Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032251.1 Gossypioides kirkii chromosome KI_09
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: 38743931
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2800 characters in sequence are not A, C, G, or T
File 24 of 144
Found at i:5966459 original size:29 final size:28
Alignment explanation
Indices: 5966130--5966461 Score: 180
Period size: 29 Copynumber: 11.5 Consensus size: 28
5966120 ACTTGGGGGC
* * *
5966130 AAAATGGTAA-TTTGGAACTTACGGGGGC
1 AAAATGGTAATTTTGGAAATT-CGAGGGT
5966158 AAAATGGTAATTTTTGGTGAAA-TCG-GGGT
1 AAAATGGTAA-TTTT-G-GAAATTCGAGGGT
* *
5966187 CAAAAATGG-AATTTTGGAAAATT-TAGGGG
1 --AAAATGGTAATTTTGG-AAATTCGAGGGT
*
5966216 AAAATGGTGATTTTGGTGAAA-TCG-GGGTT
1 AAAATGGTAATTTT-G-GAAATTCGAGGG-T
5966245 AAAAATGG-AATTTTGGAAAGTTC-AGGGGT
1 -AAAATGGTAATTTTGGAAA-TTCGA-GGGT
5966274 AAAATGGTAATTTTGGTGAAATT-G-GGGTT
1 AAAATGGTAATTTT-G-GAAATTCGAGGG-T
* *
5966303 AAAAATAG-AATTTTGGAAAGTTCAAGGGT
1 -AAAATGGTAATTTTGGAAA-TTCGAGGGT
5966332 AAAATGGTAATTTTGGTGAAATT--AGGGTT
1 AAAATGGTAATTTT-G-GAAATTCGAGGG-T
5966361 AAAAATGG-AATTTTGGAAAGTTCGAGGGT
1 -AAAATGGTAATTTTGGAAA-TTCGAGGGT
*
5966390 -AAATAGTAATTTTTGGTGAAA-TCG-GGGTT
1 AAAATGGTAA-TTTT-G-GAAATTCGAGGG-T
*
5966419 AAAAAT-GAAATTTTGGAAAGTTCGAGGGT
1 -AAAATGGTAATTTTGGAAA-TTCGAGGGT
5966448 AAAATGGTAATTTT
1 AAAATGGTAATTTT
5966462 TGGACAGTCT
Statistics
Matches: 243, Mismatches: 14, Indels: 93
0.69 0.04 0.27
Matches are distributed among these distances:
27 29 0.12
28 61 0.25
29 74 0.30
30 51 0.21
31 25 0.10
32 3 0.01
ACGTcount: A:0.36, C:0.03, G:0.29, T:0.32
Consensus pattern (28 bp):
AAAATGGTAATTTTGGAAATTCGAGGGT
Found at i:5967484 original size:3 final size:3
Alignment explanation
Indices: 5967476--5967501 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5967466 CCATTGGGTT
5967476 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5967502 TTTAAACGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5968577 original size:37 final size:36
Alignment explanation
Indices: 5968536--5968735 Score: 155
Period size: 37 Copynumber: 5.4 Consensus size: 36
5968526 AACTTGCTCT
5968536 TACTTCAATTTCAGAGATAAATACGTGTTATCCACTC
1 TACTTCAATTTCAGAGATAAA-ACGTGTTATCCACTC
* * *
5968573 TACTTCAATTTCAAGAGGATTGGAAAA-GAT-CT-TGCTCT-
1 TACTTCAATTTC-AGA-GA-T--AAAACG-TGTTATCCACTC
5968611 TACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
1 TACTTCAATTTCAGAGATAAA-ACGTGTTATCCACTC
* **
5968648 TACTTCAATTTCAAAAGGATAGGAAA--TG--ATCTTGCTC
1 TACTTCAATTTC-AGA-GATA--AAACGTGTTATC-CACTC
5968685 TTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTC
1 -TACTTCAATTTCAGAGATAAA-ACGTGTTATCCACTC
5968723 TACTTCAATTTCA
1 TACTTCAATTTCA
5968736 AGAGGATAGG
Statistics
Matches: 129, Mismatches: 12, Indels: 44
0.70 0.06 0.24
Matches are distributed among these distances:
33 3 0.02
34 4 0.03
35 4 0.03
36 13 0.10
37 47 0.36
38 34 0.26
39 13 0.10
40 4 0.03
41 4 0.03
42 3 0.02
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.34
Consensus pattern (36 bp):
TACTTCAATTTCAGAGATAAAACGTGTTATCCACTC
Found at i:5968651 original size:75 final size:75
Alignment explanation
Indices: 5968528--5968831 Score: 529
Period size: 75 Copynumber: 4.0 Consensus size: 75
5968518 TTATAATAAA
*
5968528 CTTGCTCTTACTTCAATTTCAGAGATAAATACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
*
5968593 TGGAAAAGAT
66 AGGAAAAGAT
*
5968603 CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAAAGGAT
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
*
5968668 AGGAAATGAT
66 AGGAAAAGAT
5968678 CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
5968743 AGGAAAAGAT
66 AGGAAAAGAT
* *
5968753 CTTGCTCTTACTTCAATTTCAGAGATAAAGACTTAG-TATCCAACTTTACTTCAATTTCAAGAGG
1 CTTGCTCTTACTTCAATTTCAGAGATAAAGACGT-GTTATCC-ACTCTACTTCAATTTCAAGAGG
5968817 ATAGGAAAAGAT
64 ATAGGAAAAGAT
5968829 CTT
1 CTT
5968832 AGTGCGGTCT
Statistics
Matches: 219, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
75 182 0.83
76 37 0.17
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Consensus pattern (75 bp):
CTTGCTCTTACTTCAATTTCAGAGATAAAGACGTGTTATCCACTCTACTTCAATTTCAAGAGGAT
AGGAAAAGAT
Found at i:5968802 original size:38 final size:37
Alignment explanation
Indices: 5968535--5968811 Score: 128
Period size: 38 Copynumber: 7.4 Consensus size: 37
5968525 AAACTTGCTC
* *
5968535 TTACTTCAATTTCAGAGATAAATACGT-GTTATCCACT
1 TTACTTCAATTTCAGAGATAAAGACATAG-TATCCACT
* ** * **
5968572 CTACTTCAATTTCAAGAGGAT-TGGA-AAAG-ATCTTGCT
1 TTACTTCAATTTC-AGA-GATAAAGACATAGTATC-CACT
*
5968609 CTTACTTCAATTTCAGAGATAAAGACGT-GTTATCCACT
1 -TTACTTCAATTTCAGAGATAAAGACATAG-TATCCACT
* * * * **
5968647 CTACTTCAATTTCAAAAGGAT-AGGAAAT-G-ATCTTGCT
1 TTACTTCAATTTC-AGA-GATAAAGACATAGTATC-CACT
*
5968684 CTTACTTCAATTTCAGAGATAAAGACGT-GTTATCCACT
1 -TTACTTCAATTTCAGAGATAAAGACATAG-TATCCACT
* * * **
5968722 CTACTTCAATTTCAAGAGGAT-AGGA-AAAG-ATCTTGCT
1 TTACTTCAATTTC-AGA-GATAAAGACATAGTATC-CACT
*
5968759 CTTACTTCAATTTCAGAGATAAAGACTTAGTATCCAACT
1 -TTACTTCAATTTCAGAGATAAAGACATAGTATCC-ACT
5968798 TTACTTCAATTTCA
1 TTACTTCAATTTCA
5968812 AGAGGATAGG
Statistics
Matches: 174, Mismatches: 41, Indels: 49
0.66 0.16 0.19
Matches are distributed among these distances:
36 18 0.10
37 61 0.35
38 75 0.43
39 20 0.11
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (37 bp):
TTACTTCAATTTCAGAGATAAAGACATAGTATCCACT
Found at i:5980743 original size:29 final size:30
Alignment explanation
Indices: 5980593--5980742 Score: 223
Period size: 30 Copynumber: 5.0 Consensus size: 30
5980583 CCCTAAATTG
*
5980593 TCCAGAAATTATATTTTGACCCCAAAACTTT
1 TCCA-AAATTACATTTTGACCCCAAAACTTT
5980624 TCCAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
5980654 TCTAAAATTACATTTTGACCCCAAAACTTT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
*
5980684 TCCAAAATCACATTTTGACCCCAAAAC-TT
1 TCCAAAATTACATTTTGACCCCAAAACTTT
* *
5980713 TCAAAAATTATCATTTT-ACCCCCAAACTTT
1 TCCAAAATTA-CATTTTGACCCCAAAACTTT
5980743 CCTAAATCCC
Statistics
Matches: 110, Mismatches: 7, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
29 19 0.17
30 87 0.79
31 4 0.04
ACGTcount: A:0.37, C:0.26, G:0.03, T:0.34
Consensus pattern (30 bp):
TCCAAAATTACATTTTGACCCCAAAACTTT
Found at i:5980942 original size:29 final size:29
Alignment explanation
Indices: 5980746--5980940 Score: 121
Period size: 30 Copynumber: 6.6 Consensus size: 29
5980736 AAACTTTCCT
* *
5980746 AAATCCCATTTTTAACCCCG-AT-TTCACCA
1 AAATTCCATTTTTAACCCCGAATCTT--CTA
* * * *
5980775 AAATTTACAATTTTACCCCCGAATCTTTTA
1 AAA-TTCCATTTTTAACCCCGAATCTTCTA
* ** *
5980805 AAATTCCATTTTTAACCCCGACTTCACCAA
1 AAATTCCATTTTTAACCCCGA-ATCTTCTA
5980835 AAATTACCA-TTTT-ACCCTCGAATCTTCTA
1 AAATT-CCATTTTTAACCC-CGAATCTTCTA
** ** *
5980864 AAATTCCATTTTTAACCCCGGTTTCACCAA
1 AAATTCCATTTTTAACCCC-GAATCTTCTA
* *
5980894 AAATTACCA-TTTTACCCCTCGAATCTTTTA
1 AAATT-CCATTTTTAACCC-CGAATCTTCTA
5980924 AAATTCCATTTTTAACC
1 AAATTCCATTTTTAACC
5980941 TCAATGACAC
Statistics
Matches: 123, Mismatches: 31, Indels: 23
0.69 0.18 0.13
Matches are distributed among these distances:
28 3 0.02
29 39 0.32
30 70 0.57
31 9 0.07
32 2 0.02
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (29 bp):
AAATTCCATTTTTAACCCCGAATCTTCTA
Found at i:5980952 original size:60 final size:59
Alignment explanation
Indices: 5980714--5980972 Score: 326
Period size: 59 Copynumber: 4.4 Consensus size: 59
5980704 CCAAAACTTT
* * * *
5980714 CAAAAATTATCATTTTACCCCC-AAACTTTCCT-AAATCCCATTTTTAACCCCGATTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTT--TAAAATTCCATTTTTAACCCCAATTTCAC
* * * *
5980773 CAAAATTTACAATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAATTTCAC
* * **
5980832 CAAAAATTACCATTTTACCCTCGAATCTTCTAAAATTCCATTTTTAACCCCGGTTTCAC
1 CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAATTTCAC
* **
5980891 CAAAAATTACCATTTTACCCCTCGAATCTTTTAAAATTCCATTTTTAACCTCAATGACAC
1 CAAAAATTACCATTTTACCCC-CGAATCTTTTAAAATTCCATTTTTAACCCCAATTTCAC
*
5980951 C-AAAATTACCATTTTGCCCCCG
1 CAAAAATTACCATTTTACCCCCG
5980973 GGTATCCATA
Statistics
Matches: 177, Mismatches: 20, Indels: 7
0.87 0.10 0.03
Matches are distributed among these distances:
58 3 0.02
59 135 0.76
60 39 0.22
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (59 bp):
CAAAAATTACCATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCAATTTCAC
Found at i:5980994 original size:118 final size:118
Alignment explanation
Indices: 5980714--5981007 Score: 328
Period size: 118 Copynumber: 2.5 Consensus size: 118
5980704 CCAAAACTTT
* * * *
5980714 CAAAAATTATCATTTTACCCCC-AAACTTTCCTAAA-TCCCATTTTTAACCCCGATTTCACCAAA
1 CAAAAATTACCATTTTACCCCCGAATC-ATCCAAAAGT-CCATTTTTAACCCCGATTTCACCAAA
* * *
5980777 ATTTACAATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGACTTCAC
64 AATTACAATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGAATACAC
* * * * *
5980832 CAAAAATTACCATTTTACCCTCGAATCTTCTAAAATTCCATTTTTAACCCCGGTTTCACCAAAAA
1 CAAAAATTACCATTTTACCCCCGAATCATCCAAAAGTCCATTTTTAACCCCGATTTCACCAAAAA
* *
5980897 TTACCATTTTACCCCTCGAATCTTTTAAAATTCCATTTTTAACCTC-AATGACAC
66 TTACAATTTTACCCC-CGAATCTTTTAAAATTCCATTTTTAACCCCGAAT-ACAC
* ** * * *
5980951 C-AAAATTACCATTTTGCCCCCGGGT-ATCCATAAGTCTCGTTTTTCACCCCGATTTCA
1 CAAAAATTACCATTTTACCCCCGAATCATCCAAAAGTC-CATTTTTAACCCCGATTTCA
5981008 TCATTTATCA
Statistics
Matches: 149, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
117 7 0.05
118 105 0.70
119 37 0.25
ACGTcount: A:0.31, C:0.30, G:0.05, T:0.35
Consensus pattern (118 bp):
CAAAAATTACCATTTTACCCCCGAATCATCCAAAAGTCCATTTTTAACCCCGATTTCACCAAAAA
TTACAATTTTACCCCCGAATCTTTTAAAATTCCATTTTTAACCCCGAATACAC
Found at i:5983459 original size:19 final size:16
Alignment explanation
Indices: 5983420--5983467 Score: 60
Period size: 19 Copynumber: 2.8 Consensus size: 16
5983410 CTTTTAGTGC
5983420 ATTTGGGCTTATTAGG
1 ATTTGGGCTTATTAGG
*
5983436 GTTTGGGCTTAGTTTTAGG
1 ATTTGGGCTTA---TTAGG
5983455 ATTTGGGCTTATT
1 ATTTGGGCTTATT
5983468 TGGTTTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
16 12 0.44
19 15 0.56
ACGTcount: A:0.15, C:0.06, G:0.31, T:0.48
Consensus pattern (16 bp):
ATTTGGGCTTATTAGG
Found at i:5986657 original size:19 final size:17
Alignment explanation
Indices: 5986633--5986673 Score: 55
Period size: 19 Copynumber: 2.3 Consensus size: 17
5986623 AAGACAGGAG
*
5986633 AAGAAAGGATTACAAGAAA
1 AAGAAAGAATTA-AA-AAA
5986652 AAGAAAGAATTAAAAAA
1 AAGAAAGAATTAAAAAA
5986669 AAGAA
1 AAGAA
5986674 GAAAATGGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.38
18 2 0.10
19 11 0.52
ACGTcount: A:0.71, C:0.02, G:0.17, T:0.10
Consensus pattern (17 bp):
AAGAAAGAATTAAAAAA
Found at i:5986875 original size:6 final size:6
Alignment explanation
Indices: 5986864--5986938 Score: 68
Period size: 6 Copynumber: 12.7 Consensus size: 6
5986854 TTAAATTTGT
*
5986864 TTTAAA TTTAAA TTT--A TTTAAA TTT-AC TTTAAA TTTTAAA TTTAAA
1 TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA TTTAAA -TTTAAA TTTAAA
* *
5986910 TTTACTTA TTTAAA TTT-AC TTTAAA TTTA
1 TTTA--AA TTTAAA TTTAAA TTTAAA TTTA
5986939 GGTTTAATCA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
4 4 0.07
5 8 0.14
6 33 0.59
7 6 0.11
8 5 0.09
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (6 bp):
TTTAAA
Found at i:5986886 original size:27 final size:28
Alignment explanation
Indices: 5986853--5986907 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
5986843 TTAAATGGGT
**
5986853 TTTAAATTTGTTTTAAA-TTTAAATTTA
1 TTTAAATTTACTTTAAATTTTAAATTTA
5986880 TTTAAATTTACTTTAAATTTTAAATTTA
1 TTTAAATTTACTTTAAATTTTAAATTTA
5986908 AATTTACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 15 0.60
28 10 0.40
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (28 bp):
TTTAAATTTACTTTAAATTTTAAATTTA
Found at i:5986895 original size:38 final size:36
Alignment explanation
Indices: 5986853--5986937 Score: 109
Period size: 38 Copynumber: 2.2 Consensus size: 36
5986843 TTAAATGGGT
*
5986853 TTTAAATTTGT-TTTAAATTTAAATTTATTTAAATTTAC
1 TTTAAATTT-TATTTAAATTT--ACTTATTTAAATTTAC
5986891 TTTAAATTTTAAATTTAAATTTACTTATTTAAATTTAC
1 TTTAAATTTT--ATTTAAATTTACTTATTTAAATTTAC
5986929 TTTAAATTT
1 TTTAAATTT
5986938 AGGTTTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
37 1 0.02
38 33 0.77
40 9 0.21
ACGTcount: A:0.38, C:0.04, G:0.01, T:0.58
Consensus pattern (36 bp):
TTTAAATTTTATTTAAATTTACTTATTTAAATTTAC
Found at i:5986896 original size:11 final size:11
Alignment explanation
Indices: 5986870--5986938 Score: 77
Period size: 11 Copynumber: 5.9 Consensus size: 11
5986860 TTGTTTTAAA
5986870 TTTAAATTTA-
1 TTTAAATTTAC
5986880 TTTAAATTTAC
1 TTTAAATTTAC
*
5986891 TTTAAATTTTAAA
1 TTTAAA-TTT-AC
5986904 TTTAAATTTAC
1 TTTAAATTTAC
5986915 TTATTTAAATTTAC
1 ---TTTAAATTTAC
5986929 TTTAAATTTA
1 TTTAAATTTA
5986939 GGTTTAATCA
Statistics
Matches: 51, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
10 10 0.20
11 17 0.33
12 6 0.12
13 7 0.14
14 11 0.22
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAC
Found at i:5986906 original size:34 final size:36
