Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2379
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: 32268
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.37
Found at i:79 original size:2 final size:2
Alignment explanation
Indices: 72--111 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
62 TGTAACCAAA
72 AG AG AG AG AG AG AG AG AG AG AG -G AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
112 ATTTACCTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 36 0.97
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:816 original size:16 final size:16
Alignment explanation
Indices: 773--827 Score: 60
Period size: 16 Copynumber: 3.5 Consensus size: 16
763 ATAATATTTA
*
773 ATTTATTTTTATATATT
1 ATTTATTTTTA-AAATT
*
790 -TTT-TATTTAAAATT
1 ATTTATTTTTAAAATT
*
804 ATTTATTTTTAAAAAT
1 ATTTATTTTTAAAATT
820 ATTTATTT
1 ATTTATTT
828 AATATTTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
14 4 0.12
15 8 0.25
16 20 0.62
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
ATTTATTTTTAAAATT
Found at i:1182 original size:20 final size:20
Alignment explanation
Indices: 1157--1251 Score: 78
Period size: 20 Copynumber: 5.0 Consensus size: 20
1147 AATTAATACA
1157 ATATAAATATATTAAATTTT
1 ATATAAATATATTAAATTTT
1177 ATATAAATAT-TT-AATATTT
1 ATATAAATATATTAAAT-TTT
1196 -T-TAAATATATTATAATATTT
1 ATATAAATATATTA-AAT-TTT
* **
1216 A-A-AAATATATTATATAAT
1 ATATAAATATATTAAATTTT
*
1234 ATAAAAAT-TATTAAATTT
1 ATATAAATATATTAAATTT
1252 AATTTTTTTA
Statistics
Matches: 61, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
17 7 0.11
18 8 0.13
19 15 0.25
20 31 0.51
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATATAAATATATTAAATTTT
Found at i:1304 original size:2 final size:2
Alignment explanation
Indices: 1293--1321 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
1283 CAGGGAGATC
1293 AT AT -T 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
1322 TCCAAACCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:1518 original size:15 final size:16
Alignment explanation
Indices: 1494--1528 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
1484 TAAAAAAAAA
1494 TTAATAAATTT-ATAT
1 TTAATAAATTTGATAT
*
1509 TTAATTAATTTGATAT
1 TTAATAAATTTGATAT
1525 TTAA
1 TTAA
1529 ATTATTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTAATAAATTTGATAT
Found at i:1593 original size:21 final size:21
Alignment explanation
Indices: 1569--1608 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
1559 ATTTTTTAAT
1569 TAATA-TTTATATAAATAAAAA
1 TAATATTTTA-ATAAATAAAAA
1590 TAATATTTTAATAAATAAA
1 TAATATTTTAATAAATAAA
1609 TAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAATATTTTAATAAATAAAAA
Found at i:1943 original size:3 final size:3
Alignment explanation
Indices: 1935--1965 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
1925 AACTAAACTT
1935 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1966 ATTTACAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:2478 original size:13 final size:13
Alignment explanation
Indices: 2462--2509 Score: 55
Period size: 13 Copynumber: 3.7 Consensus size: 13
2452 ATAAAATTAC
*
2462 AAAAATTAATTTT
1 AAAAAATAATTTT
2475 AAAAAAT-ATATTT
1 AAAAAATAAT-TTT
2488 AAAAAAT-ATATTT
1 AAAAAATAAT-TTT
2501 AAAAAATAA
1 AAAAAATAA
2510 AAGTGTATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
12 2 0.06
13 29 0.91
14 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AAAAAATAATTTT
Found at i:2496 original size:11 final size:13
Alignment explanation
Indices: 2472--2508 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
2462 AAAAATTAAT
2472 TTTAAAAAATATA
1 TTTAAAAAATATA
2485 TTTAAAAAATATA
1 TTTAAAAAATATA
2498 TTTAAAAAATA
1 TTTAAAAAATA
2509 AAAGTGTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAAAATATA
Found at i:2766 original size:17 final size:16
Alignment explanation
Indices: 2744--2781 Score: 58
Period size: 17 Copynumber: 2.3 Consensus size: 16
2734 TTAATATTTT
*
2744 ATTTAAATTTTATTCAA
1 ATTTAAATTTAATTC-A
2761 ATTTAAATTTAATTCA
1 ATTTAAATTTAATTCA
2777 ATTTA
1 ATTTA
2782 TGGATATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 6 0.30
17 14 0.70
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTAAATTTAATTCA
Found at i:3208 original size:13 final size:14
Alignment explanation
Indices: 3190--3219 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
3180 TTAAAAGATT
3190 AAAAAA-TTTATAA
1 AAAAAAGTTTATAA
3203 AAAAAAGTTTATAA
1 AAAAAAGTTTATAA
3217 AAA
1 AAA
3220 TTAAATAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (14 bp):
AAAAAAGTTTATAA
Found at i:3797 original size:14 final size:14
Alignment explanation
Indices: 3780--3812 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3770 TTTAAAGATA
3780 AAAAATTAT-TTTT
1 AAAAATTATGTTTT
*
3793 TAAAATTATGTTTT
1 AAAAATTATGTTTT
3807 AAAAAT
1 AAAAAT
3813 AATATTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
13 8 0.47
14 9 0.53
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (14 bp):
AAAAATTATGTTTT
Found at i:3799 original size:13 final size:13
Alignment explanation
Indices: 3781--3810 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
3771 TTAAAGATAA
*
3781 AAAATTATTTTTT
1 AAAATTATGTTTT
3794 AAAATTATGTTTT
1 AAAATTATGTTTT
3807 AAAA
1 AAAA
3811 ATAATATTCA
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:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (13 bp):
AAAATTATGTTTT
Found at i:4010 original size:3 final size:3
Alignment explanation
Indices: 4002--4039 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
3992 TGCATTTTTC
4002 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
4040 ACTTGCTTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:6119 original size:2 final size:2
Alignment explanation
Indices: 6112--6145 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
6102 GCATGATTAC
6112 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
6146 GACACTTGCA
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:10923 original size:13 final size:14
Alignment explanation
Indices: 10905--10943 Score: 53
Period size: 13 Copynumber: 2.7 Consensus size: 14
10895 GAACGTGGAT
10905 AATTTAAAAAAAA-
1 AATTTAAAAAAAAC
10918 AATTTAAAAGAAAAC
1 AATTTAAAA-AAAAC
10933 AATTTACAAAA
1 AATTTA-AAAA
10944 GATAGATTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 9 0.39
14 4 0.17
15 7 0.30
16 3 0.13
ACGTcount: A:0.69, C:0.05, G:0.03, T:0.23
Consensus pattern (14 bp):
AATTTAAAAAAAAC
Found at i:11124 original size:2 final size:2
Alignment explanation
Indices: 11113--11142 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
11103 TCAAATGTTG
11113 AT AT -T 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 AT A
11143 GGAAGAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12308 original size:19 final size:21
Alignment explanation
Indices: 12274--12321 Score: 64
Period size: 19 Copynumber: 2.4 Consensus size: 21
12264 TATTTAATAT
12274 ATTTAATAATAAAAAAATCGA
1 ATTTAATAATAAAAAAATCGA
*
12295 ATTT-ATAA-AAAAAAATTGA
1 ATTTAATAATAAAAAAATCGA
*
12314 ATTCAATA
1 ATTTAATA
12322 TTTCATTTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 13 0.54
20 7 0.29
21 4 0.17
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (21 bp):
ATTTAATAATAAAAAAATCGA
Found at i:14918 original size:3 final size:3
Alignment explanation
Indices: 14910--14938 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
14900 TGTTTCTTTA
14910 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
14939 TTTTATAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:17543 original size:22 final size:22
Alignment explanation
