Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016467.1 Corchorus olitorius cultivar O-4 contig16500, 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: 67915
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.31
Found at i:661 original size:334 final size:333
Alignment explanation
Indices: 19--2476 Score: 1905
Period size: 322 Copynumber: 7.5 Consensus size: 333
9 TTAATGGTAA
* *
19 GTTTTTAGTCAAAAACCATGATGGTTAGTACACGATTTCGGGAAAAATTTTG-CAAAAGTTGACC
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTC-GGCAAAATTTTGCCAAAA-TTGACC
* *
83 CGAAAGATTTTTCCTCAATTTTTAATTGCAATACTGGTAAAAAATATATAATTCAACGCCAAAAA
64 CGAAAGATTTTTCCTCAATTTTTAATCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAA
* * * *
148 GTTTGAAGGGGTTTTCACGCTTCAAATATTA-TTTTTTCAATTCTTTCCCGAATTAATTTCTAAT
129 GATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCTAAT
*
212 TAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATTCATTGTGGCTGAGATTTG
194 TAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGA-TTG
* * * *
277 GGATT--ATTAATATAGATATTTCAATGAGTCCTGCCGCCAAAAATCATGCAAAACTGAGCCAGC
258 GG-TTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGG
*
340 GCCCCTAAGCGT
322 GCCCCTAAGCGC
* * * * **
352 GTTTTTAGCCAAAAACCGTGACGGTTAGTACACGATTTTGGGAAAATTTTTGCCAAAGGTGACCC
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCAAAA-TTTTGCCAAAATTGACCC
* * * *
417 GAAAGATTTTTCCTCAATTTTTAATCACAATACTGGTAAAAAATAAATAATTGAACGCCAAAAAG
65 GAAAGATTTTTCCTCAATTTTTAATCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAG
*
482 TTTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCTAATT
130 ATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCTAATT
* * *
547 AAATCGAAAAAAGATTCAGATAATCGTAAAAACAAATCCTTAAATCCATTGTGACTGAGATTCGG
195 AAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATT-GG
* * *
612 GAT-GATTAACATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTAAGCCGGGGC
259 GTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGC
*
676 CCC-AGGACGC
324 CCCTAAG-CGC
*
686 GTTTTTAGCCAAAAACC------G-T-G-ACACGATTTCGGCAAAA------C----TTGACCTG
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCAAAATTTTGCCAAAATTGACCCG
* * * * ** *
732 AAAGATTTTTTCCTTAATTTTGAACCGCAATACTCGTAAAAAATATATAATTCAATGGTAGAAAG
66 AAAGA-TTTTTCCTCAATTTTTAATCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAG
* * * * * **
797 GTTGAAGGGCTTTTTAGGCTTCTAATATCATTTTTTTTTCAATT-TTTTCCGTATTAATTTCCGA
130 ATTGAAGGGCTTTTCACGCTTCTAATATCA--TTTTTTTCAATTCTTTCCCGAATTAATTTCTAA
* * * *
861 TTAAATCGAAACATGATTCAAATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGATATTT
193 TTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTG
*
926 GGTTAGATTAATATAGATATTTCAATGAGTCTTAGCGCCAAAAATCATGCAAAACTGAGCCGGGG
258 GGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGG
* * *
991 CCCCCAAACGA
323 CCCCTAAGCGC
* *
1002 GTTTTTAGCCAAAAACCATGATGGTTAGTATACGATTTCGGCAAAATTTTTGCAAAAATTGACCT
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCAAAA-TTTTGCCAAAATTGACC-
* * * *
1067 CATGAAATATTTTTCCTTAATTTTTAACCGCAATACTCGTAAAAAATATATAATTCAATGCCAAA
64 C--GAAAGATTTTTCCTCAATTTTTAATCGCAATACTCGTAAAAAATATATAATTCAACGCCAAA
* * * ** *
1132 AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTCTT--GTTTTTTCCATAATTAATTTATA
127 AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCTA
* ** * * * * * * ** *
1195 ATTAAATTGAAACCGGTTTCTGATGCTCGGAGAAACAAATCCTTAAATCTGA-CATGCCTGAGAC
192 ATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATC-CATTGTGGCTGAGA-
* * * * *
1259 TT-GGTTAGATGAATATAGATATTACAAGGAGTCTTGGCGCCAAAAATAATACAAAACTGAGCCG
255 TTGGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCG
1323 GGG-CCCTGAAGCGC
320 GGGCCCCT-AAGCGC
* * * * *
1337 GTTTTTTGCTAAAAAACTATGATGG---GTACACGATTTCGGCTTAAATTTT-CCAAAAATTGAA
1 GTTTTTAGC-CAAAAACCATGATGGTTAGTACACGATTTCGGC-AAAATTTTGCC-AAAATTGAC
** * * * * * *
1398 CCGAAAG-TTTTTCCCTCAATTTTTGGTCACAATAATCATAAAAAGTATATAATTCATCGCTAAA
63 CCGAAAGATTTTT-CCTCAATTTTTAATCGCAATACTCGTAAAAAATATATAATTCAACGCCAAA
* * ** * ** *
1462 GAAGATTGAAGGGTTTTTCACGCTTCTAATATC--GTTTTTCCTTTTTTTTTCGAGTTAATTTCT
127 -AAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCT
* * * *
1525 AATTAAATCGAAATATA-ATTCAGAT-ACTCGTAAAAACAAATCCTCAAATCCAATGTTGCTGAG
191 AATTAAATCGAAACA-AGATTCAGATGA-TCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAG
* ** * * *
1588 ATTTGGTTAGAAGAATATAGATATTTGAATAAGTCTTGGTGCCAAAAATCATGCAAAACTGAGCC
254 ATTGGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCC
** *
1653 -GGGCCTCGGAA-TGC
319 GGGGCC-CCTAAGCGC
* * * * * ** *
1667 ATTTTTAGCTAAAAA-CA--ATGATT--T---CGGTTTC-CCTCAA-TTT-CCAAAAAGTGACCC
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCAAAATTTTGCC-AAAATTGACCC
* * *** * * * *
1721 GAATGATTTTTTCCTTAATTTTTGGCCACAATCCTCATAAAAAAATATATAATTCATCGCCAAAA
65 GAAAGA-TTTTTCCTCAATTTTTAATCGCAATACTCGT-AAAAAATATATAATTCAACGCCAAAA
* * * * * * * * * * * **
1786 AAATGGAAGGACTTTTAACACATGTGATATC-GTTTTTCCTATAT-TTT-ATGAATTAATTTCTA
128 AGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAAT-TCTTTCCCGAATTAATTTCTA
* * * * * *
1848 A-TAAAACTGAAAC-TGATTTCTGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGTCTGAGA
192 ATTAAATC-GAAACAAGA-TTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGA
* * * * * * * * * * *
1911 TTCGATTAGATGAATATAGATATTTCAATTACTGTAGGAGCAAAAAATCATGC-AAAGTAAGCCG
255 TTGGGTTAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCG
*
1975 GGG-CCCTAGAACGC
320 GGGCCCCTA-AGCGC
* ** * * ** * *
1989 GTTTTGAGCCAAAAACTGTGATGTTTAGTACATGATAACGGTTAAAATTTTG-CAGAAATTGATC
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGG-CAAAATTTTGCCA-AAATTGACC
* ** * * * * *
2053 CGAATGA-TTTTCCTTCAATTTTT-GGCAACAATATTCATAAAAAA-A-AGGAATTCATCGCCAA
64 CGAAAGATTTTTCC-TCAATTTTTAATC-GCAATACTCGTAAAAAATATA-TAATTCAACGCCAA
* * * * *
2114 AAAAATGGAACGGCTTTTCACGCTTC-AA-A--A-----AT-AATT-TTT-CTGAATTAATTTCT
126 AAAGATTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCT
* * * * * *
2167 AATTAAATCGAAACATA-ATTCAGATGCTAGTAAAGACAATTCCTTAAACCCAATGT-GCTTG-G
191 AATTAAATCGAAACA-AGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGC-TGAG
* * * * * * *
2229 ATTTGGTTAGATGAATATAGATACTAT-AAGGAGTCTTGGCGCCAAAATTCATTCAAAACTAAGC
254 ATTGGGTTAGATTAATATAGATA-TTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGC
**
2293 CGGGGCCACGGAA-CGC
318 CGGGGCC-CCTAAGCGC
** ** * * * *
2309 GTTTTTAGAGAAAAACTGTGGTGGTTAGTACACGATTTCCGCTTAAATTTTGCAAAAATTGACCC
1 GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGC-AAAATTTTGCCAAAATTGACCC
* * ** * ** * *
2374 GAATGATTTTTCCTTAATTTTT-GGCTACAATACTAATTAAAAAATATATAATTCATCACCAAAA
65 GAAAGATTTTTCCTCAATTTTTAATC-GCAATACT-CGTAAAAAATATATAATTCAACGCCAAAA
* *** *
2438 AGATGGAACAACTTTTTCACACTTCTAATATCATTTTTT
128 AGATTGAAGGGC-TTTTCACGCTTCTAATATCATTTTTT
2477 ATATTTTTTC
Statistics
Matches: 1721, Mismatches: 298, Indels: 213
0.77 0.13 0.10
Matches are distributed among these distances:
314 11 0.01
315 78 0.05
316 154 0.09
317 13 0.01
318 1 0.00
319 41 0.02
320 151 0.09
321 59 0.03
322 192 0.11
323 51 0.03
324 10 0.01
325 37 0.02
326 4 0.00
327 4 0.00
328 3 0.00
329 16 0.01
330 96 0.06
331 161 0.09
332 29 0.02
333 184 0.11
334 181 0.11
335 130 0.08
336 28 0.02
338 82 0.05
339 5 0.00
ACGTcount: A:0.35, C:0.17, G:0.16, T:0.33
Consensus pattern (333 bp):
GTTTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCAAAATTTTGCCAAAATTGACCCG
AAAGATTTTTCCTCAATTTTTAATCGCAATACTCGTAAAAAATATATAATTCAACGCCAAAAAGA
TTGAAGGGCTTTTCACGCTTCTAATATCATTTTTTTCAATTCTTTCCCGAATTAATTTCTAATTA
AATCGAAACAAGATTCAGATGATCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTGGGT
TAGATTAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGGCCC
CTAAGCGC
Found at i:2374 original size:653 final size:647
Alignment explanation
Indices: 840--2483 Score: 1626
Period size: 653 Copynumber: 2.5 Consensus size: 647
830 TTTTTTCAAT
* * ** * * *
840 TTTTTCCGTATTAATTTCCGATTAAATCGAAACATGATTCAAATGATCGTAAAAACAAATCCTTA
1 TTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTA
* * * *
905 AATCCATTGTGGCTGATATTTGGTTAGATTAATATAGATATTTCAATGAGTCTTAGCGCCAAAAA
66 AATCCAATGT-GCTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAA
* ** *
970 TCATGCAAAACTGAGCCGGGGCCCCCAAACGAGTTTTTAGCCAAAAACCATGATGGTTAGTATAC
130 TCATGCAAAACTGAGCCGGGGCCACGGAACGCGTTTTTAGCCAAAAA-C-TGATGGTTAGTA-AC
* * ** *
1035 GATTTCGGCAAAATTTTTGCAAAAATTGACCTC--ATGAAATATTTTTCCTTAATTTTTAACCGC
192 GATTTCCGCTAAA-TTTTGCAAAAATTGACC-CGAATG--AT-TTTTTCCTTAATTTTTGGCCAC
* * * * * *
1098 AATACTCGTAAAAAATATATAATTCAAT-GCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATA
252 AATACTCATAAAAAATATATAATTC-ATCGCCAAAAAGATGGAAGGACTTTTAACACATCTAATA
* * * * * * *
1162 TCATTTTCTTGTTTTTTCCATAATTAATTTATAATTAAATTGAAACCGGTTTCTGATGCTCGGAG
316 TCATTTTCCTATATTTT-CATAATTAATTTATAATAAAACTGAAACCGATTTCTGATGCTCGGAA
** * *
1227 AAACAAATCCTTAAATCTGACATGCCTGAGACTTGGTTAGATGAATATAGATATTACAAGGAGTC
380 AAACAAATCCTTAAATCCAACATGCCTGAGACTTGATTAGATGAATATAGATATTACAAGGACTC
* * * * **
1292 TTGGCGCCAAAAATAATACAAAACTGAGCCGGGGCCCTGAAGCGCGTTTTTTGCTAAAAAACTAT
445 TAGGAGCAAAAAATAATACAAAACTAAGCCGGGGCCCTGAAGCGCGTTTTGAGCTAAAAAACTAT
* ** *
1357 GATGGGTACACGATTTCGGCTTAAATTTTCCAAAAATTGAACCGAAAGTTTTTCCCTCAATTTTT
510 GATGAGTACACGATAACGGCTTAAATTTTCCAAAAATTGAACCGAAAGATTTTCCCTCAATTTTT
* * * * * * *
1422 GGTCACAATAATCATAAAAAGTATATAATTCATCGCTAAAGAAGATTGAAGGGTTTTTCACGCTT
575 GGTCACAATAATCATAAAAAG-AAAGAATTCATCGCCAAAGAAAATGGAACGGCTTTTCACGCTT
* * **
1487 CTAATATCG
639 CAAAAATAA
* * *
1496 TTTTTCCTTTTTTTTTCGAGTTAATTTCTAATTAAATCGAAATATAATTCAGATACTCGTAAAAA
1 TTTTT-C--------T-GAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAA
* * * *
1561 CAAATCCTCAAATCCAATGTTGCTGAGATTTGGTTAGAAGAATATAGATATTTGAATAAGTCTTG
56 CAAATCCTTAAATCCAATG-TGCTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTG
* * * * * * *
1626 GTGCCAAAAATCATGCAAAACTGAGCC-GGGCCTCGGAATGCATTTTTAGCTAAAAAC-AATGAT
120 GCGCCAAAAATCATGCAAAACTGAGCCGGGGCCACGGAACGCGTTTTTAGCCAAAAACTGATGGT
* * * *
1689 T--T--CGGTTTCC-CTCAA-TTTCCAAAAAGTGACCCGAATGATTTTTTCCTTAATTTTTGGCC
185 TAGTAACGATTTCCGCTAAATTTTGCAAAAATTGACCCGAATGATTTTTTCCTTAATTTTTGGCC
* * * *
1748 ACAATCCTCATAAAAAAATATATAATTCATCGCCAAAAAAATGGAAGGACTTTTAACACATGTGA
250 ACAATACTCAT-AAAAAATATATAATTCATCGCCAAAAAGATGGAAGGACTTTTAACACATCTAA
* * * *
1813 TATCGTTTTTCCTATATTTT-ATGAATTAATTTCTAATAAAACTGAAACTGATTTCTGATGTTCG
314 TATC-ATTTTCCTATATTTTCAT-AATTAATTTATAATAAAACTGAAACCGATTTCTGATGCTCG
* ** * * **
1877 TAAAAACAAATCCTTAAATCCAATGTGTCTGAGA-TTCGATTAGATGAATATAGATATTTCAATT
377 GAAAAACAAATCCTTAAATCCAACATGCCTGAGACTT-GATTAGATGAATATAGATATTACAAGG
* * * * *
1941 ACTGTAGGAGCAAAAAATCATGC-AAAGTAAGCCGGGGCCCTAGAA-CGCGTTTTGAGC-CAAAA
441 ACTCTAGGAGCAAAAAATAATACAAAACTAAGCCGGGGCCCT-GAAGCGCGTTTTGAGCTAAAAA
* * * * * * *
2003 ACTGTGATGTTTAGTACATGATAACGG-TTAAAATTTTGCAGAAATTGATCCGAATGATTTTCCT
505 ACTATGATG---AGTACACGATAACGGCTT-AAATTTTCCAAAAATTGAACCGAAAGATTTTCCC
*
2067 TCAATTTTTGG-CAACAATATTCATAAAAA-AAAGGAATTCATCGCCAAA-AAAATGGAACGGCT
566 TCAATTTTTGGTC-ACAATAATCATAAAAAGAAA-GAATTCATCGCCAAAGAAAATGGAACGGCT
2129 TTTCACGCTTCAAAAATAA
629 TTTCACGCTTCAAAAATAA
* * *
2148 TTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTAGTAAAGACAATTCCTTA
1 TTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTA
* * *
2213 AACCCAATGTGCTTG-GATTTGGTTAGATGAATATAGATACTAT-AAGGAGTCTTGGCGCCAAAA
66 AATCCAATGTGC-TGAGATTTGGTTAGATGAATATAGATA-TTTCAATGAGTCTTGGCGCCAAAA
* * * ** *
2276 TTCATTCAAAACTAAGCCGGGGCCACGGAACGCGTTTTTAGAGAAAAACTGTGGTGGTTAGTACA
129 ATCATGCAAAACTGAGCCGGGGCCACGGAACGCGTTTTTAGCCAAAAAC--TGATGGTTAGTA-A
*
2341 CGATTTCCGCTTAAATTTTGCAAAAATTGACCCGAATGA-TTTTTCCTTAATTTTTGGCTACAAT
191 CGATTTCCGC-TAAATTTTGCAAAAATTGACCCGAATGATTTTTTCCTTAATTTTTGGCCACAAT
* * ** * *
2405 ACTAATTAAAAAATATATAATTCATCACCAAAAAGATGGAACAACTTTTTCACACTTCTAATATC
255 ACTCA-TAAAAAATATATAATTCATCGCCAAAAAGATGGAAGGAC-TTTTAACACATCTAATATC
*
2470 ATTTT-TTATATTTT
318 ATTTTCCTATATTTT
2484 TTCTAATGCT
Statistics
Matches: 803, Mismatches: 144, Indels: 87
0.78 0.14 0.08
Matches are distributed among these distances:
641 58 0.07
642 88 0.11
643 1 0.00
645 4 0.00
647 1 0.00
650 7 0.01
651 22 0.03
652 158 0.20
653 206 0.26
654 90 0.11
655 3 0.00
656 8 0.01
657 7 0.01
660 1 0.00
662 5 0.01
664 1 0.00
665 22 0.03
666 120 0.15
667 1 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.33
Consensus pattern (647 bp):
TTTTTCTGAATTAATTTCTAATTAAATCGAAACATAATTCAGATGCTCGTAAAAACAAATCCTTA
AATCCAATGTGCTGAGATTTGGTTAGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAAT
CATGCAAAACTGAGCCGGGGCCACGGAACGCGTTTTTAGCCAAAAACTGATGGTTAGTAACGATT
TCCGCTAAATTTTGCAAAAATTGACCCGAATGATTTTTTCCTTAATTTTTGGCCACAATACTCAT
AAAAAATATATAATTCATCGCCAAAAAGATGGAAGGACTTTTAACACATCTAATATCATTTTCCT
ATATTTTCATAATTAATTTATAATAAAACTGAAACCGATTTCTGATGCTCGGAAAAACAAATCCT
TAAATCCAACATGCCTGAGACTTGATTAGATGAATATAGATATTACAAGGACTCTAGGAGCAAAA
AATAATACAAAACTAAGCCGGGGCCCTGAAGCGCGTTTTGAGCTAAAAAACTATGATGAGTACAC
GATAACGGCTTAAATTTTCCAAAAATTGAACCGAAAGATTTTCCCTCAATTTTTGGTCACAATAA
TCATAAAAAGAAAGAATTCATCGCCAAAGAAAATGGAACGGCTTTTCACGCTTCAAAAATAA
Found at i:5270 original size:21 final size:21
Alignment explanation
Indices: 5236--5311 Score: 59
Period size: 21 Copynumber: 3.7 Consensus size: 21
5226 TTCCCAATTG
* *
5236 ACATTGAACTTTCCTTGATTC
1 ACATTCAACATTCCTTGATTC
** *
5257 ACATTCAACATTCC-CAATTA
1 ACATTCAACATTCCTTGATTC
*
5277 ACATTGAAC-TTGCCTTGATTC
1 ACATTCAACATT-CCTTGATTC
5298 AC-TATCAACATTCC
1 ACAT-TCAACATTCC
5312 CAATTGACAT
Statistics
Matches: 41, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
19 2 0.05
20 14 0.34
21 23 0.56
22 2 0.05
ACGTcount: A:0.30, C:0.28, G:0.07, T:0.36
Consensus pattern (21 bp):
ACATTCAACATTCCTTGATTC
Found at i:5349 original size:22 final size:22
Alignment explanation
Indices: 5324--5390 Score: 57
Period size: 20 Copynumber: 3.1 Consensus size: 22
5314 ATTGACATTG
5324 AACTTGCCTTATTCTCACATCC
1 AACTTGCCTTATTCTCACATCC
* * * * **
5346 AACTTTCC-CAAT-TGACATTG
1 AACTTGCCTTATTCTCACATCC
5366 AACTTGCCTTAATTCTCACATCC
1 AACTTGCCTT-ATTCTCACATCC
5389 AA
1 AA
5391 AAACATTGAA
Statistics
Matches: 30, Mismatches: 12, Indels: 5
0.64 0.26 0.11
Matches are distributed among these distances:
20 12 0.40
21 2 0.07
22 9 0.30
23 7 0.23
ACGTcount: A:0.28, C:0.31, G:0.06, T:0.34
Consensus pattern (22 bp):
AACTTGCCTTATTCTCACATCC
Found at i:5365 original size:42 final size:41
Alignment explanation
Indices: 5226--5390 Score: 226
Period size: 41 Copynumber: 4.0 Consensus size: 41
5216 CACATTGAGT
* *
5226 TTCCCAATTGACATTGAACTTTCCTTGATTCACATTCAACA
1 TTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACA
*
5267 TTCCCAATTAACATTGAACTTGCCTTGATTCACTAT-CAACA
1 TTCCCAATTGACATTGAACTTGCCTTGATTCAC-ATCCAACA
*
5308 TTCCCAATTGACATTGAACTTGCCTT-ATTCTCACATCCAACT
1 TTCCCAATTGACATTGAACTTGCCTTGA-T-TCACATCCAACA
*
5350 TTCCCAATTGACATTGAACTTGCCTTAATTCTCACATCCAA
1 TTCCCAATTGACATTGAACTTGCCTTGA-T-TCACATCCAA
5391 AAACATTGAA
Statistics
Matches: 115, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
40 1 0.01
41 64 0.56
42 36 0.31
43 14 0.12
ACGTcount: A:0.29, C:0.28, G:0.07, T:0.35
Consensus pattern (41 bp):
TTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACA
Found at i:5365 original size:83 final size:82
Alignment explanation
Indices: 5226--5380 Score: 240
Period size: 83 Copynumber: 1.9 Consensus size: 82
5216 CACATTGAGT
* *
