Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2638
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: 76437
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.32
Found at i:10995 original size:21 final size:20
Alignment explanation
Indices: 10950--10988 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
10940 CACAAACTTT
10950 TTTTTTTAAATAAATAATCA
1 TTTTTTTAAATAAATAATCA
10970 TTTTTTTAAA-AAA-AATCA
1 TTTTTTTAAATAAATAATCA
10988 T
1 T
10989 AAATTTTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.46, C:0.05, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTTTTAAATAAATAATCA
Found at i:11137 original size:2 final size:2
Alignment explanation
Indices: 11130--11159 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11120 AAGATTTTCA
11130 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11160 GCATATAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11562 original size:11 final size:11
Alignment explanation
Indices: 11546--11572 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
11536 ATTTCATATG
11546 TTTTTTTCTTT
1 TTTTTTTCTTT
11557 TTTTTTTCTTT
1 TTTTTTTCTTT
11568 TTTTT
1 TTTTT
11573 CTTCATCTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.00, C:0.07, G:0.00, T:0.93
Consensus pattern (11 bp):
TTTTTTTCTTT
Found at i:11959 original size:7 final size:8
Alignment explanation
Indices: 11935--11961 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
11925 GAAAACTTAC
11935 TTTGATTT
1 TTTGATTT
11943 TTTGATTT
1 TTTGATTT
11951 TTTGATTT
1 TTTGATTT
11959 TTT
1 TTT
11962 TACGCTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.11, C:0.00, G:0.11, T:0.78
Consensus pattern (8 bp):
TTTGATTT
Found at i:13398 original size:18 final size:18
Alignment explanation
Indices: 13371--13450 Score: 85
Period size: 18 Copynumber: 4.6 Consensus size: 18
13361 ATTCTCTTAT
13371 GGATACATTTGAAGTAGA
1 GGATACATTTGAAGTAGA
*
13389 GGATAAATTTG-AG--GA
1 GGATACATTTGAAGTAGA
** *
13404 TTATACATTTGAGGTAGA
1 GGATACATTTGAAGTAGA
**
13422 GGATACATTTGTGGTAGA
1 GGATACATTTGAAGTAGA
13440 GGATACATTTG
1 GGATACATTTG
13451 GGGTTGATAA
Statistics
Matches: 51, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
15 10 0.20
16 1 0.02
17 2 0.04
18 38 0.75
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.33
Consensus pattern (18 bp):
GGATACATTTGAAGTAGA
Found at i:13471 original size:20 final size:22
Alignment explanation
Indices: 13439--13481 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
13429 TTTGTGGTAG
*
13439 AGGATACATTTGG-GGTTGATA
1 AGGATACATTTGGTGGTTAATA
13460 AGGATA-ATTTGGTGGTTAATA
1 AGGATACATTTGGTGGTTAATA
13481 A
1 A
13482 CCATATAAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.33, C:0.02, G:0.30, T:0.35
Consensus pattern (22 bp):
AGGATACATTTGGTGGTTAATA
Found at i:14379 original size:33 final size:32
Alignment explanation
Indices: 14336--14406 Score: 79
Period size: 33 Copynumber: 2.2 Consensus size: 32
14326 AGTTGTAAAA
* * * *
14336 AATTATATAAAATAAATTATACTTATATAATAT
1 AATTAAATAAAACAAAATATA-TTAAATAATAT
* *
14369 AATTAAATAAAACAAAATATATTAAATTATTT
1 AATTAAATAAAACAAAATATATTAAATAATAT
14401 AATTAA
1 AATTAA
14407 CAATTTACCG
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
32 14 0.44
33 18 0.56
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (32 bp):
AATTAAATAAAACAAAATATATTAAATAATAT
Found at i:16799 original size:15 final size:16
Alignment explanation
Indices: 16776--16813 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
16766 TTCAAATATA
*
16776 AAATCATAAAC-TAAT
