Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020829.1 Corchorus olitorius cultivar O-4 contig20862, 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: 126229
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Found at i:1137 original size:332 final size:332
Alignment explanation
Indices: 527--1970 Score: 1901
Period size: 332 Copynumber: 4.4 Consensus size: 332
517 TCTATAAGTT
** *
527 AATTTTTGGAAAATTTTAGCCGAAATCGTGTGCTAACTATCACAGTTTTTGGCTAAAAACGCGTT
1 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTT
* * * *
592 CCGGGGCTCCGGCACAGTTTTGAATGATTTTTGGCGCCAAGACTCAATGAAATATCTATGTTCAT
66 CCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTCAT
* * * * * *
657 TTAACCAAATCTCAGCCACATCGGATTTAAGTATTTGTTTTTACGAGCATTTGAATTATTTTTCG
131 TTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
722 ATTTAATTA-GAAATTATTTCTGATAATATTGGAAAAACGATATTAGAAGTGTG-AGAAGTTGTT
196 ATTTAA-TACGAAATTATTTCTGAGAAAATTGGAAAAACGATATTAGAAGAGTGAAAAACTT-TT
**
785 CATTCTTTTTGGCTTTGAATTATATATTTTCT-GTGAGTATTGTGGCTAAAAATTAAGTAAAAAT
259 CATTCTTTTTGGCTTTGAATTATATATTTTCTAG-GAGTATTGTGGCTAAAAATTTGGTAAAAAT
849 CTTTCGGGGA
323 CTTTCGGGGA
* * * * *
859 AATTTTTCCAAAATTTTAACCGAAATCTTGTACTAACCATCACAGTTTTTGGGTTAAAACGCGTT
1 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTT
* * * * *
924 CCGGGGCCTCGGCTTAGTTTTGCATGATTTTTGGCTCTAAGACTCAATGAAATATCTATATTAAT
66 CCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTCAT
*
989 TTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATATGAATCATGTTTCG
131 TTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
*
1054 ATTTAATACGAAATTAATTTC-GAGAAAATTGGAAAAGCGATATTAGAAGAGTGAAAAACTTTTC
196 ATTTAATACGAAATT-ATTTCTGAGAAAATTGGAAAAACGATATTAGAAGAGTGAAAAACTTTTC
* * * * *
1118 ATTCTTTTTGGCGTTGAATTATATATTCTCTAGGAGTATTGTGGCTTAAAGTTTGGTAAAAATAT
260 ATTCTTTTTGGCTTTGAATTATATATTTTCTAGGAGTATTGTGGCTAAAAATTTGGTAAAAATCT
1183 TTCGGGGA
325 TTCGGGGA
* * *
1191 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCATAGTTTTAGGCTAAAAACGCATT
1 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTT
* * * *
1256 CCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCAATGGAATATCTATATTTAT
66 CCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTCAT
* * * *
1321 CTAACTAAATCTTAGCCACATAGTATTTAAGGATTTGTTTTTACGAG-ACTCTGAATCATGTTTC
131 TTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCA-TCTGAATCATGTTTC
* * * * * * * *
1385 TATTTACTAAGAAATTATTTCTGATAAAATTGGAAAAACGATATTAGAAGCA-CGAGAAGCTGTT
195 GATTTAATACGAAATTATTTCTGAGAAAATTGGAAAAACGATATTAGAAG-AGTGAAAAACTTTT
* * * *
1449 CATTCTTTTTGGATTTGAATTATATATTTTCTATGAGTATTGTGGCTAAAAATTT-TTAAAAATT
259 CATTCTTTTTGGCTTTGAATTATATATTTTCTAGGAGTATTGTGGCTAAAAATTTGGTAAAAATC
1513 TTTCGGGGA
324 TTTCGGGGA
* *
1522 AATTTTTCC-AAATTTTAGTCGAAATC--GTA-T-ACCATCACAGTTTTTGGCTAAAAACGCGTT
1 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTT
* * *
1582 TC-GAGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTCAT
66 CCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTCAT
* * *
1646 TTAACCAAATCTTAGCCACACTGTATTTAAGGATTTGTTTTTACGAGCATCTAAATCATGTTTCG
131 TTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * * * *
1711 ATTTAAT-CTGAAATTAATTCAGAGAAATTTGGAAAAACGATATTAGAAGCGTGAAAAGCTTTTC
196 ATTTAATAC-GAAATTATTTCTGAGAAAATTGGAAAAACGATATTAGAAGAGTGAAAAACTTTTC
* *
1775 ATTCTTTTTGGCATTGAATTATATATTTTCTAGGAGTATTGTGGCTAAAATTTTGGTAAAAATCT
260 ATTCTTTTTGGCTTTGAATTATATATTTTCTAGGAGTATTGTGGCTAAAAATTTGGTAAAAATCT
1840 TTCGGGGA
325 TTCGGGGA
** * * * * *
1848 AATTTTTTTATAAATTTTAGCCGAAATCGTGTATTAAATATCACAGTTTTAGGCTAAAAGCGCAT
1 AATTTTTCCA-AAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGT
* * * * *** *
1913 TACGGAGCCCCGACTCAGTTTTGCCTGATTTTTTATGACAAGACTCAATG-AATATCTA
65 TCCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTA
1971 GGGATTGAAT
Statistics
Matches: 970, Mismatches: 124, Indels: 36
0.86 0.11 0.03
Matches are distributed among these distances:
325 215 0.22
326 51 0.05
327 1 0.00
328 19 0.02
330 19 0.02
331 34 0.04
332 580 0.60
333 51 0.05
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (332 bp):
AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTTGGCTAAAAACGCGTT
CCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTCAT
TTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
ATTTAATACGAAATTATTTCTGAGAAAATTGGAAAAACGATATTAGAAGAGTGAAAAACTTTTCA
TTCTTTTTGGCTTTGAATTATATATTTTCTAGGAGTATTGTGGCTAAAAATTTGGTAAAAATCTT
TCGGGGA
Found at i:1845 original size:657 final size:663
Alignment explanation
Indices: 527--1970 Score: 2134
Period size: 664 Copynumber: 2.2 Consensus size: 663
517 TCTATAAGTT
** * * *
527 AATTTTTGGAAAATTTTAGCCGAAATCGTGTGCTAACTATCACAGTTTTTGGCTAAAAACGCGTT
1 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTAGGCTAAAAACGCATT
* * * * * *
592 CCGGGGCTCCGGCACAGTTTTGAATGATTTTTGGCGCCAAGACTCAATGAAATATCTATGTTCAT
66 CCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGGAATATCTATATTCAT
* * * * * *
657 TTAACCAAATCTCAGCCACATCGGATTTAAGTATTTGTTTTTACGAGCATTTGAATTATTTTTCG
131 CTAACCAAATCTCAGCCACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
* * *** *
722 ATTTAATTAGAAATTATTTCTGATAATATTGGAAAAACGATATTAGAAGTGTGAGAAGTTGTTCA
196 ATTTAATAAGAAATTATTTCTGATAAAATTGGAAAAACGATATTAGAAGCACGAGAAGCTGTTCA
* *
787 TTCTTTTTGGCTTTGAATTATATATTTTCTGTGAGTATTGTGGCTAAAAATTAAGTAAAAATCTT
261 TTCTTTTTGGATTTGAATTATATATTTTCTATGAGTATTGTGGCTAAAAATTAAGTAAAAATCTT
* *
852 TCGGGGAAATTTTTCCAAAATTTTAACCGAAATCTTGTACTAACCATCACAGTTTTTGGGTTAAA
326 TCGGGGAAATTTTTCCAAAATTTTAACCGAAATC-TGTACTAACCATCACAGTTTTTGGCTAAAA
* * * *
917 ACGCGTTCCGGGGCCTCGGCTTAGTTTTGCATGATTTTTGGCTCTAAGACTCAATGAAATATCTA
390 ACGCGTTCCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTA
* *
982 TATTAATTTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTTTACGAGCATATGAATCA
455 TATTAATTTAACCAAATCTCAGCCACACTGTATTTAAGGATTTGTTTTTACGAGCATATAAATCA
*
1047 TGTTTCGATTTAATACGAAATTAATTTCGAGAAAATTGGAAAAGCGATATTAGAAGAGTGAAAAA
520 TGTTTCGATTTAATACGAAATTAATTTCGAGAAAATTGGAAAAACGATATTAGAAGAGTGAAAAA
* *
1112 CTTTTCATTCTTTTTGGCGTTGAATTATATATTCTCTAGGAGTATTGTGGCTTAAAGTTTGGTAA
