Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold306
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: 585619
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.31
Warning! 41328 characters in sequence are not A, C, G, or T
File 1 of 3
Found at i:26398 original size:143 final size:143
Alignment explanation
Indices: 26140--26424 Score: 552
Period size: 143 Copynumber: 2.0 Consensus size: 143
26130 TCTCCATGTC
*
26140 TTCATCGTCTACAAGTTCCATCTCGGTGATTTTGATGGGATCTATCAAAACTAAAAAATTTTAGA
1 TTCATCGTCTACAAGTTCCATCTCGGTGAATTTGATGGGATCTATCAAAACTAAAAAATTTTAGA
26205 AAAGTTTCGAGATCTTTCTCCAACAACGTCTAACAATTTTTGCACTAATCTTTTCCTTCATATCA
66 AAAGTTTCGAGATCTTTCTCCAACAACGTCTAACAATTTTTGCACTAATCTTTTCCTTCATATCA
26270 TCAACCGAGACAA
131 TCAACCGAGACAA
*
26283 TTCATCGTCTACAAGTTCCATCTCGGTGAATTTGATGGGATCTATCGAAACTAAAAAATTTTAGA
1 TTCATCGTCTACAAGTTCCATCTCGGTGAATTTGATGGGATCTATCAAAACTAAAAAATTTTAGA
26348 AAAGTTTCGAGATCTTTCTCCAACAACGTCTAACAATTTTTGCACTAATCTTTTCCTTCATATCA
66 AAAGTTTCGAGATCTTTCTCCAACAACGTCTAACAATTTTTGCACTAATCTTTTCCTTCATATCA
26413 TCAACCGAGACA
131 TCAACCGAGACA
26425 TTTCTATTAA
Statistics
Matches: 140, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
143 140 1.00
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (143 bp):
TTCATCGTCTACAAGTTCCATCTCGGTGAATTTGATGGGATCTATCAAAACTAAAAAATTTTAGA
AAAGTTTCGAGATCTTTCTCCAACAACGTCTAACAATTTTTGCACTAATCTTTTCCTTCATATCA
TCAACCGAGACAA
Found at i:27741 original size:28 final size:28
Alignment explanation
Indices: 27698--27761 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 28
27688 TCAGCATTTA
*
27698 TTTAAAATTAAAAAAT-ATATAAAATTTATT
1 TTTAAAATTAAAAATTCAT-TAAAA-TTA-T
27728 TTTAAAATT-AAAATTCATTAAAATTAT
1 TTTAAAATTAAAAATTCATTAAAATTAT
27755 TTTAAAA
1 TTTAAAA
27762 GTATATAAAT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
27 8 0.25
28 3 0.09
29 10 0.31
30 11 0.34
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (28 bp):
TTTAAAATTAAAAATTCATTAAAATTAT
Found at i:30594 original size:20 final size:20
Alignment explanation
Indices: 30571--30611 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
30561 ATGTTTAATA
*
30571 TGGGAGTGGTTTGTTTGATG
1 TGGGAGTGGTTTGGTTGATG
30591 TGGGAGTGGTTTGGTTGATG
1 TGGGAGTGGTTTGGTTGATG
30611 T
1 T
30612 TTAGGCTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (20 bp):
TGGGAGTGGTTTGGTTGATG
Found at i:32360 original size:36 final size:37
Alignment explanation
Indices: 32320--32395 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
32310 CTCACCAATG
32320 TTACTTGACACA-CTGACCACCTATT-AAAAATATTTT
1 TTACTTGACACATC-GACCACCTATTAAAAAATATTTT
32356 TTACTTGACACATCGACCACCTATTAAAAAAATATTTT
1 TTACTTGACACATCGACCACCTATT-AAAAAATATTTT
32394 TT
1 TT
32396 CTCCATTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 23 0.62
37 1 0.03
38 13 0.35
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (37 bp):
TTACTTGACACATCGACCACCTATTAAAAAATATTTT
Found at i:32735 original size:75 final size:75
Alignment explanation
Indices: 32612--32755 Score: 288
Period size: 75 Copynumber: 1.9 Consensus size: 75
32602 CCATTTTCAT
32612 AAATAACTAATTCTTTTGAATAAGATGTGTAAAGCCCAGTTTTCTTTGCCCGGATCAACACCAAA
1 AAATAACTAATTCTTTTGAATAAGATGTGTAAAGCCCAGTTTTCTTTGCCCGGATCAACACCAAA
32677 TGAAGACACC
66 TGAAGACACC
32687 AAATAACTAATTCTTTTGAATAAGATGTGTAAAGCCCAGTTTTCTTTGCCCGGATCAACACCAAA
1 AAATAACTAATTCTTTTGAATAAGATGTGTAAAGCCCAGTTTTCTTTGCCCGGATCAACACCAAA
32752 TGAA
66 TGAA
32756 CCCAAACAAA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 69 1.00
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (75 bp):
AAATAACTAATTCTTTTGAATAAGATGTGTAAAGCCCAGTTTTCTTTGCCCGGATCAACACCAAA
TGAAGACACC
Found at i:32779 original size:16 final size:15
Alignment explanation
Indices: 32758--32794 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
32748 CAAATGAACC
32758 CAAACAAAATAAAAAA
1 CAAACAAAA-AAAAAA
32774 CAAACAAAAAAAAAA
1 CAAACAAAAAAAAAA
32789 -AAACAA
1 CAAACAA
32795 CCCAAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (15 bp):
CAAACAAAAAAAAAA
Found at i:32801 original size:18 final size:18
Alignment explanation
Indices: 32758--32794 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
32748 CAAATGAACC
32758 CAAACAAAATAAAAAACAAA
1 CAAA-AAAA-AAAAAACAAA
32778 CAAAAAAAAAAAAACAA
1 CAAAAAAAAAAAAACAA
32795 CCCAAAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (18 bp):
CAAAAAAAAAAAAACAAA
Found at i:33007 original size:20 final size:20
Alignment explanation
Indices: 32982--33025 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
32972 ACAATATTTA
* *
32982 ATGTGGGAGTGGTTTGTTTG
1 ATGTGGGAGTGATTTGGTTG
33002 ATGTGGGAGTGATTTGGTTG
1 ATGTGGGAGTGATTTGGTTG
33022 ATGT
1 ATGT
33026 TTAGGCTAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.43, T:0.43
Consensus pattern (20 bp):
ATGTGGGAGTGATTTGGTTG
Found at i:36802 original size:42 final size:42
Alignment explanation
Indices: 36755--36851 Score: 124
Period size: 42 Copynumber: 2.3 Consensus size: 42
36745 ACGGCCAAAC
* *
36755 CACACGCCCGTG-CGCATGGCCGTGTGTCACACACGGCTGAGA
1 CACACGCCCGTGTCGC-TGCCCGTATGTCACACACGGCTGAGA
* * *
36797 TACACGCCCGTGTCTCTGCCCGTATGTCACACATGGCTGAGA
1 CACACGCCCGTGTCGCTGCCCGTATGTCACACACGGCTGAGA
*
36839 CACATGCCCGTGT
1 CACACGCCCGTGT
36852 GGACAAAATA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
42 45 0.96
43 2 0.04
ACGTcount: A:0.19, C:0.35, G:0.27, T:0.20
Consensus pattern (42 bp):
CACACGCCCGTGTCGCTGCCCGTATGTCACACACGGCTGAGA
Found at i:40490 original size:21 final size:20
Alignment explanation
Indices: 40453--40493 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
40443 CTCTTAGGTT
40453 TTTAAAAAATATGTATTTTA
1 TTTAAAAAATATGTATTTTA
* *
40473 TTTATAAAAGTATTTATTTTA
1 TTTA-AAAAATATGTATTTTA
40494 ATAAATAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.41, C:0.00, G:0.05, T:0.54
Consensus pattern (20 bp):
TTTAAAAAATATGTATTTTA
Found at i:43863 original size:95 final size:95
Alignment explanation
Indices: 43700--43888 Score: 369
Period size: 95 Copynumber: 2.0 Consensus size: 95
43690 ACGACACCAG
43700 GCTATTATATAGCCTAGATATATGACACTGTACCCCTTCCCACACGGCATCAGCCTTCTACACGG
1 GCTATTATATAGCCTAGATATATGACACTGTACCCCTTCCCACACGGCATCAGCCTTCTACACGG
43765 CCCTGTGACTTCTATTTTATAATTTTGCCA
66 CCCTGTGACTTCTATTTTATAATTTTGCCA
*
43795 GCTATTATATAGCCTAGATATATGACACTGTACCCCTTCCCACACGGCATCGGCCTTCTACACGG
1 GCTATTATATAGCCTAGATATATGACACTGTACCCCTTCCCACACGGCATCAGCCTTCTACACGG
43860 CCCTGTGACTTCTATTTTATAATTTTGCC
66 CCCTGTGACTTCTATTTTATAATTTTGCC
43889 TAGAAATTTG
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
95 93 1.00
ACGTcount: A:0.23, C:0.30, G:0.14, T:0.33
Consensus pattern (95 bp):
GCTATTATATAGCCTAGATATATGACACTGTACCCCTTCCCACACGGCATCAGCCTTCTACACGG
CCCTGTGACTTCTATTTTATAATTTTGCCA
Found at i:44169 original size:38 final size:38
Alignment explanation
Indices: 44089--44162 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
44079 GTTATTGCTG
* ** * * *
44089 CTACTGCTTTTGTTTTATTGATTGCATGTTCAGCATAC
1 CTACTGCTTCTGTTAAACTGATTGCATGATAAGCATAC
44127 CTACTGCTTCTGTTAAACTGATTGCATGATAAGCAT
1 CTACTGCTTCTGTTAAACTGATTGCATGATAAGCAT
44163 GACTACTATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 30 1.00
ACGTcount: A:0.23, C:0.19, G:0.16, T:0.42
Consensus pattern (38 bp):
CTACTGCTTCTGTTAAACTGATTGCATGATAAGCATAC
Found at i:46064 original size:17 final size:17
Alignment explanation
Indices: 46028--46061 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
46018 ATAAAAAATA
*
46028 AAAGTCCATTTACAATT
1 AAAGTCCAATTACAATT
46045 AAAGTCCAAATTACAAT
1 AAAGTCC-AATTACAAT
46062 AAACCCGAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.47, C:0.18, G:0.06, T:0.29
Consensus pattern (17 bp):
AAAGTCCAATTACAATT
Found at i:47170 original size:21 final size:22
Alignment explanation
Indices: 47094--47170 Score: 61
Period size: 23 Copynumber: 3.5 Consensus size: 22
47084 AGTCCTTCTG
* * *
47094 TTATTATTTTATTTTATTATGTA
1 TTATTATTTTAATTT-TCATATA
*
47117 ATATTATTTTAAGTTTTTCATATA
1 TTATTATTTTAA--TTTTCATATA
47141 TTA-TATTTTAA-TTTCATA-A
1 TTATTATTTTAATTTTCATATA
47160 TGTATTATTTT
1 T-TATTATTTT
47171 GTTTTTTTTA
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
19 2 0.04
20 9 0.20
21 6 0.13
23 18 0.40
24 7 0.16
25 3 0.07
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.64
Consensus pattern (22 bp):
TTATTATTTTAATTTTCATATA
Found at i:47487 original size:12 final size:12
Alignment explanation
Indices: 47466--47498 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
47456 TTGTTTTAAC
*
47466 TATTACATATAT
1 TATTATATATAT
47478 TATTATATATAT
1 TATTATATATAT
47490 TATT-TATAT
1 TATTATATAT
47499 TGAGTGTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 5 0.25
12 15 0.75
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (12 bp):
TATTATATATAT
Found at i:50820 original size:20 final size:20
Alignment explanation
Indices: 50797--50837 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
50787 ATGTTTAATA
* *
50797 TGGGAGTGGTTTGTTTGATG
1 TGGGAGTGATTTGGTTGATG
50817 TGGGAGTGATTTGGTTGATG
1 TGGGAGTGATTTGGTTGATG
50837 T
1 T
50838 TTAGGCTAGA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.12, C:0.00, G:0.44, T:0.44
Consensus pattern (20 bp):
TGGGAGTGATTTGGTTGATG
Found at i:51957 original size:20 final size:20
Alignment explanation
Indices: 51934--51974 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
51924 ATGTTTAATA
*
51934 TGGGAGTGGTTTGTTTGATG
1 TGGGAGTGGTTTGGTTGATG
51954 TGGGAGTGGTTTGGTTGATG
1 TGGGAGTGGTTTGGTTGATG
51974 T
1 T
51975 TTAGGCTAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.10, C:0.00, G:0.46, T:0.44
Consensus pattern (20 bp):
TGGGAGTGGTTTGGTTGATG
Found at i:53723 original size:36 final size:37
Alignment explanation
Indices: 53683--53758 Score: 120
Period size: 36 Copynumber: 2.1 Consensus size: 37
53673 CTCACCAATG
53683 TTACTTGACACA-CTGACCACCTATT-AAAAATATTTT
1 TTACTTGACACATC-GACCACCTATTAAAAAATATTTT
53719 TTACTTGACACATCGACCACCTATTAAAAAAATATTTT
1 TTACTTGACACATCGACCACCTATT-AAAAAATATTTT
53757 TT
1 TT
53759 CTCCATTGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
36 23 0.62
37 1 0.03
38 13 0.35
ACGTcount: A:0.37, C:0.21, G:0.05, T:0.37
Consensus pattern (37 bp):
