Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022080.1 Corchorus olitorius cultivar O-4 contig22113, 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: 38893
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:370 original size:3 final size:3
Alignment explanation
Indices: 356--397 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
346 CCGGCTACCG
*
356 GAA GAT GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
398 AATAAAGCCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.64, C:0.00, G:0.33, T:0.02
Consensus pattern (3 bp):
GAA
Found at i:9535 original size:15 final size:16
Alignment explanation
Indices: 9511--9550 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
9501 AGAGGTTGAA
*
9511 AGAAATCAATTAAAC-
1 AGAAAACAATTAAACT
*
9526 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
9542 AGAAAACAA
1 AGAAAACAA
9551 AACAAACAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.17
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:12273 original size:48 final size:48
Alignment explanation
Indices: 12208--12414 Score: 277
Period size: 48 Copynumber: 4.5 Consensus size: 48
12198 ATATCCCCAA
** *
12208 TTTGCCCTTTTCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCATGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
* * *
12256 TTTGCCATTCCCAGTCGGAAGGTGTTG----C----TTTCATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
* *
12296 TTTGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
12344 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
1 TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
*
12392 TTTGCCCTTCCTGGTCGGAAGGT
1 TTTGCCCTTCCCGGTCGGAAGGT
12415 CCCAGTTTTC
Statistics
Matches: 138, Mismatches: 13, Indels: 16
0.83 0.08 0.10
Matches are distributed among these distances:
40 34 0.25
44 2 0.01
48 102 0.74
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (48 bp):
TTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCCTGT
Found at i:12300 original size:40 final size:40
Alignment explanation
Indices: 12248--12328 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 40
12238 TCAATATTTT
12248 ATTCATGTTTTGCCATTCCCAGTCGGAAGGTGTTGCTTTC
1 ATTCATGTTTTGCCATTCCCAGTCGGAAGGTGTTGCTTTC
* * * * *
12288 ATTCCTGTTTTGCCCTTCTCGGTCGGAAGGTGTTGTTTTC
1 ATTCATGTTTTGCCATTCCCAGTCGGAAGGTGTTGCTTTC
12328 A
1 A
12329 ATGTTTTATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.12, C:0.22, G:0.23, T:0.42
Consensus pattern (40 bp):
ATTCATGTTTTGCCATTCCCAGTCGGAAGGTGTTGCTTTC
Found at i:12361 original size:88 final size:88
Alignment explanation
Indices: 12208--12376 Score: 284
Period size: 88 Copynumber: 1.9 Consensus size: 88
12198 ATATCCCCAA
*
12208 TTTGCCCTTTTCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCATTCCCAGTCG
1 TTTGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCATTCCCAGTCG
12273 GAAGGTGTTGCTTTCATTCCTGT
66 GAAGGTGTTGCTTTCATTCCTGT
* * * *
12296 TTTGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCGGTCG
1 TTTGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCATTCCCAGTCG
*
12361 GAAGGTGTTGTTTTCA
66 GAAGGTGTTGCTTTCA
12377 ATATTTTATT
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
88 75 1.00
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (88 bp):
TTTGCCCTTCTCGGTCGGAAGGTGTTGTTTTCAATATTTTATTCATGTTTTGCCATTCCCAGTCG
GAAGGTGTTGCTTTCATTCCTGT
Found at i:12537 original size:43 final size:43
Alignment explanation
Indices: 12437--12993 Score: 620
Period size: 43 Copynumber: 12.7 Consensus size: 43
12427 TATCTCTTTT
* * * *
12437 CAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-TTTT
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* **
12479 CAAAAATGCCCCTTCCTAGTTGGAAGGTCCCCGTTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* *
12522 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTT
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
*
12565 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* ** * *
12608 CAAAAATGCCCGTTCCCAGTCGGAAGGTGCC-GGTTTTCAATATCTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGT-CCTTGTTTTC-AT-T-TC
* * * *
12654 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-TTTT
1 ----CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
12700 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
*
12743 CAAAAATGCCCCTTTCCTGGTTGGAAGGTCCTTATTTTCATTTC
1 CAAAAATGCCCC-TTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* *
12787 CAAAAATGCCCCTTCCTGGTCGGAAGGTCC-AGTTTTCGATATCTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTC-AT-T-TC
* * * * *
12832 TTTTCAAAAATGCCCCTTCCTGGTTGTAAGGTCTTTATTGTC-TTTT
1 ----CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* * *
12878 CAAAAGTGCCCCTTTCTGGTTGGAAGGTCCCTGTTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* * *
12921 CAAAAATGCTCATTCCTGGTTGGAAGGTCCTCGTTTTCATTTC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
* *
12964 CAAAAATGCCCCTTCCCGGTCGGAAGGTCC
1 CAAAAATGCCCCTTCCTGGTTGGAAGGTCC
12994 CAGTTTTCCT
Statistics
Matches: 433, Mismatches: 61, Indels: 41
0.81 0.11 0.08
Matches are distributed among these distances:
42 103 0.24
43 212 0.49
44 47 0.11
45 3 0.01
46 4 0.01
47 2 0.00
48 2 0.00
49 28 0.06
50 32 0.07
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.36
Consensus pattern (43 bp):
CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTC
Found at i:12927 original size:221 final size:216
Alignment explanation
Indices: 12426--12993 Score: 768
Period size: 221 Copynumber: 2.6 Consensus size: 216
12416 CCAGTTTTCG
12426 ATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCC
1 ATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCC
* *
12491 TTCCTAGTTGGAAGGTCCCCGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTAT
66 TTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTAT
* * *
12556 TTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAAAAATGCCCGT
131 TTTCATTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCC-TATTTTCATTTCCAAAAATGCCCCT
12621 TCCCAGTCGGAAGGTGCCGGTTTTCA
195 TCCCAGTCGGAAGGT-CC-G-TTT-A
12647 ATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCC
1 ATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCC
*
12712 TTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTTCCTGGTTGGAAGGTCCTTA
66 TTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGCCCC-TTCCTGGTTGGAAGGTCCTTA
