Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr2
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: 43198478
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2088848 characters in sequence are not A, C, G, or T
File 126 of 131
Found at i:41559876 original size:43 final size:43
Alignment explanation
Indices: 41559829--41559980 Score: 127
Period size: 43 Copynumber: 3.6 Consensus size: 43
41559819 TCCCAAACGT
* *
41559829 GGTCTTACATGTAATCACATATCGATGCCACTGTCCCAGACAG
1 GGTCTTACATGAAAACACATATCGATGCCACTGTCCCAGACAG
* * * * * *
41559872 GGTCTTATA-CAAATCAAATA-CGATGCCAATGTCCCAGACAT
1 GGTCTTACATGAAAACACATATCGATGCCACTGTCCCAGACAG
*
41559913 GGTCTTACA-CATAAACACA-AGTCGATGCCAAC-GTCCCAGAC-G
1 GGTCTTACATGA-AAACACATA-TCGATGCC-ACTGTCCCAGACAG
* *
41559955 TGGTCTTTCATGAAAACACGTATCGA
1 -GGTCTTACATGAAAACACATATCGA
41559981 AATCCTATGT
Statistics
Matches: 88, Mismatches: 14, Indels: 14
0.76 0.12 0.12
Matches are distributed among these distances:
41 30 0.34
42 13 0.15
43 42 0.48
44 3 0.03
ACGTcount: A:0.32, C:0.26, G:0.18, T:0.24
Consensus pattern (43 bp):
GGTCTTACATGAAAACACATATCGATGCCACTGTCCCAGACAG
Found at i:41559905 original size:41 final size:42
Alignment explanation
Indices: 41559810--41559961 Score: 141
Period size: 43 Copynumber: 3.6 Consensus size: 42
41559800 GACTCGTACA
* * ** *
41559810 ATGCCAACGTCCCAAAC-GTGGTCTTACATGTAATCACATATCG
1 ATGCCAATGTCCCAGACAG-GGTCTTACACATAATCAAATA-CG
* *
41559853 ATGCCACTGTCCCAGACAGGGTCTTATACA-AATCAAATACG
1 ATGCCAATGTCCCAGACAGGGTCTTACACATAATCAAATACG
* *
41559894 ATGCCAATGTCCCAGACATGGTCTTACACATAAACACAAGT-CG
1 ATGCCAATGTCCCAGACAGGGTCTTACACATAATCA-AA-TACG
*
41559937 ATGCCAACGTCCCAGAC-GTGGTCTT
1 ATGCCAATGTCCCAGACAG-GGTCTT
41559962 TCATGAAAAC
Statistics
Matches: 91, Mismatches: 13, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
41 29 0.32
42 12 0.13
43 48 0.53
44 2 0.02
ACGTcount: A:0.31, C:0.28, G:0.18, T:0.23
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACAGGGTCTTACACATAATCAAATACG
Found at i:41562122 original size:78 final size:77
Alignment explanation
Indices: 41562002--41562767 Score: 915
Period size: 78 Copynumber: 9.9 Consensus size: 77
41561992 TAATTTTCAA
* *
41562002 TTTTTGCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCGCACGCCGAGGTA-TT
1 TTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTT
41562066 TTTTAAATTTCTG
65 TTTTAAATTTCTG
* * * *
41562079 TTTTTCAAAAAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCGGACACATGCCGAGGTATT
1 TTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATT
41562144 TCTTTTAAATTTCTG
64 T-TTTTAAATTTCTG
* * *
41562159 TTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTT-
*
41562224 TTTTAAATTTCTA
65 TTTTAAATTTCTG
* * *
41562237 TTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCATCGGGTCACATC-CTGAGGTA--
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA-CGCCGAGGTATT
* *
41562299 TTTTTCAGTTTCTG
64 TTTTTAAATTTCTG
** * *
41562313 TTTTTCAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTTGGGTCACATC-CTGAGGTA-
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA-CGCCGAGGTAT
* * *
41562376 -TTTTTCAGTTTCTA
63 TTTTTTAAATTTCTG
* *
41562390 TTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATT
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACACGCCGAGGTATT
*
41562455 TTTTTTAATTTCTG
64 TTTTTAAATTTCTG
* * * *
41562469 TTTTTCAAAAATCAACTGATATTGCGAGAAGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTT-
41562534 TTTTAAATTTCTG
65 TTTTAAATTTCTG
* * *
41562547 TTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTGACATC-CTGAGGTA--
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGG-CACA-CGCCGAGGTATT
* *
41562609 -TTTTCAGTTTCTG
64 TTTTTAAATTTCTG
* * * * *
41562622 TTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGACAAATGCCGATGTATTT
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTT
*
41562687 CTTTTAAATTTCTA
65 -TTTTAAATTTCTG
* *
41562701 TTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGTCACACGCCGAGGTATTT
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGCACACGCCGAGGTATTT
41562766 TT
65 TT
41562768 CAATTTCAGT
Statistics
Matches: 605, Mismatches: 64, Indels: 39
0.85 0.09 0.06
Matches are distributed among these distances:
75 25 0.04
76 55 0.09
77 143 0.24
78 291 0.48
79 72 0.12
80 19 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (77 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTATTTT
TTTAAATTTCTG
Found at i:41562421 original size:154 final size:152
Alignment explanation
Indices: 41562002--41562774 Score: 1018
Period size: 154 Copynumber: 5.0 Consensus size: 152
41561992 TAATTTTCAA
* * * *
41562002 TTTTTGCAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCGCACGCCGAGGTATT-
1 TTTTT-CAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTC
* * * *
41562066 TTTTAAATTTCTGTTTTTCAAAAAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTC-GGACA
65 TTTTAAATTTCTATTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCA
*
41562130 CATGCCGAGGTATTTCTTTTAAATTTCTG
128 CAT-CCGAGGTA--T-TTTTCAATTTCTG
*
41562159 TTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTA-TTC
* *
41562224 TTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGTGAGTTGAGCATCGGGTCACA
65 TTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
41562289 TCCTGAGGTATTTTTCAGTTTCTG
130 TCC-GAGGTATTTTTCAATTTCTG
** * *
41562313 TTTTTCAAAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTTGGGTCACAT-CCTGAGGTA-
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCC-TCGGACACATGCC-GAGGTAT
* * *
41562376 T-TTTTCAGTTTCTATTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
63 TCTTTTAAATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTC
*
41562440 ACATGCCGAGGTATTTTTTTTAATTTCTG
127 ACAT-CCGAGGTA--TTTTTCAATTTCTG
* *
41562469 TTTTTCAAAAATCAACTGATATTGCGAGAAGTGAGTTGAGCCTCGGACACATGCCGAGGTATTTC
1 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTA-TTC
* * *
41562534 TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTGACA
65 TTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACA
*
41562599 TCCTGAGGTA-TTTTCAGTTTCTG
130 TCC-GAGGTATTTTTCAATTTCTG
* * *
41562622 TTTTTCAAAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGACAAATGCCGATGTATTT
1 TTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTA-TT
* *
41562687 CTTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGTCAC
64 CTTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCAC
*
41562752 ACGCCGAGGTATTTTTCAATTTC
129 A-TCCGAGGTATTTTTCAATTTC
41562775 AGTTAAAAAA
Statistics
Matches: 550, Mismatches: 47, Indels: 40
0.86 0.07 0.06
Matches are distributed among these distances:
153 34 0.06
154 204 0.37
155 88 0.16
156 170 0.31
157 36 0.07
158 18 0.03
ACGTcount: A:0.28, C:0.17, G:0.20, T:0.35
Consensus pattern (152 bp):
TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACACATGCCGAGGTATTCT
TTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACAT
CCGAGGTATTTTTCAATTTCTG
Found at i:41562579 original size:310 final size:307
Alignment explanation
Indices: 41562009--41562767 Score: 1144
Period size: 310 Copynumber: 2.4 Consensus size: 307
41561999 CAATTTTTGC
* * * *
41562009 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGCGCACGCCGAGGTATTTTTTAAAT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGCACA-TCCGAGGTATTTTTTAAAT
* * * *
41562074 TTCTGTTTTTCAAAAAAATCAACTCGTATTGCGAGAAGTGAGTTGAGCCTCGGACACATGCCGAG
65 TTCTATTTTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAG
*
41562139 GTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCG
129 GTATTT-TTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCG
*
41562204 GACACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAATCAACTCATATTGCAAGAGGT
193 GACACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAATCAACTCATATTACAAGAGGT
41562269 GAGTTGAGCATCGGGTCACATCCTGAGGTATTTTTCAGTTTCTGTTTTTCA
258 GAGTTGAGCATCGGGTCACATCCTGAGGTA-TTTTCAGTTTCTGTTTTTCA
** * *
41562320 AAAAATCAACTCATATTATGAGAGGTGAGTTGAGCCTTGGGTCACATCCTGAGGTA-TTTTTCAG
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGG-CACATCC-GAGGTATTTTTTAAA
*
41562384 TTTCTATTTTTCAAAAAATCAACTTATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGA
64 TTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCGA
* * *
41562449 GGTATTTTTTTTAATTTCTGTTTTTCAAAAATCAACTGATATTGCGAGAAGTGAGTTGAGCCTCG
128 GGTATTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCG
* *
41562514 GACACATGCCGAGGTATTTCTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAGGT
193 GACACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAATCAACTCATATTACAAGAGGT
* *
41562579 GAGTTGAGCCTCGGGTGACATCCTGAGGTATTTTCAGTTTCTGTTTTTCA
258 GAGTTGAGCATCGGGTCACATCCTGAGGTATTTTCAGTTTCTGTTTTTCA
* * * * *
41562629 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGACAAATGCCGATGTATTTCTTTTAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGCACAT-CCGAGGTA-TT-TTTTAA
* *
41562694 ATTTCTATTTTTC-AAAAATCAACTCATATTGCGAGAGATGAGTTGAGCCTCAGGTCACACGCCG
63 ATTTCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGTCACATGCCG
41562758 AGGTATTTTT
127 AGGTATTTTT
41562768 CAATTTCAGT
Statistics
Matches: 406, Mismatches: 35, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
308 9 0.02
309 58 0.14
310 238 0.59
311 92 0.23
312 9 0.02
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (307 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGGCACATCCGAGGTATTTTTTAAATT
TCTATTTTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGTCACATGCCGAGGT
ATTTTTTTAAATTTCTGTTTTTCAAAAATCAACTCATATTACGAGAAGTGAGTTGAGCCTCGGAC
ACATGCCGAGGTATTTCTTTTAAATTTCTATTTTTCAAAAATCAACTCATATTACAAGAGGTGAG
TTGAGCATCGGGTCACATCCTGAGGTATTTTCAGTTTCTGTTTTTCA
Found at i:41563023 original size:30 final size:30
Alignment explanation
Indices: 41562962--41563088 Score: 114
Period size: 30 Copynumber: 4.3 Consensus size: 30
41562952 GTTTTTAAAA
* * **
41562962 AAAATTGCATTTTGACCCCT-AACTTTTTT
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* *
41562991 AAAATTACATTTCAACCCCTAAACTTTCTT
1 AAAATTACATTTTAACCCCTAAACTTTCCT
** * *
41563021 AAAATTGTATTTTAACCCTTGAACTTTCCT
1 AAAATTACATTTTAACCCCTAAACTTTCCT
* * * *
41563051 AGAATTACATTTTGA-CCCTAAAATTTCCC
1 AAAATTACATTTTAACCCCTAAACTTTCCT
41563080 AAAATTACA
1 AAAATTACA
41563089 CTTTGGCCAC
Statistics
Matches: 78, Mismatches: 19, Indels: 2
0.79 0.19 0.02
Matches are distributed among these distances:
29 35 0.45
30 43 0.55
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.39
Consensus pattern (30 bp):
AAAATTACATTTTAACCCCTAAACTTTCCT
Found at i:41563084 original size:59 final size:59
Alignment explanation
Indices: 41562962--41563085 Score: 133
Period size: 59 Copynumber: 2.1 Consensus size: 59
41562952 GTTTTTAAAA
* ** * **
41562962 AAAATTGCATTTTGACCCCTAACTTTTTTAAAATTACATTTCAACCCCTAAACTTTCTT
1 AAAATTGCATTTTAACCCCTAACTTTCCTAAAATTACATTTCAACCCCTAAAATTTCCC
* * * **
41563021 AAAATTGTATTTTAACCCTTGAACTTTCCTAGAATTACATTTTGA-CCCTAAAATTTCCC
1 AAAATTGCATTTTAACCCCT-AACTTTCCTAAAATTACATTTCAACCCCTAAAATTTCCC
41563080 AAAATT
1 AAAATT
41563086 ACACTTTGGC
Statistics
Matches: 53, Mismatches: 11, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
59 34 0.64
60 19 0.36
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.40
Consensus pattern (59 bp):
AAAATTGCATTTTAACCCCTAACTTTCCTAAAATTACATTTCAACCCCTAAAATTTCCC
Found at i:41563619 original size:23 final size:21
Alignment explanation
Indices: 41563593--41563673 Score: 82
Period size: 20 Copynumber: 3.9 Consensus size: 21
41563583 CTGATCGTGA
41563593 AAGAAAGAAAGAAAGAAAAAG
1 AAGAAAGAAAGAAAGAAAAAG
41563614 -AG-AAGAAAGAAAGAAAGAAG
1 AAGAAAGAAAGAAAGAAA-AAG
*
41563634 AAG-AAGAAAG-AAGAAGGAAG
1 AAGAAAGAAAGAAAGAA-AAAG
41563654 AAGAAAGGGAAAGAAA-AAAA
1 AAGAAA--GAAAGAAAGAAAA
41563674 TTTAATTCAG
Statistics
Matches: 51, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
19 14 0.27
20 16 0.31
21 11 0.22
22 1 0.02
23 7 0.14
24 2 0.04
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (21 bp):
AAGAAAGAAAGAAAGAAAAAG
Found at i:41563621 original size:27 final size:28
Alignment explanation
Indices: 41563591--41563671 Score: 94
Period size: 30 Copynumber: 2.8 Consensus size: 28
41563581 CGCTGATCGT
41563591 GAAAGAAAGAAAGAAAGAAAAAG-AGAA
1 GAAAGAAAGAAAGAAAGAAAAAGAAGAA
41563618 GAAAGAAAGAAAGAAGAAGAAGAAAGAAGAA
1 GAAAGAAAGAAAG-A-AAGAA-AAAGAAGAA
*
41563649 GGAAG-AAGAAAGGGAAAGAAAAA
1 GAAAGAAAGAAA--GAAAGAAAAA
41563672 AATTTAATTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
27 13 0.28
28 1 0.02
29 8 0.17
30 15 0.32
31 9 0.19
32 1 0.02
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (28 bp):
