Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003690.1 Hibiscus syriacus cultivar Beakdansim tig00007884_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: 65802
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:8608 original size:15 final size:15
Alignment explanation
Indices: 8588--8617 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8578 CCTATTTACA
8588 CATGCAAGAAACATT
1 CATGCAAGAAACATT
*
8603 CATGCAAGAACCATT
1 CATGCAAGAAACATT
8618 TCAGAGTAGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.23, G:0.13, T:0.20
Consensus pattern (15 bp):
CATGCAAGAAACATT
Found at i:9551 original size:22 final size:22
Alignment explanation
Indices: 9524--9566 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
9514 CCCTTCCTGT
9524 TCCATTATTTGGTACATGTTCC
1 TCCATTATTTGGTACATGTTCC
9546 TCCATTATTTGGTACATGTTC
1 TCCATTATTTGGTACATGTTC
9567 TACCGCTGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.19, C:0.21, G:0.14, T:0.47
Consensus pattern (22 bp):
TCCATTATTTGGTACATGTTCC
Found at i:13306 original size:23 final size:24
Alignment explanation
Indices: 13280--13358 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 24
13270 AACTTCAAAA
*
13280 TCAAAAAACCT-TGTTTACCAGAG
1 TCAAAAAACCTATATTTACCAGAG
* * *
13303 TCAAAAAAACTATTTTTACCATAG
1 TCAAAAAACCTATATTTACCAGAG
* *
13327 TCGAAAAA-CTCTATTTACCAGAG
1 TCAAAAAACCTATATTTACCAGAG
* *
13350 CCGAAAAAC
1 TCAAAAAAC
13359 TATGTTTGTA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
23 29 0.63
24 17 0.37
ACGTcount: A:0.43, C:0.22, G:0.10, T:0.25
Consensus pattern (24 bp):
TCAAAAAACCTATATTTACCAGAG
Found at i:13357 original size:24 final size:24
Alignment explanation
Indices: 13293--13361 Score: 79
Period size: 23 Copynumber: 3.0 Consensus size: 24
13283 AAAAACCTTG
* *
13293 TTTACCAGAGTCAAAAAAACTATT
1 TTTACCAGAGTCGAAAAAACTATA
* *
13317 TTTACCATAGTCG-AAAAACTCTA
1 TTTACCAGAGTCGAAAAAACTATA
*
13340 TTTACCAGAGCCG-AAAAACTAT
1 TTTACCAGAGTCGAAAAAACTAT
13362 GTTTGTACAA
Statistics
Matches: 38, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
23 27 0.71
24 11 0.29
ACGTcount: A:0.42, C:0.20, G:0.10, T:0.28
Consensus pattern (24 bp):
TTTACCAGAGTCGAAAAAACTATA
Found at i:14902 original size:21 final size:21
Alignment explanation
Indices: 14878--14941 Score: 101
Period size: 21 Copynumber: 3.0 Consensus size: 21
14868 GCTAAAAGCA
*
14878 CTCGTGGCGATAGTAAAAACG
1 CTCGCGGCGATAGTAAAAACG
*
14899 CTCGCGGCGATAGTAAAAATG
1 CTCGCGGCGATAGTAAAAACG
*
14920 CTAGCGGCGATAGTAAAAACG
1 CTCGCGGCGATAGTAAAAACG
14941 C
1 C
14942 CACAAGAAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.17
Consensus pattern (21 bp):
CTCGCGGCGATAGTAAAAACG
Found at i:15053 original size:43 final size:42
Alignment explanation
Indices: 15002--15215 Score: 218
Period size: 43 Copynumber: 5.1 Consensus size: 42
14992 AAATAAAAAT
* * *
15002 GCCGCAAAAAGTCAAGATCTATAGCGGCATTTTTGAAACAAAC
1 GCCGCAAAAGGTCAA-ATCTGTAGCGGCGTTTTTGAAACAAAC
* * * * *
15045 GCCGCAAAAGGTCAAATCTATAGTGGTGTTTTTGTAGACAAAT
1 GCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTTG-AAACAAAC
* * *
15088 GCCGCAAAAGGTCAAATCTGTAGCAGTGTTTTTGGATACAAAC
1 GCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTT-GAAACAAAC
* * * *
15131 GCCGCAAAAGG-CTAGATTTGTAGCGGCGTTTTTG-GA-AAAT
1 GCCGCAAAAGGTC-AAATCTGTAGCGGCGTTTTTGAAACAAAC
* *
15171 GCCGCAAAAGGTCATATCTGTAGCGGCGTTTTTGGAACAAAC
1 GCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTTGAAACAAAC
15213 GCC
1 GCC
15216 ACTAATTACC
Statistics
Matches: 144, Mismatches: 21, Indels: 13
0.81 0.12 0.07
Matches are distributed among these distances:
40 33 0.23
41 3 0.02
42 24 0.17
43 83 0.58
44 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (42 bp):
GCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTTGAAACAAAC
Found at i:15162 original size:86 final size:82
Alignment explanation
Indices: 14997--15215 Score: 269
Period size: 86 Copynumber: 2.6 Consensus size: 82
14987 TTGTGAAATA
* * * *
14997 AAAATGCCGCAAAAAGTCAAGATCTATAGCGGCATTTTTGAAACAAACGCCGCAAAAGGTCAAAT
1 AAAATGCCGCAAAAGGTCAA-ATCTGTAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAAT
* *
15062 CTATAGTGGTGTTTTTGTAG
65 CTATAGCGGCGTTTTTG--G
* * *
15082 ACAAATGCCGCAAAAGGTCAAATCTGTAGCAGTGTTTTTGGATACAAACGCCGCAAAAGG-CTAG
1 A-AAATGCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTTGGA-ACAAACGCCGCAAAAGGTC-AA
* *
15146 ATTTGTAGCGGCGTTTTTGG
63 ATCTATAGCGGCGTTTTTGG
*
15166 AAAATGCCGCAAAAGGTCATATCTGTAGCGGCGTTTTTGGAACAAACGCC
1 AAAATGCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTTGGAACAAACGCC
15216 ACTAATTACC
Statistics
Matches: 117, Mismatches: 14, Indels: 9
0.84 0.10 0.06
Matches are distributed among these distances:
82 9 0.08
83 37 0.32
84 2 0.02
85 18 0.15
86 51 0.44
ACGTcount: A:0.33, C:0.18, G:0.24, T:0.25
Consensus pattern (82 bp):
AAAATGCCGCAAAAGGTCAAATCTGTAGCGGCGTTTTTGGAACAAACGCCGCAAAAGGTCAAATC
TATAGCGGCGTTTTTGG
