Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015141.1 Corchorus capsularis cultivar CVL-1 contig15162, 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: 41151
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--27 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1 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
28 TATGAGTATT
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:859 original size:328 final size:329
Alignment explanation
Indices: 152--959 Score: 936
Period size: 328 Copynumber: 2.4 Consensus size: 329
142 GACTCAGTCT
* *
152 CATTGGATTTAAGGGTTTGTTTTTACGAGCATCTC-AATCCGATTTCGATTTAATTAGAAATTAA
1 CATTGGATTTAAGGATTTGTTTTTACGAGCATC-CGAATCTG-TTTCGATTTAATTAGAAATTAA
* * * * *
216 TTCAGAAAAATATGAAAAAGACGATATTAGATGCGTGAAAAGCCTTTCAAT-TTTTTCTGCGTTG
64 TTCGGAAAAA-AAGGAAAA-ACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTT-GGCGTTG
* * * * *
280 AGTTATATAT-TTTTTATGAGTATTGTGCCCAAAAATTGAGAAGAAATTTTTTTGGGTCAATTTT
126 A-TTATATATATTTTTATGAGTATCGTGACCAAAAATTGAGAAGAAATTTTTATGAGTAAATTTT
* * **
344 TGCAAAATTTTGGCCGAAATCGTGTACTAACCATCACGATTTTTGACTAAAAACGCATTCCGGCG
190 TGCAAAATTTTGACCGAAATC-TGTACTAACCATCACGATTTTTGACTAAAAACACATTCCGAAG
** * * * * * * * *
409 TCCCTACTCTGTTTTGCATGGTTTTTTACGCTAAGTCTATTGAAATATCTATATTCATCTAACCA
254 TCCAGACTCAGTTTTGCATGATTTTTGACACCAAGACTATTGAAAAATCTATATTCATCAAACCA
*
474 AATCTCACCCA
319 AATCACACCCA
*
485 CATTGGATTTAAGGATTTGTTTTTACGAGCATCTGAATCATGTTTCG-TTTCAATTAGAAATTAA
1 CATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAATC-TGTTTCGATTT-AATTAGAAATTAA
*
549 TTCGGAAAAAAAGG-AAAACATATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGCA
64 TTCGGAAAAAAAGGAAAAAC-GATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTG-A
* *
613 TTATATATATTTTTATGATTATCGTGACCAAAAATTGAGGA-AAATTCTTTATGAGTAAATTTTT
127 TTATATATATTTTTATGAGTATCGTGACCAAAAATTGAGAAGAAATT-TTTATGAGTAAATTTTT
* * * *
677 GCAAAATTTT-ACCGAAAT-TGT-GT-ACCATCACGGTTTTTGGCTAAAAACACGTTCCGAAGTC
191 GCAAAATTTTGACCGAAATCTGTACTAACCATCACGATTTTTGACTAAAAACACATTCCGAAGTC
* *
738 CAGACTCAGTTTTGCATGATTTTTGGCACCAAGACTCCTTGAAAAATCTATATTCATCAAACCAA
256 CAGACTCAGTTTTGCATGATTTTTGACACCAAGACT-ATTGAAAAATCTATATTCATCAAACCAA
*
803 ATCACATCCA
320 ATCACACCCA
* * * *
813 TATTGAATTTACGGATTTGTTTTTACGAGCATCCGAATCTTGTTTCGATTTAATTAGATATTAAT
1 CATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAATC-TGTTTCGATTTAATTAGAAATTAAT
* * * * * **
878 TAAGAAAAAAATATGAAAAACGATATTATAAGCGTGAAAAGCCCTTCAATCTTTTTGGCACTGAA
65 T-CGGAAAAAA-AGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTG-A
*
943 TTATGTATA-TTTTATGA
127 TTATATATATTTTTATGA
960 CTATTGTGGC
