Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.04
Sequence: scaffold1583
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 1104062
ACGTcount: A:0.27, C:0.14, G:0.14, T:0.27
Warning! 201198 characters in sequence are not A, C, G, or T
File 4 of 3
Found at i:764158 original size:2 final size:2
Alignment explanation
Indices: 764151--764196 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
764141 ATATCTCTTT
764151 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
764193 TC TC
1 TC TC
764197 AGTGACTTTG
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:768259 original size:3 final size:3
Alignment explanation
Indices: 768251--768276 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
768241 TTCACTTTTC
768251 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
768277 CTTTTTTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:769180 original size:110 final size:111
Alignment explanation
Indices: 768976--769181 Score: 247
Period size: 110 Copynumber: 1.9 Consensus size: 111
768966 CTTTCTTGAA
* * *
768976 ATGATTGGATTAAATTTTACATTTTTCAAAAATATTAAACTCATTTAAATCATGTCAAAATGACC
1 ATGATTGGATTAAATTTTAAAATTTTCAAAAATATTAAACTCATGTAAATCATGTCAAAATGACC
* ** ** * *
769041 TCAGACTAATTTCAAATTATGATATTTCAGTCAAATTCTGCGTCTG
66 TCAGAATAATTTCAAAACAAAAAAATTCAGTCAAATTCTGCGTCTG
* **
769087 ATGATTGGATTAAA-TTTAAAATTTTCAAAAA-ATTTAAACTCATGTAAATCGTGTTGAAATGAC
1 ATGATTGGATTAAATTTTAAAATTTTCAAAAATA-TTAAACTCATGTAAATCATGTCAAAATGAC
*
769150 CTCA-ATATAATTTTAAAACAAAAAAATTCAGT
65 CTCAGA-ATAATTTCAAAACAAAAAAATTCAGT
769182 TTTTTAAAAC
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
109 2 0.03
110 63 0.80
111 14 0.18
ACGTcount: A:0.41, C:0.12, G:0.10, T:0.37
Consensus pattern (111 bp):
ATGATTGGATTAAATTTTAAAATTTTCAAAAATATTAAACTCATGTAAATCATGTCAAAATGACC
TCAGAATAATTTCAAAACAAAAAAATTCAGTCAAATTCTGCGTCTG
Found at i:769188 original size:23 final size:23
Alignment explanation
Indices: 769160--769205 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
769150 CTCAATATAA
*
769160 TTTTAAAACAAAAAAATTCAGTT
1 TTTTAAAACAAAAAAATACAGTT
769183 TTTTAAAACAAAAAAATACAGTT
1 TTTTAAAACAAAAAAATACAGTT
769206 GCACTTGCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.09, G:0.04, T:0.33
Consensus pattern (23 bp):
TTTTAAAACAAAAAAATACAGTT
Found at i:769425 original size:133 final size:132
Alignment explanation
Indices: 769242--769863 Score: 643
Period size: 133 Copynumber: 4.6 Consensus size: 132
769232 TTTTTTTTTC
* * * * * *
769242 GAATTGATTGGATTAAATTTTAATTTTTTTAAAATTTTAAAACTCGTTTAATTCGAGTCAAAATG
1 GAATTGATTGGATT-AA-TTTAAATTTTTCAAAATTTT-AAACTCATTTAAATCGTGTTAAAATG
* ** ** * * * * *
769307 ACCTCAGAATAATTCCAAGTCATGACATTTAAGTTGCGC-TGTAATTTTGTGTCTAATGACAGTT
63 ACCTCAGACTAATTTGAAAACATGTCATCTAAGTTGCGCTTGCAATTTTGCGTCTAATGACAGCT
769371 TTCTT
128 TTCTT
* ***
769376 GAATTGATTGGATTAGATTTAAATTTTTCAAAATTGTTAAACTTATTTAAATCGTGTTGTTATGA
1 GAATTGATTGGATTA-ATTTAAATTTTTCAAAATT-TTAAACTCATTTAAATCGTGTTAAAATGA
* * * *
769441 CCTCAGACTATTTTGAAAACATGTCATCAAAGTTGCGCTTGCAATTCTGCGTCTAATGACAGCGT
64 CCTCAGACTAATTTGAAAACATGTCATCTAAGTTGCGCTTGCAATTTTGCGTCTAATGACAGCTT
769506 TCTT
129 TCTT
* * * ** * *
769510 GAATTTATTGAATTAAATTAAAAATTTCAAAAACTTTAAACTCATTTAAATCGTGTCAAAATGAC
1 GAATTGATTGGATTAATTTAAATTTTTC-AAAATTTTAAACTCATTTAAATCGTGTTAAAATGAC
* * * ** * * * *
769575 CTCAGACTCATTTGAAAAGATGTCAGCTAAGTTGCATTTGCAATTTTTCGTCCAAAGAGAGCTTT
65 CTCAGACTAATTTGAAAACATGTCATCTAAGTTGCGCTTGCAATTTTGCGTCTAATGACAGCTTT
*
769640 CTC
130 CTT
* *
769643 GAATTGGTTGGATTAAGTTTAAATTTTTCAAAATTTTAAAACTCATTTAAATCGTGTTGAAATGA
1 GAATTGATTGGATTAA-TTTAAATTTTTCAAAATTTT-AAACTCATTTAAATCGTGTTAAAATGA
** * * *
769708 TTTCAGACTAATTTGAAAACATGCCAACTAAGTTGTGCTTGCAATTTCTGCGTCTAATGACAGCT
64 CCTCAGACTAATTTGAAAACATGTCATCTAAGTTGCGCTTGCAATTT-TGCGTCTAATGACAGCT
769773 TTCTT
128 TTCTT
* * * *
769778 GAATTGATTGAATTAAACTTAAATTTTTCAAAAATCTATTAAACTCATATAAATCGTTTTAAAAT
1 GAATTGATTGGATT-AATTTAAATTTTTC-AAAAT-T-TTAAACTCATTTAAATCGTGTTAAAAT
*
769843 GACCTCAGAATAATTTGAAAA
62 GACCTCAGACTAATTTGAAAA
769864 TTTTATATCT
Statistics
Matches: 396, Mismatches: 81, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
133 174 0.44
134 132 0.33
135 40 0.10
136 7 0.02
137 41 0.10
138 2 0.01
ACGTcount: A:0.34, C:0.13, G:0.14, T:0.38
Consensus pattern (132 bp):
GAATTGATTGGATTAATTTAAATTTTTCAAAATTTTAAACTCATTTAAATCGTGTTAAAATGACC
TCAGACTAATTTGAAAACATGTCATCTAAGTTGCGCTTGCAATTTTGCGTCTAATGACAGCTTTC
TT
Found at i:769693 original size:267 final size:271
Alignment explanation
Indices: 769370--769863 Score: 739
Period size: 267 Copynumber: 1.8 Consensus size: 271
769360 TAATGACAGT
* *
769370 TTTCTTGAATTGATTGGATTAGATTTAAATTTTTCAAAATTGTTAAACTTATTTAAATCGTGTTG
1 TTTCTCGAATTGATTGGATTAGATTTAAATTTTTCAAAATTGTTAAACTCATTTAAATCGTGTTG
** * * *
769435 TTATGACCTCAGACTATTTTGAAAACATGTCATCAAAGTTGCGCTTGCAA-TTCTGCGTCTAATG
66 AAATGACCTCAGACTAATTTGAAAACATGCCAACAAAGTTGCGCTTGCAATTTCTGCGTCTAATG
* *
769499 ACAGCGTTCTTGAATTTATTGAATTAAA-TTAAAAATTTCAAAAA-CT-TTAAACTCATTTAAAT
131 ACAGCGTTCTTGAATTGATTGAATTAAACTTAAAAATTTCAAAAATCTATTAAACTCATATAAAT
* *
769561 CGTGTCAAAATGACCTCAGACTCATTTGAAAAGATGTCAGCTAAGTTGCATTTGCAATTTTTCGT
196 CGTGTCAAAATGACCTCAGAATAATTTGAAAAGATGTCAGCTAAGTTGCATTTGCAATTTTTCGT
769626 CCAAAGAGAGC
261 CCAAAGAGAGC
*
769637 TTTCTCGAATTGGTTGGATTA-AGTTTAAATTTTTCAAAATT-TTAAAACTCATTTAAATCGTGT
1 TTTCTCGAATTGATTGGATTAGA-TTTAAATTTTTCAAAATTGTT-AAACTCATTTAAATCGTGT
** * *
769700 TGAAATGATTTCAGACTAATTTGAAAACATGCCAACTAAGTTGTGCTTGCAATTTCTGCGTCTAA
64 TGAAATGACCTCAGACTAATTTGAAAACATGCCAACAAAGTTGCGCTTGCAATTTCTGCGTCTAA
* **
769765 TGACAGCTTTCTTGAATTGATTGAATTAAACTTAAATTTTTCAAAAATCTATTAAACTCATATAA
129 TGACAGCGTTCTTGAATTGATTGAATTAAACTTAAAAATTTCAAAAATCTATTAAACTCATATAA
* *
769830 ATCGTTTTAAAATGACCTCAGAATAATTTGAAAA
194 ATCGTGTCAAAATGACCTCAGAATAATTTGAAAA
769864 TTTTATATCT
Statistics
Matches: 200, Mismatches: 21, Indels: 8
0.87 0.09 0.03
Matches are distributed among these distances:
266 3 0.01
267 98 0.49
268 40 0.20
269 14 0.07
270 2 0.01
271 43 0.22
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.38
Consensus pattern (271 bp):
TTTCTCGAATTGATTGGATTAGATTTAAATTTTTCAAAATTGTTAAACTCATTTAAATCGTGTTG
AAATGACCTCAGACTAATTTGAAAACATGCCAACAAAGTTGCGCTTGCAATTTCTGCGTCTAATG
ACAGCGTTCTTGAATTGATTGAATTAAACTTAAAAATTTCAAAAATCTATTAAACTCATATAAAT
CGTGTCAAAATGACCTCAGAATAATTTGAAAAGATGTCAGCTAAGTTGCATTTGCAATTTTTCGT
CCAAAGAGAGC
Found at i:788181 original size:13 final size:13
Alignment explanation
Indices: 788163--788193 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
788153 TTAGTAAAAG
788163 TTAGTAATAGATA
1 TTAGTAATAGATA
788176 TTAGTAATAGATA
1 TTAGTAATAGATA
788189 TTAGT
1 TTAGT
788194 TCAAGGTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.16, T:0.42
Consensus pattern (13 bp):
TTAGTAATAGATA
Found at i:788603 original size:66 final size:66
Alignment explanation
Indices: 788497--788631 Score: 270
Period size: 66 Copynumber: 2.0 Consensus size: 66
788487 TTTGCTCTAG
788497 TTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTTATT
1 TTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTTATT
788562 A
66 A
788563 TTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTTATT
1 TTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTTATT
788628 A
66 A
788629 TTA
1 TTA
788632 TTATTCTTTT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
66 69 1.00
ACGTcount: A:0.19, C:0.19, G:0.13, T:0.49
Consensus pattern (66 bp):
TTAGGGTCTTCCGTCTTCAGCGGAAGACCCTTCTATTATTCTATTGTTTCTTTTTCAATTTTATT
A
Found at i:791009 original size:446 final size:445
Alignment explanation
Indices: 789961--791209 Score: 2225
Period size: 446 Copynumber: 2.8 Consensus size: 445
789951 CCGTAAGTTA
* * *
789961 AATACCCTTTGACATTAAGACTTCAAACTTAGAACATAGGTAGATGGTATTGAAAAGGAGTGCAC
1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTAATGAGAAGGAGTGCAC
* * * * * * * *
790026 GCCACCAAAAGTTTTGACCTTGACCTATTTT-CTTTTTCAAGGTCAAACTTTTTATAAAAAACAT
66 GTCACCAAAAGTTTTGATCTTTACCTATTTTGC-TCTTCAATGTCAAGCTTTTCATAAAAAATAT
* *
790090 TGTTCGGACCATAACACAAGACTCCTTTAACTTACAGACTTTTAACTTGTATCATAGATAGATGG
130 TGTTCGGACCATAACACAAGACTCCTTTAACATACACACTTTTAACTTGTATCATAGATAGATGG
* *
790155 TATATAACCTAGTTGAACCTTACAAAAAATTTTGACCTTGACCTAGAATTATTATTTCAAAGTCA
195 TATATAACCTAGTTGAACCTTACCAAAAATTTTGACCTTGACCTAGAATTATTATTTCAAGGTCA
