Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold784
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: 40313
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:6659 original size:27 final size:26
Alignment explanation
Indices: 6621--6758 Score: 170
Period size: 27 Copynumber: 5.1 Consensus size: 26
6611 AAGCGTCTTT
*
6621 GTGGCTATGCCACAGTTATCTGATCTG
1 GTGGCTCTGCCACA-TTATCTGATCTG
*
6648 GTGGCTCTGCCACATATATCTG-TCCTA
1 GTGGCTCTGCCACAT-TATCTGAT-CTG
*
6675 GTGGCTATGCCACAATTATCTGATCTG
1 GTGGCTCTGCCAC-ATTATCTGATCTG
*
6702 GTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTCTGCCACAT-TATCTGATCTG
*
6729 GTGGCTCTGCCACAATATCTGTATCTG
1 GTGGCTCTGCCACATTATCTG-ATCTG
6756 GTG
1 GTG
6759 ACTTCGTAAC
Statistics
Matches: 97, Mismatches: 8, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
26 10 0.10
27 84 0.87
28 3 0.03
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (26 bp):
GTGGCTCTGCCACATTATCTGATCTG
Found at i:6703 original size:54 final size:54
Alignment explanation
Indices: 6621--6758 Score: 224
Period size: 54 Copynumber: 2.6 Consensus size: 54
6611 AAGCGTCTTT
*
6621 GTGGCTATGCCACAGTTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTA
1 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTA
* *
6675 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTTCTG
1 GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTA
*
6729 GTGGCTCTGCCACAA-TATCTGTATCTGGTG
1 GTGGCTATGCCACAATTATCTG-ATCTGGTG
6759 ACTTCGTAAC
Statistics
Matches: 79, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
53 6 0.08
54 73 0.92
ACGTcount: A:0.18, C:0.25, G:0.23, T:0.34
Consensus pattern (54 bp):
GTGGCTATGCCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTA
Found at i:6771 original size:81 final size:80
Alignment explanation
Indices: 6621--6776 Score: 192
Period size: 81 Copynumber: 1.9 Consensus size: 80
6611 AAGCGTCTTT
* *
6621 GTGGCTATGCCACAGTTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGGCTATGCC
1 GTGGCTATGCCACAGTTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTATGCA
6686 ACAATTATCTGATCTG
66 ACAA-TATCTGATCTG
* * * *
6702 GTGGCTCTGCCACA-TATATCTGTTCTGGTGGCTCTGCCACA-ATATCTGTATCTGGTGACT-TC
1 GTGGCTATGCCACAGT-TATCTGATCTGGTGGCTCTGCCACATATATCTGT-CCTAGTGACTAT-
*
6764 GTAACAATATCTG
63 GCAACAATATCTG
6777 GCAGCCTCGC
Statistics
Matches: 65, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
80 16 0.25
81 49 0.75
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.34
Consensus pattern (80 bp):
GTGGCTATGCCACAGTTATCTGATCTGGTGGCTCTGCCACATATATCTGTCCTAGTGACTATGCA
ACAATATCTGATCTG
Found at i:8019 original size:21 final size:21
Alignment explanation
Indices: 7994--8036 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
7984 ATACGCCAAG
7994 TAAAACAATTTCATGCTAACA
1 TAAAACAATTTCATGCTAACA
