Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01012330.1 Kokia drynarioides strain JFW-HI SEQ_127332, 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: 143461
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Warning! 128 characters in sequence are not A, C, G, or T
Found at i:4969 original size:15 final size:15
Alignment explanation
Indices: 4949--4979 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
4939 TTTCTAAGTT
4949 TAACCTTATTGAAAA
1 TAACCTTATTGAAAA
4964 TAACCTTATTGAAAA
1 TAACCTTATTGAAAA
4979 T
1 T
4980 TTCTTTTACT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.35
Consensus pattern (15 bp):
TAACCTTATTGAAAA
Found at i:5044 original size:57 final size:56
Alignment explanation
Indices: 4915--5044 Score: 158
Period size: 57 Copynumber: 2.3 Consensus size: 56
4905 TTTTTGACTG
*
4915 CAGATTTATGTTTTTACTGGTTATTTTCTAAGTTTAACCTTATTGAAAATAACCTTATT
1 CAGAATTATGTTTTTACTGGTTATTTTCTAAGTTTAACCTTATTGAAAAT-A--TTATT
* * *
4974 GAAAATT-T-CTTTTACTGGTTATTTTCTAAGTTTAACCTTATTGAAAAT-TTAATGT
1 CAGAATTATGTTTTTACTGGTTATTTTCTAAGTTTAACCTTATTGAAAATATT-AT-T
5029 CAGAATTATGTTTTTA
1 CAGAATTATGTTTTTA
5045 AAACAGGGTT
Statistics
Matches: 60, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
53 2 0.03
54 2 0.03
55 6 0.10
56 1 0.02
57 44 0.73
58 1 0.02
59 4 0.07
ACGTcount: A:0.30, C:0.10, G:0.11, T:0.49
Consensus pattern (56 bp):
CAGAATTATGTTTTTACTGGTTATTTTCTAAGTTTAACCTTATTGAAAATATTATT
Found at i:17775 original size:39 final size:39
Alignment explanation
Indices: 17731--17811 Score: 162
Period size: 39 Copynumber: 2.1 Consensus size: 39
17721 ATTAATGTAC
17731 TAAAAATAATTTCTGTAACAAAAATAATATAATTTTTTG
1 TAAAAATAATTTCTGTAACAAAAATAATATAATTTTTTG
17770 TAAAAATAATTTCTGTAACAAAAATAATATAATTTTTTG
1 TAAAAATAATTTCTGTAACAAAAATAATATAATTTTTTG
17809 TAA
1 TAA
17812 TAATTTTATA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 42 1.00
ACGTcount: A:0.49, C:0.05, G:0.05, T:0.41
Consensus pattern (39 bp):
TAAAAATAATTTCTGTAACAAAAATAATATAATTTTTTG
Found at i:26478 original size:15 final size:15
Alignment explanation
Indices: 26455--26507 Score: 56
Period size: 15 Copynumber: 3.7 Consensus size: 15
26445 CACACAAATA
*
26455 ATATTTTTAATTATT
1 ATATATTTAATTATT
26470 ATATATTTAATTATT
1 ATATATTTAATTATT
* *
26485 TTA-ATCT-ATTATT
1 ATATATTTAATTATT
*
26498 AAATATTTAA
1 ATATATTTAA
26508 ACAAACATGC
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
13 7 0.23
14 6 0.20
15 17 0.57
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (15 bp):
ATATATTTAATTATT
Found at i:32997 original size:2 final size:2
Alignment explanation
Indices: 32990--33026 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
32980 ACGTAGGTGA
32990 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33027 ATAATCACAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:42821 original size:12 final size:12
Alignment explanation
Indices: 42801--42834 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
42791 GAGTGACAGA
*
42801 ATATATATATGT
1 ATATATATACGT
*
42813 ATATGTATACGT
1 ATATATATACGT
42825 ATATATATAC
1 ATATATATAC
42835 ATGTATAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.41, C:0.06, G:0.09, T:0.44
Consensus pattern (12 bp):
ATATATATACGT
Found at i:42829 original size:20 final size:20
Alignment explanation
Indices: 42804--42841 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
42794 TGACAGAATA
* *
42804 TATATATGTATATGTATACG
1 TATATATATACATGTATACG
42824 TATATATATACATGTATA
1 TATATATATACATGTATA
42842 GAAGCAGACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.39, C:0.05, G:0.11, T:0.45
Consensus pattern (20 bp):
TATATATATACATGTATACG
Found at i:44563 original size:2 final size:2
Alignment explanation
Indices: 44558--44583 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
44548 GGTTCCTAAT
44558 GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA
44584 TAAGGTAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:51587 original size:18 final size:20
Alignment explanation
Indices: 51550--51588 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
51540 GCATTGGTCA
*
51550 ATTTTGATCCCATTAAAACC
1 ATTTTGATCCCATCAAAACC
51570 ATTTTGAT-CCA-CAAAACC
1 ATTTTGATCCCATCAAAACC
51588 A
1 A
51589 GGTTTTGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.38, C:0.26, G:0.05, T:0.31
Consensus pattern (20 bp):
ATTTTGATCCCATCAAAACC
Found at i:53207 original size:96 final size:96
Alignment explanation
Indices: 52944--53179 Score: 427
Period size: 96 Copynumber: 2.5 Consensus size: 96
52934 GTTTATCTCG
** * * *
52944 ATTTGAAGAAAGGTTGCACCTAGTAAGTTAAAGCACAAATTTTCAGAATCGAAAATAAGGAAACA
1 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAGGAAACA
53009 TTGCCTCGATTAAGGGTATTCGATTATTTCA
66 TTGCCTCGATTAAGGGTATTCGATTATTTCA
53040 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAGGAAACA
1 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAGGAAACA
53105 TTGCCTCGATTAAGGGTATTCGATTATTTCA
66 TTGCCTCGATTAAGGGTATTCGATTATTTCA
53136 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTC
1 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTC
53180 GAAACTCGAA
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
96 135 1.00
ACGTcount: A:0.39, C:0.13, G:0.19, T:0.29
Consensus pattern (96 bp):
ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAGGAAACA
TTGCCTCGATTAAGGGTATTCGATTATTTCA
Found at i:53235 original size:96 final size:96
Alignment explanation
Indices: 52944--53211 Score: 308
Period size: 96 Copynumber: 2.8 Consensus size: 96
52934 GTTTATCTCG
** * * * *
52944 ATTTGAAGAAAGGTTGCACCTAGTAAGTTAAAGCACAAATTTTCAGAATCGAAAATAAGGAAACA
1 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAAGAAACA
* * * ***
53009 TTGCCTCGATTAAGGGTATTCGATTATTTCA
66 TTGCCTCAATTAAGAGTATTCGATGAAAACA
*
53040 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAGGAAACA
1 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAAGAAACA
* * * ***
53105 TTGCCTCGATTAAGGGTATTCGATTATTTCA
66 TTGCCTCAATTAAGAGTATTCGATGAAAACA
53136 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTC-GAAACTCG-AAATAAA-AGA
1 ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAG-AA-TCGAAAATAAAGA-A
*
53198 ATATTGCCTCAATT
63 ACATTGCCTCAATT
53212 TTAAAGTTTT
Statistics
Matches: 161, Mismatches: 8, Indels: 6
0.92 0.05 0.03
Matches are distributed among these distances:
95 2 0.01
96 156 0.97
97 3 0.02
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.29
Consensus pattern (96 bp):
ATTTGAAGAAAAATTGCACGTAGTAAGTTAAGGCGCAAATTTTCAGAATCGAAAATAAAGAAACA
TTGCCTCAATTAAGAGTATTCGATGAAAACA
Found at i:53456 original size:29 final size:29
Alignment explanation
Indices: 53424--53484 Score: 79
Period size: 28 Copynumber: 2.1 Consensus size: 29
53414 AAAATGAGAC
*
53424 TTTTTAGATACCCGGGGGCAAAATGGTAA
1 TTTTTAGATACCCGAGGGCAAAATGGTAA
* * *
53453 -TTTTGGATTCTCGAGGGCAAAATGGTAA
1 TTTTTAGATACCCGAGGGCAAAATGGTAA
53481 TTTT
1 TTTT
53485 GGGAAATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 24 0.89
29 3 0.11
ACGTcount: A:0.28, C:0.11, G:0.26, T:0.34
Consensus pattern (29 bp):
TTTTTAGATACCCGAGGGCAAAATGGTAA
Found at i:53657 original size:29 final size:28
Alignment explanation
Indices: 53568--53659 Score: 87
Period size: 29 Copynumber: 3.2 Consensus size: 28
53558 AAAAATAGAA
*
53568 TTTTGGACATTCGGGGTAAAATGGTAAT
1 TTTTGGACATTCGGGGTAAAATGGTGAT
** * *
53596 TTTTGAGAGTTTCGAGGTCAAAAATGGAG-T
1 TTTTG-GACATTCGGGGT--AAAATGGTGAT
*
53626 TTTTGGACATCCGGGGGTAAAATGGTGAT
1 TTTTGGACATTC-GGGGTAAAATGGTGAT
53655 TTTTG
1 TTTTG
53660 AAAGTTTTGA
Statistics
Matches: 49, Mismatches: 10, Indels: 9
0.72 0.15 0.13
Matches are distributed among these distances:
28 13 0.27
29 19 0.39
30 10 0.20
31 7 0.14
ACGTcount: A:0.26, C:0.08, G:0.30, T:0.36
Consensus pattern (28 bp):
TTTTGGACATTCGGGGTAAAATGGTGAT
Found at i:53657 original size:59 final size:59
Alignment explanation
Indices: 53558--53843 Score: 198
Period size: 59 Copynumber: 4.9 Consensus size: 59
