Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008891.1 Corchorus capsularis cultivar CVL-1 contig08912, 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: 66863
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:3345 original size:30 final size:29
Alignment explanation
Indices: 3309--3371 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 29
3299 TGTGTTCAAG
3309 TCCATGATAAGTCCTTGGTGC-ATCATTCCC
1 TCCATGATAAG-CCTTGG-GCGATCATTCCC
3339 TCCATGATAAGCCTTGGGCGTATCATTCCC
1 TCCATGATAAGCCTTGGGCG-ATCATTCCC
3369 TCC
1 TCC
3372 CCCTTGAAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
28 2 0.06
29 6 0.19
30 23 0.74
ACGTcount: A:0.19, C:0.32, G:0.17, T:0.32
Consensus pattern (29 bp):
TCCATGATAAGCCTTGGGCGATCATTCCC
Found at i:9498 original size:156 final size:153
Alignment explanation
Indices: 9121--9490 Score: 354
Period size: 156 Copynumber: 2.4 Consensus size: 153
9111 CGTCTCAAAC
* * * * * * * *
9121 AGACTTCGTATGAAAAACTTATGCAAGTTTTTCAGTTAAGGACAATTTGGGGTGTCAAACAAACT
1 AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGAC-ATTTGAGGTGTGAAAC-TAGT
* * * * *
9186 TCTCTATGCTAGAGAGTTCGGTTTTACTTAGAATTTTTCCCATAGCTTCATGGGGATAATCTAAG
64 TCACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCTTCATGGAGATAATCTAAG
* *
9251 TCTACTGGTGGAAGATCAGCTTCGTT
129 TCTACT-GTGGAAAATCAGCTTCATT
* * ** * * *
9277 GGACTTAGAATGAAAAACTTAAGCTAGTTTTTCATTTAAGGACAACTCAGGGAGAGAAACCTAGT
1 AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACATTTGA-GGTGTGAAA-CTAGT
* * *
9342 TCACCAT-CAAGAGGAGCTCGGTTTTACTTAGAATTTTTTCCATAGTCTT-GTGGAGATAGTCTA
64 TCACCATGCAAGA-GAGCTCGGTTTTACTTAGAATTTTTCCCATAG-CTTCATGGAGATAATCTA
*
9405 AGTC-CCT-TGGCAAAATTTCAGC-TCATT
127 AGTCTACTGTGG-AAAA--TCAGCTTCATT
*
9432 CAGATTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACAGTTTGAGGTGTGAA
1 -AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACA-TTTGAGGTGTGAA
9491 GTCTAGTTTG
Statistics
Matches: 171, Mismatches: 34, Indels: 18
0.77 0.15 0.08
Matches are distributed among these distances:
153 3 0.02
154 3 0.02
155 12 0.07
156 147 0.86
157 6 0.04
ACGTcount: A:0.30, C:0.15, G:0.21, T:0.34
Consensus pattern (153 bp):
AGACTTAGAATGAAAAACTTATGCTAGTTTTTCATTTAAGGACATTTGAGGTGTGAAACTAGTTC
ACCATGCAAGAGAGCTCGGTTTTACTTAGAATTTTTCCCATAGCTTCATGGAGATAATCTAAGTC
TACTGTGGAAAATCAGCTTCATT
Found at i:12067 original size:42 final size:42
Alignment explanation
Indices: 11983--12068 Score: 145
Period size: 42 Copynumber: 2.0 Consensus size: 42
11973 TAAACCAAGC
*
11983 TCTTCATGATCCATGAACCAATTCCATCAATCACCAGGATCT
1 TCTTCATGATCCATGAACCAATTCCATCAATCACCAGAATCT
**
12025 TCTTCATGATCCATGAACCAATTCCATCAATCGTCAGAATCT
1 TCTTCATGATCCATGAACCAATTCCATCAATCACCAGAATCT
12067 TC
1 TC
12069 AATGCAATTG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.30, C:0.30, G:0.09, T:0.30
Consensus pattern (42 bp):
TCTTCATGATCCATGAACCAATTCCATCAATCACCAGAATCT