5226 TTCCCAATTGACATTGAACTTTCCTTGATTCACATTCAACATTCCCAATTAACATTGAACTTGCC
1 TTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACATTCCCAATTAACATTGAACTTGCC
*
5291 TTGATTCACTATCAACA
66 TTAATTCACTATCAACA
* *
5308 TTCCCAATTGACATTGAACTTGCCTT-ATTCTCACATCCAACTTTCCCAATTGACATTGAACTTG
1 TTCCCAATTGACATTGAACTTGCCTTGA-T-TCACATCCAACATTCCCAATTAACATTGAACTTG
5372 CCTTAATTC
64 CCTTAATTC
5381 TCACATCCAA
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
81 1 0.02
82 26 0.39
83 39 0.59
ACGTcount: A:0.28, C:0.28, G:0.08, T:0.36
Consensus pattern (82 bp):
TTCCCAATTGACATTGAACTTGCCTTGATTCACATCCAACATTCCCAATTAACATTGAACTTGCC
TTAATTCACTATCAACA
Found at i:5402 original size:33 final size:33
Alignment explanation
Indices: 5360--5507 Score: 260
Period size: 33 Copynumber: 4.5 Consensus size: 33
5350 TTCCCAATTG
5360 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
5393 ACATTGAACTTGCCTTAATTATCACATCCAAAA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
*
5426 ACATTGAACTTGCCTTAATTCTCACATCCAACA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
* *
5459 ACATTGAACTTGCCTTAATTCTCATATCCAACA
1 ACATTGAACTTGCCTTAATTCTCACATCCAAAA
5492 ACATTGAACTTGCCTT
1 ACATTGAACTTGCCTT
5508 CACTCACATT
Statistics
Matches: 111, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 111 1.00
ACGTcount: A:0.34, C:0.27, G:0.07, T:0.32
Consensus pattern (33 bp):
ACATTGAACTTGCCTTAATTCTCACATCCAAAA
Found at i:6131 original size:66 final size:66
Alignment explanation
Indices: 6054--6186 Score: 248
Period size: 66 Copynumber: 2.0 Consensus size: 66
6044 ATGCTTGAAG
*
6054 GAGATCAAAGAGAGCTTTGGCTCCAAAATTATTAAGTGCTCCAAGTTTCCAGTGGTTTGAAGCAA
1 GAGATCAAAGAGAGCTTTGGCTCCAAAATTACTAAGTGCTCCAAGTTTCCAGTGGTTTGAAGCAA
6119 A
66 A
*
6120 GAGATCAAAGAGAGCTTTGGCTCTAAAATTACTAAGTGCTCCAAGTTTCCAGTGGTTTGAAGCAA
1 GAGATCAAAGAGAGCTTTGGCTCCAAAATTACTAAGTGCTCCAAGTTTCCAGTGGTTTGAAGCAA
6185 A
66 A
6186 G
1 G
6187 CTTAACCCTG
Statistics
Matches: 65, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (66 bp):
GAGATCAAAGAGAGCTTTGGCTCCAAAATTACTAAGTGCTCCAAGTTTCCAGTGGTTTGAAGCAA
A
Found at i:14559 original size:2 final size:2
Alignment explanation
Indices: 14552--14579 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
14542 TGTTGTAATC
14552 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
14580 CAAATTCAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:16617 original size:332 final size:324
Alignment explanation
Indices: 16005--17924 Score: 1868
Period size: 332 Copynumber: 5.9 Consensus size: 324
15995 CTAAAAACTA
* * *
16005 TGATGGTTAGTACACGATTTCAG-TCAAAATTTTGCAAAAACTGTCCCGAAAAATTTTTCCTCAA
1 TGATGGTTAGTACACGATTTC-GCT-AAAATTTTGCAAAAATTGACCCGAAAAA-TTTTCCTAAA
* * * * * * *
16069 TTTTTGGCCACAACACTTATAAAAAATATATAATTTAA-ATCCAAAAAGACTT-AAGGGCTTTAG
63 TTTTT-GCCACGATAATCATAAAAAATATATAATTCAACA-CCAAAAAGA-TTGAAAGGCTTT-C
* * * ** * * *
16132 ATGCTTC-AATTTTGTTTTTCAAATTTTTTTCCGAATTAATTTCTAATCAAATCGAAACATAATT
124 ACGCTTCTAATATCGTTTTTCCTA-TTTTTTCCGAATTAATTCCTAATTAAATCGAAACATGATT
* * * * *** *
16196 AAGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGACTGACATCTCATTAGATAAATATAGAT
188 CAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGAT-TTGGTAGATGAATATAGAT
* *
16261 ATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGAACTCGGAACGCATTTTTA
252 ATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGG-CCTCGGAACGCATTTTTA
16326 GCCAAAAAC
316 GCCAAAAAC
* * * *
16335 AGTGATAGTTAGTACATGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTACTAA
1 --TGATGGTTAGTACACGATTTC-GCTAAAATTTTGCAAAAATTGACCCGAAA-AATTTTCCTAA
*
16400 ATGTTTTGCCACGATAATGATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTATTCA
62 AT-TTTTGCCACGATAATCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCT-TTCA
* * *
16465 CGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTCCTAATTGAATCGAAAAATGATTCA
125 CGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTCCTAATTAAATCGAAACATGATTCA
* * * * *
16530 TATGCTCGTAAAAGCAAATCCTTAAATCCAATTTGGTTGAGATTTGGATAGATGGATATAGATAT
190 GATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG-TAGATGAATATAGATAT
* * * * ** **
16595 TTCAATGAGACATGGGGCCAAAAATCATGCAAAA-TAGAGTCGGGTCCCCAAAACGTGTTTTTAG
254 TTCAATGAGACTTGGCGCCAAAAATCATGCAAAACT-GAGCCGGG-CCTCGGAACGCATTTTTAG
*
16659 -TAAAAAC
317 CCAAAAAC
* * * *
16666 TGTGATGGTTAGTACACGATTTCGACAAAAAATTTTGCAAAAATTGACACGAAACATTTCTCCTC
1 --TGATGGTTAGTACACGATTTCG-C-TAAAATTTTGCAAAAATTGACCCGAAAAATTT-TCCTA
* * * * * * * *
16731 AATTTCTGGCGACCATATTCATAAAAAATTTATAATTCAACATCAAAACGATTGAAGGGCTTCTC
61 AATTT-TTGCCACGATAATCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTT-TC
* * * **
16796 ACGCTTCTAATATTGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGA
124 ACGCTTCTAATATCG---TTTTTCCTATTTTTTCCGAATTAATTCCTAATTAAATCGAAACATGA
* * * *
16861 TTGAGATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGATGAATATAG
186 TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT-AGATGAATATAG
* * *
16926 ATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACTAGGGCCTCGGAACGCGA-TT
250 ATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGC-CGGGCCTCGGAACGC-ATTT
*
16990 TAAGCCAAAAAC
313 TTAGCCAAAAAC
* *
17002 CG-T-G--A-T-----A--T--CTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCTAAATT
1 TGATGGTTAGTACACGATTTCGCTAAAATTTTGCAAAAATTGACCCGAAA-AATTTTCCTAAATT
* * *
17053 TTCGGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGCTATTCACGC
65 TT-TGCCACGATAATCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCT-TTCACGC
* * * *
17118 TTCTAATATCGTTTTTCCTAATTTTTTCTGAATTAATTCCTAATTGAATTG-AACATGATTCATA
128 TTCTAATATCGTTTTTCCT-ATTTTTTCCGAATTAATTCCTAATTAAATCGAAACATGATTCAGA
* * * * *
17182 TGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGATACTC
192 TGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG-TAGATGAATATAGATATTT
* * * * * * * * *
17247 CAAAGAGACTTGGTGCCAACAATCATGCAAAACAGCGCCGGGACCCCGAAACGCGTTTTTAGTCA
256 CAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGG-CCTCGGAACGCATTTTTAGCCA
17312 AAAAC
320 AAAAC
* * * *
17317 TGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAATTGACACGAAACATTTCTCCTCA
1 --TGATGGTTAGTACACGA-TTTCGCTAAAATTTTGCAAAAATTGACCCGAAAAATTT-TCCTAA
** * * * ** * *
17382 ATTTCCGACCACCATATTCATAAAAAATTTATAATTCAACGTCAAAACGATTAAAAGGCTTCTCA
62 ATTTTTG-CCACGATAATCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTT-TCA
* * * * *
17447 CGCTTCTAATAT-TTTTTTTCTA-TTTTTCTGAATTAATTTCTAATTAAATCGAAACCA-GATTG
125 CGCTTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTCCTAATTAAATCGAAA-CATGATTC
* *
17509 AGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGATGAATATAGATA
189 AGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT-AGATGAATATAGATA
* *
17574 TTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCTCGGAACGCGA-TTTAA
253 TTTCAATGAGACTTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCTCGGAACGC-ATTTTTA
17638 GCCAAAAAC
316 GCCAAAAAC
* *
17647 CG-T-G--A-T-----A--T--CTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCTAAATT
1 TGATGGTTAGTACACGATTTCGCTAAAATTTTGCAAAAATTGACCCGAAA-AATTTTCCTAAATT
* * *
17698 TTTGGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGTTATTCACGC
65 TTT-GCCACGATAATCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCT-TTCACGC
* * *
17763 TTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATGATTCATAT
128 TTCTAATATCGTTTTTCCTATTTTTTCCGAATTAATTCCTAATTAAATCGAAACATGATTCAGAT
* * ** * *
17828 GCTCGTAAAAGCAAATCCTTAAATCCATTGTGATTGAAATTTGGTTAGATGGATATAGATATTTC
193 GCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGG-TAGATGAATATAGATATTTC
* *
17893 AATGAGACTTGGTGCCAAAAATCATGAAAAAC
257 AATGAGACTTGGCGCCAAAAATCATGCAAAAC
