Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01006278.1 Corchorus capsularis cultivar CVL-1 contig06297, 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: 36162
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1434 original size:652 final size:647
Alignment explanation
Indices: 3--1817 Score: 2700
Period size: 651 Copynumber: 2.8 Consensus size: 647
1 TT
* * *
3 ATGATTTTTGGCATTGAGAGTCCTTGAAATATCAATATTCATCTAACCAAATCCCAGCCATTGTT
1 ATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATTCTT
*** * *
68 TTTACAAAAATCTGAATCATGTTTCG-GTATAATTAGAAATTAATTCG-G-AAAAATAGAAAAAA
66 TTTACAAGTGTCTGAATCATGTTTCGATTA-AATTAGAAATTAATTCGTGAAAAAATAGGAAAAA
* * * * **
130 CGATATTAGAAGCGTGAAAAGCCTTTAAATCTTTTTGGCA-TTAAATTATATATATATTATGTCT
130 TGATATTAGAAGCGCGAAAAGCCCTTCAATCTTTTTGG-AGTTAAATTATATATATATTATGAGT
* * * * *
194 ACTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTCTTTTTTTTCCTCAAAATTTTAGCGAAAAT
194 ATTTTATCCAAAAATTGAGGAAAAATTTTTCAGGTC-ATTTTTT--TCAAATTTTTAGCCAAAAT
* * * * * *
259 TGTGTACTAACCATCAC-AGTTTTTGGCTAAAAATGCGTTTCAGGATCTCGGCTCAGTTCTGCAT
256 CGTGTACTAACCATCACGA-TTTTTGGGTAAAAACGCGTTTCAGGGTCCCGGCTCAGTTTTGCAT
* * ** * *
323 GATTTTCGGCATTGAGACTTTGCGAAATATCTATATTCATCTAATAAAACCTTAGCCACATTGTA
320 GATTTTTGGCA-CGAGACTCCGTGAAATATCTATATTCATCTAATAAAACCTTAGCCACATTGCA
* * *
388 TTTAAGGATTTGTTTTTATGTGCATCTG-ATTCTTTATTCGATTTAATTAGAA-TTAATTCAG-A
384 TTTAAGGATTTGTTTTTACGAGCATCTGAATCCTTT-TTCGATTTAATTAGAATTTAATTCAGAA
*
450 AAAATATGAAAAACGATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATA
448 AAAATATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATA
* *
515 TTTTCTAAGAATATTTTGGCTAAAAATGTAGAAAACATCTTTCGGGTCAATTTTTGCCAAATTAT
513 TTTTATAAGAATATTGTGGCTAAAAATGTAGAAAACATCTTTCGGGTCAATTTTTGCCAAATTAT
* * * *
580 AGCTGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGATGTCTGTTTCAAT
578 AGCCGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAAT
**
645 TTTGC
643 TTAAC
* * *
650 TTGATTTTTGGCATTGAGACTCCATGAAATATCAATATTCATCTAACAAAATCCAAGCCATTCTT
1 ATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATTCTT
* * *
715 TTTACAAGTGCCTGAAACATGTTTCAATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAAAT
66 TTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAAAT
* * * *
780 GATATTCGAAGCGCGAAAAACCCTTCAATCTTTTTGGAGTTAAATTATATATATAATATAAGTAT
131 GATATTAGAAGCGCGAAAAGCCCTTCAATCTTTTTGGAGTTAAATTATATATATATTATGAGTAT
*
845 TTTATCCAAAAAATTGAGGAAAAATTTTTCAGGTCATTTTTTGCAAATTTTTAGCCAAAATCGTG
196 TTTATCC-AAAAATTGAGGAAAAATTTTTCAGGTCATTTTTTTCAAATTTTTAGCCAAAATCGTG
* *
910 TACTAACCATCGCGATTTTTGGGTAAAAACGCGTTTCAGGGTCCCGGCTCAGTTTTACATGATTT
260 TACTAACCATCACGATTTTTGGGTAAAAACGCGTTTCAGGGTCCCGGCTCAGTTTTGCATGATTT
*
975 TTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAAATAAAACCTTAGCCACATTGCATTTA
325 TTGGCA-CGAGACTCCGTGAAATATCTATATTCATCT-AATAAAACCTTAGCCACATTGCATTTA
*
1040 AGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAAAAT
388 AGGATTTGTTTTTACGAGCATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAAAAT
* * *
1105 AAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTTTGCATTGAATTATATATTTT
453 ATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATA-TTTTTGGCGTTGAATTATATATTTT
* * *
1170 ATAAGATTATTGTGGCTAAAAAT-TTGAAAAATATCTTTCGGGTCAATTTTTGCCAAATTATAGC
517 ATAAGAATATTGTGGCTAAAAATGTAG-AAAACATCTTTCGGGTCAATTTTTGCCAAATTATAGC
* *
1234 CGAAATCGTGTAAGAATCATTACGGTTTTTTGCTAAAAACGGGTTCCGAGGCCTGGTTCAATTAT
581 CGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAATT-T
1299 AAC
645 AAC
1302 ATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATAT-T
1 ATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCAT-TCT
1366 TTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAAA
65 TTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAAA
* * *
1431 TGATATTAGAAGCGCGAAAAGTCCTTCAATCTTTTTAGAGTTAAATTATATATATATTTTGAGTA
130 TGATATTAGAAGCGCGAAAAGCCCTTCAATCTTTTTGGAGTTAAATTATATATATATTATGAGTA
*
1496 TTTTATCCAAAAATTGAGGAAAATATTTTT-AGGTCATTTTTTTCAAATTTTTTGCCAAAATCGT
195 TTTTATCCAAAAATTGAGGAAAA-ATTTTTCAGGTCATTTTTTTCAAATTTTTAGCCAAAATCGT
* *
1560 GTACTAACCATCACGGTTTTTGGGTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATT
259 GTACTAACCATCACGATTTTTGGGTAAAAACGCGTTTCAGGGTCCCGGCTCAGTTTTGCATGATT
* * *
1625 TTTGGCACAAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCGTTTAA
324 TTTGGCACGAGACTCCGTGAAATATCTATATTCATCTAATAAAACCTTAGCCACATTGCATTTAA
*
1690 GGATTTGTTTTTACGAGCATCTGAATCCTTTTT-TATTTAATTAGAATTTAATTCAGAAAAAAAT
389 GGATTTGTTTTTACGAGCATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAG-AAAAAAT
*
1754 ATGAAAAACAATATTAACAGCATGAAATGCCCATCAATATTTTTGGCGTTGAATTATATATTTT
453 ATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTT
1818 TGGCACCGAG
Statistics
