Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009361.1 Kokia drynarioides strain JFW-HI SEQ_124068, whole genome shotgun sequence
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: 70440
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:12528 original size:29 final size:29
Alignment explanation
Indices: 12496--12592 Score: 115
Period size: 29 Copynumber: 3.4 Consensus size: 29
12486 AAAAAATGCG
* ** *
12496 ATTTTTGGATACCCGAGGGTAAAATTGTA
1 ATTTTTGGACACTTGAGGGAAAAATTGTA
* *
12525 A-TTTTGGACACTTGAGGGCAAAATGGTA
1 ATTTTTGGACACTTGAGGGAAAAATTGTA
* *
12553 ATTTTTGGACACTTGGGGGAAAAAATGTA
1 ATTTTTGGACACTTGAGGGAAAAATTGTA
12582 ATTTTTGGACA
1 ATTTTTGGACA
12593 TACGGGGGTA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
28 23 0.40
29 35 0.60
ACGTcount: A:0.32, C:0.09, G:0.26, T:0.33
Consensus pattern (29 bp):
ATTTTTGGACACTTGAGGGAAAAATTGTA
Found at i:12529 original size:28 final size:28
Alignment explanation
Indices: 12498--12564 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
12488 AAAATGCGAT
* * *
12498 TTTTGGATACCCGAGGGTAAAATTGTAA
1 TTTTGGACACCCGAGGGCAAAATGGTAA
**
12526 TTTTGGACACTTGAGGGCAAAATGGTAA
1 TTTTGGACACCCGAGGGCAAAATGGTAA
12554 TTTTTGGACAC
1 -TTTTGGACAC
12565 TTGGGGGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 23 0.70
29 10 0.30
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (28 bp):
TTTTGGACACCCGAGGGCAAAATGGTAA
Found at i:12575 original size:28 final size:29
Alignment explanation
Indices: 12516--12615 Score: 107
Period size: 29 Copynumber: 3.5 Consensus size: 29
12506 ACCCGAGGGT
* * *
12516 AAAATTGTAA-TTTTGGACACTTGAGGGC
1 AAAATGGTAATTTTTGGACACTTGGGGGA
12544 AAAATGGTAATTTTTGGACACTTGGGGGAA
1 AAAATGGTAATTTTTGGACACTTGGGGG-A
* *
12574 AAAAT-GTAATTTTTGGACA-TACGGGGGT
1 AAAATGGTAATTTTTGGACACT-TGGGGGA
*
12602 AACATGGTAATTTT
1 AAAATGGTAATTTT
12616 CAAAAGTTCA
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
28 14 0.23
29 43 0.69
30 5 0.08
ACGTcount: A:0.33, C:0.08, G:0.26, T:0.33
Consensus pattern (29 bp):
AAAATGGTAATTTTTGGACACTTGGGGGA
Found at i:12682 original size:59 final size:58
Alignment explanation
Indices: 12619--12826 Score: 172
Period size: 59 Copynumber: 3.5 Consensus size: 58
12609 TAATTTTCAA
* **
12619 AAGTTCAGGGGCAAAAATATGATTTTTGAAATAATT-GGGGTCAAAAATGTAATTTTTGG
1 AAGTTCAGGGGCAAAAATGT-ATTTTTGAAA-AATTCAAGGTCAAAAATGTAATTTTTGG
* * * * *
12678 AAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAAGGTTAAAAATGTAATTTTTTG
1 AAGTTCAGGGGCAAAAATGT-ATTTTTGAAAAATTCAAGGTCAAAAATGTAATTTTTGG
* * * * *
12737 AAGTTC-GGGGTCAAAAATGTATTTTTTG-GAAGTTTATGGGT-AAAAATGTGATTTTTGG
1 AAGTTCAGGGG-CAAAAATGTA-TTTTTGAAAAATTCA-AGGTCAAAAATGTAATTTTTGG
* **
12795 AAAGTTTAGGGTTAAAAATGTAATTTTTGAAA
1 -AAGTTCAGGGGCAAAAATGT-ATTTTTGAAA
12827 GTTTAGGGGT
Statistics
Matches: 120, Mismatches: 21, Indels: 15
0.77 0.13 0.10
Matches are distributed among these distances:
58 29 0.24
59 86 0.72
60 5 0.04
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.38
Consensus pattern (58 bp):
AAGTTCAGGGGCAAAAATGTATTTTTGAAAAATTCAAGGTCAAAAATGTAATTTTTGG
Found at i:12689 original size:88 final size:87
Alignment explanation
Indices: 12573--12877 Score: 230
Period size: 88 Copynumber: 3.5 Consensus size: 87
12563 ACTTGGGGGA
*** * *
12573 AAAAATGTAATTTTTGGACA-TACGGGGGTAACATGGTAA-TTTT-CAAAAGTTCAGGGGCAAAA
1 AAAAATGTAATTTTTGGA-AGTTTAGGGGTAAAAT-GTAATTTTTGCAAAA-TTCAAGGGCAAAA
* *
12635 ATATGA-TTTTTGAAATAATTGGGGTC
63 ATATAATTTTTTGAAAT--TCGGGGTC
* **
12661 AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAAGGTTAAAAAT
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT-AAAATGTAATTTTTGCAAAATTCAAGGGCAAAAAT
* *
12726 GTAATTTTTTGAAGTTCGGGGTC
65 ATAATTTTTTGAAATTCGGGGTC
* * * * * * *
12749 AAAAATGTATTTTTTGGAAGTTTATGGGTAAAAATGTGATTTTTGGAAAGTT-TAGGGTTAAAAA
1 AAAAATGTAATTTTTGGAAGTTTAGGGGT-AAAATGTAATTTTTGCAAAATTCAAGGG-CAAAAA
* *
12813 TGTAA-TTTTTGAAAGTTTAGGGGT-
64 TATAATTTTTTGAAA--TTCGGGGTC
* * **
12837 TAAAATGTAA-TTTTGAAAAGTTTAGGATTAAAATGTAATTT
1 AAAAATGTAATTTTTG-GAAGTTTAGGGGTAAAATGTAATTT
12878 CTAGATAGTT
Statistics
Matches: 181, Mismatches: 27, Indels: 19
0.80 0.12 0.08
Matches are distributed among these distances:
87 28 0.15
88 111 0.61
89 29 0.16
90 13 0.07
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (87 bp):
AAAAATGTAATTTTTGGAAGTTTAGGGGTAAAATGTAATTTTTGCAAAATTCAAGGGCAAAAATA
TAATTTTTTGAAATTCGGGGTC
Found at i:12694 original size:29 final size:29
Alignment explanation
Indices: 12655--12877 Score: 245
Period size: 29 Copynumber: 7.6 Consensus size: 29
12645 TGAAATAATT
12655 GGGGTCAAAAATGTAATTTTTGGAAGTTTA
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTA
* *
12685 GGGGTAAAAATGTAATTTTTGGAAAATTCA
1 GGGGTAAAAATGTAATTTTTGG-AAGTTTA
* * * *
12715 AGGTTAAAAATGTAATTTTTTGAAG-TTC
1 GGGGTAAAAATGTAATTTTTGGAAGTTTA
*
12743 GGGGTCAAAAATGTATTTTTTGGAAGTTTA
1 GGGGT-AAAAATGTAATTTTTGGAAGTTTA
* *
12773 TGGGTAAAAATGTGATTTTTGGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTGG-AAGTTTA
* *
12803 GGGTTAAAAATGTAATTTTTGAAAGTTTA
1 GGGGTAAAAATGTAATTTTTGGAAGTTTA
* *
12832 GGGGTTAAAATGTAA-TTTTGAAAAGTTTA
1 GGGGTAAAAATGTAATTTTTG-GAAGTTTA
* *
12861 -GGATTAAAATGTAATTT
1 GGGGTAAAAATGTAATTT
12878 CTAGATAGTT
Statistics
Matches: 164, Mismatches: 23, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
28 22 0.13
29 82 0.50
30 60 0.37
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGGAAGTTTA
Found at i:12829 original size:59 final size:58
Alignment explanation
Indices: 12656--12877 Score: 250
Period size: 59 Copynumber: 3.8 Consensus size: 58
12646 GAAATAATTG
* * *
12656 GGGTCAAAAATGTAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATTCAA
1 GGGT-AAAAATGTAATTTTTGGAAGTTTAGGGTTAAAAATGTAATTTTT-GAAAGTTTAA
* * ** * * * *
12716 GGTTAAAAATGTAATTTTTTGAAGTTCGGGGTCAAAAATGTATTTTTTGGAAGTTTAT
1 GGGTAAAAATGTAATTTTTGGAAGTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTAA
* *
12774 GGGTAAAAATGTGATTTTTGGAAAGTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTAG
1 GGGTAAAAATGTAATTTTTGG-AAGTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTAA
* * *
12833 GGGTTAAAATGTAA-TTTTGAAAAGTTTAGGATT-AAAATGTAATTT
1 GGGTAAAAATGTAATTTTTG-GAAGTTTAGGGTTAAAAATGTAATTT
12878 CTAGATAGTT
Statistics
Matches: 136, Mismatches: 24, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
57 12 0.09
58 40 0.29
59 81 0.60
60 3 0.02
ACGTcount: A:0.36, C:0.02, G:0.23, T:0.39
Consensus pattern (58 bp):
GGGTAAAAATGTAATTTTTGGAAGTTTAGGGTTAAAAATGTAATTTTTGAAAGTTTAA
Found at i:14784 original size:17 final size:17
Alignment explanation
Indices: 14761--14870 Score: 123
Period size: 17 Copynumber: 6.4 Consensus size: 17
14751 GTTTGTAACC
*
14761 ATTTAAATTTAGAATAA
1 ATTTAAATTTAAAATAA
* *
14778 TTTTAAATGTAAAAATAA
1 ATTTAAAT-TTAAAATAA
* * *
14796 ATTTAAACTTATATTAA
1 ATTTAAATTTAAAATAA
*
14813 ATTTAAATTTAAAACAA
1 ATTTAAATTTAAAATAA
14830 ATTTAAATTTAAAATAA
1 ATTTAAATTTAAAATAA
*
14847 ACTT-AATCTTAAAATAA
1 ATTTAAAT-TTAAAATAA
14864 ATTTAAA
1 ATTTAAA
14871 AAAATGGGTT
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
16 3 0.04
17 57 0.76
18 15 0.20
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (17 bp):
ATTTAAATTTAAAATAA
Found at i:14802 original size:6 final size:6
Alignment explanation
Indices: 14761--14842 Score: 55
Period size: 6 Copynumber: 14.2 Consensus size: 6
14751 GTTTGTAACC
* * ** * *
14761 ATTTAA ATTTAGA A--TAA TTTTAA ATGTAA AAATAA ATTTAA ACTTAT
1 ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
**
14808 A-TTAA ATTTAA ATTTAA A-ACAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
14843 ATAAACTTAA
Statistics
Matches: 57, Mismatches: 14, Indels: 10
0.70 0.17 0.12
Matches are distributed among these distances:
4 1 0.02
5 9 0.16
6 45 0.79
7 2 0.04
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (6 bp):
ATTTAA
Found at i:14825 original size:29 final size:29
Alignment explanation
Indices: 14761--14825 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
