Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023862.1 Corchorus olitorius cultivar O-4 contig23895, 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: 12245
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Found at i:847 original size:321 final size:314
Alignment explanation
Indices: 1--851 Score: 799
Period size: 321 Copynumber: 2.6 Consensus size: 314
* * *
1 ATATCATTTTTTCCATTTTTTTAGGAA-TATTTTCTATTTAAATCGAAACAAAGATTCAGATACT
1 ATATCA-TTTTTCCA-TTTTTTCGGAATTAATTTCTATTTAAATCGAAA-AAAGATTCAGATGCT
* * * *
65 CGTAAAAACAAATCCTTATATCCAATGTGACTGGGATTTGGATCGA-AGAATATAGATATTTTAA
63 CGTAAAAACAAATCCTTAAAT-CAATTTG-CTGGGATTTGGTTCGATA-AATATAGATATTTCAA
* * *
129 GAAGTCTTTACGCCAAAAAACATACAAAACTGAGCCGGGGACCCGGAACGCGTTTTTAACAAAAA
125 GGAGTCTTTACGCCAAAAATCATACAAAACTGAG-CGGGGACCCGGAACGCGTTTTTAGCAAAAA
* ** *
194 ACCGTGATGTACACGATTTCGGCTAAAATTTTGTAAAAACTGACCCAAAAAATTTATTCTCAATT
189 ACCGTGATG-----G--TT-AG-TAAAATTAGGTAAAAACTGACCCAAAAAATTTATTCTCAACT
* * * * *
259 TTTTTGCCACAATAGTCAGGAACAATATAAGATTAGATGCAAAAAAAATGAAGGGTTTTTCATGC
245 TTTTTGCCACAATACTCAGAAAAAATATAAGATTAGACGCAAAAAAAATGAAGGGCTTTTCATGC
324 TTCTA
310 TTCTA
* * * * * *
329 ATATC-GTTTTCCATTTTTTC--AGTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTC--
1 ATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGCTCGT
* * * * * * *
389 ATAAACAAACCCTTAAATCAATTGTGGTTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAG
66 AAAAACAAATCCTTAAATCAATT-T-GCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAG
** * * * ***
454 TCTTTTTGCCAAAAAT-ATTCAAAACTGAGCTGGGG-CCTCGAAACACGTTTTTAGCCCCCAAAC
129 TCTTTACGCCAAAAATCATACAAAACTGAGC-GGGGACC-CGGAACGCGTTTTTAG-CAAAAAAC
* ** * *** * *
517 GGTGATGGTTAGTAACGAATTAGGCTAAAAACTGAGTCGAATTTTTTTTTCTGAACTTTTTT-CC
191 CGTGATGGTTAGTAA--AATTAGG-TAAAAACTGACCCAAAAAATTTATTCTCAACTTTTTTGCC
* * * *
581 ATAATACTCAGAAAAAATATATA-ATTCA-ACGCCAAAAAGATTGACGGGCTTTTCATGCTTCTA
253 ACAATACTCAGAAAAAATATA-AGATT-AGACG-CAAAAAAAATGAAGGGCTTTTCATGCTTCTA
*
644 ATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAATAAGATTCAGATGCTCGT
1 ATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGCTCGT
*
709 AAAAACAAATCCTCTAAATCGAATTTCGCTGGGATTTGGTTCGATAAATACAGATATTTCAAGGA
66 AAAAACAAATCCT-TAAATC-AATTT-GCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGA
*** * *
774 GTCTTTACAATAAAAATCATGCAAAATTGAGTCGGGGACCCGGAACGCGTTTTTAGCAAAAAACC
128 GTCTTTACGCCAAAAATCATACAAAACTGAG-CGGGGACCCGGAACGCGTTTTTAGCAAAAAACC
839 GTGATGGTTAGTA
192 GTGATGGTTAGTA
852 TATGATTTCG
Statistics
Matches: 419, Mismatches: 81, Indels: 53
0.76 0.15 0.10
Matches are distributed among these distances:
312 3 0.01
313 1 0.00
314 31 0.07
315 62 0.15
316 15 0.04
318 35 0.08
319 3 0.01
320 44 0.11
321 138 0.33
322 34 0.08
323 17 0.04
324 18 0.04
325 6 0.01
326 7 0.02
328 5 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (314 bp):
ATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAAAAAGATTCAGATGCTCGT
AAAAACAAATCCTTAAATCAATTTGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTC
TTTACGCCAAAAATCATACAAAACTGAGCGGGGACCCGGAACGCGTTTTTAGCAAAAAACCGTGA
TGGTTAGTAAAATTAGGTAAAAACTGACCCAAAAAATTTATTCTCAACTTTTTTGCCACAATACT
CAGAAAAAATATAAGATTAGACGCAAAAAAAATGAAGGGCTTTTCATGCTTCTA
Found at i:1585 original size:13 final size:13
Alignment explanation
Indices: 1578--1685 Score: 126
Period size: 13 Copynumber: 7.8 Consensus size: 13
1568 GGGTTACGGT
1578 TTAGGGTTTTAGGG
1 TTAGGG-TTTAGGG
*
1592 TTAGGATTTAGGG
1 TTAGGGTTTAGGG
1605 TTAGGGTTTAAGGG
1 TTAGGGTTT-AGGG
*
1619 TTTAGGGTTTTAGTG
1 -TTAGGG-TTTAGGG
1634 TTAGGGTTTTAGGG
1 TTAGGG-TTTAGGG
1648 TTTTAGGGTTTAGGG
1 --TTAGGGTTTAGGG
1663 TTAGGGTTTAGGG
1 TTAGGGTTTAGGG
*
1676 TTATGGTTTA
1 TTAGGGTTTA
1686 TTTCAAATTA
Statistics
Matches: 84, Mismatches: 5, Indels: 11
0.84 0.05 0.11
Matches are distributed among these distances:
13 37 0.44
14 22 0.26
15 16 0.19
16 9 0.11
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (13 bp):
TTAGGGTTTAGGG
Found at i:1593 original size:21 final size:20
Alignment explanation
Indices: 1567--1685 Score: 118
Period size: 21 Copynumber: 5.7 Consensus size: 20
1557 GAAAAAATGA
1567 AGGGTTACGGTTTAGGGTTTT
1 AGGGTTA-GGTTTAGGGTTTT
1588 AGGGTTAGGATTTAGGG--TT
1 AGGGTTAGG-TTTAGGGTTTT
1607 AGGGTTTAAGGGTTTAGGGTTTT
1 AGGG-TT-A-GGTTTAGGGTTTT
*
1630 AGTGTTAGGGTTTTAGGGTTTT
1 AGGGTTA-GG-TTTAGGGTTTT
*
1652 AGGGTTTAGGGTTAGGG-TTT
1 AGGG-TTAGGTTTAGGGTTTT
1672 AGGGTTATGGTTTA
1 AGGGTTA-GGTTTA
1686 TTTCAAATTA
Statistics
Matches: 85, Mismatches: 4, Indels: 19
0.79 0.04 0.18
Matches are distributed among these distances:
19 9 0.11
20 16 0.19
21 32 0.38
22 20 0.24
23 8 0.09
ACGTcount: A:0.17, C:0.01, G:0.39, T:0.43
Consensus pattern (20 bp):
AGGGTTAGGTTTAGGGTTTT
Found at i:1627 original size:7 final size:7
Alignment explanation
Indices: 1575--1677 Score: 115
Period size: 8 Copynumber: 14.6 Consensus size: 7
1565 GAAGGGTTAC
1575 GGTTTAG
1 GGTTTAG
1582 GGTTTTAG
1 GG-TTTAG
1590 GG-TTAG
1 GGTTTAG
*
1596 GATTTAG
1 GGTTTAG
1603 GG-TTAG
1 GGTTTAG
1609 GGTTTAAG
1 GGTTT-AG
1617 GGTTTAG
1 GGTTTAG
1624 GGTTTTAG
1 GG-TTTAG
*
1632 TG-TTAG
1 GGTTTAG
1638 GGTTTTAG
1 GG-TTTAG
1646 GGTTTTAG
1 GG-TTTAG
1654 GGTTTAG
1 GGTTTAG
1661 GG-TTAG
1 GGTTTAG
1667 GGTTTAG
1 GGTTTAG
1674 GGTT
1 GGTT
1678 ATGGTTTATT
Statistics
Matches: 84, Mismatches: 4, Indels: 16
