Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold1005
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: 71697
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Found at i:1755 original size:31 final size:30
Alignment explanation
Indices: 1719--1780 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 30
1709 CGATATTTAT
1719 ATTATTATT-TAAAATAATATTAAAAATTAAA
1 ATTATT-TTATAAAA-AATATTAAAAATTAAA
* *
1750 ATTATTTTGATATAAAATATTTAAAATTAAA
1 ATTATTTT-ATAAAAAATATTAAAAATTAAA
1781 TTTAAATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 2 0.07
31 21 0.78
32 4 0.15
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.44
Consensus pattern (30 bp):
ATTATTTTATAAAAAATATTAAAAATTAAA
Found at i:3383 original size:26 final size:27
Alignment explanation
Indices: 3353--3414 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
3343 CTCAAATTAA
3353 ATTAAAGT-CACAC-AAAATATCTTTAC
1 ATTAAA-TACACACAAAAATATCTTTAC
3379 ATT-AATACACACTAAAAATATCTTTAC
1 ATTAAATACACAC-AAAAATATCTTTAC
3406 ATT-AATACA
1 ATTAAATACA
3415 TTTAATGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
24 1 0.03
25 7 0.21
26 3 0.09
27 22 0.67
ACGTcount: A:0.48, C:0.18, G:0.02, T:0.32
Consensus pattern (27 bp):
ATTAAATACACACAAAAATATCTTTAC
Found at i:3390 original size:25 final size:26
Alignment explanation
Indices: 3361--3414 Score: 92
Period size: 27 Copynumber: 2.1 Consensus size: 26
3351 AAATTAAAGT
3361 CACAC-AAAATATCTTTACATTAATA
1 CACACAAAAATATCTTTACATTAATA
3386 CACACTAAAAATATCTTTACATTAATA
1 CACAC-AAAAATATCTTTACATTAATA
3413 CA
1 CA
3415 TTTAATGTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.19
27 22 0.81
ACGTcount: A:0.48, C:0.20, G:0.00, T:0.31
Consensus pattern (26 bp):
CACACAAAAATATCTTTACATTAATA
Found at i:8033 original size:2 final size:2
Alignment explanation
Indices: 8026--8052 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8016 ATTTTATAAC
8026 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8053 TGAATAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9176 original size:18 final size:17
Alignment explanation
Indices: 9151--9184 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
9141 AATTTAATTT
*
9151 AAATTATTTAATTAATC
1 AAATTATTAAATTAATC
9168 AAATCTATTAAATTAAT
1 AAAT-TATTAAATTAAT
9185 AACTTAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (17 bp):
AAATTATTAAATTAATC
Found at i:9515 original size:2 final size:2
Alignment explanation
Indices: 9504--9538 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9494 CAAATTGAAA
9504 AT AT -T 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
9539 GCATACCTAC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:9904 original size:30 final size:28
Alignment explanation
Indices: 9850--9905 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
9840 AATTTTAATA
9850 TTTATAATTAAATATAAATAAAATTATT
1 TTTATAATTAAATATAAATAAAATTATT
* *
9878 TTTATTATATAAATAGTAATTAAAATTA
1 TTTATAAT-TAAATA-TAAATAAAATTA
9906 CTCTTAACTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 7 0.29
29 6 0.25
30 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.46
Consensus pattern (28 bp):
TTTATAATTAAATATAAATAAAATTATT
Found at i:10440 original size:19 final size:18
Alignment explanation
Indices: 10405--10463 Score: 66
Period size: 19 Copynumber: 3.2 Consensus size: 18
10395 ACTATAATTA
10405 ATATTTTATAATT-TATTT
1 ATATTTT-TAATTATATTT
10423 ATATTTTTAATTAATATTT
1 ATATTTTTAATT-ATATTT
**
10442 ATTATAATTAATTATATTT
1 A-TATTTTTAATTATATTT
10461 ATA
1 ATA
10464 ATTATAATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
17 5 0.14
18 9 0.25
19 13 0.36
20 9 0.25
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
ATATTTTTAATTATATTT
Found at i:10451 original size:16 final size:16
Alignment explanation
Indices: 10397--10467 Score: 67
Period size: 16 Copynumber: 4.5 Consensus size: 16
10387 AATATAATAC
*
10397 TATAATTAA-TAT-TT
1 TATAATTAATTTTATT
*
10411 TATAATTTATTTATATT
1 TATAATTAATTT-TATT
*
10428 TTTAATTAATATTTA-T
1 TATAATTAAT-TTTATT
*
10444 TATAATTAATTATATT
1 TATAATTAATTTTATT
10460 TATAATTA
1 TATAATTA
10468 TAATAAATAT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
14 8 0.17
15 4 0.09
16 20 0.43
17 12 0.26
18 2 0.04
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TATAATTAATTTTATT
Found at i:13796 original size:16 final size:17
Alignment explanation
Indices: 13761--13798 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
13751 TTTTTATCTT
*
13761 TAAATATATATTAAATA
1 TAAATATATATTAAAAA
*
13778 TAAATAT-TTTTAAAAA
1 TAAATATATATTAAAAA
13794 TAAAT
1 TAAAT
13799 GATCGGTGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAATATATATTAAAAA
Found at i:15918 original size:21 final size:22
Alignment explanation
Indices: 15877--15919 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
15867 TTGATTTAAA
15877 ATTTAAAAGTTTAAATTAATTT
1 ATTTAAAAGTTTAAATTAATTT
15899 ATTT-AAA-TTTAAATTTAATTT
1 ATTTAAAAGTTTAAA-TTAATTT
15920 GCTTTAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.30
21 10 0.50
22 4 0.20
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
ATTTAAAAGTTTAAATTAATTT
Found at i:16007 original size:16 final size:16
Alignment explanation
Indices: 15996--16026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15986 TCTAAAATGA
