Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020865.1 Corchorus olitorius cultivar O-4 contig20898, 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: 80501
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:1156 original size:325 final size:325
Alignment explanation
Indices: 563--1241 Score: 954
Period size: 325 Copynumber: 2.1 Consensus size: 325
553 AAAAAAGCTT
* * *
563 AATCTTTTGGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCTTGAAAAAAAA
1 AATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCTAGAAAAAAAA
** * *
628 ATTCGGATAAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGAGTT
66 ATTCGGATAAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGAGTT
* * * *
693 TCGGGGGCCCAGGCTCAGCTTTGCATGATTTTTTGCAGAACGACTCCGTGAAATATGTATACTCA
131 TCGGAGGCCCAGGCTCAGCTTTGCATGATTTTTTGCAGAAAGACTCCGTGAAATATCTACACTCA
* * * *
758 TCTAACAAAATCTCAGCCACATTAAAATGAAGGATTTGTTTTTACGAGCATCTGAATCTAGTTCT
196 TCGAACAAAATCCCAGCCACATTAAAATGAACGATTTGTTTTTACGAGCATCCGAATCTAGTTCT
* * *
823 GATTTAATTATAAATTGATTCCGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATCCCGT
261 GATTTAATTAAAAATTAATTCCGAAAAAAA-TGGAAAAATGATATTAGAAGCATGAAAATCCCGT
888 C
325 C
*
889 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTC-AGAAAAAAAA
1 AATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCTAGAAAAAAAA
* * * *
953 ATTCTTG-TCAGTTTTTAGCCCATATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGCGT
66 ATTC-GGATAAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGAGT
* * * * *
1017 TTCGGAGGCCCCGGCTCAGTTTTGCATGA-TTTTTGATAGAAAGACTCCTTGAAATATCTACATT
130 TTCGGAGGCCCAGGCTCAGCTTTGCATGATTTTTTG-CAGAAAGACTCCGTGAAATATCTACACT
* ** * *
1081 CATCGAATC-AAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTA-
194 CATCGAA-CAAAATCCCAGCCACATTAAAATGAACGATTTGTTTTTACGAGCATCCGAATC-TAG
* * *
1144 TTTTGTTTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCC
257 TTCTGATTTAATTAAAAATTAATTCCGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCC
1209 CGTC
322 CGTC
1213 AATCTTTTTGGCGTTGAATTATATATTTT
1 AATCTTTTTGGCGTTGAATTATATATTTT
1242 GCTACATGTT
Statistics
Matches: 312, Mismatches: 37, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
324 68 0.22
325 189 0.61
326 55 0.18
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (325 bp):
AATCTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCTAGAAAAAAAA
ATTCGGATAAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGAGTT
TCGGAGGCCCAGGCTCAGCTTTGCATGATTTTTTGCAGAAAGACTCCGTGAAATATCTACACTCA
TCGAACAAAATCCCAGCCACATTAAAATGAACGATTTGTTTTTACGAGCATCCGAATCTAGTTCT
GATTTAATTAAAAATTAATTCCGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
Found at i:1659 original size:828 final size:828
Alignment explanation
Indices: 61--1745 Score: 2746
Period size: 828 Copynumber: 2.0 Consensus size: 828
51 AAAAAAGCTT
* * * * *
61 AATCTTTTGGGCGTTGAATTATAAATTTTTACTTAGTATTGTGGCAAAATATTCAGGAAAAAAAA
1 AATCTTTTTGGCGTTGAATTATATATTTTTACTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAA
** * *
126 TTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGAGTTT
66 TTCGGGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGAGTTT
* *
191 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
131 CGGAGGCCCAGGCTCAGCTTTGCATGATTTTTGATAGAAAGACTCCTTGAAATATCTACATTCAT
256 CGAATCAAATCCCAGCGACATTCGATTTAACGATTTTTTTTACGAGCATCCGAAATCTTATTTCG
196 CGAATCAAATCCCAGCGACATTCGATTTAACGATTTTTTTTACGAGCATCCGAAATCTTATTTCG
* *
321 TTTTAATTAGAAATTAATTCTGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTCA
261 TTTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTCA
* *
386 ATCTTTTTGATGTTTAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGA
326 ATCTTTTTGACGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGA
*
451 CAGATATTGCTGCAAATTGGTACTGATTATGCTACAATTGGGACAAAATAAGCCTACAACTAGGG
391 AAGATATTGCTGCAAATTGGTACTGATTATGCTACAATTGGGACAAAATAAGCCTACAACTAGGG
516 TCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTGGGCGTTGAA
456 TCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTGGGCGTTGAA
* *
581 TTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCTTGAAAAAAAAATTCGGATAAGTTTTTAG
521 TTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCTAGAAAAAAAAATTCGGATAAGCTTTTAG
* * *
646 CTGAAATCGTGTACTAACCATCACGGTTTTTGGGCTAAAAACGAGTTTCGGGGGCCCAGGCTCAG
586 CTGAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTCGGGGGCCCAGGCTCAG
* * * * * *
711 CTTTGCATGATTTTTTGCAGAACGACTCCGTGAAATATGTATACTCATCTAACAAAATCTCAGCC
651 CTTTGCATGATTTTTGGCAGAAAGACTCCGTGAAATATCTACACTCATCGAACAAAATCCCAGCC
* * * *
776 ACATTAAAATGAAGGATTTGTTTTTACGAGCATCTGAATCTAGTTCTGATTTAATTATAAATTGA
716 ACATTAAAATGAACGATTTGTTTTTACGAGCATCCGAATCTAGTTCTGATTTAATTAGAAATTAA
* * *
841 TTCCGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATCCCGTC
781 TTCCGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
* *
889 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAA
1 AATCTTTTTGGCGTTGAATTATATATTTTTACTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAA
** * *
954 TTCTTGTCAGTTTTTAGCCCATATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGCGTTT
66 TTCGGGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGAGTTT
* *
1019 CGGAGGCCCCGGCTCAGTTTTGCATGATTTTTGATAGAAAGACTCCTTGAAATATCTACATTCAT
131 CGGAGGCCCAGGCTCAGCTTTGCATGATTTTTGATAGAAAGACTCCTTGAAATATCTACATTCAT
*
1084 CGAATCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCG-AATCTTATTTT
196 CGAATCAAATCCCAGCGACATTCGATTTAACGATTT-TTTTTACGAGCATCCGAAATCTTATTTC
1148 GTTTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
260 GTTTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
*
1213 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAG
325 AATCTTTTTGACGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAG
* * *
1278 AAAGATATTGTTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAG
390 AAAGATATTGCTGCAAATTGGTACTGATTATGCTACAA-TTGGGACAAAATAAGCCTACAACTAG
1343 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTGGGCGTTG
454 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTGGGCGTTG
* * * *
1408 AATTATAAATTTTTTCTTAGTATTGTGGCAAAAAATTC-AGGAAAAAAAATTCGGGTCAGCTTTT
519 AATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCTAGAAAAAAAAATTCGGATAAGCTTTT
1472 AGCTGAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTCGGGGGCCCAGGCTC
584 AGCTGAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTCGGGGGCCCAGGCTC
* * * *
1537 AGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCATCGAACCAAATCCCAG
649 AGCTTTGCATGATTTTTGGCAGAAAGACTCCGTGAAATATCTACACTCATCGAACAAAATCCCAG
* ** * * * * *
1602 CGACATTCGATTTAACGATTTGTTTTTATGAGCATCCGAATCTTATTTC-GTTTTAATTAGAAAT
714 CCACATTAAAATGAACGATTTGTTTTTACGAGCATCCGAATC-TAGTTCTGATTTAATTAGAAAT
*
1666 TAATTCGGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
778 TAATTCCGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
1717 AATCTTTTTGGCGTTGAATTATATATTTT
1 AATCTTTTTGGCGTTGAATTATATATTTT
1746 GCTACATGTT
Statistics
Matches: 789, Mismatches: 65, Indels: 6
0.92 0.08 0.01
Matches are distributed among these distances:
828 641 0.81
829 148 0.19
ACGTcount: A:0.33, C:0.15, G:0.18, T:0.34
Consensus pattern (828 bp):
AATCTTTTTGGCGTTGAATTATATATTTTTACTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAA
TTCGGGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGAGTTT
CGGAGGCCCAGGCTCAGCTTTGCATGATTTTTGATAGAAAGACTCCTTGAAATATCTACATTCAT
CGAATCAAATCCCAGCGACATTCGATTTAACGATTTTTTTTACGAGCATCCGAAATCTTATTTCG
TTTTAATTAAAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTCA
ATCTTTTTGACGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAGA
AAGATATTGCTGCAAATTGGTACTGATTATGCTACAATTGGGACAAAATAAGCCTACAACTAGGG
TCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTGGGCGTTGAA
TTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCTAGAAAAAAAAATTCGGATAAGCTTTTAG
CTGAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTCGGGGGCCCAGGCTCAG
CTTTGCATGATTTTTGGCAGAAAGACTCCGTGAAATATCTACACTCATCGAACAAAATCCCAGCC
ACATTAAAATGAACGATTTGTTTTTACGAGCATCCGAATCTAGTTCTGATTTAATTAGAAATTAA
TTCCGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
Found at i:1891 original size:504 final size:503
Alignment explanation
Indices: 889--2236 Score: 2123
Period size: 491 Copynumber: 2.7 Consensus size: 503
879 AAATCCCGTC
* * *
889 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAA
1 AATCTTTTGGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCAG-AAAAAAAA
** ** * * * *
954 TTCTTGTCAGTTTTTAGCCCATATCGTGTACTAACCATCACGATTTTTGGGATAAAAACGCGTTT
65 TTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTT
* * * *
1019 CGGAGGCCCCGGCTCAGTTTTGCATGATTTTTGATAGAAAGACTCCTTGAAATATCTACATTCAT
130 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
* *
1084 CGAATCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTTG
195 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCG
1149 TTTTAATTAAAAATTAATTCGG-AAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
260 TTTTAATTAAAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
*
1213 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAG
325 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAG
*
1278 AAAGATATTGTTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAG
390 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAG
1343 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTT
455 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTT
*
1392 AATCTTTTGGGCGTTGAATTATAAATTTTTTCTTAGTATTGTGGCAAAAAATTCAGGAAAAAAAA
1 AATCTTTTGGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCA-GAAAAAAAA
* *
1457 TTCGGGTCAGCTTTTAGCTGAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTT
65 TTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTT
1522 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
130 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
*
1587 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTATGAGCATCCGAATCTTATTTCG
195 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCG
* *
1652 TTTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
260 TTTTAATTAAAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