12777 TTTTCATTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCC-AGTTTTCGATATCTCTTTTCAAAA
130 TTTTCATTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTA-TTTTC-AT-T-TC----CAAAA
** * *
12841 ATGCCCCTTCCTGGTTGTAAGGT-C-TTT-
187 ATGCCCCTTCCCAGTCGGAAGGTCCGTTTA
* * * ** * * * *
12868 AT-TGTCTTTTCAAAAGTGCCCCTTTCTGGTTGGAAGGTCCCTGTTTTCATTTCCAAAAATGCTC
1 ATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-TTTTCAAAAATGCCC
* * *
12932 ATTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
65 CTTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCC
12994 CAGTTTTCCT
Statistics
Matches: 314, Mismatches: 23, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
220 56 0.18
221 167 0.53
222 61 0.19
223 4 0.01
224 2 0.01
226 1 0.00
228 23 0.07
ACGTcount: A:0.20, C:0.25, G:0.18, T:0.37
Consensus pattern (216 bp):
ATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCC
TTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTAT
TTTCATTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCTATTTTCATTTCCAAAAATGCCCCTT
CCCAGTCGGAAGGTCCGTTTA
Found at i:12999 original size:178 final size:177
Alignment explanation
Indices: 12473--13001 Score: 815
Period size: 178 Copynumber: 3.0 Consensus size: 177
12463 GTCTTTATTG
* **** * *
12473 TCTTTTCAAAAATGCCCCTTCCTAGTTGGAAGGTCCCCGTTTTCATTTCCAAAAATGCCCCTTCC
1 TCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-TTTTCAAAAATGCCCCTTCC
* * *
12538 TGGTTGGAAGGTCCTTATTTTCATTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTC
65 TGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCATTCCTGGTTGGAAGGTCCTTATTTTC
* * *
12603 ATTTCCAAAAATGCCCGTTCCCAGTCGGAAGGTGCCGGTTTTCAATATC
130 ATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGT-CCAGTTTTCAATATC
12652 TCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCT
1 TCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCT
*
12717 GGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTTCCTGGTTGGAAGGTCCTTATTTTC
66 GGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATG-CCCATTCCTGGTTGGAAGGTCCTTATTTTC
* *
12782 ATTTCCAAAAATGCCCCTTCCTGGTCGGAAGGTCCAGTTTTCGATATC
130 ATTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCAGTTTTCAATATC
* * *
12830 TCTTTTCAAAAATGCCCCTTCCTGGTTGTAAGGTCTTTATTGTCTTTTCAAAAGTGCCCCTTTCT
1 TCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCT
* * **
12895 GGTTGGAAGGTCCCTGTTTTCATTTCCAAAAATGCTCATTCCTGGTTGGAAGGTCCTCGTTTTCA
66 GGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCATTCCTGGTTGGAAGGTCCTTATTTTCA
12960 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCCAGTTTTC
131 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGT-CCAGTTTTC
13002 CTTTGATAAT
Statistics
Matches: 324, Mismatches: 24, Indels: 5
0.92 0.07 0.01
Matches are distributed among these distances:
177 58 0.18
178 169 0.52
179 97 0.30
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.37
Consensus pattern (177 bp):
TCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCT
GGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCATTCCTGGTTGGAAGGTCCTTATTTTCA
TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCCAGTTTTCAATATC
Found at i:13176 original size:81 final size:81
Alignment explanation
Indices: 13010--13290 Score: 379
Period size: 81 Copynumber: 3.5 Consensus size: 81
13000 TCCTTTGATA
*
13010 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAA-TCACCAGTTTGCCATTCCTCATC
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCACCAGTTTGCCCTTCCTCATC
* *
13074 GAAAGGTGTTGTTTAA
66 GGAAGGTGTTGTTTAG
*
13090 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTAAATTC-CCAATTTGCCCTTCCTCAT
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAAATTCACCAGTTTGCCCTTCCTCAT
*
13154 CGGAAGGTGTTG-TCAG
65 CGGAAGGTGTTGTTTAG
* * * * * * * *
13170 CATTCCCAGTTTGCCTTTCCTCTTCGGAAGGTATGGTTTAAGTTCACCGGTTTGTCCTTCCTCAC
1 -ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCACCAGTTTGCCCTTCCTCAT
*
13235 CGGAAAGTGTTGTTTAG
65 CGGAAGGTGTTGTTTAG
* *
13252 ATTCCCAGTTTGCCCTTCCTCATCGGAAGTTGTTATTTA
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA
13291 GAGCCCATTC
Statistics
Matches: 174, Mismatches: 22, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
80 45 0.26
81 124 0.71
82 5 0.03
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (81 bp):
ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCACCAGTTTGCCCTTCCTCATC
GGAAGGTGTTGTTTAG
Found at i:13256 original size:121 final size:121
Alignment explanation
Indices: 13009--13285 Score: 371
Period size: 121 Copynumber: 2.3 Consensus size: 121
12999 TTCCTTTGAT
*
13009 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATCACCAGTTTGCCATTCCTCATC
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTCAAATCACCAGTTTGCCATTCCTCATC
* * * *
13074 GAAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTA
66 GAAAGGTATGGTTTAAATTCCCAGTTTGCCCTTCCTCACCGGAAAGTGTTGTTTTA
* * * *
13130 AATTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCAGCATTC-CCAGTTTGCCTTTCCTCT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTCA--AATCACCAGTTTGCCATTCCTCA
* * * *
13193 TCGGAAGGTATGGTTTAAGTTCACCGGTTTGTCCTTCCTCACCGGAAAGTGTTG-TTTA
64 TCGAAAGGTATGGTTTAAATTC-CCAGTTTGCCCTTCCTCACCGGAAAGTGTTGTTTTA
* *
13251 GATTCCCAGTTTGCCCTTCCTCATCGGAAGTTGTT
1 AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTT
13286 ATTTAGAGCC
Statistics
Matches: 137, Mismatches: 16, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
120 2 0.01
121 105 0.77
122 30 0.22
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (121 bp):
AATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTCAAATCACCAGTTTGCCATTCCTCATC
GAAAGGTATGGTTTAAATTCCCAGTTTGCCCTTCCTCACCGGAAAGTGTTGTTTTA
Found at i:13291 original size:40 final size:40
Alignment explanation
Indices: 13010--13292 Score: 347
Period size: 40 Copynumber: 7.0 Consensus size: 40
13000 TCCTTTGATA
13010 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTA-
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
* * * *
13049 AATCACCAGTTTGCCATTCCTCATCGAAAGGTGTTGTTTAA
1 ATTC-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
*
13090 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTTAA
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTG-TTTAG
* *
13131 ATTCCCAATTTGCCCTTCCTCATCGGAAGGTGTTG-TCAG
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
