Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold3127
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: 37027
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:1297 original size:10 final size:10
Alignment explanation
Indices: 1282--1375 Score: 59
Period size: 10 Copynumber: 9.4 Consensus size: 10
1272 ATTGGATTTA
1282 AAAAAAAGAG
1 AAAAAAAGAG
**
1292 AAAAAATTCA-
1 AAAAAA-AGAG
**
1302 AAAAAAATTG
1 AAAAAAAGAG
1312 AAAAAAA-A-
1 AAAAAAAGAG
1320 AAAAAAAGTGAG
1 AAAAAAA--GAG
* *
1332 CAAAAAAGAA
1 AAAAAAAGAG
*
1342 AAAAAAAGAA
1 AAAAAAAGAG
*
1352 AAAAAAAGAA
1 AAAAAAAGAG
*
1362 AAAAAAAGTG
1 AAAAAAAGAG
1372 AAAA
1 AAAA
1376 GTCTTGCGAG
Statistics
Matches: 67, Mismatches: 11, Indels: 12
0.74 0.12 0.13
Matches are distributed among these distances:
8 7 0.10
10 52 0.78
11 2 0.03
12 6 0.09
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (10 bp):
AAAAAAAGAG
Found at i:1324 original size:20 final size:19
Alignment explanation
Indices: 1301--1367 Score: 66
Period size: 18 Copynumber: 3.5 Consensus size: 19
1291 GAAAAAATTC
*
1301 AAAAAAAATTG-AAAAAAA
1 AAAAAAAAATGAAAAAAAA
* *
1319 AAAAAAAAGTGAGCAAAAAAG
1 AAAAAAAAATGA--AAAAAAA
1340 AAAAAAAAA-GAAAAAAAA
1 AAAAAAAAATGAAAAAAAA
1358 AGAAAAAAAA
1 A-AAAAAAAA
1368 AGTGAAAAGT
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 17 0.41
19 8 0.20
20 2 0.05
21 14 0.34
ACGTcount: A:0.84, C:0.01, G:0.10, T:0.04
Consensus pattern (19 bp):
AAAAAAAAATGAAAAAAAA
Found at i:1375 original size:20 final size:20
Alignment explanation
Indices: 1281--1375 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
1271 TATTGGATTT
* ***
1281 AAAAAAAAGAGAAAAAATTC
1 AAAAAAAAGTGAAAAAAAGA
*
1301 AAAAAAAATTG-AAAAAA-A
1 AAAAAAAAGTGAAAAAAAGA
1319 AAAAAAAAGTGAGCAAAAAAGA
1 AAAAAAAAGTGA--AAAAAAGA
**
1341 AAAAAAAAGAAAAAAAAAGA
1 AAAAAAAAGTGAAAAAAAGA
1361 AAAAAAAAGTGAAAA
1 AAAAAAAAGTGAAAA
1376 GTCTTGCGAG
Statistics
Matches: 62, Mismatches: 9, Indels: 8
0.78 0.11 0.10
Matches are distributed among these distances:
18 10 0.16
19 5 0.08
20 30 0.48
21 6 0.10
22 11 0.18
ACGTcount: A:0.80, C:0.02, G:0.12, T:0.06
Consensus pattern (20 bp):
AAAAAAAAGTGAAAAAAAGA
Found at i:2445 original size:15 final size:13
Alignment explanation
Indices: 2436--2492 Score: 53
Period size: 14 Copynumber: 4.2 Consensus size: 13
2426 AAAAAGTGAG
2436 AAAAAGAAAATGA
1 AAAAAGAAAATGA
2449 AGAAAAGAAAATTG-
1 A-AAAAGAAAA-TGA
*
2463 AAAAAGAAAAAGCGA
1 AAAAAG-AAAA-TGA
*
2478 AAAAAGAAATTGA
1 AAAAAGAAAATGA
2491 AA
1 AA
2493 GGAGCTTGAA
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 10 0.28
14 18 0.50
15 8 0.22
ACGTcount: A:0.72, C:0.02, G:0.18, T:0.09
Consensus pattern (13 bp):
AAAAAGAAAATGA
Found at i:2456 original size:14 final size:13
Alignment explanation
