Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013126.1 Corchorus capsularis cultivar CVL-1 contig13147, 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: 17741
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Found at i:75 original size:2 final size:2
Alignment explanation
Indices: 68--107 Score: 53
Period size: 2 Copynumber: 19.5 Consensus size: 2
58 AATTATCCAA
* *
68 AT AT AT AT AT AT AT AT AT AT CT AT AT TT AT ACT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT A
108 AAAGTACGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3554 original size:2 final size:2
Alignment explanation
Indices: 3547--3579 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3537 TTTTATTTAC
3547 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 T
3580 GACTTCTTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4792 original size:59 final size:59
Alignment explanation
Indices: 4695--4813 Score: 211
Period size: 59 Copynumber: 2.0 Consensus size: 59
4685 GTGTACGGGT
* *
4695 ATTCCTGTGCGTTTGTAATCCCAATTTCTTCAAGAAATGAAAATGATTATTATCTTAAA
1 ATTCATGTGCGTTTGTAATCCCAATTTCTTCAAGAAATGAAAATGATTATTATCTCAAA
*
4754 ATTCATGTGCGTTTGTAATCCCAATTTCTTCAAGAAATGAAAATGATTTTTATCTCAAA
1 ATTCATGTGCGTTTGTAATCCCAATTTCTTCAAGAAATGAAAATGATTATTATCTCAAA
4813 A
1 A
4814 AAAATAAAAA
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.34, C:0.15, G:0.12, T:0.39
Consensus pattern (59 bp):
ATTCATGTGCGTTTGTAATCCCAATTTCTTCAAGAAATGAAAATGATTATTATCTCAAA
Found at i:14513 original size:40 final size:38
Alignment explanation
Indices: 14468--14588 Score: 105
Period size: 40 Copynumber: 3.3 Consensus size: 38
14458 AATTCAGGGT
14468 AATTAAGAAAGGAAAGTACAATCAAGGTCCTATGTTGGAC
1 AATTAAGAAAGGAAAGTAC-ATCAAGGTCCTA-GTTGGAC
* * * *
14508 AATTAAGAAAAGTAAAGT-C-TTAA--TTC-AG--GG-T
1 AATTAAG-AAAGGAAAGTACATCAAGGTCCTAGTTGGAC
14539 AATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTGGAC
1 AATTAAGAAAGGAAAGTACA-TCAAGGTCCT-AGTTGGAC
14579 AATTAAGAAA
1 AATTAAGAAA
14589 AGTAAAGTCT
Statistics
Matches: 62, Mismatches: 8, Indels: 22
0.67 0.09 0.24
Matches are distributed among these distances:
30 9 0.15
31 8 0.13
32 2 0.03
33 3 0.05
34 1 0.02
35 3 0.05
36 2 0.03
37 2 0.03
38 3 0.05
39 2 0.03
40 18 0.29
41 9 0.15
ACGTcount: A:0.45, C:0.10, G:0.21, T:0.23
Consensus pattern (38 bp):
AATTAAGAAAGGAAAGTACATCAAGGTCCTAGTTGGAC
Found at i:14521 original size:71 final size:71
Alignment explanation
Indices: 14439--14709 Score: 404
Period size: 71 Copynumber: 3.8 Consensus size: 71
14429 GATTAAGGGA
* * *
14439 AATTAAG--AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAATCAAGGTCCTATG
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAG
14502 TTGGAC
66 TTGGAC
*
14508 AATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAG
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAG
14573 TTGGAC
66 TTGGAC
*
14579 AATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTGCAGTCAAGGTCCTAAG
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAG
*
14644 TTGGGC
66 TTGGAC
