Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019192.1 Corchorus olitorius cultivar O-4 contig19225, 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: 97213
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:1127 original size:39 final size:39
Alignment explanation
Indices: 1084--1191 Score: 207
Period size: 39 Copynumber: 2.8 Consensus size: 39
1074 TTGCTTGTTA
1084 AAACCTAGGTTTAATTTTATTTTGGGCTTGGGATCGTTG
1 AAACCTAGGTTTAATTTTATTTTGGGCTTGGGATCGTTG
1123 AAACCTAGGTTTAATTTTATTTTGGGCTTGGGATCGTTG
1 AAACCTAGGTTTAATTTTATTTTGGGCTTGGGATCGTTG
*
1162 AAACCTAGGTTTAATTTCATTTTGGGCTTG
1 AAACCTAGGTTTAATTTTATTTTGGGCTTG
1192 TCAACTATAT
Statistics
Matches: 68, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
39 68 1.00
ACGTcount: A:0.21, C:0.11, G:0.24, T:0.44
Consensus pattern (39 bp):
AAACCTAGGTTTAATTTTATTTTGGGCTTGGGATCGTTG
Found at i:9088 original size:20 final size:20
Alignment explanation
Indices: 9063--9105 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9053 CTCTCACAAG
*
9063 TTTCTAGCCGTTAGAGCTCT
1 TTTCTAGCCGTTAGAGCACT
*
9083 TTTCTAGCCGTTATAGCACT
1 TTTCTAGCCGTTAGAGCACT
9103 TTT
1 TTT
9106 TCCACTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.16, T:0.44
Consensus pattern (20 bp):
TTTCTAGCCGTTAGAGCACT
Found at i:9577 original size:21 final size:21
Alignment explanation
Indices: 9551--9592 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9541 CTCCTAGAGA
9551 AGGCTCGGAAGGAGAAGGAGG
1 AGGCTCGGAAGGAGAAGGAGG
9572 AGGCTCGGAAGGAGAAGGAGG
1 AGGCTCGGAAGGAGAAGGAGG
9593 CAGCAGAGAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.10, G:0.52, T:0.05
Consensus pattern (21 bp):
AGGCTCGGAAGGAGAAGGAGG
Found at i:9593 original size:18 final size:20
Alignment explanation
Indices: 9546--9588 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
9536 TCCATCTCCT
*
9546 AGAGAAGGCTCGGAAGGAGA
1 AGAGGAGGCTCGGAAGGAGA
9566 AGGAGGAGGCTCGGAAGGAGA
1 A-GAGGAGGCTCGGAAGGAGA
9587 AG
1 AG
9589 GAGGCAGCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 2 0.10
21 19 0.90
ACGTcount: A:0.37, C:0.09, G:0.49, T:0.05
Consensus pattern (20 bp):
AGAGGAGGCTCGGAAGGAGA
Found at i:9624 original size:51 final size:51
Alignment explanation
Indices: 9597--9702 Score: 185
Period size: 51 Copynumber: 2.1 Consensus size: 51
9587 AGGAGGCAGC
*
9597 AGAGACAGAGGATGAGCCTCGGAAGGAGGCATCAGATGAAGAGGAAGAGGA
1 AGAGACAGAGGATGAGCCTCGGAAGGAGGCATCAGAAGAAGAGGAAGAGGA
* *
9648 AGAGACAGAGGATGAGGCTCGGAAGGAGGCATCAGATGAAGAGGAAGAGGA
1 AGAGACAGAGGATGAGCCTCGGAAGGAGGCATCAGAAGAAGAGGAAGAGGA
9699 AGAG
1 AGAG
9703 GATGAAACAT
Statistics
Matches: 54, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.40, C:0.10, G:0.42, T:0.08
Consensus pattern (51 bp):
AGAGACAGAGGATGAGCCTCGGAAGGAGGCATCAGAAGAAGAGGAAGAGGA
Found at i:9683 original size:27 final size:27
Alignment explanation
Indices: 9602--9683 Score: 73
Period size: 27 Copynumber: 3.1 Consensus size: 27
9592 GCAGCAGAGA
*
9602 CAGAGGATGAGCCTCGGAAGGAGGCAT
1 CAGAGGATGAGGCTCGGAAGGAGGCAT
* * ***
9629 CAGATGAAGAGGAAGAGGAA-GA-G-A-
1 CAGAGGATGAGG-CTCGGAAGGAGGCAT
9653 CAGAGGATGAGGCTCGGAAGGAGGCAT
1 CAGAGGATGAGGCTCGGAAGGAGGCAT
9680 CAGA
1 CAGA
9684 TGAAGAGGAA
Statistics
Matches: 39, Mismatches: 11, Indels: 10
0.65 0.18 0.17
Matches are distributed among these distances:
23 4 0.10
24 12 0.31
25 2 0.05
26 2 0.05
27 15 0.38
28 4 0.10
ACGTcount: A:0.37, C:0.13, G:0.41, T:0.09
Consensus pattern (27 bp):
CAGAGGATGAGGCTCGGAAGGAGGCAT
Found at i:11977 original size:17 final size:17
Alignment explanation
Indices: 11955--11989 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
11945 GAAAGAATAC
