Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01011063.1 Kokia drynarioides strain JFW-HI SEQ_126034, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 552818
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Warning! 607 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:219938 original size:19 final size:16
Alignment explanation
Indices: 219901--219932 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
219891 GATAGTAGTT
219901 AGAGGAGAAGAGAGAA
1 AGAGGAGAAGAGAGAA
*
219917 AGAGGAGAAGAAAGAA
1 AGAGGAGAAGAGAGAA
219933 GAAAGAAGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (16 bp):
AGAGGAGAAGAGAGAA
Found at i:221062 original size:16 final size:16
Alignment explanation
Indices: 221024--221073 Score: 59
Period size: 16 Copynumber: 3.1 Consensus size: 16
221014 TTTACTTCAT
*
221024 ATAATTAATGTAAAACA
1 ATAATTAAT-TAAAATA
221041 AT-ATT-ATTCAAAATA
1 ATAATTAATT-AAAATA
221056 ATAATTAATTAAAATA
1 ATAATTAATTAAAATA
221072 AT
1 AT
221074 TAACTTATAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
14 1 0.03
15 9 0.31
16 14 0.48
17 5 0.17
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (16 bp):
ATAATTAATTAAAATA
Found at i:222121 original size:29 final size:30
Alignment explanation
Indices: 222088--222555 Score: 346
Period size: 29 Copynumber: 15.9 Consensus size: 30
222078 ATTTAGGGGT
*
222088 AAAAATGGAATTTTTAG-AGTTTCGAGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * * * *
222117 GAAAATAGAGTTTTTGGACA---TCCAGGGGC
1 AAAAATGGAATTTTTGGA-AGTTTCGA-GGTC
* * *
222146 -AAAATAGTAAATTTTGAAAGTTTCGAGGTC
1 AAAAAT-GGAATTTTTGGAAGTTTCGAGGTC
* *
222176 AAAAATGGAAATTTTGG-AGGTTCGAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* *
222205 AAAAATGGAA-TTTTAGAAGTTTCGACGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * *
222234 AAAGATGGAATTATTGGAAG-TTCGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* *
222262 AAAAATGGAATTTTTAGAAGTTTCGAGGTT
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * *
222292 AAAAATAGAATTTTTGGAAG-ATCAAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* *
222321 AAAAATGGGATTTTTGGAAGTTT-TAGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
*
222351 AAAAATGGAATTTTTTGAAGTTT-GAGGGT-
1 AAAAATGGAATTTTTGGAAGTTTCGA-GGTC
* * *
222380 AAAAATGTAATTTTTGGAAATTTTG-GAGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAG-GTC
* * *
222410 GAAAATGGAATTTTTGGAAG-TTCGGGGGC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
* * *
222439 AAAAATGGAATTTTTTGGAAATTTTGGGGTC
1 AAAAATGGAA-TTTTTGGAAGTTTCGAGGTC
* * *
222470 AAAAATGAAATTTTTAGAAG-TTCGGGGGT-
1 AAAAATGGAATTTTTGGAAGTTTC-GAGGTC
* * *
222499 AATAATGGAATTTTTGGAAATTTCGGGGTC
1 AAAAATGGAATTTTTGGAAGTTTCGAGGTC
*
222529 GAAAATGGAATTTTTGGAAG-TTCGAGG
1 AAAAATGGAATTTTTGGAAGTTTCGAGG
222556 GGACGGTTCG
Statistics
Matches: 350, Mismatches: 63, Indels: 52
0.75 0.14 0.11
Matches are distributed among these distances:
28 34 0.10
29 160 0.46
30 131 0.37
31 25 0.07
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.33
Consensus pattern (30 bp):
AAAAATGGAATTTTTGGAAGTTTCGAGGTC
Found at i:222355 original size:59 final size:59
Alignment explanation
Indices: 222084--222556 Score: 437
Period size: 59 Copynumber: 8.1 Consensus size: 59
222074 ACACATTTAG
* * * * * *
222084 GGGTAAAAATGGAATTTTT--AGAGTTTCGAGGTCGAAAATAGAGTTTTTGGACA--TCCA
1 GGGTAAAAATGGAATTTTTGGAAATTTTCG-GGTCAAAAATGGAATTTTTGGA-AGTTCGA
** * * * * *
222141 GGGGCAAAATAGTAAATTTT-GAAAGTTTCGAGGTCAAAAATGGAAATTTTGGAGGTTCGA
1 GGGTAAAAAT-GGAATTTTTGGAAATTTTCG-GGTCAAAAATGGAATTTTTGGAAGTTCGA
* * * * *
222201 GGGTAAAAATGGAA-TTTTAG-AAGTTTCGACGTCAAAGATGGAATTATTGGAAGTTCG-
1 GGGTAAAAATGGAATTTTTGGAAATTTTCG-GGTCAAAAATGGAATTTTTGGAAGTTCGA
* * * * * *
222258 GGGTAAAAATGGAATTTTTAG-AAGTTTCGAGGTTAAAAATAGAATTTTTGGAAGATCAA
1 GGGTAAAAATGGAATTTTTGGAAATTTTCG-GGTCAAAAATGGAATTTTTGGAAGTTCGA
* * * * *
222317 GGGTAAAAATGGGATTTTTGGAAGTTTTAGGGTCAAAAATGGAATTTTTTGAAGTTTGA
1 GGGTAAAAATGGAATTTTTGGAAATTTTCGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* * *
222376 GGGTAAAAATGTAATTTTTGGAAATTTT-GGAGTCGAAAATGGAATTTTTGGAAGTTCGG
1 GGGTAAAAATGGAATTTTTGGAAATTTTCGG-GTCAAAAATGGAATTTTTGGAAGTTCGA
* * * * *
222435 GGGCAAAAATGGAATTTTTTGGAAATTTTGGGGTCAAAAATGAAATTTTTAGAAGTTCGG
1 GGGTAAAAATGGAA-TTTTTGGAAATTTTCGGGTCAAAAATGGAATTTTTGGAAGTTCGA
* *
222495 GGGTAATAATGGAATTTTTGGAAA-TTTCGGGGTCGAAAATGGAATTTTTGGAAGTTCGA
1 GGGTAAAAATGGAATTTTTGGAAATTTTC-GGGTCAAAAATGGAATTTTTGGAAGTTCGA
222554 GGG
1 GGG
222557 GACGGTTCGG
Statistics
Matches: 348, Mismatches: 56, Indels: 22
0.82 0.13 0.05
Matches are distributed among these distances:
57 22 0.06
58 84 0.24
59 173 0.50
60 67 0.19
61 2 0.01
ACGTcount: A:0.34, C:0.05, G:0.28, T:0.33
Consensus pattern (59 bp):
GGGTAAAAATGGAATTTTTGGAAATTTTCGGGTCAAAAATGGAATTTTTGGAAGTTCGA
Found at i:223186 original size:3 final size:3
Alignment explanation
Indices: 223175--223251 Score: 100
Period size: 3 Copynumber: 25.3 Consensus size: 3
223165 TTTATTACTA
* ** **
223175 ATT AAT ATT ATT ATT ATT ATT ATT AAA ACA ATT ATT ATT AATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT ATT
223221 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
223252 ATGCTATCAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
3 63 0.95
4 3 0.05
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (3 bp):
ATT
Found at i:223957 original size:6 final size:6
Alignment explanation
Indices: 223940--224004 Score: 50
Period size: 6 Copynumber: 11.3 Consensus size: 6
223930 ATTTAAATAG
*
223940 ATTTAA ATTTTAA ATTTATA A--TAA ATTTAA ATTT-A A-GTAA ATTTAA
1 ATTTAA A-TTTAA ATTTA-A ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
* *
223986 ACTTAA A-ATAA ATTTAA AT
1 ATTTAA ATTTAA ATTTAA AT
224005 CTTGTTGGGC
Statistics
Matches: 47, Mismatches: 5, Indels: 14
0.71 0.08 0.21
Matches are distributed among these distances:
4 3 0.06
5 10 0.21
6 26 0.55
7 8 0.17
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (6 bp):
ATTTAA
Found at i:223968 original size:17 final size:16
Alignment explanation
Indices: 223943--224004 Score: 79
Period size: 17 Copynumber: 3.7 Consensus size: 16
223933 TAAATAGATT
223943 TAAATTTTAAATTTATAA
1 TAAA-TTTAAATTTA-AA
*
223961 TAAATTTAAATTTAAG
1 TAAATTTAAATTTAAA
*
223977 TAAATTTAAACTTAAAA
1 TAAATTTAAA-TTTAAA
223994 TAAATTTAAAT
1 TAAATTTAAAT
224005 CTTGTTGGGC
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
16 12 0.30
17 24 0.60
18 4 0.10
ACGTcount: A:0.53, C:0.02, G:0.02, T:0.44
Consensus pattern (16 bp):
TAAATTTAAATTTAAA
Found at i:224419 original size:37 final size:38
Alignment explanation
Indices: 224369--224440 Score: 92
Period size: 38 Copynumber: 1.9 Consensus size: 38
224359 CATATCACTT
* * *
224369 GTTTTGATCCACTT-CTCTGTGTTTCATCAGGAAGATG
1 GTTTTGATCCACTTCCCCCGTATTTCATCAGGAAGATG
* *
224406 GTTTTGGTTCACTTCCCCCGTATTTCATCAGGAAG
1 GTTTTGATCCACTTCCCCCGTATTTCATCAGGAAG
224441 TTAACCTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
37 12 0.41
38 17 0.59
ACGTcount: A:0.18, C:0.22, G:0.21, T:0.39
Consensus pattern (38 bp):
GTTTTGATCCACTTCCCCCGTATTTCATCAGGAAGATG
Found at i:224683 original size:205 final size:204
Alignment explanation
Indices: 224425--224982 Score: 876
Period size: 200 Copynumber: 2.8 Consensus size: 204
224415 CACTTCCCCC
* *
224425 GTATTTCATCAGGAAGTTAACCTTTTATTGCTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCT
224490 GGGGTTCGAAGATTTGTTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCA
66 GGGGTTCGAAGATTTG-TCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCA
224555 GGAAGATGACCGCATCGTTTGTTTCAATTCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGT
130 GGAAGATGACCGCATCGTTTGTTTCAATTCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGT
*
224620 CCAGTT-ATCA
195 CCACTTCA-CA
* * *
224630 GTATCTCATCAAGAAGCTAACCTTTTATTGCTTCGACCTGCTTCTCGGTGTCTCATCAGGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCT
* * * *
224695 GGGGTTCGATGATTTG---C-TCGAGTGTGGGTTTGATTTGGTCTTATTCTCAGTATCTCATCAA
66 GGGGTTCGAAGATTTGTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAG
* * *
224756 GAAGATGACCGCGTCGTTTGTTTCAATTCGCTTCTCTATATCTCATTAGGAAGACGAATTTGGTC
131 GAAGATGACCGCATCGTTTGTTTCAATTCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGTC
224821 CACTTCACA
196 CACTTCACA
* *
224830 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGATCTACTTCTCAGTGTCTCATCAAGAAGCT
1 GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCT
* *
224895 GGGGTACGAAGATTTGCTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCCCATCA
66 GGGGTTCGAAGATTTG-TCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCA
* *
224960 GGAAGATGATCGCACCG-TTGTTT
130 GGAAGATGACCGCATCGTTTGTTT
224983 GTGAATAATC
Statistics
Matches: 320, Mismatches: 27, Indels: 13
0.89 0.08 0.04
Matches are distributed among these distances:
200 183 0.57
201 2 0.01
204 7 0.02
205 128 0.40
ACGTcount: A:0.22, C:0.21, G:0.22, T:0.36
Consensus pattern (204 bp):
GTATCTCATCAGGAAGCTAACCTTTTATTGCTTCGATCTGCTTCTCAGTGTCTCATCAGGAAGCT
GGGGTTCGAAGATTTGTCACATCGAGCGTGGGTTTGATTTGGTCTTCTTCTCAGTATCTCATCAG
GAAGATGACCGCATCGTTTGTTTCAATTCGCTTCTCTATATCTCATCAAGAAGACGAATTTGGTC
CACTTCACA
Found at i:225816 original size:47 final size:47
Alignment explanation
Indices: 225736--225825 Score: 128
Period size: 47 Copynumber: 1.9 Consensus size: 47
225726 TTGGTTCTAG
* *
225736 GACGCCCTTTGCGGGTTTTCATCATGAACCCCCTTTTTTTTTTTCGA
1 GACGCCCTTTGCGGGTTTTCATCATCAACCCCCTTTTGTTTTTTCGA
* *
225783 GACGCCCTTTGTGGGTTTTCATC-TCAATTCCCCTTTTGTTTTT
1 GACGCCCTTTGCGGGTTTTCATCATCAA-CCCCCTTTTGTTTTT
225826 AGGTGAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
46 3 0.08
47 35 0.92
ACGTcount: A:0.11, C:0.27, G:0.17, T:0.46
Consensus pattern (47 bp):
GACGCCCTTTGCGGGTTTTCATCATCAACCCCCTTTTGTTTTTTCGA
Found at i:236257 original size:96 final size:96
Alignment explanation
Indices: 236068--236259 Score: 239
Period size: 96 Copynumber: 2.0 Consensus size: 96
236058 ATTTTAGGAA
** **
236068 AAGGATATTCGATTATTTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGTGCAATATTTCA
1 AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCCAATATTTCA
**
236133 GAATCGAAGATAAAGAAACATTGTCTCGATT
66 GAATCGAAGATAAAGAAACATTACCTCGATT
* *
236164 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTTAGTTAAGGCCCAA-ATTTTC
1 AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCCAATA-TTTC
*
236228 -GAAACTCGAA-ATAAA-AGAATATTACCTCGATT
65 AG-AA-TCGAAGATAAAGA-AACATTACCTCGATT
236260 TTAAAGTCTT
Statistics
Matches: 83, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
95 3 0.04
96 75 0.90
97 5 0.06
ACGTcount: A:0.37, C:0.13, G:0.19, T:0.31
Consensus pattern (96 bp):
AAGGATATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCCCAATATTTCA
GAATCGAAGATAAAGAAACATTACCTCGATT
Found at i:236511 original size:28 final size:27
Alignment explanation
Indices: 236480--236537 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
236470 AAAATGAGAC
236480 TTTGGA-TACTTGAGGGCAAAATGGTAAT
1 TTTGGACT-CTTG-GGGCAAAATGGTAAT
* *
236508 TTTGGACTTTTGGGGCAAGATGGTAAT
1 TTTGGACTCTTGGGGCAAAATGGTAAT
