Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_1453
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: 31106
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.35
Found at i:850 original size:14 final size:14
Alignment explanation
Indices: 815--899 Score: 62
Period size: 13 Copynumber: 6.5 Consensus size: 14
805 CTTACATTAC
815 AACTTACATAACTAT
1 AACTTACATAACT-T
830 AAC-TACATAACTT
1 AACTTACATAACTT
843 AACTTAC--AACTT
1 AACTTACATAACTT
* *
855 -ACATA-ATACATTT
1 AACTTACATA-ACTT
868 AACTTACAT-ACTT
1 AACTTACATAACTT
881 -ACTATACATAA--T
1 AACT-TACATAACTT
893 AACTTAC
1 AACTTAC
900 TTACATAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 21
0.70 0.05 0.26
Matches are distributed among these distances:
11 4 0.07
12 13 0.23
13 18 0.32
14 17 0.30
15 5 0.09
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.34
Consensus pattern (14 bp):
AACTTACATAACTT
Found at i:873 original size:18 final size:18
Alignment explanation
Indices: 850--985 Score: 81
Period size: 18 Copynumber: 7.4 Consensus size: 18
840 CTTAACTTAC
850 AACTTACATAATACATTT
1 AACTTACATAATACATTT
868 AACTTAC---ATAC--TT
1 AACTTACATAATACATTT
*
881 -ACTATACATAATA-ACTT
1 AACT-TACATAATACATTT
*
898 -ACTTACATAATACTTACTTAC
1 AACTTACATAATAC--A-TT-T
*
919 AACTTACATAATACACTT
1 AACTTACATAATACATTT
* *
937 AACTTACAACTTACATATAATAT
1 AACTTAC-A--TA-ATA-CATTT
960 AACTTACATAATACATTT
1 AACTTACATAATACATTT
978 AACTTACA
1 AACTTACA
986 ACTTACATAA
Statistics
Matches: 92, Mismatches: 9, Indels: 34
0.68 0.07 0.25
Matches are distributed among these distances:
12 3 0.03
13 5 0.05
15 4 0.04
16 12 0.13
17 5 0.05
18 25 0.27
19 6 0.07
20 4 0.04
21 2 0.02
22 17 0.18
23 9 0.10
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (18 bp):
AACTTACATAATACATTT
Found at i:875 original size:25 final size:25
Alignment explanation
Indices: 841--1085 Score: 210
Period size: 25 Copynumber: 10.4 Consensus size: 25
831 ACTACATAAC
841 TTAACTTACAACTTACATAATACAT
1 TTAACTTACAACTTACATAATACAT
866 TTAACTTACATACTTAC-T-ATACAT
1 TTAACTTACA-ACTTACATAATACAT
*
890 AATAACTT---ACTTACATAATAC--
1 -TTAACTTACAACTTACATAATACAT
*
911 TT-ACTTACAACTTACATAATACAC
1 TTAACTTACAACTTACATAATACAT
935 TTAACTTACAACTTACAT-ATA-AT
1 TTAACTTACAACTTACATAATACAT
*
958 ATAAC-T-----T-ACATAATACAT
1 TTAACTTACAACTTACATAATACAT
976 TTAACTTACAACTTACATAATACAT
1 TTAACTTACAACTTACATAATACAT
1001 TTAACTTACAACTTACATAATAC--
1 TTAACTTACAACTTACATAATACAT
* *
1024 TTAACTTACTTACATTACATACATTACTT
1 TTAACTTAC-AAC-TTACATA-A-TACAT
*
1053 TCATAACTTAC-ACTTACTTAATACA-
1 T--TAACTTACAACTTACATAATACAT
1078 -TAACTTAC
1 TTAACTTAC
1086 TTAACTTTAC
Statistics
Matches: 185, Mismatches: 8, Indels: 57
0.74 0.03 0.23
Matches are distributed among these distances:
16 4 0.02
17 4 0.02
18 6 0.03
19 5 0.03
20 1 0.01
21 6 0.03
22 23 0.12
23 18 0.10
24 14 0.08
25 73 0.39
26 10 0.05
27 4 0.02
28 6 0.03
29 3 0.02
31 8 0.04
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.37
Consensus pattern (25 bp):
TTAACTTACAACTTACATAATACAT
Found at i:906 original size:16 final size:15
