Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold775
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: 75633
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:5669 original size:310 final size:310
Alignment explanation
Indices: 5104--5683 Score: 921
Period size: 310 Copynumber: 1.9 Consensus size: 310
5094 AAAAACCATG
*
5104 ATGAATAACCCTGTTCAAATATATAAGTATTCATTTGAGAGTTGTCTAATGTAACTATGTAGGGA
1 ATGAATAACCCTCTTCAAATATATAAGTATTCATTTGAGAGTTGTCTAATGTAACTATGTAGGGA
* * * * * * *
5169 AGTGCATGTTCTGAGACAACTTGTTAATTACATATGCCACATCAGGTTTGGTTACTGAAAGATAC
66 AGTGCATGTACTAAGACAACTTGTTAACTACATATGCCACATCAAGTCTGGTTAATAAAAGATAC
* * * * * *
5234 TAAAGAAAGCCAACTAATTGTTTGTATGCAGTAGCTTTAGTTGAATCAATGCTATCATGAAGTTT
131 TAAAGAAAGCCAACCAATTGTTTGTATGCAATAGCTTCAATAGAACCAATGCTATCATGAAGTTT
* * * *
5299 TAATTGAGTGCTTGAAGCCATTAGGGTGATAGTATCCTTTGCATTAGATATATTAAAATTTTCAA
196 TAATTGACTGCTTGAAGCCATTAGGGTGATAGTATCCTTTGCATTAAACATATCAAAATTTTCAA
5364 GATCTTTGATTGAGAGATGAATTTCTCATTACAAAAAAAAAAAAAAAAGA
261 GATCTTTGATTGAGAGATGAATTTCTCATTACAAAAAAAAAAAAAAAAGA
* *
5414 ATGAATAACCCTCTTCAACTATATAAGTATTCATTTGAGAGTTGTCTAATGTAACTGTGTAAGGG
1 ATGAATAACCCTCTTCAAATATATAAGTATTCATTTGAGAGTTGTCTAATGTAACTATGT-AGGG
5479 -AGTGCATGTACTAAGACAACTTGTTAACTACATATGCCACATCAAGTCTGGTTAATAAAAGATA
65 AAGTGCATGTACTAAGACAACTTGTTAACTACATATGCCACATCAAGTCTGGTTAATAAAAGATA
** *
5543 -TTGAGAAAAGCCAACCAATTGTTTGTATGCAATAGCTTCAATAGAACCAGTGCTATCATGAAGT
130 CTAAAG-AAAGCCAACCAATTGTTTGTATGCAATAGCTTCAATAGAACCAATGCTATCATGAAGT
5607 TTTAATTGACTGCTTGAAGCCATTAGGGTGATAGTATCCTTTGCATTAAACATATCAAAATTTTC
194 TTTAATTGACTGCTTGAAGCCATTAGGGTGATAGTATCCTTTGCATTAAACATATCAAAATTTTC
5672 AAGATCTTTGAT
259 AAGATCTTTGAT
5684 GTATTTATGT
Statistics
Matches: 245, Mismatches: 23, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
309 3 0.01
310 238 0.97
311 4 0.02
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (310 bp):
ATGAATAACCCTCTTCAAATATATAAGTATTCATTTGAGAGTTGTCTAATGTAACTATGTAGGGA
AGTGCATGTACTAAGACAACTTGTTAACTACATATGCCACATCAAGTCTGGTTAATAAAAGATAC
TAAAGAAAGCCAACCAATTGTTTGTATGCAATAGCTTCAATAGAACCAATGCTATCATGAAGTTT
TAATTGACTGCTTGAAGCCATTAGGGTGATAGTATCCTTTGCATTAAACATATCAAAATTTTCAA
GATCTTTGATTGAGAGATGAATTTCTCATTACAAAAAAAAAAAAAAAAGA
Found at i:9176 original size:33 final size:32
Alignment explanation
Indices: 9115--9183 Score: 79
Period size: 33 Copynumber: 2.1 Consensus size: 32
9105 TATTGGAGAT
*
9115 AAGAGATAAAAATTAGTTTATCTCATCTATAC
1 AAGAGATAAAAATTAGTTTATCTCATCTATAA
*
9147 AAGAGATAAGAAATTA-TCTTA-CTTTATCTATAA
1 AAGAGATAA-AAATTAGT-TTATC-TCATCTATAA
9180 AAGA
1 AAGA
9184 TTAGCTACAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
32 11 0.34
33 21 0.66
ACGTcount: A:0.46, C:0.10, G:0.10, T:0.33
Consensus pattern (32 bp):
AAGAGATAAAAATTAGTTTATCTCATCTATAA
Found at i:16163 original size:17 final size:17
Alignment explanation
Indices: 16141--16174 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
16131 ATTTCATGCA
*
16141 TTTAGGTATATTTAAGT
1 TTTAGGTATACTTAAGT
16158 TTTAGGTATACTTAAGT
1 TTTAGGTATACTTAAGT
16175 CATTTTCTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.03, G:0.18, T:0.50
Consensus pattern (17 bp):
TTTAGGTATACTTAAGT
Found at i:16401 original size:57 final size:58
Alignment explanation
Indices: 16340--16471 Score: 148
Period size: 57 Copynumber: 2.3 Consensus size: 58
16330 CATCTTAGTT
* * *
16340 ACTATTATGCAATTTCATA-CTTTT-AGAGTTACTT-TAGTTATTTTCAAT-ATTTTAGGG
1 ACTATTATGCAATTTCATAGATTTTAAGA-TTA-TTATAGTCATGTTCAATGA-TTTAGGG
*
16397 ACTATTATGTAATTT-ATAGATTTTAAGATTATTATAGTCATGTTCAATGATTTAGGG
1 ACTATTATGCAATTTCATAGATTTTAAGATTATTATAGTCATGTTCAATGATTTAGGG
* *
16454 ACCATTATGCAAGTTCAT
1 ACTATTATGCAATTTCAT
16472 GCATTTATCC
Statistics
Matches: 63, Mismatches: 7, Indels: 9
0.80 0.09 0.11
Matches are distributed among these distances:
56 5 0.08
57 52 0.83
58 6 0.10
ACGTcount: A:0.31, C:0.10, G:0.14, T:0.45
Consensus pattern (58 bp):
ACTATTATGCAATTTCATAGATTTTAAGATTATTATAGTCATGTTCAATGATTTAGGG
Found at i:19286 original size:72 final size:73
Alignment explanation
Indices: 19162--19401 Score: 218
Period size: 76 Copynumber: 3.3 Consensus size: 73
19152 ATTCATACAA
* * * * * *
19162 AAGTTCCCACATGACCCTAGACTCT-ATTT--ATGTTACCACATAAATAACCTTAATGGACATGT
