Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold550
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: 65816
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.33
Warning! 1609 characters in sequence are not A, C, G, or T
Found at i:872 original size:22 final size:22
Alignment explanation
Indices: 831--884 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
821 TTGTATTTTC
* *
831 ATTAAAATTTTTAGTAAATAATT
1 ATTAAAGTTTTAAGTAAAT-ATT
854 ATTAAAGTTTTAAGT-AATATT
1 ATTAAAGTTTTAAGTAAATATT
*
875 -TAAAAGTTTT
1 ATTAAAGTTTT
885 TGATAAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 9 0.32
21 3 0.11
22 3 0.11
23 13 0.46
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
ATTAAAGTTTTAAGTAAATATT
Found at i:899 original size:21 final size:21
Alignment explanation
Indices: 833--899 Score: 50
Period size: 20 Copynumber: 3.2 Consensus size: 21
823 GTATTTTCAT
*
833 TAAAA-TTTTTAGTAAATAATTA
1 TAAAAGTTTTAAGT-AA-AATTA
* *
855 TTAAAGTTTTAAGTAATATT-
1 TAAAAGTTTTAAGTAAAATTA
*
875 TAAAAGTTTT-TGATAAAATTA
1 TAAAAGTTTTAAG-TAAAATTA
896 TAAA
1 TAAA
900 TTTTAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 15 0.42
21 7 0.19
22 6 0.17
23 7 0.19
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (21 bp):
TAAAAGTTTTAAGTAAAATTA
Found at i:930 original size:11 final size:11
Alignment explanation
Indices: 916--948 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
906 TTTTTTTTCC
916 TTTTTATATTT
1 TTTTTATATTT
927 TTTTTAT-TTT
1 TTTTTATATTT
*
937 TTCTTATATTT
1 TTTTTATATTT
948 T
1 T
949 GGTCCTGCCC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.15, C:0.03, G:0.00, T:0.82
Consensus pattern (11 bp):
TTTTTATATTT
Found at i:1197 original size:14 final size:14
Alignment explanation
Indices: 1170--1211 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
1160 AAACACTAAT
*
1170 TAATCTAAATCCTA
1 TAATCTAAACCCTA
*
1184 TAATCTAGACCCTA
1 TAATCTAAACCCTA
1198 -AATCCTAAACCCTA
1 TAAT-CTAAACCCTA
1212 ACCCAAATCC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
13 3 0.12
14 21 0.88
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (14 bp):
TAATCTAAACCCTA
Found at i:1224 original size:20 final size:20
Alignment explanation
Indices: 1174--1235 Score: 65
Period size: 20 Copynumber: 3.0 Consensus size: 20
1164 ACTAATTAAT
*
1174 CTAAATCCTATAA-TCTAGACC
1 CTAAATCCTA-AACCCTA-ACC
1195 CTAAATCCTAAACCCTAACC
1 CTAAATCCTAAACCCTAACC
*
1215 C-AAATCCCTAACCCCTAACC
1 CTAAAT-CCTAAACCCTAACC
1235 C
1 C
1236 CTACACCTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
19 4 0.11
20 20 0.54
21 13 0.35
ACGTcount: A:0.37, C:0.40, G:0.02, T:0.21
Consensus pattern (20 bp):
CTAAATCCTAAACCCTAACC
Found at i:1866 original size:41 final size:41
Alignment explanation
Indices: 1811--1909 Score: 171
Period size: 41 Copynumber: 2.4 Consensus size: 41
1801 GCGCTTCCTC
* *
1811 AAAAAACGCTGCTAAAGGTACGAGCATTAGCGGCGCTTATT
1 AAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCACTTATT
1852 AAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCACTTATT
1 AAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCACTTATT
*
1893 CAAAAACGCCGCTAAAG
1 AAAAAACGCCGCTAAAG
1910 ACCTAAGCAT
Statistics
Matches: 55, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 55 1.00
ACGTcount: A:0.37, C:0.22, G:0.22, T:0.18
Consensus pattern (41 bp):
AAAAAACGCCGCTAAAGGTACGAGCATTAGCGGCACTTATT
Found at i:1919 original size:41 final size:40
Alignment explanation
Indices: 1798--1953 Score: 147
Period size: 41 Copynumber: 3.8 Consensus size: 40
1788 AAATGTTTTT
** * *
1798 GCGGCGCTTCCTCAAAAAACGCTGCTAAAGGTA-CGAGCATTA
1 GCGGCGCTTATTC-AAAAACGCCGCTAAA-G-ACCAAGCATTA
* *
1840 GCGGCGCTTATTAAAAAACGCCGCTAAAGGTA-CGAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAA-G-ACCAAGCATTA
*
1881 GCGGCACTTATTCAAAAACGCCGCTAAAGACCTAAGCATTA
1 GCGGCGCTTATTCAAAAACGCCGCTAAAGACC-AAGCATTA
* *
1922 GAGGCGCTT-TTCAGAAAATGCCGCTAAAGACC
1 GCGGCGCTTATTCA-AAAACGCCGCTAAAGACC
1954 CCAAAACTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 7
0.86 0.08 0.06
Matches are distributed among these distances:
39 1 0.01
40 6 0.06
41 84 0.83
42 10 0.10
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.19
Consensus pattern (40 bp):
GCGGCGCTTATTCAAAAACGCCGCTAAAGACCAAGCATTA
Found at i:2049 original size:39 final size:41
Alignment explanation
Indices: 1986--2068 Score: 116
Period size: 40 Copynumber: 2.1 Consensus size: 41
1976 TTTGCGGCGC
1986 TTTCCAAAAAACGCCGCTAATGCTT-ATTTTTAGCAGCGTT
1 TTTCCAAAAAACGCCGCTAATGCTTCATTTTTAGCAGCGTT
* * **
2026 TTTCC-AAAAGCGCCGCTACTGCTTCATTTTTAGTGGCGTT
1 TTTCCAAAAAACGCCGCTAATGCTTCATTTTTAGCAGCGTT
2066 TTT
1 TTT
2069 TGTCCAAACG
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
39 17 0.45
40 21 0.55
ACGTcount: A:0.22, C:0.23, G:0.17, T:0.39
Consensus pattern (41 bp):
TTTCCAAAAAACGCCGCTAATGCTTCATTTTTAGCAGCGTT
Found at i:2081 original size:41 final size:38
Alignment explanation
Indices: 1993--2085 Score: 107
Period size: 39 Copynumber: 2.3 Consensus size: 38
1983 CGCTTTCCAA
1993 AAAACGCCGCTAATGCTTATTTTTAGCAGCGTTTTTCC
1 AAAACGCCGCTAATGCTTATTTTTAGCAGCGTTTTTCC
* **
2031 AAAAGCGCCGCTACTGCTTCATTTTTAGTGGCGTTTTTTGTCC
1 AAAA-CGCCGCTAATGCTT-ATTTTTAGCAGCG--TTTT-TCC
2074 -AAACGCCGCTAA
1 AAAACGCCGCTAA
2086 AAGCCTGTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
38 4 0.09
39 13 0.28
40 11 0.24
41 8 0.17
42 7 0.15
43 3 0.07
ACGTcount: A:0.23, C:0.25, G:0.18, T:0.34
Consensus pattern (38 bp):
AAAACGCCGCTAATGCTTATTTTTAGCAGCGTTTTTCC
Found at i:2883 original size:24 final size:24
Alignment explanation
Indices: 2855--2907 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2845 TTAGTAAGTC
* *
2855 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
2879 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
2903 AAATA
1 AAATA
2908 TTCTAGAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.55, C:0.09, G:0.04, T:0.32
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:7612 original size:18 final size:17
Alignment explanation
Indices: 7584--7628 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 17
