Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012367.1 Corchorus capsularis cultivar CVL-1 contig12388, 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: 30509
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.34
Found at i:13037 original size:112 final size:114
Alignment explanation
Indices: 12838--13065 Score: 442
Period size: 112 Copynumber: 2.0 Consensus size: 114
12828 GTTAAGTAAT
12838 TTAGGTGTTTTTTTTTTTGACAATGTTATGGGTTCAAATCCCATCACAAGCAAAAACTTTTTTTC
1 TTAGGTGTTTTTTTTTTTGACAATGTTATGGGTTCAAATCCCATCACAAGCAAAAACTTTTTTTC
12903 AAAATTTAAATTTTAAAATTAGTCGCCATGTCCAAACCGGTCAAAAACA
66 AAAATTTAAATTTTAAAATTAGTCGCCATGTCCAAACCGGTCAAAAACA
12952 TTAGGTG-TTTTTTTTTT-ACAATGTTATGGGTTCAAATCCCATCACAAGCAAAAACTTTTTTTC
1 TTAGGTGTTTTTTTTTTTGACAATGTTATGGGTTCAAATCCCATCACAAGCAAAAACTTTTTTTC
13015 AAAATTTAAATTTTAAAATTAGTCGCCATGTCCAAACCGGTCAAAAACA
66 AAAATTTAAATTTTAAAATTAGTCGCCATGTCCAAACCGGTCAAAAACA
13064 TT
1 TT
13066 CCGATTTTCC
Statistics
Matches: 114, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
112 97 0.85
113 10 0.09
114 7 0.06
ACGTcount: A:0.34, C:0.17, G:0.12, T:0.37
Consensus pattern (114 bp):
TTAGGTGTTTTTTTTTTTGACAATGTTATGGGTTCAAATCCCATCACAAGCAAAAACTTTTTTTC
AAAATTTAAATTTTAAAATTAGTCGCCATGTCCAAACCGGTCAAAAACA
Found at i:13225 original size:30 final size:31
Alignment explanation
Indices: 13180--13245 Score: 100
Period size: 30 Copynumber: 2.2 Consensus size: 31
13170 AAATTGCCAA
*
13180 TTGACCTCGTTAAAATGAT-AGATTTATAGTT
1 TTGACCTCATTAAAATGATAAG-TTTATAGTT
13211 TTGACCT-ATTAAAATGATAAGTTTATAGTT
1 TTGACCTCATTAAAATGATAAGTTTATAGTT
13241 TTGAC
1 TTGAC
13246 ACCATTATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.33, C:0.09, G:0.15, T:0.42
Consensus pattern (31 bp):
TTGACCTCATTAAAATGATAAGTTTATAGTT
Found at i:16858 original size:13 final size:13
Alignment explanation
Indices: 16840--16886 Score: 62
Period size: 13 Copynumber: 3.7 Consensus size: 13
16830 AAAAGCCTTT
16840 AAAGAAGAAAAAA
1 AAAGAAGAAAAAA
16853 AAAGAAGAAAAACA
1 AAAGAAGAAAAA-A
*
16867 AAA-AA-AAAAAG
1 AAAGAAGAAAAAA
16878 AAAGAAGAA
1 AAAGAAGAA
16887 CAGCGGGTCG
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
11 3 0.10
12 7 0.23
13 16 0.53
14 4 0.13
ACGTcount: A:0.83, C:0.02, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAGAAGAAAAAA
Found at i:16882 original size:22 final size:21
Alignment explanation
Indices: 16847--16888 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
16837 TTTAAAGAAG
16847 AAAAAAAAAGAAGAAAAACAA
1 AAAAAAAAAGAAGAAAAACAA
*
16868 AAAAAAAAAGAAAGAAGAACA
1 AAAAAAAAAG-AAGAAAAACA
16889 GCGGGTCGCG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.83, C:0.05, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAGAAGAAAAACAA
Found at i:23936 original size:2 final size:2
Alignment explanation
Indices: 23929--23979 Score: 95
Period size: 2 Copynumber: 26.0 Consensus size: 2
23919 TACATTAATA
23929 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
23971 TC TC T- TC TC
1 TC TC TC TC TC
23980 GTGCACCTTC
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 47 0.98
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:24052 original size:52 final size:52
Alignment explanation
Indices: 23973--24113 Score: 255
Period size: 52 Copynumber: 2.7 Consensus size: 52
23963 TCTCTCTCTC
*
23973 TCTTCTCGTGCACCTTCGTGTGCGCTGGCCTCGCCTCCTGCGGAGGCCTTTG
