Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014716.1 Corchorus olitorius cultivar O-4 contig14749, 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: 122871
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5950 original size:16 final size:16
Alignment explanation
Indices: 5929--5959 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
5919 TCAAGATGTT
5929 TATTATAATTATATAG
1 TATTATAATTATATAG
*
5945 TATTATTATTATATA
1 TATTATAATTATATA
5960 TTAAAAAAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (16 bp):
TATTATAATTATATAG
Found at i:10312 original size:14 final size:12
Alignment explanation
Indices: 10275--10300 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10265 AACAAATGTG
10275 CAAATAAAAGAA
1 CAAATAAAAGAA
10287 CAAATAAAAGAA
1 CAAATAAAAGAA
10299 CA
1 CA
10301 CAATGAATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.12, G:0.08, T:0.08
Consensus pattern (12 bp):
CAAATAAAAGAA
Found at i:19244 original size:6 final size:6
Alignment explanation
Indices: 19235--19286 Score: 50
Period size: 6 Copynumber: 8.7 Consensus size: 6
19225 CAGCTAAAAT
** ** * *
19235 TCGAGC TCGAGC TCGAAT TCGATA TCGTGT TCGAGC TCGAGC TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC TCGAGC
19283 TCGA
1 TCGA
19287 CAGGTATATA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
6 37 1.00
ACGTcount: A:0.19, C:0.27, G:0.29, T:0.25
Consensus pattern (6 bp):
TCGAGC
Found at i:28523 original size:2 final size:2
Alignment explanation
Indices: 28516--28543 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
28506 TAGTCTGATT
28516 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28544 AAGTTGGATT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:38899 original size:59 final size:57
Alignment explanation
Indices: 38796--38905 Score: 175
Period size: 59 Copynumber: 1.9 Consensus size: 57
38786 ATAGCATCAT
*
38796 GCCTCGGTCCTAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
1 GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
* *
38853 GCCTCGGTCCGAAAACGTCTTTTTTTTATGCATCTAATAAAGAACATGTCACT
1 GCCTCGGTCCGAAAACGTC--TTTTTTAGGCATCTAATAAAAAACATGTCACT
38906 TCATATTTGA
Statistics
Matches: 48, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
57 18 0.38
59 30 0.62
ACGTcount: A:0.31, C:0.23, G:0.15, T:0.32
Consensus pattern (57 bp):
GCCTCGGTCCGAAAACGTCTTTTTTAGGCATCTAATAAAAAACATGTCACTCGATAA
Found at i:86078 original size:8 final size:9
Alignment explanation
Indices: 86065--86101 Score: 53
Period size: 8 Copynumber: 4.4 Consensus size: 9
86055 AAATTAATGA
86065 ATATTAT-T
1 ATATTATAT
86073 ATATTATAT
1 ATATTATAT
86082 ATA-TATAT
1 ATATTATAT
86090 ATA-TATAT
1 ATATTATAT
86098 ATAT
1 ATAT
86102 GCATGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
8 23 0.85
9 4 0.15
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (9 bp):
ATATTATAT
Found at i:86084 original size:2 final size:2
Alignment explanation
Indices: 86072--86101 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
86062 TGAATATTAT
86072 TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
86102 GCATGTCAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:97116 original size:322 final size:323
Alignment explanation
Indices: 94998--100274 Score: 4691
Period size: 322 Copynumber: 16.1 Consensus size: 323
94988 TCATGATGGT
* * * * *
94998 AAAAATGACCCG-AAAGATTTTTCCTCAATTTTTGGCAAAAATACTCAT-AAAATATATATAATA
1 AAAAATGACCCGAAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCATGAAAA-ATATATAATT
* * ** * * * *
95061 CAATGCC-AAAAGATTGAAGGCCTTTTCACGCTT-TTATATCGTTTTT-CA-TATTTTCTGGATT
64 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATT
* *
95122 AATTTCTAATTAAATCGATACAAGATTCAGATGCACGT-AAAACAAAATCCTTAAATCCAATGTG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAATCCTTAAATCCAATGTG
* * * * * * * ** *
95186 GCTTAGATTTGATTAGATAAATAAAGATAATTGAAAGAGTCTCGACGCCAAAAATCATGCAAAAC
193 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAAC
* * * * ** *
95251 AGAGCCGTGGCC-CCGGAACGCGTATTTAGTGAAAAACCGTGATGGTTAGTATACGATTTCGGCT
258 TGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT
95315 A
323 A
** * * * *
95316 AAACCTGACCCGAAACGTTTATTTCTCAATTTTTTTCCACAATACTTA-GAAAAATATATAATTT
1 AAAAATGACCCGAAAAGTTT-TTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTC
* * * * * * **
95380 AAGGCCAAAAACATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCCTTTTTTTTTTTCTAA
65 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTT-CC---ATTTTTTTCCGA
* * * * * *
95445 ATTACTTTCTAATTAAATCGAAATAAGATTCAGATGTTTGTAAAAACAAATCCTTATATCCTATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * * * * * * **
95510 TGGCTGACATATGATTCGATGAATATAGATGTTTCGAGAAGTCTTTGCGCCAAAAATCATGCAAA
191 TGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAA
* * * * * *
95575 ATTGAGCCG-GGGCTCC-AGAACACGTTTTTAGACAAAAAAAAATCGTGATGGTTAATACACGAT
256 ACTGAGCCGAGGCCTCCGA-AACGCGTTTTTAG-C---CAAAAACCGTGATGGTTAGTACACGAT
95638 TTCGGCTAAA
316 TTCGGCT--A
* * *
95648 ATTTTGCAAAAGTTGACCCGAAAAGTTTTTCCTCAATTTTTTGCTACAATACTC-GGAAAAAATA
1 A------AAAA--TGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCATG-AAAAATA
* * * * *
95712 TATAATTTAATGCCAAAAAAAATTAAAGGATTTTTCTCGCTTCTAATATCGTTTTTCCA-TTTTT
57 TATAATTCAACGCC-AAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
* * ** *
95776 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCTGATGCTCGTAAACCCAAATCCTTAAGTC
121 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC
* *
95841 CAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAAAACA
186 CAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCC-AAAAATCA
* * * *
95906 TGCAAAATTGAGTCGAGG-CTCCGAAACGCGTTTTTAGCCAAAAACCGCGATGGTTAGTACATGA
250 TGCAAAACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA
95970 TTTCGGCTA
315 TTTCGGCTA
* * * * * *
95979 AAAATTGA-CCTAAAATTTTGTTTCTCAATTTTTTACCACAATACTCATAAAAAATATATAATTT
1 AAAAATGACCCGAAAAGTTT-TTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTC
* * *
96043 AACGCCAAAAAGATTGAACGGTTTTTCATGCTTCTAATATCGTTTTTCCA--TTTTTCCGAATTA
65 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTA
* * *
96106 ATTTCTAATTGAATCGAAACAAGATTCAGATGCTCGTAAAAGCAAATCGTTAAATCCAATGTGGC
130 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * **
96171 TGATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTACGTAAAAAATCATGCAAAACTG
195 TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTG
* * * * * * *
96236 AGCC-AGG--GCCGGAACGCGTTTTTAGCCAAAAACCGTGA---TAAGAAAACAATTTCGACTAA
260 AGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCT--
96295 AA
323 -A
* * * ** *
96297 TTTTGCAAAAACTGATCCGAAACA-TTTTTCCTCAATTCTACGCTACAATACTCA-GAAAAAATA
1 ------AAAAA-TGACCCGAAA-AGTTTTTTCTCAATTTTTTGCCACAATACTCATG-AAAAATA
* * ** * *
96360 TATAATTCAACACCAAAAAAATTGAAGGCTTTTTCATACTTCTATTATTGTTTTT-CATTTTTTT
57 TATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTT
* * * *
96424 -CGAATTTATTTCTAATT-AATCGAAACAAGATTCAGATGATTGTAAAAACAAATCCTTATATCC
122 CCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCC
* * ** *
96487 AATGTGGCTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAATCTTTGCGTCAAAAATCATG
187 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATG
* * * *
96552 CAAAATTGAGCCG-GGGCTCCGGAACGCTTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATG
252 CAAAACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA--
**
96616 TCTAAAATTTTGC-A
315 --T----TTCGGCTA
* * * *
96630 AAAACTGACCCGAAAA-TATTTTCCTCAATTTTTTGCCACAATACT-AAGAAAAA-ATATAATTT
1 AAAAATGACCCGAAAAGT-TTTTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTC
* * * * **
96692 AATGCCAAAAAAATTTATGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTTCTTAAT
65 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTTTCCGAAT
* * *
96757 TTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAATAAATCCTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * *
96822 GCTTG-GACTTGGTTAGATGAATATAGATACTTCAAGGAGTCTTTATGCCAAAAA-CTAGGCAAA
193 GC-TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATC-ATGCAAA
* * * *
96885 ACTGAGTCGAGGCCT-CAAAACGCGTTTTTAGCCAAAAACCGTGGTGGTTACTACACGATTTCGG
256 ACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGG
96949 CTA
321 CTA
** *
96952 AAAAATGACCCGAAAAGGGTTTTCTCAATTTTTTCCCACAATACTCATGAAAAATATATAATTCA
1 AAAAATGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTCA
* * * *
97017 ACGCCAAAAATATTGAAGGGTTTTTCATGCCTCTGATATCGTTTTTCCATTTTTTTCCGAATTAA
66 ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAA
* *
97082 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTAAATCGAATGTGGC-
131 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
* * * * ** *
97146 CAGGATTTGGTTTGATAAATATAGATATTTTAAGGAGTCTTTGCGCCAAAAATCATGCAAAATTG
196 GA-GATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTG
* * * * *
97211 AGCTG-GGGCTCC-AGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAATATACGATTTCGGCAA
260 AGCCGAGGCCTCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC--
97274 AAATTTTGCA
322 ------T--A
* * *
97284 AAAAACTGACCC-AAAAGGTTTTTTTTCTCAATTTCTTGCCACAATACT-AAGATTAAATATATA
1 AAAAA-TGACCCGAAAA-G--TTTTTTCTCAATTTTTTGCCACAATACTCATGA-AAAATATATA
* * * *
97347 ATTCAACGCCAAAAAATTTGAAGGGTATTTCATGCTTCTAATATCGTTTTCCCATTTTTTTCCGA
61 ATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGA
* * * **
97412 ATTTATTTCTAATTAAATCGAAACAAGATTTAGATGGTCGTAAAGCCAAATCCTTAAATCCAATG
126 ATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATG
* * *
97477 TGGCTGAGATTTGGTTAGATGAGTATATAGATATTTGAAAGAGTCTTTCTGCCAAAAATCATGCA
191 TGGCTGAGATTTGGTTAGATGA--ATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCA
* * * * * *
97542 AAACTAAGCAGAGGCCT-TGAAAC-CTGTTTTTAGACAAAAACTGTGATGAGATAGTACACGATT
254 AAACTGAGCCGAGGCCTCCGAAACGC-GTTTTTAGCCAAAAACCGTGATG-GTTAGTACACGATT
97605 TCGGCTA
317 TCGGCTA
* * * * *
97612 AAAACTGATCCGAAAAGTTTTTTTCTCAA-TTTTTG-CAGAATATTC-CGAGAAAATATATAATT
1 AAAAATGACCCGAAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCATGA-AAAATATATAATT
* * ** *
97674 CAACGCCAAAAAGATTGACGGGCGTTTCACGCTTCTAATATCGTTTTT-CAATTTTTTCCGAATT
64 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATT
*
97738 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCCTTATATCCAATGTGG
129 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *
97802 CTGAGATTTGGTTCGATGAATATAGTTATTTCAAGAAGTC-TT-TGCACGAAAAATCATGCAAAA
194 CTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGC-C-AAAAATCATGCAAAA
* * * * * *** *
97865 TTGAGTCG-GGGCTCCGTAACACGTTTTTAGCCAAAAACCGT-A-ACATA-CACACGATTTCGGT
257 CTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGG-
*
97926 TTAAA
321 CT--A
* *
97931 TTTTGCAAAAACTGA-CTGAAAAGTTTTTTCTCAATCTTTTT-CCACAATACT-A-AAATTAAAT
1 ------AAAAA-TGACCCGAAAAGTTTTTTCTCAAT-TTTTTGCCACAATACTCATGAA--AAAT
* *
97992 ATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCATGCTTCTAATATCGTTTTTCCA-TTTTT
56 ATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
* ***
98056 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGGGAAATCCTTAAATC
121 TCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATC
* * *
98121 CAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAATCAT
186 CAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCAT
* * * * * *
98186 GCAAAACTAAGCCGAGACC-CCAAAACCCGTTTTTAGCCAAAAACTGTGATGG--ATTACACGAT
251 GCAAAACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGAT
98248 TTCGGCTA
316 TTCGGCTA
* * * * * *
98256 AAAACTTATCCAAAAAGTTTTTTTCTCAATTTTTTG-CAAAATATTCAT-AGAAAATATATAATT
1 AAAAATGACCCGAAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCATGA-AAAATATATAATT
* * * *
98319 CAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTT-CAGTTTTTTTTTCGAA
64 CAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTTTTTCCGAA
* * * *
98383 TTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAGAAACAAATCCTTATATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * **
98448 GGCTGAGATTTGGTTCGATGAATATAGATATTTTTGAAGGAGTCTTTGCGCCAAAAATCATGCAA
192 GGCTGAGATTTGGTTAGATGAATATAGATA--TTTCAAGGAGTCTTTATGCCAAAAATCATGCAA
* ** * * * ** *
98513 AATTGAG-TTAGGGCTCCGAAACGTGTTTTTAGCCAAAAACCAT-AACG-TA-CACACGATTTCG
255 AACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
*
98574 GTTA
320 GCTA
* *
98578 AAATTTTGCAATAACTGACCGAAAAGTTTTTTTCTCAATCTTTTGCCACAATACTCA-GAAAAAA
1 AAA------AATGAC---CCGAAAAG-TTTTTTCTCAATTTTTTGCCACAATACTCATG-AAAAA
* * *
98642 TATATAATTCAACACCAAAAAAATTGAAGGATTTTTCACACTTCTAATATCGTTTTTCCAATTTT
55 TATATAATTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-A--TT
* * *
98707 TTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AATCTTTA
117 TTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
*
98771 AAACCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAA
182 AATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAA
* * * * * * * * ** * * *
98836 CCCTACAAAACAGAGTCGAGACAT-CAAAATACGTTTTTGGCCAAAAACCGTTATGGTTATTAC-
247 TCATGCAAAACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACA
98899 CTGATTAT-GGCTA
312 C-GATT-TCGGCTA
* * * * *
98912 AAAACTAACCCGAAATAG-TTTTTCTCAATTTTTTGCCGCAAAACTCATAAAAAATATATAATTC
1 AAAAATGACCCGAAA-AGTTTTTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTC
* * * *
98976 AACGCC-AAAAAATGGAA-GGATTTTCACGCTTCTAATTTCG-TTTTCCTATTTTTTTTTCCAAA
65 AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCC-A--TTTTTTTCCGAA
* * * *
99038 TTAATTTCTAATTAAATCAAAACAAGATTTAGATGTTCGTAAAAACAAATCCCTAAATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
** * * ** **
99103 GGCTGAGATTTAATTATATGAATGTAGATATTTCAAGGAGTCTTCCTGCTTAAAATCATGCAAAA
192 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA
* * * * * * *
99168 CTGAG-CTAGG-GTCCCGAAACACGTTTTTAGCCAAAAATCGTGATGGTTAATGCATGATTTCGG
257 CTGAGCCGAGGCCT-CCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGG
99231 CTAAAATTTTA
321 C--------TA
* * * *
99242 CAAAAACTAACCCAAAAATTTTTTTCTCAATTCTTTGCCACAATACT--TGGAAAAATTATATAA
1 -AAAAA-TGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAT-GAAAAA-TATATAA
* ** * *
99305 CTCAACGCCAAAAAAATTGAACAGTTTTTCACGCTTCTATTATCGTTTTTCCATTTTTTTCAGAA
62 TTCAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAA
* * * * ** * *
99370 TTTATTTCTAATTAATTTGAATCAAGATTTGGATGCTCGTAAACA-AAATCCATAAATCCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * * * * *
99434 GGCTGAGATTTGGTTAAATTAATATAGATATTTCAAGGATTATTTCTACCAAAAATCAAGCAAAA
192 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA
* * ** *
99499 CTGAGCCGTGGCC-CCGAAATGCGTTTTTAGCCAAAAACCGT-ACCG-TA--A-GCGATTTCGGC
257 CTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
99558 TA
322 TA
* *
99560 AAAACTGATCCGAGAAA-TTTTTTCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAATT
1 AAAAATGACCCGA-AAAGTTTTTTCTCAATTTTTTGCCACAATACTCATG-AAAAATATATAATT
** ** *
99623 CAACGCCAAAATGATTGACA-GACTTTTCACGCTTCTAATGTCGTTTTTCCA----------AAT
64 CAACGCCAAAAAAATTGA-AGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAAT
* * *
99677 TAATTTCTAATTAAATCGAAACAAAATTCGGATGCTCGTAAAAACAAATCTTTAAATCCAATGTG
128 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
*
99742 GCTGAGATTTGTTTCCATTTTGGCTGAGATTTGTTTGCACGAATATAGATATTTCAAGGAGTCTT
193 GCT--GA---G-----A-TTTGG-TTAGA------T----GAATATAGATATTTCAAGGAGTCTT
* * * * * * *
99807 TACGCCTAAAATCATGCAAAATTGAACCGTGG-CTCCGGAACGCGCTTTTAGCCAAAAACCGTGA
236 TATGCCAAAAATCATGCAAAACTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGA
**
99871 TGGTTAGTACACGATTTCTACTAAAATTTTTTTA
301 TGGTTAGTACACGATTTCGGC-----------TA
* * * *
99905 AAAAACTGACCCGAAAAG-TTTTCCTCAATTTTTTGCCACAATACTCAGGAAATATATATAATTT
1 AAAAA-TGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTC
* * * *
99969 AACACCAAAAAAATTAAAGGGGTTTT-AGCGCTTCTAATATAGTTTTTCCATTTTTTTTCCCGAA
65 AACGCCAAAAAAATTGAAGGGTTTTTCA-CGCTTCTAATATCGTTTTTCCA-TTTTTTT-CCGAA
* * * * * * * * *
100033 TTTATTTCTGATAAAATCGAAGCAAGATTCAAATGCTCGTAAAAATATATACTTAAATTCAATGT
127 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * *
100098 GGCTGAGATTTGGTTATATGAATATAGATATTTTAAGGAGTCTTTATGCCAAAAACCTTGCAAAA
192 GGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAA
* * * * * *
100163 CTGAGTCGA-GACTCCGAAACGCGTTTTTAACCAAAAACGGTAATGGTTAGTATACGATTTCGGC
257 CTGAGCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGC
100227 TA
322 TA
* ** * *
100229 AAAACTGACAAGAAAATTTTTTTTCTCAATTTTTTACCACAATACT
1 AAAAATGACCCGAAAA-GTTTTTTCTCAATTTTTTGCCACAATACT
100275 TATATATGAA
Statistics
Matches: 4061, Mismatches: 639, Indels: 511
0.78 0.12 0.10
Matches are distributed among these distances:
306 40 0.01
307 21 0.01
309 2 0.00
312 1 0.00
315 13 0.00
316 95 0.02
317 18 0.00
318 70 0.02
319 143 0.04
320 102 0.03
321 285 0.07
322 450 0.11
323 184 0.05
324 342 0.08
325 161 0.04
326 348 0.09
327 126 0.03
328 52 0.01
329 226 0.06
330 45 0.01
331 193 0.05
332 179 0.04
333 98 0.02
334 99 0.02
335 265 0.07
336 106 0.03
337 108 0.03
338 26 0.01
339 24 0.01
340 36 0.01
341 34 0.01
344 2 0.00
345 91 0.02
346 13 0.00
347 1 0.00
352 1 0.00
355 2 0.00
357 59 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (323 bp):
AAAAATGACCCGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCATGAAAAATATATAATTCA
ACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAATTAA
TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
GAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGA
GCCGAGGCCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTA
Found at i:99461 original size:653 final size:645
Alignment explanation
Indices: 94997--100274 Score: 4853
Period size: 653 Copynumber: 8.1 Consensus size: 645
94987 ATCATGATGG
* * * * * *