TTACTTGACACATCGACCACCTATTAAAAAATATTTT
Found at i:54067 original size:16 final size:15
Alignment explanation
Indices: 54046--54082 Score: 58
Period size: 16 Copynumber: 2.5 Consensus size: 15
54036 CAAATGAACC
54046 CAAACAAAATAAAAAA
1 CAAACAAAA-AAAAAA
54062 CAAACAAAAAAAAAA
1 CAAACAAAAAAAAAA
54077 -AAACAA
1 CAAACAA
54083 CCCAAAAGGC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 6 0.29
15 6 0.29
16 9 0.43
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (15 bp):
CAAACAAAAAAAAAA
Found at i:54089 original size:18 final size:18
Alignment explanation
Indices: 54046--54082 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 18
54036 CAAATGAACC
54046 CAAACAAAATAAAAAACAAA
1 CAAA-AAAA-AAAAAACAAA
54066 CAAAAAAAAAAAAACAA
1 CAAAAAAAAAAAAACAA
54083 CCCAAAAGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 9 0.53
19 4 0.24
20 4 0.24
ACGTcount: A:0.84, C:0.14, G:0.00, T:0.03
Consensus pattern (18 bp):
CAAAAAAAAAAAAACAAA
Found at i:58058 original size:20 final size:21
Alignment explanation
Indices: 58020--58058 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
58010 TTTGGCCCGT
*
58020 TTTTTTACCAAAATCTTGGTA
1 TTTTTGACCAAAATCTTGGTA
*
58041 TTTTTGACCCAAAT-TTGG
1 TTTTTGACCAAAATCTTGG
58059 GCTCTCCTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (21 bp):
TTTTTGACCAAAATCTTGGTA
Found at i:58717 original size:3 final size:3
Alignment explanation
Indices: 58711--58749 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
58701 ATTAATCTTG
58711 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
58750 GGTATTAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:59085 original size:17 final size:17
Alignment explanation
Indices: 59065--59097 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
59055 TATAACTTAT
59065 TTATATATATATGTATG
1 TTATATATATATGTATG
*
59082 TTATATCTATATGTAT
1 TTATATATATATGTAT
59098 ATATGCATGC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.33, C:0.03, G:0.09, T:0.55
Consensus pattern (17 bp):
TTATATATATATGTATG
Found at i:59293 original size:35 final size:33
Alignment explanation
Indices: 59217--59293 Score: 77
Period size: 35 Copynumber: 2.2 Consensus size: 33
59207 AATATACCCC
*
59217 TTTT-TACATACATAGTTTTTATATTTTATGAT
1 TTTTATACATACATAGTTTTTATATTTTATGAA
*
59249 TTGTATATACATACATATTTTTTCATATATTTTAT-AA
1 TT-T-TATACATACATA-GTTTT--TATATTTTATGAA
59286 TTTTATAC
1 TTTTATAC
59294 TTCATAATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
32 2 0.05
33 1 0.03
34 1 0.03
35 15 0.41
36 5 0.14
37 3 0.08
38 10 0.27
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.57
Consensus pattern (33 bp):
TTTTATACATACATAGTTTTTATATTTTATGAA
Found at i:61778 original size:9 final size:8
Alignment explanation
Indices: 61760--61806 Score: 51
Period size: 9 Copynumber: 5.5 Consensus size: 8
61750 ATCCTTTTTT
61760 TAAATAAAA
1 TAAA-AAAA
61769 TAAAAGAAA
1 TAAAA-AAA
61778 TAATAAAAA
1 TAA-AAAAA
61787 TAAAAATAA
1 TAAAAA-AA
61796 T-AAAAAA
1 TAAAAAAA
61803 TAAA
1 TAAA
61807 GTTAAACAGG
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
7 3 0.09
8 10 0.29
9 19 0.56
10 2 0.06
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:61795 original size:15 final size:16
Alignment explanation
Indices: 61762--61806 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 16
61752 CCTTTTTTTA
61762 AATAAAATAA-AAGAAAT
1 AATAAAA-AATAA-AAAT
61779 AAT-AAAAATAAAAAT
1 AATAAAAAATAAAAAT
61794 AATAAAAAATAAA
1 AATAAAAAATAAA
61807 GTTAAACAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.35
16 14 0.54
17 3 0.12
ACGTcount: A:0.80, C:0.00, G:0.02, T:0.18
Consensus pattern (16 bp):
AATAAAAAATAAAAAT
Found at i:63198 original size:21 final size:19
Alignment explanation
Indices: 63172--63210 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
63162 AACCATTCAA
*
63172 TATTATTAATATAAATGAGAT
1 TATTA-TAAAATAAA-GAGAT
63193 TATTATAAAATAAAGAGA
1 TATTATAAAATAAAGAGA
63211 AATATAGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 8 0.47
21 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (19 bp):
TATTATAAAATAAAGAGAT
Found at i:65653 original size:39 final size:40
Alignment explanation
Indices: 65593--65668 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
65583 ATGTCAGGGG
*
65593 ACGTGGCAAAAATCGCGTCCCT-GAGGGCGCGCTTTGCTT
1 ACGTGGCAAAAATCGCGTCCCTCAAGGGCGCGCTTTGCTT
* *
65632 ACGTGGACGAAAATCGC-TCCCTCAAGGGCGCGTTTTG
1 ACGTGG-CAAAAATCGCGTCCCTCAAGGGCGCGCTTTG
65669 TTGCCACGTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
39 11 0.34
40 21 0.66
ACGTcount: A:0.20, C:0.28, G:0.30, T:0.22
Consensus pattern (40 bp):
ACGTGGCAAAAATCGCGTCCCTCAAGGGCGCGCTTTGCTT
Found at i:66170 original size:124 final size:124
Alignment explanation
Indices: 65950--66318 Score: 648
Period size: 124 Copynumber: 3.0 Consensus size: 124
65940 TTTATTAAGG
** * * * **
65950 AAATCGCTCCCACGTGGACGTGCTTTTCCTACAGTAGGTCCTAAAAAAATAATTTTGAGTTGACG
1 AAATCGCTCCCACGTGGACGCACTTTTGCTACAATAGGTCCTGAAAAAATAATTTCAAGTTGACG
* * *
66015 TTTGTGAGCAAATAGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
66 TTTCTGAGAAAATTGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
66074 AAATCGCTCCCACGTGGACGCACTTTTGCTACAATAGGTCCTGAAAAAATAATTTCAAGTTGACG
1 AAATCGCTCCCACGTGGACGCACTTTTGCTACAATAGGTCCTGAAAAAATAATTTCAAGTTGACG
66139 TTTCTGAGAAAATTGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
66 TTTCTGAGAAAATTGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
66198 AAATCGCTCCCACGTGGACGCACTTTTGCTACAATAGGTCCTGAAAAAATAATTTCAAGTTGACG
1 AAATCGCTCCCACGTGGACGCACTTTTGCTACAATAGGTCCTGAAAAAATAATTTCAAGTTGACG
66263 TTTCTGAGAAAATTGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTT
66 TTTCTGAGAAAATTGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTT
66319 NNNNNNNNNN
Statistics
Matches: 235, Mismatches: 10, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
124 235 1.00
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.29
Consensus pattern (124 bp):
AAATCGCTCCCACGTGGACGCACTTTTGCTACAATAGGTCCTGAAAAAATAATTTCAAGTTGACG
TTTCTGAGAAAATTGTATAAAAACGCTTCAAGCAGGATGCTTTATCAGAAGAATTTCTA
Found at i:69357 original size:49 final size:49
Alignment explanation
Indices: 69300--69549 Score: 428
Period size: 49 Copynumber: 5.1 Consensus size: 49
69290 AGAATATTAG
* * *
69300 CTATTTTGTATTTTGTTAAATGAAATAATATCAAAATATTCAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
* * *
69349 CTATTTTGTATTTTATTAAATGAAATAATATCAAAATATTTAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
69398 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
69447 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
*
69496 CTATTTTGTATTTTATTACATCAAATAATATTAAAATATTCAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
*
69545 ATATT
1 CTATT
69550 CAAAATAATA
Statistics
Matches: 194, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
49 194 1.00
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (49 bp):
CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
Found at i:69546 original size:14 final size:14
Alignment explanation
Indices: 69527--69557 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
69517 CAAATAATAT
69527 TAAAATATTCAAAA
1 TAAAATATTCAAAA
69541 TAAAATATTCAAAA
1 TAAAATATTCAAAA
69555 TAA
1 TAA
69558 TATCAAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.06, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAATATTCAAAA
Found at i:69810 original size:18 final size:18
Alignment explanation
Indices: 69784--69826 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
69774 GACTAGAAAA
* * *
69784 AGGAAACATATAAGGGTT
1 AGGATACATAGAAGGGCT
69802 AGGATACATAGAAGGGCT
1 AGGATACATAGAAGGGCT
69820 AGGATAC
1 AGGATAC
69827 GCACCTAGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.09, G:0.30, T:0.19
Consensus pattern (18 bp):
AGGATACATAGAAGGGCT
Found at i:71685 original size:11 final size:11
Alignment explanation
Indices: 71657--71688 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
71647 TTTAAATAGA
*
71657 AATTTGAGAGG
1 AATTTGTGAGG
71668 AATTTGTGAGG
1 AATTTGTGAGG
71679 AATTTGTGAG
1 AATTTGTGAG
71689 AATATTAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.34, T:0.34
Consensus pattern (11 bp):
AATTTGTGAGG
Found at i:72857 original size:16 final size:16
Alignment explanation
Indices: 72819--72857 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
72809 GTTTAGTTCA
*
72819 CTGTAATGGAATAGGG
1 CTGTAATGGAATAGAG
* *
72835 TTATAATGGAATAGAG
1 CTGTAATGGAATAGAG
72851 CTGTAAT
1 CTGTAAT
72858 CAGTAATTCA
Statistics
Matches: 18, Mismatches: 5, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.36, C:0.05, G:0.28, T:0.31
Consensus pattern (16 bp):
CTGTAATGGAATAGAG
Found at i:73155 original size:58 final size:59
Alignment explanation
Indices: 73024--73165 Score: 155
Period size: 61 Copynumber: 2.4 Consensus size: 59
73014 TTGTTATTAA
* * ***
73024 ATTTTAATA-AGATTATTATTAAATAAAATTTAATAATAATAAAAATAAATGATTTCATCGT
1 ATTTTAATATA-ATTATTATTAAATAAAATTTAATAATAAT--AAATAAATAATTTAATAAC
* * *
73085 ATTTTAACATAATTATTATTAAATACAATTTAATAA-AAT-AATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATAAAATTTAATAATAATAAATAAATAATTTAATAAC
73142 ATTCTTAATATAATTATTATTAAA
1 ATT-TTAATATAATTATTATTAAA
73166 ATATGAATTA
Statistics
Matches: 70, Mismatches: 9, Indels: 7
0.81 0.10 0.08
Matches are distributed among these distances:
57 15 0.21
58 19 0.27
60 3 0.04
61 32 0.46
62 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.02, T:0.43
Consensus pattern (59 bp):
ATTTTAATATAATTATTATTAAATAAAATTTAATAATAATAAATAAATAATTTAATAAC
Found at i:73203 original size:23 final size:21
Alignment explanation
Indices: 73172--73214 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
73162 TAAAATATGA
73172 ATTAAAAAATCATAATATATAAT
1 ATTAAAAAA--ATAATATATAAT
*
73195 ATTATAAAAATAATATATAA
1 ATTAAAAAAATAATATATAA
73215 CTTACTTTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 11 0.58
23 8 0.42
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (21 bp):
ATTAAAAAAATAATATATAAT
Found at i:77383 original size:16 final size:15
Alignment explanation
Indices: 77359--77388 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
77349 ATTGGTAAAT
77359 AAAAAAAAACATTTC
1 AAAAAAAAACATTTC
77374 AAAAATAAAACATTT
