Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015672.1 Corchorus olitorius cultivar O-4 contig15705, 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: 179081
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:857 original size:52 final size:51
Alignment explanation
Indices: 780--883 Score: 172
Period size: 52 Copynumber: 2.0 Consensus size: 51
770 TTACCATAAT
780 AATAAACCAACCAAACCAAACCAACATAAATTTTTATGTTATACAATCAAA
1 AATAAACCAACCAAACCAAACCAACATAAATTTTTATGTTATACAATCAAA
* * *
831 AATAATACCAACTAAACCGAACCAACATAAATTTTTATGTTGTACAATCAAA
1 AATAA-ACCAACCAAACCAAACCAACATAAATTTTTATGTTATACAATCAAA
883 A
1 A
884 CCCACAAATG
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 5 0.10
52 44 0.90
ACGTcount: A:0.51, C:0.20, G:0.04, T:0.25
Consensus pattern (51 bp):
AATAAACCAACCAAACCAAACCAACATAAATTTTTATGTTATACAATCAAA
Found at i:3238 original size:13 final size:13
Alignment explanation
Indices: 3220--3244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3210 TTAACTTAAT
3220 ATAATATAACATG
1 ATAATATAACATG
3233 ATAATATAACAT
1 ATAATATAACAT
3245 AATATATTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.04, T:0.32
Consensus pattern (13 bp):
ATAATATAACATG
Found at i:4673 original size:25 final size:22
Alignment explanation
Indices: 4620--4676 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
4610 TAAGTTTTTT
*
4620 AATTAAATTAGTAAAATGATAA
1 AATTAAATTAGTAAAAGGATAA
* *
4642 AAATAAATTAGGTATAAGGATATA
1 AATTAAATTA-GTAAAAGGATA-A
4666 AGATTAAATTA
1 A-ATTAAATTA
4677 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
22 9 0.32
23 9 0.32
24 2 0.07
25 8 0.29
ACGTcount: A:0.56, C:0.00, G:0.12, T:0.32
Consensus pattern (22 bp):
AATTAAATTAGTAAAAGGATAA
Found at i:4777 original size:132 final size:132
Alignment explanation
Indices: 4595--4848 Score: 379
Period size: 132 Copynumber: 1.9 Consensus size: 132
4585 TCATTTATCC
* *
4595 AAATTCTAATATATCTAAGTTTTTTAATTAAATTAGTAAAATGATAAAAA-TAAATTAGGTATAA
1 AAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATTAAA-TAGGTATAA
* *
4659 GGATATAAGATTAAATTAAATAAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTGTATTT
65 AGATATAAGATTAAAGTAAAT-AAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTGTATTT
4724 AAAA
129 AAAA
*
4728 AAATTCTAATATATATAAG-TTTTTAATTAAAATAGTAAAATTG-TAAAAATTAAATAGTTATAA
1 AAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAA-TGATAAAAATTAAATAGGTATAA
* * * *
4791 AGATATTAGATTTAAGTAAATAAAAATAGAGTTTTTAGTTGAGTAAAATTATAAAAGT
65 AGATATAAGATTAAAGTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGT
4849 TTAAACAATG
Statistics
Matches: 110, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
131 35 0.32
132 51 0.46
133 24 0.22
ACGTcount: A:0.50, C:0.02, G:0.11, T:0.37
Consensus pattern (132 bp):
AAATTCTAATATATATAAGTTTTTTAATTAAAATAGTAAAATGATAAAAATTAAATAGGTATAAA
GATATAAGATTAAAGTAAATAAAAATAGAGTTTTTAGTTGAGCAAAACTATAAAAGTGTATTTAA
AA
Found at i:5579 original size:134 final size:130
Alignment explanation
Indices: 5360--5599 Score: 340
Period size: 134 Copynumber: 1.8 Consensus size: 130
5350 TTATTTAAAG
* *
5360 TTTTATAGTTTTATTCAACTAAAAACTCTATTTTTTATTTAATTAAGTCTAATATCCTTATAACT
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
*
5425 ATTTTATTTTTAGCAGTTTACTATTTTATTTTAATTAAAAAACTTAAAAATTAGAATTTTTTAAA
66 ATTTTATTTTTACCAGTTTACTA----A-TTTAATTAAAAAACTTAAAAATTAGAATTTTTTAAA
5490 TATAT
126 TATAT
* ** *
5495 TTTTATAGTTTTACTCAATTAAAAACTCTA-TTTTTATCTT-ATTAAATCTAATATTTTTATACC
1 TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTAT-TTAATTAAATCTAATATCCTTATAAC
*
5558 TATTTTATTTTTACCATTTTACTAATTTAATTAAAAAACTTA
65 TATTTTATTTTTACCAGTTTACTAATTTAATTAAAAAACTTA
5600 TAAAGTTTTT
Statistics
Matches: 96, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
129 17 0.18
130 1 0.01
134 48 0.50
135 30 0.31
ACGTcount: A:0.36, C:0.10, G:0.03, T:0.52
Consensus pattern (130 bp):
TTTTATAGTTTTACTCAACTAAAAACTCTATTTTTTATTTAATTAAATCTAATATCCTTATAACT
ATTTTATTTTTACCAGTTTACTAATTTAATTAAAAAACTTAAAAATTAGAATTTTTTAAATATAT
Found at i:7158 original size:22 final size:22
Alignment explanation
Indices: 7133--7174 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
7123 ACGTTAAGAC
**
7133 TTTTTTTTTTATGTGAAACATA
1 TTTTTTTTAAATGTGAAACATA
7155 TTTTTTTTAAATGTGAAACA
1 TTTTTTTTAAATGTGAAACA
7175 CTTTCCCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.31, C:0.05, G:0.10, T:0.55
Consensus pattern (22 bp):
TTTTTTTTAAATGTGAAACATA
Found at i:7884 original size:22 final size:22
Alignment explanation
Indices: 7859--7923 Score: 76
Period size: 22 Copynumber: 3.0 Consensus size: 22
7849 ACACCTATCA
* **
7859 GGTTATCAAAATTATATAGTGT
1 GGTTATCAAAATTACATAGAAT
**
7881 GGTTATCAAAATCCCATAGAAT
1 GGTTATCAAAATTACATAGAAT
*
7903 GGTTATCAAAATTTCATAGAA
1 GGTTATCAAAATTACATAGAA
7924 ATCATTATTA
Statistics
Matches: 36, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 36 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (22 bp):
GGTTATCAAAATTACATAGAAT
Found at i:7997 original size:22 final size:22
Alignment explanation
Indices: 7972--8284 Score: 168
Period size: 22 Copynumber: 14.6 Consensus size: 22
7962 TTAAGTGTAT
*
7972 TCAAAATTTCATAGGGAAGTTA
1 TCAAAATTTCATAGGGAGGTTA
*
7994 TCAAAATTTCAAAGCGG-GGTTA
1 TCAAAATTTCATAG-GGAGGTTA
* *
8016 TCGAAATTTCATAGTGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
8038 TCGATAA-TTCACA-GTATGGTTA
1 TC-AAAATTTCATAGGGA-GGTTA
*
8060 TCAAAATTTCATATGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* *
8082 T-AAAATTTCATAGTGTGGTTA
1 TCAAAATTTCATAGGGAGGTTA
**
8103 TCAAAATTTCATAAAGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * *
8125 TCGAAATTTAAT-GGTATGGTTA
1 TCAAAATTTCATAGGGA-GGTTA
* * *
8147 TTAACATTT--TA--GA-G-TG
1 TCAAAATTTCATAGGGAGGTTA
** * *
8163 T-AGTATTTTAAAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* ** *
8184 CCAAAATTTCATAGTCTA-ATTA
1 TCAAAATTTCATAG-GGAGGTTA
* *
8206 CCAAAATTTCATAGGAAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
* * * * *
8228 TTAAAATTTTATTGTGGA-ATAA
1 TCAAAATTTCATAG-GGAGGTTA
*
8250 TTAAAATTTCATAGGGAGGTTA
1 TCAAAATTTCATAGGGAGGTTA
8272 TCAAAATTTCATA
1 TCAAAATTTCATA
8285 AGAAAGTTCC
Statistics
Matches: 215, Mismatches: 56, Indels: 40
0.69 0.18 0.13
Matches are distributed among these distances:
15 5 0.02
16 2 0.01
17 2 0.01
19 3 0.01
20 2 0.01
21 29 0.13
22 163 0.76
23 9 0.04
ACGTcount: A:0.37, C:0.09, G:0.18, T:0.36
Consensus pattern (22 bp):
TCAAAATTTCATAGGGAGGTTA
Found at i:8025 original size:44 final size:44
Alignment explanation
Indices: 7858--8133 Score: 194
Period size: 44 Copynumber: 6.3 Consensus size: 44
7848 AACACCTATC
* ** *
7858 AGGTTATCAAAATTAT-ATAGTGTGGTTATCAAAATCCCATA-GA
1 AGGTTATCAAAATT-TCAAAGTGTGGTTATCAAAATTTCATAGGG
* * ** * *
7901 ATGGTTATCAAAATTTCATAGAAATCATTATTATCAAAATTTTATAGGA
1 A-GGTTATCAAAATTTC--A-AAGT-GTGGTTATCAAAATTTCATAGGG
* *
7950 ATGTTATCAAAA-TT--AAGTGT--AT-TCAAAATTTCATAGGG
1 AGGTTATCAAAATTTCAAAGTGTGGTTATCAAAATTTCATAGGG
* * * * *
