Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 26 of 438
Found at i:6575631 original size:3 final size:3
Alignment explanation
Indices: 6575623--6575789 Score: 130
Period size: 3 Copynumber: 56.0 Consensus size: 3
6575613 TTAATAGTAT
6575623 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-A ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * *
6575670 ATA ATA ATA GAAA ATA ATA AGA ACA TTA ATA ATA ATA ATA TATG TTA
1 ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA
* * ** *
6575717 ATA ACA ACA ATA AT- ATA A-A A-A AGGG A-A ATA ATA AT- ATA CTA
1 ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA
* *
6575758 ATA AGA ATG ATA ATA GATTA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA -A-TA ATA ATA ATA ATA
6575790 GTATAAGAAA
Statistics
Matches: 133, Mismatches: 21, Indels: 20
0.76 0.12 0.11
Matches are distributed among these distances:
2 11 0.08
3 113 0.85
4 7 0.05
5 2 0.02
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:6575893 original size:19 final size:20
Alignment explanation
Indices: 6575863--6575908 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
6575853 TACATAAAAT
*
6575863 AATAACATAAAATGTAAG-TA
1 AATAACATAAAA-ATAAGATA
6575883 AATAA-ATAAAAATAAGATA
1 AATAACATAAAAATAAGATA
6575902 AATAACA
1 AATAACA
6575909 AAATAAGTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 4 0.17
19 13 0.57
20 6 0.26
ACGTcount: A:0.67, C:0.04, G:0.07, T:0.22
Consensus pattern (20 bp):
AATAACATAAAAATAAGATA
Found at i:6575953 original size:3 final size:3
Alignment explanation
Indices: 6575936--6576085 Score: 58
Period size: 3 Copynumber: 49.0 Consensus size: 3
6575926 AATATGATAG
* *
6575936 TAA TAA -AA GTAA TAA TAA TAA CAA T-A TAAA TGA TAA TAA TAA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA
* ** * *
6575981 AAA TAA -AA GTAA TAA TAA T-A TGT TAA GTTA TAA TAG TAA -AA TAA
1 TAA TAA TAA -TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
* * * * * * * *
6576025 TAA TGA TAG TGA TAA TATA TAT TAA GTGA TAA TAG TGGAA TAA CAA TAG
1 TAA TAA TAA TAA TAA TA-A TAA TAA -TAA TAA TAA T--AA TAA TAA TAA
6576074 TAA TAA TAA TAA
1 TAA TAA TAA TAA
6576086 CATATTAAAC
Statistics
Matches: 105, Mismatches: 29, Indels: 26
0.66 0.18 0.16
Matches are distributed among these distances:
2 10 0.10
3 80 0.76
4 13 0.12
5 2 0.02
ACGTcount: A:0.57, C:0.01, G:0.10, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:6575977 original size:24 final size:21
Alignment explanation
Indices: 6575937--6576000 Score: 92
Period size: 24 Copynumber: 2.9 Consensus size: 21
6575927 ATATGATAGT
6575937 AATAAAAGTAATAATAATAACA
1 AATAAAAGTAATAATAATAA-A
*
6575959 ATATAAATGATAATAATAATAAA
1 A-ATAAAAG-TAATAATAATAAA
6575982 AATAAAAGTAATAATAATA
1 AATAAAAGTAATAATAATA
6576001 TGTTAAGTTA
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
21 11 0.29
22 7 0.18
23 8 0.21
24 12 0.32
ACGTcount: A:0.67, C:0.02, G:0.05, T:0.27
Consensus pattern (21 bp):
AATAAAAGTAATAATAATAAA
Found at i:6576039 original size:26 final size:27
Alignment explanation
Indices: 6575983--6576041 Score: 68
Period size: 26 Copynumber: 2.2 Consensus size: 27
6575973 AATAATAAAA
* * *
6575983 ATAAAAGTAATAATAATATGTTAAGTT
1 ATAATAGTAATAATAATATGATAAGTG
6576010 ATAATAGTAA-AATAATAATGAT-AGTG
1 ATAATAGTAATAATAAT-ATGATAAGTG
6576036 ATAATA
1 ATAATA
6576042 TATATTAAGT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
26 15 0.54
27 13 0.46
ACGTcount: A:0.54, C:0.00, G:0.12, T:0.34
Consensus pattern (27 bp):
ATAATAGTAATAATAATATGATAAGTG
Found at i:6576083 original size:43 final size:44
Alignment explanation
Indices: 6575990--6576093 Score: 113
Period size: 43 Copynumber: 2.4 Consensus size: 44
6575980 AAAATAAAAG
* * * *
6575990 TAATAATAATATGTTAAGTTATAATAGTAAAATAATAATGATAG
1 TAATAATAATATATTAAGTGATAATAGTAAAATAACAATGATAA
* **
6576034 TGATAAT-ATATATTAAGTGATAATAGTGGAATAACAAT-AGTAA
1 TAATAATAATATATTAAGTGATAATAGTAAAATAACAATGA-TAA
*
6576077 TAATAATAACATATTAA
1 TAATAATAATATATTAA
6576094 ACCAATTAAT
Statistics
Matches: 49, Mismatches: 9, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
42 1 0.02
43 34 0.69
44 14 0.29
ACGTcount: A:0.52, C:0.02, G:0.12, T:0.35
Consensus pattern (44 bp):
TAATAATAATATATTAAGTGATAATAGTAAAATAACAATGATAA
Found at i:6579775 original size:39 final size:39
Alignment explanation
Indices: 6579727--6579833 Score: 187
Period size: 39 Copynumber: 2.7 Consensus size: 39
6579717 TGTGTGAGAT
6579727 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
*
6579766 TTATATCCGGGGTAAGTCCCAAAGGCATTCGTGCTGGTG
1 TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
* *
6579805 TTATATCTGGGCTAAGTCCCGAAGGCATT
1 TTATATCCGGGCTAAGTCCCAAAGGCATT
6579834 TGTGTTGGAA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 64 1.00
ACGTcount: A:0.21, C:0.21, G:0.28, T:0.29
Consensus pattern (39 bp):
TTATATCCGGGCTAAGTCCCAAAGGCATTCGTGCTGGTG
Found at i:6585966 original size:19 final size:19
Alignment explanation
Indices: 6585942--6586039 Score: 164
Period size: 19 Copynumber: 5.2 Consensus size: 19
6585932 AATCTTTAAG
6585942 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6585961 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6585980 GATA--CAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6585997 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
6586016 GATATGCAATCTTGAAGATAT
1 GATATGCAATCTT--AGATAT
6586037 GAT
1 GAT
6586040 CTTGTAATCT
Statistics
Matches: 75, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
17 17 0.23
19 49 0.65
21 9 0.12
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:6585972 original size:36 final size:35
Alignment explanation
Indices: 6585932--6586039 Score: 112
Period size: 36 Copynumber: 2.9 Consensus size: 35
6585922 ATGGAAATAT
6585932 AATCTTTAAGGATATGCAATCTTAGATATGATATGC
1 AATCTTTAA-GATATGCAATCTTAGATATGATATGC
6585968 AATC-TT-AGATATGATACAATCTTAGATATGATATGC
1 AATCTTTAAGATATG---CAATCTTAGATATGATATGC
*
6586004 AATCTTAGATATGATATGCAATCTTGAAGATATGAT
1 AATCTT---TAAGATATGCAATCTT--AGATATGAT
6586040 CTTGTAATCT
Statistics
Matches: 61, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
33 6 0.10
34 1 0.02
35 2 0.03
36 28 0.46
37 1 0.02
38 7 0.11
40 10 0.16
41 6 0.10
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (35 bp):
AATCTTTAAGATATGCAATCTTAGATATGATATGC
Found at i:6586513 original size:22 final size:21
Alignment explanation
Indices: 6586488--6586539 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
6586478 CTATTTATTC
*
6586488 ATTTTTTTAGTGTAT-GTCATTT
1 ATTTTTTTAGTGCATAGT--TTT
6586510 ATTTTATTT-GTGCATAGTTTT
1 ATTTT-TTTAGTGCATAGTTTT
6586531 ATTTTTTTA
1 ATTTTTTTA
6586540 TATGCTATGT
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
20 3 0.12
21 8 0.31
22 10 0.38
23 5 0.19
ACGTcount: A:0.19, C:0.04, G:0.12, T:0.65
Consensus pattern (21 bp):
ATTTTTTTAGTGCATAGTTTT
Found at i:6586557 original size:25 final size:25
Alignment explanation
Indices: 6586529--6586577 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 25
6586519 GTGCATAGTT
6586529 TTATTT-TTTTATATGCTATGTTTAA
1 TTATTTCTTTTATATGCTAT-TTTAA
*
6586554 TTATTTCTTTTATGTGCTATTTTA
1 TTATTTCTTTTATATGCTATTTTA
6586578 TGATATATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 10 0.45
26 12 0.55
ACGTcount: A:0.20, C:0.06, G:0.08, T:0.65
Consensus pattern (25 bp):
TTATTTCTTTTATATGCTATTTTAA
Found at i:6589533 original size:29 final size:27
Alignment explanation
Indices: 6589501--6589602 Score: 105
Period size: 29 Copynumber: 3.6 Consensus size: 27
6589491 GTGACGAGAT
*
6589501 TGGCACTGAGTGTGCGAGCTTGTAATGTA
1 TGGCACTAAGTGTGCGAGCTTG-AAT-TA
* *
6589530 TGGCACTAAGTGTGCGAGTTTGGACTATA
1 TGGCACTAAGTGTGCGAGCTT-GAAT-TA
* * *
6589559 TGGCACTATGTGTGCGGGCTTGAATCA
1 TGGCACTAAGTGTGCGAGCTTGAATTA
6589586 CTGGCACTAAGTGTGCG
1 -TGGCACTAAGTGTGCG
6589603 TGATTGAGTA
Statistics
Matches: 61, Mismatches: 10, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