0.81 0.04 0.15
Matches are distributed among these distances:
6 22 0.26
7 28 0.33
8 34 0.40
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.44
Consensus pattern (7 bp):
GGTTTAG
Found at i:1640 original size:29 final size:28
Alignment explanation
Indices: 1578--1685 Score: 141
Period size: 29 Copynumber: 3.9 Consensus size: 28
1568 GGGTTACGGT
*
1578 TTAGGGTTTTAGGG-TTAGGATTTAGGG
1 TTAGGGTTTTAGGGTTTAGGGTTTAGGG
* *
1605 TTAGGGTTTAAGGGTTTAGGGTTTTAGTG
1 TTAGGGTTTTAGGGTTTAGGG-TTTAGGG
1634 TTAGGGTTTTAGGGTTTTAGGGTTTAGGG
1 TTAGGGTTTTAGGG-TTTAGGGTTTAGGG
*
1663 TTAGGG-TTTAGGG-TTATGGTTTA
1 TTAGGGTTTTAGGGTTTAGGGTTTA
1686 TTTCAAATTA
Statistics
Matches: 72, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
26 9 0.12
27 13 0.18
28 12 0.17
29 31 0.43
30 7 0.10
ACGTcount: A:0.17, C:0.00, G:0.39, T:0.44
Consensus pattern (28 bp):
TTAGGGTTTTAGGGTTTAGGGTTTAGGG
Found at i:2914 original size:322 final size:318
Alignment explanation
Indices: 1693--3129 Score: 1451
Period size: 322 Copynumber: 4.5 Consensus size: 318
1683 TTATTTCAAA
* * * * *
1693 TTAAATCGAAACAAGATTTAGATGCTGGTAAAAACAAACCCTTAACTCAAATGTAGCTGAG-TCT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTAGCTGGGAT-T
* * * *
1757 TGGTTAGATGAATATAGATATTTCAAGGAGTC-TTGCAGCCAAAAATATTCAAAACTGAGCTGGG
65 TGGTTTGATAAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATATGCAAAACTGAGC-GGG
* * * * *
1821 GCCCCGAAACACGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACAATTTAGGCTAAAAACGGA
128 GACCCGAAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGA
* * *
1886 GTCGGAAAATTGTTTTCTAAATCTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAA
192 CTCGAAAAATT-TTTTCTGAATCTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAA
* *
1951 AAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTGTTAGGAATTAATTTCTAT
256 AAAGATTGACGGG-TTTTCACGCTTCTAATATCATTTTTCCATTTTTTAGCAATTAATTTCTAT
* * * * * * *
2015 TTAAATCGAAACAATATTCAAATGCTCGTTAAACCAAATCCTTATATCCAATGTGGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTAGCTGGGATTT
* * *
2080 GGATCT-A-AGAATATAGATATTTCAAGAAGTCTTTACGCCAAAAATCATGCAAAACTAAGCCGG
66 GG-TTTGATA-AATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAG-CGG
** * *
2143 GGACCCGAAACGTATTTTTAACAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTG
127 GGACCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTAGGC----------
* * * * * * * * * * *
2208 TAAAAACTGACCCAAAAAATTTATCCTCAATTTTTTACCACAATAGTCAGGAACAATATATAATT
182 TAAAAACTGACTCGAAAAATTTTTTCTGAATCTTTTGCCACAATACTTAGAAAAAATATATAATT
* * * * * * * *
2273 CAATGCAAAAAAAAATGAAGGGTTTTACACGCTTCTAATATCGTTTTTCCATTTTTT--CAGTTT
247 CAACGCCAAAAAGATTGACGGGTTTT-CACGCTTCTAATATCATTTTTCCATTTTTTAGCAATTA
*
2336 ATTTCTAA
311 ATTTCTAT
* * * *
2344 TTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAAATCAAATGTAGCTGAGACTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTAGCTGGGATTT
* * * ** *
2409 -GTTTGGATGAATATAGATATTTCTAGGATTCTTTTTGCCAAAAATATTCAAAACTGAGCTGGGG
66 GGTTT-GATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATATGCAAAACTGAGC-GGGG
* * * * *
2473 TCCCGAAACGCGTTTTTAGCCCAAAAA-C-TG-T-GAT-G-ACACGATTCATGCTAAAAAACTGA
129 ACCCGAAACGCGTTTTTAG-CAAAAAACCGTGATGGTTAGTACACGATTTAGGCT-AAAAACTGA
* **
2532 CTCGAAAAAATTTTTCTGAAAT-TTTTGCCACAATA-TTCAGAAAAAATATATAATTCAACGCGG
192 CTCGAAAAATTTTTTCTG-AATCTTTTGCCACAATACTT-AGAAAAAATATATAATTCAACGCCA
*
2595 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCAATTTTTTCA-CAATTAATTTCTA
255 AAAAGATTGACGGG-TTTTCACGCTTCTAATATCATTTTTCCATTTTTT-AGCAATTAATTTCTA
2659 T
318 T
* * * * *
2660 TTAAATCGAAATAAGATTCAAATGCTCGTAAAAACAAATCGTTAAATCGAATGTGGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTAGCTGGGATTT
* *
2725 GGTTTGATAAATATAGATATTTCAAGGAGTCTTTACAACAAAAAAATATGCAAAACTGAGTCGGG
66 GGTTTGATAAATATAGATATTTCAAGGAGTCTTTAC-GC-CAAAAATATGCAAAACTGAG-CGGG
* * * *
2790 GAGCCGGAACGCGTTTTTAGCAAAAAACCGCGATGGTTAGTACACGATTTAGGCTAAAAACTGAG
128 GACCCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGAC
* *
2855 TCGAAAATTTTTTTCTGAATCTTTTGCCTCAATACTTAGAAAAAATATATAATTCAACGCCAAAA
193 TCGAAAAATTTTTTCTGAATCTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAAAA
* * *
2920 AGATTGACGGG-TTT-----TTC----GTC---TTTCCA-TTTTTAGGAATTATTTTCTAT
258 AGATTGACGGGTTTTCACGCTTCTAATATCATTTTTCCATTTTTTAGCAATTAATTTCTAT
* * * *
2967 TTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTTGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTAGCTGGGATTT
* * * * *
3032 GGTTCGA-AGAATATAAATATTTTAAGAAGTCTTTACACCAAAAATCATGCAAAACTGAGCCGGG
66 GGTTTGATA-AATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAG-CGGG
* *
3096 GACCCGGAACGCGTTTTTAACAAAAAACCGTGAT
128 GACCCGAAACGCGTTTTTAGCAAAAAACCGTGAT
3130 AACGTACACG
Statistics
Matches: 919, Mismatches: 153, Indels: 102
0.78 0.13 0.09
Matches are distributed among these distances:
305 6 0.01
306 52 0.06
307 105 0.11
308 5 0.01
311 2 0.00
313 2 0.00
314 92 0.10
315 10 0.01
316 93 0.10
317 11 0.01
318 39 0.04
319 2 0.00
320 4 0.00
321 5 0.01
322 189 0.21
323 58 0.06
324 2 0.00
325 2 0.00
326 1 0.00
327 5 0.01
328 32 0.03
329 102 0.11
330 4 0.00
331 80 0.09
332 16 0.02
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (318 bp):
TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTAGCTGGGATTT
GGTTTGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATATGCAAAACTGAGCGGGGAC
CCGAAACGCGTTTTTAGCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGACTCG
AAAAATTTTTTCTGAATCTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAAAAAGA
TTGACGGGTTTTCACGCTTCTAATATCATTTTTCCATTTTTTAGCAATTAATTTCTAT
Found at i:3290 original size:7 final size:7
Alignment explanation
Indices: 3250--3365 Score: 134
Period size: 7 Copynumber: 16.9 Consensus size: 7
3240 AAGGGCTACA
3250 GTTTAGG
1 GTTTAGG
3257 GTTTAAGG
1 GTTT-AGG
**
3265 GTTTATA
1 GTTTAGG
*
3272 GTTTATG
1 GTTTAGG
3279 G-TTAGG
1 GTTTAGG
3285 GTTTAGG
1 GTTTAGG
3292 G-TTAGG
1 GTTTAGG
3298 GTTTAGGG
1 GTTTA-GG
3306 GTTTAGG
1 GTTTAGG
3313 G-TTAGG
1 GTTTAGG
3319 GTTTAGG
1 GTTTAGG
3326 GTTTAAGG
1 GTTT-AGG
*
3334 GTTTAGT
1 GTTTAGG
3341 G-TTAGG
1 GTTTAGG
3347 GTTTAGG
1 GTTTAGG
3354 G-TTAGG
1 GTTTAGG
3360 GTTTAG
1 GTTTAG
3366 AGTACACGAT
Statistics
Matches: 95, Mismatches: 6, Indels: 16
0.81 0.05 0.14
Matches are distributed among these distances:
6 28 0.29
7 46 0.48
8 21 0.22
ACGTcount: A:0.17, C:0.00, G:0.41, T:0.42
Consensus pattern (7 bp):
GTTTAGG
Found at i:4453 original size:323 final size:322
Alignment explanation
Indices: 3840--7120 Score: 3425
Period size: 323 Copynumber: 10.1 Consensus size: 322
3830 TTATTTCAAA
* * * *
3840 TTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAAAT-CAATTGTGGTTGAGACT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAA-TGTGGCTGAGATT
* ** * * * *
3904 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAATATTCGAAATTGAGTTGGGG
65 TGGTTAGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATATGCAAAACTGAGTCGGGG
* ** * * *
3969 -CCTCGAAGCATGTTTTTAGCCCAAAAACGGTGATGGTTAGTA-ACGAATTAGGCTAAAAACTGA
130 ACC-CGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGA
* *** *
4032 GTCGAAATTTTTTGTTTTTCTGAAATTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGC
194 CTCGAAA--AAAT-TTTTTCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGC
*
4097 CAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCT
256 CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCT
4162 AT
321 AT
* * * *
4164 TTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * ** *
4229 GGTTCGATAAATACAGATATTTCAAGGAGTCTTTACAACAAAAATCAAGCAAAACTGAGTCGGGG
66 GGTTAGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAGTCGGGG
* * * *
4294 ACTCGGAACGCGTTTTTAG-CAAAAAACCGTGACGGTTAGTACACGATTTAGGCTAAAAACTGAG
130 ACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGAC
*
4358 TCGAAAAAATTTTTTTCTGAATTTTTTGCCACAATACTCT-GAAAAAATATATAATTCAATGCCA
195 TCGAAAAAA-TTTTTTCTGAATTTTTTGCCACAATACT-TAGAAAAAATATATAATTCAACGCCA
* * *
4422 AAAACATTGACGGGCATTTCACGCTTCTAATATCATTTTACCATTTTTTCGGAATTAATTTCTAT
258 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTAT
* * * *
4487 TTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAATCCATATATCCAATGTGGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * **
4552 GGATCA-A-AGAATACAGATATTTCAAGGAGTCATTACGCCAAAAATCATGCAAAACTGAGTCAA
66 GG-TTAGATA-AATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAGTCGG
* * * * * *
4615 GGACCCGGAACACGATTTTAG-CAAAAAACTGTGATGGTTAGTACACGATTTCGTCTAAAATTTT
128 GGACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGC---------
* ** * * * * *
4679 GTAAAAACTGACCCG-AAAAATTCATCCTCAATTTTATTGCCACAATAATTAGGAACAATATATA
184 -TAAAAACTGACTCGAAAAAATTTTTTCTGAATTTT-TTGCCACAATACTTAGAAAAAATATATA
* * * * * * *
4743 ATTCAAAGCAAAAAAAAAATGAAGGGTTTTTCAAGCTTCTAATATCA-TTTTCCA-TTTTTC--A
247 ATTCAACGC-CAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGA
* * *
4804 GTTTATTTCTAA
311 ATTAATTTCTAT
* * *
4816 TTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTAGCTGAGACTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA-TT
* * * * *
4881 TGATTAGATGAATATACATATTTCAAGGAGCCTTT-CTGCCAAAAATATTCAAAACTGAG-CTGG
65 TGGTTAGATAAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATATGCAAAACTGAGTC-GG
* * * *
4944 GGCCCCGAAACTCGTTTTTAGCCCAAAAACCGTTATGG--AGTACACGATTTAGGCTAAAAACTG
128 GGACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTG
* * *
5007 ACTTGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTCAGAAAAAAATATATAATTGAACGCC
193 ACTCGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTTAG-AAAAAATATATAATTCAACGCC
* *
5072 AAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTCAGAATTAATTTCTA
257 AAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTA
5137 T
322 T
* * *
5138 TTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * ** *
5203 GGTTCGAAAAATATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAAAATGAGTCGGGG
66 GGTTAGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAGTCGGGG
* * * *
5268 ACCCGTAACGCGTTTTTA-ACAAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTGT
130 ACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGC----------T
* * * * * ** * * * *
5332 AAAAACTAACCCG-AAAAATTTATCCTCAATTTTTTGGTACATTAGTTAGGAACAATATATAATT
185 AAAAACTGACTCGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATT
* * * * * **
5396 CAATG-CAAAAA-AATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTT-TTAATAT
250 CAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAAT-T
*
5458 AA-TTCTAA
314 AATTTCTAT
* * * *
5466 TTAAATCGAAATAAGATTTAGATGCTCGTAAAAACAAAACCTTAAATCCAATGTGGCTGAGACTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* *** *
