Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016441.1 Corchorus olitorius cultivar O-4 contig16474, 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: 112400
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:730 original size:333 final size:330
Alignment explanation
Indices: 3--3848 Score: 5083
Period size: 333 Copynumber: 11.7 Consensus size: 330
1 GT
* * * * *
3 AAAA-AAATCCTTAAATCCTAAATGGCTGAGATCTGGCTAGGTTAAAATAAATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * **
67 CATGGCGCCAAAAATCATGCAAAATTTAGTCGGGTCCCCGGAACGCGTTTTTAGCGTAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
132 GATGGTTAGTACACGATTTCAGCTACAATTTTGTAAAAATTGACCCGAAATATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
** * * *
197 TTTGATCACAATACTAATAAAGAACATCTAATTCAAAGCCAAAAAGACTGAACGACTTTTCACGC
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGC
* * *
262 TTCTTAGTTGTTTTT-TTCTTTTTCTGAATTAATTTTTTATTAGATCGAACCATGATTCAGATGC
261 TTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
326 TCGTA
326 TCGTA
*
331 AAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * *
396 CATGGCACCAAAAATCATGCAAAATTGAGCCGGGTCCCCTGAAGGCGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
461 GATGGTTAGTACACGATTTCGGCTATAATTTTGCAAAAATAGAAACCCGAAAGAATTTTCCTCAA
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTG--ACCCGAAAGATTTTTCCTCAA
* *
526 TTTTTTGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGGCTGAA-GACATTTTCA
194 TTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGAC-TTTTCA
*
590 CGCGTCTTAGTTGTTTTTCTTTTTTTTCCCGAATTAATTTTTTATTAAATCGAACCATGATTCAG
258 CGCTTCTTAGTTGTTTTTCTTTTTTTT-CCGAATTAATTTTTTATTAAATCGAACCATGATTCAG
655 ATGCTCGTA
322 ATGCTCGTA
* *
664 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATAAAAATTGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * *
729 CATGGCACCAAAAATCATGCAAAATTAAGCCGGGTCCCCGTAACGCGTTTTAAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
794 GATAGTTTGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCAT-AAT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCC-TCAAT
* * ** * * **
858 TTTTAGCCACAATACTCATTAAA-AATATATAATTCAGGGCCATAAATA-TAGAAGGGTTTTTCA
195 TTTTGGCCACAATACTCA-TAAAGAATATCTAATTCAAAGCCAAAAAGACT-GAAGGACTTTTCA
* * * * *** *
921 CGTTTCTAATA-TTGTTTTCGCCATTTTTTTT-CGAAATAATATCCAATTAAATC-ATAAC-TCG
258 CGCTTCT--TAGTTGTTTT--TC-TTTTTTTTCCGAATTAATTTTTTATTAAATCGA-ACCAT-G
*
982 ATTCTGATGCTCGTA
316 ATTCAGATGCTCGTA
** * *
997 AAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAAAATGGATATTTCAAGGAAT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
** * * *
1062 CGA-AACGCCAAAAATCATGCAAAATTGACCCGGGTCCCCGGAACACGTTTTTAGCTAAAAACCG
66 C-ATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCG
* * * *
1126 TCATGGTTAGTATACGTTTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
130 TGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
*
1191 TCTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAA-GATCTTTTCAC
195 TTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGA-CTTTTCAC
* * *
1255 GCTTCTTAGTTGTTTTTTTTCTTTTTTTTTCGAAATAATTTTTTATTAAATCGAACCATGATTCT
259 GCTTCTTAGTTG---TTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCA
1320 GATGCTCGTA
321 GATGCTCGTA
* * *
1330 AAAACAAATCATTAAATCCTAAATAGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* *
1395 CATGGCGTCAAAAATCATGCAAAATTGAGCCAGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* *
1460 GAT-G-TA--A-ACGATTTCGGCTACAATTTTGGAAAAATTGACACGAAAGATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
* * *
1520 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGCCTTTGCACGG
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGC
1585 TTCTTAGTTG----------TTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
261 TTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
1640 TCGTA
326 TCGTA
1645 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * *
1710 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCAGAACGCGTTTCTAGCTAAAAATCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * * *
1775 GATGGTTAGTGA-ACGATTTCAGCTACAATTTTGTAAAAATTGACCTGAAATATTTTTCCTCAAT
131 GATGGTTAGT-ACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
* * *
1839 TTTTGGCCATAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGGCTTTTCACG
195 TTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACG
* *
1904 CTTCTTAGTTGTTTTTC---TTTTCCCGAATTAATTTTCTATTAAATCGAACCATGATTCAGATG
260 CTTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATG
1966 CTCGTA
325 CTCGTA
* *
1972 AAAACAAATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTGAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * ** **
2037 CATGGCGCCAAAAATCATTCGAAATTGAGCCGGATCCCCAAAACAAGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * * *
2102 GATGGTTTA-TACACGAATTCGGCTACAAATTTGCAAAAATTGACCCGAAAGCTTTCTCCTCAAT
131 GATGG-TTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
* ** *
2166 TTTTGGCCACAATTCTCATAAAGAATATCTAATTCAAAGCCAAAAAGACT-AAATATCTTGTCAC
195 TTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGA-CTTTTCAC
* * **
2230 GCTTCTTAGTTG----T-TTTTTTTTCTGAAATAATTTTTTATTAAATCGAACCATGATTCATTT
259 GCTTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGAT
*
2290 GTTCGTA
324 GCTCGTA
* * * *
2297 AAAA-AAATCCTTAAATCCTAAATGGCTGAGATCTGGCTAGATTAAAATAAATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * **
2361 CATGGCGCCAAAAATCATGCAAAATTTAGTCGGGTCCCCGGAACGCGTTTTTAGCGTAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
2426 GATGGTTAGTACACGATTTCAGCTACAATTTTGTAAAAATTGACCCGAAATATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
** * * *
2491 TTTGATCACAATACTAATAAAGAACATCTAATTCAAAGCCAAAAAGACTGAACGACTTTTCACGC
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGC
2556 TTCTTAGTTGTTTTT-TTTTTTTT-CGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
261 TTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
2619 TCGTA
326 TCGTA
* * * *
2624 AAAAGAAATACTTCAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGGTATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* ** * ** *
2689 CATGACGCCAAAAATCATGTGAAATTG-GCCGGGTTCCCAAAACACGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
*
2753 GATGGTTAGTATACGATTTCGG---C----TT-C---AATTGACCCGAAAG-TTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
*
2806 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTCTTTTCACGC
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGC
* *
2871 TTCTTAGTTGTTTTTCTTTTTTCTTTTTTTTCGGAAATAATTTTTTATTAAATCGAACC-TGATT
261 TTCTTAGTTG-------TTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATT
* *
2935 CATATGCTAGTA
319 CAGATGCTCGTA
* * * *
2947 AAAACAAATCATTAAATCCTAAATGGCTGAGATTTGGCTAGATTAAAATAGATATTTCATGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* ** *
3012 CATGGTGCCAAAAACTCATGCAAAATTGAGTTGGGTCCCCGGAACGCGTTTTTAGCCAAAAATCG
66 CATGGCGCCAAAAA-TCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCG
* *
3077 TGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATCGACCCGAAATATTTTTCCTCAAT
130 TGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
* * * * * *
3142 TTTTGGCTACAATACTCATAAAGAATATCTGATTTAAAGGCAAAAAGACTGAAGGTCTTTTCACA
195 TTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACG
*
3207 CTTCTTAGTTGTTTTTCTTCTTCTTCTTTTCTTGCGAAATAATTTTTTATTAAATCGAACCATGA
260 CTTCTTAGTTG--TTT-TTCTT-TT-TTTTC---CGAATTAATTTTTTATTAAATCGAACCATGA
3272 TTCTA-ATGCTCGTA
317 TTC-AGATGCTCGTA
** * *
3286 AAAACAAATCCTTAAATCCAATGTGGCTGAGATCTGGTTAGATTAAAATATATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * *
3351 CACGACGCCAAAAGTCATGCAAAATTGAGCAGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
3416 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
* * * * *
3481 TTTGGCCACAATACTCGTAAAGAATATCTAATTCAAAGCCAAAAGGACTTAAGGGCTTTTTCGCG
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGAC-TTTTCACG
* * * * *
3546 CTTCAGATA-TTGTTATTCTTTTTTATTCCGAATGAAATTTATATTAAATCGAACCATGATTCAG
260 CTTC--TTAGTTGTTTTTCTTTTTT-TTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAG
* *
3610 ATTCCCGTA
322 ATGCTCGTA
* **
3619 AAAACAAATCCTTAAATCCTAAATACCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* **
3684 CTTGGCGCCAAAAATCATGCAAAATTGAATCGGGTCCCCGGAACGCGTTTTTTAGCCAAAAACCG
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCG-TTTTTAGCCAAAAACCG
* * * *
3749 TAATGATTAGTACACGATTTCGGCTACAATTTGGCAAAAATTGACCCGAAAGA-TTTTCCTTAAT
130 TGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
*
3813 TTTTGGCCACAATACTCATTAAA-AATATATAATTCA
195 TTTTGGCCACAATACTCA-TAAAGAATATCTAATTCA
3849 GGGCCATAAA
Statistics
Matches: 3093, Mismatches: 331, Indels: 183
0.86 0.09 0.05
Matches are distributed among these distances:
315 253 0.08
316 14 0.00
317 2 0.00
320 121 0.04
322 5 0.00
323 96 0.03
324 262 0.08
325 102 0.03
326 3 0.00
327 377 0.12
328 211 0.07
329 152 0.05
330 4 0.00
331 163 0.05
332 48 0.02
333 794 0.26
334 78 0.03
335 19 0.01
336 17 0.01
337 88 0.03
338 187 0.06
339 91 0.03
340 4 0.00
341 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (330 bp):
AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACGC
TTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
TCGTA
Found at i:2463 original size:651 final size:654
Alignment explanation
Indices: 3--3848 Score: 4960
Period size: 651 Copynumber: 5.9 Consensus size: 654
1 GT
* * * * *
3 AAAA-AAATCCTTAAATCCTAAATGGCTGAGATCTGGCTAGGTTAAAATAAATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * **
67 CATGGCGCCAAAAATCATGCAAAATTTAGTCGGGTCCCCGGAACGCGTTTTTAGCGTAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
132 GATGGTTAGTACACGATTTCAGCTACAATTTTGTAAAAATTGACCCGAAATATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
** * * * * *
197 TTTGATCACAATACTAATAAAGAACATCTAATTCAAAGCCAAAAAGACTGAACGACTTTTCACGC
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGTCTTTTCACGC
* * *
262 TTCTTAGTTGTTTTTTTCTTTTTCTGAATTAATTTTTTATTAGATCGAACCATGATTCAGATGCT
261 TTCTTAGTTG--TTTTT-TTTTTCTGAAATAATTTTTTATTAAATCGAACCATGATTCATATGCT
* *
327 CGTAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATAGATATTTCAAG
323 CGTAAAAACAAATCCTTAAATCCTAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAG
* * *
392 GAGTCATGGCACCAAAAATCATGCAAAATTGAGCCGGGTCCCCTGAAGGCGTTTTTAGCCAAAAA
388 GAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAA
* * * *
457 CCGTGATGGTTAGTACACGATTTCGGCTATAATTTTGCAAAAATAGAAACCCGAAAGAATTTTCC
453 CCGTGATGGTTAGTACACGATTTCAGCTACAATTTTGCAAAAATTG--ACCCGAAAGATTTTTCC
