Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014694.1 Corchorus olitorius cultivar O-4 contig14727, 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: 96098
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:9250 original size:105 final size:101
Alignment explanation
Indices: 9067--9273 Score: 283
Period size: 103 Copynumber: 2.0 Consensus size: 101
9057 TGGAATGAGC
*
9067 TCAATGTTTTTTAAGTAATGTTTAAGTTTGAGTCTTGTAAAATCCGACTTGTAAATAGGGAAAAC
1 TCAATGTTATTTAAGTAATGTTTAAGTTTGAGTCTTGTAAAATCCGACTTGTAAATAGGGAAAAC
**
9132 ATATGTTAGAAGAGCCTTTCTTATTTGAATCCAAAAAA
66 ATATGTTAGAAGAG--TTTCCCATTTGAATCCAAAAAA
** *
9170 TCAATGTTATTTAAGTAATGTTTGGGTTTCTGAGTCTTGTAAAATCCGATTTGTAAAT-GGAGAA
1 TCAATGTTATTTAAGTAATGTTTAAG-TT-TGAGTCTTGTAAAATCCGACTTGTAAATAGG-GAA
*
9234 AACATGTGTT-GAAAGAGTTTCCCATTTGAATCCAAAAAA
63 AACATATGTTAG-AAGAGTTTCCCATTTGAATCCAAAAAA
9273 T
1 T
9274 AAGTATCAGG
Statistics
Matches: 93, Mismatches: 7, Indels: 8
0.86 0.06 0.07
Matches are distributed among these distances:
103 44 0.47
104 5 0.05
105 44 0.47
ACGTcount: A:0.35, C:0.11, G:0.18, T:0.37
Consensus pattern (101 bp):
TCAATGTTATTTAAGTAATGTTTAAGTTTGAGTCTTGTAAAATCCGACTTGTAAATAGGGAAAAC
ATATGTTAGAAGAGTTTCCCATTTGAATCCAAAAAA
Found at i:20678 original size:31 final size:31
Alignment explanation
Indices: 20610--20683 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 31
20600 GGCACAATGA
* * * *
20610 GAACTCAATTAACCCAATCTTGTGAGTTCAT
1 GAACTAAATTGACTCAATCTTGTGAGTTCAG
20641 GAACTAAATTGACTCAATCTTGTGAGTAT-AG
1 GAACTAAATTGACTCAATCTTGTGAGT-TCAG
*
20672 GGACTAAATTGA
1 GAACTAAATTGA
20684 TCGCTTTTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 36 0.97
32 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (31 bp):
GAACTAAATTGACTCAATCTTGTGAGTTCAG
Found at i:47866 original size:31 final size:31
Alignment explanation
Indices: 47828--47889 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
47818 AAGTTTTGTA
47828 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
47859 AAACTTTTGAATCGCCTATTATACCCTTATT
1 AAACTTTTGAATCGCCTATTATACCCTTATT
47890 TTTAGAATAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.29, C:0.23, G:0.06, T:0.42
Consensus pattern (31 bp):
AAACTTTTGAATCGCCTATTATACCCTTATT
Found at i:48002 original size:93 final size:93
Alignment explanation
Indices: 47901--48079 Score: 295
Period size: 93 Copynumber: 1.9 Consensus size: 93
47891 TTAGAATATA
* * *
47901 TTTATAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATCTACTATTCATATAACTAT
1 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATATAACTAT
*
47966 TTTATTTTTACCATTTTACTATTTTGCT
66 TTTATTTTTACCATATTACTATTTTGCT
* *
47994 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATACCTAT
1 TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATATAACTAT
*
48059 TTTATTTTTACGATATTACTA
