Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2188
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: 73181
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.35
Found at i:2797 original size:52 final size:52
Alignment explanation
Indices: 2731--2845 Score: 194
Period size: 52 Copynumber: 2.2 Consensus size: 52
2721 ATTTATCTGT
* *
2731 ATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCTTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
* *
2783 ATGTATCGATACATTTTATAATGTATCGATACATCTTGGCAAATTTGCCTGC
1 ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
2835 ATGTATCGATA
1 ATGTATCGATA
2846 TAAAGATCGG
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.17, T:0.37
Consensus pattern (52 bp):
ATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:2860 original size:52 final size:52
Alignment explanation
Indices: 2731--2867 Score: 161
Period size: 52 Copynumber: 2.6 Consensus size: 52
2721 ATTTATCTGT
* *
2731 ATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGCTTGC
1 ATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
*** * *
2783 ATGTATCGATACATTTTATAATGTATCGATACATCTTGGCAAATTTGCCTGC
1 ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
* *
2835 ATGTATCGATATA-AAGATCGGTGTATCGATACA
1 ATGTATCGATACATAAGAT-AGTGTATCGATACA
2868 ATGTATTGAT
Statistics
Matches: 73, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
51 4 0.05
52 69 0.95
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.36
Consensus pattern (52 bp):
ATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCCTGC
Found at i:2962 original size:13 final size:13
Alignment explanation
Indices: 2944--2968 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2934 CAAAAAAATA
2944 TGTATCGATACAT
1 TGTATCGATACAT
2957 TGTATCGATACA
1 TGTATCGATACA
2969 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:2964 original size:33 final size:33
Alignment explanation
Indices: 2922--2988 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
2912 AGTAGCTTAA
2922 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
2955 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
2988 A
1 A
2989 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:3888 original size:55 final size:52
Alignment explanation
Indices: 3788--4219 Score: 374
Period size: 49 Copynumber: 8.7 Consensus size: 52
3778 GAAAAGTGAT
* * * * * * **
3788 AAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAA
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATG-G-A
* *
3842 AAAGGATGTCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
1 AAAGG-TGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
3895 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGAC-T-----T---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
3938 AAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
3988 --AGGTGCCAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* **
4036 -AAGGTGCCAATATGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGAT---
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * *
4084 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT--A-ATGGT
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* * * *
4133 GAAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGAT-G-
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
* *
4183 -AAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTG
1 AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTG
4220 GGCTTAGAAG
Statistics
Matches: 325, Mismatches: 37, Indels: 37
0.81 0.09 0.09
Matches are distributed among these distances:
43 38 0.12
44 1 0.00
46 3 0.01
47 1 0.00
48 44 0.14
49 154 0.47
51 3 0.01
52 34 0.10
53 6 0.02
54 5 0.02
55 36 0.11
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.25
Consensus pattern (52 bp):
AAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGA
Found at i:4059 original size:49 final size:49
Alignment explanation
Indices: 3851--4225 Score: 494
Period size: 49 Copynumber: 7.7 Consensus size: 49
3841 AAAAGGATGT
* *
3851 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
*
3903 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
3946 CAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG-AGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
3994 CAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
4043 CAATATGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
4092 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
4141 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
4190 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
4226 GAAGGGTTGC
Statistics
Matches: 283, Mismatches: 33, Indels: 17
0.85 0.10 0.05
Matches are distributed among these distances:
43 39 0.14
48 45 0.16
49 167 0.59
52 32 0.11
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATATGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:4125 original size:98 final size:98
Alignment explanation
Indices: 3785--4225 Score: 554
Period size: 98 Copynumber: 4.5 Consensus size: 98
3775 TGAGAAAAGT
* * * * * *
3785 GATAAAGATGCCAATATGTTGATTCACGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TG
* * *
3850 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