1 AAGTTCCCACATGACCCTAGACT-TGGTTTCAAAGATACTACCTAAATAATCTTAATGGACATGT
19224 TTTGACATG
65 TTTGACATG
* * * *
19233 AAGTTCCCATATGACCTTAGACTTTGTTTCAAAG-TACTATCTAAATAATCTTAATGGACATGTT
1 AAGTTCCCACATGACCCTAGACTTGGTTTCAAAGATACTACCTAAATAATCTTAATGGACATGTT
* *
19297 TCGACTTG
66 TTGACATG
** * * **
19305 AAAGTTTTCACATAACCCTAGACTTGGTTTTAAAGAATTGTTACCTAAATAATCTTAATGGACAT
1 -AAGTTCCCACATGACCCTAGACTTGGTTTCAAAG-A-TACTACCTAAATAATCTTAATGGACAT
* *
19370 ATTTTGCCATG
63 GTTTTGACATG
*
19381 AAGTCTCCCACATGATCCTAG
1 AAGT-TCCCACATGACCCTAG
19402 GGACTCGTTT
Statistics
Matches: 133, Mismatches: 28, Indels: 11
0.77 0.16 0.06
Matches are distributed among these distances:
70 1 0.01
71 24 0.18
72 32 0.24
73 29 0.22
75 4 0.03
76 43 0.32
ACGTcount: A:0.32, C:0.20, G:0.13, T:0.35
Consensus pattern (73 bp):
AAGTTCCCACATGACCCTAGACTTGGTTTCAAAGATACTACCTAAATAATCTTAATGGACATGTT
TTGACATG
Found at i:19866 original size:165 final size:166
Alignment explanation
Indices: 19672--19986 Score: 406
Period size: 165 Copynumber: 1.9 Consensus size: 166
19662 TTGCATCATG
** *
19672 GTCCTTAAATGCATGGAAAATGCCTTAAATGAACT-AAAAATACACGAAATTGCTTAATAA-TCT
1 GTCCTTAAATGCATGGAAAACACCTTAAATGAA-TGAAAAATACACGAAATTGCATAATAATTC-
* *
19735 CTAAATACATTA-AAAATTACATAAATGACTTAAAATACATGAATTTGCATAACAATCCCT-AGA
64 CTAAATACA-TAGAAAATTACATAAATGACCTAAAATACATGAATTTACATAACAATCCCTCA-A
**
19798 TGCATATTAAATGCTTTAAATGACTTCAAATTGCAATGTA
127 TGCATAAAAAATGCTTTAAATGACTTCAAATTGCAATGTA
* ** *
19838 GTCCTTAAAT-CATGGAAAACACCTTAAATGAATGAAAAATGCGTGAAATTGCATAATGATTCCT
1 GTCCTTAAATGCATGGAAAACACCTTAAATGAATGAAAAATACACGAAATTGCATAATAATTCCT
* * * * * *
19902 AAATGCATAGAAAATTACTTAAATGACCTAAAATGCATGCATTTACATAATAGTCCCTCAATGCA
66 AAATACATAGAAAATTACATAAATGACCTAAAATACATGAATTTACATAACAATCCCTCAATGCA
19967 TAAAAAATGCTTTAAATGAC
131 TAAAAAATGCTTTAAATGAC
19987 CAAAAATTAT
Statistics
Matches: 128, Mismatches: 17, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
164 3 0.02
165 112 0.88
166 13 0.10
ACGTcount: A:0.43, C:0.16, G:0.11, T:0.30
Consensus pattern (166 bp):
GTCCTTAAATGCATGGAAAACACCTTAAATGAATGAAAAATACACGAAATTGCATAATAATTCCT
AAATACATAGAAAATTACATAAATGACCTAAAATACATGAATTTACATAACAATCCCTCAATGCA
TAAAAAATGCTTTAAATGACTTCAAATTGCAATGTA
Found at i:20061 original size:41 final size:41
Alignment explanation
Indices: 20014--20098 Score: 152
Period size: 41 Copynumber: 2.1 Consensus size: 41
20004 TCCTTAATCA
*
20014 TAAAAAATGACTAAAATAGTTCTAGAATGCATGAAATTATG
1 TAAAAAATGACTAAAATAGTTCTAGAACGCATGAAATTATG
*
20055 TAAAAAATGACTAAAATGGTTCTAGAACGCATGAAATTATG
1 TAAAAAATGACTAAAATAGTTCTAGAACGCATGAAATTATG
20096 TAA
1 TAA
20099 TGGTCTCTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.48, C:0.08, G:0.15, T:0.28
Consensus pattern (41 bp):
TAAAAAATGACTAAAATAGTTCTAGAACGCATGAAATTATG
Found at i:21924 original size:25 final size:25
Alignment explanation
Indices: 21896--21966 Score: 65
Period size: 24 Copynumber: 2.9 Consensus size: 25
21886 AAATATTTAT
21896 TTTTAAAATTTAAAAATTTTTTAAA
1 TTTTAAAATTTAAAAATTTTTTAAA
** * **
21921 TTTT-ATTTTTAAAATTTTTTTATG
1 TTTTAAAATTTAAAAATTTTTTAAA
*
21945 TTTCTAGAATTT-AAAATTTTTT
1 TTT-TAAAATTTAAAAATTTTTT
21967 GTGTTGAATT
Statistics
Matches: 35, Mismatches: 9, Indels: 4
0.73 0.19 0.08
Matches are distributed among these distances:
24 18 0.51
25 14 0.40
26 3 0.09
ACGTcount: A:0.35, C:0.01, G:0.03, T:0.61
Consensus pattern (25 bp):
TTTTAAAATTTAAAAATTTTTTAAA
Found at i:21931 original size:13 final size:14
Alignment explanation
Indices: 21880--21938 Score: 64
Period size: 14 Copynumber: 3.9 Consensus size: 14
21870 AAAATCCAAT
21880 TTTTTAAAATATTTA
1 TTTTTAAAAT-TTTA
*
21895 TTTTTAAAATTTAAAAA
1 TTTTTAAAATTT---TA
*
21912 TTTTTTAAATTTTA
1 TTTTTAAAATTTTA
21926 TTTTTAAAATTTT
1 TTTTTAAAATTTT
21939 TTTATGTTTC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
14 15 0.41
15 10 0.27
17 12 0.32
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTTTTAAAATTTTA
Found at i:21936 original size:31 final size:33
Alignment explanation
Indices: 21877--21937 Score: 108
Period size: 31 Copynumber: 1.9 Consensus size: 33
21867 GTAAAAATCC
21877 AATTTTTTAAAATATTTATTTTTAAAATTTAAA
1 AATTTTTTAAAATATTTATTTTTAAAATTTAAA
21910 AATTTTTT-AAAT-TTTATTTTTAAAATTT
