Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020728.1 Corchorus olitorius cultivar O-4 contig20761, 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: 50201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.34
Found at i:607 original size:333 final size:328
Alignment explanation
Indices: 69--1571 Score: 1312
Period size: 333 Copynumber: 4.5 Consensus size: 328
59 ATACTTCTTA
* * * * *
69 AAATATCTATATTCAAT-TAATCAAATCTCAGCCACATTGAATTTAAGGATTTATTTTTACGAGC
1 AAATATTTATATTC-ATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGC
* * * *
133 ATGTGAATCTTGTTTCGATTTAATTAGAAATTAATTT-AGAAAAATATGAAAAATGATAATAAAA
65 ATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGA-AAAAATAGGAAAAACGATATTAAAA
* * * * * *
197 GCGCGAAAAGTCC-TCAAATATTTTTTGCGTTGAATTATATATATTTTATGAGTATTGTGGC-A-
129 GCGTGAAAAGCCCTTC-AATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACTAG
*
259 ATAATTAAGGAAAAAT-ATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATTAC
193 A-AATTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACC-TTAC
* * *
323 GATTTTTTTTTTTTTTGGTTAAAAACACGTTCTGAGGGCTCAAGTCAGTTTTGCATTATTTTTTT
256 G----TTTTTTTTTTTGGCTAAAAACGCGTTCTG-GGG-TCAAGTCAGTTTTGCATGATTTTTTT
*
388 GGCAAAAATCCTTG
315 GGCAAAACTCCTTG
* *
402 AAATATTTATATTCATCTAACCAAATCTTAGCCATATTGGATTTAAGGATTTGTTTTTACAAGCA
1 AAATATTTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* *
467 TTTGAAT-TATGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAA
66 TCTGAATCT-TGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAG
* * * * *
531 CATGAGAAGCCCTTCGATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGGCTTGAA
130 CGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACTAGAA
* * * *
596 ATTGA-GAAAAAT-ATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAGTCATGTACCTTCACGG
195 ATTGAGGAAAAATCA-TTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCTT-ACGT
* * * * * **
659 TTTTTTTTTT-GCTAAAAACGTGTTCCGGGGTCCTAGGTCAGTTTTCCATGATTTTTGGTGTTAA
258 TTTTTTTTTTGGCTAAAAACGCGTTCTGGGGT-C-AAGTCAGTTTTGCATGATTTTT-TTGGCAA
*
723 AACTCCTTA
320 AACTCCTTG
* * *
732 AAATATATCTATATTAATCTAACCAAATCTCT-GCCACATTGTATTTAAGGATTTGTTTTTATGA
1 AAATAT-T-TATATTCATCTAACCAAATCT-TAGCCACATTGGATTTAAGGATTTGTTTTTACGA
* * * ** *
796 GTATCTAAATCTTGTTTCGATTTAATCAGAAATTAATACGGAAATAAAAATAGGAAAAACAATAT
63 GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT-TTG--A-AAAAATAGGAAAAACGATAT
* * * * * * * *
861 TAGAAGCGTGGAAAAGGCTTTCAAGT-TGTTTGTCGTTGAATCATATA-TTTTTATGAGCATTTT
124 TAAAAGCGT-GAAAAGCCCTTCAA-TCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT
* * *
924 CACTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTAGCAAAATTTTAGCCGAAATCGTGTA-C
187 GACTAGAAATTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACC
* * ***** *** *
988 TAACCATCACGGTTTTTGGCTAAAAACGCGTT-TCGAGACCCAACTCAGTTTTGCATGATTTTTT
252 TTA-CGTTTTTTTTTTTGGCTAAAAACGCGTTCT-G-GGGTCAAGTCAGTTTTGCATGATTTTTT
1052 AT-GCAAAGACTCCTTG
314 -TGGCAAA-ACTCCTTG
* * * *
1068 AAATATCTATATTCATCTAACCAAATCTTAGTCATATTGGATTTAAGGATTTGTTTTTACGAGTA
1 AAATATTTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
* * * * * * *
1133 TCCGCATCTTGTTTCGATTTAATTAG-AA-TAATTCGGAAAAAAAAACAAGAAAAACAATATTAG
66 TCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TG---AAAAAATAGGAAAAACGATATTAA
* * *** * * * *
1196 AAGCGTTAAAAGCCCCTCAATCTTTTTTATGTTGAATTATATATTTTTTGTGGGTATTTTAGACA
127 AAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT-GACT
* * * * * *
1261 AGAAATTGAGGAAATATCTTTTGAGTCAATTTTTGTAAAATTTTAGCCGAAATTGTGTACACCAT
191 AGAAATTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT--ACC-T
* * * *
1326 CACG-----CTTTTTGGCTAAAAACGCGTTCTGGGGTCACGGCTCTGTTTTGCATGA-TTTTTTG
253 TACGTTTTTTTTTTTGGCTAAAAACGCGTTCTGGGGTCA-AG-TCAGTTTTGCATGATTTTTTTG
* *
1385 CGCCGAGACTCCTTG
316 -G-CAAAACTCCTTG
* * * * * * *
1400 AAATATCTT-TATTTATCTAATCAAATCTCAGGCACATTTGAATTAAGGATTTATTTTTAC-ATG
1 AAATAT-TTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGA-G
* * * * *
1463 CATCTGAATCTTGTTTCAATTTAATTAGAAACTAATTCTGAAAAAATATGAAAGACGATATTAGA
64 CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATT-TGAAAAAATAGGAAAAACGATATTAAA
** * **
1528 AGCGTGAAAAGATCTCCAATCTTTTTTACGTTGAATTTATATAT
128 AGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAA-TTATATAT
1572 ATATATATAT
Statistics
Matches: 962, Mismatches: 158, Indels: 101
0.79 0.13 0.08
Matches are distributed among these distances:
327 1 0.00
328 4 0.00
329 32 0.03
330 32 0.03
331 104 0.11
332 233 0.24
333 237 0.25
334 130 0.14
335 7 0.01
336 92 0.10
337 88 0.09
338 2 0.00
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (328 bp):
AAATATTTATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACGAGCA
TCTGAATCTTGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAAACGATATTAAAAGC
GTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGTGACTAGAAA
TTGAGGAAAAATCATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCTTACGTTTT
TTTTTTTGGCTAAAAACGCGTTCTGGGGTCAAGTCAGTTTTGCATGATTTTTTTGGCAAAACTCC
TTG
Found at i:1427 original size:332 final size:329
Alignment explanation
Indices: 1--1571 Score: 1398
Period size: 332 Copynumber: 4.7 Consensus size: 329
* * * * * * *
1 TTTTTGGCTAAAAACGCGTT-TCGGGG-CCCGACTTAGTCTTGCATGATTTTTGGCGCCGATACT
1 TTTTTGGCTAAAAACGCGTTCT-GGGGTCACGGCTCAGTTTTGCATGATTTTTTGCGCCAAAACT
* * * * * *
64 TCTTAAAATATCTATATTCAAT-TAATCAAATCTCAGCCACATTGAATTTAAGGATTTATTTTTA
65 CCTTGAAATATCTATATT-AATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTA
* * * * *
128 CGAGCATGTGAATCTTGTTTCGATTTAATTAGAAATTAATT--TAGAAAAATATGAAAAATGATA
129 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATA
* * * * * *
191 ATAAAAGCGCGAAAAGTCCTCAAATATTTTTTGCGTTGAATTATATATATTTTATGAGTATTGTG
194 TTAGAAGCGTGAAAAGCCCTC-AATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTGTG
* * * *
256 GCAA-TAATTAAGGAAAAAT-ATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCA
258 ACAAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCA
*
319 TTACGATTTTTTTTT
323 TCACG--------TT
* * * *
334 TTTTTGGTTAAAAACACGTTCTGAGGGCTCA-AG-TCAGTTTTGCATTATTTTTTTG-G-CAAAA
1 TTTTTGGCTAAAAACGCGTTCTG-GGG-TCACGGCTCAGTTTTGCATGA-TTTTTTGCGCCAAAA
* * * *
395 ATCCTTGAAATATTTATATTCATCTAACCAAATCTTAGCCATATTGGATTTAAGGATTTGTTTTT
63 CTCCTTGAAATATCTATATTAATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTT
* * *
460 ACAAGCATTTGAAT-TATGTTTCGATTTAATTAGAAATTAATT-TG-AAAAAATAGGAAAAACGA
128 ACGAGCATCTGAATCT-TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGA
* * * * * *
522 TATTAAAAACATGAGAAGCCCTTCGATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTG
192 TATTAGAAGCGTGAAAAGCCC-TCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTG
* ** * * * *
587 TGGCTTGAAATTGA-GAAAAATATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAGTCATGTAC
256 TGACAAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTAC
*
651 CTTCACGGTTTT
321 CATCAC-G--TT
* * * * * * **
663 TTTTTTGCTAAAAACGTGTTCCGGGGTC-CTAGG-TCAGTTTTCCATGATTTTTGGTGTTAAAAC
1 TTTTTGGCTAAAAACGCGTTCTGGGGTCAC--GGCTCAGTTTTGCATGATTTTTTGCGCCAAAAC
* *
726 TCCTTAAAATATATCTATATTAATCTAACCAAATCTCT-GCCACATTGTATTTAAGGATTTGTTT
64 TCCTT-GAA-ATATCTATATTAATCTAACCAAATCT-TAGCCACATTGGATTTAAGGATTTGTTT
* * * * *
790 TTATGAGTATCTAAATCTTGTTTCGATTTAATCAGAAATTAATACGGAAATAAAAATAGGAAAAA
126 TTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AA-AAAAATAGGAAAAA
* ** * * *
855 CAATATTAGAAGCGTGGAAAAGGCTTTCAA-GTTGTTTGTCGTTGAATCATATA-TTTTTATGAG
189 CGATATTAGAAGCGT-GAAAA-GCCCTCAATCTTTTTTG-CGTTGAATTATATATTTTTTATGAG
* * * * *
918 CATTTTCACTAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTAGCAAAATTTTAGCCGAAATCG
251 TATTGTGACAAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCG
*
983 TGTACTAACCATCACG-G
316 TG---T-ACCATCACGTT
* * * * ** **
1000 TTTTTGGCTAAAAACGCGTT-TCGAGACCCAACTCAGTTTTGCATGATTTTTTATG-CAAAGACT
1 TTTTTGGCTAAAAACGCGTTCTGGGGTCACGGCTCAGTTTTGCATGATTTTTTGCGCCAAA-ACT
* * *
1063 CCTTGAAATATCTATATTCATCTAACCAAATCTTAGTCATATTGGATTTAAGGATTTGTTTTTAC
65 CCTTGAAATATCTATATTAATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTAC
* * * * * *
1128 GAGTATCCGCATCTTGTTTCGATTTAATTAG-AA-TAATTCGGAAAAAAAAACAAGAAAAACAAT
130 GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG--AAAAAAATAGGAAAAACGAT
* ** * * *
1191 ATTAGAAGCGTTAAAAGCCCCTCAATCTTTTTTATGTTGAATTATATATTTTTTGTGGGTATTTT
193 ATTAGAAGCGTGAAAAG-CCCTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTGT
* * * * *
1256 AGACAAGAAATTGAGGAAATATCTTTTGAGTCAATTTTTGTAAAATTTTAGCCGAAATTGTGTAC
257 -GACAAGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT--
*
1321 ACCATCACG-C
319 ACCATCACGTT
* * *
1331 TTTTTGGCTAAAAACGCGTTCTGGGGTCACGGCTCTGTTTTGCATGATTTTTTGCGCCGAGACTC
1 TTTTTGGCTAAAAACGCGTTCTGGGGTCACGGCTCAGTTTTGCATGATTTTTTGCGCCAAAACTC
* * * * * * * *
1396 CTTGAAATATCTTTATTTATCTAATCAAATCTCAGGCACATTTGAATTAAGGATTTATTTTTAC-
66 CTTGAAATATCTATATTAATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACG
* * * * *
1460 ATGCATCTGAATCTTGTTTCAATTTAATTAGAAACTAATTCTG-AAAAAATATGAAAGACGATAT
131 A-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATAT
** *
1524 TAGAAGCGTGAAAAGATCTCCAATCTTTTTTACGTTGAATTTATATAT
195 TAGAAGCGTGAAAAGCCCT-CAATCTTTTTTGCGTTGAA-TTATATAT
1572 ATATATATAT
Statistics
Matches: 1014, Mismatches: 174, Indels: 101
0.79 0.13 0.08
Matches are distributed among these distances:
327 2 0.00
328 9 0.01
329 36 0.04
330 13 0.01
331 102 0.10
332 256 0.25
333 256 0.25
334 150 0.15
335 13 0.01
336 85 0.08
337 81 0.08
338 2 0.00
340 2 0.00
341 7 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (329 bp):
TTTTTGGCTAAAAACGCGTTCTGGGGTCACGGCTCAGTTTTGCATGATTTTTTGCGCCAAAACTC
CTTGAAATATCTATATTAATCTAACCAAATCTTAGCCACATTGGATTTAAGGATTTGTTTTTACG
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT
AGAAGCGTGAAAAGCCCTCAATCTTTTTTGCGTTGAATTATATATTTTTTATGAGTATTGTGACA
AGAAATTGAGGAAAAATCTTTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATCA
CGTT
Found at i:1427 original size:666 final size:656
Alignment explanation
Indices: 1--1538 Score: 1631
Period size: 666 Copynumber: 2.3 Consensus size: 656
* * * *
1 TTTTTGGCTAAAAACGCGTT-TCGGGGCCCGACT-TAGTCTTGCATGATTTTTGGCGCCGATACT
1 TTTTTGGCTAAAAACGCGTTCT-GGGGTCCGGCTCT-GTTTTGCATGATTTTTGGCGCCGAAACT
* *
64 TCTTAAAATATCTATATTCAAT-TAATCAAATCTCAGCCACATTGAATTTAAGGATTTATTTTTA
64 CCTTAAAATATCTATATT-AATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTATTTTTA
* ** * *
128 CGAGCATGTGAATCTTGTTTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAATGATAAT
128 -GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATCGA-AAAAATATGAAAAACGATATT
* * * * * * **
193 AAAAGCGCGAAAAGTCCTCAAATATTTTTTGCGTTGAATTATATATATTTTATGAGTATTGTGGC
191 AGAAGCGTGAAAAGGCCTCAAATATTTTGTGCGTTGAATCATATATATTTTATGAGCATTGTCAC
* *
258 AATAATTAAGGAAAAATATTCGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCATTAC
256 AATAATTAAGGAAAAATATTCGGGTCAATTTTAGCAAAATTTTAGCCGAAATCGTGTACCATAAC
* ***** * * * * *
323 GATTTTTTTTTTTTTTGGTTAAAAACACGTTCTGAGGGCTCAAGTCAGTTTTGCATTATTTTTTT
321 CA--TTCACGGTTTTTGGCTAAAAACACGTTCTGAGGACCCAACTCAGTTTTGCATGATTTTTTT
*
388 GGCAAAAATCCTTGAAATATTTATATTCATCTAACCAAATCTTAGCCATATTGGATTTAAGGATT
384 GGCAAAAATCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCATATTGGATTTAAGGATT
** * * *
453 TGTTTTTACAAGCATTTGAATTATGTTTCGATTTAATTAGAAATTAATTTGAAAAAATAGGAAAA
449 TGTTTTTACAAGCATCCGAATTATGTTTCGATTTAATTAGAAATTAATTGGAAAAAACAAGAAAA
* * * * *
518 ACGATATTAAAAACATGAGAAGCCCTTCGATCTTTTTGGCGTTGAATTATATATTTTTTATGAGT
514 ACAATATTAAAAACATGAAAAGCCCCTCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGT
* ** * *
583 ATTGTGGCTTGAAATTGAGAAAAATATTTCGGGTCAATTTTTGTAAAATTTTAGCCGAAGTCATG
579 ATTGTGACAAGAAATTGAGAAAAATATTTCGAGTCAATTTTTGTAAAATTTTAGCCGAAATCATG
* *
648 TACCTTCACGGTTTT
644 TACCATCACGG--TC
* * * * * * ***
663 TTTTTTGCTAAAAACGTGTTCCGGGGTCCTAGG-TCAGTTTTCCATGATTTTTGGTGTTAAAACT
1 TTTTTGGCTAAAAACGCGTTCTGGGGTCC--GGCTCTGTTTTGCATGATTTTTGGCGCCGAAACT
* * *
727 CCTTAAAATATATCTATATTAATCTAACCAAATCTCTGCCACATTGTATTTAAGGATTTGTTTTT
64 CCTT-AAA-ATATCTATATTAATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTATTTTT
* * * * *
792 ATGAGTATCTAAATCTTGTTTCGATTTAATCAGAAATTAATACGGAAATAAAAATAGGAAAAACA
127 A-GAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAT-C-G--A-AAAAATATGAAAAACG
* *
857 ATATTAGAAGCGTGGAAAAGGCTTTCAAGT-TGTTTGT-CGTTGAATCATATAT-TTTTATGAGC
186 ATATTAGAAGCGT-GAAAAGGC-CTCAAATAT-TTTGTGCGTTGAATCATATATATTTTATGAGC
* * *
919 ATTTTCACTAGA-AATTGAGGAAAAATCTTTCGGGTCAATTTTAGCAAAATTTTAGCCGAAATCG
248 ATTGTCAC-A-ATAATTAAGGAAAAAT-ATTCGGGTCAATTTTAGCAAAATTTTAGCCGAAATCG
*
983 TGTA-C-TAACCA-TCACGGTTTTTGGCTAAAAACGCGTT-TCGA-GACCCAACTCAGTTTTGCA
310 TGTACCATAACCATTCACGGTTTTTGGCTAAAAACACGTTCT-GAGGACCCAACTCAGTTTTGCA
* *
1043 TGATTTTTTAT-GCAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTTAGTCATATTG
374 TGATTTTTT-TGGCAAA-AATCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCATATTG
* * *
1107 GATTTAAGGATTTGTTTTTACGAGTATCCGCATCT-TGTTTCGATTTAATTAG-AA-TAATTCGG
437 GATTTAAGGATTTGTTTTTACAAGCATCCGAAT-TATGTTTCGATTTAATTAGAAATTAATT-GG
* * * * * *
1169 AAAAAAAAACAAGAAAAACAATATTAGAAGCGTTAAAAGCCCCTCAATCTTTTTTATGTTGAATT
500 ---AAAAAACAAGAAAAACAATATTAAAAACATGAAAAGCCCCTCAATCTTTTTGACGTTGAATT
* * * * * *
1234 ATATATTTTTTGTGGGTATTTTAGACAAGAAATTGAGGAAATATCTTTTGAGTCAATTTTTGTAA
562 ATATATTTTTTATGAGTATTGT-GACAAGAAATTGA-GAAAAATATTTCGAGTCAATTTTTGTAA
**
1299 AATTTTAGCCGAAATTGTGTACACCATCAC-G-C
625 AATTTTAGCCGAAATCATGT--ACCATCACGGTC
* *
1331 TTTTTGGCTAAAAACGCGTTCTGGGGTCACGGCTCTGTTTTGCATGATTTTTTGCGCCGAGACTC
1 TTTTTGGCTAAAAACGCGTTCTGGGGTC-CGGCTCTGTTTTGCATGATTTTTGGCGCCGAAACTC
* * * * * *
1396 CTTGAAATATCTTTATTTATCTAATCAAATCTCAGGCACATT-TGAATTAAGGATTTATTTTTAC
65 CTTAAAATATCTATATTAATCTAATCAAATCTCAGCCACATTGT-ATTTAAGGATTTATTTTTAG
* * *
1460 ATGCATCTGAATCTTGTTTCAATTTAATTAGAAACTAATTCTGAAAAAATATGAAAGACGATATT
129 A-GCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA-TC-GAAAAAATATGAAAAACGATATT
1525 AGAAGCGTGAAAAG
191 AGAAGCGTGAAAAG
1539 ATCTCCAATC
Statistics