Alignment explanation
Indices: 875--919 Score: 72
Period size: 15 Copynumber: 2.9 Consensus size: 15
865 TTTAACTTAC
875 ATACTTACTATACATA
1 ATACTTACT-TACATA
891 ATAACTTACTTACATA
1 AT-ACTTACTTACATA
907 ATACTTACTTACA
1 ATACTTACTTACA
920 ACTTACATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.39
16 10 0.36
17 7 0.25
ACGTcount: A:0.42, C:0.20, G:0.00, T:0.38
Consensus pattern (15 bp):
ATACTTACTTACATA
Found at i:968 original size:41 final size:43
Alignment explanation
Indices: 919--1010 Score: 152
Period size: 41 Copynumber: 2.2 Consensus size: 43
909 ACTTACTTAC
919 AACTTACATAATACACTTAACTTACAACTTACAT-ATA-ATAT
1 AACTTACATAATACACTTAACTTACAACTTACATAATACATAT
* *
960 AACTTACATAATACATTTAACTTACAACTTACATAATACATTT
1 AACTTACATAATACACTTAACTTACAACTTACATAATACATAT
1003 AACTTACA
1 AACTTACA
1011 ACTTACATAA
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
41 33 0.70
42 3 0.06
43 11 0.23
ACGTcount: A:0.46, C:0.20, G:0.00, T:0.35
Consensus pattern (43 bp):
AACTTACATAATACACTTAACTTACAACTTACATAATACATAT
Found at i:1005 original size:66 final size:66
Alignment explanation
Indices: 811--1032 Score: 275
Period size: 66 Copynumber: 3.4 Consensus size: 66
801 TACACTTACA
*
811 TTACAACTTACATA-ACTATAAC-TACAT-A-AC--TTAACTTACAACTTACATAATACATTTAA
1 TTACAACTTACATATAATATAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAA
870 C
66 C
*
871 TTACATACTTAC-TATACATAATAACTTACTTACATA-ATACTT-ACTTACAACTTACATAATAC
1 TTACA-ACTTACATATA-AT-ATAACTTACATA-ATACAT--TTAACTTACAACTTACATAATAC
*
933 ACTTAAC
60 ATTTAAC
940 TTACAACTTACATATAATATAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAA
1 TTACAACTTACATATAATATAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAA
1005 C
66 C
*
1006 TTACAACTTACATAATACT-TAACTTAC
1 TTACAACTTACAT-ATAATATAACTTAC
1033 TTACATTACA
Statistics
Matches: 140, Mismatches: 6, Indels: 26
0.81 0.03 0.15
Matches are distributed among these distances:
60 7 0.05
61 7 0.05
62 1 0.01
63 5 0.04
64 4 0.03
65 2 0.01
66 51 0.36
67 18 0.13
68 8 0.06
69 35 0.25
70 2 0.01
ACGTcount: A:0.44, C:0.21, G:0.00, T:0.36
Consensus pattern (66 bp):
TTACAACTTACATATAATATAACTTACATAATACATTTAACTTACAACTTACATAATACATTTAA
C
Found at i:1077 original size:31 final size:34
Alignment explanation
Indices: 1031--1119 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 34
1021 TACTTAACTT
* *
1031 ACTTACATTACATACATTACTTTCATAAC-TTAC
1 ACTTACATTACATACATAACTTACATAACTTTAC
*
1064 ACTTAC-TTA-ATACATAACTTACTTAACTTTAC
1 ACTTACATTACATACATAACTTACATAACTTTAC
* * * *
1096 ACGTACATAACTTACATAATTTAC
1 ACTTACATTACATACATAACTTAC
1120 TTAATACAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
31 15 0.33
32 12 0.26
33 8 0.17
34 11 0.24
ACGTcount: A:0.38, C:0.22, G:0.01, T:0.38
Consensus pattern (34 bp):
ACTTACATTACATACATAACTTACATAACTTTAC
Found at i:1122 original size:60 final size:57
Alignment explanation
Indices: 960--1122 Score: 134
Period size: 53 Copynumber: 3.0 Consensus size: 57
950 CATATAATAT
* *
960 AACTTACATAATACAT---TTAACTTACA--ACTTACATAA--TACAT-TTAACTTAC