1 TCTTCTCGTGCACCTTCGTGTGTGCTGGCCTCGCCTCCTGCGGAGGCCTTTG
24025 TCTTCTCGTGCACCTTCGTGTGTGCTGGCCTCGCCTCCTGCGGAGGCCTTTG
1 TCTTCTCGTGCACCTTCGTGTGTGCTGGCCTCGCCTCCTGCGGAGGCCTTTG
* *
24077 TCTTCTCGTGGACCTTCGTGTCTGCTGGCCTCGCCTC
1 TCTTCTCGTGCACCTTCGTGTGTGCTGGCCTCGCCTC
24114 ACTTCGTGTC
Statistics
Matches: 86, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 86 1.00
ACGTcount: A:0.04, C:0.36, G:0.28, T:0.33
Consensus pattern (52 bp):
TCTTCTCGTGCACCTTCGTGTGTGCTGGCCTCGCCTCCTGCGGAGGCCTTTG
Found at i:24126 original size:45 final size:45
Alignment explanation
Indices: 24075--24203 Score: 204
Period size: 45 Copynumber: 2.9 Consensus size: 45
24065 CGGAGGCCTT
* *
24075 TGTCTTCTCGTGGACCTTCGTGTCTGCTGGCCTCGCCTCACTTCG
1 TGTCTTCTCGTGTACCTTCGTGTCTGCTGGCCTCGCCTCACTTCC
* * *
24120 TGTCTTCTCGTGTACCCTCGTGTCTTCTGGCCTCTCCTCACTTCC
1 TGTCTTCTCGTGTACCTTCGTGTCTGCTGGCCTCGCCTCACTTCC
*
24165 TGTCTTCTGGTGTACCTTCGTGTCTGCTGGCCTCGCCTC
1 TGTCTTCTCGTGTACCTTCGTGTCTGCTGGCCTCGCCTC
24204 CTGCGGAGGT
Statistics
Matches: 75, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 75 1.00
ACGTcount: A:0.04, C:0.36, G:0.22, T:0.38
Consensus pattern (45 bp):
TGTCTTCTCGTGTACCTTCGTGTCTGCTGGCCTCGCCTCACTTCC
Found at i:24188 original size:20 final size:20
Alignment explanation
Indices: 24115--24194 Score: 61
Period size: 20 Copynumber: 3.8 Consensus size: 20
24105 CCTCGCCTCA
*
24115 CTTCGTGTCTTCTCGTGTAC
1 CTTCGTGTCTTCTGGTGTAC
* * *
24135 CCTCGTGTCTTCTGGCCTCTCCTC
1 CTTCGTGTCTTCTGG--TGT--AC
*
24159 ACTTCCTGTCTTCTGGTGTAC
1 -CTTCGTGTCTTCTGGTGTAC
*
24180 CTTCGTGTCTGCTGG
1 CTTCGTGTCTTCTGG
24195 CCTCGCCTCC
Statistics
Matches: 45, Mismatches: 10, Indels: 10
0.69 0.15 0.15
Matches are distributed among these distances:
20 26 0.58
21 1 0.02
22 2 0.04
23 2 0.04
24 1 0.02
25 13 0.29
ACGTcount: A:0.04, C:0.34, G:0.21, T:0.41
Consensus pattern (20 bp):
CTTCGTGTCTTCTGGTGTAC
Found at i:27501 original size:320 final size:319
Alignment explanation
Indices: 26152--30004 Score: 3925
Period size: 320 Copynumber: 11.9 Consensus size: 319
26142 CCCGATTCAA
** * * * * *
26152 TTTTGCATGATTTTTGATAGAAAGACTCATTGAAATATCTATATTCATTTAATCAATTCTTAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
26217 ACATTGGATTTAATGATTTGTTTTTACGAGCATCTGAAATCTTATGTTTCGATTTAATTAG-AAT
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGCATCTG-AATC-T-TGTTTCGATTTAATTAGAAAT
* * * ** * * * *
26281 TAAATTCGAGAAAAAAAAATAGAAAATCGATATTATAATTGTGAAAAACCCTTCAATTTTTTTTG
128 T-AATTC--G--AAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGG
* * * * *
26346 CGTTAAATTATACATTTTTTTCGAGTATCGTGGCAAAGAATTGACGAAAAAA-TTTTCGGGTCAG
188 CGTTAAATTATATATTTTTCT-GAGTATTGTAGCAAAAAATTGA-GAAAAAACTTTTCGGGTCAG
* * * * * * * *
26410 TTTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGTTAGAAACGCATTTCGGGAGCCTGA
251 TTTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAG-GCCCGG
*
26475 CTTAC
315 CTTAG
* ** * *
26480 TTTTGCATGATTTTTGTCAGAAAGAAGCCTTGAAATATCCATATTCATTTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * *
26545 ACATTGGATTTAAAGATTT-ATTTTACA-AGAATCTGAATATTGTTTTGATTTAATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTA-AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
26608 ATTCGGAAAATATTGAAAAACGATATTAGAAGCGTGAAAAGACCATCAATATTTTTGGTGTTGAA
130 ATTCGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT--A
* *
26673 TTATATATATATATATATATTTTGAGTATTGTA-CCAAAAATTGAGAAAAAAAACTTTTCGGGTC
