Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013833.1 Kokia drynarioides strain JFW-HI SEQ_128861, 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: 157692
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Warning! 57 characters in sequence are not A, C, G, or T
Found at i:1196 original size:11 final size:12
Alignment explanation
Indices: 1156--1204 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1146 TATTTGTGTA
1156 AAAATTAATTTG
1 AAAATTAATTTG
1168 AAAATTAATTTAAG
1 AAAATTAATTT--G
*
1182 TTGAAATTAATTTG
1 --AAAATTAATTTG
1196 AAAATTAAT
1 AAAATTAAT
1205 GAACATGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.51, C:0.00, G:0.08, T:0.41
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:1324 original size:10 final size:11
Alignment explanation
Indices: 1286--1325 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
1276 TTGAAGTTGA
1286 AATTT-AAATT
1 AATTTAAAATT
1296 ACATTTAAAATT
1 A-ATTTAAAATT
1308 AATTTAAAATT
1 AATTTAAAATT
1319 -ATTTAAA
1 AATTTAAA
1326 TAAAAAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.29
11 14 0.50
12 6 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (11 bp):
AATTTAAAATT
Found at i:1546 original size:84 final size:84
Alignment explanation
Indices: 1308--1956 Score: 953
Period size: 84 Copynumber: 7.6 Consensus size: 84
1298 ATTTAAAATT
* * * *
1308 AATTTAAAATTATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTTC
1 AATTT-AAA-TATTTAAATAAAAAA-A-TATTATTATATTAAAATTTTTATCAAATAATGTGTTG
1373 ATTTGACAATACATTATTTA-TCA
62 ATTTGACAATACATTATTTACT-A
** * *
1396 AATTTTCATATTTAAATAAAAAGATTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
1 AATTTAAATATTTAAATAAAAA-AATATTATTATATTAAAATTTTTATCAAATAATGTGTTGATT
1461 TGACAATACATTATTTACTA
65 TGACAATACATTATTTACTA
*
1481 AATTTAAATATTTAAATAAAAAAATATTATTATATTACAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAAATATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTT
*
1546 GATAATACATTATTTA-TCA
66 GACAATACATTATTTACT-A
** *
1565 AATTTTCATATTTAAATAAAAAAGATTATTATTATATTAAAATTTTTATCAAATAATATGTTGAT
1 AATTTAAATATTTAAATAAAAAA-A-TATTATTATATTAAAATTTTTATCAAATAATGTGTTGAT
1630 TTGACAATACATTATTTACTA
64 TTGACAATACATTATTTACTA
* *
1651 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTATAATTTTTATCAAATAATATGTTGAT
1 AATTTAAATATTTAAATAAAAAA-A-TATTATTATATTAAAATTTTTATCAAATAATGTGTTGAT
* *
1716 TTGACAATATATTATTTATTA
64 TTGACAATACATTATTTACTA
* * *
1737 AATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTTTATCAAATAATGTTTTAATTT
1 AATTTAAATATTTAAATAAAAAAATATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTT
1802 GACAATACATTATTTACTA
66 GACAATACATTATTTACTA
*
1821 AATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTT
1 AATTTAAATATTTAAATAAAAAAATATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTT
1886 GACAATACATTATTTACTA
66 GACAATACATTATTTACTA
* * *
1905 ATTTTAAAT-TTTCAAATAAAAAATTATTATTATATTACAATTTTTATCAAAT
1 AATTTAAATATTT-AAATAAAAAAATATTATTATATTAAAATTTTTATCAAAT
1957 TTTAAATTTA
Statistics
Matches: 521, Mismatches: 33, Indels: 18
0.91 0.06 0.03
Matches are distributed among these distances:
83 4 0.01
84 260 0.50
85 75 0.14
86 174 0.33
87 3 0.01
88 5 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (84 bp):
AATTTAAATATTTAAATAAAAAAATATTATTATATTAAAATTTTTATCAAATAATGTGTTGATTT
GACAATACATTATTTACTA
Found at i:1650 original size:170 final size:170
Alignment explanation
Indices: 1308--1956 Score: 1031
Period size: 170 Copynumber: 3.8 Consensus size: 170
1298 ATTTAAAATT
* * *
1308 AATTTAAAATTATTTAAATAAAAAAGATTATTATTATATTACAATTTATATCAAATATTGTGTTC
1 AATTT-AAA-TATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTG
*
1373 ATTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAGATTATTATTATATTATAAT
64 ATTTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAA-ATTATTATTATATTAAAAT
1438 TTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
128 TTTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
1481 AATTTAAATATTTAAATAAAAAA-A-TATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
*
1544 TTGATAATACATTATTTATCAAATTTTCATATTTAAATAAAAAAGATTATTATTATATTAAAATT
66 TTGACAATACATTATTTATCAAATTTTCATATTTAAAT-AAAAA-ATTATTATTATATTAAAATT
*
1609 TTTATCAAATAATATGTTGATTTGACAATACATTATTTACTA
129 TTTATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
* *
1651 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTATAATTTTTATCAAATAATATGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
* * **
1716 TTGACAATATATTATTTATTAAATTTAAATATTTAAATAAAAAATTATTATTATATTAAAATTTT
66 TTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATTAAAATTTT
* *
1781 TATCAAATAATGTTTTAATTTGACAATACATTATTTACTA
131 TATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
*
1821 AATTTAAATATTTAAAT-AAAAA-ATTATTATTATATTAAAATTTTTATCAAATAATGTGTTGAT
1 AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
* * *
1884 TTGACAATACATTATTTA-CTAATTTT-AAATTTTCAAATAAAAAATTATTATTATATTACAATT
66 TTGACAATACATTATTTATCAAATTTTCATA-TTT-AAATAAAAAATTATTATTATATTAAAATT
1947 TTTATCAAAT
129 TTTATCAAAT
1957 TTTAAATTTA
Statistics
Matches: 447, Mismatches: 24, Indels: 15
0.92 0.05 0.03
Matches are distributed among these distances:
166 2 0.00
167 8 0.02
168 94 0.21
169 78 0.17
170 166 0.37
171 21 0.05
172 73 0.16
173 5 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (170 bp):
AATTTAAATATTTAAATAAAAAAGATTATTATTATATTACAATTTTTATCAAATAATGTGTTGAT
TTGACAATACATTATTTATCAAATTTTCATATTTAAATAAAAAATTATTATTATATTAAAATTTT
TATCAAATAATGTGTTGATTTGACAATACATTATTTACTA
Found at i:2083 original size:22 final size:22
Alignment explanation
Indices: 2049--2109 Score: 77
Period size: 22 Copynumber: 2.8 Consensus size: 22
2039 TCGACCACTT
* *
2049 AAATTCCAGCTCACCTAAACCG
1 AAATTCCAGCTCACCAAAACCA
* * *
2071 AAATTTCAACTCAGCAAAACCA
1 AAATTCCAGCTCACCAAAACCA
2093 AAATTCCAGCTCACCAA
1 AAATTCCAGCTCACCAA
2110 CACCTCAATT
Statistics
Matches: 31, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.43, C:0.33, G:0.07, T:0.18
Consensus pattern (22 bp):
AAATTCCAGCTCACCAAAACCA
Found at i:3720 original size:30 final size:30
Alignment explanation
Indices: 3658--3749 Score: 103
Period size: 30 Copynumber: 3.1 Consensus size: 30
3648 TCCTTTTACT
* ** * *
3658 TTTTAAATTTAATTTGTAATTTTGTTTTTA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
3688 TTTTAAATTTAATTTCTAATTTCCTATATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
* * * *
3718 TTTTAATTTTATTTTCTAATTCCCTGTATA
1 TTTTAAATTTAATTTCTAATTTCCTATATA
3748 TT
1 TT
3750 CTAATTATTA
Statistics
Matches: 53, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.27, C:0.08, G:0.03, T:0.62
Consensus pattern (30 bp):
TTTTAAATTTAATTTCTAATTTCCTATATA
Found at i:3755 original size:30 final size:30
Alignment explanation
Indices: 3686--3763 Score: 102
Period size: 30 Copynumber: 2.6 Consensus size: 30
3676 ATTTTGTTTT
* * *
3686 TATTTTAAATTTAATTTCTAATTTCCTATA
1 TATTTTAATTTTATTTTCTAATTCCCTATA
*
3716 TATTTTAATTTTATTTTCTAATTCCCTGTA
1 TATTTTAATTTTATTTTCTAATTCCCTATA
*
3746 TATTCTAATTATTATTTT
1 TATTTTAATT-TTATTTT
3764 TTGAAAATTT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
30 35 0.83
31 7 0.17
ACGTcount: A:0.28, C:0.10, G:0.01, T:0.60
Consensus pattern (30 bp):
TATTTTAATTTTATTTTCTAATTCCCTATA
Found at i:4733 original size:62 final size:61
Alignment explanation
Indices: 4568--5139 Score: 539
Period size: 62 Copynumber: 9.4 Consensus size: 61
4558 GAGGGAAGTT
* ** * ***
4568 GGTGTCGGCCATTATATGACCAACACCAAAAAAATTT-AA-TTTTTTACCAAATAAAAAGGG
1 GGTGTCGACCATTGCATGACCAACACCAAAAAAATTTAAATTTTTTTATC-TGCAAAAAGGG
* * * *
4628 GGCGTCGACCATTACATGACCAACTA--AAAAAAATTCAAATTTTTTTATCTGCAAAAAGAG
1 GGTGTCGACCATTGCATGACCAAC-ACCAAAAAAATTTAAATTTTTTTATCTGCAAAAAGGG
* *
4688 TGTGTCGACCA-TGACATGACCAACACCAAAAAAATTTAAAATTTTTTAATCTGCAAAAAGGG
