Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold923
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: 96686
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Found at i:915 original size:27 final size:28
Alignment explanation
Indices: 885--941 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
875 TGGAGATAAA
*
885 AACGGGATCGGAATA-CCCCTCAGAAAT
1 AACGGGATCGGAATATCCCCTCAAAAAT
* * *
912 AACGGGGTTGGAGTATCCCCTCAAAAAT
1 AACGGGATCGGAATATCCCCTCAAAAAT
940 AA
1 AA
942 TGGAGTTGGA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
27 12 0.48
28 13 0.52
ACGTcount: A:0.37, C:0.23, G:0.23, T:0.18
Consensus pattern (28 bp):
AACGGGATCGGAATATCCCCTCAAAAAT
Found at i:933 original size:28 final size:28
Alignment explanation
Indices: 894--956 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
884 AAACGGGATC
* *
894 GGAATA-CCCCTCAGAAATAACGGGGTT
1 GGAATATCCCCTCAAAAATAACGGAGTT
* *
921 GGAGTATCCCCTCAAAAATAATGGAGTT
1 GGAATATCCCCTCAAAAATAACGGAGTT
949 GGAATATC
1 GGAATATC
957 ATCAATTGTG
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 5 0.17
28 25 0.83
ACGTcount: A:0.35, C:0.19, G:0.24, T:0.22
Consensus pattern (28 bp):
GGAATATCCCCTCAAAAATAACGGAGTT
Found at i:1132 original size:80 final size:82
Alignment explanation
Indices: 978--1201 Score: 260
Period size: 80 Copynumber: 2.8 Consensus size: 82
968 AAAATTAGTG
*
978 TTTTGAAAATAAAATCGGAGTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATT
1 TTTTGAAAATAAAATCGGAGTTGAAGTATCCCCTCAGAAAAAACGGGGTTGGAGTATCCCCGATT
* *
1043 GTGAAAAATCATTTTTT
66 ATAAAAAATCATTTTTT
* * * **
1060 TTTTGGAAATAAAATCGGGGTTGAAGTA-CCCCTCA-AAAAAATGGGGTTGGAGTATCTTCGATT
1 TTTTGAAAATAAAATCGGAGTTGAAGTATCCCCTCAGAAAAAACGGGGTTGGAGTATCCCCGATT
* *
1123 ATAAAAAATCA---ATG
66 ATAAAAAATCATTTTTT
* * * * * * *
1137 TTTTGAAAATAAAACCGGGGTTGGAGTATCCCCTTAGAAATAACAGGGTTGGGGTATCCCCGATT
1 TTTTGAAAATAAAATCGGAGTTGAAGTATCCCCTCAGAAAAAACGGGGTTGGAGTATCCCCGATT
1202 GTGGAAAATC
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
77 26 0.22
78 6 0.05
79 22 0.18
80 33 0.28
81 7 0.06
82 26 0.22
ACGTcount: A:0.33, C:0.14, G:0.23, T:0.29
Consensus pattern (82 bp):
TTTTGAAAATAAAATCGGAGTTGAAGTATCCCCTCAGAAAAAACGGGGTTGGAGTATCCCCGATT
ATAAAAAATCATTTTTT
Found at i:1239 original size:79 final size:79
Alignment explanation
Indices: 918--1258 Score: 335
Period size: 79 Copynumber: 4.3 Consensus size: 79
908 AAATAACGGG
* * * * * ** * *
918 GTTGGAGTATCCCCTCAAAAATAATGGAGTTGGAATATCATCAATTGTGAAAAATTAGTGTTTTG
1 GTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTG
983 AAAATAAAATCGGA
66 AAAATAAAATCGGA
* *
997 GTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCATTTTTTTT
1 GTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCA---GTGTT
* *
1062 TTGGAAATAAAATCGGG
63 TTGAAAATAAAATCGGA
* * ** * * *
1079 GTTGAAGTA-CCCCTCA-AAAAAATGGGGTTGGAGTATCTTCGATTATAAAAAATCAATGTTTTG
1 GTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTG
* *
1142 AAAATAAAACCGGG
66 AAAATAAAATCGGA
* * * * * * *
1156 GTTGGAGTATCCCCTTAGAAATAACAGGGTTGGGGTATCCCCGATTGTGGAAAATCGGTGCTTTG
1 GTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTG
*
1221 GAAATAAAATCGGA
66 AAAATAAAATCGGA
* * * *
1235 GTTGGATTATCCTCTCGGAAATAA
1 GTTGAAGTATCCCCTCAGAAATAA
1259 AAACATGAAT
Statistics
Matches: 213, Mismatches: 44, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
77 26 0.12
78 6 0.03
79 114 0.54
80 33 0.15
81 7 0.03
82 27 0.13
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
GTTGAAGTATCCCCTCAGAAATAACGGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTG
AAAATAAAATCGGA
Found at i:3608 original size:20 final size:20
Alignment explanation
Indices: 3583--3697 Score: 72
Period size: 20 Copynumber: 5.6 Consensus size: 20
3573 AAAAATGCCT
3583 AAATGTATCGATACATTGAA
1 AAATGTATCGATACATTGAA
*
3603 AAATGTATCGATATATCTAGATA
1 AAATGTATCGATACAT-T-GA-A
* ** *
3626 AAATCTA--GAATGTATCGATA
1 AAATGTATCG-ATACATTGA-A
* *
3646 TAATGTATCGATACAATGAA
1 AAATGTATCGATACATTGAA
* *
3666 CAATGTATCGATACAATGAA
1 AAATGTATCGATACATTGAA
* *
3686 CAATATATCGAT
1 AAATGTATCGAT
3698 GCAAAATGTG
Statistics
Matches: 77, Mismatches: 12, Indels: 12
0.76 0.12 0.12
Matches are distributed among these distances:
20 55 0.71
21 7 0.09
22 8 0.10
23 7 0.09
ACGTcount: A:0.44, C:0.11, G:0.14, T:0.30
Consensus pattern (20 bp):
AAATGTATCGATACATTGAA
Found at i:3676 original size:33 final size:33
Alignment explanation
Indices: 3584--3683 Score: 107
Period size: 33 Copynumber: 3.1 Consensus size: 33
3574 AAAATGCCTA
*
3584 AATGTATCGATACATTGAAAAATGTATCGATAT
1 AATGTATCGATACAATGAAAAATGTATCGATAT
* * ** *
3617 -ATCTA--GATAAAATCTAGAATGTATCGATAT
1 AATGTATCGATACAATGAAAAATGTATCGATAT
* *
3647 AATGTATCGATACAATGAACAATGTATCGATAC
1 AATGTATCGATACAATGAAAAATGTATCGATAT
3680 AATG
1 AATG
3684 AACAATATAT
Statistics
Matches: 52, Mismatches: 12, Indels: 6
0.74 0.17 0.09
Matches are distributed among these distances:
30 20 0.38
31 4 0.08
32 4 0.08
33 24 0.46
