Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032244.1 Gossypioides kirkii chromosome KI_01
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: 38174113
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1000 characters in sequence are not A, C, G, or T
File 126 of 126
Found at i:38052073 original size:14 final size:15
Alignment explanation
Indices: 38052054--38052082 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
38052044 TTAATTTTTT
38052054 TTAAAA-TAAAAATA
1 TTAAAATTAAAAATA
38052068 TTAAAATTAAAAATA
1 TTAAAATTAAAAATA
38052083 AAAATATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TTAAAATTAAAAATA
Found at i:38055053 original size:14 final size:14
Alignment explanation
Indices: 38055034--38055061 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
38055024 TCTAGTTAAG
38055034 CCTATTATATTTAC
1 CCTATTATATTTAC
38055048 CCTATTATATTTAC
1 CCTATTATATTTAC
38055062 TTTGAAAGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.29, C:0.21, G:0.00, T:0.50
Consensus pattern (14 bp):
CCTATTATATTTAC
Found at i:38066743 original size:19 final size:20
Alignment explanation
Indices: 38066708--38066746 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
38066698 ACCCAAATCA
38066708 TGTGAATAAATAAAAATTAGT
1 TGTGAATAAAT-AAAATTAGT
38066729 TGTGAATAAAT-AAATTAG
1 TGTGAATAAATAAAATTAG
38066747 ACTTGGTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.00, G:0.15, T:0.33
Consensus pattern (20 bp):
TGTGAATAAATAAAATTAGT
Found at i:38082906 original size:33 final size:33
Alignment explanation
Indices: 38082864--38082932 Score: 138
Period size: 33 Copynumber: 2.1 Consensus size: 33
38082854 ATTAAGAACC
38082864 TTAGTTTATAGCTTTGCTAAATAAAGATCTAAG
1 TTAGTTTATAGCTTTGCTAAATAAAGATCTAAG
38082897 TTAGTTTATAGCTTTGCTAAATAAAGATCTAAG
1 TTAGTTTATAGCTTTGCTAAATAAAGATCTAAG
38082930 TTA
1 TTA
38082933 TACACAAGCA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.36, C:0.09, G:0.14, T:0.41
Consensus pattern (33 bp):
TTAGTTTATAGCTTTGCTAAATAAAGATCTAAG
Found at i:38090856 original size:5 final size:5
Alignment explanation
Indices: 38090846--38090870 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
38090836 GTTTGATCAA
38090846 AGGCT AGGCT AGGCT AGGCT AGGCT
1 AGGCT AGGCT AGGCT AGGCT AGGCT
38090871 CATTTAAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.40, T:0.20
Consensus pattern (5 bp):
AGGCT
Found at i:38100071 original size:81 final size:83
Alignment explanation
Indices: 38099935--38100102 Score: 218
Period size: 81 Copynumber: 2.0 Consensus size: 83
38099925 AAAAGGATAT
* *
38099935 TTTTGCAATTTAGTCCTTTTATAAATAGATAAACTATAAAATAATATATAGTAAAATTTCACTTT
1 TTTTGCAATTAAGTCCTCTTATAAATAGATAAACTATAAAATAATATATAGTAAAATTTCACTTT
**
38100000 -GACTCCTCAAATGTAAAA
66 AG-CTCCTCAAAAATAAAA
* **
38100018 TTTT-CAATTAAGTCCTCTTATAAATA-A-AGAATTATAAGGTAATATATAGTAAAATTTCACTT
1 TTTTGCAATTAAGTCCTCTTATAAATAGATA-AACTATAAAATAATATATAGTAAAATTTCACTT
*
38100080 TAGCTCCTTAAAAATAAAA
65 TAGCTCCTCAAAAATAAAA