Alignment explanation
Indices: 5986863--5986937 Score: 118
Period size: 38 Copynumber: 2.1 Consensus size: 36
5986853 TTTAAATTTG
5986863 TTTTAAATTTAAA-T-TTATTTAAATTTACTTTAAA
1 TTTTAAATTTAAATTATTATTTAAATTTACTTTAAA
5986897 TTTTAAATTTAAATTTACTTATTTAAATTTACTTTAAA
1 TTTTAAATTTAAA-TTA-TTATTTAAATTTACTTTAAA
5986935 TTT
1 TTT
5986938 AGGTTTAATC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
34 13 0.35
36 1 0.03
38 23 0.62
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (36 bp):
TTTTAAATTTAAATTATTATTTAAATTTACTTTAAA
Found at i:5986922 original size:14 final size:14
Alignment explanation
Indices: 5986903--5986930 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5986893 TAAATTTTAA
5986903 ATTTAAATTTACTT
1 ATTTAAATTTACTT
5986917 ATTTAAATTTACTT
1 ATTTAAATTTACTT
5986931 TAAATTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (14 bp):
ATTTAAATTTACTT
Found at i:5987719 original size:12 final size:12
Alignment explanation
Indices: 5987704--5987728 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5987694 ACATTAATGG
5987704 TAATAATAATTT
1 TAATAATAATTT
5987716 TAATAATAATTT
1 TAATAATAATTT
5987728 T
1 T
5987729 TATTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATAATAATTT
Found at i:5988690 original size:162 final size:162
Alignment explanation
Indices: 5988512--5988842 Score: 472
Period size: 162 Copynumber: 2.0 Consensus size: 162
5988502 TTCAATTTAA
* * * *
5988512 TCCTTTGACTGTTTGACTACACCAGAGGCTGCCACGTGTCACGTTTTGGTTTATTTATGCGTTTA
1 TCCTTTGACTGTTTGACTACACCAGAGGCTGCCACGTGTCACGTTTTAGCTTATTTATGCATCTA
*
5988577 GTCCCTGTCATTTTTAAATTT-TTTTAATTTAATCCTCAAATCAACTTCTGCTTAATTACAAAAT
66 GTCCCTGTCATTTTT-AATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAAT
* *
5988641 T-GACTC-AGGAATCTTTT-GAGATTTTTAAATTAG
130 TGGA-TCGA-GAAT-TTTTCAAGATTTATAAATTAG
* * *
5988674 TCCTTTGACTGTTTGACTGCACCAGAGGCTGCCACGTGTCACTTTTTAGCTTATTTATGTATCTA
1 TCCTTTGACTGTTTGACTACACCAGAGGCTGCCACGTGTCACGTTTTAGCTTATTTATGCATCTA
* * * *
5988739 GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTTAAATCAACTTTTATTTAATTACAAGATT
66 GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAATT
5988804 GGATCGAGAATTTTTCAAGATTTATAAATTAG
131 GGATCGAGAATTTTTCAAGATTTATAAATTAG
5988836 TCCTTTG
1 TCCTTTG
5988843 GCTTCTGGGT
Statistics
Matches: 151, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
161 9 0.06
162 139 0.92
163 3 0.02
ACGTcount: A:0.25, C:0.17, G:0.14, T:0.44
Consensus pattern (162 bp):
TCCTTTGACTGTTTGACTACACCAGAGGCTGCCACGTGTCACGTTTTAGCTTATTTATGCATCTA
GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAATT
GGATCGAGAATTTTTCAAGATTTATAAATTAG
Found at i:5988991 original size:59 final size:58
Alignment explanation
Indices: 5988906--5989260 Score: 480
Period size: 59 Copynumber: 6.1 Consensus size: 58
5988896 TTTTATAGGT
* * *
5988906 CCCCAAACTTTCCAAAATTCCCTTTTTGACCCCGGTTTTACCAAAAATTACCATTTTA
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
* * **
5988964 CCCTCGAACATTCCAAAATTCCATTTTTGACCCCAATTTTA-CAAAAATTACCATTTTA
1 CCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
* * *
5989022 CCCCTGAACTTTCCAAAATTTCATTTTTAACCTCGGTTTTACCAAAACTTACCATTTTA
1 CCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
* * *
5989081 CCCTCGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACTAAGAATTACCATTTCA
1 CCC-CGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
* *
5989140 CCCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTTACCAAAAATTACCATTTTA
1 -CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
* * * *
5989199 CCCCTAAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTG
1 CCCC-GAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
5989257 CCCC
1 CCCC
5989261 CGTACGTCCA
Statistics
Matches: 264, Mismatches: 27, Indels: 12
0.87 0.09 0.04
Matches are distributed among these distances:
57 1 0.00
58 92 0.35
59 167 0.63
60 4 0.02
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (58 bp):
CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTA
Found at i:5989121 original size:117 final size:117
Alignment explanation
Indices: 5988906--5989261 Score: 518
Period size: 117 Copynumber: 3.0 Consensus size: 117
5988896 TTTTATAGGT
* *
5988906 CCCCAAACTTTCCAAAATTCCCTTTTTGACCCCGGTTTTACCAAAAATTACCATTTTACCCTCGA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTACCCTCGA
* * *
5988971 ACATTCCAAAATTCCATTTTTGACCCCAATTTTACAAAAATTACCATTTTAC
66 ACTTTCCAAAATTCCATTTTTAACCCCGATTTTACAAAAATTACCATTTTAC
** * * *
5989023 CCCTGAACTTTCCAAAATTTCATTTTTAACCTCGGTTTTACCAAAACTTACCATTTTACCCTCGA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTACCCTCGA
* * *
5989088 ACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACTAAGAATTACCATTTCAC
66 ACTTTCCAAAATTCCATTTTTAACCCCGATTTTAC-AAAAATTACCATTTTAC
* *
5989141 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCAGTTTTACCAAAAATTACCATTTTACCC-CTA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTACCCTC-G
* *
5989205 AACTTTCCAAAATTCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTTGC
65 AACTTTCCAAAATTCCATTTTTAACCCCGATTTTA-CAAAAATTACCATTTTAC
5989258 CCCC
1 CCCC
5989262 GTACGTCCAG
Statistics
Matches: 211, Mismatches: 25, Indels: 6
0.87 0.10 0.02
Matches are distributed among these distances:
117 123 0.58
118 88 0.42
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (117 bp):
CCCCAAACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTTACCCTCGA
ACTTTCCAAAATTCCATTTTTAACCCCGATTTTACAAAAATTACCATTTTAC
Found at i:5989159 original size:29 final size:28
Alignment explanation
Indices: 5988906--5989231 Score: 144
Period size: 29 Copynumber: 11.1 Consensus size: 28
5988896 TTTTATAGGT
*
5988906 CCCCAAACTTTCCAAAATTCCCTTTTTGA-
1 CCCCAAACTTTCCAAAATT-CCATTTT-AC
***
5988935 CCCC-GGTTTTACCAAAAATTACCATTTTAC
1 CCCCAAACTTT-CC-AAAATT-CCATTTTAC
* * *
5988965 CCTCGAACATTCCAAAATTCCATTTTTGA-
1 CCCCAAACTTTCCAAAATTCCA-TTTT-AC
* *
5988994 CCCC-AATTTTACAAAAATTACCATTTTAC
1 CCCCAAACTTT-CCAAAATT-CCATTTTAC
** * *
5989023 CCCTGAACTTTCCAAAATTTCATTTTTAA
1 CCCCAAACTTTCCAAAATTCCA-TTTTAC
* ***
5989052 CCTC-GGTTTTACCAAAACTTACCATTTTAC
1 CCCCAAACTTT-CCAAAA-TT-CCATTTTAC
* * *
5989082 CCTCGAACTTTCCAAAATTCCATTTTTAA
1 CCCCAAACTTTCCAAAATTCCA-TTTTAC
*** * *
5989111 CCCC-GGTTTTACTAAGAATTACCATTTCAC
1 CCCCAAACTTT-CCAA-AATT-CCATTTTAC
*
5989141 CCCCAAACTTTCCAAAATTCCATTTTTAA
1 CCCCAAACTTTCCAAAATTCCA-TTTTAC
**
5989170 CCCC-AGTTTTACCAAAAATTACCATTTTAC
1 CCCCAAACTTT-CC-AAAATT-CCATTTTAC
* *
5989200 CCCTAAACTTTCCAAAATTCCATTTTAA
1 CCCCAAACTTTCCAAAATTCCATTTTAC
5989228 CCCC
1 CCCC
5989232 GATTTCACCA
Statistics
Matches: 221, Mismatches: 51, Indels: 51
0.68 0.16 0.16
Matches are distributed among these distances:
28 40 0.18
29 87 0.39
30 74 0.33
31 20 0.09
ACGTcount: A:0.31, C:0.30, G:0.04, T:0.35
Consensus pattern (28 bp):
CCCCAAACTTTCCAAAATTCCATTTTAC
Found at i:5989228 original size:176 final size:176
Alignment explanation
Indices: 5988911--5989255 Score: 530
Period size: 176 Copynumber: 2.0 Consensus size: 176
5988901 TAGGTCCCCA
* * * * *
5988911 AACTTTCCAAAATTCCCTTTTTGACCCCGGTTTTACCAAAAATTACCATTTTACCCTCGAACATT
1 AACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTCACCCCCAAACATT
* *
5988976 CCAAAATTCCATTTTTGACCCCAATTTTACAAAAATTACCATTTTACCCCTGAACTTTCCAAAAT
66 CCAAAATTCCATTTTTAACCCCAATTTTACAAAAATTACCATTTTACCCCTAAACTTTCCAAAAT
* * * * *
5989041 TTCATTTTTAACCTCGGTTTTACCAAAACTTACCATTTTACCCTCG
131 TCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCG
* * *
5989087 AACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACTAAGAATTACCATTTCACCCCCAAACTTT
1 AACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTCACCCCCAAACATT
*
5989152 CCAAAATTCCATTTTTAACCCCAGTTTTACCAAAAATTACCATTTTACCCCTAAACTTTCCAAAA
66 CCAAAATTCCATTTTTAACCCCAATTTTA-CAAAAATTACCATTTTACCCCTAAACTTTCCAAAA
5989217 TTCCA-TTTTAACCCCGATTTCACCAAAAATTACCATTTT
130 TTCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTT
5989256 GCCCCCGTAC
Statistics
Matches: 152, Mismatches: 16, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
176 114 0.75
177 38 0.25
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.36
Consensus pattern (176 bp):
AACTTTCCAAAATTCCATTTTTAACCCCGGTTTTACCAAAAATTACCATTTCACCCCCAAACATT
CCAAAATTCCATTTTTAACCCCAATTTTACAAAAATTACCATTTTACCCCTAAACTTTCCAAAAT
TCCATTTTTAACCCCGATTTCACCAAAAATTACCATTTTACCCTCG
Found at i:5989260 original size:29 final size:30
Alignment explanation
Indices: 5988942--5989260 Score: 160
Period size: 29 Copynumber: 10.9 Consensus size: 30
5988932 TGACCCCGGT
*
5988942 TTTACCAAAAATTACCATTTTACCCTCGAAC
1 TTTACCAAAAATTACCATTTTACCC-CAAAC
* *
5988973 ATT-CC-AAAATT-CCATTTTTGACCCC-AAT
1 TTTACCAAAAATTACCA-TTTT-ACCCCAAAC
*
5989001 TTTA-CAAAAATTACCATTTTACCCCTGAAC
1 TTTACCAAAAATTACCATTTTACCCC-AAAC
* * ***
5989031 TTT-CC-AAAATT-TCATTTTTAACCTC-GGT
1 TTTACCAAAAATTACCA-TTTT-ACCCCAAAC
* *
5989059 TTTACCAAAACTTACCATTTTACCCTCGAAC
1 TTTACCAAAAATTACCATTTTACCC-CAAAC
***
5989090 TTT-CC-AAAATT-CCATTTTTAACCCC-GGT
1 TTTACCAAAAATTACCA-TTTT-ACCCCAAAC
* * *
5989118 TTTACTAAGAATTACCATTTCACCCCCAAAC
1 TTTACCAAAAATTACCATTTTA-CCCCAAAC
**
5989149 TTT-CC-AAAATT-CCATTTTTAACCCC-AGT
1 TTTACCAAAAATTACCA-TTTT-ACCCCAAAC
5989177 TTTACCAAAAATTACCATTTTACCCCTAAAC
1 TTTACCAAAAATTACCATTTTACCCC-AAAC
*
5989208 TTT-CC-AAAATT-CCATTTTAACCCC-GA-
1 TTTACCAAAAATTACCATTTT-ACCCCAAAC
*
5989234 TTTCACCAAAAATTACCATTTTGCCCC
1 TTT-ACCAAAAATTACCATTTTACCCC
5989261 CGTACGTCCA
Statistics
Matches: 220, Mismatches: 34, Indels: 70
0.68 0.10 0.22
Matches are distributed among these distances:
26 3 0.01
27 1 0.00
28 40 0.18
29 88 0.40
30 68 0.31
31 20 0.09
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (30 bp):
TTTACCAAAAATTACCATTTTACCCCAAAC
Found at i:6001637 original size:76 final size:76
Alignment explanation
Indices: 6001514--6002049 Score: 856
Period size: 76 Copynumber: 7.0 Consensus size: 76
6001504 AAGGACAAAC
* * *
6001514 ATCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
* *
6001579 GTAAGAGCAAC
66 GTAAGAACAAG
*
6001590 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATTTCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
* *
6001655 GTAAGAGCAAC
66 GTAAGAACAAG
*
6001666 ATTATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
*
6001731 TTAAGAACAAG
66 GTAAGAACAAG
*
6001742 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
6001807 GTAAGAACAAG
66 GTAAGAACAAG
*
6001818 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATTAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
*
6001883 GTAAGAGCAAG
66 GTAAGAACAAG
* * *
6001894 ATCATTTCCTATCCTCTTGAAATTGAAATAGAGTTGGATATCAAGTCTTTATCTCTGAAATTGAA
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
6001959 GTAAGAACAAG
66 GTAAGAACAAG
* * * * *
6001970 ATCATTTTCTATCCTCCTGAAATTGAAGTAAAGTTGGATAGCAAGTCTTTATCTCTCTAAAATTG
1 ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTA--TCTCTGAAATTG
*
6002035 AAGTAAGATCAAG
64 AAGTAAGAACAAG
6002048 AT
1 AT
6002050 GAAGCCTAGA
Statistics
Matches: 433, Mismatches: 25, Indels: 2
0.94 0.05 0.00
Matches are distributed among these distances:
76 408 0.94
78 25 0.06
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Consensus pattern (76 bp):
ATCATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATATCAAGTCTTTATCTCTGAAATTGAA
GTAAGAACAAG
Found at i:6002382 original size:11 final size:11
Alignment explanation
Indices: 6002333--6002388 Score: 67
Period size: 11 Copynumber: 4.9 Consensus size: 11
6002323 TTAAATGGGT
**
6002333 TTTAAATTTGT
1 TTTAAATTTAC
6002344 TTTAAATTTAC
1 TTTAAATTTAC
*
6002355 TTTAAATTTTAAA
1 TTTAAA-TTT-AC
6002368 TTTAAATTTAC
1 TTTAAATTTAC
6002379 TTTAAATTTA
1 TTTAAATTTA
6002389 GGTTTAATCA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
11 26 0.67
12 6 0.15
13 7 0.18
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (11 bp):
TTTAAATTTAC
Found at i:6003137 original size:28 final size:29
Alignment explanation
Indices: 6003083--6003137 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
6003073 CATTGAATGT
*
6003083 ACATTAATAGTAATTAATAACTATTTTCA
1 ACATTAATAGTAATTAATAAATATTTTCA
* *
6003112 ACATTAATA-TTATTAATAAATTTTTT
1 ACATTAATAGTAATTAATAAATATTTT
6003138 TAAATAACAT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 14 0.61
29 9 0.39
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.47
Consensus pattern (29 bp):
ACATTAATAGTAATTAATAAATATTTTCA
Found at i:6003161 original size:32 final size:32
Alignment explanation
Indices: 6003111--6003176 Score: 89
Period size: 32 Copynumber: 2.1 Consensus size: 32
6003101 AACTATTTTC
* *
6003111 AACATTAATATTATTAATAAATTTTT-TTAAAT
1 AACATTAATAGTAATAAT-AATTTTTATTAAAT
*
6003143 AACATTAATGGTAATAATAATTTTTATTAAAT
1 AACATTAATAGTAATAATAATTTTTATTAAAT
6003175 AA
1 AA
6003177 AAAAAGAGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 7 0.23
32 23 0.77
ACGTcount: A:0.48, C:0.03, G:0.03, T:0.45
Consensus pattern (32 bp):
AACATTAATAGTAATAATAATTTTTATTAAAT
Found at i:6004233 original size:162 final size:161
Alignment explanation