1 AATTTTTTAAAATATTTATTTTTAAAATTT
21938 TTTTATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
31 16 0.57
32 4 0.14
33 8 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (33 bp):
AATTTTTTAAAATATTTATTTTTAAAATTTAAA
Found at i:25149 original size:21 final size:21
Alignment explanation
Indices: 25123--25176 Score: 83
Period size: 20 Copynumber: 2.6 Consensus size: 21
25113 TTCTACAATT
*
25123 TGTATCGATACAATAAGTTAA
1 TGTATCGATACAATAAGTGAA
25144 TGTATCGATAC-ATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
25164 TGTATTGATACAA
1 TGTATCGATACAA
25177 GCTTGAAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.41, C:0.09, G:0.17, T:0.33
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:25160 original size:20 final size:20
Alignment explanation
Indices: 25123--25196 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 20
25113 TTCTACAATT
25123 TGTATCGATACAATAAGTTAA
1 TGTATCGATAC-ATAAGTTAA
*
25144 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTTAA
*
25164 TGTATTGATAC--AAGCTTGAAA
1 TGTATCGATACATAAG-TT--AA
25185 TGTATCGATACA
1 TGTATCGATACA
25197 AGACCATGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
18 3 0.07
19 1 0.02
20 18 0.40
21 23 0.51
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (20 bp):
TGTATCGATACATAAGTTAA
Found at i:25289 original size:52 final size:52
Alignment explanation
Indices: 25232--25371 Score: 147
Period size: 52 Copynumber: 2.7 Consensus size: 52
25222 TCTAAAAATA
* * *
25232 AAATGTATTGATACATTTTTCATTGTATCGATATATTCTGGGTTTTTGACAT
1 AAATGTATTAATACATTTTTCATTGTATCGATATATTCTGAGTTTTTAACAT
* * * ** * *
25284 AAATGTATCAATACATTCTCCATTGTATCGATACGTTTTGAGTTTTTAACCT
1 AAATGTATTAATACATTTTTCATTGTATCGATATATTCTGAGTTTTTAACAT
* * *
25336 AAATATAGTAATACACTTTTT-AATGTATCGATATAT
1 AAATGTATTAATACA-TTTTTCATTGTATCGATATAT
25372 CCAATTAAAT
Statistics
Matches: 69, Mismatches: 18, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
52 66 0.96
53 3 0.04
ACGTcount: A:0.31, C:0.12, G:0.12, T:0.44
Consensus pattern (52 bp):
AAATGTATTAATACATTTTTCATTGTATCGATATATTCTGAGTTTTTAACAT
Found at i:27848 original size:27 final size:27
Alignment explanation
Indices: 27808--27908 Score: 139
Period size: 27 Copynumber: 3.7 Consensus size: 27
27798 TGTCGTCATC
* * * *
27808 GGGGATACTATAACTCTATTTTTTCGA
1 GGGGATACTGTAACCCCATTCTTTCGA
27835 GGGGATACTGTAACCCCATTCTTTCGA
1 GGGGATACTGTAACCCCATTCTTTCGA
*
27862 GAGGATACTGTAACCCCATTCTTTCGA
1 GGGGATACTGTAACCCCATTCTTTCGA
**
27889 GGGGATACTCCAACCCCATT
1 GGGGATACTGTAACCCCATT
27909 TTTAAACTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 66 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.31
Consensus pattern (27 bp):
GGGGATACTGTAACCCCATTCTTTCGA
Found at i:30508 original size:32 final size:32
Alignment explanation
Indices: 30462--30535 Score: 121
Period size: 32 Copynumber: 2.3 Consensus size: 32
30452 ACAGTAAATG
*
30462 TATCAATACATAAGTGTTGTATCGATACAATA
1 TATCGATACATAAGTGTTGTATCGATACAATA
*
30494 TATCGATACATAAGTGTTGTATCGATACAATG
1 TATCGATACATAAGTGTTGTATCGATACAATA
*
30526 TATCGCTACA
1 TATCGATACA
30536 AAGCTACTGC
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (32 bp):
TATCGATACATAAGTGTTGTATCGATACAATA
Found at i:30518 original size:19 final size:19
Alignment explanation
Indices: 30460--30522 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
30450 AAACAGTAAA
*
30460 TGTATCAATACATAAGTGT
1 TGTATCGATACATAAGTGT
30479 TGTATCGATAC--AA----
1 TGTATCGATACATAAGTGT
*
30492 TATATCGATACATAAGTGT
1 TGTATCGATACATAAGTGT
30511 TGTATCGATACA
1 TGTATCGATACA
30523 ATGTATCGCT
Statistics
Matches: 35, Mismatches: 3, Indels: 12
0.70 0.06 0.24
Matches are distributed among these distances:
13 10 0.29
15 2 0.06
17 2 0.06
19 21 0.60
ACGTcount: A:0.37, C:0.13, G:0.16, T:0.35
Consensus pattern (19 bp):
TGTATCGATACATAAGTGT
Found at i:31564 original size:20 final size:21
Alignment explanation
Indices: 31525--31565 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
31515 TAAACCTTGA
31525 TCATGCATTTTGAGCTATGTT
1 TCATGCATTTTGAGCTATGTT
31546 TCATGC-TTTTGTAGC-ATGTT
1 TCATGCATTTTG-AGCTATGTT
31566 CAGCACCTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.17, C:0.15, G:0.20, T:0.49
Consensus pattern (21 bp):
