Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01013441.1 Kokia drynarioides strain JFW-HI SEQ_128467, 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: 236504
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 3 characters in sequence are not A, C, G, or T
Found at i:180 original size:34 final size:33
Alignment explanation
Indices: 142--220 Score: 95
Period size: 34 Copynumber: 2.4 Consensus size: 33
132 ACTTTGTTTG
*
142 AAAATAAATTTAAATTTAAATTAAATCCAAACTC
1 AAAATAAATTTAAATTTAAAGTAAATCCAAA-TC
* * * *
176 AAAATAAGTTCAAATTTAAAGTAAATTCAAATT
1 AAAATAAATTTAAATTTAAAGTAAATCCAAATC
*
209 TAAATAAATTTA
1 AAAATAAATTTA
221 GATTAAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 1
0.80 0.17 0.02
Matches are distributed among these distances:
33 10 0.27
34 27 0.73
ACGTcount: A:0.56, C:0.08, G:0.03, T:0.34
Consensus pattern (33 bp):
AAAATAAATTTAAATTTAAAGTAAATCCAAATC
Found at i:204 original size:17 final size:16
Alignment explanation
Indices: 143--218 Score: 80
Period size: 17 Copynumber: 4.6 Consensus size: 16
133 CTTTGTTTGA
*
143 AAATAAATTTAAATTT
1 AAATAAATTCAAATTT
* **
159 AAATTAAATCCAAACTCA
1 AAA-TAAATTCAAA-TTT
*
177 AAATAAGTTCAAATTT
1 AAATAAATTCAAATTT
193 AAAGTAAATTCAAATTT
1 AAA-TAAATTCAAATTT
210 AAATAAATT
1 AAATAAATT
219 TAGATTAAAA
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
16 13 0.27
17 31 0.65
18 4 0.08
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (16 bp):
AAATAAATTCAAATTT
Found at i:900 original size:209 final size:208
Alignment explanation
Indices: 533--1036 Score: 663
Period size: 209 Copynumber: 2.4 Consensus size: 208
523 ATGGTTTGGT
* * * * **
533 GTCATTGATTTGGTCTACTTCTCAATGTCTCATCAGGAAGATAATCGCATCACTTGTTTTGATCC
1 GTCATTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCC
* * * ** * * *
598 ACTTTTTTGTGTCTCATCAAGAAGACTTATCTGGTTCACTTCTCTGTATCTCATCAGAAAGGTAA
66 GCTTCTTTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAA
* * *
663 CCGCTTTATTGCTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCGAAGATTCGCTC
131 CCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTCGCTC
* *
728 ACTTTGAGCT-TGG
196 ACATCGAG-TGTGG
* * * *
741 CTTCATTAATTTGGTCTTCTTCTCAATACCTCATCAAGAAGATGACCGCATCACTTGTTTCAATC
1 -GTCATTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATC
* * * * *
806 CGCTTCTCTGTGTCTCATCAGGAAGACGAATTTGGTCCACTTTTCAGTATCTTATCAGGAAGCTA
65 CGCTTCTTTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTCATCAGAAAGCTA
* * *
871 ACCATTTTATTGCTTCGACCTACTTCTCAGTATCTTATCAGGAAGCTGAGGTTCGAAGATTTGCT
130 ACCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTCGCT
936 CACATCGAGTGTGG
195 CACATCGAGTGTGG
* *
950 GT--TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCC
1 GTCATTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCC
*
1013 GCTTCTTTGTATCTCATCAGGAAG
66 GCTTCTTTGTGTCTCATCAGGAAG
1037 CTAACCATTT
Statistics
Matches: 255, Mismatches: 39, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
206 78 0.31
208 2 0.01
209 175 0.69
ACGTcount: A:0.22, C:0.23, G:0.18, T:0.36
Consensus pattern (208 bp):
GTCATTGATTTGGTCTTCTTCTCAATATCTCATCAGGAAGATGACCGCATCACTTGTTTCAATCC
GCTTCTTTGTGTCTCATCAGGAAGACGAATCTGGTCCACTTCTCAGTATCTCATCAGAAAGCTAA
CCACTTTATTGCTTCGACCTACTTCTCAGTATCTCATCAGGAAGCTGAGGTTCGAAGATTCGCTC
ACATCGAGTGTGG
Found at i:1073 original size:48 final size:48
Alignment explanation
Indices: 965--1086 Score: 133
Period size: 48 Copynumber: 2.5 Consensus size: 48
955 ATTTGGTCTT
* * *
965 CTTCTCAGTATCTCATCAGGAAGATGACTGCATCACTTGTTTCAATCCG
1 CTTCTCAGTATCTCATCAGGAAGCTAAC-GCATCACTTGCTTCAATCCG
** *
1014 CTTCTTTGTATCTCATCAGGAAGCTAAC-CATTTTA-TTGCTTCAA-CCTG
1 CTTCTCAGTATCTCATCAGGAAGCTAACGCA--TCACTTGCTTCAATCC-G
1062 CTTCTCAGTATCTCATCAGGAAGCT
1 CTTCTCAGTATCTCATCAGGAAGCT
1087 GGGGTTCGAA
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
47 4 0.06
48 32 0.52
49 26 0.42
ACGTcount: A:0.24, C:0.26, G:0.15, T:0.35
Consensus pattern (48 bp):
CTTCTCAGTATCTCATCAGGAAGCTAACGCATCACTTGCTTCAATCCG
Found at i:1138 original size:169 final size:169
Alignment explanation
Indices: 852--1176 Score: 560
Period size: 169 Copynumber: 1.9 Consensus size: 169
842 CCACTTTTCA
* * *
852 GTATCTTATCAGGAAGCTAACCATTTTATTGCTTCGACCTACTTCTCAGTATCTTATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTACTTCTCAGTATCTCATCAGGAAGC
** *
917 TGAGGTTCGAAGATTTGCTCACATCGAGTGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 TGAGGTTCGAAGATTTGCTCACATCGAGCATGGCTTTGATTTGGTCTTCTTCTCAGTATCTCATC
*
982 AGGAAGATGACTGCATCACTTGTTTCAATCCGCTTCTTT
131 AGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTT
*
1021 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTGCTTCTCAGTATCTCATCAGGAAGC
1 GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTACTTCTCAGTATCTCATCAGGAAGC
*
1086 TGGGGTTCGAAGATTTGCTCACATCGAGCATGGCTTTGATTTGGTCTTCTTCTCAGTATCTCATC
66 TGAGGTTCGAAGATTTGCTCACATCGAGCATGGCTTTGATTTGGTCTTCTTCTCAGTATCTCATC
*
1151 AGGAAGATGACCGCATCGCTTGTTTC
131 AGGAAGATGACCGCATCACTTGTTTC
1177 GGATAACTAC
Statistics
Matches: 146, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
169 146 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (169 bp):
GTATCTCATCAGGAAGCTAACCATTTTATTGCTTCAACCTACTTCTCAGTATCTCATCAGGAAGC
TGAGGTTCGAAGATTTGCTCACATCGAGCATGGCTTTGATTTGGTCTTCTTCTCAGTATCTCATC
AGGAAGATGACCGCATCACTTGTTTCAATCCGCTTCTTT
Found at i:1972 original size:48 final size:48
Alignment explanation
Indices: 1655--1988 Score: 335
Period size: 48 Copynumber: 6.8 Consensus size: 48
1645 TCGCCATTGC
* * * *
1655 TCGTGCTACTGGATCCGTCGTTGCGGCTTAGATATTTCCCTTGTGTCT
1 TCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTATGTCT
* *
1703 TCCTGGTACTGGATCCGCTGTTGCGGCTTAGATCTTTCCCTTATGTCT
1 TCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTATGTCT
* * * *
1751 TCGCGGTACTGGATCCACTGTTGCGGCTTAGATATTTCCCTTCATGTCT
1 TCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTT-ATGTCT
* * * ** *
1800 TCGCGATACTGGATCCGCCGTTGCGGTCTTAGATATTTCCCGTCGTGTTT
1 TCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCC-TTATGTCT
** ** ** *
1850 TTATGGTACTGGATCCGCCGTTATGGTCTTAGATCTTTCCCGTCGTGTTT
1 TCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCC-TTATGTCT
* *
1900 TTGTGGTACTGGATCCGCCGTCGCGGCTTAGATCTTTCCCTTATGTCT
1 TCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTATGTCT
* * * * * *
1948 TCGTGGTATTAGATCCACCATCGCGGTTTTAGATCTTTCCC
1 TCGTGGTACTGGATCCGCCGTTGCGG-CTTAGATCTTTCCC
1989 GTCGTGTTTC
Statistics
Matches: 246, Mismatches: 36, Indels: 7
0.85 0.12 0.02
Matches are distributed among these distances:
48 106 0.43
49 56 0.23
50 83 0.34
51 1 0.00
ACGTcount: A:0.12, C:0.26, G:0.24, T:0.38
Consensus pattern (48 bp):
TCGTGGTACTGGATCCGCCGTTGCGGCTTAGATCTTTCCCTTATGTCT
Found at i:10566 original size:17 final size:16
Alignment explanation
Indices: 10541--10616 Score: 89
Period size: 17 Copynumber: 4.6 Consensus size: 16
10531 CTTTGTTTGA