94997 TAAAAA-TGACCCG-AAAGATTTTTCCTCAATTTTTGGCAAAAATACTCATAAAATATATATAAT
1 TAAAAACTGATCCGAAAAG-TTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * * * * * * *
95060 ACAATGCCAAAAGATTGAAGGCCTTTTCACGCTT-TTATATCGTTTTTCA-TATTTTCTGGATTA
64 TCAACGCCAAAAAATTGAAGG-ATTTTCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATTA
* *
95123 ATTTCTAATTAAATCGATACAAGATTCAGATGCACGT-AAAACAAAATCCTTAAATCCAATGTGG
128 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAC-AAATCCTTAAATCCAATGTGG
* * * * * * * * * *
95187 CTTAGATTTGATTAGATAAATAAAGATAATTGAAAGAGTC-TCGACGCCAAAAATCATGCAAAAC
192 CTGAGATTTGGTT-TATGAATATAGATATTTCAAGGAGTCTTC--TGCCAAAAATCATGCAAAAT
* * * * * ** * *
95251 AGAGC-CGTGG-CCCCGGAACGCGTATTTAGTGAAAAACCGTGATGGTTAGTATACGATTTCGGC
254 TGAGCTAG-GGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGC
** * * * *
95314 TAAAA-----C-----CTGACCCGAAACGTTTATTTCTCAATTTTTTTCCACAATACTTAGAAAA
318 TAAAATTTTGCAAAAACTGACCC-AAAAATTTTTTTCTCAATTCTTTGCCACAATACTAAGAAAA
* * * * * *
95369 ATATATAATTTAAGGCCAAAAACATTG-ACGGGCTTTTCACGCTTCTAATATTGTTTTTCCCTTT
382 ATATATAATTCAACGCCAAAAAAATTGAAC-GGTTTTTCACGCTTCTAATATCGTTTTT-CC--A
* * * * * *
95433 TTTTTTTTCTAAATTACTTTCTAATTAAATCGAAATAAGATTCAGATGTTTGTAAAAACAAATCC
443 TTTTTTTCCGAATTTA-TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAA-AAATCC
* * * * * * * * * **
95498 TTATATCCTATGTGGCTGACATATGATTCGATGAATATAGATGTTTCGAGAAGTCTTTGCGCCAA
505 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAA
* * * * * * *
95563 AAATCATGCAAAATTGAGCCG-GGGCTCCAGAACACGTTTTTAGACAAAAAAAAATCGTGATGGT
570 AAATCATGCAAAACTGAGTCGAGGCCT-CAAAACGCGTTTTTAG-C---CAAAAACCGTGATGG-
*
95627 TAATACACGATTTCGGC
629 TATTACACGATTTCGGC
* * * *
95644 TAAAATTTTGCAAAAGTTGACCCGAAAAGTTTTTCCTCAATTTTTTGCTACAATACTCGGAAAAA
1 T---A------AAAA-CTGATCCGAAAAGTTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAA
* * * *
95709 ATATATAATTTAATGCCAAAAAAAATTAAAGGATTTTTCTCGCTTCTAATATCGTTTTTCCA-TT
55 ATATATAATTCAACGCC--AAAAAATTGAAGGA-TTTTCACGCTTCTAATATCG-TTTTCCATTT
* * **
95773 TTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCTGATGCTCGTAAACCCAAATCCTTAA
116 TTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * *
95838 GTCCAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAAA
181 ATCCAATGTGGCTGAGATTTGGTT-TATGAATATAGATATTTCAAGGAGTC-TTCTGCC-AAAAA
* * * *
95903 ACATGCAAAATTGAG-TCGAGG-CTCCGAAACGCGTTTTTAGCCAAAAACCGCGATGGTTAGTAC
243 TCATGCAAAATTGAGCTAG-GGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATAC
* * * * *
95966 ATGATTTCGGC--------T--AAAAATTGA-CCTAAAATTTTGTTTCTCAATTTTTTACCACAA
307 ACGATTTCGGCTAAAATTTTGCAAAAACTGACCCAAAAATTTT-TTTCTCAATTCTTTGCCACAA
* * *
96020 TACTCATA-AAAAATATATAATTTAACGCCAAAAAGATTGAACGGTTTTTCATGCTTCTAATATC
371 TACT-A-AGAAAAATATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCACGCTTCTAATATC
* *
96084 GTTTTTCCA--TTTTTCCGAATTAATTTCTAATTGAATCGAAACAAGATTCAGATGCTCGTAAAA
434 GTTTTTCCATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
* * *
96147 GCAAATCGTTAAATCCAATGTGGCTGATATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTT
499 --AAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTT
* ** * * **
96212 TACGTAAAAAATCATGCAAAACTGAG-CCAGGGC-CGGAACGCGTTTTTAGCCAAAAACCGTGAT
562 TATGCCAAAAATCATGCAAAACTGAGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGAT
* ** **
96275 AAG-AAAACAATTTCGACTAAAATTTTGC
627 -GGTATTAC-A---CGA-T----TTCGGC
* ** *
96303 -AAAAACTGATCCGAAACA-TTTTTCCTCAATTCTACGCTACAATACTCAGAAAAAATATATAAT
1 TAAAAACTGATCCGAAA-AGTTTTT-CTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * ** * * *
96366 TCAACACCAAAAAAATTGAAGGCTTTTTCATACTTCTATTATTGTTTTTCATTTTTTT-CGAATT
64 TCAACGCC-AAAAAATTGAAGG-ATTTTCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATT
* * * *
96430 TATTTCTAATT-AATCGAAACAAGATTCAGATGATTGTAAAAACAAATCCTTATATCCAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
*
96494 CTGAGATTTGGTTTGATGAATATAGATATTTCAAGGAATCTT-TGCGTCAAAAATCATGCAAAAT
192 CTGAGATTTGGTTT-ATGAATATAGATATTTCAAGGAGTCTTCTGC--CAAAAATCATGCAAAAT
* * * * * *
96558 TGAGC-CGGGGCTCCGGAACGCTTTTTTAGCCAAAAACCGTGATGGTTAGTACACGA--T-GTCT
254 TGAGCTAGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCT
* * * *
96619 AAAATTTTGCAAAAACTGACCCGAAAATATTTTCCTCAATTTTTTGCCACAATACTAAGAAAAA-
319 AAAATTTTGCAAAAACTGACCCAAAAATTTTTTTCTCAATTCTTTGCCACAATACTAAGAAAAAT
* * * ** *
96683 ATATAATTTAATGCCAAAAAAATTTATGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTT
384 ATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCACGCTTCTAATATCGTTTTTCCA--TTTT
** *
96748 TTTCTTAATTTATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAATAAATCCTTAAA
447 TTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAA-AAATCCTTAAA
* *
96813 TCCAATGTGGCTTG-GACTTGGTTAGATGAATATAGATACTTCAAGGAGTCTTTATGCCAAAAA-
510 TCCAATGTGGC-TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAAT
* * *
96876 CTAGGCAAAACTGAGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGGTGGTTACTACAC
574 C-ATGCAAAACTGAGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGATGG-TATTACAC
96941 GATTTCGGC
637 GATTTCGGC
* * * *
96950 TAAAAAATGACCCGAAAAGGGTTTTCTCAATTTTTTCCCACAATACTCATG-AAAAATATATAAT
1 TAAAAACTGATCCGAAAA-GTTTTTCTCAATTTTTTGCCACAATACTCA-GAAAAAATATATAAT
* * * *
97014 TCAACGCCAAAAATATTGAAGGGTTTTTCATGCCTCTGATATCGTTTTTCCATTTTTTTCCGAAT
64 TCAACGCCAAAAA-ATTGAA-GGATTTTCACGCTTCTAATATCG-TTTTCCATTTTTTTCCGAAT
* *
97079 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAGTCCTTAAATCGAATGTG
126 TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTG
* * *
97144 GC-CAGGATTTGGTTTGATAAATATAGATATTTTAAGGAGTCTT-TGCGCCAAAAATCATGCAAA
191 GCTGA-GATTTGGTTT-ATGAATATAGATATTTCAAGGAGTCTTCT--GCCAAAAATCATGCAAA
* * *
97207 ATTGAGCT-GGGGCTCC-AGAATGCGTTTTTAGCCAAAAACCGTGATGGTTAATATACGATTTCG
252 ATTGAGCTAGGGTCTCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCG
* *
97270 GCAAAAATTTTGCAAAAAACTGACCCAAAAGGTTTTTTTTCTCAATT-TCTTGCCACAATACTAA
316 GCTAAAATTTTGC-AAAAACTGACCCAAAA--ATTTTTTTCTCAATTCT-TTGCCACAATACTAA
* * * * * *
97334 GATTAAATATATAATTCAACGCCAAAAAATTTGAAGGGTATTTCATGCTTCTAATATCGTTTTCC
377 GA-AAAATATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCACGCTTCTAATATCGTTTTTC
* * *
97399 CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTTAGATGGTCGTAAAGCCAAATC
441 CATTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA--AAAATC
* * *
97464 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAGTATATAGATATTTGAAAGAGTCTTTCTGC
504 CTTAAATCCAATGTGGCTGAGATTTGGTTAGATGA--ATATAGATATTTCAAGGAGTCTTTATGC
* ** * *
97529 CAAAAATCATGCAAAACTAAG-CAGAGGCCTTGAAAC-CTGTTTTTAGACAAAAACTGTGATGAG
567 CAAAAATCATGCAAAACTGAGTC-GAGGCCTCAAAACGC-GTTTTTAGCCAAAAACCGTGATG-G
*
97592 ATAGTACACGATTTCGGC
629 -TATTACACGATTTCGGC
* * * *
97610 TAAAAACTGATCCGAAAAGTTTTTTTCTCAA-TTTTTG-CAGAATATTCCGAGAAAATATATAAT
1 TAAAAACTGATCCGAAAAG--TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* ** * *
97673 TCAACGCCAAAAAGATTGACGGGCGTTTCACGCTTCTAATATCGTTTTTCAATTTTTTCCGAATT
64 TCAACGCCAAAAA-ATTGA-AGGATTTTCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATT
*
97738 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATCCTTATATCCAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
* * *
97802 CTGAGATTTGGTTCGATGAATATAGTTATTTCAAGAAGTCTT-TGCACGAAAAATCATGCAAAAT
192 CTGAGATTTGGTT-TATGAATATAGATATTTCAAGGAGTCTTCTGC-C-AAAAATCATGCAAAAT
* * * * *** * *
97866 TGAG-TCGGGGCTCCGTAACACGTTTTTAGCCAAAAACCGT-A-ACAT-ACACACGATTTCGGTT
254 TGAGCTAGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCT
* ** * *
97927 TAAATTTTGCAAAAACTGA-CTGAAAAGTTTTTTCTCAA-TCTTTTTCCACAATACTAA-AATTA
319 AAAATTTTGCAAAAACTGACCCAAAAATTTTTTTCTCAATTC-TTTGCCACAATACTAAGAA--A
*
97989 AATATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCATGCTTCTAATATCGTTTTTCCA-TT
381 AATATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT
*
98053 TTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAGGGAAATCCTTAA
446 TTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA--AAAATCCTTAA
* * *
98118 ATCCAATGTGGCTGAGATTTGGTTAGATAAATATAGATATTTCAAAGAGTCTTTCTGCCAAAAAT
509 ATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAAT
* * * * * *
98183 CATGCAAAACTAAGCCGAGACCCCAAAACCCGTTTTTAGCCAAAAACTGTGATGG-ATTACACGA
574 CATGCAAAACTGAGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTATTACACGA
98247 TTTCGGC
639 TTTCGGC
* * * * * *
98254 TAAAAACTTATCCAAAAAGTTTTTTTCTCAATTTTTTG-CAAAATATTCATAGAAAATATATAAT
1 TAAAAACTGATCCGAAAAG--TTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAAT
* * * *
98318 TCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCGTTTTTCAGTTTTTTTTTCGAA
64 TCAACGCCAAAAA-ATTGA-AGGATTTTCACGCTTCTAATATCGTTTTCCA--TTTTTTTCCGAA
* * * *
98383 TTAATTTCTAATTAAATTGAAACAAGATTCAGATACTCGTAGAAACAAATCCTTATATCCAATGT
125 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* *