1 AAATAATAAACTTAAT
16791 AAATAATAAACTTAAT
1 AAATAATAAACTTAAT
*
16807 ATATAAT
1 AAATAAT
16814 TATTTCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.61, C:0.08, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAATAAACTTAAT
Found at i:16951 original size:3 final size:3
Alignment explanation
Indices: 16943--16994 Score: 95
Period size: 3 Copynumber: 17.3 Consensus size: 3
16933 TATATATTCT
*
16943 ATA ATA ATA ATA AAA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
16991 ATA A
1 ATA A
16995 ATCTAATATA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
ATA
Found at i:16962 original size:12 final size:12
Alignment explanation
Indices: 16945--17017 Score: 78
Period size: 12 Copynumber: 6.1 Consensus size: 12
16935 TATATTCTAT
16945 AATAATAATAAA
1 AATAATAATAAA
*
16957 AATAATAATAAT
1 AATAATAATAAA
*
16969 AATAATAATAAT
1 AATAATAATAAA
16981 AATAATAATAATA
1 AATAATAATAA-A
*
16994 AAT-CTAATATAA
1 AATAATAATA-AA
*
17006 TATAAT-ATAAA
1 AATAATAATAAA
17017 A
1 A
17018 TTTCATAAAA
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
11 2 0.04
12 45 0.87
13 5 0.10
ACGTcount: A:0.67, C:0.01, G:0.00, T:0.32
Consensus pattern (12 bp):
AATAATAATAAA
Found at i:17355 original size:17 final size:17
Alignment explanation
Indices: 17335--17376 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
17325 ACAATATTCA
17335 AATATAAATTATAAAAT
1 AATATAAATTATAAAAT
* * *
17352 AATAAAAAATATATAAT
1 AATATAAATTATAAAAT
17369 AAT-TAAAT
1 AATATAAAT
17377 ACATCTTAAT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 3 0.15
17 17 0.85
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AATATAAATTATAAAAT
Found at i:17506 original size:68 final size:69
Alignment explanation
Indices: 17414--17546 Score: 250
Period size: 68 Copynumber: 1.9 Consensus size: 69
17404 TATAATTTAT
17414 AAATTAATGAAAAAAATTTATTTATTCACCCAAAATTTTATTTATAAAAGAAATTAATAAACTAT
1 AAATTAATGAAAAAAATTTATTTATTCACCCAAAATTTTATTTATAAAAGAAATTAATAAACTAT
17479 GCCC
66 GCCC
*
17483 AAATTAATG-AAAAATTTTATTTATTCACCCAAAATTTTATTTATAAAAGAAATTAATAAACTAT
1 AAATTAATGAAAAAAATTTATTTATTCACCCAAAATTTTATTTATAAAAGAAATTAATAAACTAT
17547 ACCTATCACT
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
68 54 0.86
69 9 0.14
ACGTcount: A:0.50, C:0.10, G:0.04, T:0.37
Consensus pattern (69 bp):
AAATTAATGAAAAAAATTTATTTATTCACCCAAAATTTTATTTATAAAAGAAATTAATAAACTAT
GCCC
Found at i:17608 original size:22 final size:26
Alignment explanation
Indices: 17558--17613 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
17548 CCTATCACTA
*
17558 TTATTTATAAAACAAATTATATAATT
1 TTATTTATAAAACAAATTATATAAAT
17584 TTATTTATAAAA-AAA-TA-A-AAAT
1 TTATTTATAAAACAAATTATATAAAT
17606 TTATTTAT
1 TTATTTAT
17614 TCACCATAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
22 11 0.38
23 1 0.03
24 2 0.07
25 3 0.10
26 12 0.41
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (26 bp):
TTATTTATAAAACAAATTATATAAAT
Found at i:18763 original size:20 final size:19
Alignment explanation
Indices: 18738--18803 Score: 84
Period size: 20 Copynumber: 3.5 Consensus size: 19
18728 ATATAATTTT
18738 TTTAATTTAAATTGATTTAA
1 TTTAATTTAAATT-ATTTAA
18758 TTTAATTTAAATTA-TT-A
1 TTTAATTTAAATTATTTAA
18775 TTTAATTATAAAATT-TTTAA
1 TTTAATT-T-AAATTATTTAA
18795 TTTAATTTA
1 TTTAATTTA
18804 GTTATAAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
17 8 0.19
18 4 0.10
19 9 0.21
20 21 0.50
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (19 bp):
TTTAATTTAAATTATTTAA
Found at i:18789 original size:25 final size:24
Alignment explanation