585 CTTTTCATTCTTTTTGGCATTGAATTATATATTCTCTAGGAGTATTGTGGCTAAAAGTTTGGTAA
1177 AAATATTTCGGGGA
650 AAATATTTCGGGGA
*
1191 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCATAGTTTTAGGCTAAAAACGCATT
1 AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTAGGCTAAAAACGCATT
* *
1256 CCGGGGCCCCGACTCAATTTTGCATGATTTTTGGCGCCAAGACTCAATGGAATATCTATATTTAT
66 CCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGGAATATCTATATTCAT
* * *
1321 CTAACTAAATCTTAGCCACATAGTATTTAAGGATTTGTTTTTACGAG-ACTCTGAATCATGTTTC
131 CTAACCAAATCTCAGCCACATAGGATTTAAGGATTTGTTTTTACGAGCA-TCTGAATCATGTTTC
* *
1385 TATTTACTAAGAAATTATTTCTGATAAAATTGGAAAAACGATATTAGAAGCACGAGAAGCTGTTC
195 GATTTAATAAGAAATTATTTCTGATAAAATTGGAAAAACGATATTAGAAGCACGAGAAGCTGTTC
** *
1450 ATTCTTTTTGGATTTGAATTATATATTTTCTATGAGTATTGTGGCTAAAAATT-TTTAAAAATTT
260 ATTCTTTTTGGATTTGAATTATATATTTTCTATGAGTATTGTGGCTAAAAATTAAGTAAAAATCT
**
1514 TTCGGGGAAATTTTTCC-AAATTTTAGTCGAAATC-GTA-T-ACCATCACAGTTTTTGGCTAAAA
325 TTCGGGGAAATTTTTCCAAAATTTTAACCGAAATCTGTACTAACCATCACAGTTTTTGGCTAAAA
*
1575 ACGCGTTTC-GAGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTA
390 ACGCGTTCCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTA
* * *
1639 TATTCATTTAACCAAATCTTAGCCACACTGTATTTAAGGATTTGTTTTTACGAGCATCTAAATCA
455 TATTAATTTAACCAAATCTCAGCCACACTGTATTTAAGGATTTGTTTTTACGAGCATATAAATCA
* *
1704 TGTTTCGATTTAAT-CTGAAATTAA-TTCAGAGAAATTTGGAAAAACGATATTAGAAGCGTGAAA
520 TGTTTCGATTTAATAC-GAAATTAATTTC-GAGAAAATTGGAAAAACGATATTAGAAGAGTGAAA
* * *
1767 AGCTTTTCATTCTTTTTGGCATTGAATTATATATTTTCTAGGAGTATTGTGGCTAAAATTTTGGT
583 AACTTTTCATTCTTTTTGGCATTGAATTATATATTCTCTAGGAGTATTGTGGCTAAAAGTTTGGT
*
1832 AAAAATCTTTCGGGGA
648 AAAAATATTTCGGGGA
** * * *
1848 AATTTTTTTATAAATTTTAGCCGAAATCGTGTATTAAATATCACAGTTTTAGGCTAAAAGCGCAT
1 AATTTTTCCA-AAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTAGGCTAAAAACGCAT
* * * *** *
1913 TACGGAGCCCCGACTCAGTTTTGCCTGATTTTTTATGACAAGACTCAAT-GAATATCTA
65 TCCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGGAATATCTA
1971 GGGATTGAAT
Statistics
Matches: 703, Mismatches: 73, Indels: 15
0.89 0.09 0.02
Matches are distributed among these distances:
656 4 0.01
657 257 0.37
658 120 0.17
659 1 0.00
660 3 0.00
662 15 0.02
663 26 0.04
664 277 0.39
ACGTcount: A:0.31, C:0.14, G:0.17, T:0.37
Consensus pattern (663 bp):
AATTTTTCCAAAATTTTAGCCGAAATCGTGTACTAACTATCACAGTTTTAGGCTAAAAACGCATT
CCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGGAATATCTATATTCAT
CTAACCAAATCTCAGCCACATAGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG
ATTTAATAAGAAATTATTTCTGATAAAATTGGAAAAACGATATTAGAAGCACGAGAAGCTGTTCA
TTCTTTTTGGATTTGAATTATATATTTTCTATGAGTATTGTGGCTAAAAATTAAGTAAAAATCTT
TCGGGGAAATTTTTCCAAAATTTTAACCGAAATCTGTACTAACCATCACAGTTTTTGGCTAAAAA
CGCGTTCCGGAGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCAATGAAATATCTAT
ATTAATTTAACCAAATCTCAGCCACACTGTATTTAAGGATTTGTTTTTACGAGCATATAAATCAT
GTTTCGATTTAATACGAAATTAATTTCGAGAAAATTGGAAAAACGATATTAGAAGAGTGAAAAAC
TTTTCATTCTTTTTGGCATTGAATTATATATTCTCTAGGAGTATTGTGGCTAAAAGTTTGGTAAA
AATATTTCGGGGA
Found at i:2881 original size:332 final size:332
Alignment explanation
Indices: 2033--3126 Score: 1661
Period size: 332 Copynumber: 3.3 Consensus size: 332
2023 ATCTTTCGGG
* ** * * *
2033 TTAGCTGAAATCGTGTGTTAACCATCGCAGTATTTGGCTAAAAACGCGTTTCGAGGCCCCGGCTC
1 TTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTC
* * * * *
2098 AG-TTTAAATGATTTTTGGCGGCAAAACTCAATGAAATATCTATATTCATCTAACCAAATTTCAG
66 AGTTTTACATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTTATCTAACCAAATCTCAG
*
2162 CCACATAGAATTTAAGGATTTGTTTTTACGAGCATCTGAATC----TTCGATTTAATAAGAAATT
131 CCACATAGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATAAGAAATT
* * *
2223 ATTTCTGATAAACATTAGAAAATTGCTATTAGAAAGGTGAGAA-CTCTTCATTCTTTTGGGCATT
196 ATTTCTGATAAACATTGGAAAAATGCTATTAG-AAGGTGAAAAGCTCTTCATTCTTTTGGGCATT
2287 GAATTATATATTTTCTATGAGCATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGGGCAATTTTT
260 GAATTATATATTTTCTATGAGCATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGGGCAATTTTT
*
2352 CCAAAAGT
325 CCAAAATT
* * *
2360 TTAGCCGAAATCGTGTAC---GCAACAGAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTC
1 TTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTC
*
2422 AGTTTTACATGATTTTTGGCGCCAAGACTCAATGATATATCTATATTTATCTAACCAAATCTCAG
66 AGTTTTACATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTTATCTAACCAAATCTCAG
*
2487 CCACATAGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTACTAAGAAATT
131 CCACATAGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATAAGAAATT
* * * * * *
2552 ATTTCTGATAAAAATTGGAAAAACGATATTAGAAGCGTGAAAAGCTTTTCATTCTTTTTGGCGTT
196 ATTTCTGATAAACATTGGAAAAATGCTATTAGAAG-GTGAAAAGCTCTTCATTCTTTTGGGCATT
* * * *
2617 GAATTATATATTCTCTATGAGTATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGAGAAATTTTT
260 GAATTATATATTTTCTATGAGCATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGGGCAATTTTT
2682 CCAAAATT
325 CCAAAATT
* * *
2690 TTAGCC-AAAGTCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTCCGGGGCACCAGCT
1 TTAGCCGAAA-TCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCT
* * *
2754 CAGTTTTGCATGATTTTTGGCACCAAG-CTCAATGAAATATCTATATTTATCTAACTAAATCTCA
65 CAGTTTTACATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTTATCTAACCAAATCTCA
* *
2818 TCCACATAGTATTTAAGGATTTGTTTTTATGAGCATCTGAATCATGTTTCGATTTAATAAGAAAT
130 GCCACATAGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATAAGAAAT
2883 TATTTCTGATAAACATTGGAAAAATGCTATTAGAAGGGTGAAAAGCTCTTCATTCTTTTGGGCAT
195 TATTTCTGATAAACATTGGAAAAATGCTATTAGAA-GGTGAAAAGCTCTTCATTCTTTTGGGCAT
2948 TGAATTATATATTTTCTATGAGCATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGGGCAATTTT
259 TGAATTATATATTTTCTATGAGCATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGGGCAATTTT
3013 TCCAAAATT
324 TCCAAAATT
* * * *
3022 TTAGCCGACATCATGTACTAACCATCACAGTTTTTGGCTAAAAACGCATTTCGGGGCCCCGACTC
1 TTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTC
** *
3087 AAATTTGCATGATTTTTGGCGCCAAGACTCAATGAAATAT
66 AGTTTTACATGATTTTTGGCGCCAAGACTCAATGAAATAT
