Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015433.1 Corchorus olitorius cultivar O-4 contig15466, 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: 118896
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:458 original size:2 final size:2
Alignment explanation
Indices: 451--485 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
441 TGAATTGTTT
451 TA TA TA TA TA 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 TA TA T
486 TTACAGACCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:3650 original size:31 final size:31
Alignment explanation
Indices: 3615--3675 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
3605 TAGTTCACCA
3615 ATCATTTTCCAGCAGCTGGGGAAAATTTATC
1 ATCATTTTCCAGCAGCTGGGGAAAATTTATC
3646 ATCATTTTCCAGCAGCTGGGGAAAATTTAT
1 ATCATTTTCCAGCAGCTGGGGAAAATTTAT
3676 GGGCTGCATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.30, C:0.18, G:0.20, T:0.33
Consensus pattern (31 bp):
ATCATTTTCCAGCAGCTGGGGAAAATTTATC
Found at i:3993 original size:31 final size:31
Alignment explanation
Indices: 3934--4038 Score: 158
Period size: 31 Copynumber: 3.4 Consensus size: 31
3924 ACAGTGTCCT
* * *
3934 ACGTGGCATGTCATGTG-TACCAAAAGTGAC
1 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
3964 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
* *
3995 ACATGGTATGCCATGTGTTTCAAAAAGTGAC
1 ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
4026 ACGTGGCATGCCA
1 ACGTGGCATGCCA
4039 CGTGCACAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 1
0.89 0.09 0.01
Matches are distributed among these distances:
30 16 0.24
31 51 0.76
ACGTcount: A:0.30, C:0.20, G:0.26, T:0.25
Consensus pattern (31 bp):
ACGTGGCATGCCATGTGTTTCAAAAAGTGAC
Found at i:7266 original size:60 final size:60
Alignment explanation
Indices: 7201--7329 Score: 170
Period size: 60 Copynumber: 2.1 Consensus size: 60
7191 GATGTTTGTC
* * *
7201 AAAATGCTCAAATAAAGGCCCGATCTCTTAATTTGGCTAAATAAG-AGCCTAATATTATCT
1 AAAATGCTCAAATAAAGGCCCGATCTCTTAATTTGACCAAATAAGAAGCC-AATATTATCG
* * * * *
7261 AAAATGCTCAAATAAGGGTCTGATCTTTTAATTTGACCAAATAAGAATCCAATATTATCG
1 AAAATGCTCAAATAAAGGCCCGATCTCTTAATTTGACCAAATAAGAAGCCAATATTATCG
7321 AAAATGCTC
1 AAAATGCTC
7330 GGGTCTAACA
Statistics
Matches: 60, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
60 57 0.95
61 3 0.05
ACGTcount: A:0.40, C:0.17, G:0.13, T:0.30
Consensus pattern (60 bp):
AAAATGCTCAAATAAAGGCCCGATCTCTTAATTTGACCAAATAAGAAGCCAATATTATCG
Found at i:19699 original size:36 final size:36
Alignment explanation
Indices: 19593--19702 Score: 166
Period size: 36 Copynumber: 3.1 Consensus size: 36
19583 CGAACCTCCA
* * *
19593 GAGCTTTGGTTTCCTTCAGAATTAGCATTTGAAGAT
1 GAGCTTTGGGTTCCTTCAGAATTAGCTTTTGATGAT
* *
19629 GAGCTTTGGGTTCCCTCAGAATTAGCTTTCGATGAT
1 GAGCTTTGGGTTCCTTCAGAATTAGCTTTTGATGAT
*
19665 GAGCTTTGGGTTCCTTCAGAATTAGTTTTTGATGAT
1 GAGCTTTGGGTTCCTTCAGAATTAGCTTTTGATGAT
19701 GA
1 GA
19703 AGATGATTTC
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.22, C:0.15, G:0.25, T:0.39
Consensus pattern (36 bp):
GAGCTTTGGGTTCCTTCAGAATTAGCTTTTGATGAT
Found at i:23299 original size:333 final size:331
Alignment explanation
Indices: 22650--28664 Score: 7179
Period size: 333 Copynumber: 18.1 Consensus size: 331
22640 AATCTCTTCT
* * * ** * *
22650 ACGATTTCAGCTAAAATTTTGC-AGAAAATGATCTGAAAAATA-ATCCTCAATTTTTGGCCACAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATATTTCCTCAATTTTT-GACACAA
* ** * * * **
22713 CAAAAAGAAAAAATATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTTAAGCATCTACTATTG
65 TAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATATCA
* * * *
22778 CTTTTCCTATTTTTTCTAAATTAATTTTTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAA
129 CTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAA
* * * *
22843 CAAATCCTTAAATCCAATGTGACCAAGATTTGGTTAGATAAATATAGATACTTT-ATGGAGTCTG
194 CAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATA-TTTCATGGAGTCTG
* * * *
22907 GGCACCAAAAATCAAGCAAAACTGAGTCGGGG-TCTCAGAATGCGTTTTTAGCCAAAAACCGTAA
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTC-CGGAACGCGTTTTTAGCCAAAAACCGTGA
22971 TGGTTAGTAC
322 TGGTTAGTAC
* *
22981 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCAAAAAATTTTTCCTCAATTTTTGGACACAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATATTTCCTCAATTTTT-GACACAA
*
23046 TAATCAGAAAAAATATATAATTCAACGCCAAACAA-ATTGAAGGGCTTTTCAAGCATCTGATATC
65 TAATCAGAAAAAATATATAATTCAACGCCAAA-AAGATTGAA-GGCTTTTCAAGCATCTAATATC
** * * * *
23110 GGTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAA
128 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAA
** * * *
23175 ACAAATCCCTAAACCCCATGTGGCCGAGATTCGGTTAGATGAATATAGATATTTCATGGAGTCTG
193 ACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTG
* *** *
23240 GGCGCCAAAAATCAAGCAAAACTAAGAAAGGGCTCCGGAACGCATTTTTAGCCAAAAACCGTGAT
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
23305 GGTTAGTAC
323 GGTTAGTAC
* * *
23314 ACGATTTCGGGTAAAATTTTGCAAAAAAA-GATCCGAAAAATATTTCCTCAATTTTTGACCACAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATATTTCCTCAATTTTTGA-CACAA
* * * * * ** * *
23378 TTATCAG-AAATATATATAATACAATGCCAAAAATATTGAAGTATTTTGCGAGCATCTAATATCG
65 TAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTT-CAAGCATCTAATATCA
* * * * * *
23442 TTTTTCCTATTTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCTGATGCTCGTTAAAA
129 CTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAA
* * * * ** *
23507 CAAATCCTTAAATCCAATGTGGCCGAGATTTGATTAGATGGATATAGTTATTTCACCGACTCTGG
194 CAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTGG
* * *
23572 GTGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCTGGAATGCGTTTTTAGCCAAAAACCGTGATG
259 GCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATG
*
23637 ATTATTAGTAC
324 ---GTTAGTAC
* * * *
23648 ACGATTTCAGCTAAAATTTTAC-AAAAAATG--CTCCAAAAAGTTTTTCCTCAATTTTTGACCTC
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAAC-CCAAAAA-TATTTCCTCAATTTTTGA-CAC
* * **
23710 AATACTCATAAAAAATATTTATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCGCGCATCTAAT
63 AATAATCAGAAAAAATA--TATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAAT
* ** * * * * * *
23775 AT-AGTTTTCCTTTTTTTTTTTCCGAATTAATTTCTAATTAAATAGAAACAAGATTTAGATGCTC
125 ATCACTTTTCCTAATTTTTCTT---AATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTC
* ** * * * * *
23839 GTAAAAACAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGCATATATATGTATCAAGG
187 GTAAAAACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGG
* ** * *
23904 AGTCTAGGCGCCAAAAATCAAGCAAAACT-AAACTGGGGC-CACGGAACGTGTTTTAAGCCAAAA
252 AGTCTGGGCGCCAAAAATCAAGCAAAACTGAGTC-GGGGCTC-CGGAACGCGTTTTTAGCC-AAA
* *
23967 AACCGTAATGGTTAGTAA
314 AACCGTGATGGTTAGTAC
* * *
23985 ACGATTTCAGCTAAAATTTTGCATAAAAATG-ACCCAAAAAATTTTTCCTCAATTTTTGGACACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCC-AAAAATATTTCCTCAATTTTT-GACACA
* * *
24049 ATAATCAGAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCAAGTATCTATTATC
64 ATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATATC
* *
24114 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATC-AAACCATGATTCTGATGCTCTTAAA
128 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAA-CATGATTCAGATGCTCGTAAA
* * * * *
24178 AAGAAATATTTAAATCCAATGTGGCCGAGATTCGGTTAGATGAATATAGATATTTCATGAAGTCC
192 AACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCT
* * * *
24243 GGGTGCCAAAAATCAAGAAAAACTGAGTTGGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
257 GGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGA
*
24308 -----CGTAC
322 TGGTTAGTAC
* * ** *
24313 ACAATATCGGCTAAAATTTTGCAAAACAAAAAAATCCCAAAAATATTTCCTCAATTGTTAT-CCA
1 ACGATTTCGGCTAAAATTTTGCAAAA-AAATGAA-CCCAAAAATATTTCCTCAATT-TT-TGACA
* * * * ** *
24377 CAATTATCAGAAAAATATATATAATACAACGCTAAAAATATTGAAGAATTTTGCGAGCATCTAAT
62 CAATAATCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGCTTTT-CAAGCATCTAAT
** * ** * * *
24442 ATCGTTTTTCCTATTTTTTCGGAATTAATTTCTGATTAAATCGAACCATGATTCAGATGCTCGTT
125 ATCACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTA
* ** *
24507 AAAACAAAT-TATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATATAGATAATTCATGGAG
190 AAAACAAATCT-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAG
* * *
24571 TCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGAAACGCGTTTTTAGCCAAAAACTG
254 TCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCG
* *
24636 TGAT-GTAACATAC
319 TGATGGTTA-GTAC
* * *
24649 AGGATTTCGGCTAAAATTTTGCATAAAAAT-TACCCAAAAAATATTTCCTCAATTTTTGGACACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCC-AAAAATATTTCCTCAATTTTT-GACACA
* *
24713 ATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTCCAAGCATCTAAGATC
64 ATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATATC
* *
24778 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAACCATGATTCGGATGCTCGTAAAA
128 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAA
* *
24843 AGAAATCTTTAAATCCAATGTGGCCGAGATTCGGTTAGATGAATATAGATATTTCATGGAGTCTG
193 ACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTG
* *
24908 GGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
24973 GGTTAGTAC
323 GGTTAGTAC
*
24982 ACGATTTCGGCTAAAATTTTGCAAAAAAA-GATCCCAAAAATATTTCCTCAATTTTTGACCACAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATATTTCCTCAATTTTTGA-CACAA
* * ** * ** *
25046 TTATCAGAAAAAA-AAATAACACAACGCCAAAAATATTGAAGAATTTTGCGAGCATCTAATATC-
65 TAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTT-CAAGCATCTAATATCA
* * * *
25109 CTTTTTACT-ATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAGAA
129 C-TTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAA
* ** * * * *
25173 ACAAAT-TATGAAATCCTTTTTGGCCCAAATTTGGTTAGATGAATATAGATAATTCATGGAGTCT
193 ACAAATCT-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCT
* * *
25237 GGGCGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGA
257 GGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGA
*
25302 TGATTAGTAC
322 TGGTTAGTAC
* * * * * *
25312 ATGATTTCGGCTAAAATTTTGCATAAAACTG-ACCAAAAAAATTTTTCCTCAATTTTTGGCCACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACC-CAAAAATATTTCCTCAATTTTT-GACACA
* * *
25376 ATAATCAGAAAAAGTATATAATTTAACGCCAAAAAGATTGAATGGCTTTTCAAGCATGTAATATC
64 ATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATATC
* * * * * * *
25441 AATTTTCCTTATATTTCTTAATGAATTTCTGATTAAATCGAACCACGATTCGGATGCTCAT-AAA
128 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAA
* ** *
25505 AGAAATCTTTAAATCCAATGTGGCCGAGATTCAGTTAGATAAATATAGATATTTCATGGAGTCTG
193 ACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTG
* * *
25570 GGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTAAGCCAAAAACCGTGAT
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
*
25635 GGTTGGTAC
323 GGTTAGTAC
*
25644 ACGATTTCGGCTAAAATTTTGCAAAAAAA-AAATCCCAAAAATATTTCCTCAATTTTTGACTACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAA-CCCAAAAATATTTCCTCAATTTTTGAC-ACA
* * * * * * ** * * *
25708 ATTATCAGAATAATATATATGATACAATGCCAAAAATATTGAAGAATTTTGAGACCATCTAAGAT
64 ATAATCAGAA-AAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCA-AGCATCTAATAT
25773 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGAAT-CTCGTAA
127 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAG-ATGCTCGTAA
* * * * *
25837 AAACAAAT-TATGAAATCCATTGTGGCCGAGATTTGGTTAGTTGAATATAGATAATACATGGAGT
191 AAACAAATCT-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGT
* * *
25901 CTGGACGCCAAAAATCAGGCAAAACTAAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGT
255 CTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
25966 AATGATTGGTAC
320 GATGGTTAGTAC
*
25978 ACGATTTCGGCTAAAATTTTGCAAAAAAA-AAATCCCAAAAATATTTCCTCAATTTTTGACTACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAA-CCCAAAAATATTTCCTCAATTTTTGAC-ACA
* * * * ** * *
26042 ATTATCAGAAAAATATATATGATTCAATGCCAAAAATATTGAAGAATTTTGAGAGCATCTAAGAT
64 ATAATCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCA-AGCATCTAATAT
* * * *
26107 CACATTTCCTAATTTTTCTTAATCAATTTGTGATTAAATCGAAACATGATTCAGAAGCTCGTAAA
127 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAA
* * * * * *
26172 AACAAAT-TATGAAATCC-TTTTAGGCCGAGATTTGGTTAGATAAATATAGATAATTGATGGAGT
192 AACAAATCT-TTAAATCCAATGT-GGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGT
* * * ** *
26235 CTAGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCGTAACGCGTTTTTAATCAAAAACTGT
255 CTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGT
*
26300 GATGGTTAGTAT
320 GATGGTTAGTAC
* ** * * *
26312 ATGATTTCGGCTAAAATTTTG-AATAAAAATG-ACCC-AATTTTTTTTCTCAATTTTTGGCCACA
1 ACGATTTCGGCTAAAATTTTGCAA-AAAAATGAACCCAAAAATATTTCCTCAATTTTT-GACACA
