Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009063.1 Hibiscus syriacus cultivar Beakdansim tig00112486_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: 79026
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:1564 original size:14 final size:15
Alignment explanation
Indices: 1545--1581 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
1535 CTTTTCAAAT
1545 TTTTTATA-TTTATA
1 TTTTTATATTTTATA
1559 TTTTTATATTTTATA
1 TTTTTATATTTTATA
1574 TGTTTTAT
1 T-TTTTAT
1582 TTGCAAGTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 8 0.38
15 7 0.33
16 6 0.29
ACGTcount: A:0.24, C:0.00, G:0.03, T:0.73
Consensus pattern (15 bp):
TTTTTATATTTTATA
Found at i:12119 original size:12 final size:12
Alignment explanation
Indices: 12102--12171 Score: 72
Period size: 12 Copynumber: 5.9 Consensus size: 12
12092 ATGCTTGAAG
*
12102 AAAAAAA-AAGA
1 AAAAAAAGAAAA
12113 AAAAAAAGAAAA
1 AAAAAAAGAAAA
*
12125 AAAAAAAGAAAG
1 AAAAAAAGAAAA
12137 AAAAAAAGAAAA
1 AAAAAAAGAAAA
* *
12149 TGAAAAAAG-AGA
1 -AAAAAAAGAAAA
*
12161 AGAAAAAGAAA
1 AAAAAAAGAAA
12172 GGGGTCAAGG
Statistics
Matches: 48, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
11 13 0.27
12 28 0.58
13 7 0.15
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.01
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:12136 original size:25 final size:26
Alignment explanation
Indices: 12102--12172 Score: 94
Period size: 24 Copynumber: 2.8 Consensus size: 26
12092 ATGCTTGAAG
12102 AAAAAA-AAAGAAAAAAAAGAAAA-A
1 AAAAAAGAAAGAAAAAAAAGAAAATA
*
12126 AAAAAAGAAAG-AAAAAAAGAAAATG
1 AAAAAAGAAAGAAAAAAAAGAAAATA
12151 AAAAAAGAGAAGAAAAAGAAAG
1 AAAAAAGA-AAGAAAAA-AAAG
12173 GGGTCAAGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 6
0.85 0.02 0.12
Matches are distributed among these distances:
24 18 0.44
25 12 0.29
26 3 0.07
27 4 0.10
28 4 0.10
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.01
Consensus pattern (26 bp):
AAAAAAGAAAGAAAAAAAAGAAAATA
Found at i:13234 original size:52 final size:52
Alignment explanation
Indices: 13110--13560 Score: 777
Period size: 52 Copynumber: 8.8 Consensus size: 52
13100 TATGTGCTCA
* * *
13110 ATAGCATCTTCTGGAAGTGTTATTTAAGTTATCTGATCTGGTTAGA-AGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
13161 ATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
13213 ATAGCATCTTCTGGAAGTGTTATTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
13265 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
13317 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
13369 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
*
13421 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAT
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
13473 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATC----TGGACAGAAC
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
* * *
13521 ATAGCATCTTCTTGAAGTTTTCTTTGAGTTATCTAATCTG
1 ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
13561 ATTAGACATA
Statistics
Matches: 387, Mismatches: 10, Indels: 7
0.96 0.02 0.02
Matches are distributed among these distances:
48 44 0.11
51 44 0.11
52 299 0.77
ACGTcount: A:0.24, C:0.14, G:0.24, T:0.38
Consensus pattern (52 bp):
ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTGGACAGAAC
Found at i:14415 original size:119 final size:118
Alignment explanation
Indices: 14194--14644 Score: 777
Period size: 119 Copynumber: 3.8 Consensus size: 118
14184 CAAATATTCA
* *
14194 AATTCATCACTTGATGGATCATCATTTCCAGAGAAAGAGTTCATAATGAGAAGAACTCGTCATCT
1 AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
14259 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
14312 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC-AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
14377 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
14431 AATTCATCAAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
1 AATTCATC-AATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATC
*
