Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011585.1 Kokia drynarioides strain JFW-HI SEQ_126575, 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: 31282
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Found at i:11653 original size:17 final size:19
Alignment explanation
Indices: 11620--11664 Score: 51
Period size: 17 Copynumber: 2.5 Consensus size: 19
11610 TATTTCTTTG
*
11620 GTCACTGCA-CTTTCA-TT
1 GTCACTGCATCTTACATTT
11637 GTCACTGCATC-TACATTT
1 GTCACTGCATCTTACATTT
*
11655 GTCATTGCAT
1 GTCACTGCAT
11665 TTCCATATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
17 12 0.50
18 12 0.50
ACGTcount: A:0.20, C:0.27, G:0.13, T:0.40
Consensus pattern (19 bp):
GTCACTGCATCTTACATTT
Found at i:14232 original size:15 final size:16
Alignment explanation
Indices: 14200--14244 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
14190 AAGAATAAAG
14200 AAAGAAATAATTATT-A
1 AAAGAAA-AATTATTAA
14216 AAAGAAAAATT-TGTAA
1 AAAGAAAAATTAT-TAA
14232 AAAG-AAAATTATT
1 AAAGAAAAATTATT
14245 TTTTAGAAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
14 1 0.04
15 12 0.46
16 13 0.50
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.29
Consensus pattern (16 bp):
AAAGAAAAATTATTAA
Found at i:20378 original size:215 final size:215
Alignment explanation
Indices: 20007--21443 Score: 1451
Period size: 215 Copynumber: 6.6 Consensus size: 215
19997 TTTATGGAAC
* * * *
20007 AAAAGTTTGTCAAGTTCGAAAGTTCGATCAAGAACCAAGAAAGAAACTCTTCTCACATAAATAA-
1 AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACCAAGAGAGAAACTATTCTCACCTAAATAAG
* * * * * * *
20071 TTTTTTATTTAAAAAACAAAAGTTTTTTACAAAATGACAATCTATTTAGAACAATTGATGGGATT
66 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGAACAAATGATGCGATT
* * *
20136 TCCCGAGCATGGAATGCTCGAAAAATTGCACGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
130 TCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC
*
20201 CGAAGTTAAAAAAGAAGTCGT
195 CGAAGTTAAAAAAGAACTCGT
* * * * *
20222 AAAAGTTTGTCAACTTCGGAAGTTCGACCGTGAACCAAGAGAGAAATTATTCTCACCTAAATAAG
1 AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACCAAGAGAGAAACTATTCTCACCTAAATAAG
* * *
20287 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGATAACTATTTAGATCAAATGATGTGATTT
66 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGAACAAATGATGCGATTT
* * * * * *
20352 CTCAAGCATGGAATGTTCAAAAAATTGCTTGAAGAAATGGATCGTCTTAAATACTTTAAGGAACT
131 CCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
*
20417 GAAGTTATAAAAGAACTCGT
196 GAAGTTAAAAAAGAACTCGT
* ** * * * * *
20437 AAAGGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACTAAGAAAAAAACAATTCTCACCTAAACAAG
1 AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACCAAGAGAGAAACTATTCTCACCTAAATAAG
* * * *
20502 -TTTTAATTCAAAGACCAAAAGTAGTTTACAAAATGACAACTGTTTAGACCTAATGATGCGATTT
66 TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGAACAAATGATGCGATTT
* ** ** * *
20566 CCCAAGCTTGGGCTGCACGGAAAATGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA--
131 CCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
* *
20629 -AACGTTATAACAGAACTCGT
196 GAA-GTTAAAAAAGAACTCGT
* * * *
20649 AAAAGTTTGTCAAGTTCGGAAGTTTGATCAAGAACCAAGAAAGAAACAATTCTCAAAGAAACAAT
1 AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACCAAG--AG-------------AGAAACTAT
* * * * * *
20714 TCTCACATAAATAACTTTTTAATTTAATGACCACAACTTGTTTACAAAATGACAATCTATTTAGA
51 TCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGA
* * * * *
20779 ACAACTGATACAATTTCCCAAGCATGGAATGTTCGAAAAATTG-TGCGAAGGAATGGGTCATCTT
115 ACAAATGATGCGATTTCCCAAGCATGGAATGTTCGAAAAATTGCT-CGAAGGAATGGATCGTCTT
* *
20843 GAATACTTTACGGAACCGAAGTTAAAAAAGAACTTGT
179 GAATACTTTAAGGAACCGAAGTTAAAAAAGAACTCGT
* * * * *
20880 AAATGTTTGTCAAGTTTGGAAGTTCTG-TCGAGAACCTAA-AGAGGAACTATTATCACCTAAATA
1 AAAAGTTTGTCAAGTTCGAAAGTTC-GATCGAGAACC-AAGAGAGAAACTATTCTCACCTAAATA
* * * * *
20943 AGTTTTTAATTCAAAGACGAAAAGTTATTTATAAAAGGACAACTATTT-GAACCAAATGATACGA
64 AGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGAA-CAAATGATGCGA
* * * * *
21007 TTT-CCAGAGCATGGATTGTTC-AGAAAATGGCTCGGAGGAATGGATAGTCTTGAAAACTTTAAG
128 TTTCCCA-AGCATGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAG
***
21070 GAATAAAAGTTATAAAAA-AACTCGT
191 GAACCGAAGTTA-AAAAAGAACTCGT
* * * * * *
21095 AAAAGTTTGTCAAGTTCAAAATTTCGGTCGAGAACCTAA-AAAGAAACAATTCTCACATAAATAA
1 AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACC-AAGAGAGAAACTATTCTCACCTAAATAA
* *
21159 GTTTTTAATTCAAAGACCAAATGTTGTTTACAAAATGACAATCTATTTAGAACAATTGATGCGAT
65 GTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGAACAAATGATGCGAT
** * * * * * * * * *
21224 TTCCCGTGAATAGAATATTTGAAAATTTGCTCGAAGGTATAGATCATCTTGAATAATTTAAGGAA
129 TTCCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
**
21289 CCGAAGTTAAAAAAGAACTCAC
194 CCGAAGTTAAAAAAGAACTCGT
* * * * ** * * * *
21311 AAAGGTTTTTGAGGTTCGAAAGTTCGGCCCAGAACCTAGAGAAAAACTATTATCACCTAAATAAG
1 AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACCAAGAGAGAAACTATTCTCACCTAAATAAG
* * *
21376 TTTTGTAATTCAAAGACCAAAAGTTGTTTATAAAATGACAACTATCTAGACCAAATGATGCGATT
66 TTTT-TAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGAACAAATGATGCGATT
21441 TCC
130 TCC
21444 TGAGCTTGGT
Statistics
Matches: 1001, Mismatches: 183, Indels: 75
0.80 0.15 0.06
Matches are distributed among these distances:
211 2 0.00
212 48 0.05
214 118 0.12
215 377 0.38
216 240 0.24
217 40 0.04
227 20 0.02
228 35 0.03
229 72 0.07
231 44 0.04
232 5 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (215 bp):
AAAAGTTTGTCAAGTTCGAAAGTTCGATCGAGAACCAAGAGAGAAACTATTCTCACCTAAATAAG
TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGAACAAATGATGCGATTT
CCCAAGCATGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACC
GAAGTTAAAAAAGAACTCGT
Found at i:20708 original size:15 final size:15
Alignment explanation
Indices: 20688--20718 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
20678 AAGAACCAAG
20688 AAAGAAACAATTCTC
1 AAAGAAACAATTCTC
20703 AAAGAAACAATTCTC
1 AAAGAAACAATTCTC
20718 A
1 A
20719 CATAAATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.19, G:0.06, T:0.19
Consensus pattern (15 bp):
AAAGAAACAATTCTC
Found at i:22048 original size:80 final size:80
Alignment explanation
Indices: 21915--22065 Score: 241
Period size: 80 Copynumber: 1.9 Consensus size: 80
21905 ACTAATTTCA
* * * *
21915 TTTTAACTCTTGTAGCGAAGCTAATGAGTCATGTCTTTTCATTAGGATCTGATGTAGTTGAAAAG
1 TTTTAACTCTTGTAGCGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAAG
*
21980 GCATGGGAATTTCGT
66 ACATGGGAATTTCGT
21995 TTTTAACTCTTGTAG-GAAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAA
1 TTTTAACTCTTGTAGCG-AAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAA
22059 GACATGG
65 GACATGG
22066 CATTTCTCTT
Statistics
Matches: 65, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
79 1 0.02
80 64 0.98
ACGTcount: A:0.28, C:0.14, G:0.23, T:0.35
Consensus pattern (80 bp):
TTTTAACTCTTGTAGCGAAGCCAATGAGTCATGTCTCTTCATTAGGATCTGATGTAGCTAAAAAG
ACATGGGAATTTCGT
Found at i:22595 original size:48 final size:48
Alignment explanation
Indices: 22514--22638 Score: 161
Period size: 48 Copynumber: 2.7 Consensus size: 48
22504 CAAGGCATTT
* * *
22514 AACAAAGATGAATTTAACAAACAAAATAGTTAAT-AGTGCAGATTACTA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGAG-GCAGATTACTA
* *
22562 AACAGAGATGCATTTAACAAACAAAACACTTAATGAGGCAGATTATTA
1 AACAAAGATGCATTTAACAAACAAAACACTTAATGAGGCAGATTACTA
22610 AACAAAGATGCA-TT-A-AAA-AAAACACTTAA
1 AACAAAGATGCATTTAACAAACAAAACACTTAA
22639 CGAAGCATAA
Statistics
Matches: 70, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
44 11 0.16
45 3 0.04
46 1 0.01
47 2 0.03
48 51 0.73
49 2 0.03
ACGTcount: A:0.53, C:0.13, G:0.12, T:0.22
Consensus pattern (48 bp):
AACAAAGATGCATTTAACAAACAAAACACTTAATGAGGCAGATTACTA
Found at i:23332 original size:215 final size:214
Alignment explanation
Indices: 22945--25910 Score: 2938
Period size: 215 Copynumber: 13.9 Consensus size: 214
22935 TCACATCACT
* * *
22945 TGGAATGTTCAAAAAATTGCTCGAAGGAAT-GATTCATCTTGAATACTTTAAGGAACTGAAG-TA
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAAC-AAAGTTA
* * * * **
23008 TAAAAGAACTTGTAAAAGTTTGTTAACTTCGAAAGTTC-ACCCTAGAACCAAGAGAGAAAGTATT
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGA-CCGAGAACCAAGAGAGAAACAATT
* * * * * *
23072 CTCAACTAAATAAGTTTTTAATTTAAAGACTAGAAGTTTTTTACAAAATTACAACTATTTAGACC
128 CTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACC
* *
23137 AAATGATGCAATTTCTCAAGCA
193 AAATGATGCGATTTCCCAAGCA
* * * * *
23159 TAGAATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTTAGGAATCGAAGTTAT
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTAT
* * * * * * * * * *
23224 GAAAGAACTAGTAAAAGTTTTTCAAGTTTGTAAGTTCGGCCAAGAACCAAAAGAAAAACAATTTT
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTCT
* * * * *
23289 CACCTAAGTAAGTTTTTAATTGAAAAACCAAAAGTAGTTTACAAAATGACAACTATTTAGACCTA
130 CACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAA
*
23354 ATGATGTGATTTCCCAAGCA
195 ATGATGCGATTTCCCAAGCA
* * * * * * *
23374 TGGACTATACTG-AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAATGAAAAAAAGGTA
1 TGGAATGTTC-GAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAA-GGAACAAAGTTA
* * * * *
23438 TAAAAGAACTTGTAAAAGTTTGTCAAGTT-TAAAGTTCGACCGAGAACTAAGAAAGAAGCAATTC
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTC
* * * * * * *
23502 TCACATAAAGAATTTTTTAACTAAAAAACCAAAATTTGTTTACAAAATGACAACTATTTAGACCA
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
* *
23567 AATAATGTGATTTCCCAAGCA
194 AATGATGCGATTTCCCAAGCA
* * * * *
23588 TGGAATGTTTGGAAATTTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAACCAAGGTTAT
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTAT
* * * * * * *
23653 AAAAGATCTCGTAAAAGTTTGTCAACTTCTG-TAGTTCGGCCCAAAACCAAGAGAGAAATAATTC
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTC-GAAAGTTCGACCGAGAACCAAGAGAGAAACAATTC
* *
23717 TCACCTAAATTAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAACTATTTAGACCA
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
*** *
23782 AATGATGCGATTTCTTGAGCT
194 AATGATGCGATTTCCCAAGCA
* *
23803 TGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCATCTT-AATTACTTTAAGGAACCAAAGTTA
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAA-TACTTTAAGGAA-CAAAGTTA
* * * * *
23867 TAAAACAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGATCGAGAACCAAGAAAGAAACAATTC
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTC
* *
23932 TCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCT
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
23997 AATGATGCGATTTCCCAAGCA
194 AATGATGCGATTTCCCAAGCA
* * * * * *
24018 TGGACTGTACGAAAAATTGCTCGAAGGAATTGATCGTGTTGAATACTTTATGGAACCCAAGTTA-
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTAT
* * * * * * *
24082 AAAAGAACTTGTAAAAGTTTGTCAAGTTCGGAAGTTTGGCCGAGAACCAAGAGAGGAACTATTAT
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTCT
* * ** * *
24147 CCCCTAAATAAGTTTTTAACTT-AAAGACCAAAAGTTGTTTATAGCATGACAACTATTTAGATCG
130 CACCTAAATAAGTTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
* ** ****
24211 TATGATGAAATTTTTTTAGCA
194 AATGATGCGATTTCCCAAGCA
* * * * *
24232 TGGAATGTTCGGAAAATTG-TGTGAAGGAATGGATCGTCTTAAATACTTTAATGAACCAATGTTA
1 TGGAATGTTCGAAAAATTGCT-CGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTA
* * * * * * ** * *
24296 TAGAAGAACTTGTAAAATTTTGTGAAGTTTGAAAGTTTGATTGAGAACTAAGAGAGAAACTATTC
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTC
*
24361 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCA
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
24426 AATGATGCGATTTCCCAAGCA
194 AATGATGCGATTTCCCAAGCA
* *
24447 TGGATTGCTTTG-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAAGTTA
1 TGGAATG-TTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC-AAAGTTA
* * * * * * * *
24511 TAAAAGACCACGTAAAAGTTTTTCAAGTTTG-AAGTTCGGCTGAGAACCAAGAAACAAACAATTC
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTC
* * * * * * *
24575 TCACATAAAGAATTTTTTAATTTAAAGACCAAAACTTGTTTACAAAATAACAAATATTTAGACCA
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
* *
24640 AATGATGCGATTTCTCGAGCA
194 AATGATGCGATTTCCCAAGCA
* * * * **
24661 TGGAATATTC-AAAAATTTCTCGAAGGAATGGATCGTCTTAAATACTTTGAGGAATTGAAGTTAT
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTAT
* * *
24725 AAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAAGTTTGACCGAGAACCAAGAGACAAAACAATTC
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGA-GAAACAATTC
* *
24790 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTGGTTTACAAAATGACAACTATTTAGACCT
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
*
24855 AATGATGCGATTTTCCAAG-A
194 AATGATGCGATTTCCCAAGCA
* * * * * * *
24875 TGGACTGTACGGAAAATGGGTCGAAGGAATGGATCATATTGAATACTTTAAGGAACAAAAGTTAT
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAAC-AAAGTTAT
* * *
24940 AAAAGAACTCGTAAAAGTTTGTCATGTTC-AGAAGTTCGACCGAGAACCAATAAAGAAACAATTC
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCGA-AAGTTCGACCGAGAACCAAGAGAGAAACAATTC
* * * ** *
25004 TCACATAAATAACTTTTTAATTTAAAGACCAAATTTTGTTTACAAAATGACAATCTATTTAGAAC
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGACC
* * *
25069 AATTGATACGATTTCCCGAGCA
193 AAATGATGCGATTTCCCAAGCA
* * *