1 GGTGTCGACCATTG-CATGACCAACACCAAAAAAATTT-AAATTTTTTTATCTGCAAAAAGGG
* * *
4750 GGTGTCGACCATTGCATGACCAACA-CAAAAAAATTTTGAAAATTTTTTATCTGAAAAAAGGA
1 GGTGTCGACCATTGCATGACCAACACCAAAAAAA-TTT-AAATTTTTTTATCTGCAAAAAGGG
* * * ** *
4812 GATGTCGGCCATTGCAT-AGCCAATA-CAAAAAAATTCGAATTTTTTTATTTGCAAAAAGGG
1 GGTGTCGACCATTGCATGA-CCAACACCAAAAAAATTTAAATTTTTTTATCTGCAAAAAGGG
* * *
4872 AGTGTCGGCCATGGCATGACCAACACC-AAAAAATTTGAAATTTTTTTATCTGCAAAAAGGG
1 GGTGTCGACCATTGCATGACCAACACCAAAAAAATTT-AAATTTTTTTATCTGCAAAAAGGG
* *
4933 GGTGTCGATCATTGCAT-AGCCAACACCAAAAAAATTTGAAATTTTTTTATCTGAAAAAAGGGG
1 GGTGTCGACCATTGCATGA-CCAACACCAAAAAAATTT-AAATTTTTTTATCTGCAAAAA-GGG
* * * *
4996 GGTGTCGACCATTGCATGGCCAACACC-CAAAAATTT-GATTTTTTTATCAG-ATAAATA-GG
1 GGTGTCGACCATTGCATGACCAACACCAAAAAAATTTAAATTTTTTTATCTGCA-AAA-AGGG
* * * * * * * *
5055 AGTGTCGGCCATTGCATGGCCAACACAAAAAAAAATTGAA-TTTTTT-T-TACAAAAAGAG
1 GGTGTCGACCATTGCATGACCAACACCAAAAAAATTTAAATTTTTTTATCTGCAAAAAGGG
**
5113 GGTGTCGGTCATTGCATGACCAACACC
1 GGTGTCGACCATTGCATGACCAACACC
5140 CAAATTAATT
Statistics
Matches: 429, Mismatches: 60, Indels: 48
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.00
58 27 0.06
59 40 0.09
60 124 0.29
61 76 0.18
62 132 0.31
63 29 0.07
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.27
Consensus pattern (61 bp):
GGTGTCGACCATTGCATGACCAACACCAAAAAAATTTAAATTTTTTTATCTGCAAAAAGGG
Found at i:4758 original size:122 final size:120
Alignment explanation
Indices: 4587--5138 Score: 529
Period size: 122 Copynumber: 4.6 Consensus size: 120
4577 CATTATATGA
** * *
4587 CCAACACCAAAAAAATTT-AATTTTTTACCAAAT--AAAAAGGGGGCGTCGACCATTACATGACC
1 CCAACACCAAAAAAATTTAAATTTTTTA--ATCTGCAAAAAGGGGGTGTCGACCATTGCATGACC
*
4649 AACTA-AAAAAAATTCAAATTTTTTTATCTGCAAAAAGAGTGTGTCGACCA-TGACAT-G
64 AAC-ACAAAAAAATTGAAATTTTTTTATCTGCAAAAAGAG-GTGTCGACCATTG-CATAG
4706 ACCAACACCAAAAAAATTTAAAATTTTTTAATCTGCAAAAAGGGGGTGTCGACCATTGCATGACC
1 -CCAACACCAAAAAAATTT-AAATTTTTTAATCTGCAAAAAGGGGGTGTCGACCATTGCATGACC
* * * *
4771 AACACAAAAAAATTTTGAAAATTTTTTATCTGAAAAAAGGAGATGTCGGCCATTGCATAG
64 AACACAAAAAAA--TTGAAATTTTTTTATCTGCAAAAA-GAGGTGTCGACCATTGCATAG
* ** * * * * *
4831 CCAATA-CAAAAAAATTCGAATTTTTTTATTTGCAAAAAGGGAGTGTCGGCCATGGCATGACCAA
1 CCAACACCAAAAAAATTTAAATTTTTTAATCTGCAAAAAGGGGGTGTCGACCATTGCATGACCAA
* * *
4895 CACCAAAAAATTTGAAATTTTTTTATCTGCAAAAAGGGGGTGTCGATCATTGCATAG
66 CA-CAAAAAAATTGAAATTTTTTTATCTGCAAAAA-GAGGTGTCGACCATTGCATAG
* * *
4952 CCAACACCAAAAAAATTTGAAATTTTTTTATCTGAAAAAAGGGGGGTGTCGACCATTGCATGGCC
1 CCAACACCAAAAAAATTT-AAATTTTTTAATCTGCAAAAA-GGGGGTGTCGACCATTGCATGACC
* * * * *
5017 AACACCCAAAAATTTG--ATTTTTTTATCAG-ATAAATAG-GAGTGTCGGCCATTGCATGG
64 AACA-CAAAAAAATTGAAATTTTTTTATCTGCA-AAA-AGAG-GTGTCGACCATTGCATAG
* * * * * **
5074 CCAACACAAAAAAAAATTGAATTTTTT--T-TACAAAAAGAGGGTGTCGGTCATTGCATGACCAA
1 CCAACACCAAAAAAATTTAAATTTTTTAATCTGCAAAAAGGGGGTGTCGACCATTGCATGACCAA
5136 CAC
66 CAC
5139 CCAAATTAAT
Statistics
Matches: 368, Mismatches: 47, Indels: 38
0.81 0.10 0.08
Matches are distributed among these distances:
116 1 0.00
117 24 0.07
118 6 0.02
119 1 0.00
120 20 0.05
121 56 0.15
122 146 0.40
123 36 0.10
124 72 0.20
125 6 0.02
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (120 bp):
CCAACACCAAAAAAATTTAAATTTTTTAATCTGCAAAAAGGGGGTGTCGACCATTGCATGACCAA
CACAAAAAAATTGAAATTTTTTTATCTGCAAAAAGAGGTGTCGACCATTGCATAG
Found at i:5167 original size:58 final size:56
Alignment explanation
Indices: 4792--5181 Score: 202
Period size: 61 Copynumber: 6.6 Consensus size: 56
4782 ATTTTGAAAA
* * * ***
4792 TTTTTTATCTGA-AAAAAGGAGATGTCGGCCATTGCATAGCCAATACAAAAAAATTCGAAT
1 TTTTTTATCAGATAAAAAGG-GGTGTCGGCCATTGCATGGCC-A-ACACCCAAATT--AAT
** * * * *
4852 TTTTTTATTTG-CAAAAAGGGAGTGTCGGCCATGGCATGACCAACACCAAAAAATTTGAAAT
1 TTTTTTATCAGATAAAAAGGG-GTGTCGGCCATTGCATGGCCAACACC--CAAA-TT--AAT
* * ** * *
4913 TTTTTTATCTGCA-AAAAGGGGGTGTCGATCATTGCATAGCCAACACCAAAAAAATTTGAAAT
1 TTTTTTATCAG-ATAAAAAGGGGTGTCGGCCATTGCATGGCCAACACC---CAAA-TT--AAT
* * *
4975 TTTTTTATCTGA-AAAAAGGGGGGTGTCGACCATTGCATGGCCAACACCCAAAAATTTGAT
1 TTTTTTATCAGATAAAAA--GGGGTGTCGGCCATTGCATGGCCAACACCC--AAA-TTAAT
* * **
5035 TTTTTTATCAGATAAATAGGAGTGTCGGCCATTGCATGGCCAACACAAAAAAAAATTGAAT
1 TTTTTTATCAGATAAAAAGGGGTGTCGGCCATTGCATGGCCAACAC----CCAAATT-AAT
* * *
5096 TTTTTT-T---ACAAAAAGAGGGTGTCGGTCATTGCATGACCAACACCCAAATTAAT
1 TTTTTTATCAGATAAAAAG-GGGTGTCGGCCATTGCATGGCCAACACCCAAATTAAT
5149 TTTTTTATCAGATTAAAAAGGGGTGTCGGCCAT
1 TTTTTTATCAGA-TAAAAAGGGGTGTCGGCCAT
5182 GCAATGGTCA
Statistics
Matches: 269, Mismatches: 37, Indels: 51
0.75 0.10 0.14
Matches are distributed among these distances:
53 9 0.03
54 6 0.02
57 19 0.07
58 33 0.12
59 28 0.10
60 53 0.20
61 56 0.21
62 38 0.14
63 27 0.10
ACGTcount: A:0.36, C:0.16, G:0.19, T:0.29
Consensus pattern (56 bp):
TTTTTTATCAGATAAAAAGGGGTGTCGGCCATTGCATGGCCAACACCCAAATTAAT
Found at i:6073 original size:8 final size:8
Alignment explanation
Indices: 6060--6084 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6050 TAGAAATACT
6060 AGAAAAGA
1 AGAAAAGA
6068 AGAAAAGA
1 AGAAAAGA
6076 AGAAAAGA
1 AGAAAAGA
6084 A
1 A
6085 AGAGTTGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:6187 original size:8 final size:8
Alignment explanation
Indices: 6174--6198 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
6164 TAGAAATACT
6174 AGAAAAGA
1 AGAAAAGA
6182 AGAAAAGA
1 AGAAAAGA
6190 AGAAAAGA
1 AGAAAAGA
6198 A
1 A
6199 AGAGTCGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:6201 original size:126 final size:126
Alignment explanation
Indices: 5973--6198 Score: 361
Period size: 126 Copynumber: 1.8 Consensus size: 126
5963 TTGTTGGCAA
5973 AATAGGGAGAATACTTCAAAGAGTTGAAAATTGAAGGTTGAAAAAAATTGAATTAGCAAAGCAAA
1 AATAGGGAGAATACTTCAAAGAGTTGAAAATTGAAGGTTGAAAAAAATTGAATTAGCAAAGCAAA
* * *
6038 TACGTAAGCAGGTAGAAATACTAGAAAAGAAGAAAAGAAGAAAAGAAAGAGTTGTGTTTGT
66 TACGTAAACAGCTAGAAATACAAGAAAAGAAGAAAAGAAGAAAAGAAAGAGTTGTGTTTGT
**
6099 AATAGGGAGAATACTTCAAAGAGTTGAAAATTGAAGGTTGAAAAAAATTGAATTAGCAAAGCAGG
1 AATAGGGAGAATACTTCAAAGAGTTGAAAATTGAAGGTTGAAAAAAATTGAATTAGCAAAGCAAA
* *
6164 TA-G-AAATA-CTAGAAA-AGAAGAAAAGAAGAAAAGAA
66 TACGTAAACAGCTAGAAATACAAGAAAAGAAGAAAAGAA
6199 AGAGTCGTGT
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
122 18 0.19
123 6 0.06
124 3 0.03
125 1 0.01
126 65 0.70
ACGTcount: A:0.52, C:0.05, G:0.23, T:0.19
Consensus pattern (126 bp):
AATAGGGAGAATACTTCAAAGAGTTGAAAATTGAAGGTTGAAAAAAATTGAATTAGCAAAGCAAA
TACGTAAACAGCTAGAAATACAAGAAAAGAAGAAAAGAAGAAAAGAAAGAGTTGTGTTTGT
Found at i:8863 original size:76 final size:72
Alignment explanation
Indices: 8765--8903 Score: 188
Period size: 76 Copynumber: 1.9 Consensus size: 72
8755 ACCCTAACTC
* * *
8765 CATCTTCTTCTATTTTTGCATTTTGTTTTCACCATTATTTTCCCTCCCTTACCTCACCATCGTTT
1 CATCTTATTCTATTTTTGCATTTCGGTTTCACCATTATTTTCCCT--C--ACCTCACCATCGTTT
8830 TCTCTCATCCT
62 TCTCTCATCCT
* * *
8841 CATCTTATTCTATTTTTTCATTTCGGTTTCACCATTGTTTTGCCTCACCTCACCATCGTTTTC
1 CATCTTATTCTATTTTTGCATTTCGGTTTCACCATTATTTTCCCTCACCTCACCATCGTTTTC
8904 CCTTTTTTCT
Statistics
Matches: 57, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 17 0.30
74 1 0.02
76 39 0.68
ACGTcount: A:0.14, C:0.31, G:0.06, T:0.50
Consensus pattern (72 bp):
CATCTTATTCTATTTTTGCATTTCGGTTTCACCATTATTTTCCCTCACCTCACCATCGTTTTCTC
TCATCCT
Found at i:23196 original size:23 final size:24
Alignment explanation
Indices: 23164--23208 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
23154 TTAATTAAAT
*
23164 AAAAAGTAAAGAAAACAAAATATG
1 AAAAAGTAAAAAAAACAAAATATG
*
23188 AAAAA-TAAAAAAAATAAAATA
1 AAAAAGTAAAAAAAACAAAATA
23209 AAATAAAAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.78, C:0.02, G:0.07, T:0.13
Consensus pattern (24 bp):
AAAAAGTAAAAAAAACAAAATATG
Found at i:23211 original size:10 final size:9
Alignment explanation
Indices: 23160--23216 Score: 51
Period size: 9 Copynumber: 5.9 Consensus size: 9
23150 AAAATTAATT