Statistics
Matches: 408, Mismatches: 54, Indels: 30
0.83 0.11 0.06
Matches are distributed among these distances:
327 59 0.14
328 90 0.22
329 21 0.05
330 50 0.12
331 61 0.15
332 63 0.15
333 63 0.15
334 1 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.37
Consensus pattern (329 bp):
CATTGGATTTAAGGATTTGTTTTTACGAGCATCCGAATCTGTTTCGATTTAATTAGAAATTAATT
CGGAAAAAAAGGAAAAACGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGATTAT
ATATATTTTTATGAGTATCGTGACCAAAAATTGAGAAGAAATTTTTATGAGTAAATTTTTGCAAA
ATTTTGACCGAAATCTGTACTAACCATCACGATTTTTGACTAAAAACACATTCCGAAGTCCAGAC
TCAGTTTTGCATGATTTTTGACACCAAGACTATTGAAAAATCTATATTCATCAAACCAAATCACA
CCCA
Found at i:3373 original size:330 final size:328
Alignment explanation
Indices: 2655--3986 Score: 1251
Period size: 330 Copynumber: 4.0 Consensus size: 328
2645 CTGAAACTTG
* * ** *
2655 TTTTGGCTAAAAACGCGTTCCGGGACCATGGTTCAGTTTTGCATGATTTTT-GACGTCAAG-ACT
1 TTTTGACTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTGGAC-TCAAGTACT
* * ** * *
2718 CATTGTAATATCTATATTCGTCTAATGAAATCTCAGCCACATTGGATTTAAGATTTATTTTTACG
65 CATTGAAATATCTATATTCATCTAAACAAATCTCACCCACATTGGATTTAAGATTTGTTTTTACG
* * * * *
2783 AGCATCTCAATCCGGTTTCGATTTAATTATAAATTAATTCGGAATAAAATAGG-AAATTGATATA
130 AGCATCTGAATCAGGTTTCGATTTAATTAGAAATTAATTCGG-A-AAAATAGGAAAATCGATATT
* ** ** *
2847 AAAAGCGTGAGAAGCCCTTCAATTTTTTTGTTGTTGCGTTATATATTTTTTATTATTATTGTGAG
193 AGAAGCGTGAGAAGCCCTTCAA-TTTTTTGGCGTTGAATTATATA---TTT-TTATGA--GT-A-
* * * * * *
2912 TTTGTGACCCAAAATTGAGGAGAAATTTTTCGGGTCAATTTTTGC-AAAATTTTGCCGAAATCGT
249 -TTGTGGCCAAAAATTGAGGAGAAATCTTTCAGGTAAATTTTTGCAAAAATTTAGCCGAAATCGT
*
2976 GTACTAACCATCACAGT
313 GTACT-ACCATCACGGT
* ** ** * *
2993 TTTTTACTAAAAATGCGTT-TTGGAGTCCCGGCTCTGTTTTGCATGATTTTTGGCACT-AAGTA-
1 TTTTGACTAAAAACACGTTCCGGGA-CCCCGGCTCAGTTTTGCATGATTTTTGG-ACTCAAGTAC
* * * *
3055 TCGTTGAAATATCTATATCCATCTAAACAAATCTTACCCACATTGGATTTAATGATTTGTTGTTA
64 TCATTGAAATATCTATATTCATCTAAACAAATCTCACCCACATTGGATTTAA-GATTTGTTTTTA
* * *
3120 CGAGCATCTGAA-CTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAAAACCGATAT
128 CGAGCATCTGAATC-AGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAATCGATAT
* * ** *
3184 TAGAAGCGTGA-ATAGCCTTTCAATATTTTGGTTTTGAATTATATATTTCTTATGAGTATCGTGG
192 TAGAAGCGTGAGA-AGCCCTTCAATTTTTTGGCGTTGAATTATATATTT-TTATGAGTATTGTGG
* * *
3248 CCGAAAATTGA-GA-AATACTCTTTCAGGTAAATTTTTACAAAAATTTAGGCGAAATCGTGTACT
255 CCAAAAATTGAGGAGAA-A-TCTTTCAGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACT
3311 ACCTATCACGGT
318 ACC-ATCACGGT
* * * * *
3323 TTTTGGCTAAAAACACGTTCTGGGACCCCGGCTCACTTTTGCACGATTTTTGGCAC-CAA-AACT
