Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021132.1 Corchorus olitorius cultivar O-4 contig21165, 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: 72285
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:4942 original size:333 final size:331
Alignment explanation
Indices: 2953--7182 Score: 3787
Period size: 332 Copynumber: 12.8 Consensus size: 331
2943 GTGGCCCTAT
* * * * * * * *
2953 AACGTGTTTTTAGCCAGAAACCGTGAAGGTTAGTATACAATTTCGGTTAAAATTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * * **
3018 GACTCGAAAGATATTT-TCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAGTTCGACATC
66 GACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * * *
3082 AAAAAGATTGAAGGGCTTTTAAAGCTTCTAATAT--TGTTT--T-TTTTTT-CGAATTAATTTCT
131 AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* * * *
3141 AATTAAATCGAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCTAATGTGGCTGAAAT
196 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * *
3206 TTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCACAAAAAATCATGCAAAACTGAGCCAG
261 TTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACC-G
*** *
3271 ATTCCAG
325 GGCCCGG
* * * * *
3278 AACGAGTTTTTAGCCGAAAATCGTGATGGTTAGTACACGATTTCGGCT-AAATTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * * *
3342 GACCCGAAAGA-ATTT-TCCTCGATTTCTAGCGATAATACTCATAAAAAATATATAATTCAATGC
66 GACCCGAAAGATATTTCT-CTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * * * * *
3405 CAAAAAAATTGAA-AGCTTTTTCACGGTTCTAATATCGTTTTTCATATTTTATTTCCAAATTAAT
130 CAAAAAGATTGAAGGGC-TTTTCACGCTTTTAATATCGTTTTTCCTA-TTT-TTTCCGAATTAAT
* * ** * * * *
3469 TTCTGATTAAATCGAAACAAGATTTAGAAACTCGTAAAAACAAATTCTTAAATACAATGTGGGTA
192 TTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTG
* * *
3534 AGATTTGGTTAGATGAATATAGATATATTTTAAGGAATCTTGGCGCCAAAAATCATGCAAAACTG
257 AGATTTGATTAGATGAATATAG--ATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
3599 -ACCTGGAGTCCCGG
320 AACC-GG-G-CCCGG
* * * **
3613 AACGCGATTTTAGCCAAAGAACCATGAAT-ATGATGGTACACGATTTCATCTAAAATTTTGCAAA
1 AACGCGTTTTTAGCCAAA-AACCGTG-ATGATTAT--TACACGATTTCGGCTAAAATTTTGCAAA
* * * * **
3677 AATTGACCCG-AA-ATATTTTTCTCAAGTTTTAGCCACAATACTCATAAAAGTTATATAATTCAA
62 AATTGACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAA
* * * *
3740 CGCCAAAAAGATTGAAGGGC-TTCCAACGCTTCTAATATCGTTTTTCCTATTTTTTTTCAAATTA
127 CGCCAAAAAGATTGAAGGGCTTTTC-ACGCTTTTAATATCGTTTTTCCTA-TTTTTTCCGAATTA
* * * * *
3804 ATTTCTAATTAAATCGAAACATGATTCAAATACTTGTAAAAACAAATCCTTAAATCCAATGTGTC
190 ATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGC
* * * * ** *
3869 TAAGATTTGGTTAGATGAATATAGATATTTCAAGAAAT-TTTCCACCAAAAATCATGCAAAACTG
255 TGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTG
* * *
3933 ACCCTGTGCCCTGA
320 AACC-GGGCCC-GG
* * *
3947 AACGTGTTTTTTGCCAACAAACC---ATGATGA-TACACGATTTCGGCTAAAA-TTTGCAAAAAT
1 AACGCGTTTTTAGCCAA-AAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * * * * * * * * * * *
4007 TAACGCGAAATATTTTTC-CTCAATTTTTATC-ACAATACTCATAGAATATACATAACTAAAGGC
65 TGACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * * * *
4070 C-AAAAGATTGGAGGACCTTTTCACGCTTTTAATATCATTTTTCATA-TTTTTCTGAATTAATTT
130 CAAAAAGATTGAAGG-GCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATTAATTT
* * * * *
4133 CTAATTAAATCGAAACAAGATTCAGATGCTCGAAAAAAGAAATTCTTAAATTCAAAT-AGGCTGA
194 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA-TCCAATGTGGCTGA
** * *
4197 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCAGCGCCAAAAATCACGCAAAA-TTAAG
258 GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAA-
*
4261 CCGGGGCCCCGA
322 CC-GGG-CCCGG
* *
4273 AACGCG-TTTTAGCCAAAAACCGTGATTG-TTACTACACGATTTCGGCTAAAATTTTGCAAAAAA
1 AACGCGTTTTTAGCCAAAAACCGTGA-TGATTATTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * * * *
4336 TGACCTGAAAAAT-TTTC-CATCAATTTTTTGTCTAAAGTACTCATAAAAAATATATATAATTTA
65 TGACCCGAAAGATATTTCTC-TCAATTTTTAG-CTAAAATACTCAT-AAAAA-ATATATAATTCA
* * * * *
4399 ACACCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCGTTTTT-C-ATATTTTCTGAATTAA
126 ACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATTAA
* ***
4462 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATAAAGCT
191 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT
* * * * * *
4527 GAGATTTGATTAGATGAATATGGATATCTCAAAGAGTGTTGGGGCCAAAAATCATGCAAAACTTA
256 GAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA
*
4592 GCCGGGGCCCCGG
321 ACC-GGG-CCCGG
* * * ** *
4605 AACGCGTTTTTAACCAAAAACCGTGATGATTATTACACGATTTTGACTCGAAGTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
* * * * * * *
4670 GACTCGAAAGTTATTTAT-TCAATTTTTAGCCACAATACTCATAAAAATTATATAATTCTACGCC
66 GACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * *
4734 AAAAAGATTGAAGGGTTTTTCATGCTTATAATATCGTTTTTCCTATTATTTTCCGAATTAATTTC
131 AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATT-TTTTCCGAATTAATTTC
* * * *** * *
4799 TAATTAAATCGAAACATGATTCATATGCTTGT-TTTACAAATCCTTAAATCCAATGTGACAGAGA
195 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * **
4863 TATGGTTAGATAAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATTGTGCAAACACTGAACC
260 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAA-ACTGAACC
4928 GGGACCCTGG
324 GGG-CCC-GG
* * * * *
4938 AACGCGTTATTAGCCAAAAATCATGATTTCGACTAACGTACACGATTTCGGCTAAAATTTTGCAA
1 AACGCGTTTTTAGCCAAAAACCGTGA--T-GA-TTA-TTACACGATTTCGGCTAAAATTTTGCAA
* * * * * * * *
5003 AAATTGA-CCTATAAAAT-TTTTTCTTAATTTTTCGCTAAAATACTCATGAAATATATATAATTT
61 AAATTGACCCGA-AAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTC
* * * * * **
5066 AATGCCAAAAAGATTGGAGGACTTTTCACGCTTTTCATATCGTTTTTCATAATTTTTTATGAATT
125 AACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCT-ATTTTTTCCGAATT
* * * * * * * * *
5131 AAATTATAATCAAATTTG-AACAAAATTTAGATGCTCGTAGAAACAAAT-CTGTAAATGCTATGT
189 AATTTCTAATTAAA-TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCT-TAAATCCAATGT
* * * *
5194 GGCTGAGATTTGATTAGATGAATATGGATATATCTCAAGGAGTCTTAGTGGCAAAAATCATGCAA
252 GGCTGAGATTTGATTAGATGAATATAGATAT-T-TCAAGGAGTCTTGGCGCCAAAAATCATGCAA