Indices: 17518--17560 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
17508 GGTATTTATA
*
17518 TGACTTTTCCTCTTGTATGGCT
1 TGACTTTTCCTCATGTATGGCT
17540 TGACTTTTCCTCATGTATGGC
1 TGACTTTTCCTCATGTATGGC
17561 ATGTGCACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.47
Consensus pattern (22 bp):
TGACTTTTCCTCATGTATGGCT
Found at i:18521 original size:13 final size:13
Alignment explanation
Indices: 18505--18535 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
18495 TATATTTATA
18505 ATATTCATATTTG
1 ATATTCATATTTG
*
18518 ATATTCATTTTTG
1 ATATTCATATTTG
18531 ATATT
1 ATATT
18536 TTAAAAATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (13 bp):
ATATTCATATTTG
Found at i:18762 original size:11 final size:11
Alignment explanation
Indices: 18726--18820 Score: 69
Period size: 11 Copynumber: 9.0 Consensus size: 11
18716 CGACACAATT
18726 ATAATAT-AAA
1 ATAATATAAAA
18736 A-AAT-TAAAA
1 ATAATATAAAA
18745 TATAATATAAAA
1 -ATAATATAAAA
*
18757 ATAATA-AAAT
1 ATAATATAAAA
18767 AT-A-ATAAAA
1 ATAATATAAAA
**
18776 ATATATATAATC
1 ATA-ATATAAAA
*
18788 ATAATAAAAAA
1 ATAATATAAAA
18799 ATAAT-TAAAAA
1 ATAATAT-AAAA
*
18810 ATAATGTAAAA
1 ATAATATAAAA
18821 TTTTATTTGA
Statistics
Matches: 67, Mismatches: 8, Indels: 19
0.71 0.09 0.20
Matches are distributed among these distances:
8 2 0.03
9 12 0.18
10 7 0.10
11 33 0.49
12 13 0.19
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (11 bp):
ATAATATAAAA
Found at i:18764 original size:21 final size:21
Alignment explanation
Indices: 18725--18820 Score: 99
Period size: 20 Copynumber: 4.6 Consensus size: 21
18715 ACGACACAAT
*
18725 TATAATATAAAAA-ATTAAAA
1 TATAATATAAAAATAATAAAA
18745 TATAATATAAAAATAATAAAA
1 TATAATATAAAAATAATAAAA
*
18766 TAT-A-ATAAAAATATATATAA
1 TATAATATAAAAATA-ATAAAA
*
18786 TCATAATAAAAAAATAATTAAAA
1 T-ATAATATAAAAATAA-TAAAA
* *
18809 AATAATGTAAAA
1 TATAATATAAAA
18821 TTTTATTTGA
Statistics
Matches: 63, Mismatches: 7, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
19 9 0.14
20 20 0.32
21 11 0.17
22 11 0.17
23 12 0.19
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (21 bp):
TATAATATAAAAATAATAAAA
Found at i:18810 original size:34 final size:32
Alignment explanation
Indices: 18726--18820 Score: 97
Period size: 31 Copynumber: 3.0 Consensus size: 32
18716 CGACACAATT
* *
18726 ATAATATAAAA-AATTAAAATATAATATAAAA
1 ATAATAAAAAATAATTAAAAAATAATATAAAA
* **
18757 ATAATAAAATATAA-T-AAAAATATATATAATC
1 ATAATAAAAAATAATTAAAAAATA-ATATAAAA
*
18788 ATAATAAAAAAATAATTAAAAAATAATGTAAAA
1 ATAAT-AAAAAATAATTAAAAAATAATATAAAA
18821 TTTTATTTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
30 6 0.12
31 21 0.42
32 10 0.20
33 6 0.12
34 7 0.14
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.28
Consensus pattern (32 bp):
ATAATAAAAAATAATTAAAAAATAATATAAAA
Found at i:18900 original size:32 final size:33
Alignment explanation
Indices: 18864--18926 Score: 92
Period size: 32 Copynumber: 1.9 Consensus size: 33
18854 AGAGAAATAT
* *
18864 ATTAATATTTTAAAATTTATAT-AATATAAATC
1 ATTAACATATTAAAATTTATATAAATATAAATC
*
18896 ATTAACGTATTAAAATTTATATAAATATAAA
1 ATTAACATATTAAAATTTATATAAATATAAA
18927 ATATTTTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
32 19 0.70
33 8 0.30
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (33 bp):
ATTAACATATTAAAATTTATATAAATATAAATC
Found at i:18947 original size:22 final size:19
Alignment explanation
Indices: 18926--18965 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
18916 ATAAATATAA
*
18926 AATATTTTAAATATAATCAT
1 AATATTTAAAATATAAT-AT
18946 AATATTTAAAATAT-ATAT
1 AATATTTAAAATATAATAT
18964 AA
1 AA
18966 GATATAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 4 0.21
19 2 0.11
20 13 0.68
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (19 bp):
AATATTTAAAATATAATAT
Found at i:18970 original size:20 final size:19
