Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015852.1 Corchorus olitorius cultivar O-4 contig15885, 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: 85233
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:691 original size:322 final size:321
Alignment explanation
Indices: 1--2419 Score: 1957
Period size: 322 Copynumber: 7.5 Consensus size: 321
* * * * *
1 TCCTTATATACAATGTGGCTGAGATTTGGTTCGATAAATATAGATATTTGAAGGAGTCTTTAC-G
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-CTG
** * * *
65 CCAAAAAATCATACAAAATTGAGCCGGGAGTCCGGAACGCGTTTTT-GCCAAAAATCGTGATAGT
65 CC-AAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGT
** * * * *
129 TAGTACACGATTTCAACTAAAATTTTGCAAAAACTGACTCG-AAATTCTTTTCCTTAATTTTTTG
128 TAGTACACGATTTCGGC--------T--AAAAACTGACACGAAAATT-TTTTTCTCAATTTTTTA
* * * * * ** ** * * * * * **
193 CCATAATAGTTAGAAAAAAATTTAATTTGACACCAAAAATATTGAAGG-GTTTTCACGTTTCTAA
182 ACAAAATACTCAGAAAAATATAAAATTCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAA
** * * * * *
257 TATCG---TT---TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAAGATT-GAGATGCTC
247 TATCGTTTTTCCATTTTTTTCAAAAATAATTTTTAATTAAATCAAAAC-AAGATTCGAGATGCTA
315 AT-AAAA-AAA
311 ATAAAAACAAA
* * ** * * ** * *
324 TTCTTA-ATTCAATTGTGACTAAGATTTTTTTAGATGAACATAGATATTTCAAGGAGTCTTTCTG
1 TCCTTATATCCAA-TGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTG
** *
388 CCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACAAGTTTTTAGCCAAAAATCATGACTGTGT
65 CCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGA-TG-GT
* * * *
453 TAGTACACGATTTCGGCTAAAAACTGACGCGAAAATTTTTTTCTCAATTTTTTAATAAAATATTT
128 TAGTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAATTTTTTAACAAAATACTC
* *
518 AGAAAAATATAAAATTCAATGCCAAAAAGACGGACGGACTTTTCACCCTTCTAATATCGTTTTTC
193 AGAAAAATATAAAATTCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAATATCGTTTTTC
* * * * *
583 CATTTGTTTAAAAAATATTTTTTAATTAAATCAAAACAAGA-TCGAGGTGGTAATAAAAACAAA
258 CATTTTTTTCAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAA
* * * * * *
646 TCTTTATATCCAATATGATTGACATTTGGTTCGATGAATATAGATATTTTAAGGAGTCTTTGTGT
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
* ** ** * * ** ** *
711 CAAAAATCCTGCAAATTTGAGCCAGCACTTTGGTACGCGTTTTTAGCCAAAAACCGTGATGGTTA
66 CAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTA
* * * **
776 GTACACGATTTCGGCTAAAATTTATCAAAAATTGAC-CCAAAAGGTTTTTCCTCAATTTTTTGCC
130 GTACACGATTTCGGCTAAAA---A-C------TGACACGAAAA-TTTTTTTCTCAATTTTTTAAC
* * * * *
840 AGAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-ATTTGAAGGA-TATTTCACGCTTCTA
184 AAAATACTCAG-AAAAATATAAAATTCAACGCCAAAAAGA-CTGACGGACT-TTTCACCCTTCTA
** ** * * * * *
903 ATATCG-TTTTCTTTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAATATTC-AGATGCT
246 ATATCGTTTTTCCATTTTTTT-CAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGCT
**
966 CGTAAAAACAAA
310 AATAAAAACAAA
* * * * ** *
978 TTCTTAAATCCAATGT-GTCTTAGATTTAATTAGATG-ATATAGATA-TTCTAA-GAGGTCTTTC
1 TCCTTATATCCAATGTGGT-TGACATTTGGTTCGATGAATATAGATATTTC-AAGGA-GTCTTTC
* * * * * *
1039 TGCCAAAAATCGTTTAAAATTTAGCTGGGATCCGAAACGCGTTTTTAGCTAAAAATCGTGATGCT
63 TGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGT
* * ** *
1104 TACTACACGATTTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAAATTTTTAATGAAATATT
128 TAGTACACGA-TTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAATTTTTTAACAAAATACT
* * * *
1169 TAGAAAAATATAAAATTCAATGCCAAAATGACTGACGGGCTTTTCACCCTTCTAATATCGTTTTT
192 CAGAAAAATATAAAATTCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAATATCGTTTTT
* * * * *
1234 CCATTTGTTTCAGAATTAATGTCTAATTAAATCAAAACAAGA-TCGAGATGCTAATAAAAACAAA
257 CCATTTTTTTCAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAA
* *
1298 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGGGTCTTTGTGC
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
* ** * * * * *
1363 CAAAAATCCTGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTCGCCAAAAACCGTGATGGTTA
66 CAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTA
* * * * * **
1428 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCTATTTTTTGCCA
130 GTACACGATTTCGGC--------T--AAAAACTGACACGAAAATTTTTTTCTCAATTTTTTAACA
* * * * * ** *
1493 AAATACTCAGGTAAAATATATAATAT-AACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAAT
185 AAATACTCA-GAAAAATATAAAAT-TCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAAT
* * ** * * *
1557 ATCGTTTTTCC-TTTTTTTCCCCCAAAATTTATTCGTAATTAAATCGATACAATATTC-AGATGC
248 ATCGTTTTTCCATTTTTTT----CAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGC
** *
1620 TCGTACAAACAAA
309 TAATAAAAACAAA
* * * ** *
1633 TTCTTAAATCCAATGTGGTTGAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTTCTGC
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
* ** * *
1698 CAAAAATCATATAAAACTGAGCTTGGATTCGAAACGCGTTTTTAGCCAAAAATCGTGATGCTTTA
66 CAAAAATCATTTAAAACTGAGCCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGATG-GTTA
* * * * * * *
1763 -TACACGATTTCGGCT-AAAACTAACCCGAAAA-GTCTTTCTCAAATTTTT-GCCAAATACTCAG
130 GTACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAATTTTTTAACAAAATACTCAG
* * * * * * * * * * *
1824 AAAAAATATATAACTCAACGCGAAATATATTGACGGGCTTTACGCGCTTCTAATATCGTTTTACC
195 -AAAAATATAAAATTCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAATATCGTTTTTCC
* * * **
1889 ATTTTTTTTTC-AAATTAATTTCTAATTAAATCGAAACAAGATTCG-GATGCTCGTAAAAACAAA
259 A--TTTTTTTCAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAA
* * * *
1952 TCCTTATATACAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTCTGC
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
**
2017 CAAAAATCATTTAAAACTGAGCCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGACAGTTAG
66 CAAAAATCATTTAAAACTGAGCCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAG
* * * *
2082 TACACGATTTCGGCTGAAAACTGACACGAAAATGTTTTTCTC-ATTTATTTAACAAAATATTTTA
131 TACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAATTT-TTTAACAAAATA-CTCA