66 TTTATTTTTACCATATTACTA
48080 ATTTATTTAA
Statistics
Matches: 79, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 79 1.00
ACGTcount: A:0.32, C:0.13, G:0.03, T:0.51
Consensus pattern (93 bp):
TTTATAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCATATAACTAT
TTTATTTTTACCATATTACTATTTTGCT
Found at i:48726 original size:16 final size:16
Alignment explanation
Indices: 48686--48719 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
48676 TTGGCCTCAA
*
48686 GTCACTCGGATTTTGG
1 GTCATTCGGATTTTGG
*
48702 GTCATTCGGGTTTTGG
1 GTCATTCGGATTTTGG
48718 GT
1 GT
48720 TTTTCGGCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.09, C:0.15, G:0.35, T:0.41
Consensus pattern (16 bp):
GTCATTCGGATTTTGG
Found at i:52863 original size:15 final size:14
Alignment explanation
Indices: 52845--52891 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
52835 TATCTAGAAC
52845 TAAATTATCTTTGAT
1 TAAATTAT-TTTGAT
* *
52860 TAAATTTTTTTTGAG
1 TAAA-TTATTTTGAT
52875 TAAA-TATTTTGAT
1 TAAATTATTTTGAT
52888 TAAA
1 TAAA
52892 ATTAGAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
13 11 0.41
15 13 0.48
16 3 0.11
ACGTcount: A:0.36, C:0.02, G:0.09, T:0.53
Consensus pattern (14 bp):
TAAATTATTTTGAT
Found at i:63611 original size:14 final size:14
Alignment explanation
Indices: 63592--63625 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
63582 ACAACTCTGG
63592 TTTTTTCTTCT-TCT
1 TTTTTTCTTCTGT-T
63606 TTTTTTCTTCTGTT
1 TTTTTTCTTCTGTT
63620 TTTTTT
1 TTTTTT
63626 TTTCATTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 18 0.95
15 1 0.05
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (14 bp):
TTTTTTCTTCTGTT
Found at i:64843 original size:105 final size:101
Alignment explanation
Indices: 64718--64921 Score: 320
Period size: 105 Copynumber: 2.0 Consensus size: 101
64708 ATGAATTATG
64718 ATTTAATATATACGATTTAAGCAATCTCTAAAGCTAGA-TTTTTTTTGAGGTCATCTCTATAGCT
1 ATTTAATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTGAGGTCA--TCTATAGCT
*
64782 AGATTATTACTAATTAATATGGGTAATTGTCTTGCCATATA
64 AGATT-GT--TAATTAATATGGGTAATTGTCTTGCCATATA
* *
64823 ATTTGATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTTAGGTCATCTATAGCTAG
1 ATTTAATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTGAGGTCATCTATAGCTAG
*
64888 ATTGTTAATTAATTTGGGTAATTGTCTTGCCATA
66 ATTGTTAATTAATATGGGTAATTGTCTTGCCATA
64922 ATATTAAAAG
Statistics
Matches: 94, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
101 28 0.30
103 1 0.01
104 14 0.15
105 37 0.39
106 14 0.15
ACGTcount: A:0.31, C:0.12, G:0.14, T:0.43
Consensus pattern (101 bp):
ATTTAATATATACGATTTAAGCAATCTCTAAAGCTAGATTTTTTTTTGAGGTCATCTATAGCTAG
ATTGTTAATTAATATGGGTAATTGTCTTGCCATATA
Found at i:77996 original size:58 final size:57
Alignment explanation
Indices: 77902--78012 Score: 161
Period size: 58 Copynumber: 1.9 Consensus size: 57
