Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008569.1 Hibiscus syriacus cultivar Beakdansim tig00111493_pilon, 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: 1513883
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 8
Found at i:809024 original size:31 final size:31
Alignment explanation
Indices: 808989--809072 Score: 109
Period size: 31 Copynumber: 2.6 Consensus size: 31
808979 TGCCCCTTAA
*
808989 TAAAATAAAAACAATATATACTTTTAAAATT
1 TAAAATAAAAAAAATATATACTTTTAAAATT
809020 TAAAATAAGAATAAAATATAT--TTTTAAAATT
1 TAAAATAA-AA-AAAATATATACTTTTAAAATT
809051 TAAAATAAGAAAAAATAATATA
1 TAAAATAA-AAAAAAT-ATATA
809073 AGAATAAAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
30 5 0.10
31 33 0.69
32 2 0.04
33 8 0.17
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (31 bp):
TAAAATAAAAAAAATATATACTTTTAAAATT
Found at i:809073 original size:15 final size:15
Alignment explanation
Indices: 809055--809087 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
809045 AAAATTTAAA
809055 ATAAGAA-AAAATAAT
1 ATAAGAATAAAAT-AT
809070 ATAAGAATAAAATAT
1 ATAAGAATAAAATAT
809085 ATA
1 ATA
809088 TTTTTAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.70, C:0.00, G:0.06, T:0.24
Consensus pattern (15 bp):
ATAAGAATAAAATAT
Found at i:809136 original size:27 final size:27
Alignment explanation
Indices: 809086--809138 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
809076 ATAAAATATA
* *
809086 TATTTTTAAATTAAAATATTAATAAAG
1 TATTCTTAAATTAAAATATAAATAAAG
**
809113 TATTCTTAAATTAAGTTATAAATAAA
1 TATTCTTAAATTAAAATATAAATAAA
809139 ATATGTTAAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (27 bp):
TATTCTTAAATTAAAATATAAATAAAG
Found at i:810131 original size:39 final size:39
Alignment explanation
Indices: 810087--810261 Score: 136
Period size: 39 Copynumber: 4.7 Consensus size: 39
810077 ATGAAACTCA
*
810087 ACGACTGCATAACGTCTTCAGACAAATAGAGAAGACCCT
1 ACGACTGCATAACGTCTTCAGGCAAATAGAGAAGACCCT
810126 ACGACTGC---A-----T-AGGCAAATAGAGAAGAACCC-
1 ACGACTGCATAACGTCTTCAGGCAAATAGAGAAG-ACCCT
** * * * *
810156 ACGACTGCATGGCGACTTCAGGCAAATGGAGAAGATCTT
1 ACGACTGCATAACGTCTTCAGGCAAATAGAGAAGACCCT
* * *
810195 AGGAGTGCATAACGTCTTCAGGCAAATGGAGAAGACCCT
1 ACGACTGCATAACGTCTTCAGGCAAATAGAGAAGACCCT
* * ** *
810234 AAGAGTTTATGACGTCTTCAGGCAAATA
1 ACGACTGCATAACGTCTTCAGGCAAATA
810262 AAAAAGACTT
Statistics
Matches: 108, Mismatches: 17, Indels: 22
0.73 0.12 0.15
Matches are distributed among these distances:
30 22 0.20
31 5 0.05
36 1 0.01
38 3 0.03
39 77 0.71
ACGTcount: A:0.36, C:0.21, G:0.24, T:0.19
Consensus pattern (39 bp):
ACGACTGCATAACGTCTTCAGGCAAATAGAGAAGACCCT
Found at i:810145 original size:30 final size:30
Alignment explanation
Indices: 810109--810165 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
810099 CGTCTTCAGA
810109 CAAATAGAGAAG-ACCCTACGACTGCATAGG
1 CAAATAGAGAAGAACCC-ACGACTGCATAGG
810139 CAAATAGAGAAGAACCCACGACTGCAT
1 CAAATAGAGAAGAACCCACGACTGCAT
810166 GGCGACTTCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.42, C:0.25, G:0.21, T:0.12
Consensus pattern (30 bp):
CAAATAGAGAAGAACCCACGACTGCATAGG
Found at i:810269 original size:39 final size:39
Alignment explanation
Indices: 810206--810304 Score: 101
Period size: 39 Copynumber: 2.5 Consensus size: 39
810196 GGAGTGCATA
** * **
810206 ACGTCTTCAGGCAAATGGAGAAGACCCTAAG-AGTTTATG
1 ACGTCTTCAGGCAAATAAAAAAGA-CCTAAGAAGTACATG
* *
810245 ACGTCTTCAGGCAAATAAAAAAGACTTCAGAAGTACATG
1 ACGTCTTCAGGCAAATAAAAAAGACCTAAGAAGTACATG
* *
810284 ACGTCTTCAGACGAATAAAAA
1 ACGTCTTCAGGCAAATAAAAA
810305 TCCTAGTTTA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
38 4 0.08
39 46 0.92
ACGTcount: A:0.40, C:0.18, G:0.20, T:0.21
Consensus pattern (39 bp):
ACGTCTTCAGGCAAATAAAAAAGACCTAAGAAGTACATG
Found at i:813586 original size:54 final size:57
Alignment explanation
Indices: 813518--813656 Score: 169
Period size: 54 Copynumber: 2.5 Consensus size: 57
813508 ATCACTGTTT
* * * *
813518 ATTTTTGATTTGGCTACT-TCTATTTTATTTTATTCATTTTAGTCACTA-T-TT-TTC
1 ATTTCTGATTTGGCTACTGT-TATTTTATTTTATGCACTTTAATCACTATTATTATTC
* *
813572 ATTTCTGATTTGGCTACTGTTATTTTATTTTATGCACTTTAATCATTATTATTATTT
1 ATTTCTGATTTGGCTACTGTTATTTTATTTTATGCACTTTAATCACTATTATTATTC
* *
813629 ATTTCTGATTTGGCTACTATTGTTTTAT
1 ATTTCTGATTTGGCTACTGTTATTTTAT
813657 GTTTTGGTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
54 41 0.56
55 2 0.03
56 2 0.03
57 28 0.38
ACGTcount: A:0.20, C:0.12, G:0.09, T:0.59
Consensus pattern (57 bp):
ATTTCTGATTTGGCTACTGTTATTTTATTTTATGCACTTTAATCACTATTATTATTC
Found at i:817532 original size:9 final size:8
Alignment explanation
Indices: 817513--817627 Score: 95
Period size: 8 Copynumber: 13.4 Consensus size: 8
817503 AAAGACATAG
*
817513 AAAAGAGA
1 AAAAAAGA
817521 AAAGAAAGA
1 AAA-AAAGA
*
817530 AAAAATGA
1 AAAAAAGA
*
817538 AAAAAGGA
1 AAAAAAGA
*
817546 AAAAAGGA
1 AAAAAAGA
817554 AAAAAAGAAA
1 AAAAAAG--A
817564 GAATAAAAGA
1 -AA-AAAAGA
817574 GAAAAAAGA
1 -AAAAAAGA
817583 GAAAAAAGA
1 -AAAAAAGA
*
817592 ATAAAAGA
1 AAAAAAGA
*
817600 ATAAAAGA
1 AAAAAAGA
817608 AAAAAAGA
1 AAAAAAGA
*
817616 GAAGAAAGA
1 -AAAAAAGA
817625 AAA
1 AAA
817628 CCGATCAAAT
Statistics
Matches: 93, Mismatches: 8, Indels: 12
0.82 0.07 0.11
Matches are distributed among these distances:
8 52 0.56
9 29 0.31
10 5 0.05
11 2 0.02
12 5 0.05
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.03
Consensus pattern (8 bp):
AAAAAAGA
Found at i:817573 original size:55 final size:55
Alignment explanation
Indices: 817513--817621 Score: 154
Period size: 55 Copynumber: 2.0 Consensus size: 55
817503 AAAGACATAG
817513 AAAAGAGAAAAGAA-AGAAAAAATGAA-AAAAGGAA-AAAAGGAAAAAAAGA-AAGAAT
1 AAAAGAGAAAA-AAGAGAAAAAA-GAATAAAA-GAATAAAA-GAAAAAAAGAGAAGAAT
817568 AAAAGAGAAAAAAGAGAAAAAAGAATAAAAGAATAAAAGAAAAAAAGAGAAGAA
1 AAAAGAGAAAAAAGAGAAAAAAGAATAAAAGAATAAAAGAAAAAAAGAGAAGAA
817622 AGAAAACCGA
Statistics
Matches: 50, Mismatches: 0, Indels: 8
0.86 0.00 0.14
Matches are distributed among these distances:
54 18 0.36
55 32 0.64
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (55 bp):
AAAAGAGAAAAAAGAGAAAAAAGAATAAAAGAATAAAAGAAAAAAAGAGAAGAAT
Found at i:817620 original size:5 final size:4
Alignment explanation
Indices: 817521--817626 Score: 53
Period size: 4 Copynumber: 25.8 Consensus size: 4
817511 AGAAAAGAGA
*
817521 AAAG AAAG AAA- AAATG AAA- AAAGG AAA- AAAGG AAAA AAAG AAAG AATA-
1 AAAG AAAG AAAG AAA-G AAAG AAA-G AAAG AAA-G AAAG AAAG AAAG AA-AG
* * *
817569 AAAG AGAAA AAAG AGAAA AAAG AATA- AAAG AATA- AAAG AAAA AAAG
1 AAAG A-AAG AAAG A-AAG AAAG AA-AG AAAG AA-AG AAAG AAAG AAAG
817615 AGAAG AAAG AAA
1 A-AAG AAAG AAA
817627 ACCGATCAAA
Statistics
Matches: 79, Mismatches: 8, Indels: 30
0.68 0.07 0.26
Matches are distributed among these distances:
3 12 0.15
4 45 0.57
5 22 0.28
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (4 bp):
AAAG
Found at i:818310 original size:28 final size:28
Alignment explanation
Indices: 818259--818331 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
818249 GCAAGAAACC
* *
818259 AACCTGGAACACATTGCTTACCCAAATT
1 AACCTGAAACACATTACTTACCCAAATT
* * *
818287 TACTTGAAACACATTACTTCCCCAAATT
1 AACCTGAAACACATTACTTACCCAAATT
818315 AACCTGAAACACATTAC
1 AACCTGAAACACATTAC
818332 ATTCTCAAGT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.38, C:0.29, G:0.07, T:0.26
Consensus pattern (28 bp):
AACCTGAAACACATTACTTACCCAAATT
Found at i:819676 original size:55 final size:55
Alignment explanation
Indices: 819598--820513 Score: 788
Period size: 55 Copynumber: 17.0 Consensus size: 55
819588 TTTTTTTAGG
* * *
819598 AACTAAGTCTGATTTTCAAAAGTTTCTTGATGATTTTTAAATAAGTTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * * * *
819653 AACTAAGTCTGATTTTTAGAAGTTTCCTGACGATTTTTAAATTAGCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * * ** *
819708 AACTAAGTCTAATTTT-AGAAGTTTCATGATGATTTTAAAAAAAGATTTT-AAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * *
819761 AACTAAGTCTGATTTTCGGAAGTTTTTTGATCATTTTTAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* ** *
819816 AACTAAGTTTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * * *
819871 AACTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTTAAATGACCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTTAAATGAGCTTTTAAAGA
* * * *
819927 AACTAAGTCTGTTTTTTAGGAGTTTCTTGATTATTTTTAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * *
819982 AACTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTTAAATGACCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTTAAATGAGCTTTTAAAGA
* * * * *
820038 AACTAAGTGT-TTTTTTAGGAGTTTCTTGATTATTTTTAAATGAGCTTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* *
820092 AACTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGA-TTTTTAAATGAGCTTTTAAAGA
* * * **
820148 AATTAAGTCTGATTTTCAGAGGTTTCTTGA-CATGATT--A--A--TTTTAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * * * ** * * *
820196 AGCTAAGCCTAATTTTTAG--GGGTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * * * *
820247 AGA-TAAGCCTGATTTTCAGGAGTTTCTTGATG-TGTTCAAATGA-ATTTTAAAGA
1 A-ACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * * * * * * *
820300 AGCTAAGCCTAATTTTTA-AGGGTTTCTTGATG-TTTTCAAATGA-ATTTGAAAGA
1 AACTAAGTCTGATTTTCAGA-AGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* ** * * * *
820353 AGCTAAG-CATGATTTTCAGGGGGTTCTTAATG-TTTTCAAATGAG-TTTAAAAGA
1 AACTAAGTC-TGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* * ** * * ** *
820406 AGCTAAGCCTGATTTTCAGGTGTTTCTTGAT-ATTTTCAAATGA-ATTAAAAAAA
1 AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
* ** * **
820459 AACTAAGCCTG-TATTTCAGGGGTTTCTTGATG-TTTTCAAATGAATTTTTAAAGA
1 AACTAAGTCTGAT-TTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
820513 A
1 A
820514 GTTAATCCTA
Statistics
Matches: 719, Mismatches: 116, Indels: 53
0.81 0.13 0.06
Matches are distributed among these distances:
46 9 0.01
48 23 0.03
50 2 0.00
51 23 0.03
52 3 0.00
53 216 0.30
54 91 0.13
55 229 0.32
56 123 0.17
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.41
Consensus pattern (55 bp):
AACTAAGTCTGATTTTCAGAAGTTTCTTGATGATTTTTAAATGAGCTTTTAAAGA
Found at i:820066 original size:221 final size:219
Alignment explanation
Indices: 819598--820177 Score: 763
Period size: 221 Copynumber: 2.6 Consensus size: 219
819588 TTTTTTTAGG
* * * * * *
819598 AACTAAGTCTGATTTTCAAAAGTTTCTTGATGATTTTTAAATAAGTTTTTAAAGAAACTAAGTCT
1 AACTAAGT-TTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGCTTTTAAAGAAACTAAGTAT
* * * * *
819663 GATTTTTAGAAGTTTCCTGACGA-TTTTTAAATTAGCTTTCAAAGAAACTAAGTCT-AATTTTAG
65 GATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTTAG
* * * *
819726 AAGTTTCATGATGATTTTAAAAAAAGATTTTAAGAAACTAAGTCTGATTTTCGGAAGTTTTTTGA
130 GAGTTTCTTGATGATTTTAAAAAAAGATTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGA
* *
819791 TCATTTTTAAATGAGCTTTTAAAGA
195 TCATTTTTAAATGACCTTTCAAAGA
* *
819816 AACTAAGTTTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAACTAAGTAT
1 AACTAAGTTT-ATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGCTTTTAAAGAAACTAAGTAT
* * *
819881 GATTTTCATAAGTTTCTTGATGATTTTTTAAATGACCTTTCAAAGAAACTAAGTCTGTTTTTTAG
65 GATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTTAG
* * ** * *
819946 GAGTTTCTTGATTATTTTTAAATGAGCTTTTAAAGAAACTAAGTCTGATTTTCATAAGTTTCTTG
130 GAGTTTCTTGATGATTTTAAAAAAAGATTTT-AAGAAACTAAGTCTGATTTTCAGAAGTTTCTTG
*
820011 ATGATTTTTTAAATGACCTTTCAAAGA
194 ATCA-TTTTTAAATGACCTTTCAAAGA
* * * *
820038 AACTAAGTGTT-TTTTTAGGAGTTTCTTGATTATTTTTAAATGAGCTTTTAAAGAAACTAAGTTT
1 AACTAAGT-TTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGCTTTTAAAGAAACTAAGTAT
* *
820102 GATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGAAATTAAGTCTGATTTTCA-
65 GATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTTAG
820166 GAGGTTTCTTGA
130 GA-GTTTCTTGA
820178 CATGATTAAT
Statistics
Matches: 315, Mismatches: 40, Indels: 11
0.86 0.11 0.03
Matches are distributed among these distances:
217 1 0.00
218 74 0.23
219 30 0.10
220 32 0.10
221 148 0.47
222 28 0.09
223 2 0.01
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.43
Consensus pattern (219 bp):
AACTAAGTTTATTTTCAGAAGTTTCTTGATAATTTTTAAATGAGCTTTTAAAGAAACTAAGTATG
ATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGAAACTAAGTCTGATTTTTAGG
AGTTTCTTGATGATTTTAAAAAAAGATTTTAAGAAACTAAGTCTGATTTTCAGAAGTTTCTTGAT
CATTTTTAAATGACCTTTCAAAGA
Found at i:820291 original size:53 final size:52