53548 AAATCGAGAA
* * *
53558 AAAAATAGAA-TTTTGGACATTC-GGGGTAAAATGGTAATTTTTGAGAGTTTCGAGGTC
1 AAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGCTC
* * * *
53615 AAAAATGGAGTTTTTGGACATCCGGGGGTAAAATGGTGATTTTTGAAAGTTTTGAGCTC
1 AAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGCTC
* * ** * * * *
53674 AAGAATGGAATTTTTAGAGGTTCGGGGGTAAAAAT-GCAATTTTT-AGAAGTTTTTG-GGTT
1 AAAAATGGAATTTTTGGACATTCGGGGGT-AAAATGGTAATTTTTGA-AAG-TTTCGAGCTC
* * * ** * *
53733 AAAAATAGAATTTTTAGA-AGTTCGAGGGTAAAA-AATAATTTTT-AGAAG-TTCGGGGTC
1 AAAAATGGAATTTTTGGACA-TTCGGGGGTAAAATGGTAATTTTTGA-AAGTTTCGAGCTC
* ***
53790 AAAAATGGAATTTTTAGA-AGTTTAAGGGTAAAAAT-GTAATTTTTGAAAGTTTCG
1 AAAAATGGAATTTTTGGACA-TTCGGGGGT-AAAATGGTAATTTTTGAAAGTTTCG
53844 GGATCTCCTA
Statistics
Matches: 188, Mismatches: 29, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
56 3 0.02
57 37 0.20
58 43 0.23
59 95 0.51
60 10 0.05
ACGTcount: A:0.35, C:0.05, G:0.26, T:0.35
Consensus pattern (59 bp):
AAAAATGGAATTTTTGGACATTCGGGGGTAAAATGGTAATTTTTGAAAGTTTCGAGCTC
Found at i:53709 original size:29 final size:29
Alignment explanation
Indices: 53677--53833 Score: 167
Period size: 29 Copynumber: 5.4 Consensus size: 29
53667 TGAGCTCAAG
*
53677 AATGGAATTTTTAGAGGTTCGGGGGTAAA
1 AATGGAATTTTTAGAAGTTCGGGGGTAAA
* ** *
53706 AATGCAATTTTTAGAAGTTTTTGGGTTAAA
1 AATGGAATTTTTAGAAG-TTCGGGGGTAAA
* *
53736 AATAGAATTTTTAGAAGTTCGAGGGTAAAA
1 AATGGAATTTTTAGAAGTTCGGGGGT-AAA
53766 AAT--AATTTTTAGAAGTTC-GGGGTCAAA
1 AATGGAATTTTTAGAAGTTCGGGGGT-AAA
***
53793 AATGGAATTTTTAGAAGTTTAAGGGTAAA
1 AATGGAATTTTTAGAAGTTCGGGGGTAAA
*
53822 AATGTAATTTTT
1 AATGGAATTTTT
53834 GAAAGTTTCG
Statistics
Matches: 107, Mismatches: 16, Indels: 10
0.80 0.12 0.08
Matches are distributed among these distances:
27 10 0.09
28 15 0.14
29 48 0.45
30 34 0.32
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (29 bp):
AATGGAATTTTTAGAAGTTCGGGGGTAAA
Found at i:53738 original size:30 final size:29
Alignment explanation
Indices: 53702--53841 Score: 135
Period size: 30 Copynumber: 4.8 Consensus size: 29
53692 GGTTCGGGGG
**
53702 TAAAAATGCAATTTTTAGAAGTTTTTGGGT
1 TAAAAATG-AATTTTTAGAAGTTTAAGGGT
**
53732 TAAAAATAGAATTTTTAGAAGTTCGAGGGT
1 TAAAAAT-GAATTTTTAGAAGTTTAAGGGT
* **
53762 AAAAAAT-AATTTTTAGAAG-TTCGGGGT
1 TAAAAATGAATTTTTAGAAGTTTAAGGGT
*
53789 CAAAAATGGAATTTTTAGAAGTTTAAGGG-
1 TAAAAAT-GAATTTTTAGAAGTTTAAGGGT
53818 TAAAAATGTAATTTTT-GAAAGTTT
1 TAAAAATG-AATTTTTAG-AAGTTT
53842 CGGGATCTCC
Statistics
Matches: 93, Mismatches: 11, Indels: 13
0.79 0.09 0.11
Matches are distributed among these distances:
27 11 0.12
28 14 0.15
29 31 0.33
30 36 0.39
31 1 0.01
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (29 bp):
TAAAAATGAATTTTTAGAAGTTTAAGGGT
Found at i:54998 original size:3 final size:3
Alignment explanation
Indices: 54990--55029 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
54980 TTTTATTTAT
* *
54990 TTA TTA TTA GTA TTAA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
55030 ATGCTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:55037 original size:15 final size:15
Alignment explanation
Indices: 54990--55038 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
54980 TTTTATTTAT
* *
54990 TTATTATTAGTATTAA
1 TTATTATTAATACT-A
*
55006 TTATTATTAATATTA
1 TTATTATTAATACTA
*
55021 TTATTATTAATGCTA
1 TTATTATTAATACTA
55036 TTA
1 TTA
55039 AAACATTTAT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (15 bp):
TTATTATTAATACTA
Found at i:55794 original size:17 final size:17
Alignment explanation
Indices: 55761--55876 Score: 151
Period size: 17 Copynumber: 6.4 Consensus size: 17
55751 ATAATAATAT
55761 TTTAAATTTTGAAAATAAA
1 TTTAAA-TTT-AAAATAAA
55780 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
55797 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
55814 TTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
55831 TTTAAATTCAAATTTAAAATAAA
1 --T---TT-AAATTTAAAATAAA
*
55854 TCTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAA
55871 TTTAAA
1 TTTAAA
55877 AGGGGCCCGA
Statistics
Matches: 89, Mismatches: 2, Indels: 14
0.85 0.02 0.13
Matches are distributed among these distances:
17 61 0.69
18 4 0.04
19 7 0.08
21 1 0.01
22 2 0.02
23 14 0.16
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (17 bp):
TTTAAATTTAAAATAAA
Found at i:55798 original size:11 final size:11
Alignment explanation
Indices: 55782--55877 Score: 78
Period size: 11 Copynumber: 9.0 Consensus size: 11
55772 AAAATAAATT
55782 TAAATTTAAAA
1 TAAATTTAAAA
*
55793 TAAATTTAAATT
1 TAAATTTAAA-A
* *
55805 TAAA-ATAAATT
1 TAAATTTAAA-A
55816 TAAATTTAAAA
1 TAAATTTAAAA
*
55827 TAAATTTAAAT
1 TAAATTTAAAA
55838 TCAAATTTAAAA
1 T-AAATTTAAAA
*
55850 TAAA--T---C
1 TAAATTTAAAA
55856 TAAATTTAAAA
1 TAAATTTAAAA
55867 TAAATTTAAAA
1 TAAATTTAAAA
55878 GGGGCCCGAT
Statistics
Matches: 69, Mismatches: 8, Indels: 16
0.74 0.09 0.17
Matches are distributed among these distances:
6 4 0.06
8 1 0.01
9 1 0.01
11 45 0.65
12 18 0.26
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:55806 original size:23 final size:23
Alignment explanation
Indices: 55776--55876 Score: 89
Period size: 23 Copynumber: 4.2 Consensus size: 23
55766 ATTTTGAAAA
55776 TAAATTTAAATTTAAAATAAATT
1 TAAATTTAAATTTAAAATAAATT
* *
55799 TAAATTTAAA-ATAAATTTAAATT
1 TAAATTTAAATTTAAA-ATAAATT
* *
55822 TAAA-ATAAATTTAAATTCAAATT
1 TAAATTTAAATTTAAAAT-AAATT
55845 TAAAATAAATCTAAATTTAAAATAAATT
1 T-AAAT---T-TAAATTTAAAATAAATT
55873 TAAA
1 TAAA
55877 AGGGGCCCGA
Statistics
Matches: 63, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
22 10 0.16
23 30 0.48
24 3 0.05
27 3 0.05
28 6 0.10
29 11 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
TAAATTTAAATTTAAAATAAATT
Found at i:55814 original size:34 final size:34
Alignment explanation
Indices: 55761--55876 Score: 151
Period size: 40 Copynumber: 3.2 Consensus size: 34
55751 ATAATAATAT
55761 TTTAAATTTTGAAAATAAATTTAAATTTAAAATAAA
1 TTTAAA-TTT-AAAATAAATTTAAATTTAAAATAAA
55797 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
1 TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
*
55831 TTTAAATTCAAATTTAAAATAAATCTAAATTTAAAATAAA
1 --T---TT-AAATTTAAAATAAATTTAAATTTAAAATAAA
55871 TTTAAA
1 TTTAAA
55877 AGGGGCCCGA
Statistics
Matches: 73, Mismatches: 1, Indels: 14
0.83 0.01 0.16
Matches are distributed among these distances:
34 28 0.38
35 5 0.07
36 7 0.10
38 1 0.01
39 2 0.03
40 30 0.41
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.41
Consensus pattern (34 bp):
TTTAAATTTAAAATAAATTTAAATTTAAAATAAA
Found at i:56546 original size:206 final size:204
Alignment explanation
Indices: 56182--56847 Score: 875
Period size: 206 Copynumber: 3.2 Consensus size: 204
56172 TCTAGTTTCA
* * * * * ** **
56182 TTGACTTGGCCTTCTTCTCAGTATCTCGTCAGAAAGATGACTGCATCACTTGTTTTGATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCACTT
* * * * * *
56247 CTCTGTGTTTTATTAGGAAGACGGATTTGGT-TCACTTCTCCGTATCTCATCAGGAAGCTAACCA
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCT-ACTTCTCAGTATCTCATCAGGAAGCTAACCA
* * * *
56311 CTTTATTGCTTCGACCTTCTTCTCAGTATCTCATCAGGAAGCTAGGGTTTGAAGATTTGTTCATA
130 TTTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGTTCATA
56376 TCGAGCGTGAGT
194 TCGAGCGTG-GT
* *
56388 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCACATCGTTTGTTTCAATCCGCTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCACTT
* *
56453 CTCAGTATCTCATCAGGAAGACAAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCAT
*
56518 TTTATTACTTCGACCTGCTTCTCAGTATCTTATCAGGAAGCTGGGGTTCGAAGATTTGTTCATAT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCT-GGGTTCGAAGATTTGTTCATAT
*
56583 TGAGCGTGGAT
195 CGAGCGTGG-T
* * **
56594 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGACGATCGTGTCGTTTGTTTCAATCCACTT
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCACTT
* * * *
56659 CTCTGTATCTCATCAGAAAGACGAATTTGGTCCACTTCTCAGTATCTCATCATGAAGCTAACTAT
66 CTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCAT
* * * * * * * **
56724 TTTATTACTTTGACCCGCTTCTCAGAATCTCATCAGGAAGATGAGATTCAAAGATTTGCTCACCT
131 TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTG-GGTTCGAAGATTTGTTCATAT
56789 CGAGCGTGGGT
195 CGAGCGT-GGT
*
56800 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGATCGCATCG
1 TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCG
56848 CTGTTTGTGG
Statistics
Matches: 404, Mismatches: 52, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
205 2 0.00
206 399 0.99
207 3 0.01
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (204 bp):
TTGATTTGGTCTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCGTTTGTTTCAATCCACTT
CTCTGTATCTCATCAGGAAGACGAATTTGGTCTACTTCTCAGTATCTCATCAGGAAGCTAACCAT
TTTATTACTTCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGTTCGAAGATTTGTTCATATC
GAGCGTGGT
Found at i:57018 original size:78 final size:77
Alignment explanation
Indices: 56889--57061 Score: 188
Period size: 78 Copynumber: 2.2 Consensus size: 77
56879 ATCGGGATAG
* * ** * * *
56889 GAGATTGGTTGATAGTGATCTGCCCCAAGCTCATTGTAAGAGATCGAATGGCTGT-AATTTACCC
1 GAGATTGGTTGAGA-TGATCTACCCCAAGCTCAGGGTAAAAGATCAAATGGCT-TCAATCT-CCC
*
56953 CT-GGCTTGAGGTAA
63 CTAGGCTCGAGGTAA
* *
56967 GAGATTGGTTGACGATGATCTACCCCAAGCTCAGGGTAAAAGATTAAATGGCTTCAATCTGCCCT
1 GAGATTGGTTGA-GATGATCTACCCCAAGCTCAGGGTAAAAGATCAAATGGCTTCAATCTCCCCT
*
57032 AGGCTCGGGGTAA
65 AGGCTCGAGGTAA
57045 GAGATTGGTTGATGATG
1 GAGATTGGTTGA-GATG
57062 TAACTTCACT
Statistics
Matches: 80, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
77 5 0.06
78 74 0.93
79 1 0.01
ACGTcount: A:0.27, C:0.17, G:0.28, T:0.28
Consensus pattern (77 bp):
GAGATTGGTTGAGATGATCTACCCCAAGCTCAGGGTAAAAGATCAAATGGCTTCAATCTCCCCTA
GGCTCGAGGTAA
Found at i:57379 original size:50 final size:49
Alignment explanation
Indices: 57318--58240 Score: 441
Period size: 50 Copynumber: 18.6 Consensus size: 49
57308 GTCATTACGA
* ** * *
57318 CTTAAACCTTTCCCCTTCAAATCTTCGTGGTACTAGATTCGCCGTTGCGG
1 CTTAAATCTTT-CCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * * *
57368 CTTAAATCTTTCCCTTCTTGTCTTCTGAGGTACACGG-TCCGCCGTTTCGA
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTAC-TGGATCCGCCGTTGCGG
** * *
57418 CTTAAA-CATTT-CCTTTTTGTATCTTTGTGGTACTGGATCCCCCGTTGCGG
1 CTTAAATC-TTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTTGCGG
* *
57468 TCTTAGATC-TTCCCTTCATGTCTTCATGGTACTGGATCCGCCGTTGCGGG
1 -CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGC-GG
** * * * *
57518 CTTGGATCTTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCAG
1 CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * * * * *
57567 CTTAAATCTTTCTCTTCTTGTCTTTTGAGGTACACGG-TCTGCCGTTGCGA
1 CTTAAATCTTTCCCTTCATGTC-TTCGTGGTAC-TGGATCCGCCGTTGCGG
* ** * * * *
57617 CTT-AGTCCTTTCCCGTTTGTATCTTTGTGGTATTGGATCCACCGTTGCGG
1 CTTAAAT-CTTTCCC-TTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
** * * * *
57667 TCTTGGATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTACAG
1 -CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * * *
57717 CTTAAATCTTTCCCTTCGTGTCTT-TTGAGTACACGG-TCCTGCCGTTACGA
1 CTTAAATCTTTCCCTTCATGTCTTCGTG-GTAC-TGGATCC-GCCGTTGCGG
* * * * * * **
57767 CTTAGACCTTTCCCTT-TTGTATCTTTGTGGTACTGGATTCACCGTTTTGG
1 CTTAAATCTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * ** * *
57817 CTTAAAACTTTCCCTTCCTGTCTTCTGAGGTACACGATCCGCCATTGCGA
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTACTGGATCCGCCGTTGCGG
* * ** *
57867 CTTAGACCTTT-CCTTTTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGG
1 CTTAAATCTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * *
57917 TCTTGAATCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTGCAG
1 -CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * * * * *
57967 CTTAAATCTTTCCCTTCTTGTCTTTTGAGGTACACGG-TTCGCTGTTGCGA
1 CTTAAATCTTTCCCTTCATGTC-TTCGTGGTAC-TGGATCCGCCGTTGCGG
* * * * * * * *
58017 CTTAGACCTTTCCCTT-TTGTATCTTTGTAGTATTGGATCCACCGTTGTGG
1 CTTAAATCTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTTGCGG
** * * * * *
58067 TCTTGGATC--T---TTC---TCTTCATGGTACTGGATTCACCGTTACAG
1 -CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
* * * * *
58109 CTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGG-TCCTTCCGTTGCGA
1 CTTAAATCTTTCCCTTCATGTCTTC-GTGGTAC-TGGATCC-GCCGTTGCGG
* * * * * *
58160 CTTAGACCTTTCCCTT-TTGTATCTTTGTGGTACTAGATCCACCGTTGCGG
1 CTTAAATCTTTCCCTTCATG--TCTTCGTGGTACTGGATCCGCCGTTGCGG
* *
58210 TCTTAGATCTTTCCCTTCATGTCTTCATGGT
1 -CTTAAATCTTTCCCTTCATGTCTTCGTGGT
58241 GCTGAGACCT
Statistics
Matches: 653, Mismatches: 166, Indels: 108
0.70 0.18 0.12
Matches are distributed among these distances:
41 6 0.01
42 21 0.03
43 1 0.00
46 5 0.01
48 2 0.00
49 145 0.22
50 344 0.53
51 113 0.17
52 16 0.02
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (49 bp):
CTTAAATCTTTCCCTTCATGTCTTCGTGGTACTGGATCCGCCGTTGCGG
Found at i:57532 original size:150 final size:150
Alignment explanation
Indices: 57325--58240 Score: 797
Period size: 150 Copynumber: 6.2 Consensus size: 150
57315 CGACTTAAAC
** * * * *
57325 CTTTCCCCTTCAAATCTTCGTGGTACTAGATTCGCCGTTGCGGCTTAAATCTTTCCCTTCTTGTC
1 CTTT-CCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTC
* *
57390 TTCTGAGGTACACGGTCCGCCGTTTCGACTTAAACATTTCCTTTTTGTATCTTTGTGGTACTGGA
65 TTCTGAGGTACACGGTCCGCCGTTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGGA
*
57455 TCCCCCGTTGCGGTCTTAGAT
130 TCCGCCGTTGCGGTCTTAGAT
* * **
57476 C-TTCCCTTCATGTCTTCATGGTACTGGATCCGCCGTTGCGGGCTTGGATCTTTCCCTTCATGTC
1 CTTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGC-GGCTTAAATCTTTCCCTTCATGTC
* * * * * * *
57540 TTC--ATGGTAC-TGGATTCACCGTTGC-AGCTTAAATCTTTCTCTTCTTGTCT-TTTGAGGTAC
65 TTCTGA-GGTACACGG-TCCGCCGTTGCGA-CTTAAACCTTTC-CTTTTTGTATCTTTGTGGTAC
* * *
57600 ACGG-TCTGCCGTTGC-GACTTAG-T
126 -TGGATCCGCCGTTGCGGTCTTAGAT
** * ** * * **
57623 CCTTTCCCGTTTGTATCTTTGTGGTATTGGATCCACCGTTGCGGTCTTGGATCTTTCCCTTCATG
1 -CTTTCCC-TTCATGTCTTCATGGTACTGGATTCACCGTTGCGG-CTTAAATCTTTCCCTTCATG
* * * * * * *
57688 TCTTC--ATGGTAC-TGGATTCGCCGTTAC-AGCTTAAATCTTTCC-CTTCGTGTCTTT-TGAGT
63 TCTTCTGA-GGTACACGG-TCCGCCGTTGCGA-CTTAAACCTTTCCTTTTTGTATCTTTGTG-GT
* * * *
57747 ACACGG-TCCTGCCGTTAC-GACTTAGAC
124 AC-TGGATCC-GCCGTTGCGGTCTTAGAT
* ** ** * *
57774 CTTTCCCTT-TTGTATCTTTGTGGTACTGGATTCACCGTTTTGGCTTAAAACTTTCCCTTCCTGT
1 CTTTCCCTTCATG--TCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGT
* * *
57838 CTTCTGAGGTACACGATCCGCCATTGCGACTTAGACCTTTCCTTTTTGTATCTTTGTGGTACTGG
64 CTTCTGAGGTACACGGTCCGCCGTTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGG
57903 ATCCGCCGTTGCGGTCTT-GAAT
129 ATCCGCCGTTGCGGTCTTAG-AT
* * *
57925 CTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCTTGTCT
1 CTTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCT
* * * * * * *
57990 TTTGAGGTACACGGTTCGCTGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTAGTATTGGAT
66 TCTGAGGTACACGGTCCGCCGTTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGGAT
* * *
58055 CCACCGTTGTGGTCTTGGAT
131 CCGCCGTTGCGGTCTTAGAT
* * *
58075 C--T---TTC---TCTTCATGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCGTGTCT
1 CTTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCT
* * * *
58132 TCTGAGGTACACGGTCCTTCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTAGA
66 TCTGAGGTACACGGTCC-GCCGTTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGGA
*
58197 TCCACCGTTGCGGTCTTAGAT
130 TCCGCCGTTGCGGTCTTAGAT
58218 CTTTCCCTTCATGTCTTCATGGT
1 CTTTCCCTTCATGTCTTCATGGT
58241 GCTGAGACCT
Statistics
Matches: 636, Mismatches: 93, Indels: 72
0.79 0.12 0.09
Matches are distributed among these distances:
142 64 0.10
143 62 0.10
145 4 0.01
147 1 0.00
148 21 0.03
149 116 0.18
150 319 0.50
151 45 0.07
152 4 0.01
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (150 bp):
CTTTCCCTTCATGTCTTCATGGTACTGGATTCACCGTTGCGGCTTAAATCTTTCCCTTCATGTCT
TCTGAGGTACACGGTCCGCCGTTGCGACTTAAACCTTTCCTTTTTGTATCTTTGTGGTACTGGAT
CCGCCGTTGCGGTCTTAGAT
Found at i:57867 original size:250 final size:250