193 --A-AT-TATATAT-T-T-TTCTGAGTATTGTAGCAAAAAATTGAG--AAAAAACTTTTCGGGTC
* ** * * *
26737 AGTTTTTAGACGAAATCGTGTACTAAAAATCACGGGTTTTTTGCTAAAAACGTGTTTCGAGGTCC
249 AGTTTTTAGCCGAAATCGTGTACTAACCATCAC-TGTTTTTGGCTAAAAACGCGTTTCGAGG-CC
26802 CGGCTTAG
312 CGGCTTAG
* * **
26810 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATAAATATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * *
26875 ACACTGGATTTAAGGATTTGTTTTTACGAGCTTCTAAATCTGGTTTCGATTTAATTA-AAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
26939 TTCGGGAAAAAAAATTGAAAAACGATATTATAAGCGTGAAAAGCCTGCCAAAT-TTTTTGGTGTT
131 TTC--G-AAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTC-AATCTTTTTGGCGTT
* * * * * * * *
27003 GAATTATATATATTTTATGAGTATTAT-GACAAAAAAAATTGGGATAAAAACTTCTCGAGTTAGC
192 AAATTATATAT-TTTTCTGAGTATTGTAG-C--AAAAAATTGAGA-AAAAACTTTTCGGGTCAGT
* * * ** * **
27067 TTTTAGTCGATATCGTGTACGAACCATCACAATTTTTGACTAAAAATACGTTTCGAGGCCCCGGC
252 TTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGG-CCCGGC
27132 TTAG
316 TTAG
* * * * *
27136 TTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATGTATATTCATGTAACCAAATCTGAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
27201 AGATTGGATTTAAGGATTTGTTTTTAAGAGCAAT-TGAATCTTGTTTTGATTTAATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* ** *
27265 ATTCAGAAAAAAATTGAAAAATGATATTAGAAGCGTGGGAAGCCCGTCAATTTTTTTGGCGTTAA
130 ATTC-GAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTAA
*
27330 ATTATATATTTTTCTGAGTA-TGTAGCAAAAAATTGAGAAAAAACATTTCGGGTCAGTTTTTAGC
194 ATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC
* * * *
27394 CGAAATCGTGTACTAACAATCACTGTTTTTGGCTAAAAACACTTTTCGAGGCCCTAGCTTAG
259 CGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGGCCC-GGCTTAG
* * * * **
27456 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAAGCAAATCTCAGTT
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * * *
27521 ACACTGGATTTAAGGATTTGGTTTTACGAGCTTCTAAATCTTGTTTTGATTTAATTA-AAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
27585 TTCGGAAAAAATTGAGAAACGATATT--AAGCGTGAAAAGCCCGTCAAAT-TTTTTGGTGTTGAA
131 TTCGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTC-AATCTTTTTGGCGTTAAA
* * * * * * * *
27647 TTATATGTATTTTATGAGTATTAT-GACAAAAAATTGGGAAAAAAAAAACTTCTCGAGTTAGCTT
195 TTATATAT-TTTTCTGAGTATTGTAG-CAAAAAATT--G--AGAAAAAACTTTTCGGGTCAGTTT
* ** *
27711 TTAGTCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAATGCGTTTCGAGGCCCCGGCTT
254 TTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGG-CCCGGCTT
27776 AG
318 AG
* * * *
27778 TTTTGCACGACTTTTGGCAGAAAGGCTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
27843 AGATTGGATTTAAGAATTTGTTTTTAAGAGCAAT-TGAATCTTGTTTCGATTTAATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* **
27907 ATTC-AGAAAAAATTGAAAAATGATATTAGAAGCGTGGGAAGCCCGTCAATCTTTTTGGCGTTAA
130 ATTCGA-AAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTAA
* * *
27971 ATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTATCGAGTCAATTTTTAGC
194 ATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC
* * *
28036 CGAAATCATGTACTAACCATCACTGTTTTTGGCTAAAAACACGTTTCGAGGCCCCGACTTAG
259 CGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGG-CCCGGCTTAG
* * * *
28098 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAAGCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * * *
28163 ATACTGGATTTAAGGATTTGTTTTTACGAGCTTCTAAATCTTGTTTCGATTTAATTA-AAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * * *
28227 TTCGGAAAAAATTGAGAAACGATATTAGAAGCGTGAAAAGCCCGTCAAAT-TTTTTGGTGTTGAA
131 TTCGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTC-AATCTTTTTGGCGTTAAA
* * * * * * * *
28291 TTATATATATTTTATGTGTATTAT-GACAAAAAAATTGGGAAAAAAAACTTCTCGAGTTAGCTTT
195 TTATATAT-TTTTCTGAGTATTGTAG-C-AAAAAATT--GAGAAAAAACTTTTCGGGTCAGTTTT
* * ** *
28355 TAGTCGAAATCGTGTACTAGCCATCACAATTTTTGGCTAAAAATGCGTTTCGAGGCCCCGGCTTA
255 TAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGG-CCCGGCTTA
28420 G
319 G
* * *
28421 TTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
28486 AGATTGGAGTTAAGGATTTGTTTTTAAGAGCAAT-TGAATCTTGTTTCGATTTAATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGC-ATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * **
28550 ATTCAGAAAAAAAATTTGAAAAATGATATTAGAAGTGTGGGAAGCCCGTCAATCTTTTTGGCGTT
130 ATTC-G-AAAAAAA-TTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* * ** *
28615 AAATTATATATTTTTCTGAGTATTGTGGCGAAAAATTGAGCTAAAACTTTTCGGGTAAGTTTTTA
192 AAATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTA
* * * * * *
28680 GCCAAAATCGTGTACTAACCATCACGGTTTTTGGTTTAAAAACGTGTTTCG-GGACCCCGACTCA
257 GCCGAAATCGTGTACTAACCATCACTGTTTTTGG-CTAAAAACGCGTTTCGAGG--CCCGGCTTA
*
28744 A
319 G
* * * *
28745 TTTTTCATGATTTTTGGCAGAAAGACTGCTTTAAATATCTATATTCATCAAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* *
28810 ACAATGGATTTAAGGATTTGTTTTTACA-AGCATCTGAATCTTGTTTCGATTTAATTAGAAATGA
66 ACATTGGATTTAAGGATTTGTTTTTA-AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * * ** * *
28874 ATTCGGAAAAAAAAATGAAAAAATGATGTTATAAGCGTG-AAAGCCCATTAATCCATTTAGCGTC
130 ATTC-G-AAAAAAATTG-AAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTT
* *
28938 AAATTATGTATTTTTTCTGAGTATTG-AGGCAAAAAATTGATAAAAAGA-TTTTCGGGATCAGTT
192 AAATTATATA-TTTTTCTGAGTATTGTA-GCAAAAAATTGAGAAAAA-ACTTTTCGGG-TCAGTT
* * * * ** * * *
29001 TTTAGCCAAAATCGTGTACAAACCATTACTCTTTTTAGAATAAAAACACGTTT--TGG---GACT
253 TTTAGCCGAAATCGTGTACTAACCATCACTGTTTTT-GGCTAAAAACGCGTTTCGAGGCCCGGCT
* *
29061 CAA
317 TAG
* * * * ** * **
29064 TTTTGCATGATTTTTGGCGGAAACACTCCTTTAAATATTTATATTCATAAAACTAAATCTCATTC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* ** *
29129 ACAATGGATTTAAGGATTTGTTTTTACTAGCATCTGAATCTTGTTCCGATTTAATTAGAAATTAA
66 ACATTGGATTTAAGGATTTGTTTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* ** * * * * * * * * *
29194 TTAGGAAAAAAAAGGGAAAACGATATTATAGGCGTGAAAAACTCATCAATATATTTAGCGTTAAA
131 TT-CGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTAAA
* * *
29259 TTA-AGTATTTTTTCTGAGTATTGTGGCAAAATATTGAGAAAAAAATTTTCGGGTCAGTTTTTAG
195 TTATA-TA-TTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG
* * * * * * *
29323 CCAAAATTGTGTACTAACCATCACTATTTTTGGACTAAAAACGCGTTACG-GGACCCTGACTCAA
258 CCGAAATCGTGTACTAACCATCACTGTTTTTGG-CTAAAAACGCGTTTCGAGG-CCC-GGCTTAG
* * * * *
29387 TTTTCCATGATTTTTGGAAGAAAGACTCCTTGAAATATTTATATTCATCAAACCAAATCGCAGCC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * * *
29452 ACATTGGATTTAAGGATTGGTTTTTACA-AGCATCTAAATTTTGTTTCGATTTGATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTA-AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * * *
29516 TTTCGGAAAAAACTGAAAAACGATATTAGAAGCGTGAAAAACCCGTTAATCTTTTT-GCTATTAA
130 ATTCGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGC-GTTAA