38100099 TTTT
1 TTTT
38100103 TTTAGTCCTT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
80 1 0.01
81 49 0.65
82 21 0.28
83 4 0.05
ACGTcount: A:0.42, C:0.11, G:0.07, T:0.39
Consensus pattern (83 bp):
TTTTGCAATTAAGTCCTCTTATAAATAGATAAACTATAAAATAATATATAGTAAAATTTCACTTT
AGCTCCTCAAAAATAAAA
Found at i:38102178 original size:19 final size:20
Alignment explanation
Indices: 38102143--38102180 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
38102133 ATAATGCCTT
*
38102143 TCTCTTTTTGTACTTTTTCC
1 TCTCATTTTGTACTTTTTCC
38102163 TCTCATTTTG-ACTTTTTC
1 TCTCATTTTGTACTTTTTC
38102181 TGACTTTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.08, C:0.24, G:0.05, T:0.63
Consensus pattern (20 bp):
TCTCATTTTGTACTTTTTCC
Found at i:38104252 original size:27 final size:27
Alignment explanation
Indices: 38104222--38104292 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 27
38104212 TTCCATTAAT
38104222 ATAATTTAAACTAATTTTTTTGTGTA-A
1 ATAATTTAAACTAATTTTTTTG-GTAGA
38104249 ATAATTTAAACTAATTTTTTTGGTAGA
1 ATAATTTAAACTAATTTTTTTGGTAGA
* *
38104276 TTAATTTAAATTAATTT
1 ATAATTTAAACTAATTT
38104293 GATCCTTCTA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
26 3 0.07
27 38 0.93
ACGTcount: A:0.38, C:0.03, G:0.07, T:0.52
Consensus pattern (27 bp):
ATAATTTAAACTAATTTTTTTGGTAGA
Found at i:38108876 original size:21 final size:22
Alignment explanation
Indices: 38108830--38108879 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
38108820 AACAGTGCAG
*
38108830 ACTTCTACCGATACAAGTGACT
1 ACTTCTACCGATACAAGTCACT
38108852 -CTTCTACCGA-AGCAAGTCA-T
1 ACTTCTACCGATA-CAAGTCACT
38108872 ACTTCTAC
1 ACTTCTAC
38108880 TGGTACTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.30, C:0.30, G:0.12, T:0.28
Consensus pattern (22 bp):
ACTTCTACCGATACAAGTCACT
Found at i:38109216 original size:13 final size:13
Alignment explanation
Indices: 38109190--38109245 Score: 55
Period size: 13 Copynumber: 4.5 Consensus size: 13
38109180 TAATTTAAGT
38109190 TATTATGAATTAA
1 TATTATGAATTAA
38109203 TATTA-GAATATAA
1 TATTATGAAT-TAA
* * *
38109216 TAATATAAATTAT
1 TATTATGAATTAA
38109229 TATT-T-AATTAA
1 TATTATGAATTAA
38109240 TATTAT
1 TATTAT
38109246 CTTATTATAT
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
11 9 0.26
12 6 0.17
13 17 0.49
14 3 0.09
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (13 bp):
TATTATGAATTAA
Found at i:38109425 original size:2 final size:2
Alignment explanation
Indices: 38109418--38109459 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
38109408 TTACTAACTA
38109418 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
38109459 A
1 A
38109460 AAAGGATAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:38113603 original size:51 final size:51
Alignment explanation
Indices: 38113529--38113761 Score: 342
Period size: 51 Copynumber: 4.6 Consensus size: 51
38113519 TTTCATTTAA
* * * * *
38113529 TACTCACGATGACATATTA-TCATCAGACCTTTAATTCGTCATGGATTCATT
1 TACTCACGATGACA-CTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