* *
2146 GAAAAATATAAAATTCAATGCCAAAAAGACTGACGGACTTTTCACCCTTCTAATATCATTTTTCC
194 GAAAAATATAAAATTCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAATATCGTTTTTCC
* * * *
2211 ATTTATTTTCAGAAATAATTTTTAAATAAATCAAAACAAGA-TCGAGGTGGTAATAAAAACAAA
259 ATTT-TTTTCAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAA
* * * *
2274 TCCTTATATCTAATATGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTGTGT
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
** ** * * * *
2339 CAAAAATCATGCAAATTTGAGCCGGCACTCCGGAACGCGTTTTTAGCTAAAAACCGTGAT-G---
66 CAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTA
2400 GTACACGATTTCGGCTAAAA
130 GTACACGATTTCGGCTAAAA
2420 TTTTACAATA
Statistics
Matches: 1681, Mismatches: 333, Indels: 168
0.77 0.15 0.08
Matches are distributed among these distances:
314 59 0.04
315 23 0.01
316 1 0.00
318 5 0.00
319 193 0.11
320 151 0.09
321 237 0.14
322 349 0.21
323 122 0.07
324 25 0.01
325 1 0.00
326 1 0.00
327 1 0.00
328 1 0.00
329 1 0.00
330 46 0.03
331 134 0.08
332 163 0.10
333 3 0.00
334 43 0.03
335 120 0.07
336 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (321 bp):
TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGC
CAAAAATCATTTAAAACTGAGCCGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGGTTAG
TACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAATTTTTTAACAAAATACTCAGA
AAAATATAAAATTCAACGCCAAAAAGACTGACGGACTTTTCACCCTTCTAATATCGTTTTTCCAT
TTTTTTCAAAAATAATTTTTAATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAA
Found at i:1263 original size:652 final size:647
Alignment explanation
Indices: 1--2101 Score: 2648
Period size: 652 Copynumber: 3.2 Consensus size: 647
* * * * **
1 TCCTTATATACAATGTGGCTGAGATTTGGTTCGATAAATATAGATATTTGAAGGAGTCTTTACGC
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTGTGC
* * * *
66 CAAAAAATCATACAAAATTGAGCCGGGAGTCCGGAACGCGTTTTT-GCCAAAAATCGTGATAGTT
66 C-AAAAATCATGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTT
** * * * * *
130 AGTACACGATTTCAACTAAAATTTTGCAAAAACTGACTCGAAATTCTTTTCCTTAATTTTTTGCC
130 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGT-TTTTCCTCAATTTTTTGCC
* * * * * * *
195 ATAATAGTTAGAAAAAA-ATTTAATTTGACACC-AAAAATATTGAAGGGTTTTCACGTTTCTAAT
194 AAAATACTCAGAAAAAATATATAA-TTAACGCCAAAAAAT-TTGAAGGGTTTTCACGCTTCTAAT
* * *
258 ATCG-----TTTTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAAGATTGAGATGCTCAT
257 ATCGTTTTCTTTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAAC-AATATTCAGATGCTCGT
* * ** *
317 -AAAA-AAATTCTT-AATTCAATTGTGACTAAGATTTTTTTAGATGAACATAGATATTTCAAGGA
321 AAAAACAAATTCTTAAATCCAA-TGTGTCTAAGATTTAATTAGATGAATATAGATATTTCAAGGA
* ** *
379 GTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAAACAAGTTTTTAGCCAAAAATCA
385 GTCTTTCTGCCAAAAATCATTTAAAACTGAGCTGGGATCCGAAACGCGTTTTTAGCCAAAAATCG
* * *
444 TGACTGTGTTAGTACACGATTTCGGCTAAAAACTGACGCGAAAATTTTTTTCTCAATTTTTTAAT
450 TGA-TG-CTTA-TACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAAATTTTTAAT
* * *
509 AAAATATTTAGAAAAATATAAAATTCAATGCCAAAAAGACGGACGGACTTTTCACCCTTCTAATA
512 AAAATATTTAGAAAAATATAAAATTCAATGCCAAAATGACTGACGGGCTTTTCACCCTTCTAATA
* * * * * *
574 TCGTTTTTCCATTTGTTTAAAAAATATTTTTTAATTAAATCAAAACAAGATCGAGGTGGTAATAA
577 TCGTTTTTCCATTTGTTT-CAAATTAATTTCTAATTAAATCAAAACAAGATCGAGATGCTAATAA
639 AAACAAA
641 AAACAAA
* * * * *
646 TCTTTATATCCAATATGATTGACATTTGGTTCGATGAATATAGATATTTTAAGGAGTCTTTGTGT
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTGTGC
* * * ** * *
711 CAAAAATCCTGCAAATTTGAGCCAGCACTTTGGTACGCGTTTTTAGCCAAAAACCGTGATGGTTA
66 CAAAAATCATGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTA
776 GTACACGATTTCGGCTAAAATTTAT-CAAAAATTGACCCAAAAGGTTTTTCCTCAATTTTTTGCC
131 GTACACGATTTCGGCTAAAATTT-TGCAAAAATTGACCCAAAA-GTTTTTCCTCAATTTTTTGCC
* *
840 AGAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATTTGAAGGATATTTCACGCTTCTAAT
194 AAAATACTCAGAAAAAATATATAATT-AACGCCAAAAAATTTGAAGGGT-TTTCACGCTTCTAAT
905 ATCGTTTTCTTTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTA
257 ATCGTTTTCTTTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTA
*
970 AAAACAAATTCTTAAATCCAATGTGTCTTAGATTTAATTAGATG-ATATAGATA-TTCTAA-GAG
322 AAAACAAATTCTTAAATCCAATGTGTCTAAGATTTAATTAGATGAATATAGATATTTC-AAGGA-
* * * *
1032 GTCTTTCTGCCAAAAATCGTTTAAAATTTAGCTGGGATCCGAAACGCGTTTTTAGCTAAAAATCG
385 GTCTTTCTGCCAAAAATCATTTAAAACTGAGCTGGGATCCGAAACGCGTTTTTAGCCAAAAATCG
*
1097 TGATGCTTACTACACGATTTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAAATTTTTAATG
450 TGATGCTTA-TACACGA-TTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAAATTTTTAATA
1162 AAATATTTAGAAAAATATAAAATTCAATGCCAAAATGACTGACGGGCTTTTCACCCTTCTAATAT
513 AAATATTTAGAAAAATATAAAATTCAATGCCAAAATGACTGACGGGCTTTTCACCCTTCTAATAT
*
1227 CGTTTTTCCATTTGTTTCAGAATTAATGTCTAATTAAATCAAAACAAGATCGAGATGCTAATAAA
578 CGTTTTTCCATTTGTTTCA-AATTAATTTCTAATTAAATCAAAACAAGATCGAGATGCTAATAAA
1292 AACAAA
642 AACAAA
* *
1298 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTCAAGGGGTCTTTGTGC
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTGTGC
* * *
1363 CAAAAATCCTGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTCGCCAAAAACCGTGATGGTTA
66 CAAAAATCATGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTA
*
1428 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAAGTTTTTCCTCTATTTTTTGCCA
131 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCC-AAAAGTTTTTCCTCAATTTTTTGCCA
** *
1493 AAATACTCAGGTAAAATATATAATATAACGCCAAAAAAATTGAAGGGTTTTTCACGCTTCTAATA
195 AAATACTCAGAAAAAATATATAAT-TAACGCCAAAAAATTTGAAGGG-TTTTCACGCTTCTAATA
** * *
1558 TCGTTTTTCCTTTTTTTCCCCCAAAATTTA-TTCGTAATTAAATCGATACAATATTCAGATGCTC
258 TCG-TTTT-CTTTTTTTTTCCC-GAATTTATTTC-TAATTAAATCGAAACAATATTCAGATGCTC
* *
1622 GTACAAACAAATTCTTAAATCCAATGTGGT-TGAGATTTAATTAGATGAATATAGATATTTCAAG
319 GTAAAAACAAATTCTTAAATCCAATGT-GTCTAAGATTTAATTAGATGAATATAGATATTTCAAG
* * *
1686 GAGTCTTTCTGCCAAAAATCATATAAAACTGAGCTTGGATTCGAAACGCGTTTTTAGCCAAAAAT