Matches: 1056, Mismatches: 96, Indels: 31
0.89 0.08 0.03
Matches are distributed among these distances:
647 201 0.19
648 113 0.11
649 196 0.19
650 99 0.09
651 251 0.24
652 195 0.18
653 1 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (647 bp):
ATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATTCTT
TTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAAAT
GATATTAGAAGCGCGAAAAGCCCTTCAATCTTTTTGGAGTTAAATTATATATATATTATGAGTAT
TTTATCCAAAAATTGAGGAAAAATTTTTCAGGTCATTTTTTTCAAATTTTTAGCCAAAATCGTGT
ACTAACCATCACGATTTTTGGGTAAAAACGCGTTTCAGGGTCCCGGCTCAGTTTTGCATGATTTT
TGGCACGAGACTCCGTGAAATATCTATATTCATCTAATAAAACCTTAGCCACATTGCATTTAAGG
ATTTGTTTTTACGAGCATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAAAATATG
AAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATTTTATAA
GAATATTGTGGCTAAAAATGTAGAAAACATCTTTCGGGTCAATTTTTGCCAAATTATAGCCGAAA
TCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAATTTAAC
Found at i:1624 original size:317 final size:318
Alignment explanation
Indices: 1048--1668 Score: 645
Period size: 317 Copynumber: 2.0 Consensus size: 318
1038 TAAGGATTTG
* * * * * * * *
1048 TTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTC-AGAAAAAATAAGAAAA
1 TTTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAA
** ** * * * *
1112 ACAATATTA-ACAGCATGAAAAGCCCATCAATATTTTTTTGCA-TTGAATTATATAT-T-TTATA
66 ATGATATTAGA-AGCGCGAAAAGCCCTTCAAT-CTTTTTAG-AGTTAAATTATATATATATTATA
* * ** * *
1173 AG-ATTATTGTGGCTAAAAATTTGA--AAAATATCTTTCGGGTCAATTTTTGCCAAA-TTATAGC
128 AGTATT-TTAT--CCAAAAA-TTGAGGAAAATAT-TTTTAGGTC-ATTTTTTCCAAATTTTTAGC
* * * * * * *
1234 CGAAATCGTGTAAGAATCATTACGGTTTTTTGCTAAAAACGGGTTCCGAGG-CCTGGTTCAATTA
187 CAAAATCGTGTAAGAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGTCCCGGCTCAATT-
* * * *
1298 TAACATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCAT
251 TTACATGATTTTTGGCATCGAGACTCCGTGAAATATCAATATTCATCTAACAAAATCCAAGCCAT
1363 AT-
316 ATC
1365 TTTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAA
1 TTTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAA
* * *
1430 ATGATATTAGAAGCGCGAAAAGTCCTTCAATCTTTTTAGAGTTAAATTATATATATATTTTGAGT
66 ATGATATTAGAAGCGCGAAAAGCCCTTCAATCTTTTTAGAGTTAAATTATATATATATTATAAGT
* *
1495 ATTTTATCCAAAAATTGAGGAAAATATTTTTAGGTCATTTTTTTCAAATTTTTTGCCAAAATCGT
131 ATTTTATCCAAAAATTGAGGAAAATATTTTTAGGTCATTTTTTCCAAATTTTTAGCCAAAATCGT
** * * * * *
1560 GTACTAACCATCACGGTTTTTGGGTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATGATT
196 GTAAGAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGTCCCGGCTCAATTTTACATGATT
* *
1625 TTTGGCA-CAAGACTCCGTGAAATATCTATATTCATCTAACAAAA
261 TTTGGCATCGAGACTCCGTGAAATATCAATATTCATCTAACAAAA
1669 CCTTAGCCAC
Statistics
Matches: 247, Mismatches: 47, Indels: 21
0.78 0.15 0.07
Matches are distributed among these distances:
316 47 0.19
317 134 0.54
318 54 0.22
319 9 0.04
320 3 0.01
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (318 bp):
TTTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGGAAAA
ATGATATTAGAAGCGCGAAAAGCCCTTCAATCTTTTTAGAGTTAAATTATATATATATTATAAGT
ATTTTATCCAAAAATTGAGGAAAATATTTTTAGGTCATTTTTTCCAAATTTTTAGCCAAAATCGT
GTAAGAACCATCACGGTTTTTGGCTAAAAACGCGTTCCGAGGTCCCGGCTCAATTTTACATGATT
TTTGGCATCGAGACTCCGTGAAATATCAATATTCATCTAACAAAATCCAAGCCATATC
Found at i:1964 original size:192 final size:191
Alignment explanation
Indices: 1622--2010 Score: 663
Period size: 192 Copynumber: 2.0 Consensus size: 191
1612 GTTTTGCATG
*
1622 ATTTTTGGCACAAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCGTT
1 ATTTTTGGCACAAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCATT
*
1687 TAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTTATTTAATTAGAATTTAATTCAGAAAAAA
66 TAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTGATTTAATTAGAATTTAATTCAGAAAAAA
* * * *
1752 ATATGAAAAACAATATTAACAGCATGAAATGCCCATCAATATTTTTGGCGTTGAATTATAT
131 ATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTCGGCATTGAATTATAT
* *
1813 ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
1 ATTTTTGGCA-CAAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
*
1878 TTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAG-AAA
65 TTAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTT-GATTTAATTAGAATTTAATTCAGAAAA
*
1942 AAATAAGAAAAACAATATTAACAGCTTGAAAAGCCCATCAATATTTTCGGCATTGAATTATAT
129 AAATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTCGGCATTGAATTATAT
2005 ATTTTT
1 ATTTTT
2011 TAAGATTATT
Statistics
Matches: 186, Mismatches: 10, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
191 10 0.05
192 154 0.83
193 22 0.12
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (191 bp):
ATTTTTGGCACAAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCATT
TAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTGATTTAATTAGAATTTAATTCAGAAAAAA
ATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTCGGCATTGAATTATAT
Found at i:2631 original size:835 final size:841
Alignment explanation
Indices: 971--2653 Score: 2936
Period size: 835 Copynumber: 2.0 Consensus size: 841
961 GTTTTACATG
*
971 ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAAATAAAACCTTAGCCACATTGCA
1 ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAAACAAAACCTTAGCCACATTGCA
1036 TTTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAA
66 TTTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAA
**
1101 AAATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTTTGCATTGAATTATATA
131 AAATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTCGGCATTGAATTATATA
*
1166 TTTTATAAGATTATTGTGGCTAAAAATTTGAAAAATATCTTTCGGGTCAATTTTTGCCAAATTAT
196 TTTTATAAGATTATTGTGGCTAAAAATTAGAAAAATATCTTTCGGGTCAATTTTTGCCAAATTAT
* *
1231 AGCCGAAATCGTGTAAGAATCATTACGGTTTTTTGCTAAAAACGGGTTCCGAGGCCTGGTTCAAT
261 AGCCGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAAT
*
1296 TATAACATGATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCC
326 TATAACATAATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCC
* * *
1361 ATATTTTTTACAAGTGTCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGTGAAAAAATAGG
391 ATATTTTTTACAAGTGTCTGAATCATCTTGCAATTAAATTAGAAATTAATTCGTGAAAAAATAGG
* * *
1426 AAAAATGATATTAGAAGCGCGAAAAGTCCTTCAATCTTTTTAGAGTTAAATTATATATATATTTT
456 AAAAATGATATTAGAAGCGCGAAAAGCCCTTCAATATTTTTAGAGTTAAA-TATATATATATTAT
* * *
1491 GAGTATTTTATCCAAAAATTGAGGAAAATATTTTTAGGTCATTTTTTTCAAATTTTTTGCCAAAA
520 GAGTATTTTATCCAAAAATGGAGGAAAATATTTTTAGGTCATTTTTTGCAAATTTTTAGCCAAAA
1556 TCGTGTACTAACCATCACGGTTTTTGGGTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCAT
585 TCGTGTACTAACCATCACGGTTTTTGGGTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCAT
*
1621 GATTTTTGGCACAAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCGT
650 GATTTTTGGCACAAGACTCCGTGAAATATCTATATGCATCTAACAAAACCTTAGCCACATTGCGT
*
1686 TTAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTTATTTAATTAGAATTTAATTCAGAAAAA
715 TCAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTTATTTAATTAGAATTTAATTCAGAAAAA
* *
1751 AATATGAAAAACAATATTAACAGCATGAAATGCCCATCAATATTTTTGGCGTTGAATTATAT
780 AATATGAAAAACAAAATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATAT
1813 ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCT-AACAAAACCTTAGCCACATTGCA
1 ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAAACAAAACCTTAGCCACATTGCA
1877 TTTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAA
66 TTTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAA
*
1942 AAATAAGAAAAACAATATTAACAGCTTGAAAAGCCCATCAATA-TTTTCGGCATTGAATTATATA
131 AAATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTCGGCATTGAATTATATA
*
2006 TTTTTTAAGATTATTGTGGCTAAAAATGTAG-AAAATATCTTTCGGGTCAATTTTTGCCAAATTA
196 TTTTATAAGATTATTGTGGCTAAAAAT-TAGAAAAATATCTTTCGGGTCAATTTTTGCCAAATTA
2070 TAGCCGAAATCGTGTAAGAATCATCACGGTTTTTGGCT-AAAACGGGTTCCGAGGCCTGGTTCAA
260 TAGCCGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAA
** * *
2134 TT-TTGCATAATTTTTGGCATTGAGGCTCCTTGAAATATCAATATTCATCTAACCAAGTCCAAG-
325 TTATAACATAATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGC
*
2197 C-TATTGTTTTAACAAGTGTCTGAATCATCTTGCAATTAAATTAGAAATTAA-TCGTGTAAAAAT
390 CATATT-TTTT-ACAAGTGTCTGAATCATCTTGCAATTAAATTAGAAATTAATTCGTGAAAAAAT
* * *
2260 AGGAAAAATGATGTTAGAAGCGTGAAAAGCCCTTCAATATTTTTGGAGTTAAA-ATATATATATT
453 AGGAAAAATGATATTAGAAGCGCGAAAAGCCCTTCAATATTTTTAGAGTTAAATATATATATATT
* *
2324 ATGAGTATTTTATCCAAAAATGGAGGAAAATGTTTTTGGGTCATTTTTTGCAAATTTTTAGCCAA
518 ATGAGTATTTTATCCAAAAATGGAGGAAAATATTTTTAGGTCATTTTTTGCAAATTTTTAGCCAA
** *
2389 AATCGTGTACTAACCATTGCGGTTTTTGGGTAGAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGC
583 AATCGTGTACTAACCATCACGGTTTTTGGGTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGC
2454 ATGATTTTTGGCACCAAGACTCCGTGAAATATCTATATGCATCTAACAAAACCTTAGCCACATTG
648 ATGATTTTTGGCA-CAAGACTCCGTGAAATATCTATATGCATCTAACAAAACCTTAGCCACATTG
2519 CGTTCAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTTATTTAATTAGAATTTAATTCAG-A
712 CGTTCAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTTATTTAATTAGAATTTAATTCAGAA
2583 AAAAATATGAAAAACAAAATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATAT
777 AAAAATATGAAAAACAAAATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATAT
2648 ATTTTT
1 ATTTTT
2654 TAGGATTATT
Statistics
Matches: 802, Mismatches: 35, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
835 215 0.27
836 116 0.14
837 64 0.08
838 93 0.12
839 28 0.03
840 114 0.14
841 131 0.16
842 41 0.05
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Consensus pattern (841 bp):
ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAAACAAAACCTTAGCCACATTGCA
TTTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAA
AAATAAGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTCGGCATTGAATTATATA
TTTTATAAGATTATTGTGGCTAAAAATTAGAAAAATATCTTTCGGGTCAATTTTTGCCAAATTAT
AGCCGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAAT
TATAACATAATTTTTGGCATTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCC
ATATTTTTTACAAGTGTCTGAATCATCTTGCAATTAAATTAGAAATTAATTCGTGAAAAAATAGG
AAAAATGATATTAGAAGCGCGAAAAGCCCTTCAATATTTTTAGAGTTAAATATATATATATTATG
AGTATTTTATCCAAAAATGGAGGAAAATATTTTTAGGTCATTTTTTGCAAATTTTTAGCCAAAAT
CGTGTACTAACCATCACGGTTTTTGGGTAAAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCATG
ATTTTTGGCACAAGACTCCGTGAAATATCTATATGCATCTAACAAAACCTTAGCCACATTGCGTT
CAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTTATTTAATTAGAATTTAATTCAGAAAAAA
ATATGAAAAACAAAATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATAT
Found at i:2735 original size:643 final size:639
Alignment explanation
Indices: 1813--3467 Score: 2251
Period size: 643 Copynumber: 2.6 Consensus size: 639
1803 TGAATTATAT
*
1813 ATTTTTGGCACCGAGGCTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
1 ATTTTTGGCACCGAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
*
1878 TTAAGGATTTGTTTTTACGAGTATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAA
66 TTAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAA
* * * *
1943 AATAAGAAAAACAATATTAACAGCTTGAAAAGCCCATCAATATTTTCGGCATTGAATTATATATT
131 AATATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATT
*
2008 TTTTAAGATTATTGTGGCTAAAAATGTAGAAAATATCTTTCGGGTCAATTTTTGCCAAATTATAG
196 TTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCCAAATTATAG
2073 CCGAAATCGTGTAAGAATCATCACGGTTTTTGGCTAAAACGGGTTCCGAGGCCTGGTTCAATTTT
261 CCGAAATCGTGTAAGAATCATCACGG-TTTTGGCTAAAACGGGTTCCGAGGCCTGGTTCAATTTT
* * *
2138 GCATAATTTTTGGCATTGAGGCTCCTTGAAATATCAATATTCATCTAACCAAGTCCAAGCTATTG
325 GCATGATTTTTGGCATTGAGGCTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATTG
*** * *
2203 TTTTAACAAGTGTCTGAATCATCTTGCAAT-TAAATTAGAAATTAA-TCGTGTAAAAATAGGAAA
390 TTTTAACAAAAATCTGAATCATCTTGCAGTAT-AATTAGAAATTAATTCG-G-AAAAATAGAAAA
* * *
2266 AATGATGTTAGAAGCGTGAAAAGCCCTTCAATATTTTTGG-AGTTAAA-ATATATATATTATGAG
452 AACGATATTAGAAGCGTGAAAAGCCCTTAAATATTTTTGGCA-TTAAATATATATATATTATGAG
* * *
2329 TATTTTATCCAAAAATGGAGG-AAAATGTTTTTGGGTCATTTTTT-GCAAATTTTTAGCCAAAAT
516 TACTTTATCCAAAAATGGAGGAAAAAT-TTTTCGGGTCATTTTTTCGCAAAATTTTAGCCAAAAT
* * * * **
2392 CGTGTAC-TAACCATTGCGGTTTTTGGGTAGAAACGCGTTTCGGGGTCCCGGCTCAGTTTTGCAT
580 CGTGTACGTAA-CA-----GTTTTTGGCTAAAAACGCGTTTCAGGATCCCGGCTCAGTCCTGCAT
2456 G
639 G
* * *
2457 ATTTTTGGCACCAAGACTCCGTGAAATATCTATATGCATCTAACAAAACCTTAGCCACATTGCGT
1 ATTTTTGGCACCGAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
* *
2522 TCAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTT-TATTTAATTAGAATTTAATTCAGAAAA
66 TTAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAA
*
2586 AATATGAAAAACAAAATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATT
131 AATATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATT
* * *
2651 TTTTAGGATTATTGTGGCTAAAAATTTAGAAAATATCTTCCAGGTCAATTTTTGCCAAATTATAG
196 TTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCCAAATTATAG
* * *
2716 CCGAAATCGTGTAAGAATCATCACGGGTTTTGTCTAAAACGGTTTCCGAGGCCTGGTTAAATTTT
261 CCGAAATCGTGTAAGAATCATCAC-GGTTTTGGCTAAAACGGGTTCCGAGGCCTGGTTCAATTTT
*
2781 GCATGATTTTTGGCATTGAGAG-TCCTTGAAATATCAATATTCATCTAACCAAATCCCAGCCATT
325 GCATGATTTTTGGCATTGAG-GCTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATT
* * * *
2845 GTTTTTACAAAAATCTGAATCATGTTTCGGTATAATTAGAAATTAATTCGGAAAAATAGAAAAAA
389 GTTTTAACAAAAATCTGAATCATCTTGCAGTATAATTAGAAATTAATTCGGAAAAATAGAAAAAA
* * * *
2910 CGATATTAGAAGCGTGAAAAGCCTTTAAATCTTTTTGGCATTAAATTATATATATTTTATGTGTA
454 CGATATTAGAAGCGTGAAAAGCCCTTAAATATTTTTGGCATTAAA-TATATATATATTATGAGTA
* ** * * *
2975 CTTTATCCAAAAATTGAGGAAAAATTTTTCGGGTTTTTTTTTCTCAAAATTTTAGCGAAAATTGT
518 CTTTATCCAAAAATGGAGGAAAAATTTTTCGGGTCATTTTTTCGCAAAATTTTAGCCAAAATCGT
* * *
3040 GTACGTTACAGTTTTTGGCTAAAAATGCGTTTCAGGATCTCGGCTCAGTCCTGCATG
583 GTACGTAACAGTTTTTGGCTAAAAACGCGTTTCAGGATCCCGGCTCAGTCCTGCATG
* ** * * *
3097 ATTTTCGGCATTGAGACTCTGTGAAATATCTATATTCATCTAATAAAACCTTAGCCACATTGTAT
1 ATTTTTGGCACCGAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
* * *
3162 TTAAGGATTTGTTTTTATGTGCATCTGAAT-CTTTATTCGATTTAATTAGAA-TTATTTCAG-AA
66 TTAAGGATTTGTTTTTACGAGCATCTGAATCCTTT-TTCGATTTAATTAGAATTTAATTCAGAAA
* * * *
3224 AAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTCGGAGTGTG-ATTAT-T
130 AAATATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTT-GGCGT-TGAATTATAT
* *
3287 -TTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTTAATTTTTGCAAAATT
193 ATTTTTT-AAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCCAAATT
* * ** * *
3351 GTAGCCGAAATTGTGTATTAATAATCACGAGTTTTGGTTAAAAACGGGTTCCGAGGCCTGGTTTC
257 ATAGCCGAAATCGTGTAAGAATCATCACG-GTTTTGGCT-AAAACGGGTTCCGAGGCCTGG-TTC
* * ** * *
3416 AATTTAGCATGATTTTTGGCATCGAAACTCATTGAAATATCTATATTCATCT
319 AATTTTGCATGATTTTTGGCATTGAGGCTCCTTGAAATATCAATATTCATCT
3468 TATAAAACCT
Statistics
Matches: 896, Mismatches: 96, Indels: 41
0.87 0.09 0.04
Matches are distributed among these distances:
638 7 0.01
639 133 0.15
640 161 0.18
641 61 0.07
642 51 0.06
643 302 0.34
644 150 0.17
645 29 0.03
646 2 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.36
Consensus pattern (639 bp):
ATTTTTGGCACCGAGACTCCGTGAAATATCTATATTCATCTAACAAAACCTTAGCCACATTGCAT
TTAAGGATTTGTTTTTACGAGCATCTGAATCCTTTTTCGATTTAATTAGAATTTAATTCAGAAAA
AATATGAAAAACAATATTAACAGCATGAAAAGCCCATCAATATTTTTGGCGTTGAATTATATATT
TTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCCAAATTATAG
CCGAAATCGTGTAAGAATCATCACGGTTTTGGCTAAAACGGGTTCCGAGGCCTGGTTCAATTTTG
CATGATTTTTGGCATTGAGGCTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCATTGT
TTTAACAAAAATCTGAATCATCTTGCAGTATAATTAGAAATTAATTCGGAAAAATAGAAAAAACG
ATATTAGAAGCGTGAAAAGCCCTTAAATATTTTTGGCATTAAATATATATATATTATGAGTACTT
TATCCAAAAATGGAGGAAAAATTTTTCGGGTCATTTTTTCGCAAAATTTTAGCCAAAATCGTGTA
CGTAACAGTTTTTGGCTAAAAACGCGTTTCAGGATCCCGGCTCAGTCCTGCATG
Found at i:3496 original size:330 final size:327
Alignment explanation
Indices: 3091--5428 Score: 2095
Period size: 330 Copynumber: 7.1 Consensus size: 327
3081 GGCTCAGTCC
* *
3091 TGCATGATTTTCGGCATTGAGACTCTGTGAAATATCTATATTCATCTAATAAAACCTTAGCCACA
1 TGCATGATTTTTGGCATCGAGACTCT-TGAAATATCTATATTCATCTAATAAAACCTTAGCCACA
* * * *
3156 TTGTATTTAAGGATTTGTTTTTATGTGCATCTGAATCTTTATTCGATTTAATTAGAATTATTTCA
65 TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTT-TTCGATTTAATTAGAATTAATTCA
3221 GAAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTCGGAGTGTGATTAT
129 GAAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTT-GGAGT-TGATTAT
*
3286 -T-TTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTTAATTTTTGCAAAA
192 ATATTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAAA
* * * *
3349 TTGTAGCCGAAATTGTGTATTAATAATCACGAGTTTTGGTTAAAAACGGGTTCCGAGGCCTGGTT
257 TTGTAGCCGAAATCGTGTAATAATCATCACGAGTTTTGGCTAAAAACGGGTTCCGAGGCCTGG-T
3414 TCAATTT
321 TCAATTT
* * *
3421 AGCATGATTTTTGGCATCGAAACTCATTGAAATATCTATATTCATCTTATAAAACCTTAGCCACA
1 TGCATGATTTTTGGCATCGAGACTC-TTGAAATATCTATATTCATCTAATAAAACCTTAGCCACA
*
3486 TTGCATTTAAGGA--TCTTTTTACGAGCATCTGAATCTATTTTCGATTTAATTAGAAATTAATTC
65 TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TTTTCGATTTAATTAG-AATTAATTC
* * * * *
3549 AGATAAAATATGATAAACGATATTAAAAGAATGAAAACCCCATCAATCTTTCTGGATTTGAATTA
128 AGA-AAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTG-ATTA
* ** *
3614 TATATTTTGT-AAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCTAGCCAATTTTTGCAAA
191 TATATTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAA
* * * *
3678 ATTGTAGTCGAAATCGTGTTATACTCATCACGTGTTTTGGCTAAAAACGGGTTCCGAGGCCTGGT
256 ATTGTAGCCGAAATCGTGTAATAATCATCACGAGTTTTGGCTAAAAACGGGTTCCGAGGCCTGGT
3743 TCAATTT
321 TCAATTT
* ** ** * **
3750 TGCATGATTTTTGGCTTTAAGACTCCTCAAAATATCAATATTCATCTAACCAAA---T--CCA-A
1 TGCATGATTTTTGGCATCGAGACT-CTTGAAATATCTATATTCATCTAATAAAACCTTAGCCACA
* * * *
3809 --GC---T----A-TTGTTTTTACAAGTATCTGAATCATGTTTCGATTAAATTAGAAATTAATTC
65 TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC-TTTTTCGATTTAATTAG-AATTAATTC
* * * * * * *
3864 GGAAAGAA-ATTGGAAAAATGATATTAGAAGCGTGTAAAGCCCTTCAATCTTTTTGGCA-TTAAA
128 AGAAA-AATA-T-GAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGG-AGTT-GA
* * * * ** * * * * *
3927 TTATATATATATATATATTATGAGTATTTTATCCAAAAATTGATGGAAAAT-TTTTTTGGGTCAT
188 TTATATAT-T-T-T-T-TAAAGATTATTGTGGCTAAAAATT--TAGAAAATATCTTTCGGGTCAA
* * * * * * * * *
3991 TTTTTGCAAATTTGTAGTCAAAAGCGTGT-GTTA-CATCATG-GTTTTTGGCTAAAAACGTGTTT
246 TTTTTGCAAAATTGTAGCCGAAATCGTGTAATAATCATCACGAG-TTTTGGCTAAAAACGGGTTC
* * ** *
4053 CGTGGTCTCGACTCAGTTT
310 CGAGGCCT-GGTTCAATTT
* * * *
4072 TGCATGATTTTTGACACCGAGACTCTGTGAAAAATCTATATTCATCTAACAAAACCTTAGCCACA
1 TGCATGATTTTTGGCATCGAGACTCT-TGAAATATCTATATTCATCTAATAAAACCTTAGCCACA
* ** * *
4137 TTGCATTTAAGTATTTAATTTTACAAGCATTTGAATCCTTTTTCGATTTAATTAGAA--AATTCA
65 TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAAT-CTTTTTCGATTTAATTAGAATTAATTCA
* * *
4200 AAAAAATATGAAAAACGATATTAAAAGCATGTAAAGCCCATCAATCTTTTTGGTGTTGAATTATA
129 GAAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTG-ATTATA
* * *
4265 TA-TTTTTAAATAGTATTGTGGCTAAAAATTTATAAAATATCTCTT-GGGTCAATTTTTGCAAAA
193 TATTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCT-TTCGGGTCAATTTTTGCAAAA
* * ** * *