77892 ATTAATCAAA
*
77902 TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAGACGTTTTCGGACCGAGCCT
1 TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGCCT
* * *
77959 TATCGAGTGACATGTTTTTTTATTAGATGTC-TAAAAAAGACGTTTTAGGACCGA
1 TATCAAGTGACATG-GTCTTTATTAGATG-CATAAAAAAGACGTTTTAGGACCGA
78013 TGCATGATGC
Statistics
Matches: 48, Mismatches: 4, Indels: 3
0.87 0.07 0.05
Matches are distributed among these distances:
57 13 0.27
58 34 0.71
59 1 0.02
ACGTcount: A:0.32, C:0.14, G:0.21, T:0.33
Consensus pattern (57 bp):
TATCAAGTGACATGGTCTTTATTAGATGCATAAAAAAGACGTTTTAGGACCGAGCCT
Found at i:79318 original size:36 final size:36
Alignment explanation
Indices: 79271--79340 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
79261 TTCAATAACC
* *
79271 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
79307 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
79341 CCAAAATCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Found at i:80227 original size:207 final size:200
Alignment explanation
Indices: 79853--80264 Score: 700
Period size: 207 Copynumber: 2.0 Consensus size: 200
79843 GCTTAATAAC
* *
79853 TTTATCAATGGTGAATGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
79918 GATACAATACAATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGCTTGAT
66 GATACAATACAATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGCTTGAT
79983 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
131 TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
80048 ATTTA
196 ATTTA
80053 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
1 TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
* *
80118 GATACAACACATTACTATTATATATATATATAGAACTATACC-AAAAAAATTAGTTGAATATTAG
66 GAT---ACA-A-TACAATTAT-TATATATA-A-AACTATACCAAAAAAAATTAGTTGAACATTAG
*
80182 TGGTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA
123 TGCTTGATTTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTA
80247 AAGATCCGATTTA
188 AAGATCCGATTTA
80260 TTTAT
1 TTTAT
80265 TATTAAGGAA
Statistics
Matches: 199, Mismatches: 5, Indels: 9
0.93 0.02 0.04
Matches are distributed among these distances:
200 66 0.33
203 3 0.02
204 1 0.01
205 8 0.04
206 8 0.04
207 104 0.52
208 9 0.05
ACGTcount: A:0.44, C:0.08, G:0.10, T:0.37
Consensus pattern (200 bp):
TTTATCAATGATGAACGTTATTAATTTTTTAAGTCTAAGATTACTAACAAAGTTGTAGTGAATAA
GATACAATACAATTATTATATATAAAACTATACCAAAAAAAATTAGTTGAACATTAGTGCTTGAT
TTATTAAATTAAATTAGATCAATGTCAAACAAAATTTCAAAATTATAAAAGATATTAAAGATCCG
ATTTA
Found at i:80434 original size:39 final size:40
Alignment explanation
Indices: 80369--80449 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
80359 CTATCAAAGA
*
80369 ATTTAATTAATATAAGGATTTCAGTTATTATA-GTATTAC
1 ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
* * *
80408 ATTTAATTAATGTAAGTATTTTAGTTATTATATATATTAC