5531 GGTTAGATGAATATAGATATTTCAAGGAGTCTTTTTACCAAAAATATTCAAAACTGAG-CTGGGG
66 GGTTAGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATATGCAAAACTGAGTC-GGGG
* * * *
5595 CCCCGAAATGCGTTTTTAGCCCAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGAG
130 ACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGAC
** *
5660 TCG-AAAAATTTTTTCTGAATTTTTTGCCACAATACTCCGAAAAAATATATTATTCAACGCCAAA
195 TCGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAAA
* * * *
5724 ACGATTGATGGGCTTTTCACGCTTCTAATTTCATTTTTCCATTTTTTCAGAATTAATTTCTAT
260 AAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTAT
** * *
5787 TTAAATCGAAGTAAGATTCAGATGCTCGTAAAAAC-AATCCTTAAATCAAATGTGGCTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * ***
5851 GGTTCGATAAATATAGAAATTTCAAGGAGTCTTTATAACAAAAATCATGCAAAACTGAGTCGGGG
66 GGTTAGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAGTCGGGG
* * * * * ** *
5916 ACCCGTAACGCGTTTTTA-ACAAAAAACCGTGACGATTTCGT-CTAAAATTT-TG-TAAAAACTG
130 ACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATG-GTTAGTAC-ACGATTTAGGCTAAAAACTG
* ** * * * * * * * *
5977 ACCCG-AAAAATTCATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATGATTCAAAGCA
193 ACTCGAAAAAATTTTTTCTGAATTTT-TTGCCACAATACTTAGAAAAAATATATAATTCAACGCC
* * * * * * * *
6041 AGAAAAAAATGAAGGGTTTTTCAAGCTTCTAATATC-GTTTTCCA-TTTTTC--AGTTTATTTCT
257 A-AAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCT
*
6102 AA
321 AT
* * *
6104 TTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTAGCTGAGACTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGA-TT
* * * *
6169 T-GTTAGATGAATATAGATATTTCAAGGAGCCTTT-CTGCCAAAAATATTCAAAACCGAG-CTGG
65 TGGTTAGATAAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATATGCAAAACTGAGTC-GG
* * * *
6231 GGCCCCGAAACACGTTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTAGGCTAAAAACTG
128 GGACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTG
* * * * *
6296 ACTCGAAAAATTTTTTTCTGATTTTTTTGCCACAATACTCAGAAAAAATATATAATTTAACGCGA
193 ACTCGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCA
* *
6361 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCTATTTTTTCGGAATTAATTTCAAT
258 AAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTAT
* * * *
6426 TTGAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGTTGGGATTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * * * * * *
6491 AGATCGA-AGAATATAGATATTTCAAGAAGTCTTTACGCCAAAATTCATGCAAAACTGAGCCGGA
66 GGTTAGATA-AATATAGATATTTCAAGGAGTCTTTACGCCAAAAAT-ATGCAAAACTGAGTCGGG
* * *
6555 GACCCGGAACGCATTTTTAG-CAAAAAACCGTGATGGTTAGTACACGATTTCGGCCAAAATTTTG
129 GACCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGG-C---------
* * * * * * * *
6619 TAAAAACTAAC-CCAAAAAATTTATCCTCAATTTTTTTGCCACAATAGTTAGGAACAATATATAA
184 TAAAAACTGACTCGAAAAAATTTTTTCTGAA-TTTTTTGCCACAATACTTAGAAAAAATATATAA
* * * * * * **
6683 TTCAATG-CAAAAA-AATGAAGGGTTTTTCACGCTTCTAATATCGTTTTTTCATTTTTT-TTAAT
248 TTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAAT
*
6745 ATAA-TTCTAA
313 -TAATTTCTAT
* * * * *
6755 TTAAATAGAAACATGATTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTT
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
* * *
6820 GGTTAGATAAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATATTCAAAATTGAGCCGGGG
66 GGTTAGATAAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATATGCAAAACTGAGTCGGGG
* * * *
6884 -CCTCGAAATGCGTTTTTAGCCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAAACTTA
130 ACC-CGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGA
* * * *
6948 CTCAAAAAAATTTTTTCTGAATTTTTTACTACAATACTCAGAAAAAATATATAATTCAACGCCAA
194 CTCGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAA
* * *
7013 AAAGATTGACCGGCTTTTCACGCTTCTAATATCAATTTTCCATTTTTTCGGAATTAATTTCAAT
259 AAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTAT
* *
7077 TTAAATTGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTA
1 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTA
7121 TTCCGAACCT
Statistics
Matches: 2438, Mismatches: 419, Indels: 202
0.80 0.14 0.07
Matches are distributed among these distances:
316 1 0.00
317 81 0.03
318 212 0.09
319 175 0.07
320 207 0.08
321 202 0.08
322 274 0.11
323 315 0.13
324 115 0.05
325 55 0.02
326 2 0.00
327 32 0.01
328 184 0.08
329 268 0.11
330 96 0.04
331 52 0.02
332 114 0.05
333 53 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (322 bp):
TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTT
GGTTAGATAAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATATGCAAAACTGAGTCGGGGA
CCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGACT
CGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTTAGAAAAAATATATAATTCAACGCCAAAA
AGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTAT
Found at i:5085 original size:651 final size:649
Alignment explanation
Indices: 3472--7120 Score: 4308
Period size: 651 Copynumber: 5.6 Consensus size: 649
3462 ATTGACAGGC
* * * *
3472 TTTTCACGCTTCTAATACCATTTTTCCATTTTTTCGGAATTAATTTC-AATTTAAATCGAAATAA
1 TTTTCAAGCTTCTAATATCA-TTTTCCATTTTTTC--AATTTATTTCTAA-TTAAATCGAAACAA
* * * * * * *
3536 GATTCAGATACTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGGGA-TTTGGTTCGATAAATA
62 GATTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATA
** * * * *
3600 TAGATATTTCAAGGAGTCTTTAC-AACAAAAATCATGCAAAACTGAG-TCGGGGACCCGGAACGC
127 TAGATATTTCAAGGAGTCTTT-CTGCCAAAAAT-ATTCAAAACTGAGCT-GGGGCCCCGAAACTC
