Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001978.1 Hibiscus syriacus cultivar Beakdansim tig00004013_pilon, 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: 2594977
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 10
Found at i:620542 original size:40 final size:40
Alignment explanation
Indices: 620498--620873 Score: 179
Period size: 40 Copynumber: 9.1 Consensus size: 40
620488 ATAACACTGC
* * *
620498 TCCTTCGTATTTAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
* * * * * *
620538 TCCTTCGTTTTAAGGA-AGTCTGGTTGTCTGAGGATGACACTGC
1 TCCTTCGTGTTGAGGAGA-TCT-G--GTCGGTGGATGACATTGT
* * * *
620581 ACCTTTGCGTTGAGGAGATCTGGTTGGTGGATGACATTGT
1 TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
* * * * * ** **
620621 TCCTTTGCGTGGAGGA-AGTCTGGTTGTCTGAGGATGACGCTAC
1 TCCTTCGTGTTGAGGAGA-TCT-G--GTCGGTGGATGACATTGT
* * *
620664 TCCTACGCGTTGAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
* * * * * * *
620704 TCCTTCCTGCTT-AGGAAGTATGGTTGTCTGAGGATGACACTGC
1 TCCTTCGTG-TTGAGG-AG-AT-CTGGTCGGTGGATGACATTGT
*
620747 TCCTTCGCGTT-ATGGAGATCTGGTCGGTGGATGACATTGT
1 TCCTTCGTGTTGA-GGAGATCTGGTCGGTGGATGACATTGT
** * * *
620787 TCCTTCGTGTTGAGGA-AGTCTGGTTATATGAGGACGACATTGC
1 TCCTTCGTGTTGAGGAGA-TCTGG---TCGGTGGATGACATTGT
* * *
620830 TCGTACGCT-TTGAGGAGATCTGGTCGGTGGACGACATTGT
1 TCCTTCG-TGTTGAGGAGATCTGGTCGGTGGATGACATTGT
620870 TCCT
1 TCCT
620874 ACATGATGAA
Statistics
Matches: 247, Mismatches: 67, Indels: 44
0.69 0.19 0.12
Matches are distributed among these distances:
39 3 0.01
40 116 0.47
41 9 0.04
42 9 0.04
43 106 0.43
44 4 0.02
ACGTcount: A:0.18, C:0.18, G:0.32, T:0.33
Consensus pattern (40 bp):
TCCTTCGTGTTGAGGAGATCTGGTCGGTGGATGACATTGT
Found at i:620572 original size:83 final size:83
Alignment explanation
Indices: 620463--620873 Score: 529
Period size: 83 Copynumber: 5.0 Consensus size: 83
620453 GTTCCTTTTC
* * * * ** *
620463 GTTGAAGAAGTCTGATTGTCTAAGGATAACACTGCTCCTTCGTATTTAGGAGATCTGGTCGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
620528 ACGACATTGTTCCTTCGT
66 ACGACATTGTTCCTTCGT
* * * * *
620546 TTTAAGGAAGTCTGGTTGTCTGAGGATGACACTGCACCTTTGCGTTGAGGAGATCTGGTTGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
* * *
620611 ATGACATTGTTCCTTTGC
66 ACGACATTGTTCCTTCGT
* * * *
620629 GTGGAGGAAGTCTGGTTGTCTGAGGATGACGCTACTCCTACGCGTTGAGGAGATCTGGTCGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
*
620694 ACGACATTGTTCCTTCCT
66 ACGACATTGTTCCTTCGT
*
620712 GCTT-AGGAAGTATGGTTGTCTGAGGATGACACTGCTCCTTCGCGTT-ATGGAGATCTGGTCGGT
1 G-TTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGA-GGAGATCTGGTCGGT
*
620775 GGATGACATTGTTCCTTCGT
64 GGACGACATTGTTCCTTCGT
* * * * * * *
620795 GTTGAGGAAGTCTGGTTATATGAGGACGACATTGCTCGTACGCTTTGAGGAGATCTGGTCGGTGG
1 GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
620860 ACGACATTGTTCCT
66 ACGACATTGTTCCT
620874 ACATGATGAA
Statistics
Matches: 280, Mismatches: 44, Indels: 8
0.84 0.13 0.02
Matches are distributed among these distances:
82 3 0.01
83 275 0.98
84 2 0.01
ACGTcount: A:0.19, C:0.18, G:0.31, T:0.32
Consensus pattern (83 bp):
GTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCGCGTTGAGGAGATCTGGTCGGTGG
ACGACATTGTTCCTTCGT
Found at i:620679 original size:43 final size:43
Alignment explanation
Indices: 620556--620853 Score: 167
Period size: 43 Copynumber: 7.1 Consensus size: 43
620546 TTTAAGGAAG
*
620556 TCTGGTTGTCTGAGGATGACACTGCACCTTTGCGTTGAGGAGA
1 TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * * *
620599 TCTGGTTG---GTGGATGACATTGTTCCTTTGCGTGGAGGA-A
1 TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * **
620638 GTCTGGTTGTCTGAGGATGACGCTACTCCTACGCGTTGAGGAGA
1 -TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * * * *
620682 TCT-G--GTCGGTGGACGACATTGTTCCTTCCTGC-TT-AGGA-A
1 TCTGGTTGTCTGAGGATGACACTGCTCCTT--TGCGTTGAGGAGA
* *
620721 GTATGGTTGTCTGAGGATGACACTGCTCCTTCGCGTT-ATGGAGA
1 -TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGA-GGAGA
* * * * * *
620765 TCT-G--GTCGGTGGATGACATTGTTCCTTCGTGTTGAGGA-A
1 TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
* * * * * ** *
620804 GTCTGGTTATATGAGGACGACATTGCTCGTACGCTTTGAGGAGA
1 -TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
620848 TCTGGT
1 TCTGGT
620854 CGGTGGACGA
Statistics
Matches: 190, Mismatches: 45, Indels: 40
0.69 0.16 0.15
Matches are distributed among these distances:
39 3 0.02
40 84 0.44
41 7 0.04
42 7 0.04
43 86 0.45
44 3 0.02
ACGTcount: A:0.17, C:0.18, G:0.33, T:0.32
Consensus pattern (43 bp):
TCTGGTTGTCTGAGGATGACACTGCTCCTTTGCGTTGAGGAGA
Found at i:621241 original size:139 final size:139
Alignment explanation
Indices: 620839--621264 Score: 579
Period size: 139 Copynumber: 3.1 Consensus size: 139
620829 CTCGTACGCT
* * *
620839 TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACATGATGAAGACGTATATCC-GTCTTTAG
1 TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAAGACTTCTA-CCAGTCTTTAG
* * * * * *
620903 GGATAATTTGGAGATAACATGGTTCCTACGTGATGAGGAAGCTTGATTGCCTAAGGATGATGTTG
65 GGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTTTGATTGCCTGAGGATGACGATG
*
620968 CTCTTACGTG
130 CTCCTACGTG
* * *
620978 TTAAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAGGA-TGCATATCCA-TCTTTA
1 TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAAGACTTC-TA-CCAGTCTTTA
*
621041 GGGATAATTTGGAGACAACACGGTTCCTAAGTGATGAGGAAGTTTGATTGCCTGAGGATGACGAT
64 GGGATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTTTGATTGCCTGAGGATGACGAT
*
621106 GCACCTACGTG
129 GCTCCTACGTG
** * * *
621117 TTGAGGAGATCTGGTTAGTGGACGATATTGTTCCTACGTGATGAACACTTCTAGCAGTCTTTAGG
1 TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAAGACTTCTACCAGTCTTTAGG
* * * *
621182 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTTTGATTGCATGAGAATGACGCTAC
66 GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTTTGATTGCCTGAGGATGACGATGC
*
621247 TCCTACGCG
131 TCCTACGTG
621256 TTGAGGAGA
1 TTGAGGAGA
621265 GCTAGTCATA
Statistics
Matches: 253, Mismatches: 30, Indels: 8
0.87 0.10 0.03
Matches are distributed among these distances:
138 2 0.01
139 249 0.98
140 2 0.01
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.30
Consensus pattern (139 bp):
TTGAGGAGATCTGGTCGGTGGACGACATTGTTCCTACGTGATGAAGACTTCTACCAGTCTTTAGG
GATAATTTGGAGACAACACGGTTCCTACGTGATGAGGAAGTTTGATTGCCTGAGGATGACGATGC
TCCTACGTG
Found at i:627805 original size:20 final size:21
Alignment explanation
Indices: 627779--627862 Score: 73
Period size: 20 Copynumber: 3.9 Consensus size: 21
627769 ACCAGTACCC
*
627779 CATGGGGGTATCGATTCCCCT
1 CATGGGGGAATCGATTCCCCT
*
627800 -ATGGGGGGCAATCGGTTCCCCTT
1 CAT-GGGGG-AATCGATTCCCC-T
* *
627823 CAAAGGGGGAATCGGTT-CCCT
1 C-ATGGGGGAATCGATTCCCCT
*
627844 CATGGGGGTATCGATTCCC
1 CATGGGGGAATCGATTCCC
627863 TCTGCACCAA
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
20 14 0.27
21 9 0.18
22 13 0.25
23 9 0.18
24 5 0.10
25 1 0.02
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.25
Consensus pattern (21 bp):
CATGGGGGAATCGATTCCCCT
Found at i:630026 original size:18 final size:19
Alignment explanation
Indices: 629998--630043 Score: 60
Period size: 19 Copynumber: 2.5 Consensus size: 19
629988 GGAAATATTT
*
629998 TTTTTACTTTA-TTCCTT-
1 TTTTTATTTTATTTCCTTA
630015 TATTTTATTTTATTTCCTTA
1 T-TTTTATTTTATTTCCTTA
630035 TTTTTATTT
1 TTTTTATTT
630044 CTATCTATCC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 1 0.04
18 9 0.36
19 14 0.56
20 1 0.04
ACGTcount: A:0.15, C:0.11, G:0.00, T:0.74
Consensus pattern (19 bp):
TTTTTATTTTATTTCCTTA
Found at i:637160 original size:162 final size:162
Alignment explanation
Indices: 636888--637194 Score: 479
Period size: 162 Copynumber: 1.9 Consensus size: 162
636878 GTTTGCAACC
* * ** * *
636888 CACGGAATTCATCATATGTTGATGAACGACCGTATAGGCACTAAGTGTGCAACCTACGGAATTCA
1 CACGAAATTCATCATATGTTGATGAACGACCATATAGGCACTAAGTGAACAACCCACGAAATTCA
* * * *
636953 TTATATGTTGATGAAAGACCGTATCAACACTAAGTGTGTAACCCACGGAATTCATCATAAGTTGA
66 TCATATGTTGATGAAAGACCGTATCAACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTGA
637018 TGAACGACCGTATCGGCATTAAGTCTGCAATG
131 TGAACGACCGTATCGGCATTAAGTCTGCAATG
637050 CACGAAATTCATCATATGTTGATGAACGACCATATAGGCACTAAGTGAACAACCCACGAAATTCA
1 CACGAAATTCATCATATGTTGATGAACGACCATATAGGCACTAAGTGAACAACCCACGAAATTCA
* * * *
637115 TCATATGTTGATGAACGACCGTATCGACACTAAGTGTGCAACCCACAGAATTCATAATATGTTTA
66 TCATATGTTGATGAAAGACCGTATCAACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTGA
*
637180 TGAACGACTGTATCG
131 TGAACGACCGTATCG
637195 ACACTGTGTG
Statistics
Matches: 130, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
162 130 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (162 bp):
CACGAAATTCATCATATGTTGATGAACGACCATATAGGCACTAAGTGAACAACCCACGAAATTCA
TCATATGTTGATGAAAGACCGTATCAACACTAAGTGTGCAACCCACAGAATTCATAATAAGTTGA
TGAACGACCGTATCGGCATTAAGTCTGCAATG
Found at i:637206 original size:54 final size:54
Alignment explanation
Indices: 636873--637199 Score: 429
Period size: 54 Copynumber: 6.1 Consensus size: 54
636863 TACTATAGGA
* * *
636873 ACTAAGTTTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATAGGC
1 ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * * *
636927 ACTAAGTGTGCAACCTACGGAATTCATTATATGTTGATGAAAGACCGTATCAAC
1 ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * *
636981 ACTAAGTGTGTAACCCACGGAATTCATCATAAGTTGATGAACGACCGTATCGGC
1 ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * ** * * * *
637035 ATTAAGTCTGCAATGCACGAAATTCATCATATGTTGATGAACGACCATATAGGC
1 ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
** *
637089 ACTAAGTGAACAACCCACGAAATTCATCATATGTTGATGAACGACCGTATCGAC
1 ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
* * * *
637143 ACTAAGTGTGCAACCCACAGAATTCATAATATGTTTATGAACGACTGTATCGAC
1 ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
637197 ACT
1 ACT
637200 GTGTGTGTGC
Statistics
Matches: 234, Mismatches: 39, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 234 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (54 bp):
ACTAAGTGTGCAACCCACGGAATTCATCATATGTTGATGAACGACCGTATCGAC
Found at i:642633 original size:54 final size:54
Alignment explanation
Indices: 642574--643062 Score: 586
Period size: 54 Copynumber: 9.1 Consensus size: 54
642564 CTATGTGTAC
* * **
642574 TATAGGCACTAAGTGTGCAAACCAC-AGAATTCATCATATGTTAATGAACGACTA
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * * * * *
642628 TATAGGCACTAAGTGTGAAACCCAAGTAACTCGTCATATGTTGATGAACGATCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * ***
642682 TATAGGCACTAAGTGTGCAACCCATGGAATTCATCATATGTTGATGAATGGTTG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
642736 TATCGGCACTATGTTTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * *
642790 TATAAGCACTAAGTGTGCAACCCACGTAATTCATCGTATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
*
642844 TATAGGCATTAAGTGTGCAACCCAC-AGAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGA-AATTCATCATATGTTGATGAACGACCG
* * * * * * *
642898 TATTGACATTAAGTGTGCAACCCTCGAAATTCTTCATTTGTTGATGAACGACCA
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * * * *
642952 TATCGACATTAAGTGTGCAACCCACGAAAATCATCATATGTTAATGAACAACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
* * * *
643006 TATCGGTATTAAGTGTGCAACCCATGAAATTCATCATATGTTGATGAACGACCG
1 TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
643060 TAT
1 TAT
643063 CGACATTAAG
Statistics
Matches: 375, Mismatches: 57, Indels: 6
0.86 0.13 0.01
Matches are distributed among these distances:
54 374 1.00
55 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.19, T:0.28
Consensus pattern (54 bp):
TATAGGCACTAAGTGTGCAACCCACGAAATTCATCATATGTTGATGAACGACCG
Found at i:644493 original size:55 final size:55
Alignment explanation
Indices: 644401--644529 Score: 138
Period size: 55 Copynumber: 2.3 Consensus size: 55
644391 TGTTGAGAGT
* * **
644401 GTATTGATACCCTTGAAAACATCGAGTGTCATATGTGTATCGGTACA-CTGAGGAGA
1 GTATCGATACCC-TCAAAACATCGAGTGTCATATGTGTATCAATACACCT-AGGAGA
* *
644457 GTATCGATACCCTCAAAACATCGAGTG-C-TACTTGTGTATCAATACACCTATGAGT
1 GTATCGATACCCTCAAAACATCGAGTGTCATA--TGTGTATCAATACACCTAGGAGA
*
644512 GTATCGATACCCTTAAAA
1 GTATCGATACCCTCAAAA
644530 TTTCGAATGC
Statistics
Matches: 63, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
53 2 0.03
54 1 0.02
55 47 0.75
56 13 0.21
ACGTcount: A:0.32, C:0.20, G:0.19, T:0.29
Consensus pattern (55 bp):
GTATCGATACCCTCAAAACATCGAGTGTCATATGTGTATCAATACACCTAGGAGA
Found at i:645335 original size:21 final size:21
Alignment explanation
Indices: 645305--645353 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
645295 TCGAGGGTCC
* *
645305 ATGTGATCCTTCGGGACAATT
1 ATGTGGTCCTCCGGGACAATT
645326 ATGTGGTCCTCCGGGACAATT
1 ATGTGGTCCTCCGGGACAATT
645347 ATGTGGT
1 ATGTGGT
645354 ACTTTGGTGC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.20, C:0.18, G:0.29, T:0.33
Consensus pattern (21 bp):
ATGTGGTCCTCCGGGACAATT
Found at i:650971 original size:21 final size:21
Alignment explanation
Indices: 650945--650992 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
650935 GTTGAGGGTC
* *
650945 TATGTGATCATTCGGGACAAT
1 TATGTGATCATCCGAGACAAT
* *
650966 TATGTGGTCCTCCGAGACAAT
1 TATGTGATCATCCGAGACAAT
650987 TATGTG
1 TATGTG
650993 GCACTTCAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
TATGTGATCATCCGAGACAAT
Found at i:651006 original size:21 final size:21
Alignment explanation
Indices: 650961--651065 Score: 63
Period size: 21 Copynumber: 4.9 Consensus size: 21
650951 ATCATTCGGG
*
650961 ACAATTATGTGGTC-CTCCGAG-
1 ACAATTATGTGG-CACTTC-AGT
650982 ACAATTATGTGGCACTTCAGT
1 ACAATTATGTGGCACTTCAGT
* *
651003 ACAACCCTATGTGGCACTTTAGT
1 ACAA--TTATGTGGCACTTCAGT
* * * *
651026 GCAAACTATATGGTC-CTTCAGG
1 AC-AATTATGTGG-CACTTCAGT
*
651048 ACAATTATGGGGCACTTC
1 ACAATTATGTGGCACTTC
651066 GGTGTAAATT
Statistics
Matches: 66, Mismatches: 11, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
20 4 0.06
21 30 0.45
22 13 0.20
23 17 0.26
24 2 0.03
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.30
Consensus pattern (21 bp):
ACAATTATGTGGCACTTCAGT
Found at i:653431 original size:24 final size:23
Alignment explanation
Indices: 653391--653442 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 23
653381 AACTGCCACA
653391 TAGAATTGCACCAAAGTGCCGCG
1 TAGAATTGCACCAAAGTGCCGCG
* * *
653414 TAGAATATGCACCGAAGTGTCTCG
1 TAGAAT-TGCACCAAAGTGCCGCG
653438 TAGAA
1 TAGAA
653443 ATGTCCCGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 6 0.24
24 19 0.76
ACGTcount: A:0.33, C:0.21, G:0.25, T:0.21
Consensus pattern (23 bp):
TAGAATTGCACCAAAGTGCCGCG
Found at i:658094 original size:20 final size:20
Alignment explanation
Indices: 658069--658106 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
658059 TTTGGTTCAC
658069 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
658089 GGAATGTAAGATTACCAG
1 GGAATGTAAGATTACCAG
658107 GGAATAGGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.37, C:0.11, G:0.29, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:658310 original size:2 final size:2
Alignment explanation
Indices: 658303--658329 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
658293 TCATAAAATT
658303 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
658330 TGTTACAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:662744 original size:139 final size:138
Alignment explanation
Indices: 662494--662872 Score: 587
Period size: 139 Copynumber: 2.7 Consensus size: 138
662484 TACTATTCAC
* * *
662494 GTGAAGGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTATCAGAGAATATGTTATCATTGCCTT
1 GTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* * *
662559 ATTATGTCACTCATGTCCCCCGGTGGCACTATTGATGTCAATACTTATTATGTTTGAGGGGACTT
66 ATTATGTCACTCATGT-CCCCGGGGGCACTATTCATGTCAATACTTATTATGTTTGAGGAGACTT
* *
662624 GGTAAAGTG
130 AGCAAAGTG
* * *
662633 GTGAAAGCGCATTCTCGGGGGGGCGCCTTCCATTATTTTGTTAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
*
662698 ATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGTACTTATTATGTTTGAGGAGACTT
66 ATTATGTCACTCATGTCCC-CGGGGGCACTATTCATGTCAATACTTATTATGTTTGAGGAGACTT
662763 AGCAAAGTG
130 AGCAAAGTG
* * *
662772 GTGAAAGCGCGTTCCCGGGGGGGCGCCTTCGATTGTTATGTCAGAGAATATGTTATCATTGCCCT
1 GTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
* *
662837 ATTATGTGAGTCATGTCCCCGGGGGCACTATTCATG
66 ATTATGTCACTCATGTCCCCGGGGGCACTATTCATG
662873 ACAGAGAATA
Statistics
Matches: 219, Mismatches: 20, Indels: 3
0.90 0.08 0.01
Matches are distributed among these distances:
138 20 0.09
139 199 0.91
ACGTcount: A:0.21, C:0.20, G:0.26, T:0.33
Consensus pattern (138 bp):
GTGAAAGCGCGTTCCCGGGGGGGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
ATTATGTCACTCATGTCCCCGGGGGCACTATTCATGTCAATACTTATTATGTTTGAGGAGACTTA
GCAAAGTG
Found at i:662912 original size:61 final size:61
Alignment explanation
Indices: 662813--662933 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 61
662803 ATTGTTATGT
* * * **
662813 CAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCCGGGGGCACTATTCATGA
1 CAGAGAATATGTTATCATTGCCATATTATGTCACTCATGTCCCCCAGGGCACTATTCATGA
* *
662874 CAGAGAATATGTTATCATTTCCATATTATGTCACTCATGTCCCCCAGGGTACTATTCATG
1 CAGAGAATATGTTATCATTGCCATATTATGTCACTCATGTCCCCCAGGGCACTATTCATG
662934 TCAGTACCTA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 53 1.00
ACGTcount: A:0.26, C:0.22, G:0.19, T:0.33
Consensus pattern (61 bp):
CAGAGAATATGTTATCATTGCCATATTATGTCACTCATGTCCCCCAGGGCACTATTCATGA
Found at i:663018 original size:200 final size:200
Alignment explanation
Indices: 662675--663056 Score: 615
Period size: 200 Copynumber: 1.9 Consensus size: 200
662665 TTATTTTGTT
* **
662675 AGAGAATATGTTATCATTGCCCTATTATGTCACTCATGTCCCTCGGGGGCACTATTCATGTCAGT
1 AGAGAATATGTTATCATTGCCATATTATGTCACTCATGTCCCTCCAGGGCACTATTCATGTCAGT
* * * * *
662740 ACTTATTATGTTTGAGGAGACTTAGCAAAGTGGTGAAAGCGCGTTCCCGGGGGGGCGCCTTCGAT
66 ACCTATTATGTTTGAGGAGACTCAACAAAGTGGTGAAAGCGAGTTCCAGGGGGGGCGCCTTCGAT
662805 TGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCCGGGGGCACTATTC
131 TGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCCGGGGGCACTATTC
662870 ATGAC
196 ATGAC
* *
662875 AGAGAATATGTTATCATTTCCATATTATGTCACTCATGTCCC-CCAGGGTACTATTCATGTCAGT
1 AGAGAATATGTTATCATTGCCATATTATGTCACTCATGTCCCTCCAGGGCACTATTCATGTCAGT
* * *
662939 ACCTATTATGTTTGAGGGGA-TGCAACAAAGTGGTGAAAGCGTATTTCTAGGGGGGGCGCCTTCG
66 ACCTATTATGTTTGAGGAGACT-CAACAAAGTGGTGAAAGCG-AGTTCCAGGGGGGGCGCCTTCG
663003 ATTGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCC
129 ATTGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCC
663057 CAGAGACACA
Statistics
Matches: 167, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
198 1 0.01
199 54 0.32
200 112 0.67
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (200 bp):
AGAGAATATGTTATCATTGCCATATTATGTCACTCATGTCCCTCCAGGGCACTATTCATGTCAGT
ACCTATTATGTTTGAGGAGACTCAACAAAGTGGTGAAAGCGAGTTCCAGGGGGGGCGCCTTCGAT
TGTTATGTCAGAGAATATGTTATCATTGCCCTATTATGTGAGTCATGTCCCCGGGGGCACTATTC
ATGAC
Found at i:663249 original size:23 final size:23
Alignment explanation
Indices: 663201--663255 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
663191 TGAAGTTTAA
* * *
663201 ATAAATTGGATTAAATGTTATGG
1 ATAAATTGGAATAAATGTGAAGG
663224 ATAAATT-GAATAAATGTGAAGTG
1 ATAAATTGGAATAAATGTGAAG-G
*
663247 ATAAGTTGG
1 ATAAATTGG
663256 TTGTGATGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 11 0.42
23 14 0.54
24 1 0.04
ACGTcount: A:0.42, C:0.00, G:0.24, T:0.35
Consensus pattern (23 bp):
ATAAATTGGAATAAATGTGAAGG
Found at i:663524 original size:34 final size:34
Alignment explanation
Indices: 663486--663554 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
663476 TTAAGTTGAA
*
663486 TTTAATGTTAATTTTTGAATACTATAATTTATAT
1 TTTAATGTTAAATTTTGAATACTATAATTTATAT
*
663520 TTTAATGTTAAATTTTGAATACTATAATTTGTAT
1 TTTAATGTTAAATTTTGAATACTATAATTTATAT
663554 T
1 T
663555 ATAAAAACAT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.35, C:0.03, G:0.07, T:0.55
Consensus pattern (34 bp):
TTTAATGTTAAATTTTGAATACTATAATTTATAT
Found at i:664110 original size:21 final size:21
Alignment explanation
Indices: 664084--664141 Score: 62
Period size: 21 Copynumber: 2.8 Consensus size: 21
664074 AAACCCTGCA
*
664084 GGCTAGGCATGTAACCTGGTG
1 GGCTAGGCATGTAACCTGGCG
* **
664105 GTCTAGGCATAAAACCTGGCG
1 GGCTAGGCATGTAACCTGGCG
* *
664126 GGATAGGAATGTAACC
1 GGCTAGGCATGTAACC
664142 CTATGGAGAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.33, T:0.21
Consensus pattern (21 bp):
GGCTAGGCATGTAACCTGGCG
Found at i:665998 original size:31 final size:31
Alignment explanation
Indices: 665963--666030 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
665953 TTAAATTAAT
*
665963 AATAATTATATAAAT-ATTATTTTAATATAAA
1 AATAA-TATATAAATAATTATATTAATATAAA
* *
665994 AATAATATTTATATAATTATATTAATATAAA
1 AATAATATATAAATAATTATATTAATATAAA
666025 ATATAA
1 A-ATAA
666031 CAACTATTTT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
30 7 0.22
31 21 0.66
32 4 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (31 bp):
AATAATATATAAATAATTATATTAATATAAA
Found at i:666007 original size:17 final size:17
Alignment explanation
Indices: 665960--666009 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