Indices: 6003949--6004241 Score: 444
Period size: 162 Copynumber: 1.8 Consensus size: 161
6003939 TTCAATTTAA
* * * *
6003949 TCCTTTGACTGTTTAACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTATTTATACGTTTA
1 TCCTTTGACTATTTAACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTATA-GTTTA
*
6004014 GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGCTTAATTACAAAATT
65 GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAATT
6004079 GACCTAGGAATCTTTTGAGATTTTTAAATTAG
130 GACCTAGGAATCTTTTGAGATTTTTAAATTAG
*
6004111 TCCTTTGACTATTTGACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTAT-GTATCT
1 TCCTTTGACTATTTAACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTATAGT-T-T
* * * * * *
6004175 AGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAATTTTTATTTAATTACAAGAT
64 AGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAAT
6004240 TG
129 TG
6004242 GCCCGAGAAT
Statistics
Matches: 117, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
160 2 0.02
161 1 0.01
162 114 0.97
ACGTcount: A:0.25, C:0.17, G:0.13, T:0.45
Consensus pattern (161 bp):
TCCTTTGACTATTTAACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTATAGTTTAG
TCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAATTG
ACCTAGGAATCTTTTGAGATTTTTAAATTAG
Found at i:6004271 original size:162 final size:161
Alignment explanation
Indices: 6003949--6004282 Score: 442
Period size: 162 Copynumber: 2.1 Consensus size: 161
6003939 TTCAATTTAA
* * * *
6003949 TCCTTTGACTGTTTAACTGCACCAGAGGCTGCCACGTGTCACTTTTTGGTTTATTTATACGTTTA
1 TCCTTTGACTATTTAACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTATA-GTTTA
*
6004014 GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTGCTTAATTACAAAATT
65 GTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAATT
* * *
6004079 GACCTAGGAATCTTTTGAGATTTTTAAATTAG
130 GACCGAGGAATCTTTTAAGATTTATAAATTAG
*
6004111 TCCTTTGACTATTTGACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTAT-GTATCT
1 TCCTTTGACTATTTAACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTATAGT-T-T
* * * * * *
6004175 AGTCCCTGTTATTTTTAATTTGTTTTAATTTAATCCTTAAATCAATTTTTATTTAATTACAAGAT
64 AGTCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAAT
*
6004240 TGGCCCGA-GAAT-TTTTCAAGATTTATAAATTAG
129 T-GACCGAGGAATCTTTT-AAGATTTATAAATTAG
6004273 TCAC-TTGACT
1 TC-CTTTGACT
6004283 TCTGGTACCT
Statistics
Matches: 151, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
160 2 0.01
161 5 0.03
162 139 0.92
163 5 0.03
ACGTcount: A:0.26, C:0.17, G:0.13, T:0.44
Consensus pattern (161 bp):
TCCTTTGACTATTTAACTACACCAGAGACTGCCACGTGTCACTTTTTGGCTTATTTATAGTTTAG
TCCCTGTCATTTTTAATTTGTTTTAATTTAATCCTCAAATCAACTTCTACTTAATTACAAAATTG
ACCGAGGAATCTTTTAAGATTTATAAATTAG
Found at i:6004638 original size:177 final size:178
Alignment explanation
Indices: 6004342--6004699 Score: 585
Period size: 177 Copynumber: 2.0 Consensus size: 178
6004332 TTTTATAGGT
* *
6004342 CCCCAAACTTTCCAAAATTCCATTTTTGACCCTGATTTTACCAAAAATTACCATTTTACCCCCAA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCCAA
* * *
6004407 ACTTTCCAAAATTCCATTTTTGACCCCAGTTTTACCAAAAATTACCATTTTACCCCCGAACTTTC
66 ACTTTCCAAAATTCCATTTTTAACCCCAGTTTTACCAAAAATCACCAATTTACCCCCGAACTTTC
* * * *
6004472 CAAAATTCTATTTTTAACCTCGGTTTTACCAAGAATTACCATTTT-AC
131 CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTGAC
**
6004519 CCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCTGA
1 CCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCCAA
*
6004584 ACTTTCCAAAATTCCATTTTTAACCTC-GATTTTACCAAAAATCACCAATTTACCCCCGAACTTT
66 ACTTTCCAAAATTCCATTTTTAACCCCAG-TTTTACCAAAAATCACCAATTTACCCCCGAACTTT
6004648 CCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTGAC
130 CCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTGAC
6004697 CCC
1 CCC
6004700 GTACGTCCAG
Statistics
Matches: 167, Mismatches: 12, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
176 1 0.01
177 161 0.96
178 5 0.03
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (178 bp):
CCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACCAAAAATTACCATTTTACCCCCAA
ACTTTCCAAAATTCCATTTTTAACCCCAGTTTTACCAAAAATCACCAATTTACCCCCGAACTTTC
CAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTGAC
Found at i:6004721 original size:59 final size:59
Alignment explanation
Indices: 6004342--6004699 Score: 529
Period size: 59 Copynumber: 6.1 Consensus size: 59
6004332 TTTTATAGGT
* * *
6004342 CCCCAAACTTTCCAAAATTCCATTTTTGACCCTGATTTTACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTAC
* *
6004401 CCCCAAACTTTCCAAAATTCCATTTTTGACCCC-AGTTTTACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGA-TTTTACCAAAAATTACCATTTTAC
* * * *
6004460 CCCCGAACTTTCCAAAATTCTATTTTTAACCTCGGTTTTACCAAGAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTAC
* **
6004519 CCCCAAACTTTCCAAAATTCCATTTTTAACCCTAATTTTACCAAAAATTACCATTTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTAC
* * * *
6004578 CCCTGAACTTTCCAAAATTCCATTTTTAACCTCGATTTTACCAAAAATCACCAATTTAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTAC
* *
6004637 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGGTTTCACCAAAAATTACCATTTTGAC
1 CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTT-AC
6004697 CCC
1 CCC
6004700 GTACGTCCAG
Statistics
Matches: 269, Mismatches: 27, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
58 1 0.00
59 263 0.98
60 5 0.02
ACGTcount: A:0.32, C:0.30, G:0.04, T:0.34
Consensus pattern (59 bp):
CCCCGAACTTTCCAAAATTCCATTTTTAACCCCGATTTTACCAAAAATTACCATTTTAC
Found at i:6010225 original size:6 final size:6
Alignment explanation
Indices: 6010211--6010391 Score: 272
Period size: 6 Copynumber: 30.2 Consensus size: 6
6010201 TGTTTCGACA
*
6010211 ATTACT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * * *
6010259 ATTATT ATTATT ATTATT ACTATT ATTACT ATTATT ATTACT ATTACT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * *
6010307 ATTACT ATTACT ATTACT ATTATT ATTATT ATTATT ATTATT ATTATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* *
6010355 ATTATT ATTATT ATTCTT ATTATT ATTATT GTTATT A
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT A
6010392 CTATGCGAAA
Statistics
Matches: 164, Mismatches: 11, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 164 1.00
ACGTcount: A:0.33, C:0.05, G:0.01, T:0.62
Consensus pattern (6 bp):
ATTATT
Found at i:6016809 original size:6 final size:6
Alignment explanation
Indices: 6016788--6016877 Score: 57
Period size: 6 Copynumber: 15.8 Consensus size: 6
6016778 AATTTTAGAC
* * *
6016788 ATTT-A ATTTAA TTTTAA ATTTAA ATTTATA A--TAA ATTCAA ATTT-T
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTA-A ATTTAA ATTTAA ATTTAA
** * * *
6016833 ATACAA ATTTAA ATTCAA A-ATAA ATTT-A ATTTAA AATTAA ATTTA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTA
6016878 TATCTTTATT
Statistics
Matches: 62, Mismatches: 16, Indels: 13
0.68 0.18 0.14
Matches are distributed among these distances:
4 2 0.03
5 16 0.26
6 42 0.68
7 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:6016809 original size:12 final size:12
Alignment explanation
Indices: 6016788--6016877 Score: 57
Period size: 11 Copynumber: 7.9 Consensus size: 12
6016778 AATTTTAGAC
6016788 ATTT-AATTTAA
1 ATTTAAATTTAA
*
6016799 TTTTAAATTTAA
1 ATTTAAATTTAA
6016811 ATTTATAA--TAA
1 ATTTA-AATTTAA
* *
6016822 ATTCAAATTT-T
1 ATTTAAATTTAA
**
6016833 ATACAAATTTAA
1 ATTTAAATTTAA
* *
6016845 ATTCAAA-ATAA
1 ATTTAAATTTAA
6016856 ATTT-AATTTAA
1 ATTTAAATTTAA
*
6016867 AATTAAATTTA
1 ATTTAAATTTA
6016878 TATCTTTATT
Statistics
Matches: 61, Mismatches: 11, Indels: 13
0.72 0.13 0.15
Matches are distributed among these distances:
10 4 0.07
11 31 0.51
12 24 0.39
13 2 0.03
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (12 bp):
ATTTAAATTTAA
Found at i:6016822 original size:17 final size:17
Alignment explanation
Indices: 6016802--6016877 Score: 82
Period size: 17 Copynumber: 4.5 Consensus size: 17
6016792 AATTTAATTT
*
6016802 TAAATTTAAATTTATAA
1 TAAATTTAAATTTAAAA
* * *
6016819 TAAATTCAAATTTTATA
1 TAAATTTAAATTTAAAA
* *
6016836 CAAATTTAAATTCAAAA
1 TAAATTTAAATTTAAAA
6016853 TAAATTT-AATTTAAAA
1 TAAATTTAAATTTAAAA
6016869 TTAAATTTA
1 -TAAATTTA
6016878 TATCTTTATT
Statistics
Matches: 46, Mismatches: 11, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
16 8 0.17
17 38 0.83
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (17 bp):
TAAATTTAAATTTAAAA
Found at i:6016875 original size:34 final size:34
Alignment explanation
Indices: 6016788--6016877 Score: 101
Period size: 34 Copynumber: 2.6 Consensus size: 34
6016778 AATTTTAGAC
* * *
6016788 ATTTAATTTAATTTTAAATTTAAATTTATAATAA
1 ATTTAATTTAATATTAAATTTAAATTCAAAATAA
* * *
6016822 ATTCAAATTTTATA-CAAATTTAAATTCAAAATAA
1 ATT-TAATTTAATATTAAATTTAAATTCAAAATAA
*
6016856 ATTTAATTTAAAATTAAATTTA
1 ATTTAATTTAATATTAAATTTA
6016878 TATCTTTATT
Statistics
Matches: 44, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
33 7 0.16
34 30 0.68
35 7 0.16
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (34 bp):
ATTTAATTTAATATTAAATTTAAATTCAAAATAA
Found at i:6020445 original size:29 final size:30
Alignment explanation
Indices: 6020406--6020475 Score: 85
Period size: 29 Copynumber: 2.4 Consensus size: 30
6020396 TTTTCAGAAA
6020406 TTAT-GAATTTAA-TTTTTATATTTTTAT-T
1 TTATAGAATTTAATTTTTTAT-TTTTTATAT
*
6020434 TTATAGAATTTAGTTTTTTATTTTTTATAT
1 TTATAGAATTTAATTTTTTATTTTTTATAT
*
6020464 TTTTA-AATTTAA
1 TTATAGAATTTAA
6020476 GTTTATCTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
28 4 0.11
29 20 0.56
30 12 0.33
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (30 bp):
TTATAGAATTTAATTTTTTATTTTTTATAT
Found at i:6022059 original size:19 final size:19
Alignment explanation
Indices: 6022025--6022062 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6022015 CCACCGTCAC
**
6022025 CCACCGTAATTGAATTTGT
1 CCACCGTAATCAAATTTGT
6022044 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
6022063 TATTAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:6024231 original size:89 final size:90
Alignment explanation
Indices: 6024069--6024248 Score: 265
Period size: 89 Copynumber: 2.0 Consensus size: 90
6024059 AATAAAAAAT
** *
6024069 TCACTTGATAATTATATAATTAAAAATAAGACAGTTGTAATTAGCTTGAATTTAACAAAAAAAAA
1 TCACTTGATAACCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAAAAAAA
* *
6024134 TATTTAATAGTGGTAATAGTTAAAC
66 TATTTAATAGTGGTAACAATTAAAC
* * *
6024159 TCACTTGATAACCATGTAATTAAAAATAAGAC-GTTGCAATTAGCTTGAATTTAA-AAAATATAT
1 TCACTTGATAACCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAA-AAAA
6024222 ATATTTAATAGTGGTAACAATTAAAC
65 ATATTTAATAGTGGTAACAATTAAAC
6024248 T
1 T
6024249 TAAATTTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 4 0.05
89 48 0.59
90 29 0.36
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.34
Consensus pattern (90 bp):
TCACTTGATAACCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAAAAAAA
TATTTAATAGTGGTAACAATTAAAC
Found at i:6024651 original size:21 final size:22
Alignment explanation
Indices: 6024625--6024665 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6024615 ATTATATTGT
* *
6024625 TATTTTTG-TGCTTTTTTTTAC
1 TATTTTGGTTGCTGTTTTTTAC
6024646 TATTTTGGTTGCTGTTTTTT
1 TATTTTGGTTGCTGTTTTTT
6024666 GTTGTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.71
Consensus pattern (22 bp):
TATTTTGGTTGCTGTTTTTTAC
Found at i:6024722 original size:21 final size:21
Alignment explanation
Indices: 6024698--6024764 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 21
6024688 ACTGGTTTGG
*
6024698 TGTTGTTTTTACTGCTATTTT
1 TGTTGTTTTTATTGCTATTTT
6024719 TGTTGTTATTT-TTGTTACTATTTT
1 TGTTGTT-TTTATTG---CTATTTT
*
6024743 TGTTGTTTTTATTGTTATTTT
1 TGTTGTTTTTATTGCTATTTT
6024764 T
1 T
6024765 ATTATTTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 16 0.41
22 3 0.08
23 3 0.08
24 17 0.44
ACGTcount: A:0.10, C:0.04, G:0.13, T:0.72
Consensus pattern (21 bp):
TGTTGTTTTTATTGCTATTTT
Found at i:6024728 original size:12 final size:12
Alignment explanation
Indices: 6024713--6024758 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
6024703 TTTTTACTGC
6024713 TATTTTTGTTGT
1 TATTTTTGTTGT
**
6024725 TATTTTTGTTAC
1 TATTTTTGTTGT
6024737 TATTTTTGTTGT
1 TATTTTTGTTGT
6024749 T-TTTATTGTT
1 TATTT-TTGTT
6024759 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 3 0.10
12 26 0.90
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.74
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:6024757 original size:24 final size:24
Alignment explanation
Indices: 6024712--6024759 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
6024702 GTTTTTACTG
6024712 CTATTTTTGTTGTTATTTTTGTTA
1 CTATTTTTGTTGTTATTTTTGTTA
6024736 CTATTTTTGTTGTT-TTTATTGTTA
1 CTATTTTTGTTGTTATTT-TTGTTA
6024760 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.12, C:0.04, G:0.12, T:0.71
Consensus pattern (24 bp):
CTATTTTTGTTGTTATTTTTGTTA
Found at i:6024943 original size:12 final size:12
Alignment explanation