383 GAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCTGGGATCCGAAACGCGTTTTTAGCCAAAAAT
* * * * **
1751 CGTGATGCTTTATACACGATTTCGGCT-AAAACTAACCCGAAAA-GTCTTTCTCAAATTTTT-GC
448 CGTGATGC-TTATACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAAATTTTTAAT
* * * * * * * * * * *
1813 CAAATACTCAGAAAAAATATATAACTCAACGCGAAATAT-ATTGACGGGCTTTACGCGCTTCTAA
512 AAAATATTTAG-AAAAATATAAAATTCAATGCCAAA-ATGACTGACGGGCTTTTCACCCTTCTAA
* * * *
1877 TATCGTTTTACCATTTTTTTTTCAAATTAATTTCTAATTAAATCGAAACAAGATTCG-GATGCTC
575 TATCGTTTTTCCA--TTTGTTTCAAATTAATTTCTAATTAAATCAAAACAAGA-TCGAGATGCTA
*
1941 GTAAAAACAAA
637 ATAAAAACAAA
* * * *
1952 TCCTTATATACAATGTGGCTGAGATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTCTGC
1 TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTGTGC
** * * * * *
2017 CAAAAATCATTTAAAACTGAGCCGGGA-TCCGAAACGCGTTTTTAGCCAAAAATCGTGACAGTTA
66 CAAAAATCATGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTA
2081 GTACACGATTTCGGCTGAAAA
131 GTACACGATTTCGGCT-AAAA
2102 CTGACACGAA
Statistics
Matches: 1278, Mismatches: 139, Indels: 69
0.86 0.09 0.05
Matches are distributed among these distances:
644 34 0.03
645 142 0.11
646 19 0.01
647 24 0.02
651 12 0.01
652 440 0.34
653 228 0.18
654 185 0.14
655 102 0.08
656 84 0.07
657 8 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (647 bp):
TCCTTATATCCAATGTGGTTGACATTTGGTTCGATGAATATAGATATTTGAAGGAGTCTTTGTGC
CAAAAATCATGCAAAATTGAGCCGGCACTCCGGAACGCGTTTTTAGCCAAAAACCGTGATAGTTA
GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCAAAAGTTTTTCCTCAATTTTTTGCCAA
AATACTCAGAAAAAATATATAATTAACGCCAAAAAATTTGAAGGGTTTTCACGCTTCTAATATCG
TTTTCTTTTTTTTTCCCGAATTTATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAAAA
CAAATTCTTAAATCCAATGTGTCTAAGATTTAATTAGATGAATATAGATATTTCAAGGAGTCTTT
CTGCCAAAAATCATTTAAAACTGAGCTGGGATCCGAAACGCGTTTTTAGCCAAAAATCGTGATGC
TTATACACGATTTCGGCTAAAAACTGACACGAAAATTTTTTTCTCAAATTTTTAATAAAATATTT
AGAAAAATATAAAATTCAATGCCAAAATGACTGACGGGCTTTTCACCCTTCTAATATCGTTTTTC
CATTTGTTTCAAATTAATTTCTAATTAAATCAAAACAAGATCGAGATGCTAATAAAAACAAA
Found at i:5446 original size:651 final size:651
Alignment explanation
Indices: 2446--10364 Score: 7743
Period size: 651 Copynumber: 12.1 Consensus size: 651
2436 CAAAACTCCG
* * * ** *
2446 GAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCTTTATTTCCAAAATTTATTCCTAATTAAATC
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCTTTTTTTTCCCGAATTTATTTCTAATTAAATC
* * * * * *
2511 GAAAC-AATATTCAGATGCTCGTACAAACAAATTCTTAAATCCAATGTGGTTGAGATTATATTAG
66 GAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTAG
*
2575 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATTCGAA
131 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAA
*
2640 ACGCGTTTTTAGCCAAAAATCGTGATGCTTAGTACACGATTTCGGCTAAAAACTAACCCGAAAAG
196 ACGCGTTTTTAGCCAAAAATCGTGATG-TTAGTACACGATTTCGGCTAAAAACTAACACGAAAAG
** * * * *
2705 GCTTTCTCAATTTTTTGCAAAATATTCATA-AAAAATATATAATTCTATGCCAAATTA-ATTGAC
260 TTTTTCTCAATTTTTTACGAAATATT--TAGAAAAATATATAATTCAATGCCAAA-AAGATTGAC
** * * * *
2768 GGGCTTTTTGCGCTTCTAATATCGTTTTCCCATTT-TTCCA-AATTAATTTCTAATTAAATCGAA
322 GGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAA
* ** * * * *
2831 ATAAGATTCG-GATGCTCGTAAAAACAAATCGTTATATACAATGTGGCTCAAATTTGGTTCGATG
387 ACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATG
**
2895 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGGTGGGACTCCGGAAC
452 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAAC
* * * * *
2960 GCGTTTTTTTTGCCAAAAACCATGATAGTTACTACACGATTTCGGCTAAAA-TTTGAAAAAACTG
517 GCG--TTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTT
* * * * * *
3024 ACTC-AAAATTTTTTTCCTCCA-TTTTTGCCATAATAGTC--AAAAAATATATAAGTTGACGCCA
580 ACCCGAAAA-GTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCCA
3085 AAAATATT
644 AAAATATT
* *
3093 GAAGGG-TTTTCAGGTTTCTAATATCGGTTTTCCTTTTTTTTCCCGAATTTATTTCTAATTAAAT
1 GAAGGGTTTTTCACGTTTCTAATATC-GTTTTTCTTTTTTTTCCCGAATTTATTTCTAATTAAAT
* * * *
3157 TGAAACAAAGATTGAGATGCTCATAAAAA-AAA-TCTTAAATCCATTGTGGCTAAGATTTTTTTA
65 CGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTA
3220 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGA
130 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGA
* * *
3285 AACGCGTTTTTAGCCAAAAATCGTGATAGCTAGTACACGATTTCGGCTAAAAACTGATACGAAAA
195 AACGCGTTTTTAGCCAAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAAACTAACACGAAAA
* * *
3350 TTTTTTTCTCAATTTTTTAACGAAATATTTAGAAAAATATAAAATTCAATGCCAAAAAGACTGAC
259 -GTTTTTCTCAATTTTTT-ACGAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGAC
* *
3415 GGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAAATAATTTTTAATTAAATCAAA
322 GGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAA
* * * * *
3480 ACATGA-TCGAGGTGGTAATAAAAACAAATCCTTATATCCAATGTGGTTGACATTTGGTTCAATG
387 ACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATG
* ** * * * * * *
3544 AATAAAGATATTTCAAGGAGTCTTTGTGTCAAAAATCCTGCACATTTGAGACGGCACTCCGGAAC
452 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAAC
* ** * **
3609 GCGTTTTTAGTTAAAAACCGTGATGGTTAGTACACGATTTTTGCTAAAATTTTGCAAAAA-TTGA
517 GCGTTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTT-A
* * *
3673 CCCGAAAAGTTTTTCCTCAATCTTTTGCCAGAATACTCAGAAAAAATATATAATTCAACGCCAAA
581 CCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCCAAA
*
3738 AAAATT
646 AATATT
* ** *
3744 GAAGGGGTTTTCACCCTTCTAATATCGTTTTTCCTTTTTTTCCCGAATTTATTTCTAATTAAATC
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCTTTTTTTTCCCGAATTTATTTCTAATTAAATC
* * * *
3809 GAAAC-AATATTAAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTAG
66 GAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTAG
* * *
3873 ATGGATATATATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCTGAA
131 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAA
* * * * *
3938 ACGCGTTATTAGCCAAAAATCGTGATGCTTAGAAGACGATTTCGGCTATAAACTAACCCGAAAAG