665950 AATTTAAATT
*
665960 AATAATAATTATATAAA
1 AATAATATTTATATAAA
* *
665977 TATTAT-TTTAATATAAA
1 AATAATATTT-ATATAAA
665994 AATAATATTTATATAA
1 AATAATATTTATATAA
666010 TTATATTAAT
Statistics
Matches: 26, Mismatches: 5, Indels: 4
0.74 0.14 0.11
Matches are distributed among these distances:
16 2 0.08
17 21 0.81
18 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
AATAATATTTATATAAA
Found at i:668228 original size:3 final size:3
Alignment explanation
Indices: 668213--668324 Score: 172
Period size: 3 Copynumber: 37.0 Consensus size: 3
668203 CTATTTTAAT
* * *
668213 TTA TTA CTA TTA TTA TT- TTGT TTA TTA TTA TTAA TTC TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A TTA TTA TTA TTA
668259 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
668307 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
668325 CAAATGTACA
Statistics
Matches: 101, Mismatches: 5, Indels: 6
0.90 0.04 0.05
Matches are distributed among these distances:
2 2 0.02
3 94 0.93
4 5 0.05
ACGTcount: A:0.31, C:0.02, G:0.01, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:668746 original size:50 final size:51
Alignment explanation
Indices: 668624--668752 Score: 170
Period size: 52 Copynumber: 2.5 Consensus size: 51
668614 TTAGCAGTAA
** * *
668624 AGCGCGCCCCCTGCACCGCGCTATACGATGATTTGGTGCCACGTGGGGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTAGCGCCACGT-GGGGTAT
*
668676 AGCGCGCCCCCTGCACCGCGCTATACGGTGAGCTAGCGCCACGT-GGGTAT
1 AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTAGCGCCACGTGGGGTAT
* * *
668726 AGCGTGGCCCCTGCAACGCGCTATACG
1 AGCGCGCCCCCTGCACCGCGCTATACG
668753 CCACGTAGGG
Statistics
Matches: 69, Mismatches: 8, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 30 0.43
52 39 0.57
ACGTcount: A:0.16, C:0.34, G:0.32, T:0.18
Consensus pattern (51 bp):
AGCGCGCCCCCTGCACCGCGCTATACGATGAGCTAGCGCCACGTGGGGTAT
Found at i:674770 original size:16 final size:16
Alignment explanation
Indices: 674718--674771 Score: 60
Period size: 16 Copynumber: 3.4 Consensus size: 16
674708 TGCAAAAAGA
*
674718 ATTATATTAGTAAAAT
1 ATTATAATAGTAAAAT
674734 ATTA-AATAAAGTAAAA-
1 ATTATAAT--AGTAAAAT
674750 A-TATAATAGTAAAAT
1 ATTATAATAGTAAAAT
674765 ATTATAA
1 ATTATAA
674772 AATATACCTT
Statistics
Matches: 32, Mismatches: 1, Indels: 10
0.74 0.02 0.23
Matches are distributed among these distances:
14 7 0.22
15 5 0.16
16 13 0.41
17 7 0.22
ACGTcount: A:0.59, C:0.00, G:0.06, T:0.35
Consensus pattern (16 bp):
ATTATAATAGTAAAAT
Found at i:674801 original size:12 final size:10
Alignment explanation
Indices: 674787--674827 Score: 57
Period size: 10 Copynumber: 4.1 Consensus size: 10
674777 ACCTTAAAAA
*
674787 GAGAGTATTT
1 GAGAGAATTT
674797 GAGAGAAATTT
1 GAGAG-AATTT
674808 -AGAGAATTT
1 GAGAGAATTT
674817 GAGAGAATTT
1 GAGAGAATTT
674827 G
1 G
674828 GTGTGATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 5 0.18
10 19 0.68
11 4 0.14
ACGTcount: A:0.39, C:0.00, G:0.29, T:0.32
Consensus pattern (10 bp):
GAGAGAATTT
Found at i:674992 original size:50 final size:51
Alignment explanation
Indices: 674938--675064 Score: 166
Period size: 51 Copynumber: 2.5 Consensus size: 51
674928 AGATATACAG
* * **
674938 GTATAGCGCGCTGCAGGGGCCGCGCTATA-CCCACGTGGCGCCAGCTCACC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACC
* * *
674988 GTATAGCGCGGTGCAGGGGGCGCACTATACCCCACGTGGTGCCAAATCATC
1 GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACC
* *
675039 GTATAACGCGGTGGAGGGGGCGCGCT
1 GTATAGCGCGGTGCAGGGGGCGCGCT
675065 TTACTGCTAA
Statistics
Matches: 66, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
50 26 0.39
51 40 0.61
ACGTcount: A:0.18, C:0.31, G:0.35, T:0.16
Consensus pattern (51 bp):
GTATAGCGCGGTGCAGGGGGCGCGCTATACCCCACGTGGCGCCAAATCACC
Found at i:682152 original size:105 final size:106
Alignment explanation
Indices: 682009--682329 Score: 370
Period size: 106 Copynumber: 3.0 Consensus size: 106
681999 TAAAATTCTT
682009 TCTCGTTTGAGACATTTTTTT-CTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
1 TCTCGTTTGAGACATTTTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
* *
682073 TTGATCTCATTTGAGATCGCTTTCTTAAAAAACAAACTCTG
66 TTGATCTCAATTGAGATCGATTTCTTAAAAAACAAACTCTG
* ** * *
682114 TCTTGTTTGAGACATTTTTTTCCTTTGA-CCTACAAATTTTGAATTTGATTCAC-TTGAAACAAA
1 TCTCGTTTGAGACATTTTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATT-AAAC-AA
* * * * *
682177 AATTAATCTCAATTGAGATTGTTATTTCTTTCAAAATA-AAATTC-G
64 AGTTGATCTCAATTGAGATCG--ATTTC-TT-AAAAAACAAACTCTG
* *
682222 TCTCATTTGAGACA--TTTTTCATTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
1 TCTCGTTTGAGACATTTTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
* * * *
682285 TTGATCTCACTTGAGATCGTTTTC-TCAAAAACAAACTTTG
66 TTGATCTCAATTGAGATCGATTTCTTAAAAAACAAACTCTG
682325 TCTCG
1 TCTCG
682330 CATGAGATAG
Statistics
Matches: 176, Mismatches: 29, Indels: 24
0.77 0.13 0.10
Matches are distributed among these distances:
101 4 0.02
102 5 0.03
103 5 0.03
104 6 0.03
105 45 0.26
106 55 0.31
107 25 0.14
108 19 0.11
109 7 0.04
110 5 0.03
ACGTcount: A:0.32, C:0.16, G:0.12, T:0.41
Consensus pattern (106 bp):
TCTCGTTTGAGACATTTTTTTCCTTTGAGAATACAAATTTCGAATTTGTTTCACATTAAACAAAG
TTGATCTCAATTGAGATCGATTTCTTAAAAAACAAACTCTG
Found at i:682399 original size:37 final size:35
Alignment explanation
Indices: 682311--682415 Score: 111
Period size: 36 Copynumber: 2.9 Consensus size: 35
682301 TCGTTTTCTC
* *
682311 AAAAACAAACTTTGTCTCGCATGAGATAGTTTCCCT
1 AAAAACAAA-TTTGTCTCGCTTGAGATAATTTCCCT
* * * *
682347 AAAAACAATTTTTGTCTCGTTTGAGACAATTTCTCT
1 AAAAACAA-ATTTGTCTCGCTTGAGATAATTTCCCT
*
682383 AAAAAACAAATGTTGTCTCACTTGAGATAATTT
1 -AAAAACAAAT-TTGTCTCGCTTGAGATAATTT
682416 TCCAAATTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
36 30 0.54
37 26 0.46
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (35 bp):
AAAAACAAATTTGTCTCGCTTGAGATAATTTCCCT
Found at i:682752 original size:66 final size:63
Alignment explanation
Indices: 682576--682761 Score: 185
Period size: 64 Copynumber: 2.9 Consensus size: 63
682566 TAAAACAAAA
* ** * * * * *
682576 TGAAAAAATCTTTGAGTATATTTCTT-TGATAACAAAATTTTGTCTCTTTCGATAAAGTTTCTTT
1 TGAAAAAATCTTTAAGTACGTTT-TTATGAAAAC-AAATTTTGTCTCTTTTGAGACAGTTCCTTT
* * * * *
682640 TGAAAGAATCTTTGAGTATGTTTTTTTGGAAACACAATTTTGTCTCTTTTGAGACAGTTCCTTT
1 TGAAAAAATCTTTAAGTACGTTTTTATGAAAACA-AATTTTGTCTCTTTTGAGACAGTTCCTTT
*
682704 TGAATAAAAATCTTTAAGTCCGTTTTTATGAAAACAAATGTTTGTCTCTTTTGAGACA
1 TG-A-AAAAATCTTTAAGTACGTTTTTATGAAAACAAAT-TTTGTCTCTTTTGAGACA
682762 ATTTCTCTTA
Statistics
Matches: 103, Mismatches: 14, Indels: 8
0.82 0.11 0.06
Matches are distributed among these distances:
63 3 0.03
64 53 0.51
65 4 0.04
66 43 0.42
ACGTcount: A:0.30, C:0.12, G:0.14, T:0.44
Consensus pattern (63 bp):
TGAAAAAATCTTTAAGTACGTTTTTATGAAAACAAATTTTGTCTCTTTTGAGACAGTTCCTTT
Found at i:682819 original size:33 final size:33
Alignment explanation
Indices: 682780--682842 Score: 108
Period size: 33 Copynumber: 1.9 Consensus size: 33
682770 TAAAACAAAC
682780 ATCTTTGAGATTGTTTCCCTTGAAACAAAATTT
1 ATCTTTGAGATTGTTTCCCTTGAAACAAAATTT
* *
682813 ATCTTTGAGTTTGTTTCTCTTGAAACAAAA
1 ATCTTTGAGATTGTTTCCCTTGAAACAAAA
682843 GTCTGTGAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (33 bp):
ATCTTTGAGATTGTTTCCCTTGAAACAAAATTT
Found at i:682864 original size:29 final size:29
Alignment explanation
Indices: 682826--682900 Score: 80
Period size: 29 Copynumber: 2.6 Consensus size: 29
682816 TTTGAGTTTG
*
682826 TTTCTCTTGAAACAAAAGTCTGTGAG-TCA
1 TTTCTTTTGAAACAAAA-TCTGTGAGTTCA
* **
682855 TTTCTTTTGAAACCAAAATCTTTGAGTTTG
1 TTTCTTTTGAAA-CAAAATCTGTGAGTTCA
*
682885 TTTATTTTGAAACAAA
1 TTTCTTTTGAAACAAA
682901 GTTTTGTCTC
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
29 22 0.56
30 17 0.44
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.41
Consensus pattern (29 bp):
TTTCTTTTGAAACAAAATCTGTGAGTTCA
Found at i:682893 original size:30 final size:30
Alignment explanation
Indices: 682775--682897 Score: 106
Period size: 30 Copynumber: 4.0 Consensus size: 30
682765 TCTCTTAAAA
* **
682775 CAAACATCTTTGAGATTGTTTCCCTTGAAAC
1 CAAA-ATCTTTGAGTTTGTTTCTTTTGAAAC
* *
682806 AAAATTTATCTTTGAGTTTGTTTCTCTTGAAA-
1 CAAA---ATCTTTGAGTTTGTTTCTTTTGAAAC
* **
682838 CAAAAGTCTGTGAG-TCATTTCTTTTGAAAC
1 CAAAA-TCTTTGAGTTTGTTTCTTTTGAAAC
*
682868 CAAAATCTTTGAGTTTGTTTATTTTGAAAC
1 CAAAATCTTTGAGTTTGTTTCTTTTGAAAC
682898 AAAGTTTTGT
Statistics
Matches: 74, Mismatches: 13, Indels: 11
0.76 0.13 0.11
Matches are distributed among these distances:
29 20 0.27
30 25 0.34
31 3 0.04
32 3 0.04
33 23 0.31
ACGTcount: A:0.29, C:0.15, G:0.14, T:0.42
Consensus pattern (30 bp):
CAAAATCTTTGAGTTTGTTTCTTTTGAAAC
Found at i:683308 original size:43 final size:42
Alignment explanation
Indices: 683201--683433 Score: 124
Period size: 43 Copynumber: 5.4 Consensus size: 42
683191 GATGGCTAGA
* * * *
683201 ACTCTTCATCACGTATGAGCCGTGTCATCTCCT-G--ACCAG
1 ACTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATACCAG
* *
683240 ATCTCTTCATCACGTAGGAGTCGTGTCA-CCCCTAGATAACCAG
1 A-CTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGAT-ACCAG
* **
683283 ACGTCCTCATCACGTAGGAACCGTGTTATCACCCTTCCTAAAGATGGCAG
1 AC-TCCTCATCACGTAGGAGCCGTG---TCACCC--CCT--AGATACCAG
* * * *
683333 AACTCTTCATCACGTATGAGCCATGTCATCCCC--G--ACCAG
1 -ACTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATACCAG
* *
683372 ATCTCCTCATCGCGTAGGAGCTGTGTCA-CCCCTAGATAACCAG
1 A-CTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGAT-ACCAG
* *
683415 CCGTCCTCATCGCGTAGGA
1 AC-TCCTCATCACGTAGGA
683434 ACCGAGTTAT
Statistics
Matches: 151, Mismatches: 21, Indels: 40
0.71 0.10 0.19
Matches are distributed among these distances:
38 5 0.03
39 29 0.19
40 26 0.17
41 1 0.01
42 2 0.01
43 46 0.30
45 2 0.01
46 3 0.02
47 7 0.05
49 3 0.02
50 21 0.14
51 6 0.04
ACGTcount: A:0.24, C:0.33, G:0.19, T:0.24
Consensus pattern (42 bp):
ACTCCTCATCACGTAGGAGCCGTGTCACCCCCTAGATACCAG
Found at i:683436 original size:132 final size:133
Alignment explanation
Indices: 683185--683542 Score: 542
Period size: 132 Copynumber: 2.7 Consensus size: 133
683175 AATCATTATC
* * * *
683185 CCTAAAGATGGCTAGAACTCTTCATCACGTATGAGCCGTGTCATCTCCTGACCAGATCTCTTCAT
1 CCTAAAGATGGCAAGAACTCTTCATCACGTATGAGCCATGTCATC-CCCGACCAGATCTCCTCAT
*
683250 CACGTAGGAG-TCGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGTGTTATCA
65 CACGTAGGAGCT-GTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCA
683314 CCCTT
129 CCCTT
683319 CCTAAAGATGGC-AGAACTCTTCATCACGTATGAGCCATGTCATCCCCGACCAGATCTCCTCATC
1 CCTAAAGATGGCAAGAACTCTTCATCACGTATGAGCCATGTCATCCCCGACCAGATCTCCTCATC