1717 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAG
325 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAG
1782 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAG
390 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAG
1847 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTT
455 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTT
1896 AATCTTTTTGGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGG---------C----AAAAAA
1 AATC-TTTTGGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAA
* * *
1948 TTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTACGCTAAAAATGAGTTT
65 TTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTT
* * *
2013 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCTTGAAATATCTATATTCAT
130 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
* * * * ** * * * *
2078 CTAACCGAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTT-GTTCT
195 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTC-
* * * * * *
2142 GATTTAATTATAAATTGATTCCGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATCCCGT
259 GTTTTAATTAAAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGT
*
2207 CAATCTTTTTGGAGTTGAATTATATATTTT
324 CAATCTTTTTGGCGTTGAATTATATATTTT
2237 TTCTGAGTAT
Statistics
Matches: 788, Mismatches: 53, Indels: 20
0.92 0.06 0.02
Matches are distributed among these distances:
490 3 0.00
491 264 0.34
496 1 0.00
503 258 0.33
504 223 0.28
505 39 0.05
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.35
Consensus pattern (503 bp):
AATCTTTTGGGCGTTGAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAT
TCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTC
GGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCATC
GAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGT
TTTAATTAAAAATTAATTCGGAAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTCA
ATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAGA
AAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAGG
GTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTT
Found at i:2305 original size:324 final size:323
Alignment explanation
Indices: 1942--2559 Score: 907
Period size: 324 Copynumber: 1.9 Consensus size: 323
1932 GTATTGTGGC
** * *
1942 AAAAAATTCGGGTCAGTTTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTACGCTAAAAAT
1 AAAAAATTCGGGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTACGCTAAAAAC
* *
2007 GAGTTTCGGGGGCC-CAGGCTCAGCTTTGCATGATTTTTGGCAGAACGACTCCTTGAAATATCTA
66 GAGTTTCGGAGGCCTC-GGCTCAGCTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTA
* * * * * *
2071 TATTCATCTAACCGAATCTCAGCCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCT
130 CATTCATCGAACCAAATCCCAGCCACATTAAATTGAACGATTTGTTTTTACGAGCATCCGAATCT
* * * *
2136 T-GTTCTGATTTAATTATAAATTGATTCCGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAA
195 TATTTC-GATTTAATTAGAAATTAATTCCGAAAAAAA-TGGAAAAATGATATTAGAAGCATGAAA
2200 ATCCCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGA
258 ATCCCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGA
2265 A
323 A
** * * **
2266 AAAAAATTCTTGTTAGTTTTTAGCCCAAATCGTGTACTAATCATCACGATTTTTGGGCTAAAAAC
1 AAAAAATTCGGGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTACGCTAAAAAC
* * *
2331 GCGTTTCGGAGGCCTCGGCTCAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTAC
66 GAGTTTCGGAGGCCTCGGCTCAGCTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTAC
* ** *
2396 ATTCATCGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTT
131 ATTCATCGAACCAAATCCCAGCCACATTAAATTGAACGATTTGTTTTTACGAGCATCCGAATCTT
* *
2461 ATTTCGTTTTAATTAGAAATTAATTCGGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATC
196 ATTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATC
*
2526 CCGTCAATCTTTTTGGCGTTGAATTATATATTTT
261 CCGTCAATCTTTTTGGAGTTGAATTATATATTTT
2560 GCTACATGTT
Statistics
Matches: 260, Mismatches: 32, Indels: 5
0.88 0.11 0.02
Matches are distributed among these distances:
323 62 0.24
324 194 0.75
325 4 0.02
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Consensus pattern (323 bp):
AAAAAATTCGGGTCAGTTTTTAGCCCAAATCGTGTACTAACCATCACGATTTTTACGCTAAAAAC
GAGTTTCGGAGGCCTCGGCTCAGCTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTAC
ATTCATCGAACCAAATCCCAGCCACATTAAATTGAACGATTTGTTTTTACGAGCATCCGAATCTT
ATTTCGATTTAATTAGAAATTAATTCCGAAAAAAATGGAAAAATGATATTAGAAGCATGAAAATC
CCGTCAATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAA
Found at i:3096 original size:826 final size:815
Alignment explanation
Indices: 1392--3113 Score: 2959
Period size: 826 Copynumber: 2.1 Consensus size: 815
1382 AAAAAAGCTT
* * * *
1392 AATCTTTTGGGCGTTGAATTATAAATTTTTTCTTAGTATTGTGGCAAAAAATTCAGGAAAAAAAA
1 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCA-GAAAAAAAA
** * **
1457 TTCGGGTCAGCTTTTAGCTGAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTT
65 TTCTTGTCAGTTTTTAGCCCAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTT
*
1522 CGGGGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
130 CGGAGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