7574 TTTTGGGGGT
*
7584 TTATT-TTATTAATATTG
1 TTATTATTATT-ATATTA
7601 TTATTATTATTATATTA
1 TTATTATTATTATATTA
7618 TATATTATTAT
1 T-TATTATTAT
7629 ACCTACATAT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 11 0.44
18 14 0.56
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (17 bp):
TTATTATTATTATATTA
Found at i:12943 original size:28 final size:29
Alignment explanation
Indices: 12894--12963 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
12884 AAATTAAAAA
*
12894 TTACCAAAATGT-TATAATTTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTTAT
*
12922 TTACTAAAATATATATAA-TTTTTTTTAT
1 TTACCAAAATATATATAATTTTTTTTTAT
12950 TTACCAAAATATAT
1 TTACCAAAATATAT
12964 CCAAAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
28 33 0.87
29 5 0.13
ACGTcount: A:0.39, C:0.07, G:0.01, T:0.53
Consensus pattern (29 bp):
TTACCAAAATATATATAATTTTTTTTTAT
Found at i:13060 original size:27 final size:27
Alignment explanation
Indices: 13022--13128 Score: 151
Period size: 27 Copynumber: 4.0 Consensus size: 27
13012 ACTCCCTCGG
13022 ACAAGGGAACCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
* * *
13049 ACAATGAAACCCTGTTGGCAGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
13076 ACAAGGGTTCCCTGTTGGCGGCACCAA
1 ACAAGGGAACCCTGTTGGCGGCACCAA
**
13103 ACAAGGGTTCCCTGTTGGCGGCACCA
1 ACAAGGGAACCCTGTTGGCGGCACCA
13129 NNNNNNNNNN
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 72 1.00
ACGTcount: A:0.27, C:0.30, G:0.27, T:0.16
Consensus pattern (27 bp):
ACAAGGGAACCCTGTTGGCGGCACCAA
Found at i:13248 original size:15 final size:14
Alignment explanation
Indices: 13208--13236 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
13198 TTTTTGTATC
13208 AATTTAATTATTCT
1 AATTTAATTATTCT
13222 AATTTAATTATTCT
1 AATTTAATTATTCT
13236 A
1 A
13237 GTTTTAGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (14 bp):
AATTTAATTATTCT
Found at i:16358 original size:19 final size:19
Alignment explanation
Indices: 16289--16357 Score: 106
Period size: 19 Copynumber: 3.7 Consensus size: 19
16279 NNNNNNNNNT
16289 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
* *
16308 TTATTAAATGAGAATAGA-
1 TTATTAAATTAAAATAGAG
16326 TTATTAAATTAAAATAGAG
1 TTATTAAATTAAAATAGAG
16345 TTATTAAA-TAAAA
1 TTATTAAATTAAAA
16358 AAATGAGTTG
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
18 21 0.47
19 24 0.53
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (19 bp):
TTATTAAATTAAAATAGAG
Found at i:16481 original size:27 final size:27
Alignment explanation
Indices: 16432--16509 Score: 106
Period size: 27 Copynumber: 2.9 Consensus size: 27
16422 CTTTTTTTTC
*
16432 CTTTGGCACCA-TGGTGCCGCCAATGA
1 CTTTGGCACCATTGGTGCCACCAATGA
*
16458 CTTTGGCACCATTGGTGCCACCAATTTA
1 CTTTGGCACCATTGGTGCCACCAA-TGA
*
16486 -TTTGGCACCTTTGGTGCCACCAAT
1 CTTTGGCACCATTGGTGCCACCAAT
16510 TTAATTGGCC
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
26 12 0.26
27 33 0.70
28 2 0.04
ACGTcount: A:0.19, C:0.29, G:0.22, T:0.29