236535 TTT
1 TTT
236538 AGGGAAGTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
27 17 0.63
28 9 0.33
29 1 0.04
ACGTcount: A:0.26, C:0.07, G:0.29, T:0.38
Consensus pattern (27 bp):
TTTGGACTCTTGGGGCAAAATGGTAAT
Found at i:236687 original size:59 final size:57
Alignment explanation
Indices: 236497--236747 Score: 145
Period size: 58 Copynumber: 4.3 Consensus size: 57
236487 ACTTGAGGGC
** * * *
236497 AAAATGGTAATTTTGGAC-TTTTGGGGCAAGATGGTAATTTTAGGGAAGTTT-GAGGTTA
1 AAAATGGTAATTTTGGACATTAGGGGGCAAAAT-GTAATTTT--TGAAGTTTCGAGGTCA
* ** * * *
236555 AAAGATGG-AATTTTTAGACATTTAGGGGTAAAAATGGAATTTTTGGAGTTTCGAGGTCG
1 AAA-ATGGTAA-TTTTGGACA-TTAGGGGGCAAAATGTAATTTTTGAAGTTTCGAGGTCA
* *
236614 AAAATAGAGT--TTTTGGACATTCGGGGGCAAAATGATAATTTTTGAAAGTTTCGGGGTCA
1 AAAAT-G-GTAATTTTGGACATTAGGGGGCAAAATG-TAATTTTTG-AAGTTTCGAGGTCA
** * ** * ** * *
236673 AAAATGGTAATTTTGGAGGTTCGAGGGTAAAAATGGAATTTTACAAATTTCGAGGTTA
1 AAAATGGTAATTTTGGACATTAG-GGGGCAAAATGTAATTTTTGAAGTTTCGAGGTCA
236731 AAAATGG-AATTCTTGGA
1 AAAATGGTAATT-TTGGA
236748 AGTTCGAAGG
Statistics
Matches: 150, Mismatches: 29, Indels: 28
0.72 0.14 0.14
Matches are distributed among these distances:
57 18 0.12
58 53 0.35
59 53 0.35
60 17 0.11
61 9 0.06
ACGTcount: A:0.33, C:0.06, G:0.28, T:0.33
Consensus pattern (57 bp):
AAAATGGTAATTTTGGACATTAGGGGGCAAAATGTAATTTTTGAAGTTTCGAGGTCA
Found at i:236701 original size:117 final size:115
Alignment explanation
Indices: 236554--237074 Score: 509
Period size: 117 Copynumber: 4.4 Consensus size: 115
236544 GTTTGAGGTT
* * * * * *
236554 AAAAGATGGAATTTTTAGACATTTAG-GGGTAAAAATGGAATTTTTGGAGTTTCGAGGTCGAAAA
1 AAAA-ATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTAGAAATTTCGAGGTCGAAAA
* * * *
236618 TAGAGTTTTTGGACA-TTCGGGGGCAAAATGATAATTTTTGAAAGTTTCGGGGTC
64 TGGAATTTTTGGA-AGTTCGGGGGAAAAATG-GAATTTTTGAAA-TTTCGGGGTC
* * **
236672 AAAAATGGTAA-TTTTGGAGGTTCGAGGGTAAAAATGGAATTTTACAAATTTCGAGGTTAAAAAT
1 AAAAATGG-AATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTAGAAATTTCGAGGTCGAAAAT
* * * * * *
236736 GGAATTCTTGGAAGTTCGAAGGTAAAAATGGGATTTTTTGAAGTTTCGGGGTT
65 GGAATTTTTGGAAGTTCG-GGGGAAAAAT-GGAATTTTTGAAATTTCGGGGTC
* * * *
236789 AAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTCAAAAATTTCGGGGTTGAAAAT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT-AGAAATTTCGAGGTCGAAAAT
* *
236854 GGAATTTTTGGAAGTT-GGGGGCAAAAATGGAATTTTGGGAAATATT-GGGGTT
65 GGAATTTTTGGAAGTTCGGGGG-AAAAATGGAATTTT-TGAAAT-TTCGGGGTC
* *
236906 AAAAATGGAATTTTTGGAAGTTC-AGGGCAAAAATGGAATTTTTAGAAATTT-TAGGGTCGAAAA
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAA-TTTTAGAAATTTCGA-GGTCGAAAA
* ***
236969 TGGAATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTAGAAATTTTAAGGTC
64 TGGAATTTTTGGAAGTTCGGGGG-AAAAATGGAATTTTT-GAAATTTCGGGGTC
* * *
237023 AAAAATGGGATTTTTGGAAGTTCGA-GGCAAAAATGTAATTTTCAGACAATTT
1 AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTT-AGA-AATTT
237075 AGGGACCTCC
Statistics
Matches: 340, Mismatches: 45, Indels: 36
0.81 0.11 0.09
Matches are distributed among these distances:
116 66 0.19
117 210 0.62
118 63 0.19
119 1 0.00
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (115 bp):
AAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTAGAAATTTCGAGGTCGAAAATG
GAATTTTTGGAAGTTCGGGGGAAAAATGGAATTTTTGAAATTTCGGGGTC
Found at i:236807 original size:59 final size:59
Alignment explanation
Indices: 236550--237074 Score: 496
Period size: 59 Copynumber: 8.9 Consensus size: 59
236540 GGAAGTTTGA
* * * * * *
236550 GGTTAAAAGATGGAATTTTTAGACATTTAG-GGGTAAAAATGGAATTTTT-GGAGTTTCGA
1 GGTTAAAA-ATGGAATTTTTGGA-AGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
** * * ** *
236609 GGTCGAAAATAGAGTTTTTGGACA-TTCG-GGGGCAAAATGATAATTTTT-GAAAGTTTCGG
1 GGTTAAAAATGGAATTTTTGGA-AGTTCGAGGGTAAAAATG-GAATTTTTAGAAA-TTTCGG
* * * *
236668 GGTCAAAAATGGTAA-TTTTGGAGGTTCGAGGGTAAAAATGGAA-TTTTACAAATTTCGA
1 GGTTAAAAATGG-AATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
* * * * *
236726 GGTTAAAAATGGAATTCTTGGAAGTTCGAAGGTAAAAATGGGATTTTTTGAAGTTTCGG
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
* * *
236785 GGTTAAAAATGAAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTCAAAAATTTCGG
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
* * * **
236844 GGTTGAAAATGGAATTTTTGGAAGTT-GGGGGCAAAAATGGAATTTTGGGAAATATT-GG
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAAT-TTCGG
* **
236902 GGTTAAAAATGGAATTTTTGGAAGTTC-AGGGCAAAAATGGAATTTTTAGAAATTTTAG
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
** * * ***
236960 GGTCGAAAATGGAATTTTTGAAAGTTCGGGGGTAAAAATGGAATTTTTAGAAATTTTAA
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
* * * * *
237019 GGTCAAAAATGGGATTTTTGGAAGTTCGA-GGCAAAAATGTAATTTTCAGACAATTT
1 GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGA-AATTT
237075 AGGGACCTCC
Statistics
Matches: 390, Mismatches: 63, Indels: 26
0.81 0.13 0.05
Matches are distributed among these distances:
57 16 0.04
58 181 0.46
59 183 0.47
60 10 0.03
ACGTcount: A:0.35, C:0.05, G:0.27, T:0.33
Consensus pattern (59 bp):
GGTTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAATTTCGG
Found at i:238104 original size:3 final size:3
Alignment explanation
Indices: 238096--238205 Score: 123
Period size: 3 Copynumber: 36.0 Consensus size: 3
238086 CGTTTCTTTT
* * * * **
238096 TTA TTA TTA TTAA TTA ATA ATA ATA TTA TTA TTA TTA TTA -AA ACA
1 TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
238141 GTTA TTA TTAA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 -TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
238188 TTA TTA CTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
238206 ATGCTATCAG
Statistics
Matches: 95, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
2 1 0.01
3 87 0.92
4 7 0.07
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:238212 original size:15 final size:14
Alignment explanation
Indices: 238142--238251 Score: 75
Period size: 15 Copynumber: 7.7 Consensus size: 14
238132 ATTAAAACAG
238142 TTATTATTAAT-TA
1 TTATTATTAATCTA
238155 TTATTATT-AT-TA
1 TTATTATTAATCTA
238167 TTATTATTATTAT-TA
1 TTATTATTA--ATCTA
*
238182 TTATTATTATTACTA
1 TTATTATTAAT-CTA
238197 TTATTATTAATGCTA
1 TTATTATTAAT-CTA
* ** * *
238212 TCAGCATCATATTTA
1 TTATTATTA-ATCTA
*
238227 TTATTATTAAAGCTA
1 TTATTATT-AATCTA
238242 TTATTATTAA
1 TTATTATTAA
238252 AACATTTGAA
Statistics
Matches: 76, Mismatches: 14, Indels: 13
0.74 0.14 0.13
Matches are distributed among these distances:
12 12 0.16
13 9 0.12
14 2 0.03
15 50 0.66
16 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.56
Consensus pattern (14 bp):
TTATTATTAATCTA
Found at i:240288 original size:23 final size:24
Alignment explanation
Indices: 240239--240300 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 24
240229 TTAACAATGG
240239 AATAAATTAAAGATCTAAGTTCCAAAA
1 AATAAA-TAAA-ATCTAAGTTCC-AAA
*
240266 AATAAATAAAATCT-AGTT-TAAA
1 AATAAATAAAATCTAAGTTCCAAA
240288 AATAAATATAAAT
1 AATAAATA-AAAT
240301 AATATAACAA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
22 11 0.33
23 4 0.12
24 4 0.12
25 4 0.12
26 4 0.12
27 6 0.18
ACGTcount: A:0.60, C:0.06, G:0.05, T:0.29
Consensus pattern (24 bp):
AATAAATAAAATCTAAGTTCCAAA
Found at i:242492 original size:3 final size:3
Alignment explanation
Indices: 242484--242509 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
242474 TAAGCTCGAC
242484 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
242510 GTAATTAGGG
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:242561 original size:104 final size:105
Alignment explanation
Indices: 242402--242613 Score: 374
Period size: 104 Copynumber: 2.0 Consensus size: 105
242392 TGGAGTGAAT
242402 TTAGTAATTAGGGGCAGCCTCTACCCCCATGGCACAGCCCCTAGTAAGAATAATAAATAAAAAGT
1 TTAGTAATTAGGGGCAGCCTCTACCCCCATGGCACAGCCCCTAGTAAGAATAATAAATAAAAAGT
242467 GATATTAT-AAGCTCGACTATTATTATTATTATTATTATTA
66 GATATTATAAAG-TCGACTATTATTATTATTATTATTATTA
242507 TTAGTAATTAGGGGCAGCCTCTA-CCCCATGGCACAGCCCCTAGTAAGAATAATAAATAAAAAGT
1 TTAGTAATTAGGGGCAGCCTCTACCCCCATGGCACAGCCCCTAGTAAGAATAATAAATAAAAAGT
* * *
242571 GATATTATAAAGTTGATTTTTATTATTATTATTATTATTA
66 GATATTATAAAGTCGACTATTATTATTATTATTATTATTA
242611 TTA
1 TTA
242614 TTATTATTAT
Statistics
Matches: 103, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
104 77 0.75
105 26 0.25
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.34
Consensus pattern (105 bp):
TTAGTAATTAGGGGCAGCCTCTACCCCCATGGCACAGCCCCTAGTAAGAATAATAAATAAAAAGT
GATATTATAAAGTCGACTATTATTATTATTATTATTATTA
Found at i:242598 original size:3 final size:3
Alignment explanation
Indices: 242590--242632 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
242580 AAGTTGATTT
242590 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
242633 AAAAACCTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:243783 original size:31 final size:31
Alignment explanation
Indices: 243745--243808 Score: 101
Period size: 31 Copynumber: 2.1 Consensus size: 31
243735 CTCTGAATAA
*
243745 TATCCTCCGATAGCCAGAGTCGAAAAAGATC
1 TATCCTCCGATAGCCAAAGTCGAAAAAGATC
* *
243776 TATCCTCCGATGGCCAAAGTTGAAAAAGATC
1 TATCCTCCGATAGCCAAAGTCGAAAAAGATC
243807 TA
1 TA
243809 GATTCCAACG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.22
Consensus pattern (31 bp):
TATCCTCCGATAGCCAAAGTCGAAAAAGATC
Found at i:248918 original size:36 final size:36
Alignment explanation
Indices: 248873--248958 Score: 120
Period size: 37 Copynumber: 2.4 Consensus size: 36
248863 ACGTGTGCAG
248873 GGAATCCCACTAAG-GTTTTTTATTTGTTTCTCTTA
1 GGAATCCCACTAAGTGTTTTTTATTTGTTTCTCTTA
* * *
248908 GGAACTCCCACCAAGTTTTTTTTATTTGTTTCTGTTA
1 GGAA-TCCCACTAAGTGTTTTTTATTTGTTTCTCTTA
248945 GGAAATCCCACTAA
1 GG-AATCCCACTAA
248959 ATGGACAAGA
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
35 4 0.09
36 9 0.20
37 29 0.66
38 2 0.05
ACGTcount: A:0.23, C:0.20, G:0.14, T:0.43
Consensus pattern (36 bp):
GGAATCCCACTAAGTGTTTTTTATTTGTTTCTCTTA
Found at i:250368 original size:3 final size:3
Alignment explanation
Indices: 250360--250404 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
250350 GCCATCTCTT
* * *
250360 TTA TTA TTA TTA TTA TTA TTA GTA TTA GTA TTA TTA TTA TAA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
250405 CTTGGTGTAT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.36, C:0.00, G:0.04, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:250522 original size:24 final size:24
Alignment explanation
Indices: 250494--250546 Score: 97
Period size: 24 Copynumber: 2.2 Consensus size: 24
250484 AGCTCATTTT
250494 CATATTCTCCATATCTAGAGAACA
1 CATATTCTCCATATCTAGAGAACA
250518 CATATTCTCCATATCTAGAGAACA
1 CATATTCTCCATATCTAGAGAACA
*
250542 TATAT
1 CATAT
250547 ATTCCTTTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.32
Consensus pattern (24 bp):
CATATTCTCCATATCTAGAGAACA
Found at i:251064 original size:17 final size:18
Alignment explanation
Indices: 251042--251079 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
251032 TAATAAAAAT
*
251042 ATAATTTA-ATTTTTATA
1 ATAATTTATATATTTATA
251059 ATAATTTATATATTTATA