*
26374 ATAATCAGAAAAAGTATATAATTCAACGCCAAAAAGATTGAATGGCTTTTCAAGCATCTAATATC
64 ATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATATC
* * * * * *
26439 ACTTTTCCTTATATTTCTTAATGAATTTCTGATTAAATCGAACCACGATTCGGATGCTCATAAAA
128 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAA
* ***
26504 AGAAATCTTTAAATCCAATGTGGCCGAGATGCAGTTAGATGAATATAGATATTTCATGGAGTCTG
193 ACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTG
* * * *
26569 GGTGACAAAAATCAAGCAAAATTGAGTCGGGGCTCCGGAACGCGGTTTTAGCCAAAAACCGTGAT
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
*
26634 GGTTGGTAC
323 GGTTAGTAC
**
26643 ACGATTTCGGCTAAAATTTTGCAAAAAAAAAAATCCCAAAAATATTTCCTCAATTTTTGACTACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAA-CCCAAAAATATTTCCTCAATTTTTGAC-ACA
* * ** * * ** * *
26708 ATTATCAGAAAAATATATATGATAAAATGCCAAAAATATTGAAGAATTTTGAGAGCATCTAAGAT
64 ATAATCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCA-AGCATCTAATAT
* * *
26773 CACTTTTCCTAGTTTTTCTTAATGAATTTATGATTAAATCGAAACATGATTCAGAAGCTCGTAAA
127 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAA
* * * * *
26838 AACAAAT-TCTGAAATCCATTGTGGCCGAGATTTGGTTAGTTGAATATAGATAATACATGGAGTC
192 AACAAATCT-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTC
* * * * * * *
26902 TGGACGCCAAAAATCAGGCAAAATTGAGTCGGGGCTTCAGAATGCGTTTTTAGCCAAAAACTGTG
256 TGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTG
26967 ATGGTT-GTTAC
321 ATGGTTAG-TAC
* * *
26978 ACGATTTCGGCTAAAATTTTGCATAAAAATG-ACCCAAAAAATTTTTCCTCAATTTTTGGCCACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCC-AAAAATATTTCCTCAATTTTT-GACACA
*
27042 ATAATCAG-AAAAATATATAATTCAACGCCAAAAAGATTGATGGGCTTTTCAAGCATCTAATATC
64 ATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA-AGGCTTTTCAAGCATCTAATATC
* * * * *
27106 ACTTTTCCTAATATTTCTTAATGAATTTCAGATTAAATCGAACCATGATTCGGATGCTCAT-AAA
128 ACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAA
* ***
27170 AGAAATCTTTAAATCCAATGTGGCCGAGATGCAGTTAGATGAATATAGATATTTCATGGAGTCTG
193 ACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTG
* * *
27235 GGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGGTTTTAGCCAAAAACCGTGAT
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
*
27300 GGTTGGTAC
323 GGTTAGTAC
*
27309 ACGATTTCGGCTAAAATTTTGCAAAAAAA--AATCCCAAAAATACTTCCTCAATTTTTGACTACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAA-CCCAAAAATATTTCCTCAATTTTTGAC-ACA
* * * * ** ** * *
27372 ATTATCAGAAAAATATATATGATACAATGCCAAAATTATTGAAGAATTTTGAGAGCATCTAAGAT
64 ATAATCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCA-AGCATCTAATAT
*
27437 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGAAGCTCGTAAA
127 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAA
* * * * * *
27502 AACAAAT-TATGAAATCCATTGTGGACGAGATTTGGTTAGATGAATATAGATAATTCTTGGTGTC
192 AACAAATCT-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTC
* * * * *
27566 TAGACGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTG
256 TGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTG
*
27631 ATGGTTATTAC
321 ATGGTTAGTAC
* *
27642 ACGATTTCGGCTAAAATTTTGCATAAAAATG-ACCCAAAAA-ATTTTACCTCAATTTTTCGCCAC
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATA-TTT-CCTCAATTTTT-GACAC
*
27705 AATAATCAGAAAAAGTATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATAT
63 AATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATAT
* * * * *
27770 CACTTTTCCTAATATTTCTTAATGAATTTCTGATCAAATCGAACCATGATTCGGATGCTCATAAA
127 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAA
* **
27835 AAGAAATCTTTAAATCCAATGTGGCCGAGATTCAGTTAGATGAATATAGATATTTCATGGAGTCT
192 AACAAATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCT
* *
27900 GGGTGACC-AAAATCAAGCAAAACTGAGTCGGGTC-CTCGGAACGCGTTTTTAGCCAAAAACCGT
257 GGGCG-CCAAAAATCAAGCAAAACTGAGTCGGGGCTC-CGGAACGCGTTTTTAGCCAAAAACCGT
*
27963 GATGGTTGGTAC
320 GATGGTTAGTAC
* *
27975 ACGATTTCGGCTAAAATTTTGCAAAAAAA-AAATCCCAAAAATATTTCCTCAATTTTTTACCACA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAA-CCCAAAAATATTTCCTCAATTTTTGA-CACA
* * * * ** * *
28039 ATTATCAGAAAAATATATATAATACAATGCCAAAAATATTGAAGAATTTTGAGAGCATCTAACAT
64 ATAATCAGAAAAA-ATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCA-AGCATCTAATAT
*
28104 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGAAGCTCGTAAA
127 CACTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAA
* ** *
28169 AACAAAT-TATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATATAGATAATTCATGGAGTC
192 AACAAATCT-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTC
* *
28233 TGGGCG-CAAGAAATCAAGCAAAACTGAGTC-GGGCCCCGGAACGCATTTTTAGCCAAAAA-C-T
256 TGGGCGCCAA-AAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGT
28294 G-T-G--ACGTAC
320 GATGGTTA-GTAC
* * *
28303 ACGATTTCGGCTAAAATTTTGCATAAAAATG-ACCCAAAAATTTTTCCTCAATTTTTGGCCACAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATATTTCCTCAATTTTT-GACACAA
* *
28367 TAATCAGAAAAGATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCAAGCATCTAATATCA
65 TAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAA-GGCTTTTCAAGCATCTAATATCA
* * * *
28432 CTTTTCCTAATATTTCTTAATGAATTTCTGATTAAATCGAAGCATGATTCGGATGCTCATAAAAA
129 CTTTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAA
* ***
28497 GAAATCTTTAAAATCCAATGTGGCCGAGATGCAGTTAGATGAATATAGATATTTCATGGAGTCTG
194 CAAATCTTT-AAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTG
* *
28562 GGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
258 GGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGAT
*
28627 GGTTGGTAC
323 GGTTAGTAC
28636 ACGATTTCGGCTAAAATTTTGCAAAAAAA
1 ACGATTTCGGCTAAAATTTTGCAAAAAAA
28665 AAATCCCAAA
Statistics
Matches: 4874, Mismatches: 673, Indels: 272
0.84 0.12 0.05
Matches are distributed among these distances:
326 103 0.02
327 117 0.02
328 88 0.02
329 8 0.00
330 285 0.06
331 922 0.19
332 552 0.11
333 1211 0.25
334 972 0.20
335 252 0.05
336 82 0.02
337 78 0.02
338 50 0.01
339 142 0.03
340 12 0.00
ACGTcount: A:0.37, C:0.16, G:0.16, T:0.30
Consensus pattern (331 bp):
ACGATTTCGGCTAAAATTTTGCAAAAAAATGAACCCAAAAATATTTCCTCAATTTTTGACACAAT
AATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGCTTTTCAAGCATCTAATATCACT
TTTCCTAATTTTTCTTAATGAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGTAAAAACA
AATCTTTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATATTTCATGGAGTCTGGGC
GCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGT
TAGTAC
Found at i:29127 original size:510 final size:498
Alignment explanation
Indices: 28168--29178 Score: 1668
Period size: 511 Copynumber: 2.0 Consensus size: 498
28158 AAGCTCGTAA
*
28168 AAACAAATTATGAAATCCTTTGTGGCCGAGATTTGGTTAGATGAATATAGATAATTCATGGAGTC
1 AAACAAATTATGAAATCCTTTGAGGCCGAGATTTGGTTAGATGAATATAGATAATTCATGGAGTC
*
28233 TGGGCGCAAGAAATCAAGCAAAACTGAGTCGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGA
66 TAGGCGCAAGAAATCAAGCAAAACTGAGTCGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGA
* *** *
28298 CGTACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAATTTTTCCTCAATTTTTGGCC
131 AGTACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAACATTCCACAATTTTTGGCC
28363 ACAATAATCAGAAAAGATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCAAGCATCTAAT
196 ACAATAATCAGAAAAGATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCAAGCATCTAAT
* *
28428 ATCACTTTTCCTAATATTTCTTAATGAATTTCTGATTAAATCGAAGCATGATTCGGATGCTCATA
261 ATCACTTTTCCTAATATTTCTTAATGAATTTCTAATTAAATCGAACCATGATTCGGATGCTCATA
* *
28493 AAAAGAAATCTTTAAAATCCAATGTGGCCGAGATGCAGTTAGATGAATATAGATATTTCATGGAG
326 AAAAGAAATCTGTAAAATCCAATGTGGCCGAGATGCAGTTAGATGAATAAAGATATTTCATGGAG
28558 TCTGGGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCG
391 TCTGGGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCG
**
28623 TGATGGTTGGTACACGATTTCGGCTAAAATTTTGCAAAAAAAAAATCCC
456 T-A----ACGTACACGATTTCGGCTAAAATTTTGC-AAAAAAAAATCCC
*
28672 AAACAAATTATGAAATCCTTTGAGGCCGAGATTTGGTTAGATGAATATAGATAATTGATGGAGTC
1 AAACAAATTATGAAATCCTTTGAGGCCGAGATTTGGTTAGATGAATATAGATAATTCATGGAGTC
*
28737 TAGGCGCCAA-AAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACTGT
66 TAGGCG-CAAGAAATCAAGCAAAACTGAGTCG-GGCCCCGGAACGCATTTTTAGCCAAAAACTGT
*
28801 GATGGTTAGTACATGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAACATTCCACAAT
129 GA-----AGTACACGATTTCGGCTAAAATTTTGCATAAAAATGACCC-AAAAAACATTCCACAAT
* *
28866 TTTTGGCCACAATAATCAGAAAA-AGTATATAATTCAACGCCAAAAAGATTGAATGGCTTTTCAA
188 TTTTGGCCACAATAATCAGAAAAGA-TATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCAA
28930 GCATCTAATATCACTTTTCCTAATATTTCTTAATGAATTTCTAATTAAATCGAACCATGATTCGG
252 GCATCTAATATCACTTTTCCTAATATTTCTTAATGAATTTCTAATTAAATCGAACCATGATTCGG
* *
28995 ATGCTCGTAAAAAGAAATCTGT-AAATCCAATGTGGCCGAGATTCAGTTAGATGAATAAAGATAT
317 ATGCTCATAAAAAGAAATCTGTAAAATCCAATGTGGCCGAGATGCAGTTAGATGAATAAAGATAT
*
29059 TTCATGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGC
382 TTCATGGAGTCTGGGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGC
*
29124 CAAAAACCGTAACGTACACGATTTCGGCTAAAATTTTGCAAAAAAAGATCCC
447 CAAAAACCGTAACGTACACGATTTCGGCTAAAATTTTGCAAAAAAAAATCCC
29176 AAA
1 AAA
29179 AATATTTCCT
Statistics
Matches: 476, Mismatches: 22, Indels: 18
0.92 0.04 0.03
Matches are distributed among these distances:
504 104 0.22
505 62 0.13
509 1 0.00
510 153 0.32
511 156 0.33
ACGTcount: A:0.37, C:0.17, G:0.19, T:0.27
Consensus pattern (498 bp):
AAACAAATTATGAAATCCTTTGAGGCCGAGATTTGGTTAGATGAATATAGATAATTCATGGAGTC
TAGGCGCAAGAAATCAAGCAAAACTGAGTCGGGCCCCGGAACGCATTTTTAGCCAAAAACTGTGA
AGTACACGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAACATTCCACAATTTTTGGCC
ACAATAATCAGAAAAGATATATAATTCAACACCAAAAAGATTGAAGGGCTTTTCAAGCATCTAAT
ATCACTTTTCCTAATATTTCTTAATGAATTTCTAATTAAATCGAACCATGATTCGGATGCTCATA
AAAAGAAATCTGTAAAATCCAATGTGGCCGAGATGCAGTTAGATGAATAAAGATATTTCATGGAG
TCTGGGTGACAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCG
TAACGTACACGATTTCGGCTAAAATTTTGCAAAAAAAAATCCC
Found at i:30026 original size:331 final size:327
Alignment explanation
Indices: 28672--30749 Score: 2055
Period size: 331 Copynumber: 6.3 Consensus size: 327
28662 AAAAAATCCC
* ** * * *
28672 AAACAAATTATGAAATCCTTTGAGGCCGAGATTTGGTTAGATGAATATAGATAATTGATGGAGTC
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATTATTCATGGAGTC
* * *
28737 TAGGCGCCAAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTG
66 TGGGCGCCAAAAATCAAGCAAAACTGAGTCG-GGGCCCGGAACGCGTTTTTAGCCAAAAACCGTG
* * * *
28802 ATGGTTAGTACATGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAACATTCCACAA-T
130 AT-G--AGTACACGATTTCGGCTAAAATTTTACA-AAAAATGACCCAAAAAAATATTCCTCAATT
* * *
28866 TTTTGGCCACAATAATCAGAAAAA-GTATATAATTCAACGCCAAAAAGATTGAATGGCTTTTCAA
191 TTTTGACCACAAT-ATCAGAAAAATATATATAATTCAACGCCAAAAAGATTGAA-GGATTTTCAA
* * * * * *
28930 GCATCTAATATCACTTTTCCTAATATTTCTTAATGAATTTCTAATTAAATCGAACCATGATTCGG
254 GCATCTAATATCACTTTTCCT-ATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAG
28995 ATGCTCGTAA
318 ATGCTCGTAA
* * ** *
29005 AAAGAAATCT-GTAAATCCAATGTGGCCGAGATTCAGTTAGATGAATAAAGA-TATTTCATGGAG
1 AAACAAAT-TATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATTA-TTCATGGAG
*
29068 TCTGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCCAAAAACCG
64 TCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGC-CCGGAACGCGTTTTTAGCCAAAAACCG
* * *
29133 T-A--ACGTACACGATTTCGGCTAAAATTTTGCAAAAAAAGATCCCAAAAATAT-TTCCTCAA-T
128 TGATGA-GTACACGATTTCGGCTAAAATTTTACAAAAAATGA-CCCAAAAAAATATTCCTCAATT
* * * *
29193 TTTTGACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAATTTTGAGA
191 TTTTGACCACAA-TATCAGAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGATTTTCA-A
** * *
29258 GCATCTAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTGATTAAATCGAAACATGATTCTGA
254 GCATCTAATATCACTTTTCCTATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGA
*
29323 TGCTCGTTA
319 TGCTCGTAA
* * * ** *
29332 AAACAAATCT-TTAAATCCAATGTGGCCGAGATTTGATTTGATGGATATAG-TTGATTCATCAAC
1 AAACAAAT-TATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATT-ATTCATGGAG
* * * *
29395 TCTGGGTGCCAAAAATCAAACAAAACTGAGTCGGGGCTTCGGAACGCATTTTTAGCCAAAAACCG
64 TCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGC-CCGGAACGCGTTTTTAGCCAAAAACCG
* ** * *
29460 TGAT--G---ACGATTTCGGTTAAAATTTTACAAAAAATGACCCAAAAAGTTTTTCCT-AAATTT
128 TGATGAGTACACGATTTCGGCTAAAATTTTACAAAAAATGACCCAAAAAAATATTCCTCAATTTT
* * * **
29519 TTGACCTCAATACTCATAAAAGAATATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCGC
193 TTGACCACAATA-TCA-GAAA-AATATATATAATTCAACGCCAAAAAGATTG-AAGGATTTTCAA
** * * * * * * *
29584 GCATCTAATATCATTCTTCTATTTTTTTTTTCCGAAATAATTTCTAATTTAATGGAAACAAGATT