Indices: 18741--18813 Score: 64
Period size: 25 Copynumber: 3.1 Consensus size: 24
18731 TAATTTTTTT
*
18741 AATTTAAA-TTGATTTAATT-T--
1 AATTTAAATTTAATTTAATTATAA
*
18761 AATTTAAATTATTATTTAATTATAA
1 AATTTAAATT-TAATTTAATTATAA
* *
18786 AATTTTTAATTTAATTTAGTTATAA
1 AA-TTTAAATTTAATTTAATTATAA
18811 AAT
1 AAT
18814 AAATAAATAT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
20 8 0.19
21 1 0.02
22 9 0.21
23 1 0.02
24 1 0.02
25 16 0.37
26 7 0.16
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (24 bp):
AATTTAAATTTAATTTAATTATAA
Found at i:20297 original size:5 final size:5
Alignment explanation
Indices: 20287--20348 Score: 70
Period size: 5 Copynumber: 11.4 Consensus size: 5
20277 GTGACTTAAC
*
20287 AAAGA AAAGA AAGATGA AAAGCA AAAGA AGAAGAA AAAAA AAAGA AAAGA
1 AAAGA AAAGA AA-A-GA AAAG-A AAAGA A-AAG-A AAAGA AAAGA AAAGA
20337 AAAGA AAAGA AA
1 AAAGA AAAGA AA
20349 TGAAGATATA
Statistics
Matches: 50, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
5 32 0.64
6 12 0.24
7 6 0.12
ACGTcount: A:0.77, C:0.02, G:0.19, T:0.02
Consensus pattern (5 bp):
AAAGA
Found at i:21121 original size:11 final size:11
Alignment explanation
Indices: 21105--21131 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
21095 GAAGATGAAG
21105 AAAAAAAAGAA
1 AAAAAAAAGAA
21116 AAAAAAAAGAA
1 AAAAAAAAGAA
21127 AAAAA
1 AAAAA
21132 CATATGAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:21524 original size:2 final size:2
Alignment explanation
Indices: 21517--21548 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
21507 ATTTATATGC
21517 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
21549 TGAAAATCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:21722 original size:20 final size:18
Alignment explanation
Indices: 21690--21728 Score: 60
Period size: 20 Copynumber: 2.1 Consensus size: 18
21680 TTTAAAATTT
21690 ATGATTTTTTTTAAAAAA
1 ATGATTTTTTTTAAAAAA
21708 ATGATTATTTATTTAAAAAA
1 ATGATT-TTT-TTTAAAAAA
21728 A
1 A
21729 AAGTTTGTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
19 3 0.16
20 10 0.53
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (18 bp):
ATGATTTTTTTTAAAAAA
Found at i:29551 original size:13 final size:13
Alignment explanation
Indices: 29533--29559 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
29523 GTGAATATAG
29533 CATTGTAGACCAA
1 CATTGTAGACCAA
29546 CATTGTAGACCAA
1 CATTGTAGACCAA
29559 C
1 C
29560 TAAGCAAACA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.26, G:0.15, T:0.22
Consensus pattern (13 bp):
CATTGTAGACCAA
Found at i:42120 original size:13 final size:13
Alignment explanation
Indices: 42102--42128 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
42092 ACATTATGCT
42102 TTGTATCGATACA
1 TTGTATCGATACA
42115 TTGTATCGATACA
1 TTGTATCGATACA
42128 T
1 T
42129 GGACAATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:44355 original size:18 final size:18
Alignment explanation
Indices: 44334--44376 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44324 GCATCCTTCT
44334 CAAAAAACAAAAAAAAAA
1 CAAAAAACAAAAAAAAAA
* *
44352 CAAAAACCAAAAAAATAA
1 CAAAAAACAAAAAAAAAA
*
44370 TAAAAAA
1 CAAAAAA
44377 GATAGGGGCC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.84, C:0.12, G:0.00, T:0.05
Consensus pattern (18 bp):
CAAAAAACAAAAAAAAAA
Found at i:45618 original size:12 final size:14
Alignment explanation
Indices: 45566--45624 Score: 56
Period size: 13 Copynumber: 4.5 Consensus size: 14
45556 AAAGGTTGTT
45566 AAGAAAT-TATCGTC
1 AAGAAATGT-TCGTC
* *
45580 AAGAACT-TTTGTC