* * * *
29580 ATTATATATTTTTTTGAGTATTGTGGCAAAAGATTTAGAAAAAACTTTTCGGGTCAGTTTTTAGC
194 ATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGC
* * * * * * *
29645 TGAAATCGTGTACTAACAATCAC-GATTTTTGACTAAAAACGCGTTTCG-GGACCCTGATACAA
259 CGAAATCGTGTACTAACCATCACTG-TTTTTGGCTAAAAACGCGTTTCGAGG-CCCGGCT-TAG
* * * * *
29707 TTTTGCAAGATTTTTGGCAGAAAGACTCCTTTAAATATCAATATTCATCAAACCAAATCTCAGTC
1 TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
* * *
29772 ACATTGGATTTAAGGGTTTGATTTTACA-AGCATCTGAATCTTGATTCGATTTAATTAGAAATTA
66 ACATTGGATTTAAGGATTTGTTTTTA-AGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTA
* * * * *
29836 ATTTCG-AAAAAATTAAAAAACGATATTAGAAGCGTGAAAAGTCCATCAATCTATTTAGCGTTAA
130 A-TTCGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTAA
* * * * * *
29900 ATTATGA-ATTTTCTCTGAGTATTGTGGAAAAAAATTGAGATAAAATTTTTCGAGTTAGTTTTTA
194 ATTAT-ATATTTT-TCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTA
* *
29964 GCCGAAATCGTGTACTAACCATCACTATTTTTGGCAAAAAA
257 GCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAA
30005 ATTGAGAAAT
Statistics
Matches: 2976, Mismatches: 450, Indels: 205
0.82 0.12 0.06
Matches are distributed among these distances:
316 36 0.01
317 81 0.03
318 109 0.04
319 211 0.07
320 614 0.21
321 184 0.06
322 229 0.08
323 426 0.14
324 276 0.09
325 168 0.06
326 173 0.06
327 133 0.04
328 100 0.03
329 46 0.02
330 112 0.04
331 28 0.01
332 1 0.00
333 46 0.02
334 3 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (319 bp):
TTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATCTAACCAAATCTCAGCC
ACATTGGATTTAAGGATTTGTTTTTAAGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
TTCGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCGTCAATCTTTTTGGCGTTAAAT
TATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCG
AAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACGCGTTTCGAGGCCCGGCTTAG
Found at i:27913 original size:642 final size:643
Alignment explanation
Indices: 26152--30004 Score: 4265
Period size: 642 Copynumber: 6.0 Consensus size: 643
26142 CCCGATTCAA
** * * * * * *
26152 TTTTGCATGATTTTTGATAGAAAGAC-TCATTGAAATATCTATATTCATTTAATCAATTCTTAGC
1 TTTTGCATGATTTTTGGCAAAAAGACTTC-TTGAAATATATATATTCATCTAACCAAATCTCAGC
* * *
26216 CACATTGGATTTAATGATTTGTTTTTACGAGCATCTGAAATCTTATGTTTCGATTTAATTAGAAT
65 CACACTGGATTTAAGGATTTGTTTTTACGAGCATCT-AAATC-T-TGTTTCGATTTAATTAAAAT
* * ** * * * *
26281 TAAATTCGAGAAAAAAAAATAGAAAATCGATATTATAATTGTGAAAAACCCTTCAATTTTTTTTG
127 T-AATTCG-G--AAAAAAATTGAAAAACGATA-TATAAGCGTGAAAAGCCCGTCAAATTTTTTGG
* * * ** * * ** * *
26346 CGTTAAATTATACAT-TTTTTTCGAGTATCGTGGCAAAGAATTGACGAAAAAA-TTTTCGGGTCA
187 TGTTAAATTATATATATTTTAT-GAGTATTATGACAAAAAATTGAAAAAAAAACTTCTCGAGTCA
* ** ** * * * *
26409 GTTTTTAGTCGAAATCGTGTACTAACCATCACGGTTTTTGGTTAGAAACGCATTTCG-GGAGCCT
251 GCTTTTAGTCGAAATCGTGTACTAACCATCACAATTTTTGACTAAAAACGCGTTTCGAGG-CCCC
* * * * * ** * *
26473 GACTTACTTTTGCATGATTTTTGTCAGAAAGAAGCCTTGAAATATCCATATTCATTTAACCAAAT
315 GGCTTAGTTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAAT
* * * *
26538 CTCAGCCACATTGGATTTAAAGATTT-ATTTTACA-AG-AATCTGAATATTGTTTTGATTTAATT
380 CTCAGCCACATTGGATTTAAGGATTTGTTTTTA-AGAGCAATCTGAATCTTGTTTCGATTTAATT
* * * *
26600 AGAAATTAATTC-GGAAAATATTGAAAAACGATATTAGAAGCGTGAAAAGACCATCAATATTTTT
444 AGAAATTAATTCAGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTT
* * *