*
10541 AAATAAATTTAAATTT
1 AAATAAATTCAAATTT
**
10557 AAATTAAATTCAAACTCA
1 AAA-TAAATTCAAA-TTT
*
10575 AAATAAGTTCAAATTT
1 AAATAAATTCAAATTT
10591 AAAGTAAATTCAAATTT
1 AAA-TAAATTCAAATTT
10608 AAATAAATT
1 AAATAAATT
10617 TAGATTAAAA
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
16 13 0.26
17 33 0.66
18 4 0.08
ACGTcount: A:0.55, C:0.07, G:0.03, T:0.36
Consensus pattern (16 bp):
AAATAAATTCAAATTT
Found at i:10589 original size:34 final size:34
Alignment explanation
Indices: 10540--10604 Score: 103
Period size: 34 Copynumber: 1.9 Consensus size: 34
10530 ACTTTGTTTG
* *
10540 AAAATAAATTTAAATTTAAATTAAATTCAAACTC
1 AAAATAAATTCAAATTTAAAGTAAATTCAAACTC
*
10574 AAAATAAGTTCAAATTTAAAGTAAATTCAAA
1 AAAATAAATTCAAATTTAAAGTAAATTCAAA
10605 TTTAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 28 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (34 bp):
AAAATAAATTCAAATTTAAAGTAAATTCAAACTC
Found at i:16001 original size:49 final size:50
Alignment explanation
Indices: 15920--16016 Score: 151
Period size: 49 Copynumber: 2.0 Consensus size: 50
15910 CGTATAGAAT
* * *
15920 TATATTTCTTCTATTCGATATTGATTAGAATAAGGTT-TTTCAACCTTAC
1 TATACTTCATCTATTCGATATTGATTAGAATAAGATTCTTTCAACCTTAC
*
15969 TATACTTCATCTATTTGATATTGATTAGAATAAGATTCTTTCAACCTT
1 TATACTTCATCTATTCGATATTGATTAGAATAAGATTCTTTCAACCTT
16017 CAAATAGATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
49 33 0.77
50 10 0.23
ACGTcount: A:0.30, C:0.14, G:0.09, T:0.46
Consensus pattern (50 bp):
TATACTTCATCTATTCGATATTGATTAGAATAAGATTCTTTCAACCTTAC
Found at i:19073 original size:332 final size:332
Alignment explanation
Indices: 18467--19130 Score: 1274
Period size: 332 Copynumber: 2.0 Consensus size: 332
18457 ATGCACAAAG
18467 ATGATTGAATCTTCAAAGAAAGTTAGGAATTTGTACTATCCCATAAACCAAAGTGATAGCAAGTA
1 ATGATTGAATCTTCAAAGAAAGTTAGGAATTTGTACTATCCCATAAACCAAAGTGATAGCAAGTA
18532 CCAATAAAAAGGCTTTTAGCACGGCTTCATATCTCACGATTATTTCTTGATGGAGTGATAACCGG
66 CCAATAAAAAGGCTTTTAGCACGGCTTCATATCTCACGATTATTTCTTGATGGAGTGATAACCGG
18597 ACTAAGGCTAAAAAGGAATTTAGTGACACATGATTTTAATCACGCTTGATGGATGAATGTGGTGA
131 ACTAAGGCTAAAAAGGAATTTAGTGACACATGATTTTAATCACGCTTGATGGATGAATGTGGTGA
*
18662 TTTGTTTGTGATTATGTAGAATGGAAAGAGGGAAGAATTGATATAGCAATTATGCAAATTTGCAA
196 TTTGTTTGTGATTATGTAGAATGGAAAGAGGGAAGAATTGATATAGCAATTAGGCAAATTTGCAA
18727 AAGAATGAAATGGAAATAAAAATGGCAGAGAAAGAGCACCGTCAATTTGGTAGAAAAAGAAAATA
261 AAGAATGAAATGGAAATAAAAATGGCAGAGAAAGAGCACCGTCAATTTGGTAGAAAAAGAAAATA
18792 AATAAAT
326 AATAAAT
18799 ATGATTGAATCTTCAAAGAAAGTTAGGAATTTGTACTATCCCATAAACCAAAGTGATAGCAAGTA
1 ATGATTGAATCTTCAAAGAAAGTTAGGAATTTGTACTATCCCATAAACCAAAGTGATAGCAAGTA
* *
18864 CCAATAAAAAGGCTTTTAGCACGGTTTTATATCTCACGATTATTTCTTGATGGAGTGATAACCGG
66 CCAATAAAAAGGCTTTTAGCACGGCTTCATATCTCACGATTATTTCTTGATGGAGTGATAACCGG
*
18929 ACTAAGGTTAAAAAGGAATTTAGTGACACATGATTTTAATCACGCTTGATGGATGAATGTGGTGA
131 ACTAAGGCTAAAAAGGAATTTAGTGACACATGATTTTAATCACGCTTGATGGATGAATGTGGTGA
*
18994 TTTGTTTGTGATTATGTAGAATGGAAAGAGGGAAGGATTGATATAGCAATTAGGCAAATTTGCAA
196 TTTGTTTGTGATTATGTAGAATGGAAAGAGGGAAGAATTGATATAGCAATTAGGCAAATTTGCAA
*
19059 AAGAATGAAATGGAAATAAAAATGGCAGAGAAAGAGCACTGTCAATTTGGTAGAAAAAGAAAATA
261 AAGAATGAAATGGAAATAAAAATGGCAGAGAAAGAGCACCGTCAATTTGGTAGAAAAAGAAAATA
19124 AATAAAT
326 AATAAAT
19131 GCTCAATTGC
Statistics
Matches: 326, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
332 326 1.00
ACGTcount: A:0.40, C:0.11, G:0.22, T:0.28
Consensus pattern (332 bp):
ATGATTGAATCTTCAAAGAAAGTTAGGAATTTGTACTATCCCATAAACCAAAGTGATAGCAAGTA
CCAATAAAAAGGCTTTTAGCACGGCTTCATATCTCACGATTATTTCTTGATGGAGTGATAACCGG
ACTAAGGCTAAAAAGGAATTTAGTGACACATGATTTTAATCACGCTTGATGGATGAATGTGGTGA
TTTGTTTGTGATTATGTAGAATGGAAAGAGGGAAGAATTGATATAGCAATTAGGCAAATTTGCAA
AAGAATGAAATGGAAATAAAAATGGCAGAGAAAGAGCACCGTCAATTTGGTAGAAAAAGAAAATA
AATAAAT
Found at i:26162 original size:6 final size:6
Alignment explanation
Indices: 26153--26232 Score: 76
Period size: 6 Copynumber: 13.7 Consensus size: 6
26143 GATTTATTTC
* ** *
26153 TAAATT TAAATT TAAATT TAAATT CATTTT TAAATT TAAATT T-ATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
* *
26200 TAAATT TGAAA-- TAATTT TAAACT TAAATT TAAA
1 TAAATT T-AAATT TAAATT TAAATT TAAATT TAAA
26233 ATCAATTACA
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
4 2 0.03
5 5 0.09
6 48 0.83
7 3 0.05
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (6 bp):
TAAATT
Found at i:26165 original size:18 final size:17
Alignment explanation
Indices: 26153--26230 Score: 86
Period size: 17 Copynumber: 4.5 Consensus size: 17
26143 GATTTATTTC
*
26153 TAAATTTAAATTTAAATT
1 TAAATTT-ATTTTAAATT
*
26171 TAAATTCATTTTTAAATT
1 TAAATTTA-TTTTAAATT
26189 TAAATTTATTTTAAATT
1 TAAATTTATTTTAAATT
* *
26206 TGAAA-TAATTTTAAACT
1 T-AAATTTATTTTAAATT
26223 TAAATTTA
1 TAAATTTA
26231 AAATCAATTA
Statistics
Matches: 51, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
16 3 0.06
17 24 0.47
18 24 0.47
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (17 bp):
TAAATTTATTTTAAATT
Found at i:26166 original size:24 final size:24
Alignment explanation
Indices: 26139--26211 Score: 78
Period size: 24 Copynumber: 3.0 Consensus size: 24
26129 TTAGATGGGT
*
26139 TTTAGATTTATTTCTAAATTTAAA
1 TTTAAATTTATTTCTAAATTTAAA
* **
26163 TTTAAATTTAAATTC-ATTTTTAAA
1 TTTAAATTT-ATTTCTAAATTTAAA
26187 TTTAAATTTATTT-TAAATTTGAAA
1 TTTAAATTTATTTCTAAATTT-AAA
26211 T
1 T
26212 AATTTTAAAC
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
23 7 0.18
24 28 0.72
25 4 0.10
ACGTcount: A:0.40, C:0.03, G:0.03, T:0.55
Consensus pattern (24 bp):
TTTAAATTTATTTCTAAATTTAAA
Found at i:27419 original size:59 final size:60
Alignment explanation
Indices: 27327--27580 Score: 241
Period size: 59 Copynumber: 4.2 Consensus size: 60
27317 TAAATTGTCA
* * * *
27327 AAAAAATCCATTTTTGACTCAAAAACTTTCAAAAATTA-TATTTTTACCCCCGAACTTCT
1 AAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTTCT
* * * *
27386 AAAAATTCCATTTTTAACCCTAAAACTTCCAAAAATTAC-ATTTTTACTCCTGAACCTCT
1 AAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTTCT
* ** * * * ** * *
27445 AAAAATTCCATTTTTGACCCCAAAACTTTTAAAAATTACAATTTTAACCCCTGATGTCCAAA
1 AAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTTC--T
*
27507 AAAAACTT-CATTTTTGACCCTAAAAC-TCTCAAAAATTACTA-TTTTACCCCCGAA-TGTCC
1 AAAAA-TTCCATTTTTGACCCTAAAACTTC-CAAAAATTACTATTTTTACCCCCGAACT-TCT
*
27566 AAAAATTCTATTTTT
1 AAAAATTCCATTTTT
27581 TTATCTTGGT
Statistics
Matches: 158, Mismatches: 29, Indels: 16
0.78 0.14 0.08
Matches are distributed among these distances:
58 2 0.01
59 96 0.61
60 14 0.09
61 12 0.08
62 32 0.20
63 2 0.01
ACGTcount: A:0.38, C:0.23, G:0.04, T:0.35
Consensus pattern (60 bp):
AAAAATTCCATTTTTGACCCTAAAACTTCCAAAAATTACTATTTTTACCCCCGAACTTCT
Found at i:27420 original size:30 final size:29
Alignment explanation
Indices: 27348--27495 Score: 136
Period size: 30 Copynumber: 5.0 Consensus size: 29
27338 TTTTGACTCA
*
