Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold587
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: 51991
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1645 original size:96 final size:94
Alignment explanation
Indices: 1513--1687 Score: 248
Period size: 96 Copynumber: 1.8 Consensus size: 94
1503 GCCCCTAAGT
*
1513 GAACTCGGACTCAAGCTCAACGAGCTCTGGCGTTCGCATCCATAAGTGAATCTCGCGGACTCAGA
1 GAACTCGGACTCAAGCTCAACGAGCTCTGGCATTCGCATCCATAAGTGAA-CT--CGGACTCA-A
1578 CTC-ACGAGTTCGGATGCCTAGTTACATCTCGC
62 CTCAACGAGTTCGGATGCCTAGTTACATCTCGC
* * *
1610 GAACTCGGACTCAA-CTCAACGAGTTC-GGACATTCGCATCCATAGGTGAACTTGGACTCAACTC
1 GAACTCGGACTCAAGCTCAACGAGCTCTGG-CATTCGCATCCATAAGTGAACTCGGACTCAACTC
1673 AACGAGTTCGGATGC
65 AACGAGTTCGGATGC
1688 TCAACCATCC
Statistics
Matches: 72, Mismatches: 4, Indels: 8
0.86 0.05 0.10
Matches are distributed among these distances:
92 4 0.06
93 21 0.29
95 4 0.06
96 29 0.40
97 14 0.19
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (94 bp):
GAACTCGGACTCAAGCTCAACGAGCTCTGGCATTCGCATCCATAAGTGAACTCGGACTCAACTCA
ACGAGTTCGGATGCCTAGTTACATCTCGC
Found at i:4729 original size:17 final size:17
Alignment explanation
Indices: 4707--4742 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4697 TGATTTGTTT
4707 GATCAGCTAAAAGGAGC
1 GATCAGCTAAAAGGAGC
4724 GATCAGCTAAAAGGAGC
1 GATCAGCTAAAAGGAGC
4741 GA
1 GA
4743 CATGGTTTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.42, C:0.17, G:0.31, T:0.11
Consensus pattern (17 bp):
GATCAGCTAAAAGGAGC
Found at i:8115 original size:45 final size:45
Alignment explanation
Indices: 8065--8232 Score: 186
Period size: 45 Copynumber: 3.7 Consensus size: 45
8055 TGGTTGAGCA
8065 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
* *
8110 TCCGAACTCGTTGAGTTGAGTCCGAGTT--C-GTGAGATG-TAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATG-GATGCGAA-T--G
*
8155 CATCCGAACTCG-TGAGTTGAGT-CGAGTTCACTTATGGATGCGAACG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAATG
* *
8201 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACT
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACT
8233 TAGGGGCGGG
Statistics
Matches: 103, Mismatches: 7, Indels: 26
0.76 0.05 0.19
Matches are distributed among these distances:
42 4 0.04
43 6 0.06
44 8 0.08
45 46 0.45
46 20 0.19
47 11 0.11
48 4 0.04
49 4 0.04
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.28
Consensus pattern (45 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATG
Found at i:8218 original size:91 final size:92
Alignment explanation
Indices: 8062--8229 Score: 286
Period size: 91 Copynumber: 1.8 Consensus size: 92
8052 GGATGGTTGA
* *
8062 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAATGTCCGAACTCGTTGAGTT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGCCCGAACTCGTTGAGTT
8127 GAGTCCGAGTTCGTGAGATGTAACTAG
66 GAGTCCGAGTTCGTGAGATGTAACTAG
*
8154 GCATCCGAACTCG-TGAGTTGAGT-CGAGTTCACTTATGGATGCGAACGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCAC-TATGGATGCGAACGCCCGAACTCGTTGAGT
8217 TGAGTCCGAGTTC
65 TGAGTCCGAGTTC
8230 ACTTAGGGGC
Statistics
Matches: 72, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
90 9 0.12
91 50 0.69
92 13 0.18
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.27
Consensus pattern (92 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTATGGATGCGAACGCCCGAACTCGTTGAGTT
GAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:9710 original size:24 final size:25
Alignment explanation
Indices: 9653--9710 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
9643 AGGAAGTGCA
*
9653 AAAAG-GGCTTTGCCCTAGTTTATC
1 AAAAGAGGCTTTGCCCCAGTTTATC
*
9677 AAAA-AGGGCTTTGCCCCAG-TTATT
1 AAAAGA-GGCTTTGCCCCAGTTTATC