* * *
683383 GCGTAGGAGCTGTGTCACCCCTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGAGTTATCACC
66 ACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACC
683448 CTT
131 CTT
*
683451 CCTAAAGATGGCCAAGAACTCTTCATCACGTATGAG-CAGTGTCATCCCTCGACCAGATTTCCTC
1 CCTAAAGATGG-CAAGAACTCTTCATCACGTATGAGCCA-TGTCATCCC-CGACCAGATCTCCTC
* * *
683515 ATCACGTAGGAACCGTGTCACCCTTAGA
63 ATCACGTAGGAGCTGTGTCACCCCTAGA
683543 CGACCCGAAC
Statistics
Matches: 207, Mismatches: 12, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
132 91 0.44
133 35 0.17
134 43 0.21
135 38 0.18
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (133 bp):
CCTAAAGATGGCAAGAACTCTTCATCACGTATGAGCCATGTCATCCCCGACCAGATCTCCTCATC
ACGTAGGAGCTGTGTCACCCCTAGATAACCAGACGTCCTCATCACGTAGGAACCGAGTTATCACC
CTT
Found at i:683576 original size:43 final size:40
Alignment explanation
Indices: 683465--683581 Score: 119
Period size: 43 Copynumber: 2.9 Consensus size: 40
683455 AAGATGGCCA
683465 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
** * * * *
683505 AGATTTCCTCATCACGTAGGAACCGTGTCA-CCCTTAGACGACC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC-T---CGACC
* *
683548 CGAACTCTTCATCACGTATGAGCAGTGTCGTCCC
1 AGAACTCTTCATCACGTATGAGCAGTGTCATCCC
683582 CAACAACTAA
Statistics
Matches: 58, Mismatches: 14, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
39 3 0.05
40 25 0.43
43 27 0.47
44 3 0.05
ACGTcount: A:0.24, C:0.32, G:0.19, T:0.25
Consensus pattern (40 bp):
AGAACTCTTCATCACGTATGAGCAGTGTCATCCCTCGACC
Found at i:683753 original size:3 final size:3
Alignment explanation
Indices: 683738--683801 Score: 85
Period size: 3 Copynumber: 21.0 Consensus size: 3
683728 CTATTTTAAT
* *
683738 TTA TTA CTA TTA TTA TT- TTGT TTA TTA TTA TTAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TT-A TTA TTA TTA TTA
683784 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
683802 ATACAAATGG
Statistics
Matches: 55, Mismatches: 3, Indels: 6
0.86 0.05 0.09
Matches are distributed among these distances:
2 2 0.04
3 48 0.87
4 5 0.09
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:683781 original size:28 final size:28
Alignment explanation
Indices: 683745--683798 Score: 83
Period size: 28 Copynumber: 1.9 Consensus size: 28
683735 AATTTATTAC
*
683745 TATTATTATT-TTGTTTATTATTATTAAT
1 TATTATTATTATT-ATTATTATTATTAAT
683773 TATTATTATTATTATTATTATTATTA
1 TATTATTATTATTATTATTATTATTA
683799 TTAATACAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
28 22 0.92
29 2 0.08
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (28 bp):
TATTATTATTATTATTATTATTATTAAT
Found at i:683783 original size:31 final size:31
Alignment explanation
Indices: 683740--683803 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
683730 ATTTTAATTT
*
683740 ATTACTATTATTATT-TTGTTTATTATTATTA
1 ATTACTATTATTATTATT-ATTATTATTATTA
*
683771 ATTATTATTATTATTATTATTATTATTATTA
1 ATTACTATTATTATTATTATTATTATTATTA
683802 AT
1 AT
683804 ACAAATGGAC
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (31 bp):
ATTACTATTATTATTATTATTATTATTATTA
Found at i:686430 original size:14 final size:14
Alignment explanation
Indices: 686408--686437 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
686398 ATCAAACAGC
*
686408 ATTAGAAAAAAAAT
1 ATTAAAAAAAAAAT
686422 ATTAAAAAAAAAAT
1 ATTAAAAAAAAAAT
686436 AT
1 AT
686438 GTCAGTTACG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.23
Consensus pattern (14 bp):
ATTAAAAAAAAAAT
Found at i:687059 original size:21 final size:21
Alignment explanation
Indices: 687003--687060 Score: 57
Period size: 23 Copynumber: 2.7 Consensus size: 21
686993 TTCTATACTT
*
687003 TATAATATAC-ACATCAAAAC
1 TATAATATACAATATCAAAAC
*
687023 TAT-ATAATATCTAATATGAAAAC
1 TATAAT-ATA-C-AATATCAAAAC
687046 TATAATATACAATAT
1 TATAATATACAATAT
687061 TTAATATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 2 0.06
20 6 0.19
21 6 0.19
22 1 0.03
23 14 0.45
24 2 0.06
ACGTcount: A:0.53, C:0.12, G:0.02, T:0.33
Consensus pattern (21 bp):
TATAATATACAATATCAAAAC
Found at i:687059 original size:28 final size:28
Alignment explanation
Indices: 687023--687082 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
687013 ACATCAAAAC
* *
687023 TATATAATATCTAATATGAAAACTATAA
1 TATACAATATCTAATATAAAAACTATAA
* * *
687051 TATACAATATTTAATATAAAAATTATAC
1 TATACAATATCTAATATAAAAACTATAA
687079 TATA
1 TATA
687083 TACTATGTAT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.53, C:0.07, G:0.02, T:0.38
Consensus pattern (28 bp):
TATACAATATCTAATATAAAAACTATAA
Found at i:687633 original size:19 final size:19
Alignment explanation
Indices: 687609--687649 Score: 73
Period size: 19 Copynumber: 2.2 Consensus size: 19
687599 GGGTCGGGTC
*
687609 AAGTTTCTAAGTTATTTCT
1 AAGTTTCTAAGTTATTTAT
687628 AAGTTTCTAAGTTATTTAT
1 AAGTTTCTAAGTTATTTAT
687647 AAG
1 AAG
687650 CGGAACAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.07, G:0.12, T:0.49
Consensus pattern (19 bp):
AAGTTTCTAAGTTATTTAT
Found at i:691523 original size:77 final size:79
Alignment explanation
Indices: 691395--691543 Score: 187
Period size: 77 Copynumber: 1.9 Consensus size: 79
691385 ATATAGTAAG
**
691395 TAAAAATTAAAAGAATGTAATTTTGATCATAACTCTTTTAATCGATATTTAATTCGGAA-TAATT
1 TAAAAATTAAAAGAATGTAATTCAGATCATAACTCTTTTAATCGATATTTAATT-GGAATTAATT
691459 AAATAATAGTTTAAA
65 AAATAATAGTTTAAA
* * * * * * *
691474 TAAACATTAAAA-ATTGTAATTCAGATTATAAGTC-TTTAATGGATGTTTAATTTGAATTAATTA
1 TAAAAATTAAAAGAATGTAATTCAGATCATAACTCTTTTAATCGATATTTAATTGGAATTAATTA
691537 AATAATA
66 AATAATA
691544 TTTTTTATTA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
76 3 0.05
77 29 0.48
78 17 0.28
79 11 0.18
ACGTcount: A:0.45, C:0.05, G:0.09, T:0.40
Consensus pattern (79 bp):
TAAAAATTAAAAGAATGTAATTCAGATCATAACTCTTTTAATCGATATTTAATTGGAATTAATTA
AATAATAGTTTAAA
Found at i:695460 original size:17 final size:17
Alignment explanation
Indices: 695423--695465 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
695413 AATATTTGTT
* * *
695423 TCTCGAATGAGAGTTTT
1 TCTCGAAAGAGAATTTC
695440 TCTCGAAAGAGAATTTC
1 TCTCGAAAGAGAATTTC
695457 TCTC-AAAGA
1 TCTCGAAAGA
695466 AAGGGAATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 5 0.22
17 18 0.78
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (17 bp):
TCTCGAAAGAGAATTTC
Found at i:700849 original size:32 final size:32
Alignment explanation
Indices: 700805--700866 Score: 106
Period size: 32 Copynumber: 1.9 Consensus size: 32
700795 CGACACCCCA
*
700805 ATGCATGGCGCATGGAGCACCATGCGTTACCT
1 ATGCATGGCGCATGGAACACCATGCGTTACCT
*
700837 ATGCTTGGCGCATGGAACACCATGCGTTAC
1 ATGCATGGCGCATGGAACACCATGCGTTAC
700867 ATTTTTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.27, G:0.27, T:0.23
Consensus pattern (32 bp):
ATGCATGGCGCATGGAACACCATGCGTTACCT
Found at i:703437 original size:4 final size:4
Alignment explanation
Indices: 703430--705379 Score: 3208
Period size: 4 Copynumber: 492.0 Consensus size: 4
703420 AGTATATATA
*
703430 TATG TATG TATG TATG TATG TATG TATT TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
703478 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
703526 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
703574 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
703622 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
703670 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
703716 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
703764 TATG TATG TATG TATG TATG TATG TATG TATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* ** * * *
703812 CATG TATG TATG TATG TATG TAAA TAAG -AAG GATG TGAATG -ATG ATAATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG T--ATG TATG -T-ATG
*
703862 -ATAG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TAT-G TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
703910 TATG TATG TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
703958 TATG TATG TATG TATG TATG TATG TATG TA-- TATA TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
704004 TATG TATG TATA TATG TATG TATG TATG TATG TGTG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
704052 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
704100 CATG TATG TATA TATG TATG TATG TATG CATG CATG CATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
704148 TATG TATG CATG CATG CATG AATG CATG CATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
704196 TATG TATG TATG TATG CATG TATG TATG TATG CATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
704244 TATG TATG TATG TATG TATG TATG CATG CATG TATG CATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * *
704292 TATG CATG TATG TATG TATG TATG TATG TATA TATG TATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
704340 TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * *
704388 CATG CATG CATG TATG TATG TATG CATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
704436 TATG TATA TATG TATG CATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* *
704484 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG CATG CATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
* * * * * *
704532 CATG CATG CATG CATG CATG CATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704580 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG --TG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704626 TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704672 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704720 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704768 TATG TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704814 TATG TATG TATG TATG TATG TATG TATG TA-G TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704861 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704909 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
704957 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
705005 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATA
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
705053 TATG TATG TATG TA-- TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
705099 TATG TATG TATG TATG TATG TAT- TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
705146 TATG TATG TATG TATG TATG TA-- TATG TATG TATG TATG TA-- TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
705190 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
705238 TATG TATG TATG TCTG TATG TATG --TG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
*
705284 TATA TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