14496 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTG
65 TGAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
* * * *
14550 AATTCATCAGTTGATGGATCAACATTACCAG-GTAA-AGTTCATAATGAGAAGAA--C-TCATCT
1 AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
*
14610 GAAGAAGGAAGAAAAAGTTCATAATGAGAAGAACT
66 GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACT
14645 CATCAAGAGC
Statistics
Matches: 323, Mismatches: 9, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
113 39 0.12
114 1 0.00
116 18 0.06
117 3 0.01
118 28 0.09
119 234 0.72
ACGTcount: A:0.38, C:0.14, G:0.21, T:0.27
Consensus pattern (118 bp):
AATTCATCAATTGATGGATCATCATTTCCAGAGGAAGAGTTCATAATGAGAAGAACTCGTCATCT
GAAGAAGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTGCTTG
Found at i:14907 original size:3 final size:3
Alignment explanation
Indices: 14893--14973 Score: 90
Period size: 3 Copynumber: 27.0 Consensus size: 3
14883 TTTATCCATT
* * * *
14893 TTA TTA TCA TTA TTA TTA ATA TTA TTA TTA TCA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * *
14941 TCA TTA TTT TTA TTA TTA TTA TTT TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
14974 AATATATTAA
Statistics
Matches: 64, Mismatches: 14, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 64 1.00
ACGTcount: A:0.32, C:0.04, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:14908 original size:12 final size:12
Alignment explanation
Indices: 14884--14959 Score: 75
Period size: 12 Copynumber: 6.3 Consensus size: 12
14874 ATACTATTTT
14884 TTATCCATT-TTA
1 TTAT-CATTATTA
14896 TTATCATTATTA
1 TTATCATTATTA
14908 TTAAT-ATTATTA
1 TT-ATCATTATTA
14920 TTATCATTATTA
1 TTATCATTATTA
* * *
14932 ATATTATTATCA
1 TTATCATTATTA
**
14944 TTATTTTTATTA
1 TTATCATTATTA
14956 TTAT
1 TTAT
14960 TATTTTTTTT
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
11 6 0.11
12 47 0.85
13 2 0.04
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.61
Consensus pattern (12 bp):
TTATCATTATTA
Found at i:16410 original size:22 final size:20
Alignment explanation
Indices: 16369--16413 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
16359 ATAGAATTAT
**
16369 TATTTTATTATATTGTTAAA
1 TATTTTATTATATTCATAAA
16389 TATTTTGATATATATTCATAAA
1 TATTTT-AT-TATATTCATAAA
16411 TAT
1 TAT
16414 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 2 0.10
22 13 0.62
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (20 bp):
TATTTTATTATATTCATAAA
Found at i:17522 original size:16 final size:18
Alignment explanation
Indices: 17493--17531 Score: 64
Period size: 16 Copynumber: 2.3 Consensus size: 18
17483 AATTTCAAGA
17493 AAATATATTAATTTTTAT
1 AAATATATTAATTTTTAT
17511 AAATATA-T-ATTTTTAT
1 AAATATATTAATTTTTAT
17527 AAATA
1 AAATA
17532 AGATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (18 bp):
AAATATATTAATTTTTAT
Found at i:17537 original size:17 final size:16
Alignment explanation
Indices: 17503--17539 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
17493 AAATATATTA
*
17503 ATTTTTATAAATATAT
1 ATTTTTATAAATAGAT
17519 ATTTTTATAAATAAGAT
1 ATTTTTATAAAT-AGAT
17536 ATTT
1 ATTT
17540 ATTTATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTTTATAAATAGAT
Found at i:17759 original size:139 final size:139
Alignment explanation
Indices: 17550--17831 Score: 383
Period size: 139 Copynumber: 2.0 Consensus size: 139
17540 ATTTATTTAG
*
17550 AAATATCAGAAAAAGGCTTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATTAAAAAATAAAT
1 AAATATCAGAAAAAGGATTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATTAAAAAATAAAT
*
17615 AAATAACTAAAACATTTTCTTAAAATAATAAT-AATAAA-AAAATATTTTAATATAGTAAGATAT
66 AAATAACT-AAACA-TTTCTTAAAATAAGAATAAATAAATAAAATATTTTAATATA-TAAGATAT
17678 TTATTTATTTAA
128 TTATTTATTTAA
* * *
17690 AAATATCAG-AAAGGGATTCTAGTTGTTTTAAGACAACTCTTTTCTTCGAT-TTAAAAAAATAAA
1 AAATATCAGAAAAAGGATTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATT-AAAAAATAAA
* * *
17753 TAAATAACTAAATATTTCTTAAAATAAGAATAAAATAAATTTAAAATATATATAATTTATAAGGA
