:0.06, G:0.38, T:0.16
Consensus pattern (19 bp):
ATTGCAGGGAAAAGAGAGA
Found at i:63351 original size:20 final size:20
Alignment explanation
Indices: 63305--63352 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
63295 TGCAGGTAAG
**
63305 AGGGAGAATTGCAGGAGAAA
1 AGGGAGAATTGCAAAAGAAA
*
63325 AGAGAGAATTGCAAAAGAAA
1 AGGGAGAATTGCAAAAGAAA
*
63345 GGGGAGAA
1 AGGGAGAA
63353 AAAAACCCAG
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.50, C:0.04, G:0.38, T:0.08
Consensus pattern (20 bp):
AGGGAGAATTGCAAAAGAAA
Found at i:66937 original size:30 final size:30
Alignment explanation
Indices: 66903--66993 Score: 114
Period size: 30 Copynumber: 3.1 Consensus size: 30
66893 ACAGACGCTC
*
66903 AAATTGAGAGTTCAGGGGGTAAAATGTCCA
1 AAATTGAGAGTTCAGGGGGCAAAATGTCCA
**
66933 AAATTGAGAGTT-ATAGGGCAAAATGTCCA
1 AAATTGAGAGTTCAGGGGGCAAAATGTCCA
* *
66962 AAATTGA-AGTTCAGGGGGGGAAAACGTCCA
1 AAATTGAGAGTTCA-GGGGGCAAAATGTCCA
66992 AA
1 AA
66994 CGCTACAAGT
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
28 4 0.08
29 22 0.42
30 26 0.50
ACGTcount: A:0.40, C:0.11, G:0.29, T:0.21
Consensus pattern (30 bp):
AAATTGAGAGTTCAGGGGGCAAAATGTCCA
Found at i:67161 original size:31 final size:31
Alignment explanation
Indices: 67123--67182 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
67113 CCACATTGCA
67123 CACCTAATTTTAGTGTTGGTTTTAGTGAGAC
1 CACCTAATTTTAGTGTTGGTTTTAGTGAGAC
*
67154 CACCTAATTTTGGTGTTGGTTTTAGTGAG
1 CACCTAATTTTAGTGTTGGTTTTAGTGAG
67183 TCTACCAAGG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.20, C:0.12, G:0.25, T:0.43
Consensus pattern (31 bp):
CACCTAATTTTAGTGTTGGTTTTAGTGAGAC
Found at i:71783 original size:39 final size:40
Alignment explanation
Indices: 71725--71808 Score: 152
Period size: 39 Copynumber: 2.1 Consensus size: 40
71715 TCCAACTCAA
71725 TCTAATTCTAATCTAGCCTATTTTGTTGAATTCTAAACCT
1 TCTAATTCTAATCTAGCCTATTTTGTTGAATTCTAAACCT
*
71765 TCTAATTCT-ATCTAGCCTATTTTGTTGAATTCTAACCCT
1 TCTAATTCTAATCTAGCCTATTTTGTTGAATTCTAAACCT
71804 TCTAA
1 TCTAA
71809 CCCTTCGCTA
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
39 34 0.79
40 9 0.21
ACGTcount: A:0.26, C:0.21, G:0.07, T:0.45
Consensus pattern (40 bp):
TCTAATTCTAATCTAGCCTATTTTGTTGAATTCTAAACCT
Found at i:83994 original size:44 final size:44
Alignment explanation
Indices: 83944--84032 Score: 169
Period size: 44 Copynumber: 2.0 Consensus size: 44
83934 TAATGGCCTA
*
83944 TGCCTAATCCTACAATGGTATTTTCCATCCACATCATTAAGTAT
1 TGCCTAATCCTACAATGGTATTTTCCATCCACATCATCAAGTAT
83988 TGCCTAATCCTACAATGGTATTTTCCATCCACATCATCAAGTAT
1 TGCCTAATCCTACAATGGTATTTTCCATCCACATCATCAAGTAT
84032 T
1 T
84033 CATATCTGTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 44 1.00
ACGTcount: A:0.29, C:0.26, G:0.09, T:0.36
Consensus pattern (44 bp):
TGCCTAATCCTACAATGGTATTTTCCATCCACATCATCAAGTAT
Found at i:85668 original size:21 final size:20
Alignment explanation
Indices: 85639--85677 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
85629 TGTCTACTTT
85639 TAACACAAAGGCCGGTGGAG
1 TAACACAAAGGCCGGTGGAG
85659 TAACAACAAAGGCCGGTGG
1 TAAC-ACAAAGGCCGGTGG
85678 CTGTTTATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.36, C:0.21, G:0.33, T:0.10
Consensus pattern (20 bp):
TAACACAAAGGCCGGTGGAG
Found at i:92021 original size:23 final size:23
Alignment explanation
Indices: 91978--92021 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
91968 TAATATTTTT
*
91978 AATTAAAATAGTAAAATGGTAAA
1 AATTAAAATAGTAAAAGGGTAAA
*
92001 AATT-AAATAGTTATAAGGGTA
1 AATTAAAATAG-TAAAAGGGTA
92022 TTATATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 6 0.33
23 12 0.67
ACGTcount: A:0.55, C:0.00, G:0.16, T:0.30
Consensus pattern (23 bp):
AATTAAAATAGTAAAAGGGTAAA
Found at i:97067 original size:105 final size:104
Alignment explanation
Indices: 96882--97142 Score: 364
Period size: 105 Copynumber: 2.5 Consensus size: 104
96872 AATTTTAACC
* * *
96882 TTAATTTCACTAAGTTTAGCTCAAATTAAAATTTTATTTTATTTTAAAGGTAAATTTCAAAATTA
1 TTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTA
*
96947 ATAATTTATTGTTATAGGGTTTTAGAAATATAATACAAAA
66 ATAA-TTATTGTTATAGGGTTTTAGAAATAAAATACAAAA
* *
96987 TTAATTTCACTAAATTTAGCCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCATAAT
1 TTAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTA-TTTTATTTTAAGGGTAAATTCCAAAAT
* *
97052 TAATAA-TATTGTTATAGGGTTTTAGAAATAAAATATATAA
64 TAATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAA
* ** *
97092 CTAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATCTTATTTTAAGGGT
1 TTAATTTCACTAAGTTTAGCCCAAATTAAAATT-TTATTTTATTTTAAGGGT
97143 TAGAAAAATT
Statistics
Matches: 140, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
103 28 0.20
104 14 0.10
105 52 0.37
106 16 0.11
107 30 0.21
ACGTcount: A:0.41, C:0.08, G:0.09, T:0.42
Consensus pattern (104 bp):
TTAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTATTGTTATAGGGTTTTAGAAATAAAATACAAAA
Done.