25091 TGGAATGTTCGAAAAATTACGT-GAAGGAATGGATCATCTTGAATAGTTTAAGGAACCAAAGTTA
1 TGGAATGTTCGAAAAATTGC-TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTA
* * * * * *
25155 AAAAAGAATTCGTAAATGTTTGTCAAGTTCGAAAGTTTGGCCGAGAACCAAGAGA-AGAACTATT
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGA-AACAATT
* ** * * ** * * *
25219 ATCACCTAAATAAGTTTTTTAATT-AAA-AGGAGAACTACTTAGACCAAATTATG-CGA-TTTTT
128 CTCACCTAAATAAG-TTTTTAATTCAAAGACCAAAAGTTGTT-TA-CAAA--ATGACAACTATTT
* * *
25280 AGAGC---T--T-CGATTGTTCGAA--A
188 AGACCAAATGATGCGATT-TCCCAAGCA
* * *
25300 ---AATG---G-------C-TCGAAGGAATGGATCGTCTTGAATACTTTAAGAAATAAAAGTTAT
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTAT
* ** * * * *
25351 AAAAGAACTCGTAAAAGTTTTTCAAGTTCGAAAGTTCGGTCAAGAACCTAGAAAGAAATAATTCT
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTCT
* * *
25416 CACATAAATAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA-GACAATCTATTTAGAACA
130 CACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGACCA
* ** * *
25480 ATTGATATGATTTCCCGAGAA
194 AATGATGCGATTTCCCAAGCA
* * * * * *
25501 TGGAATGTTAGAAAAATTGCTCGAAGGTATAGATCGTCTTGAATAATTTAAGGAAACGAAGTTAA
1 TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGG-AACAAAGTTAT
* * * * *
25566 AAAAGAACTCGTAAAGGTTT-TCCAAGTTC-AGATGTTCGACCCAGAACCTAGAGAGAAACTATT
65 AAAAGAACTCGTAAAAGTTTGT-CAAGTTCGA-AAGTTCGACCGAGAACCAAGAGAGAAACAATT
* * * * * *
25629 ATCACATAAATAAGTTTTTAATTCAAAGACCAAAA-TTAATTCATAAAATGATAACTATTTAGAC
128 CTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAACTATTTAGAC
*** *
25693 CAAATGATGC-ATTTTCTTGAGCT
192 CAAATGATGCGA-TTTCCCAAGCA
** * **
25716 TGCTATTTTC-AGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGCAGTTA
1 TGGAATGTTCGA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAAAGTTA
* * * * * * * *
25780 TAAAAGAACACGTAAAAGTTTGTCAACTTCGGATGTTCGGCCTAGAAACAAGAGAGAAACTATTC
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTC
* *
25845 TCACCTAAATAAGTTTTTAATTCAAAGACCAAATG-T-TTTACAAAATTACAACTATTTAGACCA
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
25908 AAT
194 AAT
25911 CATATGATTT
Statistics
Matches: 2264, Mismatches: 409, Indels: 159
0.80 0.14 0.06
Matches are distributed among these distances:
191 1 0.00
192 3 0.00
194 22 0.01
195 103 0.05
196 8 0.00
197 1 0.00
199 4 0.00
200 4 0.00
201 1 0.00
203 1 0.00
204 4 0.00
206 4 0.00
207 1 0.00
209 1 0.00
210 5 0.00
211 4 0.00
213 106 0.05
214 604 0.27
215 1222 0.54
216 144 0.06
217 16 0.01
218 2 0.00
219 3 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (214 bp):
TGGAATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAAAGTTATA
AAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAGAGAAACAATTCTC
ACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAA
TGATGCGATTTCCCAAGCA
Found at i:23760 original size:429 final size:428
Alignment explanation
Indices: 22957--25932 Score: 3030
Period size: 429 Copynumber: 7.0 Consensus size: 428
22947 GAATGTTCAA
* **
22957 AAAATTGCTCGAAGGAAT-GATTCATCTTGAATACTTTAAGGAACTGAAG-TATAAAAGAACTTG
1 AAAATTGCTCGAAGGAATGGA-TCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTG
* * * * * *
23020 TAAAAGTTTGTTAACTTCGAAAGTTC-ACCCTAGAACCAAGAGAGAAAGTATTCTCAACTAAATA
65 TAAAAGTTTGTCAAGTTCGAAAGTTCGA-CCGAGAACCAAGAAAGAAACTATTCTCACCTAAATA
* * * * *
23084 AGTTTTTAATTTAAAGACTAGAAGTTT-TTTACAAAATTACAACTATTTAGACCAAATGATGCAA
129 AGTTTTTAATTCAAAGACCA-AAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA
* * * * *
23148 TTTCTCAAGCATAGAATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAATACTTTTAGGA
193 TTTCCCAAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGA
* * * * *
23213 ATCGAAGTTATGAAAGAACTAGTAAAAGTTTTTCAAGTT-TGTAAGTTCGG-CCAAGAACCAAAA
258 A-CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTG-AAGTTCGGCCCAA-AACCAAGA
* * * * * * *
23276 GAAAAACAATTTTCACCTAAGTAAGTTTTTAATTGAAAAACCAAAAGTAGTTTACAAAATGACAA
320 GAGAAATAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA
* * * * * *
23341 CTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTATACTG
385 CTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTC-G
* * ** *
23386 AAAATTGCTCGAAGGAATGGATCGCCTTGAATACTTTAATGAAAAAAAGGTATAAAAGAACTTGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTGT
* * * * * * *
23451 AAAAGTTTGTCAAGTT-TAAAGTTCGACCGAGAACTAAGAAAGAAGCAATTCTCACATAAAGAAT
66 AAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAAAGAAACTATTCTCACCTAAATAAG
* * * * *
23515 TTTTTAACTAAAAAACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATAATGTGATTT
131 TTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTT
* *
23580 CCCAAGCATGGAATGTTTGGAAATTTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAACC
196 CCCAAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-C
* * * *
23645 AAGGTTATAAAAGATCTCGTAAAAGTTTGTCAACTTCTGTAGTTCGGCCCAAAACCAAGAGAGAA
260 AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTGAAGTTCGGCCCAAAACCAAGAGAGAA
* *
23710 ATAATTCTCACCTAAATTAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAACTATT
325 ATAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATT
* * *
23775 TAGACCAAATGATGCGATTTCTTGAGCTTGGAATGTTCGG
390 TAGACCAAATGATGCGATTTCTCGAGCATGGAATATTC-G
* * *
23815 AAAATTGCTCGAAGGAATGGATCATCTT-AATTACTTTAAGGAACCAAAGTTATAAAACAACTCG
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAA-TACTTTAAGGAACCAAAGTTATAAAAGAACTTG
* * * *
23879 TAAAAGTTTGACAAGTTCGGAAGTTCGATCGAGAACCAAGAAAGAAACAATTCTCACCTAAATAA
65 TAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAAAGAAACTATTCTCACCTAAATAA
* * *
23944 GTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCTAATGATGCGATT
130 GTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATT
* ** * * * *
24009 TCCCAAGCATGGACTGTACGAAAAATTGCTCGAAGGAATTGATCGTGTTGAATACTTTATGGAAC
195 TCCCAAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-
* * * * * *
24074 CCAAGTTA-AAAAGAACTTGTAAAAGTTTGTCAAGTTCGGAAGTTTGGCCGAGAACCAAGAGAGG
259 CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTGAAGTTCGGCCCAAAACCAAGAGA-G
* * * * **
24138 AACT-ATTATCCCCTAAATAAGTTTTTAACTT-AAAGACCAAAAGTTGTTTATAGCATGACAACT
323 AAATAATTCTCACCTAAATAAGTTTTTAA-TTCAAAGACCAAAAGTTGTTTACAAAATGACAACT
* ** ** * ** *
24201 ATTTAGATCGTATGATGAAATTTTTTTAGCATGGAATGTTCGG
387 ATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTC-G
* * * * *
24244 AAAATTG-TGTGAAGGAATGGATCGTCTTAAATACTTTAATGAACCAATGTTATAGAAGAACTTG
1 AAAATTGCT-CGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTG
* * * * ** * *
24308 TAAAATTTTGTGAAGTTTGAAAGTTTGATTGAGAACTAAGAGAGAAACTATTCTCACCTAAATAA
65 TAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAAAGAAACTATTCTCACCTAAATAA