8015 TAAAACAATTTCATGCTAACA
1 TAAAACAATTTCATGCTAACA
8036 T
1 T
8037 GTGGCAGAAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.19, G:0.05, T:0.30
Consensus pattern (21 bp):
TAAAACAATTTCATGCTAACA
Found at i:14532 original size:40 final size:40
Alignment explanation
Indices: 14427--14602 Score: 220
Period size: 40 Copynumber: 4.5 Consensus size: 40
14417 CGGATGATAA
* *
14427 CCGGGCTAAGTCCCGAAGGCATCTGTG-GAAGTGACTA-ATT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACTATA-T
* *
14467 CCGGGCTAAG-CCCGAAGGCAATTGTGCGAGTTATTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
14506 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
*
14546 CCGGGCTAAGTCCCGAAGGCATTTGAGC-AG-TAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTA-CTATAT
**
14585 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
14603 TACTTGGTTG
Statistics
Matches: 123, Mismatches: 9, Indels: 10
0.87 0.06 0.07
Matches are distributed among these distances:
38 16 0.13
39 41 0.33
40 66 0.54
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAT
Found at i:14584 original size:79 final size:79
Alignment explanation
Indices: 14427--14602 Score: 218
Period size: 79 Copynumber: 2.2 Consensus size: 79
14417 CGGATGATAA
*
14427 CCGGGCTAAGTCCCGAAGGCATCTGTGGAAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGT
1 CCGGGCTAAGTCCCGAAGGCATCTGTGGAAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGA
*
14492 GCGAGTTATTATAT
66 GCGAGTTACTATAT
* * *
14506 CCGGGCTAAGTCCCGAAGGCATTTGTGCG-AGTTACT-ATATCCGGGCTAAGTCCCGAAGGCATT
1 CCGGGCTAAGTCCCGAAGGCATCTGTG-GAAGTGACTAAT-TCCGGGCTAAG-CCCGAAGGCAAT
14569 TGAGC-AG-TAGCTATAT
63 TGAGCGAGTTA-CTATAT
**
14585 CC-GGCTAAACCCCGAAGG
1 CCGGGCTAAGTCCCGAAGG
14603 TACTTGGTTG
Statistics
Matches: 86, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
78 18 0.21
79 52 0.60
80 16 0.19
ACGTcount: A:0.25, C:0.24, G:0.28, T:0.23
Consensus pattern (79 bp):
CCGGGCTAAGTCCCGAAGGCATCTGTGGAAGTGACTAATTCCGGGCTAAGCCCGAAGGCAATTGA
GCGAGTTACTATAT
Found at i:23951 original size:20 final size:19
Alignment explanation
Indices: 23924--23965 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
23914 CTTTCCAAAT
23924 TTTCTTACTTT-CATTTGCA
1 TTTCTTACTTTCCA-TTGCA
23943 TTTCATTACTTTCCATTGCA
1 TTTC-TTACTTTCCATTGCA
23963 TTT
1 TTT
23966 AATTTCTTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.17, C:0.21, G:0.05, T:0.57
Consensus pattern (19 bp):
TTTCTTACTTTCCATTGCA
Found at i:26469 original size:27 final size:26
Alignment explanation
Indices: 26421--26480 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
26411 GCGAGGCTGC
*
26421 CAGATATTGTGACGAAGTCACCAGATA
1 CAGATATTGTGACGAAGCCACCAGA-A
* * *
26448 CAGATATTGTGGCTAGGCCACCAGAA
1 CAGATATTGTGACGAAGCCACCAGAA
*
26474 TAGATAT
1 CAGATAT
26481 ATATATGTGG