*
1587 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTATGAGCATCCGAATCTTATTTCG
195 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCG
1652 TTTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
260 TTTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
1717 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAG
325 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAG
*
1782 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAATTAG
390 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAACTAG
*
1847 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTTGGGCGTT
455 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTTAGGCGTT
1912 GAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCGGGTCAGTTTTTAGCTGAAATCGTGT
520 GAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCGGGTCAGTTTTTAGCTGAAATCGTGT
*
1977 ACTAACCATCACGGTTTTTACGCTAAAAATGAGTTTCGGGGGCCCAGGCTCAGCTTTGCATGATT
585 ACTAACCATCACGGTTTTTACGCTAAAAACGAGTTTCGGGGGCCCAGGCTCAGCTTTGCATGATT
* * *
2042 TTTGGCAGAACGACTCCTTGAAATATCTATATTCATCTAACCGAATCTCAGCCACATTAAATTGA
650 TTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTAAATTGA
2107 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTGATTTAATTATAAATTGATTCCGAAAAAAA
715 AGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTGATTTAATTATAAATTGATTCCGAAAAAAA
2172 TTGGAAAAATGATATTAGAAGCGTGAAAATCCCGTC
780 TTGGAAAAATGATATTAGAAGCGTGAAAATCCCGTC
2208 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAT
1 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAT
* * * * *
2273 TCTTGTTAGTTTTTAGCCCAAATCGTGTACTAATCATCACGATTTTTGGGCTAAAAACGCGTTTC
66 TCTTGTCAGTTTTTAGCCCAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTC
*
2338 GGAGGCCTC-GGCTCAGTTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
131 GGAGGCC-CAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCAT
2402 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCG
195 CGAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCG
*
2467 TTTTAATTAGAAATTAATTCGG-AAAAAAATGGAAAAATGATATTAGAAGCATGAAAATCCCGTC
260 TTTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTC
*
2531 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAATTAG
325 AATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAG
2596 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAACTAG
390 AAAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAACTAG
*
2661 GGTCCGTTTGGCCCAGCTTATTTAACAGTTTATCTACTGAAAAAAGCTTAATC-TTTTAGGCGTT
455 GGTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTTAGGCGTT
2725 GAATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCAGGAAAAAAAATTCGGGTCAGTTTTT
520 GAATTATAAATTTTTTCTGAGTATTGTGG---------C-----AAAAAATTCGGGTCAGTTTTT
* **
2790 AGCTGACATCGTGTACTAACCATCACGGTTTTTGGGCT-AAAACGAGTTTCGGGGGCCCAGGCTC
571 AGCTGAAATCGTGTACTAACCATCACGGTTTTTACGCTAAAAACGAGTTTCGGGGGCCCAGGCTC
*
2854 AGCTTTGCATGATTTTTGGCAGAACGCCTCCGTGAAATATCTATATTCATCTAACCAAATCTCAA
636 AGCTTTGCATGATTTTTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAACCAAATCTCAA
2919 CCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTGATTTAATTATAAATT
701 CCACATTAAATTGAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTCTGATTTAATTATAAATT
*
2984 GATTCTGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATCCCGTC
766 GATTCCGAAAAAAATTGGAAAAATGATATTAGAAGCGTGAAAATCCCGTC
3034 AATCTTTTTGGAGTTGAATTATATA-TTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAA
1 AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAG---AAAAAA
3098 AATTCTTGTCAGTTTT
63 AATTCTTGTCAGTTTT
3114 GGCCGTCGGT
Statistics
Matches: 856, Mismatches: 32, Indels: 24
0.94 0.04 0.03
Matches are distributed among these distances:
813 39 0.05
814 221 0.26
815 211 0.25
816 52 0.06
822 1 0.00
825 30 0.04
826 225 0.26
827 56 0.07
828 21 0.02
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (815 bp):
AATCTTTTTGGAGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAAAAAAT
TCTTGTCAGTTTTTAGCCCAAATCATGTACTAACCATCACGATTTTTAGGCTAAAAACGAGTTTC
GGAGGCCCAGGCTCAGCTTTGCATGATTTTTGGTAGAAAGACTCCTTGAAATATCTACATTCATC
GAACCAAATCCCAGCGACATTCGATTTAACGATTTGTTTTTACGAGCATCCGAATCTTATTTCGT
TTTAATTAGAAATTAATTCGGAAAAAAAATGAAAAAATGATATTAGAAGCATGAAAATCCCGTCA
ATCTTTTTGGCGTTGAATTATATATTTTGCTACATGTTAAATCCCTTTAAGAATGGTGAAGTAGA
AAGATATTGCTGCAAATTGGTCCTGATTATGCTACAATTTGGGACAAAATAAGCCTACAACTAGG
GTCCGTTTGGCCCAGCTTATTTAACAGCTTATCTACTGAAAAAAGCTTAATCTTTTTAGGCGTTG
AATTATAAATTTTTTCTGAGTATTGTGGCAAAAAATTCGGGTCAGTTTTTAGCTGAAATCGTGTA
CTAACCATCACGGTTTTTACGCTAAAAACGAGTTTCGGGGGCCCAGGCTCAGCTTTGCATGATTT
TTGGCAGAACGACTCCGTGAAATATCTATATTCATCTAACCAAATCTCAACCACATTAAATTGAA
GGATTTGTTTTTACGAGCATCTGAATCTTGTTCTGATTTAATTATAAATTGATTCCGAAAAAAAT
TGGAAAAATGATATTAGAAGCGTGAAAATCCCGTC
Found at i:4988 original size:649 final size:644
Alignment explanation
Indices: 3537--5781 Score: 2549
Period size: 650 Copynumber: 3.5 Consensus size: 644
3527 GAGGTTCTCT
* * * ** *
3537 AAACGTGTTTTTAGCCCAAAAATCGTGATAGTTAGTACACGATTTC--GAATAAAAACTTA-CAC
1 AAACGCGTTTTTA-CCCAAAAACCGTGATGGTTAGTACACGATTTCATGTGTAAAAACTGATC-C