23160 AAATAAAAA
1 AAATAAAAA
*
23169 GTAAAGAAAACA
1 --AAATAAAA-A
**
23181 AAATATGAA
1 AAATAAAAA
23190 AAATAAAAA
1 AAATAAAAA
23199 AAATAAAATA
1 AAATAAAA-A
23209 AAATAAAA
1 AAATAAAA
23217 GCGTAGCTAT
Statistics
Matches: 38, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
9 16 0.42
10 14 0.37
11 7 0.18
12 1 0.03
ACGTcount: A:0.79, C:0.02, G:0.05, T:0.14
Consensus pattern (9 bp):
AAATAAAAA
Found at i:24602 original size:17 final size:17
Alignment explanation
Indices: 24589--24636 Score: 69
Period size: 17 Copynumber: 2.8 Consensus size: 17
24579 ATAAATTTCC
24589 AATAAATTTAAATTTAA
1 AATAAATTTAAATTTAA
* *
24606 AATAAATTTAATTTTAG
1 AATAAATTTAAATTTAA
*
24623 AATTAATTTAAATT
1 AATAAATTTAAATT
24637 CTATTGGGCC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (17 bp):
AATAAATTTAAATTTAA
Found at i:25186 original size:98 final size:98
Alignment explanation
Indices: 25066--25673 Score: 717
Period size: 98 Copynumber: 6.2 Consensus size: 98
25056 GCCGTTGCGA
* * * * * *
25066 CTTAAAT-TTTCCTTTCATGCTTCTGAGGTATAAGGTTCGCCATTACGACTTAAATCTTTCTCTT
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
** * * * * * *
25130 TGTGTCTTCATGGTAGTGGATTTGTAGTTGTAG
66 CATATCTTCGTGGTACTGGATTCGCAGTTGTGG
* **
25163 CTTAAATCTTTCCCTTTATGCTTCTGAGGTACAAGGTTCGTTGTTGCGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
*
25228 CCA-ATCTTCGTGGTACTGGATTCGCCA-TTGCGG
66 -CATATCTTCGTGGTACTGGATTCG-CAGTTGTGG
* * * * *
25261 CTTAAGTCTTTCCCTTCATGCTTTTGAGGTACAAGGTTTGTCGTTGCGACTTAAACCTTTCCCTC
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* *
25326 CATATCTTCGTGGTACTAGATTCGCCGTTGTGG
66 CATATCTTCGTGGTACTGGATTCGCAGTTGTGG
* * *
25359 CTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGCCGTTGCGAC--AAACCTCTCCCTC
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * **
25422 CATATCTTCGTGGTACTAGATTCGCCGTTACGG
66 CATATCTTCGTGGTACTGGATTCGCAGTTGTGG
* * * *
25455 CTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCGTTGCCACTTAAACCTTTCCCTC
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * *
25520 CATATCTTCGTGGTACTAGAATCGTC-GTTGCGG
66 CATATCTTCGTGGTACTGGATTCG-CAGTTGTGG
* * * * *
25553 CTTAAATATTTCCCTTCATCCTTCTGAGATACAAGGTTCGCTGTTACGACTTAAACCTTTCCCTT
1 CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
* * *
25618 CA-ATCTTCGTGGTACTGGATTGGCCGTTGCGG
66 CATATCTTCGTGGTACTGGATTCGCAGTTGTGG
25650 CTTAAATCTTTCCCTTCATGCTTC
1 CTTAAATCTTTCCCTTCATGCTTC
25674 GTGGAACTAA
Statistics
Matches: 450, Mismatches: 52, Indels: 18
0.87 0.10 0.03
Matches are distributed among these distances:
96 92 0.20
97 57 0.13
98 299 0.66
99 2 0.00
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (98 bp):
CTTAAATCTTTCCCTTCATGCTTCTGAGGTACAAGGTTCGCCGTTGCGACTTAAACCTTTCCCTT
CATATCTTCGTGGTACTGGATTCGCAGTTGTGG
Found at i:25216 original size:49 final size:48
Alignment explanation
Indices: 25056--25674 Score: 348
Period size: 49 Copynumber: 12.7 Consensus size: 48
25046 TACTAAATTT
*
25056 GCCGTTGCGACTTAAAT-TTT-CCTTTCATGCTTCTGAGGTATAAGGTTC
1 GCCGTTGCGACTTAAATCTTTCCCTTT-ATGCTTC-GAGGTACAAGGTTC
* * * * ** *
25104 GCCATTACGACTTAAATCTTTCTCTTTGTGTCTTC-ATGGTA-GTGGATTT
1 GCCGTTGCGACTTAAATCTTTCCCTTTATG-CTTCGA-GGTACAAGG-TTC
** *
25153 GTAGTTG-TAGCTTAAATCTTTCCCTTTATGCTTCTGAGGTACAAGGTTC
1 GCCGTTGCGA-CTTAAATCTTTCCCTTTATGCTTC-GAGGTACAAGGTTC
** * * * *
25202 GTTGTTGCGACTTAAACCTTTCCCTTCCAAT-CTTCGTGGTAC-TGGATTC
1 GCCGTTGCGACTTAAATCTTTCCCTT--TATGCTTCGAGGTACAAGG-TTC
* * * * * *
25251 GCCATTGCGGCTTAAGTCTTTCCCTTCATGCTTTTGAGGTACAAGGTTT
1 GCCGTTGCGACTTAAATCTTTCCCTTTATGC-TTCGAGGTACAAGGTTC
* * * * * *
25300 GTCGTTGCGACTTAAACCTTTCCCTCCATAT-CTTCGTGGTACTAGATTC
1 GCCGTTGCGACTTAAATCTTTCCCT--TTATGCTTCGAGGTACAAGGTTC
* * * *
25349 GCCGTTGTGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTC
1 GCCGTTGCGACTTAAATCTTTCCCTTTATGC-TTCGAGGTACAAGGTTC
* * * * * *
25398 GCCGTTGCGAC--AAACCTCTCCCTCCATAT-CTTCGTGGTACTAGATTC
1 GCCGTTGCGACTTAAATCTTTCCCT--TTATGCTTCGAGGTACAAGGTTC
* * * *
25445 GCCGTTACGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTC
1 GCCGTTGCGACTTAAATCTTTCCCTTTATGC-TTCGAGGTACAAGGTTC
* * * * * * **
25494 GTCGTTGCCACTTAAACCTTTCCCTCCATAT-CTTCGTGGTACTAGAATC
1 GCCGTTGCGACTTAAATCTTTCCCT--TTATGCTTCGAGGTACAAGGTTC
* * * * * *
25543 GTCGTTGCGGCTTAAATATTTCCCTTCATCCTTCTGAGATACAAGGTTC
1 GCCGTTGCGACTTAAATCTTTCCCTTTATGCTTC-GAGGTACAAGGTTC
* * * * * * *
25592 GCTGTTACGACTTAAACCTTTCCCTTCAAT-CTTCGTGGTAC-TGGATTG
1 GCCGTTGCGACTTAAATCTTTCCCTT-TATGCTTCGAGGTACAAGG-TTC
* *
25640 GCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTCG
1 GCCGTTGCGACTTAAATCTTTCCCTTTATGCTTCG
25675 TGGAACTAAG
Statistics
Matches: 423, Mismatches: 115, Indels: 66
0.70 0.19 0.11
Matches are distributed among these distances:
47 44 0.10
48 67 0.16
49 284 0.67
50 22 0.05
51 6 0.01
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (48 bp):
GCCGTTGCGACTTAAATCTTTCCCTTTATGCTTCGAGGTACAAGGTTC
Found at i:25487 original size:194 final size:194
Alignment explanation
Indices: 25044--25672 Score: 830
Period size: 194 Copynumber: 3.2 Consensus size: 194
25034 CAATCCGCAC
* * * * * * * *
25044 GGTACTAAATTTGCCGTTGCGACTTAAAT-TTTCCTTTCATGCTTCTGAGGTATAAGGTTCGCCA
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCG
* * * *** * * * * * * *
25108 TTACGACTTAAATCTTTCTCTTTGTGTCTTCATGGTAGTGGATTTGTAGTTGTAGCTTAAATCTT
66 TTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTT
* *
25173 TCCCTTTATGCTTCTGAGGTACAAGGTTCGTTGTTGCGACTTAAACCTTTCCCTTCCAATCTTCG
131 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCTGTTGCGAC-TAAACCTTTCCC-TCCAATCTTCG
25238 T
194 T
* * * *
25239 GGTACTGGATTCGCCATTGCGGCTTAAGTCTTTCCCTTCATGCTTTTGAGGTACAAGGTTTGTCG
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCG
*
25304 TTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGCCGTTGTGGCTTAAATCTT
66 TTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTT
* * *
25369 TCCCTTCATGCTTTTGAGGTACAAGGTTCGCCGTTGCGAC-AAACCTCTCCCTCCATATCTTCGT
131 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCTGTTGCGACTAAACCTTTCCCTCCA-ATCTTCGT
*
25433 GGTACTAGATTCGCCGTTACGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCG
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCG
* * * *
25498 TTGCCACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGAATCGTCGTTGCGGCTTAAATATT
66 TTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTT
* * * *
25563 TCCCTTCATCCTTCTGAGATACAAGGTTCGCTGTTACGACTTAAACCTTTCCCTTCAATCTTCGT
131 TCCCTTCATGCTTCTGAGGTACAAGGTTCGCTGTTGCGAC-TAAACCTTTCCCTCCAATCTTCGT
* *
25628 GGTACTGGATTGGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
1 GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTT
25673 CGTGGAACTA
Statistics
Matches: 379, Mismatches: 51, Indels: 8
0.87 0.12 0.02
Matches are distributed among these distances:
193 4 0.01
194 173 0.46
195 73 0.19
196 129 0.34
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (194 bp):
GGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCATGCTTTTGAGGTACAAGGTTCGTCG
TTGCGACTTAAACCTTTCCCTCCATATCTTCGTGGTACTAGATTCGTCGTTGTGGCTTAAATCTT
TCCCTTCATGCTTCTGAGGTACAAGGTTCGCTGTTGCGACTAAACCTTTCCCTCCAATCTTCGT
Found at i:37578 original size:29 final size:28
Alignment explanation
Indices: 37546--37745 Score: 92
Period size: 30 Copynumber: 6.9 Consensus size: 28
37536 GGACACTCGG
*
37546 GGGTGAAATGGTAATTTTTAGAAGGTTCA
1 GGGTAAAATGGTAATTTTTAGAA-GTTCA
* * *
37575 GGGTCAAAAGTAG-AATTTTTAGACATTTGA
1 GGGT-AAAA-TGGTAATTTTTAGA-AGTTCA
* *
37605 GGGTAAAATGGTAATTTTTGGAAAGTTTA
1 GGGTAAAATGGTAATTTTTAG-AAGTTCA
* * *
37634 GGGTTACGAAT-GAAATTTTTAGACA-TCTGA
1 GGG-TA-AAATGGTAATTTTTAGA-AGT-TCA
*
37664 GGGTAAAATGGTAATTTTTGGAAAAGTTC-
1 GGGTAAAATGGTAATTTTT--AGAAGTTCA
*
37693 GGGTTAAAAATAG-AATTTTTAGACA--TCTA
1 GGG-T-AAAATGGTAATTTTTAGA-AGTTC-A
*
37722 GGGGT-AAATGGTAATTTTTGGAAG
1 -GGGTAAAATGGTAATTTTTAGAAG
37746 GTTTGGGGTT