GAAAGAAAGAAAGAAAGAAAAAGAAGAA
Found at i:41563669 original size:4 final size:4
Alignment explanation
Indices: 41563591--41563645 Score: 66
Period size: 4 Copynumber: 14.8 Consensus size: 4
41563581 CGCTGATCGT
41563591 GAAA GAAA GAAA GAAA G-AA -AAA GAGAA GAAA GAAA GAAA G-AA G-AA
1 GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA
41563636 G-AA GAAA GAA
1 GAAA GAAA GAA
41563646 GAAGGAAGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
3 13 0.28
4 30 0.64
5 4 0.09
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:41563935 original size:14 final size:14
Alignment explanation
Indices: 41563899--41563944 Score: 58
Period size: 14 Copynumber: 3.3 Consensus size: 14
41563889 AGCAGTCCAG
*
41563899 AAAAAAAAGAGGAA
1 AAAAAAAAAAGGAA
*
41563913 GAAAAAAAAA-GAA
1 AAAAAAAAAAGGAA
41563926 AAAAAGAAAAAGGAA
1 AAAAA-AAAAAGGAA
41563941 AAAA
1 AAAA
41563945 CCAAGCTCGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
13 7 0.26
14 13 0.48
15 7 0.26
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAGGAA
Found at i:41564443 original size:16 final size:15
Alignment explanation
Indices: 41564411--41564444 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
41564401 CCTTTTAAAA
41564411 AAATTCTCGTGTTTC
1 AAATTCTCGTGTTTC
*
41564426 AAATTTTCGTGTTTTC
1 AAATTCTCGTG-TTTC
41564442 AAA
1 AAA
41564445 AATTTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.26, C:0.15, G:0.12, T:0.47
Consensus pattern (15 bp):
AAATTCTCGTGTTTC
Found at i:41564449 original size:18 final size:18
Alignment explanation
Indices: 41564409--41564549 Score: 79
Period size: 18 Copynumber: 8.3 Consensus size: 18
41564399 GTCCTTTTAA
*
41564409 AAAAATTCTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
41564426 --AAATTTTCGTGTTTTC
1 AAAAATTTTCGTGTTTTC
*
41564442 AAAAATTTT-TTGTGTTTC
1 AAAAATTTTCGTGT-TTTC
*
41564460 -AAAAGTTTCGTG-TTTC
1 AAAAATTTTCGTGTTTTC
* *
41564476 AAAAA-ATTCCTGTGTTTC
1 AAAAATTTTCGTGT-TTTC
* * *
41564494 AAAAATTTCCTTGTCTTC
1 AAAAATTTTCGTGTTTTC
*
41564512 AAAAAATATT-GTG-TTTC
1 -AAAAATTTTCGTGTTTTC
* *
41564529 -AAAATTATCGAGTTTT-
1 AAAAATTTTCGTGTTTTC
41564545 AAAAA
1 AAAAA
41564550 AAATTTCGTA
Statistics
Matches: 94, Mismatches: 17, Indels: 26
0.69 0.12 0.19
Matches are distributed among these distances:
15 16 0.17
16 15 0.16
17 24 0.26
18 27 0.29
19 12 0.13
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (18 bp):
AAAAATTTTCGTGTTTTC
Found at i:41564457 original size:34 final size:34
Alignment explanation
Indices: 41564409--41564550 Score: 126
Period size: 34 Copynumber: 4.1 Consensus size: 34
41564399 GTCCTTTTAA
* *
41564409 AAAAATTCTCGTGTTTC-AAATTTTCGTGTTTTC
1 AAAAATTATTGTGTTTCAAAATTTTCGTGTTTTC
* *
41564442 AAAAATTTTTTGTGTTTCAAAAGTTTCGTG-TTTC
1 AAAAA-TTATTGTGTTTCAAAATTTTCGTGTTTTC
** * * *
41564476 AAAAAATTCCTGTGTTTCAAAAATTTCCTTGTCTTC
1 -AAAAATTATTGTGTTTC-AAAATTTTCGTGTTTTC
* * * *
41564512 AAAAAATATTGTGTTTCAAAATTATCGAGTTTTA
1 AAAAATTATTGTGTTTCAAAATTTTCGTGTTTTC
41564546 AAAAA
1 AAAAA
41564551 AATTTCGTAT
Statistics
Matches: 86, Mismatches: 18, Indels: 9
0.76 0.16 0.08
Matches are distributed among these distances:
33 5 0.06
34 40 0.47
35 38 0.44
36 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.11, T:0.44
Consensus pattern (34 bp):
AAAAATTATTGTGTTTCAAAATTTTCGTGTTTTC
Found at i:41564474 original size:16 final size:16
Alignment explanation
Indices: 41564409--41564532 Score: 99
Period size: 16 Copynumber: 7.2 Consensus size: 16
41564399 GTCCTTTTAA
41564409 AAAAATTCTCGTGTTTC
1 AAAAATT-TCGTGTTTC
*
41564426 -AAATTTTCGTGTTTTC
1 AAAAATTTCGTG-TTTC
*
41564442 AAAAATTTTTTGTGTTTC
1 AAAAA--TTTCGTGTTTC
*
41564460 AAAAGTTTCGTGTTTC
1 AAAAATTTCGTGTTTC
*
41564476 AAAAAATTCCTGTGTTTC
1 -AAAAATTTC-GTGTTTC
*
41564494 AAAAATTTCCTTGTCTTC
1 AAAAATTT-CGTGT-TTC
41564512 AAAAAATATT-GTGTTTC
1 -AAAAAT-TTCGTGTTTC
41564529 AAAA
1 AAAA
41564533 TTATCGAGTT
Statistics
Matches: 87, Mismatches: 10, Indels: 21
0.74 0.08 0.18
Matches are distributed among these distances:
15 5 0.06
16 23 0.26
17 23 0.26
18 22 0.25
19 12 0.14
20 2 0.02
ACGTcount: A:0.31, C:0.13, G:0.11, T:0.44
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:41564551 original size:34 final size:32
Alignment explanation
Indices: 41564403--41564565 Score: 121
Period size: 35 Copynumber: 4.7 Consensus size: 32
41564393 CGATACGTCC
*
41564403 TTTTAAAAAAATTCTCGTGTTTCAAATTTTCGTG
1 TTTTAAAAAAATT-T-GTGTTTCAAAATTTCGTG
**
41564437 TTTTCAAAAATTTTTTGTGTTTCAAAAGTTTCGTG
1 TTTT-AAAAA-AATTTGTGTTTCAAAA-TTTCGTG
* *
41564472 -TTTCAAAAAATTCCTGTGTTTCAAAAATTTCCTTG
1 TTTTAAAAAAATT--TGTGTTTC-AAAATTT-CGTG
* * *
41564507 TCTTCAAAAAATATTGTGTTTCAAAATTATCGAG
1 TTTTAAAAAAAT-TTGTGTTTCAAAATT-TCGTG
*
41564541 TTTTAAAAAAAATTTCGTATTTCAA
1 TTTT-AAAAAAATTT-GTGTTTCAA
41564566 TCGGATCACG
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
32 2 0.02
33 4 0.04
34 41 0.39
35 44 0.42
36 12 0.12
37 1 0.01
ACGTcount: A:0.33, C:0.12, G:0.10, T:0.45
Consensus pattern (32 bp):
TTTTAAAAAAATTTGTGTTTCAAAATTTCGTG
Found at i:41573703 original size:15 final size:15
Alignment explanation
Indices: 41573683--41573734 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
41573673 ACTACAAAAC
41573683 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
41573698 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
41573717 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
41573732 ATT
1 ATT
41573735 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:41585236 original size:20 final size:21
Alignment explanation
Indices: 41585209--41585252 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
41585199 ACATTAAAAA
41585209 ATATAAAA-T-AGAAATAAAT
1 ATATAAAATTCAGAAATAAAT
*
41585228 ATATAAAAATTCAGAAATATAT
1 ATAT-AAAATTCAGAAATAAAT
41585250 ATA
1 ATA
41585253 ATCTAGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 4 0.19
21 1 0.05
22 12 0.57
ACGTcount: A:0.64, C:0.02, G:0.05, T:0.30
Consensus pattern (21 bp):
ATATAAAATTCAGAAATAAAT
Found at i:41586530 original size:79 final size:80
Alignment explanation
Indices: 41586426--41586585 Score: 313
Period size: 79 Copynumber: 2.0 Consensus size: 80
41586416 TAGAATTAAA
41586426 TATAAAATATTTTTGAAATTTTAGTATTTACCCTATAGTGAGACTATATGTATTAAATAAGATAA
1 TATAAAATATTTTTGAAATTTTAGTATTTACCCTATAGTGAGACTATATGTATTAAATAAGATAA
41586491 AATTATAAGCAATTT
66 AATTATAAGCAATTT
41586506 TATAAAATA-TTTTGAAATTTTAGTATTTACCCTATAGTGAGACTATATGTATTAAATAAGATAA
1 TATAAAATATTTTTGAAATTTTAGTATTTACCCTATAGTGAGACTATATGTATTAAATAAGATAA
41586570 AATTATAAGCAATTT
66 AATTATAAGCAATTT
41586585 T
1 T
41586586 GAAAAACTAC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
79 71 0.89
80 9 0.11
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.41
Consensus pattern (80 bp):
TATAAAATATTTTTGAAATTTTAGTATTTACCCTATAGTGAGACTATATGTATTAAATAAGATAA
AATTATAAGCAATTT
Found at i:41589050 original size:3 final size:3
Alignment explanation
Indices: 41589044--41589091 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
41589034 TTTACACTAC
* *
41589044 TAT TAT TAT TAT TAT TAT T-T TA- AAT TAT TAT TAT TAT AAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41589090 TA
1 TA
41589092 GTACGTTTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 3 0.08
3 36 0.92
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:41589065 original size:28 final size:28
Alignment explanation
Indices: 41589033--41589090 Score: 80
Period size: 28 Copynumber: 2.1 Consensus size: 28
41589023 TCTGTCATTT
* *
41589033 TTTTACACTACTATTATTATTATTATTA
1 TTTTAAACTACTATTATTATAATTATTA
* *
41589061 TTTTAAATTATTATTATTATAATTATTA
1 TTTTAAACTACTATTATTATAATTATTA
41589089 TT
1 TT
41589091 AGTACGTTTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.60
Consensus pattern (28 bp):
TTTTAAACTACTATTATTATAATTATTA
Found at i:41589072 original size:16 final size:15
Alignment explanation
Indices: 41589044--41589091 Score: 73
Period size: 15 Copynumber: 3.3 Consensus size: 15
41589034 TTTACACTAC
*
41589044 TATTATTATTATTAT
1 TATTATTATAATTAT
41589059 TATT-TTA-AATTAT
1 TATTATTATAATTAT
41589072 TATTATTATAATTAT
1 TATTATTATAATTAT
41589087 TATTA
1 TATTA
41589092 GTACGTTTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
13 9 0.30
14 6 0.20
15 15 0.50
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (15 bp):
TATTATTATAATTAT
Found at i:41591099 original size:50 final size:50
Alignment explanation
Indices: 41591021--41591263 Score: 342
Period size: 50 Copynumber: 4.8 Consensus size: 50
41591011 ATTTGGGTAA
*
41591021 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
41591071 AGGGGTCCCATGTAAGACCATGTTTGGGACATGACATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * *
41591121 AGAGGTCCCATATAGGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
* * * * *
41591171 AGAGGTCCCCTGTAAAACCATGTCTGGGACATGGCATGGGCACCGACACG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
41591221 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
41591264 TGTTATTATC
Statistics
Matches: 168, Mismatches: 24, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
50 134 0.80
51 34 0.20
ACGTcount: A:0.26, C:0.23, G:0.30, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:41594155 original size:3 final size:3
Alignment explanation
Indices: 41594147--41594174 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
41594137 CCCCTCAAGT
41594147 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41594175 ATAATACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:41594672 original size:230 final size:231
Alignment explanation
Indices: 41594258--41594718 Score: 915
Period size: 230 Copynumber: 2.0 Consensus size: 231
41594248 ACATTATTTA
41594258 ATATATAATTATTTTTTATAAATTTAATTTTTAAATATAACTTATCATAAATACTAATATATGTA
1 ATATATAATTATTTTTTATAAATTTAATTTTTAAATATAACTTATCATAAATACTAATATATGTA
41594323 TATTCTATTCTTTATTTTAAATATGTTCTTAAATCTTAATTAATTTATTATATATTCAAATTTAA
66 TATTCTATTCTTTATTTTAAATATGTTCTTAAATCTTAATTAATTTATTATATATTCAAATTTAA
41594388 TGTATTTAATGGTCATTTTTAATTCTAATTTTATCACCACTGTGTTTAAATTAAAATACACATCT
131 TGTATTTAATGGTCATTTTTAATTCTAATTTTATCACCACTGTGTTTAAATTAAAATACACATCT
41594453 CTCAGCTAATTTTAATCTCATTATTATAATTATTGC
196 CTCAGCTAATTTTAATCTCATTATTATAATTATTGC
41594489 ATATATAATT-TTTTTTATAAATTTAATTTTTAAATATAACTTATCATAAATACTAATATATGTA
1 ATATATAATTATTTTTTATAAATTTAATTTTTAAATATAACTTATCATAAATACTAATATATGTA
41594553 TATTCTATTCTTTATTTTAAATATGTTCTTAAATCTTAATTAATTTATTATATATTCAAATTTAA
66 TATTCTATTCTTTATTTTAAATATGTTCTTAAATCTTAATTAATTTATTATATATTCAAATTTAA
41594618 TGTATTTAATGGTCATTTTTAATTCTAATTTTATCACCACTGTGTTTAAATTAAAATACACATCT
131 TGTATTTAATGGTCATTTTTAATTCTAATTTTATCACCACTGTGTTTAAATTAAAATACACATCT
41594683 CTCAGCTAATTTTAATCTCATTATTATAATTATTGC
196 CTCAGCTAATTTTAATCTCATTATTATAATTATTGC
41594719 TCTCCCGCCA
Statistics
Matches: 230, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
230 220 0.96
231 10 0.04
ACGTcount: A:0.36, C:0.10, G:0.04, T:0.50
Consensus pattern (231 bp):
ATATATAATTATTTTTTATAAATTTAATTTTTAAATATAACTTATCATAAATACTAATATATGTA
TATTCTATTCTTTATTTTAAATATGTTCTTAAATCTTAATTAATTTATTATATATTCAAATTTAA
TGTATTTAATGGTCATTTTTAATTCTAATTTTATCACCACTGTGTTTAAATTAAAATACACATCT
CTCAGCTAATTTTAATCTCATTATTATAATTATTGC
Found at i:41595311 original size:15 final size:15
Alignment explanation
Indices: 41595291--41595322 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
41595281 AACAAAATTG
41595291 AATCCAAGTCAGATA
1 AATCCAAGTCAGATA
41595306 AATCCAAGTCAGATA
1 AATCCAAGTCAGATA
41595321 AA
1 AA
41595323 AAAATTAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.50, C:0.19, G:0.12, T:0.19
Consensus pattern (15 bp):
AATCCAAGTCAGATA
Found at i:41597306 original size:2 final size:2
Alignment explanation
Indices: 41597299--41597329 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
41597289 ATTTCATTCC
41597299 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41597330 ATCACATAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41598770 original size:28 final size:28
Alignment explanation
Indices: 41598644--41598769 Score: 171
Period size: 28 Copynumber: 4.5 Consensus size: 28
41598634 ATTAATAAGT
** * *
41598644 TCGCACACTTAGTGCTGAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* * *
41598672 TCGCACACGTAGTGCTTTGCCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
41598700 TCGCACACTTAGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
41598728 TCGCACACTTAGTGTTTTACAATTAAAT
1 TCGCACACTTAGTGCTTTACAATTAAAC
41598756 TCGCACACTTAGTG
1 TCGCACACTTAGTG
41598770 TCGAAAGTCA