*
5259 AACTG-ACTCGGGACTCTGG
315 AACTGAAC-CGGG-C-CCGG
* *
5278 AACACGTTTTTAGCCAAAAACTGTGATGATTATT--AC-A--T--GCTAAAATTTTGCAAAAATT
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
* *
5336 GACCGGAAAGATATTT-TCTCAATTTTTGGCTAAAATACTCATAAAAAATATATAATTCAACGCC
66 GACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCC
* * * *
5400 AAAAATATTGAAGGGTTTTTTACGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
131 AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
* * * * *
5465 AATTAAATCAAAACAAGATTTAGATGCTTGT---AAC---TACTTAAATCGAATGTGGCTGAGAT
196 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
* * * * *
5524 TTGATTAGATAAATATACATATTTCAAGGAGTCTAGGTGCCAAAAATCATGCAAAACTGACCCAG
261 TTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACC-G
5589 GGCTCCGG
325 GGC-CCGG
** * * ***** ** * * *
5597 ATTGTGTTTTTAGCAAAAAAAAAAAAAAAACTGTGATGTTACACGATTTCGGTTAATATTTTACA
1 AACGCGTTTTTAGC-CAAAAACCGTGATGA-T-T-A--TTACACGATTTCGGCTAAAATTTTGCA
* * * *
5662 AAAATTGAACC-AAA-ATATTTGTCCTCAATTTTTAGCCACAATACTCATAAAAAATATATAATT
60 AAAATTGACCCGAAAGATATTTCT-CTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATT
* * *
5725 CAACGCTAAAAAGATTGAAGGGCGTTT--CG-----AATATTGTTTTTCCTTATTTTTTTCCGAA
124 CAACGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCC-TA-TTTTTTCCGAA
* * * * * * *
5783 TTAATTTTTAATTAAAACGAAATATGATTGAGATGCTTGT-------AA-----GAA--CAA--T
187 TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGT
* * * **
5832 GGCTGGGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTCGGCGTAAAAAATCATTG-AAA
252 GGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCA-TGCAAA
*
5896 ACCGAACCGGGCCCCGG
316 ACTGAACCGGG-CCCGG
**
5913 AACGCGTTTTTAGCC-AAAACCTGTGATGATTATTACACGATTTTAGCTAAAATTTTGCAAAAAT
1 AACGCGTTTTTAGCCAAAAACC-GTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAAT
* *
5977 TGACCCGAAAGATATTTC-CTCAATTTTTATGC-ATAACACTCATAAAAAATATATAATTCAACG
65 TGACCCGAAAGATATTTCTCTCAATTTTTA-GCTAAAATACTCATAAAAAATATATAATTCAACG
* * * ** *
6040 CCAAAAAGATTGAAGGGCTTTTTACGCTTTTAATATCGTTTTTCATTTTCTTTTTTGTATTAATT
129 CCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATT-TTTTCCGAATTAATT
* * * * * *
6105 TCTAATTACATCAAAACAAAATTCAGATGCTCGTAAAAACAAATCCTTGAATGCAATGTGGCTAA
193 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * * * * *
6170 AACTTT-ATTAGATGTATATAGATATTTCAAGGAGTGTCGGCGCAAAAAATCATGCAAAATTGAG
258 GA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAA
*
6234 CCGGGGCCTCGA
322 CC-GGGCC-CGG
* * * * * *
6246 AACGCGTTTTTAACCAAAAACCGTGATGAGTAGTACATGATTTTGGCTAAAATTTTGCAAAAAAA
1 AACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGC-AAAAAT
* * * * * * * *
6311 TGACCCGAAAAATTTTTC-CTTAATTTTTGGATAAAATAATCATAAAAAATATATAATTTAACAC
65 TGACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * * ** * *
6375 CAAAAAGATTGGAGGACTTTTCATGCTTTTAATATAATTTTTCATA-TTTTTCTGAATTAATTTC
130 CAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTC
* * * *
6439 AAACTAAATC-AAACAAGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGA
195 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA
* * * * * *
6503 TTTGATTAGATGAATATGGATATCTCAAGGAGTCTTGGTGCCAAAAATCATGTAAAACTGAGTCG
260 TTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGA-ACC
*
6568 GGGCCCCAG
324 GGG-CCCGG
* * * * *
6577 AACGCCTTTTTATCCAAAAACTGTGAT-AGTTATTACACGATTTCGGCTAACATTTTGTAAAAAT
1 AACGCGTTTTTAGCCAAAAACCGTGATGA-TTATTACACGATTTCGGCTAAAATTTTGCAAAAAT
* * *
6641 TGATCCGAAAGATATTTC-CTCAATTTTTGGATAAAATACTCATAAAAAATATATAATTCAACGC
65 TGACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * * **
6705 CAAAAAGATTGAAGGGTTTTTGAC-ATTTCTAATATCGTTTTTCCTA-TTTTTCAAAATTAATTT
130 CAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTCCTATTTTTTCCGAATTAATTT
* * * * *
6768 CTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCTAATGTGACTTAA
194 CTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG
* * * * * * *
6833 ATTTGATTAGATGAATGTAGATAATTCAAGTAGTCTCGGAG--ATAAAATCATGCAAAATTGAGC
259 ATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCA-AAAATCATGCAAAACTGAAC
6896 CGGGTTCCCGG
323 CGGG--CCCGG
* ** * * *
6907 AATGTATTTTTAGCCAAAAACCGTGATGGTTTTGTTAGTACACGATTTCGGTTAAAA-TTTGCAA
1 AACGCGTTTTTAGCCAAAAACCGTGAT-G----ATTATTACACGATTTCGGCTAAAATTTTGCAA
* * *
6971 AAATTGACACGAAAG--ATTTCTCCTCAATTTTTGGCTAAAATACTCAT-AAGAATATATAATTC
61 AAATTGACCCGAAAGATATTTCT-CTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTC
* * * * * * * **
7033 AACGCCAAAAACATTGGAGGGTTTTTTTACGCTTTTAATATCATATTTCTTATTTTTTCTAAATT
125 AACGCCAAAAAGATTGAAGGG-CTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATT
* ** *
7098 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACCAATTTTTTAAATCCAATGTT
189 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-CAAATCCTTAAATCCAATGTG
* *
7163 GTTGAGATTTGGTTAGATGA
253 GCTGAGATTTGATTAGATGA
7183 TGTAAAGTAT
Statistics
Matches: 3193, Mismatches: 556, Indels: 301
0.79 0.14 0.07
Matches are distributed among these distances:
310 92 0.03
311 5 0.00
312 9 0.00
313 1 0.00
314 5 0.00
315 4 0.00
316 56 0.02
317 73 0.02
318 2 0.00
319 51 0.02
320 12 0.00
321 41 0.01
322 3 0.00
323 10 0.00
324 97 0.03
325 159 0.05
326 53 0.02
327 158 0.05
328 168 0.05
329 46 0.01
330 233 0.07
331 260 0.08
332 483 0.15
333 277 0.09
334 262 0.08
335 113 0.04
336 42 0.01
337 105 0.03
338 238 0.07
339 73 0.02
340 34 0.01
341 28 0.01
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (331 bp):
AACGCGTTTTTAGCCAAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATT
GACCCGAAAGATATTTCTCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCC
AAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCCTATTTTTTCCGAATTAATTTCT
AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT
TTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACCGG
GCCCGG
Found at i:7434 original size:13 final size:13
Alignment explanation
Indices: 7418--7445 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
7408 TTTAAATTAA
7418 ATAAATAAAAATT
1 ATAAATAAAAATT
7431 ATAAATAAAAATT
1 ATAAATAAAAATT