** * * *
3599 G-AATTTTTTTCCTGAATTTTTTGCCACAAT-ACACAGAAAAAACTATATAATTCAACGCCAAAA
64 GAAAAATTTTTCCTCAATTCTTTGCCACAATAAC-CAGAAAAAAATATATAATTCAACGCCAAAA
* ** * *
3662 AGATTGATAATC-TTTCACATTTCTAATATC-ATTTTCCAA-TTTTTTT-CAAATTAATTTCTAA
128 AGATTGATAGTCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTTCCGAATTAATTTCTAA
* * * *
3723 TTAAATTGAAACAAGATTCATATGCTCGTAAAAACAAATCCTTATATACAATGTGGCTGACATTT
193 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTT
* ** * * *
3788 GGTTCAAAAAATATTAGATATTTCAA-GAGT-TTT-TGCGCTTAAAATCATTCAAAATTGAGTCA
258 GGTTCGATGAATA-TAGATATTTCAAGGAGTCTTTCTGC-C-AAAAATCATGCAAAATTGAGCCA
* *
3850 GGGCTCCAAAACGTGTTTTTAG-CTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTG
320 GGGCTCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACT-
*
3914 ACCCGAAAAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
384 A--C-AAGAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCA
*
3979 AAAAGATTGACGGGCTTTACACGCATCTAATATCATTTTTCCATTTTTTTCGAATTAAATTCTAA
446 AAAAGATTGACGGGCTTTACACGCATCTAATATCATTTTTCCATTTTTTTCGAATTAATTTCTAA
4044 TTAAATCGAAACAAGATTGAA-ATGCTC-AAAAAA-AAATCCTTATATCCAATATGGCTGAGATT
511 TTAAATCGAAACAAGATT-AAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATT
* * * * *
4106 TGGTTCGATAAATATAGATATTTCAAGGAATCTTTACGCCAAATATCTTGCAAAACTGAGCCGGG
575 TGGTTAGATAAATATAGATATTTCAAGGAGTCTTT-CACCAAAAATCTTGCAAAACTGAGCGGGG
4171 CCCCGG
639 CCCCGG
* * * * * *
4177 GAACGCGTTTTTAGCCATAAACCGTGAT-G--AGTAAACGATTTCGAATAAAATTGTGCAAAAAT
1 AAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTACACGATTTC-------A-TGTGTAAAAAC
* *
4239 TGATCCGAAAAAATTTTCCTCCATTCTTTGCCACAATAACCAGAAAAAAATATATAATTCAACGC
58 TGATCCGAAAAATTTTTCCTCAATTCTTTGCCACAATAACCAGAAAAAAATATATAATTCAACGC
* * *
4304 CAAAAAGATTGA-AGGGT-TTTTCAAGCTTTTAATATCGTTTTTCCAATTTTTATTCCGAATTAA
123 CAAAAAGATTGATA--GTCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTTCCGAATTAA
* * * * *
4367 TTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAA-AAATCATTAAATCGAATGTCGCT
186 TTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCT
* * * *
4431 GGGATTTGGTTCGATGAATGTAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGA
251 GAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGA
* * * *
4496 GCCAGGACCCCCAAAACGCATTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAA
316 GCCAGG-GCTCCAAAACGCGTTTTTAG-CCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAA
* *
4561 AAACTACAAGACTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAATAAATATATAATTCAACG
379 AAACTACAAGAATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAA-AAATATATAATTCAACG
* * * * *
4626 CCAAAAAGATTGAAGGGATTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCGGAATCAATT
443 CCAAAAAGATTGACGGGCTTTACACGCATCTAATATCATTTTTCC-ATTTTTTTC-GAATTAATT
* * * * ** *
4691 TCTAATTAAATCGGAACAAGATTCAGATACTCGTAAAAAACAAATCCTTAAATTTAATGTGGCTG
506 TCTAATTAAATCGAAACAAGATTAAGATGCTCG-AAAAAACAAATCCTTATATCCAATATGGCTG
* * *
4756 AGATTTGGTTAGATGAATATAGATATTTCACGGAGTCTTTCTACCAAAAATCATGCAAAGA-TGA
570 AGATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTTC-ACCAAAAATCTTGCAAA-ACTGA
*
4820 GTCGGGGCCCCCG
633 G-CGGGGCCCCGG
4833 AAACGCGTTTTTATCCCAAAAACCGTGATGGTTAGTACACGATTTCA-GT-TAAAAACTG-TCCC
1 AAACGCGTTTTTA-CCCAAAAACCGTGATGGTTAGTACACGATTTCATGTGTAAAAACTGAT-CC
* * * * * * * * *
4895 GAATATTTTTTCCTGAATTTTTTGCCACGAT-ACTCA-AAAAAAATTTATACTTGAACGCCCAAA
64 GAAAAATTTTTCCTCAATTCTTTGCCACAATAAC-CAGAAAAAAATATATAATTCAACGCCAAAA
*
4958 AGATTGATAGTCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTTCCGAATTAATTTCTAA
128 AGATTGATAGTCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTTCCGAATTAATTTCTAA
*
5023 TTAAATCGAAACAAGATTCAGATGCTCCTAAAAACAAATCCTTATATCCAATGTGGCTGACG-TT
193 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGA-GATT
* * * * * *
5087 TGGTTCGATGAATATAGGTATTTTAAGGAGTATTTGC-GCTAAAAATTATGCAAAAATTGAGCCG
257 TGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATCATGC-AAAATTGAGCCA
** * * *
5151 GGGCTCCGGAACGCGTTTTTGGCCAAAAACCGTGAT-GTAAAGTTCACGATTTCGGCTAAAAACT
320 GGGCTCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGT-TAGTACACGATTTCGGCTAAAAACT
* *
5215 A-ATACGAAAAGTTTTTTCTCAATTTTTTGCCACAATACTCA-AAAAATATATATAATTCAACAC
384 ACA-A-G--AATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAA-ATATATAATTCAACGC
* * *
5278 CAAAAAGATTGACGGGCTTTACACGCGTCTAATATCGTTATTCCATTTTTTTCGAATTAATTTCT
444 CAAAAAGATTGACGGGCTTTACACGCATCTAATATCATTTTTCCATTTTTTTCGAATTAATTTCT
*
5343 AATTAAATCGAAACAAGATTAAGATGCTCGAAAAAACAAATACTTATATCCAATATGGCTGAGAT
509 AATTAAATCGAAACAAGATTAAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGAT
*
5408 TTGGTTCA-ATAAATATAGATATTTCAAGGAGTCTTTAAGCCAAAAATCTTGCAAAACTGAGCCG
574 TTGGTT-AGATAAATATAGATATTTCAAGGAGTCTTTCA-CCAAAAATCTTGCAAAACTGAG-CG
*
5472 GGG--TCGG
636 GGGCCCCGG
* * * * * * * ** *** *
5479 GAACACGTTTTTAGCTATAAACCGTGATGAGTAAATGATTTCGAATAAAATTGTGTAAATACTGA
1 AAACGCGTTTTTACCCAAAAACCGTGATG-GTTAGT-A-CACG-ATTTCA-TGTGTAAAAACTGA
5544 TCCGAAAAATTTTTCCTCAATTCTTTGCCACAATAACCAG-AAAAAATATATAATTCAACGCCAA