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.30, C:0.25, G:0.14, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:41601333 original size:51 final size:51
Alignment explanation
Indices: 41601257--41601355 Score: 171
Period size: 51 Copynumber: 1.9 Consensus size: 51
41601247 GCGAGAGACA
** *
41601257 CGTCGAGCATTATTTGTACGAAGACGAGGCTGATCAACTTTATCTTCCTAG
1 CGTCGAGCATTATTTACACGAAGACGAGGCTGATCAACCTTATCTTCCTAG
41601308 CGTCGAGCATTATTTACACGAAGACGAGGCTGATCAACCTTATCTTCC
1 CGTCGAGCATTATTTACACGAAGACGAGGCTGATCAACCTTATCTTCC
41601356 CAATTACGAT
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.29
Consensus pattern (51 bp):
CGTCGAGCATTATTTACACGAAGACGAGGCTGATCAACCTTATCTTCCTAG
Found at i:41604071 original size:15 final size:16
Alignment explanation
Indices: 41604038--41604071 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41604028 TTTAGGCTGA
41604038 TTTGGGCTTGTAATTG
1 TTTGGGCTTGTAATTG
*
41604054 TTTGGGCTT-TATTTG
1 TTTGGGCTTGTAATTG
41604069 TTT
1 TTT
41604072 AACGGGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.09, C:0.06, G:0.26, T:0.59
Consensus pattern (16 bp):
TTTGGGCTTGTAATTG
Found at i:41604525 original size:44 final size:44
Alignment explanation
Indices: 41604460--41604618 Score: 183
Period size: 44 Copynumber: 3.6 Consensus size: 44
41604450 GCCAGTATGG
* * *
41604460 GAAGATAAGATCTGCTATCTTCGATCTACTTCACGTCAATACAT
1 GAAGATAAGATCTACTTTCTTCGATCTACTTCACGCCAATACAT
** * * ***
41604504 GAAGACGAGATCTACTTTCTTCGATCTACTTCGCCACCAATATGG
1 GAAGATAAGATCTACTTTCTTCGATCTACTTC-ACGCCAATACAT
* *
41604549 GAAGATAAGATCTAGTTTCGTCGATCTACTTCACGCCAATACAT
1 GAAGATAAGATCTACTTTCTTCGATCTACTTCACGCCAATACAT
* *
41604593 AAAGATAAGACCTACTTTCTTCGATC
1 GAAGATAAGATCTACTTTCTTCGATC
41604619 GATTCCACTG
Statistics
Matches: 91, Mismatches: 23, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
44 57 0.63
45 34 0.37
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (44 bp):
GAAGATAAGATCTACTTTCTTCGATCTACTTCACGCCAATACAT
Found at i:41604560 original size:45 final size:44
Alignment explanation
Indices: 41604436--41604618 Score: 177
Period size: 44 Copynumber: 4.1 Consensus size: 44
41604426 CTTGTATCTC
* * ** * *
41604436 CGATCTACTTCGCCGCCAGTATGGGAAGATAAGATCTGCTATCTT
1 CGATCTACTTC-ACGCCAATACAGGAAGATAAGATCTACTTTCTT
* * **
41604481 CGATCTACTTCACGTCAATACATGAAGACGAGATCTACTTTCTT
1 CGATCTACTTCACGCCAATACAGGAAGATAAGATCTACTTTCTT
* * ** * *
41604525 CGATCTACTTCGCCACCAATATGGGAAGATAAGATCTAGTTTCGT
1 CGATCTACTTC-ACGCCAATACAGGAAGATAAGATCTACTTTCTT
** *
41604570 CGATCTACTTCACGCCAATACATAAAGATAAGACCTACTTTCTT
1 CGATCTACTTCACGCCAATACAGGAAGATAAGATCTACTTTCTT
41604614 CGATC
1 CGATC
41604619 GATTCCACTG
Statistics
Matches: 108, Mismatches: 29, Indels: 3
0.77 0.21 0.02
Matches are distributed among these distances:
44 63 0.58
45 45 0.42
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (44 bp):
CGATCTACTTCACGCCAATACAGGAAGATAAGATCTACTTTCTT
Found at i:41604589 original size:89 final size:89
Alignment explanation
Indices: 41604436--41604618 Score: 269
Period size: 89 Copynumber: 2.1 Consensus size: 89
41604426 CTTGTATCTC
* * * *
41604436 CGATCTACTTCGCCGCCAGTATGGGAAGATAAGATCTGCTATCTTCGATCTACTTCACGTCAATA
1 CGATCTACTTCGCCACCAATATGGGAAGATAAGATCTGCTATCGTCGATCTACTTCACGCCAATA
* * *
41604501 CATGAAGACGAGATCTACTTTCTT
66 CATAAAGACAAGACCTACTTTCTT
*
41604525 CGATCTACTTCGCCACCAATATGGGAAGATAAGATCTAG-TTTCGTCGATCTACTTCACGCCAAT
1 CGATCTACTTCGCCACCAATATGGGAAGATAAGATCT-GCTATCGTCGATCTACTTCACGCCAAT
*
41604589 ACATAAAGATAAGACCTACTTTCTT
65 ACATAAAGACAAGACCTACTTTCTT
41604614 CGATC
1 CGATC
41604619 GATTCCACTG
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
89 83 0.99
90 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (89 bp):
CGATCTACTTCGCCACCAATATGGGAAGATAAGATCTGCTATCGTCGATCTACTTCACGCCAATA
CATAAAGACAAGACCTACTTTCTT
Found at i:41604803 original size:43 final size:44
Alignment explanation
Indices: 41604622--41604803 Score: 115
Period size: 44 Copynumber: 4.2 Consensus size: 44
41604612 TTCGATCGAT
*
41604622 TCCACTGCTGA-CCAGGGAGATAGAAT-TACTGGCTTCAATATAC
1 TCCACTGCT-ACCCAGGGAGATAGAATCTACTGGCTTCAATCTAC
* * * * *** ** *
41604665 TCCACTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGC
1 TCCACTGCTACC-CAGGGAGATAGAATCTACTGGCTTCAATCTAC
* * ** * *
41604710 TCCACTACTGCTTAGGGAGATA-AGATCTGTAAT--CTTCAATCTAT
1 TCCACTGCTACCCAGGGAGATAGA-ATC--TACTGGCTTCAATCTAC
*
41604754 TCCACTGCTACCCAGGGAGATAGAAT-TACTGGCTTCAATGTAC
1 TCCACTGCTACCCAGGGAGATAGAATCTACTGGCTTCAATCTAC
41604797 TCCACTG
1 TCCACTG
41604804 TAACCACAAG
Statistics
Matches: 99, Mismatches: 31, Indels: 18
0.67 0.21 0.12
Matches are distributed among these distances:
41 3 0.03
42 1 0.01
43 26 0.26
44 50 0.51
45 18 0.18
46 1 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
TCCACTGCTACCCAGGGAGATAGAATCTACTGGCTTCAATCTAC
Found at i:41604817 original size:132 final size:132
Alignment explanation
Indices: 41604610--41605058 Score: 697
Period size: 132 Copynumber: 3.4 Consensus size: 132
41604600 AGACCTACTT
* * * *
41604610 TCTTCGATCGATTCCACTGCTGA-CCAGGGAGATAGAATTACTGGCTTCAATATACTCCACTGCA
1 TCTTCAATCTATTCCACTGCT-ACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTA
* *
41604674 ACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTG
65 ACCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
*
41604739 TAA
130 AAA
41604742 TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
1 TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* * *
41604807 CCACAAGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGTTTAGGGAGACAAGATCTGA
66 CCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
41604872 AA
131 AA
* * *
41604874 TCTTCAATCTATTCCACTGCTGCCCAGGGAAATAGAATTACTGGCTTCAATGTACTTCACTGTAA
1 TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
* *
41604939 CCTCAGGGAGGTAAAAT-TCACCATCTTTGATCTGCCCCATTACTGCTTAGGGAGACAAGATCTG
66 CCTCAGGGAGGTAAAATCT-ACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTG
41605003 AAA
130 AAA
* *
41605006 TCTTCAATCTATTCTACTGCTGCCCAGGGA-AGTAGAATTACTGGCTTCAATGT
1 TCTTCAATCTATTCCACTGCTACCCAGGGAGA-TAGAATTACTGGCTTCAATGT
41605059 NNNNNNNNNN
Statistics
Matches: 295, Mismatches: 19, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
131 3 0.01
132 292 0.99
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
TCTTCAATCTATTCCACTGCTACCCAGGGAGATAGAATTACTGGCTTCAATGTACTCCACTGTAA
CCTCAGGGAGGTAAAATCTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAAGATCTGA
AA
Found at i:41605543 original size:14 final size:14
Alignment explanation
Indices: 41605514--41605559 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
41605504 AATTTACAAC
*
41605514 ATATACGAATAAAT
1 ATATACAAATAAAT
* *
41605528 ATTTACAAATACAT
1 ATATACAAATAAAT
41605542 ATATACAAATATAAT
1 ATATACAAATA-AAT
41605557 ATA
1 ATA
41605560 ACAGTAAAGT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
14 21 0.81
15 5 0.19
ACGTcount: A:0.57, C:0.09, G:0.02, T:0.33
Consensus pattern (14 bp):
ATATACAAATAAAT
Found at i:41607917 original size:43 final size:43
Alignment explanation
Indices: 41607777--41607918 Score: 140
Period size: 44 Copynumber: 3.2 Consensus size: 43
41607767 ACCGATATAA
* * *
41607777 GAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGACCTG-TTTCTTTGATCTACTTCACGCTAGTACAT
* * * * * * * **
41607821 GAAGATAAAATCTATTTTCTTCGATCTACTCCACCACTAGTACGG
1 GAAGACAAGACCT-GTTTCTTTGATCTACTTCA-CGCTAGTACAT
*
41607866 GGAGACAAGACCTGTTTCTTTGATCTACTTCACGCTAGTACAT
1 GAAGACAAGACCTGTTTCTTTGATCTACTTCACGCTAGTACAT
41607909 GAAGACAAGA
1 GAAGACAAGA
41607919 ACATGAAGAT
Statistics
Matches: 73, Mismatches: 23, Indels: 5
0.72 0.23 0.05
Matches are distributed among these distances:
43 17 0.23
44 40 0.55
45 16 0.22
ACGTcount: A:0.30, C:0.24, G:0.18, T:0.28
Consensus pattern (43 bp):
GAAGACAAGACCTGTTTCTTTGATCTACTTCACGCTAGTACAT
Found at i:41607993 original size:101 final size:102
Alignment explanation
Indices: 41607817--41608019 Score: 383
Period size: 101 Copynumber: 2.0 Consensus size: 102
41607807 TCACGCCAGT
41607817 ACATGAAGATAAAATCTATTTTCTTCGATCTACTCCACCACTAGTACGGGGAGACAAGACCTGTT
1 ACATGAAGATAAAATCTATTTTCTTCGATCTACTCCACCACTAGTACGGGGAGACAAGACCTGTT
41607882 TCTTTGATCTACTTCACGCTAGTAC-ATGAAGACAAGA
66 TCTTTGATCTACTTCACGCTAGTACAAT-AAGACAAGA
41607919 ACATGAAGAT-AAATCTATTTTCTTCGATCTACTCCACCACTAGTACGGGGAGACAAGACCTGTT
1 ACATGAAGATAAAATCTATTTTCTTCGATCTACTCCACCACTAGTACGGGGAGACAAGACCTGTT
41607983 TCTTTGATCTACTTCACGCTAGTACAATAAGACAAGA
66 TCTTTGATCTACTTCACGCTAGTACAATAAGACAAGA
41608020 TCTGTTTTCT
Statistics
Matches: 100, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
101 88 0.88
102 12 0.12
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.29
Consensus pattern (102 bp):
ACATGAAGATAAAATCTATTTTCTTCGATCTACTCCACCACTAGTACGGGGAGACAAGACCTGTT
TCTTTGATCTACTTCACGCTAGTACAATAAGACAAGA
Found at i:41608294 original size:133 final size:133
Alignment explanation
Indices: 41608078--41608532 Score: 813
Period size: 133 Copynumber: 3.4 Consensus size: 133
41608068 GAAATCTTCA
*
41608078 ATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCAC-A
1 ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA
* * ** * *
41608142 GGGAGGTAAAATCTACCATCTTTGATCAGCTTCGCTGTCTATACAGGAAGGCAAGATCTGCTATC
66 -GGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATCTGCTATC
41608207 TTTG
130 TTTG
* *
41608211 ATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA
1 ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA
41608276 GGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATCTGCTATCT
66 GGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATCTGCTATCT
41608341 TTG
131 TTG
41608344 ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA
1 ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA
41608409 GGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATCTGCTATCT
66 GGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATCTGCTATCT
41608474 TTG
131 TTG
41608477 ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTG
1 ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTG
41608533 NNNNNNNNNN
Statistics
Matches: 312, Mismatches: 9, Indels: 2
0.97 0.03 0.01
Matches are distributed among these distances:
133 311 1.00
134 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (133 bp):
ATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTAACCACGA
GGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATCTGCTATCT
TTG
Found at i:41609729 original size:44 final size:43
Alignment explanation
Indices: 41609676--41609820 Score: 148
Period size: 44 Copynumber: 3.3 Consensus size: 43
41609666 GGACCTGCTA
* * *
41609676 TCTTTGATCTACTTCACGCCAGTACATGAAGATAAAATCTATTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCT-TTT
* ** * * *
41609720 TCTTCGATCTACTCCAC-CACTAGTACGGGGAGACAAGACCTGTT
1 TCTTCGATCTACTTCACGC-C-AGTACATGAAGACAAGATCTTTT
* *
41609764 TCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCT-TTT
41609808 TCTTCGATCTACT
1 TCTTCGATCTACT
41609821 CCACCACCAG
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
43 17 0.22
44 47 0.59
45 15 0.19
ACGTcount: A:0.27, C:0.24, G:0.15, T:0.34
Consensus pattern (43 bp):
TCTTCGATCTACTTCACGCCAGTACATGAAGACAAGATCTTTT
Found at i:41609776 original size:88 final size:89
Alignment explanation
Indices: 41609659--41609845 Score: 286
Period size: 88 Copynumber: 2.1 Consensus size: 89
41609649 ACCGATATAA
* *
41609659 GAAGACAGGACCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGATAAAATCTATTTTCTT
1 GAAGACAAGACCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTATTTTCTT
*
41609724 CGATCTACTCCACCACTAGTACGG
66 CGATCTACTCCACCACCAGTACGG
* * * * *
41609748 GGAGACAAGACCTG-TTTCTTTGATCTACTTCACGCTAGTACATGAAGACAAGATCTGTTTTCTT
1 GAAGACAAGACCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTATTTTCTT
*
41609812 CGATCTACTCCACCACCAGTATGG
66 CGATCTACTCCACCACCAGTACGG
41609836 GAAGACAAGA
1 GAAGACAAGA
41609846 TTTGAAATCT
Statistics
Matches: 88, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
88 76 0.86
89 12 0.14
ACGTcount: A:0.29, C:0.25, G:0.18, T:0.28
Consensus pattern (89 bp):
GAAGACAAGACCTGCTATCTTTGATCTACTTCACGCCAGTACATGAAGACAAAATCTATTTTCTT
CGATCTACTCCACCACCAGTACGG
Found at i:41609857 original size:45 final size:44
Alignment explanation
Indices: 41609718--41609846 Score: 161
Period size: 44 Copynumber: 2.9 Consensus size: 44
41609708 TAAAATCTAT
* *
41609718 TTTCTTCGATCTACTCCACCACTAGTACGGGGAGACAAGACCTG
1 TTTCTTCGATCTACTCCACCACTAGTACGGGAAGACAAGATCTG
* * * **
41609762 TTTCTTTGATCTACTTCA-CGCTAGTACATGAAGACAAGATCTG
1 TTTCTTCGATCTACTCCACCACTAGTACGGGAAGACAAGATCTG
* *
41609805 TTTTCTTCGATCTACTCCACCACCAGTATGGGAAGACAAGAT