3127 TTGAAGCATG
Statistics
Matches: 689, Mismatches: 64, Indels: 22
0.89 0.08 0.03
Matches are distributed among these distances:
324 40 0.06
325 97 0.14
327 15 0.02
328 3 0.00
329 54 0.08
330 100 0.15
332 302 0.44
333 78 0.11
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (332 bp):
TTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCGGCTC
AGTTTTACATGATTTTTGGCGCCAAGACTCAATGAAATATCTATATTTATCTAACCAAATCTCAG
CCACATAGTATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATAAGAAATT
ATTTCTGATAAACATTGGAAAAATGCTATTAGAAGGTGAAAAGCTCTTCATTCTTTTGGGCATTG
AATTATATATTTTCTATGAGCATTGTGGCTAAAAATTTAGTAAAAATCTTTCGGGGCAATTTTTC
CAAAATT
Found at i:4426 original size:336 final size:333
Alignment explanation
Indices: 3123--5550 Score: 2729
Period size: 336 Copynumber: 7.3 Consensus size: 333
3113 ACTCAATGAA
**
3123 ATATTTGAAGCATG-AAAAGGCTTGAAATCTTTTTGGCGTTTGAATTATATATTTTTTATGAGTA
1 ATATTTGAAGCATGAAAAACCCTT-AAATCTTTTTGGCG-TTGAATTATATATTTTTTATGAGTA
* * *
3187 TTATGGCCAAAATATGTGAAAAAAAAAAATTTCGGATCAGTTTTTACAAAATTTTAGCTGAAATC
64 TTGTGGCC-AAATATTTG--AAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATC
* * * *
3252 ATGTACTAACGATCACGGTTTCTGGCTGAAAA-GTCGTTCC-GGGCCCTGGC-CAGTTTTGCAAG
126 GTGTACTAACTATCACGGTTTCTGACTGAAAACG-CGTTCCGGGGCCCCGGCTCAGTTTTGCAAG
* * * * *
3314 TTTTTTGGCGTTGAGACTCCTTGAAATAAT-TATATTCATCTAATCAAATCTCAGCCACATTGGA
190 ATTTTTGGCGTCGAAACTCCTTGAAAT-ATCTATATTAATCTAATCAAATCTCAGTCACATTGGA
* * * * ** *
3378 TTTAAGGATAAG-TTTTACCAGCTACTAAATCTTAATTCGAATTTATTAGAAATTAATTGGATAA
254 TTTAAGGATATGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGATAA
3442 AAAAAAGGAAAAACC
319 AAAAAAGGAAAAACC
* * * *
3457 ATATTTGAAGCATGAAAAGCCCTTAAATCGTTTTGGCGTTGAATTCTATA-CTTTTATGAGTATT
1 ATATTTGAAGCATGAAAAACCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
* * * * *
3521 G-GAGCTAAA-AATTGAGAAAAAAAATTTTCAGATAAGTTTTTGCAAAATTTTAACTGAAATCGT
66 GTG-GCCAAATATTTGA-AAAAAAAA-TTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCGT
* * * * * * *
3584 GTAC--A--A-CACGGCTTCTTGA-TGAGAACGCATTCCGAGGCTCCGGCTCAGTTTTACATGAT
128 GTACTAACTATCACGGTTTC-TGACTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGAT
* *
3643 TTATGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTGGATTT
192 TTTTGGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTGGATTT
* *
3708 AAGGATATGTTTTTACGAGCTTCTGAATCTTGATTCGGTTTTATCAAAAATTAATTGGAT-AAAA
257 AAGGATATGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGATAAAAA
* *
3772 GAATGAAAAACC
322 AAAGGAAAAACC
** * *
3784 ATATTTGAAGCATG-AAAAGGCTTGAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAATAC
1 ATATTTGAAGCATGAAAAACCCTT-AAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTAT
* * ** * *
3848 TATGGCCAAAAATTGTGAAAAAAAAATTTTCATATCAGTTTTTGCAAAATTTTAGCTTAAATCAT
65 TGTGGCCAAATATT-TGAAAAAAAAA-TTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCGT
** *
3913 GTACTAA-TCATCACGGTTTCTGACTGAAAACGCGTTCTAGGGCCCCGACTCAGTTTTGCAAGAT
128 GTACTAACT-ATCACGGTTTCTGACTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGAT
* * * * *
3977 TTTTGGCGTCGATACTCCTTGAACTATCTATATGAATCTAATCAAACCTCAG-CTACAATGGATT
192 TTTTGGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTC-ACATTGGATT
* * *
4041 TAAGGATATGTTTTCACGAG-TATC-GAGATCTTCATTCGATTTTATCAGAAATTAATTGGATAA
256 TAAGGATATGTTTTTACGAGCT-TCTGA-ATCTTAATTCGGTTTTATCAGAAATTAATTGGAT--
4104 AAAAAAGAAGGAAAAACC
317 AAAAAA-AAGGAAAAACC
* * * *
4122 ATATTTTAAGCATGAAAAACCCTTAAATCTGTTTGGCGTTAAATTATATATTTTCTATGAGTATT
1 ATATTTGAAGCATGAAAAACCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
* * *
4187 GGGGCCAAATATTTAGAAAAAAAAATTTCGGATCAGATTTTGCAAAATTTGAGCTGAAATCGTGT
66 GTGGCCAAATATTT-GAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCGTGT
* * * * *
4252 AATAACTATCACGATTTCTTACTGAAAACGCGTTCCGGGGCCCCAGCTC-GTTTTGCATGATTTT
130 ACTAACTATCACGGTTTCTGACTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTT
** * * * *
4316 TTACATTGAAACTCCTTGAAGTATCAATATTAATCTAATCAAATCTCAGTCACATTGGATTTAAG
195 TGGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTGGATTTAAG
* *
4381 AATATGTTTTTACGAGCTTCTGAATAC-TGATTCGGTTTTATCAGAAATTAATTGGATAAAAAAA
260 GATATGTTTTTACGAGCTTCTGAAT-CTTAATTCGGTTTTATCAGAAATTAATTGGATAAAAAAA
4445 A-GAAAAACC
324 AGGAAAAACC
* * * *
4454 ATATTTGAAGCATGAAAAGCCCTGAAATTTTTTTGGCGTTGAATTATAT-TTTTTTATGAGCATT
1 ATATTTGAAGCATGAAAAACCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
* * * * *
4518 TTGGCAAAATATTCTG-AAAAAAATTTTCGGATCAGTTTTTGCAAAATTTCAACTGAAATCGTGT
66 GTGGCCAAATATT-TGAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCGTGT
* * * *
4582 ACTAACCATCACGGTTT-TCAGCTGAAAA-GTCGTTCCGAGCCCCCGGCTCAGTTTTGCAAGATT
130 ACTAACTATCACGGTTTCTGA-CTGAAAACG-CGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATT
* * * * *
4645 TTTGGCATCGAAACACCTTGAAATATCTATATTGATCTAATCAAATCTTAGAT-ACATTGTATTT
193 TTTGGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAG-TCACATTGGATTT
*
4709 AAGGATAGGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGATTAAAA
257 AAGGATATGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGA-T---A
*
4774 AAAAAAAGGAAAACCC
318 AAAAAAAGGAAAAACC
* ** *
4790 ATATTTGAAGCATGAAAAGCCCTTAAATCTTTTTCACGTTGAATTATATA-TTTTTATGAGTCTT
1 ATATTTGAAGCATGAAAAACCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
* * * *
4854 GTGGCTAAAAATTGAGAAAAAAAAATATTTTTCGAATCAGTTTTTGCAAAATTTTAGCTGAAATC
66 GTGGCCAAATATT-TG-AAAAAAAA-A--TTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATC
* * * ** * * * *
4919 GTGTACTAATTATCACGGTTTCTGGCTGAAAACGCATTTTGGGGCCCCAGCCTCAGATTTACATG
126 GTGTACTAACTATCACGGTTTCTGACTGAAAACGCGTTCCGGGGCCCC-GGCTCAGTTTTGCAAG
* * *
4984 A-TTCTGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTAAGTCACATTGGAT
190 ATTTTTGGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTGGAT
* * *
5048 TTAAGGATATGTTTTTAAGAGCTTTTGAATCTTGATTCGGTTTTATCAGAAATTAATTGGAT-AA
255 TTAAGGATATGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGATAAA
*
5112 AAAAACGAAAAACC
320 AAAAAGGAAAAACC
** * *
5126 ATATTTGAAGCATG-AAAAGGCTTGAAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTAC
1 ATATTTGAAGCATGAAAAACCCTT-AAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTAT
* *
5190 TGTGGCCAAATATTGTGAAAAAAAAATTTCGGATCAGTTTTTGAAAAATTTTAGCTGAAATCATG
65 TGTGGCCAAATATT-TGAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCGTG
* * * * * *
5255 TACTAACCATCACTGTTTCTCG-CTGAAAA-GTCGTTAC-GGGCCCTGTCTCAGTTTTGCAAGTT
129 TACTAACTATCACGGTTTCT-GACTGAAAACG-CGTTCCGGGGCCCCGGCTCAGTTTTGCAAG-A
* * * * * *
5317 TTTTTGGCATCGAGACTCCTTGAAATAACTATATTCATCTAATCATATCTCAGCCACATTGGATT
191 TTTTTGGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTGGATT
* * * * ** * * *
5382 TAAGGATAAG-TTTTACCAGCTTATAAATCTTAATTCGAATTTATTATAAATTAATTAGATAAAA
256 TAAGGATATGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGAT-AAA
5446 AAAAAGGAAAAACC
320 AAAAAGGAAAAACC
* * *
5460 ATATTGGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTAAATTATATATATTTTTATGAGTAT
1 ATATTTGAAGCATGAAAAACCCTTAAATCTTTTTGGCGTTGAATTATATAT-TTTTTATGAGTAT
* * *
5525 TAG-GACTAAA-AATTGAAAAAAAAATT
65 T-GTGGCCAAATATTTGAAAAAAAAATT
5551 CAGATAAGTT
Statistics
Matches: 1773, Mismatches: 254, Indels: 135
0.82 0.12 0.06
Matches are distributed among these distances:
325 18 0.01
326 19 0.01
327 127 0.07
328 60 0.03
329 60 0.03
330 125 0.07
331 160 0.09
332 116 0.07
333 161 0.09
334 235 0.13
335 45 0.03
336 248 0.14
337 109 0.06
338 87 0.05
339 7 0.00
340 2 0.00
341 179 0.10
342 15 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (333 bp):
ATATTTGAAGCATGAAAAACCCTTAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATT
GTGGCCAAATATTTGAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCGTGTA
CTAACTATCACGGTTTCTGACTGAAAACGCGTTCCGGGGCCCCGGCTCAGTTTTGCAAGATTTTT
GGCGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTGGATTTAAGG
ATATGTTTTTACGAGCTTCTGAATCTTAATTCGGTTTTATCAGAAATTAATTGGATAAAAAAAAG
GAAAAACC
Found at i:4436 original size:670 final size:666
Alignment explanation
Indices: 3123--5548 Score: 3202
Period size: 670 Copynumber: 3.6 Consensus size: 666
3113 ACTCAATGAA
*
3123 ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCGTTTGAATTATATATTTTTTATGAGTAT
1 ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCG-TTGAATTATATATTTTTTATGAGTAC
* *
3188 TATGGCC-AAAATATGTGAAAAAAAAAAATTTCGGATCAGTTTTTACAAAATTTTAGCTGAAATC
65 TATGGCCAAAAAT-TGTG-AAAAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATC
* * * * *
3252 ATGTACTAACGATCACGGTTTCTGGCTGAAAAGTCGTTCCGGGCCCTGGC-CAGTTTTGCAAGTT
128 ATGTACTAACCATCACGGTTTCTGACTGAAAAGTCGTTCAGGGCCCCGGCTCAGTTTTGCAAGAT
* * *
3316 TTTTGGCGTTGAGACTCCTTGAAATAAT-TATATTCATCTAATCAAATCTCAGCCACATTGGATT
193 TTTTGGCATCGAGACTCCTTGAAAT-ATCTATATGCATCTAATCAAATCTCAGCCACATTGGATT
* *
3380 TAAGGATAAGTTTTACCAGCTA-CTAAATCTTAATTCGAATTTATTAGAAATTAATTGGAT-AAA
257 TAAGGATAAGTTTTACCAGCTATCGAAATCTTAATTCGAATTTATCAGAAATTAATTGGATAAAA
* *
3443 AAAAAGGAAAAACCATATTTGAAGCATGAAAAGCCCTTAAATC-GTTTTGGCGTTGAATTCTATA
322 AAAAAGGAAAAACCATATTTGAAGCATGAAAAGCCCTTAAATCTG-TTTGGCGTTAAATTATATA
* * * * *
3507 CTTTTATGAGTATTGGAGCTAAAAATTGAGAAAAAAAATTTTCAGATAAGTTTTTGCAAAATTTT
386 TTTTTATGAGTATTGGGGCTAAAAATTGAGAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTT
* * * * * * *
3572 AACTGAAATCGTG--T-AC-AACACGGCTTCTTGA-TGAGAACGCATTCCGAGGCTCCGGCTCAG
451 AGCTGAAATCGTGTATAACTATCACGGTTTCTT-ACTGAAAACGCATTCCGGGGCCCCAGCTCAG
3632 TTTTACATGATTTATGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTC
515 TTTTACATGATTTATGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTC
*
3697 ACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGATTCGGTTTTATCAAAAATTAA
580 ACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGATTCGGTTTTATCAGAAATTAA
* *
3762 TTGGATAAAAGAATGAAAAACC
645 TTGGATAAAAAAAAGAAAAACC
*
3784 ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAATACT
1 ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTACT
** *
3849 ATGGCCAAAAATTGTGAAAAAAAAATTTTCATATCAGTTTTTGCAAAATTTTAGCTTAAATCATG
66 ATGGCCAAAAATTGTGAAAAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCATG
* *
3914 TACTAATCATCACGGTTTCTGACTGAAAACG-CGTTCTAGGGCCCCGACTCAGTTTTGCAAGATT
131 TACTAACCATCACGGTTTCTGACTGAAAA-GTCGTTC-AGGGCCCCGGCTCAGTTTTGCAAGATT
* * * * * * *
3978 TTTGGCGTCGATACTCCTTGAACTATCTATATGAATCTAATCAAACCTCAGCTACAATGGATTTA
194 TTTGGCATCGAGACTCCTTGAAATATCTATATGCATCTAATCAAATCTCAGCCACATTGGATTTA
* * * * *
4043 AGGATATGTTTTCACGAG-TATCGAGATCTTCATTCGATTTTATCAGAAATTAATTGGATAAAAA
259 AGGATAAGTTTT-ACCAGCTATCGAAATCTTAATTCGAATTTATCAGAAATTAATTGGAT-AAAA
* *
4107 AAAGAAGGAAAAACCATATTTTAAGCATGAAAAACCCTTAAATCTGTTTGGCGTTAAATTATATA
322 AAA-AAGGAAAAACCATATTTGAAGCATGAAAAGCCCTTAAATCTGTTTGGCGTTAAATTATATA
* * * *
4172 TTTTCTATGAGTATTGGGGCCAAATATTTAGAAAAAAAAATTTCGGATCAGATTTTGCAAAATTT
386 TTTT-TATGAGTATTGGGGCTAAAAATTGAGAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTT
* * *
4237 GAGCTGAAATCGTGTAATAACTATCACGATTTCTTACTGAAAACGCGTTCCGGGGCCCCAGCTC-
450 TAGCTGAAATCGTGT-ATAACTATCACGGTTTCTTACTGAAAACGCATTCCGGGGCCCCAGCTCA
* * * * * * *
4301 GTTTTGCATGATTTTTTACATTGAAACTCCTTGAAGTATCAATATTAATCTAATCAAATCTCAGT
514 GTTTTACATGATTTATGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGT
*
4366 CACATTGGATTTAAGAATATGTTTTTACGAGCTTCTGAATAC-TGATTCGGTTTTATCAGAAATT
579 CACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAAT-CTTGATTCGGTTTTATCAGAAATT
4430 AATTGGATAAAAAAAAGAAAAACC
643 AATTGGATAAAAAAAAGAAAAACC
* * * * *
4454 ATATTTGAAGCATGAAAAGCCCTGAAATTTTTTTGGCGTTGAATTATAT-TTTTTTATGAGCATT
1 ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTACT
* * * * *
4518 TTGG-CAAAATATTCTG--AAAAAAATTTTCGGATCAGTTTTTGCAAAATTTCAACTGAAATCGT
66 ATGGCCAAAA-ATTGTGAAAAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCAT
* * *
4580 GTACTAACCATCACGGTTT-TCAGCTGAAAAGTCGTTCCGAGCCCCCGGCTCAGTTTTGCAAGAT
130 GTACTAACCATCACGGTTTCTGA-CTGAAAAGTCGTTCAG-GGCCCCGGCTCAGTTTTGCAAGAT
* * * ** *
4644 TTTTGGCATCGAAACACCTTGAAATATCTATATTG-ATCTAATCAAATCTTAGATACATTGTATT
193 TTTTGGCATCGAGACTCCTTGAAATATCTATA-TGCATCTAATCAAATCTCAGCCACATTGGATT
* * **
4708 TAAGGATAGGTTTTTACGAGCT-TCTG-AATCTTAATTCGGTTTTATCAGAAATTAATTGGATTA
257 TAAGGATAAG-TTTTACCAGCTATC-GAAATCTTAATTCGAATTTATCAGAAATTAATTGGA-T-