4328 TTATA-CACGAAATCGTGTAAGAATCATCACG-GTTTTTCACTAAAAACGGGTTCCTAGGCCTAG
257 TTGTAGC-CGAAATCGTGTAATAATCATCACGAG-TTTTGGCTAAAAACGGGTTCCGAGGCCTGG
*
4391 TTAAATTT
320 TTCAATTT
* ** * *
4399 TGCATGATTTTTGG--TGCTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTCAG-C-
1 TGCATGATTTTTGGCAT-C-GAGACT-CTTGAAATATCTATATTCATCTAATAAAACCTTAGCCA
* * * * *
4460 CATTGC--------------TTTTACAAGAATCTGAATCATGTTTAC-ATATAATTATAAATTAA
63 CATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC-T-TTTTCGATTTAATTA-GAATTAA
* * * * *
4510 TTCGGAAAAA-ATAGAATAAACGATATTAGAAGCGTGAAAAG-CCTTACAATCATTTTGGCA-TT
125 TTCAGAAAAATAT-GAA-AAACGATATTAAAAGCATGAAAAGCCCAT-CAATCTTTTTGG-AGTT
* * * * * * *
4572 AAATTATATATATATATATATATTA-TGTGCACTTTATCCAAAAATTGAGGAAAAT-T-TTT---
186 -GATTATATAT-TTTTTAAAGATTATTGTG-GC----T--AAAAATTTA-GAAAATATCTTTCGG
** * * * * *
4631 -TTGATTTTTGCAAATTTTTAG-CGAAAATTGTGTAGTAACCATCAC-AGTTTTGTGCTAAAAAC
241 GTCAATTTTTGCAAAATTGTAGCCG-AAATCGTGTAATAATCATCACGAGTTTTG-GCTAAAAAC
* * * * *
4693 GCGTTTCG-GGATCTCGGCTT-AGTTC
304 GGGTTCCGAGG-CCT-GG-TTCAATTT
* *
4718 TGCATGATTTTTGGCA-CTGAGACTCTATGAAATATCTATATACATCTAATAAAACCTTAGCCAT
1 TGCATGATTTTTGGCATC-GAGACTCT-TGAAATATCTATATTCATCTAATAAAACCTTAGCCAC
*
4782 ATTGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTTATTCGATTTAATTAGAATTAATTC
64 ATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTT-TTCGATTTAATTAGAATTAATTC
*
4847 AGAAAAATATGAAAAACAATATTAAAAGCATGAAAAGCCCATCAATCTTTTTCGGAGTTGGATTA
128 AGAAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTT-GGAGTT-GATTA
*
4912 TTTATTTTTT-AAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTT-CAAA
191 TATATTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAA
* * *
4975 ATTGTAGCCGAAATCGTGTAATAATCATCACGTGTTTTGCCTAAAAATGGGTTCCGAGGCCTGGT
256 ATTGTAGCCGAAATCGTGTAATAATCATCACGAGTTTTGGCTAAAAACGGGTTCCGAGGCCTGGT
5040 TCAATTT
321 TCAATTT
* * * * *
5047 AGCATGATTTTTGACACCGAAACTCCTTGAAACATCTATATTCATCTAATAAAACCTTAGCCACA
1 TGCATGATTTTTGGCATCGAGACT-CTTGAAATATCTATATTCATCTAATAAAACCTTAGCCACA
* *
5112 TTGCATTTATGGATTTGTTTTTACGAGCATCTAAATCTATTTTCGATTTAATTAGAAATTAATTC
65 TTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT-TTTTCGATTTAATTAG-AATTAATTC
* *
5177 AGAAAAAATATGAAAAACAATATTAAAAGCATGAAAAGCCCATCAATCTTTTGGGAGTTGAATTA
128 AG-AAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTG-ATTA
* *
5242 TATATTTTTT-AAGAGTATTGTGGCAAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAA
191 TATATTTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAA
* * * * * *
5306 ATTATAGTCGAAATAGTGTAAGAATCATCACGGATTTTTGGCTAAAAACGCGTTCCGAGGCGC-G
256 ATTGTAGCCGAAATCGTGTAATAATCATCAC-GAGTTTTGGCTAAAAACGGGTTCCGAGGC-CTG
5370 GTTCAATTT
319 GTTCAATTT
* * *
5379 TGGCATGATTTTTTACGC-T-GAGACTCCTTGAAATATCAATATTTATCTAA
1 T-GCATGA-TTTTT-GGCATCGAGACT-CTTGAAATATCTATATTCATCTAA
5429 CCAAATCCCA
Statistics
Matches: 1622, Mismatches: 257, Indels: 255
0.76 0.12 0.12
Matches are distributed among these distances:
310 1 0.00
311 25 0.02
312 6 0.00
313 2 0.00
314 20 0.01
315 90 0.06
316 51 0.03
317 20 0.01
318 53 0.03
319 54 0.03
320 4 0.00
321 43 0.03
322 66 0.04
323 43 0.03
324 15 0.01
325 19 0.01
326 43 0.03
327 78 0.05
328 72 0.04
329 181 0.11
330 350 0.22
331 104 0.06
332 40 0.02
333 125 0.08
334 44 0.03
335 36 0.02
337 3 0.00
338 33 0.02
339 1 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (327 bp):
TGCATGATTTTTGGCATCGAGACTCTTGAAATATCTATATTCATCTAATAAAACCTTAGCCACAT
TGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTTTTCGATTTAATTAGAATTAATTCAGA
AAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTGATTATATAT
TTTTTAAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTGT
AGCCGAAATCGTGTAATAATCATCACGAGTTTTGGCTAAAAACGGGTTCCGAGGCCTGGTTCAAT
TT
Found at i:5074 original size:648 final size:647
Alignment explanation
Indices: 3422--5095 Score: 2242
Period size: 649 Copynumber: 2.6 Consensus size: 647
3412 TTTCAATTTA
* *
3422 GCATGATTTTTGGCA-TCGAAACTC-ATTGAAATATCTATATTCATCTTATAAAACCTTAGCCAC
1 GCATGATTTTTGGCACT-GAGACTCTA-TGAAATATCTATATTCATCTAATAAAACCTTAGCCAC
* *
3485 ATTGCATTTAAGGA--TCTTTTTACGAGCATCTGAATCTATTTTCGATTTAATTAGAAATTAATT
64 ATTGCATTTAAGGATTTATTTTTACGAGCATTTGAATCT-TTTTCGATTTAATTAG-AATTAATT
* * * * *
3548 CAGATAAAATATGATAAACGATATTAAAAGAATGAAAACCCCATCAATCTTTCTGGATTTGAATT
127 CAGA-AAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTGAATT
* ** *
3613 ATATATTTTGTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCTAGCCAATTTTTGCAAA
191 ATATATTTTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAA
* * * *
3678 ATTGTAGTCGAAATCGTGTTATACTCATCACGTGTTTTGGCTAAAAACGGGTTCCGAGGCCTGGT
256 ATTGTAGCCGAAATCGTGTAATAATCATCACGTGTTTTGCCTAAAAACGGGTTCCGAGGCCTGGT
* * **
3743 TCAATTTTGCATGATTTTTGGCTTTAAGACTCCTCAAAATATCAATATTCATCTAACCAAATCCA