1 AACTTACATAATACATAACTT-ACTTACATTACATACATAACTTACATATTTACTTAC
* * *
1010 AACTTACATAATACTTAACTTACTTACATTACATACATTACTTTCATA---ACTTAC
1 AACTTACATAATACATAACTTACTTACATTACATACATAACTTACATATTTACTTAC
* *
1064 -ACTTACTTAATACATAACTTACTTAACTTTACACGTACATAACTTACATAATTTACTTA
1 AACTTACATAATACATAACTTACTT-ACATTACA--TACATAACTTACAT-ATTTACTTA
1123 ATACAAATAT
Statistics
Matches: 89, Mismatches: 9, Indels: 20
0.75 0.08 0.17
Matches are distributed among these distances:
50 15 0.17
52 7 0.08
53 24 0.27
54 21 0.24
56 16 0.18
57 1 0.01
60 5 0.06
ACGTcount: A:0.40, C:0.21, G:0.01, T:0.38
Consensus pattern (57 bp):
AACTTACATAATACATAACTTACTTACATTACATACATAACTTACATATTTACTTAC
Found at i:1127 original size:25 final size:26
Alignment explanation
Indices: 1066--1127 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
1056 TAACTTACAC
*
1066 TTACTTAATACATAACTTACTTAACT
1 TTACTTAATACATAACTTACATAACT
*
1092 TTAC--ACGTACATAACTTACATAA-T
1 TTACTTA-ATACATAACTTACATAACT
1116 TTACTTAATACA
1 TTACTTAATACA
1128 AATATATTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
24 6 0.20
25 19 0.63
26 5 0.17
ACGTcount: A:0.40, C:0.19, G:0.02, T:0.39
Consensus pattern (26 bp):
TTACTTAATACATAACTTACATAACT
Found at i:5130 original size:42 final size:42
Alignment explanation
Indices: 5068--5280 Score: 345
Period size: 42 Copynumber: 5.0 Consensus size: 42
5058 AGTGGCGTTT
* * * *
5068 TTGTATAAAAGCGCCACTAAAGAATATGTTCTTTAGCGGCGC
1 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
5110 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
1 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
*
5152 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAACGGCGC
1 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
**
5194 TTGTAAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCAT
1 TTGT-AAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
*
5237 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGTGGCGC
1 TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
5279 TT
1 TT
5281 TTGTTTGTAA
Statistics
Matches: 159, Mismatches: 11, Indels: 2
0.92 0.06 0.01
Matches are distributed among these distances:
42 120 0.75
43 39 0.25
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.26
Consensus pattern (42 bp):
TTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGC
Found at i:5241 original size:85 final size:84
Alignment explanation
Indices: 5067--5280 Score: 347
Period size: 85 Copynumber: 2.5 Consensus size: 84
5057 TAGTGGCGTT
* * * *
5067 TTTGTATAAAAGCGCCACTAAAGAATATGTTCTTTAGCGGCGCTTGTAAAAAAACGCCGCTAAAG
1 TTTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTGTAAAAAAACGCCGCTAAAG
*
5132 AACATGTTCTTTAGCGGCG
66 AACATGTTCTTTAGCGGCA
* *
5151 CTTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAACGGCGCTTGTAAAAAAAACGCCGCTAAA
1 TTTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTGT-AAAAAAACGCCGCTAAA
5216 GAACATGTTCTTTAGCGGCA
65 GAACATGTTCTTTAGCGGCA
*
5236 TTTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGTGGCGCTT
1 TTTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTT
5281 TTGTTTGTAA
Statistics
Matches: 119, Mismatches: 10, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
84 41 0.34
85 78 0.66
ACGTcount: A:0.34, C:0.20, G:0.20, T:0.27
Consensus pattern (84 bp):
TTTGTAAAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTGTAAAAAAACGCCGCTAAAG
AACATGTTCTTTAGCGGCA
Found at i:5833 original size:31 final size:30
Alignment explanation
Indices: 5795--5896 Score: 84
Period size: 31 Copynumber: 3.3 Consensus size: 30
5785 CACATCAATT
5795 TTAAATTAATAAAATATTATCTATATAAATA
1 TTAAATTAATAAAATA-TATCTATATAAATA
** * *
5826 TTAAATTAAATTTAATATCTCGTAT-T-CATA
1 TTAAATT-AATAAAATATATC-TATATAAATA
* *
5856 TTAAATTAATCAAAA-ACTATCTAGATAATTA
1 TTAAATTAAT-AAAATA-TATCTATATAAATA
5887 TTAAATTAAT
1 TTAAATTAAT
5897 TATTAAATTC
Statistics
Matches: 55, Mismatches: 10, Indels: 12
0.71 0.13 0.16
Matches are distributed among these distances:
29 6 0.11
30 16 0.29
31 23 0.42
32 10 0.18
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (30 bp):
TTAAATTAATAAAATATATCTATATAAATA
Found at i:5898 original size:12 final size:12
Alignment explanation
Indices: 5881--5910 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
5871 ACTATCTAGA
5881 TAATTATTAAAT
1 TAATTATTAAAT
5893 TAATTATTAAAT
1 TAATTATTAAAT
*
5905 TCATTA
1 TAATTA
5911 AAACAATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (12 bp):
TAATTATTAAAT
Found at i:6238 original size:13 final size:13
Alignment explanation
Indices: 6220--6247 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
6210 TTCAACCAGT
6220 TTTTGGGTTTTGG
1 TTTTGGGTTTTGG
6233 TTTTGGGTTTTGG
1 TTTTGGGTTTTGG
6246 TT
1 TT
6248 CTCGGGTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.00, C:0.00, G:0.36, T:0.64
Consensus pattern (13 bp):
TTTTGGGTTTTGG
Found at i:15453 original size:30 final size:30
Alignment explanation
Indices: 15419--15541 Score: 219
Period size: 30 Copynumber: 4.1 Consensus size: 30
15409 ACTTAACAAG
*
15419 CAAATGCCTCTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
*
15449 CAAATGCCTTTAGAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
*
15479 CAAATGCCTTTAGAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
15509 CAAATGCCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTTTAAAATAATAACAAAATTAA
15539 CAA
1 CAA
15542 TAAATAAGTT
Statistics
Matches: 90, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.55, C:0.15, G:0.05, T:0.25
Consensus pattern (30 bp):
CAAATGCCTTTAAAATAATAACAAAATTAA
Found at i:16522 original size:14 final size:14
Alignment explanation
Indices: 16498--16531 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
16488 AACATACGTA
16498 GCAATAGTGTGGGTG
1 GCAA-AGTGTGGGTG
16513 GCAAAGTGTGGGTG
1 GCAAAGTGTGGGTG
16527 GCAAA
1 GCAAA
16532 ACAGAAGGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 15 0.79
15 4 0.21
ACGTcount: A:0.26, C:0.09, G:0.44, T:0.21
Consensus pattern (14 bp):
GCAAAGTGTGGGTG
Found at i:20411 original size:30 final size:30
Alignment explanation
