Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_617 ID=scaffold_617-JGI_221_v2.0
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: 5212
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.31
Found at i:168 original size:86 final size:86
Alignment explanation
Indices: 19--183 Score: 242
Period size: 86 Copynumber: 1.9 Consensus size: 86
9 ACTATCTTGA
* *
19 GAAGATAAGATTCACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGAAATCTT
1 GAAGATAAGATTCACCATCTTCGATCCGCTCCACAACTACTTAGGGTAACAGAATCTCAAATCTT
*
84 CAACCTACTCCACTGTATTGG
66 CAACCGACTCCACTGTATTGG
* * * *
105 GAAGATAAGATTCCCCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATC-CACAATCT
1 GAAGATAAGATTCACCATCTTCGATCCGCTCCACAACTACTTAGGGTAACAGAATCTCA-AATCT
*
169 TTAACCGACTCCACT
65 TCAACCGACTCCACT
184 ACTTCTTATG
Statistics
Matches: 70, Mismatches: 8, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
85 1 0.01
86 69 0.99
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (86 bp):
GAAGATAAGATTCACCATCTTCGATCCGCTCCACAACTACTTAGGGTAACAGAATCTCAAATCTT
CAACCGACTCCACTGTATTGG
Found at i:262 original size:132 final size:132
Alignment explanation
Indices: 91--681 Score: 740
Period size: 132 Copynumber: 4.5 Consensus size: 132
81 CTTCAACCTA
* ** * *
91 CTCCACTGTATTGGGAAGATAAGATTCCCCATCTTCGATCTGCTCCACTACTACTTAGGGTGACA
1 CTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * * * * * * *
156 GAATCCACAATCTTTAACCGACTCCACTACTTCTTATGGTGATAAGACTAACGGCATAAATCTGC
66 GAATCTACAATCTTCAACCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGC
221 TT
131 TT
* * *
223 CTCCACTGTATTAGGAAAATAAGATTCATCATATTCGATCTGCTTCACTACTGTTTAGGGTGACA
1 CTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * * * *
288 GAATCTACAATCTTCAACCAACTCCACTA-TGGCTGAGGGAGATAGGATTAATAGCTTAAATGTT
66 GAATCTACAATCTTCAACCTACTCCACTACT-GCTGAGGGTGATAGGACTAATGGCTTAAATCTG
*
352 CCT
130 CTT
355 CTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACA
1 CTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * *
420 GACTCTGCAATCTTTAGCCTACTCCACTAC-GACTGAGGGTGATAGGACTAATGGCTTAAATCTG
66 GAATCTACAATCTTCAACCTACTCCACTACTG-CTGAGGGTGATAGGACTAATGGCTTAAATCTG
484 CTT
130 CTT
* * * * * *
487 CTCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCCGCTACACAACTGCTTAGGGTAACA
1 CTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACA
* * * *
552 GAATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGC
66 GAATCTACAATCTTCAACCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGC
617 TT
131 TT
* * * *
619 CTCCACTGTATTAGGAAGATAAGATTCA-CA-ATCTCCAACCTACTCCACCACTGCTTAGGGTGA
1 CTCCACTGTATTAGGAAGATAAGATTCATCATAT-T-CGATCTGCTCCACTACTGCTTAGGGTGA
682 TAGGACTAAT
Statistics
Matches: 395, Mismatches: 58, Indels: 12
0.85 0.12 0.03
Matches are distributed among these distances:
130 1 0.00
131 5 0.01
132 388 0.98
133 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.29
Consensus pattern (132 bp):
CTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACA
GAATCTACAATCTTCAACCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGC
TT
Found at i:693 original size:88 final size:88
Alignment explanation
Indices: 559--769 Score: 314
Period size: 88 Copynumber: 2.4 Consensus size: 88
549 ACAGAATCTG
* *
559 CAATCTTCAACCTACTCCACTGCTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCA
624 CTGTATTAGGAAGATAAGATTCA
66 CTGTATTAGGAAGATAAGATTCA
* * *
647 CAATCTCCAACCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCA
* * *
712 CTGTATTTGGAAGGTAAGATTTA
66 CTGTATTAGGAAGATAAGATTCA
* * * *
735 CCATCTTCGATCTGCTCCACTACTGCTTAGGGTGA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGA
770 CCGAATCAGC
Statistics
Matches: 109, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 109 1.00
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.30
Consensus pattern (88 bp):
CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCA
CTGTATTAGGAAGATAAGATTCA
Found at i:698 original size:220 final size:220
Alignment explanation
Indices: 437--901 Score: 698
Period size: 220 Copynumber: 2.1 Consensus size: 220
427 CAATCTTTAG
