Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2045
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: 191657
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Found at i:3977 original size:25 final size:25
Alignment explanation
Indices: 3949--4047 Score: 76
Period size: 25 Copynumber: 3.8 Consensus size: 25
3939 AATAAAAATT
3949 AGCCACCAATTTTGACAAATA-AACA
1 AGCCACCAATTTTGACAAATACAA-A
*
3974 AGCCTCC-ATATTTGACAAATACAAA
1 AGCCACCAAT-TTTGACAAATACAAA
* *
3999 AGAAACCACCATTTTTGACAAACACAAAA
1 AG---CCACCAATTTTGACAAATAC-AAA
* *
4028 TAACCACCATTTTTGACAAA
1 -AGCCACCAATTTTGACAAA
4048 CAAATGGGTA
Statistics
Matches: 61, Mismatches: 5, Indels: 14
0.76 0.06 0.17
Matches are distributed among these distances:
24 2 0.03
25 20 0.33
26 2 0.03
27 17 0.28
28 15 0.25
29 4 0.07
30 1 0.02
ACGTcount: A:0.46, C:0.24, G:0.07, T:0.22
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATACAAA
Found at i:4018 original size:28 final size:27
Alignment explanation
Indices: 3951--4047 Score: 110
Period size: 28 Copynumber: 3.6 Consensus size: 27
3941 TAAAAATTAG
*
3951 CCACCAATTTTGACAAATA-AACAAG--
1 CCACCATTTTTGACAAATACAA-AAGAA
* *
3976 CCTCCATATTTGACAAATACAAAAGAAA
1 CCACCATTTTTGACAAATACAAAAG-AA
* *
4004 CCACCATTTTTGACAAACACAAAATAA
1 CCACCATTTTTGACAAATACAAAAGAA
4031 CCACCATTTTTGACAAA
1 CCACCATTTTTGACAAA
4048 CAAATGGGTA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
25 19 0.31
26 2 0.03
27 19 0.31
28 21 0.34
ACGTcount: A:0.46, C:0.25, G:0.06, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAATACAAAAGAA
Found at i:4048 original size:27 final size:28
Alignment explanation
Indices: 3979--4049 Score: 108
Period size: 27 Copynumber: 2.6 Consensus size: 28
3969 AAACAAGCCT
* *
3979 CCATATTTGACAAATACAAAAGAAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
*
4007 CCATTTTTGACAAACACAAAA-TAACCA
1 CCATTTTTGACAAACACAAAAGAAACCA
4034 CCATTTTTGACAAACA
1 CCATTTTTGACAAACA
4050 AATGGGTAGC
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
27 21 0.52
28 19 0.47
ACGTcount: A:0.48, C:0.24, G:0.06, T:0.23
Consensus pattern (28 bp):
CCATTTTTGACAAACACAAAAGAAACCA
Found at i:8565 original size:15 final size:15
Alignment explanation
Indices: 8545--8573 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
8535 TATATATACC
8545 AAAGGTTTTATATTG
1 AAAGGTTTTATATTG
8560 AAAGGTTTTATATT
1 AAAGGTTTTATATT
8574 ATTTATTCAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.34, C:0.00, G:0.17, T:0.48
Consensus pattern (15 bp):
AAAGGTTTTATATTG
Found at i:14950 original size:57 final size:57
Alignment explanation
Indices: 14862--14972 Score: 195
Period size: 57 Copynumber: 1.9 Consensus size: 57
14852 AAATGTTTTG
* * *
14862 GCTTTTTTTTATCGATTTGGAGACGATATTTGTCTCTAAAACTTTGGGGATAAATTA
1 GCTTTTTTTTATCAATTTGGAGACAATATTTGTCCCTAAAACTTTGGGGATAAATTA
14919 GCTTTTTTTTATCAATTTGGAGACAATATTTGTCCCTAAAACTTTGGGGATAAA
1 GCTTTTTTTTATCAATTTGGAGACAATATTTGTCCCTAAAACTTTGGGGATAAA
14973 GTTCATCTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
57 51 1.00
ACGTcount: A:0.28, C:0.12, G:0.18, T:0.42
Consensus pattern (57 bp):
GCTTTTTTTTATCAATTTGGAGACAATATTTGTCCCTAAAACTTTGGGGATAAATTA
Found at i:17353 original size:24 final size:24
Alignment explanation
Indices: 17325--17370 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
17315 ATAAAAAATT
17325 AGCCACCAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
17349 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
17371 AAATAACCAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.43, C:0.28, G:0.07, T:0.22
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:17398 original size:28 final size:28
Alignment explanation
Indices: 17351--17428 Score: 99
Period size: 28 Copynumber: 2.9 Consensus size: 28
17341 AAACAACAAG
* *
17351 CCACCATTTTTTAC-AA-ACAAA-AATAA
1 CCACCATATTTGACAAATACAAAGAA-AA
*
17377 CCACCATATTTGACAAATACAAAGGAAA
1 CCACCATATTTGACAAATACAAAGAAAA
17405 CCACCATATTTGACAAATACAAAG
1 CCACCATATTTGACAAATACAAAG
17429 GGTGGCATTT
Statistics
Matches: 46, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
26 12 0.26
27 2 0.04
28 31 0.67
29 1 0.02
ACGTcount: A:0.49, C:0.23, G:0.06, T:0.22
Consensus pattern (28 bp):
CCACCATATTTGACAAATACAAAGAAAA
Found at i:17429 original size:28 final size:28
Alignment explanation
Indices: 17375--17429 Score: 110
Period size: 28 Copynumber: 2.0 Consensus size: 28
17365 AAACAAAAAT
17375 AACCACCATATTTGACAAATACAAAGGA
1 AACCACCATATTTGACAAATACAAAGGA
17403 AACCACCATATTTGACAAATACAAAGG
1 AACCACCATATTTGACAAATACAAAGG
17430 GTGGCATTTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.49, C:0.22, G:0.11, T:0.18
Consensus pattern (28 bp):
AACCACCATATTTGACAAATACAAAGGA
Found at i:21960 original size:24 final size:24
Alignment explanation
Indices: 21932--21977 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
21922 ATAAAAAATT
*
21932 AGCCACTAATTTTGACAAACAACA
1 AGCCACCAATTTTGACAAACAACA
* *
21956 AGCCACCATTTTTTACAAACAA
1 AGCCACCAATTTTGACAAACAA
21978 AAATAATCAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.43, C:0.26, G:0.07, T:0.24
Consensus pattern (24 bp):
AGCCACCAATTTTGACAAACAACA
Found at i:25710 original size:19 final size:18
Alignment explanation
Indices: 25671--25711 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
25661 TGTAATGAGC
*
25671 AAAGAAAAAAAATGAGAA
1 AAAGAAAAAAAATAAGAA
25689 AAAGACAAAAAAATTAAGAA
1 AAAGA-AAAAAAA-TAAGAA
25709 AAA
1 AAA
25712 ATATTTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 7 0.35
20 8 0.40
ACGTcount: A:0.78, C:0.02, G:0.12, T:0.07
Consensus pattern (18 bp):
AAAGAAAAAAAATAAGAA
Found at i:26571 original size:2 final size:2
Alignment explanation
Indices: 26564--26607 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
26554 ATGTGAAATG
26564 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
26606 TA
1 TA
26608 AAGGAAGGAT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:28991 original size:14 final size:14
Alignment explanation
Indices: 28969--29011 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
28959 TTTTATCATG
*
28969 TATTCATATTATAT
1 TATTTATATTATAT
*
28983 TATTTATATCATAT
1 TATTTATATTATAT
*
28997 TTTTTATATTATAT
1 TATTTATATTATAT
29011 T
1 T