Indices: 6024926--6024950 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6024916 AATTTGTTTA
6024926 TATTTTAATGTT
1 TATTTTAATGTT
6024938 TATTTTAATGTT
1 TATTTTAATGTT
6024950 T
1 T
6024951 TTAAGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTAATGTT
Found at i:6026543 original size:14 final size:13
Alignment explanation
Indices: 6026507--6026553 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
6026497 CATGATGTCA
6026507 TTTT-TTTTTCGTT
1 TTTTCTTTTTC-TT
*
6026520 TTTTCCTTTTCTT
1 TTTTCTTTTTCTT
6026533 TTATTCTTTTTCTT
1 TT-TTCTTTTTCTT
6026547 TTCTTCT
1 TT-TTCT
6026554 CATTCTCCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
13 8 0.28
14 21 0.72
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.79
Consensus pattern (13 bp):
TTTTCTTTTTCTT
Found at i:6026558 original size:20 final size:20
Alignment explanation
Indices: 6026519--6026559 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
6026509 TTTTTTTCGT
*
6026519 TTTTTCCTTTTCTTTTATTC
1 TTTTTCCTTTTCTTTCATTC
6026539 TTTTT-CTTTTCTTCTCATTC
1 TTTTTCCTTTTCTT-TCATTC
6026559 T
1 T
6026560 CCTCCTCTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.05, C:0.22, G:0.00, T:0.73
Consensus pattern (20 bp):
TTTTTCCTTTTCTTTCATTC
Found at i:6029726 original size:119 final size:118
Alignment explanation
Indices: 6029544--6029856 Score: 425
Period size: 119 Copynumber: 2.6 Consensus size: 118
6029534 ATCCGGTGGC
* * * * * * *
6029544 AAAATGGTAA-TTTTGGTGAAGTCGGGGTTAAAACT-CAATTTTTTTGACAGTTCGGGGGTAAAA
1 AAAACGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAA--TTTTAGAAAGTTCGGGGGTAAAA
* *
6029607 TGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
64 TGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
*
6029662 AAAACGGTAATTTTTGGT-AAAGTCGAGGTTAAAAATGGTATTTTAGAAAGTTCGGGGGGTAAAA
1 AAAACGGTAATTTTTGGTGAAA-TCGAGGTTAAAAATGGAATTTTAGAAAGTTC-GGGGGTAAAA
* *
6029726 TGGTAATTTTCGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
64 TGGTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
* * *
6029781 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGTAAAATG
1 AAAACGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATG
*
6029846 GTAAATTTTGG
66 GTAATTTTTGG
6029857 AAGTTTCGGG
Statistics
Matches: 172, Mismatches: 18, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
118 43 0.25
119 125 0.73
120 4 0.02
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.34
Consensus pattern (118 bp):
AAAACGGTAATTTTTGGTGAAATCGAGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGTAAAATG
GTAATTTTTGGTGAAATCAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
Found at i:6029839 original size:30 final size:29
Alignment explanation
Indices: 6029803--6029866 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
6029793 TTTGGTGAAA
*
6029803 TCGGGGTTAAAAATGG-AATTTTAGAAGGT
1 TCGGGGGT-AAAATGGAAATTTTAGAAGGT
* *
6029832 TCGGGGGTAAAATGGTAAATTTTGGAAGTT
1 TCGGGGGTAAAATGG-AAATTTTAGAAGGT
6029862 TCGGG
1 TCGGG
6029867 TCAAAATGTA
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
28 7 0.23
29 7 0.23
30 16 0.53
ACGTcount: A:0.30, C:0.05, G:0.34, T:0.31
Consensus pattern (29 bp):
TCGGGGGTAAAATGGAAATTTTAGAAGGT
Found at i:6029866 original size:59 final size:59
Alignment explanation
Indices: 6029544--6029856 Score: 389
Period size: 59 Copynumber: 5.3 Consensus size: 59
6029534 ATCCGGTGGC
* * * * *
6029544 AAAATGGTAA-TTTTGGTGAAGTCGGGGTTAAAACT-CAATTTTTTTGACAGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA--TTTTAGAAAGTTCGGGGGT
* * **
6029603 AAAATGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGT
* * *
6029662 AAAACGGTAATTTTTGGT-AAAGTCGAGGTTAAAAATGGTATTTTAGAAAGTTCGGGGGGT
1 AAAATGGTAATTTTTGGTGAAA-TCGGGGTTAAAAATGGAATTTTAGAAAGTTC-GGGGGT
* ** * **
6029722 AAAATGGTAATTTTCGGTGAAATTAGGGTTAAAAATGGAATTTTGGAAAGTTTAGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGT
*
6029781 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTCGGGGGT
1 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGT
*
6029840 AAAATGGTAAATTTTGG
1 AAAATGGTAATTTTTGG
6029857 AAGTTTCGGG
Statistics
Matches: 217, Mismatches: 32, Indels: 10
0.84 0.12 0.04
Matches are distributed among these distances:
58 3 0.01
59 140 0.65
60 69 0.32
61 5 0.02
ACGTcount: A:0.33, C:0.04, G:0.30, T:0.34
Consensus pattern (59 bp):
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAAGTTCGGGGGT
Found at i:6031002 original size:6 final size:6
Alignment explanation
Indices: 6030991--6031025 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
6030981 TTCATTGCTC
* *
6030991 ATTAAT ATTAAT ATTAAT AATAAT ATTATT ATTAA
1 ATTAAT ATTAAT ATTAAT ATTAAT ATTAAT ATTAA
6031026 AAGTATTAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (6 bp):
ATTAAT
Found at i:6031747 original size:11 final size:11
Alignment explanation
Indices: 6031730--6031805 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
6031720 TTATAATAAT
6031730 ATTAAATTTAA
1 ATTAAATTTAA
* *
6031741 CTTAAATTCAA
1 ATTAAATTTAA
*
6031752 ATTTAAATTAAA
1 A-TTAAATTTAA
*
6031764 ATTGAATTTAA
1 ATTAAATTTAA
*
6031775 AATAAATTTAA
1 ATTAAATTTAA
*
6031786 GATTAAA-ATAA
1 -ATTAAATTTAA
*
6031797 ATTTAATTT
1 ATTAAATTT
6031806 TCAAATGGTT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
10 5 0.10
11 30 0.60
12 15 0.30
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:6031781 original size:34 final size:34
Alignment explanation
Indices: 6031716--6031782 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
6031706 TTTTCTTTTT
* **
6031716 AAATTTATAATAATATTAAATTTAACTTAAATTC
1 AAATTTATAATAAAATTAAATTTAAAATAAATTC
*
6031750 AAATTTA-AATTAAAATTGAATTTAAAATAAATT
1 AAATTTATAA-TAAAATTAAATTTAAAATAAATT
6031783 TAAGATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
AAATTTATAATAAAATTAAATTTAAAATAAATTC
Found at i:6032220 original size:76 final size:76
Alignment explanation
Indices: 6032132--6033149 Score: 1357
Period size: 76 Copynumber: 13.8 Consensus size: 76
6032122 TCAATGTCAG
* * * *
6032132 AGAGATAAAGACTTGTTATCCAACTTTACCTCGATTTCAAGAGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032197 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
6032208 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAATGATCTTGTTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032273 ACTTCAATTTC
66 ACTTCAATTTC
* * *
6032284 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032348 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
6032359 AGAGATAAAGACGTGTTATCC-ACTTTACTTCAATTCCAAGCGGACAGGAAATGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032423 ACTTCAATTTC
66 ACTTCAATTTC
* * *
6032434 AGAGATAAAGACGTGTTATCC-GCTCTACTTCAATTTTCAAGGGGATAGGAAATGATCTTGCTCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAA-TTTCAAGCGGATAGGAAATGATCTTGCTCT
*
6032498 TACTTCAGTTTC
65 TACTTCAATTTC
* * * *
6032510 AGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCAGATAGGAAATGATCTTACTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032575 ACTTCAATTTC
66 ACTTCAATTTC
* *
6032586 AGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032644 A-TTCAATTTC
66 ACTTCAATTTC
* *
6032654 AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032712 ACTTCAATTTC
66 ACTTCAATTTC
*
6032723 AGAGATAAAGA-TGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCT
1 AGAGATAAAGACT-TGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCT
6032787 TACTTCAATTTC
65 TACTTCAATTTC
* * *
6032799 AGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGAT--G--ACG---TTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032857 ACTTCAATTTC
66 ACTTCAATTTC
* * *
6032868 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTACTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6032933 ACTTCAATTTC
66 ACTTCAATTTC
* * *
6032944 AGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGAT----AACG--C-TGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6033002 ACTTCAATTTC
66 ACTTCAATTTC
* * * * *
6033013 GGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
6033078 ACTTCAATTTC
66 ACTTCAATTTC
* * * **
6033089 AGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAGTGGACAGGAAAAAATCTTGCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCT
6033150 GTGGTCTGAT
Statistics
Matches: 852, Mismatches: 64, Indels: 53
0.88 0.07 0.05
Matches are distributed among these distances:
68 67 0.08
69 180 0.21
70 1 0.00
71 2 0.00
72 7 0.01
73 7 0.01
74 2 0.00
75 187 0.22
76 388 0.46
77 11 0.01
ACGTcount: A:0.32, C:0.20, G:0.16, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
ACTTCAATTTC
Found at i:6032237 original size:38 final size:37
Alignment explanation
Indices: 6032132--6033051 Score: 278
Period size: 38 Copynumber: 25.0 Consensus size: 37
6032122 TCAATGTCAG
* *
6032132 AGAGATAAAGACTTGTTATCCAACTTTACCTCGATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* ** ***
6032170 AAGAGGAT-AGGAAATG-ATCTTGCTCTTACTTCAATTTC
1 -AGA-GATAAAGACTTGTATCCAACT-TTACTTCAATTTC
6032208 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* ** ****
6032246 AAGAGGAT-AGGAAATG-ATCTTGTTCTTACTTCAATTTC
1 -AGA-GATAAAGACTTGTATCCAACT-TTACTTCAATTTC
* *
6032284 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* * *** *** *
6032321 AAGCGGAT-AGGAAAAG-ATCTTGCTCCTACTTCAATTTC
1 -AG-AGATAAAGACTTGTATCCAACT-TTACTTCAATTTC
* *
6032359 AGAGATAAAGACGTGTTATCC-ACTTTACTTCAATTCC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* * * ** ***
6032396 AAGCGGA-CAGGAAATG-ATCTTGCTCTTACTTCAATTTC
1 -AG-AGATAAAGACTTGTATCCAACT-TTACTTCAATTTC
* * *
6032434 AGAGATAAAGACGTGTTATCC-GCTCTACTTCAATTTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAA-TTTC
* * ** *** *
6032472 AAGGGGAT-AGGAAATG-ATCTTGCTCTTACTTCAGTTTC
1 -A-GAGATAAAGACTTGTATCCAACT-TTACTTCAATTTC
*
6032510 AGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* ** **
6032548 AAGCAGAT-AGGAAATG-ATCTTACTCTTACTTCAATTTC
1 -AG-AGATAAAGACTTGTATCCAACT-TTACTTCAATTTC
* *
6032586 AGAGATGAAGACTTGTTATCCAACTCTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
*** * * *
6032624 A-AGCGGATGAC--GT-TGC-TC-TTA-TTCAATTTC
1 AGAGATAAAGACTTGTATCCAACTTTACTTCAATTTC
*
6032654 AGAGATAAAGACTTGATATCCAACTCTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
*** * * *
6032692 A-AGCGGATGAC--GT-TGC-TC-TTACTTCAATTTC
1 AGAGATAAAGACTTGTATCCAACTTTACTTCAATTTC
6032723 AGAGATAAAGA-TGTGTTATCCAACTTTACTTCAATTTC
1 AGAGATAAAGACT-TG-TATCCAACTTTACTTCAATTTC
* * ** ***
6032761 AAGCGGAT-AGGAAATG-ATCTTGCTCTTACTTCAATTTC
1 -AG-AGATAAAGACTTGTATCCAACT-TTACTTCAATTTC
* *
6032799 AGAGATGAAGACTTGATATCCAACTCTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
*** * * *
6032837 A-AGCGGATGAC--GT-TGC-TC-TTACTTCAATTTC
1 AGAGATAAAGACTTGTATCCAACTTTACTTCAATTTC
6032868 AGAGATAAAGACTTGATATCCAACTTTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* * ** **
6032906 AAGCGGAT-AGGAAATG-ATCTTACTCTTACTTCAATTTC
1 -AG-AGATAAAGACTTGTATCCAACT-TTACTTCAATTTC
* *
6032944 AGAGATGAAGACTTGATATCCAACTCTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
* * *
6032982 AAGCGGATAACG-C-TG----C-TC-TTACTTCAATTTC
1 -AG-AGATAAAGACTTGTATCCAACTTTACTTCAATTTC
* *
6033013 GGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTC
1 AGAGATAAAGACTTG-TATCCAACTTTACTTCAATTTC
6033051 A
1 A
6033052 AGCGGATAGG
Statistics
Matches: 635, Mismatches: 160, Indels: 173
0.66 0.17 0.18
Matches are distributed among these distances:
29 6 0.01
30 12 0.02
31 48 0.08
32 15 0.02
33 8 0.01
34 6 0.01
35 7 0.01
36 37 0.06
37 145 0.23
38 232 0.37
39 94 0.15
40 25 0.04
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.34
Consensus pattern (37 bp):
AGAGATAAAGACTTGTATCCAACTTTACTTCAATTTC
Found at i:6032844 original size:145 final size:145
Alignment explanation
Indices: 6032132--6033128 Score: 1281
Period size: 145 Copynumber: 6.8 Consensus size: 145
6032122 TCAATGTCAG
* * *
6032132 AGAGATAAAGACT-TGTTATCCAACTTTACCTCGATTTCAAGAGGATAGGAAATGATCTTGCTCT
1 AGAGATAAAGA-TGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCT
* * *
6032196 TACTTCAATTTCAGAGATAAAGACTTGATATCCAACTTTACTTCAATTTCAAGAGGATAGGAAAT
65 TACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGAT--G--AC
*
6032261 GATCTTGTTCTTACTTCAATTTC
126 G---TTGCTCTTACTTCAATTTC
* * * *
6032284 AGAGATAAAGACGTGTTATCC-ACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGATGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
* * * *
6032348 ACTTCAATTTCAGAGATAAAGACGTGTTATCC-ACTTTACTTCAATTCCAAGCGGACAGGAAATG
66 ACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAA---G-C-GG--ATG
6032412 ATC-TTGCTCTTACTTCAATTTC
124 A-CGTTGCTCTTACTTCAATTTC
* * * *
6032434 AGAGATAAAGACGTGTTATCC-GCTCTACTTCAATTTTCAAGGGGATAGGAAATGATCTTGCTCT
1 AGAGATAAAGATGTGTTATCCAACTTTACTTCAA-TTTCAAGCGGATAGGAAATGATCTTGCTCT
* * * *
6032498 TACTTCAGTTTCAGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCAGATAGGAAAT
65 TACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGC-----GG--AT
*
6032563 GATC-TTACTCTTACTTCAATTTC
123 GA-CGTTGCTCTTACTTCAATTTC
* * *
6032586 AGAGATGAAGACT-TGTTATCCAACTCTACTTCAATTTCAAGCGGAT--G--ACG---TTGCTCT