24373 GTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATT
130 GTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATT
*
24438 TCCCAAGCATGGATTGCTTT-GAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
195 TCCCAAGCATGGAATG-TTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * ** * * *
24502 CAAAAGTTATAAAAGACCACGTAAAAGTTTTTCAAGTT-TGAAGTTCGGCTGAGAACCAAGAAAC
259 C-AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTGAAGTTCGGCCCAAAACCAAGAGAG
* * * * * * * *
24566 AAACAATTCTCACATAAAGAATTTTTTAATTTAAAGACCAAAACTTGTTTACAAAATAACAAATA
323 AAATAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTA
*
24631 TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTCA
388 TTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTCG
* * * *** *
24672 AAAATTTCTCGAAGGAATGGATCGTCTTAAATACTTTGAGGAATTGAAGTTATAAAAGAACTCGT
1 AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTGT
* * *
24737 AAAAGTTTGTCAAGTTCAAAAGTTTGACCGAGAACCAAGAGACA-AAACAATTCTCACCTAAATA
66 AAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGA-A-AGAAACTATTCTCACCTAAATA
* * *
24801 AGTTTTTAATTCAAAGACCAAAAGTGGTTTACAAAATGACAACTATTTAGACCTAATGATGCGAT
129 AGTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGAT
* * ** * * * *
24866 TTTCCAAG-ATGGACTGTACGGAAAATGGGTCGAAGGAATGGATCATATTGAATACTTTAAGGAA
194 TTCCCAAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA
* * * * * * *
24930 CAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCATGTTCAGAAGTTCGACCGAGAACCAATAAAG
259 C-AAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTGAAGTTCGGCCCAAAACCAAGAGAG
* * * * **
24995 AAACAATTCTCACATAAATAACTTTTTAATTTAAAGACCAAATTTTGTTTACAAAATGACAATCT
323 AAATAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CT
* * * * *
25060 ATTTAGAACAATTGATACGATTTCCCGAGCATGGAATGTTCG
387 ATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTCG
* * * *
25102 AAAAATTACGT-GAAGGAATGGATCATCTTGAATAGTTTAAGGAACCAAAGTTAAAAAAGAA-TT
1 -AAAATTGC-TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTT
* * * *
25165 CGTAAATGTTTGTCAAGTTCGAAAGTTTGGCCGAGAACCAAGAGAAG-AACTATTATCACCTAAA
64 -GTAAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGA-AAGAAACTATTCTCACCTAAA
* * * *
25229 TAAG-TTTT--TT----------AA-----TT--AAAAGGAGAACTACTTAGACCAAATTATGCG
127 TAAGTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCG
** * * * * * *
25274 ATTT-TTAGAGCTTCGATTGTTCGAAAAATGGCTCGAAGGAATGGATCGTCTTGAATACTTTAAG
192 ATTTCCCA-AGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAG
* * * * *
25338 AAATAAAAGTTATAAAAGAACTCGTAAAAGTTTTTCAAGTTC-GAAAGTTCGG-TCAAGAACCTA
256 GAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTG-AAGTTCGGCCCAA-AACCAA
* * *
25401 GAAAGAAATAATTCTCACATAAATAACTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAA-GAC
318 GAGAGAAATAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
* * ** * * * *
25465 AATCTATTTAGAACAATTGATATGATTTCCCGAGAATGGAATGTTAG
383 AA-CTATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTCG
* * * * * * *
25512 AAAAATTGCTCGAAGGTATAGATCGTCTTGAATAATTTAAGGAAACGAAGTTAAAAAAGAACTCG
1 -AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTG
* * * * * * *
25577 TAAAGGTTT-TCCAAGTTC-AGATGTTCGACCCAGAACCTAGAGAGAAACTATTATCACATAAAT
65 TAAAAGTTTGT-CAAGTTCGA-AAGTTCGACCGAGAACCAAGAAAGAAACTATTCTCACCTAAAT
** * * *
25640 AAGTTTTTAATTCAAAGACCAAAATTAATTCATAAAATGATAACTATTTAGACCAAATGATGC-A
128 AAGTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGA
*** * ** *
25704 TTTTCTTGAGCTTGCTAT-TTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAG
193 -TTTCCCAAGCATGGAATGTTT-GGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAG
** * * * * *
25768 GAACCGCAGTTATAAAAGAACACGTAAAAGTTTGTCAACTTCGGATGTTCGGCCTAGAAA-CAAG
256 GAA-CAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTGAAGTTCGGCCCA-AAACCAAG
* *
25832 AGAGAAACT-ATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAATG-T-TTTACAAAATTAC
319 AGAGAAA-TAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGAC
* **
25894 AACTATTTAGACCAAATCATATGATTTCTCGAGCATGGA
383 AACTATTTAGACCAAATGATGCGATTTCTCGAGCATGGA
25933 TGATGTGAGC
Statistics
Matches: 2150, Mismatches: 332, Indels: 131
0.82 0.13 0.05
Matches are distributed among these distances:
409 6 0.00
410 185 0.09
411 155 0.07
412 2 0.00
413 2 0.00
417 2 0.00
423 2 0.00
427 3 0.00
428 222 0.10
429 1022 0.48
430 450 0.21
431 97 0.05
432 2 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (428 bp):
AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAAAGTTATAAAAGAACTTGT
AAAAGTTTGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAAAGAAACTATTCTCACCTAAATAAG
TTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATGATGCGATTT
CCCAAGCATGGAATGTTTGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACA
AAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCTGAAGTTCGGCCCAAAACCAAGAGAGAAA
TAATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTT
AGACCAAATGATGCGATTTCTCGAGCATGGAATATTCG
Found at i:24234 original size:644 final size:642
Alignment explanation
Indices: 22945--25910 Score: 3156
Period size: 644 Copynumber: 4.6 Consensus size: 642
22935 TCACATCACT
** * * *
22945 TGGAATGTTCAAAAAATTGCTCGAAGGAATGATTCATCTTGAATACTTTAAGGAACTGAAG-TAT
1 TGGAATGTTCGGAAAATTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAAC-CAAGTTAT
* * * *
23009 AAAAGAACTTGTAAAAGTTTGTTAACTTC-GAAAGTTC-ACCCTAGAACCAAGAGAGAAAGTATT
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCAG-AAGTTCGACCC-AGAACCAAGAGAGAAACTATT
* * * * * *
23072 CTCAACTAAATAAGTTTTTAATTTAAAGACTAGAAGTTTTTTACAAAATTACAACTATTTAGACC
128 CTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACC
* * * * * *
23137 AAATGATGCAATTTCTCAAGCATAGAATGTTTGAAAAATTGCTCAAAGGAATGGATCGTCTTGAA
193 AAATGATGCGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCGTCTTGAA
* * * * * * * * *
23202 TACTTTTAGGAATCGAAGTTATGAAAGAACTAGTAAAAGTTTTTCAAGTTTGTAAGTTCGGCCAA
258 TACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGA
* * * * *
23267 GAACCAA-AAGAAAAACAATTTTCACCTAAGTAAGTTTTTAATTGAAAAACCAAAAGTAGTTTAC
323 GAACCAAGAA-AGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTAC
* *
23331 AAAATGACAACTATTTAGACCTAATGATGTGATTTCCCAAGCATGGACTATACTG-AAAATTGCT
387 AAAATGACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGACTATAC-GAAAAATTGCT
* * * *
23395 CGAAGGAATGGATCGCCTTGAATACTTTAAT-GAAAAAAAGGTATAAAAGAACTTGTAAAAGTTT
451 CGAAGGAATGGATCGTCTTGAATACTTTAATGGAATAAAAGTTATAAAAGAACTCGTAAAAGTTT
* * * * *
23459 GTCAAGTT-TAAAGTTCGACCGAGAACTAAGAAAGAAGCAATTCTCACATAAAGAATTTTTTAAC
516 GTCAAGTTCGAAAGTTCGACCGAGAACCAAGAAAGAA-CAATTCTCACATAAATAAGTTTTTAAT
* * * * *
23523 TAAAAAACCAAAATTTGTTTACAAAATGACAACTATTTAGACCAAATAATGTGATTTCCCAAGCA