705332 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
705380 CAATGGTTAT
Statistics
Matches: 1856, Mismatches: 62, Indels: 56
0.94 0.03 0.03
Matches are distributed among these distances:
2 18 0.01
3 14 0.01
4 1816 0.98
5 2 0.00
6 6 0.00
ACGTcount: A:0.26, C:0.02, G:0.24, T:0.48
Consensus pattern (4 bp):
TATG
Found at i:722376 original size:27 final size:28
Alignment explanation
Indices: 722330--722389 Score: 86
Period size: 27 Copynumber: 2.2 Consensus size: 28
722320 ATATTATTCA
* *
722330 AAAATTATTCGAACCCTAATATATGAAT
1 AAAATTATTCGAACCCTAATACATAAAT
*
722358 AAAATT-TTTGAACCCTAATACATAAAT
1 AAAATTATTCGAACCCTAATACATAAAT
722385 AAAAT
1 AAAAT
722390 AAATTACCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
27 23 0.79
28 6 0.21
ACGTcount: A:0.50, C:0.13, G:0.05, T:0.32
Consensus pattern (28 bp):
AAAATTATTCGAACCCTAATACATAAAT
Found at i:728583 original size:29 final size:30
Alignment explanation
Indices: 728540--728602 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 30
728530 TAAATTTATA
728540 ATATTTTATATTCTTAACTT-TTAAA-ATT
1 ATATTTTATATTCTTAACTTATTAAATATT
*
728568 ATATTTTACTTTTCTTAACTTATTAAATATT
1 ATATTTTA-TATTCTTAACTTATTAAATATT
728599 -TATT
1 ATATT
728603 CTCATTTTAC
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 8 0.26
29 11 0.35
30 9 0.29
31 3 0.10
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (30 bp):
ATATTTTATATTCTTAACTTATTAAATATT
Found at i:728674 original size:29 final size:28
Alignment explanation
Indices: 728621--728717 Score: 86
Period size: 29 Copynumber: 3.3 Consensus size: 28
728611 ACATAAAAAT
* * * *
728621 ATATATTTTAATATCATCTTCACTTAAA
1 ATATATTTTACTCTTATCTTAACTTAAA
*
728649 AGTATATTTTACTCTTATTTTAACTTAAAA
1 A-TATATTTTACTCTTATCTTAACTT-AAA
* * *
728679 ATATAATTTATTCTTATCTTAATTTTCAAA
1 ATATATTTTACTCTTATCTTAA-CTT-AAA
728709 ATATATTTT
1 ATATATTTT
728718 TAAATTATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
28 1 0.02
29 37 0.67
30 17 0.31
ACGTcount: A:0.37, C:0.10, G:0.01, T:0.52
Consensus pattern (28 bp):
ATATATTTTACTCTTATCTTAACTTAAA
Found at i:728873 original size:2 final size:2
Alignment explanation
Indices: 728866--728937 Score: 78
Period size: 2 Copynumber: 36.5 Consensus size: 2
728856 TGATAAGAAT
* *
728866 TA TA TA TA TA TA TA TA -A T- TCA T- TGA AA TA AA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA T-A TA T-A TA TA TA TA TA TA TA TA
*
728907 TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
728938 TTTAAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
1 3 0.05
2 55 0.93
3 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:728948 original size:16 final size:15
Alignment explanation
Indices: 728928--728971 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 15
728918 ATATATATAT
728928 ATAAATATATTTTAA
1 ATAAATATATTTTAA
*
728943 ATTAAAATATTTTTTAA
1 A-T-AAATATATTTTAA
728960 A-AAATATATTTT
1 ATAAATATATTTT
728972 TAAGTGAAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
14 10 0.40
15 1 0.04
16 1 0.04
17 13 0.52
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATAAATATATTTTAA
Found at i:728971 original size:15 final size:16
Alignment explanation
Indices: 728930--728974 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
728920 ATATATATAT
*
728930 AAATATATTTTAAATTA
1 AAATATATTTTTAA-TA
728947 AAATAT-TTTTTAA-A
1 AAATATATTTTTAATA
728961 AAATATATTTTTAA
1 AAATATATTTTTAA
728975 GTGAAGATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
14 7 0.27
15 7 0.27
16 6 0.23
17 6 0.23
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAATATATTTTTAATA
Found at i:729052 original size:29 final size:29
Alignment explanation
Indices: 729015--729071 Score: 78
Period size: 29 Copynumber: 2.0 Consensus size: 29
729005 CATTAAAATA
*
729015 AAAACAAATAATATTTTATAAGTTAAGAC
1 AAAACAAATAATATTTTAAAAGTTAAGAC
* * *
729044 AAAATAAATTATATTTTAAAATTTAAGA
1 AAAACAAATAATATTTTAAAAGTTAAGA
729072 TATATAAAAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.56, C:0.04, G:0.05, T:0.35
Consensus pattern (29 bp):
AAAACAAATAATATTTTAAAAGTTAAGAC
Found at i:731018 original size:16 final size:16
Alignment explanation
Indices: 730997--731028 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
730987 ACGTTCCTTG
730997 GTTTAACAACCCTAAA
1 GTTTAACAACCCTAAA
731013 GTTTAACAACCCTAAA
1 GTTTAACAACCCTAAA
731029 TACTTATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.06, T:0.25
Consensus pattern (16 bp):
GTTTAACAACCCTAAA
Found at i:734422 original size:2 final size:2
Alignment explanation
Indices: 734415--734445 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
734405 ATTTTGTAAA
734415 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
734446 AATTTTATGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:734663 original size:20 final size:20
Alignment explanation
Indices: 734638--734675 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
734628 ATCCTATTAC
*
734638 CTGGTAATCTTATATTCCCA
1 CTGGTAATCTTACATTCCCA
734658 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
734676 GTAAACCAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.24, C:0.26, G:0.11, T:0.39
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:734813 original size:3 final size:3
Alignment explanation
Indices: 734790--734850 Score: 86
Period size: 3 Copynumber: 20.3 Consensus size: 3
734780 GTTAAACACC
* * * *
734790 AAG AGG AAG AGG AAA AAG AAG AAG AAG AAG ATG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
734838 AAG AAG AAG AAG A
1 AAG AAG AAG AAG A
734851 TCTCCTCCAC
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.64, C:0.00, G:0.34, T:0.02
Consensus pattern (3 bp):
AAG
Found at i:748329 original size:65 final size:64
Alignment explanation
Indices: 748258--748417 Score: 234
Period size: 65 Copynumber: 2.5 Consensus size: 64
748248 GAATAAATTG
* *
748258 AACATCGAATGCATTTTATGCATCGATGCACATA-CCATGCATTGATGCACTCAGGGCT-TTATG
1 AACATCGAATGCATTTGATGCATCGATGCACA-AGCCATGCATCGATGCACTCA-GGCTATTATG
748321 AA
64 -A
* *
748323 AACATCGAATGCATTTGATGCATCGATGCACAAGTCATGCATCGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTATGA
*
748387 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
748418 TCTTAGTAAA
Statistics
Matches: 88, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
64 36 0.41
65 52 0.59
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTGATGCATCGATGCACAAGCCATGCATCGATGCACTCAGGCTATTATGA
Found at i:748433 original size:64 final size:65
Alignment explanation
Indices: 748258--748442 Score: 180
Period size: 65 Copynumber: 2.9 Consensus size: 65
748248 GAATAAATTG
* * ** **
748258 AACATCGAATGCATTTTATGCATCGATGCACATAC-CATGCATTGATGCACTCAGGGCTTTATGA
1 AACATCGAATGCACTTGATGCATCGATGCACA-ACTCATAAACCGATGCACTCAGGGCTTTATGA
748322 A
65 A
* * ** * *
748323 AACATCGAATGCATTTGATGCATCGATGCACAAGTCATGCATCGATGCACTCA-GGCTATTTTG-
1 AACATCGAATGCACTTGATGCATCGATGCACAACTCATAAACCGATGCACTCAGGGCT-TTATGA
748386 A
65 A
* * *
748387 AACATCGAATGCACTTGATGCATCGATGCAC-TCTTAGTAAACCGATGCACTAAGGG
1 AACATCGAATGCACTTGATGCATCGATGCACAACTCA-TAAACCGATGCACTCAGGG
748443 TCCAACGATC
Statistics
Matches: 104, Mismatches: 12, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.02
64 48 0.46
65 54 0.52
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (65 bp):
AACATCGAATGCACTTGATGCATCGATGCACAACTCATAAACCGATGCACTCAGGGCTTTATGAA
Found at i:753855 original size:21 final size:21
Alignment explanation
Indices: 753790--753884 Score: 77
Period size: 23 Copynumber: 4.4 Consensus size: 21
753780 TTGTGCTTAA
*
753790 TGCATCGATACACC-T-AACAG
1 TGCATCGATACACCTTGAA-TG
* *
753810 TACATCGATGCATCCTTGAATG
1 TGCATCGATACA-CCTTGAATG
* *
753832 TGCATCGATACACCATGAAGG
1 TGCATCGATACACCTTGAATG
* *
753853 TGCACCGATGCACTCCTTGAATG
1 TGCATCGAT--ACACCTTGAATG
753876 TGCATCGAT
1 TGCATCGAT
753885 GCACAAGGTA
Statistics
Matches: 58, Mismatches: 12, Indels: 7
0.75 0.16 0.09
Matches are distributed among these distances:
20 10 0.17
21 17 0.29
22 12 0.21
23 19 0.33
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (21 bp):
TGCATCGATACACCTTGAATG
Found at i:753878 original size:23 final size:23
Alignment explanation
Indices: 753812--753888 Score: 97
Period size: 23 Copynumber: 3.5 Consensus size: 23
753802 CCTAACAGTA
753812 CATCGATGCA-TCCTTGAATGTG
1 CATCGATGCACTCCTTGAATGTG
* * *
753834 CATCGAT--ACACCATGAAGGTG
1 CATCGATGCACTCCTTGAATGTG
*
753855 CACCGATGCACTCCTTGAATGTG
1 CATCGATGCACTCCTTGAATGTG
753878 CATCGATGCAC
1 CATCGATGCAC
753889 AAGGTAATGC
Statistics
Matches: 44, Mismatches: 8, Indels: 5
0.77 0.14 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.34
22 7 0.16
23 21 0.48
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (23 bp):
CATCGATGCACTCCTTGAATGTG
Found at i:753879 original size:44 final size:42
Alignment explanation
Indices: 753790--753884 Score: 129
Period size: 44 Copynumber: 2.2 Consensus size: 42
753780 TTGTGCTTAA
*
753790 TGCATCGATACACCTAACAGTACATCGATGCATCCTTGAATG
1 TGCATCGATACACCTAACAGTACACCGATGCATCCTTGAATG
* *
753832 TGCATCGATACACCATGAA-GGTGCACCGATGCACTCCTTGAATG
1 TGCATCGATACACC-T-AACAGTACACCGATGCA-TCCTTGAATG
753876 TGCATCGAT
1 TGCATCGAT
753885 GCACAAGGTA
Statistics
Matches: 47, Mismatches: 3, Indels: 4
0.87 0.06 0.07
Matches are distributed among these distances:
42 14 0.30
43 12 0.26
44 21 0.45
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.25
Consensus pattern (42 bp):
TGCATCGATACACCTAACAGTACACCGATGCATCCTTGAATG
Found at i:753905 original size:43 final size:42
Alignment explanation
Indices: 753812--753910 Score: 128
Period size: 44 Copynumber: 2.3 Consensus size: 42
753802 CCTAACAGTA
* *
753812 CATCGATGCATCCTTGAATGTGCATCGATACACCATGAAGGTG
1 CATCGATGCATCCTTGAATGTGCATCGATACACAAGGAA-GTG
* *
753855 CACCGATGCACTCCTTGAATGTGCATCGATGCACAAGGTAA-TG
1 CATCGATGCA-TCCTTGAATGTGCATCGATACACAAGG-AAGTG
753898 CATCGATGCATCC
1 CATCGATGCATCC
753911 GTCGGGTTTT
Statistics
Matches: 49, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
42 3 0.06
43 20 0.41
44 24 0.49
45 2 0.04
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (42 bp):
CATCGATGCATCCTTGAATGTGCATCGATACACAAGGAAGTG
Found at i:756587 original size:65 final size:64
Alignment explanation
Indices: 756483--756642 Score: 216
Period size: 65 Copynumber: 2.5 Consensus size: 64
756473 GAATAAATTG
* *
756483 AACATCGAATGCATTTTATGCATCGATGCACATACCATGCATCGTTGCACTCAGGGCT-TTATGA
1 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTCA-GGCTATTATG-
756547 A
64 A
* * * *
756548 AACATCGAATGCATTTGATGCATCGATGCACA-AGTCATGCATTGATGCACTCAGGCTATTTTGA
1 AACATCGAATGCATTTCATGCATCGATGCACATA-CCATGCATCGATGCACTCAGGCTATTATGA