Alignment explanation
Indices: 57544--58063 Score: 808
Period size: 250 Copynumber: 2.1 Consensus size: 250
57534 CATGTCTTCA
* * * * * *
57544 TGGTACTGGATTCACCGTTGCAGCTTAAATCTTTCTCTTCTTGTCTTTTGAGGTACACGGTCTGC
1 TGGTACTGGATTCACCGTTGCAGCTTAAAACTTTCCCTTCCTGTCTTCTGAGGTACACGATCCGC
* * * *
57609 CGTTGCGACTTAGTCCTTTCCCGTTTGTATCTTTGTGGTATTGGATCCACCGTTGCGGTCTTGGA
66 CATTGCGACTTAGACCTTTCCCGTTTGTATCTTTGTGGTACTGGATCCACCGTTGCGGTCTTGAA
57674 TCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTACAGCTTAAATCTTTCCCTTCGTGTC
131 TCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTACAGCTTAAATCTTTCCCTTCGTGTC
57739 TTTTGA-GTACACGGTCCTGCCGTTACGACTTAGACCTTTCCCTTTTGTATCTTTG
196 TTTTGAGGTACACGGTCC-GCCGTTACGACTTAGACCTTTCCCTTTTGTATCTTTG
***
57794 TGGTACTGGATTCACCGTTTTGGCTTAAAACTTTCCCTTCCTGTCTTCTGAGGTACACGATCCGC
1 TGGTACTGGATTCACCGTTGCAGCTTAAAACTTTCCCTTCCTGTCTTCTGAGGTACACGATCCGC
** *
57859 CATTGCGACTTAGACCTTTCCTTTTTGTATCTTTGTGGTACTGGATCCGCCGTTGCGGTCTTGAA
66 CATTGCGACTTAGACCTTTCCCGTTTGTATCTTTGTGGTACTGGATCCACCGTTGCGGTCTTGAA
* *
57924 TCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCTTGTC
131 TCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTACAGCTTAAATCTTTCCCTTCGTGTC
* * *
57989 TTTTGAGGTACACGGTTCGCTGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTG
196 TTTTGAGGTACACGGTCCGCCGTTACGACTTAGACCTTTCCCTTTTGTATCTTTG
* * *
58044 TAGTATTGGATCCACCGTTG
1 TGGTACTGGATTCACCGTTG
58064 TGGTCTTGGA
Statistics
Matches: 244, Mismatches: 25, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
250 234 0.96
251 10 0.04
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.40
Consensus pattern (250 bp):
TGGTACTGGATTCACCGTTGCAGCTTAAAACTTTCCCTTCCTGTCTTCTGAGGTACACGATCCGC
CATTGCGACTTAGACCTTTCCCGTTTGTATCTTTGTGGTACTGGATCCACCGTTGCGGTCTTGAA
TCTTTCCCTTCATGTCTTCATGGTACTGGATTCGCCGTTACAGCTTAAATCTTTCCCTTCGTGTC
TTTTGAGGTACACGGTCCGCCGTTACGACTTAGACCTTTCCCTTTTGTATCTTTG
Found at i:58171 original size:51 final size:51
Alignment explanation
Indices: 58116--58235 Score: 120
Period size: 51 Copynumber: 2.4 Consensus size: 51
58106 CAGCTTAAAT
* *
58116 CTTTCCCTTCGTGTCTTCTGAGGTAC-ACGGTCCTTCCGTTGC-GACTTAGAC
1 CTTTCCCTTCGTGTCTTCTGAGGTACTA-GATCC-ACCGTTGCGGACTTAGAC
* * * * *
58167 CTTTCCCTTTTGTATCTT-TGTGGTACTAGATCCACCGTTGCGGTCTTAGAT
1 CTTTCCC-TTCGTGTCTTCTGAGGTACTAGATCCACCGTTGCGGACTTAGAC
*
58218 CTTTCCCTTCATGTCTTC
1 CTTTCCCTTCGTGTCTTC
58236 ATGGTGCTGA
Statistics
Matches: 55, Mismatches: 10, Indels: 8
0.75 0.14 0.11
Matches are distributed among these distances:
50 14 0.25
51 32 0.58
52 9 0.16
ACGTcount: A:0.12, C:0.29, G:0.18, T:0.41
Consensus pattern (51 bp):
CTTTCCCTTCGTGTCTTCTGAGGTACTAGATCCACCGTTGCGGACTTAGAC
Found at i:58228 original size:143 final size:141
Alignment explanation
Indices: 57939--58230 Score: 440
Period size: 143 Copynumber: 2.0 Consensus size: 141
57929 CCCTTCATGT
* * * *
57939 CTTCATGGTACTGGATTCGCCGTTGCAGCTTAAATCTTTCCCTTCTTGTCTTTTGAGGTACACGG
1 CTTCATGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCCTGTCTTCTGAGGTACACGG
* * * * *
58004 TTCGCTGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTAGTATTGGATCCACCGTTGTGGTC
66 TCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCACCGTTGCGGTC
*
58069 TTGGATCTTTCT
131 TT-GATCTTTCC
*
58081 CTTCATGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCGTGTCTTCTGAGGTACACGG
1 CTTCATGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCCTGTCTTCTGAGGTACACGG
* *
58146 TCCTTCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTAGATCCACCGTTGCGGT
66 TCC-GCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCACCGTTGCGGT
58211 CTTAGATCTTTCC
130 CTT-GATCTTTCC
58224 CTTCATG
1 CTTCATG
58231 TCTTCATGGT
Statistics
Matches: 136, Mismatches: 13, Indels: 1
0.91 0.09 0.01
Matches are distributed among these distances:
142 63 0.46
143 73 0.54
ACGTcount: A:0.14, C:0.25, G:0.20, T:0.40
Consensus pattern (141 bp):
CTTCATGGTACTGGATTCACCGTTACAGCTTAAATCTTTCCCTTCCTGTCTTCTGAGGTACACGG
TCCGCCGTTGCGACTTAGACCTTTCCCTTTTGTATCTTTGTGGTACTGGATCCACCGTTGCGGTC
TTGATCTTTCC
Found at i:59494 original size:6 final size:6
Alignment explanation
Indices: 59460--59550 Score: 60
Period size: 6 Copynumber: 14.8 Consensus size: 6
59450 CTTTTTTGTA
* * *
59460 TTTTTG TTTTTC TTCTTG TTTTTGC -TTTTC TTTTT- TTCTTTC TTTTCTTC
1 TTTTTC TTTTTC TTTTTC TTTTT-C TTTTTC TTTTTC TT-TTTC -TTT-TTC
* * * * *
59510 TTCTTC TTCTTC TTTTTC TTCTTC TTCTTC TTCTTC TTTTT
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTT
59551 TTGTATCTGA
Statistics
Matches: 70, Mismatches: 9, Indels: 12
0.77 0.10 0.13
Matches are distributed among these distances:
5 3 0.04
6 59 0.84
7 3 0.04
8 5 0.07
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (6 bp):
TTTTTC
Found at i:59510 original size:3 final size:3
Alignment explanation
Indices: 59469--59547 Score: 83
Period size: 3 Copynumber: 26.7 Consensus size: 3
59459 ATTTTTGTTT
* * *
59469 TTC TTC TTG TTT TTGC TT- TTC TT- TTT TTC TTTC TT- TTC TTC TTC
1 TTC TTC TTC TTC TT-C TTC TTC TTC TTC TTC -TTC TTC TTC TTC TTC
*
59513 TTC TTC TTC TTT TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
59548 TTTTTGTATC
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
2 6 0.09
3 54 0.83
4 5 0.08
ACGTcount: A:0.00, C:0.24, G:0.03, T:0.73
Consensus pattern (3 bp):
TTC
Found at i:65232 original size:29 final size:29
Alignment explanation
Indices: 65182--65340 Score: 138
Period size: 29 Copynumber: 5.4 Consensus size: 29
65172 ACATGGTGAA
* *
65182 TTTTGAAAGTTTCGAGGTTAAAAATGGAAT
1 TTTTGGAAGTTT-GAGGGTAAAAATGGAAT
** * * *
65212 TTTTGGTTGTTTGGGGGTAAAATTGTAAT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAAT
* * *
65241 TTTTAGAAGTTTTAGGGTCAAAATGGAAT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAAT
* * * *
65270 TTTTAGAAGTTTTAAGGTCAAAAATGAAAT
1 TTTTGGAAGTTTGAGGGT-AAAAATGGAAT
* * *
65300 TTTTGGAAGTTTGGGGGTAAAAGTGTAAT
1 TTTTGGAAGTTTGAGGGTAAAAATGGAAT
*
65329 TTTTGAAAGTTT
1 TTTTGGAAGTTT
65341 CGGGACATCC
Statistics
Matches: 103, Mismatches: 25, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
29 71 0.69
30 32 0.31
ACGTcount: A:0.32, C:0.02, G:0.25, T:0.41
Consensus pattern (29 bp):
TTTTGGAAGTTTGAGGGTAAAAATGGAAT
Found at i:65293 original size:88 final size:87
Alignment explanation
Indices: 65179--65340 Score: 227
Period size: 88 Copynumber: 1.9 Consensus size: 87
65169 GTAACATGGT
* * * ** *
65179 GAATTTTGAAAGTTTCGAGGTTAAAAATGGAATTTTTGGTTGTTTGGGGGTAAAATTGTAATTTT
1 GAATTTTGAAAGTTTCAAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAGTGTAATTTT
65244 T-AGAAGTTTTAGGGTCAAAATG
66 TGA-AAGTTTTAGGGTCAAAATG
* *
65266 GAATTTTTAGAAGTTTTAAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAGTGTAATTT
1 GAATTTTGA-AAGTTTCAAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAGTGTAATTT
65331 TTGAAAGTTT
65 TTGAAAGTTT
65341 CGGGACATCC
Statistics
Matches: 65, Mismatches: 8, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
87 8 0.12
88 56 0.86
89 1 0.02
ACGTcount: A:0.33, C:0.02, G:0.25, T:0.40
Consensus pattern (87 bp):
GAATTTTGAAAGTTTCAAGGTCAAAAATGAAATTTTTGGAAGTTTGGGGGTAAAAGTGTAATTTT
TGAAAGTTTTAGGGTCAAAATG
Found at i:66489 original size:3 final size:3
Alignment explanation
Indices: 66483--66522 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
66473 TTTTTTTTAT
* *
66483 TTA TTA TTA GTA TTAA TTA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA
66523 ATGCTATTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
3 29 0.91
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:66530 original size:15 final size:15
Alignment explanation
Indices: 66483--66531 Score: 53
Period size: 15 Copynumber: 3.2 Consensus size: 15
66473 TTTTTTTTAT
* *
66483 TTATTATTAGTATTAA
1 TTATTATTAATACT-A
*
66499 TTATTATTAATATTA
1 TTATTATTAATACTA
*
66514 TTATTATTAATGCTA
1 TTATTATTAATACTA
66529 TTA
1 TTA
66532 AAACATTTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 17 0.57
16 13 0.43