9701 AAAAGAGGCT
1 AAAAGAGGCT
9711 AGGCCTCCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.31, C:0.19, G:0.22, T:0.28
Consensus pattern (25 bp):
AAAAGAGGCTTTGCCCCAGTTTATC
Found at i:15071 original size:46 final size:46
Alignment explanation
Indices: 15018--15190 Score: 170
Period size: 46 Copynumber: 3.7 Consensus size: 46
15008 TTGGGCATCT
15018 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * * * * * * * *
15064 GAACTCGTTAAGTTGAGTCTGAGTTC-GTGAAATGTA-ACTAGGCATCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-ACGTCC
* *
15111 GAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCC
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
* * * *
15157 GAGCTCATTGAGTTGAGTCCAAGTTCGCTTATGG
1 GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGG
15191 GCGGGTTACA
Statistics
Matches: 99, Mismatches: 23, Indels: 10
0.75 0.17 0.08
Matches are distributed among these distances:
45 1 0.01
46 62 0.63
47 35 0.35
48 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (46 bp):
GAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCC
Found at i:15182 original size:93 final size:93
Alignment explanation
Indices: 15011--15183 Score: 274
Period size: 93 Copynumber: 1.9 Consensus size: 93
15001 AGGACATTTG
* * *
15011 GGCATCTGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGTCCGAACTCGTTAAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTAAG
**
15076 TTGAGTCTGAGTTCGTGAAATGTAACTA
66 TTGAGTCCAAGTTCGTGAAATGTAACTA
* * *
15104 GGCATCCGAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAG
1 GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTAAG
15169 TTGAGTCCAAGTTCG
66 TTGAGTCCAAGTTCG
15184 CTTATGGGCG
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
93 72 1.00
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.29
Consensus pattern (93 bp):
GGCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAACTCATTAAG
TTGAGTCCAAGTTCGTGAAATGTAACTA
Found at i:17822 original size:46 final size:48
Alignment explanation
Indices: 17755--17872 Score: 141
Period size: 48 Copynumber: 2.5 Consensus size: 48
17745 GGACAGGACA
* * *
17755 AGACAGAAATGAGCCATGTAAGTCCATATCA-GT-TATATGGCTTTGG
1 AGACAGGAATGAGCCATGTAAGTCCATATCATATATATATGGCATTGG
* *
17801 AGACAGGAATGAGCCATGTAAGCCCATATTATATATATATGGCATTGG
1 AGACAGGAATGAGCCATGTAAGTCCATATCATATATATATGGCATTGG
* * **
17849 AGACAAGAATAATTCATGTAAGTC
1 AGACAGGAATGAGCCATGTAAGTC
17873 AATGTCGAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
46 28 0.47
47 1 0.02
48 31 0.52
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.27
Consensus pattern (48 bp):
AGACAGGAATGAGCCATGTAAGTCCATATCATATATATATGGCATTGG
Found at i:20746 original size:15 final size:15
Alignment explanation
Indices: 20726--20790 Score: 62
Period size: 15 Copynumber: 4.4 Consensus size: 15
20716 ATATCTTGGG
20726 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
*
20741 TTTCTTTATTCTGGG
1 TTTCTTTATTCTGGA
* *
20756 TTTC-TCAATCTTGGA
1 TTTCTTTATTC-TGGA
* *
20771 TTTTTTTATTC-GGT
1 TTTCTTTATTCTGGA
20785 TTTCTT
1 TTTCTT
20791 GTTATCTTTA
Statistics
Matches: 39, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
14 11 0.28
15 24 0.62
16 4 0.10
ACGTcount: A:0.11, C:0.14, G:0.14, T:0.62
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:20758 original size:30 final size:31
Alignment explanation
Indices: 20722--20790 Score: 81
Period size: 30 Copynumber: 2.3 Consensus size: 31
20712 TATCATATCT
* *
20722 TGGGTTTCTTTATTC-TGGATTTCTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
*
20752 TGGGTTTC-TCAATCTTGGATTTTTTTATTC
1 TGGGTTTCTTCAATCTTGGATTTCTTTATTC
*
20782 -GGTTTTCTT
1 TGGGTTTCTT
20791 GTTATCTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