27 1 0.02
28 18 0.30
29 41 0.67
30 1 0.02
ACGTcount: A:0.21, C:0.17, G:0.33, T:0.29
Consensus pattern (27 bp):
TGGCACTAAGTGTGCGAGCTTGAATTA
Found at i:6596701 original size:46 final size:44
Alignment explanation
Indices: 6596642--6596756 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
6596632 ACAGGACAGA
* *
6596642 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
6596688 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
6596732 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
6596757 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:6596737 original size:44 final size:45
Alignment explanation
Indices: 6596642--6596775 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
6596632 ACAGGACAGA
* *
6596642 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
6596688 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
6596732 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
6596776 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:6604062 original size:46 final size:44
Alignment explanation
Indices: 6604003--6604117 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
6603993 ACAGGACAGA
* *
6604003 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
6604049 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
6604093 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
6604118 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:6604098 original size:44 final size:45
Alignment explanation
Indices: 6604003--6604136 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
6603993 ACAGGACAGA
* *
6604003 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
6604049 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
6604093 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
6604137 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:6606242 original size:3 final size:3
Alignment explanation
Indices: 6606234--6606271 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
6606224 ACCATTTGTA
6606234 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
6606272 ATAAATAAAT
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:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:6606276 original size:4 final size:4
Alignment explanation
Indices: 6606267--6606294 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
6606257 TAATAATAAT
6606267 AATA AATA AATA AATA AATA AATA AATA
1 AATA AATA AATA AATA AATA AATA AATA
6606295 TATTTTACTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AATA
Found at i:6606319 original size:34 final size:35
Alignment explanation
Indices: 6606276--6606342 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
6606266 TAATAAATAA
*
6606276 ATAAATAAATAAATAA-ATATATTT-TACTTAATTT
1 ATAAATAAATAAATAACATACATTTGTA-TTAATTT
* *
6606310 ATAAGTAAATATATAACATACATTTGTATTAAT
1 ATAAATAAATAAATAACATACATTTGTATTAAT
6606343 AATTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 14 0.50
35 12 0.43
36 2 0.07
ACGTcount: A:0.51, C:0.04, G:0.03, T:0.42
Consensus pattern (35 bp):
ATAAATAAATAAATAACATACATTTGTATTAATTT
Found at i:6614374 original size:30 final size:30
Alignment explanation
Indices: 6614338--6614398 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 30
6614328 TCATACATAG
*
6614338 TCCGTGGAGTAGGATTTTGATTACCCGCAA
1 TCCGTGGAGTAGAATTTTGATTACCCGCAA
*
6614368 TCCGTGGAGTAGAATTTTGATTAGCCGCAA
1 TCCGTGGAGTAGAATTTTGATTACCCGCAA
6614398 T
1 T
6614399 TGCAGAAGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.31
Consensus pattern (30 bp):
TCCGTGGAGTAGAATTTTGATTACCCGCAA
Found at i:6614630 original size:3 final size:3
Alignment explanation
Indices: 6614617--6614650 Score: 59
Period size: 3 Copynumber: 11.0 Consensus size: 3
6614607 AAAAGTAAAT
6614617 TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6614651 AATTAAATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 27 0.90
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:6620485 original size:3 final size:3
Alignment explanation
Indices: 6620479--6620529 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
6620469 TATATAAGTA
6620479 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
6620527 TAT
1 TAT
6620530 ATATAAAATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:6620563 original size:21 final size:21
Alignment explanation
Indices: 6620534--6620593 Score: 54
Period size: 21 Copynumber: 2.9 Consensus size: 21
6620524 TATTATATAT
*
6620534 AAAATAAAAGAAAGTA-AAAGA
1 AAAAGAAAAGAAA-TAGAAAGA
6620555 AAAAGAAAA-AGAATAGAAAGA
1 AAAAGAAAAGA-AATAGAAAGA
* *
6620576 AACAGAGAAGAAAT-GAAA
1 AAAAGAAAAGAAATAGAAA
6620594 CAGGGGAGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
20 7 0.21
21 25 0.76
22 1 0.03
ACGTcount: A:0.73, C:0.02, G:0.18, T:0.07
Consensus pattern (21 bp):
AAAAGAAAAGAAATAGAAAGA
Found at i:6620632 original size:14 final size:14
Alignment explanation
Indices: 6620534--6620640 Score: 56
Period size: 15 Copynumber: 7.3 Consensus size: 14
6620524 TATTATATAT
*
6620534 AAAATAAAAGAAAG
1 AAAAGAAAAGAAAG
*
6620548 TAAAAGAAAA-AGA-
1 -AAAAGAAAAGAAAG
*
6620561 AAAAGAATAGAAAG
1 AAAAGAAAAGAAAG
*
6620575 AAACAGAGAAGAAATG
1 AAA-AGAAAAGAAA-G
***
6620591 AAACAGGGGAGAAAG
1 AAA-AGAAAAGAAAG
*
6620606 AAGGAGAAAAAGAAAG
1 AA-AAG-AAAAGAAAG
*
6620622 GAAAGAAAAGAAAAG
1 AAAAGAAAAG-AAAG
6620637 AAAA
1 AAAA
6620641 AGGGGAAATA
Statistics
Matches: 70, Mismatches: 15, Indels: 14
0.71 0.15 0.14
Matches are distributed among these distances:
12 8 0.11
13 2 0.03
14 10 0.14
15 30 0.43
16 20 0.29
ACGTcount: A:0.70, C:0.02, G:0.24, T:0.04
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:6620642 original size:21 final size:21
Alignment explanation
Indices: 6620601--6620643 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
6620591 AAACAGGGGA
* *
6620601 GAAAGAAGGAGAAAAAGAAAG
1 GAAAGAAGAAGAAAAAAAAAG
6620622 GAAAGAA-AAGAAAAGAAAAAG
1 GAAAGAAGAAGAAAA-AAAAAG
6620643 G
1 G
6620644 GGAAATAAGG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (21 bp):
GAAAGAAGAAGAAAAAAAAAG
Found at i:6621673 original size:6 final size:6
Alignment explanation
Indices: 6621662--6621688 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
6621652 TGTGTACCGC
6621662 TACTGT TACTGT TACTGT TACTGT TAC
1 TACTGT TACTGT TACTGT TACTGT TAC
6621689 CCTTACGGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.15, T:0.48
Consensus pattern (6 bp):
TACTGT
Found at i:6623238 original size:11 final size:11
Alignment explanation
Indices: 6623222--6623246 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
6623212 TCATATCAAG
6623222 AAACATTACTC
1 AAACATTACTC
6623233 AAACATTACTC
1 AAACATTACTC
6623244 AAA
1 AAA
6623247 TGTTAATGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (11 bp):
AAACATTACTC
Found at i:6624450 original size:7 final size:7
Alignment explanation
Indices: 6624438--6624470 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
6624428 CTGTTATGGC
6624438 AGTTAGT
1 AGTTAGT
6624445 AGTTAGT
1 AGTTAGT
6624452 AGTTAG-
1 AGTTAGT
6624458 AGCTTAGT
1 AG-TTAGT
6624466 AGTTA
1 AGTTA
6624471 TGGTTGTTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 2 0.08
7 20 0.83
8 2 0.08
ACGTcount: A:0.30, C:0.03, G:0.27, T:0.39
Consensus pattern (7 bp):
AGTTAGT
Found at i:6626421 original size:2 final size:2
Alignment explanation
Indices: 6626414--6626443 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
6626404 TAAATGATTA
6626414 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
6626444 TATTTTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6627094 original size:3 final size:3
Alignment explanation
Indices: 6627086--6627131 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
6627076 TAATAAAATC
6627086 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT T
6627132 TTGCTGTTTG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:6627185 original size:2 final size:2