** * * * *
14650 -AGCAAGGAAGAGTAAAGTCTTAATTCAGGCTAATTAAGAAAAGAAGGTATAGTCAAGGTC
1 AATTAA-GAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTC
14710 ATAATTTAGA
Statistics
Matches: 187, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
69 7 0.04
70 3 0.02
71 177 0.95
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.24
Consensus pattern (71 bp):
AATTAAGAAAAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAG
TTGGAC
Found at i:14546 original size:31 final size:31
Alignment explanation
Indices: 14508--14626 Score: 98
Period size: 31 Copynumber: 3.6 Consensus size: 31
14498 TATGTTGGAC
14508 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
* * * *
14539 AATTAAG-AAAGGAAAGTACAGTCAAGGTCCTAAGTTGGAC
1 AATTAAGAAAAGTAAAGT-C--TTAA--T--TCAG--GG-T
14579 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
1 AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
14610 AATTAAGAAAAG-AAAGT
1 AATTAAGAAAAGTAAAGT
14627 GCAGTCAAGG
Statistics
Matches: 69, Mismatches: 8, Indels: 23
0.69 0.08 0.23
Matches are distributed among these distances:
30 14 0.20
31 20 0.29
32 2 0.03
33 3 0.04
34 3 0.04
35 1 0.01
36 1 0.01
37 3 0.04
38 3 0.04
39 2 0.03
40 8 0.12
41 9 0.13
ACGTcount: A:0.47, C:0.08, G:0.21, T:0.24
Consensus pattern (31 bp):
AATTAAGAAAAGTAAAGTCTTAATTCAGGGT
Found at i:14734 original size:71 final size:71
Alignment explanation
Indices: 14446--14761 Score: 400
Period size: 71 Copynumber: 4.5 Consensus size: 71
14436 GGAAATTAAG
* * *
14446 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAATCAAGGTCCTATGTTGGACAAT
1 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGACAAT
*
14511 TAAGAA
66 CAAGAA
*
14517 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAGGAAAGTACAGTCAAGGTCCTAAGTTGGACAAT
1 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGACAAT
*
14582 TAAGAA
66 CAAGAA
* * *
14588 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTGCAGTCAAGGTCCTAAGTTGGGC-AG
1 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGACAAT
14652 CAAGGAA
66 CAA-GAA
* * * * * * * *
14659 GAGTAAAGTCTTAATTCAGGCTAATTAAGAAAAGAAGGTATAGTCAAGGTCATAATTTAGATAAT
1 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGACAAT
*
14724 CAAGAT
66 CAAGAA
* * * * **
14730 GAGTAAAGTTTTCATCCAGGGCGATTAAGAAA
1 AAGTAAAGTCTTAATTCAGGGTAATTAAGAAA
14762 GTCAGATTAG
Statistics
Matches: 218, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
70 3 0.01
71 211 0.97
72 4 0.02
ACGTcount: A:0.42, C:0.10, G:0.23, T:0.25
Consensus pattern (71 bp):
AAGTAAAGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGGTCCTAAGTTGGACAAT
CAAGAA
Found at i:14859 original size:37 final size:37
Alignment explanation
Indices: 14806--14914 Score: 157
Period size: 37 Copynumber: 2.9 Consensus size: 37
14796 AAGAAAAGAG
*
14806 CAGTCAAAGAACTTAATTCTGGGTAATTAAGTAAACA
1 CAGTCAAAGAGCTTAATTCTGGGTAATTAAGTAAACA
* *
14843 CAGTTAAAGAGCTTAATTCAGGGTAATTAAGTAAACA
1 CAGTCAAAGAGCTTAATTCTGGGTAATTAAGTAAACA
* *
14880 CAGTCAAAGAGCTTAATT-TAAGGAAATTAAGTAAA
1 CAGTCAAAGAGCTTAATTCT-GGGTAATTAAGTAAA
14915 AGCAGTTAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.45, C:0.11, G:0.17, T:0.27