29 10 0.30
30 23 0.70
ACGTcount: A:0.10, C:0.13, G:0.17, T:0.59
Consensus pattern (31 bp):
TGGGTTTCTTCAATCTTGGATTTCTTTATTC
Found at i:24017 original size:22 final size:22
Alignment explanation
Indices: 23989--24034 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
23979 TCAACGGACC
23989 ATCTCGGTATGGTGGCTTGCAT
1 ATCTCGGTATGGTGGCTTGCAT
24011 ATCTCGGTATGGTGGCTTGCAT
1 ATCTCGGTATGGTGGCTTGCAT
24033 AT
1 AT
24035 TTTGGCATGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.17, G:0.30, T:0.37
Consensus pattern (22 bp):
ATCTCGGTATGGTGGCTTGCAT
Found at i:26365 original size:40 final size:40
Alignment explanation
Indices: 26271--26455 Score: 207
Period size: 40 Copynumber: 4.6 Consensus size: 40
26261 TATTCGAATG
*
26271 ATATCCGGGCTAAG-TCCCGAAGGCTTTTGTGCTAGGTGACT
1 ATATCCGGGCTAAGAT-CCGAAGGCATTTGTGCTA-GTGACT
* * * *
26312 ATAAT-CGGACTAAGATCCAAAGGCATTCGTGCAAGTTG-CT
1 AT-ATCCGGGCTAAGATCCGAAGGCATTTGTGCTAG-TGACT
* *
26352 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGCGACT
1 ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
* *
26392 ATATCCGGGCTAAG-TCTCGAAGGCGTTTATGCTAGTGACT
1 ATATCCGGGCTAAGATC-CGAAGGCATTTGTGCTAGTGACT
*
26432 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGATCCGAAGGC
26456 CTTGTGCAAG
Statistics
Matches: 121, Mismatches: 16, Indels: 15
0.80 0.11 0.10
Matches are distributed among these distances:
39 4 0.03
40 87 0.72
41 27 0.22
42 3 0.02
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (40 bp):
ATATCCGGGCTAAGATCCGAAGGCATTTGTGCTAGTGACT
Found at i:26441 original size:80 final size:81
Alignment explanation
Indices: 26271--26455 Score: 234
Period size: 80 Copynumber: 2.3 Consensus size: 81
26261 TATTCGAATG
* * *
26271 ATATCCGGGCTAAGTCCCGAAGGCTTTTGTGCTAGGTGACTATAATCGGACTAAGATCCAAAGGC
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAATCGGACTAAGATCCAAAGGC
*
26336 ATTCGTGCAAGTTGCT
66 ATTCATGCAAGTTGCT
* *
26352 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTA-GCGACTAT-ATCCGGGCTAAG-TCTCGAAG
1 ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAAT-CGGACTAAGATC-CAAAG
* * *
26414 GCGTTTATGCTAG-TGACT
64 GCATTCATGCAAGTTG-CT
26432 ATATCCGGGCTAAGACCCGAAGGC
1 ATATCCGGGCTAAGACCCGAAGGC
26456 CTTGTGCAAG
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
79 6 0.07
80 54 0.59
81 32 0.35
ACGTcount: A:0.25, C:0.23, G:0.27, T:0.25
Consensus pattern (81 bp):
ATATCCGGGCTAAGACCCGAAGGCATTTGTGCTAGGCGACTATAATCGGACTAAGATCCAAAGGC
ATTCATGCAAGTTGCT
Found at i:31975 original size:47 final size:45
Alignment explanation
Indices: 31865--31984 Score: 127
Period size: 47 Copynumber: 2.6 Consensus size: 45
31855 TCTCGTAGCT
* * *
31865 GATGCATGTCCCAGACATATCTTACACTGGCTCTCGTCTCAATGTC
1 GATGCATGTCCCAGACATGTCTTACACTGGCTATCG-ATCAATGTC
* **
31911 AATGCATGTCCTGGACATGTCTTACACTGGCATATC-AT-AATGTGGTC
1 GATGCATGTCCCAGACATGTCTTACACTGGC-TATCGATCAA--T-GTC
31958 GATGCATGTCCCAGACATGTCTTACAC
1 GATGCATGTCCCAGACATGTCTTACAC
31985 GAGCACACAC
Statistics
Matches: 61, Mismatches: 9, Indels: 7
0.79 0.12 0.09
Matches are distributed among these distances:
44 2 0.03
45 1 0.02
46 28 0.46
47 30 0.49
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (45 bp):
GATGCATGTCCCAGACATGTCTTACACTGGCTATCGATCAATGTC
Found at i:34519 original size:15 final size:15
Alignment explanation
Indices: 34484--34524 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 15
34474 TCCATAACGG
34484 AGAAATCCAGAATATA
1 AGAAATCCA-AATATA
34500 A-AAATCCAACATA-A
1 AGAAATCCAA-ATATA
34514 AGAAATCCAAA
1 AGAAATCCAAA
34525 ACAAGAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 4 0.17
15 18 0.78
16 1 0.04
ACGTcount: A:0.61, C:0.17, G:0.07, T:0.15