TCATGCATTTTGAGCTATGTT
Found at i:35329 original size:17 final size:17
Alignment explanation
Indices: 35309--35358 Score: 57
Period size: 17 Copynumber: 3.0 Consensus size: 17
35299 CTTAATTAAA
35309 CTATTTAATTAAGTCAT
1 CTATTTAATTAAGTCAT
* *
35326 CTATTTAATTTA-TCTT
1 CTATTTAATTAAGTCAT
* *
35342 TTATTTAACTAAGTCAT
1 CTATTTAATTAAGTCAT
35359 ACTTAATTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
16 12 0.46
17 14 0.54
ACGTcount: A:0.32, C:0.12, G:0.04, T:0.52
Consensus pattern (17 bp):
CTATTTAATTAAGTCAT
Found at i:36219 original size:33 final size:32
Alignment explanation
Indices: 36182--36244 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 32
36172 TACCATTGTT
36182 TGTATCGATACATG-GCACATTGTATCGATATAA
1 TGTATCGATACATGAG-A-ATTGTATCGATATAA
36215 TGTATCGATACATGATGAATTGTATCGATA
1 TGTATCGATACATGA-GAATTGTATCGATA
36245 CATTGCTTCT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 26 0.93
34 1 0.04
35 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGTATCGATACATGAGAATTGTATCGATATAA
Found at i:44679 original size:22 final size:24
Alignment explanation
Indices: 44625--44686 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 24
44615 AATATCACAA
*
44625 ATTTAAAAACTATTTACATGATTGAC
1 ATTTGAAAACTATTTACATG--TGAC
*
44651 ATATGAAAAC-ATTTACATG-GAC
1 ATTTGAAAACTATTTACATGTGAC
44673 ATTTGAACAACTAT
1 ATTTGAA-AACTAT
44687 ACCAAATAGG
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
22 9 0.29
23 3 0.10
24 2 0.06
25 9 0.29
26 8 0.26
ACGTcount: A:0.44, C:0.13, G:0.10, T:0.34
Consensus pattern (24 bp):
ATTTGAAAACTATTTACATGTGAC
Found at i:45169 original size:19 final size:18
Alignment explanation
Indices: 45145--45203 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 18
45135 GAAGTGCGAG
45145 AGAAAAAAAAAAAAAGACA
1 AGAAAAAAAAAAAAAGA-A
* *
45164 AGAAAAGAAAAATAAGAA
1 AGAAAAAAAAAAAAAGAA
*
45182 AAAAAAATGAAAGAAAAAGAA
1 AGAAAAA--AAA-AAAAAGAA
45203 A
1 A
45204 ATATTTTTTA
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
18 6 0.19
19 15 0.47
20 3 0.09
21 8 0.25
ACGTcount: A:0.81, C:0.02, G:0.14, T:0.03
Consensus pattern (18 bp):
AGAAAAAAAAAAAAAGAA
Found at i:45180 original size:14 final size:15
Alignment explanation
Indices: 45163--45204 Score: 52
Period size: 14 Copynumber: 2.8 Consensus size: 15
45153 AAAAAAAGAC
45163 AAGAAAAGAAAAAT-
1 AAGAAAAGAAAAATA
45177 AAGAAAA-AAAAATGA
1 AAGAAAAGAAAAAT-A
45192 AAGAAAAAGAAAA
1 AAG-AAAAGAAAA
45205 TATTTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
13 6 0.25
14 7 0.29
15 3 0.12
16 4 0.17
17 4 0.17
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (15 bp):
AAGAAAAGAAAAATA
Found at i:45185 original size:11 final size:10
Alignment explanation
Indices: 45147--45204 Score: 57
Period size: 10 Copynumber: 5.9 Consensus size: 10
45137 AGTGCGAGAG
45147 AAAA-AAAAA
1 AAAAGAAAAA
* *
45156 AAAAGACAAG
1 AAAAGAAAAA
45166 AAAAG-AAAA
1 AAAAGAAAAA
*
45175 ATAAGAAAAA
1 AAAAGAAAAA
*
45185 AAAATGAAAGA
1 AAAA-GAAAAA
45196 AAAAGAAAA
1 AAAAGAAAA
45205 TATTTTTTAA
Statistics
Matches: 38, Mismatches: 8, Indels: 5
0.75 0.16 0.10
Matches are distributed among these distances:
9 10 0.26
10 19 0.50
11 9 0.24
ACGTcount: A:0.83, C:0.02, G:0.12, T:0.03
Consensus pattern (10 bp):
AAAAGAAAAA
Found at i:45617 original size:23 final size:23
Alignment explanation
Indices: 45586--45650 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
45576 TTATATTGAT
*
45586 ATTTATAATTAAATTTATATAAAA
1 ATTT-TAATTAAATTTAAATAAAA
* *
45610 ATTTTAA-TATTATTTAAATAATA
1 ATTTTAATTA-AATTTAAATAAAA
*
45633 ATTTAAATTAAA-TTAAAT
1 ATTTTAATTAAATTTAAAT
45651 TAATTCAATT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
22 8 0.24
23 20 0.59
24 6 0.18
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTTTAATTAAATTTAAATAAAA
Found at i:45731 original size:25 final size:26
Alignment explanation
Indices: 45697--45749 Score: 90
Period size: 25 Copynumber: 2.1 Consensus size: 26
45687 CTAATAGACC
45697 GGACAAGCTGTTTGGCCGATGA-GAA
1 GGACAAGCTGTTTGGCCGATGAGGAA
*
45722 GGACAAGCTGTTTGGCGGATGAGGAA
1 GGACAAGCTGTTTGGCCGATGAGGAA
45748 GG
1 GG
45750 CATATATGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
25 21 0.81
26 5 0.19
ACGTcount: A:0.26, C:0.13, G:0.42, T:0.19