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (33 bp):
AATGTATCGATACAATGAAAAATGTATCGATAT
Found at i:3683 original size:13 final size:13
Alignment explanation
Indices: 3634--3663 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3624 TAAAATCTAG
*
3634 AATGTATCGATAT
1 AATGTATCGATAC
3647 AATGTATCGATAC
1 AATGTATCGATAC
3660 AATG
1 AATG
3664 AACAATGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (13 bp):
AATGTATCGATAC
Found at i:4440 original size:18 final size:17
Alignment explanation
Indices: 4381--4441 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
4371 TAAACATTAA
4381 AATTAAAATTTA-AAATT
1 AATT-AAATTTATAAATT
*
4398 -ATTAAATATTATATATT
1 AATTAAAT-TTATAAATT
* *
4415 TATAAAATTTAATAAATT
1 AATTAAATTT-ATAAATT
4433 AATTAAATT
1 AATTAAATT
4442 AAACTTTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
15 4 0.11
16 6 0.17
17 6 0.17
18 19 0.54
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAAATTTATAAATT
Found at i:4580 original size:2 final size:2
Alignment explanation
Indices: 4575--4603 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
4565 TACTCTTTAC
4575 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4604 AAACAATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6083 original size:18 final size:19
Alignment explanation
Indices: 6046--6084 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
6036 AGGATAAACA
6046 AAAGAAGAAATAATAAATG
1 AAAGAAGAAATAATAAATG
* *
6065 AAAGAGGAAATTA-AAATG
1 AAAGAAGAAATAATAAATG
6083 AA
1 AA
6085 TTAAACTTGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (19 bp):
AAAGAAGAAATAATAAATG
Found at i:10104 original size:160 final size:161
Alignment explanation
Indices: 9896--10194 Score: 379
Period size: 160 Copynumber: 1.9 Consensus size: 161
9886 AGGAGAAAGG
* * * * *
9896 GTTATAAATATTAAGATTCAACTTTCAAACTTATTAAAAATAAAATATATTTTGTAATAAATATC
1 GTTACAAATATTAAGATTCAACTTTCAAACTTAATAAAAACAAAATATATTTCGAAATAAATATC
* * *
9961 TTGT-GGTTTAAGGTAAAATAAATTCCCATCTTAACTTCGAACCTTAATACTTAACTTTTTGGTA
66 TT-TAGGTTTAAGGTAAAATAAATTCACATCTTAACTTCGAACCTTAATACTTAACTTCTTGGCA
*
10025 CAAACGAGATTGTAATTTAGAGATAAAAAAAA
130 CAAACAAGATTGTAATTTAGAGATAAAAAAAA
* **
10057 GTTACAAATATTAGGATTCAAGC-TT-AAACTTAATAAATGCAAAATATATTTCGAAATAAATAT
1 GTTACAAATATTAAGATTCAA-CTTTCAAACTTAATAAAAACAAAATATATTTCGAAATAAATAT
* * * * * * * *
10120 CTTTATGTTTAAGGTGACATAAATTCACATTTTAACTTTGAATCTTGATATTTAACTTCTTGGCA
65 CTTTAGGTTTAAGGTAAAATAAATTCACATCTTAACTTCGAACCTTAATACTTAACTTCTTGGCA
10185 CAAACAAGAT
130 CAAACAAGAT
10195 CAAATTTTAA
Statistics
Matches: 116, Mismatches: 20, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
159 1 0.01
160 93 0.80
161 21 0.18
162 1 0.01
ACGTcount: A:0.41, C:0.11, G:0.10, T:0.37
Consensus pattern (161 bp):
GTTACAAATATTAAGATTCAACTTTCAAACTTAATAAAAACAAAATATATTTCGAAATAAATATC
TTTAGGTTTAAGGTAAAATAAATTCACATCTTAACTTCGAACCTTAATACTTAACTTCTTGGCAC
AAACAAGATTGTAATTTAGAGATAAAAAAAA
Found at i:12032 original size:20 final size:18
Alignment explanation
Indices: 11986--12035 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
11976 GAAAAATATA
*
11986 TAAAAAATCAGAAAAATG
1 TAAAAAATCAAAAAAATG
* *
12004 TAGAAAATCAAAAAAGATTT
1 TAAAAAATCAAAAAA-A-TG
12024 TAAAAAATCAAA
1 TAAAAAATCAAA
12036 TAGCATACAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 13 0.50
19 1 0.04
20 12 0.46
ACGTcount: A:0.66, C:0.06, G:0.08, T:0.20
Consensus pattern (18 bp):
TAAAAAATCAAAAAAATG
Found at i:12548 original size:2 final size:2
Alignment explanation
Indices: 12541--12574 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
12531 TACTAGAGTG
12541 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12575 CATACTTTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:14744 original size:33 final size:33
Alignment explanation
Indices: 14668--14744 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 33
14658 AAATTACATA
* *
14668 AATATAATATAAATATACGAATATATCAAAATT
1 AATATAATATAAATATACGAACATAACAAAATT
* * **
14701 TATATGATATAAATAT-TTAACATAACAAAATT
1 AATATAATATAAATATACGAACATAACAAAATT
14733 AATATAAATATA
1 AATAT-AATATA
14745 TAAAAATAAT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
32 16 0.46
33 19 0.54
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.35
Consensus pattern (33 bp):
AATATAATATAAATATACGAACATAACAAAATT
Found at i:14770 original size:26 final size:27
Alignment explanation
Indices: 14731--14782 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
14721 CATAACAAAA
14731 TTAATATAAATATATAAAAATAATATT
1 TTAATATAAATATATAAAAATAATATT
* *
14758 TTAA-ATAAATATATGAATATAATAT
1 TTAATATAAATATATAAAAATAATAT
14783 AAATATATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 19 0.83
27 4 0.17
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (27 bp):
TTAATATAAATATATAAAAATAATATT
Found at i:15832 original size:16 final size:16
Alignment explanation
Indices: 15809--15850 Score: 68
Period size: 16 Copynumber: 2.6 Consensus size: 16
15799 ATGTAGGTAT