7444 AT
1 AT
7446 TCCTAATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
ATAAATAAAAATT
Found at i:7564 original size:15 final size:17
Alignment explanation
Indices: 7539--7572 Score: 54
Period size: 15 Copynumber: 2.1 Consensus size: 17
7529 GACTAGAAAT
7539 AATACTATTATAAT-TA
1 AATACTATTATAATCTA
7555 AATA-TATTATAATCTA
1 AATACTATTATAATCTA
7571 AA
1 AA
7573 AAATAATTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.53, C:0.06, G:0.00, T:0.41
Consensus pattern (17 bp):
AATACTATTATAATCTA
Found at i:7812 original size:37 final size:37
Alignment explanation
Indices: 7771--7846 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
7761 CTAAGGGTAT
* *
7771 TTATGAAATTTCCCAATTAAAATTTTTGAGTTCGTAA
1 TTATGAAATTTCCCAATTAAAATTTTTGAGCTCATAA
7808 TTATGAAATTTCCCAATTAAAATTTTTGAGCTCATAA
1 TTATGAAATTTCCCAATTAAAATTTTTGAGCTCATAA
7845 TT
1 TT
7847 TTATATAGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (37 bp):
TTATGAAATTTCCCAATTAAAATTTTTGAGCTCATAA
Found at i:7868 original size:5 final size:5
Alignment explanation
Indices: 7858--7896 Score: 64
Period size: 5 Copynumber: 8.2 Consensus size: 5
7848 TATATAGTAG
7858 TAAGA TAAGA TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
7897 GGTAAGATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 27 0.84
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:7886 original size:23 final size:23
Alignment explanation
Indices: 7851--7905 Score: 87
Period size: 23 Copynumber: 2.5 Consensus size: 23
7841 ATAATTTTAT
7851 ATAGT-AG-TAAGATAAGATAAG
1 ATAGTAAGATAAGATAAGATAAG
7872 ATAGTAAGATAAGATAAGATAAG
1 ATAGTAAGATAAGATAAGATAAG
*
7895 ATGGTAAGATA
1 ATAGTAAGATA
7906 TACTTTGTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 5 0.16
22 2 0.06
23 24 0.77
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (23 bp):
ATAGTAAGATAAGATAAGATAAG
Found at i:7905 original size:18 final size:18
Alignment explanation
Indices: 7855--7892 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
7845 TTTTATATAG
7855 TAGTAAGATAAGATAAGA
1 TAGTAAGATAAGATAAGA
7873 TAGTAAGATAAGATAAGA
1 TAGTAAGATAAGATAAGA
7891 TA
1 TA
7893 AGATGGTAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (18 bp):
TAGTAAGATAAGATAAGA
Found at i:12477 original size:24 final size:23
Alignment explanation
Indices: 12445--12501 Score: 66
Period size: 20 Copynumber: 2.6 Consensus size: 23
12435 GCCTTATACA
**
12445 CAAACTAATGATATGTTTAGGATT
1 CAAACTAATGATATGTACA-GATT
12469 CAAACTAATG---TGTACAGATT
1 CAAACTAATGATATGTACAGATT
12489 CAAACTAATGATA
1 CAAACTAATGATA
12502 AACAATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
20 14 0.50
21 4 0.14
24 10 0.36
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (23 bp):
CAAACTAATGATATGTACAGATT
Found at i:19034 original size:29 final size:28
Alignment explanation
Indices: 18999--19067 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 28
18989 ACACAAAAGG
* * *
18999 GCCAAATAAGCCTCTGAACTC-TAATTACA
1 GCCAAATAAGCCCCCGAACTCTTAA--AAA
19028 GCCAAATAAGCCCCCGAACTCTTAAAAA
1 GCCAAATAAGCCCCCGAACTCTTAAAAA
19056 GCCAAATAAGCC
1 GCCAAATAAGCC
19068 ATTTTCTGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
28 14 0.39
29 19 0.53
30 3 0.08
ACGTcount: A:0.41, C:0.30, G:0.12, T:0.17
Consensus pattern (28 bp):
GCCAAATAAGCCCCCGAACTCTTAAAAA
Found at i:19815 original size:24 final size:23
Alignment explanation
Indices: 19767--19812 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
19757 TCACTTCAAT
*
19767 TTTCCAGATCTAATAAATAAAAA
1 TTTCCAGATATAATAAATAAAAA
19790 TTTCCAGATATAATAAATAAAAA
1 TTTCCAGATATAATAAATAAAAA
19813 ATTATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.54, C:0.11, G:0.04, T:0.30
Consensus pattern (23 bp):
TTTCCAGATATAATAAATAAAAA
Found at i:19823 original size:23 final size:23
Alignment explanation
Indices: 19771--19830 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
19761 TTCAATTTTC
* * *
19771 CAGATCTAATAAATAAAAATTTC
1 CAGATATAATAAATAAAAAATTA
19794 CAGATATAATAAATAAAAAATTA
1 CAGATATAATAAATAAAAAATTA
* * *
19817 TATATATCATAAAT
1 CAGATATAATAAAT
19831 TTACAGTGAT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.57, C:0.08, G:0.03, T:0.32
Consensus pattern (23 bp):
CAGATATAATAAATAAAAAATTA
Found at i:22115 original size:43 final size:45
Alignment explanation
Indices: 22062--22152 Score: 143
Period size: 43 Copynumber: 2.1 Consensus size: 45
22052 AAACCTGACT
22062 ATTCTTTAAAA-AATATATGAAACTTCAACTTGATATAGCAAAA-A
1 ATTCTTTAAAATAA-ATATGAAACTTCAACTTGATATAGCAAAATA
*
22106 ATTC-TTAAAATAAATATGAAGCTTCAACTTGATATAGCAAAATA
1 ATTCTTTAAAATAAATATGAAACTTCAACTTGATATAGCAAAATA
22150 ATT
1 ATT
22153 ATCTATCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
43 34 0.77
44 10 0.23
ACGTcount: A:0.48, C:0.11, G:0.08, T:0.33
Consensus pattern (45 bp):
ATTCTTTAAAATAAATATGAAACTTCAACTTGATATAGCAAAATA
Found at i:22682 original size:15 final size:15
Alignment explanation
Indices: 22662--22707 Score: 58
Period size: 15 Copynumber: 3.0 Consensus size: 15
22652 TTAAAATATT
22662 TTATAAGGTTACTAA
1 TTATAAGGTTACTAA
22677 TTATAAGGCTTA-TAA
1 TTATAAGG-TTACTAA
*
22692 TTAATAAGATTACTAA
1 TT-ATAAGGTTACTAA
22708 AAATGCTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (15 bp):
TTATAAGGTTACTAA
Found at i:22744 original size:21 final size:22
Alignment explanation
Indices: 22701--22767 Score: 79
Period size: 21 Copynumber: 3.2 Consensus size: 22
22691 ATTAATAAGA
*
22701 TTACTAAAAATGCTTATGA-AGT
1 TTACTAAAAACGCTTAT-ATAGT
22723 TT-CTAAAAACGCTTATATAGT
1 TTACTAAAAACGCTTATATAGT
*
22744 TTACTTAAAAC-CTTATAT-GT
1 TTACTAAAAACGCTTATATAGT
22764 TTAC
1 TTAC
22768 CTATAAATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
20 7 0.17
21 25 0.61
22 9 0.22
ACGTcount: A:0.37, C:0.13, G:0.09, T:0.40
Consensus pattern (22 bp):
TTACTAAAAACGCTTATATAGT
Found at i:23630 original size:12 final size:12
Alignment explanation
Indices: 23613--23639 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
23603 CGACTTATTA
23613 AAGAAATCTTAT
1 AAGAAATCTTAT
23625 AAGAAATCTTAT
1 AAGAAATCTTAT