38113580 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
38113631 TACTCACGATGACATTTAGTCATCGGACCTTTAATTCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* * *
38113682 TACTCATGATGACACTTAGTCACCTGACCTTTAATCCGTAAAGGATTCATT
1 TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
* *
38113733 TGCTCACGATGACACTTAGTCACCGGACC
1 TACTCACGATGACACTTAGTCATCGGACC
38113762 CTTTCGTTTA
Statistics
Matches: 166, Mismatches: 15, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
50 3 0.02
51 163 0.98
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.33
Consensus pattern (51 bp):
TACTCACGATGACACTTAGTCATCGGACCTTTAATCCGTAAAGGATTCATT
Found at i:38119609 original size:51 final size:51
Alignment explanation
Indices: 38119522--38119758 Score: 305
Period size: 51 Copynumber: 4.6 Consensus size: 51
38119512 GCTATAAACG
* *
38119522 AAAGAGTCCGGTGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGGATT
1 AAAG-GTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* ** * *
38119574 AAAGGTCTGATGACTAAGTGTCATCGTGAGTAAATGAATTATTTATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* *
38119625 AAAGGTCCGATGACTAAGTGTTATCGTGAGCAAATGAATCCTTTACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* * * *
38119676 AAAGATCCGATGACTAAGTGTAATCGTGAGTAAATGAATCCATGACGAATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
* * *
38119727 AAAGGTCTGATGAC-AATATGTCATCATGAGTA
1 AAAGGTCCGATGACTAA-GTGTCATCGTGAGTA
38119759 TCAAATGAAA
Statistics
Matches: 162, Mismatches: 22, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
50 2 0.01
51 156 0.96
52 4 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.30
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTTACGAATT
Found at i:38124064 original size:21 final size:21
Alignment explanation
Indices: 38124039--38124094 Score: 71
Period size: 21 Copynumber: 2.7 Consensus size: 21
38124029 AATAGTGCAG
38124039 ACTTCTACCGATACAAGTGAC-T
1 ACTTCTACCGATACAAGT--CTT
*
38124061 -CTTCTACCGAAACAAGTCTT
1 ACTTCTACCGATACAAGTCTT
38124081 ACTTCTACCGATAC
1 ACTTCTACCGATAC
38124095 TAAAAACTCC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
19 1 0.03
20 1 0.03
21 28 0.93
ACGTcount: A:0.30, C:0.30, G:0.11, T:0.29
Consensus pattern (21 bp):
ACTTCTACCGATACAAGTCTT
Found at i:38124848 original size:61 final size:61
Alignment explanation
Indices: 38124772--38124920 Score: 246
Period size: 61 Copynumber: 2.4 Consensus size: 61
38124762 TTTGATAACT
* *
38124772 ACGATGCCGTAAAGACATCA-GACCTTTAATCCATAATAGGATTCATTTTCATGTAATACTC
1 ACGATGACATAAAGACAT-AGGACCTTTAATCCATAATAGGATTCATTTTCATGTAATACTC
38124833 ACGATGACATAAAGACATAGGACCTTTAATCCATAATAGGATTCATTTTCATGTAATACTC
1 ACGATGACATAAAGACATAGGACCTTTAATCCATAATAGGATTCATTTTCATGTAATACTC
* *
38124894 ACGATGACATAAAGACATTGAACCTTT
1 ACGATGACATAAAGACATAGGACCTTT
38124921 TTGCATTTAC
Statistics
Matches: 83, Mismatches: 4, Indels: 2
0.93 0.04 0.02
Matches are distributed among these distances:
60 1 0.01
61 82 0.99