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (15 bp):
TTATTATTAATACTA
Found at i:66548 original size:2 final size:2
Alignment explanation
Indices: 66541--66566 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
66531 AAAACATTTA
66541 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
66567 TTATTACACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:67275 original size:19 final size:18
Alignment explanation
Indices: 67251--67294 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
67241 ATAATAATCT
67251 TTTAAATTTTGAAAATATA
1 TTTAAATTTTGAAAATA-A
*
67270 TTTAAA-TTTGAAATTAA
1 TTTAAATTTTGAAAATAA
67287 TTTAAATT
1 TTTAAATT
67295 CAAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 7 0.30
18 10 0.43
19 6 0.26
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTAAATTTTGAAAATAA
Found at i:67289 original size:17 final size:18
Alignment explanation
Indices: 67251--67294 Score: 63
Period size: 17 Copynumber: 2.4 Consensus size: 18
67241 ATAATAATCT
67251 TTTAAATTTTGAAAATATA
1 TTTAAA-TTTGAAAATATA
*
67270 TTTAAATTTGAAATTA-A
1 TTTAAATTTGAAAATATA
67287 TTTAAATT
1 TTTAAATT
67295 CAAATTTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 9 0.38
18 9 0.38
19 6 0.25
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (18 bp):
TTTAAATTTGAAAATATA
Found at i:67312 original size:11 final size:11
Alignment explanation
Indices: 67272--67316 Score: 54
Period size: 11 Copynumber: 4.0 Consensus size: 11
67262 AAAATATATT
*
67272 TAAATTTGAAA
1 TAAATTTAAAA
* *
67283 TTAATTTAAAT
1 TAAATTTAAAA
67294 TCAAATTTAAAA
1 T-AAATTTAAAA
67306 TAAATTTAAAA
1 TAAATTTAAAA
67317 GGGGCTCGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
11 19 0.68
12 9 0.32
ACGTcount: A:0.56, C:0.02, G:0.02, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:71428 original size:62 final size:62
Alignment explanation
Indices: 71331--71455 Score: 216
Period size: 62 Copynumber: 2.0 Consensus size: 62
71321 TGAAGACATG
71331 TGTGAAGTGATGGGTTGAATTCAAATTTGGGGGACATTGAAGGCTTAATTGCAAAGAAGTTC
1 TGTGAAGTGATGGGTTGAATTCAAATTTGGGGGACATTGAAGGCTTAATTGCAAAGAAGTTC
* *
71393 TGTGAAGAT-ATGGGTTGTATTCAAATTTGGGGGACATTGAAGGTTTAATTGCAAAGAAGTTC
1 TGTGAAG-TGATGGGTTGAATTCAAATTTGGGGGACATTGAAGGCTTAATTGCAAAGAAGTTC
71455 T
1 T
71456 TAGTTGAAAT
Statistics
Matches: 60, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
62 59 0.98
63 1 0.02
ACGTcount: A:0.30, C:0.07, G:0.30, T:0.33
Consensus pattern (62 bp):
TGTGAAGTGATGGGTTGAATTCAAATTTGGGGGACATTGAAGGCTTAATTGCAAAGAAGTTC
Found at i:71537 original size:43 final size:42
Alignment explanation
Indices: 71478--71569 Score: 148
Period size: 43 Copynumber: 2.2 Consensus size: 42
71468 TCAAATAAGC
* *
71478 TTATTCAAAGCTGTTATTTTCTTAATTTTATTTTGATTAAAT
1 TTATTTAAAGCTGTTATTTTCTTAATTTTAATTTGATTAAAT
*
71520 TATATTTAAAGTTGTTATTTTCTTAATTTTAATTTGATTAAAT
1 T-TATTTAAAGCTGTTATTTTCTTAATTTTAATTTGATTAAAT
71563 TTATTTA
1 TTATTTA
71570 TTTTAAGTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
42 7 0.15
43 39 0.85
ACGTcount: A:0.30, C:0.04, G:0.07, T:0.59
Consensus pattern (42 bp):
TTATTTAAAGCTGTTATTTTCTTAATTTTAATTTGATTAAAT
Found at i:72125 original size:16 final size:18
Alignment explanation
Indices: 72104--72143 Score: 57
Period size: 16 Copynumber: 2.3 Consensus size: 18
72094 ACTTTATTTA
*
72104 TTTTATTTTA-TTT-TCG
1 TTTTATTTTAGTTTAACG
72120 TTTTATTTTAGTTTAACG
1 TTTTATTTTAGTTTAACG
72138 TTTTAT
1 TTTTAT
72144 CTCTAAACCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 10 0.48
17 3 0.14
18 8 0.38
ACGTcount: A:0.17, C:0.05, G:0.07, T:0.70
Consensus pattern (18 bp):
TTTTATTTTAGTTTAACG
Found at i:78280 original size:22 final size:22
Alignment explanation
Indices: 78239--78279 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
78229 ATCGAAGATA
78239 AAAATTTTATTACTTAAAAATG
1 AAAATTTTATTACTTAAAAATG
78261 AAAA-TTTATTACTTAAAAA
1 AAAATTTTATTACTTAAAAA
78280 ACTATATTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
AAAATTTTATTACTTAAAAATG
Found at i:78895 original size:3 final size:3
Alignment explanation
Indices: 78887--78915 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
78877 CATAAATTTG
78887 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC AT
78916 GTCGGTTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
ATC
Found at i:86797 original size:31 final size:29
Alignment explanation
Indices: 86761--86819 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
86751 TTATTGTTAT
86761 ATAATTT-ATACTATTGATTTTTATTTTTTTA
1 ATAATTTAAT-CTATT--TTTTTATTTTTTTA
86792 ATAATTTAATCTATTTTTTTATTTTTTT
1 ATAATTTAATCTATTTTTTTATTTTTTT
86820 CATCGCACTT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 13 0.48
31 12 0.44
32 2 0.07
ACGTcount: A:0.27, C:0.03, G:0.02, T:0.68
Consensus pattern (29 bp):
ATAATTTAATCTATTTTTTTATTTTTTTA
Found at i:86962 original size:12 final size:12
Alignment explanation
Indices: 86930--86968 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
86920 CATTTCGATG
86930 AAATAATTATTA
1 AAATAATTATTA
*
86942 AAATCAATTTTTA
1 AAAT-AATTATTA
*
86955 ATATAATTATTA
1 AAATAATTATTA
86967 AA
1 AA
86969 TATTGTATTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
12 12 0.55
13 10 0.45
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (12 bp):
AAATAATTATTA
Found at i:90769 original size:24 final size:26
Alignment explanation
Indices: 90711--90769 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
90701 AAATAGTGTC
*
90711 AAAT-TTAAGTATTAAATTACATAAA
1 AAATGTTAAGTATCAAATTACATAAA
*
90736 AAAAGCTTAAGTATCAAATTA-A-AAA
1 AAATG-TTAAGTATCAAATTACATAAA
90761 AAATGTTAA
1 AAATGTTAA
90770 ATTCAAGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
24 4 0.14
25 10 0.34
26 1 0.03
27 14 0.48
ACGTcount: A:0.58, C:0.05, G:0.07, T:0.31
Consensus pattern (26 bp):
AAATGTTAAGTATCAAATTACATAAA
Found at i:93451 original size:18 final size:18
Alignment explanation
Indices: 93416--93451 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
93406 TTGTTTGTAG
93416 ATTTTAAAAATATATATT
1 ATTTTAAAAATATATATT
93434 ATTTATAAAAATAT-TATT
1 ATTT-TAAAAATATATATT
93452 TTAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
ATTTTAAAAATATATATT
Found at i:93458 original size:17 final size:19
Alignment explanation
Indices: 93420--93459 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
93410 TTGTAGATTT
*
93420 TAAAAATATATATTATTTA
1 TAAAAATATATATTATTAA
93439 TAAAAATAT-TATT-TTAA
1 TAAAAATATATATTATTAA
93456 TAAA
1 TAAA
93460 TAAATTTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 7 0.35
18 4 0.20
19 9 0.45
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
TAAAAATATATATTATTAA
Found at i:93464 original size:19 final size:19
Alignment explanation
Indices: 93416--93464 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 19
93406 TTGTTTGTAG
*
93416 ATTTTAA-AAATATATATT
1 ATTTTAATAAATAAATATT
93434 A-TTT-AT-AA-AAATATT
1 ATTTTAATAAATAAATATT
93449 ATTTTAATAAATAAAT
1 ATTTTAATAAATAAAT
93465 TTCATTTTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 9
0.71 0.03 0.26
Matches are distributed among these distances:
15 7 0.28
16 6 0.24
17 5 0.20
18 3 0.12
19 4 0.16
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (19 bp):
ATTTTAATAAATAAATATT
Found at i:93649 original size:55 final size:56
Alignment explanation
Indices: 93560--93665 Score: 171
Period size: 55 Copynumber: 1.9 Consensus size: 56
93550 AAATGAACGT
*
93560 TTAATTATATACGTATATTTTTTAAAAAGTTTTTTAAATTTTAATTTTAAAATTTTA
1 TTAATTATATAC-TATATTTTTTAAAAAGTTTTTTAAATTTAAATTTTAAAATTTTA
93617 TTAATTATATA-TATTATTTTTT-AAAAGTTTTTTAAATTTAAATTTTAAA
1 TTAATTATATACTA-TATTTTTTAAAAAGTTTTTTAAATTTAAATTTTAAA
93666 TTCTTAAGAA
Statistics
Matches: 47, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
55 28 0.60
56 8 0.17
57 11 0.23
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.57
Consensus pattern (56 bp):
TTAATTATATACTATATTTTTTAAAAAGTTTTTTAAATTTAAATTTTAAAATTTTA
Found at i:95100 original size:17 final size:17
