Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008214.1 Hibiscus syriacus cultivar Beakdansim tig00110840_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: 2117680
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:1050897 original size:2 final size:2
Alignment explanation
Indices: 1050881--1050938 Score: 93
Period size: 2 Copynumber: 29.5 Consensus size: 2
1050871 AGTTAATTAC
1050881 TA TA -A TA TCA TA TA TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1050922 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
1050939 GCACTTCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 2 0.04
2 49 0.92
3 2 0.04
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1053163 original size:24 final size:23
Alignment explanation
Indices: 1053133--1053190 Score: 64
Period size: 23 Copynumber: 2.5 Consensus size: 23
1053123 TGCTTTGATT
1053133 TAATTTAATTACTAAATTAATATA
1 TAATTTAATTACTAAATTAAT-TA
* * *
1053157 TAATTTAA-TATTTATTTAATTA
1 TAATTTAATTACTAAATTAATTA
1053179 TAATTGTAATTA
1 TAATT-TAATTA
1053191 TTATGTTAGT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 7 0.24
23 12 0.41
24 10 0.34
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.52
Consensus pattern (23 bp):
TAATTTAATTACTAAATTAATTA
Found at i:1053164 original size:12 final size:11
Alignment explanation
Indices: 1053133--1053191 Score: 57
Period size: 12 Copynumber: 5.1 Consensus size: 11
1053123 TGCTTTGATT
1053133 TAATTTAATTA
1 TAATTTAATTA
*
1053144 CTAAATTAATATA
1 -TAATTTAAT-TA
1053157 TAATTTAA-TA
1 TAATTTAATTA
*
1053167 TTTATTTAATTA
1 -TAATTTAATTA
1053179 TAATTGTAATTA
1 TAATT-TAATTA
1053191 T
1 T
1053192 TATGTTAGTG
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
10 2 0.05
11 11 0.28
12 24 0.62
13 2 0.05
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.53
Consensus pattern (11 bp):
TAATTTAATTA
Found at i:1054683 original size:2 final size:2
Alignment explanation
Indices: 1054676--1054716 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1054666 ATGAAGTTCA
1054676 AT AT AT AT 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 AT AT AT AT A
1054717 CTGCAATTCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1056762 original size:14 final size:14
Alignment explanation
Indices: 1056743--1056822 Score: 86
Period size: 14 Copynumber: 6.3 Consensus size: 14
1056733 CGTTCATGAA
1056743 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1056757 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
1056771 CG-T---TTATGTT
1 CGTTCGGTTATGTT
1056781 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
*
1056795 CG-T---TTACGTT
1 CGTTCGGTTATGTT
*
1056805 CATTCGGTTATGTT
1 CGTTCGGTTATGTT
1056819 CGTT
1 CGTT
1056823 TATGTTCATT
Statistics
Matches: 54, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
10 16 0.30
11 2 0.04
13 2 0.04
14 34 0.63
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:1056771 original size:24 final size:24
Alignment explanation
Indices: 1056744--1056829 Score: 145
Period size: 24 Copynumber: 3.6 Consensus size: 24
1056734 GTTCATGAAC
*
1056744 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1056768 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
* *
1056792 GTTCGTTTACGTTCATTCGGTTAT
1 GTTCGTTTATGTTCGTTCGGTTAT
1056816 GTTCGTTTATGTTC
1 GTTCGTTTATGTTC
1056830 ATTCATTTAT
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 58 1.00
ACGTcount: A:0.09, C:0.14, G:0.24, T:0.52
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGGTTAT
Found at i:1056816 original size:38 final size:37
Alignment explanation
Indices: 1056743--1056822 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 37
1056733 CGTTCATGAA
*
1056743 CGTTCGGTTATGTTCGTTCGGTTATGTTCGTTTATGTT
1 CGTTCGGTTATGTTCGTTCGGTTA-GTTCGGTTATGTT
1056781 CGTTCGGTTATGTTCGTTTAC-GTTCA-TTCGGTTATGTT
1 CGTTCGGTTATGTTCG-TT-CGGTT-AGTTCGGTTATGTT
1056819 CGTT