Indices: 2435--2472 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
2425 GAAAAAGTGA
2435 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
2447 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
2462 GAAAAAGAAAA
1 GAAAAAGAAAA
2473 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:5804 original size:17 final size:17
Alignment explanation
Indices: 5782--5827 Score: 74
Period size: 17 Copynumber: 2.7 Consensus size: 17
5772 TGTATTGGAT
5782 AAAAAAAAAAAAAATTC
1 AAAAAAAAAAAAAATTC
**
5799 AAAAAAAAATGAAATTC
1 AAAAAAAAAAAAAATTC
5816 AAAAAAAAAAAA
1 AAAAAAAAAAAA
5828 TGAGCAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.83, C:0.04, G:0.02, T:0.11
Consensus pattern (17 bp):
AAAAAAAAAAAAAATTC
Found at i:5844 original size:8 final size:8
Alignment explanation
Indices: 5833--5863 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
5823 AAAAATGAGC
5833 AAAAAAAG
1 AAAAAAAG
*
5841 AAAAAAAA
1 AAAAAAAG
5849 AAAAAAAG
1 AAAAAAAG
5857 AAAAAAA
1 AAAAAAA
5864 AAGTGAAAAG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:5852 original size:16 final size:16
Alignment explanation
Indices: 5833--5865 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5823 AAAAATGAGC
5833 AAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
5849 AAAAAAAGAAAAAAAA
1 AAAAAAAGAAAAAAAA
5865 A
1 A
5866 GTGAAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.94, C:0.00, G:0.06, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAAAAA
Found at i:5861 original size:25 final size:25
Alignment explanation
Indices: 5816--5864 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5806 AATGAAATTC
** *
5816 AAAAAAAAAAAATGAGCAAAAAAAG
1 AAAAAAAAAAAAAAAGAAAAAAAAG
5841 AAAAAAAAAAAAAAAGAAAAAAAA
1 AAAAAAAAAAAAAAAGAAAAAAAA
5865 AGTGAAAAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (25 bp):
AAAAAAAAAAAAAAAGAAAAAAAAG
Found at i:5872 original size:12 final size:12
Alignment explanation
Indices: 5817--5865 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
5807 ATGAAATTCA
5817 AAAAAAAAAAATG
1 AAAAAAAAAAA-G
*
5830 AGCAAAAAAAGAAAA
1 A--AAAAAAA-AAAG
5845 AAAAAAAAAAAG
1 AAAAAAAAAAAG
5857 AAAAAAAAA
1 AAAAAAAAA
5866 GTGAAAAGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 7
0.77 0.05 0.17
Matches are distributed among these distances:
12 12 0.39
13 8 0.26
15 8 0.26
16 3 0.10
ACGTcount: A:0.88, C:0.02, G:0.08, T:0.02
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:5872 original size:27 final size:27
Alignment explanation
Indices: 5816--5866 Score: 77
Period size: 27 Copynumber: 1.9 Consensus size: 27
5806 AATGAAATTC
* *
5816 AAAAAAAAAAAATGAGCAAAAAAAGAA
1 AAAAAAAAAAAAAGAGAAAAAAAAGAA
5843 AAAAAAAAAAAAAGA-AAAAAAAAG
1 AAAAAAAAAAAAAGAGAAAAAAAAG