1 AAAAA-AAAACATTT
77389 TTTATGTGCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.10, G:0.00, T:0.23
Consensus pattern (15 bp):
AAAAAAAAACATTTC
Found at i:77891 original size:23 final size:23
Alignment explanation
Indices: 77861--77906 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
77851 ATCCGTGTGG
*
77861 CCTTAGGCGATTCGTTCGTCCAA
1 CCTTAGGCAATTCGTTCGTCCAA
77884 CCTTAGGCAATTCGTTCGTCCAA
1 CCTTAGGCAATTCGTTCGTCCAA
77907 ACTCCCCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.20, C:0.30, G:0.20, T:0.30
Consensus pattern (23 bp):
CCTTAGGCAATTCGTTCGTCCAA
Found at i:88202 original size:29 final size:30
Alignment explanation
Indices: 88119--88205 Score: 92
Period size: 29 Copynumber: 3.0 Consensus size: 30
88109 TTTGAGTTTA
*
88119 TGAATAAA-ATATTTATTAATTAAAAATAT
1 TGAAAAAATATATTTATTAATTAAAAATAT
* * *
88148 TTAAAAAGATGA-A-TTA-AAATTAAAAAAAT
1 TGAAAAA-AT-ATATTTATTAATTAAAAATAT
88177 TGAAAAAATATATTTATTAATTAAAAATA
1 TGAAAAAATATATTTATTAATTAAAAATA
88206 AAACAACCTT
Statistics
Matches: 45, Mismatches: 7, Indels: 11
0.71 0.11 0.17
Matches are distributed among these distances:
27 1 0.02
28 3 0.07
29 25 0.56
30 14 0.31
31 1 0.02
32 1 0.02
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (30 bp):
TGAAAAAATATATTTATTAATTAAAAATAT
Found at i:113986 original size:85 final size:84
Alignment explanation
Indices: 113791--114075 Score: 259
Period size: 84 Copynumber: 3.4 Consensus size: 84
113781 TTGTTACGGG
* * * * ** * * ***
113791 GCACAACATATTTGCATATTAAAAAAAACTACCACTTGGTTCGTTATTGAACCACACTGATTGTG
1 GCACAACATATTTGCAGATT-AAACAAACTGCAACTCAGTTTGTGATTGAACCACA-T-ATTCCA
113856 GTTACTGCCACTTCTTGTGAGT
63 GTTACTGCCACTTCTTGTGAGT
** * * ** ** * *
113878 GCATGACATATTTGTAGA-CAAACAAACTGTGACTTGGTTTGTGATTTAACCACATATTTTCAGT
1 GCACAACATATTTGCAGATTAAACAAACTGCAACTCAGTTTGTGATTGAACCACATA-TTCCAGT
* *
113942 TACTGCCACTTGTTGTAAGT
65 TACTGCCACTTCTTGTGAGT
* * * *
113962 GCACAATATATTTACAGATTAAACAAACTCCAACTCAGTTTGTGATTGAACCACATATTCCAATT
1 GCACAACATATTTGCAGATTAAACAAACTGCAACTCAGTTTGTGATTGAACCACATATTCCAGTT
*
114027 ACT-CCAACTTTTTGTGAGT
66 ACTGCC-ACTTCTTGTGAGT
114046 GCACAACATATTTGCAGATTAAACAAACTG
1 GCACAACATATTTGCAGATTAAACAAACTG
114076 ATAATACTCT
Statistics
Matches: 159, Mismatches: 36, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
83 3 0.02
84 83 0.52
85 59 0.37
87 14 0.09
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (84 bp):
GCACAACATATTTGCAGATTAAACAAACTGCAACTCAGTTTGTGATTGAACCACATATTCCAGTT
ACTGCCACTTCTTGTGAGT
Found at i:114425 original size:7 final size:7
Alignment explanation
Indices: 114415--114691 Score: 554
Period size: 7 Copynumber: 39.6 Consensus size: 7
114405 TTATTTATCT
114415 TTTAGGG
1 TTTAGGG
114422 TTTAGGG
1 TTTAGGG
114429 TTTAGGG
1 TTTAGGG
114436 TTTAGGG
1 TTTAGGG
114443 TTTAGGG
1 TTTAGGG
114450 TTTAGGG
1 TTTAGGG
114457 TTTAGGG
1 TTTAGGG
114464 TTTAGGG
1 TTTAGGG
114471 TTTAGGG
1 TTTAGGG
114478 TTTAGGG
1 TTTAGGG
114485 TTTAGGG
1 TTTAGGG
114492 TTTAGGG
1 TTTAGGG
114499 TTTAGGG
1 TTTAGGG
114506 TTTAGGG
1 TTTAGGG
114513 TTTAGGG
1 TTTAGGG
114520 TTTAGGG
1 TTTAGGG
114527 TTTAGGG
1 TTTAGGG
114534 TTTAGGG
1 TTTAGGG
114541 TTTAGGG
1 TTTAGGG
114548 TTTAGGG
1 TTTAGGG
114555 TTTAGGG
1 TTTAGGG
114562 TTTAGGG
1 TTTAGGG
114569 TTTAGGG
1 TTTAGGG
114576 TTTAGGG
1 TTTAGGG
114583 TTTAGGG
1 TTTAGGG
114590 TTTAGGG
1 TTTAGGG
114597 TTTAGGG
1 TTTAGGG
114604 TTTAGGG
1 TTTAGGG
114611 TTTAGGG
1 TTTAGGG
114618 TTTAGGG
1 TTTAGGG
114625 TTTAGGG
1 TTTAGGG
114632 TTTAGGG
1 TTTAGGG
114639 TTTAGGG
1 TTTAGGG
114646 TTTAGGG
1 TTTAGGG
114653 TTTAGGG
1 TTTAGGG
114660 TTTAGGG
1 TTTAGGG
114667 TTTAGGG
1 TTTAGGG
114674 TTTAGGG
1 TTTAGGG
114681 TTTAGGG
1 TTTAGGG
114688 TTTA
1 TTTA
114692 CATCTACTAT
Statistics
Matches: 270, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 270 1.00
ACGTcount: A:0.14, C:0.00, G:0.42, T:0.43
Consensus pattern (7 bp):
TTTAGGG
Found at i:116071 original size:85 final size:84
Alignment explanation
Indices: 115876--116160 Score: 259
Period size: 84 Copynumber: 3.4 Consensus size: 84
115866 TTGTTACGGG
* * * * ** * * ***
115876 GCACAACATATTTGCATATTAAAAAAAACTACCACTTGGTTCGTTATTGAACCACACTGATTGTG
1 GCACAACATATTTGCAGATT-AAACAAACTGCAACTCAGTTTGTGATTGAACCACA-T-ATTCCA
115941 GTTACTGCCACTTCTTGTGAGT
63 GTTACTGCCACTTCTTGTGAGT
** * * ** ** * *
115963 GCATGACATATTTGTAGA-CAAACAAACTGTGACTTGGTTTGTGATTTAACCACATATTTTCAGT
1 GCACAACATATTTGCAGATTAAACAAACTGCAACTCAGTTTGTGATTGAACCACATA-TTCCAGT
* *
116027 TACTGCCACTTGTTGTAAGT
65 TACTGCCACTTCTTGTGAGT
* * * *
116047 GCACAATATATTTACAGATTAAACAAACTCCAACTCAGTTTGTGATTGAACCACATATTCCAATT
1 GCACAACATATTTGCAGATTAAACAAACTGCAACTCAGTTTGTGATTGAACCACATATTCCAGTT
*
116112 ACT-CCAACTTTTTGTGAGT
66 ACTGCC-ACTTCTTGTGAGT
116131 GCACAACATATTTGCAGATTAAACAAACTG
1 GCACAACATATTTGCAGATTAAACAAACTG
116161 ATAATACTCT
Statistics
Matches: 159, Mismatches: 36, Indels: 9
0.78 0.18 0.04
Matches are distributed among these distances:
83 3 0.02
84 83 0.52
85 59 0.37
87 14 0.09
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.33
Consensus pattern (84 bp):
GCACAACATATTTGCAGATTAAACAAACTGCAACTCAGTTTGTGATTGAACCACATATTCCAGTT
ACTGCCACTTCTTGTGAGT
Found at i:116510 original size:7 final size:7
Alignment explanation
Indices: 116500--116574 Score: 141
Period size: 7 Copynumber: 10.6 Consensus size: 7
116490 TTATTTATCT
116500 TTTAGGG
1 TTTAGGG
116507 TTTAGGG
1 TTTAGGG
116514 TTTAGGG
1 TTTAGGG
116521 TTTAGGG
1 TTTAGGG
116528 TTTAGGG
1 TTTAGGG
116535 TTTAGGG
1 TTTAGGG
116542 TTTAGGG
1 TTTAGGG
116549 TTTAGGG
1 TTTAGGG
116556 TTTTAGGG
1 -TTTAGGG
116564 TTTAGGG
1 TTTAGGG
116571 TTTA
1 TTTA
116575 AACTAGGTTT
Statistics
Matches: 67, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
7 60 0.90
8 7 0.10
ACGTcount: A:0.15, C:0.00, G:0.40, T:0.45
Consensus pattern (7 bp):
TTTAGGG
Found at i:119923 original size:14 final size:14
Alignment explanation
Indices: 119904--119930 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
119894 TATTTACATA
119904 TATTTTCTTTTTTC
1 TATTTTCTTTTTTC
119918 TATTTTCTTTTTT
1 TATTTTCTTTTTT
119931 TTTAGTTTCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.11, G:0.00, T:0.81
Consensus pattern (14 bp):
TATTTTCTTTTTTC
Found at i:119931 original size:15 final size:15
Alignment explanation
Indices: 119904--119942 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
119894 TATTTACATA
119904 TATTTTC-TTTTTTC
1 TATTTTCTTTTTTTC
*
119918 TATTTTCTTTTTTTT
1 TATTTTCTTTTTTTC
*
119933 TAGTTTCTTT
1 TATTTTCTTT
119943 CATGTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 7 0.32
15 15 0.68
ACGTcount: A:0.08, C:0.10, G:0.03, T:0.79
Consensus pattern (15 bp):
TATTTTCTTTTTTTC
Found at i:120597 original size:101 final size:102
Alignment explanation
Indices: 120472--120674 Score: 399
Period size: 101 Copynumber: 2.0 Consensus size: 102
120462 ATGTACAGCA
120472 GGCCGAACATGCGACAAAATCAGCAAGGAAATTATTCCCCAAATTCCCTTCTTGCTAGCGGTGGC
1 GGCCGAACATGCGACAAAATCAGCAAGGAAATTATTCCCCAAATTCCCTTCTTGCTAGCGGTGGC
120537 CGACTTCAATTAATTCAAGGAAATCAAATCAGCCTTG
66 CGACTTCAATTAATTCAAGGAAATCAAATCAGCCTTG
120574 GGCCGAACAT-CGACAAAATCAGCAAGGAAATTATTCCCCAAATTCCCTTCTTGCTAGCGGTGGC
1 GGCCGAACATGCGACAAAATCAGCAAGGAAATTATTCCCCAAATTCCCTTCTTGCTAGCGGTGGC
120638 CGACTTCAATTAATTCAAGGAAATCAAATCAGCCTTG
66 CGACTTCAATTAATTCAAGGAAATCAAATCAGCCTTG
120675 AAGAGTTCAA
Statistics
Matches: 101, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
101 91 0.90
102 10 0.10
ACGTcount: A:0.33, C:0.26, G:0.18, T:0.24
Consensus pattern (102 bp):
GGCCGAACATGCGACAAAATCAGCAAGGAAATTATTCCCCAAATTCCCTTCTTGCTAGCGGTGGC
CGACTTCAATTAATTCAAGGAAATCAAATCAGCCTTG
Found at i:121488 original size:29 final size:30
Alignment explanation
Indices: 121429--121486 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
121419 TCCGAGCCTT
*
121429 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
121459 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
121487 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:121716 original size:13 final size:13
Alignment explanation
Indices: 121698--121729 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
121688 TTTCCAGCAA
121698 TTATGAATTTATT
1 TTATGAATTTATT
121711 TTATGAATTTATT
1 TTATGAATTTATT
*
121724 TGATGA
1 TTATGA
121730 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:127702 original size:6 final size:6
Alignment explanation
Indices: 127683--127727 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
127673 CTTAAGGAAA
**
127683 AAAAAG AAGGAG AAAAAG AAAAAG --AAAG AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
127728 AGAAGTAAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
4 4 0.12
6 29 0.88
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:127710 original size:22 final size:21
Alignment explanation
Indices: 127679--127738 Score: 75
Period size: 22 Copynumber: 2.7 Consensus size: 21
127669 TATTCTTAAG
**
127679 GAAAAAAAAGAAGGAGAAAAA
1 GAAAAAAAAGAAAAAGAAAAA
127700 GAAAAAGAAAGAAAAAGAAAAA
1 GAAAAA-AAAGAAAAAGAAAAA
127722 GAAAAAAGAAGTAAAAA
1 GAAAAAA-AAG-AAAAA
127739 ATAATAATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
21 7 0.21
22 22 0.65
23 5 0.15
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (21 bp):
GAAAAAAAAGAAAAAGAAAAA
Found at i:127712 original size:16 final size:16
Alignment explanation
Indices: 127683--127738 Score: 69
Period size: 16 Copynumber: 3.3 Consensus size: 16
127673 CTTAAGGAAA
127683 AAAAAGAAGGAGAAAAAG
1 AAAAAGAA--AGAAAAAG
127701 AAAAAGAAAGAAAAAG
1 AAAAAGAAAGAAAAAG
127717 AAAAAGAAA-AAAGAAG
1 AAAAAGAAAGAAA-AAG
127733 TAAAAA
1 -AAAAA
127739 ATAATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.08
16 20 0.56
17 5 0.14
18 8 0.22
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.02
Consensus pattern (16 bp):
AAAAAGAAAGAAAAAG
Found at i:128333 original size:12 final size:12
Alignment explanation
Indices: 128318--128352 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
128308 AATTTGAATT
*
128318 TTATTAGGATTA
1 TTATTAAGATTA
128330 TTATTAAGATTA
1 TTATTAAGATTA
*
128342 TTATTTAGATT
1 TTATTAAGATT
128353 TAATTTCAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (12 bp):
TTATTAAGATTA