Found at i:19137 original size:41 final size:41
Alignment explanation
Indices: 19080--19419 Score: 351
Period size: 41 Copynumber: 8.2 Consensus size: 41
19070 AGAGGCAACT
* *
19080 CACTAAA-TACAAGTCTATAGTGGCGTTTGTATAAAAACGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
* ** * *
19120 CACTAATGTACGAGTCTATAGCAACGTTTGTACAAAAATGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
* * * * *
19161 CACTAAAGTACAAGCCTATTGCGGCATTTGTAAACACAAACGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATA-A-AAACGC
* * * * * *
19204 CACTAAAGTACAAGCCTATTA-CGACATTTGTAAACACAAACAC
1 CACTAAAGTACGAGTCTA-TAGCGGCGTTTGTATA-A-AAACGC
*
19247 CACTAAAGTACGAGTCTATAGCGACGTTTGTATAAAAACGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
* * *
19288 CACTAAAGTAGGAGTCTATAGTGGCATTTGTATAAAAACGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
* * * *
19329 CGCTAAAGTACTACTCTATCGCGGCGTTTGTATAAAAACGC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
* * * *
19370 CACTGAAGTACGAGTCTATAGTGGCGTTTTTATAAAAACTC
1 CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
19411 CACTAAAGT
1 CACTAAAGT
19420 TACCATTTTG
Statistics
Matches: 251, Mismatches: 44, Indels: 9
0.83 0.14 0.03
Matches are distributed among these distances:
40 6 0.02
41 170 0.68
42 4 0.02
43 70 0.28
44 1 0.00
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (41 bp):
CACTAAAGTACGAGTCTATAGCGGCGTTTGTATAAAAACGC
Found at i:23382 original size:2 final size:2
Alignment explanation
Indices: 23377--23437 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
23367 TATCTTAATT
23377 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
23419 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
23438 CTTTGTTATT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:29645 original size:37 final size:38
Alignment explanation
Indices: 29578--29653 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 38
29568 AGAATTTTCG
*
29578 AATTTCTCCATAAGAAATTTCTTAGTTAGAAAAAACGA
1 AATTTCTCCATAAGAAATTTCTTAGCTAGAAAAAACGA
* * *
29616 AATTTCT-CATAAGTAGTTTTTTAGCTAGAAAAAACGA
1 AATTTCTCCATAAGAAATTTCTTAGCTAGAAAAAACGA
29653 A
1 A
29654 TGAAGTGGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
37 27 0.79
38 7 0.21
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (38 bp):
AATTTCTCCATAAGAAATTTCTTAGCTAGAAAAAACGA
Found at i:31616 original size:108 final size:104
Alignment explanation
Indices: 31441--31660 Score: 277
Period size: 108 Copynumber: 2.1 Consensus size: 104
31431 TAATTCTCGC
31441 GTGT-TTTTGAATGTTAGCCACATGTAAGGACTGATTCTGATATTTACCCATTTCTTATGCATGT
1 GTGTGTTTTGAATGTTAGCCACATGTAAGGACTGATTCTGATATTTACCCATTTCTTATGCATGT
31505 TATATATTTTTTGGGATAATTGTTGCTTAGTCCCCATAGTTTA
66 TATA-A--TTTTGGGATAATTGTTGCTTAGT-CCCATAGTTTA
* * * * *
31548 GTGTGTTTTGCATGTTGGTCACCTGTAAGGACTGAATT-TGCTATTTACCC-TTT-TTATGCATG
1 GTGTGTTTTGAATGTTAGCCACATGTAAGGACTG-ATTCTGATATTTACCCATTTCTTATGCATG
* *
31610 CTTTATAATTTTGGGATATTTGTTGTTTAGTCCCATAGTTTA
65 --TTATAATTTTGGGATAATTGTTGCTTAGTCCCATAGTTTA
*
31652 GCGTGTTTT
1 GTGTGTTTT
31661 TACATTTTGG
Statistics
Matches: 101, Mismatches: 8, Indels: 11
0.84 0.07 0.09
Matches are distributed among these distances:
104 19 0.19
105 21 0.21
106 9 0.09
107 8 0.08
108 41 0.41
109 3 0.03
ACGTcount: A:0.20, C:0.14, G:0.20, T:0.46
Consensus pattern (104 bp):
GTGTGTTTTGAATGTTAGCCACATGTAAGGACTGATTCTGATATTTACCCATTTCTTATGCATGT
TATAATTTTGGGATAATTGTTGCTTAGTCCCATAGTTTA
Found at i:31673 original size:105 final size:108
Alignment explanation
Indices: 31463--31673 Score: 290
Period size: 105 Copynumber: 2.0 Consensus size: 108
31453 GTTAGCCACA
*
31463 TGTAAGGACTGATTCTGATATTTACCCATTTCTTATGCATGTTATATATTTTTTGGGATAATTGT
1 TGTAAGGACTGATTCTGATATTTACCCATTTCTTATGCATGTTATATATATTTTGGGATAATTGT
* *
31528 TGCTTAGTCCCCATAGTTTAGTGTGTTTTGCATGTTGGTCACC
66 TGCTTAGTCCCCATAGTTTAGCGTGTTTTACATGTTGGTCACC
* *
31571 TGTAAGGACTGAATT-TGCTATTTACCC-TTT-TTATGCATGCTT-TATA-ATTTTGGGATATTT
1 TGTAAGGACTG-ATTCTGATATTTACCCATTTCTTATGCATG-TTATATATATTTTGGGATAATT
* *
31631 GTTGTTTAGT-CCCATAGTTTAGCGTGTTTTTACATTTTGGTCA
64 GTTGCTTAGTCCCCATAGTTTAGCGTG-TTTTACATGTTGGTCA
31674 TATGTAGTGA
Statistics
Matches: 93, Mismatches: 7, Indels: 9
0.85 0.06 0.08
Matches are distributed among these distances:
104 15 0.16
105 35 0.38
106 13 0.14
107 5 0.05
108 22 0.24
109 3 0.03
ACGTcount: A:0.20, C:0.14, G:0.19, T:0.47
Consensus pattern (108 bp):
TGTAAGGACTGATTCTGATATTTACCCATTTCTTATGCATGTTATATATATTTTGGGATAATTGT
TGCTTAGTCCCCATAGTTTAGCGTGTTTTACATGTTGGTCACC
Found at i:32749 original size:131 final size:131
Alignment explanation
Indices: 32507--32857 Score: 515
Period size: 131 Copynumber: 2.7 Consensus size: 131
32497 AGTAATATCT
* * * * *
32507 TCTT-ATTTCGGTTGGAGTAATAAATGATTGCTTTAAGGCATAAGTGATCATTTATTCTCAATGG
1 TCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGATCATTTATTCTCGATTG
* * * * ** **
32571 GAAATAATTATATATTATCATTTTCTCTCGAATCAATATTGATTTTTAAGACGGAATAATGATGT