11955 AGTATTATAATCCATAT
1 AGTATTATAATCCATAT
11972 AGTATTATAATCCATAT
1 AGTATTATAATCCATAT
11989 A
1 A
11990 ACACTATTCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (17 bp):
AGTATTATAATCCATAT
Found at i:16938 original size:663 final size:653
Alignment explanation
Indices: 15592--17824 Score: 2350
Period size: 663 Copynumber: 3.4 Consensus size: 653
15582 CAACGGTTTT
* * * * *
15592 AAATCTCACCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATAATGTTTCGATTCAA
1 AAATCTCACCCATATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCAGGTTTCGATTTAA
* * *
15657 TTAGAAATTAATTCGG-AAAAATACGAAAAACGATATTAAAAGCGTGAAAAGCTTTTCAAT-TTT
66 TTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAAAAGCGTGAAAAGCCTTTCAATCTTT
* * * * *
15720 TCTGGCGTTGAACTATATATTTTTTATAAGTATCGTAGCCAAAAATTGAGAAAAATCCTTTCGGG
131 T-TGGCATTGAATTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGGG
*
15785 T-AATTTTT-TACAAAATTTTAGCCGAAATCGTGTATTAACTATCACGATTTTTGACTAAAAACA
195 TCAATTTTTGT--AAAATTTTAGCCGAAATCGTGTACTAAC-ATCACGATTTTTGACTAAAAACA
* * **
15848 CATTCTGAGGCCCAGGCTCAGTTTT-CATAATTTTTTGCGTTAAGACTTCTTGAAATATCT-TAA
257 CGTTCTG-GGCCCAGGCTCA-TTTTGCATAATTTTTAGCGCCAAGAC-TCTTGAAATATCTAT-A
*
15911 TTCTTCTAACTAAATCTCATCCACATTGGATTTAAGGATTTGTTTTACGAGCATCTGAATCTTGT
318 TTCATCTAACTAAATCTCATCCACATTGGATTTAA-GATTTGTTTTACGAGCATCTGAATCTTGT
* * * * *
15976 TTCTATTTAAATAGAAATTAATTTGGAAAAAAGATAGGGAAAACAATATCAAAAACGTGAAAACA
382 TTCGATTTAATTAGAAATTAATTCGG-AAAAA-ATA-GGAAAACAATAT-AGAAGCGTGAAAAC-
** * ** **
16041 C-TTCAATAGTTTTGGCATTGAATTATATA--TATTATGAGTATTGTGGTTAAAAATTGAGGGAG
442 CTTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATCATGGCCAAAAATTGA---AG
* * * * * *
16103 AAAA--CTTTCGGTTAAATTTTTGCAAAATTTTAGTCGAAATCATGTAAC-TAACCATCACGGTT
504 AAAATTCTTTCGGATAAATTTTTGCAAAATTTTA-CCGAAATCATGTACCATCACGATTA-GG-T
* * * * * *
16165 TTTGGCTAAAAACGCGTTCTGGGGTCCCGGCTCAGTTTTGCATGATTTTTTGTGCCGAGACTCTT
566 TTTAGCTAAAAACGCG-TCTCGGGACCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCAT
*
16230 TGAAATATCTATATTCATCTAACG
630 TGAAATATCTATATTCATCTAACC
* ** * * * * *
16254 AAATCTTAGGCACAATGGATTTAAGGATTTGTTTTTACGAGCATATCAATCCGGTTTCGATTTAA
1 AAATCTCACCCATATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCAGGTTTCGATTTAA
* * *
16319 TTAGAATTTAATTCGGGAAAAAAAAGGAAAAACGATATTAAAAGTGTGAAAAGCCCTTCAATCTT
66 TTAGAAATTAATTC-GGAAAAAAAAGGAAAAACGATATTAAAAGCGTGAAAAGCCTTTCAATCTT
* * * * * *
16384 TTTGACATT-AAGTTATATTTTTTTTATGAGTATTGTGGCCAAAAACTGGGGAGAAATT-TTTCG
130 TTTGGCATTGAA-TTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGA-AAATTCTTTCG
* *
16447 GGTCAATTTTTGTAAAATTTTAGTCGAAATCATGTACTAATCATCAC-AGTTTTTGACTAAAAAC
193 GGTCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAA-CATCACGA-TTTTTGACTAAAAAC
* * * * *
16511 GCGTTCTGGGCCCTGGCTCTATTTTGTAT-ATTTTTAGCGCCAAGTCTCATTGAAATTTCTATAT
256 ACGTTCTGGGCCCAGGCTC-ATTTTGCATAATTTTTAGCGCCAAGACTC-TTGAAATATCTATAT
* * * * * *
16575 CCATATAACCAAATAC-CACCCACATTGGATTTAAAATTTTGTTTTTACGAGCATCTGAATCATG
319 TCATCTAACTAAAT-CTCATCCACATTGGATTTAAGA-TTTG-TTTTACGAGCATCTGAATCTTG
* *
16639 TTTCGATTTAATTAGAAA-TAATTCAGAAAAAATAGGAAAACCGATACTAGAAGCGTGAAAAGCC
381 TTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGAAAA-CAATA-TAGAAGCGTGAAAA-CC
* ** * * *
16703 TTTCAGTCTTTTTACCGTTGAATTATATATTTTTTATGAGTATCATGACCAATAATTGAAGAAAA
443 TTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAA
* *
16768 TTCTTTCGGATAAATTTTTACAAAATTTTACCGAAATCATGTACCATCACGGTTTAGGTTCTTAG
508 TTCTTTCGGATAAATTTTTGCAAAATTTTACCGAAATCATGTACCATCAC-GATTAGGTT-TTAG
* * * * * **
16833 CCAAAAACACGTCCCGGGACCCAGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTCAAAA
571 CTAAAAACGCGTCTCGGGACCC-GGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAA
16898 TATCTATATTCATCTAACC
635 TATCTATATTCATCTAACC
* * * * *
16917 AAATATCATCCATATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAATCATGTTTTGATTTAA
1 AAATCTCACCCATATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCAGGTTTCGATTTAA
* * * *
16982 TTAGAAATTAATTCGGAAAAAATAGGAAAACCCGATATTAGAAGCGTGAATAGCCTTTCAATC-T
66 TTAGAAATTAATTCGGAAAAAAAAGGAAAA-ACGATATTAAAAGCGTGAAAAGCCTTTCAATCTT
** * * *
17046 TTTGGTGTTGAATTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGACAATTCTCTCGGT
130 TTTGGCATTGAATTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGGG
* * *
17111 TCAA-TTTTGCAAAATTTTAGCCGAAATCGTGTAC---CATCACGGTTTTTGCCTAAAAACACGT
195 TCAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACATCACGATTTTTGACTAAAAACACGT
* * * * * * *
17172 CCCGAGCCCAAGGCTCATATTTGCATGA-TTTTGGCTCCAAGAGTCCTTGAAATATCTATATTCA
260 TCTGGGCCC-AGGCTCAT-TTTGCATAATTTTTAGCGCCAAGACT-CTTGAAATATCTATATTCA
* * * *
17236 TCTAACTAAATCTAATCCACATTGGATTTTAGGATTTGCTTTTACGAACATCTGAATCTTTTTTC
322 TCTAACTAAATCTCATCCACATTGGA-TTTAAGATTTG-TTTTACGAGCATCTGAATCTTGTTTC
** * * *
17301 GAAATAATTATAAATTAATTCGGAAAAAATAGGATAAACAATATTAGAAGCATAAAAAACCCTTT
385 GATTTAATTAGAAATTAATTCGGAAAAAATAGGA-AAACAATA-TAGAAGCGT-GAAAA-CCTTT
* * *
17366 CAATCTTTTTGGCATTGAATTATATATTTTTTATAAGTATCCTGGCCAAAAATTGAGGAAAATTC
446 CAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTC
* * * *
17431 TTTCGGATAATTTTTTGCAAAATTTTAACTGTAATCATGTATTAACCATCACGATT--G-TTGA-
511 TTTCGGATAAATTTTTGCAAAATTTT-ACCGAAATCATG---T-ACCATCACGATTAGGTTTTAG
* * * * * *
17492 CTAAAAACGCGTTTCGGAGCCCCGGCTCTGTTTTGTATGATTTTTTGCGTCAAGTCTCATTGAAA
571 CTAAAAACGCGTCTCGG-GACCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAA
* * *
17557 TATCTATATCCATGTAATC
635 TATCTATATTCATCTAACC
* *
17576 AAATCTCGCCCACT-TTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATC-GTGTTTCGATTT
1 AAATCTCACCCA-TATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCAG-GTTTCGATTT
* * * * *
17639 AATTAGAAATTAATTC-AAAAAAAATAGGAAAACCGATATTAGAAGCATGAAAAGCCTTTCAATT
64 AATTAGAAATTAATTCGGAAAAAAA-AGGAAAAACGATATTAAAAGCGTGAAAAGCCTTTCAATC
* *
17703 TTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCTAAAAATTGAGGAAAATTCTTTCG
128 TTTTTGGCATTGAATTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCG
* * *
17768 TGTAAATTTTTGCAAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTG
193 GGTCAATTTTTG--TAAAATTTTAGCCGAAATCGTGTACTAA-CATCACGATTTTTG
17825 GCAACAAAGC
Statistics
Matches: 1305, Mismatches: 208, Indels: 112
0.80 0.13 0.07
Matches are distributed among these distances:
657 32 0.02
658 132 0.10
659 237 0.18
660 110 0.08
661 67 0.05
662 213 0.16
663 273 0.21
664 203 0.16
665 24 0.02
666 14 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (653 bp):
AAATCTCACCCATATTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCAGGTTTCGATTTAA
TTAGAAATTAATTCGGAAAAAAAAGGAAAAACGATATTAAAAGCGTGAAAAGCCTTTCAATCTTT
TTGGCATTGAATTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGGGT
CAATTTTTGTAAAATTTTAGCCGAAATCGTGTACTAACATCACGATTTTTGACTAAAAACACGTT
CTGGGCCCAGGCTCATTTTGCATAATTTTTAGCGCCAAGACTCTTGAAATATCTATATTCATCTA
ACTAAATCTCATCCACATTGGATTTAAGATTTGTTTTACGAGCATCTGAATCTTGTTTCGATTTA
ATTAGAAATTAATTCGGAAAAAATAGGAAAACAATATAGAAGCGTGAAAACCTTTCAATCTTTTT
GGCATTGAATTATATATTTTTTATGAGTATCATGGCCAAAAATTGAAGAAAATTCTTTCGGATAA
ATTTTTGCAAAATTTTACCGAAATCATGTACCATCACGATTAGGTTTTAGCTAAAAACGCGTCTC
GGGACCCGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCATCTA
ACC
Found at i:17651 original size:333 final size:330
Alignment explanation