Consensus pattern (15 bp):
AGAAATCCAAATATA
Found at i:37381 original size:40 final size:40
Alignment explanation
Indices: 37337--37608 Score: 429
Period size: 40 Copynumber: 6.8 Consensus size: 40
37327 GAGTATAGCT
* * *
37337 ACTCGCTCGAATGCCTTCGGGACATAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
37377 ACTCGCACCAATGCCTTCGGGACTTAGCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
* *
37417 ACTCGCACAAATGCCTTCGAGACTTAGCCTGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
37457 ACTCGCACAAATGCCTTCGGGACTTATCCCGGATATAGTA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
37497 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGCA
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
*
37537 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGA-ACTAGTC
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATA-TAGTA
* *
37577 ACTAGCGCAAATGCCTTCGGGACTTAGCCCGG
1 ACTCGCACAAATGCCTTCGGGACTTAGCCCGG
37609 TTATCATCCA
Statistics
Matches: 216, Mismatches: 15, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
39 1 0.00
40 215 1.00
ACGTcount: A:0.26, C:0.29, G:0.23, T:0.22
Consensus pattern (40 bp):
ACTCGCACAAATGCCTTCGGGACTTAGCCCGGATATAGTA
Found at i:37664 original size:18 final size:19
Alignment explanation
Indices: 37622--37664 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
37612 TCATCCAAAT
37622 ATTCATGCACACATCAATA
1 ATTCATGCACACATCAATA
* *
37641 AATCATG-ACACATCTATA
1 ATTCATGCACACATCAATA
*
37659 TTTCAT
1 ATTCAT
37665 TTTCATAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.33
Consensus pattern (19 bp):
ATTCATGCACACATCAATA
Found at i:44002 original size:78 final size:81
Alignment explanation
Indices: 43881--44062 Score: 230
Period size: 78 Copynumber: 2.3 Consensus size: 81
43871 TCCTCGTTCA
* *
43881 AATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGG
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTC-GGATCTTAACCCGG
* *
43944 ATTTAGTAAC-TCGCAC
65 ATATAGTAACTTAGCAC
* **
43960 AATGCCTTCGGG-CTTAGCCCGGAAT-TAGTATCTCGCACAAATGCCTTCGGATCTTAGTCCGGA
1 AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
* *
44023 TATGGTCACTTAGCAC
66 TATAGTAACTTAGCAC
*
44039 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAGCCCGGA
44063 CATCATTCAA
Statistics
Matches: 89, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
77 3 0.03
78 46 0.52
79 29 0.33
80 11 0.12
ACGTcount: A:0.25, C:0.27, G:0.23, T:0.25
Consensus pattern (81 bp):
AATGCCTTCGGGACTTAGCCCGGAATATAGTAACTCGCACAAATGCCTTCGGATCTTAACCCGGA
TATAGTAACTTAGCAC
Found at i:44062 original size:40 final size:40
Alignment explanation
Indices: 43879--44062 Score: 225
Period size: 40 Copynumber: 4.7 Consensus size: 40
43869 GCTCCTCGTT
* *
43879 CAAATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
* *
43919 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
*
43959 C-AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATA-TAGTAACTCGCA
* * * *
43997 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATATAGTAAC-TCGCA
44038 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
44063 CATCATTCAA
Statistics
Matches: 124, Mismatches: 13, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
38 24 0.19
39 21 0.17
40 67 0.54
41 12 0.10
ACGTcount: A:0.25, C:0.28, G:0.23, T:0.24
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATATAGTAACTCGCA
Found at i:48419 original size:40 final size:40
Alignment explanation
Indices: 48335--48518 Score: 205
Period size: 40 Copynumber: 4.6 Consensus size: 40
48325 TTGAATGCTG
* * * *
48335 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACT-AT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGC-GAGTTATTAAT