* * ** *
4771 AAAAAAAAAAGGAAAACCCATATTTGAAGCATGAAAAGCCCTTAAATCTTTTTCACGTTGAATTA
318 -AAAAAAAAAGGAAAAACCATATTTGAAGCATGAAAAGCCCTTAAATCTGTTTGGCGTTAAATTA
* * *
4836 TATATTTTTATGAGTCTTGTGGCTAAAAATTGAGAAAAAAAAATATTTTTCGAATCAGTTTTTGC
382 TATATTTTTATGAGTATTGGGGCTAAAAATTGAG-AAAAAAAA-A--TTTCGGATCAGTTTTTGC
* ** **
4901 AAAATTTTAGCTGAAATCGTGTACTAATTATCACGGTTTCTGGCTGAAAACGCATTTTGGGGCCC
443 AAAATTTTAGCTGAAATCGTGTA-TAACTATCACGGTTTCTTACTGAAAACGCATTCCGGGGCCC
* *
4966 CAGCCTCAGATTTACATGA-TTCTGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAA
507 CAG-CTCAGTTTTACATGATTTATGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAA
* * *
5030 ATCTAAGTCACATTGGATTTAAGGATATGTTTTTAAGAGCTTTTGAATCTTGATTCGGTTTTATC
571 ATCTCAGTCACATTGGATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGATTCGGTTTTATC
*
5095 AGAAATTAATTGGATAAAAAAACGAAAAACC
636 AGAAATTAATTGGATAAAAAAAAGAAAAACC
*
5126 ATATTTGAAGCATGAAAAGGCTTGAAATATTTTTGGCGTTGAATTATATATTTTTTATGAGTACT
1 ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTACT
* * *
5191 GTGGCCAAATATTGTGAAAAAAAAA-TTTCGGATCAGTTTTTGAAAAATTTTAGCTGAAATCATG
66 ATGGCCAAAAATTGTGAAAAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCATG
* * * *
5255 TACTAACCATCACTGTTTCTCG-CTGAAAAGTCGTT-ACGGGCCCTGTCTCAGTTTTGCAAGTTT
131 TACTAACCATCACGGTTTCT-GACTGAAAAGTCGTTCA-GGGCCCCGGCTCAGTTTTGCAAG-AT
* * *
5318 TTTTGGCATCGAGACTCCTTGAAATAACTATATTCATCTAATCATATCTCAGCCACATTGGATTT
193 TTTTGGCATCGAGACTCCTTGAAATATCTATATGCATCTAATCAAATCTCAGCCACATTGGATTT
* * *
5383 AAGGATAAGTTTTACCAGCTTAT--AAATCTTAATTCGAATTTATTATAAATTAATTAGATAAAA
258 AAGGATAAGTTTTACCAGC-TATCGAAATCTTAATTCGAATTTATCAGAAATTAATTGGATAAAA
* *
5446 AAAAAGGAAAAACCATATTGGAAGCATGAAAAGCCCTTAAATCTTTTTGGCGTTAAATTATATAT
322 AAAAAGGAAAAACCATATTTGAAGCATGAAAAGCCCTTAAATCTGTTTGGCGTTAAA-T-TATAT
* *
5511 ATTTTTATGAGTATTAGGACTAAAAATTGA-AAAAAAAA
385 ATTTTTATGAGTATTGGGGCTAAAAATTGAGAAAAAAAA
5549 TTCAGATAAG
Statistics
Matches: 1540, Mismatches: 174, Indels: 93
0.85 0.10 0.05
Matches are distributed among these distances:
659 75 0.05
660 46 0.03
661 124 0.08
662 37 0.02
664 6 0.00
665 58 0.04
666 69 0.04
667 212 0.14
668 80 0.05
669 30 0.02
670 254 0.16
671 109 0.07
672 209 0.14
673 88 0.06
674 134 0.09
675 9 0.01
ACGTcount: A:0.35, C:0.14, G:0.16, T:0.35
Consensus pattern (666 bp):
ATATTTGAAGCATGAAAAGGCTTGAAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTACT
ATGGCCAAAAATTGTGAAAAAAAAATTTTCGGATCAGTTTTTGCAAAATTTTAGCTGAAATCATG
TACTAACCATCACGGTTTCTGACTGAAAAGTCGTTCAGGGCCCCGGCTCAGTTTTGCAAGATTTT
TGGCATCGAGACTCCTTGAAATATCTATATGCATCTAATCAAATCTCAGCCACATTGGATTTAAG
GATAAGTTTTACCAGCTATCGAAATCTTAATTCGAATTTATCAGAAATTAATTGGATAAAAAAAA
AGGAAAAACCATATTTGAAGCATGAAAAGCCCTTAAATCTGTTTGGCGTTAAATTATATATTTTT
ATGAGTATTGGGGCTAAAAATTGAGAAAAAAAAATTTCGGATCAGTTTTTGCAAAATTTTAGCTG
AAATCGTGTATAACTATCACGGTTTCTTACTGAAAACGCATTCCGGGGCCCCAGCTCAGTTTTAC
ATGATTTATGACGTCGAAACTCCTTGAAATATCTATATTAATCTAATCAAATCTCAGTCACATTG
GATTTAAGGATATGTTTTTACGAGCTTCTGAATCTTGATTCGGTTTTATCAGAAATTAATTGGAT
AAAAAAAAGAAAAACC
Found at i:9262 original size:11 final size:11
Alignment explanation
Indices: 9246--9282 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
9236 TCAACAAAAG
9246 GAAAATTTTTA
1 GAAAATTTTTA
9257 GAAAATTTTTCA
1 GAAAATTTTT-A
9269 -AAAATTTTTA
1 GAAAATTTTTA
9279 GAAA
1 GAAA
9283 TTTACCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
10 1 0.04
11 22 0.92
12 1 0.04
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.41
Consensus pattern (11 bp):
GAAAATTTTTA
Found at i:23534 original size:2 final size:2
Alignment explanation
Indices: 23527--23565 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
23517 AATACAAAGA
23527 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
23566 AAAGTCTATC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:27098 original size:4 final size:4
Alignment explanation
Indices: 27089--27120 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
27079 TACTCGGAAA
27089 AAAT AAAT AAAT AAAT AAAT AAAT AAAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAA
27121 AAGAGAGAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:38202 original size:13 final size:13
Alignment explanation
Indices: 38184--38213 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
38174 CATTGAAAAA
38184 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
38197 AAAAGAAAGAAAG
1 AAAAGAAAGAAAG
38210 AAAA
1 AAAA
38214 CTATATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (13 bp):
AAAAGAAAGAAAG
Found at i:38205 original size:17 final size:17
Alignment explanation
Indices: 38180--38212 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
38170 AATACATTGA
38180 AAAAAAAAGAAAGAAAG
1 AAAAAAAAGAAAGAAAG
*
38197 AAAAGAAAGAAAGAAA
1 AAAAAAAAGAAAGAAA
38213 ACTATATCAT
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:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAAAGAAAG
Found at i:43112 original size:3 final size:3
Alignment explanation
Indices: 43106--43172 Score: 62
Period size: 3 Copynumber: 22.3 Consensus size: 3
43096 GACTGCTCCC
* * * * * ** *
43106 CAT CAT CCT CCT CCT CAT CAT AAT CAA CAT CCC CAT CAT CAT AAT CAT
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT
43154 CAT CAT CAT CAT CAT CAT C
1 CAT CAT CAT CAT CAT CAT C
43173 CACATTCACT
Statistics
Matches: 52, Mismatches: 12, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.31, C:0.39, G:0.00, T:0.30
Consensus pattern (3 bp):
CAT
Found at i:57115 original size:24 final size:24
Alignment explanation
Indices: 57062--57109 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
57052 ACTTGGATTG
* *
57062 TATGATGCACATGGACTTGGGTGA
1 TATGATGAACATGGACTTGGCTGA
57086 TATGATGAACATGGACTT-GCTGA
1 TATGATGAACATGGACTTGGCTGA
57109 T
1 T
57110 GCTGATCCTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.27, C:0.12, G:0.29, T:0.31
Consensus pattern (24 bp):
TATGATGAACATGGACTTGGCTGA
Found at i:60651 original size:25 final size:26
Alignment explanation
Indices: 60612--60660 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