Indices: 15591--17824 Score: 2274
Period size: 332 Copynumber: 6.7 Consensus size: 330
15581 TCAACGGTTT
* * * *
15591 TAAATCTCACCCACATTGGATTTAAAGATTTGTTTTTACGAGCATCTAAATAATGTTTCGATTCA
1 TAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
* * *
15656 ATTAGAAATTAATTCGG-AAAAATACGAAAAACGATATTAAAAGCGTGAAAAGCTTTTCAAT-TT
66 ATTAGAAATTAATTCGGAAAAAATA-GGAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTT
* * * * * *
15719 TTCTGGCGTTGAACTATATATTTTTTATAAGTATCGTAGCCAAAAATTGAGAAAAATCCTTTCGG
130 TT-TGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGG
* * * * * * *
15784 GTAATTTTTTACAAAATTTTAGCCGAAATCGTGTATTAACTATCACGATTTTTGACTAAAAACAC
194 ATAAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACGATTTTTGACTAAAAACAC
* * * **
15849 ATTCTGAGGCCCAGGCTCAGTTTT-CATAATTTTTTGCGTTAAGACTTC-TTGAAATATCT-TAA
259 GTTCGGA-GCCCAGGCTCAGTTTTGCATGATTTTTTGCGCCAAGAC-TCATTGAAATATCTAT-A
*
15911 TTCTTCTAAC
321 TTCATCTAAC
* * *
15921 TAAATCTCATCCACATTGGATTTAAGGATTTG-TTTTACGAGCATCTGAATCTTGTTTCTATTTA
1 TAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
* * * * * *
15985 AATAGAAATTAATTTGGAAAAAAGATAGGGAAAACAATATCAAAAACGTGAAAA-CAC-TTCAAT
66 ATTAGAAATTAATTCGG-AAAAA-ATA-GGAAAACGATATTAGAAGCGTGAAAAGC-CTTTCAAT
** * * ** *
16048 AGTTTTGGCATTGAATTATATA--TATTATGAGTATTGTGGTTAAAAATTGAGGGAGAAA-ACTT
127 CTTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGA-GGA-AAATTCTT
* ** * *
16110 TCGGTTAAATTTTTGCAAAATTTTAGTCGAAATCATGTAACTAACCATCACGGTTTTTGGCTAAA
190 TCGGATAAATTTTTGCAAAATTTTAACCGAAATCATGT-ACTAACCATCACGATTTTTGACTAAA
* * * * *
16175 AACGCGTTCTGGGGTCCC-GGCTCAGTTTTGCATGATTTTTTGTGCCGAGACTCTTTGAAATATC
254 AACACGTTC-GGAG-CCCAGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATC
16239 TATATTCATCTAAC
317 TATATTCATCTAAC
* * ** * * * **
16253 GAAATCTTAGGCACAATGGATTTAAGGATTTGTTTTTACGAGCATATCAATCCGGTTTCGATTTA
1 TAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
* * * * *
16318 ATTAGAATTTAATTCGGGAAAAAAAAGGAAAAACGATATTAAAAGTGTGAAAAGCCCTTCAATCT
66 ATTAGAAATTAATTC-GGAAAAAATAGG-AAAACGATATTAGAAGCGTGAAAAGCCTTTCAATCT
* * * * *
16383 TTTTGACATT-AAGTTATATTTTTTTTATGAGTATTGTGGCCAAAAACTGGGGAGAAATT-TTTC
129 TTTTGGCATTGAA-TTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGA-AAATTCTTTC
* * * ** *
16446 GGGTCAATTTTTGTAAAATTTTAGTCGAAATCATGTACTAATCATCAC-AGTTTTTGACTAAAAA
192 GGATAAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACGA-TTTTTGACTAAAAA
* * * * * *
16510 CGCGTTCTGG-GCCCTGGCTCTA-TTTTGTAT-ATTTTTAGCGCCAAGTCTCATTGAAATTTCTA
256 CACGTTC-GGAGCCCAGGCTC-AGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTA
* *
16572 TATCCATATAAC
319 TATTCATCTAAC
* *
16584 CAAATAC-CACCCACATTGGATTTAA-AATTTTGTTTTTACGAGCATCTGAATCATGTTTCGATT
1 TAAAT-CTCACCCACATTGGATTTAAGGA-TTTGTTTTTACGAGCATCTGAATCATGTTTCGATT
* * *
16647 TAATTAGAAA-TAATTCAGAAAAAATAGGAAAACCGATACTAGAAGCGTGAAAAGCCTTTCAGTC
64 TAATTAGAAATTAATTCGGAAAAAATAGGAAAA-CGATATTAGAAGCGTGAAAAGCCTTTCAATC
** * * * * *
16711 TTTTTACCGTTGAATTATATATTTTTTATGAGTATCATGACCAATAATTGAAGAAAATTCTTTCG
128 TTTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCG
* * * *
16776 GATAAATTTTTACAAAATTTT-ACCGAAATCATG---T-ACCATCACGGTTTAGGTTCTTAGCCA
193 GATAAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCAC-GATT---TT-TGA-CTA
* * * **
16836 AAAACACGTCCCGG-GACCCAGGCTCAGTTTTGCATGATTTTTGGCGCCAAGACTCCTCAAAATA
252 AAAACACGT-TCGGAG-CCCAGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATA
16900 TCTATATTCATCTAAC
315 TCTATATTCATCTAAC
* * * * * * *
16916 CAAATATCATCCATATTGGATTTAAGGATTTGCTTTTACGAGCATCTAAATCATGTTTTGATTTA
1 TAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
*