Consensus pattern (26 bp):
GGACAAGCTGTTTGGCCGATGAGGAA
Found at i:48874 original size:2 final size:2
Alignment explanation
Indices: 48867--48913 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
48857 CCCTCCCCAA
48867 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
48909 TC TC T
1 TC TC T
48914 ATATATATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:48918 original size:2 final size:2
Alignment explanation
Indices: 48913--48947 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
48903 TCTCTCTCTC
48913 TA 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 TA T
48948 TAATCTCCTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:57394 original size:16 final size:16
Alignment explanation
Indices: 57375--57406 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
57365 AGAAAGAGGC
57375 CAAGAAAATGATTTTG
1 CAAGAAAATGATTTTG
*
57391 CAAGAAGATGATTTTG
1 CAAGAAAATGATTTTG
57407 AATGGTGTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.06, G:0.22, T:0.31
Consensus pattern (16 bp):
CAAGAAAATGATTTTG
Found at i:63280 original size:13 final size:13
Alignment explanation
Indices: 63262--63287 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
63252 TACACAAAGT
63262 ATGTATCGATACA
1 ATGTATCGATACA
63275 ATGTATCGATACA
1 ATGTATCGATACA
63288 CCATAAAATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:63304 original size:33 final size:32
Alignment explanation
Indices: 63244--63307 Score: 94
Period size: 33 Copynumber: 2.0 Consensus size: 32
63234 TAGCCAAATT
*
63244 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAGAATGTATCGATACAA
63276 TGTATCGATACACCATAA-AATGTATCGATACA
1 TGTATCGATACA-CA-AAGAATGTATCGATACA
63308 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 12 0.41
33 15 0.52
34 2 0.07
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAGAATGTATCGATACAA
Found at i:65516 original size:104 final size:104
Alignment explanation
Indices: 65320--65528 Score: 330
Period size: 104 Copynumber: 2.0 Consensus size: 104
65310 GCTCGCCTGT
*
65320 ACCAAAAGCCTCGTGGCCTTGTTTATTTCACTTTTGCACACCATTAATAAACCTCAAGACAAGAC
1 ACCAAAAGCCTCGTGGCCTTGTTTATTTCACTTTTGCACACCATTAATAAACCCCAAGACAAGAC
* * * *
65385 ATCAGAACATACTGTTATCCTTACACTTTGTTGGTCGTA
66 AACAGAACAGACTGCTATCCTTACACTTTCTTGGTCGTA
*
65424 ACCAAAAGCCTCGTGGCCTTGTTTATTTCACTTTTGCACGCCATTAATAAACCCCAAGACAAGAC
1 ACCAAAAGCCTCGTGGCCTTGTTTATTTCACTTTTGCACACCATTAATAAACCCCAAGACAAGAC
* *
65489 AACAGGACAGACTGCTA-CTCTTTCACTTTCTTGGTCGTA
66 AACAGAACAGACTGCTATC-CTTACACTTTCTTGGTCGTA
65528 A
1 A
65529 ATAGTTTAAG
Statistics
Matches: 96, Mismatches: 8, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
103 1 0.01
104 95 0.99
ACGTcount: A:0.29, C:0.26, G:0.14, T:0.30
Consensus pattern (104 bp):
ACCAAAAGCCTCGTGGCCTTGTTTATTTCACTTTTGCACACCATTAATAAACCCCAAGACAAGAC
AACAGAACAGACTGCTATCCTTACACTTTCTTGGTCGTA
Found at i:66355 original size:21 final size:20
Alignment explanation
Indices: 66329--66371 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
66319 AAATTTAAAT
66329 AAAAATATAATATTATAATTA
1 AAAAATATAATATTA-AATTA
* *
66350 AAAAATATTATTTTAAATTA
1 AAAAATATAATATTAAATTA
66370 AA
1 AA
66372 TTAATTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 7 0.35
21 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAAATATAATATTAAATTA
Found at i:66361 original size:19 final size:21
Alignment explanation
Indices: 66324--66371 Score: 57
Period size: 20 Copynumber: 2.4 Consensus size: 21
66314 TAATTAAATT
66324 TAAA-TAAAAATATAATATTA
1 TAAATTAAAAATATAATATTA
* *
66344 T-AATTAAAAA-ATATTATTT
1 TAAATTAAAAATATAATATTA
66363 TAAATTAAA
1 TAAATTAAA
66372 TTAATTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTAAAAATATAATATTA
Found at i:67128 original size:28 final size:27
Alignment explanation
Indices: 67067--67132 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
67057 TGTAGGAATC
67067 CTAATTAAAAATTTTATATGAAGGGATT
1 CTAATTAAAAATTTTATATGAA-GGATT
* *
67095 -AAATTAAAAATTTTATGTGCCAA-GATT
1 CTAATTAAAAATTTTATATG--AAGGATT
67122 CTAATTAAAAA
1 CTAATTAAAAA
67133 AACTATATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
27 21 0.66
28 9 0.28
29 2 0.06
ACGTcount: A:0.47, C:0.06, G:0.11, T:0.36
Consensus pattern (27 bp):
CTAATTAAAAATTTTATATGAAGGATT
