Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016459.1 Corchorus capsularis cultivar CVL-1 contig16480, 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: 104978
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:4919 original size:45 final size:45
Alignment explanation
Indices: 4870--4958 Score: 124
Period size: 45 Copynumber: 2.0 Consensus size: 45
4860 CACCACATGA
4870 TTGTTCGCACCATTGTGGTTCGCACCATTATGGTTTGCACCATTG
1 TTGTTCGCACCATTGTGGTTCGCACCATTATGGTTTGCACCATTG
* * * * * *
4915 TTGTTGGCGCCATTGTGGTTTGCACCATTGTTGTTTGCGCCATT
1 TTGTTCGCACCATTGTGGTTCGCACCATTATGGTTTGCACCATT
4959 CACCCTAGCA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
45 38 1.00
ACGTcount: A:0.12, C:0.22, G:0.25, T:0.40
Consensus pattern (45 bp):
TTGTTCGCACCATTGTGGTTCGCACCATTATGGTTTGCACCATTG
Found at i:4946 original size:30 final size:30
Alignment explanation
Indices: 4876--4958 Score: 121
Period size: 30 Copynumber: 2.8 Consensus size: 30
4866 ATGATTGTTC
* *
4876 GCACCATTGTGGTTCGCACCATTATGGTTT
1 GCACCATTGTTGTTCGCGCCATTATGGTTT
* *
4906 GCACCATTGTTGTTGGCGCCATTGTGGTTT
1 GCACCATTGTTGTTCGCGCCATTATGGTTT
*
4936 GCACCATTGTTGTTTGCGCCATT
1 GCACCATTGTTGTTCGCGCCATT
4959 CACCCTAGCA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 48 1.00
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (30 bp):
GCACCATTGTTGTTCGCGCCATTATGGTTT
Found at i:4950 original size:15 final size:15
Alignment explanation
Indices: 4876--4958 Score: 103
Period size: 15 Copynumber: 5.5 Consensus size: 15
4866 ATGATTGTTC
*
4876 GCACCATTGTGGTTC
1 GCACCATTGTGGTTT
*
4891 GCACCATTATGGTTT
1 GCACCATTGTGGTTT
* *
4906 GCACCATTGTTGTTG
1 GCACCATTGTGGTTT
*
4921 GCGCCATTGTGGTTT
1 GCACCATTGTGGTTT
*
4936 GCACCATTGTTGTTT
1 GCACCATTGTGGTTT
*
4951 GCGCCATT
1 GCACCATT
4959 CACCCTAGCA
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
15 57 1.00
ACGTcount: A:0.13, C:0.23, G:0.25, T:0.39
Consensus pattern (15 bp):
GCACCATTGTGGTTT
Found at i:5605 original size:15 final size:15
Alignment explanation
Indices: 5585--5614 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5575 CAAAGAAAAC
5585 GAAAAAGAAAGGGAA
1 GAAAAAGAAAGGGAA
5600 GAAAAAGAAAGGGAA
1 GAAAAAGAAAGGGAA
5615 AATAACGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
GAAAAAGAAAGGGAA
Found at i:9255 original size:17 final size:17
Alignment explanation
Indices: 9233--9265 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
9223 GTAATCCAGC
9233 ACCTCATGCTACCTAGT
1 ACCTCATGCTACCTAGT
*
9250 ACCTCATGTTACCTAG
1 ACCTCATGCTACCTAG
9266 GTATCATGAG
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:0.24, C:0.33, G:0.12, T:0.30
Consensus pattern (17 bp):
ACCTCATGCTACCTAGT
Found at i:11049 original size:31 final size:31
Alignment explanation
Indices: 11011--11069 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
11001 TTTGTGAAAC
*
11011 TTTTGAAATACCTATTATACCCTTATTTAAT
1 TTTTGAAACACCTATTATACCCTTATTTAAT
* *
11042 TTTTGAAACGCCTATTATATCCTTATTT
1 TTTTGAAACACCTATTATACCCTTATTT
11070 GTCTAACATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.29, C:0.17, G:0.05, T:0.49
Consensus pattern (31 bp):
TTTTGAAACACCTATTATACCCTTATTTAAT
Found at i:11124 original size:9 final size:9
Alignment explanation
Indices: 11110--11134 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
11100 CAATTAATTT
11110 TTAATTTTG
1 TTAATTTTG
11119 TTAATTTTG
1 TTAATTTTG
11128 TTAATTT
1 TTAATTT
11135 GCATTTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (9 bp):
TTAATTTTG
Found at i:11944 original size:239 final size:239
Alignment explanation
Indices: 11525--12002 Score: 771
Period size: 239 Copynumber: 2.0 Consensus size: 239
11515 AAAATTGAGG
* * * *
11525 GATGTTGACTAGTCACCTAATGATATTCAATATTCATTCTAAAACTGAAAATCCATAAATTGCAA
1 GATGTTGACCAGTCACCTAATGACATTCAATATTCAATCTAAAACTGAAAACCCATAAATTGCAA
*
11590 AAATAACTTTAACACCAGTATCATAGGTCATTTCAGTTTCTGATTGAGCGGATTTTTTTGGTCGA
66 AAATAACTTTAACACCAGTATCATAGGTCATTTCAGTTTCGGATTGAGCGGATTTTTTTGGTCGA
*
11655 ATCGAGTTGGATAGAGTTTGGCTTCAAGCAGTCGAGTTAGTAGTATACTTAAGATTTTAATTTTC
131 ATCGAGTTAGATAGAGTTTGGCTTCAAGCAGTCGAGTTAGTAGTATACTTAAGATTTTAATTTTC
*
11720 ATTTCATTTAAACATATTAGGTCACGTGCAAAGCACGTGAAAGT
196 ATTTAATTTAAACATATTAGGTCACGTGCAAAGCACGTGAAAGT
* *
11764 GATGTTGACCGGTCACCTAATGACATTCAATGTTCAATCTAAAACTGAAAACCCATAAATTGCAA
1 GATGTTGACCAGTCACCTAATGACATTCAATATTCAATCTAAAACTGAAAACCCATAAATTGCAA
**
11829 AAATAACTTTAACACCAGTGATCATAGGTCATTTTGGTTTCGGATTGAGCGGA-TTTTTTGGTCG
66 AAATAACTTTAACACCAGT-ATCATAGGTCATTTCAGTTTCGGATTGAGCGGATTTTTTTGGTCG
* * * * *
11893 AATTGGGTTAGATA-AGGTTTGGTTTCAAGCGGTTGAGTTAGTAGTATACTTAAGATTTTAATTT
130 AATCGAGTTAGATAGA-GTTTGGCTTCAAGCAGTCGAGTTAGTAGTATACTTAAGATTTTAATTT