* * *
522 TCAATTTTTTGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGGCTGAA-GACATT
516 TCAATTTTTGGCCACAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGAC-TT
* *
586 TTCACGCGTCTTAGTTGTTTTTCTTTTTTTTCCCGAATTAATTTTTTATTAAATCGAACCATGAT
580 TTCACGCTTCTTAGTTG--TTT-TTTCTTTTCCCGAATTAATTTTTTATTAAATCGAACCATGAT
651 TCAGATGCTCGTA
642 TCAGATGCTCGTA
* *
664 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATAAAAATTGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * *
729 CATGGCACCAAAAATCATGCAAAATTAAGCCGGGTCCCCGTAACGCGTTTTAAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * *
794 GATAGTTTGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCAT-AAT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCC-TCAAT
* * ** * *
858 TTTTAGCCACAATACTCATTAAA-AATATATAATTCAGGGCCATAAATA-TAGAAGGGT-TTTTC
195 TTTTGGCCACAATACTCA-TAAAGAATATCTAATTCAAAGCCAAAAAGACTA-AA-GGTCTTTTC
* * * *** *
920 ACGTTTCTAATA-TTGTTTTCGCCATTTTTTTTCGAAATAATATCCAATTAAATC-ATAAC-TCG
257 ACGCTTCT--TAGTTGTTTT-----TTTTTTCT-GAAATAATTTTTTATTAAATCGA-ACCAT-G
*
982 ATTC-TGATGCTCGTAAAAACAAATCCTTAAATCC-AATGTGGCTGAGATTTGGTTAGATTAAAA
312 ATTCAT-ATGCTCGTAAAAACAAATCCTTAAATCCTAA-ATGGCTGAGATTTGGTTAGATTAAAA
* * ** * *
1045 TGGATATTTCAAGGAATCGA-AACGCCAAAAATCATGCAAAATTGACCCGGGTCCCCGGAACACG
375 TAGATATTTCAAGGAGTC-ATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCG
* * * *
1109 TTTTTAGCTAAAAACCGTCATGGTTAGTATACGTTTTCAGCTACAATTTTGCAAAAATTGACCCG
439 TTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCG
* *
1174 AAAGATTTTTCCTCAATTCTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGA
504 AAAGATTTTTCCTCAATTTTTGGCCACAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGA
** *
1239 CTGAA-GATCTTTTCACGCTTCTTAGTTGTTTTTTTTCTTTTTTTTTCGAAATAATTTTTTATTA
569 CTGAAGGA-CTTTTCACGCTTCTTAGTTG--TTTTTTC---TTTTCCCGAATTAATTTTTTATTA
*
1303 AATCGAACCATGATTCTGATGCTCGTA
628 AATCGAACCATGATTCAGATGCTCGTA
* * *
1330 AAAACAAATCATTAAATCCTAAATAGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* *
1395 CATGGCGTCAAAAATCATGCAAAATTGAGCCAGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* *
1460 GAT-G-TA--A-ACGATTTCGGCTACAATTTTGGAAAAATTGACACGAAAGATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
* * * *
1520 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGCCTTTGCACGG
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGTCTTTTCACGC
* * *
1585 TTCTTAGTTG------TTTTCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCTCGT
261 TTCTTAGTTGTTTTTTTTTTCTGAAATAATTTTTTATTAAATCGAACCATGATTCATATGCTCGT
*
1644 AAAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAG
326 AAAAACAAATCCTTAAATCCTAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAG
* * * *
1709 TCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCAGAACGCGTTTCTAGCTAAAAATCG
391 TCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCG
* * *
1774 TGATGGTTAGTGA-ACGATTTCAGCTACAATTTTGTAAAAATTGACCTGAAATATTTTTCCTCAA
456 TGATGGTTAGT-ACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA
* *
1838 TTTTTGGCCATAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGGCTTTTCAC
520 TTTTTGGCCACAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCAC
*
1903 GCTTCTTAGTTG-TTTTTCTTTTCCCGAATTAATTTTCTATTAAATCGAACCATGATTCAGATGC
585 GCTTCTTAGTTGTTTTTTCTTTTCCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
1967 TCGTA
650 TCGTA
* *
1972 AAAACAAATCCTTAAATTCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTGAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * ** **
2037 CATGGCGCCAAAAATCATTCGAAATTGAGCCGGATCCCCAAAACAAGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
* * * *
2102 GATGGTTTA-TACACGAATTCGGCTACAAATTTGCAAAAATTGACCCGAAAGCTTTCTCCTCAAT
131 GATGG-TTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
* ** *
2166 TTTTGGCCACAATTCTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAATATCTTGTCACG
195 TTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGTCTTTTCACG
* *
2231 CTTCTTAGTTG-TTTTTTTTTCTGAAATAATTTTTTATTAAATCGAACCATGATTCATTTGTTCG
260 CTTCTTAGTTGTTTTTTTTTTCTGAAATAATTTTTTATTAAATCGAACCATGATTCATATGCTCG
* * *
2295 TAAAAA-AAATCCTTAAATCCTAAATGGCTGAGATCTGGCTAGATTAAAATAAATATTTCAAGGA
325 TAAAAACAAATCCTTAAATCCTAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGA
* * **
2359 GTCATGGCGCCAAAAATCATGCAAAATTTAGTCGGGTCCCCGGAACGCGTTTTTAGCGTAAAACC
390 GTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACC
* *
2424 GTGATGGTTAGTACACGATTTCAGCTACAATTTTGTAAAAATTGACCCGAAATATTTTTCCTCAA
455 GTGATGGTTAGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAA
** * *
2489 TTTTTGATCACAATACTAATAAAGAACATCTAATTCAAAGCCAAAAAGACTGAACGACTTTTCAC
520 TTTTTGGCCACAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCAC
* **
2554 GCTTCTTAGTTGTTTTTTTTTTTTTCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
585 GCTTCTTAGTTGTTTTTTCTTTTCCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGC
2619 TCGTA
650 TCGTA
* * * *
2624 AAAAGAAATACTTCAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGGTATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* ** * ** *
2689 CATGACGCCAAAAATCATGTGAAATTG-GCCGGGTTCCCAAAACACGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
*