14751 GTTTGTAACC
*
14761 ATTTAAATTTAGAATAATTTTAAATGTAA
1 ATTTAAATTTAGAATAATATTAAATGTAA
** * *
14790 AAATAAATTTA-AACTTATATTAAATTTAA
1 ATTTAAATTTAGAA-TAATATTAAATGTAA
14819 ATTTAAA
1 ATTTAAA
14826 ACAAATTTAA
Statistics
Matches: 28, Mismatches: 7, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
28 2 0.07
29 26 0.93
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (29 bp):
ATTTAAATTTAGAATAATATTAAATGTAA
Found at i:15645 original size:39 final size:38
Alignment explanation
Indices: 15602--16287 Score: 308
Period size: 39 Copynumber: 17.8 Consensus size: 38
15592 GCTGATGATG
* * *
15602 ATCTGCCTTAGGCTTGAGGTAAGAGATCGAATGGTTGCA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * * *
15641 ATCTGCC-CAAGCTCGAGGTAAGAAATTC-ACTGG-TGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGA-TCGAATGGTTGA
* * *
15677 TGATCTGCC-CTAGGCTCGAGGTAGGAGATCGAATGGCTGCA
1 --ATCTGCCTC-AGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * ** * *
15718 ATCTGCCCCAGGCTCGGGGTAAGAAAT-TTATTGATGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTGA
* *
15755 TGATCTCCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCA
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * *
15796 ATCTACCTCAAGCTCGGGGTAAGAGATTCG-TTGGTGATGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGA-TCGAATGGT--TGA
* * *
15836 A-CTGCCTTAGGCT-GGGGTAAAAGATCGAATGGCTGCA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * * *
15873 ATCTATCC-CAGGCTCGGGGTAACAGATTC-ACT-GATGA
1 ATCT-GCCTCAGGCTCGGGGTAAGAGA-TCGAATGGTTGA
**
15910 TGATCTGCCT-AGGCTCGGGGTAAGAGATCGAATGACTGTA
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* *
15950 ATCTGCC-CGAAGCTCGAGGTAAGAGATTTGCTG-ATGG-TG-
1 ATCTGCCTC-AGGCTCGGGGTAAGAGA--T-C-GAATGGTTGA
*
15989 ATCTGCCTCAGGCT-TGGGTAAGAGATCGAATGGTTGTA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * * *
16027 ATCTGCCTCAGGCTTGGGGTAAGAGATTTG--TTGATGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGA-TCGAATGGTTGA
* * ** *
16064 TGATCTGCCTCAGACTTGCTGTAAGTGATCGAATGGTTGCA
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * *
16105 ATTTG-C-CAGGCTCGTGGTAAGAGATCGAATGATTGCA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTG-A
* * *
16142 ATCTGCC-CAAGGCTTGGGGTAAGAGATTGGTTGATGG-TG-
1 ATCTGCCTC-AGGCTCGGGGTAAGAGA-TCG--AATGGTTGA
* * * * **
16181 ATCTGCCCCAAGCTCGGGGTAAGAGATCGAACGACTACA
1 ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATG-GTTGA
* * * *
16220 ATCTACCCCAGGCTCAGGGTAAGAGATTCG-TTGG-TGA
1 ATCTGCCTCAGGCTCGGGGTAAGAGA-TCGAATGGTTGA
* * *
16257 TGATCTGCCCCAAGCTTGGGGTAAGAGATCG
1 --ATCTGCCTCAGGCTCGGGGTAAGAGATCG
16288 GGATCTTCAA
Statistics
Matches: 497, Mismatches: 93, Indels: 115
0.70 0.13 0.16
Matches are distributed among these distances:
34 1 0.00
35 5 0.01
36 8 0.02
37 42 0.08
38 120 0.24
39 274 0.55
40 29 0.06
41 10 0.02
42 7 0.01
43 1 0.00
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.25
Consensus pattern (38 bp):
ATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGTTGA
Found at i:15678 original size:77 final size:77
Alignment explanation
Indices: 15579--16168 Score: 582
Period size: 77 Copynumber: 7.6 Consensus size: 77
15569 CCCGTTGATA
** * *
15579 GGGTAAGAGATTGGCTGATGATGATCTGCCTTAGGCTTGAGGTAAGAGATCGAATGGTTGCAATC
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
*
15644 TGCCCAAGCTCG
66 TGCCCAGGCTCG
* * * * * * *
15656 AGGTAAGAAATTCACTGGTGATGATCTGCCCTAGGCTCGAGGTAGGAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
15721 TGCCCCAGGCTCG
66 TG-CCCAGGCTCG
* * * * * *
15734 GGGTAAGAAATTTATTGATGATGATCTCCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
* *
15799 TACCTCAAGCTCG
66 TGCC-CAGGCTCG
** * * *
15812 GGGTAAGAGATTCGTTGGTGATGAACTGCCTTAGGC-TGGGGTAAAAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
*
15876 TATCCCAGGCTCG
66 T-GCCCAGGCTCG
* * * *
15889 GGGTAACAGATTCACTGATGATGATCTGCC-TAGGCTCGGGGTAAGAGATCGAATGACTGTAATC
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
*
15953 TGCCCGAAGCTCG
66 TGCCC-AGGCTCG
* ** * * * *
15966 AGGTAAGAGATTTGCTGATGGTGATCTGCCTCAGGCTT-GGGTAAGAGATCGAATGGTTGTAATC
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
*
16030 TGCCTCAGGCTTG
66 TGCC-CAGGCTCG
*** * * ** * * *
16043 GGGTAAGAGATTTGTTGATGATGATCTGCCTCAGACTTGCTGTAAGTGATCGAATGGTTGCAATT
1 GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
16108 TG-CCAGGCTCG
66 TGCCCAGGCTCG
* * **
16119 TGGTAAGAGA-TCGAATGAT--TGCAATCTGCCCAAGGCTTGGGGTAAGAGAT
1 GGGTAAGAGATTC-ACTGATGATG--ATCTGCCTTAGGCTTGGGGTAAGAGAT
16169 TGGTTGATGG
Statistics
Matches: 428, Mismatches: 74, Indels: 23
0.82 0.14 0.04
Matches are distributed among these distances:
74 2 0.00
75 1 0.00
76 49 0.11
77 243 0.57
78 133 0.31
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (77 bp):
GGGTAAGAGATTCACTGATGATGATCTGCCTTAGGCTTGGGGTAAGAGATCGAATGGCTGCAATC
TGCCCAGGCTCG
Found at i:15861 original size:155 final size:154
Alignment explanation
Indices: 15579--16129 Score: 656
Period size: 155 Copynumber: 3.6 Consensus size: 154
15569 CCCGTTGATA
*** * * * *
15579 GGGTAAGAGATTGGCTGATGATGATCTGCCTTAGGCTTGAGGTAAGAGATCGAATGGTTGCAATC
1 GGGTAAGAGATTTATTGATGATGATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* * * * *
15644 TGCCCAAGCTCGAGGTAAGAAATTCACTGGTGATGATCTGCCCTAGGCTCGAGGTAGGAGATCGA
66 TGCCCAAGCTCGAGGTAAGAGATTCGCTGGTGATGATCTGCCTTAGGCT-GGGGTAAGAGATCGA
15709 ATGGCTGCAATCTGCCCCAGGCTCG
130 ATGGCTGCAATCTGCCCCAGGCTCG
* *
15734 GGGTAAGAAATTTATTGATGATGATCTCCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
1 GGGTAAGAGATTTATTGATGATGATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* * * * *
15799 TACCTCAAGCTCGGGGTAAGAGATTCGTTGGTGATGAACTGCCTTAGGCTGGGGTAAAAGATCGA
66 TGCC-CAAGCTCGAGGTAAGAGATTCGCTGGTGATGATCTGCCTTAGGCTGGGGTAAGAGATCGA
**
15864 ATGGCTGCAATCTATCCCAGGCTCG
130 ATGGCTGCAATCTGCCCCAGGCTCG
* * * * *
15889 GGGTAACAGATTCACTGATGATGATCTGCCT-AGGCTCGGGGTAAGAGATCGAATGACTGTAATC
1 GGGTAAGAGATTTATTGATGATGATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* * * * *
15953 TGCCCGAAGCTCGAGGTAAGAGATTTGCTGATGGTGATCTGCCTCAGGCTTGGGTAAGAGATCGA
66 TGCCC-AAGCTCGAGGTAAGAGATTCGCTGGTGATGATCTGCCTTAGGCTGGGGTAAGAGATCGA
* * * *
16018 ATGGTTGTAATCTGCCTCAGGCTTG
130 ATGGCTGCAATCTGCCCCAGGCTCG
* * * ** * * *
16043 GGGTAAGAGATTTGTTGATGATGATCTGCCTCAGACTTGCTGTAAGTGATCGAATGGTTGCAATT
1 GGGTAAGAGATTTATTGATGATGATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
* *
16108 TG-CCAGGCTCGTGGTAAGAGAT
66 TGCCCAAGCTCGAGGTAAGAGAT
16130 CGAATGATTG
Statistics
Matches: 334, Mismatches: 59, Indels: 8
0.83 0.15 0.02
Matches are distributed among these distances:
153 17 0.05
154 132 0.40
155 146 0.44
156 39 0.12
ACGTcount: A:0.25, C:0.18, G:0.31, T:0.26
Consensus pattern (154 bp):
GGGTAAGAGATTTATTGATGATGATCTGCCTCAGGCTCGGGGTAAGAGATCGAATGGCTGCAATC
TGCCCAAGCTCGAGGTAAGAGATTCGCTGGTGATGATCTGCCTTAGGCTGGGGTAAGAGATCGAA
TGGCTGCAATCTGCCCCAGGCTCG
Found at i:24474 original size:58 final size:58
Alignment explanation
Indices: 24393--24513 Score: 147
Period size: 58 Copynumber: 2.1 Consensus size: 58
24383 CAAAAATGCG
* * * *
24393 ATTTTTGGATACTC-GGGGTTAAAATGGTAA-TTTTAGTCACTCAGAGGGTAAAATGATA
1 ATTTTTGGACACTCGGGGGTAAAAAT-GTAATTTTTAGACACTC-GAGGGTAAAATGAAA
* * *
24451 ATTTTTGGACACTTGGGGGTAAAAATGTAATTTTTAGACATTCGGGGGTAAAATGAAA
1 ATTTTTGGACACTCGGGGGTAAAAATGTAATTTTTAGACACTCGAGGGTAAAATGAAA
24509 ATTTT
1 ATTTT
24514 CAAAGGTTTA
Statistics
Matches: 54, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
58 34 0.63
59 20 0.37
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (58 bp):
ATTTTTGGACACTCGGGGGTAAAAATGTAATTTTTAGACACTCGAGGGTAAAATGAAA
Found at i:24511 original size:29 final size:29
Alignment explanation
Indices: 24393--24513 Score: 104
Period size: 29 Copynumber: 4.2 Consensus size: 29
24383 CAAAAATGCG
* * * * *
24393 ATTTTTGGATACTCGGGGTTAAAATGGTA
1 ATTTTTAGACACTTGGGGGTAAAATGATA
* * *
24422 A-TTTTAGTCACTCAGAGGGTAAAATGATA
1 ATTTTTAGACACT-TGGGGGTAAAATGATA
*