Statistics
Matches: 130, Mismatches: 20, Indels: 43
0.67 0.10 0.22
Matches are distributed among these distances:
27 8 0.06
28 16 0.12
29 40 0.31
30 51 0.39
31 15 0.12
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.34
Consensus pattern (28 bp):
GGGTAAAATGGTAATTTTTAGAAGTTCA
Found at i:37614 original size:59 final size:58
Alignment explanation
Indices: 37529--37769 Score: 258
Period size: 59 Copynumber: 4.1 Consensus size: 58
37519 GTAAAGCGAT
* * * * * *
37529 AATTTTTGGACA-CTCGGGGGTGAAATGGTAATTTTTAGAAGGTTCAGGGTCAAAAGTAG
1 AATTTTTAGACATCT-GAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTAAAA-TAG
* * *
37588 AATTTTTAGACATTTGAGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTACGAAT-G
1 AATTTTTAGACATCTGAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTA-AAATAG
37646 AAATTTTTAGACATCTGAGGGTAAAATGGTAATTTTTGGAAAAGTTC-GGGTTAAAAATAG
1 -AATTTTTAGACATCTGAGGGTAAAATGGTAATTTTTGG-AAAGTTCAGGGTT-AAAATAG
* ** *
37706 AATTTTTAGACATCT-AGGGGT-AAATGGTAATTTTTGGAAGGTTTGGGGTTAAATATGG
1 AATTTTTAGACATCTGA-GGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTAAA-ATAG
37764 AATTTT
1 AATTTT
37770 GGAAAATTTA
Statistics
Matches: 158, Mismatches: 15, Indels: 19
0.82 0.08 0.10
Matches are distributed among these distances:
57 8 0.05
58 32 0.20
59 107 0.68
60 11 0.07
ACGTcount: A:0.33, C:0.05, G:0.27, T:0.36
Consensus pattern (58 bp):
AATTTTTAGACATCTGAGGGTAAAATGGTAATTTTTGGAAAGTTCAGGGTTAAAATAG
Found at i:37708 original size:118 final size:117
Alignment explanation
Indices: 37529--37756 Score: 309
Period size: 118 Copynumber: 1.9 Consensus size: 117
37519 GTAAAGCGAT
* * * * *
37529 AATTTTTGGACACTCGGGGGTGAAATGGTAATTTTTAGAAGGTTCAGGGTCAAAAGTAGAATTTT
1 AATTTTTAGACACTCGAGGGTAAAATGGTAATTTTTAGAAAGTTCAGGGTCAAAAATAGAATTTT
*
37594 TAGACAT-TTGAGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTACGAATGA
66 TAGACATCTAG-GGGT-AAATGGTAATTTTTGGAAAGTTTAGGGTTACGAATGA
* *
37647 AATTTTTAGACA-TCTGAGGGTAAAATGGTAATTTTTGGAAAAGTTC-GGGTTAAAAATAGAATT
1 AATTTTTAGACACTC-GAGGGTAAAATGGTAATTTTTAG-AAAGTTCAGGGTCAAAAATAGAATT
* *
37710 TTTAGACATCTAGGGGTAAATGGTAATTTTTGGAAGGTTTGGGGTTA
64 TTTAGACATCTAGGGGTAAATGGTAATTTTTGGAAAGTTTAGGGTTA
37757 AATATGGAAT
Statistics
Matches: 97, Mismatches: 10, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
117 30 0.31
118 59 0.61
119 8 0.08
ACGTcount: A:0.32, C:0.05, G:0.27, T:0.35
Consensus pattern (117 bp):
AATTTTTAGACACTCGAGGGTAAAATGGTAATTTTTAGAAAGTTCAGGGTCAAAAATAGAATTTT
TAGACATCTAGGGGTAAATGGTAATTTTTGGAAAGTTTAGGGTTACGAATGA
Found at i:37782 original size:58 final size:58
Alignment explanation
Indices: 37545--37884 Score: 250
Period size: 59 Copynumber: 5.8 Consensus size: 58
37535 TGGACACTCG
* * * * * * * *
37545 GGGGTGAAATGGTAATTTTTAGAAGGTTCAGGGTCAAAAGTAGAATTTT-TAGACATTT-
1 GGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTAAAA-TGGAATTTTGGA-AAATTTA
* * * * *
37603 GAGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTACGAATGAAATTTT-TAGACATCT-
1 G-GGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTA-AAATGGAATTTTGGA-AAATTTA
* * * * *
37662 GAGGGTAAAATGGTAATTTTTGGAAAAG-TTCGGGTTAAAAATAGAATTTT-TAGACATCTA
1 G-GGGTAAAATGGTAATTTTTGG-AAAGTTTAGGGTT-AAAATGGAATTTTGGA-AAATTTA
* *
37722 GGGGT-AAATGGTAATTTTTGGAAGGTTTGGGGTTAAATATGGAATTTTGGAAAATTTA
1 GGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTAAA-ATGGAATTTTGGAAAATTTA
*** * * *
37780 GGGGTAAAAAATTAA-TTTTAGAAAGTTTAAGGTTAAAATGGAATTTTGGAAAGTTTA
1 GGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTAAAATGGAATTTTGGAAAATTTA
* *
37837 GGGGTAAAAT-GTAATTTTTGTG-AAGTTTAAGGGTCAAAATGCAATTTT
1 GGGGTAAAATGGTAATTTTTG-GAAAGTTT-AGGGTTAAAATGGAATTTT
37885 TGATAACTTC
Statistics
Matches: 237, Mismatches: 33, Indels: 24
0.81 0.11 0.08
Matches are distributed among these distances:
56 3 0.01
57 44 0.19
58 78 0.33
59 104 0.44
60 8 0.03
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (58 bp):
GGGGTAAAATGGTAATTTTTGGAAAGTTTAGGGTTAAAATGGAATTTTGGAAAATTTA
Found at i:37837 original size:57 final size:58
Alignment explanation
Indices: 37720--37884 Score: 178
Period size: 58 Copynumber: 2.9 Consensus size: 58
37710 TTTAGACATC
* * * *
37720 TAGGGGT-AAATGGTAATTTTTGGAAGGTTT-GGGGTTAAATATGGAATTTTGGAAAATT
1 TAGGGGTAAAAT-GTAATTTTAGTAAAGTTTAAGGGTTAAA-ATGGAATTTTGGAAAATT
*
37778 TAGGGGTAAAAAAT-TAATTTTAG-AAAGTTTAA-GGTTAAAATGGAATTTTGGAAAGTT
1 TAGGGGT--AAAATGTAATTTTAGTAAAGTTTAAGGGTTAAAATGGAATTTTGGAAAATT
* * * *
37835 TAGGGGTAAAATGTAATTTTTGTGAAGTTTAAGGGTCAAAATGCAATTTT
1 TAGGGGTAAAATGTAATTTTAGTAAAGTTTAAGGGTTAAAATGGAATTTT
37885 TGATAACTTC
Statistics
Matches: 92, Mismatches: 8, Indels: 14
0.81 0.07 0.12
Matches are distributed among these distances:
55 5 0.05
56 8 0.09
57 32 0.35
58 35 0.38
59 8 0.09
61 4 0.04
ACGTcount: A:0.36, C:0.01, G:0.26, T:0.37
Consensus pattern (58 bp):
TAGGGGTAAAATGTAATTTTAGTAAAGTTTAAGGGTTAAAATGGAATTTTGGAAAATT
Found at i:37865 original size:29 final size:28
Alignment explanation
Indices: 37605--37886 Score: 143
Period size: 29 Copynumber: 9.7 Consensus size: 28
37595 AGACATTTGA
37605 GGGTAAAATGGTAATTTTTGGAAAGTTTAG
1 GGGTAAAAT-GTAATTTTTGG-AAGTTTAG
* * * * *
37635 GGTTACGAATGAAATTTTTAGACA-TCT-G
1 GGGTA-AAATGTAATTTTTGGA-AGTTTAG
*
37663 AGGGTAAAATGGTAATTTTTGGAAAAG-TTCG
1 -GGGTAAAAT-GTAATTTTTGG--AAGTTTAG
* * *
37694 GGTTAAAAATAG-AATTTTTAGACA-TCTAG
1 GGGT-AAAAT-GTAATTTTTGGA-AGTTTAG
37723 GGGT-AAATGGTAATTTTTGGAAGGTTT-G
1 GGGTAAAAT-GTAATTTTTGGAA-GTTTAG
* *
37751 GGGTTAAATATGGAA-TTTTGGAAAATTTAG
1 GGG-TAAA-ATGTAATTTTTGG-AAGTTTAG
* * *
37781 GGGTAAAAAAT-TAATTTTAGAAAGTTTAA
1 GGGT--AAAATGTAATTTTTGGAAGTTTAG
* *
37810 GGTTAAAATGGAA-TTTTGGAAAGTTTAG
1 GGGTAAAATGTAATTTTTGG-AAGTTTAG
*
37838 GGGTAAAATGTAATTTTTGTGAAGTTTAA
1 GGGTAAAATGTAATTTTTG-GAAGTTTAG
*
37867 GGGTCAAAATGCAATTTTTG
1 GGGT-AAAATGTAATTTTTG
37887 ATAACTTCAA
Statistics
Matches: 190, Mismatches: 35, Indels: 54
0.68 0.13 0.19
Matches are distributed among these distances:
27 15 0.08
28 38 0.20
29 62 0.33
30 59 0.31
31 16 0.08
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (28 bp):
GGGTAAAATGTAATTTTTGGAAGTTTAG
Found at i:37883 original size:30 final size:30
Alignment explanation
Indices: 37802--37906 Score: 103
Period size: 30 Copynumber: 3.6 Consensus size: 30
37792 TAATTTTAGA
* *
37802 AAGTTTAA-GGTTAAAATGGAA-TTTTG-G
1 AAGTTTAAGGGTCAAAATGCAATTTTTGTG
* *
37829 AAAGTTTAGGGGT-AAAATGTAATTTTTGTG
1 -AAGTTTAAGGGTCAAAATGCAATTTTTGTG
37859 AAGTTTAAGGGTCAAAATGCAATTTTTGAT-
1 AAGTTTAAGGGTCAAAATGCAATTTTTG-TG
* *
37889 AACTTCAAGGGTCAAAAT
1 AAGTTTAAGGGTCAAAAT
37907 ATGATTTCTA
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
28 15 0.23
29 19 0.29
30 31 0.47
31 1 0.02
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.35
Consensus pattern (30 bp):
AAGTTTAAGGGTCAAAATGCAATTTTTGTG
Found at i:39699 original size:6 final size:6
Alignment explanation
Indices: 39688--39756 Score: 58
Period size: 6 Copynumber: 12.0 Consensus size: 6
39678 ATTATTTAAA
* *
39688 TAAATT TAAATT TAAATT T--ATGA TAAATT TAAATT TAAA-A TAAATT
1 TAAATT TAAATT TAAATT TAAAT-T TAAATT TAAATT TAAATT TAAATT
*
39734 TAATTT TAGAA-- TAAATT TAAATT
1 TAAATT TA-AATT TAAATT TAAATT
39757 CTGTTATGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
4 4 0.08
5 7 0.14
6 36 0.72
7 3 0.06
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (6 bp):
TAAATT
Found at i:39716 original size:17 final size:16
Alignment explanation
Indices: 39694--39756 Score: 81
Period size: 17 Copynumber: 3.8 Consensus size: 16
39684 TAAATAAATT
39694 TAAATTTAAATTTATGA
1 TAAATTTAAATTTA-GA
*
39711 TAAATTTAAATTTAAAA
1 TAAATTTAAATTT-AGA
*
39728 TAAATTTAATTTTAGAA
1 TAAATTTAAATTTAG-A
39745 TAAATTTAAATT
1 TAAATTTAAATT
39757 CTGTTATGCC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
16 1 0.03
17 38 0.95