1 CGTT
1056823 TATGTTCATT
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
38 31 0.82
39 5 0.13
40 2 0.05
ACGTcount: A:0.09, C:0.15, G:0.25, T:0.51
Consensus pattern (37 bp):
CGTTCGGTTATGTTCGTTCGGTTAGTTCGGTTATGTT
Found at i:1056830 original size:24 final size:24
Alignment explanation
Indices: 1056744--1056842 Score: 144
Period size: 24 Copynumber: 4.1 Consensus size: 24
1056734 GTTCATGAAC
* *
1056744 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
*
1056768 GTTCGTTTATGTTCGTTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
*
1056792 GTTCGTTTACGTTCATTCGGTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
**
1056816 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGTTTATGTTCATTCGGTTAT
1056840 GTT
1 GTT
1056843 TAACTCAATT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.11, C:0.13, G:0.22, T:0.54
Consensus pattern (24 bp):
GTTCGTTTATGTTCATTCGGTTAT
Found at i:1057355 original size:23 final size:23
Alignment explanation
Indices: 1057325--1057412 Score: 113
Period size: 23 Copynumber: 3.8 Consensus size: 23
1057315 TGGGATAATG
*
1057325 TCGACCTTGAATTGAGCTCAGAA
1 TCGACCTTGAATCGAGCTCAGAA
*
1057348 TCGACCTTGAATTGAGCTCAGAA
1 TCGACCTTGAATCGAGCTCAGAA
* * *
1057371 TCGAGCTTGAATCGAGCTTAGAC
1 TCGACCTTGAATCGAGCTCAGAA
* *
1057394 TCGAGCTTCAATCGAGCTC
1 TCGACCTTGAATCGAGCTC
1057413 GAGTCTCGAG
Statistics
Matches: 59, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 59 1.00
ACGTcount: A:0.27, C:0.24, G:0.23, T:0.26
Consensus pattern (23 bp):
TCGACCTTGAATCGAGCTCAGAA
Found at i:1057384 original size:11 final size:11
Alignment explanation
Indices: 1057325--1057411 Score: 75
Period size: 11 Copynumber: 7.6 Consensus size: 11
1057315 TGGGATAATG
*
1057325 TCGACCTTGAA
1 TCGAGCTTGAA
* *
1057336 TTGAGCTCAGAA
1 TCGAGCT-TGAA
*
1057348 TCGACCTTGAA
1 TCGAGCTTGAA
* *
1057359 TTGAGCTCAGAA
1 TCGAGCT-TGAA
1057371 TCGAGCTTGAA
1 TCGAGCTTGAA
*
1057382 TCGAGCTTAGAC
1 TCGAGCTT-GAA
*
1057394 TCGAGCTTCAA
1 TCGAGCTTGAA
1057405 TCGAGCT
1 TCGAGCT
1057412 CGAGTCTCGA
Statistics
Matches: 59, Mismatches: 14, Indels: 6
0.75 0.18 0.08
Matches are distributed among these distances:
11 32 0.54
12 27 0.46
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:1057411 original size:46 final size:47
Alignment explanation
Indices: 1057325--1057436 Score: 118
Period size: 46 Copynumber: 2.4 Consensus size: 47
1057315 TGGGATAATG
* * * *
1057325 TCGACCTTGAATTGAGCTCAGAATCGACCTTGAATTGAGCTC-AGAA
1 TCGAGCTTGAATCGAGCTCAGAATCGACCTTCAATCGAGCTCGAGAA
* * * **
1057371 TCGAGCTTGAATCGAGCTTAGACTCGAGCTTCAATCGAGCTCGAGTC
1 TCGAGCTTGAATCGAGCTCAGAATCGACCTTCAATCGAGCTCGAGAA
* *
1057418 TCGAGTTTTAATCGAGCTC
1 TCGAGCTTGAATCGAGCTC
1057437 TTAATTTTTT
Statistics
Matches: 53, Mismatches: 12, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
46 35 0.66
47 18 0.34
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.28
Consensus pattern (47 bp):
TCGAGCTTGAATCGAGCTCAGAATCGACCTTCAATCGAGCTCGAGAA
Found at i:1057430 original size:24 final size:24
Alignment explanation
Indices: 1057338--1057436 Score: 87
Period size: 23 Copynumber: 4.2 Consensus size: 24
1057328 ACCTTGAATT
* * * *
1057338 GAGCTC-AGAATCGACCTTGAATT
1 GAGCTCGAGACTCGAGCTTCAATC
* *
1057361 GAGCTC-AGAATCGAGCTTGAATC
1 GAGCTCGAGACTCGAGCTTCAATC
*
1057384 GAGCT-TAGACTCGAGCTTCAATC
1 GAGCTCGAGACTCGAGCTTCAATC
* * *
1057407 GAGCTCGAGTCTCGAGTTTTAATC
1 GAGCTCGAGACTCGAGCTTCAATC
1057431 GAGCTC
1 GAGCTC
1057437 TTAATTTTTT
Statistics
Matches: 66, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
23 46 0.70
24 20 0.30
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.26
Consensus pattern (24 bp):
GAGCTCGAGACTCGAGCTTCAATC
Found at i:1057657 original size:16 final size:16
Alignment explanation
Indices: 1057635--1057696 Score: 115
Period size: 16 Copynumber: 3.9 Consensus size: 16
1057625 GGTCTCTAAT