Alignment explanation
Indices: 819600--820539 Score: 488
Period size: 53 Copynumber: 17.5 Consensus size: 52
819590 TTTTTAGGAA
* ** * *
819600 CTAAGTCTGATTTTCAAAAGTTTCTTGATGATTTTTAAAT-AAGTTTTTAAAGAAA
1 CTAAGCCTGATTTTC-AGGGTTTCTTGATG-TTTTCAAATGAA--TTTTAAAGAAG
* * * * * * * * * *
819655 CTAAGTCTGATTTTTAGAAGTTTCCTGACGATTTTTAAATTAGCTTTCAAAGAAA
1 CTAAGCCTGATTTTCAG-GGTTTCTTGATG-TTTTCAAATGA-ATTTTAAAGAAG
* * * * * ** *
819710 CTAAGTCTAATTTT-AGAAGTTTCATGATGATTTTAAAAAAAGATTTT-AAGAAA
1 CTAAGCCTGATTTTCAG-GGTTTCTTGATG-TTTTCAAATGA-ATTTTAAAGAAG
* * * * * *
819763 CTAAGTCTGATTTTC-GGAAGTTTTTTGATCATTTTTAAATGAGCTTTTAAAGAAA
1 CTAAGCCTGATTTTCAGG--GTTTCTTGAT-GTTTTCAAATGA-ATTTTAAAGAAG
** * ** * *
819818 CTAAGTTTGATTTTCAGAAGTTTCTTGACAATTTTCAAATGAGCTTTTAAAGAAA
1 CTAAGCCTGATTTTCAG-GGTTTCTTGA-TGTTTTCAAATGA-ATTTTAAAGAAG
** ** * * * *
819873 CTAAGTATGATTTTCATAAGTTTCTTGATGATTTTTTAAATGACCTTTCAAAGAAA
1 CTAAGCCTGATTTTCA-GGGTTTCTTGATG--TTTTCAAATGA-ATTTTAAAGAAG
* * * * * * *
819929 CTAAGTCTGTTTTTTAGGAGTTTCTTGATTATTTTTAAATGAGCTTTTAAAGAAA
1 CTAAGCCTGATTTTCAGG-GTTTCTTGA-TGTTTTCAAATGA-ATTTTAAAGAAG
* ** * * * *
819984 CTAAGTCTGATTTTCATAAGTTTCTTGATGATTTTTTAAATGACCTTTCAAAGAAA
1 CTAAGCCTGATTTTCA-GGGTTTCTTGATG--TTTTCAAATGA-ATTTTAAAGAAG
* * * * * *
820040 CTAAG--TGTTTTTTTAGGAGTTTCTTGATTATTTTTAAATGAGCTTTTAAAGAAA
1 CTAAGCCTG-ATTTTCAGG-GTTTCTTGA-TGTTTTCAAATGA-ATTTTAAAGAAG
** * * * * *
820094 CTAAGTTTGATTTTCAGAAGTTTCTTGATGATTTTTTAAATGAGCTTTCAAAGAAA
1 CTAAGCCTGATTTTCAG-GGTTTCTTGATG--TTTTCAAATGA-ATTTTAAAGAAG
* * * *
820150 TTAAGTCTGATTTTCAGAGGTTTCTTGA------CATGATTAATTTTAAAGAAG
1 CTAAGCCTGATTTTCAG-GGTTTCTTGATGTTTTCA-AATGAATTTTAAAGAAG
* * * *
820198 CTAAGCCTAATTTTTAGGG-GTCTTGATGTTTTCAAATGAATTTGAAAGAAG
1 CTAAGCCTGATTTTCAGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAG
* *
820249 ATAAGCCTGATTTTCAGGAGTTTCTTGATGTGTTCAAATGAATTTTAAAGAAG
1 CTAAGCCTGATTTTCAGG-GTTTCTTGATGTTTTCAAATGAATTTTAAAGAAG
* * *
820302 CTAAGCCTAATTTTTAAGGGTTTCTTGATGTTTTCAAATGAATTTGAAAGAAG
1 CTAAGCCTGA-TTTTCAGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAG
* * * * *
820355 CTAAGCATGATTTTCAGGGGGTTCTTAATGTTTTCAAATGAGTTTAAAAGAAG
1 CTAAGCCTGATTTTCA-GGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAG
* ** * *
820408 CTAAGCCTGATTTTCAGGTGTTTCTTGATATTTTCAAATGAATTAAAAAAAAA
1 CTAAGCCTGATTTTCAGG-GTTTCTTGATGTTTTCAAATGAATTTTAAAGAAG
820461 CTAAGCCTG-TATTTCAGGGGTTTCTTGATGTTTTCAAATGAATTTTTAAAGAAG
1 CTAAGCCTGAT-TTTCA-GGGTTTCTTGATGTTTTCAAATGAA-TTTTAAAGAAG
* * *
820515 TTAATCCT-ATTTTTAGGGATTTCTT
1 CTAAGCCTGATTTTCAGGG-TTTCTT
820540 AATGATAAAT
Statistics
Matches: 728, Mismatches: 113, Indels: 90
0.78 0.12 0.10
Matches are distributed among these distances:
46 6 0.01
47 2 0.00
48 23 0.03
49 3 0.00
51 29 0.04
52 14 0.02
53 217 0.30
54 102 0.14
55 208 0.29
56 123 0.17
57 1 0.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (52 bp):
CTAAGCCTGATTTTCAGGGTTTCTTGATGTTTTCAAATGAATTTTAAAGAAG
Found at i:821120 original size:36 final size:37
Alignment explanation
Indices: 821050--821135 Score: 102
Period size: 36 Copynumber: 2.4 Consensus size: 37
821040 AATATAAATT
* *
821050 TTGAAATTGTTTCACTTGAAAAAAAAATTTATCTCAC
1 TTGAGATTGTTTCACTTGAAAAAAAAATTCATCTCAC
** *
821087 TTGAGATTGTTTTTCTT-AAAACAAAATTCATCTCAC
1 TTGAGATTGTTTCACTTGAAAAAAAAATTCATCTCAC
* *
821123 TAGAGATAGTTTC
1 TTGAGATTGTTTC
821136 CCTCGAAACA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 27 0.66
37 14 0.34
ACGTcount: A:0.36, C:0.14, G:0.10, T:0.40
Consensus pattern (37 bp):
TTGAGATTGTTTCACTTGAAAAAAAAATTCATCTCAC
Found at i:821181 original size:36 final size:36
Alignment explanation
Indices: 821077--821186 Score: 116
Period size: 36 Copynumber: 3.1 Consensus size: 36
821067 GAAAAAAAAA
* * * * * *
821077 TTTATCTCACTTGAGATTGTTTTTCTTAAAACAAAA
1 TTTATCTCACCTAAGATAGTTTCTCTTCAAACAAAT
* *
821113 TTCATCTCA-CTAGAGATAGTTTC-CCTCGAAACAAAT
1 TTTATCTCACCTA-AGATAGTTTCTCTTC-AAACAAAT
821149 TTTATCTCACCTAAGATAGTTTCTCTTCAAACAAAT
1 TTTATCTCACCTAAGATAGTTTCTCTTCAAACAAAT
821185 TT
1 TT
821187 CTTTTTATTC
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
35 3 0.05
36 51 0.85
37 6 0.10
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (36 bp):
TTTATCTCACCTAAGATAGTTTCTCTTCAAACAAAT
Found at i:821768 original size:140 final size:136
Alignment explanation
Indices: 821453--821768 Score: 370
Period size: 136 Copynumber: 2.3 Consensus size: 136
821443 GGGTAAGCCA
* *
821453 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTCATCCGATAGAGGGAGAAGAAGTTCA
1 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCA
* * * * *** *
821518 TAATGAGAAGATCCTATTCGACCTATCATTCGATTCATGGCATTTTGAATCAGTGACGCCTCACT
66 TAATGAGAAGAACCTATTCGACATATCACTCGATTCATCGCATTTTGAATCAACAACACCTCACT
*
821583 TGAAGG
131 CGAAGG
821589 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTTATCC-AGCAGAGGGAGAAGAAGTTC
1 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTTATCCGA-CAGAGGGAGAAGAAGTTC
* * *
821653 ATAATGAGAAGAACTTGTTC-A-ATATTAGCTCGATTCATCGCATATAGAGTTGAATCAACAACA
65 ATAATGAGAAGAACCTATTCGACATATCA-CTCGATTCATCGCAT-T----TTGAATCAACAACA
821716 CCTCACTCGATA-G
124 CCTCACTCGA-AGG
* * * *
821729 ATCAACATTTCCAGTGAAGAGTTCATAATGAGAAAAACTT
1 ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTT
821769 GTTCAACCTT
Statistics
Matches: 154, Mismatches: 18, Indels: 12
0.84 0.10 0.07
Matches are distributed among these distances:
134 4 0.03
135 15 0.10
136 78 0.51
140 56 0.36
141 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.20, T:0.26
Consensus pattern (136 bp):
ATCAACATTTCAAATGGAGAGTTCATAATGAGAAGAACTTATCCGACAGAGGGAGAAGAAGTTCA
TAATGAGAAGAACCTATTCGACATATCACTCGATTCATCGCATTTTGAATCAACAACACCTCACT
CGAAGG
Found at i:821821 original size:100 final size:99
Alignment explanation
Indices: 821643--821868 Score: 317
Period size: 100 Copynumber: 2.3 Consensus size: 99
821633 AGCAGAGGGA
* *
821643 GAAGAAGTTCATAATGAGAAGAACTTGTTCAATATTAGCTCGATTCATCGCATATAGAGTTGAAT
1 GAAG-AGTTCATAATGAGAAGAACTTGTTCAACATTAGCTCGATTCATCGCATATAGAGTTAAAT
* *
821708 CAACAACACCTCACTCGATAGATCAACATTTCCAGT
65 CAACAACACCTCACTCGAGAGATCAACATGTCCA-T
* * * * *
821744 GAAGAGTTCATAATGAGAAAAACTTGTTCAACCTTAGTTCGATTCATCGTATATGGAGTTAAATC
1 GAAGAGTTCATAATGAGAAGAACTTGTTCAACATTAGCTCGATTCATCGCATATAGAGTTAAATC
* *
821809 AGCAACACCTCACTCGAGGGATCAACATGTCCAT
66 AACAACACCTCACTCGAGAGATCAACATGTCCAT
*
821843 GAGAGAGTTAATAATGAGAAGAACTT
1 GA-AGAGTTCATAATGAGAAGAACTT
821869 ATCCGATAAG
Statistics
Matches: 111, Mismatches: 13, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
99 3 0.03
100 104 0.94
101 4 0.04
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.27
Consensus pattern (99 bp):
GAAGAGTTCATAATGAGAAGAACTTGTTCAACATTAGCTCGATTCATCGCATATAGAGTTAAATC
AACAACACCTCACTCGAGAGATCAACATGTCCAT
Found at i:823574 original size:54 final size:55
Alignment explanation
Indices: 823496--823618 Score: 178
Period size: 54 Copynumber: 2.3 Consensus size: 55
823486 ATCACTATTT
*
823496 ATTTCTGATTTGGCTACTGCTATTTTATTTTATGCATTTTAG-TCACTA-TTTTTC
1 ATTTCTGATTTGGCAACTGCTATTTTATTTTATGCATTTTAGAT-ACTATTTTTTC
* * * *
823550 ATTTCTGATTTGGCAATTGTTATTTTATTTTATGCATTTTAGATATTATTTTTTT
1 ATTTCTGATTTGGCAACTGCTATTTTATTTTATGCATTTTAGATACTATTTTTTC
823605 ATTTCTGATTTGGC
1 ATTTCTGATTTGGC
823619 TACTATTTTT
Statistics
Matches: 62, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
54 42 0.68
55 20 0.32
ACGTcount: A:0.20, C:0.11, G:0.12, T:0.58
Consensus pattern (55 bp):
ATTTCTGATTTGGCAACTGCTATTTTATTTTATGCATTTTAGATACTATTTTTTC
Found at i:823625 original size:26 final size:26
Alignment explanation
Indices: 823493--823629 Score: 71
Period size: 26 Copynumber: 5.1 Consensus size: 26
823483 TCAATCACTA
** *
823493 TTTATTTCTGATTTGGCTACTGCTAT
1 TTTATTTCTGATTTGGCTACTATTTT
* *
823519 TTTATTTTATGCATTTTAG-TCACTA-TTT
1 TTTA-TTTCTG-A-TTTGGCT-ACTATTTT
* * * * *
823547 TTCATTTCTGATTTGGCAATTGTTAT
1 TTTATTTCTGATTTGGCTACTATTTT
* * * *
823573 TTTATTTTATGCATTTTAGATATTATTTT
1 TTTA-TTTCTG-A-TTTGGCTACTATTTT
823602 TTTATTTCTGATTTGGCTACTATTTT
1 TTTATTTCTGATTTGGCTACTATTTT
823628 TT
1 TT
823630 ATTACATTTT
Statistics
Matches: 80, Mismatches: 22, Indels: 18
0.67 0.18 0.15
Matches are distributed among these distances:
25 6 0.08
26 24 0.30
27 16 0.20
28 13 0.16
29 21 0.26
ACGTcount: A:0.19, C:0.10, G:0.11, T:0.60
Consensus pattern (26 bp):
TTTATTTCTGATTTGGCTACTATTTT
Found at i:823630 original size:54 final size:53
Alignment explanation
Indices: 823493--823632 Score: 174
Period size: 54 Copynumber: 2.6 Consensus size: 53
823483 TCAATCACTA
* *
823493 TTTATTTCTGATTTGGCTACTGCTATTTTATTTTATGCATTTTAGTCACTATTT
1 TTTATTTCTGATTTGGCTACT-ATTTTTTATTTTATGCATTTTAGTCACTATTT
* * * * *
823547 TTCATTTCTGATTTGGCAATTGTTATTTTATTTTATGCATTTTAGAT-ATTATTTT
1 TTTATTTCTGATTTGGCTACTATT-TTTTATTTTATGCATTTTAG-TCACTA-TTT
823602 TTTATTTCTGATTTGGCTACTATTTTTTATT
1 TTTATTTCTGATTTGGCTACTATTTTTTATT
823633 ACATTTTGGT
Statistics
Matches: 73, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
53 1 0.01
54 48 0.66
55 24 0.33
ACGTcount: A:0.19, C:0.10, G:0.11, T:0.60
Consensus pattern (53 bp):
TTTATTTCTGATTTGGCTACTATTTTTTATTTTATGCATTTTAGTCACTATTT
Found at i:824698 original size:23 final size:23
Alignment explanation
Indices: 824651--824700 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
824641 AATAACATAT
* **
824651 TAGGTATCGCTTATATAATGTAA
1 TAGGTAGCGCTTATATAATAAAA
*
824674 TAGGTAGCGTTTATATAATAAAA
1 TAGGTAGCGCTTATATAATAAAA
824697 TAGG
1 TAGG
824701 CATTTAACTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.06, G:0.20, T:0.36
Consensus pattern (23 bp):
TAGGTAGCGCTTATATAATAAAA
Found at i:824760 original size:87 final size:87
Alignment explanation
Indices: 824614--824776 Score: 292
Period size: 87 Copynumber: 1.9 Consensus size: 87
824604 TATGTTATAT
824614 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTATCGCTTATATAATGTAATAGGT
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTATCGCTTATATAATGTAATAGGT
*
824679 AGCGTTTATATAATAAAATAGG
66 AGCGCTTATATAATAAAATAGG
*
824701 CATTTAACTGGAAATATTATCAAGTACAATAACATATTAGGTAGT-GCTTATATAATGTAATAGG
1 CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTA-TCGCTTATATAATGTAATAGG
824765 TAGCGCTTATAT
65 TAGCGCTTATAT
824777 TGACCTATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
87 72 0.99
88 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.15, T:0.34
Consensus pattern (87 bp):
CATTTAACCGGAAATATTATCAAGTACAATAACATATTAGGTATCGCTTATATAATGTAATAGGT
AGCGCTTATATAATAAAATAGG
Found at i:825401 original size:200 final size:198
Alignment explanation
Indices: 824776--825491 Score: 853
Period size: 200 Copynumber: 3.6 Consensus size: 198
824766 AGCGCTTATA
* * *
824776 TTGACCTATTTTCTAAGT-TAACCGATATATTTATACCGGTAACATTGCAAATTTACCTATTACA
1 TTGACCTATTTTCTAA-TAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACA
* * * * *
824840 TTATAATTCTCGGTTTTGAT-TTTTTTGGATCGATACAATTT--TAAATGTATCGACACTTTATT
65 TTATAATTATCGGTTTCGATGTTTTTGGGATCGATAC-TTTTAATAAATGTATCGACACTTTATG
* * *
824902 CTTGCACCTCG-TTGGGCATTCATTCTGGA-AAAAGTATCGACACAAACTTAAAAAGTGTTGATA
129 CGTGCACCTCGTTTGGGCATTCATTCTGGATAAAAGTATCGACACAAA-TTAACAAGTGTCGATA
824965 CATTA-
193 CATTAG
* * * *
824970 TTAGACCTATTTTCTCATAAAACCGGTATATTTATACCGGGTACATTGTAAATTTACCTATCACA
1 TT-GACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACA
* * * * *
825035 TTGTAATTTTC-CTTTCGATGTTTTTGGGATCAATACTTTTAATAAATGTATCGACACTCTATGC
65 TTATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGC
* * *
825099 GTGCACCCCGTTT-GGTATTCATTATGGATAAAATGTATCGACACAAATTTAACAAGTGTCGATA
130 GTGCACCTCGTTTGGGCATTCATTCTGGATAAAA-GTATCGACACAAA-TTAACAAGTGTCGATA
*
825163 CTTTATG
193 CATTA-G
* * * * *
825170 CTGACCTATTTTCTCATAAAACTGGTATATTTATATCGGTTACATTGTAAATTTACCTATTACAT
1 TTGACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* *
825235 TATAATTATCGGTTTCGATGTTTTTGGGATTGATACTTTTAATAAATGCATCGACACTTTATGCG
66 TATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG
*
825300 TGCACCTCGTTTGGGCATTCATTCTGGATAATAAGTATCGACACAAATTCCACAAGTGTCGATAC
131 TGCACCTCGTTTGGGCATTCATTCTGGATAA-AAGTATCGACACAAATT-AACAAGTGTCGATAC
825365 ATTACG
194 ATTA-G
* * * * * * *
825371 TTGAACTGTTTTCTAAT-TAACAGATATATTTATACCAGTTACATTATTAATTTACCTATTACAT
1 TTGACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
* * * *
825435 TATAATTATTGGTTTTGATGTTTTTTGGG-TCGATACTTGTAGA-AAATATATCGACAC
66 TATAATTATCGGTTTCGATG-TTTTTGGGATCGATACTTTTA-ATAAATGTATCGACAC