23637 AAG
1 AAG
23640 TTACTAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (12 bp):
AAGAAATCTTAT
Found at i:25286 original size:28 final size:28
Alignment explanation
Indices: 25246--25304 Score: 118
Period size: 28 Copynumber: 2.1 Consensus size: 28
25236 CCTACTAAAT
25246 ATTCTAATCCTTGTGCGAATGATTATTA
1 ATTCTAATCCTTGTGCGAATGATTATTA
25274 ATTCTAATCCTTGTGCGAATGATTATTA
1 ATTCTAATCCTTGTGCGAATGATTATTA
25302 ATT
1 ATT
25305 TAGATTGGGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.44
Consensus pattern (28 bp):
ATTCTAATCCTTGTGCGAATGATTATTA
Found at i:30584 original size:331 final size:328
Alignment explanation
Indices: 29669--32086 Score: 2073
Period size: 333 Copynumber: 7.4 Consensus size: 328
29659 ATCGTAATGG
* * * * * * *
29669 TTGCAAAAATTGACTCAAAAGATT-TTTCCTCGATTTCTAGT-GAAAATGCTCATAAAAAATATA
1 TTGCAAAAATTGACCCGAAA-ATTATTTCCTCAATTTTTA-TCTAAAATACTCATAAAAATTATA
* ** * * * **
29732 TAATTAAACACCCAAAAA-ATTGAAAGCCTTTTTCACACTTTTAATAAAGTTTTTCATATTTTTC
64 TAATTCAA-TGCCAAAAAGATTGAAGGGC-TTTTCACGCTTTTAATATCGTTTTTCATATTTTTC
* * * *
29796 TGAATTAATTTCTAATTAAATCGAAACAAGATGT-AGATACTTGTAAAAAAAATCCTTAAATTCA
127 TGAATTAATTTCTAATTAAATCGAAACAAGAT-TCAGATGCTCGTAAAACAAATCCTTAAATCCA
* * * *
29860 ATGTGGCTGAGATTTGAGTAGATGAACATAGATATTTCATTCAAGGAATCTCGGCAAT-AAAAAT
191 ATGTGGCTGAGATTTGATTAGATGAATATAGATA--T--TTCAAGG-A-GTCGGC-GTCAAAAAT
** * * * * * * *
29924 TTTGCAAAACTGAGTC-GGGCCCCGAAATGCGTGTTTAACCGAAAACCGTGATGCTTAGTACACG
249 CATGCAAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACG
29988 ATTTCGGCTAAAATT
314 ATTTCGGCTAAAATT
* ** *
30003 TTACAAAAATTGACCCGAAAGATT-TTTCCATCAATTTTTGGCTAAAATACTCAT-AATA-TATA
1 TTGCAAAAATTGACCCGAAA-ATTATTTCC-TCAATTTTTATCTAAAATACTCATAAAAATTATA
* * * * * * *
30065 TAATTTAACGTCAAAAAGATTGTAGGACTTTTCGCGCTTTTAATATCGTTTTTCATATTTTTCTC
64 TAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTG
* * *
30130 AATTAATTTCTAATTAAATCGAAACAAGATTCGGATGCTCGTAAAAACAAATTCTTCAATCCAAT
129 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCAAT
* * * * * * * **
30195 GTCGCTGAGATTAGATTAAATGATTATGGATATCTCAAAGAGTCTTGGCACCAAAAATCATGCAA
193 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC--GGCGTCAAAAATCATGCAA
* * * *
30260 AACTTAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACCATGATGATTATTACACGATTTCG
256 AACTGAGACGGGGCCCCGAAACGCGTTTTTAGCC-AAAAACCGTGATGGTTATTACACGATTTCG
*
30325 GCTAGAATT
320 GCTAAAATT
* * ** * * * *
30334 TTACGAAAATTGACTTGAAAGTTATTTCCTCAATTTTTATCCACAATAATCATAAAAATTATATA
1 TTGCAAAAATTGACCCGAAAATTATTTCCTCAATTTTTATCTAAAATACTCATAAAAATTATATA
* * * * *
30399 ATTCAATGCCAAAAAGATTGAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCG
66 ATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-T-TTTTCTG
* * * *** *
30464 AATTAATTTCTAATTAAATAGAAACATGATTCAGATGCTTGTTTTACAAATCCTTAAATTCAATG
129 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATG
* * * ***
30529 TGGCTGAGATTTGGTTAGATGAATGTAGATATTTCAAGGAGTCGGCGTAAAAAATCATGCAACGT
194 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCGGCGTCAAAAATCATGCAAAAC
* * * * *
30594 TGTA-CCGTGGCCCCGAAACGTGTTTTTAACCAAAAACCGTGAT--TTCGACTAACGTACGATTT
259 TG-AGACGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTT--A-TTAC--ACGATTT
*
30656 CGGCTAATATT
318 CGGCTAAAATT
* * *
30667 TTGCAAAAATTGACCAGAAATATT-TTTCCTAAATTTTTGTCTAAAATACTCAT-AAAATATATA
1 TTGCAAAAATTGACCCGAAA-ATTATTTCCTCAATTTTTATCTAAAATACTCATAAAAAT-TATA
* * * * * *
30730 AAATTCAATTCCAAAAAGATTGGAGGACTTTTCTCACTTTTAATATCGTTTTTCATATTTTTCTG
64 TAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTG
* * * *
30795 AATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTAAATCAAATCCTTAAATGCAATA
129 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATG
** * *
30860 TGGCT--GA---GATT---T-AATATAGATATTTCGGGGAGTTTCGAC-TCCAAAAATCTTGCAA
194 TGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG--TCGGCGT-CAAAAATCATGCAA
* * * * * * *
30915 AACTGAGCCGGGACCCCGAAATGTGTTTTTAGCAAAAAAACAGTGATGGTTAGTACACGATTTCG
256 AACTGAGACGGGGCCCCGAAACGCGTTTTTAGC-CAAAAACCGTGATGGTTATTACACGATTTCG
*
30980 GCTAAAACT
320 GCTAAAATT
* * * * * * *
30989 TTGCAAAAAATGACCAGAAAAATA-TTCTCTCAATTTTTAGCCATAATACTCATAAAAAATATAT
1 TTGCAAAAATTGACCCGAAAATTATTTC-CTCAATTTTTATCTAAAATACTCATAAAAATTATAT
* *
31053 AATTCAATGCCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTG
65 AATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTG
* * * * * *
31117 AATTAATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT--AA-AAA--C---AAT----GG
129 AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATG
* * * *
31170 TTG--GA-ATTTTG-TTAGATGAATATAGATATCTCAAGGAGTC-TCAGTGCCAAAAATCATTCA
194 TGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGTCGGC-GT--CAAAAATCATGCA
* * * * * *
31230 AAATTGA-ACCGGG-CCCTAGAACACG-TTTTAGCCAAAAATCGTGATGATTATTACACGATTTC
255 AAACTGAGACGGGGCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTC
31292 GGCTAAAATT
319 GGCTAAAATT
* * *
31302 TTGCAAAAATTGACCCGAAAGA-TATCTCCTCAATTTTTAGT-TATAATACTCATAAAAAGCTAT
1 TTGCAAAAATTGACCCGAAA-ATTATTTCCTCAATTTTTA-TCTAAAATACTCATAAAAA-TTAT
* * *
31365 ATAATTCAACGCCAAAAAGATTGAATGGCTTTTCACGCTTTTAATATC-ATTTTCATATTTTTTC
63 ATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTC
* *
31429 TGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATGCA
127 TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATCCA
* * * ** *
31494 ATGTGGCTAAGATTTTATTAGATGAATGTAGATATTTCAAGGAGTGCCGGCACCAAAAACCATGC
191 ATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT--CGGCGTCAAAAATCATGC
* * * * * * *
31559 AAAACTGAGCCGGGGTCACGAAACGCGTTTTTAGCCTAAAACAGTGATGGTTAGTACACGATTTT
254 AAAACTGAGACGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTC
*
31624 GGCTAAAAACT
319 GGCT-AAAATT
* * * ***
31635 TTGCAAAAACTGACCCGAAAAATT-TTTCCCCTATTTTCTGGATAAAATACTCATACAATATATA
1 TTGCAAAAATTGACCCG-AAAATTATTTCCTCAATTTT-TATCTAAAATACTCATA-AA-A-AT-
* * * ** * *
31699 TATATAATTTAATGCCAAAAATATTGGAGAACTTTTCATGCTTTTAATATCATTTTTCATATTTT
60 TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTT
* * * *
31764 TCTGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATACTCGTAAAAACAAATTCTTAACTC
125 TCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-AAAACAAATCCTTAAATC
* * * *
31829 CAATGTGGTTGAGATCTGATTAGATGAATATGGATATCTCAAGGAGTCTTGGCGTCAAAAATCAT
189 CAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC--GGCGTCAAAAATCAT
* * ** ** *
31894 GCAAAACTGAGCCGGGG-CCC-ATAATGTTTTTTTAGTTAAAAACTGTGATGGTTATTACACGAT
252 GCAAAACTGAGACGGGGCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGAT
31957 TTCGGCTAAAATT
316 TTCGGCTAAAATT
* * *** * * * *
31970 TTGTAAGAATTGATTAGAAAAATATTTCCTCAGTTTTT-TGCTAAAATATTCATAAAAAATATAT
1 TTGCAAAAATTGACCCGAAAATTATTTCCTCAATTTTTAT-CTAAAATACTCATAAAAATTATAT
* * * * *
32034 AATTCAACGCTAAAAAGATTGAAGAGCTTTTGA-GGTTTCTAATATCGTTTTTC
65 AATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAATATCGTTTTTC
32087 CTAATACTTT
Statistics
Matches: 1677, Mismatches: 315, Indels: 188
0.77 0.14 0.09
Matches are distributed among these distances:
309 1 0.00
310 2 0.00
312 2 0.00
313 83 0.05
314 91 0.05
315 35 0.02
316 35 0.02
317 3 0.00
318 3 0.00
319 3 0.00
320 2 0.00
321 38 0.02
322 135 0.08
323 10 0.01
324 42 0.03
325 12 0.01
326 3 0.00
327 7 0.00
328 4 0.00
329 36 0.02
330 141 0.08
331 179 0.11
332 173 0.10
333 255 0.15
334 109 0.06
335 47 0.03
336 42 0.03
337 176 0.10
338 8 0.00
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (328 bp):
TTGCAAAAATTGACCCGAAAATTATTTCCTCAATTTTTATCTAAAATACTCATAAAAATTATATA
ATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAA
TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAACAAATCCTTAAATCCAATGTG
GCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCGGCGTCAAAAATCATGCAAAACTG
AGACGGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTATTACACGATTTCGGCTAAA
ATT
Found at i:30704 original size:333 final size:326
Alignment explanation
Indices: 28411--32086 Score: 2990
Period size: 331 Copynumber: 11.2 Consensus size: 326
28401 TTTTTGGAAA
* * * * * * *
28411 AAAATACTCA-AAAAATACATATAGTTCAACGCCAAAAGGATTGGAGAGCTTTTCACGCTTTCAA
1 AAAATACTCATAAAAAT-TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA
* *
28475 TATCGTTTTTCATATATTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCACAT
65 TATCGTTTTTCATAT-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * *
28540 AAAAACAAATCCTTAAATTCAATGTGCCTGAGATTTGATTAGATGAATAAAGATATTTCAAGGAG
129 -AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * * * * * * **
28605 TCTAGGTGCCAAAAATCATACAAAACAGAGCTGTGG-CCCTATAACGCATTTTTAGTAAAAAAAA
193 TC--GGCGTCAAAAATCATGCAAAACTGAGCCG-GGCCCCGA-AACGCGTTTTTAG----CCAAA
* * *
28669 AACAGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATTTCC
250 AACCGTGAT-GTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCC
**
28734 TCAATTTTTGGCT
314 TCAATTTTTATCT
* * * * *
28747 AAAATACTCATAAAAAAATATATAATTCGACAT--CAAAAAGATTAAAGGGCTTTTTACACTTCT
1 AAAATACTCAT-AAAAATTATATAATTC-A-ATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTT
* * * *
28810 AATATTGTTTTTCCTATTTTT-TCAACTTAATTTCTAATTAAATCGAAATAAGATTCAGATGCTC
63 AATATCGTTTTTCATATTTTTCTGAA-TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* ** *
28874 ATAAAAACAAATCCTTAAATTTAATGTCGCTGAGATTTTG-TTAGATGAATATAGATATTTCAAG
127 GT-AAAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAG
* ** * * * * **
28938 GAGTTTTGGCACCAAAAATCATGCAAAACTGAGCTGGGGCCCAGAGA-GCGGTTTTAGCTGAAAA
190 GAG--TCGGCGTCAAAAATCATGCAAAACTGAGC-CGGGCCCCGAAACGCGTTTTTAGCCAAAAA
* * * * *
29002 CCGTGATAGTTAGTACATGATTTCGGCTAAAACTTTGCAAAAATTGATCCAAAAGATTTTTCCTC
252 CCGTGAT-GTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTC
* ** * *
29067 GATTTCCAGCG
316 AATTTTTATCT
* * ** * * *
29078 AAAATACTCATAAAAAATATATAATTCAACGTTAAAAGGATTTG-AGGACTTCTCACG-TATTTA
1 AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGA-TTGAAGGGCTTTTCACGCT-TTTA
* * * *
29141 ATATCGTTTTT--TATATTT-TGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATTCACAT
64 ATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * * * *
29203 AAAAAAAATACTTAAATCAAACGT-GCTTGAGATTTGATTAGATGAATAAAGATATTTTAAGGAG
129 AAAACAAATCCTTAAATCCAATGTGGC-TGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
* * * * * *
29267 TCTCGGCGCCAAAAACCATGCAAAACAT-AACCGTGGCCCTGGAACGCGTTTTTAGCCAAAAACT
193 --TCGGCGTCAAAAATCATGCAAAAC-TGAGCCG-GGCCCCGAAACGCGTTTTTAGCCAAAAACC
** * ** * *
29331 GTGATGCTTAAAGACATGATTTCGGCTAAAATTTTTTAAAAATTGATCCGAAAGATATTTCCTCA
254 GTGATG-TT-ATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCA
**
29396 ATTTTTGGCT
317 ATTTTTATCT
* * * * **
29406 AAAATACTCATAAAAAATATATAATTCGATGTCAAAAAGATTGAAGGGCTTTTAACGCTTCCAAT
1 AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
** * *
29471 ATTATCTTTCCAT-TTTTTC-AAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
66 ATCGT-TTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-
* * *
29534 AAAACAAATCCTTAAATCTAATGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAAT
129 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG-A-
* * ** * * * *
29599 TTTGGCACCAAAAATCGTGCAAAACTGAGCCAGGCCCCCGAAACACAG-TTTTAGCCGAAAA---
192 GTCGGCGTCAAAAATCATGCAAAACTGAGCC-GGGCCCCGAAACGC-GTTTTTAGCCAAAAACCG
* * * *
29660 T--CG----T--A--A--T-GG--------TTGCAAAAATTGACTCAAAAGATTTTTCCTCGATT
255 TGATGTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
* *
29704 TCTAGT-G
320 TTTA-TCT
* * * ** * * *
29711 AAAATGCTCATAAAAAATATATAATTAAACACCCAAAAA-ATTGAAAGCCTTTTTCACACTTTTA
1 AAAATACTCATAAAAATTATATAATTCAA-TGCCAAAAAGATTGAAGGGC-TTTTCACGCTTTTA
** * *
29775 ATAAAGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATGT-AGATACTTG
64 ATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGAT-TCAGATGCTCG
* * * *
29839 TAAAAAAAATCCTTAAATTCAATGTGGCTGAGATTTGAGTAGATGAACATAGATATTTCATTCAA
128 TAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATA--T--TTCAA
* * ** * * * * *
29904 GGAATCTCGGCAAT-AAAAATTTTGCAAAACTGAGTCGGGCCCCGAAATGCGTGTTTAACCGAAA
189 GG-A-GTCGGC-GTCAAAAATCATGCAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAA
* *