16981 ATTAGAAATTAATTCGGAAAAAATAGGAAAACCCGATATTAGAAGCGTGAATAGCCTTTCAATC-
66 ATTAGAAATTAATTCGGAAAAAATAGGAAAA--CGATATTAGAAGCGTGAAAAGCCTTTCAATCT
** * * *
17045 TTTTGGTGTTGAATTATATATTTTTTATAAGTATCGTGGCCAAAAATTGAGGACAATTCTCTCGG
129 TTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGG
* * * * * *
17110 TTCAA-TTTTGCAAAATTTTAGCCGAAATC--GT-GT-ACCATCACGGTTTTTGCCTAAAAACAC
194 ATAAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACGATTTTTGACTAAAAACAC
* * * * * *
17170 GTCCCGAGCCCAAGGCTCA-TATTTGCATGA-TTTTGGCTCCAAGAGTCCTTGAAATATCTATAT
259 GTTCGGAGCCC-AGGCTCAGT-TTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATAT
17233 TCATCTAAC
322 TCATCTAAC
* * * * * * * **
17242 TAAATCTAATCCACATTGGATTTTAGGATTTGCTTTTACGAACATCTGAATCTTTTTTCGAAATA
1 TAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
* * * * *
17307 ATTATAAATTAATTCGGAAAAAATAGGATAAACAATATTAGAAGCATAAAAAACCCTTTCAATCT
66 ATTAGAAATTAATTCGGAAAAAATAGGA-AAACGATATTAGAAGCGT-GAAAAGCCTTTCAATCT
* *
17372 TTTTGGCATTGAATTATATATTTTTTATAAGTATCCTGGCCAAAAATTGAGGAAAATTCTTTCGG
129 TTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGG
* * * * * *
17437 ATAATTTTTTGCAAAATTTTAACTGTAATCATGTATTAACCATCACGATTGTTGACTAAAAACGC
194 ATAAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACGATTTTTGACTAAAAACAC
* * * * * *
17502 GTTTCGGAGCCCCGGCTCTGTTTTGTATGATTTTTTGCGTCAAGTCTCATTGAAATATCTATATC
259 G-TTCGGAGCCCAGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATT
*
17567 CATGTAA-
323 CATCTAAC
* * * *
17574 TCAAATCTCGCCCACTTTGGATTTAAGGATTTGTTTTTACGAGCATCTTAATCGTGTTTCGATTT
1 T-AAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTT
** * *
17639 AATTAGAAATTAATTCAAAAAAAATAGGAAAACCGATATTAGAAGCATGAAAAGCCTTTCAATTT
65 AATTAGAAATTAATTCGGAAAAAATAGGAAAA-CGATATTAGAAGCGTGAAAAGCCTTTCAATCT
*
17704 TTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCTAAAAATTGAGGAAAATTCTTTCGT
129 TTTTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCG-
* *
17769 G-TAAATTTTTGCAAAAAATTTTAGCCGAAATCGTGTACTAACCATCACGATTTTTG
193 GATAAATTTTTGC--AAAATTTTAACCGAAATCATGTACTAACCATCACGATTTTTG
17825 GCAACAAAGC
Statistics
Matches: 1588, Mismatches: 249, Indels: 130
0.81 0.13 0.07
Matches are distributed among these distances:
324 7 0.00
325 16 0.01
326 138 0.09
327 93 0.06
328 43 0.03
329 166 0.10
330 93 0.06
331 189 0.12
332 376 0.24
333 333 0.21
334 111 0.07
335 23 0.01
ACGTcount: A:0.33, C:0.15, G:0.15, T:0.36
Consensus pattern (330 bp):
TAAATCTCACCCACATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTA
ATTAGAAATTAATTCGGAAAAAATAGGAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTT
TTGGCATTGAATTATATATTTTTTATGAGTATCGTGGCCAAAAATTGAGGAAAATTCTTTCGGAT
AAATTTTTGCAAAATTTTAACCGAAATCATGTACTAACCATCACGATTTTTGACTAAAAACACGT
TCGGAGCCCAGGCTCAGTTTTGCATGATTTTTTGCGCCAAGACTCATTGAAATATCTATATTCAT
CTAAC
Found at i:21588 original size:24 final size:24
Alignment explanation
Indices: 21556--21609 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
21546 GGGAAATTTA
21556 GATGCCTGTAACTCTGACAGCTAG
1 GATGCCTGTAACTCTGACAGCTAG
21580 GATGCCTGTAACTCTGACAGCTAG
1 GATGCCTGTAACTCTGACAGCTAG
*
21604 AATGCC
1 GATGCC
21610 AGCAATAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (24 bp):
GATGCCTGTAACTCTGACAGCTAG
Found at i:26307 original size:100 final size:100
Alignment explanation
Indices: 26134--26336 Score: 352
Period size: 100 Copynumber: 2.0 Consensus size: 100
26124 TATTCAAAGT
*
26134 TCAAATTAACTGAGGTTTCAAGTCAATAAAAGATCTTCAATTCAAACTAAAAACAACTCTTCAAT
1 TCAAATTAACTGAGGTTTCAAGTCAATAAAAGATCTACAATTCAAACTAAAAACAACTCTTCAAT
*
26199 CAAAACCATCCATACTGACACAGCATTCTCGAGAG
66 CAAAACCATCCATACTGACACAGCATTCACGAGAG