7988 AAGTTATCAAAATTTCAAAGCGGGGTTATCGAAATTTCATAGTG
1 AGGTTATCAAAATTTCAAAGTGTGGTTATCAAAATTTCATAGGG
* * * *
8032 AGGTTATCGATAA-TTCACAGTATGGTTATCAAAATTTCATATGG
1 AGGTTATC-AAAATTTCAAAGTGTGGTTATCAAAATTTCATAGGG
* **
8076 AGGTTAT-AAAATTTCATAGTGTGGTTATCAAAATTTCATAAAG
1 AGGTTATCAAAATTTCAAAGTGTGGTTATCAAAATTTCATAGGG
*
8119 AGGTTATCGAAATTT
1 AGGTTATCAAAATTT
8134 AATGGTATGG
Statistics
Matches: 182, Mismatches: 35, Indels: 31
0.73 0.14 0.12
Matches are distributed among these distances:
38 25 0.14
39 3 0.02
41 5 0.03
42 6 0.03
43 37 0.20
44 71 0.39
45 3 0.02
46 1 0.01
47 4 0.02
48 24 0.13
49 3 0.02
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.36
Consensus pattern (44 bp):
AGGTTATCAAAATTTCAAAGTGTGGTTATCAAAATTTCATAGGG
Found at i:8147 original size:87 final size:88
Alignment explanation
Indices: 7972--8132 Score: 236
Period size: 87 Copynumber: 1.9 Consensus size: 88
7962 TTAAGTGTAT
* **
7972 TCAAAATTTCATAGGGAAGTTATCAAAATTTCAAAGCGGGGTTATCGAAATTTCATAGTGAGGTT
1 TCAAAATTTCATAGGGAAGTTATCAAAATTTCAAAGCGGGGTTATCAAAATTTCATAAAGAGGTT
8037 ATCGATAATTCACAGTATGGTTA
66 ATCGATAATTCACAGTATGGTTA
* * * * *
8060 TCAAAATTTCATATGGAGGTTAT-AAAATTTCATAGTGTGGTTATCAAAATTTCATAAAGAGGTT
1 TCAAAATTTCATAGGGAAGTTATCAAAATTTCAAAGCGGGGTTATCAAAATTTCATAAAGAGGTT
8124 ATCGA-AATT
66 ATCGATAATT
8133 TAATGGTATG
Statistics
Matches: 65, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
86 4 0.06
87 40 0.62
88 21 0.32
ACGTcount: A:0.37, C:0.10, G:0.19, T:0.35
Consensus pattern (88 bp):
TCAAAATTTCATAGGGAAGTTATCAAAATTTCAAAGCGGGGTTATCAAAATTTCATAAAGAGGTT
ATCGATAATTCACAGTATGGTTA
Found at i:8636 original size:22 final size:23
Alignment explanation
Indices: 8611--8667 Score: 75
Period size: 22 Copynumber: 2.6 Consensus size: 23
8601 TAAGCATATA
8611 AAATTTTGATAACT-ATC-TTATG
1 AAATTTTGATAACTGA-CATTATG
8633 AAATTTTGATAA-TGACATTATG
1 AAATTTTGATAACTGACATTATG
*
8655 TAATTTTGATAAC
1 AAATTTTGATAAC
8668 CTCTAAGTGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
21 2 0.06
22 29 0.94
ACGTcount: A:0.39, C:0.07, G:0.11, T:0.44
Consensus pattern (23 bp):
AAATTTTGATAACTGACATTATG
Found at i:8704 original size:44 final size:43
Alignment explanation
Indices: 8611--8723 Score: 104
Period size: 44 Copynumber: 2.6 Consensus size: 43
8601 TAAGCATATA
* * * **
8611 AAATTTTGATAACTATCTTATGAAATTTTGATAATGACATTATG
1 AAATTTTGATAAC-CTCTAATGAAATATTGATAATGACACAATG
*
8655 TAATTTTGATAACCTCTAAGTGAAATATTGATAA-GCACACAATG
1 AAATTTTGATAACCTCTAA-TGAAATATTGATAATG-ACACAATG
* *
8699 AAATTTT-ACAACCTCCATATGAAAT
1 AAATTTTGATAACCTCTA-ATGAAAT
8724 GTTAGTAATC
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
43 19 0.33
44 38 0.67
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (43 bp):
AAATTTTGATAACCTCTAATGAAATATTGATAATGACACAATG
Found at i:9480 original size:61 final size:61
Alignment explanation
Indices: 9385--9506 Score: 235
Period size: 61 Copynumber: 2.0 Consensus size: 61
9375 TATGATTATG
*
9385 AAAATTACTTACTGATTTCATCTCCTTAAAAAAACGTCGTGTACAATTTTAAGGTATGCTA
1 AAAATTACTTACTGATTTCATCTCCTTAAAAAAACGTCGTGCACAATTTTAAGGTATGCTA
9446 AAAATTACTTACTGATTTCATCTCCTTAAAAAAACGTCGTGCACAATTTTAAGGTATGCTA
1 AAAATTACTTACTGATTTCATCTCCTTAAAAAAACGTCGTGCACAATTTTAAGGTATGCTA
9507 CTCATTCTCA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
61 60 1.00
ACGTcount: A:0.36, C:0.17, G:0.11, T:0.35
Consensus pattern (61 bp):
AAAATTACTTACTGATTTCATCTCCTTAAAAAAACGTCGTGCACAATTTTAAGGTATGCTA
Found at i:9735 original size:22 final size:21
Alignment explanation
Indices: 9710--9767 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 21
9700 AATGACATTG
*
9710 TGAAATATTGATAATCACACTA
1 TGAAAT-TTGATAACCACACTA
*
9732 TGAAATTGTGATAACCTCACTA
1 TGAAATT-TGATAACCACACTA
9754 TGAAATTTTGATAA
1 TGAAA-TTTGATAA
9768 ACCATCTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 1 0.03
22 29 0.91
23 2 0.06
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.34
Consensus pattern (21 bp):
TGAAATTTGATAACCACACTA
Found at i:9802 original size:22 final size:21
Alignment explanation
Indices: 9734--9807 Score: 60
Period size: 22 Copynumber: 3.3 Consensus size: 21
9724 TCACACTATG
* * *
9734 AAATTGTGATAACCTCACTATG
1 AAATTTTGATAACCTC-CTTTA
9756 AAATTTTGATAAACCAT-CTTATA
1 AAATTTTGAT-AACC-TCCTT-TA
9779 AAATTTTGATAACCTCCGTTTA
1 AAATTTTGATAACCTCC-TTTA
*
9801 AATTTTT
1 AAATTTT
9808 ATGACAACAA
Statistics
Matches: 43, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
21 1 0.02
22 24 0.56
23 17 0.40
24 1 0.02
ACGTcount: A:0.36, C:0.15, G:0.08, T:0.41
Consensus pattern (21 bp):
AAATTTTGATAACCTCCTTTA
Found at i:9881 original size:22 final size:21
Alignment explanation
Indices: 9856--9911 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
9846 GTAACCTTAT
*
9856 TATGAAATGTTGTTAACCTCCC
1 TATGAAATGTTGATAACC-CCC
*
9878 TATGAAATTTTGATAACCCCC
1 TATGAAATGTTGATAACCCCC
*
9899 TATGAAATTTTGA
1 TATGAAATGTTGA
9912 AAACTAAACT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
21 16 0.50
22 16 0.50
ACGTcount: A:0.32, C:0.18, G:0.12, T:0.38
Consensus pattern (21 bp):
TATGAAATGTTGATAACCCCC
Found at i:9945 original size:22 final size:22
Alignment explanation
Indices: 9856--9984 Score: 120
Period size: 22 Copynumber: 6.0 Consensus size: 22
9846 GTAACCTTAT
* *
9856 TATGAAATGTTGTTAACCTCCC
1 TATGAAATTTTGATAACCTCCC
9878 TATGAAATTTTGATAACC-CCC
1 TATGAAATTTTGATAACCTCCC
* **
9899 TATGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT-CCC
*
9921 TATGAAATTTCGATAACCTCCC
1 TATGAAATTTTGATAACCTCCC
* * * **
9943 TAT-AAAATTTAATAACATTTC
1 TATGAAATTTTGATAACCTCCC
*
9964 TATGAAATTTTAATAACCTCC
1 TATGAAATTTTGATAACCTCC
9985 ATCTAAAATA
Statistics
Matches: 84, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
20 3 0.04
21 31 0.37
22 46 0.55
23 4 0.05
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.36
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTCCC
Found at i:9967 original size:43 final size:43
Alignment explanation
Indices: 9877--9993 Score: 123
Period size: 43 Copynumber: 2.7 Consensus size: 43
9867 GTTAACCTCC
*
9877 CTATGAAATTTTGATAACC-CCCTATGAAATTTTGAAAACTAAA
1 CTATGAAATTTTGATAACCTCCCTAT-AAAATTTGAAAACTAAA
* **
9920 CTATGAAATTTCGATAACCTCCCTATAAAATTT-AATAAC-ATTT
1 CTATGAAATTTTGATAACCTCCCTATAAAATTTGAA-AACTA-AA
* * *
9963 CTATGAAATTTTAATAACCTCCATCTAAAAT
1 CTATGAAATTTTGATAACCTCCCTATAAAAT
9994 ACCACACATT
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
42 3 0.05
43 54 0.86
44 6 0.10
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (43 bp):
CTATGAAATTTTGATAACCTCCCTATAAAATTTGAAAACTAAA
Found at i:12285 original size:22 final size:22
Alignment explanation
Indices: 12252--12319 Score: 70
Period size: 22 Copynumber: 3.0 Consensus size: 22
12242 ATATACTATT
12252 AAATAA-ATAATAAATATATTTA
1 AAATAATA-AATAAATATATTTA
*
12274 AAATAATAAAT-AAT-TAGTTCA
1 AAATAATAAATAAATATA-TTTA
12295 AAATAAATAAATAATATATATTTA
1 AAAT-AATAAATAA-ATATATTTA
12319 A
1 A
12320 TTACTAAACG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