**
48374 ATCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTATTAAT
1 -TCCGGGTTAAG-TCCCGAAGGCATTTGTGCGAGTTATTAAT
* * *
48415 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGATACTAAT
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
* *
48455 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTT-TTAAAA
1 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATT-AAT
48495 TCCGGGTTAAGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
48519 GAATGAGTTA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
39 2 0.02
40 113 0.90
41 10 0.08
ACGTcount: A:0.24, C:0.21, G:0.27, T:0.28
Consensus pattern (40 bp):
TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTATTAAT
Found at i:48472 original size:80 final size:81
Alignment explanation
Indices: 48335--48515 Score: 230
Period size: 80 Copynumber: 2.3 Consensus size: 81
48325 TTGAATGCTG
* *
48335 TCCGGGCTAAGTCCCGAAGG-CTTTGTGCTAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
* *
48399 TGTGCGAGTTATT-AAT
66 CGTGCGAGTT-TTAAAA
**
48415 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCG-AGAT-ACTA-ATTCCGGGTTAAG-TCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAG-TGACTATA-TCCGGACTAAGAT-CCGAAGGC
48476 ATTCGTGCGAGTTTTAAAA
63 ATTCGTGCGAGTTTTAAAA
48495 TCCGGGTTAAGTCCCGAAGGC
1 TCCGGGTTAAGTCCCGAAGGC
48516 ATTGAATGAG
Statistics
Matches: 90, Mismatches: 6, Indels: 10
0.85 0.06 0.09
Matches are distributed among these distances:
79 4 0.04
80 77 0.86
81 9 0.10
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.27
Consensus pattern (81 bp):
TCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAAGTGACTATATCCGGACTAAGATCCGAAGGCATT
CGTGCGAGTTTTAAAA
Found at i:48539 original size:39 final size:38
Alignment explanation
Indices: 48388--48565 Score: 133
Period size: 40 Copynumber: 4.5 Consensus size: 38
48378 GGACTAAGAT
** * *
48388 CCGAAGGCATTTGTGCGAGTTATTAATTCCGGGTTAAGTC
1 CCGAAGGCA-TTGAACGAGTTACTAA-ACCGGGTTAAGTC
* ** * *
48428 CCGAAGGCCTTTGTGCGAGATACTAATTCCGGGTTAAGTC
1 CCGAAGG-CATTGAACGAGTTACTAA-ACCGGGTTAAGTC
** *
48468 CCGAAGGCATTCGTGCGAGTT-TTAAAATCCGGGTTAAGTC
1 CCGAAGGCATT-GAACGAGTTACT-AAA-CCGGGTTAAGTC
* * *
48508 CCGAAGGCATTGAATGAGTTACTATAACCGGGCTATGTC
1 CCGAAGGCATTGAACGAGTTACTA-AACCGGGTTAAGTC
48547 CCGAAGGCACTTGAACGAG
1 CCGAAGGCA-TTGAACGAG
48566 GAGCTATATC
Statistics
Matches: 117, Mismatches: 14, Indels: 14
0.81 0.10 0.10
Matches are distributed among these distances:
39 30 0.26
40 86 0.74
41 1 0.01
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (38 bp):
CCGAAGGCATTGAACGAGTTACTAAACCGGGTTAAGTC
Found at i:48573 original size:40 final size:39
Alignment explanation
Indices: 48336--48578 Score: 104
Period size: 40 Copynumber: 6.1 Consensus size: 39
48326 TGAATGCTGT
* ** * *
48336 CCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTGAAC-GAGTGACTATAA
* ** *
48376 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTA-T-TAA
1 CCGGGCTAAG-TCCCGAAGGCA-TTGAACGAGTGACTATAA
* * ** *
48414 TTCCGGGTTAAGTCCCGAAGGCCTTTGTGCGAGAT-ACTA-ATT
1 --CCGGGCTAAGTCCCGAAGG-CATTGAACGAG-TGACTATA-A
* ** ** *
48456 CCGGGTTAAGTCCCGAAGGCATTCGTGCGAGT-TTTAAAA
1 CCGGGCTAAGTCCCGAAGGCATT-GAACGAGTGACTATAA
* * *
48495 TCCGGGTTAAGTCCCGAAGGCATTGAATGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
* *
48535 CCGGGCTATGTCCCGAAGGCACTTGAACGAG-GAGCTATAT
1 CCGGGCTAAGTCCCGAAGGCA-TTGAACGAGTGA-CTATAA
48575 CCGG
1 CCGG
48579 TTAAATTCCG
Statistics
Matches: 163, Mismatches: 24, Indels: 32
0.74 0.11 0.15
Matches are distributed among these distances:
38 2 0.01
39 33 0.20
40 117 0.72
41 11 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.26
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTGAACGAGTGACTATAA
Done.