27348 AAAACTT-TCAAAAATTATATTTTTACCCC
1 AAAACTTCT-AAAAATTACATTTTTACCCC
** * *
27377 CGAACTTCTAAAAATTCCATTTTTAACCCT
1 AAAACTTCTAAAAATTACATTTTT-ACCCC
* *
27407 AAAACTTCCAAAAATTACATTTTTACTCC
1 AAAACTTCTAAAAATTACATTTTTACCCC
** * *
27436 TGAACCTCTAAAAATTCCATTTTTGACCCC
1 AAAACTTCTAAAAATTACATTTTT-ACCCC
* *
27466 AAAACTTTTAAAAATTACAATTTTAACCCC
1 AAAACTTCTAAAAATTAC-ATTTTTACCCC
27496 TGATGTCCAA
Statistics
Matches: 92, Mismatches: 23, Indels: 7
0.75 0.19 0.06
Matches are distributed among these distances:
29 40 0.43
30 47 0.51
31 5 0.05
ACGTcount: A:0.39, C:0.24, G:0.02, T:0.35
Consensus pattern (29 bp):
AAAACTTCTAAAAATTACATTTTTACCCC
Found at i:27711 original size:28 final size:29
Alignment explanation
Indices: 27656--27716 Score: 88
Period size: 28 Copynumber: 2.1 Consensus size: 29
27646 AAATTTCCCA
*
27656 AAAATTACCATTTTGCCCTCGAGAATCC-
1 AAAATTACCATTTTACCCTCGAGAATCCT
* *
27684 AAAATTACCATTTTACCCTCGGGTATCCT
1 AAAATTACCATTTTACCCTCGAGAATCCT
27713 AAAA
1 AAAA
27717 GTCTCATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 25 0.86
29 4 0.14
ACGTcount: A:0.34, C:0.26, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAATTACCATTTTACCCTCGAGAATCCT
Found at i:38707 original size:3 final size:3
Alignment explanation
Indices: 38655--38690 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
38645 TTTCAAAATG
38655 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
38691 ATATAGCTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39789 original size:28 final size:29
Alignment explanation
Indices: 39747--39905 Score: 107
Period size: 29 Copynumber: 5.4 Consensus size: 29
39737 GGAGGTCCCT
*
39747 AAACTGTCTAAAAATTTCATTTTTAACCTC
1 AAACT-TCTAAAAATTTCATTTTTAACCCC
*
39777 -AACTTCTAAAAATTAT-ATTTTTACCCCC
1 AAACTTCTAAAAATT-TCATTTTTAACCCC
* * *
39805 AAACTTCCAAAAATTCCATTTTTAACCCTA
1 AAACTTCTAAAAATTTCATTTTTAACCC-C
*
39835 AAACTT-TCAAAAATTACCA-TTTT-ACCGCC
1 AAACTTCT-AAAAATT-TCATTTTTAACC-CC
* * * *
39864 GAA-TGTCCAAAAACTTCATTTTTTACCCC
1 AAACT-TCTAAAAATTTCATTTTTAACCCC
39893 AAAAC-TCTAAAAA
1 -AAACTTCTAAAAA
39906 ATTACCATTT
Statistics
Matches: 102, Mismatches: 14, Indels: 27
0.71 0.10 0.19
Matches are distributed among these distances:
28 23 0.23
29 53 0.52
30 23 0.23
31 3 0.03
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.34
Consensus pattern (29 bp):
AAACTTCTAAAAATTTCATTTTTAACCCC
Found at i:39846 original size:30 final size:30
Alignment explanation
Indices: 39743--39857 Score: 112
Period size: 29 Copynumber: 3.9 Consensus size: 30
39733 CCTTGGAGGT
* *
39743 CCCTAAACTGTCTAAAAATTTCATTTTTAA
1 CCCTAAACTTTCTAAAAATTCCATTTTTAA
* ** *
39773 -CCTCAAC-TTCTAAAAATTATATTTTTAC
1 CCCTAAACTTTCTAAAAATTCCATTTTTAA
* *
39801 CCCCAAAC-TTCCAAAAATTCCATTTTTAA
1 CCCTAAACTTTCTAAAAATTCCATTTTTAA
39830 CCCTAAAACTTTC-AAAAATTACCATTTT
1 CCCT-AAACTTTCTAAAAATT-CCATTTT
39858 ACCGCCGAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 7
0.78 0.14 0.08
Matches are distributed among these distances:
28 17 0.25
29 31 0.45
30 11 0.16
31 10 0.14
ACGTcount: A:0.37, C:0.24, G:0.01, T:0.37
Consensus pattern (30 bp):
CCCTAAACTTTCTAAAAATTCCATTTTTAA
Found at i:39858 original size:59 final size:58
Alignment explanation
Indices: 39751--40039 Score: 220
Period size: 59 Copynumber: 4.9 Consensus size: 58
39741 GTCCCTAAAC
* * *
39751 TGTCTAAAAATTTCATTTTTAA-CCT-CAAC-TTCTAAAAATTA-TATTTTTACCCCCAAA
1 TGTCCAAAAA-TTCATTTTTAACCCTAAAACTTTC-AAAAATTACCA-TTTTACCCCCAAA
* *
39808 CT-TCCAAAAATTCCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTACCGCCGAA
1 -TGTCCAAAAATT-CATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTACCCCCAAA
* * * * * *
39867 TGTCCAAAAACTTCATTTTTTACCCCAAAACTCTAAAAAATTACCATTTTACCCTCGAA
1 TGTCCAAAAA-TTCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTACCCCCAAA
* ** * *
39926 TGTCCAAAAAATTCATTTTTTATCCCGT---TTTTTCTAAAAATTACCGTTTTACCCTCAAA
1 TGTCC-AAAAATTCA-TTTTTAACCC-TAAAACTTTC-AAAAATTACCATTTTACCCCCAAA
* * * *
39985 TGT-CTAAAATTCTATTTTAAACCCTAAAA-TTTCCCAAAATTACCATTTTGCCCCC
1 TGTCCAAAAATTC-ATTTTTAACCCTAAAACTTT-CAAAAATTACCATTTTACCCCC
40040 GGGTATCCAA
Statistics
Matches: 187, Mismatches: 28, Indels: 32
0.76 0.11 0.13
Matches are distributed among these distances:
56 3 0.02
57 31 0.17
58 29 0.16
59 105 0.56
60 19 0.10
ACGTcount: A:0.35, C:0.25, G:0.03, T:0.37
Consensus pattern (58 bp):
TGTCCAAAAATTCATTTTTAACCCTAAAACTTTCAAAAATTACCATTTTACCCCCAAA
Found at i:39890 original size:30 final size:29
Alignment explanation
Indices: 39854--39952 Score: 94
Period size: 30 Copynumber: 3.3 Consensus size: 29
39844 AAAATTACCA
*
39854 TTTTACCGCCGAATGTCCAAAAACTTCATT
1 TTTTACC-CCGAATGTCCAAAAAATTCATT
* ** *
39884 TTTTACCCCAAAACTCTAAAAAATTACCA--
1 TTTTACCCCGAATGTCCAAAAAATT--CATT
39913 TTTTACCCTCGAATGTCCAAAAAATTCATT
1 TTTTACCC-CGAATGTCCAAAAAATTCATT
*
39943 TTTTATCCCG
1 TTTTACCCCG
39953 TTTTTTCTAA
Statistics
Matches: 54, Mismatches: 10, Indels: 11
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.04
29 23 0.43
30 27 0.50
31 2 0.04
ACGTcount: A:0.33, C:0.26, G:0.06, T:0.34
Consensus pattern (29 bp):
TTTTACCCCGAATGTCCAAAAAATTCATT
Found at i:39916 original size:29 final size:29
Alignment explanation
Indices: 39784--39920 Score: 84
Period size: 30 Copynumber: 4.7 Consensus size: 29
39774 CTCAACTTCT
** * *
39784 AAAAATTATATTTTTACCCCCAAACT-TCC
1 AAAAATTCCATTTTTACCCCAAAACTCT-A
* * *
39813 AAAAATTCCATTTTTAACCCTAAAACTTTC
1 AAAAATTCCATTTTT-ACCCCAAAACTCTA
* ** *
39843 AAAAATTACCA-TTTTACCGCCGAATGTCCA
1 AAAAATT-CCATTTTTACC-CCAAAACTCTA
*
39873 AAAACTT-CATTTTTTACCCCAAAACTCTA
1 AAAAATTCCA-TTTTTACCCCAAAACTCTA
39902 AAAAATTACCA-TTTTACCC
1 AAAAATT-CCATTTTTACCC
39921 TCGAATGTCC
Statistics
Matches: 83, Mismatches: 17, Indels: 16
0.72 0.15 0.14
Matches are distributed among these distances:
28 2 0.02
29 37 0.45
30 38 0.46
31 6 0.07
ACGTcount: A:0.39, C:0.26, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCAAAACTCTA
Found at i:39934 original size:29 final size:28
Alignment explanation
Indices: 39842--39935 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 28
39832 CTAAAACTTT
39842 CAAAAATTACCATTTTACCGCCGAATGTC
1 CAAAAATTACCATTTTACC-CCGAATGTC
* **
39871 CAAAAACTT--CATTTTTTACCCCAAAACTC
1 CAAAAA-TTACCA--TTTTACCCCGAATGTC
*
39900 TAAAAAATTACCATTTTACCCTCGAATGTC
1 -CAAAAATTACCATTTTACCC-CGAATGTC
39930 CAAAAA
1 CAAAAA
39936 ATTCATTTTT
Statistics
Matches: 50, Mismatches: 8, Indels: 14
0.69 0.11 0.19
Matches are distributed among these distances:
28 2 0.04
29 27 0.54
30 19 0.38
31 2 0.04
ACGTcount: A:0.39, C:0.27, G:0.05, T:0.29
Consensus pattern (28 bp):
CAAAAATTACCATTTTACCCCGAATGTC
Found at i:39945 original size:29 final size:28
Alignment explanation
Indices: 39854--39945 Score: 87
Period size: 29 Copynumber: 3.1 Consensus size: 28
39844 AAAATTACCA
*
39854 TTTTACCGCCGAATGTCCAAAAACTTCATT
1 TTTTACC-CCGAATGTCCAAAAAATTCA-T
* ** *