24451 ATTTTTGGACACTTGGGGGTAAAAATG-TA
1 ATTTTTAGACACTTGGGGGT-AAAATGATA
*
24480 ATTTTTAGACA-TTCGGGGGTAAAATGAAA
1 ATTTTTAGACACTT-GGGGGTAAAATGATA
24509 ATTTT
1 ATTTT
24514 CAAAGGTTTA
Statistics
Matches: 74, Mismatches: 13, Indels: 10
0.76 0.13 0.10
Matches are distributed among these distances:
28 16 0.22
29 43 0.58
30 15 0.20
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (29 bp):
ATTTTTAGACACTTGGGGGTAAAATGATA
Found at i:24588 original size:88 final size:88
Alignment explanation
Indices: 24471--24787 Score: 266
Period size: 88 Copynumber: 3.6 Consensus size: 88
24461 ACTTGGGGGT
* * * * * *
24471 AAAAATGTAATTTTTAGACA-TTCGGGGGT-AAAATGAAAATTTTCAAAGGTTTAGGGGCAAAAA
1 AAAAATGTAATTTTTGGA-AGTTCGAGGGTAAAAATGTAATTTTTGAAA-GTTCAGGGGCAAAAA
24534 TATGATTTTTGGAAAAATGAATGTC
64 TATGATTTTTGGAAAAATGAATGTC
* * *
24559 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTCAAGGTCAAAAAT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTG-AAAGTTCAGGGGCAAAAAT
* *** **
24624 ATAATTTTTGGAAGTTTGGGTGT-
65 ATGATTTTTGGAAAAATGAATGTC
* * * * * * **
24647 AAAAATGTGATTTTTGGAAAGTT-TAGGATCAAAGATGTAATTTTTGGAAGTTCGGGGGTGAAAA
1 AAAAATGTAATTTTTGG-AAGTTCGAGGGT-AAAAATGTAATTTTTGAAAGTTCAGGGGCAAAAA
* * ** * *
24711 TGTGATTTTTGG-AAAGTTTAGGGC
64 TATGATTTTTGGAAAAATGAATGTC
* *
24735 AAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAAGTTC
1 AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTG-AAAGTTC
24788 GAGGTTTAAA
Statistics
Matches: 179, Mismatches: 42, Indels: 16
0.76 0.18 0.07
Matches are distributed among these distances:
87 23 0.13
88 93 0.52
89 60 0.34
90 3 0.02
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (88 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTAATTTTTGAAAGTTCAGGGGCAAAAATA
TGATTTTTGGAAAAATGAATGTC
Found at i:24592 original size:29 final size:29
Alignment explanation
Indices: 24559--24837 Score: 269
Period size: 29 Copynumber: 9.5 Consensus size: 29
24549 AATGAATGTC
24559 AAAAATGTAATTTTTGGAAGTTCGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
24588 AAAAATGTGATTTTTGAAAAGTTC-AAGGT
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
* *
24617 CAAAAATATAATTTTTGGAAGTTTG-GGTGT
1 -AAAAATGTAATTTTTGGAAGTTCGAGG-GT
* * *
24647 AAAAATGTGATTTTTGGAAAGTT-TAGGAT
1 AAAAATGTAATTTTTGG-AAGTTCGAGGGT
* *
24676 CAAAGATGTAATTTTTGGAAGTTCGGGGGT
1 -AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * * *
24706 GAAAATGTGATTTTTGGAAAGTT-TAGGGC
1 AAAAATGTAATTTTTGG-AAGTTCGAGGGT
*
24735 AAAAATGTAATTTTTGGAAGTTTGAGGGT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
* * *
24764 AAAAATGTGATTTTTGAAAAGTTCGAGGTT
1 AAAAATGTAATTTTTG-GAAGTTCGAGGGT
* * *
24794 TAAAATGTAATTTTTGAAAGTTCGAGGTT
1 AAAAATGTAATTTTTGGAAGTTCGAGGGT
*
24823 CAAAATGTAATTTTT
1 AAAAATGTAATTTTT
24838 AAAAAGTTCA
Statistics
Matches: 205, Mismatches: 34, Indels: 22
0.79 0.13 0.08
Matches are distributed among these distances:
28 5 0.02
29 124 0.60
30 76 0.37
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AAAAATGTAATTTTTGGAAGTTCGAGGGT
Found at i:24788 original size:88 final size:89
Alignment explanation
Indices: 24558--24837 Score: 322
Period size: 88 Copynumber: 3.2 Consensus size: 89
24548 AAATGAATGT
* *
24558 CAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTC-AAGGTCAAAA
1 CAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAAGTTCGAGGGT-AAAA
* *
24622 ATATAATTTTTGG-AAGTTTGGGTG
65 ATGTAATTTTTGGAAAGTTTAGGTG
* * * * * * * *
24646 TAAAAATGTGATTTTTGGAAAGTTT-AGGATCAAAGATGTAATTTTTG-GAAGTTCGGGGGTGAA
1 CAAAAATGTAATTTTTGG-AAGTTTGAGGGT-AAAAATGTGATTTTTGAAAAGTTCGAGGGTAAA
*
24709 AATGTGATTTTTGGAAAGTTTAGG-G
64 AATGTAATTTTTGGAAAGTTTAGGTG
* *
24734 CAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAAGTTCGAGGTTTAAAA
1 CAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAAGTTCGAGGGTAAAAA
* *
24799 TGTAATTTTT-GAAAGTTCGAGGTT
66 TGTAATTTTTGGAAAGTT-TAGGTG
24823 C-AAAATGTAATTTTT
1 CAAAAATGTAATTTTT
24838 AAAAAGTTCA
Statistics
Matches: 159, Mismatches: 25, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
87 27 0.17
88 101 0.64
89 31 0.19
ACGTcount: A:0.35, C:0.04, G:0.25, T:0.37
Consensus pattern (89 bp):
CAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAAGTTCGAGGGTAAAAA
TGTAATTTTTGGAAAGTTTAGGTG
Found at i:24843 original size:59 final size:59
Alignment explanation
Indices: 24556--24846 Score: 381
Period size: 59 Copynumber: 4.9 Consensus size: 59
24546 AAAAATGAAT
*
24556 GTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTCAAG
1 GTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTCTAG
* * *
24615 GTCAAAAATATAATTTTTGGAAGTTTG-GGTGTAAAAATGTGATTTTTGGAAAGTT-TAG
1 GTCAAAAATGTAATTTTTGGAAGTTCGAGG-GTAAAAATGTGATTTTTGAAAAGTTCTAG
* * * *
24673 GATCAAAGATGTAATTTTTGGAAGTTCGGGGGTGAAAATGTGATTTTTGGAAAGTT-TAG
1 G-TCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTCTAG
* * *
24732 GGCAAAAATGTAATTTTTGGAAGTTTGAGGGTAAAAATGTGATTTTTGAAAAGTTCGAG
1 GTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTCTAG
** * * * * *
24791 GTTTAAAATGTAATTTTTGAAAGTTCGAGGTTCAAAATGTAATTTTTAAAAAGTTC
1 GTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTC
24847 AGGGGTAAAA
Statistics
Matches: 204, Mismatches: 24, Indels: 8
0.86 0.10 0.03
Matches are distributed among these distances:
58 53 0.26
59 149 0.73
60 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.37
Consensus pattern (59 bp):
GTCAAAAATGTAATTTTTGGAAGTTCGAGGGTAAAAATGTGATTTTTGAAAAGTTCTAG
Found at i:24857 original size:29 final size:29
Alignment explanation
Indices: 24466--24856 Score: 219
Period size: 29 Copynumber: 13.3 Consensus size: 29
24456 TGGACACTTG
* *
24466 GGGGTAAAAATGTAATTTTTAGACA-TTCG
1 GGGGTAAAAATGTAATTTTT-GAAAGTTCA
* * * *
24495 GGGGT-AAAATGAAAATTTTCAAAGGTTTA
1 GGGGTAAAAATGTAATTTTTGAAA-GTTCA
* * * ** *
24524 GGGGCAAAAATATGATTTTTGGAAAAATGA
1 GGGGTAAAAATGTAATTTTT-GAAAGTTCA
** *
24554 -ATGTCAAAAATGTAATTTTTGGAAGTTC-
1 GGGGT-AAAAATGTAATTTTTGAAAGTTCA
*
24582 GAGGGTAAAAATGTGATTTTTGAAAAGTTCA
1 G-GGGTAAAAATGTAATTTTTG-AAAGTTCA
* * * *
24613 -AGGTCAAAAATATAATTTTTGGAAGTT-T
1 GGGGT-AAAAATGTAATTTTTGAAAGTTCA
* *
24641 GGGTGTAAAAATGTGATTTTTGGAAAGTTTA
1 GGG-GTAAAAATGTAATTTTT-GAAAGTTCA
* * * *
24672 -GGATCAAAGATGTAATTTTTGGAAGTTCG
1 GGGGT-AAAAATGTAATTTTTGAAAGTTCA
* * *
24701 GGGGTGAAAATGTGATTTTTGGAAAGTTTA
1 GGGGTAAAAATGTAATTTTT-GAAAGTTCA
* * *
24731 -GGGCAAAAATGTAATTTTTGGAAGTT-T
1 GGGGTAAAAATGTAATTTTTGAAAGTTCA
*
24758 GAGGGTAAAAATGTGATTTTTGAAAAGTTC-
1 G-GGGTAAAAATGTAATTTTTG-AAAGTTCA
* *
24788 GAGGTTTAAAATGTAATTTTTGAAAGTTC-
1 G-GGGTAAAAATGTAATTTTTGAAAGTTCA
* * *
24817 GAGGTTCAAAATGTAATTTTTAAAAAGTTCA
1 G-GGGTAAAAATGTAATTTTT-GAAAGTTCA
24848 GGGGTAAAA
1 GGGGTAAAA
24857 TATGATTTTT
Statistics
Matches: 273, Mismatches: 66, Indels: 45
0.71 0.17 0.12
Matches are distributed among these distances:
27 2 0.01
28 18 0.07
29 133 0.49
30 116 0.42
31 4 0.01
ACGTcount: A:0.37, C:0.04, G:0.25, T:0.35
Consensus pattern (29 bp):
GGGGTAAAAATGTAATTTTTGAAAGTTCA
Found at i:24996 original size:21 final size:20
Alignment explanation
Indices: 24968--25006 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
24958 TTGTTTTAAA
*
24968 TTTAAAATATCAATGTCCCT
1 TTTAAAATATCAAAGTCCCT
*
24988 TTTACAAATTTCAAAGTCC
1 TTTA-AAATATCAAAGTCC
25007 AATTCCGAAA
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:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTAAAATATCAAAGTCCCT
Found at i:25535 original size:33 final size:33
Alignment explanation
Indices: 25493--25560 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
25483 ATATTCTATT
*
25493 GATATTGAGAGTAAAGCTTTTGTTATGTTTTTA
1 GATATTGAGACTAAAGCTTTTGTTATGTTTTTA
*
25526 GATATTGAGACTAAAGTTTTTGTTATGTTTTTA
1 GATATTGAGACTAAAGCTTTTGTTATGTTTTTA
25559 GA
1 GA
25561 GCTTGTCCCT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.28, C:0.03, G:0.21, T:0.49
Consensus pattern (33 bp):
GATATTGAGACTAAAGCTTTTGTTATGTTTTTA
Found at i:27316 original size:39 final size:39
Alignment explanation