1 ATAATTTATATATTTATA
251077 ATA
1 ATA
251080 TTTGAAAGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.42
18 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (18 bp):
ATAATTTATATATTTATA
Found at i:252279 original size:22 final size:23
Alignment explanation
Indices: 252231--252281 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 23
252221 CGAAATTTGT
* *
252231 AATTTTTATAATAGTAAAAATAT
1 AATTTTTATAAAAGTAAAAATAA
* *
252254 AATTTTTA-AAAAGTTAAATTAA
1 AATTTTTATAAAAGTAAAAATAA
252276 AATTTT
1 AATTTT
252282 ATCATTTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 16 0.67
23 8 0.33
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (23 bp):
AATTTTTATAAAAGTAAAAATAA
Found at i:252289 original size:30 final size:31
Alignment explanation
Indices: 252257--252314 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
252247 AAAATATAAT
*
252257 TTTTAAAA-AG-TTAAATTAAAATTTTATCA
1 TTTTAAAAGAGATAAAATTAAAATTTTATCA
252286 TTTTAAAAGAGATAAAATTAAAATTTTAT
1 TTTTAAAAGAGATAAAATTAAAATTTTAT
252315 TTTTATTCAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
29 8 0.31
30 2 0.08
31 16 0.62
ACGTcount: A:0.50, C:0.02, G:0.05, T:0.43
Consensus pattern (31 bp):
TTTTAAAAGAGATAAAATTAAAATTTTATCA
Found at i:256752 original size:33 final size:33
Alignment explanation
Indices: 256710--256802 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 33
256700 AGTCACACAA
* *
256710 GCTGCATTTACAA-GAGCTGCAGTCGCATAAACT
1 GCTGCATTTACAAGGA-CTACAGTCACATAAACT
*
256743 GCTGCATTTACATGGACTACAGTCACATAAACT
1 GCTGCATTTACAAGGACTACAGTCACATAAACT
** *
256776 ATTGCATTTACACA-AACTACAGTCACA
1 GCTGCATTTACA-AGGACTACAGTCACA
256803 CGAGCTGTAT
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
33 49 0.96
34 2 0.04
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (33 bp):
GCTGCATTTACAAGGACTACAGTCACATAAACT
Found at i:256835 original size:30 final size:30
Alignment explanation
Indices: 256796--256907 Score: 118
Period size: 30 Copynumber: 3.7 Consensus size: 30
256786 CACAAACTAC
* * *
256796 AGTCACACGAGCTGTATTTACACGGGTTGC
1 AGTCGCACGAGCTGCATTTACACGGGTTGT
* * * *
256826 AATCGCACGAGTTGCATTTACACGGATCGT
1 AGTCGCACGAGCTGCATTTACACGGGTTGT
* *
256856 AGTCGCACGAACT-CTGATTTACATGGGTTGT
1 AGTCGCACGAGCTGC--ATTTACACGGGTTGT
256887 AGTCGCACGAGCTGCATTTAC
1 AGTCGCACGAGCTGCATTTAC
256908 GAGCTGTATC
Statistics
Matches: 65, Mismatches: 14, Indels: 6
0.76 0.16 0.07
Matches are distributed among these distances:
29 1 0.02
30 39 0.60
31 24 0.37
32 1 0.02
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (30 bp):
AGTCGCACGAGCTGCATTTACACGGGTTGT
Found at i:263571 original size:46 final size:47
Alignment explanation
Indices: 263504--263595 Score: 177
Period size: 46 Copynumber: 2.0 Consensus size: 47
263494 ACTCTACTAC
263504 ACCCTCTTGTTGTTCAACAAACTTGCCAATCAAAATGTT-AAGATCT
1 ACCCTCTTGTTGTTCAACAAACTTGCCAATCAAAATGTTAAAGATCT
263550 ACCCTCTTGTTGTTCAACAAACTTGCCAATCAAAATGTTAAAGATC
1 ACCCTCTTGTTGTTCAACAAACTTGCCAATCAAAATGTTAAAGATC
263596 CTTTCTCTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 39 0.87
47 6 0.13
ACGTcount: A:0.34, C:0.24, G:0.11, T:0.32
Consensus pattern (47 bp):
ACCCTCTTGTTGTTCAACAAACTTGCCAATCAAAATGTTAAAGATCT
Found at i:271887 original size:18 final size:18
Alignment explanation
Indices: 271860--271906 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
271850 CCTACGAAGT
271860 TGTCGACACAACTGCCCA
1 TGTCGACACAACTGCCCA
*
271878 TGTTGACACAACTGCCCA
1 TGTCGACACAACTGCCCA
271896 TGTCGACACAA
1 TGTCGACACAA
271907 TCGGTTATAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.30, C:0.34, G:0.17, T:0.19
Consensus pattern (18 bp):
TGTCGACACAACTGCCCA
Found at i:274635 original size:23 final size:23
Alignment explanation
Indices: 274580--274635 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
274570 GTCACTGCGT
*
274580 TCCTGAAGAAGAAATGCTATCTA
1 TCCTGAAGTAGAAATGCTATCTA
*
274603 TCTTGAAGTAGAAATGCTATCTA
1 TCCTGAAGTAGAAATGCTATCTA
*
274626 TCCTGGAGTA
1 TCCTGAAGTA
274636 TTGTCACGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (23 bp):
TCCTGAAGTAGAAATGCTATCTA
Found at i:277564 original size:3 final size:3
Alignment explanation
Indices: 277547--277600 Score: 53
Period size: 3 Copynumber: 18.7 Consensus size: 3
277537 GAAGAAAAAT
*
277547 AGA A-A AGA A-A AGA AGA AGGA A-A AGA AG- AGA AGGA AAA AGA AGA
1 AGA AGA AGA AGA AGA AGA A-GA AGA AGA AGA AGA A-GA AGA AGA AGA
277590 AGA AGA AGA AG
1 AGA AGA AGA AG
277601 TTGTCTCGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
2 8 0.19
3 29 0.67
4 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:278156 original size:13 final size:12
Alignment explanation
Indices: 278118--278150 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
278108 TGCAGACACT
278118 AAGTTTGG-GGG
1 AAGTTTGGAGGG
278129 AAAGTTTGGAGGG
1 -AAGTTTGGAGGG
278142 AAGTTTGGA
1 AAGTTTGGA
278151 ATGGAAATGC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 17 0.85
13 3 0.15
ACGTcount: A:0.27, C:0.00, G:0.45, T:0.27
Consensus pattern (12 bp):
AAGTTTGGAGGG
Found at i:284122 original size:19 final size:20
Alignment explanation
Indices: 284091--284131 Score: 66
Period size: 19 Copynumber: 2.1 Consensus size: 20
284081 TCGAAGGCCT
284091 AATTTGTTAACCCAATACCC
1 AATTTGTTAACCCAATACCC
*
284111 AATTTG-TAACCCATTACCC
1 AATTTGTTAACCCAATACCC
284130 AA
1 AA
284132 CCCAAACCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.37, C:0.29, G:0.05, T:0.29
Consensus pattern (20 bp):
AATTTGTTAACCCAATACCC
Found at i:287557 original size:22 final size:21
Alignment explanation
Indices: 287529--287570 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
287519 TTCAGGGTGT
287529 CTTCAGGGGTATGTCGCGACAC
1 CTTCA-GGGTATGTCGCGACAC
* *
287551 CTTCAGGTTGTGTCGCGACA
1 CTTCAGGGTATGTCGCGACA
287571 ACAACGACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.26, G:0.31, T:0.26
Consensus pattern (21 bp):
CTTCAGGGTATGTCGCGACAC
Found at i:289042 original size:25 final size:25
Alignment explanation
Indices: 289012--289065 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
289002 ATTAAATAGT
*
289012 TAAATCTATCAACGTAAATATAACA
1 TAAATCTATCAACATAAATATAACA
289037 TAAATCTATCAACATAAATATAACA
1 TAAATCTATCAACATAAATATAACA
289062 TAAA
1 TAAA
289066 ATGTCAGAGC
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.56, C:0.15, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAATCTATCAACATAAATATAACA
Found at i:289052 original size:14 final size:14
Alignment explanation
Indices: 289012--289055 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
289002 ATTAAATAGT
*
289012 TAAATCTATCAACG
1 TAAATCTATCAACA
289026 TAAA--TAT-AACA
1 TAAATCTATCAACA
289037 TAAATCTATCAACA
1 TAAATCTATCAACA
289051 TAAAT
1 TAAAT
289056 ATAACATAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 7 0.27
12 3 0.12
13 3 0.12
14 13 0.50
ACGTcount: A:0.52, C:0.16, G:0.02, T:0.30
Consensus pattern (14 bp):
TAAATCTATCAACA
Found at i:289063 original size:11 final size:11
Alignment explanation
Indices: 289026--289065 Score: 53
Period size: 11 Copynumber: 3.4 Consensus size: 11
289016 TCTATCAACG
289026 TAAATATAACA
1 TAAATATAACA
289037 TAAATCTATCAACA
1 TAAA--TAT-AACA
289051 TAAATATAACA
1 TAAATATAACA
289062 TAAA
1 TAAA
289066 ATGTCAGAGC
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 12 0.46
12 3 0.12
13 3 0.12
14 8 0.31
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (11 bp):
TAAATATAACA
Found at i:290659 original size:18 final size:19
Alignment explanation
Indices: 290619--290670 Score: 63
Period size: 20 Copynumber: 2.8 Consensus size: 19
290609 TATACATATT
*
290619 TTTTTTTTCTTTTTATCAAC
1 TTTTCTTTCTTTTT-TCAAC
*
290639 TTTTCTTTCTTTTTTC-TC
1 TTTTCTTTCTTTTTTCAAC
290657 TTTTC-TTCTTTTTT
1 TTTTCTTTCTTTTTT
290671 TATGCGATTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
17 9 0.30
18 6 0.20
19 2 0.07
20 13 0.43
ACGTcount: A:0.06, C:0.17, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTTCTTTCTTTTTTCAAC
Found at i:291716 original size:15 final size:14
Alignment explanation
Indices: 291694--291739 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 14
291684 GAACAACTTC
291694 TTCTTCTTTTCAT-T
1 TTCTTCTTTTC-TCT
291708 TTCCTTCTTTTCTCT
1 TT-CTTCTTTTCTCT
291723 TTCTTCTTTTTCTCT
1 TTCTTC-TTTTCTCT
291738 TT
1 TT
291740 TCTATTCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
14 7 0.24
15 22 0.76
ACGTcount: A:0.02, C:0.26, G:0.00, T:0.72
Consensus pattern (14 bp):
TTCTTCTTTTCTCT
Found at i:293544 original size:24 final size:25
Alignment explanation
Indices: 293511--293566 Score: 71
Period size: 24 Copynumber: 2.3 Consensus size: 25
293501 TTATTCTTGC
*
293511 AAAAACTAAAGA-AACAAATTAA-AG
1 AAAAATTAAAGACAA-AAATTAACAG
*
293535 TAAAATTAAAGACAAAAATTAACAG
1 AAAAATTAAAGACAAAAATTAACAG
293560 AAAAATT
1 AAAAATT
293567 TGCAATCACA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
24 17 0.63
25 10 0.37
ACGTcount: A:0.68, C:0.07, G:0.07, T:0.18
Consensus pattern (25 bp):
AAAAATTAAAGACAAAAATTAACAG
Found at i:293552 original size:13 final size:12
Alignment explanation
Indices: 293511--293564 Score: 56
Period size: 13 Copynumber: 4.3 Consensus size: 12
293501 TTATTCTTGC
*
293511 AAAAACTAAAGA
1 AAAAATTAAAGA
293523 AACAAATTAAAG-
1 AA-AAATTAAAGA
*
293535 TAAAATTAAAGA
1 AAAAATTAAAGA
293547 CAAAAATTAACAGA
1 -AAAAATTAA-AGA
293561 AAAA
1 AAAA
293565 TTTGCAATCA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
11 9 0.26
12 3 0.09
13 20 0.57
14 3 0.09
ACGTcount: A:0.70, C:0.07, G:0.07, T:0.15
Consensus pattern (12 bp):
AAAAATTAAAGA
Found at i:297906 original size:18 final size:18
Alignment explanation
Indices: 297885--297928 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
297875 AAACATGTGG
297885 TTGCATCTAGTTAAATGA
1 TTGCATCTAGTTAAATGA
*
297903 TTGCATCTAGTTATATGA
1 TTGCATCTAGTTAAATGA
297921 TTGCATCT
1 TTGCATCT
297929 GAGTATGCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.27, C:0.14, G:0.16, T:0.43
Consensus pattern (18 bp):
TTGCATCTAGTTAAATGA
Found at i:303553 original size:7 final size:7
Alignment explanation
Indices: 303541--303571 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
303531 GGCTGGGCAT
303541 GAGGAGA
1 GAGGAGA
303548 GAGGAGA
1 GAGGAGA
303555 GAGGAGA
1 GAGGAGA
*
303562 GAGAAGA
1 GAGGAGA
303569 GAG
1 GAG
303572 AAAAAAAGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.45, C:0.00, G:0.55, T:0.00
Consensus pattern (7 bp):
GAGGAGA
Found at i:304026 original size:30 final size:30
Alignment explanation
Indices: 303987--304185 Score: 142
Period size: 30 Copynumber: 6.8 Consensus size: 30
303977 CCCTTAAATT
* *
303987 TCTCAAAAATTACATTTTTACCCTCGAACC
1 TCTCAAAAATTACATTTTAACCCTCAAACC
* * *
304017 TCTCTAAAATTACATTTT-TCCC-CAAACT
1 TCTCAAAAATTACATTTTAACCCTCAAACC
* **
304045 TC-CAAACATTACATTTTAACCC-CTAAATT
1 TCTCAAAAATTACATTTTAACCCTC-AAACC
*
304074 TCTCAAAAATTACATTTTAACCCT-AAACT
1 TCTCAAAAATTACATTTTAACCCTCAAACC
* * * * * *
304103 TTTCCAAAATTTCATTTTGA-CCTCGAATC
1 TCTCAAAAATTACATTTTAACCCTCAAACC
* * *
304132 TTTCAAAAATTACATTTTGACCC-CTAAACT
1 TCTCAAAAATTACATTTTAACCCTC-AAACC