*
756612 AACATCGAATGCACTTCATGCATCGATGCAC
1 AACATCGAATGCATTTCATGCATCGATGCAC
756643 TCTTAGTAAA
Statistics
Matches: 86, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
64 35 0.41
65 51 0.59
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.28
Consensus pattern (64 bp):
AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTCAGGCTATTATGA
Found at i:762385 original size:21 final size:21
Alignment explanation
Indices: 762333--762388 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
762323 AAATACATCC
*
762333 CTCAGTAAAAAGAATCGATCT
1 CTCAGTAAAAAGAATCGATCA
* * * *
762354 CTTAATTAAAAGAATCGCTCA
1 CTCAGTAAAAAGAATCGATCA
762375 CTCAGTGAAAAAGA
1 CTCAGT-AAAAAGA
762389 TTGACCCATT
Statistics
Matches: 26, Mismatches: 8, Indels: 1
0.74 0.23 0.03
Matches are distributed among these distances:
21 20 0.77
22 6 0.23
ACGTcount: A:0.45, C:0.18, G:0.14, T:0.23
Consensus pattern (21 bp):
CTCAGTAAAAAGAATCGATCA
Found at i:762442 original size:21 final size:21
Alignment explanation
Indices: 762391--762444 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
762381 GAAAAAGATT
*
762391 GACCCATTCCTTTAAAGGATC
1 GACCCATTTCTTTAAAGGATC
*
762412 GACCCCTTTCTTTAAAGGATC
1 GACCCATTTCTTTAAAGGATC
762433 GACCCATTTCTT
1 GACCCATTTCTT
762445 GCAACAGTCG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (21 bp):
GACCCATTTCTTTAAAGGATC
Found at i:765308 original size:23 final size:23
Alignment explanation
Indices: 765269--765324 Score: 80
Period size: 23 Copynumber: 2.4 Consensus size: 23
765259 TGCAGGAGGC
765269 ATCGATACCCCCTTTGAATGGGT
1 ATCGATACCCCCTTTGAATGGGT
765292 A-CTGATACCCTCC-TTGAATGGGT
1 ATC-GATACCC-CCTTTGAATGGGT
765315 ATCGATACCC
1 ATCGATACCC
765325 ACACGTGAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
22 1 0.03
23 26 0.87
24 3 0.10
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.29
Consensus pattern (23 bp):
ATCGATACCCCCTTTGAATGGGT
Found at i:773228 original size:21 final size:20
Alignment explanation
Indices: 773189--773237 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
773179 CTCTAAATCA
* *
773189 TTTTTCAAAATTTCATTTTG
1 TTTTTCAAAATCTAATTTTG
773209 TTTTTCAAAATCTAATTTT-
1 TTTTTCAAAATCTAATTTTG
*
773228 TGTTTCAAAA
1 TTTTTCAAAA
773238 GAAAAACGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.31, C:0.10, G:0.04, T:0.55
Consensus pattern (20 bp):
TTTTTCAAAATCTAATTTTG
Found at i:779137 original size:15 final size:15
Alignment explanation
Indices: 779117--779147 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
779107 GGTCTTTTGA
779117 TAACTATTACATCAT
1 TAACTATTACATCAT
779132 TAACTATTACATCAT
1 TAACTATTACATCAT
779147 T
1 T
779148 CTTACTGTCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.39, C:0.19, G:0.00, T:0.42
Consensus pattern (15 bp):
TAACTATTACATCAT
Found at i:780088 original size:22 final size:22
Alignment explanation
Indices: 780063--780120 Score: 107
Period size: 22 Copynumber: 2.6 Consensus size: 22
780053 CAATTTCAAT
780063 TTAATTTAATTTTTGTTACATA
1 TTAATTTAATTTTTGTTACATA
780085 TTAATTTAATTTTTGTTACATA
1 TTAATTTAATTTTTGTTACATA
*
780107 TTAATTTTATTTTT
1 TTAATTTAATTTTT
780121 CTTTGAATTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.29, C:0.03, G:0.03, T:0.64
Consensus pattern (22 bp):
TTAATTTAATTTTTGTTACATA
Found at i:793381 original size:17 final size:16
Alignment explanation
Indices: 793359--793392 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
793349 TAAAAACAGT
793359 AAATAAAAAGATAAATA
1 AAATAAAAAGA-AAATA
*
793376 AAATAAGAAGAAAATA
1 AAATAAAAAGAAAATA
793392 A
1 A
793393 TCCTCACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (16 bp):
AAATAAAAAGAAAATA
Found at i:797277 original size:23 final size:23
Alignment explanation
Indices: 797203--797277 Score: 71
Period size: 23 Copynumber: 3.1 Consensus size: 23
797193 AAGATGAGTA
* *
797203 AAAGAGAGAGAAAAAGTAAAAGTT
1 AAAGAAAGAG-AAAAGAAAAAGTT
* *
797227 AACATGAAAGAGAAAA-AAAATGAAT
1 AA-A-GAAAGAGAAAAGAAAAAG-TT
797252 AAAGAAAGAGAAAAGAAAAAGTT
1 AAAGAAAGAGAAAAGAAAAAGTT
797275 AAA
1 AAA
797278 AAATTTGGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
23 15 0.37
24 12 0.29
25 8 0.20
26 6 0.15
ACGTcount: A:0.68, C:0.01, G:0.20, T:0.11
Consensus pattern (23 bp):
AAAGAAAGAGAAAAGAAAAAGTT
Found at i:805189 original size:111 final size:111
Alignment explanation
Indices: 805027--805260 Score: 339
Period size: 111 Copynumber: 2.1 Consensus size: 111
805017 TGGAAAGTGT
* * * *
805027 ATCCATTAAATCAGGGTAGACTTGTTCCGCTGTCACTTAGGAATATCAAATCTTGAAAGAGAAGG
1 ATCCATTGAATTAGGGCAGACTTGTTCCGCTGTCACTCAGGAATATCAAATCTTGAAAGAGAAGG
* * * *
805092 ATCTATTCCGCTTCTTTGAAAGGGAATATCAGATTTG-AGGGAGTTG
66 ATCTATCCCACTTCTTTGAAAGGGAATATCAAATCTGTA-GGAGTTG
805138 ATCCATTGAATTAGGGCAGACTCT-TT-CGCTGTCACTCAGAGAATATCAAATCTTGAAAGAGAA
1 ATCCATTGAATTAGGGCAGACT-TGTTCCGCTGTCACTCAG-GAATATCAAATCTTGAAAGAGAA
*
805201 GGATCTGTCCCACTTCTTTGAAAGGGAATATCAAATCTGTAGGAGTTG
64 GGATCTATCCCACTTCTTTGAAAGGGAATATCAAATCTGTAGGAGTTG
805249 ATCCATTGAATT
1 ATCCATTGAATT
805261 GGGATCAAAC
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
110 12 0.11
111 97 0.87
112 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.22, T:0.30
Consensus pattern (111 bp):
ATCCATTGAATTAGGGCAGACTTGTTCCGCTGTCACTCAGGAATATCAAATCTTGAAAGAGAAGG
ATCTATCCCACTTCTTTGAAAGGGAATATCAAATCTGTAGGAGTTG
Found at i:814846 original size:12 final size:12
Alignment explanation
Indices: 814829--814860 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
814819 GTTGATGGTA
814829 AAAGAAGAAAAG
1 AAAGAAGAAAAG
*
814841 AAAGAAGAGAAG
1 AAAGAAGAAAAG
814853 AAAGAAGA
1 AAAGAAGA
814861 CAAAAAACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
AAAGAAGAAAAG
Found at i:815584 original size:32 final size:32
Alignment explanation
Indices: 815546--815609 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
815536 TATATTTATT
*
815546 TTATATAGCACTTTAAAGCTTCAATTAAGTTA
1 TTATATAACACTTTAAAGCTTCAATTAAGTTA
815578 TTATATAACACTTTAAAGCTTCAATTAAGTTA
1 TTATATAACACTTTAAAGCTTCAATTAAGTTA
815610 AAAATAAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.39, C:0.12, G:0.08, T:0.41
Consensus pattern (32 bp):
TTATATAACACTTTAAAGCTTCAATTAAGTTA
Found at i:818961 original size:40 final size:39
Alignment explanation
Indices: 818906--819009 Score: 135
Period size: 40 Copynumber: 2.7 Consensus size: 39
818896 TAAAAAACTA
818906 TATATTTATATATGTTTTCAAAATAATATGTTTT-TAAAAAC
1 TATA-TTATATATGTTTTCAAAA-AATAT-TTTTCTAAAAAC
**
818947 TATATTATATATGTTTTCAAAACCT-TTTTTCTAAAAAC
1 TATATTATATATGTTTTCAAAAAATATTTTTCTAAAAAC
818985 TATATT-T-TATGTTTTCAAAAAATAT
1 TATATTATATATGTTTTCAAAAAATAT
819010 ATTATATATG
Statistics
Matches: 57, Mismatches: 4, Indels: 8
0.83 0.06 0.12
Matches are distributed among these distances:
36 14 0.25
37 6 0.11
38 14 0.25
39 1 0.02
40 18 0.32
41 4 0.07
ACGTcount: A:0.39, C:0.08, G:0.04, T:0.49
Consensus pattern (39 bp):
TATATTATATATGTTTTCAAAAAATATTTTTCTAAAAAC
Found at i:818982 original size:38 final size:37
Alignment explanation
Indices: 818868--819004 Score: 129
Period size: 38 Copynumber: 3.6 Consensus size: 37
818858 CAAGATTATA
* * *
818868 TATATTATATAGGTTTTCAAAAACC--GTTTAAAAAAC
1 TATATTATATATGTTTTC-AAAACCTTTTTTTAAAAAC
**
818904 TATATATTTATATATGTTTTCAAAATAATATGTTTTTAAAAAC
1 --TATA-TTATATATGTTTTCAAAA-CCT-T-TTTTTAAAAAC
818947 TATATTATATATGTTTTCAAAACCTTTTTTCTAAAAAC
1 TATATTATATATGTTTTCAAAACCTTTTTT-TAAAAAC
818985 TATATT-T-TATGTTTTCAAAA
1 TATATTATATATGTTTTCAAAA
819005 AATATATTAT
Statistics
Matches: 85, Mismatches: 7, Indels: 16
0.79 0.06 0.15
Matches are distributed among these distances:
36 13 0.15
37 5 0.06
38 22 0.26
39 14 0.16
40 18 0.21
41 4 0.05
43 9 0.11
ACGTcount: A:0.40, C:0.09, G:0.05, T:0.46
Consensus pattern (37 bp):
TATATTATATATGTTTTCAAAACCTTTTTTTAAAAAC
Found at i:819005 original size:22 final size:22
Alignment explanation
Indices: 818973--819038 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 22
818963 TCAAAACCTT
818973 TTTTCTAAAAACTATATTTTATG
1 TTTTC-AAAAACTATATTTTATG
*
818996 TTTTCAAAAAATATATTATATATG
1 TTTTCAAAAACTATATT-T-TATG
*
819020 TTTTCAAAAACCAT-TTTTA
1 TTTTCAAAAACTATATTTTA
819039 AAAAACTATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 2 0.05
22 12 0.32
23 8 0.21
24 16 0.42
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.48
Consensus pattern (22 bp):
TTTTCAAAAACTATATTTTATG
Found at i:819006 original size:24 final size:24
Alignment explanation
Indices: 818973--819029 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
818963 TCAAAACCTT
*
818973 TTTTCTAAAAACTATATT-T-TATG
1 TTTTC-AAAAAATATATTATATATG
818996 TTTTCAAAAAATATATTATATATG
1 TTTTCAAAAAATATATTATATATG
819020 TTTTCAAAAA
1 TTTTCAAAAA
819030 CCATTTTTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
22 11 0.35
23 6 0.19
24 14 0.45
ACGTcount: A:0.42, C:0.07, G:0.04, T:0.47
Consensus pattern (24 bp):
TTTTCAAAAAATATATTATATATG
Found at i:819025 original size:60 final size:62
Alignment explanation
Indices: 818931--819072 Score: 209
Period size: 60 Copynumber: 2.3 Consensus size: 62
818921 TTTCAAAATA
* * *
818931 ATATGTTTTTAAAAACTATATTATATATGTTTTC-AAAACCTTTTTTCTAAAAACTATAT-TT
1 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCATTTTT-AAAAAACTATATATT
*
818992 -TATGTTTTCAAAAAATATATTATATATGTTTTCAAAAACCATTTTTAAAAAACTATATATT
1 ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCATTTTTAAAAAACTATATATT
*
819053 ATATATTTTCAAAAACTATA
1 ATATGTTTTCAAAAACTATA
819073 CTGCATCTTC
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
60 42 0.58
61 13 0.18
62 17 0.24
ACGTcount: A:0.42, C:0.09, G:0.03, T:0.46
Consensus pattern (62 bp):
ATATGTTTTCAAAAACTATATTATATATGTTTTCAAAAACCATTTTTAAAAAACTATATATT
Found at i:819056 original size:38 final size:37
Alignment explanation
Indices: 818996--819068 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
818986 ATATTTTATG
*
818996 TTTTCAAAAAATATATTATATATGTTTTCAAAAACCA
1 TTTTCAAAAAATATATTATATATATTTTCAAAAACCA
*
819033 TTTTTAAAAAACTATA-TATTATATATTTTCAAAAAC
1 TTTTCAAAAAA-TATATTA-TATATATTTTCAAAAAC
819069 TATACTGCAT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
37 12 0.38
38 20 0.62
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (37 bp):
TTTTCAAAAAATATATTATATATATTTTCAAAAACCA
Found at i:820466 original size:20 final size:20
Alignment explanation
Indices: 820441--820495 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
820431 CATAAAAGAG
820441 TAGTATCGATACTATAGTGA
1 TAGTATCGATACTATAGTGA
820461 TAGTATCGATACTATAGTGA
1 TAGTATCGATACTATAGTGA
* *
820481 TAATACCGATACTAT