1 TTTTGACTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTGG-ACTCAAGTACT
* ** * *
3386 CATTGAAATATCTTTATTCATCTAATA-AAATCTCAAACAAATTGGATTTAAGGTTTTGTTTTTA
65 CATTGAAATATCTATATTCATCTAA-ACAAATCTCACCCACATTGGATTTAA-GATTTGTTTTTA
* * * * *
3450 CGAGCATCTGAATCCGGTTTCGATTAAATTAGAAATTACTTTGGAAAAATAGGAAAAACGATATT
128 CGAGCATCTGAATCAGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAATCGATATT
*
3515 AGAAGCGTGAGAAGCCCTTCAATCTTTTTTGGCGTTGAGTTATATATATATTTATGAGTATTGTG
193 AGAAGCGTGAGAAGCCCTTCAA--TTTTTTGGCGTTGAATTATATAT-T-TTTATGAGTATTGTG
* * * *
3580 GCCAAAAATTGAGGAGAAATGTTTCCATGTCAATTTTTGCAAAATTTTAGCCGAAATC--G---T
254 GCCAAAAATTGAGGAGAAATCTTT-CAGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACT
3640 --CA-CA--GT
318 ACCATCACGGT
* * * **
3646 TTTTTACTAAAAACACGTTCCGGGATCCCGGCTCTGTTTTGCATGATTTTTGGTGTCAAGT-CTC
1 TTTTGACTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTGGACTCAAGTACTC
* * ** *
3710 ATTGAAACATTTATATTTGTCTAAACAAATCCCACCCACATTGGATTTAAGAATTTTGTTTTTAC
66 ATTGAAATATCTATATTCATCTAAACAAATCTCACCCACATTGGATTTAAG-A-TTTGTTTTTAC
* * * * * *
3775 GAGCATCTGAATCATGTTTCGATTTAAATAAAAAAAGTAATTCGGGAAAATAGGAAAATTGATAT
129 GAGCATCTGAATCAGGTTTCGATTT-AAT-TAGAAATTAATTCGGAAAAATAGGAAAATCGATAT
* *
3840 TAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTA-TGATG
192 TAGAAGCGTGAGAAGCCCTTCAAT-TTTTTGGCGTTGAATTATATA-TTTTTATGAGTATTG-TG
* * * * * *
3904 GCCAAAAATTTAGGA-AAATTCTTTCAAGTAAATTTTTGTAAAATTTTAGTCGAAATCATGTACA
254 GCCAAAAATTGAGGAGAAA-TCTTTCAGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTAC-
*
3968 AACCATCACGGT
317 TACCATCACGGT
3980 TTTTGAC
1 TTTTGAC
3987 AACGAAGCAC
Statistics
Matches: 818, Mismatches: 129, Indels: 98
0.78 0.12 0.09
Matches are distributed among these distances:
322 2 0.00
323 127 0.16
324 64 0.08
325 27 0.03
326 50 0.06
327 3 0.00
328 3 0.00
329 35 0.04
330 201 0.25
331 10 0.01
332 24 0.03
333 29 0.04
334 48 0.06
335 2 0.00
337 29 0.04
338 112 0.14
339 50 0.06
340 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (328 bp):
TTTTGACTAAAAACACGTTCCGGGACCCCGGCTCAGTTTTGCATGATTTTTGGACTCAAGTACTC
ATTGAAATATCTATATTCATCTAAACAAATCTCACCCACATTGGATTTAAGATTTGTTTTTACGA
GCATCTGAATCAGGTTTCGATTTAATTAGAAATTAATTCGGAAAAATAGGAAAATCGATATTAGA
AGCGTGAGAAGCCCTTCAATTTTTTGGCGTTGAATTATATATTTTTATGAGTATTGTGGCCAAAA
ATTGAGGAGAAATCTTTCAGGTAAATTTTTGCAAAAATTTAGCCGAAATCGTGTACTACCATCAC
GGT
Found at i:3950 original size:668 final size:655
Alignment explanation
Indices: 2655--3984 Score: 1601
Period size: 668 Copynumber: 2.0 Consensus size: 655
2645 CTGAAACTTG
* * * * * ** *
2655 TTTTGGCTAAAAACGCGTTCCGGGACCATGGTTCAGTTTTGCATGATTTTTGACGTCAAGACTCA