*
437 CCTACTCCACTAC-GACTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
1 CCTACTCCACTACTG-CTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
* *
501 GAAGATAAGATTCATCATCTTCGATCCGCTACACAACTGCTTAGGGTAACAGAATCTGCAATCTT
65 GAAGATAAGATTCACCATCTTCGATCCGCTACACAACTGCTTAGGGTAACAGAATCAGCAATCTT
*
566 CAACCTACTCCACTGCTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATT
130 CAACCTACTCCACTACTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATT
631 AGGAAGATAAGATTCACAATCTCCAA
195 AGGAAGATAAGATTCACAATCTCCAA
* *
657 CCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTTGG
1 CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
* * * * * * * *
722 AAGGTAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACCGAATCAGCAATCTTT
66 AAGATAAGATTCACCATCTTCGATCCGCTACACAACTGCTTAGGGTAACAGAATCAGCAATCTTC
* * * *
787 AGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTG
131 AACCTACTCCACTACTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTA
* * *
852 GGAAGATAAGATTCACCATCTTCGA
196 GGAAGATAAGATTCACAATCTCCAA
* * *
877 GCTTCTCCACTATTGCTTAGGGTGA
1 CCTACTCCACTACTGCTTAGGGTGA
902 CAGAATCTGC
Statistics
Matches: 219, Mismatches: 25, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
220 218 1.00
221 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (220 bp):
CCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCACTGTATTGGG
AAGATAAGATTCACCATCTTCGATCCGCTACACAACTGCTTAGGGTAACAGAATCAGCAATCTTC
AACCTACTCCACTACTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTA
GGAAGATAAGATTCACAATCTCCAA
Found at i:732 original size:352 final size:352
Alignment explanation
Indices: 294--998 Score: 1063
Period size: 352 Copynumber: 2.0 Consensus size: 352
284 GACAGAATCT
* * * * *
294 ACAATCTTCAACCAACTCCACTATGGCTGAGGGAGATAGGATTAATAGCTTAAATGTTCCTCTCC
1 ACAATCTCCAACCAACTCCACCATGGCTGAGGGAGATAGGACTAATAGCTTAAATCTGCCTCTCC
* *
359 ACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGACT
66 ACTGTATTAGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
*
424 CTGCAATCTTTAGCCTACTCCACTAC-GACTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTC
131 CAGCAATCTTTAGCCTACTCCACTACTG-CTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTC
* *
488 TCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCCGCTACACAACTGCTTAGGGTAACAG
195 TCCACTGTATTGGGAAGATAAGATTCACCATCTTCGAGCCGCTACACAACTGCTTAGGGTAACAG
* * *
553 AATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCT
260 AATCTGCAATCTTCAACCTACTCCACTACTGCTCAAGGTCATAGGACAAATGGCTTAAATCTGCT
*
618 TCTCCACTGTATTAGGAAGATAAGATTC
325 TCTCCACTGTATTAGGAACATAAGATTC
* * * * *
646 ACAATCTCCAACCTACTCCACCACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTC
1 ACAATCTCCAACCAACTCCACCA-TGGCTGAGGGAGATAGGACTAATAGCTTAAATCTGCCTCTC
* * * * *
710 CACTGTATTTGGAAGGTAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACCGAA
65 CACTGTATTAGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAA
775 TCAGCAATCTTTAGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTC
130 TCAGCAATCTTTAGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTC
** * * * *
840 TCCACTGTATTGGGAAGATAAGATTCACCATCTTCGAGCTTCTCCACTATTGCTTAGGGTGACAG
195 TCCACTGTATTGGGAAGATAAGATTCACCATCTTCGAGCCGCTACACAACTGCTTAGGGTAACAG
* * * *
905 AATCTGCACTCTTCAACCTACTCCACTACTTCTTAAGGTCATAGGACTAATGGCTTAAATCTGCT
260 AATCTGCAATCTTCAACCTACTCCACTACTGCTCAAGGTCATAGGACAAATGGCTTAAATCTGCT
*
970 TCTCCACTGTATTGGGAACATAAGATTC
325 TCTCCACTGTATTAGGAACATAAGATTC
998 A
1 A
999 TCATATTCGA
Statistics
Matches: 316, Mismatches: 35, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
352 314 0.99
353 2 0.01
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (352 bp):
ACAATCTCCAACCAACTCCACCATGGCTGAGGGAGATAGGACTAATAGCTTAAATCTGCCTCTCC
ACTGTATTAGGAAGATAAGATTCACCATATTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
CAGCAATCTTTAGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTCT
CCACTGTATTGGGAAGATAAGATTCACCATCTTCGAGCCGCTACACAACTGCTTAGGGTAACAGA
ATCTGCAATCTTCAACCTACTCCACTACTGCTCAAGGTCATAGGACAAATGGCTTAAATCTGCTT
CTCCACTGTATTAGGAACATAAGATTC