15809 AAATTTTAAAA-TTAA
1 AAATTTTAAAATTTAA
15824 AAATATTTAAAATTTAA
1 AAAT-TTTAAAATTTAA
15841 AAATTTTAAA
1 AAATTTTAAA
15851 TATCAAATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.16
16 13 0.52
17 8 0.32
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AAATTTTAAAATTTAA
Found at i:15959 original size:16 final size:16
Alignment explanation
Indices: 15938--15971 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15928 ATTTTATTTT
*
15938 AAATATAATTATAAAA
1 AAATATAATAATAAAA
*
15954 AAATATCATAATAAAA
1 AAATATAATAATAAAA
15970 AA
1 AA
15972 TATTAAAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAATATAATAATAAAA
Found at i:16412 original size:20 final size:21
Alignment explanation
Indices: 16384--16424 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
16374 AAATGAATTA
16384 TTTTATTATGAT-ATTTTTCT
1 TTTTATTATGATAATTTTTCT
* *
16404 TTTTTTTATTATAATTTTTCT
1 TTTTATTATGATAATTTTTCT
16425 CCCTTTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTTATTATGATAATTTTTCT
Found at i:16699 original size:15 final size:15
Alignment explanation
Indices: 16645--16706 Score: 54
Period size: 15 Copynumber: 3.9 Consensus size: 15
16635 TTGAATTGAG
*
16645 TTATTTTAAATTTAGA
1 TTATTTTTAATTTA-A
*
16661 TTTATTTTAAATTTAA
1 -TTATTTTTAATTTAA
*
16677 TTACTTTTAATTTGAA
1 TTATTTTTAATTT-AA
16693 -TATTTTTGAATTTA
1 TTATTTTT-AATTTA
16707 GTTTTTTCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
15 18 0.45
16 8 0.20
17 14 0.35
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.60
Consensus pattern (15 bp):
TTATTTTTAATTTAA
Found at i:17925 original size:32 final size:30
Alignment explanation
Indices: 17884--17942 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
17874 TGCAAAAATA
*
17884 TTTAAGAATTAAAAAAATTTTATTTTATTGAT
1 TTTAAGAATT--AAAAATTATATTTTATTGAT
* *
17916 TTTAGGAATTGAAAATTATATTTTATT
1 TTTAAGAATTAAAAATTATATTTTATT
17943 TAAATATATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 15 0.62
32 9 0.38
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (30 bp):
TTTAAGAATTAAAAATTATATTTTATTGAT
Found at i:18414 original size:23 final size:25
Alignment explanation
Indices: 18346--18415 Score: 65
Period size: 23 Copynumber: 2.8 Consensus size: 25
18336 AAAAATTCAC
18346 TATT-AATCATTTTTATTGATAATAAAT
1 TATTAAAT-ATTTTT-TT-ATAATAAAT
** *
18373 TATTAAATATAATTATATAAT-AAT
1 TATTAAATATTTTTTTATAATAAAT
18397 TA-TAAATATTTTTTTATAA
1 TATTAAATATTTTTTTATAA
18416 ATTAAATATT
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
23 14 0.39
24 5 0.14
25 5 0.14
26 1 0.03
27 8 0.22
28 3 0.08
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (25 bp):
TATTAAATATTTTTTTATAATAAAT
Found at i:18418 original size:21 final size:21
Alignment explanation
Indices: 18367--18430 Score: 60
Period size: 23 Copynumber: 3.0 Consensus size: 21
18357 TTTATTGATA
**
18367 ATAAATTATTAAATATAATTAT
1 ATAAATTA-TAAATATTTTTAT
*
18389 ATAATAATTATAAATATTTTTTT
1 AT-A-AATTATAAATATTTTTAT
18412 ATAAA-T-TAAATATTTTTAT
1 ATAAATTATAAATATTTTTAT
18431 TTAAGAAAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
19 12 0.33
20 1 0.03
21 2 0.06
22 3 0.08
23 13 0.36
24 5 0.14
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATAAATTATAAATATTTTTAT
Found at i:18472 original size:34 final size:34
Alignment explanation
Indices: 18434--18503 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
18424 TTTTTATTTA
*
18434 AGAAAATTTTAATCATTTATTTATTTATACTTTT
1 AGAAAAATTTAATCATTTATTTATTTATACTTTT
18468 AGAAAAATTTAATCATTTATTTATTTATACTTTT
1 AGAAAAATTTAATCATTTATTTATTTATACTTTT
18502 AG
1 AG
18504 TTTAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.37, C:0.06, G:0.04, T:0.53
Consensus pattern (34 bp):
AGAAAAATTTAATCATTTATTTATTTATACTTTT
Found at i:18674 original size:15 final size:15
Alignment explanation
Indices: 18653--18718 Score: 62
Period size: 16 Copynumber: 4.3 Consensus size: 15
18643 TTTCGGATTG
18653 AATTTTTGTAAATATA
1 AATTTTTGTAAAT-TA
*
18669 AATTTTTTTAAATTA
1 AATTTTTGTAAATTA
*
18684 AATTTTTTTAAAATTTA
1 AATTTTTGT-AAA-TTA
* *
18701 AAATTTT-TAATTTA
1 AATTTTTGTAAATTA
18715 AATT
1 AATT
18719 GTAAATTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
14 6 0.14
15 13 0.30
16 16 0.36
17 9 0.20
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTTTGTAAATTA
Found at i:18688 original size:31 final size:31
Alignment explanation
Indices: 18653--18718 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
18643 TTTCGGATTG
*
18653 AATTTTTGT-AAATATAAATTTTTTTAAATTA
1 AATTTTTGTAAAATATAAA-ATTTTTAAATTA
* * *
18684 AATTTTTTTAAAATTTAAAATTTTTAATTTA
1 AATTTTTGTAAAATATAAAATTTTTAAATTA
18715 AATT
1 AATT
18719 GTAAATTTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 22 0.73
32 8 0.27
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (31 bp):
AATTTTTGTAAAATATAAAATTTTTAAATTA
Found at i:18737 original size:22 final size:22
Alignment explanation
Indices: 18691--18770 Score: 83
Period size: 22 Copynumber: 3.7 Consensus size: 22