17925 AGAGGCGAGA
Statistics
Matches: 1307, Mismatches: 220, Indels: 139
0.78 0.13 0.08
Matches are distributed among these distances:
313 92 0.07
314 19 0.01
315 245 0.19
316 29 0.02
317 2 0.00
318 96 0.07
319 7 0.01
321 1 0.00
322 2 0.00
323 1 0.00
324 2 0.00
326 1 0.00
327 2 0.00
328 1 0.00
329 28 0.02
330 122 0.09
331 56 0.04
332 423 0.32
333 23 0.02
334 2 0.00
335 143 0.11
336 10 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (324 bp):
TGATGGTTAGTACACGATTTCGCTAAAATTTTGCAAAAATTGACCCGAAAAATTTTCCTAAATTT
TTGCCACGATAATCATAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTTTCACGCTTC
TAATATCGTTTTTCCTATTTTTTCCGAATTAATTCCTAATTAAATCGAAACATGATTCAGATGCT
CGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTAGATGAATATAGATATTTCAATG
AGACTTGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCTCGGAACGCATTTTTAGCCAAAAAC
Found at i:17275 original size:315 final size:314
Alignment explanation
Indices: 16694--19127 Score: 1567
Period size: 315 Copynumber: 7.6 Consensus size: 314
16684 ATTTCGACAA
* * * *
16694 AAAATTTTGCAAAAATTGACACGAAACATTTCTCCTCAA-TTTCTGGCGACCATATTCATAAAAA
1 AAAATTTTGCAAAAATTGACACGAAAAATTTCTCCTAAATTTTC-GGCCACCATAATCATAAAAA
* * * * * *
16758 ATTTATAATTCAACATCAAAACGATTGAAGGGCTTCTCACGCTTCTAATATTGTTTTTTTTTCTA
65 ATATATAATTCAACACCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATATCG---TTTTTCCTA
* * ** * *
16823 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACCGGATTGAGATGTTCGTAAAAACAAATCCTT
127 TTTTTTCTGAATTAATTCCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTT
* *
16888 AAATCGAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAA
192 AAATCCAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAA
*
16953 ATCATGCAAAACTGAACTAGGGCCTCGGAACGCGATTTAAGCCAAAAACCGTGATATCT
257 ATCATGCAAAACTGAGC-AGGGCCTCGGAACGCGATTTAAGCCAAAAACCGTGATATCT
* * * *
17012 AAAATTTTGTAAAAATTGACCCGAAAGAATTT-TCCTAAATTTTCGGCCACGATAATCATAAAGA
1 AAAATTTTGCAAAAATTGACACGAAA-AATTTCTCCTAAATTTTCGGCCACCATAATCATAAAAA
*
17076 ATATATAATTTAACACCAAAAAGATTGAAAGGCTAT-TCACGCTTCTAATATCGTTTTTCCTAAT
65 ATATATAATTCAACACCAAAAAGATTGAAAGGCT-TCTCACGCTTCTAATATCGTTTTTCCT-AT
* * * *
17140 TTTTTCTGAATTAATTCCTAATTGAATTG-AACATGATTCATATGCTCGTAAAAGCAAATCCTTA
128 TTTTTCTGAATTAATTCCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTA
* * * * * * * * *
17204 AATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGATACTCCAAAGAGACTTGGTGCCAACAA
193 AATCCAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAA
* * * * * * * * *
17269 TCATGCAAAACAGCGCCGGGACCCCGAAACGCGTTTTTAGTCAAAAACTGTGATGGTTAGTACAC
258 TCATGCAAAACTGAGCAGGG-CCTCGGAACGCGATTTAAGCCAAAAAC--CG-T-G--A-T----
17334 GATTTTAGCT
311 -A---T--CT
* * * * *
17344 AAAATTTTGCAAAAATTGACACGAAACATTTCTCCTCAATTTCCGACCACCATATTCATAAAAAA
1 AAAATTTTGCAAAAATTGACACGAAAAATTTCTCCTAAATTTTCGGCCACCATAATCATAAAAAA
* ** * * * *
17409 TTTATAATTCAACGTCAAAACGATTAAAAGGCTTCTCACGCTTCTAATAT-TTTTTTTCTA-TTT
66 TATATAATTCAACACCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATATCGTTTTTCCTATTTT
* *
17472 TTCTGAATTAATTTCTAATTAAATCGAAACCA-GATTGAGATGCTCGTAAAAACAAATCCTTAAA
131 TTCTGAATTAATTCCTAATTAAATCGAAA-CATGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* *
17536 TCGAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATC
195 TCCAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATC
17601 ATGCAAAACTGAGCCAGGGCCTCGGAACGCGATTTAAGCCAAAAACCGTGATATCT
260 ATGCAAAACTGAG-CAGGGCCTCGGAACGCGATTTAAGCCAAAAACCGTGATATCT
* * * * *
17657 AAAATTTTGTAAAAATTGACCCGAAAGAATTT-TCCTAAATTTTTGGCCACGATAATCATAAAGA
1 AAAATTTTGCAAAAATTGACACGAAA-AATTTCTCCTAAATTTTCGGCCACCATAATCATAAAAA
* *
17721 ATATATAATTTAACACCAAAAAGATTGAAAGG-TTATTCACGCTTCTAATATCGTTTTTCCTATT
65 ATATATAATTCAACACCAAAAAGATTGAAAGGCTT-CTCACGCTTCTAATATCGTTTTTCCTATT
* * *
17785 TTTTCTGAATTAATTCCTAATTGAATCGAAACATGATTCATATGCTCGTAAAAGCAAATCCTTAA
129 TTTTCTGAATTAATTCCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAA
* ** * * * * *
17850 ATCCATTGTGATTGAAATTTGGTTAGATGGATATAGATATTTCAATGAGACTTGGTGCCAAAAAT
194 ATCCAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAAT
* * * * *
17915 CATGAAAAAC--AG-A-GG---C-GAGACCCGA---AA--C-----GCGT-ATTTCGGG
259 CATGCAAAACTGAGCAGGGCCTCGGA-ACGCGATTTAAGCCAAAAACCGTGATATC--T
* * * * * * **** * * * **
17955 AAAATTTTGCCAAAGTTGACCCGAAAGATTTTTCCTTAATTTTTAATCGCAATACTGGTAAAAAA
1 AAAATTTTGCAAAAATTGACACGAAAAATTTCTCCTAAATTTTCGGCCACCATAATCATAAAAAA
* * * * * * *
18020 TATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTCATGCTTCTAATATCATTTATT-CAATTC
66 TATATAATTCAACACCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATATCGTTT-TTCCTATT-
* * * * **
18084 TTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATAATCGTAAAAACAAATCCTTAA
129 TTTTCTGAATTAATTCCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * ** * * * *
18149 AACCATTGTGACTGAGA-TTCGGGATGATTAATATAGATATTTCAATGAGTCTTTGCGCCAAAAC
194 ATCCAATGTGGCTGAGATTTCGTCA-GATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAA
* * * *
18213 TCATGCAAAACTGAGCCAGGGCCCCGGGACGCGTTTTTAGCCAAAAACCGTGATAGTTAGTACAC
258 TCATGCAAAACTGAG-CAGGGCCTCGGAACGCGATTTAAGCCAAAAACCGTG--A--TA-T---C
18278 GATTT
314 ----T
* * * * * **
18283 CGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCTTAATTTT--G-AACCGCAA-CAT
1 -----AAAATTTTGCAAAAATTGACACGAAA-AATTTCTCCTAAATTTTCGGCCACCATAATCAT
** **** *** * * * * * * *
18344 -----ACCT-TGCGCCAACGGTAGAAAGGTTGAAGGGCTTTTTAGGCTTCTAATATCTTTTTTTT
60 AAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATATC--GTTTTT
* * * * * * * *
18403 TCAATTTTTTCCGTATTAATTTCCGATTTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAA
123 CCTATTTTTTCTGAATTAA-TTCCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAA
* ** * *
18468 TCCTTAAATCCATTGTGGCTGAGATTT-GGGATGATTAATATAGATATTTCAATGAGTCTTGGCG
187 TCCTTAAATCCAATGTGGCTGAGATTTCGTCA-GATGAATATAGATATTTCAATGAGACTTGGCG
* * * *
18532 CCAAAAATCATGCAAAACTGAGTCGGGGCAC-CGGAACGCGTTTTTAGCCAAAAATCGTGATGGT
251 CCAAAAATCATGCAAAACTGAG-CAGGGC-CTCGGAACGCGATTTAAGCCAAAAACCGTGA----
18596 TAGTACACGATTT
310 TA-T---C----T
* * * * * * * * * *
18609 CGGCAAAAGCTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTT-GAACCGCAATACTCGT
1 ----AAAA-TTTTGCAAAAATTGACACGAAAAATTTCTCCTAAATTTTCG-GCCACCATAATCAT
** * * * *
18673 AAAAAATATATAATTCAAC-GGAAGAAAGATTGAAGGGCTTTTCA-GCCGTCTAATATCATTTTT
60 AAAAAATATATAATTCAACACCAA-AAAGATTGAAAGGCTTCTCACG-CTTCTAATATC-GTTTT
* * * * * *
18736 TTCAATTTTTTCCGTATTAATTTCC-GATTAAATCGAAAC-TAGATTCAGATGCTCGTAAAATCA
122 TCCTATTTTTTCTGAATTAA-TTCCTAATTAAATCGAAACAT-GATTCAGATGCTCGTAAAAACA
* ** *
18799 AATCCTTAAGTCCAATGTGGCTGAGATTT-GAGATGATGAATATAGATATTTCAATGAGTCTTGG
185 AATCCTTAAATCCAATGTGGCTGAGATTTCGTCA-GATGAATATAGATATTTCAATGAGACTTGG
* * * * * * * *
18863 CTCCAAAAATCATGCAAAACTAAGTCGGGGCAC-CGAAACGTGTTTTTATCCAAAAACCGTGATG
249 CGCCAAAAATCATGCAAAACTGAG-CAGGGC-CTCGGAACGCGATTTAAGCCAAAAACCGTGA--
18927 GTTAT-T
310 --TATCT
* * ** * * * * * *
18933 ACACGATTTCGACAAAAATTTTCA--AATACTTAC-CCTACTCAATTTT-TGCCAACAATACTCA
1 A-A-AATTTTG-CAAAAATTGACACGAAAAATTTCTCCTA---AATTTTCGGCC-ACCATAATCA
* * * * * * * * *
18994 TAAAAAATATATAATTCAACGCCATAAATATTGAATGGCTTTTCATGCTTCTAATAGCTTTTTTT
59 TAAAAAATATATAATTCAACACCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATATCGTTTTTC
* * * * *
19059 TTCATTTTTTCCGAATTAATTTCTATTTAAATCGAAACATGAGTT-AGTTGCTCGTAAAAACAAA
124 CT-ATTTTTTCTGAATTAATTCCTAATTAAATCGAAACATGA-TTCAGATGCTCGTAAAAACAAA
19123 TCCTT
187 TCCTT
19128 TCGGTGCGAC
Statistics
Matches: 1713, Mismatches: 292, Indels: 218
0.77 0.13 0.10
Matches are distributed among these distances:
296 4 0.00
297 7 0.00
298 100 0.06
299 117 0.07
301 2 0.00
302 1 0.00
303 1 0.00
304 4 0.00
306 2 0.00