1 AAGAAATGTTCGTC
45593 AAG-AATGTTCGTC
1 AAGAAATGTTCGTC
45606 -AGAAATGTT-GTC
1 AAGAAATGTTCGTC
45618 AAGAAAT
1 AAGAAAT
45625 TTTTGTCAAC
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 7 0.18
13 24 0.63
14 7 0.18
ACGTcount: A:0.39, C:0.12, G:0.19, T:0.31
Consensus pattern (14 bp):
AAGAAATGTTCGTC
Found at i:45779 original size:29 final size:29
Alignment explanation
Indices: 45642--46100 Score: 364
Period size: 28 Copynumber: 15.5 Consensus size: 29
45632 AACACGACTT
* **
45642 CTTTTCAAAGCCCATAAGTCA-TGGC-TT
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
45669 TTTTTCAAAACCCACAAGTCAGTGGCAACC
1 CTTTTCAAAGCCCACAAGTCAGTGGC-ACC
* *
45699 CTTTTCAAAGCCCACAAATTAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
*
45728 CTTTT-AAAGCCCACAAGTTAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
*
45756 CTTTTCAAAGCTCACAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
*
45785 CTTTTCAAAGCTCACAAGTCAGTGGCACC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
* *
45814 C-TTTCAAAAGCCCACAAATCAGTGACACC
1 CTTTTC-AAAGCCCACAAGTCAGTGGCACC
* *
45843 C-TTTCAAAGCCCACAAGTTAGTGGTATCC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-CC
* * *
45872 TTTTAATCCTTTCAAAAGCCCACAAGTTAGTGGTA-C
1 -------CTTTTC-AAAGCCCACAAGTCAGTGGCACC
* *
45908 CATTTCAAAAGCCCACAAATCAGTGGCACC
1 CTTTTC-AAAGCCCACAAGTCAGTGGCACC
* *
45938 C-TTCCAAAGCCCACAAGTTAGTGGCATCC
1 CTTTTCAAAGCCCACAAGTCAGTGGCA-CC
* *
45967 TTTCAATTCTTTCAAAAGCCCGCAAGTCAGTAGCACC
1 ---C---T-TTTC-AAAGCCCACAAGTCAGTGGCACC
* *
46004 CTTTT-AAAGCCCACAAGTCAATGACA-C
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
* * * *
46031 CTTTTTAAAGCCCACAAGTAAATGGCA-T
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
* * *
46059 TTTTTCAAAGCCCACAAGTTAGTGGCAAC
1 CTTTTCAAAGCCCACAAGTCAGTGGCACC
46088 C-TTTCAAAGCCCA
1 CTTTTCAAAGCCCA
46101 TACAAGTTGA
Statistics
Matches: 361, Mismatches: 43, Indels: 55
0.79 0.09 0.12
Matches are distributed among these distances:
27 24 0.07
28 142 0.39
29 115 0.32
30 27 0.07
31 1 0.00
32 1 0.00
34 1 0.00
36 2 0.01
37 9 0.02
38 39 0.11
ACGTcount: A:0.31, C:0.29, G:0.15, T:0.25
Consensus pattern (29 bp):
CTTTTCAAAGCCCACAAGTCAGTGGCACC
Found at i:45947 original size:95 final size:95
Alignment explanation
Indices: 45787--46058 Score: 368
Period size: 95 Copynumber: 2.9 Consensus size: 95
45777 GTGGCACCCT
*
45787 TTTC-AAAGCTCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATCAGTGACACCCTTTCAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATCAGTGACACCCTTTCAAA
* *
45851 GCCCACAAGTTAGTGGTATCCTTTTAATCC
66 GCCCACAAGTTAGTGGCATCCTTTCAATCC
* * * * *
45881 TTTCAAAAGCCCACAAGTTAGTGGTACCATTTCAAAAGCCCACAAATCAGTGGCACCCTTCCAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATCAGTGACACCCTTTCAAA
*
45946 GCCCACAAGTTAGTGGCATCCTTTCAATTC
66 GCCCACAAGTTAGTGGCATCCTTTCAATCC
* * * * * * *
45976 TTTCAAAAGCCCGCAAGTCAGTAGCACCCTTT-TAAAGCCCACAAGTCAATGACACCTTTTTAAA
1 TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATCAGTGACACCCTTTCAAA
* *
46040 GCCCACAAGTAAATGGCAT
66 GCCCACAAGTTAGTGGCAT
46059 TTTTTCAAAG
Statistics
Matches: 154, Mismatches: 23, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
94 46 0.30
95 108 0.70
ACGTcount: A:0.32, C:0.29, G:0.14, T:0.24
Consensus pattern (95 bp):
TTTCAAAAGCCCACAAGTCAGTGGCACCCTTTCAAAAGCCCACAAATCAGTGACACCCTTTCAAA
GCCCACAAGTTAGTGGCATCCTTTCAATCC
Found at i:46108 original size:30 final size:28
Alignment explanation
Indices: 46003--46118 Score: 92
Period size: 28 Copynumber: 4.1 Consensus size: 28
45993 TCAGTAGCAC
* ** *