1057635 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
*
1057651 ATTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
1057667 GTTTATGTTCGTGTTC
1 GTTTATGTTCGTGTTC
1057683 GTTTATGTTCGTGT
1 GTTTATGTTCGTGT
1057697 AACACCCTCA
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 44 1.00
ACGTcount: A:0.08, C:0.11, G:0.24, T:0.56
Consensus pattern (16 bp):
GTTTATGTTCGTGTTC
Found at i:1058345 original size:30 final size:30
Alignment explanation
Indices: 1058305--1058461 Score: 287
Period size: 30 Copynumber: 5.2 Consensus size: 30
1058295 TCCGAATGAC
1058305 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1058335 CTATCTAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1058365 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1058395 CTATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1058425 CTATCCAGAGGTCATAAAGATCCTCGATAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1058455 CTATCCA
1 CTATCCA
1058462 TATGTTCCTT
Statistics
Matches: 122, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 122 1.00
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1058697 original size:4 final size:4
Alignment explanation
Indices: 1058688--1058946 Score: 495
Period size: 4 Copynumber: 65.2 Consensus size: 4
1058678 ATATAACCAT
1058688 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1058736 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
1058784 TACA TACA TACA TACA TACA TATA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1058832 TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1058878 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1058926 TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA T
1058947 GTCATCATTT
Statistics
Matches: 251, Mismatches: 2, Indels: 4
0.98 0.01 0.02
Matches are distributed among these distances:
2 2 0.01
4 249 0.99
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:1059864 original size:19 final size:19
Alignment explanation
Indices: 1059840--1059889 Score: 100
Period size: 19 Copynumber: 2.6 Consensus size: 19
1059830 TTTAATGGGG
1059840 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1059859 TGCATCGATGCACTCCTTA
1 TGCATCGATGCACTCCTTA
1059878 TGCATCGATGCA
1 TGCATCGATGCA
1059890 TCGATGGCAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.18, T:0.30
Consensus pattern (19 bp):
TGCATCGATGCACTCCTTA
Found at i:1064474 original size:30 final size:30
Alignment explanation
Indices: 1064316--1064472 Score: 287
Period size: 30 Copynumber: 5.2 Consensus size: 30
1064306 TCCGAAAAAC
1064316 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1064346 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1064376 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1064406 CTATCCAGAGGTCATAAAGACCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
1064436 CTATCCATAGATCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1064466 CTATCCA
1 CTATCCA
1064473 TATGTTCCTT
Statistics
Matches: 123, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 123 1.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1064717 original size:4 final size:4
Alignment explanation
Indices: 1064700--1064736 Score: 65
Period size: 4 Copynumber: 9.2 Consensus size: 4
1064690 ATATAACCAT
*
1064700 TACA TACA TCCA TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA T
1064737 GTCATCGTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 31 1.00
ACGTcount: A:0.46, C:0.27, G:0.00, T:0.27
Consensus pattern (4 bp):
TACA
Found at i:1066862 original size:18 final size:19
Alignment explanation
Indices: 1066841--1066882 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
1066831 AGTATTTTTT
1066841 TAAAATTAT-GATTTTAAA
1 TAAAATTATAGATTTTAAA
*
1066859 T-AAATTATATATTTTAAA
1 TAAAATTATAGATTTTAAA
*
1066877 AAAAAT
1 TAAAAT
1066883 CATTTTTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 9 0.45