20 2 0.05
21 10 0.26
22 16 0.42
23 2 0.05
24 6 0.16
25 2 0.05
ACGTcount: A:0.62, C:0.01, G:0.01, T:0.35
Consensus pattern (22 bp):
AAATAATAAATAAATATATTTA
Found at i:16574 original size:16 final size:15
Alignment explanation
Indices: 16553--16588 Score: 63
Period size: 16 Copynumber: 2.3 Consensus size: 15
16543 AGAAATAAAC
16553 ATATATATATACTAA
1 ATATATATATACTAA
16568 TATATATATATACTAA
1 -ATATATATATACTAA
16584 ATATA
1 ATATA
16589 CTAAATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 5 0.25
16 15 0.75
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.42
Consensus pattern (15 bp):
ATATATATATACTAA
Found at i:16589 original size:9 final size:9
Alignment explanation
Indices: 16559--16596 Score: 53
Period size: 9 Copynumber: 4.4 Consensus size: 9
16549 AAACATATAT
16559 ATATACT-A
1 ATATACTAA
*
16567 ATATA-TAT
1 ATATACTAA
16575 ATATACTAA
1 ATATACTAA
16584 ATATACTAA
1 ATATACTAA
16593 ATAT
1 ATAT
16597 TATTTGAAAC
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
7 1 0.04
8 10 0.38
9 15 0.58
ACGTcount: A:0.53, C:0.08, G:0.00, T:0.39
Consensus pattern (9 bp):
ATATACTAA
Found at i:17016 original size:379 final size:380
Alignment explanation
Indices: 16570--17331 Score: 1445
Period size: 379 Copynumber: 2.0 Consensus size: 380
16560 TATACTAATA
*
16570 TATATATATACTAAATATACTAAATATTATTTGAAACATCCAATGAAATTACTAAAGGCTCCAAA
1 TATATATATACT-AATATACTAAATATTATTTGAAACACCCAATGAAATTACTAAAGGCTCCAAA
16635 TCAAGATTGATGAGGAGCCAGCATTTTGTCCTTTTTTGCCTTTTCTTACTTGGTAAATTATAGAA
65 TCAAGATTGATGAGGAGCCAGCATTTTGTCCTTTTTTGCCTTTTCTTACTTGGTAAATTATAGAA
*
16700 AAGTCCATACTAGATTTTTATCTTTCCTTTACCTATTTGGTCATTTTGGTAATTGCATGTCCTTT
130 AAGTCCAAACTAGATTTTTATCTTTCCTTTACCTATTTGGTCATTTTGGTAATTGCATGTCCTTT
* *
16765 GAAACTGTTTTGGGAAGTCATTAGTGTAGATATATTTATTGTTGGGAGAATTCCTCCTTAGTGTA
195 GAAACCGTTTTGGGAAGTCATTAGTGTAGACATATTTATTGTTGGGAGAATTCCTCCTTAGTGTA
16830 TTGAAAAGCTAAATAATCCATGATTGGTGATATAGAGAAAATTAATCCTTCATCTATACTAACTA
260 TTGAAAAGCTAAATAATCCATGATTGGTGATATAGAGAAAATTAATCCTTCATCTATACTAACTA
*
16895 TTTTTTTAATTAAATAGAACTTTGCATTAACTATATAAAGAAGTGGAATTAATAGT
325 TTTTTTTAATTAAATAGAACTTTACATTAACTATATAAAGAAGTGGAATTAATAGT
16951 TATATATATACT-ATATACTAAATATTATTTGAAACACCCAATGAAATTACTAAAGGCTCCAAAT
1 TATATATATACTAATATACTAAATATTATTTGAAACACCCAATGAAATTACTAAAGGCTCCAAAT
* *
17015 CAGGATTGATGAGGAGCCAGCATTTTGTCCTTTTTTGTCTTTTCTTACTTGGTAAATTATAGAAA
66 CAAGATTGATGAGGAGCCAGCATTTTGTCCTTTTTTGCCTTTTCTTACTTGGTAAATTATAGAAA
17080 AGTCCAAACTAGATTTTTATCTTTCCTTTACCTATTTGGTCATTTTGGTAATTGCATGTCCTTTG
131 AGTCCAAACTAGATTTTTATCTTTCCTTTACCTATTTGGTCATTTTGGTAATTGCATGTCCTTTG
17145 AAACCGTTTTGGGAAGTCATTAGTGTAGACATATTTATTGTTGGGAGAATTCCTCCTTAGTGTAT
196 AAACCGTTTTGGGAAGTCATTAGTGTAGACATATTTATTGTTGGGAGAATTCCTCCTTAGTGTAT
17210 TGAAAAGCTAAATAATCCATGATTGGTGATATAGAGAAAATTAATCCTTCATCTATACTAACTAT
261 TGAAAAGCTAAATAATCCATGATTGGTGATATAGAGAAAATTAATCCTTCATCTATACTAACTAT
17275 TTTTTTAATTAAATAGAACTTTACATTAACTATATAAAGAAGTGGAATTAATAGT
326 TTTTTTAATTAAATAGAACTTTACATTAACTATATAAAGAAGTGGAATTAATAGT
17330 TA
1 TA
17332 CTTAGTTCAA
Statistics
Matches: 374, Mismatches: 7, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
379 362 0.97
381 12 0.03
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.39
Consensus pattern (380 bp):
TATATATATACTAATATACTAAATATTATTTGAAACACCCAATGAAATTACTAAAGGCTCCAAAT
CAAGATTGATGAGGAGCCAGCATTTTGTCCTTTTTTGCCTTTTCTTACTTGGTAAATTATAGAAA
AGTCCAAACTAGATTTTTATCTTTCCTTTACCTATTTGGTCATTTTGGTAATTGCATGTCCTTTG
AAACCGTTTTGGGAAGTCATTAGTGTAGACATATTTATTGTTGGGAGAATTCCTCCTTAGTGTAT
TGAAAAGCTAAATAATCCATGATTGGTGATATAGAGAAAATTAATCCTTCATCTATACTAACTAT
TTTTTTAATTAAATAGAACTTTACATTAACTATATAAAGAAGTGGAATTAATAGT
Found at i:18173 original size:29 final size:29
Alignment explanation
Indices: 18129--18213 Score: 143
Period size: 29 Copynumber: 2.9 Consensus size: 29
18119 TAGTTGATCA
* *
18129 AAGTGATTCGGTATTCATTTTTCTTAATC
1 AAGTGATTTGCTATTCATTTTTCTTAATC
*
18158 AAGTTATTTGCTATTCATTTTTCTTAATC
1 AAGTGATTTGCTATTCATTTTTCTTAATC
18187 AAGTGATTTGCTATTCATTTTTCTTAA
1 AAGTGATTTGCTATTCATTTTTCTTAA
18214 ATAAGGTTAA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.25, C:0.13, G:0.11, T:0.52
Consensus pattern (29 bp):
AAGTGATTTGCTATTCATTTTTCTTAATC
Found at i:20305 original size:29 final size:30
Alignment explanation
Indices: 20272--20345 Score: 105
Period size: 30 Copynumber: 2.5 Consensus size: 30
20262 TTGTAGCGTA
* * *
20272 TGGACGTTTTGGCCGCTAAACT-TCAATTT
1 TGGACGTTTTGCCCCCTAAACTCTCAATCT
*
20301 TGGACATTTTGCCCCCTAAACTCTCAATCT
1 TGGACGTTTTGCCCCCTAAACTCTCAATCT
20331 TGGACGTTTTGCCCC
1 TGGACGTTTTGCCCC
20346 TCTCAACCGA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 19 0.49
30 20 0.51
ACGTcount: A:0.19, C:0.28, G:0.18, T:0.35
Consensus pattern (30 bp):
TGGACGTTTTGCCCCCTAAACTCTCAATCT
Found at i:20346 original size:29 final size:28
Alignment explanation
Indices: 20272--20346 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 28
20262 TTGTAGCGTA
* *
20272 TGGACGTTTTGGCCGCTAAACTTCAATTT
1 TGGACGTTTT-GCCCCTAAACTTCAATCT
*
20301 TGGACATTTTGCCCCCTAAACTCTCAATCT
1 TGGACGTTTTG-CCCCTAAACT-TCAATCT
20331 TGGACGTTTTGCCCCT
1 TGGACGTTTTGCCCCT
20347 CTCAACCGAT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
28 1 0.03
29 23 0.57
30 16 0.40
ACGTcount: A:0.19, C:0.28, G:0.17, T:0.36
Consensus pattern (28 bp):
TGGACGTTTTGCCCCTAAACTTCAATCT
Found at i:20568 original size:17 final size:17
Alignment explanation
Indices: 20543--20575 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20533 TTGAGAGTTC
20543 AGGGGGCAAAATGTCCT
1 AGGGGGCAAAATGTCCT
*
20560 AGGGTGCAAAATGTCC
1 AGGGGGCAAAATGTCC
20576 AAACGCTACA
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:0.30, C:0.18, G:0.33, T:0.18
Consensus pattern (17 bp):
AGGGGGCAAAATGTCCT
Found at i:25870 original size:23 final size:23
Alignment explanation
Indices: 25843--25898 Score: 103
Period size: 23 Copynumber: 2.4 Consensus size: 23
25833 CAAAAAACTA
25843 AACAGAAACTGCTTATTTATACT
1 AACAGAAACTGCTTATTTATACT
25866 AACAGAAACTGCTTATTTATACT
1 AACAGAAACTGCTTATTTATACT
*
25889 AACACAAACT
1 AACAGAAACT
25899 TGGCCTCCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.07, T:0.30
Consensus pattern (23 bp):
AACAGAAACTGCTTATTTATACT
Found at i:26643 original size:84 final size:82
Alignment explanation
Indices: 26549--26703 Score: 238
Period size: 84 Copynumber: 1.9 Consensus size: 82
26539 TATGGCGGCT
* * *
26549 AAGCTAGTATATTATGACGGCTTATTGGGTGCCCCAACCCTTTATTGTCAGAATAAAAATAATGC
1 AAGCTAGTATAATATGACGGCTTATTGGGTGCCCCAACACTTCATTGTCAGAAT--AAATAATGC
*
26614 TAGTAGTAAATAATACTAC
64 TACTAGTAAATAATACTAC
**
26633 AAGCTAGTATAATATGACGGCTTATTGGGTGCCCCAACACTTCATTGTCATCATAAATAATGCTA
1 AAGCTAGTATAATATGACGGCTTATTGGGTGCCCCAACACTTCATTGTCAGAATAAATAATGCTA
26698 CTAGTA
66 CTAGTA
26704 GTACTTTCAT
Statistics
Matches: 65, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
82 16 0.25
84 49 0.75
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Consensus pattern (82 bp):