46003 CCTTTTAAAGCCCACAAGTCAATGAC-A
1 CCTTTCAAAGCCCACAAGTTGATGGCAA
* ** *
46030 CCTTTTTAAAGCCCACAAGTAAATGGCAT
1 CC-TTTCAAAGCCCACAAGTTGATGGCAA
**
46059 TTTTTCAAAGCCCACAAGTT-AGTGGCAA
1 CCTTTCAAAGCCCACAAGTTGA-TGGCAA
46087 CCTTTCAAAGCCCATACAAGTTGATGGCAA
1 CCTTTCAAAGCCC--ACAAGTTGATGGCAA
46117 CC
1 CC
46119 CTTCTAAACT
Statistics
Matches: 73, Mismatches: 10, Indels: 9
0.79 0.11 0.10
Matches are distributed among these distances:
27 3 0.04
28 54 0.74
30 15 0.21
31 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.15, T:0.25
Consensus pattern (28 bp):
CCTTTCAAAGCCCACAAGTTGATGGCAA
Found at i:47205 original size:17 final size:17
Alignment explanation
Indices: 47168--47220 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
47158 GGTTAAAGGC
* **
47168 AAGAAAAAAAGAAGATG
1 AAGAAAAAAAAAAGAAA
* **
47185 AAGAAGAAATGAAGAAA
1 AAGAAAAAAAAAAGAAA
47202 AAGAAAAAAAAAAGAAA
1 AAGAAAAAAAAAAGAAA
47219 AA
1 AA
47221 AACATATAAA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
17 29 1.00
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.04
Consensus pattern (17 bp):
AAGAAAAAAAAAAGAAA
Found at i:47607 original size:2 final size:2
Alignment explanation
Indices: 47600--47635 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
47590 ATTTATATGC
47600 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
47636 TGAAAATCTC
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:50057 original size:400 final size:400
Alignment explanation
Indices: 49317--50123 Score: 1578
Period size: 400 Copynumber: 2.0 Consensus size: 400
49307 ATCTCTATGT
49317 TTCCCATCTCTCTGGAGCGCATATATAATTAAAATTTTTCTCAAAACCTGGATTCATTTTTACAT
1 TTCCCATCTCTCTGGAGCGCATATATAATTAAAATTTTTCTCAAAACCTGGATTCATTTTTACAT
49382 AAAATTCATGCATTCAAGGGGATTATATCAAAATGATTTCAAGTCAAAACCATTGAAACCAATGT
66 AAAATTCATGCATTCAAGGGGATTATATCAAAATGATTTCAAGTCAAAACCATTGAAACCAATGT
* *
49447 CAAGTTAAAATGTAGCTAGTAAGGTACCAATTTTGGACGTTGCGAGGAGATTCATATCTCTTTGC
131 CAAGTTAAAATGTAGCTAGTAAGGTACCAATTTCGGACGTCGCGAGGAGATTCATATCTCTTTGC
49512 GCGTAACCAACTCCCAGACCCAACCGATGAGTCTCTTAATTACGTAGACCACAAGATCGATGTCT
196 GCGTAACCAACTCCCAGACCCAACCGATGAGTCTCTTAATTACGTAGACCACAAGATCGATGTCT
*
49577 CAAGTTTCGTAACTCAAGACATAGGTTTCAATAGGCATCCGATCATGCTTAGCCCAAAATGATCG
261 CAAGTTTCGTAACTCAAGACATAGATTTCAATAGGCATCCGATCATGCTTAGCCCAAAATGATCG
49642 GTGGCGACTTCAAAATTTCGGTCATTTCGTGGTGACCGTCGAAGATCGATTAGATAGACGATTCA
326 GTGGCGACTTCAAAATTTCGGTCATTTCGTGGTGACCGTCGAAGATCGATTAGATAGACGATTCA
49707 TCTATGGATC
391 TCTATGGATC
49717 TTCCCATCTCTCTGGAGCGCATATATAATTAAAATTTTTCTCAAAACCTGGATTCATTTTTACAT
1 TTCCCATCTCTCTGGAGCGCATATATAATTAAAATTTTTCTCAAAACCTGGATTCATTTTTACAT
49782 AAAATTCATGCATTCAAGGGGATTATATCAAAATGATTTCAAGTCAAAACCATTGAAACCAATGT
66 AAAATTCATGCATTCAAGGGGATTATATCAAAATGATTTCAAGTCAAAACCATTGAAACCAATGT
49847 CAAGTTAAAATGTAGCTAGTAAGGTACCAATTTCGGACGTCGCGAGGAGATTCATATCTCTTTGC
131 CAAGTTAAAATGTAGCTAGTAAGGTACCAATTTCGGACGTCGCGAGGAGATTCATATCTCTTTGC
49912 GCGTAACCAACTCCCAGACCCAACCGATGAGTCTCTTAATTACGTAGACCACAAGATCGATGTCT
196 GCGTAACCAACTCCCAGACCCAACCGATGAGTCTCTTAATTACGTAGACCACAAGATCGATGTCT
49977 CAAGTTTCGTAACTCAAGACATAGATTTCAATAGGCATCCGATCATGCTTAGCCCAAAATGATCG
261 CAAGTTTCGTAACTCAAGACATAGATTTCAATAGGCATCCGATCATGCTTAGCCCAAAATGATCG
*
50042 GTGGCGACTTCAAAATTTCGGTCATTTCGTGGTGACCGTCGAAGATCGATTAGATGGACGATTCA
326 GTGGCGACTTCAAAATTTCGGTCATTTCGTGGTGACCGTCGAAGATCGATTAGATAGACGATTCA
50107 TCTATGGATC
391 TCTATGGATC
50117 TTCCCAT
1 TTCCCAT
50124 TTTAATCAAT
Statistics
Matches: 403, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