580 TCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-C-AATGATGAGATTTCCCAAGCA
* *
23588 TGGAATGTTTGGAAATTTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAACCAAGGTTAT
1 TGGAATGTTCGGAAAATTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAACCAA-GTTAT
* * * * * *
23653 AAAAGATCTCGTAAAAGTTTGTCAACTTCTGTAGTTCGGCCCAAAACCAAGAGAGAAA-TAATTC
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCAGAAGTTCGACCCAGAACCAAGAGAGAAACT-ATTC
* *
23717 TCACCTAAATTAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATAACAACTATTTAGACCA
129 TCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCA
* * *
23782 AATGATGCGATTTCTTGAGCTTGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCATCTT-AAT
194 AATGATGCGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCGTCTTGAA-
* * **
23846 TACTTTAAGGAACCAAAGTTATAAAACAACTCGTAAAAGTTTGACAAGTTCGGAAGTTCGATCGA
258 TACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGA
23911 GAACCAAGAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACA
323 GAACCAAGAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACA
* *
23976 AAATGACAACTATTTAGACCTAATGATGCGATTTCCCAAGCATGGACTGTACGAAAAATTGCTCG
388 AAATGACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGACTATACGAAAAATTGCTCG
* * *** *
24041 AAGGAATTGATCGTGTTGAATACTTT-ATGGAACCCAAGTTA-AAAAGAACTTGTAAAAGTTTGT
453 AAGGAATGGATCGTCTTGAATACTTTAATGGAATAAAAGTTATAAAAGAACTCGTAAAAGTTTGT
* * * * * * * *
24104 CAAGTTCGGAAGTTTGGCCGAGAACCAAGAGAGGAACTATTATCCCCTAAATAAGTTTTTAACTT
518 CAAGTTCGAAAGTTCGACCGAGAACCAAGA-AAGAACAATTCTCACATAAATAAGTTTTTAA-TT
* ** * * ****
24169 -AAAGACCAAAAGTTGTTTATAGCATGACAACTATTTAGATCGTATGATGAAATTTTTTTAGCA
581 CAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-C-AATGATGAGATTTCCCAAGCA
* * * *
24232 TGGAATGTTCGGAAAATTG-TGTGAAGGAATGGATCGTCTTAAATACTTTAATGAACCAATGTTA
1 TGGAATGTTCGGAAAATTGCT-CGAAGGAATGAATCGTCTTGAATACTTTAAGGAACCAA-GTTA
* * * * * * *** *
24296 TAGAAGAACTTGTAAAATTTTGTGAAGTT-TGAAAGTTTGATTGAGAACTAAGAGAGAAACTATT
64 TAAAAGAACTCGTAAAAGTTTGTCAAGTTCAG-AAGTTCGACCCAGAACCAAGAGAGAAACTATT
*
24360 CTCACCTAAATAAGTTTTTAATTCAAAGACCAAAATTTGTTTACAAAATGACAACTATTTAGACC
128 CTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACC
* * * *
24425 AAATGATGCGATTTCCCAAGCATGGATTGCTT-TGAAAATTGCTCGAAGGAATGGATCGTCTTGA
193 AAATGATGCGATTTCTCGAGCATGGAATG-TTCGGAAAATTGCTCGAAGGAATGGATCGTCTTGA
* * * * * *
24489 ATACTTTAAGGAACAAAAGTTATAAAAGACCACGTAAAAGTTTTTCAAGTT-TGAAGTTCGGCTG
257 ATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCG
* * * * * * *
24553 AGAACCAAGAAACAAACAATTCTCACATAAAGAATTTTTTAATTTAAAGACCAAAACTTGTTTAC
322 AGAACCAAGAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTAC
* * * * * * *
24618 AAAATAACAAATATTTAGACCAAATGATGCGATTTCTCGAGCATGGAATATTC-AAAAATTTCTC
387 AAAATGACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGACTATACGAAAAATTGCTC
* * **
24682 GAAGGAATGGATCGTCTTAAATACTTTGA-GGAATTGAAGTTATAAAAGAACTCGTAAAAGTTTG
452 GAAGGAATGGATCGTCTTGAATACTTTAATGGAATAAAAGTTATAAAAGAACTCGTAAAAGTTTG
* * * *
24746 TCAAGTTCAAAAGTTTGACCGAGAACCAAGAGACAAAACAATTCTCACCTAAATAAGTTTTTAAT
517 TCAAGTTCGAAAGTTCGACCGAGAACCAAGA-A-AGAACAATTCTCACATAAATAAGTTTTTAAT
* * *
24811 TCAAAGACCAAAAGTGGTTTACAAAATGACAACTATTTAGACCTAATGATGCGATTTTCCAAG-A
580 TCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGA-C-AATGATGAGATTTCCCAAGCA
* * * * * * * *
24875 TGGACTGTACGGAAAATGGGTCGAAGGAATGGATCATATTGAATACTTTAAGGAACAAAAGTTAT
1 TGGAATGTTCGGAAAATTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAAC-CAAGTTAT
* * * * *
24940 AAAAGAACTCGTAAAAGTTTGTCATGTTCAGAAGTTCGACCGAGAACCAATAAAGAAACAATTCT
65 AAAAGAACTCGTAAAAGTTTGTCAAGTTCAGAAGTTCGACCCAGAACCAAGAGAGAAACTATTCT
* * * ** *
25005 CACATAAATAACTTTTTAATTTAAAGACCAAATTTTGTTTACAAAATGACAATCTATTTAGAACA
130 CACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAGACCA
* * * * * *
25070 ATTGATACGATTTCCCGAGCATGGAATGTTCGAAAAATTACGT-GAAGGAATGGATCATCTTGAA
194 AATGATGCGATTTCTCGAGCATGGAATGTTCGGAAAATTGC-TCGAAGGAATGGATCGTCTTGAA
* * * * * *
25134 TAGTTTAAGGAACCAAAGTTAAAAAAGAATTCGTAAATGTTTGTCAAGTTCGAAAGTTTGGCCGA
258 TACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGA
* *
25199 GAACCAAGAGAAG-AACTATTATCACCTAAATAAGTTTTTTAATT--------AAAAG--G----
323 GAACCAAGA-AAGAAACAATTCTCACCTAAATAAG-TTTTTAATTCAAAAACCAAAAGTTGTTTA
* * ** * * * * * *
25249 ----A-G--AACTACTTAGACCAAATTATGCGATTT-TTAGAGCTTCGATTGTTCGAAAAATGGC
386 CAAAATGACAACTATTTAGACCAAATGATGCGATTTCCCA-AGCATGGACTATACGAAAAATTGC
*
25306 TCGAAGGAATGGATCGTCTTGAATACTTTAA-GAAATAAAAGTTATAAAAGAACTCGTAAAAGTT
450 TCGAAGGAATGGATCGTCTTGAATACTTTAATGGAATAAAAGTTATAAAAGAACTCGTAAAAGTT
* ** * * * *
25370 TTTCAAGTTCGAAAGTTCGGTCAAGAACCTAGAAAGAAATAATTCTCACATAAATAACTTTTTAA
515 TGTCAAGTTCGAAAGTTCGACCGAGAACCAAGAAAG-AACAATTCTCACATAAATAAGTTTTTAA
*
25435 TTCAAAGACCAAAAGTTGTTTACAAAA-GACAATCTATTTAGAACAATTGAT-ATGATTTCCCGA
579 TTCAAAGACCAAAAGTTGTTTACAAAATGACAA-CTATTTAG-ACAA-TGATGA-GATTTCCCAA
*
25498 GAA
640 GCA
* * * * *
25501 TGGAATGTTAGAAAAATTGCTCGAAGGTAT-AGATCGTCTTGAATAATTTAAGGAAACGAAGTTA
1 TGGAATGTTCGGAAAATTGCTCGAAGGAATGA-ATCGTCTTGAATACTTTAAGG-AACCAAGTTA
* * * *
25565 AAAAAGAACTCGTAAAGGTTT-TCCAAGTTCAGATGTTCGACCCAGAACCTAGAGAGAAACTATT
64 TAAAAGAACTCGTAAAAGTTTGT-CAAGTTCAGAAGTTCGACCCAGAACCAAGAGAGAAACTATT
* * * * * *
25629 ATCACATAAATAAGTTTTTAATTCAAAGACCAAAA-TTAATTCATAAAATGATAACTATTTAGAC
128 CTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTT-GTTTACAAAATGACAACTATTTAGAC
* * ** * *
25693 CAAATGATGC-ATTTTCTTGAGCTTGCTATTTTCAGAAAATTGCTCGAAGGAATGGATCGTCTTG
192 CAAATGATGCGA-TTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCGTCTTG
** * * *
25757 AATACTTTAAGGAACCGCAGTTATAAAAGAACACGTAAAAGTTTGTCAACTTCGGATGTTCGGCC
256 AATACTTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCC
* * * * * *
25822 TAGAAACAAGAGAGAAACTATTCTCACCTAAATAAGTTTTTAATTCAAAGACCAAATG-T-TTTA
321 GAGAACCAAGAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTA
*
25885 CAAAATTACAACTATTTAGACCAAAT
386 CAAAATGACAACTATTTAGACCAAAT
25911 CATATGATTT
Statistics
Matches: 1944, Mismatches: 314, Indels: 130
0.81 0.13 0.05
Matches are distributed among these distances:
624 22 0.01
625 251 0.13
626 237 0.12
627 3 0.00
628 1 0.00
632 4 0.00
636 1 0.00
638 4 0.00
640 1 0.00
642 46 0.02
643 421 0.22
644 890 0.46
645 52 0.03
646 11 0.01
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (642 bp):
TGGAATGTTCGGAAAATTGCTCGAAGGAATGAATCGTCTTGAATACTTTAAGGAACCAAGTTATA
AAAGAACTCGTAAAAGTTTGTCAAGTTCAGAAGTTCGACCCAGAACCAAGAGAGAAACTATTCTC
ACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAA
TGATGCGATTTCTCGAGCATGGAATGTTCGGAAAATTGCTCGAAGGAATGGATCGTCTTGAATAC
TTTAAGGAACCAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCGGCCGAGAA
CCAAGAAAGAAACAATTCTCACCTAAATAAGTTTTTAATTCAAAAACCAAAAGTTGTTTACAAAA
TGACAACTATTTAGACCAAATGATGCGATTTCCCAAGCATGGACTATACGAAAAATTGCTCGAAG
GAATGGATCGTCTTGAATACTTTAATGGAATAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAA
GTTCGAAAGTTCGACCGAGAACCAAGAAAGAACAATTCTCACATAAATAAGTTTTTAATTCAAAG
ACCAAAAGTTGTTTACAAAATGACAACTATTTAGACAATGATGAGATTTCCCAAGCA
Found at i:27147 original size:50 final size:51
Alignment explanation
Indices: 27061--27175 Score: 144
Period size: 50 Copynumber: 2.3 Consensus size: 51
27051 TGCATGACTT
*
27061 GATTTAATGATGCAAACTTTAACTAACATGGGAGTTACATAATGCATG-ATAG
1 GATTT-ATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGTA-AG
* * * *
27113 GATTTATGATGCATA-TTTAACTAACATGTAAGTTACTTAATGCATGTAAT
1 GATTTATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGTAAG
*
27163 TATTTATGATGCA
1 GATTTATGATGCA
27176 GATTAATAGT
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
50 41 0.73
51 10 0.18
52 5 0.09
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (51 bp):
GATTTATGATGCAAACTTTAACTAACATGGAAGTTACATAATGCATGTAAG
Found at i:27271 original size:77 final size:80
Alignment explanation
Indices: 27185--27359 Score: 275
Period size: 77 Copynumber: 2.2 Consensus size: 80
27175 AGATTAATAG
* *
27185 TGCAAGACATAATTAAATCACAATCTTAATAAACATAGGAGAAG-TTTT-T-ATGAGTGAATTAA
1 TGCAAGACATAATTAAATCACAATCGTAATAAACATAGGAGAAGCTTTTATAATGACTGAATTAA
27247 ATGCAAAACACTTAA
66 ATGCAAAACACTTAA
* *
27262 TGCAAGACATAATTAAATCACAATCGTAATAAACATAGGAGATGCTTTTATGAATGACTTAATTA
1 TGCAAGACATAATTAAATCACAATCGTAATAAACATAGGAGAAGCTTTTAT-AATGACTGAATTA
*
27327 AATGCAAATCACTTAA
65 AATGCAAAACACTTAA
27343 TGCAAGACATAATTAAA
1 TGCAAGACATAATTAAA
27360 GATGCAAACA
Statistics
Matches: 89, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
77 42 0.47
78 4 0.04
79 1 0.01
81 42 0.47
ACGTcount: A:0.46, C:0.13, G:0.13, T:0.29
Consensus pattern (80 bp):
TGCAAGACATAATTAAATCACAATCGTAATAAACATAGGAGAAGCTTTTATAATGACTGAATTAA
ATGCAAAACACTTAA
Found at i:27405 original size:17 final size:17
Alignment explanation
Indices: 27374--27406 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
27364 CAAACACTTA
27374 TTAAACTAAAATAAAAC
1 TTAAACTAAAATAAAAC
27391 TTAAA-TAAAATTAAAA
1 TTAAACTAAAA-TAAAA
27407 AAATCCTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (17 bp):
TTAAACTAAAATAAAAC
Found at i:27931 original size:214 final size:215
Alignment explanation
Indices: 27545--29791 Score: 2315
Period size: 214 Copynumber: 10.5 Consensus size: 215
27535 ACATCAATGA
* ** *
27545 AATGTTCAAAAAATTGCTAAAAGGAATGGATCGTCTTGAATACTTTAAGGAATC-GAAGTTATGA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAGAAGTTATAA
* * *
27609 AAGAAC-CTATAAAAGTTTTTCAAGTTCGAAAGTTCGGCCGAAAACCAA-AGGAGAAACAATTCT
65 AAGAACTC-GTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGA-GAGAAACAATTCT
* * * **
27672 CACCTAAGTAAGTTTTTAATTCAAAGACCAAAAGTAATTTACAAAATGACAACTATTTAAACCTA
128 CACATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACC-A
* *
27737 AA-GATGTGATTTCCAAAGCATGG
192 AATGATGCGATTTCCCAAGCATGG
* * * * * * * * *
27760 ACTATACGAAAAATTGCTCGAAGGAATAGATCGTCTTGAGTACTTTAATGAACAAAACTTAAAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATAAA
* *
27825 AGAACTTGTAAAAGTTTGTCAAGTTC-AAAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCAC
66 AGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTCAC
*
27889 ATAAAGAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAAATG
131 ATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAAATG
* *
27954 ATGTGATTTCCCTAGCATGG
196 ATGCGATTTCCCAAGCATGG
* * * *
27974 AATGTTC-AGAAAATTGCTCGAAGGAATGGATCTTTTTTAATACTTTTAAGGAACAAAAGTTATA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATAC-TTTAAGGAACAGAAGTTATA
* * * * * *
28038 AAAGAACTCGTAAAAGTTTGTCAAGCTCGAAAGTTCGACTGAGAACCAACAAAGAAACAATTATC
64 AAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTC
* * * *
28103 ACAAAAATAACTTTTTAATTTAAAGACCAAAAGTAT-TTTACAAAATGACAATCTATTCAGAA-C
129 ACATAAATAATTTTTTAATTCAAAGACCAAAAGT-TGTTTACAAAATGACAA-CTATTTA-AACC
* * * *
28166 AATTAATGC-ACTTTCCCAAGGATAG
191 AAATGATGCGA-TTTCCCAAGCATGG
* * *
28191 AATGTTCAAAAAAATTGCAT-GAAGGAATGGATCGTCTTGAATACTGTAAGGAACCGAAGTTA-A
1 AATGTTC-GAAAAATTGC-TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATA
* * * * * * ** **
28254 AAAAAACTCGTAAATGTTTGTCAAGTTGGGAAGTTCGACCGAGAACCAAGAGGGAAAGTATAATC
64 AAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTC
* * * * *
28319 ACCTAAATAAGTTTTTAATTCAAAGA-CGAAAGTTGTTTATAAAATGATAACTATTTAGAA-CAA
129 ACATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTA-AACCAA
* *
28382 ATGATGCAATTTCCTAAGCATGG
193 ATGATGCGATTTCCCAAGCATGG
* * * ** *
28405 GATGTTCGAAAAATTGCTCGAAGGAATGGATAGTCTTGAATACTTTAAGGAACCGAACATATAAC
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATAAA
* ** * * * *
28470 AGAACTCGTAAAAGTTTGTCAAGTTCAAAAGTTAAGCCAAGCACCAAGAGGGAAACTATTCTCAC
66 AGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTCAC
* ** * * *
28535 CTAAATAAGATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCGAATA
131 ATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAAATG
** ** *
28600 ATTTGATTTCCTTAGCATGT
196 ATGCGATTTCCCAAGCATGG
* * * ** * * *
28620 AATGTTCAAAAAATTGCTTGAAGGAATGAATCAACTTGAATGCTTCAAGAAATC-GAAGTTATAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAGAAGTTATAA
* *
28684 AAGAACTCGTAAAAATTTGTCAAGTTCG-AAGTTCGGCCGAGAACCAAGAAAGAAACAATTCTCA
65 AAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTCA
* * * * *
28748 CATGAAGAATTTTTTAATTCAAAGACCAAAACTTATTTACAAAATGACAACTATTTATACCAAAT
130 CATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAAAT
28813 GATGCGATTTCCCAAGCATGG
195 GATGCGATTTCCCAAGCATGG
* * * * * *
28834 ACTGTTC-AGGAAATTGCTCGAAGGAATAGATCGTCTTGAACACTCTAAGGAACAAAAGTTATAA
1 AATGTTCGA-AAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATAA
* * * * ** *
28898 CAA-AACTCGTTAAAGTTAGTCAGGTTCGGAAGTTCGATCGAGAACCAAGAAAGAAACAATTCTC
65 -AAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTC
* * * *
28962 ATATAAATAACTTTTTAATTTAAAGACCAAAAGTTTTTTTACAAAATGACAATCTATTTAGAA-C
129 ACATAAATAATTTTTTAATTCAAAGACCAAAAG-TTGTTTACAAAATGACAA-CTATTTA-AACC
* * ** *
29026 AATTGATGCGATTTCTCGGGCGTGG
191 AAATGATGCGATTTCCCAAGCATGG
* * *
29051 AAGGTTTGAAAAATTGCACGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCA-AAGTTA-AA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAA-CAGAAGTTATAA
* * * * ** *
29114 ATGGAACTCGTAGAAGTTTGTCAAGTTCGAATGTTCGACCGAGAACCAAGAGAGAAACTGTTATC
65 A-AGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTC
* * * *