1 AGAGATAAAGA-TGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCT
6032643 TA-TTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATGACGTTG
65 TACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATGACGTTG
6032707 CTCTTACTTCAATTTC
130 CTCTTACTTCAATTTC
6032723 AGAGATAAAGATGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
1 AGAGATAAAGATGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
*
6032788 ACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATGACGTTGC
66 ACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATGACGTTGC
6032853 TCTTACTTCAATTTC
131 TCTTACTTCAATTTC
* *
6032868 AGAGATAAAGACT-TGATATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTACTCT
1 AGAGATAAAGA-TGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCT
* * *
6032932 TACTTCAATTTCAGAGATGAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATAACGCTG
65 TACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATGACGTTG
6032997 CTCTTACTTCAATTTC
130 CTCTTACTTCAATTTC
* * * *
6033013 GGAGATAAAGACGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCCT
1 AGAGATAAAGATGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
* *
6033078 ACTTCAATTTCAGAGATAAAGACATGTTATCC-ACTCTACTTCAATTTCAAG
66 ACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAG
6033129 TGGACAGGAA
Statistics
Matches: 769, Mismatches: 47, Indels: 66
0.87 0.05 0.07
Matches are distributed among these distances:
136 2 0.00
137 64 0.08
139 3 0.00
141 2 0.00
144 75 0.10
145 312 0.41
146 1 0.00
148 3 0.00
149 1 0.00
150 68 0.09
151 126 0.16
152 94 0.12
153 13 0.02
155 3 0.00
157 2 0.00
ACGTcount: A:0.31, C:0.20, G:0.15, T:0.33
Consensus pattern (145 bp):
AGAGATAAAGATGTGTTATCCAACTTTACTTCAATTTCAAGCGGATAGGAAATGATCTTGCTCTT
ACTTCAATTTCAGAGATAAAGACTTGATATCCAACTCTACTTCAATTTCAAGCGGATGACGTTGC
TCTTACTTCAATTTC
Found at i:6035465 original size:267 final size:266
Alignment explanation
Indices: 6034990--6035523 Score: 1059
Period size: 267 Copynumber: 2.0 Consensus size: 266
6034980 CGACCAATAG
6034990 TACCCAAATCTCATGATCTGCCTAGCCATCTTGAATCCATTCGCGTGTGTTCCACAAATCCCTTC
1 TACCCAAATCTCATGATCTGCCTAGCCATCTTGAATCCATTCGCGTGTGTTCCACAAATCCCTTC
6035055 ATGGACTTCTTCTAAGATCTTTTTAGCCTCGATTGAATCCACACATCTCAACAACACCTGATCCT
66 ATGGACTTCTTCTAAGATCTTTTTAGCCTCGATTGAATCCACACATCTCAACAACACCTGATCCT
6035120 TCCTTCTCTTATACAAGATTTCTCCATCCAGGACGTACTCATTTGCGAGCCTTCTCAATGTCCTT
131 TCCTTCTCTTATACAAGATTTCTCCATCCAGGACGTACTCATTTGCGAGCCTTCTCAATGTCCTT
6035185 TTGTCATTTTCAGTTGCTCCTTCGGGGTATTTTCGGCCCTTCACATATTGGAGAATGTCCTGGTA
196 TTGTCATTTTCAGTTGCTCCTTCGGGGTATTTTC-GCCCTTCACATATTGGAGAATGTCCTGGTA
6035250 CCAAGGA
260 CCAAGGA
6035257 TACCCAAATCTCATGATCTGCCTAGCCATCTTGAATCCATTCGCGTGTGTTCCACAAATCCCTTC
1 TACCCAAATCTCATGATCTGCCTAGCCATCTTGAATCCATTCGCGTGTGTTCCACAAATCCCTTC
6035322 ATGGACTTCTTCTAAGATCTTTTTAGCCTCGATTGAATCCACACATCTCAACAACACCTGATCCT
66 ATGGACTTCTTCTAAGATCTTTTTAGCCTCGATTGAATCCACACATCTCAACAACACCTGATCCT
6035387 TCCTTCTCTTATACAAGATTTCTCCATCCAGGACGTACTCATTTGCGAGCCTTCTCAATGTCCTT
131 TCCTTCTCTTATACAAGATTTCTCCATCCAGGACGTACTCATTTGCGAGCCTTCTCAATGTCCTT
6035452 TTGTCATTTTCAGTTGCTCCTTCGGGGTATTTTCGCCCTTCACATATTGGAGAATGTCCTGGTAC
196 TTGTCATTTTCAGTTGCTCCTTCGGGGTATTTTCGCCCTTCACATATTGGAGAATGTCCTGGTAC
6035517 CAAGGA
261 CAAGGA
6035523 T
1 T
6035524 GCCCCTCTTT
Statistics
Matches: 267, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
266 38 0.14
267 229 0.86
ACGTcount: A:0.22, C:0.29, G:0.15, T:0.34
Consensus pattern (266 bp):
TACCCAAATCTCATGATCTGCCTAGCCATCTTGAATCCATTCGCGTGTGTTCCACAAATCCCTTC
ATGGACTTCTTCTAAGATCTTTTTAGCCTCGATTGAATCCACACATCTCAACAACACCTGATCCT
TCCTTCTCTTATACAAGATTTCTCCATCCAGGACGTACTCATTTGCGAGCCTTCTCAATGTCCTT
TTGTCATTTTCAGTTGCTCCTTCGGGGTATTTTCGCCCTTCACATATTGGAGAATGTCCTGGTAC
CAAGGA
Found at i:6038263 original size:14 final size:15
Alignment explanation
Indices: 6038233--6038266 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
6038223 TGTCGTGCTC
*
6038233 TTCTTGTCTCTTTCT
1 TTCTTGTCTATTTCT
6038248 TTCTT-TCTATTTCT
1 TTCTTGTCTATTTCT
6038262 TTCTT
1 TTCTT
6038267 CCTTTCTTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 13 0.72
15 5 0.28
ACGTcount: A:0.03, C:0.24, G:0.03, T:0.71
Consensus pattern (15 bp):
TTCTTGTCTATTTCT
Found at i:6045720 original size:59 final size:59
Alignment explanation
Indices: 6045532--6046015 Score: 645
Period size: 59 Copynumber: 8.2 Consensus size: 59
6045522 GGGGGCAAAG
* * * *
6045532 TGGTAA-TTTTGGTGAAGTCGGGGTTAAAAATAGAATTTTTTTGAGAGTTTGAGGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAA--TTTTGGAAAGTTTGAGGGTAAAA
* ** * *
6045592 TTGTAAATTTTT-GTGAAATCAAGGTTAAAAATGGAA-TTTGGAATGTTTGGGGGTAAAA
1 TGGT-AATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
* * *
6045650 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGGAAGTTCGAGGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
*
6045709 TGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTG-GGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
* ** * ** ** *
6045767 CGGTAATTTTTGGTGAAGCCGGGGTTAAAAATGGTATTTTAAAAAGTCCGCGGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
6045826 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
* *
6045885 TGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAG-TTCAGAGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAG-GGTAAAA
* * *
6045944 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTTGGGGGTAAAA
1 TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
*
6046003 TGGTAAATTTTGG
1 TGGTAATTTTTGG
6046016 AAGTTTCGGG
Statistics
Matches: 370, Mismatches: 47, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
57 7 0.02
58 95 0.26
59 236 0.64
60 6 0.02
61 22 0.06
62 4 0.01
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.34
Consensus pattern (59 bp):
TGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTTGAGGGTAAAA
Found at i:6045946 original size:118 final size:118
Alignment explanation
Indices: 6045522--6046015 Score: 674
Period size: 117 Copynumber: 4.2 Consensus size: 118
6045512 TTGGACACCC
* * * * * *
6045522 GGGGGCAAAGTGGTAA-TTTTGGTGAAGTCGGGGTTAAAAATAGAATTTTTTTGAGAGTTTGAGG
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAA--TTTTGGAAAGTTCGAGG
* ** *
6045586 GTAAAATTGTAAATTTTT-GTGAAATCAAGGTTAAAAATGGAA-TTTGGAATGTTT
64 GTAAAATGGT-AATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
*
6045640 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGGAAGTTCGAGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
*
6045705 AAAATGGTGATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* ** * * ** * *
6045758 -GGGGTAAAACGGTAATTTTTGGTGAAGCCGGGGTTAAAAATGGTATTTTAAAAAGTCCGCGGGT
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
6045822 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
66 AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
* * *
6045875 GAGGGTAAAATGGTAATTTTTGGTGAAATCGGGATTAAAAATGGAATTTTGGAAAGTTC-AGAGG
1 GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAG-GG
* *
6045939 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTAGAAGGTTT
65 TAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
*
6045993 GGGGGTAAAATGGTAAATTTTGG
1 GGGGGTAAAATGGTAATTTTTGG
6046016 AAGTTTCGGG
Statistics
Matches: 334, Mismatches: 37, Indels: 10
0.88 0.10 0.03
Matches are distributed among these distances:
116 6 0.02
117 151 0.45
118 149 0.45
119 28 0.08
ACGTcount: A:0.33, C:0.03, G:0.30, T:0.33
Consensus pattern (118 bp):
GGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATAGAATTTTGGAAAGTTCGAGGGT
AAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGAATTTTGGAAAGTTT
Found at i:6045998 original size:30 final size:29
Alignment explanation
Indices: 6045962--6046027 Score: 73
Period size: 30 Copynumber: 2.2 Consensus size: 29
6045952 TTTGGTGAAA
6045962 TCGGGGTTAAAAATGG-AATTTTAGAAGGTT
1 TCGGGGTT-AAAATGGAAATTTTAGAA-GTT
* *
6045992 T-GGGGGTAAAATGGTAAATTTTGGAAGTT
1 TCGGGGTTAAAATGG-AAATTTTAGAAGTT
6046021 TCGGGGT
1 TCGGGGT
6046028 GAGAATGCAA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
28 7 0.23
29 9 0.30
30 14 0.47
ACGTcount: A:0.29, C:0.03, G:0.35, T:0.33
Consensus pattern (29 bp):
TCGGGGTTAAAATGGAAATTTTAGAAGTT
Found at i:6046001 original size:29 final size:28
Alignment explanation
Indices: 6045971--6046027 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
6045961 ATCGGGGTTA
6045971 AAAATGG-AATTTTAGAAGGTTTGGGGGT
1 AAAATGGAAATTTTAGAA-GTTTGGGGGT
* *
6045999 AAAATGGTAAATTTTGGAAGTTTCGGGGT
1 AAAATGG-AAATTTTAGAAGTTTGGGGGT
6046028 GAGAATGCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 7 0.28
29 9 0.36
30 9 0.36
ACGTcount: A:0.32, C:0.02, G:0.33, T:0.33
Consensus pattern (28 bp):
AAAATGGAAATTTTAGAAGTTTGGGGGT
Found at i:6047920 original size:11 final size:11
Alignment explanation
Indices: 6047903--6047978 Score: 64
Period size: 11 Copynumber: 6.8 Consensus size: 11
6047893 TTATAATAAT
6047903 ATTAAATTTAA
1 ATTAAATTTAA
* *
6047914 CTTAAATTCAA
1 ATTAAATTTAA
*
6047925 ATTTAAATTAAA
1 A-TTAAATTTAA
*
6047937 ATTGAATTTAA
1 ATTAAATTTAA
*
6047948 AATAAATTTAA
1 ATTAAATTTAA
*
6047959 GATTAAA-ATAA
1 -ATTAAATTTAA
*
6047970 ATTTAATTT
1 ATTAAATTT
6047979 TCAAATGATT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
10 5 0.10
11 30 0.60
12 15 0.30
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:6047954 original size:34 final size:34
Alignment explanation
Indices: 6047889--6047955 Score: 82
Period size: 34 Copynumber: 2.0 Consensus size: 34
6047879 TTTTCTTTTT
* **
6047889 AAATTTATAATAATATTAAATTTAACTTAAATTC
1 AAATTTATAATAAAATTAAATTTAAAATAAATTC
*
6047923 AAATTTA-AATTAAAATTGAATTTAAAATAAATT
1 AAATTTATAA-TAAAATTAAATTTAAAATAAATT
6047956 TAAGATTAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 26 0.93
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (34 bp):
AAATTTATAATAAAATTAAATTTAAAATAAATTC
Found at i:6052529 original size:31 final size:31
Alignment explanation
Indices: 6052482--6052556 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
6052472 TTTTCAGAAA
* *
6052482 TTATGAATTTAA-TTTTTATA-TTTTTAT-T
1 TTATAAATTTAAGTTTTTTTATTTTTTATAT
6052510 TTATAGAATTT-AGTTTTTTTATTTTTTATAT
1 TTATA-AATTTAAGTTTTTTTATTTTTTATAT
*
6052541 TTTTAAATTTAAGTTT
1 TTATAAATTTAAGTTT
6052557 ATCTATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
28 5 0.13
29 12 0.31
30 12 0.31
31 10 0.26
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (31 bp):
TTATAAATTTAAGTTTTTTTATTTTTTATAT
Found at i:6054177 original size:19 final size:19
Alignment explanation
Indices: 6054143--6054180 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
6054133 CCACCGTCAC
**
6054143 CCACCGTAATTGAATTTGT
1 CCACCGTAATCAAATTTGT
6054162 CCACCGTAATCAAATTTGT
1 CCACCGTAATCAAATTTGT
6054181 TATTAACTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.29, C:0.24, G:0.13, T:0.34
Consensus pattern (19 bp):
CCACCGTAATCAAATTTGT
Found at i:6054742 original size:28 final size:27
Alignment explanation
Indices: 6054710--6054764 Score: 74
Period size: 30 Copynumber: 1.9 Consensus size: 27
6054700 AGGATAGGAG
*
6054710 GAGAGTAAAAGTTTTAGGAGGAAAATGAGA
1 GAGAGAAAAAGTTTT-GG-GGAAAAT-AGA
6054740 GAGAGAAAAAGTTTTGGGGAAAATA
1 GAGAGAAAAAGTTTTGGGGAAAATA
6054765 AAAAGTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 1 0.04
28 7 0.29
29 2 0.08
30 14 0.58
ACGTcount: A:0.47, C:0.00, G:0.33, T:0.20
Consensus pattern (27 bp):
GAGAGAAAAAGTTTTGGGGAAAATAGA
Found at i:6056478 original size:89 final size:90
Alignment explanation
Indices: 6056316--6056495 Score: 265
Period size: 89 Copynumber: 2.0 Consensus size: 90
6056306 AATAAAAAAT
** *
6056316 TCACTTGATAATTATATAATTAAAAATAAGACAGTTGTAATTAGCTTGAATTTAACAAAAAAAAA
1 TCACTTGATAACCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAAAAAAA
* *
6056381 TATTTAATAGTGGTAATAGTTAAAC
66 TATTTAATAGTGGTAACAATTAAAC
* * *
6056406 TCACTTGATAACCATGTAATTAAAAATAAGAC-GTTGCAATTAGCTTGAATTTAA-AAAATATAT
1 TCACTTGATAACCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAA-AAAA
6056469 ATATTTAATAGTGGTAACAATTAAAC
65 ATATTTAATAGTGGTAACAATTAAAC
6056495 T
1 T
6056496 TAAATTTTAA
Statistics
Matches: 81, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
88 4 0.05
89 48 0.59
90 29 0.36
ACGTcount: A:0.46, C:0.08, G:0.11, T:0.34
Consensus pattern (90 bp):
TCACTTGATAACCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAAAAAAA
TATTTAATAGTGGTAACAATTAAAC
Found at i:6056898 original size:21 final size:22
Alignment explanation
Indices: 6056872--6056912 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6056862 ATTATATTGT
* *
6056872 TATTTTTG-TGCTTTTTTTTAC
1 TATTTTGGTTGCTGTTTTTTAC
6056893 TATTTTGGTTGCTGTTTTTT
1 TATTTTGGTTGCTGTTTTTT
6056913 GTTGTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.71
Consensus pattern (22 bp):
TATTTTGGTTGCTGTTTTTTAC
Found at i:6056969 original size:21 final size:21
Alignment explanation
Indices: 6056945--6057011 Score: 73
Period size: 24 Copynumber: 3.0 Consensus size: 21
6056935 ACTGGTTTGG
*