* * * * *
3663 GTTTTTAG-CAAAAAACCGTGATTGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATAGACC
189 GTTTTTAGCCCAAAAACCGTGA-TGGTAGTACACGATTTAGGCT---A------AAAACT-GACT
* * * * * * * * * * *
3727 CG-AAAAATTTATCCTCAATTTTTTTCCCACAATAGTTAGGAACAATATATGATTCAATGCAAAA
243 CGAAAAAATTTTTTCTGAA-TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAA
* * * ** *
3791 AAAATTAAAGGATTTTTCACGCTTCTAATATCGTTTTT---TTTATTTC------AA-----A-T
307 AAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTCCATTT-TTTCGGAATTAATTTCTATT
* * * * * *
3841 TAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACCCTTAAATCAATTGTGGTTGAGACTTG
371 TAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTTG
* * ** **** * * * *
3906 GTTAGATGAATATAGATATTTCAAGGAGTCTTTTTGCCAAAAAT-ATTCGAAATTGAGTTGGGG-
436 GATCGAAAAATATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAGTCGGGGA
* * * * * * * *
3969 CCTC-GAA-GCATGTTTTTAGCCCAAAAACGGTGATGGTTAGTA-ACGAATTAGGCTAAAAACTG
501 CC-CGGAACGC--GATTTTA-ACAAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AAAATTT
* ** ***** * * * * * * *
4031 AGTCGAAA-TTTTTTG-----TT-TTTCTGAAATTT-TTGCCACAATACTTAGAAAAAATATATA
561 TGTAAAAACTAACCCGAAAAATTCATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATA
* * * *
4088 ATTCAACGCCAAAAAGATTGACGGGC
626 ATTCAAAG-CAAAAA-AATGAAGGGT
* * * *
4114 TTTTCATGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAATAAG
1 TTTTCAAGCTTCTAATATCA-TTTTCCATTTTTTC--AATTTATTTCTAATTAAATCGAAACAAG
* * * * * * * *
4179 ATTCAGTTGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGA-TTTGGTTCGATAAATAC
63 ATTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATAT
** ** * * * *
4243 AGATATTTCAAGGAGTCTTTAC-AACAAAAATCAAGCAAAACTGAG-TCGGGGACTCGGAACGCG
128 AGATATTTCAAGGAGTCTTT-CTGCCAAAAAT-ATTCAAAACTGAGCT-GGGGCCCCGAAACTCG
* * *
4306 TTTTTAG-CAAAAAACCGTGACGGTTAGTACACGATTTAGGCTAAAAACTGAGTCGAAAAAATTT
190 TTTTTAGCCCAAAAACCGTGATGG-TAGTACACGATTTAGGCTAAAAACTGACTCGAAAAAA-TT
* * *
4370 TTTTCTGAATTTTTTGCCACAATACTCTGAAAAAATATATAATTCAATGCCAAAAACATTGACGG
253 TTTTCTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGG
* * *
4435 GCATTTCACGCTTCTAATATCATTTTACCATTTTTTCGGAATTAATTTCTATTTAAATTGAAACA
318 GCTTTTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAACA
* * *
4500 AGATTCAGATGCTCGTAAAAACAAATCCATATATCCAATGTGGCTGGGATTTGGATC-AAAGAAT
383 AGATTCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTTGGATCGAAA-AAT
* * ** ** *
4564 ACAGATATTTCAAGGAGTCATTACGCCAAAAATCATGCAAAACTGAGTCAAGGACCCGGAACACG
447 ATAGATATTTCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCG
* * * *
4629 ATTTTAGCAAAAAACTGTGATGGTTAGTACACGATTTCGTCTAAAATTTTGTAAAAACTGACCCG
512 ATTTTAACAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCG
*
4694 AAAAATTCATCCTCAATTTTATTGCCACAATAATTAGGAACAATATATAATTCAAAGCAAAAAAA
577 AAAAATTCATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATAATTCAAAGC---AAAA
4759 AAATGAAGGGT
639 AAATGAAGGGT
*
4770 TTTTCAAGCTTCTAATATCATTTTCCA-TTTTTCAGTTTATTTCTAATTAAATCGAAACAAGATT
1 TTTTCAAGCTTCTAATATCATTTTCCATTTTTTCAATTTATTTCTAATTAAATCGAAACAAGATT
* * *
4834 TAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTAGCTGAGACTTTGATTAGATGAATATACA
66 TAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATATAGA
*
4899 TATTTCAAGGAGCCTTTCTGCCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAACTCGTTTTTA
131 TATTTCAAGGAGTCTTTCTGCCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAACTCGTTTTTA
* *
4964 GCCCAAAAACCGTTATGG-AGTACACGATTTAGGCTAAAAACTGACTTGAAAAAATTTTTTCTGA
196 GCCCAAAAACCGTGATGGTAGTACACGATTTAGGCTAAAAACTGACTCGAAAAAATTTTTTCTGA
*
5028 ATTTTTTGCCACAATACTCAGAAAAAAATATATAATTGAACGCCAAAAAGATTGACGGGCTTTTC
261 ATTTTTTGCCACAATACTCAG-AAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTC
* * *
5093 ACGCTTCTAATATCATTTTTCCAATTTTTCAGAATTAATTTCTATTTAAATCGAAATAAGATTCA
325 ACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCA
* * *
5158 GTTGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGAGATTTGGTTCGAAAAATATAGATAT
390 GATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTTGGATCGAAAAATATAGATAT
* * *
5223 TTCAAGGAGTCTTTACAACAAAAATCATGCAAAAATGAGTCGGGGACCCGTAACGCGTTTTTAAC
455 TTCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGATTTTAAC
* *
5288 AAAAAACCATGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAAAATTT
520 AAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAAAATTC
** * *
5353 ATCCTCAATTTT-TTGGTACATTAGTTAGGAACAATATATAATTCAATGCAAAAAAATGAAGGGT
585 ATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATAATTCAAAGCAAAAAAATGAAGGGT
* * * * * *
5417 TTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTAATATAATTCTAATTAAATCGAAATAAGA
1 TTTTCAAGCTTCTAATATC-ATTTTCCA-TTTTTTCAATTTATTTCTAATTAAATCGAAACAAGA
*
5482 TTTAGATGCTCGTAAAAACAAAACCTTAAATCCAATGTGGCTGAGAC-TTGGTTAGATGAATATA
64 TTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATATA
* *
5546 GATATTTCAAGGAGTCTTTTTACCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAA-TGCGTTT
129 GATATTTCAAGGAGTCTTTCTGCCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAACT-CGTTT
*
5610 TTAGCCCAAAAACCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGAGTCG-AAAAATTTTTT
193 TTAGCCCAAAAACCGTGATGG-TAGTACACGATTTAGGCTAAAAACTGACTCGAAAAAATTTTTT
* * * *
5674 CTGAATTTTTTGCCACAATACTCCGAAAAAATATATTATTCAACGCCAAAACGATTGATGGGCTT
