Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014717.1 Corchorus olitorius cultivar O-4 contig14750, 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: 143278
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:784 original size:322 final size:323
Alignment explanation
Indices: 66--876 Score: 925
Period size: 322 Copynumber: 2.5 Consensus size: 323
56 TCTCGCTTTA
* * *
66 AATATCATTTTTCTATTTTTTTCCGAATCT-ATTTCTAATTAAATGGAAACAATATTTAGATGCT
1 AATATCATTTTTCCATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAACAATATTAAGATGCT
* * * *
130 CGAAAAAACAAATCCTTAAATCTAACGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATA
65 CGTAAAAACAAATCCTTAAATCCAACGTGGCT--GA--C--A-TTTGGTTTGATGAATATAGATA
* * * *
195 TTTCAAGGAGTCTTTCTGCCAAAGATCATGCAAAACTGTCCCGGGGCCCCCCGAAAACGCGTTTT
123 TTTCAAGGAGTCTTAC-GCCAAAAATCATGCAAAACTGACCCGGGG--CCCCGAAAACGCGATTT
* * *
260 TAGCCCAAAAACCATGATGGTTAGTACAAGATTTTCGGCTAAAATCTGACCCAGAATTTTTTTAT
185 TAGCCCAAAAACCATGATGGTTAGTACAAGATTTTCGGCAAAAAACTGACCCAGAAGTTTTTTAT
* * * *
325 GAATTTTTTTCCACAATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCATTT
250 CAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACACCAAAAAAATTGACGGTCATTT
*
390 CACGCTTTT
315 CACGCTTCT
* * *
399 AATATCATTTTTCCAATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAATATTCAGATGCTC
1 AATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTAAGATGCTC
* * *
464 GTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAATG
66 GTAAAAACAAATCCTTAAATCCAACGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGG
* * ** * ** *
529 AGTCTCTGCGCCAAAAATCATGCAAAATTGAGTCGGGG-CTCGGGAACGCGATTTTAG-CCGAAA
131 AGTCT-TACGCCAAAAATCATGCAAAACTGACCCGGGGCCCCGAAAACGCGATTTTAGCCCAAAA
** * * ** *
592 ACTGTGATGGTTATTACACGA-TTTCGGCAAAAAACTGATCGGAGAAGTTTTTTCTCAATTTTTT
195 ACCATGATGGTTAGTACAAGATTTTCGGCAAAAAACTGA-CCCAGAAGTTTTTTATCAATTTTTT
* * * *
656 GCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGTCTTTTCATGCTTCT
259 GCCACAATACTCAAAAAAAATATATAATTCAACACCAAAAAAATTGACGGTCATTTCACGCTTCT
* * *
721 AATATC-TTTTTCCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAA-AAGATTAAGATGC
1 AATATCATTTTT-CCATTT-TTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTAAGATGC
** * ** * *
784 TCGTAAAAACAAATATTTAAATCGAACGTGG-TGGGATTTTGTTTGATGAATATATATATTTCAA
64 TCGTAAAAACAAATCCTTAAATCCAACGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAA
* *
848 GGAGTATTTACGTCAAAAATCATGCAAAA
129 GGAGT-CTTACGCCAAAAATCATGCAAAA
877 ACAAAAAAAT
Statistics
Matches: 412, Mismatches: 60, Indels: 24
0.83 0.12 0.05
Matches are distributed among these distances:
321 72 0.17
322 148 0.36
323 44 0.11
326 56 0.14
327 3 0.01
329 1 0.00
331 2 0.00
332 1 0.00
333 85 0.21
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (323 bp):
AATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTAAGATGCTC
GTAAAAACAAATCCTTAAATCCAACGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGG
AGTCTTACGCCAAAAATCATGCAAAACTGACCCGGGGCCCCGAAAACGCGATTTTAGCCCAAAAA
CCATGATGGTTAGTACAAGATTTTCGGCAAAAAACTGACCCAGAAGTTTTTTATCAATTTTTTGC
CACAATACTCAAAAAAAATATATAATTCAACACCAAAAAAATTGACGGTCATTTCACGCTTCT
Found at i:1604 original size:322 final size:322
Alignment explanation
Indices: 933--1754 Score: 926
Period size: 322 Copynumber: 2.5 Consensus size: 322
923 AATTGAAATA
* * * *
933 TTTTCTCGCTTTAAATATCATTTTTCTATTTTTTTCCGATTCTATTTTCTAATTAAATCGAAACA
1 TTTTCACGCTTT-AATATCATTTTTCCATTTTTTTCCGAAT-TAATTTCTAATTAAATCGAAACA
* * * * * *
998 ATATTCAGATGCTGC-TAAAAACAAATTCTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTA
64 AGATTCAGATGC-GCGTAAAAACAAATACTTAAATCCAATGTGGCT--GA--C--A-TTTGGTTT
* * *
1062 GATAAATATAGATATTTCAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGAGCCCCC
121 GATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGAGACCCC
1127 GAAACGCATTTTTAGCCCAAAAACCATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCG
186 GAAACGCATTTTTAGCCCAAAAACCATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCG
** *
1192 GAATTTTTTTTTCTGAATTTTTTCCACAATACTAAAAAAAAAAATAATTCAACACCAAAAAGATT
251 GAAAGTTTTTTTCTCAATTTTTTCCACAATACTAAAAAAAAAAATAATTCAACACCAAAAAGATT
1257 GATGGTC
316 GATGGTC
* *
1264 TTTTCACGCTTTTAATATCATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATGGAAACA
1 TTTTCACGC-TTTAATATCATTTTTCC-ATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * *
1329 AGATTCAGATGCGCGTAAAAATAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATA
64 AGATTCAGATGCGCGTAAAAACAAATACTTAAATCCAATGTGGCTGACATTTGGTTTGATGAATA
* * * * * * * *
1394 TAGATATTTCAAGGAGTCTCTGCGCCAAAAATCATGCAAAATTGAGTCGG-GACTCGGGAACGCG
129 TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGAGACCCCGAAACGCA
* * * *
1458 TTTTTAG-CCAAAAACCGTGA-TG-TAGTACACGA-TTTCGGCTAAAATCTTA-TCGGAAAAGTT
194 TTTTTAGCCCAAAAACCATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGG-AAAGTT
* * * * * *
1518 TTTTTCTCAATTTTTTGCCACAATGCTCTGAAAAAATATATAATTCAACACGAAAAAGATTGTCT
258 TTTTTCTCAATTTTTT-CCACAAT--ACTAAAAAAAAAAATAATTCAACACCAAAAAGATTG-AT
1583 GG-C
319 GGTC
* * * *
1586 TTTTCACGCTTCTAATATCGTTTTTCCATTTATTTTCTGAATTAATTTTTAATTAAATTGAAA-A
1 TTTTCACGCTT-TAATATCATTTTTCCATTT-TTTTCCGAATTAATTTCTAATTAAATCGAAACA
* * * * * * **
1650 AGATTAAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCAG-GATTTTTTTTGATGAATA
64 AGATTCAGATGCGCGTAAAAACAAATACTTAAATCCAATGTGGCTGACATTTGGTTTGATGAATA
* *
1714 TAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAA
129 TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAA
1755 ACAAAAAAAA
Statistics
Matches: 423, Mismatches: 58, Indels: 31
0.83 0.11 0.06
Matches are distributed among these distances:
318 3 0.01
319 35 0.08
320 69 0.16
321 45 0.11
322 95 0.22
323 19 0.04
324 58 0.14
325 1 0.00
327 1 0.00
329 2 0.00
330 2 0.00
331 78 0.18
332 15 0.04
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (322 bp):
TTTTCACGCTTTAATATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAG
ATTCAGATGCGCGTAAAAACAAATACTTAAATCCAATGTGGCTGACATTTGGTTTGATGAATATA
GATATTTCAAGGAGTCTTTACGCCAAAAATCATGCAAAACTGAGCCGGAGACCCCGAAACGCATT
TTTAGCCCAAAAACCATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAAAGTTTTT
TTCTCAATTTTTTCCACAATACTAAAAAAAAAAATAATTCAACACCAAAAAGATTGATGGTC
Found at i:3021 original size:881 final size:881
Alignment explanation
Indices: 12--4021 Score: 6551
Period size: 881 Copynumber: 4.5 Consensus size: 881
2 TATTTTCGGA
* *
12 AAAAAATATACAATTCAAAGCAAAAAATAAAATTGAAATATTTTTCTCGCTTTAAATATCATTTT
1 AAAAAATACACAATTCAACGC-AAAAA-AAAATTGAAATA-TTTTCTCGCTTTAAATATCATTTT
* * * *
77 TCTATTTTTTTCCGAATCTA-TTTCTAATTAAATGGAAACAATATTTAGATGCT-CGAAAAAACA
63 TCTATTTTTTTCCGAACCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGC-TAAAAACA
** *
140 AATCCTTAAATCTAACGTGGCTGAGAGCCTGAGATTGGTTAGATGAATATAGATATTTCAAGGAG
127 AATCCTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAG
* * **
205 TCTTTCTGCCAAAGATCATGCAAAACTGTCCCGGGGCCCCCCGAAAACGCGTTTTTAGCCCAAAA
192 TCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGG-CCCCCG-AAACGCGTTTTTAGCCCAAAA
* * * *
270 ACCATGATGGTTAGTACAAGATTTTCGGCTAAAATCTGACCCAGAA-TTTTTTTATGAATTTTTT
255 ACCATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTTCTGAATTTTTT
*
334 TCCACAATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCATTTCACGCTTTT
320 TCCACAATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTT
*
399 AATATCATTTTTCC-AATTTTTTCCGAATTAATTTCTAATTAAATCGAAATAATATTCAGATGCT
385 AATATCATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
*
463 CGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAT
450 CGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAG
*