15996 TTTAAACTTAAAATAG
1 TTTAAACTTAAAATAG
*
16012 TTTTAACTTAAAATA
1 TTTAAACTTAAAATA
16027 ACTCAAACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (16 bp):
TTTAAACTTAAAATAG
Found at i:16760 original size:21 final size:21
Alignment explanation
Indices: 16736--16778 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
16726 TTGATTTGAA
*
16736 TATTAAAAATTTTAA-TTAATT
1 TATT-AAAATTTAAATTTAATT
*
16757 TATTTAAATTTAAATTTAATT
1 TATTAAAATTTAAATTTAATT
16778 T
1 T
16779 GATTTGATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (21 bp):
TATTAAAATTTAAATTTAATT
Found at i:16940 original size:430 final size:427
Alignment explanation
Indices: 15759--17027 Score: 1640
Period size: 429 Copynumber: 3.0 Consensus size: 427
15749 ATCAATTGCG
* *** * *
15759 AAGAATAAAATTACAAATGATGTCACGTAGTATTTTAATAGCCCAAACAATAAAAAAGATTTCAT
1 AAGAATAAAATTACATATGATGTCACG--G-ATTACGATAGCCTAAACAGTAAAAAAGATTTCAT
* * * * *
15824 TTCAGTAATGATGTACCATGGCTTTTTTTAAAGTAGGATAAA-CTTGATTT-AAAATTTAAAAGT
63 TTAAGTAATGATGTACCA-GGCTTTTTTT-AAGAAGG-TAAATTTTGATTTGAATA-TTAAAAAT
* * * *
15887 TTAAATTAATTTATTTAAATTTAAATTTAATTTGCTTTAATTAGAAAAGTTAACAATTTAAAATT
124 TTAAATTAATTTATTTAAATTTAAATTTAATTTGATTTGATTAGAAAAGTTAATAATTCAAAATT
* * *
15952 AATTAAATTAAATTTAAATTTAAAATGACTCATATCTAAAATGATTTAAACTTAAAATAGTTTTA
189 AATTAAATTAAATTTAAATTTAAAATGACTCATATCTAAAATGATTTGAACTTGAAATAGTTTAA
* * ** * * *
16017 ACTTAAAATAACTCAAACTCGAATTAATCTGAACAATTAACTGAAATGACTCAAATCTAAATTA-
254 ACTTAAAACAACTCAAACTCGAATTGATCTGAACAATTAACCAAAATAACTCAAATCAAAATGAC
* * * *
16081 TGAAACCTGATGAACTTAAATATTAAATCTAATTGACTTGAAACTGATTAATTTCAATACTAAAC
319 T-AAACCTGATGAACCTAAATATTAAATCTAATTGACTTGAAACTGATTAATTTGAGTATTAAAC
* *
16146 TCAATTGACTTAAACTTGAAATAACATAAAAGCATTTTTGTTTAC
383 TCAATTGACCTAAACTTGAAATAACATAAAAACATTTTTGTTTAC
* * *
16191 AAGAATAAAATTACATATGATGTCACGTACTACGATAGCCTAAACAGTAAAAAAAAATTT-ATTT
1 AAGAATAAAATTACATATGATGTCACGGATTACGATAGCCTAAACAGT-AAAAAAGATTTCATTT
* ** * *
16255 TAGTAATGATGTACCATTCTTTTTCTTAAGTAAGGTAAATTTTGATTTGAATTTTAAAAATTTGA
65 AAGTAATGATGTACCAGGCTTTTT-TTAAG-AAGGTAAATTTTGATTTGAATATTAAAAATTTAA
16320 ATTAATTTATTTAAATTTAAATTTAATTTGATTTGATTAGAAAAGTTAATAATTCAAAATTAATT
128 ATTAATTTATTTAAATTTAAATTTAATTTGATTTGATTAGAAAAGTTAATAATTCAAAATTAATT
*
16385 AAATTAAATTTAAGTTTAAAATGACTCATATCTAAAATGATTTGAACTTGAAATAGTTTAAACTT
193 AAATTAAATTTAAATTTAAAATGACTCATATCTAAAATGATTTGAACTTGAAATAGTTTAAACTT
* * * *
16450 AAAACAACTCAAATTTGAATTGATCTGAACAATTAATCAAAATGAA-TCAAAACAAAATGACTAA
258 AAAACAACTCAAACTCGAATTGATCTGAACAATTAACCAAAAT-AACTCAAATCAAAATGACTAA
*
16514 ACCTGATGAACCTAAATATTAAATCTAATGGACTTGAAACTGATTAATTTGAGTATTAAACTCAA
322 ACCTGATGAACCTAAATATTAAATCTAATTGACTTGAAACTGATTAATTTGAGTATTAAACTCAA
*
16579 TTGACCTAAA-TATGAAATAACATAAAAATATTTTTGTTTAC
387 TTGACCTAAACT-TGAAATAACATAAAAACATTTTTGTTTAC
* *
16620 AAGAATAAAATTACATATGATGTCACGGATTACGATAGTCTAAACAGTAAGAAAGATTTCATTTA
1 AAGAATAAAATTACATATGATGTCACGGATTACGATAGCCTAAACAGTAAAAAAGATTTCATTTA
* *
16685 AGTAAAGATGTACCAGGACCTTTTTTTAAGCAAGGTAAATTTTGATTTGAATATTAAAAATTTTA
66 AGTAATGATGTACCAGG--CTTTTTTTAAG-AAGGTAAATTTTGATTTGAATATTAAAAATTTAA
* ** * *
16750 ATTAATTTATTTAAATTTAAATTTAATTTGATTTGATTAAAAAAGTTAATAGCTCGAAATTGATT
128 ATTAATTTATTTAAATTTAAATTTAATTTGATTTGATTAGAAAAGTTAATAATTCAAAATTAATT
* * * * *
16815 AAATCAAATTTAAATTTAAAATAATTCATAT-TCAAAATGATTTGAATTTGAAATAGTTTGAACT
193 AAATTAAATTTAAATTTAAAATGACTCATATCT-AAAATGATTTGAACTTGAAATAGTTTAAACT
* * * *
16879 TTAAACAACTCAAACTCGAATTGATTTGAATAATTAACCAAAATAACTCCAATTC-AAATGACTA
257 TAAAACAACTCAAACTCGAATTGATCTGAACAATTAACCAAAATAACT-CAAATCAAAATGACTA
* * * * * * *
16943 AA-TTCGATGAATCTAAGTATTAAACCTAATTGACCTGAAACT-AATAACTTGAGTATTAAACTC
321 AACCT-GATGAACCTAAATATTAAATCTAATTGACTTGAAACTGATTAATTTGAGTATTAAACTC
* *
17006 AATTGACTTGAACTTGAAATAA
385 AATTGACCTAAACTTGAAATAA
17028 TCTGAACTCA
Statistics
Matches: 735, Mismatches: 86, Indels: 35
0.86 0.10 0.04
Matches are distributed among these distances:
428 23 0.03
429 426 0.58
430 250 0.34
431 10 0.01
432 26 0.04
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (427 bp):
AAGAATAAAATTACATATGATGTCACGGATTACGATAGCCTAAACAGTAAAAAAGATTTCATTTA
AGTAATGATGTACCAGGCTTTTTTTAAGAAGGTAAATTTTGATTTGAATATTAAAAATTTAAATT
AATTTATTTAAATTTAAATTTAATTTGATTTGATTAGAAAAGTTAATAATTCAAAATTAATTAAA
TTAAATTTAAATTTAAAATGACTCATATCTAAAATGATTTGAACTTGAAATAGTTTAAACTTAAA
ACAACTCAAACTCGAATTGATCTGAACAATTAACCAAAATAACTCAAATCAAAATGACTAAACCT
GATGAACCTAAATATTAAATCTAATTGACTTGAAACTGATTAATTTGAGTATTAAACTCAATTGA
CCTAAACTTGAAATAACATAAAAACATTTTTGTTTAC
Found at i:24953 original size:34 final size:34
Alignment explanation
Indices: 24907--25158 Score: 332
Period size: 34 Copynumber: 7.5 Consensus size: 34
24897 GTAAAAACCA
*
24907 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
24941 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
24975 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
25009 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
25043 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
25076 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
25110 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
25143 CCATTTAATCAACAAT
1 CCATTTAATCAACAAT
25159 TCTCCCACTT
Statistics
Matches: 196, Mismatches: 17, Indels: 11
0.88 0.08 0.05
Matches are distributed among these distances:
33 45 0.23
34 149 0.76
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:25116 original size:67 final size:68
Alignment explanation
Indices: 24907--25158 Score: 373
Period size: 68 Copynumber: 3.7 Consensus size: 68
24897 GTAAAAACCA
* * *
24907 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
24972 CAC
66 CAC
* *
24975 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
**
25040 TTC
66 CAC
* * *
25043 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
25107 CAC
66 CAC
* * *
25110 CCATTTAATCAACAATGGTAAACTACTAAATC-ACCATTTAATCAACAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAAT
25159 TCTCCCACTT
Statistics
Matches: 166, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
67 73 0.44
68 93 0.56
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
CAC
Found at i:29615 original size:34 final size:34
Alignment explanation
Indices: 29569--29818 Score: 328
Period size: 34 Copynumber: 7.4 Consensus size: 34
29559 GTAAAAACCA
*
29569 CCATTTAATCAACAATGGCAACCTACCAAATCTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
29603 CCATTTAGTCAACAATGGTAAGCC-ACCAAATCAC
1 CCATTTAATCAACAATGGTAA-CCTACCAAATCTC
* *
29637 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* *
29671 CCATTTAATCAACAATGGTAAGCTACCAAATTTC
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
*
29705 CCATTTAATCAACAATGGTAAGCTACCAAATCT-
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
* * *
29738 CCATTTAGTCAACAATGGCAAACC-ACCAAATCAC
1 CCATTTAATCAACAATGG-TAACCTACCAAATCTC
* * *
29772 CCATTTAATCAACAATGGTAAACTACTAAATC-A
1 CCATTTAATCAACAATGGTAACCTACCAAATCTC
29805 CCATTTAATCAACA
1 CCATTTAATCAACA
29819 GTGCATAATC
Statistics
Matches: 194, Mismatches: 17, Indels: 11
0.87 0.08 0.05
Matches are distributed among these distances:
33 43 0.22
34 149 0.77
35 2 0.01
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (34 bp):
CCATTTAATCAACAATGGTAACCTACCAAATCTC
Found at i:29778 original size:67 final size:68
Alignment explanation
Indices: 29569--29818 Score: 369
Period size: 68 Copynumber: 3.7 Consensus size: 68
29559 GTAAAAACCA
* * *
29569 CCATTTAATCAACAATGGCAACCTACCAAATCTCCCATTTAGTCAACAATGGTAAGCCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
29634 CAC
66 CAC
* *
29637 CCATTTAATCAACAATGGTAAGCTACCAAATTTCCCATTTAATCAACAATGGTAAGCTACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
**
29702 TTC
66 CAC
* * *
29705 CCATTTAATCAACAATGGTAAGCTACCAAATCT-CCATTTAGTCAACAATGGCAAACCACCAAAT
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
29769 CAC
66 CAC
* * *
29772 CCATTTAATCAACAATGGTAAACTACTAAATC-ACCATTTAATCAACA
1 CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACA
29819 GTGCATAATC
Statistics
Matches: 164, Mismatches: 17, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
67 71 0.43
68 93 0.57
ACGTcount: A:0.40, C:0.27, G:0.08, T:0.25
Consensus pattern (68 bp):
CCATTTAATCAACAATGGTAAGCTACCAAATCTCCCATTTAATCAACAATGGTAAGCCACCAAAT
CAC
Found at i:30453 original size:14 final size:14
Alignment explanation
Indices: 30396--30472 Score: 58
Period size: 13 Copynumber: 5.9 Consensus size: 14
30386 ATTAATATTT
*
30396 TAATAATTA-AATA
1 TAATAATTATAAAA
*
30409 TAATAAATAT-AAA
1 TAATAATTATAAAA
*
30422 TAATAA--A-AAAT
1 TAATAATTATAAAA
30433 TAA-AATTATAAAA
1 TAATAATTATAAAA
*
30446 TAATAATTATAATA
1 TAATAATTATAAAA
* *
30460 TTATAAATATAAA
1 TAATAATTATAAA
30473 TTTTCTTATG
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
10 2 0.04
11 6 0.12
12 1 0.02
13 22 0.44
14 19 0.38
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAATAATTATAAAA
Found at i:31379 original size:17 final size:17
Alignment explanation
Indices: 31357--31394 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
31347 TCAATGCTTA
31357 ATGTTAACATTGCAAAG
1 ATGTTAACATTGCAAAG
* *
31374 ATGTTAGCATTGTAAAG
1 ATGTTAACATTGCAAAG
31391 ATGT
1 ATGT
31395 GTCATGAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.37, C:0.08, G:0.21, T:0.34
Consensus pattern (17 bp):
ATGTTAACATTGCAAAG
Found at i:31579 original size:19 final size:18
Alignment explanation
Indices: 31551--31593 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 18
31541 ATAATGATTG
31551 TATTAATTTTT-TATATTT
1 TATT-ATTTTTATATATTT
*
31569 ATATTATTTTTATCTATTT
1 -TATTATTTTTATATATTT
31588 TATTAT
1 TATTAT
31594 ATTATAATTA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
TATTATTTTTATATATTT
Found at i:31628 original size:22 final size:24
Alignment explanation
Indices: 31595--31638 Score: 58
Period size: 22 Copynumber: 1.9 Consensus size: 24
31585 TTTTATTATA
31595 TTATAATTATAT-TTAA-AATATT
1 TTATAATTATATATTAATAATATT
31617 TTAT-ATTGATATATTAATAATA
1 TTATAATT-ATATATTAATAATA
31639 CATATTATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
21 3 0.16
22 8 0.42
23 4 0.21
24 4 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTATAATTATATATTAATAATATT
Found at i:32781 original size:7 final size:7
Alignment explanation
Indices: 32772--32803 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
32762 GTGAATTTCA
*
32772 AATTTTA
1 AATTTTG
32779 AATTTTG
1 AATTTTG
32786 AATTTTG
1 AATTTTG
32793 AATTTTG
1 AATTTTG
32800 AATT
1 AATT
32804 AATATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.56
Consensus pattern (7 bp):
AATTTTG
Found at i:35937 original size:17 final size:17