AAGCTAGTATAATATGACGGCTTATTGGGTGCCCCAACACTTCATTGTCAGAATAAATAATGCTA
CTAGTAAATAATACTAC
Found at i:38087 original size:19 final size:19
Alignment explanation
Indices: 38063--38099 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
38053 GTACAATATC
*
38063 TAATTTGATATGTACAGTG
1 TAATTTCATATGTACAGTG
*
38082 TAATTTCATCTGTACAGT
1 TAATTTCATATGTACAGT
38100 ACCTAAACGG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.16, T:0.43
Consensus pattern (19 bp):
TAATTTCATATGTACAGTG
Found at i:47508 original size:5 final size:5
Alignment explanation
Indices: 47498--47522 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
47488 TGTATACGAC
47498 CTTTT CTTTT CTTTT CTTTT CTTTT
1 CTTTT CTTTT CTTTT CTTTT CTTTT
47523 TCTAATGCGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
CTTTT
Found at i:61911 original size:49 final size:49
Alignment explanation
Indices: 61839--61968 Score: 195
Period size: 41 Copynumber: 2.8 Consensus size: 49
61829 GCAATGTATA
*
61839 CACTGTCAGTGCATCTAATATAAATCCATACTATATTACTATATTACTC
1 CACTGTTAGTGCATCTAATATAAATCCATACTATATTACTATATTACTC
61888 CACTGTTAGTGCATCTAATATAAAT-C---C---A-TACTATATTACTC
1 CACTGTTAGTGCATCTAATATAAATCCATACTATATTACTATATTACTC
61929 CACTGTTAGTGCATCTAATATAAATCCATACTATATTACT
1 CACTGTTAGTGCATCTAATATAAATCCATACTATATTACT
61969 CCATATATTT
Statistics
Matches: 72, Mismatches: 1, Indels: 16
0.81 0.01 0.18
Matches are distributed among these distances:
41 38 0.53
42 2 0.03
45 2 0.03
48 2 0.03
49 28 0.39
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.37
Consensus pattern (49 bp):
CACTGTTAGTGCATCTAATATAAATCCATACTATATTACTATATTACTC
Found at i:62050 original size:18 final size:18
Alignment explanation
Indices: 62027--62062 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
62017 TTTTAGGCTG
62027 AGAGCCTGAGACTAACCC
1 AGAGCCTGAGACTAACCC
62045 AGAGCCTGAGACTAACCC
1 AGAGCCTGAGACTAACCC
62063 CTTTCGAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.33, G:0.22, T:0.11
Consensus pattern (18 bp):
AGAGCCTGAGACTAACCC
Found at i:65486 original size:18 final size:17
Alignment explanation
Indices: 65455--65488 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
65445 CCAAGCATGA
65455 ATTTTTGTTTTTTTAAC
1 ATTTTTGTTTTTTTAAC
*
65472 ATTTTTTTTTGTTTTAA
1 ATTTTTGTTT-TTTTAA
65489 TTAGTGGTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 9 0.60
18 6 0.40
ACGTcount: A:0.18, C:0.03, G:0.06, T:0.74
Consensus pattern (17 bp):
ATTTTTGTTTTTTTAAC
Found at i:78478 original size:1 final size:1
Alignment explanation
Indices: 78472--78496 Score: 50
Period size: 1 Copynumber: 25.0 Consensus size: 1
78462 TAGCATAGAG
78472 TTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTT
78497 AAATAAGTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 24 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:78767 original size:19 final size:19
Alignment explanation
Indices: 78743--78779 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
78733 ATACAGTACT
*
78743 TAATCTAATTTGTACAGTG
1 TAATCTAATCTGTACAGTG
*
78762 TAATCTCATCTGTACAGT
1 TAATCTAATCTGTACAGT
78780 TGCTACAGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:78795 original size:28 final size:28
Alignment explanation
Indices: 78755--78812 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
78745 ATCTAATTTG
*
78755 TACAGTGTAATCTCATCTGTACAGTTGC
1 TACAGTGTAATCTCATCTATACAGTTGC
78783 TACAGTGTAATCTCATCTATACAGTTGC
1 TACAGTGTAATCTCATCTATACAGTTGC
78811 TA
1 TA
78813 AATAGTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.36
Consensus pattern (28 bp):
TACAGTGTAATCTCATCTATACAGTTGC
Found at i:81193 original size:2 final size:2
Alignment explanation
Indices: 81186--81211 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
81176 TTAATACATA
81186 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
81212 TACGATTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:82648 original size:16 final size:16
Alignment explanation
Indices: 82629--82663 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
82619 GATCCGAAAA
82629 ACCCAAAACCCGAATG
1 ACCCAAAACCCGAATG
* *
82645 ACCCAGAACCCGAGTG
1 ACCCAAAACCCGAATG
82661 ACC
1 ACC
82664 TAGGGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.37, C:0.40, G:0.17, T:0.06
Consensus pattern (16 bp):
ACCCAAAACCCGAATG
Found at i:83572 original size:62 final size:60
Alignment explanation
Indices: 83478--83608 Score: 192
Period size: 62 Copynumber: 2.1 Consensus size: 60
83468 AATTAGTAAA
*
83478 ATGGT-AAAAAAAAAGGTATAAGGATATTAGATTTAATTAAATGAAAATAGAGGTTTTAG
1 ATGGTAAAAAAAAAAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAG
* *
83537 ATGGTAAAAATAAAATAGGTATAAGGATATTAGATTTGATTAAATAAAAATAGAGTTTTTAG
1 ATGGTAAAAA-AAAA-AGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAG
*
83599 TTGAGTAAAA
1 ATG-GTAAAA
83609 CTATAAAAGA
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
59 5 0.08
60 4 0.06
61 4 0.06
62 45 0.70
63 6 0.09
ACGTcount: A:0.49, C:0.00, G:0.19, T:0.32
Consensus pattern (60 bp):
ATGGTAAAAAAAAAAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGGTTTTAG
Found at i:84922 original size:123 final size:120
Alignment explanation
Indices: 84631--84929 Score: 275
Period size: 123 Copynumber: 2.4 Consensus size: 120
84621 AATAATTATA
* * * * *
84631 AAATTATTGAATTTGATTAAATGAAAATAGAGTTTTTTTGTAAAATAAAACTGTATATTAAAAAA
1 AAATTATTAAATTTAATTAAATAAAAATAGAG-TTTTTAGTAGAATAAAACTGTATATTAAAAAA
* *
84696 TTTTAATATATCCAAGTTTTTAATGAACAATAGTAAAATGGTAGAAATAAACTTTT
65 TTTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGAAGAAATAAACTTTT
* * ** * * ** *
84752 AAATTA--AAATGGTAAAAATAAAATAATTATAAAATATTGAATTTAGAATAAAACTGTATATT-
1 AAATTATTAAAT--T--TAATTAAATAAAAATAGAGT-TTTTA-GTAGAATAAAACTGTATATTA
* * *
84814 AAAAATTTTTATATATCCTAGTTTTTAATGAAAAATATTAAAATAGTGAAAAGAAAGT-AA-TTT
60 AAAAATTTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAAT-G-G--AAGAAA-TAAACTTT
84877 T
120 T
84878 AAATATATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACT
1 AAAT-TATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACT
84930 ATAATAGTTT
Statistics
Matches: 136, Mismatches: 28, Indels: 26
0.72 0.15 0.14
Matches are distributed among these distances:
119 3 0.02
121 7 0.05
122 1 0.01
123 65 0.48
124 22 0.16
125 15 0.11
126 8 0.06
127 10 0.07
128 1 0.01
129 4 0.03
ACGTcount: A:0.50, C:0.03, G:0.09, T:0.37
Consensus pattern (120 bp):
AAATTATTAAATTTAATTAAATAAAAATAGAGTTTTTAGTAGAATAAAACTGTATATTAAAAAAT
TTTAATATATCCAAGTTTTTAATGAAAAATAGTAAAATGGAAGAAATAAACTTTT
Found at i:86083 original size:21 final size:23
Alignment explanation
Indices: 86039--86099 Score: 90
Period size: 21 Copynumber: 2.7 Consensus size: 23
86029 GGACCAAATT
86039 TGGTTGGATCCTTTCATGAAAAAAA
1 TGGTTGGATCC-TT-ATGAAAAAAA
86064 TGGTTGGATCCTT-T-AAAAAAA
1 TGGTTGGATCCTTATGAAAAAAA
86085 TGGTTGGATCCTTAT
1 TGGTTGGATCCTTAT
86100 TTAAATCCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
21 20 0.57
22 2 0.06