196 ACGCGTTTTTAGCCAAAAATCGTGATG-TTAGTACACGATTTCGGCTAAAAACTAACACGAAAAG
* * * * * * *
4003 TTTTTCTCAATTTTTTGCAAAATATTCATAAAACATATATAATTTAACGCCAAAAAGATTGACAG
260 TTTTTCTCAATTTTTTACGAAATATTTAGAAAA-ATATATAATTCAATGCCAAAAAGATTGACGG
* * * * **
4068 GCTTTTCTCGCTTCCAATATCGTTTTTCCA-TT-TTTCCGAATTAAATTT-TAATTAAATTGAAA
324 GCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATT-AATTTCTAATTAAATCAAAA
** * * * * *
4130 CAAGATTCG-GATGCTCGTAAAAAGAAATCTTTATATACAATGTGGCTGAGATTTGCTTCGATGA
388 CAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATGA
*
4194 ATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGAGTCCGGAACG
453 ATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAACG
*
4259 CGTTTTTTGACAAAAACCGTGATAGTTAGTACACGATTTCGTTGGCAAAAAAAAGCACACGATTT
518 CGTTTTTTGCCAAAAACCGTGATAG-T--T-----A----G-T-------------ACACGATTT
* *
4324 CAGCTAAAATTTTGCAAAAACTTACACGAAAAGTTTTTCCTCAATTTTTTGCCATAATTCTCAGA
557 CAGCTAAAATTTTGCAAAAACTTACCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGA
4389 AAAAATATATAATTTAACGCCAAAAATATT
622 AAAAATATATAATTTAACGCCAAAAATATT
* *
4419 GAAGGGTTTTTCATGTTTCTAATATCGTTTTTCCTTTTCTTTT-TCGAATTTATTTCTAATTAAA
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTT-CTTTT-TTTTCCCGAATTTATTTCTAATTAAA
* * * *
4483 TCGAAACAAAGATTGAGATGCTCGTAAAAATAAATTCTGAAATCCATCGTGGCTTAGA---T-TT
64 TCGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATT
* *
4544 ---TG--T-T--ATA--TCAAGGAGTCTTTCTGCAAAAAATCATTTAAAACTTAGCCGGGATCCG
129 AGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCG
* * * * *
4599 AAAAGCGTTTTTGGCCAAAAATCGTAAAAGTTAGTACACGATTTCGGCTAAAAACTGACACGAAA
194 AAACGCGTTTTTAGCCAAAAATCGT-GATGTTAGTACACGATTTCGGCTAAAAACTAACACG-AA
* * * *
4664 AAGTTTTTCTCAATTTTTTAACGAAATATTTAGAAAATTTTAAAATTCAATGCCAAAAAGACTGA
257 AAGTTTTTCTCAATTTTTT-ACGAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGA
* ** * * *
4729 CGAGCTTTTCACCCTTC-AATATCGTTTTTCCATTTGTTTTTGAAATAATTTTTAATTTAATCAA
321 CGGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAA
* * * *
4793 AACAAGA-TCGAGGTGGTAATAAAAACAAATCCTTATATCCAATGTGGTTAACATTTGGTTCGAT
386 AACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGAT
* ** * *
4857 GAATATAGATATTTCAAGGAGTGTTTGTGCC-AAAATCATGCGAAATTGAGCCGGGACTCTGGAA
451 GAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAA
* * * * *
4921 CG-GTTTTTTTTGCCAAATATCGTGATAGTTAGTACATGATTTCGGCTAAAATTTTACAAAAACT
516 CGCG--TTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACT
* ** * * *
4985 TACTCGAAATTTTTTTCCTCAATTTTTTGTCATAATAGTCAG-AAAAA-ATATAATTTGACGCCA
579 TACCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCCA
5048 AAAATATT
644 AAAATATT
5056 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCTTTTTTTTTCCCGAATTTATTTCTAATTAAAT
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTC-TTTTTTTTCCCGAATTTATTTCTAATTAAAT
* *
5121 CGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTAAGATTTTGTTA
65 CGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTA
* * *
5186 GATGAATATAGATATTTCAAGGAATCTTCCTGCAAAAAATCATTTAAAACTGAGCCGGGATCCGA
130 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGA
* *
5251 AACGTGTTTTTAGCCAAAAATCGTGATAGTTAGTACACGATTTCGGCTAAAAACTTACACGAAAA
195 AACGCGTTTTTAGCCAAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAAACTAACACGAAAA
* *
5316 TTTTTTCTCAATTTTTTTACGAAATATTTAGAAAAATATATAATTCAATACCAAAAAGATTGACG
259 GTTTTTCTCAA-TTTTTTACGAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGACG
*
5381 GGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATGTCTAATTAAATCAAAA
323 GGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAA
* * * * *
5446 CAA-AATCGAGAAGCTAATAAAAACAAATCTTTATATCCAATGTGGTTGACATTTGGTTCGACGA
388 CAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATGA
** * *
5510 ATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTGCAAAATTGAGCCGGCACTCCGGAACG
453 ATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAACG
* * * * *
5575 CGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTCCAAAAA-TTGAC
518 CGTTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTT-AC
* * * * *
5639 CCGAAAAGTTTTTCCTCTATTTTTTGCCAGAATACTAAGGAAAAATATATAATTCAACGCCAAAA
582 CCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCCAAAA
*
5704 AAATT
647 ATATT
* * * * *
5709 GAAGGGTTTTTCATGCTTCTAATATCGTTTTTCCTTTTTTTCCCCAAATTTATTTCAAATTAAAT
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTT-CTTTTTTTTCCCGAATTTATTTCTAATTAAAT
* * * * * * *
5774 CCAAA-TAATATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGTTGAGATTTAATTA
65 CGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTA
* **
5838 GATGAATATAGAGATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGATGGGATCCGA
130 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGA
* * *
5903 AACGCATTTTT-GTCCAAAAATCATGATGCTTTA-TACACGATTTCGGCTAAAAACTAACCCGAA
195 AACGCGTTTTTAG-CCAAAAATCGTGATG--TTAGTACACGATTTCGGCTAAAAACTAACACGAA
* * * * * *
5966 AAGTCTTTCTCAAATTTTTACCAAATACTCAGTAAAAATATATAATTCAACGCCAAAAAGATTGA
257 AAGTTTTTCTCAATTTTTTACGAAATATTTAG-AAAAATATATAATTCAATGCCAAAAAGATTGA
* * * * *
6031 CGGGCTTTTCGCGCTTCTAATATCGTTTTTCAATTTTTTTTTCCGAATTAATTTCTAATTAAATC
321 CGGGCTTTTCACCCTTCTAATATCGTTTTTCCA--TTTGTTTCAGAATTAATTTCTAATTAAATC
* ** * * * *
6096 GAAACAAGATTCG-GATGCTCGTAAAAACAAATCC-T-TAT--AATGTGGCTGAGATTTGATTCA
384 AAAACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCG
* *
6156 ATGAATGTAGATATTTCAAGGAGACTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGG
449 ATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGG
* * * *
6221 AGCGCGTTTTTTGCCAAAAATCGTGATAGTTAATACACGATTTTAGCTAAAATTTTGCAAAAACT
514 AACGCGTTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACT
* ** * * * *
6286 AACCCGAAATTTTTTTCCTCAATTTTTTGCCATAATAGTCAGAAAAAAAAATATAATTTGATGCC
579 TACCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAG-AAAAAATATATAATTTAACGCC
6351 AAAAATATT
643 AAAAATATT
*
6360 GAAGGG-TTTTCACGTTTCTAATATCGTTTTTCCTTTTTTT-CCGAATTTATTTCTAATTAAATC