60 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
3889 GATGGAAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
* *
3948 ATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAA
63 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * * *
3984 GGT-GAGGTGCCAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
4048 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
4081 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
4146 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * *
4179 GATGAAGGTGCCAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTA
4226 GAAGGGTTGC
Statistics
Matches: 299, Mismatches: 28, Indels: 26
0.85 0.08 0.07
Matches are distributed among these distances:
91 39 0.13
95 41 0.14
96 4 0.01
97 43 0.14
98 131 0.44
103 1 0.00
104 3 0.01
107 37 0.12
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
Found at i:4185 original size:147 final size:142
Alignment explanation
Indices: 3851--4225 Score: 547
Period size: 147 Copynumber: 2.6 Consensus size: 142
3841 AAAAGGATGT
*
3851 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAAGGTGCCAATATGCTGATT
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGCCAATATGCTGATT
* *
3916 CAAGGCCAGCTATATTGGAC-T-TAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGAC
63 CAAGGCCAGCTATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGAC
3979 TTAAAGGTGAGGTGC
128 TTAAAGGTGAGGTGC
* * *
3994 CAATGTGCTGATTCAAGACCAGCTATATTGGACTTAAAGATGAAGGTGCCAATATGCTGAGTCAA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
* * *
4059 GGCCAGCTACATTGGTCTTAAAGATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGA
66 GGCCAGCTATATTGGACTT----ATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGA
*
4124 CTTAATGGTGAAGGTGC
127 CTTAAAGGTG-AGGTGC
* *
4141 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAG
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
*
4206 GGCCAGCTATATTGGGCTTA
66 GGCCAGCTATATTGGACTTA
4226 GAAGGGTTGC
Statistics
Matches: 208, Mismatches: 17, Indels: 14
0.87 0.07 0.06
Matches are distributed among these distances:
140 37 0.18
141 1 0.00
142 1 0.00
143 39 0.19
146 47 0.23
147 83 0.40
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (142 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATATGCTGATTCAA
GGCCAGCTATATTGGACTTATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTACATTGGACTTA
AAGGTGAGGTGC
Found at i:17925 original size:27 final size:28
Alignment explanation
Indices: 17894--17964 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
17884 TAATATGGAA
*
17894 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
17921 ATAATAATAT-ATAAATTTTATTTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
*
17948 ATAATAATTTAATAAAT
1 ATAATAATATAATAAAT
17965 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.25
27 24 0.60
28 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATAATATAATAAATTTTATTTTTAT
Found at i:19527 original size:21 final size:20
Alignment explanation
Indices: 19496--19534 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
19486 ATTTTTATTT
19496 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
19516 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
19535 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:19661 original size:21 final size:22
Alignment explanation
Indices: 19618--19667 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
19608 TGTGAATAAA
*
19618 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
19640 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
19661 TTCATTA
1 TTTATTA
19668 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:19827 original size:22 final size:22
Alignment explanation
Indices: 19755--19816 Score: 124
Period size: 22 Copynumber: 2.8 Consensus size: 22
19745 AATATAAAAA
19755 AGAATAAACTTTATATTAGTGG
1 AGAATAAACTTTATATTAGTGG
19777 AGAATAAACTTTATATTAGTGG
1 AGAATAAACTTTATATTAGTGG
19799 AGAATAAACTTTATATTA
1 AGAATAAACTTTATATTA
19817 TTGGCATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 40 1.00
ACGTcount: A:0.44, C:0.05, G:0.15, T:0.37
Consensus pattern (22 bp):
AGAATAAACTTTATATTAGTGG
Found at i:20151 original size:9 final size:9
Alignment explanation
Indices: 20137--20166 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
20127 ACTCCCAAAT
*
20137 TTCCTCCTC
1 TTCCTCTTC
20146 TTCCTCTTC
1 TTCCTCTTC
20155 TTCCTCTTC
1 TTCCTCTTC
20164 TTC
1 TTC
20167 TTCGTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:23445 original size:3 final size:3
Alignment explanation
Indices: 23437--23474 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
23427 GTGTTACCTT
23437 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
23475 TGTTAATAAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:25659 original size:22 final size:22
Alignment explanation
Indices: 25624--25666 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
25614 AAATCTCTTT
** *
25624 TTTTTATTTGAATTCAAATATC
1 TTTTTATTCCAATTAAAATATC
25646 TTTTTATTCCAATTAAAATAT
1 TTTTTATTCCAATTAAAATAT
25667 TAACAATGTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.35, C:0.09, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTTATTCCAATTAAAATATC
Found at i:36465 original size:1 final size:1
Alignment explanation
Indices: 36459--36521 Score: 72
Period size: 1 Copynumber: 63.0 Consensus size: 1
36449 TGGCAATTGG
* * ** * *
36459 AAAAAAAAAAAAAAAAAACAAAACAAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
36522 GTGAAGATTT
Statistics
Matches: 52, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
1 52 1.00
ACGTcount: A:0.90, C:0.05, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:36498 original size:30 final size:30
Alignment explanation
Indices: 36463--36522 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
36453 AATTGGAAAA
*
36463 AAAAAAAAAAAAAACAAAACAAAAAAAAAGG
1 AAAAAGAAAAAAAA-AAAACAAAAAAAAAGG
36494 AAAAAGAAAAAAAAAAAACAAAAAAAAAG
1 AAAAAGAAAAAAAAAAAACAAAAAAAAAG
36523 TGAAGATTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 15 0.54
31 13 0.46
ACGTcount: A:0.88, C:0.05, G:0.07, T:0.00
Consensus pattern (30 bp):
AAAAAGAAAAAAAAAAAACAAAAAAAAAGG
Found at i:56236 original size:22 final size:22
Alignment explanation
Indices: 56194--56236 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
56184 ATACAAATAG
*
56194 ATAACAATTGGTATTTATTTTA
1 ATAACAATTGGTATGTATTTTA
* *
56216 ATAATAATTGGTATGTCTTTT
1 ATAACAATTGGTATGTATTTT
56237 CTGCTCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.33, C:0.05, G:0.12, T:0.51
Consensus pattern (22 bp):
ATAACAATTGGTATGTATTTTA
Found at i:60252 original size:19 final size:18
Alignment explanation
Indices: 60228--60295 Score: 74
Period size: 19 Copynumber: 3.9 Consensus size: 18
60218 CAGTAGCTGA
60228 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
60247 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
60262 -T-TGTATCGATACAACAC
1 TTATGTATCGATACAA-AC
*
60279 TTATATATCGATACAAA
1 TTATGTATCGATACAAA
60296 TCGTTGAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 13
0.75 0.02 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 2 0.05
19 26 0.62
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:60268 original size:13 final size:13
Alignment explanation
Indices: 60250--60274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60240 ACAATACTTA
60250 TGTATCGATACAT
1 TGTATCGATACAT
60263 TGTATCGATACA
1 TGTATCGATACA
60275 ACACTTATAT
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:60269 original size:32 final size:32
Alignment explanation
Indices: 60231--60293 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
60221 TAGCTGATTA
* *
60231 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAACACTTATATATCGATACAT
60263 TGTATCGATACAACACTTATATATCGATACA
1 TGTATCGATACAACACTTATATATCGATACA
60294 AATCGTTGAA
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:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAACACTTATATATCGATACAT
Found at i:63123 original size:27 final size:28
Alignment explanation
Indices: 63092--63162 Score: 110
Period size: 27 Copynumber: 2.6 Consensus size: 28
63082 TAATATGGAA
*
63092 ATAATTATATAATAAATTTTA-TTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
63119 ATAATAATAT-ATAAATTTTATTTTTAT
1 ATAATAATATAATAAATTTTATTTTTAT
*
63146 ATAATAATTTAATAAAT
1 ATAATAATATAATAAAT
63163 ATATAAAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 10 0.25
27 24 0.60
28 6 0.15
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATAATATAATAAATTTTATTTTTAT
Found at i:64743 original size:21 final size:20
Alignment explanation
Indices: 64712--64750 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
64702 ATTTTTATTT
64712 TTTAAATTTTTAAGTTTTAC
1 TTTAAATTTTTAAGTTTTAC
*
64732 TTTAAGATTTTTATGTTTT
1 TTTAA-ATTTTTAAGTTTT
64751 TAGATTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.26, C:0.03, G:0.08, T:0.64
Consensus pattern (20 bp):
TTTAAATTTTTAAGTTTTAC
Found at i:64877 original size:21 final size:22
Alignment explanation
Indices: 64834--64883 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
64824 TGTGAATAAA
*
64834 TTTATTATTAAATTTATAAATT
1 TTTATTATAAAATTTATAAATT
*
64856 TTTATTATAAAATTT-TACATT
1 TTTATTATAAAATTTATAAATT
*
64877 TTCATTA
1 TTTATTA
64884 ACTTTAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
21 11 0.44
22 14 0.56
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (22 bp):
TTTATTATAAAATTTATAAATT
Found at i:65344 original size:9 final size:9
Alignment explanation
Indices: 65330--65359 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
65320 ACTCCCAAAT
*
65330 TTCCTCCTC
1 TTCCTCTTC
65339 TTCCTCTTC
1 TTCCTCTTC
65348 TTCCTCTTC
1 TTCCTCTTC
65357 TTC
1 TTC
65360 TTCGTCTTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (9 bp):
TTCCTCTTC
Found at i:65922 original size:2 final size:2
Alignment explanation
Indices: 65917--65947 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
65907 TCTCTCTCTC
65917 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 T
65948 GCACGCACAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:68632 original size:3 final size:3
Alignment explanation
Indices: 68624--68660 Score: 67
Period size: 3 Copynumber: 12.7 Consensus size: 3
68614 GTGTTACCTT
68624 TTA TTA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
68661 TGTTAATAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Done.