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCACCAATGA
Found at i:16510 original size:27 final size:26
Alignment explanation
Indices: 16433--16518 Score: 102
Period size: 27 Copynumber: 3.2 Consensus size: 26
16423 TTTTTTTTCC
* * *
16433 TTTGGCACCATGGTGCCGCCAA-TGA
1 TTTGGCACCTTGGTGCCACCAATTTA
16458 CTTTGGCACCATTGGTGCCACCAATTTA
1 -TTTGGCACC-TTGGTGCCACCAATTTA
16486 TTTGGCACCTTTGGTGCCACCAATTTA
1 TTTGGCACC-TTGGTGCCACCAATTTA
*
16513 ATTGGC
1 TTTGGC
16519 CTGATCAGGT
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
26 9 0.17
27 42 0.79
28 2 0.04
ACGTcount: A:0.20, C:0.27, G:0.22, T:0.31
Consensus pattern (26 bp):
TTTGGCACCTTGGTGCCACCAATTTA
Found at i:24365 original size:27 final size:27
Alignment explanation
Indices: 24307--24367 Score: 90
Period size: 25 Copynumber: 2.3 Consensus size: 27
24297 AATCAAACAC
24307 CAGAAAATATTTTCCAGTAAATCATTTT
1 CAGAAAATA-TTTCCAGTAAATCATTTT
24335 -AGAAAATA-TTCCAGTAAATCATTTT
1 CAGAAAATATTTCCAGTAAATCATTTT
24360 ACAGAAAA
1 -CAGAAAA
24368 GTAAAACATT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
25 17 0.55
27 14 0.45
ACGTcount: A:0.46, C:0.13, G:0.08, T:0.33
Consensus pattern (27 bp):
CAGAAAATATTTCCAGTAAATCATTTT
Found at i:27244 original size:6 final size:6
Alignment explanation
Indices: 27233--27257 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
27223 ATCCATGAAA
27233 GAAAAG GAAAAG GAAAAG GAAAAG G
1 GAAAAG GAAAAG GAAAAG GAAAAG G
27258 CTCAAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (6 bp):
GAAAAG
Found at i:29560 original size:6 final size:6
Alignment explanation
Indices: 29549--29579 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
29539 ACTGTAAAAC
29549 CCTCGA CCTCGA CCTCGA CCTCGA CCTCGA C
1 CCTCGA CCTCGA CCTCGA CCTCGA CCTCGA C
29580 GGCTGGGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.52, G:0.16, T:0.16
Consensus pattern (6 bp):
CCTCGA
Found at i:37361 original size:6 final size:6
Alignment explanation
Indices: 37350--37375 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
37340 CTAAAGCATG
37350 CAGCAA CAGCAA CAGCAA CAGCAA CA
1 CAGCAA CAGCAA CAGCAA CAGCAA CA
37376 AGCAGTAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.50, C:0.35, G:0.15, T:0.00
Consensus pattern (6 bp):
CAGCAA
Found at i:40259 original size:21 final size:21
Alignment explanation
Indices: 40233--40308 Score: 64
Period size: 21 Copynumber: 3.5 Consensus size: 21
40223 ATTTTTGAAA
40233 AAAATATTTAATAATGTTTAT
1 AAAATATTTAATAATGTTTAT
* **
40254 AAAATATTTACA-AATATCAAAT
1 AAAATATTTA-ATAATGT-TTAT
* *
40276 AAACGATATTAAATAATGTTTAG
1 AAA--ATATTTAATAATGTTTAT
40299 AAAATATTTA
1 AAAATATTTA
40309 CAAATATCAA
Statistics
Matches: 41, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
21 20 0.49
22 6 0.15
23 5 0.12
24 10 0.24
ACGTcount: A:0.53, C:0.04, G:0.05, T:0.38
Consensus pattern (21 bp):
AAAATATTTAATAATGTTTAT
Found at i:40285 original size:45 final size:45
Alignment explanation
Indices: 40236--40324 Score: 160
Period size: 45 Copynumber: 2.0 Consensus size: 45