Alignment explanation
Indices: 6627178--6627206 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
6627168 CGTAATACAA
6627178 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
6627207 GAAAGTGGAC
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:6632816 original size:19 final size:20
Alignment explanation
Indices: 6632777--6632816 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
6632767 AATAATTTTT
* *
6632777 AAAATTTTAAATTATTTATA
1 AAAATTCTAAATTATTCATA
6632797 AAAATTCTAAATT-TTCATA
1 AAAATTCTAAATTATTCATA
6632816 A
1 A
6632817 TTTTTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (20 bp):
AAAATTCTAAATTATTCATA
Found at i:6635171 original size:10 final size:10
Alignment explanation
Indices: 6635152--6635304 Score: 67
Period size: 10 Copynumber: 15.9 Consensus size: 10
6635142 AAAAAATTCG
*
6635152 ATTATTAAAA
1 ATTATAAAAA
6635162 ATTATAAAAA
1 ATTATAAAAA
6635172 ATATATTAAAAA
1 AT-TA-TAAAAA
*
6635184 ATTGT--AAA
1 ATTATAAAAA
* *
6635192 ATTTTATAAA
1 ATTATAAAAA
*
6635202 ATTGTAAAAA
1 ATTATAAAAA
6635212 A-T-TAAAAA
1 ATTATAAAAA
*
6635220 A-TATATAGAA
1 ATTATA-AAAA
6635230 A-TAT-AAAA
1 ATTATAAAAA
*
6635238 ATTAT-ATAA
1 ATTATAAAAA
*
6635247 ATT-TATAAA
1 ATTATAAAAA
* * *
6635256 GTCATGAGAAA
1 ATTAT-AAAAA
*
6635267 ATTATACAAA
1 ATTATAAAAA
*
6635277 ATGTA-AAGAA
1 AT-TATAAAAA
6635287 A-TATAAAAA
1 ATTATAAAAA
6635296 ATTATAAAA
1 ATTATAAAA
6635305 GTTATCGTTC
Statistics
Matches: 111, Mismatches: 19, Indels: 26
0.71 0.12 0.17
Matches are distributed among these distances:
8 22 0.20
9 20 0.18
10 49 0.44
11 12 0.11
12 8 0.07
ACGTcount: A:0.61, C:0.01, G:0.05, T:0.32
Consensus pattern (10 bp):
ATTATAAAAA
Found at i:6635220 original size:18 final size:18
Alignment explanation
Indices: 6635176--6635221 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
6635166 TAAAAAATAT
*
6635176 ATTAAAAAATTGTAAAAT
1 ATTAAAAAATTGTAAAAA
* *
6635194 TTTATAAAATTGTAAAAA
1 ATTAAAAAATTGTAAAAA
6635212 ATTAAAAAAT
1 ATTAAAAAAT
6635222 ATATAGAAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (18 bp):
ATTAAAAAATTGTAAAAA
Found at i:6635231 original size:18 final size:19
Alignment explanation
Indices: 6635210--6635245 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
6635200 AAATTGTAAA
6635210 AAAT-TAAAAAATATATAG
1 AAATATAAAAAATATATAG
*
6635228 AAATATAAAAATTATATA
1 AAATATAAAAAATATATA
6635246 AATTTATAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 4 0.25
19 12 0.75
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (19 bp):
AAATATAAAAAATATATAG
Found at i:6635296 original size:29 final size:28
Alignment explanation
Indices: 6635178--6635304 Score: 100
Period size: 27 Copynumber: 4.5 Consensus size: 28
6635168 AAAAATATAT
* * * *
6635178 TAAAAAATTGTAAAATTTTATA-AAATTG
1 TAAAAAATTATAAAAATATATAGAAA-TA
6635206 TAAAAAATTA-AAAAATATATAGAAATA
1 TAAAAAATTATAAAAATATATAGAAATA
* * *
6635233 T-AAAAATTATATAAATTTATA-AAGTCA
1 TAAAAAATTATAAAAATATATAGAAAT-A
* * *
6635260 TGAGAAAATTATACAAAATGTAAAGAAATA
1 T-AAAAAATTATA-AAAATATATAGAAATA
6635290 TAAAAAATTATAAAA
1 TAAAAAATTATAAAA
6635305 GTTATCGTTC
Statistics
Matches: 79, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
26 11 0.14
27 22 0.28
28 15 0.19
29 19 0.24
30 9 0.11
31 3 0.04
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (28 bp):
TAAAAAATTATAAAAATATATAGAAATA
Found at i:6642148 original size:30 final size:30
Alignment explanation
Indices: 6642114--6642173 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
6642104 ACTTAACAAG
6642114 CAAATACCTCTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
*
6642144 CAAATACCTTTAAAATAATAACAAAATTAA
1 CAAATACCTCTAAAATAATAACAAAATTAA
6642174 TAATAAAATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.15, G:0.00, T:0.25
Consensus pattern (30 bp):
CAAATACCTCTAAAATAATAACAAAATTAA
Found at i:6644044 original size:15 final size:15
Alignment explanation
Indices: 6644015--6644052 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
6644005 TTTGAGGTTT
*
6644015 AATATT-TTTTTATA
1 AATATTATTTTAATA
6644029 AATATTATTTTAATA
1 AATATTATTTTAATA
*
6644044 AATAATATT
1 AATATTATT
6644053 AATAAATTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 6 0.29
15 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
AATATTATTTTAATA
Found at i:6649155 original size:19 final size:19
Alignment explanation
Indices: 6649131--6649167 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
6649121 GAAAACCAAT
6649131 TAATAACAACT-AATTCAAA
1 TAATAACAA-TGAATTCAAA
6649150 TAATAACAATGAATTCAA
1 TAATAACAATGAATTCAA
6649168 TAAATTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 1 0.06
19 16 0.94
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.27
Consensus pattern (19 bp):
TAATAACAATGAATTCAAA
Found at i:6654225 original size:7 final size:7
Alignment explanation
Indices: 6654209--6654237 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
6654199 TAATTAAATA
6654209 TTTTTA-
1 TTTTTAC
6654215 TTTTTAC
1 TTTTTAC
6654222 TTTTTAC
1 TTTTTAC
6654229 TTTTTAC
1 TTTTTAC
6654236 TT
1 TT
6654238 CTTTTAACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.14, C:0.10, G:0.00, T:0.76
Consensus pattern (7 bp):
TTTTTAC
Found at i:6654643 original size:30 final size:30
Alignment explanation
Indices: 6654602--6654663 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
6654592 AAATTACACC
6654602 AACAATCACTCAACTTTGAG-AAAATAATAA
1 AACAATCACTCAA-TTTGAGAAAAATAATAA
* *
6654632 AACAGTCACTCAATTTTAGAAAAATAATAA
1 AACAATCACTCAATTTGAGAAAAATAATAA
6654662 AA
1 AA
6654664 TAGTTACCCA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 24 0.83
ACGTcount: A:0.55, C:0.15, G:0.06, T:0.24
Consensus pattern (30 bp):
AACAATCACTCAATTTGAGAAAAATAATAA
Found at i:6655566 original size:3 final size:3
Alignment explanation
Indices: 6655552--6655581 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
6655542 GTATCTCCAT
6655552 TTC TTC TT- TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
6655582 ACTGCCCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TTC
Found at i:6655765 original size:29 final size:29
Alignment explanation
Indices: 6655720--6655796 Score: 82
Period size: 29 Copynumber: 2.6 Consensus size: 29
6655710 TGTTATTTTT
*
6655720 TTTTCTAAAGTTTAGTGATTGAGTTGTAAC
1 TTTTC-AAAGTTAAGTGATTGAGTTGTAAC
* * * *
6655750 TTTTCAAAGTTAAGTGGTTGATTTGTTAT
1 TTTTCAAAGTTAAGTGATTGAGTTGTAAC
6655779 TTTACTCAAAGTTAAGTG
1 TTT--TCAAAGTTAAGTG
6655797 GCTAATGGTG
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
29 22 0.55
30 5 0.12
31 13 0.32
ACGTcount: A:0.27, C:0.06, G:0.19, T:0.47
Consensus pattern (29 bp):
TTTTCAAAGTTAAGTGATTGAGTTGTAAC
Found at i:6655814 original size:31 final size:31
Alignment explanation
Indices: 6655753--6655814 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
6655743 TTGTAACTTT
* * * *
6655753 TCAAAGTTAAGTGGTTGATTTGTTATTTTAC
1 TCAAAGTTAAGTGGCTAATGTGTTACTTTAC
6655784 TCAAAGTTAAGTGGCTAATG-GTGTACTTTAC
1 TCAAAGTTAAGTGGCTAATGTGT-TACTTTAC
6655815 CTTTTTTTAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 2 0.08
31 24 0.92
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (31 bp):
TCAAAGTTAAGTGGCTAATGTGTTACTTTAC
Found at i:6656905 original size:2 final size:2
Alignment explanation
Indices: 6656898--6656951 Score: 90
Period size: 2 Copynumber: 27.0 Consensus size: 2
6656888 AGATATAATG
* *
6656898 TA TA TA TA TA CA TA TA TA TC 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
6656940 TA TA TA TA TA TA
1 TA TA TA TA TA TA
6656952 AAGCAAAACT
Statistics
Matches: 48, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6658502 original size:14 final size:14
Alignment explanation
Indices: 6658485--6658518 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
6658475 ATTATGATTA
6658485 AGGATTTATAGATG
1 AGGATTTATAGATG
*
6658499 AGGATTTATAGGTG
1 AGGATTTATAGATG
6658513 AGGATT
1 AGGATT
6658519 AGGCCTTTGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.32, T:0.35