321 TCAATTTTGCATGATTTTTGGCCTGAA-ACTCCTTGAAATATCAATATTCATCTAACCAAATCCA
* * *
3808 AGCTATTGTTTTTACAAGTATCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGGAAAGAAA
385 AGCCATTGCTTTTACAAGAATCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGGAAAGAAA
* * * *
3873 TTGGAAAAATGATATTAGAAGCGTGTAAAGCCCTTCAATCTTTTTGGCATTAAATTATATATATA
450 TTAGAAAAACGATATTAGAAGCGTGAAAAGCCCTTCAATCATTTTGGCATTAAATTATATATATA
* *
3938 TATATATTATGAGTATTTTATCCAAAAATTGATGGAAAATTTTTTTGGGTCATTTTTTGCAAATT
515 TATATATTATGAGCACTTTATCCAAAAATTGATGGAAAATTTTTTT-GG-CATTTTTTGCAAATT
* ** *
4003 TGTAGTCAAAAGCGTGTGTTACATCATGGTTTTTGGCTAAAAACGTGTTTCGTGGTCTCGACTCA
578 TGTAGTCAAAAGCGTGTGTAACATCACAGTTTTTGGCTAAAAACGCGTTTCGTGGTCTCGACTCA
*
4068 GTTTT
643 GTTCT
* * * * *
4073 GCATGATTTTTGACACCGAGACTCTGTGAAAAATCTATATTCATCTAACAAAACCTTAGCCACAT
1 GCATGATTTTTGGCACTGAGACTCTATGAAATATCTATATTCATCTAATAAAACCTTAGCCACAT
* * * *
4138 TGCATTTAAGTATTTAATTTTACAAGCATTTGAATCCTTTTTCGATTTAATTAGAA--AATTCAA
66 TGCATTTAAGGATTTATTTTTACGAGCATTTGAAT-CTTTTTCGATTTAATTAGAATTAATTCAG
* *
4201 AAAAATATGAAAAACGATATTAAAAGCATGTAAAGCCCATCAATCTTTTTGGTGTTGAATTATAT
130 AAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTGAATTATAT
* * * *
4266 ATTTTTAAATAGTATTGTGGCTAAAAATTTATAAAATATCTCTT-GGGTCAATTTTTGCAAAATT
195 ATTTTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCT-TTCGGGTCAATTTTTGCAAAATT
* * * * *
4330 ATA-CACGAAATCGTGTAAGAATCATCACG-GTTTTTCACTAAAAACGGGTTCCTAGGCCTAGTT
259 GTAGC-CGAAATCGTGTAATAATCATCACGTGTTTTGC-CTAAAAACGGGTTCCGAGGCCTGGTT
* * *
4393 AAATTTTGCATGATTTTTGGTGCTGAGACTCCTTGAAATATCAATATTCATCTAACCAAATCTC-
322 CAATTTTGCATGATTTTTGG-CCTGAAACTCCTTGAAATATCAATATTCATCTAACCAAATC-CA
*
4457 AGCCATTGCTTTTACAAGAATCTGAATCATGTTTAC-A-TATAATTATAAATTAATTCGGAAA-A
385 AGCCATTGCTTTTACAAGAATCTGAATCATGTTT-CGATTA-AATTAGAAATTAATTCGGAAAGA
4519 AA-TAGAATAAACGATATTAGAAGCGTGAAAAG-CCTTACAATCATTTTGGCATTAAATTATATA
448 AATTAGAA-AAACGATATTAGAAGCGTGAAAAGCCCTT-CAATCATTTTGGCATTAAA-T-TATA
*
4582 TATATATATATATTATGTGCACTTTATCCAAAAATTGA-GGAAAATTTTTTT-G-A-TTTTTGCA
509 TATATATATATATTATGAGCACTTTATCCAAAAATTGATGGAAAATTTTTTTGGCATTTTTTGCA
* **
4643 AATTTTTAG-CGAAAATTGTGTAGTAACCATCACAG-TTTTGTGCTAAAAACGCGTTTCG-GGAT
574 AATTTGTAGTC-AAAAGCGTGT-GTAA-CATCACAGTTTTTG-GCTAAAAACGCGTTTCGTGG-T
* *
4705 CTCGGCTTAGTTCT
634 CTCGACTCAGTTCT
* *
4719 GCATGATTTTTGGCACTGAGACTCTATGAAATATCTATATACATCTAATAAAACCTTAGCCATAT
1 GCATGATTTTTGGCACTGAGACTCTATGAAATATCTATATTCATCTAATAAAACCTTAGCCACAT
*
4784 TGCATTTAAGGATTTGTTTTTACGAGCATTTGAATCTTTATTCGATTTAATTAGAATTAATTCAG
66 TGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTT-TTCGATTTAATTAGAATTAATTCAG
* * *
4849 AAAAATATGAAAAACAATATTAAAAGCATGAAAAGCCCATCAATCTTTTTCGGAGTTGGATTATT
130 AAAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTT-GGAGTTGAATTATA
4914 TATTTTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTT-CAAAATT
194 TATTTTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAAATT
*
4978 GTAGCCGAAATCGTGTAATAATCATCACGTGTTTTGCCTAAAAATGGGTTCCGAGGCCTGGTTCA
259 GTAGCCGAAATCGTGTAATAATCATCACGTGTTTTGCCTAAAAACGGGTTCCGAGGCCTGGTTCA
* * * * *
5043 ATTTAGCATGATTTTTGACACCGAAACTCCTTGAAACATCTATATTCATCTAA
324 ATTTTGCATGATTTTTGGC-CTGAAACTCCTTGAAATATCAATATTCATCTAA
5096 TAAAACCTTA
Statistics
Matches: 894, Mismatches: 100, Indels: 61
0.85 0.09 0.06
Matches are distributed among these distances:
643 1 0.00
644 24 0.03
645 15 0.02
646 139 0.16
647 9 0.01
648 207 0.23
649 343 0.38
650 52 0.06
651 67 0.07
652 2 0.00
653 33 0.04
654 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Consensus pattern (647 bp):
GCATGATTTTTGGCACTGAGACTCTATGAAATATCTATATTCATCTAATAAAACCTTAGCCACAT
TGCATTTAAGGATTTATTTTTACGAGCATTTGAATCTTTTTCGATTTAATTAGAATTAATTCAGA
AAAATATGAAAAACGATATTAAAAGCATGAAAAGCCCATCAATCTTTTTGGAGTTGAATTATATA
TTTTTTAAGATTATTGTGGCTAAAAATTTAGAAAATATCTTTCGGGTCAATTTTTGCAAAATTGT
AGCCGAAATCGTGTAATAATCATCACGTGTTTTGCCTAAAAACGGGTTCCGAGGCCTGGTTCAAT
TTTGCATGATTTTTGGCCTGAAACTCCTTGAAATATCAATATTCATCTAACCAAATCCAAGCCAT
TGCTTTTACAAGAATCTGAATCATGTTTCGATTAAATTAGAAATTAATTCGGAAAGAAATTAGAA
AAACGATATTAGAAGCGTGAAAAGCCCTTCAATCATTTTGGCATTAAATTATATATATATATATA
TTATGAGCACTTTATCCAAAAATTGATGGAAAATTTTTTTGGCATTTTTTGCAAATTTGTAGTCA
AAAGCGTGTGTAACATCACAGTTTTTGGCTAAAAACGCGTTTCGTGGTCTCGACTCAGTTCT
Found at i:6682 original size:2 final size:2
Alignment explanation
Indices: 6675--6701 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6665 GGTGTTGAAT
6675 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
6702 TACGAGTATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7571 original size:323 final size:320
Alignment explanation
Indices: 6860--7981 Score: 876
Period size: 324 Copynumber: 3.5 Consensus size: 320
6850 GTGGTAAAAA
* * **