61 TCCGAAAAATTTTTCCTCAATTCTTTGCCACAATAACCAGAAAAAAATATATAATTCAACGCCAA
** * * *
5608 AAAGATTGACGGGCATTTCACGCTTCTAATATCGTTTTT-C-TTTTTTTTTCCGAATTAATTTCT
126 AAAGATTGATAGTCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTTCCGAATTAATTTCT
* * * * *
5671 AATTAAATCGAAACAAGATTGAGATGCT-GGAAAAA-AAATCCTCATTTCCAATATGGCTGAGAT
191 AATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGAT
*
5734 TTGGTTCGATGAATATAGATAGTTCAAGGAGTCTTTAC-GCCAAAAATC
256 TTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT-CTGCCAAAAATC
5782 TTACCTGAGT
Statistics
Matches: 1349, Mismatches: 189, Indels: 126
0.81 0.11 0.08
Matches are distributed among these distances:
636 12 0.01
638 1 0.00
639 12 0.01
640 11 0.01
645 13 0.01
646 28 0.02
647 64 0.05
648 174 0.13
649 256 0.19
650 297 0.22
651 150 0.11
652 159 0.12
653 43 0.03
654 7 0.01
655 74 0.05
656 22 0.02
657 13 0.01
658 1 0.00
660 12 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.32
Consensus pattern (644 bp):
AAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTACACGATTTCATGTGTAAAAACTGATCCGA
AAAATTTTTCCTCAATTCTTTGCCACAATAACCAGAAAAAAATATATAATTCAACGCCAAAAAGA
TTGATAGTCTTTTCACGCTTCTAATATCGTTTTTCCAATTTTTTTTCCGAATTAATTTCTAATTA
AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGT
TCGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAATTGAGCCAGGGCTC
CAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTACAAGAA
TTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATTGA
CGGGCTTTACACGCATCTAATATCATTTTTCCATTTTTTTCGAATTAATTTCTAATTAAATCGAA
ACAAGATTAAGATGCTCGAAAAAACAAATCCTTATATCCAATATGGCTGAGATTTGGTTAGATAA
ATATAGATATTTCAAGGAGTCTTTCACCAAAAATCTTGCAAAACTGAGCGGGGCCCCGG
Found at i:5091 original size:326 final size:323
Alignment explanation
Indices: 3537--5769 Score: 2216
Period size: 327 Copynumber: 6.9 Consensus size: 323
3527 GAGGTTCTCT
* * * * *
3537 AAACGTGTTTTTAGCCCAAAAATCGTGATAGTTAGTACACGATTTC-GAATAAAAACT-TACACG
1 AAACGCGTTTTTA-CCCAAAAACCGTGATGGTTAGTACACGATTTCAG-CTAAAAACTGT-CCCG
* * * *
3600 -AATTTTTTTCCTGAATTTTTTGCCACAATACACAGAAAAAACTATATAATTCAACGCCAAAAAG
63 AAAATTTTTTCCTCAATTTTTTGCCACAATACTCA-AAAAAAATATATAATTCAACGCCAAAAAG
* ** ** *
3664 ATTGATAATC-TTTCACATTTCTAATATCA-TTTTCCAATTTTTTT-CAAATTAATTTCTAATTA
127 ATTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTA
* * * *
3726 AATTGAAACAAGATTCATATGCTCGTAAAAACAAATCCTTATATACAATGTGGCTGACATTTGGT
192 AATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGT
* ** * * * * * *
3791 TCAAAAAATATTAGATATTTCAA-GAGT-TTT-TGCGCTTAAAATCATTCAAAATTGAGTCAGGG
257 TCGATGAATA-TAGATATTTCAAGGAGTCTTTCTAC-C-AAAAATCATGCAAAACTGAGCCGGGG
* *
3853 CTCCA
319 CCCCG
* * * * *
3858 AAACGTGTTTTTA-GCTAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAACTGACCCGAAA
1 AAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGTCCCG-AA
* *
3922 AATTTTTTTCTCAATTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAGATT
65 AATTTTTTCCTCAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATT
* * * *
3987 GACGGGCTTTACACGCATCTAATATCATTTTTCC-ATTTTTTT-CGAATTAAATTCTAATTAAAT
130 GACAGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAAT
* * * *
4050 CGAAACAAGATTGAAATGCTC--AAAAAAAAATCCTTATATCCAATATGGCTGAGATTTGGTTCG
195 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCG
* * * * *
4113 ATAAATATAGATATTTCAAGGAATCTTTAC-GCCAAATATCTTGCAAAACTGAGCC-GGGCCCCG
260 ATGAATATAGATATTTCAAGGAGTCTTT-CTACCAAAAATCATGCAAAACTGAGCCGGGGCCCC-
4176 G
323 G
* * * *
4177 GAACGCGTTTTTAGCCATAAACCGTGAT-G--AGTAAACGATTTCGAATAAAATTG-TGCAAAAA
1 AAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTACACGATTTC-------A--GCT--AAAAA
* ** * *
4238 TTGAT-CCGAAAAAATTTTCCTCCATTCTTTGCCACAATAAC-CAGAAAAAAATATATAATTCAA
55 CTG-TCCCGAAAATTTTTTCCTCAATTTTTTGCCACAAT-ACTCA-AAAAAAATATATAATTCAA
* * * *
4301 CGCCAAAAAGATTGA-AGGGTTTTTCAAGCTTTTAATATCGTTTTTCCAATTTTTATTCCGAATT
117 CGCCAAAAAGATTGACA-GGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTT-TTCCGAATT
* * * * *
4365 AATTTCTAATTAAATCAAAACAAGATTCAGATGCTCGTAAAAA-AAATCATTAAATCGAATGTCG
180 AATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGG
* *
4429 CTGGGATTTGGTTCGATGAATGTAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACT
245 CTGAGATTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACT
** *
4494 GAGCCAGGACCCCCA
310 GAGCC-GGGGCCCCG
* * * *
4509 AAACGCATTTTTAGCCCAAAAATCGTGATGGTTAGTACACGATTTCGGCTAAAAAC--T-AC-AA
1 AAACGCGTTTTTA-CCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGTCCCGAA
* * * *
4570 GACTTTTTTTCTGAATTTTTTGCCACAATACTCAGAAATAAATATATAATTCAACGCCAAAAAGA
65 -AATTTTTTCCTCAATTTTTTGCCACAATACTCA-AAAAAAATATATAATTCAACGCCAAAAAGA
* * *
4635 TTGA-AGGGATTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCGGAATCAATTTCTAATTA
128 TTGACA-GGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTA
* * * **
4699 AATCGGAACAAGATTCAGATACTCGTAAAAAACAAATCCTTAAATTTAATGTGGCTGAGATTTGG
192 AATCGAAACAAGATTCAGATGCTCGT-AAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGG
* * *
4764 TTAGATGAATATAGATATTTCACGGAGTCTTTCTACCAAAAATCATGCAAAGA-TGAGTCGGGGC