825492 ATATTTAGGT
Statistics
Matches: 447, Mismatches: 59, Indels: 26
0.84 0.11 0.05
Matches are distributed among these distances:
194 12 0.03
195 76 0.17
196 41 0.09
197 6 0.01
198 31 0.07
199 67 0.15
200 143 0.32
201 69 0.15
202 2 0.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (198 bp):
TTGACCTATTTTCTAATAAAACCGATATATTTATACCGGTTACATTGTAAATTTACCTATTACAT
TATAATTATCGGTTTCGATGTTTTTGGGATCGATACTTTTAATAAATGTATCGACACTTTATGCG
TGCACCTCGTTTGGGCATTCATTCTGGATAAAAGTATCGACACAAATTAACAAGTGTCGATACAT
TAG
Found at i:829216 original size:199 final size:200
Alignment explanation
Indices: 828793--829753 Score: 1506
Period size: 199 Copynumber: 4.8 Consensus size: 200
828783 CTCGTTATTT
* *
828793 AAAAGTATCAACAC-AAATTTAAAAGTGTCGATACAT-TATGTAGACCTATTCTCTCATAAAACC
1 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAACC
* *
828856 GGTATATTTATACCGATTATATTACAAAATTACCTATTATATTATAATTATGGGTTTCGATGTTT
65 GGTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTT
* * *
828921 TTGGGATCGACACGTTTTGAAAATGTATCGACACTTTATGAGTTCAACCTTTTTGGAATTCATTC
130 TTGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGAGTTCACCCTTTTTGGCATTCATTC
828986 TGGACA
195 TGGACA
828992 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCT-TTCTCTCATAAAA-CG
1 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
* *
829055 GTATATTTATACCGGTTATATTACAAAATTACCTATTATATTATAATTATGGATTTCGATGTTTT
66 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
829120 TGAGATCGACACTTTTTGAAAATGTATCGACACTTTATGCGTTCACCCTTTTTTGGCATTCATTT
131 TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGAGTTCACCC-TTTTTGGCATTCATTC
*
829185 TGTACA
195 TGGACA
829191 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
1 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
* * * *
829256 GAATGTTTATACCAGTTATATTACAAAATTACCTATTACA-TATAATTATGGGTTTCGATATTTT
66 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
*
829320 TGGGATTGACACTTTTTGAAAATGTATCGACACTTTAT-ATGTTCACCCTTTTTGGCATTCATTC
131 TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGA-GTTCACCCTTTTTGGCATTCATTC
*
829384 TGTACA
195 TGGACA
* *
829390 AAAAGTATCAACACAAAATTAAAAAGTGTCGATACATGTTGTAGACATATTCTCTCATAAAACCG
1 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
*
829455 GTATATTTATACCGATTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
66 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
*
829520 TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGAGTTCACCATTTTTGGCATTCATTCT
131 TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGAGTTCACCCTTTTTGGCATTCATTCT
829585 GGACA
196 GGACA
* * *
829590 AAAAGTATCGACACAATATTAAAAAGTGTCGATACATGTTATAGACCTATT-TTTCATAAAACCG
1 AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
* * * ** * *
829654 ATATATTTATACCTGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTCGATGTTTT
66 GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
* * *
829719 TAGGG-TAGATACTTTTTAAAAATGTATCGACACTT
131 T-GGGATCGACACTTTTTGAAAATGTATCGACACTT
829754 AATGGGAAAC
Statistics
Matches: 706, Mismatches: 47, Indels: 18
0.92 0.06 0.02
Matches are distributed among these distances:
198 109 0.15
199 310 0.44
200 247 0.35
201 40 0.06
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.38
Consensus pattern (200 bp):
AAAAGTATCGACACAAAATTAAAAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCG
GTATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTT
TGGGATCGACACTTTTTGAAAATGTATCGACACTTTATGAGTTCACCCTTTTTGGCATTCATTCT
GGACA
Found at i:831136 original size:6 final size:6
Alignment explanation
Indices: 831107--831146 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
831097 CTTGTTTGAA
* * *
831107 TCATCA TCATCG TCATCT TCATCT TCATCT TTATCT TCAT
1 TCATCT TCATCT TCATCT TCATCT TCATCT TCATCT TCAT
831147 TGACCGCTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.20, C:0.30, G:0.03, T:0.47
Consensus pattern (6 bp):
TCATCT
Found at i:833000 original size:200 final size:199
Alignment explanation
Indices: 832620--833770 Score: 1518
Period size: 200 Copynumber: 5.8 Consensus size: 199
832610 ATTTAAAATG
* ** * * * * *
832620 GTATCGACGCAAATTTAACAATTGTCGATACTTTTTG-ATGACTTATTTTCTCATAAAACCGGTA
1 GTATCGACACAAATTCCACAAGTGTCGATACATGTTGTA-GACCTATTCTCTCATAAAACCGGTA
* * * *
832684 TATTTACACTGGTTACATTGGAAATTTACTTATTACATTATAATTATGGGTTTCGATGTTTTTGG
65 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* * *
832749 GATCGACAC-TTTTAAAAATGTATCGACACTTTATGGGTGCACCTTTTTTGGGTTTTGATTCTTG
130 GATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCA-CTCTTTTGGGCTTTGATTCTGG
832813 ATCAAAA
194 A-CAAAA
* **
832820 GTATCGACACAAATTCCACAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAAACCAATAT
1 GTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
* * * *
832885 ATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGTGTTTCGATGTTTCTGGG
66 ATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
* * * * **
832950 ATCGATACTTTTTATAAATGTATCGACACTTTATGAGTGCACTCTTTTGGGCATTCCTTCTGGAC
131 ATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACTCTTTTGGGCTTTGATTCTGGAC
833015 AAACA
196 AAA-A
* * * *
833020 GTATCGACATAAATTCCAGAAGTGTCGATACAT-TATGTTGACCTATTCTCTCATAAAATCGGTA
1 GTATCGACACAAATTCCACAAGTGTCGATACATGT-TGTAGACCTATTCTCTCATAAAACCGGTA
* * *
833084 TAGTTATAACGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
65 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* *
833149 GATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTATGGGCTTTGATTCTGG
130 GATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACTCTTT-TGGGCTTTGATTCTGG
833214 ACAAAAA
194 AC-AAAA
* *
833221 ATATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTATCTCATAAAACCGGTAT
1 GTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
* * * *
833286 ATTTATACCAGTTATATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTATGGG
66 ATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
* * * * * * *
833351 ATCGATACTTTTTATAAATATATCGACACTTTATAGGTGCACCCTTTTGGGCATTCATTCTGGAC
131 ATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACTCTTTTGGGCTTTGATTCTGGAC
833416 AAATA
196 AAA-A
* * * * * *
833421 GTATCGACACAATATT-AAAAAGTGTCGATACATGTTATATACCTATT-TTTCATAAAATCGGTA
1 GTATCGACACAA-ATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTA
* * * *
833484 TATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTAGATGTTTTTGG
65 TATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
* *
833549 GATCGACACTTTTTAAAAATGTATCGAAACTTTATGGGTGCA------T--ACTTTGATTCTGGA
130 GATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACTCTTTTGGGCTTTGATTCTGGA
833606 CCAAAA
195 -CAAAA
* * *
833612 GTATCGACACAAATTACACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACTGATAT
1 GTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
*
833677 ATTTATACCGGTTACATTGAAGATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
66 ATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
*
833742 ATCGACACTTTTTATAAATGTATCGACAC
131 ATCGACACTTTTTAAAAATGTATCGACAC
833771 ATATGCTTAC
Statistics
Matches: 835, Mismatches: 104, Indels: 32
0.86 0.11 0.03
Matches are distributed among these distances:
190 3 0.00
191 51 0.06
192 104 0.12
193 1 0.00
199 116 0.14
200 347 0.42
201 209 0.25
202 4 0.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (199 bp):
GTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGGTAT
ATTTATACCGGTTACATTGAAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGG
ATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACTCTTTTGGGCTTTGATTCTGGAC
AAAA
Found at i:833362 original size:401 final size:397
Alignment explanation
Indices: 832620--833770 Score: 1684
Period size: 401 Copynumber: 2.9 Consensus size: 397
832610 ATTTAAAATG
* * * * * * *
832620 GTATCGACGCAA-ATTTAACAATTGTCGATACTTTTTGATGACTTATTTTCTCATAAAACCGGTA
1 GTATCGACACAATA-TTAAAAAGTGTCGATACATTATGATGACCTA-TTTCTCATAAAATCGGTA
* *
832684 TATT-TACACTGGTTACATTGGAAATTTACTTATTACATTATAATTATGGGTTTCGATGTTTTTG
64 TATTATA-AC-GGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTG
* * *
832748 GGATCGACAC-TTTTAAAAATGTATCGACACTTTATGGGTGCACCTTTTTTGGGTTTTGATTCTT
127 GGATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACC-TTTATGGGCTTTGATTCTG
*
832812 GATCAAAAGTATCGACACAAATTCCACAAGTGTTGATACATGTTGTAGACCTATTCTCTCATAAA
191 GA-CAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAA
* *
832877 ACCAATATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGTGTTTCGATG
255 ACCGATATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATG
* *
832942 TTTCTGGGATCGATACTTTTTATAAATGTATCGACACTTTAT-GAGTGCACTCTTTTGGGCATTC
320 TTTATGGGATCGATACTTTTTATAAATGTATCGACACTTTATAG-GTGCACCCTTTTGGGCATTC
*
833006 CTTCTGGACAAACA
384 ATTCTGGACAAACA
* * * *
833020 GTATCGACATAA-ATTCCAGAAGTGTCGATACATTATGTTGACCTATTCTCTCATAAAATCGGTA
1 GTATCGACACAATATT-AAAAAGTGTCGATACATTATGATGACCTATT-TCTCATAAAATCGGTA
833084 TAGTTATAACGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
64 TA-TTATAACGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
*
833149 GATCGATACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCCTTTATGGGCTTTGATTCTGG
128 GATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCA-CCTTTATGGGCTTTGATTCTGG
* *
833214 ACAAAAAATATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTATCTCATAAAA
192 AC-AAAAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAA
* *
833279 CCGGTATATTTATACCAGTTATATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
256 CCGATATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGT
*
833344 TTATGGGATCGATACTTTTTATAAATATATCGACACTTTATAGGTGCACCCTTTTGGGCATTCAT
321 TTATGGGATCGATACTTTTTATAAATGTATCGACACTTTATAGGTGCACCCTTTTGGGCATTCAT
*
833409 TCTGGACAAATA
386 TCTGGACAAACA
*
833421 GTATCGACACAATATTAAAAAGTGTCGATACATGTTAT-AT-ACCTATTTTTCATAAAATCGGTA
1 GTATCGACACAATATTAAAAAGTGTCGATACA--TTATGATGACCTATTTCTCATAAAATCGGTA
* * *
833484 TATTTATATCGGTTACATTGTAAATTTACCTATTACATTATAATTATCGGTTTAGATGTTTTTGG
64 TA-TTATAACGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGG
*
833549 GATCGACACTTTTTAAAAATGTATCGAAACTTTATGGGTGCA----TA----CTTTGATTCTGGA
128 GATCGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCTTTATGGGCTTTGATTCTGGA
*
833606 CCAAAAGTATCGACACAAATTACACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
193 -CAAAAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAAC
* * * *
833671 TGATATATTTATACCGGTTACATTGAAGATTTACCTATTACATTATAATTATGGGTTTCGATGTT
257 CGATATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTT
* *
833736 TTTGGGATCGACACTTTTTATAAATGTATCGACAC
322 TATGGGATCGATACTTTTTATAAATGTATCGACAC
833771 ATATGCTTAC
Statistics
Matches: 688, Mismatches: 51, Indels: 33
0.89 0.07 0.04
Matches are distributed among these distances:
391 164 0.24
392 1 0.00
395 2 0.00
399 4 0.01
400 228 0.33
401 276 0.40
402 9 0.01
403 4 0.01
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (397 bp):
GTATCGACACAATATTAAAAAGTGTCGATACATTATGATGACCTATTTCTCATAAAATCGGTATA
TTATAACGGTTACATTGTAAATTTACCTATTACATTATAATTATGGGTTTCGATGTTTTTGGGAT
CGACACTTTTTAAAAATGTATCGACACTTTATGGGTGCACCTTTATGGGCTTTGATTCTGGACAA
AAGTATCGACACAAATTCCACAAGTGTCGATACATGTTGTAGACCTATTCTCTCATAAAACCGAT
ATATTTATACCAGTTACATTGAAAAATTACCTATTACATTATAATTATGGGTTTCGATGTTTATG
GGATCGATACTTTTTATAAATGTATCGACACTTTATAGGTGCACCCTTTTGGGCATTCATTCTGG
ACAAACA
Found at i:834692 original size:4 final size:4
Alignment explanation
Indices: 834683--836096 Score: 2807
Period size: 4 Copynumber: 354.2 Consensus size: 4
834673 AATGTCCTTT
834683 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
834731 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
834779 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
834827 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
834875 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
834923 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