790220 TATTAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAA
260 TATTAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAA
790285 CAAAGAACAATAATAATACACTTAGGTGTACTA-TTGAATAATATTTGACCTTGACCTTGGTTTA
325 CAAAGAACAATAATAATACACTTAGGTGTACTATTTGAATAATATTTGACCTTGACCTTGGTTTA
790349 CTCAAGGTCAAATTAATTAGAAAAAAATAAGAAAATTTTGTCTGGATCATAACTTT
390 CTCAAGGTCAAATTAATTAGAAAAAAATAAGAAAATTTTGTCTGGATCATAACTTT
790405 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTAATGAGAAGGAGTGCAC
1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTAATGAGAAGGAGTGCAC
790470 GTCACCAAAAGTTTTGATCTTTACCTATTTTGCTCTTCAATGTCAAGCTTTTCATAAAAAATATT
66 GTCACCAAAAGTTTTGATCTTTACCTATTTTGCTCTTCAATGTCAAGCTTTTCATAAAAAATATT
790535 GTTCGGACCATAACACAAGACTCCTTTAACATACACACTTTTAACTTGTATCATAGATAGATGGT
131 GTTCGGACCATAACACAAGACTCCTTTAACATACACACTTTTAACTTGTATCATAGATAGATGGT
790600 ATATAACCTAGTTGAACCTTACCAAAAATTTTGACCTTGACCTAGAATTATTATTTCAAGGTCAT
196 ATATAACCTAGTTGAACCTTACCAAAAATTTTGACCTTGACCTAGAATTATTATTTCAAGGTCAT
790665 ATTAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC
261 ATTAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC
* *
790730 AAAGAACAATAATAATACACTTAGGTGTACTATTTAATAATAATATTTGACCTTGACCTTGTTTT
326 AAAGAACAATAATAATACACTTAGGTGTACTATTT--GAATAATATTTGACCTTGACCTTGGTTT
790795 ACTCAAGGTCAAATTAA-TAGAAAAAAATAAGAAAATTTTGTCTGGATCATAACTTT
389 ACTCAAGGTCAAATTAATTAGAAAAAAATAAGAAAATTTTGTCTGGATCATAACTTT
790851 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTAATGAGAAGGAGTGCAC
1 AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTAATGAGAAGGAGTGCAC
790916 GTCACCAAAAGTTTTGATCTTTACCTATTTTGCTCTTCAATGTCAAGCTTTTCATAAAAAATATT
66 GTCACCAAAAGTTTTGATCTTTACCTATTTTGCTCTTCAATGTCAAGCTTTTCATAAAAAATATT
* *
790981 GTTCGGACCATAACACAAGACTCCTTTAACATACACACTTTTAACTTGTATCAGATATAGATGGT
131 GTTCGGACCATAACACAAGACTCCTTTAACATACACACTTTTAACTTGTATCATAGATAGATGGT
* * *
791046 ATATAACCTAGTTGAACCTTACCAAAATTTTTGACCTTGACCTAGAATTTTTATTTCAAGGTCAA
196 ATATAACCTAGTTGAACCTTACCAAAAATTTTGACCTTGACCTAGAATTATTATTTCAAGGTCAT
* *
791111 ATTAGAAAAAACTTCATTGTTCAACTCCTGAATATACTTTGACAGAAGTACTTCAAACTTTAAAC
261 ATTAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC
*
791176 AAAGAACAATAATAATACACGTAGGTGTACTATT
326 AAAGAACAATAATAATACACTTAGGTGTACTATT
791210 GATTTANATT
Statistics
Matches: 776, Mismatches: 25, Indels: 6
0.96 0.03 0.01
Matches are distributed among these distances:
444 340 0.44
445 3 0.00
446 390 0.50
447 43 0.06
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (445 bp):
AATACCCTTTGACATTAAGACTTCAAACTTGGAACATAGGTAGATGGTAATGAGAAGGAGTGCAC
GTCACCAAAAGTTTTGATCTTTACCTATTTTGCTCTTCAATGTCAAGCTTTTCATAAAAAATATT
GTTCGGACCATAACACAAGACTCCTTTAACATACACACTTTTAACTTGTATCATAGATAGATGGT
ATATAACCTAGTTGAACCTTACCAAAAATTTTGACCTTGACCTAGAATTATTATTTCAAGGTCAT
ATTAGAAAAAACTTCATTGTTCAACTTCTGAATATACTTTGACAGAAGGACTTCAAACTTTAAAC
AAAGAACAATAATAATACACTTAGGTGTACTATTTGAATAATATTTGACCTTGACCTTGGTTTAC
TCAAGGTCAAATTAATTAGAAAAAAATAAGAAAATTTTGTCTGGATCATAACTTT
Found at i:794534 original size:4 final size:4
Alignment explanation
Indices: 794525--794580 Score: 112
Period size: 4 Copynumber: 14.0 Consensus size: 4
794515 ATTCCGAAGA
794525 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
1 AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT AGAT
794573 AGAT AGAT
1 AGAT AGAT
794581 GCAACATTCT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.25, T:0.25
Consensus pattern (4 bp):
AGAT
Found at i:798776 original size:4 final size:4
Alignment explanation
Indices: 798769--798867 Score: 189
Period size: 4 Copynumber: 24.8 Consensus size: 4
798759 TGGATGGATG
798769 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
*
798817 AATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
798865 GAT
1 GAT
798868 TGATGATTCA
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
4 93 1.00
ACGTcount: A:0.51, C:0.00, G:0.24, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:803632 original size:163 final size:164
Alignment explanation
Indices: 803302--803829 Score: 754
Period size: 163 Copynumber: 3.2 Consensus size: 164
803292 GCATCCTCAG
* * * *
803302 GTTGTGAAAATTATGACCCCCGGTGGTAGGGTGGGACCACAATGGGGGAGGGGGTCGAAGTTTAA
1 GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCATAATGGGGGA-----TCGAAGTTTAA
* * *
803367 CATAGGAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCGGTCAGGAAAGGT
61 CATAGGAATATATAGAGTAAATCTTTAAAAA--TTCTTCTCAGAAACTAATCAGCCAGGAAAGCT
* *
803432 GACACTTGTGTGAAAGCATCCTCAGGTAGTGTAGATTCAAA
124 GAAACTTGTTTGAAAGCATCCTCAGGTAGTGTAGATTCAAA
*
803473 GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCATAATGGGGGATCGAAGTTTTACATAG
1 GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCATAATGGGGGATCGAAGTTTAACATAG
* *
803538 GAATATTTAGAGTAAATCTTTAAAAA-TCTTCTCAGATACTAATCAGCCAGGAAAGCTGAAACTT
66 GAATATATAGAGTAAATCTTTAAAAATTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTT
* * *
803602 GTTTGAAAGCATCCTAAGATAATGTAGATTCAAA
131 GTTTGAAAGCATCCTCAGGTAGTGTAGATTCAAA
* * *
803636 GTTGTGAAAATCATGACCCCCGCGGGTAGGGTGGGGCCATAATGGGGGATCGAAGGTTAACAAAG
1 GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCATAATGGGGGATCGAAGTTTAACATAG
*
803701 GAATATATAGAGTAAATCTTTAAAAATCTTCTTCTCAGAAACTAATCAGCCAGCAAAGCTGAAAC
66 GAATATATAGAGTAAATCTTTAAAAA--TTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAAC
*
803766 TTGTGTTG-AAGCATCCTCAGGTAGTGTAGATTTAAA
129 TTGT-TTGAAAGCATCCTCAGGTAGTGTAGATTCAAA
* *
803802 GTTGTGAAAATCATGATCCCCAGGGGTA
1 GTTGTGAAAATCATGACCCCCGGGGGTA
803830 TATATAGGGT
Statistics
Matches: 324, Mismatches: 29, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
163 149 0.46
166 127 0.39
167 3 0.01
171 45 0.14
ACGTcount: A:0.33, C:0.15, G:0.26, T:0.26
Consensus pattern (164 bp):
GTTGTGAAAATCATGACCCCCGGGGGTAGGGTGGGGCCATAATGGGGGATCGAAGTTTAACATAG
GAATATATAGAGTAAATCTTTAAAAATTCTTCTCAGAAACTAATCAGCCAGGAAAGCTGAAACTT
GTTTGAAAGCATCCTCAGGTAGTGTAGATTCAAA
Found at i:808649 original size:116 final size:112
Alignment explanation
Indices: 808445--808668 Score: 313
Period size: 116 Copynumber: 2.0 Consensus size: 112
808435 GTTCGTTCGT
* * *
808445 GTATATCTAATTAGAGTCTATTGTTTGTTTTACTTACGAAAACCCCTGAAACTAACACAGAATAT
1 GTATATCTAATTAGAGTCTATTGTTTGTCTTAATTAAGAAAACCCCTGAAACTAACACAGAATAT
* ** *
808510 ACAAGATATACACAACATATGTGTCTTGTGCCCGGGTGCACGTTTGC
66 ACAAGATATACACAACAGATGTGTAGTGTGCCCAGGTGCACGTTTGC
* *
808557 GTATATCTAATTAGAGTCTATTGTTTGTCCAACTTAATTAAGAAAACTCCTGGAACTAACACAGA
1 GTATATCTAATTAGAGTCTATTGTTTGT----CTTAATTAAGAAAACCCCTGAAACTAACACAGA
* *
808622 ATATACAAGATATACACAACAGGTGTGTAGTGTGCCCATGTGCACGT
62 ATATACAAGATATACACAACAGATGTGTAGTGTGCCCAGGTGCACGT
808669 CAGTGTTTCT
Statistics
Matches: 97, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
112 28 0.29
116 69 0.71
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (112 bp):
GTATATCTAATTAGAGTCTATTGTTTGTCTTAATTAAGAAAACCCCTGAAACTAACACAGAATAT
ACAAGATATACACAACAGATGTGTAGTGTGCCCAGGTGCACGTTTGC
Found at i:809681 original size:11 final size:11
Alignment explanation
Indices: 809665--809696 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
809655 ATTTTTTGAA
809665 TAGCTTAAAGG
1 TAGCTTAAAGG
809676 TAGCTTAAAGG
1 TAGCTTAAAGG
*
809687 TGGCTTAAAG
1 TAGCTTAAAG
809697 AAGTTTGGAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.34, C:0.09, G:0.28, T:0.28
Consensus pattern (11 bp):
TAGCTTAAAGG
Found at i:809787 original size:22 final size:22
Alignment explanation
Indices: 809761--809813 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
809751 TTAAAGATAG
809761 TCTTTAAGCTGCCTTTAAGCCA
1 TCTTTAAGCTGCCTTTAAGCCA
* **
809783 TCTTTACGCTTTCTTTAAGCCA
1 TCTTTAAGCTGCCTTTAAGCCA
*
809805 CCTTTAAGC
1 TCTTTAAGC
809814 AACATATATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.21, C:0.28, G:0.11, T:0.40
Consensus pattern (22 bp):
TCTTTAAGCTGCCTTTAAGCCA
Found at i:810994 original size:178 final size:180
Alignment explanation
Indices: 810499--811115 Score: 990
Period size: 178 Copynumber: 3.4 Consensus size: 180
810489 ACCCTACATG
* * *
810499 TATATGCAACATTTTGCCAAAAAATGAC-ATGGTTCAAAAGCTAGTATTTTTTTC-ATAAAGTAT
1 TATATGCAACATTTTGCCAAAAAATGACTA-AGTTCAAAAGCTGGTA-TTTTTTCGATAAATTAT
* *
810562 CGGAAATCAAAATCCCAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACA
64 CAGAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAG---A
*
810627 ACTAACTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCATACAATGAGGGTACCC
126 AC-AACTTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
810683 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
* *
810748 GAAGTCAAAATCCTAGCAATATGCACACCTCTAATATATGTACAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
* *
810813 TTCCTATCTTGAGAACTGTAGGAGGAGCTATCCGTACAATGAGGGTATCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* * *
810863 TATATGCAATATTTTGCCAAAAAAT-TCTAAGTTCAAAAGCTGGTATTTTTTC-ATAAATAATCA
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
* *
810926 GAAATCAAAATCCTAGCAAAATGCACACCTCTGATATATGTATAATTGATCTGCAAAAGAACAAC
66 GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
*
810991 TTCCTATCTTGAAAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
131 TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
* *
811041 TATATGCAATATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCG
1 TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
811106 GAAATCAAAA
66 GAAATCAAAA
811116 NNNNNNNNNN
Statistics
Matches: 406, Mismatches: 23, Indels: 12
0.92 0.05 0.03
Matches are distributed among these distances:
178 143 0.35
179 52 0.13
180 93 0.23
181 3 0.01
183 7 0.02
184 107 0.26
185 1 0.00
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (180 bp):
TATATGCAACATTTTGCCAAAAAATGACTAAGTTCAAAAGCTGGTATTTTTTCGATAAATTATCA
GAAATCAAAATCCTAGCAATATGCACACCTCTGATATATGTACAATTGATCTGCAAAAGAACAAC
TTCCTATCTTGAGAACTGTAGGAGGAGTTATCCGTACAATGAGGGTACCC
Found at i:813810 original size:20 final size:20
Alignment explanation
Indices: 813785--813826 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
813775 ACCTAATTTG
*
813785 TTCATGTCAGGGCGGAAAGA
1 TTCATGTCAAGGCGGAAAGA
813805 TTCATGTCAAGGCGGAAAGA
1 TTCATGTCAAGGCGGAAAGA
813825 TT
1 TT
813827 TAGTCCATGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.31, C:0.14, G:0.31, T:0.24
Consensus pattern (20 bp):
TTCATGTCAAGGCGGAAAGA
Found at i:825460 original size:31 final size:30
Alignment explanation
Indices: 825418--825481 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 30
825408 TTCTTCACAT
825418 CTATAAGATTTTTAAAAAATAAA-ATCAATAA
1 CTATAAGATTTTTAAAAAA-AAATA-CAATAA
*
825449 CTATAATATTTTTAAAAAAAAATACAATAA
1 CTATAAGATTTTTAAAAAAAAATACAATAA
825479 CTA
1 CTA
825482 GCCAGTAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
30 12 0.39
31 19 0.61
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (30 bp):
CTATAAGATTTTTAAAAAAAAATACAATAA
Found at i:825477 original size:30 final size:31
Alignment explanation
Indices: 825418--825481 Score: 96
Period size: 30 Copynumber: 2.1 Consensus size: 31
825408 TTCTTCACAT
825418 CTATAAGATTTTTAAAAAATAAAATCAATAA
1 CTATAAGATTTTTAAAAAATAAAATCAATAA
*
825449 CTATAATATTTTT-AAAAA-AAAATACAATAA
1 CTATAAGATTTTTAAAAAATAAAAT-CAATAA
825479 CTA
1 CTA
825482 GCCAGTAGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
29 5 0.16
30 14 0.45
31 12 0.39
ACGTcount: A:0.58, C:0.08, G:0.02, T:0.33
Consensus pattern (31 bp):
CTATAAGATTTTTAAAAAATAAAATCAATAA
Found at i:850714 original size:21 final size:21
Alignment explanation
Indices: 850673--850787 Score: 151
Period size: 21 Copynumber: 5.4 Consensus size: 21
850663 TTCTGTCCTT
*
850673 ACATGCAAGATAAATTTTGTCA
1 ACATGCAAGA-AAATTATGTCA
850695 ACATGCAAGAAAATTATGTCA
1 ACATGCAAGAAAATTATGTCA
850716 ACATGCAAGAAAATTATGTCA
1 ACATGCAAGAAAATTATGTCA
* *
850737 ACATGCAAGATAATTATGTCG
1 ACATGCAAGAAAATTATGTCA
** *
850758 ACATGCTTGATAATTATGT-A
1 ACATGCAAGAAAATTATGTCA
850778 TACATGCAAG
1 -ACATGCAAG
850788 TTACAAATCT
Statistics
Matches: 84, Mismatches: 8, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
21 74 0.88
22 10 0.12
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.29
Consensus pattern (21 bp):
ACATGCAAGAAAATTATGTCA
Found at i:850990 original size:21 final size:21
Alignment explanation
Indices: 850961--851069 Score: 101
Period size: 21 Copynumber: 5.1 Consensus size: 21
850951 ACATGCAAAA
*
850961 AATTAATGTCAACATGCGAGAT
1 AATT-ATGTTAACATGCGAGAT
* **
850983 AATTATGTTGACATGCGACTTT
1 AATTATGTTAACATGCGA-GAT
** * *
851005 TTTTATGTTAACATGCAAGTT
1 AATTATGTTAACATGCGAGAT
*
851026 AATTATGTTAACATGCAAGAT
1 AATTATGTTAACATGCGAGAT
* *
851047 AGTTATGTCAACATGCGAGAT
1 AATTATGTTAACATGCGAGAT
851068 AA
1 AA
851070 CTAGTTTAAA
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
21 51 0.73
22 19 0.27
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.35
Consensus pattern (21 bp):
AATTATGTTAACATGCGAGAT
Found at i:851042 original size:85 final size:84
Alignment explanation
Indices: 850901--851069 Score: 214
Period size: 85 Copynumber: 2.0 Consensus size: 84
850891 TGCGACTTGT
* * *
850901 TTATATTGACATGCGACTTACTTATGTGAACATGCAGGTTAGTTGTAATAACATGCAA-AAAATT
1 TTATATTGACATGCGACTTACTTATGTGAACATGCAAGTTAATTATAATAACATGCAAGAAAATT
850965 AATGTCAACATGCGAGATAA
66 -ATGTCAACATGCGAGATAA
* ** * ** * *
850985 TTATGTTGACATGCGACTTTTTTTATGTTAACATGCAAGTTAATTATGTTAACATGCAAGATAGT
1 TTATATTGACATGCGAC-TTACTTATGTGAACATGCAAGTTAATTATAATAACATGCAAGAAAAT
851050 TATGTCAACATGCGAGATAA
65 TATGTCAACATGCGAGATAA
851070 CTAGTTTAAA
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
84 16 0.22
85 52 0.72
86 4 0.06
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.34
Consensus pattern (84 bp):
TTATATTGACATGCGACTTACTTATGTGAACATGCAAGTTAATTATAATAACATGCAAGAAAATT
ATGTCAACATGCGAGATAA
Found at i:854012 original size:2 final size:2
Alignment explanation
Indices: 854005--854039 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
853995 TTAACCATGG
854005 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
854040 GAATTCCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:857894 original size:29 final size:29
Alignment explanation
Indices: 857862--858272 Score: 130
Period size: 29 Copynumber: 14.2 Consensus size: 29
857852 AGAGACAAGC
*
857862 AAACCTGTCATAACGAACCATTCATATAG
1 AAACCTGTCATAACGAACCATACATATAG
** * *
857891 AAACCCATCAAAACGAACCAAACATATAG
1 AAACCTGTCATAACGAACCATACATATAG
* * * *
857920 AAACTTCTTATAACGAACAAGACATATATATAG
1 AAACCTGTCATAACGAAC----CATACATATAG
* *
857953 AAACCTGTC-TAAC-AACTGAGACATATAG
1 AAACCTGTCATAACGAAC-CATACATATAG
* *
857981 AAACATGTTATAACGAA-C---C----AG
1 AAACCTGTCATAACGAACCATACATATAG
* * *
858002 AAACCTGTTATAACGAACCAGACATGTAG
1 AAACCTGTCATAACGAACCATACATATAG
* * * *
858031 AAACCTGTTACAACGAACAAGACATATAG
1 AAACCTGTCATAACGAACCATACATATAG
* * * *
858060 AAACCTGCCATAAAGAGCAAGGTACACGTATATAG
1 AAACCTGTCATAACGAACCA--T--AC--ATATAG
** * * ***
858095 AAATTTAT-ATTTACGAACCAGGTATATAG
1 AAACCTGTCA-TAACGAACCATACATATAG
* * * *
858124 AAACCTATTATAACGAACCAGACATATAA
1 AAACCTGTCATAACGAACCATACATATAG
** * * *
858153 AAACCAATGACAATG-ACCATATC-TACT-G
1 AAACCTGTCATAACGAACCATA-CATA-TAG
* * * * *
858181 AAACCTGCCACAATGAACCATACACACAG
1 AAACCTGTCATAACGAACCATACATATAG
** *
858210 AAACCTGTCATAACGATTCAGACATATAG
1 AAACCTGTCATAACGAACCATACATATAG
* * * *
858239 AAACCTTTCAGAACGAACCAGACGTATAG
1 AAACCTGTCATAACGAACCATACATATAG
858268 AAACC
1 AAACC
858273 AAAAAGAACC
Statistics
Matches: 281, Mismatches: 74, Indels: 54
0.69 0.18 0.13
Matches are distributed among these distances:
21 18 0.06
22 1 0.00
25 2 0.01
28 34 0.12
29 182 0.65
30 3 0.01
31 3 0.01
32 4 0.01
33 17 0.06
34 1 0.00
35 16 0.06
ACGTcount: A:0.45, C:0.22, G:0.13, T:0.20
Consensus pattern (29 bp):
AAACCTGTCATAACGAACCATACATATAG
Found at i:858003 original size:21 final size:21
Alignment explanation
Indices: 857979--858023 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
857969 TGAGACATAT
857979 AGAAACATGTTATAACGAACC
1 AGAAACATGTTATAACGAACC
*
858000 AGAAACCTGTTATAACGAACC
1 AGAAACATGTTATAACGAACC
858021 AGA
1 AGA
858024 CATGTAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.20, G:0.16, T:0.18
Consensus pattern (21 bp):
AGAAACATGTTATAACGAACC
Found at i:871939 original size:2 final size:2
Alignment explanation
Indices: 871926--871991 Score: 114
Period size: 2 Copynumber: 33.0 Consensus size: 2
871916 TGGGAAACAA
* *
871926 AG AG AA AG AG AG AG AG AG AA AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
871968 AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG
871992 GGGTATAATT
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:873478 original size:53 final size:52
Alignment explanation
Indices: 873398--873504 Score: 196
Period size: 53 Copynumber: 2.0 Consensus size: 52
873388 TCAAGCAATA