6860 TCCTTGAAATA--TATATTCATCTAACCAAATCTTAGCCACATTGGATTTAAAAATTTGTTTTTA
1 TCCTTGAAATATCTATATTCATCTAACTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * * * * * * *
6923 TGAGCATTTGAATCATGTTTCGATTTAATTA-AAATTAATTTGAAAAAAAAAGAAGGAAAAACGA
66 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCG--GAAAAAA-TACGAAAAACAA
* * * * * *
6987 TATTAGAAGAC-TG-AGAAGCCCTTCAATCTTTTTTG-CGTTGAATTATATATTTTTTATAAGTA
128 TATTAAAAG-CGTGAAAAAGCTCTTCAATC-TTTTTGATGTCGAATTATATATTTTTTATGAGTA
* * ** * * *
7049 TTGT-GCCTAAAAATTGA-GAAAAATATTTTGGGTCAACTTTTGCTAAATTTTAGCCGAAATCGT
191 TTTTAG-CTAAAAATTAAGGAAAAACCTTTCGGG-----TTTTGCAAAATTTTAGCTGAAATCGT
* ** * * * * * ** * *
7112 G---T-ACCATCACAGTTTTTTTGACTAGAAACGCGTTTCGGGGCCCCGGGTAAATTTTGCATGA
250 GTACTAACCATCAC-GGTTTTCAG-CTAAAAACGCATTCCAGGGCCACGACTCAGTTTTG-A-G-
****
7173 TTTTTGGTGTAAAGAC
310 ---TT--AACCAAGAC
* * *
7189 TCCTTAAAATATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATTTAAGGATTTGTTTT
1 TCCTT-GAA-ATATCTATATTCATCTAACTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * *
7254 TACGAGTATCTAAATCTTGTTTCGATTTAATCAGAAATTAATTTGGAAATAAAATACGAAAAACA
64 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGG-AA-AAAATACGAAAAACA
* * * * *
7319 ATATTATAAGCGTGAAAAAGGCT-TTCAAT-TTTTTGGGTGTTGAATTGTATATTTTTTATGATT
127 ATATTAAAAGCGTGAAAAA-GCTCTTCAATCTTTTT-GATGTCGAATTATATATTTTTTATGAGT
* * * * *
7382 ATTTTCA-CTAGAAATTGAGGAAAAATCTTTCTGGTCAATTTTTGCAAAATTTTAG-TCGAAGTC
190 ATTTT-AGCTAAAAATTAAGGAAAAACCTTTC-GG----GTTTTGCAAAATTTTAGCT-GAAATC
* *
7445 GTGTACTAACCATCACGGTTTTCGGCTAAAAACGCATTCC-GGGACC-CGGCTCAGTTTTG-G-T
248 GTGTACTAACCATCACGGTTTTCAGCTAAAAACGCATTCCAGGG-CCACGACTCAGTTTTGAGTT
*
7506 -GCCAAGAC
312 AACCAAGAC
** * *
7514 TTTTTGAAATATCTATATTCATCTAACTAAATCTCAGCCACATTGGATTTTAGGATTTGCTTTTA
1 TCCTTGAAATATCTATATTCATCTAACTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
* * * *
7579 CGAGCATCTGCATCTTGTTTTGATTTAATTAGAAATTAATTCGGAAAAATTAGGAAAAACAATAT
66 CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATACGAAAAACAATAT
* * * *
7644 TAGAAGCAT-CAAAAGCTCTTCAATCTTTTTTATGTCGAATTATATATTTTTTATGAGTATTTTA
131 TAAAAGCGTGAAAAAGCTCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTA
* *
7708 GTTAAAAATTAAGGAAATACCTTTCGGGTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCAT
196 GCTAAAAATTAAGGAAAAACCTTTCGGGTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCAT
* * * * * *
7773 CACGGTTTTTAGCTAAAAATGCCTTCCAGGGCCATGACTCTGTTTTGCATGATTTTTTACACCGA
261 CACGGTTTTCAGCTAAAAACGCATTCCAGGGCCACGACTCAGTTTTG-A-G-----TTA-ACCAA
7838 GAC
318 GAC
*
7841 TCCTTGAAATA--TAT-TT-ATTCTAA-TCAAATCTCAGCCACATTGGATATAAGGATTTGTTTT
1 TCCTTGAAATATCTATATTCA-TCTAACT-AAATCTCAGCCACATTGGATTTAAGGATTTGTTTT
* * * *
7901 TACGTGCATTTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATATGAAAAACGAT
64 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATACGAAAAACAAT
7966 ATTAAAAGCGTGAAAA
129 ATTAAAAGCGTGAAAA
7982 GTCCTCCAAT
Statistics
Matches: 652, Mismatches: 95, Indels: 96
0.77 0.11 0.11
Matches are distributed among these distances:
315 59 0.09
316 14 0.02
319 7 0.01
320 57 0.09
321 29 0.04
322 2 0.00
323 93 0.14
324 108 0.17
325 16 0.02
327 15 0.02
328 1 0.00
329 5 0.01
330 2 0.00
331 3 0.00
332 6 0.01
333 96 0.15
334 60 0.09
335 35 0.05
336 15 0.02
337 14 0.02
338 7 0.01
339 8 0.01
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (320 bp):
TCCTTGAAATATCTATATTCATCTAACTAAATCTCAGCCACATTGGATTTAAGGATTTGTTTTTA
CGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATACGAAAAACAATAT
TAAAAGCGTGAAAAAGCTCTTCAATCTTTTTGATGTCGAATTATATATTTTTTATGAGTATTTTA
GCTAAAAATTAAGGAAAAACCTTTCGGGTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCAT
CACGGTTTTCAGCTAAAAACGCATTCCAGGGCCACGACTCAGTTTTGAGTTAACCAAGAC
Found at i:8013 original size:2 final size:2
Alignment explanation
Indices: 8006--8037 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
7996 TGGCGTTGAA
8006 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8038 TATGAGTATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15687 original size:3 final size:3
Alignment explanation
Indices: 15679--15708 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
15669 ATTGCTGGGC
15679 GGT GGT GGT GGT GGT GGT GGT GGGT GGT GG
1 GGT GGT GGT GGT GGT GGT GGT -GGT GGT GG
15709 GGAGGGGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.00, C:0.00, G:0.70, T:0.30
Consensus pattern (3 bp):
GGT
Found at i:29284 original size:3 final size:3
Alignment explanation
Indices: 29271--29309 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
29261 ATATATATAG
*
29271 GAA GCA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
29310 AGAATATGAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.03, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Done.