18681 TTAAATTTTT
* * *
18691 TTAAAATTTAAAATTTTT-AAT
1 TTAAATTTTAAATTTTTTCAAA
*
18712 TTAAATTGTAAATTTTTTCAAA
1 TTAAATTTTAAATTTTTTCAAA
**
18734 TTAAATTTTAAATTAATTCAAA
1 TTAAATTTTAAATTTTTTCAAA
18756 -TAAATTTTTAAATTT
1 TTAAA-TTTTAAATTT
18771 AAACTTGGCT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
21 19 0.39
22 30 0.61
ACGTcount: A:0.45, C:0.03, G:0.01, T:0.51
Consensus pattern (22 bp):
TTAAATTTTAAATTTTTTCAAA
Found at i:18740 original size:15 final size:15
Alignment explanation
Indices: 18653--18742 Score: 81
Period size: 15 Copynumber: 5.4 Consensus size: 15
18643 TTTCGGATTG
*
18653 AATTTTTGTAAATATA
1 AATTTTTTTAAAT-TA
18669 AATTTTTTTAAATTA
1 AATTTTTTTAAATTA
18684 AATTTTTTTAAAATTTAA
1 AATTTTTTT-AAA-TT-A
18702 AATTTTTAATTTAAATTGTA
1 AA-TTTT--TTTAAA-T-TA
*
18722 AATTTTTTCAAATTA
1 AATTTTTTTAAATTA
18737 AATTTT
1 AATTTT
18743 AAATTAATTC
Statistics
Matches: 65, Mismatches: 2, Indels: 15
0.79 0.02 0.18
Matches are distributed among these distances:
15 19 0.29
16 16 0.25
17 7 0.11
18 3 0.05
19 8 0.12
20 8 0.12
21 4 0.06
ACGTcount: A:0.41, C:0.01, G:0.02, T:0.56
Consensus pattern (15 bp):
AATTTTTTTAAATTA
Found at i:19209 original size:28 final size:28
Alignment explanation
Indices: 19169--19225 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
19159 AATTTGAGGG
19169 ATCGTTTTTTTTGTTCTCAGACAAAGTT
1 ATCGTTTTTTTTGTTCTCAGACAAAGTT
19197 ATCGTTTTTTTTGTTCTCAGACAAAGTT
1 ATCGTTTTTTTTGTTCTCAGACAAAGTT
19225 A
1 A
19226 AGTTTTTGCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.23, C:0.14, G:0.14, T:0.49
Consensus pattern (28 bp):
ATCGTTTTTTTTGTTCTCAGACAAAGTT
Found at i:19232 original size:28 final size:28
Alignment explanation
Indices: 19172--19232 Score: 106
Period size: 28 Copynumber: 2.2 Consensus size: 28
19162 TTGAGGGATC
*
19172 GTTTTTTTTGTTCTCAGACAAAGTTATC
1 GTTTTTTTTGTTCTCAGACAAAGTTATA
19200 GTTTTTTTTGTTCTCAGACAAAGTTA-A
1 GTTTTTTTTGTTCTCAGACAAAGTTATA
19227 GTTTTT
1 GTTTTT
19233 GCAGAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 6 0.19
28 26 0.81
ACGTcount: A:0.21, C:0.11, G:0.15, T:0.52
Consensus pattern (28 bp):
GTTTTTTTTGTTCTCAGACAAAGTTATA
Found at i:20482 original size:2 final size:2
Alignment explanation
Indices: 20475--20508 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20465 GTTGAGCGAC
20475 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
20509 GTTGGTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:22172 original size:30 final size:30
Alignment explanation
Indices: 22136--22224 Score: 151
Period size: 30 Copynumber: 3.0 Consensus size: 30
22126 AACTTTCTAG
*
22136 CTGGGACATGCTTTGTATCTCCATGCGTTT
1 CTGGGACATGCTCTGTATCTCCATGCGTTT
*
22166 CTGGGACATGCTCTGTATCTCCATACGTTT
1 CTGGGACATGCTCTGTATCTCCATGCGTTT
*
22196 CTGGGACATGCTCTGTATCTCTATGCGTT
1 CTGGGACATGCTCTGTATCTCCATGCGTT
22225 GGGTCTAGTT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 55 1.00
ACGTcount: A:0.15, C:0.25, G:0.22, T:0.38
Consensus pattern (30 bp):
CTGGGACATGCTCTGTATCTCCATGCGTTT
Found at i:22268 original size:3 final size:3
Alignment explanation
Indices: 22262--22291 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
22252 AATAACAATA
22262 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
22292 TTTCTGTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:27658 original size:2 final size:2
Alignment explanation
Indices: 27651--27697 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
27641 TGAACTGTTC
27651 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
27693 TA TA T
1 TA TA T
27698 TTGAAGTTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29449 original size:1 final size:1
Alignment explanation
Indices: 29404--29433 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
29394 TGATATTCTG
*
29404 TTTTTTTTTTTTTTTTTTTTTTTTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
29434 GGTTGGATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:30557 original size:15 final size:15
Alignment explanation
Indices: 30534--30563 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
30524 AAAAAAAAAA
*
30534 TAAATATATTTTTAT
1 TAAAAATATTTTTAT
30549 TAAAAATATTTTTAT
1 TAAAAATATTTTTAT
30564 ATTTGATATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TAAAAATATTTTTAT
Found at i:31047 original size:16 final size:16
Alignment explanation
Indices: 31026--31057 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
31016 TAATAATATG
31026 TGTCACATTATTATTA
1 TGTCACATTATTATTA
31042 TGTCACATTATTATTA
1 TGTCACATTATTATTA
31058 ATTAAAAGAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.12, G:0.06, T:0.50
Consensus pattern (16 bp):
TGTCACATTATTATTA
Found at i:35820 original size:13 final size:13
Alignment explanation
Indices: 35802--35826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
35792 AACTCACTCA
35802 GTATCGATACATT
1 GTATCGATACATT
35815 GTATCGATACAT
1 GTATCGATACAT
35827 GGTCAAATGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:36269 original size:23 final size:23