Found at i:131455 original size:19 final size:20
Alignment explanation
Indices: 131431--131477 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 20
131421 ACAATTAACA
131431 CATGCA-AAAGAAAAACAAT
1 CATGCACAAAGAAAAACAAT
*
131450 CATGCAACTAAAGAGAAACAAT
1 CATGC-AC-AAAGAAAAACAAT
131472 CATGCA
1 CATGCA
131478 TACTTACTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
19 5 0.21
20 1 0.04
21 1 0.04
22 17 0.71
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (20 bp):
CATGCACAAAGAAAAACAAT
Found at i:136136 original size:35 final size:36
Alignment explanation
Indices: 136090--136166 Score: 129
Period size: 35 Copynumber: 2.1 Consensus size: 36
136080 ATAAGGCACC
*
136090 TTGTACGTACAATAACAAATATAGATAAAACT-ACA
1 TTGTACGTACAATAACAAATACAGATAAAACTAACA
136125 TTGTACGTACAATAACAAATACAGATAAAACTAACA
1 TTGTACGTACAATAACAAATACAGATAAAACTAACA
136161 TATGTA
1 T-TGTA
136167 TTATTCACAA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
35 31 0.79
36 4 0.10
37 4 0.10
ACGTcount: A:0.51, C:0.14, G:0.09, T:0.26
Consensus pattern (36 bp):
TTGTACGTACAATAACAAATACAGATAAAACTAACA
Found at i:136834 original size:23 final size:23
Alignment explanation
Indices: 136804--136850 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
136794 TGTATTTATC
136804 GTTTCTTGGCAAGGATTAAAGAT
1 GTTTCTTGGCAAGGATTAAAGAT
*
136827 GTTTCTTGGCAAGGATTAAGGAT
1 GTTTCTTGGCAAGGATTAAAGAT
136850 G
1 G
136851 CTATTTAACG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.34
Consensus pattern (23 bp):
GTTTCTTGGCAAGGATTAAAGAT
Found at i:140983 original size:24 final size:24
Alignment explanation
Indices: 140923--140989 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
140913 GCTCCGAAGG
* *
140923 GCTATTAACGGGAAGTTCATGAGA
1 GCTAATAACGGGAAGCTCATGAGA
* * *
140947 GCCAAATATCGGGATGCTCATGAGA
1 G-CTAATAACGGGAAGCTCATGAGA
*
140972 GCTAATAACGGGACGCTC
1 GCTAATAACGGGAAGCTC
140990 TTTTGAGCTG
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
24 15 0.44
25 19 0.56
ACGTcount: A:0.31, C:0.19, G:0.28, T:0.21
Consensus pattern (24 bp):
GCTAATAACGGGAAGCTCATGAGA
Found at i:147364 original size:48 final size:50
Alignment explanation
Indices: 147264--147381 Score: 152
Period size: 49 Copynumber: 2.4 Consensus size: 50
147254 ACTCTCTCTC
* * * *
147264 GAGCCATATAA-CGGGAAGCTCATATGATCCATGTAACAGGAAGCTCCGGA
1 GAGCCAT-TAATCGGGAAGCTCATACGAGCCATATAACAGGAAGCTCCAGA
* *
147314 GAGCCTTTAAT-GGGAAGCTCATACGAGCCA-ATATCAGGAAGCTCCAGA
1 GAGCCATTAATCGGGAAGCTCATACGAGCCATATAACAGGAAGCTCCAGA
147362 GAGCCATTAATCGGGAAGCT
1 GAGCCATTAATCGGGAAGCT
147382 TATGAAAGAG
Statistics
Matches: 59, Mismatches: 7, Indels: 5
0.83 0.10 0.07
Matches are distributed among these distances:
48 25 0.42
49 28 0.47
50 6 0.10
ACGTcount: A:0.33, C:0.22, G:0.26, T:0.19
Consensus pattern (50 bp):
GAGCCATTAATCGGGAAGCTCATACGAGCCATATAACAGGAAGCTCCAGA
Found at i:147381 original size:25 final size:25
Alignment explanation
Indices: 147263--147420 Score: 85
Period size: 25 Copynumber: 6.3 Consensus size: 25
147253 AACTCTCTCT
*
147263 CGAGCCATATAA-CGGGAAGCTCATA
1 CGAGCCAT-TAATCGGGAAGCTCAGA
* * * *
147288 TGATCCATGTAA-CAGGAAGCTCCGGA
1 CGAGCCAT-TAATCGGGAAGCT-CAGA
* *
147314 -GAGCCTTTAAT-GGGAAGCTCATA
1 CGAGCCATTAATCGGGAAGCTCAGA
* *
147337 CGAGCCAAT-ATCAGGAAGCTCCAGA
1 CGAGCCATTAATCGGGAAGCT-CAGA
*
147362 -GAGCCATTAATCGGGAAGCTTATGAA
1 CGAGCCATTAATCGGGAAGCTCA-G-A
* * * *
147388 AGAGCCTTTAATCAGGAAGCTCTGA
1 CGAGCCATTAATCGGGAAGCTCAGA
*
147413 AGAGCCAT
1 CGAGCCAT
147421 ATATTAGGAC
Statistics
Matches: 101, Mismatches: 23, Indels: 18
0.71 0.16 0.13
Matches are distributed among these distances:
23 4 0.04
24 31 0.31
25 44 0.44
26 4 0.04
27 18 0.18
ACGTcount: A:0.34, C:0.22, G:0.25, T:0.20
Consensus pattern (25 bp):
CGAGCCATTAATCGGGAAGCTCAGA
Found at i:147417 original size:52 final size:47
Alignment explanation
Indices: 147264--147441 Score: 131
Period size: 49 Copynumber: 3.6 Consensus size: 47
147254 ACTCTCTCTC
* * * * * *
147264 GAGCCATATAACGGGAAGCTCATATGATCCATGTAACAGGAAGCTCCGGA
1 GAGCCAT-TAATGGGAAGCTCATAAGAGCCA-ATATCAGGAAGCT-CGAA
* * *
147314 GAGCCTTTAATGGGAAGCTCATACGAGCCAATATCAGGAAGCTCCAGA
1 GAGCCATTAATGGGAAGCTCATAAGAGCCAATATCAGGAAGCTCGA-A
* **
147362 GAGCCATTAATCGGGAAGCTTATGAAAGAGCCTTTAATCAGGAAGCTCTGAA
1 GAGCCATTAAT-GGGAAGCTCAT--AAGAGCCAAT-ATCAGGAAGCTC-GAA
* * *
147414 GAGCCATATATTAGGACGCTCATAAGAG
1 GAGCCAT-TAATGGGAAGCTCATAAGAG
147442 TTATGGTGTG
Statistics
Matches: 103, Mismatches: 18, Indels: 14
0.76 0.13 0.10
Matches are distributed among these distances:
47 1 0.01
48 22 0.21
49 30 0.29
50 11 0.11
51 7 0.07
52 28 0.27
53 4 0.04
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.20
Consensus pattern (47 bp):
GAGCCATTAATGGGAAGCTCATAAGAGCCAATATCAGGAAGCTCGAA
Found at i:147582 original size:24 final size:25
Alignment explanation
Indices: 147526--147588 Score: 83
Period size: 25 Copynumber: 2.6 Consensus size: 25
147516 CAATAACCAT
**
147526 ATAACGGGAAACTCATGAGAGCCAA
1 ATAACGGGATGCTCATGAGAGCCAA
* *
147551 ATATCGGGATGCTCATGAGAG-CTA
1 ATAACGGGATGCTCATGAGAGCCAA
147575 ATAACGGGATGCTC
1 ATAACGGGATGCTC
147589 TTTCGAGCTG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
24 15 0.45
25 18 0.55
ACGTcount: A:0.35, C:0.19, G:0.27, T:0.19
Consensus pattern (25 bp):
ATAACGGGATGCTCATGAGAGCCAA
Found at i:147927 original size:21 final size:20
Alignment explanation
Indices: 147903--147945 Score: 59
Period size: 21 Copynumber: 2.1 Consensus size: 20
147893 TAAATTTAGC
*
147903 TCAATTTAATACAATTCATAT
1 TCAATTCAATACAATTCA-AT
*
147924 TCAATTCAATTCAATTCAAT
1 TCAATTCAATACAATTCAAT
147944 TC
1 TC
147946 CCATCTTAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 4 0.20
21 16 0.80
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (20 bp):
TCAATTCAATACAATTCAAT
Found at i:147932 original size:5 final size:5
Alignment explanation
Indices: 147903--147945 Score: 59
Period size: 5 Copynumber: 8.4 Consensus size: 5
147893 TAAATTTAGC
* *
147903 TCAAT TTAAT ACAAT TCATAT TCAAT TCAAT TCAAT TCAAT TC
1 TCAAT TCAAT TCAAT TCA-AT TCAAT TCAAT TCAAT TCAAT TC
147946 CCATCTTAGG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 28 0.85
6 5 0.15
ACGTcount: A:0.40, C:0.19, G:0.00, T:0.42
Consensus pattern (5 bp):
TCAAT
Found at i:150206 original size:41 final size:41
Alignment explanation
Indices: 150143--150247 Score: 165
Period size: 41 Copynumber: 2.5 Consensus size: 41
150133 CTTAATTTAA
* *
150143 CAGATTCACCGGCACTTGGCCTGCTAGGCTTATAGCCTGATT
1 CAGA-TCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
* *
150185 CAGATCACCGGCACCTAGCCTGCTAGGTTTATAACCTGATT
1 CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
150226 CAGATCACCGGCACTTAGCCTG
1 CAGATCACCGGCACTTAGCCTG
150248 NNNNNNNNNN
Statistics
Matches: 58, Mismatches: 5, Indels: 1
0.91 0.08 0.02
Matches are distributed among these distances:
41 54 0.93
42 4 0.07
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.26
Consensus pattern (41 bp):
CAGATCACCGGCACTTAGCCTGCTAGGCTTATAACCTGATT
Found at i:159073 original size:18 final size:19
Alignment explanation
Indices: 159038--159074 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
159028 AATAAACATT
159038 TTTAAAATTTATTAAATAA
1 TTTAAAATTTATTAAATAA
*
159057 TTTAAAA-TTATTTAATAA
1 TTTAAAATTTATTAAATAA
159075 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTAAAATTTATTAAATAA
Found at i:159077 original size:19 final size:20
Alignment explanation
Indices: 159037--159083 Score: 62
Period size: 19 Copynumber: 2.4 Consensus size: 20
159027 AAATAAACAT
159037 TTTTAAAATTTATTAAATAA
1 TTTTAAAATTTATTAAATAA
*
159057 -TTTAAAA-TTATTTAATAAA
1 TTTTAAAATTTATTAAAT-AA
159076 TTTTAAAA
1 TTTTAAAA
159084 ATAAACACGT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
18 8 0.33
19 9 0.38
20 7 0.29
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (20 bp):
TTTTAAAATTTATTAAATAA
Found at i:161417 original size:2 final size:2
Alignment explanation
Indices: 161410--161434 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
161400 TGAATCTAAC
161410 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
161435 NNNNNNNNNN
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:161594 original size:2 final size:2
Alignment explanation
Indices: 161587--161658 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
161577 NNNNNNNNCC
161587 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
161629 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
161659 ATTTACACTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:162957 original size:14 final size:14
Alignment explanation
Indices: 162938--162964 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
162928 TTTACCCTAA
162938 AAATTAAATATTTC
1 AAATTAAATATTTC
162952 AAATTAAATATTT
1 AAATTAAATATTT
162965 ATTTCATTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
AAATTAAATATTTC
Found at i:163474 original size:16 final size:16
Alignment explanation
Indices: 163450--163483 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
163440 GTTATTGTTA
163450 TTTTTTAAAATAT-TT
1 TTTTTTAAAATATATT
163465 TTTTTATAAAATATATT
1 TTTTT-TAAAATATATT
163482 TT
1 TT
163484 ATCATTTTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTTTAAAATATATT
Found at i:165933 original size:19 final size:18
Alignment explanation
Indices: 165882--165936 Score: 56
Period size: 19 Copynumber: 2.9 Consensus size: 18
165872 AAAAATCATA
*
165882 ATAAAATTATTAGAAATTT
1 ATAAAATT-TTAGAAAATT
* *
165901 ATAATTATTATAGAAAATT
1 ATAA-AATTTTAGAAAATT
165920 ATTAAAATTTTAGAAAA
1 A-TAAAATTTTAGAAAA
165937 AATTTAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.40
Consensus pattern (18 bp):
ATAAAATTTTAGAAAATT
Found at i:166004 original size:8 final size:8
Alignment explanation
Indices: 165993--166030 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
165983 AACATATTCA
165993 AAAATTAT
1 AAAATTAT
166001 AAAAATTAT
1 -AAAATTAT
166010 AAAATTAT
1 AAAATTAT
*
166018 AAAAGT-T
1 AAAATTAT
166025 AAAATT
1 AAAATT
166031 TGGCTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
7 6 0.22
8 13 0.48
9 8 0.30
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:166006 original size:9 final size:9
Alignment explanation