256 TTCGATGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAA-ACTGAGCCGGGG-
4828 CCCCG
319 CCCCG
*
4833 AAACGCGTTTTTATCCCAAAAACCGTGATGGTTAGTACACGATTTCAGTTAAAAACTGTCCCGAA
1 AAACGCGTTTTTA-CCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGTCCCGAA
* * * * * * *
4898 TATTTTTTCCTGAATTTTTTGCCACGATACTCAAAAAAAATTTATACTTGAACGCCCAAAAGATT
65 AATTTTTTCCTCAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATT
* *
4963 GATAGTCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTTCCGAATTAATTTCTAATTAAA
130 GACAGGCTTTTCACGCTTCTAATATCATTTTTCCAA-TTTTTTTCCGAATTAATTTCTAATTAAA
*
5028 TCGAAACAAGATTCAGATGCTCCTAAAAACAAATCCTTATATCCAATGTGGCTGACG-TTTGGTT
194 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGA-GATTTGGTT
* * * * * * * *
5092 CGATGAATATAGGTATTTTAAGGAGTATTTGC-GCTAAAAATTATGCAAAAATTGAGCCGGGGCT
258 CGATGAATATAGATATTTCAAGGAGTCTTT-CTACCAAAAATCATGC-AAAACTGAGCCGGGGCC
5156 CCG
321 CCG
* ** * * * * *
5159 GAACGCGTTTTTGGCCAAAAACCGTGAT-GTAAAGTTCACGATTTCGGCTAAAAACTAAT-ACGA
1 AAACGCGTTTTTACCCAAAAACCGTGATGGT-TAGTACACGATTTCAGCTAAAAACT-GTCCCGA
* *
5222 AAAGTTTTTT-CTCAATTTTTTGCCACAATACTCAAAAAATATATATAATTCAACACCAAAAAGA
64 AAA-TTTTTTCCTCAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGA
* * * * *
5286 TTGACGGGCTTTACACGCGTCTAATATCGTTATTCC-ATTTTTTT-CGAATTAATTTCTAATTAA
128 TTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAA
* * * *
5349 ATCGAAACAAGATTAAGATGCTCGAAAAAACAAATACTTATATCCAATATGGCTGAGATTTGGTT
193 ATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTT
* * * * *
5414 CAATAAATATAGATATTTCAAGGAGTCTTT-AAGCCAAAAATCTTGCAAAACTGAGCCGGGG-TC
258 CGATGAATATAGATATTTCAAGGAGTCTTTCTA-CCAAAAATCATGCAAAACTGAGCCGGGGCCC
*
5477 GG
322 CG
* * * * * * * ** ** *
5479 GAACACGTTTTTAGCTATAAACCGTGATGAGTAAATGATTTCGAATAAAATTGTG-TAAATACTG
1 AAACGCGTTTTTACCCAAAAACCGTGATG-GTTAGT-A-CACG-AT----TTCAGCTAAAAACTG
* * *
5543 AT-CCGAAAAATTTTTCCTCAATTCTTTGCCACAATAAC-CAGAAAAAATATATAATTCAACGCC
58 -TCCCGAAAATTTTTTCCTCAATTTTTTGCCACAAT-ACTCAAAAAAAATATATAATTCAACGCC
* * * **
5606 AAAAAGATTGACGGGCATTTCACGCTTCTAATATCGTTTTT-CTTTTTTTTTCCGAATTAATTTC
121 AAAAAGATTGACAGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTC
* * * * *
5670 TAATTAAATCGAAACAAGATTGAGATGCT-GGAAAAA-AAATCCTCATTTCCAATATGGCTGAGA
186 TAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGA
*
5733 TTTGGTTCGATGAATATAGATAGTTCAAGGAGTCTTT
251 TTTGGTTCGATGAATATAGATATTTCAAGGAGTCTTT
5770 ACGCCAAAAA
Statistics
Matches: 1609, Mismatches: 227, Indels: 147
0.81 0.11 0.07
Matches are distributed among these distances:
317 12 0.01
318 18 0.01
319 112 0.07
320 76 0.05
321 123 0.08
322 166 0.10
323 110 0.07
324 140 0.09
325 117 0.07
326 251 0.16
327 266 0.17
328 54 0.03
329 2 0.00
330 39 0.02
331 77 0.05
332 16 0.01
333 17 0.01
334 1 0.00
336 12 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (323 bp):
AAACGCGTTTTTACCCAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAAACTGTCCCGAAA
ATTTTTTCCTCAATTTTTTGCCACAATACTCAAAAAAAATATATAATTCAACGCCAAAAAGATTG
ACAGGCTTTTCACGCTTCTAATATCATTTTTCCAATTTTTTTCCGAATTAATTTCTAATTAAATC
GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTCGA
TGAATATAGATATTTCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCGGGGCCCCG
Found at i:7693 original size:18 final size:18
Alignment explanation
Indices: 7667--7705 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
7657 AGGAGATAGA
7667 TGTGATAATTATGGAATT
1 TGTGATAATTATGGAATT
* *
7685 TGTGGTAATTATGGTATT
1 TGTGATAATTATGGAATT
7703 TGT
1 TGT
7706 AACATTAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.49
Consensus pattern (18 bp):
TGTGATAATTATGGAATT
Found at i:23863 original size:16 final size:16
Alignment explanation
Indices: 23818--23867 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
23808 TCGTTTGGCA
*
23818 TCGTTTTCGTTTT-TC
1 TCGTTTTCGTTTTGTT
23833 T-GTTTTTCTGTTTTTGTT
1 TCG-TTTTC-G-TTTTGTT
23851 TCGTTTTCGTTTTGTT
1 TCGTTTTCGTTTTGTT
23867 T
1 T
23868 TTGTTGCGCT
Statistics
Matches: 29, Mismatches: 1, Indels: 9
0.74 0.03 0.23
Matches are distributed among these distances:
14 1 0.03
15 6 0.21
16 9 0.31
17 5 0.17
18 7 0.24
19 1 0.03
ACGTcount: A:0.00, C:0.12, G:0.16, T:0.72
Consensus pattern (16 bp):
TCGTTTTCGTTTTGTT
Found at i:36330 original size:17 final size:18
Alignment explanation
Indices: 36304--36339 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
36294 AAGTAGTACA
*
36304 CAATTGAAATA-CAACTT
1 CAATTCAAATACCAACTT
36321 CAATTCAAATACCAACTT
1 CAATTCAAATACCAACTT
36339 C
1 C
36340 TTATTAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.44, C:0.25, G:0.03, T:0.28
Consensus pattern (18 bp):
CAATTCAAATACCAACTT
Found at i:41551 original size:3 final size:3
Alignment explanation
Indices: 41543--41572 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
41533 GTTTATTACC
41543 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
1 TGT TGT TGT TGT TGT TGT TGT TGT TGT TGT
41573 ATGGAAGCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TGT
Found at i:44241 original size:18 final size:18
Alignment explanation