Alignment explanation
Indices: 36243--36286 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
36233 GTATTCAACC
*
36243 TTGGTGTACAATCTTTT-AAGAAT
1 TTGGGGTACAAT-TTTTGAAGAAT
*
36266 TTGGGGTATAATTTTTGAAGA
1 TTGGGGTACAATTTTTGAAGA
36287 GATTGAGAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.30, C:0.05, G:0.23, T:0.43
Consensus pattern (23 bp):
TTGGGGTACAATTTTTGAAGAAT
Found at i:42019 original size:21 final size:21
Alignment explanation
Indices: 41986--42034 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
41976 CAAGTATTCT
* *
41986 TCAAATTTCATCT-TTTTCACA
1 TCAAAATTAATCTGTTTT-ACA
*
42007 TCAAAATTAATCTGTTTTTCA
1 TCAAAATTAATCTGTTTTACA
42028 TCAAAAT
1 TCAAAAT
42035 CATCAACAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.18, G:0.02, T:0.45
Consensus pattern (21 bp):
TCAAAATTAATCTGTTTTACA
Found at i:43675 original size:31 final size:32
Alignment explanation
Indices: 43637--43715 Score: 151
Period size: 32 Copynumber: 2.5 Consensus size: 32
43627 GGAAAAGTTT
43637 CTTATTGATTGGTATCA-TTTTTTTTGTTTCC
1 CTTATTGATTGGTATCATTTTTTTTTGTTTCC
43668 CTTATTGATTGGTATCATTTTTTTTTGTTTCC
1 CTTATTGATTGGTATCATTTTTTTTTGTTTCC
43700 CTTATTGATTGGTATC
1 CTTATTGATTGGTATC
43716 TTATTGATCT
Statistics
Matches: 47, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 17 0.36
32 30 0.64
ACGTcount: A:0.14, C:0.13, G:0.14, T:0.59
Consensus pattern (32 bp):
CTTATTGATTGGTATCATTTTTTTTTGTTTCC
Found at i:44575 original size:19 final size:20
Alignment explanation
Indices: 44532--44580 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
44522 TACCTAGATA
44532 TATCGATACATATTGCTTAG
1 TATCGATACATATTGCTTAG
* *
44552 TATCGATACATGTT-CTTGG
1 TATCGATACATATTGCTTAG
44571 TATCGATACA
1 TATCGATACA
44581 CAGTAAATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
19 14 0.52
20 13 0.48
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.39
Consensus pattern (20 bp):
TATCGATACATATTGCTTAG
Found at i:44666 original size:13 final size:13
Alignment explanation
Indices: 44629--44666 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
44619 AACTCACTCC
*
44629 GTATCGATACAGT
1 GTATCGATACATT
44642 GTATCGATACATT
1 GTATCGATACATT
44655 GTATCGATACAT
1 GTATCGATACAT
44667 GGTCAAATGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:46719 original size:97 final size:97
Alignment explanation
Indices: 46471--46708 Score: 334
Period size: 97 Copynumber: 2.5 Consensus size: 97
46461 GAAAAACGAA
* * *
46471 GTTGGAGTATCCCCTCGGAGGAATGAGGTTGGAGTGTACCTGATGATGACAATTTAAGTGAGAAT
1 GTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTACCCGATGATGACAATTTAAGTGAGAAT
*
46536 AAAATTTAAACTTTGATGCATTTAAAAACGGG
66 AAAATTTAAACTTTGATGCATTTAAAAACAGG
* * *
46568 GTTGGAGTATCCCCTCGGAA-GAATGGGGTTGAAGTGTACCCAATGGTGACAATTTAAGTGAGAA
1 GTTGGAGTATCCCCTC-GAAGGAATGGGGTTGGAGTGTACCCGATGATGACAATTTAAGTGAGAA
* ** *
46632 TAAGATTTAAACTTTGATGTGTTTAAAAGCAGG
65 TAAAATTTAAACTTTGATGCATTTAAAAACAGG
* * *
46665 GTTGGAGTATCCTCTCGAAGGAATGGGGTTGGAGTATCCCCGAT
1 GTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTACCCGAT
46709 AAATAAAATT
Statistics
Matches: 123, Mismatches: 16, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
96 3 0.02
97 118 0.96
98 2 0.02
ACGTcount: A:0.30, C:0.13, G:0.29, T:0.29
Consensus pattern (97 bp):
GTTGGAGTATCCCCTCGAAGGAATGGGGTTGGAGTGTACCCGATGATGACAATTTAAGTGAGAAT
AAAATTTAAACTTTGATGCATTTAAAAACAGG
Found at i:52954 original size:142 final size:138
Alignment explanation
Indices: 52667--52935 Score: 333
Period size: 142 Copynumber: 1.9 Consensus size: 138
52657 AATAAACTTG
* * *
52667 AGCTTTCAAATTGTTTTCATGAGATTATAATTACGTGTTTAAATTACAATAGAAATCAATAAATT
1 AGCTTTCAAATTGTTTTCATGAAATTATAATTACGTGTTCAAATTACAATAGAAATAAATAAATT
* * * * ** * * *
52732 ATATATAACTAGATAAATTTAATGTGAAATTATGGGCAATTGATACATGATTAAATTTGAACGCG
66 ACATAGAACTAGATAAATTTAATATAAAATTATGACCAATTGATACAGGAATAAATCTGAACGCG
52797 ACAGCATA
131 ACAGCATA
* **
52805 AGCTTTCACATTGTTTTCATGAAATTATAATTGTGTGTTCAAATTACAATAGGAACCATTAAATA
1 AGCTTTCAAATTGTTTTCATGAAATTATAATTACGTGTTCAAATTACAATA-GAA--A-TAAATA
* *
52870 AATTACATAGAACTAGATAAATTTAATATAAAATTA-GACCAAATTTATATAGGAATAAATCTGA
62 AATTACATAGAACTAGATAAATTTAATATAAAATTATGACC-AATTGATACAGGAATAAATCTGA
52934 AC
126 AC
52936 ATGGGAATTT
Statistics
Matches: 109, Mismatches: 17, Indels: 6
0.83 0.13 0.05
Matches are distributed among these distances:
138 46 0.42
139 3 0.03
141 3 0.03
142 57 0.52
ACGTcount: A:0.43, C:0.10, G:0.12, T:0.35
Consensus pattern (138 bp):
AGCTTTCAAATTGTTTTCATGAAATTATAATTACGTGTTCAAATTACAATAGAAATAAATAAATT
ACATAGAACTAGATAAATTTAATATAAAATTATGACCAATTGATACAGGAATAAATCTGAACGCG
ACAGCATA
Found at i:54294 original size:5 final size:6
Alignment explanation
Indices: 54260--54291 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
54250 ATTTTTTAGA
54260 TTAATT TTAATT TTAATT TTAATT TT-ATT TTA
1 TTAATT TTAATT TTAATT TTAATT TTAATT TTA