Consensus pattern (14 bp):
AGGATTTATAGATG
Found at i:6667459 original size:22 final size:21
Alignment explanation
Indices: 6667416--6667456 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
6667406 TTTTAGATAT
*
6667416 TTTAGAATTTTTAACAATTTG
1 TTTAGAAATTTTAACAATTTG
6667437 TTTAGAAAATTTTAA-AATTT
1 TTTAG-AAATTTTAACAATTT
6667457 TGTACTAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 8 0.44
ACGTcount: A:0.39, C:0.02, G:0.07, T:0.51
Consensus pattern (21 bp):
TTTAGAAATTTTAACAATTTG
Found at i:6668353 original size:20 final size:20
Alignment explanation
Indices: 6668328--6668368 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6668318 AAAAATGATA
6668328 AAAATT-TAATTCAATCTTTT
1 AAAATTATAATTCAAT-TTTT
*
6668348 AAAATTATAATTTAATTTTT
1 AAAATTATAATTCAATTTTT
6668368 A
1 A
6668369 CCCTAAAACC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (20 bp):
AAAATTATAATTCAATTTTT
Found at i:6672721 original size:20 final size:19
Alignment explanation
Indices: 6672682--6672732 Score: 84
Period size: 20 Copynumber: 2.6 Consensus size: 19
6672672 TTTTTATACA
6672682 TATTTTGAATTTTAAAATT
1 TATTTTGAATTTTAAAATT
*
6672701 TATTTTGAATATTTGAAATT
1 TATTTTGAAT-TTTAAAATT
6672721 TATTTTGAATTT
1 TATTTTGAATTT
6672733 ATTTTGTAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 12 0.40
20 18 0.60
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (19 bp):
TATTTTGAATTTTAAAATT
Found at i:6672731 original size:11 final size:12
Alignment explanation
Indices: 6672690--6672744 Score: 57
Period size: 11 Copynumber: 5.0 Consensus size: 12
6672680 CATATTTTGA
*
6672690 ATTTTAAAATTT
1 ATTTTGAAATTT
6672702 ATTTTG-AA--T
1 ATTTTGAAATTT
6672711 A-TTTGAAATTT
1 ATTTTGAAATTT
6672722 ATTTTG-AATTT
1 ATTTTGAAATTT
*
6672733 ATTTTGTAATTT
1 ATTTTGAAATTT
6672745 TTGTTGAGAG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
8 4 0.11
9 4 0.11
11 15 0.41
12 14 0.38
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (12 bp):
ATTTTGAAATTT
Found at i:6674569 original size:21 final size:20
Alignment explanation
Indices: 6674543--6674586 Score: 70
Period size: 20 Copynumber: 2.1 Consensus size: 20
6674533 CGTTAAATGC
6674543 TGGTCAAAGGGGCTTTCCCGG
1 TGGTC-AAGGGGCTTTCCCGG
*
6674564 TGGTCAATGGGCTTTCCCGG
1 TGGTCAAGGGGCTTTCCCGG
6674584 TGG
1 TGG
6674587 GCTGCGGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.11, C:0.23, G:0.39, T:0.27
Consensus pattern (20 bp):
TGGTCAAGGGGCTTTCCCGG
Found at i:6676550 original size:12 final size:12
Alignment explanation
Indices: 6676535--6676561 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
6676525 ATTATATAAC
6676535 AAATATATTTAT
1 AAATATATTTAT
6676547 AAATATATTTAT
1 AAATATATTTAT
6676559 AAA
1 AAA
6676562 GGTTGGTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATATATTTAT
Found at i:6678057 original size:5 final size:5
Alignment explanation
Indices: 6678047--6678071 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6678037 TATTTAATTG
6678047 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
6678072 GTTCTTCTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:6679130 original size:27 final size:27
Alignment explanation
Indices: 6679099--6679154 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
6679089 GAGGTTGGGC
6679099 CAAGTCGGGCTAAAGAGGAACTAGAGG
1 CAAGTCGGGCTAAAGAGGAACTAGAGG
6679126 CAAGTCGGGCTAAAGAGGAACTAGAGG
1 CAAGTCGGGCTAAAGAGGAACTAGAGG
6679153 CA
1 CA
6679155 GATGAATTCC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.38, C:0.16, G:0.36, T:0.11
Consensus pattern (27 bp):
CAAGTCGGGCTAAAGAGGAACTAGAGG
Found at i:6687344 original size:25 final size:24
Alignment explanation
Indices: 6687295--6687347 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 24
6687285 AATAATACTA
*
6687295 ATAT-TACATAAAGATATACTTAT
1 ATATATACATAAAGATATACTCAT
6687318 ATATATACATTAAAGATATA-TGCAT
1 ATATATACA-TAAAGATATACT-CAT
6687343 ATATA
1 ATATA
6687348 ATAAAATACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
23 4 0.15
24 5 0.19
25 17 0.65
ACGTcount: A:0.49, C:0.08, G:0.06, T:0.38
Consensus pattern (24 bp):
ATATATACATAAAGATATACTCAT
Found at i:6687433 original size:18 final size:19
Alignment explanation
Indices: 6687402--6687441 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
6687392 TAAAATAGAG
* *
6687402 ATAATAATATACATAATAT
1 ATAATAATACACATAACAT
6687421 ATAA-AATACACATAACAT
1 ATAATAATACACATAACAT
6687439 ATA
1 ATA
6687442 CGTACATAGC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.60, C:0.10, G:0.00, T:0.30
Consensus pattern (19 bp):
ATAATAATACACATAACAT
Found at i:6687836 original size:29 final size:30
Alignment explanation
Indices: 6687813--6687881 Score: 86
Period size: 31 Copynumber: 2.3 Consensus size: 30
6687803 ATATACTTAT
6687813 ATAATAAGAGTAT-ATACTAATATATAATA
1 ATAATAAGAGTATAATACTAATATATAATA
* * *
6687842 ATAATAATAGTATAATATTAATAATATAAAA
1 ATAATAAGAGTATAATACTAAT-ATATAATA
*
6687873 ATAAAAAGA
1 ATAATAAGA
6687882 ATATTTAATA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 12 0.36
30 7 0.21
31 14 0.42
ACGTcount: A:0.61, C:0.01, G:0.06, T:0.32
Consensus pattern (30 bp):
ATAATAAGAGTATAATACTAATATATAATA
Found at i:6687857 original size:17 final size:16
Alignment explanation
Indices: 6687830--6687892 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
6687820 GAGTATATAC
6687830 TAATATATAATAATAA
1 TAATATATAATAATAA
*
6687846 TAATAGTATAATATTAA
1 TAATA-TATAATAATAA
* *
6687863 TAATATAAAAATAAAAA
1 TAATAT-ATAATAATAA
* *
6687880 GAATATTTAATAA
1 TAATATATAATAA
6687893 AGAAATGAAA
Statistics
Matches: 38, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
16 11 0.29
17 27 0.71
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TAATATATAATAATAA
Found at i:6687858 original size:14 final size:14
Alignment explanation
Indices: 6687813--6687876 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
6687803 ATATACTTAT
*
6687813 ATAATAAGAGTATA
1 ATAATAATAGTATA
6687827 TACTAAT-ATA-TAATA
1 -A-TAATAATAGT-ATA
6687842 ATAATAATAGTATA
1 ATAATAATAGTATA
* *
6687856 ATATTAATAATATA
1 ATAATAATAGTATA
*
6687870 AAAATAA
1 ATAATAA
6687877 AAAGAATATT
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
13 4 0.10
14 25 0.62
15 7 0.17
16 4 0.10
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (14 bp):
ATAATAATAGTATA
Found at i:6698953 original size:41 final size:41
Alignment explanation
Indices: 6698896--6698973 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
6698886 AAAATGATTG
6698896 TTTTTATACTTTACCCTTTTAACTTTACCTAAATTTATTTA
1 TTTTTATACTTTACCCTTTTAACTTTACCTAAATTTATTTA
6698937 TTTTTATACTTTACCCTTTTAACTTTACCTAAATTTA
1 TTTTTATACTTTACCCTTTTAACTTTACCTAAATTTA
6698974 GACATTTAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (41 bp):
TTTTTATACTTTACCCTTTTAACTTTACCTAAATTTATTTA
Found at i:6700271 original size:28 final size:27
Alignment explanation
Indices: 6700237--6700302 Score: 78
Period size: 30 Copynumber: 2.3 Consensus size: 27
6700227 ATTTCGATTA
6700237 ATTTAAAATATTTCAATTCGGTTAATG
1 ATTTAAAATATTTCAATTCGGTTAATG
* **
6700264 TATTTAAAATTTTTTTTGATTCGGTTAATG
1 -ATTTAAAA--TATTTCAATTCGGTTAATG
6700294 ATTTAAAAT
1 ATTTAAAAT
6700303 TTTTACATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
27 1 0.03
28 8 0.24
29 8 0.24
30 16 0.48
ACGTcount: A:0.35, C:0.05, G:0.11, T:0.50
Consensus pattern (27 bp):
ATTTAAAATATTTCAATTCGGTTAATG
Found at i:6701371 original size:13 final size:14
Alignment explanation
Indices: 6701355--6701390 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
6701345 CAATCTCATA
6701355 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
6701368 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
6701381 TCTC-ATTTCA
1 TCTCAATTTCA
6701391 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:6701380 original size:18 final size:19
Alignment explanation
Indices: 6701342--6701382 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