1 TTTTGGCTAAAAACACGTTCCGGGACCACGGCTCACTTTTGCACGATTTTTGACACCAAAACTCA
* * * ** *
2720 TTGTAATATCTATATTCGTCTAATGAAATCTCAGCCACATTGGATTTAAGATTTATTTTTACGAG
66 TTGAAATATCTATATTCATCTAATAAAATCTCAAACAAATTGGATTTAAGATTTATTTTTACGAG
* * **
2785 CATCTCAATCCGGTTTCGATTTAATTATAAATTAATTCGGAATAAAATAGGAAATTGATATAAAA
131 CATCTCAATCCGGTTTCGATTAAATTAGAAATTAATTCGGAATAAAATAGGAAAACGATATAAAA
** * *
2850 AGCGTGAGAAGCCCTTCAATTTTTTTGTTGTTGCGTTATATATTTTTTATTATTATTGTGAGTTT
196 AGCGTGAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATA----TTATTATTATTATGAGTTT
* * *
2915 GTGACCCAAAATTGAGGAGAAATTTTTCGGGTCAATTTTTGCAAAATTTTGCCGAAATCGTGTAC
257 GTGACCAAAAATTGAGGAGAAATTTTCCAGGTCAATTTTTGCAAAATTTTGCCGAAATCG-G---
** **
2980 TAACCATCACAGTTTTTTACTAAAAATGCGTTTTGGAGTCCCGGCTCTGTTTTGCATGATTTTTG
318 -----ATCACAGTTTTTTACTAAAAACACGTTCGGGAGTCCCGGCTCTGTTTTGCATGATTTTTG
* * **
3045 GCACTAAGTATCGTTGAAATATCTATATCCATCTAAACAAATCTTACCCACATTGGATTTAATGA
378 GCACTAAGTATCATTGAAACATCTATATCCATCTAAACAAATCCCACCCACATTGGATTTAATGA
* * *
3110 TTTGTTGTTACGAGCATCTGAACTATGTTTCGATTTAATTAGAAATTAATTCAGAAAAATAGGAA
443 TTTGTTGTTACGAGCATCTGAACTATGTTTCGATTTAATAAAAAAGTAATTCAGAAAAATAGGAA
* **
3175 AACCGATATTAGAAGCGTGAATAGCCTTTCAATATTTTGGTTTTGAATTATATATTTCTTATGAG
508 AACCGATATTAGAAGCGTGAAAAGCCTTTCAATATTTTGGCGTTGAATTATATATTTCTTATGAG
*
3240 TATCGTGGCCGAAAATTGAGAAATACTCTTTCAGGTAAATTTTTACAAAAATTTAGGCGAAATCG
573 TATCGTGGCCAAAAATTGAGAAATACTCTTTCAGGTAAATTTTTACAAAAATTTAGGCGAAATCG
3305 TGTACTACCTATCACGGT
638 TGTACTACCTATCACGGT
* * *
3323 TTTTGGCTAAAAACACGTTCTGGGACCCCGGCTCACTTTTGCACGATTTTTGGCACCAAAACTCA
1 TTTTGGCTAAAAACACGTTCCGGGACCACGGCTCACTTTTGCACGATTTTTGACACCAAAACTCA
* * *
3388 TTGAAATATCTTTATTCATCTAATAAAATCTCAAACAAATTGGATTTAAGGTTTTGTTTTTACGA
66 TTGAAATATCTATATTCATCTAATAAAATCTCAAACAAATTGGATTTAA-GATTTATTTTTACGA
* * * *
3453 GCATCTGAATCCGGTTTCGATTAAATTAGAAATTACTTTGG-A-AAAATAGGAAAAACGATATTA
130 GCATCTCAATCCGGTTTCGATTAAATTAGAAATTAATTCGGAATAAAATAGG-AAAACGATATAA
*
3516 GAAGCGTGAGAAGCCCTTCAATCTTTTTTGGCGTTGAGTTATATA-TA-TA-T-TTATGAGTATT
194 AAAGCGTGAGAAGCCCTTCAAT-TTTTTTGGCGTTGAGTTATATATTATTATTATTATGAGT-TT
* *
3577 GTGGCCAAAAATTGAGGAGAAATGTTTCCATGTCAATTTTTGCAAAATTTTAGCCGAAATC-G-T
257 GTGACCAAAAATTGAGGAGAAAT-TTTCCAGGTCAATTTTTGCAAAATTTT-GCCGAAATCGGAT
**
3640 CACAGTTTTTTACTAAAAACACGTTCCGGGA-TCCCGGCTCTGTTTTGCATGATTTTTGG-TGTC
320 CACAGTTTTTTACTAAAAACACGTT-CGGGAGTCCCGGCTCTGTTTTGCATGATTTTTGGCACT-
* * ***
3703 AAGTCTCATTGAAACATTTATATTTGTCTAAACAAATCCCACCCACATTGGATTTAA-GAATTTT
383 AAGTATCATTGAAACATCTATATCCATCTAAACAAATCCCACCCACATTGGATTTAATG-A-TTT
* * *
3767 GTTTTTACGAGCATCTGAA-TCATGTTTCGATTTAAATAAAAAAAGTAATTCGGGAAAATAGGAA