54292 TTTCTTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (6 bp):
TTAATT
Found at i:54408 original size:26 final size:26
Alignment explanation
Indices: 54379--54428 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
54369 AATTAAAATA
*
54379 ATTTAATTTATTAATTAAT-TATTTTT
1 ATTTAATTT-TTAAATAATATATTTTT
*
54405 ATTTGATTTTTAAATAATATATTT
1 ATTTAATTTTTAAATAATATATTT
54429 AAAGTATTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (26 bp):
ATTTAATTTTTAAATAATATATTTTT
Found at i:57783 original size:27 final size:27
Alignment explanation
Indices: 57734--57787 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
57724 CTTATAATGA
*
57734 AGCACTCTTCCCTCGATCCAAAAGCTT
1 AGCACTCTTCCCTCGAACCAAAAGCTT
* * *
57761 AGCACTCTTCCTTTGAACTAAAAGCTT
1 AGCACTCTTCCCTCGAACCAAAAGCTT
57788 TGATACCAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.28, C:0.31, G:0.11, T:0.30
Consensus pattern (27 bp):
AGCACTCTTCCCTCGAACCAAAAGCTT
Found at i:59145 original size:21 final size:22
Alignment explanation
Indices: 59119--59163 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
59109 GTTGATGTAA
59119 TAATTTAATTATT-AAATT-AAT
1 TAATTTAA-TATTAAAATTGAAT
59140 TAATTTAATATTAAAATTGAAT
1 TAATTTAATATTAAAATTGAAT
59162 TA
1 TA
59164 TTATGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 4 0.18
21 13 0.59
22 5 0.23
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (22 bp):
TAATTTAATATTAAAATTGAAT
Found at i:59428 original size:13 final size:13
Alignment explanation
Indices: 59385--59433 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
59375 ATTAGAAAAA
*
59385 TTTTCTCTTTCGTT
1 TTTTCTCTTT-TTT
*
59399 TTTTC-CTTTTTCA
1 TTTTCTCTTTTT-T
59412 TTTTCTCTTTTTT
1 TTTTCTCTTTTTT
59425 TTTTCTCTT
1 TTTTCTCTT
59434 GCTTTTTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
12 1 0.03
13 18 0.60
14 11 0.37
ACGTcount: A:0.02, C:0.20, G:0.02, T:0.76
Consensus pattern (13 bp):
TTTTCTCTTTTTT
Found at i:65453 original size:2 final size:2
Alignment explanation
Indices: 65448--65472 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
65438 TAAATGACAA
65448 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
65473 GTAGTATACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:65613 original size:14 final size:14
Alignment explanation
Indices: 65591--65630 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
65581 CGTGTAATTT
* *
65591 ATTTTATTTTATAA
1 ATTTAATTTAATAA
65605 ATTTAATTTAATAA
1 ATTTAATTTAATAA
65619 ATTTAATTTAAT
1 ATTTAATTTAAT
65631 TTAATTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAATTTAATAA
Found at i:65636 original size:24 final size:23
Alignment explanation
Indices: 65604--65750 Score: 78
Period size: 23 Copynumber: 6.5 Consensus size: 23
65594 TTATTTTATA
65604 AATTTAATTTAATAAATTTAATTT
1 AATTTAATTTAATAAATTT-ATTT
*
65628 AATTTAATTT-AT-TATTTA-TT
1 AATTTAATTTAATAAATTTATTT
* *
65648 AATTTAA-ATAATATATTTATTT
1 AATTTAATTTAATAAATTTATTT
* * *
65670 AAATTTAAATTAA-AAATATA-TA
1 -AATTTAATTTAATAAATTTATTT
*
65692 AAATTAA-TTAA-AAATATT-TTAAT
1 AATTTAATTTAATAAAT-TTATT--T
* * * *
65715 AATTTAAATTATTAAATTAAATT
1 AATTTAATTTAATAAATTTATTT
65738 AATTTAAATTTAA
1 AATTT-AATTTAA
65751 ACTTAATTTA
Statistics
Matches: 95, Mismatches: 15, Indels: 26
0.70 0.11 0.19
Matches are distributed among these distances:
19 1 0.01
20 19 0.20
21 15 0.16
22 7 0.07
23 26 0.27
24 22 0.23
25 5 0.05
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AATTTAATTTAATAAATTTATTT
Found at i:65654 original size:5 final size:5
Alignment explanation
Indices: 65604--65638 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
65594 TTATTTTATA
*
65604 AATTT AATTT AA-TA AATTT AATTT AATTT AATTT A
1 AATTT AATTT AATTT AATTT AATTT AATTT AATTT A
65639 TTATTTATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 3 0.11
5 24 0.89
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (5 bp):
AATTT
Found at i:65675 original size:43 final size:42
Alignment explanation
Indices: 65585--65677 Score: 109
Period size: 43 Copynumber: 2.2 Consensus size: 42
65575 GCGGGTCGTG
* *
65585 TAATTTATTTTATTTTATAAATTTAATTTAATAAATTTAATT
1 TAATTTAATTTATTTTATAAATTTAATATAATAAATTTAATT
* *
65627 TAATTTAATTTATTATTTATTAATTTAA-ATAATATATTT-ATT
1 TAATTTAATTTA-T-TTTATAAATTTAATATAATAAATTTAATT
65669 TAAATTTAA
1 T-AATTTAA
65678 ATTAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
42 15 0.34
43 17 0.39
44 12 0.27
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (42 bp):
TAATTTAATTTATTTTATAAATTTAATATAATAAATTTAATT
Found at i:65760 original size:17 final size:16
Alignment explanation
Indices: 65604--65761 Score: 67
Period size: 15 Copynumber: 10.4 Consensus size: 16
65594 TTATTTTATA
*
65604 AATTT-AATTT-AATA
1 AATTTAAATTTAAATT
*
65618 AATTT-AATTTAATTT
1 AATTTAAATTTAAATT
*
65633 AATTTATTATTT--ATT
1 AATTTA-AATTTAAATT
* *
65648 AATTTAAATAATATATT
1 AATTTAAAT-TTAAATT
*
65665 TATTTAAATTTAAATT
1 AATTTAAATTTAAATT
*
65681 AA---AAATATATAA--
1 AATTTAAATTTA-AATT
* *