1 -TTTCTTCGATCTACTCCACCACTAGTACGGGAAGACAAGAT
41609847 TTGAAATCTT
Statistics
Matches: 69, Mismatches: 14, Indels: 3
0.80 0.16 0.03
Matches are distributed among these distances:
43 20 0.29
44 32 0.46
45 17 0.25
ACGTcount: A:0.27, C:0.26, G:0.18, T:0.29
Consensus pattern (44 bp):
TTTCTTCGATCTACTCCACCACTAGTACGGGAAGACAAGATCTG
Found at i:41609993 original size:132 final size:134
Alignment explanation
Indices: 41609838--41610744 Score: 1045
Period size: 132 Copynumber: 6.8 Consensus size: 134
41609828 CAGTATGGGA
* *
41609838 AGACAAGATTTGAAATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCAA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
*
41609903 TGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATATTTGATCTGC-CCT-ACTACTGCTT
66 TGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCTGACTACTGCTT
41609966 AAGG
131 AAGG
* *
41609970 AGACAAAATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAG
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
* * * *
41610035 TGTACTCCACTGTAACCACAGGGAGGTAAAATCTACCATCTTTGATCAGCTTC-G-CT-GT-CTA
66 TGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCTGACTACTGCT-
41610096 TACAGG
130 TA-AGG
* ** ** * *
41610102 AAGGCAAGATCTGCTATCTTTGATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCA
1 -AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCA
* * *
41610167 ATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTA-T
65 ATGTACTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATCTTTGATCTGC-TC-CTGACTACT
*
41610230 GCAGTAA-G
127 GC-TTAAGG
** **
41610238 -G-CAAGATCTGCTATCTTTGATCTATTCCACTGCTGCCCAGGGAAGTAGAATTA-TCGGCTTCA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACT-GGCTTCA
41610300 ATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCGCCATCTTTGATCTGCTCC--ACTACTGC
65 ATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCTGACTACTGC
*
41610362 TTAGGG
129 TTAAGG
* * * *
41610368 AGGCAAGATCTGAAATCTCCAATCTATTCCGCTGCTGCCCAGAG-AGATAGAATTACTGGCTTCA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCA
* * *
41610432 ATGTACTCCACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTAATCTG--CCTCACTACTGC
65 ATGTACTCCACTGTAACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCTGACTACTGC
*
41610494 TTAGGG
129 TTAAGG
* * * *
41610500 AGATAAGCTCTGAAATCTTCAATCTATTCCGCTGCTGCCCAGGG-AGATAGAATTACTAGCTTCA
1 AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCA
* *
41610564 ATGTACTCCACTGTAACCAC-GAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGTCTA-T
65 ATGTACTCCACTGTAACCACAG-GGAGGTAAAATCTGCCATCTTTGATCTGC-TC-CTGACTACT
41610627 GC---AGG
127 GCTTAAGG
* ** * * * *
41610632 AAGGCAAGATCTGCTATCTTTAATCTGTTCCACTGCTGCCCAGGGAAGTAGAATTACTGTCATCA
1 -AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCA
* * * *
41610697 ATGTACTCCACTGTAACTACATGGAGGAAAAATCTGCCATCTTCGATC
65 ATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATC
41610745 AGATTCGCTG
Statistics
Matches: 676, Mismatches: 66, Indels: 65
0.84 0.08 0.08
Matches are distributed among these distances:
129 5 0.01
130 8 0.01
131 8 0.01
132 332 0.49
133 299 0.44
134 5 0.01
135 5 0.01
136 7 0.01
137 4 0.01
138 3 0.00
ACGTcount: A:0.28, C:0.24, G:0.20, T:0.28
Consensus pattern (134 bp):
AGACAAGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAA
TGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCTGACTACTGCTT
AAGG
Found at i:41610752 original size:133 final size:132
Alignment explanation
Indices: 41609852--41610787 Score: 1096
Period size: 133 Copynumber: 7.1 Consensus size: 132
41609842 AAGATTTGAA
*
41609852 ATCTTCAATCTATTCCACTGTTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
* * * * *
41609917 ACCACAGGGAGGTAAAATCTGCCATATTTGATCTG--CCCT-ACTACTGCTTAAGG-AGACAAAA
66 ACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGTTCGCTGTCTA-TGC---AGGAAGGCAAGA
**
41609978 TCTGAA
127 TCTGCT
*
41609984 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAGTGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
* * *
41610049 ACCACAGGGAGGTAAAATCTACCATCTTTGATCAGCTTCGCTGTCTATACAGGAAGGCAAGATCT
66 ACCACAGGGAGGTAAAATCTGCCATCTTTGATCTG-TTCGCTGTCTATGCAGGAAGGCAAGATCT
41610114 GCT
130 GCT
** * *
41610117 ATCTTTGATCTATTCCACTGTTGTCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
* * *
41610182 ACCAC-GAGGAGGTAAAATCTGCCATCTTCGATTTGCTTCGCTGTCTATGCAGTAAGGCAAGATC
66 ACCACAG-GGAGGTAAAATCTGCCATCTTTGATCTG-TTCGCTGTCTATGCAGGAAGGCAAGATC
41610246 TGCT
129 TGCT
**
41610250 ATCTTTGATCTATTCCACTGCTGCCCAGGGAAGTAGAATTA-TCGGCTTCAATGTACTCCACTGT
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACT-GGCTTCAATGTACTCCACTGT
* * *
41610314 AACCACAGGGAGGTAAAAT-TCGCCATCTTTGATCTGCTC-C--ACTACTGCTTAGGGAGGCAAG
65 AACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGTTCGCTGTCTA-TGC--AGGAAGGCAAG
**
41610375 ATCTGAA
126 ATCTGCT
* * *
41610382 ATCTCCAATCTATTCCGCTGCTGCCCAGAG-AGATAGAATTACTGGCTTCAATGTACTCCACTGT
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGT
* * ** * **
41610446 AACCACAGGGAGGTAAAAT-TCACCATCTTTAATCTG--C-CTCACTACTGCTTAGGGAGATAAG
65 AACCACAGGGAGGTAAAATCT-GCCATCTTTGATCTGTTCGCTGTCTA-TGC--AGGAAGGCAAG
* **
41610507 CTCTGAA
126 ATCTGCT
* *
41610514 ATCTTCAATCTATTCCGCTGCTGCCCAGGG-AGATAGAATTACTAGCTTCAATGTACTCCACTGT
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTACTCCACTGT
*
41610578 AACCAC-GAGGAGGTAAAATCTGCCATCTTCGATCTGCTTCGCTGTCTATGCAGGAAGGCAAGAT
65 AACCACAG-GGAGGTAAAATCTGCCATCTTTGATCTG-TTCGCTGTCTATGCAGGAAGGCAAGAT
41610642 CTGCT
128 CTGCT
* * * *
41610647 ATCTTTAATCTGTTCCACTGCTGCCCAGGGAAGTAGAATTACTGTCATCAATGTACTCCACTGTA
1 ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
* * * * * *
41610712 ACTACATGGAGGAAAAATCTGCCATCTTCGATCAGATTCGCTGTCTATGCAGAAAGGCAAGATCT
66 ACCACAGGGAGGTAAAATCTGCCATCTTTGATCTG-TTCGCTGTCTATGCAGGAAGGCAAGATCT
41610777 GCT
130 GCT
41610780 ATCTTCAA
1 ATCTTCAA
41610788 CTTGCTCTAC
Statistics
Matches: 710, Mismatches: 70, Indels: 47
0.86 0.08 0.06
Matches are distributed among these distances:
129 3 0.00
130 5 0.01
131 4 0.01
132 320 0.45
133 358 0.50
134 3 0.00
135 9 0.01
136 8 0.01
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (132 bp):
ATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACTCCACTGTA
ACCACAGGGAGGTAAAATCTGCCATCTTTGATCTGTTCGCTGTCTATGCAGGAAGGCAAGATCTG
CT
Found at i:41617964 original size:15 final size:16
Alignment explanation
Indices: 41617931--41617964 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
41617921 TTTAGGCTGA
41617931 TTTGGGCTTGTAATTG
1 TTTGGGCTTGTAATTG
*
41617947 TTTGGGCTT-TATTTG
1 TTTGGGCTTGTAATTG
41617962 TTT
1 TTT
41617965 AACGGGTCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.09, C:0.06, G:0.26, T:0.59
Consensus pattern (16 bp):
TTTGGGCTTGTAATTG
Found at i:41618439 original size:12 final size:14
Alignment explanation
Indices: 41618407--41618443 Score: 53
Period size: 12 Copynumber: 2.9 Consensus size: 14
41618397 ACTAAAAAAT
41618407 TAAAAT-AAATAAC
1 TAAAATCAAATAAC
41618420 TAAAATCAAATAA-
1 TAAAATCAAATAAC
41618433 T-AAATCAAATA
1 TAAAATCAAATA
41618444 TTAAGGAAGC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
12 10 0.43
13 7 0.30
14 6 0.26
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAAATCAAATAAC
Found at i:41618939 original size:19 final size:19
Alignment explanation
Indices: 41618898--41618939 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
41618888 AAAAATTCGG
*
41618898 AATAAAATCATAATAAAAT
1 AATAAAATCATAATAAAAC
*
41618917 AATAAAAT-ATGATAAATAC
1 AATAAAATCATAATAAA-AC
41618936 AATA
1 AATA
41618940 TTGAGTTTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 7 0.35
19 13 0.65
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (19 bp):
AATAAAATCATAATAAAAC
Found at i:41620943 original size:25 final size:25
Alignment explanation
Indices: 41620915--41620962 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
41620905 AAAATTGAAG
41620915 TAATTTCCTACAAAACCCTAGATCT
1 TAATTTCCTACAAAACCCTAGATCT
41620940 TAATTTCCTACAAAACCCTAGAT
1 TAATTTCCTACAAAACCCTAGAT
41620963 ATTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.27, G:0.04, T:0.31
Consensus pattern (25 bp):
TAATTTCCTACAAAACCCTAGATCT
Found at i:41627220 original size:3 final size:3
Alignment explanation
Indices: 41627212--41627794 Score: 1116
Period size: 3 Copynumber: 195.0 Consensus size: 3
41627202 ATACATTGTT
* * * *
41627212 ATA ATA ATA ATA ATA ATA ATT ACA ATA ATA GTA AT- TTA A-A ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627258 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627306 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627354 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627402 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627450 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627498 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627546 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627594 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627642 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627690 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627738 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
41627786 ATA ATA ATA
1 ATA ATA ATA
41627795 GAGTGTAAAA
Statistics
Matches: 570, Mismatches: 8, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
2 3 0.01
3 567 0.99
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:41629960 original size:73 final size:73
Alignment explanation
Indices: 41629853--41629991 Score: 201
Period size: 73 Copynumber: 1.9 Consensus size: 73
41629843 TTCTCGGTAA
* ** *
41629853 GCGTCGCAAAAAGACTTCAGCCCCACGATGCCGTTTTCTGAGCTTT-TGGGGATTTAGTGGCGTT
1 GCGTCGCAAAAAGACTTCAGCCCAACGACACCGTTTT-TGAGCTTTCGGGGGATTTAGTGGCGTT
41629917 TTTGGGGAT
65 TTTGGGGAT
*
41629926 GCGTCGC-AAACGTACTTCAGCCCAACGACACCGTTTTTGAGCTTTCGGGGGATTTAGTGGCGTT
1 GCGTCGCAAAAAG-ACTTCAGCCCAACGACACCGTTTTTGAGCTTTCGGGGGATTTAGTGGCGTT
41629990 TT
65 TT
41629992 CATGAAATCG
Statistics
Matches: 59, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
72 12 0.20
73 47 0.80
ACGTcount: A:0.18, C:0.22, G:0.29, T:0.31
Consensus pattern (73 bp):
GCGTCGCAAAAAGACTTCAGCCCAACGACACCGTTTTTGAGCTTTCGGGGGATTTAGTGGCGTTT
TTGGGGAT
Found at i:41630076 original size:187 final size:185
Alignment explanation
Indices: 41629745--41630106 Score: 451
Period size: 187 Copynumber: 1.9 Consensus size: 185
41629735 GGTAAAGCGC
* *
41629745 CGCAAAAGACTTCAGCCCAACGACGCCGTTTTCTGAGCTGAGAAGGATTTAATGGTGATTTTATG
1 CGCAAAAGACTTCAGCCCAACGACACCGTTTTCTGAGCTGAGAAGGATTTAATGGCGATTTTATG
* * **
41629810 AAAGCGCCGCCAATTATCAGTCTTTAGCGGCGTTTCTCGGTAAGCGTCGCAAAAAGACTTCAGCC
66 AAAGCGCCGCCAATGATCAGTCTTTAGCGGCGTTTCTCGGAAAGCACCGCAAAAAGACTTCAGCC
* ** *
41629875 CCACGATGCCGTTTTCTGAGCTTTTGGGGATTTAGTGGCGTTTTTGGGGATGCGT
131 CAACGACACCGTTTTCTGAGCTTTTGGGGATTTAGTGGCATTTTTGGGGATGCGT
* ** ** *
41629930 CGCAAACGTACTTCAGCCCAACGACACCGTTTT-TGAGCTTTCGGGGGATTTAGTGGCG-TTTTC
1 CGCAAAAG-ACTTCAGCCCAACGACACCGTTTTCTGAGC-TGAGAAGGATTTAATGGCGATTTT-
* * * * * * *
41629993 ATGAAATCGCCGCTAATGCTGAGGTCTTTAGCGGCGTTTTTGGGAAAGCACCGC-AAACGTACTT
63 ATGAAAGCGCCGCCAATGATCA-GTCTTTAGCGGCGTTTCTCGGAAAGCACCGCAAAAAG-ACTT
41630057 CAGCCCAACGACACCGTTTTCTGAGCTTTTGGGGATTTAGTGGCATTTTT
126 CAGCCCAACGACACCGTTTTCTGAGCTTTTGGGGATTTAGTGGCATTTTT
41630107 ATTAAAGCGC
Statistics
Matches: 149, Mismatches: 23, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
185 16 0.11
186 57 0.38
187 76 0.51
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (185 bp):
CGCAAAAGACTTCAGCCCAACGACACCGTTTTCTGAGCTGAGAAGGATTTAATGGCGATTTTATG
AAAGCGCCGCCAATGATCAGTCTTTAGCGGCGTTTCTCGGAAAGCACCGCAAAAAGACTTCAGCC
CAACGACACCGTTTTCTGAGCTTTTGGGGATTTAGTGGCATTTTTGGGGATGCGT
Found at i:41630118 original size:114 final size:114
Alignment explanation
Indices: 41629904--41630591 Score: 852
Period size: 114 Copynumber: 6.0 Consensus size: 114
41629894 GCTTTTGGGG
* * * * * * *
41629904 ATTTAGTGGCGTTTTTGGGGATGCGTCGCAAACGTACTTCAGCCCAACGACACCGTTTT-TGAGC
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCACAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
* * * * * *
41629968 TTTCGGGGGATTTAGTGGCGTTTTCATGAAATCGCCGCTAATGCTGAGGT
66 TTTC-GGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGT
* * * * *
41630018 CTTTAGCGGCGTTTTTGGGAAAGCACCGCAAACGTACTTCAGCCCAACGACACCGTTTTCTGAGC
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCACAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
* * * *
41630083 TTTTGGGGATTTAGTGGCATTTTTATTAAAGCGCCGCTAATACTCAGGG
66 TTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGT
*