*
11957 TCATTTAATTTAAACATATTAGGTCACGTGCAAGGCACGTGAAAGT
194 TCATTTAATTTAAACATATTAGGTCACGTGCAAAGCACGTGAAAGT
12003 AAACATTTAA
Statistics
Matches: 220, Mismatches: 17, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
238 1 0.00
239 189 0.86
240 30 0.14
ACGTcount: A:0.32, C:0.14, G:0.19, T:0.35
Consensus pattern (239 bp):
GATGTTGACCAGTCACCTAATGACATTCAATATTCAATCTAAAACTGAAAACCCATAAATTGCAA
AAATAACTTTAACACCAGTATCATAGGTCATTTCAGTTTCGGATTGAGCGGATTTTTTTGGTCGA
ATCGAGTTAGATAGAGTTTGGCTTCAAGCAGTCGAGTTAGTAGTATACTTAAGATTTTAATTTTC
ATTTAATTTAAACATATTAGGTCACGTGCAAAGCACGTGAAAGT
Found at i:12329 original size:152 final size:156
Alignment explanation
Indices: 12168--12470 Score: 461
Period size: 160 Copynumber: 1.9 Consensus size: 156
12158 GCTTTTTTTA
* * *
12168 TTTTAATGTATTTATTTTTTAGAGAAATTCTATTCTACTAATCTTTC-TTTTTTTGGCCAA-AGT
1 TTTTAATGTATTTAATTTTTAGAGAAATTCTACTCTACTAATCTTTCTTTTTTTTGACCAAGAGT
*
12231 ACTCTACTAATCC-GACTATTTTTCTCTACTATTTTTTCCTTTTTCCAATTTTTCGTTTATTT-A
66 ACTCTACTAATCCTGACTATTTTTCTCTACTATTTTTTCCTTTTTCCAATTTTTCATTTATTTAA
12294 AAAAATTATAAACTCTACTATCAATT
131 AAAAATTATAAACTCTACTATCAATT
*
12320 TTTTAATGTATTTAATTTTTAGAGAAGTTCTACTCTACTAATCTTTCTTTTTTTTTTTGACCAAG
1 TTTTAATGTATTTAATTTTTAGAGAAATTCTACTCTACTAATCTTTC---TTTTTTTTGACCAAG
* * *
12385 AGTACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTCTTTTTTCAATTTTTCATTTT
63 AGTACTCTACTAATCC--TGACTATTTTTCTCTACTATTTTTTCCTTTTTCCAATTTTTCATTTA
12450 TTTAAAAAAATTATAAACTCT
126 TTTAAAAAAATTATAAACTCT
12471 TTATAATTGC
Statistics
Matches: 134, Mismatches: 8, Indels: 9
0.89 0.05 0.06
Matches are distributed among these distances:
152 44 0.33
156 12 0.09
157 16 0.12
160 45 0.34
161 17 0.13
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (156 bp):
TTTTAATGTATTTAATTTTTAGAGAAATTCTACTCTACTAATCTTTCTTTTTTTTGACCAAGAGT
ACTCTACTAATCCTGACTATTTTTCTCTACTATTTTTTCCTTTTTCCAATTTTTCATTTATTTAA
AAAAATTATAAACTCTACTATCAATT
Found at i:12846 original size:36 final size:36
Alignment explanation
Indices: 12803--12877 Score: 150
Period size: 36 Copynumber: 2.1 Consensus size: 36
12793 TTTATACCTA
12803 TTTTATTTTTACCATTTTACTAATCTAATTAAAGTT
1 TTTTATTTTTACCATTTTACTAATCTAATTAAAGTT
12839 TTTTATTTTTACCATTTTACTAATCTAATTAAAGTT
1 TTTTATTTTTACCATTTTACTAATCTAATTAAAGTT
12875 TTT
1 TTT
12878 AAAAATAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.29, C:0.11, G:0.03, T:0.57
Consensus pattern (36 bp):
TTTTATTTTTACCATTTTACTAATCTAATTAAAGTT
Found at i:19597 original size:13 final size:13
Alignment explanation
Indices: 19579--19606 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
19569 CATCATAATT
19579 ATAATTAGTATAG
1 ATAATTAGTATAG
19592 ATAATTAGTATAG
1 ATAATTAGTATAG
19605 AT
1 AT
19607 GGTCTCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.46, C:0.00, G:0.14, T:0.39
Consensus pattern (13 bp):
ATAATTAGTATAG
Found at i:21565 original size:18 final size:19
Alignment explanation
Indices: 21531--21567 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21521 TCAACTTGTG
21531 GACTATTATTCTAAATCAA
1 GACTATTATTCTAAATCAA
*
21550 GACTATTCTT-TAAATCAA
1 GACTATTATTCTAAATCAA
21568 CAATATAATC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (19 bp):
GACTATTATTCTAAATCAA
Found at i:21815 original size:18 final size:19
Alignment explanation
Indices: 21781--21817 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
21771 TGATCAAATG
21781 GACTATTATTCTAAATCAA
1 GACTATTATTCTAAATCAA
*
21800 GACTATTGTT-TAAATCAA
1 GACTATTATTCTAAATCAA
21818 CAATATTAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.41, C:0.14, G:0.08, T:0.38
Consensus pattern (19 bp):
GACTATTATTCTAAATCAA
Found at i:22072 original size:67 final size:68
Alignment explanation
Indices: 21994--22131 Score: 215
Period size: 69 Copynumber: 2.0 Consensus size: 68
21984 TAAAAACTAA
* * *
21994 ACCAACCTCTATAAACACTAAGGGAG-ATAAAAAAATGATATGACATGAAATCTAAATCCTAACA
1 ACCAACCTCTATAAACACTAAGGGAGAAAAAAAAAATGACATGACATGAAATCTAAACCCTAACA
22058 ATG
66 ATG
*
22061 ACCAACCTCTATAAACACTAAGGGAGACAAAAAAAAATGACATGATATGAAATCTAAACCCTAAC
1 ACCAACCTCTATAAACACTAAGGGAGA-AAAAAAAAATGACATGACATGAAATCTAAACCCTAAC
*
22126 TATG
65 AATG
22130 AC
1 AC
22132 ATGACAAACC
Statistics
Matches: 64, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
67 26 0.41
69 38 0.59
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.20
Consensus pattern (68 bp):
ACCAACCTCTATAAACACTAAGGGAGAAAAAAAAAATGACATGACATGAAATCTAAACCCTAACA
ATG
Found at i:41167 original size:11 final size:11
Alignment explanation
Indices: 41151--41182 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
41141 GAAGTTCGTG
41151 TTTGAAGATTA