Indices: 165992--166021 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
165982 TAACATATTC
165992 AAAAATTAT
1 AAAAATTAT
166001 AAAAATTAT
1 AAAAATTAT
166010 -AAAATTAT
1 AAAAATTAT
166018 AAAA
1 AAAA
166022 GTTAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.40
9 12 0.60
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAAATTAT
Found at i:171742 original size:20 final size:20
Alignment explanation
Indices: 171719--171765 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
171709 GGCACGATTA
*
171719 TTCAATCAGAGACATCGAAG
1 TTCAATCAGAGACACCGAAG
*
171739 TTCAAAT-AGAGGCACCGAAG
1 TTC-AATCAGAGACACCGAAG
*
171759 TGCAATC
1 TTCAATC
171766 CTGTACTAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
19 3 0.14
20 16 0.73
21 3 0.14
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.19
Consensus pattern (20 bp):
TTCAATCAGAGACACCGAAG
Found at i:177370 original size:30 final size:30
Alignment explanation
Indices: 177334--177396 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
177324 ATACATAAAA
*
177334 TAAAAAAAGAGTAAA-ATTACAAAAAAAATG
1 TAAAAAAACAG-AAATATTACAAAAAAAATG
* *
177364 TAAAAAAACAGAAATTTTTCAAAAAAAATG
1 TAAAAAAACAGAAATATTACAAAAAAAATG
177394 TAA
1 TAA
177397 CATATGAGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.67, C:0.05, G:0.08, T:0.21
Consensus pattern (30 bp):
TAAAAAAACAGAAATATTACAAAAAAAATG
Found at i:177484 original size:19 final size:20
Alignment explanation
Indices: 177460--177505 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
177450 ATTTTTTTTC
*
177460 AAAAATAGATA-AAAATAAA
1 AAAAATAGAGAGAAAATAAA
* *
177479 AAAAATAGGGAGAAAATGAA
1 AAAAATAGAGAGAAAATAAA
177499 AAAAATA
1 AAAAATA
177506 CAAAATTCAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (20 bp):
AAAAATAGAGAGAAAATAAA
Found at i:178486 original size:14 final size:14
Alignment explanation
Indices: 178463--178501 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
178453 TAGTATTTTC
*
178463 AGTTACAGTTGGTT
1 AGTTAAAGTTGGTT
*
178477 AGTTGAAGTTGGTT
1 AGTTAAAGTTGGTT
178491 AGTTAAAGTTG
1 AGTTAAAGTTG
178502 CAAGTATTAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.26, C:0.03, G:0.31, T:0.41
Consensus pattern (14 bp):
AGTTAAAGTTGGTT
Found at i:188436 original size:10 final size:9
Alignment explanation
Indices: 188417--188468 Score: 50
Period size: 10 Copynumber: 5.3 Consensus size: 9
188407 ATTTATTTTA
188417 AAAAAGTTAT
1 AAAAA-TTAT
188427 AAAAACTTAT
1 AAAAA-TTAT
* *
188437 TAAAAGTATT
1 AAAAATTA-T
188447 AAAAAGTTAT
1 AAAAA-TTAT
188457 AAAAATTAT
1 AAAAATTAT
188466 AAA
1 AAA
188469 TATGTAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
9 9 0.26
10 24 0.69
11 2 0.06
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.31
Consensus pattern (9 bp):
AAAAATTAT
Found at i:188443 original size:20 final size:19
Alignment explanation
Indices: 188418--188468 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
188408 TTTATTTTAA
188418 AAAAGTTATAAAAACTTATT
1 AAAAGTTATAAAAACTTA-T
*
188438 AAAAG-TATTAAAAAGTTAT
1 AAAAGTTA-TAAAAACTTAT
*
188457 AAAAATTATAAA
1 AAAAGTTATAAA
188469 TATGTAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.61, C:0.02, G:0.06, T:0.31
Consensus pattern (19 bp):
AAAAGTTATAAAAACTTAT
Found at i:188480 original size:30 final size:30
Alignment explanation
Indices: 188417--188485 Score: 90
Period size: 30 Copynumber: 2.3 Consensus size: 30
188407 ATTTATTTTA
*
188417 AAAAAGTTATAAAAACTTATTAAAAGTATT
1 AAAAAGTTATAAAAACTTATTAAAAGTAAT
188447 AAAAAGTTATAAAAA-TTA-TAAATATGTAAT
1 AAAAAGTTATAAAAACTTATTAAA-A-GTAAT
188477 -AAAAGTTAT
1 AAAAAGTTAT
188486 TTGGAGTGCT
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
28 4 0.11
29 13 0.36
30 19 0.53
ACGTcount: A:0.58, C:0.01, G:0.07, T:0.33
Consensus pattern (30 bp):
AAAAAGTTATAAAAACTTATTAAAAGTAAT
Found at i:194823 original size:9 final size:9
Alignment explanation
Indices: 194809--194848 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
194799 TTTGGTTAAA
194809 AATTACCCG
1 AATTACCCG
*
194818 AATTACCAG
1 AATTACCCG
194827 AATTACCCG
1 AATTACCCG
*
194836 AATTACCCA
1 AATTACCCG
194845 AATT
1 AATT
194849 GAATCACTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.28, G:0.07, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:194878 original size:17 final size:17
Alignment explanation
Indices: 194856--194955 Score: 74
Period size: 17 Copynumber: 5.5 Consensus size: 17
194846 ATTGAATCAC
194856 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
* * *
194873 TACATAAATCTTAGAATCAC
1 TACAT-AA--TTAAAAACAT
*
194893 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
194910 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
194930 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
194947 TACATAATT
1 TACATAATT
194956 CTTTAATATT
Statistics
Matches: 61, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
17 33 0.54
18 2 0.03
19 2 0.03
20 24 0.39
ACGTcount: A:0.50, C:0.14, G:0.03, T:0.33
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:194898 original size:20 final size:20
Alignment explanation
Indices: 194873--194936 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 20
194863 TTAAAAACAT
194873 TACATAAATCTTAGAATCAC
1 TACATAAATCTTAGAATCAC
* * *
194893 TACAT-AAT-TAAAAAT-AT
1 TACATAAATCTTAGAATCAC
* *
194910 TACATAAGTCTTTGAATCAC
1 TACATAAATCTTAGAATCAC
194930 TACATAA
1 TACATAA
194937 TTAAAAACAT
Statistics
Matches: 33, Mismatches: 8, Indels: 6
0.70 0.17 0.13
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 7 0.21
20 13 0.39
ACGTcount: A:0.47, C:0.16, G:0.05, T:0.33
Consensus pattern (20 bp):
TACATAAATCTTAGAATCAC
Found at i:194959 original size:37 final size:37
Alignment explanation
Indices: 194847--194959 Score: 190
Period size: 37 Copynumber: 3.1 Consensus size: 37
194837 ATTACCCAAA
194847 TTGAATCACTACATAATTAAAAACATTACATAAATCT
1 TTGAATCACTACATAATTAAAAACATTACATAAATCT
* * *
194884 TAGAATCACTACATAATTAAAAATATTACATAAGTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAATCT
*
194921 TTGAATCACTACATAATTAAAAACATTACATAATTCT
1 TTGAATCACTACATAATTAAAAACATTACATAAATCT
194958 TT
1 TT
194960 AATATTCTCC
Statistics
Matches: 70, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 70 1.00
ACGTcount: A:0.47, C:0.15, G:0.04, T:0.35
Consensus pattern (37 bp):
TTGAATCACTACATAATTAAAAACATTACATAAATCT
Found at i:200757 original size:24 final size:24
Alignment explanation
Indices: 200722--200792 Score: 106
Period size: 24 Copynumber: 3.0 Consensus size: 24
200712 TTGAATTATG
*
200722 TGAATATACATGAATGATTTTGAT
1 TGAATATACATGAATGATCTTGAT
*
200746 TGAATATGCATGAATGATCTTGAT
1 TGAATATACATGAATGATCTTGAT
* *
200770 TGAAAATATATGAATGATCTTGA
1 TGAATATACATGAATGATCTTGA
200793 CTAAATTCTT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.38, C:0.06, G:0.18, T:0.38
Consensus pattern (24 bp):
TGAATATACATGAATGATCTTGAT
Found at i:226447 original size:23 final size:24
Alignment explanation
Indices: 226399--226451 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
226389 TTAGTAAGTC
* * *
226399 AAATAAATTATGCTAATAAATGCT
1 AAATATATTATACTAATAAATACT
226423 AAATATATTATACT-ATAAATACT
1 AAATATATTATACTAATAAATACT
226446 AAATAT
1 AAATAT
226452 TCTAGAAAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.53, C:0.08, G:0.04, T:0.36
Consensus pattern (24 bp):
AAATATATTATACTAATAAATACT
Found at i:228386 original size:24 final size:24
Alignment explanation
Indices: 228358--228409 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
228348 TTAGTAAGTC
* *
228358 AAATAAACTATGCTAATAAATGCT
1 AAATAAACTATACTAATAAATACT
* *
228382 AAATATATTATACTAATAAATACT
1 AAATAAACTATACTAATAAATACT
228406 AAAT
1 AAAT
228410 CTTCTAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.54, C:0.10, G:0.04, T:0.33
Consensus pattern (24 bp):
AAATAAACTATACTAATAAATACT
Found at i:228658 original size:13 final size:13
Alignment explanation
Indices: 228642--228671 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
228632 TTGAATTAAG
228642 ATTATGAATAAAT
1 ATTATGAATAAAT
*
228655 ATTATTAATAAAT
1 ATTATGAATAAAT
228668 ATTA
1 ATTA
228672 CAATATATGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.43
Consensus pattern (13 bp):
ATTATGAATAAAT
Found at i:245277 original size:11 final size:11
Alignment explanation
Indices: 245261--245358 Score: 73
Period size: 11 Copynumber: 9.3 Consensus size: 11
245251 TCAATTATTT
245261 TCTCAATTTCC
1 TCTCAATTTCC
245272 TCTCAATTTCC
1 TCTCAATTTCC
* *
245283 TCTCAAATTGC
1 TCTCAATTTCC
245294 TCTCAATTTCC
1 TCTCAATTTCC
245305 T-TCCAAATTT-C
1 TCT-C-AATTTCC
*
245316 TCTCAA-ATCC
1 TCTCAATTTCC
* **
245326 -AT--ATTTAA
1 TCTCAATTTCC
*
245334 TCTCAATTTGC
1 TCTCAATTTCC
245345 TCTCAATTTCC
1 TCTCAATTTCC
245356 TCT
1 TCT
245359 TAAATTTCTC
Statistics
Matches: 66, Mismatches: 13, Indels: 16
0.69 0.14 0.17
Matches are distributed among these distances:
7 1 0.02
8 1 0.02
9 3 0.05
10 4 0.06
11 51 0.77
12 6 0.09
ACGTcount: A:0.23, C:0.31, G:0.02, T:0.44
Consensus pattern (11 bp):
TCTCAATTTCC
Found at i:245299 original size:33 final size:33
Alignment explanation
Indices: 245261--245323 Score: 94
Period size: 33 Copynumber: 1.9 Consensus size: 33
245251 TCAATTATTT
245261 TCTCAATTTCC-TCTC-AATTTCCTCTCAAATTGC
1 TCTCAATTTCCTTC-CAAATTT-CTCTCAAATTGC
245294 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
1 TCTCAATTTCCTTCCAAATTTCTCTCAAAT
245324 CCATATTTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.24, C:0.32, G:0.02, T:0.43
Consensus pattern (33 bp):
TCTCAATTTCCTTCCAAATTTCTCTCAAATTGC
Found at i:247182 original size:18 final size:18
Alignment explanation
Indices: 247159--247201 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
247149 TGCCATGTGC
*
247159 GTATCCTAACCCTTTTAT
1 GTATCCTAACCCTTATAT
247177 GTATCCTAACCCTTATAT
1 GTATCCTAACCCTTATAT
*
247195 GTTTCCT
1 GTATCCT
247202 TTTTCTAGTC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.21, C:0.28, G:0.07, T:0.44
Consensus pattern (18 bp):
GTATCCTAACCCTTATAT
Found at i:247652 original size:49 final size:49
Alignment explanation
Indices: 247599--247719 Score: 233
Period size: 49 Copynumber: 2.5 Consensus size: 49
247589 GTTTATATTA
247599 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTG
*