18 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (16 bp):
TAAATTTAAATTTAGA
Found at i:39902 original size:17 final size:17
Alignment explanation
Indices: 39876--39917 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
39866 TCTCTCGATC
*
39876 TTTAAATTTATAATAAA
1 TTTAAATTTAGAATAAA
*
39893 TTTAATTTTAGAATAAA
1 TTTAAATTTAGAATAAA
39910 TTTAAATT
1 TTTAAATT
39918 CTGTTAGGCC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (17 bp):
TTTAAATTTAGAATAAA
Found at i:47827 original size:16 final size:16
Alignment explanation
Indices: 47806--47864 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
47796 TGATTATAAC
*
47806 TCTATTCCATTACAGT
1 TCTATTCCATTACAAT
*
47822 TTTATTCCATTACAAT
1 TCTATTCCATTACAAT
*
47838 TCTATTTCATTACAAT
1 TCTATTCCATTACAAT
* *
47854 CCTATTACATT
1 TCTATTCCATT
47865 CTAGTGAATC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.29, C:0.22, G:0.02, T:0.47
Consensus pattern (16 bp):
TCTATTCCATTACAAT
Found at i:57738 original size:14 final size:15
Alignment explanation
Indices: 57719--57747 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
57709 AGGGGACTCT
57719 TAAAGAAG-AGGACG
1 TAAAGAAGAAGGACG
57733 TAAAGAAGAAGGACG
1 TAAAGAAGAAGGACG
57748 ATGCCCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.52, C:0.07, G:0.34, T:0.07
Consensus pattern (15 bp):
TAAAGAAGAAGGACG
Found at i:58738 original size:13 final size:12
Alignment explanation
Indices: 58720--58758 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
58710 CACAAAATGA
58720 AAGAAGAAGAAAG
1 AAGAAGAA-AAAG
58733 AAGAAGAAAAGAG
1 AAGAAGAAAA-AG
58746 AA-AAGAAAAAG
1 AAGAAGAAAAAG
58757 AA
1 AA
58759 ATATATTGCC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
11 4 0.16
12 9 0.36
13 12 0.48
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (12 bp):
AAGAAGAAAAAG
Found at i:62718 original size:78 final size:75
Alignment explanation
Indices: 62631--62784 Score: 191
Period size: 75 Copynumber: 2.0 Consensus size: 75
62621 CAACATCAAC
* * *
62631 CCAAATAAACAATATGAGTCCAAGTGAACAACAACAACAATACAACAACATAATAATAAAAAAAA
1 CCAAATAAACAACACGAGTCAAAGT--A-AACAACAACAATACAACAACATAATAATAAAAAAAA
62696 CATAAGAAAAAGT
63 CATAAGAAAAAGT
* * * * * *
62709 CCAAGTAAACAACCCGAGTCAAAGTAAACAACAACAATACAATAAGATTATAATAAAAAAAATAT
1 CCAAATAAACAACACGAGTCAAAGTAAACAACAACAATACAACAACATAATAATAAAAAAAACAT
*
62774 AAGCAAAAGT
66 AAGAAAAAGT
62784 C
1 C
62785 TAAAATAGAG
Statistics
Matches: 66, Mismatches: 10, Indels: 3
0.84 0.13 0.04
Matches are distributed among these distances:
75 45 0.68
76 1 0.02
78 20 0.30
ACGTcount: A:0.60, C:0.17, G:0.08, T:0.15
Consensus pattern (75 bp):
CCAAATAAACAACACGAGTCAAAGTAAACAACAACAATACAACAACATAATAATAAAAAAAACAT
AAGAAAAAGT
Found at i:62877 original size:14 final size:16
Alignment explanation
Indices: 62838--62889 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 16
62828 AAATAAAAAG
62838 AACACAACAAATTCTAAT
1 AACACAACAAA--CTAAT
62856 AA-ACCAAC-AAC-AAT
1 AACA-CAACAAACTAAT
62870 AACACAACAAACTAAT
1 AACACAACAAACTAAT
62886 AACA
1 AACA
62890 ATAACACATC
Statistics
Matches: 30, Mismatches: 0, Indels: 10
0.75 0.00 0.25
Matches are distributed among these distances:
14 9 0.30
15 5 0.17
16 7 0.23
17 3 0.10
18 6 0.20
ACGTcount: A:0.62, C:0.25, G:0.00, T:0.13
Consensus pattern (16 bp):
AACACAACAAACTAAT
Found at i:74462 original size:60 final size:59
Alignment explanation
Indices: 74314--74462 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 59
74304 GAATTTACAA
* * * * *
74314 TTTTTCTTAATTTAGTACCTAAATTTTTTTTACCTAATTTGATACCTGAACTTAACACT
1 TTTTTCCTAATTTGGTACTTAAATTTTTTTGACCCAATTTGATACCTGAACTTAACACT
* * * * ** *
74373 TTTTT-CTAATTTGGTATTTAAACTCTTTTTGGACCCAATTTGGTACTTGAACTTGGCATT
1 TTTTTCCTAATTTGGTACTTAAA-T-TTTTTTGACCCAATTTGATACCTGAACTTAACACT
*
74433 TTTTTCCTAATTTGGTACTTAAGTTTTTTT
1 TTTTTCCTAATTTGGTACTTAAATTTTTTT
74463 TTTAATTCAA
Statistics
Matches: 72, Mismatches: 15, Indels: 6
0.77 0.16 0.06
Matches are distributed among these distances:
58 13 0.18
59 11 0.15
60 33 0.46
61 15 0.21
ACGTcount: A:0.23, C:0.15, G:0.10, T:0.52
Consensus pattern (59 bp):
TTTTTCCTAATTTGGTACTTAAATTTTTTTGACCCAATTTGATACCTGAACTTAACACT
Found at i:79995 original size:53 final size:53
Alignment explanation
Indices: 79937--80039 Score: 197
Period size: 53 Copynumber: 1.9 Consensus size: 53
79927 AGGATTAAAA
*
79937 TTTCAAAATTCAAAAAGTATAAAAACTAAAATTGATCAAATTAAAATACAAAT
1 TTTCAAAATTCAAAAAATATAAAAACTAAAATTGATCAAATTAAAATACAAAT
79990 TTTCAAAATTCAAAAAATATAAAAACTAAAATTGATCAAATTAAAATACA
1 TTTCAAAATTCAAAAAATATAAAAACTAAAATTGATCAAATTAAAATACA
80040 TGTACTAATT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 49 1.00
ACGTcount: A:0.59, C:0.10, G:0.03, T:0.28
Consensus pattern (53 bp):
TTTCAAAATTCAAAAAATATAAAAACTAAAATTGATCAAATTAAAATACAAAT
Found at i:81633 original size:10 final size:10
Alignment explanation
Indices: 81618--81651 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
81608 TTATTAATTT
81618 AAAATTTTTA
1 AAAATTTTTA
*
81628 AAAATTTTAA
1 AAAATTTTTA
*
81638 AAAATTTATA
1 AAAATTTTTA
81648 AAAA
1 AAAA
81652 AAATTTTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (10 bp):
AAAATTTTTA
Found at i:86296 original size:15 final size:16
Alignment explanation
Indices: 86273--86303 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
86263 CTAGTAGATT
86273 GATTGGTTTAAAATTG
1 GATTGGTTTAAAATTG
86289 GATT-GTTTAAAATTG
1 GATTGGTTTAAAATTG
86304 TCAAATAGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.32, C:0.00, G:0.23, T:0.45
Consensus pattern (16 bp):
GATTGGTTTAAAATTG
Found at i:87983 original size:20 final size:20
Alignment explanation
Indices: 87953--87991 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
87943 TTCTACATCT
87953 ATATTTATA-TTTTAAAATA
1 ATATTTATATTTTTAAAATA
87972 ATATTATATATTTTTAAAAT
1 ATATT-TATATTTTTAAAAT
87992 TTTATTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 4 0.22
21 9 0.50
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATATTTATATTTTTAAAATA
Found at i:89213 original size:20 final size:19
Alignment explanation
Indices: 89190--89237 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 19
89180 AAGCTCTTTT
89190 AAAATTTAAAATTAATAAAA
1 AAAATTTAAAATT-ATAAAA
* *
89210 AAAATCATAAAATTATAAAC
1 AAAAT-TTAAAATTATAAAA
89230 AAAATTTA
1 AAAATTTA
89238 TAAAAAAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
19 2 0.08
20 15 0.62
21 7 0.29
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (19 bp):
AAAATTTAAAATTATAAAA
Found at i:89233 original size:12 final size:11
Alignment explanation
Indices: 89197--89253 Score: 55
Period size: 12 Copynumber: 5.1 Consensus size: 11
89187 TTTAAAATTT
89197 AAAATTAATAAA
1 AAAATT-ATAAA
* *
89209 AAAA--ATCAT
1 AAAATTATAAA
89218 AAAATTATAAA
1 AAAATTATAAA
89229 CAAAATTTATAAA
1 -AAAA-TTATAAA
89242 AAAATTATAAA
1 AAAATTATAAA
89253 A
1 A
89254 TTATAATTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
9 7 0.19
11 11 0.30
12 12 0.32
13 7 0.19
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATTATAAA
Found at i:89242 original size:21 final size:21
Alignment explanation
Indices: 89196--89234 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
89186 TTTTAAAATT
89196 TAAAATTAATAAAAAAAATCA
1 TAAAATTAATAAAAAAAATCA
*
89217 TAAAATT-ATAAACAAAAT
1 TAAAATTAATAAAAAAAAT
89235 TTATAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAATTAATAAAAAAAATCA
Found at i:89252 original size:32 final size:33
Alignment explanation
Indices: 89197--89259 Score: 101
Period size: 32 Copynumber: 1.9 Consensus size: 33
89187 TTTAAAATTT
89197 AAAATTAATAAAAAAAATCATAAAATTATAAAC
1 AAAATTAATAAAAAAAATCATAAAATTATAAAC
* *
89230 AAAATTTAT-AAAAAAATTATAAAATTATAA
1 AAAATTAATAAAAAAAATCATAAAATTATAA
89260 TTTTTATTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
32 20 0.71
33 8 0.29
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (33 bp):