873398 TATACATATTTCATAATATATTTCGTAAAAGCAATACAACAACCACTTTGCC
1 TATACATATTTCATAATATATTTCGTAAAAGCAATACAACAACCACTTTGCC
*
873450 NTATACATATTTCATAATATATTTCGTAAAAGCAATACAATAACCACTTTGCC
1 -TATACATATTTCATAATATATTTCGTAAAAGCAATACAACAACCACTTTGCC
873503 TA
1 TA
873505 CTAAGAGTTA
Statistics
Matches: 53, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
52 2 0.04
53 51 0.96
ACGTcount: A:0.40, C:0.20, G:0.06, T:0.34
Consensus pattern (52 bp):
TATACATATTTCATAATATATTTCGTAAAAGCAATACAACAACCACTTTGCC
Found at i:886238 original size:20 final size:20
Alignment explanation
Indices: 886209--886260 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
886199 CCAGGACGGT
886209 GGGAAATACTGGTAATTCCC
1 GGGAAATACTGGTAATTCCC
* *
886229 GGGAATTACTGGTATTTCCC
1 GGGAAATACTGGTAATTCCC
886249 GGGAAATACTGG
1 GGGAAATACTGG
886261 GAAATAAAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.27, C:0.17, G:0.29, T:0.27
Consensus pattern (20 bp):
GGGAAATACTGGTAATTCCC
Found at i:887898 original size:13 final size:14
Alignment explanation
Indices: 887863--887899 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
887853 AGACCAATCA
*
887863 ATTATAATATAAAT
1 ATTATAATATTAAT
887877 A-TATAATATTAAT
1 ATTATAATATTAAT
887890 ATTAT-ATATT
1 ATTATAATATT
887900 CTATATCATA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
ATTATAATATTAAT
Found at i:908532 original size:2 final size:2
Alignment explanation
Indices: 908525--908578 Score: 92
Period size: 2 Copynumber: 27.5 Consensus size: 2
908515 TTATAACTTT
*
908525 GA GA GA GA GA GA GA G- GA GA GA GA GA GA GA GG GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
908566 GA GA GA GA GA GA G
1 GA GA GA GA GA GA G
908579 GTGAAATCGA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.46, C:0.00, G:0.54, T:0.00
Consensus pattern (2 bp):
GA
Found at i:912674 original size:3 final size:3
Alignment explanation
Indices: 912666--912699 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
912656 CTTACAGATA
* *
912666 AAT AAT AAT AAT AAT AAT AAT ACT TAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
912700 TTCCAACCAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (3 bp):
AAT
Found at i:916034 original size:20 final size:20
Alignment explanation
Indices: 916009--916046 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
915999 ATTAATATAC
*
916009 AAGAGAGAGAGAGAAAGACA
1 AAGAGACAGAGAGAAAGACA
916029 AAGAGACAGAGAGAAAGA
1 AAGAGACAGAGAGAAAGA
916047 GAGATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.61, C:0.05, G:0.34, T:0.00
Consensus pattern (20 bp):
AAGAGACAGAGAGAAAGACA
Found at i:920683 original size:1 final size:1
Alignment explanation
Indices: 920679--920709 Score: 53
Period size: 1 Copynumber: 31.0 Consensus size: 1
920669 TTCCCCCACG
*
920679 CCCCCCCCCCACCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
920710 ATTTTAGACT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.03, C:0.97, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:920689 original size:13 final size:12
Alignment explanation
Indices: 920671--920709 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
920661 TCGGGGGGTT
920671 CCCCCACGCCCCC
1 CCCCCAC-CCCCC
920684 CCCCCACCCCCC
1 CCCCCACCCCCC
920696 CCCCC-CCCCCC
1 CCCCCACCCCCC
920707 CCC
1 CCC
920710 ATTTTAGACT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 9 0.35
12 10 0.38
13 7 0.27
ACGTcount: A:0.05, C:0.92, G:0.03, T:0.00
Consensus pattern (12 bp):
CCCCCACCCCCC
Found at i:926438 original size:2 final size:2
Alignment explanation
Indices: 926431--926475 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
926421 TTTCCGGTAC
926431 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
926473 GA G
1 GA G
926476 TCTATTCAAC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:933701 original size:20 final size:20
Alignment explanation
Indices: 933676--933757 Score: 137
Period size: 20 Copynumber: 4.1 Consensus size: 20
933666 TCATGACGAA
*
933676 ATATGAAACAATGTCGGAAT
1 ATATGAGACAATGTCGGAAT
933696 ATATGAGACAATGTCGGAAT
1 ATATGAGACAATGTCGGAAT
*
933716 ATATGAGACAATGTCGAAAT
1 ATATGAGACAATGTCGGAAT
*
933736 ATATGAGACAACGTCGGAAT
1 ATATGAGACAATGTCGGAAT
933756 AT
1 AT
933758 TTACATGTTT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (20 bp):
ATATGAGACAATGTCGGAAT
Found at i:934016 original size:2 final size:2
Alignment explanation
Indices: 934009--934065 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
933999 TCTTATCTGT
934009 GA GA GA GA GA GA -A GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
934050 GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA
934066 TTCTAAAGTC
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
GA
Found at i:936018 original size:4 final size:4
Alignment explanation
Indices: 936009--936080 Score: 51
Period size: 4 Copynumber: 18.0 Consensus size: 4
935999 CTGCACGATT
* *
936009 AATC AATC AATA AATC AATC AATC ACCA-C AAT- AA-C AATC GATC AATC
1 AATC AATC AATC AATC AATC AATC A--ATC AATC AATC AATC AATC AATC
* **
936056 AAATT GTTC AATC AATC AATC AATC
1 -AATC AATC AATC AATC AATC AATC
936081 GTTGGCAATT
Statistics
Matches: 52, Mismatches: 10, Indels: 12
0.70 0.14 0.16
Matches are distributed among these distances:
3 5 0.10
4 41 0.79
5 5 0.10
6 1 0.02
ACGTcount: A:0.49, C:0.24, G:0.03, T:0.25
Consensus pattern (4 bp):
AATC
Found at i:940336 original size:17 final size:17
Alignment explanation
Indices: 940314--940347 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
940304 AAGCTACTAT
*
940314 ATAGTAGCTTTTCTCCC
1 ATAGTAGCATTTCTCCC
*
940331 ATAGTAGGATTTCTCCC
1 ATAGTAGCATTTCTCCC
940348 TAACGTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.26, G:0.15, T:0.38
Consensus pattern (17 bp):
ATAGTAGCATTTCTCCC
Found at i:941488 original size:166 final size:165
Alignment explanation
Indices: 941139--941566 Score: 730
Period size: 166 Copynumber: 2.6 Consensus size: 165
941129 AGAACCAGAA
* * * *
941139 AGCCAGGAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTGAAAGCTGTGAAATT
1 AGCCAGTAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT
* *
941204 CATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGTCGAAGTTTTACATAGGAATATGTAGAG
66 CATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGTCGAAATTTTACATAGGAATATATAGAG
941269 TAAATCTTTAAAAATCTTCTTCTTAGAAACTAATC
131 TAAATCTTTAAAAATCTTCTTCTTAGAAACTAATC
*
941304 AGCCAGTAAAGCTGAAACTTATGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT
1 AGCCAGTAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT
* *
941369 CATGACCCCTGGGAGTAGAGTGGGGCCACAATGGGGGCTCGAAATTTTACATAGGAATATATAGA
66 CATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGG-TCGAAATTTTACATAGGAATATATAGA
941434 GTAAATCTTTAAAAATCTTCTTCTTAGAAACTAATC
130 GTAAATCTTTAAAAATCTTCTTCTTAGAAACTAATC
* *
941470 AGCCAGTAAAGCTGAAACTTGTGTGGAAGCATCCTCAAGAAGTGTAGATTTAAAGTTGTGAAAAT
1 AGCCAGTAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT
* *
941535 CGTGACCCCTGGGGGTAGGGTGGGGCAACAAT
66 CATGACCCCTGGGGGTAGGGTGGGGCCACAAT
941567 CTTCTTCTCA
Statistics
Matches: 246, Mismatches: 16, Indels: 1
0.94 0.06 0.00
Matches are distributed among these distances:
165 95 0.39
166 151 0.61
ACGTcount: A:0.32, C:0.15, G:0.26, T:0.26
Consensus pattern (165 bp):
AGCCAGTAAAGCTGAAACTTGTGTGGAAGCATCCTCAGGTAGTGTAGATTTAAAGTTGTGAAAAT
CATGACCCCTGGGGGTAGGGTGGGGCCACAATGGGGGTCGAAATTTTACATAGGAATATATAGAG
TAAATCTTTAAAAATCTTCTTCTTAGAAACTAATC
Found at i:952916 original size:18 final size:19
Alignment explanation
Indices: 952893--952932 Score: 73
Period size: 18 Copynumber: 2.2 Consensus size: 19
952883 AGGTTTTTCC
952893 TATCTAAATACATATAA-A
1 TATCTAAATACATATAATA
952911 TATCTAAATACATATAATA
1 TATCTAAATACATATAATA
952930 TAT
1 TAT
952933 ATGTCTAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 17 0.81
19 4 0.19
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (19 bp):
TATCTAAATACATATAATA
Found at i:954818 original size:15 final size:16
Alignment explanation
Indices: 954798--954827 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
954788 CTGTAACTTA
954798 AACTTTATTT-GCAAC
1 AACTTTATTTCGCAAC
954813 AACTTTATTTCGCAA
1 AACTTTATTTCGCAA
954828 TTTATTAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.33, C:0.20, G:0.07, T:0.40
Consensus pattern (16 bp):
AACTTTATTTCGCAAC
Found at i:958672 original size:12 final size:12
Alignment explanation