5867 TGAAAAGTCT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 8 0.36
27 14 0.64
ACGTcount: A:0.86, C:0.02, G:0.10, T:0.02
Consensus pattern (27 bp):
AAAAAAAAAAAAAGAGAAAAAAAAGAA
Found at i:6876 original size:17 final size:17
Alignment explanation
Indices: 6850--6941 Score: 73
Period size: 17 Copynumber: 5.4 Consensus size: 17
6840 CATTGAGCGA
* * *
6850 GAAAAGGAAAAGAGATT
1 GAAAAAGAAAAGAAATC
*
6867 GAAAAAGAAATTGAAA--
1 GAAAAAGAAA-AGAAATC
*
6883 GAAAACA-AAAAGAAAAC
1 GAAAA-AGAAAAGAAATC
*
6900 GAAAAAGAAAAAGAAATT
1 GAAAAAG-AAAAGAAATC
*
6918 GCAAAAGAAAAGAAATC
1 GAAAAAGAAAAGAAATC
6935 GAAAAAG
1 GAAAAAG
6942 TGAGAGAAAA
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.07
16 9 0.15
17 30 0.50
18 17 0.28
ACGTcount: A:0.68, C:0.04, G:0.20, T:0.08
Consensus pattern (17 bp):
GAAAAAGAAAAGAAATC
Found at i:6906 original size:12 final size:12
Alignment explanation
Indices: 6880--6998 Score: 66
Period size: 12 Copynumber: 9.6 Consensus size: 12
6870 AAAGAAATTG
6880 AAAGAAAAC-AA
1 AAAGAAAACGAA
6891 AAAGAAAACGAA
1 AAAGAAAACGAA
*
6903 AAAGAAAAAGAA
1 AAAGAAAACGAA
**
6915 ATTGCAAAA-G-A
1 AAAG-AAAACGAA
*
6926 AAAGAAATCGAA
1 AAAGAAAACGAA
* *
6938 AAAGTGAGA-GAA
1 AAAG-AAAACGAA
*
6950 AAAGAAAATGAAGA
1 AAAGAAAACG-A-A
*
6964 AAAGAAAATTGAA
1 AAAGAAAA-CGAA
6977 AAAGAAAAAGCGAAA
1 AAAG-AAAA-CG-AA
6992 AAAGAAA
1 AAAGAAA
6999 TTGAAAGAGA
Statistics
Matches: 84, Mismatches: 13, Indels: 19
0.72 0.11 0.16
Matches are distributed among these distances:
10 3 0.04
11 15 0.18
12 29 0.35
13 11 0.13
14 18 0.21
15 8 0.10
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.06
Consensus pattern (12 bp):
AAAGAAAACGAA
Found at i:6910 original size:18 final size:18
Alignment explanation
Indices: 6884--6986 Score: 73
Period size: 18 Copynumber: 5.6 Consensus size: 18
6874 AAATTGAAAG
*
6884 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
6902 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
*
6920 AAAAG-AAAAGAAATCGA
1 AAAAGAAAAAGAAAACGA
** * *
6937 AAAAGTGAGAGAAAAAGA
1 AAAAGAAAAAGAAAACGA
* *
6955 AAATGAAGAAAAGAAAATTGA
1 AAAAG-A-AAAAGAAAA-CGA
6976 AAAAGAAAAAG
1 AAAAGAAAAAG
6987 CGAAAAAAGA
Statistics
Matches: 65, Mismatches: 16, Indels: 7
0.74 0.18 0.08
Matches are distributed among these distances:
17 15 0.23
18 31 0.48
19 5 0.08
20 8 0.12
21 6 0.09
ACGTcount: A:0.71, C:0.04, G:0.18, T:0.07
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:6912 original size:6 final size:6
Alignment explanation
Indices: 6880--6986 Score: 65
Period size: 6 Copynumber: 17.7 Consensus size: 6
6870 AAAGAAATTG
* * ** *
6880 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAG-A
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