Alignment explanation
Indices: 35909--35980 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
35899 ATAATTAAAA
35909 TAAATTT-A-AATA-TT
1 TAAATTTAATAATATTT
35923 TAATATTTAATAATATTT
1 TAA-ATTTAATAATATTT
35941 TAAATTTAA-AA-ATTAT
1 TAAATTTAATAATATT-T
*
35957 ATAAATTT-TTAATATTT
1 -TAAATTTAATAATATTT
35974 T-AATTTA
1 TAAATTTA
35981 CGTAAATAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 16
0.74 0.02 0.25
Matches are distributed among these distances:
14 3 0.06
15 12 0.25
16 5 0.10
17 20 0.42
18 8 0.17
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TAAATTTAATAATATTT
Found at i:35945 original size:32 final size:33
Alignment explanation
Indices: 35909--35980 Score: 87
Period size: 32 Copynumber: 2.2 Consensus size: 33
35899 ATAATTAAAA
* *
35909 TAAATTTAAATATT-TA-ATATTTAATAATATTT
1 TAAATTTAAAAATTATATAAATTT-ATAATATTT
*
35941 TAAATTTAAAAATTATATAAATTTTTAATATTT
1 TAAATTTAAAAATTATATAAATTTATAATATTT
35974 T-AATTTA
1 TAAATTTA
35981 CGTAAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
32 19 0.54
33 11 0.31
34 5 0.14
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (33 bp):
TAAATTTAAAAATTATATAAATTTATAATATTT
Found at i:35964 original size:24 final size:24
Alignment explanation
Indices: 35907--35973 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
35897 ATATAATTAA
* * *
35907 AATAAATTTAAATATTTAATATTT
1 AATAAATTTTAATATTTAAAAATT
35931 AATAATATTTTAA-ATTTAAAAATT
1 AATAA-ATTTTAATATTTAAAAATT
35955 ATATAAATTTTTAATATTT
1 A-ATAAA-TTTTAATATTT
35974 TAATTTACGT
Statistics
Matches: 36, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 16 0.44
25 16 0.44
26 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (24 bp):
AATAAATTTTAATATTTAAAAATT
Found at i:39594 original size:23 final size:23
Alignment explanation
Indices: 39551--39594 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
39541 CAATATAATA
* *
39551 TTATATAAATATATTTTTTAAAT
1 TTATATAAATATAATTATTAAAT
39574 TTATAT-AATATAAATTATTAA
1 TTATATAAATAT-AATTATTAA
39595 TAAATTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATATAAATATAATTATTAAAT
Found at i:39610 original size:32 final size:29
Alignment explanation
Indices: 39570--39629 Score: 84
Period size: 32 Copynumber: 2.0 Consensus size: 29
39560 TATATTTTTT
39570 AAATTTATATAATATAAATTATTAATAAATTA
1 AAATTTATATAA-ATAAA-T-TTAATAAATTA
*
39602 AAATTTATATAAATATATTTAATAAATT
1 AAATTTATATAAATAAATTTAATAAATT
39630 TTATAAATAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 10 0.37
30 1 0.04
31 4 0.15
32 12 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAATTTATATAAATAAATTTAATAAATTA
Found at i:39613 original size:16 final size:17
Alignment explanation
Indices: 39570--39618 Score: 59
Period size: 16 Copynumber: 3.0 Consensus size: 17
39560 TATATTTTTT
39570 AAATTTATAT-AATATA
1 AAATTTATATAAATATA
*
39586 AATTATTA-ATAAAT-TA
1 AAAT-TTATATAAATATA
39602 AAATTTATATAAATATA
1 AAATTTATATAAATATA
39619 TTTAATAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
15 3 0.11
16 16 0.59
17 8 0.30
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
AAATTTATATAAATATA
Found at i:39892 original size:31 final size:31
Alignment explanation
Indices: 39827--39894 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
39817 AATATATATA
* *
39827 AATATATTAAATTTATATAATATGAATTATT
1 AATATATTAAATTTATATAATATGAATAAAT
*
39858 AATATATTAAAAATTTATATATTAT-AA-AAAT
1 AATATATT--AAATTTATATAATATGAATAAAT
39889 AATATA
1 AATATA
39895 AATACATGAA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
31 16 0.50
32 2 0.06
33 14 0.44
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (31 bp):
AATATATTAAATTTATATAATATGAATAAAT
Found at i:40721 original size:16 final size:17
Alignment explanation
Indices: 40686--40724 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
40676 ATAATATATT
40686 TAAATTATTTATATTCA
1 TAAATTATTTATATTCA
40703 TAAATTAATTTAT-TT-A
1 TAAATT-ATTTATATTCA
40719 TAAATT
1 TAAATT
40725 TTACAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.33
17 8 0.38
18 6 0.29
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (17 bp):
TAAATTATTTATATTCA
Found at i:45545 original size:14 final size:14
Alignment explanation
Indices: 45526--45564 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
45516 TCTTTGTCAG
45526 ATATAATTAAATAA
1 ATATAATTAAATAA
*
45540 ATATAATATAAGTAA
1 ATATAAT-TAAATAA
45555 A-ATAATTAAA
1 ATATAATTAAA
45565 ATATTAGATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
13 3 0.14
14 12 0.55
15 7 0.32
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (14 bp):
ATATAATTAAATAA
Found at i:45964 original size:23 final size:23
Alignment explanation
Indices: 45912--45986 Score: 71
Period size: 23 Copynumber: 3.2 Consensus size: 23
45902 AAAATAATAA
*
45912 TTAAATATATTTAATT-TTATTTT
1 TTAAATAT-TTTAATTATAATTTT
*
45935 TAATAAATATTTTAATTATAATTAT
1 T--TAAATATTTTAATTATAATTTT
** *
45960 TTAAATAAATTAATTAAAATTTT
1 TTAAATATTTTAATTATAATTTT
45983 TTAA
1 TTAA
45987 TTTAATTTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
23 23 0.53
24 7 0.16
25 13 0.30
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (23 bp):
TTAAATATTTTAATTATAATTTT
Found at i:46059 original size:16 final size:16
Alignment explanation
Indices: 46011--46072 Score: 56
Period size: 16 Copynumber: 3.9 Consensus size: 16