Indices: 958655--958680 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
958645 CCGTCATCCC
958655 TCTGTCTGTCCG
1 TCTGTCTGTCCG
958667 TCTGTCTGTCCG
1 TCTGTCTGTCCG
958679 TC
1 TC
958681 CATCCGTCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.35, G:0.23, T:0.42
Consensus pattern (12 bp):
TCTGTCTGTCCG
Found at i:969405 original size:19 final size:19
Alignment explanation
Indices: 969381--969421 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
969371 CGACAGCCCT
*
969381 GGTTAAGGTTTTAGGAGCA
1 GGTTAAAGTTTTAGGAGCA
* *
969400 GGTTAAAGTTTTTGGTGCA
1 GGTTAAAGTTTTAGGAGCA
969419 GGT
1 GGT
969422 GCTTTTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.22, C:0.05, G:0.37, T:0.37
Consensus pattern (19 bp):
GGTTAAAGTTTTAGGAGCA
Found at i:970635 original size:12 final size:12
Alignment explanation
Indices: 970618--970644 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
970608 ATTGTCCGGC
970618 GTCCGTCTGTCT
1 GTCCGTCTGTCT
970630 GTCCGTCTGTCT
1 GTCCGTCTGTCT
970642 GTC
1 GTC
970645 TGTAAACTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.33, G:0.26, T:0.41
Consensus pattern (12 bp):
GTCCGTCTGTCT
Found at i:971333 original size:163 final size:164
Alignment explanation
Indices: 970778--971566 Score: 1048
Period size: 166 Copynumber: 4.7 Consensus size: 164
970768 TAAAAAAATC
*
970778 TTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATATTTGTGTGGAAGCATCCTCAGATAGTGTA
1 TTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGATAGTGTA
*
970843 GATTCAAGTTTGTTCAAATCATGGT-CCTCGGGGGTAAGGT-GGGCCTCAATAGGGGGTCGAATT
66 GATTCAAGTTTGTTCAAATCATGGTCCCT-GGGGGTAAGGTGGGGCCTCAATGGGGGGTCGAATT
*
970906 TTTACATCGGAGTATATAGAGTTAATTTTTAAAAA
130 TTTACATCGGAGTATATAGAGTTAATCTTTAAAAA
* * * *
970941 TCTTCTTCTCAAAAATCATTTGACCAGAGAAGCTGATATTTGTGTGGAAGCATCCTCAGATAGTG
1 --TTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGATAGTG
* *
971006 TACCGGTAGGTTCAAGTTTGTTCAAATCATGGTCCCTGAGGGTAATGTGGGGCCTCAATAGGGGG
64 TA---G-A--TTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAAT-GGGGG
* *
971071 GTCGAATTTTTACATCGGAATATATAGAGGTAATCTTTAAAAA
122 GTCGAATTTTTACATCGGAGTATATAGAGTTAATCTTTAAAAA
* *
971114 TCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGATAGTG
1 --TTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGATAGTG
*
971179 TAGGTTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGTCGAAT
64 TAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGTCGAAT
*
971244 TTTTACATAGGAGTATATAGAGTTAATCTTTAAAAA
129 TTTTACATCGGAGTATATAGAGTTAATCTTTAAAAA
* *
971280 -TCTTCTCAAAAACCATTTGGCCAGAAAAGCGGATACTTGTGTCGAAGCATCCTCAGATAGTGTA
1 TTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGATAGTGTA
* * ** * * * *
971344 GATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTTATGTGAAGCCACAATAGGGGGTCAAAGTT
66 GATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGTCGAATTT
* * * *
971409 TTACATCGAAGTATATGGAGTTAAACTTTCAAAAT
131 TTACATCGGAGTATATAGAGTTAATCTTT-AAAAA
* ** * * *
971444 TTATATCTCAAAAACCATAAGGCCA-AATAAGCTGCTACTTGTGTGAAAGCATCCTCAGATGGTG
1 TTCT-TCTCAAAAACCATTTGGCCAGAA-AAGCTGATACTTGTGTGGAAGCATCCTCAGATAGTG
* * * *
971508 TAGATTTAAGTTAGTTCAAATCATGGTCCCTGGGGGT-AGTGTGGTGCCACAATGGGGGG
64 TAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAG-GTGGGGCCTCAATGGGGGG
971567 GGGGGTTCAA
Statistics
Matches: 559, Mismatches: 51, Indels: 27
0.88 0.08 0.04
Matches are distributed among these distances:
163 141 0.25
164 4 0.01
165 67 0.12
166 145 0.26
167 47 0.08
168 1 0.00
169 1 0.00
170 1 0.00
171 32 0.06
172 13 0.02
173 107 0.19
ACGTcount: A:0.29, C:0.16, G:0.24, T:0.30
Consensus pattern (164 bp):
TTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGATAGTGTA
GATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGTCGAATTT
TTACATCGGAGTATATAGAGTTAATCTTTAAAAA
Found at i:971532 original size:329 final size:334
Alignment explanation
Indices: 970771--971566 Score: 1110
Period size: 329 Copynumber: 2.4 Consensus size: 334
970761 GATATTTTAA
* *
970771 AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATATTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTATTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
*
970836 TAGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCTCGGGGGTAAGGT-GGGCCTCAATAGGGGG
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCT-GGGGGTAAGGTGGGGCCTCAATGGGGGG
* * *
970899 TCGAATTTTTACATCGGAGTATATAGAGTTAATTTTTAAAAATCTTCTTCTCAAAAATCATTTGA
130 TCGAATTTTTACATAGGAGTATATAGAGTTAATCTTTAAAAA--TTCTTCTCAAAAACCATTTGA
* * * *
970964 CCAGAGAAGCTGATATTTGTGTGGAAGCATCCTCAGATAGTGTACCGGTAGGTTCAAGTTTGTTC
193 CCAGAAAAGCGGATACTTGTGTCGAAGCATCCTCAGATAGTGTA-C-GTA-GTTCAAGTTTGTTC
** * * *
971029 AAATCATGGTCCCTGAGGGTAATGTGGGGCCTCAATAGGGGGGTCGAATTTTTACATCGGAATAT
255 AAATCATGGTCCCTGAGGGTAATGTGAAGCCACAATAGGGGGGTCAAAGTTTTACATCGGAATAT
*
971094 ATAGAGGTAATCTTT
320 ATAGAGGTAAACTTT
* * *
971109 AAAAATCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTATTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
*
971174 TAGTGTAGGTTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGT
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGT
*
971239 CGAATTTTTACATAGGAGTATATAGAGTTAATCTTTAAAAA-TCTTCTCAAAAACCATTTGGCCA
131 CGAATTTTTACATAGGAGTATATAGAGTTAATCTTTAAAAATTCTTCTCAAAAACCATTTGACCA
971303 GAAAAGCGGATACTTGTGTCGAAGCATCCTCAGATAGTGTA-G-A-TTCAAGTTTGTTCAAATCA
196 GAAAAGCGGATACTTGTGTCGAAGCATCCTCAGATAGTGTACGTAGTTCAAGTTTGTTCAAATCA
* * *
971365 TGGTCCCTGGGGGTTATGTGAAGCCACAATA-GGGGGTCAAAGTTTTACATC-GAAGTATATGGA
261 TGGTCCCTGAGGGTAATGTGAAGCCACAATAGGGGGGTCAAAGTTTTACATCGGAA-TATATAGA
*
971428 GTTAAACTTT
325 GGTAAACTTT
* ** * *
971438 CAAAAT-TTATATCTCAAAAACCATAAGGCCA-AATAAGCTGCTACTTGTGTGAAAGCATCCTCA
1 AAAAATCTTAT-TCTCAAAAACCATTTGGCCAGAA-AAGCTGATACTTGTGTGGAAGCATCCTCA
* * * * *
971501 GATGGTGTAGATTTAAGTTAGTTCAAATCATGGTCCCTGGGGGT-AGTGTGGTGCCACAATGGGG
64 GATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAG-GTGGGGCCTCAATGGGG
971565 GG
128 GG
971567 GGGGGTTCAA
Statistics
Matches: 415, Mismatches: 37, Indels: 21
0.88 0.08 0.04
Matches are distributed among these distances:
328 10 0.02
329 138 0.33
330 45 0.11
332 1 0.00
333 1 0.00
336 58 0.14
338 104 0.25
339 58 0.14
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (334 bp):
AAAAATCTTATTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGT
CGAATTTTTACATAGGAGTATATAGAGTTAATCTTTAAAAATTCTTCTCAAAAACCATTTGACCA
GAAAAGCGGATACTTGTGTCGAAGCATCCTCAGATAGTGTACGTAGTTCAAGTTTGTTCAAATCA
TGGTCCCTGAGGGTAATGTGAAGCCACAATAGGGGGGTCAAAGTTTTACATCGGAATATATAGAG
GTAAACTTT
Found at i:971537 original size:166 final size:166
Alignment explanation
Indices: 970771--971566 Score: 1077
Period size: 163 Copynumber: 4.8 Consensus size: 166
970761 GATATTTTAA
*
970771 AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATATTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
*
970836 TAGTGTAGATTCAAGTTTGTTCAAATCATGGT-CCTCGGGGGTAAGGT-GGGCCTCAATAGGGGG
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCT-GGGGGTAATGTGGGGCCTCAATAGGGGG
* *
970899 TCGAATTTTTACATCGGAGTATATAGAGTTAATTTTT
130 TCGAATTTTTACATCGAAGTATATAGAGTTAATCTTT
* * * *
970936 AAAAATCTTCTTCTCAAAAATCATTTGACCAGAGAAGCTGATATTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
*
971001 TAGTGTACCGGTAGGTTCAAGTTTGTTCAAATCATGGTCCCTGAGGGTAATGTGGGGCCTCAATA
66 TAGTGTA---G-A--TTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAATGTGGGGCCTCAATA
*
971066 GGGGGGTCGAATTTTTACATCGGAA-TATATAGAGGTAATCTTT
125 -GGGGGTCGAATTTTTACATC-GAAGTATATAGAGTTAATCTTT
* *
971109 AAAAATCTTCTTCTCAAAAATCATTTGGCCAGAAAAGCTGAAACTTGTGTGGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
* * *
971174 TAGTGTAGGTTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAAGGTGGGGCCTCAATGGGGGGT
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAATGTGGGGCCTCAATAGGGGGT
* *
971239 CGAATTTTTACATAGGAGTATATAGAGTTAATCTTT
131 CGAATTTTTACATCGAAGTATATAGAGTTAATCTTT
* *
971275 AAAAA---TCTTCTCAAAAACCATTTGGCCAGAAAAGCGGATACTTGTGTCGAAGCATCCTCAGA
1 AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
* ** *
971337 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTTATGTGAAGCCACAATAGGGGGT
66 TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAATGTGGGGCCTCAATAGGGGGT
* * * *
971402 CAAAGTTTTACATCGAAGTATATGGAGTTAAACTTT
131 CGAATTTTTACATCGAAGTATATAGAGTTAATCTTT
* * ** * *