834971 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835019 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835067 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835115 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835163 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835211 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835259 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835307 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835355 CATA CATA CATA CATA CATA CATA CATA CATA C-TA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835402 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835450 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835498 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835546 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835594 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835642 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835690 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835738 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835786 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835834 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835882 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835930 CATA CATA CATA CATA CAT- -ATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
835976 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
836024 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA CATA
836072 CATA CATA CATA CATA CATA CATA C
1 CATA CATA CATA CATA CATA CATA C
836097 CAATCTCTTA
Statistics
Matches: 1407, Mismatches: 0, Indels: 6
1.00 0.00 0.00
Matches are distributed among these distances:
2 2 0.00
3 3 0.00
4 1402 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:837098 original size:18 final size:18
Alignment explanation
Indices: 837075--837123 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
837065 ATTTTCTCTA
837075 TCTTTTCTTCTTCCTCCC
1 TCTTTTCTTCTTCCTCCC
837093 TCTTTTCTTCTTCCTCCC
1 TCTTTTCTTCTTCCTCCC
*
837111 TATTTTCTTCTTC
1 TCTTTTCTTCTTC
837124 ATATTTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.02, C:0.39, G:0.00, T:0.59
Consensus pattern (18 bp):
TCTTTTCTTCTTCCTCCC
Found at i:837344 original size:33 final size:33
Alignment explanation
Indices: 837307--837373 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
837297 CCATCTTAAG
837307 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
*
837340 TTCACCCCTCAACACCTCAACTTCTTTCATCAC
1 TTCACCCCTCAACACCTCAACTTCTTTCACCAC
837373 T
1 T
837374 CTATCTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.24, C:0.46, G:0.00, T:0.30
Consensus pattern (33 bp):
TTCACCCCTCAACACCTCAACTTCTTTCACCAC
Found at i:837432 original size:21 final size:21
Alignment explanation
Indices: 837407--837450 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
837397 CCCCTTATGC
837407 CTCTCAACTGTCTCTTCGACT
1 CTCTCAACTGTCTCTTCGACT
* * *
837428 CTCTCAAGTTTCTCTTCTACT
1 CTCTCAACTGTCTCTTCGACT
837449 CT
1 CT
837451 TGATTGTCTT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.14, C:0.36, G:0.07, T:0.43
Consensus pattern (21 bp):
CTCTCAACTGTCTCTTCGACT
Found at i:840037 original size:181 final size:181
Alignment explanation
Indices: 839805--840618 Score: 1103
Period size: 182 Copynumber: 4.5 Consensus size: 181
839795 TACACGTACT
* ** * * * *
839805 TATTAAAGTATCGAAACTTTCGATATATCTGGTAGCTCTTTACCGGTTTTATCATTGCGAGACCG
1 TATTAAAGTATCGACACTTTAAATATATCT-GTAGCGCTTTACCAGTTTTATCCTTTCGAGACCG
* *
839870 GTTTTGTTATATTTTTACCTGTTATATCGTTATGGATCGATACATTTTTATAAAATATCGACACT
65 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACT
* *
839935 TTATAGGCGCTAAAA-TACTTCTGTTTTAAATTTACAAAGTGTCGATACTTA
130 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * *
839986 TAATAAAGTATCGACACTTTAAATATATCCTGTAGCGCTTTACCAGTTTTATCCTTTAGAGACTG
1 TATTAAAGTATCGACACTTTAAATATAT-CTGTAGCGCTTTACCAGTTTTATCCTTTCGAGACCG
* * * *
840051 ATTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTGTTATAAAGTATCGACATT
65 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACT
* *
840116 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCTCAAAGTGTCGATACTTA
130 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * * *
840168 TATTAAAGTATCGACACTTTCAATATATACGGTCGCTCTATA-CTGATTTTATCCTTTAGAGACC
1 TATTAAAGTATCGACACTTTAAATATAT-CTGTAGCGCTTTACCAG-TTTTATCCTTTCGAGACC
* * ** *
840232 GATTTTATCATATTTTTACCTGTTATATCGTTGTGGATTAATATATTTTTATAAAATATCGACAC
64 GGTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACAC
840297 TTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
129 TTTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * *
840350 TATTAAAGTATCGACACTTTAAATATATCTGGTAGTGCTTTACCGGTTTTGTCTTTTCGTGACCG
1 TATTAAAGTATCGACACTTTAAATATATCT-GTAGCGCTTTACCAGTTTTATCCTTTCGAGACCG
* * * * * *
840415 GTTCTGTTATATTTTTACCTGTTATATCGTGGTGGATCGATACATTTTTATACAGTATCAACACT
65 GTTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACT
*
840480 TTATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
130 TTATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
* * * * * *
840532 TATTAAAGTATCGACACTGTAAATATAACCGGTAGCGCTTTACCAGTTTT-TCTTTTCGTGGCCG
1 TATTAAAGTATCGACACTTTAAATAT-ATCTGTAGCGCTTTACCAGTTTTATCCTTTCGAGACCG
840596 GTTTTGTCATATTTTTACCTGTT
65 GTTTTGTCATATTTTTACCTGTT
840619 TTATTAATAT
Statistics
Matches: 558, Mismatches: 69, Indels: 12
0.87 0.11 0.02
Matches are distributed among these distances:
181 163 0.29
182 391 0.70
183 4 0.01
ACGTcount: A:0.28, C:0.16, G:0.14, T:0.41
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTAAATATATCTGTAGCGCTTTACCAGTTTTATCCTTTCGAGACCGG
TTTTGTCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTATAAAATATCGACACTT
TATAGGCGCTAAAACTACTTCTCTTTTAAATTCACAAAGTGTCGATACTTA
Found at i:842117 original size:76 final size:76
Alignment explanation
Indices: 842010--842164 Score: 249
Period size: 76 Copynumber: 2.0 Consensus size: 76
842000 TTAATAAATA
* * *
842010 AATTAGTTTATAAATGAGTCGATAAATAAATTTATTCATGAACATAAACGAACTAAATACACATT
1 AATTAGTTTATAAATGAATCAATAAACAAATTTATTCATGAACATAAACGAACTAAATACACATT
842075 TTTTCGTGTTC
66 TTTTCGTGTTC
*
842086 AATT-GTTTATTAAATGAATCAATAAACAAATTTATTTATGAACATAAACGAACTAAATACACAT
1 AATTAGTTTA-TAAATGAATCAATAAACAAATTTATTCATGAACATAAACGAACTAAATACACAT
*
842150 TTTTTTGTGTTC
65 TTTTTCGTGTTC
842162 AAT
1 AAT
842165 AGAAAATAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
75 5 0.07
76 68 0.93
ACGTcount: A:0.42, C:0.11, G:0.09, T:0.38
Consensus pattern (76 bp):
AATTAGTTTATAAATGAATCAATAAACAAATTTATTCATGAACATAAACGAACTAAATACACATT
TTTTCGTGTTC
Found at i:845226 original size:4 final size:4
Alignment explanation
Indices: 845217--845276 Score: 75
Period size: 4 Copynumber: 15.0 Consensus size: 4
845207 AAAAAAGCAA
* * *
845217 AAAG AAAG AAAA AAAG AAAA AAAG AAAG AAAG AAAA AAAG AAAG AAAG
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
* *
845265 AATG AATG AAAG
1 AAAG AAAG AAAG
845277 TATTACTGCA
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.03
Consensus pattern (4 bp):
AAAG
Found at i:845231 original size:20 final size:19
Alignment explanation
Indices: 845206--845266 Score: 70
Period size: 20 Copynumber: 3.1 Consensus size: 19
845196 ATACAATATC
845206 AAAAAAAGCAAAAAGAAAGA
1 AAAAAAAG-AAAAAGAAAGA
*
845226 AAAAAAGAAAAAAAGAAAGA
1 AAAAAA-AGAAAAAGAAAGA
845246 AAGAAAAA-AAGAAAGAAAGA
1 AA-AAAAAGAA-AAAGAAAGA
845266 A
1 A
845267 TGAATGAAAG
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
19 2 0.05
20 30 0.81
21 5 0.14
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAAAAGAAAGA
Found at i:845232 original size:8 final size:8
Alignment explanation
Indices: 845206--845266 Score: 77
Period size: 8 Copynumber: 7.2 Consensus size: 8
845196 ATACAATATC
845206 AAAAAAAG
1 AAAAAAAG
845214 CAAAAAGAAAG
1 --AAAA-AAAG
845225 AAAAAAAG
1 AAAAAAAG
845233 AAAAAAAG
1 AAAAAAAG
*
845241 AAAGAAAG
1 AAAAAAAG
845249 AAAAAAAG
1 AAAAAAAG
*
845257 AAAGAAAG
1 AAAAAAAG
845265 AA
1 AA
845267 TGAATGAAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
8 35 0.74
9 4 0.09
10 4 0.09
11 4 0.09
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:854065 original size:8 final size:8
Alignment explanation
Indices: 854054--854122 Score: 52
Period size: 8 Copynumber: 8.2 Consensus size: 8
854044 CTAAAATATT
854054 AAAAAATA
1 AAAAAATA
*
854062 AAAATTATTA
1 AAAA--AATA
854072 TAAACAAAT-
1 -AAA-AAATA
854081 AAAAAATA
1 AAAAAATA
*
854089 AATAAAATT
1 AA-AAAATA
854098 AAAAAAT-
1 AAAAAATA
*
854105 TAAAAATA
1 AAAAAATA
854113 AAAAAATA
1 AAAAAATA
854121 AA
1 AA
854123 TGAAGTTAAA
Statistics
Matches: 49, Mismatches: 5, Indels: 14
0.72 0.07 0.21
Matches are distributed among these distances:
7 10 0.20
8 23 0.47
9 7 0.14
10 5 0.10
11 3 0.06
12 1 0.02
ACGTcount: A:0.77, C:0.01, G:0.00, T:0.22
Consensus pattern (8 bp):
AAAAAATA
Found at i:854093 original size:19 final size:19
Alignment explanation
Indices: 854053--854104 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 19
854043 TCTAAAATAT
* *
854053 TAAAAAATAAAAATTATTA
1 TAAAAAATAAAAAATATAA
854072 TAAACAAATAAAAAATA-AA
1 TAAA-AAATAAAAAATATAA
*
854091 T-AAAATTAAAAAAT
1 TAAAAAATAAAAAAT
854105 TAAAAATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
17 10 0.34
18 2 0.07
19 6 0.21
20 11 0.38
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (19 bp):
TAAAAAATAAAAAATATAA
Found at i:854101 original size:15 final size:14
Alignment explanation
Indices: 854083--854122 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
854073 AAACAAATAA
*
854083 AAAATAAATAAAATT
1 AAAA-AAATAAAAAT
*
854098 AAAAAATTAAAAAT
1 AAAAAAATAAAAAT
854112 AAAAAAATAAA
1 AAAAAAATAAA
854123 TGAAGTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
14 18 0.82
15 4 0.18
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (14 bp):
AAAAAAATAAAAAT
Found at i:854109 original size:24 final size:24
Alignment explanation
Indices: 854053--854119 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
854043 TCTAAAATAT
*
854053 TAAAAAATAAAAATTATTATAAACAAA
1 TAAAAAATAAAAA--AAT-TAAACAAA
854080 TAAAAAATAAATAAAATTAAA-AAA
1 TAAAAAATAAA-AAAATTAAACAAA
*
854104 TTAAAAATAAAAAAAT
1 TAAAAAATAAAAAAAT
854120 AAATGAAGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
23 5 0.14
24 13 0.35
25 4 0.11
26 2 0.05
27 11 0.30
28 2 0.05
ACGTcount: A:0.75, C:0.01, G:0.00, T:0.24
Consensus pattern (24 bp):
TAAAAAATAAAAAAATTAAACAAA
Found at i:854122 original size:32 final size:31
Alignment explanation
Indices: 854077--854138 Score: 88
Period size: 32 Copynumber: 2.0 Consensus size: 31
854067 TATTATAAAC
854077 AAATAAAAAATAAATAAAATTAAAAAATTAA
1 AAATAAAAAATAAATAAAATTAAAAAATTAA
* * *
854108 AAATAAAAAAATAAATGAAGTTAAATAATTA
1 AAAT-AAAAAATAAATAAAATTAAAAAATTA
854139 CCTTCCAGCC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 4 0.15
32 23 0.85
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (31 bp):
AAATAAAAAATAAATAAAATTAAAAAATTAA
Found at i:855603 original size:31 final size:31
Alignment explanation
Indices: 855560--855621 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
855550 ATACAATCAT
* *
855560 TTTCGTTTTTATTTTATTAAAATATGGTCAC
1 TTTCATTTTTATTTAATTAAAATATGGTCAC
* *
855591 TTTCATTTTTATTTAATTAAGATGTGGTCAC
1 TTTCATTTTTATTTAATTAAAATATGGTCAC
855622 CCCGAGTTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.26, C:0.10, G:0.11, T:0.53
Consensus pattern (31 bp):
TTTCATTTTTATTTAATTAAAATATGGTCAC
Found at i:855875 original size:23 final size:23
Alignment explanation
Indices: 855849--855915 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
855839 ATAATATTTT
*
855849 ATATATATATATTAACTTAAAAA
1 ATATATTTATATTAACTTAAAAA
* *
855872 ATATTTTTATATTAACTT-ATAA
1 ATATATTTATATTAACTTAAAAA
855894 ATATATTTTATTATTAACTTAA
1 ATATA-TTTA-TATTAACTTAA
855916 TTTAAAATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.19
23 20 0.54
24 9 0.24
25 1 0.03
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (23 bp):
ATATATTTATATTAACTTAAAAA
Found at i:855905 original size:29 final size:29
Alignment explanation
Indices: 855873--855936 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
855863 ACTTAAAAAA
855873 TATTTTTATA-TTAACTTATAAA-TATATTT
1 TATTTTTA-ACTTAACTTA-AAATTATATTT
* * *
855902 TATTATTAACTTAATTTAAAATTTTATTT
1 TATTTTTAACTTAACTTAAAATTATATTT
855931 TATTTT
1 TATTTT
855937 CATTTAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 4 0.14
29 25 0.86
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (29 bp):
TATTTTTAACTTAACTTAAAATTATATTT
Found at i:855908 original size:24 final size:23
Alignment explanation
Indices: 855856--855915 Score: 86
Period size: 23 Copynumber: 2.6 Consensus size: 23
855846 TTTATATATA
855856 TATATTAACTTAAAAAATATTTT
1 TATATTAACTTAAAAAATATTTT
*
855879 TATATTAACTT-ATAAATATATTT
1 TATATTAACTTAAAAAATAT-TTT
855902 TATTATTAACTTAA
1 TA-TATTAACTTAA
855916 TTTAAAATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