40226 TTTGAAAAAA
* *
40236 ATATTTAATAATGTTTATAAAATATTTACAAATATCAAATAAACG
1 ATATTAAATAATGTTTAGAAAATATTTACAAATATCAAATAAACG
40281 ATATTAAATAATGTTTAGAAAATATTTACAAATATCAAATAAAC
1 ATATTAAATAATGTTTAGAAAATATTTACAAATATCAAATAAAC
40325 AATGTTCTAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.53, C:0.07, G:0.04, T:0.36
Consensus pattern (45 bp):
ATATTAAATAATGTTTAGAAAATATTTACAAATATCAAATAAACG
Found at i:41580 original size:20 final size:21
Alignment explanation
Indices: 41555--41593 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
41545 CAAAAATGTA
41555 ACTATT-CGATAA-TTTTAATG
1 ACTATTACG-TAAGTTTTAATG
41575 ACTATTACGTAAGTTTTAA
1 ACTATTACGTAAGTTTTAA
41594 AAGTTGAGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (21 bp):
ACTATTACGTAAGTTTTAATG
Found at i:43976 original size:20 final size:20
Alignment explanation
Indices: 43959--44001 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
43949 AATCAACTTT
43959 TTTTTGGAATATTCAACTAA
1 TTTTTGGAATATTCAACTAA
43979 TTTTTGGAATATTCAACTAA
1 TTTTTGGAATATTCAACTAA
43999 TTT
1 TTT
44002 AGTCTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.49
Consensus pattern (20 bp):
TTTTTGGAATATTCAACTAA
Found at i:46399 original size:17 final size:17
Alignment explanation
Indices: 46377--46435 Score: 59
Period size: 17 Copynumber: 3.4 Consensus size: 17
46367 GTATACAATC
46377 AAAAATAGATGATATAT
1 AAAAATAGATGATATAT
*
46394 AAAAAT--ATGTATACAAT
1 AAAAATAGATG-ATA-TAT
*
46411 CAAAAATAGATGACATAT
1 -AAAAATAGATGATATAT
46429 AAAAATA
1 AAAAATA
46436 TAAAATAGTT
Statistics
Matches: 34, Mismatches: 3, Indels: 10
0.72 0.06 0.21
Matches are distributed among these distances:
15 3 0.09
16 3 0.09
17 15 0.44
18 8 0.24
19 2 0.06
20 3 0.09
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.25
Consensus pattern (17 bp):
AAAAATAGATGATATAT
Found at i:46406 original size:35 final size:35
Alignment explanation
Indices: 46365--46436 Score: 135
Period size: 35 Copynumber: 2.1 Consensus size: 35
46355 AAAAATAGCA
*
46365 ATGTATACAATCAAAAATAGATGATATATAAAAAT
1 ATGTATACAATCAAAAATAGATGACATATAAAAAT
46400 ATGTATACAATCAAAAATAGATGACATATAAAAAT
1 ATGTATACAATCAAAAATAGATGACATATAAAAAT
46435 AT
1 AT
46437 AAAATAGTTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (35 bp):
ATGTATACAATCAAAAATAGATGACATATAAAAAT
Found at i:48802 original size:24 final size:24
Alignment explanation
Indices: 48755--48802 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
48745 ATATATCACG
* *
48755 TATGTACGTATGTATGTGTATGTA
1 TATGTACGCATGTATGTATATGTA
*
48779 TATGTACGCATGTATGTATGTGTA
1 TATGTACGCATGTATGTATATGTA
48803 GGGATATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.25, C:0.06, G:0.25, T:0.44
Consensus pattern (24 bp):
TATGTACGCATGTATGTATATGTA
Found at i:49838 original size:23 final size:23
Alignment explanation
Indices: 49808--49863 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
49798 AATGCAACAA
* *
49808 GAGACCAGCAGCAGTTCAGCATG
1 GAGACCAGCAGCAGCTCAACATG
49831 GAGACCAGCAGCAGCTCAACATG
1 GAGACCAGCAGCAGCTCAACATG