446 GTTGTTACGAGCATCTGAACT-ATGTTTCGATTT-AAT-AAAAAAGTAATTCAGAAAAATAGGAA
** * *
3831 AATTGATATTAGAAGCGTGAAAAGCCTTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGA
508 AACCGATATTAGAAGCGTGAAAAGCCTTTCAAT-ATTTTGGCGTTGAATTATATATTTCTTATGA
* * * ** * *
3896 GTAT-GATGGCCAAAAATTTAGGAAA-ATTCTTTCAAGTAAATTTTTGTAAAATTTTAGTCGAAA
572 GTATCG-TGGCCAAAAATTGA-GAAATACTCTTTCAGGTAAATTTTTACAAAAATTTAGGCGAAA
* *
3959 TCATGTACAAACC-ATCACGGT
635 TCGTGTAC-TACCTATCACGGT
3980 TTTTG
1 TTTTG
3985 ACAACGAAGC
Statistics
Matches: 569, Mismatches: 76, Indels: 45
0.82 0.11 0.07
Matches are distributed among these distances:
652 2 0.00
653 102 0.18
654 36 0.06
655 3 0.01
656 52 0.09
657 95 0.17
658 7 0.01
661 7 0.01
662 25 0.04
663 26 0.05
664 11 0.02
667 8 0.01
668 127 0.22
669 68 0.12
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.37
Consensus pattern (655 bp):
TTTTGGCTAAAAACACGTTCCGGGACCACGGCTCACTTTTGCACGATTTTTGACACCAAAACTCA
TTGAAATATCTATATTCATCTAATAAAATCTCAAACAAATTGGATTTAAGATTTATTTTTACGAG
CATCTCAATCCGGTTTCGATTAAATTAGAAATTAATTCGGAATAAAATAGGAAAACGATATAAAA
AGCGTGAGAAGCCCTTCAATTTTTTTGGCGTTGAGTTATATATTATTATTATTATGAGTTTGTGA
CCAAAAATTGAGGAGAAATTTTCCAGGTCAATTTTTGCAAAATTTTGCCGAAATCGGATCACAGT
TTTTTACTAAAAACACGTTCGGGAGTCCCGGCTCTGTTTTGCATGATTTTTGGCACTAAGTATCA
TTGAAACATCTATATCCATCTAAACAAATCCCACCCACATTGGATTTAATGATTTGTTGTTACGA
GCATCTGAACTATGTTTCGATTTAATAAAAAAGTAATTCAGAAAAATAGGAAAACCGATATTAGA
AGCGTGAAAAGCCTTTCAATATTTTGGCGTTGAATTATATATTTCTTATGAGTATCGTGGCCAAA
AATTGAGAAATACTCTTTCAGGTAAATTTTTACAAAAATTTAGGCGAAATCGTGTACTACCTATC
ACGGT
Found at i:4238 original size:11 final size:11
Alignment explanation
Indices: 4222--4247 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
4212 GCGTTCGGCC
4222 ACGTGCAATGT
1 ACGTGCAATGT
4233 ACGTGCAATGT
1 ACGTGCAATGT
4244 ACGT
1 ACGT
4248 AAAAATGAAT
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:0.27, C:0.19, G:0.27, T:0.27
Consensus pattern (11 bp):
ACGTGCAATGT
Found at i:4465 original size:2 final size:2
Alignment explanation
Indices: 4458--4493 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
4448 AGGCCATGGA
4458 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4494 CACTAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14311 original size:7 final size:7
Alignment explanation
Indices: 14295--14328 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
14285 AATGGTTGGG
14295 CATGTTT
1 CATGTTT
*
14302 CATATTT
1 CATGTTT
*
14309 CATGTCT
1 CATGTTT
14316 CATGTTT
1 CATGTTT
14323 CATGTT
1 CATGTT
14329 GTAGATATAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.12, T:0.53
Consensus pattern (7 bp):
CATGTTT