2753 GATGGTTAGTATACGATTTCGG---C----TT-C---AATTGACCCGAAAG-TTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
*
2806 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGTCTTTTCACGC
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGTCTTTTCACGC
2871 TTCTTAGTTGTTTTTCTTTTTTCTTTTTTTTCGGAAATAATTTTTTATTAAATCGAACC-TGATT
261 TTCTTAGTTG-TTTT-TTTTTTC-------T--GAAATAATTTTTTATTAAATCGAACCATGATT
* * *
2935 CATATGCTAGTAAAAACAAATCATTAAATCCTAAATGGCTGAGATTTGGCTAGATTAAAATAGAT
315 CATATGCTCGTAAAAACAAATCCTTAAATCCTAAATGGCTGAGATTTGGTTAGATTAAAATAGAT
* * **
3000 ATTTCATGGAGTCATGGTGCCAAAAACTCATGCAAAATTGAGTTGGGTCCCCGGAACGCGTTTTT
380 ATTTCAAGGAGTCATGGCGCCAAAAA-TCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTT
* * * *
3065 AGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATCGACCCGAAATA
444 AGCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGA
* * * * *
3130 TTTTTCCTCAATTTTTGGCTACAATACTCATAAAGAATATCTGATTTAAAGGCAAAAAGACTGAA
509 TTTTTCCTCAATTTTTGGCCACAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAA
* * *
3195 GGTCTTTTCACACTTCTTAGTTGTTTTTCTTCTTCTTCTTTTCTTGCGAAATAATTTTTTATTAA
574 GGACTTTTCACGCTTCTTAGTTG-TTTT-TTCTT-TTC----C---CGAATTAATTTTTTATTAA
3260 ATCGAACCATGATTCTA-ATGCTCGTA
629 ATCGAACCATGATTC-AGATGCTCGTA
** * *
3286 AAAACAAATCCTTAAATCCAATGTGGCTGAGATCTGGTTAGATTAAAATATATATTTCAAGGAGT
1 AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
* * * *
3351 CACGACGCCAAAAGTCATGCAAAATTGAGCAGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
66 CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
3416 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
131 GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
* * * * *
3481 TTTGGCCACAATACTCGTAAAGAATATCTAATTCAAAGCCAAAAGGACTTAAGGGCTTTTTCGCG
196 TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGTC-TTTTCACG
* * * * * *
3546 CTTCAGATATTGTTATTCTTTTTTATTCCG-AATGAAATTTATATTAAATCGAACCATGATTCAG
260 CTTC---T-TAGTTGTT-TTTTTT-TTCTGAAAT-AATTTTTTATTAAATCGAACCATGATTCAT
* * **
3610 ATTCCCGTAAAAACAAATCCTTAAATCCTAAATACCTGAGATTTGGTTAGATTAAAATAGATATT
318 ATGCTCGTAAAAACAAATCCTTAAATCCTAAATGGCTGAGATTTGGTTAGATTAAAATAGATATT
* **
3675 TCAAGGAGTCTTGGCGCCAAAAATCATGCAAAATTGAATCGGGTCCCCGGAACGCGTTTTTTAGC
383 TCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCG-TTTTTAGC
* * * *
3740 CAAAAACCGTAATGATTAGTACACGATTTCGGCTACAATTTGGCAAAAATTGACCCGAAAGA-TT
447 CAAAAACCGTGATGGTTAGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* * *
3804 TTCCTTAATTTTTGGCCACAATACTCATTAAA-AATATATAATTCA
512 TTCCTCAATTTTTGGCCACAATACT-AATAAAGAATATCTAATTCA
3849 GGGCCATAAA
Statistics
Matches: 2802, Mismatches: 287, Indels: 182
0.86 0.09 0.06
Matches are distributed among these distances:
639 82 0.03
640 14 0.00
641 3 0.00
642 172 0.06
643 2 0.00
644 2 0.00
645 8 0.00
646 1 0.00
647 115 0.04
648 275 0.10
649 11 0.00
650 22 0.01
651 390 0.14
652 357 0.13
653 4 0.00
654 4 0.00
655 2 0.00
659 2 0.00
660 10 0.00
661 106 0.04
662 340 0.12
663 66 0.02
664 99 0.04
665 12 0.00
666 351 0.13
667 1 0.00
670 5 0.00
671 87 0.03
672 153 0.05
674 14 0.00
675 65 0.02
676 11 0.00
679 7 0.00
680 9 0.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (654 bp):
AAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAGT
CATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCGT
GATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAATT
TTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGTCTTTTCACGC
TTCTTAGTTGTTTTTTTTTTCTGAAATAATTTTTTATTAAATCGAACCATGATTCATATGCTCGT
AAAAACAAATCCTTAAATCCTAAATGGCTGAGATTTGGTTAGATTAAAATAGATATTTCAAGGAG
TCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGCCAAAAACCG
TGATGGTTAGTACACGATTTCAGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTTCCTCAAT
TTTTGGCCACAATACTAATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGACTTTTCACG
CTTCTTAGTTGTTTTTTCTTTTCCCGAATTAATTTTTTATTAAATCGAACCATGATTCAGATGCT
CGTA
Found at i:5281 original size:332 final size:330
Alignment explanation
Indices: 3939--6713 Score: 3662
Period size: 331 Copynumber: 8.4 Consensus size: 330
3929 AAATTTATAA
* * * * * *
3939 TTCAAGGAGTCACGGCGCCAAAAGTCATTCAAAATTGAGCGGGGTCCCCGGAACGCGTTTTTTGT
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
* *
4004 CAAATACCGTGATGGTTAGTACACGATTTCGACTACAATTTTGCAAAAATTGACCCGAAAGATTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* *
4069 TTCCTCAAATTTTGGCCACAATACTCATAAAGAATATCCAATTCAAAGCCAAAAAGACTGAAGGT
131 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGT
* * * *
4134 CTTTTCA--C-ACTTAGTTGATTTTCCTTTTTTTTCTGAATTAATTTTCTATTAAATCGAACCAT
196 CTTTTCACGCTTCTTAGTTG-TTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCAT
* * * * * * *
4196 AATTCAGATGCTCGTAAAAACAAATTCTTAAATCTAAAATGACTGAGATTTGATTAGATTAAAAT
260 GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAAAT
4261 AGATAT
325 AGATAT
* *
4267 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACACGTTTCTAGC
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
* *
4332 CAAAAACC------G-T--TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAG-TTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* * *
4387 TT-CTCAATTTTTGGCCACAATACTCGTAAAGAATATCTAATTCAAAGCCAAAAAGACTAAAGGG
131 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGT
** * * * * *
4451 CTTTTTTGCGCTTCAGATA-TTTTTTTGTTTTTTTTATTCCGAATTAATTTTTTGTTAATTCGAA
196 C-TTTTCACGCTTC--TTAGTTGTTTT-TCTTTTTT-TTCCGAATTAATTTTTTATTAAATCGAA
* * *
4515 CCACGATTCTGATGCTCGTAAAAACAATTCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTA
256 CCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTA
* *
4580 AAATTGATAC
321 AAATAGATAT
* *
4590 TGCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTCTTTAGC
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
* * *
4655 CAAAAACCATGATGGTTAGTACACGATTTCGGCTACTATTTTGCAAAAATTGACCCGAAATATTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* * *
4720 TTCCTCAATTTTTGGCCACAATACTCATAAAGAGTATCTAATTCAAAGCCAAAAAGACAGCAGGT
131 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGT
* *
4785 CTTTTCAGGCTTCTTAGTTG-TTTTCTTTTTTTTCCGAAATAATTTTTTATTAAATCGAACCATG
196 CTTTTCACGCTTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATG
* *
4849 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGCTTTGGTTAGATTAAAATA
261 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAAATA
4914 GATAT
326 GATAT
* * ** * * *
4919 TTCAATGAGTCAGGGCGCCAAAGGTCATGCAAAATTGAGCCAGGTCCCCTGAACTCGTTTTTAGC
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
*
4984 CAAAAACTGTGATGGTTAGTACACGATTTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATT
66 CAAAAACCGTGATGGTTAGTACACGA-TTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATT
* *
5049 TTTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTATTTCATAGCCAAAAAGACTGAAGG
130 TTTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGG
* *
5114 TCTTTTCACGCTTCTTAGTTGTTTTTCTTTTATTTTCTGAATTAATTTTTTATTAGATCGAACCA
195 TCTTTTCACGCTTCTTAGTTGTTTTTCTTTT-TTTTCCGAATTAATTTTTTATTAAATCGAACCA
*
5179 TGATT-TAGATGCTCGTAAAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAA
259 TGATTCT-GATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAA
*
5243 ATTGATAT
323 ATAGATAT
* * *
5251 TTCAAGGAGCCATGGCGCCAAAATTCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGC
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
* * *
5316 CAAAAACTGTGATGGTTAGTAGACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGACTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* * * * * * ** * *
5381 TTCCACAATTTTTTGCCAGAATACTCGTTTAA-AATATATAATTCACGGCCATAAATA-TAGAAG
131 TTCCTCAATTTTTGGCCACAATACTC-ATAAAGAATATCTAATTCAAAGCCAAAAAGACT-GAA-
* * * ** * * *
5444 GGT-TTTTCACGTTTCTAATA-TCGTTTTTCCCATTTTTTT-CGAATTAACATCTAATTAAAT-T
193 GGTCTTTTCACGCTTCT--TAGTTGTTTTT--CTTTTTTTTCCGAATTAATTTTTTATTAAATCG
* * *
5505 ATAAC-TCGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAG
254 A-ACCAT-GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAG
5569 ATTAAAATAGATAT
317 ATTAAAATAGATAT
* * * * *
5583 TTCAAGGAATCA-AGCGCCAAAAATCATGCAAAATTGAGTCGGGTCCCCGGAACGCGTTCTTAGG
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
*
5647 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* * * *
5712 TTCCTTAATTTTTGGCCACAATACTCATAAAGTATATCTAATTCAAAGCCAAAAATATTGAAGGT
131 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGT
* * *
5777 CTTTTCACGCTTCCTAATTGTTTTTC-TTTTTTTCCGAATTAATTTTTTATTAAATCGAGCCATG
196 CTTTTCACGCTTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATG
5841 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAAATA
261 ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAAATA
5906 GATAT
326 GATAT
* * *
5911 CTCAAGGAG-CAATGGCGCCAAAAATCATGCAAAATTGAGTCGAGTCCCCGGAACGCGTTTTTAG
1 TTCAAGGAGTC-ATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAG
* * *
5975 CCAAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATCGATCCGAAATAT
65 CC-AAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGAT
* * * *
6040 TTTTCCTCAATTTTTGGTCACAATACTCATAAAGAATATTTAATTTAAAGCCAAAAAGACTAAAG
129 TTTTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAG
* *
6105 GTCTTTTCACGCTTCTTAGTTGTTTTTCTTCTTCTTTTTTTTCCCAAATAA-TTTTTATTAAATC
194 GTCTTTTCACGCTTCTTAGTTG----T-TT-TTCTTTTTTTTCCGAATTAATTTTTTATTAAATC
* * * *
6169 GAACCATGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTTGGTTAGA
253 GAACCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGA
*
6234 TTAAAATATATAT
318 TTAAAATAGATAT
* * * * *
6247 TTCAAGGAGTCACGGCGCCAAAAGTCATGCAAAATTGAACGGGGTCCCCGAAACGCGTTTTTAGC
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
* * * * *
6312 CCAAAACCGTGATGGTTCGTACACGATTTTGGCTACAATTTTGTAAAAATTGACCCGAAATATTT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
* * * *
6377 TTCCTCTATTTTTTGCCACAATACTCATAAAGAATATCAAATTCAAAGCCAAAAAGACTGAATGT
131 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGT
*
6442 CTTTTCACGCTTCTTAGTTGTTTTTCTTTTTTTTTCCGAATTAATATTTTATTAAATCGAACCAT
196 CTTTTCACGCTTCTTAGTTGTTTTTC-TTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCAT
* * * * *
6507 GATTCAGATGATCGTAAAAACAAATCCTTAAATTCAAAATGGCTGAGATTTAGTTAGATTAAAAT
260 GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAAAT
6572 AGATAT
325 AGATAT
* * * * * * * * * *
6578 TTCATGGAGTCATGGCACTATAAATCATGCAAAATTGAGTCAGGTTCCCGAAACGTGTTTTTAGG
1 TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
* * * * * *
6643 CAAAAACCGTGATGGTTTGTATACGATTTCGACTACAACTTTGCAATAATAGAAACCCGAAAGAT