66 GAAATCATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAATGATAA
32636 C
131 C
*
32637 TCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATTTATTCTCGATTG
1 TCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGATCATTTATTCTCGATTG
* * *
32702 GAAATCGTTAGATATTATCATTTTCACTCGAATCAATATTTAATTTTAAGACAAAATAGTGATAA
66 GAAATCATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAATGATAA
32767 C
131 C
* *
32768 TCTTCATTTTGATTGGAGTAATAAATGACTGCTTTAAGGCATGAGAGATCATTTATTCTCGATTG
1 TCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGATCATTTATTCTCGATTG
*
32833 GAAATCATTAGATATTATCGTTTTC
66 GAAATCATTAGATATTATCATTTTC
32858 TTTCTTAAAA
Statistics
Matches: 198, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
130 4 0.02
131 194 0.98
ACGTcount: A:0.32, C:0.12, G:0.17, T:0.40
Consensus pattern (131 bp):
TCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGATCATTTATTCTCGATTG
GAAATCATTAGATATTATCATTTTCACTCGAATCAATATTGAATTTTAAGACAAAATAATGATAA
C
Found at i:34503 original size:18 final size:18
Alignment explanation
Indices: 34480--34532 Score: 88
Period size: 18 Copynumber: 2.9 Consensus size: 18
34470 GCGTAGAATT
*
34480 TGTCCCGTAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
34498 TGTCCCGAAGGACCACTG
1 TGTCCCGAAGGACCACTA
34516 TGTCCCGAAGGACCACT
1 TGTCCCGAAGGACCACT
34533 TCTTAAGAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 33 1.00
ACGTcount: A:0.23, C:0.34, G:0.25, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:35488 original size:24 final size:20
Alignment explanation
Indices: 35431--35488 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 20
35421 TTCCCATTGA
*
35431 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
*
35451 AGTGTATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
35474 ATGTGCATCGATGCA
1 A-GTGCATCGATGCA
35489 CTATCCATGC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
20 15 0.48
22 1 0.03
23 3 0.10
24 12 0.39
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.33
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:40311 original size:341 final size:335
Alignment explanation
Indices: 39651--40327 Score: 1072
Period size: 341 Copynumber: 2.0 Consensus size: 335
39641 AACTCGATAA
* *
39651 ATTTTTATTTTTGCATGAAATTACAAAATACATATAATCTAGTATAGGAAAACTTTGAGGGTAAA
1 ATTTTGATTTTTGCATGAAATTACAAAATACATATAATCTAGTATACGAAAACTTTGAGGGTAAA
* *
39716 CATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACTAGTATTTCTTTTACAAAATGATGAT
66 CATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAATATTTCTTTTACAAAATGATGAT
* * *
39781 GATGATAATAAATATTTTATAATTTAAAGAATTATAAATTTTATATATTTTTGAAAAACTTATTA
131 GATGATAATAAATATTTTATAATTTAAAGAATTATAAATTTCATATATTTGTGAAAAAATTATTA
* *
39846 ACTTTTAAAATTAATTGTTTAAAAATATAACAATTATTAAAATAAACTTTTAATTACAATTGAGG
196 ACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTGAGG
* *
39911 GATCAATTGAATTCTTATTCATTAATTATTATTTTTAACAATAGTTAATAATATTTATTCATTTT
261 GATCAAATGAATTATTATTCATTAATTATTATTTTTAACAATAGTTAATAATATTTATTCATTTT
39976 TAATAAAATT
326 TAATAAAATT
* *
39986 ATTTTGATTTTTGCATGAAATTACACAATACATATAATCTAGTATACGAAAACTTTGAGGGTAAG
1 ATTTTGATTTTTGCATGAAATTACAAAATACATATAATCTAGTATACGAAAACTTTGAGGGTAAA
*
40051 TATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAATATTTCTTTTACAAAATATTGAT
66 CATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAATATTTCTTTTAC-AAA-A-TGAT
*
40116 GATAATGATGATAATAAATATTTTATAGTTTAAA-AATTATAAATTTCATATATTTGTGAAAAAA
128 G---ATGATGATAATAAATATTTTATAATTTAAAGAATTATAAATTTCATATATTTGTG-AAAAA
*
40180 ATTATTGACTTTTAAAATTAATTGTTT-AAAATATTAAAAAATATTAAAATAAACTTTTAATTAC
189 ATTATTAACTTTTAAAATTAATTGTTTAAAAATA-TAAAAAATATTAAAATAAACTTTTAATTAC
* * * *
40244 AATTGATGGATTAAATGAATTATTATTCATTAATTATTATTTTTAACAACT-TTTAATAATGTTT
253 AATTGAGGGATCAAATGAATTATTATTCATTAATTATTATTTTTAACAA-TAGTTAATAATATTT
40308 ATTCATTTTTAATAAAATT
317 ATTCATTTTTAATAAAATT
40327 A
1 A
40328 GAATTTAATA
Statistics
Matches: 313, Mismatches: 20, Indels: 12
0.91 0.06 0.03
Matches are distributed among these distances:
335 112 0.36
336 3 0.01
337 1 0.00
338 5 0.02
340 28 0.09
341 163 0.52
342 1 0.00
ACGTcount: A:0.43, C:0.06, G:0.08, T:0.44
Consensus pattern (335 bp):
ATTTTGATTTTTGCATGAAATTACAAAATACATATAATCTAGTATACGAAAACTTTGAGGGTAAA
CATTTTAAAATATGAATAATTTTATAAAAGTTTTATAACCAATATTTCTTTTACAAAATGATGAT
GATGATAATAAATATTTTATAATTTAAAGAATTATAAATTTCATATATTTGTGAAAAAATTATTA
ACTTTTAAAATTAATTGTTTAAAAATATAAAAAATATTAAAATAAACTTTTAATTACAATTGAGG
GATCAAATGAATTATTATTCATTAATTATTATTTTTAACAATAGTTAATAATATTTATTCATTTT
TAATAAAATT
Found at i:40435 original size:10 final size:10
Alignment explanation
Indices: 40420--40472 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
40410 TACATTATTT
40420 TTTTATTGAA
1 TTTTATTGAA
40430 TTTTATTGAA
1 TTTTATTGAA
*
40440 TTTTAATT-AT
1 TTTT-ATTGAA
*
40450 TTTTATTGCA
1 TTTTATTGAA
40460 TTTTATTG-A
1 TTTTATTGAA
40469 TTTT
1 TTTT
40473 TTTTAAAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