Alignment explanation
Indices: 95075--95154 Score: 69
Period size: 16 Copynumber: 4.8 Consensus size: 17
95065 TTAGGCCCAC
95075 AAATA-TTATTTT-TTT
1 AAATATTTATTTTATTT
95090 AAAATATTTATTTTATTT
1 -AAATATTTATTTTATTT
* * *
95108 TAATATTTA-ATCATTT
1 AAATATTTATTTTATTT
* *
95124 ATATATTTTTATTTATTT
1 AAATATTTAT-TTTATTT
95142 AAATA-TTATTTTA
1 AAATATTTATTTTA
95155 ATGTTTATAT
Statistics
Matches: 50, Mismatches: 10, Indels: 8
0.74 0.15 0.12
Matches are distributed among these distances:
16 20 0.40
17 18 0.36
18 12 0.24
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.62
Consensus pattern (17 bp):
AAATATTTATTTTATTT
Found at i:96464 original size:3 final size:3
Alignment explanation
Indices: 96458--96484 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
96448 TATTATTAAT
96458 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
96485 ATATTTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:96512 original size:15 final size:15
Alignment explanation
Indices: 96456--96515 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
96446 ATTATTATTA
*
96456 ATTAATAATAATAAT
1 ATTAATAATAAAAAT
*
96471 AATAATAATAATAAAT
1 ATTAATAATAA-AAAT
** *
96487 ATTTTTAATAAAAAC
1 ATTAATAATAAAAAT
96502 ATTAATAATAAAAA
1 ATTAATAATAAAAA
96516 AGAAAACAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
15 25 0.69
16 11 0.31
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (15 bp):
ATTAATAATAAAAAT
Found at i:96902 original size:21 final size:20
Alignment explanation
Indices: 96863--96902 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
96853 GGAGAGAGCT
* *
96863 TTTTTTTTGAAAAATGAAAA
1 TTTTTTTTAAAAAAGGAAAA
96883 TTTTTTTTAAAACAAGGAAA
1 TTTTTTTTAAAA-AAGGAAA
96903 CAAAATGAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (20 bp):
TTTTTTTTAAAAAAGGAAAA
Found at i:97466 original size:29 final size:29
Alignment explanation
Indices: 97425--97820 Score: 292
Period size: 29 Copynumber: 13.5 Consensus size: 29
97415 CTAAATGTCT
* **
97425 AAAAATTACATTTTTACCCCCGAACTTTT
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* * *
97454 AAAAATTCCATTTTTAACCTCGAAACATCC
1 AAAAATTCCATTTTTACCCCCG-AACTTCC
* *
97484 AAAAATTCCATTTTTACCCACGAACTTCA
1 AAAAATTCCATTTTTACCCCCGAACTTCC
*
97513 AAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
***
97542 AAAAATTCCATTTTTGACCCAAAAACTTCC
1 AAAAATTCCATTTTT-ACCCCCGAACTTCC
*
97572 AAAAATTCCATTTTTACCCCCGAACCTT-T
1 AAAAATTCCATTTTTACCCCCGAA-CTTCC
*
97601 AAAAATTCCATTTTTGA-CCCTGAGACTTCC
1 AAAAATTCCATTTTT-ACCCCCGA-ACTTCC
* * *
97631 AAAAATTCCATTTTTACTCCTGAACCTCC
1 AAAAATTCCATTTTTACCCCCGAACTTCC
* * *
97660 AAAATTTCTATTTTTGA--CCCGAAACTTTC
1 AAAAATTCCATTTTT-ACCCCCG-AACTTCC
* *
97689 AAAAATTACCA-TTTTGCCCCCGGA-TGTCC
1 AAAAATT-CCATTTTTACCCCCGAACT-TCC
* * *
97718 AAAAACTCCATTTTCGA-CCTCGAAAC-TCTC
1 AAAAATTCCATTTT-TACCCCCG-AACTTC-C
* *
97748 -AAAATTACC-CTTTTACCCCCGAA-TATCT
1 AAAAATT-CCATTTTTACCCCCGAACT-TCC
** *
97776 AAAAATTCCATTTTTAATCCCAAACTTTCC
1 AAAAATTCCATTTTTACCCCCGAAC-TTCC
*
97806 CAAAATTACCATTTT
1 AAAAATT-CCATTTT
97821 GCCCCCCGGG
Statistics
Matches: 291, Mismatches: 49, Indels: 52
0.74 0.12 0.13
Matches are distributed among these distances:
28 12 0.04
29 177 0.61
30 94 0.32
31 8 0.03
ACGTcount: A:0.34, C:0.28, G:0.05, T:0.33
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCCCGAACTTCC
Found at i:97498 original size:59 final size:59
Alignment explanation
Indices: 97425--97703 Score: 309
Period size: 59 Copynumber: 4.7 Consensus size: 59
97415 CTAAATGTCT
* ** * *
97425 AAAAATTACATTTTT-ACCCCCGAACTTTTAAAAATTCCATTTTTAACCTCGAAACATCC
1 AAAAATTCCATTTTTGACCCCCGAACTTCCAAAAATTCCATTTTTACCCTCG-AACCTCC
* * *
97484 AAAAATTCCATTTTT-ACCCACGAACTTCAAAAAATTCCATTTTTACCCTCGAACTTCC
1 AAAAATTCCATTTTTGACCCCCGAACTTCCAAAAATTCCATTTTTACCCTCGAACCTCC
*** * **
97542 AAAAATTCCATTTTTGACCCAAAAACTTCCAAAAATTCCATTTTTACCCCCGAACCTTT
1 AAAAATTCCATTTTTGACCCCCGAACTTCCAAAAATTCCATTTTTACCCTCGAACCTCC
*
97601 AAAAATTCCATTTTTGA-CCCTGAGACTTCCAAAAATTCCATTTTTACTCCT-GAACCTCC
1 AAAAATTCCATTTTTGACCCCCGA-ACTTCCAAAAATTCCATTTTTAC-CCTCGAACCTCC
* * *
97660 AAAATTTCTATTTTTGA--CCCGAAACTTTCAAAAATTACCATTTT
1 AAAAATTCCATTTTTGACCCCCG-AACTTCCAAAAATT-CCATTTT
97704 GCCCCCGGAT
Statistics
Matches: 192, Mismatches: 23, Indels: 10
0.85 0.10 0.04
Matches are distributed among these distances:
58 39 0.20
59 151 0.79
60 2 0.01
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.34
Consensus pattern (59 bp):
AAAAATTCCATTTTTGACCCCCGAACTTCCAAAAATTCCATTTTTACCCTCGAACCTCC
Found at i:97661 original size:88 final size:84
Alignment explanation
Indices: 97424--97703 Score: 294
Period size: 88 Copynumber: 3.2 Consensus size: 84
97414 CCTAAATGTC
* * ** *
97424 TAAAAATTACATTTTTACCCCCGAACTTTTAAAAATTCCATTTTTAACCTCGAAACATCCAAAAA
1 TAAAAATTCCATTTTTA-CCCTGAACTTCCAAAAATTCCATTTTTACCCT-G-AACATCCAAAAA
*
97489 TTCCATTTTTACCCACGAACTT
63 TTCCATTTTTACCCCCGAACTT
* ** *
97511 CAAAAAATTCCATTTTTACCCTCGAACTTCCAAAAATTCCATTTTTGACCCAAAAACTTCCAAAA
1 -TAAAAATTCCATTTTTACCCT-GAACTTCCAAAAATTCCATTTTT-ACCC-TGAACATCCAAAA
97576 ATTCCATTTTTACCCCCGAACCTT
62 ATTCCATTTTTACCCCCGAA-CTT
* *
97600 TAAAAATTCCATTTTTGACCCTGAGACTTCCAAAAATTCCATTTTTACTCCTGAACCTCCAAAAT
1 TAAAAATTCCATTTTT-ACCCTGA-ACTTCCAAAAATTCCATTTTTAC-CCTGAACATCCAAAAA
*
97665 TTCTATTTTTGA--CCCGAAACTT
63 TTCCATTTTT-ACCCCCG-AACTT
97687 TCAAAAATTACCATTTT
1 T-AAAAATT-CCATTTT
97704 GCCCCCGGAT
Statistics
Matches: 165, Mismatches: 16, Indels: 21
0.82 0.08 0.10
Matches are distributed among these distances:
87 11 0.07
88 112 0.68
89 42 0.25
ACGTcount: A:0.35, C:0.26, G:0.04, T:0.35
Consensus pattern (84 bp):
TAAAAATTCCATTTTTACCCTGAACTTCCAAAAATTCCATTTTTACCCTGAACATCCAAAAATTC
CATTTTTACCCCCGAACTT
Found at i:97750 original size:59 final size:57
Alignment explanation
Indices: 97539--97840 Score: 198
Period size: 59 Copynumber: 5.1 Consensus size: 57
97529 CCCTCGAACT
* * * * * **
97539 TCCAAAAATTCCATTTTTGACCCAAAAACTTCCAAAAATT-CCATTTTTACCCCCGAACC
1 TCCAAAAACTCCATTTTTGACCC-GAAACTTTC-AAAATTACCA-TTTTGCCCCCGGATA
** * * * ** * *
97598 TTTAAAAATTCCATTTTTGACCCTGAGACTTCCAAAAATT-CCATTTTTACTCCTGA-A
1 TCCAAAAACTCCATTTTTGACCC-GAAACTTTC-AAAATTACCATTTTGCCCCCGGATA
** * *
97655 CCTCCAAAATTTCTATTTTTGACCCGAAACTTTCAAAAATTACCATTTTGCCCCCGGATG
1 --TCCAAAAACTCCATTTTTGACCCGAAACTTTC-AAAATTACCATTTTGCCCCCGGATA
* * * * *
97715 TCCAAAAACTCCATTTTCGACCTCGAAACTCTCAAAATTACCCTTTTACCCCCGAATA
1 TCCAAAAACTCCATTTTTGACC-CGAAACTTTCAAAATTACCATTTTGCCCCCGGATA
* * * *
97773 TCTAAAAATTCCATTTTTAATCCC-AAACTTTCCCAAAATTACCATTTTGCCCCCCGGGTA
1 TCCAAAAACTCCATTTTTGA-CCCGAAACTTT--CAAAATTACCATTTTG-CCCCCGGATA
97833 TCCAAAAA
1 TCCAAAAA
97841 GTCTCATTCT
Statistics
Matches: 193, Mismatches: 41, Indels: 17
0.77 0.16 0.07
Matches are distributed among these distances:
57 6 0.03
58 78 0.40
59 94 0.49
60 15 0.08
ACGTcount: A:0.32, C:0.29, G:0.06, T:0.32
Consensus pattern (57 bp):
TCCAAAAACTCCATTTTTGACCCGAAACTTTCAAAATTACCATTTTGCCCCCGGATA
Found at i:109304 original size:115 final size:115
Alignment explanation
Indices: 109162--109378 Score: 319
Period size: 115 Copynumber: 1.9 Consensus size: 115
109152 TCAAACCCAC
* * * * * * * *
109162 GCTCGATGTGAGCAAATCTTCGAATCCCAGCTTCTTGATGAGA-TATTGAGAAGCAGGTCGAAGT
1 GCTCGATGTGAGAAAATCTTCGAATCCCAGCTTCCTGATGAGACAACTAAGAAGCAGGGCAAAGC
109226 AATAAAATGGTTAGCTTCCTGACGAGATACAGAGAAGTATACCAACTCAGG
66 AATAAAA-GGTTAGCTTCCTGACGAGATACAGAGAAGTATACCAACTCAGG
*
109277 GCTCGATGTGAGAAAATCTTTGAATCCCAGCTTCCTGATGAGACAACTAAGAAGCAGGGCAAAGC
1 GCTCGATGTGAGAAAATCTTCGAATCCCAGCTTCCTGATGAGACAACTAAGAAGCAGGGCAAAGC
* *
109342 AATAAAAGGTTAGCTTCCTGATGAGATACTGAGAAGT
66 AATAAAAGGTTAGCTTCCTGACGAGATACAGAGAAGT
109379 GGACCAAATT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
115 68 0.76
116 22 0.24
ACGTcount: A:0.34, C:0.18, G:0.24, T:0.24
Consensus pattern (115 bp):
GCTCGATGTGAGAAAATCTTCGAATCCCAGCTTCCTGATGAGACAACTAAGAAGCAGGGCAAAGC
AATAAAAGGTTAGCTTCCTGACGAGATACAGAGAAGTATACCAACTCAGG
Found at i:109597 original size:202 final size:200