39884 TTTTACCCCAAAACTCTAAAAAATTACCA-
1 TTTTACCCCGAATGTCCAAAAAATT--CAT
39913 TTTTACCCTCGAATGTCCAAAAAATTCAT
1 TTTTACCC-CGAATGTCCAAAAAATTCAT
39942 TTTT
1 TTTT
39946 TATCCCGTTT
Statistics
Matches: 49, Mismatches: 9, Indels: 9
0.73 0.13 0.13
Matches are distributed among these distances:
28 2 0.04
29 25 0.51
30 20 0.41
31 2 0.04
ACGTcount: A:0.35, C:0.25, G:0.05, T:0.35
Consensus pattern (28 bp):
TTTTACCCCGAATGTCCAAAAAATTCAT
Found at i:41512 original size:19 final size:19
Alignment explanation
Indices: 41454--41513 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
41444 TTATGATTTT
*
41454 TTTAATAATTTTTATAAGT-
1 TTTATTAATTTTTATAA-TA
* **
41473 TTATATCAA-TTTTATTTTA
1 TT-TATTAATTTTTATAATA
41492 TTTATTAATTTTTATAATA
1 TTTATTAATTTTTATAATA
41511 TTT
1 TTT
41514 TATGATTATT
Statistics
Matches: 31, Mismatches: 7, Indels: 6
0.70 0.16 0.14
Matches are distributed among these distances:
18 6 0.19
19 21 0.68
20 4 0.13
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (19 bp):
TTTATTAATTTTTATAATA
Found at i:48596 original size:14 final size:15
Alignment explanation
Indices: 48554--48598 Score: 65
Period size: 17 Copynumber: 2.9 Consensus size: 15
48544 TTTATGTCAT
48554 TTTTTTATAAATATA
1 TTTTTTATAAATATA
48569 TTTGTTTCATAAATATA
1 TTT-TTT-ATAAATATA
48586 -TTTTTATAAATAT
1 TTTTTTATAAATAT
48599 TTATACTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 8 0.29
15 6 0.21
16 5 0.18
17 9 0.32
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (15 bp):
TTTTTTATAAATATA
Found at i:50521 original size:11 final size:11
Alignment explanation
Indices: 50494--50525 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
50484 ATAGCATGTT
50494 AAAATGTTATC
1 AAAATGTTATC
50505 --AATGTTATC
1 AAAATGTTATC
50514 AAAATGTTATC
1 AAAATGTTATC
50525 A
1 A
50526 TGTAGATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (11 bp):
AAAATGTTATC
Found at i:50537 original size:20 final size:20
Alignment explanation
Indices: 50494--50542 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 20
50484 ATAGCATGTT
* *
50494 AAAATGTTATCAATGTTATC
1 AAAATGTTATCAATGTGATA
50514 AAAATGTTATC-ATGTAGATA
1 AAAATGTTATCAATGT-GATA
*
50534 AAAAAGTTA
1 AAAATGTTA
50543 AATATTAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 4 0.16
20 21 0.84
ACGTcount: A:0.47, C:0.06, G:0.12, T:0.35
Consensus pattern (20 bp):
AAAATGTTATCAATGTGATA
Found at i:52758 original size:15 final size:15
Alignment explanation
Indices: 52723--52761 Score: 55
Period size: 14 Copynumber: 2.7 Consensus size: 15
52713 ATTGACAGAG
52723 ATAATAAAA-TATAC
1 ATAATAAAATTATAC
52737 ATAATAAAATTATA-
1 ATAATAAAATTATAC
52751 ATATATAAAAT
1 ATA-ATAAAAT
52762 AAATTAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 12 0.52
15 11 0.48
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAAAATTATAC
Found at i:55868 original size:21 final size:21
Alignment explanation
Indices: 55827--55878 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
55817 AGGTCCGCTC
55827 ATATTATTTTTTTAAAATATTT
1 ATATTATTTTTTT-AAATATTT
55849 ATATTATTTATTTT-AATATTT
1 ATATTATTT-TTTTAAATATTT
*
55870 A-ATAATTTT
1 ATATTATTTT
55879 ATACATTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 1 0.04
20 6 0.21
21 8 0.29
22 9 0.32
23 4 0.14
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTATTTTTTTAAATATTT
Found at i:64922 original size:27 final size:28
Alignment explanation
Indices: 64879--64942 Score: 87
Period size: 27 Copynumber: 2.4 Consensus size: 28
64869 TTCGCTAATA
* *
64879 TGTG-GGTGAGCTAGGGGTTTTCTAGTT
1 TGTGTGGTGAGCTAGGGGTCTGCTAGTT
*
64906 TGTTTGGTGAGCT-GGGGTCTGCTAGTT
1 TGTGTGGTGAGCTAGGGGTCTGCTAGTT
64933 TGTGTGGTGA
1 TGTGTGGTGA
64943 ATAGGGCTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
27 24 0.75
28 8 0.25
ACGTcount: A:0.09, C:0.08, G:0.42, T:0.41
Consensus pattern (28 bp):
TGTGTGGTGAGCTAGGGGTCTGCTAGTT
Found at i:68853 original size:22 final size:22
Alignment explanation
Indices: 68843--68887 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
68833 AGTATGTTCT
68843 TCATGCCATGTGACTAATTATG
1 TCATGCCATGTGACTAATTATG
*
68865 TCATGCCATGTGACTAACTATG
1 TCATGCCATGTGACTAATTATG
68887 T
1 T
68888 TGTGCTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.36
Consensus pattern (22 bp):
TCATGCCATGTGACTAATTATG
Found at i:69708 original size:38 final size:38
Alignment explanation
Indices: 69666--69748 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 38
69656 TGAGTCTATT
* *
69666 CAGAATTGCGCCCGAAATTGTCACTACATGA-CAATGTC
1 CAGAATTGCGCCCAAAATTGTCACTACATGAGC-ATGCC
* * *
69704 CAGAATTGTGCCCAAAATTGTTACTGCATGAGCATGCC
1 CAGAATTGCGCCCAAAATTGTCACTACATGAGCATGCC
69742 CAGAATT
1 CAGAATT
69749 ACCGCTTCAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 38 0.97
39 1 0.03
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.25
Consensus pattern (38 bp):
CAGAATTGCGCCCAAAATTGTCACTACATGAGCATGCC
Found at i:84232 original size:21 final size:20
Alignment explanation
Indices: 84208--84284 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 20
84198 AACATTCACC
84208 GGTTCTGGTTCTGGTGAAATT
1 GGTTCTGGTTCTGGT-AAATT
*
84229 GGTTCTGGTTCTAGTAAAGTT
1 GGTTCTGGTTCTGGTAAA-TT
* * * *
84250 TGTTTTGATTCCGGTAAAATT
1 GGTTCTGGTTCTGGT-AAATT
*
84271 GGTTCTAGTTCTGG
1 GGTTCTGGTTCTGG
84285 CAAAGTTGGA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
20 3 0.07
21 37 0.86
22 3 0.07
ACGTcount: A:0.17, C:0.10, G:0.29, T:0.44
Consensus pattern (20 bp):
GGTTCTGGTTCTGGTAAATT
Found at i:85964 original size:33 final size:35
Alignment explanation
Indices: 85893--85975 Score: 100
Period size: 33 Copynumber: 2.4 Consensus size: 35
85883 TCACATATGC
* *
85893 GGTTTATCCG-CTAGGCACTGGGTGCCATGATTGTT
1 GGTTTATCCGACTA-GCACTGGGTGACATAATTGTT
85928 GGTTTATCCGACTAGCACTGGGT-ACA-AATTGTT
1 GGTTTATCCGACTAGCACTGGGTGACATAATTGTT
* *
85961 GGTTAATCCAACTAG
1 GGTTTATCCGACTAG
85976 AGCTGGGCTC
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
33 19 0.44
34 2 0.05
35 19 0.44
36 3 0.07
ACGTcount: A:0.22, C:0.19, G:0.27, T:0.33
Consensus pattern (35 bp):
GGTTTATCCGACTAGCACTGGGTGACATAATTGTT
Found at i:104780 original size:79 final size:80
Alignment explanation
Indices: 104649--104872 Score: 256
Period size: 79 Copynumber: 2.8 Consensus size: 80
104639 TTTATTTATG
**
104649 TTGTCAGTTTAACTGACTAGAGCTGGGCTCAC-TTTCGCGACTTATCCGCTAGGCACTGGGTGCC
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTT-GCGGTTTATCCGCTAGGCACTGGGTGCC
* *
104713 AAGACTTGATGGA-CC
65 AAGACTTGACGGATAC
*
104728 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCTCTAGGCACTGGGTGCCA
1 TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCA
* * *
104793 GGATTTGACGGATAT
66 AGACTTGACGGATAC
* * ** * ** * *
104808 TTGT-TGGTTAATCCAACCAGAGCTGGGCTCACACCTACGGTTTATCCGCTAGGCATTGGGTGCC
1 TTGTCAGTTTAA-CTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCC
104872 A
65 A
104873 TGATTGTCAG