* * * *
13170 CATTCCCAGTTTGCCTTTCCTCTTCGGAAGGTATGGTTTA-
1 -ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
* * * *
13210 AGTTCACCGGTTTGTCCTTCCTCACCGGAAAGTGTTGTTTAG
1 A-TTC-CCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
* *
13252 ATTCCCAGTTTGCCCTTCCTCATCGGAAGTTGTTATTTAG
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
13292 A
1 A
13293 GCCCATTCTT
Statistics
Matches: 207, Mismatches: 29, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
39 6 0.03
40 126 0.61
41 74 0.36
42 1 0.00
ACGTcount: A:0.18, C:0.25, G:0.20, T:0.37
Consensus pattern (40 bp):
ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAG
Found at i:13354 original size:40 final size:40
Alignment explanation
Indices: 13308--13508 Score: 159
Period size: 40 Copynumber: 4.8 Consensus size: 40
13298 TTCTTTCAAG
*
13308 TTTGCCCTTCCCCACCGGAAGGTGTTTATTTCATTCCCGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCGT
* *
13348 TTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCGT
***** * **
13388 TTTGCCCTTCCTGGTAGGAAGGTGTTGTTTTCAATGTTTTATTCTTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTG------A--TTTCATTCCCGT
* * *
13436 GTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCGT
* *** *
13476 TTTTCCCTTCCCGGTCGGAAGGTGTTGTTTTCA
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCA
13509 ATGTTTTATT
Statistics
Matches: 132, Mismatches: 21, Indels: 16
0.78 0.12 0.09
Matches are distributed among these distances:
40 98 0.74
42 1 0.01
46 1 0.01
48 32 0.24
ACGTcount: A:0.11, C:0.26, G:0.22, T:0.41
Consensus pattern (40 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCGT
Found at i:13384 original size:128 final size:127
Alignment explanation
Indices: 13220--13505 Score: 281
Period size: 128 Copynumber: 2.2 Consensus size: 127
13210 AGTTCACCGG
* * * * * * *
13220 TTTGTCCTTCCTCACCGGAAAGTGTTGTTTAGATTCCCAG-TTTGCCCTTCCTCATCGGAAGTTG
1 TTTGCCCTTCCCCGCCGGAAGGTGTTGTTT-CATT-CCAGTTTTGCCCTTCCTCATAGGAAGGTG
* * *
13284 TTATTTAGAGCCCATTCT-TTCAAGT-TTGCCCTTCCCCACCGGAAGGTGTTTATTTCATTCCCG
64 TTATTTACA--ACATTCTATTCAAGTGTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCG
13347 T
127 T
* **
13348 TTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCTGGTAGGAAGGTGT
1 TTTGCCCTTCCCCGCCGGAAGGTGTTG-TTTCATTCCAGTTTTGCCCTTCCTCATAGGAAGGTGT
* * ** * ** * *
13413 TGTTTTCAATGTTTTATTCTTGTGTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGT
65 TATTTACAACATTCTATTCAAGTGTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCGT
* * *
13476 TTTTCCCTTCCCGGTCGGAAGGTGTTGTTT
1 TTTGCCCTTCCCCGCCGGAAGGTGTTGTTT
13506 TCAATGTTTT
Statistics
Matches: 129, Mismatches: 25, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
126 3 0.02
127 11 0.09
128 112 0.87
129 3 0.02
ACGTcount: A:0.13, C:0.26, G:0.21, T:0.40
Consensus pattern (127 bp):
TTTGCCCTTCCCCGCCGGAAGGTGTTGTTTCATTCCAGTTTTGCCCTTCCTCATAGGAAGGTGTT
ATTTACAACATTCTATTCAAGTGTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCCCGT
Found at i:13441 original size:88 final size:88
Alignment explanation
Indices: 13340--13808 Score: 692
Period size: 88 Copynumber: 5.3 Consensus size: 88
13330 TGTTTATTTC
* *
13340 ATTCCCGTTTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCTGGTAG
1 ATTCCTGTTTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTAG
13405 GAAGGTGTTGTTTTCAATGTTTT
66 GAAGGTGTTGTTTTCAATGTTTT
* * * *
13428 ATTCTTGTGTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTTCCCTTCCCGGTCG
1 ATTCCTGTTTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTAG
13493 GAAGGTGTTGTTTTCAATGTTTT
66 GAAGGTGTTGTTTTCAATGTTTT
* * ** * * *
13516 ATTCCTGTTTTGCCCTTCCTCAG-GGGAAGACGTCGTTTTCATTCTTGTTTTGCCCTTCCCGGTA
1 ATTCCTGTTTTGCCCTTCC-CCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTA
13580 GGAAGGTGTTGTTTTCAATGTTTT
65 GGAAGGTGTTGTTTTCAATGTTTT
* *
13604 ATTCCTGTTTTGCCCTTCCCCGCGGGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCCGGTAG
1 ATTCCTGTTTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTAG
13669 GAAGGTGTTGTTTTCAATGTTTT
66 GAAGGTGTTGTTTTCAATGTTTT
* ** * * *
13692 ATTCTTGTTTTGCCCTTCCCCAG-CGGAAGACGTCGTTTTCATTCCTGTTTTGCCCTTCCCGGTC
1 ATTCCTGTTTTGCCCTTCCCC-GCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTA
13756 GGAAGGTGTTG-TTTCAATGTTTT
65 GGAAGGTGTTGTTTTCAATGTTTT
**
13779 ATTCCTGTTTTGCCCTTCCCCATCGGAAGG
1 ATTCCTGTTTTGCCCTTCCCCGCCGGAAGG
13809 AGTCGTTCAT
Statistics
Matches: 343, Mismatches: 34, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
87 40 0.12
88 300 0.87
89 3 0.01
ACGTcount: A:0.12, C:0.24, G:0.23, T:0.42
Consensus pattern (88 bp):
ATTCCTGTTTTGCCCTTCCCCGCCGGAAGGTGTTGATTTCATTCCTGTTTTGCCCTTCCCGGTAG
GAAGGTGTTGTTTTCAATGTTTT
Found at i:13584 original size:40 final size:40
Alignment explanation
Indices: 13510--13769 Score: 177
Period size: 40 Copynumber: 6.1 Consensus size: 40
13500 TTGTTTTCAA
**
13510 TGTTTT-ATTCCTGTTTTGCCCTTCCTCAGG--GGAAGACGT
1 TGTTTTCATTCCTGTTTTGCCCTTCC-C-GGTAGGAAGGTGT
* *
13549 CGTTTTCATTCTTGTTTTGCCCTTCCCGGTAGGAAGGTGT
1 TGTTTTCATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
* **
13589 TGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCCCCGCGGGAAGGTGT
1 TGTTTTC--------ATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
* *
13637 TGATTTCATTCATGTTTTGCCCTTCCCGGTAGGAAGGTGT
1 TGTTTTCATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
* * * **
13677 TGTTTTCAATGTTTTATTCTTGTTTTGCCCTTCCCCAG-CGGAAGACGT
1 TGTTTTC--------ATTCCTGTTTTGCCCTT-CCCGGTAGGAAGGTGT
* *
13725 CGTTTTCATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGT
1 TGTTTTCATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
13765 TGTTT
1 TGTTT
13770 CAATGTTTTA
Statistics
Matches: 174, Mismatches: 26, Indels: 41
0.72 0.11 0.17
Matches are distributed among these distances:
38 2 0.01
39 10 0.06
40 94 0.54
48 64 0.37
49 4 0.02
ACGTcount: A:0.12, C:0.23, G:0.23, T:0.43
Consensus pattern (40 bp):
TGTTTTCATTCCTGTTTTGCCCTTCCCGGTAGGAAGGTGT
Found at i:14331 original size:14 final size:15
Alignment explanation
Indices: 14298--14335 Score: 60
Period size: 14 Copynumber: 2.6 Consensus size: 15
14288 AAATGGTTGC
14298 TTTGTTTTGTTTCAG
1 TTTGTTTTGTTTCAG
*
14313 TTTGTTTTG-TTCTG
1 TTTGTTTTGTTTCAG
14327 TTTGTTTTG
1 TTTGTTTTG
14336 GTGTTTTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 13 0.59
15 9 0.41
ACGTcount: A:0.03, C:0.05, G:0.21, T:0.71