46001 TGGTCAATTC
*
46011 TAAATATGAATAGTTTA
1 TAAATATTAATA-TTTA
* *
46028 AAAATA-TAATA-ATA
1 TAAATATTAATATTTA
46042 TAAATATTAATATTTA
1 TAAATATTAATATTTA
*
46058 TAATTATTAAATATT
1 TAAATATT-AATATT
46073 ATTTTTTAAA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
14 7 0.19
15 5 0.14
16 13 0.36
17 11 0.31
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.44
Consensus pattern (16 bp):
TAAATATTAATATTTA
Found at i:55453 original size:17 final size:17
Alignment explanation
Indices: 55431--55465 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
55421 AAAAAGTTAT
*
55431 TTTAATAAATTTATATA
1 TTTAATAAATTTAAATA
55448 TTTAATAAATTTAAATA
1 TTTAATAAATTTAAATA
55465 T
1 T
55466 CCTAATGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (17 bp):
TTTAATAAATTTAAATA
Found at i:56691 original size:16 final size:16
Alignment explanation
Indices: 56670--56701 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
56660 TATCATATAA
*
56670 ATTAAATTTTAAATTT
1 ATTAAATATTAAATTT
56686 ATTAAATATTAAATTT
1 ATTAAATATTAAATTT
56702 TTTTTAAACT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTAAATATTAAATTT
Found at i:57472 original size:8 final size:8
Alignment explanation
Indices: 57459--57553 Score: 56
Period size: 8 Copynumber: 11.9 Consensus size: 8
57449 TTATATTACA
57459 AATATATT
1 AATATATT
57467 AATATATT
1 AATATATT
*
57475 AAAATATAT
1 AATATAT-T
*
57484 AAAATA-T
1 AATATATT
*
57491 AATTTATT
1 AATATATT
57499 AATATATTTT
1 AATATA--TT
* *
57509 AAATTTATA
1 -AATATATT
*
57518 AAAATATAT
1 AATATAT-T
57527 AATATATT
1 AATATATT
57535 AA-ATA-T
1 AATATATT
57541 AAT-TA-T
1 AATATATT
57547 AATATAT
1 AATATAT
57554 AAAAATTATT
Statistics
Matches: 68, Mismatches: 10, Indels: 18
0.71 0.10 0.19
Matches are distributed among these distances:
6 9 0.13
7 10 0.15
8 28 0.41
9 14 0.21
10 2 0.03
11 5 0.07
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
AATATATT
Found at i:57499 original size:32 final size:34
Alignment explanation
Indices: 57463--57559 Score: 108
Period size: 36 Copynumber: 2.8 Consensus size: 34
57453 ATTACAAATA
57463 TATTAATATA-TTAAAATATAT-AAAATATAATT
1 TATTAATATATTTAAAATATATAAAAATATAATT
* * *
57495 TATTAATATATTTTAAATTTATAAAAATATATAATA
1 TATTAATATATTTAAAATATAT-AAAA-ATATAATT
* *
57531 TATTAAATATAATTATAATATATAAAAAT
1 TATT-AATATATTTAAAATATATAAAAAT
57560 TATTAAAAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
32 10 0.19
33 9 0.17
35 5 0.09
36 15 0.28
37 14 0.26
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (34 bp):
TATTAATATATTTAAAATATATAAAAATATAATT
Found at i:57499 original size:43 final size:43
Alignment explanation
Indices: 57452--57533 Score: 103
Period size: 43 Copynumber: 1.9 Consensus size: 43
57442 ATCAAATTTA
*
57452 TATTACAAATATATT-AATATATTAAAATATATAAAATATAATT
1 TATTA-AAATATATTAAATATATAAAAATATATAAAATATAATT
* * * *
57495 TATTAATATATTTTAAATTTATAAAAATATATAATATAT
1 TATTAAAATATATTAAATATATAAAAATATATAAAATAT
57534 TAAATATAAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
42 7 0.21
43 26 0.79
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (43 bp):
TATTAAAATATATTAAATATATAAAAATATATAAAATATAATT
Found at i:57522 original size:34 final size:32
Alignment explanation
Indices: 57463--57525 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
57453 ATTACAAATA
57463 TATTAATATATTAAAATATATAAAATATAATT
1 TATTAATATATTAAAATATATAAAATATAATT
* *
57495 TATTAATATATTTTAAATTTATAAAAATATA
1 TATTAATATA-TTAAAATATAT-AAAATATA
57526 TAATATATTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 10 0.37
33 9 0.33
34 8 0.30
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
TATTAATATATTAAAATATATAAAATATAATT
Found at i:57863 original size:28 final size:26
Alignment explanation
Indices: 57823--57901 Score: 72
Period size: 27 Copynumber: 3.0 Consensus size: 26
57813 TAATTTTTAA
* *
57823 TTTTTTCAA-ATATTT-ATATTAATAT
1 TTTTTTAAATATATTTAAAATTAA-AT
*
57848 TTATTTTAAATTATATTTAAAATTTAAT
1 TT-TTTTAAA-TATATTTAAAATTAAAT
*
57876 TTTTTTAAATATATTAAAAAATTAAA
1 TTTTTTAAATATATT-TAAAATTAAA
57902 AATAATATAA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
25 2 0.05
26 12 0.27
27 15 0.34
28 10 0.23
29 5 0.11
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.54
Consensus pattern (26 bp):
TTTTTTAAATATATTTAAAATTAAAT
Found at i:57896 original size:27 final size:28
Alignment explanation
Indices: 57846--57900 Score: 78
Period size: 26 Copynumber: 2.0 Consensus size: 28
57836 TTATATTAAT
*
57846 ATTTATTTTAAATTATATTTAAAATTTA
1 ATTTATTTTAAATTATATTAAAAATTTA
*
57874 ATTT-TTTTAAA-TATATTAAAAAATTA
1 ATTTATTTTAAATTATATTAAAAATTTA
57900 A
1 A
57901 AAATAATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 14 0.56
27 7 0.28
28 4 0.16
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (28 bp):
ATTTATTTTAAATTATATTAAAAATTTA
Found at i:57957 original size:26 final size:24
Alignment explanation
Indices: 57923--57986 Score: 69
Period size: 26 Copynumber: 2.6 Consensus size: 24
57913 TTTATTAATT
*
57923 TATAATTTTTATATATT-TATATTA
1 TATATTTTTTATATATTATATA-TA
*
57947 TAATTATTTTTTAAATATTATATATA
1 T-A-TATTTTTTATATATTATATATA
57973 TATATTTTTT-TATA
1 TATATTTTTTATATA
57987 ATATTCTCAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
23 3 0.09
24 9 0.26
25 2 0.06
26 16 0.47