Consensus pattern (37 bp):
CAGTCAAAGAGCTTAATTCTGGGTAATTAAGTAAACA
Found at i:14940 original size:37 final size:38
Alignment explanation
Indices: 14830--14941 Score: 144
Period size: 37 Copynumber: 3.0 Consensus size: 38
14820 AATTCTGGGT
* *
14830 AATTAAGTAAACACAGTTAAAGAGCTTAA-TTCAGGGT
1 AATTAAGTAAACACAGTTAAAGAGCTTAATTTCAAGGA
*
14867 AATTAAGTAAACACAGTCAAAGAGCTTAATTT-AAGGA
1 AATTAAGTAAACACAGTTAAAGAGCTTAATTTCAAGGA
14904 AATTAAGTAAA-AGCAGTTAAAG-GAC-TAATTTCAAGGA
1 AATTAAGTAAACA-CAGTTAAAGAG-CTTAATTTCAAGGA
14941 A
1 A
14942 GGAAATTAGG
Statistics
Matches: 67, Mismatches: 4, Indels: 8
0.85 0.05 0.10
Matches are distributed among these distances:
36 8 0.12
37 57 0.85
38 2 0.03
ACGTcount: A:0.47, C:0.10, G:0.18, T:0.25
Consensus pattern (38 bp):
AATTAAGTAAACACAGTTAAAGAGCTTAATTTCAAGGA
Found at i:14974 original size:41 final size:41
Alignment explanation
Indices: 14929--15092 Score: 232
Period size: 41 Copynumber: 4.1 Consensus size: 41
14919 GTTAAAGGAC
14929 TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
1 TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
* * *
14970 TAA-TTC-AGG-A--TAATTAAGTAAAGTA-AAGCACATACT
1 TAATTTCAAGGAAGGAAATTAGGTAAAG-ACAAGCACAGACT
* *
15006 TAATTTCAAGGAAAGAAATTAGGTAAAGACAAGCATAGACT
1 TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
15047 TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
1 TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
15088 TAATT
1 TAATT
15093 CAGGGTAATT
Statistics
Matches: 107, Mismatches: 9, Indels: 14
0.82 0.07 0.11
Matches are distributed among these distances:
36 24 0.22
37 4 0.04
38 4 0.04
39 4 0.04
40 4 0.04
41 67 0.63
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (41 bp):
TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACT
Found at i:14988 original size:77 final size:75
Alignment explanation
Indices: 14891--15092 Score: 192
Period size: 77 Copynumber: 2.5 Consensus size: 75
14881 AGTCAAAGAG
* * *
14891 CTTAATTTAAGGAAATTAAGTAAA-AGCAGTTAAAGGAC-TAATTTCAAGGAAGGAAATTAGGTA
1 CTTAA-TTAAGGAAATTAAGTAAAGA-AAG-CAAA-GACTTAATTTCAAGGAAAGAAATTAGGTA
14954 AAGACAAGCACAGA
62 AAGACAAGCACAGA
* * *
14968 CTTAATTCAGGATAATTAAGTAAAGTAAAGCACATACTTAATTTCAAGGAAAGAAATTAGGTAAA
1 CTTAATTAAGGA-AATTAAGTAAAG-AAAGCAAAGACTTAATTTCAAGGAAAGAAATTAGGTAAA
*
15033 GACAAGCATAGA
64 GACAAGCACAGA
* *
15045 CTTAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATT
1 CTTAA-TT-----AAGGAAATTAAGTAAAGA-AAGCAAAGACTTAATT
15093 CAGGGTAATT
Statistics
Matches: 104, Mismatches: 10, Indels: 17
0.79 0.08 0.13
Matches are distributed among these distances:
76 8 0.08
77 60 0.58
78 4 0.04
79 1 0.01
81 1 0.01
82 26 0.25
83 4 0.04
ACGTcount: A:0.47, C:0.10, G:0.19, T:0.24
Consensus pattern (75 bp):
CTTAATTAAGGAAATTAAGTAAAGAAAGCAAAGACTTAATTTCAAGGAAAGAAATTAGGTAAAGA
CAAGCACAGA
Found at i:15109 original size:77 final size:75
Alignment explanation
Indices: 14929--15092 Score: 195
Period size: 77 Copynumber: 2.1 Consensus size: 75
14919 GTTAAAGGAC
*
14929 TAATTTCAAGGAAGGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGATAATTAAGTAAAGT
1 TAATTTCAAGG-A-GAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGAAAATTAAGTAAAGT
*
14994 AAAGCACATACT
64 AAAGCACAGACT
* *
15006 TAATTTCAAGGAAAGAAATTAGGTAAAGACAAGCATAGACTTAATTTCAAGGAAGGAAATTAGGT
1 TAATTTCAAGG--AGAAATTAGGTAAAGACAAGCACAGACTTAA-TTC-AGG-A--AAATTAAGT
15071 AAAG-ACAAGCACAGACT
59 AAAGTA-AAGCACAGACT
15088 TAATT
1 TAATT
15093 CAGGGTAATT
Statistics
Matches: 76, Mismatches: 4, Indels: 9
0.85 0.04 0.10
Matches are distributed among these distances:
77 40 0.53
78 5 0.07
79 3 0.04
80 1 0.01
81 1 0.01
82 26 0.34
ACGTcount: A:0.47, C:0.11, G:0.19, T:0.23
Consensus pattern (75 bp):
TAATTTCAAGGAGAAATTAGGTAAAGACAAGCACAGACTTAATTCAGGAAAATTAAGTAAAGTAA
AGCACAGACT
Found at i:15192 original size:35 final size:35
Alignment explanation
Indices: 15099--15229 Score: 171
Period size: 35 Copynumber: 3.8 Consensus size: 35
15089 AATTCAGGGT
*
15099 AATTAAGT-AAATTAGCAAAGACTTAATTT--TAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCAAAG
* *
15131 AATTAAGTAAAATTAGCAGAGGCTTAATTTCACAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCA-AAG
15167 AATTAAGT-AAATTAGCAAAGACTTAATTTCATAAG
1 AATTAAGTAAAATTAGCAAAGACTTAATTTCA-AAG
* *
15202 AATTAAGTAAAATCATCAAAGACTTAAT
1 AATTAAGTAAAATTAGCAAAGACTTAAT
15230 CCAAAGATGA
Statistics
Matches: 86, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
32 8 0.09
33 19 0.22
35 32 0.37
36 27 0.31
ACGTcount: A:0.48, C:0.09, G:0.12, T:0.31
Consensus pattern (35 bp):
AATTAAGTAAAATTAGCAAAGACTTAATTTCAAAG
Found at i:15317 original size:37 final size:37
Alignment explanation
Indices: 15271--15582 Score: 278
Period size: 37 Copynumber: 8.8 Consensus size: 37
15261 ACTTAACCCT
* * ** * *
15271 AGGGGATTAAGTAAAGAAAAGGACTTAGTTCCAAGAA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
**
15308 AGGGAA-T---TA-AGTTAAGGACTTGGTTCCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
* ** *
15340 AGGGAGTTAAGTAGAGCAAAGGACTTAATTTCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
*
15377 AGGAAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
* * *
15414 AGAGAATTAAGTAGAGTTAAGGGCTTAATTTCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
* *
15451 AGGAAATTAAGT--AG---AGGACTTAATTTCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
* *
15483 AGGAAATTAAGT--AG---AGGACTTGATTCCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
** *
15515 AGGGAATTAAGTAGAGTTAAGGGTTTAATTTCAAGGA
1 AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
* *
15552 AGGAAATTAAGTCA-AGTCAAGGACTTAATTC
1 AGGGAATTAAGT-AGAGTTAAGGACTTAATTC
15583 AGGGTAATTA
Statistics
Matches: 229, Mismatches: 35, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
32 82 0.36
33 3 0.01
34 2 0.01
35 2 0.01
36 3 0.01
37 136 0.59
38 1 0.00
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (37 bp):
AGGGAATTAAGTAGAGTTAAGGACTTAATTCCAAGGA
Found at i:15325 original size:32 final size:32
Alignment explanation
Indices: 15289--15526 Score: 174
Period size: 32 Copynumber: 7.0 Consensus size: 32
15279 AAGTAAAGAA
* *