Indices: 27191--27694 Score: 310
Period size: 39 Copynumber: 12.9 Consensus size: 39
27181 CCATCAGCCA
* * * * *
27191 ATCTCTTACCCCAAGCTTGGGGTAGATTACA-ACATCTG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* *
27229 ATCTTTTACCCCGAGCTTGGGGTAGA-T-CA-CCATTAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCA-T--CCG
* * *
27268 ATCTCTTACCCCGAGCTTAGGGCAGATTACAGCTATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* * * * *
27307 ATCTTTTACCCCGAGCTCGGGGCAGATCACCA-TCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTA-CAGCCATCCG
* * * * * * *
27346 ATCTCTTACCCCGTGCTTGGGACATATTATAGCCATTCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* * * * * *
27385 ATCTTTTACCCTGAGCTTGGAGCAGATCATCA-TCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTA-CAGCCATCCG
* * * **
27424 AT-TTCTTACACCGAGCCTGGGGTAGATTGTAGCCATCCG
1 ATCTT-TTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* * * * * * *
27463 ATCTTTTACCCTGAGCCTGAGGCAGATCACCA-TCAGCCA
1 ATCTTTTACCCCGAGCTTGGGGCAGATTA-CAGCCATCCG
* * *
27502 ATCTCTTACCCCGAGCTTGGGGTAAATTACAGCCATCCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* *
27541 ATCTTTTACCCCGAGCCTGAGGCAGA-T-CA-CCATCAGCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATC--CG
* * * * * *
27579 AATCTCTTACCCCGAGCCTGGGGTAGGTTGCAGCCATCTG
1 -ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* * * *
27619 ATCTTTTACCCTGAGCTTGGGGCAGATTGCAACCATTCG
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
* * * *
27658 ATCTTTTACCCCGATCATGGGGCAGATTGCAACCATC
1 ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATC
27695 TAATGTCTTA
Statistics
Matches: 354, Mismatches: 92, Indels: 39
0.73 0.19 0.08
Matches are distributed among these distances:
36 9 0.03
37 4 0.01
38 33 0.09
39 287 0.81
40 9 0.03
41 5 0.01
42 7 0.02
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.27
Consensus pattern (39 bp):
ATCTTTTACCCCGAGCTTGGGGCAGATTACAGCCATCCG
Found at i:27345 original size:78 final size:78
Alignment explanation
Indices: 27171--27645 Score: 587
Period size: 78 Copynumber: 6.1 Consensus size: 78
27161 TAATTAAGTA
* * *
27171 GGGCAGATCACCATCAGCCAATCTCTTACCCCAAGCTTGGGGTAGATTACA-ACATCTGATCTTT
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
*
27235 TACCCCGAGCTTG
66 TACCCCGAGCTCG
* * * * *
27248 GGGTAGATCACCATTAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTACAGCTATCCGATCTTT
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
27313 TACCCCGAGCTCG
66 TACCCCGAGCTCG
* ** * * * *
27326 GGGCAGATCACCATCAGCCAATCTCTTACCCCGTGCTTGGGACATATTATAGCCATTCAATCTTT
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
* *
27391 TACCCTGAGCTTG
66 TACCCCGAGCTCG
* * * * * **
27404 GAGCAGATCATCATCAGCCAATTTCTTACACCGAGCCTGGGGTAGATTGTAGCCATCCGATCTTT
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
*
27469 TACCCTGAGC-CTG
66 TACCCCGAGCTC-G
* *
27482 AGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAAATTACAGCCATCCGATCTTT
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
27547 TACCCCGAGC-CTG
66 TACCCCGAGCTC-G
* * * * * *
27560 AGGCAGATCACCATCAGCGAATCTCTTACCCCGAGCCTGGGGTAGGTTGCAGCCATCTGATCTTT
1 GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
* *
27625 TACCCTGAGCTTG
66 TACCCCGAGCTCG
27638 GGGCAGAT
1 GGGCAGAT
27646 TGCAACCATT
Statistics
Matches: 342, Mismatches: 53, Indels: 5
0.86 0.13 0.01
Matches are distributed among these distances:
77 46 0.13
78 296 0.87
ACGTcount: A:0.23, C:0.30, G:0.21, T:0.26
Consensus pattern (78 bp):
GGGCAGATCACCATCAGCCAATCTCTTACCCCGAGCTTGGGGTAGATTACAGCCATCCGATCTTT
TACCCCGAGCTCG
Found at i:28288 original size:21 final size:20
Alignment explanation
Indices: 28260--28298 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
28250 TTGTTTTAAA
*
28260 TTTAAAATATCAATGTCCCT
1 TTTAAAATATCAAAGTCCCT
*
28280 TTTACAAATTTCAAAGTCC
1 TTTA-AAATATCAAAGTCC
28299 AATTCCGAAA
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:0.36, C:0.21, G:0.05, T:0.38
Consensus pattern (20 bp):
TTTAAAATATCAAAGTCCCT
Found at i:28665 original size:25 final size:26
Alignment explanation
Indices: 28632--28684 Score: 99
Period size: 25 Copynumber: 2.1 Consensus size: 26
28622 AGATTCTTAG
28632 TTTTTTTGTCGATTATGCCTGCC-CT
1 TTTTTTTGTCGATTATGCCTGCCGCT
28657 TTTTTTTGTCGATTATGCCTGCCGCT
1 TTTTTTTGTCGATTATGCCTGCCGCT
28683 TT
1 TT
28685 AGATCATCCA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 23 0.85
26 4 0.15
ACGTcount: A:0.08, C:0.23, G:0.17, T:0.53
Consensus pattern (26 bp):
TTTTTTTGTCGATTATGCCTGCCGCT
Found at i:32915 original size:16 final size:15
Alignment explanation
Indices: 32886--32928 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 15
32876 ATCATAAATA
*
32886 AATAATAAAGTATATT
1 AATAATAAA-TATAAT
32902 AATAAATAAATATAAT
1 AAT-AATAAATATAAT
32918 AATAATAAATA
1 AATAATAAATA
32929 GTAAAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 8 0.32
16 11 0.44
17 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (15 bp):
AATAATAAATATAAT
Found at i:33644 original size:17 final size:17
Alignment explanation
Indices: 33622--33657 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
33612 CAAAACTGTG
*
33622 CCGTTTTTTGACTCGAC
1 CCGTTTTCTGACTCGAC
33639 CCGTTTTCTGACTCGAC
1 CCGTTTTCTGACTCGAC
33656 CC
1 CC
33658 AAAAGGAGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.11, C:0.36, G:0.17, T:0.36
Consensus pattern (17 bp):
CCGTTTTCTGACTCGAC
Found at i:33959 original size:11 final size:11
Alignment explanation
Indices: 33943--33967 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
33933 GCCCAAGTAA
33943 TTTTGAATTAT
1 TTTTGAATTAT
33954 TTTTGAATTAT
1 TTTTGAATTAT
33965 TTT
1 TTT
33968 ATTATAAATC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (11 bp):
TTTTGAATTAT
Found at i:34088 original size:30 final size:29
Alignment explanation
Indices: 34049--34218 Score: 123
Period size: 29 Copynumber: 5.8 Consensus size: 29
34039 AAAGGTCTCT
*
34049 AAACTTTCCATAAATCATATTTTGACCTCG
1 AAACTTTCCA-AAATTATATTTTGACCTCG
* * * * *
34079 AACCTTTCCAAAATTACATTTTAACCCCT
1 AAACTTTCCAAAATTATATTTTGACCTCG
* *
34108 AAACTTCTCAAAAATTATATTTTTGCCCTC-
1 AAACTT-TCCAAAATTATA-TTTTGACCTCG
* *
34138 AAACTTCCCAAAATAATATTTTGACCTCG
1 AAACTTTCCAAAATTATATTTTGACCTCG
* * *
34167 -AACTTCTCAAAAATTACATTTT-ACCCCCG
1 AAACTT-TCCAAAATTATATTTTGA-CCTCG
* * *
34196 -AACTTCCCAAAATCACATTTTGA
1 AAACTTTCCAAAATTATATTTTGA
34219 ACCCCGAACT
Statistics
Matches: 110, Mismatches: 24, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
28 28 0.25
29 50 0.45
30 25 0.23
31 7 0.06
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.34
Consensus pattern (29 bp):
AAACTTTCCAAAATTATATTTTGACCTCG
Found at i:34099 original size:29 final size:28
Alignment explanation
Indices: 34050--34410 Score: 189
Period size: 30 Copynumber: 12.4 Consensus size: 28
34040 AAGGTCTCTA
* * *
34050 AACTTTCCATAAATCATATTTTGACCTCG
1 AACTTTCCA-AAATTACATTTTGACCCCG
* *
34079 AACCTTTCCAAAATTACATTTTAACCCCTA
1 AA-CTTTCCAAAATTACATTTTGACCCC-G
* * *
34109 AACTTCTCAAAAATTATATTTTTG-CCCTCA
1 AACTT-TCCAAAATTACA-TTTTGACCC-CG
* * * *
34139 AACTTCCCAAAATAATATTTTGACCTCG
1 AACTTTCCAAAATTACATTTTGACCCCG
*
34167 AACTTCTCAAAAATTACATTTT-ACCCCCG
1 AACTT-TCCAAAATTACATTTTGA-CCCCG
* *
34196 AACTTCCCAAAATCACATTTTGAACCCCG
1 AACTTTCCAAAATTACATTTTG-ACCCCG
* **
34225 AAC--TCAAAAATTACATTTTTCCCCCG
1 AACTTTCCAAAATTACATTTTGACCCCG
* * *
34251 AACTTTCCAAAATCACATTTTTACTCCCA
1 AACTTTCCAAAATTACATTTTGAC-CCCG
*
34280 AAC-TTCTCAAAATTTACATTTGTG-CCCCTA
1 AACTTTC-CAAAA-TTACATTT-TGACCCC-G
* * * *
34310 AACTTCCCAAAATCACATTTTTTACCCCTA
1 AACTTTCCAAAATTACA-TTTTGACCCC-G
* * *
34340 AATTTATCAAAAATTACATTTTTG-CCCTCA
1 AACTT-TCCAAAATTACA-TTTTGACCC-CG
* *
34370 AACTTCTCAAAAATTACTATTTTGCCCCCG
1 AACTT-TCCAAAATTAC-ATTTTGACCCCG
*
34400 AAC-ATCCAAAA
1 AACTTTCCAAAA
34411 ATCACCCTTT
Statistics
Matches: 263, Mismatches: 45, Indels: 49
0.74 0.13 0.14
Matches are distributed among these distances:
26 8 0.03
27 13 0.05
28 50 0.19
29 78 0.30