400 403 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.30
Consensus pattern (400 bp):
TTCCCATCTCTCTGGAGCGCATATATAATTAAAATTTTTCTCAAAACCTGGATTCATTTTTACAT
AAAATTCATGCATTCAAGGGGATTATATCAAAATGATTTCAAGTCAAAACCATTGAAACCAATGT
CAAGTTAAAATGTAGCTAGTAAGGTACCAATTTCGGACGTCGCGAGGAGATTCATATCTCTTTGC
GCGTAACCAACTCCCAGACCCAACCGATGAGTCTCTTAATTACGTAGACCACAAGATCGATGTCT
CAAGTTTCGTAACTCAAGACATAGATTTCAATAGGCATCCGATCATGCTTAGCCCAAAATGATCG
GTGGCGACTTCAAAATTTCGGTCATTTCGTGGTGACCGTCGAAGATCGATTAGATAGACGATTCA
TCTATGGATC
Found at i:54353 original size:39 final size:38
Alignment explanation
Indices: 54310--54446 Score: 100
Period size: 39 Copynumber: 3.5 Consensus size: 38
54300 ATCCCTGAAC
* *
54310 GCATTCAGTTGAGGCTGCAACTGCTGATTATCACCAACG
1 GCATTCAATTGAGGCTGCAACTGCTGATTATC-CCAAAG
* * * *
54349 GCATTGAATTGAGACTCCAGCTGCTGATTATTCCCAAAG
1 GCATTCAATTGAGGCTGCAACTGCTGATTA-TCCCAAAG
* * * * *
54388 TCATT-TAGTGTAGGATGCAACTGCCT-ATTATCCCCAATG
1 GCATTCAATTG-AGGCTGCAACTG-CTGATTAT-CCCAAAG
54427 GCATTCAATTG-GAGCTGCAA
1 GCATTCAATTGAG-GCTGCAA
54447 TGGTTGATCC
Statistics
Matches: 74, Mismatches: 18, Indels: 12
0.71 0.17 0.12
Matches are distributed among these distances:
38 5 0.07
39 62 0.84
40 7 0.09
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.28
Consensus pattern (38 bp):
GCATTCAATTGAGGCTGCAACTGCTGATTATCCCAAAG
Found at i:54518 original size:39 final size:39
Alignment explanation
Indices: 54442--54520 Score: 97
Period size: 39 Copynumber: 2.0 Consensus size: 39
54432 CAATTGGAGC
* * * *
54442 TGCAATGGTTGATCCATCAGATTTGTATTTGATTGGGGT
1 TGCAATGGTAGATCCATCAGATTTATACTTGACTGGGGT
*
54481 TGCAATTGTAGATCCATCA-AGTTTATACTTGACTGGGGT
1 TGCAATGGTAGATCCATCAGA-TTTATACTTGACTGGGGT
54520 T
1 T
54521 TCAACTGCCA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
38 1 0.03
39 33 0.97
ACGTcount: A:0.23, C:0.13, G:0.25, T:0.39
Consensus pattern (39 bp):
TGCAATGGTAGATCCATCAGATTTATACTTGACTGGGGT
Found at i:54535 original size:39 final size:39
Alignment explanation
Indices: 54492--54566 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 39
54482 GCAATTGTAG
* *
54492 ATCCATCAAGTTTATACTTGACTGGGGTTTCAACTGCCA
1 ATCCATCAAGCTTATACTTGACTGGGGTTCCAACTGCCA
*** *
54531 ATCCATGTGGCTTATATTTGACTGGGGTTCCAACTG
1 ATCCATCAAGCTTATACTTGACTGGGGTTCCAACTG
54567 GTAACTTACC
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
39 30 1.00
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.35
Consensus pattern (39 bp):
ATCCATCAAGCTTATACTTGACTGGGGTTCCAACTGCCA
Found at i:57238 original size:22 final size:21
Alignment explanation
Indices: 57213--57260 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
57203 TATATATGAG
57213 AAATAGTAATTTATCAAAAAAT
1 AAATA-TAATTTATCAAAAAAT
* *
57235 AAATTATATTTTATCAAAAAGT
1 AAA-TATAATTTATCAAAAAAT
57257 AAAT
1 AAAT
57261 TATGTCATGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 1 0.04
22 20 0.87
23 2 0.09
ACGTcount: A:0.56, C:0.04, G:0.04, T:0.35
Consensus pattern (21 bp):
AAATATAATTTATCAAAAAAT
Found at i:57261 original size:22 final size:22
Alignment explanation
Indices: 57222--57263 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
57212 GAAATAGTAA
57222 TTTATCAAAAAATAAATTATAT
1 TTTATCAAAAAATAAATTATAT
*
57244 TTTATCAAAAAGTAAATTAT
1 TTTATCAAAAAATAAATTAT
57264 GTCATGAGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.40
Consensus pattern (22 bp):
TTTATCAAAAAATAAATTATAT
Found at i:58167 original size:18 final size:18
Alignment explanation
Indices: 58146--58206 Score: 63
Period size: 18 Copynumber: 3.4 Consensus size: 18