1 ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
80448 AT
1 AT
80450 AGGAATTAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.38, C:0.04, G:0.09, T:0.49
Consensus pattern (40 bp):
ATTTAATTAATATAAGGATTTCAGTTATTATATATATTAC
Found at i:81723 original size:29 final size:29
Alignment explanation
Indices: 81690--81755 Score: 71
Period size: 30 Copynumber: 2.2 Consensus size: 29
81680 CAATTCAAAT
* *
81690 CTAAATCTTT-GAAGCGCTCCAAATTAGGC
1 CTAAATCTTTCGAA-AGCTACAAATTAGGC
* *
81719 CTAAATGTTTTCGAAATCTACAAATTAGGC
1 CTAAAT-CTTTCGAAAGCTACAAATTAGGC
81749 CTAAATC
1 CTAAATC
81756 AGACGGAGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
29 6 0.20
30 21 0.70
31 3 0.10
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (29 bp):
CTAAATCTTTCGAAAGCTACAAATTAGGC
Found at i:90228 original size:17 final size:14
Alignment explanation
Indices: 90194--90222 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
90184 AAACTGGTGA
90194 AGGATGGTTTTATC
1 AGGATGGTTTTATC
90208 AGGATGGTTTTATC
1 AGGATGGTTTTATC
90222 A
1 A
90223 TCAGGAACTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.24, C:0.07, G:0.28, T:0.41
Consensus pattern (14 bp):
AGGATGGTTTTATC
Found at i:90592 original size:26 final size:26
Alignment explanation
Indices: 90563--90893 Score: 509
Period size: 26 Copynumber: 12.7 Consensus size: 26
90553 CAAAATCAAC
**
90563 TATAGTTGCATATTCAGTAGGGCTCA
1 TATAGTTGCATATTCAGTAGGGGACA
** *
90589 TATAGTCACATATTCAATAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
**
90615 TATAGTTGCATATTCAGTAGGGCTCA
1 TATAGTTGCATATTCAGTAGGGGACA
90641 TATAGTTGCATATTCAGTAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
90667 TATAGTTGCATATTCAGTAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
**
90693 TATAGTTGCATATTCAGTAGGGCCCA
1 TATAGTTGCATATTCAGTAGGGGACA
90719 TATAGTTGCATATTCAGTAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
*
90745 TATAGTTGCATATTCAATAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
**
90771 TATAGTTGCATATTCAGTAGGGCTCA
1 TATAGTTGCATATTCAGTAGGGGACA
* **
90797 TATAGTTCCATATTCAGTAGGGCCCA
1 TATAGTTGCATATTCAGTAGGGGACA
*
90823 TATAGCTGCATATTCAGTAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
90849 TATAGTTGCATATTCAGTAGGGGACA
1 TATAGTTGCATATTCAGTAGGGGACA
*
90875 TATAGTTGCATATTTAGTA
1 TATAGTTGCATATTCAGTA
90894 CAAGATTGGA
Statistics
Matches: 277, Mismatches: 28, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 277 1.00
ACGTcount: A:0.30, C:0.14, G:0.24, T:0.32
Consensus pattern (26 bp):
TATAGTTGCATATTCAGTAGGGGACA
Found at i:91289 original size:5 final size:5
Alignment explanation
Indices: 91279--91323 Score: 62
Period size: 5 Copynumber: 9.8 Consensus size: 5
91269 AATTATTTTA
91279 CTTAT CTTAT CTTAT CTTAT CTTA- C-TAT CTTAT CTTA- C-TAT CTTA
1 CTTAT CTTAT CTTAT CTTAT CTTAT CTTAT CTTAT CTTAT CTTAT CTTA