30 87 0.33
31 27 0.10
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (28 bp):
AACTTTCCAAAATTACATTTTGACCCCG
Found at i:34284 original size:113 final size:114
Alignment explanation
Indices: 34114--34412 Score: 307
Period size: 113 Copynumber: 2.6 Consensus size: 114
34104 CCCTAAACTT
* * * * *
34114 CTCAAAAATTATATTTTTGCCCTCAAACTTCCCAAAATAATATTTTGACCTCGAACTTCTCAAAA
1 CTCAAAAATTACATTTTTGCCCCCAAACTTCCCAAAATAACATTTTGACCCCAAACTTCTCAAAA
*
34179 ATTACATTT-TACCCCCGAACTTCCCAAAATCACATTTTGAACCCCGAA
66 ATTACATTTGTACCCCCAAACTTCCCAAAATCACATTTTGAACCCCGAA
* * * *
34227 CTCAAAAATTACATTTTT-CCCCCGAACTTTCCAAAATCACATTTTTACTCCCAAACTTCTCAAA
1 CTCAAAAATTACATTTTTGCCCCCAAACTTCCCAAAATAACATTTTGAC-CCCAAACTTCTCAAA
* * * ** *
34291 ATTTACATTTGTGCCCCTAAACTTCCCAAAATCACATTTTTTACCCCTAAA
65 AATTACATTTGTACCCCCAAACTTCCCAAAATCACATTTTGAACCCC-GAA
* * * * * * *
34342 TTTATCAAAAATTACATTTTTGCCCTCAAACTTCTCAAAAATTACTATTTTGCCCCCGAACATC-
1 ---CTCAAAAATTACATTTTTGCCCCCAAACTTC-CCAAAATAAC-ATTTTGACCCCAAACTTCT
34406 CAAAAAT
61 CAAAAAT
34413 CACCCTTTTC
Statistics
Matches: 150, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
112 24 0.16
113 39 0.26
114 31 0.21
115 2 0.01
118 17 0.11
119 15 0.10
120 16 0.11
121 6 0.04
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.33
Consensus pattern (114 bp):
CTCAAAAATTACATTTTTGCCCCCAAACTTCCCAAAATAACATTTTGACCCCAAACTTCTCAAAA
ATTACATTTGTACCCCCAAACTTCCCAAAATCACATTTTGAACCCCGAA
Found at i:34313 original size:30 final size:30
Alignment explanation
Indices: 34088--34397 Score: 197
Period size: 30 Copynumber: 10.6 Consensus size: 30
34078 GAACCTTTCC
**
34088 AAAATTACATTTTAACCCCTAAACTTCTCA
1 AAAATTACATTTTTGCCCCTAAACTTCTCA
* *
34118 AAAATTATATTTTTG-CCCTCAAACTTC-CC
1 AAAATTACATTTTTGCCCCT-AAACTTCTCA
* *
34147 AAAA-TA-ATATTTTG-ACCTCGAACTTCTCA
1 AAAATTACAT-TTTTGCCCCT-AAACTTCTCA
* ** *
34176 AAAATTACA-TTTTACCCCCGAACTTC-CC
1 AAAATTACATTTTTGCCCCTAAACTTCTCA
* *
34204 AAAATCACA-TTTTGAACCCC-GAA---CTCA
1 AAAATTACATTTTTG--CCCCTAAACTTCTCA
** *
34231 AAAATTACATTTTT-CCCCCGAACTT-TCC
1 AAAATTACATTTTTGCCCCTAAACTTCTCA
* *
34259 AAAATCACATTTTTACTCCC-AAACTTCTCA
1 AAAATTACATTTTTGC-CCCTAAACTTCTCA
* * *
34289 AAATTTACATTTGTGCCCCTAAACTTC-CC
1 AAAATTACATTTTTGCCCCTAAACTTCTCA
* * * *
34318 AAAATCACATTTTTTACCCCTAAATTTATCA
1 AAAATTACA-TTTTTGCCCCTAAACTTCTCA
34349 AAAATTACATTTTTG-CCCTCAAACTTCTCA
1 AAAATTACATTTTTGCCCCT-AAACTTCTCA
34379 AAAATTAC-TATTTTGCCCC
1 AAAATTACAT-TTTTGCCCC
34398 CGAACATCCA
Statistics
Matches: 222, Mismatches: 35, Indels: 45
0.74 0.12 0.15
Matches are distributed among these distances:
25 4 0.02
26 4 0.02
27 11 0.05
28 49 0.22
29 50 0.23
30 91 0.41
31 13 0.06
ACGTcount: A:0.35, C:0.28, G:0.04, T:0.34
Consensus pattern (30 bp):
AAAATTACATTTTTGCCCCTAAACTTCTCA
Found at i:34479 original size:30 final size:30
Alignment explanation
Indices: 34460--34522 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
34450 CAACCTCAAT
34460 TTTTCCAA-AAATTCGATTTTAATCCCAAA
1 TTTTCCAACAAATTCGATTTTAATCCCAAA
* * *
34489 TTTTCTAACAACTTCGATTTTGATCCCTAAA
1 TTTTCCAACAAATTCGATTTTAATCCC-AAA
34520 TTT
1 TTT
34523 CTCAGGAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 7 0.24
30 16 0.55
31 6 0.21
ACGTcount: A:0.32, C:0.21, G:0.05, T:0.43
Consensus pattern (30 bp):
TTTTCCAACAAATTCGATTTTAATCCCAAA
Found at i:45640 original size:39 final size:37
Alignment explanation
Indices: 45533--46193 Score: 360
Period size: 39 Copynumber: 17.2 Consensus size: 37
45523 TAAATTACAG
* *
45533 CCATTCGATCTCTTACCCCGAGCCTAGGGCAGA-TCA
1 CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
* * * * *
45569 CAATTAGCCATCTCTTACCCTGAGCATGGGGCAGATTGTA
1 CCATT--CAATCTCTTACCCCGAGCCTGGGGCAGATT-CA
* *
45609 GCCATTCAATCTTTTACCCCGAGCCTAGGGCAGA-TCA
1 -CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
* *
45646 CAATTAGCCAATCTCTTACCTCGAGCCTGGGGCAGATTGCA
1 CCATT---CAATCTCTTACCCCGAGCCTGGGGCAGATT-CA
* *
45687 GCCATTCAATCTTTTACCCCGAGCCTAGGGCAGA-TCA
1 -CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
* * *
45724 CCATTAGCCAATCTTTTACCCTGAGCCTGGGGCAAATTACA
1 CCATT---CAATCTCTTACCCCGAGCCTGGGGCAGATT-CA
* * * * *
45765 GTCATTCGATCTCTTACCCTGAGCCTGGGGTAGATCACTA
1 -CCATTCAATCTCTTACCCCGAGCCTGGGGCAGAT-TC-A
** * * *
45805 CCAGCCAATCTCTTACCCCAAACCTAGGGCA-ATTGCA
1 CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATT-CA
* * * **
45842 GCCATCCGATCTTTTACCTTGAGCAC-GGGGCAGATCATCA
1 -CCATTCAATCTCTTACCCCGAGC-CTGGGGCAGAT--TCA
** *
45882 CCAGCCAATCTTTTACCCCGAGCCTGGGGCAG--TCA
1 CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
** * ** * * *
45917 CCGTCAACCAATCTCTTACCCCGAGCTTAAGGTA-AATCG
1 -C--CATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
* * *
45956 CCA-TCAAGATCTCTTACCCCAAGCTTGGGGTAGATTGCAA
1 CCATTC-A-ATCTCTTACCCCGAGCCTGGGGCAGATT-C-A
* ** *
45996 CCATTCAATCTCTTACCCTGAGCCCAGGGTAGA-TCA
1 CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
*
46032 CCATCAGTCAATCTCTTACCCCGAGCCTGAGGCAGATTGCA
1 CCAT---TCAATCTCTTACCCCGAGCCTGGGGCAGATT-CA
* *
46073 GCCATTCGATCTCTTACCCCGAGCCTGGGGTAGA-TCA
1 -CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
* *
46110 CCATTAACCAATCTCTTACCTCGAGCCTGGGGCA-AATCA
1 CCATT---CAATCTCTTACCCCGAGCCTGGGGCAGATTCA
* * *
46149 CCATCAACCAATCTCTTACCTCGAGCCTGGGGCGGA-TCA
1 CCAT---TCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
46188 CC-TTCA
1 CCATTCA
46194 GCCAATCTCT
Statistics
Matches: 490, Mismatches: 84, Indels: 103
0.72 0.12 0.15
Matches are distributed among these distances:
35 6 0.01
36 27 0.06
37 28 0.06
38 82 0.17
39 310 0.63
40 12 0.02
41 13 0.03
42 12 0.02
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.24
Consensus pattern (37 bp):
CCATTCAATCTCTTACCCCGAGCCTGGGGCAGATTCA
Found at i:45697 original size:78 final size:78
Alignment explanation
Indices: 45530--46287 Score: 660
Period size: 78 Copynumber: 9.8 Consensus size: 78
45520 GGGTAAATTA
* * *
45530 CAGCCATTCGATCTCTTACCCCGAGCCTAGGGCAGATCACAATTAGCC-ATCTCTTACCCTGAGC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
*
45594 ATGGGGCAGATTG
66 CTGGGGCAGATTG
* * * *
45607 TAGCCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACAATTAGCCAATCTCTTACCTCGAGC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
45672 CTGGGGCAGATTG
66 CTGGGGCAGATTG
* * *
45685 CAGCCATTCAATCTTTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTTTTACCCTGAGC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
* *
45750 CTGGGGCAAATTA
66 CTGGGGCAGATTG
* * * * * * ** * *
45763 CAGTCATTCGATCTCTTACCCTGAGCCTGGGGTAGATCACTACCAGCCAATCTCTTACCCCAAAC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
*
45828 CTAGGGCA-ATTG
66 CTGGGGCAGATTG
* * * ** * * ** *
45840 CAGCCATCCGATCTTTTACCTTGAGCAC-GGGGCAGATCATCACCAGCCAATCTTTTACCCCGAG
1 CAGCCATTCAATCTCTTACCCCGAGC-CTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAG
**
45904 CCTGGGGCAG-TCA
65 CCTGGGGCAGATTG
* * ** * * * * * * *
45917 CCGTCAACCAATCTCTTACCCCGAGCTTAAGGTAAATCGCCA-T--CAAGATCTCTTACCCCAAG
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCA-ATCTCTTACCCCGAG
* *
45979 CTTGGGGTAGATTG
65 CCTGGGGCAGATTG
* * * * * *
45993 CAACCATTCAATCTCTTACCCTGAGCCCAGGGTAGATCACCATCAGTCAATCTCTTACCCCGAGC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
*
46058 CTGAGGCAGATTG
66 CTGGGGCAGATTG
* * * * *
46071 CAGCCATTCGATCTCTTACCCCGAGCCTGGGGTAGATCACCATTAACCAATCTCTTACCTCGAGC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
*
46136 CTGGGGCA-AAT-
66 CTGGGGCAGATTG
* * * *
46147 CA-CCATCAACCAATCTCTTACCTCGAGCCTGGGGCGGATCACC-TTCAGCCAATCTCTTACCCC
1 CAGCCAT---TCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATT-AGCCAATCTCTTACCCC
* *
46210 -ATGCGTGGGGTAGATTG
62 GA-GCCTGGGGCAGATTG
* * * * * * * * *
46227 CAGTCATTCGATCTTTTACCTCGAGTCT-GGGACAAATCATCATTAGTCAATCTTTTACCCC
1 CAGCCATTCAATCTCTTACCCCGAGCCTAGGG-CAGATCACCATTAGCCAATCTCTTACCCC
46288 AATCATGGGG
Statistics
Matches: 550, Mismatches: 112, Indels: 37
0.79 0.16 0.05
Matches are distributed among these distances:
74 2 0.00
75 25 0.05
76 34 0.06
77 144 0.26
78 335 0.61
79 5 0.01
80 2 0.00
81 3 0.01
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (78 bp):
CAGCCATTCAATCTCTTACCCCGAGCCTAGGGCAGATCACCATTAGCCAATCTCTTACCCCGAGC
CTGGGGCAGATTG
Found at i:46219 original size:39 final size:39
Alignment explanation
Indices: 46081--46224 Score: 159
Period size: 39 Copynumber: 3.7 Consensus size: 39
46071 CAGCCATTCG
*
46081 ATCTCTTACC-CCGAGCCTGGGGTAGATCACCATT-AACCA
1 ATCTCTTACCTCC-AGCCTGGGGCAGATCACC-TTCAACCA
* * *
46120 ATCTCTTACCTCGAGCCTGGGGCAAATCACCATCAACCA
1 ATCTCTTACCTCCAGCCTGGGGCAGATCACCTTCAACCA
* * *
46159 ATCTCTTACCTCGAGCCTGGGGCGGATCACCTTCAGCCA
1 ATCTCTTACCTCCAGCCTGGGGCAGATCACCTTCAACCA
* *
46198 ATCTCTTACC-CCATGCGTGGGGTAGAT
1 ATCTCTTACCTCCA-GCCTGGGGCAGAT
46225 TGCAGTCATT
Statistics
Matches: 90, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 3 0.03
39 86 0.96
40 1 0.01
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCTCCAGCCTGGGGCAGATCACCTTCAACCA
Found at i:46794 original size:17 final size:17
Alignment explanation
Indices: 46765--46828 Score: 83
Period size: 17 Copynumber: 3.7 Consensus size: 17
46755 CTGTGAATCA
*
46765 AAATTTTAATTTATTTT
1 AAATTTAAATTTATTTT
* *
46782 AAGTTTGAATTTATTTT
1 AAATTTAAATTTATTTT
46799 AAATTTAAATTTATTTT
1 AAATTTAAATTTATTTT
*
46816 AAAATTGAAATTT
1 -AAATTTAAATTT
46829 GAAAGTTGCT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
17 30 0.73
18 11 0.27
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (17 bp):
AAATTTAAATTTATTTT
Found at i:47475 original size:20 final size:19
Alignment explanation
Indices: 47445--47520 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 19
47435 TAATAGATGG
47445 TAATAAATAAATAATAAAGTA
1 TAAT-AATAAATAATAAA-TA
*
47466 TATTAATAAATAAATAAATA
1 TAATAATAAAT-AATAAATA
47486 TAATAAT-AATAAT-AATAA
1 TAATAATAAATAATAAAT-A
*
47504 TAATAATAAATAGTAAA
1 TAATAATAAATAATAAA
47521 AAGAAGGTAA
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
17 3 0.06
18 11 0.23
19 8 0.17
20 17 0.35
21 9 0.19
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.32
Consensus pattern (19 bp):
TAATAATAAATAATAAATA
Found at i:47493 original size:3 final size:3
Alignment explanation
Indices: 47485--47512 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
47475 ATAAATAAAT
47485 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
47513 ATAGTAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:47493 original size:12 final size:12
Alignment explanation
Indices: 47445--47515 Score: 67
Period size: 12 Copynumber: 5.8 Consensus size: 12
47435 TAATAGATGG
47445 TAATAAATA-AA
1 TAATAAATATAA
*
47456 TAATAAAGTATAT
1 TAATAAA-TATAA
47469 TAATAAATA-AA
1 TAATAAATATAA
47480 TAAATATAATAATAA
1 T-AATA-AAT-ATAA
47495 TAAT-AATAATAA
1 TAATAAAT-ATAA
47507 TAATAAATA
1 TAATAAATA
47516 GTAAAAAGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
11 9 0.18
12 21 0.41
13 14 0.27
14 4 0.08
15 3 0.06
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.32
Consensus pattern (12 bp):
TAATAAATATAA
Found at i:48728 original size:29 final size:30
Alignment explanation
Indices: 48635--48900 Score: 210
Period size: 30 Copynumber: 9.0 Consensus size: 30
48625 AAAAGGTCTC
48635 TAAACTT-TCAAAAA-T-CATATTTTGACCCT
1 TAAACTTCTCAAAAATTACAT-TTTTG-CCCT
** * * * *
48664 CGAACTTTTCCAAAATTACA-TGTTGACCCC
1 TAAACTTCTCAAAAATTACATTTTTG-CCCT
*
48694 TGAACTTCTCAAAAATTACA-TTTTGCCCT
1 TAAACTTCTCAAAAATTACATTTTTGCCCT
* *
48723 TAAACTTC-CTAAAATCACA-TTTTGACCCT
1 TAAACTTCTCAAAAATTACATTTTTG-CCCT
* * *
48752 TGAACTTCTCAAAAATTACATTTTTTCCCC
1 TAAACTTCTCAAAAATTACATTTTTGCCCT
* *
48782 TAAACTTC-CCAAAATTATATTTTTG-CCT
1 TAAACTTCTCAAAAATTACATTTTTGCCCT
* *
48810 CTAAACTTTTCAAAAAGTTACATTTTTACCCT
1 -TAAACTTCTCAAAAA-TTACATTTTTGCCCT
* * * *
48842 TGAACTTC-CTAAAATCACATTTTTACCCT
1 TAAACTTCTCAAAAATTACATTTTTGCCCT
**
48871 TAAACTTCTTTAAAATTACATTTTTGCCCT
1 TAAACTTCTCAAAAATTACATTTTTGCCCT
48901 CGAATTTTTG
Statistics
Matches: 191, Mismatches: 35, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
28 16 0.08
29 68 0.36
30 82 0.43
31 20 0.10
32 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.05, T:0.39
Consensus pattern (30 bp):
TAAACTTCTCAAAAATTACATTTTTGCCCT
Found at i:48788 original size:88 final size:90
Alignment explanation
Indices: 48632--48901 Score: 316
Period size: 88 Copynumber: 3.0 Consensus size: 90
48622 CCCAAAAGGT
* * * * * * *
48632 CTCTAAACTTTCAAAAATCATATTTTGACCCTCGAACTTTTCCAAAATTACATGTTGACCCCTGA
1 CTCTAAACTTTCAAAAATCACATTTTGACCCTTGAACTTCTCAAAAATTACATTTTTACCCCTAA
48697 ACTTCTCAAAAATTACA-TTTTGCC
66 ACTTCTCAAAAATTACATTTTTGCC
* * *
48721 CT-TAAACTTCCTAAAATCACATTTTGACCCTTGAACTTCTCAAAAATTACATTTTTTCCCCTAA
1 CTCTAAACTTTCAAAAATCACATTTTGACCCTTGAACTTCTCAAAAATTACATTTTTACCCCTAA
* *
48785 ACTTC-CCAAAATTATATTTTTG-C
66 ACTTCTCAAAAATTACATTTTTGCC
* * * * *
48808 CTCTAAACTTTTCAAAAAGTTACATTTTTACCCTTGAACTTC-CTAAAATCACATTTTTACCCTT
1 CTCTAAAC-TTTCAAAAA-TCACATTTTGACCCTTGAACTTCTCAAAAATTACATTTTTACCCCT
**
48872 AAACTTCTTTAAAATTACATTTTTGCC
64 AAACTTCTCAAAAATTACATTTTTGCC
48899 CTC
1 CTC
48902 GAATTTTTGA
Statistics
Matches: 152, Mismatches: 23, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
87 12 0.08
88 67 0.44
89 34 0.22
90 35 0.23
91 4 0.03
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (90 bp):
CTCTAAACTTTCAAAAATCACATTTTGACCCTTGAACTTCTCAAAAATTACATTTTTACCCCTAA
ACTTCTCAAAAATTACATTTTTGCC
Found at i:48817 original size:59 final size:59
Alignment explanation
Indices: 48696--48900 Score: 245
Period size: 59 Copynumber: 3.5 Consensus size: 59
48686 TTGACCCCTG
* *
48696 AACTTCTCAAAAATTACA-TTTTGCCCTTAAACTTCCTAAAATCACA-TTTTGACCCTTG
1 AACTTCTCAAAAATTACATTTTTACCCTTAAACTTCCTAAAATCACATTTTTG-CCCTTA
* * * * *
48754 AACTTCTCAAAAATTACATTTTTTCCCCTAAACTTCCCAAAATTATATTTTTG-CCTCTA
1 AACTTCTCAAAAATTACATTTTTACCCTTAAACTTCCTAAAATCACATTTTTGCCCT-TA
* * *
48813 AACTTTTCAAAAAGTTACATTTTTACCCTTGAACTTCCTAAAATCACATTTTTACCCTTA
1 AACTTCTCAAAAA-TTACATTTTTACCCTTAAACTTCCTAAAATCACATTTTTGCCCTTA
** *
48873 AACTTCTTTAAAATTACATTTTTGCCCT
1 AACTTCTCAAAAATTACATTTTTACCCT
48901 CGAATTTTTG
Statistics
Matches: 124, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
58 21 0.17
59 50 0.40
60 50 0.40
61 3 0.02
ACGTcount: A:0.32, C:0.24, G:0.03, T:0.40
Consensus pattern (59 bp):
AACTTCTCAAAAATTACATTTTTACCCTTAAACTTCCTAAAATCACATTTTTGCCCTTA
Found at i:50978 original size:33 final size:33
Alignment explanation
Indices: 50879--50998 Score: 138
Period size: 33 Copynumber: 3.7 Consensus size: 33
50869 CCATTTATGA
50879 TAAAAATAATTTTTCCCTACGATACAATAGAGG
1 TAAAAATAATTTTTCCCTACGATACAATAGAGG
* * * *** ** *
50912 T-AACA-CA-TTCTGATTACGGCACAATAGATG
1 TAAAAATAATTTTTCCCTACGATACAATAGAGG
50942 TAAAAATAATTTTTCCCTACGATACAATAGAGG
1 TAAAAATAATTTTTCCCTACGATACAATAGAGG
50975 TAAAAATAATTTTTCCCTACGATA
1 TAAAAATAATTTTTCCCTACGATA
50999 TTGTGCTTAC
Statistics
Matches: 66, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
30 17 0.26
31 4 0.06
32 4 0.06
33 41 0.62
ACGTcount: A:0.41, C:0.17, G:0.12, T:0.31
Consensus pattern (33 bp):
TAAAAATAATTTTTCCCTACGATACAATAGAGG
Found at i:57391 original size:59 final size:56
Alignment explanation
Indices: 57318--57800 Score: 239
Period size: 59 Copynumber: 8.3 Consensus size: 56
57308 GACATTCGGA
* * *
57318 GGTAAAATGGTAATTTTGGAAAAAATCGGGATCAAGAATAGAATTTTTGGAAGTTTAGG
1 GGTAAAATGGTAATTTTGG-AAAAATCGGG-TCAAAAATGGAA-TTTAGGAAGTTTAGG
* *
57377 GGTAAAATGGTAATTTTGGGAAAATCAGGGTCAAAAATGGAATTTAGGAAG-TTCGTG
1 GGTAAAATGGTAATTTTGGAAAAATC-GGGTCAAAAATGGAATTTAGGAAGTTTAG-G
*** ** * * * *
57434 GGTAAAAACATAATTTTTTGGAAAAATCAAAGTCAAAGATGGAATTTTGGAAGCTTGGG
1 GGTAAAATGGTAA--TTTTGGAAAAATC-GGGTCAAAAATGGAATTTAGGAAGTTTAGG
*
57493 GGTAAAATGGTAATTTTGGGAAAAATCGAGGTCAAAAATGGAATTCTAGGAAGTTT-GCA
1 GGTAAAATGGTAATTTT-GGAAAAATCG-GGTCAAAAATGGAATT-TAGGAAGTTTAG-G
* *** * * * *
57552 AGTAAAAAT-GTAATTTTTGGAAGTTTAGGGGT--AAAATGTAATTTTCGAAAGTTTAGG
1 GGT-AAAATGGTAA-TTTTGGAAAAAT-CGGGTCAAAAATGGAA-TTTAGGAAGTTTAGG