9 8 0.21
10 27 0.71
11 3 0.08
ACGTcount: A:0.25, C:0.02, G:0.08, T:0.66
Consensus pattern (10 bp):
TTTTATTGAA
Found at i:40453 original size:20 final size:20
Alignment explanation
Indices: 40420--40473 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
40410 TACATTATTT
*
40420 TTTTATTGAATTTTATTGAA
1 TTTTATTGATTTTTATTGAA
*
40440 TTTTAATT-ATTTTTATTGCA
1 TTTT-ATTGATTTTTATTGAA
40460 TTTTATTGATTTTT
1 TTTTATTGATTTTT
40474 TTTAAAAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 3 0.10
20 24 0.80
21 3 0.10
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (20 bp):
TTTTATTGATTTTTATTGAA
Found at i:42535 original size:2 final size:2
Alignment explanation
Indices: 42525--42594 Score: 51
Period size: 2 Copynumber: 36.5 Consensus size: 2
42515 AAATGAAAAA
*
42525 AT AT A- AT AT AT AT AT AT AT AT A- AT AT A- AA AT -T 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
* * *
42563 AA ACT AT AT TT AT AT -T AT AA ACT AT AT AT AT A
1 AT A-T AT AT AT AT AT AT AT AT A-T AT AT AT AT A
42595 AATTATATTT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
1 5 0.09
2 47 0.87
3 2 0.04
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (2 bp):
AT
Found at i:42547 original size:17 final size:17
Alignment explanation
Indices: 42531--42692 Score: 76
Period size: 18 Copynumber: 8.6 Consensus size: 17
42521 AAAAATATAA
42531 TATATATATATATATAA-
1 TATATATATATATA-AAC
*
42548 TATAAAATTATATATAAAC
1 TAT-ATA-TATATATAAAC
*
42567 TATATTTATATTATAAAC
1 TATATATATA-TATAAAC
* **
42585 TATATATATAAATTATATT
1 TATATATATATA-TA-AAC
42604 TATGTGAACTATATATATAAAC
1 TA--T--A-TATATATATAAAC
*
42626 TATGTATATAAAATTATAAAC
1 TA--TATAT-ATA-TATAAAC
*
42647 TATATTTATATTATAAAC
1 TATATATATA-TATAAAC
*
42665 TATATA-ATTATTATAAGC
1 TATATATA-TA-TATAAAC
42683 TATATATATA
1 TATATATATA
42693 AATTATGTTT
Statistics
Matches: 115, Mismatches: 15, Indels: 29
0.72 0.09 0.18
Matches are distributed among these distances:
17 9 0.08
18 55 0.48
19 22 0.19
20 3 0.03
21 10 0.09
22 6 0.05
23 3 0.03
24 7 0.06
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.44
Consensus pattern (17 bp):
TATATATATATATAAAC
Found at i:42656 original size:21 final size:18
Alignment explanation
Indices: 42613--42692 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 18
42603 TTATGTGAAC
42613 TATATA-TATAAACTATGTA
1 TATATATTATAAACTA--TA
*
42632 TATAAAATTATAAACTATA
1 TAT-ATATTATAAACTATA
*
42651 TTTATATTATAAACTATA
1 TATATATTATAAACTATA
*
42669 TA-ATTATTATAAGCTATA
1 TATA-TATTATAAACTATA
42687 TATATA
1 TATATA
42693 AATTATGTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 9
0.79 0.08 0.14
Matches are distributed among these distances:
17 1 0.02
18 32 0.62
19 8 0.15
20 2 0.04
21 9 0.17
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.44
Consensus pattern (18 bp):
TATATATTATAAACTATA
Found at i:42686 original size:98 final size:97
Alignment explanation
Indices: 42555--42735 Score: 310
Period size: 98 Copynumber: 1.9 Consensus size: 97
42545 TAATATAAAA
*
42555 TTATATATAAACTATATTTATATTATAAACTATATATATAAATTATATTTATGTGAACTATATAT
1 TTATATATAAACTATATATATATTATAAACTATATATATAAATTATATTTATGTGAACTATATAT
42620 ATAAACTATGTATATAAAATTATAAACTATAT
66 ATAAACTATGTATATAAAATTATAAACTATAT
* *
42652 TTATATTATAAACTATATA-ATTATTATAAGCTATATATATAAATTATGTTTATGTGAACTATAT
1 TTATA-TATAAACTATATATA-TATTATAAACTATATATATAAATTATATTTATGTGAACTATAT
42716 ATATAAACTATGTATATAAA
64 ATATAAACTATGTATATAAA
42736 CTATATATGT
Statistics
Matches: 79, Mismatches: 3, Indels: 3
0.93 0.04 0.04
Matches are distributed among these distances:
97 6 0.08
98 73 0.92
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.44
Consensus pattern (97 bp):
TTATATATAAACTATATATATATTATAAACTATATATATAAATTATATTTATGTGAACTATATAT
ATAAACTATGTATATAAAATTATAAACTATAT
Found at i:42755 original size:15 final size:13
Alignment explanation
Indices: 42530--42757 Score: 122
Period size: 13 Copynumber: 16.4 Consensus size: 13
42520 AAAAAATATA
*
42530 ATATATATATA-T
1 ATATATATAAACT
*
42542 ATATAATATAAAAT
1 ATAT-ATATAAACT
42556 -TATATATAAACTAT
1 ATATATATAAAC--T
42570 ATTTATATTATAAACT
1 A--TATA-TATAAACT
*
42586 ATATATATAAATT
1 ATATATATAAACT
* *
42599 ATATTTATGTGAACT
1 ATA--TATATAAACT
42614 ATATATATAAACT
1 ATATATATAAACT
* *
42627 ATGTATATAAAAT
1 ATATATATAAACT
* *
42640 -TATAAACTATA-T
1 ATATATA-TAAACT
*
42652 TTATATTATAAACT
1 ATATA-TATAAACT
42666 ATATAATTATTATAAGCT
1 ATAT-A-TA-TA-AA-CT
*
42684 ATATATATAAATT
1 ATATATATAAACT
* * *
42697 ATGTTTATGTGAACT
1 A--TATATATAAACT
42712 ATATATATAAACT
1 ATATATATAAACT
*
42725 ATGTATATAAACT
1 ATATATATAAACT
42738 ATATATGTATAAACT
1 ATATA--TATAAACT
42753 ATATA
1 ATATA
42758 AAATATATAG
Statistics
Matches: 168, Mismatches: 26, Indels: 41
0.71 0.11 0.17
Matches are distributed among these distances:
12 16 0.10
13 75 0.45
14 13 0.08
15 38 0.23
16 6 0.04
17 7 0.04
18 13 0.08
ACGTcount: A:0.48, C:0.05, G:0.04, T:0.43