29012 CATGTTGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.63
Consensus pattern (14 bp):
TATTTATATTATAT
Found at i:28996 original size:19 final size:19
Alignment explanation
Indices: 28972--29010 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
28962 TATCATGTAT
28972 TCATATTATATTAT-TTATA
1 TCATATT-TATTATATTATA
*
28991 TCATATTTTTTATATTATA
1 TCATATTTATTATATTATA
29010 T
1 T
29011 TCATGTTGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 13 0.72
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (19 bp):
TCATATTTATTATATTATA
Found at i:28997 original size:25 final size:25
Alignment explanation
Indices: 28946--28997 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 25
28936 TATATTAGAG
28946 TCATATTTATATATTTTATCATGTAT
1 TCATATTTATATATTTTATCA-GTAT
28972 TCATA-TTATATTATTTATATCA-TAT
1 TCATATTTATA-TATTT-TATCAGTAT
28997 T
1 T
28998 TTTTATATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
25 9 0.38
26 10 0.42
27 5 0.21
ACGTcount: A:0.33, C:0.08, G:0.02, T:0.58
Consensus pattern (25 bp):
TCATATTTATATATTTTATCAGTAT
Found at i:37113 original size:22 final size:22
Alignment explanation
Indices: 37088--37160 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 22
37078 CACATTTCAC
37088 GGTAAAAATTCCGTAATCCATT
1 GGTAAAAATTCCGTAATCCATT
*
37110 GGTAATAGACCA-T-C-TAGTCCAATT
1 GGTAA-A-A--ATTCCGTAATCC-ATT
*
37134 TGTAAAAATTCCGTAATCCATT
1 GGTAAAAATTCCGTAATCCATT
37156 GGTAA
1 GGTAA
37161 TAGACCATCT
Statistics
Matches: 39, Mismatches: 4, Indels: 16
0.66 0.07 0.27
Matches are distributed among these distances:
20 1 0.03
21 1 0.03
22 14 0.36
23 12 0.31
24 9 0.23
25 1 0.03
26 1 0.03
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.32
Consensus pattern (22 bp):
GGTAAAAATTCCGTAATCCATT
Found at i:37156 original size:46 final size:46
Alignment explanation
Indices: 37089--37180 Score: 184
Period size: 46 Copynumber: 2.0 Consensus size: 46
37079 ACATTTCACG
37089 GTAAAAATTCCGTAATCCATTGGTAATAGACCATCTAGTCCAATTT
1 GTAAAAATTCCGTAATCCATTGGTAATAGACCATCTAGTCCAATTT
37135 GTAAAAATTCCGTAATCCATTGGTAATAGACCATCTAGTCCAATTT
1 GTAAAAATTCCGTAATCCATTGGTAATAGACCATCTAGTCCAATTT
37181 CCAAATTAAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 46 1.00
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.33
Consensus pattern (46 bp):
GTAAAAATTCCGTAATCCATTGGTAATAGACCATCTAGTCCAATTT
Found at i:41483 original size:12 final size:12
Alignment explanation
Indices: 41430--41487 Score: 57
Period size: 12 Copynumber: 4.7 Consensus size: 12
41420 TCATCTCATA
41430 TTTT-TATTATT
1 TTTTATATTATT
41441 TTTTATATCGTATAT
1 TTTTATAT--TAT-T
*
41456 TTTTATATTATA
1 TTTTATATTATT
41468 TTTTA-ATTACTT
1 TTTTATATTA-TT
41480 TTTTATAT
1 TTTTATAT
41488 CGTGTCGAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
11 8 0.21
12 14 0.36
13 5 0.13
14 3 0.08
15 9 0.23
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:45197 original size:8 final size:8
Alignment explanation
Indices: 45184--45209 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
45174 GTGTTCAAAG
45184 AAAAAATA
1 AAAAAATA
45192 AAAAAATA
1 AAAAAATA
45200 AAAAAATA
1 AAAAAATA
45208 AA
1 AA
45210 GGTTTGGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAATA
Found at i:46671 original size:22 final size:22
Alignment explanation
Indices: 46646--46694 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
46636 TAAATCTTAT
*
46646 TATA-TAAATTTTGATATTTTTA
1 TATATTAAATGTT-ATATTTTTA
*
46668 TATATTTAATGTTATATTTTTA
1 TATATTAAATGTTATATTTTTA
46690 T-TATT
1 TATATT
46695 TTTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 4 0.17
22 14 0.58
23 6 0.25
ACGTcount: A:0.33, C:0.00, G:0.04, T:0.63
Consensus pattern (22 bp):
TATATTAAATGTTATATTTTTA
Found at i:46714 original size:15 final size:13
Alignment explanation
Indices: 46665--46745 Score: 64
Period size: 11 Copynumber: 6.3 Consensus size: 13
46655 TTTGATATTT
* *
46665 TTATATATTTAATG
1 TTATAT-TTTTATA
46679 TTATA-TTTT-TA
1 TTATATTTTTATA
46690 TTAT-TTTTTATA
1 TTATATTTTTATA
46702 TCGTATATTTTTATA
1 T--TATATTTTTATA
46717 TTATA-TTTTA-A
1 TTATATTTTTATA
*
46728 TTACTTTTTTTATA
1 TTA-TATTTTTATA
46742 TTAT
1 TTAT
46746 GTCGAAAGAT
Statistics
Matches: 56, Mismatches: 3, Indels: 17
0.74 0.04 0.22
Matches are distributed among these distances:
11 13 0.23
12 12 0.21
13 10 0.18
14 12 0.21
15 9 0.16
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (13 bp):
TTATATTTTTATA
Found at i:51291 original size:25 final size:25
Alignment explanation
Indices: 51229--51326 Score: 101
Period size: 24 Copynumber: 3.8 Consensus size: 25
51219 AATAAAAATT
*
51229 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
51253 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
* *
51278 AGCCTCC-ATATTTGACAAATACAAAGGA
1 AGCCACCAAT-TTTGACAAAT--AAA-CA
* *
51306 AACCACCATTTTTGACAAATA
1 AGCCACCAATTTTGACAAATA
51327 CAAAATAACC
Statistics
Matches: 62, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
24 21 0.34
25 20 0.32
26 1 0.02
27 3 0.05
28 16 0.26
29 1 0.02
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.21
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:51322 original size:28 final size:27
Alignment explanation
Indices: 51231--51351 Score: 101
Period size: 25 Copynumber: 4.6 Consensus size: 27
51221 TAAAAATTAG
* * *
51231 CCACCAATTTTGAC-AA-ACAACA-AG
1 CCACCATTTTTGACAAATACAAAATAA
* * *
51255 CCACCAATTTTGACAAATA-AACA-AG
1 CCACCATTTTTGACAAATACAAAATAA
* *
51280 CCTCCATATTTGACAAATACAAAGGA-AA
1 CCACCATTTTTGACAAATACAAA--ATAA
51308 CCACCATTTTTGACAAATACAAAATAA
1 CCACCATTTTTGACAAATACAAAATAA
*
51335 CCACCATTTTTTACAAA
1 CCACCATTTTTGACAAA
51352 CAAATGGGTG
Statistics
Matches: 83, Mismatches: 8, Indels: 9
0.83 0.08 0.09
Matches are distributed among these distances:
24 14 0.17
25 24 0.29
26 4 0.05
27 18 0.22
28 23 0.28
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (27 bp):
CCACCATTTTTGACAAATACAAAATAA
Found at i:55885 original size:25 final size:25
Alignment explanation
Indices: 55823--55945 Score: 106
Period size: 27 Copynumber: 4.8 Consensus size: 25
55813 AATAAAAATT
*
55823 AGCCACCAATTTTGACAAA-CAACA
1 AGCCACCAATTTTGACAAATAAACA
55847 AGCCACCAATTTTGACAAATAAACA
1 AGCCACCAATTTTGACAAATAAACA
* *
55872 AGCCTCC-ATATTTGACAAATACAAAGGA