41630132 ATTTAGCGGCGTTTTTGTGAAAGCGCCAC-AACAATACTTCAGCCCAACGACGCCGTTTTCTGAG
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCACAAAC-ATACTTCAGCCCAACGACGCCGTTTTCTGAG
* * *
41630196 CTTTCGGGGATTTAGTGGTGTTTTTATTAAAGCGCCATTAATACTCAGGG
65 CTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGT
*
41630246 ATTTAGCGGCGTTTTTGTGAAAGCGCCAC-AACAATACTTCAGCCCAACGACGCCGTTTTCTGAG
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCACAAAC-ATACTTCAGCCCAACGACGCCGTTTTCTGAG
* *
41630310 CTTTCGGGGATTTAGTGGTGTTTTTATTAAAGCGCCATTAATACTCA-GT
65 CTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGT
* * *
41630359 GATTTAGCGGCGTTTTTGTGAAAGCGTCACAATA-ATACTTCTGCCCAACGACGCCGTTTTCTGA
1 -ATTTAGCGGCGTTTTTGGGAAAGCGCCACAA-ACATACTTCAGCCCAACGACGCCGTTTTCTGA
** * * * *
41630423 GC-TGAGAAGGATTTAGTGGCGTTTTTATGT-ATGCGCCGCTAATGCTCAGGT
64 GCTTTCG-GGGATTTAGTGGCGTTTTTAT-TAAAGCGCCACTAATACTCAGGT
* * * * *
41630474 CTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACTTCAGCCCAACGACGCCGTTTTTTTAGC
1 ATTTAGCGGCGTTTTTGGGAAAGCGCCACAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
* *
41630539 TTTCGGGGATTTAGTGGCGTTTTTA-TGAAGCGCCACTAATACTCAGGG
66 TTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGT
41630587 ATTTA
1 ATTTA
41630592 AAATAAATTA
Statistics
Matches: 512, Mismatches: 51, Indels: 23
0.87 0.09 0.04
Matches are distributed among these distances:
112 1 0.00
113 28 0.05
114 468 0.91
115 14 0.03
116 1 0.00
ACGTcount: A:0.22, C:0.21, G:0.25, T:0.32
Consensus pattern (114 bp):
ATTTAGCGGCGTTTTTGGGAAAGCGCCACAAACATACTTCAGCCCAACGACGCCGTTTTCTGAGC
TTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGT
Found at i:41630304 original size:228 final size:227
Alignment explanation
Indices: 41629938--41630591 Score: 938
Period size: 228 Copynumber: 2.9 Consensus size: 227
41629928 GTCGCAAACG
* * * *
41629938 TACTTCAGCCCAACGACACCGTTTT-TGAGCTTTCGGGGGATTTAGTGGCGTTTTCATGAAATCG
1 TACTTCAGCCCAACGACGCCGTTTTCTGAGCTTTC-GGGGATTTAGTGGCGTTTTTATTAAAGCG
* * *
41630002 CCGCTAATGCTGAGGTCTTTAGCGGCGTTTTTGGGAAAGCACCGCAAACGTACTTCAGCCCAACG
65 CCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAA-ATACTTCAGCCCAACG
* * * *
41630067 ACACCGTTTTCTGAGCTTTTGGGGATTTAGTGGCATTTTTATTAAAGCGCCGCTAATACTCAGGG
129 ACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGG
41630132 ATTTAGCGGCGTTTTTGTGAAAGCGCCACAACAA
194 ATTTAGCGGCGTTTTTGTGAAAGCGCCACAACAA
*
41630166 TACTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGTGTTTTTATTAAAGCGC
1 TACTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGC
** * ** * *
41630231 CATTAATACTCAGGGATTTAGCGGCGTTTTTGTGAAAGCGCCACAACAATACTTCAGCCCAACGA
66 CGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAA-AATACTTCAGCCCAACGA
* * *
41630296 CGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGTGTTTTTATTAAAGCGCCATTAATACTCAGTGA
130 CGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGGA
* *
41630361 TTTAGCGGCGTTTTTGTGAAAGCGTCACAATAA
195 TTTAGCGGCGTTTTTGTGAAAGCGCCACAACAA
* ** * *
41630394 TACTTCTGCCCAACGACGCCGTTTTCTGAGC-TGAGAAGGATTTAGTGGCGTTTTTATGT-ATGC
1 TACTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCG-GGGATTTAGTGGCGTTTTTAT-TAAAGC
41630457 GCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAATACTTCAGCCCAAC
64 GCCGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGC-AAAATACTTCAGCCCAAC
* * *
41630522 GACGCCGTTTTTTTAGCTTTCGGGGATTTAGTGGCGTTTTTA-TGAAGCGCCACTAATACTCAGG
128 GACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGG
41630586 GATTTA
193 GATTTA
41630592 AAATAAATTA
Statistics
Matches: 378, Mismatches: 43, Indels: 11
0.88 0.10 0.03
Matches are distributed among these distances:
227 27 0.07
228 338 0.89
229 13 0.03
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.31
Consensus pattern (227 bp):
TACTTCAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGC
CGCTAATGCTCAGGTCTTTAGCGGCGTTTTTGGGAAAGCGCCGCAAAATACTTCAGCCCAACGAC
GCCGTTTTCTGAGCTTTCGGGGATTTAGTGGCGTTTTTATTAAAGCGCCACTAATACTCAGGGAT
TTAGCGGCGTTTTTGTGAAAGCGCCACAACAA
Found at i:41630919 original size:14 final size:14
Alignment explanation
Indices: 41630882--41630912 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
41630872 GATTTAAGGT
41630882 TTATGGGTTAGGGG
1 TTATGGGTTAGGGG
41630896 TTATGGGTTAGGGG
1 TTATGGGTTAGGGG
41630910 TTA
1 TTA
41630913 GATGTTAAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (14 bp):
TTATGGGTTAGGGG
Found at i:41630919 original size:21 final size:21
Alignment explanation
Indices: 41630886--41630929 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41630876 TAAGGTTTAT
* * *
41630886 GGGTTAGGGGTTATGGGTTAG
1 GGGTTAGAGGTTAAGAGTTAG
*
41630907 GGGTTAGATGTTAAGAGTTAG
1 GGGTTAGAGGTTAAGAGTTAG
41630928 GG
1 GG
41630930 ATTTAGGGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.20, C:0.00, G:0.48, T:0.32
Consensus pattern (21 bp):
GGGTTAGAGGTTAAGAGTTAG
Found at i:41631025 original size:7 final size:7
Alignment explanation
Indices: 41631013--41631073 Score: 61
Period size: 7 Copynumber: 8.7 Consensus size: 7
41631003 TAAATAAGGT
41631013 TTAGGGG
1 TTAGGGG
41631020 TTAGGGG
1 TTAGGGG
*
41631027 TTAGAGG
1 TTAGGGG
*
41631034 TTATGGG
1 TTAGGGG
*
41631041 TTAAGGGT
1 TT-AGGGG
41631049 TTA-GGG
1 TTAGGGG
*
41631055 TTAAGGG
1 TTAGGGG
*
41631062 TTAAGGG
1 TTAGGGG
41631069 TTAGG
1 TTAGG
41631074 AGTCAGGGAT
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 5 0.11
7 35 0.78
8 5 0.11
ACGTcount: A:0.21, C:0.00, G:0.46, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:41631042 original size:21 final size:20
Alignment explanation
Indices: 41631017--41631073 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 20
41631007 TAAGGTTTAG
*
41631017 GGGTTAGGGGTTAGAGGTTAT
1 GGGTTAGGGGTTAG-GGTTAA
*
41631038 GGGTTAAGGGTTTAGGGTTAA
1 GGGTT-AGGGGTTAGGGTTAA
*
41631059 GGGTTAAGGGTTAGG
1 GGGTTAGGGGTTAGG
41631074 AGTCAGGGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
20 8 0.26
21 15 0.48
22 8 0.26
ACGTcount: A:0.21, C:0.00, G:0.47, T:0.32
Consensus pattern (20 bp):
GGGTTAGGGGTTAGGGTTAA
Found at i:41643342 original size:17 final size:17
Alignment explanation
Indices: 41643303--41643343 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41643293 CTCATTATTA
* *
41643303 TTTTATTTTATTTTTTC
1 TTTTATTTTATTATTCC
*
41643320 TGTTATTTTATTATTCC
1 TTTTATTTTATTATTCC
41643337 TTTTATT
1 TTTTATT
41643344 ATTTTTGGCA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.15, C:0.07, G:0.02, T:0.76
Consensus pattern (17 bp):
TTTTATTTTATTATTCC
Found at i:41647475 original size:26 final size:26
Alignment explanation
Indices: 41647415--41647475 Score: 61
Period size: 26 Copynumber: 2.3 Consensus size: 26
41647405 TATTTAGAGC
* *
41647415 TCCTAATTAAATACTCTTTGTGAGCT
1 TCCTAATTAAATACTCTTTGTAAACT
* * *
41647441 TTCTGATTAAA-AGTTCTTTGTAAACT
1 TCCTAATTAAATA-CTCTTTGTAAACT
41647467 TCCTAATTA
1 TCCTAATTA
41647476 TGGCTCTTAT
Statistics
Matches: 27, Mismatches: 7, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 1 0.04
26 26 0.96
ACGTcount: A:0.30, C:0.16, G:0.10, T:0.44
Consensus pattern (26 bp):
TCCTAATTAAATACTCTTTGTAAACT
Found at i:41647577 original size:26 final size:26
Alignment explanation
Indices: 41647512--41647579 Score: 81
Period size: 26 Copynumber: 2.7 Consensus size: 26
41647502 AGCCCGGATA
*
41647512 AGCTTCCTG--ATA-GGCTTTTTGTG
1 AGCTTCCTGTTATATGGCTCTTTGTG
*
41647535 AGCTTCCCGATTA-ATGGCTCTTTGTG
1 AGCTTCCTG-TTATATGGCTCTTTGTG
41647561 AGCTTCCTGTTATATGGCT
1 AGCTTCCTGTTATATGGCT
41647580 TAAGAGAGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
23 8 0.22
25 4 0.11
26 25 0.68
ACGTcount: A:0.15, C:0.21, G:0.24, T:0.41
Consensus pattern (26 bp):
AGCTTCCTGTTATATGGCTCTTTGTG
Found at i:41680843 original size:3 final size:3
Alignment explanation
Indices: 41680837--41680861 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
41680827 GATGATTCCA
41680837 ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG A
41680862 GGAGGAGGAG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:41689862 original size:43 final size:42
Alignment explanation
Indices: 41689757--41689887 Score: 151
Period size: 43 Copynumber: 3.1 Consensus size: 42
41689747 TAACCGTCAC
41689757 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
*
41689799 ACGG-GGAATCAGCACATAGCAACC-CCTT-TCACAGTCAAGGAT
1 ACGGTGGAATCAGCACTTAGCAACCACCTTAT-A-A-TCAAGGAT
* * * * *
41689841 ATGGTGGAATCAACACTTAGCAACCACATTTATATTCAATGAT
1 ACGGTGGAATCAGCACTTAGCAACCAC-CTTATAATCAAGGAT
41689884 ACGG
1 ACGG
41689888 ATTCACATAG
Statistics
Matches: 74, Mismatches: 8, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 20 0.27
42 15 0.20
43 28 0.38
44 1 0.01
45 3 0.04
46 1 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
ACGGTGGAATCAGCACTTAGCAACCACCTTATAATCAAGGAT
Found at i:41689920 original size:26 final size:26
Alignment explanation
Indices: 41689891--41689971 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
41689881 GATACGGATT
41689891 CACATAGTAGCATGCACATAGTACTA
1 CACATAGTAGCATGCACATAGTACTA
* *
41689917 CACAT-GTGACCAT-CAC-TA-TCCGATA
1 CACATAGT-AGCATGCACATAGTAC--TA
* * *
41689942 CACGTAGTAGCCTGCATATAGTACTA
1 CACATAGTAGCATGCACATAGTACTA
41689968 CACA
1 CACA
41689972 CGTGATCGAA
Statistics
Matches: 40, Mismatches: 8, Indels: 14
0.65 0.13 0.23
Matches are distributed among these distances:
23 2 0.05
24 2 0.05
25 14 0.35
26 18 0.45
27 2 0.05
28 2 0.05
ACGTcount: A:0.35, C:0.27, G:0.15, T:0.23
Consensus pattern (26 bp):
CACATAGTAGCATGCACATAGTACTA
Found at i:41689963 original size:51 final size:51
Alignment explanation
Indices: 41689895--41690077 Score: 185
Period size: 51 Copynumber: 3.6 Consensus size: 51
41689885 CGGATTCACA
* * *
41689895 TAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
* * * *
41689946 TAGTAGCCTGCATATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATCA-CTATCCGGTACACG
* *** * *
41689997 TAGTAGCCTGCACATAGTACTACAAATACGACCTATCA-T-TCTGGTATACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACC-ATCACTATCCGGTACACG
*
41690047 TAGTAGCCTACACATAGTACTACACACGTGA
1 TAGTAGCCTGCACATAGTACTACACACGTGA
41690078 TCGANNNNNN
Statistics
Matches: 105, Mismatches: 22, Indels: 11
0.76 0.16 0.08
Matches are distributed among these distances:
50 35 0.33
51 67 0.64
52 2 0.02
53 1 0.01
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.25
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATCACTATCCGGTACACG
Found at i:41690072 original size:101 final size:102
Alignment explanation
Indices: 41689893--41690081 Score: 274
Period size: 101 Copynumber: 1.9 Consensus size: 102
41689883 TACGGATTCA
* ** *
41689893 CATAGTAGCATGCACATAGTACTACACATGTGACCATCACTATCCGATACACGTAGTAGCCTGCA
1 CATAGTAGCATGCACATAGTACTACAAATACGACCATCACTATCCGATACACGTAGTAGCCTACA
*
41689958 TATAGTACTACACACGTGATCGAAGCTATCCGGTACG
66 CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
* * * *
41689995 CATAGTAGCCTGCACATAGTACTACAAATACGACCTATCA-T-TCTGGTATACGTAGTAGCCTAC
1 CATAGTAGCATGCACATAGTACTACAAATACGACC-ATCACTATCCGATACACGTAGTAGCCTAC
41690058 ACATAGTACTACACACGTGATCGA
65 ACATAGTACTACACACGTGATCGA
41690082 NNNNNNNNNN
Statistics
Matches: 77, Mismatches: 9, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
101 41 0.53
102 32 0.42
103 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.17, T:0.24
Consensus pattern (102 bp):
CATAGTAGCATGCACATAGTACTACAAATACGACCATCACTATCCGATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCGAAGCTATCCGGTACG
Found at i:41691250 original size:26 final size:26
Alignment explanation
Indices: 41691194--41691252 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 26
41691184 TTTAGAGAAC
* * *
41691194 CTGATTAAAGGCTCTTTGTGATCTTT
1 CTGATTAAAAGCTCTTTGTAAACTTT
*
41691220 CTGATTAAAAGTTCTTTGTAAAC-TT
1 CTGATTAAAAGCTCTTTGTAAACTTT
41691245 CTTGATTA
1 C-TGATTA
41691253 TGGCTCTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.25, C:0.14, G:0.15, T:0.46
Consensus pattern (26 bp):
CTGATTAAAAGCTCTTTGTAAACTTT
Found at i:41691354 original size:26 final size:26
Alignment explanation
Indices: 41691289--41691356 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
41691279 AGCCCGGATA
*
41691289 AGCTTCCTG--ATA-GGCTTTTTGTG
1 AGCTTCCTGTTATATGGCTCTTTGTG
41691312 AGCTT-CTCGATTA-ATGGCTCTTTGTG
1 AGCTTCCT-G-TTATATGGCTCTTTGTG
41691338 AGCTTCCTGTTATATGGCT
1 AGCTTCCTGTTATATGGCT
41691357 TGAGAGAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 11
0.76 0.02 0.22
Matches are distributed among these distances:
22 2 0.05
23 6 0.16
25 4 0.11
26 23 0.62
27 2 0.05
ACGTcount: A:0.15, C:0.19, G:0.24, T:0.43
Consensus pattern (26 bp):
AGCTTCCTGTTATATGGCTCTTTGTG