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.25
27 21 0.75
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.23
Consensus pattern (26 bp):
CAGATATTGTGACGAAGCCACCAGAA
Found at i:26729 original size:27 final size:27
Alignment explanation
Indices: 26697--26782 Score: 111
Period size: 27 Copynumber: 3.2 Consensus size: 27
26687 ATAATCCTAG
26697 GGGTAAAATCGTAATTCTGTAAATCGA
1 GGGTAAAATCGTAATTCTGTAAATCGA
*
26724 GGGTAAAA-CAGTAATTCTGTAAATCAA
1 GGGTAAAATC-GTAATTCTGTAAATCGA
* * * *
26751 GGGTAACATAGTAATTTTGTAATTCGA
1 GGGTAAAATCGTAATTCTGTAAATCGA
26778 GGGTA
1 GGGTA
26783 CTTTAATAAT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
26 1 0.02
27 50 0.98
ACGTcount: A:0.37, C:0.09, G:0.23, T:0.30
Consensus pattern (27 bp):
GGGTAAAATCGTAATTCTGTAAATCGA
Found at i:26833 original size:27 final size:27
Alignment explanation
Indices: 26803--26928 Score: 100
Period size: 27 Copynumber: 4.7 Consensus size: 27
26793 TTTACATGTC
*
26803 GAGGGTATTTCAGTAATTTTGCAAACT
1 GAGGGTATTTCAGTAATTTTACAAACT
*
26830 GAGGGAATTTC-GATAATTTTACAAA-T
1 GAGGGTATTTCAG-TAATTTTACAAACT
* * ** *
26856 CGAGGATAGTTGGGTAATTTTATAAACCT
1 -GAGGGTATTTCAGTAATTTTACAAA-CT
*
26885 G-GGGTACTTT-GGTAATTTTAC-AACT
1 GAGGGTA-TTTCAGTAATTTTACAAACT
*
26910 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCAGTAATTT
26929 GGTAAACTAA
Statistics
Matches: 80, Mismatches: 11, Indels: 17
0.74 0.10 0.16
Matches are distributed among these distances:
25 6 0.08
26 16 0.20
27 53 0.66
28 4 0.05
29 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (27 bp):
GAGGGTATTTCAGTAATTTTACAAACT
Found at i:26834 original size:54 final size:55
Alignment explanation
Indices: 26776--26928 Score: 152
Period size: 54 Copynumber: 2.8 Consensus size: 55
26766 TTTGTAATTC
* ** *
26776 GAGGGTACTTTAATAATTTTACATGTCGAGGGTATTTCAGTAATTTTGCAAA-CT
1 GAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACCT
* * * ** *
26830 GAGGG-AATTTCGATAATTTTACAAATCGAGGATAGTTGGGTAATTTTATAAACCT
1 GAGGGTACTTT-GATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACCT
* * *
26885 G-GGGTACTTTGGTAATTTTACAACT-GGGGGTATTTCAGTAATTT
1 GAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTT
26929 GGTAAACTAA
Statistics
Matches: 78, Mismatches: 18, Indels: 7
0.76 0.17 0.07
Matches are distributed among these distances:
53 18 0.23
54 53 0.68
55 7 0.09
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (55 bp):
GAGGGTACTTTGATAATTTTACAAATCGAGGGTATTTCAGTAATTTTACAAACCT
Found at i:26925 original size:26 final size:26
Alignment explanation
Indices: 26776--26928 Score: 89
Period size: 27 Copynumber: 5.7 Consensus size: 26
26766 TTTGTAATTC
* **
26776 GAGGGTACTTT-AATAATTTTACATGT
1 GAGGGTA-TTTCAGTAATTTTACAACT
*
26802 CGAGGGTATTTCAGTAATTTTGCAAACT
1 -GAGGGTATTTCAGTAATTTTAC-AACT
* *