** ** * * *
6926 AAAGAA ATCGAA AAAGTG AGAGAA AAAGAA AATGAAGA AAAGAA AATTGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAG-A-A AAAGAA AA-AGAA
6977 AAAGAA AAAG
1 AAAGAA AAAG
6987 CGAAAAAAGA
Statistics
Matches: 74, Mismatches: 23, Indels: 9
0.70 0.22 0.08
Matches are distributed among these distances:
5 8 0.11
6 55 0.74
7 7 0.09
8 4 0.05
ACGTcount: A:0.71, C:0.04, G:0.19, T:0.07
Consensus pattern (6 bp):
AAAGAA
Found at i:6968 original size:14 final size:13
Alignment explanation
Indices: 6947--6984 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
6937 AAAAGTGAGA
6947 GAAAAAGAAAA-T
1 GAAAAAGAAAATT
6959 GAAGAAAAGAAAATT
1 G-A-AAAAGAAAATT
6974 GAAAAAGAAAA
1 GAAAAAGAAAA
6985 AGCGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 10 0.43
14 10 0.43
15 2 0.09
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (13 bp):
GAAAAAGAAAATT
Found at i:6998 original size:21 final size:21
Alignment explanation
Indices: 6948--6998 Score: 50
Period size: 21 Copynumber: 2.4 Consensus size: 21
6938 AAAGTGAGAG
*
6948 AAAAAGAAAATGAAGAAAAGA
1 AAAAAGAAAAAGAAGAAAAGA
** *
6969 AAATTGAAAAAGAA-AAAGCGA
1 AAAAAGAAAAAGAAGAAA-AGA
6990 AAAAAGAAA
1 AAAAAGAAA
6999 TTGAAAGAGA
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
20 3 0.13
21 20 0.87
ACGTcount: A:0.75, C:0.02, G:0.18, T:0.06
Consensus pattern (21 bp):
AAAAAGAAAAAGAAGAAAAGA
Found at i:7038 original size:33 final size:33
Alignment explanation
Indices: 7001--7063 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
6991 AAAAGAAATT
7001 GAAAGAGAG-CT-TGAAAAGAAATCAAGTGAAAAA
1 GAAAGAGAGTCTGT-AAAAGAAA-CAAGTGAAAAA
*
7034 GAAAGAGAGTCTGTAAAAGAAACGAGTGAA
1 GAAAGAGAGTCTGTAAAAGAAACAAGTGAA
7064 GTGAGTAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.54, C:0.06, G:0.27, T:0.13
Consensus pattern (33 bp):
GAAAGAGAGTCTGTAAAAGAAACAAGTGAAAAA
Found at i:12233 original size:12 final size:12
Alignment explanation
Indices: 12216--12249 Score: 54
Period size: 11 Copynumber: 3.0 Consensus size: 12
12206 AAACCGTATG
12216 CAATTTTTTTTT
1 CAATTTTTTTTT
12228 CAA-TTTTTTTT
1 CAATTTTTTTTT
12239 -AATTTTTTTTT
1 CAATTTTTTTTT
12250 GAACTCCTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.10
11 16 0.76
12 3 0.14
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:12248 original size:10 final size:11
Alignment explanation
Indices: 12220--12248 Score: 51
Period size: 10 Copynumber: 2.7 Consensus size: 11
12210 CGTATGCAAT
12220 TTTTTTTTCAA
1 TTTTTTTTCAA
12231 TTTTTTTT-AA
1 TTTTTTTTCAA
12241 TTTTTTTT
1 TTTTTTTT
12249 TGAACTCCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 10 0.56
11 8 0.44
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTTTTTTCAA
Found at i:12260 original size:22 final size:22
Alignment explanation