65 TAAATAACTAAACATTTCTTAAAATAAGAAT-AAATAAA--TAAAATAT-TTTAATATATAA-GA
17818 TATTTATTTATTTA
125 TATTTATTTATTTA
17832 TTTAAACAAA
Statistics
Matches: 126, Mismatches: 8, Indels: 13
0.86 0.05 0.09
Matches are distributed among these distances:
137 16 0.13
138 6 0.05
139 62 0.49
140 9 0.07
142 10 0.08
143 23 0.18
ACGTcount: A:0.48, C:0.07, G:0.07, T:0.38
Consensus pattern (139 bp):
AAATATCAGAAAAAGGATTCTAGTTGCTTTAAGACAACTCTTTTATTCGATATTAAAAAATAAAT
AAATAACTAAACATTTCTTAAAATAAGAATAAATAAATAAAATATTTTAATATATAAGATATTTA
TTTATTTAA
Found at i:17929 original size:25 final size:24
Alignment explanation
Indices: 17862--17923 Score: 69
Period size: 25 Copynumber: 2.7 Consensus size: 24
17852 TATGACTAAG
17862 ATAATAATAA-ATA-AT-AAAAGTA
1 ATAATAA-AATATATATCAAAAGTA
*
17884 ATAATTTAAATATATATCAAAAGTA
1 ATAA-TAAAATATATATCAAAAGTA
17909 ATAATAAAATA-ATAT
1 ATAATAAAATATATAT
17924 TACAAATGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
22 6 0.18
23 9 0.26
24 8 0.24
25 11 0.32
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (24 bp):
ATAATAAAATATATATCAAAAGTA
Found at i:18210 original size:2 final size:2
Alignment explanation
Indices: 18203--18262 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
18193 CCTAAAATAA
18203 AT AT AT AT AT 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 AT AT AT AT AT
18245 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
18263 TGCAATGACT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19091 original size:24 final size:24
Alignment explanation
Indices: 19057--19121 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
19047 GTGCAGCTGC
*
19057 GACGTGTAGGGGCTGCTGGTGAGG
1 GACGTGGAGGGGCTGCTGGTGAGG
* *
19081 GACGTGGAGGGGCTACTGGTGTGG
1 GACGTGGAGGGGCTGCTGGTGAGG
19105 GACGTGGAGGGGCTGCT
1 GACGTGGAGGGGCTGCT
19122 CGGGTAAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.12, C:0.14, G:0.54, T:0.20
Consensus pattern (24 bp):
GACGTGGAGGGGCTGCTGGTGAGG
Found at i:19630 original size:45 final size:45
Alignment explanation
Indices: 19563--19683 Score: 179
Period size: 45 Copynumber: 2.7 Consensus size: 45
19553 GAGGTCTTAT
* * * *
19563 CATCTTGCACTGTAGGTTTTACAGATGACCCGAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
*
19608 CATCATGCACTGAAGGACTTACAGATGACCCAAAGGTTTTGAAAA
1 CATCATGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
* *
19653 CATCATGCACTAAAGGTCTTACAAATGACCC
1 CATCATGCACTGAAGGTCTTACAGATGACCC
19684 TGAGGCTTTA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 68 1.00
ACGTcount: A:0.34, C:0.21, G:0.19, T:0.26
Consensus pattern (45 bp):
CATCATGCACTGAAGGTCTTACAGATGACCCAAAGGTTTTGAAAA
Found at i:19811 original size:76 final size:74
Alignment explanation
Indices: 19644--20203 Score: 922
Period size: 74 Copynumber: 7.5 Consensus size: 74
19634 GACCCAAAGG
** *
19644 TTTTGAAAACATCATGCACTAAAGGTCTTACAAATGACCCTGAGGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
19709 CCGAAGGCT
66 CCGAAGGCT
* * *
19718 TTTTGAAAACATCATGCACTGTAGGTCATACAGATGACCCTAAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATATCAAAAAGC
**
19783 TCATGAAGGCT
64 TCCCGAAGGCT
* *
19794 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATATCAAAAAGC
*
19859 TCCCAAAGGCT
64 TCCCGAAGGCT
19870 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
19935 CCGAAGGCT
66 CCGAAGGCT
*
19944 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATATCAAAAAGC
*
20009 TCCCAAAGGCT
64 TCCCGAAGGCT
20020 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
*
20085 CTGAAGGCT
66 CCGAAGGCT
*
20094 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAAGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
20159 CCGAAGGCT
66 CCGAAGGCT
*
20168 TTTTGAAAACATCATGCACTATAGGTCTTACAGATG
1 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
20204 TGGGAAATAG
Statistics
Matches: 457, Mismatches: 25, Indels: 8
0.93 0.05 0.02
Matches are distributed among these distances:
74 245 0.54
76 212 0.46
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (74 bp):
TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATCAAAAAGCTC
CCGAAGGCT
Found at i:19941 original size:150 final size:148
Alignment explanation
Indices: 19644--20203 Score: 931
Period size: 150 Copynumber: 3.7 Consensus size: 148
19634 GACCCAAAGG
* * *
19644 TTTTGAAAACATCATGCACTAAAGGTCTTACAAATGACCCTGAGGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAACATCAAAAAGCTC
* * * *
19709 CCGAAGGCTTTTTGAAAACATCATGCACTGTAGGTCATACAGATGACCCTAAGGCTTTAAAAACA
66 CCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTT--AAATA
*
19774 TCAAAAAGCTCATGAAGGCT
129 TCAAAAAGCTCCTGAAGGCT
19794 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTT--AAACATCAAAAAGC
19859 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
64 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
*
19924 TCAAAAAGCTCCCGAAGGCT
129 TCAAAAAGCTCCTGAAGGCT
*
19944 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAAAACATCAAAAAGC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTT--AAACATCAAAAAGC
20009 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
64 TCCCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATA
20074 TCAAAAAGCTCCTGAAGGCT
129 TCAAAAAGCTCCTGAAGGCT
* * *
20094 TTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAAGCTTTAAATATCAAAAAGCTC
1 TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAACATCAAAAAGCTC
* *
20159 CCGAAGGCTTTTTGAAAACATCATGCACTATAGGTCTTACAGATG
66 CCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATG
20204 TGGGAAATAG
Statistics
Matches: 393, Mismatches: 15, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
148 58 0.15
150 265 0.67
152 70 0.18
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (148 bp):
TTTTGAAAACATCATGCACTATAGGTCTTACAGATGACCCTGAGGCTTTAAACATCAAAAAGCTC
CCAAAGGCTTTTTGAAAACATCATGCACTGTAGGTCTTACAGATGACCCTGAGGCTTTAAATATC
AAAAAGCTCCTGAAGGCT
Found at i:27539 original size:14 final size:15
Alignment explanation
Indices: 27520--27557 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
27510 ATGTAAGTGT
*
27520 AAATACAAACAT-AA
1 AAATACAAAAATGAA
*
27534 AAATACAAAAATGCA
1 AAATACAAAAATGAA
27549 AAATACAAA
1 AAATACAAA
27558 TGCATGTATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 11 0.52
15 10 0.48
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (15 bp):
AAATACAAAAATGAA
Found at i:30430 original size:18 final size:16
Alignment explanation
Indices: 30407--30445 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 16
30397 AATTTCAAGA
30407 AAATATATTAATTTTTAT
1 AAATATA-T-ATTTTTAT
30425 AAATATATATTTTTAT
1 AAATATATATTTTTAT
30441 AAATA
1 AAATA
30446 AGATATTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 13 0.62
17 1 0.05
18 7 0.33
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
AAATATATATTTTTAT
Found at i:30451 original size:17 final size:16
Alignment explanation
Indices: 30417--30453 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
30407 AAATATATTA
*
30417 ATTTTTATAAATATAT
1 ATTTTTATAAATAGAT
30433 ATTTTTATAAATAAGAT
1 ATTTTTATAAAT-AGAT
30450 ATTT
1 ATTT
30454 ATTTATTTAG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
ATTTTTATAAATAGAT
Found at i:30670 original size:140 final size:142
Alignment explanation
Indices: 30443--30750 Score: 462
Period size: 140 Copynumber: 2.2 Consensus size: 142
30433 ATTTTTATAA
* * *
30443 ATAAGATATTTATTTATTTAGAAATATCAGAAAATGGCTTCTAGTTGCTTTAAGACAACTCTTTT
1 ATAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGTTGCTTTAAGACAACTCATTT
* *
30508 CTTTGATATTAAAAAATAAATAAATAACTAAAACATTTTCTTAAAATAATAAT-AATAAA-AAAT
66 CTTCGATATTAAAAAATAAATAAATAACTAAAACATTTTCTTAAAATAATAATAAATAAATAAAA
*
30571 TAT-TTTAATAT
131 TATATATAATAT
30582 AGTAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGTTGCTTTAAGACAACTCATT
1 A-TAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGTTGCTTTAAGACAACTCATT
*
30647 TCTTCGAT-TTAAAAAAATAAATAAATAACTAAAATATTTTCTTAAAATAATAATGAAATAAATT
65 TCTTCGATATT-AAAAAATAAATAAATAACTAAAACATTTTCTTAAAATAATAAT-AAATAAA--
*
30711 TAAAATATATATAATTT