Indices: 20285--20555 Score: 301
Period size: 30 Copynumber: 8.9 Consensus size: 30
20275 GTATATGTTT
* *
20285 TATACATTGCCGAATTGATTTGTACATGTA
1 TATACATTGCCGAATTGATTTGTATATGGA
** * * *
20315 TATGTATTGTC-AAATGATTTGTATATGTTTA
1 TATACATTGCCGAATTGATTTGTATATG--GA
* * *
20346 CATATATTGTCGAATTGATTTGTATATGGATA
1 TATACATTGCCGAATTGATTTGTATATGG--A
*
20378 TATATATTGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
20408 TATACATAGCCGAATTGATTTGTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
** *
20438 TATACATTATCGAATTGATTTGTATATGTA
1 TATACATTGCCGAATTGATTTGTATATGGA
*
20468 TATACATTGCCGAATTGATTTTTATATGGA
1 TATACATTGCCGAATTGATTTGTATATGGA
* * * *
20498 GATACGTTGCCGAATTGATTTGTACATGTA
1 TATACATTGCCGAATTGATTTGTATATGGA
* *
20528 TATATATTGCCGAAATGATTTGTATATG
1 TATACATTGCCGAATTGATTTGTATATG
20556 TTTACATATA
Statistics
Matches: 205, Mismatches: 31, Indels: 10
0.83 0.13 0.04
Matches are distributed among these distances:
29 14 0.07
30 137 0.67
31 11 0.05
32 43 0.21
ACGTcount: A:0.31, C:0.08, G:0.18, T:0.43
Consensus pattern (30 bp):
TATACATTGCCGAATTGATTTGTATATGGA
Found at i:20556 original size:90 final size:91
Alignment explanation
Indices: 20274--20555 Score: 343
Period size: 90 Copynumber: 3.1 Consensus size: 91
20264 TGAATTCAAA
* * * * ** * *
20274 TGTATATGTTTTATACATTGCCGAATTGATTTGTACATGTATATGTATTGTC-AAATGATTTGTA
1 TGTATATGATATATACATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
*
20338 TATGTTTACATATATTGTCGAATTGATT
66 TATG--TATATATATTGTCGAATTGATT
* *
20366 TGTATATGGATATATATATTGCCGAATTGATTTGTATATGGATATACATAGCCGAATTGATTTGT
1 TGTATAT-GATATATACATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGT
* * *
20431 ATATGGATATACATTATCGAATTGATT
65 ATATGTATATATATTGTCGAATTGATT
* * *
20458 TGTATATG-TATATACATTGCCGAATTGATTTTTATATGGAGATACGTTGCCGAATTGATTTGTA
1 TGTATATGATATATACATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
* * *
20522 CATGTATATATATTGCCGAAATGATT
66 TATGTATATATATTGTCGAATTGATT
20548 TGTATATG
1 TGTATATG
20556 TTTACATATA
Statistics
Matches: 163, Mismatches: 25, Indels: 6
0.84 0.13 0.03
Matches are distributed among these distances:
90 79 0.48
91 1 0.01
92 32 0.20
93 36 0.22
94 15 0.09
ACGTcount: A:0.30, C:0.08, G:0.18, T:0.44
Consensus pattern (91 bp):
TGTATATGATATATACATTGCCGAATTGATTTGTATATGGATATACATTGCCGAATTGATTTGTA
TATGTATATATATTGTCGAATTGATT
Found at i:20751 original size:41 final size:40
Alignment explanation
Indices: 20706--20785 Score: 124
Period size: 41 Copynumber: 2.0 Consensus size: 40
20696 GAGGTGTGAT
*
20706 TTCGTATAAGACCATGTCTGGGACATTGGCATCGTATATGA
1 TTCGTATAAGACCATGTCTGGGACAGTGGCATCG-ATATGA
* *
20747 TTCGTATAAGACCTTGTCTTGGACAGTGGCATCGATATG
1 TTCGTATAAGACCATGTCTGGGACAGTGGCATCGATATG
20786 CGTTAAAATG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
40 5 0.14
41 31 0.86
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (40 bp):
TTCGTATAAGACCATGTCTGGGACAGTGGCATCGATATGA
Found at i:24325 original size:89 final size:87
Alignment explanation
Indices: 24224--24448 Score: 238