* * * * *
57609 GGTAAAAAT-ATATTTTTTGG-AAAATTGATGTCAAAAATGGAATTTTGGAAAGTTTAGG
1 GGT-AAAATGGTA-ATTTTGGAAAAATCG-GGTCAAAAATGGAATTTAGG-AAGTTTAGG
* ** ** * * **
57667 GGTAAAAAT-GTAATTTTTAGAAAGTTCGAGGTCAAAAATATAATTTTGAAAAGTTCGGG
1 GGT-AAAATGGTAA-TTTTGGAAAAATCG-GGTCAAAAATGGAATTTAG-GAAGTTTAGG
** * *** * *
57726 GGTGAAAAT-GTAATTTTTAAAAAATTAGGGTCAAAAATATCATTTTGGAAAGTTTAGT
1 GGT-AAAATGGTAATTTTGGAAAAA-TCGGGTCAAAAATGGAATTTAGG-AAGTTTAGG
57784 GGTAAAAAT-GTAATTTT
1 GGT-AAAATGGTAATTTT
57801 AAAAAAGTTT
Statistics
Matches: 333, Mismatches: 67, Indels: 49
0.74 0.15 0.11
Matches are distributed among these distances:
55 1 0.00
56 7 0.02
57 59 0.18
58 123 0.37
59 130 0.39
60 13 0.04
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.32
Consensus pattern (56 bp):
GGTAAAATGGTAATTTTGGAAAAATCGGGTCAAAAATGGAATTTAGGAAGTTTAGG
Found at i:57406 original size:29 final size:29
Alignment explanation
Indices: 57318--57406 Score: 74
Period size: 29 Copynumber: 3.0 Consensus size: 29
57308 GACATTCGGA
*
57318 GGTAAAATGGTAATTTTGGAAAAAATC-GG
1 GGTAAAATGGTAATTTTGG-GAAAATCAGG
* * * ** *
57347 GATCAAGAATAG-AATTTTTGGAAGTTTAGG
1 GGT-AA-AATGGTAATTTTGGGAAAATCAGG
57377 GGTAAAATGGTAATTTTGGGAAAATCAGG
1 GGTAAAATGGTAATTTTGGGAAAATCAGG
57406 G
1 G
57407 TCAAAAATGG
Statistics
Matches: 43, Mismatches: 13, Indels: 8
0.67 0.20 0.12
Matches are distributed among these distances:
28 4 0.09
29 22 0.51
30 13 0.30
31 4 0.09
ACGTcount: A:0.38, C:0.03, G:0.29, T:0.29
Consensus pattern (29 bp):
GGTAAAATGGTAATTTTGGGAAAATCAGG
Found at i:57412 original size:29 final size:28
Alignment explanation
Indices: 57321--57421 Score: 71
Period size: 29 Copynumber: 3.4 Consensus size: 28
57311 ATTCGGAGGT
*
57321 AAAATGGTAATTTTGGAAAAAATC-GGGATC
1 AAAATGG-AATTTTGG-GAAAATCAGGG-TC
* * ** *
57351 AAGAATAGAATTTTTGGAAGTTTAGGGGT-
1 AA-AATGGAATTTTGGGAAAATCA-GGGTC
57380 AAAATGGTAATTTTGGGAAAATCAGGGTC
1 AAAATGG-AATTTTGGGAAAATCAGGGTC
57409 AAAAATGGAATTT
1 -AAAATGGAATTT
57422 AGGAAGTTCG
Statistics
Matches: 54, Mismatches: 11, Indels: 13
0.69 0.14 0.17
Matches are distributed among these distances:
28 8 0.15
29 22 0.41
30 17 0.31
31 7 0.13
ACGTcount: A:0.41, C:0.04, G:0.26, T:0.30
Consensus pattern (28 bp):
AAAATGGAATTTTGGGAAAATCAGGGTC
Found at i:57585 original size:29 final size:29
Alignment explanation
Indices: 57553--57844 Score: 211
Period size: 29 Copynumber: 10.0 Consensus size: 29
57543 AAGTTTGCAA
*
57553 GTAAAAATGTAATTTTTGGAAGTTTAGGG
1 GTAAAAATGTAATTTTTGAAAGTTTAGGG
*
57582 GT-AAAATGTAATTTTCGAAAGTTTAGGG
1 GTAAAAATGTAATTTTTGAAAGTTTAGGG
* * * **
57610 GTAAAAATATATTTTTTGGAAA-ATT-GAT
1 GTAAAAATGTAATTTTT-GAAAGTTTAGGG
* *
57638 GTCAAAAATGGAATTTTGGAAAGTTTAGGG
1 GT-AAAAATGTAATTTTTGAAAGTTTAGGG
* *
57668 GTAAAAATGTAATTTTTAGAAAG-TTCGAG
1 GTAAAAATGTAATTTTT-GAAAGTTTAGGG
* **
57697 GTCAAAAATATAA-TTTTGAAAAGTTCGGGG
1 GT-AAAAATGTAATTTTTG-AAAGTTTAGGG
* * **
57727 GTGAAAATGTAATTTTTAAAAAATTA-GG
1 GTAAAAATGTAATTTTTGAAAGTTTAGGG
* * * *
57755 GTCAAAAATATCATTTTGGAAAGTTTAGTG
1 GT-AAAAATGTAATTTTTGAAAGTTTAGGG
**
57785 GTAAAAATGTAATTTTAAAAAAGTTT-GAGG
1 GTAAAAATGTAATTTT-TGAAAGTTTAG-GG
* * *
57815 GTTAAAATATAATTTTTGGATAGTTTAGGG
1 GTAAAAATGTAATTTTT-GAAAGTTTAGGG
57845 ACCTTCAAGG
Statistics
Matches: 199, Mismatches: 48, Indels: 31
0.72 0.17 0.11
Matches are distributed among these distances:
28 38 0.19
29 97 0.49
30 63 0.32
31 1 0.01
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (29 bp):
GTAAAAATGTAATTTTTGAAAGTTTAGGG
Found at i:57662 original size:58 final size:57
Alignment explanation
Indices: 57362--57800 Score: 327
Period size: 58 Copynumber: 7.6 Consensus size: 57
57352 AGAATAGAAT
* *
57362 TTTTGGAAGTTTAGGGGT-AAAATGGTAATTTTGGGAAAA-TCAGGGTCAAAAATGGAA
1 TTTTGGAAGTTTAGGGGTAAAAAT-GTAATTTTTGGAAAATTGA-GGTCAAAAATGGAA
* * ** ** * *
57419 TTTAGGAAG-TTCGTGGGTAAAAACATAATTTTTTGGAAAAATCAAAGTCAAAGATGGAA
1 TTTTGGAAGTTTAG-GGGTAAAAATGTAA-TTTTTGG-AAAATTGAGGTCAAAAATGGAA
* * * *
57478 TTTTGGAAGCTTGGGGGT-AAAATGGTAATTTTGGGAAAAATCGAGGTCAAAAATGGAA
1 TTTTGGAAGTTTAGGGGTAAAAAT-GTAATTTTTGG-AAAATTGAGGTCAAAAATGGAA
* ** ** * *
57536 TTCTAGGAAGTTT-GCAAGTAAAAATGTAATTTTTGGAAGTTTAGGGGT--AAAATGTAA
1 TT-TTGGAAGTTTAG-GGGTAAAAATGTAATTTTTGGAAAATT-GAGGTCAAAAATGGAA
* * * *
57593 TTTTCGAAAGTTTAGGGGTAAAAATATATTTTTTGGAAAATTGATGTCAAAAATGGAA
1 TTTT-GGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATTGAGGTCAAAAATGGAA
* * **
57651 TTTTGGAAAGTTTAGGGGTAAAAATGTAATTTTTAGAAAGTTCGAGGTCAAAAATATAA
1 TTTTGG-AAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATT-GAGGTCAAAAATGGAA
* ** * ** ***
57710 TTTTGAAAAGTTCGGGGGTGAAAATGTAATTTTTAAAAAATT-AGGGTCAAAAATATCA
1 TTTTG-GAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATTGA-GGTCAAAAATGGAA
*
57768 TTTTGGAAAGTTTAGTGGTAAAAATGTAATTTT
1 TTTTGG-AAGTTTAGGGGTAAAAATGTAATTTT
57801 AAAAAAGTTT
Statistics
Matches: 304, Mismatches: 58, Indels: 39
0.76 0.14 0.10
Matches are distributed among these distances:
56 7 0.02
57 55 0.18
58 130 0.43
59 103 0.34
60 9 0.03
ACGTcount: A:0.39, C:0.04, G:0.24, T:0.33
Consensus pattern (57 bp):
TTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGGAAAATTGAGGTCAAAAATGGAA
Found at i:57750 original size:117 final size:114
Alignment explanation
Indices: 57490--57830 Score: 323
Period size: 117 Copynumber: 2.9 Consensus size: 114
57480 TTGGAAGCTT
* * * *
57490 GGGGGTAAAATGGTAATTTTGGGAAAAATCGAGGTCAAAAATGGAATTCTAGG-AAGTTT-GCAA
1 GGGGGTAAAAT-GTAATTTT-TGAAAAATTGAGGTCAAAAATGGAATT-TTGGAAAGTTTAG-AG
* * * *
57553 GTAAAAATGTAATTTTT-GGAAGTTTAGGGGTAAAATGTAATTTTCGAAAGTTT
62 GTAAAAATGTAATTTTTAGAAAG-TTAGAGGTAAAATATAATTTTCGAAAGTTC
* * * * * *
57606 AGGGGTAAAAATATATTTTTTGGAAAATTGATGTCAAAAATGGAATTTTGGAAAGTTTAGGGGTA
1 GGGGGT-AAAATGTAATTTTTGAAAAATTGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGTA
*
57671 AAAATGTAATTTTTAGAAAGTTCGAGGTCAAAAATATAATTTT-GAAAAGTTC
65 AAAATGTAATTTTTAGAAAGTTAGAGGT--AAAATATAATTTTCG-AAAGTTC
* *** *
57723 GGGGGTGAAAATGTAATTTTTAAAAAATT-AGGGTCAAAAATATCATTTTGGAAAGTTTAGTGGT
1 GGGGGT-AAAATGTAATTTTTGAAAAATTGA-GGTCAAAAATGGAATTTTGGAAAGTTTAGAGGT
* * *
57787 AAAAATGTAATTTTAAAAAAGTTTGAGGGTTAAAATATAATTTT
64 AAAAATGTAATTTTTAGAAAGTTAGA-GG-TAAAATATAATTTT
57831 TGGATAGTTT
Statistics
Matches: 186, Mismatches: 29, Indels: 19
0.79 0.12 0.08
Matches are distributed among these distances:
114 3 0.02
115 52 0.28
116 18 0.10
117 110 0.59
118 2 0.01
119 1 0.01
ACGTcount: A:0.40, C:0.03, G:0.23, T:0.34
Consensus pattern (114 bp):
GGGGGTAAAATGTAATTTTTGAAAAATTGAGGTCAAAAATGGAATTTTGGAAAGTTTAGAGGTAA
AAATGTAATTTTTAGAAAGTTAGAGGTAAAATATAATTTTCGAAAGTTC
Found at i:57806 original size:58 final size:59
Alignment explanation
Indices: 57553--57844 Score: 281
Period size: 58 Copynumber: 5.0 Consensus size: 59
57543 AAGTTTGCAA
** ** * * *
57553 GTAAAAATGTAATTTTTGGAAGTTTAGGGGT--AAAATGTAATTTTCGAAAGTTTAGGG
1 GTAAAAATGTAATTTTTAAAAAATTAGAGGTCAAAAATATAATTTTGGAAAGTTTAGGG
* * ** * **
57610 GTAAAAATATATTTTTTGGAAAATT-GATGTCAAAAATGGAATTTTGGAAAGTTTAGGG
1 GTAAAAATGTAATTTTTAAAAAATTAGAGGTCAAAAATATAATTTTGGAAAGTTTAGGG
* * * * **
57668 GTAAAAATGTAATTTTTAGAAAGTTCGAGGTCAAAAATATAATTTTGAAAAGTTCGGGG
1 GTAAAAATGTAATTTTTAAAAAATTAGAGGTCAAAAATATAATTTTGGAAAGTTTAGGG
* * *
57727 GTGAAAATGTAATTTTTAAAAAATTAG-GGTCAAAAATATCATTTTGGAAAGTTTAGTG
1 GTAAAAATGTAATTTTTAAAAAATTAGAGGTCAAAAATATAATTTTGGAAAGTTTAGGG
* * *
57785 GTAAAAATGTAA-TTTTAAAAAAGTTTGAGGGT-TAAAATATAATTTTTGGATAGTTTAGGG
1 GTAAAAATGTAATTTTTAAAAAA-TTAGA-GGTCAAAAATATAA-TTTTGGAAAGTTTAGGG
57845 ACCTTCAAGG
Statistics
Matches: 195, Mismatches: 33, Indels: 11
0.82 0.14 0.05
Matches are distributed among these distances:
56 3 0.02
57 31 0.16
58 85 0.44
59 58 0.30
60 18 0.09
ACGTcount: A:0.39, C:0.02, G:0.22, T:0.36
Consensus pattern (59 bp):
GTAAAAATGTAATTTTTAAAAAATTAGAGGTCAAAAATATAATTTTGGAAAGTTTAGGG
Found at i:59680 original size:26 final size:25
Alignment explanation
Indices: 59631--59678 Score: 71
Period size: 25 Copynumber: 1.9 Consensus size: 25