6701332 TGGTTCATGT
6701342 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
6701361 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
6701379 TTTC
1 TTTC
6701383 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:6701572 original size:39 final size:38
Alignment explanation
Indices: 6701505--6701639 Score: 101
Period size: 39 Copynumber: 3.4 Consensus size: 38
6701495 ACCAATATGG
* * *
6701505 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATATTTGA
1 CACCCAGTGCCTCATCGGCTAG-CCGAAGAAATATTTGA
* * * *
6701544 CACCCAGTGTCTCATCGGCCTAGCCGAAGTAA-AGTTGG
1 CACCCAGTGCCTCATCGG-CTAGCCGAAGAAATATTTGA
* * * * *
6701582 TACCCAGTACCTCATCGAATCTATCCGAAGAAATATAGTGA
1 CACCCAGTGCCTCATCG--GCTAGCCGAAGAAATAT-TTGA
*
6701623 CACCCAGTGTCTCATCG
1 CACCCAGTGCCTCATCG
6701640 ACTCGAGGTC
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
38 18 0.25
39 35 0.48
40 4 0.05
41 16 0.22
ACGTcount: A:0.28, C:0.28, G:0.20, T:0.24
Consensus pattern (38 bp):
CACCCAGTGCCTCATCGGCTAGCCGAAGAAATATTTGA
Found at i:6701905 original size:18 final size:19
Alignment explanation
Indices: 6701879--6701917 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
6701869 TTTCAATTCA
*
6701879 ATTCAAATAATCAATTTAT
1 ATTCAAATAATCAATATAT
*
6701898 ATTC-AATATTCAATATAT
1 ATTCAAATAATCAATATAT
6701916 AT
1 AT
6701918 ATCTATATAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (19 bp):
ATTCAAATAATCAATATAT
Found at i:6703243 original size:5 final size:5
Alignment explanation
Indices: 6703233--6703285 Score: 61
Period size: 5 Copynumber: 10.0 Consensus size: 5
6703223 TTACTTATTT
* *
6703233 ATATA ATATAA TATATA ATATA ATATA CTATA ATATA ATAATA ATTTA
1 ATATA ATAT-A -ATATA ATATA ATATA ATATA ATATA AT-ATA ATATA
6703281 ATATA
1 ATATA
6703286 TATTTTAACA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
5 30 0.73
6 7 0.17
7 4 0.10
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:6703249 original size:12 final size:12
Alignment explanation
Indices: 6703232--6703287 Score: 69
Period size: 12 Copynumber: 4.5 Consensus size: 12
6703222 TTTACTTATT
6703232 TATATAATATAA
1 TATATAATATAA
6703244 TATATAATATAATA
1 TATATAATAT-A-A
6703258 TACTATAATATAA
1 TA-TATAATATAA
*
6703271 TA-ATAATTTAA
1 TATATAATATAA
6703282 TATATA
1 TATATA
6703288 TTTTAACACA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 10 0.26
12 13 0.33
13 4 0.10
14 4 0.10
15 8 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (12 bp):
TATATAATATAA
Found at i:6713971 original size:18 final size:18
Alignment explanation
Indices: 6713950--6713987 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6713940 TTCAATGTAA
*
6713950 TTAAAT-ATGTATTTATAT
1 TTAAATAATATATTT-TAT
6713968 TTAAATAATATATTTTAT
1 TTAAATAATATATTTTAT
6713986 TT
1 TT
6713988 TATTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (18 bp):
TTAAATAATATATTTTAT
Found at i:6714138 original size:22 final size:21
Alignment explanation
Indices: 6714094--6714147 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
6714084 TTGAAAAAAT
*
6714094 AATATTAGTATTTTAATTATA
1 AATATTAGTATTATAATTATA
6714115 AATATATAG-ATTATAATTTATA
1 AATAT-TAGTATTATAA-TTATA
6714137 AATATTTAGTA
1 AATA-TTAGTA
6714148 ATAAATGTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
21 11 0.39
22 15 0.54
23 2 0.07
ACGTcount: A:0.46, C:0.00, G:0.06, T:0.48
Consensus pattern (21 bp):
AATATTAGTATTATAATTATA
Found at i:6715273 original size:31 final size:31
Alignment explanation
Indices: 6715205--6715273 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
6715195 TAAGAAAATT
* *
6715205 AATAGTGTAATGACTTAAATAAAAACATTTA
1 AATAGTTTAATGAATTAAATAAAAACATTTA
* * *
6715236 AATAGTTTAGTGAATTAAATAAGAACTTTTA
1 AATAGTTTAATGAATTAAATAAAAACATTTA
6715267 AATAGTT
1 AATAGTT
6715274 CAATAACCGG
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (31 bp):
AATAGTTTAATGAATTAAATAAAAACATTTA
Found at i:6716103 original size:4 final size:4
Alignment explanation
Indices: 6716094--6716122 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
6716084 AGCAAACGTG
6716094 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
6716123 TAGAAAAGGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:6716949 original size:47 final size:47
Alignment explanation
Indices: 6716885--6716995 Score: 154
Period size: 47 Copynumber: 2.4 Consensus size: 47
6716875 GACATTGAGT
*
6716885 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCCGGATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
6716932 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
6716979 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
6716996 CTTATCCCGG
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
47 52 0.93
48 4 0.07
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:6718285 original size:4 final size:4
Alignment explanation
Indices: 6718276--6718300 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
6718266 AGCAAACGTG
6718276 AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA A
6718301 TAGAAAAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:6719126 original size:46 final size:47
Alignment explanation
Indices: 6719063--6719172 Score: 145
Period size: 47 Copynumber: 2.4 Consensus size: 47
6719053 GACATTGAGT
*
6719063 CGATG-AGACACTATGTGT-CGACTACTGTTAAAGTTCC-GATTTGTTC
1 CGATGAAG-CACTATGTGTACGA-TAATGTTAAAGTTCCGGATTTGTTC
* * *
6719109 CGATGAAGTACTTTGTGTACTATAATGTTAAAGTTCCGGATTTGTTC
1 CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
6719156 CGATGAAGCACTATGTG
1 CGATGAAGCACTATGTG
6719173 CTTATCCCGG
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
46 27 0.49
47 28 0.51
ACGTcount: A:0.25, C:0.16, G:0.23, T:0.35
Consensus pattern (47 bp):
CGATGAAGCACTATGTGTACGATAATGTTAAAGTTCCGGATTTGTTC
Found at i:6720696 original size:16 final size:17
Alignment explanation
Indices: 6720675--6720717 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
6720665 ATAAAAACTG
*
6720675 AAATTAACAAATT-TAA
1 AAATTAAAAAATTATAA
6720691 AAATTATAAAAATTATAA
1 AAATTA-AAAAATTATAA
6720709 AAATTAAAA
1 AAATTAAAA
6720718 TTAATCAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (17 bp):
AAATTAAAAAATTATAA
Found at i:6720700 original size:9 final size:9
Alignment explanation
Indices: 6720683--6720714 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
6720673 TGAAATTAAC
6720683 AAATT-TAA
1 AAATTATAA
6720691 AAATTATAA
1 AAATTATAA
6720700 AAATTATAA
1 AAATTATAA
6720709 AAATTA
1 AAATTA
6720715 AAATTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
8 5 0.22
9 18 0.78
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:6720719 original size:40 final size:40
Alignment explanation
Indices: 6720647--6720732 Score: 104
Period size: 40 Copynumber: 2.2 Consensus size: 40
6720637 TAGAATTTTT
* *
6720647 TTTAAAAATAATAAAGGTATAAAAACTGAAATTAA-CAAA
1 TTTAAAAATAATAAAAGTATAAAAACTAAAATTAATCAAA
* * *
6720686 TTTAAAAATTATAAAAATTATAAAAATTAAAATTAATCAAA
1 TTTAAAAATAAT-AAAAGTATAAAAACTAAAATTAATCAAA
6720727 -TTAAAA
1 TTTAAAA
6720733 TATAGATACC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
39 11 0.28
40 25 0.62
41 4 0.10
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (40 bp):
TTTAAAAATAATAAAAGTATAAAAACTAAAATTAATCAAA
Found at i:6720802 original size:25 final size:25
Alignment explanation
Indices: 6720774--6720824 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
6720764 AGTTTAACTC
6720774 TCATTATCACCTAACCTAACATTTT
1 TCATTATCACCTAACCTAACATTTT
6720799 TCATTATCACCTAACCTAACATTTT
1 TCATTATCACCTAACCTAACATTTT
6720824 T
1 T
6720825 TTCCACCGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.41
Consensus pattern (25 bp):
TCATTATCACCTAACCTAACATTTT
Found at i:6721328 original size:14 final size:14
Alignment explanation
Indices: 6721308--6721342 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
6721298 ATTTACAAAT
6721308 TAAAAAATAATTATA
1 TAAAAAATAA-TATA
*
6721323 TTAAAAATAATATA