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.30
Consensus pattern (61 bp):
ACGATGACATAAAGACATAGGACCTTTAATCCATAATAGGATTCATTTTCATGTAATACTC
Found at i:38128381 original size:22 final size:22
Alignment explanation
Indices: 38128356--38128399 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38128346 TCAAGAATTG
* * *
38128356 AAATATATTTAATTTAAATTCA
1 AAATAAATTTAAATAAAATTCA
38128378 AAATAAATTTAAATAAAATTCA
1 AAATAAATTTAAATAAAATTCA
38128400 CAAAATTTAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (22 bp):
AAATAAATTTAAATAAAATTCA
Found at i:38128429 original size:37 final size:39
Alignment explanation
Indices: 38128366--38128440 Score: 102
Period size: 37 Copynumber: 2.0 Consensus size: 39
38128356 AAATATATTT
* *
38128366 AATTTAAATTCAAAATAAATTTAAATA-AA-ATTCACAA
1 AATTTAAAATCAAAATAAATTGAAATATAACATTCACAA
38128403 AATTTAAAATCAAAAT-AATATGAAATATAACATTCACA
1 AATTTAAAATCAAAATAAAT-TGAAATATAACATTCACA
38128441 TTATGTTATA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 3 0.09
37 21 0.64
38 2 0.06
39 7 0.21
ACGTcount: A:0.59, C:0.09, G:0.01, T:0.31
Consensus pattern (39 bp):
AATTTAAAATCAAAATAAATTGAAATATAACATTCACAA
Found at i:38145733 original size:23 final size:23
Alignment explanation
Indices: 38145707--38145829 Score: 140
Period size: 23 Copynumber: 5.3 Consensus size: 23
38145697 AGTGCTGGGC
*
38145707 AACAGAGAGCACACACAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* * *
38145730 AACAGAGAGTACACAAAGTACTA
1 AACAGAGAGCACACACAGTGCTA
* *
38145753 ATCAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACACAGTGCTA
*
38145776 ATCAGAGAGCACACACAGTGCTAA
1 AACAGAGAGCACACACAGTGCT-A
*
38145800 TAACAGAGAGCACGAGAC-GTGCTA
1 -AACAGAGAGCAC-ACACAGTGCTA
38145824 AACAGA
1 AACAGA
38145830 AACCGCGCTA
Statistics
Matches: 89, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
23 68 0.76
24 2 0.02
25 16 0.18
26 3 0.03
ACGTcount: A:0.46, C:0.22, G:0.21, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACACAGTGCTA
Found at i:38145782 original size:69 final size:68
Alignment explanation
Indices: 38145666--38145809 Score: 177
Period size: 69 Copynumber: 2.1 Consensus size: 68
38145656 CGGAAAAAAT
* *
38145666 AGAGTACCAAAGTACTAACAGAGAGCAGATAAGTGCTGGGCAACAGAGAGCACACACAGTACT-A
1 AGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCT--G-AACAGAGAGCACACACAGTACTAA
38145730 -AACAG
63 TAACAG
*
38145735 AGAGTACACAAAGTACTAATCAGAGAGCACACAAAGTGCT-AATCAGAGAGCACACACAGTGCTA
1 AGAGTAC-CAAAGTACTAA-CAGAGAGCACA-AAAGTGCTGAA-CAGAGAGCACACACAGTACTA
38145799 ATAACAG
62 ATAACAG
38145806 AGAG
1 AGAG
38145810 CACGAGACGT
Statistics
Matches: 66, Mismatches: 3, Indels: 10
0.84 0.04 0.13
Matches are distributed among these distances:
68 2 0.03
69 26 0.39
70 12 0.18
71 19 0.29
72 7 0.11
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.12
Consensus pattern (68 bp):
AGAGTACCAAAGTACTAACAGAGAGCACAAAAGTGCTGAACAGAGAGCACACACAGTACTAATAA
CAG
Found at i:38151881 original size:22 final size:23
Alignment explanation