60602 GCTCATATTT
60612 ATTTTTTAAAAT-AAAATAATAATTAA
1 ATTTTTTAAAATAAAAATAA-AATTAA
*
60638 ATTTTTT-AATTAAAAATAAAATT
1 ATTTTTTAAAATAAAAATAAAATT
60661 TAAACATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTTTTAAAATAAAAATAAAATTAA
Found at i:62735 original size:29 final size:29
Alignment explanation
Indices: 62663--62735 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
62653 GTTGAGGGGA
*
62663 GCAAAACGTCCCAAAATTGAAGTCTAAGGG
1 GCAAAACAT-CCAAAATTGAAGTCTAAGGG
* ** *
62693 GTAAAATGTCCAAAATTGAAGTTTAAGGG
1 GCAAAACATCCAAAATTGAAGTCTAAGGG
*
62722 GCAAAACATTCAAA
1 GCAAAACATCCAAA
62736 CACTACAAGT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
29 29 0.81
30 7 0.19
ACGTcount: A:0.44, C:0.15, G:0.21, T:0.21
Consensus pattern (29 bp):
GCAAAACATCCAAAATTGAAGTCTAAGGG
Found at i:67744 original size:14 final size:14
Alignment explanation
Indices: 67725--67753 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
67715 ATAATATCCT
67725 ACCCTTAAAACAAA
1 ACCCTTAAAACAAA
67739 ACCCTTAAAACAAA
1 ACCCTTAAAACAAA
67753 A
1 A
67754 TCATATTTGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.59, C:0.28, G:0.00, T:0.14
Consensus pattern (14 bp):
ACCCTTAAAACAAA
Found at i:67907 original size:36 final size:38
Alignment explanation
Indices: 67851--67925 Score: 127
Period size: 36 Copynumber: 2.0 Consensus size: 38
67841 TATTCAATTA
*
67851 TTGTCTAGCCTTTGGAGGGTTTAGCCGTTAAGTTTGGG
1 TTGTCTAGCCCTTGGAGGGTTTAGCCGTTAAGTTTGGG
67889 TTGTCTA-CCCTT-GAGGGTTTAGCCGTTAAGTTTGGG
1 TTGTCTAGCCCTTGGAGGGTTTAGCCGTTAAGTTTGGG
67925 T
1 T
67926 GACTAGTGAG
Statistics
Matches: 36, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 25 0.69
37 4 0.11
38 7 0.19
ACGTcount: A:0.13, C:0.15, G:0.32, T:0.40
Consensus pattern (38 bp):
TTGTCTAGCCCTTGGAGGGTTTAGCCGTTAAGTTTGGG
Found at i:78472 original size:38 final size:38
Alignment explanation
Indices: 78423--78513 Score: 166
Period size: 38 Copynumber: 2.4 Consensus size: 38
78413 TTGAAAATTA
*
78423 CAAAAATGTATAAAACACCAAAAAGTTTGCATACTTGT
1 CAAAATTGTATAAAACACCAAAAAGTTTGCATACTTGT
78461 CAAAATTGTATAAAACACCAAAAAGTTTGCATACTTGT
1 CAAAATTGTATAAAACACCAAAAAGTTTGCATACTTGT
78499 C-AAATTGTATAAAAC
1 CAAAATTGTATAAAAC
78514 GAATCAGAAC
Statistics
Matches: 52, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
37 14 0.27
38 38 0.73
ACGTcount: A:0.47, C:0.15, G:0.10, T:0.27
Consensus pattern (38 bp):
CAAAATTGTATAAAACACCAAAAAGTTTGCATACTTGT
Found at i:88680 original size:7 final size:7
Alignment explanation
Indices: 88668--88698 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
88658 ATACTAATAT
88668 ATACTAA
1 ATACTAA
88675 ATACTAA
1 ATACTAA
88682 ATACTAA
1 ATACTAA
88689 ATACTAA
1 ATACTAA
88696 ATA
1 ATA
88699 AATATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (7 bp):
ATACTAA
Found at i:89357 original size:160 final size:163
Alignment explanation
Indices: 89093--89417 Score: 548
Period size: 160 Copynumber: 2.0 Consensus size: 163
89083 ATGGCTTAAG
*
89093 ACATGCAATTATTTTCTCCAATTGGAGTAGACTTTAATTTTTGTGATATTAGATAAAAAAAATAG
1 ACATGCAATTATTTTCTCCAATTGGAGTAGACTTTAATTTTTGTGATACTAGATAAAAAAAATAG
*
89158 GTTAATCATTTAGGTATTATATGTTCTTAAACAGTAGAC-AT-T-AACAAGCTTTACAATTTAGA
66 GTTAATCATTTAGGTATTATATGTTCTTAAACAGTAGACTATATAAACAAACTTTACAATTTAGA
*
89220 TGATATAATATGTTTCAAGCAAATCTAGTTTTC
131 TGATATAATATGTTTCAAGCAAATCCAGTTTTC
*
89253 ACATGCAATTATTTTCTCCAATTGGCGTAGACTTTAATTTTTGTGATACTAGATAAAAAAAATAG
1 ACATGCAATTATTTTCTCCAATTGGAGTAGACTTTAATTTTTGTGATACTAGATAAAAAAAATAG
* * *
89318 GTTAATCATTTAGGTATTGTATGTTTTTAAACAGTAGACATTATATAAACAAATTTTACAATTTA
66 GTTAATCATTTAGGTATTATATGTTCTTAAACAGTAGAC--TATATAAACAAACTTTACAATTTA
89383 GATGATATAATATGTTTCAAGCAAATCCAGTTTTC
129 GATGATATAATATGTTTCAAGCAAATCCAGTTTTC
89418 CATTTATAGA
Statistics
Matches: 153, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
160 100 0.65
163 2 0.01
164 1 0.01
165 50 0.33
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (163 bp):
ACATGCAATTATTTTCTCCAATTGGAGTAGACTTTAATTTTTGTGATACTAGATAAAAAAAATAG
GTTAATCATTTAGGTATTATATGTTCTTAAACAGTAGACTATATAAACAAACTTTACAATTTAGA
TGATATAATATGTTTCAAGCAAATCCAGTTTTC
Found at i:91285 original size:19 final size:20
Alignment explanation
Indices: 91261--91302 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
91251 AAAGGTAGAA
91261 TTAATGGCAAATT-TAATTT
1 TTAATGGCAAATTGTAATTT
*
91280 TTAATGTCAAATTGTAATTT
1 TTAATGGCAAATTGTAATTT
91300 TTA
1 TTA
91303 GGCTTTATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.05, G:0.10, T:0.50
Consensus pattern (20 bp):
TTAATGGCAAATTGTAATTT
Found at i:99834 original size:1 final size:1
Alignment explanation
Indices: 99828--99857 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
99818 GGTTTTCGTG
*
99828 AAAAAAAAAAAAAAAAAAAAAAAAAGAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
99858 CGTGAAAACT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.97, C:0.00, G:0.03, T:0.00
Consensus pattern (1 bp):
A
Found at i:123000 original size:320 final size:318
Alignment explanation
Indices: 121827--124084 Score: 1933
Period size: 320 Copynumber: 7.0 Consensus size: 318
121817 TACTGATAAT
* * * *
121827 ATATATAATTCAACGCCAAAAAAATTGGAGGACTTTTCACACTTTTAATATCGTTTTT-CATATT
1 ATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTT
* *
121891 TTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCAT-GTAAAAACAAATCCTTAAA
66 TTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGC-TCGTAAAAACAAATCCTTAAA
* * *** *
121955 TCCAATGTGGCTGAGATTTGGTTAGATGAATAAAGATATTTCAAGGAGTCCCGAC-ACCAAAAAT
130 TCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGT-CTTTCTGCCAAAAAT
** * * * * * * *
122019 CATGCAAAACAGAACCGTGGCCTTGGAACGCGTTTTTAGTC-AAAAACTGTAATGGTTATTACAC
194 CATGCAAAACTCAGCCGGGGCC-CGAAACGCGTTTTTAGCCAAAAAAC-GTGATGGTTAGTACAC
* ** *
122083 GATTTAGGCTAAAAACGGACCCGAAACATATTT--TCTCAAGTTTTTGCCACAATACTCAGAAAA
257 GATTTCGGCTAAAAATTG--CCGAAA-ATATTTACTCACAAGTTTTTG-CACAATACTCAGAAAA
122146 A
318 A
* * * * * * *
122147 ATAAAAAATTTAATGCCAAAAAAATTGATA-GGCGTTTCACGCTTCTAATAACGTTTTTCCATTT