Period size: 88 Copynumber: 2.5 Consensus size: 87
24214 TTAATTGGGT
* ** * * *
24224 AAAAAGTCCTCAAATTTTTTTTAAAAAGTAATTAAGTT-CTTACTTTTTTTTCGCACTCATTTGG
1 AAAAAGCCCTCAAATTTTTTAAAAAAAGAAATTAA-TTCCCTACTTTTTTTT-GCACTCAATTGG
* *
24288 GTACTTGAACTTTTAAAATATATAA
64 GTACTTGAACTTTCAAAATACAT-A
* * *
24313 AAAAAGCCCTCAAACCTTTTCAAAAAAA-AAATTAATTCCCTACTTTTTTTTGTACTCAATTGGG
1 AAAAAGCCCTCAAA-TTTTTTAAAAAAAGAAATTAATTCCCTACTTTTTTTTGCACTCAATTGGG
* *
24377 TACTTGAACTTTCAAAATGCATC
65 TACTTGAACTTTCAAAATACATA
* **
24400 AAAAAGACCCTCAAACTTTTTTAAAAAAAGCAATTAAACCCCTACTTTT
1 AAAAAG-CCCTCAAA-TTTTTTAAAAAAAGAAATTAATTCCCTACTTTT
24449 ATTAAAAATT
Statistics
Matches: 114, Mismatches: 18, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
87 6 0.05
88 52 0.46
89 47 0.41
90 9 0.08
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.37
Consensus pattern (87 bp):
AAAAAGCCCTCAAATTTTTTAAAAAAAGAAATTAATTCCCTACTTTTTTTTGCACTCAATTGGGT
ACTTGAACTTTCAAAATACATA
Found at i:24382 original size:88 final size:90
Alignment explanation
Indices: 24264--24448 Score: 241
Period size: 88 Copynumber: 2.1 Consensus size: 90
24254 ATTAAGTTCT
* * *
24264 TACTTTTTTTTCGCACTCATTTGGGTACTTGAACTTTTAAAATATATAAAAAA-AGCCCTCAAAC
1 TACTTTTTTTTCGCACTCAATTGGGTACTTGAACTTTCAAAATACATAAAAAAGA-CCCTCAAAC
**
24328 CTTTTCAAAAAAA-AAATTAATTCCC
65 CTTTTCAAAAAAAGAAATTAAACCCC
* * * *
24353 TACTTTTTTTT-GTACTCAATTGGGTACTTGAACTTTCAAAATGCATCAAAAAGACCCTCAAACT
1 TACTTTTTTTTCGCACTCAATTGGGTACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAACC
* *
24417 TTTTTAAAAAAAGCAATTAAACCCC
66 TTTTCAAAAAAAGAAATTAAACCCC
24442 TACTTTT
1 TACTTTT
24449 ATTAAAAATT
Statistics
Matches: 83, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
88 55 0.66
89 28 0.34
ACGTcount: A:0.37, C:0.19, G:0.08, T:0.36
Consensus pattern (90 bp):
TACTTTTTTTTCGCACTCAATTGGGTACTTGAACTTTCAAAATACATAAAAAAGACCCTCAAACC
TTTTCAAAAAAAGAAATTAAACCCC
Found at i:24552 original size:10 final size:11
Alignment explanation
Indices: 24526--24551 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
24516 ATAAAATATT
24526 AAAAATTAGAA
1 AAAAATTAGAA
24537 AAAAATTAGAA
1 AAAAATTAGAA
24548 AAAA
1 AAAA
24552 TATAAAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.77, C:0.00, G:0.08, T:0.15
Consensus pattern (11 bp):
AAAAATTAGAA
Found at i:24558 original size:9 final size:9
Alignment explanation
Indices: 24536--24634 Score: 56
Period size: 9 Copynumber: 10.4 Consensus size: 9
24526 AAAAATTAGA
*
24536 AAAAAATTAG
1 AAAAAA-TAT
24546 AAAAAATAT
1 AAAAAATAT
** *
24555 AAAATTTGT
1 AAAAAATAT
24564 AAAAAATAT
1 AAAAAATAT
* *
24573 AAAAATTGT
1 AAAAAATAT
*
24582 ATAAAAATCGT
1 A-AAAAAT-AT
24593 AAAAAA-ATT
1 AAAAAATA-T
*
24602 ATAAAATAT
1 AAAAAATAT
*
24611 ATAGAAATAT
1 A-AAAAATAT
24621 AAAAAATTAT
1 AAAAAA-TAT
24631 AAAA
1 AAAA
24635 TTTTATAAAG
Statistics
Matches: 68, Mismatches: 15, Indels: 12
0.72 0.16 0.13
Matches are distributed among these distances:
9 34 0.50
10 31 0.46
11 3 0.04
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (9 bp):
AAAAAATAT