Alignment explanation
Indices: 18920--18970 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 19
18910 ATTTATATAA
*
18920 ATATA-AAATATTTTAAAT
1 ATATATAAATATTTAAAAT
18938 ATA-ATCATAATATTTAAAAT
1 ATATAT-A-AATATTTAAAAT
18958 ATATATAAGATAT
1 ATATATAA-ATAT
18971 AAATATATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 1 0.04
18 3 0.11
19 2 0.07
20 19 0.70
21 2 0.07
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (19 bp):
ATATATAAATATTTAAAAT
Found at i:18999 original size:46 final size:46
Alignment explanation
Indices: 18874--18980 Score: 119
Period size: 46 Copynumber: 2.2 Consensus size: 46
18864 ATTAATATTT
*
18874 TAAAAT-TTATATAATATAAATCATTAACGTA-TTAAAATTTATATAAATA
1 TAAAATATTATA-AATAT-AATCA-TAA--TATTTAAAATATATATAAATA
*
18923 TAAAATATTTTAAATATAATCATAATATTTAAAATATATATAAGATA
1 TAAAATATTATAAATATAATCATAATATTTAAAATATATATAA-ATA
18970 TAAATATATTA
1 TAAA-ATATTA
18981 ATAATTTAAT
Statistics
Matches: 51, Mismatches: 3, Indels: 9
0.81 0.05 0.14
Matches are distributed among these distances:
45 2 0.04
46 14 0.27
47 10 0.20
48 10 0.20
49 11 0.22
50 4 0.08
ACGTcount: A:0.54, C:0.03, G:0.02, T:0.41
Consensus pattern (46 bp):
TAAAATATTATAAATATAATCATAATATTTAAAATATATATAAATA
Found at i:19882 original size:2 final size:2
Alignment explanation
Indices: 19875--19902 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
19865 TCTCAACCTC
19875 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
19903 CACACACAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20154 original size:32 final size:32
Alignment explanation
Indices: 20102--20183 Score: 87
Period size: 32 Copynumber: 2.6 Consensus size: 32
20092 ATAATTAAAT
*
20102 TTAAAAATTATATATTTATATAAATTTTAATACA
1 TTAATAATT-TAT-TTTATATAAATTTTAATACA
* * *
20136 TTAATAATTTATTTTATATAATTTTTTATATA
1 TTAATAATTTATTTTATATAAATTTTAATACA
*
20168 TTTAT-A-TTATTTTATA
1 TTAATAATTTATTTTATA
20184 ATTTATATCC
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
30 10 0.23
31 1 0.02
32 21 0.49
33 3 0.07
34 8 0.19
ACGTcount: A:0.41, C:0.01, G:0.00, T:0.57
Consensus pattern (32 bp):
TTAATAATTTATTTTATATAAATTTTAATACA
Found at i:20197 original size:17 final size:18
Alignment explanation
Indices: 20159--20200 Score: 59
Period size: 17 Copynumber: 2.4 Consensus size: 18
20149 TTATATAATT
*
20159 TTTTATATATTTATATTA
1 TTTTATATATTTATATCA
*
20177 TTTTATA-ATTTATATCC
1 TTTTATATATTTATATCA
20194 TTTTATA
1 TTTTATA
20201 GAGGCTGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTTATATATTTATATCA
Found at i:20607 original size:19 final size:19
Alignment explanation
Indices: 20583--20622 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
20573 AAATATTAAA
*
20583 AATATTT-TATATTAATATT
1 AATATTTATA-ATTAAAATT
20602 AATATTTATAATTAAAATT
1 AATATTTATAATTAAAATT
20621 AA
1 AA
20623 ATAAAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTTATAATTAAAATT
Found at i:23292 original size:14 final size:13
Alignment explanation
Indices: 23260--23303 Score: 63
Period size: 14 Copynumber: 3.3 Consensus size: 13
23250 GTCAGACGTG
23260 AATAATTTAAAAA
1 AATAATTTAAAAA
23273 AA-AATTTAAGAAA
1 AATAATTTAA-AAA
23286 AATAATTTACAAAA
1 AATAATTTA-AAAA
23300 AATA
1 AATA
23304 GATTCTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
12 7 0.25
13 7 0.25
14 13 0.46
15 1 0.04
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.27
Consensus pattern (13 bp):
AATAATTTAAAAA
Found at i:23472 original size:2 final size:2
Alignment explanation
Indices: 23461--23496 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
23451 TCAGATGTTG
23461 AT AT -T AT 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 AT AT AT AT A
23497 GAGGAAGAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24382 original size:20 final size:19
Alignment explanation