Consensus pattern (13 bp):
ATATATATAAACT
Found at i:42994 original size:7 final size:7
Alignment explanation
Indices: 42982--43067 Score: 86
Period size: 7 Copynumber: 12.4 Consensus size: 7
42972 TATACATACA
42982 TTAGGGT
1 TTAGGGT
42989 TTAGGGT
1 TTAGGGT
**
42996 TTAGTAT
1 TTAGGGT
*
43003 TTATGGT
1 TTAGGGT
43010 TTAGGGT
1 TTAGGGT
*
43017 TTA--TT
1 TTAGGGT
*
43022 ATTATGGT
1 -TTAGGGT
43030 TTAGGGT
1 TTAGGGT
43037 TTAGGGT
1 TTAGGGT
43044 TTAGGGT
1 TTAGGGT
* *
43051 TTATGAT
1 TTAGGGT
43058 TTAGGGT
1 TTAGGGT
43065 TTA
1 TTA
43068 AAGTTTATAT
Statistics
Matches: 63, Mismatches: 13, Indels: 6
0.77 0.16 0.07
Matches are distributed among these distances:
5 1 0.02
6 3 0.05
7 58 0.92
8 1 0.02
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (7 bp):
TTAGGGT
Found at i:43028 original size:20 final size:20
Alignment explanation
Indices: 42981--43040 Score: 93
Period size: 20 Copynumber: 3.0 Consensus size: 20
42971 TTATACATAC
*
42981 ATTAGGGTTTAGGGTTTAGT
1 ATTATGGTTTAGGGTTTAGT
*
43001 ATTTATGGTTTAGGGTTTATT
1 A-TTATGGTTTAGGGTTTAGT
43022 ATTATGGTTTAGGGTTTAG
1 ATTATGGTTTAGGGTTTAG
43041 GGTTTAGGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
20 18 0.50
21 18 0.50
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (20 bp):
ATTATGGTTTAGGGTTTAGT
Found at i:43073 original size:21 final size:21
Alignment explanation
Indices: 43036--43075 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
43026 TGGTTTAGGG
**
43036 TTTAGGGTTTAGGGTTTATGA
1 TTTAGGGTTTAAAGTTTATGA
43057 TTTAGGGTTTAAAGTTTAT
1 TTTAGGGTTTAAAGTTTAT
43076 ATAAACTATA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (21 bp):
TTTAGGGTTTAAAGTTTATGA
Found at i:43074 original size:14 final size:14
Alignment explanation
Indices: 43028--43074 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
43018 TATTATTATG
**
43028 GTTTAGGGTTTAGG
1 GTTTAGGGTTTAAA
*
43042 GTTTAGGGTTT-AT
1 GTTTAGGGTTTAAA
43055 GATTTAGGGTTTAAA
1 G-TTTAGGGTTTAAA
43070 GTTTA
1 GTTTA
43075 TATAAACTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.04
14 25 0.89
15 2 0.07
ACGTcount: A:0.21, C:0.00, G:0.32, T:0.47
Consensus pattern (14 bp):
GTTTAGGGTTTAAA
Found at i:43345 original size:19 final size:19
Alignment explanation
Indices: 43302--43365 Score: 92
Period size: 19 Copynumber: 3.3 Consensus size: 19
43292 AAATTTTCTA
* *
43302 TTCCCTCTAAATTTCTCATT
1 TTCCCTCTAAA-TTCCCAAT
*
43322 TTCCCTCGAAATTCCCAAT
1 TTCCCTCTAAATTCCCAAT
43341 TTCCCTCTAAATTCCCAAT
1 TTCCCTCTAAATTCCCAAT
43360 TTCCCT
1 TTCCCT
43366 ATATTATCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
19 30 0.75
20 10 0.25
ACGTcount: A:0.22, C:0.36, G:0.02, T:0.41
Consensus pattern (19 bp):
TTCCCTCTAAATTCCCAAT
Found at i:43515 original size:22 final size:24
Alignment explanation
Indices: 43474--43517 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
43464 ACTTTGAATA
*
43474 ATATATATAAGTATATACATAAAT
1 ATATATATAAGTATAAACATAAAT
43498 ATATATATAA-T-TAAACATAA
1 ATATATATAAGTATAAACATAA
43518 GTGGCTAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 1 0.05
24 10 0.53
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (24 bp):
ATATATATAAGTATAAACATAAAT
Found at i:43957 original size:2 final size:2
Alignment explanation
Indices: 43950--44002 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
43940 TATGTTTAAT
43950 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
43992 TA TA TA TA TA T
1 TA TA TA TA TA T
44003 TATTCAAAGT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:44162 original size:20 final size:20
Alignment explanation
Indices: 44095--44164 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
44085 TAGGAATTTA
*
44095 TTAGAGGGAAATTAGGAAAT
1 TTAGAGGGAAATTGGGAAAT
* *
44115 TTTGA--GAATATAGGGAAAT
1 TTAGAGGGAA-ATTGGGAAAT
*
44134 TGGAGAGGGAAATTGGGAAAT
1 T-TAGAGGGAAATTGGGAAAT
44155 TTAGAGGGAA
1 TTAGAGGGAA
44165 CATAAAAGTT
Statistics
Matches: 39, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
18 3 0.08
19 9 0.23
20 14 0.36
21 10 0.26
22 3 0.08
ACGTcount: A:0.41, C:0.00, G:0.34, T:0.24
Consensus pattern (20 bp):
TTAGAGGGAAATTGGGAAAT
Found at i:44653 original size:14 final size:14
Alignment explanation
Indices: 44634--44680 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
44624 ATTTTTTCTT
44634 TATATAAATTAAAC
1 TATATAAATTAAAC
44648 TATAT-AATT----
1 TATATAAATTAAAC
44657 TATATAAATTAAAC
1 TATATAAATTAAAC
*
44671 TATATTAATT
1 TATATAAATT
44681 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:44658 original size:23 final size:24
Alignment explanation
Indices: 44632--44681 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
44622 TTATTTTTTC
44632 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
44655 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
44679 TTT
1 TTT
44682 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:45819 original size:14 final size:15
Alignment explanation