Found at i:12578 original size:72 final size:72
Alignment explanation
Indices: 12463--12597 Score: 184
Period size: 72 Copynumber: 1.9 Consensus size: 72
12453 ACCATAAAGA
* *
12463 TCAATTTTTGACAATCTAAAAATTTCAGCAGAAAATTTCGCATCCAAA-TCAGAATCCCACAAAC
1 TCAATTTTTGACAATCTAAAAACTTCAGCAGAAAATTTCGCATCAAAACT-AGAATCCCACAAAC
12527 CTTCAAAC
65 CTTCAAAC
* * * *
12535 TCAATTTTTGGCAATCTCAAGACTTCAGCAGTAAACTTT-GCATCAAAACTAGAATCCCACAAA
1 TCAATTTTTGACAATCTAAAAACTTCAGCAG-AAAATTTCGCATCAAAACTAGAATCCCACAAA
12598 ACAAGATCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
72 48 0.87
73 7 0.13
ACGTcount: A:0.40, C:0.24, G:0.09, T:0.27
Consensus pattern (72 bp):
TCAATTTTTGACAATCTAAAAACTTCAGCAGAAAATTTCGCATCAAAACTAGAATCCCACAAACC
TTCAAAC
Found at i:15984 original size:17 final size:19
Alignment explanation
Indices: 15964--16002 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
15954 TTAATTTCCA
*
15964 TATTTTTA-TA-ATTATTT
1 TATTTTTACTATATTAATT
15981 TATTTTTACTATATTAATT
1 TATTTTTACTATATTAATT
16000 TAT
1 TAT
16003 AAAAATTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 8 0.42
18 2 0.11
19 9 0.47
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (19 bp):
TATTTTTACTATATTAATT
Found at i:20849 original size:32 final size:32
Alignment explanation
Indices: 20810--21131 Score: 252
Period size: 32 Copynumber: 9.9 Consensus size: 32
20800 GAAAAATCAA
*
20810 GAGTAAAAGTAAAAGAAATAATCAGTAGAAGG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGG
* **
20842 GAGTAAAAGTAAAAGAAGTAATCAGTAACAATAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGT----AGAAGG
*
20878 GAGTAAAAGTAAAAGAAGTAATCAGTA-ACAGTAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGA-AG--G
*
20912 AAG-AAGAAGTAAAAGAAGTAATCAGTAGAAGG
1 GAGTAA-AAGTAAAAGAAGTAATCAGTAGAAGG
**
20944 GAGTAAAAGTAAAAGAAGTAATCAGTAACAGTAAAA
1 GAGTAAAAGTAAAAGAAGTAATCAGT---AG-AAGG
*
20980 GAGTAAAAGTAAAAGAAGTAATCAGCA-AAGTG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAG-G
* *
21012 AAGTAAAAGTAAAAGAAGTAATCAGCA-AAGTG
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAG-G
* * ** * *
21044 AAGTAAAAGTAAAAAAAAAAAATCAGCAGAATG
1 GAGTAAAAGT-AAAAGAAGTAATCAGTAGAAGG
* *
21077 AAGT-AAAGTAAGAGAAGTAATC---AGAA--
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGG
*
21103 GAGTAATAGTAAAAGAAGTAATCAG-AGAA
1 GAGTAAAAGTAAAAGAAGTAATCAGTAGAA
21132 ACAGAAAAAT
Statistics
Matches: 245, Mismatches: 25, Indels: 43
0.78 0.08 0.14
Matches are distributed among these distances:
26 3 0.01
27 16 0.07
28 4 0.02
29 4 0.02
31 12 0.05
32 95 0.39
33 24 0.10
34 28 0.11
35 3 0.01
36 56 0.23
ACGTcount: A:0.58, C:0.05, G:0.22, T:0.16
Consensus pattern (32 bp):
GAGTAAAAGTAAAAGAAGTAATCAGTAGAAGG
Found at i:20885 original size:68 final size:67
Alignment explanation
Indices: 20780--21166 Score: 265
Period size: 68 Copynumber: 5.8 Consensus size: 67
20770 AACTAAAAAG
* * * *
20780 AGTAAAAG--AAAG-AGTAAACAGAAAAAT-CAAGAGTAAAAGTAAAAGAAATAATCAGTAGAAG