Consensus pattern (15 bp):
TTTGTTTTGTTTCAG
Found at i:15206 original size:66 final size:66
Alignment explanation
Indices: 15085--15211 Score: 164
Period size: 66 Copynumber: 1.9 Consensus size: 66
15075 CATGTCTCGC
* * ** * ** * *
15085 GCATCTGTTCATCAACATAGTTTGTTATGTCATGCATCTTTTGTAGGTATTCATCAGCATGCTCA
1 GCATCTGCTCATCAACAAAGTTTGCCATGCCATGCATCTTTTCAAGATATCCATCAGCATGCTCA
15150 T
66 T
*
15151 GCATCTGCTCATCAACAAAGTTTGCCATGCCATGCATCTTTTCAATATATCCATCAGCATG
1 GCATCTGCTCATCAACAAAGTTTGCCATGCCATGCATCTTTTCAAGATATCCATCAGCATG
15212 AGACTTTGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
66 51 1.00
ACGTcount: A:0.25, C:0.24, G:0.15, T:0.36
Consensus pattern (66 bp):
GCATCTGCTCATCAACAAAGTTTGCCATGCCATGCATCTTTTCAAGATATCCATCAGCATGCTCA
T
Found at i:17920 original size:20 final size:20
Alignment explanation
Indices: 17895--17934 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
17885 GCAAAAGGGG
17895 ACATTGTATTCATATTGCAA
1 ACATTGTATTCATATTGCAA
*
17915 ACATTGTATTTATATTGCAA
1 ACATTGTATTCATATTGCAA
17935 GCATGCCATG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.42
Consensus pattern (20 bp):
ACATTGTATTCATATTGCAA
Found at i:21716 original size:101 final size:101
Alignment explanation
Indices: 21518--21968 Score: 367
Period size: 101 Copynumber: 4.4 Consensus size: 101
21508 AGATGAAGTC
* * * *
21518 TTTAAGTAATTTGTAAATAAAAATTAAATTTTTAACCAAAA-ATTGAATCTTTTAAGCAATTTGT
1 TTTAAGTAATTTGTAAATAAAGATTAAATTTTTAATCAAAAGATTGAATCATTTAAGTAATTTGT
** * * * * *
21582 AAATAAAAGTGGGA-TTTTTAATTAAGAGTTTGAACT
66 AAATAAAAGTGAAACCTTTGAGTAAAG-GATTGAACT
* * * * **
21618 ATTAAGTAATTGTGTAAATAAAGGTTGAATTTTTAATCAAAAGGTTGAATC-TTTAAGTGGTTTG
1 TTTAAGTAATT-TGTAAATAAAGATTAAATTTTTAATCAAAAGATTGAATCATTTAAGTAATTTG
* *
21682 TAAATAAAAATGAAACCTTTGAGTGAAGGATTGAACT
65 TAAATAAAAGTGAAACCTTTGAGTAAAGGATTGAACT
* * * *
21719 TTTAAATAATTTTGTAAATAAAGGTTAAATTTCTAATTAAAAAAAGATTGAATCATTTAAGTAAT
1 TTTAAGTAA-TTTGTAAATAAAGATTAAATTTTTAA-T--CAAAAGATTGAATCATTTAAGTAAT
* * *
21784 ATGTAAATAAAAGTGAAGCCTTTGAGTAAAAGATTGAAGCT
62 TTGTAAATAAAAGTGAAACCTTTGAGTAAAGGATTGAA-CT
* ** * * * * *
21825 TTTAAGTAATTTGCAAATAAAGATTGGA-TTTTGATTAAAAGA-TGAAACTTTTAAGTGATTTGT
1 TTTAAGTAATTTGTAAATAAAGATTAAATTTTTAATCAAAAGATTGAATCATTTAAGTAATTTGT
* * * * * *
21888 GAATAAAGATTG-AA-TTTTACAATAAAAGATTGAAGCT
66 AAATAAA-AGTGAAACCTTT-GAGTAAAGGATTGAA-CT
** * *
21925 TTTAAGTAATTTGTAAATAAAGATTGGATTTTTGATTAAAAGAT
1 TTTAAGTAATTTGTAAATAAAGATTAAATTTTTAATCAAAAGAT
21969 AAAATTTTGA
Statistics
Matches: 289, Mismatches: 49, Indels: 24
0.80 0.14 0.07
Matches are distributed among these distances:
99 3 0.01
100 77 0.27
101 108 0.37
102 18 0.06
103 1 0.00
104 16 0.06
105 56 0.19
106 10 0.03
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (101 bp):
TTTAAGTAATTTGTAAATAAAGATTAAATTTTTAATCAAAAGATTGAATCATTTAAGTAATTTGT
AAATAAAAGTGAAACCTTTGAGTAAAGGATTGAACT
Found at i:21946 original size:51 final size:50
Alignment explanation
Indices: 21506--21968 Score: 318
Period size: 51 Copynumber: 9.1 Consensus size: 50
21496 CTTTGTGTTG
* * * *
21506 AAAGA-TGAAG-TCTTTAAGTAATTTGTAAATAAAAATTAAATTTTTAACCA
1 AAAGATTGAAGCT-TTTAAGTAATTTGTAAATAAAGATTGAATTTTGAA-TA
* * * * *
21556 AAA-ATTGAATCTTTTAAGCAATTTGTAAATAAA-AGTGGGATTTTTAATTA
1 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGA-TTGAATTTTGAA-TA
* * * * *
21606 AGAGTTTGAA-CTATTAAGTAATTGTGTAAATAAAGGTTGAATTTTTAATCA
1 AAAGATTGAAGCTTTTAAGTAATT-TGTAAATAAAGATTGAATTTTGAAT-A
* * ** * * * *
21657 AAAGGTTGAATC-TTTAAGTGGTTTGTAAATAAA-AATGAAACCTTTGAGTG
1 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTG-AA-TTTTGAATA
* * * *
21707 AAGGATTGAA-CTTTTAAATAATTTTGTAAATAAAGGTTAAATTTCT-AATTAAAA
1 AAAGATTGAAGCTTTTAAGTAA-TTTGTAAATAAAGATTGAATTT-TGAA-T---A
* * * * * *
21761 AAAGATTGAATCATTTAAGTAATATGTAAATAAA-AGTGAAGCCTTTGAGTA
1 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGAA--TTTTGAATA
* * *
21812 AAAGATTGAAGCTTTTAAGTAATTTGCAAATAAAGATTGGATTTTGATTA
1 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTGAATA
* * * *
21862 AAAGA-TGAAACTTTTAAGTGATTTGTGAATAAAGATTGAATTTTACAATA
1 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGAATTTT-GAATA
* *
21912 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGGATTTTTGATTA
1 AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATT-GAATTTTGAATA
21963 AAAGAT
1 AAAGAT
21969 AAAATTTTGA
Statistics
Matches: 321, Mismatches: 66, Indels: 51
0.73 0.15 0.12
Matches are distributed among these distances:
49 39 0.12
50 100 0.31
51 133 0.41
52 12 0.04
53 3 0.01
54 22 0.07
55 12 0.04
ACGTcount: A:0.43, C:0.04, G:0.16, T:0.37
Consensus pattern (50 bp):
AAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGAATTTTGAATA
Found at i:21994 original size:100 final size:100
Alignment explanation
Indices: 21810--21995 Score: 295
Period size: 100 Copynumber: 1.9 Consensus size: 100
21800 AGCCTTTGAG
*
21810 TAAAAGATTGAAGCTTTTAAGTAATTTGCAAATAAAGATTGGATTTTGATTAAAAGATGAAACTT
1 TAAAAGATTGAAGCTTTTAAGTAATTTGCAAATAAAGATTGGATTTTGATTAAAAGATGAAAATT
*
21875 TTAAGTGATTTGTGAATAAAGATTGAATTTTACAA
66 TTAAGTAATTTGTGAATAAAGATTGAATTTTACAA
*
21910 TAAAAGATTGAAGCTTTTAAGTAATTTGTAAATAAAGATTGGATTTTTGATTAAAAGAT-AAAAT
1 TAAAAGATTGAAGCTTTTAAGTAATTTGCAAATAAAGATTGGA-TTTTGATTAAAAGATGAAAAT
* *
21974 TTTGATTCAATTTGTG-ATAAAG
65 TTTAAGT-AATTTGTGAATAAAG
21996 GTGAAATCTT
Statistics
Matches: 79, Mismatches: 5, Indels: 4
0.90 0.06 0.05
Matches are distributed among these distances:
100 57 0.72
101 22 0.28
ACGTcount: A:0.42, C:0.03, G:0.17, T:0.38
Consensus pattern (100 bp):
TAAAAGATTGAAGCTTTTAAGTAATTTGCAAATAAAGATTGGATTTTGATTAAAAGATGAAAATT
TTAAGTAATTTGTGAATAAAGATTGAATTTTACAA
Found at i:22018 original size:50 final size:50
Alignment explanation
Indices: 21964--22112 Score: 165
Period size: 50 Copynumber: 2.9 Consensus size: 50
21954 TTTTGATTAA
**
21964 AAGATAAAATTTTGATTCAATTTGTGATAAAGGTGAAATCTTTAAGCT-AC
1 AAGATAAAATTTTGATT-AATTTGTGATAAAAATGAAATCTTTAAGCTAAC
* * * *
22014 AAGATGAAACTTTCGATTAATTTATGATAAAAATGAAACCTTTAAGCTAAC
1 AAGAT-AAAATTTTGATTAATTTGTGATAAAAATGAAATCTTTAAGCTAAC
* *
22065 AAGTGAAAAAATTTTTTGATTAATTTGTGATAAAAATAAAATCTTTAA
1 AA--GATAAAA--TTTTGATTAATTTGTGATAAAAATGAAATCTTTAA
22113 ATTAAGAGAT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
50 31 0.38
51 14 0.17
52 3 0.04
53 2 0.02
54 31 0.38
ACGTcount: A:0.44, C:0.07, G:0.13, T:0.36