26830 GAGGGAATTTC-GATAATTTTACAAAT
1 GAGGGTATTTCAG-TAATTTTACAACT
* * ** *
26856 CGAGGATAGTTGGGTAATTTTATAAACCT
1 -GAGGGTATTTCAGTAATTTTA-CAA-CT
*
26885 G-GGGTACTTT-GGTAATTTTACAACT
1 GAGGGTA-TTTCAGTAATTTTACAACT
*
26910 GGGGGTATTTCAGTAATTT
1 GAGGGTATTTCAGTAATTT
26929 GGTAAACTAA
Statistics
Matches: 99, Mismatches: 17, Indels: 21
0.72 0.12 0.15
Matches are distributed among these distances:
25 6 0.06
26 21 0.21
27 63 0.64
28 8 0.08
29 1 0.01
ACGTcount: A:0.29, C:0.10, G:0.23, T:0.38
Consensus pattern (26 bp):
GAGGGTATTTCAGTAATTTTACAACT
Found at i:29293 original size:27 final size:27
Alignment explanation
Indices: 29261--29319 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 27
29251 ATAATCCTAG
29261 GGGTAAAATCA-TAATTCTGTAAATCGA
1 GGGTAAAA-CAGTAATTCTGTAAATCGA
* *
29288 GGGTAAAACAGTAATTTTGTAATTCGA
1 GGGTAAAACAGTAATTCTGTAAATCGA
29315 GGGTA
1 GGGTA
29320 CTTTAATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 2 0.07
27 27 0.93
ACGTcount: A:0.37, C:0.08, G:0.24, T:0.31
Consensus pattern (27 bp):
GGGTAAAACAGTAATTCTGTAAATCGA
Found at i:29329 original size:27 final size:27
Alignment explanation
Indices: 29271--29386 Score: 94
Period size: 27 Copynumber: 4.3 Consensus size: 27
29261 GGGTAAAATC
* * ***
29271 ATAATTCTGTAAATCGAGGGTAAAACA
1 ATAATTTTGTAATTCGAGGGTATTTCA
*
29298 GTAATTTTGTAATTCGAGGGTACTTT-A
1 ATAATTTTGTAATTCGAGGGTA-TTTCA
*
29325 ATAATTTTAT-ATGTCGAGGGTATTTCA
1 ATAATTTTGTAAT-TCGAGGGTATTTCA
* * *
29352 GTAATTTTGCAAATT-GAGGGTATTTCG
1 ATAATTTTG-TAATTCGAGGGTATTTCA
29379 ATAATTTT
1 ATAATTTT
29387 ACAAATCGAG
Statistics
Matches: 71, Mismatches: 13, Indels: 10
0.76 0.14 0.11
Matches are distributed among these distances:
26 5 0.07
27 63 0.89
28 1 0.01
29 2 0.03
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.41
Consensus pattern (27 bp):
ATAATTTTGTAATTCGAGGGTATTTCA
Found at i:29391 original size:27 final size:27
Alignment explanation
Indices: 29311--29465 Score: 113
Period size: 27 Copynumber: 5.8 Consensus size: 27
29301 ATTTTGTAAT
* * **
29311 TCGAGGGTACTTT-AATAATTTTATATG
1 TCGAGGGTA-TTTCGATAATTTTACAAA
*
29338 TCGAGGGTATTTC-AGTAATTTTGCAAA
1 TCGAGGGTATTTCGA-TAATTTTACAAA
*
29365 TTGAGGGTATTTCGATAATTTTACAAA
1 TCGAGGGTATTTCGATAATTTTACAAA
* * * *
29392 TCGAGGATATTTGGGTAATTTTATAAA
1 TCGAGGGTATTTCGATAATTTTACAAA
* * *
29419 -CTGGGGGTACTTT-GGTAATTTTACAAC
1 TC-GAGGGTA-TTTCGATAATTTTACAAA
*
29446 TCG-GGGTATTTCAATAATTT
1 TCGAGGGTATTTCGATAATTT
29466 GGTAAACTAA
Statistics
Matches: 104, Mismatches: 17, Indels: 15
0.76 0.12 0.11
Matches are distributed among these distances:
25 3 0.03
26 16 0.15
27 80 0.77
28 5 0.05
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.41
Consensus pattern (27 bp):
TCGAGGGTATTTCGATAATTTTACAAA
Found at i:29396 original size:54 final size:53
Alignment explanation