Matches: 719, Mismatches: 123, Indels: 68
0.79 0.14 0.07
Matches are distributed among these distances:
662 30 0.04
663 51 0.07
664 13 0.02
665 119 0.17
666 192 0.27
667 6 0.01
668 120 0.17
669 53 0.07
670 78 0.11
671 50 0.07
672 7 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (656 bp):
TTTTTGGCTAAAAACGCGTTCTGGGGTCCGGCTCTGTTTTGCATGATTTTTGGCGCCGAAACTCC
TTAAAATATCTATATTAATCTAATCAAATCTCAGCCACATTGTATTTAAGGATTTATTTTTAGAG
CATCTGAATCTTGTTTCGATTTAATTAGAAATTAATCGAAAAAATATGAAAAACGATATTAGAAG
CGTGAAAAGGCCTCAAATATTTTGTGCGTTGAATCATATATATTTTATGAGCATTGTCACAATAA
TTAAGGAAAAATATTCGGGTCAATTTTAGCAAAATTTTAGCCGAAATCGTGTACCATAACCATTC
ACGGTTTTTGGCTAAAAACACGTTCTGAGGACCCAACTCAGTTTTGCATGATTTTTTTGGCAAAA
ATCCTTGAAATATCTATATTCATCTAACCAAATCTTAGCCATATTGGATTTAAGGATTTGTTTTT
ACAAGCATCCGAATTATGTTTCGATTTAATTAGAAATTAATTGGAAAAAACAAGAAAAACAATAT
TAAAAACATGAAAAGCCCCTCAATCTTTTTGACGTTGAATTATATATTTTTTATGAGTATTGTGA
CAAGAAATTGAGAAAAATATTTCGAGTCAATTTTTGTAAAATTTTAGCCGAAATCATGTACCATC
ACGGTC
Found at i:1570 original size:2 final size:2
Alignment explanation
Indices: 1565--1589 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1555 ACGTTGAATT
1565 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 T
1590 TATGATTATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10895 original size:334 final size:330
Alignment explanation
Indices: 10165--13815 Score: 2732
Period size: 335 Copynumber: 11.1 Consensus size: 330
10155 AAATCCTTAA
* * * * * *
10165 CTTAAATCCAATGTGGCTAAGATTTGGTCAAATGAATATAGATATTTCAAGGAGTTTTGCCA-CC
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTG-GAGCC
* * * * * *
10229 AAAAATCATGCAAAACTAACCCGAGGTCCCGGAATGAGTTTTTAACCAAAAAAACC--G-TGATT
65 AAAAATCATGCAAAACTAAGCCG-GGGCCCGAAACGCGTTTTTAGCC-AAAAAACCGTGATGATT
* * * * ** * * *
10291 GGTACACGATTTTGACTAAAATTTTACAAACTTTGACCCGAAATATGTTTCCTCAATTTTTAGCC
128 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATAT-TTTCCTCAATTTTTGGCT
* * * * * *
10356 ACAGTACTCATAAATTATATATAATTCAACGCAAAAAAGATTTGA-GAATTTCTCACGCTTTTAA
192 AAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTT-TCACGCTTTTAA
* * *
10420 TATCATTTTTCATATTTTTCTGAAT--TAA-TTCTAA-TAAATCGAAACAAGATTCAAATGCTCG
256 TATCGTTTTTCATATTTTT-TCAATAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
*
10481 TTAAAACAAATC
320 -TAAAACAAATT
* * * **
10493 CTTAAATTCAATGTGGCTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTCGGCTCCA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
*
10558 AAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTAGCCAAAAAAACTGTGATGGA-T
66 AAAATCATGCAAAACTAAGCCGGGGCCC-GAAACGCGTTTTTAGCC-AAAAAACCGTGAT-GATT
* * * * *
10622 AGTACACTATTTCGACTGAAATTTTGCAAAAAATGACCTGAAAAATTTATCCGTCAATTTTTGGC
128 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATATTT-TCC-TCAATTTTTGGC
* * *
10687 TAAAATACTCATAAAATATATATAATTTAACGCCAACAA-ATTGGAGGACTGTTCACGCTTTTAA
191 TAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAA
10751 TATCGTTTTTCATATTTTTTCAATTAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
256 TATCGTTTTTCATATTTTTTCAA-TAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCG
*
10816 TAAAAGAAATT
320 TAAAACAAATT
* * * * *
10827 CTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCAAAGAGTTTTGGAGCCA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
* * *
10892 AAAATCATGCGAAACTTAA-CCGGGGCCCCAGAACGCGTTTTTAGCCAAAAAAAAACCATGATGA
66 AAAATCATGCAAAAC-TAAGCCGGGGCCCGA-AACGCGTTTTTAGCC---AAAAAACCGTGATGA
* * *
10956 TTATTACACGATTTCGGCTAGAATTTTGCAAAACTT--CGCTCGAAAGTTATTTT-CTCAATTTT
126 TTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CT-GAAA--TATTTTCCTCAATTTT
* *** * ** * * * ** **
11018 TAGCCGCAATACTCATAAAAAATATATAATTCATTGGCAAAAAAATTGAAGGGTTTTTCATTCTT
187 TGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTT
* * * * **
11083 CTTAA-ATCG-TCTTCACTA-----T---T-AT--TTCCGAATTAAATTGAAACGTGATTCAGAT
252 -TTAATATCGTTTTTCA-TATTTTTTCAATAATAATTTCTAATTAAATCGAAACAAGATTCAGAT
* ***
11135 GCTTGTTTTACAAATT
315 GCTCGTAAAACAAATT
* * * * * * ** * *
11151 CTTAAACCCAATGTGGCTAAAATTTGGTTAGATGAATATAGGTATTTTAAGGAGTCTCAGCGCGA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
* * *
11216 AAAATCATGCAACACTGAA-CAGGGGCCCCATAACGCGTTTTTAG-CAAAAAACCGTGATTTTGA
66 AAAATCATGCAAAACT-AAGCCGGGGCCCGA-AACGCGTTTTTAGCCAAAAAACCGTGA---TGA
* * * * * *
11279 CTAACGTACACGATTTCGCCTAATATTTTGAAAAAATTGATCAGAAATATTTTTCCTCAATTTTT
126 -TTA-GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATA-TTTTCCTCAATTTTT
** * * * * * *
11344 ATCTAGAATACTCATAAATTATATATAATTCAACTCCATAAAGATCGGAGGACTTTTCACGATTT
188 GGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTT
* * * * *