22 7 0.21
23 16 0.48
24 9 0.27
25 1 0.03
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (23 bp):
TATATTAACTTAAAAAATATTTT
Found at i:856126 original size:31 final size:31
Alignment explanation
Indices: 856088--856155 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
856078 TGATGAGCAC
*
856088 ATCTTAATTAAATAAAAACGAAAGTAACCAT
1 ATCTTAATTAAATAAAAACGAAAGTAACAAT
*
856119 ATCTTAATTAAATAAAAACGAAAGTGACAAT
1 ATCTTAATTAAATAAAAACGAAAGTAACAAT
856150 ATCTTA
1 ATCTTA
856156 TGTTTTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.53, C:0.12, G:0.07, T:0.28
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACGAAAGTAACAAT
Found at i:857554 original size:20 final size:20
Alignment explanation
Indices: 857531--857573 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
857521 TGAGTATCGG
* *
857531 TACTCAAGGTTCGGTATAGA
1 TACTCAAGGGTCAGTATAGA
* *
857551 TACTGAAGGGTCAGTATCGA
1 TACTCAAGGGTCAGTATAGA
857571 TAC
1 TAC
857574 CCACAGATAG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (20 bp):
TACTCAAGGGTCAGTATAGA
Found at i:861453 original size:16 final size:17
Alignment explanation
Indices: 861421--861457 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
861411 TATGTTACAT
*
861421 GTGTTATATGTATTAAA
1 GTGTTATATGAATTAAA
861438 GTGTTATA-GAATTAAA
1 GTGTTATATGAATTAAA
861454 GTGT
1 GTGT
861458 GGATACCATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.35, C:0.00, G:0.22, T:0.43
Consensus pattern (17 bp):
GTGTTATATGAATTAAA
Found at i:867261 original size:40 final size:40
Alignment explanation
Indices: 867206--867292 Score: 129
Period size: 40 Copynumber: 2.2 Consensus size: 40
867196 ATTTTGCTAA
* * * *
867206 AAGGAAATCAGGTGTCCTGGCTATTTCTCGAGCATCAAAC
1 AAGGATATCAGGTGTCATGGCTACTTCCCGAGCATCAAAC
*
867246 AAGGATATCAGGTGTCATGGCTGCTTCCCGAGCATCAAAC
1 AAGGATATCAGGTGTCATGGCTACTTCCCGAGCATCAAAC
867286 AAGGATA
1 AAGGATA
867293 GTTTTATGTC
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (40 bp):
AAGGATATCAGGTGTCATGGCTACTTCCCGAGCATCAAAC
Found at i:869078 original size:18 final size:18
Alignment explanation
Indices: 869057--869105 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
869047 CGTATAATTC
869057 CCACTAGAACACGTAGGA
1 CCACTAGAACACGTAGGA
* *
869075 CCACTATG-TCCCGTAGGA
1 CCACTA-GAACACGTAGGA
869093 CCACGTAGAACAC
1 CCAC-TAGAACAC
869106 ATATGTCCCG
Statistics
Matches: 24, Mismatches: 4, Indels: 5
0.73 0.12 0.15
Matches are distributed among these distances:
18 19 0.79
19 5 0.21
ACGTcount: A:0.33, C:0.33, G:0.20, T:0.14
Consensus pattern (18 bp):
CCACTAGAACACGTAGGA
Found at i:869128 original size:18 final size:18
Alignment explanation
Indices: 869107--869178 Score: 117
Period size: 18 Copynumber: 4.0 Consensus size: 18
869097 GTAGAACACA
*
869107 TATGTCCCGTAGGACTAC
1 TATGTCCCGTAGGACCAC
869125 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
869143 TATGTCCCGTAGGACCAC
1 TATGTCCCGTAGGACCAC
* *
869161 TATATCCCGTAAGACCAC
1 TATGTCCCGTAGGACCAC
869179 GTAGAACCCT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 51 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (18 bp):
TATGTCCCGTAGGACCAC
Found at i:869687 original size:25 final size:25
Alignment explanation
Indices: 869659--869708 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
869649 TTTAACACCA
869659 TATCACTACATATTTATGCTTCAGT
1 TATCACTACATATTTATGCTTCAGT
* *
869684 TATCCCTACATGTTTATGCTTCAGT
1 TATCACTACATATTTATGCTTCAGT
869709 ACCCTAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.10, T:0.44
Consensus pattern (25 bp):
TATCACTACATATTTATGCTTCAGT
Found at i:872014 original size:23 final size:24
Alignment explanation
Indices: 871973--872017 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
871963 TTTCTTGTGC
*
871973 TTTCTTCTTTGAAATTTCTTTTCT
1 TTTCTTCTTTGAAACTTCTTTTCT
*
871997 TTTCTTCTTTG-TACTTCTTTT
1 TTTCTTCTTTGAAACTTCTTTT
872018 TGTTGTTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
23 8 0.42
24 11 0.58
ACGTcount: A:0.09, C:0.18, G:0.04, T:0.69
Consensus pattern (24 bp):
TTTCTTCTTTGAAACTTCTTTTCT
Found at i:874756 original size:24 final size:24
Alignment explanation
Indices: 874739--874874 Score: 209
Period size: 24 Copynumber: 5.7 Consensus size: 24
874729 ATCATAACAT
* *
874739 AATCCAGGTCAAGTATCAGATCAA
1 AATCCAGGTCAAGTATCCGATCAG
874763 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
* *
874787 AATCTAGGTCACGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
874811 AATCCAGGTCAAGCATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
874835 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
* *
874859 AATCCATGTCAGGTAT
1 AATCCAGGTCAAGTAT
874875 TATAATAGAA
Statistics
Matches: 102, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 102 1.00
ACGTcount: A:0.34, C:0.24, G:0.20, T:0.22
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:874774 original size:12 final size:13
Alignment explanation
Indices: 874739--874869 Score: 75
Period size: 12 Copynumber: 10.8 Consensus size: 13
874729 ATCATAACAT
874739 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
874752 TAT-CAGATCAA-
1 AATCCAGGTCAAG
874763 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
874776 TATCC-GATC-AG
1 AATCCAGGTCAAG
* *
874787 AATCTAGGTCACG
1 AATCCAGGTCAAG
* *
874800 TATCC-GATC-AG
1 AATCCAGGTCAAG
874811 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
874824 CATCC-GATC-AG
1 AATCCAGGTCAAG
874835 AATCCAGGTCAAG
1 AATCCAGGTCAAG
* *
874848 TATCC-GATC-AG
1 AATCCAGGTCAAG
*
874859 AATCCATGTCA
1 AATCCAGGTCA
874870 GGTATTATAA
Statistics
Matches: 83, Mismatches: 25, Indels: 20
0.65 0.20 0.16
Matches are distributed among these distances:
11 24 0.29
12 37 0.45
13 22 0.27
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.21
Consensus pattern (13 bp):
AATCCAGGTCAAG
Found at i:877390 original size:15 final size:15
Alignment explanation
Indices: 877370--877402 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
877360 TGGTCAACGT
877370 CGGTCAAC-GAGTCAA
1 CGGTCAACAG-GTCAA
877385 CGGTCAACAGGTCAA
1 CGGTCAACAGGTCAA
877400 CGG
1 CGG
877403 GTCGGGTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.30, C:0.27, G:0.30, T:0.12
Consensus pattern (15 bp):
CGGTCAACAGGTCAA
Found at i:877416 original size:13 final size:13
Alignment explanation
Indices: 877398--877422 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
877388 TCAACAGGTC
877398 AACGGGTCGGGTT
1 AACGGGTCGGGTT
877411 AACGGGTCGGGT
1 AACGGGTCGGGT
877423 CAGTAGGTAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.16, G:0.48, T:0.20
Consensus pattern (13 bp):
AACGGGTCGGGTT
Found at i:879603 original size:24 final size:24
Alignment explanation
Indices: 879576--879663 Score: 131
Period size: 24 Copynumber: 3.7 Consensus size: 24
879566 ATCATAACAT
* ** *
879576 AATCCAGGTCAAGTGTTAGATCAA
1 AATCCAGGTCAAGTATCCGATCAG
879600 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
879624 AATCCAGGTCAAGTATCCGATCAG
1 AATCCAGGTCAAGTATCCGATCAG
*
879648 AATCCAGGTCAGGTAT
1 AATCCAGGTCAAGTAT
879664 TATAATAGAA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 59 1.00
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (24 bp):
AATCCAGGTCAAGTATCCGATCAG
Found at i:882188 original size:13 final size:13
Alignment explanation
Indices: 882170--882199 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
882160 ACGAGTCAAC
882170 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
882183 GGTCAATGGGTCG
1 GGTCAACGGGTCG
882196 GGTC
1 GGTC
882200 GAGTCAGCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.20, G:0.47, T:0.20
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:886239 original size:15 final size:15
Alignment explanation
Indices: 886216--886245 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
886206 GTTACCTGAT
886216 GAGAGGGAGCAGGCC
1 GAGAGGGAGCAGGCC
*
886231 GAGATGGAGCAGGCC
1 GAGAGGGAGCAGGCC
886246 AGAAGAACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.50, T:0.03
Consensus pattern (15 bp):
GAGAGGGAGCAGGCC
Found at i:891391 original size:15 final size:15
Alignment explanation
Indices: 891368--891397 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
891358 GTTACCTGAT
891368 GAGAGGGAGCAGGCC
1 GAGAGGGAGCAGGCC
*
891383 GAGATGGAGCAGGCC
1 GAGAGGGAGCAGGCC
891398 AAAAGCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.20, G:0.50, T:0.03
Consensus pattern (15 bp):
GAGAGGGAGCAGGCC
Found at i:891835 original size:38 final size:38
Alignment explanation
Indices: 891782--891922 Score: 219
Period size: 38 Copynumber: 3.7 Consensus size: 38
891772 ATTTATTTGA
*
891782 TCTATTTTAATTTAATGTAATTTGTTTAAATTTAAATGG
1 TCTACTTT-ATTTAATGTAATTTGTTTAAATTTAAATGG
891821 TCTACTTTATTTAATGTAATTTGTTTAAATTTAAATGG
1 TCTACTTTATTTAATGTAATTTGTTTAAATTTAAATGG
* * *
891859 TCTACTTTATTTAATGTTATTTGTTTAAATTTAATTGA
1 TCTACTTTATTTAATGTAATTTGTTTAAATTTAAATGG
* *
891897 TCTATTTTATTTAATGTGATTTGTTT
1 TCTACTTTATTTAATGTAATTTGTTT
891923 TTTTACATAA
Statistics
Matches: 96, Mismatches: 6, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
38 89 0.93
39 7 0.07
ACGTcount: A:0.29, C:0.04, G:0.10, T:0.57
Consensus pattern (38 bp):
TCTACTTTATTTAATGTAATTTGTTTAAATTTAAATGG
Found at i:891885 original size:18 final size:18
Alignment explanation
Indices: 891864--891927 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
891854 AATGGTCTAC
*
891864 TTTATTTAATGTTATTTG
1 TTTATTTAATGTGATTTG
891882 TTTAAATTTAAT-TGATCTAT-
1 TTT--ATTTAATGTGAT-T-TG
891902 TTTATTTAATGTGATTTG
1 TTTATTTAATGTGATTTG
*
891920 TTTTTTTA
1 TTTATTTA
891928 CATAATATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
17 1 0.03
18 18 0.47
19 7 0.18
20 11 0.29
21 1 0.03
ACGTcount: A:0.25, C:0.02, G:0.09, T:0.64
Consensus pattern (18 bp):
TTTATTTAATGTGATTTG
Found at i:892267 original size:23 final size:23
Alignment explanation
Indices: 892234--892285 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
892224 TATGACATGT
*
892234 TCTCTGTCTTTATGACAAGTTTA
1 TCTCTGCCTTTATGACAAGTTTA
* * * *
892257 TCTCTGCCTTTGTGGCACGTTTT
1 TCTCTGCCTTTATGACAAGTTTA
892280 TCTCTG
1 TCTCTG
892286 TCTCTTGGTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (23 bp):
TCTCTGCCTTTATGACAAGTTTA
Found at i:894464 original size:150 final size:148
Alignment explanation
Indices: 894210--894529 Score: 468
Period size: 150 Copynumber: 2.1 Consensus size: 148
894200 GTAGGGTCTA
*
894210 CAGGATCTTCCATGTCATTGTCACTATCGATATCAACTACCTCAACCTTAACTTCCTTCTCCATT
1 CAGGATCTTCCATGTCATTGCCACTATCGATATCAACTACCTCAACCTTAACTTCCTTCTCCATT
894275 GCACCATCAGGGTCCCTGACAACTGCCTCAATCTTCTGGACTT-TAGTTTCTTGACCAAGAGCAA
66 GCACCATCAGGGTCCCTGACAACTGCCTCAA--TTCTGGACTTCT-GTTTCTTGACCAAGAGCAA
894339 CCTCATCTTCCTCTT-CAATGT
128 CCTCATCTTCCT-TTCCAATGT
* * * *
894360 CAGTATCTTCCATGTCATTGCCACTATCGATGTCAACTACCTCGATCTTAACTTCCTTCTCCATT
1 CAGGATCTTCCATGTCATTGCCACTATCGATATCAACTACCTCAACCTTAACTTCCTTCTCCATT
* **
894425 -CTTCCTTCATCAGGGTCCCTGACAACTGCCTCAA-TCTGGACTTCTGTTTCTTGATGAAGAGCA
66 GC--AC--CATCAGGGTCCCTGACAACTGCCTCAATTCTGGACTTCTGTTTCTTGACCAAGAGCA
894488 ACCTCATCTTCCTTTCCAATGT
127 ACCTCATCTTCCTTTCCAATGT
894510 CAGGATCTTCCATGTCATTG
1 CAGGATCTTCCATGTCATTG
894530 TTGGCATCTA
Statistics
Matches: 155, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
149 3 0.02
150 123 0.79
151 2 0.01
153 27 0.17
ACGTcount: A:0.22, C:0.31, G:0.13, T:0.34
Consensus pattern (148 bp):
CAGGATCTTCCATGTCATTGCCACTATCGATATCAACTACCTCAACCTTAACTTCCTTCTCCATT
GCACCATCAGGGTCCCTGACAACTGCCTCAATTCTGGACTTCTGTTTCTTGACCAAGAGCAACCT
CATCTTCCTTTCCAATGT
Found at i:894650 original size:141 final size:141
Alignment explanation
Indices: 894396--894653 Score: 317
Period size: 141 Copynumber: 1.8 Consensus size: 141
894386 TCGATGTCAA
* * ** *
894396 CTACCTCGATCTTAACTTCCTTCTCCATTCTTCCTTCATCAGGGTCCCTGACAACTGCCTCAATC
1 CTACCTCGATCTCAACTTCCTTCTCCATTCTGCCTTCATCAGCATCCCAGACAACTGCCTCAATC
* *
894461 TGGACTTCTGTTTCTTGATGAAGAGCAACCTCATCTTCCTTTCCAATGTCAGGATCTTCCATGTC
66 TGGACTTCTGTTTCTTGATCAAGAGCAACCTCATCTTCCTATCCAATGTCAGGATCTTCCATGTC
894526 ATTGTTGGCAT
131 ATTGTTGGCAT
* * * *
894537 CTACCTC-AGTCTCAACTTCCTTCTCCATTGTGCCTTCATCAGCATCCCCAG-TATCTGCCTCGA
1 CTACCTCGA-TCTCAACTTCCTTCTCCATTCTGCCTTCATCAGCAT-CCCAGACAACTGCCTCAA
* ** *
894600 TCTGGACTTTTGTTTCTCT-ATCTTGAGCAACCTCCTCTTCCTCAT-CAATGTCAG
64 TCTGGACTTCTGTTTCT-TGATCAAGAGCAACCTCATCTTCCT-ATCCAATGTCAG
894654 CAGCACTACC
Statistics