Indices: 24353--24398 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
24343 AATAATTTAA
* *
24353 ATTCATATCAATTAAAATTT
1 ATTCAAATCAAAT-AAATTT
24373 ATTCAAATCAAATAAATTT
1 ATTCAAATCAAATAAATTT
24392 -TTCAAAT
1 ATTCAAAT
24399 TTAAGTTACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.29
19 6 0.25
20 11 0.46
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (19 bp):
ATTCAAATCAAATAAATTT
Found at i:24918 original size:16 final size:18
Alignment explanation
Indices: 24897--24929 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
24887 TAATAAAATC
24897 ATAATG-AAAAA-AATTA
1 ATAATGCAAAAACAATTA
24913 ATAATGCAAAAACAATT
1 ATAATGCAAAAACAATT
24930 GGTAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 5 0.33
18 4 0.27
ACGTcount: A:0.64, C:0.06, G:0.06, T:0.24
Consensus pattern (18 bp):
ATAATGCAAAAACAATTA
Found at i:29878 original size:22 final size:22
Alignment explanation
Indices: 29853--29895 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
29843 GGTATTTATA
*
29853 TGACTTTTCCTCTTGTATGGCT
1 TGACTTTTCCTCATGTATGGCT
29875 TGACTTTTCCTCATGTATGGC
1 TGACTTTTCCTCATGTATGGC
29896 ATGTGCACGG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.47
Consensus pattern (22 bp):
TGACTTTTCCTCATGTATGGCT
Found at i:30160 original size:54 final size:54
Alignment explanation
Indices: 30078--30185 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
30068 TGCTGCCTTA
*
30078 GTCATTATCCTGATCAAGTGGTGACTATTGCCTGCAACAAATAGCTCTGAAACC
1 GTCATTATCCTGATCAAGTGGTGACTATTGCCTGCAACAAATAGCTCAGAAACC
30132 GTCATTATCCTGATCAAGTGGTGACTATTGCCTGCAACAAATAGCTCAGAAACC
1 GTCATTATCCTGATCAAGTGGTGACTATTGCCTGCAACAAATAGCTCAGAAACC
30186 ATCAGTTGTG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.27
Consensus pattern (54 bp):
GTCATTATCCTGATCAAGTGGTGACTATTGCCTGCAACAAATAGCTCAGAAACC
Found at i:30805 original size:19 final size:20
Alignment explanation
Indices: 30766--30806 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
30756 AAGGTCATAT
*
30766 TTTATATAATATAGTATTATC
1 TTTATATAATATA-TAGTATC
30787 TTTATATAATAT-TAGTATC
1 TTTATATAATATATAGTATC
30806 T
1 T
30807 GAAAATGTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
21 12 0.63
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTATATAATATATAGTATC
Found at i:31222 original size:18 final size:18
Alignment explanation
Indices: 31178--31243 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
31168 TAACAATTAT
31178 AATATAA-AAAATT-A-A
1 AATATAATAAAATTAATA
31193 AATATGATATAAAATTAATA
1 AATAT-A-ATAAAATTAATA
*
31213 AATATAATAAAAATATATA
1 AATATAATAAAATTA-ATA
31232 TAATCATAATAA
1 -AAT-ATAATAA
31244 TAAAATAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 10
0.79 0.02 0.19
Matches are distributed among these distances:
15 5 0.12
16 1 0.02
17 1 0.02
18 14 0.33
19 5 0.12
20 9 0.21
21 7 0.17
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (18 bp):
AATATAATAAAATTAATA
Found at i:31370 original size:17 final size:17
Alignment explanation
Indices: 31341--31398 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
31331 CGCCGTACGT
31341 TAAA-ATTTATATAACTA
1 TAAATATTT-TATAACTA
*
31358 TAAATATTTTATATCTCA
1 TAAATATTTTATAACT-A
*
31376 T-AATATTTTA-AAATA
1 TAAATATTTTATAACTA
*
31391 TAGATATT
1 TAAATATT
31399 AACACACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
15 2 0.06
16 7 0.21
17 19 0.56
18 6 0.18
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (17 bp):
TAAATATTTTATAACTA
Found at i:32115 original size:15 final size:15
Alignment explanation
Indices: 32095--32126 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
32085 CCAAATTGCT
32095 AAAAATAAAAAAATA
1 AAAAATAAAAAAATA
*
32110 AAAAATAAATAAATA
1 AAAAATAAAAAAATA
32125 AA
1 AA
32127 GTAAATGGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (15 bp):
AAAAATAAAAAAATA
Done.