247648 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTG
247697 ATGTAATAAAATACAAAATAGTT
1 ATGTAATAAAATACAAAATAGTT
247720 AATATTCTTA
Statistics
Matches: 71, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 71 1.00
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTAATTTGAATATTTTGATATTATTTG
Found at i:248218 original size:14 final size:14
Alignment explanation
Indices: 248197--248232 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
248187 CATCCCATAG
248197 TCGCAAGTCCTATT
1 TCGCAAGTCCTATT
* *
248211 TTGCAAGTCTTATT
1 TCGCAAGTCCTATT
248225 TCGCAAGT
1 TCGCAAGT
248233 GTACACGATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (14 bp):
TCGCAAGTCCTATT
Found at i:251081 original size:124 final size:124
Alignment explanation
Indices: 250817--251225 Score: 629
Period size: 125 Copynumber: 3.3 Consensus size: 124
250807 AAACATTCTA
* ** * *
250817 CTGTAGCAAAAGCGCGTTCACGTGGGAGCGATTTCAAAAATTCTTTCAATAAAACATCCTGCTTG
1 CTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTTTGATAAAGCATTCTGCTTG
* * *
250882 AAGCATTTTTTATACTATTTGTTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACTTC
66 AAGC-GTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACTTC
*
250942 CTGTAGCAAAAGCGCGTCCATGTGGGAGCGATTTCAAAAATTCTTTTGATAAAGCATTCTGCTTG
1 CTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTTTGATAAAGCATTCTGCTTG
251007 AAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACTTC
66 AAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACTTC
** * *
251066 CTGTAGCAAAAGCGCGTCCACGTAAGAGCGATTTCAGAAATTCTTCTGATAAAGCATTCTGCTTG
1 CTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTTTGATAAAGCATTCTGCTTG
* * *
251131 AAGCGTTTTTTATACTATTTGCTCAGAAACATCAACTCAAAATTATTTTTTCAGGACCTA
66 AAGCG-TTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACTTC
* * *
251191 CTGTATCAAAAACGCGTCCTCGTGGGAGCGATTTC
1 CTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTC
251226 CTTAATAAAT
Statistics
Matches: 261, Mismatches: 22, Indels: 2
0.92 0.08 0.01
Matches are distributed among these distances:
124 117 0.45
125 144 0.55
ACGTcount: A:0.30, C:0.20, G:0.17, T:0.33
Consensus pattern (124 bp):
CTGTAGCAAAAGCGCGTCCACGTGGGAGCGATTTCAAAAATTCTTTTGATAAAGCATTCTGCTTG
AAGCGTTTTTATACTATTTGCTCAGAAACGTCAACTCAAAATTATTTTTTCAGGACTTC
Found at i:254398 original size:49 final size:49
Alignment explanation
Indices: 254336--254433 Score: 153
Period size: 49 Copynumber: 2.0 Consensus size: 49
254326 ATTTTATAAA
** *
254336 TACACATAACAAATGTGTATTATATATGAGTGTTTTCTTTTTGAGAATT
1 TACACATAACAAATGCATATTATATATGAGTGTTTTCTTCTTGAGAATT
254385 TACACA-AAGCAAATGCATATTATATATGAGTGTTTTCTTCTTGAGAATT
1 TACACATAA-CAAATGCATATTATATATGAGTGTTTTCTTCTTGAGAATT
254434 GTTTTCCAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
48 2 0.04
49 43 0.96
ACGTcount: A:0.34, C:0.10, G:0.14, T:0.42
Consensus pattern (49 bp):
TACACATAACAAATGCATATTATATATGAGTGTTTTCTTCTTGAGAATT
Found at i:259515 original size:91 final size:90
Alignment explanation
Indices: 259355--259543 Score: 254
Period size: 91 Copynumber: 2.1 Consensus size: 90
259345 CTAATTAAAA
* * * * *
259355 ATTTCTCTACAACTGTTGGTTGTTGATATTCAATTGTTGTTTTTCTCGACATTTCTTTAAACTTA
1 ATTTCTCGACAACTGTTGATTGTTGATATTCAATTGTAGTTTTTCTCAACATTTCTCTAAACTTA
*
259420 TTTTTTTTGAACTTCTTATCGGCAAG
66 -TTTTTTTGAACTTCTTATCGACAAG
* * * *
259446 ATTTCTCGACAATTTTTGATTGTTGCTATTCAATTGCTAG-TTTTCTCAACATTTCTCTAGACTT
1 ATTTCTCGACAACTGTTGATTGTTGATATTCAATTG-TAGTTTTTCTCAACATTTCTCTAAACTT
*
259510 CTTTTTTTGAACTTCTTATCGACAAG
65 ATTTTTTTGAACTTCTTATCGACAAG
259536 ATTTCTCG
1 ATTTCTCG
259544 GAAGCTGTTG
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
90 32 0.37
91 52 0.60
92 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.49
Consensus pattern (90 bp):
ATTTCTCGACAACTGTTGATTGTTGATATTCAATTGTAGTTTTTCTCAACATTTCTCTAAACTTA
TTTTTTTGAACTTCTTATCGACAAG
Found at i:259563 original size:90 final size:91
Alignment explanation
Indices: 259381--259572 Score: 219
Period size: 90 Copynumber: 2.1 Consensus size: 91
259371 TGGTTGTTGA
* * * * *
259381 TATTCAATTGTTGTTTTTCTCGACATTTCTTTAAACTTATTTTTTTTGAACTTCTTATCGGCAAG
1 TATTCAATTGTAGTTTTTCTCAACATTTCTCTAAACTTACTTTTTTTGAACTTCTTATCGACAAG
* * * **
259446 ATTTCTCGACAATTTTTGATTGTTGC
66 ATTTCTCGACAACTGTTGACTACTGC
*
259472 TATTCAATTGCTAG-TTTTCTCAACATTTCTCTAGACTT-CTTTTTTTGAACTTCTTATCGACAA
1 TATTCAATTG-TAGTTTTTCTCAACATTTCTCTAAACTTACTTTTTTTGAACTTCTTATCGACAA
* *
259535 GATTTCTCGGA-AGCTGTTGGCTACTGC
65 GATTTCTC-GACAACTGTTGACTACTGC
*
259562 TATTTAATTGT
1 TATTCAATTGT
259573 TATTTTAAGG
Statistics
Matches: 85, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
89 1 0.01
90 49 0.58
91 33 0.39
92 2 0.02
ACGTcount: A:0.21, C:0.17, G:0.13, T:0.48
Consensus pattern (91 bp):
TATTCAATTGTAGTTTTTCTCAACATTTCTCTAAACTTACTTTTTTTGAACTTCTTATCGACAAG
ATTTCTCGACAACTGTTGACTACTGC
Found at i:262989 original size:23 final size:23
Alignment explanation
Indices: 262934--262994 Score: 77
Period size: 23 Copynumber: 2.7 Consensus size: 23
262924 TCACCTCAAG
*
262934 GGCATTACAGAACATGCCACACA
1 GGCATTACAGAACATGCCACAAA
* * *
262957 TGCATCACAGAATATGCCACAAA
1 GGCATTACAGAACATGCCACAAA
*
262980 GGCTTTACAGAACAT
1 GGCATTACAGAACAT
262995 TACATGTTTA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.16, T:0.18
Consensus pattern (23 bp):
GGCATTACAGAACATGCCACAAA
Found at i:264202 original size:16 final size:16
Alignment explanation
Indices: 264181--264217 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
264171 GGCGTATCCC
*
264181 TTCATAGGCTCACTCT
1 TTCATAGGCGCACTCT
264197 TTCATAGGCGCACTCT
1 TTCATAGGCGCACTCT
264213 TTCAT
1 TTCAT
264218 TTCTAAGAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.19, C:0.30, G:0.14, T:0.38
Consensus pattern (16 bp):
TTCATAGGCGCACTCT
Found at i:272563 original size:20 final size:20
Alignment explanation
Indices: 272523--272564 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
272513 GATTGAATAC
*
272523 AAAAGAAAAAATATTCAGAG
1 AAAAGAAAAAAGATTCAGAG
272543 AAAAGAAAAACAGATTC-GAG
1 AAAAGAAAAA-AGATTCAGAG
272563 AA
1 AA
272565 GGTGATTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.64, C:0.07, G:0.17, T:0.12
Consensus pattern (20 bp):
AAAAGAAAAAAGATTCAGAG
Found at i:273261 original size:18 final size:18
Alignment explanation
Indices: 273238--273274 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
273228 TCATCATTAT
273238 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
273256 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
273274 T
1 T
273275 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Found at i:276024 original size:25 final size:25
Alignment explanation
Indices: 275990--276040 Score: 93
Period size: 25 Copynumber: 2.0 Consensus size: 25
275980 GGAATCGATG
*
275990 CAAAAGATCTGATCTTGGTTCCAGA
1 CAAAAGATCTGAGCTTGGTTCCAGA
276015 CAAAAGATCTGAGCTTGGTTCCAGA
1 CAAAAGATCTGAGCTTGGTTCCAGA
276040 C
1 C
276041 TTAGTACTCC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (25 bp):
CAAAAGATCTGAGCTTGGTTCCAGA
Found at i:276422 original size:132 final size:134
Alignment explanation
Indices: 276216--276483 Score: 506
Period size: 132 Copynumber: 2.0 Consensus size: 134
276206 AAATGGTACA
276216 ATCAATTGAGCCACACCAAGATTGGTTCATGGAGGGACCTAGCTCAAGCATTCATGAGGCAATAC
1 ATCAATTGAGCCACACCAAGATTGGTTCATGGAGGGACCTAGCTCAAGCATTCATGAGGCAATAC
276281 AATCATGTGACAGATATGGCGCCCGATAGA-ATTGTAATAGCCTGAATTTTTAGTGGTGTCGGAA
66 AATCATGTGACAGATATGGCGCCCGATAGAGA-TGTAATAGCCTGAATTTTTAGTGGTGTCGGAA
276345 TGGTG
130 TGGTG
276350 ATCAATTGAG-C-CACCAAGATTGGTTCATGGAGGGACCTAGCTCAAGCATTCATGAGGCAATAC
1 ATCAATTGAGCCACACCAAGATTGGTTCATGGAGGGACCTAGCTCAAGCATTCATGAGGCAATAC
276413 AATCATGTGACAGATATGGCGCCCGATAGAGATGTAATAGCCTGAATTTTTAGTGGTGTCGGAAT
66 AATCATGTGACAGATATGGCGCCCGATAGAGATGTAATAGCCTGAATTTTTAGTGGTGTCGGAAT
276478 GGTG
131 GGTG
276482 AT
1 AT
276484 TCGAGATCAC
Statistics
Matches: 133, Mismatches: 0, Indels: 4
0.97 0.00 0.03
Matches are distributed among these distances:
132 121 0.91
133 2 0.02
134 10 0.08
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (134 bp):
ATCAATTGAGCCACACCAAGATTGGTTCATGGAGGGACCTAGCTCAAGCATTCATGAGGCAATAC
AATCATGTGACAGATATGGCGCCCGATAGAGATGTAATAGCCTGAATTTTTAGTGGTGTCGGAAT
GGTG
Found at i:277326 original size:30 final size:30
Alignment explanation
Indices: 277292--277503 Score: 424
Period size: 30 Copynumber: 7.1 Consensus size: 30
277282 AATTAAGGTT
277292 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277322 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277352 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277382 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277412 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277442 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277472 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
1 TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
277502 TG
1 TG
277504 TAGTAGTCTA
Statistics
Matches: 182, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 182 1.00
ACGTcount: A:0.20, C:0.07, G:0.37, T:0.37
Consensus pattern (30 bp):
TGGTGTTGCGGTTTTGAGTATGAAAGGCTA
Found at i:277987 original size:46 final size:45
Alignment explanation
Indices: 277935--278131 Score: 234
Period size: 46 Copynumber: 4.6 Consensus size: 45
277925 TTTGAGTACT
277935 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTA
**
277981 TCTGATCAAGAAACAAAGTGATAA---GT-G----GCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTA
* *
278018 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAG-TTTAGCTACACTTA
** **
278064 TCTGATCAAGTGGTAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTA
278109 TCTGATCAAG-GAC-AAGTGATAAG
1 TCTGATCAAGTGACAAAGTGATAAG
278132 AGGTCATATG
Statistics
Matches: 131, Mismatches: 11, Indels: 21
0.80 0.07 0.13
Matches are distributed among these distances:
37 31 0.24
40 2 0.02
41 1 0.01
42 1 0.01
43 12 0.09
44 1 0.01
45 21 0.16
46 62 0.47
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.28
Consensus pattern (45 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTAGCTACACTTA
Found at i:278012 original size:37 final size:37
Alignment explanation
Indices: 277971--278045 Score: 123
Period size: 37 Copynumber: 2.0 Consensus size: 37