Found at i:24558 original size:18 final size:19
Alignment explanation
Indices: 24537--24634 Score: 73
Period size: 18 Copynumber: 5.2 Consensus size: 19
24527 AAAATTAGAA
24537 AAAAATTAG-AAAAAATAT
1 AAAAATTAGTAAAAAATAT
*
24555 -AAAATTTGTAAAAAATAT
1 AAAAATTAGTAAAAAATAT
*
24573 AAAAATT-GTATAAAAATCGTAA
1 AAAAATTAGTA-AAAAA---TAT
*
24595 AAAAATTA-TAAAATATAT
1 AAAAATTAGTAAAAAATAT
*
24613 AGAAA-TA-TAAAAAATTAT
1 AAAAATTAGTAAAAAA-TAT
24631 AAAA
1 AAAA
24635 TTTTATAAAG
Statistics
Matches: 65, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
17 15 0.23
18 24 0.37
19 11 0.17
21 4 0.06
22 11 0.17
ACGTcount: A:0.66, C:0.01, G:0.05, T:0.28
Consensus pattern (19 bp):
AAAAATTAGTAAAAAATAT
Found at i:24567 original size:29 final size:28
Alignment explanation
Indices: 24518--24634 Score: 64
Period size: 29 Copynumber: 4.1 Consensus size: 28
24508 ATTAAAAAAT
*
24518 AAAATATTAAAAATTAGAAAAAA-ATTAGAA
1 AAAATA-T-AAAATTAGTAAAAAAATTA-AA
*
24548 AAAATATAAAATTTGT-AAAAAATATAAA
1 AAAATATAAAATTAGTAAAAAAAT-TAAA
** * *
24576 AATTGTATAAAAATCGTAAAAAAATTATAA
1 AA-AATATAAAATTAGTAAAAAAATTA-AA
* *
24606 AATATATAGAAA-TA-T-AAAAAATTATA
1 AAAATATA-AAATTAGTAAAAAAATTAAA
24632 AAA
1 AAA
24635 TTTTATAAAG
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
26 3 0.04
27 13 0.18
28 14 0.20
29 21 0.30
30 20 0.28
ACGTcount: A:0.67, C:0.01, G:0.05, T:0.27
Consensus pattern (28 bp):
AAAATATAAAATTAGTAAAAAAATTAAA
Found at i:24604 original size:20 final size:19
Alignment explanation
Indices: 24581--24705 Score: 62
Period size: 19 Copynumber: 6.5 Consensus size: 19
24571 ATAAAAATTG
24581 TATAAAAATCGTAAAAAAAT
1 TATAAAAAT-GTAAAAAAAT
* * *
24601 TAT-AAAATATATAGAAA-
1 TATAAAAATGTAAAAAAAT
*
24618 TATAAAAAAT-T-ATAAAAT
1 TAT-AAAAATGTAAAAAAAT
* * *
24636 TTTATAAAGTCGTAAGAAAAT
1 TATA-AAAAT-GTAAAAAAAT
24657 TATACAAAATGTAAAAAAA-
1 TATA-AAAATGTAAAAAAAT
* **
24676 TACAAATTTTGTAAAAGAAAT
1 TATAAA-AATGTAAAA-AAAT
24697 TATAAAAAT
1 TATAAAAAT
24706 TATCATATAC
Statistics
Matches: 76, Mismatches: 19, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
17 7 0.09
18 15 0.20
19 20 0.26
20 16 0.21
21 18 0.24
ACGTcount: A:0.61, C:0.03, G:0.06, T:0.30
Consensus pattern (19 bp):
TATAAAAATGTAAAAAAAT
Found at i:24981 original size:15 final size:15
Alignment explanation
Indices: 24961--24999 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
24951 AAATTTAATA
24961 ATTTTTCTAAAATTT
1 ATTTTTCTAAAATTT
* *
24976 ATTTTTTTATAATTT
1 ATTTTTCTAAAATTT
24991 -TTTTTCTAA
1 ATTTTTCTAA
25000 TTTTTAATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.67
Consensus pattern (15 bp):
ATTTTTCTAAAATTT
Found at i:28386 original size:14 final size:15
Alignment explanation
Indices: 28361--28392 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
28351 TTCTTTAAAA
28361 TATAATTAATATTAT
1 TATAATTAATATTAT
28376 TATAA-TAATATTAT
1 TATAATTAATATTAT
28390 TAT
1 TAT
28393 CTTTTAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 12 0.71
15 5 0.29
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATAATTAATATTAT
Done.