Indices: 45802--45835 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
45792 TTTTAATAAA
45802 ATTTAAAA-AATATT
1 ATTTAAAATAATATT
*
45816 ATTTAAAATATTATT
1 ATTTAAAATAATATT
45831 ATTTA
1 ATTTA
45836 TACTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
ATTTAAAATAATATT
Found at i:48941 original size:19 final size:19
Alignment explanation
Indices: 48913--48963 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
48903 AATATATACA
48913 TGTT-AGTTCATTTTAGCT
1 TGTTAAGTTCATTTTAGCT
48931 TGTTAAGTTCATTTTAGCT
1 TGTTAAGTTCATTTTAGCT
48950 TGTTAAGTTCATTT
1 TGTTAAGTTCATTT
48964 AAATTTTCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
18 4 0.12
19 28 0.88
ACGTcount: A:0.20, C:0.10, G:0.16, T:0.55
Consensus pattern (19 bp):
TGTTAAGTTCATTTTAGCT
Found at i:49475 original size:55 final size:55
Alignment explanation
Indices: 49416--49524 Score: 146
Period size: 55 Copynumber: 2.0 Consensus size: 55
49406 AGGAATATGA
* * * *
49416 GAAAAAGCTTAAAAAAGCCAGAATGAGAAATAGCTTAGCAAAGCTATTAGAGAAT
1 GAAAAAGCTTAAAAAAGCAAGAACGAGAAATAGCTTAGAAAAGCTATGAGAGAAT
** * *
49471 GAAAAAGCTTAGCAAAGCAAGGACGAGAAATAGCTTTGAAAAGCTATGAGAGAA
1 GAAAAAGCTTAAAAAAGCAAGAACGAGAAATAGCTTAGAAAAGCTATGAGAGAA
49525 AAGGTGAAGC
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.50, C:0.11, G:0.23, T:0.17
Consensus pattern (55 bp):
GAAAAAGCTTAAAAAAGCAAGAACGAGAAATAGCTTAGAAAAGCTATGAGAGAAT
Found at i:49604 original size:16 final size:16
Alignment explanation
Indices: 49583--49622 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
49573 TAGCTGCAGC
*
49583 TAGTATTGTAGTGTTG
1 TAGTATTGCAGTGTTG
49599 TAGTATTGCAGTGTTG
1 TAGTATTGCAGTGTTG
*
49615 TAATATTG
1 TAGTATTG
49623 AGGTAATGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.23, C:0.03, G:0.28, T:0.47
Consensus pattern (16 bp):
TAGTATTGCAGTGTTG
Found at i:50546 original size:55 final size:55
Alignment explanation
Indices: 50481--50589 Score: 137
Period size: 55 Copynumber: 2.0 Consensus size: 55
50471 AGGAATATGA
* * * * * *
50481 GAAAAGGCTTAGAAAAGCCAGAATGAGAAATAGGTTAGCAAAGCTATTAGAGAAT
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAGCTTAGAAAAGCTATGAGAGAAT
* * *
50536 GAAAAAGCTTAGCAAAGCAAGGACGAGAAATAGCTTTGAAAAGCTATGAGAGAA
1 GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAGCTTAGAAAAGCTATGAGAGAA
50590 AGGTGAAGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
55 45 1.00
ACGTcount: A:0.48, C:0.10, G:0.26, T:0.17
Consensus pattern (55 bp):
GAAAAAGCTTAGAAAAGCAAGAACGAGAAATAGCTTAGAAAAGCTATGAGAGAAT
Found at i:50669 original size:16 final size:16
Alignment explanation
Indices: 50648--50678 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
50638 AGCTGCAGCT
*
50648 AGTATTGTAGTGTTGC
1 AGTATTGCAGTGTTGC
50664 AGTATTGCAGTGTTG
1 AGTATTGCAGTGTTG
50679 TAATATTGAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.42
Consensus pattern (16 bp):
AGTATTGCAGTGTTGC
Found at i:55098 original size:3 final size:3
Alignment explanation
Indices: 55090--55118 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
55080 AAAATTATAT
55090 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
55119 TTCATTAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:55396 original size:42 final size:42
Alignment explanation
Indices: 55248--55495 Score: 155
Period size: 42 Copynumber: 5.8 Consensus size: 42
55238 GGACCTTAAT
* *
55248 TTTTTTCAATCCCATTTTTTTTTACATTTATAATTGATGATCCTAA
1 TTTTTTCAATCCCA---TTTTTTACATTTATAATTGAAGCT-CTAA
* ** * * *
55294 GTTTTTCAATCCCACCTTATACCTTTATAATT-AAGCTACT-G
1 TTTTTTCAATCCCATTTTTTACATTTATAATTGAAGCT-CTAA
* * *
55335 CTTTTTCAATCTCACTTTTTACATTTATAATTGAAGCATCTAA
1 TTTTTTCAATCCCATTTTTTACATTTATAATTGAAGC-TCTAA
* * * *
55378 TTTTTTCAATCCCATTTTTTTAC-TCATATAATTTAGGCCCCTAA
1 TTTTTTCAATCCCA-TTTTTTACAT-TTATAATTGAAG-CTCTAA
* * * *
55422 TTTATTTCAAT--CACTTTTTACATTTAAAATTGATGCTCTTA
1 TTT-TTTCAATCCCATTTTTTACATTTATAATTGAAGCTCTAA
* ** * *
55463 TTTTTTTAATATCACTTTTTACCTTTATAATTG
1 TTTTTTCAATCCCATTTTTTACATTTATAATTG
55496 GGGTCTCTAT
Statistics
Matches: 160, Mismatches: 32, Indels: 24
0.74 0.15 0.11
Matches are distributed among these distances:
40 6 0.04
41 34 0.21
42 45 0.28
43 31 0.19
44 23 0.14
45 8 0.05
46 13 0.08
ACGTcount: A:0.27, C:0.18, G:0.05, T:0.50
Consensus pattern (42 bp):
TTTTTTCAATCCCATTTTTTACATTTATAATTGAAGCTCTAA
Found at i:55524 original size:86 final size:87
Alignment explanation
Indices: 55336--55528 Score: 205
Period size: 84 Copynumber: 2.2 Consensus size: 87
55326 AAGCTACTGC
* * *
55336 TTTTTCAATCTCACTTTTTACATTTATAATTGAAGCATCTAATTTTTTCAATCCCATTTTTTTAC
1 TTTTTCAATCT-ACTTTTTACATTTAAAATTGAAGCATCTAATTTTTTCAATACCATCTTTTTAC
*
55401 TCATATAATTTAGGCCCCTAATT
65 TCATATAATTGAGGCCCCTAATT
* * * * *
55424 TATTTCAATC-ACTTTTTACATTTAAAATTGATGC-TCTTATTTTTTTAATATCA-CTTTTTAC-
1 TTTTTCAATCTACTTTTTACATTTAAAATTGAAGCATCTAATTTTTTCAATACCATCTTTTTACT
* * * * *
55485 CTTTATAATTGGGGTCTCTATTT
66 C-ATATAATTGAGGCCCCTAATT