58136 TAATAAATAT
58146 TAAAAAATTAATTTTATA
1 TAAAAAATTAATTTTATA
* *
58164 TAAAAAATTAAATATATA
1 TAAAAAATTAATTTTATA
* *
58182 T-AAATATAAATTTTA-A
1 TAAAAAATTAATTTTATA
58198 TAAATAAAT
1 TAAA-AAAT
58207 ATATTTAAAA
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
16 2 0.06
17 12 0.35
18 20 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAAAAAATTAATTTTATA
Found at i:58179 original size:16 final size:16
Alignment explanation
Indices: 58139--58210 Score: 53
Period size: 16 Copynumber: 4.6 Consensus size: 16
58129 TTTGTAATAA
58139 TAAATAT-TAAAAAAT
1 TAAATATATAAAAAAT
*
58154 TAATTTTATATAAAAAAT
1 TAA--ATATATAAAAAAT
*
58172 TAAATATAT-ATAAAT
1 TAAATATATAAAAAAT
* *
58187 ATAAAT-TTTAATAAA-
1 -TAAATATATAAAAAAT
58202 TAAATATAT
1 TAAATATAT
58211 TTAAAATAAT
Statistics
Matches: 46, Mismatches: 5, Indels: 12
0.73 0.08 0.19
Matches are distributed among these distances:
14 5 0.11
15 12 0.26
16 15 0.33
17 3 0.07
18 11 0.24
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
TAAATATATAAAAAAT
Found at i:58929 original size:20 final size:20
Alignment explanation
Indices: 58898--58962 Score: 56
Period size: 20 Copynumber: 3.6 Consensus size: 20
58888 TTCAAGATTA
58898 ATATATTTTATATAAATTTTG
1 ATATA-TTTATATAAATTTTG
58919 ATATA-TT-TAT-AA--TT-
1 ATATATTTATATAAATTTTG
58933 -TAT-TTTATATAAATTTTG
1 ATATATTTATATAAATTTTG
*
58951 ATCTATTTATAT
1 ATATATTTATAT
58963 TTTATGTTGT
Statistics
Matches: 35, Mismatches: 1, Indels: 17
0.66 0.02 0.32
Matches are distributed among these distances:
13 5 0.14
14 3 0.09
15 4 0.11
17 4 0.11
18 3 0.09
19 4 0.11
20 7 0.20
21 5 0.14
ACGTcount: A:0.37, C:0.02, G:0.03, T:0.58
Consensus pattern (20 bp):
ATATATTTATATAAATTTTG
Found at i:58938 original size:32 final size:32
Alignment explanation
Indices: 58896--58967 Score: 117
Period size: 32 Copynumber: 2.2 Consensus size: 32
58886 TATTCAAGAT
*
58896 TAATATATTTTATATAAATTTTGATATATTTA
1 TAATTTATTTTATATAAATTTTGATATATTTA
*
58928 TAATTTATTTTATATAAATTTTGATCTATTTA
1 TAATTTATTTTATATAAATTTTGATATATTTA
*
58960 TATTTTAT
1 TAATTTAT
58968 GTTGTATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (32 bp):
TAATTTATTTTATATAAATTTTGATATATTTA
Found at i:58961 original size:18 final size:17
Alignment explanation
Indices: 58908--58961 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
58898 ATATATTTTA
58908 TATAAATTTTGATATATT
1 TATAAATTTTGAT-TATT
58926 TAT-AA-TTT-ATT-TT
1 TATAAATTTTGATTATT
58939 ATATAAATTTTGATCTATT
1 -TATAAATTTTGAT-TATT
58958 TATA
1 TATA
58962 TTTTATGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 12
0.71 0.00 0.29
Matches are distributed among these distances:
13 2 0.07
14 4 0.13
15 4 0.13
16 6 0.20
17 4 0.13
18 8 0.27
19 2 0.07
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (17 bp):
TATAAATTTTGATTATT
Found at i:59472 original size:29 final size:29
Alignment explanation
Indices: 59440--59500 Score: 88
Period size: 29 Copynumber: 2.1 Consensus size: 29
59430 TAAGCAAAGA
59440 GGTAATTGTGTTATTAAGAT-AAAGTTGAG
1 GGTAATTGTGTTATTAAGATGAAA-TTGAG
* *
59469 GGTAATTTTGTTATTATGATGAAATTGAG
1 GGTAATTGTGTTATTAAGATGAAATTGAG
59498 GGT
1 GGT
59501 TGATTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.31, C:0.00, G:0.28, T:0.41
Consensus pattern (29 bp):
GGTAATTGTGTTATTAAGATGAAATTGAG
Found at i:72905 original size:52 final size:52
Alignment explanation
Indices: 72808--72947 Score: 140
Period size: 52 Copynumber: 2.7 Consensus size: 52
72798 AATTGTCAGC
* * * * * * *
72808 ATGTATCAATA-TATTAAAGAATGTATCGATATATTTAGATAAAAAACCCAGA