AAAATTAATAAAAAAAATCATAAAATTATAAAC
Found at i:89630 original size:52 final size:52
Alignment explanation
Indices: 89552--89652 Score: 193
Period size: 52 Copynumber: 1.9 Consensus size: 52
89542 ATAAAAGAGT
89552 AAAGATTAAATTGAATAAATTAATAAAAGTCAAGGGTTATATTTGCTATCGA
1 AAAGATTAAATTGAATAAATTAATAAAAGTCAAGGGTTATATTTGCTATCGA
*
89604 AAAGATTAAATTGAATAAATTTATAAAAGTCAAGGGTTATATTTGCTAT
1 AAAGATTAAATTGAATAAATTAATAAAAGTCAAGGGTTATATTTGCTAT
89653 TACGCTTTAT
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.46, C:0.05, G:0.15, T:0.35
Consensus pattern (52 bp):
AAAGATTAAATTGAATAAATTAATAAAAGTCAAGGGTTATATTTGCTATCGA
Found at i:91840 original size:31 final size:31
Alignment explanation
Indices: 91805--91883 Score: 97
Period size: 31 Copynumber: 2.5 Consensus size: 31
91795 AACCTCCAAA
*
91805 AGTTTAAGTACCAACTTTAA-AAAAAGTGTTT
1 AGTTTAAGTACCAA-ATTAAGAAAAAGTGTTT
**
91836 AGTTTAAGTACCAAATTAAGAAAAAGTGTCA
1 AGTTTAAGTACCAAATTAAGAAAAAGTGTTT
* *
91867 AGTTTGAGTATCAAATT
1 AGTTTAAGTACCAAATT
91884 GGACAAAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 4 0.10
31 38 0.90
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.33
Consensus pattern (31 bp):
AGTTTAAGTACCAAATTAAGAAAAAGTGTTT
Found at i:91917 original size:90 final size:90
Alignment explanation
Indices: 91753--91922 Score: 227
Period size: 90 Copynumber: 1.9 Consensus size: 90
91743 AAAAGATTAG
* *** *
91753 GTACCAAATTAGGAAAAAGAGTCAAGTTAAGGTATCAAATTGAACCTCCAAAAGTTTAAGTACCA
1 GTACCAAATTAAGAAAAAGAGTCAAGTTAAGGTATCAAATTGAACCAAAAAAAATTTAAGTACCA
*
91818 ACTTTAAAAAAAGTGTTTAGTTTAA
66 AATTTAAAAAAAGTGTTTAGTTTAA
* * * *
91843 GTACCAAATTAAGAAAAAGTGTCAAGTT-TGAGTATCAAATTGGA-CAAAAAAAATTTAAGTACT
1 GTACCAAATTAAGAAAAAGAGTCAAGTTAAG-GTATCAAATTGAACCAAAAAAAATTTAAGTACC
91906 AAATTTAAAAAAAGTGT
65 AAATTTAAAAAAAGTGT
91923 CAAGTTCATG
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
89 31 0.45
90 38 0.55
ACGTcount: A:0.47, C:0.10, G:0.15, T:0.28
Consensus pattern (90 bp):
GTACCAAATTAAGAAAAAGAGTCAAGTTAAGGTATCAAATTGAACCAAAAAAAATTTAAGTACCA
AATTTAAAAAAAGTGTTTAGTTTAA
Found at i:93361 original size:32 final size:31
Alignment explanation
Indices: 93312--93371 Score: 77
Period size: 32 Copynumber: 1.9 Consensus size: 31
93302 CATCCAAACC
*
93312 AAACCTATAAATTTTCTTTATTTTGTGTTTCA
1 AAACCTATAAATTTTCTTT-TTTGGTGTTTCA
*
93344 AAACTTAT-AATTATTCTTTTTTGGTGTT
1 AAACCTATAAATT-TTCTTTTTTGGTGTT
93372 GGGAGCAGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 12 0.48
32 13 0.52
ACGTcount: A:0.27, C:0.10, G:0.08, T:0.55
Consensus pattern (31 bp):
AAACCTATAAATTTTCTTTTTTGGTGTTTCA
Found at i:95258 original size:17 final size:17
Alignment explanation
Indices: 95235--95297 Score: 83
Period size: 17 Copynumber: 3.6 Consensus size: 17
95225 ACCCAACAGG
95235 ATTTAAATTTACTTTAA
1 ATTTAAATTTACTTTAA
* *
95252 GTTTAAATTTACTTAAA
1 ATTTAAATTTACTTTAA
95269 ATTTAAATTTA-TTATAA
1 ATTTAAATTTACTT-TAA
95286 ATTTAAAGTTTA
1 ATTTAAA-TTTA
95298 AATCTATTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
16 2 0.05
17 34 0.85
18 4 0.10
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
ATTTAAATTTACTTTAA
Found at i:95297 original size:24 final size:23
Alignment explanation
Indices: 95264--95310 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
95254 TTAAATTTAC
*
95264 TTAAAATTTAAATTTATTATAAAT
1 TTAAAATTTAAATCTATT-TAAAT
*
95288 TTAAAGTTTAAATCTATTTAAAT
1 TTAAAATTTAAATCTATTTAAAT
95311 AAAGTCCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.24
24 16 0.76
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (23 bp):
TTAAAATTTAAATCTATTTAAAT
Found at i:95299 original size:7 final size:6
Alignment explanation
Indices: 95235--95300 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
95225 ACCCAACAGG
* * * *
95235 ATTTAA ATTT-A CTTTAA GTTTAA ATTT-A CTTAAA ATTTAA ATTT--
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
95279 ATTATAA ATTTAA AGTTTAA AT
1 ATT-TAA ATTTAA A-TTTAA AT
95301 CTATTTAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
4 3 0.06
5 8 0.17
6 27 0.57
7 9 0.19
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.50
Consensus pattern (6 bp):
ATTTAA
Found at i:95996 original size:3 final size:3
Alignment explanation
Indices: 95988--96027 Score: 62
Period size: 3 Copynumber: 13.0 Consensus size: 3
95978 TTAATAGCAT
*
95988 TAA TAA TAA TAA TAA TAA TAA TAAA TAA TAC TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
96028 CATTAATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:97114 original size:30 final size:30
Alignment explanation
Indices: 96998--97105 Score: 132
Period size: 30 Copynumber: 3.7 Consensus size: 30
96988 CCCTGAAGGT
* * *
96998 CCCCCAAACTTCCTAAAATTCTATTTTTGA
1 CCCCGAAACTTCCAAAAATTCCATTTTTGA
97028 CCCCGAAACTTCCAAAAATTCCA-TTTT-A
1 CCCCGAAACTTCCAAAAATTCCATTTTTGA
*
97056 CCCCCG-AACTTCCCAAAATTCCATTTTTGA
1 -CCCCGAAACTTCCAAAAATTCCATTTTTGA
* *
97086 CCCTGAAACTTTCAAAAATT
1 CCCCGAAACTTCCAAAAATT
97106 ACTATTTTGC
Statistics
Matches: 67, Mismatches: 7, Indels: 8
0.82 0.09 0.10
Matches are distributed among these distances:
28 17 0.25
29 17 0.25
30 33 0.49
ACGTcount: A:0.32, C:0.31, G:0.05, T:0.31
Consensus pattern (30 bp):
CCCCGAAACTTCCAAAAATTCCATTTTTGA
Found at i:97199 original size:58 final size:59
Alignment explanation
Indices: 97012--97199 Score: 170
Period size: 58 Copynumber: 3.2 Consensus size: 59
97002 CAAACTTCCT
* * * *
97012 AAAATTCTATTTTTGACCCCGAAACT-TCCAAAAATT-CCATTTTACCCCCGAACT-TCCC
1 AAAATTCCATTTTCGACCCTGAAACTCT-CAAAAATTACCATTTTACCCCCGAA-TGTCCA
* * * * * *
97070 AAAATTCCATTTTTGACCCTGAAACTTTCAAAAATTACTATTTTGCCTCCGGATGTCCA
1 AAAATTCCATTTTCGACCCTGAAACTCTCAAAAATTACCATTTTACCCCCGAATGTCCA
* * * * * *
97129 GAAACTCAATTTTCGA-CCTAGAAACTCTC-GAAATTACCCTTTTACCCCCGAATGTCTA
1 AAAATTCCATTTTCGACCCT-GAAACTCTCAAAAATTACCATTTTACCCCCGAATGTCCA
97187 AAAATTCCATTTT
1 AAAATTCCATTTT
97200 TAACCCTAAA
Statistics
Matches: 104, Mismatches: 22, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
58 68 0.65
59 36 0.35
ACGTcount: A:0.31, C:0.28, G:0.08, T:0.33
Consensus pattern (59 bp):
AAAATTCCATTTTCGACCCTGAAACTCTCAAAAATTACCATTTTACCCCCGAATGTCCA
Found at i:97276 original size:28 final size:27
Alignment explanation
Indices: 97215--97276 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
97205 CTAAATTTTC
*
97215 CCAAAAATACCATTTTGCCCCTGGGAAT
1 CCAAAAATACCATTTTGCCCCCGGG-AT
*
97243 CCAAAATTACCATTTTGCCCCCGGTG-T
1 CCAAAAATACCATTTTGCCCCCGG-GAT
97270 CCAAAAA
1 CCAAAAA
97277 GTCTCATTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
27 7 0.23
28 22 0.73
29 1 0.03
ACGTcount: A:0.32, C:0.31, G:0.13, T:0.24
Consensus pattern (27 bp):
CCAAAAATACCATTTTGCCCCCGGGAT
Found at i:101918 original size:42 final size:42
Alignment explanation
Indices: 101870--102091 Score: 187
Period size: 43 Copynumber: 5.2 Consensus size: 42
101860 AAAAAATGCT
* *
101870 GCTAAAGAATATGGTCTTTAGCGGCGCTTTATCACAAACGTC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTTATCACAAACGCC
* * * *
101912 ACTAAAGAACATGGTTTTTACCGGCGCTTTCCA-CACAAATGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTTT--ATCACAAACGCC
** * * *
101955 GCTAAAGAACATGGTCTTTAGTAGCTCTTCTACCACAAATGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGCTT-TATCACAAACGCC
* * * *
101998 GCTAAAGAAAAAGGTTTTTAGCGACGCTTTTACTCACAAACGCC
1 GCTAAAGAACATGGTCTTTAGCGGCGC-TTTA-TCACAAACGCC
* * * * *
102042 GCTATAGATA-ATGTTCTTTAGCGGCGGTTTTTCCACAAACTCC
1 GCTAAAGA-ACATGGTCTTTAGCGGCGCTTTAT-CACAAACGCC
102085 GCTAAAG
1 GCTAAAG
102092 TTAGCAGATT
Statistics
Matches: 142, Mismatches: 30, Indels: 15
0.76 0.16 0.08
Matches are distributed among these distances:
42 28 0.20
43 81 0.57
44 32 0.23
45 1 0.01
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (42 bp):
GCTAAAGAACATGGTCTTTAGCGGCGCTTTATCACAAACGCC