27 4 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (24 bp):
TATATTTTTTATATATTATATATA
Found at i:57989 original size:26 final size:26
Alignment explanation
Indices: 57927--57991 Score: 75
Period size: 25 Copynumber: 2.5 Consensus size: 26
57917 TTAATTTATA
57927 ATTTTTAT-ATATTTATATTATAATT
1 ATTTTTATAATATTTATATTATAATT
57952 ATTTTT-TAA-ATATTATATATATATATT
1 ATTTTTATAATAT-TTATAT-TATA-ATT
57979 -TTTTTATAATATT
1 ATTTTTATAATATT
57992 CTCATCACGT
Statistics
Matches: 34, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
24 3 0.09
25 13 0.38
26 9 0.26
27 7 0.21
28 2 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (26 bp):
ATTTTTATAATATTTATATTATAATT
Found at i:58504 original size:36 final size:35
Alignment explanation
Indices: 58463--58539 Score: 95
Period size: 36 Copynumber: 2.2 Consensus size: 35
58453 AACGAATATT
* *
58463 TATAAATATTT-TTTAAATTATTTGATTTTTTTAAAA
1 TATAAAT-TTTATTTAAATTAATT-ATTTTTATAAAA
58499 TATAAATTTTACTTTAAATTAATTATTTTTATAAAA
1 TATAAATTTTA-TTTAAATTAATTATTTTTATAAAA
58535 T-TAAA
1 TATAAA
58540 AATAATATTG
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
35 7 0.19
36 19 0.51
37 11 0.30
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (35 bp):
TATAAATTTTATTTAAATTAATTATTTTTATAAAA
Found at i:58600 original size:30 final size:30
Alignment explanation
Indices: 58566--58648 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 30
58556 TATTAATTAT
58566 TAAAAATAT-TAATATAAATTATAATATAA-A
1 TAAAAATATATAATA-AAATTAT-ATATAATA
*
58596 TAAAAATATATATTAAAATTATATATAATA
1 TAAAAATATATAATAAAATTATATATAATA
*
58626 TAAAATAGTAACATAATAAAATT
1 TAAAA-A-T-ATATAATAAAATT
58649 TGATTTAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 7
0.82 0.05 0.13
Matches are distributed among these distances:
29 6 0.13
30 22 0.49
31 5 0.11
32 1 0.02
33 11 0.24
ACGTcount: A:0.61, C:0.01, G:0.01, T:0.36
Consensus pattern (30 bp):
TAAAAATATATAATAAAATTATATATAATA
Found at i:59330 original size:11 final size:12
Alignment explanation
Indices: 59296--59342 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
59286 TTTGTAAATT
*
59296 TAAAAA-TAATA
1 TAAAAATTAAAA
59307 TATAAAATGTAAAA
1 TA-AAAAT-TAAAA
59321 -AAAAATTAAAA
1 TAAAAATTAAAA
59332 TAAAAATTAAA
1 TAAAAATTAAA
59343 TAATTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 7 0.23
12 19 0.61
13 1 0.03
14 4 0.13
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (12 bp):
TAAAAATTAAAA
Found at i:59342 original size:23 final size:24
Alignment explanation
Indices: 59297--59342 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
59287 TTGTAAATTT
*
59297 AAAAATAATATATAAAATGTAAAA
1 AAAAATAAAATATAAAATGTAAAA
59321 AAAAATTAAAATA-AAAAT-TAAA
1 AAAAA-TAAAATATAAAATGTAAA
59343 TAATTTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 10 0.50
25 6 0.30
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAAATAAAATATAAAATGTAAAA
Found at i:59383 original size:99 final size:95
Alignment explanation
Indices: 59253--59458 Score: 220
Period size: 93 Copynumber: 2.1 Consensus size: 95
59243 GAATAAAGTG
* * *
59253 ATATTTATAAAAAATATAATTAATATGTTATTTTTTGTAAATTTAA-AAATAATATATAAAATGT
1 ATATTTAT--AAAATATAATTAATATATTATTCTTT-T-AATTCAATAAA-AATA-AT--AAT-T
59317 AAAAAAAAATTAAAATAAAAATTAAATAATTTTTAATTA
57 AAAAAAAAATTAAAATAAAAATTAAATAATTTTTAATTA
* * * *
59356 ATA-TTATAAAAT-TAATTAATATATTATTCTTTTAATTCAATAAAAGTAATAATTAAATATAAT
1 ATATTTATAAAATATAATTAATATATTATTCTTTTAATTCAATAAAAATAATAATTAAAAAAAAA
** *
59419 TTGTAATAATAATTAAATAATTTTTAATTA
66 TTAAAATAAAAATTAAATAATTTTTAATTA
59449 ATATTTATAA
1 ATATTTATAA
59459 GTATGGATTA
Statistics
Matches: 91, Mismatches: 10, Indels: 13
0.80 0.09 0.11
Matches are distributed among these distances:
93 37 0.41
94 9 0.10
96 2 0.02
97 9 0.10
98 4 0.04
99 18 0.20
100 5 0.05
102 4 0.04
103 3 0.03
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.44
Consensus pattern (95 bp):
ATATTTATAAAATATAATTAATATATTATTCTTTTAATTCAATAAAAATAATAATTAAAAAAAAA
TTAAAATAAAAATTAAATAATTTTTAATTA
Found at i:59550 original size:21 final size:21
Alignment explanation
Indices: 59520--59567 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
59510 TAAAAATTCA
*
59520 ATAA-AATTAATATATTAAAT
1 ATAATAATTAATATAATAAAT
*
59540 ATAATAATTAATATAATAATT
1 ATAATAATTAATATAATAAAT
59561 A-AATAAT
1 ATAATAAT
59568 CTTTAATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 10 0.40
21 15 0.60
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATAATAATTAATATAATAAAT
Found at i:59554 original size:12 final size:12
Alignment explanation
Indices: 59527--59567 Score: 57
Period size: 12 Copynumber: 3.3 Consensus size: 12
59517 TCAATAAAAT
59527 TAATATATTAAATA
1 TAATA-ATT-AATA
59541 TAATAATTAATA
1 TAATAATTAATA
59553 TAATAATTAA-A
1 TAATAATTAATA
59564 TAAT
1 TAAT
59568 CTTTAATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
11 5 0.19
12 14 0.52
13 3 0.11
14 5 0.19
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (12 bp):
TAATAATTAATA
Found at i:59772 original size:24 final size:24
Alignment explanation
Indices: 59731--59788 Score: 82
Period size: 24 Copynumber: 2.5 Consensus size: 24
59721 TTCGGGCCTC
*
59731 ATCTTTT-AAAAAAGTTAAATATA
1 ATCTTTTAAAAAAAATTAAATATA
*
59754 ATCTTTTAAAAAAAATTAAATATT
1 ATCTTTTAAAAAAAATTAAATATA
*
59778 ATTTTTTAAAA
1 ATCTTTTAAAA
59789 TAACTATATA