Found at i:41698074 original size:16 final size:16
Alignment explanation
Indices: 41698053--41698100 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 16
41698043 TATTGATTCT
41698053 CATTATTAGTATTTCA
1 CATTATTAGTATTTCA
41698069 CATTATTACCATAGTATTTCA
1 CATTA-T----TAGTATTTCA
41698090 CATTATTAGTA
1 CATTATTAGTA
41698101 GTAATTAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 10
0.73 0.00 0.27
Matches are distributed among these distances:
16 10 0.37
17 1 0.04
20 1 0.04
21 15 0.56
ACGTcount: A:0.33, C:0.15, G:0.06, T:0.46
Consensus pattern (16 bp):
CATTATTAGTATTTCA
Found at i:41709905 original size:6 final size:6
Alignment explanation
Indices: 41709894--41709922 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
41709884 TGATGCCCAT
41709894 GTTTAA GTTTAA GTTTAA GTTTAA GTTTA
1 GTTTAA GTTTAA GTTTAA GTTTAA GTTTA
41709923 TGTATTATTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.17, T:0.52
Consensus pattern (6 bp):
GTTTAA
Found at i:41713006 original size:73 final size:73
Alignment explanation
Indices: 41712919--41713248 Score: 651
Period size: 73 Copynumber: 4.5 Consensus size: 73
41712909 ACAACTTGAC
41712919 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
41712984 CACTAACA
66 CACTAACA
41712992 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
41713057 CACTAACA
66 CACTAACA
41713065 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
41713130 CACTAACA
66 CACTAACA
41713138 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
41713203 CACTAACA
66 CACTAACA
*
41713211 AACTTAGTTGGAATACAACTAAGTTACATCATTACATC
1 AACTTAGTTGGAATACAACTAAGTTTCATCATTACATC
41713249 CAAATAATAA
Statistics
Matches: 256, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 256 1.00
ACGTcount: A:0.42, C:0.24, G:0.06, T:0.28
Consensus pattern (73 bp):
AACTTAGTTGGAATACAACTAAGTTTCATCATTACATCAACTTAAAATAAATCACCACCTACTAC
CACTAACA
Found at i:41713259 original size:3 final size:3
Alignment explanation
Indices: 41713251--41713276 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41713241 ATTACATCCA
41713251 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
41713277 ATAAAACATG
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:41726328 original size:35 final size:36
Alignment explanation
Indices: 41726282--41726352 Score: 135
Period size: 35 Copynumber: 2.0 Consensus size: 36
41726272 AACCTTCCTG
41726282 TGTAAGAGTTAGTTCGCTC-AAATATTCTTCAACCA
1 TGTAAGAGTTAGTTCGCTCAAAATATTCTTCAACCA
41726317 TGTAAGAGTTAGTTCGCTCAAAATATTCTTCAACCA
1 TGTAAGAGTTAGTTCGCTCAAAATATTCTTCAACCA
41726353 AATTGCTTGA
Statistics
Matches: 35, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 19 0.54
36 16 0.46
ACGTcount: A:0.32, C:0.20, G:0.14, T:0.34
Consensus pattern (36 bp):
TGTAAGAGTTAGTTCGCTCAAAATATTCTTCAACCA
Found at i:41742250 original size:16 final size:16
Alignment explanation
Indices: 41742229--41742259 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
41742219 TGGTTCGCTG
41742229 TATTGGATTAGAGGTA
1 TATTGGATTAGAGGTA
41742245 TATTGGATTAGAGGT
1 TATTGGATTAGAGGT
41742260 GTAATAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.32, T:0.39
Consensus pattern (16 bp):
TATTGGATTAGAGGTA
Found at i:41761036 original size:23 final size:23
Alignment explanation
Indices: 41760992--41761036 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
41760982 TCTTATTTTG
* *
41760992 TTGATTTGTGTATAATTTATTTA
1 TTGATTTGTATATAATTGATTTA
**
41761015 TTGATTTGTATATTGTTGATTT
1 TTGATTTGTATATAATTGATTT
41761037 CAAATCTCTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.22, C:0.00, G:0.16, T:0.62
Consensus pattern (23 bp):
TTGATTTGTATATAATTGATTTA
Found at i:41765497 original size:30 final size:30
Alignment explanation
Indices: 41765456--41765512 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
41765446 ATACACCATC
* *
41765456 GACATTTGCATGCTGCTGTATTGTTGCTTG
1 GACACTTGCATGCTGCTGAATTGTTGCTTG
41765486 GACACTTGCATGCTGCTGAATTGTTGC
1 GACACTTGCATGCTGCTGAATTGTTGC
41765513 CAAATTTCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.16, C:0.19, G:0.26, T:0.39
Consensus pattern (30 bp):
GACACTTGCATGCTGCTGAATTGTTGCTTG
Found at i:41771571 original size:17 final size:17
Alignment explanation
Indices: 41771545--41771577 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
41771535 CTTTGCTTGA
*
41771545 AAACCTAAAGAAGAATC
1 AAACCAAAAGAAGAATC
41771562 AAACCAAAAGAAGAAT
1 AAACCAAAAGAAGAAT
41771578 ATACAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.64, C:0.15, G:0.12, T:0.09
Consensus pattern (17 bp):
AAACCAAAAGAAGAATC
Found at i:41776986 original size:28 final size:27
Alignment explanation
Indices: 41776926--41776979 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
41776916 TATTTTTTAT
*
41776926 TTTTTTATTTTTAAATATTTTTAAAATA
1 TTTTTTATTTTT-AATATTTTAAAAATA
*
41776954 TTTTTTATTTTT-TTATTTTAAAAATA
1 TTTTTTATTTTTAATATTTTAAAAATA
41776980 AATTTTTGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
26 12 0.50
28 12 0.50
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (27 bp):
TTTTTTATTTTTAATATTTTAAAAATA
Found at i:41781486 original size:134 final size:132
Alignment explanation
Indices: 41781246--41781514 Score: 448
Period size: 134 Copynumber: 2.0 Consensus size: 132
41781236 GGGTTTTCCC
* **
41781246 TGTTTGCGAACATGTTTTTCATTTTAGTTGCATAGATAACTGGTTGAGAAAACATTTAACTTGTC
1 TGTTTCCGAACATGTTTTTCATTTTAGTTGCATAGATAACTGGTTGAGAAAACATGGAACTTGTC
*
41781311 CGATTTGTCGGAATTGTATAGTAGATAGTATGAGCATGACATTGAGAATGTAAGTATATATATAC
66 CGAGTTGTCGGAATTGTATAGTAGATAGTATGAGCATGACATTGAGAATGTAA--ATATATATAC
41781376 TTTT
129 TTTT
* *
41781380 TGTTTCCGAACATGTTTTTCATTTTAGTTGCATAGATAACTGGTTGAGAAATCATGGAACTTGTT
1 TGTTTCCGAACATGTTTTTCATTTTAGTTGCATAGATAACTGGTTGAGAAAACATGGAACTTGTC
* *
41781445 CGAGTTGTCGGAATTGTATGGTAGATAGTATGAGCATGACATTGAGAATGTAAATATATATATTT
66 CGAGTTGTCGGAATTGTATAGTAGATAGTATGAGCATGACATTGAGAATGTAAATATATATACTT
41781510 TT
131 TT
41781512 TGT
1 TGT
41781515 ATATGTATAG
Statistics
Matches: 127, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
132 16 0.13
134 111 0.87
ACGTcount: A:0.30, C:0.09, G:0.21, T:0.40
Consensus pattern (132 bp):
TGTTTCCGAACATGTTTTTCATTTTAGTTGCATAGATAACTGGTTGAGAAAACATGGAACTTGTC
CGAGTTGTCGGAATTGTATAGTAGATAGTATGAGCATGACATTGAGAATGTAAATATATATACTT
TT
Found at i:41786314 original size:75 final size:75
Alignment explanation
Indices: 41786136--41786320 Score: 194
Period size: 75 Copynumber: 2.5 Consensus size: 75
41786126 TGGGCACACA
* * * * * * *
41786136 ATCGTCGGTTTATCCGACTAGCACTAGACGCAAACACTGTTGGTTCATCCAACTAGAGTTGGGCT
1 ATCGTCGGTTAATCCGACTAGCGCTGGGCACAAACACTGTTGGTTCATCCAACGAGAGTTGGGAT
*
41786201 CACATTTAAT
66 CACATTCAAT
* ** * * *
41786211 ATCATCGG-TATATCCGACTAATGTTGGGCACAAACATTGTTGGTTTATCCAACGAGAGTTGGGA
1 ATCGTCGGTTA-ATCCGACTAGCGCTGGGCACAAACACTGTTGGTTCATCCAACGAGAGTTGGGA
41786275 TCACATTCAAT
65 TCACATTCAAT
* *
41786286 A-CTGTCGGTTAACCCGACTAGCGCTGGGCTCAAAC
1 ATC-GTCGGTTAATCCGACTAGCGCTGGGCACAAAC
41786321 TCCTCTATAG
Statistics
Matches: 87, Mismatches: 20, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
74 2 0.02
75 83 0.95
76 2 0.02
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (75 bp):
ATCGTCGGTTAATCCGACTAGCGCTGGGCACAAACACTGTTGGTTCATCCAACGAGAGTTGGGAT
CACATTCAAT
Found at i:41787700 original size:48 final size:46
Alignment explanation
Indices: 41787598--41787703 Score: 117
Period size: 48 Copynumber: 2.3 Consensus size: 46
41787588 GGCGTTACAT
* *
41787598 AACAGGTGACCAGGCACTATTATTCAATTCATGTAGGTTTAACCAGG
1 AACAGGTAACCAGGCACTATAATTCAATTCATGTAGGTTTAACCA-G
* * *
41787645 AA-GGGTAACTAGGCACTATAATTCATTATTCGTGTAGGTTTAACCCA-
1 AACAGGTAACCAGGCACTATAATTCA--ATTCATGTAGGTTTAA-CCAG
41787692 AACAGGTAACCA
1 AACAGGTAACCA
41787704 AACACTATTA
Statistics
Matches: 48, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
46 19 0.40
47 4 0.08
48 22 0.46
49 3 0.06
ACGTcount: A:0.34, C:0.19, G:0.20, T:0.27
Consensus pattern (46 bp):
AACAGGTAACCAGGCACTATAATTCAATTCATGTAGGTTTAACCAG
Found at i:41791616 original size:3 final size:3
Alignment explanation
Indices: 41791608--41791663 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
41791598 GAATTAGTCC
41791608 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41791656 TAT TAT TA
1 TAT TAT TA
41791664 CCTATTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41792129 original size:22 final size:23
Alignment explanation
Indices: 41792074--41792129 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
41792064 TAAAATATAC
*
41792074 TTTATATATTTTGTTAATTCATG
1 TTTATATATATTGTTAATTCATG
* * * *
41792097 TATACACATATT-TTAGTTCATG
1 TTTATATATATTGTTAATTCATG
41792119 TTTATATATAT
1 TTTATATATAT
41792130 CTTTTTATAC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (23 bp):
TTTATATATATTGTTAATTCATG
Found at i:41804295 original size:48 final size:48
Alignment explanation
Indices: 41804242--41804695 Score: 198
Period size: 48 Copynumber: 9.3 Consensus size: 48
41804232 AGCCACAGTG
*
41804242 GCGAATCTTACTTCTGGCGATGCAACGGAGCAGATTGAAGCTACAACA
1 GCGAATCTCACTTCTGGCGATGCAACGGAGCAGATTGAAGCTACAACA
* ** *** ** * * * *
41804290 ACGAATCTCACTTC-CCCGACATTGCAATTTAAAAGATCGAAGCCACAGCG
1 GCGAATCTCACTTCTGGCG--A-TGCAACGGAGCAGATTGAAGCTACAACA
* * *
41804340 GCGAATCTTACTTCTGGCGACGCAGCGGAGCAGATTGAAGCTACAACA
1 GCGAATCTCACTTCTGGCGATGCAACGGAGCAGATTGAAGCTACAACA
** *** ** * *
41804388 GCGAATCTCACTTC-CCCGACATTGCAATTTAAAAGATTGAAGCCACAGCA
1 GCGAATCTCACTTCTGGCG--A-TGCAACGGAGCAGATTGAAGCTACAACA
* * *
41804438 GCGAATCTTACTTCTGGCGATACAGCGGAGCAGATTGAAGCTACAACA
1 GCGAATCTCACTTCTGGCGATGCAACGGAGCAGATTGAAGCTACAACA
* ** *** ** * * * *
41804486 ACGAATCTCACTTC-CCCGACATTGCAATTTAAAAGGTCGAAGCCACAACG
1 GCGAATCTCACTTCTGGCG--A-TGCAACGGAGCAGATTGAAGCTACAACA
** * **
41804536 GTAAATCTTAC-TCTTGGCGATGCAGTGGAGCAGATTGAAGCTACAACA
1 GCGAATCTCACTTC-TGGCGATGCAACGGAGCAGATTGAAGCTACAACA
* *** ** * * *
41804584 GCGAATCTCACTTCCTCGAC-ATTGCAATTTAAAAGATCGAAGCCACAACG
1 GCGAATCTCACTT-CT-GGCGA-TGCAACGGAGCAGATTGAAGCTACAACA
* * * * * * *
41804634 GTGAATCTTATTTTTGGCGATGCAATGGAACAGATTGAAGCTACAACG
1 GCGAATCTCACTTCTGGCGATGCAACGGAGCAGATTGAAGCTACAACA
*
41804682 GCGAACCTCACTTC
1 GCGAATCTCACTTC
41804696 CCCGACATTG
Statistics
Matches: 279, Mismatches: 109, Indels: 36
0.66 0.26 0.08
Matches are distributed among these distances:
47 6 0.02
48 134 0.48
49 13 0.05
50 120 0.43
51 6 0.02
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (48 bp):
GCGAATCTCACTTCTGGCGATGCAACGGAGCAGATTGAAGCTACAACA
Found at i:41804382 original size:98 final size:98
Alignment explanation
Indices: 41804213--41804788 Score: 868
Period size: 98 Copynumber: 5.9 Consensus size: 98
41804203 AAACCATAGT
** *
41804213 TTGCAATTTAAAAGATCGAAGCCACAGTGGCGAATCTTACTTCTGGCGATGCAACGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
*
41804278 GAAGCTACAACAACGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* *
41804311 TTGCAATTTAAAAGATCGAAGCCACAGCGGCGAATCTTACTTCTGGCGACGCAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
41804376 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * *
41804409 TTGCAATTTAAAAGATTGAAGCCACAGCAGCGAATCTTACTTCTGGCGATACAGCGGAGCAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
*
41804474 GAAGCTACAACAACGAATCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* ** *
41804507 TTGCAATTTAAAAGGTCGAAGCCACAACGGTAAATCTTAC-TCTTGGCGATGCAGTGGAGCAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTC-TGGCGATGCAGCGGAGCAGAT
*
41804571 TGAAGCTACAACAGCGAATCTCACTTCCTCGACA
65 TGAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * * ** *
41804605 TTGCAATTTAAAAGATCGAAGCCACAACGGTGAATCTTATTTTTGGCGATGCAATGGAACAGATT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
* *
41804670 GAAGCTACAACGGCGAACCTCACTTCCCCGACA
66 GAAGCTACAACAGCGAATCTCACTTCCCCGACA
* * *
41804703 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCCAGGCGACGCAGCGGAACAGAT
1 TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTT-CTGGCGATGCAGCGGAGCAGAT
41804768 TGAAGCCT-CAACAGCGAATCT
65 TGAAG-CTACAACAGCGAATCT
41804789 TTTCCTCGGC
Statistics
Matches: 437, Mismatches: 37, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
97 2 0.00
98 399 0.91
99 34 0.08
100 2 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.21
Consensus pattern (98 bp):
TTGCAATTTAAAAGATCGAAGCCACAACGGCGAATCTTACTTCTGGCGATGCAGCGGAGCAGATT
GAAGCTACAACAGCGAATCTCACTTCCCCGACA
Found at i:41805720 original size:10 final size:9
Alignment explanation
Indices: 41805695--41805719 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
41805685 TCTTTTGTTG
41805695 TTTTTTTAT
1 TTTTTTTAT
41805704 TTTTTTTAT
1 TTTTTTTAT