98448 GGCTGAGATTTGGTTCGATGAATATAGATATTTTTGAAGGAGTCTT-TGCGCCAAAAATCATGCA
190 GGCTGAGATTTGGTT-TATGAATATAGATA--TTTCAAGGAGTCTTCT--GCCAAAAATCATGCA
* * * ** *
98512 AAATTGAGTTAGGG-CTCCGAAACGTGTTTTTAGCCAAAAACCAT-AACG-T-ACACACGATTTC
250 AAATTGAGCTAGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTC
* * * * *
98573 GGTTAAAATTTTGCAATAACTGACCGAAAAGTTTTTTTCTCAA-TCTTTTGCCACAATACTCAGA
315 GGCTAAAATTTTGCAAAAACTGACCCAAAAATTTTTTTCTCAATTC-TTTGCCACAATACTAAG-
* *
98637 AAAAATATATAATTCAACACCAAAAAAATTGAA-GGATTTTTCACACTTCTAATATCGTTTTTCC
378 AAAAATATATAATTCAACGCCAAAAAAATTGAACGG-TTTTTCACGCTTCTAATATCGTTTTTCC
*
98701 AATTTTTTTTTCCAAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAT
442 -A--TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAT
* *
98766 CTTTAAAACCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCC
503 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCC
* * * * * * ** * *
98831 AAAAACCCTACAAAACAGAGTCGAGACATCAAAATACGTTTTTGGCCAAAAACCGTTATGGTTAT
568 AAAAATCATGCAAAACTGAGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGATGG-TAT
98896 TAC-CTGATTAT-GGC
632 TACAC-GATT-TCGGC
* * * * *
98910 TAAAAACTAACCCGAAATAGTTTTTCTCAATTTTTTGCCGCAAAACTCATAAAAAATATATAATT
1 TAAAAACTGATCCGAAA-AGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
* * *
98975 CAACGCCAAAAAATGGAAGGATTTTCACGCTTCTAATTTCGTTTTCCTATTTTTTTTTCCAAATT
65 CAACGCCAAAAAATTGAAGGATTTTCACGCTTCTAATATCGTTTTCC-A--TTTTTTTCCGAATT
* * * *
99040 AATTTCTAATTAAATCAAAACAAGATTTAGATGTTCGTAAAAACAAATCCCTAAATCCAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
** * ** *
99105 CTGAGATTTAATTATATGAATGTAGATATTTCAAGGAGTCTTCCTGCTTAAAATCATGCAAAACT
192 CTGAGATTTGGTT-TATGAATATAGATATTTCAAGGAGTCTT-CTGCCAAAAATCATGCAAAATT
* * * *
99170 GAGCTAGGGTC-CCGAAACACGTTTTTAGCCAAAAATCGTGATGGTTAATGCATGATTTCGGCTA
255 GAGCTAGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTA
* * **
99234 AAATTTTACAAAAACTAACCCAAAAATTTTTTTCTCAATTCTTTGCCACAATACTTGGAAAAATT
320 AAATTTTGCAAAAACTGACCCAAAAATTTTTTTCTCAATTCTTTGCCACAATACTAAGAAAAA-T
* * *
99299 ATATAACTCAACGCCAAAAAAATTGAACAGTTTTTCACGCTTCTATTATCGTTTTTCCATTTTTT
384 ATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT
* * * * ** *
99364 TCAGAATTTATTTCTAATTAATTTGAATCAAGATTTGGATGCTCGTAAACAAAATCCATAAATCC
449 TCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA-AAAATCCTTAAATCC
* * * * * * *
99429 AATGTGGCTGAGATTTGGTTAAATTAATATAGATATTTCAAGGATTATTTCTACCAAAAATCAAG
513 AATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATG
* * * * * ** *
99494 CAAAACTGAGCCGTGGCCCCGAAATGCGTTTTTAGCCAAAAACCGT-ACCGTA--A-GCGATTTC
578 CAAAACTGAGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTATTACACGATTTC
99555 GGC
643 GGC
*
99558 TAAAAACTGATCCGAGAAATTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
1 TAAAAACTGATCCGA-AAAGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATT
* * *
99623 CAACGCCAAAATGATTGACA-GACTTTTCACGCTTCT-A-AT-G---T-C--GTTTTTCCAAATT
65 CAACGCCAAAA-AATTGA-AGGA-TTTTCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATT
* * *
99678 AATTTCTAATTAAATCGAAACAAAATTCGGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGG
127 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGG
*
99743 CTGAGATTTGTTTCCATTTTGGCTGAGATTTGTTTGCACGAATATAGATATTTCAAGGAGTCTT-
192 CT--GA---G-----A--TT---T--G----GTTT--ATGAATATAGATATTTCAAGGAGTCTTC
* * * * *
99807 TACGCCTAAAATCATGCAAAATTGAAC-CGTGG-CTCCGGAACGCGCTTTTAGCCAAAAACCGTG
234 T--GCCAAAAATCATGCAAAATTGAGCTAG-GGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTG
* ** ** * * *
99870 ATGGTTAGTACACGATTTCTACTAAAATTTTTTTAAAAAACTGACCCGAAAA-GTTTTCCTCAAT
296 ATGGTTAATACACGATTTCGGCTAAAA--TTTTGCAAAAACTGACCCAAAAATTTTTTTCTCAAT
* * * * * * * *
99934 TTTTTGCCACAATACTCAGGAAATATATATAATTTAACACCAAAAAAATTAAAGGGGTTTT-AGC
359 TCTTTGCCACAATACT-AAGAAAAATATATAATTCAACGCCAAAAAAATTGAACGGTTTTTCA-C
* * * *
99998 GCTTCTAATATAGTTTTTCCATTTTTTTTCCCGAATTTATTTCTGATAAAATCGAAGCAAGATTC
422 GCTTCTAATATCGTTTTTCCA-TTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAGATTC
* * * *
100063 AAATGCTCGTAAAAATATATACTTAAATTCAATGTGGCTGAGATTTGGTTATATGAATATAGATA
485 AGATGCTCGTAAAAA-A-ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATA
* * * * *
100128 TTTTAAGGAGTCTTTATGCCAAAAACCTTGCAAAACTGAGTCGA-GACTCCGAAACGCGTTTTTA
548 TTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGTCGAGGCCT-CAAAACGCGTTTTTA
* * * * *