19 4 0.20
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (19 bp):
TAAAATTATAGATTTTAAA
Found at i:1070632 original size:25 final size:26
Alignment explanation
Indices: 1070584--1070634 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
1070574 GTCGGTGCAT
1070584 ACAGATTTCCAACATCATTGTTGCCA
1 ACAGATTTCCAACATCATTGTTGCCA
1070610 ACAGATTTCCAAC-TCATTGTTGCCA
1 ACAGATTTCCAACATCATTGTTGCCA
1070635 TTAACTTATA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 12 0.48
26 13 0.52
ACGTcount: A:0.29, C:0.27, G:0.12, T:0.31
Consensus pattern (26 bp):
ACAGATTTCCAACATCATTGTTGCCA
Found at i:1073260 original size:35 final size:35
Alignment explanation
Indices: 1073184--1073261 Score: 90
Period size: 35 Copynumber: 2.2 Consensus size: 35
1073174 TTAAATACAA
1073184 AAAACTTACAATAAGAATTAAATGGTAAATGATAAC
1 AAAA-TTACAATAAGAATTAAATGGTAAATGATAAC
*
1073220 CAAATTACAATAACTGATATTAAATGGT-AAT-A-AAC
1 AAAATTACAATAA--GA-ATTAAATGGTAAATGATAAC
1073255 AAAATTA
1 AAAATTA
1073262 ACTGAAATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
35 18 0.49
36 4 0.11
37 5 0.14
38 10 0.27
ACGTcount: A:0.55, C:0.09, G:0.09, T:0.27
Consensus pattern (35 bp):
AAAATTACAATAAGAATTAAATGGTAAATGATAAC
Found at i:1073487 original size:3 final size:3
Alignment explanation
Indices: 1073481--1073542 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
1073471 GCTGTCATCA
* * * * * *
1073481 TCG TCG TCG TTG TCG TCT TCG TCG TCG TTG TCA TCG TCA TCG TCG TCA
1 TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG TCG
1073529 TCG TCG TCG TCG TC
1 TCG TCG TCG TCG TC
1073543 ATCCTGAGCA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.05, C:0.31, G:0.26, T:0.39
Consensus pattern (3 bp):
TCG
Found at i:1073504 original size:15 final size:15
Alignment explanation
Indices: 1073484--1073545 Score: 88
Period size: 15 Copynumber: 4.1 Consensus size: 15
1073474 GTCATCATCG
* *
1073484 TCGTCGTTGTCGTCT
1 TCGTCGTCGTCGTCA
*
1073499 TCGTCGTCGTTGTCA
1 TCGTCGTCGTCGTCA
*
1073514 TCGTCATCGTCGTCA
1 TCGTCGTCGTCGTCA
1073529 TCGTCGTCGTCGTCA
1 TCGTCGTCGTCGTCA
1073544 TC
1 TC
1073546 CTGAGCAGGT
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 41 1.00
ACGTcount: A:0.06, C:0.31, G:0.24, T:0.39
Consensus pattern (15 bp):
TCGTCGTCGTCGTCA
Found at i:1075645 original size:17 final size:18
Alignment explanation
Indices: 1075602--1075642 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1075592 GAATTATATT
1075602 AGTAAAATA-TTAAATAA
1 AGTAAAATACTTAAATAA
1075619 AGTAAAATACTTAAATAA
1 AGTAAAATACTTAAATAA
*
1075637 ATTAAA
1 AGTAAA
1075643 TACATAATAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.29
Consensus pattern (18 bp):
AGTAAAATACTTAAATAA
Found at i:1077005 original size:75 final size:75
Alignment explanation
Indices: 1076882--1077064 Score: 244
Period size: 75 Copynumber: 2.4 Consensus size: 75
1076872 CTTAACTGGT
** * * * * *
1076882 TAAAATAAAATAAACGTTACCTATTATGTTAAATTACTTACTGGTTTGTTTGAAGGTTACTAATA
1 TAAAATAAAATAAGGGCTACATATTATGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
*
1076947 ATGTAAACGG
66 ATATAAACGG
1076957 TAAAATAAAAT-AGGTGCTACATATTATGTTAAAATA-TCTACCGGTTTGTTTAAAGGTTACTAA
1 TAAAATAAAATAAGG-GCTACATATTATGTTAAAATACT-TACCGGTTTGTTTAAAGGTTACTAA
1077020 TAATATAAACGG
64 TAATATAAACGG
* *
1077032 TAAAATAAAATAAGGGCTGCCTATTATGTTAAA
1 TAAAATAAAATAAGGGCTACATATTATGTTAAA
1077065 TAGGTGCTCT
Statistics
Matches: 95, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
74 2 0.02
75 90 0.95
76 3 0.03
ACGTcount: A:0.41, C:0.09, G:0.15, T:0.35
Consensus pattern (75 bp):
TAAAATAAAATAAGGGCTACATATTATGTTAAAATACTTACCGGTTTGTTTAAAGGTTACTAATA
ATATAAACGG
Found at i:1077223 original size:75 final size:75
Alignment explanation
Indices: 1077094--1077262 Score: 257
Period size: 75 Copynumber: 2.3 Consensus size: 75
1077084 GTTAAACAAA
* * * * *
1077094 CGCTAGCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGTAAA
1 CGCTACCTATTACGTTAAAATAGCTACCAGTTTGTTTAAAGATTAATAATAATGTAAAAGGTAAA
1077159 ATAAAATAGG
66 ATAAAATAGG
* * *
1077169 TGCTACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGATTACTAATAATGTAAAAGGTAAA
1 CGCTACCTATTACGTTAAAATAGCTACCAGTTTGTTTAAAGATTAATAATAATGTAAAAGGTAAA
*
1077234 ATAAAATTGG
66 ATAAAATAGG
1077244 CGCTACCTATTACGTTAAA
1 CGCTACCTATTACGTTAAA
1077263 TAAGCGCTAC
Statistics
Matches: 84, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
75 84 1.00
ACGTcount: A:0.39, C:0.13, G:0.15, T:0.33
Consensus pattern (75 bp):
CGCTACCTATTACGTTAAAATAGCTACCAGTTTGTTTAAAGATTAATAATAATGTAAAAGGTAAA
ATAAAATAGG
Found at i:1077263 original size:198 final size:196
Alignment explanation
Indices: 1076893--1077553 Score: 662
Period size: 198 Copynumber: 3.4 Consensus size: 196
1076883 AAAATAAAAT
* * * ** * * *
1076893 AAACGTTACCTATTATGTTAAATTA-CTTACTGGTTTGTTTGAAGGTTACTAATAATGTAAACGG
1 AAACGCTACCTATTACGTTAAACTAGC-TACCAGTTTGTTTAAAGGTTAATAATAATATAAACGG
* *
1076957 TAAAATAAAATAGGTGCTACATATTATGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAATA
65 TAAAATAAAATAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATA
* * * *
1077022 ATATAAACGGTAAAATAAAATAAGG-GCTGCCTATTATGTTAAATAGGTGCTCTACCTATTACGT
130 ATGTAAAAGGTAAAATAAAAT-AGGCGCTACCTATTATGTTAAATA-G-GCGCTACCTATTACGT
1077086 TAAAC
192 TAAAC
* * *
1077091 AAACGCTAGCTATTACGTTAAACTAGCTACCGGTTTGTTTAAAGGTTAATAATAATGTAAACGGT
1 AAACGCTACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATATAAACGGT
* *
1077156 AAAATAAAATAGGTGCTACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGATTACTAATAA
66 AAAATAAAATAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAA
* * *
1077221 TGTAAAAGGTAAAATAAAATTGGCGCTACCTATTACGTTAAATAAGCGCTACCTATTACGTTAAA
131 TGTAAAAGGTAAAATAAAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTATTACGTTAAA
1077286 C
196 C
* * * * * * * * * **
1077287 TAA--TTA-CTGATT-TGTTTAAA--GGTTACTAATAATG--TAAACGG-TAA-AATAAAATAGT
1 AAACGCTACCT-ATTACG-TTAAACTAGCTACCAGT-TTGTTTAAA-GGTTAATAATAATATAAA
* * * * ** *
1077342 CGCTACATATTATGTTAACTAAGCACTACATATTACGTTAAAATATTTACCAGTTTGTTTAAAGG
62 CGGTA-A-A--A--TAAAATAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGG
* * * *
1077407 TTACTGATAATGTAAATGATAAAATAAAATAGGCACTACCTATTATGTTAAATAGGCGCTACCTA
121 TTACTAATAATGTAAAAGGTAAAATAAAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTA
* *
1077472 TTATGTTAAAT
186 TTACGTTAAAC
* * * *
1077483 AAGCGCTACCTATTACGTTAAACTAGTTATCAGTTTGTTTAAAGGTTAATCATAATATAAACGGT
1 AAACGCTACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATATAAACGGT
1077548 AAAATA
66 AAAATA
1077554 TATACAACTT
Statistics
Matches: 377, Mismatches: 64, Indels: 46
0.77 0.13 0.09
Matches are distributed among these distances:
190 11 0.03
191 8 0.02
192 8 0.02
193 5 0.01
194 11 0.03
196 134 0.36
197 2 0.01
198 164 0.44
199 6 0.02
200 9 0.02
201 8 0.02
202 11 0.03
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (196 bp):
AAACGCTACCTATTACGTTAAACTAGCTACCAGTTTGTTTAAAGGTTAATAATAATATAAACGGT
AAAATAAAATAGGTGCTACATATTACGTTAAAATATCTACCAGTTTGTTTAAAGGTTACTAATAA
TGTAAAAGGTAAAATAAAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTATTACGTTAAA
C
Found at i:1077264 original size:98 final size:97
Alignment explanation
Indices: 1077170--1077481 Score: 428
Period size: 98 Copynumber: 3.2 Consensus size: 97
1077160 TAAAATAGGT
*
1077170 GCTACCTATTACGTTAAAATATCTACCAGTTTGTTTAAAGATTACTAATAATGTAAAAGGTAAAA
1 GCTACCTATTACGTTAAAATAT-TACCAGTTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAA
* *
1077235 TAAAATTGGCGCTACCTATTACGTTAAATAAGC
65 TAAAATAGGCGCTACCTATTATGTTAAATAAGC
* * *
1077268 GCTACCTATTACGTTAAACTAATTA-CTGATTTGTTTAAAGGTTACTAATAATGTAAACGGTAAA
1 GCTACCTATTACGTTAAAAT-ATTACCAG-TTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAA
* * *
1077332 ATAAAATAGTCGCTACATATTATGTTAACTAAGC