1 AGTAAAAGTAAAAGAAGTAATCAGTAAAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTA-AAG
**
20841 -GG
65 TAA
20843 AGTAAAAGTAAAAGAAGTAATCAGTAACAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAACA
1 AGTAAAAGTAAAAGAAGTAATCAGTAA-AATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAA-A
20908 GTAAA
64 GT-AA
* **
20913 AG-AAGAAGTAAAAGAAGTAATCAGT---AGAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAACA
1 AGTAA-AAGTAAAAGAAGTAATCAGTAAAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAA-A
20974 GTAAAA
64 GT--AA
* * * *
20980 GAGTAAAAGTAAAAGAAGTAATCAGCAAAGT--GA-AGTAAAAGTAAAAGAAGTAATCAGCAAAG
1 -AGTAAAAGTAAAAGAAGTAATCAGTAAAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAG
*
21042 TGA
65 TAA
* ** * * * *
21045 AGTAAAAGTAAAAAAAAAAAATCAGCAGAAT--GA-AGT-AAAGTAAGAGAAGTAATCAG-AAGA
1 AGTAAAAGT-AAAAGAAGTAATCAGTAAAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAA-A
21105 GTAA
64 GTAA
* * * *
21109 TAGTAAAAG-AAGTAATCAGAG-AAACAGAAAAAT-CAAGAGTAAAAGTAAAAGAAGTAAT
1 -AGTAAAAGTAA--AA-GA-AGTAATCAGTAAAATAAAAGAGTAAAAGTAAAAGAAGTAAT
21167 TGGAAAAAAG
Statistics
Matches: 270, Mismatches: 29, Indels: 44
0.79 0.08 0.13
Matches are distributed among these distances:
63 12 0.04
64 32 0.12
65 36 0.13
66 55 0.20
67 12 0.04
68 80 0.30
69 21 0.08
70 22 0.08
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (67 bp):
AGTAAAAGTAAAAGAAGTAATCAGTAAAATAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAAAGT
AA
Found at i:20934 original size:102 final size:100
Alignment explanation
Indices: 20775--21057 Score: 396
Period size: 102 Copynumber: 2.8 Consensus size: 100
20765 AATTAAACTA
* * * *
20775 AAAAGAGTAAAAG--AAAG-AGTAAACAGAAAAATCAAGAGTAAAAGTAAAAGAAATAATCAGTA
1 AAAAGAGTAAAAGTAAAAGAAGTAATCAGCAAAGT-AA-AGTAAAAGTAAAAGAAGTAATCAGTA
20837 GAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAACAAT
64 GAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAACAAT
*
20874 AAAAGAGTAAAAGTAAAAGAAGTAATCAGTAACAGTAAAAG-AAGAAGTAAAAGAAGTAATCAGT
1 AAAAGAGTAAAAGTAAAAGAAGTAATCAGCAA-AGT-AAAGTAA-AAGTAAAAGAAGTAATCAGT
*
20938 AGAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAACAGT
63 AGAAGGGAGTAAAAGTAAAAGAAGTAATCAGTAACAAT
* *
20976 AAAAGAGTAAAAGTAAAAGAAGTAATCAGCAAAGTGAAGTAAAAGTAAAAGAAGTAATCAGCA-A
1 AAAAGAGTAAAAGTAAAAGAAGTAATCAGCAAAGTAAAGTAAAAGTAAAAGAAGTAATCAGTAGA
*
21040 AGTGAAGTAAAAGTAAAA
66 AG-GGAGTAAAAGTAAAA
21058 AAAAAAAATC
Statistics
Matches: 167, Mismatches: 10, Indels: 13
0.88 0.05 0.07
Matches are distributed among these distances:
99 16 0.10
100 37 0.22
101 11 0.07
102 99 0.59
103 4 0.02
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (100 bp):
AAAAGAGTAAAAGTAAAAGAAGTAATCAGCAAAGTAAAGTAAAAGTAAAAGAAGTAATCAGTAGA
AGGGAGTAAAAGTAAAAGAAGTAATCAGTAACAAT
Found at i:21009 original size:15 final size:15
Alignment explanation
Indices: 20991--21041 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