1 AGCCACCAAT-TTTGACAAAT--AAA-CA
* * *
55900 AACCACCATTTTTGACAAATACAAAA
1 AGCCACCAATTTTGACAAATA-AACA
* *
55926 TAACCACCATTTTTGACAAA
1 -AGCCACCAATTTTGACAAA
55946 CAAATGGGTG
Statistics
Matches: 84, Mismatches: 7, Indels: 13
0.81 0.07 0.12
Matches are distributed among these distances:
24 21 0.25
25 20 0.24
26 2 0.02
27 24 0.29
28 16 0.19
29 1 0.01
ACGTcount: A:0.46, C:0.24, G:0.08, T:0.22
Consensus pattern (25 bp):
AGCCACCAATTTTGACAAATAAACA
Found at i:55938 original size:27 final size:26
Alignment explanation
Indices: 55825--55945 Score: 122
Period size: 25 Copynumber: 4.7 Consensus size: 26
55815 TAAAAATTAG
* * *
55825 CCACCAATTTTGAC-AA-ACAACAAG
1 CCACCATTTTTGACAAATACAAAAAA
* * *
55849 CCACCAATTTTGACAAATA-AACAAG
1 CCACCATTTTTGACAAATACAAAAAA
* *
55874 CCTCCATATTTGACAAATACAAAGGAAA
1 CCACCATTTTTGACAAATACAAA--AAA
55902 CCACCATTTTTGACAAATACAAAATAA
1 CCACCATTTTTGACAAATACAAAA-AA
55929 CCACCATTTTTGACAAA
1 CCACCATTTTTGACAAA
55946 CAAATGGGTG
Statistics
Matches: 84, Mismatches: 7, Indels: 9
0.84 0.07 0.09
Matches are distributed among these distances:
24 14 0.17
25 24 0.29
26 4 0.05
27 19 0.23
28 23 0.27
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.22
Consensus pattern (26 bp):
CCACCATTTTTGACAAATACAAAAAA
Found at i:55950 original size:24 final size:24
Alignment explanation
Indices: 55825--55950 Score: 92
Period size: 24 Copynumber: 4.9 Consensus size: 24
55815 TAAAAATTAG
* *
55825 CCACCAATTTTGACAAACAACA-AG
1 CCACCATTTTTGACAAACAA-ATAA
* * *
55849 CCACCAATTTTGACAAATAAACAA
1 CCACCATTTTTGACAAACAAATAA
* * *
55873 GCCTCCATATTTGACAAATACAAAGGAAA
1 -CCACCATTTTTGAC-AA-ACAAA--TAA
55902 CCACCATTTTTGACAAATACAAAATAA
1 CCACCATTTTTGAC-AA-AC-AAATAA
55929 CCACCATTTTTGACAAACAAAT
1 CCACCATTTTTGACAAACAAAT
55951 GGGTGGCTTT
Statistics
Matches: 85, Mismatches: 10, Indels: 14
0.78 0.09 0.13
Matches are distributed among these distances:
23 1 0.01
24 24 0.28
25 13 0.15
26 4 0.05
27 20 0.24
28 18 0.21
29 5 0.06
ACGTcount: A:0.46, C:0.25, G:0.07, T:0.22
Consensus pattern (24 bp):
CCACCATTTTTGACAAACAAATAA
Found at i:63093 original size:2 final size:2
Alignment explanation
Indices: 63086--63134 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
63076 ACTCCAAACT
63086 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
63128 TA TA TA T
1 TA TA TA T
63135 GTTCTTTTGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:63464 original size:93 final size:93
Alignment explanation
Indices: 63301--63488 Score: 340
Period size: 93 Copynumber: 2.0 Consensus size: 93
63291 TGGAAACTTA
* *
63301 ATTAACCGGTGGTAATCCCTCTAGCTCATGTCACTTCATTTGGTAACTTGGCCTCCGGTCTTTAC
1 ATTAACCAGTGGTAATCCCTCTAGCTCATGTCACTTCATTTGGTAACTTGGCCTCCGGTCTTCAC
*
63366 ATCTTCATTAATTGACTTTGTGGATGCT
66 ATCTTCATTAATCGACTTTGTGGATGCT
63394 ATTAACCAGTGGTAATCCCTCTAGCTCATGTCACTTCATTTGGTAACTTGGCCTCCGGTCTTCAC
1 ATTAACCAGTGGTAATCCCTCTAGCTCATGTCACTTCATTTGGTAACTTGGCCTCCGGTCTTCAC
*
63459 GTCTTCATTAATCGACTTTGTGGATGCT
66 ATCTTCATTAATCGACTTTGTGGATGCT
63487 AT
1 AT
63489 AATTAATTCA
Statistics
Matches: 91, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.38
Consensus pattern (93 bp):
ATTAACCAGTGGTAATCCCTCTAGCTCATGTCACTTCATTTGGTAACTTGGCCTCCGGTCTTCAC
ATCTTCATTAATCGACTTTGTGGATGCT
Found at i:68174 original size:20 final size:20
Alignment explanation
Indices: 68149--68195 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
68139 AAGAATTGAA
*
68149 GAGGGATACAAGAGAGGGAT
1 GAGGGATACAAGAGAGGGAG
* **
68169 GAGGGATGCTTGAGAGGGAG
1 GAGGGATACAAGAGAGGGAG
68189 GAGGGAT
1 GAGGGAT
68196 CCTCCTTTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.32, C:0.04, G:0.51, T:0.13
Consensus pattern (20 bp):
GAGGGATACAAGAGAGGGAG
Found at i:68310 original size:27 final size:27
Alignment explanation
Indices: 68243--68345 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
68233 TAAAAATTAG
* *
68243 CCACCAATTTTGACAAACAACAA-G--
1 CCACCATTTTTGACAAACAAAAAGGAA
* *
68267 CTACAATTTTTGACAAACAAAAAGGAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* * * *
68294 CCATCATTTTTGACAAATATAAAGTAA
1 CCACCATTTTTGACAAACAAAAAGGAA
* *
68321 CCACCATTGTTGACAAACACAAAGG
1 CCACCATTTTTGACAAACAAAAAGG
68346 GTGGCTTTTG
Statistics
Matches: 61, Mismatches: 15, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
24 19 0.31
25 1 0.02
27 41 0.67
ACGTcount: A:0.46, C:0.21, G:0.11, T:0.22
Consensus pattern (27 bp):
CCACCATTTTTGACAAACAAAAAGGAA
Found at i:72847 original size:23 final size:25
Alignment explanation
Indices: 72813--72882 Score: 81
Period size: 24 Copynumber: 2.8 Consensus size: 25
72803 AATAAAAATT
72813 AGCCACCAA-TTTTGACAAACAACA
1 AGCCACCAATTTTTGACAAACAACA
*
72837 AGCCA-CAATTTTTGACAAACAAAA
1 AGCCACCAATTTTTGACAAACAACA
**
72861 AGGAACCATTATTTTTGACAAA
1 AGCCACCA--ATTTTTGACAAA
72883 TATAAAGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
23 3 0.08
24 22 0.56
25 2 0.05
27 12 0.31
ACGTcount: A:0.46, C:0.21, G:0.10, T:0.23
Consensus pattern (25 bp):
AGCCACCAATTTTTGACAAACAACA
Found at i:72882 original size:27 final size:27
Alignment explanation
Indices: 72844--72917 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
72834 ACAAGCCACA
*
72844 ATTTTTGACAAACAAAAAGGAACCATT
1 ATTTTTGACAAACAAAAAGGAACCATC
* * *
72871 ATTTTTGACAAATATAAAGTAACCATC
1 ATTTTTGACAAACAAAAAGGAACCATC
* *
72898 ATTGTTGACAAACACAAAGG
1 ATTTTTGACAAACAAAAAGG
72918 GTGGCTTTTG
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (27 bp):
ATTTTTGACAAACAAAAAGGAACCATC
Found at i:73242 original size:23 final size:23
Alignment explanation
Indices: 73216--73296 Score: 73
Period size: 21 Copynumber: 3.7 Consensus size: 23
73206 TGTTCTATAA
*
73216 ATTTTGATATATTTTATATATTT
1 ATTTTCATATATTTTATATATTT
73239 A-TTTCATATA-TTTAT-TATTT
1 ATTTTCATATATTTTATATATTT
* *
73259 TTTATATCATATATTTTATAT-TAT
1 ATT-T-TCATATATTTTATATATTT
*
73283 ATTTTAAT-TATTTT
1 ATTTTCATATATTTT
73297 TTCATATCGT
Statistics
Matches: 48, Mismatches: 5, Indels: 12
0.74 0.08 0.18
Matches are distributed among these distances:
20 5 0.10
21 12 0.25
22 12 0.25
23 9 0.19
24 9 0.19
25 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.65
Consensus pattern (23 bp):
ATTTTCATATATTTTATATATTT
Found at i:73247 original size:13 final size:13
Alignment explanation