1 TAAAAAATAATATA
6721337 TAAAAA
1 TAAAAA
6721343 TATTCAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
TAAAAAATAATATA
Found at i:6721341 original size:12 final size:15
Alignment explanation
Indices: 6721310--6721344 Score: 56
Period size: 13 Copynumber: 2.5 Consensus size: 15
6721300 TTACAAATTA
6721310 AAAAATAATTATATT
1 AAAAATAATTATATT
6721325 AAAAATAA-TATA-T
1 AAAAATAATTATATT
6721338 AAAAATA
1 AAAAATA
6721345 TTCAATAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 8 0.40
14 4 0.20
15 8 0.40
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AAAAATAATTATATT
Found at i:6721405 original size:26 final size:27
Alignment explanation
Indices: 6721370--6721434 Score: 80
Period size: 27 Copynumber: 2.5 Consensus size: 27
6721360 GTCAAAATTT
*
6721370 TAAAA-AAAATTATAAATAT-TTTTAA
1 TAAAATAAAATTATAAATATATTATAA
*
6721395 TAAAATAAAATTTTAAATATATTATAA
1 TAAAATAAAATTATAAATATATTATAA
* *
6721422 TTAAATTAAATTA
1 TAAAATAAAATTA
6721435 ATTTTTAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
25 5 0.15
26 13 0.39
27 15 0.45
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (27 bp):
TAAAATAAAATTATAAATATATTATAA
Found at i:6721426 original size:28 final size:27
Alignment explanation
Indices: 6721369--6721431 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 27
6721359 TGTCAAAATT
*
6721369 TTAAAA-AAAATTATAAATATTTTTAA
1 TTAAAATAAAATTATAAATATTTATAA
*
6721395 -TAAAATAAAATTTTAAATATATTATAA
1 TTAAAATAAAATTATAAATAT-TTATAA
*
6721422 TTAAATTAAA
1 TTAAAATAAA
6721432 TTAATTTTTA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 5 0.16
26 13 0.42
27 5 0.16
28 8 0.26
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (27 bp):
TTAAAATAAAATTATAAATATTTATAA
Found at i:6734161 original size:20 final size:19
Alignment explanation
Indices: 6734123--6734167 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
6734113 ATAAGGTTGT
* *
6734123 ATAAAAAAAATATTTAAGG
1 ATAAAAAAAAAATTAAAGG
6734142 ATAAAAAAGAAAATTAAAGG
1 ATAAAAAA-AAAATTAAAGG
*
6734162 TTAAAA
1 ATAAAA
6734168 TGTTGCTATC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.67, C:0.00, G:0.11, T:0.22
Consensus pattern (19 bp):
ATAAAAAAAAAATTAAAGG
Found at i:6735577 original size:27 final size:26
Alignment explanation
Indices: 6735529--6735581 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 26
6735519 TTTCATCTCC
**
6735529 ATCTTGATCATCATTACAATCAATCAA
1 ATCTTGATCATCACCACAATC-ATCAA
6735556 ATCTTGATCATCACCATC-ATCATCAA
1 ATCTTGATCATCACCA-CAATCATCAA
6735582 GAAATTTAAG
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 5 0.22
27 17 0.74
28 1 0.04
ACGTcount: A:0.38, C:0.26, G:0.04, T:0.32
Consensus pattern (26 bp):
ATCTTGATCATCACCACAATCATCAA
Found at i:6736463 original size:25 final size:25
Alignment explanation
Indices: 6736413--6736463 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
6736403 TTTAAAATGT
* * *
6736413 AAAATAATAATAATTAAAAATTAGA
1 AAAATAAAAATAATGAAAAATAAGA
6736438 AAAATAAAAAT-ATGAAAATATAAGA
1 AAAATAAAAATAATGAAAA-ATAAGA
6736463 A
1 A
6736464 TTTTTATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 6 0.27
25 16 0.73
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (25 bp):
AAAATAAAAATAATGAAAAATAAGA
Found at i:6736601 original size:19 final size:19
Alignment explanation
Indices: 6736577--6736613 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
6736567 CAAAAGTTTG
*
6736577 GTTTTTTTTTTCAATTTTC
1 GTTTTTTTTATCAATTTTC
6736596 GTTTTTTTTATCAATTTT
1 GTTTTTTTTATCAATTTT
6736614 AAATTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.14, C:0.08, G:0.05, T:0.73
Consensus pattern (19 bp):
GTTTTTTTTATCAATTTTC
Found at i:6737301 original size:39 final size:42
Alignment explanation
Indices: 6737252--6737329 Score: 117
Period size: 39 Copynumber: 1.9 Consensus size: 42
6737242 GTCTCAAAAT
6737252 TATTATTTTAGAAAATTTTT-AAAATTTTA-ACTTTTTTATA
1 TATTATTTTAGAAAATTTTTAAAAATTTTAGACTTTTTTATA
* *
6737292 TATT-TTTTAGAAATTTTTTAAAAATTTTAGATTTTTTT
1 TATTATTTTAGAAAATTTTTAAAAATTTTAGACTTTTTT
6737330 TAAATATAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 14 0.41
40 13 0.38
41 7 0.21
ACGTcount: A:0.35, C:0.01, G:0.04, T:0.60
Consensus pattern (42 bp):
TATTATTTTAGAAAATTTTTAAAAATTTTAGACTTTTTTATA
Found at i:6737366 original size:20 final size:20
Alignment explanation
Indices: 6737255--6737390 Score: 63
Period size: 19 Copynumber: 6.8 Consensus size: 20
6737245 TCAAAATTAT
*
6737255 TATTTTAGAAAATTTT-TAAA
1 TATTTT-GAAATTTTTATAAA
* *
6737275 -ATTTT-AACTTTTTTATATA
1 TATTTTGAA-ATTTTTATAAA
*
6737294 TTTTTTAGAAATTTTT-TAAA
1 TATTTT-GAAATTTTTATAAA
* * *
6737314 AATTTT-AGATTTTTTTTAAA
1 TATTTTGA-AATTTTTATAAA
6737334 TATAAAATTTGAAATTTTTATAAA
1 TAT----TTTGAAATTTTTATAAA
*
6737358 TATTTTG-AA-TTTTAAAAA
1 TATTTTGAAATTTTTATAAA
6737376 TTATTTTG-AATTTTT
1 -TATTTTGAAATTTTT
6737391 GAAAAAAAAT
Statistics
Matches: 89, Mismatches: 13, Indels: 28
0.68 0.10 0.22
Matches are distributed among these distances:
17 2 0.02
18 13 0.15
19 25 0.28
20 25 0.28
21 5 0.06
22 2 0.02
24 16 0.18
25 1 0.01
ACGTcount: A:0.38, C:0.01, G:0.04, T:0.57
Consensus pattern (20 bp):
TATTTTGAAATTTTTATAAA
Found at i:6737368 original size:19 final size:20
Alignment explanation
Indices: 6737341--6737396 Score: 71
Period size: 19 Copynumber: 2.8 Consensus size: 20
6737331 AAATATAAAA
*
6737341 TTTGAAATTTTTATAAA-TAT
1 TTTG-AATTTTTAAAAATTAT
6737361 TTTGAA-TTTTAAAAATTAT
1 TTTGAATTTTTAAAAATTAT
6737380 TTTGAATTTTTGAAAAA
1 TTTGAATTTTT-AAAAA
6737397 AAATTGTAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.25
19 11 0.34
20 8 0.25
21 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (20 bp):
TTTGAATTTTTAAAAATTAT
Found at i:6737685 original size:31 final size:31
Alignment explanation
Indices: 6737636--6737697 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
6737626 AATTGTACTC
* * *
6737636 ACCCAATGAAATAGATGATTAGATTAGGGAG
1 ACCCAACGAAATAAATGATTAGAATAGGGAG
*
6737667 ACCCAACGAGATAAATGATTAGAATAGGGAG
1 ACCCAACGAAATAAATGATTAGAATAGGGAG
6737698 GAACAAGGAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.44, C:0.11, G:0.26, T:0.19
Consensus pattern (31 bp):
ACCCAACGAAATAAATGATTAGAATAGGGAG
Found at i:6740175 original size:28 final size:28
Alignment explanation
Indices: 6740141--6740199 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
6740131 AATTATTTTT
*
6740141 AAATAA-TTTTAATGATTTTAAATTTTAA
1 AAATAATTTTTAA-AATTTTAAATTTTAA
6740169 AAATAATTTTTAAAATTTTAAATTTTAA
1 AAATAATTTTTAAAATTTTAAATTTTAA
6740197 AAA
1 AAA
6740200 ACTAATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (28 bp):
AAATAATTTTTAAAATTTTAAATTTTAA
Found at i:6740179 original size:39 final size:36
Alignment explanation
Indices: 6740120--6740197 Score: 104
Period size: 39 Copynumber: 2.1 Consensus size: 36
6740110 AAATTTTAAA
*
6740120 AAATATTTAAAAATTATTTTTAAATAATTTTAATGATTTT
1 AAATATTTAAAAATAATTTTT-AA-AATTTTAA--ATTTT
6740160 AAAT-TTTAAAAATAATTTTTAAAATTTTAAATTTT
1 AAATATTTAAAAATAATTTTTAAAATTTTAAATTTT
6740195 AAA
1 AAA
6740198 AAACTAATTA
Statistics
Matches: 37, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
35 8 0.22
37 8 0.22
38 2 0.05
39 15 0.41
40 4 0.11
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (36 bp):
AAATATTTAAAAATAATTTTTAAAATTTTAAATTTT
Found at i:6740191 original size:19 final size:19
Alignment explanation
Indices: 6740095--6740191 Score: 57
Period size: 19 Copynumber: 5.4 Consensus size: 19
6740085 CACATAAGCA
*
6740095 TTTAATTAATTTTTAAAAT
1 TTTAAATAATTTTTAAAAT
* *
6740114 TTTAAAAAATATTTAAAA-
1 TTTAAATAATTTTTAAAAT
* *
6740132 ATT--AT--TTTTAAATAAT
1 TTTAAATAATTTTTAA-AAT
*
6740148 TTT-AATGA-TTTT-AAAT
1 TTTAAATAATTTTTAAAAT
6740164 TTTAAAAATAATTTTTAAAAT
1 TTT--AAATAATTTTTAAAAT
6740185 TTTAAAT
1 TTTAAAT
6740192 TTTAAAAAAC
Statistics
Matches: 58, Mismatches: 10, Indels: 20
0.66 0.11 0.23
Matches are distributed among these distances:
14 5 0.09
15 2 0.03
16 9 0.16