Found at i:765 original size:132 final size:132
Alignment explanation
Indices: 647--5197 Score: 3743
Period size: 132 Copynumber: 34.5 Consensus size: 132
637 ATAAGATTCA
* *
647 CAATCTCCAACCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * *
712 CTGTATTTGGAAGGTAAGATTTACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACCGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
*
777 AG
131 TG
* * *
779 CAATCTTTAGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * *
844 CTGTATTGGGAAGATAAGATTCACCATCTTCGAGCTTCTCCACTATTGCTTAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
909 TG
131 TG
* * * *
911 CACTCTTCAACCTACTCCACTACTTCTTAAGGTCATAGGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * ** *
976 CTGTATTGGGAACATAAGATTCATCATATTCGACCTGCTCCACTACTG-TTCAGGGCAACAAAAT
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTT-AGGGTGACAGAAT
*
1040 TTG
130 CTG
* * * * * *
1043 TAATTTTTAACCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTGTCCT
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * *
1108 CTGTATTAGGAAGATAAGATTAACCATCTTCAATCTGCTCCACTACTACTTAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
1173 TG
131 TG
* * * * *
1175 CAATCTTTAACCGACTCCACTACTTCTTAGGGTGATAGGACTAATGGCTGAAATCTACTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * *
1240 CTGTATTGGGAAGATAAGATTCACCATTTTCGATCTACTCCACTACTGCTTAGGGTGGCAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
*
1305 TA
131 TG
* * * * *
1307 CAATCTTCATCCTACTCCACCACTGCTTAGGATGACAGGACTAATTGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * *
1372 CTGTATTGGGAAAATAAGATTCATCATATTCGATCTGCAT-CAGTACTGTTTAGGGTGACAGAAT
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGC-TCCACTACTGCTTAGGGTGACAGAAT
*
1436 ATG
130 CTG
* * *
1439 CAATCTTCAACCAACTCCACTA-TGGCTTAGGGAGATAGAACTAATGGCTTAAATCTGCTTCTCC
1 CAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
** * * * *
1503 ACTCCATTGGGAAGATAAGATTCACCATCTTCGATCTCCGCCACTATTACTTAGGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
1568 CTG
130 CTG
* *
1571 TAATCTTCAACCTACT-CATCTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCT
1 CAATCTTCAACCTACTCCA-CTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
*
1635 ACTGTATTGGGAAGATAATATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
1700 CT-
130 CTG
* * * *
1702 CTAATCTTCAACCTGCTCCAGTACTGCTTAGGGTGATAGGATTAATGGCTTAAATATGCTTCTCC
1 C-AATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
* * * * * *
1767 ATTGTATTGGGAAGATAAGATTCATCATATTCGATCTGCTCAACTACTGTTTAAGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
1832 CTG
130 CTG
* * * ** * *
1835 TAATCTTCAACCTACTCCACTACTGCTTTGGGAGATAGGTTTAATGGCTTAAATCTGCTCCTCTA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * *
1900 CTATAATGGGTAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
1965 TG
131 TG
* * * * * * *
1967 CAATCCTCAACCTACTCCACCACTGCTTAGGGAGATTA-GACTAATGGCTTACATTTACTTCTCT
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGA-TAGGACTAATGGCTTAAATCTGCTTCTCC
* * * * * * *
2031 ACTATCTTGAGAAGATATGATTCACCATCTTCGATCCGCTGCACTACTGCTTAGGATGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
2096 CTG
130 CTG
* * *
2099 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGACTTAAATCTACTTGTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* *
2164 TTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAAGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
2229 TG
131 TG
* * *
2231 CAATTTTCAACCTACACCACTACTGCTTAGGATGATAGGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * *
2296 CTGTATTGCGAAGATAGGATTCACCATCTTCGATCTG-TATCACTACTGGTTAGGGTGACAGAAT
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCT-CCACTACTGCTTAGGGTGACAGAAT
2360 CTG
130 CTG
* * * *
2363 TAATCTTCAACCGACTCCACTACTACTTAGGATGATAGGACTAATGGCTTAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* *
2428 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGGTGAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
2493 TG
131 TG
* * *
2495 CAATCTTCAACCGACTCCACTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCGCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * **
2560 TTGTATTTGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACCACTTAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
*
2625 TA
131 TG
* * * * * *
2627 CAATCTTCAACCTACTCCAGTACTACTTAAGGTGA-ATGGACTAATGGCTTAAATTTGTTTCTCT
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATA-GGACTAATGGCTTAAATCTGCTTCTCC
* * * * * * * *
2691 ACTGTATTGGGAAGATAAGATTTATCATATTCGATCTGCTACACTACTGTTTAGGGAGATAGGA-
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
2755 C--
130 CTG
* * * * * * * * * * ** *
2756 AAATGGCTTAAATCTGCTTCTCTACTG-TATCGGGAAGATAAGATTCACCAT--CTTTGATCTAC
1 CAAT--CTTCAACCTACTCCACTACTGCT-TAGGG-TGATAGGACT-A--ATGGCTTAAATCTGC
* * * * * * * * * * * * *
2818 TCCACTACTGCT-TAGGG-TGAT-AGAATCTGCAATCCTCAACCTACTCCACTACTGCTTAGGGA
59 TTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGCTTAGGGT
** *
2880 GATTGGA-CT-
122 GACAGAATCTG
* * ** * * * ** *
2889 C-ATGGCTTACATCTGCTTCTCCACTA-T-CTT-GAGAAGATATGATTCACTATCTTCAATCTGC
1 CAAT--CTT-CAAC--CTACTCCACTACTGCTTAG-GGTGATAGGACT-AATGGCTTAAATCTGC
* * * ** * * * * * * * * *
2950 TGCACTACTGCT-TACGG-TGA-CAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGAT
59 TTCTCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGCTTAGGGT
* *
3012 GATAGGA-CT-
122 GACAGAATCTG
* * * * * * * * * * **
3021 -AATGGCTTAAATCTGCTTCTCCACTG-TATTGGGAAGATAAGATTCACCAT--CTTCGATCTGC
1 CAAT--CTTCAACCTACTCCACTACTGCT-TAGGG-TGATAGGACT-A--ATGGCTTAAATCTGC
* * * ** * * * * * * * * *
3082 TCCACTACT-CCTT-AG-AG-TGACAGAATCTACAATCTTCAACCTACTCGAGTACTGCTTAAGG
59 TTCTCCACTGTATTGGGAAGAT-A-AGATTC-ACCATCTTCGATCTGCTCCACTACTGCTTAGGG
*
3143 TGA-ATGGA-CT-
121 TGACA-GAATCTG
* * ** * * * * * * *** **
3153 -AATGGCTTAAATCTGTTTC-CTCACTG-TATTGGGAAGATAAGATTCATCATATTCGATCTGCT
1 CAAT--CTTCAACCTACTCCACT-ACTGCT-TAGGG-TGATAGGACTAAT-GGCTTAAATCTGCT
* * * * * *** * * * * * *
3215 CCTCTACTGT-TTAGGG-TGA-CAGAATCTGTAATCTTCAACCTACTCCACTACAGTTTTGGGTG
60 TCTCCACTGTATT-GGGAAGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGCTTAGGGTG
* *
3277 ATAGGA-CT-
123 ACAGAATCTG
* * * * * ** * * * * *
3285 -AATGGCTTAAATCTTCTTCTC-CT-CAGTATTAGGAAGATAAGATTAA--CCAT-ATTC-GATC
1 CAAT--CTTCAACCTAC-TC-CACTACTG-CTTAGGGTGATAGGACTAATGGCTTAAATCTG--C
* * * * * * ** * * * *
3343 TGCTCCACTACTACTTAGGG-TGACAACA-TCTACAATCTTTAACCTACTCCACTACTACTGAGG
59 TTCTCCACT-GTA-TT-GGGAAGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGCTTAGG
* *
3406 GTGATAGGA-CT-
120 GTGACAGAATCTG
* * * * * * * * ** * * ** *
3417 -AATGGCTTAAATCTAGTTCTCCACTGTATTTGGAAGATAAGATTCACCAT--CTTCGATCTACT
1 CAAT--CTTCAACCTACTCCACTACTG-CTTAGGGTGATAGGACT-A--ATGGCTTAAATCTGCT
* * * * * * * * * * *
3479 CCACTACTGCT-TAGGG-TGACTGA-ATCTGCA--ATATTC-AACATACTCCACTACAGCTTTTG
60 TCTCCACTG-TATTGGGAAGA-TAAGAT-T-CACCATCTTCGATC-TGCTCCACTACTGC-TTAG
*
3538 GAGATTGGACA-AATGGCTT
119 G-G--T-GACAGAAT--CTG
* * * ** * * ** * *
3557 AAATC-T---GCTTCTCCACTA-T-CTTTA-GAAGATAAGATTCACCAT--CTTCGATCCGCTCC
1 CAATCTTCAACCTACTCCACTACTGC-TTAGGGTGATAGGACT-A--ATGGCTTAAATCTGCTTC
* * * * * * * * * * *
3613 ACAACTGCT-TAGGGTA-A-CAGAATCTGCAATCTTCAACCTACTCCACTACTGCTTAGGGTGAC
62 TCCACTG-TATTGGGAAGATAAGATTC-ACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGAC
3675 AGAATCTG
125 AGAATCTG
* ** * * * *
3683 CAATCTTCAACCTACTTCACTACAACTTAGGGAGATTGGACTAATGGCTTAAATCTGGTTCTTCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * *
3748 CTATCTTGAG-AGAGTAAGATTCACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAAT
66 CTGTATTGGGAAGA-TAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
3812 CTG
130 CTG
* * * **
3815 CAATCTTCAACCAACTCCACTA-TGGCTTAGGGAGATAGGACTATTAACTTAAATCTGCTTCTCC
1 CAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
* *
3879 ACTATATTGGGAAGATAAGATTCACCATCTTCGATCTCCTCCACTACTGCTTAGGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
3944 CTG
130 CTG
* * *
3947 TAATCTTCAACCTACTCCACTACTTCTTAGGGTGATAGGACTAATGGCTTATATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * *
4012 CTATATTGGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGTTTAGGGTGACAAAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
*
4077 AG
131 TG
* * * * * *
4079 CATTCTTTAACCTACTCCACTACTGCTCT-GGGAGATTGGTCTAATGGCTTAAATCTACTTCTCC
1 CAATCTTCAACCTACTCCACTACTGCT-TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
* * *
4143 ACTGTATTTGGAAGATAAGGTTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
4208 CTG
130 CTG
* * * * * *
4211 CAATCTTCAGCCTACTCCAGTACTGCGTAAGGGAGATTGGACTACTGGCTTAAATCTGCTTCTCC
1 CAATCTTCAACCTACTCCACTACTGC-TTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
* * * *
4276 ACTATATTGGGAAGATAAGATTCACCATCTTCGATCTCCTCCACTATTGCTTAGGCTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
4341 CTG
130 CTG
* * * *
4344 CAATCTTCAGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATTGCTTAGATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
*
4409 CTGTATTGGGAAGAT-AGA-TCACCATCTTCGATCTGCTCCACTACTACTTAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
4472 TG
131 TG
* * *
4474 CAATCTTCAA-CGACTCCACTACTTCTTAGGGTGATAGGACTAATGGCTTAAATCTGCATCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * * * *
4538 CTGTATTGGGAAAATAAGATTTATCATATTTGATCCGCTTCACTACTGTTTAGGGTGACAGAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
4603 TG
131 TG
* * * * * *
4605 TAATATTCAACCAACTCCACCA-TGGCTTAGGGAGATAGGACTAATGGCTTAAATTTGCTTCTCC
1 CAATCTTCAACCTACTCCACTACT-GCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
* *
4669 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTCCTCCACTATTGCTTAGGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
4734 CTG
130 CTG
* * * *
4737 CAATCTTCAACCTACTCCACTACTTCTTATGGTGATAGGACTAATGGCATATATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * * *
4802 CTGTGTTGGGAAGATAAGATTCATCATATTCAATCTGCTCCACTACTGTTTAGGGTGAGAAAATC
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
**
4867 AA
131 TG
* * * * *
4869 CATTCTTTAACCTACTCCACTACTGCTCT-GAGAGATAGGACTAATGGCTTAAATCTACTTCTCC
1 CAATCTTCAACCTACTCCACTACTGCT-TAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCC
* * *
4933 ACTATATTTGGAAGATAAGATTCACCATCTTCGATCTACTCCACTACTGCTTAGGGTGACAGAAT
65 ACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAAT
4998 CTG
130 CTG
* * * **
5001 CAATCTTCAACCTACTCCACTACAGCTTAGGGAGATTGGACTAATGGCTTAAATCTGCTTCTTTA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
* * * * * * * * * *
5066 CTATCTTGAGAAGATAAGATTCACCATCTTCGATCCGTTTCACAACTGCTTAGGGTAACTGAATT
66 CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
5131 TG
131 TG
* * *
5133 CAGTCTTCAACCTACTCCACTACTACTTAGGGTGATAGGACTAATGGCATAAATCTGCTTCTCCA
1 CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
5198 GCAATACCAC
Statistics
Matches: 3683, Mismatches: 612, Indels: 248
0.81 0.13 0.05
Matches are distributed among these distances:
126 6 0.00
127 6 0.00
128 6 0.00
129 86 0.02
130 77 0.02
131 118 0.03
132 3147 0.85
133 181 0.05
134 14 0.00
135 28 0.01
136 4 0.00
137 3 0.00
138 1 0.00
139 3 0.00
141 3 0.00
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (132 bp):
CAATCTTCAACCTACTCCACTACTGCTTAGGGTGATAGGACTAATGGCTTAAATCTGCTTCTCCA
CTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGTGACAGAATC
TG
Found at i:927 original size:484 final size:483
Alignment explanation
Indices: 19--1165 Score: 1409
Period size: 484 Copynumber: 2.4 Consensus size: 483
9 ACTATCTTGA
*
19 GAAGATAAGATTCACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGAAATCTT
1 GAAGATAAGATTCATCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGAAATCTT
* * * * ** ** *
84 CAACCTACTCCACTG-T-ATTGGGAAGATAAGATTCCCCAT--CTTCGATCTG---CTCCACTAC
66 CAACCTACTCCACTGCTGCTAGGG-TGATAGGA---CAAATGGCTTAAATCTGCTTCTCCACT-G
** * * * * * *
142 TACTTAGGGTGA-CAGAATCCACAATCTTTAACCGACTCCACTACTTCTTATGGTGATAAGACTA
126 TA-TTAGGAAGATAAG-ATTCACAATCTTCAACCTACTCCACTACTACTTAGGGTGATAAGACTA
* *
206 ACGGCATAAATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCGATCTGCTTCAC
189 ACGGCATAAATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCACCATATTCGATCTGCTCCAC
* *
271 TACTGTTTAGGGTGACAGAATCTACAATCTTCAACCAACTCCACTATGGCTGAGGGAGATAGGAT