64 ATAAAATAGGCGCTACCTATTATGTTAAATAAGC
* * * * *
1077366 ACTACATATTACGTTAAAATATTTACCAGTTTGTTTAAAGGTTACTGATAATGTAAATGATAAAA
1 GCTACCTATTACGTTAAAATA-TTACCAGTTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAA
* *
1077431 TAAAATAGGCACTACCTATTATGTTAAATAGGC
65 TAAAATAGGCGCTACCTATTATGTTAAATAAGC
*
1077464 GCTACCTATTATGTTAAA
1 GCTACCTATTACGTTAAA
1077482 TAAGCGCTAC
Statistics
Matches: 186, Mismatches: 24, Indels: 8
0.85 0.11 0.04
Matches are distributed among these distances:
97 3 0.02
98 179 0.96
99 4 0.02
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.34
Consensus pattern (97 bp):
GCTACCTATTACGTTAAAATATTACCAGTTTGTTTAAAGGTTACTAATAATGTAAAAGGTAAAAT
AAAATAGGCGCTACCTATTATGTTAAATAAGC
Found at i:1077462 original size:23 final size:23
Alignment explanation
Indices: 1077433--1077504 Score: 117
Period size: 23 Copynumber: 3.1 Consensus size: 23
1077423 TGATAAAATA
*
1077433 AAATAGGCACTACCTATTATGTT
1 AAATAGGCGCTACCTATTATGTT
1077456 AAATAGGCGCTACCTATTATGTT
1 AAATAGGCGCTACCTATTATGTT
* *
1077479 AAATAAGCGCTACCTATTACGTT
1 AAATAGGCGCTACCTATTATGTT
1077502 AAA
1 AAA
1077505 CTAGTTATCA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTATGTT
Found at i:1077474 original size:121 final size:121
Alignment explanation
Indices: 1077335--1077553 Score: 321
Period size: 121 Copynumber: 1.8 Consensus size: 121
1077325 CGGTAAAATA
* * *
1077335 AAATAGTCGCTACATATTATGTTAACTAAGCACTACATATTACGTTAAAATATTTACCAGTTTGT
1 AAATAGGCGCTACATATTATGTTAAATAAGCACTACATATTACGTTAAAATAGTTACCAGTTTGT
* * * *
1077400 TTAAAGGTTACTGATAATGTAAATGATAAAATAAAATAGGCACTACCTATTATGTT
66 TTAAAGGTTAATCATAATATAAACGATAAAATAAAATAGGCACTACCTATTATGTT
* * * * *
1077456 AAATAGGCGCTACCTATTATGTTAAATAAGCGCTACCTATTACGTTAAACTAGTTATCAGTTTGT
1 AAATAGGCGCTACATATTATGTTAAATAAGCACTACATATTACGTTAAAATAGTTACCAGTTTGT
*
1077521 TTAAAGGTTAATCATAATATAAACGGTAAAATA
66 TTAAAGGTTAATCATAATATAAACGATAAAATA
1077554 TATACAACTT
Statistics
Matches: 85, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
121 85 1.00
ACGTcount: A:0.39, C:0.13, G:0.13, T:0.35
Consensus pattern (121 bp):
AAATAGGCGCTACATATTATGTTAAATAAGCACTACATATTACGTTAAAATAGTTACCAGTTTGT
TTAAAGGTTAATCATAATATAAACGATAAAATAAAATAGGCACTACCTATTATGTT
Found at i:1077818 original size:154 final size:154
Alignment explanation
Indices: 1077535--1077957 Score: 735
Period size: 154 Copynumber: 2.8 Consensus size: 154
1077525 AGGTTAATCA
* * * * *
1077535 TAATATAAACGGTAAAATATATACAACTTAATTGTTTTAAATA--TTTTTTAAAATTCGAAAGTA
1 TAATGTAAACGATAAAATATATACAACTTAACTGCTTGAAATATTTTTTTTAAAATTCGAAAGTA
* * *
1077598 T-GAATATTTACTCTAAAAGTATGAATACTCTAAAGGTTAATAATAATGTATCTATACTTACTCT
66 TAG-ATACTTACTCTAAAAGTATGAATACTCTAAAAGCTAATAATAATGTATCTATACTTACTCT
1077662 AAAAGTATGGATGCTATTTCGACAG
130 AAAAGTATGGATGCTATTTCGACAG
1077687 TAATGTAAACGATAAAATATATACAACTTAACTGCTTGAAATATTTTTTTTAAAATTCGAAAGTA
1 TAATGTAAACGATAAAATATATACAACTTAACTGCTTGAAATATTTTTTTTAAAATTCGAAAGTA
1077752 TAGATACTTACTCTAAAAGTATGAATACTCTAAAAGCTAATAATAATGTATCTATACTTACTCTA
66 TAGATACTTACTCTAAAAGTATGAATACTCTAAAAGCTAATAATAATGTATCTATACTTACTCTA
1077817 AAAGTATGGATGCTATTTCGACAG
131 AAAGTATGGATGCTATTTCGACAG
1077841 TAATGTAAACGATAAAATATATACAACTTAACTGCTTGAAATATTTTTTTTAAAATTCGAAAGTA
1 TAATGTAAACGATAAAATATATACAACTTAACTGCTTGAAATATTTTTTTTAAAATTCGAAAGTA
*
1077906 TAGATACTTACTCTAAAAGTATGAATACTCTAAAAGCTAATAATAATATATC
66 TAGATACTTACTCTAAAAGTATGAATACTCTAAAAGCTAATAATAATGTATC
1077958 CATAATAATG
Statistics
Matches: 259, Mismatches: 9, Indels: 4
0.95 0.03 0.01
Matches are distributed among these distances:
152 38 0.15
154 220 0.85
155 1 0.00
ACGTcount: A:0.43, C:0.11, G:0.10, T:0.36
Consensus pattern (154 bp):
TAATGTAAACGATAAAATATATACAACTTAACTGCTTGAAATATTTTTTTTAAAATTCGAAAGTA
TAGATACTTACTCTAAAAGTATGAATACTCTAAAAGCTAATAATAATGTATCTATACTTACTCTA
AAAGTATGGATGCTATTTCGACAG
Found at i:1079086 original size:85 final size:85
Alignment explanation