Alignment explanation
Indices: 109240--109873 Score: 772
Period size: 206 Copynumber: 3.1 Consensus size: 200
109230 AAATGGTTAG
** * * * * *
109240 CTTCCTGACGAGATACAGAGAAGTATACCAACTCAGGGCTCGATGTGAGAAAATCTTTGAATCCC
1 CTTCCTGATAAGATACAAAGAAGAATACCAACTCA-GGCTCGATGTGAGCAAATCTTCGAACCCC
* *
109305 AGCTTCCTGATGAGACAACTAAGAAGCAGGGCAAAGCAATAAAA-GGTTAGCTTCCTGATGAGAT
65 AGCTTCCTGATGAGA-TACTAAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCCTGATGAGAT
* * * * *
109369 ACTGAGAAGTGGACCAAATTCGTCTTCCTGATGAGGTACGGAGAAGTGGATTGAAACAAGTAAAG
129 ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATG
109434 CGGTCAT
194 CGGTCAT
* **
109441 CTTCCTGATAAGATACAAAGAAGAATACCAACTCGAGGCTCAATGCCAGCAAATCTTCGAACCCC
1 CTTCCTGATAAGATACAAAGAAGAATACCAACTC-AGGCTCGATGTGAGCAAATCTTCGAA-CCC
*
109506 CAGCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAATGGTTAACTTCCTGATGAGAT
64 CAGCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCCTGATGAGAT
* *
109571 ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGCGGATTGAAACAAGCGATG
129 ACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATG
*
109636 CGATCAT
194 CGGTCAT
* * * * **
109643 CTTCCTGATGAGATATTGAGAAGAGGACCGAAT-CAAACCCACACTCGATGTGAGCAAATCTTCG
1 CTTCCTGATAAGATA--CA-AAGA--A--GAATACCAACTCAGGCTCGATGTGAGCAAATCTTCG
* * *
109707 AACCCCAGCTTCCTGATGAGATATTGAGAAGCAAGTCGAAA-CAATAAAATGGTTAGCTTCCTGA
59 AACCCCAGCTTCCTGATGAGATACTAAGAAGCAGGTC-AAAGCAATAAAATGGTTAGCTTCCTGA
* * * * * **
109771 TGAGATACGGAGAAGTGAACCAAATCCGTCTTCCTGATGAAACACAAAGAAGTGGATCAAAACAA
123 TGAGATACTGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAA
109836 GTGATGCGGTCAT
188 GTGATGCGGTCAT
**
109849 CTTCCT-AGTAAGATACTGAGAAGAA
1 CTTCCTGA-TAAGATACAAAGAAGAA
109874 GGCCAAATCA
Statistics
Matches: 373, Mismatches: 48, Indels: 26
0.83 0.11 0.06
Matches are distributed among these distances:
199 3 0.01
201 77 0.21
202 116 0.31
203 3 0.01
204 1 0.00
205 5 0.01
206 134 0.36
207 25 0.07
208 5 0.01
209 4 0.01
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.22
Consensus pattern (200 bp):
CTTCCTGATAAGATACAAAGAAGAATACCAACTCAGGCTCGATGTGAGCAAATCTTCGAACCCCA
GCTTCCTGATGAGATACTAAGAAGCAGGTCAAAGCAATAAAATGGTTAGCTTCCTGATGAGATAC
TGAGAAGTGAACCAAATTCGTCTTCCTGATGAGATACAGAGAAGTGGATTGAAACAAGTGATGCG
GTCAT
Found at i:110279 original size:22 final size:20
Alignment explanation
Indices: 110247--110289 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 20
110237 AAATTAGTTT
110247 AAATTTATTTTTAAATTTAA
1 AAATTTATTTTTAAATTTAA
110267 AAATTTATCTTTTTAAATTTAA
1 AAATTTA--TTTTTAAATTTAA
110289 A
1 A
110290 TTTGCTTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.33
22 14 0.67
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (20 bp):
AAATTTATTTTTAAATTTAA
Found at i:112251 original size:30 final size:30
Alignment explanation
Indices: 112134--112499 Score: 304
Period size: 29 Copynumber: 12.5 Consensus size: 30
112124 TAAATTATCT
* * *
112134 AAAAATTACATTTTTACCCCCG-AACGTCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
112163 AAAAATTCCATTTTTGACCC-CGAGAACTTCC
1 AAAAATTCCATTTTT-ACCCTCGA-AACTTCC
112194 AAAAATTCCATTTTTACCCTC-AAACTTCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
*
112223 AAACATTCCATTTTTACCCTCGAAACTTCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
*
112253 AAAAATTCCATTTTT-CCC-CCAAACTTCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
*
112281 AAAAATTCCATTTTTGA-CCTCGAGACTTCC
1 AAAAATTCCATTTTT-ACCCTCGAAACTTCC
*
112311 AAAAATTCCATTTTTACCCTCG-AACCTCC
1 AAAAATTCCATTTTTACCCTCGAAACTTCC
* * *
112340 AAAATTTCCATTTCTGA-CC-CGAAACTTTC
1 AAAAATTCCATTT-TTACCCTCGAAACTTCC
* *
112369 AAAAATTACCA-TTTTGCCCTCG-GA-TGTCC
1 AAAAATT-CCATTTTTACCCTCGAAACT-TCC
* * * *
112398 AAAAACTCTATTTTCGA-CCTTGAAAC-TCTC
1 AAAAATTCCATTTT-TACCCTCGAAACTTC-C
* *
112428 -AAAATTACC-CTTTTACCC-CG-AA-TGTCT
1 AAAAATT-CCATTTTTACCCTCGAAACT-TCC
*
112455 AAAAATTCCATTTTTAACCTCG-AACTTTCC
1 AAAAATTCCATTTTTACCCTCGAAAC-TTCC
*
112485 CAAAATTACCATTTT
1 AAAAATT-CCATTTT
112500 GGCCCCCGGG
Statistics
Matches: 273, Mismatches: 34, Indels: 58
0.75 0.09 0.16
Matches are distributed among these distances:
27 4 0.01
28 47 0.17
29 115 0.42
30 77 0.28
31 30 0.11
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.33
Consensus pattern (30 bp):
AAAAATTCCATTTTTACCCTCGAAACTTCC
Found at i:112381 original size:59 final size:60
Alignment explanation
Indices: 112134--112499 Score: 380
Period size: 58 Copynumber: 6.2 Consensus size: 60
112124 TAAATTATCT
* *
112134 AAAAATTA-CATTTTTACCCCCGAACGTCCAAAAATTCCATTTTTGACCCCGAGAACTTCC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGACCTCGA-AACTTCC
* * *
112194 AAAAATT-CCATTTTTACCCTCAAACTTCCAAACATTCCATTTTT-ACCCTCGAAACTTCC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGA-CCTCGAAACTTCC
* * * *
112253 AAAAATT-CCATTTTT-CCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGAGACTTCC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
* * * *
112311 AAAAATT-CCATTTTTACCCTCGAACCTCCAAAATTTCCATTTCTGACC-CGAAACTTTC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
* * * * * * *
112369 AAAAATTACCA-TTTTGCCCTCGGATGTCCAAAAACTCTATTTTCGACCTTGAAAC-TCTC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGACCTCGAAACTTC-C
* * * *
112428 -AAAATTACC-CTTTTACCC-CGAATGTCTAAAAATTCCATTTTTAACCTCG-AACTTTCC
1 AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGACCTCGAAAC-TTCC
*
112485 CAAAATTACCATTTT
1 AAAAATTACCATTTT
112500 GGCCCCCGGG
Statistics
Matches: 259, Mismatches: 35, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
56 3 0.01
57 25 0.10
58 124 0.48
59 63 0.24
60 44 0.17
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.33
Consensus pattern (60 bp):
AAAAATTACCATTTTTACCCTCGAACGTCCAAAAATTCCATTTTTGACCTCGAAACTTCC
Found at i:113770 original size:104 final size:101
Alignment explanation
Indices: 113623--113831 Score: 278
Period size: 104 Copynumber: 2.0 Consensus size: 101
113613 AATTGGTTCC
*
113623 GAATAGGATATTCAATTATTTAGGTTCAAAGAAAAATCATACCCAACACGTTAATG-CACAATTC
1 GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTT--TGACACAATTC
* *
113687 CTCGACTTCCCTAAAATAAA-AGAATATTGTCTCGATTGTT
64 CTCGACTTCCCT-AAATAAAGA-AACATTGCCTCGATT-TT
* * * *
113727 GAATAGGATATTCAATTACTTAGGTTCGAAGAAAAATCGTACCCAATACGTTTGACCACAATTTC
1 GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTTTGA-CACAATTCC
*
113792 TCGAGTTCCCTAAATAAAGAAACATTGCCTCGATTTT
65 TCGACTTCCCTAAATAAAGAAACATTGCCTCGATTTT
113829 GAA
1 GAA
113832 AATATTTATG
Statistics
Matches: 94, Mismatches: 8, Indels: 8
0.85 0.07 0.07
Matches are distributed among these distances:
102 7 0.07
103 20 0.21
104 67 0.71
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (101 bp):
GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAACACGTTTGACACAATTCCT
CGACTTCCCTAAATAAAGAAACATTGCCTCGATTTT
Found at i:114242 original size:60 final size:59
Alignment explanation
Indices: 114178--114385 Score: 197
Period size: 60 Copynumber: 3.5 Consensus size: 59
114168 AGTTCAAAAA
** *
114178 CAAAATTTTGAAAAGTTCGAGGGTCAAAAACAAAATTTTGGAAAGTTTGATGGTCAAATT
1 CAAAATTTTGAAAAGTTCGAGGGTCAAAAATGAAATTTTGGAAAGTTTG-GGGTCAAATT
* * * ** *
114238 CAAAATTTTAAAAAGTTTG-GGGTTAAATTTGAATTTTTGGAAAGTTTTGGGGTCAAATT
1 CAAAATTTTGAAAAGTTCGAGGGTCAAAAATGAAATTTTGGAAAG-TTTGGGGTCAAATT
* * ** * *
114297 CAAATTTTTGGAAAGTTTAAGGGTCAAAAATGAAATTTTAGAAAAAG-TAGGGGTCAAATT
1 CAAAATTTTGAAAAGTTCGAGGGTCAAAAATGAAATTTT-G-GAAAGTTTGGGGTCAAATT
* *
114357 CGAATTTTTGAAAAGTTCGTA-GGTCAAAA
1 CAAAATTTTGAAAAGTTCG-AGGGTCAAAA
114386 TATCATTTTA
Statistics
Matches: 120, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
59 43 0.36
60 71 0.59
61 2 0.02
62 4 0.03
ACGTcount: A:0.39, C:0.06, G:0.21, T:0.33
Consensus pattern (59 bp):
CAAAATTTTGAAAAGTTCGAGGGTCAAAAATGAAATTTTGGAAAGTTTGGGGTCAAATT
Found at i:114255 original size:30 final size:30
Alignment explanation
Indices: 114171--114341 Score: 130
Period size: 30 Copynumber: 5.7 Consensus size: 30