Indices: 12217--12260 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
12207 AACCGTATGC
* **
12217 AATTTTTTTTTCAATTTTTTTT
1 AATTTTTTTTTCAACTCCTTTT
*
12239 AATTTTTTTTTGAACTCCTTTT
1 AATTTTTTTTTCAACTCCTTTT
12261 TTTTACGTAC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.18, C:0.09, G:0.02, T:0.70
Consensus pattern (22 bp):
AATTTTTTTTTCAACTCCTTTT
Found at i:12527 original size:22 final size:22
Alignment explanation
Indices: 12497--12540 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12487 TTTGGTATTT
*
12497 GGGAATTGGTATGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
*
12519 GGGATTTGGTACGAAATGGTAA
1 GGGAATTGGTACGAAATGGTAA
12541 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.34, C:0.02, G:0.36, T:0.27
Consensus pattern (22 bp):
GGGAATTGGTACGAAATGGTAA
Found at i:15374 original size:13 final size:12
Alignment explanation
Indices: 15344--15377 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
15334 AATGTGAAAC
*
15344 AAAAAGAAATTG
1 AAAAAGAAGTTG
15356 AAAAAGAAGTTG
1 AAAAAGAAGTTG
15368 AAGAAAGAAG
1 AA-AAAGAAG
15378 AGAAAATGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 13 0.65
13 7 0.35
ACGTcount: A:0.65, C:0.00, G:0.24, T:0.12
Consensus pattern (12 bp):
AAAAAGAAGTTG
Found at i:17391 original size:809 final size:812
Alignment explanation
Indices: 15884--17481 Score: 3000
Period size: 809 Copynumber: 2.0 Consensus size: 812
15874 ATGTGGTTGT
15884 ACATGAAGTTTGAGTTCCATTTGACAAACGTTAACTCAACAACGAGATTCGACTACACTATGCCC
1 ACATGAAGTTTGAGTTCCATTTGACAAACGTTAACTCAACAACGAGATTCGACTACACTATGCCC
15949 CCGATGAGCGAAGGTTTGTTTTAAATGAAAAAGGTAAAATCGACCCTTATTCTTCTGCTTATCGA
66 CCGATGAGCGAAGGTTTGTTTTAAATGAAAAAGGTAAAATCGACCCTTATTCTTCTGCTTATCGA
16014 GGTAAGATGCTTGAAACCTTTGAAACACTTTTGTACTCCTCGGATAGTGATAAAGATCGTGTTGA
131 GGTAAGATGCTTGAAACCTTTGAAACACTTTTGTACTCCTCGGATAGTGATAAAGATCGTGTTGA
*
16079 TGAACACTTAGATCGAAACGTGCTTGACTGTCCTATTTTATTTATTGATGATCTATCTGTTTTGA
196 TGAACACTTAGATCAAAACGTGCTTGACTGTCCTATTTTATTTATTGATGATCTATCTGTTTTGA
16144 TGGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATTA
261 TGGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATTA
*
16209 ATGCATGGTATGATTATGCAACTCTGTGAACCATGTGAATCTTTTCAAATACCTACTTGTGACGA
326 ATGCATGGTATGATTATGCAACTCTATGAACCATGTGAATCTTTTCAAATACCTACTTGTGACGA
16274 TTATGTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACGA
391 TTATGTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACGA
16339 CTGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTAAATTA
456 CTGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTAAATTA
*
16404 GATTGTTTGCATGGTAATCTGAATCTGTCCATTCACATGCGTTATACCTGTTCTGTTATGCTTAT
521 GATTGTTTGCATGGTAATCTGAATCTGTCCATTCACATACGTTATACCTGTTCTGTTATGCTTAT