20981 AGTAAAAGTA
20991 AAAGAAGTAATCAGC
1 AAAGAAGTAATCAGC
* *
21006 AAAGTGAAGTAA-AAGTA
1 AAA--GAAGTAATCAG-C
21023 AAAGAAGTAATCAGC
1 AAAGAAGTAATCAGC
21038 AAAG
1 AAAG
21042 TGAAGTAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 8
0.70 0.10 0.20
Matches are distributed among these distances:
15 14 0.50
16 4 0.14
17 10 0.36
ACGTcount: A:0.57, C:0.08, G:0.22, T:0.14
Consensus pattern (15 bp):
AAAGAAGTAATCAGC
Found at i:21016 original size:17 final size:17
Alignment explanation
Indices: 20994--21049 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
20984 AAAAGTAAAA
20994 GAAGTAATCAGCAAAGT
1 GAAGTAATCAGCAAAGT
* * *
21011 GAAGTAA-AAGTAAA-A
1 GAAGTAATCAGCAAAGT
21026 GAAGTAATCAGCAAAGT
1 GAAGTAATCAGCAAAGT
21043 GAAGTAA
1 GAAGTAA
21050 AAGTAAAAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
15 7 0.23
16 10 0.32
17 14 0.45
ACGTcount: A:0.54, C:0.07, G:0.23, T:0.16
Consensus pattern (17 bp):
GAAGTAATCAGCAAAGT
Found at i:21114 original size:27 final size:26
Alignment explanation
Indices: 21078--21128 Score: 84
Period size: 27 Copynumber: 1.9 Consensus size: 26
21068 AGCAGAATGA
*
21078 AGTAAAGTAAGAGAAGTAATCAGAAG
1 AGTAAAGTAAAAGAAGTAATCAGAAG
21104 AGTAATAGTAAAAGAAGTAATCAGA
1 AGTAA-AGTAAAAGAAGTAATCAGA
21129 GAAACAGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.55, C:0.04, G:0.24, T:0.18
Consensus pattern (26 bp):
AGTAAAGTAAAAGAAGTAATCAGAAG
Found at i:21140 original size:24 final size:26
Alignment explanation
Indices: 21089--21140 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
21079 GTAAAGTAAG
* *
21089 AGAAGTAATCAGAAGAGTAATAGTAAA
1 AGAAGTAATCAGAAGAG-AACAGAAAA
21116 AGAAGTAATCAG-AGA-AACAGAAAA
1 AGAAGTAATCAGAAGAGAACAGAAAA
21140 A
1 A
21141 TCAAGAGTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 8 0.35
26 3 0.13
27 12 0.52
ACGTcount: A:0.60, C:0.06, G:0.21, T:0.13
Consensus pattern (26 bp):
AGAAGTAATCAGAAGAGAACAGAAAA
Found at i:21414 original size:103 final size:104
Alignment explanation
Indices: 21249--21461 Score: 288
Period size: 103 Copynumber: 2.0 Consensus size: 104
21239 GTAATGGGTT
* * *
21249 TAATTCAGAGTAATTAAACTAAGAAGTAAAAGAATGACTAAACGGTAGTAATTAGCTTAATTCAG
1 TAATTCAGAGAAATTAAACTAAGAAGTAAAAG-A-GACTAAACAGCAGTAATTAGCTTAATTCAG
* *
21314 AGTAATTAAGTTAATCGAGAAGTAAAAAGAG-AAATCAGTAG
64 AGTAATTAAGCTAATCAAGAAGTAAAAAGAGTAAAT-AGTAG
* *
21355 TAATTCAGAGGAAATTAATC-AAGAAGTAAAAG-GAGTAAACAGCAGTAATTAGCTTAATTCAGA
1 TAATTCAGA-GAAATTAAACTAAGAAGTAAAAGAGACTAAACAGCAGTAATTAGCTTAATTCAGA
**
21418 GTAATTAAGCTAATCAAGAAGTAAAGGGAGTAAATAGTAG
65 GTAATTAAGCTAATCAAGAAGTAAAAAGAGTAAATAGTAG
21458 TAAT
1 TAAT
21462 CAGCTTAATT
Statistics
Matches: 96, Mismatches: 9, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
103 63 0.66
104 4 0.04
106 21 0.22
107 8 0.08
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.25
Consensus pattern (104 bp):