254 GCATCTAATATCA--CTT-T-TCCTATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATT
* *
29649 TACATGCTCGTAA
315 CAGATGCTCGTAA
** * ** * * *
29662 AAACAAATCCTTAAATTCAATGTGGTTGAGATTTGGTTAGATGCATATATATGTA-TCAAGGAGT
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGAT-TATTCATGGAGT
* * * * * * *
29726 CTCGGCACCAAAAATCAATCAAAACTAAG-CTGGGGCCATGGAACGCATTTTTAGTCAAAAAACC
65 CTGGGCGCCAAAAATCAAGCAAAACTGAGTC-GGGGCC-CGGAACGCGTTTTTAG-CCAAAAACC
* * * * *
29790 GTTATGGTTAGTAAACTATTTCGGCTAAAATTTTACAGAAAATGA-CCAAAAAAATAATCCTCAA
127 GTGAT-G--AGTACACGATTTCGGCTAAAATTTTACAAAAAATGACCCAAAAAAATATTCCTCAA
* * *
29854 TTTTTTG-CCACAATACTTAGAAAAA-ATATATAATTCAATGTCAAAAAGATTGAAGGATTTTCA
189 TTTTTTGACCACAATA-TCAGAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGATTTTCA
** * *
29917 AGCATCTAATATTGCTTTTCCTATTTAATCTGAATTAATTTCTGATTAAATTGAAACATGATTCA
253 AGCATCTAATATCACTTTTCCTATTT-TTCTGAATTAATTTCTGATTAAATCGAAACATGATTCA
*
29982 AATGCTCGTAA
317 GATGCTCGTAA
** * *
29993 AAACAAATTATTAAATCCCTTGTGGCCGAGATTTGG--AGATGAATATAGATAATTCATGGCGTC
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATTATTCATGGAGTC
* * * *
30056 TGGGCGTCAAAAATCAAGCAAAACTAAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTG
66 TGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGG-CCCGGAACGCGTTTTTAGCCAAAAACCGTG
* * * * * *
30121 ATGATTAGTTATCGATTTCGGCTAATATTTTGCATAAAAATGACCC-ATAAAATTTATCCTCAAT
130 ATGAGTA--CA-CGATTTCGGCTAAAATTTTACA-AAAAATGACCCAAAAAAATAT-TCCTCAAT
* * * *
30185 TTTTTG-CCACAATAAACAGAAAAA-ATATATAATTTAACGCCAAAAAGATTGAAGGGCTCTTCA
190 TTTTTGACCACAAT-ATCAGAAAAATATATATAATTCAACGCCAAAAAGATTGAA-GGATTTTCA
* * * * * *
30248 AGCATCTAATATCATTTTTCCTAATTTTTCTTAATCAATTTCTGATTAAATTGAACCATGATTCG
253 AGCATCTAATATCACTTTTCCT-ATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCA
30313 GATGCTCGTAA
317 GATGCTCGTAA
* * * *
30324 AAAGAAA-TATTTAAATCCAATGTGGCCGAGATTCGATTAGATGAATATAGA-TATTTCATGGAA
1 AAACAAATTA-TTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATTA-TTCATGGAG
* * * *
30387 TCCGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGATCCCGGAACGCGTTTTTAGCAAAAAACCG
64 TCTGGGCGCCAAAAATCAAGCAAAACTGAGTCGGG-GCCCGGAACGCGTTTTTAGCCAAAAACCG
* ** *
30452 TGATG-GTACACGATTTCGACTAAAATTTTACAAAAAAAAAATCCCAAAAATAT-TTCCTCAA-T
128 TGATGAGTACACGATTTCGGCTAAAATTTTAC-AAAAAATGA-CCCAAAAAAATATTCCTCAATT
* * * *
30514 TTTTGACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAATTTTTGCG
191 TTTTGACCACAA-TATCAGAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGA-TTTT-CA
* *
30579 AGCATCTAATATCATTTTTCCTATTTTTTCTAAATTAATTTCTGATTAAATCGAAACATGATTCT
253 AGCATCTAATATCACTTTTCCTA-TTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTC-
* *
30644 A-ATGCTCATTA
316 AGATGCTCGTAA
** * * * *
30655 AAACAAATCCTTAAATCCAATGTGACCGAGATTTGGTTAGATGGATATAG-TTATTTCATGTACT
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATTA-TTCATGGAGT
* * *
30719 CTGGGTGCCAAAAACCAAGCAAAACTAAGTC
65 CTGGGCGCCAAAAATCAAGCAAAACTGAGTC
30750 AGGACTTCGG
Statistics
Matches: 1447, Mismatches: 231, Indels: 136
0.80 0.13 0.07
Matches are distributed among these distances:
323 13 0.01
324 48 0.03
325 6 0.00
326 40 0.03
327 210 0.15
328 123 0.09
329 123 0.09
330 236 0.16
331 335 0.23
332 16 0.01
333 187 0.13
334 21 0.01
335 25 0.02
336 3 0.00
337 3 0.00
338 22 0.02
339 36 0.02
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (327 bp):
AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTTAGATGAATATAGATTATTCATGGAGTC
TGGGCGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCGGAACGCGTTTTTAGCCAAAAACCGTGA
TGAGTACACGATTTCGGCTAAAATTTTACAAAAAATGACCCAAAAAAATATTCCTCAATTTTTTG
ACCACAATATCAGAAAAATATATATAATTCAACGCCAAAAAGATTGAAGGATTTTCAAGCATCTA
ATATCACTTTTCCTATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCAGATGCTCGT
AA
Found at i:30600 original size:662 final size:654
Alignment explanation
Indices: 28672--30749 Score: 2463
Period size: 662 Copynumber: 3.1 Consensus size: 654
28662 AAAAAATCCC
* ** * * *
28672 AAACAAATTATGAAATCCTTTGAGGCCGAGATTTGGTTAGATGAATATAGATAATTGATGGAGTC
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGG-TAGATGAATATAGATAATTCAT-GACTC
* * *
28737 TAGGCGCCAAAAATCAAGCAAAACTGAGTCGAGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTG
64 TGGGCGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTG
* *** *
28802 ATGGTTAGTA-CATGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAAAACATTCCACAAT
129 ATGATTAGTATC--GATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAATTTA-TCCTCAAT
* * *
28866 TTTTGGCCACAATAATCAGAAAAAGTATATAATTCAACGCCAAAAAGATTGAATGGCTTTTCAAG
191 TTTTTGCCACAATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCAAG
* *
28931 CATCTAATATCACTTTTCCTAATATTTCTTAATGAATTTCTAATTAAATCGAACCATGATTCGGA
256 CATCTAATATCATTTTTCCTAATTTTTCTTAAT-AATTTCTAATTAAATCGAACCATGATTCGGA
* *
28996 TGCTCGTAAAAAGAAATCTGTAAATCCAATGTGGCCGAGATTC-AGTTAGATGAATAAAGATATT
320 TGCTCGTAAAAAGAAATCTTTAAATCCAATGTGGCCGAGATTCGA-TTAGATGAATATAGATATT
* *
29060 TCATGGAGTCTGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGGCTCCGGAACGCGTTTTTAGCC
384 TCATGGAGTCCGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGGC-CCGGAACGCGTTTTTAGCA
** *
29125 AAAAACCGTAACGTACACGATTTCGGCTAAAATTTTGCAAAAAAAGATCCCAAAAATATTTCCTC
448 AAAAACCGTATGGTACACGATTTCGGCTAAAATTTTACAAAAAAAGATCCCAAAAATATTTCCTC
29190 AATTTTTGACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAATTTTG
513 AATTTTTGACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAATTTTG
* *
29255 AGAGCATCTAATATCGTTTTTCCTATTTTTTTGAATTAATTTCTGATTAAATCGAAACATGATTC
578 CGAGCATCTAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTC
*
29320 TGATGCTCGTTA
643 TAATGCTCGTTA
* * * * * *
29332 AAACAAATCT-TTAAATCCAATGTGGCCGAGATTTGATTTGATGGATATAGTTGATTCATCAACT
1 AAACAAAT-TATTAAATCCAATGTGGCCGAGATTTG-GTAGATGAATATAGATAATTCAT-GACT
* * * ** * *
29396 CTGGGTGCCAAAAATCAAACAAAACTGAGTCGGGGCTTCGGAACGCATTTTTAGCCAAAAAC--C
63 CTGGGCGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGT
* * * *
29459 G-TGA-T-G-A-CGATTTCGGTTAAAATTTTACA-AAAAATGACCCAAAAAGTTTTTCCT-AAAT
128 GATGATTAGTATCGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAA-TTTATCCTCAATT
* * *
29517 TTTTGACCTCAATACTCATAAAAGAATATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTC
192 TTTTG-CCACAATAATCA-GAAA-AA-ATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTC
** * * * * * * *
29582 GCGCATCTAATATCATTCTT-CTATTTTTTTTTTCCGAAATAATTTCTAATTTAATGGAAACAAG
253 AAGCATCTAATATCATTTTTCCTA-ATTTTTCTT----AATAATTTCTAATTAAATCGAACCATG
*** * * * ** * * *
29646 ATTTACATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGTTGAGATTTGGTTAGATGCATATA
313 ATTCGGATGCTCGTAAAAAGAAATCTTTAAATCCAATGTGGCCGAGATTCGATTAGATGAATATA
* * * * ** * * * *
29711 TATGTATCAAGGAGTCTC-GGCACCAAAAATCAATCAAAACTAAG-CTGGGGCCATGGAACGCAT
378 GATATTTCATGGAGTC-CGGGTGCCAAAAATCAAGCAAAACTGAGTC-GGGGCC-CGGAACGCGT
* * * *
29774 TTTTAGTCAAAAAACCGTTATGGTTAGTAAACTATTTCGGCTAAAATTTTACAGAAAATGA--CC
440 TTTTAG-CAAAAAACCG-TAT-G---GTACACGATTTCGGCTAAAATTTTACAAAAAAAGATCCC
* * * * * *
29837 AAAAAAATAATCCTCAATTTTTTG-CCACAA-TACTTAGAAAAA-ATATATAATTCAATGTCAAA
499 AAAAATAT-TTCCTCAA-TTTTTGACCACAATTA-TCAGAAAAATATATATAATACAACGCCAAA
* * * * * *
29899 AAGATTGAAGGATTTT-CAAGCATCTAATATTGCTTTTCCTATTTAATCTGAATTAATTTCTGAT
561 AATATTGAAGAATTTTGCGAGCATCTAATATCGTTTTTCCTATTT-TTCTGAATTAATTTCTGAT
* * *
29963 TAAATTGAAACATGATTCAAATGCTCGTAA
625 TAAATCGAAACATGATTCTAATGCTCGTTA
** *
29993 AAACAAATTATTAAATCCCTTGTGGCCGAGATTTGG-AGATGAATATAGATAATTCATGGCGTCT
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTAGATGAATATAGATAATTCATGAC-TCT
* *
30057 GGGCGTCAAAAATCAAGCAAAACTAAGTCGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGA
65 GGGCGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGA
*
30122 TGATTAGTTATCGATTTCGGCTAATATTTTGCATAAAAATGACCCATAAAATTTATCCTCAATTT
130 TGATTAG-TATCGATTTCGGCTAAAATTTTGCATAAAAATGACCCA-AAAATTTATCCTCAATTT
* * * *
30187 TTTGCCACAATAAACAGAAAAAATATATAATTTAACGCCAAAAAGATTGAAGGGCTCTTCAAGCA
193 TTTGCCACAATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCAAGCA
* *
30252 TCTAATATCATTTTTCCTAATTTTTCTTAATCAATTTCTGATTAAATTGAACCATGATTCGGATG
258 TCTAATATCATTTTTCCTAATTTTTCTTAAT-AATTTCTAATTAAATCGAACCATGATTCGGATG
*
30317 CTCGTAAAAAGAAATATTTAAATCCAATGTGGCCGAGATTCGATTAGATGAATATAGATATTTCA
322 CTCGTAAAAAGAAATCTTTAAATCCAATGTGGCCGAGATTCGATTAGATGAATATAGATATTTCA
* *
30382 TGGAATCCGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGATCCCGGAACGCGTTTTTAGCAAAA
387 TGGAGTCCGGGTGCCAAAAATCAAGCAAAACTGAGTCGGG-GCCCGGAACGCGTTTTTAGCAAAA
* *
30447 AACCGTGATGGTACACGATTTCGACTAAAATTTTACAAAAAAAAAATCCCAAAAATATTTCCTCA
451 AACCGT-ATGGTACACGATTTCGGCTAAAATTTTAC-AAAAAAAGATCCCAAAAATATTTCCTCA
30512 ATTTTTGACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAATTTTTG
514 ATTTTTGACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAA-TTTTG
* *
30577 CGAGCATCTAATATCATTTTTCCTATTTTTTCTAAATTAATTTCTGATTAAATCGAAACATGATT
578 CGAGCATCTAATATCGTTTTTCCTA-TTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATT
*
30642 CTAATGCTCATTA
642 CTAATGCTCGTTA
** * * * *
30655 AAACAAATCCTTAAATCCAATGTGACCGAGATTTGGTTAGATGGATATAGTTATTTCATGTACTC
1 AAACAAATTATTAAATCCAATGTGGCCGAGATTTGG-TAGATGAATATAGATAATTCATG-ACTC
* *
30720 TGGGTGCCAAAAACCAAGCAAAACTAAGTC
64 TGGGCGCCAAAAATCAAGCAAAACTAAGTC
30750 AGGACTTCGG
Statistics
Matches: 1164, Mismatches: 197, Indels: 110
0.79 0.13 0.07
Matches are distributed among these distances:
650 7 0.01
651 29 0.02
652 22 0.02
653 5 0.00
654 60 0.05
655 1 0.00
656 3 0.00
657 149 0.13
658 26 0.02
659 95 0.08
660 168 0.14
661 138 0.12
662 241 0.21
663 43 0.04
664 49 0.04
665 60 0.05
666 6 0.01
667 22 0.02
668 28 0.02
669 12 0.01
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.31
Consensus pattern (654 bp):
AAACAAATTATTAAATCCAATGTGGCCGAGATTTGGTAGATGAATATAGATAATTCATGACTCTG
GGCGCCAAAAATCAAGCAAAACTAAGTCGGGGCCCCGGAACGCGTTTTTAGCCAAAAACTGTGAT
GATTAGTATCGATTTCGGCTAAAATTTTGCATAAAAATGACCCAAAAATTTATCCTCAATTTTTT
GCCACAATAATCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGGCTTTTCAAGCATCT
AATATCATTTTTCCTAATTTTTCTTAATAATTTCTAATTAAATCGAACCATGATTCGGATGCTCG
TAAAAAGAAATCTTTAAATCCAATGTGGCCGAGATTCGATTAGATGAATATAGATATTTCATGGA
GTCCGGGTGCCAAAAATCAAGCAAAACTGAGTCGGGGCCCGGAACGCGTTTTTAGCAAAAAACCG
TATGGTACACGATTTCGGCTAAAATTTTACAAAAAAAGATCCCAAAAATATTTCCTCAATTTTTG
ACCACAATTATCAGAAAAATATATATAATACAACGCCAAAAATATTGAAGAATTTTGCGAGCATC
TAATATCGTTTTTCCTATTTTTCTGAATTAATTTCTGATTAAATCGAAACATGATTCTAATGCTC
GTTA
Found at i:31119 original size:30 final size:30
Alignment explanation
Indices: 31085--31160 Score: 104
Period size: 29 Copynumber: 2.6 Consensus size: 30
31075 ATTAATCATC
*
31085 TCATAAAACCAT-ATCATATGTCAATATTTT
1 TCATAAAACAATGATCA-ATGTCAATATTTT
31115 TCAT-AAACAATGATCAATGTCAATATTTT
1 TCATAAAACAATGATCAATGTCAATATTTT
*
31144 TTAT-AAACAATGATCAA
1 TCATAAAACAATGATCAA
31161 AATTTAGTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
29 35 0.81
30 8 0.19
ACGTcount: A:0.43, C:0.14, G:0.05, T:0.37
Consensus pattern (30 bp):
TCATAAAACAATGATCAATGTCAATATTTT
Found at i:31134 original size:29 final size:29
Alignment explanation
Indices: 31097--31160 Score: 110
Period size: 29 Copynumber: 2.2 Consensus size: 29
31087 ATAAAACCAT
31097 ATCATATGTCAATATTTTTCATAAACAATG
1 ATCA-ATGTCAATATTTTTCATAAACAATG
*
31127 ATCAATGTCAATATTTTTTATAAACAATG
1 ATCAATGTCAATATTTTTCATAAACAATG
31156 ATCAA
1 ATCAA
31161 AATTTAGTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 29 0.88
30 4 0.12
ACGTcount: A:0.42, C:0.12, G:0.06, T:0.39
Consensus pattern (29 bp):
ATCAATGTCAATATTTTTCATAAACAATG
Found at i:32372 original size:20 final size:20
Alignment explanation
Indices: 32343--32413 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
32333 CAGCACATTC
*
32343 ACATTTAACTTTCCCAATTG
1 ACATTGAACTTTCCCAATTG
* ** *
32363 ACATTGAACTTGCCTTATTC
1 ACATTGAACTTTCCCAATTG
** *
32383 ACATCCAACTTTCCCAAATG
1 ACATTGAACTTTCCCAATTG
32403 ACATTGAACTT
1 ACATTGAACTT
32414 GCCTTAATTC
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.31, C:0.27, G:0.07, T:0.35
Consensus pattern (20 bp):
ACATTGAACTTTCCCAATTG
Found at i:32384 original size:40 final size:41
Alignment explanation
Indices: 32339--32659 Score: 196
Period size: 32 Copynumber: 9.2 Consensus size: 41
32329 CACGCAGCAC
** *
32339 ATTCACATTTAACTTTCCCAATTGACATTGAACTTGCCTT-
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32379 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32420 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32452 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTT-
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
*