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (24 bp):
ATCTTTTAAAAAAAATTAAATATA
Found at i:59890 original size:15 final size:15
Alignment explanation
Indices: 59870--59907 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
59860 ATATTCACTT
59870 AAATATAAAAAAATA
1 AAATATAAAAAAATA
*
59885 AAATAT-AAATAATA
1 AAATATAAAAAAATA
*
59899 AAATTTAAA
1 AAATATAAA
59908 CTTTTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (15 bp):
AAATATAAAAAAATA
Found at i:61471 original size:2 final size:2
Alignment explanation
Indices: 61464--61524 Score: 115
Period size: 2 Copynumber: 31.0 Consensus size: 2
61454 TCCTTGTCTT
61464 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61505 TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
61525 GGTTAAACAA
Statistics
Matches: 58, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:62195 original size:6 final size:6
Alignment explanation
Indices: 62175--62208 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
62165 ATTATTTAAG
*
62175 TTAAA- TTAAAT TTAAAC TTAAAT TTAAAT TTAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAA
62209 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (6 bp):
TTAAAT
Found at i:62203 original size:18 final size:17
Alignment explanation
Indices: 62175--62208 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
62165 ATTATTTAAG
62175 TTAAATTAAATTTAAAC
1 TTAAATTAAATTTAAAC
62192 TTAAATTTAAATTTAAA
1 TTAAA-TTAAATTTAAA
62209 ATTTTTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (17 bp):
TTAAATTAAATTTAAAC
Found at i:62478 original size:18 final size:19
Alignment explanation
Indices: 62451--62486 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
62441 GTAATAGTAT
62451 TGAAAGTTTT-ATATATTC
1 TGAAAGTTTTAATATATTC
*
62469 TGAAATTTTTAATATATT
1 TGAAAGTTTTAATATATT
62487 AATAATTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (19 bp):
TGAAAGTTTTAATATATTC
Found at i:63066 original size:14 final size:14
Alignment explanation
Indices: 63047--63090 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
63037 ACAAACTCGA
*
63047 ATTTTAATTTAATT
1 ATTTTAATATAATT
63061 ATTTT-ATATAATT
1 ATTTTAATATAATT
*
63074 AGTTTTAAAATAATT
1 A-TTTTAATATAATT
63089 AT
1 AT
63091 AAATATTAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
13 8 0.31
14 10 0.38
15 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
ATTTTAATATAATT
Found at i:63111 original size:17 final size:17
Alignment explanation
Indices: 63089--63152 Score: 50
Period size: 17 Copynumber: 4.0 Consensus size: 17
63079 TAAAATAATT
*
63089 ATAAA-TATTAATATTTA
1 ATAAATTATAAATA-TTA
63106 ATAAATTATAAATATTA
1 ATAAATTATAAATATTA
63123 AT--ATT-TAAA-ATTA
1 ATAAATTATAAATATTA
*
63136 A-AATTTATAAAATATTA
1 ATAAATTAT-AAATATTA
63153 TTTTTTAAGC
Statistics
Matches: 39, Mismatches: 2, Indels: 12
0.74 0.04 0.23
Matches are distributed among these distances:
13 5 0.13
14 6 0.15
15 4 0.10
16 3 0.08
17 14 0.36
18 7 0.18
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
ATAAATTATAAATATTA
Found at i:63112 original size:24 final size:24
Alignment explanation
Indices: 63085--63130 Score: 92
Period size: 24 Copynumber: 1.9 Consensus size: 24
63075 GTTTTAAAAT
63085 AATTATAAATATTAATATTTAATA
1 AATTATAAATATTAATATTTAATA
63109 AATTATAAATATTAATATTTAA
1 AATTATAAATATTAATATTTAA
63131 AATTAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (24 bp):
AATTATAAATATTAATATTTAATA
Found at i:63149 original size:30 final size:27
Alignment explanation
Indices: 63078--63152 Score: 84
Period size: 24 Copynumber: 2.7 Consensus size: 27
63068 ATAATTAGTT
63078 TTAAAATAATTATAAATATTAATATTTAA
1 TTAAAAT--TTATAAATATTAATATTTAA
63107 -T-AAA-TTATAAATATTAATATTTAAAA
1 TTAAAATTTATAAATATTAATATTT--AA
63133 TTAAAATTTATAAAATATTA
1 TTAAAATTTAT-AAATATTA
63153 TTTTTTAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
24 18 0.45
26 2 0.05
27 4 0.10
28 4 0.10
29 4 0.10
30 8 0.20
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (27 bp):
TTAAAATTTATAAATATTAATATTTAA
Found at i:63330 original size:2 final size:2
Alignment explanation
Indices: 63323--63348 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63313 TCAGTAAAAT
63323 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
63349 CAATAATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:66794 original size:64 final size:63
Alignment explanation
Indices: 66697--66822 Score: 216
Period size: 64 Copynumber: 2.0 Consensus size: 63
66687 GCAAAAAAAC
* * *
66697 AAAAGGGTATAGGAAAGGTGTTGGCAGGTAACCCAGAAATCATAACTTGTCTACAACATTAAA
1 AAAAGGGAATAGAAAAGGTGCTGGCAGGTAACCCAGAAATCATAACTTGTCTACAACATTAAA
66760 AAAAGGGGAATAGAAAAGGTGCTGGCAGGTAACCCAGAAATCATAACTTGTCTACAACATTAA
1 AAAA-GGGAATAGAAAAGGTGCTGGCAGGTAACCCAGAAATCATAACTTGTCTACAACATTAA
66823 TGGAGGCTAC
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
63 4 0.07
64 55 0.93
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (63 bp):
AAAAGGGAATAGAAAAGGTGCTGGCAGGTAACCCAGAAATCATAACTTGTCTACAACATTAAA
Found at i:68616 original size:5 final size:5
Alignment explanation
Indices: 68589--68637 Score: 59
Period size: 5 Copynumber: 10.2 Consensus size: 5
68579 AATACAAAAA
*
68589 AATAT -ATAT -ATAT AATA- AATAT AATAT AATATT AAGAT AATAT AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATA-T AATAT AATAT AATAT
68637 A