126 TAAAATATATATAATAT
30728 ATAAGGATATTTATTTATTTAAA
1 ATAA-GATATTTATTTATTTAAA
30751 CAAATATATA
Statistics
Matches: 152, Mismatches: 8, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
139 3 0.02
140 109 0.72
142 6 0.04
145 9 0.06
146 25 0.16
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.39
Consensus pattern (142 bp):
ATAAGATATTTATTTATTTAAAAATATCAGAAAAGGGCTTCTAGTTGCTTTAAGACAACTCATTT
CTTCGATATTAAAAAATAAATAAATAACTAAAACATTTTCTTAAAATAATAATAAATAAATAAAA
TATATATAATAT
Found at i:30847 original size:25 final size:24
Alignment explanation
Indices: 30780--30841 Score: 71
Period size: 25 Copynumber: 2.8 Consensus size: 24
30770 ATGACTAAGA
30780 TAATAAT-AAA-ATA-AT-AAAAG
1 TAATAATAAAATATATATCAAAAG
*
30800 TAATAATTTAAATATATATCAAAAG
1 TAATAA-TAAAATATATATCAAAAG
30825 TAATAATAAAATA-ATAT
1 TAATAATAAAATATATAT
30842 TGCAAATGAA
Statistics
Matches: 36, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
20 6 0.17
21 1 0.03
22 3 0.08
23 7 0.19
24 8 0.22
25 11 0.31
ACGTcount: A:0.63, C:0.02, G:0.03, T:0.32
Consensus pattern (24 bp):
TAATAATAAAATATATATCAAAAG
Found at i:31131 original size:2 final size:2
Alignment explanation
Indices: 31124--31187 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
31114 ATTTTACCTA
31124 AT AT AT AT AT 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 AT AT AT AT AT
31166 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
31188 TGCAATGACT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32382 original size:15 final size:16
Alignment explanation
Indices: 32357--32386 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
32347 AAATGTGAAT
32357 ACAATTATTTTTTGTG
1 ACAATTATTTTTTGTG
32373 ACAA-TATTTTTTGT
1 ACAATTATTTTTTGT
32387 AATAATTATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.27, C:0.07, G:0.10, T:0.57
Consensus pattern (16 bp):
ACAATTATTTTTTGTG
Found at i:32845 original size:417 final size:417
Alignment explanation
Indices: 32058--32908 Score: 1107
Period size: 417 Copynumber: 2.0 Consensus size: 417
32048 ATAACTATAA
* *
32058 ATTTT-TTACTATATAACATTTTTTGCACCAAAAAATACGTAGAAATGTCTATAATAATATAATT
1 ATTTTGTTACTATATAACATTTTTTGCACCAAAAAATAAGGAGAAATGTCTATAATAATATAATT
* *
32122 TTACATAATGATTAAAATATATAACTAAAAAAATAATTGATTACAAAAAACTTGAATTTTATTGT
66 TTACATAATGATTAAAATATATAACTAAAAAAATAATTGATTACAAAAAACCTGAATTTTATTAT
* * * * *
32187 ATGATGTGATATTTTTTTTATAAAAATAACTATAATTTATAATTACAAAACGTATGAATATAAAT
131 ATGATGTGATATTTTTTCTATAAAAATAACTATAAATTATAATTACAAAAAGTATCAATATAAAC
*
32252 TTTTGAAACAAAAAAAAAAGTGGAGAAAAATATTTATCACAATATATGTTATCACTATAATTAAA
196 TTTTGAAAC---AAAAAAAGTGGAGAAAAATATTTAACACAATATATGTTATCACTATAATTAAA
* *
32317 ATTTATAACTACAAGTATAGTTTGTCACAAAAATGTGAATACAATTATTTTTTGTGACAATATTT
258 ATTTATAAATACAAATATAGTTTGTCACAAAAATGTGAATACAATTATTTTTTGTGACAATATTT
32382 TTTGTAATAATTATAAACACTTATAGTTACAAAAATTGTTACTATATGA-TTTTTTGGCACAATA
323 TTTGTAATAATTATAAACACTTATAGTTACAAAAATTGTTACTATATGATTTTTTTGGCACAA-A
* * *
32446 AAA-TATGGAGTAAAATCTTTATGACAATAT
387 AAATTATAGAGGAAAATCTTTATGACAATAC
* * * * *
32476 ATTTTGTTACTATATAATA-TTTTTGACACTAAAAAATAAGGATAAATGGT-TATGATAGTATAA
1 ATTTTGTTACTATATAACATTTTTTG-CACCAAAAAATAAGGAGAAAT-GTCTATAATAATATAA
* *
32539 TTTTTCATAATGATTAAAATATATAAGT-AAAAAATAATTGATTA-AAAAAACCTGAATTTTATT
64 TTTTACATAATGATTAAAATATATAACTAAAAAAATAATTGATTACAAAAAACCTGAATTTTATT
* * * * *
32602 ATTTGATGTGATAATTTTTTCTATAACAATAACTATAAATTATAATTATAAAAATTGTCAATAT-
129 ATATGATGTGAT-ATTTTTTCTATAAAAATAACTATAAATTATAATTACAAAAAGTATCAATATA
* *
32666 AACTTTTGAAAC-AAAAAAGTGGAGAAAAATAGTTATAACAATTAATATATGTTATCACTATAGT
193 AACTTTTGAAACAAAAAAAGTGGAGAAAAATA-TT-TAAC-A-CAATATATGTTATCACTATAAT
32730 TAAAATTTATAAATACAAATATAAG-TTGTCACAAAAAATGTGAATATC-ATTA-TTTTTGTGAC
254 TAAAATTTATAAATACAAATAT-AGTTTGTCAC-AAAAATGTGAATA-CAATTATTTTTTGTGAC
* * * * * * *
32792 AATGTTTTTTGTAATAATTATTAACACTTATATTTA-TAAATTTTTTCACTATATGATTTTTTTT
316 AATATTTTTTGTAATAATTATAAACACTTATAGTTACAAAAATTGTT-ACTATATGATTTTTTTG
* * *
32856 GCGCAAAAAATTATAGAGGGAAATCTTTGTGACAATAC