66 CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTG--ACCCGAAAGAT
6708 TTTTCC
129 TTTTCC
6714 ATCCGTTACA
Statistics
Matches: 2141, Mismatches: 250, Indels: 107
0.86 0.10 0.04
Matches are distributed among these distances:
317 58 0.03
318 9 0.00
319 39 0.02
320 1 0.00
321 6 0.00
322 9 0.00
323 158 0.07
327 8 0.00
328 160 0.07
329 232 0.11
330 290 0.14
331 453 0.21
332 323 0.15
333 37 0.02
334 62 0.03
335 137 0.06
336 144 0.07
337 15 0.01
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (330 bp):
TTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTTTAGC
CAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTAATTCAAAGCCAAAAAGACTGAAGGT
CTTTTCACGCTTCTTAGTTGTTTTTCTTTTTTTTCCGAATTAATTTTTTATTAAATCGAACCATG
ATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTAAAATA
GATAT
Found at i:6064 original size:992 final size:986
Alignment explanation
Indices: 3940--6713 Score: 3738
Period size: 992 Copynumber: 2.8 Consensus size: 986
3930 AATTTATAAT
* * * * *
3940 TCAAGGAGTCACGGCGCCAAAAGTCATTCAAAATTGAGCGGGGTCCCCGGAACGCGTTTTTTGTC
1 TCAAGGAGTCAGGGCGCCAAAAGTCATGCAAAATTGAGC-GAGTCCCCGGAACGCGTTTTTAGCC
* *
4005 AAATACCGTGATGGTTAGTACACGATTTCGACTACAATTTTGCAAAAATTGACCCGAAAGATTTT
65 AAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTT
* * *
4070 TCCTCAAATTTTGGCCACAATACTCATAAAGAATATCCAATTCAAAGCCAAAAAGACTGAAGGTC
130 TCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTATTTCAAAGCCAAAAAGACTGAAGGTC
* * * * *
4135 TTTTCA--C-ACTTAGTTGATTTTCCTTTTTTTTCTGAATTAATTTTCTATTAAATCGAACCATA
195 TTTTCACGCTTCTTAGTTGTTTTTTCTTTTTTTTCTGAATTAATTTTTTATTAAATCGAACCATG
* * * *
4197 ATTCAGATGCTCGTAAAAACAAATTCTTAAATCTAAAATGACTGAGATTTGATTAGATTAAAATA
260 ATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATT
*
4262 GATATTTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACACGTTT
325 GATATTTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTT
* * *
4327 CTAGCCAAAAAC-----CG-T-TACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAG-
390 TTAGCCAAAAACGTGATGGTTGTACACGATTTCGGCTACAATTTTGTAAAAATTGACCCGAAAGA
* * *
4384 TTTTTCTCAATTTTTGGCCACAATACTCGTAAAGAATATCTAATTCAAAGCCAAAAAGACTA-AA
455 TTTTCCTCAATTTTTTGCCACAATACTCGTAAAGAATATATAATTCAAAGCCAAAAAGACTAGAA
** * * * *
4448 GGGCTTTTTTGCGCTTC-AGATATTTTTTTGTTTTTTTTATTCCGAATTAATTTTTTGTT-AATT
520 GGG-TTTTTCACGCTTCTA-ATATGTTTTT-CTTTTTTT-TTCCGAATTAATATTTTATTAAATT
*
4511 CGAACCACGATTCTGATGCTCGTAAAAACAATTCCTTAAATCCAATGTGGCTGAGATTTGGTTAG
581 CGAA-C-CGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAG
* * * * *
4576 ATTAAAATTGATACTGCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGG
644 ATTAAAATAGATATTTCAAGGAGTCA-AGCGCCAAAAATCATGCAAAATTGAGTCGGGTCCCCGG
* * *
4641 AACGCG-TCTTTAGCCAAAAACCATGATGGTTAGTACACGATTTCGGCTACTATTTTGCAAAAAT
708 AACGCGTTC-TTAGGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAAT
*
4705 TGACCCGAAATATTTTTCCTCAATTTTTGGCCACAATACTCATAAAGAGTATCTAATTCAAAGCC
772 TGACCCGAAAGATTTTTCCTCAATTTTTGGCCACAATACTCATAAAGAGTATCTAATTCAAAGCC
* * * *
4770 AAAAAGACAGCAGGTCTTTTCAGGCTTCTTAGTTGTTTTCTTTTTTTTCCGAAATAATTTTTTAT
837 AAAAAGACAGAAGGTCTTTTCACGCTTCCTAATTGTTTTCTTTTTTTTCCGAAATAATTTTTTAT
* *
4835 TAAATCGAACCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGCTTTG
902 TAAATCGAACCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTG
*
4900 GTTAGATTAAAATAGATATT
967 GTTAGATTAAAATAGATATC
* * * * *
4920 TCAATGAGTCAGGGCGCCAAAGGTCATGCAAAATTGAGCCAGGTCCCCTGAACTCGTTTTTAGCC
1 TCAAGGAGTCAGGGCGCCAAAAGTCATGCAAAATTGAGCGA-GTCCCCGGAACGCGTTTTTAGCC
*
4985 AAAAACTGTGATGGTTAGTACACGATTTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
65 AAAAACCGTGATGGTTAGTACACGA-TTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTT
*
5050 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTATTTCATAGCCAAAAAGACTGAAGGT
129 TTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCTATTTCAAAGCCAAAAAGACTGAAGGT
*
5115 CTTTTCACGCTTCTTAGTTG-TTTTTCTTTTATTTTCTGAATTAATTTTTTATTAGATCGAACCA
194 CTTTTCACGCTTCTTAGTTGTTTTTTCTTTT-TTTTCTGAATTAATTTTTTATTAAATCGAACCA
* *
5179 TGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCAAAATGGCTGAGATTTGGTTAGATTAAAA
258 TGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAA
* * *
5244 TTGATATTTCAAGGAGCCATGGCGCCAAAATTCATGCAAAATTGAGCCGGGTCTCCGGAACGCGT
323 TTGATATTTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGT
* *
5309 TTTTAGCCAAAAACTGTGATGGTTAGTAGACGATTTCGGCTACAATTTTGCAAAAATTGACCCGA
388 TTTTAGCCAAAAAC-GTGATGGTT-GTACACGATTTCGGCTACAATTTTGTAAAAATTGACCCGA
* * * ** * *
5374 AAGACTTTTCCACAATTTTTTGCCAGAATACTCGTTTAA-AATATATAATTCACGGCCATAAATA
451 AAGA-TTTTCCTCAATTTTTTGCCACAATACTCG-TAAAGAATATATAATTCAAAGCCAAAAAGA
* ** * * *
5438 -TAGAAGGGTTTTTCACGTTTCTAATATCGTTTTTCCCATTTTTTT-CGAATTAACATCTAATTA
514 CTAGAAGGGTTTTTCACGCTTCTAATAT-GTTTTT-CTTTTTTTTTCCGAATTAATATTTTATTA
** *
5501 AATTATAACTCGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGT
577 AATTCGAAC-CGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGT
*
5566 TAGATTAAAATAGATATTTCAAGGAATCAAGCGCCAAAAATCATGCAAAATTGAGTCGGGTCCCC
641 TAGATTAAAATAGATATTTCAAGGAGTCAAGCGCCAAAAATCATGCAAAATTGAGTCGGGTCCCC
*
5631 GGAACGCGTTCTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAA
706 GGAACGCGTTCTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAA
*
5696 TTGACCCGAAAGATTTTTCCTTAATTTTTGGCCACAATACTCATAAAGTA-TATCTAATTCAAAG
771 TTGACCCGAAAGATTTTTCCTCAATTTTTGGCCACAATACTCATAAAG-AGTATCTAATTCAAAG
* ** *
5760 CCAAAAATATTGAAGGTCTTTTCACGCTTCCTAATTGTTTT-TCTTTTTTTCCGAATTAATTTTT
835 CCAAAAAGACAGAAGGTCTTTTCACGCTTCCTAATTGTTTTCT-TTTTTTTCCGAAATAATTTTT
*
5824 TATTAAATCGAGCCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGAT
899 TATTAAATCGAACCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGAT
5889 TTGGTTAGATTAAAATAGATATC
964 TTGGTTAGATTAAAATAGATATC
* *
5912 TCAAGGAG-CAATGGCGCCAAAAATCATGCAAAATTGAGTCGAGTCCCCGGAACGCGTTTTTAGC
1 TCAAGGAGTC-AGGGCGCCAAAAGTCATGCAAAATTGAG-CGAGTCCCCGGAACGCGTTTTTAGC
* * *
5976 CAAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATCGATCCGAAATATT
64 C-AAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATT
* * *
6041 TTTCCTCAATTTTTGGTCACAATACTCATAAAGAATATTTAATTT-AAAGCCAAAAAGACTAAAG
128 TTTCCTCAATTTTTGGCCACAATACTCATAAAGAATATCT-ATTTCAAAGCCAAAAAGACTGAAG
** *
6105 GTCTTTTCACGCTTCTTAGTTGTTTTTCTTCTTCTTTTTTTTCCCAAATAA-TTTTTATTAAATC
192 GTCTTTTCACGCTTCTTAGTTG---TT-TT-TTCTTTTTTTTCTGAATTAATTTTTTATTAAATC
* **
6169 GAACCATGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGACTGAGATTTGGTTAGA
252 GAACCATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGA
* * * * *
6234 TTAAAATAT-ATATTTCAAGGAGTCACGGCGCCAAAAGTCATGCAAAATTGAACGGGGTCCCCGA
317 TTAAAAT-TGATATTTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGG
* *
6298 AACGCGTTTTTAGCCCAAAACCGTGATGGTTCGTACACGATTTTGGCTACAATTTTGTAAAAATT
381 AACGCGTTTTTAG-CCAAAAACGTGATGGTT-GTACACGATTTCGGCTACAATTTTGTAAAAATT
* * *
6363 GACCCGAAATATTTTTCCTCTATTTTTTGCCACAATACTCATAAAGAATATCA-AATTCAAAGCC
444 GACCCGAAAGA-TTTTCCTCAATTTTTTGCCACAATACTCGTAAAGAATAT-ATAATTCAAAGCC
* *
6427 AAAAAGACT-GAA-TGTCTTTTCACGCTTCTTAGT-TGTTTTTCTTTTTTTTTCCGAATTAATAT
507 AAAAAGACTAGAAGGGT-TTTTCACGCTTC-TAATATGTTTTTCTTTTTTTTTCCGAATTAATAT
* * * **
6489 TTTATTAAA-TCGAACCATGATTCAGATGATCGTAAAAACAAATCCTTAAATTCAAAATGGCTGA
570 TTTATTAAATTCGAACC--GATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGA
* * * *
6553 GATTTAGTTAGATTAAAATAGATATTTCATGGAGTCATG-GCACTATAAATCATGCAAAATTGAG
633 GATTTGGTTAGATTAAAATAGATATTTCAAGGAGTCAAGCGC-C-AAAAATCATGCAAAATTGAG
* * * * * * * * *
6617 TCAGGTTCCCGAAACGTGTTTTTAGGCAAAAACCGTGATGGTTTGTATACGATTTCGACTACAAC
696 TCGGGTCCCCGGAACGCGTTCTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAAT
* *
6682 TTTGCAATAATAGAAACCCGAAAGATTTTTCC
761 TTTGCAAAAATTG--ACCCGAAAGATTTTTCC
6714 ATCCGTTACA
Statistics
Matches: 1576, Mismatches: 169, Indels: 80
0.86 0.09 0.04
Matches are distributed among these distances:
980 77 0.05
981 106 0.07
983 10 0.01
984 171 0.11
990 1 0.00
991 3 0.00
992 455 0.29
993 164 0.10
994 38 0.02
995 165 0.10
996 337 0.21
997 25 0.02
998 24 0.02
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (986 bp):
TCAAGGAGTCAGGGCGCCAAAAGTCATGCAAAATTGAGCGAGTCCCCGGAACGCGTTTTTAGCCA
AAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAAAGATTTTT
CCTCAATTTTTGGCCACAATACTCATAAAGAATATCTATTTCAAAGCCAAAAAGACTGAAGGTCT
TTTCACGCTTCTTAGTTGTTTTTTCTTTTTTTTCTGAATTAATTTTTTATTAAATCGAACCATGA
TTCAGATGCTCGTAAAAACAAATCCTTAAATCCAAAATGACTGAGATTTGGTTAGATTAAAATTG
ATATTTCAAGGAGTCATGGCGCCAAAAATCATGCAAAATTGAGCCGGGTCCCCGGAACGCGTTTT
TAGCCAAAAACGTGATGGTTGTACACGATTTCGGCTACAATTTTGTAAAAATTGACCCGAAAGAT
TTTCCTCAATTTTTTGCCACAATACTCGTAAAGAATATATAATTCAAAGCCAAAAAGACTAGAAG
GGTTTTTCACGCTTCTAATATGTTTTTCTTTTTTTTTCCGAATTAATATTTTATTAAATTCGAAC
CGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGGTTAGATTAAAA
TAGATATTTCAAGGAGTCAAGCGCCAAAAATCATGCAAAATTGAGTCGGGTCCCCGGAACGCGTT
CTTAGGCAAAAACCGTGATGGTTAGTACACGATTTCGGCTACAATTTTGCAAAAATTGACCCGAA
AGATTTTTCCTCAATTTTTGGCCACAATACTCATAAAGAGTATCTAATTCAAAGCCAAAAAGACA
GAAGGTCTTTTCACGCTTCCTAATTGTTTTCTTTTTTTTCCGAAATAATTTTTTATTAAATCGAA
CCATGATTCTGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGGTTAGATTA
AAATAGATATC
Found at i:13147 original size:13 final size:13
Alignment explanation
Indices: 13131--13157 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13121 CAGAGTAAAC
13131 GTGCAAAATGAAT
1 GTGCAAAATGAAT
13144 GTGCAAAATGAAT
1 GTGCAAAATGAAT
13157 G
1 G
13158 GGTCTATTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.44, C:0.07, G:0.26, T:0.22
Consensus pattern (13 bp):
GTGCAAAATGAAT
Found at i:31762 original size:3 final size:3
Alignment explanation
Indices: 31754--31810 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
31744 GAATAAAAAT
* * * * * *
31754 GCA GCA GCA GCA GCA GCA TCA ACA GCA GCA ACA ACA ACA GCA ACA GCA
1 GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA GCA
31802 GCA GCA GCA
1 GCA GCA GCA
31811 ACATCATAAA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.42, C:0.33, G:0.23, T:0.02
Consensus pattern (3 bp):
GCA
Found at i:33417 original size:25 final size:26
Alignment explanation
Indices: 33380--33447 Score: 88
Period size: 25 Copynumber: 2.7 Consensus size: 26
33370 GAGAAAGAAC
33380 AAAAGGAAA-AAGAAGAAAGG-AAAG
1 AAAAGGAAAGAAGAAGAAAGGAAAAG
* *
33404 GAAAGGAAAGAAGAACAAAGGAAAAG
1 AAAAGGAAAGAAGAAGAAAGGAAAAG
*
33430 AAAAGAAAAGAA-AAGAAA
1 AAAAGGAAAGAAGAAGAAA
33448 CCCAGGAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.22
25 15 0.41
26 14 0.38