Indices: 73225--73274 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
73215 AATTTTGATA
*
73225 TATTTTATATATT
1 TATTTCATATATT
73238 TATTTCATATATT
1 TATTTCATATATT
*
73251 TA-TT-AT-TTTT
1 TATTTCATATATT
*
73261 TATATCATATATT
1 TATTTCATATATT
73274 T
1 T
73275 TATATTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
10 5 0.17
11 3 0.10
12 4 0.13
13 18 0.60
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.66
Consensus pattern (13 bp):
TATTTCATATATT
Found at i:73293 original size:37 final size:39
Alignment explanation
Indices: 73230--73304 Score: 104
Period size: 37 Copynumber: 2.0 Consensus size: 39
73220 TGATATATTT
73230 TATATATTTATTTCATATATTTATTATTTTTT-ATATCA
1 TATATATTTATTTCATATATTTATTATTTTTTCATATCA
73268 TATAT-TTTATATT-ATAT-TTTAATTATTTTTTCATATC
1 TATATATTTAT-TTCATATATTT-ATTATTTTTTCATATC
73305 GTGTCGAAAG
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
36 3 0.09
37 19 0.56
38 12 0.35
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (39 bp):
TATATATTTATTTCATATATTTATTATTTTTTCATATCA
Found at i:77419 original size:28 final size:27
Alignment explanation
Indices: 77364--77434 Score: 90
Period size: 27 Copynumber: 2.6 Consensus size: 27
77354 GCCACCCATT
*
77364 TGTTTGTCAAAAATGATGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
77391 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
77419 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
77435 AGGCTTGTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 20 0.51
28 18 0.46
ACGTcount: A:0.24, C:0.07, G:0.23, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:81992 original size:28 final size:27
Alignment explanation
Indices: 81937--82007 Score: 99
Period size: 27 Copynumber: 2.6 Consensus size: 27
81927 GCCACCCATT
81937 TGTTTGTCAAAAATGGTGGTTATTTTG
1 TGTTTGTCAAAAATGGTGGTTATTTTG
81964 TGTTTGTCAAAAATGGTGGTT-TCCTTTG
1 TGTTTGTCAAAAATGGTGGTTAT--TTTG
* *
81992 TATTTGTCAAATATGG
1 TGTTTGTCAAAAATGG
82008 AGGCTTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
26 1 0.03
27 21 0.52
28 18 0.45
ACGTcount: A:0.23, C:0.07, G:0.24, T:0.46
Consensus pattern (27 bp):
TGTTTGTCAAAAATGGTGGTTATTTTG
Found at i:82109 original size:20 final size:20
Alignment explanation
Indices: 82084--82129 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
82074 AAATAGAGGC
*
82084 TCCCTCCTCCCTCTCAAGTA
1 TCCCTCATCCCTCTCAAGTA
**
82104 TCCCTCATCCCTCTCTTGTA
1 TCCCTCATCCCTCTCAAGTA
82124 TCCCTC
1 TCCCTC
82130 TTCAATTCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.11, C:0.50, G:0.04, T:0.35
Consensus pattern (20 bp):
TCCCTCATCCCTCTCAAGTA
Found at i:90860 original size:14 final size:14
Alignment explanation
Indices: 90843--90875 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
90833 TGTGTTATTT
*
90843 TATTTTTTATATCA
1 TATTTTTCATATCA
90857 TATTTTTCATATCA
1 TATTTTTCATATCA
90871 TATTT
1 TATTT
90876 ATATTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (14 bp):
TATTTTTCATATCA
Found at i:92384 original size:16 final size:16
Alignment explanation
Indices: 92365--92401 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
92355 TTCTATGCAT
92365 AATTGACTTCGAACCC
1 AATTGACTTCGAACCC
*
92381 AATTTTACTTCGAACCC
1 AA-TTGACTTCGAACCC
92398 AATT
1 AATT
92402 TTTACTCTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.32, C:0.27, G:0.08, T:0.32
Consensus pattern (16 bp):
AATTGACTTCGAACCC
Found at i:92407 original size:18 final size:17
Alignment explanation
Indices: 92370--92403 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
92360 TGCATAATTG
92370 ACTTCGAACCCAATTTT
1 ACTTCGAACCCAATTTT
92387 ACTTCGAACCCAATTTT
1 ACTTCGAACCCAATTTT
92404 TACTCTACTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.29, G:0.06, T:0.35
Consensus pattern (17 bp):
ACTTCGAACCCAATTTT
Found at i:94496 original size:11 final size:11
Alignment explanation
Indices: 94475--94522 Score: 55
Period size: 10 Copynumber: 4.5 Consensus size: 11
94465 TTTTAATATT
94475 TTTTTAT-ATA
1 TTTTTATCATA
*
94485 TTTATATCATA
1 TTTTTATCATA
*
94496 TTTTTATTAT-
1 TTTTTATCATA
94506 TTTTTATCATA
1 TTTTTATCATA
94517 TATTTT
1 T-TTTT
94523 TATATTATAT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
10 15 0.48
11 12 0.39
12 4 0.13
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (11 bp):
TTTTTATCATA
Found at i:94500 original size:23 final size:21
Alignment explanation
Indices: 94470--94528 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 21
94460 ATAAATTTTA
94470 ATATTTTTTTATATATTTATATC
1 ATATTTTTTTATAT-TTT-TATC
94493 ATATTTTTATTAT-TTTTTATC
1 ATATTTTT-TTATATTTTTATC
*
94514 ATATATTTTTATATT
1 ATATTTTTTTATATT
94529 ATATTTTAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 4 0.12
21 13 0.39
22 3 0.09
23 9 0.27
24 4 0.12
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (21 bp):
ATATTTTTTTATATTTTTATC
Found at i:94501 original size:13 final size:12
Alignment explanation
Indices: 94470--94535 Score: 68
Period size: 13 Copynumber: 5.6 Consensus size: 12
94460 ATAAATTTTA
94470 ATATTTTT-T-T
1 ATATTTTTATAT
*
94480 ATATATTTATAT
1 ATATTTTTATAT
94492 CATATTTTTAT-T
1 -ATATTTTTATAT
94504 AT-TTTTTATCAT
1 ATATTTTTAT-AT
94516 ATATTTTTATATT
1 ATATTTTTATA-T
94529 ATATTTT
1 ATATTTT
94536 AATTACCTCT
Statistics
Matches: 47, Mismatches: 2, Indels: 11
0.78 0.03 0.18
Matches are distributed among these distances:
10 14 0.30
11 3 0.06
12 6 0.13
13 24 0.51
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (12 bp):
ATATTTTTATAT
Found at i:94817 original size:15 final size:16
Alignment explanation
Indices: 94770--94821 Score: 54
Period size: 18 Copynumber: 3.2 Consensus size: 16
94760 TTTTTTAAAA
*
94770 AAAATTATAAGTAGAATT
1 AAAATTATAA--AAAATT
94788 AAAATTATAAAAAATT
1 AAAATTATAAAAAATT
94804 AAGAATT-T-AAAAATT
1 AA-AATTATAAAAAATT
94819 AAA
1 AAA
94822 TAAAAAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
14 1 0.03
15 9 0.28
16 8 0.25
17 4 0.12
18 10 0.31
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (16 bp):
AAAATTATAAAAAATT
Found at i:95023 original size:2 final size:2
Alignment explanation
Indices: 95010--95039 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
95000 AATGTGAAAC
*
95010 AT AT AT AC 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