Statistics
Matches: 124, Mismatches: 18, Indels: 5
0.84 0.12 0.03
Matches are distributed among these distances:
79 72 0.58
80 52 0.42
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.29
Consensus pattern (80 bp):
TTGTCAGTTTAACTGACTAGAGCTGGGCTCACATTTGCGGTTTATCCGCTAGGCACTGGGTGCCA
AGACTTGACGGATAC
Found at i:120993 original size:13 final size:13
Alignment explanation
Indices: 120975--121001 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
120965 TTCGTTATTA
120975 TCGTATCATGAAT
1 TCGTATCATGAAT
120988 TCGTATCATGAAT
1 TCGTATCATGAAT
121001 T
1 T
121002 GGTTCGAGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TCGTATCATGAAT
Found at i:121695 original size:57 final size:57
Alignment explanation
Indices: 121623--121744 Score: 183
Period size: 57 Copynumber: 2.1 Consensus size: 57
121613 ATTTCCAAGT
* * * *
121623 CATTTTCATTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGATTTC-ATTTCTC
1 CATTTTCATTTTCATTTTAGAGAAAACCACAATAATTTCCAAATG-TTCCTATTTCTC
*
121680 CATTTTCATTTTCATTTTAGAGAAAACCATAATAATTTCCAAATGTTCCTATTTCTC
1 CATTTTCATTTTCATTTTAGAGAAAACCACAATAATTTCCAAATGTTCCTATTTCTC
121737 CATTTTCA
1 CATTTTCA
121745 CCATTTTTGT
Statistics
Matches: 59, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
56 3 0.05
57 56 0.95
ACGTcount: A:0.30, C:0.20, G:0.06, T:0.44
Consensus pattern (57 bp):
CATTTTCATTTTCATTTTAGAGAAAACCACAATAATTTCCAAATGTTCCTATTTCTC
Found at i:134357 original size:22 final size:22
Alignment explanation
Indices: 134329--134371 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
134319 CACCAATAGT
134329 TCTTCAAACACAAACTTTTATC
1 TCTTCAAACACAAACTTTTATC
**
134351 TCTTCAAAGTCAAACTTTTAT
1 TCTTCAAACACAAACTTTTAT
134372 TTGTCCACTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.02, T:0.40
Consensus pattern (22 bp):
TCTTCAAACACAAACTTTTATC
Found at i:138435 original size:25 final size:22
Alignment explanation
Indices: 138385--138438 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 22
138375 CTACTCTACT
*
138385 AAATAAAAAATTAATAACAAATC
1 AAAT-AAAAATTAATAACAAAAC
138408 AAATAAAAATTAAATTAAACAAAAC
1 AAATAAAAATT-AA-T-AACAAAAC
138433 AAATAA
1 AAATAA
138439 CTTAATAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
22 7 0.26
23 6 0.22
24 1 0.04
25 13 0.48
ACGTcount: A:0.72, C:0.07, G:0.00, T:0.20
Consensus pattern (22 bp):
AAATAAAAATTAATAACAAAAC
Found at i:140459 original size:29 final size:27
Alignment explanation
Indices: 140394--140460 Score: 64
Period size: 29 Copynumber: 2.3 Consensus size: 27
140384 ATTTACGATC
*
140394 TTAAGTTTAAAAGTTTAGGATTTTTTATT
1 TTAA-TTT-AAAGTTTAGGATTTTTTATA
140423 TTGAATTTAAAGTTTTAGGATTTATTTATAA
1 TT-AATTTAAAG-TTTAGGATTT-TTTAT-A
140454 TT-ATTTA
1 TTAATTTA
140461 TTATTTAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
28 4 0.12
29 20 0.61
30 7 0.21
31 2 0.06
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (27 bp):
TTAATTTAAAGTTTAGGATTTTTTATA
Found at i:144541 original size:13 final size:13
Alignment explanation
Indices: 144523--144550 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
144513 CCTGTTAATG
144523 ATTATACATACAA
1 ATTATACATACAA
144536 ATTATACATACAA
1 ATTATACATACAA
144549 AT
1 AT
144551 CGTTTGTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.32
Consensus pattern (13 bp):
ATTATACATACAA
Found at i:145021 original size:46 final size:46
Alignment explanation
Indices: 144988--145092 Score: 147
Period size: 46 Copynumber: 2.3 Consensus size: 46
144978 TATATGATAT
* * *
144988 TTAAATTTAAATTTAAATTGAAGTTGAAATTAAATACAAGTTAAAA
1 TTAAATTGAAATTAAAATTGAAGTTGAAATTAAATACAAGTGAAAA
* * *
145034 TTAAGTTGAAATTAAAATTGAAGTTGAAATTAAGTACAAGTTAAAA
1 TTAAATTGAAATTAAAATTGAAGTTGAAATTAAATACAAGTGAAAA
*
145080 TTAAGTTGAAATT
1 TTAAATTGAAATT
145093 TAAGAAGTTA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 55 1.00
ACGTcount: A:0.50, C:0.02, G:0.12, T:0.36
Consensus pattern (46 bp):
TTAAATTGAAATTAAAATTGAAGTTGAAATTAAATACAAGTGAAAA
Found at i:145059 original size:18 final size:17
Alignment explanation
Indices: 145028--145066 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
145018 TAAATACAAG
145028 TTAAAATTAAGTTGAAA
1 TTAAAATTAAGTTGAAA
145045 TTAAAATTGAAGTTGAAA
1 TTAAAATT-AAGTTGAAA
145063 TTAA
1 TTAA
145067 GTACAAGTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 8 0.38
18 13 0.62
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (17 bp):
TTAAAATTAAGTTGAAA
Found at i:145121 original size:46 final size:46
Alignment explanation
Indices: 144996--145115 Score: 145
Period size: 46 Copynumber: 2.6 Consensus size: 46
144986 ATTTAAATTT
* * *
144996 AAATTTAAATTGAAGTTGAAATTAAATACAAGTTAAAATTAAGTTG
1 AAATTAAAATTGAAATTGAAATGAAATACAAGTTAAAATTAAGTTG
* * *
145042 AAATTAAAATTGAAGTTGAAATTAAGTACAAGTTAAAATTAAGTTG
1 AAATTAAAATTGAAATTGAAATGAAATACAAGTTAAAATTAAGTTG
145088 AAATTTAAGAAGTT-AAATT-AAATGAAAT
1 AAA-TTAA-AA-TTGAAATTGAAATGAAAT
145116 TAAGTTGAAA
Statistics
Matches: 66, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
46 47 0.71
47 11 0.17
48 6 0.09
49 2 0.03
ACGTcount: A:0.52, C:0.02, G:0.13, T:0.33
Consensus pattern (46 bp):
AAATTAAAATTGAAATTGAAATGAAATACAAGTTAAAATTAAGTTG
Found at i:145126 original size:11 final size:11
Alignment explanation
Indices: 145025--145127 Score: 50
Period size: 11 Copynumber: 9.0 Consensus size: 11
145015 AATTAAATAC
*
145025 AAGTTAAAATT
1 AAGTTGAAATT
145036 AAGTTGAAATT
1 AAGTTGAAATT
* *
145047 AAAATTGAAGTT
1 -AAGTTGAAATT
* * *
145059 GAAATT-AAGTAC
1 -AAGTTGAAAT-T
*
145071 AAGTTAAAATT
1 AAGTTGAAATT
145082 AAGTTGAAATTT
1 AAGTTGAAA-TT
145094 AAGAAGTT-AAATT
1 ---AAGTTGAAATT
*
145107 AA-ATGAAATT
1 AAGTTGAAATT
145117 AAGTTGAAATT
1 AAGTTGAAATT
145128 TGAAATTAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
9 1 0.01
10 9 0.12
11 33 0.46
12 19 0.26
13 2 0.03
14 3 0.04
15 5 0.07
ACGTcount: A:0.50, C:0.01, G:0.15, T:0.34
Consensus pattern (11 bp):
AAGTTGAAATT
Found at i:145134 original size:28 final size:28
Alignment explanation
Indices: 145102--145196 Score: 94
Period size: 28 Copynumber: 3.5 Consensus size: 28
145092 TTAAGAAGTT
145102 AAATTAAATGAAATTAAGTTGAAATTTG
1 AAATTAAATGAAATTAAGTTGAAATTTG
*
145130 AAATTAAATG--AGT--GTTGAAA-TTG
1 AAATTAAATGAAATTAAGTTGAAATTTG
* * *
145153 AAATGAAATTAAATTGAAATTGAAATTTG
1 AAATTAAATGAAATT-AAGTTGAAATTTG
145182 -AATTGAAATGAAATT
1 AAATT-AAATGAAATT
145197 TAAAATTTAA
Statistics
Matches: 53, Mismatches: 7, Indels: 13
0.73 0.10 0.18
Matches are distributed among these distances:
23 11 0.21
24 7 0.13
25 2 0.04
26 2 0.04
28 19 0.36
29 12 0.23
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (28 bp):
AAATTAAATGAAATTAAGTTGAAATTTG
Found at i:145155 original size:6 final size:6
Alignment explanation
Indices: 145102--145196 Score: 73
Period size: 5 Copynumber: 16.8 Consensus size: 6
145092 TTAAGAAGTT
* **
145102 AAATT- AAA-TG AAATT- AAGTTG AAATTTG AAATT- AAA-TG AGTGTTG