26664 GGTGTTGAATTATATATATATATATATATTTTGAGTATTGTA-CCAAAAATTGAGAAAAAAAACT
509 GGCGTT--A--A-AT-TATATAT-T-T-TTCTGAGTATTGTAGCAAAAAATTGAG--AAAAAACT
* ** * * *
26728 TTTCGGGTCAGTTTTTAGACGAAATCGTGTACTAAAAATCACGGGTTTTTTGCTAAAAACGTGTT
563 TTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC-TGTTTTTGGCTAAAAACCT-TT
* *
26793 TCGAGG-TCCCGGCTTAG
626 TCGAGGACCCCGACTTAG
*
26810 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATAAATATTCATCTAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAACCAAATCTCAGCC
* *
26875 ACACTGGATTTAAGGATTTGTTTTTACGAGCTTCTAAATCTGGTTTCGATTTAATTAAAATTAAT
66 ACACTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAATTAAT
* * *
26940 TCGGGAAAAAAAATTGAAAAACGATATTATAAGCGTGAAAAGCCTGCCAAATTTTTTGGTGTTGA
131 TC-GG-AAAAAAATTGAAAAACGATA-TATAAGCGTGAAAAGCCCGTCAAATTTTTTGGTGTTAA
** * *
27005 ATTATATATATTTTATGAGTATTATGACAAAAAAAATTGGGATAAAAACTTCTCGAGTTAGCTTT
193 ATTATATATATTTTATGAGTATTATGAC--AAAAAATTGAAAAAAAAACTTCTCGAGTCAGCTTT
* * **
27070 TAGTCGATATCGTGTACGAACCATCACAATTTTTGACTAAAAATACGTTTCGAGGCCCCGGCTTA
256 TAGTCGAAATCGTGTACTAACCATCACAATTTTTGACTAAAAACGCGTTTCGAGGCCCCGGCTTA
* *
27135 GTTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATGTATATTCATGTAACCAAATCTGAGC
321 GTTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGC
* *
27200 CAGATTGGATTTAAGGATTTGTTTTTAAGAGCAAT-TGAATCTTGTTTTGATTTAATTAGAAATT
386 CACATTGGATTTAAGGATTTGTTTTTAAGAGCAATCTGAATCTTGTTTCGATTTAATTAGAAATT
* ** * *
27264 AATTCAGAAAAAAATTGAAAAATGATATTAGAAGCGTGGGAAGCCCGTCAATTTTTTTGGCGTTA
451 AATTCAGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCGTTA
*
27329 AATTATATATTTTTCTGAGTA-TGTAGCAAAAAATTGAGAAAAAACATTTCGGGTCAGTTTTTAG
516 AATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG
* *
27393 CCGAAATCGTGTACTAACAATCACTGTTTTTGGCTAAAAACACTTTTCGAGG--CCCTAGCTTAG
581 CCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAAC-CTTTTCGAGGACCCCGA-CTTAG
* **
27456 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAAGCAAATCTCAGTT
1 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAACCAAATCTCAGCC
* * *
27521 ACACTGGATTTAAGGATTTGGTTTTACGAGCTTCTAAATCTTGTTTTGATTTAATTAAAATTAAT
66 ACACTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAATTAAT
* *
27586 TCGG-AAAAAATTGAGAAACGATAT-TAAGCGTGAAAAGCCCGTCAAATTTTTTGGTGTTGAATT
131 TCGGAAAAAAATTGAAAAACGATATATAAGCGTGAAAAGCCCGTCAAATTTTTTGGTGTTAAATT
* *
27649 ATATGTATTTTATGAGTATTATGACAAAAAATTGGGAAAAAAAAAACTTCTCGAGTTAGCTTTTA
196 ATATATATTTTATGAGTATTATGACAAAAAATT--G-AAAAAAAAACTTCTCGAGTCAGCTTTTA
* *
27714 GTCGAAATCGTGTACTAACCATCACAATTTTTGGCTAAAAATGCGTTTCGAGGCCCCGGCTTAGT
258 GTCGAAATCGTGTACTAACCATCACAATTTTTGACTAAAAACGCGTTTCGAGGCCCCGGCTTAGT
*
27779 TTTGCACGACTTTTGGCAGAAAGGCTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCCA
323 TTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCCA
* *
27844 GATTGGATTTAAGAATTTGTTTTTAAGAGCAAT-TGAATCTTGTTTCGATTTAATTAGAAATTAA
388 CATTGGATTTAAGGATTTGTTTTTAAGAGCAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* ** *
27908 TTCAG-AAAAAATTGAAAAATGATATTAGAAGCGTGGGAAGCCCGTCAATCTTTTTGGCGTTAAA
453 TTCAGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCGTTAAA
* * *
27972 TTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTATCGAGTCAATTTTTAGCC
518 TTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCC
* *
28037 GAAATCATGTACTAACCATCACTGTTTTTGGCTAAAAACACGTTTCGAGG-CCCCGACTTAG