Matches: 98, Mismatches: 15, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
140 1 0.01
141 91 0.93
142 6 0.06
ACGTcount: A:0.18, C:0.33, G:0.13, T:0.36
Consensus pattern (141 bp):
CTACCTCGATCTCAACTTCCTTCTCCATTCTGCCTTCATCAGCATCCCAGACAACTGCCTCAATC
TGGACTTCTGTTTCTTGATCAAGAGCAACCTCATCTTCCTATCCAATGTCAGGATCTTCCATGTC
ATTGTTGGCAT
Found at i:895304 original size:19 final size:19
Alignment explanation
Indices: 895280--895319 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
895270 AACGAGAAGA
895280 ATCACCAAGTACTCCGTAC
1 ATCACCAAGTACTCCGTAC
*
895299 ATCACCAAGTACTCCTTAC
1 ATCACCAAGTACTCCGTAC
895318 AT
1 AT
895320 TTCTATTTCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.35, G:0.07, T:0.25
Consensus pattern (19 bp):
ATCACCAAGTACTCCGTAC
Found at i:903740 original size:2 final size:2
Alignment explanation
Indices: 903733--903786 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
903723 GTTTATCACC
903733 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
903775 AT AT AA AT AT AT
1 AT AT AT AT AT AT
903787 CAATTATTGC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:915808 original size:20 final size:20
Alignment explanation
Indices: 915750--915809 Score: 75
Period size: 21 Copynumber: 3.0 Consensus size: 20
915740 CCGTTAGACA
* * *
915750 GGGGGGAATCGATACCCCTT
1 GGGGGGAATCGGTTCCCCTG
*
915770 GGGGGGAATCTGTTCCCCCTG
1 GGGGGGAATCGGTT-CCCCTG
915791 GGGGGGAATCGGTTCCCCT
1 GGGGGGAATCGGTTCCCCT
915810 AGGCAATCTG
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
20 16 0.47
21 18 0.53
ACGTcount: A:0.13, C:0.27, G:0.38, T:0.22
Consensus pattern (20 bp):
GGGGGGAATCGGTTCCCCTG
Found at i:921186 original size:15 final size:17
Alignment explanation
Indices: 921154--921190 Score: 60
Period size: 15 Copynumber: 2.3 Consensus size: 17
921144 AGAGGAGACA
921154 TTTTAGTTTTCATATCT
1 TTTTAGTTTTCATATCT
921171 TTTTAG-TTTC-TATCT
1 TTTTAGTTTTCATATCT
921186 TTTTA
1 TTTTA
921191 TATCCCTCCG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 10 0.50
16 4 0.20
17 6 0.30
ACGTcount: A:0.16, C:0.11, G:0.05, T:0.68
Consensus pattern (17 bp):
TTTTAGTTTTCATATCT
Found at i:927494 original size:20 final size:19
Alignment explanation
Indices: 927453--927497 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
927443 CCTCTTAGAA
* *
927453 ATTTTAATTTTTTTTTTAT
1 ATTTTAATATTTTATTTAT
*
927472 ATTTTAGATATTTTATTTGT
1 ATTTTA-ATATTTTATTTAT
927492 ATTTTA
1 ATTTTA
927498 CATGAATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (19 bp):
ATTTTAATATTTTATTTAT
Found at i:930631 original size:32 final size:30
Alignment explanation
Indices: 930590--930658 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 30
930580 AATAAAATAT
**
930590 ATATATATTATTATGTATATATTTTTATTAAA
1 ATATATATTAAAAT-TATATATTTTTA-TAAA
*
930622 ATATATATTAAAATTTTATATTTTTATAAA
1 ATATATATTAAAATTATATATTTTTATAAA
930652 ATATATA
1 ATATATA
930659 GGTAAATTAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
30 11 0.32
31 11 0.32
32 12 0.35
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.54
Consensus pattern (30 bp):
ATATATATTAAAATTATATATTTTTATAAA
Found at i:930666 original size:30 final size:32
Alignment explanation
Indices: 930607--930672 Score: 93
Period size: 30 Copynumber: 2.1 Consensus size: 32
930597 TTATTATGTA
*
930607 TATATTTTTATTAAAATATATATTAAAATT-T
1 TATATTTTTATTAAAATATATAGTAAAATTAT
930638 TATATTTTTA-TAAAATATATAGGT-AAATTAT
1 TATATTTTTATTAAAATATATA-GTAAAATTAT
930669 TATA
1 TATA
930673 AATATATATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 16 0.50
31 16 0.50
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (32 bp):
TATATTTTTATTAAAATATATAGTAAAATTAT
Found at i:930686 original size:22 final size:23
Alignment explanation
Indices: 930636--930686 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
930626 ATATTAAAAT
* *
930636 TTTATATTTTTATAAAATATATA
1 TTTAAATTATTATAAAATATATA
**
930659 GGTAAATTATTAT-AAATATATA
1 TTTAAATTATTATAAAATATATA
930681 TTTAAA
1 TTTAAA
930687 ATTTTGTAAT
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
TTTAAATTATTATAAAATATATA
Found at i:941302 original size:18 final size:18
Alignment explanation
Indices: 941279--941313 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
941269 GCGATGACGA
*
941279 CATCATATATGGCTGCGG
1 CATCATAAATGGCTGCGG
*
941297 CATCATAAATGGTTGCG
1 CATCATAAATGGCTGCG
941314 ATGGCTGCTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.26, C:0.20, G:0.26, T:0.29
Consensus pattern (18 bp):
CATCATAAATGGCTGCGG
Found at i:943036 original size:17 final size:18
Alignment explanation
Indices: 942993--943033 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
942983 AAATTATATT
942993 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
943010 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
943028 ATTAAA
1 AGTAAA
943034 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:945494 original size:18 final size:18
Alignment explanation
Indices: 945473--945519 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
945463 TGCAAAATAT
945473 GTACCGATACTCAAATGA
1 GTACCGATACTCAAATGA
945491 GTACCGATACTCAAATGA
1 GTACCGATACTCAAATGA
*
945509 GTACCAATACT
1 GTACCGATACT
945520 ACTTTACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.23
Consensus pattern (18 bp):
GTACCGATACTCAAATGA
Found at i:949370 original size:31 final size:31
Alignment explanation
Indices: 949334--949416 Score: 103
Period size: 31 Copynumber: 2.7 Consensus size: 31
949324 TTAACATGTC
*
949334 TAGTACCTAAACTATTAATTTTGGTATGTTT
1 TAGTACCTAAACTATTAATTTTAGTATGTTT
** * *
949365 TAGTACCTAAACTACCACTTTTAGTCTGTTT
1 TAGTACCTAAACTATTAATTTTAGTATGTTT
* *
949396 TAGTAGCTAAACTTTTAATTT
1 TAGTACCTAAACTATTAATTT
949417 CTTTCAAAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (31 bp):
TAGTACCTAAACTATTAATTTTAGTATGTTT
Found at i:953933 original size:18 final size:20
Alignment explanation
Indices: 953889--953934 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
953879 ACTTTATTTC
953889 AACAAA-AATATATATAATA
1 AACAAATAATATATATAATA
*
953908 AACTAATAATATATATAA-A
1 AACAAATAATATATATAATA
953927 AA-AAATAA
1 AACAAATAA
953935 AATAAATGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 5 0.21
19 8 0.33
20 11 0.46
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (20 bp):
AACAAATAATATATATAATA
Found at i:954032 original size:13 final size:13
Alignment explanation
Indices: 954016--954041 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
954006 CGTTAGTTTT
954016 TGTTTGAGAAACG
1 TGTTTGAGAAACG
954029 TGTTTGAGAAACG
1 TGTTTGAGAAACG
954042 AGAAAAAAGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.31, T:0.31
Consensus pattern (13 bp):
TGTTTGAGAAACG
Found at i:954376 original size:23 final size:23
Alignment explanation
Indices: 954346--954389 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
954336 TGATAGGCAC
954346 TTCTTCTTCTTCAACCCAACCCT
1 TTCTTCTTCTTCAACCCAACCCT
*
954369 TTCTTCTTCTTTAACCCAACC
1 TTCTTCTTCTTCAACCCAACC
954390 AAATCGGTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.18, C:0.41, G:0.00, T:0.41
Consensus pattern (23 bp):
TTCTTCTTCTTCAACCCAACCCT
Found at i:954744 original size:21 final size:21
Alignment explanation
Indices: 954719--954764 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
954709 TCTCAGCTTC
* *
954719 TCCCTAGCTTTTTCTCTTTTT
1 TCCCTACCATTTTCTCTTTTT
*
954740 TCCCTCCCATTTTCTCTTTTT
1 TCCCTACCATTTTCTCTTTTT
954761 TCCC
1 TCCC
954765 ATTCTTTCTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.04, C:0.37, G:0.02, T:0.57
Consensus pattern (21 bp):
TCCCTACCATTTTCTCTTTTT
Found at i:959370 original size:3 final size:3
Alignment explanation
Indices: 959362--959444 Score: 76
Period size: 3 Copynumber: 27.0 Consensus size: 3
959352 AAATTTAAAT
** * * * * *
959362 TTA TTA TTA TTA TTA AAA TTA TTA TTA TTT TTA TAA TAA TAA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
959410 TTA TTA TTA ATA TTA TTA TTA TATA TTA TTTA TTA
1 TTA TTA TTA TTA TTA TTA TTA T-TA TTA -TTA TTA
959445 AATATTACAA
Statistics
Matches: 68, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
3 62 0.91
4 6 0.09
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (3 bp):
TTA
Found at i:961119 original size:23 final size:24
Alignment explanation
Indices: 961089--961147 Score: 79
Period size: 23 Copynumber: 2.5 Consensus size: 24
961079 TTGTAATATT
961089 ATTATTACTTTTAA-TA-TATTTTA
1 ATTATTACTTTTAATTATTA-TTTA
961112 ATTATTAC-TTTAATTATTATTTA
1 ATTATTACTTTTAATTATTATTTA
*
961135 ATTATTATTTTTA
1 ATTATTACTTTTA
961148 TCTTAGCCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
22 5 0.16
23 21 0.66
24 6 0.19
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.63
Consensus pattern (24 bp):
ATTATTACTTTTAATTATTATTTA
Found at i:961125 original size:12 final size:12
Alignment explanation
Indices: 961089--961141 Score: 67
Period size: 11 Copynumber: 4.6 Consensus size: 12
961079 TTGTAATATT
961089 ATTATTACTTTTA
1 ATTATTAC-TTTA
*
961102 A-TA-TATTTTA
1 ATTATTACTTTA
961112 ATTATTACTTTA
1 ATTATTACTTTA
961124 ATTATTA-TTTA
1 ATTATTACTTTA
961135 ATTATTA
1 ATTATTA
961142 TTTTTATCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
10 5 0.14
11 15 0.42
12 15 0.42
13 1 0.03
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATTACTTTA
Found at i:961426 original size:119 final size:119
Alignment explanation
Indices: 961192--961422 Score: 267
Period size: 119 Copynumber: 2.0 Consensus size: 119
961182 GTTTAAATAA
* * *
961192 TAATATTTACTTATTTTTAATATTAAAGAAAATGACTGTCTTAAAGCACCTAGTAGTCCGTTTTC
1 TAATATTTACTTATTTTTAATATTAAAGAAAACGACTGTCTTAAAGCACCTAGAAGTCCCTTTTC
* ** * *
961257 TGATACTTTTTATCCTATAAAATATATATATTAATTTTTAAATAAATATTTAAT
66 TGATACTTTCTATAATAAAAAATATATATATTAATATTTAAATAAATATTTAAT
* *
961311 TAATATTTATTTATTTTTTAATA-TAGAAG-AAACGAGTTGTCTTAAAGCACCTAGAAG-CCCTT
1 TAATATTTACTTA-TTTTTAATATTA-AAGAAAACGA-CTGTCTTAAAGCACCTAGAAGTCCCTT
* * *
961373 TTCTGATA-TTTCTA-AATAAATAAATATCT-TATTTATATTTAAATTAATAT
63 TTCTGATACTTTCTATAATAAA-AAATATATATATTAATATTTAAATAAATAT
961423 ATTTTCATAA
Statistics
Matches: 95, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
117 21 0.22
118 12 0.13
119 31 0.33
120 31 0.33
ACGTcount: A:0.38, C:0.10, G:0.07, T:0.45
Consensus pattern (119 bp):
TAATATTTACTTATTTTTAATATTAAAGAAAACGACTGTCTTAAAGCACCTAGAAGTCCCTTTTC
TGATACTTTCTATAATAAAAAATATATATATTAATATTTAAATAAATATTTAAT
Found at i:964532 original size:15 final size:14
Alignment explanation
Indices: 964493--964531 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
964483 TTTAAATAAA
964493 TTACATTTTTGCAT
1 TTACATTTTTGCAT
964507 TTATGCA-TTTTGCAT
1 TTA--CATTTTTGCAT
964522 TTACATTTTT
1 TTACATTTTT
964532 TATTTGTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
13 2 0.09
14 7 0.32
15 11 0.50
16 2 0.09
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (14 bp):
TTACATTTTTGCAT
Found at i:966721 original size:72 final size:74
Alignment explanation
Indices: 966579--966779 Score: 246
Period size: 72 Copynumber: 2.7 Consensus size: 74
966569 ACACAATAAA
* * *
966579 GCTTAAGTTGTCCCCCTAAAGCAATTGGTTAATAGCCTCGGCTTTATGGATAATATTCAGCTAGT
1 GCTTAAGTTGTCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAGT
*
966644 TTA-T-TAT
66 CTATTATAT
* *
966651 GCTTGAGTTGTCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGTTA-T
1 GCTTAAGTTGTCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAGT
966715 ACTATTATAT
66 -CTATTATAT
* ** * * *
966725 GCAATAAAACTGTCCCTCTAGAGCAATTGGTTGATCGCCCTGGCTTTATGGATAA
1 GC--TTAAGTTGTCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAA
966780 GTTTTAATTA
Statistics
Matches: 111, Mismatches: 13, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
71 1 0.01
72 60 0.54
73 1 0.01
74 5 0.05
76 44 0.40
ACGTcount: A:0.26, C:0.19, G:0.19, T:0.35
Consensus pattern (74 bp):
GCTTAAGTTGTCCCTCTAGAGCAATTGGTTAATAGCCCCGGCTTTATGGATAATATTCAGCTAGT
CTATTATAT
Found at i:971342 original size:22 final size:22
Alignment explanation
Indices: 971317--971393 Score: 84
Period size: 22 Copynumber: 3.5 Consensus size: 22
971307 ATCTACACTT
971317 TTCAAAGATGATAGACTCTTTC
1 TTCAAAGATGATAGACTCTTTC
* * * *
971339 TTCAAATATGATAGCCTATCTC
1 TTCAAAGATGATAGACTCTTTC
* *
971361 TTTAAAGATGATAGATTCTCTT-
1 TTCAAAGATGATAGACTCT-TTC
971383 TTCAAAGATGA
1 TTCAAAGATGA
971394 AAGCTTTATT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
22 42 0.98
23 1 0.02