528 GAGTCTCTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCGAAAA
515 GAGTCTCTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCAAAAA
* * * *
593 CTGTGATGGTTATTACACGATTTCGGCAAAAAACTGATCGGAGAAGTTTTTTCTCAATTTTTTGC
580 CCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGC
* *
658 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATTGACGGTCTTTTCATGCTTCTAA
645 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGTCTTTTCACGCTTCTAA
723 TATC-TTTTTCCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCG
710 TATCGTTTTT-CCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCG
* * *
787 TAAAAACAAATATTTAAATCGAACGTGGTGGGATTTTGTTTGATGAATATATATATTTCAAGGAG
774 TAAAAACAAATACTTAAATCGAACGTGGCGGGATTTTGTTTGATGAATATAGATATTTCAAGGAG
*
852 TATTTACGTCAAAAATCATGCAAAAACAAAAAAATATTCCGGC
839 TATTTACGTCAAAAATCATGCAAAAACAAAAAAAAATTCCGGC
895 AAAAAATACACAATTCAACGCAAAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTTTCT
1 AAAAAATACACAATTCAACGCAAAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTTTCT
** *
960 ATTTTTTTCCGATTCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGCTAAAAACAAATT
66 ATTTTTTTCCGAACCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGCTAAAAACAAATC
1025 CTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAGTCTT
131 CTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAGTCTT
* *
1090 TATGCCAAAAATCATGCAAAACTGAGCCGGAGCCCCCGAAACGCATTTTTAGCCCAAAAACCATG
196 TATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATG
1155 AGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTTTCTGAA-TTTTTTCCAC
261 AGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAA-TTTTTTTTCTGAATTTTTTTCCAC
*
1219 AATACT-AAAAAAAA-AAATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATAT
325 AATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATAT
* * *
1282 CATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATGGAAACAAGATTCAGATGCGCGTAA
390 CATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAA
*
1347 AAATAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTC
455 AAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTC
* *
1412 TCTGCGCCAAAAATCATGCAAAATTGAGTCGGGACTCGGGAACGCGTTTTTAGCCAAAAACCGTG
520 TCTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCAAAAACCGTG
* *
1477 AT-G-TAGTACACGATTTCGGCTAAAATCTTATCGGAAAAGTTTTTTTCTCAATTTTTTGCCACA
585 ATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAG-TTTTTTCTCAATTTTTTGCCACA
* * * * *
1540 ATGCTCTGAAAAAATATATAATTCAACACGAAAAAGATTGTCTGG-CTTTTCACGCTTCTAATAT
649 ATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGAC-GGTCTTTTCACGCTTCTAATAT
*
1604 CGTTTTTCCATTTATTTTCTGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAA
713 CGTTTTTCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAA
* *
1669 AACAAATACTTAAATCGAACGTGGCAGGATTTTTTTTGATGAATATAGATATTTCAAGGAGTATT
778 AACAAATACTTAAATCGAACGTGGCGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATT
1734 TACGTCAAAAATCATGCAAAAACAAAAAAAAATATCCGGC
843 TACGTCAAAAATCATGCAAAAACAAAAAAAAAT-TCCGGC
*
1774 AAAAAATACACAATTCAACGCAAAAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTCTC
1 AAAAAATACACAATTCAACGC-AAAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTTTC
* *
1839 TATTTTTTTTTCCGAATCC-A-TTTCTAGTTAAATCGAAACAATATTCAGATCCTGCTAAAAACA
65 TA--TTTTTTTCCGAA-CCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGCTAAAAACA
* * * *
1902 AATCCTTAAATCTGATGTGGCTAAGAGCCTAAGATTGGTTAGATAAATATAGATATTTCAAGGAG
127 AATCCTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAG
* * * *
1967 TCTTTCTGTCAAAAATCATGCAAAACTGAGTCGGGGCCCCTGAAACGCGTTTTTAGCCCAAAAAC
192 TCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAAC
* * *
2032 CATGATGGTTTA-AACACGATTTTCGGCTAAAATCTGACCCAGAATTTTTTTTAC-GAATTTTTT
257 CATGA-GGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTT-CTGAATTTTTT
* * *
2095 TCCACAATACTCAGAAAAAATATATAATTCAACACAAAAAAGATTGATGGTCTTTTCACGCTATT
320 TCCACAATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTT
* * * ** *
2160 AATATCATTTTTACAATTTTTTTCTGAATTAATTTAAAATTAAATCGAAACAATATTCAGATGCC
385 AATATCATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCT
*
2225 CGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAA
450 CGTAAAAACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAG
*
2290 GAGTCTCTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAACCAAAAA
515 GAGTCTCTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCAAAAA
* * *
2355 CTGTGATGGTTATTACACAATTTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGC
580 CCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGC
*
2420 CACAATACTCAGAAAAAATATATAATTCAATGCCAAAAAGATTGACGGTCTTTTCACGCTTCTAA
645 CACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGTCTTTTCACGCTTCTAA
*
2485 TATCGTTTTTTCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGT
710 TATCGTTTTTCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGT
* * * *
2550 AAAAACAAAAATTTAAATCGAACGTGGTGGGATTTTGTTTGATGAATATATATATTTCAAGGAGT
775 AAAAACAAATACTTAAATCGAACGTGGCGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGT
*
2615 ATTTACGTCAAAAATCATGCAAAATCAAAAAAAAATTCCGGC
840 ATTTACGTCAAAAATCATGCAAAAACAAAAAAAAATTCCGGC
* *
2657 AAAAAATACACAATTCAACACAAAAAAAAATTGAAATATTTTCTCTCTTTAAATATCATTTTTCT
1 AAAAAATACACAATTCAACGCAAAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTTTCT
*
2722 ATTTTTTTCCGAACCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTACTAAAAACAAATC
66 ATTTTTTTCCGAACCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGCTAAAAACAAATC
2787 CTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAGTCTT
131 CTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAGTCTT
* * * *
2852 TATGGCAAAAATCATGCAAAACTGAGCCGGAGCCCCTGAAACGCATTTTTAGCCCAAAAACCATG
196 TATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATG
*
2917 AGGGTTAATACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTTCTGAATTTTTTTCCACA
261 AGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTTCTGAATTTTTTTCCACA
* *
2982 ATACTCAGAAAAAATATATAATCCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATATC
326 ATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATATC
* *
3047 ATTTTTCCAAATTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
391 ATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAA
3112 AACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCT
456 AACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCT
*
3177 CTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAAACCGTGA
521 CTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCAAAAACCGTGA
*
3242 TGGTTAGTACACGATTTCGGCTAAAATCTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
586 TGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
* * * *
3307 ACTTAGAAATAATATATAATTCAACGCCAAAAAGATTGACAGACTTTTCACGCTTCTAATATCGT
651 ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGTCTTTTCACGCTTCTAATATCGT
*
3372 TTTTCCATTTATTTTCCGAATTAATATTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAAC
716 TTTTCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAAC
* * *
3437 AAATACTTAAATCGAACGTGGCGGGGTTTTGTTTGAAGAATATAGATATTTCAAGGAGTATTTAT
781 AAATACTTAAATCGAACGTGGCGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTAC
* *
3502 GTTAAAAATCATGCAAAAACAAAAAAAAAAACTTTCGGC
846 GTCAAAAATCATGCAAAAAC--AAAAAAAAA-TTCCGGC
*
3541 AAAAAATACACAATT-AACCGCAAAAAAAAATTGAAATATTTATCTCGTTTTAAATATCATTTTT
1 AAAAAATACACAATTCAA-CGCAAAAAAAAATTGAAATATTT-TCTCGCTTTAAATATCATTTTT
* *
3605 CTATTTTTTTTCCGATA-CTATTTTCTAATTAAATCGAAACAATATTCAGATGATGCTAAAAATA
64 CTA-TTTTTTTCCGA-ACCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGCTAAAAACA
*
3669 AATCCTTAAATCTAATAGGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAG
127 AATCCTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAG
* * *
3734 TCTTTATTCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTGAGGCCAAAAAC
192 TCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAAC
* *
3799 CATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGTAATTTTTTTTCTGAATTTTTTGC
257 CATGAGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTTCTGAATTTTTTTC
*
3864 CACAATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGTTCTTTTCACGCTTTTAA
322 CACAATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAA
* * *
3929 TATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATCGAAATAATATTTAGATGCTCG
387 TATCATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCG
*
3994 TAAAAACAAATCATTATATCCAATGTGG
452 TAAAAACAAATCCTTATATCCAATGTGG
4022 GAAAATAAGA
Statistics
Matches: 2909, Mismatches: 186, Indels: 61
0.92 0.06 0.02
Matches are distributed among these distances:
877 31 0.01
878 284 0.10
879 284 0.10
880 139 0.05
881 1090 0.37
882 73 0.03
883 288 0.10
884 276 0.09
885 55 0.02
886 388 0.13
887 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (881 bp):
AAAAAATACACAATTCAACGCAAAAAAAAATTGAAATATTTTCTCGCTTTAAATATCATTTTTCT
ATTTTTTTCCGAACCTATTTTCTAATTAAATCGAAACAATATTCAGATGCTGCTAAAAACAAATC
CTTAAATCTAATATGGCTGAGAGCCTGAGATTGGTTAGATAAATATAGATATTTCAAGGAGTCTT
TATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCGTTTTTAGCCCAAAAACCATG
AGGGTTAGTACACGATTTTCGGCTAAAATCTGACCCGGAATTTTTTTTCTGAATTTTTTTCCACA
ATACTCAAAAAAAATATATAATTCAACACCAAAAAGATTGATGGTCTTTTCACGCTTTTAATATC
ATTTTTCCAAATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAATATTCAGATGCTCGTAAA
AACAAATCCTTATATCCAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCT
CTGCGCCAAAAATCATGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCAAAAACCGTGA
TGGTTAGTACACGATTTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAAT
ACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGACGGTCTTTTCACGCTTCTAATATCGT
TTTTCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAAC
AAATACTTAAATCGAACGTGGCGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTAC
GTCAAAAATCATGCAAAAACAAAAAAAAATTCCGGC
Found at i:5896 original size:323 final size:328
Alignment explanation
Indices: 5184--6011 Score: 915
Period size: 323 Copynumber: 2.5 Consensus size: 328
5174 AATTGAAATA
* * * *
5184 TTTTCTCGCTT-TAAATATCATT-TTTCTATT-TTTTCCAAATCT-ATTTTATAATTAAATCGAA
1 TTTTCACGCTTCT-AATATCATTCTTCCAATTATTTTCCGAAT-TAATTTT-TAATTAAATCGAA
* * * * *
5245 ACAATATTCAGATGCT-GCTAAAAACAAATCCTTAAATCTAATGCGGCTGAGAGCCTAAGATAGG
63 ACAATATTCAGATGCTCG-TAAAAACAAATCCTTAAATCCAATGTGG-T-TGA--C--A-TTTGG
* * * * * *
5309 CTAGATGAATATAGATATTTAAAGGAGTCTTTATGCTAAAAATCATGCAAAAGTGAGCCGGGGCC
120 TTTGATGAATATAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAAAGTGAGCCGGGGCC
* *
5374 CCCGAAACGCATTTTTAGCCCAAAAACCATAAGGGTTAGTATACGATTTTCAGCTAAAATCTGAC
185 CCCGAAACGCATTTTTAGCCCAAAAACCATAAGGGTTAGTACACGATTTTCAGCTAAAAACTGAC
** *
5439 CCGGAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAA
250 CCGGAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAA
* * *
5504 AACGATTGATGGTC
315 AAAGATTGACGGGC
* *
5518 TTTTCACGCTTTTAATATCATTCTTCCAATTATTTTCCGAATTAATTTCTAATTAAATCGAAACA
1 TTTTCACGCTTCTAATATCATTCTTCCAATTATTTTCCGAATTAATTTTTAATTAAATCGAAACA
* *
5583 ATATTCAGATACTCGTAAAAACAAATCCTTATATCCAATGTGGTTGACATTTGGTTTGATGAATA
66 ATATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTTGATGAATA
* * * ** * * * *
5648 TAGATATTTCAAGGAGTCTCTGCGCCAAAAATCATGAAAAATTGAGTTGGGG-CTCGGGAACGCG
131 TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAAAGTGAGCCGGGGCCCCCGAAACGCA
* * * * * *
5712 TTTTTAG-CCAAAGACCGTGATGGTTAGTACACGA-TTTCGGCTAAAAACTGA-TCGGAAAAGTT
196 TTTTTAGCCCAAAAACCATAAGGGTTAGTACACGATTTTCAGCTAAAAACTGACCCGG-AAAGTT
*
5774 TTTTCTCAATTTTTTGCCACAATACTCAGAAAA-A-ATATATAATTCAACGCCAAAAAGATTGAC
260 TTTTCTCAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAAAAAGATTGAC
5837 GGGC
325 GGGC
** * * *
5841 TTTTCACGCTTCTAATATTGTTTTTCCATTTATTTTCCGAATTAATTTTTAATTAAATTGAAA-A
1 TTTTCACGCTTCTAATATCATTCTTCCAATTATTTTCCGAATTAATTTTTAATTAAATCGAAACA
* * * * * * ** * *
5905 AGATTAAGATGCTCGTAAAAACAAATACTTAAATCGAACGTGGCTGGGATTTTGTTTGAAGAATA
66 ATATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTTGATGAATA
* *
5970 TAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAAAAA
131 TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATG-AAAAA
6012 CAAAAAAATT
Statistics
Matches: 422, Mismatches: 65, Indels: 25
0.82 0.13 0.05
Matches are distributed among these distances:
322 86 0.20
323 90 0.21
324 4 0.01
325 51 0.12
326 22 0.05
327 15 0.04
328 55 0.13
329 1 0.00
331 1 0.00
333 2 0.00
334 20 0.05
335 61 0.14
336 14 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (328 bp):
TTTTCACGCTTCTAATATCATTCTTCCAATTATTTTCCGAATTAATTTTTAATTAAATCGAAACA
ATATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGTTGACATTTGGTTTGATGAATA
TAGATATTTCAAGGAGTCTTTACGCCAAAAATCATGAAAAAGTGAGCCGGGGCCCCCGAAACGCA
TTTTTAGCCCAAAAACCATAAGGGTTAGTACACGATTTTCAGCTAAAAACTGACCCGGAAAGTTT
TTTCTCAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAAAAAGATTGACG
GGC
Found at i:6604 original size:886 final size:880
Alignment explanation
Indices: 4737--6960 Score: 3587
Period size: 881 Copynumber: 2.5 Consensus size: 880
4727 GGGCGTGACA
*
4737 CAATGTGGCTGACATTTGCTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAAT-AT
1 CAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCA-
* * * * *
4801 TGCAAAATTGAGTCGGGGCTCGGGAACGCGATTTTAGCCAAAAACTGTGATGGTTATTACACAAT
65 TACAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTACACGAT
*
4866 TTCGGCTAAAAACTGATCGGAAATGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATAT
129 TTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATAT
** ** * * *
4931 ATAATTCAATTCCAAAAAGATTGACGGTTTTTTCACGCTTCTCATATCGTTTTTCCATTTAGTTT
194 ATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTATTTT
** *
4996 CTAAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAACGAATACTTAAATCGA
259 CCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAACAAATACTTAAATCGA
*
5061 ACATGG-TGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGC
324 ACGTGGCTGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGC
* *
5125 AAAAACAAAAAGAAAAATTCTGGC-AAAAATACACAATTCAACGCAAAAAAATTGAAATATTTTC
389 AAAAAC-AAAA-AAATATTCCGGCAAAAAATACACAATTCAACGCAAAAAAATTGAAATATTTTC
*
5189 TCGCTTTAAATATCATTTTTCTATTTTTTCCAAATCTATTTTATAATTAAATCGAAACAATATTC
452 TCGCTTTAAATATCATTTCTCTATTTTTTCCAAATCTATTTTATAATTAAATCGAAACAATATTC
*
5254 AGATGCTGCTAAAAACAAATCCTTAAATCTAATGCGGCTGAGAGCCTAAGATAGGCTAGATGAAT
517 AGATCCTGCTAAAAACAAATCCTTAAATCTAATGCGGCTGAGAGCCTAAGATAGGCTAGATGAAT
* *
5319 ATAGATATTTAAAGGAGTCTTTATGCTAAAAATCATGCAAAAGTGAGCCGGGGCCCCCGAAACGC
582 ATAGATATTTAAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGC
* *
5384 ATTTTTAGCCCAAAAACCATAAGGGTTAGTATACGATTTTCAGCTAAAATCTGACCCGGAATTTT
647 AGTTTTAGCCCAAAAACCATAAGGGTTAGTACACGATTTTCAGCTAAAATCTGACCCGGAATTTT
*
5449 TTTTCTGAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAAAACGATTGAT
712 TTTTCTGAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAAAAAGATTGAT
5514 GGTCTTTTCACGCTTTTAATATCATTCTTCCAATTATTTTCCGAATTAATTTCTAATTAAATCGA
777 GGTCTTTTCACGCTTTTAATATCATTCTTCCAATTATTTTCCGAATTAATTTCTAATTAAATCGA
*
5579 AACAATATTCAGATACTCGTAAAAACAAATCCTTATATC
842 AACAAGATTCAGATACTCGTAAAAACAAATCCTTATATC
*
5618 CAATGTGGTTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCAT
1 CAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCAT
*
5683 GA-AAAATTGAGTTGGGGCTCGGGAACGCGTTTTTAGCCAAAGACCGTGATGGTTAGTACACGAT
66 -ACAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAA-ACCGTGATGGTTAGTACACGAT
*
5747 TTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATAT
129 TTCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATAT
5812 ATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTATTTT
194 ATAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTATTTT
5877 CCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAACAAATACTTAAATCGA
259 CCGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAACAAATACTTAAATCGA
*
5942 ACGTGGCTGGGATTTTGTTTGAAGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGC
324 ACGTGGCTGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGC
6007 AAAAACAAAAAAATTTATATCCGGCAAAAAATACACAATTCAACGCAAAAAAATTTTGAAATATT
389 AAAAACAAAAAAA--TAT-TCCGGCAAAAAATACACAATTCAACGCAAAAAAA--TTGAAATA-T
* * *
6072 TTTCTCGCTTTAAATATCATTTCTCTATTTTTTTCCGAATCTA-TTTCTAGTTAAATCGAAACAA
448 TTTCTCGCTTTAAATATCATTTCTCTA-TTTTTTCCAAATCTATTTTATAATTAAATCGAAACAA
* * * *
6136 TATTCAGATCCT-CGTAAAAACAAATCCTTAAATCTAATGTGGCTGAGAGCCTGAGATTGGTTAG
512 TATTCAGATCCTGC-TAAAAACAAATCCTTAAATCTAATGCGGCTGAGAGCCTAAGATAGGCTAG
* *
6200 ATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCG
576 ATGAATATAGATATTTAAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCG
* * * *
6265 AAACGCGGTTTTAGCCCAAAAACCATGATGGTTTAGTACACGATTTTCGGCTAAAATCTGACCCG
641 AAACGCAGTTTTAGCCCAAAAACCAT-AAGGGTTAGTACACGATTTTCAGCTAAAATCTGACCCG
6330 GAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAA-A-ATATATAATTCAACACCAAAAA
705 GAATTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAAAAA
* * *
6393 GATTGATGGTC-TTTCACGCTTTTAATATCATTTTTCCAATTTTTTTTCTGAATTAATTTCTAAT
770 GATTGATGGTCTTTTCACGCTTTTAATATCATTCTTCCAA-TTATTTTCCGAATTAATTTCTAAT
* * *
6457 TAAATCGAAACAAGATTCGGGTGCTCGTAAAAACAAATCCTTATATC
834 TAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTATATC
*
6504 CAATATGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCAT
1 CAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCAT
* *
6569 ACAAAATTGAGTCGGGGCTCGGGAACGTGTTTTTAGCTAAAATCC----------G--CACGATT
66 ACAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAA-CCGTGATGGTTAGTACACGATT
*
6622 TCGGCTAAAAACTGATCGGAAAAGATTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATA
130 TCGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATA
6687 TAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTATTTTC
195 TAATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTATTTTC
* *
6752 CGAATTAATTTTTAATTAAATTGAAAAGGATTAAGATGCTCGTGAAAACAAATACTTAAATCGAA
260 CGAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAACAAATACTTAAATCGAA
*
6817 CGTGGC-AGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCA
325 CGTGGCTGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCA
6881 AAAA-AAAAAAAT-TTCCGGCAAAAAATACACAATTCAACGCAAAAAAAAATTGAAATATTTTCT
390 AAAACAAAAAAATATTCCGGCAAAAAATACACAATTCAACGC--AAAAAAATTGAAATATTTTCT
6944 CGCTTTAAATATCATTT
453 CGCTTTAAATATCATTT
6961 AAAAAAAAAA
Statistics
Matches: 1262, Mismatches: 62, Indels: 52
0.92 0.05 0.04
Matches are distributed among these distances:
867 23 0.02
868 35 0.03
869 1 0.00
870 8 0.01
872 7 0.01
873 60 0.05
874 204 0.16
876 1 0.00
880 6 0.00
881 306 0.24
882 66 0.05
883 5 0.00
884 27 0.02
885 29 0.02
886 207 0.16
887 189 0.15
888 88 0.07
ACGTcount: A:0.36, C:0.16, G:0.15, T:0.33
Consensus pattern (880 bp):
CAATGTGGCTGACATTTGGTTTGATGAATATAGATATTTCAAGGAGTCTCTGCGCCAAAAATCAT
ACAAAATTGAGTCGGGGCTCGGGAACGCGTTTTTAGCCAAAACCGTGATGGTTAGTACACGATTT
CGGCTAAAAACTGATCGGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTTAGAAAAAATATAT
AATTCAACGCCAAAAAGATTGACGGGCTTTTCACGCTTCTAATATTGTTTTTCCATTTATTTTCC
GAATTAATTTTTAATTAAATTGAAAAAGATTAAGATGCTCGTAAAAACAAATACTTAAATCGAAC
GTGGCTGGGATTTTGTTTGATGAATATAGATATTTCAAGGAGTATTTACGTCAAAAATCATGCAA
AAACAAAAAAATATTCCGGCAAAAAATACACAATTCAACGCAAAAAAATTGAAATATTTTCTCGC
TTTAAATATCATTTCTCTATTTTTTCCAAATCTATTTTATAATTAAATCGAAACAATATTCAGAT
CCTGCTAAAAACAAATCCTTAAATCTAATGCGGCTGAGAGCCTAAGATAGGCTAGATGAATATAG
ATATTTAAAGGAGTCTTTATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCCGAAACGCAGTT
TTAGCCCAAAAACCATAAGGGTTAGTACACGATTTTCAGCTAAAATCTGACCCGGAATTTTTTTT
CTGAATTTTTTGCCACAATACTCAGAAAATATATATATAATTCAACACCAAAAAGATTGATGGTC
TTTTCACGCTTTTAATATCATTCTTCCAATTATTTTCCGAATTAATTTCTAATTAAATCGAAACA
AGATTCAGATACTCGTAAAAACAAATCCTTATATC
Found at i:16668 original size:26 final size:26
Alignment explanation
Indices: 16621--16676 Score: 78
Period size: 26 Copynumber: 2.2 Consensus size: 26
16611 TTTTAATAAG
*
16621 TATTCTTTTTAATCATTTAACTTTTT
1 TATTCTTTTTAATCATTCAACTTTTT
*
16647 TATT-TTTTTAGATGATTCAACTTTTT
1 TATTCTTTTTA-ATCATTCAACTTTTT
16673 TATT
1 TATT
16677 AATTATGGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 6 0.22
26 21 0.78
ACGTcount: A:0.23, C:0.09, G:0.04, T:0.64
Consensus pattern (26 bp):
TATTCTTTTTAATCATTCAACTTTTT
Found at i:20230 original size:2 final size:2
Alignment explanation
Indices: 20223--20254 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
20213 TTAAAATTAA
20223 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
20255 TCATCTAACT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21348 original size:672 final size:666
Alignment explanation
Indices: 20571--22463 Score: 2294
Period size: 672 Copynumber: 2.8 Consensus size: 666
20561 TTCACTCTTA
* * *
20571 CTTGAAATATCTATACTCATCAAACCAAATCTCACTCACATTGGATATAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCGAACCAAATCTCACCCACATTGGATATAAGGATTTGTTTTTACG
* * * *
20636 AGCACCTGAATTTTGTTTTGATTTAATTAAAAATTAATTCGGAAAAGAATAATGGAAAAATGATA
66 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAA-AATAATGGAAAAATGATA
**
20701 TTATAAGCGTAAAAAGGCCGTCAAAATTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTG
130 TTATAAGCGTAAAAAGGCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTG
*
20766 CAAAAAATTGGGAAAAAACTTTTCGTGTAACTTTTTAGCCGAAATCGTGTACTATCACTGCTTTT
195 CAAAAAATTGGGAAAAAACTTTTCG-GTAAGTTTTTAGCCGAAA-CGTGTACTATCAC-G-TTTT
**
20831 GGCTAAAAACGCGTTTCGAGTCCCAGACTCTGTTTTGCATGATTCCTGGCAGAAAGACTCCTTGA
256 GGCTAAAAACGCGTTTCGAG-CCCAGACTCTGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGA
* * * *
20896 AATATCTCTATTCATCTAACCAAATCTCAGCCACATTGG-TATAAGGATTTGATTTTACA-AGTT
320 AATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACACAGTT
*
20959 TGTTTCGATTTAATTAGAAATAAATTC-GAAAAAAAAAGGAAAACGATATTTGAAGTGTGAAAAA
385 TGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAAGGAAAACGATATTTGAAGCGTGAAAAA
*
21023 CTCTTCAATTTTTTTGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTGAGGAA
450 CTCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGA-GAA
* * * *
21088 AAACTTTTAGGGTCAATTTTTGCAAAATTTTAGTCGAAATCGTGTACTTTTTATTTTTTGCCAAC
514 AAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC--ATT-TTTTTTCCCAAC
* * ** *
21153 GAAATCGTGTACTAACCATCACGGTTTTTTGC-CTAAAAATGCGTTCCGGAGTCTCGGCTAAATT
576 GAAATCGTGTACTAACCATCACGATTTTTGGCAAGAAAAACGCGTTCCGGAGTCTCGGCTAAATT
* *
21217 TTGCATGATTTTTGGTGCAGAGACTC
641 TTGCATGATTTTTGGCGCAAAGACTC
*
21243 TTTGAAATATCTATATTCATCGAACCAAATCTCACCCACATTGGATATAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCGAACCAAATCTCACCCACATTGGATATAAGGATTTGTTTTTACG
*
21308 AGTATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAATGGAAAAATGATA
66 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AAAAAATAATGGAAAAATGATA
* * * *
21373 TTAGT-AGCGTCAAAAGGCCATCAATCTTTTTGGCGTTAAATTATATATTTTTT-TAAATATTTT
130 TTA-TAAGCGTAAAAAGGCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTT
*
21436 GCAAAAAATTGAGAAAAAAAACTTTTCAGGTAAGTTTTTAGCCGAAACCGTG-----T-A-----
194 GCAAAAAATTG-G-GAAAAAACTTTTC-GGTAAGTTTTTAGCCGAAA-CGTGTACTATCACGTTT
* * * * * *
21490 ---CTAAAAACGAGTTTC-ATGGCCCCGACTCAGTTTTGAATGTTTTTTGGCAGAAAGACTCATT
255 TGGCTAAAAACGCGTTTCGA--GCCCAGACTCTGTTTTGCATGATTTTTGGCAGAAAGACTCCTT
*
21551 GAAATATCTATATTCATCTAACCAAATCTCAACCACAGTGGATTTAAGGATTTGTTTTTACGAGC
318 GAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTAC-A-C
*
21616 ATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAATGGAAAAACGATATTA
381 A---G----TTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAA-GG-AAAACGATATTT
* * * *
21681 GAAGCGTGAAAACCCCTTCAATTCTTTTTTGCGTTGAATTATATATTTTATCTGAGTATTGTGGC
437 GAAGCGTGAAAAACTCTTCAATT-TTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC
*
21746 AAAAAATTGAAGAAAAACTTTTCGGGTCAAATTTTGCAAAATTTTAGCCGAAATCGTGTACATTT
501 AAAAAATTG-AGAAAAACTTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACATTT
*
21811 TTTTTCCCAACGAAATCGTGTACTAACTATCACGATTTTTGGCAAAGAAAAACGCGTTCCGGAGT
565 TTTTTCCCAACGAAATCGTGTACTAACCATCACGATTTTTGGC-AAGAAAAACGCGTTCCGGAGT
* * *
21876 CTCGGCTCAATTTTGCATGATTTTTGGCGTAAATACTC
629 CTCGGCTAAATTTTGCATGATTTTTGGCGCAAAGACTC
* * * *
21914 CTTAAAATATCTATATTCATCGAACAAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTACG
1 CTTGAAATATCTATATTCATCGAACCAAATCTCACCCACATTGGATATAAGGATTTGTTTTTACG
* * *
21979 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC--AGAAAA-AATGGAAAAACGATAG
66 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAATGGAAAAATGATAT
* * * * *
22041 TAGAAACGTGAAAAGCCCGTCAATCTTTTTGGTGTTGAATTATATATTTTTTCTGAATATTTTGC
131 TATAAGCGTAAAAAGGCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGC
* *** *
22106 AAAAAATTTGAGCTTAAA-TGTTTCGGGTCAGTTTTTAGCCGAAACTGTGTACTAACCATCACGG
196 AAAAAA-TTGGGAAAAAACT-TTTC-GGTAAGTTTTTAGCCGAAAC-GTGTACT----ATCAC-G
* **
22170 TTTTTGGCTAAAAACGCGTTTTCG-GGCCACGACTCTGTTTTGCATGATTTTTGGC-GCCGAGAC
252 -TTTTGGCTAAAAACGCG-TTTCGAGCCCA-GACTCTGTTTTGCATGATTTTTGGCAG-AAAGAC
* * *
22233 TCCTTGAAATATCTTTATTCATCTAATCAAATCTCAACCTCATTGGATTTAAGGATTTGTTTTTA
313 TCCTTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTT-
* * * **
22298 GGAGCATCTGAATCTTGTTTCAATTTAATTAGAAATTAATTCGGAAAAAAATGGGAAAACGATAT
377 --A-CA-C--AGT-TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAAAAGGAAAACGATAT
* * * * * *
22363 TTAAAGCGTGAAAAGGCT-GTCAATATTTTTGGTGTTGAATTATATATTTTTTCTAAGTATTGTG
435 TTGAAGCGTGAAAA-ACTCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTG
* *
22427 GCAAAAAATTGAGAATAAACGTTTCGGGTCAGTTTTT
499 GCAAAAAATTGAGAA-AAACTTTTCGGGTCAATTTTT
22464 AGCCGAAATT
Statistics
Matches: 1048, Mismatches: 110, Indels: 115
0.82 0.09 0.09
Matches are distributed among these distances:
656 1 0.00
657 87 0.08
658 18 0.02
659 1 0.00
661 1 0.00
664 1 0.00
666 2 0.00
667 87 0.08
668 52 0.05
669 53 0.05
670 4 0.00
671 200 0.19
672 257 0.25
673 39 0.04
674 1 0.00
676 1 0.00
677 1 0.00
682 4 0.00
683 64 0.06
684 27 0.03
685 4 0.00
686 39 0.04
687 95 0.09
688 4 0.00
690 3 0.00
691 1 0.00
692 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (666 bp):
CTTGAAATATCTATATTCATCGAACCAAATCTCACCCACATTGGATATAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAATGGAAAAATGATAT
TATAAGCGTAAAAAGGCCGTCAATCTTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGC
AAAAAATTGGGAAAAAACTTTTCGGTAAGTTTTTAGCCGAAACGTGTACTATCACGTTTTGGCTA
AAAACGCGTTTCGAGCCCAGACTCTGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATC
TATATTCATCTAACCAAATCTCAACCACATTGGATTTAAGGATTTGTTTTTACACAGTTTGTTTC
GATTTAATTAGAAATAAATTCGGAAAAAAAAAGGAAAACGATATTTGAAGCGTGAAAAACTCTTC
AATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTGAGAAAAACTTT
TCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACATTTTTTTTCCCAACGAAATCGTGT
ACTAACCATCACGATTTTTGGCAAGAAAAACGCGTTCCGGAGTCTCGGCTAAATTTTGCATGATT
TTTGGCGCAAAGACTC
Found at i:22510 original size:322 final size:322
Alignment explanation
Indices: 22007--22749 Score: 1125
Period size: 322 Copynumber: 2.3 Consensus size: 322
21997 CGATTTAATT
* * *
22007 AGAAATTAATTCAG-AAAAAATGGAAAAACGATA-GTAGAAACGTGAAAAGCCCGTCAATCTTTT
1 AGAAATTAATTCGGAAAAAAATGGAAAAACGATATTTA-AAGCGTGAAAAGCCCGTCAATCTTTT
* ** *
22070 TGGTGTTGAATTATATATTTTTTCTGAA-TATTTTGCAAAAAATTTGAGCTTAAATGTTTCGGGT
65 TGGTGTTGAATTATATATTTTTTCT-AAGTATTTGGCAAAAAATTTGAGAATAAACGTTTCGGGT
* *
22134 CAGTTTTTAGCCGAAACTGTGTACTAACCATCACGGTTTTTGGCTAAAAACGCGTTTTCGGGCCA
129 CAGTTTTTAGCCGAAACTGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTTCCGGGCCA
22199 CGACTCTGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAA
194 CGACTCTGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAA
* *
22264 TCTCAACCTCATTGGATTTAAGGATTTGTTTTTAGGAGCATCTGAATCTTGTTTCAATTTAATT
259 TCTCAACCTCATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * *
22328 AGAAATTAATTCGGAAAAAAATGGGAAAACGATATTTAAAGCGTGAAAAGGCTGTCAATATTTTT
1 AGAAATTAATTCGGAAAAAAATGGAAAAACGATATTTAAAGCGTGAAAAGCCCGTCAATCTTTTT
22393 GGTGTTGAATTATATATTTTTTCTAAGTATTGTGGCAAAAAA-TTGAGAATAAACGTTTCGGGTC
66 GGTGTTGAATTATATATTTTTTCTAAGTATT-TGGCAAAAAATTTGAGAATAAACGTTTCGGGTC
*
22457 AGTTTTTAGCCGAAATTGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTTCCGGGCCAC
130 AGTTTTTAGCCGAAACTGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTTCCGGGCCAC
*
22522 GACTCTGTTTTGCATGATTTTTTGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAAT
195 GACTCTGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAAT
* *
22587 CTCAACCTCATTGGATTTAAGGATTTGTTTTTACGTGCATCTGAATTTTGTTTCGATTTAATT
260 CTCAACCTCATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
* * * * * **
22650 AGAAATTAATTTAGAAAAAAAAATATGAAAAACGATATTAAAAGCGTGAAAAGTCCACCAATCTT
1 AGAAATTAA-TTCG-GAAAAAAAT-GGAAAAACGATATTTAAAGCGTGAAAAGCCCGTCAATCTT
* * * * *
22715 TTTGGCGTTCAATTATATATATTTTATGAGTATTT
63 TTTGGTGTTGAATTATATATTTTTTCTAAGTATTT
22750 TTATCAAAAA
Statistics
Matches: 381, Mismatches: 34, Indels: 11
0.89 0.08 0.03
Matches are distributed among these distances:
321 15 0.04
322 282 0.74
323 14 0.04
324 9 0.02
325 61 0.16
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (322 bp):
AGAAATTAATTCGGAAAAAAATGGAAAAACGATATTTAAAGCGTGAAAAGCCCGTCAATCTTTTT
GGTGTTGAATTATATATTTTTTCTAAGTATTTGGCAAAAAATTTGAGAATAAACGTTTCGGGTCA
GTTTTTAGCCGAAACTGTGTACTAACCATCACGGTTTTTGACTAAAAACGCGTTTCCGGGCCACG
ACTCTGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTTTATTCATCTAATCAAATC
TCAACCTCATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT
Found at i:23747 original size:15 final size:15
Alignment explanation
Indices: 23727--23756 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
23717 ATCAATTGCA
23727 AAAAAAAAAAAAAGG
1 AAAAAAAAAAAAAGG
*
23742 AAAAAAGAAAAAAGG
1 AAAAAAAAAAAAAGG
23757 GCAGACTTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAAGG
Found at i:24241 original size:16 final size:16
Alignment explanation
Indices: 24207--24294 Score: 88
Period size: 16 Copynumber: 5.6 Consensus size: 16
24197 CGGGCTCGGG
**
24207 CGGGTTCGGG-TACTT
1 CGGGTTCGGGTTTTTT
24222 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
24238 CGGGTTCGGGTTTTTT
1 CGGGTTCGGGTTTTTT
* * * *
24254 CGGGCTCGTGTTATGT
1 CGGGTTCGGGTTTTTT
* * *
24270 CGGGTTTGAGTATTTT
1 CGGGTTCGGGTTTTTT
24286 CGGGTTCGG
1 CGGGTTCGG
24295 TCTCGAGTAG
Statistics
Matches: 58, Mismatches: 14, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
15 10 0.17
16 48 0.83
ACGTcount: A:0.05, C:0.15, G:0.39, T:0.42
Consensus pattern (16 bp):
CGGGTTCGGGTTTTTT
Found at i:24776 original size:31 final size:31
Alignment explanation
Indices: 24741--24812 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