Indices: 38151851--38151897 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
38151841 ACGCTAGCGC
*
38151851 GCTTACTGTTCAGCATTGTGAGT
1 GCTTACTGTTCAGCACTGTGAGT
*
38151874 GCTT-CTGTTCAGCACTGTGTGT
1 GCTTACTGTTCAGCACTGTGAGT
38151896 GC
1 GC
38151898 CTATTGTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.13, C:0.21, G:0.28, T:0.38
Consensus pattern (23 bp):
GCTTACTGTTCAGCACTGTGAGT
Found at i:38151938 original size:25 final size:24
Alignment explanation
Indices: 38151902--38151979 Score: 129
Period size: 25 Copynumber: 3.2 Consensus size: 24
38151892 GTGTGCCTAT
38151902 TGTTTCCCAGCACTTATGTGCTTC
1 TGTTTCCCAGCACTTATGTGCTTC
*
38151926 TGTTTCTCTAGCACTTATGTGCTTC
1 TGTTTC-CCAGCACTTATGTGCTTC
38151951 TGTTTCCCCAGCACTTATGTGCTTC
1 TGTTT-CCCAGCACTTATGTGCTTC
38151976 TGTT
1 TGTT
38151980 AAGTACTTCG
Statistics
Matches: 50, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
24 6 0.12
25 43 0.86
26 1 0.02
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (24 bp):
TGTTTCCCAGCACTTATGTGCTTC
Found at i:38154388 original size:25 final size:25
Alignment explanation
Indices: 38154358--38154406 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
38154348 CGGTTTCTGT
38154358 TTAGCA-CGTCTCGTGCTCTCTGTTA
1 TTAGCATCGTCT-GTGCTCTCTGTTA
* *
38154383 TTAGCATTGTGTGTGCTCTCTGTT
1 TTAGCATCGTCTGTGCTCTCTGTT
38154407 GCCCAGCACT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 18 0.86
26 3 0.14
ACGTcount: A:0.10, C:0.22, G:0.22, T:0.45
Consensus pattern (25 bp):
TTAGCATCGTCTGTGCTCTCTGTTA
Found at i:38167331 original size:34 final size:35
Alignment explanation
Indices: 38167258--38167336 Score: 151
Period size: 35 Copynumber: 2.3 Consensus size: 35
38167248 CAAAGTAATT
38167258 AATAAATCCTCATCTCGTCCAAAAAGAAATAAATA
1 AATAAATCCTCATCTCGTCCAAAAAGAAATAAATA
38167293 AATAAATCCTCATCTCGTCCAAAAAGAAA-AAATA
1 AATAAATCCTCATCTCGTCCAAAAAGAAATAAATA
38167327 AATAAATCCT
1 AATAAATCCT
38167337 GAATTTGTGA
Statistics
Matches: 44, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
34 15 0.34
35 29 0.66
ACGTcount: A:0.52, C:0.20, G:0.05, T:0.23
Consensus pattern (35 bp):
AATAAATCCTCATCTCGTCCAAAAAGAAATAAATA
Found at i:38167902 original size:33 final size:33
Alignment explanation
Indices: 38167865--38167930 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
38167855 TAACATAGAA
38167865 TTTTCATGGCTTAAATTGAGCCAATAAGTAGTG
1 TTTTCATGGCTTAAATTGAGCCAATAAGTAGTG
38167898 TTTTCATGGCTTAAATTGAGCCAATAAGTAGTG
1 TTTTCATGGCTTAAATTGAGCCAATAAGTAGTG
38167931 AAAATTCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.36
Consensus pattern (33 bp):
TTTTCATGGCTTAAATTGAGCCAATAAGTAGTG
Found at i:38168202 original size:25 final size:25
Alignment explanation
Indices: 38168151--38168217 Score: 73
Period size: 25 Copynumber: 2.7 Consensus size: 25
38168141 ATCCAAACTG
*
38168151 AATCCTAAACCAAAACTAAAATCAA
1 AATCCTAAACTAAAACTAAAATCAA
**
38168176 AATCCTAAACTAAAA-TCGAATCTAA
1 AATCCTAAACTAAAACTAAAATC-AA
* *
38168201 AACCCGAAACTAAAACT
1 AATCCTAAACTAAAACT