91324 CTACTATGTA
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
3 4 0.11
4 4 0.11
5 28 0.78
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (5 bp):
CTTAT
Found at i:91309 original size:13 final size:13
Alignment explanation
Indices: 91279--91323 Score: 72
Period size: 13 Copynumber: 3.3 Consensus size: 13
91269 AATTATTTTA
91279 CTTATCTTATCTTAT
1 CTTATCTTA-C-TAT
91294 CTTATCTTACTAT
1 CTTATCTTACTAT
91307 CTTATCTTACTAT
1 CTTATCTTACTAT
91320 CTTA
1 CTTA
91324 CTACTATGTA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
13 20 0.67
14 1 0.03
15 9 0.30
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (13 bp):
CTTATCTTACTAT
Found at i:92420 original size:334 final size:328
Alignment explanation
Indices: 91987--92888 Score: 1040
Period size: 323 Copynumber: 2.7 Consensus size: 328
91977 ATTATTTGAA
* * * *
91987 ATATTCATCTAACCGAATGTCAGCCACATTGGATTTAAGGATTTGTTTTTACAAGTATCTGAATC
1 ATATTCATCAAACCAAATCTCA-CCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATC
* *
92052 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATAATAGAATCGTGAACA
65 TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAA-A
*
92117 ACCCTTTCAATTTTTTTGGCGTTAAATTATATATTTTTTCTGAGTATTGTGGCAAAATATTTATA
129 ACCC-TTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAA-ATTTATA
* * *
92182 AAAAACTTTTCGGGTCAGTTTTTGCAAAATTTTAGCGGAAATTTGTGTACTAAAC-ATTAC-GGT
192 AAAAACTATTCGGGTCAGTTTTTGCAAAATTTTAGC-GAAA-TCGTGTACT-AACTATCACTGGT
* * ** * *
92245 TTTTGGCTAAAAATGCGTTAAGGAGTCCTGCCTCAATTTTGCATGATTTTTGGCACAAAGACTCC
254 TTTTGGCTAAAAACGAGTTAAGGAGTCC-AACTCAATTTTGCATGATTTTTCGCACAAAGAATCC
92310 TTGAAATATCT
318 TTGAAATATCT
* *
92321 ATATTCATCAAACCAAATCTCTACCACATTGGATATAAGGATTTGTTTTTACTAGCATCTGAATC
1 ATATTCATCAAACCAAATCTC-ACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATC
*
92386 TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAATGGAAAAACGATATTAGAAGCGTGA
65 TTGTTTCGATTTAATTAGAAATAAATTCGG--AAAAA-AATGGAAAAACGATATTAGAAGCGTGA
** * *
92451 AAGA-CAGTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAATATT-TTGCAAAAATTTGA
127 AA-ACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTT-A
* * * * *
92514 GAAAAAACTATTCTGGTTAG----T------TTTTAGCCAAAATCGTGTACTAACTATCACTGTT
190 TAAAAAACTATTCGGGTCAGTTTTTGCAAAATTTTAG-CGAAATCGTGTACTAACTATCACTGGT
** * * * * *
92569 TTTTGGCTAAAAACGAGTTTCGGGGTCCAACTCAGTTTTGCCTGATTTTTCGTAGAAAGAATCCT
254 TTTTGGCTAAAAACGAGTTAAGGAGTCCAACTCAATTTTGCATGATTTTTCGCACAAAGAATCCT
92634 TGAAATATCT
319 TGAAATATCT
* * * * * *
92644 ACATTCATCAAACCAAATCTCAACCAAAATAGATTTAAGAATTTGTTTTTACGAGCATCTGAATC
1 ATATTCATCAAACCAAATCTC-ACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATC
* * *
92709 TTTGTTTCGATTTAATTAGAAATAAATTTGGAAAGAATTGGAAAAACGATATTAGAAGCGTGAAA
65 -TTGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTG-AA