Indices: 29281--29465 Score: 167
Period size: 54 Copynumber: 3.5 Consensus size: 53
29271 ATAATTCTGT
*** * * *
29281 AAATCGAGGGTAAAACAGTAATTTTGTAATTCGAGGGTACTTTAATAATTTTAT
1 AAATCGAGGGTATTTCAGTAATTTTGAAATT-GAGGGTACTTTGATAATTTTAC
**
29335 ATGTCGAGGGTATTTCAGTAATTTTGCAAATTGAGGGTA-TTTCGATAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTTG-AAATTGAGGGTACTTT-GATAATTTTAC
* ** * * * *
29389 AAATCGAGGATATTTGGGTAATTTTATAAACTGGGGGTACTTTGGTAATTTTAC
1 AAATCGAGGGTATTTCAGTAATTTT-GAAATTGAGGGTACTTTGATAATTTTAC
* *
29443 AACTCG-GGGTATTTCAATAATTT
1 AAATCGAGGGTATTTCAGTAATTT
29466 GGTAAACTAA
Statistics
Matches: 105, Mismatches: 22, Indels: 9
0.77 0.16 0.07
Matches are distributed among these distances:
53 16 0.15
54 82 0.78
55 7 0.07
ACGTcount: A:0.31, C:0.09, G:0.21, T:0.39
Consensus pattern (53 bp):
AAATCGAGGGTATTTCAGTAATTTTGAAATTGAGGGTACTTTGATAATTTTAC
Found at i:31564 original size:27 final size:26
Alignment explanation
Indices: 31516--31575 Score: 66
Period size: 27 Copynumber: 2.3 Consensus size: 26
31506 GCGAAGCTGC
* *
31516 CAGATATTGTGACAAAGTCACCAGATA
1 CAGATATTGTGACAAAGCCACCA-AAA
* * *
31543 CAGATATTGTGGCTAGGCCACCAAAA
1 CAGATATTGTGACAAAGCCACCAAAA
31569 CAGATAT
1 CAGATAT
31576 ATATATGTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.38, C:0.20, G:0.20, T:0.22
Consensus pattern (26 bp):
CAGATATTGTGACAAAGCCACCAAAA
Found at i:31889 original size:54 final size:53
Alignment explanation
Indices: 31831--32006 Score: 173
Period size: 54 Copynumber: 3.3 Consensus size: 53
31821 GAAGGTAAAA
* *
31831 CAGTAATTTTGTAATCCGAGGGTACTTTGATAATTTTACATCTCGAGCGTATTT
1 CAGTAATTTTGTAAACCGAGGGTACTTTGATAATTTTACAACTCGAG-GTATTT
* * * *
31885 CAGTAATTTTGTAAACTGAGGGTA-TTTCGAAAATTTTACAAATCGAGGATTTTT
1 CAGTAATTTTGTAAACCGAGGGTACTTT-GATAATTTTACAACTCGAGG-TATTT
* * *
31939 C--TAAATTTTATAAACC-AGGGGTACTTTTG-TAATTTTACAACTGGGGGTATTT
1 CAGT-AATTTTGTAAACCGA-GGGTAC-TTTGATAATTTTACAACTCGAGGTATTT
*
31991 CAGTAATTTGGTAAAC
1 CAGTAATTTTGTAAAC
32007 TAAAGTATTC
Statistics
Matches: 99, Mismatches: 15, Indels: 17
0.76 0.11 0.13
Matches are distributed among these distances:
52 7 0.07
53 44 0.44
54 45 0.45
55 3 0.03
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (53 bp):
CAGTAATTTTGTAAACCGAGGGTACTTTGATAATTTTACAACTCGAGGTATTT
Found at i:31909 original size:27 final size:27
Alignment explanation
Indices: 31831--31912 Score: 80
Period size: 27 Copynumber: 3.0 Consensus size: 27
31821 GAAGGTAAAA
*
31831 CAGTAATTTTGTAATCCGAGGGTACTTT
1 CAGTAATTTTGTAATCTGAGGGTA-TTT
* *
31859 GA-TAA-TTT-TACATCTCGAGCGTATTT
1 CAGTAATTTTGTA-ATCT-GAGGGTATTT
*
31885 CAGTAATTTTGTAAACTGAGGGTATTT
1 CAGTAATTTTGTAATCTGAGGGTATTT
31912 C
1 C
31913 GAAAATTTTA
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
25 2 0.05
26 10 0.23
27 22 0.51
28 7 0.16
29 2 0.05