11409 TAATATCGTTTTTCATATTTTTCTTAGA-ATTAATTTCTAATAAAATCGAAACAAAATTTAGATG
253 TAATATCGTTTTTCATATTTTT-TCA-ATAATAATTTCTAATTAAATCGAAACAAGATTCAGATG
*
11473 CTCGTAAAA-AAAAT
316 CTCGTAAAACAAATT
* * * ** **
11487 CTTTAAATGCAATTTGGCTGAGAATTGATTAGACAAATATAGATATTTCAAGGAGTC-TCAATGC
1 C-TTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGA-GC
* * * * *
11551 CAAAAATCATGCAAAACTGAGCCGGGGCCCCAAAACGCATATTTAGCAAAAAAACCGTGATGATT
64 CAAAAATCATGCAAAACTAAGCCGGGG-CCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGATT
* * ** * *
11616 AGTACACAATTTCGGCTAAAATTTTGCAAAAAATGACAAGAAAAAATTTTTCTTCAATTTTTGGC
128 AGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTG-AAATA-TTTTCCTCAATTTTTGGC
* ** * *
11681 TAAAATACTCATGAAATATATATATAATTTAATACCAAAAATATTGGAGGACTTTTCACACTTTT
191 TAAAATACTCAT-AAA-ATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTT
* *
11746 CATATCGTTTTTCATATTTTTT--ATGAATTAATTTCTAATTAAATCGAAACAAGACTT-TGATG
254 AATATCGTTTTTCATATTTTTTCAAT-AA-TAATTTCTAATTAAATCGAAACAAGA-TTCAGATG
*
11808 CTCGTAAAAACAAATC
316 CTCGT-AAAACAAATT
* * * * * * * * *
11824 CTTAAATGCAATATGGCTGAGATTCGATTAAATAAATATGGATATCTCGAGGAGTCTT-AACGCC
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGA-GCC
* * * * * *
11888 AAAAATAATGCAAAACTGACCCGGGGCCCTAGAACACGTTTTTATCC-AAAAACCGTGATGATTA
65 AAAAATCATGCAAAACTAAGCCGGGGCCCGA-AACGCGTTTTTAGCCAAAAAACCGTGATGATTA
* * ** *
11952 TTACACGATTTCGGATAAAATTTTGCAAAAATTGACGGCT-AGGTA-TTTCCTAAATTTTTGGCT
129 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC--CTGAAATATTTTCCTCAATTTTTGGCT
* * * ** * *
12015 AAAATACTCATAAAA-AAATATAATTCAACGCCAAAAATATTGAAGGGTTTTTTAAGCTTTTAAT
192 AAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAAT
* *
12079 ATCGTTTTT-ACTACTTTTTCCGAAT--TAATTTCTAATTAAATCGAAACAAGATTTAGATGCTC
257 ATCGTTTTTCA-TA-TTTTTTC-AATAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
*
12141 GTAAAAACAAATC
319 GT-AAAACAAATT
* * * * *
12154 CTGAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAAATATTTCAAGGAGTCTTGGCGTCA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
* * *
12219 AAAATCATGCAAAACTAA-CCTGGGGCCTTGGAACACGTTTTTAGCCAAAAAAAAAACCGTGA--
66 AAAATCATGCAAAACTAAGCC-GGGGCC-CGAAACGCGTTTTTAGCC----AAAAAACCGTGATG
* * ** **
12281 CTT--TACACGATTTCGGCTAATATTTTGCAAAAATTGATCCCCAAAATATTTTTTTATCAATTT
125 ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA--CCTGAAATA--TTTTCCTCAATTT
* * * * * * *
12344 TTAGCCACAATACT-A-AAAA-AAATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACGCT
186 TTGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCT
* * * * * **
12406 TCTAATATCGTTTTTCTTATTTTTTTCCAA-ATTAACTTCTAATAAAAAGGAAACATA-ATTCAG
251 TTTAATATCGTTTTTCATA-TTTTTT-CAATAATAATTTCTAATTAAATCGAAACA-AGATTCAG
*
12469 ATGCT--T---A-TAA--
313 ATGCTCGTAAAACAAATT
* * * *
12479 ---AAA--CAA--TGACT-AGGATTTGGTTAGATG-A-ATAGATATTTCAAGGAGTCTCGGTGCC
1 CTTAAATCCAATGTGGCTGA-GATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCC
* ** * * * *
12534 AAAAATCATTCAAATTTGAA-CCGGGTCACGGAACGCGTTTTTAGCC-CAAAACCGTGATGATTA
65 AAAAATCATGCAAAACT-AAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGATTA
* * * *
12597 TTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGATAGATA-TTTCCTCAATTTTTAGCC
129 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGA-A-ATATTTTCCTCAATTTTTGGCT
* * * * * *
12661 ATAATACTAATAAAA-A-ATATAATTCAACGCCAGAAAGATTGAAGGATTTTTCACGCTTGTAAT
192 AAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAAT
* * * *
12724 ATCATTTTTTATATTTTTTCCAA-ATTAATTTCTAATTAAAT-GAAAACAAG----A-AT-C-AG
257 ATCGTTTTTCATATTTTTT-CAATAATAATTTCTAATTAAATCG-AAACAAGATTCAGATGCTCG
*
12780 --AAAGAAA-T
320 TAAAACAAATT
* * * * * * * *
12788 CTTTAATGCAATGTGGCTAAGATTTTATTTGATGAATATAGATATTTCAAGGAGTGTCGGTGCCA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
** *
12853 AAAATCATGCAAAACTAAGTTGGGGCCCCGAAACGCGTTTTTTGCC-AAAAACCG-G--G---A-
66 AAAATCATGCAAAACTAAGCCGGGG-CCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGATTAG
* * * * * *
12910 T--ACGGTTTTGGCTAAAATTTTGTAAAAAATGACCTGAAATTTTTTTTCCTCAA-TTTTGGATA
130 TACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAA--TATTTTCCTCAATTTTTGGCTA
* * ** * * * *
12972 AAATATTCATAAAATATATATATAGTTTAACGGAAAAAATATTGGTGGATTTTTCACACTTTTAA
193 AAATACTCATAAAATATATATA-A-TTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAA
* *
13037 TATCGTTTTCTTTATATTTTTCTGAAT--TAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
256 TATCG-TTT-TTCATATTTTT-TCAATAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
*
13100 TGTAAAAACAAATT
318 CGT-AAAACAAATT
* * * *
13114 CTTAAATCCAATGTGGCTGAGATTTGATTAAATGAATATAAATATCTCAAGGAGTCTTGGTGCCA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