380 GCACAAAAAATTATAGAGGAAAATCTTTATGACAATAC
*
32894 ATTTTTGTCACTATA
1 A-TTTTGTTACTATA
32909 ATTAAAACAT
Statistics
Matches: 378, Mismatches: 40, Indels: 29
0.85 0.09 0.06
Matches are distributed among these distances:
413 19 0.05
414 2 0.01
415 3 0.01
416 8 0.02
417 142 0.38
418 123 0.33
419 79 0.21
420 2 0.01
ACGTcount: A:0.44, C:0.08, G:0.09, T:0.39
Consensus pattern (417 bp):
ATTTTGTTACTATATAACATTTTTTGCACCAAAAAATAAGGAGAAATGTCTATAATAATATAATT
TTACATAATGATTAAAATATATAACTAAAAAAATAATTGATTACAAAAAACCTGAATTTTATTAT
ATGATGTGATATTTTTTCTATAAAAATAACTATAAATTATAATTACAAAAAGTATCAATATAAAC
TTTTGAAACAAAAAAAGTGGAGAAAAATATTTAACACAATATATGTTATCACTATAATTAAAATT
TATAAATACAAATATAGTTTGTCACAAAAATGTGAATACAATTATTTTTTGTGACAATATTTTTT
GTAATAATTATAAACACTTATAGTTACAAAAATTGTTACTATATGATTTTTTTGGCACAAAAAAT
TATAGAGGAAAATCTTTATGACAATAC
Found at i:32992 original size:16 final size:17
Alignment explanation
Indices: 32961--32993 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
32951 TTGAATCTCA
*
32961 TTATTTGTTGTGACAAT
1 TTATTTGTTGTAACAAT
32978 TTATTT-TTGTAACAAT
1 TTATTTGTTGTAACAAT
32994 AATTAGAGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.27, C:0.06, G:0.12, T:0.55
Consensus pattern (17 bp):
TTATTTGTTGTAACAAT
Found at i:33453 original size:21 final size:21
Alignment explanation
Indices: 33427--33534 Score: 94
Period size: 21 Copynumber: 5.2 Consensus size: 21
33417 ACCCGAATAT
*
33427 AGCCCAACTTCTCCATCATAC
1 AGCCCAACATCTCCATCATAC
*
33448 AGCCCAACATCACCATCATAC
1 AGCCCAACATCTCCATCATAC
* * *
33469 AACCCAACATCT-CTTCGTAC
1 AGCCCAACATCTCCATCATAC
* * * *
33489 AGCCCAACCT-TACCCTCCTAT
1 AGCCCAACATCT-CCATCATAC
* *
33510 AGCCCCACATCTCTATCATAC
1 AGCCCAACATCTCCATCATAC
33531 AGCC
1 AGCC
33535 GTACTTCACC
Statistics
Matches: 67, Mismatches: 17, Indels: 6
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.01
20 14 0.21
21 51 0.76
22 1 0.01
ACGTcount: A:0.30, C:0.44, G:0.06, T:0.21
Consensus pattern (21 bp):
AGCCCAACATCTCCATCATAC
Found at i:33630 original size:21 final size:21
Alignment explanation
Indices: 33579--33641 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
33569 GCACAGTCTA
* *
33579 ACCTCTCCAAGTTACAGTCCG
1 ACCTCTCCAAGCTACAGCCCG
* * * *
33600 ACATCACCAAGCTATAGCCCT
1 ACCTCTCCAAGCTACAGCCCG
* *
33621 ACCTCTCCAAGTTACAACCCG
1 ACCTCTCCAAGCTACAGCCCG
33642 CAGTCAGCCA
Statistics
Matches: 30, Mismatches: 12, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.29, C:0.40, G:0.11, T:0.21
Consensus pattern (21 bp):
ACCTCTCCAAGCTACAGCCCG
Found at i:40719 original size:64 final size:64
Alignment explanation
Indices: 40633--40842 Score: 221
Period size: 65 Copynumber: 3.2 Consensus size: 64
40623 TGCACTAAGA
* * * *
40633 GTGCAGCGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGACTGCATCGATGCATGGTTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
** *
40697 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTCAGTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATATCCAGAGTGCATCGATGCATGGT-
40761 T-
63 TG
* * ** *
40762 GTGCATCGATGCATGAAATGCATTCGAT-ATTCAATTTAATTCATG-GTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAAT-ATCCA-GAGTGCATCGATGCATGG-T
40825 TG
63 TG
*
40827 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
40843 CTTTGATAAA
Statistics
Matches: 121, Mismatches: 17, Indels: 15
0.79 0.11 0.10
Matches are distributed among these distances:
62 1 0.01
63 4 0.03
64 46 0.38
65 66 0.55
66 4 0.03
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATATCCAGAGTGCATCGATGCATGGTTG
Found at i:41297 original size:2 final size:2
Alignment explanation
Indices: 41290--41322 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
41280 AATTGATTAA
41290 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
41323 GGTTAAGCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41933 original size:21 final size:21
Alignment explanation
Indices: 41908--41951 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
41898 CCGGAGTAGG
*