307 11 0.01
308 1 0.00
310 3 0.00
311 1 0.00
312 3 0.00
313 94 0.05
314 17 0.01
315 248 0.14
316 27 0.02
317 4 0.00
318 93 0.05
319 13 0.01
320 6 0.00
321 17 0.01
322 124 0.07
323 7 0.00
324 40 0.02
325 35 0.02
326 197 0.12
327 5 0.00
328 3 0.00
329 28 0.02
330 121 0.07
331 20 0.01
332 96 0.06
333 178 0.10
334 50 0.03
335 33 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.32
Consensus pattern (314 bp):
AAAATTTTGCAAAAATTGACACGAAAAATTTCTCCTAAATTTTCGGCCACCATAATCATAAAAAA
TATATAATTCAACACCAAAAAGATTGAAAGGCTTCTCACGCTTCTAATATCGTTTTTCCTATTTT
TTCTGAATTAATTCCTAATTAAATCGAAACATGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
CCAATGTGGCTGAGATTTCGTCAGATGAATATAGATATTTCAATGAGACTTGGCGCCAAAAATCA
TGCAAAACTGAGCAGGGCCTCGGAACGCGATTTAAGCCAAAAACCGTGATATCT
Found at i:17733 original size:645 final size:643
Alignment explanation
Indices: 15996--17946 Score: 2803
Period size: 645 Copynumber: 3.0 Consensus size: 643
15986 GGAGTTGGCC
* * * * * *
15996 TAAAAACTATGATGGTTAGTACACGATTTCAG-TCAAAATTTTGCAAAAACTGTCCCGAAAAATT
1 TAAAAACTGTGATGGTTAGTACACGATTTTAGCT-AAAATTTTGCAAAAATTGACACGAAACATT
* * * * * * *
16060 TTTCCTCAATTTTTGGCCACAACACTT-ATAAAAAATATATAATTTAA-ATCCAAAAAGACTTAA
65 TCTCCTCAATTTCTGGCCACCATA-TTCATAAAAAATTTATAATTCAACAT-CAAAACGA-TTAA
* * * *
16123 GGGCTT-TAGATGCTTC-AAT-TTTGTTTTTCAAATTTTTTTCCGAATTAATTTCTAATCAAATC
127 GGGCTTCT-CACGCTTCTAATATTT-TTTTTC---TATTTTTCCGAATTAATTTCTAATTAAATC
* * * * * * * *
16185 GAAA-CATAATTAAGATGTTCGTAAAAACAAATCCTTAAATCCAATGTGACTGACATCTCATTAG
187 GAAACCA-GATTGAGATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAG
* *
16249 ATAAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCC-GGGAACTCG
251 ATGAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGG-CCTCG
* *
16313 GAACGC-ATTTTTAGCCAAAAACAGTGATAGTTAGTACATGATTTCGGCTAAAATTTTGTAAAAA
315 GAACGCGA-TTTAAGCCAAAAAC------CG-T-G---AT-A--T---CTAAAATTTTGTAAAAA
* * * *
16377 TTGACCCGAAAGAATTTTACTAAATGTTTT-GCCACGATAATGATAAAAAATATATAATTCAACA
362 TTGACCCGAAAGAATTTTCCTAAAT-TTTTGGCCACGATAATCATAAAGAATATATAATTTAACA
**
16441 CCAAAAAGATTGAAAGGCTATTCACGCTTCTAATATCGTTTTTCCTATTTTTTCCAAATTAATTC
426 CCAAAAAGATTGAAAGGCTATTCACGCTTCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTC
* *
16506 CTAATTGAATCGAAAAATGATTCATATGCTCGTAAAAGCAAATCCTTAAATCCAATTTGGTTGAG
491 CTAATTGAATCGAAACATGATTCATATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGTTGAG
* * * * *
16571 ATTTGGATAGATGGATATAGATATTTCAATGAGACATGGGGCCAAAAATCATGCAAAATAGAGTC
556 ATTTGGTTAGATGGATATAGATATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCC
* * *
16636 GGGTCCCCAAAACGTGTTTTTAG
621 GGGACCCCGAAACGCGTTTTTAG
* *
16659 TAAAAACTGTGATGGTTAGTACACGA-TTTCGACAAAAAATTTTGCAAAAATTGACACGAAACAT
1 TAAAAACTGTGATGGTTAGTACACGATTTTAG-C-TAAAATTTTGCAAAAATTGACACGAAACAT
*
16723 TTCTCCTCAATTTCTGGCGACCATATTCATAAAAAATTTATAATTCAACATCAAAACGATTGAAG
64 TTCTCCTCAATTTCTGGCCACCATATTCATAAAAAATTTATAATTCAACATCAAAACGATT-AAG
16788 GGCTTCTCACGCTTCTAATATTGTTTTTTTTTCTATTTTTTCCGAATTAATTTCTAATTAAATCG
128 GGCTTCTCACGCTTCTAATA----TTTTTTTTCTA-TTTTTCCGAATTAATTTCTAATTAAATCG
*
16853 AAACCGGATTGAGATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGAT
188 AAACCAGATTGAGATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGAT
* *
16918 GAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAACTAGGGCCTCGGAA
253 GAATATAGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCTCGGAA
16983 CGCGATTTAAGCCAAAAACCGTGATATCTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCT
318 CGCGATTTAAGCCAAAAACCGTGATATCTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCT
*
17048 AAATTTTCGGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGCTATT
383 AAATTTTTGGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGCTATT
*
17113 CACGCTTCTAATATCGTTTTTCCTAATTTTTTCTGAATTAATTCCTAATTGAATTG-AACATGAT
448 CACGCTTCTAATATCGTTTTTCCT-ATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATGAT
17177 TCATATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGA
512 TCATATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGA
* * * * *
17242 TACTCCAAAGAGACTTGGTGCCAACAATCATGCAAAACAGCGCCGGGACCCCGAAACGCGTTTTT
577 TATTTCAATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGACCCCGAAACGCGTTTTT
17307 AG
642 AG
17309 TCAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAATTGACACGAAACATT
1 T-AAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAATTGACACGAAACATT
* * * *
17374 TCTCCTCAATTTCCGACCACCATATTCATAAAAAATTTATAATTCAACGTCAAAACGATTAAAAG
65 TCTCCTCAATTTCTGGCCACCATATTCATAAAAAATTTATAATTCAACATCAAAACGATT-AAGG
*
17439 GCTTCTCACGCTTCTAATATTTTTTTTCTATTTTTCTGAATTAATTTCTAATTAAATCGAAACCA
129 GCTTCTCACGCTTCTAATATTTTTTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACCA
*
17504 GATTGAGATGCTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGATGAATAT
194 GATTGAGATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGATGAATAT
17569 AGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCTCGGAACGCGAT
259 AGATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCTCGGAACGCGAT
17634 TTAAGCCAAAAACCGTGATATCTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCTAAATTT
324 TTAAGCCAAAAACCGTGATATCTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCTAAATTT
*
17699 TTGGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGTTATTCACGCT
389 TTGGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGCTATTCACGCT
17764 TCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATGATTCATATG
454 TCTAATATCGTTTTTCCTATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATGATTCATATG
* * *
17829 CTCGTAAAAGCAAATCCTTAAATCCATTGTGATTGAAATTTGGTTAGATGGATATAGATATTTCA
519 CTCGTAAAAGCAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGATATTTCA
* * *
17894 ATGAGACTTGGTGCCAAAAATCATGAAAAACAGAGGCGAGA-CCCGAAACGCGT
584 ATGAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGACCCCGAAACGCGT
17947 ATTTCGGGAA
Statistics
Matches: 1181, Mismatches: 85, Indels: 63
0.89 0.06 0.05
Matches are distributed among these distances:
644 42 0.04
645 416 0.35
646 11 0.01
649 3 0.00
650 352 0.30
651 54 0.05
652 4 0.00
653 1 0.00
655 1 0.00
656 2 0.00
659 1 0.00
660 1 0.00
661 1 0.00
662 3 0.00
663 29 0.02
664 84 0.07
665 6 0.01
666 1 0.00
667 155 0.13
668 5 0.00
669 6 0.01
670 3 0.00
ACGTcount: A:0.37, C:0.17, G:0.15, T:0.32
Consensus pattern (643 bp):
TAAAAACTGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGCAAAAATTGACACGAAACATTT
CTCCTCAATTTCTGGCCACCATATTCATAAAAAATTTATAATTCAACATCAAAACGATTAAGGGC
TTCTCACGCTTCTAATATTTTTTTTCTATTTTTCCGAATTAATTTCTAATTAAATCGAAACCAGA
TTGAGATGTTCGTAAAAACAAATCCTTAAATCGAATGTGGCTGAGATTTCGTCAGATGAATATAG
ATATTTCAATGAGTCTTGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCTCGGAACGCGATTT
AAGCCAAAAACCGTGATATCTAAAATTTTGTAAAAATTGACCCGAAAGAATTTTCCTAAATTTTT
GGCCACGATAATCATAAAGAATATATAATTTAACACCAAAAAGATTGAAAGGCTATTCACGCTTC
TAATATCGTTTTTCCTATTTTTTCTGAATTAATTCCTAATTGAATCGAAACATGATTCATATGCT
CGTAAAAGCAAATCCTTAAATCCAATGTGGTTGAGATTTGGTTAGATGGATATAGATATTTCAAT
GAGACTTGGTGCCAAAAATCATGCAAAACAGAGCCGGGACCCCGAAACGCGTTTTTAG
Found at i:18871 original size:333 final size:331
Alignment explanation
Indices: 17947--19127 Score: 1376
Period size: 326 Copynumber: 3.6 Consensus size: 331
17937 CGAAACGCGT
* * * * * *
17947 ATTTCGGGAAAATTTTGCCAAAGTTGACCCGAAAGATTTTTCCTTAATTTTTAATCGCAATACTG
1 ATTTCGGCAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTGAACCGCAATACTC
* *
18012 GTAAAAAATATATAATTCAACGCCAA-AAAGTTTGAAGGGCTTTTCATGCTTCTAATATCA-TTT
66 GTAAAAAATATATAATTCAACG-GAAGAAAGATTGAAGGGCTTTTCA-GCTTCTAATATCATTTT
* * * ** *
18075 ATTCAATTCTTTCCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATAATCGTAAAAACA
129 TTTCAATT-TTTTCCGTATTAATTTCCGATTAAATCGAAACAAGATTCAGATGATCGTAAAAACA
* * * *
18140 AATCCTTAAAACCATTGTGACTGAGATTCGGGATGATTAATATAGATATTTCAATGAGTCTTTGC
193 AATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGC
* * * * * *
18205 GCCAAAACTCATGCAAAACTGAGCCAGGGCCCCGGGACGCGTTTTTAGCCAAAAACCGTGATAGT
258 GCCAAAAATCATGCAAAACTGAGTCGGGGCACCGGAACGCGTTTTTAGCCAAAAACCGTGATGGT
18270 TAGTACACG
323 TAGTACACG
18279 ATTTCGGCAAAAATTTTGCAAAAATTGACCCGAAAGATTTTTTCCTTAATTTTGAACCGC-A-A-
1 ATTTCGGC-AAAATTTTGCAAAAATTGACCCGAAAGA-TTTTTCCTTAATTTTGAACCGCAATAC
* ** **** * * * *
18341 -C-----ATACCT-TGCGCCAACGGTAGAAAGGTTGAAGGGCTTTTTAGGCTTCTAATATCTTTT
64 TCGTAAAAAATATATAATTCAACGGAAGAAAGATTGAAGGGCTTTTCA-GCTTCTAATATC-ATT
18399 TTTTTCAATTTTTTCCGTATTAATTTCCGATTTAAATCGAAACAAGATTCAGATGATCGTAAAAA
127 TTTTTCAATTTTTTCCGTATTAATTTCCGA-TTAAATCGAAACAAGATTCAGATGATCGTAAAAA
18464 CAAATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTG
191 CAAATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTG
*
18529 GCGCCAAAAATCATGCAAAACTGAGTCGGGGCACCGGAACGCGTTTTTAGCCAAAAATCGTGATG
256 GCGCCAAAAATCATGCAAAACTGAGTCGGGGCACCGGAACGCGTTTTTAGCCAAAAACCGTGATG
18594 GTTAGTACACG
321 GTTAGTACACG
*
18605 ATTTCGGCAAAAGCTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTGAACCGCAATACT
1 ATTTCGGCAAAA-TTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTGAACCGCAATACT
*
18670 CGTAAAAAATATATAATTCAACGGAAGAAAGATTGAAGGGCTTTTCAGCCGTCTAATATCATTTT
65 CGTAAAAAATATATAATTCAACGGAAGAAAGATTGAAGGGCTTTTCAG-CTTCTAATATCATTTT
* * *
18735 TTTCAATTTTTTCCGTATTAATTTCCGATTAAATCGAAACTAGATTCAGATGCTCGTAAAATCAA
129 TTTCAATTTTTTCCGTATTAATTTCCGATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAA
* * * * *
18800 ATCCTTAAGTCCAATGTGGCTGAGATTTGAGATGATGAATATAGATATTTCAATGAGTCTTGGCT
194 ATCCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCG
* * * *
18865 CCAAAAATCATGCAAAACTAAGTCGGGGCACCGAAACGTGTTTTTATCCAAAAACCGTGATGGTT
259 CCAAAAATCATGCAAAACTGAGTCGGGGCACCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTT
*
18930 ATTACACG
324 AGTACACG
* * * * *
18938 ATTTCGACAAAAATTTT-CAAATACTT-ACCC----------TACTCAATTTTTG--CCAACAAT
1 ATTTCGGC-AAAATTTTGCAAA-AATTGACCCGAAAGATTTTTCCTTAA-TTTTGAACC-GCAAT
* ** * * * * *
18989 ACTCATAAAAAATATATAATTCAACGCCATAAATATTGAATGGCTTTTCATGCTTCTAATAGCTT
62 ACTCGTAAAAAATATATAATTCAACGGAAGAAAGATTGAAGGGCTTTTCA-GCTTCTAATATC-A
* * * * *
19054 TTTTTTTC-ATTTTTTCCGAATTAATTT-CTATTTAAATCGAAACATGAGTT-AGTTGCTCGTAA
125 TTTTTTTCAATTTTTTCCGTATTAATTTCCGA-TTAAATCGAAACAAGA-TTCAGATGATCGTAA
19116 AAACAAATCCTT
188 AAACAAATCCTT
19128 TCGGTGCGAC
Statistics
Matches: 739, Mismatches: 84, Indels: 62
0.84 0.09 0.07
Matches are distributed among these distances:
321 4 0.01
322 116 0.16
323 17 0.02
324 36 0.05
325 45 0.06
326 205 0.28
327 1 0.00
329 1 0.00
332 16 0.02
333 201 0.27
334 60 0.08
335 37 0.05
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.33
Consensus pattern (331 bp):
ATTTCGGCAAAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTTAATTTTGAACCGCAATACTC
GTAAAAAATATATAATTCAACGGAAGAAAGATTGAAGGGCTTTTCAGCTTCTAATATCATTTTTT
TCAATTTTTTCCGTATTAATTTCCGATTAAATCGAAACAAGATTCAGATGATCGTAAAAACAAAT
CCTTAAATCCATTGTGGCTGAGATTTGGGATGATTAATATAGATATTTCAATGAGTCTTGGCGCC
AAAAATCATGCAAAACTGAGTCGGGGCACCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAG
TACACG
Found at i:19768 original size:334 final size:333
Alignment explanation
Indices: 19134--20224 Score: 927
Period size: 334 Copynumber: 3.3 Consensus size: 333
19124 CCTTTCGGTG
* * * * * *
19134 CGACTCAATTTTCCATG-GTTTTGGCATAAAGACTCCTTGAAATATTTATATTCATCTAACCAAA
1 CGACTCAATATTACATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAA
* * * * * * **
19198 TCTTAGCCACATTGGATTTATGGTTTGGCTTTACGAGTATCTGAGTCTTGTTTTGATTTAATTAG
66 TCCTAGCCACATTGGATTTAAGGTTTGACTTTACAAGCATCTGAATCTTGTTTCAATTTAATTAG
* * * *
19263 AAATAAATTCGGGAAAATAATGGAAAAACAATATTAGAAGCGTGTAAAACCATTCAATTTTTTTT
131 AAATAAATTCGAGAAAAAAAAGGAAAAACAATATTAGAAGCGTGAAAAACCATTCAATTTTTTTT
*
19328 GGCGTTGAATCATATATTCTTCCCGAATATTGTGCCAAAAAATTGAGGAAAAACTTTTCGGGTTA
196 GGCGTTGAATCATATATTCTTCCCGAATATTGTGCCAAAAAATTGAGGAAAAACTTTTCAGGTTA
* * * * * *
19393 GTTTTTACAAAATTTTAGCCGAAATCGTGTATTATCCATCACAGTTTTTTGCTAAAAACAAG-TT
261 GTTTTTACAAAAATTTAGCCGAAATCATATACTAACCATCACAGTTTTTGGCTAAAAAC--GCTT
19457 T-CGG-GGCC
324 TCCGGAGGCC
* * * * * **
19465 CGGCCTCAGTTTTAGATGATTTTTTGCGTAAAGACTTCTTGAAATATCTATATTCAT-TAAATTA
1 C-GACTCAATATTACATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCT-AACCA
* * *
19529 AATCCCT-GCCACATTGGATTTAAGGATTTGATTTTACAAGCATCTTAATCTTGTTTCAATTTAC
64 AAT-CCTAGCCACATTGGATTTAAGG-TTTGACTTTACAAGCATCTGAATCTTGTTTCAATTTAA
* ** *
19593 TTAGAAATTAATTCAGAGAAAAAAAAGGAAAAACGGTATTAGAAGCGTGAAAAAACCCTTCAA-T
127 TTAGAAATAAATTC-GAGAAAAAAAAGGAAAAACAATATTAGAAGCGTG-AAAAACCATTCAATT
* * * * * *
19657 TTTTTTGGTGTTGAATTATATATT-TTCTCTGAGTATTGTGGC-AAATATTGAGGAAAAACTTTT
190 TTTTTTGGCGTTGAATCATATATTCTTC-CCGAATATTGTGCCAAAAAATTGAGGAAAAACTTTT
19720 CAGGTTAGTTTCTT-CAAAAATTTAGCCGAAATCATATACTAACCATCACAGTTTTTGGCTAAAA
254 CAGGTTAGTTT-TTACAAAAATTTAGCCGAAATCATATACTAACCATCACAGTTTTTGGCTAAAA
*
19784 ACGCTTTCCGGAGTCC
318 ACGCTTTCCGGAGGCC
* * * *
19800 CGACTTAATATTACATGATTTTTGGCGCAAAGA-TTCCTTGAAATATCTATATTCATCGAAACAA
1 CGACTCAATATTACATGATTTTTGGCGTAAAGACTT-CTTGAAATATCTATATTCATCTAACCAA
* ** * * * **
19864 ATCTTAGCCTA-ATTGGATACAAGGATTTGTAC-ATACGAGCATTTGAATCTTGTTTCGTTTTAA
65 ATCCTAGCC-ACATTGGATTTAAGG-TTTG-ACTTTACAAGCATCTGAATCTTGTTTCAATTTAA
** * * * * *
19927 TTAGAAATTCATT--TG--TAAAAA--AAAAACGATATTAGAAGCGTGAAAAGCCCA-TCAA-TC
127 TTAGAAATAAATTCGAGAAAAAAAAGGAAAAACAATATTAGAAGCGTGAAAA-ACCATTCAATTT
* * * * * * * * *
19984 TTTTTGGCGTTTAATTATATATTTTTTCTGAATATTTTG-CAAAAAATTTAGAAAAAACATTTC-
191 TTTTTGGCGTTGAATCATATATTCTTCCCGAATATTGTGCCAAAAAATTGAGGAAAAACTTTTCA
* * * * * *
20047 GG---G----T-C-AGATTTTTGCCGAAATCGTGTACTAACCCATCACAGATTTTGGCTAAAAAC
256 GGTTAGTTTTTACAAAAATTTAGCCGAAATCATATACTAA-CCATCACAGTTTTTGGCTAAAAAC
* *
20103 G-TGTTTCGGAGTCC
320 GCT-TTCCGGAGGCC
* * * * *
20117 CGACTCAGTTTTGCATGATTTTTGGCAG-AAAGACTCCTTGAAATATCTATATTTATCTAACCAA
1 CGACTCAATATTACATGATTTTTGGC-GTAAAGACTTCTTGAAATATCTATATTCATCTAACCAA
* * ** * ** *
20181 ATCCCAGTCACATTCAATTTAAGGATTGTTTTTACGAGCATCTG
65 ATCCTAGCCACATTGGATTTAAGGTTTGACTTTACAAGCATCTG
20225 GACTTAATTA
Statistics
Matches: 626, Mismatches: 108, Indels: 67
0.78 0.13 0.08
Matches are distributed among these distances:
316 37 0.06
317 103 0.16
318 2 0.00
322 1 0.00
325 3 0.00
326 58 0.09
327 24 0.04
329 5 0.01
331 2 0.00
332 14 0.02
333 63 0.10
334 232 0.37
335 71 0.11
336 11 0.02
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.36
Consensus pattern (333 bp):
CGACTCAATATTACATGATTTTTGGCGTAAAGACTTCTTGAAATATCTATATTCATCTAACCAAA
TCCTAGCCACATTGGATTTAAGGTTTGACTTTACAAGCATCTGAATCTTGTTTCAATTTAATTAG
AAATAAATTCGAGAAAAAAAAGGAAAAACAATATTAGAAGCGTGAAAAACCATTCAATTTTTTTT
GGCGTTGAATCATATATTCTTCCCGAATATTGTGCCAAAAAATTGAGGAAAAACTTTTCAGGTTA
GTTTTTACAAAAATTTAGCCGAAATCATATACTAACCATCACAGTTTTTGGCTAAAAACGCTTTC
CGGAGGCC
Found at i:21237 original size:826 final size:826
Alignment explanation
Indices: 19480--21712 Score: 3325
Period size: 826 Copynumber: 2.7 Consensus size: 826
19470 TCAGTTTTAG
* * ** * * * * *
19480 ATGATTTTTTG-CGTAAAGACTTCTTGAAATATCTATATTCATTAAATTAAATCCCTGCCACATT
1 ATGA-TTTTTGACGTTAAGACTCCTTGAAATATCTATATTCATCGAACTAAGTCCCAGCTACTTT
* * * * * * **
19544 GGATTTAAGGATTTGATTTTACAAGCATCTTAATCTTGTTTCAATTTACTTAGAAATTAATTCAG
65 GGATTTAACGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGTATTAATTCAG
* * * ***
19609 AGAAAAAAAA-GGAAAAACGGTATTAGAAGCGTGAAAAAACCCTTCAATTTTTTTGGTGTTGAAT
130 A-AAAAAAAATGAAAAAACGATATTAGAAGCGTG-AAAAACCCTTCAATCTTTTTGACATTGAAT