1 ATATATAATTCAACGCCAAAAAAATTGA-AGGGCTTTTCACACTTCTAATATCGTTTTTCCA-TT
* *
122211 TTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCACATGCTCGTAAAAACAAATCCTT
64 TTTTTT--GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT
* * * * * * **
122276 ATATCCAATGTGGATGACATTTGATTTGATGAATATAGAAATTTCAAGGAGTCTTTGAGCCAAAA
127 AAATCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAA
* ** * * * * *
122341 ATCATGC-AAATTTGGACCGGGGCTCCGGAATGCGTTTTTACCCAAAAACCGTGATGGCTAGTAC
192 ATCATGCAAAACTCAG-CCGGGGC-CCGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTAC
* * * * ** * *
122405 ACGATTTTGGCTAAAATTTTGCAAAACCTGACCCGACAAGTTTTTCCTCA-ATTTTTTTCCACAG
255 ACGATTTCGGCTAAAA-ATTG-----CC-GA----A-AA-TATTTACTCACAAGTTTTTGCACAA
122469 TACTCAGAAAAA
307 TACTCAGAAAAA
* * * * * * * *
122481 ATATATAATTCAACGCTAAAAAGA-TAAACGAGCTTTTAACGCTTCTACTATCGTTTTCCCATTT
1 ATATATAATTCAACGCCAAAAAAATTGAA-GGGCTTTTCACACTTCTAATATCGTTTTTCCATTT
** * * * * * * * *
122545 TTTCCGAATTAATTTCTAATAAAATCGTAACAAGATTTAGATACTCGTAAAAACACATCGTTATA
65 TTTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* * * * * ** * * *
122610 TCCAATGTGGCTGAGATTTGTTTCGATGAATTTAGATATTCCAAAAAATCTTTGC-ACCAGAAAT
130 TCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAAT
* * * * * *
122674 CATGCAAAATTAAGCCGGGGCTCCGGAACGCGTTTTTAGCCAACAAAACGTAAAGGTTAGTGCAC
194 CATGCAAAACTCAGCCGGGGC-CCGAAACGCGTTTTTAGCCAA-AAAACGTGATGGTTAGTACAC
* * * * * * *
122739 GATTTCGGCTAAAATTTTG-C-AAAA-ACTGACCCGAAAAGTTTTT-CACAATACTTATAAAAA
257 GATTTCGGCTAAAA-ATTGCCGAAAATATTTACTC-ACAAGTTTTTGCACAATACTCAGAAAAA
* * * *
122799 ATATATAATTCAACGCCCAAAAAATTGAAGGGTTTTTGACACTACTAATATCGTTTTTCCATTTT
1 ATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCCA-TTT
* * * *
122864 TGTTTTGAATTTATTTCTAATTAAATCGAAAAAAGATTCAGATCCTCGAAAAAACCAATCCTTAA
65 T-TTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAA
* * * * *
122929 ATCTATTGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAAGTGTCTTTCTGTCAAAAAT
129 ATCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAAT
* * * * *
122994 CATGCAAAACTGAGCCGGGTCCCGAAAGGCGTTTTTAGCC-AAAAACGTTGATGGTTAAATAAAC
194 CATGCAAAACTCAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAAACG-TGATGGTT-AGTACAC
* ** * * * *
123058 GATTTCGGCTTAAAACTAACCCGAAAAGTATTT-CT--CAATTTTTTGCAAAATATTCAGAGAAA
257 GATTTCGGC-TAAAAAT-TGCCGAAAA-TATTTACTCACAAGTTTTTGCACAATACTCAGAAAAA
* ** *
123120 ATATATAATTCAA--CCAAAAAGATTGACTGGCTTTTCACGCTTCTAATATCGTTTTTCCA-TTT
1 ATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTT
* *
123182 TTTTGAATTTATTTCTAATTATATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTTAAAA
66 TTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTT-AAA
* * *
123247 TCCATTGTGGCTGAAATTTGGTTCGATGAGTATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
130 TCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
* * * * * * *
123312 ATGCAAAACTCAGTCGAGGCTCCAAAACGCATTTTTAG-CAAAAAA-TTG-T-GAT-GTACATGA
195 ATGCAAAACTCAGCCGGGGC-CCGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGA
* *
123372 TTTCGGCTAAAAATTGACCCGAAAATTTTTTTCTCA-ATA-TTTTTGCCACAATACTCA-AAAAA
259 TTTCGGCTAAAAATTG--CCGAAAA-TATTTACTCACA-AGTTTTTG-CACAATACTCAGAAAAA
* * **
123434 ATATATAATTGAACGCC-AAAAAACTGAAGGATTTTTCA-AGCTTCTAATATCGTTTTTCCA-TT
1 ATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACA-CTTCTAATATCGTTTTTCCATTT
** * * * * *
123496 TTTCCGAATTTATTTCTACTTATATCGAAACAAGATTAAGATGCTCGTAAGAACAAATCCTTATA
65 TTTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAA
* * * * *
123561 TCCAATGTGGCTGAGATTTGATTCGATGAATATATATATTTCAAGGAGTGTTTCTGCCAAAAATC
130 TCCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATC
* * * *
123626 ATGCAAAACTCAGTCGGGGCGCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTAAGTGCACGA
195 ATGCAAAACTCAGCCGGGGC-CCGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGA
* ** * *
123691 TTTCGGCTAAAAACTGACCCGAAAAGT-TTTTTTCTCAATTTTTTGCCACAATACT--GAAAAA
259 TTTCGGCTAAAAATTG--CCGAAAA-TATTTACTCACAAGTTTTTG-CACAATACTCAGAAAAA
* * * * *
123752 AAATATAATTCAACGCGAAAAAAATTGAAGGAG-TTTT--CACTTTTAATATCATTTTCCCATTT
1 ATATATAATTCAACGCCAAAAAAATTGAAGG-GCTTTTCACACTTCTAATATCGTTTTTCCATTT
* * * *
123814 TTTTTCCGAATTTATTTCTAATTATATCGAAACAAGATTCAAATGTTCGTAAGAAAAAAATCCTT
65 TTTTT--GAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA-AAACAAATCCTT
* *
123879 AAATCCAATGTGGCT-AAGATTTTGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCAAAA
127 AAATCCAATGTGGCTGAA-ATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAA
* * * * * * *
123943 AATCAAGCAAAATTCAGCCGGGGCCTGAAACCCGTTTTTAGCC-AAACACTATGATGATTAGTAC
191 AATCATGCAAAACTCAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAAAC-GTGATGGTTAGTAC
* *
124007 ACGATTTCGGCTAAAAATTGACCCAAAATTTATTT-CT--C-ATTTTTATGCCACAATACTCAGA
255 ACGATTTCGGCTAAAAATTG-CCGAAAA--TATTTACTCACAAGTTTT-TG-CACAATACTCAGA
124068 AAAA
315 AAAA
*
124072 ATATACAATTCAA
1 ATATATAATTCAA
124085 GGAGTCTTTG
Statistics
Matches: 1579, Mismatches: 281, Indels: 156
0.78 0.14 0.08
Matches are distributed among these distances:
311 6 0.00
312 23 0.01
313 2 0.00
314 120 0.08
315 110 0.07
316 61 0.04
317 115 0.07
318 133 0.08
319 159 0.10
320 284 0.18
321 117 0.07
322 11 0.01
323 6 0.00
324 161 0.10
325 7 0.00
326 1 0.00
328 3 0.00
329 2 0.00
331 135 0.09
332 41 0.03
333 10 0.01
334 64 0.04
335 6 0.00
336 2 0.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (318 bp):
ATATATAATTCAACGCCAAAAAAATTGAAGGGCTTTTCACACTTCTAATATCGTTTTTCCATTTT
TTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAAT
CCAATGTGGCTGAAATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCA
TGCAAAACTCAGCCGGGGCCCGAAACGCGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATT
TCGGCTAAAAATTGCCGAAAATATTTACTCACAAGTTTTTGCACAATACTCAGAAAAA
Found at i:125013 original size:315 final size:310
Alignment explanation
Indices: 124221--125246 Score: 1168
Period size: 306 Copynumber: 3.3 Consensus size: 310
124211 AATTCTTTGC
* * * * *
124221 CACAATACTCAGAAAAAAT-TAATGATTCAATG-CTAAAAAAAATTGAAGGGTATTTCACGGTTT
1 CACAATACTCAGAAAAAATAT-ATAATTCAACGAC--AAAAAAATTGAAGGGTTTTTCACGCTTC