Consensus pattern (50 bp):
AAGATAAAATTTTGATTAATTTGTGATAAAAATGAAATCTTTAAGCTAAC
Found at i:22711 original size:40 final size:40
Alignment explanation
Indices: 22659--22739 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
22649 TCAATATTTT
*
22659 ATTCATGTTTTGCACTTCTCAGTCGCAAGGTGTTGCTTTC
1 ATTCATGTTTTGCACTTCCCAGTCGCAAGGTGTTGCTTTC
* * * * *
22699 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTC
1 ATTCATGTTTTGCACTTCCCAGTCGCAAGGTGTTGCTTTC
22739 A
1 A
22740 ATGTTTTCAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.12, C:0.23, G:0.22, T:0.42
Consensus pattern (40 bp):
ATTCATGTTTTGCACTTCCCAGTCGCAAGGTGTTGCTTTC
Found at i:22819 original size:48 final size:48
Alignment explanation
Indices: 22699--22874 Score: 307
Period size: 48 Copynumber: 3.6 Consensus size: 48
22689 TGTTGCTTTC
22699 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
22747 CATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
1 -ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
**
22796 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
* *
22844 ATTCCTATTTTGCCCTTCCTGGTCGGAAGGT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGT
22875 CCCAGTTTTC
Statistics
Matches: 123, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
48 75 0.61
49 48 0.39
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (48 bp):
ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
Found at i:22824 original size:97 final size:96
Alignment explanation
Indices: 22699--22874 Score: 307
Period size: 97 Copynumber: 1.8 Consensus size: 96
22689 TGTTGCTTTC
** *
22699 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTCATTCCTGTTTTGCCCT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTT-ATTCCTATTTTGCCCT
22764 TCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
65 TCCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
22796 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTATTCCTATTTTGCCCTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTATTCCTATTTTGCCCTT
*
22861 CCTGGTCGGAAGGT
66 CCCGGTCGGAAGGT
22875 CCCAGTTTTC
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
96 29 0.39
97 46 0.61
ACGTcount: A:0.12, C:0.22, G:0.22, T:0.44
Consensus pattern (96 bp):
ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTATTCCTATTTTGCCCTT
CCCGGTCGGAAGGTGTTGTTTTCAATGTTTT
Found at i:22907 original size:97 final size:97
Alignment explanation
Indices: 22709--22924 Score: 231
Period size: 97 Copynumber: 2.2 Consensus size: 97
22699 ATTCCTGTTT
** *
22709 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAATGTTTTCATTCCTGTTTTGCCCTTCCCGGTCGG
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTCATTCCTATTTTGCCCTTCCCGGTCGG
*** * * *****
22774 AAGGTGTTGTTTTCAATGTTTTATTCCTGTTT
66 AAGGTCCAGTTTTCAATCTCTTATTCCAAAAA
*
22806 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTT-ATTCCTATTTTGCCCTTCCTGGTCGG
1 TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTCATTCCTATTTTGCCCTTCCCGGTCGG
22870 AAGGTCCCAGTTTTCCATATCTCTT-TT-CAAAAA
66 AAGGT-CCAGTTTT-CA-ATCTCTTATTCCAAAAA
* *
22903 TGCCCCTTCCTGGTTGGAAGGT
1 TG-CCCTTCCCGGTCGGAAGGT
22925 CTTTATTGTC
Statistics
Matches: 99, Mismatches: 16, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
96 29 0.29
97 44 0.44
98 21 0.21
99 5 0.05
ACGTcount: A:0.14, C:0.24, G:0.21, T:0.41
Consensus pattern (97 bp):
TGCCCTTCCCGGTCGGAAGGTGTTGTTTTCAAAATTTTCATTCCTATTTTGCCCTTCCCGGTCGG
AAGGTCCAGTTTTCAATCTCTTATTCCAAAAA
Found at i:22950 original size:42 final size:43
Alignment explanation
Indices: 22893--23581 Score: 703
Period size: 43 Copynumber: 15.8 Consensus size: 43
22883 TCCATATCTC
* *
22893 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
*
22935 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTT-CTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGT-CCTTATTTTCA
* *
22978 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * *
23021 TTTCCAAAAAATGCCCTTTCCTGGTTGGAATGTCCTTATTTTCA
1 TTTTC-AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* *
23065 TTTCCAAAAATACCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * ** * *
23108 TTTCCAAAAATGCCCTTTCCCAGTCGGAAGGTCCCGGTT-TTCGATATCTC
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGT-CC--TTATT---T-TC-A
** * * *
23158 TTTTCAAAAATGCCCCTTCCCAGTTGAAAGGTCTTTATTGTC-
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* *
23200 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * * * *
23243 TTTTAAAAAAGGCCCC-TCCTGGGTGGAAGGTCTTTATTGTC-
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * *
23284 TTTTCAAAAATGCCCCATCTTGGTTGGAAGGTCC-CAGTTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTA-TTTTCA
*
23327 TTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * * *
23370 TTTCCAAAAATGTCCCTTCCCGGTTGGAAGGTCCCAGTT-TTCGATATCTC
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGT-CC--TTATT---T-TC-A
* *
23420 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCTTTATTGTC-
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * * *
23462 TTTTCAAAAGTCCCCCTTCCTGGTTGGAAGGTCCATGTTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * **
23505 TTTCCAAAACTGCCCCTTCCTGGTTGGAAGGTCCTCGTTTTCA
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
* * *
23548 TTTCCAAAAATGCCCCTTCCCGGTCGGAAGGTCC
1 TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCC
23582 CAGTTTTCCT
Statistics
Matches: 547, Mismatches: 72, Indels: 55
0.81 0.11 0.08
Matches are distributed among these distances:
41 15 0.03
42 147 0.27
43 256 0.47
44 48 0.09
45 4 0.01
46 4 0.01
47 4 0.01
48 6 0.01
49 6 0.01
50 57 0.10
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (43 bp):
TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCA
Found at i:23412 original size:262 final size:263
Alignment explanation
Indices: 22854--23589 Score: 1129
Period size: 262 Copynumber: 2.8 Consensus size: 263
22844 ATTCCTATTT
* *
22854 TGCCCTTCCTGGTCGGAAGGTCCCAGTTTTCCATATCTCTTTTCAAAAATGCCCCTTCCTGGTTG
1 TGCCCTTCCCGGTCGGAAGGTCCCAGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCTGGTTG
22919 GAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCT-TCTTTCATTTTC
66 GAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGT-TTTCATTTTC
* *
22983 AAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTCCAAAAAATGCCCTTTCCTGGTTG
130 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCC-AAAAATGCCCCTTCCTGGTTG