TAATTCAGAGAAATTAAACTAAGAAGTAAAAGAGACTAAACAGCAGTAATTAGCTTAATTCAGAG
TAATTAAGCTAATCAAGAAGTAAAAAGAGTAAATAGTAG
Found at i:21448 original size:58 final size:58
Alignment explanation
Indices: 21370--21481 Score: 170
Period size: 58 Copynumber: 1.9 Consensus size: 58
21360 CAGAGGAAAT
*
21370 TAATCAAGAAGTAAAAGGAGTAAACAGCAGTAATTAGCTTAATTCAGAGTAATTAAGC
1 TAATCAAGAAGTAAAAGGAGTAAACAGCAGTAATCAGCTTAATTCAGAGTAATTAAGC
* * * * *
21428 TAATCAAGAAGTAAAGGGAGTAAATAGTAGTAATCAGCTTAATTCGGGGTAATT
1 TAATCAAGAAGTAAAAGGAGTAAACAGCAGTAATCAGCTTAATTCAGAGTAATT
21482 GAGTCAGTAG
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
58 48 1.00
ACGTcount: A:0.44, C:0.09, G:0.21, T:0.26
Consensus pattern (58 bp):
TAATCAAGAAGTAAAAGGAGTAAACAGCAGTAATCAGCTTAATTCAGAGTAATTAAGC
Found at i:23689 original size:26 final size:28
Alignment explanation
Indices: 23654--23728 Score: 79
Period size: 26 Copynumber: 2.8 Consensus size: 28
23644 GAGAAAGAAG
*
23654 AAGAAGAGAAAAAAGGA-AAAAG-GAAAAT
1 AAGAA-AGAAAAAAGAAGAAAAGAG-AAAT
23682 AA-AAAG-AAAAAGAAGAAAAGAGAAAT
1 AAGAAAGAAAAAAGAAGAAAAGAGAAAT
23708 AAGAAAGAAAAGAA-AAGAAAA
1 AAGAAAGAAAA-AAGAAGAAAA
23729 AAATCCACGT
Statistics
Matches: 41, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
25 7 0.17
26 13 0.32
27 7 0.17
28 12 0.29
29 2 0.05
ACGTcount: A:0.76, C:0.00, G:0.21, T:0.03
Consensus pattern (28 bp):
AAGAAAGAAAAAAGAAGAAAAGAGAAAT
Found at i:27142 original size:12 final size:12
Alignment explanation
Indices: 27116--27148 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
27106 TAACGAACTA
27116 TAAACGAAT-TT
1 TAAACGAATATT
27127 TAAACGAATATT
1 TAAACGAATATT
*
27139 TAAATGAATA
1 TAAACGAATA
27149 ATAAACGAGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (12 bp):
TAAACGAATATT
Found at i:39386 original size:33 final size:33
Alignment explanation
Indices: 39338--39401 Score: 110
Period size: 33 Copynumber: 1.9 Consensus size: 33
39328 AAAAAAAGGC
* *
39338 CTAGCCATTGTCCATGCCGCCCACGCTGGGCAG
1 CTAGCCAATGGCCATGCCGCCCACGCTGGGCAG
39371 CTAGCCAATGGCCATGCCGCCCACGCTGGGC
1 CTAGCCAATGGCCATGCCGCCCACGCTGGGC
39402 GGTAAGGCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.16, C:0.41, G:0.28, T:0.16
Consensus pattern (33 bp):
CTAGCCAATGGCCATGCCGCCCACGCTGGGCAG
Found at i:39511 original size:11 final size:11
Alignment explanation
Indices: 39495--39567 Score: 74
Period size: 11 Copynumber: 5.9 Consensus size: 11
39485 TTAGTTTATG
39495 TTTAATTAGTA
1 TTTAATTAGTA
39506 TTTAATTAGATTA
1 TTTAATTAG--TA
39519 TGATTAATTAGTA
1 T--TTAATTAGTA
39532 TTTAATTAGTTTA
1 TTTAATTAG--TA
39545 TGATTAATTAGTA
1 T--TTAATTAGTA
39558 TTTAATTAGT
1 TTTAATTAGT
39568 TTATGATTAA
Statistics
Matches: 54, Mismatches: 0, Indels: 16
0.77 0.00 0.23
Matches are distributed among these distances:
11 26 0.48
13 12 0.22
15 16 0.30
ACGTcount: A:0.36, C:0.00, G:0.11, T:0.53
Consensus pattern (11 bp):
TTTAATTAGTA