41908 AGGAGGAGCACGAGAAAAGCT
1 AGGAGCAGCACGAGAAAAGCT
* * *
41929 AGGAGCAGCTCGTGAAGAGCT
1 AGGAGCAGCACGAGAAAAGCT
41950 AG
1 AG
41952 CTCCCGAGGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.16, G:0.39, T:0.09
Consensus pattern (21 bp):
AGGAGCAGCACGAGAAAAGCT
Found at i:43544 original size:22 final size:21
Alignment explanation
Indices: 43475--43569 Score: 86
Period size: 21 Copynumber: 4.4 Consensus size: 21
43465 GACCCTTTGC
*
43475 ATCGATGCACATTCAAGGCGTGG
1 ATCGATGCACATTCAA-G-GTGT
* * * *
43498 ATTGGTGCACCTTCATGGTGT
1 ATCGATGCACATTCAAGGTGT
43519 ATCGATGCACATTCAAGGATGT
1 ATCGATGCACATTCAAGG-TGT
*
43541 ATCGATGCACTATT--AGGTGG
1 ATCGATGCAC-ATTCAAGGTGT
43561 ATCGATGCA
1 ATCGATGCA
43570 TGAAGCATAA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
20 11 0.18
21 20 0.33
22 14 0.23
23 15 0.25
ACGTcount: A:0.25, C:0.19, G:0.27, T:0.28
Consensus pattern (21 bp):
ATCGATGCACATTCAAGGTGT
Found at i:43566 original size:20 final size:20
Alignment explanation
Indices: 43514--43569 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 20
43504 GCACCTTCAT
43514 GGTGTATCGATGCACATTCAA
1 GGTGTATCGATGCACATT-AA
43535 GGATGTATCGATGCACTATT-A
1 GG-TGTATCGATGCAC-ATTAA
*
43556 GGTGGATCGATGCA
1 GGTGTATCGATGCA
43570 TGAAGCATAA
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 11 0.34
21 5 0.16
22 13 0.41
23 3 0.09
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (20 bp):
GGTGTATCGATGCACATTAA
Found at i:49393 original size:64 final size:63
Alignment explanation
Indices: 49322--49501 Score: 159
Period size: 65 Copynumber: 2.8 Consensus size: 63
49312 TTGAACCCTT
* *
49322 AGTGCATCGGTGCA-CTAAGAGTGCATCAATGCATTAAGTGCATTCGATG-TTTCA-AAATAGCC
1 AGTGCATCGGTGCAGCT--G-GTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAA-AGCC
*
49384 AG
62 AC
* * * *
49386 AGTGCATCGATGCATGGCTGGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTC
1 AGTGCATCGGTGCA--GCTGGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
* * * * *
49451 AGTGCATCGGTGCATGGTATGTGCATCGATGCATGAAATGCATTTGATGTT
1 AGTGCATCGGTGCA-GCT-GGTGCATCAATGCATCAAATGCATTCGATGTT
49502 CAATTTAATT
Statistics
Matches: 97, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
64 41 0.42
65 51 0.53
66 3 0.03
67 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.24, T:0.30
Consensus pattern (63 bp):
AGTGCATCGGTGCAGCTGGTGCATCAATGCATCAAATGCATTCGATGTTTTCATAAAAGCCAC
Found at i:49540 original size:65 final size:63
Alignment explanation
Indices: 49342--49551 Score: 196
Period size: 65 Copynumber: 3.3 Consensus size: 63
49332 TGCACTAAGA
* * * * *
49342 GTGCATCAATGCATTAAGTGCATTCGATGTTTCA-AAATAGC-CAGAGTGCATCGATGCATGGCT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAA-ATCTC--AGTGCATCGATGCATGGTT
49405 G
63 G
*
49406 GTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATCCTCAGTGCATCGGTGCATGGTAT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCATAAAAT-CTCAGTGCATCGATGCATGGT-T
49471 -
63 G
* * **
49471 GTGCATCGATGCATGAAATGCATTTGATG-TTCAATTTAAT-TCATGGTGCATCGATGCATGGAT
1 GTGCATCGATGCATCAAATGCATTCGATGTTTC-ATAAAATCTCA--GTGCATCGATGCATGG-T
49534 TG
62 TG
*
49536 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
49552 CTTTGATAAA
Statistics
Matches: 123, Mismatches: 13, Indels: 19
0.79 0.08 0.12
Matches are distributed among these distances:
62 3 0.02
63 3 0.02
64 47 0.38
65 64 0.52
66 5 0.04
67 1 0.01
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (63 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCATAAAATCTCAGTGCATCGATGCATGGTTG
Found at i:51095 original size:2 final size:2
Alignment explanation
Indices: 51088--51167 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
51078 ACATACTGTT
51088 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
51130 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
51168 AATGTAAGAA
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:60016 original size:44 final size:43
Alignment explanation
Indices: 59908--60018 Score: 107
Period size: 44 Copynumber: 2.5 Consensus size: 43