* * * * * * *
13179 AGAATCATGCAAAATTGAGCCGGGGCCCCAGAACGCTTTTTTATCC-AAAAACTGTGAT-AGTTA
66 AAAATCATGCAAAACTAAGCCGGGGCCCGA-AACGCGTTTTTAGCCAAAAAACCGTGATGA-TTA
* * * * * *
13242 TTACACGATTTCGGCTAAAATTTT---TAAATTGACCCGAAAGATATTTCCCCAATTTTTGACTA
129 GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATAT-TTTCCTCAATTTTTGGCTA
* * * *
13304 AAATACTCATAAAATATATATAATTCAACGCTAAAAAGATTGAAGTG-CTTTT---GATTCTAAT
193 AAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAG-GACTTTTCACGCTTTTAAT
* * * * * *
13365 ATCGTTTTTCCTATTTTTCCCAA-ATTAATTTCTAATTAATTCGAAACAAGATTCAAATACTCGT
257 ATCGTTTTTCATATTTTT-TCAATAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGT
*
13429 AAAAACAAATC
321 -AAAACAAATT
* * * * * * * **
13440 CTTAAATCGAATGTGGGTCA-ATTTGATTAGATGTATATAGATATTTCAAGTAGTCTCGCAGTTA
1 CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
* * * * * * *
13504 AAAATCATGCAAAATTGAGTCAGGTCTTCGGAACGCGTTTTTAGCC-AAAAACCGTGATGGTTTG
66 AAAATCATGCAAAACTAAGCCGGGGC-CCGAAACGCGTTTTTAGCCAAAAAACCGTGA-----TG
* * *
13568 TTATTAGTACACGATTTCGGCTAAAATTTTACAAAAATTGACATGAAAGATTTCTCCTCAATTTT
125 --ATTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATATTT-TCCTCAATTTT
* * * * *
13633 TGGCTAAAATAATCATAAAA-ATATATAATTCAACGCAAAAAAAATTGGAGGGCTTTTTACGCTT
187 TGGCTAAAATACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTT
* * * * * * *
13697 TTAATATCATATTTCTTGTTTTTTCTAA-ATTAATTTCTAATTAAATCAAAATAAGATTCAGATG
252 TTAATATCGTTTTTCATATTTTTTC-AATAATAATTTCTAATTAAATCGAAACAAGATTCAGATG
* *
13761 GTCGTAAAAAAATATT
316 CTCGTAAAACAA-ATT
* **
13777 CTTAAATCCAATTTTACTGAGATTT-AGTTAGATG-ATATA
1 CTTAAATCCAATGTGGCTGAGATTTGA-TTAGATGAATATA
13816 AAGTATTAAA
Statistics
Matches: 2668, Mismatches: 471, Indels: 359
0.76 0.13 0.10
Matches are distributed among these distances:
305 1 0.00
306 2 0.00
307 2 0.00
308 3 0.00
309 1 0.00
310 61 0.02
311 63 0.02
312 67 0.03
313 8 0.00
314 74 0.03
315 42 0.02
316 71 0.03
317 11 0.00
318 60 0.02
319 25 0.01
320 16 0.01
321 1 0.00
322 4 0.00
323 7 0.00
324 134 0.05
325 193 0.07
326 169 0.06
327 19 0.01
328 98 0.04
329 5 0.00
330 209 0.08
331 128 0.05
332 124 0.05
333 135 0.05
334 210 0.08
335 268 0.10
336 230 0.09
337 196 0.07
338 31 0.01
ACGTcount: A:0.37, C:0.15, G:0.14, T:0.33
Consensus pattern (330 bp):
CTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTTGGAGCCA
AAAATCATGCAAAACTAAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAAACCGTGATGATTAGT
ACACGATTTCGGCTAAAATTTTGCAAAAATTGACCTGAAATATTTTCCTCAATTTTTGGCTAAAA
TACTCATAAAATATATATAATTCAACGCCAAAAAGATTGGAGGACTTTTCACGCTTTTAATATCG
TTTTTCATATTTTTTCAATAATAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAC
AAATT
Found at i:11776 original size:661 final size:656
Alignment explanation
Indices: 10486--12416 Score: 1545
Period size: 661 Copynumber: 2.9 Consensus size: 656
10476 GCTCGTTAAA
** * *
10486 ACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTACATGAATATAGATATTTCAAGGAGTCTC
1 ACAAATCCTTAAACCCAATGTGGCTAAAATTTGATTACATGAATATAGATATTTCAAGGAGTCTC
* * * * *
10551 GGCTCCAAAAATCATGCAAAACTAAGCCGGGGCCCTGAAACGCGTTTTTAGCCAAAAAAACTGTG
66 AGCGCCAAAAATCATGCAAAACTAAGCAGGGGCCCTCAAACGCGTTTTTAGCCAAAAAAACCGTG
* *
10616 ATGGATAGTACACTATTTCGACTGAAATTTTGCAAAAAATGACCTGAAAAATTTATCCGTCAATT
131 ATGGATAGTACACGATTTCGACTGAAATTTTGCAAAAAATGACCAGAAAAATTTATCCGTCAATT
* * * *
10681 TTTGGCTAAAATACTCATAAAATATATATAATTTAACGCCAACAAATTGGAGGACTGTTCACGCT
196 TTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAACAAATCGGAGGACTGTTCACGAT
* *
10746 TTTAATATCGTTTTTCATATTTTTTCAATTAATAATTTCTAATTAAATCGAAACAAGATTCAGAT
261 TTTAATATCGTTTTTCATATTTTTTC-ATTAATAATTTCTAATAAAATCGAAACAAAATTCAGAT
* * ** *
10811 GCTCGTAAAAGAAATTCTTAAATCCAATGTAGCTGAGATTTGATTAGATGAATATGGATATCTCA
325 GCTCGTAAAAAAAATTCTTAAATCCAATGTAGCTGAGAATTGATTAGACAAATATAGATATCTCA
* ** * * * * *
10876 AAGAGTTTTGGAGCCAAAAATCATGCGAAACTTAACCGGGGCCCCAGAACGCGTTTTTAGCCAAA
390 AAGAGTTCTCAAGCCAAAAATCATGCAAAACTGAACCGGGGCCCCAAAACGCATATTTAGCC-AA
* * * ** ** **
10941 AAAAAACCATGATGATTATTACACGATTTCGGCTAGAATTTTGCAAAACTTCGCTCGAAAGTTAT
454 AAAAAACCATGATGATTAGTACACAATTTCGGCTAAAATTTTGCAAAAAATCGCAAGAAAAATAT
** * ** *
11006 TTTCTCAATTTTTAGCCGCAATACTCATAAAAAATATATAATTCATTGGCAAAAAAATTGAAGGG
519 TTTCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCAATACCAAAAAAATTGAAGGA
* ** *
11071 TTTTTCATTCTTCTTAAATCGTCTTCACTATTATTTCCGAATTAAATTGAAACGTGATTCAGATG
584 CTTTTCACACTTCTTAAATCGTCTTCACTATTATTTACGAATTAAATTGAAACGTGATTCAGATG
11136 CTTGTTTT
649 CTTGTTTT
* * * * *
11144 ACAAATTCTTAAACCCAATGTGGCTAAAATTTGGTTAGATGAATATAGGTATTTTAAGGAGTCTC
1 ACAAATCCTTAAACCCAATGTGGCTAAAATTTGATTACATGAATATAGATATTTCAAGGAGTCTC
* *