Indices: 44220--44254 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
44210 TAAAGAAGTT
44220 TTTAGTTTTATTTATTTA
1 TTTAGTTTTATTTATTTA
* *
44238 TTTATTTTTTTTTATTT
1 TTTAGTTTTATTTATTT
44255 TGGAGGCAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (18 bp):
TTTAGTTTTATTTATTTA
Found at i:46319 original size:21 final size:21
Alignment explanation
Indices: 46294--46336 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
46284 TTGAAATCTG
*
46294 ATAACACCTGCTCTTGAACCT
1 ATAACACCTGCTCTTAAACCT
46315 ATAACACCTGCTCTTAAACCT
1 ATAACACCTGCTCTTAAACCT
46336 A
1 A
46337 GAAACTAGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.33, G:0.07, T:0.28
Consensus pattern (21 bp):
ATAACACCTGCTCTTAAACCT
Found at i:49020 original size:33 final size:33
Alignment explanation
Indices: 48978--49045 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
48968 AAACCTATAC
48978 ATAATTGAGCATTATATGTAATTATAAAGATTA
1 ATAATTGAGCATTATATGTAATTATAAAGATTA
49011 ATAATTGAGCATTATATGTAATTATAAAGATTA
1 ATAATTGAGCATTATATGTAATTATAAAGATTA
49044 AT
1 AT
49046 TAGTATAAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.46, C:0.03, G:0.12, T:0.40
Consensus pattern (33 bp):
ATAATTGAGCATTATATGTAATTATAAAGATTA
Found at i:55478 original size:78 final size:78
Alignment explanation
Indices: 55349--55503 Score: 265
Period size: 78 Copynumber: 2.0 Consensus size: 78
55339 CTGGTAACAA
55349 TGGAAGTCCAACCATGACGGAGCCAATGGTTCCCAAACCCAAACGAACTCCACCATCTGATCAGA
1 TGGAAGTCCAACCATGACGGAGCCAATGGTTCCCAAACCCAAACGAACTCCACCATCTGATCAGA
55414 CGAACCAGAGTTC
66 CGAACCAGAGTTC
* * ** *
55427 TGGAAGTCCAATCATGGCGGAGCCAATGGTTTTCAAAGCCAAACGAACTCCACCATCTGATCAGA
1 TGGAAGTCCAACCATGACGGAGCCAATGGTTCCCAAACCCAAACGAACTCCACCATCTGATCAGA
55492 CGAACCAGAGTT
66 CGAACCAGAGTT
55504 TGAGTTTGAT
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 72 1.00
ACGTcount: A:0.33, C:0.29, G:0.21, T:0.17
Consensus pattern (78 bp):
TGGAAGTCCAACCATGACGGAGCCAATGGTTCCCAAACCCAAACGAACTCCACCATCTGATCAGA
CGAACCAGAGTTC
Found at i:57196 original size:2 final size:2
Alignment explanation
Indices: 57189--57217 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
57179 GAAACTCTTT
57189 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
57218 GATAGTAATT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:70092 original size:16 final size:16
Alignment explanation
Indices: 70068--70101 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
70058 TTATGTACAT
70068 TTATGTATGTATTTCA
1 TTATGTATGTATTTCA
*
70084 TTATTTATGTATTTCA
1 TTATGTATGTATTTCA
70100 TT
1 TT
70102 TCACTACTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.24, C:0.06, G:0.09, T:0.62
Consensus pattern (16 bp):
TTATGTATGTATTTCA
Found at i:70098 original size:59 final size:60
Alignment explanation
Indices: 70027--70146 Score: 181
Period size: 59 Copynumber: 2.0 Consensus size: 60
70017 TAAGCCAAAC
70027 ATTTATGTATTTCATTTCACTACTAC-CCAAATTATGTACATTTATGTATGT-ATTTCATT
1 ATTTATGTATTTCATTTCACTACTACACCAAATTATGTAC-TTTATGTATGTCATTTCATT
*
70086 ATTTATGTATTTCATTTCACTACTACTAAGCCAAATTATGTACTTTATGTATTTCATTTCA
1 ATTTATGTATTTCATTTCACTACTAC--A-CCAAATTATGTACTTTATGTATGTCATTTCA
70147 CTACTACTCC
Statistics
Matches: 55, Mismatches: 1, Indels: 6
0.89 0.02 0.10
Matches are distributed among these distances:
59 26 0.47
62 10 0.18
63 19 0.35
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.48
Consensus pattern (60 bp):
ATTTATGTATTTCATTTCACTACTACACCAAATTATGTACTTTATGTATGTCATTTCATT
Found at i:72918 original size:12 final size:12
Alignment explanation
Indices: 72901--72934 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
72891 TAACCTCCGG
*
72901 CAAATCTACCTC
1 CAAATCCACCTC
72913 CAAATCCACCTC
1 CAAATCCACCTC
72925 CAAATCCACC
1 CAAATCCACC
72935 ATTAGCTCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.35, C:0.47, G:0.00, T:0.18
Consensus pattern (12 bp):
CAAATCCACCTC
Found at i:74887 original size:38 final size:38
Alignment explanation
Indices: 74843--74925 Score: 139
Period size: 38 Copynumber: 2.2 Consensus size: 38
74833 TGATTTCGCA
*
74843 CTTGATTCTTCATTTTTCTTATCTTTCTACCCTGAAAT
1 CTTGATTCTTCATTTTTCTTATCTTTCAACCCTGAAAT
* *
74881 CTTGATTCTTCCTTTTTCTTGTCTTTCAACCCTGAAAT
1 CTTGATTCTTCATTTTTCTTATCTTTCAACCCTGAAAT
74919 CTTGATT
1 CTTGATT
74926 TACTAGATGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
38 42 1.00
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.52
Consensus pattern (38 bp):
CTTGATTCTTCATTTTTCTTATCTTTCAACCCTGAAAT
Found at i:77005 original size:31 final size:33
Alignment explanation
Indices: 76926--77006 Score: 98
Period size: 31 Copynumber: 2.6 Consensus size: 33
76916 GGTATTGCTG
76926 ACGTGGCAATG-CCACGTCGGACCAAAAATGCC
1 ACGTGGCAATGACCACGTCGGACCAAAAATGCC
** * *
76958 ACGTGATAATGA-CACGTTGGATC-AAAATGCC
1 ACGTGGCAATGACCACGTCGGACCAAAAATGCC
76989 ACGTGGCAA-GACCACGTC
1 ACGTGGCAATGACCACGTC
77007 AACAATATCG
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
30 2 0.05
31 20 0.50
32 18 0.45
ACGTcount: A:0.32, C:0.27, G:0.25, T:0.16
Consensus pattern (33 bp):
ACGTGGCAATGACCACGTCGGACCAAAAATGCC
Done.