24 2 0.06
25 11 0.31
ACGTcount: A:0.31, C:0.11, G:0.21, T:0.36
Consensus pattern (23 bp):
TGGTTGGATCCTTATGAAAAAAA
Found at i:87419 original size:16 final size:16
Alignment explanation
Indices: 87398--87441 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
87388 TACAAAGGAC
87398 AATTATTTAGAAATTA
1 AATTATTTAGAAATTA
**
87414 AATTATTTCAAGATCTTA
1 AATTATTT--AGAAATTA
87432 AATTATTTAG
1 AATTATTTAG
87442 GAGATTGTTG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 10 0.42
18 14 0.58
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (16 bp):
AATTATTTAGAAATTA
Found at i:87641 original size:24 final size:25
Alignment explanation
Indices: 87594--87642 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
87584 AGATTGTTAT
87594 AACTTTCTAAAAACTCAGACTCAAA
1 AACTTTCTAAAAACTCAGACTCAAA
**
87619 AACTTTCTAATCAC-CAGACTCAAA
1 AACTTTCTAAAAACTCAGACTCAAA
87643 CAGAGTAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.45
25 12 0.55
ACGTcount: A:0.45, C:0.27, G:0.04, T:0.24
Consensus pattern (25 bp):
AACTTTCTAAAAACTCAGACTCAAA
Found at i:99293 original size:16 final size:15
Alignment explanation
Indices: 99274--99307 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
99264 AACACCGTAT
*
99274 ATATATATGACA-TG
1 ATATATATGATACTG
99288 ATATATATGATACTG
1 ATATATATGATACTG
99303 ATATA
1 ATATA
99308 GTTGGATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (15 bp):
ATATATATGATACTG
Found at i:116315 original size:66 final size:65
Alignment explanation
Indices: 116231--116371 Score: 196
Period size: 66 Copynumber: 2.1 Consensus size: 65
116221 ATAAAGTTAT
* *
116231 GCATGTTTCATAGGAATATTGCTCTTCAATTGGTTTATATT-TGGAAAGTGTGTATATTGGTCAA
1 GCATGTTTTATAGGAATATTGCTCTTCAA-TCGTTTAT-TTCTGGAAAGTGTGTATATTGGTCAA
116295 AA
64 AA
* *
116297 GCATGTTTTATTGGAATATTGCTCTTTAATCGTTTATTTCGTGGAAAGTGTGTATATTGGTCAAA
1 GCATGTTTTATAGGAATATTGCTCTTCAATCGTTTATTTC-TGGAAAGTGTGTATATTGGTCAAA
116362 A
65 A
116363 G-ACTGTTTT
1 GCA-TGTTTT
116372 TGGTTTACTT
Statistics
Matches: 68, Mismatches: 4, Indels: 6
0.87 0.05 0.08
Matches are distributed among these distances:
64 2 0.03
65 8 0.12
66 58 0.85
ACGTcount: A:0.26, C:0.09, G:0.21, T:0.43
Consensus pattern (65 bp):
GCATGTTTTATAGGAATATTGCTCTTCAATCGTTTATTTCTGGAAAGTGTGTATATTGGTCAAAA
Found at i:117501 original size:2 final size:2
Alignment explanation
Indices: 117494--117535 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
117484 CCAAGTATGC
117494 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
117536 AGGTACCTGT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:122228 original size:54 final size:46
Alignment explanation
Indices: 122122--122240 Score: 139
Period size: 54 Copynumber: 2.4 Consensus size: 46
122112 ATGGAGCCTC
* * *
122122 TTATTTTGTATAGGTCCTTTAATTTGTAATTATCTAGAGGAGGCAT
1 TTATTTTGTATAGGTCCTTTAATTTGCAATGATCTAGAGGAGGCAG
122168 TTATTTTGTATAGGTCACTAATTAATTTGCAATGATCTAAGGAAGAAGAGGCAG
1 TTATTTTGTATAGGTC-CT--TTAATTTGCAATGATCT-A-G-AG--GAGGCAG
122222 TTATTTTGTATAGGTCCTT
1 TTATTTTGTATAGGTCCTT
122241 GATTTTTAGG
Statistics
Matches: 62, Mismatches: 3, Indels: 11
0.82 0.04 0.14
Matches are distributed among these distances:
46 16 0.26
47 2 0.03
49 15 0.24
50 1 0.02
51 2 0.03
52 2 0.03
53 2 0.03
54 22 0.35
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (46 bp):
TTATTTTGTATAGGTCCTTTAATTTGCAATGATCTAGAGGAGGCAG
Found at i:122535 original size:19 final size:18
Alignment explanation
Indices: 122497--122536 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
122487 TTTAAACTTT
*
122497 AAAAGGAAAAAGAAAACG
1 AAAACGAAAAAGAAAACG
*
122515 AAAACGAAAACAGAGAACG
1 AAAACGAAAA-AGAAAACG
122534 AAA
1 AAA
122537 GAAAGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.47
19 10 0.53
ACGTcount: A:0.70, C:0.10, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAACGAAAAAGAAAACG
Found at i:128537 original size:30 final size:30
Alignment explanation
Indices: 128489--128566 Score: 111
Period size: 30 Copynumber: 2.6 Consensus size: 30
128479 TGGTTTTTAT
* *
128489 TCTTCTTTGTTAAAATTTTTTTTTGGCGATA
1 TCTTCTTTGTT-AAATTTTTTTTTGGCCACA
*
128520 TCTTCTTTGTTAAATTTTTTTTTTGCCACA
1 TCTTCTTTGTTAAATTTTTTTTTGGCCACA
*
128550 ACTTCTTTGTTAAATTT
1 TCTTCTTTGTTAAATTT
128567 AGATAGCTTG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
30 32 0.74
31 11 0.26
ACGTcount: A:0.19, C:0.13, G:0.09, T:0.59
Consensus pattern (30 bp):
TCTTCTTTGTTAAATTTTTTTTTGGCCACA
Found at i:129285 original size:44 final size:44
Alignment explanation
Indices: 129235--129367 Score: 248
Period size: 44 Copynumber: 3.0 Consensus size: 44
129225 GAATAATTAT
* *
129235 TTGATACGCTGACGGTGTAAATTTTGAACTCCACAAACGGGTTG
1 TTGATACGCTGACGGTGTAAATTTTGAACTCCATAAGCGGGTTG
129279 TTGATACGCTGACGGTGTAAATTTTGAACTCCATAAGCGGGTTG
1 TTGATACGCTGACGGTGTAAATTTTGAACTCCATAAGCGGGTTG
129323 TTGATACGCTGACGGTGTAAATTTTGAACTCCATAAGCGGGTTG
1 TTGATACGCTGACGGTGTAAATTTTGAACTCCATAAGCGGGTTG
129367 T
1 T
129368 AGAGTTGACA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 87 1.00
ACGTcount: A:0.26, C:0.17, G:0.26, T:0.32
Consensus pattern (44 bp):
TTGATACGCTGACGGTGTAAATTTTGAACTCCATAAGCGGGTTG
Found at i:132233 original size:90 final size:90
Alignment explanation
Indices: 132080--132244 Score: 330
Period size: 90 Copynumber: 1.8 Consensus size: 90
132070 GCATATATGC
132080 CTTGATAGATATCCTTGGAAATAAGTAACTTTTTGAAGTTTGAATTCCAAGAAGATAATGCTTGT
1 CTTGATAGATATCCTTGGAAATAAGTAACTTTTTGAAGTTTGAATTCCAAGAAGATAATGCTTGT
132145 TGCATGTCTTTTCCTATTGAGTTGT
66 TGCATGTCTTTTCCTATTGAGTTGT
132170 CTTGATAGATATCCTTGGAAATAAGTAACTTTTTGAAGTTTGAATTCCAAGAAGATAATGCTTGT
1 CTTGATAGATATCCTTGGAAATAAGTAACTTTTTGAAGTTTGAATTCCAAGAAGATAATGCTTGT
132235 TGCATGTCTT
66 TGCATGTCTT
132245 GTAGTCTTGT
Statistics
Matches: 75, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 75 1.00
ACGTcount: A:0.29, C:0.12, G:0.19, T:0.40
Consensus pattern (90 bp):
CTTGATAGATATCCTTGGAAATAAGTAACTTTTTGAAGTTTGAATTCCAAGAAGATAATGCTTGT
TGCATGTCTTTTCCTATTGAGTTGT
Found at i:134970 original size:39 final size:39
Alignment explanation
Indices: 134927--135005 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
134917 AGTTTCCCAC
134927 TATTTTGTATCCTTTGTTGAGTTTGATGAATTGTGCAGA
1 TATTTTGTATCCTTTGTTGAGTTTGATGAATTGTGCAGA
134966 TATTTTGTATCCTTTGTTGAGTTTGATGAATTGTGCAGA
1 TATTTTGTATCCTTTGTTGAGTTTGATGAATTGTGCAGA
135005 T
1 T
135006 CTTGTTGCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.08, G:0.23, T:0.49
Consensus pattern (39 bp):
TATTTTGTATCCTTTGTTGAGTTTGATGAATTGTGCAGA
Found at i:137268 original size:38 final size:38
Alignment explanation
Indices: 137198--137274 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 38
137188 AAATTTTCCA
*
137198 TACTCATGGTTAGGTTCTGTTGTTTACATGAGCTGATTG
1 TACTCATGGTTAGGCTCTGTTGTTTACATGAGCTG-TTG
137237 TACTCATGGTTA-GCTCATG-TGTTTACATGAGCTGTTG
1 TACTCATGGTTAGGCTC-TGTTGTTTACATGAGCTGTTG
137274 T
1 T
137275 TTACAAATTT
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