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCTTTTTTTTCCCGAATTTATTTCTAATTAAATC
* *
6423 GAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTAAGATTTTGTTAG
66 GAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTAG
* * * *
6488 ATGAATATAGATATTTCAAGGAATCTTCCTGCAAAAAATCATTTAAAACTGAGCCAGGATCCGAA
131 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAA
* * * * *
6553 ACGCGTTTTTAGCCAAAAAAAACTGTGATGGTTAGTGCACGATTTCAGCTAGAAACTAACCCGAA
196 ACGCGTTTTTAGCC--AAAAATC-GTGAT-GTTAGTACACGATTTCGGCTAAAAACTAACACGAA
* * * * * *
6618 AAGTTTTTCTCAACTTTTTGCAAAATATTCGTA-AAAAAAATATAATTCAACGCCAAAAAGATTA
257 AAGTTTTTCTCAATTTTTTACGAAATATT--TAGAAAAATATATAATTCAATGCCAAAAAGATTG
* * ** *
6682 ACAGGCTTTTCGCGTTTCTAATATCGTTTTTCCATTTTTTTCCA-AATTAATTTCTAATTAAATC
320 ACGGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTT-CAGAATTAATTTCTAATTAAATC
* * ** * * *
6746 GAAACAAGATTC-CGATGCTCGTAAAAACAAATCCTTATATACAATGTGGCTGAGATTCGGTTCG
384 AAAACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCG
* *
6810 ATGAATATAAATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGAGTCCGG
449 ATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGG
*
6875 ACCGCGTTTTTGTGCCAAAAACCGTGATAGTTAGTACACTATTTCGTCGGCAAAAAAAAAGTACA
514 AACGCGTTTTT-TGCCAAAAACCGTG--A--TAG---------T--T------------AGTACA
* * * * * *
6940 CGATTTCGGCTAAAATTTTGAAAAAACTGACACGGAAAGTTTTTCCTCAATTTTTTTCCATAATA
551 CGATTTCAGCTAAAATTTTGCAAAAACTTACCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATA
7005 CTCAGAAAAAATATATAATTTAACGCCAAAAATATT
616 CTCAGAAAAAATATATAATTTAACGCCAAAAATATT
* * *
7041 GAAGGG-TTTTCACATTTGTAATATCGTTTTTCTCTTTTTTT-TCGAATTTATTTCTAATTAAAT
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCT-TTTTTTTCCCGAATTTATTTCTAATTAAAT
* * * *
7104 CGAAACAAAGATTGAGATGCTCGTAAAAATAAATTCTTAAATCCATTGTAGCTAAGATTTTGTTA
65 CGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTA
* * * *
7169 GATGAATATAGATATTTCAAGGAGTCTTTCTTCCAAAAATCAATTAAAACTAAGTCGGGATCCGA
130 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGA
* * * * **
7234 AACGCGCTTTTAGCCAAAAATCGTGATGGTTAGTTCACGATTTTGGCTAAAAACTGACATAAAAA
195 AACGCGTTTTTAGCCAAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAAACTAACA-CGAAA
* * * * * * *
7299 ATTTTTTCTCCATTGTTTACGAAATATTTATAAAAAATATTTAATTCAA-GCGAAAAAGATAGAC
258 AGTTTTTCTCAATTTTTTACGAAATATTTA-GAAAAATATATAATTCAATGCCAAAAAGATTGAC
*
7363 GTGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAA
322 GGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAA
* *
7428 ACAAGA-TCGAGATGCTAATAAAAA-AAAT-C-----GA-GA--T-GTTGACATTTGGTTCGATG
387 ACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATG
** * * * *
7481 AATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCATGCAAATTTGAGTCGGCACTCCAGAAC
452 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAAC
* * * * * *
7546 GCGATTTTAGTCAAAAACCGTGATGGTTAGTACACGATTTTAGCTAAAATTTTGGAAAAA-TTGA
517 GCGTTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTT-A
* * *
7610 CCCGAAAAGTTTTTCCTCGATTTTTTGCCATAATACTCAG-AAAAATATATAATTCAATGCCAAA
581 CCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCC-AA
*
7674 AAAAATT
645 AAATATT
**
7681 GAAGGGTTTTTCACACTTCTAATATCGTTTTTCCTTTTTTTTCCCGAATTTATTTCTAATTAAAT
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTT-CTTTTTTTTCCCGAATTTATTTCTAATTAAAT
* * * *
7746 CGAAAC-AATATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTA
65 CGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTA
* * *
7810 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGTCAGGATCTGA
130 GATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGA
* * * *
7875 AACGCGTTTTTAGCCAAAAATCGTGATGCTTAGAAGACGATTTCGGCTATAAACTAACCCGAAAA
195 AACGCGTTTTTAGCCAAAAATCGTGATG-TTAGTACACGATTTCGGCTAAAAACTAACACGAAAA
* * * * *
7940 ATTTTTCTCAATTTTTTGCAAAATATTCAGAAAACATATATAATTCAACGCCAAAAAGATTGACG
259 GTTTTTCTCAATTTTTTACGAAATATTTAGAAAA-ATATATAATTCAATGCCAAAAAGATTGACG
* * * * * ** **
8005 AGCTTTTCGCGCTTCCAATATCGTTTTCCCA-TT-TTAAACGAATTAATTTCTAATTAAATTGAA
323 GGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCA-GAATTAATTTCTAATTAAATCAAA
** * * * * *
8068 ACAAGATTCG-GATGCTCGTAAAAAGAAATCTTTATATACAATGTGGCTGAGATTTTGTTCGATG
387 ACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATG
* * * *
8132 AATATAGATATTTCAATGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCTGGGAGTTCGGAAC
452 AATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAAC
*
8197 GCGTTTTTTGCCAAAAAAAAACGTGATAGTTAGTACACGATTTCGTTGGCAAAAAAAAGCACAAG
517 GCGTTTTTTGCC---AAAAACCGTGATAG-T--T-----A----G-T----------A-CAC--G
* * *
8262 ATTTCAGCTAAAATTTTGCAAAAACTGACACGAAAAGTTTTTCCTCAATTTTTTTGCCATAATTC
553 ATTTCAGCTAAAATTTTGCAAAAACTTACCCGAAAAGTTTTTCCTCAA-TTTTTTGCCATAATAC
*
8327 TCAGAAAAAATATATAATTTAATGCCAAAAATATT
617 TCAGAAAAAATATATAATTTAACGCCAAAAATATT
** * * * * *
8362 GACTGATTTTTCACTTTTCTAATATCGTTTTTC-----CTT------TTTATTTCGAATTAAACC
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCTTTTTTTTCCCGAATTTATTTCTAATTAAATC
* *
8416 GAAACAAAGATTGAGATGCTCGTAAAAATAAATTCTTAAATCCATTGTGGCTTAGA---T-TT--
66 GAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTAG
*
8475 -TG--T-TAG--A--TCAAGGAGTCTTTCTGCCAAAAATCATTT--AACTGAGCCAGGATCCGAA
131 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAA
* *
8530 ACGCGTTTTTAGCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAGCTGACACGAAAAA
196 ACGCGTTTTTAGCCAAAAATCGTGAT-GTTAGTACACGATTTCGGCTAAAAACTAACACG--AAA
** *
8595 AAATTTTCTCAATTTTTTACGAAATATTTAGAAAAAAATATATAATTCAATGCCGAAAAGATTGA
258 AGTTTTTCTCAATTTTTTACGAAATATTTAG--AAAAATATATAATTCAATGCCAAAAAGATTGA
* * *
8660 CAGGTTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAAAATTAATTTCTAATTAAATCAA
321 CGGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAA
* * *
8725 AACAAGA-TCGAGATGCTAATAAAAACGAATCCTTATATCCAATGTGGTTGACATTTGTTTCGAT
386 AACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGAT
** * * * * *
8789 GAATATAGATATTTCAAGGAGTCTTTGTGCCAAAAATCCTACAAACTTGAGCCAGCACTCCGGAA
451 GAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAA
* * ** ** * * *
8854 TGTGTTTTCAGCCAAAAGTCGTGATGGTTTGTACACGATTTCAGCTAAAATTTGGCAAAAA-TTG
516 CGCGTTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTT-
* * *
8918 ATCCGAAAAGTTTTTCCTCAATTTTTTGCCAGAATACTCAG-AAAAA-ATATAATTCAACGCCAA
580 ACCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCCAA
*
8981 AAAAATT
645 AAATATT
* *
8988 GATGGG-TTTTCACGCTTCTAATATCGTTTTTCCTTTTTTTTCTCCGAATTTATTTCTAATTAAA
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTT-CTTTTTTTTC-CCGAATTTATTTCTAATTAAA
* * * *
9052 TCGAAAC-AATATTCAGATGCTCGTAAAAACAAATTCTTAAATCCATTATGGCTGAGATTTAATT
64 TCGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATT
* * ** ** *
9116 AGATGAATATAGATATTTGTAA-GAGCCTTTCTGCTTAAAATCATGCAAAACTGAGGCGGGA-CC
129 AGATGAATATAGATATTT-CAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCC
* * * * * * * *
9179 TGAAACGCGTTTTTAGCAAAAAAAAACTGTGATGGTTTGTGCACAATTTCTGTTAAAATTTCGAT
193 -GAAACGCGTTTTTAGC--CAAAAATC-GTGAT-GTTAGTACACGATTTCGGCTAAAA--AC--T
* * * * * * *
9244 AAATTTACATGAAAAAATTTTCCTCAATTTTTTACCACAATACTCAGAAAAAATATATAACTCAA
249 --A---ACACG-AAAAGTTTTTCTCAATTTTTTACGA-AATATTTAG-AAAAATATATAATTCAA
* * * ** * * *
9309 AGACAAAAA-ATTTGAAGGATTTTTCACGCTTCTAATA-------T-CA-TT-TTTCCGAATTTA
306 TGCCAAAAAGA-TTGACGGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAA
* * * * ** * * * *
9363 TTTCTAATTAAATCTAAACAAAATT-TAGACGCTCGTAAAAACAAATCCGTAAATCCAATGTAGT
370 TTTCTAATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGT
* * * * * * * *
9427 TGAGATTTGGTTAGATGAATATAAATATTTCATGGATTCTTT-CTACAAAAAATCATGCAAAACT
435 TGACATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTAC-GCCAAAAATCATGCAAAATT
* * * * * * * *
9491 GA-ACGGG-GTCGCGAAACGCGTTTTTAGCCAAAAACCATAAT-G-T-GTATACGATTTCGGC--
499 GAGCCGGGACTC-CGGAACGCGTTTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTA
* * * * * ** *
9549 ------T--AAAAACTAACCCGAAAAAATTTTTTCTAAATTTTTTGGCGCAATACTCATAAAAAA
563 AAATTTTGCAAAAACTTACCCG-AAAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAA
* *
9606 TATATAATTCAACGCCAAAAATTTT
627 TATATAATTTAACGCCAAAAATATT
* * ** * * * * *
9631 GACGGGCTTTTCGGGCTTCTAATATCGGTTTTCCATTTTTTTTTCCAAATTAATTTCTAATTAAA
1 GAAGGGTTTTTCACGTTTCTAATATC-GTTTTTC-TTTTTTTTCCCGAATTTATTTCTAATTAAA
* * * * **
9696 TTGAAACAAA-ATTCAGAAGCTCGTAAAAACAAA-TCTTCAAATCCAATGTGGCTGAGATTTGGT
64 TCGAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTT-AAATCCATTGTGGCTGAGATTTTAT
* * * * *
9759 TCGATGAATATAGATATTTCAAGGAGTCTTTGC-ACCAAAAATCATGTAAAATTGAGCCGAGACT
128 TAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATTTAAAACTGAGCCGGGA-T
* * *
9823 CTGGAACGCGTTTTTAGCCAAAAA-CGGTGATAGCCGTTAGTACATGATTTCGGCT-AAAACTTT
191 CCGAAACGCGTTTTTAGCCAAAAATC-GTGAT----GTTAGTACACGATTTCGGCTAAAAAC---
* ** ** ** *
9886 GTAAAAGAACTGACCCGAAAATTTTTTCCTCAATTTGTTGCCTCAATACTCAAAAAAAATATATA
248 -T-----AAC--A--CGAAAAGTTTTT-CTCAATTT-TTTACGAAATA-TTTAGAAAAATATATA
* * * * * * * * *
9951 ATTCCA--CACAAAAAAATTCGAAGGGGTTTTCACACTTTTAATATCGTTTTT-CTTTTTTTTCT
300 ATTCAATGC-CAAAAAGATT-GACGGGCTTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCA
* ** * * * *
10013 GAACTT-ATTT-TAAATAAAATCAAAACAAGATTC-AGATGCTCGTAAAAAAAAATCTTTAAATC
363 GAA-TTAATTTCT-AATTAAATCAAAACAAGATTCGAGATGCTAATAAAAACAAATCCTTATATA
* * * * * * * * *
10075 CAATGTGGCTGAGATTTGATTAC-ATTAGTATAGATTTTTCAAGGA-TTTTGTATGCCAAAAACC
426 CAATGTGGTTGACATTTGGTT-CGATGAATATAGATATTTCAAGGAGTCTT-TACGCCAAAAATC
* ** * * ** * *
10138 ATGCAAAACTGAGTGGAGGCCT-CGGTACGCGTTTTTAACCAAAAACAGTGATGGTTAGTACACG
489 ATGCAAAATTGAGCCG-GGACTCCGGAACGCGTTTTTTGCCAAAAACCGTGATAGTTAGTACACG
* * * ** *
10202 ATTTCGGC--------T--AAAAACTGACACGAAAAAATTTT-CTCAATTTTTTGCCACAATACT
553 ATTTCAGCTAAAATTTTGCAAAAACTTACCCGAAAAGTTTTTCCTCAATTTTTTGCCATAATACT
* * *
10256 CAGAATAAAAAAAATATAATTCAACGCCAAAAAGATT
618 CAG---AAAAAATATATAATTTAACGCCAAAAATATT
* ** * * *
10293 GAAGGG-TCTTCACACTTCTAATATCATTTTTCCATTTATTTTT--TGAATTAATTTCTAATTAA
1 GAAGGGTTTTTCACGTTTCTAATATCGTTTTT-C-TTT-TTTTTCCCGAATTTATTTCTAATTAA
10355 ATCGAAACAA
63 ATCGAAACAA
10365 CACGATTTTG
Statistics
Matches: 6096, Mismatches: 862, Indels: 615
0.80 0.11 0.08
Matches are distributed among these distances:
625 23 0.00
626 25 0.00
627 5 0.00
628 19 0.00
629 43 0.01
631 5 0.00
632 1 0.00
636 5 0.00
637 177 0.03
638 26 0.00
639 91 0.01
640 172 0.03
641 270 0.04
642 42 0.01
643 39 0.01
644 143 0.02
645 45 0.01
646 173 0.03
647 181 0.03
648 129 0.02
649 424 0.07
650 382 0.06
651 625 0.10
652 559 0.09
653 141 0.02
654 338 0.06
655 41 0.01
656 92 0.02
657 168 0.03
658 168 0.03
659 30 0.00
660 45 0.01
661 48 0.01
662 41 0.01
663 115 0.02
664 169 0.03
665 141 0.02
666 3 0.00
667 14 0.00
668 81 0.01
669 22 0.00
670 48 0.01
671 1 0.00
672 1 0.00
673 2 0.00
675 123 0.02
676 33 0.01
677 49 0.01
678 13 0.00
679 116 0.02
680 89 0.01
681 113 0.02
682 247 0.04
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.34
Consensus pattern (651 bp):
GAAGGGTTTTTCACGTTTCTAATATCGTTTTTCTTTTTTTTCCCGAATTTATTTCTAATTAAATC
GAAACAAAGATTGAGATGCTCGTAAAAACAAATTCTTAAATCCATTGTGGCTGAGATTTTATTAG
ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATTTAAAACTGAGCCGGGATCCGAA
ACGCGTTTTTAGCCAAAAATCGTGATGTTAGTACACGATTTCGGCTAAAAACTAACACGAAAAGT
TTTTCTCAATTTTTTACGAAATATTTAGAAAAATATATAATTCAATGCCAAAAAGATTGACGGGC
TTTTCACCCTTCTAATATCGTTTTTCCATTTGTTTCAGAATTAATTTCTAATTAAATCAAAACAA
GATTCGAGATGCTAATAAAAACAAATCCTTATATACAATGTGGTTGACATTTGGTTCGATGAATA
TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAATTGAGCCGGGACTCCGGAACGCGT
TTTTTGCCAAAAACCGTGATAGTTAGTACACGATTTCAGCTAAAATTTTGCAAAAACTTACCCGA
AAAGTTTTTCCTCAATTTTTTGCCATAATACTCAGAAAAAATATATAATTTAACGCCAAAAATAT
T
Found at i:10523 original size:175 final size:175
Alignment explanation
Indices: 10211--10532 Score: 391
Period size: 175 Copynumber: 1.8 Consensus size: 175
10201 GATTTCGGCT