38168218 CTTAATTAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 5 0.14
25 29 0.83
26 1 0.03
ACGTcount: A:0.55, C:0.24, G:0.03, T:0.18
Consensus pattern (25 bp):
AATCCTAAACTAAAACTAAAATCAA
Found at i:38169821 original size:22 final size:22
Alignment explanation
Indices: 38169796--38169842 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
38169786 TGTTTGTGTG
38169796 ATAAATGCTATATATTTTGGCT
1 ATAAATGCTATATATTTTGGCT
38169818 ATAAATGCTATATATTTTGGCT
1 ATAAATGCTATATATTTTGGCT
38169840 ATA
1 ATA
38169843 CATGATCTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.34, C:0.09, G:0.13, T:0.45
Consensus pattern (22 bp):
ATAAATGCTATATATTTTGGCT
Found at i:38170050 original size:18 final size:18
Alignment explanation
Indices: 38170014--38170051 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
38170004 TCGAATTTCG
*
38170014 AATTCGAATAACTCGAAT
1 AATTCGAATAACTCAAAT
38170032 AATTCGAATAAAC-CAAAT
1 AATTCGAAT-AACTCAAAT
38170050 AA
1 AA
38170052 AATTATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (18 bp):
AATTCGAATAACTCAAAT
Found at i:38170970 original size:21 final size:21
Alignment explanation
Indices: 38170946--38171018 Score: 69
Period size: 21 Copynumber: 3.5 Consensus size: 21
38170936 AGGGGTTTGG
38170946 GGTTTAAGGTTCAGAGCTTAA
1 GGTTTAAGGTTCAGAGCTTAA
* *
38170967 GGTTTAGGGTTC-GAGCTTGA
1 GGTTTAAGGTTCAGAGCTTAA
* * * *
38170987 GGTTTGAGGGTT-AGGGTTTAG
1 GGTTT-AAGGTTCAGAGCTTAA
38171008 GGTTTAAGGTT
1 GGTTTAAGGTT
38171019 TGAGGTTTAG
Statistics
Matches: 43, Mismatches: 7, Indels: 5
0.78 0.13 0.09
Matches are distributed among these distances:
20 17 0.40
21 26 0.60
ACGTcount: A:0.19, C:0.05, G:0.38, T:0.37
Consensus pattern (21 bp):
GGTTTAAGGTTCAGAGCTTAA
Found at i:38170984 original size:20 final size:21
Alignment explanation
Indices: 38170946--38170998 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
38170936 AGGGGTTTGG
*
38170946 GGTTTAAGGTTCAGAGCTTAA
1 GGTTTAGGGTTCAGAGCTTAA
*
38170967 GGTTTAGGGTTC-GAGCTTGA
1 GGTTTAGGGTTCAGAGCTTAA
38170987 GGTTTGAGGGTT
1 GGTTT-AGGGTT
38170999 AGGGTTTAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.19, C:0.08, G:0.38, T:0.36
Consensus pattern (21 bp):
GGTTTAGGGTTCAGAGCTTAA
Found at i:38171018 original size:14 final size:14
Alignment explanation
Indices: 38170939--38171030 Score: 60
Period size: 14 Copynumber: 6.6 Consensus size: 14
38170929 GAGGGTCAGG
*
38170939 GGTTTGGGGTTTAA
1 GGTTTAGGGTTTAA
* * *
38170953 GGTTCAGAGCTTAA
1 GGTTTAGGGTTTAA
**
38170967 GGTTTAGGGTTCGA
1 GGTTTAGGGTTTAA
* * *
38170981 GCTTGA-GGTTTGA
1 GGTTTAGGGTTTAA
* *
38170994 GGGTTAGGGTTTAG
1 GGTTTAGGGTTTAA
* *
38171008 GGTTTAAGGTTTGA
1 GGTTTAGGGTTTAA
38171022 GGTTTAGGG
1 GGTTTAGGG
38171031 CTCAGAGTTT
Statistics
Matches: 55, Mismatches: 22, Indels: 2
0.70 0.28 0.03
Matches are distributed among these distances:
13 9 0.16
14 46 0.84
ACGTcount: A:0.17, C:0.04, G:0.41, T:0.37
Consensus pattern (14 bp):
GGTTTAGGGTTTAA
Found at i:38171040 original size:28 final size:28