15289 AAGGACTTAGTTCCAAGAAAGGGAATTAAGTT
1 AAGGACTTAATTCCAAGGAAGGGAATTAAGTT
** * *
15321 AAGGACTTGGTTCCAAGGAAGGGAGTTAAGTAGAGCA
1 AAGGACTTAATTCCAAGGAAGGGAATTAAGT-----T
* *
15358 AAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGGAA-T---TA-AGTT
*
15395 AAGGACTTAATTCCAAGGAAGAGAATTAAGTAGAGTT
1 AAGGACTTAATTCCAAGGAAGGGAA-T---TA-AGTT
* * *
15432 AAGGGCTTAATTTCAAGGAAGGAAATTAAG-T
1 AAGGACTTAATTCCAAGGAAGGGAATTAAGTT
* *
15463 AGAGGACTTAATTTCAAGGAAGGAAATTAAG-T
1 A-AGGACTTAATTCCAAGGAAGGGAATTAAGTT
*
15495 AGAGGACTTGATTCCAAGGAAGGGAATTAAGT
1 A-AGGACTTAATTCCAAGGAAGGGAATTAAGT
15527 AGAGTTAAGG
Statistics
Matches: 173, Mismatches: 21, Indels: 23
0.80 0.10 0.11
Matches are distributed among these distances:
31 2 0.01
32 87 0.50
33 2 0.01
36 1 0.01
37 75 0.43
38 1 0.01
41 2 0.01
42 3 0.02
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (32 bp):
AAGGACTTAATTCCAAGGAAGGGAATTAAGTT
Found at i:15386 original size:106 final size:98
Alignment explanation
Indices: 15289--15563 Score: 250
Period size: 101 Copynumber: 2.6 Consensus size: 98
15279 AAGTAAAGAA
* ** * *
15289 AAGGACTTAGTTCCAAGAAAGGGAATTAAGTTAAGGACTTGGTTCCAAGGAAGGGAGTTAAGTAG
1 AAGGACTTAGTTCCAAGGAAGGGAATTAAGTTAAGGACTTAATTCCAAGGAAGGAAATTAAGT--
15354 AGCAAAGGACTTAATTTCAAGGAAGGAAATTAAGTAGAG
64 AG---AGGACTTAATTTCAAGGAAGGAAATTAAGTA-AG
* * * *
15393 TTAAGGACTTAATTCCAAGGAAGAGAATTAAGTAGAGTTAAGGGCTTAATTTCAAGGAAGGAAAT
1 --AAGGACTTAGTTCCAAGGAAGGGAA-T---TA-AGTTAAGGACTTAATTCCAAGGAAGGAAAT
15458 TAAGTAGAGGACTTAATTTCAAGGAAGGAAATTAAGT-AG
59 TAAGTAGAGGACTTAATTTCAAGGAAGGAAATTAAGTAAG
** *
15497 -AGGACTT-GATTCCAAGGAAGGGAATTAAGTAGAGTTAAGGGTTTAATTTCAAGGAAGGAAATT
1 AAGGACTTAG-TTCCAAGGAAGGGAA-T---TA-AGTTAAGGACTTAATTCCAAGGAAGGAAATT
15560 AAGT
60 AAGT
15564 CAAGTCAAGG
Statistics
Matches: 151, Mismatches: 12, Indels: 17
0.84 0.07 0.09
Matches are distributed among these distances:
101 63 0.42
104 2 0.01
106 52 0.34
107 1 0.01
109 2 0.01
110 2 0.01
111 29 0.19
ACGTcount: A:0.41, C:0.07, G:0.27, T:0.25
Consensus pattern (98 bp):
AAGGACTTAGTTCCAAGGAAGGGAATTAAGTTAAGGACTTAATTCCAAGGAAGGAAATTAAGTAG
AGGACTTAATTTCAAGGAAGGAAATTAAGTAAG
Found at i:15543 original size:101 final size:103
Alignment explanation
Indices: 15359--15563 Score: 342
Period size: 101 Copynumber: 2.0 Consensus size: 103
15349 AGTAGAGCAA
15359 AGGACTTAATTTCAAGGAAGGAAATTAAGTAGAGTTAAGGACTTAATTCCAAGGAAGAGAATTAA
1 AGGACTTAATTTCAAGGAAGGAAATTAAGTA-AG-T-AGGACTTAATTCCAAGGAAGAGAATTAA
15424 GTAGAGTTAAGGGCTTAATTTCAAGGAAGGAAATTAAGTAG
63 GTAGAGTTAAGGGCTTAATTTCAAGGAAGGAAATTAAGTAG
* *
15465 AGGACTTAATTTCAAGGAAGGAAATTAAGT-AG-AGGACTTGATTCCAAGGAAGGGAATTAAGTA
1 AGGACTTAATTTCAAGGAAGGAAATTAAGTAAGTAGGACTTAATTCCAAGGAAGAGAATTAAGTA
*
15528 GAGTTAAGGGTTTAATTTCAAGGAAGGAAATTAAGT
66 GAGTTAAGGGCTTAATTTCAAGGAAGGAAATTAAGT
15564 CAAGTCAAGG
Statistics
Matches: 96, Mismatches: 3, Indels: 5
0.92 0.03 0.05
Matches are distributed among these distances:
101 64 0.67
104 2 0.02
106 30 0.31
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.26
Consensus pattern (103 bp):