1 TAGTATCGATACTAT
820496 TGAGCCTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (20 bp):
TAGTATCGATACTATAGTGA
Found at i:821352 original size:21 final size:21
Alignment explanation
Indices: 821305--821425 Score: 86
Period size: 23 Copynumber: 5.6 Consensus size: 21
821295 GGTCCCTCGG
* *
821305 GACATATATGTGCTCTTGGGA
1 GACATATATGTGGTCTTTGGA
*
821326 -ACATATATGTGGTCTTTCGA
1 GACATATATGTGGTCTTTGGA
*
821346 GACATATATTTGGTCCTTTGGAA
1 GACATATATGTGGT-CTTTGG-A
* * *
821369 TATATATATGTGGTCATTAGG-
1 GACATATATGTGGTC-TTTGGA
* *
821390 GACAATTCTATATGGTCCTTTGG-
1 GAC-A-TATATGTGGT-CTTTGGA
821413 GACATATATGTGG
1 GACATATATGTGG
821426 CCCTTCGGGA
Statistics
Matches: 77, Mismatches: 16, Indels: 14
0.72 0.15 0.13
Matches are distributed among these distances:
20 17 0.22
21 20 0.26
22 8 0.10
23 31 0.40
24 1 0.01
ACGTcount: A:0.26, C:0.12, G:0.24, T:0.38
Consensus pattern (21 bp):
GACATATATGTGGTCTTTGGA
Found at i:821420 original size:44 final size:44
Alignment explanation
Indices: 821320--821458 Score: 140
Period size: 44 Copynumber: 3.1 Consensus size: 44
821310 ATATGTGCTC
* * * *
821320 TTGGGAACATATATGTGGTCTTTCGAGAC-A-TATATTTGGTCCT
1 TTGGG-ACATATATGTGGTCATTCGGGACAATTCTATATGGTCCT
* * *
821363 TTGGAATATATATATGTGGTCATTAGGGACAATTCTATATGGTCCT
1 TTGG--GACATATATGTGGTCATTCGGGACAATTCTATATGGTCCT
* *
821409 TTGGGACATATATGTGGCCCTTCGGGACAATTCTATGA-GGTCCT
1 TTGGGACATATATGTGGTCATTCGGGACAATTCTAT-ATGGTCCT
821453 TTGGGA
1 TTGGGA
821459 TAATTTTATA
Statistics
Matches: 79, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
43 4 0.05
44 58 0.73
45 2 0.03
46 15 0.19
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (44 bp):
TTGGGACATATATGTGGTCATTCGGGACAATTCTATATGGTCCT
Found at i:821435 original size:21 final size:21
Alignment explanation
Indices: 821295--821437 Score: 101
Period size: 21 Copynumber: 6.7 Consensus size: 21
821285 GGTTCTACGC
*
821295 GGTCCCTCGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
*
821316 GCT-CTT-GGGAACATATATGT
1 GGTCCTTCGGG-ACATATATGT
* * *
821336 GGTCTTTCGAGACATATATTT
1 GGTCCTTCGGGACATATATGT
* * *
821357 GGTCCTTTGGAATATATATATGT
1 GGTCCTTCGG--GACATATATGT
* * * *
821380 GGTCATTAGGGACAATTCTATAT
1 GGTCCTTCGGGAC-A-TATATGT
*
821403 GGTCCTTTGGGACATATATGT
1 GGTCCTTCGGGACATATATGT
*
821424 GGCCCTTCGGGACA
1 GGTCCTTCGGGACA
821438 ATTCTATGAG
Statistics
Matches: 91, Mismatches: 24, Indels: 14
0.71 0.19 0.11
Matches are distributed among these distances:
19 3 0.03
20 14 0.15
21 38 0.42
22 4 0.04
23 32 0.35
ACGTcount: A:0.23, C:0.17, G:0.25, T:0.35
Consensus pattern (21 bp):
GGTCCTTCGGGACATATATGT
Found at i:821453 original size:23 final size:23
Alignment explanation
Indices: 821388--821463 Score: 77
Period size: 23 Copynumber: 3.4 Consensus size: 23
821378 GTGGTCATTA
821388 GGGACAATTCTAT-ATGGTCCTTT
1 GGGACAATTCTATGA-GGTCCTTT
* * * *
821411 GGGAC-A-TATATGTGGCCCTTC
1 GGGACAATTCTATGAGGTCCTTT
821432 GGGACAATTCTATGAGGTCCTTT
1 GGGACAATTCTATGAGGTCCTTT
*
821455 GGGATAATT
1 GGGACAATT
821464 TTATATGGCA
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
21 15 0.37
22 2 0.05
23 24 0.59
ACGTcount: A:0.22, C:0.17, G:0.26, T:0.34
Consensus pattern (23 bp):
GGGACAATTCTATGAGGTCCTTT
Found at i:821602 original size:5 final size:5
Alignment explanation
Indices: 821594--821618 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
821584 AACAAAGTTC
821594 ATGTG ATGTG ATGTG ATGTG ATGTG
1 ATGTG ATGTG ATGTG ATGTG ATGTG
821619 TGCTTTGTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
ATGTG
Found at i:827060 original size:28 final size:28
Alignment explanation
Indices: 827020--827082 Score: 83
Period size: 28 Copynumber: 2.2 Consensus size: 28
827010 ATTTGTCCTG
827020 TAGAACCATTATGTCCCGAAGGACCACA
1 TAGAACCATTATGTCCCGAAGGACCACA
* *
827048 TAGAACACA-TATGTCCGGTAGGACCACA
1 TAGAAC-CATTATGTCCCGAAGGACCACA
*
827076 TAAAACC
1 TAGAACC
827083 CTATGCCAAC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
27 1 0.03
28 28 0.90
29 2 0.06
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.17
Consensus pattern (28 bp):
TAGAACCATTATGTCCCGAAGGACCACA
Found at i:827335 original size:21 final size:23
Alignment explanation
Indices: 827292--827335 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 23
827282 CATATATTCA
**
827292 CATATATATGTTCTCATGTAATT
1 CATATATATGTTCTCATACAATT
827315 CATAT-TAT-TTCTCATACAATT
1 CATATATATGTTCTCATACAATT
827336 ACTTCACTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 11 0.58
22 3 0.16
23 5 0.26
ACGTcount: A:0.32, C:0.16, G:0.05, T:0.48
Consensus pattern (23 bp):
CATATATATGTTCTCATACAATT
Found at i:835755 original size:36 final size:37
Alignment explanation
Indices: 835704--835871 Score: 150
Period size: 36 Copynumber: 4.6 Consensus size: 37
835694 AGATTATATA
** *
835704 TATTATATACATTTTCAAAAACCGTTTTTTAAAAAAC
1 TATTATATATGTTTTCAAAAAACGTTTTTTAAAAAAC
** *
835741 TA-TATATATGTTTTCAAAATAATATGTTTTTAAAAACC
1 TATTATATATGTTTTCAAAA-AACGT-TTTTTAAAAAAC
*
835779 ATATTATATATGTTTTC-AAAATCGTTTTTT-AAAAAC
1 -TATTATATATGTTTTCAAAAAACGTTTTTTAAAAAAC
* ** *
835815 TA-TATTATATGTTTT-AAAAAATGTTTTCGAAAACTAC
1 TATTA-TATATGTTTTCAAAAAACGTTTTTTAAAA-AAC
835852 -ATTATATATGTTTTCAAAAA
1 TATTATATATGTTTTCAAAAA
835872 CTATACTATA
Statistics
Matches: 106, Mismatches: 15, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
34 2 0.02
35 21 0.20
36 34 0.32
37 18 0.17
38 13 0.12
39 5 0.05
40 13 0.12
ACGTcount: A:0.42, C:0.09, G:0.05, T:0.44
Consensus pattern (37 bp):
TATTATATATGTTTTCAAAAAACGTTTTTTAAAAAAC
Found at i:835881 original size:24 final size:24
Alignment explanation
Indices: 835835--835882 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
835825 GTTTTAAAAA
* *
835835 ATGTTTTCGAAAACTACATTATAT
1 ATGTTTTCAAAAACTACACTATAT
*
835859 ATGTTTTCAAAAACTATACTATAT
1 ATGTTTTCAAAAACTACACTATAT
835883 CTTCAAAAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.12, G:0.06, T:0.42
Consensus pattern (24 bp):
ATGTTTTCAAAAACTACACTATAT
Found at i:835889 original size:20 final size:19
Alignment explanation
Indices: 835854--835901 Score: 69
Period size: 20 Copynumber: 2.5 Consensus size: 19
835844 AAAACTACAT
* *
835854 TATATATGTTTTCAAAAAC
1 TATATATATCTTCAAAAAC
835873 TATACTATATCTTCAAAAAC
1 TATA-TATATCTTCAAAAAC
835893 TATATATAT
1 TATATATAT
835902 TATAAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 9 0.35
20 17 0.65
ACGTcount: A:0.44, C:0.12, G:0.02, T:0.42
Consensus pattern (19 bp):
TATATATATCTTCAAAAAC
Found at i:835924 original size:2 final size:2
Alignment explanation
Indices: 835917--835968 Score: 104
Period size: 2 Copynumber: 26.0 Consensus size: 2
835907 ATTTTGAAAT
835917 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
835959 TA TA TA TA TA
1 TA TA TA TA TA
835969 AGTAAAGAAG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:840166 original size:21 final size:21
Alignment explanation
Indices: 840142--840202 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
840132 TTTTTTTTAC
840142 AAGGGATTGATCATTTTTCAA
1 AAGGGATTGATCATTTTTCAA
* *
840163 AAGGAATTAAT-ACTTTTTCAA
1 AAGGGATTGATCA-TTTTTCAA
* * *
840184 AAGAGATCGATCAATTTTC
1 AAGGGATTGATCATTTTTC
840203 TCGAAGATGT
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 29 0.94
22 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (21 bp):
AAGGGATTGATCATTTTTCAA
Found at i:841672 original size:3 final size:3
Alignment explanation
Indices: 841659--841688 Score: 53
Period size: 3 Copynumber: 10.3 Consensus size: 3
841649 AGTTTATTTT
841659 TAA TAA T-A TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
841689 TGTTCCGGTG
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.08
3 24 0.92
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:843560 original size:148 final size:148
Alignment explanation
Indices: 843292--843587 Score: 540
Period size: 148 Copynumber: 2.0 Consensus size: 148
843282 TTTGACTCTC
* *
843292 ATATAGGATAACACTTGCTTCCAACGATACATGAATCTTACCCATTCTTGGCATGCAGCAATTTG
1 ATATAGGATAACACTTGCTTCCAACAATACATGAATCTTACCCATTCTTGGCATGCAACAATTTG
*
843357 GTAAGGAAAGGGAAACACAATATATGTAATATAATATAGAGTTTTGGTACATTTACGCATAGTAT
66 GTAAGGAAAGGGAAAAACAATATATGTAATATAATATAGAGTTTTGGTACATTTACGCATAGTAT
843422 ATAGACCTTATGTTAGAT
131 ATAGACCTTATGTTAGAT
*
843440 ATATAGGATAACACTTGCTTCCAACAATACATGAATCTTACTCATTCTTGGCATGCAACAATTTG
1 ATATAGGATAACACTTGCTTCCAACAATACATGAATCTTACCCATTCTTGGCATGCAACAATTTG
843505 GTAAGGAAA-GGAAAGAACAATATATGTAATATAATATAGAGTTTTGGTACATTTACGCATAGTA
66 GTAAGGAAAGGGAAA-AACAATATATGTAATATAATATAGAGTTTTGGTACATTTACGCATAGTA
843569 TATAGACCTTATGTTAGAT
130 TATAGACCTTATGTTAGAT
843588 TATTGTTGAT
Statistics
Matches: 143, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
147 5 0.03
148 138 0.97
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (148 bp):
ATATAGGATAACACTTGCTTCCAACAATACATGAATCTTACCCATTCTTGGCATGCAACAATTTG
GTAAGGAAAGGGAAAAACAATATATGTAATATAATATAGAGTTTTGGTACATTTACGCATAGTAT
ATAGACCTTATGTTAGAT
Found at i:845726 original size:12 final size:11
Alignment explanation
Indices: 845709--845774 Score: 59
Period size: 10 Copynumber: 6.0 Consensus size: 11
845699 GACTTAAGAT
845709 AATAATAATGAA
1 AATAATAAT-AA
845721 AATAATAATTTAA
1 AATAATAA--TAA
845734 ACAT-ATAA-AA
1 A-ATAATAATAA
845744 AATAAT-ATAA
1 AATAATAATAA
*
845754 AACAA-AATAA
1 AATAATAATAA
845764 AATAATAATAA
1 AATAATAATAA
845775 TCAAAATGAA
Statistics
Matches: 45, Mismatches: 2, Indels: 15
0.73 0.03 0.24
Matches are distributed among these distances:
9 3 0.07
10 19 0.42
11 5 0.11
12 8 0.18
13 7 0.16
14 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.02, T:0.26
Consensus pattern (11 bp):
AATAATAATAA
Found at i:845745 original size:23 final size:24
Alignment explanation
Indices: 845719--845780 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
845709 AATAATAATG
* *
845719 AAAATAATAATTTAAAC-ATATAA
1 AAAATAATAATTAAAACAAAATAA
845742 AAAATAAT-A-TAAAACAAAATAA
1 AAAATAATAATTAAAACAAAATAA
*
845764 AATAATAATAATCAAAA
1 AA-AATAATAATTAAAA
845781 TGAAAGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
21 5 0.16
22 8 0.25
23 14 0.44
24 1 0.03
25 4 0.12
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (24 bp):
AAAATAATAATTAAAACAAAATAA
Found at i:845885 original size:33 final size:35
Alignment explanation
Indices: 845829--845895 Score: 120
Period size: 33 Copynumber: 2.0 Consensus size: 35
845819 TATCAAACTG
845829 TTAGGGATTGAAATATAAAATATATAAATTAATAC
1 TTAGGGATTGAAATATAAAATATATAAATTAATAC
845864 TTAGGGATT-AAA-ATAAAATATATAAATTAATA
1 TTAGGGATTGAAATATAAAATATATAAATTAATA
845896 GCCTAATTCA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 20 0.62