Alignment explanation
Indices: 38170966--38171041 Score: 91
Period size: 28 Copynumber: 2.8 Consensus size: 28
38170956 TCAGAGCTTA
* *
38170966 AGGTTTAGGGTTC-GAGCTTGAGGTTTG
1 AGGTTTAGGGTTCAGAGTTTAAGGTTTG
* * *
38170993 AGGGTTAGGGTTTAGGGTTTAAGGTTTG
1 AGGTTTAGGGTTCAGAGTTTAAGGTTTG
*
38171021 AGGTTTAGGGCTCAGAGTTTA
1 AGGTTTAGGGTTCAGAGTTTA
38171042 GGGCTCGAGA
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
27 11 0.28
28 28 0.72
ACGTcount: A:0.18, C:0.05, G:0.39, T:0.37
Consensus pattern (28 bp):
AGGTTTAGGGTTCAGAGTTTAAGGTTTG
Found at i:38171222 original size:8 final size:7
Alignment explanation
Indices: 38171177--38171311 Score: 70
Period size: 7 Copynumber: 19.7 Consensus size: 7
38171167 TTAAGGCTTG
*
38171177 GGGTTTG
1 GGGTTTA
38171184 GGGTTT-
1 GGGTTTA
38171190 -GGTTTA
1 GGGTTTA
38171196 GGGTTTA
1 GGGTTTA
*
38171203 GAGTTTAA
1 GGGTTT-A
38171211 GGGTTTA
1 GGGTTTA
38171218 GGGGTTT-
1 -GGGTTTA
38171225 GAGGTTTA
1 G-GGTTTA
*
38171233 -AGTTTA
1 GGGTTTA
38171239 GGGTTATA
1 GGGTT-TA
*
38171247 AGG-TTA
1 GGGTTTA
38171253 GGG-TT-
1 GGGTTTA
* *
38171258 GGGGTTG
1 GGGTTTA
*
38171265 GGGTTAA
1 GGGTTTA
38171272 GGG-TTA
1 GGGTTTA
38171278 GGGGTTTA
1 -GGGTTTA
* *
38171286 GAGTTCA
1 GGGTTTA
38171293 GGGTTTA
1 GGGTTTA
* *
38171300 AGGTTTC
1 GGGTTTA
38171307 GGGTT
1 GGGTT
38171312 AAAGTTTCGA
Statistics
Matches: 99, Mismatches: 17, Indels: 24
0.71 0.12 0.17
Matches are distributed among these distances:
5 8 0.08
6 16 0.16
7 56 0.57
8 19 0.19
ACGTcount: A:0.16, C:0.01, G:0.43, T:0.39
Consensus pattern (7 bp):
GGGTTTA
Found at i:38171457 original size:7 final size:7
Alignment explanation
Indices: 38171435--38171476 Score: 57
Period size: 7 Copynumber: 5.9 Consensus size: 7
38171425 TCGAGGGTCG
38171435 GGGTTTA
1 GGGTTTA
38171442 GGGGTTTA
1 -GGGTTTA
*
38171450 GAGTTTA
1 GGGTTTA
*
38171457 GGATTTA
1 GGGTTTA
38171464 GGGTTTA
1 GGGTTTA
38171471 GGGTTT
1 GGGTTT
38171477 CAGTGGGTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
7 23 0.77
8 7 0.23
ACGTcount: A:0.17, C:0.00, G:0.40, T:0.43
Consensus pattern (7 bp):
GGGTTTA
Found at i:38173382 original size:22 final size:21
Alignment explanation
Indices: 38173357--38173425 Score: 68
Period size: 22 Copynumber: 3.2 Consensus size: 21
38173347 TGTAATTTAT
* *
38173357 GGTTTAAGGTTTAAAAGTTAAG
1 GGTTTAAGGTTT-AAGGTTAGG
* *
38173379 GG-TTATGGGTTTAAGGTTTGG
1 GGTTTA-AGGTTTAAGGTTAGG
38173400 GGTTTAAGGTTTTAAGGTTAGG
1 GGTTTAAGG-TTTAAGGTTAGG
38173422 GGTT
1 GGTT
38173426 AGGGCTTGAG
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 13 0.34
22 25 0.66
ACGTcount: A:0.23, C:0.00, G:0.36, T:0.41
Consensus pattern (21 bp):
GGTTTAAGGTTTAAGGTTAGG
Found at i:38173931 original size:7 final size:7
Alignment explanation
Indices: 38173417--38174113 Score: 909
Period size: 7 Copynumber: 100.0 Consensus size: 7
38173407 GGTTTTAAGG
*
38173417 TTAGGGG
1 TTAGGGC
38173424 TTAGGGC
1 TTAGGGC
38173431 TT-GAGGC
1 TTAG-GGC
38173438 TTTA-GG-
1 -TTAGGGC
*