1 AAATTG AAATTG AAATTG AAATTG AAA-TTG AAATTG AAATTG A-AATTG
145147 AAATTG AAA-TG AAATT- AAATTG AAATTG AAATTTG -AATTG AAA-TG
1 AAATTG AAATTG AAATTG AAATTG AAATTG AAA-TTG AAATTG AAATTG
145192 AAATT
1 AAATT
145197 TAAAATTTAA
Statistics
Matches: 72, Mismatches: 6, Indels: 23
0.71 0.06 0.23
Matches are distributed among these distances:
4 2 0.03
5 32 0.44
6 26 0.36
7 12 0.17
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (6 bp):
AAATTG
Found at i:145161 original size:11 final size:12
Alignment explanation
Indices: 145102--145196 Score: 73
Period size: 11 Copynumber: 8.4 Consensus size: 12
145092 TTAAGAAGTT
145102 AAATT-AAA-TG
1 AAATTGAAATTG
*
145112 AAATT-AAGTTG
1 AAATTGAAATTG
145123 AAATTTGAAATT-
1 AAA-TTGAAATTG
**
145135 AAA-TGAGTGTTG
1 AAATTGA-AATTG
145147 AAATTGAAA-TG
1 AAATTGAAATTG
145158 AAATT-AAATTG
1 AAATTGAAATTG
145169 AAATTGAAATTTG
1 AAATTGAAA-TTG
145182 -AATTGAAA-TG
1 AAATTGAAATTG
145192 AAATT
1 AAATT
145197 TAAAATTTAA
Statistics
Matches: 69, Mismatches: 6, Indels: 19
0.73 0.06 0.20
Matches are distributed among these distances:
10 15 0.22
11 25 0.36
12 19 0.28
13 10 0.14
ACGTcount: A:0.49, C:0.00, G:0.16, T:0.35
Consensus pattern (12 bp):
AAATTGAAATTG
Found at i:145178 original size:17 final size:17
Alignment explanation
Indices: 144994--145196 Score: 88
Period size: 17 Copynumber: 12.1 Consensus size: 17
144984 ATATTTAAAT
* *
144994 TTAAATTTAAATTGAAG
1 TTAAATTGAAATTGAAA
** *
145011 TTGAAATT-AAATACAAG
1 TT-AAATTGAAATTGAAA
*
145028 TTAAAATT-AAGTTGAAA
1 TT-AAATTGAAATTGAAA
*
145045 TTAAAATTGAAGTTGAAA
1 TT-AAATTGAAATTGAAA
* ** * *
145063 TTAAGTACAAGTTAAAA
1 TTAAATTGAAATTGAAA
* *
145080 TTAAGTTGAAATTTAAGAAG
1 TTAAATTGAAA-TT--GAAA
145100 TTAAATT-AAA-TGAAA
1 TTAAATTGAAATTGAAA
*
145115 TTAAGTTGAAATTTGAAA
1 TTAAATTGAAA-TTGAAA
*
145133 TTAAA-TG--AGTG---
1 TTAAATTGAAATTGAAA
145144 TTGAAATTGAAA-TGAAA
1 TT-AAATTGAAATTGAAA
145161 TTAAATTGAAATTGAAA
1 TTAAATTGAAATTGAAA
*
145178 TTTGAATTGAAA-TGAAA
1 -TTAAATTGAAATTGAAA
145195 TT
1 TT
145197 TAAAATTTAA
Statistics
Matches: 147, Mismatches: 22, Indels: 35
0.72 0.11 0.17
Matches are distributed among these distances:
11 2 0.01
12 3 0.02
13 2 0.01
14 4 0.03
15 11 0.07
16 14 0.10
17 63 0.43
18 37 0.25
19 3 0.02
20 8 0.05
ACGTcount: A:0.49, C:0.01, G:0.15, T:0.35
Consensus pattern (17 bp):
TTAAATTGAAATTGAAA
Found at i:145197 original size:17 final size:18
Alignment explanation
Indices: 145121--145203 Score: 95
Period size: 17 Copynumber: 4.8 Consensus size: 18
145111 GAAATTAAGT
145121 TGAAATTTGAAATT-AAA
1 TGAAATTTGAAATTGAAA
*
145138 TG-AGTGTTGAAATTGAAA
1 TGAAAT-TTGAAATTGAAA
145156 TGAAA-TT-AAATTGAAA
1 TGAAATTTGAAATTGAAA
145172 TTGAAATTTG-AATTGAAA
1 -TGAAATTTGAAATTGAAA
*
145190 TGAAATTTAAAATT
1 TGAAATTTGAAATT
145204 TAAAATAAAG
Statistics
Matches: 56, Mismatches: 3, Indels: 13
0.78 0.04 0.18
Matches are distributed among these distances:
16 11 0.20
17 25 0.45
18 19 0.34
19 1 0.02
ACGTcount: A:0.48, C:0.00, G:0.16, T:0.36
Consensus pattern (18 bp):
TGAAATTTGAAATTGAAA
Found at i:145374 original size:31 final size:31
Alignment explanation
Indices: 145339--145409 Score: 142
Period size: 31 Copynumber: 2.3 Consensus size: 31
145329 ATCAGCAGGC
145339 TGGGCATGTCTCAACCCCTTGTCACATCAAT
1 TGGGCATGTCTCAACCCCTTGTCACATCAAT
145370 TGGGCATGTCTCAACCCCTTGTCACATCAAT
1 TGGGCATGTCTCAACCCCTTGTCACATCAAT
145401 TGGGCATGT
1 TGGGCATGT
145410 GTTATGGTCG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.21, C:0.30, G:0.20, T:0.30
Consensus pattern (31 bp):
TGGGCATGTCTCAACCCCTTGTCACATCAAT
Found at i:150945 original size:17 final size:17
Alignment explanation
Indices: 150910--150963 Score: 63
Period size: 18 Copynumber: 3.1 Consensus size: 17
150900 ATGTAACTAC
* *
150910 AATGCAAATGCACTAACA
1 AATG-AAATGCAATGACA
150928 AATGAAATGCAATGACA
1 AATGAAATGCAATGACA
*
150945 AATAAAAATGCAATGACA
1 AAT-GAAATGCAATGACA
150963 A
1 A
150964 CTAAATAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
17 14 0.44
18 18 0.56
ACGTcount: A:0.56, C:0.15, G:0.13, T:0.17
Consensus pattern (17 bp):
AATGAAATGCAATGACA
Found at i:150955 original size:18 final size:18
Alignment explanation
Indices: 150932--150968 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
150922 CTAACAAATG
150932 AAATGCAATGACAAATAA
1 AAATGCAATGACAAATAA
*
150950 AAATGCAATGACAACTAA
1 AAATGCAATGACAAATAA
150968 A
1 A
150969 TAAAATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.59, C:0.14, G:0.11, T:0.16
Consensus pattern (18 bp):
AAATGCAATGACAAATAA
Found at i:151462 original size:18 final size:18
Alignment explanation
Indices: 151441--151478 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
151431 TCTTTCATTC
151441 TCTTGCTC-ATTTTCTTCT
1 TCTTGCTCTA-TTTCTTCT
*
151459 TCTTTCTCTATTTCTTCT
1 TCTTGCTCTATTTCTTCT
151477 TC
1 TC
151479 CTCAGTCTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 17 0.94
19 1 0.06
ACGTcount: A:0.05, C:0.29, G:0.03, T:0.63
Consensus pattern (18 bp):
TCTTGCTCTATTTCTTCT
Found at i:153317 original size:20 final size:20
Alignment explanation
Indices: 153292--153336 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
153282 TGCATAAGAC
153292 TAAAAAGA-AACAAGTAAAAG
1 TAAAAAGATAA-AAGTAAAAG
*
153312 TAAAAAGATAAAAGTAAATG
1 TAAAAAGATAAAAGTAAAAG
153332 TAAAA
1 TAAAA
153337 TTACATTGGC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 21 0.91
21 2 0.09
ACGTcount: A:0.69, C:0.02, G:0.13, T:0.16
Consensus pattern (20 bp):
TAAAAAGATAAAAGTAAAAG
Found at i:165104 original size:6 final size:5
Alignment explanation
Indices: 165070--165100 Score: 53
Period size: 5 Copynumber: 6.0 Consensus size: 5
165060 TAATTATGAA
165070 ATTTT ATTTT ATTTT ATTTT ATGTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT
165101 TATTCAAGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 20 0.80
6 5 0.20
ACGTcount: A:0.19, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
ATTTT
Found at i:167227 original size:15 final size:15
Alignment explanation
Indices: 167182--167228 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
167172 AACGAAAAAG
*
167182 AAAAAGATGCCGAGGA
1 AAAAAGATGCTGA-GA
* *
167198 AGAAA-ATGTTGAGA
1 AAAAAGATGCTGAGA
167212 AAAAAGATGCTGAGA
1 AAAAAGATGCTGAGA
167227 AA
1 AA
167229 GAATCAGCTA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
14 6 0.24
15 15 0.60
16 4 0.16
ACGTcount: A:0.53, C:0.06, G:0.28, T:0.13
Consensus pattern (15 bp):
AAAAAGATGCTGAGA
Found at i:183013 original size:14 final size:14
Alignment explanation
Indices: 182994--183067 Score: 51
Period size: 14 Copynumber: 5.3 Consensus size: 14
182984 ACCCAAAAAT
*
182994 TCAATGATCAACTG
1 TCAATGATCAACGG
*
183008 TCAATGGTCAACGG
1 TCAATGATCAACGG
* * * * **
183022 TGAACGGTTAACTA
1 TCAATGATCAACGG
183036 TCAACT-ATCAACGG
1 TCAA-TGATCAACGG
*
183050 TCAATGATCAATGG
1 TCAATGATCAACGG
183064 TCAA
1 TCAA