37 4 0.11
38 18 0.50
39 14 0.39
ACGTcount: A:0.18, C:0.14, G:0.25, T:0.43
Consensus pattern (38 bp):
TACTCATGGTTAGGCTCTGTTGTTTACATGAGCTGTTG
Found at i:139343 original size:64 final size:64
Alignment explanation
Indices: 139234--139363 Score: 206
Period size: 64 Copynumber: 2.0 Consensus size: 64
139224 CGTCACGTAC
* * ** *
139234 CTAGTTATGGTGGTTGAGTCACTCAAAGGGCAGCTACGTTTTCAAGCGTATGTAAGATCTTGAA
1 CTAGTTATGGTGGCTGAGTCACTCAAAGGGCAGCTACGTTCTCAAGCGTACATAAGATCTCGAA
*
139298 CTAGTTATGGTGGCTGAGTCACTCAAAGGGCAGCTATGTTCTCAAGCGTACATAAGATCTCGAA
1 CTAGTTATGGTGGCTGAGTCACTCAAAGGGCAGCTACGTTCTCAAGCGTACATAAGATCTCGAA
139362 CT
1 CT
139364 TGAGACTTAC
Statistics
Matches: 60, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
64 60 1.00
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.29
Consensus pattern (64 bp):
CTAGTTATGGTGGCTGAGTCACTCAAAGGGCAGCTACGTTCTCAAGCGTACATAAGATCTCGAA
Found at i:147775 original size:748 final size:752
Alignment explanation
Indices: 146696--148165 Score: 2761
Period size: 748 Copynumber: 2.0 Consensus size: 752
146686 AAAGAGTTCT
*
146696 TTTATCGGCAACACAAGTGTCAGAGTACCATTCCAAAGACTTGAAGATGAAACGATTCAGAGGAC
1 TTTATCGGCAACACAAGTGTCAGAGTACCATTCCAAAGACTTGAAGATGAAACAATTCAGAGGAC
146761 AAGAACAACCTATAAAAGGTTCTATATTAGCAGGGAAAAACCTTGGCATCCAACACTCTTCTGGC
66 AAGAACAACCTATAAAAGGTTCTATATTAGCAGGGAAAAACCTTGGCATCCAACACTCTTCTGGC
*
146826 AAGTTCCTCCACCTCAAGGTATGGCCAAATAGAAGAAAAATTCTCTATCTTTTCTGTCTTCCATT
131 AAGTTCCTCAACCTCAAGGTATGGCCAAATAGAAGAAAAATTCTCTATCTTTTCTGTCTTCCATT
146891 TTCTGGGTTTTAGGGTATTTTGATGTTATGGTTTCTAAGAATAAATGGGTTTTCTTTTGATTCAG
196 TTCTGGGTTTTAGGGTATTTTGATGTTATGGTTTCTAAGAATAAATGGGTTTTCTTTTGATTCAG
*
146956 GAGAGGGATGACTTCTTTGAAGTTGGGAATGGGAGCCGGGATGACAGATATGGGTAGGGTAACCT
261 GAGAGGGATGACTTCTTTGAAGTTGGGAATGGGAGCCGAGATGACAGATATGGGTAGGGTAACCT
*
147021 CAGATTA-CTCTTTTTTT-TTC-CTCTCTCTCTTTGAATTAATGCTTTTGTTGTCGGGTTTTGTA
326 CAGATTACCTCTTTTTTTCTTCTCTCTCTCTCTTTGAATTAATGCTTTTGTTGTCGGGTTTTATA
147083 GGAGTATGTTCTTGAAGTCAACTTTGGTCGGTTGCATTCTTTTATATTTAGGCTCAATGCTAGTT
391 GGAGTATGTTCTTGAAGTCAACTTTGGTCGGTTGCATTCTTTTATATTTAGGCTCAATGCTAGTT
147148 TTACAGATTTTTTTTGGGGGATTTTGATTCTCATCAAGAAAGTAAAGTGCATAGAAATCTTGAGT
456 TTACAGATTTTTTTTGGGGGATTTTGATTCTCATCAAGAAAGTAAAGTGCATAGAAATCTTGAGT
147213 T-AGACAAGGGTTAGTAAAAGATGGGCTTCTAATTAGGTTTTGGGATATGTTTACCATTGTAATT
521 TAAGACAAGGGTTAGTAAAAGATGGGCTTCTAATTAGGTTTTGGGATATGTTTACCATTGTAATT
147277 TCTGATTTTTTTGTGTTGAAGTTTTTCTTTAGTGCTTGTGGATGTAAGGGAATAGGTTCACCTTT
586 TCTGATTTTTTTGTGTTGAAGTTTTTCTTTAGTGCTTGTGGATGTAAGGGAATAGGTTCACCTTT
147342 CACAAACTACACATATATTAGGCTGCACTCTATTTATCACTTCTTTTCTTCTTTTGAGTTTCTTG
651 CACAAACTACACATATATTAGGCTGCACTCTATTTATCACTTCTTTTCTTCTTTTGAGTTTCTTG
147407 ACTGCACTCTATTAATCACTTCTTTTCTTCTTTTGAG
716 ACTGCACTCTATTAATCACTTCTTTTCTTCTTTTGAG
*
147444 TTTATCGGCAACACAAGTGTCAGAGTACCATTGCAAAGACTTGAAGATGAAACAATTCAGAGGAC
1 TTTATCGGCAACACAAGTGTCAGAGTACCATTCCAAAGACTTGAAGATGAAACAATTCAGAGGAC
147509 AAGAACAACCT-TCAAAAGGTTCTATATTAGCAGGGAAAAACCTTGGCATCCAACACTCTTCTGG
66 AAGAACAACCTAT-AAAAGGTTCTATATTAGCAGGGAAAAACCTTGGCATCCAACACTCTTCTGG
*
147573 CAAGTTCCTCAACCTCAAGGTATGGCCAAATAGAAGAAAAATTCTTTATCTTTTCTGTCTTCCAT
130 CAAGTTCCTCAACCTCAAGGTATGGCCAAATAGAAGAAAAATTCTCTATCTTTTCTGTCTTCCAT
*
147638 TTTCTGGGTTTTAGGGTATTTTGATGTTATGGTTTCTAAGGATAAATGGGTTTTCTTTTGATTCA
195 TTTCTGGGTTTTAGGGTATTTTGATGTTATGGTTTCTAAGAATAAATGGGTTTTCTTTTGATTCA
* *
147703 GGAGAGGGATGACTTTTTTGAAGTTGGGAATGGGAGCCGAGATGACAGGTATGGGTAGGGTAACC
260 GGAGAGGGATGACTTCTTTGAAGTTGGGAATGGGAGCCGAGATGACAGATATGGGTAGGGTAACC
147768 TCAGATTACTCTCTTTTTTTCCTTCTCTCTCTCTCTTTGAATTAATGCTTTTGTTGTCGGGTTTT
325 TCAGATTAC-CTCTTTTTTT-CTTCTCTCTCTCTCTTTGAATTAATGCTTTTGTTGTCGGGTTTT
*
147833 ATAGGAGTATGTTCTTGAAGTCAATTTTGGTCGGTTGCATTCTTTTATATTTAGGCTCAATGCTA
388 ATAGGAGTATGTTCTTGAAGTCAACTTTGGTCGGTTGCATTCTTTTATATTTAGGCTCAATGCTA
*
147898 GTTTTACAGATTTTTTTTTGGGGATTTTGATTCTCATCAAGAAAGTAAAGTGCATAGAAATCTTG
453 GTTTTACAGATTTTTTTTGGGGGATTTTGATTCTCATCAAGAAAGTAAAGTGCATAGAAATCTTG
147963 AGTTAGAGACAAGGGTTAGTAAAAGATGGGCTTCTAATTAGGTTTTGGGATATGTTTACCATTGT
518 AGTTA-AGACAAGGGTTAGTAAAAGATGGGCTTCTAATTAGGTTTTGGGATATGTTTACCATTGT
148028 AATTTCTGATTTTTTTGTGTTGAAGTTTTTCTTTAGTGCTTGTGGATGTAAGGGAATAGGTTCAC
582 AATTTCTGATTTTTTTGTGTTGAAGTTTTTCTTTAGTGCTTGTGGATGTAAGGGAATAGGTTCAC
*
148093 CTTTCACGAACTACACATATATTAGGCTGCACTCTATTTATCACTTCTTTTCTTCTTTTGAGTTT
647 CTTTCACAAACTACACATATATTAGGCTGCACTCTATTTATCACTTCTTTTCTTCTTTTGAGTTT
148158 CTTGACTG
712 CTTGACTG
148166 GTTGTTTTCT
Statistics
Matches: 702, Mismatches: 12, Indels: 9
0.97 0.02 0.01
Matches are distributed among these distances:
747 1 0.00
748 322 0.46
750 10 0.01
752 3 0.00
753 170 0.24
755 196 0.28
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (752 bp):
TTTATCGGCAACACAAGTGTCAGAGTACCATTCCAAAGACTTGAAGATGAAACAATTCAGAGGAC
AAGAACAACCTATAAAAGGTTCTATATTAGCAGGGAAAAACCTTGGCATCCAACACTCTTCTGGC
AAGTTCCTCAACCTCAAGGTATGGCCAAATAGAAGAAAAATTCTCTATCTTTTCTGTCTTCCATT
TTCTGGGTTTTAGGGTATTTTGATGTTATGGTTTCTAAGAATAAATGGGTTTTCTTTTGATTCAG
GAGAGGGATGACTTCTTTGAAGTTGGGAATGGGAGCCGAGATGACAGATATGGGTAGGGTAACCT
CAGATTACCTCTTTTTTTCTTCTCTCTCTCTCTTTGAATTAATGCTTTTGTTGTCGGGTTTTATA
GGAGTATGTTCTTGAAGTCAACTTTGGTCGGTTGCATTCTTTTATATTTAGGCTCAATGCTAGTT
TTACAGATTTTTTTTGGGGGATTTTGATTCTCATCAAGAAAGTAAAGTGCATAGAAATCTTGAGT
TAAGACAAGGGTTAGTAAAAGATGGGCTTCTAATTAGGTTTTGGGATATGTTTACCATTGTAATT
TCTGATTTTTTTGTGTTGAAGTTTTTCTTTAGTGCTTGTGGATGTAAGGGAATAGGTTCACCTTT
CACAAACTACACATATATTAGGCTGCACTCTATTTATCACTTCTTTTCTTCTTTTGAGTTTCTTG
ACTGCACTCTATTAATCACTTCTTTTCTTCTTTTGAG
Found at i:162371 original size:40 final size:40
Alignment explanation
Indices: 162314--162397 Score: 134
Period size: 40 Copynumber: 2.1 Consensus size: 40
162304 AAATTGCATG
*
162314 TAATTAGAAGATGAATAAATCATT-AAATAAGCTAGCCAA
1 TAATTAGAAGATAAATAAATCATTAAAATAAGCTAGCCAA
*
162353 TAATTAAGAAGATAAATAAATCATTAAAATTAGCTAGCCAA
1 TAATT-AGAAGATAAATAAATCATTAAAATAAGCTAGCCAA
162394 TAAT
1 TAAT
162398 GAGTTTTCAG
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
39 5 0.12
40 18 0.44
41 18 0.44
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (40 bp):
TAATTAGAAGATAAATAAATCATTAAAATAAGCTAGCCAA
Found at i:168109 original size:18 final size:18
Alignment explanation
Indices: 168086--168120 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
168076 ACAAAAACTG
168086 AAATTGTTCATAAACAAA
1 AAATTGTTCATAAACAAA
*
168104 AAATTGTTCATGAACAA
1 AAATTGTTCATAAACAA
168121 TGTAATAATC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (18 bp):
AAATTGTTCATAAACAAA
Found at i:168261 original size:18 final size:18
Alignment explanation
Indices: 168240--168279 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
168230 ATATTATTTT
168240 TATAATTT-TTATTAATAA
1 TATAATTTATTATTAA-AA
168258 TAT-ATTTATTATTAAAA
1 TATAATTTATTATTAAAA
168275 TATAA
1 TATAA
168280 ATAATTATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TATAATTTATTATTAAAA
Found at i:168276 original size:17 final size:17