* * *
304162 TTTCTAAAATTATATTTTAACCCT
1 TCTCAAAAATTACATTTTAACCCT
304186 AAATTTTCTA
Statistics
Matches: 136, Mismatches: 25, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
27 13 0.10
28 13 0.10
29 50 0.37
30 60 0.44
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (30 bp):
TCTCAAAAATTACATTTTAACCCTCAAACC
Found at i:304058 original size:57 final size:58
Alignment explanation
Indices: 303992--304185 Score: 198
Period size: 57 Copynumber: 3.3 Consensus size: 58
303982 AAATTTCTCA
* * * *
303992 AAAATTACATTTTTACCCTCGAACCTCTCTAAAATTACATTTT-TCCCCAAAC-TTCC
1 AAAATTACATTTTAACCCTCGAATCTCTCAAAAATTACATTTTAACCCCAAACTTTCC
* * *
304048 AAACATTACATTTTAACCC-CTAAATTTCTCAAAAATTACATTTTAACCCTAAACTTTTCC
1 AAA-ATTACATTTTAACCCTC-GAATCTCTCAAAAATTACATTTTAACCCCAAAC-TTTCC
* * * * *
304108 AAAATTTCATTTTGA-CCTCGAATCTTTCAAAAATTACATTTTGACCCCTAAACTTTTCT
1 AAAATTACATTTTAACCCTCGAATCTCTCAAAAATTACATTTTAACCCC-AAAC-TTTCC
*
304167 AAAATTATATTTTAACCCT
1 AAAATTACATTTTAACCCT
304186 AAATTTTCTA
Statistics
Matches: 112, Mismatches: 18, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
56 4 0.04
57 33 0.29
58 33 0.29
59 32 0.29
60 10 0.09
ACGTcount: A:0.35, C:0.25, G:0.02, T:0.38
Consensus pattern (58 bp):
AAAATTACATTTTAACCCTCGAATCTCTCAAAAATTACATTTTAACCCCAAACTTTCC
Found at i:304111 original size:29 final size:29
Alignment explanation
Indices: 303992--304209 Score: 187
Period size: 29 Copynumber: 7.5 Consensus size: 29
303982 AAATTTCTCA
* * * *
303992 AAAATTACATTTTTACCCTCGAACCTCTCT
1 AAAATTACATTTTAACCCT-AAACTTTTCT
* * *
304022 AAAATTACATTTT-TCCCCAAAC--TTCC
1 AAAATTACATTTTAACCCTAAACTTTTCT
*
304048 AAACATTACATTTTAACCCCTAAA-TTTCTCA
1 AAA-ATTACATTTTAA-CCCTAAACTTT-TCT
*
304079 AAAATTACATTTTAACCCTAAACTTTTCC
1 AAAATTACATTTTAACCCTAAACTTTTCT
* * * * *
304108 AAAATTTCATTTTGACCTCGAATC-TTTCA
1 AAAATTACATTTTAACC-CTAAACTTTTCT
*
304137 AAAATTACATTTTGACCCCTAAACTTTTCT
1 AAAATTACATTTT-AACCCTAAACTTTTCT
*
304167 AAAATTATATTTTAACCCTAAA-TTTTCT
1 AAAATTACATTTTAACCCTAAACTTTTCT
*
304195 AAAATTATATTTTAA
1 AAAATTACATTTTAA
304210 ACTTCCTTTG
Statistics
Matches: 156, Mismatches: 22, Indels: 22
0.78 0.11 0.11
Matches are distributed among these distances:
26 5 0.03
27 10 0.06
28 24 0.15
29 61 0.39
30 51 0.33
31 5 0.03
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTAAACTTTTCT
Found at i:304140 original size:58 final size:58
Alignment explanation
Indices: 303992--304209 Score: 196
Period size: 59 Copynumber: 3.8 Consensus size: 58
303982 AAATTTCTCA
* * * * * *
303992 AAAATTACATTTTTACCCTCGAACCTCTCTAAAATTACATTTT-TCCCCAAAC--TTCC
1 AAAATTACA-TTTTAACCTCGAATCTTTCAAAAATTACATTTTAACCCTAAACTTTTCC
* *
304048 AAACATTACATTTTAACCCCTAAAT-TTCTCAAAAATTACATTTTAACCCTAAACTTTTCC
1 AAA-ATTACATTTTAACCTC-GAATCTT-TCAAAAATTACATTTTAACCCTAAACTTTTCC
* * * *
304108 AAAATTTCATTTTGACCTCGAATCTTTCAAAAATTACATTTTGACCCCTAAACTTTTCT
1 AAAATTACATTTTAACCTCGAATCTTTCAAAAATTACATTTT-AACCCTAAACTTTTCC
* * * *
304167 AAAATTATATTTTAACC-CTAAAT-TTTCTAAAATTATATTTTAA
1 AAAATTACATTTTAACCTC-GAATCTTTCAAAAATTACATTTTAA
304210 ACTTCCTTTG
Statistics
Matches: 132, Mismatches: 21, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
56 12 0.09
57 24 0.18
58 43 0.33
59 46 0.35
60 7 0.05
ACGTcount: A:0.36, C:0.22, G:0.02, T:0.39
Consensus pattern (58 bp):
AAAATTACATTTTAACCTCGAATCTTTCAAAAATTACATTTTAACCCTAAACTTTTCC
Found at i:304665 original size:30 final size:30
Alignment explanation
Indices: 304631--304729 Score: 155
Period size: 30 Copynumber: 3.3 Consensus size: 30
304621 TCTTTTGGGG
304631 TTACATTTTAAACCTTGAACTTTTCCAAAA
1 TTACATTTTAAACCTTGAACTTTTCCAAAA
* *
304661 TTACATTTTAAA-CTCTAAAATTTTCCAAAA
1 TTACATTTTAAACCT-TGAACTTTTCCAAAA
*
304691 TTACATTTTAACCCTTGAACTTTTCCAAAA
1 TTACATTTTAAACCTTGAACTTTTCCAAAA
304721 TTACATTTT
1 TTACATTTT
304730 TACCCCAAAC
Statistics
Matches: 62, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
29 2 0.03
30 58 0.94
31 2 0.03
ACGTcount: A:0.36, C:0.19, G:0.02, T:0.42
Consensus pattern (30 bp):
TTACATTTTAAACCTTGAACTTTTCCAAAA
Found at i:304758 original size:29 final size:28
Alignment explanation
Indices: 304717--304819 Score: 118
Period size: 28 Copynumber: 3.6 Consensus size: 28
304707 GAACTTTTCC
*
304717 AAAATTACATTTTTACCC-CAAACTTCAA
1 AAAATCACATTTTTACCCTCAAACTTC-A
* *
304745 AAAAACACATTTTTACCCTCGAACTTCCA
1 AAAATCACATTTTTACCCTCAAACTT-CA
** *
304774 AAAATCACATTCATACCCTCAAACTTCT
1 AAAATCACATTTTTACCCTCAAACTTCA
*
304802 AAAATCACATTTTGACCC
1 AAAATCACATTTTTACCC
304820 CGAACTTTTC
Statistics
Matches: 62, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
28 32 0.52
29 29 0.47
30 1 0.02
ACGTcount: A:0.40, C:0.29, G:0.02, T:0.29
Consensus pattern (28 bp):
AAAATCACATTTTTACCCTCAAACTTCA
Found at i:304797 original size:58 final size:55
Alignment explanation
Indices: 304693--304826 Score: 144
Period size: 57 Copynumber: 2.4 Consensus size: 55
304683 TTCCAAAATT
* * **
304693 ACATTTTAACCCTTGAACTTTTCCAAAATTACATTTTTACCCCAAACTTCAAAAAAAC
1 ACATTTTAACCCTCGAAC--TTCCAAAATCACATTCATACCCCAAACTTC-AAAAAAC
* * *
304751 ACATTTTTACCCTCGAACTTCCAAAAATCACATTCATACCCTCAAACTTCTAAAATC
1 ACATTTTAACCCTCGAACTTCC-AAAATCACATTCATACCC-CAAACTTCAAAAAAC
*
304808 ACATTTTGACCC-CGAACTT
1 ACATTTTAACCCTCGAACTT
304827 TTCGAAACTT
Statistics
Matches: 66, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
56 11 0.17
57 31 0.47
58 24 0.36
ACGTcount: A:0.37, C:0.29, G:0.03, T:0.31
Consensus pattern (55 bp):
ACATTTTAACCCTCGAACTTCCAAAATCACATTCATACCCCAAACTTCAAAAAAC
Found at i:305459 original size:46 final size:46
Alignment explanation
Indices: 305392--305484 Score: 186
Period size: 46 Copynumber: 2.0 Consensus size: 46
305382 TTATGCATTT
305392 AAGGATCGTATTTTAGAACTTCACTCGAGTTTTCAAAATTTTACAA
1 AAGGATCGTATTTTAGAACTTCACTCGAGTTTTCAAAATTTTACAA
305438 AAGGATCGTATTTTAGAACTTCACTCGAGTTTTCAAAATTTTACAA
1 AAGGATCGTATTTTAGAACTTCACTCGAGTTTTCAAAATTTTACAA
305484 A
1 A
305485 CAAGACCATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 47 1.00
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (46 bp):
AAGGATCGTATTTTAGAACTTCACTCGAGTTTTCAAAATTTTACAA
Found at i:314477 original size:3 final size:3
Alignment explanation
Indices: 314469--314498 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
314459 TTATGATATT
314469 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
314499 AGGGATGGCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:316746 original size:39 final size:39
Alignment explanation
Indices: 316702--317103 Score: 299
Period size: 39 Copynumber: 10.3 Consensus size: 39
316692 GAAGATTTCG
*
316702 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGTCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* *
316741 ATCTCTTACCTCGAGCCTAGGGCAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * * * *
316780 ATCTCTTA-CTCGAGCTTAGGGCAGATTGCTGCCATCTG---
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-C-ACCATCAGCCA
*
316818 ATCTCTTACCCCTAGCCTGGGGCA-AGTCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGA-TCACCATCAGCCA
* * *
316857 ATCTCTTTCCCCGAGCTTGGGGCAGAATGCAGCCAT---CCG
1 ATCTCTTACCCCGAGCCTGGGGCAG-AT-CA-CCATCAGCCA
* * * *
316896 ATCTTTTACCCCAAGCCTGGGGCAGATAATCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * *
316935 ATCTTTTACCCCGAGCTTGAGGCAGATTGCAGCCAATC-G---
1 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CC-ATCAGCCA
* * *
316974 ATCTTTTACCTCGAGCCTGGGGTAGATCACCATCAGCCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
* * *** ** *
317013 ATCTTTTACCCCGAGCCTGGGACAGAT-TGTAGTCATTCG
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCA-TCAGCCA
* * * *
317052 ATCTTTTACCCCGAGCCTGAGGCAAATCACCATCAACCA
1 ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
317091 ATCTCTTACCCCG
1 ATCTCTTACCCCG
317104 CGACAAGGGC
Statistics
Matches: 287, Mismatches: 52, Indels: 48
0.74 0.13 0.12
Matches are distributed among these distances:
35 3 0.01
36 12 0.04
37 4 0.01
38 30 0.10
39 215 0.75
40 4 0.01
41 10 0.03
42 6 0.02
43 3 0.01
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (39 bp):
ATCTCTTACCCCGAGCCTGGGGCAGATCACCATCAGCCA
Found at i:316905 original size:78 final size:78
Alignment explanation
Indices: 316702--317103 Score: 424
Period size: 78 Copynumber: 5.2 Consensus size: 78
316692 GAAGATTTCG
* * * * * *
316702 ATCTCTTACCCCGAGCCTGGGGCAGA-T-CA-CCATCAGTCAATCTCTTACCTCGAGCCTAGGGC
1 ATCTCTTTCCCCGAGCTTGGGGCAGATTGCAGCCATC---CGATCTTTTACCCCGAGCCTGGGGC
316764 AGATCACCATCAGCCA
63 AGATCACCATCAGCCA
* * * * * * *
316780 ATCTC-TTACTCGAGCTTAGGGCAGATTGCTGCCATCTGATCTCTTACCCCTAGCCTGGGGCA-A
1 ATCTCTTTCCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
316843 GTCACCATCAGCCA
66 -TCACCATCAGCCA
* *
316857 ATCTCTTTCCCCGAGCTTGGGGCAGAATGCAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAGA
1 ATCTCTTTCCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* *
316922 TAATCATCAGCCA
66 TCACCATCAGCCA
* * *
316935 ATCT-TTTACCCCGAGCTTGAGGCAGATTGCAGCCAAT-CGATCTTTTACCTCGAGCCTGGGGTA
1 ATCTCTTT-CCCCGAGCTTGGGGCAGATTGCAGCC-ATCCGATCTTTTACCCCGAGCCTGGGGCA
316998 GATCACCATCAGCCA
64 GATCACCATCAGCCA
* * * * * * *
317013 ATCT-TTTACCCCGAGCCTGGGACAGATTGTAGTCATTCGATCTTTTACCCCGAGCCTGAGGCAA
1 ATCTCTTT-CCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAG
*
317077 ATCACCATCAACCA
65 ATCACCATCAGCCA
*
317091 ATCTCTTACCCCG
1 ATCTCTTTCCCCG
317104 CGACAAGGGC
Statistics
Matches: 275, Mismatches: 39, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
76 1 0.00
77 59 0.21
78 204 0.74
79 6 0.02
80 5 0.02
ACGTcount: A:0.23, C:0.33, G:0.20, T:0.24
Consensus pattern (78 bp):
ATCTCTTTCCCCGAGCTTGGGGCAGATTGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
TCACCATCAGCCA
Found at i:317025 original size:156 final size:156
Alignment explanation
Indices: 316702--317127 Score: 474
Period size: 156 Copynumber: 2.7 Consensus size: 156
316692 GAAGATTTCG
* * * * *
316702 ATCTCTTACCCCGAGCCTGGGGCAG-AT-CA-CCATCAGTCAATCTCTTACCTCGAGCCTAGGGC
1 ATCTTTTACCCCGAGCCTGGGGCAGAATGCAGCCATC---CGATCTTTTACCCCGAGCCTGGGGC
* *
316764 AGATCACCATCAGCCAATCTCTTA-CTCGAGCTTAGGGCAGATTGCTGCCATCTGATCTCTTACC
63 AGATCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCTGATCTCTTACC
*
316828 CCTAGCCTGGGGCAAGTCACCATCAGCCA
128 CCGAGCCTGGGGCAAGTCACCATCAGCCA
* *
316857 ATCTCTTT-CCCCGAGCTTGGGGCAGAATGCAGCCATCCGATCTTTTACCCCAAGCCTGGGGCAG
1 ATCT-TTTACCCCGAGCCTGGGGCAGAATGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAG
* * * *
316921 ATAATCATCAGCCAATCTTTTACCCCGAGCTT-GAGGCAGATTGCAGCCAATC-GATCTTTTACC
65 ATCACCATCAGCCAATCTCTTACCCCGAGCTTAG-GGCAGATTGCAGCC-ATCTGATCTCTTACC
* *
316984 TCGAGCCTGGGG-TAGATCACCATCAGCCA
128 CCGAGCCTGGGGCAAG-TCACCATCAGCCA
* * * * * * *
317013 ATCTTTTACCCCGAGCCTGGGACAGATTGTAGTCATTCGATCTTTTACCCCGAGCCTGAGGCAAA
1 ATCTTTTACCCCGAGCCTGGGGCAGAATGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
* * * *
317078 TCACCATCAACCAATCTCTTACCCCGCGAC-AAGGGCAGATTGCAACCATC
66 TCACCATCAGCCAATCTCTTACCCCGAG-CTTAGGGCAGATTGCAGCCATC
317128 CAATATCTTA
Statistics
Matches: 228, Mismatches: 32, Indels: 22
0.81 0.11 0.08