29968 ACCGTGATGCTTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACCCGAAAGATTTTTCCA
251 ACCGTGATG-TTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCC-
**
30033 TCAATTTTTGGCT
314 TCAATTTTTATCT
* * * * * * *
30046 AAAATACTCAT-AATA-TATATAATTTAACGTCAAAAAGATTGTAGGACTTTTCGCGCTTTTAAT
1 AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
* *
30109 ATCGTTTTTCATATTTTTCTCAATTAATTTCTAATTAAATCGAAACAAGATTCGGATGCTCGTAA
66 ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT-A
* * * * * * * * *
30174 AAACAAATTCTTCAATCCAATGTCGCTGAGATTAGATTAAATGATTATGGATATCTCAAAGAGTC
130 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTC
** * * * *
30239 TTGGCACCAAAAATCATGCAAAACTTAGACGGGGCCCCGGAACGCGTTTTTAGCCAAAAAACCAT
195 --GGCGTCAAAAATCATGCAAAACTGAG-CCGGGCCCCGAAACGCGTTTTTAGCC-AAAAACCGT
* * * **
30304 GATGATTATTACACGATTTCGGCTAGAATTTTACGAAAATTGACTTGAAAG-TTATTTCCTCAAT
256 GATG-TTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATT-TTTCCTCAAT
*
30368 TTTTATCC
319 TTTTATCT
* * * * *
30376 ACAATAATCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGTTTTTCATGCTTCTAAT
1 AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
* * * * *
30441 ATCGTTTTTCCTATTATTTTCCGAATTAATTTCTAATTAAATAGAAACATGATTCAGATGCTTGT
66 ATCGTTTTTCATA-T-TTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*** * * *
30506 TTTACAAATCCTTAAATTCAATGTGGCTGAGATTTGGTTAGATGAATGTAGATATTTCAAGGAGT
129 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGT
* *** * *
30571 CGGCGTAAAAAATCATGCAACGTTGTA-CCGTGGCCCCGAAACGTGTTTTTAACCAAAAACCGTG
194 CGGCGTCAAAAATCATGCAAAACTG-AGCCG-GGCCCCGAAACGCGTTTTTAGCCAAAAACCGTG
* * * * *
30635 AT-TTCGACTAACGTACGATTTCGGCTAATATTTTGCAAAAATTGACCAGAAATATTTTTCCTAA
257 ATGTT--A-TTAC--ACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCA
*
30699 ATTTTTGTCT
317 ATTTTTATCT
* * * * * *
30709 AAAATACTCAT-AAAATATATAAAATTCAATTCCAAAAAGATTGGAGGACTTTTCTCACTTTTAA
1 AAAATACTCATAAAAAT-TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA
*
30773 TATCGTTTTTCATATTTTTCTGAATTAATTTCAAATTAAATCGAAACAAGATTCAGATGCTCGTA
65 TATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * **
30838 AATCAAATCCTTAAATGCAATATGGCT--GA---GATT---T-AATATAGATATTTCGGGGAGTT
130 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG--
* * * * * *
30894 TCGAC-TCCAAAAATCTTGCAAAACTGAGCCGGGACCCCGAAATGTGTTTTTAGCAAAAAAACAG
193 TCGGCGT-CAAAAATCATGCAAAACTGAGCCGGG-CCCCGAAACGCGTTTTTAGC-CAAAAACCG
* * * * * *
30958 TGATGGTTAGTACACGATTTCGGCTAAAACTTTGCAAAAAATGACCAGAAA-AATATTCTCTCAA
255 TGAT-GTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTC-CTCAA
* *
31022 TTTTTAGCC
318 TTTTTATCT
* * *
31031 ATAATACTCATAAAAAATATATAATTCAATGCCAAAAA-ATTGAAGGGCTTTTCACGCTTCTAAT
1 AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
* * * * * *
31095 ATCGTTTTTCCTATTTTTTCTGAATTAATTTCTAATTAAAACGAAACATGATTCAAATGTTTGT-
66 ATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * *
31159 -AA-AAA--C---AAT----GGTTG--GA-ATTTTG-TTAGATGAATATAGATATCTCAAGGAGT
130 AAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAAGGAGT
* * * * * * *
31209 C-TCAGTGCCAAAAATCATTCAAAATTGAACCGGG-CCCTAGAACACG-TTTTAGCCAAAAATCG
194 CGGC-GT--CAAAAATCATGCAAAACTGAGCCGGGCCCCGA-AACGCGTTTTTAGCCAAAAACCG
* *
31271 TGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATATCTCCTCAAT
255 TGATG-TTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
31336 TTTTAGT-T
319 TTTTA-TCT
* * * *
31344 ATAATACTCATAAAAAGCTATATAATTCAACGCCAAAAAGATTGAATGGCTTTTCACGCTTTTAA
1 AAAATACTCATAAAAA-TTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAA
* *
31409 TATC-ATTTTCATATTTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGT
65 TATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
* * * *
31473 AAAAACAAATCCTTAAATGCAATGTGGCTAAGATTTTATTAGATGAATGTAGATATTTCAAGGAG
129 -AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAG
** * * * * *
31538 TGCCGGCACCAAAAACCATGCAAAACTGAGCCGGGGTCACGAAACGCGTTTTTAGCCTAAAACAG
193 T--CGGCGTCAAAAATCATGCAAAACTGAGCC-GGGCCCCGAAACGCGTTTTTAGCCAAAAACCG
* * * * * * *
31603 TGATGGTTAGTACACGATTTTGGCTAAAAACTTTGCAAAAACTGACCCGAAAAATTTTTCCCCTA
255 TGAT-GTTATTACACGATTTCGGCT-AAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA
***
31668 TTTTCTGGAT
318 TTTT-TATCT
* * * ** *
31678 AAAATACTCATACAATATATATATATAATTTAATGCCAAAAATATTGGAGAACTTTTCATGCTTT
1 AAAATACTCATA-AA-A-AT-TATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTT
* * *
31743 TAATATCATTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAGGATTCAGATACTC
62 TAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * * * * *
31808 GTAAAAACAAATTCTTAACTCCAATGTGGTTGAGATCTGATTAGATGAATATGGATATCTCAAGG
127 GT-AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* * ** **
31873 AGTCTTGGCGTCAAAAATCATGCAAAACTGAGCCGGGGCCC-ATAATGTTTTTTTAGTTAAAAAC
191 AGTC--GGCGTCAAAAATCATGCAAAACTGAGCCGGGCCCCGA-AACGCGTTTTTAGCCAAAAAC
* * * *** * *
31937 TGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAGAATTGATTAGAAAAATATTTCCTCA
253 CGTGAT-GTTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCA
*
32002 GTTTTT-TGCT
317 ATTTTTAT-CT
* * * * * * *
32012 AAAATATTCATAAAAAATATATAATTCAACGCTAAAAAGATTGAAGAGCTTTTGA-GGTTTCTAA
1 AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTT-TAA
32076 TATCGTTTTTC
65 TATCGTTTTTC
32087 CTAATACTTT
Statistics
Matches: 2683, Mismatches: 495, Indels: 330
0.76 0.14 0.09
Matches are distributed among these distances:
305 70 0.03
306 73 0.03
307 38 0.01
308 3 0.00
309 23 0.01
310 35 0.01
311 1 0.00
312 4 0.00
313 82 0.03
314 93 0.03
315 32 0.01
316 41 0.02
317 3 0.00
318 4 0.00
319 4 0.00
320 2 0.00
321 39 0.01
322 135 0.05
323 13 0.00
324 41 0.02
325 20 0.01
326 87 0.03
327 70 0.03
328 121 0.05
329 41 0.02
330 233 0.09
331 355 0.13
332 176 0.07
333 260 0.10
334 100 0.04
335 64 0.02
336 179 0.07
337 225 0.08
338 15 0.01
339 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.33
Consensus pattern (326 bp):
AAAATACTCATAAAAATTATATAATTCAATGCCAAAAAGATTGAAGGGCTTTTCACGCTTTTAAT
ATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
AACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCG
GCGTCAAAAATCATGCAAAACTGAGCCGGGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGT
TATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATTTTTATC
T
Found at i:53111 original size:31 final size:31
Alignment explanation
Indices: 53076--53155 Score: 108
Period size: 31 Copynumber: 2.6 Consensus size: 31
53066 CTTAATGCGC
* *
53076 TTTTGCCTCCTAAACTTGTACGATTTTGT-CG
1 TTTTGCCCCCTAAACTTGTACGATTTT-TACA
*
53107 TTTTGCCCCCTAAATTTGTACGATTTTTACA
1 TTTTGCCCCCTAAACTTGTACGATTTTTACA
*
53138 TTTTACCCCCTAAACTTG
1 TTTTGCCCCCTAAACTTG
53156 CAATTTGGAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
30 1 0.02
31 42 0.98
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.44
Consensus pattern (31 bp):
TTTTGCCCCCTAAACTTGTACGATTTTTACA
Found at i:53382 original size:63 final size:63
Alignment explanation
Indices: 53283--53410 Score: 247
Period size: 63 Copynumber: 2.0 Consensus size: 63
53273 ACATATGCAA
*
53283 TATGGTTTGAGAGGGACTAAAATGGCTCCAAATTGTAAGTTAAAGATGCAAAATGACTCAAAT
1 TATGGTTTGAGAGGGACTAAAATGGCTCCAAATTGTAAGTTAAAGATGCAAAATGACCCAAAT
53346 TATGGTTTGAGAGGGACTAAAATGGCTCCAAATTGTAAGTTAAAGATGCAAAATGACCCAAAT
1 TATGGTTTGAGAGGGACTAAAATGGCTCCAAATTGTAAGTTAAAGATGCAAAATGACCCAAAT
53409 TA
1 TA
53411 ATGTTTAGGG
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
63 64 1.00
ACGTcount: A:0.40, C:0.12, G:0.22, T:0.27
Consensus pattern (63 bp):
TATGGTTTGAGAGGGACTAAAATGGCTCCAAATTGTAAGTTAAAGATGCAAAATGACCCAAAT
Found at i:53400 original size:31 final size:31
Alignment explanation
Indices: 53301--53409 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
53291 GAGAGGGACT
*
53301 AAAATGGCTCCAAATTGTAAGTTAAAGATGC
1 AAAATGACTCCAAATTGTAAGTTAAAGATGC
* * ** *
53332 AAAATGACT-CAAATTAT-GGTTTGAGAGGGAC
1 AAAATGACTCCAAATTGTAAGTTAAAGA-TG-C
*
53363 TAAAATGGCTCCAAATTGTAAGTTAAAGATGC
1 -AAAATGACTCCAAATTGTAAGTTAAAGATGC
53395 AAAATGAC-CCAAATT
1 AAAATGACTCCAAATT
53410 AATGTTTAGG
Statistics
Matches: 60, Mismatches: 13, Indels: 11
0.71 0.15 0.13
Matches are distributed among these distances:
29 6 0.10
30 15 0.25
31 16 0.27
32 9 0.15
33 8 0.13
34 6 0.10
ACGTcount: A:0.42, C:0.13, G:0.19, T:0.26
Consensus pattern (31 bp):
AAAATGACTCCAAATTGTAAGTTAAAGATGC
Found at i:62054 original size:52 final size:47
Alignment explanation
Indices: 61992--62091 Score: 146
Period size: 47 Copynumber: 2.0 Consensus size: 47
61982 GCTGTGTACG
61992 TAATATAATGTTTTTGTAAAACTATATTTGAAAAGATTAAATTTGTCCAAAT
1 TAATATAATG-TTTT-TAAAA--AT-TTTGAAAAGATTAAATTTGTCCAAAT
*
62044 TAATATAATGTTTTTATAAATTTTGAAAAGATTAAATTTGTCCAAAT
1 TAATATAATGTTTTTAAAAATTTTGAAAAGATTAAATTTGTCCAAAT
62091 T
1 T
62092 CCTAAAAATT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
47 27 0.57
48 2 0.04
50 4 0.09
51 4 0.09
52 10 0.21
ACGTcount: A:0.42, C:0.05, G:0.09, T:0.44
Consensus pattern (47 bp):
TAATATAATGTTTTTAAAAATTTTGAAAAGATTAAATTTGTCCAAAT
Found at i:63145 original size:22 final size:22
Alignment explanation
Indices: 63111--63344 Score: 199
Period size: 22 Copynumber: 10.7 Consensus size: 22
63101 TTCCAACGTA
*
63111 GAAATATTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* *
63133 GAAGA-TTTGATAACCTCATTAT
1 GAA-ATTTTGATAACCACACTAT
* *
63155 GAAATTTTGATAACCTCCCTAT
1 GAAATTTTGATAACCACACTAT
* *
63177 -AAATATTTGATAACCACATTGT
1 GAAAT-TTTGATAACCACACTAT
*
63199 CAAATTTTGATAACCACACTAT
1 GAAATTTTGATAACCACACTAT
* * * *
63221 GAAATTTTGATAAACTCAGTGT
1 GAAATTTTGATAACCACACTAT
* *
63243 GAAATTTTGATAATCTC-CGTAT
1 GAAATTTTGATAACCACAC-TAT
*
63265 GAAATTTTGATAATCACACTAT
1 GAAATTTTGATAACCACACTAT
* * *
63287 TAAA--TTGGTAACCGCACTAT
1 GAAATTTTGATAACCACACTAT
*
63307 GAAAATTTTGATAACCACACCAT
1 G-AAATTTTGATAACCACACTAT
* * *
63330 AAAATATCGATAACC
1 GAAATTTTGATAACC
63345 TCCATATGAG
Statistics
Matches: 172, Mismatches: 31, Indels: 18
0.78 0.14 0.08
Matches are distributed among these distances:
20 13 0.08
21 8 0.05
22 132 0.77
23 19 0.11
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.33
Consensus pattern (22 bp):
GAAATTTTGATAACCACACTAT
Found at i:64654 original size:334 final size:327
Alignment explanation
Indices: 64048--65071 Score: 997
Period size: 334 Copynumber: 3.1 Consensus size: 327
64038 CAAAAATTAT
* * ** *
64048 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCCAAATATATTTCCTCAATTTTTAGCCAC
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGA-CCCAAAGAT-TTTCCTCAATTTTT-GTAAA
* * ** * ** *
64113 AATACTATTAAAAAATATATAATTCAAAGCCAAAAAGATTGAAGGTGTTTTCTCATTTTTAAAAT
63 AATACTAATAAAAAATATATAATTCAAAGCCAAAATGATTGAAGGACTTTTCACGCTTTTAATAT
*
64178 CGTTTTCATATTTTTTCGGAATTAATTTCTAATTAAATCGAAACAAGATTC-GAAT-CTCGTAAA
128 CGTTTTCATATTTTTTCTGAATTAATTTCTAATTAAA-CGAAACAAGATTCAG-ATGCTCGTAAA
** * * *
64241 AACAAATCCTTAAATGCAATGTGGCTAAGATTTCATTAGATGAATATAGATATTTCAATGAGTCT
191 AACAAATTATTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
* * * * *
64306 CGGTGCCTAAAATCATGCAAAACTGAGCTGGGGCCCCGAAACGCGTTTTTAGCTAAAAATCAT-A
256 CGGAGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCATGA
*
64370 TTGGTTAG
321 -TGGTAAG
*
64378 TACACGATTTTGGCTAAAATTTTGTTAAAAA-TGACCCAAAAGAATTTTTCCTCAATTTTTGGAT
1 TACACGATTTCGGCTAAAATTTTG-TAAAAATTGACCC-AAAG-A-TTTTCCTCAATTTTT-G-T
** * * * *
64442 AAAAATACTCCTAAAATATATATAATTTAATGCCAAATATGATTGGAGGACTTTTCACGCTTTTA
60 AAAAATACTAATAAAAAATATATAATTCAAAGCCAAA-ATGATTGAAGGACTTTTCACGCTTTTA
* * *
64507 ATATCGTGTTTCATA-TTTTTCTGAATTAATTTTTAATTAAACCGAAATAAAATTCAGATGCTCG
124 ATATCGT-TTTCATATTTTTTCTGAATTAATTTCTAATTAAA-CGAAACAAGATTCAGATGCTCG
* * * * * * * *
64571 TAAAACCAAATTTTTAAATCCAATGTGGATGAGATTTGATTAGATTAATATGGATGTCTCAAGGA
187 TAAAAACAAATTATTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGA
* * * ***
64636 GTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGTG-CCTGGAACATTTTTTTAGCCAAAAAT
252 GTCTCGGAGCCAAAAATCATGCAAAACTGAGCCGGG-GCCCCGGAACGCGTTTTTAGCCAAAAAT
** *
64700 TGTGATGGTAAT
316 CATGATGGTAAG
* * * *
64712 TACACGATTTCGACTAAAATTTTATAAAAATTGACCC---G---GTCCTCAATTTTTGTTTAAAA