* * * *
10211 AAAAACTGACACGAAAAAATTTTCTCAATTTTTTGCCACAATACTCAGAATAAAAAAAATATAAT
1 AAAAACTGACACGAAAAAATTTCCTCAATTTTTGGCCAAAATACTC--AATAAAAAAAATATAAC
* *
10276 TCAACGCCAAAAAGATTGAAGGGTCTTCACACTTCTAATATCATTTTTCCATTTATTTTTTGAAT
64 TCAACGCCAAAAAGATTGAAGGGTCTTAACACTTCTAATATCATTTTTCCATTTATTTTCTGAAT
*
10341 TAATTTCTAATTAAATCGAAACAACACGATTTTGGGTAAAGTTTTGC
129 AAATTTCTAATTAAATCGAAACAACACGATTTTGGGTAAAGTTTTGC
* * * * *
10388 AAAAATTGACTCGAAAGATATTTCCTCAATTTTTGGCTAAAATACTC-ATAAAAAATATATAACT
1 AAAAACTGACACGAAA-AAATTTCCTCAATTTTTGGCCAAAATACTCAATAAAAAAAATATAACT
** * * * **
10452 CGGCGTCAAAAATATTGAAGGG-CGTTTAACGCTTCTAATATTGTTTTTCC-TATT-TTTTCTGA
65 CAACGCCAAAAAGATTGAAGGGTC--TTAACACTTCTAATATCATTTTTCCAT-TTATTTTCTGA
10514 ATAAATTTCTAATTAAATC
127 ATAAATTTCTAATTAAATC
10533 TTAACAGGAT
Statistics
Matches: 122, Mismatches: 19, Indels: 10
0.81 0.13 0.07
Matches are distributed among these distances:
174 1 0.01
175 59 0.48
176 23 0.19
177 14 0.11
178 25 0.20
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.36
Consensus pattern (175 bp):
AAAAACTGACACGAAAAAATTTCCTCAATTTTTGGCCAAAATACTCAATAAAAAAAATATAACTC
AACGCCAAAAAGATTGAAGGGTCTTAACACTTCTAATATCATTTTTCCATTTATTTTCTGAATAA
ATTTCTAATTAAATCGAAACAACACGATTTTGGGTAAAGTTTTGC
Found at i:11351 original size:25 final size:24
Alignment explanation
Indices: 11316--11365 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
11306 TTCCATAATT
* *
11316 AATAAAGAAGTTGAATCATCTAAAA
1 AATAAAAAAGTTAAATCA-CTAAAA
*
11341 AATAAAAAAGTTAAATGACTAAAA
1 AATAAAAAAGTTAAATCACTAAAA
11365 A
1 A
11366 GAATACTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
24 7 0.32
25 15 0.68
ACGTcount: A:0.62, C:0.06, G:0.10, T:0.22
Consensus pattern (24 bp):
AATAAAAAAGTTAAATCACTAAAA
Found at i:16774 original size:24 final size:24
Alignment explanation
Indices: 16743--16793 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
16733 ATGTCCATTT
16743 TTTTAATTAATTAAGTTTTAAATA
1 TTTTAATTAATTAAGTTTTAAATA
16767 TTTTAATTAATTAAGTTTTAAATA
1 TTTTAATTAATTAAGTTTTAAATA
16791 TTT
1 TTT
16794 CAATCTAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.00, G:0.04, T:0.57
Consensus pattern (24 bp):
TTTTAATTAATTAAGTTTTAAATA
Found at i:26308 original size:22 final size:22
Alignment explanation
Indices: 26280--26321 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
26270 AAAAAAGGGA
* *
26280 AAAAAAACTTTTTTTTTTACAT
1 AAAAAAACTTATATTTTTACAT
26302 AAAAAAACTTATATTTTTAC
1 AAAAAAACTTATATTTTTAC
26322 TTTGAAATGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (22 bp):
AAAAAAACTTATATTTTTACAT
Found at i:27971 original size:89 final size:89
Alignment explanation
Indices: 27820--28279 Score: 823
Period size: 89 Copynumber: 5.2 Consensus size: 89
27810 AACCGTTTTT
* *
27820 TCTATATATCTATATAAATTATGACATTAGGTGGGACAGGCCATGTCAGTGAATATTAAACTGTT
1 TCTATATATCTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
27885 TCTTTTCATATTTATAAAAACTTA
66 TCTTTTCATATTTATAAAAACTTA
27909 TCTATATATCTATATAAATTATGACATTAGGT-GTGACAGGCCATGCCAGTGAATATTAAACTGT
1 TCTATATATCTATATAAATTATGACATTAGGTAG-GACAGGCCATGCCAGTGAATATTAAACTGT
*
27973 TTCTTTTCATATTTATAAGAACTTA
65 TTCTTTTCATATTTATAAAAACTTA
*
27998 TCTATATATCTATATAAATTATGAAATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
1 TCTATATATCTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
* *
28063 TCTTTTCATATTTATAAGAGCTTA
66 TCTTTTCATATTTATAAAAACTTA
*
28087 TCTATATATTTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
1 TCTATATATCTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
28152 TCTTTTCATATTTATAAAAACTTA
66 TCTTTTCATATTTATAAAAACTTA
28176 TCTATATATCTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
1 TCTATATATCTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
*
28241 TCTTTTCATATTTATAAAAATTTA
66 TCTTTTCATATTTATAAAAACTTA
*
28265 TTTATATATCTATAT
1 TCTATATATCTATAT
28280 CTATATGAAG
Statistics
Matches: 358, Mismatches: 11, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
88 1 0.00
89 356 0.99
90 1 0.00
ACGTcount: A:0.35, C:0.12, G:0.13, T:0.40
Consensus pattern (89 bp):
TCTATATATCTATATAAATTATGACATTAGGTAGGACAGGCCATGCCAGTGAATATTAAACTGTT
TCTTTTCATATTTATAAAAACTTA
Found at i:28938 original size:2 final size:2
Alignment explanation
Indices: 28931--29043 Score: 58
Period size: 2 Copynumber: 58.5 Consensus size: 2
28921 CTATATTTTA
* * * * *
28931 AT AT AT AT AT AT AT AT AT -T AT A- AT AC AT AT CT TT AT TT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
** * *
28971 CG AA AT AT AT AT AT AT AT AT AT AT A- AT AT AT AT A- AC AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT
* * *
29012 A- AT AT AT AT -T AT ACT AA AT AA AT AT AT TT AT A
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT A
29044 AAAAAGTATG
Statistics
Matches: 85, Mismatches: 18, Indels: 16
0.71 0.15 0.13
Matches are distributed among these distances:
1 6 0.07
2 75 0.88
3 4 0.05
ACGTcount: A:0.48, C:0.05, G:0.01, T:0.46
Consensus pattern (2 bp):
AT
Found at i:29001 original size:19 final size:19
Alignment explanation
Indices: 28973--29043 Score: 62
Period size: 19 Copynumber: 3.9 Consensus size: 19
28963 TTATTTTTCG
28973 AAAT-ATATATATATATAT
1 AAATAATATATATATATAT
* *
28991 ATATAATATATATA-ACAT
1 AAATAATATATATATATAT
*
29009 -CATAATATATAT-TATACT
1 AAATAATATATATATATA-T
*
29027 AAATAA-ATATATTTATA
1 AAATAATATATATATATA
29044 AAAAAGTATG
Statistics
Matches: 43, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
17 13 0.30
18 13 0.30
19 17 0.40
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAATATATATATATAT
Found at i:34009 original size:15 final size:15
Alignment explanation
Indices: 33991--34024 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
33981 TCATCATCAC
*
33991 TCTCCTTATCCAATT
1 TCTCCTTATCCAAAT
*
34006 TCTCCTTTTCCAAAT
1 TCTCCTTATCCAAAT
34021 TCTC
1 TCTC
34025 TTTCAACATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.18, C:0.35, G:0.00, T:0.47