254 TACTGCTTAGGGTGACAGAATCTACAATCTTCAACCAACTCCACTATGGCTGAGGGAGATAGGAC
* * * *
336 TAATAGCTTAAATGTTCCTCTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCC
319 TAATAGCTTAAATCTGCCTCTCCACTGTATTAGGAAGATAAGATTCACCATATTCGAGCTGCTCC
* * * * *
401 ACTACTGCTTAGGGTGACAGACTCTGCAATCTTTAGCCTACTCCACTACGACTGAGGGTGATAGG
384 ACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACGACTGAAGGTCATAGG
466 ACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
449 ACTAATGGCTTAAATCTGCTTCTCCACTGTATTGG
* *
501 GAAGATAAGATTCATCATCTTCGATCCGCTACACAACTGCTTAGGGTAACAGAATCTGCAATCTT
1 GAAGATAAGATTCATCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGAAATCTT
566 CAACCTACTCCACTGCTGCTCAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATT
66 CAACCTACTCCACTGCTGCT-AGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATT
* * * * * *
631 AGGAAGATAAGATTCACAATCTCCAACCTACTCCACCACTGCTTAGGGTGATAGGACTAATGGCT
130 AGGAAGATAAGATTCACAATCTTCAACCTACTCCACTACTACTTAGGGTGATAAGACTAACGGCA
* ** * *
696 TAAATCTGCTTCTCCACTGTATTTGGAAGGTAAGATTTACCATCTTCGATCTGCTCCACTACTGC
195 TAAATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCACCATATTCGATCTGCTCCACTACTGC
* * * * *
761 TTAGGGTGACCGAATC-AGCAATCTTTAGCCTACTCCACTACT-GCTGAGGGTGATAGGACTAAT
260 TTAGGGTGACAGAATCTA-CAATCTTCAACCAACTCCACTA-TGGCTGAGGGAGATAGGACTAAT
* * * * *
824 GGCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGAGCTTCTCCACTA
323 AGCTTAAATCTGCCTCTCCACTGTATTAGGAAGATAAGATTCACCATATTCGAGCTGCTCCACTA
* * ** *
889 TTGCTTAGGGTGACAGAATCTGCACTCTTCAACCTACTCCACTACTTCTTAAGGTCATAGGACTA
388 CTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACGACTGAAGGTCATAGGACTA
954 ATGGCTTAAATCTGCTTCTCCACTGTATTGG
453 ATGGCTTAAATCTGCTTCTCCACTGTATTGG
* * * * * * * *
985 GAACATAAGATTCATCATATTCGA-CCTGCTCCACTACTG-TTCAGGGCAACAAAATTTGTAATT
1 GAAGATAAGATTCATCATCTTCGATCC-GCTCCACAACTGCTT-AGGGTAACAGAATCTGAAATC
* * * * *
1048 TTTAACCTACTCCACTACTGCTGAGGGTGATAGGACTAATGGCTTAAATCTGCTTGTCCTCTGTA
64 TTCAACCTACTCCACTGCTGCT-AGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTA
* * * *
1113 TTAGGAAGATAAGATTAACCATCTTCAATCTGCTCCACTACTACTTAGGGTGA
128 TTAGGAAGATAAGATTCACAATCTTCAACCTACTCCACTACTACTTAGGGTGA
1166 CAGAATCTGC
Statistics
Matches: 572, Mismatches: 80, Indels: 24
0.85 0.12 0.04
Matches are distributed among these distances:
481 3 0.01
482 77 0.13
483 14 0.02
484 463 0.81
485 8 0.01
486 7 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (483 bp):
GAAGATAAGATTCATCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGAAATCTT
CAACCTACTCCACTGCTGCTAGGGTGATAGGACAAATGGCTTAAATCTGCTTCTCCACTGTATTA
GGAAGATAAGATTCACAATCTTCAACCTACTCCACTACTACTTAGGGTGATAAGACTAACGGCAT
AAATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCACCATATTCGATCTGCTCCACTACTGCT
TAGGGTGACAGAATCTACAATCTTCAACCAACTCCACTATGGCTGAGGGAGATAGGACTAATAGC
TTAAATCTGCCTCTCCACTGTATTAGGAAGATAAGATTCACCATATTCGAGCTGCTCCACTACTG
CTTAGGGTGACAGAATCTGCAATCTTCAACCTACTCCACTACGACTGAAGGTCATAGGACTAATG
GCTTAAATCTGCTTCTCCACTGTATTGG
Found at i:1280 original size:616 final size:613
Alignment explanation
Indices: 19--1326 Score: 1719
Period size: 616 Copynumber: 2.1 Consensus size: 613
9 ACTATCTTGA
** *
19 GAAGATAAGATTCACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGAAATCTT
1 GAAGATAAGATTCACCATCTTCGATCTACTCCACAACTGCTTAGGGTGACAGAATCT-AAATCTT
* *
84 CAACCTACTCCACTGTATTGGGAAGATAAGATTCCCCATCTTCGATCTGCTCCACTACTACTTAG
65 AAACCTACTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAG
* * *
149 GGTGACAGAATCCACAATCTTTAACCGACTCCACTACTTCTTATGGTGATAAGACTAACGGCATA
130 GGTGACAGAATCCACAATCTTTAACCGACTCCACTACTGCTGAGGGTGATAAGACTAACGGCATA
* * * *
214 AATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCATCATATTCGATCTGCTTCACTACTGTTT
195 AATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCACCATATTCGAGCTGCTCCACTACTGCTT
* * *
279 AGGGTGACAGAATCTACAATCTTCAACCAACTCCACTATGGCTGAGGGAGATAGGATTAATAGCT
260 AGGGTGACAGAATCTACAATCTTCAACCAACTCCACTATGGCTGAAGGACATAGGACTAATAGCT
* * * *
344 TAAATGTTCCTCTCCACTGTATTAGGAAGATAAGATTCATCATATTCGATCTGCTCCACTACTGC