971438 CAAAAT-TTATATCTCAAAAACCATAAGGCCA-AATAAGCTGCTACTTGTGTGAAAGCATCCTCA
1 AAAAATCTTCT-TCTCAAAAACCATTTGGCCAGAA-AAGCTGATACTTGTGTGGAAGCATCCTCA
* * * * * * *
971501 GATGGTGTAGATTTAAGTTAGTTCAAATCATGGTCCCTGGGGGTAGTGTGGTGCCACAATGGGGG
64 GATAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAATGTGGGGCCTCAATAGGGG
971566 G
129 G
971567 GGGGGTTCAA
Statistics
Matches: 564, Mismatches: 52, Indels: 29
0.87 0.08 0.04
Matches are distributed among these distances:
163 145 0.26
165 75 0.13
166 142 0.25
167 47 0.08
168 1 0.00
169 1 0.00
170 1 0.00
171 32 0.06
172 14 0.02
173 104 0.18
174 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (166 bp):
AAAAATCTTCTTCTCAAAAACCATTTGGCCAGAAAAGCTGATACTTGTGTGGAAGCATCCTCAGA
TAGTGTAGATTCAAGTTTGTTCAAATCATGGTCCCTGGGGGTAATGTGGGGCCTCAATAGGGGGT
CGAATTTTTACATCGAAGTATATAGAGTTAATCTTT
Found at i:977679 original size:36 final size:34
Alignment explanation
Indices: 977633--977704 Score: 90
Period size: 36 Copynumber: 2.1 Consensus size: 34
977623 ATACCAATTA
* * *
977633 TATCCCCTACCACCGAGCATACCAAATGTATACCAC
1 TATCCACTACCACCAAACATACC-AAT-TATACCAC
*
977669 TATCCACTACCATCAAACATACCAATTATACCAC
1 TATCCACTACCACCAAACATACCAATTATACCAC
977703 TA
1 TA
977705 CCATCAAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 10 0.31
35 3 0.09
36 19 0.59
ACGTcount: A:0.38, C:0.36, G:0.04, T:0.22
Consensus pattern (34 bp):
TATCCACTACCACCAAACATACCAATTATACCAC
Found at i:977872 original size:61 final size:62
Alignment explanation
Indices: 977795--977948 Score: 195
Period size: 61 Copynumber: 2.5 Consensus size: 62
977785 GCTAGCATCG
* * ** *
977795 AACATACCAATGATATCCACAACCATTGATTAAACCAATTATACCA-TATTCACTACACTCA
1 AACATACCAATTATATCCACTACCATTGAACAAACCAATTATACCACTATCCACTACACTCA
* * **
977856 AACATACCAATTATATCCACTACCATTGAACATACCAATTATACCACTATCCACTACCCTTG
1 AACATACCAATTATATCCACTACCATTGAACAAACCAATTATACCACTATCCACTACACTCA
* *
977918 AACATACCAATT-TATTCACTACCATCGAACA
1 AACATACCAATTATATCCACTACCATTGAACA
977949 CACCGACTAC
Statistics
Matches: 81, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
61 58 0.72
62 23 0.28
ACGTcount: A:0.40, C:0.30, G:0.03, T:0.27
Consensus pattern (62 bp):
AACATACCAATTATATCCACTACCATTGAACAAACCAATTATACCACTATCCACTACACTCA
Found at i:977876 original size:28 final size:28
Alignment explanation
Indices: 977840--977904 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
977830 CAATTATACC
*
977840 ATATTCACTA-CACTCAAACATACCAATT
1 ATATCCACTACCA-TCAAACATACCAATT
**
977868 ATATCCACTACCATTGAACATACCAATT
1 ATATCCACTACCATCAAACATACCAATT
977896 ATA-CCACTA
1 ATATCCACTA
977905 TCCACTACCC
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 6 0.18
28 25 0.76
29 2 0.06
ACGTcount: A:0.42, C:0.29, G:0.02, T:0.28
Consensus pattern (28 bp):
ATATCCACTACCATCAAACATACCAATT
Found at i:981012 original size:14 final size:14
Alignment explanation
Indices: 980988--981022 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
980978 GCAGGTAGAT
980988 ATTTT-TTTTTAAA
1 ATTTTATTTTTAAA
*
981001 TTTTTATTTTTAAA
1 ATTTTATTTTTAAA
981015 ATTTTATT
1 ATTTTATT
981023 AATTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
13 4 0.21
14 15 0.79
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
ATTTTATTTTTAAA
Found at i:987531 original size:53 final size:53
Alignment explanation
Indices: 987472--987580 Score: 209
Period size: 53 Copynumber: 2.1 Consensus size: 53
987462 TTCCTTTAAC
987472 ATTAAAAATAAAACTACAAAAGTTATTTTTTCCTAAGTCAGTATAAGCAAACT
1 ATTAAAAATAAAACTACAAAAGTTATTTTTTCCTAAGTCAGTATAAGCAAACT
*
987525 ATTAAAAATAAAACTACAAAAGTTATTTTTTCCTAAGTCAGTATAAGCACACT
1 ATTAAAAATAAAACTACAAAAGTTATTTTTTCCTAAGTCAGTATAAGCAAACT
987578 ATT
1 ATT
987581 TCTCAATGTA
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.46, C:0.14, G:0.07, T:0.33
Consensus pattern (53 bp):
ATTAAAAATAAAACTACAAAAGTTATTTTTTCCTAAGTCAGTATAAGCAAACT
Found at i:994451 original size:16 final size:16
Alignment explanation
Indices: 994430--994460 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
994420 ATTTACACAC
994430 TTTAAAACAACATTAT
1 TTTAAAACAACATTAT
*
994446 TTTAAAACCACATTA
1 TTTAAAACAACATTA
994461 ATAAAGGAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.35
Consensus pattern (16 bp):
TTTAAAACAACATTAT
Found at i:1006145 original size:11 final size:11
Alignment explanation
Indices: 1006129--1006160 Score: 64
Period size: 11 Copynumber: 2.9 Consensus size: 11
1006119 CAAATCAACA
1006129 AACCAATACAG
1 AACCAATACAG
1006140 AACCAATACAG
1 AACCAATACAG
1006151 AACCAATACA
1 AACCAATACA
1006161 AAGACTTTCG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.56, C:0.28, G:0.06, T:0.09
Consensus pattern (11 bp):
AACCAATACAG
Found at i:1008679 original size:170 final size:170
Alignment explanation
Indices: 1008448--1008941 Score: 758
Period size: 169 Copynumber: 2.9 Consensus size: 170
1008438 TTAAAAGATT
1008448 TTCCTATG-AAAAATTTCGACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCA
1 TTCCTATGTAAAAA-TTCGA---CCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCA
* * *
1008512 TTTGAAAAAAACTTGAACCTTCACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTTTGGCT
62 TTTGAAAAAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCT
*
1008577 GATTAGTTTCAGTGAAGAAGATTTTTAAAGATTTACTCTATATA
127 GATTAGTTTCAGAGAAGAAGATTTTTAAAGATTTACTCTATATA
* * *
1008621 TTCCTATGTAAAAATTCGACCCCCCCCCATTGTGGTCCCACCCTACCCCTTGGGATCATCTTTTG
1 TTCCTATGTAAAAATTCGACCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTTG
* * * * *
1008686 -AACAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTACAGCTCTTCCGGCTAATC
66 AAAAAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCTGATT
*
1008750 AGTTTCAGAGAAAAAGATTTTTAAAGATTTACTCTATATA
131 AGTTTCAGAGAAGAAGATTTTTAAAGATTTACTCTATATA
1008790 TTCCTATGTAAAAATTCGACCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTTG
1 TTCCTATGTAAAAATTCGACCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTTG
* * * *
1008855 AACAAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGGCCGAAT
66 AAAAAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCTGATT
* **
1008920 GGTTTTTGAGAAGAAGATTTTT
131 AGTTTCAGAGAAGAAGATTTTT
1008942 GAAAAATACC
Statistics
Matches: 290, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
169 156 0.54
170 116 0.40
173 13 0.04
174 5 0.02
ACGTcount: A:0.28, C:0.27, G:0.15, T:0.30
Consensus pattern (170 bp):
TTCCTATGTAAAAATTCGACCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTTG
AAAAAAACTTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCTGATT
AGTTTCAGAGAAGAAGATTTTTAAAGATTTACTCTATATA
Found at i:1008878 original size:339 final size:331
Alignment explanation
Indices: 1008192--1008941 Score: 883
Period size: 339 Copynumber: 2.2 Consensus size: 331
1008182 TTCGAACAAT
* * * * * * *
1008192 TTGAATCTTCCCTACTTGAAGATGCTTCCACACAAGTTGCAGCTTTTCTGCCCAATCGGTTTC-T
1 TTGAATCTTCACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCCGATTGGTTTCGT
* *
1008256 G-AGAAGATTTTTTAAAGATATTTCTCTATATATTCAAATGAGAAACTTCGAACCCCCTCCCCCA
66 GAAGAAGA-TTTTTAAAGATATTACTCTATATATTCAAATGAGAAAATTCGAACCCCCTCCCCCA
* * * *
1008320 CTGTGGCCCACCCTACCCCTCGGGATCATGATTTTATCTATCTTGAATCTACTCTAACCGAGAAT
130 CTGTGGCCCACCCTACCCCTCGGGATCATGATTTTAACAAACTTGAATCTACACTAACCGAGAAT
* * * * * * *
1008385 GCTTTCACACAAGTTAAAGCTTTTCTGGCCGATCGGTTTCTGAGAAGAAGATTTTAAAAGATTTT
195 GCTTCCACACAAGTTAAAGCTCTTCCGGCCAATCAGTTTCAGAGAAAAAGATTTTAAAAGATTTT
1008450 CCTATGAAAAATTTCGACCCCCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTT
260 CCTATGAAAAATTTCGA--CCCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTT
1008515 GAAAAAAAC
323 GAAAAAAAC
* * * *
1008524 TTGAACCTTCACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTTTGGCTGATTAGTTTCAG
1 TTGAATCTTCACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCCGATTGGTTTC-G
**
1008589 TGAAGAAGATTTTTAAAGAT-TTACTCTATATATTCCTATGTA-AAAATTCG-A-CCCC-CCCCC
65 TGAAGAAGATTTTTAAAGATATTACTCTATATATTCAAATG-AGAAAATTCGAACCCCCTCCCCC
* * *
1008649 ATTGTGGTCCCACCCTACCCCTTGGGATCAT-CTTTTGAACAAACTTGAATCTACACT-ACCTGA
129 ACTGTGG-CCCACCCTACCCCTCGGGATCATGATTTT-AACAAACTTGAATCTACACTAACC-GA
* * *
1008712 GGATGCTTCCACACAAGTTACAGCTCTTCCGGCTAATCAGTTTCAGAGAAAAAGATTTTTAAAGA
191 GAATGCTTCCACACAAGTTAAAGCTCTTCCGGCCAATCAGTTTCAGAGAAAAAGA-TTTT-AA-A
*
1008777 TTTACTCTATATATTCCTATGTAAAAA-TTCGA-CCCCCCCCCATTGTGGCCCCACCCTACCCCT