257 CTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* * **
5739 TTCACGCTTCTAATTTCATTTTTCCATTTTTTCAGAATTAATTTCTATTTAAATCGAAGTAAGAT
322 TTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGAT
* *
5804 TCAGATGCTCGTAAAAAC-AATCCTTAAATCAAATGTGGCTGGGATTTGGTTCGATAAATATAGA
387 TCAGATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTTGGATCGAAAAATATAGA
* * * *
5868 AATTTCAAGGAGTCTTTATAACAAAAATCATGCAAAACTGAGTCGGGGACCCGTAACGCGTTTTT
452 TATTTCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGATTTT
* *
5933 AACAAAAAACC------G-T-G---ACGATTTCGTCTAAAATTTTGTAAAAACTGACCCGAAAAA
517 AACAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAAAA
*
5987 TTCATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATGATTCAAAGCAAGAAAAAAATG
582 TTCATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATAATTCAAAGC---AAAAAAATG
6052 AAGGGT
644 AAGGGT
* *
6058 TTTTCAAGCTTCTAATATCGTTTTCCA-TTTTTCAGTTTATTTCTAATTAAATCGAAACAAGATT
1 TTTTCAAGCTTCTAATATCATTTTCCATTTTTTCAATTTATTTCTAATTAAATCGAAACAAGATT
*
6122 TAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTAGCTGAGACTTT-GTTAGATGAATATAGA
66 TAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATATAGA
* * *
6186 TATTTCAAGGAGCCTTTCTGCCAAAAATATTCAAAACCGAGCTGGGGCCCCGAAACACGTTTTTA
131 TATTTCAAGGAGTCTTTCTGCCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAACTCGTTTTTA
* *
6251 GCCCAAAAATCGTGATGGTTAGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTTCTG
196 GCCCAAAAACCGTGATGG-TAGTACACGATTTAGGCTAAAAACTGACTCGAAAAAATTTTTTCTG
* * *
6316 ATTTTTTTGCCACAATACTCAGAAAAAATATATAATTTAACGCGAAAAAGATTGACGGGCTTTTC
260 AATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTC
* * *
6381 ACGCTTCTAATATCATTTTTCTATTTTTTCGGAATTAATTTCAATTTGAATCGAAACAAGATTCA
325 ACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCA
* * * * *
6446 GATGCTCGTAAAAACAAATCCTTATATCCAATGTGGTTGGGATTTAGATCGAAGAATATAGATAT
390 GATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTTGGATCGAAAAATATAGATAT
* ** * * * *
6511 TTCAAGAAGTCTTTACGCCAAAATTCATGCAAAACTGAGCCGGAGACCCGGAACGC-ATTTTTAG
455 TTCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGA-TTTTAA
* *
6575 CAAAAAACCGTGATGGTTAGTACACGATTTCGGCCAAAATTTTGTAAAAACTAACCCAAAAAATT
519 CAAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAAAATT
* * *
6640 TATCCTCAATTTTTTTGCCACAATAGTTAGGAACAATATATAATTCAATGCAAAAAAATGAAGGG
584 CATCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATAATTCAAAGCAAAAAAATGAAGGG
6705 T
649 T
* * * * * * * *
6706 TTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTTAATATAATTCTAATTAAATAGAAACATGA
1 TTTTCAAGCTTCTAATATC-ATTTTCCA-TTTTTTCAATTTATTTCTAATTAAATCGAAACAAGA
*
6771 TTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGAC-TTGGTTAGATAAATATA
64 TTTAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATATA
* * *
6835 GATATTTCAAGGAGTCTTTCTGCCAAAAATATTCAAAATTGAGCCGGGGCCTCGAAA-TGCGTTT
129 GATATTTCAAGGAGTCTTTCTGCCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAACT-CGTTT
* * *
6899 TTAGCCCAAAAACCGTGATAGTTAGTACACGATTTAGGCTAAAAACTTACTCAAAAAAATTTTTT
193 TTAGCCCAAAAACCGTGAT-GGTAGTACACGATTTAGGCTAAAAACTGACTCGAAAAAATTTTTT
* * *
6964 CTGAATTTTTTACTACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACCGGCTT
257 CTGAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTT
* * *
7029 TTCACGCTTCTAATATCAATTTTCCATTTTTTCGGAATTAATTTCAATTTAAATTGAAACAAGAT
322 TTCACGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGAT
*
7094 TCAGATACTCGTAAAAACAAATCCTTA
387 TCAGATGCTCGTAAAAACAAATCCTTA
7121 TTCCGAACCT
Statistics
Matches: 2650, Mismatches: 283, Indels: 139
0.86 0.09 0.05
Matches are distributed among these distances:
632 4 0.00
633 77 0.03
634 8 0.00
635 4 0.00
636 3 0.00
637 52 0.02
638 230 0.09
639 147 0.06
640 111 0.04
641 37 0.01
642 219 0.08
643 1 0.00
646 3 0.00
647 154 0.06
648 190 0.07
649 220 0.08
650 175 0.07
651 776 0.29
652 100 0.04
653 54 0.02
654 15 0.01
655 39 0.01
656 26 0.01
657 5 0.00
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.32
Consensus pattern (649 bp):
TTTTCAAGCTTCTAATATCATTTTCCATTTTTTCAATTTATTTCTAATTAAATCGAAACAAGATT
TAGATGCTCGTAAAAACAAACCCTTAAATCCAATGTGGCTGAGACTTTGGTTAGATGAATATAGA
TATTTCAAGGAGTCTTTCTGCCAAAAATATTCAAAACTGAGCTGGGGCCCCGAAACTCGTTTTTA
GCCCAAAAACCGTGATGGTAGTACACGATTTAGGCTAAAAACTGACTCGAAAAAATTTTTTCTGA
ATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCA
CGCTTCTAATATCATTTTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAACAAGATTCAG
ATGCTCGTAAAAACAAATCCTTAAATCAAATGTGGCTGGGATTTGGATCGAAAAATATAGATATT
TCAAGGAGTCTTTACAACAAAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGATTTTAACA
AAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAAAATTCA
TCCTCAATTTTATTGCCACAATAGTTAGGAACAATATATAATTCAAAGCAAAAAAATGAAGGGT
Found at i:6393 original size:318 final size:319
Alignment explanation
Indices: 3366--7120 Score: 3674
Period size: 318 Copynumber: 11.6 Consensus size: 319
3356 TAGGGTTTAG
* * * *
3366 AGTACACGATTTACGCTAAAAACTGAGTCGAAAATTTTTTTTTCTGAATTTTTAGCCACAATACT
1 AGTACACGATTTAGGCTAAAAACTGACTCGAAAA--ATTTTTTCTGAATTTTTTGCCACAATACT
* * * *
3431 CAGAAAAAATATATAGTTCAACGACAAAAAGATTGACAGGCTTTTCACGCTTCTAATACCATTTT
64 CAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTT
* *
3496 TCCATTTTTTCGGAATTAATTTC-AATTTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAA
129 TCCATTTTTTC--AATTAATTTCTAA-TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA
* * * * *
3560 TCCTTAAATCGAATGTGGCTGGGATTTGGTTCGATAAATATAGATATTTCAAGGAGTCTTTAC-A
191 TCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTG
* * * *
3624 ACAAAAATCATGCAAAACTGAGTCGGGGACCCGGAACGCGTTTTTAG-CAAAAAACCGTGATTGT
255 CCAAAAATCATGCAAAACTGAGT-GGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGT
3688 T
319 T
* * * * * * *
3689 AGTACACGATTTCGGCTAAAATTTTGTAAAAATAGACCCGAAAAATTTATCCTCAATTTTTTTCC
1 AGTACACGATTTAGGCT---A------AAAACT-GACTCGAAAAATTTTTTCTGAA-TTTTTTGC
* * * * * * * * * * **
3754 CACAATAGTTAGGAACAATATATGATTCAATGCAAAAAAAATTAAAGGATTTTTCACGCTTCT-A
55 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAA
* * *
3818 -AT-A----T-CGTTTTTT---TT-ATTTCAAATTAAATCGAAACAAGATTTAGATGCTCGTAAA
120 TATCATTTTTCCATTTTTTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * *
3872 AACAAACCCTTAAAT-CAATTGTGGTTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTC
185 AACAAATCCTTAAATCCAA-TGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * * ** *
3936 TTTTTGCCAAAAAT-ATTCGAAATTGAGTTGGGG-CCTCGAAGCATGTTTTTAGCCCAAAAACGG
249 TTTCTGCCAAAAATCATGCAAAACTGAG-TGGGGACC-CGAAACGCGTTTTTAGCCCAAAAACCG
3999 TGATGGTT
312 TGATGGTT
* * ** *
4007 AGTA-ACGAATTAGGCTAAAAACTGAGTCGAAATTTTTTGTTTTTCTGAAATTTTTGCCACAATA
1 AGTACACGATTTAGGCTAAAAACTGACTCGAAA---AAT-TTTTTCTGAATTTTTTGCCACAATA
* *
4071 CTTAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCATGCTTCTAATATCATT
62 CTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATT
* * *
4136 TTTCCATTTTTTCGGAATTAATTTCTATTTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAA
127 TTTCCATTTTTTC--AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * * *
4201 ATCCTTAAATCAAATGTGGCTGGGATTTGGTTCGATAAATACAGATATTTCAAGGAGTCTTTAC-
190 ATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CT
** * * * * *
4265 AACAAAAATCAAGCAAAACTGAGTCGGGGACTCGGAACGCGTTTTTAG-CAAAAAACCGTGACGG
254 GCCAAAAATCATGCAAAACTGAGT-GGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGG
4329 TT
318 TT
*
4331 AGTACACGATTTAGGCTAAAAACTGAGTCGAAAAAATTTTTTTCTGAATTTTTTGCCACAATACT
1 AGTACACGATTTAGGCTAAAAACTGACTCG-AAAAA-TTTTTTCTGAATTTTTTGCCACAATACT
* * * *
4396 CTGAAAAAATATATAATTCAATGCCAAAAACATTGACGGGCATTTCACGCTTCTAATATCATTTT
64 CAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTT
* * *
4461 ACCATTTTTTCGGAATTAATTTCTATTTAAATTGAAACAAGATTCAGATGCTCGTAAAAACAAAT
129 TCCATTTTTTC--AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * * * *
4526 CCATATATCCAATGTGGCTGGGATTTGGATCA-AAGAATACAGATATTTCAAGGAGTCATTAC-G
192 CCTTAAATCCAATGTGGCTGAGATTTGG-TTAGATGAATATAGATATTTCAAGGAGTC-TTTCTG
** * * * * *
4589 CCAAAAATCATGCAAAACTGAGTCAAGGACCCGGAACACGATTTTAG-CAAAAAACTGTGATGGT
255 CCAAAAATCATGCAAAACTGAGT-GGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGT
4653 T
319 T
* * * ** * *
4654 AGTACACGATTTCGTCTAAAATTTTGTAAAAACTGACCCGAAAAATTCATCCTCAATTTTATTGC
1 AGTACACGATTTAGGC----------TAAAAACTGACTCGAAAAATTTTTTCTGAATTTT-TTGC
* * * * * * * * * * *
4719 CACAATAATTAGGAACAATATATAATTCAAAGCAAAAAAAAAATGAAGGGTTTTTCAAGCTTCTA
55 CACAATACTCAGAAAAAATATATAATTCAACGC-CAAAAAGATTGACGGGCTTTTCACGCTTCTA
* * *
4784 ATATCA-TTTTCCA-TTTTTCAGTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAA
119 ATATCATTTTTCCATTTTTTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * *
4847 AAACAAACCCTTAAATCCAATGTAGCTGAGACTTTGATTAGATGAATATACATATTTCAAGGAGC
184 AAACAAATCCTTAAATCCAATGTGGCTGAGA-TTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * *
4912 CTTTCTGCCAAAAAT-ATTCAAAACTGAGCTGGGGCCCCGAAACTCGTTTTTAGCCCAAAAACCG
248 CTTTCTGCCAAAAATCATGCAAAACTGAG-TGGGGACCCGAAACGCGTTTTTAGCCCAAAAACCG
*
4976 TTATGG--
312 TGATGGTT
*
4982 AGTACACGATTTAGGCTAAAAACTGACTTGAAAAAATTTTTTCTGAATTTTTTGCCACAATACTC
1 AGTACACGATTTAGGCTAAAAACTGACTCG-AAAAATTTTTTCTGAATTTTTTGCCACAATACTC
*
5047 AGAAAAAAATATATAATTGAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTT
65 AG-AAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTT
* * * *
5112 TCCAATTTTTCAGAATTAATTTCTATTTAAATCGAAATAAGATTCAGTTGCTCGTAAAAACAAAT
129 TCCATTTTTTC--AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * ** **
5177 CCTTAAATCAAATGTGGCTGAGATTTGGTTCGAAAAATATAGATATTTCAAGGAGTCTTTAC-AA
192 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGC
* * * * *
5241 CAAAAATCATGCAAAAATGAGTCGGGGACCCGTAACGCGTTTTTA-ACAAAAAACCATGATGGTT
256 CAAAAATCATGCAAAACTGAGT-GGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTT
* * * * * * **
5305 AGTACACGATTTCGGCTAAAATTTTGTAAAAACTAACCCGAAAAATTTATCCTCAATTTTTTGGT
1 AGTACACGATTTAGGC----------TAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCC
* * * * * * * * *
5370 ACATTAGTTAGGAACAATATATAATTCAATG-CAAAAA-AATGAAGGGTTTTTCACGCTTCTAAT
56 ACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAAT
* * * *
5433 ATCGTTTTTCCATTTTTTTTAATATAA-TTCTAATTAAATCGAAATAAGATTTAGATGCTCGTAA
121 ATCATTTTTCCA-TTTTTTCAAT-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* *
5497 AAACAAAACCTTAAATCCAATGTGGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTC
184 AAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * *
5562 TTTTTACCAAAAAT-ATTCAAAACTGAGCTGGGGCCCCGAAATGCGTTTTTAGCCCAAAAACCGT
249 TTTCTGCCAAAAATCATGCAAAACTGAG-TGGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGT
5626 GATGGTT
313 GATGGTT
* *