95040 CATTATTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:95101 original size:29 final size:31
Alignment explanation
Indices: 95041--95101 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
95031 TATATATATC
* *
95041 ATTATTAAGAAATCATGATAGACAAGTTAAT
1 ATTATTAAGAAATCATGATAGAAAAGTAAAT
* *
95072 ATTATTTAGATAT-ATGAT-GAAAAGTAAAT
1 ATTATTAAGAAATCATGATAGAAAAGTAAAT
95101 A
1 A
95102 ATAATATAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
29 10 0.38
30 5 0.19
31 11 0.42
ACGTcount: A:0.49, C:0.03, G:0.13, T:0.34
Consensus pattern (31 bp):
ATTATTAAGAAATCATGATAGAAAAGTAAAT
Found at i:98056 original size:39 final size:39
Alignment explanation
Indices: 98002--98080 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
97992 AATTATTTTC
98002 AAAATTTAAAGAGAACAATTTTATTAGATATCTAATCAT
1 AAAATTTAAAGAGAACAATTTTATTAGATATCTAATCAT
98041 AAAATTTAAAGAGAACAATTTTATTAGATATCTAATCAT
1 AAAATTTAAAGAGAACAATTTTATTAGATATCTAATCAT
98080 A
1 A
98081 CCTAGCTTAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (39 bp):
AAAATTTAAAGAGAACAATTTTATTAGATATCTAATCAT
Found at i:99033 original size:34 final size:34
Alignment explanation
Indices: 98966--99181 Score: 292
Period size: 34 Copynumber: 6.4 Consensus size: 34
98956 AGTTACATCC
* * *
98966 TGTTGATTAAAT-GGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * *
98999 TGTTGATTAAATGGGTGATTTGGTGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
99033 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
99066 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
99100 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
99134 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
99168 TGTTGATTAAATGG
1 TGTTGATTAAATGG
99182 TGGTTTTTAC
Statistics
Matches: 162, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 40 0.25
34 122 0.75
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:99147 original size:68 final size:67
Alignment explanation
Indices: 98966--99183 Score: 319
Period size: 67 Copynumber: 3.2 Consensus size: 67
98956 AGTTACATCC
* * * * *
98966 TGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
99031 AT
66 AT
* * * *
99033 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
99098 AT
66 AT
* * *
99100 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
99165 CAT
65 CAT
99168 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
99184 GTTTTTACCA
Statistics
Matches: 134, Mismatches: 16, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
67 73 0.54
68 61 0.46
ACGTcount: A:0.24, C:0.08, G:0.28, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:99528 original size:20 final size:20
Alignment explanation
Indices: 99486--99549 Score: 87
Period size: 19 Copynumber: 3.3 Consensus size: 20
99476 TGGTTGTCGA
**
99486 GGTACTATTCAC-GTATATA
1 GGTACTATTCACAGTATACG
99505 GGTACTATTCACAGTATACG
1 GGTACTATTCACAGTATACG
99525 GGTACTATTCA-AGTATACG
1 GGTACTATTCACAGTATACG
*
99544 GTTACT
1 GGTACT
99550 GTACACGTGA
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
19 25 0.61
20 16 0.39
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (20 bp):
GGTACTATTCACAGTATACG
Found at i:103684 original size:34 final size:34
Alignment explanation
Indices: 103615--103832 Score: 296
Period size: 34 Copynumber: 6.5 Consensus size: 34
103605 AAGTGGGAGA
* * *
103615 ATTGTTGATTAAAT-GGTGATTTAGTAGTTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * * *
103648 ATTGTTGATTAAATGGGTGATTTGGTGGTTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
103682 ATTGTTGACTAAAT-GGAGATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
*
103715 ATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* *
103749 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
* * *
103783 ATTGTTGACTAAATGGGAGATTTGGTAGGTTGCC
1 ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
103817 ATTGTTGATTAAATGG
1 ATTGTTGATTAAATGG
103833 TGGTTTTTAC
Statistics
Matches: 164, Mismatches: 19, Indels: 3
0.88 0.10 0.02
Matches are distributed among these distances:
33 42 0.26
34 122 0.74
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (34 bp):
ATTGTTGATTAAATGGGAGATTTGGTAGCTTACC
Found at i:103798 original size:68 final size:67
Alignment explanation
Indices: 103615--103834 Score: 323
Period size: 67 Copynumber: 3.3 Consensus size: 67
103605 AAGTGGGAGA
* * * * *
103615 ATTGTTGATTAAATGGTGATTTAGTAGTTTACCATTGTTGATTAAATGGGTGATTTGGTGGTTTG
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
103680 CC
66 CC
* * * *
103682 ATTGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTA
1 ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
103747 CC
66 CC
* * *
103749 ATTGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTT
1 ATTGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTT
103814 GCC
65 GCC
103817 ATTGTTGATTAAATGGTG
1 ATTGTTGATTAAATGGTG
103835 GTTTTTACCA
Statistics
Matches: 136, Mismatches: 16, Indels: 2
0.88 0.10 0.01
Matches are distributed among these distances:
67 75 0.55
68 61 0.45
ACGTcount: A:0.25, C:0.08, G:0.27, T:0.40
Consensus pattern (67 bp):
ATTGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTG
CC
Found at i:106554 original size:13 final size:13
Alignment explanation
Indices: 106536--106569 Score: 54
Period size: 12 Copynumber: 2.8 Consensus size: 13
106526 TTTTATATCG
106536 TATATTTTTAAAT
1 TATATTTTTAAAT
106549 TATA-TTTT-AAT
1 TATATTTTTAAAT
106560 TATATTTTTA
1 TATATTTTTA
106570 TATCGTGTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
11 7 0.37
12 8 0.42
13 4 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (13 bp):
TATATTTTTAAAT
Found at i:110452 original size:17 final size:17
Alignment explanation
Indices: 110422--110454 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
110412 TTGATCAATT
110422 AATTTTAATATTTTTAA
1 AATTTTAATATTTTTAA
110439 AATTTATAAT-TTTTTA
1 AATTT-TAATATTTTTA
110455 GTACAAAGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AATTTTAATATTTTTAA
Found at i:114435 original size:28 final size:27
Alignment explanation
Indices: 114385--114465 Score: 83
Period size: 28 Copynumber: 2.9 Consensus size: 27
114375 AGCCACCAAT
* *
114385 AAATAAGCCTCCATATTTGACAAATACA
1 AAATAA-CCACCATTTTTGACAAATACA