Matches are distributed among these distances:
155 70 0.31
156 146 0.64
157 7 0.03
158 5 0.02
ACGTcount: A:0.24, C:0.32, G:0.20, T:0.24
Consensus pattern (156 bp):
ATCTTTTACCCCGAGCCTGGGGCAGAATGCAGCCATCCGATCTTTTACCCCGAGCCTGGGGCAGA
TCACCATCAGCCAATCTCTTACCCCGAGCTTAGGGCAGATTGCAGCCATCTGATCTCTTACCCCG
AGCCTGGGGCAAGTCACCATCAGCCA
Found at i:317146 original size:3 final size:3
Alignment explanation
Indices: 317138--317241 Score: 118
Period size: 3 Copynumber: 34.7 Consensus size: 3
317128 CAATATCTTA
*
317138 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAN
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*** *** ***
317186 NNN NNN NNN AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
317234 AAT AAT AA
1 AAT AAT AA
317242 AATTCTTACC
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 95 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:318379 original size:4 final size:4
Alignment explanation
Indices: 318370--318410 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
318360 ATAACTACAT
*
318370 AATA AATA AATA TAAT- ATTA AATA AAT- AATA AATA AATA AA
1 AATA AATA AATA -AATA AATA AATA AATA AATA AATA AATA AA
318411 AAGGAAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 5 0.16
4 24 0.75
5 3 0.09
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AATA
Found at i:318393 original size:16 final size:15
Alignment explanation
Indices: 318370--318410 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
318360 ATAACTACAT
318370 AATAAATAAAT-ATA
1 AATAAATAAATAATA
318384 ATATTAAATAAATAATA
1 A-A-TAAATAAATAATA
318401 AATAAATAAA
1 AATAAATAAA
318411 AAGGAAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 10 0.42
17 4 0.17
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AATAAATAAATAATA
Found at i:318402 original size:11 final size:11
Alignment explanation
Indices: 318374--318409 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
318364 CTACATAATA
318374 AATAAATATAAT
1 AATAAATA-AAT
*
318386 ATTAAATAAAT
1 AATAAATAAAT
318397 AATAAATAAAT
1 AATAAATAAAT
318408 AA
1 AA
318410 AAAGGAAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 15 0.68
12 7 0.32
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AATAAATAAAT
Found at i:319436 original size:29 final size:29
Alignment explanation
Indices: 319376--319804 Score: 304
Period size: 30 Copynumber: 14.4 Consensus size: 29
319366 AAATTTCTCA
** *
319376 AAAATTACATTTTTGCCCTCGAA-TTTCTC
1 AAAATTACATTTTAACCCTCAAACTTTC-C
* *
319405 AAAAATTACATTTTTACCCTTAAAC-TTCC
1 -AAAATTACATTTTAACCCTCAAACTTTCC
* * *
319434 AAAAATCACATTTCAACCCTCGAA-TTTCTC
1 -AAAATTACATTTTAACCCTCAAACTTTC-C
*
319464 -AAATTACATTTTAACCC-CTAAACTTTTCT
1 AAAATTACATTTTAACCCTC-AAAC-TTTCC
** *
319493 AAAATTTTATTTTAA-CCTTAAATCTTTCC
1 AAAATTACATTTTAACCCTCAAA-CTTTCC
* * *
319522 AAAATTACGTTTTAACCCCCCCAAACTTTTCT
1 AAAATTACATTTTAA--CCCTCAAAC-TTTCC
*
319554 AAAATTACATTTTAAACCTCAAACTTTTCC
1 AAAATTACATTTTAACCCTCAAAC-TTTCC
* ** *
319584 AAAATTACATTTTAACCGTTGAACTTTTTC
1 AAAATTACATTTTAACCCTCAAAC-TTTCC
*
319614 AAAATTACATTTTGA-CCTCTAAACTTTTCC
1 AAAATTACATTTTAACCCTC-AAAC-TTTCC
*
319644 AAAATTACATTTTAAACCTCAAACTTTTCC
1 AAAATTACATTTTAACCCTCAAAC-TTTCC
319674 AAAATTACATTTTGAA-CCTCCAAACTTTTCC
1 AAAATTACATTTT-AACCCT-CAAAC-TTTCC
** *
319705 AAAATTACATTTTGGCCCCCAAAC-TTCC
1 AAAATTACATTTTAACCCTCAAACTTTCC
* * *
319733 AAAAATCACATTATT-ACCCTTAAACTTTCA
1 -AAAATTACATT-TTAACCCTCAAACTTTCC
* * * *
319763 AAAATAACATTTTAACCCCCGAACTTTTC
1 AAAATTACATTTTAACCCTCAAACTTTCC
319792 AAAACTT-CATTTT
1 AAAA-TTACATTTT
319805 TGACTCCGTT
Statistics
Matches: 324, Mismatches: 52, Indels: 47
0.77 0.12 0.11
Matches are distributed among these distances:
27 1 0.00
28 23 0.07
29 93 0.29
30 151 0.47
31 33 0.10
32 23 0.07
ACGTcount: A:0.36, C:0.24, G:0.03, T:0.37
Consensus pattern (29 bp):
AAAATTACATTTTAACCCTCAAACTTTCC
Found at i:319578 original size:91 final size:89
Alignment explanation
Indices: 319406--319779 Score: 352
Period size: 90 Copynumber: 4.2 Consensus size: 89
319396 GAATTTCTCA
* * * * * *
319406 AAAATTACATTTTTACCCTTAAAC--TTCCAAAAATCACATTTCAACCCTCGAA--TTTCTCAAA
1 AAAATTACA-TTTTAACCTTAAACTTTTCC-AAAATTACATTTTAACCCCCAAACTTTTCTAAAA
* *
319467 TTACATTTT-AACCCCTAAACTTTTCT
64 TTACATTTTAAACCTC-AAACTTTTCC
** *
319493 AAAATTTTATTTTAACCTTAAA-TCTTTCCAAAATTACGTTTTAACCCCCCCAAACTTTTCTAAA
1 AAAATTACATTTTAACCTTAAACT-TTTCCAAAATTACATTTTAA--CCCCCAAACTTTTCTAAA
319557 ATTACATTTTAAACCTCAAACTTTTCC
63 ATTACATTTTAAACCTCAAACTTTTCC
* * * * * *
319584 AAAATTACATTTTAACCGTTGAACTTTTTCAAAATTACATTTTGACCTCTAAACTTTTCCAAAAT
1 AAAATTACATTTTAACC-TTAAACTTTTCCAAAATTACATTTTAACCCCCAAACTTTTCTAAAAT
319649 TACATTTTAAACCTCAAACTTTTCC
65 TACATTTTAAACCTCAAACTTTTCC
* ** * *
319674 AAAATTACATTTTGAACCTCCAAACTTTTCCAAAATTACATTTTGGCCCCCAAAC-TTCCAAAAA
1 AAAATTACATTTT-AACCT-TAAACTTTTCCAAAATTACATTTTAACCCCCAAACTTTTCTAAAA
* * * *
319738 TCACATTATT-ACCCTTAAAC-TTTCA
64 TTACATT-TTAAACCTCAAACTTTTCC
*
319763 AAAATAACATTTTAACC
1 AAAATTACATTTTAACC
319780 CCCGAACTTT
Statistics
Matches: 241, Mismatches: 33, Indels: 25
0.81 0.11 0.08
Matches are distributed among these distances:
86 12 0.05
87 19 0.08
88 8 0.03
89 22 0.09
90 77 0.32
91 76 0.32
92 26 0.11
93 1 0.00
ACGTcount: A:0.37, C:0.24, G:0.02, T:0.37
Consensus pattern (89 bp):
AAAATTACATTTTAACCTTAAACTTTTCCAAAATTACATTTTAACCCCCAAACTTTTCTAAAATT
ACATTTTAAACCTCAAACTTTTCC
Found at i:319638 original size:60 final size:60
Alignment explanation
Indices: 319464--319804 Score: 349
Period size: 60 Copynumber: 5.7 Consensus size: 60
319454 CGAATTTCTC
* **
319464 AAATTACATTTTAACCCCTAAACTTTTCTAAAATTTTATTTTAACCT-TAAA-TCTTTCCA
1 AAATTACATTTTAACCCCCAAACTTTTCTAAAATTACATTTTAACCTCTAAACT-TTTCCA
*
319523 AAATTACGTTTTAACCCCCCCAAACTTTTCTAAAATTACATTTTAAACCTC-AAACTTTTCCA
1 AAATTACATTTTAA--CCCCCAAACTTTTCTAAAATTACATTTT-AACCTCTAAACTTTTCCA
**** *
319585 AAATTACATTTTAACCGTTGAACTTTT-TCAAAATTACATTTTGACCTCTAAACTTTTCCA
1 AAATTACATTTTAACCCCCAAACTTTTCT-AAAATTACATTTTAACCTCTAAACTTTTCCA
* * * *
319645 AAATTACATTTTAAACCTCAAACTTTTCCAAAATTACATTTTGAACCTCCAAACTTTTCCA
1 AAATTACATTTTAACCCCCAAACTTTTCTAAAATTACATTTT-AACCTCTAAACTTTTCCA
** * * * * *
319706 AAATTACATTTTGGCCCCCAAAC-TTCCAAAAATCACATTATTACCCT-TAAAC-TTTCAA
1 AAATTACATTTTAACCCCCAAACTTTTCTAAAATTACATT-TTAACCTCTAAACTTTTCCA
* *
319764 AAATAACATTTTAACCCCCGAACTTTTC-AAAACTT-CATTTT
1 AAATTACATTTTAACCCCCAAACTTTTCTAAAA-TTACATTTT
319805 TGACTCCGTT
Statistics
Matches: 237, Mismatches: 33, Indels: 26
0.80 0.11 0.09
Matches are distributed among these distances:
57 2 0.01
58 32 0.14
59 27 0.11
60 86 0.36
61 62 0.26
62 27 0.11
63 1 0.00
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (60 bp):
AAATTACATTTTAACCCCCAAACTTTTCTAAAATTACATTTTAACCTCTAAACTTTTCCA
Found at i:322418 original size:29 final size:31
Alignment explanation
Indices: 322365--322428 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
322355 AGCTTTGAAC
* *
322365 TTATTTATTTATATTTAGTTGGTTTTT-ATT
1 TTATTTATTTATATCTAATTGGTTTTTGATT
*
322395 TTATTTTTTTA-ATCTAATTGGTTTTTGATT
1 TTATTTATTTATATCTAATTGGTTTTTGATT
322425 TTAT
1 TTAT
322429 GTTCCATCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 13 0.43
30 17 0.57
ACGTcount: A:0.20, C:0.02, G:0.09, T:0.69
Consensus pattern (31 bp):
TTATTTATTTATATCTAATTGGTTTTTGATT
Found at i:322964 original size:25 final size:25
Alignment explanation
Indices: 322935--322984 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
322925 TATTGGGTTC
322935 TTTATTAATGATATTTAAAAACTAA
1 TTTATTAATGATATTTAAAAACTAA
322960 TTTATTAATGATATTTAAAAACTAA
1 TTTATTAATGATATTTAAAAACTAA
322985 CTTTTATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.48, C:0.04, G:0.04, T:0.44
Consensus pattern (25 bp):
TTTATTAATGATATTTAAAAACTAA
Found at i:325357 original size:24 final size:22
Alignment explanation
Indices: 325329--325394 Score: 71
Period size: 24 Copynumber: 2.9 Consensus size: 22
325319 CCAACGAAAT
325329 TAAATTATAATTTTTATAATAGA
1 TAAATTATAATTTTTATAATA-A
* **
325352 TAAAATATAATTTTATTATTTTAA
1 TAAATTATAA-TTT-TTATAATAA
325376 TAAATTAT-ATTTTTATAAT
1 TAAATTATAATTTTTATAAT
325395 TTTTGAAAGA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 5 0.14
22 3 0.09
23 10 0.29
24 11 0.31
25 6 0.17
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (22 bp):
TAAATTATAATTTTTATAATAA
Found at i:325446 original size:30 final size:30
Alignment explanation
Indices: 325385--325457 Score: 76
Period size: 30 Copynumber: 2.3 Consensus size: 30
325375 ATAAATTATA
* *
325385 TTTTTATAATTTTTGAAAGAATAAATTAAATT
1 TTTTTAT-A-TTTAGAAAGAATAAATAAAATT
325417 TTTTTATATTTAGAAA-AATAAAATAAAATT
1 TTTTTATATTTAGAAAGAAT-AAATAAAATT
*
325447 TTATTTTTATT
1 TT-TTTATATT
325458 AATTTAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 3 0.08
30 18 0.50
31 8 0.22
32 7 0.19
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.52
Consensus pattern (30 bp):
TTTTTATATTTAGAAAGAATAAATAAAATT
Found at i:326859 original size:59 final size:57
Alignment explanation
Indices: 326790--327066 Score: 276
Period size: 59 Copynumber: 4.7 Consensus size: 57
326780 AAAAGGGTAA
* * *
326790 TTTTGAAAGTTTTGAGGTCGAAAATGGAGA-TTTTGGAAGTTTGAGGGCAAAAATGAAAT
1 TTTTGGAAGTTTCGAGGTC-AAAATGGA-ATTTTTGGAAGTTTG-GGGTAAAAATGAAAT
** * *
326849 TTTTGGAAGTTTCG-GGATCAAAAACGAGATTTTTGGAAGTTCGGGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCGAGG-TCAAAATGGA-ATTTTTGGAAGTT-TGGGGTAAAAATGAAAT
326908 TTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTTTGGGGTAAAAAT-AGAAT
1 TTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAG-TTTGGGGTAAAAATGA-AAT
* * * **
326966 TTTTGGAAG-TTCAGGGGTCAAAAATGGAATTTTTGGATGTTTCGGGGTTAAAAGTGGGAT
1 TTTTGGAAGTTTC-GAGGTC-AAAATGGAATTTTTGGAAGTTT-GGGG-TAAAAATGAAAT
* *
327026 TTTTGGAAG-TTCGAGGGTAAAAATGAAATTTTTGGAAGTTT
1 TTTTGGAAGTTTCGA-GGTCAAAATGGAATTTTTGGAAGTTT
327067 AGGGACCTTC
Statistics
Matches: 186, Mismatches: 20, Indels: 24
0.81 0.09 0.10
Matches are distributed among these distances:
57 3 0.02
58 52 0.28
59 105 0.56
60 26 0.14
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (57 bp):
TTTTGGAAGTTTCGAGGTCAAAATGGAATTTTTGGAAGTTTGGGGTAAAAATGAAAT
Found at i:326902 original size:88 final size:88
Alignment explanation
Indices: 326805--327070 Score: 310
Period size: 88 Copynumber: 3.0 Consensus size: 88
326795 AAAGTTTTGA
* * *
326805 GGTCGAAAATGGAGA-TTTTGGAAGTTT-GAGGGCAAAAATGAAATTTTTGGAAGTTTCGGGATC
1 GGTCAAAAATGGA-ATTTTTGGAAGTTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTCGGGGT-
*
326868 AAAAACGAGATTTTTGGAAGTTCGGG
64 AAAAA-GAGATTTTTGGAAGTTCAGG
* *
326894 GGT-AAAAATGGAATTTTTGGAAGTTTCGAGGTC-AAAATGGAATTTTTGGAAGTTTTGGGGTAA
1 GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
*
326957 AAATAGAATTTTTGGAAGTTCAGG
66 AAAGAG-ATTTTTGGAAGTTCAGG
* * * *
326981 GGTCAAAAATGGAATTTTTGGATGTTTCG-GGGTTAAAAGTGGGATTTTTGGAAG-TTCGAGGGT
1 GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGG-CAAAAATGGAATTTTTGGAAGTTTCG-GGGT
* *
327044 AAAAATGAAATTTTTGGAAGTTTAGG
64 AAAAA-GAGATTTTTGGAAGTTCAGG
327070 G
1 G
327071 ACCTTCAGGG
Statistics
Matches: 153, Mismatches: 16, Indels: 16