* *
26234 TCAAATTAACTGAGGTTTCAAGTCAATAAAAGATCTACAATTCAAACTGAAAACAACTCTTTAAT
1 TCAAATTAACTGAGGTTTCAAGTCAATAAAAGATCTACAATTCAAACTAAAAACAACTCTTCAAT
* *
26299 CAAAACCATCCCTACTGACACAGCATTCAGGAGAG
66 CAAAACCATCCATACTGACACAGCATTCACGAGAG
26334 TCA
1 TCA
26337 CTAGCAATAA
Statistics
Matches: 97, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.42, C:0.23, G:0.11, T:0.25
Consensus pattern (100 bp):
TCAAATTAACTGAGGTTTCAAGTCAATAAAAGATCTACAATTCAAACTAAAAACAACTCTTCAAT
CAAAACCATCCATACTGACACAGCATTCACGAGAG
Found at i:26812 original size:20 final size:20
Alignment explanation
Indices: 26774--26812 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
26764 TATCTAGAAC
*
26774 AATCTTTTAAAATATAAAAG
1 AATCTTTTAAAATAAAAAAG
26794 AATCTTTTCAAAA-AAAAAA
1 AATCTTTT-AAAATAAAAAA
26813 TAAAATTAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
AATCTTTTAAAATAAAAAAG
Found at i:27466 original size:30 final size:30
Alignment explanation
Indices: 27430--27498 Score: 113
Period size: 30 Copynumber: 2.3 Consensus size: 30
27420 TTCGAATTTC
27430 CATTTGTCATGTTTTGGCAATAAGAA-TCTA
1 CATTTGTCATGTTTTGGCAATAA-AATTCTA
*
27460 CATTTGTCATGTTTTGGCAATAAAATTTTA
1 CATTTGTCATGTTTTGGCAATAAAATTCTA
27490 CATTTGTCA
1 CATTTGTCA
27499 AATCCTTCAT
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
29 2 0.05
30 35 0.95
ACGTcount: A:0.29, C:0.13, G:0.14, T:0.43
Consensus pattern (30 bp):
CATTTGTCATGTTTTGGCAATAAAATTCTA
Found at i:29091 original size:16 final size:17
Alignment explanation
Indices: 29059--29092 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
29049 TTTTTATTTT
*
29059 TATTTATTGATATATAA
1 TATTTATTGAAATATAA
29076 TATTTATT-AAATATAA
1 TATTTATTGAAATATAA
29092 T
1 T
29093 TTATACATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (17 bp):
TATTTATTGAAATATAA
Found at i:33184 original size:19 final size:19
Alignment explanation
Indices: 33160--33196 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
33150 GTATAGTACC
33160 TAATCTAATCTGTACAGTG
1 TAATCTAATCTGTACAGTG
* *
33179 TAATCTCATTTGTACAGT
1 TAATCTAATCTGTACAGT
33197 TGCTAAACAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.41
Consensus pattern (19 bp):
TAATCTAATCTGTACAGTG
Found at i:33992 original size:12 final size:12
Alignment explanation
Indices: 33958--33986 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
33948 TCACCCAATT
33958 TTCTTTCTTTTC
1 TTCTTTCTTTTC
33970 TTCTTTCTTTTC
1 TTCTTTCTTTTC
33982 TTCTT
1 TTCTT
33987 ATTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TTCTTTCTTTTC
Found at i:39521 original size:17 final size:16
Alignment explanation
Indices: 39499--39532 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
39489 CTTAAACCCA
39499 AGTAATCAAAGATCACT
1 AGTAATCAAAGAT-ACT
*
39516 AGTAATCTAAGATACT
1 AGTAATCAAAGATACT
39532 A
1 A
39533 ACCAAACGCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (16 bp):
AGTAATCAAAGATACT
Found at i:52211 original size:65 final size:65
Alignment explanation
Indices: 52098--52229 Score: 219
Period size: 65 Copynumber: 2.0 Consensus size: 65
52088 AAGAGTCCAA
* *
52098 TACTCTACTACCAGACCAAATGTCTGATGACTAATTTTTGTTTAATCATTTCTTCAACTCTTCAG
1 TACTCTACCACCAGACCAAATGTCTGATGACTAATTTTTGTTTAATCATTTCTTAAACTCTTCAG
* * *
52163 TACTTTACCACCAGATCAAATGTCTGATGGCTAATTTTTGTTTAATCATTTCTTAAACTCTTCAG
1 TACTCTACCACCAGACCAAATGTCTGATGACTAATTTTTGTTTAATCATTTCTTAAACTCTTCAG
52228 TA
1 TA
52230 ATTATTATAA
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 62 1.00
ACGTcount: A:0.28, C:0.21, G:0.10, T:0.41
Consensus pattern (65 bp):
TACTCTACCACCAGACCAAATGTCTGATGACTAATTTTTGTTTAATCATTTCTTAAACTCTTCAG
Found at i:56865 original size:15 final size:15