ACGTcount: A:0.72, C:0.01, G:0.26, T:0.00
Consensus pattern (26 bp):
AAAAGGAAAGAAGAAGAAAGGAAAAG
Found at i:33432 original size:5 final size:5
Alignment explanation
Indices: 33395--33447 Score: 52
Period size: 5 Copynumber: 10.4 Consensus size: 5
33385 GAAAAAGAAG
* * * * *
33395 AAAGG AAAGG AAAGG AAAGA AGAACA AAGGA AAAGA AAAGA AAAGA AAAGA
1 AAAGA AAAGA AAAGA AAAGA A-AAGA AAAGA AAAGA AAAGA AAAGA AAAGA
33446 AA
1 AA
33448 CCCAGGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
5 38 0.90
6 4 0.10
ACGTcount: A:0.72, C:0.02, G:0.26, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:53380 original size:13 final size:13
Alignment explanation
Indices: 53360--53397 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
53350 TACATGACCC
*
53360 TCCAATTTGTCCT
1 TCCAATTTGTCCA
*
53373 TTCAATTTGTCCA
1 TCCAATTTGTCCA
53386 TCCAATTTGTCC
1 TCCAATTTGTCC
53398 CTCCTGACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.29, G:0.08, T:0.45
Consensus pattern (13 bp):
TCCAATTTGTCCA
Found at i:53561 original size:41 final size:42
Alignment explanation
Indices: 53499--53583 Score: 127
Period size: 41 Copynumber: 2.0 Consensus size: 42
53489 ATTTATAACT
* *
53499 AGGGACTAAACCTAGATTTAATTTCTTACCTTAATTATTAGG
1 AGGGACTAAACCTAGATTTAATTTATTACCCTAATTATTAGG
* *
53541 AGGG-CTAAACCTGGATTTAATTTATTTCCCTAATTATTAGG
1 AGGGACTAAACCTAGATTTAATTTATTACCCTAATTATTAGG
53582 AG
1 AG
53584 AGTTAAGTTG
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 35 0.90
42 4 0.10
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.38
Consensus pattern (42 bp):
AGGGACTAAACCTAGATTTAATTTATTACCCTAATTATTAGG
Found at i:84745 original size:11 final size:11
Alignment explanation
Indices: 84729--84754 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
84719 GTAAGATAGA
84729 ATTAATAATCT
1 ATTAATAATCT
84740 ATTAATAATCT
1 ATTAATAATCT
84751 ATTA
1 ATTA
84755 CTCAAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.08, G:0.00, T:0.46
Consensus pattern (11 bp):
ATTAATAATCT
Found at i:85528 original size:48 final size:49
Alignment explanation
Indices: 85472--85565 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
85462 TTAATTTGTA
85472 AATATACC-AAAAAAATCTATTAATCGACACATTTTAATTGATTGATGT
1 AATATACCAAAAAAAATCTATTAATCGACACATTTTAATTGATTGATGT
*
85520 AATATACCAAAAAAAATCTATTAATCGACACATTTTAGTTGATTGA
1 AATATACCAAAAAAAATCTATTAATCGACACATTTTAATTGATTGA
85566 CCACCTCATG
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 8 0.18
49 36 0.82
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.34
Consensus pattern (49 bp):
AATATACCAAAAAAAATCTATTAATCGACACATTTTAATTGATTGATGT
Found at i:100935 original size:36 final size:36
Alignment explanation
Indices: 100888--100959 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
100878 CTCCGGCAAC
100888 TGACCCTGATGAGCCGCCACCATATTTTTTTCTTCT
1 TGACCCTGATGAGCCGCCACCATATTTTTTTCTTCT
100924 TGACCCTGATGAGCCGCCACCATATTTTTTTCTTCT
1 TGACCCTGATGAGCCGCCACCATATTTTTTTCTTCT
100960 AGCTTGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.17, C:0.31, G:0.14, T:0.39
Consensus pattern (36 bp):
TGACCCTGATGAGCCGCCACCATATTTTTTTCTTCT
Found at i:109645 original size:25 final size:25
Alignment explanation
Indices: 109611--109661 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
109601 TCTTATGTGC
* *
109611 TGAATTCAACATTATTTTGGTTTGT
1 TGAATTCAACAGTAGTTTGGTTTGT
109636 TGAATTCAACAGTAGTTTGGTTTGT
1 TGAATTCAACAGTAGTTTGGTTTGT
109661 T
1 T
109662 TGTTTGATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.49
Consensus pattern (25 bp):
TGAATTCAACAGTAGTTTGGTTTGT
Found at i:110459 original size:61 final size:62
Alignment explanation
Indices: 110339--110462 Score: 214
Period size: 61 Copynumber: 2.0 Consensus size: 62
110329 TATAGTAAGT
110339 GTGGATTTAGATTAGACTCTACTTACTAATTACTCTGTTTTAGTGGGAAAACAGAGCTCTTGC
1 GTGGATTTAGATTAGACTCTACTTACT-ATTACTCTGTTTTAGTGGGAAAACAGAGCTCTTGC
* *
110402 GTGGATTTAGATTAGACTCTACTTACT-TTGCTCTGTTTTAGTGTGAAAACAGAGCTCTTGC
1 GTGGATTTAGATTAGACTCTACTTACTATTACTCTGTTTTAGTGGGAAAACAGAGCTCTTGC
110463 TTTTCTTTAC
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 32 0.54
63 27 0.46
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (62 bp):
GTGGATTTAGATTAGACTCTACTTACTATTACTCTGTTTTAGTGGGAAAACAGAGCTCTTGC
Found at i:111667 original size:72 final size:72
Alignment explanation
Indices: 111576--111781 Score: 349
Period size: 75 Copynumber: 2.8 Consensus size: 72
111566 GGAGGAGTCC
* *
111576 GAGGAGACATCATAGATGGAGGAGCGGGTGCTGGTTGTTTTGGAGGCGGCGGTGGAGGTCTAACT
1 GAGGAGACATCATAGATGGAGGAGCGGGTGCTGGTTGCTTTGGAGGCGGCGGTGGAGGTCGAACT
111641 ATCACCG
66 ATCACCG
*
111648 GAGGAGACATCATGGATGGAGGAGCGGGTGCTGGTTGCTTTGGAGGCGGCGGCGGTGGAGGTCGA
1 GAGGAGACATCATAGATGGAGGAGCGGGTGCTGGTTGCTTTGGA---GGCGGCGGTGGAGGTCGA
*
111713 ATTATCACCG
63 ACTATCACCG
111723 GAGGAGACATCATAGATGGAGGAGCGGGTGCTGGTTGCTTTGGAGGCGGCGGTGGAGGT
1 GAGGAGACATCATAGATGGAGGAGCGGGTGCTGGTTGCTTTGGAGGCGGCGGTGGAGGT
111782 GGGGGTCGGT
Statistics
Matches: 126, Mismatches: 5, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
72 57 0.45
75 69 0.55
ACGTcount: A:0.19, C:0.15, G:0.45, T:0.21
Consensus pattern (72 bp):
GAGGAGACATCATAGATGGAGGAGCGGGTGCTGGTTGCTTTGGAGGCGGCGGTGGAGGTCGAACT
ATCACCG
Done.