Indices: 1078982--1079155 Score: 330
Period size: 85 Copynumber: 2.0 Consensus size: 85
1078972 TAAATGTTTA
1078982 TATATCATTGCAGATATGATATTGGAACTCGAAATCTTAAGAGATAACATCAATTTCTTAATCAT
1 TATATCATTGCAGATATGATATTGGAACTCGAAATCTTAAGAGATAACATCAATTTCTTAATCAT
1079047 TAAAGTCTCTTGGTTCATGC
66 TAAAGTCTCTTGGTTCATGC
*
1079067 TATATCATTGCATATATGATATTGGAACTCGAAATCTTAAGAGATAACATCAATTTCTTAATCAT
1 TATATCATTGCAGATATGATATTGGAACTCGAAATCTTAAGAGATAACATCAATTTCTTAATCAT
*
1079132 TAAAGTCTCTTGGTTCGTGC
66 TAAAGTCTCTTGGTTCATGC
1079152 TATA
1 TATA
1079156 ACAACAAGTA
Statistics
Matches: 87, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
85 87 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (85 bp):
TATATCATTGCAGATATGATATTGGAACTCGAAATCTTAAGAGATAACATCAATTTCTTAATCAT
TAAAGTCTCTTGGTTCATGC
Found at i:1079715 original size:17 final size:19
Alignment explanation
Indices: 1079693--1079738 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
1079683 TTATTTTAGG
1079693 TAAGAATT-AT-TATGAAT
1 TAAGAATTCATATATGAAT
*
1079710 TAAGAATTCTTCATATGAAT
1 TAAGAATTCAT-ATATGAAT
1079730 TAAGAATTC
1 TAAGAATTC
1079739 TTCATAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 8 0.32
18 1 0.04
20 16 0.64
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.39
Consensus pattern (19 bp):
TAAGAATTCATATATGAAT
Found at i:1079728 original size:20 final size:20
Alignment explanation
Indices: 1079703--1079751 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
1079693 TAAGAATTAT
1079703 TATGAATTAAGAATTCTTCA
1 TATGAATTAAGAATTCTTCA
1079723 TATGAATTAAGAATTCTTCA
1 TATGAATTAAGAATTCTTCA
*
1079743 TAAGAATTA
1 TATGAATTA
1079752 TTGGTGATCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.08, G:0.10, T:0.39
Consensus pattern (20 bp):
TATGAATTAAGAATTCTTCA
Found at i:1079857 original size:18 final size:20
Alignment explanation
Indices: 1079821--1079860 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
1079811 TTTGGGAGAA
*
1079821 GTAATCTTTTTAGGATTTAT
1 GTAATCTTTTGAGGATTTAT
1079841 GTAA-CTTTTGAGG-TTTAT
1 GTAATCTTTTGAGGATTTAT
1079859 GT
1 GT
1079861 TACAAAGATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 7 0.37
19 8 0.42
20 4 0.21
ACGTcount: A:0.23, C:0.05, G:0.20, T:0.53
Consensus pattern (20 bp):
GTAATCTTTTGAGGATTTAT
Found at i:1085111 original size:17 final size:18
Alignment explanation
Indices: 1085074--1085114 Score: 66
Period size: 18 Copynumber: 2.3 Consensus size: 18
1085064 ATATTATGTA
*
1085074 TTTAATTTATTTAAGTAT
1 TTTACTTTATTTAAGTAT
1085092 TTTACTTTATTTAA-TAT
1 TTTACTTTATTTAAGTAT
1085109 TTTACT
1 TTTACT
1085115 ACTATAAATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.63
Consensus pattern (18 bp):
TTTACTTTATTTAAGTAT
Found at i:1086850 original size:24 final size:23
Alignment explanation
Indices: 1086823--1086896 Score: 60
Period size: 24 Copynumber: 3.1 Consensus size: 23
1086813 TTTATTATAT
1086823 TTGTATTTGCTTTATTTTGTTAAA
1 TTGTATTT-CTTTATTTTGTTAAA
* * *
1086847 TTGTAATTTTTTTATTAT-TTAAT
1 TTGT-ATTTCTTTATTTTGTTAAA
* *
1086870 TTAATACTTACTTTATTTTGTTAAA
1 TT-GTA-TTTCTTTATTTTGTTAAA
1086895 TT
1 TT
1086897 TGTTGGACTT
Statistics
Matches: 38, Mismatches: 8, Indels: 7
0.72 0.15 0.13
Matches are distributed among these distances:
23 7 0.18
24 21 0.55
25 10 0.26
ACGTcount: A:0.26, C:0.04, G:0.07, T:0.64
Consensus pattern (23 bp):
TTGTATTTCTTTATTTTGTTAAA
Found at i:1091523 original size:21 final size:20
Alignment explanation
Indices: 1091485--1091525 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
1091475 AATATTTATT
1091485 TATTTATTAAATTAAATAAA
1 TATTTATTAAATTAAATAAA
* *
1091505 TATTTATATCAATTTAATAAA
1 TATTTAT-TAAATTAAATAAA
1091526 GAAACAGACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
TATTTATTAAATTAAATAAA
Found at i:1091687 original size:29 final size:29
Alignment explanation
Indices: 1091655--1091710 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