1 TTTGAAGATTA
*
41162 TTTGAAGATAA
1 TTTGAAGATTA
41173 TTTGAAGATT
1 TTTGAAGATT
41183 TGAAGACAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.44
Consensus pattern (11 bp):
TTTGAAGATTA
Found at i:41179 original size:22 final size:22
Alignment explanation
Indices: 41151--41210 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
41141 GAAGTTCGTG
*
41151 TTTGAAGATTATTTGAAGATAA
1 TTTGAAGATTATTTGAAGACAA
41173 TTTGAAG---ATTTGAAGACAA
1 TTTGAAGATTATTTGAAGACAA
*
41192 -TTGAAGAATTATTTCAAGA
1 TTTGAAG-ATTATTTGAAGA
41211 AGCAAGAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 6 0.19
19 11 0.34
22 15 0.47
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (22 bp):
TTTGAAGATTATTTGAAGACAA
Found at i:41185 original size:19 final size:18
Alignment explanation
Indices: 41161--41198 Score: 58
Period size: 19 Copynumber: 2.1 Consensus size: 18
41151 TTTGAAGATT
*
41161 ATTTGAAGATAATTTGAAG
1 ATTTGAAGACAA-TTGAAG
41180 ATTTGAAGACAATTGAAG
1 ATTTGAAGACAATTGAAG
41198 A
1 A
41199 ATTATTTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.45, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
ATTTGAAGACAATTGAAG
Found at i:42567 original size:5 final size:6
Alignment explanation
Indices: 42516--42547 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
42506 ATAATTGTCA
42516 TAGATT TAGATT TAGATT TAGATT TA-ATT TAG
1 TAGATT TAGATT TAGATT TAGATT TAGATT TAG
42548 TTTGCTTTGT
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:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TAGATT
Found at i:49287 original size:2 final size:2
Alignment explanation
Indices: 49280--49316 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
49270 AAATCCTTTG
49280 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
49317 CTAGCATGTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:54495 original size:38 final size:38
Alignment explanation
Indices: 54451--54601 Score: 180
Period size: 38 Copynumber: 3.9 Consensus size: 38
54441 GCTTTTTGAC
*
54451 GGGATCTTTCCCCAAATTGAAAACTTTGAAAACTGGAT
1 GGGATCTTTCCCTAAATTGAAAACTTTGAAAACTGGAT
54489 GGGATCTTTCCCTAAATTGAAAACTTTGAAAACTTGG-T
1 GGGATCTTTCCCTAAATTGAAAACTTTGAAAAC-TGGAT
* * **
54527 GGGATTTTTCCCTAAATCT-TAAACTTAAAAAAAAACTGGAT
1 GGGATCTTTCCCTAAAT-TGAAAACTT---TGAAAACTGGAT
**
54568 TTGATCTTTCCCTAAATTGAAAACTTTGAAAACT
1 GGGATCTTTCCCTAAATTGAAAACTTTGAAAACT
54602 TCTTTTTGAT
Statistics
Matches: 95, Mismatches: 11, Indels: 14
0.79 0.09 0.12
Matches are distributed among these distances:
38 61 0.64
39 4 0.04
40 4 0.04
41 26 0.27
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.33
Consensus pattern (38 bp):
GGGATCTTTCCCTAAATTGAAAACTTTGAAAACTGGAT
Found at i:58772 original size:30 final size:30
Alignment explanation
Indices: 58736--58829 Score: 84
Period size: 30 Copynumber: 3.1 Consensus size: 30
58726 CTGTGTTATA
58736 TGTGTTTGGGGACTTTAGTATAGATGCCTC
1 TGTGTTTGGGGACTTTAGTATAGATGCCTC
* * * *
58766 TGTGTTTAGGGATTTTAATATAGATACC-C
1 TGTGTTTGGGGACTTTAGTATAGATGCCTC
* ** *
58795 TTGTGCTTGAAGACTTT-GATGTAGATGCCTC
1 -TGTGTTTGGGGACTTTAG-TATAGATGCCTC
58826 TGTG
1 TGTG
58830 CTTAGGGATG
Statistics
Matches: 49, Mismatches: 12, Indels: 6
0.73 0.18 0.09
Matches are distributed among these distances:
29 1 0.02
30 47 0.96
31 1 0.02
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (30 bp):
TGTGTTTGGGGACTTTAGTATAGATGCCTC
Found at i:58888 original size:53 final size:54
Alignment explanation
Indices: 58784--58921 Score: 149
Period size: 57 Copynumber: 2.5 Consensus size: 54
58774 GGGATTTTAA
* * *
58784 TATAGATACCCTTGTGCTTGAAGAC-TTTGATGTAGATGCCTCTGTGCTTAGGG
1 TATAAATACCCTTGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGCTTAGGG
* *
58837 -ATGAATACCCTTGTGTTTGAGGACTTTTGA-G-AGATGTGCCTCTGTGTTTAGGG
1 TATAAATACCCTTGTGTTTGAGGACTTTTGATGTAGA--TGCCTCTGTGCTTAGGG
*
58890 ACTTATAAATGCCCTTGTGTTTGAGGACTTTT
1 ---TATAAATACCCTTGTGTTTGAGGACTTTT
58922 AATTGTTGGG
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
51 3 0.04
52 21 0.30
53 21 0.30
57 26 0.37
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.38
Consensus pattern (54 bp):
TATAAATACCCTTGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGCTTAGGG
Found at i:58913 original size:57 final size:56
Alignment explanation
Indices: 58736--58921 Score: 179
Period size: 60 Copynumber: 3.3 Consensus size: 56
58726 CTGTGTTATA
* * *
58736 TGTGTTTGGGGACTTTAG-TATAGATGCCTCTGTGTTTAGGGATTTTAATATAGATACCCT
1 TGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGTTTAGGGA--TT-ATA-A-ATACCCT
* * * *
58796 TGTGCTTGAAGAC-TTTGATGTAGATGCCTCTGTGCTTAGGG---ATGAATACCCT
1 TGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGTTTAGGGATTATAAATACCCT
*
58848 TGTGTTTGAGGACTTTTGA-G-AGATGTGCCTCTGTGTTTAGGGACTTATAAATGCCCT
1 TGTGTTTGAGGACTTTTGATGTAGA--TGCCTCTGTGTTTAGGGA-TTATAAATACCCT
58905 TGTGTTTGAGGACTTTT
1 TGTGTTTGAGGACTTTT
58922 AATTGTTGGG
Statistics
Matches: 106, Mismatches: 12, Indels: 19
0.77 0.09 0.14
Matches are distributed among these distances:
51 3 0.03
52 19 0.18
53 22 0.21
54 2 0.02
57 26 0.25
59 3 0.03
60 31 0.29
ACGTcount: A:0.20, C:0.13, G:0.27, T:0.40
Consensus pattern (56 bp):
TGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGTTTAGGGATTATAAATACCCT
Found at i:71167 original size:30 final size:30
Alignment explanation
Indices: 71123--71216 Score: 102
Period size: 30 Copynumber: 3.1 Consensus size: 30
71113 TATATGTTTG
* *
71123 GGGACTTTAGTATAGATGCCTCTGTGTTTA
1 GGGACTTTAATATAGATGCCTCTGTGCTTA
* *
71153 GGGATTTTAATATAGATACC-CTTGTGCTT-
1 GGGACTTTAATATAGATGCCTC-TGTGCTTA
* *
71182 GAGGACTTTGATGTAGATGCCTCTGTGCTTA
1 G-GGACTTTAATATAGATGCCTCTGTGCTTA
71213 GGGA
1 GGGA
71217 TGAATACCCT
Statistics
Matches: 52, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
29 2 0.04
30 48 0.92
31 2 0.04
ACGTcount: A:0.21, C:0.14, G:0.28, T:0.37
Consensus pattern (30 bp):
GGGACTTTAATATAGATGCCTCTGTGCTTA
Found at i:71268 original size:53 final size:54
Alignment explanation
Indices: 71163--71300 Score: 158
Period size: 57 Copynumber: 2.5 Consensus size: 54
71153 GGGATTTTAA
* *
71163 TATAGATACCCTTGTGCTTGAGGAC-TTTGATGTAGATGCCTCTGTGCTTAGGG
1 TATAAATACCCTTGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGCTTAGGG
* *
71216 -ATGAATACCCTTGTGTTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGG
1 TATAAATACCCTTGTGTTTGAGGACTTTTGATGTAGA--TGCCTCTGTGCTTAGGG
*
71269 ACTTATAAATGCCCTTGTGTTTGAGGACTTTT
1 ---TATAAATACCCTTGTGTTTGAGGACTTTT
71301 AATTGTTGGG
Statistics
Matches: 72, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
51 3 0.04
52 22 0.31
53 21 0.29
57 26 0.36
ACGTcount: A:0.20, C:0.15, G:0.28, T:0.38
Consensus pattern (54 bp):
TATAAATACCCTTGTGTTTGAGGACTTTTGATGTAGATGCCTCTGTGCTTAGGG
Found at i:71298 original size:57 final size:56
Alignment explanation
Indices: 71117--71300 Score: 184
Period size: 60 Copynumber: 3.3 Consensus size: 56
71107 GTGTTATATA
* * *
71117 TGTTTGGGGACTTTAG-TATAGATGCCTCTGTGTTTAGGGATTTTAATATAGATACCCTTG
1 TGTTTGAGGACTTTTGATGTAGATGCCTCTGTGTTTAGGGA--TT-ATA-A-ATACCCTTG
* * *
71177 TGCTTGAGGAC-TTTGATGTAGATGCCTCTGTGCTTAGGG---ATGAATACCCTTG
1 TGTTTGAGGACTTTTGATGTAGATGCCTCTGTGTTTAGGGATTATAAATACCCTTG
*
71229 TGTTTGAGGACTTTTGA-G-AGAGGTGCCTCTGTGTTTAGGGACTTATAAATGCCCTTG
1 TGTTTGAGGACTTTTGATGTAGA--TGCCTCTGTGTTTAGGGA-TTATAAATACCCTTG
71286 TGTTTGAGGACTTTT
1 TGTTTGAGGACTTTT
71301 AATTGTTGGG
Statistics
Matches: 106, Mismatches: 10, Indels: 19
0.79 0.07 0.14
Matches are distributed among these distances:
51 3 0.03
52 20 0.19
53 22 0.21
54 2 0.02
57 26 0.25
59 3 0.03
60 30 0.28
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.39
Consensus pattern (56 bp):
TGTTTGAGGACTTTTGATGTAGATGCCTCTGTGTTTAGGGATTATAAATACCCTTG
Found at i:74399 original size:9 final size:7
Alignment explanation
Indices: 74370--74397 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
74360 TGAACTTTAA
74370 TATATAT
1 TATATAT
74377 TATATAT
1 TATATAT
74384 TATATAT
1 TATATAT
74391 TATATAT
1 TATATAT
74398 ATGTCATCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
TATATAT
Found at i:86896 original size:14 final size:14
Alignment explanation
Indices: 86877--86911 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
86867 GTGCGTGGCA
*
86877 AAAAAAAAATCAAC
1 AAAAAAAAAGCAAC
86891 AAAAAAAAAGCAAC
1 AAAAAAAAAGCAAC
86905 AAAAAAA
1 AAAAAAA
86912 TGGAAAAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.83, C:0.11, G:0.03, T:0.03
Consensus pattern (14 bp):
AAAAAAAAAGCAAC
Found at i:88064 original size:69 final size:70
Alignment explanation
Indices: 87981--88127 Score: 201
Period size: 69 Copynumber: 2.1 Consensus size: 70
87971 TGCATTTTAA
* *
87981 TTGACCCA-AGGCAGT-TTTGCTTCAGTTTATTTCAATGGACCCATGACGACCTTTCTTCAGTTT
1 TTGACCCAGAGGCAGTCTTT-CTTAAGTTTATTTCAATGGACCCAGGACGACCTTTCTTCAGTTT
88044 ATTCAG
65 ATTCAG
* * * **
88050 TTGACCCAGA-GCAGTCTTTCTTAAGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTCAGTTTA
1 TTGACCCAGAGGCAGTCTTTCTTAAGTTTATTTCAATGGACCCAGGACGACCTTTCTTCAGTTTA
88114 TTCAG
66 TTCAG
88119 TTGACCCAG
1 TTGACCCAG
88128 GGTGGTCTTG
Statistics
Matches: 69, Mismatches: 7, Indels: 4
0.86 0.09 0.05
Matches are distributed among these distances:
69 65 0.94
70 4 0.06
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.37
Consensus pattern (70 bp):
TTGACCCAGAGGCAGTCTTTCTTAAGTTTATTTCAATGGACCCAGGACGACCTTTCTTCAGTTTA