277961 GGTAGTTTTA
277971 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
** *
278008 GCTACACTTATCTGATCAAGTGATAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
278045 G
1 G
278046 TAGCTTCAGC
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:278039 original size:83 final size:83
Alignment explanation
Indices: 277935--278091 Score: 251
Period size: 83 Copynumber: 1.9 Consensus size: 83
277925 TTTGAGTACT
* *
277935 TCTGATCAAGTGACAAAGTGATAAGTGGTAGTTTTAGCTACACTTATCTGATCAAGAAACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGAAACAAAGT
278000 GATAAGTGGCTACACTTA
66 GATAAGTGGCTACACTTA
* ****
278018 TCTGATCAAGTGATAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGTGGTAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGAAACAAAGT
278083 GATAAGTGG
66 GATAAGTGG
278092 TAGCCTAGCT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
83 67 1.00
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.29
Consensus pattern (83 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTCAGCTACACTTATCTGATCAAGAAACAAAGT
GATAAGTGGCTACACTTA
Found at i:282114 original size:7 final size:7
Alignment explanation
Indices: 282097--282161 Score: 94
Period size: 7 Copynumber: 8.7 Consensus size: 7
282087 TGAGTCAGAA
282097 AAAATATG
1 AAAA-ATG
282105 AAAAATG
1 AAAAATG
282112 AAAAAAATG
1 --AAAAATG
282121 AAAAATG
1 AAAAATG
282128 AAAAATG
1 AAAAATG
282135 AAAAAATG
1 -AAAAATG
282143 AAAAATG
1 AAAAATG
282150 AAAAATG
1 AAAAATG
282157 AAAAA
1 AAAAA
282162 AAAATGGAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
7 36 0.67
8 11 0.20
9 7 0.13
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:282124 original size:15 final size:16
Alignment explanation
Indices: 282094--282163 Score: 94
Period size: 16 Copynumber: 4.5 Consensus size: 16
282084 CTCTGAGTCA
282094 GAAAAAATATGAAAAAT
1 GAAAAAA-ATGAAAAAT
282111 GAAAAAAATGAAAAAT
1 GAAAAAAATGAAAAAT
282127 G--AAAAATGAAAAAAT
1 GAAAAAAATG-AAAAAT
282142 G--AAAAATGAAAAAT
1 GAAAAAAATGAAAAAT
282156 GAAAAAAA
1 GAAAAAAA
282164 AATGGAGAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.28
15 14 0.28
16 15 0.30
17 7 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
GAAAAAAATGAAAAAT
Found at i:282138 original size:22 final size:22
Alignment explanation
Indices: 282097--282162 Score: 114
Period size: 22 Copynumber: 2.9 Consensus size: 22
282087 TGAGTCAGAA
282097 AAAATATGAAAAATGAAAAAAATG
1 AAAA-ATGAAAAATG-AAAAAATG
282121 AAAAATGAAAAATGAAAAAATG
1 AAAAATGAAAAATGAAAAAATG
282143 AAAAATGAAAAATGAAAAAA
1 AAAAATGAAAAATGAAAAAA
282163 AAATGGAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 28 0.67
23 10 0.24
24 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAAATGAAAAATGAAAAAATG
Found at i:282977 original size:926 final size:926
Alignment explanation
Indices: 281348--283200 Score: 3706
Period size: 926 Copynumber: 2.0 Consensus size: 926
281338 ACCCGAAAAG
281348 GGTGACTTAAATTTTGAGCAAAATGGGGCATGGACATCACCATTATCGAAGAATTCTAATGGGCA
1 GGTGACTTAAATTTTGAGCAAAATGGGGCATGGACATCACCATTATCGAAGAATTCTAATGGGCA
281413 TTGTTTCATTTTTTATATCATTAGAGGCTGCTTCATACGCAAATGCCATTATATGCCGATCCTAG
66 TTGTTTCATTTTTTATATCATTAGAGGCTGCTTCATACGCAAATGCCATTATATGCCGATCCTAG
281478 AGAGGATGGTATTGGAAAATGCATTGAACTTGAATGATAGCATGATAGCTGAGGGCTGTAATCAA
131 AGAGGATGGTATTGGAAAATGCATTGAACTTGAATGATAGCATGATAGCTGAGGGCTGTAATCAA
281543 TTCAAAATCAGACACCACACTTTGTCACTGTATTGCAAAATAATGAATTGCAAAAATGACTGAGA
196 TTCAAAATCAGACACCACACTTTGTCACTGTATTGCAAAATAATGAATTGCAAAAATGACTGAGA
281608 CTTACAAGGGTTGGCATGTGAAGTTACCATCTGCCTTCTTTGTTTTTGAACGTTTATCGGAACTT
261 CTTACAAGGGTTGGCATGTGAAGTTACCATCTGCCTTCTTTGTTTTTGAACGTTTATCGGAACTT
281673 TGACTGGGGCAACACTGTTTTCCCTGGTTTACAAGACGGAAGTAGTTCTACCTATTGAAGTAGAA
326 TGACTGGGGCAACACTGTTTTCCCTGGTTTACAAGACGGAAGTAGTTCTACCTATTGAAGTAGAA
281738 ATCCCTGTTCTCTAGGTTTTAGTTGAGTAGAATGAATCCAATCTAATCAAAAGGAAAGGCTAAAA
391 ATCCCTGTTCTCTAGGTTTTAGTTGAGTAGAATGAATCCAATCTAATCAAAAGGAAAGGCTAAAA
281803 GCTATTCAGTACAGCAGATGTACCAAAGGTAAATAATGTGAGCCTACAATCAAAAGTTTTGTCTC
456 GCTATTCAGTACAGCAGATGTACCAAAGGTAAATAATGTGAGCCTACAATCAAAAGTTTTGTCTC
281868 AGAGAATTCCATAAAGGGAACCTAATTTGGAGGAATATTCTTCCTACACAAAAGGATTTTAGAGG
521 AGAGAATTCCATAAAGGGAACCTAATTTGGAGGAATATTCTTCCTACACAAAAGGATTTTAGAGG
281933 AAAATGGATGCCAAAGGCCTTTTCCGAAGAAGCTCTGATCTTAAGTAGGATAGATGGTAAAAACT
586 AAAATGGATGCCAAAGGCCTTTTCCGAAGAAGCTCTGATCTTAAGTAGGATAGATGGTAAAAACT
281998 TGCAAAATCCTGTAAACTTAGATTCAGTCAAGAATTACCTCGCCTGAAGAAGGAGAAATGACCAA
651 TGCAAAATCCTGTAAACTTAGATTCAGTCAAGAATTACCTCGCCTGAAGAAGGAGAAATGACCAA
282063 TGTGAAAACCCGCAAAGGGCACTCTGAGTCAGAAAAAATATGAAAAATGAAAAAAATGAAAAATG
716 TGTGAAAACCCGCAAAGGGCACTCTGAGTCAGAAAAAATATGAAAAATGAAAAAAATGAAAAATG
282128 AAAAATGAAAAAATGAAAAATGAAAAATGAAAAAAAAATGGAGAGGCTAAGGGGAAAACCCGTAA
781 AAAAATGAAAAAATGAAAAATGAAAAATGAAAAAAAAATGGAGAGGCTAAGGGGAAAACCCGTAA
282193 AGGGCACCTTAGGCCAAAGGGGATTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAATATTGATTA
846 AGGGCACCTTAGGCCAAAGGGGATTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAATATTGATTA
282258 AAATGAGGCATGAGGC
911 AAATGAGGCATGAGGC
282274 GGTGACTTAAATTTTGAGCAAAATGGGGCATGGACATCACCATTATCGAAGAATTCTAATGGGCA
1 GGTGACTTAAATTTTGAGCAAAATGGGGCATGGACATCACCATTATCGAAGAATTCTAATGGGCA
282339 TTGTTTCATTTTTTATATCATTAGAGGCTGCTTCATACGCAAATGCCATTATATGCCGATCCTAG
66 TTGTTTCATTTTTTATATCATTAGAGGCTGCTTCATACGCAAATGCCATTATATGCCGATCCTAG
282404 AGAGGATGGTATTGGAAAATGCATTGAACTTGAATGATAGCATGATAGCTGAGGGCTGTAATCAA
131 AGAGGATGGTATTGGAAAATGCATTGAACTTGAATGATAGCATGATAGCTGAGGGCTGTAATCAA
282469 TTCAAAATCAGACACCACACTTTGTCACTGTATTGCAAAATAATGAATTGCAAAAATGACTGAGA
196 TTCAAAATCAGACACCACACTTTGTCACTGTATTGCAAAATAATGAATTGCAAAAATGACTGAGA
282534 CTTACAAGGGTTGGCATGTGAAGTTACCATCTGCCTTCTTTGTTTTTGAACGTTTATCGGAACTT
261 CTTACAAGGGTTGGCATGTGAAGTTACCATCTGCCTTCTTTGTTTTTGAACGTTTATCGGAACTT
282599 TGACTGGGGCAACACTGTTTTCCCTGGTTTACAAGACGGAAGTAGTTCTACCTATTGAAGTAGAA
326 TGACTGGGGCAACACTGTTTTCCCTGGTTTACAAGACGGAAGTAGTTCTACCTATTGAAGTAGAA
282664 ATCCCTGTTCTCTAGGTTTTAGTTGAGTAGAATGAATCCAATCTAATCAAAAGGAAAGGCTAAAA
391 ATCCCTGTTCTCTAGGTTTTAGTTGAGTAGAATGAATCCAATCTAATCAAAAGGAAAGGCTAAAA
282729 GCTATTCAGTACAGCAGATGTACCAAAGGTAAATAATGTGAGCCTACAATCAAAAGTTTTGTCTC
456 GCTATTCAGTACAGCAGATGTACCAAAGGTAAATAATGTGAGCCTACAATCAAAAGTTTTGTCTC
282794 AGAGAATTCCATAAAGGGAACCTAATTTGGAGGAATATTCTTCCTACACAAAAGGATTTTAGAGG
521 AGAGAATTCCATAAAGGGAACCTAATTTGGAGGAATATTCTTCCTACACAAAAGGATTTTAGAGG
282859 AAAATGGATGCCAAAGGCCTTTTCCGAAGAAGCTCTGATCTTAAGTAGGATAGATGGTAAAAACT
586 AAAATGGATGCCAAAGGCCTTTTCCGAAGAAGCTCTGATCTTAAGTAGGATAGATGGTAAAAACT
282924 TGCAAAATCCTGTAAACTTAGATTCAGTCAAGAATTACCTCGCCTGAAGAAGGAGAAATGACCAA
651 TGCAAAATCCTGTAAACTTAGATTCAGTCAAGAATTACCTCGCCTGAAGAAGGAGAAATGACCAA
282989 TGTGAAAACCCGCAAAGGGCACTCTGAGTCAGAAAAAATATGAAAAATGAAAAAAATGAAAAATG
716 TGTGAAAACCCGCAAAGGGCACTCTGAGTCAGAAAAAATATGAAAAATGAAAAAAATGAAAAATG
283054 AAAAATGAAAAAATGAAAAATGAAAAATGAAAAAAAAATGGAGAGGCTAAGGGGAAAACCCGTAA
781 AAAAATGAAAAAATGAAAAATGAAAAATGAAAAAAAAATGGAGAGGCTAAGGGGAAAACCCGTAA
283119 AGGGCACCTTAGGCCAAAGGGGATTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAATATTGATTA
846 AGGGCACCTTAGGCCAAAGGGGATTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAATATTGATTA
283184 AAATGAGGCATGAGGC
911 AAATGAGGCATGAGGC
283200 G
1 G
283201 ATCAGAGCAA
Statistics
Matches: 927, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
926 927 1.00
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.26
Consensus pattern (926 bp):
GGTGACTTAAATTTTGAGCAAAATGGGGCATGGACATCACCATTATCGAAGAATTCTAATGGGCA
TTGTTTCATTTTTTATATCATTAGAGGCTGCTTCATACGCAAATGCCATTATATGCCGATCCTAG
AGAGGATGGTATTGGAAAATGCATTGAACTTGAATGATAGCATGATAGCTGAGGGCTGTAATCAA
TTCAAAATCAGACACCACACTTTGTCACTGTATTGCAAAATAATGAATTGCAAAAATGACTGAGA
CTTACAAGGGTTGGCATGTGAAGTTACCATCTGCCTTCTTTGTTTTTGAACGTTTATCGGAACTT
TGACTGGGGCAACACTGTTTTCCCTGGTTTACAAGACGGAAGTAGTTCTACCTATTGAAGTAGAA
ATCCCTGTTCTCTAGGTTTTAGTTGAGTAGAATGAATCCAATCTAATCAAAAGGAAAGGCTAAAA
GCTATTCAGTACAGCAGATGTACCAAAGGTAAATAATGTGAGCCTACAATCAAAAGTTTTGTCTC
AGAGAATTCCATAAAGGGAACCTAATTTGGAGGAATATTCTTCCTACACAAAAGGATTTTAGAGG
AAAATGGATGCCAAAGGCCTTTTCCGAAGAAGCTCTGATCTTAAGTAGGATAGATGGTAAAAACT
TGCAAAATCCTGTAAACTTAGATTCAGTCAAGAATTACCTCGCCTGAAGAAGGAGAAATGACCAA
TGTGAAAACCCGCAAAGGGCACTCTGAGTCAGAAAAAATATGAAAAATGAAAAAAATGAAAAATG
AAAAATGAAAAAATGAAAAATGAAAAATGAAAAAAAAATGGAGAGGCTAAGGGGAAAACCCGTAA
AGGGCACCTTAGGCCAAAGGGGATTTGAGTTGAAAACCCGAAAAAGGCGGCTCAAATATTGATTA
AAATGAGGCATGAGGC
Found at i:283040 original size:7 final size:7
Alignment explanation
Indices: 283023--283087 Score: 94
Period size: 7 Copynumber: 8.7 Consensus size: 7
283013 TGAGTCAGAA
283023 AAAATATG
1 AAAA-ATG
283031 AAAAATG
1 AAAAATG
283038 AAAAAAATG
1 --AAAAATG
283047 AAAAATG
1 AAAAATG
283054 AAAAATG
1 AAAAATG
283061 AAAAAATG
1 -AAAAATG
283069 AAAAATG
1 AAAAATG
283076 AAAAATG
1 AAAAATG
283083 AAAAA
1 AAAAA
283088 AAAATGGAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 7
0.89 0.00 0.11
Matches are distributed among these distances:
7 36 0.67
8 11 0.20
9 7 0.13
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:283050 original size:15 final size:16
Alignment explanation
Indices: 283020--283089 Score: 94
Period size: 16 Copynumber: 4.5 Consensus size: 16
283010 CTCTGAGTCA
283020 GAAAAAATATGAAAAAT
1 GAAAAAA-ATGAAAAAT
283037 GAAAAAAATGAAAAAT
1 GAAAAAAATGAAAAAT
283053 G--AAAAATGAAAAAAT
1 GAAAAAAATG-AAAAAT
283068 G--AAAAATGAAAAAT
1 GAAAAAAATGAAAAAT
283082 GAAAAAAA
1 GAAAAAAA
283090 AATGGAGAGG
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
14 14 0.28
15 14 0.28
16 15 0.30
17 7 0.14
ACGTcount: A:0.74, C:0.00, G:0.13, T:0.13
Consensus pattern (16 bp):
GAAAAAAATGAAAAAT
Found at i:283064 original size:22 final size:22
Alignment explanation
Indices: 283023--283088 Score: 114
Period size: 22 Copynumber: 2.9 Consensus size: 22
283013 TGAGTCAGAA
283023 AAAATATGAAAAATGAAAAAAATG
1 AAAA-ATGAAAAATG-AAAAAATG
283047 AAAAATGAAAAATGAAAAAATG
1 AAAAATGAAAAATGAAAAAATG
283069 AAAAATGAAAAATGAAAAAA
1 AAAAATGAAAAATGAAAAAA
283089 AAATGGAGAG
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 28 0.67
23 10 0.24
24 4 0.10
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.14
Consensus pattern (22 bp):