11209 AGCGCGAAAAATCATGCAACACTGAA-CAGGGGCCC-CATAACGCGTTTTTAG-C-AAAAAACCG
66 AGCGCCAAAAATCATGCAAAACT-AAGCAGGGGCCCTCA-AACGCGTTTTTAGCCAAAAAAACCG
* * * * *
11270 TGATTTTGACTAACGTACACGATTTCGCCT-AATATTTTG-AAAAAATTGATCAGAAATATTTTT
129 TGA--TGGA-T-A-GTACACGATTTCGACTGAA-ATTTTGCAAAAAA-TGACCAGAAAAATTTAT
* * * *
11333 CC-TCAATTTTTATCTAGAATACTCATAAATTATATATAATTCAACTCCATA-AAGATCGGAGGA
187 CCGTCAATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCA-ACAA-ATCGGAGGA
*
11396 CTTTTCACGATTTTAATATCGTTTTTCATA-TTTTTC-TTAGAATTAATTTCTAATAAAATCGAA
250 CTGTTCACGATTTTAATATCGTTTTTCATATTTTTTCATT--AA-TAATTTCTAATAAAATCGAA
* * * *
11459 ACAAAATTTAGATGCTCGTAAAAAAAA-TCTTTAAATGCAATTTGGCTGAGAATTGATTAGACAA
312 ACAAAATTCAGATGCTCGTAAAAAAAATTC-TTAAATCCAATGTAGCTGAGAATTGATTAGACAA
* * *
11523 ATATAGATATTTCAAGGAG-TCTCAATGCCAAAAATCATGCAAAACTGAGCCGGGGCCCCAAAAC
376 ATATAGATATCTCAAAGAGTTCTCAA-GCCAAAAATCATGCAAAACTGAACCGGGGCCCCAAAAC
*
11587 GCATATTTAG-C-AAAAAAACCGTGATGATTAGTACACAATTTCGGCTAAAATTTTGCAAAAAAT
440 GCATATTTAGCCAAAAAAAACCATGATGATTAGTACACAATTTCGGCTAAAATTTTGCAAAAAAT
* * * *
11650 -GACAAGAAAAA-ATTTTTCTTCAATTTTTGGCTAAAATACTCATGAAATATATATATAATTTAA
505 CG-CAAGAAAAATA-TTTTC-TCAATTTTTAGCCAAAATACTCAT-AAA-AAATATATAATTCAA
* * * *
11713 TACCAAAAATATTGGAGGACTTTTCACACTT-TTCATATCGTTTTTCA-TATTTTTTATGAATTA
565 TACCAAAAAAATTGAAGGACTTTTCACACTTCTT-AAATCG-TCTTCACTA----TTAT---TT-
* * ** * * ***
11776 ATTTCTAATTAAATCGAAACAAGACTT-TGATGCTCGTAAAA
620 A---CGAATTAAATTGAAACGTGA-TTCAGATGCTTGT-TTT
** * * * * * * * * * *
11817 ACAAATCCTTAAATGCAATATGGCTGAGATTCGATTAAATAAATATGGATATCTCGAGGAGTCTT
1 ACAAATCCTTAAACCCAATGTGGCTAAAATTTGATTACATGAATATAGATATTTCAAGGAGTCTC
* * * * * * *
11882 AACGCCAAAAATAATGCAAAACTGACCCGGGGCCCT-AGAACACGTTTTTATCC--AAAAACCGT
66 AGCGCCAAAAATCATGCAAAACTAAGCAGGGGCCCTCA-AACGCGTTTTTAGCCAAAAAAACCGT
* * * * ** ** *
11944 GAT-GATTATTACACGATTTCGGA-TAAAATTTTGCAAAAATTGA-CGGCTAGGTATT-TCC-TA
130 GATGGA-TAGTACACGATTTC-GACTGAAATTTTGCAAAAAATGACCAGAAAAAT-TTATCCGTC
* * * * * ** * *
12004 AATTTTTGGCTAAAATACTCATAAAA-AAATATAATTCAACGCCAAAAATATTGAAGGGTTTTTT
192 AATTTTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAACAA-ATCGGAGGACTGTTC
* * * ** * *
12068 AAGCTTTTAATATCGTTTTT-ACTACTTTTTC-CGAATTAATTTCTAATTAAATCGAAACAAGAT
256 ACGATTTTAATATCGTTTTTCA-TATTTTTTCATTAA-TAATTTCTAATAAAATCGAAACAAAAT
* * * * * * ** *
12131 TTAGATGCTCGTAAAAACAAATCCTGAAATCCAATGTGGTTGAGATTTGATTAGATGAATATAAA
319 TCAGATGCTCGTAAAAA-AAATTCTTAAATCCAATGTAGCTGAGAATTGATTAGACAAATATAGA
* * ** **** * * *
12196 TATTTCAAGGAG-TCT-TGGCGTCAAAAATCATGCAAAACT-AACCTGGGGCCTTGGAACACGTT
383 TATCTCAAAGAGTTCTCAAGC--CAAAAATCATGCAAAACTGAACC-GGGGCCCCAAAACGCATA
* *
12258 TTTAGCCAAAAAAAAAACC--G-TGACTT--TACACGATTTCGGCTAATATTTTGCAAAAATTGA
445 TTTAGCC--AAAAAAAACCATGATGA-TTAGTACACAATTTCGGCTAAAATTTTGCAAAAA---A
* * * * * * **
12318 TCCCCAA-AATATTTTTTTATCAATTTTTAGCCACAATACT-A-AAAAAA-ATATAATTCAACGC
504 T-CGCAAGAAAAATATTTTCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCAATAC
* *
12379 CAAAAAAATTGAAGGGCTTTTCACGCTTC-TAATATCGT
568 CAAAAAAATTGAAGGACTTTTCACACTTCTTAA-ATCGT
12417 TTTTCTTATT
Statistics
Matches: 1027, Mismatches: 182, Indels: 124
0.77 0.14 0.09
Matches are distributed among these distances:
656 11 0.01
657 4 0.00
658 157 0.15
659 23 0.02
660 71 0.07
661 243 0.24
662 7 0.01
663 40 0.04
664 4 0.00
665 57 0.06
666 161 0.16
667 42 0.04
668 46 0.04
669 18 0.02
670 15 0.01
671 1 0.00
672 25 0.02
673 101 0.10
674 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.32
Consensus pattern (656 bp):
ACAAATCCTTAAACCCAATGTGGCTAAAATTTGATTACATGAATATAGATATTTCAAGGAGTCTC
AGCGCCAAAAATCATGCAAAACTAAGCAGGGGCCCTCAAACGCGTTTTTAGCCAAAAAAACCGTG
ATGGATAGTACACGATTTCGACTGAAATTTTGCAAAAAATGACCAGAAAAATTTATCCGTCAATT
TTTAGCTAAAATACTCATAAAATATATATAATTCAACGCCAACAAATCGGAGGACTGTTCACGAT
TTTAATATCGTTTTTCATATTTTTTCATTAATAATTTCTAATAAAATCGAAACAAAATTCAGATG
CTCGTAAAAAAAATTCTTAAATCCAATGTAGCTGAGAATTGATTAGACAAATATAGATATCTCAA
AGAGTTCTCAAGCCAAAAATCATGCAAAACTGAACCGGGGCCCCAAAACGCATATTTAGCCAAAA
AAAACCATGATGATTAGTACACAATTTCGGCTAAAATTTTGCAAAAAATCGCAAGAAAAATATTT
TCTCAATTTTTAGCCAAAATACTCATAAAAAATATATAATTCAATACCAAAAAAATTGAAGGACT
TTTCACACTTCTTAAATCGTCTTCACTATTATTTACGAATTAAATTGAAACGTGATTCAGATGCT
TGTTTT
Found at i:19175 original size:27 final size:26
Alignment explanation
Indices: 19139--19207 Score: 120
Period size: 27 Copynumber: 2.6 Consensus size: 26
19129 TGATTGCAGA
19139 CTTTGATGACTTAATTTCAAAGTTCC
1 CTTTGATGACTTAATTTCAAAGTTCC
*
19165 CTTTGCTTGACTTAATTTCAAAGTTCC
1 CTTTG-ATGACTTAATTTCAAAGTTCC
19192 CTTTGATGACTTAATT
1 CTTTGATGACTTAATT
19208 CCTGCAATTT
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 15 0.38