TTCAG
Found at i:88128 original size:34 final size:35
Alignment explanation
Indices: 87981--88136 Score: 174
Period size: 35 Copynumber: 4.5 Consensus size: 35
87971 TGCATTTTAA
* * *
87981 TTGACCCAAGGCAGT-TTTGCTTCAGTTTATTTCAA
1 TTGACCCAGGGCGGTCTTT-CTTCAGTTTATTTCAG
* * * **
88016 TGGACCCATGACGACCTTTCTTCAGTTTA-TTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
* * *
88050 TTGACCCAGAGCAGTCTTTCTTAAGTTTATTTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
88085 TTGACCCAGGGCGGTCTTTCTTCAGTTTA-TTCAG
1 TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
*
88119 TTGACCCAGGGTGGTCTT
1 TTGACCCAGGGCGGTCTT
88137 GCGTATAAGT
Statistics
Matches: 100, Mismatches: 19, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
34 47 0.47
35 50 0.50
36 3 0.03
ACGTcount: A:0.19, C:0.22, G:0.21, T:0.38
Consensus pattern (35 bp):
TTGACCCAGGGCGGTCTTTCTTCAGTTTATTTCAG
Found at i:88152 original size:34 final size:33
Alignment explanation
Indices: 88039--88149 Score: 114
Period size: 35 Copynumber: 3.2 Consensus size: 33
88029 ACCTTTCTTC
* * *
88039 AGTTTATTCAGTTGACCCAGAGCAGTCTTTCTTA
1 AGTTT-TTCAGTTGACCCAGGGCGGTCTTGCTTA
* *
88073 AGTTTATTTCAGTTGACCCAGGGCGGTCTTTCTTC
1 AG-TT-TTTCAGTTGACCCAGGGCGGTCTTGCTTA
*
88108 AGTTTATTCAGTTGACCCAGGGTGGTCTTGCGTATA
1 AGTTT-TTCAGTTGACCCAGGGCGGTCTTGC-T-TA
88144 AGTTTT
1 AGTTTT
88150 CAGAGGTCAG
Statistics
Matches: 66, Mismatches: 6, Indels: 9
0.81 0.07 0.11
Matches are distributed among these distances:
33 1 0.02
34 27 0.41
35 31 0.47
36 7 0.11
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (33 bp):
AGTTTTTCAGTTGACCCAGGGCGGTCTTGCTTA
Found at i:88182 original size:35 final size:35
Alignment explanation
Indices: 88143--88318 Score: 199
Period size: 35 Copynumber: 5.3 Consensus size: 35
88133 TCTTGCGTAT
88143 AAGTTTTCAGAGGTCAGAGTTGATCTTATTTCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTTATTTCAAG
*
88178 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTTATTTCAAG
* * **
88213 AAGTTTTCATA-TTCA-A---GA-AGT-TTTC-AG
1 AAGTTTTCAGAGGTCAGAGTTGATCTTATTTCAAG
* *
88240 AAGTTTTCGGAGGTCAGAGTTGAT-TTCATTTCGAG
1 AAGTTTTCAGAGGTCAGAGTTGATCTT-ATTTCAAG
* *
88275 AAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAAT
1 AAGTTTTCAGAGGTCAGAGTTGATCTTATTTCAAG
88310 AAGTTTTCA
1 AAGTTTTCA
88319 TTTCAAGAAG
Statistics
Matches: 117, Mismatches: 14, Indels: 20
0.77 0.09 0.13
Matches are distributed among these distances:
27 11 0.09
28 7 0.06
29 1 0.01
30 2 0.02
32 3 0.03
33 1 0.01
34 7 0.06
35 84 0.72
36 1 0.01
ACGTcount: A:0.28, C:0.12, G:0.22, T:0.38
Consensus pattern (35 bp):
AAGTTTTCAGAGGTCAGAGTTGATCTTATTTCAAG
Found at i:88229 original size:17 final size:16
Alignment explanation
Indices: 88203--88238 Score: 63
Period size: 17 Copynumber: 2.2 Consensus size: 16
88193 AGAGTTGATC
88203 TCATTTCAAGAAGTTT
1 TCATTTCAAGAAGTTT
88219 TCATATTCAAGAAGTTT
1 TCAT-TTCAAGAAGTTT
88236 TCA
1 TCA
88239 GAAGTTTTCG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (16 bp):
TCATTTCAAGAAGTTT
Found at i:88321 original size:16 final size:16
Alignment explanation
Indices: 88300--88332 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
88290 AGAGTTGATC
*
88300 TCATTTCAATAAGTTT
1 TCATTTCAAGAAGTTT
88316 TCATTTCAAGAAGTTT
1 TCATTTCAAGAAGTTT
88332 T
1 T
88333 TAGAGGTCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.12, G:0.09, T:0.48
Consensus pattern (16 bp):
TCATTTCAAGAAGTTT
Found at i:88328 original size:51 final size:51
Alignment explanation
Indices: 88263--88369 Score: 178
Period size: 51 Copynumber: 2.1 Consensus size: 51
88253 TCAGAGTTGA
* * *
88263 TTTCATTTCGAGAAGTTTTCAGAGGTCAGAGTTGATCTCATTTCAATAAGT
1 TTTCATTTCAAGAAGTTTTCAGAGGTCAGAATTGATCTCATTTCAAGAAGT
*
88314 TTTCATTTCAAGAAGTTTTTAGAGGTCAGAATTGATCTCATTTCAAGAAGT
1 TTTCATTTCAAGAAGTTTTCAGAGGTCAGAATTGATCTCATTTCAAGAAGT
88365 TTTCA
1 TTTCA
88370 GAGGTCAGAG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.29, C:0.13, G:0.18, T:0.40
Consensus pattern (51 bp):
TTTCATTTCAAGAAGTTTTCAGAGGTCAGAATTGATCTCATTTCAAGAAGT
Found at i:88332 original size:86 final size:85
Alignment explanation
Indices: 88234--88402 Score: 257
Period size: 86 Copynumber: 2.0 Consensus size: 85
88224 TTCAAGAAGT
* * * *
88234 TTTCAGAAGTTTTCGGAGGTCAGAGTTGATTTCATTTCGAGAAGTTTTCAGAGGTCAGAGTTGAT
1 TTTCAGAAGTTTTCAGAGGTCAGAATTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGAT
* *
88299 CTCATTTCAATAAGTTTTCA
66 ATCATTTCAAGAAGTTTTCA
*
88319 TTTCAAGAAGTTTTTAGAGGTCAGAATTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGA
1 TTTC-AGAAGTTTTCAGAGGTCAGAATTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGA
*