59621 CTATTTGGGC
59631 TTTGATTTGTTTTTGGACATTTTAT
1 TTTGATTTGTTTTTGGACATTTTAT
*
59656 TTTGTATTTG-TTTTGGACCTTTT
1 TTTG-ATTTGTTTTTGGACATTTT
59679 TAATTTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.12, C:0.06, G:0.17, T:0.65
Consensus pattern (25 bp):
TTTGATTTGTTTTTGGACATTTTAT
Found at i:59715 original size:6 final size:6
Alignment explanation
Indices: 59704--59790 Score: 53
Period size: 6 Copynumber: 15.3 Consensus size: 6
59694 TTTTTAAATC
* **
59704 AATTTA AATTT- AA-TTA AATTCA AATTTA AA-GCA AATTTA AA---A
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA
** *
59746 AATTTA AATTTAA AAGGATA AATTTA AATTTA AA-ATA AATTTA AA
1 AATTTA AATTT-A AA-TTTA AATTTA AATTTA AATTTA AATTTA AA
59791 CTAATTTAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 18
0.67 0.13 0.20
Matches are distributed among these distances:
3 3 0.05
4 2 0.03
5 11 0.18
6 37 0.62
7 6 0.10
8 1 0.02
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.38
Consensus pattern (6 bp):
AATTTA
Found at i:59761 original size:27 final size:27
Alignment explanation
Indices: 59709--59759 Score: 77
Period size: 26 Copynumber: 1.9 Consensus size: 27
59699 AAATCAATTT
*
59709 AAATTTAATTAAATTCAAATTTAAAGC
1 AAATTTAATAAAATTCAAATTTAAAGC
*
59736 AAATTTAA-AAAATTTAAATTTAAA
1 AAATTTAATAAAATTCAAATTTAAA
59760 AGGATAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 14 0.64
27 8 0.36
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (27 bp):
AAATTTAATAAAATTCAAATTTAAAGC
Found at i:60254 original size:50 final size:50
Alignment explanation
Indices: 60094--60365 Score: 148
Period size: 50 Copynumber: 5.4 Consensus size: 50
60084 CATCTTTCTC
* * * *
60094 TTACTACAACTTCAGAGAGATAAAGACCTGCTATTG-TTTTTAATCCAACT
1 TTACTGCAACTTCA-AGAGATAAAGACTTACTATTGATTTTCAATCCAACT
* * * ** ***
60144 TTACTGCAAGTTCAAGAGGAT-AGGAATTGACGT-TTGAAGCTTC-ATCTTGCT
1 TTACTGCAACTTCAAGA-GATAAAGACTT-AC-TATTG-ATTTTCAATCCAACT
60195 CTTACTGCAACTTCAGAGAGATAAAGACTTACTATTG-TTTTCAATCCAACT
1 -TTACTGCAACTTCA-AGAGATAAAGACTTACTATTGATTTTCAATCCAACT
* * * ** ***
60246 TTACTGCAACTTCAAGAGGAT-AGGAATTGA-TGTTTGAAGCTTC-ATCTTGCT
1 TTACTGCAACTTCAAGA-GATAAAGACTT-ACT-ATTG-ATTTTCAATCCAACT
* * * *
60297 CTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGCTTTT-AATCCCACT
1 -TTACTGCAACTTCA-AGAGATAAAGACTTACTATTGATTTTCAATCCAACT
60348 TTACTGCAACTTCAAGAG
1 TTACTGCAACTTCAAGAG
60366 GATAGGAATT
Statistics
Matches: 162, Mismatches: 40, Indels: 41
0.67 0.16 0.17
Matches are distributed among these distances:
49 20 0.12
50 56 0.35
51 24 0.15
52 45 0.28
53 17 0.10
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.33
Consensus pattern (50 bp):
TTACTGCAACTTCAAGAGATAAAGACTTACTATTGATTTTCAATCCAACT
Found at i:60260 original size:102 final size:102
Alignment explanation
Indices: 60080--60945 Score: 1423
Period size: 102 Copynumber: 8.5 Consensus size: 102
60070 TGATGTCGAG
* * *
60080 GCTTCATCTTTCTCTTACTACAACTTCAGAGAGATAAAGACCTGCTATTGTTTTTAATCCAACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
* *
60145 TACTGCAAGTTCAAGAGGATAGGAATTGACGTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
* * * *
60182 GCTTCATCTTGCTCTTACTGCAACTTCAGAGAGATAAAGACTTACTATTGTTTTCAATCCAACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
60247 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
*
60284 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGCTTTTAATCCCACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
*
60349 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTTAA
66 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
*
60386 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTCGCTA-T-TTTTTAATCCCACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
* * *
60449 TACTGCAACTTCAAGAGGATAGAAATTTATATTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTGAT-GTTTGAA
* *
60487 GCTTCATCTTGTTCTTACTACAACTTCAGAGAGATGAAGACTTGCTATTGTTTTTAATCCCACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
*
60552 TACTGCAAGTTCAAGAGGATAGGAATTGATGTTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTGATG-TTTGAA
* * *
60590 GCTTCAACTTGCTCTTACTACAACTTCAGAGAGATAAATACTTGCAATTGTTTTTAATCCCACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
* *
60655 TACTGCAACTTCAAGAGGACAGAAATTGATGTTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTGATG-TTTGAA
* **
60693 GCTTTATCTTGCTCTTACTACAAC-TCTAGAGAGATAAAGACTTGCTATTGTTTTTAATCTTACT
1 GCTTCATCTTGCTCTTACTACAACTTC-AGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACT
*
60757 TTACTACAACTTCAAGAGGATAGGAATTGATGTTTGAA
65 TTACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
*
60795 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCAACTT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
60860 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
66 TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
60897 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATT
1 GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATT
60946 TTTACTTGAT
Statistics
Matches: 711, Mismatches: 47, Indels: 12
0.92 0.06 0.02
Matches are distributed among these distances:
100 42 0.06
101 50 0.07
102 390 0.55
103 229 0.32
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.35
Consensus pattern (102 bp):
GCTTCATCTTGCTCTTACTACAACTTCAGAGAGATAAAGACTTGCTATTGTTTTTAATCCCACTT
TACTGCAACTTCAAGAGGATAGGAATTGATGTTTGAA
Found at i:60764 original size:50 final size:51
Alignment explanation
Indices: 60698--60945 Score: 152
Period size: 51 Copynumber: 4.9 Consensus size: 51
60688 TTGAAGCTTT
*
60698 ATCTTGCTCTTACTACAACTCTAGAGAGATAAAGACTTGCTATTGTTTTTA
1 ATCTTACTCTTACTACAACTCTAGAGAGATAAAGACTTGCTATTGTTTTTA
* * * * * *** *
60749 ATCTTACT-TTACTACAACTTCAAGAG-GAT-AGGAATTGATGTTTGAAGCTTC
1 ATCTTACTCTTACTACAAC-TCTAGAGAGATAAAGACTTGCT-ATTG-TTTTTA
*
60800 ATCTTGCTCTTACTACAACT-TCAGAGAGATAAAGACTTGCTATTGTTTTTA
1 ATCTTACTCTTACTACAACTCT-AGAGAGATAAAGACTTGCTATTGTTTTTA
** * * * * * * *** *
60851 ATCCAACT-TTACTGCAACTTCAAGAG-GAT-AGGAATTGATGTTTGAAGCTTC
1 ATCTTACTCTTACTACAAC-TCTAGAGAGATAAAGACTTGCT-ATTG-TTTTTA
*
60902 ATCTTGCTCTTACTACAACT-TCAGAGAGATAAAGACTTGCTATT
1 ATCTTACTCTTACTACAACTCT-AGAGAGATAAAGACTTGCTATT
60946 TTTACTTGAT
Statistics
Matches: 140, Mismatches: 42, Indels: 29
0.66 0.20 0.14
Matches are distributed among these distances:
49 14 0.10
50 31 0.22
51 51 0.36
52 30 0.21
53 14 0.10
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.36
Consensus pattern (51 bp):
ATCTTACTCTTACTACAACTCTAGAGAGATAAAGACTTGCTATTGTTTTTA
Found at i:61239 original size:100 final size:102
Alignment explanation
Indices: 61092--61280 Score: 247
Period size: 100 Copynumber: 1.9 Consensus size: 102
61082 GCCGTTACGG
* * * * *
61092 CTTAAATCTTTCCTTTCATGCTTCTAAGGTACACGGTCCGCCGTTGCGACTTAGACC-TTTCCCT
1 CTTAAATCCTTCCTTTCATGCTTCTAAGGTACAAGGTCCGCCATTGCGACTTAAACCTTTTACCT
* *
61156 TTTGT-ATCTTTGCGGTACTGGATCCGCTATTGCGGT
66 TGTGTCATCATTGCGGTACTGGATCCGCTATTGCGGT
* * * * *
61192 CTTAGATCCTTCCTTTCATTCTTCTGAGGTATAAGGTTCGCCATTGCGACTTAAACCTTTTACCT
1 CTTAAATCCTTCCTTTCATGCTTCTAAGGTACAAGGTCCGCCATTGCGACTTAAACCTTTTACCT
*
61257 TGTGTCTTCATTGCGGTACTGGAT
66 TGTGTCATCATTGCGGTACTGGAT
61281 TCGCCATTAT
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
100 48 0.65
101 10 0.14
102 16 0.22
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.39
Consensus pattern (102 bp):
CTTAAATCCTTCCTTTCATGCTTCTAAGGTACAAGGTCCGCCATTGCGACTTAAACCTTTTACCT
TGTGTCATCATTGCGGTACTGGATCCGCTATTGCGGT
Found at i:66085 original size:18 final size:19
Alignment explanation
Indices: 66043--66085 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
66033 ACCTGTCGTG
66043 CTTTTCTCATCTCTCGCTT
1 CTTTTCTCATCTCTCGCTT
* **
66062 CCTTTCT-ATCTCTTTCTT
1 CTTTTCTCATCTCTCGCTT
66080 CTTTTC
1 CTTTTC
66086 CTTCACATCT
Statistics
Matches: 20, Mismatches: 4, Indels: 1
0.80 0.16 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.05, C:0.35, G:0.02, T:0.58
Consensus pattern (19 bp):
CTTTTCTCATCTCTCGCTT
Done.