27 25 0.62
ACGTcount: A:0.25, C:0.19, G:0.12, T:0.45
Consensus pattern (26 bp):
CTTTGATGACTTAATTTCAAAGTTCC
Found at i:27282 original size:11 final size:11
Alignment explanation
Indices: 27266--27294 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
27256 CATAACACGC
27266 TTTCTTTTTCT
1 TTTCTTTTTCT
27277 TTTCTTTTTCT
1 TTTCTTTTTCT
27288 TTTCTTT
1 TTTCTTT
27295 CTTTATTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:31059 original size:10 final size:11
Alignment explanation
Indices: 31028--31057 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
31018 TAACTGTAGG
31028 AAACAAAAATA
1 AAACAAAAATA
31039 AAACAAAAATA
1 AAACAAAAATA
31050 AAACAAAA
1 AAACAAAA
31058 TATAGAAGCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.83, C:0.10, G:0.00, T:0.07
Consensus pattern (11 bp):
AAACAAAAATA
Found at i:37556 original size:66 final size:66
Alignment explanation
Indices: 37448--37571 Score: 185
Period size: 66 Copynumber: 1.9 Consensus size: 66
37438 TATGTATCCG
* * * ** *
37448 TTTAACGATTTATGATTAAATTCTATTCGAATTGGGTCATCTTATTATGAGAATAAAATCCTCCA
1 TTTAACAATTTATGACTAAATTCTATTCAAATTGAATCATCTTATTATGAAAATAAAATCCTCCA
37513 T
66 T
*
37514 TTTAACAATTTATGACTAAATTCTATTCAAATTGAATTATCTTATTATGAAAATAAAA
1 TTTAACAATTTATGACTAAATTCTATTCAAATTGAATCATCTTATTATGAAAATAAAA
37572 CTCTCATAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (66 bp):
TTTAACAATTTATGACTAAATTCTATTCAAATTGAATCATCTTATTATGAAAATAAAATCCTCCA
T
Found at i:42606 original size:14 final size:14
Alignment explanation
Indices: 42587--42613 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42577 GATGACCAAA
42587 AAAAAGAAAAAAAG
1 AAAAAGAAAAAAAG
42601 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
42614 AATGAGAGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAG
Found at i:46234 original size:102 final size:102
Alignment explanation
Indices: 46058--46263 Score: 412
Period size: 102 Copynumber: 2.0 Consensus size: 102
46048 ATTCATGGAA
46058 TAGTGTATACTACAGATCAATTTATGTTAGGAACTCCTCCCATTCTTTTCCTACTAAATCTCCTA
1 TAGTGTATACTACAGATCAATTTATGTTAGGAACTCCTCCCATTCTTTTCCTACTAAATCTCCTA
46123 ATAAACCACCATACTCTTGTTAAAAAGTAACTACTTT
66 ATAAACCACCATACTCTTGTTAAAAAGTAACTACTTT
46160 TAGTGTATACTACAGATCAATTTATGTTAGGAACTCCTCCCATTCTTTTCCTACTAAATCTCCTA
1 TAGTGTATACTACAGATCAATTTATGTTAGGAACTCCTCCCATTCTTTTCCTACTAAATCTCCTA
46225 ATAAACCACCATACTCTTGTTAAAAAGTAACTACTTT
66 ATAAACCACCATACTCTTGTTAAAAAGTAACTACTTT
46262 TA
1 TA
46264 ATTGTCTCTG
Statistics
Matches: 104, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
102 104 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (102 bp):
TAGTGTATACTACAGATCAATTTATGTTAGGAACTCCTCCCATTCTTTTCCTACTAAATCTCCTA
ATAAACCACCATACTCTTGTTAAAAAGTAACTACTTT
Found at i:46604 original size:10 final size:10
Alignment explanation
Indices: 46589--46618 Score: 51
Period size: 10 Copynumber: 2.9 Consensus size: 10
46579 CTTTTTTCCA
46589 AAAAAAAAAC
1 AAAAAAAAAC
46599 AAAAAAAAAC
1 AAAAAAAAAC
46609 AAAAACAAAA
1 AAAAA-AAAA
46619 GGATCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 15 0.79
11 4 0.21
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:46612 original size:16 final size:15
Alignment explanation
Indices: 46588--46618 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
46578 TCTTTTTTCC
46588 AAAAAAAAAACAAAA
1 AAAAAAAAAACAAAA
46603 AAAAACAAAAACAAAA
1 AAAAA-AAAAACAAAA
46619 GGATCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.33
16 10 0.67
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAACAAAA
Found at i:47190 original size:2 final size:2
Alignment explanation
Indices: 47185--47220 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47175 AAAAAAGTTG
47185 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
47221 GTACTATTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:48056 original size:23 final size:24
Alignment explanation
Indices: 48030--48075 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
48020 GTTTTTTTCA
48030 GGACTCCTTAGTGAGAG-TTTTTG
1 GGACTCCTTAGTGAGAGCTTTTTG
*
48053 GGACTCCTTTGTGAGAGCTTTTT
1 GGACTCCTTAGTGAGAGCTTTTT
48076 CTATTGTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 16 0.76
24 5 0.24
ACGTcount: A:0.15, C:0.15, G:0.28, T:0.41
Consensus pattern (24 bp):
GGACTCCTTAGTGAGAGCTTTTTG
Found at i:48457 original size:15 final size:15
Alignment explanation
Indices: 48437--48468 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
48427 ATTTTCTTCT
48437 TGTAATTTTAATTAA
1 TGTAATTTTAATTAA
48452 TGTAATTTTAATTAA
1 TGTAATTTTAATTAA
48467 TG
1 TG
48469 GTGTTTGGAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (15 bp):
TGTAATTTTAATTAA
Done.