253 ---A---GAT-T-TTCCTATG-AAAAATTTCGACCCCCCCCCCATTGTGGCCCCACCCTACCCCT
*
1008840 GGGGATCATCATTTGAACAAAAC
309 GGGGATCATCATTTGAAAAAAAC
* * * *
1008863 TTGAATCTACACTACCTGAGGATGCTTCCACACAAGTTTCAGCTTTTCTGGCCGAATGGTTTTTG
1 TTGAATCTTCACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCCGATTGG-TTTCG
*
1008928 AGAAGAAGATTTTT
65 TGAAGAAGATTTTT
1008942 GAAAAATACC
Statistics
Matches: 355, Mismatches: 43, Indels: 33
0.82 0.10 0.08
Matches are distributed among these distances:
330 18 0.05
331 89 0.25
332 57 0.16
333 26 0.07
334 15 0.04
335 6 0.02
337 1 0.00
339 119 0.34
340 5 0.01
341 1 0.00
342 13 0.04
343 5 0.01
ACGTcount: A:0.27, C:0.26, G:0.15, T:0.31
Consensus pattern (331 bp):
TTGAATCTTCACTACCTGAGGATGCTTCCACACAAGTTACAGCTTTTCTGGCCGATTGGTTTCGT
GAAGAAGATTTTTAAAGATATTACTCTATATATTCAAATGAGAAAATTCGAACCCCCTCCCCCAC
TGTGGCCCACCCTACCCCTCGGGATCATGATTTTAACAAACTTGAATCTACACTAACCGAGAATG
CTTCCACACAAGTTAAAGCTCTTCCGGCCAATCAGTTTCAGAGAAAAAGATTTTAAAAGATTTTC
CTATGAAAAATTTCGACCCCCCCCCCATTGTGGCCCCACCCTACCCCTGGGGATCATCATTTGAA
AAAAAC
Found at i:1039166 original size:19 final size:20
Alignment explanation
Indices: 1039142--1039181 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
1039132 AAAGCAATAG
*
1039142 AACTTTTTTTAAAAC-TTTT
1 AACTTTTTTAAAAACATTTT
1039161 AACTTTTTTAAAAACATTTT
1 AACTTTTTTAAAAACATTTT
1039181 A
1 A
1039182 CTCAATGTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.53
Consensus pattern (20 bp):
AACTTTTTTAAAAACATTTT
Found at i:1074662 original size:164 final size:165
Alignment explanation
Indices: 1074427--1074816 Score: 455
Period size: 164 Copynumber: 2.3 Consensus size: 165
1074417 CTACATAACG
* * * * **
1074427 ATGCTTCCAAATAAGTTTCAGCTTTCCTAACCTAGTGG-TTTTGAGAAGATTTTTTTTAAAGATT
1 ATGCTTCCATATAAGTTTCAGCTTTCCTGACATAATGGTTTTTGAGAAGA-GATTTTTAAAGATT
1074491 AACTCTATATATTCATATGTAAAAAGTCGT-CCC-CCATTGTGGCCCCA-CTGAACCCCCGAGGG
65 AACTCTATATATTCATATGTAAAAAGTCGTCCCCTCCATTGTGGCCCCATCT-AACCCCC-AGGG
* *
1074553 TCATGATTTTCACAACTTTGAATTTTCACTACCTGAGA
128 TCATGATTTTCACAACTTTGAATCTACACTACCTGAGA
* * * *
1074591 ATGCTTCCATACAAGTTTCAGCTTTCCTGGCATAATGGTTTTTGAGAACAGATTTTTAAAGATTT
1 ATGCTTCCATATAAGTTTCAGCTTTCCTGACATAATGGTTTTTGAGAAGAGATTTTTAAAGATTA
* * * * *
1074656 ACTCTATATATTCCTTTGTGAAAATTCGTCCCCCCCCCTCCATTGTGGCCCCATCTTACCCCCAG
66 ACTCTATATATTCATATGTAAAAAGTCGT-----CCCCTCCATTGTGGCCCCATCTAACCCCCAG
* *
1074721 GGTCATGGTTTTCACAACTTTGAATCTACACTACCTGAGG
126 GGTCATGATTTTCACAACTTTGAATCTACACTACCTGAGA
* * * * *
1074761 ATGCTTCCATATAAGTTTCAACTTTTCTTGCCAAAATGGTTCTTGAGAAGAGATTT
1 ATGCTTCCATATAAGTTTCAGC-TTTCCTGACATAATGGTTTTTGAGAAGAGATTT
1074817 AATATATGTG
Statistics
Matches: 190, Mismatches: 26, Indels: 13
0.83 0.11 0.06
Matches are distributed among these distances:
164 69 0.36
165 10 0.05
170 61 0.32
171 48 0.25
172 2 0.01
ACGTcount: A:0.26, C:0.23, G:0.15, T:0.35
Consensus pattern (165 bp):
ATGCTTCCATATAAGTTTCAGCTTTCCTGACATAATGGTTTTTGAGAAGAGATTTTTAAAGATTA
ACTCTATATATTCATATGTAAAAAGTCGTCCCCTCCATTGTGGCCCCATCTAACCCCCAGGGTCA
TGATTTTCACAACTTTGAATCTACACTACCTGAGA
Found at i:1074828 original size:2 final size:2
Alignment explanation
Indices: 1074823--1074979 Score: 305
Period size: 2 Copynumber: 78.5 Consensus size: 2
1074813 ATTTAATATA
1074823 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1074865 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1074907 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
*
1074949 TG TG TG TG TG TG TG TT TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1074980 ATCTTTTTGT
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
2 153 1.00
ACGTcount: A:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:1076408 original size:160 final size:163
Alignment explanation
Indices: 1076095--1076631 Score: 458
Period size: 165 Copynumber: 3.3 Consensus size: 163
1076085 AAGGGTCATG
* * * *
1076095 AGTTTCAGCTTTCCTGGCTTAATGGTTTTGAGAAGAAGATTTTTAAAGATTTTCTCTATATATTC
1 AGTTTCAGCTTTCCTTGCTAAATGGTTTTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTC
* * *
1076160 AAATGT-GAAAATTGAACCCCCCATTATGCCTTTACCCTACTCCCAGGGCTCATGATTTTTACAA
66 ATATGTAAAAAATTGAACCCCCCA-TAT--CTTGACCCTACTCCCAGGGCTCATGATTTTTACAA
** *
1076224 GTTTGAATCTACTCTACCTGAGGATACTTCCACACA
128 CCTTGAATCTACACTACCTGAGGATACTTCCACACA
*
1076260 AGTTTCAGCTTTCCTTGCCAAATGGTTCTTGAGAAGAAGATTTTTTAAAGATTTACTCTAAATAT
1 AGTTTCAGCTTTCCTTGCTAAATGGTT-TTGAGAAGAAGA-TTTTTAAAGATTTACTCTAAATAT
* * * *
1076325 TCTTATGTTAAAAAATTG-ACCCCCCA-AT-TTGACCCTAC-CCCCGGGAGTCGTGA-TTTT-C-
64 TCATATG-TAAAAAATTGAACCCCCCATATCTTGACCCTACTCCCAGGG-CTCATGATTTTTACA
* *
1076383 ACCTTGAATCTACACTACCTGAGGATGCTTCCACACT
127 ACCTTGAATCTACACTACCTGAGGATACTTCCACACA
* * *
1076420 AGTTTCAGC-TTCCTTGGCTGATTGCTTTCTGAGAAGAAGATTTTTAAAGATTTACTC-AATATA
1 AGTTTCAGCTTTCCTT-GCTAAATGGTTT-TGAGAAGAAGATTTTTAAAGATTTACTCTAA-ATA
* * * * * *
1076483 TTCCTATGT-AAAAATTCAA--CCCCA-A-CTGTGGCCCCATCCTACCCTCGGGAGTCATGATTT
63 TTCATATGTAAAAAATTGAACCCCCCATATCT-T-GACCC-TACT-CCC-AGGG-CTCATGATTT
* * * * * *
1076543 TCACAACCTTGAATTTACTCTACAC-AAGGATGCTCCCACACA
122 TTACAACCTTGAATCTACACTAC-CTGAGGATACTTCCACACA
* * * * * *
1076585 AGTTTCAGATTTCCTGGCTGATTGCTTTCTGAGAAGAAGATCTTTAA
1 AGTTTCAGCTTTCCTTGCTAAATGGTTT-TGAGAAGAAGATTTTTAA
1076632 CAAGAGGCTA
Statistics
Matches: 316, Mismatches: 35, Indels: 42
0.80 0.09 0.11
Matches are distributed among these distances:
156 7 0.02
157 8 0.03
158 8 0.03
159 36 0.11
160 59 0.19
161 4 0.01
162 21 0.07
163 17 0.05
164 1 0.00
165 92 0.29
166 20 0.06
167 27 0.09
168 9 0.03
169 7 0.02
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (163 bp):
AGTTTCAGCTTTCCTTGCTAAATGGTTTTGAGAAGAAGATTTTTAAAGATTTACTCTAAATATTC
ATATGTAAAAAATTGAACCCCCCATATCTTGACCCTACTCCCAGGGCTCATGATTTTTACAACCT
TGAATCTACACTACCTGAGGATACTTCCACACA
Found at i:1077496 original size:173 final size:170
Alignment explanation
Indices: 1077120--1077529 Score: 635
Period size: 173 Copynumber: 2.4 Consensus size: 170
1077110 CCCCCCATGT
* * ** * *
1077120 CCTGAACCCCTTACCCAGGGGCCATGAATTTCACAATTTTGAAAGAGGGCCTCATTGACTTCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
* *
1077185 ACCAGGCATTTGGTTTTGAACAAATATATATATGGGAGTAGAGAAAAAGATTTTCTAAGATTTAA
66 ACCAGGCATTTAGTTTTGAACAAATATATATATGGAAGTAGAGAAAAAGATTTTCTAAGATTTAA
*
1077250 TACATTTTTACTATTTGGCCATATTGGCCCCACCCTAGAG
131 TACATTTTTACTATGTGGCCATATTGGCCCCACCCTAGAG
*
1077290 CCTGCACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1077355 ACCAGGCATTTAGTTTTGAACAAATATACATGTATATGGAAGTAGA-AAAGAAGATTTTCTAAGA
66 ACCAGGCATTTAGTTTTGAACAAATAT--A--TATATGGAAGTAGAGAAA-AAGATTTTCTAAGA
1077419 TTTAATACA-TTTTACTATGTGGCCATATTGGCCCCACCCTAGAG
126 TTTAATACATTTTTACTATGTGGCCATATTGGCCCCACCCTAGAG
* * **
1077463 CCTGAACCTCTGACCCAGGGGTCATGAATTTCACAATTTAGGTAGAGGGTTTCATGGACATCATA
1 CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
1077528 AC
66 AC
1077530 TATGAACCCA
Statistics
Matches: 220, Mismatches: 15, Indels: 7
0.91 0.06 0.03
Matches are distributed among these distances:
170 84 0.38
172 1 0.00
173 99 0.45
174 36 0.16
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (170 bp):
CCTGAACCCCTGACCCAGGGGTCATGAATTTCACAATTTTGGTAGAGGGCCTCATGGACATCATA
ACCAGGCATTTAGTTTTGAACAAATATATATATGGAAGTAGAGAAAAAGATTTTCTAAGATTTAA
TACATTTTTACTATGTGGCCATATTGGCCCCACCCTAGAG
Found at i:1082161 original size:103 final size:103
Alignment explanation
Indices: 1081933--1082429 Score: 459
Period size: 103 Copynumber: 4.9 Consensus size: 103
1081923 ACCGGAAGTT
* * * *
1081933 ACAGCTATTAAAACAACTAAAGGTGCCATA-TT-AAGTACATGTTTGGCTGCCATCTTTTTAACA
1 ACAGCTA-TAAAACAACTAAAGGTACCATACTTGAA--ACATGTTTGGCCGCCATCTTTGTCACA
* * * * *
1081996 ATCAC--ATAGAC--T-TTCGCTGAT-ATAAACAAATACTC
63 ATCTCTGATAGACAATATTCACAGATAACAAACAACTACTC
* * * *
1082031 ACAGCTATAAAACAATTAAAGGCACCATACTTGAAACTTGTTTGGCCGCCATCTTTATCACAATC
1 ACAGCTATAAAACAACTAAAGGTACCATACTTGAAACATGTTTGGCCGCCATCTTTGTCACAATC
*
1082096 TCTGTTAGACAATATTCACAGATAACAAACAACTACTC
66 TCTGATAGACAATATTCACAGATAACAAACAACTACTC
* * *
1082134 ACAGCCATAAAACAACT-AAGGATACCATACTTGAAACATGTTCGGCTGCCATCTTTGTCACAAT
1 ACAGCTATAAAACAACTAAAGG-TACCATACTTGAAACATGTTTGGCCGCCATCTTTGTCACAAT
* *
1082198 CTC--ATAGAC--TATTCGCAGAT-ATAAACATACT-CTC
65 CTCTGATAGACAATATTCACAGATAACAAACA-ACTACTC
* * * * * *
1082232 ACAGCTATAAAACAATTAAGGGTGCCATACTTCAAACTTGTTTGGCCGCCATCTTTGTCACAATT
1 ACAGCTATAAAACAACTAAAGGTACCATACTTGAAACATGTTTGGCCGCCATCTTTGTCACAATC