* *
49854 AAGATCAGCA
1 GAGACCAGCA
49864 TTGGAGTTGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.36, C:0.27, G:0.27, T:0.11
Consensus pattern (23 bp):
GAGACCAGCAGCAGCTCAACATG
Found at i:55155 original size:11 final size:11
Alignment explanation
Indices: 55141--55227 Score: 51
Period size: 11 Copynumber: 8.3 Consensus size: 11
55131 TCAATTATTT
55141 TCTCAATTTCC
1 TCTCAATTTCC
* *
55152 TCTCAAATTGC
1 TCTCAATTTCC
55163 TCTCAATTTCC
1 TCTCAATTTCC
55174 TGC-CAACTTT-C
1 T-CTCAA-TTTCC
*
55185 TCTCAA-ATCC
1 TCTCAATTTCC
* **
55195 -AT--ATTTAA
1 TCTCAATTTCC
*
55203 TCTCAATTTGC
1 TCTCAATTTCC
55214 TCTCAATTTCC
1 TCTCAATTTCC
55225 TCT
1 TCT
55228 TAAATTTCTC
Statistics
Matches: 55, Mismatches: 13, Indels: 16
0.65 0.15 0.19
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 2 0.04
11 44 0.80
12 4 0.07
ACGTcount: A:0.23, C:0.31, G:0.03, T:0.43
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:55208 original size:51 final size:51
Alignment explanation
Indices: 55152--55251 Score: 139
Period size: 51 Copynumber: 2.0 Consensus size: 51
55142 CTCAATTTCC
*
55152 TCTCAAATTGCTCTCAATTTCCTGC-CAACTTTCTCTCAAATCCATATTTAA
1 TCTCAAATTGCTCTCAATTTCCT-CTCAAATTTCTCTCAAATCCATATTTAA
* * * *
55203 TCTCAATTTGCTCTCAATTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTT
55252 TTAATTATTT
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
50 1 0.02
51 42 0.98
ACGTcount: A:0.25, C:0.28, G:0.03, T:0.44
Consensus pattern (51 bp):
TCTCAAATTGCTCTCAATTTCCTCTCAAATTTCTCTCAAATCCATATTTAA
Found at i:57414 original size:49 final size:49
Alignment explanation
Indices: 57358--57524 Score: 316
Period size: 49 Copynumber: 3.4 Consensus size: 49
57348 TTATACAAAA
57358 TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
1 TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
57407 TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
1 TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
57456 TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
1 TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
* *
57505 TATTTCATTTAATAAAATAC
1 TATTTGATGTAATAAAATAC
57525 GNNNNNNNNN
Statistics
Matches: 116, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 116 1.00
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (49 bp):
TATTTGATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATAT
Found at i:60936 original size:124 final size:124
Alignment explanation
Indices: 60780--61064 Score: 498
Period size: 124 Copynumber: 2.3 Consensus size: 124
60770 CCTAAACATG
*
60780 CTACTGTAGCAAAAACGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
* * *
60845 TTGAAGCTTTTTTATACTATTTCCTCAGAAACGTCAACTCAAATTTATTTTTTCAGGAT
66 TTGAAGCTTTTTTATACTATTTCCTCAGAAACGTCAACGCAAAATTATTTTTTCAGGAC
* *
60904 CTACTGTAGCAAAAGCACGTCCAAGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
*
60969 TTGAAGCTTTTTTATACTATTTGCTCAGAAACGTCAACGCAAAATTATTTTTTCAGGAC
66 TTGAAGCTTTTTTATACTATTTCCTCAGAAACGTCAACGCAAAATTATTTTTTCAGGAC
*
61028 CTACTGTAGCAAAAGCGCTTCCACGTGGGAGCGATTT