41805713 TTTTTTT
1 TTTTTTT
41805720 TCTATTTGTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (9 bp):
TTTTTTTAT
Found at i:41806165 original size:3 final size:3
Alignment explanation
Indices: 41806157--41806212 Score: 112
Period size: 3 Copynumber: 18.7 Consensus size: 3
41806147 GAATTAGTCC
41806157 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
41806205 TAT TAT TA
1 TAT TAT TA
41806213 CCTATTTATT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 53 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:41806612 original size:22 final size:23
Alignment explanation
Indices: 41806557--41806612 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 23
41806547 TAAAATATAC
*
41806557 TTTATATATTTTGTTAATTCATG
1 TTTATATATATTGTTAATTCATG
* * * *
41806580 TATACACATATT-TTAGTTCATG
1 TTTATATATATTGTTAATTCATG
41806602 TTTATATATAT
1 TTTATATATAT
41806613 CTTTTTATAC
Statistics
Matches: 25, Mismatches: 8, Indels: 1
0.74 0.24 0.03
Matches are distributed among these distances:
22 17 0.68
23 8 0.32
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.55
Consensus pattern (23 bp):
TTTATATATATTGTTAATTCATG
Found at i:41806669 original size:84 final size:84
Alignment explanation
Indices: 41806573--41806740 Score: 327
Period size: 84 Copynumber: 2.0 Consensus size: 84
41806563 TATTTTGTTA
*
41806573 ATTCATGTATACACATATTTTAGTTCATGTTTATATATATCTTTTTATACTTAATTGTATTTGCT
1 ATTCATGTATACACATATTTTAATTCATGTTTATATATATCTTTTTATACTTAATTGTATTTGCT
41806638 ATTTATTTATTTCATTTTT
66 ATTTATTTATTTCATTTTT
41806657 ATTCATGTATACACATATTTTAATTCATGTTTATATATATCTTTTTATACTTAATTGTATTTGCT
1 ATTCATGTATACACATATTTTAATTCATGTTTATATATATCTTTTTATACTTAATTGTATTTGCT
41806722 ATTTATTTATTTCATTTTT
66 ATTTATTTATTTCATTTTT
41806741 GTTATTATTT
Statistics
Matches: 83, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 83 1.00
ACGTcount: A:0.27, C:0.10, G:0.05, T:0.58
Consensus pattern (84 bp):
ATTCATGTATACACATATTTTAATTCATGTTTATATATATCTTTTTATACTTAATTGTATTTGCT
ATTTATTTATTTCATTTTT
Found at i:41807344 original size:103 final size:103
Alignment explanation
Indices: 41807230--41807434 Score: 383
Period size: 103 Copynumber: 2.0 Consensus size: 103
41807220 CTCGATTAAC
* * *
41807230 GTGAATTATATTTCTTTTTCCAAAAATTTTCATTTTAATACAAGGATTGTATTTTTAATTCTTTC
1 GTGAAATATATTTCTTTTTCCAAAAATTTTCATTTTAATACAAGGATCGTATTTTTAATTATTTC
41807295 AAGTTCTCAATTTTCGACATCAAGACATTAGATAATCT
66 AAGTTCTCAATTTTCGACATCAAGACATTAGATAATCT
41807333 GTGAAATATATTTCTTTTTCCAAAAATTTTCATTTTAATACAAGGATCGTATTTTTAATTATTTC
1 GTGAAATATATTTCTTTTTCCAAAAATTTTCATTTTAATACAAGGATCGTATTTTTAATTATTTC
41807398 AAGTTCTCAATTTTCGACATCAAGACATTAGATAATC
66 AAGTTCTCAATTTTCGACATCAAGACATTAGATAATC
41807435 AACTAGGTAC
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
103 99 1.00
ACGTcount: A:0.33, C:0.14, G:0.09, T:0.44
Consensus pattern (103 bp):
GTGAAATATATTTCTTTTTCCAAAAATTTTCATTTTAATACAAGGATCGTATTTTTAATTATTTC
AAGTTCTCAATTTTCGACATCAAGACATTAGATAATCT
Found at i:41824509 original size:16 final size:16
Alignment explanation
Indices: 41824488--41824556 Score: 120
Period size: 16 Copynumber: 4.2 Consensus size: 16
41824478 TTTGGTTCGC
*
41824488 TGTATTGGATTATAGG
1 TGTATTGGATTAGAGG
41824504 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41824520 TGTATTGGGATTAGAGG
1 TGTATT-GGATTAGAGG
41824537 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
41824553 TGTA
1 TGTA
41824557 ATAGCTAATC
Statistics
Matches: 51, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
16 35 0.69
17 16 0.31
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:41824538 original size:33 final size:32
Alignment explanation
Indices: 41824488--41824556 Score: 120
Period size: 33 Copynumber: 2.1 Consensus size: 32
41824478 TTTGGTTCGC
*
41824488 TGTATTGGATTATAGGTGTATTGGATTAGAGG
1 TGTATTGGATTAGAGGTGTATTGGATTAGAGG
41824520 TGTATTGGGATTAGAGGTGTATTGGATTAGAGG
1 TGTATT-GGATTAGAGGTGTATTGGATTAGAGG
41824553 TGTA
1 TGTA
41824557 ATAGCTAATC
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 6 0.17
33 29 0.83
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (32 bp):
TGTATTGGATTAGAGGTGTATTGGATTAGAGG
Found at i:41824621 original size:44 final size:45
Alignment explanation
Indices: 41824537--41824627 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
41824527 GGATTAGAGG
* * *
41824537 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
41824582 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
41824626 TG
1 TG
41824628 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:41824810 original size:7 final size:7
Alignment explanation
Indices: 41824798--41825260 Score: 926
Period size: 7 Copynumber: 66.1 Consensus size: 7
41824788 TTAAATATAT
41824798 TACTTGA
1 TACTTGA
41824805 TACTTGA
1 TACTTGA
41824812 TACTTGA
1 TACTTGA
41824819 TACTTGA
1 TACTTGA
41824826 TACTTGA
1 TACTTGA
41824833 TACTTGA
1 TACTTGA
41824840 TACTTGA
1 TACTTGA
41824847 TACTTGA
1 TACTTGA
41824854 TACTTGA
1 TACTTGA
41824861 TACTTGA
1 TACTTGA
41824868 TACTTGA
1 TACTTGA
41824875 TACTTGA
1 TACTTGA
41824882 TACTTGA
1 TACTTGA
41824889 TACTTGA
1 TACTTGA
41824896 TACTTGA
1 TACTTGA
41824903 TACTTGA
1 TACTTGA
41824910 TACTTGA
1 TACTTGA
41824917 TACTTGA
1 TACTTGA
41824924 TACTTGA
1 TACTTGA
41824931 TACTTGA
1 TACTTGA
41824938 TACTTGA
1 TACTTGA
41824945 TACTTGA
1 TACTTGA
41824952 TACTTGA
1 TACTTGA
41824959 TACTTGA
1 TACTTGA
41824966 TACTTGA
1 TACTTGA
41824973 TACTTGA
1 TACTTGA
41824980 TACTTGA
1 TACTTGA
41824987 TACTTGA
1 TACTTGA
41824994 TACTTGA
1 TACTTGA
41825001 TACTTGA
1 TACTTGA
41825008 TACTTGA
1 TACTTGA
41825015 TACTTGA
1 TACTTGA
41825022 TACTTGA
1 TACTTGA
41825029 TACTTGA
1 TACTTGA
41825036 TACTTGA
1 TACTTGA
41825043 TACTTGA
1 TACTTGA
41825050 TACTTGA
1 TACTTGA
41825057 TACTTGA
1 TACTTGA
41825064 TACTTGA
1 TACTTGA
41825071 TACTTGA
1 TACTTGA
41825078 TACTTGA
1 TACTTGA
41825085 TACTTGA
1 TACTTGA
41825092 TACTTGA
1 TACTTGA
41825099 TACTTGA
1 TACTTGA
41825106 TACTTGA
1 TACTTGA
41825113 TACTTGA
1 TACTTGA
41825120 TACTTGA
1 TACTTGA
41825127 TACTTGA
1 TACTTGA
41825134 TACTTGA
1 TACTTGA
41825141 TACTTGA
1 TACTTGA
41825148 TACTTGA
1 TACTTGA
41825155 TACTTGA
1 TACTTGA
41825162 TACTTGA
1 TACTTGA
41825169 TACTTGA
1 TACTTGA
41825176 TACTTGA
1 TACTTGA
41825183 TACTTGA
1 TACTTGA
41825190 TACTTGA
1 TACTTGA
41825197 TACTTGA
1 TACTTGA
41825204 TACTTGA
1 TACTTGA
41825211 TACTTGA
1 TACTTGA
41825218 TACTTGA
1 TACTTGA
41825225 TACTTGA
1 TACTTGA
41825232 TACTTGA
1 TACTTGA
41825239 TACTTGA
1 TACTTGA
41825246 TACTTGA
1 TACTTGA
41825253 TACTTGA
1 TACTTGA
41825260 T
1 T
41825261 TTCCACATAT
Statistics
Matches: 456, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 456 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (7 bp):
TACTTGA
Found at i:41826337 original size:485 final size:485
Alignment explanation
Indices: 41825428--41826475 Score: 2096
Period size: 485 Copynumber: 2.2 Consensus size: 485
41825418 AATGGGCATC
41825428 AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
1 AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
41825493 AAACCTCATATCATCAATTTGAAACCTACAGATTGGCATTAGCATATTTTTGGATTATCCTTGGA
66 AAACCTCATATCATCAATTTGAAACCTACAGATTGGCATTAGCATATTTTTGGATTATCCTTGGA
41825558 CTTGCAGAAAATAATTGATAAATTCCCCCAAGGTGGATGTAATTTGACGAATTTATAAAGGGATA
131 CTTGCAGAAAATAATTGATAAATTCCCCCAAGGTGGATGTAATTTGACGAATTTATAAAGGGATA
41825623 CCCTCAGTTCCTGGTTCTCATCTTTCTTTGCTAAATACATACAAGTTGAGGCATTCATTATATAA
196 CCCTCAGTTCCTGGTTCTCATCTTTCTTTGCTAAATACATACAAGTTGAGGCATTCATTATATAA
41825688 ATTGATGATCCAAGTAGTCTAGTTTTTCATTTGAATACAATACAGCAGCTGTATGTATGCATGTG
261 ATTGATGATCCAAGTAGTCTAGTTTTTCATTTGAATACAATACAGCAGCTGTATGTATGCATGTG
41825753 TGTTGTGTAAGCGCATAGATTGAAATATAGCATAGCATTAGCTCTTAATAAACCACTCCCATTTT
326 TGTTGTGTAAGCGCATAGATTGAAATATAGCATAGCATTAGCTCTTAATAAACCACTCCCATTTT
41825818 AGGTGGAACTGTGTAGACCTCTACCGCACTCGTTGCCCAGCATTTAGTCAGAGGATGTTCTCTCT
391 AGGTGGAACTGTGTAGACCTCTACCGCACTCGTTGCCCAGCATTTAGTCAGAGGATGTTCTCTCT
41825883 TCTTTTATCCCTTTATTCTACTCCTTTTTA
456 TCTTTTATCCCTTTATTCTACTCCTTTTTA
41825913 AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
1 AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
41825978 AAACCTCATATCATCAATTTGAAACCTACAGATTGGCATTAGCATATTTTTGGATTATCCTTGGA
66 AAACCTCATATCATCAATTTGAAACCTACAGATTGGCATTAGCATATTTTTGGATTATCCTTGGA
41826043 CTTGCAGAAAATAATTGATAAATTCCCCCAAGGTGGATGTAATTTGACGAATTTATAAAGGGATA
131 CTTGCAGAAAATAATTGATAAATTCCCCCAAGGTGGATGTAATTTGACGAATTTATAAAGGGATA
41826108 CCCTCAGTTCCTGGTTCTCATCTTTCTTTGCTAAATACATACAAGTTGAGGCATTCATTATATAA
196 CCCTCAGTTCCTGGTTCTCATCTTTCTTTGCTAAATACATACAAGTTGAGGCATTCATTATATAA
41826173 ATTGATGATCCAAGTAGTCTAGTTTTTCATTTGAATACAATACAGCAGCTGTATGTATGCATGTG
261 ATTGATGATCCAAGTAGTCTAGTTTTTCATTTGAATACAATACAGCAGCTGTATGTATGCATGTG
41826238 TGTTGTGTAAGCGCATAGATTGAAATATAGCATAGCATTAGCTCTTAATAAACCACTCCCATTTT
326 TGTTGTGTAAGCGCATAGATTGAAATATAGCATAGCATTAGCTCTTAATAAACCACTCCCATTTT
41826303 AGGTGGAACTGTGTAGACCTCTACCGCACTCGTTGCCCAGCATTTAGTCAGAGGATGTTCTCTCT
391 AGGTGGAACTGTGTAGACCTCTACCGCACTCGTTGCCCAGCATTTAGTCAGAGGATGTTCTCTCT
41826368 TCTTTTATCCCTTTATTCTACTCCTTTTTA
456 TCTTTTATCCCTTTATTCTACTCCTTTTTA
41826398 AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
1 AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
41826463 AAACCTCATATCA
66 AAACCTCATATCA
41826476 GCAAATACAG
Statistics
Matches: 563, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
485 563 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (485 bp):
AAGGTGGTTTTTTTTCATAAGAAAATGTAATTAGAAGGGAGAAGAGATTTACAAATACAAATATT
AAACCTCATATCATCAATTTGAAACCTACAGATTGGCATTAGCATATTTTTGGATTATCCTTGGA
CTTGCAGAAAATAATTGATAAATTCCCCCAAGGTGGATGTAATTTGACGAATTTATAAAGGGATA
CCCTCAGTTCCTGGTTCTCATCTTTCTTTGCTAAATACATACAAGTTGAGGCATTCATTATATAA
ATTGATGATCCAAGTAGTCTAGTTTTTCATTTGAATACAATACAGCAGCTGTATGTATGCATGTG
TGTTGTGTAAGCGCATAGATTGAAATATAGCATAGCATTAGCTCTTAATAAACCACTCCCATTTT
AGGTGGAACTGTGTAGACCTCTACCGCACTCGTTGCCCAGCATTTAGTCAGAGGATGTTCTCTCT
TCTTTTATCCCTTTATTCTACTCCTTTTTA
Found at i:41827027 original size:18 final size:18
Alignment explanation
Indices: 41827004--41827038 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
41826994 GTTTCGGACG
41827004 TGAGAAAGAAATGAGAAA
1 TGAGAAAGAAATGAGAAA
41827022 TGAGAAAGAAATGAGAA
1 TGAGAAAGAAATGAGAA
41827039 GACGGCTGGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (18 bp):
TGAGAAAGAAATGAGAAA
Found at i:41843986 original size:12 final size:12
Alignment explanation
Indices: 41843969--41843999 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
41843959 TATTAAAAAA
41843969 TTATTTTATTTT
1 TTATTTTATTTT
*
41843981 TTATTTAATTTT
1 TTATTTTATTTT
41843993 TTATTTT
1 TTATTTT
41844000 TAAGTCTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (12 bp):
TTATTTTATTTT
Found at i:41858266 original size:28 final size:28
Alignment explanation
Indices: 41858218--41858280 Score: 67
Period size: 28 Copynumber: 2.2 Consensus size: 28
41858208 TAGTCCACTG
41858218 TTTTTTTAGAACTGAATAAAATAATAAT-
1 TTTTTTTAGAACTGAATAAAAT-ATAATA
** *
41858246 TTTTTTTATCACTAGAA-AAAATCTAATA
1 TTTTTTTAGAACT-GAATAAAATATAATA
41858274 TTTTTTT
1 TTTTTTT
41858281 CCTTCAAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 23 0.77
29 3 0.10
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (28 bp):
TTTTTTTAGAACTGAATAAAATATAATA
Found at i:41864978 original size:4 final size:4
Alignment explanation
Indices: 41864965--41864994 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
41864955 TTAGTATGTC
41864965 TTTA -TTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
41864995 GGTATACTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 3 0.12
4 22 0.88
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTTA
Found at i:41866316 original size:19 final size:19
Alignment explanation
Indices: 41866294--41866330 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
41866284 ATAAATATAT
41866294 AACACTTTTATAATATTTA
1 AACACTTTTATAATATTTA
* *
41866313 AACATTTTTATTATATTT
1 AACACTTTTATAATATTT
41866331 TTTTGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (19 bp):
AACACTTTTATAATATTTA
Found at i:41867098 original size:12 final size:12
Alignment explanation
Indices: 41867081--41867105 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41867071 TTGACGGGGG
41867081 TTTTTGTTTTTT
1 TTTTTGTTTTTT
41867093 TTTTTGTTTTTT
1 TTTTTGTTTTTT
41867105 T
1 T
41867106 CGTAAATACA
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:0.00, C:0.00, G:0.08, T:0.92
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:41869804 original size:23 final size:23
Alignment explanation