* *
19673 TATATATTTTCTCTGAGTATTGTGGCAAAT-ATTGA-GGAAAAACTTTTCAGGTTAGTTTCTT-C
193 TATATATTTTTTCTGAGTATTGTGGCAAATAATTGAGGGAAAAA-TTTTCAGGTAAGTTT-TTGC
** * * * * * *
19735 AAAA-ATTTAGCCGAAATCATATACTAACCATCACAGTTTTTGGCTAAAAACGCT-TTCCGGAGT
256 AAAATA-TTAGCTAAAATCATGTACTAACCATTACGGTTTTTGGTTAAAAACG-TGTTCCGGTGC
* * * * * * * *
19798 CCCGACTTAATATTACATGATTTTTGGCGCAAAGATTCCTTGAAATATCTATATTCATCGAAACA
319 CCCGGCTCAATTTTGCATTATTTTTGGCGCAAA-ACTCCTTGAAATATCTATATTCATTGAACCA
* * *** * * **
19863 AATCTTAGCCTA-ATTGGATACAAGGATTTGTACATACGAGCATTTGAATCTTGTTTCGTTTTAA
383 AATCTTAGCC-ACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTTCAATTTAA
* * * * * * *
19927 TTAGAAATTCATT-TGTAAAAA---AAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTT
447 TTATAAATTAATTCGGGAAAAATGGAAAAACTATATTAGAAGCGTGAAAAGCCCGTCAATATTTT
* * * * *
19988 TGGCGTTTAATTATATATTTTTTCTGAATATTTTGCAAAAAATT--TAGAAAAAACATTTCGGGT
512 TGGCGTTGAATTATATATTTTTTCTGAATATTTCGCAAAAAATTCAAAAAAAAAACTTTTCGGGT
* *
20051 CAGATTTTTGCCGAAATCGTGTACTAACCCATCACAGATTTTGGCTAAAAACGTGTTTCGGAGTC
577 CAGATTTTAGCCGAAATCGTGTACTAACCCATCACAGATTTTGGCTAAAAACGCGTTTCGGAGTC
20116 CCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAA
642 CCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAA
*
20181 ATCCCAGTCACATTCAATTTAAGGATTGTTTTTACGAGCATCTGGACTTAATTAAAAATAAATTC
707 ATCCCAGCCACATTCAATTTAAGGATTGTTTTTACGAGCATCTGGACTTAATTAAAAATAAATTC
20246 GGAAAAAAAAAAAAGAAACACGATCTTAGAAGCGTGAAAACCCTTTCAATTTTGC
772 GGAAAAAAAAAAAAGAAACACGATCTTAGAAGCGTGAAAACCCTTTCAATTTTGC
*
20301 ATGATTTTTGACGTTAAGGCTCCTTGAAATATCTATATTCATCGAACTAAGTCCCAGCTACTTTG
1 ATGATTTTTGACGTTAAGACTCCTTGAAATATCTATATTCATCGAACTAAGTCCCAGCTACTTTG
* * *
20366 CATTTAATGATTTGTTTTTACGAGCATATGAATCTTGTTTCGATTTAATTAGGTATTAATTCAGA
66 GATTTAACGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGTATTAATTCAGA
* *
20431 AAAAAAAATGAAAAAACAAATATTAGAAGCGTGAAAAACCTTTCAATCTTTTTGACATTGAATTA
131 AAAAAAAATGAAAAAAC-GATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGACATTGAATTA
* *
20496 TATATTTTTTCTGAGTACTGTGGCAAATAATTGAGGGAAAAATTTTCGGGTAAGTTTTTGCAAAA
195 TATATTTTTTCTGAGTATTGTGGCAAATAATTGAGGGAAAAATTTTCAGGTAAGTTTTTGCAAAA
*
20561 TATTAGCTAAAATCGTGTACTAACCATTACGGTTTTTGGTTAAAAACGTGTTCCGGTGCCCCGGC
260 TATTAGCTAAAATCATGTACTAACCATTACGGTTTTTGGTTAAAAACGTGTTCCGGTGCCCCGGC
20626 TCAATTTTGCATTATTTTTGGCGCATAAACTCCTTGAAATATCTATATTCATTGAACCAAATCTT
325 TCAATTTTGCATTATTTTTGGCGCA-AAACTCCTTGAAATATCTATATTCATTGAACCAAATCTT
20691 AGCCACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTTCAATTTAATTATAAA
389 AGCCACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTTCAATTTAATTATAAA
*
20756 TTAATTCGGGAAAAATGGAAAAACTATATTAGAAGCATGAAAAGCCCGTCAATATTTTTGGCGTT
454 TTAATTCGGGAAAAATGGAAAAACTATATTAGAAGCGTGAAAAGCCCGTCAATATTTTTGGCGTT
* *
20821 GAATCATAT-TTTTTTCTAAATATTTCGCAAAAAATTCAAAAAAAAAAACTTTTCGGGTCAGATT
519 GAATTATATATTTTTTCTGAATATTTCGCAAAAAATTC-AAAAAAAAAACTTTTCGGGTCAGATT
* *
20885 TTAGCCGAAATCGTGTACTAA-CCATCACAGATTTTGGCTAAAAATGCGTTTCGGAGTCCCGGCT
583 TTAGCCGAAATCGTGTACTAACCCATCACAGATTTTGGCTAAAAACGCGTTTCGGAGTCCCGACT
20949 CAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCCCA
648 CAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCCCA
* *
21014 GCCACATTCGATTTAAGGATTGTTTTTACGAGCATCTGGACTTAATTAAAAATAAATTCGG-GAA
713 GCCACATTCAATTTAAGGATTGTTTTTACGAGCATCTGGACTTAATTAAAAATAAATTCGGAAAA
21078 AAAAAAAAGAAACACGATCTT-GAAAGCGTGAAAACCCTTTCAATTTTGC
778 AAAAAAAAGAAACACGATCTTAG-AAGCGTGAAAACCCTTTCAATTTTGC
* * *
21127 CTGATTTTTGATGTTAAGACTCCTTGAAATATCTATATTCATCGAACTAAGTCCCAGTTACTTTG
1 ATGATTTTTGACGTTAAGACTCCTTGAAATATCTATATTCATCGAACTAAGTCCCAGCTACTTTG
*
21192 GATTTAACGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGTATTAATTCGGA
66 GATTTAACGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGTATTAATTCAGA
*
21257 AAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAACCCCTTCAATCTTTTTGACATTGAATTAT
131 AAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGACATTGAATTAT
21322 ATATTTTTTCTGAGTATTGTGGCAAATAATTGAGGG-AAAATTTTCAGGTAAGTTTTTGCAAAAT
196 ATATTTTTTCTGAGTATTGTGGCAAATAATTGAGGGAAAAATTTTCAGGTAAGTTTTTGCAAAAT
* * *
21386 ATTAGCTAAAATCATGTACTAACAATTACGGTTTTTGGTTAAAAATGTGTTTCGGTGCCCCGGCT
261 ATTAGCTAAAATCATGTACTAACCATTACGGTTTTTGGTTAAAAACGTGTTCCGGTGCCCCGGCT
* * *
21451 CAATTTTGCATTATTTTTGGTGCAAAAGCTCCTTGAAATATTTATATTCATTGAACCAAATCTCA
326 CAATTTTGCATTATTTTTGGCGCAAAA-CTCCTTGAAATATCTATATTCATTGAACCAAATCTTA
*
21516 GTCACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTTCAATTTAATTATAAAT
390 GCCACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTTCAATTTAATTATAAAT
* *
21581 TAATTCGGGAAAAATGGAAAAACTATATTAGAAGCGTGAAAAAAACCCGTCAATATTTTTGGCAT
455 TAATTCGGGAAAAATGGAAAAACTATATTAGAAGCGTG--AAAAGCCCGTCAATATTTTTGGCGT
*
21646 TGAATTATATATTTTTTCTGAATATTTCGCAAAAAATTCAAAAAAAAAACTTTTCGGGTCAGTTT
518 TGAATTATATATTTTTTCTGAATATTTCGCAAAAAATTCAAAAAAAAAACTTTTCGGGTCAGATT
21711 TT
583 TT
21713 TCAAAATTTT
Statistics
Matches: 1283, Mismatches: 107, Indels: 39
0.90 0.07 0.03
Matches are distributed among these distances:
820 14 0.01
821 167 0.13
822 200 0.16
823 19 0.01
824 247 0.19
825 106 0.08
826 297 0.23
827 191 0.15
828 42 0.03
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (826 bp):
ATGATTTTTGACGTTAAGACTCCTTGAAATATCTATATTCATCGAACTAAGTCCCAGCTACTTTG
GATTTAACGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGTATTAATTCAGA
AAAAAAAATGAAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTGACATTGAATTAT
ATATTTTTTCTGAGTATTGTGGCAAATAATTGAGGGAAAAATTTTCAGGTAAGTTTTTGCAAAAT
ATTAGCTAAAATCATGTACTAACCATTACGGTTTTTGGTTAAAAACGTGTTCCGGTGCCCCGGCT
CAATTTTGCATTATTTTTGGCGCAAAACTCCTTGAAATATCTATATTCATTGAACCAAATCTTAG
CCACATTGGACATAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTTCAATTTAATTATAAATT
AATTCGGGAAAAATGGAAAAACTATATTAGAAGCGTGAAAAGCCCGTCAATATTTTTGGCGTTGA
ATTATATATTTTTTCTGAATATTTCGCAAAAAATTCAAAAAAAAAACTTTTCGGGTCAGATTTTA
GCCGAAATCGTGTACTAACCCATCACAGATTTTGGCTAAAAACGCGTTTCGGAGTCCCGACTCAG
TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTTATCTAACCAAATCCCAGCC
ACATTCAATTTAAGGATTGTTTTTACGAGCATCTGGACTTAATTAAAAATAAATTCGGAAAAAAA
AAAAAGAAACACGATCTTAGAAGCGTGAAAACCCTTTCAATTTTGC
Found at i:23064 original size:257 final size:250
Alignment explanation
Indices: 22615--23112 Score: 739
Period size: 257 Copynumber: 2.0 Consensus size: 250
22605 ATCTTATATT
* * * *
22615 TTTTTGAGTATTGTGGCAAAAATTTGAGAAAGAATTTTTTAGGTCAGTTTTTAACCGAAATCTTG
1 TTTTTGAGTATTGTGGCAAAAAATTGAGAAAGAATTTTTCAAGTCAGTTTTTAACCGAAATCTTA
* * * *
22680 TCACGGTTTTTGGCTAAAATCGTGTTCCGGAGCCCCGGCTCAATTTCGCATTATTTTTTGCGCAA
66 TCACGGTTTTTGACTAAAAACGTGTTCCGGAGCCCCGACTCAATTTCGCATTATTTTTGGCGCAA
**
22745 AAACTCCTTGAAATATCTAGATTCATTGAACCAAATCTCAGCCACATTTTACATAAGGATTTGTT
131 AAACTCCTTGAAATATCTAGATTCATTGAACCAAATCTCAGCCACATTGGACATAAGGATTTGTT
* *
22810 TTTACGAGCATCTGAACCTTTTTTCAATTTAATTAGAAATAAATTCAAAGATTTC
196 TTTACGAGCATCTAAACCTTTTTTAAATTTAATTAGAAATAAATTCAAAGATTTC
22865 TTTTTGAGTATTGTGGCAAAAAATTGAGAAAGAA-TTTTCAAGTCAG-TTTTAACCGAAATCGTG
1 TTTTTGAGTATTGTGGCAAAAAATTGAGAAAGAATTTTTCAAGTCAGTTTTTAACCGAAATC---
**
22928 TACTAACCATCACGGTTTTTGACTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTTCATTATTT
63 T--T----ATCACGGTTTTTGACTAAAAACGTGTTCCGGAGCCCCGACTCAATTTCGCATTATTT
* *
22993 TTGGCGTAAAAACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGCCACATTGGACATAA
122 TTGGCGCAAAAACTCCTTGAAATATCTAGATTCATTGAACCAAATCTCAGCCACATTGGACATAA
* *
23058 GGATTTGTTTTTACGAGCATCTAAATCTTTTTTAAATTTAATTAGAAATTAATTC
187 GGATTTGTTTTTACGAGCATCTAAACCTTTTTTAAATTTAATTAGAAATAAATTC
23113 TGAAAAAAAT
Statistics
Matches: 221, Mismatches: 18, Indels: 11
0.88 0.07 0.04