17 3 0.05
18 5 0.09
19 23 0.40
20 4 0.07
21 7 0.12
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (19 bp):
TTTAAATAATTTTTAAAAT
Found at i:6748679 original size:27 final size:27
Alignment explanation
Indices: 6748637--6748688 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
6748627 ATCTAAATCA
*
6748637 TCCAACACTTGTGTTTCGC-CACCAAAG
1 TCCAACACTTGAGTTTC-CTCACCAAAG
6748664 TCCAACACTTGAGTTTCCTCACCAA
1 TCCAACACTTGAGTTTCCTCACCAA
6748689 GGTTTAGAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 1 0.04
27 22 0.96
ACGTcount: A:0.27, C:0.35, G:0.12, T:0.27
Consensus pattern (27 bp):
TCCAACACTTGAGTTTCCTCACCAAAG
Found at i:6755796 original size:43 final size:43
Alignment explanation
Indices: 6755735--6755891 Score: 278
Period size: 43 Copynumber: 3.7 Consensus size: 43
6755725 CCGGCATTAC
*
6755735 GCCTGCTAGGCACGAAGGCCCGAATACACATCACTGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
6755778 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
* *
6755821 GCCTGCTAGGTACGAAGGCCCGAATACACATCACCGGCACAAA
1 GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
*
6755864 GCCTACTAGGCACGAAGGCCCGAATACA
1 GCCTGCTAGGCACGAAGGCCCGAATACA
6755892 ATACCAACAC
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 109 1.00
ACGTcount: A:0.31, C:0.33, G:0.25, T:0.11
Consensus pattern (43 bp):
GCCTGCTAGGCACGAAGGCCCGAATACACATCACCGGCACGAA
Found at i:6755950 original size:38 final size:38
Alignment explanation
Indices: 6755906--6756004 Score: 144
Period size: 38 Copynumber: 2.6 Consensus size: 38
6755896 CAACACTAGG
*
6755906 CTGCGGGATTTATCCCGGATATAATACCAGCACGAAGC
1 CTGCGGGATTTAACCCGGATATAATACCAGCACGAAGC
**
6755944 CTGCGGGATTTAACCCGGATATTTTACCAGCACGAAGC
1 CTGCGGGATTTAACCCGGATATAATACCAGCACGAAGC
*
6755982 CTGCGGGTCTTTAAGCCCGGATA
1 CTGCGGG-ATTTAA-CCCGGATA
6756005 CACATCAAAT
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
38 42 0.76
39 5 0.09
40 8 0.15
ACGTcount: A:0.25, C:0.26, G:0.25, T:0.23
Consensus pattern (38 bp):
CTGCGGGATTTAACCCGGATATAATACCAGCACGAAGC
Found at i:6760652 original size:88 final size:88
Alignment explanation
Indices: 6760554--6760751 Score: 224
Period size: 94 Copynumber: 2.2 Consensus size: 88
6760544 TTAATGGTGC
* * * *
6760554 AAAAAGCCCTCAAACTTTA-AAAAA-AA-AAAGCCCTTACTCTTTTCTT-TTTTTCACTCAATTG
1 AAAAAACCCTCAAACTTTAGAAAAACAATAAAGCCCCTACT-TTTT-TTCTTTTGCAATCAATTG
* *
6760615 GGTACTTTAACTTTCAAAATGCATCAA
64 GGTACTTAAAATTTCAAAATGCAT--A
* *
6760642 AAAAAACCCTCAAACTTTTTTAGAAAAACCAATTAAGCCCCTACTTTTTTTCTTTTGCAATTAAT
1 AAAAAACCCTCAAAC---TTTAGAAAAA-CAATAAAGCCCCTACTTTTTTTCTTTTGCAATCAAT
6760707 TGGGTACTTAAAATTTCAAAATGCATA
62 TGGGTACTTAAAATTTCAAAATGCATA
6760734 AAAAAACCCTCAAACTTT
1 AAAAAACCCTCAAACTTT
6760752 TTCAAAAAGG
Statistics
Matches: 94, Mismatches: 8, Indels: 15
0.80 0.07 0.13
Matches are distributed among these distances:
88 14 0.15
89 3 0.03
91 4 0.04
92 21 0.22
93 2 0.02
94 40 0.43
95 10 0.11
ACGTcount: A:0.39, C:0.21, G:0.07, T:0.34
Consensus pattern (88 bp):
AAAAAACCCTCAAACTTTAGAAAAACAATAAAGCCCCTACTTTTTTTCTTTTGCAATCAATTGGG
TACTTAAAATTTCAAAATGCATA
Found at i:6761091 original size:10 final size:9
Alignment explanation
Indices: 6761044--6761193 Score: 56
Period size: 9 Copynumber: 15.6 Consensus size: 9
6761034 CATGCGGCAA
6761044 AAAAATTAT
1 AAAAATTAT
*
6761053 AATAA--AT
1 AAAAATTAT
*
6761060 AAAAATAAAT
1 AAAAAT-TAT
*
6761070 AAAAGTTAT
1 AAAAATTAT
6761079 AAAAATTAGT
1 AAAAATTA-T
**
6761089 AAATTTTAATT
1 AAAAATT-A-T
6761100 AAAAA-TATT
1 AAAAATTA-T
*
6761109 AAAATTTTATT
1 AAAA-ATTA-T
6761120 AAAAATTAGAAT
1 AAAAATT---AT
6761132 AAAAAATTAT
1 -AAAAATTAT
* *
6761142 AAAAACCATAA
1 AAAAA--TTAT
6761153 AAAAATTAT
1 AAAAATTAT
6761162 -AAAATTAT
1 AAAAATTAT
*
6761170 AAAATTTTAT
1 AAAA-ATTAT
*
6761180 AAAAATCAT
1 AAAAATTAT
6761189 AAAAA
1 AAAAA
6761194 AATTAATAAA
Statistics
Matches: 107, Mismatches: 19, Indels: 30
0.69 0.12 0.19
Matches are distributed among these distances:
7 6 0.06
8 8 0.07
9 38 0.36
10 26 0.24
11 20 0.19
12 1 0.01
13 8 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.32
Consensus pattern (9 bp):
AAAAATTAT
Found at i:6761104 original size:21 final size:21
Alignment explanation
Indices: 6761078--6761128 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
6761068 ATAAAAGTTA
6761078 TAAAAATTAGT-AAATTTTAAT
1 TAAAAATTAGTAAAATTTT-AT
*
6761099 TAAAAA-TATTAAAATTTTAT
1 TAAAAATTAGTAAAATTTTAT
6761119 TAAAAATTAG
1 TAAAAATTAG
6761129 AATAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.41
Consensus pattern (21 bp):
TAAAAATTAGTAAAATTTTAT
Found at i:6761155 original size:20 final size:20
Alignment explanation
Indices: 6761132--6761216 Score: 95
Period size: 20 Copynumber: 4.3 Consensus size: 20
6761122 AAATTAGAAT
*
6761132 AAAAAATTATAAAAACCATA
1 AAAAAATTATAAAAATCATA
*
6761152 AAAAAATTAT-AAAATTAT-
1 AAAAAATTATAAAAATCATA
**
6761170 AAAATTTTATAAAAATCATA
1 AAAAAATTATAAAAATCATA
6761190 AAAAAATTA-ATAAAATGCATA
1 AAAAAATTATA-AAAAT-CATA
6761211 AAAAAA
1 AAAAAA
6761217 AACTCTTTAA
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.15
19 14 0.26
20 22 0.41
21 10 0.19
ACGTcount: A:0.68, C:0.05, G:0.01, T:0.26
Consensus pattern (20 bp):
AAAAAATTATAAAAATCATA
Found at i:6769126 original size:15 final size:15
Alignment explanation
Indices: 6769103--6769140 Score: 67
Period size: 15 Copynumber: 2.5 Consensus size: 15
6769093 TTTATACTAC
6769103 AAAATATTTATTATT
1 AAAATATTTATTATT
*
6769118 AATATATTTATTATT
1 AAAATATTTATTATT
6769133 AAAATATT
1 AAAATATT
6769141 AATATTGAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:6769239 original size:20 final size:18
Alignment explanation
Indices: 6769216--6769258 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
6769206 TAAAACAAAA
*
6769216 ATTAAAATATTAAATATTTT
1 ATTAAAATAAT-AA-ATTTT
*
6769236 ATTAAATTAATAAATTTT
1 ATTAAAATAATAAATTTT
6769254 ATTAA
1 ATTAA
6769259 TAATTTTATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 10 0.48
19 2 0.10
20 9 0.43
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATTAAAATAATAAATTTT
Found at i:6769250 original size:27 final size:27
Alignment explanation
Indices: 6769220--6769287 Score: 66
Period size: 30 Copynumber: 2.4 Consensus size: 27
6769210 ACAAAAATTA
*
6769220 AAATATTAAATATTTTATTAAATTAAT
1 AAATATTAAATATTTTATTAAATGAAT
* * *
6769247 AAATTTTATTAATAATTTTATTACATGACT
1 AAATATTA--AAT-ATTTTATTAAATGAAT
6769277 AAATA-TAAATA
1 AAATATTAAATA
6769288 ATTAAATATG
Statistics
Matches: 33, Mismatches: 5, Indels: 7
0.73 0.11 0.16
Matches are distributed among these distances:
26 1 0.03
27 10 0.30
29 5 0.15
30 17 0.52
ACGTcount: A:0.50, C:0.03, G:0.01, T:0.46
Consensus pattern (27 bp):
AAATATTAAATATTTTATTAAATGAAT
Found at i:6769265 original size:12 final size:13
Alignment explanation
Indices: 6769241--6769269 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
6769231 ATTTTATTAA
6769241 ATTAATAAATTTT
1 ATTAATAAATTTT
6769254 ATTAAT-AATTTT
1 ATTAATAAATTTT
6769266 ATTA
1 ATTA
6769270 CATGACTAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 10 0.62
13 6 0.38
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATTAATAAATTTT
Found at i:6769280 original size:30 final size:30
Alignment explanation
Indices: 6769223--6769280 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
6769213 AAAATTAAAA
*
6769223 TATTAAATATTTTATTAAATTAATAAATTT
1 TATTAAATATTTTATTAAATGAATAAATTT
* *
6769253 TATT-AATAATTTTATTACATGACTAAAT
1 TATTAAAT-ATTTTATTAAATGAATAAAT
6769281 ATAAATAATT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 3 0.12
30 21 0.88
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.50
Consensus pattern (30 bp):
TATTAAATATTTTATTAAATGAATAAATTT
Found at i:6781460 original size:28 final size:28
Alignment explanation
Indices: 6781420--6781477 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
6781410 GACTCAACGA
6781420 AGTTCAAACTAAACTAGAATATGTTTCT
1 AGTTCAAACTAAACTAGAATATGTTTCT