6056945 TGTTGTTTTTACTGCTATTTT
1 TGTTGTTTTTATTGCTATTTT
6056966 TGTTGTTATTT-TTGTTACTATTTT
1 TGTTGTT-TTTATTG---CTATTTT
*
6056990 TGTTGTTTTTATTGTTATTTT
1 TGTTGTTTTTATTGCTATTTT
6057011 T
1 T
6057012 ATTATTTGGA
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 16 0.41
22 3 0.08
23 3 0.08
24 17 0.44
ACGTcount: A:0.10, C:0.04, G:0.13, T:0.72
Consensus pattern (21 bp):
TGTTGTTTTTATTGCTATTTT
Found at i:6056975 original size:12 final size:12
Alignment explanation
Indices: 6056960--6057005 Score: 58
Period size: 12 Copynumber: 3.8 Consensus size: 12
6056950 TTTTTACTGC
6056960 TATTTTTGTTGT
1 TATTTTTGTTGT
**
6056972 TATTTTTGTTAC
1 TATTTTTGTTGT
6056984 TATTTTTGTTGT
1 TATTTTTGTTGT
6056996 T-TTTATTGTT
1 TATTT-TTGTT
6057006 ATTTTTATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
11 3 0.10
12 26 0.90
ACGTcount: A:0.11, C:0.02, G:0.13, T:0.74
Consensus pattern (12 bp):
TATTTTTGTTGT
Found at i:6057004 original size:24 final size:24
Alignment explanation
Indices: 6056959--6057006 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
6056949 GTTTTTACTG
6056959 CTATTTTTGTTGTTATTTTTGTTA
1 CTATTTTTGTTGTTATTTTTGTTA
6056983 CTATTTTTGTTGTT-TTTATTGTTA
1 CTATTTTTGTTGTTATTT-TTGTTA
6057007 TTTTTATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 3 0.13
24 20 0.87
ACGTcount: A:0.12, C:0.04, G:0.12, T:0.71
Consensus pattern (24 bp):
CTATTTTTGTTGTTATTTTTGTTA
Found at i:6057190 original size:12 final size:12
Alignment explanation
Indices: 6057173--6057197 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6057163 AATTTGTTTA
6057173 TATTTTAATGTT
1 TATTTTAATGTT
6057185 TATTTTAATGTT
1 TATTTTAATGTT
6057197 T
1 T
6057198 TTAAGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTAATGTT
Found at i:6063389 original size:89 final size:90
Alignment explanation
Indices: 6063217--6063400 Score: 273
Period size: 89 Copynumber: 2.1 Consensus size: 90
6063207 TTTAAATAAA
* *
6063217 AAACTCACTTGATAATTATATAATTAAAAATAAGACAGTTGTAATTAGCTTGAATTTAACAAAAA
1 AAACTCACTTGATAATCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAAA
* *
6063282 AAAATATTTAATAATGGTAATAGTT
66 AAAATATTTAATAATGGTAACAATT
*
6063307 AAACTCACTTGATAATCATGTAATTAAAAATAAGAC-GTTGCAATTAGCTTGAATTTAA-AAAAT
1 AAACTCACTTGATAATCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAA-
* * *
6063370 ATATATATTTAATAGTGGTAACAATT
65 AAAAATATTTAATAATGGTAACAATT
6063396 AAACT
1 AAACT
6063401 TAAATTTTAA
Statistics
Matches: 85, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
88 4 0.05
89 47 0.55
90 34 0.40
ACGTcount: A:0.47, C:0.08, G:0.10, T:0.34
Consensus pattern (90 bp):
AAACTCACTTGATAATCATATAATTAAAAATAAGACAGTTGCAATTAGCTTGAATTTAACAAAAA
AAAATATTTAATAATGGTAACAATT
Found at i:6063803 original size:21 final size:22
Alignment explanation
Indices: 6063777--6063817 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
6063767 ATTATATTGT
* *
6063777 TATTTTTG-TGCTTTTTTTTAC
1 TATTTTGGTTGCTGTTTTTTAC
6063798 TATTTTGGTTGCTGTTTTTT
1 TATTTTGGTTGCTGTTTTTT
6063818 GTTGTTTTGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.07, C:0.07, G:0.15, T:0.71
Consensus pattern (22 bp):
TATTTTGGTTGCTGTTTTTTAC
Found at i:6063848 original size:18 final size:19
Alignment explanation
Indices: 6063825--6063864 Score: 55
Period size: 20 Copynumber: 2.1 Consensus size: 19
6063815 TTTGTTGTTT
*
6063825 TGGTTT-TGTTTTTTTTAC
1 TGGTTTGTGTTATTTTTAC
6063843 TGGTTTGGTGTTATTTTTAC
1 TGGTTT-GTGTTATTTTTAC
6063863 TG
1 TG
6063865 CTATTTTTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.07, C:0.05, G:0.23, T:0.65
Consensus pattern (19 bp):
TGGTTTGTGTTATTTTTAC
Found at i:6063849 original size:23 final size:23
Alignment explanation
Indices: 6063788--6063860 Score: 69
Period size: 23 Copynumber: 3.2 Consensus size: 23
6063778 ATTTTTGTGC
* *
6063788 TTTTTTTTACTATTTTGGTTGCTG
1 TTTTTTTTACTGTTTTGGTT-TTG
*
6063812 TTTTTTGT--TGTTTTGGTTTTG
1 TTTTTTTTACTGTTTTGGTTTTG
* * *
6063833 TTTTTTTTACTGGTTTGGTGTTA
1 TTTTTTTTACTGTTTTGGTTTTG
6063856 TTTTT
1 TTTTT
6063861 ACTGCTATTT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
21 9 0.22
22 9 0.22
23 15 0.38
24 7 0.17
ACGTcount: A:0.05, C:0.04, G:0.19, T:0.71
Consensus pattern (23 bp):
TTTTTTTTACTGTTTTGGTTTTG
Found at i:6063898 original size:12 final size:12
Alignment explanation
Indices: 6063883--6063919 Score: 58
Period size: 12 Copynumber: 3.2 Consensus size: 12
6063873 GTTACTATTT
6063883 TTGTTGTTTTTA
1 TTGTTGTTTTTA
6063895 TTGTTG-TTTTA
1 TTGTTGTTTTTA
*
6063906 TTGTTATTTTTA
1 TTGTTGTTTTTA
6063918 TT
1 TT
6063920 ATTTGGATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 10 0.43
12 13 0.57
ACGTcount: A:0.11, C:0.00, G:0.14, T:0.76
Consensus pattern (12 bp):
TTGTTGTTTTTA
Found at i:6063932 original size:76 final size:77
Alignment explanation
Indices: 6063774--6063937 Score: 187
Period size: 76 Copynumber: 2.1 Consensus size: 77
6063764 AAAATTATAT
* * *
6063774 TGTTATTTTT-GTGCTTTTTTTTACTATTTTGGTTGCTGTTTTTTGTTGTTTTGGTTTTGTTTTT
1 TGTTATTTTTACTGCTTTTTTTTACTATTTTGGTTGCTGTTTTTTGTTGTTTT-GTATTGTTATT
*
6063838 TTTACTGGTTTGG
65 TTTACTGATTTGG
*
6063851 TGTTATTTTTACTGCTATTTTTGTTACTATTTTTGTTG-T-TTTTATTGTTG-TTT-TATTGTTA
1 TGTTATTTTTACTGCT-TTTTT-TTACTATTTTGGTTGCTGTTTT-TTGTTGTTTTGTATTGTTA
*
6063912 TTTTTA-TTATTTGG
63 TTTTTACTGATTTGG
6063926 ATGTTATTTTTA
1 -TGTTATTTTTA
6063938 TACGTTTTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
75 6 0.08
76 23 0.30
77 10 0.13
78 11 0.14
79 12 0.16
80 14 0.18
ACGTcount: A:0.10, C:0.04, G:0.16, T:0.69
Consensus pattern (77 bp):
TGTTATTTTTACTGCTTTTTTTTACTATTTTGGTTGCTGTTTTTTGTTGTTTTGTATTGTTATTT
TTACTGATTTGG
Found at i:6064095 original size:12 final size:12
Alignment explanation
Indices: 6064078--6064102 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6064068 AATTTGTTTA
6064078 TATTTTAATGTT
1 TATTTTAATGTT
6064090 TATTTTAATGTT
1 TATTTTAATGTT
6064102 T
1 T
6064103 TTAAGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.08, T:0.68
Consensus pattern (12 bp):
TATTTTAATGTT
Found at i:6076316 original size:16 final size:16
Alignment explanation
Indices: 6076297--6076334 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
6076287 AAATTAGATT
6076297 TTAATTAAAAAATAAA
1 TTAATTAAAAAATAAA
**
6076313 TTAATTAAATGATAAA
1 TTAATTAAAAAATAAA
6076329 TTAATT
1 TTAATT
6076335 TAATTAAGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
TTAATTAAAAAATAAA
Found at i:6076776 original size:18 final size:18
Alignment explanation
Indices: 6076744--6076783 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
6076734 TAATTATTTC
*
6076744 ATTTTTTAATCAAAATCGA
1 ATTTTTTAATAAAAATC-A
6076763 ATTTTTTAA-AAAAATCA
1 ATTTTTTAATAAAAATCA
6076780 ATTT
1 ATTT
6076784 CTTCCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 5 0.25
18 6 0.30
19 9 0.45
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (18 bp):
ATTTTTTAATAAAAATCA
Found at i:6079260 original size:8 final size:8
Alignment explanation
Indices: 6079225--6079270 Score: 56
Period size: 8 Copynumber: 5.8 Consensus size: 8
6079215 CTGTGTTTTT
6079225 ATATATAC
1 ATATATAC
*
6079233 ATACATAC
1 ATATATAC
*
6079241 ATACATAC
1 ATATATAC
*
6079249 ATATATAT
1 ATATATAC
*
6079257 ATATATAT
1 ATATATAC
6079265 ATATAT
1 ATATAT
6079271 TTTGTGTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 35 1.00
ACGTcount: A:0.50, C:0.11, G:0.00, T:0.39
Consensus pattern (8 bp):
ATATATAC
Found at i:6079270 original size:12 final size:12
Alignment explanation
Indices: 6079225--6079267 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
6079215 CTGTGTTTTT
6079225 ATATATACATAC
1 ATATATACATAC
*
6079237 ATACATACATAC
1 ATATATACATAC
* *
6079249 ATATATATATAT
1 ATATATACATAC
6079261 ATATATA
1 ATATATA
6079268 TATTTTGTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.51, C:0.12, G:0.00, T:0.37
Consensus pattern (12 bp):
ATATATACATAC
Found at i:6081534 original size:16 final size:17
Alignment explanation
Indices: 6081505--6081541 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6081495 TTTATAACAT
6081505 ATAAATTATTTTTTATA
1 ATAAATTATTTTTTATA
*
6081522 ATAAATT-TTTTTTATC
1 ATAAATTATTTTTTATA
6081538 ATAA
1 ATAA
6081542 CTTTAGAAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.57
Consensus pattern (17 bp):
ATAAATTATTTTTTATA
Found at i:6082348 original size:138 final size:138
Alignment explanation
Indices: 6082195--6082463 Score: 529
Period size: 138 Copynumber: 1.9 Consensus size: 138
6082185 ATTTTAATTA
6082195 TTATATATAAAATAAAGTATCAAATAATTATTTATATTCGGGTCGTGTTAAATCAAGCTTGAAAA
1 TTATATATAAAATAAAGTATCAAATAATTATTTATATTCGGGTCGTGTTAAATCAAGCTTGAAAA
*
6082260 TATTTATCAAAAGTCTAGTTATTTGGGCTGGACAAAAATTGATGGAATCCGATTAAATTGATTGA
66 TATTTATCAAAAGTCTAGTTATTTGGGCTGGACAAAAATTGATGAAATCCGATTAAATTGATTGA
6082325 AAGTCTAG
131 AAGTCTAG
6082333 TTATATATAAAATAAAGTATCAAATAATTATTTATATTCGGGTCGTGTTAAATCAAGCTTGAAAA
1 TTATATATAAAATAAAGTATCAAATAATTATTTATATTCGGGTCGTGTTAAATCAAGCTTGAAAA
6082398 TATTTATCAAAAGTCTAGTTATTTGGGCTGGACAAAAATTGATGAAATCCGATTAAATTGATTGA
66 TATTTATCAAAAGTCTAGTTATTTGGGCTGGACAAAAATTGATGAAATCCGATTAAATTGATTGA
6082463 A
131 A
6082464 TCTAATTAAA
Statistics
Matches: 130, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
138 130 1.00
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (138 bp):
TTATATATAAAATAAAGTATCAAATAATTATTTATATTCGGGTCGTGTTAAATCAAGCTTGAAAA
TATTTATCAAAAGTCTAGTTATTTGGGCTGGACAAAAATTGATGAAATCCGATTAAATTGATTGA
AAGTCTAG
Found at i:6096376 original size:20 final size:20
Alignment explanation
Indices: 6096320--6096378 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
6096310 TGCTGATGTT
*
6096320 GCTCGATGCT-GCCTGATGCT
1 GCTCGATGCTAG-CTGATGCC
* *
6096340 GCTTGATACTA-CTTGATGCC
1 GCTCGATGCTAGC-TGATGCC
6096360 GCTCGATGCTAGCTGATGC
1 GCTCGATGCTAGCTGATGC
6096379 AGTTGGCTCA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
19 1 0.03
20 29 0.94
21 1 0.03
ACGTcount: A:0.15, C:0.27, G:0.27, T:0.31
Consensus pattern (20 bp):
GCTCGATGCTAGCTGATGCC
Found at i:6103490 original size:148 final size:149
Alignment explanation
Indices: 6103260--6103671 Score: 544
Period size: 148 Copynumber: 2.8 Consensus size: 149
6103250 GATCTTGGGA
* * ** * * *
6103260 AAAGTTTTGATTTTTTTAAATAATTTCGAAATAAGTGTTTTGAGTTTTAAGAAAAATAGTAATTT
1 AAAGTTTTGATTTTTTTTAATTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAATAATGATTT
* ** * *
6103325 TCTTTTAAGAAAAGAAAGTTTAGAATTTTAAAAATAAAAATATGTTTTTTAGTCATTTTAAA-AA
66 TCATAAAAAAAAAGAAAGTTTAGAATTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAA
6103389 AAAATTCAAATTTTTAAAC
131 AAAATTCAAATTTTTAAAC
* * * *
6103408 AAAGTTTTGATTTTTTTTAATTACTTCAAAATAAAAATTTGGAGTTTTAAAAAAAATAATGATTT
1 AAAGTTTTGATTTTTTTTAATTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAATAATGATTT
*
6103473 TCATAAAAAAAAAGAAAGTTTAGAGTTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAA
66 TCATAAAAAAAAAGAAAGTTTAGAATTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAA
* *
6103538 AAATTTTAAATTTTTAAAC
131 AAAATTCAAATTTTTAAAC
* *
6103557 AAATTTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAATAATGATTT
1 AAAGTTTTGATTTTTTTTAATTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAATAATGATTT
* * * *
6103621 TCATAAAAAAGAAGAAGAAAGTCTAG-ATTTT-TAAATAAAATTTTATTTTTT
66 TCAT-AAAAA-AA-AAGAAAGTTTAGAATTTTAAAAATAAAAATATATTTTTT
6103672 TTAACTATTT
Statistics
Matches: 230, Mismatches: 30, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
148 163 0.71
149 50 0.22
150 6 0.03
151 11 0.05
ACGTcount: A:0.45, C:0.03, G:0.10, T:0.42
Consensus pattern (149 bp):
AAAGTTTTGATTTTTTTTAATTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAATAATGATTT
TCATAAAAAAAAAGAAAGTTTAGAATTTTAAAAATAAAAATATATTTTTTAGTCATTTTAAAGAA
AAAATTCAAATTTTTAAAC
Found at i:6103730 original size:100 final size:100
Alignment explanation
Indices: 6103547--6103729 Score: 262
Period size: 100 Copynumber: 1.8 Consensus size: 100
6103537 AAAATTTTAA
*
6103547 ATTTTTAAACAAATTTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAA
1 ATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAA
6103612 TAATGATTTTCATAAAAAAGAAGAAGAAAGTCTAG
66 TAATGATTTTCATAAAAAAGAAGAAGAAAGTCTAG
* * * * *
6103647 ATTTTTAAATAAAATTTT-ATTTTTTTTAACTATTTTGATATAAAAGTTTGGATTTTTAA-TAAA
1 ATTTTTAAACAAAATTTTGA-TTTTTTTAACTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAA
* **
6103710 ATAGTGATTTTTTTAAAAAA
65 ATAATGATTTTCATAAAAAA
6103730 AAAAAGTTTA
Statistics
Matches: 73, Mismatches: 9, Indels: 3
0.86 0.11 0.04
Matches are distributed among these distances:
99 21 0.29
100 52 0.71
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.44
Consensus pattern (100 bp):
ATTTTTAAACAAAATTTTGATTTTTTTAACTATTTCGAAATAAAAGTTTGGAGTTTTAAGAAAAA
TAATGATTTTCATAAAAAAGAAGAAGAAAGTCTAG
Found at i:6103818 original size:244 final size:249
Alignment explanation
Indices: 6103398--6103865 Score: 644
Period size: 244 Copynumber: 1.9 Consensus size: 249
6103388 AAAAATTCAA
* *
6103398 ATTTTTAAACAAAGTTTTGATTTTTTTTAATTACTTCAAAATAAAAATTTGGAGTTTTAAAAAAA