* *
23048 GAATGTCCTTA-TTTTCATTTCCAAAAATACCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTC
194 GAAGGTCC-CAGTTTTCATTTCCAAAAATACCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTC
23112 CAAAAA
258 CAAAAA
* * **
23118 TGCCCTTTCCCAGTCGGAAGGTCCCGGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCCAGTT
1 TGCCC-TTCCCGGTCGGAAGGTCCCAGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCTGGTT
* *
23183 GAAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTTA
65 GGAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTTC
* * * * * * * *
23248 AAAAAGGCCCC-TCCTGGGTGGAAGGTCTTTATTGTC-TTTTCAAAAATGCCCCATCTTGGTTGG
130 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGG
*
23311 AAGGTCCCAGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCA
195 AAGGTCCCAGTTTTCATTTCCAAAAATACCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCA
23376 AAAA
260 AAAA
*
23380 TGTCCCTTCCCGGTTGGAAGGTCCCAGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCTGGTT
1 TG-CCCTTCCCGGTCGGAAGGTCCCAGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCTGGTT
* * * *
23445 GGAAGGTCTTTATTGTCTTTTCAAAAGTCCCCCTTCCTGGTTGGAAGGTCCATGTTTTCATTTCC
65 GGAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTTC
* * * *
23510 AAAACTGCCCCTTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGCCCCTTCCCGGTCGG
130 AAAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGG
23575 AAGGTCCCAGTTTTC
195 AAGGTCCCAGTTTTC
23590 CTTCGATAAT
Statistics
Matches: 422, Mismatches: 44, Indels: 12
0.88 0.09 0.03
Matches are distributed among these distances:
261 1 0.00
262 207 0.49
263 27 0.06
264 62 0.15
265 124 0.29
266 1 0.00
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (263 bp):
TGCCCTTCCCGGTCGGAAGGTCCCAGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCTGGTTG
GAAGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTTCA
AAAATGCCCCTTCCTGGTTGGAAGGTCCTTGTTTTCATTTCCAAAAATGCCCCTTCCTGGTTGGA
AGGTCCCAGTTTTCATTTCCAAAAATACCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAA
AAA
Found at i:23488 original size:178 final size:176
Alignment explanation
Indices: 22856--23589 Score: 877
Period size: 178 Copynumber: 4.2 Consensus size: 176
22846 TCCTATTTTG
*
22856 CCCTTCCTGGTCGGAAGGTCCCAGTTTTCCATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGA
1 CCCTTCCTGGTTGGAAGGTCCCAGTTTT-CATAT-TCTTTTCAAAAATGCCCCTTCCTGGTTGGA
* *
22921 AGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCC-TTCTTTCATTTTCAA
64 AGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGT-TTTCATTTCCAA
* *
22985 AAATGCCCCTTCCTGGTTGGAAGGTCCCTGTTTTCATTTCCAAAAAATGC
128 AAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCC-AAAAATGC
* * * *
23035 CCTTTCCTGGTTGGAATGTCCTTA-TTTTCAT-TTC----CAAAAATACCCCTTCCTGGTTGGAA
1 CCCTTCCTGGTTGGAAGGTCC-CAGTTTTCATATTCTTTTCAAAAATGCCCCTTCCTGGTTGGAA
* * * * ** * *
23094 GGTCCTTATTTTCATTTCCAAAAATGCCCTTTCCCAGTCGGAAGGTCCCGGTTTTCGATATCTCT
65 GGTCTTTATTGTC-TTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTC-AT-T-TC-
** * * * *
23159 TTTCAAAAATGCCCCTTCCCAGTTGAAAGGTCTTTATTGTC-TTTTCAAAAATGC
125 ---CAAAAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAAAAATGC
* * * *
23213 CCCTTCCTGGTTGGAAGGTCCCTGTTTTC--A---TTTTAAAAAAGGCCCC-TCCTGGGTGGAAG
1 CCCTTCCTGGTTGGAAGGTCCCAGTTTTCATATTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAG
* *
23272 GTCTTTATTGTCTTTTCAAAAATGCCCCATCTTGGTTGGAAGGTCCCAGTTTTCATTTCCAAAAA
66 GTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCATTTCCAAAAA
*
23337 TGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAAAAATGT
131 TGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAAAAATGC
*
23383 CCCTTCCCGGTTGGAAGGTCCCAGTTTTCGATATCTCTTTTCAAAAATGCCCCTTCCTGGTTGGA
1 CCCTTCCTGGTTGGAAGGTCCCAGTTTTC-ATAT-TCTTTTCAAAAATGCCCCTTCCTGGTTGGA
* *
23448 AGGTCTTTATTGTCTTTTCAAAAGTCCCCCTTCCTGGTTGGAAGGT-CCATGTTTTCATTTCCAA
64 AGGTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCA-GTTTTCATTTCCAA
* **
23512 AACTGCCCCTTCCTGGTTGGAAGGTCCTCGTTTTCATTTCCAAAAATGC
128 AAATGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAAAAATGC
* *
23561 CCCTTCCCGGTCGGAAGGTCCCAGTTTTC
1 CCCTTCCTGGTTGGAAGGTCCCAGTTTTC
23590 CTTCGATAAT
Statistics
Matches: 468, Mismatches: 61, Indels: 53
0.80 0.10 0.09
Matches are distributed among these distances:
169 33 0.07
170 38 0.08
172 35 0.07
173 37 0.08
174 4 0.01
175 3 0.01
176 37 0.08
177 40 0.09
178 183 0.39
179 26 0.06
180 32 0.07
ACGTcount: A:0.20, C:0.26, G:0.18, T:0.36
Consensus pattern (176 bp):
CCCTTCCTGGTTGGAAGGTCCCAGTTTTCATATTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAG
GTCTTTATTGTCTTTTCAAAAATGCCCCTTCCTGGTTGGAAGGTCCCAGTTTTCATTTCCAAAAA
TGCCCCTTCCTGGTTGGAAGGTCCTTATTTTCATTTCCAAAAATGC
Found at i:23654 original size:41 final size:40
Alignment explanation
Indices: 23597--23800 Score: 257
Period size: 41 Copynumber: 5.0 Consensus size: 40
23587 TTCCTTCGAT
* *
23597 AATTCCCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTCTTA
1 AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGT-TTA
*
23638 AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTG-TCA
1 AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTA
* * * *
23677 GCATTCCTAGTTTGCCCTTCCTCATCGGAAGGTATTGTTTA
1 -AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTA
* * * *
23718 AGTTCACCAGTTTGTCCTTCCTCACCAGAAAGTGTTGTTTA
1 AATTC-CCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTA
* *
23759 GATTCCCAGTTTGCCATTCCTCATCAGAAGGTGTTGTTTA
1 AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTA
23799 AA
1 AA
23801 GCCCATTCTT
Statistics
Matches: 137, Mismatches: 23, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
39 2 0.01
40 67 0.49
41 68 0.50
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (40 bp):
AATTCCCAGTTTGCCCTTCCTCATCAGAAGGTGTTGTTTA
Found at i:23737 original size:81 final size:80
Alignment explanation
Indices: 23598--23800 Score: 282
Period size: 81 Copynumber: 2.5 Consensus size: 80
23588 TCCTTCGATA
* *
23598 ATTCCCAGTTTGCCCTTTCTCATCGGAAGGTGTTGTCTTAAATTCCCAGTTTGCCCTTCCTCATC
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGT-TTAAATTCCCAGTTTGCCCTTCCTCACC
*
23663 AGAAGGTGTTG-TCAG
65 AGAAAGTGTTGTTCAG
* * * *
23678 CATTCCTAGTTTGCCCTTCCTCATCGGAAGGTATTGTTTAAGTTCACCAGTTTGTCCTTCCTCAC
1 -ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTC-CCAGTTTGCCCTTCCTCAC