114161 AAAAACAAGT
*
114171 TCAAAAACAAAATTTTGAAAAGTTCGAGGG
1 TCAAAAACAAAATTTTGAAAAGTTTGAGGG
* *
114201 TCAAAAACAAAATTTTGGAAAGTTTGATGG
1 TCAAAAACAAAATTTTGAAAAGTTTGAGGG
** *
114231 TCAAATTCAAAATTTTAAAAAGTTTG-GGG
1 TCAAAAACAAAATTTTGAAAAGTTTGAGGG
* **** * *
114260 TTAAATTTGAATTTTTGGAAAGTTTTG-GGG
1 TCAAAAACAAAATTTTGAAAAG-TTTGAGGG
** * * *
114290 TCAAATTCAAATTTTTGGAAAGTTTAAGGG
1 TCAAAAACAAAATTTTGAAAAGTTTGAGGG
**
114320 TCAAAAATGAAATTTTAGAAAA
1 TCAAAAACAAAATTTT-GAAAA
114342 AGTAGGGGTC
Statistics
Matches: 114, Mismatches: 24, Indels: 5
0.80 0.17 0.03
Matches are distributed among these distances:
29 21 0.18
30 89 0.78
31 4 0.04
ACGTcount: A:0.42, C:0.06, G:0.19, T:0.33
Consensus pattern (30 bp):
TCAAAAACAAAATTTTGAAAAGTTTGAGGG
Found at i:114282 original size:89 final size:89
Alignment explanation
Indices: 114183--114385 Score: 225
Period size: 89 Copynumber: 2.3 Consensus size: 89
114173 AAAAACAAAA
* * *
114183 TTTTGAAAAGTTCGAGGGTCAAAAACAAAATTTTGGAAAGTTTGATGGTC-AAATTCAAAATTTT
1 TTTTGAAAAGTTCGAGGGTCAAAAACAAAATTTTGGAAAGTTTAAGGGTCAAAAAT-AAAATTTT
* * *
114247 -AAAAAGTTTGGGGTTAAATTTGAAT
65 AAAAAAG-TAGGGGTCAAATTCGAAT
* * ** * *
114272 TTTTGGAAAGTTTTG-GGGTCAAATTCAAATTTTTGGAAAGTTTAAGGGTCAAAAATGAAATTTT
1 TTTTGAAAAG-TTCGAGGGTCAAAAACAAAATTTTGGAAAGTTTAAGGGTCAAAAATAAAATTTT
114336 AGAAAAAGTAGGGGTCAAATTCGAAT
65 A-AAAAAGTAGGGGTCAAATTCGAAT
114362 TTTTGAAAAGTTCGTA-GGTCAAAA
1 TTTTGAAAAGTTCG-AGGGTCAAAA
114386 TATCATTTTA
Statistics
Matches: 93, Mismatches: 15, Indels: 11
0.78 0.13 0.09
Matches are distributed among these distances:
89 49 0.53
90 38 0.41
91 6 0.06
ACGTcount: A:0.38, C:0.06, G:0.22, T:0.34
Consensus pattern (89 bp):
TTTTGAAAAGTTCGAGGGTCAAAAACAAAATTTTGGAAAGTTTAAGGGTCAAAAATAAAATTTTA
AAAAAGTAGGGGTCAAATTCGAAT
Found at i:119378 original size:58 final size:59
Alignment explanation
Indices: 119286--119399 Score: 169
Period size: 58 Copynumber: 1.9 Consensus size: 59
119276 TTTGATAGTT
* * *
119286 GTCTTCAATTTTAGGACCGTTTTCTGTTAAAGCTTTTAT-AGTGGCAAGTTTCACATCTA
1 GTCTTCAATTTCAGGACCATTTTCTGTTAAAGCTTTTATAAG-GGCAAGTATCACATCTA
*
119345 GTCTTCAATTTCAGGATCATTTT-TGTTAAAGCTTTTATAAGGGCAAGTATCACAT
1 GTCTTCAATTTCAGGACCATTTTCTGTTAAAGCTTTTATAAGGGCAAGTATCACAT
119400 TCTTTTAAGA
Statistics
Matches: 50, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
58 28 0.56
59 22 0.44
ACGTcount: A:0.26, C:0.16, G:0.17, T:0.41
Consensus pattern (59 bp):
GTCTTCAATTTCAGGACCATTTTCTGTTAAAGCTTTTATAAGGGCAAGTATCACATCTA
Found at i:126433 original size:44 final size:44
Alignment explanation
Indices: 126384--126474 Score: 182
Period size: 44 Copynumber: 2.1 Consensus size: 44
126374 CTTTGTGAAA
126384 TACTTTCTTCAGTATGAAGTTCTAACCATTAATGATATCAATTT
1 TACTTTCTTCAGTATGAAGTTCTAACCATTAATGATATCAATTT
126428 TACTTTCTTCAGTATGAAGTTCTAACCATTAATGATATCAATTT
1 TACTTTCTTCAGTATGAAGTTCTAACCATTAATGATATCAATTT
126472 TAC
1 TAC
126475 ATGACAAAGA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.32, C:0.16, G:0.09, T:0.43
Consensus pattern (44 bp):
TACTTTCTTCAGTATGAAGTTCTAACCATTAATGATATCAATTT
Found at i:131690 original size:2 final size:2
Alignment explanation
Indices: 131683--131712 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
131673 TATTAGTACA
131683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
131713 TGGGGATTAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:133330 original size:20 final size:20
Alignment explanation
Indices: 133305--133376 Score: 76
Period size: 20 Copynumber: 3.5 Consensus size: 20
133295 TTTAATTTCA
133305 AATTAACTATTAACTCTTTG
1 AATTAACTATTAACTCTTTG
* **
133325 AATTAACTAATTTTAA--GTTCA
1 AATTAACT-A--TTAACTCTTTG
133346 AATTAACTATTAACTCTTTG
1 AATTAACTATTAACTCTTTG
133366 AATTAACTATT
1 AATTAACTATT
133377 TTTTAAATAA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
18 4 0.10
20 22 0.54
21 11 0.27
23 4 0.10
ACGTcount: A:0.39, C:0.12, G:0.04, T:0.44
Consensus pattern (20 bp):
AATTAACTATTAACTCTTTG
Found at i:133337 original size:41 final size:41
Alignment explanation
Indices: 133291--133379 Score: 160
Period size: 41 Copynumber: 2.2 Consensus size: 41
133281 ATTTTATCTG
*
133291 TAATTTTAATTTCAAATTAACTATTAACTCTTTGAATTAAC
1 TAATTTTAAGTTCAAATTAACTATTAACTCTTTGAATTAAC
133332 TAATTTTAAGTTCAAATTAACTATTAACTCTTTGAATTAAC
1 TAATTTTAAGTTCAAATTAACTATTAACTCTTTGAATTAAC
*
133373 TATTTTT
1 TAATTTT
133380 TAAATAATTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 46 1.00
ACGTcount: A:0.37, C:0.11, G:0.03, T:0.48
Consensus pattern (41 bp):
TAATTTTAAGTTCAAATTAACTATTAACTCTTTGAATTAAC
Found at i:138767 original size:5 final size:5
Alignment explanation
Indices: 138759--138786 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
138749 ATAAAAGAAA
138759 AATCT AATCT AATCT AATCT AATCT AAT
1 AATCT AATCT AATCT AATCT AATCT AAT
138787 GTTATAAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (5 bp):
AATCT
Found at i:143023 original size:59 final size:58
Alignment explanation
Indices: 142941--143083 Score: 166
Period size: 58 Copynumber: 2.5 Consensus size: 58
142931 AGTTTCGAAG
* *
142941 AGTTTGA-GGTTAAAATGTGATTTTGGGAAATTTTAGGGTC-AAAATGTGATTTTTAGAA
1 AGTTTGAGGGTCAAAATGTGATTTTGGGAAA-TTTAGGGGCTAAAATGT-ATTTTTAGAA
** * *
142999 AGTTT-AGGAGTCAAAATGTGATTTTAAGAAATTTAGGGGCTTAAATGTATTTTTGGAA
1 AGTTTGAGG-GTCAAAATGTGATTTTGGGAAATTTAGGGGCTAAAATGTATTTTTAGAA
* *
143057 AGTTTGAGGGTTAAAATGTAATTTTGG
1 AGTTTGAGGGTCAAAATGTGATTTTGG
143084 AAAAGTTGTC
Statistics
Matches: 71, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
57 1 0.01
58 42 0.59
59 28 0.39
ACGTcount: A:0.33, C:0.02, G:0.26, T:0.39
Consensus pattern (58 bp):
AGTTTGAGGGTCAAAATGTGATTTTGGGAAATTTAGGGGCTAAAATGTATTTTTAGAA
Found at i:143082 original size:29 final size:29
Alignment explanation
Indices: 142941--143146 Score: 146
Period size: 29 Copynumber: 7.2 Consensus size: 29
142931 AGTTTCGAAG
* *
142941 AGTTTGA-GGTTAAAATGTGATTTTGGGAA
1 AGTTTGAGGGTCAAAATGTAATTTT-GGAA
* * *
142970 A-TTTTAGGGTCAAAATGTGATTTTTAGAA
1 AGTTTGAGGGTCAAAATGT-AATTTTGGAA
* *
142999 AGTTT-AGGAGTCAAAATGTGATTTTAAGAA
1 AGTTTGAGG-GTCAAAATGTAATTTT-GGAA
* * *
143029 A-TTT-AGGGGCTTAAATGTATTTTTGGAA
1 AGTTTGAGGGTC-AAAATGTAATTTTGGAA
*
143057 AGTTTGAGGGTTAAAATGTAATTTTGGAAA
1 AGTTTGAGGGTCAAAATGTAATTTTGG-AA
143087 AG-TT----GTCAAAATGTAATTTTGGAA
1 AGTTTGAGGGTCAAAATGTAATTTTGGAA
* *
143111 AGGTTCGAGAGTCAAAA-GTAATTTTGGAAA
1 A-GTTTGAGGGTCAAAATGTAATTTTGG-AA
143141 AGTTTG
1 AGTTTG
143147 GAGATAAAAA
Statistics
Matches: 142, Mismatches: 19, Indels: 32
0.74 0.10 0.17
Matches are distributed among these distances:
24 3 0.02
25 18 0.13
26 1 0.01
28 10 0.07
29 70 0.49
30 40 0.28
ACGTcount: A:0.35, C:0.03, G:0.25, T:0.37
Consensus pattern (29 bp):
AGTTTGAGGGTCAAAATGTAATTTTGGAA
Found at i:143098 original size:25 final size:26
Alignment explanation
Indices: 143069--143144 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 26
143059 TTTGAGGGTT
143069 AAAATGTAATTTTGGAAAAGTT-GTC
1 AAAATGTAATTTTGGAAAAGTTAGTC
*
143094 AAAATGTAATTTTGGAAAGGTTCGAGAGTC
1 AAAATGTAATTTTGGAAAAGTT----AGTC
143124 AAAA-GTAATTTTGGAAAAGTT
1 AAAATGTAATTTTGGAAAAGTT
143145 TGGAGATAAA
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
25 21 0.48
29 16 0.36
30 7 0.16
ACGTcount: A:0.41, C:0.04, G:0.22, T:0.33
Consensus pattern (26 bp):
AAAATGTAATTTTGGAAAAGTTAGTC
Found at i:143132 original size:54 final size:54
Alignment explanation
Indices: 143041--143144 Score: 156
Period size: 54 Copynumber: 1.9 Consensus size: 54
143031 TTAGGGGCTT
* * * *
143041 AAATGTATTTTTGGAAAGTTTGAGGGTTAAAATGTAATTTTGGAAAAGTTGTCA
1 AAATGTAATTTTGGAAAGTTCGAGAGTCAAAATGTAATTTTGGAAAAGTTGTCA
143095 AAATGTAATTTTGGAAAGGTTCGAGAGTCAAAA-GTAATTTTGGAAAAGTT
1 AAATGTAATTTTGGAAA-GTTCGAGAGTCAAAATGTAATTTTGGAAAAGTT
143145 TGGAGATAAA
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 33 0.73
55 12 0.27
ACGTcount: A:0.38, C:0.03, G:0.24, T:0.36
Consensus pattern (54 bp):
AAATGTAATTTTGGAAAGTTCGAGAGTCAAAATGTAATTTTGGAAAAGTTGTCA
Done.