0.83 0.09 0.09
Matches are distributed among these distances:
86 2 0.01
87 27 0.18
88 72 0.47
89 51 0.33
90 1 0.01
ACGTcount: A:0.32, C:0.05, G:0.31, T:0.33
Consensus pattern (88 bp):
GGTCAAAAATGGAATTTTTGGAAGTTTCGAGGGCAAAAATGGAATTTTTGGAAGTTTCGGGGTAA
AAAGAGATTTTTGGAAGTTCAGG
Found at i:327013 original size:30 final size:30
Alignment explanation
Indices: 326790--327066 Score: 288
Period size: 29 Copynumber: 9.4 Consensus size: 30
326780 AAAAGGGTAA
* * * *
326790 TTTTGAAAGTTTTGAGGTCGAAAATGGAGA-
1 TTTTGGAAGTTTCGGGGTCAAAAATGGA-AT
*
326820 TTTTGGAAGTTT-GAGGG-CAAAAATGAAAT
1 TTTTGGAAGTTTCG-GGGTCAAAAATGGAAT
* *
326849 TTTTGGAAGTTTCGGGATCAAAAA-CGAGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGA-AT
326879 TTTTGGAAG-TTCGGGGGT-AAAAATGGAAT
1 TTTTGGAAGTTTC-GGGGTCAAAAATGGAAT
*
326908 TTTTGGAAGTTTCGAGGTC-AAAATGGAAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
* *
326937 TTTTGGAAGTTTTGGGGT-AAAAATAGAAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
326966 TTTTGGAAG-TTCAGGGGTCAAAAATGGAAT
1 TTTTGGAAGTTTC-GGGGTCAAAAATGGAAT
* * * *
326996 TTTTGGATGTTTCGGGGTTAAAAGTGGGAT
1 TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
*
327026 TTTTGGAAG-TTCGAGGGT-AAAAATGAAAT
1 TTTTGGAAGTTTCG-GGGTCAAAAATGGAAT
327055 TTTTGGAAGTTT
1 TTTTGGAAGTTT
327067 AGGGACCTTC
Statistics
Matches: 209, Mismatches: 23, Indels: 30
0.80 0.09 0.11
Matches are distributed among these distances:
28 3 0.01
29 117 0.56
30 86 0.41
31 3 0.01
ACGTcount: A:0.32, C:0.04, G:0.30, T:0.34
Consensus pattern (30 bp):
TTTTGGAAGTTTCGGGGTCAAAAATGGAAT
Found at i:328220 original size:15 final size:15
Alignment explanation
Indices: 328200--328229 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
328190 TTTTATTAAT
328200 TAATATTAATAATAA
1 TAATATTAATAATAA
*
328215 TAATATTATTAATAA
1 TAATATTAATAATAA
328230 AACATTTACT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
TAATATTAATAATAA
Found at i:328330 original size:21 final size:21
Alignment explanation
Indices: 328292--328331 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
328282 GGTCATTAAT
* *
328292 ATTATTATTATTACTAAAACA
1 ATTATTAATACTACTAAAACA
*
328313 ATTATTAATACTATTAAAA
1 ATTATTAATACTACTAAAA
328332 GTTATTGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (21 bp):
ATTATTAATACTACTAAAACA
Found at i:328999 original size:18 final size:18
Alignment explanation
Indices: 328976--329029 Score: 69
Period size: 17 Copynumber: 3.1 Consensus size: 18
328966 CATTTTAAAT
328976 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
328994 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
329011 ATTTAAA-TTTAAACTTA
1 AATTAAATTTTAAACTTA
329028 AA
1 AA
329030 AGAAAAGTCT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
17 24 0.75
18 8 0.25
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:329016 original size:17 final size:16
Alignment explanation
Indices: 328967--329028 Score: 63
Period size: 17 Copynumber: 3.8 Consensus size: 16
328957 TTTGAACTTC
*
328967 ATTTTAAA-TAATTAA
1 ATTTTAAATTAATTTA
*
328982 ATTTTAAATTCAAATTA
1 ATTTTAAATT-AATTTA
328999 ATTTTAAACTTAATTTA
1 ATTTTAAA-TTAATTTA
*
329016 AATTTAAACTTAA
1 ATTTTAAA-TTAA
329029 AAGAAAAGTC
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
15 8 0.20
16 1 0.03
17 29 0.73
18 2 0.05
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.47
Consensus pattern (16 bp):
ATTTTAAATTAATTTA
Found at i:329534 original size:37 final size:37
Alignment explanation
Indices: 329467--329621 Score: 103
Period size: 37 Copynumber: 3.9 Consensus size: 37
329457 TATCACTTGT
* * * * *
329467 TTTGTTCCACTTCTCTGTGTTTCATTAGGAAGATGAA
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGAA
*
329504 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGACCGCGTCG
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGA-------A
* * * *
329548 TTTGTTTCAATCCGCTTCTCTGTATCTCATCAGGAAGACGAA
1 TTTG-----GTCCACTTCTCAGTATCTCATCAGGAAGATGAA
*
329590 TTTGGTCCACTTCTCAATATCTCATCAGGAAG
1 TTTGGTCCACTTCTCAGTATCTCATCAGGAAG
329622 TTAACCATTT
Statistics
Matches: 91, Mismatches: 15, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
37 55 0.60
42 4 0.04
44 4 0.04
49 28 0.31
ACGTcount: A:0.23, C:0.23, G:0.19, T:0.35
Consensus pattern (37 bp):
TTTGGTCCACTTCTCAGTATCTCATCAGGAAGATGAA
Found at i:341404 original size:29 final size:29
Alignment explanation
Indices: 341372--341465 Score: 77
Period size: 29 Copynumber: 3.2 Consensus size: 29
341362 TTTGAGGTCG
341372 AAAATGAAGATTTTGGAAGTTCGAGGGCAA
1 AAAATGAAGATTTTGGAAGTTCGAGGG-AA
* **
341402 AAACAT-AA-TTTTTGGAAGTTTCGAGATAA
1 AAA-ATGAAGATTTTGGAAG-TTCGAGGGAA
* * *
341431 AAAACG-GGATGTTTGGAAGTTCGAGGGTA
1 AAAATGAAGAT-TTTGGAAGTTCGAGGGAA
341460 AAAATG
1 AAAATG
341466 GAATTTTTAG
Statistics
Matches: 49, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
28 1 0.02
29 27 0.55
30 19 0.39
31 2 0.04
ACGTcount: A:0.39, C:0.06, G:0.28, T:0.27
Consensus pattern (29 bp):
AAAATGAAGATTTTGGAAGTTCGAGGGAA
Found at i:341478 original size:29 final size:30
Alignment explanation
Indices: 341382--341754 Score: 311
Period size: 30 Copynumber: 12.4 Consensus size: 30
341372 AAAATGAAGA
* ***
341382 TTTTGGAAG-TTCGAGGGCAAAAACATAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
* * *
341411 TTTTGGAAGTTTCGA-GATAAAAAACGGGAT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGAAT
*
341441 GTTTGGAAG-TTCGAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
* *
341470 TTTTAGAAGTTTTG-GGGTTAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGG-TAAAAATGGAAT
*
341500 TTTTGGAAGTTT-GGGGGT-AAAATGGAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
* *
341528 TTTTGGAAGTTTCGAAGTTAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
* * *
341558 TTTTAGAAGTTTC-TGGGTCAAAATGGAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
*
341587 TTTTGGAAGTTTTG-GGGTCAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGGT-AAAAATGGAAT
* *
341617 TTTTGAAAGTTTTG-GGGTAAAAATAGAATTTTTGGAAT
1 TTTTGGAAGTTTCGAGGGT---AA-A-AA----TGGAAT
*
341655 TTTTGGAAG-TTCAAGGGTAAAAATGGAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
* * *
341684 TTTTGGAAGTTTTG-GGGTTAAAATTGGGAT
1 TTTTGGAAGTTTCGAGGG-TAAAAATGGAAT
**
341714 TTTTGGAAG-TTCGAGGGTAAAAATAAAAT
1 TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
*
341743 TTTTGAAAGTTT
1 TTTTGGAAGTTT
341755 AGGAACCTCC
Statistics
Matches: 282, Mismatches: 39, Indels: 45
0.77 0.11 0.12
Matches are distributed among these distances:
28 22 0.08
29 103 0.37
30 127 0.45
32 2 0.01
33 3 0.01
34 3 0.01
35 2 0.01
37 2 0.01
38 18 0.06
ACGTcount: A:0.34, C:0.03, G:0.27, T:0.36
Consensus pattern (30 bp):
TTTTGGAAGTTTCGAGGGTAAAAATGGAAT
Found at i:341493 original size:59 final size:59
Alignment explanation
Indices: 341382--341660 Score: 294
Period size: 59 Copynumber: 4.7 Consensus size: 59
341372 AAAATGAAGA
* *** * * * * * *
341382 TTTTGGAAGTTCGAGGGCAAAAACATAATTTTTGGAAGTTTCGAGATAAAAAACGGGAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAT
* *
341441 GTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGAAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAT
* * * **
341500 TTTTGGAAGTTTGGGGGT-AAAATGGAATTTTTGGAAGTTTCGAAGTTAAAAATGGAAT
1 TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAT
* * * *
341558 TTTTAGAAGTTTC-TGGGTCAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAAT
1 TTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAT
* * * *
341617 TTTTGAAAGTTTTG-GGGTAAAAATAGAATTTTTGGAATTTTTGG
1 TTTTGGAAG-TTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGG
341661 AAGTTCAAGG
Statistics
Matches: 185, Mismatches: 32, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
58 48 0.26
59 137 0.74
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.36
Consensus pattern (59 bp):
TTTTGGAAGTTCGAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAAATGGAAT
Found at i:341502 original size:117 final size:115
Alignment explanation
Indices: 341334--341653 Score: 322
Period size: 117 Copynumber: 2.7 Consensus size: 115
341324 TTTTTAGACA
* * * * *
341334 TTCGGGGTAAAAGGGTAATTTTGAG-AGTTTTGAGGTCGAAAATGAAGATTTTGGAAGTTCGAGG
1 TTCGGGGTAAAATGG-AATTTTTAGAAGTTTTGGGGTCAAAAATGGA-ATTTTGGAAGTTCG-GG
* * *
341398 GCAAAAACATAATTTTTGGAAGTTTCG-AGATAAAAAACGGGATGTTTGGAAG-
63 GCAAAAACAGAATTTTTGGAAGTTTCGAAG-TAAAAAACGGAATGTTTAGAAGT
* *
341450 TTCGAGGGTAAAAATGGAATTTTTAGAAGTTTTGGGGTTAAAAATGGAATTTTTGGAAGTTTGGG
1 TTCG-GGGT-AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAA-TTTTGGAAGTTCGGG
** ** * * *
341515 GGTAAAATGGAATTTTTGGAAGTTTCGAAGTTAAAAATGGAATTTTTAGAAGT
63 GCAAAAACAGAATTTTTGGAAGTTTCGAAGTAAAAAACGGAATGTTTAGAAGT
* * * *
341568 TTCTGGGTCAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGAAAGTTTTGGG
1 TTCGGGGT-AAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAA-TTTTGGAAG-TTCGGG
* *
341633 GTAAAAATAGAATTTTTGGAA
63 GCAAAAACAGAATTTTTGGAA
341654 TTTTTGGAAG
Statistics
Matches: 172, Mismatches: 25, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
116 4 0.02
117 104 0.60
118 64 0.37
ACGTcount: A:0.34, C:0.04, G:0.28, T:0.34
Consensus pattern (115 bp):
TTCGGGGTAAAATGGAATTTTTAGAAGTTTTGGGGTCAAAAATGGAATTTTGGAAGTTCGGGGCA
AAAACAGAATTTTTGGAAGTTTCGAAGTAAAAAACGGAATGTTTAGAAGT
Found at i:341654 original size:38 final size:38
Alignment explanation
Indices: 341611--341697 Score: 120
Period size: 38 Copynumber: 2.3 Consensus size: 38
341601 GGGTCAAAAA
***
341611 TGGAATTTTTGAAAGTTTTGGGGTAAAAATAGAATTTT
1 TGGAATTTTTGAAAGTTCAAGGGTAAAAATAGAATTTT
* *
341649 TGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTT
1 TGGAATTTTTGAAAGTTCAAGGGTAAAAATAGAATTTT
*
341687 TGGAAGTTTTG
1 TGGAATTTTTG
341698 GGGTTAAAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.32, C:0.01, G:0.26, T:0.40
Consensus pattern (38 bp):
TGGAATTTTTGAAAGTTCAAGGGTAAAAATAGAATTTT
Found at i:341660 original size:68 final size:68
Alignment explanation
Indices: 341581--341721 Score: 203
Period size: 68 Copynumber: 2.1 Consensus size: 68
341571 TGGGTCAAAA
***
341581 TGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAATTTTTGAAAGTTTTGGGG-TAAAAATAGAA
1 TGGAATTTTTGGAAGTTCAAGGGT-AAAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATAGAA
341645 TTTT
65 TTTT
* * * *
341649 TGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATTGGGAT
1 TGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATAGAAT
341714 TTT
66 TTT
341717 TGGAA
1 TGGAA
341722 GTTCGAGGGT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
67 27 0.42
68 38 0.58
ACGTcount: A:0.31, C:0.01, G:0.28, T:0.39
Consensus pattern (68 bp):
TGGAATTTTTGGAAGTTCAAGGGTAAAAATGGAATTTTTGAAAGTTTTGGGGTTAAAAATAGAAT
TTT
Found at i:341678 original size:97 final size:97
Alignment explanation
Indices: 341552--341747 Score: 279
Period size: 97 Copynumber: 2.0 Consensus size: 97
341542 AAGTTAAAAA
* *
341552 TGGAATTTTTAGAAGTTTCTGGGTCAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAAT
1 TGGAATTTTTAGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAAT
* *
341617 TTTTGAAAGTTTTG-GGGTAAAAATAGAATTTT
66 TTTTGAAAG-TTCGAGGGTAAAAATAAAATTTT