Found at i:67237 original size:54 final size:54
Alignment explanation
Indices: 67179--67299 Score: 163
Period size: 54 Copynumber: 2.2 Consensus size: 54
67169 CAAAAATTTA
*
67179 AATAAAAATTCTATATTTAAAATGTCTAA-TGAAAATCTTCATGTGTGAAAGTTC
1 AATAAAAATTCTATATTTAAAAAGTCTAATTGAAAAT-TTCATGTGTGAAAGTTC
* * * * *
67233 AATAAAAAATATATGTTTAAAAAGTTTAATTGAAAATTTTATGTGTGAAAGTTC
1 AATAAAAATTCTATATTTAAAAAGTCTAATTGAAAATTTCATGTGTGAAAGTTC
*
67287 AATTAAAATTCTA
1 AATAAAAATTCTA
67300 AGAGGTTCGC
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
54 50 0.88
55 7 0.12
ACGTcount: A:0.45, C:0.06, G:0.11, T:0.38
Consensus pattern (54 bp):
AATAAAAATTCTATATTTAAAAAGTCTAATTGAAAATTTCATGTGTGAAAGTTC
Found at i:67283 original size:27 final size:27
Alignment explanation
Indices: 67208--67296 Score: 83
Period size: 27 Copynumber: 3.3 Consensus size: 27
67198 AAATGTCTAA
*
67208 TGAAAATCTTCATGTGTGAAAGTTCAA-
1 TGAAAAT-TTTATGTGTGAAAGTTCAAT
* * * * * *
67235 TAAAAAATATATGTTTAAAAAGTTTAAT
1 TGAAAATTTTATGTGT-GAAAGTTCAAT
67263 TGAAAATTTTATGTGTGAAAGTTCAAT
1 TGAAAATTTTATGTGTGAAAGTTCAAT
67290 T-AAAATT
1 TGAAAATT
67297 CTAAGAGGTT
Statistics
Matches: 47, Mismatches: 13, Indels: 5
0.72 0.20 0.08
Matches are distributed among these distances:
26 12 0.26
27 23 0.49
28 12 0.26
ACGTcount: A:0.44, C:0.04, G:0.13, T:0.38
Consensus pattern (27 bp):
TGAAAATTTTATGTGTGAAAGTTCAAT
Found at i:67699 original size:36 final size:35
Alignment explanation
Indices: 67659--67847 Score: 109
Period size: 36 Copynumber: 5.3 Consensus size: 35
67649 CACATCCAAG
*
67659 GAAATATCCTCGAGAGAAAG-TCTAAAAATATCTTAT
1 GAAATATCCTCAAGAG-AAGCTCTAAAAATATC-TAT
* * *
67695 GAAATCTCCTCAAGAGATGCTCTAAAAATCTCTAT
1 GAAATATCCTCAAGAGAAGCTCTAAAAATATCTAT
* * * * * * *
67730 GAAACATCTTTAAG-GGAGACTTTGAAAA-ACCTTAT
1 GAAATATCCTCAAGAGAAG-CTCTAAAAATATC-TAT
* * * *
67765 CGAAATATCCTTAAAAGAAGCTCTGAAAATATTTAAT
1 -GAAATATCCTCAAGAGAAGCTCTAAAAATATCT-AT
* *
67802 GAAATATCCTTAAGA-AAGGCTCTAAAAATCAAT-AAT
1 GAAATATCCTCAAGAGAA-GCTCTAAAAAT--ATCTAT
67838 GAAATATCCT
1 GAAATATCCT
67848 TAAAAGAGGC
Statistics
Matches: 119, Mismatches: 24, Indels: 20
0.73 0.15 0.12
Matches are distributed among these distances:
34 3 0.03
35 27 0.23
36 81 0.68
37 6 0.05
38 2 0.02
ACGTcount: A:0.43, C:0.16, G:0.13, T:0.28
Consensus pattern (35 bp):
GAAATATCCTCAAGAGAAGCTCTAAAAATATCTAT
Found at i:67866 original size:36 final size:36
Alignment explanation
Indices: 67766--67866 Score: 134
Period size: 36 Copynumber: 2.8 Consensus size: 36
67756 AAACCTTATC
* *
67766 GAAATATCCTTAAAAGAAGCTCTGAAAATATTTAAT
1 GAAATATCCTTAAAAGAGGCTCTGAAAATATATAAT
*
67802 GAAATATCCTTAAGAA-AGGCTCTAAAAATCA-ATAAT
1 GAAATATCCTTAA-AAGAGGCTCTGAAAAT-ATATAAT
*
67838 GAAATATCCTTAAAAGAGGCTTTGAAAAT
1 GAAATATCCTTAAAAGAGGCTCTGAAAAT
67867 GTATTTATCA
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
35 2 0.04
36 52 0.91
37 3 0.05
ACGTcount: A:0.48, C:0.12, G:0.13, T:0.28
Consensus pattern (36 bp):
GAAATATCCTTAAAAGAGGCTCTGAAAATATATAAT
Found at i:68117 original size:38 final size:37
Alignment explanation
Indices: 68058--68157 Score: 105
Period size: 37 Copynumber: 2.7 Consensus size: 37
68048 GTACTCGATG
* * * *
68058 AAATATCC-TAAAGAGAAGCTTTGAAAATGTCTTTATTA
1 AAATATCCTTAAA-AGAGGCTTTGAAAATCTC-TAATAA
*
68096 GAATATCCTTGAAAA-AGGCTTTGAAAATCTCTAATAA
1 AAATATCCTT-AAAAGAGGCTTTGAAAATCTCTAATAA
*
68133 AAATATCCTTAAAAGAGGATTTGAA
1 AAATATCCTTAAAAGAGGCTTTGAA
68158 GATACCTTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 7
0.79 0.11 0.11
Matches are distributed among these distances:
36 4 0.08
37 22 0.42
38 21 0.40
39 2 0.04
40 3 0.06
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.31
Consensus pattern (37 bp):
AAATATCCTTAAAAGAGGCTTTGAAAATCTCTAATAA
Found at i:68233 original size:61 final size:61
Alignment explanation
Indices: 68111--68234 Score: 148
Period size: 62 Copynumber: 2.0 Consensus size: 61
68101 TCCTTGAAAA
*
68111 AGGCTTTGAAAATCTCTAATAAAAATATCCTTAAAAGAGGATTTGAAGATACCTTTAATGAT
1 AGGCTTTGAAAATCTCTAATAAAAATATCCTTAAAAGAGGATTTGAAAATA-CTTTAATGAT
* *
68173 AGGCTTTGAGAAT-TCTAAT-AAAATATCCTTTTTAAAAGA-GATTGTGAAAATA-TTTGATGAT
1 AGGCTTTGAAAATCTCTAATAAAAATATCC---TTAAAAGAGGATT-TGAAAATACTTTAATGAT
68234 A
1 A