325 TAAATCTGCCTCTCCACTGTATTAGGAACATAAGATTCATCATATTCGACCTGCTCCACTACTGC
** * * *
409 TTAGGGTGACAGACTCTGCAATCTTTAGCCTACTCCACTACGACTGAGGGTGATAGGACTAATGG
390 TTAGGGCAACAAAATCTGCAATCTTTAACCTACTCCACTACGACTGAGGGTGATAGGACTAATGG
* * * *
474 CTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCATCATCTTCGATCCGCTACACAACT
455 CTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTCAATCCGCTACACAACT
* * *
539 GCTTAGGGTAACAGAATCTGCAATCTTCAACCTACTCCACTGCTGCTCAGGGTGATAGGACAAAT
520 ACTTAGGGTAACAGAATCTGCAATCTTCAACCGACTCCACTACTGCTCAGGGTGATAGGACAAAT
* *
604 GGCTTAAATCTGCTTCTCCACTGTATTAG
585 GGCTGAAATCTACTTCTCCACTGTATTAG
* * * * * * *
633 GAAGATAAGATTCACAATCTCCAACCTACTCCACCACTGCTTAGGGTGATAGGA-CT-AATGGCT
1 GAAGATAAGATTCACCATCTTCGATCTACTCCACAACTGCTTAGGGTGACAGAATCTAAAT--CT
* * * * *
696 TAAATCTGCTTCTCCACTGTATTTGGAAGGTAAGATTTACCATCTTCGATCTGCTCCACTACTGC
64 TAAA-C--CTACTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTAC
* * * * *
761 TTAGGGTGACCGAAT-CAGCAATCTTTAGCCTACTCCACTACTGCTGAGGGTGATAGGACTAATG
126 TTAGGGTGACAGAATCCA-CAATCTTTAACCGACTCCACTACTGCTGAGGGTGATAAGACTAACG
* * * * * *
825 GCTTAAATCTGCTTCTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGAGCTTCTCCACTAT
190 GCATAAATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCACCATATTCGAGCTGCTCCACTAC
* * * * * *
890 TGCTTAGGGTGACAGAATCTGCACTCTTCAACCTACTCCACTACT-TCTTAAGGTCATAGGACTA
255 TGCTTAGGGTGACAGAATCTACAATCTTCAACCAACTCCACTA-TGGCTGAAGGACATAGGACTA
* * *
954 ATGGCTTAAATCTGCTTCTCCACTGTATTGGGAACATAAGATTCATCATATTCGACCTGCTCCAC
319 ATAGCTTAAATCTGCCTCTCCACTGTATTAGGAACATAAGATTCATCATATTCGACCTGCTCCAC
* * *
1019 TACTG-TTCAGGGCAACAAAATTTGTAATTTTTAACCTACTCCACTACTG-CTGAGGGTGATAGG
384 TACTGCTT-AGGGCAACAAAATCTGCAATCTTTAACCTACTCCACTAC-GACTGAGGGTGATAGG
* * *
1082 ACTAATGGCTTAAATCTGCTTGTCCTCTGTATTAGGAAGATAAGATTAACCATCTTCAATCTGCT
447 ACTAATGGCTTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTCAATCCGCT
* * * * * *
1147 CCACTACTACTTAGGGTGACAGAATCTGCAATCTTTAACCGACTCCACTACTTCTTAGGGTGATA
512 ACACAACTACTTAGGGTAACAGAATCTGCAATCTTCAACCGACTCCACTACTGCTCAGGGTGATA
* *
1212 GGACTAATGGCTGAAATCTACTTCTCCACTGTATTGG
577 GGACAAATGGCTGAAATCTACTTCTCCACTGTATTAG
* * *
1249 GAAGATAAGATTCACCATTTTCGATCTACTCCACTACTGCTTAGGGTGGCAGAATCTACAATCTT
1 GAAGATAAGATTCACCATCTTCGATCTACTCCACAACTGCTTAGGGTGACAGAATCTA-AATCTT
* *
1314 CATCCTACTCCAC
65 AAACCTACTCCAC
1327 CACTGCTTAG
Statistics
Matches: 591, Mismatches: 91, Indels: 24
0.84 0.13 0.03
Matches are distributed among these distances:
611 3 0.01
613 7 0.01
614 53 0.09
615 4 0.01
616 513 0.87
617 8 0.01
619 3 0.01
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (613 bp):
GAAGATAAGATTCACCATCTTCGATCTACTCCACAACTGCTTAGGGTGACAGAATCTAAATCTTA
AACCTACTCCACTGTATTGGGAAGATAAGATTCACCATCTTCGATCTGCTCCACTACTACTTAGG
GTGACAGAATCCACAATCTTTAACCGACTCCACTACTGCTGAGGGTGATAAGACTAACGGCATAA
ATCTGCTTCTCCACTGTATTAGGAAAATAAGATTCACCATATTCGAGCTGCTCCACTACTGCTTA
GGGTGACAGAATCTACAATCTTCAACCAACTCCACTATGGCTGAAGGACATAGGACTAATAGCTT
AAATCTGCCTCTCCACTGTATTAGGAACATAAGATTCATCATATTCGACCTGCTCCACTACTGCT
TAGGGCAACAAAATCTGCAATCTTTAACCTACTCCACTACGACTGAGGGTGATAGGACTAATGGC
TTAAATCTGCTTCTCCACTGTATTAGGAAGATAAGATTAACCATCTTCAATCCGCTACACAACTA
CTTAGGGTAACAGAATCTGCAATCTTCAACCGACTCCACTACTGCTCAGGGTGATAGGACAAATG
GCTGAAATCTACTTCTCCACTGTATTAG
Found at i:2809 original size:220 final size:220
Alignment explanation
Indices: 2512--2963 Score: 582
Period size: 220 Copynumber: 2.1 Consensus size: 220
2502 CAACCGACTC
* * * **
2512 CACTACTGCTTAGGGTGAAAGGACTAATGGCTTAAATCTGCTTCGCCATTGTATTTGGAAGATAA
1 CACTACTGCTTAGGGAGAAAGGACAAATGGCTTAAATCTGCTTCGCCACTGTATCGGGAAGATAA
* *
2577 GATTCACCATCTTCGATCTGCTCCACTACCACTTAGGGTGACAGAATCTACAATCTTCAACCTAC
66 GATTCACCATCTTCGATCTACTCCACTACCACTTAGGGTGACAGAATCTACAATCCTCAACCTAC
* * * * * * *
2642 TCCAGTACTACTTAAGGTGAATGGACTAATGGCTTAAATTTGTTTCTCTACTGTATTGGGAAGAT
131 TCCACTACTACTTAAGGAGAATGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGAGAAGAT
* *
2707 AAGATTTA-TCATATTCGATCTGCTA
196 AAGATTCACT-ATATTCAATCTGCTA
* * * *
2732 CACTACTGTTTAGGGAGATAGGACAAATGGCTTAAATCTGCTTCTCTACTGTATCGGGAAGATAA