* *
114413 AAGGA-AACCACCATTTTTTACAAACACA
1 AA--ATAACCACCATTTTTGACAAATACA
*
114441 AAATAACCATCATTTTTGACAAATA
1 AAATAACCACCATTTTTGACAAATA
114466 AATGAGATTA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
26 1 0.02
27 18 0.42
28 21 0.49
29 2 0.05
30 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.06, T:0.26
Consensus pattern (27 bp):
AAATAACCACCATTTTTGACAAATACA
Found at i:114555 original size:28 final size:27
Alignment explanation
Indices: 114509--114589 Score: 92
Period size: 28 Copynumber: 2.9 Consensus size: 27
114499 AGCCACCAAT
* *
114509 AAATAAGCCTCCATATTTGACAAATACA
1 AAATAA-CCACCATTTTTGACAAATACA
*
114537 AAGGA-AACCACCATTTTTGACAAACACA
1 AA--ATAACCACCATTTTTGACAAATACA
*
114565 AAATAACCATCATTTTTGACAAATA
1 AAATAACCACCATTTTTGACAAATA
114590 AATGAGTAGC
Statistics
Matches: 45, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
26 1 0.02
27 19 0.42
28 22 0.49
29 2 0.04
30 1 0.02
ACGTcount: A:0.47, C:0.21, G:0.07, T:0.25
Consensus pattern (27 bp):
AAATAACCACCATTTTTGACAAATACA
Found at i:114568 original size:124 final size:124
Alignment explanation
Indices: 114348--114595 Score: 487
Period size: 124 Copynumber: 2.0 Consensus size: 124
114338 TCTAATAAAA
114348 ATTAGCCACCAATTTTGACAAACAACAAGCCACCAATAAATAAGCCTCCATATTTGACAAATACA
1 ATTAGCCACCAATTTTGACAAACAACAAGCCACCAATAAATAAGCCTCCATATTTGACAAATACA
*
114413 AAGGAAACCACCATTTTTTACAAACACAAAATAACCATCATTTTTGACAAATAAATGAG
66 AAGGAAACCACCATTTTTGACAAACACAAAATAACCATCATTTTTGACAAATAAATGAG
114472 ATTAGCCACCAATTTTGACAAACAACAAGCCACCAATAAATAAGCCTCCATATTTGACAAATACA
1 ATTAGCCACCAATTTTGACAAACAACAAGCCACCAATAAATAAGCCTCCATATTTGACAAATACA
114537 AAGGAAACCACCATTTTTGACAAACACAAAATAACCATCATTTTTGACAAATAAATGAG
66 AAGGAAACCACCATTTTTGACAAACACAAAATAACCATCATTTTTGACAAATAAATGAG
114596 TAGCTTTTGT
Statistics
Matches: 123, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
124 123 1.00
ACGTcount: A:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (124 bp):
ATTAGCCACCAATTTTGACAAACAACAAGCCACCAATAAATAAGCCTCCATATTTGACAAATACA
AAGGAAACCACCATTTTTGACAAACACAAAATAACCATCATTTTTGACAAATAAATGAG
Found at i:114580 original size:27 final size:27
Alignment explanation
Indices: 114519--114587 Score: 86
Period size: 27 Copynumber: 2.5 Consensus size: 27
114509 AAATAAGCCT
* *
114519 CCATATTTGACAAATACAAAGGAAACCA
1 CCATTTTTGACAAACACAAA-GAAACCA
114547 CCATTTTTGACAAACACAAA-ATAACCA
1 CCATTTTTGACAAACACAAAGA-AACCA
*
114574 TCATTTTTGACAAA
1 CCATTTTTGACAAA
114588 TAAATGAGTA
Statistics
Matches: 37, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
26 1 0.03
27 18 0.49
28 18 0.49
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.25
Consensus pattern (27 bp):
CCATTTTTGACAAACACAAAGAAACCA
Found at i:115900 original size:25 final size:24
Alignment explanation
Indices: 115872--115996 Score: 97
Period size: 27 Copynumber: 4.9 Consensus size: 24
115862 AAGCCACCCA
115872 TTTGTTTGTCAAAAATGGTGGTTATT
1 TTTGTTTGTCAAAAATGGTGG-T-TT
115898 TTGTGTTTGTCAAAAATGGTGGTTT
1 TT-TGTTTGTCAAAAATGGTGGTTT
* * * *
115923 CCTTTGTATTTGTTAAATATGGAGGCTTG
1 --TTTG--TTTGTCAAAAATGGTGG-TTT
* * *
115952 TTTATTTGTCAAAATTGGTGGCTT
1 TTTGTTTGTCAAAAATGGTGGTTT
* *
115976 GTTGTTTGTCAAAATTGGTGG
1 TTTGTTTGTCAAAAATGGTGG
115997 CTAATTTTTA
Statistics
Matches: 80, Mismatches: 13, Indels: 14
0.75 0.12 0.13
Matches are distributed among these distances:
24 20 0.25
25 15 0.19
26 5 0.06
27 24 0.30
28 14 0.17
29 2 0.03
ACGTcount: A:0.21, C:0.06, G:0.26, T:0.47
Consensus pattern (24 bp):
TTTGTTTGTCAAAAATGGTGGTTT
Found at i:115934 original size:28 final size:27
Alignment explanation
Indices: 115876--115996 Score: 92
Period size: 25 Copynumber: 4.6 Consensus size: 27
115866 CACCCATTTG
*
115876 TTTGTCAAAAATGGTGGTTATTTTGTG
1 TTTGTCAAAAATGGTGGTTATTTTGTA
115903 TTTGTCAAAAATGGTGGTT-TCCTTTGTA
1 TTTGTCAAAAATGGTGGTTAT--TTTGTA
* * * * *
115931 TTTGTTAAATATGGAGGCT-TGTT-TA
1 TTTGTCAAAAATGGTGGTTATTTTGTA
* * *
115956 TTTGTCAAAATTGGTGGCT-TGTTG--
1 TTTGTCAAAAATGGTGGTTATTTTGTA
*
115980 TTTGTCAAAATTGGTGG
1 TTTGTCAAAAATGGTGG
115997 CTAATTTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
24 17 0.21
25 21 0.26
26 3 0.04
27 19 0.23
28 21 0.26
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (27 bp):
TTTGTCAAAAATGGTGGTTATTTTGTA
Found at i:115983 original size:24 final size:25
Alignment explanation
Indices: 115929--115998 Score: 90
Period size: 24 Copynumber: 2.8 Consensus size: 25
115919 GTTTCCTTTG
* *
115929 TATTTGT-TAAATATGGAGGCTTGTT
1 TATTTGTCAAAAT-TGGTGGCTTGTT
115954 TATTTGTCAAAATTGGTGGCTTG-T
1 TATTTGTCAAAATTGGTGGCTTGTT
*
115978 TGTTTGTCAAAATTGGTGGCT
1 TATTTGTCAAAATTGGTGGCT
115999 AATTTTTATT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
24 21 0.51
25 16 0.39
26 4 0.10
ACGTcount: A:0.21, C:0.07, G:0.26, T:0.46
Consensus pattern (25 bp):
TATTTGTCAAAATTGGTGGCTTGTT
Found at i:122781 original size:2 final size:2
Alignment explanation
Indices: 122774--122814 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
122764 TAGATGTGAA
*
122774 AC AC AC AC AC AC AC AT AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
122815 TATATATATA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.46, G:0.00, T:0.02
Consensus pattern (2 bp):
AC
Found at i:125196 original size:2 final size:2
Alignment explanation
Indices: 125189--125216 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
125179 AAGATACGTG
125189 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
125217 GATACATATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:127044 original size:27 final size:26
Alignment explanation
Indices: 126978--127044 Score: 64
Period size: 27 Copynumber: 2.5 Consensus size: 26
126968 TAATGCTTTC
*
126978 AATATATATTTAAATTTTAAAATTTTT
1 AATAT-TATTTAAATATTAAAATTTTT
* **
127005 TATATTAAATAAATAATTAAATATTTTT
1 AATATTATTTAAAT-ATTAAA-ATTTTT
127033 AAT-TTATTTAAA
1 AATATTATTTAAA
127045 AATCAATGTG
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
26 7 0.23
27 16 0.52
28 8 0.26
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (26 bp):
AATATTATTTAAATATTAAAATTTTT
Found at i:129008 original size:13 final size:13
Alignment explanation
Indices: 128972--129010 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