29179 AC-TAAAT-CTGCTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAA
129 ACATAAATAAT-TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAA
* *** * **
29242 ATTATGCGATTTCTTGAGAATTA
193 ATGATGCGATTTCCCAAGCATGG
* * * *
29265 AATGTT--AAGAAATTTGCTCGAAGGAATGGATCATTTTGAATACTTAAAGGAACCGAAGTTATA
1 AATGTTCGAA-AAA-TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATA
* * * * *
29328 AAAGAACTCGTAAAAGTTTGTCAACTTCAAAAGTTCGGCCGTGAACCAGGAGAGAAACTATTCTC
64 AAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTC
* * * *
29393 ATC-TAAATAA-TTTTTAATTTAATGATCAAAAGTTGTTTACAAAATGATAACTATTTAAACCAA
129 A-CATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAA
* * *
29456 ATGATGCGATTTCTCGAGCATGA
193 ATGATGCGATTTCCCAAGCATGG
* * * *
29479 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGGCTTAAATAC-TTCAGGAACTGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATAAA
* * * * *
29543 AGAACACGTAAATGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACAAAGTGATAAACAATTCTCAC
66 AGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTCAC
* * * * * * *
29608 CTAAAT-ATGTTTTTAATTCAAAGCCCAAAAGTAGTTTGCAAAATGACAACTATTTAGACCTAAC
131 ATAAATAAT-TTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAAAT
* *
29672 GATGCGATTTCCCAAACGT-G
195 GATGCGATTTCCCAAGCATGG
* * * * * * *
29692 AACTGTACGAAAAATGGCTTGAAGGAATAGATCGTCTTGAA-ACTTTAAGGACCAAAAGTAATAA
1 AA-TGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATAA
*
29756 AAGAACTCGTAAAAATTTGTCAAGTTC-AGAAGTTCG
65 AAGAACTCGTAAAAGTTTGTCAAGTTCGA-AAGTTCG
29792 AATGTTCAGA
Statistics
Matches: 1692, Mismatches: 292, Indels: 97
0.81 0.14 0.05
Matches are distributed among these distances:
212 5 0.00
213 140 0.08
214 784 0.46
215 350 0.21
216 202 0.12
217 174 0.10
218 35 0.02
219 2 0.00
ACGTcount: A:0.40, C:0.15, G:0.17, T:0.28
Consensus pattern (215 bp):
AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACAGAAGTTATAAA
AGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAACCAAGAGAGAAACAATTCTCAC
ATAAATAATTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAAATG
ATGCGATTTCCCAAGCATGG
Found at i:29657 original size:859 final size:854
Alignment explanation
Indices: 27540--29792 Score: 2796
Period size: 860 Copynumber: 2.6 Consensus size: 854
27530 TGTTCACATC
** * *
27540 AATGAAATGTTCAAAAAATTGCTAAAAGGAATGGATCGTCTTGAATACTTTAAGGAATCGAAGTT
1 AATGAAATGTTC-AAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTT
* * * * * * *
27605 ATGAAAGAAC-CTATAAAAGTTTTTCAAGTTCGAAAGTTCGGCCGAAAACCAAAGGAGAAACAAT
65 ATAAAAGAACTC-GTAAAAGTTTGTCAAGTTCAAAAGTTCGGCCGAGAACCAGA-GAGAAACTAT
* **
27669 TCTCACCTAAGTAAGTTTTTAATTCAAAGACCAAAAGTAATTTACAAAATGACAACTATTTAAAC
128 TCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAAC
* * * * * *
27734 CTAAA-GATGTGATTTCCAAAGCATGGACTATACGAAAAATTGCTCGAAGGAATAGATCGTCTTG
193 C-AAATGATGTGATTTCCAAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATCGACTTG
* * ** * * *
27798 AGTACTTTAATGAACAAAACTTAAAAAAGAACTTGTAAAAGTTTGTCAAGTTC-AAAGTTCGGCC
257 AATACTTCAA-GAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCC
*
27862 GAGAACCAAGAAAGAAACAATTCTCACATAAAGAATTTTTTAATTCAAAGACCAAAAGTTGTTTA
321 GAGAACCAAGAAAGAAACAATTCTCACAT-AA-AATTTTTTAATTCAAAGACCAAAAGTAGTTTA
* * *
27927 CAAAATGACAACTATTTAAACCAAATGATGTGATTTCCCTAGCATGGAATGTTCAGAAAATTGCT
384 CAAAATGACAACTATTTAAACCAAATGATGCGATTTCCCAAGCATGGACTGTTCAGAAAATTGCT
* * * *
27992 CGAAGGAATGGATCTTTTTTAATACTTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTT
449 CGAAGGAATAGATCGTCTTGAA-AC-TTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTT
* *
28057 GTCAAGCTCGAAAGTTCGACTGAGAACCAACAAAGAAACAATTATCACAAAAATAACTTTTTAAT
512 GTCAAGTTCGGAAGTTCGACTGAGAACCAACAAAGAAACAATTATCACAAAAATAACTTTTTAAT
28122 TTAAAGACCAAAAGTATTTTACAAAATGACAATCTATTCAGAACAATTAATGCACTTTCCCAAGG
577 TTAAAGACCAAAAGTATTTTACAAAATGACAATCTATTCAGAACAATTAATGCACTTTCCCAAGG
* * *
28187 ATAGAATGTTCAAAAAAATTGCATGAAGGAATGGATCGTCTTGAATACTGTAAGGAACCGAAGTT
642 ATAGAAGGTTCAAAAAAATTGCACGAAGGAATGGATCGTCTTGAATACTGTAAGGAACCAAAGTT
* * *
28252 AAAAAAAACTCGTAAATGTTTGTCAAGTTGGGAAGTTCGACCGAGAACCAAGAGGGAAAGTATAA
707 AAAAAAAACTCGTAAATGTTTGTCAAGTTGCGAAGTTCGACCGAGAACCAAGAGAGAAACTATAA
* * * *
28317 TCACCTAAATAAGTTTTTAATTCAAAGACGAAAGTTGTTTATAAAATGATAACTATTTAGAACAA
772 TCACCTAAATAAGCTTTTAATTCAAAGACAAAAGTTGTTTACAAAATGACAACTATTTAGAACAA
28382 ATGATGCAATTTCCTAAG
837 ATGATGCAATTTCCTAAG
* ** **
28400 CATGGGATGTTCGAAAAATTGCTCGAAGGAATGGAT-AGTCTTGAATACTTTAAGGAACCGAACA
1 AATGAAATGTTC-AAAAATTGCTCGAAGGAATGGATCA-TCTTGAATACTTTAAGGAACCGAAGT
* ** * * *
28464 TATAACAGAACTCGTAAAAGTTTGTCAAGTTCAAAAGTTAAGCCAAGCACCAAGAGGGAAACTAT
64 TATAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAAGTTCGGCCGAGAACC-AGAGAGAAACTAT
* *
28529 TCTCACCTAAATAAGATTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGAC
128 TCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAAC
* * * ** * * * * *
28594 CGAATAATTTGATTTCCTTAGCATGTAATGTTCAAAAAATTGCTTGAAGGAATGAATCAACTTGA
193 CAAATGATGTGATTTCCAAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATCGACTTGA
* * *
28659 ATGCTTCAAGAAATCGAAGTTATAAAAGAACTCGTAAAAATTTGTCAAGTTCG-AAGTTCGGCCG
258 ATACTTCAAGAACT-GAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCG
*
28723 AGAACCAAGAAAGAAACAATTCTCACATGAAGAATTTTTTAATTCAAAGACCAAAACTTA-TTTA
322 AGAACCAAGAAAGAAACAATTCTCACAT-AA-AATTTTTTAATTCAAAGACCAAAA-GTAGTTTA
* *
28787 CAAAATGACAACTATTTATACCAAATGATGCGATTTCCCAAGCATGGACTGTTCAGGAAATTGCT
384 CAAAATGACAACTATTTAAACCAAATGATGCGATTTCCCAAGCATGGACTGTTCAGAAAATTGCT
* * *
28852 CGAAGGAATAGATCGTCTTGAACACTCTAAGGAACAAAAGTTATAACAA-AACTCGTTAAAGTTA
449 CGAAGGAATAGATCGTCTTGAA-ACTTTAAGGAACAAAAGTTATAA-AAGAACTCGTAAAAGTTT
* * * * *
28916 GTCAGGTTCGGAAGTTCGA-TCGAGAACCAAGAAAGAAACAATTCTCATATAAATAACTTTTTAA
512 GTCAAGTTCGGAAGTTCGACT-GAGAACCAACAAAGAAACAATTATCACAAAAATAACTTTTTAA
* * * *
28980 TTTAAAGACCAAAAGTTTTTTTACAAAATGACAATCTATTTAGAACAATTGATGCGA-TTTCTC-
576 TTTAAAGACCAAAAG-TATTTTACAAAATGACAATCTATTCAGAACAATTAATGC-ACTTTCCCA
* * * ** *
29043 GGGCGTGGAAGGTT-TGAAAAATTGCACGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCAA
639 AGG-ATAGAAGGTTCAAAAAAATTGCACGAAGGAATGGATCGTCTTGAATACTGTAAGGAACCAA
**
29107 AGTTAAAATGGAACTCGTAGAA-GTTTGTCAAGTT-CGAATGTTCGACCGAGAACCAAGAGAGAA
703 AGTTAAAA-AAAACTCGTA-AATGTTTGTCAAGTTGCGAA-GTTCGACCGAGAACCAAGAGAGAA
* * ** *
29170 ACTGTTATCA-CTAAATCTGCTTTTAATTTAAAGACCAAAAGTTGTTTACAAAATGACAACTATT
765 ACTATAATCACCTAAATAAGCTTTTAATTCAAAGA-CAAAAGTTGTTTACAAAATGACAACTATT
* * * * *
29234 TAGACCAAATTATGCGATTTCTTGAG
829 TAGAACAAATGATGCAATTTCCTAAG
* * *
29260 AATTAAATGTT-AAGAAATTTGCTCGAAGGAATGGATCATTTTGAATACTTAAAGGAACCGAAGT