ACGTcount: A:0.27, C:0.13, G:0.20, T:0.40
Consensus pattern (27 bp):
CAGTAATTTTGTAATCTGAGGGTATTT
Found at i:33804 original size:27 final size:27
Alignment explanation
Indices: 33762--33813 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
33752 GAAATGTGAA
*
33762 AGGGGTTGCTATGTGCTGATTCCCCCG
1 AGGGGTTGCTAAGTGCTGATTCCCCCG
33789 AGGGGTTGCTAAGTGCTGATTCCCC
1 AGGGGTTGCTAAGTGCTGATTCCCC
33814 GTTCATTGGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.13, C:0.25, G:0.33, T:0.29
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:33853 original size:102 final size:104
Alignment explanation
Indices: 33686--33907 Score: 351
Period size: 103 Copynumber: 2.2 Consensus size: 104
33676 TGTATATAAA
** * * *
33686 AGGGGTTGCTGTGTGCTGATTCCCCGATTTATGGGTGGTGCTATGTGCGTGATCCACCATATCTT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCACATCTT
*
33751 TGAAATGTGAAA-GGGGTTGCTATGTGCTGATTCCCCCG
66 TGAAATGTGAAAGGGGGTTGCTATATGCTGATTCCCCCG
*
33789 AGGGGTTGCTAAGTGCTGATTCCCCG-TTCATTGGTGGTGCTAAGTGCGAT-ATCCACCACATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCG-TGATCCACCACATCT
33852 TTGAAATGTGAAAGGGGGTTGCTATATGCTGATTCCCCCG
65 TTGAAATGTGAAAGGGGGTTGCTATATGCTGATTCCCCCG
33892 AGGGGTTGCTAAGTGC
1 AGGGGTTGCTAAGTGC
33908 GATATCCATT
Statistics
Matches: 110, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
102 44 0.40
103 66 0.60
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (104 bp):
AGGGGTTGCTAAGTGCTGATTCCCCGATTCATGGGTGGTGCTAAGTGCGTGATCCACCACATCTT
TGAAATGTGAAAGGGGGTTGCTATATGCTGATTCCCCCG
Found at i:33960 original size:71 final size:72
Alignment explanation
Indices: 33826--33977 Score: 234
Period size: 71 Copynumber: 2.1 Consensus size: 72
33816 TCATTGGTGG
* *
33826 TGCTAAGTGCGATATCCACCACATCTTTGAAATGTGAAAGGGGGTTGCTATATGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCACATATTTGAAATGTAAAAGGGGGTTGCTATATGCTGATTCCCCC
33891 GAGGGGT
66 GAGGGGT
**** *
33898 TGCTAAGTGCGATATCCATTGTATATTTGAAATG-AAAAGGGGGTTGCTATGTGCTGATTCCCCC
1 TGCTAAGTGCGATATCCACCACATATTTGAAATGTAAAAGGGGGTTGCTATATGCTGATTCCCCC
33962 GAGGGGT
66 GAGGGGT
33969 TGCTAAGTG
1 TGCTAAGTG
33978 ATGATTCCCC
Statistics
Matches: 73, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 44 0.60
72 29 0.40
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.30
Consensus pattern (72 bp):
TGCTAAGTGCGATATCCACCACATATTTGAAATGTAAAAGGGGGTTGCTATATGCTGATTCCCCC
GAGGGGT
Found at i:38871 original size:22 final size:22
Alignment explanation
Indices: 38845--38889 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
38835 TTGTAACAAA
38845 ATGTTTAATCTGTCAACAAGTG
1 ATGTTTAATCTGTCAACAAGTG
38867 ATGTTTAATCTGTCAACAAGTG
1 ATGTTTAATCTGTCAACAAGTG
38889 A
1 A
38890 AGGCTGAGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (22 bp):
ATGTTTAATCTGTCAACAAGTG
Done.