Indices: 41869777--41869829 Score: 88
Period size: 23 Copynumber: 2.3 Consensus size: 23
41869767 AGTGTTATTG
*
41869777 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGACTACAT
*
41869800 TTCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGACTACAT
41869823 ATCAGTG
1 ATCAGTG
41869830 TGGCACTTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.25, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGACTACAT
Found at i:41874167 original size:21 final size:21
Alignment explanation
Indices: 41874131--41874189 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
41874121 GATAGTAGGC
* *
41874131 AAGGTATCGGTTCTTTTGTCA
1 AAGGTATCGATACTTTTGTCA
* * *
41874152 GAGGTATTGATAC-TTTGTTA
1 AAGGTATCGATACTTTTGTCA
41874172 AAGGTATCGATACTTTTG
1 AAGGTATCGATACTTTTG
41874190 ATTTTTTAAA
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 17 0.57
21 13 0.43
ACGTcount: A:0.24, C:0.10, G:0.24, T:0.42
Consensus pattern (21 bp):
AAGGTATCGATACTTTTGTCA
Found at i:41875704 original size:51 final size:49
Alignment explanation
Indices: 41875623--41875767 Score: 166
Period size: 51 Copynumber: 2.9 Consensus size: 49
41875613 AGCTTGATGG
* * ** *
41875623 CTGAGATGATAAAACAAGTCTCTCTACATGATTTGATGGAAGTTTAACGA
1 CTGAAATGATAAAACAAGTCTCT-TTCATGATTTGATGGAAGCCTAACAA
* * * *
41875673 CTGAAATGATAAAAACAAGTCTGTTTGCATGAGTTGATGGAAGCCTGATAA
1 CTGAAATGAT-AAAACAAGTCTCTTT-CATGATTTGATGGAAGCCTAACAA
*
41875724 CTGAAATGATAAAACAAGTCTCTTT-ATGATTTGATGGAAACCTA
1 CTGAAATGATAAAACAAGTCTCTTTCATGATTTGATGGAAGCCTA
41875768 TTCAATAATA
Statistics
Matches: 80, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
48 16 0.20
50 24 0.30
51 40 0.50
ACGTcount: A:0.37, C:0.13, G:0.20, T:0.30
Consensus pattern (49 bp):
CTGAAATGATAAAACAAGTCTCTTTCATGATTTGATGGAAGCCTAACAA
Found at i:41882843 original size:13 final size:12
Alignment explanation
Indices: 41882820--41882879 Score: 57
Period size: 13 Copynumber: 4.5 Consensus size: 12
41882810 TTAAATTATG
41882820 ATTATTATTTAAA
1 ATTATT-TTTAAA
41882833 ATTAGTTTTTAAA
1 ATTA-TTTTTAAA
*
41882846 ATTTAATTTATTTAA
1 A-TT-ATTT-TTAAA
41882861 ATTATATTTTAAA
1 ATTAT-TTTTAAA
41882874 ATTATT
1 ATTATT
41882880 GATATTGTAT
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
12 1 0.03
13 22 0.55
14 11 0.28
15 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (12 bp):
ATTATTTTTAAA
Found at i:41887169 original size:21 final size:22
Alignment explanation
Indices: 41887144--41887184 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
41887134 GTGTTCATTG
41887144 TGTTTTAAATATGTT-ATATCT
1 TGTTTTAAATATGTTCATATCT
41887165 TGTTTTAAATATGTTCATAT
1 TGTTTTAAATATGTTCATAT
41887185 ATGTTTTTCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.79
22 4 0.21
ACGTcount: A:0.29, C:0.05, G:0.10, T:0.56
Consensus pattern (22 bp):
TGTTTTAAATATGTTCATATCT
Found at i:41887189 original size:21 final size:21
Alignment explanation
Indices: 41887135--41887191 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 21
41887125 TCTTTGTATG
*
41887135 TGTTCAT-TGTGTTTTAAATA
1 TGTTCATATATGTTTTAAATA
*
41887155 TGTT-ATATCTTGTTTTAAATA
1 TGTTCATAT-ATGTTTTAAATA
41887176 TGTTCATATATGTTTT
1 TGTTCATATATGTTTT
41887192 TCTACCAAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 2 0.06
20 5 0.16
21 21 0.66
22 4 0.12
ACGTcount: A:0.25, C:0.05, G:0.12, T:0.58
Consensus pattern (21 bp):
TGTTCATATATGTTTTAAATA
Found at i:41895347 original size:19 final size:19
Alignment explanation
Indices: 41895311--41895349 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
41895301 TTTTCAAAAT
*
41895311 TATTTTAATTTGGGTTCGA
1 TATTTTAATTTAGGTTCGA
*
41895330 TATTTTAATTTAGTTTCGA
1 TATTTTAATTTAGGTTCGA
41895349 T
1 T
41895350 TATATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.23, C:0.05, G:0.15, T:0.56
Consensus pattern (19 bp):
TATTTTAATTTAGGTTCGA
Found at i:41895891 original size:2 final size:2
Alignment explanation
Indices: 41895884--41895910 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
41895874 ATAAGAGAAA
41895884 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
41895911 AAAAGAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:41900244 original size:20 final size:20
Alignment explanation
Indices: 41900219--41900263 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
41900209 AGTAAAAGCT
41900219 TTTACCAAAATATCTAACGA
1 TTTACCAAAATATCTAACGA
* * *
41900239 TTTACCAATATTTCTAACGG
1 TTTACCAAAATATCTAACGA
41900259 TTTAC
1 TTTAC
41900264 TACCAATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.36, C:0.20, G:0.07, T:0.38
Consensus pattern (20 bp):
TTTACCAAAATATCTAACGA
Found at i:41900271 original size:23 final size:23
Alignment explanation
Indices: 41900221--41900286 Score: 75
Period size: 23 Copynumber: 3.0 Consensus size: 23
41900211 TAAAAGCTTT
* *
41900221 TACCAAAATATCTAACGA-TT--
1 TACCAATATTTCTAACGATTTAC
*
41900241 TACCAATATTTCTAACGGTTTAC
1 TACCAATATTTCTAACGATTTAC
*
41900264 TACCAATATTTTTAACGATTTAC
1 TACCAATATTTCTAACGATTTAC
41900287 AATGTAAGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
20 15 0.39
21 2 0.05
23 21 0.55
ACGTcount: A:0.36, C:0.20, G:0.06, T:0.38
Consensus pattern (23 bp):
TACCAATATTTCTAACGATTTAC
Found at i:41905670 original size:12 final size:12
Alignment explanation
Indices: 41905653--41905677 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
41905643 CTTCGGGTCC
41905653 TTTTTTATTTTA
1 TTTTTTATTTTA
41905665 TTTTTTATTTTA
1 TTTTTTATTTTA
41905677 T
1 T
41905678 AAAAGAATAT
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:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTTTATTTTA
Found at i:41911499 original size:25 final size:25
Alignment explanation
Indices: 41911445--41911549 Score: 119
Period size: 25 Copynumber: 4.3 Consensus size: 25
41911435 CACTAATGAA
*
41911445 CAGAGAGCACTAAAGTGCT--ATA-
1 CAGAGAGCACTAACGTGCTAAATAT
* *
41911467 CAGAGAGCACTGACATGCTAAATAT
1 CAGAGAGCACTAACGTGCTAAATAT
* *
41911492 CAAAGAGCACCAACGTGCT-AATAGT
1 CAGAGAGCACTAACGTGCTAAATA-T
*
41911517 CAGAGAGCACTAACGTGCTAAAAAT
1 CAGAGAGCACTAACGTGCTAAATAT
41911542 CAGAGAGC
1 CAGAGAGC
41911550 GCGCTAAGTT
Statistics
Matches: 68, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
22 16 0.24
24 7 0.10
25 42 0.62
26 3 0.04
ACGTcount: A:0.41, C:0.21, G:0.22, T:0.16
Consensus pattern (25 bp):
CAGAGAGCACTAACGTGCTAAATAT
Found at i:41915091 original size:50 final size:54
Alignment explanation
Indices: 41915029--41915177 Score: 198
Period size: 50 Copynumber: 2.8 Consensus size: 54
41915019 TGATCATAAC
41915029 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC-G-TCTC-GG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAGATCTCAGG
* *
41915080 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATGATCTCAAGG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCA-GATCTC-AGG
* * * *
41915135 ATGCCAATGCAATATCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
41915178 TTACCCAAAT
Statistics
Matches: 85, Mismatches: 7, Indels: 7
0.86 0.07 0.07
Matches are distributed among these distances:
50 41 0.48
52 1 0.01
53 4 0.05
55 2 0.02
56 37 0.44
ACGTcount: A:0.25, C:0.30, G:0.21, T:0.25
Consensus pattern (54 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAGATCTCAGG
Found at i:41916588 original size:226 final size:225
Alignment explanation
Indices: 41916195--41916648 Score: 746
Period size: 226 Copynumber: 2.0 Consensus size: 225
41916185 ATTTTGATAA
*
41916195 TGAGGGTGAAGATTTTAGGTCCCAGTGATATCAACGACGAAGGTGTGGATTATGATGAAAATGTT
1 TGAGGGTGAAGATTTTAGGTCCCAGTGATATCAACGACGAAGGTGTGGATGATGATGAAAATGTT
* **
41916260 TACGCCCCTTTGATCAAGAACCCGGGTTGTGGCATTGTCATACACAATGACCCTGAAGCGCACAT
66 TACGCCCCTTTGATCAAGAACCCGAGTCATGGCATTGTCATACACAATGACCCTGAAGCGCACAT
** * * * *
41916325 GTCGAGTGTAAATCTTGATGTGTCGCATGTGTTCGAGTTCCCCAAGTACCCTAATATAATATTTG
131 GTCGAGCATAAATCCTGATGCGTCGCATGCGTTCGAGTTCCCCAAGTACCCCAATATAATATTTG
*
41916390 CTCATTGATTGGCGGCATATCGAGCCTTCT
196 CTCATTGATTGGCAGCATATCGAGCCTTCT
* *
41916420 TGAGGGTGAAGATTTTAGGTCCCAGATGATATCGATGACGAAGGTGTGGATGATGATGAAAATGT
1 TGAGGGTGAAGATTTTAGGTCCCAG-TGATATCAACGACGAAGGTGTGGATGATGATGAAAATGT
41916485 TTACGCCCCTTTGATCAAGAACCCGAGTCATGGCATTGTCATACACAATGACCCTGAAGCGCACA
65 TTACGCCCCTTTGATCAAGAACCCGAGTCATGGCATTGTCATACACAATGACCCTGAAGCGCACA
*
41916550 TGTCGAGCATAAATCCTGATGCGTCGCATGCGTTCGAGTTCCCCGAGTACCCCAATATAATATTT
130 TGTCGAGCATAAATCCTGATGCGTCGCATGCGTTCGAGTTCCCCAAGTACCCCAATATAATATTT
* * *
41916615 TCTCATTGATTGGCAGTATATTGAGCCTTCT
195 GCTCATTGATTGGCAGCATATCGAGCCTTCT
41916646 TGA
1 TGA
41916649 ATGGATAGTT
Statistics
Matches: 211, Mismatches: 17, Indels: 1
0.92 0.07 0.00
Matches are distributed among these distances:
225 25 0.12
226 186 0.88
ACGTcount: A:0.26, C:0.20, G:0.24, T:0.29
Consensus pattern (225 bp):
TGAGGGTGAAGATTTTAGGTCCCAGTGATATCAACGACGAAGGTGTGGATGATGATGAAAATGTT
TACGCCCCTTTGATCAAGAACCCGAGTCATGGCATTGTCATACACAATGACCCTGAAGCGCACAT
GTCGAGCATAAATCCTGATGCGTCGCATGCGTTCGAGTTCCCCAAGTACCCCAATATAATATTTG
CTCATTGATTGGCAGCATATCGAGCCTTCT
Found at i:41920363 original size:16 final size:16
Alignment explanation
Indices: 41920326--41920363 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 16
41920316 ACTCTAAAAT
41920326 TATAAAAAAAAGTTTA
1 TATAAAAAAAAGTTTA
41920342 TAATAAAAAATAA-TTTA
1 T-ATAAAAAA-AAGTTTA
41920359 TATAA
1 TATAA
41920364 TATATTTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.25
17 13 0.65
18 2 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (16 bp):
TATAAAAAAAAGTTTA
Found at i:41920365 original size:19 final size:17
Alignment explanation
Indices: 41920327--41920360 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
41920317 CTCTAAAATT
41920327 ATAAAAAAAAGTTTATA
1 ATAAAAAAAAGTTTATA
41920344 ATAAAAAATAA-TTTATA
1 ATAAAAAA-AAGTTTATA
41920361 TAATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.88
18 2 0.12
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.32
Consensus pattern (17 bp):
ATAAAAAAAAGTTTATA
Found at i:41920491 original size:108 final size:108
Alignment explanation
Indices: 41920342--41920597 Score: 467
Period size: 108 Copynumber: 2.3 Consensus size: 108
41920332 AAAAAGTTTA
*
41920342 TAATAAAAAATAATTTATATAATATATTTATTTATAAAAAGTTATGACTTAAAAATGTGGAGATA
1 TAATAAAAAAT--TTTA-ATTATA-ATTTATTTATAAAAAGTTATGACTTAAAAATGTGGAGATA
41920407 ATTTATTTATATTTCCATATTATATATCATAAAAATAATATGCTTAT
62 ATTTATTTATATTTCCATATTATATATCATAAAAATAATATGCTTAT
41920454 TAATAAAAAATTTTAATTATAATTTATTTATAAAAAGTTATGACTTAAAAATGTGGAGATAATTT
1 TAATAAAAAATTTTAATTATAATTTATTTATAAAAAGTTATGACTTAAAAATGTGGAGATAATTT
41920519 ATTTATATTTCCATATTATATATCATAAAAATAATATGCTTAT
66 ATTTATATTTCCATATTATATATCATAAAAATAATATGCTTAT
41920562 TAATAAAAAATTTTAATTATAATTTATTTATAAAAA
1 TAATAAAAAATTTTAATTATAATTTATTTATAAAAA
41920598 ATAACTTTCT
Statistics
Matches: 143, Mismatches: 1, Indels: 4
0.97 0.01 0.03
Matches are distributed among these distances:
108 123 0.86
109 5 0.03
110 4 0.03
112 11 0.08
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.43
Consensus pattern (108 bp):
TAATAAAAAATTTTAATTATAATTTATTTATAAAAAGTTATGACTTAAAAATGTGGAGATAATTT
ATTTATATTTCCATATTATATATCATAAAAATAATATGCTTAT
Found at i:41921591 original size:23 final size:26
Alignment explanation
Indices: 41921537--41921595 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
41921527 GAAAACATTC
* *
41921537 AAAAACTATTTCTAACATTCTTTAAA
1 AAAAATTATTTCTAACATTCTATAAA
41921563 AAAAATTATTTCTAACA-T-TATAAA
1 AAAAATTATTTCTAACATTCTATAAA
*
41921587 AAAATTTAT
1 AAAAATTAT
41921596 ATATACAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
24 13 0.43
25 1 0.03
26 16 0.53
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.39
Consensus pattern (26 bp):
AAAAATTATTTCTAACATTCTATAAA
Found at i:41923432 original size:19 final size:18
Alignment explanation
Indices: 41923398--41923436 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
41923388 GCAATCCTTT
* *
41923398 TTAATTATTTATTAAAATA
1 TTAATTATTCACT-AAATA
41923417 TTAATTATTCACTAAATA
1 TTAATTATTCACTAAATA
41923435 TT
1 TT
41923437 TTACTAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (18 bp):
TTAATTATTCACTAAATA
Found at i:41933499 original size:20 final size:21
Alignment explanation
Indices: 41933476--41933518 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
41933466 ACTTTTCCCG
*
41933476 TTTTT-TA-AGAGTTAGGGTT
1 TTTTTCTACAGAGCTAGGGTT
41933495 TTTTTCTACTAGAGCTAGGGTT
1 TTTTTCTAC-AGAGCTAGGGTT
41933517 TT
1 TT
41933519 AGGGGTTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
22 13 0.65
ACGTcount: A:0.19, C:0.07, G:0.23, T:0.51
Consensus pattern (21 bp):
TTTTTCTACAGAGCTAGGGTT
Done.