128962 CCATGTAGTA
*
128972 TTTATATTATTTT
1 TTTATATTATATT
128985 TTTATCA-TATATT
1 TTTAT-ATTATATT
128998 TTTATATTATATT
1 TTTATATTATATT
129011 GTAATTACTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
12 1 0.04
13 21 0.91
14 1 0.04
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTATATTATATT
Found at i:129492 original size:2 final size:2
Alignment explanation
Indices: 129485--129509 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
129475 TGTGAAACAT
129485 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 T
129510 CACTATTAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:134076 original size:1 final size:1
Alignment explanation
Indices: 134070--134127 Score: 71
Period size: 1 Copynumber: 58.0 Consensus size: 1
134060 TGGCAATTGG
* ** * *
134070 AAAAAAAAAAAAAAAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
134128 GGTGAAGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.91, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:134100 original size:29 final size:29
Alignment explanation
Indices: 134068--134125 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
134058 CATGGCAATT
134068 GGAAAAAAAAAAAAAAAAAACAAAAAAAA
1 GGAAAAAAAAAAAAAAAAAACAAAAAAAA
*
134097 GGAAAAAGAAAAAAAAAAAACAAAAAAAA
1 GGAAAAAAAAAAAAAAAAAACAAAAAAAA
134126 AAGGTGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (29 bp):
GGAAAAAAAAAAAAAAAAAACAAAAAAAA
Found at i:134109 original size:31 final size:30
Alignment explanation
Indices: 134068--134129 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
134058 CATGGCAATT
*
134068 GGAAAAAAAAAAAAAAAAA-ACAAAAAAAA
1 GGAAAAAAAAAAAAAAAAACAAAAAAAAAA
134097 GGAAAAAGAAAAAAAAAAAACAAAAAAAAAA
1 GGAAAAA-AAAAAAAAAAAACAAAAAAAAAA
134128 GG
1 GG
134130 TGAAGATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 7 0.23
30 12 0.40
31 11 0.37
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (30 bp):
GGAAAAAAAAAAAAAAAAACAAAAAAAAAA
Found at i:142658 original size:1 final size:1
Alignment explanation
Indices: 142652--142709 Score: 71
Period size: 1 Copynumber: 58.0 Consensus size: 1
142642 TGGCAATTGG
* ** * *
142652 AAAAAAAAAAAAAAAAAACAAAAAAAAGGAAAAAGAAAAAAAAAAAACAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
142710 GGTGAAGATT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.91, C:0.03, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:142682 original size:29 final size:29
Alignment explanation
Indices: 142650--142707 Score: 107
Period size: 29 Copynumber: 2.0 Consensus size: 29
142640 CATGGCAATT
142650 GGAAAAAAAAAAAAAAAAAACAAAAAAAA
1 GGAAAAAAAAAAAAAAAAAACAAAAAAAA
*
142679 GGAAAAAGAAAAAAAAAAAACAAAAAAAA
1 GGAAAAAAAAAAAAAAAAAACAAAAAAAA
142708 AAGGTGAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.88, C:0.03, G:0.09, T:0.00
Consensus pattern (29 bp):
GGAAAAAAAAAAAAAAAAAACAAAAAAAA
Found at i:142691 original size:31 final size:30
Alignment explanation
Indices: 142650--142711 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
142640 CATGGCAATT
*
142650 GGAAAAAAAAAAAAAAAAA-ACAAAAAAAA
1 GGAAAAAAAAAAAAAAAAACAAAAAAAAAA
142679 GGAAAAAGAAAAAAAAAAAACAAAAAAAAAA
1 GGAAAAA-AAAAAAAAAAAACAAAAAAAAAA
142710 GG
1 GG
142712 TGAAGATTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 7 0.23
30 12 0.40
31 11 0.37
ACGTcount: A:0.85, C:0.03, G:0.11, T:0.00
Consensus pattern (30 bp):
GGAAAAAAAAAAAAAAAAACAAAAAAAAAA
Found at i:149592 original size:31 final size:31
Alignment explanation
Indices: 149551--149631 Score: 83
Period size: 31 Copynumber: 2.6 Consensus size: 31
149541 ATAAAAGAAT
*
149551 ATTAATAAAAA-TATTATTAAAACTATATTTA
1 ATTAATAAAAATTA-TATTAAAAATATATTTA
* *
149582 ATTATTAAAAATTATGTTAAAAATATATTTTA
1 ATTAATAAAAATTATATTAAAAATATA-TTTA
** *
149614 AAAAATAAAAATAATATT
1 ATTAATAAAAATTATATT
149632 GGTAGATCTA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
31 21 0.52
32 19 0.47
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.41
Consensus pattern (31 bp):
ATTAATAAAAATTATATTAAAAATATATTTA
Found at i:150182 original size:20 final size:21
Alignment explanation
Indices: 150148--150193 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
150138 TTTTATTTTT
150148 AAATATAATTATAAAAAATCA
1 AAATATAATTATAAAAAATCA
*
150169 AAAT-TAATTGTAAAAAATCA
1 AAATATAATTATAAAAAATCA
150189 AAATA
1 AAATA
150194 ACTGAAAACT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 19 0.83
21 4 0.17
ACGTcount: A:0.65, C:0.04, G:0.02, T:0.28
Consensus pattern (21 bp):
AAATATAATTATAAAAAATCA
Found at i:150513 original size:9 final size:8
Alignment explanation
Indices: 150499--150523 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
150489 ATATACAGAC
150499 AAAAAAAT
1 AAAAAAAT
150507 AAAAAAAT
1 AAAAAAAT
150515 AAAAAAAT
1 AAAAAAAT
150523 A
1 A
150524 TTAATAAATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (8 bp):
AAAAAAAT
Found at i:150530 original size:22 final size:22
Alignment explanation
Indices: 150504--150549 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
150494 CAGACAAAAA
150504 AATAAAAAAATAAAAAAATATT
1 AATAAAAAAATAAAAAAATATT
** * *
150526 AATAAATGAATGAAATAATATT
1 AATAAAAAAATAAAAAAATATT
150548 AA
1 AA
150550 AATAAATTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.04, T:0.26
Consensus pattern (22 bp):
AATAAAAAAATAAAAAAATATT
Found at i:154246 original size:1 final size:1
Alignment explanation
Indices: 154240--154265 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
154230 GTTAGGTCTT
154240 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
154266 AAAAAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:164265 original size:72 final size:72
Alignment explanation
Indices: 164148--164287 Score: 253
Period size: 72 Copynumber: 1.9 Consensus size: 72
164138 AACTTAGCCG
* *
164148 TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCTATCATCCTTCTATTTCTTCACTTTAAA
1 TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
164213 CTGTCTC
66 CTGTCTC
*
164220 TATTTAAGCAATGATTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
1 TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
164285 CTG
66 CTG
164288 CGATCAAGAA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
72 65 1.00
ACGTcount: A:0.21, C:0.27, G:0.11, T:0.41