88384 TATCATTTTAAGAAGTTTT
65 TATCATTTCAAGAAGTTTT
88403 TAGAGGTCAG
Statistics
Matches: 75, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
85 4 0.05
86 71 0.95
ACGTcount: A:0.28, C:0.11, G:0.21, T:0.39
Consensus pattern (85 bp):
TTTCAGAAGTTTTCAGAGGTCAGAATTGATCTCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGAT
ATCATTTCAAGAAGTTTTCA
Found at i:88362 original size:35 final size:35
Alignment explanation
Indices: 88316--88624 Score: 425
Period size: 35 Copynumber: 9.0 Consensus size: 35
88306 CAATAAGTTT
* *
88316 TCATTTCAAGAAGTTTTTAGAGGTCAGAATTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
88351 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATA
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
88386 TCATTTTAAGAAGTTTTTAGAGGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
88421 TCATTTCAAGAAGTTTTCAGAGGTCATAGTTGATT
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
88456 TCATTTCAAGAAGTTTTCAGAAGTCATAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
88491 TCATTTCAAGATGTTTTTAGAGGTC---GTT--T-
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
88520 TCATTTCAAGAAGTTTTCAGAAGTCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
* *
88555 TCATTTCAAGAAGTTTTCAGAAGTCAGAGTTTATC
1 TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
*
88590 TCATTTCAAGAAGTTTTC-GATGATCAGAGTTGATC
1 TCATTTCAAGAAGTTTTCAGA-GGTCAGAGTTGATC
88625 CAGTGCGGCT
Statistics
Matches: 245, Mismatches: 22, Indels: 14
0.87 0.08 0.05
Matches are distributed among these distances:
29 22 0.09
30 1 0.00
32 6 0.02
34 3 0.01
35 213 0.87
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.38
Consensus pattern (35 bp):
TCATTTCAAGAAGTTTTCAGAGGTCAGAGTTGATC
Found at i:89783 original size:80 final size:81
Alignment explanation
Indices: 89667--89908 Score: 324
Period size: 80 Copynumber: 2.9 Consensus size: 81
89657 GGTTTCATGT
* * *
89667 AATAAATTATAAAATTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGAGGAAGGTTT
1 AATAAA-TATAAAATTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTT
89732 AGGAGATATTTTAAG-A
65 AGGAGATATTTTAAGAA
* * *
89748 AATAGATATAAAATTGAATAATAATGAAAATATTTTCTAAATCTTTCCAAATTGTGGGAGATTTA
1 AATAAATATAAAATTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTA
89813 GGAGATATTTTAAGAAATA
66 GGAGATATTTTAAG--A-A
* * *
89832 AATAAATAATAAAGATTGAATAGTAATGAGAATATTTCTCTAAATCTTGTCAGATTGTGGGAGAT
1 AATAAAT-ATAAA-ATTGAATAATAATGAGAATATTT-TCTAAATCTTGCCAAATTGTGGGAGAT
*
89897 TTATGAGATATT
63 TTAGGAGATATT
89909 AAATAATAAT
Statistics
Matches: 141, Mismatches: 13, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
80 68 0.48
81 5 0.04
84 7 0.05
85 5 0.04
86 21 0.15
87 35 0.25
ACGTcount: A:0.43, C:0.05, G:0.16, T:0.36
Consensus pattern (81 bp):
AATAAATATAAAATTGAATAATAATGAGAATATTTTCTAAATCTTGCCAAATTGTGGGAGATTTA
GGAGATATTTTAAGAA
Found at i:90495 original size:41 final size:41
Alignment explanation
Indices: 90440--90584 Score: 254
Period size: 41 Copynumber: 3.5 Consensus size: 41
90430 CGTTACGACA
* *
90440 CCTTCCTTGAAATTAAGTTTGTGCTTGTCTTTACCTAATTT
1 CCTTCATTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT
*
90481 CCTTCCTTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT
1 CCTTCATTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT
*
90522 CCTTCATTGAAATTAAGTCTATGCTTGTCTTTACCTAATTT
1 CCTTCATTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT
90563 CCTTCATTGAAATTAAGTCTGT
1 CCTTCATTGAAATTAAGTCTGT
90585 TGATTGCCAT
Statistics
Matches: 100, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 100 1.00
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.46
Consensus pattern (41 bp):
CCTTCATTGAAATTAAGTCTGTGCTTGTCTTTACCTAATTT
Found at i:90638 original size:40 final size:40
Alignment explanation
Indices: 90594--90670 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 40
90584 TTGATTGCCA
90594 TTTTTACTTAATTTCTAAGAATTAAGTCTTTTAACTGATG
1 TTTTTACTTAATTTCTAAGAATTAAGTCTTTTAACTGATG
*
90634 TTTTTTCTTAATTTCTAAGAATTAAGTCTTTTAACTG
1 TTTTTACTTAATTTCTAAGAATTAAGTCTTTTAACTG
90671 TTCTTATTAC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.29, C:0.10, G:0.09, T:0.52
Consensus pattern (40 bp):
TTTTTACTTAATTTCTAAGAATTAAGTCTTTTAACTGATG
Found at i:90689 original size:32 final size:31
Alignment explanation
Indices: 90664--90783 Score: 84
Period size: 30 Copynumber: 3.6 Consensus size: 31
90654 ATTAAGTCTT
90664 TTAACTGTTCTT-ATTACCCTGAATTAAGCC
1 TTAACTGTTCTTAATTACCCTGAATTAAGCC
* *
90694 TTAACTTTTCTTAATTA-CC-AAATTAAGACC
1 TTAACTGTTCTTAATTACCCTGAATTAAG-CC
* *
90724 TTGACCGTGCTTACTTCTCTTAATTACCCTGAATTAAGAC
1 TT-AAC-TG------T-TCTTAATTACCCTGAATTAAGCC
90764 TCTAACTGTTCTTAATTACC