1 AATGAAATGTTCAA-AAA-TTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGT
* *
29324 TATAAAAGAACTCGTAAAAGTTTGTCAACTTCAAAAGTTCGGCCGTGAACCAGGAGAGAAACTAT
64 TATAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAAGTTCGGCCGAGAACCA-GAGAGAAACTAT
* * * * *
29389 TCTCATCTAAATAA-TTTTTAATTTAATGATCAAAAGTTGTTTACAAAATGATAACTATTTAAAC
128 TCTCACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAAC
* * * *
29453 CAAATGATGCGATTTCTC-GAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATCGGCTTA
193 CAAATGATGTGATTTC-CAAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATCGACTTG
* * *
29517 AATACTTCAGGAACTGAAGTTATAAAAGAACACGTAAATGTTTGTCAAGTTCGAAAGTTCGGCCG
257 AATACTTCAAGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCG
* ** * * * *
29582 AGAACAAAGTGATAAACAATTCTCACCTAAATATGTTTTTAATTCAAAGCCCAAAAGTAGTTTGC
322 AGAACCAAGAAAGAAACAATTCTCACATAAA-AT-TTTTTAATTCAAAGACCAAAAGTAGTTTAC
* * * * * * * *
29647 AAAATGACAACTATTTAGACCTAACGATGCGATTTCCCAAACGTGAACTGTAC-GAAAAATGGCT
385 AAAATGACAACTATTTAAACCAAATGATGCGATTTCCCAAGCATGGACTGTTCAG-AAAATTGCT
* * * *
29711 TGAAGGAATAGATCGTCTTGAAACTTTAAGGACCAAAAGTAATAAAAGAACTCGTAAAAATTTGT
449 CGAAGGAATAGATCGTCTTGAAACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGT
*
29776 CAAGTTCAGAAGTTCGA
514 CAAGTTCGGAAGTTCGA
29793 ATGTTCAGAA
Statistics
Matches: 1191, Mismatches: 175, Indels: 56
0.84 0.12 0.04
Matches are distributed among these distances:
857 3 0.00
858 94 0.08
859 428 0.36
860 658 0.55
861 8 0.01
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.28
Consensus pattern (854 bp):
AATGAAATGTTCAAAAATTGCTCGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTA
TAAAAGAACTCGTAAAAGTTTGTCAAGTTCAAAAGTTCGGCCGAGAACCAGAGAGAAACTATTCT
CACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAAACCAA
ATGATGTGATTTCCAAAGCATGAAATGTTCGAAAAATTGCTCGAAGGAATGGATCGACTTGAATA
CTTCAAGAACTGAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTCGAAAGTTCGGCCGAGAA
CCAAGAAAGAAACAATTCTCACATAAAATTTTTTAATTCAAAGACCAAAAGTAGTTTACAAAATG
ACAACTATTTAAACCAAATGATGCGATTTCCCAAGCATGGACTGTTCAGAAAATTGCTCGAAGGA
ATAGATCGTCTTGAAACTTTAAGGAACAAAAGTTATAAAAGAACTCGTAAAAGTTTGTCAAGTTC
GGAAGTTCGACTGAGAACCAACAAAGAAACAATTATCACAAAAATAACTTTTTAATTTAAAGACC
AAAAGTATTTTACAAAATGACAATCTATTCAGAACAATTAATGCACTTTCCCAAGGATAGAAGGT
TCAAAAAAATTGCACGAAGGAATGGATCGTCTTGAATACTGTAAGGAACCAAAGTTAAAAAAAAC
TCGTAAATGTTTGTCAAGTTGCGAAGTTCGACCGAGAACCAAGAGAGAAACTATAATCACCTAAA
TAAGCTTTTAATTCAAAGACAAAAGTTGTTTACAAAATGACAACTATTTAGAACAAATGATGCAA
TTTCCTAAG
Found at i:30293 original size:215 final size:215
Alignment explanation
Indices: 29873--31254 Score: 1569
Period size: 215 Copynumber: 6.4 Consensus size: 215
29863 GTAATAATAG
* * *
29873 AATGTTCGAAAAATTGCACGAAGGAATGGATCATCTTGAATACTTTAAGGAACCGAAGTTAAAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * **
29938 AGAACTCGTAAAAGTTTGTCAAGTTCGGATGTTCAATCGAGAACCAAGAGGGAAAGTATAATCAC
66 AGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCAACCAAGAACCAAGAGAGAAACTATTCTCAC
* * * * * *
30003 CTAAATAAGTTTTTAATTCAAAGACCAAAAGTTCTTTATAAAATTATAACTATTTTGAACAAATG
131 CTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATG
*
30068 ATGCGATTTCCTAAGCATCG-
196 ATGCGATTTCCTGAGCAT-GT
* * * * * * *
30088 GATGTTCAAAAAATTGCTCGAACGAATGGATAGTCTTGAATACTTTAAGGAACCTAACTTATAAT
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * *
30153 AGAACTCGTAAAAGTTTGTCAAGTACGGAAGTT-AAGCCAAGCATCAAGAGGGAAACTATTCTCA
66 AGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCAA-CCAAGAACCAAGAGAGAAACTATTCTCA
* *
30217 CCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAAATATTTAGACCGAAT
130 CCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAAT
* ** *
30282 AATTTGATTTCCTTAGCATGT
195 GATGCGATTTCCTGAGCATGT
* * * *
30303 AATGTTCGAAAAATTGCTTGAAGGAATGAATCATCTTGAATGCTTTAAGGAACCGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * *** * *
30368 AGAACTTGTAAAAGTTTCTCAAGTTC-GAAGTTTGTCCAAGAACCAAGAAAGAAACAATTCTCAC
66 AGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCAACCAAGAACCAAGAGAGAAACTATTCTCAC
* * * * * * *
30432 ATAAAGAATTTTTTAATTCAAAAACCAAAACTTATTTACAAAATGACAACTATTTATACCAAATG
131 CTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATG
** *
30497 ATGCGATTTCCCAAGCATGG
196 ATGCGATTTCCTGAGCATGT
* ** * * **
30517 ATTGTTCGGGAAATTGCTCGAAGGAATAGATCGTATTGAATACTTTAAGGAACAAAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* * * * * * **
30582 AGAACTCGTTAAAGTTTGTCAGGTTCGGAAGTTCGACCGAGAGCCAAGAAAGAAAAAATTCTCAC
66 AGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCAACCAAGAACCAAGAGAGAAACTATTCTCAC
* * * * * * *
30647 ATAAATAACTTTTTAATTTAACGACCAAAAGTTTTTTTACAAAATGACAATCTATTTAGAACAAT
131 CTAAATAAGTTTTTAATTCAAAGACCAAAAG-TTGTTTACAAAATGACAA-CTATTTAGACCAAA
*
30712 TGATGCGATTT-CTCGGGCATGT
194 TGATGCGATTTCCT-GAGCATGT
* * *
30734 AATGTTTGAAAAATTGCAT-GAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGCAGATA-AA
1 AATGTTCGAAAAATTGC-TCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAA
* * ** * *
30797 AAGGAAGTCGTAAAAGTTTGTCAAGTTCGAAAGTTCAACCGGGAACAAAGAGAGAAACTATTATC
65 AA-GAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCAACCAAGAACCAAGAGAGAAACTATTCTC
*
30862 ACCTAAATATGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAA
129 ACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAA
* * * * *
30927 TTATGCAATTTCTTGAGAATGG
194 TGATGCGATTTCCTGAGCATGT
*
30949 AATGTT--AAGAAATTTGCTCGAAGGAATGGATCGTCTTGAATACTTAAAGGAACCGAAGTTATA
1 AATGTTCGAA-AAA-TTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATA
* * * **
31012 AAAGAACACGTAAAAGTTTGTCAACTTC-GAATGTTCTACCGTGAACCAAGAGAGAAACTATTCT
64 AAAGAACTCGTAAAAGTTTGTCAAGTTCGGAA-GTTCAACCAAGAACCAAGAGAGAAACTATTCT
* * * * *
31076 TACCTAAATAAGTTTTTAATTTAAAGATCAAAAGTTGTTTACAAAATGATAACTATTTAGATCAA
128 CACCTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAA
* * *
31141 ATTATGCGAATT-CTCGAGCATGA
193 ATGATGCGATTTCCT-GAGCATGT
* * * * *
31164 AATGATCGAAAAGTTACTCGAAGGAATGGATCGTCTTAAATACTTTAAGGAACTGAAGTTATAAA
1 AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
* *
31229 AGACCACGTAAAAGTTTGTCAAGTTC
66 AGAACTCGTAAAAGTTTGTCAAGTTC
31255 AAAAGTTCGG
Statistics
Matches: 982, Mismatches: 167, Indels: 36
0.83 0.14 0.03
Matches are distributed among these distances:
213 2 0.00
214 186 0.19
215 591 0.60
216 46 0.05
217 156 0.16
218 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.17, T:0.29
Consensus pattern (215 bp):
AATGTTCGAAAAATTGCTCGAAGGAATGGATCGTCTTGAATACTTTAAGGAACCGAAGTTATAAA
AGAACTCGTAAAAGTTTGTCAAGTTCGGAAGTTCAACCAAGAACCAAGAGAGAAACTATTCTCAC
CTAAATAAGTTTTTAATTCAAAGACCAAAAGTTGTTTACAAAATGACAACTATTTAGACCAAATG
ATGCGATTTCCTGAGCATGT
Done.