55508 TTTTTCAATCATACTTTTTAC
1 TTTTTCAATC-TACTTTTTAC
55529 TTGTATAGTT
Statistics
Matches: 87, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
83 1 0.01
84 31 0.36
85 15 0.17
86 31 0.36
88 9 0.10
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (87 bp):
TTTTTCAATCTACTTTTTACATTTAAAATTGAAGCATCTAATTTTTTCAATACCATCTTTTTACT
CATATAATTGAGGCCCCTAATT
Found at i:55526 original size:44 final size:43
Alignment explanation
Indices: 55336--55528 Score: 116
Period size: 42 Copynumber: 4.5 Consensus size: 43
55326 AAGCTACTGC
* * *
55336 TTTTTCAATC-TCACTTTTTACATTTATAATTGAAGCATC-TAAT
1 TTTTTCAATCAT-ACTTTTTACATTTAAAATTGAGGC-TCTTATT
* * * * * *
55379 TTTTTCAATCCCAT-TTTTTTAC-TCATATAATTTAGGCCCCTAATT
1 TTTTTCAAT--CATACTTTTTACAT-TTAAAATTGAGG-CTCTTATT
* *
55424 TATTTCAATC--ACTTTTTACATTTAAAATTGATGCTCTTATT
1 TTTTTCAATCATACTTTTTACATTTAAAATTGAGGCTCTTATT
* * *
55465 TTTTT-AAT-ATCACTTTTTACCTTTATAATTG-GGGTCTCTATTT
1 TTTTTCAATCAT-ACTTTTTACATTTAAAATTGAGGCTCT-TA-TT
55508 TTTTTCAATCATACTTTTTAC
1 TTTTTCAATCATACTTTTTAC
55529 TTGTATAGTT
Statistics
Matches: 115, Mismatches: 20, Indels: 29
0.70 0.12 0.18
Matches are distributed among these distances:
40 3 0.03
41 14 0.12
42 35 0.30
43 19 0.17
44 29 0.25
45 14 0.12
46 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.05, T:0.52
Consensus pattern (43 bp):
TTTTTCAATCATACTTTTTACATTTAAAATTGAGGCTCTTATT
Found at i:56461 original size:3 final size:3
Alignment explanation
Indices: 56453--56485 Score: 57
Period size: 3 Copynumber: 10.7 Consensus size: 3
56443 TTTCGCTGAA
56453 ATT ATT ATT ATT ATT ATT ATT ATT ATT AATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT -ATT AT
56486 ATTTATTTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:58986 original size:131 final size:131
Alignment explanation
Indices: 58630--58986 Score: 410
Period size: 131 Copynumber: 2.7 Consensus size: 131
58620 CAATATTGAG
* * *
58630 AATAATAATATAT-TTTCATTTCAGTTGGAGTAATAAATGACTGTTTTAAGGCATGAGAGGTCAC
1 AATAATAATATCTCTTT-ATTTCAATTGGAGTAATAAATGACTGTTTTAAGGCATGAGAGGTCAT
* ** * * * * * *
58694 TTATTTTTTATTGGAAATAATTCGATATTACCGTTTTCTCTTGAATCAATTTTGATTTTTAAGAC
65 TTATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTAGAATCAATATTGAATTTTAAGAC
*
58759 GG
130 GA
** * * * * * * *
58761 AATGTTGATATCTCTTCATTTCGATTGGAGTAATAAATAATTGTTTTAAGGTATGAGAGGCCATT
1 AATAATAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAAGGCATGAGAGGTCATT
* * * ***
58826 TATTCTCGATTGGAAATCATCAAATATTATCGTTTTCACTAGAATTGCTATTGAATTTTAAGACG
66 TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTAGAATCAATATTGAATTTTAAGACG
58891 A
131 A
* * *
58892 AATAATAATATCTCTTTATTTCAATTGGAGTAATAAATGACCGTTTTAAGGCATAAAAGGTCATT
1 AATAATAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAAGGCATGAGAGGTCATT
*
58957 TATTCTCGAATGGAAATAATTAGATATTAT
66 TATTCTCGATTGGAAATAATTAGATATTAT
58987 ATTTTCTCTC
Statistics
Matches: 181, Mismatches: 44, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
131 179 0.99
132 2 0.01
ACGTcount: A:0.34, C:0.10, G:0.16, T:0.40
Consensus pattern (131 bp):
AATAATAATATCTCTTTATTTCAATTGGAGTAATAAATGACTGTTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTAGATATTATCGTTTTCACTAGAATCAATATTGAATTTTAAGACG
A
Found at i:62956 original size:149 final size:149
Alignment explanation
Indices: 62685--62982 Score: 339
Period size: 149 Copynumber: 2.0 Consensus size: 149
62675 AGTAGCGTCA
* * * * * * *
62685 AGAGGGAGTCTACCTTCCAAGGAGACTATCTAGAAATTTGCATGCTGAGGTAACAAGTTGGACTC
1 AGAGGGAGTCTACCTACCAAGGAGACGATCCAGAAATTTGCATACTGAAGTAACAAGGTGGACTA
* * * * *
62750 GAGATGATTCAAAGCTGAAGCTAACAATTGAAGATTACGAACCAGCTCGAAAGATTTCTAGAAA-
66 AAGAAGATTCAAAGCTGAAGCCAACAATTGAAGATCACGAACCAGCTCAAAAGATTTCT-GAAAG
* *
62814 TAAGAGTTGAAGTAGGAGCT
130 TAAGAGATGAAGTAGAAGCT
* * *
62834 AGAGGGAGTCTATCTACCAATGAGACGATCCAGACATTTAGC-TACTGAAGTAACAAGGTGGACT
1 AGAGGGAGTCTACCTACCAAGGAGACGATCCAGAAATTT-GCATACTGAAGTAACAAGGTGGACT
* * * * * * *
62898 AAAGAAGATTCGATGTTGAAGCCAACAGTTGAAGATCATGAACCAGTTCAAAATATTTCTGAAAG
65 AAAGAAGATTCAAAGCTGAAGCCAACAATTGAAGATCACGAACCAGCTCAAAAGATTTCTGAAAG
*
62963 TAGGAGATGAAGTAGAAGCT
130 TAAGAGATGAAGTAGAAGCT
62983 TTGAAGATGA
Statistics
Matches: 122, Mismatches: 25, Indels: 4
0.81 0.17 0.03
Matches are distributed among these distances:
148 4 0.03
149 116 0.95
150 2 0.02
ACGTcount: A:0.37, C:0.15, G:0.24, T:0.23
Consensus pattern (149 bp):
AGAGGGAGTCTACCTACCAAGGAGACGATCCAGAAATTTGCATACTGAAGTAACAAGGTGGACTA
AAGAAGATTCAAAGCTGAAGCCAACAATTGAAGATCACGAACCAGCTCAAAAGATTTCTGAAAGT
AAGAGATGAAGTAGAAGCT
Found at i:64248 original size:2 final size:2
Alignment explanation
Indices: 64241--64279 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
64231 TTATCCTTTC
64241 AT AT AT AT AT AT AT -T 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
64280 CCATTGTTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:64593 original size:8 final size:8
Alignment explanation