* ** * * *
92774 AACCCTTCAATTTTTTTGGCGTTGAATTATTTATTTTTTCAAAGCAATGTGGCAAAAAATTAATA
128 AACCCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGC-AAAAATTTATA
** * *
92839 AAAAACCCTTCGGCTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACT
192 AAAAACTATTCGGGTCAGTTTTTGCAAAATTTTAG-CGAAATCGTGTACT
92889 TTTTTTATTT
Statistics
Matches: 479, Mismatches: 65, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
321 26 0.05
322 47 0.10
323 125 0.26
324 69 0.14
325 1 0.00
327 1 0.00
330 1 0.00
333 24 0.05
334 110 0.23
335 41 0.09
336 7 0.01
337 27 0.06
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (328 bp):
ATATTCATCAAACCAAATCTCACCACATTGGATTTAAGGATTTGTTTTTACAAGCATCTGAATCT
TGTTTCGATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTAGAAGCGTGAAAAC
CCTTCAATTTTTTTGGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAAAATTTATAAAAA
ACTATTCGGGTCAGTTTTTGCAAAATTTTAGCGAAATCGTGTACTAACTATCACTGGTTTTTGGC
TAAAAACGAGTTAAGGAGTCCAACTCAATTTTGCATGATTTTTCGCACAAAGAATCCTTGAAATA
TCT
Found at i:93690 original size:685 final size:680
Alignment explanation
Indices: 92226--93874 Score: 2114
Period size: 685 Copynumber: 2.4 Consensus size: 680
92216 GCGGAAATTT
* * * * ** * *
92226 GTGTACTAAACATTACGGTTTTTGGCTAAAAATGCGTTAAGGAGTCCTGCCTCAATTTTGCATGA
1 GTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGA
* * *
92291 TTTTTGGCACAAAGACTCCTTGAAATATCTATATTCATCAAACCAAATCTCTACCACATTGGATA
66 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC-ACCACATTGTATA
* **
92356 TAAGGATTTGTTTTTACTAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAA
130 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTA-AAATTAATTTAG-AAAA
*
92421 AATAATGGAAAAACGATATTAGAAGCGTG-AAAGACAGTCAATTTTTTTGGCGTTGAATTATATA
193 AATAATGGAAAAACGATATTAGAAGCGTGAAAAGCCA-TCAATTTTTTTGGCGTTGAATTATATA
* * *
92485 TTTTTTCTGAATATTTTGCAAAAATTTGAGAAAAAACTATTCTGGTTAGTTTTTAGCCAAAATCG
257 TTTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTATTCGGGTCAGTTTTTAGCCAAAATCG
* * * * ***
92550 TGTACTAACTATCACTGTTTTTTGGCTAAAAACGAGTTTCGGGGTCCAACTCAGTTTTGCCTGAT
322 TGTACTAACCATCACTGGTTTTTGGCTAAAAACGAGTTTCAGGGCCCAACTCAGTTTTAAATGAT
* *
92615 TTTTCGTAGAAAGAATCCTTGAAATATCTACATTCATCAAACCAAATCTCAACCAAAATAGATTT
387 TTTTCGCAGAAAGAATCCTAGAAATATCTACATTCATCAAACCAAATCTCAACCAAAATAGATTT
** * * * *
92680 AAGAATTTGTTTTTACGAGCATCTGAATCTTTGTTTCGATTTAATTAGAAATAAATTTGGAAAGA
452 AAGAATTTGAGTTTACGAGCATCTGAATCTTTATTTCGATTCAATTAGAAATAAATTAGGAAAAA
** * *
92745 ATTGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAATTTTTTTGGCGTTGAATTATTTATTT
517 AAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGGCGTTGAATTATATATTT
* *
92810 TTTCAAAGCAATGTGGCAAAAAATTAATAAAAAACCCTTCGGCTCAATTTTTGCAAAATTTTAGC
582 CTTCAAAGCAATGTGGCAAAAAATTAAGAAAAAACCCTTCGGCTCAATTTTTGCAAAATTTTAGC