24731 TAAATTATTG
*
24741 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
24772 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
24803 CAAATTAAAA
1 CAAATTAAAA
24813 GCTGATAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:25256 original size:17 final size:17
Alignment explanation
Indices: 25234--25266 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
25224 TCAAATTATT
25234 TCGGGTTCGGGCTCGGG
1 TCGGGTTCGGGCTCGGG
*
25251 TCGGGTTCGGTCTCGG
1 TCGGGTTCGGGCTCGG
25267 TCTCGGGTCG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.24, G:0.48, T:0.27
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGGG
Found at i:25266 original size:23 final size:23
Alignment explanation
Indices: 25240--25283 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
25230 TATTTCGGGT
*
25240 TCGGGCTCGGGTCGGGTTCGGTC
1 TCGGGCTCGGGTCGAGTTCGGTC
*
25263 TCGGTCTCGGGTCGAGTTCGG
1 TCGGGCTCGGGTCGAGTTCGG
25284 ATTGCCTCGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.02, C:0.25, G:0.45, T:0.27
Consensus pattern (23 bp):
TCGGGCTCGGGTCGAGTTCGGTC
Found at i:25958 original size:91 final size:91
Alignment explanation
Indices: 25803--25984 Score: 301
Period size: 91 Copynumber: 2.0 Consensus size: 91
25793 AGATCATGTG
* * *
25803 GAGAAATTATTAGGTGGACCGGATCCACCATGTCATCCGTGGTCTCAACCAATAAGATTTTGACA
1 GAGAAACTATTAGGTGGACCGGATCCACCACGTCATCCGTGGTCCCAACCAATAAGATTTTGACA
25868 AGTCAGATTTTTTCCTACAATTTCTA
66 AGTCAGATTTTTTCCTACAATTTCTA
* * *
25894 GAGAAACTATTAGGTGGATCGGGTCCACCACGTCATCCGTGGTCCCGACCAATAAGATTTTGACA
1 GAGAAACTATTAGGTGGACCGGATCCACCACGTCATCCGTGGTCCCAACCAATAAGATTTTGACA
*
25959 AGTCATATTTTTTCCTACAATTTCTA
66 AGTCAGATTTTTTCCTACAATTTCTA
25985 AAACCCTAGC
Statistics
Matches: 84, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 84 1.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (91 bp):
GAGAAACTATTAGGTGGACCGGATCCACCACGTCATCCGTGGTCCCAACCAATAAGATTTTGACA
AGTCAGATTTTTTCCTACAATTTCTA
Found at i:26871 original size:14 final size:13
Alignment explanation
Indices: 26851--26883 Score: 57
Period size: 14 Copynumber: 2.5 Consensus size: 13
26841 ATAGTAGTAG
26851 TATATATATAATA
1 TATATATATAATA
26864 TAATATATATAATA
1 T-ATATATATAATA
26878 TATATA
1 TATATA
26884 ATAGAGAACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 6 0.32
14 13 0.68
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
TATATATATAATA
Found at i:26873 original size:9 final size:9
Alignment explanation
Indices: 26851--26886 Score: 58
Period size: 9 Copynumber: 4.2 Consensus size: 9
26841 ATAGTAGTAG
26851 TATATAT-A
1 TATATATAA
26859 TA-ATATAA
1 TATATATAA
26867 TATATATAA
1 TATATATAA
26876 TATATATAA
1 TATATATAA
26885 TA
1 TA
26887 GAGAACAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 4 0.15
8 5 0.19
9 17 0.65
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
TATATATAA
Found at i:29454 original size:23 final size:23
Alignment explanation
Indices: 29424--29467 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
29414 TGGAGGAAGA
29424 GGGTTAGTGGTGACTGTTTTGAT
1 GGGTTAGTGGTGACTGTTTTGAT
*
29447 GGGTTAGTGGTGATTGTTTTG
1 GGGTTAGTGGTGACTGTTTTG
29468 GTGCATTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.11, C:0.02, G:0.41, T:0.45
Consensus pattern (23 bp):
GGGTTAGTGGTGACTGTTTTGAT
Found at i:31268 original size:29 final size:29
Alignment explanation
Indices: 31210--31268 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
31200 TATATATCTT
* *
31210 ATCTTATTTTACTATCTTACTACTATATA
1 ATCTTATCTTACTATCTTACTACTACATA
*
31239 ATCTTATCTTACTATCTTACTAGTACATA
1 ATCTTATCTTACTATCTTACTACTACATA
31268 A
1 A
31269 AATCACGAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.32, C:0.19, G:0.02, T:0.47
Consensus pattern (29 bp):
ATCTTATCTTACTATCTTACTACTACATA
Found at i:31711 original size:65 final size:65
Alignment explanation
Indices: 31607--31736 Score: 242
Period size: 65 Copynumber: 2.0 Consensus size: 65
31597 AAATCACGTT
*
31607 CCTATTTATAAAACGTGAAACAACACAACCTCTGGAAACCGTCTCCTAATTAAAAGGTATCTATC
1 CCTATTTATAAAACGTGAAACAACACAACCTCTGGAAACCGTCTCCTAACTAAAAGGTATCTATC
*
31672 CCTATTTATAAAACGTGAAACAACACAATCTCTGGAAACCGTCTCCTAACTAAAAGGTATCTATC
1 CCTATTTATAAAACGTGAAACAACACAACCTCTGGAAACCGTCTCCTAACTAAAAGGTATCTATC
31737 AGATAAAAGA
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.26
Consensus pattern (65 bp):
CCTATTTATAAAACGTGAAACAACACAACCTCTGGAAACCGTCTCCTAACTAAAAGGTATCTATC
Found at i:31840 original size:50 final size:50
Alignment explanation
Indices: 31782--31877 Score: 183
Period size: 50 Copynumber: 1.9 Consensus size: 50
31772 ATTTTCTTTA
31782 AGGAAAATAAAAAATTAAGACTTAGAATTTCTTAAGTCATCAAGGCACTT
1 AGGAAAATAAAAAATTAAGACTTAGAATTTCTTAAGTCATCAAGGCACTT
*
31832 AGGAAAATAAAAAATTAAGACTTGGAATTTCTTAAGTCATCAAGGC
1 AGGAAAATAAAAAATTAAGACTTAGAATTTCTTAAGTCATCAAGGC
31878 CCAAGTGCCC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 45 1.00
ACGTcount: A:0.46, C:0.11, G:0.16, T:0.27
Consensus pattern (50 bp):
AGGAAAATAAAAAATTAAGACTTAGAATTTCTTAAGTCATCAAGGCACTT
Found at i:32338 original size:37 final size:37
Alignment explanation
Indices: 32297--32371 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
32287 ATCTCTGGAA
32297 CGTCTGCACCAATTACATCACATATACTTATCTTGTG
1 CGTCTGCACCAATTACATCACATATACTTATCTTGTG
32334 CGTCTGCACCAATTACATCACATATACTTATCTTGTG
1 CGTCTGCACCAATTACATCACATATACTTATCTTGTG
32371 C
1 C
32372 CTCACAAGTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.27, C:0.28, G:0.11, T:0.35
Consensus pattern (37 bp):
CGTCTGCACCAATTACATCACATATACTTATCTTGTG
Found at i:33621 original size:24 final size:24
Alignment explanation
Indices: 33594--33642 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
33584 ATAGGTATTC
*
33594 TTTTTAG-TCATTTAACTTTTTTAT
1 TTTTTAGATCATTCAA-TTTTTTAT
*
33618 TTTTTAGATGATTCAATTTTTTAT
1 TTTTTAGATCATTCAATTTTTTAT
33642 T
1 T
33643 AATTATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 16 0.73
25 6 0.27
ACGTcount: A:0.22, C:0.06, G:0.06, T:0.65
Consensus pattern (24 bp):
TTTTTAGATCATTCAATTTTTTAT
Found at i:40216 original size:13 final size:13
Alignment explanation
Indices: 40195--40231 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
40185 GATAATTCTT
40195 TTTGACCCTCCAA
1 TTTGACCCTCCAA
*
40208 TTTGTCCCTCCAA
1 TTTGACCCTCCAA
*
40221 CTTGACCCTCC
1 TTTGACCCTCC
40232 TAATAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.16, C:0.43, G:0.08, T:0.32
Consensus pattern (13 bp):
TTTGACCCTCCAA
Found at i:40292 original size:40 final size:40
Alignment explanation
Indices: 40230--40310 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
40220 ACTTGACCCT
*
40230 CCTAATAATTAAGGAAATAAATTAAATCCAGGTTTAGCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
* *
40270 CCTAATAATTAAGGTAAGAAATTAAATCCAGGTTTATCCC
1 CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
40310 C
1 C
40311 TAGTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (40 bp):
CCTAATAATTAAGGAAAGAAATTAAATCCAGGTTTAGCCC
Found at i:41219 original size:3 final size:3
Alignment explanation
Indices: 41211--41270 Score: 120
Period size: 3 Copynumber: 20.0 Consensus size: 3
41201 ACTAACATAT
41211 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
41259 TTA TTA TTA TTA
1 TTA TTA TTA TTA
41271 AGCTTATTCG
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:43818 original size:19 final size:18
Alignment explanation
Indices: 43794--43839 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 18
43784 TACAAGTTAA
43794 TTTTAATTTATTCATATAT
1 TTTTAATTTATTCAT-TAT
43813 TTTTAATTTATTCATTAT
1 TTTTAATTTATTCATTAT
43831 TATTTAATT