1 A
68638 TATTTTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 12 0.31
5 23 0.59
6 4 0.10
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (5 bp):
AATAT
Found at i:68619 original size:27 final size:27
Alignment explanation
Indices: 68574--68680 Score: 69
Period size: 27 Copynumber: 4.0 Consensus size: 27
68564 AGATATGGTT
* * *
68574 TAATAAATACAAAAAAATATATATATA
1 TAATAAATATAATATAATATATATATA
*
68601 TAATAAATATAATATAATAT-TA-AGA
1 TAATAAATATAATATAATATATATATA
** * *
68626 TAATATAATAT-ATATTTTATTTATATT
1 TAATA-AATATAATATAATATATATATA
* * *
68653 TAATAATTTATATTAT-ATTTATATATA
1 TAATAA-ATATAATATAATATATATATA
68680 T
1 T
68681 GATTATCATT
Statistics
Matches: 61, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
25 14 0.23
26 10 0.16
27 34 0.56
28 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.46
Consensus pattern (27 bp):
TAATAAATATAATATAATATATATATA
Found at i:68646 original size:5 final size:6
Alignment explanation
Indices: 68636--68676 Score: 50
Period size: 6 Copynumber: 6.8 Consensus size: 6
68626 TAATATAATA
68636 TATATT T-TATT TATATT TAATAATT TATA-T TATATT TATAT
1 TATATT TATATT TATATT T-AT-ATT TATATT TATATT TATAT
68677 ATATGATTAT
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
5 10 0.32
6 13 0.42
7 4 0.13
8 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (6 bp):
TATATT
Found at i:68810 original size:18 final size:20
Alignment explanation
Indices: 68772--68810 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
68762 ATTAATTTTT
*
68772 ATATATTAAATAAAACCATA
1 ATATATTAAATAAAACAATA
68792 ATATA-TAAATAAAA-AATA
1 ATATATTAAATAAAACAATA
68810 A
1 A
68811 AAATTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 4 0.22
19 9 0.50
20 5 0.28
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (20 bp):
ATATATTAAATAAAACAATA
Found at i:70536 original size:65 final size:65
Alignment explanation
Indices: 70427--70551 Score: 196
Period size: 65 Copynumber: 1.9 Consensus size: 65
70417 GAGGTCATGG
* * *
70427 TAATGAGTTATTGTACCAAGTTTTCAAGATTTAAATAAGAAAGATGACTCAAAGACTTCGTATAA
1 TAATAAGTTACTGTACCAAGTTTTCAAGATTTAAATAAGAAAGATGACTCAAAAACTTCGTATAA
* **
70492 TAATAAGTTACTGTATCAAGTTTTTGAGATTTAAATAAGAAAGATGACTCAAAAACTTCG
1 TAATAAGTTACTGTACCAAGTTTTCAAGATTTAAATAAGAAAGATGACTCAAAAACTTCG
70552 GTTTCTCCAA
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (65 bp):
TAATAAGTTACTGTACCAAGTTTTCAAGATTTAAATAAGAAAGATGACTCAAAAACTTCGTATAA
Found at i:71212 original size:7 final size:7
Alignment explanation
Indices: 71196--71333 Score: 63
Period size: 7 Copynumber: 19.1 Consensus size: 7
71186 TAAAGGTGAT
71196 TATATTA
1 TATATTA
*
71203 TATTTTA
1 TATATTA
71210 TATATTA
1 TATATTA
71217 TA-ATTA
1 TATATTA
71223 TAT-TTAA
1 TATATT-A
* *
71230 AATATTT
1 TATATTA
71237 TAGTA-TA
1 TA-TATTA
* *
71244 AATTTTAA
1 TATATT-A
71252 TATATTA
1 TATATTA
71259 -ATAATT-
1 TAT-ATTA
*
71265 TATGTTA
1 TATATTA
71272 TATATTA
1 TATATTA
*
71279 TCTATTCA
1 TATATT-A
*
71287 TATCATAA
1 TAT-ATTA
71295 TTATATTA
1 -TATATTA
*
71303 T-TATTT
1 TATATTA
71309 TATAATATA
1 TAT-AT-TA
71318 TTATATTA
1 -TATATTA
71326 TATATTA
1 TATATTA
71333 T
1 T
71334 TTTAATTAAT
Statistics
Matches: 97, Mismatches: 18, Indels: 32
0.66 0.12 0.22
Matches are distributed among these distances:
6 18 0.19
7 48 0.49
8 20 0.21
9 8 0.08
10 3 0.03
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (7 bp):
TATATTA
Found at i:71224 original size:20 final size:20
Alignment explanation
Indices: 71194--71346 Score: 83
Period size: 20 Copynumber: 7.8 Consensus size: 20
71184 AATAAAGGTG
71194 ATTAT-ATTATATTTTATAT
1 ATTATAATTATATTTTATAT
* *
71213 ATTATAATTATATTTAAAAT
1 ATTATAATTATATTTTATAT
* * *
71233 ATTTTAGTATAAATTTTAATAT
1 ATTATAAT-TATATTTT-ATAT
*
71255 ATTAATAATT-TATGTTATAT
1 ATT-ATAATTATATTTTATAT
* *
71275 ATTATCTATTCATA--TCATA-
1 ATTAT-AATT-ATATTTTATAT
71294 ATTAT-ATTATTATTTTATA-
1 ATTATAATTA-TATTTTATAT
*
71313 A-TAT-ATTATATTATATATT
1 ATTATAATTATATTTTATA-T
*
71332 ATTTTAATTA-ATTTT
1 ATTATAATTATATTTT
71347 TATTTAAACA
Statistics
Matches: 103, Mismatches: 17, Indels: 27
0.70 0.12 0.18
Matches are distributed among these distances:
16 1 0.01
17 13 0.13
18 7 0.07
19 18 0.17
20 38 0.37
21 14 0.14
22 9 0.09
23 3 0.03
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (20 bp):
ATTATAATTATATTTTATAT
Found at i:71299 original size:24 final size:23
Alignment explanation
Indices: 71272--71333 Score: 72
Period size: 23 Copynumber: 2.6 Consensus size: 23
71262 ATTTATGTTA
*
71272 TATATTATCTATTCATATCATA-AT
1 TATATTAT-TATT-ATATAATATAT
*
71296 TATATTATTATTTTATAATATAT
1 TATATTATTATTATATAATATAT
71319 TATATTATATATTAT
1 TATATTAT-TATTAT
71334 TTTAATTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
22 6 0.18
23 14 0.42
24 13 0.39
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (23 bp):
TATATTATTATTATATAATATAT
Found at i:71334 original size:15 final size:15
Alignment explanation
Indices: 71296--71334 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
71286 ATATCATAAT
*
71296 TATATTATTATTTTA
1 TATATTATTATATTA
71311 TA-ATATATTATATTA
1 TATAT-TATTATATTA
71326 TATATTATT
1 TATATTATT
71335 TTAATTAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 2 0.10
15 17 0.81
16 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATATTATTATATTA
Done.