ACGTcount: A:0.34, C:0.16, G:0.13, T:0.38
Consensus pattern (22 bp):
TTCAAAGATGATAGACTCTTTC
Found at i:972245 original size:46 final size:46
Alignment explanation
Indices: 972111--972675 Score: 893
Period size: 46 Copynumber: 12.3 Consensus size: 46
972101 GGGAGCTTTT
*
972111 TGATATTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
972156 TGATGTTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTGAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
972201 TGATGTTTTCAAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
972247 TGATGTTTTCAAAAACATTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
972293 TGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
972339 TGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
972386 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
972432 TGATGTTTTCAAAAACCTTCAGGTCATCTGTAAGCCCTTCAATGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
972478 TGATGTTTTCAAAAAAATCGTCGGGTCATCTGTAAGTCCTTCAGTGCA
1 TGATGTTTTC--AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
972526 TGATGTTTTCAAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTGGA
1 TGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* *
972573 TGATGTTTTCAAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
*
972619 TGATGTTTT-TAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
972664 TGATGTTTTCAA
1 TGATGTTTTCAA
972676 CATTTCCATC
Statistics
Matches: 484, Mismatches: 31, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
45 95 0.20
46 261 0.54
47 87 0.18
48 41 0.08
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (46 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:972312 original size:92 final size:92
Alignment explanation
Indices: 972111--972675 Score: 893
Period size: 93 Copynumber: 6.1 Consensus size: 92
972101 GGGAGCTTTT
*
972111 TGATATTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAACCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
*
972174 CGGGTCATCTGTAAGCCCTTGAGTGCA
66 CGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
972201 TGATGTTTTCAAAAACCTTCGGGTCATCTATAAGTCCTTCAGTGCATGATGTTTTCAAAAACATT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
*
972266 CGGGTCATCTGTAAGTCCTTCAGTGCA
66 CGGGTCATCTGTAAGCCCTTCAGTGCA
*
972293 TGATGTTTTCAAAAGCCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCT
*
972358 TCGGGTCATCTGTAAGTCCTTCAGTGCA
65 TCGGGTCATCTGTAAGCCCTTCAGTGCA
*
972386 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
* *
972451 CAGGTCATCTGTAAGCCCTTCAATGCA
66 CGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
972478 TGATGTTTTCAAAAAAATCGTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAAAC
1 TGATGTTTTC--AAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAAC
* * *
972543 CTTCAGGTCATCTGTAAGTCCTTCAGTGGA
63 CTTCGGGTCATCTGTAAGCCCTTCAGTGCA
* * *
972573 TGATGTTTTCAAAAGCCTTCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT-TAAAACCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
972637 CGGGTCATCTGTAAGCCCTTCAGTGCA
66 CGGGTCATCTGTAAGCCCTTCAGTGCA
972664 TGATGTTTTCAA
1 TGATGTTTTCAA
972676 CATTTCCATC
Statistics
Matches: 440, Mismatches: 29, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
90 9 0.02
91 87 0.20
92 128 0.29
93 129 0.29
94 44 0.10
95 43 0.10
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (92 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTT
CGGGTCATCTGTAAGCCCTTCAGTGCA
Found at i:972397 original size:139 final size:138
Alignment explanation
Indices: 972111--972675 Score: 938
Period size: 139 Copynumber: 4.1 Consensus size: 138
972101 GGGAGCTTTT
* *
972111 TGATATTTTC-AAAACCTTCGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAA-CCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCTT
* * *
972174 CGGGTCATCTGTAAGCCCTTGAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTATAAGTCCT
66 CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
972239 TCAGTGCA
131 TCAGTGCA
*
972247 TGATGTTTTCAAAAACATTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCTT
*
972312 CGGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAAACCTTCGGGTCATCTGTAAGTCC
66 CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGTCC
972377 TTCAGTGCA
130 TTCAGTGCA
*
972386 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAACCTT
1 TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCTT
* * *
972451 CAGGTCATCTGTAAGCCCTTCAATGCATGATGTTTTCAAAAAAATCGTCGGGTCATCTGTAAGTC
66 CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTC--AAAAACCTTCGGGTCATCTGTAAGTC
972516 CTTCAGTGCA
129 CTTCAGTGCA
* *
972526 TGATGTTTTCAAAAAACCTTCAGGTCATCTGTAAGTCCTTCAGTGGATGATGTTTTCAAAAGCCT
1 TGATGTTTTC-AAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCT
* *
972591 TCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTT-TAAAACCTTCGGGTCATCTGTAAGCCC
65 TCAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCC
972655 TTCAGTGCA
130 TTCAGTGCA
972664 TGATGTTTTCAA
1 TGATGTTTTCAA
972676 CATTTCCATC
Statistics
Matches: 405, Mismatches: 19, Indels: 9
0.94 0.04 0.02
Matches are distributed among these distances:
136 9 0.02
137 49 0.12
138 82 0.20
139 133 0.33
140 45 0.11
141 87 0.21
ACGTcount: A:0.25, C:0.22, G:0.19, T:0.34
Consensus pattern (138 bp):
TGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCTTCAGTGCATGATGTTTTCAAAAGCCTT
CAGGTCATCTGTAAGCCCTTCAGTGCATGATGTTTTCAAAAACCTTCGGGTCATCTGTAAGTCCT
TCAGTGCA
Found at i:972831 original size:3 final size:3
Alignment explanation
Indices: 972808--972876 Score: 77
Period size: 3 Copynumber: 23.0 Consensus size: 3
972798 AAATTTAAAT
* ** *
972808 TTA TTA TTC TTA TTA AAA TTA TTA TTA TTA TTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
972856 TTA TTA TATA TT- TTT TTA TTA
1 TTA TTA T-TA TTA TTA TTA TTA
972877 AATATTACAA
Statistics
Matches: 55, Mismatches: 9, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
2 2 0.04
3 50 0.91
4 3 0.05
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:976195 original size:12 final size:12
Alignment explanation
Indices: 976178--976202 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
976168 TTTATCCGCA
976178 AAATAATTTTTT
1 AAATAATTTTTT
976190 AAATAATTTTTT
1 AAATAATTTTTT
976202 A
1 A
976203 TTTAAAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (12 bp):
AAATAATTTTTT
Found at i:986373 original size:30 final size:30
Alignment explanation
Indices: 986330--986387 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
986320 ATATTTTATC
*
986330 TTAATTTACTAAATATATTATACTATTACT
1 TTAAATTACTAAATATATTATACTATTACT
* * *
986360 TTAAATTATTAAATATATTTTATTATTA
1 TTAAATTACTAAATATATTATACTATTA
986388 TCTTAACTTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.53
Consensus pattern (30 bp):
TTAAATTACTAAATATATTATACTATTACT
Found at i:986474 original size:27 final size:26
Alignment explanation
Indices: 986412--986482 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
986402 TATTTTAACA
*
986412 TAAAATATATATTTTTAAATTAAAAT
1 TAAAATAAATATTTTTAAATTAAAAT
*
986438 TAAAATAAATATTTTTAAATT-AATT
1 TAAAATAAATATTTTTAAATTAAAAT
*
986463 TAATAATGAAATATATTTAA
1 TAA-AAT-AAATATTTTTAA
986483 TAAGTTAATA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
25 6 0.15
26 23 0.57
27 11 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (26 bp):
TAAAATAAATATTTTTAAATTAAAAT
Found at i:987725 original size:20 final size:21
Alignment explanation
Indices: 987681--987725 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
987671 CTATATTTTT
*
987681 ATTTTCTTTTATTTTGATCTC
1 ATTTTCTTTTATTTTGATATC
987702 -TTTTC-TTTATTTT-ATTATC
1 ATTTTCTTTTATTTTGA-TATC
987721 ATTTT
1 ATTTT
987726 AGTCATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 1 0.05
19 11 0.52
20 9 0.43
ACGTcount: A:0.16, C:0.11, G:0.02, T:0.71
Consensus pattern (21 bp):
ATTTTCTTTTATTTTGATATC
Found at i:988943 original size:45 final size:45
Alignment explanation
Indices: 988894--988988 Score: 118
Period size: 45 Copynumber: 2.1 Consensus size: 45
988884 TAATTATATG
* * *
988894 TCTTTATATTGAAAGAATAAATTTGTTTGCTGTACATTATTTGTT
1 TCTTTAGATTGAAAGAATAAATTTGTGTGCTGTACATTATTTATT
* * * * *
988939 TCTTTAGATTTAATGATTATATTTGTGTGTTGTACATTATTTATT
1 TCTTTAGATTGAAAGAATAAATTTGTGTGCTGTACATTATTTATT
988984 TCTTT
1 TCTTT
988989 GTATGTTTTT
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.56
Consensus pattern (45 bp):
TCTTTAGATTGAAAGAATAAATTTGTGTGCTGTACATTATTTATT
Found at i:993847 original size:9 final size:8
Alignment explanation
Indices: 993822--993846 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
993812 CTCATTCATC
993822 AGAAAAAA
1 AGAAAAAA
993830 AGAAAAAA
1 AGAAAAAA
993838 AGAAAAAA
1 AGAAAAAA
993846 A
1 A
993847 AATATTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:995488 original size:51 final size:52
Alignment explanation
Indices: 995409--995543 Score: 220
Period size: 51 Copynumber: 2.6 Consensus size: 52
995399 ATCTATCTGG
995409 GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTG-
1 GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
* *
995460 GGTATCTTAAAGGCTCACATTAGCATGAAAAAGACAGAAGTAATCCATGTGA
1 GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
* *
995512 GGCATCTTGAAGGCTCACACCAGCAT-AAAAAG
1 GGCATCTTAAAGGCTCACATCAGCATGAAAAAG
995544 GTTGGGATAT
Statistics
Matches: 77, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
51 55 0.71
52 22 0.29
ACGTcount: A:0.39, C:0.19, G:0.21, T:0.20
Consensus pattern (52 bp):
GGCATCTTAAAGGCTCACATCAGCATGAAAAAGACAGAAGTAATCCATGTGA
Found at i:996780 original size:42 final size:42
Alignment explanation
Indices: 996712--996793 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
996702 CACAAATTCG
* * *
996712 TAAATCCTTCGGGTCATCTGTTAGTCTTTCAAGCATGATGCT
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGCT
*
996754 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATG
996794 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.23, C:0.22, G:0.21, T:0.34
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTGTCAGTCTTTCAAGCAAGATGCT
Found at i:997087 original size:248 final size:249
Alignment explanation
Indices: 996627--997489 Score: 1478
Period size: 249 Copynumber: 3.5 Consensus size: 249
996617 CCCAACCAAC
* * * *
996627 AAGTTTCTCATTTAATCTTTTTTAGAAAATGAAATTCTTGAAAAGTAA-AAGTTTCTTACCCAGT
1 AAGTTTCTCATTTAA--TGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGT
* *
996691 AAAGTATTTCCCACAAATTCGTAAATCCTTCGGGTCATCTGTTAGTCTTTCAAGCATGATGCTTA
64 AAAGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTA
996756 AAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
129 AAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGC
* *
996821 CTTTGGGTAGGATGTTCACATATGATTTTTGCATGAAAATGAGATAGCAATTTTCA
194 CTTTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
* * *
996877 AAATTTCTCATTTAATGTTCTAGAAAATAAAATTCTTGAAAAGTAAGAAGCTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
996942 AGTATTTCCCACAAATTTGTAAATCCTTC-GGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
** * * *
997006 ACCTTCGGGTCATCTACCAGTCTTTCAAGAAAGATGATAAGTCCTTAGGGCCATTCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
*
997071 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATATCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
* * *
997125 AAGTTTCTCATTTAATGTTCTAAAAAAGCAAATTCTTGAAAGGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
997190 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
*
997255 ACCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
131 ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
997320 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
196 TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
*
997374 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTATTGAAAAGTAAGAAGTTTCTTACCTAGTAA
1 AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
* *
997439 AGTATTTCCCACAAATTTGTATATCCTTCGGGTCATCTGTCAGTCTTTCGA
66 AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGA
997490 ACAAGATGAT
Statistics
Matches: 576, Mismatches: 35, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
248 261 0.45
249 301 0.52
250 14 0.02
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (249 bp):
AAGTTTCTCATTTAATGTTCTAGAAAATCAAATTCTTGAAAAGTAAGAAGTTTCTTACCTAGTAA
AGTATTTCCCACAAATTTGTAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCTTAAA
ACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCCATCCGTAAAGCCT
TTGGGTAGGATGTTCACATATGATTTTCGCATGAAAATGAGATAGCGATTTTCA
Found at i:997277 original size:42 final size:42
Alignment explanation
Indices: 997209--997290 Score: 128
Period size: 42 Copynumber: 2.0 Consensus size: 42
997199 CACAAATTTG
* * *
997209 TAAATCCTTCGGGTCATCTGTTAGTCTTTCGAGCATGATGCT
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
*
997251 TAAAACCTTCGGGTTATCTGTCAGTCTTTCGAGCAAGATG
1 TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATG
997291 ATAAGTCCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.35
Consensus pattern (42 bp):
TAAAACCTTCGGGTCATCTGTCAGTCTTTCGAGCAAGATGCT
Found at i:997709 original size:48 final size:46
Alignment explanation
Indices: 997629--997724 Score: 147
Period size: 48 Copynumber: 2.0 Consensus size: 46
997619 GGTAATTTGT
*
997629 AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAGGAAGTTTTTCA
1 AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGAAG-TTTTCA
* *
997676 AAAAGCCTTTGGGTCATCCATAAGACCTTCAGTGCAAGATGTTTTCA
1 AAAA-CCTTCGGGTCATCCATAAGACCTTCAGTGCAAGAAGTTTTCA
997723 AA
1 AA
997725 TGAGATTTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
47 12 0.27
48 33 0.73
ACGTcount: A:0.31, C:0.22, G:0.19, T:0.28
Consensus pattern (46 bp):
AAAACCTTCGGGTCATCCATAAGACCTTCAGTGCAAGAAGTTTTCA
Found at i:998066 original size:20 final size:20
Alignment explanation
Indices: 998041--998086 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
998031 ATCTGAAGAG
998041 GAAGAAGAAATTCATAATCT
1 GAAGAAGAAATTCATAATCT
998061 GAAGAAGAAATTCATAATCT
1 GAAGAAGAAATTCATAATCT
998081 GAAGAA
1 GAAGAA
998087 CTTATTCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.52, C:0.09, G:0.17, T:0.22
Consensus pattern (20 bp):
GAAGAAGAAATTCATAATCT
Found at i:998993 original size:20 final size:21
Alignment explanation
Indices: 998949--998993 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 21
998939 CTATATTTTT
*
998949 ATTTTCCTTTATTTTGATCTC
1 ATTTTCCTTTATTTTGATATC
998970 -TTTT-CTTTATTTT-ATTATC
1 ATTTTCCTTTATTTTGA-TATC
998989 ATTTT
1 ATTTT
998994 AGTCATTAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 5
0.78 0.04 0.19
Matches are distributed among these distances:
18 1 0.05
19 12 0.57
20 8 0.38
ACGTcount: A:0.16, C:0.13, G:0.02, T:0.69
Consensus pattern (21 bp):
ATTTTCCTTTATTTTGATATC
Found at i:999177 original size:24 final size:24
Alignment explanation
Indices: 999144--999202 Score: 61
Period size: 23 Copynumber: 2.5 Consensus size: 24
999134 TTTGTGCCCC
*
999144 TTTTTGTTTTATTT-ATATTTAAGT-
1 TTTTTATTTTATTTAATA-TTAA-TA
999168 TTTTTATTTT-TTTAATATTAATA
1 TTTTTATTTTATTTAATATTAATA
*
999191 CTTTTATTTTAT
1 TTTTTATTTTAT
999203 GCAATTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
22 1 0.03
23 16 0.53
24 13 0.43
ACGTcount: A:0.24, C:0.02, G:0.03, T:0.71
Consensus pattern (24 bp):
TTTTTATTTTATTTAATATTAATA
Found at i:1001912 original size:66 final size:67
Alignment explanation
Indices: 1001831--1001969 Score: 199
Period size: 66 Copynumber: 2.1 Consensus size: 67
1001821 GTCATTGCTA
* * * *
1001831 GTTAAGCTCGTTAAAATGTTGCTCGACTCGTTCTCATTAAGAAG-TTTGTTGCTTGACTCGTTGA
1 GTTAAGCTCGTTAAAATGTTGCTCGACTCGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
1001895 TC
66 TC
* * * *
1001897 GTTAAGCTTGTTAAAATTTTTCTCGACTTGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
1 GTTAAGCTCGTTAAAATGTTGCTCGACTCGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
1001962 TC
66 TC
1001964 GTTAAG
1 GTTAAG
1001970 TTCATTATTC
Statistics
Matches: 64, Mismatches: 8, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
66 39 0.61
67 25 0.39
ACGTcount: A:0.22, C:0.18, G:0.19, T:0.40
Consensus pattern (67 bp):
GTTAAGCTCGTTAAAATGTTGCTCGACTCGTACTCATTAAGAAGTTTTGTTGCTCGACTCCTCGA
TC
Found at i:1002608 original size:20 final size:19
Alignment explanation
Indices: 1002585--1002638 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 19
1002575 GTTGCGATTT
1002585 AGAAAATCGCAACGTAAAAA
1 AGAAAATCGCAACGT-AAAA
*
1002605 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAAC-GTAAAA
1002625 AGAAAATCGCAACG
1 AGAAAATCGCAACG
1002639 CGAGCTTCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
19 1 0.03
20 29 0.91
21 2 0.06
ACGTcount: A:0.54, C:0.19, G:0.19, T:0.09
Consensus pattern (19 bp):
AGAAAATCGCAACGTAAAA
Found at i:1002698 original size:20 final size:20
Alignment explanation
Indices: 1002673--1002906 Score: 261
Period size: 20 Copynumber: 11.4 Consensus size: 20
1002663 TTTAGAAGAA
*
1002673 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
1002693 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
1002713 ATTCGCAATGCGATTGAGAAGAG
1 AATCGCAATGCGATT--G-AGAG
*
1002736 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
*
1002756 AATCGCAATGCGATTGATAG
1 AATCGCAATGCGATTGAGAG
* *
1002776 AATCGCAATGCGATTTATAG
1 AATCGCAATGCGATTGAGAG
* *
1002796 AATCGCAACGCGATTAAGAG
1 AATCGCAATGCGATTGAGAG
* * *
1002816 ATTCGCAACGCGATTAAGAG
1 AATCGCAATGCGATTGAGAG
* *
1002836 ATTCGCAACGCGATTGAGAG
1 AATCGCAATGCGATTGAGAG
* *
1002856 ATTCGCAACGCGATTTAGAAGAG
1 AATCGCAATGCGA-TT-G-AGAG
*
1002879 AATCGCAATGCGACTGAGAG
1 AATCGCAATGCGATTGAGAG
1002899 AATCGCAA
1 AATCGCAA
1002907 CGTTGAAAAT
Statistics
Matches: 195, Mismatches: 13, Indels: 12
0.89 0.06 0.05
Matches are distributed among these distances:
20 156 0.80
21 4 0.02
22 3 0.02
23 32 0.16
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGATTGAGAG
Found at i:1002740 original size:63 final size:61
Alignment explanation
Indices: 1002651--1002908 Score: 268
Period size: 63 Copynumber: 4.1 Consensus size: 61
1002641 AGCTTCCAAG
* * * *
1002651 TTCGCAACGCGATTTAGAAGAAAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGA
1 TTCGCAACGCGA-TT-GAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
* * * *
1002714 TTCGCAATGCGATTGAGAAGAGAATCGCAATGCGATTGATAGAATCGCAATGCGATTGATAGA
1 TTCGCAACGCGATT--GAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
* * * * * * * *
1002777 ATCGCAATGCGATT-TATAGAATCGCAACGCGATTAAGAGATTCGCAACGCGATTAAGAGA
1 TTCGCAACGCGATTGAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
* *
1002837 TTCGCAACGCGATTG-AGAGATTCGCAACGCGATTTAGAAGAGAATCGCAATGCGACTGAGAGA
1 TTCGCAACGCGATTGAAGAGAATCGCAACGCGA-TT-G-AGAGAATCGCAATGCGATTGAGAGA
*
1002900 ATCGCAACG
1 TTCGCAACG
1002909 TTGAAAATAA
Statistics
Matches: 168, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
60 64 0.38
61 2 0.01
62 2 0.01
63 100 0.60
ACGTcount: A:0.35, C:0.17, G:0.26, T:0.22
Consensus pattern (61 bp):
TTCGCAACGCGATTGAAGAGAATCGCAACGCGATTGAGAGAATCGCAATGCGATTGAGAGA
Found at i:1003027 original size:6 final size:6
Alignment explanation
Indices: 1003016--1003143 Score: 207
Period size: 6 Copynumber: 22.5 Consensus size: 6
1003006 GACACGTATT
1003016 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1003064 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1003111 ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
1003144 GAGACGAGAC
Statistics
Matches: 121, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
5 35 0.29
6 86 0.71
ACGTcount: A:0.30, C:0.53, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:1003848 original size:6 final size:6
Alignment explanation
Indices: 1003837--1003917 Score: 144
Period size: 6 Copynumber: 13.5 Consensus size: 6
1003827 TCTCGTCTCG
1003837 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
**
1003885 GGTCGT GGTCGT GGTCGT GGTAAT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
1003918 AATACGTGTC
Statistics
Matches: 71, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
6 71 1.00
ACGTcount: A:0.02, C:0.15, G:0.49, T:0.33
Consensus pattern (6 bp):
GGTCGT
Found at i:1004028 original size:20 final size:20
Alignment explanation
Indices: 1004005--1004302 Score: 175
Period size: 20 Copynumber: 14.6 Consensus size: 20
1003995 TTCTTTTTAA
1004005 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1004025 CGTTGCGATTCTCTCAATCA
1 CGTTGCGATTTTCTAAATCG
* * *
1004045 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1004065 CATTGCGATTCTCTCAGTCG
1 CGTTGCGATTTTCTAAATCG
*
1004085 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
* * *
1004108 CGTTGCGAATCTCTCAATCG
1 CGTTGCGATTTTCTAAATCG
* * *
1004128 CATTGCGATTCTATAAATCG
1 CGTTGCGATTTTCTAAATCG
* * * *
1004148 CATTGCGATTCTATCAATCG
1 CGTTGCGATTTTCTAAATCG
*
1004168 CATTGCGATTTTCTTCTAAATCG
1 CGTTGCGA--TT-TTCTAAATCG
** ** *
1004191 CGTTGCGAACTTGGAAGCTCG
1 CGTTGCGATTTTCTAA-ATCG
*** **
1004212 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
*** **
1004232 CGTTGCGATTTTCTTTTTAA
1 CGTTGCGATTTTCTAAATCG
1004252 CGTTGCGATTTTCTAAATCG
1 CGTTGCGATTTTCTAAATCG
* *
1004272 CGTTGCGATTTT-GATATCG
1 CGTTGCGATTTTCTAAATCG
1004291 CGTTGCGATTTT
1 CGTTGCGATTTT
1004303 ATTGGTTATT
Statistics
Matches: 224, Mismatches: 47, Indels: 15
0.78 0.16 0.05
Matches are distributed among these distances:
19 17 0.08
20 161 0.72
21 14 0.06
22 4 0.02
23 28 0.12
ACGTcount: A:0.20, C:0.22, G:0.18, T:0.40
Consensus pattern (20 bp):
CGTTGCGATTTTCTAAATCG
Found at i:1004051 original size:40 final size:40
Alignment explanation
Indices: 1004007--1004198 Score: 240
Period size: 40 Copynumber: 4.7 Consensus size: 40
1003997 CTTTTTAACG
*
1004007 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCACA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
1004047 TTGCGATTCTATAAATCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
*
1004087 TTGCGATTTTCTTCTAAATCGCGTTGCGAATCTCTCAATCGCA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGATTCTCTCAATCGCA
* * * *
1004130 TTGCGATTCTATAAATCGCATTGCGATTCTATCAATCGCA
1 TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1004170 TTGCGATTTTCTTCTAAATCGCGTTGCGA
1 TTGCGA--TT-TTCTAAATCGCGTTGCGA
1004199 ACTTGGAAGC
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
40 74 0.58
41 2 0.02
42 4 0.03
43 48 0.38
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.37
Consensus pattern (40 bp):
TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
Found at i:1004115 original size:83 final size:83
Alignment explanation
Indices: 1004015--1004199 Score: 334
Period size: 83 Copynumber: 2.2 Consensus size: 83
1004005 CGTTGCGATT
* *
1004015 TTCTAAATCGCGTTGCGATTCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTCTC
1 TTCTAAATCGCGTTGCGAATCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTATC
*
1004080 AGTCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
*
1004098 TTCTAAATCGCGTTGCGAATCTCTCAATCGCATTGCGATTCTATAAATCGCATTGCGATTCTATC
1 TTCTAAATCGCGTTGCGAATCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTATC
1004163 AATCGCATTGCGATTTTC
66 AATCGCATTGCGATTTTC
1004181 TTCTAAATCGCGTTGCGAA
1 TTCTAAATCGCGTTGCGAA
1004200 CTTGGAAGCT
Statistics
Matches: 98, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 98 1.00
ACGTcount: A:0.23, C:0.24, G:0.16, T:0.36
Consensus pattern (83 bp):
TTCTAAATCGCGTTGCGAATCTCTCAATCACATTGCGATTCTATAAATCGCATTGCGATTCTATC
AATCGCATTGCGATTTTC
Found at i:1008097 original size:27 final size:24
Alignment explanation
Indices: 1008050--1008121 Score: 67
Period size: 26 Copynumber: 2.9 Consensus size: 24
1008040 GTTAATGAAA
1008050 TTAATATAATTATATATTTAATAC
1 TTAATATAATTATATATTTAATAC
* *
1008074 TTAATATATATTTTATTAATTTAAT-T
1 TTAATATA-ATTATA-T-ATTTAATAC
*
1008100 TTAATTTTAATTATA-ATTTAAT
1 TTAA-TATAATTATATATTTAAT
1008122 TAAATAATTT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
23 7 0.17
24 8 0.20
25 5 0.12
26 10 0.25
27 10 0.25
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.57
Consensus pattern (24 bp):
TTAATATAATTATATATTTAATAC
Found at i:1008105 original size:11 final size:11
Alignment explanation
Indices: 1008089--1008122 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
1008079 ATATATTTTA
1008089 TTAATTTAATT
1 TTAATTTAATT
1008100 TTAATTTTAATT
1 TTAA-TTTAATT
*
1008112 ATAATTTAATT
1 TTAATTTAATT
1008123 AAATAATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (11 bp):
TTAATTTAATT
Found at i:1008122 original size:17 final size:17
Alignment explanation
Indices: 1008089--1008122 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1008079 ATATATTTTA
1008089 TTAATTTAATTTTAATT
1 TTAATTTAATTTTAATT
1008106 TTAATTATAA-TTTAATT
1 TTAATT-TAATTTTAATT
1008123 AAATAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 13 0.81
18 3 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
TTAATTTAATTTTAATT
Done.