583 GAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAAC-CTTTTCGAGGACCCCGACTTAG
*
28098 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAAGCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAACCAAATCTCAGCC
* *
28163 ATACTGGATTTAAGGATTTGTTTTTACGAGCTTCTAAATCTTGTTTCGATTTAATTAAAATTAAT
66 ACACTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAATTAAT
* * *
28228 TCGG-AAAAAATTGAGAAACGATATTAGAAGCGTGAAAAGCCCGTCAAATTTTTTGGTGTTGAAT
131 TCGGAAAAAAATTGAAAAACGATA-TATAAGCGTGAAAAGCCCGTCAAATTTTTTGGTGTTAAAT
* * *
28292 TATATATATTTTATGTGTATTATGACAAAAAAATTGGGAAAAAAAACTTCTCGAGTTAGCTTTTA
195 TATATATATTTTATGAGTATTATGAC-AAAAAATT-GAAAAAAAAACTTCTCGAGTCAGCTTTTA
* * *
28357 GTCGAAATCGTGTACTAGCCATCACAATTTTTGGCTAAAAATGCGTTTCGAGGCCCCGGCTTAGT
258 GTCGAAATCGTGTACTAACCATCACAATTTTTGACTAAAAACGCGTTTCGAGGCCCCGGCTTAGT
28422 TTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCCA
323 TTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCCA
* *
28487 GATTGGAGTTAAGGATTTGTTTTTAAGAGCAAT-TGAATCTTGTTTCGATTTAATTAGAAATTAA
388 CATTGGATTTAAGGATTTGTTTTTAAGAGCAATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
* * ** *
28551 TTCAGAAAAAAAATTTGAAAAATGATATTAGAAGTGTGGGAAGCCCGTCAATCTTTTTGGCGTTA
453 TTCAG-AAAAAAA-TTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCGTTA
* * ** *
28616 AATTATATATTTTTCTGAGTATTGTGGCGAAAAATTGAGCTAAAACTTTTCGGGTAAGTTTTTAG
516 AATTATATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAG
* * * * * *
28681 CCAAAATCGTGTACTAACCATCACGGTTTTTGGTTTAAAAACGTGTTTCG-GGACCCCGACTCAA
581 CCGAAATCGTGTACTAACCATCACTGTTTTTGG-CTAAAAACCT-TTTCGAGGACCCCGACTTAG
* * * * * *
28745 TTTTTCATGATTTTTGGCAGAAAGACTGCTTTAAATATCTATATTCATCAAACCAAATCTCAGCC
1 TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAACCAAATCTCAGCC
* * * *
28810 ACAATGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCTTGTTTCGATTTAATTAGAAATGAA
66 ACACTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA-AAATTAA
* * * * * ** * * *
28875 TTCGGAAAAAAAAATGAAAAAATGATGTTATAAGCGTG-AAAGCCCAT-TAATCCATTTAGCGTC
130 TTCGG-AAAAAAATTG-AAAAACGAT-ATATAAGCGTGAAAAGCCCGTCAAAT-TTTTTGGTGTT
* * * * * * * * *
28938 AAATTATGTATTTTTTCTGAGTATTGA-GGCAAAAAATTGATAAAAAGA-TTTTCGGGATCAGTT
191 AAATTATATATATTTTATGAGTATT-ATGACAAAAAATTGAAAAAAAAACTTCTCGAG-TCAGCT
* * * * ** * * * *
29001 TTTAGCCAAAATCGTGTACAAACCATTACTCTTTTTAGAATAAAAACACGTTT--TGG----GAC
254 TTTAGTCGAAATCGTGTACTAACCATCACAATTTTT-GACTAAAAACGCGTTTCGAGGCCCCGGC
* * * * * * * * ** *
29060 TCAATTTTGCATGATTTTTGGCGGAAACACTCCTTTAAATATTTATATTCATAAAACTAAATCTC
318 TTAGTTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTC
** * ** *
29125 ATTCACAATGGATTTAAGGATTTGTTTTTACTAGC-ATCTGAATCTTGTTCCGATTTAATTAGAA
383 AGCCACATTGGATTTAAGGATTTGTTTTTAAGAGCAATCTGAATCTTGTTTCGATTTAATTAGAA
** * * * * * * * *
29189 ATTAATT-AGGAAAAAAAAGGGAAAACGATATTATAGGCGTGAAAAACTCATCAATATATTTAGC
448 ATTAATTCA-GAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGC
* * *
29253 GTTAAATTA-AGTATTTTTTCTGAGTATTGTGGCAAAATATTGAGAAAAAAATTTTCGGGTCAGT
512 GTTAAATTATA-TA-TTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGT
* * * * * *
29317 TTTTAGCCAAAATTGTGTACTAACCATCACTATTTTTGGACTAAAAACGCGTTACG-GGACCCTG
575 TTTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGG-CTAAAAAC-CTTTTCGAGGACCCCG
* *
29381 ACTCAA
638 ACTTAG
* * * * *
29387 TTTTCCATGATTTTTGG-AAGAAAGACTCCTTGAAATATTTATATTCATCAAACCAAATCGCAGC
1 TTTTGCATGATTTTTGGCAA-AAAGACTTCTTGAAATATATATATTCATCTAACCAAATCTCAGC