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAGATTTTCCTCAATTTTTG-TAAAAA
* * * **
64771 TACTAATAAAAAATATATAATTGAACA-CCAAAAAT-ATTGAAGGGCTTTTGACGCTACTAATAT
65 TACTAATAAAAAATATATAATTCAA-AGCC-AAAATGATTGAAGGACTTTTCACGCTTTTAATAT
* *
64834 CGTTTTTCCTATTTTTTCTGTATTAATTTCT-A-T---CGAAACAAGATTCAGATGCTCGTAAAA
128 CG-TTTTCATATTTTTTCTGAATTAATTTCTAATTAAACGAAACAAGATTCAGATGCTCGTAAAA
* * * *
64894 ACAAATTATTAAACCCAACGTGGCTCAGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTC
192 ACAAATTATTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
* * * * * *
64959 GGAGCCAAAAAATCATGCGAAATTGAGCCGGGTCCCCGGAACGCGCGTTTTTTGTCAAAAATCGT
257 GGAGCC-AAAAATCATGCAAAACTGAGCCGGGGCCCCGGAA--CGCGTTTTTAGCCAAAAATCAT
65024 GATGGTTAGTTAG
319 GATGG-TA---AG
* *
65037 TACACGATTTCGGCTATAATTTTGCAAAAATTGAC
1 TACACGATTTCGGCTAAAATTTTGTAAAAATTGAC
65072 ATGAAAGATT
Statistics
Matches: 570, Mismatches: 100, Indels: 53
0.79 0.14 0.07
Matches are distributed among these distances:
318 83 0.15
319 29 0.05
321 21 0.04
322 3 0.01
323 32 0.06
324 49 0.09
325 47 0.08
329 3 0.01
330 30 0.05
331 21 0.04
332 31 0.05
333 69 0.12
334 150 0.26
335 2 0.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (327 bp):
TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAGATTTTCCTCAATTTTTGTAAAAAT
ACTAATAAAAAATATATAATTCAAAGCCAAAATGATTGAAGGACTTTTCACGCTTTTAATATCGT
TTTCATATTTTTTCTGAATTAATTTCTAATTAAACGAAACAAGATTCAGATGCTCGTAAAAACAA
ATTATTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGAG
CCAAAAATCATGCAAAACTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCAAAAATCATGATGGTA
AG
Found at i:65121 original size:2 final size:2
Alignment explanation
Indices: 65114--65142 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
65104 ATACTCATAA
65114 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 A
65143 ATTCAATGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65647 original size:21 final size:21
Alignment explanation
Indices: 65623--65674 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 21
65613 AATATCCTTA
65623 CATAATTAAAATAAAAAGT-TT
1 CATAATTAAAATAAAAA-TATT
* *
65644 CATAACTATAAATAATAATATT
1 CATAATTA-AAATAAAAATATT
65666 -ATAATTAAA
1 CATAATTAAA
65675 TATATTATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
20 2 0.08
21 14 0.54
22 10 0.38
ACGTcount: A:0.58, C:0.06, G:0.02, T:0.35
Consensus pattern (21 bp):
CATAATTAAAATAAAAATATT
Found at i:66061 original size:21 final size:21
Alignment explanation
Indices: 65994--66073 Score: 99
Period size: 21 Copynumber: 3.8 Consensus size: 21
65984 TGAATATTTT
65994 TATGAAATTTTGATAATTACCC
1 TATGAAATTTTGATAATTA-CC
* *
66016 TATAAAATTTT-ATAACTACGC
1 TATGAAATTTTGATAATTAC-C
66037 TATGAAATTTTGATAATTACC
1 TATGAAATTTTGATAATTACC
* *
66058 TATGGAATTATGATAA
1 TATGAAATTTTGATAA
66074 ACTCTATACG
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
20 1 0.02
21 32 0.64
22 17 0.34
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (21 bp):
TATGAAATTTTGATAATTACC
Found at i:66143 original size:21 final size:21
Alignment explanation
Indices: 66102--66179 Score: 77
Period size: 21 Copynumber: 3.6 Consensus size: 21
66092 ATAACCAAAA
*
66102 TATGAAATTTTAATAAACCTTTC
1 TATGAAATTTT-GT-AACCTTTC
*
66125 TATGAAATTTTGTAACCTTTT
1 TATGAAATTTTGTAACCTTTC
* *
66146 TATG-ATTTTTGATAACCTTCC
1 TATGAAATTTTG-TAACCTTTC
*
66167 TATGAGATTTTGT
1 TATGAAATTTTGT
66180 TAATCTCCTT
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 6 0.13
21 23 0.50
22 6 0.13
23 11 0.24
ACGTcount: A:0.29, C:0.12, G:0.10, T:0.49
Consensus pattern (21 bp):
TATGAAATTTTGTAACCTTTC
Found at i:66196 original size:42 final size:43
Alignment explanation
Indices: 66117--66202 Score: 104
Period size: 42 Copynumber: 2.0 Consensus size: 43
66107 AATTTTAATA
* **
66117 AACCTTTCTATGAAATTTTGTAACCTTTTTATGA-TTTTTGAT
1 AACCTTCCTATGAAATTTTGTAACCTCCTTATGATTTTTTGAT
* *
66159 AACCTTCCTATGAGATTTTGTTAATCTCCTTAT-ATTTTTTGAT
1 AACCTTCCTATGAAATTTTG-TAACCTCCTTATGATTTTTTGAT
66202 A
1 A
66203 TTATAGTATG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
42 19 0.51
43 18 0.49
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (43 bp):
AACCTTCCTATGAAATTTTGTAACCTCCTTATGATTTTTTGAT
Found at i:68816 original size:11 final size:10
Alignment explanation
Indices: 68784--68810 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
68774 TTCGCAAGTT
68784 AAAAAAGACA
1 AAAAAAGACA
68794 AAAAAAGACA
1 AAAAAAGACA
68804 AAAAAAG
1 AAAAAAG
68811 TTCAAATGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.81, C:0.07, G:0.11, T:0.00
Consensus pattern (10 bp):
AAAAAAGACA
Found at i:69202 original size:42 final size:43
Alignment explanation
Indices: 69151--69244 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
69141 AGTGCATTAT
*
69151 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
*
69192 CTAATATTCTACTCCTCCATCTCTAGATAATTTATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
69237 CTAATATT
1 CTAATATT
69245 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.38, C:0.21, G:0.05, T:0.35
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:71504 original size:2 final size:2
Alignment explanation
Indices: 71497--71539 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
71487 GCTATTTTCT
*
71497 TA TA TA TA TA TA TA CA 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 TA TA TA TA TA TA TA
71539 T
1 T
71540 GCAGTATGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:72171 original size:12 final size:12
Alignment explanation
Indices: 72154--72178 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
72144 CTTAACAGAA
72154 CGTTAGTCATAC
1 CGTTAGTCATAC
72166 CGTTAGTCATAC
1 CGTTAGTCATAC
72178 C
1 C
72179 ATAATACCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.32
Consensus pattern (12 bp):
CGTTAGTCATAC
Found at i:72256 original size:2 final size:2
Alignment explanation
Indices: 72249--72278 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
72239 TTATGATACA
72249 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
72279 TATCTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.