1 ATTTTTAAACAAAATTTTGATTTTTTTTAACTACTTCAAAATAAAAATTTGGAGTTTTAAAAAAA
6103463 ATAATGATTTTCATAAAAAAAAAGAAAGTTTAGAGTTTTAAAAATAAAAATATATTTTTTAGTCA
66 ATAATGATTTTCATAAAAAAAAAGAAAGTTTAGAGTTTTAAAAATAAAAATATATTTTTTAGTCA
* * *
6103528 TTTTAAAGAAAAATTTTAAATTTTTAAACAAATTTTTGATTTTTTTAACTATTTCGAAATAAAAG
131 TTTTAAAGAAAAAGTTTAAATTTTTAAACAAATATTTGATTTTTTTAACTATTTCGAAATAAAAA
6103593 TTTGGAGTTTTAAGAAAAATAATGATTTTCATAAAAAAGAAGAAGAAAGTCTAG
196 TTTGGAGTTTTAAGAAAAATAATGATTTTCATAAAAAAGAAGAAGAAAGTCTAG
* * ** * * * *
6103647 ATTTTTAAATAAAATTTT-ATTTTTTTTAACTATTTTGATATAAAAGTTTGGA-TTTTTAATAAA
1 ATTTTTAAACAAAATTTTGATTTTTTTTAACTACTTCAAAATAAAAATTTGGAGTTTTAAAAAAA
* * * * * *
6103710 ATAGTGATTTT-TTTAAAAAAAA-AAAGTTTAGA-TTTTAAAAATCAAATTATGTTTTTTAGTCA
66 ATAATGATTTTCATAAAAAAAAAGAAAGTTTAGAGTTTTAAAAATAAAAATATATTTTTTAGTCA
* * *
6103772 TTTTAAGAGAGAAAAGTTTAGATTTTTAAACAAA-ATTTGA-TTTTTTAATTATTTGGAAATAAA
131 TTTTAA-AGA-AAAAGTTTAAATTTTTAAACAAATATTTGATTTTTTTAACTATTTCGAAATAAA
* * *
6103835 AATTTTGATTTTTAAGAAAAGTAATGATTTT
194 AATTTGGAGTTTTAAGAAAAATAATGATTTT
6103866 GTTTTAAAAA
Statistics
Matches: 192, Mismatches: 25, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
244 81 0.42
245 18 0.09
246 30 0.16
247 19 0.10
248 28 0.15
249 16 0.08
ACGTcount: A:0.44, C:0.03, G:0.10, T:0.43
Consensus pattern (249 bp):
ATTTTTAAACAAAATTTTGATTTTTTTTAACTACTTCAAAATAAAAATTTGGAGTTTTAAAAAAA
ATAATGATTTTCATAAAAAAAAAGAAAGTTTAGAGTTTTAAAAATAAAAATATATTTTTTAGTCA
TTTTAAAGAAAAAGTTTAAATTTTTAAACAAATATTTGATTTTTTTAACTATTTCGAAATAAAAA
TTTGGAGTTTTAAGAAAAATAATGATTTTCATAAAAAAGAAGAAGAAAGTCTAG
Found at i:6106403 original size:56 final size:58
Alignment explanation
Indices: 6106270--6106423 Score: 190
Period size: 56 Copynumber: 2.7 Consensus size: 58
6106260 TATATTATGA
* *
6106270 TTTTTATT-AATTCATAATTTAATAGTAATTATATTAAAA-ATGTTATTAAATTATATACT
1 TTTTTATTAAATT-AT-ATTTAATAATAATCATATTAAAATATG-TATTAAATTATATACT
* * * *
6106329 ATTTTATTAAATTGTATTTAATAATAATCATGTTAAAATATG-ATTAAATTATTTA-T
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGTATTAAATTATATACT
*
6106385 TTTTTATTAAATTATATTTAATAATAATCTTATTAAAAT
1 TTTTTATTAAATTATATTTAATAATAATCATATTAAAAT
6106424 TTAATAATAA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
56 36 0.43
57 12 0.14
58 20 0.24
59 11 0.13
60 4 0.05
ACGTcount: A:0.43, C:0.03, G:0.03, T:0.51
Consensus pattern (58 bp):
TTTTTATTAAATTATATTTAATAATAATCATATTAAAATATGTATTAAATTATATACT
Found at i:6112782 original size:158 final size:158
Alignment explanation
Indices: 6112487--6112807 Score: 464
Period size: 158 Copynumber: 2.0 Consensus size: 158
6112477 ATTTCGGGAT
* * * * * *
6112487 TTACAGGTTATATGGGTGCCGGTCCTAGATGTCCTACTGATGGTTGAGATCTAGCATTTGTTGTG
1 TTACAAGTTATATGGGTGCCAGTCCTAGATGTCCAACTAATGGCTGAGATCTAGCATTTGTTGCG
* *
6112552 GATTCTCCACAGCTCATGTGAGCAGCATCGTGTAGACTAACATCTTGACCCACAGCTCGTGTAAG
66 GATTCTCCACAGCTCATGTGAGCAGCATCGTATAGACTAACATCTCGACCCACAGCTCGTGTAAG
**
6112617 CAAGCCCACTTCACAGCTCGTGTGAGCA
131 CAAGCCCACTTCACAGCTCGCATGAGCA
* *
6112645 TTACAAGTTATATGGGTGCTAGTTCTAGATGTCCAACTAATGGCTGAGATCT-GACATTTGTTGC
1 TTACAAGTTATATGGGTGCCAGTCCTAGATGTCCAACTAATGGCTGAGATCTAG-CATTTGTTGC
* * * *
6112709 GGATTCTCCACAGCTCATGTGAGTAGCATCGTATAGCCTAACATCTCGACCCATAGCTCGTGTGA
65 GGATTCTCCACAGCTCATGTGAGCAGCATCGTATAGACTAACATCTCGACCCACAGCTCGTGTAA
* *
6112774 GCAGGCCCACTTCACGGCTCGCATGAGCA
130 GCAAGCCCACTTCACAGCTCGCATGAGCA
6112803 TTACA
1 TTACA
6112808 TGATACAGAG
Statistics
Matches: 144, Mismatches: 18, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
157 1 0.01
158 143 0.99
ACGTcount: A:0.24, C:0.24, G:0.24, T:0.28
Consensus pattern (158 bp):
TTACAAGTTATATGGGTGCCAGTCCTAGATGTCCAACTAATGGCTGAGATCTAGCATTTGTTGCG
GATTCTCCACAGCTCATGTGAGCAGCATCGTATAGACTAACATCTCGACCCACAGCTCGTGTAAG
CAAGCCCACTTCACAGCTCGCATGAGCA
Found at i:6121549 original size:36 final size:36
Alignment explanation
Indices: 6121502--6121580 Score: 140
Period size: 36 Copynumber: 2.2 Consensus size: 36
6121492 TGTGCAAACC
*
6121502 GTGCACCAGGATGATCTAAGATATGCTTCCAAGTAA
1 GTGCATCAGGATGATCTAAGATATGCTTCCAAGTAA
*
6121538 GTGCATCAGGATGATCTAAGATGTGCTTCCAAGTAA
1 GTGCATCAGGATGATCTAAGATATGCTTCCAAGTAA
6121574 GTGCATC
1 GTGCATC
6121581 CATGGTCTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (36 bp):
GTGCATCAGGATGATCTAAGATATGCTTCCAAGTAA
Found at i:6134043 original size:6 final size:6
Alignment explanation
Indices: 6134019--6134090 Score: 67
Period size: 6 Copynumber: 12.3 Consensus size: 6
6134009 AGTTTATTTC
* * * * **
6134019 TAAAAT TAAATT T-ACTT TAAATT TAAAAT TAAATT CATTTT TAAATT
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT
*
6134066 TAAATT T-ATTT TAAATT TAAATT TA
1 TAAATT TAAATT TAAATT TAAATT TA
6134091 GTCTAAATTT
Statistics
Matches: 51, Mismatches: 13, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
5 8 0.16
6 43 0.84
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (6 bp):
TAAATT
Found at i:6134045 original size:23 final size:24
Alignment explanation
Indices: 6134019--6134069 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 24
6134009 AGTTTATTTC
*
6134019 TAAAATTAAATTTA-CTTTAAATT
1 TAAAATTAAATTCATCTTTAAATT
*
6134042 TAAAATTAAATTCATTTTTAAATT
1 TAAAATTAAATTCATCTTTAAATT
6134066 TAAA
1 TAAA
6134070 TTTATTTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (24 bp):
TAAAATTAAATTCATCTTTAAATT
Found at i:6134047 original size:18 final size:17
Alignment explanation
Indices: 6134040--6134120 Score: 83
Period size: 17 Copynumber: 4.7 Consensus size: 17
6134030 TTACTTTAAA
* *
6134040 TTTAAAATTAAATTCATT
1 TTTAAATTTAAATTTA-T
6134058 TTTAAATTTAAATTTAT
1 TTTAAATTTAAATTTAT
*
6134075 TTTAAATTTAAATTTAG
1 TTTAAATTTAAATTTAT
* *
6134092 TCTAAATTTGAAA-TAAT
1 TTTAAATTT-AAATTTAT
*
6134109 TTTAAAATTAAA
1 TTTAAATTTAAA
6134121 ATAAAAAAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
16 3 0.06
17 34 0.63
18 17 0.31
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (17 bp):
TTTAAATTTAAATTTAT
Found at i:6134090 original size:23 final size:22
Alignment explanation
Indices: 6134019--6134086 Score: 72
Period size: 23 Copynumber: 3.2 Consensus size: 22
6134009 AGTTTATTTC
6134019 TAAAATTAAATTTACTTTAAATT
1 TAAAATTAAATTTA-TTTAAATT
*
6134042 TAAAATTAAATTCA-TT---TT
1 TAAAATTAAATTTATTTAAATT
*
6134060 TAAATTTAAATTTATTTTAAATT
1 TAAAATTAAATTTA-TTTAAATT
6134083 TAAA
1 TAAA
6134087 TTTAGTCTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 10
0.74 0.06 0.20
Matches are distributed among these distances:
18 14 0.38
20 2 0.05
21 2 0.05
23 19 0.51
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAAATTAAATTTATTTAAATT
Found at i:6134124 original size:17 final size:17
Alignment explanation
Indices: 6134024--6134120 Score: 79
Period size: 17 Copynumber: 5.6 Consensus size: 17
6134014 ATTTCTAAAA
** *
6134024 TTAAATTTACTTTAAAT
1 TTAAATTTAAATTAATT
* *
6134041 TTAAAATTAAATTCATTT
1 TTAAATTTAAATT-AATT
*
6134059 TTAAATTTAAATTTATT
1 TTAAATTTAAATTAATT
* *
6134076 TTAAATTTAAATTTAGT
1 TTAAATTTAAATTAATT
*
6134093 CTAAATTTGAAA-TAATT
1 TTAAATTT-AAATTAATT
*
6134110 TTAAAATTAAA
1 TTAAATTTAAA
6134121 ATAAAAAAAA
Statistics
Matches: 64, Mismatches: 14, Indels: 5
0.77 0.17 0.06
Matches are distributed among these distances:
16 3 0.05
17 44 0.69
18 17 0.27
ACGTcount: A:0.45, C:0.03, G:0.02, T:0.49
Consensus pattern (17 bp):
TTAAATTTAAATTAATT
Found at i:6136247 original size:59 final size:58
Alignment explanation
Indices: 6135998--6136364 Score: 477
Period size: 58 Copynumber: 6.3 Consensus size: 58
6135988 CTTGGATGGT
* * * *
6135998 CCAAAAATTACCGTTTTACCCCTAAACCTTCCAAAATTCCATTTTTACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
* * *
6136056 CCAAAAGTTACCATTTTACCCCCGAACTTTCCAAAATTCCATTTTAGCCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
* * * *
6136114 CCAAAAATTACCATTTTACCCCT-AAATTCTCTAAAATTCCATTTTAACCCTGATTTTA
1 CCAAAAATTACCATTTTACCCCTGAACTT-TCCAAAATTCCATTTTAACCCCGATTTCA
* * *
6136172 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAGCCCTGATTTTA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCA
* * **
6136231 CTAAAAATTTCCATTTTACCCCCAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCA-TTTTAACCCCGATTTCA
* * *
6136290 CCAAAAATTACCATTTTA-CCCTCGAACTTTCCAAAATTCCATTTAAACCCTGATTTTA
1 CCAAAAATTACCATTTTACCCCT-GAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
* *
6136348 TCAAAATTTACCATTTT
1 CCAAAAATTACCATTTT
6136365 GCCCTCGAGA
Statistics
Matches: 272, Mismatches: 33, Indels: 8
0.87 0.11 0.03
Matches are distributed among these distances:
57 4 0.01
58 163 0.60
59 105 0.39
ACGTcount: A:0.32, C:0.29, G:0.04, T:0.35
Consensus pattern (58 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTAACCCCGATTTCA
Found at i:6136293 original size:29 final size:27
Alignment explanation
Indices: 6136028--6136364 Score: 195
Period size: 29 Copynumber: 11.6 Consensus size: 27
6136018 CCTAAACCTT
*
6136028 CCAAAATTCCATTTTTACCCCGATTTCA
1 CCAAAATTCCATTTTAACCCCGATTT-A
*
6136056 CCAAAAGTTACCATTTTACCCCCGAACTTT-
1 CCAAAA-TT-CCATTTTAACCCCG-A-TTTA
*
6136086 CCAAAATTCCATTTTAGCCCCGATTTCA
1 CCAAAATTCCATTTTAACCCCGATTT-A
*
6136114 CCAAAAATTACCATTTT-ACCCCTAAATTCT-
1 CC-AAAATT-CCATTTTAACCCC--GATT-TA
* *
6136144 CTAAAATTCCATTTTAACCCTGATTTTA
1 CCAAAATTCCATTTTAACCCCGA-TTTA
6136172 CCAAAAATTACCATTTT-ACCCCTGAACTTT-
1 CC-AAAATT-CCATTTTAACCCC-G-A-TTTA
* *
6136202 CCAAAATTCCATTTTTAGCCCTGATTTTA
1 CCAAAATTCCA-TTTTAACCCCGA-TTTA
* * *
6136231 CTAAAAATTTCCATTTTACCCCCAAACTTT-
1 C-CAAAA-TTCCATTTTAACCCC-GA-TTTA
6136261 CCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAATTCCA-TTTTAACCCCGATTT-A
6136290 CCAAAAATTACCATTTT-ACCCTCGAACTTT-
1 CC-AAAATT-CCATTTTAACCC-CG-A-TTTA
* *
6136320 CCAAAATTCCATTTAAACCCTGATTTTA
1 CCAAAATTCCATTTTAACCCCGA-TTTA
*
6136348 TCAAAATTTACCATTTT
1 CCAAAA-TT-CCATTTT
6136365 GCCCTCGAGA
Statistics
Matches: 246, Mismatches: 27, Indels: 70
0.72 0.08 0.20
Matches are distributed among these distances:
26 3 0.01
27 10 0.04
28 56 0.23
29 77 0.31
30 72 0.29
31 21 0.09
32 7 0.03
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (27 bp):
CCAAAATTCCATTTTAACCCCGATTTA
Found at i:6136410 original size:28 final size:28
Alignment explanation
Indices: 6136346--6136410 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
6136336 ACCCTGATTT
6136346 TATCAAAATTTACCATTTTGCCCTCGAG
1 TATCAAAATTTACCATTTTGCCCTCGAG
*
6136374 -AGTCCAAAA-TTACCATTTTGCCCTCGGG
1 TA-T-CAAAATTTACCATTTTGCCCTCGAG
6136402 TATCTAAAA
1 TATC-AAAA
6136411 GTCCCGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
27 2 0.06
28 24 0.75
29 6 0.19
ACGTcount: A:0.31, C:0.25, G:0.12, T:0.32
Consensus pattern (28 bp):
TATCAAAATTTACCATTTTGCCCTCGAG
Found at i:6148763 original size:92 final size:91
Alignment explanation
Indices: 6148600--6148824 Score: 342
Period size: 92 Copynumber: 2.5 Consensus size: 91
6148590 GAGCGAGATT
* * * *
6148600 ATTTCTTATCCTCTTGAAATTAAAGTAAAGCTGGGTAACAAGCCTTCGTCCCTCTGAAATTGAAG
1 ATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTATGAAATTGAAG
*
6148665 TAAGAGTGAGAAGAAGGACCAACATC
66 CAAGAGTGAGAAGAAGGACCAACATC
*
6148691 ATTTTCCTATCCTCTTGAAATTGAAGTAAAGCTAGATAACAAGCCTTCGTCCCTATGAAATTGAA
1 A-TTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTATGAAATTGAA
* *
6148756 GCGAGAGTGAGAAGAAGGACCAACGTC
65 GCAAGAGTGAGAAGAAGGACCAACATC
* * *
6148783 ATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAG
1 ATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAG
6148825 TCTTTATCTC
Statistics
Matches: 121, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
91 38 0.31
92 83 0.69
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.27
Consensus pattern (91 bp):
ATTTCCTATCCTCTTGAAATTGAAGTAAAGCTGGATAACAAGCCTTCGTCCCTATGAAATTGAAG
CAAGAGTGAGAAGAAGGACCAACATC
Found at i:6148879 original size:38 final size:37
Alignment explanation
Indices: 6148776--6149416 Score: 251
Period size: 38 Copynumber: 16.9 Consensus size: 37
6148766 GAAGAAGGAC
*
6148776 CAACGTCATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
1 CAACGTCAT-TCCTATCCTCTTGAAATTGAAGTA-AG--AG
*
6148817 ATAACAAGTC-TT--TAT-CTC-TGAAATTGAAGTAAGAG
1 -CAAC--GTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
* *
6148852 CAACGTCATCTCCTATCCTCTTTAAATTGAAGTAGAGTTGG
1 CAACGTCAT-TCCTATCCTCTTGAAATTGAAGTA-AG--AG
*
6148893 ATAACAAGTC-TT--TAT-CTC-TGAAATTGAAGTAAGAG
1 -CAAC--GTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
* *
6148928 CAACGTCATCTCCTATCCTCTTTAAATTGAAGTAGAGTTGG
1 CAACGTCAT-TCCTATCCTCTTGAAATTGAAGTA-AG--AG
*
6148969 ATAACAAGTC-TT--TAT-CTC-TGAAATTGAAGTAAGAG
1 -CAAC--GTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
*
6149004 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
1 CAACGTCA-TTCCTATCCTCTTGAAATTGAAGTA-AG--AG
* *
6149045 ATAACAAGTC-TT--TAT-CTC-TAAAATTGAAGTAAGAG
1 -CAAC--GTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
*
6149080 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
1 CAACGTCA-TTCCTATCCTCTTGAAATTGAAGTA-AG--AG
* *
6149121 ATAACAAGTC-TT--TAT-CTC-TGAAATCGAAGTAAGAG