* * * *
341649 TGGAATTTTTGGAAG-TTCAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTTAAAATTGGGA
1 TGGAATTTTTAGAAGTTTC-AGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAA
*
341713 TTTTTGGAAGTTCGAGGGTAAAAATAAAATTTT
65 TTTTTGAAAGTTCGAGGGTAAAAATAAAATTTT
341746 TG
1 TG
341748 AAAGTTTAGG
Statistics
Matches: 88, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
96 6 0.07
97 82 0.93
ACGTcount: A:0.32, C:0.03, G:0.27, T:0.38
Consensus pattern (97 bp):
TGGAATTTTTAGAAGTTTCAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGAAT
TTTTGAAAGTTCGAGGGTAAAAATAAAATTTT
Found at i:342928 original size:31 final size:31
Alignment explanation
Indices: 342892--342954 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 31
342882 TAATAATATT
*
342892 ATTATTAA-TAAAACATTTACTATTATTAATG
1 ATTATTAAGGAAAAC-TTTACTATTATTAATG
**
342923 ATTATTAAGGAAAACTTTTTTATTATTAATG
1 ATTATTAAGGAAAACTTTACTATTATTAATG
342954 A
1 A
342955 GGTCATTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 23 0.82
32 5 0.18
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (31 bp):
ATTATTAAGGAAAACTTTACTATTATTAATG
Found at i:343688 original size:17 final size:17
Alignment explanation
Indices: 343648--343701 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
343638 CATTTTAAAT
343648 AATTATATTTTAAA-TTCA
1 AATTA-ATTTTAAACTT-A
343666 AATTAATTTTAAACTTA
1 AATTAATTTTAAACTTA
* *
343683 ATTTAAATTTAAACTTA
1 AATTAATTTTAAACTTA
343700 AA
1 AA
343702 AGAAAAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
17 25 0.78
18 7 0.22
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTAATTTTAAACTTA
Found at i:349593 original size:27 final size:27
Alignment explanation
Indices: 349523--349594 Score: 69
Period size: 27 Copynumber: 2.7 Consensus size: 27
349513 TTTTATTTTT
*
349523 TTAT-TTTTTAAAAATTTTCAAAATAAC
1 TTATATTTTT-AACATTTTCAAAATAAC
* *
349550 TTATATTTTTAATATTTTCAAAATTA-
1 TTATATTTTTAACATTTTCAAAATAAC
349576 TTA-ATTGTTATAACATTTT
1 TTATATT-TT-TAACATTTT
349595 TTATATGATA
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
25 3 0.08
26 5 0.13
27 26 0.67
28 5 0.13
ACGTcount: A:0.39, C:0.06, G:0.01, T:0.54
Consensus pattern (27 bp):
TTATATTTTTAACATTTTCAAAATAAC
Found at i:350470 original size:24 final size:24
Alignment explanation
Indices: 350442--350492 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
350432 AGTTTGATTC
*
350442 AAACAAATAAACAGAATTTAATTG
1 AAACAAATAAACAGAATTTAACTG
* *
350466 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAATTTAACTG
350490 AAA
1 AAA
350493 GATTATTTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.57, C:0.10, G:0.10, T:0.24
Consensus pattern (24 bp):
AAACAAATAAACAGAATTTAACTG
Found at i:352447 original size:24 final size:24
Alignment explanation
Indices: 352416--352490 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 24
352406 AATAAGACTC
*
352416 AAACAAATAAATAGAGTTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* * *
352440 AAATAAATAAACAAAATTTAATTG
1 AAACAAATAAACAGAGTTTAATTG
* *
352464 AAACAATTAAACAGAGTTTAACTG
1 AAACAAATAAACAGAGTTTAATTG
352488 AAA
1 AAA
352491 GATTATTTCT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 42 1.00
ACGTcount: A:0.57, C:0.07, G:0.09, T:0.27
Consensus pattern (24 bp):
AAACAAATAAACAGAGTTTAATTG
Found at i:354269 original size:17 final size:19
Alignment explanation
Indices: 354233--354270 Score: 53
Period size: 17 Copynumber: 2.1 Consensus size: 19
354223 AACATCCTCT
354233 TTAATGACTATGAGTTTTA
1 TTAATGACTATGAGTTTTA
*
354252 TTAATG-CTTTGA-TTTTA
1 TTAATGACTATGAGTTTTA
354269 TT
1 TT
354271 TGCCAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 7 0.39
18 5 0.28
19 6 0.33
ACGTcount: A:0.26, C:0.05, G:0.13, T:0.55
Consensus pattern (19 bp):
TTAATGACTATGAGTTTTA
Found at i:357174 original size:13 final size:13
Alignment explanation
Indices: 357132--357174 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
357122 TGTAAGGTTG
*
357132 TTAAATGTTTTAT
1 TTAAATTTTTTAT
* * *
357145 TTGAATTTTATAA
1 TTAAATTTTTTAT
357158 TTAAATTTTTTAT
1 TTAAATTTTTTAT
357171 TTAA
1 TTAA
357175 TTTAATGTTA
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (13 bp):
TTAAATTTTTTAT
Found at i:362789 original size:20 final size:20
Alignment explanation
Indices: 362752--362790 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
362742 ACAAAAAACA
**
362752 AAAACAAAAATACTGAAAAT
1 AAAACAAAAATAAAGAAAAT
*
362772 AAAAGAAAAATAAAGAAAA
1 AAAACAAAAATAAAGAAAA
362791 ATGCAATAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.77, C:0.05, G:0.08, T:0.10
Consensus pattern (20 bp):
AAAACAAAAATAAAGAAAAT
Found at i:369383 original size:13 final size:13
Alignment explanation
Indices: 369365--369391 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
369355 ACATTTATTG
369365 TATAATATATATA
1 TATAATATATATA
369378 TATAATATATATA
1 TATAATATATATA
369391 T
1 T
369392 TCTTTCTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TATAATATATATA
Found at i:369406 original size:10 final size:10
Alignment explanation
Indices: 369391--369451 Score: 63
Period size: 10 Copynumber: 6.0 Consensus size: 10
369381 AATATATATA
369391 TTCTTTCTTT
1 TTCTTTCTTT
369401 TTCTTTCTTT
1 TTCTTTCTTT
* *
369411 TTC-ATCAACTT
1 TTCTTTC--TTT
369422 TTCTTTCTTT
1 TTCTTTCTTT
369432 TTCTTT-TTT
1 TTCTTTCTTT
369441 TTCTTTTCTTT
1 TTC-TTTCTTT
369452 ATGCGACTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
9 8 0.19
10 24 0.57
11 8 0.19
12 2 0.05
ACGTcount: A:0.05, C:0.20, G:0.00, T:0.75
Consensus pattern (10 bp):
TTCTTTCTTT
Found at i:370539 original size:15 final size:15
Alignment explanation
Indices: 370519--370554 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
370509 TCTTCTTTCT
*
370519 CTTCATCTCTTGCTC
1 CTTCATCTCGTGCTC
*
370534 CTTCATCTCGTGCTT
1 CTTCATCTCGTGCTC
370549 CTTCAT
1 CTTCAT
370555 TGGCTCCAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.08, C:0.36, G:0.08, T:0.47
Consensus pattern (15 bp):
CTTCATCTCGTGCTC
Found at i:396838 original size:28 final size:28
Alignment explanation
Indices: 396792--396924 Score: 162
Period size: 28 Copynumber: 4.8 Consensus size: 28
396782 ATAACACACA
*
396792 TTTCGAGCCAGAA-CAGAATATCGCTC-
1 TTTCGAGCTAGAATCAGAATATCGCTCT
* **
396818 TTTCTGAGCTAAAATCAGAATATCAATCT
1 TTTC-GAGCTAGAATCAGAATATCGCTCT
* *
396847 TTTCAAGCTAGTATCAGAATATCGCTCT
1 TTTCGAGCTAGAATCAGAATATCGCTCT
* *
396875 TTTCGATCTAGTATCAGAATATCGCTCT
1 TTTCGAGCTAGAATCAGAATATCGCTCT
*
396903 TTCCGAGCTAGAATCAGAATAT
1 TTTCGAGCTAGAATCAGAATAT
396925 TTATTAAGTC
Statistics
Matches: 90, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
26 4 0.04
27 7 0.08
28 75 0.83
29 4 0.04
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (28 bp):
TTTCGAGCTAGAATCAGAATATCGCTCT
Found at i:400022 original size:22 final size:21
Alignment explanation
Indices: 399996--400036 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
399986 TAATTTGTTG
* *
399996 TAATATATGTAAAATATAAATT
1 TAATAGATATAAAA-ATAAATT
400018 TAATAGATATAAAAATAAA
1 TAATAGATATAAAAATAAA
400037 CTCAATTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (21 bp):
TAATAGATATAAAAATAAATT
Found at i:400224 original size:13 final size:14
Alignment explanation
Indices: 400202--400235 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
400192 AGTAATTTAT
400202 TTTTCAGAAA-TCA
1 TTTTCAGAAAGTCA
*
400215 TTTTCCGAAAGTCA
1 TTTTCAGAAAGTCA
400229 TTTTCAG
1 TTTTCAG
400236 TCAAACAAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (14 bp):
TTTTCAGAAAGTCA
Found at i:400576 original size:12 final size:12
Alignment explanation
Indices: 400559--400584 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
400549 TGGTTAGACG
400559 AAATAAGTAGAA
1 AAATAAGTAGAA
400571 AAATAAGTAGAA
1 AAATAAGTAGAA
400583 AA
1 AA
400585 TGCTTTCCAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.15
Consensus pattern (12 bp):
AAATAAGTAGAA
Found at i:402061 original size:260 final size:260
Alignment explanation
Indices: 401588--402107 Score: 871
Period size: 260 Copynumber: 2.0 Consensus size: 260
401578 ATATTTTATT
*
401588 GCTTTTAAGGCCAAATGAGGCCTAAAGATTAGCTAACCTGCTTCGTGAGTGCACATGAGACTATT
1 GCTTTTAAGGCCAAATGAGGCCTAAAGATTAGATAACCTGCTTCGTGAGTGCACATGAGACTATT
*
401653 AGCAGCTGAGCAAAAGTGATACTGACCACTTCATCACGACATAAGAAGCTCTATGTCGCAACAAA
66 AGCAGCTGAGCAAAAGTGATACTGACCACTTCATCACGACATAAGAAGCTCTATATCGCAACAAA
401718 GGGGCCAGCAACGAAGAATAGAGAAATTGCTTACTTTGTTACGACACAAGACTTGGTGTGTCGCG
131 GGGGCCAGCAACGAAGAATAGAGAAATTGCTTACTTTGTTACGACACAAGACTTGGTGTGTCGCG
* **
401783 ACATCGACCCCAGACTGCAACTCTGCATCGAGTGACGGGCATTTTCGTCTTCTTAATGTGACTTA
196 ACATCGACCCAAGACTGCAACTCTGCATCGAGTGACGGGCATTTTCGTCTTCACAATGTGACTTA
**
401848 GCTTTTAAGGCCAAATGAGGCCTAAAGATTAGATAATTTGCTTCGTGAGTGCACATGAGACTATT
1 GCTTTTAAGGCCAAATGAGGCCTAAAGATTAGATAACCTGCTTCGTGAGTGCACATGAGACTATT
* * *
401913 AGCAGTTGAGCAAAAGTGATACTGACCACTTCGTCATGACATAAGAAGCTCTATATCGCAACAAA
66 AGCAGCTGAGCAAAAGTGATACTGACCACTTCATCACGACATAAGAAGCTCTATATCGCAACAAA
* * * * *
401978 GGGGCCAGCAGCGAAGCATAGAGAAATTGTTTGCTTTGTTGCGACACAAGACTTGGTGTGTCGCG
131 GGGGCCAGCAACGAAGAATAGAGAAATTGCTTACTTTGTTACGACACAAGACTTGGTGTGTCGCG
* *
402043 ACATTGA-CCAAGGACTGCAACTCTGCATCGAGTGAGGGGCATTTTCGTCTTCACAATGTGACTT
196 ACATCGACCCAA-GACTGCAACTCTGCATCGAGTGACGGGCATTTTCGTCTTCACAATGTGACTT
402107 A
260 A
402108 AGCACGAAGG
Statistics
Matches: 242, Mismatches: 17, Indels: 2
0.93 0.07 0.01
Matches are distributed among these distances:
259 3 0.01
260 239 0.99
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (260 bp):
GCTTTTAAGGCCAAATGAGGCCTAAAGATTAGATAACCTGCTTCGTGAGTGCACATGAGACTATT
AGCAGCTGAGCAAAAGTGATACTGACCACTTCATCACGACATAAGAAGCTCTATATCGCAACAAA
GGGGCCAGCAACGAAGAATAGAGAAATTGCTTACTTTGTTACGACACAAGACTTGGTGTGTCGCG
ACATCGACCCAAGACTGCAACTCTGCATCGAGTGACGGGCATTTTCGTCTTCACAATGTGACTTA
Found at i:404815 original size:12 final size:12
Alignment explanation
Indices: 404800--404837 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
404790 GAAGCGGAAG
404800 AAGAGGAATGAA
1 AAGAGGAATGAA
*
404812 AAGA-GAA-AAA
1 AAGAGGAATGAA
404822 AAGAGGAATGAA
1 AAGAGGAATGAA
404834 AAGA
1 AAGA
404838 AGTTGAAGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
10 6 0.27
11 6 0.27
12 10 0.45
ACGTcount: A:0.66, C:0.00, G:0.29, T:0.05
Consensus pattern (12 bp):
AAGAGGAATGAA
Found at i:405289 original size:17 final size:17
Alignment explanation
Indices: 405269--405316 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
405259 CAAATTCCCT
*
405269 TTGTCATTGCATTTTAA
1 TTGTCATTGCATTTGAA
* *
405286 TTGTCACTGCATTTGCA
1 TTGTCATTGCATTTGAA
*
405303 TTGTCATTACATTT
1 TTGTCATTGCATTT
405317 CCTTTTGTCA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.21, C:0.17, G:0.12, T:0.50
Consensus pattern (17 bp):
TTGTCATTGCATTTGAA
Found at i:411857 original size:27 final size:27
Alignment explanation
Indices: 411772--411865 Score: 100
Period size: 27 Copynumber: 3.5 Consensus size: 27
411762 TTTGCCATAC
* ** *
411772 ATATCGTTCCTTCAAAGTTCGTCATGA
1 ATATCATTCCTTCAGTGTTCATCATGA
*
411799 ATATCATTCCTTCAGTTTTCATCATGA
1 ATATCATTCCTTCAGTGTTCATCATGA