Found at i:39513 original size:26 final size:26
Alignment explanation
Indices: 39484--39577 Score: 170
Period size: 26 Copynumber: 3.6 Consensus size: 26
39474 TACTTAGTTT
*
39484 ATTAGTTTATGTTTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
*
39510 ATTAGATTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
39536 ATTAGTTTATGATTAATTAGTATTTA
1 ATTAGTTTATGATTAATTAGTATTTA
39562 ATTAGTTTATGATTAA
1 ATTAGTTTATGATTAA
39578 AATGAAGGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.53
Consensus pattern (26 bp):
ATTAGTTTATGATTAATTAGTATTTA
Found at i:39618 original size:24 final size:25
Alignment explanation
Indices: 39587--39641 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
39577 AAATGAAGGA
*
39587 AAAT-AAATTTGAAG-ATTTGTTAG
1 AAATGAAATTTGAAGAAGTTGTTAG
39610 AAATGAAATTTGAAGAAGTTGTTAG
1 AAATGAAATTTGAAGAAGTTGTTAG
39635 AAATGAA
1 AAATGAA
39642 GTTTAAGGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 4 0.14
24 10 0.34
25 15 0.52
ACGTcount: A:0.47, C:0.00, G:0.20, T:0.33
Consensus pattern (25 bp):
AAATGAAATTTGAAGAAGTTGTTAG
Found at i:41186 original size:16 final size:16
Alignment explanation
Indices: 41145--41189 Score: 56
Period size: 15 Copynumber: 2.9 Consensus size: 16
41135 TCGGATTTTG
**
41145 TCGGTTTCGGGTTATC
1 TCGGTTTCGGGTTAAA
*
41161 TC-GATTCGGGTTAAA
1 TCGGTTTCGGGTTAAA
41176 TCGGTTTCGGGTTA
1 TCGGTTTCGGGTTA
41190 TAGTACTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
15 12 0.50
16 12 0.50
ACGTcount: A:0.13, C:0.16, G:0.31, T:0.40
Consensus pattern (16 bp):
TCGGTTTCGGGTTAAA
Found at i:44299 original size:27 final size:26
Alignment explanation
Indices: 44267--44331 Score: 96
Period size: 27 Copynumber: 2.5 Consensus size: 26
44257 TTATTTTTTC
44267 AAGTCCTCCTTTTTTGATTAAAAAAA
1 AAGTCCTCCTTTTTTGATTAAAAAAA
* *
44293 AATGTCCTCTTTTTTTGATTGAAAAAA
1 AA-GTCCTCCTTTTTTGATTAAAAAAA
44320 AAGTCCT-CTTTT
1 AAGTCCTCCTTTT
44332 GGTCCATACA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
25 4 0.11
26 7 0.20
27 24 0.69
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (26 bp):
AAGTCCTCCTTTTTTGATTAAAAAAA
Found at i:44317 original size:26 final size:27
Alignment explanation
Indices: 44267--44331 Score: 96
Period size: 26 Copynumber: 2.4 Consensus size: 27
44257 TTATTTTTTC
*
44267 AAGTCCTCCTTTTTTGATTAAAAAAAA
1 AAGTCCTCTTTTTTTGATTAAAAAAAA
* *
44294 ATGTCCTCTTTTTTTGATT-GAAAAAA
1 AAGTCCTCTTTTTTTGATTAAAAAAAA
44320 AAGTCCTCTTTT
1 AAGTCCTCTTTT
44332 GGTCCATACA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
26 17 0.50
27 17 0.50
ACGTcount: A:0.32, C:0.15, G:0.09, T:0.43
Consensus pattern (27 bp):
AAGTCCTCTTTTTTTGATTAAAAAAAA
Found at i:55950 original size:2 final size:2
Alignment explanation
Indices: 55943--55973 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
55933 GACAAACTCA
55943 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