Indices: 64582--64651 Score: 63
Period size: 8 Copynumber: 8.8 Consensus size: 8
64572 AGATAGATAG
64582 AAAAAAAT
1 AAAAAAAT
64590 AAAAAAAT
1 AAAAAAAT
64598 AGAAAAAAT
1 A-AAAAAAT
64607 AGAAAAAAT
1 A-AAAAAAT
* *
64616 GAAAAAAG
1 AAAAAAAT
*
64624 AAAAAGA-
1 AAAAAAAT
*
64631 AAAATAA-
1 AAAAAAAT
*
64638 AAAAAAAG
1 AAAAAAAT
64646 AAAAAA
1 AAAAAA
64652 GAAGAAGAAG
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
7 11 0.21
8 26 0.49
9 16 0.30
ACGTcount: A:0.84, C:0.00, G:0.09, T:0.07
Consensus pattern (8 bp):
AAAAAAAT
Found at i:64596 original size:9 final size:9
Alignment explanation
Indices: 64582--64643 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
64572 AGATAGATAG
64582 AAAAAAAT-
1 AAAAAAATA
64590 AAAAAAATA
1 AAAAAAATA
*
64599 GAAAAAATA
1 AAAAAAATA
*
64608 GAAAAAATGA
1 AAAAAAAT-A
64618 AAAAAGAA-A
1 AAAAA-AATA
64627 AAGAAAAATA
1 AA-AAAAATA
64637 AAAAAAA
1 AAAAAAA
64644 AGAAAAAAGA
Statistics
Matches: 47, Mismatches: 2, Indels: 9
0.81 0.03 0.16
Matches are distributed among these distances:
8 8 0.17
9 26 0.55
10 11 0.23
11 2 0.04
ACGTcount: A:0.84, C:0.00, G:0.08, T:0.08
Consensus pattern (9 bp):
AAAAAAATA
Found at i:64627 original size:6 final size:6
Alignment explanation
Indices: 64618--64690 Score: 64
Period size: 6 Copynumber: 12.5 Consensus size: 6
64608 GAAAAAATGA
* * *
64618 AAAAAG AAAAAG AAAAA- TAAAA- AAAAAG AAAAAAG AAGAAG AAGAA-
1 AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG -AAAAAG AAAAAG AAAAAG
*
64664 AAAGAG AAAAAG -AAAAG AAGAAAG AAA
1 AAAAAG AAAAAG AAAAAG AA-AAAG AAA
64691 CCGATCAAAC
Statistics
Matches: 56, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
5 16 0.29
6 28 0.50
7 12 0.21
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:64634 original size:22 final size:22
Alignment explanation
Indices: 64617--64679 Score: 51
Period size: 22 Copynumber: 2.9 Consensus size: 22
64607 AGAAAAAATG
* *
64617 AAAAAAGAAAAAGAAAAATAA-A
1 AAAAAAG-AAAAGAAGAAAAAGA
*
64639 AAAAAAGAAAA-AAGAAGAAGA
1 AAAAAAGAAAAGAAGAAAAAGA
64660 AGAAAAAGAGAAA-AAGAAAA
1 A-AAAAAGA-AAAGAAGAAAA
64680 GAAGAAAGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
20 6 0.17
21 6 0.17
22 14 0.40
23 9 0.26
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAGAAGAAAAAGA
Found at i:64636 original size:46 final size:46
Alignment explanation
Indices: 64584--64679 Score: 135
Period size: 46 Copynumber: 2.1 Consensus size: 46
64574 ATAGATAGAA
*
64584 AAAAATAAAAAAATAGAAAAAATAGAA-AA-AATGAAAAA-AGAAAAAG
1 AAAAATAAAAAAAAAG-AAAAA-AGAAGAAGAA-GAAAAAGAGAAAAAG
64630 AAAAATAAAAAAAAAGAAAAAAGAAGAAGAAGAAAAAGAGAAAAAG
1 AAAAATAAAAAAAAAGAAAAAAGAAGAAGAAGAAAAAGAGAAAAAG
64676 AAAA
1 AAAA
64680 GAAGAAAGAA
Statistics
Matches: 46, Mismatches: 1, Indels: 6
0.87 0.02 0.11
Matches are distributed among these distances:
44 4 0.09
45 13 0.28
46 29 0.63
ACGTcount: A:0.81, C:0.00, G:0.14, T:0.05
Consensus pattern (46 bp):
AAAAATAAAAAAAAAGAAAAAAGAAGAAGAAGAAAAAGAGAAAAAG
Found at i:64643 original size:38 final size:38
Alignment explanation
Indices: 64592--64686 Score: 115
Period size: 38 Copynumber: 2.5 Consensus size: 38
64582 AAAAAAATAA
*
64592 AAAAATAGAAAAAATAGAAAAAATGAA-AA-AAGAAAAAG
1 AAAAATA-AAAAAAAAGAAAAAA-GAAGAAGAAGAAAAAG
64630 AAAAATAAAAAAAAAGAAAAAAGAAGAAGAAGAAAAAG
1 AAAAATAAAAAAAAAGAAAAAAGAAGAAGAAGAAAAAG
* *
64668 AGAAAA-AGAAAAGAAGAAA
1 A-AAAATAAAAAAAAAGAAA
64687 GAAACCGATC
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
36 3 0.06
37 16 0.31
38 28 0.55
39 4 0.08
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.04
Consensus pattern (38 bp):
AAAAATAAAAAAAAAGAAAAAAGAAGAAGAAGAAAAAG
Found at i:64648 original size:29 final size:29
Alignment explanation
Indices: 64601--64686 Score: 102
Period size: 29 Copynumber: 2.9 Consensus size: 29
64591 AAAAAATAGA
* *
64601 AAAAATAGAAAAAATGAAAAAAGAAAAAG
1 AAAAATAAAAAAAAAGAAAAAAGAAAAAG
*
64630 AAAAATAAAAAAAAAGAAAAAAGAAGAAG
1 AAAAATAAAAAAAAAGAAAAAAGAAAAAG
*
64659 AAGAAA-AAGAGAAAAAGAAAAGAAGAAA
1 AA-AAATAA-AAAAAAAGAAAA-AAGAAA
64687 GAAACCGATC
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
29 30 0.61
30 14 0.29
31 5 0.10
ACGTcount: A:0.80, C:0.00, G:0.16, T:0.03
Consensus pattern (29 bp):
AAAAATAAAAAAAAAGAAAAAAGAAAAAG
Found at i:64649 original size:9 final size:9
Alignment explanation
Indices: 64582--64666 Score: 59
Period size: 9 Copynumber: 9.4 Consensus size: 9
64572 AGATAGATAG
*
64582 AAAAAAATA
1 AAAAAAAGA
64591 AAAAAATAGA
1 AAAAAA-AGA
*
64601 AAAAATAG-
1 AAAAAAAGA
*
64609 AAAAAATGA
1 AAAAAAAGA
64618 AAAAAGAA-A
1 AAAAA-AAGA
*
64627 AAGAAAAATA
1 AA-AAAAAGA
64637 AAAAAAA-A
1 AAAAAAAGA
*
64645 GAAAAAAGA
1 AAAAAAAGA
* *
64654 AGAAGAAGA
1 AAAAAAAGA
64663 AAAA
1 AAAA
64667 GAGAAAAAGA
Statistics
Matches: 60, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
8 13 0.22
9 33 0.55
10 14 0.23
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (9 bp):
AAAAAAAGA
Done.