183068 CGTGTTCGAT
Statistics
Matches: 44, Mismatches: 14, Indels: 4
0.71 0.23 0.06
Matches are distributed among these distances:
13 1 0.02
14 43 0.98
ACGTcount: A:0.35, C:0.20, G:0.19, T:0.26
Consensus pattern (14 bp):
TCAATGATCAACGG
Found at i:183059 original size:21 final size:21
Alignment explanation
Indices: 182994--183069 Score: 55
Period size: 21 Copynumber: 3.6 Consensus size: 21
182984 ACCCAAAAAT
* * *
182994 TCAATGATCAACTGTCAATGG
1 TCAACGATCAACGGTCAATGA
* * *
183015 TCAACGGTGAACGGTTAACT-A
1 TCAACGATCAACGGTCAA-TGA
*
183036 TCAACTATCAACGGTCAATGA
1 TCAACGATCAACGGTCAATGA
* *
183057 TCAATGGTCAACG
1 TCAACGATCAACG
183070 TGTTCGATTC
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (21 bp):
TCAACGATCAACGGTCAATGA
Found at i:183087 original size:18 final size:18
Alignment explanation
Indices: 183064--183103 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
183054 TGATCAATGG
*
183064 TCAACGTGTTCGATTCAA
1 TCAACGGGTTCGATTCAA
* *
183082 TCAACGGGTTCGGTTCAG
1 TCAACGGGTTCGATTCAA
183100 TCAA
1 TCAA
183104 TGGGCGGATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (18 bp):
TCAACGGGTTCGATTCAA
Found at i:191931 original size:83 final size:83
Alignment explanation
Indices: 191832--191988 Score: 296
Period size: 83 Copynumber: 1.9 Consensus size: 83
191822 TTCATGGAAT
191832 TAGTCCATCCATATGCATGCACAAGATCATTCTAGAAAATAGAAAGAAAGGGACGATTGATGGAC
1 TAGTCCATCCATATGCATGCACAAGATCATTCTAGAAAATAGAAAGAAAGGGACGATTGATGGAC
*
191897 AACGGAGATAATCAAGTC
66 AAAGGAGATAATCAAGTC
*
191915 TAGTCCATCCATATGCATGCACAAGATCATTCTAGAAAATAGAAAGAACGGGACGATTGATGGAC
1 TAGTCCATCCATATGCATGCACAAGATCATTCTAGAAAATAGAAAGAAAGGGACGATTGATGGAC
191980 AAAGGAGAT
66 AAAGGAGAT
191989 CATTCTAGAA
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
83 72 1.00
ACGTcount: A:0.41, C:0.17, G:0.22, T:0.20
Consensus pattern (83 bp):
TAGTCCATCCATATGCATGCACAAGATCATTCTAGAAAATAGAAAGAAAGGGACGATTGATGGAC
AAAGGAGATAATCAAGTC
Found at i:198988 original size:24 final size:24
Alignment explanation
Indices: 198949--199047 Score: 117
Period size: 24 Copynumber: 4.1 Consensus size: 24
198939 AAAGACAACA
* * * *
198949 TTAGCTCTCACTAGCCCAGGATTG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
198973 TTAGCTCTTATGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
*
198997 TTAGCTCTTACGAGCCCAAAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
* *
199021 TTAGTTCTTACGAGCCTAGAATGG
1 TTAGCTCTTACGAGCCCAGAATGG
199045 TTA
1 TTA
199048 ACCAGTATAC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 63 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (24 bp):
TTAGCTCTTACGAGCCCAGAATGG
Found at i:199003 original size:48 final size:48
Alignment explanation
Indices: 198949--199047 Score: 135
Period size: 48 Copynumber: 2.1 Consensus size: 48
198939 AAAGACAACA
* ** * *
198949 TTAGCTCTCACTAGCCCAGGATTGTTAGCTCTTATGAGCCTAGAATGG
1 TTAGCTCTCACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGG
* *
198997 TTAGCTCTTACGAGCCCAAAATGGTTAGTTCTTACGAGCCTAGAATGG
1 TTAGCTCTCACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGG
199045 TTA
1 TTA
199048 ACCAGTATAC
Statistics
Matches: 44, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
48 44 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (48 bp):
TTAGCTCTCACGAGCCCAAAATGGTTAGCTCTTACGAGCCTAGAATGG
Found at i:199201 original size:82 final size:82
Alignment explanation
Indices: 199059--199278 Score: 298
Period size: 82 Copynumber: 2.7 Consensus size: 82
199049 CCAGTATACG
* * * * *
199059 ATGCTACTCACACAATCTAATGAGAATTCATGACATACACGAAGGCTCAACCATCAATACGATCC
1 ATGCTGCTCACACAAGCTAATGAGAATTCATAACATACACGAAGACTCAACCATCGATACGATCC
199124 AGAATTTCCCACTCTCA
66 AGAATTTCCCACTCTCA
* * ** * *
199141 ATGCTGCTCACAAAAGCTGATGAGAATTCGCAACATACACGAAGACTCAACCATCGATACGGTCT
1 ATGCTGCTCACACAAGCTAATGAGAATTCATAACATACACGAAGACTCAACCATCGATACGATCC
*
199206 AGAATTTCCCACTCTCG
66 AGAATTTCCCACTCTCA
* *
199223 ATGCTGCTCACACAAGCTAATGAGAATTCATAACATATGA-GAAGACTCAGCCATCG
1 ATGCTGCTCACACAAGCTAATGAGAATTCATAACATA-CACGAAGACTCAACCATCG
199279 GAGGGGTCCA
Statistics
Matches: 119, Mismatches: 18, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
82 118 0.99
83 1 0.01
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.22
Consensus pattern (82 bp):
ATGCTGCTCACACAAGCTAATGAGAATTCATAACATACACGAAGACTCAACCATCGATACGATCC
AGAATTTCCCACTCTCA
Found at i:203730 original size:24 final size:24
Alignment explanation
Indices: 203703--203821 Score: 130
Period size: 24 Copynumber: 5.0 Consensus size: 24
203693 ACAATATTAC
* *
203703 CTCTCACAAGCCCAAGATGGTTAG
1 CTCTTACAAGCCCAAAATGGTTAG
* * * *
203727 CTCTTATAAGCCTAGAATGGTTCG
1 CTCTTACAAGCCCAAAATGGTTAG
* *
203751 CACTTACGAGCCCAAAATGGTTAG
1 CTCTTACAAGCCCAAAATGGTTAG
*
203775 CTCTTACGAGCCCAAAATGGTTAG
1 CTCTTACAAGCCCAAAATGGTTAG
** *
203799 CTCTTATGAGCCCAGAATGGTTA
1 CTCTTACAAGCCCAAAATGGTTA
203822 ACCAATATAC
Statistics
Matches: 80, Mismatches: 15, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 80 1.00
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (24 bp):
CTCTTACAAGCCCAAAATGGTTAG
Found at i:208985 original size:21 final size:21
Alignment explanation
Indices: 208948--208988 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
208938 TGACCAAATA
*
208948 ATTTATTTCCATTTTAACTTT
1 ATTTATTTCAATTTTAACTTT
208969 ATTTATTT-AATTATTAACTT
1 ATTTATTTCAATT-TTAACTT
208989 GCCACAAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.29, C:0.10, G:0.00, T:0.61
Consensus pattern (21 bp):
ATTTATTTCAATTTTAACTTT
Found at i:209529 original size:30 final size:30
Alignment explanation
Indices: 209465--209529 Score: 89
Period size: 29 Copynumber: 2.2 Consensus size: 30
209455 AGACAACCAA
*
209465 TTAAGGGAGGAGGGAGCCCAAACCGTCCAC
1 TTAAGGGAGGAAGGAGCCCAAACCGTCCAC
*
209495 -TAAGGGAGGAAAGGAG-CCTAACCGTCCAC
1 TTAAGGGAGG-AAGGAGCCCAAACCGTCCAC
209524 TTAAGG
1 TTAAGG
209530 TGCCTAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
29 21 0.68
30 10 0.32
ACGTcount: A:0.32, C:0.23, G:0.32, T:0.12
Consensus pattern (30 bp):
TTAAGGGAGGAAGGAGCCCAAACCGTCCAC
Found at i:209813 original size:15 final size:15
Alignment explanation
Indices: 209784--209827 Score: 63
Period size: 15 Copynumber: 3.0 Consensus size: 15
209774 CAAGCAATTG
209784 TCATT-ATTCACTCA
1 TCATTCATTCACTCA
*
209798 TCATTCATTCATTCA
1 TCATTCATTCACTCA
*
209813 TCTTTCATTCACTCA
1 TCATTCATTCACTCA
209828 CTACACATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 5 0.19
15 21 0.81
ACGTcount: A:0.25, C:0.30, G:0.00, T:0.45
Consensus pattern (15 bp):
TCATTCATTCACTCA
Found at i:219772 original size:29 final size:26
Alignment explanation
Indices: 219738--219791 Score: 72
Period size: 29 Copynumber: 2.0 Consensus size: 26
219728 AAAACAATTG
219738 AAAAGAAAAAAGAAAAGATGAGTAGAGAC
1 AAAAGAAAAAA-AAAA-ATGAGT-GAGAC
*
219767 AAAAGAGAAAAAAAAATGAGTGAGA
1 AAAAGAAAAAAAAAAATGAGTGAGA