65693 AA-TT-AATTAAAAAT
1 AATTTAAATTTAAATT
*
65707 ATTTTAATAATTTAAATT
1 AATTT-A-AATTTAAATT
65725 -A-TTAAA-TTAAATT
1 AATTTAAATTTAAATT
65738 AATTTAAATTTAAACTT
1 AATTTAAATTTAAA-TT
65755 AATTTAA
1 AATTTAA
65762 CATATAATTG
Statistics
Matches: 108, Mismatches: 17, Indels: 35
0.68 0.11 0.22
Matches are distributed among these distances:
12 4 0.04
13 17 0.16
14 18 0.17
15 24 0.22
16 13 0.12
17 24 0.22
18 8 0.07
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTTAAATTTAAATT
Found at i:66492 original size:12 final size:13
Alignment explanation
Indices: 66470--66501 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
66460 GCGGATCGAA
66470 TTAAA-TTAAA-T
1 TTAAATTTAAATT
66481 TTAAATTTAAATT
1 TTAAATTTAAATT
66494 TTAAATTT
1 TTAAATTT
66502 TTTTCAAGTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.26
12 5 0.26
13 9 0.47
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (13 bp):
TTAAATTTAAATT
Found at i:67242 original size:26 final size:27
Alignment explanation
Indices: 67211--67270 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
67201 TTGAAAATTT
67211 TTAATATTTATA-AATATTT-AATAAAA
1 TTAATATTTATATAA-ATTTAAATAAAA
*
67237 TTAATATTTATATAAATTTAAATTAAA
1 TTAATATTTATATAAATTTAAATAAAA
67264 TT-ATATT
1 TTAATATT
67271 AAATAATTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
26 21 0.68
27 10 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATATTTATATAAATTTAAATAAAA
Found at i:67244 original size:16 final size:17
Alignment explanation
Indices: 67223--67257 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
67213 AATATTTATA
67223 AATATTTA-ATAAAATT
1 AATATTTATATAAAATT
*
67239 AATATTTATATAAATTT
1 AATATTTATATAAAATT
67256 AA
1 AA
67258 ATTAAATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATATTTATATAAAATT
Found at i:67259 original size:22 final size:21
Alignment explanation
Indices: 67234--67274 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 21
67224 ATATTTAATA
67234 AAATTAATATT-TATATAAATTT
1 AAATTAA-ATTATAT-TAAATTT
67256 AAATTAAATTATATTAAAT
1 AAATTAAATTATATTAAAT
67275 AATTATTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (21 bp):
AAATTAAATTATATTAAATTT
Found at i:67321 original size:17 final size:17
Alignment explanation
Indices: 67286--67326 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
67276 ATTATTATTT
*
67286 ATTTAAATATTTTTGTA
1 ATTTAAATATTTTTATA
67303 ATTTAAA-ATTTTATATA
1 ATTTAAATATTTT-TATA
67320 A-TTAAAT
1 ATTTAAAT
67327 TTGAAATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (17 bp):
ATTTAAATATTTTTATA
Found at i:68080 original size:12 final size:12
Alignment explanation
Indices: 68047--68121 Score: 62
Period size: 12 Copynumber: 6.0 Consensus size: 12
68037 CACCATATGA
68047 ATAAAAAATAAT
1 ATAAAAAATAAT
*
68059 -TAAAATATAAT
1 ATAAAAAATAAT
68070 ATAAAAAATAAT
1 ATAAAAAATAAT
* *
68082 ATGAATATATGAAT
1 AT-AAAAAAT-AAT
* *
68096 GTATCAAAATATAT
1 ATA-AAAAATA-AT
68110 ATAAAAAATAAT
1 ATAAAAAATAAT
68122 TAATGTATAA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
11 10 0.21
12 14 0.29
13 13 0.27
14 11 0.23
ACGTcount: A:0.64, C:0.01, G:0.04, T:0.31
Consensus pattern (12 bp):
ATAAAAAATAAT
Found at i:68213 original size:23 final size:23
Alignment explanation
Indices: 68158--68237 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 23
68148 TTAATATTTT
*
68158 AAATATAAAAAATAATATGAACATA
1 AAATATAAAAAATAAT-T-AAAATA
* *
68183 ATAT-TAAAAATTAATTAAAATA
1 AAATATAAAAAATAATTAAAATA
* *
68205 AAATATAAAAAATAAAT-ATA-A
1 AAATATAAAAAATAATTAAAATA
68226 AAATATAAAAAA
1 AAATATAAAAAA
68238 AATATTTATA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
21 13 0.28
22 10 0.21
23 11 0.23
24 10 0.21
25 3 0.06
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (23 bp):
AAATATAAAAAATAATTAAAATA
Found at i:68218 original size:14 final size:14
Alignment explanation
Indices: 68199--68235 Score: 58
Period size: 13 Copynumber: 2.6 Consensus size: 14
68189 AAAATTAATT
68199 AAAATAAAATATAA
1 AAAATAAAATATAA
68213 AAAAT-AAATATAA
1 AAAATAAAATATAA
68226 AAATATAAAA
1 AAA-ATAAAA
68236 AAAATATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.52
14 7 0.33
15 3 0.14
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (14 bp):
AAAATAAAATATAA
Found at i:68238 original size:11 final size:11
Alignment explanation
Indices: 68158--68242 Score: 59
Period size: 11 Copynumber: 7.5 Consensus size: 11
68148 TTAATATTTT
68158 AAATATAAAAA
1 AAATATAAAAA
* *
68169 ATAATATGAACA
1 A-AATATAAAAA
*
68181 TAATATTAAAAA
1 AAATA-TAAAAA
*
68193 TTAAT-TAAAATA
1 -AAATATAAAA-A
68205 AAATATAAAAA
1 AAATATAAAAA
*
68216 ATAA-AT-ATAA
1 A-AATATAAAAA
68226 AAATATAAAAA
1 AAATATAAAAA
68237 AAATAT
1 AAATAT
68243 TTATAAATAT
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
9 2 0.03
10 6 0.10
11 26 0.45
12 20 0.34
13 4 0.07
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.27
Consensus pattern (11 bp):
AAATATAAAAA
Found at i:68249 original size:23 final size:21
Alignment explanation