AGGACTTAATTTCAAGGAAGGAAATTAAGTAAGTAGGACTTAATTCCAAGGAAGAGAATTAAGTA
GAGTTAAGGGCTTAATTTCAAGGAAGGAAATTAAGTAG
Found at i:15597 original size:32 final size:32
Alignment explanation
Indices: 15556--15627 Score: 126
Period size: 32 Copynumber: 2.2 Consensus size: 32
15546 CAAGGAAGGA
15556 AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
1 AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
* *
15588 AATTAAGTCAAGTTAGGGACTTAATTCAGGGT
1 AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
15620 AATTAAGT
1 AATTAAGT
15628 AGCGTCAATA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
32 38 1.00
ACGTcount: A:0.38, C:0.10, G:0.22, T:0.31
Consensus pattern (32 bp):
AATTAAGTCAAGTCAAGGACTTAATTCAGGGT
Found at i:15612 original size:69 final size:66
Alignment explanation
Indices: 15381--15613 Score: 176
Period size: 69 Copynumber: 3.4 Consensus size: 66
15371 CAAGGAAGGA
* * *
15381 AATTAAGTAGAGTTAAGGACTTAATTCCAAGGAA-GAGAATTAAGTAGAGTTAAGGGCTTAATTT
1 AATTAAGTAGAGTTAGGGACTTAATTTCAAGGAAGGA-AATTAAGTA-AG-TAAGGACTTAA-TT
*
15445 CAAGG
62 CAGGG
** * *
15450 AAGGAAATTA-AG-TAGAGGACTTAATTTCAAGGAAGGAAATTAAGT-AG--AGGACTTGATTCC
1 AA-TTAAGTAGAGTTAG-GGACTTAATTTCAAGGAAGGAAATTAAGTAAGTAAGGACTTAATT-C
15510 AAGGAAGGG
63 -----AGGG
*
15519 AATTAAGTAGAGTTAAGGG-TTTAATTTCAAGGAAGGAAATTAAGTCAAGTCAAGGACTTAATTC
1 AATTAAGTAGAGTT-AGGGACTTAATTTCAAGGAAGGAAATTAAGT-AAGT-AAGGACTTAATTC
15583 AGGG
63 AGGG
15587 TAATTAAGTCA-AGTTAGGGACTTAATT
1 -AATTAAGT-AGAGTTAGGGACTTAATT
15614 CAGGGTAATT
Statistics
Matches: 130, Mismatches: 14, Indels: 40
0.71 0.08 0.22
Matches are distributed among these distances:
63 2 0.02
64 8 0.06
67 2 0.02
68 14 0.11
69 79 0.61
70 10 0.08
71 4 0.03
73 1 0.01
74 10 0.08
ACGTcount: A:0.40, C:0.07, G:0.25, T:0.27
Consensus pattern (66 bp):
AATTAAGTAGAGTTAGGGACTTAATTTCAAGGAAGGAAATTAAGTAAGTAAGGACTTAATTCAGG
G
Found at i:15654 original size:36 final size:36
Alignment explanation
Indices: 15573--15757 Score: 154
Period size: 36 Copynumber: 5.2 Consensus size: 36
15563 TCAAGTCAAG
**
15573 GACTTAATTCAGGGTAATTAAGTCA-AGT---T-AGG
1 GACTTAATTCAGGGTAATTAAGT-AGAGTCAATAAAA
*
15605 GACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* * *
15641 GGCTTAATTCAGGGTAATTAAATGGAGTCAAT-AAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
* * **
15676 GCACTTAATCTAAGAAG-AGATTAAGTA-AAACAATAAAA
1 G-ACTTAAT-TCAG-GGTA-ATTAAGTAGAGTCAATAAAA
*
15714 GACTTAATTCAGGGTAATTAAGTGGAGTCAAT-AAA
1 GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
15749 GAACTTAAT
1 G-ACTTAAT
15758 CTAAAAAGGG
Statistics
Matches: 121, Mismatches: 19, Indels: 22
0.75 0.12 0.14
Matches are distributed among these distances:
31 1 0.01
32 25 0.21
35 17 0.14
36 51 0.42
37 16 0.13
38 11 0.09
ACGTcount: A:0.43, C:0.10, G:0.20, T:0.28
Consensus pattern (36 bp):
GACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAA
Found at i:15711 original size:37 final size:37
Alignment explanation
Indices: 15669--15795 Score: 111
Period size: 38 Copynumber: 3.4 Consensus size: 37
15659 TAAATGGAGT
15669 CAAT-AAAGCACTTAATCTAAGAAGAGATTAAGTAAAA