Alignment explanation
Indices: 168244--168278 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
168234 TATTTTTATA
168244 ATTTTTATTAATAATAT
1 ATTTTTATTAATAATAT
168261 ATTTATTATTAA-AATAT
1 ATTT-TTATTAATAATAT
168278 A
1 A
168279 AATAATTATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTTATTAATAATAT
Found at i:168366 original size:35 final size:35
Alignment explanation
Indices: 168320--168394 Score: 150
Period size: 35 Copynumber: 2.1 Consensus size: 35
168310 TTATATAAAC
168320 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
168355 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
168390 GAACA
1 GAACA
168395 TAAACGAACT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.21
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:177405 original size:10 final size:10
Alignment explanation
Indices: 177390--177427 Score: 53
Period size: 10 Copynumber: 3.9 Consensus size: 10
177380 TTTAGAAATA
177390 TATCTATATC
1 TATCTATATC
177400 TATCTATATC
1 TATCTATATC
177410 TAT-T-TATC
1 TATCTATATC
177418 TATACTATAT
1 TAT-CTATAT
177428 AAAAAGTACG
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
8 7 0.28
9 1 0.04
10 14 0.56
11 3 0.12
ACGTcount: A:0.32, C:0.16, G:0.00, T:0.53
Consensus pattern (10 bp):
TATCTATATC
Found at i:177763 original size:21 final size:22
Alignment explanation
Indices: 177739--177860 Score: 106
Period size: 22 Copynumber: 5.6 Consensus size: 22
177729 AATTTTGGAA
* *
177739 GTTATCAAAA-TTCATTGTGTG
1 GTTATCAAAATTTTATAGTGTG
*
177760 GTTA-CTAAAATTTTATAGTGCG
1 GTTATC-AAAATTTTATAGTGTG
*
177782 GTTTTCAAAATTTTATAGTGTG
1 GTTATCAAAATTTTATAGTGTG
* *
177804 GTTACCAAAATTTCATAG-GTAG
1 GTTATCAAAATTTTATAGTGT-G
* * * *
177826 GATGTTAAAATTTTATAGTGTA
1 GTTATCAAAATTTTATAGTGTG
*
177848 GTTATCACAATTT
1 GTTATCAAAATTT
177861 CATGGGATGT
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
20 1 0.01
21 10 0.13
22 64 0.82
23 3 0.04
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (22 bp):
GTTATCAAAATTTTATAGTGTG
Found at i:177962 original size:44 final size:44
Alignment explanation
Indices: 177872--178034 Score: 150
Period size: 44 Copynumber: 3.7 Consensus size: 44
177862 ATGGGATGTT
* * * ** * *
177872 AAATTTCATAAGGAGGTTATCGAAA-TTCATGGGAAGGTTGTCA
1 AAATTTCATAGGGAGATTATCAAAATTTCATATGCAGGTTATCA
* * * *
177915 AAATTTCACAGGGAGATTACCAAAATTTCATATTCTGGTTATCA
1 AAATTTCATAGGGAGATTATCAAAATTTCATATGCAGGTTATCA
* * * * *
177959 AAATTTCATAGGGCGATTATCGAAATCTT-ATATGGAAGTTATTA
1 AAATTTCATAGGGAGATTATCAAAAT-TTCATATGCAGGTTATCA
*
178003 AAATTTCATAGGAAGATTATCAAAATTTCATA
1 AAATTTCATAGGGAGATTATCAAAATTTCATA
178035 GTGTGCTTAT
Statistics
Matches: 94, Mismatches: 23, Indels: 5
0.77 0.19 0.04
Matches are distributed among these distances:
43 22 0.23
44 70 0.74
45 2 0.02
ACGTcount: A:0.38, C:0.11, G:0.17, T:0.34
Consensus pattern (44 bp):
AAATTTCATAGGGAGATTATCAAAATTTCATATGCAGGTTATCA
Found at i:177978 original size:22 final size:22
Alignment explanation
Indices: 177872--178063 Score: 122
Period size: 22 Copynumber: 8.8 Consensus size: 22
177862 ATGGGATGTT
* * *
177872 AAATTTCATAAGGAGGTTATCG
1 AAATTTCATAGGGAGATTATCA
* *
177894 AAA-TTCAT-GGGAAGGTTGTCA
1 AAATTTCATAGGG-AGATTATCA
* *
177915 AAATTTCACAGGGAGATTACCA
1 AAATTTCATAGGGAGATTATCA
**** *
177937 AAATTTCATATTCTGGTTATCA
1 AAATTTCATAGGGAGATTATCA
* *
177959 AAATTTCATAGGGCGATTATCG
1 AAATTTCATAGGGAGATTATCA
* *
177981 AAATCTT-ATATGGA-AGTTATTA
1 AAAT-TTCATAGGGAGA-TTATCA
*
178003 AAATTTCATAGGAAGATTATCA
1 AAATTTCATAGGGAGATTATCA
* * * *
178025 AAATTTCATAGTGTGCTTATAA
1 AAATTTCATAGGGAGATTATCA
* *
178047 AAATTACATAGTGAGAT
1 AAATTTCATAGGGAGAT
178064 AGAGTGAGCT
Statistics
Matches: 128, Mismatches: 35, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
20 2 0.02
21 18 0.14
22 102 0.80
23 6 0.05
ACGTcount: A:0.38, C:0.10, G:0.18, T:0.34
Consensus pattern (22 bp):
AAATTTCATAGGGAGATTATCA
Found at i:178050 original size:44 final size:43
Alignment explanation
Indices: 177914--178063 Score: 142
Period size: 44 Copynumber: 3.4 Consensus size: 43
177904 GAAGGTTGTC
* * * *
177914 AAAATTTCACAGGGAGATTACCAAAATTTCATATTCTGGTTATC
1 AAAATTTCATAGGGAGATTATCAAAATTTCATA-TGTGGTTATA
* * *
177958 AAAATTTCATAGGGCGATTATCGAAATCTT-ATATG-GAAGTTATT
1 AAAATTTCATAGGGAGATTATCAAAAT-TTCATATGTG--GTTATA
* *
178002 AAAATTTCATAGGAAGATTATCAAAATTTCATAGTGTGCTTATA
1 AAAATTTCATAGGGAGATTATCAAAATTTCATA-TGTGGTTATA
* *
178046 AAAATTACATAGTGAGAT
1 AAAATTTCATAGGGAGAT
178064 AGAGTGAGCT
Statistics
Matches: 86, Mismatches: 14, Indels: 12
0.77 0.12 0.11
Matches are distributed among these distances:
42 1 0.01
43 3 0.03
44 77 0.90
45 4 0.05
46 1 0.01
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.35
Consensus pattern (43 bp):
AAAATTTCATAGGGAGATTATCAAAATTTCATATGTGGTTATA
Found at i:178175 original size:22 final size:23
Alignment explanation
Indices: 178139--178193 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
178129 ATAGAGGTAA
*
178139 CAAAATTTCATAGGGAAG-TTAT
1 CAAAATTTCAGAGGGAAGATTAT
* * *
178161 CGAAATTTTAGAGGGGAGATTAT
1 CAAAATTTCAGAGGGAAGATTAT
178184 CAAAATTTCA
1 CAAAATTTCA
178194 TAGTGTGGTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 14 0.54
23 12 0.46
ACGTcount: A:0.40, C:0.09, G:0.20, T:0.31
Consensus pattern (23 bp):
CAAAATTTCAGAGGGAAGATTAT
Found at i:178246 original size:61 final size:60
Alignment explanation
Indices: 178165--178281 Score: 164
Period size: 61 Copynumber: 1.9 Consensus size: 60
178155 AGTTATCGAA
* *
178165 ATTTTAGAGGGGAGATTATCAAAATTTCATAGTGTGGTTA-ATAAAATTTTATAATGTGGT
1 ATTTCAGAGGGGAGATTATCAAAATTTCATAGTGTGG-TAGATAAAATTTCATAATGTGGT
* * *
178225 ATTTCAGAGGGAGAGATTATCAAATTTTCATTGTGTGGTAGTTAAAATTTCATAATG
1 ATTTCAGAGGG-GAGATTATCAAAATTTCATAGTGTGGTAGATAAAATTTCATAATG
178282 AGTTTATCGA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
60 12 0.24
61 38 0.76
ACGTcount: A:0.34, C:0.05, G:0.21, T:0.39
Consensus pattern (60 bp):
ATTTCAGAGGGGAGATTATCAAAATTTCATAGTGTGGTAGATAAAATTTCATAATGTGGT
Found at i:178315 original size:21 final size:22
Alignment explanation
Indices: 178268--178366 Score: 92
Period size: 22 Copynumber: 4.5 Consensus size: 22
178258 TGTGGTAGTT
* * *
178268 AAAATTTCATAATGAGTTTATC
1 AAAATTTCATAGTGAGATTAAC
*
178290 GAAATTT-ATAGTGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
* * * **
178311 AAAATTTGATAGTGTGGTTCTC
1 AAAATTTCATAGTGAGATTAAC
* *
178333 AAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAGTGAGATTAAC
178355 AAAATTTCATAG
1 AAAATTTCATAG
178367 GTAAGTTATC
Statistics
Matches: 60, Mismatches: 16, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
21 17 0.28
22 43 0.72
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.36
Consensus pattern (22 bp):
AAAATTTCATAGTGAGATTAAC
Found at i:178383 original size:44 final size:42
Alignment explanation
Indices: 178268--178383 Score: 108
Period size: 44 Copynumber: 2.6 Consensus size: 42
178258 TGTGGTAGTT
* * *
178268 AAAATTTCATA-ATGAGTTTATCGAAATTTATAGTGAGATTAAC