34 3 0.09
35 9 0.28
ACGTcount: A:0.54, C:0.01, G:0.10, T:0.34
Consensus pattern (35 bp):
TTAGGGATTGAAATATAAAATATATAAATTAATAC
Found at i:847046 original size:3 final size:3
Alignment explanation
Indices: 847038--847093 Score: 60
Period size: 3 Copynumber: 19.0 Consensus size: 3
847028 TAAAATTATT
* * * *
847038 TAA TAA TAA TAA TAA -AA TAA TTA TAA TTA TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
847085 AAA TAA TAA
1 TAA TAA TAA
847094 AACCGGGATA
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
2 2 0.05
3 42 0.95
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:847699 original size:20 final size:21
Alignment explanation
Indices: 847676--847718 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
847666 GTTGAACAAG
847676 TTCTTCTCATTATGAACTTCTTC
1 TTCTTCTCATTATGAA--TCTTC
847699 TTCTTCTCATTATGAA-CTTC
1 TTCTTCTCATTATGAATCTTC
847719 AGGTGCTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
23 16 0.80
ACGTcount: A:0.19, C:0.26, G:0.05, T:0.51
Consensus pattern (21 bp):
TTCTTCTCATTATGAATCTTC
Found at i:847982 original size:36 final size:35
Alignment explanation
Indices: 847942--848057 Score: 99
Period size: 36 Copynumber: 3.2 Consensus size: 35
847932 AGTGAAACTG
847942 TCTCAAGCGAGACAAATCTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGACAAAT-TTGTTTTAAGAAAAACAA
* * *** * *
847978 TCTCAAGTGAGATAAATTGTTGTTTCGGGAGAAACTA
1 TCTCAAGCGAGACAAA-T-TTGTTTTAAGAAAAACAA
* *
848015 TCTCAAGCGAAATGC-AGTTTGTTTTAAGAAAAACAA
1 TCTCAAGCGAGA--CAAATTTGTTTTAAGAAAAACAA
848051 TCTCAAG
1 TCTCAAG
848058 TTAGATAAAT
Statistics
Matches: 60, Mismatches: 17, Indels: 6
0.72 0.20 0.07
Matches are distributed among these distances:
36 34 0.57
37 25 0.42
38 1 0.02
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.28
Consensus pattern (35 bp):
TCTCAAGCGAGACAAATTTGTTTTAAGAAAAACAA
Found at i:848970 original size:22 final size:22
Alignment explanation
Indices: 848911--848974 Score: 67
Period size: 22 Copynumber: 2.9 Consensus size: 22
848901 GAAATCCAAT
* * *
848911 AAATCTTTCATCTTTTAAAAGA
1 AAATCTATCATCTTTGAAGAGA
*
848933 GAATCTATCA-CATTTGAAGAGA
1 AAATCTATCATC-TTTGAAGAGA
*
848955 AAATTTATCATCTTTGAAGA
1 AAATCTATCATCTTTGAAGA
848975 ATGTAGATGT
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 1 0.03
22 32 0.94
23 1 0.03
ACGTcount: A:0.41, C:0.12, G:0.11, T:0.36
Consensus pattern (22 bp):
AAATCTATCATCTTTGAAGAGA
Found at i:856435 original size:43 final size:43
Alignment explanation
Indices: 856367--856448 Score: 128
Period size: 43 Copynumber: 1.9 Consensus size: 43
856357 TGCATCAAAC
*
856367 AAAACTTTACATATATGGGACAACTTTCAATCCTAACTTCAAT
1 AAAACTTTACATATAGGGGACAACTTTCAATCCTAACTTCAAT
* **
856410 AAAACTTTACATATAGGGGATAACTTTCCCTCCTAACTT
1 AAAACTTTACATATAGGGGACAACTTTCAATCCTAACTT
856449 TCTAAAGCCA
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.37, C:0.22, G:0.09, T:0.33
Consensus pattern (43 bp):
AAAACTTTACATATAGGGGACAACTTTCAATCCTAACTTCAAT
Found at i:858694 original size:2 final size:2
Alignment explanation
Indices: 858687--858718 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
858677 AAATAAATAA
858687 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
858719 GATAAGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:858793 original size:6 final size:5
Alignment explanation
Indices: 858759--858810 Score: 50
Period size: 5 Copynumber: 9.8 Consensus size: 5
858749 ACATATATAA
* * *
858759 AAAAT AATAT AAAAT AAAAT AATAAT CAAAAT CAAAAT GAAAT AAATT
1 AAAAT AAAAT AAAAT AAAAT AA-AAT -AAAAT -AAAAT AAAAT AAAAT
858807 AAAA
1 AAAA
858811 GCAATAATAT
Statistics
Matches: 39, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
5 25 0.64
6 12 0.31
7 2 0.05
ACGTcount: A:0.71, C:0.04, G:0.02, T:0.23
Consensus pattern (5 bp):
AAAAT
Found at i:859357 original size:14 final size:14
Alignment explanation
Indices: 859338--859364 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
859328 TAACCGGCCC
859338 TTTATCAGCTCTCT
1 TTTATCAGCTCTCT
859352 TTTATCAGCTCTC
1 TTTATCAGCTCTC
859365 AACGGAGAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.30, G:0.07, T:0.48
Consensus pattern (14 bp):
TTTATCAGCTCTCT
Found at i:860051 original size:3 final size:3
Alignment explanation
Indices: 860008--860063 Score: 51
Period size: 3 Copynumber: 19.0 Consensus size: 3
859998 ATAAATTATT
* * * * *
860008 TAA TAA TAC TAA TAA -AA TAA TTA TAA TTA TAA TTA TTA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
860055 AAA TAA TAA
1 TAA TAA TAA
860064 AACCGGGATA
Statistics
Matches: 42, Mismatches: 10, Indels: 2
0.78 0.19 0.04
Matches are distributed among these distances:
2 2 0.05
3 40 0.95
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:865938 original size:21 final size:21
Alignment explanation
Indices: 865914--865954 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
865904 TTTTGCATTT
865914 TATCATTTTATCG-GTTTTTTC
1 TATCATTTTAT-GAGTTTTTTC
*
865935 TATCTTTTTATGAGTTTTTT
1 TATCATTTTATGAGTTTTTT
865955 AACCCGACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.15, C:0.10, G:0.10, T:0.66
Consensus pattern (21 bp):
TATCATTTTATGAGTTTTTTC
Found at i:867477 original size:17 final size:17
Alignment explanation
Indices: 867430--867477 Score: 53
Period size: 17 Copynumber: 2.8 Consensus size: 17
867420 TTTAAAAAAT
** *
867430 ATATTTTATACTTCTAA
1 ATATTTTATTTTTGTAA
867447 AT-TTTTATTATTTGTAA
1 ATATTTTATT-TTTGTAA
867464 ATATTTTATTTTTG
1 ATATTTTATTTTTG
867478 GTTTTTTACA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
16 6 0.23
17 13 0.50
18 7 0.27
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.62
Consensus pattern (17 bp):
ATATTTTATTTTTGTAA
Found at i:867616 original size:22 final size:22
Alignment explanation
Indices: 867572--867616 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
867562 TTCTGCCATT
**
867572 TAATTTAATAAAAAAATTCAAA
1 TAATTTAATAAAAAAATAAAAA
867594 TAATTTAATAAAAATAA-AAAAA
1 TAATTTAATAAAAA-AATAAAAA
867616 T
1 T
867617 CCAAAAATAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 18 0.90
23 2 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TAATTTAATAAAAAAATAAAAA
Found at i:869714 original size:23 final size:23
Alignment explanation
Indices: 869679--869735 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
869669 TTATCGCAAG
*
869679 GTAATTTTTTAAAATT-ATTTTTT
1 GTAA-TTTTTAAAATTGAATTTTT
869702 GTGAATTTTT-AAATTGAATTTTT
1 GT-AATTTTTAAAATTGAATTTTT
*
869725 GTATTTTTTAA
1 GTAATTTTTAA
869736 TTTTTGACGT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
22 11 0.38
23 16 0.55
24 2 0.07
ACGTcount: A:0.30, C:0.00, G:0.09, T:0.61
Consensus pattern (23 bp):
GTAATTTTTAAAATTGAATTTTT
Found at i:876541 original size:15 final size:15
Alignment explanation
Indices: 876521--876549 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
876511 GAAAAATAAT
876521 GAGTCATCAACAGAG
1 GAGTCATCAACAGAG
876536 GAGTCATCAACAGA
1 GAGTCATCAACAGA
876550 AATAAATAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.14
Consensus pattern (15 bp):
GAGTCATCAACAGAG
Found at i:878640 original size:18 final size:19
Alignment explanation
Indices: 878619--878656 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
878609 TATCAAACCT
878619 AAAATGG-GTATCGATACC
1 AAAATGGAGTATCGATACC
878637 AAAATGGAGTATCGATACC
1 AAAATGGAGTATCGATACC
878656 A
1 A
878657 TAGTATAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 7 0.37
19 12 0.63
ACGTcount: A:0.42, C:0.16, G:0.21, T:0.21
Consensus pattern (19 bp):
AAAATGGAGTATCGATACC
Found at i:878694 original size:95 final size:94
Alignment explanation
Indices: 878476--878696 Score: 239
Period size: 94 Copynumber: 2.3 Consensus size: 94
878466 ATCGATGAGG
* * * * * * *
878476 TAGTATCGATACCATGGTAAGGGTATCGATATCAGGAAACATCGAATCTAAAATTGGTATCGATA
1 TAGTATCCATACCAGGGTAAGAGTATCGATACCAGGAAACATCAAACCTAAAATGGGTATCGATA
** * * *
878541 CCGGAAGGGGTATCGGTACTATAGTATGA
66 CCAAAAGGAGTATCGATACCATAGTATGA
* * * *
878570 TAGTATCCATACCATGGTAAGGGTATCGATACCAGGCAATATCAAACCTAAAATGGGTATCGATA
1 TAGTATCCATACCAGGGTAAGAGTATCGATACCAGGAAACATCAAACCTAAAATGGGTATCGATA
878635 CCAAAATGGAGTATCGATACCATAGTATAGA
66 CCAAAA-GGAGTATCGATACCATAGTAT-GA
**
878666 -AGTATCGGTACCAGGGT-AGTAGTATCGATAC
1 TAGTATCCATACCAGGGTAAG-AGTATCGATAC
878697 TATTGAGCTT
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
94 64 0.59
95 42 0.39
96 2 0.02
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (94 bp):
TAGTATCCATACCAGGGTAAGAGTATCGATACCAGGAAACATCAAACCTAAAATGGGTATCGATA
CCAAAAGGAGTATCGATACCATAGTATGA
Found at i:879278 original size:78 final size:79
Alignment explanation
Indices: 879100--879306 Score: 301
Period size: 78 Copynumber: 2.6 Consensus size: 79
879090 GAATGAATGA
* * * *
879100 ATAAAAGAATAATGCATATAGGTGCATTATTGGCATGAAAAGATGACATAGCTGAAATGGATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
* *
879165 GGTGCATTCTTAGC
66 AGTGCATTCTGAGC
* *
879179 ATAAAAGAATAATTCACATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTG-AATGCATATG
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
879243 AGTGCATTCTCGA-C
66 AGTGCATTCT-GAGC
* *
879257 ATAAAAGAATAATGCATATGGGTGCATTATTGGAATGAAAGAATGCCATA
1 ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATA
879307 ATTGAAAATG
Statistics
Matches: 115, Mismatches: 12, Indels: 3
0.88 0.09 0.02
Matches are distributed among these distances:
78 65 0.57
79 50 0.43
ACGTcount: A:0.38, C:0.12, G:0.23, T:0.27
Consensus pattern (79 bp):
ATAAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCATAGCTGAAATGCATATG
AGTGCATTCTGAGC
Found at i:879436 original size:20 final size:20
Alignment explanation
Indices: 879411--879582 Score: 83
Period size: 20 Copynumber: 7.5 Consensus size: 20
879401 ATTGAAAATT
*
879411 CATGAACGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
* *
879431 CATGAAAGGATTTCATAATTAAAAATG
1 CATGAAAGGA-TGC---ATT---AAGG
*
879458 CATGAATGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
879478 CATGAAAGGATGCCATAACTAAAAATG
1 CATGAAAGGATG-CAT---T---AAGG
*
879505 CATGAACGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
*
879525 CATGAAAGGATGCCATAACTAAAAATG
1 CATGAAAGGATG-CAT---T---AAGG
*
879552 CATGAACGGATGCATTAAGG
1 CATGAAAGGATGCATTAAGG
879572 CATGAAAGGAT
1 CATGAAAGGAT
879583 ACCGTAATTG
Statistics
Matches: 116, Mismatches: 15, Indels: 42
0.67 0.09 0.24
Matches are distributed among these distances:
20 50 0.43
21 8 0.07
23 5 0.04
24 5 0.04
26 8 0.07
27 40 0.34
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.22
Consensus pattern (20 bp):
CATGAAAGGATGCATTAAGG
Done.