5633 AGTACACGATTTAGGCTAAAAACTGAGTCGAAAAATTTTTTCTGAATTTTTTGCCACAATACTCC
1 AGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCCACAATACTCA
* * * *
5698 GAAAAAATATATTATTCAACGCCAAAACGATTGATGGGCTTTTCACGCTTCTAATTTCATTTTTC
66 GAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTC
* **
5763 CATTTTTTCAGAATTAATTTCTATTTAAATCGAAGTAAGATTCAGATGCTCGTAAAAAC-AATCC
131 CATTTTTTC--AATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCC
* * * * * * **
5827 TTAAATCAAATGTGGCTGGGATTTGGTTCGATAAATATAGAAATTTCAAGGAGTCTTTATAACAA
194 TTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAA
* * * * *
5892 AAATCATGCAAAACTGAGTCGGGGACCCGTAACGCGTTTTTA-ACAAAAAACCGTGACGATTT
259 AAATCATGCAAAACTGAGT-GGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATG-GTT
* ** * * ** * * *
5954 CGT-CTAAAATTT-TG-TAAAAACTGACCCGAAAAATTCATCCTCAATTTTATTGCCACAATAGT
1 AGTAC-ACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTT-TTGCCACAATACT
* * * * * * * * * * * *
6016 TAGGAACAATATATGATTCAAAGCAAGAAAAAAATGAAGGGTTTTTCAAGCTTCTAATATC-GTT
64 CAGAAAAAATATATAATTCAACGCCA-AAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTT
* * * *
6080 TTCCA-TTTTTCAGTTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAACC
128 TTCCATTTTTTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATC
* *
6144 CTTAAATCCAATGTAGCTGAGACTTT-GTTAGATGAATATAGATATTTCAAGGAGCCTTTCTGCC
193 CTTAAATCCAATGTGGCTGAGA-TTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCC
* * * * *
6208 AAAAAT-ATTCAAAACCGAGCTGGGGCCCCGAAACACGTTTTTAGCCCAAAAATCGTGATGGTT
257 AAAAATCATGCAAAACTGAG-TGGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTT
*
6271 AGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTTCTGATTTTTTTGCCACAATACTC
1 AGTACACGATTTAGGCTAAAAACTGACTCGAAAAA-TTTTTTCTGAATTTTTTGCCACAATACTC
* *
6336 AGAAAAAATATATAATTTAACGCGAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTT
65 AGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTT
* *
6401 CTATTTTTTCGGAATTAATTTC-AATTTGAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
130 CCATTTTTTC--AATTAATTTCTAA-TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
* * * * * * * *
6465 CCTTATATCCAATGTGGTTGGGATTTAGATCGAAGAATATAGATATTTCAAGAAGTCTTTAC-GC
192 CCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGC
* * * * * *
6529 CAAAATTCATGCAAAACTGAGCCGGAGACCCGGAACGCATTTTTAG-CAAAAAACCGTGATGGTT
256 CAAAAATCATGCAAAACTGAG-TGGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTT
* * * * * * *
6593 AGTACACGATTTCGGCCAAAATTTTGTAAAAACTAACCCAAAAAATTTATCCTCAATTTTTTTGC
1 AGTACACGATTTAGG-C---------TAAAAACTGACTCGAAAAATTTTTTCTGAA-TTTTTTGC
* * * * * * * *
6658 CACAATAGTTAGGAACAATATATAATTCAATG-CAAAAA-AATGAAGGGTTTTTCACGCTTCTAA
55 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAA
* * * * * *
6721 TATCGTTTTTTCATTTTTTTTAATATAA-TTCTAATTAAATAGAAACATGATTTAGATGCTCGTA
120 TATCATTTTTCCA-TTTTTTCAAT-TAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * *
6785 AAAACAAACCCTTAAATCCAATGTGGCTGAGACTTGGTTAGATAAATATAGATATTTCAAGGAGT
183 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGT
* * * *
6850 CTTTCTGCCAAAAAT-ATTCAAAATTGAGCCGGGG-CCTCGAAATGCGTTTTTAGCCCAAAAACC
248 CTTTCTGCCAAAAATCATGCAAAACTGAG-TGGGGACC-CGAAACGCGTTTTTAGCCCAAAAACC
*
6913 GTGATAGTT
311 GTGATGGTT
* * * *
6922 AGTACACGATTTAGGCTAAAAACTTACTCAAAAAAATTTTTTCTGAATTTTTTACTACAATACTC
1 AGTACACGATTTAGGCTAAAAACTGACTC-GAAAAATTTTTTCTGAATTTTTTGCCACAATACTC
* *
6987 AGAAAAAATATATAATTCAACGCCAAAAAGATTGACCGGCTTTTCACGCTTCTAATATCAATTTT
65 AGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTT
* *
7052 CCATTTTTTCGGAATTAATTTC-AATTTAAATTGAAACAAGATTCAGATACTCGTAAAAACAAAT
130 CCATTTTTTC--AATTAATTTCTAA-TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAAT
7116 CCTTA
192 CCTTA
7121 TTCCGAACCT
Statistics
Matches: 2802, Mismatches: 491, Indels: 279
0.78 0.14 0.08
Matches are distributed among these distances:
307 7 0.00
308 5 0.00
310 58 0.02
311 8 0.00
312 2 0.00
313 1 0.00
314 1 0.00
316 2 0.00
317 120 0.04
318 339 0.12
319 191 0.07
320 203 0.07
321 201 0.07
322 271 0.10
323 329 0.12
324 129 0.05
325 52 0.02
326 5 0.00
327 32 0.01
328 184 0.07
329 265 0.09
330 97 0.03
331 60 0.02
332 179 0.06
333 61 0.02
ACGTcount: A:0.37, C:0.16, G:0.15, T:0.32
Consensus pattern (319 bp):
AGTACACGATTTAGGCTAAAAACTGACTCGAAAAATTTTTTCTGAATTTTTTGCCACAATACTCA
GAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATCATTTTTC
CATTTTTTCAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
AAATCCAATGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
ATCATGCAAAACTGAGTGGGGACCCGAAACGCGTTTTTAGCCCAAAAACCGTGATGGTT
Found at i:7657 original size:4 final size:4
Alignment explanation
Indices: 7648--7672 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
7638 GGGATTTAAG
7648 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
7673 AGGAAAAATC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:8699 original size:14 final size:15
Alignment explanation
Indices: 8670--8705 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
8660 CCAAAGGAAA
8670 ATACTATCATATATAT
1 ATACT-TCATATATAT
8686 ATACTTCA-ATATAT
1 ATACTTCATATATAT
8700 ATACTT
1 ATACTT
8706 AACAGTGTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 12 0.60
15 3 0.15
16 5 0.25
ACGTcount: A:0.42, C:0.14, G:0.00, T:0.44
Consensus pattern (15 bp):
ATACTTCATATATAT
Done.