16469 GATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTCATGGCTATTCTTTTCAGTGGACTC
586 GATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTCATGGCTATTCTTTTCAGTGGACTC
16534 AATTGCCATTAGTCCCGTTCGATAGAGGAAAGTCGAGTTCATTTGATTTTTCAGATTCGAGGACG
651 AATTGCCATTAGTCCCGTTCGATAGAGGAAAGTCGAGTTCATTTGATTTTTCAGATTCGAGGACG
*
16599 AATCTTTTTGAGGAAGGGGGAATGATACGAGTCACAAAAGCCCAAATTCTTGAAGGCGAGG-CCA
716 AATCTTTTTGAGGAAGGGGGAATGATACGAGTCACAAAAG-CCAAATTCTTG-AGGCAAGGCCCA
*
16663 ATAAGCAAATTTGTTTCAATTTAATTCGTGCAAA
779 ATAAGAAAATTTGTTTCAATTTAATTCGTGCAAA
*
16697 ACATGAAGTTTGAGTTCCATTTGACGAACGTTAACTCAACAACGAAGATTCGACTACACTATGCC
1 ACATGAAGTTTGAGTTCCATTTGACAAACGTTAACTCAACAACG-AGATTCGACTACACTATGCC
16762 CCCGATGAGCGAAGGTTTGTTTTAAAATGAAAAAGGTAAAATCGA-CC-TATTCTTCTGCTTATC
65 CCCGATGAGCGAAGGTTTGTTTT-AAATGAAAAAGGTAAAATCGACCCTTATTCTTCTGCTTATC
16825 -AGGTAAGATGCTTGAAACCTTTGAAACACTTTTGTACTCCTCGGATAGTGAT-AAGATCGTGTT
129 GAGGTAAGATGCTTGAAACCTTTGAAACACTTTTGTACTCCTCGGATAGTGATAAAGATCGTGTT
16888 GATGAACACTTAGATCAAAACGTGCTTGACTGTCCTATTTTATTTTATTGATGATCTATCTGTTT
194 GATGAACACTTAGATCAAAACGTGCTTGACTGTCCTATTTTA-TTTATTGATGATCTATCTGTTT
16953 TGATGGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTG-GTGAATCTATAGACCG-CGA
258 TGATGGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGA
17016 TTAATGCATGGTATGATTATGCAACTCTATGAACCATGTGAATCTTTTCAAATACCTACTTGTGA
323 TTAATGCATGGTATGATTATGCAACTCTATGAACCATGTGAATCTTTTCAAATACCTACTTGTGA
*
17081 CGATTATATTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAAATGTGA
388 CGATTAT-GTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAAC-AATGTGA
17146 GACGACTGAATGCCTTAAAACATGT-CAT-TTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTA
451 GACGACTGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTA
17209 AATTAGATTGTTTGCATGGTAA-CTGAATCTGTCCATTCACATACGTTATACCTGTTCTGTTATG
516 AATTAGATTGTTTGCATGGTAATCTGAATCTGTCCATTCACATACGTTATACCTGTTCTGTTATG
17273 CTTATGATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTCATGGCTATTCTTTTCAGTG
581 CTTATGATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTCATGGCTATTCTTTTCAGTG
17338 GACTCAATTGCCATTAGTCCCGTTCGATAGAGGAAAGTCGAGTTCATTTGATTTTTCAGATTCGA
646 GACTCAATTGCCATTAGTCCCGTTCGATAGAGGAAAGTCGAGTTCATTTGATTTTTCAGATTCGA
17403 GGACGAATCTTTTTGAGGAAGGGGGAATGATACGAGTCACAAAAGCCAAATTCTTGAGGCAAGGC
711 GGACGAATCTTTTTGAGGAAGGGGGAATGATACGAGTCACAAAAGCCAAATTCTTGAGGCAAGGC
17468 CCAATAAGAAAATT
776 CCAATAAGAAAATT
17482 CCCAGCCCAA
Statistics
Matches: 772, Mismatches: 7, Indels: 17
0.97 0.01 0.02
Matches are distributed among these distances:
807 7 0.01
808 24 0.03
809 216 0.28
810 131 0.17
811 119 0.15
812 150 0.19
813 59 0.08
814 45 0.06
815 21 0.03
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.35
Consensus pattern (812 bp):