Alignment explanation
Indices: 56845--56875 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
56835 AAGAGTTTAC
56845 TTATATCAATAAGAA
1 TTATATCAATAAGAA
56860 TTATATCAATAAGAA
1 TTATATCAATAAGAA
56875 T
1 T
56876 GAATCAATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.52, C:0.06, G:0.06, T:0.35
Consensus pattern (15 bp):
TTATATCAATAAGAA
Found at i:69735 original size:11 final size:11
Alignment explanation
Indices: 69719--69744 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
69709 TTATTTTTCC
69719 CAATTAGGATA
1 CAATTAGGATA
69730 CAATTAGGATA
1 CAATTAGGATA
69741 CAAT
1 CAAT
69745 GTAGCTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.46, C:0.12, G:0.15, T:0.27
Consensus pattern (11 bp):
CAATTAGGATA
Found at i:79557 original size:56 final size:56
Alignment explanation
Indices: 79491--79601 Score: 188
Period size: 56 Copynumber: 2.0 Consensus size: 56
79481 AATTTATAGG
*
79491 ATAATTAAGTAGAGATAGGGGGATA-GCATTTATTATAATATTTATTGTGTAAAAGA
1 ATAATTAAGTAGAGATAGGGGGATATG-ATTTATTATAACATTTATTGTGTAAAAGA
*
79547 ATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAAAG
1 ATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTAAAAG
79602 GAAATAGATA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
56 51 0.98
57 1 0.02
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.36
Consensus pattern (56 bp):
ATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTAAAAGA
Found at i:83888 original size:21 final size:21
Alignment explanation
Indices: 83864--83930 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
83854 AATTCTCTGT
83864 AAATTAAGAAATACTTAACTC
1 AAATTAAGAAATACTTAACTC
* * * *
83885 AAATCATAGAAAATTCTT--TTT
1 AAATTA-AG-AAATACTTAACTC
*
83906 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTTAACTC
83927 AAAT
1 AAAT
83931 CCTGATCCTT
Statistics
Matches: 33, Mismatches: 9, Indels: 8
0.66 0.18 0.16
Matches are distributed among these distances:
19 6 0.18
20 2 0.06
21 16 0.48
22 2 0.06
23 7 0.21
ACGTcount: A:0.51, C:0.13, G:0.04, T:0.31
Consensus pattern (21 bp):
AAATTAAGAAATACTTAACTC
Found at i:83910 original size:42 final size:42
Alignment explanation
Indices: 83851--83931 Score: 135
Period size: 42 Copynumber: 1.9 Consensus size: 42
83841 GCTAAGTCTT
*
83851 GAAAATTCTCTGTAAATTAAGAAATACTTAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
* *
83893 GAAAATTCTTTTTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
83932 CTGATCCTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.47, C:0.15, G:0.06, T:0.32
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:84247 original size:2 final size:2
Alignment explanation
Indices: 84240--84267 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
84230 TAATATGTAG
84240 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
84268 CTAGTTTTAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:86455 original size:352 final size:352
Alignment explanation
Indices: 85805--86495 Score: 956
Period size: 352 Copynumber: 2.0 Consensus size: 352
85795 ATTGCCAAGC
* * * *
85805 CAGATGTCTTGAAGTCTAAATCTAATATTCTTAGACCCGATTCGTAACTGTGGAAGCCCAAAGAA
1 CAGATGTCTTGAAGTCTAAATCTAATATTCTTAAACCCAATTCGTAACTATGGAAGCCAAAAGAA
* * * * *
85870 GGAGTTCAAGTCCAATAAGTAATTATGATGCAATAATGATTCAGCTCTGATGTAGCATTGTTAAA
66 GGAGTCCAAGTCCAATAAGTAATTATGATGCAATAATGATTCACCCCTAATGCAGCATTGTTAAA
*** * * * * ** *
85935 TCCTATTTGGAGGATGACTTCAAAAGAGCAGTTTTTGAAGAAAATTCATAGTTTTTGATCCGGAA
131 TCCTATTCAAAAGAGGACTTCAAAAGAGCAGTTTTGGAAGAAAATCCATAACTTTTGATCCAGAA
*
86000 CTCAGAAAATTGAAAATGAGGTACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTTA
196 CTCAGAAAATTGAAAATGAGATACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTTA
* * * *
86065 CCTCGAGACCTAATTCTGCAATTCTAGTGGACGATTTTGCCCTTGAAATTTCTTGATAGAATTGA
261 CCTCGAGACCTAATTCTGCAATTCTAGTGGACGATTTTGCCCTTGAAATTTCTGGACAAAATTAA
86130 TCTTCTCCTAAACCCGGTTTGGAGAGT
326 TCTTCTCCTAAACCCGGTTTGGAGAGT
* *
86157 CAGATGTCTTGAAGTCTAAATCTGATATTCTTAAACCCAATTCGTTAA-TATGGAAGTCAAAAGA
1 CAGATGTCTTGAAGTCTAAATCTAATATTCTTAAACCCAATTCG-TAACTATGGAAGCCAAAAGA
* * *
86221 AGGAGTCCAAGTCCAATGAGTAATTATGATGTATTAATGATTCACCCCTAATGCAGCATTGTTAA
65 AGGAGTCCAAGTCCAATAAGTAATTATGATGCAATAATGATTCACCCCTAATGCAGCATTGTTAA
* * * *
86286 ATCCTATTCAAAAGAGGATTTCACAAGAGCAGTTTTGGAAGAAAATCCATAACTTTTGGTCTAGA
130 ATCCTATTCAAAAGAGGACTTCAAAAGAGCAGTTTTGGAAGAAAATCCATAACTTTTGATCCAGA
* * * *
86351 GCTCAGAAAAATT-CAAATGAGATACCGTTGGAAAGATGATTCCAAGGTCTACAACTTTTATGTT
195 ACTCAG-AAAATTGAAAATGAGATACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTT
* * * * *
86415 TATCTCGAGACCTAATTCTGCAGTT-TCAGTGGATGATTTTGCCCTTTAATTTTCTGGACAAAAT
259 TACCTCGAGACCTAATTCTGCAATTCT-AGTGGACGATTTTGCCCTTGAAATTTCTGGACAAAAT
86479 TAATCTTCTCCTAAACC
323 TAATCTTCTCCTAAACC
86496 GACTTGGAGA
Statistics
Matches: 294, Mismatches: 42, Indels: 6
0.86 0.12 0.02
Matches are distributed among these distances:
351 1 0.00
352 284 0.97
353 9 0.03
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Consensus pattern (352 bp):
CAGATGTCTTGAAGTCTAAATCTAATATTCTTAAACCCAATTCGTAACTATGGAAGCCAAAAGAA
GGAGTCCAAGTCCAATAAGTAATTATGATGCAATAATGATTCACCCCTAATGCAGCATTGTTAAA
TCCTATTCAAAAGAGGACTTCAAAAGAGCAGTTTTGGAAGAAAATCCATAACTTTTGATCCAGAA
CTCAGAAAATTGAAAATGAGATACCGTTGGAAAGAAGATTCCAAGATCTACAACTTTTATGTTTA
CCTCGAGACCTAATTCTGCAATTCTAGTGGACGATTTTGCCCTTGAAATTTCTGGACAAAATTAA
TCTTCTCCTAAACCCGGTTTGGAGAGT
Found at i:88948 original size:20 final size:20
Alignment explanation
Indices: 88923--88965 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
88913 AAATTTATAC
88923 ATTTTGACAATCTTCCCACA
1 ATTTTGACAATCTTCCCACA
*
88943 ATTTTGACAATTTTCCCACA
1 ATTTTGACAATCTTCCCACA
88963 ATT
1 ATT
88966 GAGTTGCAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.26, G:0.05, T:0.40
Consensus pattern (20 bp):
ATTTTGACAATCTTCCCACA
Found at i:91323 original size:2 final size:2
Alignment explanation
Indices: 91316--91345 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
91306 GATAAACTTG
91316 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
91346 CCTAACAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92639 original size:22 final size:22
Alignment explanation
Indices: 92614--92659 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
92604 TGAATTGACA
*
92614 AAATACAATTAATGA-AGAATTT
1 AAATACAAATAATGATA-AATTT
*
92636 AAATCCAAATAATGATAAATTT
1 AAATACAAATAATGATAAATTT
92658 AA
1 AA
92660 TCTAAAAGTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 20 0.95
23 1 0.05
ACGTcount: A:0.57, C:0.07, G:0.07, T:0.30
Consensus pattern (22 bp):
AAATACAAATAATGATAAATTT
Found at i:93209 original size:2 final size:2
Alignment explanation
Indices: 93202--93236 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
93192 TCTTTTTATT
93202 TA TA TA TA 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 TA TA TA TA T
93237 GTCACTTTGC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:95604 original size:6 final size:6
Alignment explanation
Indices: 95593--95617 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
95583 AATTCATCAA
95593 GTGCAT GTGCAT GTGCAT GTGCAT G
1 GTGCAT GTGCAT GTGCAT GTGCAT G
95618 ACAGGATTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.36, T:0.32
Consensus pattern (6 bp):
GTGCAT
Done.