92875 CGAAATCGTGTACTTTTTTTATTTTGCCAACGAAATC
647 CGAAATCGTGTA---TTTTTATTTTGCCAACGAAATC
* * * * * * *
92912 TTGTACTTACCATCACGATTTTTGCCTAAAAACGCATTCCTGAGTCTCGGCTCAATTTTGCATGA
1 GTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGA
** * *
92977 TTTTTACCGCAAAGACTCCTTAAAATATCTATATTCATCGAACCAAATCTCAGTCACATTGTATA
66 TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCA-CCACATTGTATA
* *
93042 TAAGAATTTGTTTTTACGAGCATCTAAATCTTGTTTCGATTTAATTAATAATTAATTTAGAAAAA
130 TAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAA-AATTAATTTAGAAAAA
* * * *
93107 ATAATGGAAAAACGATATTAGAAGCGTGAAAAGGCCATCAATCTTTTTAGCTTTGAATAATATA-
194 ATAATGGAAAAACGATATTAGAAGCGTGAAAA-GCCATCAATTTTTTTGGCGTTGAATTATATAT
*
93171 TTTTTCTGAATATTTTGCAAAAAATTGAG-AAAAACTTTTCGGGTCAGTTTTTAGCCGAAAA-CG
258 TTTTTCTGAATATTTTGCAAAAAATTGAGAAAAAACTATTCGGGTCAGTTTTTAGCC-AAAATCG
* * * * ** *
93234 TGTACTAACCATCAC-GGTTTTTGGTTAAAATCGTGTTTCATGGCCTCGGCTTAGTTTTAAATGA
322 TGTACTAACCATCACTGGTTTTTGGCTAAAAACGAGTTTCAGGGCC-CAACTCAGTTTTAAATGA
* * * * * * *
93298 TTTTTGGCAGAAAGACTCCTAGAAATATTTACATTCATCTAACCAGATCTCAGCTAAAATAGATT
386 TTTTTCGCAGAAAGAATCCTAGAAATATCTACATTCATCAAACCAAATCTCAACCAAAATAGATT
* * *
93363 TTAGGATTTGAGTTTACGAGCATCTGAATCTTTATTTTGATTCAATTAGAAATAAATTAGGAAAA
451 TAAGAATTTGAGTTTACGAGCATCTGAATCTTTATTTCGATTCAATTAGAAATAAATTAGGAAAA
93428 AAGAAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGGCGTTGAATTATATAT
516 AA-AAGGAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGGCGTTGAATTATATAT
** * * * * *
93493 TTCTTCTCAGTATTGTGGCAAAAAAATTGAGAAAAAACCTTTCGGGTCAATTTTTGCAAAATTTT
580 TTCTTCAAAGCAATGTGGC-AAAAAATTAAGAAAAAACCCTTCGGCTCAATTTTTGCAAAATTTT
*
93558 AGCCGAAATCGTGTA-TTTT-TTTT-CCTACGAAATC
644 AGCCGAAATCGTGTATTTTTATTTTGCCAACGAAATC
* * * * * *
93592 GTGTACTAACTATCATGGTTTTTTTTTTGGCTAAAAACGTGTTCCGGAGTCCCGACTCAATTCTA
1 GTGTACTAACCATCA-CG----ATTTTTGGCTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTG
* * * * *
93657 CATGATTTTTGGCGTATAGACTCCTTGAAATATCTATATTCATCGTACCAAATATCAACCACGTT
61 CATGATTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTC-ACCACATT
* * *
93722 GTATATAAGGATTTGTTTTTACGAGCATATGAATCTTATTTCGATTTAATTAAAAATTAA-TTCG
125 GTATATAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATT-AAAATTAATTTAG
* * *
93786 GAAAAA-AATGGAAAAACGATATTAGAAGCATGAACAA-CACGTCAATTTTTTTGGCGTTGAATT
189 AAAAAATAATGGAAAAACGATATTAGAAGCGTGAA-AAGC-CATCAATTTTTTTGGCGTTGAATT
*
93849 ATATATTTTTTCTAAATATTTTGCAA
252 ATATATTTTTTCTGAATATTTTGCAA
93875 TTTTTTTCTC
Statistics
Matches: 829, Mismatches: 116, Indels: 38
0.84 0.12 0.04
Matches are distributed among these distances:
680 22 0.03
681 5 0.01
682 5 0.01
683 74 0.09
684 195 0.24
685 280 0.34
686 245 0.30
687 3 0.00
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.36
Consensus pattern (680 bp):
GTGTACTAACCATCACGATTTTTGGCTAAAAACGCGTTCCGGAGTCCCGACTCAATTTTGCATGA
TTTTTGGCGCAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCACCACATTGTATAT
AAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAAAATTAATTTAGAAAAAAT
AATGGAAAAACGATATTAGAAGCGTGAAAAGCCATCAATTTTTTTGGCGTTGAATTATATATTTT
TTCTGAATATTTTGCAAAAAATTGAGAAAAAACTATTCGGGTCAGTTTTTAGCCAAAATCGTGTA
CTAACCATCACTGGTTTTTGGCTAAAAACGAGTTTCAGGGCCCAACTCAGTTTTAAATGATTTTT
CGCAGAAAGAATCCTAGAAATATCTACATTCATCAAACCAAATCTCAACCAAAATAGATTTAAGA
ATTTGAGTTTACGAGCATCTGAATCTTTATTTCGATTCAATTAGAAATAAATTAGGAAAAAAAAG
GAAAAACGATATTAGAAGCGTGAAAAACCCTTCAAATTTTTTGGCGTTGAATTATATATTTCTTC
AAAGCAATGTGGCAAAAAATTAAGAAAAAACCCTTCGGCTCAATTTTTGCAAAATTTTAGCCGAA
ATCGTGTATTTTTATTTTGCCAACGAAATC
Found at i:95356 original size:307 final size:308
Alignment explanation
Indices: 94845--95419 Score: 720
Period size: 307 Copynumber: 1.9 Consensus size: 308
94835 TTTTTGCCAA
* * *
94845 CGAAAACGTGTACTAACTATCATGGTTTTTTGGCTAAAAACGCGTTCCAGAGTCCCGACTCAATT
1 CGAAAACGTGTACTAACCATCATGGTTTTTTGGCTAAAAACACGTTCCAGAGGCCCGACTCAATT
** * *
94910 TTGCATCAGTTTTGGCGTAAAGATTCCTTGAAATATTTATATTCATCGTACCAAATCTCAGCCAT
66 TTGCATCAGTTTTGGCGTAAAGATTCCTTGAAATAGCTATATTCATCGTACCAAATCTCAGCAAC
** * * * * *
94975 GTTGTATATAAGGATTTGTTTTTACGAGCATATGAATCTTATTTCGATTTAATTAGCAATTAGTT
131 AATGGATATAAGGATTTGTTTTTACGAGCATATCAATCTTATTTCGATTTAATTAGAAATAAATT
*
95040 CGGAAAAAAATG-GA-AAAACGATATTAGAAGCAT-AAACAGCCCGTAAAGTTTTTTGGCGTTGA
196 C-GAAAAAAA-GAAAGAAAACGATATTAGAAGCATGAAA-A-CCCGTAAAGTTTTTTGGCGTTGA
95102 ATTATATATTTTTTCTAAATATTTTGCAAAAATTGAGCTTTCGAGTTAGAGC
257 ATTATATATTTTTTCTAAATATTTTGCAAAAATTGAGCTTTCGAGTTAGAGC
* * *
95154 CGAAATCGTGTACTAACCATCATGG-TTTTTGGCTAAAAACACGTTTC-G-GGCCTCGACTCAGT
1 CGAAAACGTGTACTAACCATCATGGTTTTTTGGCTAAAAACACGTTCCAGAGGCC-CGACTCAAT
* *
95216 TTTGCATGA-TTTTAGGCAG-AAAGATTCCTTGAAATAGCTATATTCATC-TAACCAAATCTTAG
65 TTTGCATCAGTTTT-GGC-GTAAAGATTCCTTGAAATAGCTATATTCATCGT-ACCAAATCTCAG
* * * *
95278 TAACAATGGATTTAAGGATTTGTTTTTACGAGCATCTCAATCTTTGTTTCGATTTAATTAGAAAA
127 CAACAATGGATATAAGGATTTGTTTTTACGAGCATATCAATC-TTATTTCGATTTAATTAG-AAA
* * * *
95343 TAAATTC-AAAAAAAGAAAAGAAAACGATATTAGAAGCGTGAAAACCCTTCAATTTTTTTGGCGT
190 TAAATTCGAAAAAAAG-AAAGAAAACGATATTAGAAGCATGAAAACCCGTAAAGTTTTTTGGCGT
*
95407 TGAATTATTTATT
254 TGAATTATATATT
95420 CTTTATGAGT
Statistics
Matches: 227, Mismatches: 29, Indels: 21
0.82 0.10 0.08
Matches are distributed among these distances:
306 9 0.04
307 98 0.43
308 68 0.30
309 49 0.22
310 3 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (308 bp):
CGAAAACGTGTACTAACCATCATGGTTTTTTGGCTAAAAACACGTTCCAGAGGCCCGACTCAATT
TTGCATCAGTTTTGGCGTAAAGATTCCTTGAAATAGCTATATTCATCGTACCAAATCTCAGCAAC
AATGGATATAAGGATTTGTTTTTACGAGCATATCAATCTTATTTCGATTTAATTAGAAATAAATT
CGAAAAAAAGAAAGAAAACGATATTAGAAGCATGAAAACCCGTAAAGTTTTTTGGCGTTGAATTA
TATATTTTTTCTAAATATTTTGCAAAAATTGAGCTTTCGAGTTAGAGC
Done.