32483 ATT----T-C-AC-AT-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
* *
32516 ATT--CA--C-A---T-CCAAATAACATTGAACTTGCCTCA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32548 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32580 ATT--CA--C-A---T-CCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32612 A-TCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
1 ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
32652 ATTCACAT
1 ATTCACAT
32660 TGGCCCTCAA
Statistics
Matches: 257, Mismatches: 7, Indels: 33
0.87 0.02 0.11
Matches are distributed among these distances:
30 2 0.01
31 4 0.02
32 165 0.64
33 6 0.02
34 2 0.01
35 1 0.00
36 2 0.01
37 1 0.00
39 3 0.01
40 62 0.24
41 9 0.04
ACGTcount: A:0.33, C:0.26, G:0.08, T:0.32
Consensus pattern (41 bp):
ATTCACATCCAACTTTCCCAAATGACATTGAACTTGCCTTA
Found at i:32437 original size:32 final size:32
Alignment explanation
Indices: 32396--32659 Score: 420
Period size: 32 Copynumber: 8.0 Consensus size: 32
32386 TCCAACTTTC
32396 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
32428 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
32460 CCAAATGACATTGAACTTGCCTTATTTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
32492 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
* *
32524 CCAAATAACATTGAACTTGCCTCAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
32556 CCAAATGACATTGAACTTGCCTTAATTCACAT
1 CCAAATGACATTGAACTTGCCTTAATTCACAT
*
32588 CCAAATGACATTGAACTTGCCTTAATCACATCCAACTTT
1 CCAAATGACATTGAACTTGCCTTAAT----T-C-AC-AT
32627 CCCAAATGACATTGAACTTGCCTTAATTCACAT
1 -CCAAATGACATTGAACTTGCCTTAATTCACAT
32660 TGGCCCTCAA
Statistics
Matches: 216, Mismatches: 8, Indels: 15
0.90 0.03 0.06
Matches are distributed among these distances:
32 180 0.83
33 1 0.00
34 2 0.01
35 1 0.00
36 2 0.01
37 1 0.00
38 2 0.01
39 1 0.00
40 26 0.12
ACGTcount: A:0.34, C:0.26, G:0.09, T:0.31
Consensus pattern (32 bp):
CCAAATGACATTGAACTTGCCTTAATTCACAT
Found at i:32624 original size:20 final size:20
Alignment explanation
Indices: 32601--32659 Score: 55
Period size: 20 Copynumber: 2.9 Consensus size: 20
32591 AATGACATTG
32601 AACTTGCCTTAATCACATCC
1 AACTTGCCTTAATCACATCC
* ** * **
32621 AACTTTCCCAAATGACATTG
1 AACTTGCCTTAATCACATCC
32641 AACTTGCCTTAATTCACAT
1 AACTTGCCTTAA-TCACAT
32660 TGGCCCTCAA
Statistics
Matches: 28, Mismatches: 10, Indels: 1
0.72 0.26 0.03
Matches are distributed among these distances:
20 23 0.82
21 5 0.18
ACGTcount: A:0.32, C:0.29, G:0.07, T:0.32
Consensus pattern (20 bp):
AACTTGCCTTAATCACATCC
Found at i:36548 original size:565 final size:565
Alignment explanation
Indices: 35479--36612 Score: 2135
Period size: 565 Copynumber: 2.0 Consensus size: 565
35469 GAGTATGAGC
*
35479 AAACCCCCAACCTAATTCGCTCCTTCGAAAGAAAAACACAGTTCCTTGCCACCCATTCCCCCACC
1 AAACCCCCAACCTAATTCGCTCCTTCGAAAGAAAAACACAGTTCCTTACCACCCATTCCCCCACC
*
35544 AGCCACGCAAGTGATGAGTAAATGTGGCTGTTCTAGAATACCGGCATGAGACCTCCCATCACGAA
66 AGCCACGCAAGTGATGAGTAAATGTGGCTGTTCTAGAATACCGGCATGAGACCTCCCATCACAAA
*
35609 CCAGATGCTGTACATGAAGAATTAAAATTCATCAGTAGCTCAGTGGTTTAAAAGCTTAAAAAATC
131 CCAGATGCTGTACATGAAGAATTAAAATTCATCAGTAACTCAGTGGTTTAAAAGCTTAAAAAATC
35674 AGAAGTGAAAACTTTCAAAACAAAGCACTTAGAAAATAAACTGCCCATTTCAAGGACAATCACAT
196 AGAAGTGAAAACTTTCAAAACAAAGCACTTAGAAAATAAACTGCCCATTTCAAGGACAATCACAT
35739 CAACCAACCAATTACAAAGATGAGGAAAGAGATCACCCAATACTACTCAAAACATGTTACCAACA
261 CAACCAACCAATTACAAAGATGAGGAAAGAGATCACCCAATACTACTCAAAACATGTTACCAACA
35804 AACCTGGTAGCCATATCACAAAACATGCAAGTATCATGACAAGGAAGAAAAGAGGAATCACACAG
326 AACCTGGTAGCCATATCACAAAACATGCAAGTATCATGACAAGGAAGAAAAGAGGAATCACACAG
*
35869 AAAACATAGCAATTATTCAAACAGCTTCCAACTGCAAATAAGAATATTTGGCACATTCTGCAAGT
391 AAAACATAGCAATTATTCAAACAGCTTCCAAATGCAAATAAGAATATTTGGCACATTCTGCAAGT
*
35934 GGGAAACATTTTAATGTAATCTTTCCCTTCAAACATTGCATTTACATTTTTCACAACTGAAAATG
456 CGGAAACATTTTAATGTAATCTTTCCCTTCAAACATTGCATTTACATTTTTCACAACTGAAAATG
35999 ACCAACCCAAATACACCGAAAACATGAGATCAATAAAGAGTCTGT
521 ACCAACCCAAATACACCGAAAACATGAGATCAATAAAGAGTCTGT
36044 AAACCCCCAACCTAATTCGCTCCTTCGAAAGAAAAACACAGTTCCTTACCACCCATTCCCCCACC
1 AAACCCCCAACCTAATTCGCTCCTTCGAAAGAAAAACACAGTTCCTTACCACCCATTCCCCCACC
* *
36109 TGCCAC-CAAAGTGATGAGTAAATGTGGCTGTTCTAGAATACCGGCATGGGACCTCCCATCACAA
66 AGCCACGC-AAGTGATGAGTAAATGTGGCTGTTCTAGAATACCGGCATGAGACCTCCCATCACAA
* * *
36173 ACCAGCTGCTGTACATGAAGAATTAGAATTCATCAGTAACTCAGTGGTTTAAAAGCTTAACAAAT
130 ACCAGATGCTGTACATGAAGAATTAAAATTCATCAGTAACTCAGTGGTTTAAAAGCTTAAAAAAT
36238 CAGAAGTGAAAACTTTCAAAACAAAGCACTTAGAAAATAAACTGCCCATTTCAAGGACAATCACA
195 CAGAAGTGAAAACTTTCAAAACAAAGCACTTAGAAAATAAACTGCCCATTTCAAGGACAATCACA
36303 TCAACCAACCAATTACAAAGATGAGGAAAGAGATCACCCAATACTACTCAAAACATGTTACCAAC
260 TCAACCAACCAATTACAAAGATGAGGAAAGAGATCACCCAATACTACTCAAAACATGTTACCAAC
*
36368 AAACCTGGTAGCCATATCACAAAACATGTAAGTATCATGACAAGGAAGAAAAGAGGAATCACACA
325 AAACCTGGTAGCCATATCACAAAACATGCAAGTATCATGACAAGGAAGAAAAGAGGAATCACACA
*
36433 GAAAACATAGCAATTATTTAAACAGCTTCCAAATGCAAATAAGAATATTTGGCACATTCTGCAAG
390 GAAAACATAGCAATTATTCAAACAGCTTCCAAATGCAAATAAGAATATTTGGCACATTCTGCAAG
36498 TCGGAAACATTTTAATGTAATCTTTCCCTTCAAACATTGCATTTACATTTTTCACAACTGAAAAT
455 TCGGAAACATTTTAATGTAATCTTTCCCTTCAAACATTGCATTTACATTTTTCACAACTGAAAAT
*
36563 GACCAACCCAAATACACCGAAAACATGTGATCAATAAAGAGTCTGT
520 GACCAACCCAAATACACCGAAAACATGAGATCAATAAAGAGTCTGT
36609 AAAC
1 AAAC
36613 AATAACCATT
Statistics
Matches: 555, Mismatches: 13, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
564 1 0.00
565 554 1.00
ACGTcount: A:0.40, C:0.24, G:0.14, T:0.22
Consensus pattern (565 bp):
AAACCCCCAACCTAATTCGCTCCTTCGAAAGAAAAACACAGTTCCTTACCACCCATTCCCCCACC
AGCCACGCAAGTGATGAGTAAATGTGGCTGTTCTAGAATACCGGCATGAGACCTCCCATCACAAA
CCAGATGCTGTACATGAAGAATTAAAATTCATCAGTAACTCAGTGGTTTAAAAGCTTAAAAAATC
AGAAGTGAAAACTTTCAAAACAAAGCACTTAGAAAATAAACTGCCCATTTCAAGGACAATCACAT
CAACCAACCAATTACAAAGATGAGGAAAGAGATCACCCAATACTACTCAAAACATGTTACCAACA
AACCTGGTAGCCATATCACAAAACATGCAAGTATCATGACAAGGAAGAAAAGAGGAATCACACAG
AAAACATAGCAATTATTCAAACAGCTTCCAAATGCAAATAAGAATATTTGGCACATTCTGCAAGT
CGGAAACATTTTAATGTAATCTTTCCCTTCAAACATTGCATTTACATTTTTCACAACTGAAAATG
ACCAACCCAAATACACCGAAAACATGAGATCAATAAAGAGTCTGT
Found at i:43429 original size:38 final size:38
Alignment explanation
Indices: 43378--43454 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
43368 CCAATATTGA
43378 TTGATATTTCGATGTACGGGAATTTGAACCAGGTTTCT