* ** * * * *
1082297 TCCGATAGGATTATATTCATAGATAATAAA-AACAAAATC
66 TCTGATA-GACAATATTCACAGATAACAAACAAC-TACTC
* * ** *
1082336 ACAGATATAAAACAACTAAAGGTATCATACTTTTAACATGTTTGGCTGCCATCTTTGTCACAATC
1 ACAGCTATAAAACAACTAAAGGTACCATACTTGAAACATGTTTGGCCGCCATCTTTGTCACAATC
* * *
1082401 CCTGTTAAACAATATTCACAGATAACAAA
66 TCTGATAGACAATATTCACAGATAACAAA
1082430 TCACGGAAGT
Statistics
Matches: 325, Mismatches: 55, Indels: 33
0.79 0.13 0.08
Matches are distributed among these distances:
97 46 0.14
98 72 0.22
99 23 0.07
100 3 0.01
101 8 0.02
102 13 0.04
103 94 0.29
104 66 0.20
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (103 bp):
ACAGCTATAAAACAACTAAAGGTACCATACTTGAAACATGTTTGGCCGCCATCTTTGTCACAATC
TCTGATAGACAATATTCACAGATAACAAACAACTACTC
Found at i:1082285 original size:201 final size:201
Alignment explanation
Indices: 1081941--1082400 Score: 590
Period size: 201 Copynumber: 2.3 Consensus size: 201
1081931 TTACAGCTAT
* * *
1081941 TAAAACAACTAAAGGTGCCATA-TT-AAGTACATGTTTGGCTGCCATCTTTTTAACAATCACATA
1 TAAAACAACTAAAGGTACCATACTTGAA--ACATGTTTGGCTGCCATCTTTGTCACAATCACATA
* *
1082004 GACTTTCGCTGATATAAACAAATACTCACAGCTATAAAACAATTAAAGGCACCATACTTGAAACT
64 GACTTTCGCAGATATAAACAAATACTCACAGCTATAAAACAATTAAAGGCACCATACTTCAAACT
* * * *
1082069 TGTTTGGCCGCCATCTTTATCACAATCTCTGTTA-GACAATATTCACAGATAACAAACAAC-TAC
129 TGTTTGGCCGCCATCTTTATCACAATCTCCGATAGGACAATATTCACAGATAACAAA-AACAAAA
*
1082132 TCACAGCCA
193 TCACAGACA
* *
1082141 TAAAACAACT-AAGGATACCATACTTGAAACATGTTCGGCTGCCATCTTTGTCACAATCTCATAG
1 TAAAACAACTAAAGG-TACCATACTTGAAACATGTTTGGCTGCCATCTTTGTCACAATCACATAG
* * **
1082205 ACTATTCGCAGATATAAACATACT-CTCACAGCTATAAAACAATTAAGGGTGCCATACTTCAAAC
65 ACT-TTCGCAGATATAAACA-AATACTCACAGCTATAAAACAATTAAAGGCACCATACTTCAAAC
* * ** * *
1082269 TTGTTTGGCCGCCATCTTTGTCACAATTTCCGATAGGATTATATTCATAGATAATAAAAACAAAA
128 TTGTTTGGCCGCCATCTTTATCACAATCTCCGATAGGACAATATTCACAGATAACAAAAACAAAA
*
1082334 TCACAGATA
193 TCACAGACA
* **
1082343 TAAAACAACTAAAGGTATCATACTTTTAACATGTTTGGCTGCCATCTTTGTCACAATC
1 TAAAACAACTAAAGGTACCATACTTGAAACATGTTTGGCTGCCATCTTTGTCACAATC
1082401 CCTGTTAAAC
Statistics
Matches: 225, Mismatches: 27, Indels: 14
0.85 0.10 0.05
Matches are distributed among these distances:
199 4 0.02
200 51 0.23
201 87 0.39
202 79 0.35
203 4 0.02
ACGTcount: A:0.37, C:0.22, G:0.12, T:0.29
Consensus pattern (201 bp):
TAAAACAACTAAAGGTACCATACTTGAAACATGTTTGGCTGCCATCTTTGTCACAATCACATAGA
CTTTCGCAGATATAAACAAATACTCACAGCTATAAAACAATTAAAGGCACCATACTTCAAACTTG
TTTGGCCGCCATCTTTATCACAATCTCCGATAGGACAATATTCACAGATAACAAAAACAAAATCA
CAGACA
Found at i:1087272 original size:4 final size:4
Alignment explanation
Indices: 1087260--1087295 Score: 63
Period size: 4 Copynumber: 8.8 Consensus size: 4
1087250 AAGCAAAAAA
1087260 AAAC AAAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1 AAAC -AAAC AAAC AAAC AAAC AAAC AAAC AAAC AAA
1087296 ATGACAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.78, C:0.22, G:0.00, T:0.00
Consensus pattern (4 bp):
AAAC
Found at i:1089840 original size:27 final size:27
Alignment explanation
Indices: 1089802--1090120 Score: 525
Period size: 27 Copynumber: 11.9 Consensus size: 27
1089792 ATGCAACAAC
* *
1089802 TCCATCAACTGCCAGTATAAGGCACAG
1 TCCATCAACTGCCAGTATTAGACACAG
* *
1089829 TCCATCAACTGCCAGGA-TATGACAGAG
1 TCCATCAACTGCCAGTATTA-GACACAG
1089856 TCCATCAACTGCCAGTATT-GACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
1089882 TCCATCAACTGCCAGTATTAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
*
1089909 TTCATCAACTGCCAGTATTAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
*
1089936 TCCATCAACTGCCAGTATAAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
1089963 TCCATCAACTGCCAGTATTAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
1089990 TCCATCAACTGCCAGTATTAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
*
1090017 TACATCAACTGCCAGTATTAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
*
1090044 TCCATCAACTGCCAATATTAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
*
1090071 TCCATCAACTGCCAGTATAAGACACAG
1 TCCATCAACTGCCAGTATTAGACACAG
*
1090098 TCCATCAACTGCCAGTATAAGAC
1 TCCATCAACTGCCAGTATTAGAC
1090121 CNNNNNNNNN
Statistics
Matches: 274, Mismatches: 15, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
26 26 0.09
27 247 0.90
28 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.21
Consensus pattern (27 bp):
TCCATCAACTGCCAGTATTAGACACAG
Found at i:1094463 original size:27 final size:27
Alignment explanation
Indices: 1094425--1094567 Score: 234
Period size: 27 Copynumber: 5.3 Consensus size: 27
1094415 NNNNNNNNNN
1094425 AGACACAGTCCATCAACTGCCAGTATA
1 AGACACAGTCCATCAACTGCCAGTATA
*
1094452 AGACCCAGTCCATCAACTGCCAGTATA
1 AGACACAGTCCATCAACTGCCAGTATA
* *
1094479 AGACCCAGTCCATCAACTGCCAGTATT
1 AGACACAGTCCATCAACTGCCAGTATA
1094506 AGACACAGTCCATCAACTGCCAGTAT-
1 AGACACAGTCCATCAACTGCCAGTATA
* *
1094532 TGACACAGTCCATCAACTGCCAGTATT
1 AGACACAGTCCATCAACTGCCAGTATA
1094559 AGACACAGT
1 AGACACAGT
1094568 TATCGTAAAA
Statistics
Matches: 110, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 25 0.23
27 85 0.77
ACGTcount: A:0.34, C:0.31, G:0.15, T:0.20
Consensus pattern (27 bp):
AGACACAGTCCATCAACTGCCAGTATA
Found at i:1096601 original size:8 final size:8
Alignment explanation
Indices: 1096588--1096669 Score: 85
Period size: 8 Copynumber: 10.2 Consensus size: 8
1096578 TTCCTCTGCA
*
1096588 TCCGTCAG
1 TCCGTCTG
1096596 TCCGTCTG
1 TCCGTCTG
*
1096604 TCTGTCTG
1 TCCGTCTG
*
1096612 TCTGTCTG
1 TCCGTCTG
*
1096620 TCCGTCCG
1 TCCGTCTG
1096628 TCCGTGC-G
1 TCCGT-CTG
*
1096636 TCCGTCCG
1 TCCGTCTG
1096644 TCCGTCTG
1 TCCGTCTG
* *
1096652 TCTGTCCG
1 TCCGTCTG
1096660 TCCGTCTG
1 TCCGTCTG
1096668 TC
1 TC
1096670 TGTCCCACTT
Statistics
Matches: 63, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
7 1 0.02
8 61 0.97
9 1 0.02
ACGTcount: A:0.01, C:0.38, G:0.26, T:0.35
Consensus pattern (8 bp):
TCCGTCTG
Found at i:1096608 original size:4 final size:4
Alignment explanation
Indices: 1096599--1096673 Score: 62
Period size: 4 Copynumber: 18.8 Consensus size: 4
1096589 CCGTCAGTCC
* * * * * *
1096599 GTCT GTCT GTCT GTCT GTCT GTCC GTCC GTCC GTGC- GTCC GTCC GTCC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTCT GTCT GT-CT GTCT GTCT GTCT
* *
1096647 GTCT GTCT GTCC GTCC GTCT GTCT GTC
1 GTCT GTCT GTCT GTCT GTCT GTCT GTC
1096674 CCACTTCAGT
Statistics
Matches: 65, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
3 1 0.02
4 63 0.97
5 1 0.02
ACGTcount: A:0.00, C:0.36, G:0.27, T:0.37
Consensus pattern (4 bp):
GTCT
Found at i:1096620 original size:16 final size:16
Alignment explanation
Indices: 1096595--1096674 Score: 108
Period size: 16 Copynumber: 5.0 Consensus size: 16
1096585 GCATCCGTCA
*
1096595 GTCCGTCTGTCTGTCT
1 GTCCGTCTGTCTGTCC
* *
1096611 GTCTGTCTGTCCGTCC
1 GTCCGTCTGTCTGTCC
*
1096627 GTCCGTGC-GTCCGTCC
1 GTCCGT-CTGTCTGTCC
1096643 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
1096659 GTCCGTCTGTCTGTCC
1 GTCCGTCTGTCTGTCC
1096675 CACTTCAGTT
Statistics
Matches: 57, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
15 1 0.02
16 55 0.96
17 1 0.02
ACGTcount: A:0.00, C:0.38, G:0.26, T:0.36
Consensus pattern (16 bp):
GTCCGTCTGTCTGTCC
Found at i:1096674 original size:12 final size:12
Alignment explanation
Indices: 1096588--1096674 Score: 93
Period size: 12 Copynumber: 7.2 Consensus size: 12
1096578 TTCCTCTGCA
*
1096588 TCCGTCAGTCCG
1 TCCGTCTGTCCG
* *
1096600 TCTGTCTGTCTG
1 TCCGTCTGTCCG
*
1096612 TCTGTCTGTCCG
1 TCCGTCTGTCCG
* *
1096624 TCCGTCCGTGCG
1 TCCGTCTGTCCG
*
1096636 TCCGTCCGTCCG
1 TCCGTCTGTCCG
*
1096648 TCTGTCTGTCCG
1 TCCGTCTGTCCG
*
1096660 TCCGTCTGTCTG
1 TCCGTCTGTCCG
1096672 TCC
1 TCC
1096675 CACTTCAGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 63 1.00
ACGTcount: A:0.01, C:0.38, G:0.25, T:0.36
Consensus pattern (12 bp):
TCCGTCTGTCCG
Found at i:1100838 original size:20 final size:22
Alignment explanation
Indices: 1100810--1100858 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
1100800 GAAAAACAAG
* *
1100810 GTTTAACGG-TTGTAAACTATA
1 GTTTAACGGATAGAAAACTATA
1100831 GTTT-ACGGATAGAAAACTATA
1 GTTTAACGGATAGAAAACTATA
1100852 G-TTAACG
1 GTTTAACG
1100859 ACAATAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 6 0.25
21 18 0.75
ACGTcount: A:0.37, C:0.10, G:0.20, T:0.33
Consensus pattern (22 bp):
GTTTAACGGATAGAAAACTATA
Done.