Matches are distributed among these distances:
248 14 0.06
249 10 0.05
250 33 0.15
251 1 0.00
253 1 0.00
257 162 0.73
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.37
Consensus pattern (250 bp):
TTTTTGAGTATTGTGGCAAAAAATTGAGAAAGAATTTTTCAAGTCAGTTTTTAACCGAAATCTTA
TCACGGTTTTTGACTAAAAACGTGTTCCGGAGCCCCGACTCAATTTCGCATTATTTTTGGCGCAA
AAACTCCTTGAAATATCTAGATTCATTGAACCAAATCTCAGCCACATTGGACATAAGGATTTGTT
TTTACGAGCATCTAAACCTTTTTTAAATTTAATTAGAAATAAATTCAAAGATTTC
Found at i:23448 original size:580 final size:569
Alignment explanation
Indices: 22433--23744 Score: 1672
Period size: 580 Copynumber: 2.3 Consensus size: 569
22423 TTTTTACATT
* * * * * * *
22433 AAAACTCCTTTAAATTTCTATATTCATCGAATCAAGTCCCAGCTACATTGGATTTAATGATTTGT
1 AAAACTCCTTGAAATATCTATATTCATTGAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
**
22498 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGGTATTAATTCAGAAAAAAA-GGAAAAAC
66 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGGAAAAAC
* * * * *
22562 GATATTAGAAGCGTGAAAAACCCTTCAATCTTTTTAACATTGAATCTTATATTTTTTTGAGTATT
131 GATATTAGAAGCGTG-AAAATCCTTCAATATTTTTAACAGTGAATCTTATATTTTTTTAAATATT
* * * * **
22627 GTGGCAAAAATTTGAGAAAGAATTTTTTAGGTCAGTTTTTAACCGAAATCTTGTCACGGTTTTTG
195 GTGGCAAAAAATTGAGAAAAAACTTTTCAGGTCAGTTTTTAACCGAAATCTCATCACGGTTTTTG
* * * * * * * *
22692 GCTAAAATCGTGTTCCGGAGCCCCGGCTCAATTTCGCATTATTTTTTGCGCAAAAACTCCTTGAA
260 GCGAAAAACGCGTTCCGGAGCCCCGACTCAATTTCGCATGATTTTTTGCGCAAAAACACATTAAA
* ** * *
22757 ATATCTAGATTCATTGAACCAAATCTCAGCCACATTTTACATAAGGATTTGTTTTTACGAGCATC
325 ATATCTAGATTCATTGAACCAAATCTCAGCCACAGTGGACATAAGGATTTCTTTTTACAAGCATC
* *
22822 TGAACCTTTTTTCAATTTAATTAGAAATAAATTCAAAGATTTCTTTTTGAGTATTGTGGCAAAAA
390 TAAACCTTGTTTCAATTTAATTAGAAATAAATTCAAAGATTTCTTTTTGAGTATTGTGGCAAAAA
22887 ATTGAGAAAGAA-TTTTCAAGTCAG-TTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGA
455 ATTGAGAAAGAATTTTTCAAGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGA
* *
22950 CTAAAAACGTGTTCCGGAGCCCCGACTCAATTTTTCATTATTTTTGGCGTA
520 CTAAAAACGTGTTCCGAAGCCCCGACTCAATTTTGCATTATTTTTGGCG-A
* **
23001 AAAACTCCTTGAAATATCTATATTCATTGAACCAAATCTCAGCCACATTGGACATAAGGATTTGT
1 AAAACTCCTTGAAATATCTATATTCATTGAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* * ** *
23066 TTTTACGAGCATCTAAATCTTTTTTAAATTTAATTAGAAATTAATTCTGAAAAAAATGGAAAAAC
66 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGGAAAAAC
* * ** *
23131 TATATTAGAAGCGTGAAAAGTCCGTCAATATTTTTGGCGGTGAAT-TATATATTTTTTCTAAATA
131 GATATTAGAAGCGTGAAAA-TCCTTCAATATTTTTAACAGTGAATCT-TATATTTTTT-TAAATA
* *
23195 TT-TTGCAAAAAATTGAGAAAAAAAACTTTTCAGGTCAGTTTTTAGCCGAAACCATGTACTAACC
193 TTGTGGCAAAAAATTGAG--AAAAAACTTTTCAGGTCAGTTTTTAACCG-AA--A--T-CT---C
* * *
23259 ATCACGGTTTTTGGCGAAAAACGCGTTTC-GAGGCCCCGACTCAGTTTTGCATGATTTTTTGCTG
247 ATCACGGTTTTTGGCGAAAAACGCGTTCCGGA-GCCCCGACTCAATTTCGCATGATTTTTTGC-G
* ** *
23323 -AAAAACACATTAAAATATCTATATTCATAT-AATTAAATCTCAGCCACAGTGGA-TTCAAGGAT
310 CAAAAACACATTAAAATATCTAGATTCAT-TGAACCAAATCTCAGCCACAGTGGACAT-AAGGAT
* * * * *
23385 TTCTTTTTACAAGTATCTAAATCTTGTTTCGATTTAATTAGAAATAAATTCAAGGTTTTCTTTTT
373 TTCTTTTTACAAGCATCTAAACCTTGTTTCAATTTAATTAGAAATAAATTCAAAGATTTCTTTTT
* * *
23450 GAGTATTGTGGCAAAAAATTGAGAAAGAATTTTTCAGGTTAGTTTTTAGCCGAAATCGTGTACTA
438 GAGTATTGTGGCAAAAAATTGAGAAAGAATTTTTCAAGTCAGTTTTTAACCGAAATCGTGTACTA
* *
23515 ACCATCACGGTTTTTGGCTAAAAACGTGTTCCGAAGTCCCGACTCAATTTTGCATTATTTTTGGC
503 ACCATCACGGTTTTTGACTAAAAACGTGTTCCGAAGCCCCGACTCAATTTTGCATTATTTTTGGC
23580 GA
568 GA
*
23582 AAAACTCCTTGAAATATCTATATTCATTGAATCAAATCTCAGCCACATTGGATTTAAGGATTTGG
1 AAAACTCCTTGAAATATCTATATTCATTGAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
* * * * *
23647 CTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAAAAATTATTTCAGAAAAATATGGAAAAAC
66 TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGGAAAAAC
* * *
23712 GATATTAAAAACATGAAAATCCTTCAA-ATTTTT
131 GATATTAGAAGCGTGAAAATCCTTCAATATTTTT
23745 TTATGTTAGA
Statistics
Matches: 635, Mismatches: 88, Indels: 31
0.84 0.12 0.04
Matches are distributed among these distances:
568 109 0.17
569 63 0.10
570 6 0.01
571 25 0.04
572 2 0.00
574 1 0.00
576 1 0.00
577 2 0.00
579 9 0.01
580 190 0.30
581 144 0.23
582 83 0.13
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (569 bp):
AAAACTCCTTGAAATATCTATATTCATTGAATCAAATCTCAGCCACATTGGATTTAAGGATTTGT
TTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAAATGGAAAAAC
GATATTAGAAGCGTGAAAATCCTTCAATATTTTTAACAGTGAATCTTATATTTTTTTAAATATTG
TGGCAAAAAATTGAGAAAAAACTTTTCAGGTCAGTTTTTAACCGAAATCTCATCACGGTTTTTGG
CGAAAAACGCGTTCCGGAGCCCCGACTCAATTTCGCATGATTTTTTGCGCAAAAACACATTAAAA
TATCTAGATTCATTGAACCAAATCTCAGCCACAGTGGACATAAGGATTTCTTTTTACAAGCATCT
AAACCTTGTTTCAATTTAATTAGAAATAAATTCAAAGATTTCTTTTTGAGTATTGTGGCAAAAAA
TTGAGAAAGAATTTTTCAAGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTGAC
TAAAAACGTGTTCCGAAGCCCCGACTCAATTTTGCATTATTTTTGGCGA
Found at i:24436 original size:20 final size:20
Alignment explanation
Indices: 24408--24446 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
24398 CCCCGAATTC
*
24408 AATACTAATATTTGAAAATA
1 AATAATAATATTTGAAAATA
*
24428 AATAATAATTTTTGAAAAT
1 AATAATAATATTTGAAAAT
24447 TTCATTTATG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.54, C:0.03, G:0.05, T:0.38
Consensus pattern (20 bp):
AATAATAATATTTGAAAATA
Found at i:38292 original size:16 final size:17
Alignment explanation
Indices: 38271--38304 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
38261 GTATGTATAA
*
38271 ATTATAT-TTAATAAAT
1 ATTATATATCAATAAAT
38287 ATTATATATCAATAAAT
1 ATTATATATCAATAAAT
38304 A
1 A
38305 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTATATATCAATAAAT
Found at i:43491 original size:5 final size:5
Alignment explanation
Indices: 43492--43523 Score: 50
Period size: 5 Copynumber: 6.8 Consensus size: 5
43482 ATTCAATTCA
43492 AATT- AATTT AATTT AATTT AATTT AA-TT AATT
1 AATTT AATTT AATTT AATTT AATTT AATTT AATT
43524 GGGATTTCGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
4 8 0.31
5 18 0.69
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (5 bp):
AATTT
Found at i:43504 original size:15 final size:15
Alignment explanation
Indices: 43481--43519 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
43471 AACCTCTTGG
*
43481 AATTCAATTCAAATT
1 AATTTAATTCAAATT
* *
43496 AATTTAATTTAATTT
1 AATTTAATTCAAATT
43511 AATTTAATT
1 AATTTAATT
43520 AATTGGGATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
AATTTAATTCAAATT
Found at i:48245 original size:2 final size:2
Alignment explanation
Indices: 48238--48274 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
48228 GTTTGTGCAG
48238 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 A
48275 ATAGATTTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:54285 original size:38 final size:39
Alignment explanation
Indices: 54254--54422 Score: 150
Period size: 38 Copynumber: 4.2 Consensus size: 39
54244 GGAATCTAAT
54254 TGATAATCACATTGATCCCGATTAGTTTGGAATCGAA-C
1 TGATAATCACATTGATCCCGATTAGTTTGGAATCGAAGC
* *
54292 TGATAGTCACATTAAGT-CCGATTAGTCTAGAGTGAAGCTAGAGT-GAAGC
1 TGATAATCACATTGA-TCCCGATTAGT-T----TG--G--A-A-TCGAAGC
* *
54341 TGATAATCACATTGATCCCGATTAGTCTAGAAT-GAAGC
1 TGATAATCACATTGATCCCGATTAGTTTGGAATCGAAGC
*
54379 TGATAATCACATTGATCCCGATTAGTTTGGAACCG-AGC
1 TGATAATCACATTGATCCCGATTAGTTTGGAATCGAAGC
54417 TGATAA
1 TGATAA
54423 GACAATGTTT
Statistics
Matches: 107, Mismatches: 9, Indels: 30
0.73 0.06 0.21
Matches are distributed among these distances:
38 67 0.63
39 4 0.04
40 1 0.01
42 1 0.01
43 2 0.02
44 1 0.01
45 1 0.01
47 1 0.01
48 5 0.05
49 24 0.22
ACGTcount: A:0.33, C:0.17, G:0.21, T:0.29
Consensus pattern (39 bp):
TGATAATCACATTGATCCCGATTAGTTTGGAATCGAAGC
Done.