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTT
61065 CCTTAATAAA
Statistics
Matches: 151, Mismatches: 10, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
124 151 1.00
ACGTcount: A:0.29, C:0.20, G:0.18, T:0.32
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTTAGAAATTCTTCTGATAAAGCATCCTGC
TTGAAGCTTTTTTATACTATTTCCTCAGAAACGTCAACGCAAAATTATTTTTTCAGGAC
Found at i:61839 original size:67 final size:67
Alignment explanation
Indices: 61751--61890 Score: 178
Period size: 67 Copynumber: 2.1 Consensus size: 67
61741 AATATAGGCA
* * * * *
61751 AAAC-AAAAAAGAATTGCAATAATATTTTAAATTAAATTATAAAAACTCAAA-AATTAAAGGGGT
1 AAACAAAAAAAGAATTACAATAAGATTATAAAATAAATTATAAAAACACAAACAA-TAAAGGGGT
61814 TAT
65 TAT
* * *
61817 AAACAAAAAAAGATTTATAATAAGGTTATAAAATAAATTATAAAAACACAAACAATAAAGGGGTT
1 AAACAAAAAAAGAATTACAATAAGATTATAAAATAAATTATAAAAACACAAACAATAAAGGGGTT
61882 AT
66 AT
61884 AAA-AAAA
1 AAACAAAA
61891 TTTCACCAAA
Statistics
Matches: 64, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
66 8 0.12
67 54 0.84
68 2 0.03
ACGTcount: A:0.60, C:0.06, G:0.09, T:0.25
Consensus pattern (67 bp):
AAACAAAAAAAGAATTACAATAAGATTATAAAATAAATTATAAAAACACAAACAATAAAGGGGTT
AT
Found at i:62806 original size:22 final size:22
Alignment explanation
Indices: 62756--62806 Score: 52
Period size: 22 Copynumber: 2.3 Consensus size: 22
62746 ATAGAGGGAG
62756 AAATAAAAGAGAATGAAAAAAA
1 AAATAAAAGAGAATGAAAAAAA
**
62778 AGTTAAAAGA-ACAT-AAAAGAAA
1 AAATAAAAGAGA-ATGAAAA-AAA
62800 AAATAAA
1 AAATAAA
62807 TTGCTCAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.22
22 18 0.78
ACGTcount: A:0.75, C:0.02, G:0.12, T:0.12
Consensus pattern (22 bp):
AAATAAAAGAGAATGAAAAAAA
Found at i:63858 original size:22 final size:21
Alignment explanation
Indices: 63814--63863 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 21
63804 CGCGAATCAA
*
63814 TTTTTATATTAAAATATATATT
1 TTTTTA-AATAAAATATATATT
63836 TTGTTTAAATAAAATAT-TAATT
1 TT-TTTAAATAAAATATAT-ATT
63858 TTTTTA
1 TTTTTA
63864 TTTTTATTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
21 5 0.20
22 16 0.64
23 4 0.16
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (21 bp):
TTTTTAAATAAAATATATATT
Found at i:65367 original size:82 final size:82
Alignment explanation
Indices: 65214--65371 Score: 235
Period size: 82 Copynumber: 1.9 Consensus size: 82
65204 ATGTAAGAAA
* * * * * *
65214 ATAGACTGTTTTTGGATAGAGTGTGTGAAAGCGAATGAGCTTTCTTACTGATATATTAAGGAAAG
1 ATAGACCGTTTTTGGAGAGAGTGTGTGAAAGCGAACGAGCTTTCTTACTGACATATCAAGAAAAG
65279 CACACCCAGTTGAACAC
66 CACACCCAGTTGAACAC
*
65296 ATAGACCGTTTTTGGAGAGAGTGTGTGAAAGCGAACGAGCTTTCTTACTGACATGTCAAGAAAAG
1 ATAGACCGTTTTTGGAGAGAGTGTGTGAAAGCGAACGAGCTTTCTTACTGACATATCAAGAAAAG
**
65361 TGCACCCAGTT
66 CACACCCAGTT
65372 AAACGCATTT
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
82 67 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.28
Consensus pattern (82 bp):
ATAGACCGTTTTTGGAGAGAGTGTGTGAAAGCGAACGAGCTTTCTTACTGACATATCAAGAAAAG
CACACCCAGTTGAACAC
Done.