Consensus pattern (15 bp):
TCTCCTTATCCAAAT
Found at i:34423 original size:13 final size:14
Alignment explanation
Indices: 34398--34427 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
34388 ACAAGAACGT
34398 AAAAGAAATAAAGA
1 AAAAGAAATAAAGA
34412 AAAAGAAA-AAAGA
1 AAAAGAAATAAAGA
34425 AAA
1 AAA
34428 TACCCAAACT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.83, C:0.00, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAGAAATAAAGA
Found at i:40467 original size:22 final size:24
Alignment explanation
Indices: 40437--40480 Score: 65
Period size: 23 Copynumber: 1.9 Consensus size: 24
40427 GACTTAAACT
40437 AAATGTTCC-ACGAAAAAGAAAAA
1 AAATGTTCCAACGAAAAAGAAAAA
*
40460 AAAT-TTCCAATGAAAAAGAAA
1 AAATGTTCCAACGAAAAAGAAA
40481 CTTTTTTGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.61, C:0.11, G:0.11, T:0.16
Consensus pattern (24 bp):
AAATGTTCCAACGAAAAAGAAAAA
Found at i:44426 original size:12 final size:13
Alignment explanation
Indices: 44411--44442 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
44401 ACAGGAGCTT
44411 CAACAACAAC-AG
1 CAACAACAACAAG
44423 CAACAACAACAAG
1 CAACAACAACAAG
44436 -AACAACA
1 CAACAACA
44443 CCAACAGTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 17 0.89
13 2 0.11
ACGTcount: A:0.62, C:0.31, G:0.06, T:0.00
Consensus pattern (13 bp):
CAACAACAACAAG
Found at i:44432 original size:18 final size:18
Alignment explanation
Indices: 44390--44439 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
44380 GCAACTACTG
* *
44390 CAACAACAACAACAGGAG
1 CAACAACAACAACAGCAA
**
44408 CTTCAACAACAACAGCAA
1 CAACAACAACAACAGCAA
*
44426 CAACAACAAGAACA
1 CAACAACAACAACA
44440 ACACCAACAG
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.56, C:0.30, G:0.10, T:0.04
Consensus pattern (18 bp):
CAACAACAACAACAGCAA
Found at i:45926 original size:6 final size:6
Alignment explanation
Indices: 45917--45941 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
45907 ATATAAAAAC
45917 AGAACA AGAACA AGAACA AGAACA A
1 AGAACA AGAACA AGAACA AGAACA A
45942 AAATCTCTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.16, T:0.00
Consensus pattern (6 bp):
AGAACA
Found at i:46181 original size:1 final size:1
Alignment explanation
Indices: 46175--46206 Score: 64
Period size: 1 Copynumber: 32.0 Consensus size: 1
46165 TGCTTTTGGG
46175 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
46207 GCCTCTTCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 31 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:49803 original size:17 final size:16
Alignment explanation
Indices: 49769--49800 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
49759 TATTAGTATG
*
49769 TGAAAAGAAGAAAAAA
1 TGAAAAGAAAAAAAAA
49785 TGAAAAGAAAAAAAAA
1 TGAAAAGAAAAAAAAA
49801 ATGTAAAGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.78, C:0.00, G:0.16, T:0.06
Consensus pattern (16 bp):
TGAAAAGAAAAAAAAA
Found at i:63964 original size:44 final size:44
Alignment explanation
Indices: 63901--63989 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
63891 CTCAACACAT
63901 GTTAGATCGGGCAGAAAGATCGTTCGATAAATAAGAAATCACTC
1 GTTAGATCGGGCAGAAAGATCGTTCGATAAATAAGAAATCACTC
63945 GTTAGATCGGGCAGAAAGATCGTTCGATAAATAAGAAATCACTC
1 GTTAGATCGGGCAGAAAGATCGTTCGATAAATAAGAAATCACTC
63989 G
1 G
63990 ATAAATAAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.22
Consensus pattern (44 bp):
GTTAGATCGGGCAGAAAGATCGTTCGATAAATAAGAAATCACTC
Found at i:63992 original size:19 final size:19
Alignment explanation
Indices: 63968--64005 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
63958 GAAAGATCGT
63968 TCGATAAATAAGAAATCAC
1 TCGATAAATAAGAAATCAC
63987 TCGATAAATAAGAAATCAC
1 TCGATAAATAAGAAATCAC
64006 AAAAAGACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.16, G:0.11, T:0.21
Consensus pattern (19 bp):
TCGATAAATAAGAAATCAC
Found at i:64262 original size:14 final size:14
Alignment explanation
Indices: 64243--64271 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
64233 ATATTTCATA
64243 ACGGTTGCTTTCTT
1 ACGGTTGCTTTCTT
64257 ACGGTTGCTTTCTT
1 ACGGTTGCTTTCTT
64271 A
1 A
64272 TTTAGGGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.10, C:0.21, G:0.21, T:0.48
Consensus pattern (14 bp):
ACGGTTGCTTTCTT
Found at i:68099 original size:17 final size:18
Alignment explanation
Indices: 68064--68101 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
68054 TATGAATTGG
68064 AATGAAGCAAGCACAAGC
1 AATGAAGCAAGCACAAGC
* *
68082 AATG-AGCAATCACTAGC
1 AATGAAGCAAGCACAAGC
68099 AAT
1 AAT
68102 ATTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 14 0.78
18 4 0.22
ACGTcount: A:0.47, C:0.21, G:0.18, T:0.13
Consensus pattern (18 bp):
AATGAAGCAAGCACAAGC
Found at i:81396 original size:24 final size:23
Alignment explanation
Indices: 81364--81451 Score: 74
Period size: 24 Copynumber: 3.7 Consensus size: 23
81354 AAAAAAATCT
81364 TAGACAAAATCAAAAATTAAATAAA
1 TAGA-AAAAT-AAAAATTAAATAAA
* **
81389 TAGAAAAATAAAAAAATTTTAATGTA
1 TAGAAAAAT--AAAAA-TTAAATAAA
81415 T-G-AAAA-AAAAATTAAATAAA
1 TAGAAAAATAAAAATTAAATAAA
81435 TAGAAAAATTAAAAATT
1 TAGAAAAA-TAAAAATT
81452 TTAGATATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
20 7 0.14
21 6 0.12
22 4 0.08
24 16 0.32
25 10 0.20
26 7 0.14
ACGTcount: A:0.67, C:0.02, G:0.06, T:0.25
Consensus pattern (23 bp):
TAGAAAAATAAAAATTAAATAAA
Found at i:83646 original size:31 final size:30
Alignment explanation
Indices: 83608--83683 Score: 91
Period size: 31 Copynumber: 2.5 Consensus size: 30
83598 CTGACATGTG
*
83608 AACTTTTAAAAT-TTAATTATTTTGCCCCATA
1 AACTTTTAAAATCTTAA-CATTTTGCCCC-TA
* **
83639 AACTTTTAAAATCTTAACGTTTTGTTCCTA
1 AACTTTTAAAATCTTAACATTTTGCCCCTA
83669 AACTTTTAAAATCTT
1 AACTTTTAAAATCTT
83684 GACGTTTTAT
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
30 17 0.43
31 19 0.47
32 4 0.10
ACGTcount: A:0.34, C:0.16, G:0.04, T:0.46
Consensus pattern (30 bp):
AACTTTTAAAATCTTAACATTTTGCCCCTA
Done.