1 ATGTATCAATACAATGAAA-AATGCATCGATACATTTGGGTCAAAAACCCAGA
* * * *
72860 ATGTATTAATACAATGAATAATGTAT-GAATACATTTGGGTCAAAAACCTAGA
1 ATGTATCAATACAATGAAAAATGCATCG-ATACATTTGGGTCAAAAACCCAGA
*
72912 ATGTATCGATACAATGAAAAATGCATCGATACATTT
1 ATGTATCAATACAATGAAAAATGCATCGATACATTT
72948 TCTTTCCATA
Statistics
Matches: 72, Mismatches: 13, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
51 1 0.01
52 66 0.92
53 5 0.07
ACGTcount: A:0.45, C:0.11, G:0.14, T:0.31
Consensus pattern (52 bp):
ATGTATCAATACAATGAAAAATGCATCGATACATTTGGGTCAAAAACCCAGA
Found at i:73026 original size:20 final size:20
Alignment explanation
Indices: 73003--73056 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
72993 CATTTCAAAC
* *
73003 ATGTATCGATATATTCACTT
1 ATGTATCGATACACTCACTT
73023 ATGTATCGATACACTCACTT
1 ATGTATCGATACACTCACTT
*
73043 ATTATATCGATACA
1 A-TGTATCGATACA
73057 AATTATATGA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 19 0.63
21 11 0.37
ACGTcount: A:0.33, C:0.19, G:0.09, T:0.39
Consensus pattern (20 bp):
ATGTATCGATACACTCACTT
Found at i:73525 original size:20 final size:21
Alignment explanation
Indices: 73480--73526 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
73470 TAAAGATTAC
73480 ATTA-TTATCAAATAATAAAA
1 ATTATTTATCAAATAATAAAA
* * *
73500 AATATTTATCTAA-AATAATA
1 ATTATTTATCAAATAATAAAA
73520 ATTATTT
1 ATTATTT
73527 TTGTAATTCA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 15 0.68
21 7 0.32
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (21 bp):
ATTATTTATCAAATAATAAAA
Found at i:73673 original size:45 final size:44
Alignment explanation
Indices: 73617--73701 Score: 161
Period size: 45 Copynumber: 1.9 Consensus size: 44
73607 TTTATTTATA
73617 ATAATTATTCAAAAAAATTATTATGTAAACTATTAATCATTAAT
1 ATAATTATTCAAAAAAATTATTATGTAAACTATTAATCATTAAT
73661 ATAATTATTTCAAAAAAATTATTATGTAAACTATTAATCAT
1 ATAATTA-TTCAAAAAAATTATTATGTAAACTATTAATCAT
73702 AAATTTTCAC
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
44 7 0.17
45 33 0.82
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.41
Consensus pattern (44 bp):
ATAATTATTCAAAAAAATTATTATGTAAACTATTAATCATTAAT
Found at i:73863 original size:22 final size:22
Alignment explanation
Indices: 73838--73906 Score: 81
Period size: 22 Copynumber: 3.2 Consensus size: 22
73828 TTTAAAAAAA
*
73838 AATAAAAAATAAATATTAATTT
1 AATAAAAAATAAATATAAATTT
* *
73860 AATATATAATAAA-ATAATATTT
1 AATAAAAAATAAATATAA-ATTT
73882 AATAAAAAAT-AATA-AAATTT
1 AATAAAAAATAAATATAAATTT
73902 AATAA
1 AATAA
73907 TTTATCTTAC
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
20 9 0.22
21 7 0.17
22 24 0.60
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATAAAAAATAAATATAAATTT
Found at i:73877 original size:15 final size:15
Alignment explanation
Indices: 73859--73896 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
73849 AATATTAATT
73859 TAATATATAATAAAA
1 TAATATATAATAAAA
*
73874 TAATATTTAATAAAA
1 TAATATATAATAAAA
73889 -AATA-ATAA
1 TAATATATAA
73897 AATTTAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 3 0.14
14 4 0.19
15 14 0.67
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
TAATATATAATAAAA
Found at i:75295 original size:13 final size:13
Alignment explanation
Indices: 75277--75304 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
75267 CTTTACTCAA
75277 TGTATCGATACAT
1 TGTATCGATACAT
75290 TGTATCGATACAT
1 TGTATCGATACAT
75303 TG
1 TG
75305 ATCTTTGTAT
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:0.29, C:0.14, G:0.18, T:0.39
Consensus pattern (13 bp):
TGTATCGATACAT
Done.