Indices: 68158--68237 Score: 72
Period size: 23 Copynumber: 3.6 Consensus size: 21
68148 TTAATATTTT
68158 AAATATAAAAAAT-AATATGAA
1 AAATATAAAAAATAAATAT-AA
* * *
68179 CATAATATTAAAAATTAATTAAAATA
1 -A-AATA-TAAAAAATAAAT-ATA-A
68205 AAATATAAAAAATAAATATAA
1 AAATATAAAAAATAAATATAA
68226 AAATATAAAAAA
1 AAATATAAAAAA
68238 AATATTTATA
Statistics
Matches: 47, Mismatches: 6, Indels: 11
0.73 0.09 0.17
Matches are distributed among these distances:
21 13 0.28
22 3 0.06
23 14 0.30
24 11 0.23
25 4 0.09
26 2 0.04
ACGTcount: A:0.71, C:0.01, G:0.01, T:0.26
Consensus pattern (21 bp):
AAATATAAAAAATAAATATAA
Found at i:77567 original size:12 final size:12
Alignment explanation
Indices: 77537--77569 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
77527 ATTTCATTTA
77537 AAATATATGTTT
1 AAATATATGTTT
*
77549 -GATATATGTTT
1 AAATATATGTTT
77560 AAATATATGT
1 AAATATATGT
77570 ATACATTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
11 10 0.56
12 8 0.44
ACGTcount: A:0.39, C:0.00, G:0.12, T:0.48
Consensus pattern (12 bp):
AAATATATGTTT
Found at i:77986 original size:12 final size:11
Alignment explanation
Indices: 77961--77993 Score: 57
Period size: 11 Copynumber: 2.9 Consensus size: 11
77951 TTTTGTTGTA
77961 TTTTATATTATT
1 TTTTA-ATTATT
77973 TTTTAATTATT
1 TTTTAATTATT
77984 TTTTAATTAT
1 TTTTAATTAT
77994 ACTTATGCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (11 bp):
TTTTAATTATT
Found at i:82728 original size:19 final size:20
Alignment explanation
Indices: 82704--82759 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 20
82694 TATATCGATA
82704 CATTGTATCGATACATGC-T
1 CATTGTATCGATACATGCTT
*
82723 CATTGTATCGATACATACTT
1 CATTGTATCGATACATGCTT
*
82743 AATTGTATCGATACATG
1 CATTGTATCGATACATG
82760 AAACTGGTAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (20 bp):
CATTGTATCGATACATGCTT
Found at i:90209 original size:23 final size:26
Alignment explanation
Indices: 90179--90234 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 26
90169 AATTATATAT
90179 ATTAAAAT-TATGTTCATAA-A-TAA
1 ATTAAAATATATGTTCATAATATTAA
* *
90202 ATTAAAATATATTTTTATAATATTAA
1 ATTAAAATATATGTTCATAATATTAA
90228 ATTAAAA
1 ATTAAAA
90235 ATAATTAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 8 0.29
24 9 0.32
25 1 0.04
26 10 0.36
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAAAATATATGTTCATAATATTAA
Found at i:91376 original size:16 final size:17
Alignment explanation
Indices: 91353--91406 Score: 67
Period size: 16 Copynumber: 3.2 Consensus size: 17
91343 TATATAAATA
91353 TCAATATAAAATAATTT
1 TCAATATAAAATAATTT
*
91370 T-AATATATAAT-ATTT
1 TCAATATAAAATAATTT
91385 TCAATAATAAAATAGATTT
1 TCAAT-ATAAAATA-ATTT
91404 TCA
1 TCA
91407 GATCCAACGG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
15 5 0.16
16 12 0.39
17 7 0.23
19 7 0.23
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.43
Consensus pattern (17 bp):
TCAATATAAAATAATTT
Found at i:91376 original size:30 final size:34
Alignment explanation
Indices: 91341--91404 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 34
91331 TTATTATGAA
91341 AATATATAA-A-TATCAAT-ATAAAATA-ATTTT
1 AATATATAATATTATCAATAATAAAATAGATTTT
*
91371 AATATATAATATTTTCAATAATAAAATAGATTTT
1 AATATATAATATTATCAATAATAAAATAGATTTT
91405 CAGATCCAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
30 9 0.31
31 1 0.03
32 6 0.21
33 8 0.28
34 5 0.17
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.42
Consensus pattern (34 bp):
AATATATAATATTATCAATAATAAAATAGATTTT
Found at i:92200 original size:26 final size:25
Alignment explanation
Indices: 92143--92202 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
92133 TATAGTTATA
* * *
92143 AATATAATAAATATTTATTATGATT
1 AATATTATAAATATTAATTATAATT
92168 AATTATTATAAATATTAATTATAATGT
1 AA-TATTATAAATATTAATTATAAT-T
*
92195 TATATTAT
1 AATATTAT
92203 GATTGTTATT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 2 0.07
26 25 0.86
27 2 0.07
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (25 bp):
AATATTATAAATATTAATTATAATT
Found at i:94469 original size:20 final size:19
Alignment explanation
Indices: 94444--94494 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
94434 CTATTTTTTC
94444 ATATTATA-ATAATATTTAAA
1 ATATTATATAT-ATATTT-AA
*
94464 ATATTATATATTTATTTAA
1 ATATTATATATATATTTAA
94483 ATATTA-ATATAT
1 ATATTATATATAT
94495 TAATAATTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 5 0.18
19 8 0.29
20 13 0.46
21 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (19 bp):
ATATTATATATATATTTAA
Found at i:94495 original size:20 final size:20
Alignment explanation
Indices: 94456--94495 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
94446 ATTATAATAA
94456 TATTTAAAATATTATATATT
1 TATTTAAAATATTATATATT
94476 TATTT-AAATATTAATATATT
1 TATTTAAAATATT-ATATATT
94496 AATAATTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 12 0.63
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TATTTAAAATATTATATATT
Done.