* * * *
124284 CAATATCGTTTTTTCCATTTTTTTACCGAATTTATTTCTAATTAAATCAAAATAAGATTCAGATA
63 CAATATCG-TTTTACCA--TTTTTACCGAATTTATTTCTAATTAAATCAAAACAAAATTCAGATG
* * *
124349 CTCGTAAAAACAAATCCTTAAATCCATCGTGGTTGAGATTTGGTTAGATGAATATAGATATTTCA
125 CTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCA
* *
124414 ATGACTCTTT-CTGCCAAAAATCATGCAAAACTGAGATGGGACCTGAAACACGTTTTTAGCCAAA
190 ATGAGTCTTTGC-G-CAAAAATCATGCAAAACTGAG-TGGG-CCCGAAACACGTTTTTAGCCAAA
* * * * *
124478 GACCGTGATTGTAATACACGAGTTCGGCTAAAAACTGACCCG-AAATTTTT----TTTC--
251 AACCGTGATGGT-GTACACGATTTCGGCTAAAAACTGACCTGAAAATTTTTCCAATTTCTG
* * *
124532 CACAATACTCAGAAAAAATATATAATTCAACGATAAAAAAATTGAAGGGTTTTTCACGCATCTAA
1 CACAATACTCAGAAAAAATATATAATTCAACGACAAAAAAATTGAAGGGTTTTTCACGCTTCCAA
* * * *
124597 TATCATTTTCCCATTTTTCCCGAATTTATTTC-AATTAAATTAAAACAAAATTCAGATGCTCGTA
66 TATCGTTTTACCATTTTTACCGAATTTATTTCTAATTAAATCAAAACAAAATTCAGATGCTCGTA
* * *
124661 AAAACAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTCGATGAAAATAGATATTT-AAAGAAG
131 AAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAATG-AG
* * *
124725 TCTTTGCGCAAAAAATCATGCAAAACTGAGTCGAGCCACGAAACACATTTTTAGCAAAAAACCGT
195 TCTTTGCGC-AAAAATCATGCAAAACTGAGT-GGGCC-CGAAACACGTTTTTAGCCAAAAACCGT
*
124790 GATGGTGTAAACGATTTCGGCTAAAAACTGACCTGAAAAGTTTTTCCCCAATTTCTGG
257 GATGGTGTACACGATTTCGGCTAAAAACTGACCTGAAAA-TTTTT--CCAATTTCT-G
* * * *
124848 CAACAATACTTAG-AAAAATATATAATTCAACGCCGAAATAATTGAAGGGTTTTTCACGCTTCCA
1 C-ACAATACTCAGAAAAAATATATAATTCAACGACAAAAAAATTGAAGGGTTTTTCACGCTTCCA
* * * *
124912 CTATTGTTTTACCATTTTT-CCG-ATTTATTTCTAATTATATCGAAACAAAATTCAGATGCTCGT
65 ATATCGTTTTACCATTTTTACCGAATTTATTTCTAATTAAATCAAAACAAAATTCAGATGCTCGT
* *
124975 AAAAACGAATCCTTAAATCCATTGTGGCTGAAATTTGGTTCGATGAATATAGATATTTCAATGAG
130 AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAATGAG
* * *
125040 TCTTCTGC-CAAAAATCATGCAAAACTCAACTGGGGCCTCGAAACGCGTTTTTAGCCAAAAACCG
195 TCTT-TGCGCAAAAATCATGCAAAACT-GAGT-GGGCC-CGAAACACGTTTTTAGCCAAAAACCG
* * *
125104 TGATGATATGTACACGATTTCGGCTAAAAACTGACCTGAATATTTTTCTCAATTTTTTG
256 TGATG--GTGTACACGATTTCGGCTAAAAACTGACCTGAAAATTTTTC-CAA-TTTCTG
* * * * * *
125163 CCACAATACTCAGAAAAAATATATAATTTGAA-AACTAAAAAATTGAAGAGTTTTTCACGTTTCA
1 -CACAATACTCAGAAAAAATATATAA-TTCAACGACAAAAAAATTGAAGGGTTTTTCACGCTTCC
125227 AATATCGTTTTACCATTTTT
64 AATATCGTTTTACCATTTTT
125247 TTCCTAATTT
Statistics
Matches: 611, Mismatches: 74, Indels: 55
0.83 0.10 0.07
Matches are distributed among these distances:
305 32 0.05
306 140 0.23
307 24 0.04
309 7 0.01
310 30 0.05
311 28 0.05
312 1 0.00
313 4 0.01
314 27 0.04
315 140 0.23
316 132 0.22
317 46 0.08
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (310 bp):
CACAATACTCAGAAAAAATATATAATTCAACGACAAAAAAATTGAAGGGTTTTTCACGCTTCCAA
TATCGTTTTACCATTTTTACCGAATTTATTTCTAATTAAATCAAAACAAAATTCAGATGCTCGTA
AAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTTCAATGAGT
CTTTGCGCAAAAATCATGCAAAACTGAGTGGGCCCGAAACACGTTTTTAGCCAAAAACCGTGATG
GTGTACACGATTTCGGCTAAAAACTGACCTGAAAATTTTTCCAATTTCTG
Found at i:125893 original size:321 final size:321
Alignment explanation
Indices: 125355--126229 Score: 1150
Period size: 322 Copynumber: 2.7 Consensus size: 321
125345 AAATGAAGGG
*
125355 TTTTTGGCACAATA-TTCAGAAAAAATATATAATTCGAAGCCAAAAAAAATTGAAGGGTTTTTTA
1 TTTTTGGCACAATACTT-AG-AAAAATATATAATTCAAAGCC-AAAAAAATTGAAGGG-TTTTT-
* * * *
125419 CACGCTTCTAATATCGTTGTACCATTTTTTTTCCTAATTTATATT-TAATTATATCGAAACAAGA
61 CACGATTCTACTATCGTTTTACCA-TTTTTTCCCTAATTTAT-TTCTAATTATATCGAAACAA-A
* *
125483 TTCAGATGCTTGTAAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCAATGAATATA
123 TTCAGATGCTAGT-AAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATA
* * ** * *
125548 GATATTTCAGGGTGTGTTTCTGCCAAAAATTATTCAAAACTCAGCCAGGGCCCCGAAACACGTTT
187 GATATTCCAAGGAATGTATCTGCCAAAAATTATGCAAAACTCAGCCAGGGCCCCGAAACACGTTT
* * *
125613 TTAGCCAAAAACTATGATGGTAAGTTTACGATTTCGGCTAAAAACTTACCCG-AAATTTTTTTTC
252 TTAGCCAAAAACCATGATGGTAAGTATACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTC
125677 -CAAT
317 TCAAT
*
125681 TTTTTGCCACAATACTTAGAAAACATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCACG
1 TTTTTGGCACAATACTTAGAAAA-ATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCACG
* *
125746 AATCTACTATCGTTTTACCATTTTTTCCCGAATTTATTTCTAATTATATCGAAACAACATTCAGA
65 ATTCTACTATCGTTTTACCATTTTTTCCCTAATTTATTTCTAATTATATCGAAACAA-ATTCAGA
** * * *
125811 AACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGATATTTGGTTCGATGAATATAGGTATTC
129 TGCTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTC
* * * * *
125876 CAATGAATGTATCTGCCAAAAATTATGCGAAACTCAGCCGGGGCCTCGAAACGCGTTTTTAGCCA
194 CAAGGAATGTATCTGCCAAAAATTATGCAAAACTCAGCCAGGGCCCCGAAACACGTTTTTAGCCA
* *
125941 AAAACCGTGATGGTAAGTATACGATTTCGGCTAAAAACTGACTCGAAAATTTTTTTTCTCAAT
259 AAAACCATGATGGTAAGTATACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAAT
* * *
126004 TTTTTGGGACAATAC-TA-AAAAAAATATAATTCAAAGCAAAAAAAATTTTGAAGGGTTTTTCAC
1 TTTTTGGCACAATACTTAGAAAAATATATAATTCAAAGCCAAAAAAA--TTGAAGGGTTTTTCAC
* * * *
126067 GTTTCTACTATCGTTTTTCCATTTTTTCCCTAATTTATATCTAATTATATCGCAACAAAGTTCAG
64 GATTCTACTATCGTTTTACCATTTTTTCCCTAATTTATTTCTAATTATATCGAAACAAA-TTCAG
* * *
126132 ATGCTAGTAAAATCAAATCCTTAAATCCATTGTGGTTGAGATTTAGTTCGATGAATATAGATATT
128 ATGCTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATT
* * * * * * *
126197 TCAGGGAGTGTTTCTACCAGAAATTAAGCAAAA
193 CCAAGGAATGTATCTGCCAAAAATTATGCAAAA
Statistics
Matches: 483, Mismatches: 58, Indels: 20
0.86 0.10 0.04
Matches are distributed among these distances:
320 22 0.05
321 156 0.32
322 211 0.44
323 37 0.08
324 5 0.01
325 19 0.04
326 31 0.06
327 2 0.00
ACGTcount: A:0.35, C:0.16, G:0.14, T:0.34
Consensus pattern (321 bp):
TTTTTGGCACAATACTTAGAAAAATATATAATTCAAAGCCAAAAAAATTGAAGGGTTTTTCACGA
TTCTACTATCGTTTTACCATTTTTTCCCTAATTTATTTCTAATTATATCGAAACAAATTCAGATG
CTAGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGATTTGGTTCGATGAATATAGATATTCCA
AGGAATGTATCTGCCAAAAATTATGCAAAACTCAGCCAGGGCCCCGAAACACGTTTTTAGCCAAA
AACCATGATGGTAAGTATACGATTTCGGCTAAAAACTGACCCGAAAATTTTTTTTCTCAAT
Done.