6781448 AGTTCAAACTAAACTAGAATATGTTTCT
1 AGTTCAAACTAAACTAGAATATGTTTCT
6781476 AG
1 AG
6781478 CCAACCCAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.40, C:0.14, G:0.12, T:0.34
Consensus pattern (28 bp):
AGTTCAAACTAAACTAGAATATGTTTCT
Found at i:6787037 original size:13 final size:13
Alignment explanation
Indices: 6787012--6787053 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
6787002 TTGAGATTTA
6787012 AGGTTTGATGTTTG
1 AGGTTT-ATGTTTG
6787026 AGGTTTATGTTTG
1 AGGTTTATGTTTG
*
6787039 TA-GTTTAAGTTTG
1 -AGGTTTATGTTTG
6787052 AG
1 AG
6787054 TTTTGATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 17 0.68
14 7 0.28
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (13 bp):
AGGTTTATGTTTG
Found at i:6789220 original size:6 final size:6
Alignment explanation
Indices: 6789211--6789266 Score: 58
Period size: 6 Copynumber: 8.7 Consensus size: 6
6789201 TTTTATAATA
* *
6789211 AATTTT AATTGAT AATTTT AATTTT AATTTT AATTTTTT AATTTAT AATGTT
1 AATTTT AATT-TT AATTTT AATTTT AATTTT AA--TTTT AATTT-T AATTTT
6789263 AATT
1 AATT
6789267 GAAAACAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
6 26 0.62
7 10 0.24
8 6 0.14
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.61
Consensus pattern (6 bp):
AATTTT
Found at i:6789264 original size:21 final size:20
Alignment explanation
Indices: 6789226--6789266 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
6789216 TAATTGATAA
*
6789226 TTTTAATTTTAATTTTAATT
1 TTTTAATTTTAATGTTAATT
6789246 TTTTAATTTATAATGTTAATT
1 TTTTAATTT-TAATGTTAATT
6789267 GAAAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (20 bp):
TTTTAATTTTAATGTTAATT
Found at i:6791655 original size:12 final size:12
Alignment explanation
Indices: 6791638--6791663 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6791628 AAAATAGGGC
6791638 TTTAGCGGCGTT
1 TTTAGCGGCGTT
6791650 TTTAGCGGCGTT
1 TTTAGCGGCGTT
6791662 TT
1 TT
6791664 ATCAAAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.08, C:0.15, G:0.31, T:0.46
Consensus pattern (12 bp):
TTTAGCGGCGTT
Found at i:6792379 original size:24 final size:24
Alignment explanation
Indices: 6792352--6792400 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
6792342 CGTATATTTA
*
6792352 TTAAAAGTTTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
6792376 TTAAAAGTCTATATAAAAATTAAT
1 TTAAAAGTCTATATAAAAATTAAT
6792400 T
1 T
6792401 GTTATTTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (24 bp):
TTAAAAGTCTATATAAAAATTAAT
Found at i:6792499 original size:7 final size:7
Alignment explanation
Indices: 6792445--6792592 Score: 50
Period size: 7 Copynumber: 20.9 Consensus size: 7
6792435 TTTTTATTAA
6792445 GGTTTAT
1 GGTTTAT
*
6792452 GGATTAT
1 GGTTTAT
*
6792459 GGATTAT
1 GGTTTAT
6792466 GGGTTTAT
1 -GGTTTAT
*
6792474 GGATTAT
1 GGTTTAT
* *
6792481 GATTTAC
1 GGTTTAT
*
6792488 AGTTTAT
1 GGTTTAT
*
6792495 GGTTTAA
1 GGTTTAT
* **
6792502 GGGTTGG
1 GGTTTAT
*
6792509 GGTTTAA
1 GGTTTAT
6792516 GGTTTA-
1 GGTTTAT
6792522 GGTGTTA-
1 GGT-TTAT
*
6792529 GGTGTTAG
1 GGT-TTAT
* *
6792537 GGGTTAG
1 GGTTTAT
*
6792544 GGGTTAT
1 GGTTTAT
*
6792551 GGGTTAT
1 GGTTTAT
*
6792558 GGGTTTAA
1 -GGTTTAT
*
6792566 GGGTTAT
1 GGTTTAT
6792573 -GTTGTAT
1 GGTT-TAT
* *
6792580 GATTTAG
1 GGTTTAT
6792587 GGTTTA
1 GGTTTA
6792593 GGGGATAAAA
Statistics
Matches: 108, Mismatches: 27, Indels: 12
0.73 0.18 0.08
Matches are distributed among these distances:
6 5 0.05
7 88 0.81
8 15 0.14
ACGTcount: A:0.20, C:0.01, G:0.36, T:0.44
Consensus pattern (7 bp):
GGTTTAT
Found at i:6792543 original size:21 final size:21
Alignment explanation
Indices: 6792519--6792573 Score: 58
Period size: 22 Copynumber: 2.6 Consensus size: 21
6792509 GGTTTAAGGT
*
6792519 TTAGGTGTTA-GGTGTTAGGGG
1 TTAGGGGTTATGG-GTTAGGGG
*
6792540 TTAGGGGTTATGGGTTATGGGT
1 TTAGGGGTTATGGGTTA-GGGG
*
6792562 TTAAGGGTTATG
1 TTAGGGGTTATG
6792574 TTGTATGATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 13 0.45
22 16 0.55
ACGTcount: A:0.16, C:0.00, G:0.44, T:0.40
Consensus pattern (21 bp):
TTAGGGGTTATGGGTTAGGGG
Found at i:6792571 original size:15 final size:15
Alignment explanation
Indices: 6792532--6792573 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
6792522 GGTGTTAGGT
*
6792532 GTTAGGGGTTA-GGG
1 GTTAAGGGTTATGGG
*
6792546 GTTATGGGTTATGGG
1 GTTAAGGGTTATGGG
*
6792561 TTTAAGGGTTATG
1 GTTAAGGGTTATG
6792574 TTGTATGATT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
14 10 0.42
15 14 0.58
ACGTcount: A:0.17, C:0.00, G:0.45, T:0.38
Consensus pattern (15 bp):
GTTAAGGGTTATGGG
Found at i:6792928 original size:21 final size:21
Alignment explanation
Indices: 6792891--6792934 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
6792881 AATTTAATCT
*
6792891 AATTATTTTAAATATTACTTA
1 AATTATTTTAAAAATTACTTA
*
6792912 AATT-TTTTAAAAAATTATTTA
1 AATTATTTT-AAAAATTACTTA
6792933 AA
1 AA
6792935 ATTAATATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTATTTTAAAAATTACTTA
Found at i:6792946 original size:22 final size:23
Alignment explanation
Indices: 6792921--6792984 Score: 71
Period size: 22 Copynumber: 2.9 Consensus size: 23
6792911 AAATTTTTTA
*
6792921 AAAAATTATTTAAAATT-AATAT
1 AAAAATTATTAAAAATTCAATAT
6792943 AAAAGA-TA-TAAAAATTCAATAT
1 AAAA-ATTATTAAAAATTCAATAT
* *
6792965 AAAAATTATAAAAAAGTCAA
1 AAAAATTATTAAAAATTCAA
6792985 ACATTAGCGG
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
21 8 0.23
22 17 0.49
23 10 0.29
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.30
Consensus pattern (23 bp):
AAAAATTATTAAAAATTCAATAT
Found at i:6793020 original size:40 final size:40
Alignment explanation
Indices: 6792976--6793098 Score: 176
Period size: 40 Copynumber: 3.1 Consensus size: 40
6792966 AAAATTATAA
* *
6792976 AAAAGTCAAACATTAGCGGCGTTTATGATAAAAACGCCGC
1 AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
*
6793016 AAAAGACAAGCAATAGCGGCGTTTAT-ATAAAAACGCCGC
1 AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
* * * *
6793055 AAAAGGCAATCAATAGCAGCGTTTATGATAAAAACGCCAC
1 AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
6793095 AAAA
1 AAAA
6793099 AGTAATTTAT
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
39 36 0.48
40 39 0.52
ACGTcount: A:0.45, C:0.20, G:0.19, T:0.17
Consensus pattern (40 bp):
AAAAGACAAACAATAGCGGCGTTTATGATAAAAACGCCGC
Found at i:6793057 original size:39 final size:40
Alignment explanation
Indices: 6792989--6793098 Score: 177
Period size: 39 Copynumber: 2.8 Consensus size: 40
6792979 AGTCAAACAT
6792989 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
* *
6793029 TAGCGGCGTTTAT-ATAAAAACGCCGCAAAAGGCAATCAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
* *
6793068 TAGCAGCGTTTATGATAAAAACGCCACAAAA
1 TAGCGGCGTTTATGATAAAAACGCCGCAAAA
6793099 AGTAATTTAT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
39 36 0.55
40 29 0.45
ACGTcount: A:0.43, C:0.20, G:0.20, T:0.17
Consensus pattern (40 bp):
TAGCGGCGTTTATGATAAAAACGCCGCAAAAGACAAGCAA
Found at i:6793288 original size:20 final size:19
Alignment explanation
Indices: 6793267--6793304 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
6793257 TATTTCTCTC
*
6793267 CCCCGATTCCCTTTTCTTT
1 CCCCAATTCCCTTTTCTTT
6793286 -CCCAATTCCCTTTTCTTT
1 CCCCAATTCCCTTTTCTTT
6793304 C
1 C
6793305 TCAGCCTTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.08, C:0.42, G:0.03, T:0.47
Consensus pattern (19 bp):
CCCCAATTCCCTTTTCTTT
Found at i:6796228 original size:33 final size:33
Alignment explanation
Indices: 6796177--6796243 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
6796167 ATCCTTTGGA
* *
6796177 TCTCTTTGCTACTAGTTCCAATGTGTATCTTCT
1 TCTCATTGCTACTAGTTCCAATGCGTATCTTCT
* *
6796210 TCTCATTGCTACTGGTTCCAATGCGTATGTTCT
1 TCTCATTGCTACTAGTTCCAATGCGTATCTTCT
6796243 T
1 T
6796244 AAGTATGAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.15, C:0.24, G:0.15, T:0.46
Consensus pattern (33 bp):
TCTCATTGCTACTAGTTCCAATGCGTATCTTCT
Done.