1 T-TAACTGTTCTTAATTACC
90784 AAATTAAGAC
Statistics
Matches: 69, Mismatches: 7, Indels: 26
0.68 0.07 0.25
Matches are distributed among these distances:
29 7 0.10
30 17 0.25
31 6 0.09
32 12 0.17
33 1 0.01
38 1 0.01
39 11 0.16
40 6 0.09
41 8 0.12
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.40
Consensus pattern (31 bp):
TTAACTGTTCTTAATTACCCTGAATTAAGCC
Found at i:90782 original size:71 final size:71
Alignment explanation
Indices: 90671--91107 Score: 573
Period size: 71 Copynumber: 6.2 Consensus size: 71
90661 CTTTTAACTG
* * * * * *
90671 TTCTT-ATTACCCTGAATTAAGCCTTAACTTTTCTTAATTA-CCAAATTAAGACCTTGACCGTGC
1 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAAGACCTTGACTGTAC
90734 TTACTT
66 TTACTT
* * * * * *
90740 CTCTTAATTACCCTGAATTAAGACTCTAACTGTTCTTAATTA-CCAAATTAAGACCTTGACTATG
1 TTCTTAATTACCCTGAATTAAGACT-TTACTCTTCTTAATTACCCAACTTAAGACCTTGACTGTA
90804 CTTACTT
65 CTTACTT
* * * ** *
90811 TTCTTAATTATCCTGAATTAAGA-TTCTGCAT-TTCTTAATT-TCCATGTTAAGACCTTGACTAT
1 TTCTTAATTACCCTGAATTAAGACTT-TAC-TCTTCTTAATTACCCAACTTAAGACCTTGACTGT
*
90873 GCTTACTT
64 ACTTACTT
*
90881 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGACTGTAC
1 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAAGACCTTGACTGTAC
*
90946 TTTCTT
66 TTACTT
*
90952 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGACTGTAC
1 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAAGACCTTGACTGTAC
*
91017 TTTCTT
66 TTACTT
91023 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTT-AGTACCTTGACTGTA
1 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAAG-ACCTTGACTGTA
*
91087 CTTTCTT
65 CTTACTT
91094 TTCTTAATTACCCT
1 TTCTTAATTACCCT
91108 TTACTTTTCT
Statistics
Matches: 338, Mismatches: 21, Indels: 16
0.90 0.06 0.04
Matches are distributed among these distances:
69 6 0.02
70 90 0.27
71 242 0.72
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (71 bp):
TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAAGACCTTGACTGTAC
TTACTT
Found at i:90815 original size:39 final size:39
Alignment explanation
Indices: 90772--90892 Score: 118
Period size: 39 Copynumber: 3.3 Consensus size: 39
90762 ACTCTAACTG
90772 TTCTTAATTACCAAATTAAGACCTTGACTATGCTTACTT
1 TTCTTAATTACCAAATTAAGACCTTGACTATGCTTACTT
*
90811 TTCTTAATTATCCTGAATTAAGA--TT--C--TGC--A--T
1 TTCTTAATTA-CC-AAATTAAGACCTTGACTATGCTTACTT
* **
90842 TTCTTAATTTCCATGTTAAGACCTTGACTATGCTTACTT
1 TTCTTAATTACCAAATTAAGACCTTGACTATGCTTACTT
90881 TTCTTAATTACC
1 TTCTTAATTACC
90893 CTGAATTAAG
Statistics
Matches: 64, Mismatches: 6, Indels: 24
0.68 0.06 0.26
Matches are distributed among these distances:
29 6 0.09
30 2 0.03
31 12 0.19
33 2 0.03
35 6 0.09
37 2 0.03
39 24 0.38
40 2 0.03
41 8 0.12
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (39 bp):
TTCTTAATTACCAAATTAAGACCTTGACTATGCTTACTT
Found at i:90910 original size:31 final size:31
Alignment explanation
Indices: 90875--91066 Score: 131
Period size: 31 Copynumber: 5.6 Consensus size: 31
90865 TTGACTATGC
*
90875 TTACTTTTCTTAATTACCCTGAATTAAGACT
1 TTACTCTTCTTAATTACCCTGAATTAAGACT
90906 TTACTCTTCTTAATTACCC--AACTTAGGACCTTGACT
1 TTACTCTTCTTAATTACCCTGAA-TTA--A----GACT
*
90942 GTACTTTCTTTTCTTAATTACCCTGAATTAAGACT
1 TTAC--TC--TTCTTAATTACCCTGAATTAAGACT
90977 TTACTCTTCTTAATTACCC--AACTTAGGACCTTGACT
1 TTACTCTTCTTAATTACCCTGAA-TTA--A----GACT
*
91013 GTACTTTCTTTTCTTAATTACCCTGAATTAAGACT
1 TTAC--TC--TTCTTAATTACCCTGAATTAAGACT
91048 TTACTCTTCTTAATTACCC
1 TTACTCTTCTTAATTACCC
91067 AACTTAGTAC
Statistics
Matches: 130, Mismatches: 5, Indels: 52
0.70 0.03 0.28
Matches are distributed among these distances:
29 4 0.03
30 6 0.05
31 44 0.34
32 2 0.02
33 4 0.03
35 14 0.11
36 14 0.11
38 4 0.03
39 2 0.02
40 26 0.20
41 6 0.05
42 4 0.03
ACGTcount: A:0.26, C:0.24, G:0.07, T:0.43
Consensus pattern (31 bp):
TTACTCTTCTTAATTACCCTGAATTAAGACT
Found at i:90959 original size:40 final size:39
Alignment explanation
Indices: 90903--91106 Score: 169
Period size: 40 Copynumber: 5.5 Consensus size: 39
90893 CTGAATTAAG
*
90903 ACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGACTGT
1 ACTTT-CTTTTCTTAATTACCCAACTTA-GACCTTGACTGT
*
90944 ACTTTCTTTTCTTAATTACCCTGAA-TTA-A----GACTTT
1 ACTTTCTTTTCTTAATTACCC--AACTTAGACCTTGACTGT
90979 AC--TC--TTCTTAATTACCCAACTTAGGACCTTGACTGT
1 ACTTTCTTTTCTTAATTACCCAACTTA-GACCTTGACTGT
*
91015 ACTTTCTTTTCTTAATTACCCTGAA-TTA-A----GACTTT
1 ACTTTCTTTTCTTAATTACCC--AACTTAGACCTTGACTGT
91050 AC--TC--TTCTTAATTACCCAACTTAGTACCTTGACTGT
1 ACTTTCTTTTCTTAATTACCCAACTTAG-ACCTTGACTGT
91086 ACTTTCTTTTCTTAATTACCC
1 ACTTTCTTTTCTTAATTACCC
91107 TTTACTTTTC
Statistics
Matches: 132, Mismatches: 5, Indels: 53
0.69 0.03 0.28