1 T-TTTAATT
43840 ATAAAGTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 4 0.15
19 22 0.85
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.65
Consensus pattern (18 bp):
TTTTAATTTATTCATTAT
Found at i:45979 original size:12 final size:12
Alignment explanation
Indices: 45962--46004 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
45952 TTGAAATTGT
45962 TAAGGAACCATC
1 TAAGGAACCATC
*
45974 TAAGGAGCCATC
1 TAAGGAACCATC
* * *
45986 CAAGCAGCCATC
1 TAAGGAACCATC
45998 TAAGGAA
1 TAAGGAA
46005 GGAGAACCAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (12 bp):
TAAGGAACCATC
Found at i:46638 original size:27 final size:27
Alignment explanation
Indices: 46600--46655 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
46590 CTATCGGTCG
*
46600 ATACACTTACAATTAGTTAACAAGTCC
1 ATACACTTACAATTAGTTAACAACTCC
*
46627 ATACACTTACAATTAGTTAGCAACTCC
1 ATACACTTACAATTAGTTAACAACTCC
46654 AT
1 AT
46656 TGTCACACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.30
Consensus pattern (27 bp):
ATACACTTACAATTAGTTAACAACTCC
Found at i:52524 original size:30 final size:29
Alignment explanation
Indices: 52483--52571 Score: 97
Period size: 29 Copynumber: 2.9 Consensus size: 29
52473 ACCGTTTAAG
*
52483 AGGGACTAAAACGTCCAAAATTAAGAATTTA
1 AGGGA-TAAAACATCCAAAATTAA-AATTTA
*
52514 AGGGATAAAACATCCAAAATTAAAGTTTA
1 AGGGATAAAACATCCAAAATTAAAATTTA
* * *
52543 CGGAACAAAACATCCAAAATGTACAAATT
1 AGGGATAAAACATCCAAAAT-TA-AAATT
52572 CAGCCGCAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 22 0.44
30 19 0.38
31 9 0.18
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.21
Consensus pattern (29 bp):
AGGGATAAAACATCCAAAATTAAAATTTA
Found at i:52870 original size:21 final size:20
Alignment explanation
Indices: 52846--52916 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
52836 CTCGGTTTTT
52846 AAAAAACTACCCATTT-AAA
1 AAAAAACTACCCATTTAAAA
* * * *
52865 ACAAAACCACTCAATTAAAA
1 AAAAAACTACCCATTTAAAA
* *
52885 AGAAAACTACACATTTAAAA
1 AAAAAACTACCCATTTAAAA
52905 AAGAAAACTACC
1 AA-AAAACTACC
52917 ATAAACTACC
Statistics
Matches: 40, Mismatches: 10, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
19 12 0.30
20 20 0.50
21 8 0.20
ACGTcount: A:0.59, C:0.21, G:0.03, T:0.17
Consensus pattern (20 bp):
AAAAAACTACCCATTTAAAA
Found at i:53595 original size:115 final size:115
Alignment explanation
Indices: 53451--53681 Score: 426
Period size: 115 Copynumber: 2.0 Consensus size: 115
53441 CCATATTTTT
* *
53451 GTAACTTAGGGAAATTACTCACAAACCCTTTCAACTTTTAACCTAAAAAAACTTTTTCCCTCGAT
1 GTAACCTAGGGAAATTACTCACAAACCCTTTCAACTTTTAACCTAAAAAAACTTTTTCCCTCGAC
*
53516 AAATTACTCAATAATTCTTATGTTATATGTGGTTTGTGTTGAGTTTGTTG
66 AAATTACTCAATAATCCTTATGTTATATGTGGTTTGTGTTGAGTTTGTTG
53566 GTAACCTAGGGAAATTACTCACAAACCCTTTCAACTTTTAACCTAAAAAAACTTTTTCCCTCGAC
1 GTAACCTAGGGAAATTACTCACAAACCCTTTCAACTTTTAACCTAAAAAAACTTTTTCCCTCGAC
*
53631 AAATTACTCAATAATCCTTATGTTCTATGTGGTTTGTGTTGAGTTTGTTG
66 AAATTACTCAATAATCCTTATGTTATATGTGGTTTGTGTTGAGTTTGTTG
53681 G
1 G
53682 GTTATAAAAG
Statistics
Matches: 112, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
115 112 1.00
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (115 bp):
GTAACCTAGGGAAATTACTCACAAACCCTTTCAACTTTTAACCTAAAAAAACTTTTTCCCTCGAC
AAATTACTCAATAATCCTTATGTTATATGTGGTTTGTGTTGAGTTTGTTG
Found at i:56175 original size:48 final size:51
Alignment explanation
Indices: 56122--56226 Score: 153
Period size: 54 Copynumber: 2.1 Consensus size: 51
56112 AAAACCTTCC
*
56122 TTGAGGCATGATTGTTTAC-ATTATCTTAT-CT-TAAGATATATTATAGAA
1 TTGAGGCATGATTGTTTACTATTATCTTATAATATAAGATATATTATAGAA
56170 TTGAGGCATGATTGTTTACATTATTATCTTATAATAATAAGATATATTATAGAA
1 TTGAGGCATGATTGTTTAC--TATTATCTTATAAT-ATAAGATATATTATAGAA
56224 TTG
1 TTG
56227 CTATATATAT
Statistics
Matches: 50, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
48 19 0.38
51 10 0.20
52 1 0.02
54 20 0.40
ACGTcount: A:0.35, C:0.07, G:0.14, T:0.44
Consensus pattern (51 bp):
TTGAGGCATGATTGTTTACTATTATCTTATAATATAAGATATATTATAGAA
Found at i:56779 original size:2 final size:2
Alignment explanation
Indices: 56772--56812 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
56762 CATATGCATG
56772 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
56813 GCACAATTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:59591 original size:12 final size:12
Alignment explanation
Indices: 59574--59661 Score: 69
Period size: 12 Copynumber: 7.7 Consensus size: 12
59564 CTTTTAATAT
59574 TTATATATATAA
1 TTATATATATAA
* **
59586 TTATATATTTGT
1 TTATATATATAA
59598 TTATA-AT-TAA
1 TTATATATATAA
59608 TTATATATATAA
1 TTATATATATAA
59620 TT-TA-AT-TATA
1 TTATATATATA-A
* **
59630 TTATATATTTTT
1 TTATATATATAA
59642 TTATATATATAA
1 TTATATATATAA
*
59654 TTTTATAT
1 TTATATAT
59662 TTTGTTTTAT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
9 2 0.03
10 11 0.19
11 8 0.14
12 37 0.63
13 1 0.02
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (12 bp):
TTATATATATAA
Found at i:59613 original size:34 final size:33
Alignment explanation
Indices: 59574--59686 Score: 129
Period size: 34 Copynumber: 3.3 Consensus size: 33
59564 CTTTTAATAT
59574 TTATATATATAATTATATATTTGTTTATAATTAA
1 TTATATATATAATT-TATATTTGTTTATAATTAA
* * **
59608 TTATATATATAATTTA-ATTATATTATATATTTTT
1 TTATATATATAATTTATATT-TGTT-TATAATTAA
59642 TTATATATATAATTTTATATTTTGTTTTATAATTAA
1 TTATATATATAA-TTTATA-TTTG-TTTATAATTAA
59678 TTATATATA
1 TTATATATA
59687 ATATAATTAT
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
32 3 0.05
33 5 0.08
34 32 0.49
35 4 0.06
36 17 0.26
37 4 0.06
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (33 bp):
TTATATATATAATTTATATTTGTTTATAATTAA
Found at i:59614 original size:24 final size:24
Alignment explanation
Indices: 59587--59686 Score: 95
Period size: 24 Copynumber: 4.2 Consensus size: 24
59577 TATATATAAT
59587 TATATATTTGTTTATAATTAATTA
1 TATATATTTGTTTATAATTAATTA
**
59611 TATATA--TAATT-TAATTATATTA
1 TATATATTTGTTTATAATTA-ATTA
*
59633 TATAT-TTT-TTTATATATATAATTT
1 TATATATTTGTTTATA-AT-TAATTA
59657 TATAT-TTTGTTTTATAATTAATTA
1 TATATATTTG-TTTATAATTAATTA
59681 TATATA
1 TATATA
59687 ATATAATTAT
Statistics
Matches: 62, Mismatches: 5, Indels: 17
0.74 0.06 0.20
Matches are distributed among these distances:
21 6 0.10
22 14 0.23
23 3 0.05
24 29 0.47
25 4 0.06
26 6 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (24 bp):
TATATATTTGTTTATAATTAATTA
Found at i:59650 original size:14 final size:14
Alignment explanation
Indices: 59608--59705 Score: 53
Period size: 12 Copynumber: 6.9 Consensus size: 14
59598 TTATAATTAA
59608 TTATATATATAATTT
1 TTATATATATAA-TT
*
59623 AATTATATTATATATTTTT
1 --TTATA-TATATA--ATT
59642 TTATATATATAATT
1 TTATATATATAATT
**
59656 TTATAT-T-TTGTT
1 TTATATATATAATT
59668 TTATA-AT-TAATT
1 TTATATATATAATT
*
59680 ATATATAATATAATT
1 TTATAT-ATATAATT
*
59695 ATA-ATATATAA
1 TTATATATATAA
59706 ATTTCCATTC
Statistics
Matches: 67, Mismatches: 7, Indels: 18
0.73 0.08 0.20
Matches are distributed among these distances:
12 16 0.24
13 7 0.10
14 12 0.18
15 8 0.12
16 6 0.09
17 10 0.15
18 6 0.09
19 2 0.03
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (14 bp):
TTATATATATAATT
Found at i:59683 original size:68 final size:68
Alignment explanation
Indices: 59573--59704 Score: 205
Period size: 68 Copynumber: 1.9 Consensus size: 68
59563 TCTTTTAATA
* *
59573 TTTATATATATAATTATATATTTGTTTATAATTAATTATATATATAATTTAATTATATTATATAT
1 TTTATATATATAATTATATATTTGTTTATAATTAATTATATATATAATATAATTATAATATATAT
59638 TTT
66 TTT
*
59641 TTTATATATATAATTTTATATTTTGTTTTATAATTAA-T-TATATATAATATAATTATAATATAT
1 TTTATATATATAATTATATA-TTTG-TTTATAATTAATTATATATATAATATAATTATAATATAT