ACATGAAGTTTGAGTTCCATTTGACAAACGTTAACTCAACAACGAGATTCGACTACACTATGCCC
CCGATGAGCGAAGGTTTGTTTTAAATGAAAAAGGTAAAATCGACCCTTATTCTTCTGCTTATCGA
GGTAAGATGCTTGAAACCTTTGAAACACTTTTGTACTCCTCGGATAGTGATAAAGATCGTGTTGA
TGAACACTTAGATCAAAACGTGCTTGACTGTCCTATTTTATTTATTGATGATCTATCTGTTTTGA
TGGTTGATAAAAAGATTCTTGTTTTTGATAATGCATGTGTGAGTGAATCTATAGACCGTCGATTA
ATGCATGGTATGATTATGCAACTCTATGAACCATGTGAATCTTTTCAAATACCTACTTGTGACGA
TTATGTTTACCATTTGATTTATTACTCGCAATTTATTCATGGTTTGTGGGAACAATGTGAGACGA
CTGAATGCCTTAAAACATGTCCATCTTTGTTTCAAATATTTGACGAGGCAGTGGTGAGTAAATTA
GATTGTTTGCATGGTAATCTGAATCTGTCCATTCACATACGTTATACCTGTTCTGTTATGCTTAT
GATTGGACTACAAGCTTGTTTCCGTTGCTATTTACTATCTCATGGCTATTCTTTTCAGTGGACTC
AATTGCCATTAGTCCCGTTCGATAGAGGAAAGTCGAGTTCATTTGATTTTTCAGATTCGAGGACG
AATCTTTTTGAGGAAGGGGGAATGATACGAGTCACAAAAGCCAAATTCTTGAGGCAAGGCCCAAT
AAGAAAATTTGTTTCAATTTAATTCGTGCAAA
Found at i:22170 original size:20 final size:20
Alignment explanation
Indices: 22141--22192 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 20
22131 TCTGCTTTTT
22141 ATTATTTTATTTTAAAA-TA
1 ATTATTTTATTTTAAAATTA
*
22160 ATTATTTTTATCTTAAAATTA
1 ATTA-TTTTATTTTAAAATTA
22181 ATTAGTTTTATT
1 ATTA-TTTTATT
22193 ATCATTATTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
19 4 0.14
20 12 0.43
21 12 0.43
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (20 bp):
ATTATTTTATTTTAAAATTA
Found at i:22803 original size:16 final size:17
Alignment explanation
Indices: 22782--22815 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22772 CATACATATT
*
22782 TACATATATTTTT-ACA
1 TACATAGATTTTTCACA
22798 TACATAGATTTTTCACA
1 TACATAGATTTTTCACA
22815 T
1 T
22816 TTTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.35, C:0.15, G:0.03, T:0.47
Consensus pattern (17 bp):
TACATAGATTTTTCACA
Found at i:28386 original size:30 final size:31
Alignment explanation
Indices: 28352--28420 Score: 106
Period size: 30 Copynumber: 2.3 Consensus size: 31
28342 TTGTTTTGTC
28352 CCCTGTAATATAG-GAAAAATCTCATTTTGA-
1 CCCTGTAATATAGTG-AAAATCTCATTTTGAT
*
28382 CCCTGTAATATAGTGAAAATCTTATTTTGAT
1 CCCTGTAATATAGTGAAAATCTCATTTTGAT
28413 CCCTGTAA
1 CCCTGTAA
28421 ATTGCCTGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
30 27 0.75
31 9 0.25
ACGTcount: A:0.33, C:0.17, G:0.13, T:0.36
Consensus pattern (31 bp):
CCCTGTAATATAGTGAAAATCTCATTTTGAT
Found at i:35089 original size:18 final size:19
Alignment explanation
Indices: 35066--35103 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
35056 GGAAGCAAGC
*
35066 AATGATTGAAGA-AATCAG
1 AATGATTGAAAAGAATCAG
35084 AATGATTGAAAAGAATCAG
1 AATGATTGAAAAGAATCAG
35103 A
1 A
35104 CCTGGAGTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.53, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AATGATTGAAAAGAATCAG
Done.