*
23743 CAGAAAGTGTTGTTTAG
64 CAGAAAGTGTTGTTCAG
* *
23760 ATTCCCAGTTTGCCATTCCTCATCAGAAGGTGTTGTTTAAA
1 ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAA
23801 GCCCATTCTT
Statistics
Matches: 107, Mismatches: 13, Indels: 4
0.86 0.10 0.03
Matches are distributed among these distances:
80 7 0.07
81 97 0.91
82 3 0.03
ACGTcount: A:0.20, C:0.25, G:0.19, T:0.37
Consensus pattern (80 bp):
ATTCCCAGTTTGCCCTTCCTCATCGGAAGGTGTTGTTTAAATTCCCAGTTTGCCCTTCCTCACCA
GAAAGTGTTGTTCAG
Found at i:23875 original size:39 final size:40
Alignment explanation
Indices: 23816--23905 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 40
23806 TTCTTTCCAG
* * *
23816 TTTGCCCTTCCCCACTGGAAGGT-TTGATTTTATTCCTGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCATGT
* *
23855 TTTGCCCTTTCCCGCCGGAAGGTGTTGATTTCATTCATGT
1 TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCATGT
23895 TTTGCCCTTCC
1 TTTGCCCTTCC
23906 TGGTAGGATG
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
39 20 0.45
40 24 0.55
ACGTcount: A:0.11, C:0.28, G:0.19, T:0.42
Consensus pattern (40 bp):
TTTGCCCTTCCCCACCGGAAGGTGTTGATTTCATTCATGT
Found at i:23959 original size:48 final size:48
Alignment explanation
Indices: 23887--24263 Score: 249
Period size: 48 Copynumber: 8.4 Consensus size: 48
23877 TGTTGATTTC
* * *
23887 ATTCATGTTTTGCCCTTCCTGGTAGGATGGTGTCGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTAGGATGGTGTTGTTTTCAATGTTTT
*
23935 ATTCATGTTTTGCCCTTCCCGGTAGGAAT-GTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTAGG-ATGGTGTTGTTTTCAATGTTTT
* * ** * *
23983 ATTCCTATTTTGCCCTTCCCTGCCGGAAGGTGTTG------A--TTTC
1 ATTCCTGTTTTGCCCTTCCCGGTAGGATGGTGTTGTTTTCAATGTTTT
* *
24023 ATTCATGTTTTGCCCTTCCCGGTCGGAAT-GTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTAGG-ATGGTGTTGTTTTCAATGTTTT
* * * ** *
24071 ATTCCTGTTTTGCCCTTCCTCAG-CGGAAGACGTCGTTTTC--------
1 ATTCCTGTTTTGCCCTTCC-CGGTAGGATGGTGTTGTTTTCAATGTTTT
* * *
24111 ATTCCTATTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTT
1 ATTCCTGTTTTGCCCTTCCCGGTAGGATGGTGTTGTTTTCAATGTTTT
* * * *
24159 ATTCCTGTTTTGCCCTTCCCCGTCGGAAGGTGTTG------A--TTTC
1 ATTCCTGTTTTGCCCTTCCCGGTAGGATGGTGTTGTTTTCAATGTTTT
* *
24199 ATTCCTATTTTGCCCTTCCCTGTA--A-GGTGTTGTTATT-AATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTAGGATGGTGTTGTT-TTCAATGTTTT
*
24244 ATTCCGGTTTTGCCCTTCCC
1 ATTCCTGTTTTGCCCTTCCC
24264 CAGCGGAAGA
Statistics
Matches: 262, Mismatches: 37, Indels: 63
0.72 0.10 0.17
Matches are distributed among these distances:
37 7 0.03
38 1 0.00
39 2 0.01
40 86 0.33
41 1 0.00
42 2 0.01
43 1 0.00
45 21 0.08
46 1 0.00
47 2 0.01
48 134 0.51
49 4 0.02
ACGTcount: A:0.13, C:0.22, G:0.20, T:0.45
Consensus pattern (48 bp):
ATTCCTGTTTTGCCCTTCCCGGTAGGATGGTGTTGTTTTCAATGTTTT
Found at i:24027 original size:88 final size:86
Alignment explanation
Indices: 23935--24348 Score: 487
Period size: 88 Copynumber: 4.8 Consensus size: 86
23925 TCAATGTTTT
* * *
23935 ATTCATGTTTTGCCCTTCCCGGTAGGAATGTGTTGTTTTCAATGTTTTATTCCTATTTTGCCCTT
1 ATTCCTGTTTTGCCCTTCCCGGT-GGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTT
* ** *
24000 CCCTGCCGGAAGGTGTTGATTTC
65 CCCAG-CGGAAGACGTCGATTTC
* *
24023 ATTCATGTTTTGCCCTTCCCGGTCGGAATGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTT
1 ATTCCTGTTTTGCCCTTCCCGGT-GGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTT
*
24088 CCTCAGCGGAAGACGTCGTTTTC
65 CC-CAGCGGAAGACGTCGATTTC
* *
24111 ATTCCTATTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTT
1 ATTCCTGTTTTGCCCTTCCCGGT-GGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTT
* ** *
24176 CCCCGTCGGAAGGTGTTGATTTC
65 CCCAG-CGGAAGACGTCGATTTC
* * *
24199 ATTCCTATTTTGCCCTTCCC--TGTAAGGTGTTGTTATT-AATGTTTTATTCCGGTTTTGCCCTT
1 ATTCCTGTTTTGCCCTTCCCGGTGGAAGGTGTTGTT-TTCAATGTTTTATTCCTGTTTTGCCCTT
*
24261 CCCCAGCGGAAGACGTCGTTTTC
65 -CCCAGCGGAAGACGTCGATTTC
* * * * * *
24284 ATTCCCGTTTTGCCCTTCCCGGTCGAAAG-GTTG-TTTCAATGTTTTATTCCCGTTTTTCCTTTC
1 ATTCCTGTTTTGCCCTTCCCGGTGGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTC
24347 CC
66 CC
24349 CATCAGAAGG
Statistics
Matches: 286, Mismatches: 33, Indels: 18
0.85 0.10 0.05
Matches are distributed among these distances:
84 5 0.02
85 89 0.31
86 11 0.04
87 6 0.02
88 173 0.60
89 2 0.01
ACGTcount: A:0.13, C:0.24, G:0.19, T:0.43
Consensus pattern (86 bp):
ATTCCTGTTTTGCCCTTCCCGGTGGAAGGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTC
CCAGCGGAAGACGTCGATTTC
Found at i:24037 original size:136 final size:136
Alignment explanation
Indices: 23843--24089 Score: 417
Period size: 136 Copynumber: 1.8 Consensus size: 136
23833 GAAGGTTTGA
* *
23843 TTTTATTCCTGTTTTGCCCTTTCCCGCCGGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCTG
1 TTTTATTCCTATTTTGCCCTTTCCCGCCGGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCCG
23908 GTAGG-ATGGTGTCGTTTTCAATGTTTTATTCATGTTTTGCCCTTCCCGGTAGGAATGTGTTGTT
66 GTAGGAAT-GTGTCGTTTTCAATGTTTTATTCATGTTTTGCCCTTCCCGGTAGGAATGTGTTGTT
23972 TTCAATG
130 TTCAATG
23979 TTTTATTCCTATTTTGCCC-TTCCCTGCCGGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCC
1 TTTTATTCCTATTTTGCCCTTTCCC-GCCGGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCC
* * *
24043 GGTCGGAATGTGTTGTTTTCAATGTTTTATTCCTGTTTTGCCCTTCC
65 GGTAGGAATGTGTCGTTTTCAATGTTTTATTCATGTTTTGCCCTTCC
24090 TCAGCGGAAG
Statistics
Matches: 104, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
135 5 0.05
136 97 0.93
137 2 0.02
ACGTcount: A:0.12, C:0.22, G:0.20, T:0.46
Consensus pattern (136 bp):
TTTTATTCCTATTTTGCCCTTTCCCGCCGGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCCG
GTAGGAATGTGTCGTTTTCAATGTTTTATTCATGTTTTGCCCTTCCCGGTAGGAATGTGTTGTTT
TCAATG
Found at i:24050 original size:40 final size:40
Alignment explanation
Indices: 23983--24218 Score: 168
Period size: 40 Copynumber: 5.5 Consensus size: 40
23973 TCAATGTTTT
* * *
23983 ATTCCTATTTTGCCCTTCCCTGCCGGAAGGTGTTGATTTC
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGATTTC
* * *
24023 ATTCATGTTTTGCCCTTCCCGGTCGGAATGTGTTGTTTTCAATGTTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAA-G-G-TG--TT-GA--TTTC
* ** * *
24071 ATTCCTGTTTTGCCCTTCCTCAG-CGGAAGACGTCGTTTTC
1 ATTCCTGTTTTGCCCTTCC-CGGTCGGAAGGTGTTGATTTC
* * *
24111 ATTCCTATTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTT
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTG--------ATTTC
*