100192 ACCAAAAACGGTAATGGTTAGTATACGATTTCGGC
612 GCCAAAAACCGTGATGG-TATTACACGATTTCGGC
* * *
100227 TAAAAACTGA-CAAGAAAATTTTTTTTCTCAATTTTTTACCACAATACT
1 TAAAAACTGATC-CGAAAA--GTTTTTCTCAATTTTTTGCCACAATACT
100275 TATATATGAA
Statistics
Matches: 3913, Mismatches: 509, Indels: 395
0.81 0.11 0.08
Matches are distributed among these distances:
638 72 0.02
640 2 0.00
641 2 0.00
642 1 0.00
643 7 0.00
644 110 0.03
645 162 0.04
646 24 0.01
647 178 0.05
648 256 0.07
649 184 0.05
650 224 0.06
651 291 0.07
652 23 0.01
653 348 0.09
654 191 0.05
655 239 0.06
656 194 0.05
657 333 0.09
658 133 0.03
659 191 0.05
660 156 0.04
661 95 0.02
662 167 0.04
663 168 0.04
664 104 0.03
665 2 0.00
666 2 0.00
668 5 0.00
669 22 0.01
670 27 0.01
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (645 bp):
TAAAAACTGATCCGAAAAGTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTC
AACGCCAAAAAATTGAAGGATTTTCACGCTTCTAATATCGTTTTCCATTTTTTTCCGAATTAATT
TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
GATTTGGTTTATGAATATAGATATTTCAAGGAGTCTTCTGCCAAAAATCATGCAAAATTGAGCTA
GGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAATACACGATTTCGGCTAAAATTT
TGCAAAAACTGACCCAAAAATTTTTTTCTCAATTCTTTGCCACAATACTAAGAAAAATATATAAT
TCAACGCCAAAAAAATTGAACGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTCCGAAT
TTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAAATCCTTAAATCCAATGTGGC
TGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTG
AGTCGAGGCCTCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTATTACACGATTTCGGC
Found at i:122470 original size:150 final size:150
Alignment explanation
Indices: 122181--122478 Score: 569
Period size: 151 Copynumber: 2.0 Consensus size: 150
122171 TGAGTCGGCA
*
122181 CTCCGAAACGCGTTTTTCGCCAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAA
1 CTCCGAAACGCGTTTTTCGCCAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAA
*
122246 AAAATGACCCGAAAAGTTTTTCCTAAATTTTTTGCTTGAATACTCAGAAAAAATATGTAATTCAA
66 AAAATGACCCGAAAAGTTTTTCCTAAATTTTTTGCTAGAATACTCAGAAAAAATATGTAATTCAA
122311 CGCCAAAAAAATTGAAGTTT
131 CGCCAAAAAAATTGAAGTTT
122331 CTCCGAAACGCGTTTTTCGCCAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAA
1 CTCCGAAACGCGTTTTTCGCCAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAA
122396 AAAATAGACCCGAAAAGTTTTTCCTAAATTTTTTGCTAGAATACTCAGAAAAAATATGTAATTCA
66 AAAAT-GACCCGAAAAGTTTTTCCTAAATTTTTTGCTAGAATACTCAGAAAAAATATGTAATTCA
122461 ACGCCAAAAAAATTGAAG
130 ACGCCAAAAAAATTGAAG
122479 GGTCTTTAAC
Statistics
Matches: 145, Mismatches: 2, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
150 69 0.48
151 76 0.52
ACGTcount: A:0.37, C:0.18, G:0.15, T:0.30
Consensus pattern (150 bp):
CTCCGAAACGCGTTTTTCGCCAAAACCGTGATGGTTAGTAAACGATTTCGGCTAAAATTTTGCAA
AAAATGACCCGAAAAGTTTTTCCTAAATTTTTTGCTAGAATACTCAGAAAAAATATGTAATTCAA
CGCCAAAAAAATTGAAGTTT
Found at i:122710 original size:200 final size:200
Alignment explanation
Indices: 122367--122737 Score: 496
Period size: 200 Copynumber: 1.9 Consensus size: 200
122357 CGTGATGGTT
* *
122367 AGTAAACGATTTCGGCTAAAATTTTGCAAAAAATAGACCCGAAAAGTTTTTCCTAAATTTTTTGC
1 AGTAAACGATTTCGACTAAAATTTTGCAAAAAATAGACCCGAAAAGTTTTTACTAAATTTTTTGC
* * ** * * * *
122432 TAGAATACTCAGAAAAAATATGTAATTCAACGCCAAAAAAATTGAAGGGTCTTTAACGCTTCGAT
66 GACAATACAAAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTCTTTAACACCTCGAA
*
122497 TATCGTTTTTCCTT-TTTTTCCCCGAATTTATTTCTAATTAAATCGAAAGTATATTCAGAAAACC
131 TATCGTTTTTCCTTATTTCT-CCCGAATTTATTTCTAATTAAATCGAAAGTATATTCAGAAAACC
122561 ATGATG
195 ATGATG
* * ** *
122567 AGTAAACGATTTCGACTAAAATTTTGCAAAAACT-GACCTGAAACTTTTTTACTCAATTTTTTGC
1 AGTAAACGATTTCGACTAAAATTTTGCAAAAAATAGACCCGAAAAGTTTTTACTAAATTTTTTGC
* * * *
122631 GACAATACAAAGAAAAAAATATATAATTCGACGCCAAAAAAATTGACGGGT-TTCTCACACCTCT
66 GACAATACAAAG-AAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTCTT-TAACACCTCG
**
122695 AATATCGTTTTTCCTTATTTCTCTTGAATTTATTTCTAATTAA
129 AATATCGTTTTTCCTTATTTCTCCCGAATTTATTTCTAATTAA
122738 TTAAATCGCG
Statistics
Matches: 146, Mismatches: 22, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
199 35 0.24
200 107 0.73
201 4 0.03
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (200 bp):
AGTAAACGATTTCGACTAAAATTTTGCAAAAAATAGACCCGAAAAGTTTTTACTAAATTTTTTGC
GACAATACAAAGAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGTCTTTAACACCTCGAA
TATCGTTTTTCCTTATTTCTCCCGAATTTATTTCTAATTAAATCGAAAGTATATTCAGAAAACCA
TGATG
Done.