68235 ATATTTTCTT
Statistics
Matches: 55, Mismatches: 3, Indels: 9
0.82 0.04 0.13
Matches are distributed among these distances:
60 9 0.16
61 15 0.27
62 16 0.29
63 15 0.27
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (61 bp):
AGGCTTTGAAAATCTCTAATAAAAATATCCTTAAAAGAGGATTTGAAAATACTTTAATGAT
Found at i:69355 original size:28 final size:28
Alignment explanation
Indices: 69294--69375 Score: 96
Period size: 28 Copynumber: 2.9 Consensus size: 28
69284 TTTTGGAGAT
*
69294 AATAACGGGGTTGGAGTGTTCCCTCG--GA
1 AATAACGGGGTTGGAGT-ATCCC-CGATGA
*
69322 AGTAACGGGGTTGGAGTATCCCCGATGA
1 AATAACGGGGTTGGAGTATCCCCGATGA
* *
69350 AATAACGAGGTTGGAGTATCCTCGAT
1 AATAACGGGGTTGGAGTATCCCCGAT
69376 TGTGAAAAAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
26 2 0.04
27 4 0.09
28 41 0.87
ACGTcount: A:0.26, C:0.17, G:0.33, T:0.24
Consensus pattern (28 bp):
AATAACGGGGTTGGAGTATCCCCGATGA
Found at i:69517 original size:51 final size:51
Alignment explanation
Indices: 69355--69526 Score: 186
Period size: 52 Copynumber: 3.3 Consensus size: 51
69345 GATGAAATAA
*
69355 CGAGGTTGGAGTAT-CCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAAT
1 CGAGGTTGGAGTATCCCT-GATTATGAAAAATTGGTA-TTTTGGAAATAAAAT
* * * * * *
69407 CG-GTGTTGGAGTATCCCCGATTAAAGGAAAATTGGTGTTTTGAAAATAAAAC
1 CGAG-GTTGGAGTATCCCTGATT-ATGAAAAATTGGTATTTTGGAAATAAAAT
* *** *
69459 CGGGGTTGGAGTATCCCTGATTATGAAAAATCAATATTTTGGAAATAAAGT
1 CGAGGTTGGAGTATCCCTGATTATGAAAAATTGGTATTTTGGAAATAAAAT
69510 CGAGGTTGGAGTATCCC
1 CGAGGTTGGAGTATCCC
69527 CTCGGAAATA
Statistics
Matches: 98, Mismatches: 18, Indels: 9
0.78 0.14 0.07
Matches are distributed among these distances:
51 37 0.38
52 48 0.49
53 13 0.13
ACGTcount: A:0.33, C:0.11, G:0.26, T:0.31
Consensus pattern (51 bp):
CGAGGTTGGAGTATCCCTGATTATGAAAAATTGGTATTTTGGAAATAAAAT
Found at i:69548 original size:28 final size:27
Alignment explanation
Indices: 69513--69584 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
69503 ATAAAGTCGA
**
69513 GGTTGGAGTATCCCCTCGGAAATAACGG
1 GGTTGGAGTATCCCCGAGG-AATAACGG
* *
69541 GGTTGGAGTATCCCCGATGATTAACGG
1 GGTTGGAGTATCCCCGAGGAATAACGG
*
69568 GGTTGGAGTGTCCCCGA
1 GGTTGGAGTATCCCCGA
69585 TTGTGAAGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
27 23 0.59
28 16 0.41
ACGTcount: A:0.21, C:0.21, G:0.35, T:0.24
Consensus pattern (27 bp):
GGTTGGAGTATCCCCGAGGAATAACGG
Found at i:69650 original size:211 final size:211
Alignment explanation
Indices: 69302--69685 Score: 592
Period size: 211 Copynumber: 1.8 Consensus size: 211
69292 ATAATAACGG
* * *
69302 GGTTGGAGTGTTCCCTCGGAAGTAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
69367 ATCCTCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGTGTTGGAGTATCCCCGATTAAA
66 ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
** * *
69432 GGAAAATTGGTGTTTTGAAAATAAAACCGGGGTTGGAGTATCCCTGATTATGAAAAATCAATATT
131 GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCTGATTATGAAAAATCAATATT
69497 TTGGAAATAAAGTCGA
196 TTGGAAATAAAGTCGA
* *
69513 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATG-ATTAACGGGGTTGGAGT
1 GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
* *
69577 GTCCCCGATTGTGAAGAAATTGGTGTTTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
66 ATCCCCGATTGTGAA-AAATTGGT-ATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTA
* * *
69642 TA-GAAAATTAATGTTTTGAAAGTAAAATCGGAGTTGGAATATCC
129 AAGGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCC
69686 TCGATTGTGG
Statistics
Matches: 155, Mismatches: 16, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
210 28 0.18
211 88 0.57
212 39 0.25
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.29
Consensus pattern (211 bp):
GGTTGGAGTATCCCCTCGGAAATAACGGGGTTGGAGTATCCCCGATGAAATAACGAGGTTGGAGT
ATCCCCGATTGTGAAAAATTGGTATTTTTGGAAATAAAATCGGAGTTGGAGTATCCCCGATTAAA
GGAAAATTAATGTTTTGAAAATAAAACCGGAGTTGGAATATCCCTGATTATGAAAAATCAATATT
TTGGAAATAAAGTCGA
Found at i:71769 original size:20 final size:20
Alignment explanation
Indices: 71746--71819 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
71736 ACAATTCAAA
71746 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
****
71766 GTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCA-AT
71787 GTATCGATACATGTTGCAAT