Found at i:102177 original size:15 final size:15
Alignment explanation
Indices: 102157--102189 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
102147 TTTTCCTATA
102157 AATTCAAATCCAACC
1 AATTCAAATCCAACC
*
102172 AATTCAAATTCAACC
1 AATTCAAATCCAACC
102187 AAT
1 AAT
102190 AACTTCAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.48, C:0.27, G:0.00, T:0.24
Consensus pattern (15 bp):
AATTCAAATCCAACC
Found at i:102453 original size:21 final size:21
Alignment explanation
Indices: 102429--102468 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
102419 TTTCGCAACT
* *
102429 CTCGCTGCTGCCTCTGCTTCC
1 CTCGCTGCTACCTCCGCTTCC
*
102450 CTCGTTGCTACCTCCGCTT
1 CTCGCTGCTACCTCCGCTT
102469 TAAGTTGTAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.03, C:0.45, G:0.17, T:0.35
Consensus pattern (21 bp):
CTCGCTGCTACCTCCGCTTCC
Found at i:107883 original size:18 final size:18
Alignment explanation
Indices: 107862--107913 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
107852 TTTAAATTTT
107862 AAAATATTTATTAGTGAC
1 AAAATATTTATTAGTGAC
107880 AAAAT-TTTACTTA---A-
1 AAAATATTTA-TTAGTGAC
*
107894 AAAATATATATTAGTGAC
1 AAAATATTTATTAGTGAC
107912 AA
1 AA
107914 CATTTTACTT
Statistics
Matches: 27, Mismatches: 1, Indels: 12
0.68 0.03 0.30
Matches are distributed among these distances:
14 8 0.30
15 4 0.15
17 5 0.19
18 10 0.37
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.37
Consensus pattern (18 bp):
AAAATATTTATTAGTGAC
Found at i:107899 original size:32 final size:32
Alignment explanation
Indices: 107862--107926 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
107852 TTTAAATTTT
*
107862 AAAATATTTATTAGTGACAAAATTTTACTTAA
1 AAAATATATATTAGTGACAAAATTTTACTTAA
*
107894 AAAATATATATTAGTGACAACATTTTACTTAA
1 AAAATATATATTAGTGACAAAATTTTACTTAA
107926 A
1 A
107927 TATTTGAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (32 bp):
AAAATATATATTAGTGACAAAATTTTACTTAA
Found at i:108015 original size:14 final size:15
Alignment explanation
Indices: 107990--108053 Score: 69
Period size: 14 Copynumber: 4.2 Consensus size: 15
107980 TGGGTTGTTT
107990 TTTTATAATTAAATA
1 TTTTATAATTAAATA
108005 TTTTA-AATTAAATA
1 TTTTATAATTAAATA
* *
108019 TTTAATTAACT-AATA
1 TTTTA-TAATTAAATA
108034 CTGTTTATAATTAAATA
1 -T-TTTATAATTAAATA
108051 TTT
1 TTT
108054 AATTTAAAAT
Statistics
Matches: 40, Mismatches: 4, Indels: 10
0.74 0.07 0.19
Matches are distributed among these distances:
14 13 0.32
15 11 0.28
16 9 0.22
17 7 0.17
ACGTcount: A:0.44, C:0.03, G:0.02, T:0.52
Consensus pattern (15 bp):
TTTTATAATTAAATA
Found at i:108063 original size:14 final size:15
Alignment explanation
Indices: 108046--108077 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
108036 GTTTATAATT
108046 AAATATTTAATT-TA
1 AAATATTTAATTATA
108060 AAATATTTAATTATA
1 AAATATTTAATTATA
108075 AAA
1 AAA
108078 AACAACCCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
AAATATTTAATTATA
Found at i:111158 original size:19 final size:20
Alignment explanation
Indices: 111119--111159 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
111109 TTAATGATAT
*
111119 TTTATTAAATGAAAATAATA
1 TTTAATAAATGAAAATAATA
*
111139 TTTAATAAAT-AAAATTATA
1 TTTAATAAATGAAAATAATA
111158 TT
1 TT
111160 ATAAAATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 10 0.53
20 9 0.47
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (20 bp):
TTTAATAAATGAAAATAATA
Found at i:112251 original size:41 final size:40
Alignment explanation
Indices: 111930--112243 Score: 421
Period size: 41 Copynumber: 7.7 Consensus size: 40
111920 GCTCTGACCT
* *
111930 AAGCGCCGCTAATGGCCTGACTTTTAGCGGCGCTTATGAGAA
1 AAGCGCCGCTAAT-GCCTGACCTTTAGCGGCGCTTATG-GGA
* * * *
111972 AAGCGTCGCTAATGACCAGACCTTTAGCGGTGCTTATAGGA
1 AAGCGCCGCTAATG-CCTGACCTTTAGCGGCGCTTATGGGA
*
112013 AAGCGCCGCTAATGCCTTGACCTTTAGTGGCGCTTATGGGA
1 AAGCGCCGCTAATGCC-TGACCTTTAGCGGCGCTTATGGGA
*
112054 AAGCGCCGCTAATGCCTTGACCTTTAGCGACGCTTATGGGA
1 AAGCGCCGCTAATGCC-TGACCTTTAGCGGCGCTTATGGGA
* **
112095 AAGCGCCACTAATGCCTTGACCTTTAGCGGCGCTTATACGA
1 AAGCGCCGCTAATGCC-TGACCTTTAGCGGCGCTTATGGGA
* * *
112136 ATGCGCTGCTAATGACCTGACCTTTAGCGACGCTTATGGGA
1 AAGCGCCGCTAATG-CCTGACCTTTAGCGGCGCTTATGGGA
*
112177 AAGCGCCGCTAATGCCTGACCTTTAGTGGCGCTTATGGGA
1 AAGCGCCGCTAATGCCTGACCTTTAGCGGCGCTTATGGGA
112217 AAGCGCCGCTAATGACCTGACCTTTAG
1 AAGCGCCGCTAATG-CCTGACCTTTAG
112244 TAACGCTTTG
Statistics
Matches: 241, Mismatches: 27, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
40 40 0.17
41 168 0.70
42 33 0.14
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (40 bp):
AAGCGCCGCTAATGCCTGACCTTTAGCGGCGCTTATGGGA
Found at i:112354 original size:94 final size:93
Alignment explanation
Indices: 112192--112379 Score: 358
Period size: 94 Copynumber: 2.0 Consensus size: 93
112182 CCGCTAATGC
112192 CTGACCTTTAGTGGCGCTTATGGGAAAGCGCCGCTAATGACCTGACCTTTAGTAACGCTTTGACA
1 CTGACCTTTAGTGGCGCTTATGGGAAAGCGCCGCTAATGACCTGACCTTTAGTAACGCTTTGACA
*
112257 TAAACACCTCTAATGGTCAAAGAATTAG
66 TAAACACCTCTAAAGGTCAAAGAATTAG
112285 CNTGACCTTTAGTGGCGCTTATGGGAAAGCGCCGCTAATGACCTGACCTTTAGTAACGCTTTGAC
1 C-TGACCTTTAGTGGCGCTTATGGGAAAGCGCCGCTAATGACCTGACCTTTAGTAACGCTTTGAC
112350 ATAAACACCTCTAAAGGTCAAAGAATTAG
65 ATAAACACCTCTAAAGGTCAAAGAATTAG
112379 C
1 C
112380 GGCGCTTTCC
Statistics
Matches: 93, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 1 0.01
94 92 0.99
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (93 bp):
CTGACCTTTAGTGGCGCTTATGGGAAAGCGCCGCTAATGACCTGACCTTTAGTAACGCTTTGACA
TAAACACCTCTAAAGGTCAAAGAATTAG
Found at i:112423 original size:41 final size:40
Alignment explanation
Indices: 112378--112509 Score: 142
Period size: 40 Copynumber: 3.3 Consensus size: 40
112368 CAAAGAATTA
** * *
112378 GCGGCGCTTTCCCAATAAATGCCGCTACTGCTTTACCTTTT
1 GCGGCGCTTTCGGAA-AAACGCCGCTATTGCTTTACCTTTT
*
112419 GCGGCGCTTAT-GGAAAAACGCCGCTATTGCTTTACCTTCT
1 GCGGCGCTT-TCGGAAAAACGCCGCTATTGCTTTACCTTTT
* * *
112459 GGGGCG-TTTATGGAAAAACGCCGCTATTGCTTTACTTTTT
1 GCGGCGCTTT-CGGAAAAACGCCGCTATTGCTTTACCTTTT
*
112499 GCGGCGTTTTC
1 GCGGCGCTTTC
112510 TTTCCAAACG
Statistics
Matches: 77, Mismatches: 10, Indels: 9
0.80 0.10 0.09
Matches are distributed among these distances:
38 1 0.01
39 2 0.03
40 59 0.77
41 14 0.18
42 1 0.01
ACGTcount: A:0.17, C:0.26, G:0.23, T:0.34
Consensus pattern (40 bp):
GCGGCGCTTTCGGAAAAACGCCGCTATTGCTTTACCTTTT
Found at i:112505 original size:40 final size:40
Alignment explanation
Indices: 112398--112507 Score: 175
Period size: 40 Copynumber: 2.8 Consensus size: 40
112388 CCCAATAAAT
* *
112398 GCCGCTACTGCTTTACCTTTTGCGGCGCTTATGGAAAAAC
1 GCCGCTATTGCTTTACCTTTTGCGGCGTTTATGGAAAAAC
* *
112438 GCCGCTATTGCTTTACCTTCTGGGGCGTTTATGGAAAAAC
1 GCCGCTATTGCTTTACCTTTTGCGGCGTTTATGGAAAAAC
*
112478 GCCGCTATTGCTTTACTTTTTGCGGCGTTT
1 GCCGCTATTGCTTTACCTTTTGCGGCGTTT
112508 TCTTTCCAAA
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (40 bp):
GCCGCTATTGCTTTACCTTTTGCGGCGTTTATGGAAAAAC
Found at i:112744 original size:15 final size:16
Alignment explanation
Indices: 112724--112761 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
112714 TAGGTGGAGC
112724 AATAATATTATTA-AA
1 AATAATATTATTACAA
*
112739 AATAATATTTTTATCAA
1 AATAATATTATTA-CAA
112756 AATAAT
1 AATAAT
112762 TATAATAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 12 0.60
17 8 0.40
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
AATAATATTATTACAA
Found at i:112958 original size:36 final size:37
Alignment explanation
Indices: 112904--112975 Score: 92
Period size: 37 Copynumber: 2.0 Consensus size: 37
112894 CTAATTTAAC
* **
112904 TTAAAAAATAGTTATAA-TTTAATTTAAAATTATTAG
1 TTAAAAAATAGTGATAATTTTAAAATAAAATTATTAG
* *
112940 TTAAAAAATTGTGCTAATTTTAAAATAAAATTATTA
1 TTAAAAAATAGTGATAATTTTAAAATAAAATTATTA
112976 CTTGGATAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 14 0.47
37 16 0.53