Consensus pattern (72 bp):
TATTTAAGCAATGACTTTGGGGCTCTTCCCTGACCTCCATCATCCTTCTATTTCATCACTTTAAA
CTGTCTC
Found at i:170504 original size:14 final size:15
Alignment explanation
Indices: 170476--170504 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
170466 AATTATGACA
170476 TAATAAATATATTTT
1 TAATAAATATATTTT
170491 TAATAAAT-TATTTT
1 TAATAAATATATTTT
170505 ATAGTCGTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
TAATAAATATATTTT
Found at i:171051 original size:11 final size:12
Alignment explanation
Indices: 171035--171063 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
171025 GTGATTTTTC
171035 ATTTTG-ATATG
1 ATTTTGAATATG
171046 ATTTTGAATATG
1 ATTTTGAATATG
171058 ATTTTG
1 ATTTTG
171064 TTAAAGTTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.17, T:0.55
Consensus pattern (12 bp):
ATTTTGAATATG
Found at i:171348 original size:31 final size:31
Alignment explanation
Indices: 171312--171390 Score: 122
Period size: 31 Copynumber: 2.5 Consensus size: 31
171302 TGTCACAGGT
171312 TAAGAATAGTGGTTTTTACCGTGCCACCAGA
1 TAAGAATAGTGGTTTTTACCGTGCCACCAGA
** * *
171343 TAAGAATAGTATTTTTTACTGTGCCACCGGA
1 TAAGAATAGTGGTTTTTACCGTGCCACCAGA
171374 TAAGAATAGTGGTTTTT
1 TAAGAATAGTGGTTTTT
171391 GTTCCAACTA
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.29, C:0.14, G:0.22, T:0.35
Consensus pattern (31 bp):
TAAGAATAGTGGTTTTTACCGTGCCACCAGA
Found at i:173098 original size:19 final size:19
Alignment explanation
Indices: 173076--173132 Score: 53
Period size: 19 Copynumber: 3.0 Consensus size: 19
173066 AACCCAAAAA
173076 AATAAAATAAATAAATATT
1 AATAAAATAAATAAATATT
* *
173095 AAT-AAATGAATGAAATAAT
1 AATAAAATAAAT-AAATATT
* * *
173114 ATTAAAATATATTAATATT
1 AATAAAATAAATAAATATT
173133 TTAAATTATA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
18 7 0.24
19 16 0.55
20 6 0.21
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (19 bp):
AATAAAATAAATAAATATT
Found at i:173146 original size:17 final size:18
Alignment explanation
Indices: 173115--173150 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
173105 TGAAATAATA
173115 TTAAAATATATTAATATT
1 TTAAAATATATTAATATT
*
173133 TTAAATTATA-TAATATT
1 TTAAAATATATTAATATT
173150 T
1 T
173151 GAATGAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (18 bp):
TTAAAATATATTAATATT
Found at i:173164 original size:27 final size:25
Alignment explanation
Indices: 173130--173190 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 25
173120 ATATATTAAT
173130 ATTTTAAATTATATAATATTTGAATGA
1 ATTTTAAATTAT-T-ATATTTGAATGA
*
173157 ATTTT-AA--ATTATCTTTGAATGA
1 ATTTTAAATTATTATATTTGAATGA
173179 ATTTTAAATTAT
1 ATTTTAAATTAT
173191 CTCTTAAATG
Statistics
Matches: 30, Mismatches: 1, Indels: 8
0.77 0.03 0.21
Matches are distributed among these distances:
22 16 0.53
23 3 0.10
24 2 0.07
25 2 0.07
26 2 0.07
27 5 0.17
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (25 bp):
ATTTTAAATTATTATATTTGAATGA
Found at i:173173 original size:22 final size:22
Alignment explanation
Indices: 173148--173206 Score: 100
Period size: 22 Copynumber: 2.6 Consensus size: 22
173138 TTATATAATA
173148 TTTGAATGAATTTTAAATTATC
1 TTTGAATGAATTTTAAATTATC
173170 TTTGAATGAATTTTAAATTATC
1 TTTGAATGAATTTTAAATTATC
*
173192 TCTTAAATGAATTTT
1 T-TTGAATGAATTTT
173207 GTAAACGAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
22 23 0.66
23 12 0.34
ACGTcount: A:0.36, C:0.05, G:0.08, T:0.51
Consensus pattern (22 bp):
TTTGAATGAATTTTAAATTATC
Found at i:174253 original size:26 final size:25
Alignment explanation
Indices: 174223--174281 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 25
174213 TAAATTTAGA
*
174223 TATTTTTATAT-ATTTATTATTTATAT
1 TATTTTTATATCATATATT-TTTA-AT
174249 TATTTTATATATCATATATTTTTAAT
1 TATTTT-TATATCATATATTTTTAAT
174275 TATTTTT
1 TATTTTT
174282 TCGTATTGTG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 1 0.03
26 14 0.47
27 9 0.30
28 6 0.20
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.68
Consensus pattern (25 bp):
TATTTTTATATCATATATTTTTAAT
Found at i:174255 original size:17 final size:17
Alignment explanation
Indices: 174223--174279 Score: 50
Period size: 17 Copynumber: 3.5 Consensus size: 17
174213 TAAATTTAGA
174223 TATT-TTTATA-TA-TT
1 TATTATTTATATTATTT
174237 TATTATTTATATTATTT
1 TATTATTTATATTATTT
*
174254 TATATATCATATATT-TTT
1 TAT-TAT-TTATATTATTT
*
174272 AATTATTT
1 TATTATTT
174280 TTTCGTATTG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
14 4 0.11
15 6 0.17
16 3 0.09
17 8 0.23
18 8 0.23
19 6 0.17
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.67
Consensus pattern (17 bp):
TATTATTTATATTATTT
Found at i:174268 original size:25 final size:26
Alignment explanation
Indices: 174226--174280 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
174216 ATTTAGATAT
*
174226 TTTTATATATTTATTATTTAT-ATTA
1 TTTTATATATATATTATTTATAATTA
*
174251 TTTTATATATCATA-TATTTTTAATTA
1 TTTTATATAT-ATATTATTTATAATTA
174277 TTTT
1 TTTT
174281 TTCGTATTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 16 0.62
26 10 0.38
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (26 bp):
TTTTATATATATATTATTTATAATTA
Found at i:176622 original size:2 final size:2
Alignment explanation
Indices: 176615--176640 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
176605 CACTCTAATC
176615 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
176641 GTTTTTTTTG
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):
AT
Found at i:177115 original size:2 final size:2
Alignment explanation
Indices: 177108--177148 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
177098 AACAAGATTC
177108 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
177149 CATTTGAAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:179911 original size:21 final size:21
Alignment explanation
Indices: 179887--179942 Score: 94
Period size: 21 Copynumber: 2.7 Consensus size: 21
179877 TTTTTTCAGA
179887 TTTAGAAGCTTATTTTACATC
1 TTTAGAAGCTTATTTTACATC
*
179908 TTTAGAAGCTTAGTTTACATC
1 TTTAGAAGCTTATTTTACATC
*
179929 TTTAGAAGTTTATT
1 TTTAGAAGCTTATT
179943 CAAGATCCAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.29, C:0.11, G:0.12, T:0.48
Consensus pattern (21 bp):
TTTAGAAGCTTATTTTACATC
Done.