AAAAATGAAAAATGAAAAAATG
Found at i:283446 original size:96 final size:96
Alignment explanation
Indices: 283280--283486 Score: 317
Period size: 96 Copynumber: 2.1 Consensus size: 96
283270 AGGATAGGCA
*
283280 ACATCTTGGGCCATCGACAAAGCACTGTAGATCTCCTAAACACATGTCAAACTCAGAATGGTCTT
1 ACATCTTGGG-CATCGACAAAGCACTGTAGATCTCCTAAACACATGTCAAACTCAAAATGGTCTT
* *
283345 CAGAAAGTTTGTACGGAGAAGTTCAAGCTGCG
65 CAGAAAGTTTGTACAGAGAAGTTCAAGCTACG
* *
283377 ACATCTTGAGGCATCGACAAAGCAGT-TAGATCTCTTAAACACATGTCAAACTCAAAATGGTCTT
1 ACATCTTG-GGCATCGACAAAGCACTGTAGATCTCCTAAACACATGTCAAACTCAAAATGGTCTT
*
283441 GAGAAAGTTTGTACAGAGAAGTTCAAGCTACG
65 CAGAAAGTTTGTACAGAGAAGTTCAAGCTACG
* *
283473 ATATCTGGGGCATC
1 ACATCTTGGGCATC
283487 CAATTCTCAT
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
95 6 0.06
96 71 0.70
97 22 0.22
98 2 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (96 bp):
ACATCTTGGGCATCGACAAAGCACTGTAGATCTCCTAAACACATGTCAAACTCAAAATGGTCTTC
AGAAAGTTTGTACAGAGAAGTTCAAGCTACG
Found at i:284695 original size:128 final size:128
Alignment explanation
Indices: 284466--285113 Score: 996
Period size: 128 Copynumber: 5.0 Consensus size: 128
284456 AAAACCTAGC
* * *
284466 TCCCTGGTCAGCATTGGAGTAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGT
1 TCCCTGGTCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGC
*
284531 AGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCCACAAGTCCTATG
65 AGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* *
284595 TCCCTGTTCAGCAGTGGAATAGGTTGGAAATTACCA-ATCTTGTCTCCCTAAGCAGTAACGGAGC
1 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTA-CAGATCTTGTCTCCCTAAGCAGTAGCGGAGC
* * *
284659 AGATCAAAGACGGCGAATCTTATCTTCGAGTGTAAGGAAGTAGATTTAAGCCACAAGTCGTATG
65 AGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
*
284723 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
1 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* *
284788 GATCGAAAG-CGGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAACCACAAGTCCTATG
66 GATC-AAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
* * * *
284851 TCTCTGGTCAGCAGTGGAGTAGGTTGAGAAATTACAGATCTTGTCTCCTTAAGCAGTAGCAGAGC
1 TCCCTGGTCAGCAGTGGAATAGGTTG-GAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGC
* * *
284916 AGATCAAAGACGGTGAATTTTATCTTCAAGTGTAAGGAAGCAGATTTAATCCACAAGTCCTATG
65 AGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
*
284980 TCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
1 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* * * * * *
285045 GATCGAAGATGGCGCATCTTATCTTCAAGTGTAAGGAAGCAGATTGAAGCCGATAAG-CCTATC
66 GATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCC-ACAAGTCCTATG
285108 TCCCTG
1 TCCCTG
285114 AAGTTGTAGT
Statistics
Matches: 475, Mismatches: 38, Indels: 13
0.90 0.07 0.02
Matches are distributed among these distances:
127 1 0.00
128 326 0.69
129 148 0.31
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (128 bp):
TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
GATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
Found at i:284950 original size:257 final size:257
Alignment explanation
Indices: 284466--285089 Score: 995
Period size: 257 Copynumber: 2.4 Consensus size: 257
284456 AAAACCTAGC
* * *
284466 TCCCTGGTCAGCATTGGAGTAGGTTGGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGT
1 TCCCTGGTCAGCAGTGGAATAGGTT-GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGC
* *
284531 AGATC-AAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAAATTTAAGCCACAAGTCCTATG
65 AGATCGAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAACCACAAGTCCTATG
* *
284595 TCCCTGTTCAGCAGTGGAATAGGTTGGAAATTACCAATCTTGTCTCCCTAAGCAGTAACGGAGCA
130 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACCAATCTTGTCTCCCTAAGCAGTAACAGAGCA
* * *
284660 GATCAAAGACGGCGAATCTTATCTTCGAGTGTAAGGAAGTAGATTTAAGCCACAAGTCGTATG
195 GATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
*
284723 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTATAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
1 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
*
284788 GATCGAAAG-CGGTGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAACCACAAGTCCTATGT
66 GATCGAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAACCACAAGTCCTATGT
* * * *
284852 CTCTGGTCAGCAGTGGAGTAGGTTGAGAAATTA-CAGATCTTGTCTCCTTAAGCAGTAGCAGAGC
131 CCCTGGTCAGCAGTGGAATAGGTTG-GAAATTACCA-ATCTTGTCTCCCTAAGCAGTAACAGAGC
* * *
284916 AGATCAAAGACGGTGAATTTTATCTTCAAGTGTAAGGAAGCAGATTTAATCCACAAGTCCTATG
194 AGATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
*
284980 TCCCTGGTCAGCAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
1 TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
* *
285045 GATCG-AAGATGGCGCATCTTATCTTCAAGTGTAAGGAAGCAGATT
66 GATCGAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATT
285090 GAAGCCGATA
Statistics
Matches: 339, Mismatches: 24, Indels: 8
0.91 0.06 0.02
Matches are distributed among these distances:
256 121 0.36
257 218 0.64
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (257 bp):
TCCCTGGTCAGCAGTGGAATAGGTTGGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCA
GATCGAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAACCACAAGTCCTATGT
CCCTGGTCAGCAGTGGAATAGGTTGGAAATTACCAATCTTGTCTCCCTAAGCAGTAACAGAGCAG
ATCAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATG
Found at i:285370 original size:44 final size:44
Alignment explanation
Indices: 285104--285598 Score: 207
Period size: 44 Copynumber: 11.4 Consensus size: 44
285094 CCGATAAGCC
* ** *
285104 TATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGTTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAGATCT
* * * ** * *
285148 TATCTCTCTAAAGTTGCAGT--AG-A-ATGGATCG-CATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGAT-TAAAGTAAT-AGATCT
* * * * * * *
285189 TATCTCCCTGAAGTTGCAGCGAAGCACACT-GAGTAAGCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-TAGATCT
* ** * * *
285233 TATAC-CCCTGAAGTTGCAGTGGGGCAGATCGAAGATTACAAATCT
1 TAT-CTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TAATAGATCT
* * *
285278 TATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGTCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-AATAGATCT
* *
285322 TATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAGATCT
** * ** * * *
285366 TATCTCTTTGAAGTTGCAGTAGAGTGGA-T--CG-CATCAGGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAAT-AGATCT
* * * * * *
285407 CATCTCCCTGAGGTTGCAGTGGAGTAGACTGAGAA--AACA-AGTTT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGA-TTA-AAGTAATAGA-TCT
* ** * * * * *
285451 TATCCCCCTGAAGTCACAGTGGGGCAGACTGAAG-AAGCAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAA-TAGATCT
* * * * *
285495 TATCTCCTTGAGGTTGCAGTGGAGCAGATTGAAGTCGATA-ATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGT-AATAGATCT
* * *
285539 TATCTCCCTGAGGTTGTAGTGGGAG-GGATTAAAGTAATAGATCT
1 TATCTCCCTGAAGTTGCAGT-GGAGCAGATTAAAGTAATAGATCT
*
285583 TATCTCTCTGAAGTTG
1 TATCTCCCTGAAGTTG
285599 TAGTAGAGTG
Statistics
Matches: 334, Mismatches: 89, Indels: 56
0.70 0.19 0.12
Matches are distributed among these distances:
40 6 0.02
41 52 0.16
42 4 0.01
43 12 0.04
44 211 0.63
45 46 0.14
46 3 0.01
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.29
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTAATAGATCT
Found at i:285580 original size:217 final size:217
Alignment explanation
Indices: 285082--285623 Score: 784
Period size: 218 Copynumber: 2.5 Consensus size: 217
285072 AGTGTAAGGA
* * * *
285082 AGCAGATTGAAGCCGATAAGCCTATCTCCCTGAAGTTGTAGTGGAGTGGATTAAAGTAATAGTTC
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * *
285147 TTATCTCTCTAAAGTTGCAGTAGAATGGATCGCATCAGGTCTTATCTCCCTGAAGTTGCAGCGAA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTCATCTCCCTGAAGTTGCAGCGAA
* * * **
285212 GCACACTGAGTAAGCAGGTCTTATACCCCTGAAGTTGCAGTGGGGCAGATCGAAGATTACAAATC
131 GCACACTGAGAAAACAAGTCTTATACCCCTGAAGTCACAGTGGGGCAGATCGAAGA-TACAAATC
285277 TTATCTCCCTGAAGTTACAGTGG
195 TTATCTCCCTGAAGTTACAGTGG
*
285300 AGCAGATTAAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
* * * *
285365 TTATCTCTTTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTCATCTCCCTGAGGTTGCAGTGGA
66 TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTCATCTCCCTGAAGTTGCAGCGAA
* * * *
285430 GTAGACTGAGAAAACAAGTTTTATCCCCCTGAAGTCACAGTGGGGCAGA-CTGAAGA-AGCAAAT
131 GCACACTGAGAAAACAAGTCTTATACCCCTGAAGTCACAGTGGGGCAGATC-GAAGATA-CAAAT
* * *
285493 CTTATCTCCTTGAGGTTGCAGTGG
194 CTTATCTCCCTGAAGTTACAGTGG
*
285517 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAGGTTGTAGTGGGAG-GGATTAAAGTAATAGAT
1 AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGT-GGAGCGGATTAAAGTAATAGAT
* *
285581 CTTATCTCTCTGAAGTTGTAGTAGAGTGGATCGCATCAAGTCT
65 CTTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCT
285624 TGCCGACTAG
Statistics
Matches: 292, Mismatches: 29, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
216 1 0.00
217 124 0.42
218 167 0.57
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.28
Consensus pattern (217 bp):
AGCAGATTGAAGTCGATAATCCTATCTCCCTGAAGTTGTAGTGGAGCGGATTAAAGTAATAGATC
TTATCTCTCTGAAGTTGCAGTAGAGTGGATCGCATCAGGTCTCATCTCCCTGAAGTTGCAGCGAA
GCACACTGAGAAAACAAGTCTTATACCCCTGAAGTCACAGTGGGGCAGATCGAAGATACAAATCT
TATCTCCCTGAAGTTACAGTGG
Found at i:286403 original size:21 final size:19
Alignment explanation
Indices: 286367--286408 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
286357 GATTGAATAC
286367 AAAAGAAAAAACATTCAGAG
1 AAAAGAAAAAACATTC-GAG
*
286387 AAAAGAAAAATAGATTCGAG
1 AAAAGAAAAA-ACATTCGAG
286407 AA
1 AA
286409 GGTGATTCGC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.64, C:0.07, G:0.17, T:0.12
Consensus pattern (19 bp):
AAAAGAAAAAACATTCGAG
Found at i:287106 original size:18 final size:18
Alignment explanation
Indices: 287083--287119 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
287073 TCATCATTAT
287083 TATTAGTATTAT-TATTTA
1 TATTAGT-TTATATATTTA
287101 TATTAGTTTATATATTTA
1 TATTAGTTTATATATTTA
287119 T
1 T
287120 CTACATATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.32, C:0.00, G:0.05, T:0.62
Consensus pattern (18 bp):
TATTAGTTTATATATTTA
Done.