Matches are distributed among these distances:
29 4 0.03
30 6 0.05
31 26 0.20
32 2 0.02
33 4 0.03
35 14 0.11
36 14 0.11
38 4 0.03
39 2 0.02
40 41 0.31
41 11 0.08
42 4 0.03
ACGTcount: A:0.25, C:0.25, G:0.07, T:0.43
Consensus pattern (39 bp):
ACTTTCTTTTCTTAATTACCCAACTTAGACCTTGACTGT
Found at i:91053 original size:142 final size:140
Alignment explanation
Indices: 90671--91107 Score: 601
Period size: 141 Copynumber: 3.1 Consensus size: 140
90661 CTTTTAACTG
* * *
90671 TTCTT-ATTACCCTGAATTAAGCCTTAACTTTTCTTAATTACCAAATTAAGACCTTGACCGTGCT
1 TTCTTAATTACCCTGAATTAAGACTTTAC-TTTCTTAATTACCAAATTAAGACCTTGACTGTGCT
* * * * *
90735 TACTTCTCTTAATTACCCTGAATTAAGACTCTAACTGTTCTTAATTA-CCAAATTAAGACCTTGA
65 TACTTTTCTTAATTACCCTGAATTAAGACT-TTACTCTTCTTAATTACCCAACTTAGGACCTTGA
* * *
90799 CTATGCTTACTT
129 CTGTACTTTCTT
* * * ** *
90811 TTCTTAATTATCCTGAATTAAGA-TTCTGCATTTCTTAATTTCCATGTTAAGACCTTGACTATGC
1 TTCTTAATTACCCTGAATTAAGACTT-TAC-TTTCTTAATTACCAAATTAAGACCTTGACTGTGC
90875 TTACTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGA
64 TTACTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGA
90940 CTGTACTTTCTT
129 CTGTACTTTCTT
* * *
90952 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGACTGTAC
1 TTCTTAATTACCCTGAATTAAGACTTTACT-TTCTTAATTA-CCAAATTAAGACCTTGACTGTGC
* *
91017 TTTCTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGTACCTTGA
64 TTACTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGA
91082 CTGTACTTTCTT
129 CTGTACTTTCTT
91094 TTCTTAATTACCCT
1 TTCTTAATTACCCT
91108 TTACTTTTCT
Statistics
Matches: 263, Mismatches: 28, Indels: 10
0.87 0.09 0.03
Matches are distributed among these distances:
140 22 0.08
141 132 0.50
142 109 0.41
ACGTcount: A:0.27, C:0.23, G:0.08, T:0.42
Consensus pattern (140 bp):
TTCTTAATTACCCTGAATTAAGACTTTACTTTCTTAATTACCAAATTAAGACCTTGACTGTGCTT
ACTTTTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGACT
GTACTTTCTT
Found at i:91128 original size:212 final size:211
Alignment explanation
Indices: 90671--91134 Score: 539
Period size: 212 Copynumber: 2.2 Consensus size: 211
90661 CTTTTAACTG
* *
90671 TTCTT-ATTACCCTGAATTAAGCCTTAACTT-TTCTTAATTA-CCAAATTAAGACCTTGACCGTG
1 TTCTTAATTACCCTGAATT-AGACTTAA-TTCTTCTTAATTACCCAAATTAAGACCTTGACCGTA
*
90733 CTTACTTCTCTTAATTACCCTGAATTAAGACTCTAACTGTTCTTAATTACCAAATTAAGACCTTG
64 CTTACTTCTCTTAATTACCCTGAATTAAGACTCTAACTCTTCTTAATTACCAAATTAAGACCTTG
* * * * **
90798 ACTATGCTTACTTTTCTTAATTATCCTGAATTAAGATTCTGCATTTCTTAATTTCCATGTTAAGA
129 ACTATACTTACTTTTCTTAATTACCCTGAATTAAGATTCTACATTTCTTAATTCCCAACTTAAGA
*
90863 CCTTGACTATGCTTACTT
194 CCTTGACTATACTTACTT
* * * * *
90881 TTCTTAATTACCCTGAATTAAGACTTTACTCTTCTTAATTACCCAACTTAGGACCTTGACTGTAC
1 TTCTTAATTACCCTGAATT-AGACTTAATTCTTCTTAATTACCCAAATTAAGACCTTGACCGTAC
* * * * *
90946 TTTCTTTTCTTAATTACCCTGAATTAAGACT-TTACTCTTCTTAATTACCCAACTTAGGACCTTG
65 TTACTTCTCTTAATTACCCTGAATTAAGACTCTAACTCTTCTTAATTA-CCAAATTAAGACCTTG
* *
91010 ACTGTACTTTCTTTTCTTAATTACCCTGAATTAAGACTT-TAC-TCTTCTTAATTACCCAACTT-
129 ACTATACTTACTTTTCTTAATTACCCTGAATTAAGA-TTCTACAT-TTCTTAATT-CCCAACTTA
* *
91072 AGTACCTTGACTGTACTTTCTT
191 AG-ACCTTGACTATACTTACTT
* * **
91094 TTCTTAATTACCCTTTACTT-TTCTTAATTCTTCTTAATTAC
1 TTCTTAATTACCC-TGAATTAGACTTAATTCTTCTTAATTAC
91135 AATGAATTAA
Statistics
Matches: 215, Mismatches: 30, Indels: 16
0.82 0.11 0.06
Matches are distributed among these distances:
210 6 0.03
211 45 0.21
212 124 0.58
213 36 0.17
214 4 0.02
ACGTcount: A:0.26, C:0.23, G:0.08, T:0.43
Consensus pattern (211 bp):
TTCTTAATTACCCTGAATTAGACTTAATTCTTCTTAATTACCCAAATTAAGACCTTGACCGTACT
TACTTCTCTTAATTACCCTGAATTAAGACTCTAACTCTTCTTAATTACCAAATTAAGACCTTGAC
TATACTTACTTTTCTTAATTACCCTGAATTAAGATTCTACATTTCTTAATTCCCAACTTAAGACC
TTGACTATACTTACTT
Found at i:97820 original size:29 final size:29
Alignment explanation
Indices: 97765--97820 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
97755 TTTTCTAATC
** **
97765 AAAATCACACCCAAACTCTGTGTCAAAAA
1 AAAATCACACCCAAACTCCATAACAAAAA
97794 AAAATCACACCCAAACTCCATAACAAA
1 AAAATCACACCCAAACTCCATAACAAA
97821 TCATTTCTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.52, C:0.30, G:0.04, T:0.14
Consensus pattern (29 bp):
AAAATCACACCCAAACTCCATAACAAAAA
Found at i:101950 original size:18 final size:16
Alignment explanation
Indices: 101927--101961 Score: 52
Period size: 18 Copynumber: 2.1 Consensus size: 16
101917 AGAAGAAGTA
101927 TGCTTTATAATTATTGTT
1 TGCTTTAT-ATT-TTGTT
101945 TGCTTTATATTTTGTT
1 TGCTTTATATTTTGTT
101961 T
1 T
101962 TAGATTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.35
17 3 0.18
18 8 0.47
ACGTcount: A:0.17, C:0.06, G:0.11, T:0.66
Consensus pattern (16 bp):
TGCTTTATATTTTGTT
Done.