1 CAATAAAAG-ACTTAATCTAAGAAGAGATTAAGTAAAA
* * * **
15706 CAATAAAAGACTTAAT-TCAG-GGTA-ATTAAGTGGAGT
1 CAATAAAAGACTTAATCTAAGAAG-AGATTAAGT-AAAA
* *
15742 CAAT-AAAGAACTTAATCTAAAAAGGGATTAAGTAAAA
1 CAATAAAAG-ACTTAATCTAAGAAGAGATTAAGTAAAA
15779 CAATAAAAGGACTTAAT
1 CAATAAAA-GACTTAAT
15796 TTATAAAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 17
0.70 0.12 0.17
Matches are distributed among these distances:
35 12 0.17
36 16 0.23
37 18 0.26
38 22 0.32
39 1 0.01
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (37 bp):
CAATAAAAGACTTAATCTAAGAAGAGATTAAGTAAAA
Found at i:15720 original size:73 final size:73
Alignment explanation
Indices: 15633--15796 Score: 274
Period size: 73 Copynumber: 2.2 Consensus size: 73
15623 TAAGTAGCGT
* * *
15633 CAATAAAAGGCTTAATTCAGGGTAATTAAATGGAGTCAATAAAGCACTTAATCTAAGAAGAGATT
1 CAATAAAAGACTTAATTCAGGGTAATTAAATGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
15698 AAGTAAAA
66 AAGTAAAA
* *
15706 CAATAAAAGACTTAATTCAGGGTAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGGGATT
1 CAATAAAAGACTTAATTCAGGGTAATTAAATGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
15771 AAGTAAAA
66 AAGTAAAA
15779 CAATAAAAGGACTTAATT
1 CAATAAAA-GACTTAATT
15797 TATAAAAATT
Statistics
Matches: 85, Mismatches: 5, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
73 76 0.89
74 9 0.11
ACGTcount: A:0.49, C:0.09, G:0.17, T:0.25
Consensus pattern (73 bp):
CAATAAAAGACTTAATTCAGGGTAATTAAATGGAGTCAATAAAGAACTTAATCTAAAAAGAGATT
AAGTAAAA
Found at i:15772 original size:38 final size:37
Alignment explanation
Indices: 15657--15774 Score: 93
Period size: 37 Copynumber: 3.2 Consensus size: 37
15647 ATTCAGGGTA
* * *
15657 ATTAAATGGAGTCAATAAAGCACTTAATCTAAGAAGAG
1 ATTAAGTGGAGTCAATAAAGAACTTAATCTAA-AAGGG
* ** *
15695 ATTAAGT-AAAACAATAAA-AGACTTAAT-T--CAGGG
1 ATTAAGTGGAGTCAATAAAGA-ACTTAATCTAAAAGGG
15728 TAATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAAGGG
1 --ATTAAGTGGAGTCAATAAAGAACTTAATCT-AAAAGGG
15768 ATTAAGT
1 ATTAAGT
15775 AAAACAATAA
Statistics
Matches: 60, Mismatches: 11, Indels: 18
0.67 0.12 0.20
Matches are distributed among these distances:
33 3 0.05
35 7 0.12
36 16 0.27
37 17 0.28
38 13 0.22
40 4 0.07
ACGTcount: A:0.48, C:0.08, G:0.18, T:0.25
Consensus pattern (37 bp):
ATTAAGTGGAGTCAATAAAGAACTTAATCTAAAAGGG
Found at i:15793 original size:38 final size:36
Alignment explanation
Indices: 15669--15795 Score: 107
Period size: 37 Copynumber: 3.4 Consensus size: 36
15659 TAAATGGAGT
* *
15669 CAATAAAGCACTTAATCTAAGAAGAGATTAAGTAAAA
1 CAATAAAGGACTTAATCTAA-AAGGGATTAAGTAAAA
* * * **
15706 CAATAAAAGACTTAAT-T--CAGGGTAATTAAGTGGAGT
1 CAATAAAGGACTTAATCTAAAAGGG--ATTAAGT-AAAA
*
15742 CAATAAAGAACTTAATCTAAAAAGGGATTAAGTAAAA
1 CAATAAAGGACTTAATCT-AAAAGGGATTAAGTAAAA
15779 CAATAAAAGGACTTAAT
1 CAAT-AAAGGACTTAAT
15796 TTATAAAAAT
Statistics
Matches: 68, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
33 3 0.04
35 7 0.10
36 16 0.24
37 20 0.29
38 18 0.26
40 4 0.06
ACGTcount: A:0.51, C:0.09, G:0.16, T:0.24
Consensus pattern (36 bp):
CAATAAAGGACTTAATCTAAAAGGGATTAAGTAAAA
Done.