55974 GCTAACGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:56177 original size:7 final size:7
Alignment explanation
Indices: 56165--56191 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
56155 GGAGAGTCTT
56165 GATTTTA
1 GATTTTA
56172 GATTTTA
1 GATTTTA
56179 GATTTTA
1 GATTTTA
56186 GATTTT
1 GATTTT
56192 TTATTTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.26, C:0.00, G:0.15, T:0.59
Consensus pattern (7 bp):
GATTTTA
Found at i:66746 original size:364 final size:364
Alignment explanation
Indices: 66077--66805 Score: 1253
Period size: 364 Copynumber: 2.0 Consensus size: 364
66067 ACGCTTTCGT
66077 GGAAGTACGCAAAACCTCCTTTCTATTTTTCTTTTCTTCCGCCGCACAAGAAGCGCTCTTGTAAG
1 GGAAGTACGCAAAACCTCCTTTCTATTTTTCTTTTCTTCCGCCGCACAAGAAGCGCTCTTGTAAG
*
66142 TCCTCATCATATTCATTATCAAAAAAATTCACTCCTCCACTAAAGTCAATATCTTCATATAAGGT
66 ACCTCATCATATTCATTATCAAAAAAATTCACTCCTCCACTAAAGTCAATATCTTCATATAAGGT
* *
66207 GCCTAGCTACCACCTACAAAAACAAATTTCAACTGAGGCGTTAAATCATATTACAATTTAACTCA
131 GCCTAGCTACCACCTACAAAAACAAACTACAACTGAGGCGTTAAATCATATTACAATTTAACTCA
*
66272 ACATAAATTTTTTTGGCTTAGTGCTCAAAATGGCCCCTCAACTTACACAAAACGGCCAAATAAAC
196 ACATAAATTTTTTTGGCTTAGTGCTCAAAATGGCCCCTCAACTTACACAAAACGACCAAATAAAC
* **
66337 CCCTAAACTCTAATTGCAGTCAAATAAGCCCCTGAACTCTTAAAAAATACCAAATAAGCCCTTTT
261 CCCTAAACTCTAATTGCAGTCAAATAAGCCCCTGAACTCTTAAAAAAGACCAAATAAGCCCTAAT
*
66402 CTGTCGGCTAAATACTGAAATAAGGACTAAACGTTTCAA
326 CTGACGGCTAAATACTGAAATAAGGACTAAACGTTTCAA
*
66441 GGAAGTACGCAAAACCTCCTTTCTATTTTTCTTTTCTTCCGCCGCACAAGAAGCGTTCTTGTAAG
1 GGAAGTACGCAAAACCTCCTTTCTATTTTTCTTTTCTTCCGCCGCACAAGAAGCGCTCTTGTAAG
66506 ACCTCATCATATTCATTATCAAAAAAATTCACTCCTCCACTAAAGTCAATATCTTCATATAAGGT
66 ACCTCATCATATTCATTATCAAAAAAATTCACTCCTCCACTAAAGTCAATATCTTCATATAAGGT
** *
66571 GCCTAGCTACCACCTACAAAAACAAACTACAGTTGAGGCGTTAAATCATATTAC-GTTCTAACTC
131 GCCTAGCTACCACCTACAAAAACAAACTACAACTGAGGCGTTAAATCATATTACAATT-TAACTC
* * **
66635 AACATAATTTTTTTTGGCTTATTGCTCAAAATGGCTTCTCAACTTACACAAAACGACCAAATAAA
195 AACATAAATTTTTTTGGCTTAGTGCTCAAAATGGCCCCTCAACTTACACAAAACGACCAAATAAA
* *
66700 CCCCTGAACTCTAATTGCAGTCAAATAAGCCCCTGAACTCTTAAAAAAGGCCAAATAAGCCCTAA
260 CCCCTAAACTCTAATTGCAGTCAAATAAGCCCCTGAACTCTTAAAAAAGACCAAATAAGCCCTAA
* * *
66765 TCTGACGGCTAAATGCTGAAATAATGACTAAATGTTTCAA
325 TCTGACGGCTAAATACTGAAATAAGGACTAAACGTTTCAA
66805 G
1 G
66806 ATTTTCTCAA
Statistics
Matches: 343, Mismatches: 21, Indels: 2
0.94 0.06 0.01
Matches are distributed among these distances:
363 2 0.01
364 341 0.99
ACGTcount: A:0.35, C:0.25, G:0.12, T:0.29
Consensus pattern (364 bp):
GGAAGTACGCAAAACCTCCTTTCTATTTTTCTTTTCTTCCGCCGCACAAGAAGCGCTCTTGTAAG
ACCTCATCATATTCATTATCAAAAAAATTCACTCCTCCACTAAAGTCAATATCTTCATATAAGGT
GCCTAGCTACCACCTACAAAAACAAACTACAACTGAGGCGTTAAATCATATTACAATTTAACTCA
ACATAAATTTTTTTGGCTTAGTGCTCAAAATGGCCCCTCAACTTACACAAAACGACCAAATAAAC
CCCTAAACTCTAATTGCAGTCAAATAAGCCCCTGAACTCTTAAAAAAGACCAAATAAGCCCTAAT
CTGACGGCTAAATACTGAAATAAGGACTAAACGTTTCAA
Done.