1 CACTACTGCTTAGGGAGAAAGGACAAATGGCTTAAATCTGCTTCGCCACTGTATCGGGAAGATAA
* ** * *
2797 GATTCACCATCTTTGATCTACTCCACTACTGCTTAGGGTGATAGAATCTGCAATCCTCAACCTAC
66 GATTCACCATCTTCGATCTACTCCACTACCACTTAGGGTGACAGAATCTACAATCCTCAACCTAC
* * * * * *
2862 TCCACTACTGCTTAGGGAGATTGGACTCATGGCTTACATCTGCTTCTCCACTATCTTGAGAAGAT
131 TCCACTACTACTTAAGGAGAATGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGAGAAGAT
* * *
2927 ATGATTCACTATCTTCAATCTGCTG
196 AAGATTCACTATATTCAATCTGCTA
2952 CACTACTGCTTA
1 CACTACTGCTTA
2964 CGGTGACAGA
Statistics
Matches: 196, Mismatches: 35, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
220 195 0.99
221 1 0.01
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.32
Consensus pattern (220 bp):
CACTACTGCTTAGGGAGAAAGGACAAATGGCTTAAATCTGCTTCGCCACTGTATCGGGAAGATAA
GATTCACCATCTTCGATCTACTCCACTACCACTTAGGGTGACAGAATCTACAATCCTCAACCTAC
TCCACTACTACTTAAGGAGAATGGACTAATGGCTTAAATCTGCTTCTCCACTATATTGAGAAGAT
AAGATTCACTATATTCAATCTGCTA
Found at i:2824 original size:88 final size:88
Alignment explanation
Indices: 2664--2840 Score: 246
Period size: 88 Copynumber: 2.0 Consensus size: 88
2654 TAAGGTGAAT
* * * * * * *
2664 GGACTAATGGCTTAAATTTGTTTCTCTACTGTATTGGGAAGATAAGATTTATCATATTCGATCTG
1 GGACAAATGGCTTAAATCTGCTTCTCTACTGTATCGGGAAGATAAGATTCACCATATTCGATCTA
*
2729 CTACACTACTGTTTAGGGAGATA
66 CTACACTACTGCTTAGGGAGATA
* *
2752 GGACAAATGGCTTAAATCTGCTTCTCTACTGTATCGGGAAGATAAGATTCACCATCTTTGATCTA
1 GGACAAATGGCTTAAATCTGCTTCTCTACTGTATCGGGAAGATAAGATTCACCATATTCGATCTA
* *
2817 CTCCACTACTGCTTAGGGTGATA
66 CTACACTACTGCTTAGGGAGATA
2840 G
1 G
2841 AATCTGCAAT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
88 77 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (88 bp):
GGACAAATGGCTTAAATCTGCTTCTCTACTGTATCGGGAAGATAAGATTCACCATATTCGATCTA
CTACACTACTGCTTAGGGAGATA
Found at i:3682 original size:176 final size:176
Alignment explanation
Indices: 3465--3846 Score: 606
Period size: 176 Copynumber: 2.2 Consensus size: 176
3455 AAGATTCACC
* * *
3465 ATCTTCGATCTACTCCACTACTGCTTAGGGTGACTGAATCTGCAATATTCAACATACTCCACTAC
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATATTCAACATACTCCACTAC
* ** *
3530 AGCTTTTGGAGATTGGACAAATGGCTTAAATCTGCTTCTCCACTATCTTTAGA-AGATAAGATTC
66 AACTTAGGGAGATTGGACAAATGGCTTAAATCTGCTTCTCCACTATCTTGAGAGAG-TAAGATTC
3594 ACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGCA
130 ACCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGCA
* * *
3641 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTACTTCACTAC
1 ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATATTCAACATACTCCACTAC
* * *
3706 AACTTAGGGAGATTGGACTAATGGCTTAAATCTGGTTCTTCACTATCTTGAGAGAGTAAGATTCA
66 AACTTAGGGAGATTGGACAAATGGCTTAAATCTGCTTCTCCACTATCTTGAGAGAGTAAGATTCA
3771 CCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGCA
131 CCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGCA
*
3817 ATCTTCAACCAACTCCACTA-TGGCTTAGGG
1 ATCTTCAACCTACTCCACTACT-GCTTAGGG
3847 AGATAGGACT
Statistics
Matches: 190, Mismatches: 14, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
175 1 0.01
176 187 0.98
177 2 0.01
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.29
Consensus pattern (176 bp):
ATCTTCAACCTACTCCACTACTGCTTAGGGTGACAGAATCTGCAATATTCAACATACTCCACTAC
AACTTAGGGAGATTGGACAAATGGCTTAAATCTGCTTCTCCACTATCTTGAGAGAGTAAGATTCA
CCATCTTCGATCCGCTCCACAACTGCTTAGGGTAACAGAATCTGCA
Found at i:3704 original size:44 final size:44
Alignment explanation
Indices: 3609--3714 Score: 167
Period size: 44 Copynumber: 2.4 Consensus size: 44
3599 CTTCGATCCG
*
3609 CTCCACAACTGCTTAGGGTAACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTAACAGAATCTGCAATCTTCAACCTA
*
3653 CTCCACTACTGCTTAGGGTGACAGAATCTGCAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGTAACAGAATCTGCAATCTTCAACCTA
* **
3697 CTTCACTACAACTTAGGG
1 CTCCACTACTGCTTAGGG
3715 AGATTGGACT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
44 57 1.00
ACGTcount: A:0.29, C:0.29, G:0.15, T:0.26
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGTAACAGAATCTGCAATCTTCAACCTA
Done.