1 AAAATTTCATAGGT-AG-TTATCGAATTTTATAGGGAGATTAAC
* * * *
178311 AAAATTTGATAGTGTGGTTCTCAAAATTTTATAGGGAGATTAAC
1 AAAATTTCATAG-GTAGTTATC-GAATTTTATAGGGAGATTAAC
178355 AAAATTTCATAGGTAAGTTATCGTAATTT
1 AAAATTTCATAGGT-AGTTATCG-AATTT
178384 CATGGTGTAA
Statistics
Matches: 57, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
43 16 0.28
44 40 0.70
45 1 0.02
ACGTcount: A:0.39, C:0.07, G:0.16, T:0.38
Consensus pattern (42 bp):
AAAATTTCATAGGTAGTTATCGAATTTTATAGGGAGATTAAC
Found at i:178424 original size:21 final size:21
Alignment explanation
Indices: 178398--178451 Score: 99
Period size: 21 Copynumber: 2.6 Consensus size: 21
178388 GTGTAATTAA
*
178398 TTATCAAAATTTTGTTGGGGG
1 TTATCAAAATTTTATTGGGGG
178419 TTATCAAAATTTTATTGGGGG
1 TTATCAAAATTTTATTGGGGG
178440 TTATCAAAATTT
1 TTATCAAAATTT
178452 AATAGTGTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.30, C:0.06, G:0.20, T:0.44
Consensus pattern (21 bp):
TTATCAAAATTTTATTGGGGG
Found at i:178503 original size:22 final size:21
Alignment explanation
Indices: 178477--178612 Score: 86
Period size: 22 Copynumber: 6.4 Consensus size: 21
178467 AAAATTTCGT
178477 AGGAGGTTAACAAAAGTTTATA
1 AGGAGGTTAACAAAA-TTTATA
*
178499 AGGAGGTTATAAAAAATTTAT-
1 AGGAGGTTA-ACAAAATTTATA
* *
178520 AGGATGTTATCAAAATTTCATA
1 AGGAGGTTAACAAAATTT-ATA
*
178542 A-GATGGTTATCAAAATTTCAT-
1 AGGA-GGTTAACAAAATTT-ATA
* *
178563 --GAGATTATCAAAATTTGA-A
1 AGGAGGTTAACAAAATTT-ATA
*
178582 ATGGAGGTTATCAAAATGTTATA
1 A-GGAGGTTAACAAAAT-TTATA
*
178605 GGGAGGTT
1 AGGAGGTT
178613 TATAAAAATT
Statistics
Matches: 95, Mismatches: 9, Indels: 20
0.77 0.07 0.16
Matches are distributed among these distances:
19 14 0.15
20 9 0.09
21 12 0.13
22 52 0.55
23 8 0.08
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (21 bp):
AGGAGGTTAACAAAATTTATA
Found at i:178523 original size:43 final size:44
Alignment explanation
Indices: 178467--178578 Score: 110
Period size: 43 Copynumber: 2.6 Consensus size: 44
178457 TGTTCTTATC
*
178467 AAAATTTCGTAGGAGGTTAACAAAAGTTT-ATAAGGA-GGTTATAA
1 AAAATTTCATAGGAGGTTAACAAAA-TTTCATAA-GATGGTTATAA
* * *
178511 AAAATTT-ATAGGATGTTATCAAAATTTCATAAGATGGTTAT-C
1 AAAATTTCATAGGAGGTTAACAAAATTTCATAAGATGGTTATAA
* *
178553 AAAATTTCAT--GAGATTATCAAAATTT
1 AAAATTTCATAGGAGGTTAACAAAATTT
178579 GAAATGGAGG
Statistics
Matches: 59, Mismatches: 6, Indels: 9
0.80 0.08 0.12
Matches are distributed among these distances:
41 14 0.24
42 12 0.20
43 26 0.44
44 7 0.12
ACGTcount: A:0.43, C:0.06, G:0.16, T:0.35
Consensus pattern (44 bp):
AAAATTTCATAGGAGGTTAACAAAATTTCATAAGATGGTTATAA
Found at i:178572 original size:19 final size:21
Alignment explanation
Indices: 178511--178670 Score: 93
Period size: 22 Copynumber: 7.5 Consensus size: 21
178501 GAGGTTATAA
178511 AAAATTT-ATAGGATG-TTATC
1 AAAATTTCATA-GATGATTATC
*
178531 AAAATTTCATAAGATGGTTATC
1 AAAATTTCAT-AGATGATTATC
178553 AAAATTTCAT-GA-GATTATC
1 AAAATTTCATAGATGATTATC
*
178572 AAAATTTGA-A-ATGGAGGTTATC
1 AAAATTTCATAGAT-GA--TTATC
* * *
178594 AAAATGTT-ATAGGGAGGTTTATA
1 AAAAT-TTCATA--GATGATTATC
*
178617 AAAATTTCATAG-TGAGGTATC
1 AAAATTTCATAGATGA-TTATC
* * *
178638 ACAATTTCATGATATGTTTATC
1 AAAATTTCAT-AGATGATTATC
178660 AAAATTTCATA
1 AAAATTTCATA
178671 ATGTGATTAC
Statistics
Matches: 109, Mismatches: 14, Indels: 33
0.70 0.09 0.21
Matches are distributed among these distances:
18 1 0.01
19 14 0.13
20 12 0.11
21 20 0.18
22 43 0.39
23 17 0.16
25 1 0.01
26 1 0.01
ACGTcount: A:0.40, C:0.07, G:0.16, T:0.37
Consensus pattern (21 bp):
AAAATTTCATAGATGATTATC
Found at i:178620 original size:23 final size:23
Alignment explanation
Indices: 178462--178634 Score: 68
Period size: 22 Copynumber: 8.0 Consensus size: 23
178452 AATAGTGTTC
* *
178462 TTATCAAAATTTCGTA-GGAGGT
1 TTATAAAAATTTCATAGGGAGGT
* * * *
178484 TAACAAAAGTTT-ATAAGGAGG-
1 TTATAAAAATTTCATAGGGAGGT
*
178505 TTATAAAAAATTT-ATA-GGATG-
1 TTAT-AAAAATTTCATAGGGAGGT
* *
178526 TTATCAAAATTTCATA-AGATGG-
1 TTATAAAAATTTCATAGGGA-GGT
* *
178548 TTATCAAAATTTCAT---GA-GA
1 TTATAAAAATTTCATAGGGAGGT
* * * *
178567 TTATCAAAATTTGAAATGGAGG-
1 TTATAAAAATTTCATAGGGAGGT
*
178589 TTATCAAAATGTT-ATAGGGAGGT
1 TTATAAAAAT-TTCATAGGGAGGT
*
178612 TTATAAAAATTTCATAGTGAGGT
1 TTATAAAAATTTCATAGGGAGGT
178635 ATCACAATTT
Statistics
Matches: 121, Mismatches: 18, Indels: 23
0.75 0.11 0.14
Matches are distributed among these distances:
18 1 0.01
19 13 0.11
20 9 0.07
21 17 0.14
22 60 0.50
23 21 0.17
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.35
Consensus pattern (23 bp):
TTATAAAAATTTCATAGGGAGGT
Found at i:178665 original size:107 final size:105
Alignment explanation
Indices: 178462--178669 Score: 262
Period size: 107 Copynumber: 2.0 Consensus size: 105
178452 AATAGTGTTC
* *
178462 TTATCAAAATTTCGTAGGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGATGT
1 TTATCAAAATTTCGAAGGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGATGG
178527 TATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGA
66 TATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGA
* *
178567 TTATCAAAATTT-GAAATGGAGGTTATCAAAA-TGTTATAGGGAGGTT-TATAAAAATTTCATAG
1 TTATCAAAATTTCG-AA-GGAGGTTAACAAAAGT-TTATAAGGAGGTTATA-AAAAATTT-ATAG
* * * *
178629 TGA-GGTATCACAATTTCATGATATGTTTATCAAAATTTCAT
61 -GATGGTATCAAAATTTCATAAGATGGTTATCAAAATTTCAT
178670 AATGTGATTA
Statistics
Matches: 89, Mismatches: 8, Indels: 10
0.83 0.07 0.09
Matches are distributed among these distances:
104 1 0.01
105 16 0.18
106 33 0.37
107 37 0.42
108 2 0.02
ACGTcount: A:0.40, C:0.07, G:0.17, T:0.36
Consensus pattern (105 bp):
TTATCAAAATTTCGAAGGAGGTTAACAAAAGTTTATAAGGAGGTTATAAAAAATTTATAGGATGG
TATCAAAATTTCATAAGATGGTTATCAAAATTTCATGAGA
Found at i:178770 original size:22 final size:22
Alignment explanation
Indices: 178745--178800 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
178735 CATTGGGAGT
178745 TTATTAAAATTTCATAAGATAG
1 TTATTAAAATTTCATAAGATAG
* * * *
178767 TTATCAAAATTTCATTAGGTGG
1 TTATTAAAATTTCATAAGATAG
*
178789 TTGTTAAAATTT
1 TTATTAAAATTT
178801 TTATTAGGGA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (22 bp):
TTATTAAAATTTCATAAGATAG
Found at i:178915 original size:22 final size:21
Alignment explanation
Indices: 178890--178956 Score: 75
Period size: 22 Copynumber: 3.1 Consensus size: 21
178880 TATCGTCCTA
*
178890 AAAACTTTATAGTGTATTTATC
1 AAAATTTTATAGTG-ATTTATC
*
178912 AAAATTTTATA-TGGAGATTATC
1 AAAATTTTATAGT-GA-TTTATC
178934 AAAATTTTATAGTG-TTTATC
1 AAAATTTTATAGTGATTTATC
178954 AAA
1 AAA
178957 TTTCATAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
20 8 0.21
21 2 0.05
22 28 0.72
23 1 0.03
ACGTcount: A:0.40, C:0.06, G:0.10, T:0.43
Consensus pattern (21 bp):
AAAATTTTATAGTGATTTATC
Found at i:179029 original size:2 final size:2
Alignment explanation
Indices: 179022--179048 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
179012 TTAAAACTAG
179022 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 T
179049 TTAATTTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.