219792 AAGTATATGA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 4 0.17
27 6 0.25
28 4 0.17
29 10 0.42
ACGTcount: A:0.67, C:0.02, G:0.24, T:0.07
Consensus pattern (26 bp):
AAAAGAAAAAAAAAAATGAGTGAGAC
Found at i:224312 original size:18 final size:17
Alignment explanation
Indices: 224286--224321 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
224276 TAACTTTTGC
224286 TTTTACTTTCTATTTTA
1 TTTTACTTTCTATTTTA
*
224303 TTTTATCTTTTTATTTTA
1 TTTTA-CTTTCTATTTTA
224321 T
1 T
224322 GCTCTCAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTACTTTCTATTTTA
Found at i:225049 original size:23 final size:23
Alignment explanation
Indices: 225008--225051 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
224998 GAGGCAATTG
* *
225008 TTATACCTTGTGTACTGAGCCAT
1 TTATACCTTATATACTGAGCCAT
*
225031 TTATACCTTATATAGTGAGCC
1 TTATACCTTATATACTGAGCC
225052 TCATGGACCT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (23 bp):
TTATACCTTATATACTGAGCCAT
Found at i:225067 original size:21 final size:21
Alignment explanation
Indices: 225041--225082 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
225031 TTATACCTTA
*
225041 TATAGTG-AGCCTCATGGACCT
1 TATAGTGTA-CCTCATGAACCT
225062 TATAGTGTACCTCATGAACCT
1 TATAGTGTACCTCATGAACCT
225083 CAAGTGCATC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 18 0.95
22 1 0.05
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (21 bp):
TATAGTGTACCTCATGAACCT
Found at i:227054 original size:22 final size:23
Alignment explanation
Indices: 227012--227067 Score: 66
Period size: 22 Copynumber: 2.6 Consensus size: 23
227002 TATATTTTTT
*
227012 ATAATATACAAA-TTAAGTAAAA
1 ATAATATATAAATTTAAGTAAAA
*
227034 ATAATATATAAATTTTA-TAAAA
1 ATAATATATAAATTTAAGTAAAA
227056 A-AAT-TATAAATT
1 ATAATATATAAATT
227068 GTCGAATAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
20 8 0.26
21 3 0.10
22 17 0.55
23 3 0.10
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (23 bp):
ATAATATATAAATTTAAGTAAAA
Found at i:228412 original size:27 final size:28
Alignment explanation
Indices: 228360--228413 Score: 76
Period size: 27 Copynumber: 2.0 Consensus size: 28
228350 ACAACTACAG
*
228360 CTTTTATTATCCTAAATTATCTCCTTTC
1 CTTTTATTATCCAAAATTATCTCCTTTC
228388 CTTTTATTAT-CAAAATTA-CTACCTTT
1 CTTTTATTATCCAAAATTATCT-CCTTT
228414 TACTTTCAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 2 0.08
27 12 0.50
28 10 0.42
ACGTcount: A:0.26, C:0.22, G:0.00, T:0.52
Consensus pattern (28 bp):
CTTTTATTATCCAAAATTATCTCCTTTC
Found at i:228419 original size:28 final size:28
Alignment explanation
Indices: 228360--228419 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 28
228350 ACAACTACAG
* *
228360 CTTTTATTATCCTAAATTATCTCCTTTC
1 CTTTTATTATCCAAAATTATCTCCTTTA
228388 CTTTTATTAT-CAAAATTA-CTACCTTTTA
1 CTTTTATTATCCAAAATTATCT-CC-TTTA
228416 CTTT
1 CTTT
228420 CAACTTTCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.07
27 9 0.32
28 17 0.61
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (28 bp):
CTTTTATTATCCAAAATTATCTCCTTTA
Found at i:234927 original size:18 final size:18
Alignment explanation
Indices: 234904--234955 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
234894 TTGAACTTTA
234904 ATTTTTAATTATTTTAGG
1 ATTTTTAATTATTTTAGG
** *
234922 ATTTTTTTTTATTTTAAG
1 ATTTTTAATTATTTTAGG
*
234940 ACTTTTAATT-TTTTAG
1 ATTTTTAATTATTTTAG
234956 ATAATTTCTT
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
17 5 0.19
18 22 0.81
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.65
Consensus pattern (18 bp):
ATTTTTAATTATTTTAGG
Found at i:235129 original size:11 final size:12
Alignment explanation
Indices: 235108--235217 Score: 50
Period size: 11 Copynumber: 9.3 Consensus size: 12
235098 GATTTATTTC
*
235108 TAAAATTAAATT
1 TAAATTTAAATT
*
235120 T-ACTTTAAATT
1 TAAATTTAAATT
235131 TAAATTTAAATT
1 TAAATTTAAATT
***
235143 CATTTTTTTAAATT
1 --TAAATTTAAATT
*
235157 TAAATTT-ATTT
1 TAAATTTAAATT
**
235168 TAAATTTCTATT
1 TAAATTTAAATT
*
235180 T-AGTTTAAATT
1 TAAATTTAAATT
*
235191 TGAAA--TAATTT
1 T-AAATTTAAATT
* *
235202 TAAACTTAAAAT
1 TAAATTTAAATT
235214 TAAA
1 TAAA
235218 AATCAATTAC
Statistics
Matches: 71, Mismatches: 19, Indels: 16
0.67 0.18 0.15
Matches are distributed among these distances:
10 3 0.04
11 33 0.46
12 25 0.35
13 1 0.01
14 9 0.13
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (12 bp):
TAAATTTAAATT
Found at i:235132 original size:6 final size:6
Alignment explanation
Indices: 235108--235217 Score: 50
Period size: 6 Copynumber: 18.7 Consensus size: 6
235098 GATTTATTTC
* * ***
235108 TAAAAT TAAATT T-ACTT TAAATT TAAATT TAAATT CATTTTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT --TAAATT TAAATT
* ** * *
235157 TAAATT T-ATTT TAAATT TCTATT T-AGTT TAAATT TGAAA-- TAATTT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T-AAATT TAAATT
* *
235202 TAAACT TAAAAT TAAA
1 TAAATT TAAATT TAAA
235218 AATCAATTAC
Statistics
Matches: 76, Mismatches: 20, Indels: 16
0.68 0.18 0.14
Matches are distributed among these distances:
4 2 0.03
5 12 0.16
6 56 0.74
7 3 0.04
8 3 0.04
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:235154 original size:20 final size:20
Alignment explanation
Indices: 235129--235168 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
235119 TTACTTTAAA
235129 TTTAAATTTAAATTCATTTT
1 TTTAAATTTAAATTCATTTT
*
235149 TTTAAATTTAAATTTATTTT
1 TTTAAATTTAAATTCATTTT
235169 AAATTTCTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (20 bp):
TTTAAATTTAAATTCATTTT
Found at i:235170 original size:17 final size:17
Alignment explanation
Indices: 235094--235211 Score: 74
Period size: 17 Copynumber: 7.4 Consensus size: 17
235084 TTAGATGGAT
*
235094 TTTAGATTTATTTCTAAA
1 TTTAAATTTATTT-TAAA
* *
235112 ATTAAATTTACTTTAAA
1 TTTAAATTTATTTTAAA
235129 TTT-AA---A-TTTAAA
1 TTTAAATTTATTTTAAA
*
235141 -TT-CATTT-TTTTAAA
1 TTTAAATTTATTTTAAA
235155 TTTAAATTTATTTTAAA
1 TTTAAATTTATTTTAAA
** *
235172 TTTCTATTTAGTTTAAA
1 TTTAAATTTATTTTAAA
*
235189 TTTGAAA-TAATTTTAAA
1 TTT-AAATTTATTTTAAA
*
235206 CTTAAA
1 TTTAAA
235212 ATTAAAAATC
Statistics
Matches: 78, Mismatches: 14, Indels: 18
0.71 0.13 0.16
Matches are distributed among these distances:
11 3 0.04
12 6 0.08
13 1 0.01
14 6 0.08
15 2 0.03
16 9 0.12
17 40 0.51
18 11 0.14
ACGTcount: A:0.40, C:0.04, G:0.03, T:0.53
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:236435 original size:30 final size:30
Alignment explanation
Indices: 236401--236470 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
236391 CAGCGAAGGT
* * *
236401 GTCGGATGACAACGCGTGACAGCGACGTGC
1 GTCGGACGACAACGCGCGACAGCGACGCGC
236431 GTCGGACGACAACGCGCGACAGCGACGCGC
1 GTCGGACGACAACGCGCGACAGCGACGCGC
236461 GTCGGACGAC
1 GTCGGACGAC
236471 GATCGAAGGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.23, C:0.31, G:0.37, T:0.09
Consensus pattern (30 bp):
GTCGGACGACAACGCGCGACAGCGACGCGC
Done.