ACGTcount: A:0.50, C:0.01, G:0.06, T:0.43
Consensus pattern (37 bp):
TTAAAAAATAGTGATAATTTTAAAATAAAATTATTAG
Found at i:113627 original size:59 final size:59
Alignment explanation
Indices: 113535--113653 Score: 238
Period size: 59 Copynumber: 2.0 Consensus size: 59
113525 TTTTAACAAC
113535 TAACTAGCACATATATCTTAATATTCCCCCATCAACTTTTCTTCTCCACTCTTGTTTTA
1 TAACTAGCACATATATCTTAATATTCCCCCATCAACTTTTCTTCTCCACTCTTGTTTTA
113594 TAACTAGCACATATATCTTAATATTCCCCCATCAACTTTTCTTCTCCACTCTTGTTTTA
1 TAACTAGCACATATATCTTAATATTCCCCCATCAACTTTTCTTCTCCACTCTTGTTTTA
113653 T
1 T
113654 CCAAGCTGTA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 60 1.00
ACGTcount: A:0.25, C:0.29, G:0.03, T:0.43
Consensus pattern (59 bp):
TAACTAGCACATATATCTTAATATTCCCCCATCAACTTTTCTTCTCCACTCTTGTTTTA
Found at i:119124 original size:21 final size:21
Alignment explanation
Indices: 119089--119138 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
119079 TACAGATTTT
* * *
119089 TACCAATATATGTATTAGTTC
1 TACCAATACAAGTATAAGTTC
*
119110 TACCAATACAAGTATAATTTC
1 TACCAATACAAGTATAAGTTC
*
119131 TAACAATA
1 TACCAATA
119139 AATGTCATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.16, G:0.06, T:0.36
Consensus pattern (21 bp):
TACCAATACAAGTATAAGTTC
Found at i:120082 original size:51 final size:51
Alignment explanation
Indices: 119946--120084 Score: 134
Period size: 54 Copynumber: 2.7 Consensus size: 51
119936 TCGGACCTTT
* * * * * *
119946 TAATCCGTAAAGGATCCATATACTTACAATGACACTTAGTCATTGAACCTT
1 TAATCCGTAAAGGATTCATATACTCACGATGACACTTAATCATCGAACCTC
** * * * *
119997 TAAATCTATAAAAGGATTTCATATACCCATGATGACTCTTAATCATCGAATCTC
1 T-AATCCGT-AAAGGA-TTCATATACTCACGATGACACTTAATCATCGAACCTC
*
120051 TAATCCGTAAAGGATTCATTTACTCACGATGACA
1 TAATCCGTAAAGGATTCATATACTCACGATGACA
120085 TAGTCATCGG
Statistics
Matches: 67, Mismatches: 18, Indels: 6
0.74 0.20 0.07
Matches are distributed among these distances:
51 17 0.25
52 11 0.16
53 11 0.16
54 28 0.42
ACGTcount: A:0.36, C:0.21, G:0.12, T:0.32
Consensus pattern (51 bp):
TAATCCGTAAAGGATTCATATACTCACGATGACACTTAATCATCGAACCTC
Found at i:123629 original size:2 final size:2
Alignment explanation
Indices: 123609--123645 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
123599 TGATGAGGAA
123609 AT AT A- AT AT -T AT A- 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 AT AT AT AT AT AT AT
123646 TTTTTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
1 3 0.09
2 29 0.91
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:135868 original size:14 final size:14
Alignment explanation
Indices: 135849--135900 Score: 50
Period size: 14 Copynumber: 3.5 Consensus size: 14
135839 TCTTGAAAAA
**
135849 AAAAATAAGGAAGT
1 AAAAATAAAAAAGT
135863 AAAAATAAAAAAGT
1 AAAAATAAAAAAGT
135877 AAAAAAGTAAAAAAAGT
1 -AAAAA-T-AAAAAAGT
*
135894 GAAAATA
1 AAAAATA
135901 CAAGACCCTC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 13 0.41
15 6 0.19
16 5 0.16
17 8 0.25
ACGTcount: A:0.73, C:0.00, G:0.13, T:0.13
Consensus pattern (14 bp):
AAAAATAAAAAAGT
Found at i:135898 original size:8 final size:8
Alignment explanation
Indices: 135859--135890 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
135849 AAAAATAAGG
135859 AAGT-AAA
1 AAGTAAAA
135866 AA-TAAAA
1 AAGTAAAA
135873 AAGTAAAA
1 AAGTAAAA
135881 AAGTAAAA
1 AAGTAAAA
135889 AA
1 AA
135891 AGTGAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
6 1 0.04
7 7 0.30
8 15 0.65
ACGTcount: A:0.78, C:0.00, G:0.09, T:0.12
Consensus pattern (8 bp):
AAGTAAAA
Found at i:138432 original size:12 final size:12
Alignment explanation
Indices: 138419--138519 Score: 84
Period size: 12 Copynumber: 8.8 Consensus size: 12
138409 CTAAATAACC
*
138419 AAAATAACAACC
1 AAAATAACAACA
*
138431 AAAACAACAACA
1 AAAATAACAACA
*
138443 AGAAT---AACA
1 AAAATAACAACA
*
138452 ATAA-AACAACA
1 AAAATAACAACA
**
138463 AAAATTGCAACA
1 AAAATAACAACA
* *
138475 AAAATAACAGCT
1 AAAATAACAACA
138487 AAAATAACAACA
1 AAAATAACAACA
* *
138499 AAAACAACAATA
1 AAAATAACAACA
138511 AAAATAACA
1 AAAATAACA
138520 TCATCAAAAC
Statistics
Matches: 68, Mismatches: 17, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
9 7 0.10
11 7 0.10
12 54 0.79
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (12 bp):
AAAATAACAACA
Found at i:138448 original size:24 final size:23
Alignment explanation
Indices: 138418--138519 Score: 93
Period size: 24 Copynumber: 4.4 Consensus size: 23
138408 TCTAAATAAC
*
138418 CAAAATAACAACCAAAACAACAA
1 CAAAATAACAACAAAAACAACAA
*
138441 CAAGAATAACAA-TAAAACAAC-A
1 CAA-AATAACAACAAAAACAACAA
** * *
138463 -AAAATTGCAACAAAAATAACAG
1 CAAAATAACAACAAAAACAACAA
138485 CTAAAATAACAACAAAAACAACAA
1 C-AAAATAACAACAAAAACAACAA
*
138509 TAAAAATAACA
1 -CAAAATAACA
138520 TCATCAAAAC
Statistics
Matches: 62, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
20 6 0.10
21 9 0.15
22 1 0.02
23 11 0.18
24 35 0.56
ACGTcount: A:0.69, C:0.19, G:0.03, T:0.10
Consensus pattern (23 bp):
CAAAATAACAACAAAAACAACAA
Found at i:146967 original size:63 final size:62
Alignment explanation
Indices: 146835--146968 Score: 164
Period size: 63 Copynumber: 2.1 Consensus size: 62
146825 TTTAAGTTAT
** *
146835 ATTTGCATTTTCATTTTCATTTTGGAGAAAAGCACATTCTTTTTCAAACGATTCTGTTTCTCC
1 ATTT-CATTTTCATTTTCATTTTGGAGAAAAGCACATAATTTTTCAAACGATTCTATTTCTCC
* *
146898 ATTTTCATTTTCATTTTCATTTTGGAGAAAA-C-CATAATTATTTCCAAATGTTTCATATTTCTC
1 A-TTTCATTTTCATTTTCATTTTGGAGAAAAGCACATAATT-TTT-CAAACGATTC-TATTTCTC
146961 C
62 C
146962 ATTTCAT
1 ATTTCAT
146969 CATTTATATT
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
61 5 0.08
62 4 0.06
63 41 0.66
64 12 0.19
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (62 bp):
ATTTCATTTTCATTTTCATTTTGGAGAAAAGCACATAATTTTTCAAACGATTCTATTTCTCC
Found at i:151497 original size:20 final size:20
Alignment explanation
Indices: 151474--151519 Score: 53
Period size: 20 Copynumber: 2.4 Consensus size: 20
151464 TGGGTTTATG
151474 ATATATATT-ATAAAAATAAT
1 ATATATATTCATAAAAA-AAT
151494 ATAT-TAATTCATAAAAAAAT
1 ATATAT-ATTCATAAAAAAAT
151514 AT-TATA
1 ATATATA
151520 GTTTTTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 3 0.13
20 13 0.57
21 7 0.30
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (20 bp):
ATATATATTCATAAAAAAAT
Found at i:154792 original size:29 final size:27
Alignment explanation
Indices: 154722--154796 Score: 87
Period size: 29 Copynumber: 2.6 Consensus size: 27
154712 TTTTTGATTC
* *
154722 AATTTGATACTTGAATTTGACATTTTTT
1 AATTTG-TACTTAAACTTGACATTTTTT
*
154750 AATTTGGTAATTAAACTTGACAATTTTTT
1 AATTT-GTACTTAAACTTGAC-ATTTTTT
154779 ATATTTGTACTTAAACTT
1 A-ATTTGTACTTAAACTT
154797 TTTGGGGTCC
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
28 16 0.40
29 20 0.50
30 4 0.10
ACGTcount: A:0.32, C:0.08, G:0.09, T:0.51
Consensus pattern (27 bp):
AATTTGTACTTAAACTTGACATTTTTT
Found at i:155135 original size:60 final size:59
Alignment explanation
Indices: 155001--155185 Score: 218
Period size: 60 Copynumber: 3.2 Consensus size: 59
154991 AATAAATTTT
** * * * * *
155001 GGTACCAAATTGAATCTAAAAAAAA-CTTAGGAACCAAATTAGGAAAAAATGCCAAGTTCA
1 GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTA--AGAAAATGTCAAGTTCA
* * *
155061 AGTATCAAACTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAAGTGTCAAGTTCA
1 GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAA-TGTCAAGTTCA
155121 GGTACCAAATTGGGT-C--AAAAAAGTTTAGGTACCAAATT-AGAAAATGTCAAGTTCA
1 GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAATGTCAAGTTCA
155176 GGTACCAAAT
1 GGTACCAAAT
155186 GTTATATAAA
Statistics
Matches: 110, Mismatches: 13, Indels: 9
0.83 0.10 0.07
Matches are distributed among these distances:
55 21 0.19
56 6 0.05
57 22 0.20
59 6 0.05
60 41 0.37
61 14 0.13
ACGTcount: A:0.45, C:0.14, G:0.18, T:0.23
Consensus pattern (59 bp):
GGTACCAAATTGGGTCCAAAAAAAAGTTTAGGTACCAAATTAAGAAAATGTCAAGTTCA
Done.