* * *
411826 ATATCATTCCTTTAGTGTTCGTC-TTA
1 ATATCATTCCTTCAGTGTTCATCATGA
411852 AGTATCATTCCTTC
1 A-TATCATTCCTTC
411866 TATGTTTGCC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 3 0.05
27 53 0.95
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (27 bp):
ATATCATTCCTTCAGTGTTCATCATGA
Found at i:421553 original size:245 final size:245
Alignment explanation
Indices: 421123--421610 Score: 922
Period size: 245 Copynumber: 2.0 Consensus size: 245
421113 GGATGCATTA
421123 GAATTAGTTGAGCTATTTGAACCAAACATCAGCTAATAAACACAATAATTGAAAAGTGCATGCTT
1 GAATTAGTTGAGCTATTTGAACCAAACATCAGCTAATAAACACAATAATTGAAAAGTGCATGCTT
*
421188 AATTTATATCCGACCCAAAATAAATTAATGGTTTGTAATAACTTGACCGAGATCTATTACCTTGC
66 AATTTATATCCGACCCAAAATAAATTAATGGTTCGTAATAACTTGACCGAGATCTATTACCTTGC
421253 ATGGCTTTTAGGTTCATATGATTAAATTGTTTTAAATCGACCTAGTCCCTATTACTTCACATGAA
131 ATGGCTTTTAGGTTCATATGATTAAATTGTTTTAAATCGACCTAGTCCCTATTACTTCACATGAA
* *
421318 TACGAAGAAATCCTTAGTTTAATATGATCAGTAAAATGCACGTTTCACAT
196 TACGAAGAAATCATTAGTTTAATATGATCAGTAAAATGCACATTTCACAT
421368 GAATTAGTTGAGCTATTTGAACCAAACATCAGCTAATAAACACAATAATTGAAAAGTGCATGCTT
1 GAATTAGTTGAGCTATTTGAACCAAACATCAGCTAATAAACACAATAATTGAAAAGTGCATGCTT
*
421433 AATTTATATCCGACCCAAAATAAATTAATGGTTCGTAATAACTTGACCGAGCTCTATTACCTTGC
66 AATTTATATCCGACCCAAAATAAATTAATGGTTCGTAATAACTTGACCGAGATCTATTACCTTGC
*
421498 ATGGCTTTTAGGTTCATGTGATTAAATTGTTTTAAATCGACCTAGTCCCTATTACTTCACATGAA
131 ATGGCTTTTAGGTTCATATGATTAAATTGTTTTAAATCGACCTAGTCCCTATTACTTCACATGAA
*
421563 TACTAAGAAATCATTAGTTTAATATGATCAGTAAAATGCACATTTCAC
196 TACGAAGAAATCATTAGTTTAATATGATCAGTAAAATGCACATTTCAC
421611 TAAGTAAAAG
Statistics
Matches: 237, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
245 237 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (245 bp):
GAATTAGTTGAGCTATTTGAACCAAACATCAGCTAATAAACACAATAATTGAAAAGTGCATGCTT
AATTTATATCCGACCCAAAATAAATTAATGGTTCGTAATAACTTGACCGAGATCTATTACCTTGC
ATGGCTTTTAGGTTCATATGATTAAATTGTTTTAAATCGACCTAGTCCCTATTACTTCACATGAA
TACGAAGAAATCATTAGTTTAATATGATCAGTAAAATGCACATTTCACAT
Found at i:423227 original size:10 final size:10
Alignment explanation
Indices: 423195--423227 Score: 50
Period size: 10 Copynumber: 3.4 Consensus size: 10
423185 TTTCTATTGA
423195 TTTTGTTAAT
1 TTTTGTTAAT
*
423205 GTTTGTTAAT
1 TTTTGTTAAT
423215 TTTTGTT-AT
1 TTTTGTTAAT
423224 TTTT
1 TTTT
423228 CTATTAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 6 0.29
10 15 0.71
ACGTcount: A:0.15, C:0.00, G:0.12, T:0.73
Consensus pattern (10 bp):
TTTTGTTAAT
Found at i:424328 original size:16 final size:16
Alignment explanation
Indices: 424309--424345 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
424299 TTATCCAAAC
424309 CCAAAATAATCTAAAT
1 CCAAAATAATCTAAAT
424325 CCAAAATAATCTAAAT
1 CCAAAATAATCTAAAT
424341 CCAAA
1 CCAAA
424346 GACAACTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (16 bp):
CCAAAATAATCTAAAT
Found at i:424447 original size:26 final size:26
Alignment explanation
Indices: 424411--424461 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
424401 AGTCGTAATG
424411 AAAAAAATATTCAAATAGTTCTTGTT
1 AAAAAAATATTCAAATAGTTCTTGTT
424437 AAAAAAATATTCAAATAGTTCTTGT
1 AAAAAAATATTCAAATAGTTCTTGT
424462 ACCATAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.47, C:0.08, G:0.08, T:0.37
Consensus pattern (26 bp):
AAAAAAATATTCAAATAGTTCTTGTT
Found at i:424959 original size:24 final size:25
Alignment explanation
Indices: 424908--424965 Score: 116
Period size: 25 Copynumber: 2.3 Consensus size: 25
424898 AAAAAATTAT
424908 AAAAAAATTCCTAAAATTCTGAGAA
1 AAAAAAATTCCTAAAATTCTGAGAA
424933 AAAAAAATTCCTAAAATTCTGAGAA
1 AAAAAAATTCCTAAAATTCTGAGAA
424958 AAAAAAAT
1 AAAAAAAT
424966 AGCTTTTTTC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 33 1.00
ACGTcount: A:0.60, C:0.10, G:0.07, T:0.22
Consensus pattern (25 bp):
AAAAAAATTCCTAAAATTCTGAGAA
Found at i:428163 original size:10 final size:9
Alignment explanation
Indices: 427972--428169 Score: 51
Period size: 9 Copynumber: 20.6 Consensus size: 9
427962 TCTTATCATA
427972 TATAAAAAT
1 TATAAAAAT
*
427981 CATAGCAAAAT
1 TATA--AAAAT
*
427992 CATAAAAACT
1 TATAAAAA-T
*
428002 TATAAATAT
1 TATAAAAAT
428011 TATAATAAAT
1 TATAA-AAAT
* *
428021 TCTAAAAAA
1 TATAAAAAT
*
428030 AATAAAACA-
1 TATAAAA-AT
*
428039 TATTAAAAT
1 TATAAAAAT
* *
428048 AATTAAAACCT
1 TA-TAAAA-AT
* *
428059 TTTATAAATT
1 TATA-AAAAT
*
428069 TATACAAAT
1 TATAAAAAT
428078 TATAAAAAAATT
1 TAT--AAAAA-T
* *
428090 TCAAAAAAACA
1 T-ATAAAAA-T
*
428101 TATAAATAT
1 TATAAAAAT
*
428110 TATAAAAAC
1 TATAAAAAT
428119 TA-ATAAAAT
1 TATA-AAAAT
*
428128 TCTAATAAAT
1 TATAA-AAAT
* *
428138 TATCAATAT
1 TATAAAAAT
428147 T-TAAAAACT
1 TATAAAAA-T
428156 TATAAAAAT
1 TATAAAAAT
*
428165 CATAA
1 TATAA
428170 TAAGTTCTAA
Statistics
Matches: 135, Mismatches: 36, Indels: 36
0.65 0.17 0.17
Matches are distributed among these distances:
8 6 0.04
9 59 0.44
10 44 0.33
11 23 0.17
12 2 0.01
13 1 0.01
ACGTcount: A:0.60, C:0.08, G:0.01, T:0.32
Consensus pattern (9 bp):
TATAAAAAT
Found at i:428197 original size:25 final size:25
Alignment explanation
Indices: 428161--428208 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
428151 AAACTTATAA
428161 AAATCATAATAAGTTCTAATAAATT
1 AAATCATAATAAGTTCTAATAAATT
* *
428186 AAAT-ATATATAATTTTTAATAAA
1 AAATCATA-ATAAGTTCTAATAAA
428209 ATTATAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 3 0.15
25 17 0.85
ACGTcount: A:0.54, C:0.04, G:0.02, T:0.40
Consensus pattern (25 bp):
AAATCATAATAAGTTCTAATAAATT
Found at i:429302 original size:10 final size:10
Alignment explanation
Indices: 429287--429355 Score: 97
Period size: 10 Copynumber: 7.0 Consensus size: 10
429277 TAATCTCTAT
429287 TTTTTTATAA
1 TTTTTTATAA
429297 TTTTTTATAA
1 TTTTTTATAA
429307 TTTTTTAT-A
1 TTTTTTATAA
*
429316 TTGTTTATAA
1 TTTTTTATAA
*
429326 GTTTTTATGAA
1 TTTTTTAT-AA
429337 TTTTTTATAA
1 TTTTTTATAA
429347 -TTTTTATAA
1 TTTTTTATAA
429356 GTATATATCA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
9 17 0.32
10 27 0.51
11 9 0.17
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:429310 original size:9 final size:9
Alignment explanation
Indices: 429288--429388 Score: 80
Period size: 10 Copynumber: 10.4 Consensus size: 9
429278 AATCTCTATT
429288 TTTTTATAA
1 TTTTTATAA
429297 TTTTTTATAA
1 -TTTTTATAA
429307 TTTTT-TATA
1 TTTTTATA-A
429316 TTGTTTATAA
1 TT-TTTATAA
429326 GTTTTTATGAA
1 -TTTTTAT-AA
429337 TTTTTTATAA
1 -TTTTTATAA
429347 TTTTTATAA
1 TTTTTATAA
* *
429356 GTATATATCAA
1 -TTTTTAT-AA
*
429367 TTTTAAT-A
1 TTTTTATAA
429375 TTTTTAATAA
1 TTTTT-ATAA
429385 TTTT
1 TTTT
429389 ATGATGTTAA
Statistics
Matches: 75, Mismatches: 7, Indels: 18
0.75 0.07 0.18
Matches are distributed among these distances:
8 7 0.09
9 19 0.25
10 34 0.45
11 15 0.20
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:429379 original size:28 final size:29
Alignment explanation
Indices: 429288--429380 Score: 91
Period size: 30 Copynumber: 3.2 Consensus size: 29
429278 AATCTCTATT
* * *
429288 TTTTTATAATTTTTTAT-AATTTTTTATA
1 TTTTTATAAGTATATATCAATTTTTTATA
* * *
429316 TTGTTTATAAGTTTTTATGAATTTTTTATAA
1 TT-TTTATAAGTATATATCAATTTTTTAT-A
*
429347 TTTTTATAAGTATATATCAA-TTTTAATA
1 TTTTTATAAGTATATATCAATTTTTTATA
429375 TTTTTA
1 TTTTTA
429381 ATAATTTTAT
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
28 9 0.16
29 20 0.35
30 25 0.44
31 3 0.05
ACGTcount: A:0.31, C:0.01, G:0.04, T:0.63
Consensus pattern (29 bp):
TTTTTATAAGTATATATCAATTTTTTATA
Found at i:433847 original size:15 final size:15
Alignment explanation
Indices: 433829--433881 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
433819 TGTTTTGCTC
433829 TATTTTGTTATGTTT
1 TATTTTGTTATGTTT
433844 TATTTTGGTT-TGTTT
1 TATTTT-GTTATGTTT
* * *
433859 TGTTATGTTAGGTTT
1 TATTTTGTTATGTTT
*
433874 TGTTTTGT
1 TATTTTGT
433882 CTAGTTTTGG
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
14 3 0.09
15 26 0.81
16 3 0.09
ACGTcount: A:0.09, C:0.00, G:0.21, T:0.70
Consensus pattern (15 bp):
TATTTTGTTATGTTT
Found at i:433868 original size:30 final size:30
Alignment explanation
Indices: 433834--433897 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
433824 TGCTCTATTT
* * *
433834 TGTTATGTTTTATTTTGGT-TTGTTTTGTTA
1 TGTTAGGTTTTATTTT-GTCTAGTTTTGGTA
*
433864 TGTTAGGTTTTGTTTTGTCTAGTTTTGGTA
1 TGTTAGGTTTTATTTTGTCTAGTTTTGGTA
433894 TGTT
1 TGTT
433898 GTACTTCCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 2 0.07
30 27 0.93
ACGTcount: A:0.09, C:0.02, G:0.23, T:0.66
Consensus pattern (30 bp):
TGTTAGGTTTTATTTTGTCTAGTTTTGGTA
Found at i:433874 original size:25 final size:25
Alignment explanation
Indices: 433831--433881 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
433821 TTTTGCTCTA
**
433831 TTTTGTTATGTTTTATTTTGGTTTG
1 TTTTGTTATGTTAGATTTTGGTTTG
* *
433856 TTTTGTTATGTTAGGTTTTGTTTTG
1 TTTTGTTATGTTAGATTTTGGTTTG
433881 T
1 T
433882 CTAGTTTTGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.08, C:0.00, G:0.22, T:0.71
Consensus pattern (25 bp):
TTTTGTTATGTTAGATTTTGGTTTG
Found at i:433888 original size:15 final size:15
Alignment explanation
Indices: 433855--433897 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
433845 ATTTTGGTTT
433855 GTTTTGTTATGTTAG
1 GTTTTGTTATGTTAG
*
433870 GTTTTGTTTTGTCTA-
1 GTTTTGTTATGT-TAG
*
433885 GTTTTGGTATGTT
1 GTTTTGTTATGTT
433898 GTACTTCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
14 1 0.04
15 21 0.88
16 2 0.08
ACGTcount: A:0.09, C:0.02, G:0.26, T:0.63
Consensus pattern (15 bp):
GTTTTGTTATGTTAG
Found at i:438412 original size:15 final size:16
Alignment explanation
Indices: 438385--438414 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
438375 GTTTTATTTT
438385 AATAATAAATTTTAAC
1 AATAATAAATTTTAAC
438401 AATAAT-AATTTTAA
1 AATAATAAATTTTAA
438415 ATTTTAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (16 bp):
AATAATAAATTTTAAC
Found at i:438479 original size:27 final size:28
Alignment explanation
Indices: 438448--438521 Score: 71
Period size: 30 Copynumber: 2.5 Consensus size: 28
438438 ATTATTGAAG
438448 AATATTTATAT-TAA-TATTGTAATAATA
1 AATATTTATATATAAGTATT-TAATAATA
* *
438475 AATATTACAATTTATAAGTATTTAATAATA
1 AATATT--TATATATAAGTATTTAATAATA
438505 AATATTTTATAGTATAA
1 AATA-TTTATA-TATAA
438522 AATATGAATA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
27 6 0.16
29 5 0.14
30 20 0.54
31 6 0.16
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (28 bp):
AATATTTATATATAAGTATTTAATAATA
Found at i:438480 original size:15 final size:14
Alignment explanation
Indices: 438448--438511 Score: 51
Period size: 14 Copynumber: 4.5 Consensus size: 14
438438 ATTATTGAAG
*
438448 AATATTT-AT-ATT
1 AATATTTAATAATA
438460 AATATTGTAATAATA
1 AATATT-TAATAATA
* *
438475 AATATTACAATTTATA
1 AATATT-TAA-TAATA
*
438491 AGTATTTAATAATA
1 AATATTTAATAATA
438505 AATATTT
1 AATATTT
438512 TATAGTATAA
Statistics
Matches: 40, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
12 6 0.15
13 1 0.03
14 12 0.30
15 12 0.30
16 9 0.22
ACGTcount: A:0.48, C:0.02, G:0.03, T:0.47
Consensus pattern (14 bp):
AATATTTAATAATA
Done.