Found at i:22406 original size:27 final size:27
Alignment explanation
Indices: 22376--22432 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
22366 CATTGTTTAA
22376 TTTAT-ATTAA-ATTTTTCTTTTTACTTT
1 TTTATGATTAAGA-TTTT-TTTTTACTTT
* *
22403 TTTATGCTTAAGATTTTTTTTTATTTT
1 TTTATGATTAAGATTTTTTTTTACTTT
22430 TTT
1 TTT
22433 TTTGCACATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
27 17 0.65
28 8 0.31
29 1 0.04
ACGTcount: A:0.19, C:0.05, G:0.04, T:0.72
Consensus pattern (27 bp):
TTTATGATTAAGATTTTTTTTTACTTT
Found at i:36023 original size:90 final size:90
Alignment explanation
Indices: 35869--36047 Score: 250
Period size: 90 Copynumber: 2.0 Consensus size: 90
35859 ACCGGAGGAC
* * * * * *
35869 AAAACAGGAAAGAAAAACGGAGAATCAAAGTCAAGTGGCTGAGTCTCGGCATCAGTGTTTGGATT
1 AAAACAGAAAAGAAAAACGCAGAATCAAAGTCAAGAGGCTGAGTCTCGGCATCAGCGCTCGGATT
* *
35934 CTTCTCAGAAGGTTTACTTTCGCCA
66 CTTCTCAAAAGGTTTAATTTCGCCA
* * *
35959 AAAACAGAAAAGGAAAACTCAGAATCAAAGTCAAGAGGCTGAGTCTCGGCATCGGCGCTCGGATT
1 AAAACAGAAAAGAAAAACGCAGAATCAAAGTCAAGAGGCTGAGTCTCGGCATCAGCGCTCGGATT
*
36024 GTTCTCAAAAGGTTTAATTTCGCC
66 CTTCTCAAAAGGTTTAATTTCGCC
36048 CTTGTCGTCT
Statistics
Matches: 77, Mismatches: 12, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
90 77 1.00
ACGTcount: A:0.34, C:0.19, G:0.24, T:0.23
Consensus pattern (90 bp):
AAAACAGAAAAGAAAAACGCAGAATCAAAGTCAAGAGGCTGAGTCTCGGCATCAGCGCTCGGATT
CTTCTCAAAAGGTTTAATTTCGCCA
Found at i:37522 original size:23 final size:23
Alignment explanation
Indices: 37496--37572 Score: 75
Period size: 23 Copynumber: 3.2 Consensus size: 23
37486 AACATTTCAG
37496 TGATTTTCTTTTTATAATATGAA
1 TGATTTTCTTTTTATAATATGAA
* * * *
37519 TGATTATTATTTGATTA-ACATTTCAG
1 TGATT-TTCTTT--TTATA-ATATGAA
37545 TGATTTTCTTTTTATAATATGAA
1 TGATTTTCTTTTTATAATATGAA
37568 TGATT
1 TGATT
37573 ATTATTTGAT
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
23 17 0.41
24 6 0.15
25 6 0.15
26 12 0.29
ACGTcount: A:0.30, C:0.05, G:0.10, T:0.55
Consensus pattern (23 bp):
TGATTTTCTTTTTATAATATGAA
Found at i:37558 original size:49 final size:49
Alignment explanation
Indices: 37486--37585 Score: 200
Period size: 49 Copynumber: 2.0 Consensus size: 49
37476 AGCTTTCCTA
37486 AACATTTCAGTGATTTTCTTTTTATAATATGAATGATTATTATTTGATT
1 AACATTTCAGTGATTTTCTTTTTATAATATGAATGATTATTATTTGATT
37535 AACATTTCAGTGATTTTCTTTTTATAATATGAATGATTATTATTTGATT
1 AACATTTCAGTGATTTTCTTTTTATAATATGAATGATTATTATTTGATT
37584 AA
1 AA
37586 TTATTGCAAA
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 51 1.00
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (49 bp):
AACATTTCAGTGATTTTCTTTTTATAATATGAATGATTATTATTTGATT
Done.