38173444 TTAGGGT
1 TTAGGGC
*
38173451 TTAAGG-
1 TTAGGGC
* *
38173457 TTTGGGA
1 TTAGGGC
*
38173464 TTAGTGC
1 TTAGGGC
*
38173471 TTAGGGT
1 TTAGGGC
*
38173478 TTAGGGT
1 TTAGGGC
*
38173485 TTAGGGT
1 TTAGGGC
*
38173492 TTAGGGT
1 TTAGGGC
*
38173499 TTAGGGT
1 TTAGGGC
*
38173506 TTAGGGT
1 TTAGGGC
*
38173513 TTAGGGT
1 TTAGGGC
*
38173520 TTAGGGT
1 TTAGGGC
38173527 TTAGGG-
1 TTAGGGC
*
38173533 TTAGGGT
1 TTAGGGC
*
38173540 TTAGGGT
1 TTAGGGC
*
38173547 TTAGGGT
1 TTAGGGC
*
38173554 TTAGGGT
1 TTAGGGC
*
38173561 TTAGGGT
1 TTAGGGC
*
38173568 TTAGGGT
1 TTAGGGC
*
38173575 TTAGGGT
1 TTAGGGC
*
38173582 TTAGGGT
1 TTAGGGC
38173589 TTAGGGC
1 TTAGGGC
38173596 TTAGGGC
1 TTAGGGC
38173603 TTAGGGC
1 TTAGGGC
38173610 TTAGGGC
1 TTAGGGC
38173617 TTAGGGC
1 TTAGGGC
38173624 TTAGGGC
1 TTAGGGC
38173631 TTAGGGC
1 TTAGGGC
38173638 TTAGGGC
1 TTAGGGC
38173645 TTAGGGC
1 TTAGGGC
38173652 TTAGGGC
1 TTAGGGC
38173659 TTAGGGC
1 TTAGGGC
38173666 TTAGGGC
1 TTAGGGC
38173673 TTAGGGC
1 TTAGGGC
38173680 TTAGGGC
1 TTAGGGC
38173687 TTAGGGC
1 TTAGGGC
38173694 TTAGGGC
1 TTAGGGC
38173701 TTAGGGC
1 TTAGGGC
38173708 TTAGGGC
1 TTAGGGC
38173715 TTAGGGC
1 TTAGGGC
38173722 TTAGGGC
1 TTAGGGC
38173729 TTAGGGC
1 TTAGGGC
38173736 TTAGGGC
1 TTAGGGC
38173743 TTAGGGC
1 TTAGGGC
38173750 TTAGGGC
1 TTAGGGC
38173757 TTAGGGC
1 TTAGGGC
38173764 TTAGGGC
1 TTAGGGC
38173771 TTAGGGC
1 TTAGGGC
38173778 TTAGGGC
1 TTAGGGC
38173785 TTAGGGC
1 TTAGGGC
38173792 TTAGGGC
1 TTAGGGC
38173799 TTAGGGC
1 TTAGGGC
38173806 TTAGGGC
1 TTAGGGC
38173813 TTAGGGC
1 TTAGGGC
38173820 TTAGGGC
1 TTAGGGC
38173827 TTAGGGC
1 TTAGGGC
38173834 TTAGGGC
1 TTAGGGC
38173841 TTAGGGC
1 TTAGGGC
38173848 TTAGGGC
1 TTAGGGC
38173855 TTAGGGC
1 TTAGGGC
38173862 TTAGGGC
1 TTAGGGC
38173869 TTAGGGC
1 TTAGGGC
38173876 TTAGGGC
1 TTAGGGC
38173883 TTAGGGC
1 TTAGGGC
38173890 TTAGGGC
1 TTAGGGC
38173897 TTAGGGC
1 TTAGGGC
38173904 TTAGGGC
1 TTAGGGC
38173911 TTAGGGC
1 TTAGGGC
38173918 TTAGGGC
1 TTAGGGC
38173925 TTAGGGC
1 TTAGGGC
*
38173932 TTCGGGC
1 TTAGGGC
*
38173939 TTCGGGC
1 TTAGGGC
*
38173946 TTCGGGC
1 TTAGGGC
*
38173953 TTCGGGC
1 TTAGGGC
*
38173960 TTCGGGC
1 TTAGGGC
*
38173967 TTCGGGC
1 TTAGGGC
*
38173974 TTCGGGC
1 TTAGGGC
*
38173981 TTCGGGC
1 TTAGGGC
*
38173988 TTCGGGC
1 TTAGGGC
*
38173995 TTCGGGC
1 TTAGGGC
*
38174002 TTCGGGC
1 TTAGGGC
*
38174009 TTCGGGC
1 TTAGGGC
*
38174016 TTCGGGC
1 TTAGGGC
*
38174023 TTCGGGC
1 TTAGGGC
*
38174030 TTCGGGC
1 TTAGGGC
*
38174037 TTCGGGC
1 TTAGGGC
*
38174044 TTCGGGC
1 TTAGGGC
*
38174051 TTCGGGC
1 TTAGGGC
*
38174058 TTCGGGC
1 TTAGGGC
*
38174065 TTCGGGC
1 TTAGGGC
*
38174072 TTCGGGC
1 TTAGGGC
*
38174079 TTCGGGC
1 TTAGGGC
*
38174086 TTCGGGC
1 TTAGGGC
*
38174093 TTCGGGC
1 TTAGGGC
*
38174100 TTCGGGC
1 TTAGGGC
*
38174107 TTCGGGC
1 TTAGGGC
Statistics
Matches: 672, Mismatches: 11, Indels: 14
0.96 0.02 0.02
Matches are distributed among these distances:
5 3 0.00
6 13 0.02
7 654 0.97
8 2 0.00
ACGTcount: A:0.11, C:0.15, G:0.43, T:0.32
Consensus pattern (7 bp):
TTAGGGC
Done.