1 GTATCGATACATGTTGCAAT
71807 GTATCGATACATG
1 GTATCGATACATG
71820 AAAAAGATGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
20 29 0.64
21 16 0.36
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (20 bp):
GTATCGATACATGTTGCAAT
Found at i:71790 original size:21 final size:21
Alignment explanation
Indices: 71764--71839 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
71754 ACATGTTGCA
71764 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
****
71785 ATGTATCGATACATGTTGCA-
1 ATGTATCGATACATGAAAAAG
71805 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
71826 ATGTATCGATACAT
1 ATGTATCGATACAT
71840 TTCTTGGCAG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 16 0.35
21 30 0.65
ACGTcount: A:0.41, C:0.12, G:0.18, T:0.29
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:71797 original size:41 final size:41
Alignment explanation
Indices: 71746--71839 Score: 188
Period size: 41 Copynumber: 2.3 Consensus size: 41
71736 ACAATTCAAA
71746 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
71787 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
1 GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
71828 GTATCGATACAT
1 GTATCGATACAT
71840 TTCTTGGCAG
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 53 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (41 bp):
GTATCGATACATGTTGCAATGTATCGATACATGAAAAAGAT
Found at i:71896 original size:13 final size:13
Alignment explanation
Indices: 71878--71903 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
71868 TACAGAAAGT
71878 ATGTATCGATACA
1 ATGTATCGATACA
71891 ATGTATCGATACA
1 ATGTATCGATACA
71904 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:71901 original size:32 final size:33
Alignment explanation
Indices: 71860--71923 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
71850 TAGCCAAACT
* **
71860 TGTATCGATACAGAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
71892 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
71924 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:74432 original size:19 final size:19
Alignment explanation
Indices: 74410--74477 Score: 76
Period size: 19 Copynumber: 3.9 Consensus size: 19
74400 AATTCAACAA
*
74410 TTTGTATTGATACATAAGT
1 TTTGTATCGATACATAAGT
74429 TTTGTATCGATAC--AA--
1 TTTGTATCGATACATAAGT
74444 --TGTATCGATACATAAGT
1 TTTGTATCGATACATAAGT
*
74461 ATTGTATCGATACATAA
1 TTTGTATCGATACATAA
74478 TTAGCTACTG
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 2 0.05
19 27 0.64
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (19 bp):
TTTGTATCGATACATAAGT
Found at i:74448 original size:32 final size:32
Alignment explanation
Indices: 74412--74474 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
74402 TTCAACAATT
* *
74412 TGTATTGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTATTGTATCGATACAA
74444 TGTATCGATACATAAGTATTGTATCGATACA
1 TGTATCGATACATAAGTATTGTATCGATACA
74475 TAATTAGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.35, C:0.11, G:0.16, T:0.38
Consensus pattern (32 bp):
TGTATCGATACATAAGTATTGTATCGATACAA
Found at i:74449 original size:13 final size:13
Alignment explanation
Indices: 74431--74455 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
74421 ACATAAGTTT
74431 TGTATCGATACAA
1 TGTATCGATACAA
74444 TGTATCGATACA
1 TGTATCGATACA
74456 TAAGTATTGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:74534 original size:13 final size:13
Alignment explanation
Indices: 74516--74541 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
74506 ACATTTTCTG
74516 TGTATCGATACAT
1 TGTATCGATACAT
74529 TGTATCGATACAT
1 TGTATCGATACAT
74542 GGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:74558 original size:33 final size:32
Alignment explanation
Indices: 74497--74562 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 32
74487 GCCAAGGAAA
**
74497 TGTATCGATACATTTTCTGTGTATCGATACAT
1 TGTATCGATACATGATCTGTGTATCGATACAT
*
74529 TGTATCGATACATGGATCTTTGTATCGATACAT
1 TGTATCGATACAT-GATCTGTGTATCGATACAT
74562 T
1 T
74563 TGGAATTTAC
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 13 0.43
33 17 0.57
ACGTcount: A:0.26, C:0.15, G:0.17, T:0.42
Consensus pattern (32 bp):
TGTATCGATACATGATCTGTGTATCGATACAT
Done.