59898 TAGCAAAGTA
* * * * *
59908 TGAAATCTTCACAGAAGAGTAGTGGAGTAATCCAAGTTTGAGTT
1 TGAAAT-TTCACGGAAGAGTAGTGGAGAAATCCAACTTTGAATC
* * *
59952 TGAAATTTCACGAAATAGTAGTGGAAGCAAATTCAACTTTGAATC
1 TGAAATTTCACGGAAGAGTAGTGG-AG-AAATCCAACTTTGAATC
*
59997 TGATA-TTCACGGAAGAGTAGTG
1 TGAAATTTCACGGAAGAGTAGTG
60019 AAATTAGATT
Statistics
Matches: 54, Mismatches: 11, Indels: 4
0.78 0.16 0.06
Matches are distributed among these distances:
43 15 0.28
44 23 0.43
45 16 0.30
ACGTcount: A:0.36, C:0.12, G:0.23, T:0.29
Consensus pattern (43 bp):
TGAAATTTCACGGAAGAGTAGTGGAGAAATCCAACTTTGAATC
Found at i:64485 original size:312 final size:311
Alignment explanation
Indices: 63913--64833 Score: 1407
Period size: 312 Copynumber: 3.0 Consensus size: 311
63903 AAGCCTACCT
*
63913 AAGTTTACTAATGTCAAGGAAATACCTTGGGGCCTCAAAGCCTACCCAAGTGTCACCTTAGGTCC
1 AAGTTTACTGATGTCAA-GAAATACCTTGGGGCCTCAAAGCCTACCCAAGTGTCACCTTAGGTCC
* *
63978 GTAAGGATTTACCAACTTGATCAGAGCTGAACCTCCATACTCCAGAATTCTACCCAGACAATATC
65 GTAAGGATTTACCAGCTTGATCAGAGCTGAACCTCCATACTCCAGAATTCTACCCAGACAGTATC
* * *
64043 CCAA-AATATCAATTCATATAATAATCCAGTAATTTCCATGATCTATAAATCAAACATAATTATA
130 CCAATAA-ATCAGTTCATACAATAATCCAGTAATTTCCATGATCTATAAATCAGACATAATTATA
* * *
64107 TTTTCTAGTGAAAATAGGTAACCAGAGAACACATATCATGTAGCCATAGTTTATAAACAATAAAT
194 TTTTATAGTGAAAATAGGTAACCAGAGAGCACATATCATGTAGCCATAGTTTATAAACAGTAAAT
*
64172 CAATACATCAGTAAGTCAGAATATCGAACAGTTAAAATATCCAACAATTAAAC
259 CAATACATCAGTAAGTCAGAATATCGAACAGTTAAAATATCCAACAATAAAAC
* *
64225 AAGTTTACTGATGTCAAGTAAATACCTTGGGGCCTCAAAGCCTACCCAGGTGTCACCTTAGGTTC
1 AAGTTTACTGATGTCAAG-AAATACCTTGGGGCCTCAAAGCCTACCCAAGTGTCACCTTAGGTCC
* * *
64290 GTAAAGATTTACCAGCTTGATCAGAGCTGAACCTCCATATTCCAGAATTCAACCCAGACAGTATC
65 GTAAGGATTTACCAGCTTGATCAGAGCTGAACCTCCATACTCCAGAATTCTACCCAGACAGTATC
* * * * *
64355 TCAATAAATCCGTTTATACATTAATCCAGTAATTTCCATGATCTATAAATCAGATATAATTATAT
130 CCAATAAATCAGTTCATACAATAATCCAGTAATTTCCATGATCTATAAATCAGACATAATTATAT
* * *
64420 TTTTTAGTGAAAATAGGTAACCAGAGAGTACAAATCATGTAGCCATAGTTTATAAACAGTAAATC
195 TTTATAGTGAAAATAGGTAACCAGAGAGCACATATCATGTAGCCATAGTTTATAAACAGTAAATC
** * **
64485 AATACATCAGTACTTCAGAATATCAAACAGTTAAAATATCCAGTAATAAAAC
260 AATACATCAGTAAGTCAGAATATCGAACAGTTAAAATATCCAACAATAAAAC
* * *
64537 AAGTTTACTGATCTAAAGAAATACCTTTGGGCCTCAAAGCCTACCCAAGTGTCACCTTAGG-CCT
1 AAGTTTACTGATGTCAAGAAATACCTTGGGGCCTCAAAGCCTACCCAAGTGTCACCTTAGGTCC-
* * *
64601 GTAAGGATTTACCTGCTTGATCAGAGTTGAATCTCCATACTCCAGAATTCTACCCAGACAGTATC
65 GTAAGGATTTACCAGCTTGATCAGAGCTGAACCTCCATACTCCAGAATTCTACCCAGACAGTATC
* * * *
64666 CCAATAAATCAGTTCATACAGTAATCCAGTAATTTCCATGATCCATAAATTAGGCATAATTATAT
130 CCAATAAATCAGTTCATACAATAATCCAGTAATTTCCATGATCTATAAATCAGACATAATTATAT
* * *
64731 TTTATAGTGAAAATAGGTAACTAGAGAGCACATATCATGTAGCCATAATTCATAAACAGTAAATC
195 TTTATAGTGAAAATAGGTAACCAGAGAGCACATATCATGTAGCCATAGTTTATAAACAGTAAATC
*
64796 AATACATTAGTAAGTCAGAATATCGAA-AGTTAAAATAT
260 AATACATCAGTAAGTCAGAATATCGAACAGTTAAAATAT
64834 TCAGTAAATC
Statistics
Matches: 550, Mismatches: 56, Indels: 8
0.90 0.09 0.01
Matches are distributed among these distances:
310 12 0.02
311 240 0.44
312 296 0.54
313 2 0.00
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (311 bp):
AAGTTTACTGATGTCAAGAAATACCTTGGGGCCTCAAAGCCTACCCAAGTGTCACCTTAGGTCCG
TAAGGATTTACCAGCTTGATCAGAGCTGAACCTCCATACTCCAGAATTCTACCCAGACAGTATCC
CAATAAATCAGTTCATACAATAATCCAGTAATTTCCATGATCTATAAATCAGACATAATTATATT
TTATAGTGAAAATAGGTAACCAGAGAGCACATATCATGTAGCCATAGTTTATAAACAGTAAATCA
ATACATCAGTAAGTCAGAATATCGAACAGTTAAAATATCCAACAATAAAAC
Found at i:68292 original size:22 final size:20
Alignment explanation
Indices: 68264--68305 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
68254 GCAATTACTA
68264 CCACACCACCATCATTCCATTT
1 CCACACCA--ATCATTCCATTT
*
68286 CCACACCATTCATTCCATTT
1 CCACACCAATCATTCCATTT
68306 TGCCACATCA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 11 0.58
22 8 0.42
ACGTcount: A:0.26, C:0.43, G:0.00, T:0.31
Consensus pattern (20 bp):
CCACACCAATCATTCCATTT
Done.