1 -CAAC--GTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
* * *
6149156 CAAAGATCATTTCCTAACC-CTTGTAATTGAAGTAA-AG
1 CAACG-TCA-TTCCTATCCTCTTGAAATTGAAGTAAGAG
* * * *
6149193 CTGGACATCAAATCTTTAT-CTC-TGAAATTGAAGTAAGAG
1 C--AACGTC-ATTC-CTATCCTCTTGAAATTGAAGTAAGAG
*
6149232 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGG
1 CAACGTCA-TTCCTATCCTCTTGAAATTGAAGTA-AG--AG
*
6149273 ATAACAAGTC-TT--TAT-CTC-TGAAATTGAAGTAAGAG
1 -CAAC--GTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
* *
6149308 CAAAGATCATTTCCTATCCTCTTGAAATTGAGGTAA-AG
1 CAACG-TCA-TTCCTATCCTCTTGAAATTGAAGTAAGAG
* * * *
6149346 CTGGACATCAAATCTTTAT-CTC-TGAAATTGAAGTAAGAG
1 C--AACGTC-ATTC-CTATCCTCTTGAAATTGAAGTAAGAG
*
6149385 CAA-GATCATTCCTATCCTCGTGAAATTGAAGT
1 CAACG-TCATTCCTATCCTCTTGAAATTGAAGT
6149417 TGGATAGCAA
Statistics
Matches: 455, Mismatches: 57, Indels: 179
0.66 0.08 0.26
Matches are distributed among these distances:
32 14 0.03
33 6 0.01
34 22 0.05
35 13 0.03
36 22 0.05
37 57 0.13
38 186 0.41
39 59 0.13
40 23 0.05
41 5 0.01
42 27 0.06
43 3 0.01
44 18 0.04
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (37 bp):
CAACGTCATTCCTATCCTCTTGAAATTGAAGTAAGAG
Found at i:6148902 original size:76 final size:76
Alignment explanation
Indices: 6148776--6149459 Score: 1042
Period size: 76 Copynumber: 9.0 Consensus size: 76
6148766 GAAGAAGGAC
*
6148776 CAACGTCATCTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
6148841 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
6148852 CAACGTCATCTCCTATCCTCTTTAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
6148917 TGAAGTAAGAG
66 TGAAGTAAGAG
* *
6148928 CAACGTCATCTCCTATCCTCTTTAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
6148993 TGAAGTAAGAG
66 TGAAGTAAGAG
*
6149004 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTAAAAT
1 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
6149069 TGAAGTAAGAG
66 TGAAGTAAGAG
6149080 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
*
6149145 CGAAGTAAGAG
66 TGAAGTAAGAG
* * * * * * * *
6149156 CAAAGATCATTTCCTAACC-CTTGTAATTGAAGTAAAGCTGGACATCAAATCTTTATCTCTGAAA
1 CAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
6149220 TTGAAGTAAGAG
65 TTGAAGTAAGAG
6149232 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
1 CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
6149297 TGAAGTAAGAG
66 TGAAGTAAGAG
* * * * * * *
6149308 CAAAGATCATTTCCTATCCTCTTGAAATTGAGGTAAAGCTGGACATCAAATCTTTATCTCTGAAA
1 CAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAA
6149373 TTGAAGTAAGAG
65 TTGAAGTAAGAG
* * *
6149385 CAA-GATCA-TTCCTATCCTCGTGAAATT---G-A-AGTTGGATAGCAAATCTTTATCTCTCTGA
1 CAACG-TCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTA--TCTCTGA
6149443 AATTGAAGTAAGAG
63 AATTGAAGTAAGAG
6149457 CAA
1 CAA
6149460 GATGAAGCAT
Statistics
Matches: 569, Mismatches: 34, Indels: 14
0.92 0.06 0.02
Matches are distributed among these distances:
70 17 0.03
71 1 0.00
72 25 0.04
75 30 0.05
76 416 0.73
77 80 0.14
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (76 bp):
CAACGTCATTTCCTATCCTCTTGAAATTGAAGTAGAGTTGGATAACAAGTCTTTATCTCTGAAAT
TGAAGTAAGAG
Found at i:6149451 original size:35 final size:34
Alignment explanation
Indices: 6149354--6149459 Score: 105
Period size: 35 Copynumber: 3.1 Consensus size: 34
6149344 AGCTGGACAT
6149354 CAAATCTTTA--TCTCTGAAATTGAAG-TAAGAG
1 CAAATCTTTATCTCTCTGAAATTGAAGTTAAGAG
* *
6149385 CAAGATCATTCCTATC-CTCGTGAAATTGAAGTTGGATAG
1 CAA-ATC-TT--TATCTCTC-TGAAATTGAAGTT-AAGAG
6149424 CAAATCTTTATCTCTCTGAAATTGAAG-TAAGAG
1 CAAATCTTTATCTCTCTGAAATTGAAGTTAAGAG
6149457 CAA
1 CAA
6149460 GATGAAGCAT
Statistics
Matches: 61, Mismatches: 4, Indels: 18
0.73 0.05 0.22
Matches are distributed among these distances:
31 3 0.05
32 3 0.05
33 8 0.13
34 1 0.02
35 17 0.28
36 6 0.10
37 13 0.21
38 4 0.07
39 6 0.10
ACGTcount: A:0.36, C:0.16, G:0.17, T:0.31
Consensus pattern (34 bp):
CAAATCTTTATCTCTCTGAAATTGAAGTTAAGAG
Found at i:6149792 original size:17 final size:18
Alignment explanation
Indices: 6149753--6149797 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
6149743 TAAAATGGTT
* *
6149753 TTTAAGTTTATTTCTAAA
1 TTTAAATTTACTTCTAAA
*
6149771 ATTAAATTTACTT-TAAA
1 TTTAAATTTACTTCTAAA
6149788 TTTAAATTTA
1 TTTAAATTTA
6149798 AATTCATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 13 0.57
18 10 0.43
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.53
Consensus pattern (18 bp):
TTTAAATTTACTTCTAAA
Found at i:6151732 original size:29 final size:29
Alignment explanation
Indices: 6151700--6151977 Score: 164
Period size: 29 Copynumber: 9.4 Consensus size: 29
6151690 TAAACCTTCC
*
6151700 AAAATTCTATTTTTACCCCGATTTCTCCA
1 AAAATTCCATTTTTACCCCGATTTCTCCA
*
6151729 AAAATTACCA-TTTTACCCCCGAACTT-TCC-
1 AAAATT-CCATTTTTA-CCCCG-ATTTCTCCA
* **
6151758 AAAATTCTATTTTTAGCCCCGATTTGACCAA
1 AAAATTCCATTTTTA-CCCCGATTTCTCC-A
* * *
6151789 AAAATACCA-TTTTACCCCTGAATTCT-CT
1 AAAATTCCATTTTTACCCC-GATTTCTCCA
* *
6151817 AAAATTCCATTTTTAACCTCGATTTCACCA
1 AAAATTCCATTTTT-ACCCCGATTTCTCCA
* *
6151847 AAAATTACCA-TTTTACCCCTAAACTT-TCC-
1 AAAATT-CCATTTTTACCCC--GATTTCTCCA
*
6151876 AAAATTCCATTTTTAACCCCGATTTCACCA
1 AAAATTCCATTTTT-ACCCCGATTTCTCCA
* *
6151906 AAAATTACCA-TTTTACCCTTGAACTT-TCC-
1 AAAATT-CCATTTTTACCC-CG-ATTTCTCCA
* ** *
6151935 AAAATTCCATTTTAACCCTAATTTCACCA
1 AAAATTCCATTTTTACCCCGATTTCTCCA
*
6151964 AAATTTACCATTTT
1 AAAATT-CCATTTT
6151978 GCCCCCGAGA
Statistics
Matches: 192, Mismatches: 32, Indels: 49
0.70 0.12 0.18
Matches are distributed among these distances:
27 3 0.02
28 25 0.13
29 81 0.42
30 61 0.32
31 22 0.11
ACGTcount: A:0.33, C:0.28, G:0.03, T:0.36
Consensus pattern (29 bp):
AAAATTCCATTTTTACCCCGATTTCTCCA
Found at i:6151803 original size:59 final size:59
Alignment explanation
Indices: 6151668--6152005 Score: 425
Period size: 59 Copynumber: 5.8 Consensus size: 59
6151658 CCTGGATGGT
* * * * * * *
6151668 CCAAAAATTATCGTTTTACCCTTAAACCTTCCAAAATTCTATTTTT-ACCCCGATTTCT
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * * *
6151726 CCAAAAATTACCATTTTACCCCCGAACTTTCCAAAATTCTATTTTTAGCCCCGATTTGA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
6151785 CCAAAAAATACCATTTTACCCCTGAA-TTCTCTAAAATTCCATTTTTAACCTCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTT-TCCAAAATTCCATTTTTAACCCCGATTTCA
*
6151844 CCAAAAATTACCATTTTACCCCTAAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* **
6151903 CCAAAAATTACCATTTTACCCTTGAACTTTCCAAAATTCCA-TTTTAACCCTAATTTCA
1 CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
* * *
6151961 CCAAAATTTACCATTTTGCCCCCGAGA--TTCCAAAATTACCATTTT
1 CCAAAAATTACCATTTTACCCCTGA-ACTTTCCAAAATT-CCATTTT
6152006 GCCCCCGGGT
Statistics
Matches: 246, Mismatches: 28, Indels: 11
0.86 0.10 0.04
Matches are distributed among these distances:
57 10 0.04
58 81 0.33
59 153 0.62
60 2 0.01
ACGTcount: A:0.32, C:0.28, G:0.04, T:0.36
Consensus pattern (59 bp):
CCAAAAATTACCATTTTACCCCTGAACTTTCCAAAATTCCATTTTTAACCCCGATTTCA
Found at i:6167721 original size:20 final size:21
Alignment explanation
Indices: 6167693--6167733 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
6167683 ACTTTATCAA
*
6167693 TAATATTAAAACTAATTTTTT
1 TAATATTAAAACAAATTTTTT
*
6167714 TAAT-TTAAAGCAAATTTTTT
1 TAATATTAAAACAAATTTTTT
6167734 ATGAATGTTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.51
Consensus pattern (21 bp):
TAATATTAAAACAAATTTTTT
Found at i:6168116 original size:14 final size:15
Alignment explanation
Indices: 6168097--6168127 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
6168087 TGAATATGTG
6168097 TTTAATATT-TATTT
1 TTTAATATTGTATTT
6168111 TTTAATATTGTATTT
1 TTTAATATTGTATTT
6168126 TT
1 TT
6168128 AATTGAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.56
15 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTAATATTGTATTT
Found at i:6168233 original size:20 final size:22
Alignment explanation
Indices: 6168210--6168251 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
6168200 CAATTCACAT
*
6168210 ATTATAA-TAGAA-ATTTTTAA
1 ATTATAATTAAAATATTTTTAA
6168230 ATTATAATTAAAATATTTTTAA
1 ATTATAATTAAAATATTTTTAA
6168252 CATATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 4 0.21
22 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (22 bp):
ATTATAATTAAAATATTTTTAA
Found at i:6170242 original size:80 final size:80
Alignment explanation
Indices: 6170108--6170266 Score: 264
Period size: 80 Copynumber: 2.0 Consensus size: 80
6170098 TGTAATTATA
* *
6170108 GGTTTTTTATTCATTTTAAAATTGAAGACAGGATCAGGGCAATATTTAGATAAAGCTCATAATGA
1 GGTTTTTTATTCATTTTAAAATTGAAGACAGGATCAAGGCAATACTTAGATAAAGCTCATAATGA
6170173 CAAGTGTTGGGATTC
66 CAAGTGTTGGGATTC
* * * *
6170188 GGTTTTTTATTCATTTTGAAGTTGAAGATAGGATCAAGGCAATACTTAGGTAAAGCTCATAATGA
1 GGTTTTTTATTCATTTTAAAATTGAAGACAGGATCAAGGCAATACTTAGATAAAGCTCATAATGA
6170253 CAAGTGTTGGGATT
66 CAAGTGTTGGGATT
6170267 GATCTGATTA
Statistics
Matches: 73, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
80 73 1.00
ACGTcount: A:0.33, C:0.09, G:0.23, T:0.35
Consensus pattern (80 bp):
GGTTTTTTATTCATTTTAAAATTGAAGACAGGATCAAGGCAATACTTAGATAAAGCTCATAATGA
CAAGTGTTGGGATTC
Found at i:6174526 original size:23 final size:25
Alignment explanation
Indices: 6174485--6174538 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 25
6174475 TTATTACTGC
*
6174485 AGAAAATTAAAAAAGAGAATTAAA-
1 AGAAAATTAAAAAAGAGAAGTAAAT
* *
6174509 AGAAAA-TAAAATATAGAAGTAAAT
1 AGAAAATTAAAAAAGAGAAGTAAAT
6174533 AGAAAA
1 AGAAAA
6174539 ATTGTAATAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
23 14 0.54
24 12 0.46
ACGTcount: A:0.70, C:0.00, G:0.13, T:0.17
Consensus pattern (25 bp):
AGAAAATTAAAAAAGAGAAGTAAAT
Found at i:6192580 original size:13 final size:13
Alignment explanation
Indices: 6192543--6192581 Score: 51
Period size: 15 Copynumber: 2.8 Consensus size: 13
6192533 TTACTATAAT
6192543 AATATAAAAAAAG
1 AATATAAAAAAAG
6192556 AATAGTACAAAAAATG
1 AATA-TA-AAAAAA-G
6192572 AATATAAAAA
1 AATATAAAAA
6192582 CAAAACCTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 4 0.17
14 6 0.26
15 8 0.35
16 5 0.22
ACGTcount: A:0.72, C:0.03, G:0.08, T:0.18
Consensus pattern (13 bp):
AATATAAAAAAAG
Found at i:6192850 original size:12 final size:12
Alignment explanation
Indices: 6192833--6192858 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
6192823 GACATACTTC
6192833 AATAACAAGTTT
1 AATAACAAGTTT
6192845 AATAACAAGTTT
1 AATAACAAGTTT
6192857 AA
1 AA
6192859 ACGAGCATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.08, T:0.31
Consensus pattern (12 bp):
AATAACAAGTTT
Found at i:6206085 original size:13 final size:13
Alignment explanation
Indices: 6206067--6206091 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6206057 AAACATACAT
6206067 TTTAACCATTAAC
1 TTTAACCATTAAC
6206080 TTTAACCATTAA
1 TTTAACCATTAA
6206092 AGTTAACAAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.20, G:0.00, T:0.40
Consensus pattern (13 bp):
TTTAACCATTAAC
Found at i:6207001 original size:22 final size:23
Alignment explanation
Indices: 6206955--6207001 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
6206945 TCCATCAAGA
*
6206955 TTGAAGATCTCATTTTGATTTCT
1 TTGAAGATCTCATTTGGATTTCT
6206978 TTGAAGAT-T-ATTTGGAGTTTCT
1 TTGAAGATCTCATTTGGA-TTTCT
6207000 TT
1 TT
6207002 ATTTTTTGTG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 6 0.27
22 8 0.36
23 8 0.36
ACGTcount: A:0.21, C:0.09, G:0.17, T:0.53
Consensus pattern (23 bp):
TTGAAGATCTCATTTGGATTTCT
Found at i:6216138 original size:29 final size:29
Alignment explanation
Indices: 6216104--6216170 Score: 89
Period size: 29 Copynumber: 2.3 Consensus size: 29
6216094 TCATGTAGGC
* *
6216104 CACACGGGTATGTGTTAGGCCGTATGGGT
1 CACACGGGCATGTGTTAGGCCATATGGGT
* * *
6216133 CACACGAGCATGTGTTAGGCTATGTGGGT
1 CACACGGGCATGTGTTAGGCCATATGGGT
6216162 CACACGGGC
1 CACACGGGC
6216171 TGATCATTTG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (29 bp):
CACACGGGCATGTGTTAGGCCATATGGGT
Found at i:6221871 original size:20 final size:20
Alignment explanation
Indices: 6221835--6221872 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
6221825 AAAAGGACCT
**
6221835 TTGACCATTAATTTTAACAG
1 TTGACCATTAAAGTTAACAG
6221855 TTGACCATTAAAGTTAAC
1 TTGACCATTAAAGTTAAC
6221873 TGTTTATAAT
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:0.37, C:0.16, G:0.11, T:0.37
Consensus pattern (20 bp):
TTGACCATTAAAGTTAACAG
Found at i:6222547 original size:32 final size:32
Alignment explanation
Indices: 6222452--6222538 Score: 135
Period size: 32 Copynumber: 2.8 Consensus size: 32
6222442 GGTTCCTAGA
*
6222452 TTTGGGGA-TTTT-GG-TTTAGGTTTCAAAAA
1 TTTGGGGATTTTTAGGATTTAGGTTTCAAAAT
*
6222481 TTTGGGGATTTTTAGGTTTTAGGTTTCAAAAT
1 TTTGGGGATTTTTAGGATTTAGGTTTCAAAAT
6222513 TTTGGGGATTTTTAGGATTTAGGTTT
1 TTTGGGGATTTTTAGGATTTAGGTTT
6222539 GGGCATTTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
29 8 0.15
30 4 0.08
31 2 0.04
32 39 0.74
ACGTcount: A:0.21, C:0.02, G:0.28, T:0.49
Consensus pattern (32 bp):
TTTGGGGATTTTTAGGATTTAGGTTTCAAAAT
Done.