59704 A
64 A
59705 AATTTCCATT
Statistics
Matches: 59, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
68 43 0.73
69 5 0.08
70 11 0.19
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (68 bp):
TTTATATATATAATTATATATTTGTTTATAATTAATTATATATATAATATAATTATAATATATAT
TTT
Found at i:59687 original size:34 final size:34
Alignment explanation
Indices: 59577--59688 Score: 104
Period size: 36 Copynumber: 3.3 Consensus size: 34
59567 TTAATATTTA
*
59577 TATATATAATTATATA-TTTG-TTTATAATTAAT
1 TATATATAATTTTATATTTTGTTTTATAATTAAT
* * * * * **
59609 TATATATATAATTTA-ATTATATTATATATTTTTTT
1 TATATATA-ATTTTATATTTTGTTTTATA-ATTAAT
59644 ATATATATAATTTTATATTTTGTTTTATAATTAAT
1 -TATATATAATTTTATATTTTGTTTTATAATTAAT
59679 TATATATAAT
1 TATATATAAT
59689 ATAATTATAA
Statistics
Matches: 59, Mismatches: 15, Indels: 10
0.70 0.18 0.12
Matches are distributed among these distances:
32 9 0.15
33 6 0.10
34 15 0.25
35 11 0.19
36 18 0.31
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (34 bp):
TATATATAATTTTATATTTTGTTTTATAATTAAT
Found at i:59695 original size:15 final size:15
Alignment explanation
Indices: 59669--59705 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
59659 TATTTTGTTT
59669 TATAAT-TAATTATA
1 TATAATATAATTATA
59683 TATAATATAATTATA
1 TATAATATAATTATA
59698 -AT-ATATAA
1 TATAATATAA
59706 ATTTCCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.27
14 8 0.36
15 8 0.36
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
TATAATATAATTATA
Found at i:59739 original size:21 final size:21
Alignment explanation
Indices: 59713--59757 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
59703 TAAATTTCCA
*
59713 TTCGGTTTCGGTTTGGTCGGT
1 TTCGGTTTCGGTTTGGTCAGT
*
59734 TTCGGTTTTGGTTTGGTCAGT
1 TTCGGTTTCGGTTTGGTCAGT
59755 TTC
1 TTC
59758 ATAGTTAGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.02, C:0.13, G:0.33, T:0.51
Consensus pattern (21 bp):
TTCGGTTTCGGTTTGGTCAGT
Found at i:72771 original size:30 final size:30
Alignment explanation
Indices: 72735--72797 Score: 126
Period size: 30 Copynumber: 2.1 Consensus size: 30
72725 CTCCTTTGCA
72735 TGTTATTTGGGTTTTGTGGTTGTTCCTAAG
1 TGTTATTTGGGTTTTGTGGTTGTTCCTAAG
72765 TGTTATTTGGGTTTTGTGGTTGTTCCTAAG
1 TGTTATTTGGGTTTTGTGGTTGTTCCTAAG
72795 TGT
1 TGT
72798 AAGCTTCTCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.10, C:0.06, G:0.30, T:0.54
Consensus pattern (30 bp):
TGTTATTTGGGTTTTGTGGTTGTTCCTAAG
Found at i:75626 original size:20 final size:20
Alignment explanation
Indices: 75597--75636 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
75587 TCACGAATAG
*
75597 GCTTCTTAGTTCATTAAGCA
1 GCTTCGTAGTTCATTAAGCA
75617 GCTTCGTAGTTCATTAAGCA
1 GCTTCGTAGTTCATTAAGCA
75637 CAATAACATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.25, C:0.20, G:0.17, T:0.38
Consensus pattern (20 bp):
GCTTCGTAGTTCATTAAGCA
Found at i:83803 original size:73 final size:73
Alignment explanation
Indices: 83684--83823 Score: 246
Period size: 73 Copynumber: 1.9 Consensus size: 73
83674 ATTTATTTCC
83684 TTATTAGAAGGGTCAAGTTGGAGGGACAAATTGGAGAGTTCCTTATCACATCAAAGCAACTTCAC
1 TTATTAGAAGGGTCAAGTTGGAGGGACAAATTGGAGAGTTCCTTATCACATCAAAGCAACTTCAC
83749 ATCCTTAA
66 ATCCTTAA
* *
83757 TTATTAGGAGGGTCAAGTTGGAGTGACAAATTGGAG-GATTCCTTATCACATCAAAGCAACTTCA
1 TTATTAGAAGGGTCAAGTTGGAGGGACAAATTGGAGAG-TTCCTTATCACATCAAAGCAACTTCA
83821 CAT
65 CAT
83824 TTGCAGCCAT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
72 1 0.02
73 63 0.98
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (73 bp):
TTATTAGAAGGGTCAAGTTGGAGGGACAAATTGGAGAGTTCCTTATCACATCAAAGCAACTTCAC
ATCCTTAA
Found at i:113896 original size:13 final size:12
Alignment explanation
Indices: 113878--113916 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 12
113868 TTTAATACTC
*
113878 TAATAATTACTA
1 TAATAATTAATA
113890 TACATAATTAATA
1 TA-ATAATTAATA
113903 TAATAA-TAATA
1 TAATAATTAATA
113914 TAA
1 TAA
113917 AATATTTTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
11 8 0.32
12 6 0.24
13 11 0.44
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (12 bp):
TAATAATTAATA
Found at i:119989 original size:21 final size:21
Alignment explanation
Indices: 119960--120010 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
119950 TCCCGCCGCC
*
119960 GTCCGATGATCAAGATGAGGT
1 GTCCGATGATCAAGATGAGCT
*
119981 GTCTGATGATCAAGATGAGCT
1 GTCCGATGATCAAGATGAGCT
120002 GTCCGATGA
1 GTCCGATGA
120011 GGCATTGATA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (21 bp):
GTCCGATGATCAAGATGAGCT
Found at i:125987 original size:2 final size:2
Alignment explanation
Indices: 125980--126008 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
125970 ATTTATGGAG
125980 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
126009 AAGTCTTATG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:136846 original size:130 final size:130
Alignment explanation
Indices: 136607--136994 Score: 668
Period size: 130 Copynumber: 3.0 Consensus size: 130
136597 GAAGCTCTTG
* * *
136607 CATCTTTTTCGGTATACATATTGGCGAGGAAGGGGAGACTAGAATTCAAATTCCAACCCTTAGAG
1 CATCTTTTTCGGTATACATATTGGCGAGGAAGGGGAGACTAGAATCCAAATTCCAACCCCTAGAA
* * *
136672 CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTTTAGACTGAGCACTCAGTTTTTTCATCTTTTG
66 CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTCTAGACTGAGCACTCAGATTTTTCATCTTTTA
* * *
136737 TATCTTTTTCGGTATACATATTGACGAGAAAGGGGAGACTAGAATCCAAATTCCAACCCCTAGAA
1 CATCTTTTTCGGTATACATATTGGCGAGGAAGGGGAGACTAGAATCCAAATTCCAACCCCTAGAA
* *
136802 CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTCTAGACAGAGCACTCAGCTTTTTCATCTTTTA
66 CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTCTAGACTGAGCACTCAGATTTTTCATCTTTTA
136867 CATCTTTTTCGGTATACATATTGGCGAGGAAGGGGAGACTAGAATCCAAATTCCAACCCCTAGAA
1 CATCTTTTTCGGTATACATATTGGCGAGGAAGGGGAGACTAGAATCCAAATTCCAACCCCTAGAA
*
136932 CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTCTAGACTGAGCACTCAAATTTTTCATCTTT
66 CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTCTAGACTGAGCACTCAGATTTTTCATCTTT
136995 GCTACTTAAT
Statistics
Matches: 242, Mismatches: 16, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
130 242 1.00
ACGTcount: A:0.28, C:0.23, G:0.18, T:0.32
Consensus pattern (130 bp):
CATCTTTTTCGGTATACATATTGGCGAGGAAGGGGAGACTAGAATCCAAATTCCAACCCCTAGAA
CGTTTTAATGAACTCCCTAAGCCTCTGGCTACTCTAGACTGAGCACTCAGATTTTTCATCTTTTA
Found at i:138132 original size:3 final size:3
Alignment explanation
Indices: 138124--138158 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
138114 CAAGGGCTAT
138124 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
138159 GTTGTTGTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:138163 original size:3 final size:3
Alignment explanation
Indices: 138157--138182 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
138147 ATTATTATTA
138157 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
138183 ATATATACTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:138825 original size:53 final size:52
Alignment explanation
Indices: 138739--138838 Score: 148
Period size: 53 Copynumber: 1.9 Consensus size: 52
138729 ATCATTTGTG
*
138739 TATTCAATATTCATGTGTAAACTCAGGTCCAAATTTTAAAAAACTGTCGGGTC
1 TATTCAATATTCATATGTAAACTCAGGTCCAAA-TTTAAAAAACTGTCGGGTC
* *
138792 TATTCAATATTCATATGTAAA-TCTAGGTTCAAATTTAAAAAATTGTC
1 TATTCAATATTCATATGTAAACTC-AGGTCCAAATTTAAAAAACTGTC
138839 TCCACGCAGA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
52 15 0.35
53 28 0.65
ACGTcount: A:0.37, C:0.14, G:0.12, T:0.37
Consensus pattern (52 bp):
TATTCAATATTCATATGTAAACTCAGGTCCAAATTTAAAAAACTGTCGGGTC
Done.