1 TTGATATTTCGATGTACGGGAATTTGAACCAGGTTTCT
43416 TTGATATTTCGATGTACGGGAATTTGAACCAGGTTTCT
1 TTGATATTTCGATGTACGGGAATTTGAACCAGGTTTCT
43454 T
1 T
43455 ACTTTCTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.23, C:0.13, G:0.23, T:0.40
Consensus pattern (38 bp):
TTGATATTTCGATGTACGGGAATTTGAACCAGGTTTCT
Found at i:46195 original size:17 final size:17
Alignment explanation
Indices: 46173--46210 Score: 76
Period size: 17 Copynumber: 2.2 Consensus size: 17
46163 TAAACAATTT
46173 CATGAATAATAATACAA
1 CATGAATAATAATACAA
46190 CATGAATAATAATACAA
1 CATGAATAATAATACAA
46207 CATG
1 CATG
46211 TCTGAAATCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.55, C:0.13, G:0.08, T:0.24
Consensus pattern (17 bp):
CATGAATAATAATACAA
Found at i:48687 original size:66 final size:66
Alignment explanation
Indices: 48581--48719 Score: 235
Period size: 66 Copynumber: 2.1 Consensus size: 66
48571 GTATCTGTAA
* *
48581 CTGTTTCACCACCATTTGATCGTTTCATCACCGATTTGGATCCAAACGAAACTTAAGTGTAAACT
1 CTGTTTCACCACCATTCGACCGTTTCATCACCGATTTGGATCCAAACGAAACTTAAGTGTAAACT
48646 C
66 C
* *
48647 CTGTTTCACCACCATTCGACCGTTTCATCACCGTTTTGGATCCAAACGAAGCTTAAGTGTAAACT
1 CTGTTTCACCACCATTCGACCGTTTCATCACCGATTTGGATCCAAACGAAACTTAAGTGTAAACT
48712 C
66 C
48713 C-GTTTCA
1 CTGTTTCA
48720 ATTGTTATTC
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
65 6 0.09
66 63 0.91
ACGTcount: A:0.27, C:0.27, G:0.14, T:0.32
Consensus pattern (66 bp):
CTGTTTCACCACCATTCGACCGTTTCATCACCGATTTGGATCCAAACGAAACTTAAGTGTAAACT
C
Found at i:56438 original size:1 final size:1
Alignment explanation
Indices: 56432--56467 Score: 72
Period size: 1 Copynumber: 36.0 Consensus size: 1
56422 ATATTAAGGG
56432 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
56468 GACGAGAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 35 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:71611 original size:2 final size:2
Alignment explanation
Indices: 71604--71636 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
71594 CAAATAATGA
71604 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
71637 AGGAAATGTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:84698 original size:42 final size:42
Alignment explanation
Indices: 84639--84808 Score: 331
Period size: 42 Copynumber: 4.0 Consensus size: 42
84629 GTCAGATTCA
84639 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
1 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
*
84681 TATAAAATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
1 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
84723 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
1 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
84765 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
1 TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
84807 TA
1 TA
84809 CTTAATGAAC
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 126 1.00
ACGTcount: A:0.34, C:0.33, G:0.02, T:0.31
Consensus pattern (42 bp):
TATAAGATCACTCTCCCAACACCTTCATTATTCTCAAAACCT
Found at i:84746 original size:24 final size:24
Alignment explanation
Indices: 84719--84789 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
84709 TATTCTCAAA
84719 ACCTTATAAGATCACTCTCCCAAC
1 ACCTTATAAGATCACTCTCCCAAC
* *
84743 ACCTTCAT----T-A-T-TCTCAAA
1 ACCTT-ATAAGATCACTCTCCCAAC
84761 ACCTTATAAGATCACTCTCCCAAC
1 ACCTTATAAGATCACTCTCCCAAC
84785 ACCTT
1 ACCTT
84790 CATTATTCTC
Statistics
Matches: 35, Mismatches: 4, Indels: 16
0.64 0.07 0.29
Matches are distributed among these distances:
17 2 0.06
18 10 0.29
19 1 0.03
20 1 0.03
21 2 0.06
22 1 0.03
23 1 0.03
24 15 0.43
25 2 0.06
ACGTcount: A:0.32, C:0.35, G:0.03, T:0.30
Consensus pattern (24 bp):
ACCTTATAAGATCACTCTCCCAAC
Found at i:87975 original size:54 final size:54
Alignment explanation
Indices: 87893--88001 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
87883 AAAGCAAACA
87893 CCGTCGAAATTTTTGGCTAACTCCCAGATCTCCATAATTAAGCAAGCTCCTTCC
1 CCGTCGAAATTTTTGGCTAACTCCCAGATCTCCATAATTAAGCAAGCTCCTTCC
87947 CCGTCGAAATTTTTGGCTAACTCCCAGATCTCCATAATTAAGCAAGCTCCTTCC
1 CCGTCGAAATTTTTGGCTAACTCCCAGATCTCCATAATTAAGCAAGCTCCTTCC
88001 C
1 C
88002 ATAACATTTG
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.26, C:0.32, G:0.13, T:0.29
Consensus pattern (54 bp):
CCGTCGAAATTTTTGGCTAACTCCCAGATCTCCATAATTAAGCAAGCTCCTTCC
Found at i:95400 original size:19 final size:19
Alignment explanation
Indices: 95349--95407 Score: 73
Period size: 19 Copynumber: 3.0 Consensus size: 19
95339 TGTTGCTTTA
*
95349 ATAATCTCATATGTACAGT
1 ATAATCTCATCTGTACAGT
*
95368 ACCTAATCTAATCTGTACAGT
1 A--TAATCTCATCTGTACAGT
*
95389 ATAATTTCATCTGTACAGT
1 ATAATCTCATCTGTACAGT
95408 TGCTAAACAG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
19 17 0.50
21 17 0.50
ACGTcount: A:0.34, C:0.19, G:0.10, T:0.37
Consensus pattern (19 bp):
ATAATCTCATCTGTACAGT
Found at i:96502 original size:2 final size:2
Alignment explanation
Indices: 96497--96536 Score: 53
Period size: 2 Copynumber: 20.0 Consensus size: 2
96487 ACAAAAAATG
* * *
96497 AT AT AT AT AT AT AT AT AT AC AC AT AT AT GT 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
96537 GTATTTAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:97545 original size:2 final size:2
Alignment explanation
Indices: 97538--97578 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
97528 AGAGAATGGC
97538 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
97579 AGCTTAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:102205 original size:4 final size:4
Alignment explanation
Indices: 102196--102221 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
102186 TCTCTTCGAA
102196 TAAT TAAT TAAT TAAT TAAT TAAT TA
1 TAAT TAAT TAAT TAAT TAAT TAAT TA
102222 TCTTTTTCCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (4 bp):
TAAT
Found at i:110069 original size:13 final size:15
Alignment explanation
Indices: 110051--110083 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
110041 AAAAACCTAA
110051 AATTAGTAA-T-ATT
1 AATTAGTAATTAATT
110064 AATTAGTAATTAATT
1 AATTAGTAATTAATT
110079 AATTA
1 AATTA
110084 ATTAATTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 9 0.50
14 1 0.06
15 8 0.44
ACGTcount: A:0.48, C:0.00, G:0.06, T:0.45
Consensus pattern (15 bp):
AATTAGTAATTAATT
Done.