* * * * *
29451 CACATTGGATTTAAGGATTGGTTTTTACAAGCATCTAAATTTTGTTTCGATTTGATTAGAAATTA
65 CACACTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTA-AAATTA
* * * * * * *
29516 TTTCGG-AAAAAACTGAAAAACGATATTAGAAGCGTGAAAAACCCGT-TAATCTTTTTGCTATTA
129 ATTCGGAAAAAAATTGAAAAACGATA-TATAAGCGTGAAAAGCCCGTCAAAT-TTTTTGGTGTTA
* * * * * * * * *
29579 AATTATATAT-TTTTTTGAGTATTGTGGCAAAAGATT-TAGAAAAAACTTTTCGGGTCAGTTTTT
192 AATTATATATATTTTATGAGTATTATGACAAAAAATTGAAAAAAAAACTTCTCGAGTCAGCTTTT
* * * * * *
29642 AG-CTGAAATCGTGTACTAACAATCACGATTTTTGACTAAAAACGCGTTTCG-GGACCCTGATAC
257 AGTC-GAAATCGTGTACTAACCATCACAATTTTTGACTAAAAACGCGTTTCGAGGCCCCGGCT-T
* * * * * **
29705 AATTTTGCAAGATTTTTGGCAGAAAGACTCCTTTAAATATCAATATTCATCAAACCAAATCTCAG
320 AGTTTTGCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAG
* * * *
29770 TCACATTGGATTTAAGGGTTTGATTTTACA-AGC-ATCTGAATCTTGATTCGATTTAATTAGAAA
385 CCACATTGGATTTAAGGATTTGTTTTTA-AGAGCAATCTGAATCTTGTTTCGATTTAATTAGAAA
* * * *
29833 TTAATTTC-G-AAAAAATTAAAAAACGATATTAGAAGCGTGAAAAGTCCATCAATCTATTTAGCG
449 TTAA-TTCAGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCG
* * * * * *
29896 TTAAATTATGA-ATTTTCTCTGAGTATTGTGGAAAAAAATTGAGATAAAATTTTTCGAGTTAGTT
513 TTAAATTAT-ATATTTT-TCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTT
* *
29960 TTTAGCCGAAATCGTGTACTAACCATCACTATTTTTGGCAAAAAA
576 TTTAGCCGAAATCGTGTACTAACCATCACTGTTTTTGGCTAAAAA
30005 ATTGAGAAAT
Statistics
Matches: 2808, Mismatches: 326, Indels: 139
0.86 0.10 0.04
Matches are distributed among these distances:
637 15 0.01
638 41 0.01
639 55 0.02
640 35 0.01
641 193 0.07
642 822 0.29
643 481 0.17
644 66 0.02
645 19 0.01
646 292 0.10
647 187 0.07
648 55 0.02
649 42 0.01
650 45 0.02
651 18 0.01
652 7 0.00
653 67 0.02
654 12 0.00
655 33 0.01
656 137 0.05
657 47 0.02
658 137 0.05
659 2 0.00
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.35
Consensus pattern (643 bp):
TTTTGCATGATTTTTGGCAAAAAGACTTCTTGAAATATATATATTCATCTAACCAAATCTCAGCC
ACACTGGATTTAAGGATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAAAATTAAT
TCGGAAAAAAATTGAAAAACGATATATAAGCGTGAAAAGCCCGTCAAATTTTTTGGTGTTAAATT
ATATATATTTTATGAGTATTATGACAAAAAATTGAAAAAAAAACTTCTCGAGTCAGCTTTTAGTC
GAAATCGTGTACTAACCATCACAATTTTTGACTAAAAACGCGTTTCGAGGCCCCGGCTTAGTTTT
GCACGACTTTTGGCAGAAAGACTCCTTGAAATATCTATATTCATGTAACCAAATCTCAGCCACAT
TGGATTTAAGGATTTGTTTTTAAGAGCAATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTC
AGAAAAAAATTGAAAAACGATATTAGAAGCGTGAAAAGCCCATCAATCTTTTTGGCGTTAAATTA
TATATTTTTCTGAGTATTGTAGCAAAAAATTGAGAAAAAACTTTTCGGGTCAGTTTTTAGCCGAA
ATCGTGTACTAACCATCACTGTTTTTGGCTAAAAACCTTTTCGAGGACCCCGACTTAG
Found at i:30010 original size:72 final size:72
Alignment explanation
Indices: 29927--30060 Score: 189
Period size: 72 Copynumber: 1.9 Consensus size: 72
29917 AGTATTGTGG
* * * *
29927 AAAAAAATTGAGATAA-AATTTTTCGAGTTAGTTTTTAGCCGAAATCGTGTACTAACCATCACTA
1 AAAAAAATTGAGA-AATAACTATTCGAGTCAGTTTTTAGCAGAAATCGTGTACTAACCATCACTA
29991 TTTTTGGC
65 TTTTTGGC
* * *
29999 AAAAAAATTGAGAAATACCTATTCGGGTCAGTTTTTAGTAGAAATCGTGTACTAACCATCAC
1 AAAAAAATTGAGAAATAACTATTCGAGTCAGTTTTTAGCAGAAATCGTGTACTAACCATCAC
30061 GGTTTTTGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
71 2 0.04
72 52 0.96
ACGTcount: A:0.37, C:0.15, G:0.16, T:0.33
Consensus pattern (72 bp):
AAAAAAATTGAGAAATAACTATTCGAGTCAGTTTTTAGCAGAAATCGTGTACTAACCATCACTAT
TTTTGGC
Done.