24159 ATTCCTGTTTTGCCCTTCCCCGTCGGAAGGTGTTGATTTC
1 ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGATTTC
*
24199 ATTCCTATTTTGCCCTTCCC
1 ATTCCTGTTTTGCCCTTCCC
24219 TGTAAGGTGT
Statistics
Matches: 151, Mismatches: 27, Indels: 36
0.71 0.13 0.17
Matches are distributed among these distances:
39 2 0.01
40 76 0.50
41 1 0.01
42 1 0.01
43 3 0.02
45 3 0.02
46 1 0.01
47 1 0.01
48 61 0.40
49 2 0.01
ACGTcount: A:0.13, C:0.25, G:0.19, T:0.43
Consensus pattern (40 bp):
ATTCCTGTTTTGCCCTTCCCGGTCGGAAGGTGTTGATTTC
Found at i:24126 original size:176 final size:173
Alignment explanation
Indices: 23942--24333 Score: 585
Period size: 176 Copynumber: 2.3 Consensus size: 173
23932 TTTATTCATG
* *
23942 TTTTGCCCTTCCCGGTAGGAATGTGTTGTTTTCAATGTTTTATTCCTATTTTGCCCTTCCCTGCC
1 TTTTGCCCTTCCCGGTAGGAAAGTGTTGTTTTCAATGTTTTATTCCTATTTTGCCCTTCCCCGCC
* *
24007 GGAAGGTGTTGATTTCATTCATGTTTTGCCCTTCCCGGTCGGAATGTGTTGTT-TTCAATGTTTT
66 GGAAGGTGTTGATTTCATTCATATTTTGCCCTTCCC--T-GGAAGGTGTTGTTATT-AATGTTTT
* * *
24071 ATTCCTGTTTTGCCCTTCCTCAGCGGAAGACGTCGTTTTCATTCCTA
127 ATTCCGGTTTTGCCCTTCCCCAGCGGAAGACGTCGTTTTCATTCCCA
* * * *
24118 TTTTGCCCTTCCCGGTAGGAAGGTGTTGTTTTCAATATTTTATTCCTGTTTTGCCCTTCCCCGTC
1 TTTTGCCCTTCCCGGTAGGAAAGTGTTGTTTTCAATGTTTTATTCCTATTTTGCCCTTCCCCGCC
* *
24183 GGAAGGTGTTGATTTCATTCCTATTTTGCCCTTCCCTGTAAGGTGTTGTTATTAATGTTTTATTC
66 GGAAGGTGTTGATTTCATTCATATTTTGCCCTTCCCTGGAAGGTGTTGTTATTAATGTTTTATTC
*
24248 CGGTTTTGCCCTTCCCCAGCGGAAGACGTCGTTTTCATTCCCG
131 CGGTTTTGCCCTTCCCCAGCGGAAGACGTCGTTTTCATTCCCA
*
24291 TTTTGCCCTTCCCGGT-CGAAAG-GTTG-TTTCAATGTTTTATTCC
1 TTTTGCCCTTCCCGGTAGGAAAGTGTTGTTTTCAATGTTTTATTCC
24334 CGTTTTTCCT
Statistics
Matches: 199, Mismatches: 16, Indels: 8
0.89 0.07 0.04
Matches are distributed among these distances:
170 16 0.08
171 4 0.02
172 4 0.02
173 78 0.39
174 3 0.02
176 94 0.47
ACGTcount: A:0.13, C:0.24, G:0.20, T:0.43
Consensus pattern (173 bp):
TTTTGCCCTTCCCGGTAGGAAAGTGTTGTTTTCAATGTTTTATTCCTATTTTGCCCTTCCCCGCC
GGAAGGTGTTGATTTCATTCATATTTTGCCCTTCCCTGGAAGGTGTTGTTATTAATGTTTTATTC
CGGTTTTGCCCTTCCCCAGCGGAAGACGTCGTTTTCATTCCCA
Found at i:26373 original size:28 final size:28
Alignment explanation
Indices: 26333--26392 Score: 102
Period size: 28 Copynumber: 2.1 Consensus size: 28
26323 AAAGAAAACT
26333 AAAACTTGATGGGAACTTTCCCAATTTG
1 AAAACTTGATGGGAACTTTCCCAATTTG
* *
26361 AAAACTTGATGGGAAGTTTCCCAGTTTG
1 AAAACTTGATGGGAACTTTCCCAATTTG
26389 AAAA
1 AAAA
26393 GAGCTAAATT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (28 bp):
AAAACTTGATGGGAACTTTCCCAATTTG
Found at i:28180 original size:19 final size:19
Alignment explanation
Indices: 28156--28202 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
28146 CTAAAATCTA
28156 AAGCCCAACG-AAATTTAAG
1 AAGCCCAACGTAAA-TTAAG
*
28175 AAGCCCAAAGTAAATTAAG
1 AAGCCCAACGTAAATTAAG
28194 AAGCCCAAC
1 AAGCCCAAC
28203 CTATACTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.88
20 3 0.12
ACGTcount: A:0.49, C:0.23, G:0.15, T:0.13
Consensus pattern (19 bp):
AAGCCCAACGTAAATTAAG
Found at i:33372 original size:6 final size:6
Alignment explanation
Indices: 33361--33394 Score: 52
Period size: 6 Copynumber: 5.7 Consensus size: 6
33351 ATGGGAAATG
33361 AAAAGA AAAAGA AAAAGA AAAA-A GAAAAGA AAAA
1 AAAAGA AAAAGA AAAAGA AAAAGA -AAAAGA AAAA
33395 AGTGTTGCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 1 0.04
6 24 0.92
7 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAGA
Found at i:33378 original size:12 final size:12
Alignment explanation
Indices: 33360--33396 Score: 58
Period size: 12 Copynumber: 3.1 Consensus size: 12
33350 GATGGGAAAT
33360 GAAAAG-AAAAA
1 GAAAAGAAAAAA
33371 GAAAAAGAAAAAA
1 G-AAAAGAAAAAA
33384 GAAAAGAAAAAA
1 GAAAAGAAAAAA
33396 G
1 G
33397 TGTTGCTGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 1 0.04
12 17 0.71
13 6 0.25
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
GAAAAGAAAAAA
Found at i:35089 original size:41 final size:41
Alignment explanation
Indices: 34913--35671 Score: 987
Period size: 40 Copynumber: 18.9 Consensus size: 41
34903 AAGACAAGAT
* *
34913 TAAACAACACCTTCCGACG-GGAAGGGCAAACTGGGAAAAG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* * *
34953 TGAACAACACCTTCCGATGAGGAAGGGTAAACT-GG-AATT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* *
34992 TAAACAACACCTTCCGATGAGGAAGGGCAAACTCGG-AATT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
35032 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
*
35073 TAAACGACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
*
35114 TAAACAACACCTTCCGATGAGGAAGGGCAAATTGGGAAATG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* * *
35155 TAAACAACACCTTCCGGTGAGGAAGGGCAAACTTGG-AATT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* *
35195 TAAAAAACACCTTCCGATGGGGAAGGGCAAACTGGGCAAA-G
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGG-AAATG
*
35236 TAAAGAACACCTTCCGATGAGGAAGGGCAAACT-GGAAATG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* *
35276 CT-GACAACACCTTCCGATGAGGAAGGGCAAACTGGTAAACT-
1 -TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAA-TG
* * * * *
35317 T-AACAACACCTTTCAATTACGAAGGGCAAACTGGG-AATT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
** * * *
35356 TTGACAACACCTTCCGATGACGAAGGGCAAACT-AGCAATG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
** *
35396 TTGACAACACCTTCCGATGAGGAAGGGCAAACT-GGAATTG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
*
35436 TAAACAACACATTCCGATGAGGAAGGGCAAACT-GGAAATG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* * *
35476 TAAACAACACCTTCCGGTGGGGAAGGGCAAACT-GG-AATT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* * *
35515 TAAACAACACCTTCCAATGGGGAAGGGCAAACTGGGAAAAG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* *
35556 TAAACAACATCTTCCGATGAGGAAGGGCAAACT-GGAAATT
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
* *
35596 TAAACAACACCTTTCGATG-GAGAAGGGCAAACTGGGAAAAG
1 TAAACAACACCTTCCGATGAG-GAAGGGCAAACTGGGAAATG
35637 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
1 TAAACAACACCTTCCGATGAGGAAGGGCAAACTGG
35672 AATGTTGAAG
Statistics
Matches: 638, Mismatches: 64, Indels: 33
0.87 0.09 0.04
Matches are distributed among these distances:
38 1 0.00
39 75 0.12
40 326 0.51
41 232 0.36
42 4 0.01
ACGTcount: A:0.38, C:0.20, G:0.26, T:0.16
Consensus pattern (41 bp):
TAAACAACACCTTCCGATGAGGAAGGGCAAACTGGGAAATG
Done.