1091645 TTATCCCCTA
1091655 AAATTTTATAAATTCAAGTTCGCCTCCTG
1 AAATTTTATAAATTCAAGTTCGCCTCCTG
*
1091684 AAATTTTATAAGTTCAAGTTCGCCTCC
1 AAATTTTATAAATTCAAGTTCGCCTCC
1091711 ACTAACATAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.21, G:0.11, T:0.38
Consensus pattern (29 bp):
AAATTTTATAAATTCAAGTTCGCCTCCTG
Found at i:1091774 original size:15 final size:16
Alignment explanation
Indices: 1091754--1091783 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1091744 CAAACAAATA
1091754 TATATTTAT-TTTATT
1 TATATTTATATTTATT
1091769 TATATTTATATTTAT
1 TATATTTATATTTAT
1091784 AAATAAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATATTTATATTTATT
Found at i:1092013 original size:16 final size:17
Alignment explanation
Indices: 1091986--1092028 Score: 61
Period size: 16 Copynumber: 2.6 Consensus size: 17
1091976 ATAAATTGGG
1091986 TGGGTCGGGTCAATTTT
1 TGGGTCGGGTCAATTTT
*
1092003 TGGGT-GGGTCAGTTTT
1 TGGGTCGGGTCAATTTT
*
1092019 CGGGTCGGGT
1 TGGGTCGGGT
1092029 GATTATCGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
16 14 0.61
17 9 0.39
ACGTcount: A:0.07, C:0.12, G:0.44, T:0.37
Consensus pattern (17 bp):
TGGGTCGGGTCAATTTT
Found at i:1092211 original size:2 final size:2
Alignment explanation
Indices: 1092204--1092236 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1092194 GAATCTAATC
1092204 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
1092237 ATTGATTTAT
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:1092398 original size:16 final size:16
Alignment explanation
Indices: 1092379--1092435 Score: 78
Period size: 16 Copynumber: 3.6 Consensus size: 16
1092369 TTCGGGTTGC
1092379 TTTCGGTTCAAATTGT
1 TTTCGGTTCAAATTGT
1092395 TTTCGGTTCAAATTGT
1 TTTCGGTTCAAATTGT
* * **
1092411 TTTCAGTTCAAGTTAA
1 TTTCGGTTCAAATTGT
1092427 TTTCGGTTC
1 TTTCGGTTC
1092436 GGTTTGCTTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.19, C:0.14, G:0.18, T:0.49
Consensus pattern (16 bp):
TTTCGGTTCAAATTGT
Found at i:1092403 original size:32 final size:32
Alignment explanation
Indices: 1092362--1092445 Score: 80
Period size: 32 Copynumber: 2.7 Consensus size: 32
1092352 GATCGGGTTA
* *
1092362 AATTT-GGTTCGGGTTGCTTTCGGTTCAAATT
1 AATTTCGGTTCGGATTGCTTTCAGTTCAAATT
** ** * *
1092393 GTTTTCGGTTCAAATTGTTTTCAGTTCAAGTT
1 AATTTCGGTTCGGATTGCTTTCAGTTCAAATT
*
1092425 AATTTCGGTTCGGTTTGCTTT
1 AATTTCGGTTCGGATTGCTTT
1092446 TGATTCGGGT
Statistics
Matches: 38, Mismatches: 14, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
31 3 0.08
32 35 0.92
ACGTcount: A:0.15, C:0.13, G:0.23, T:0.49
Consensus pattern (32 bp):
AATTTCGGTTCGGATTGCTTTCAGTTCAAATT
Found at i:1093115 original size:20 final size:20
Alignment explanation
Indices: 1093041--1093115 Score: 62
Period size: 21 Copynumber: 3.6 Consensus size: 20
1093031 TATACCAAAT
* *
1093041 GGATCGATCCTTTTTGGGAAG
1 GGATCGATCC-TTTTCGCAAG
* *
1093062 GGATCGATCCTTTTCCTCGAG
1 GGATCGATCCTTTT-CGCAAG
* *
1093083 GGATAGATTCTTTT-GCAATG
1 GGATCGATCCTTTTCGCAA-G
1093103 GGATCGATCCTTT
1 GGATCGATCCTTT
1093116 GAGCCAGAGA
Statistics
Matches: 42, Mismatches: 10, Indels: 5
0.74 0.18 0.09
Matches are distributed among these distances:
19 2 0.05
20 16 0.38
21 24 0.57
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.36
Consensus pattern (20 bp):
GGATCGATCCTTTTCGCAAG
Found at i:1093176 original size:21 final size:20
Alignment explanation
Indices: 1093152--1093197 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
1093142 TATAAAGCGC
* *
1093152 GAAAACGTTCGAGTATGTTTT
1 GAAAACGTTCGACTAAG-TTT
*
1093173 GAAAAGGTTCGACTAAGTTT
1 GAAAACGTTCGACTAAGTTT
1093193 GAAAA
1 GAAAA
1093198 ACATTTAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (20 bp):
GAAAACGTTCGACTAAGTTT
Found at i:1096362 original size:66 final size:66
Alignment explanation
Indices: 1096256--1096387 Score: 255
Period size: 66 Copynumber: 2.0 Consensus size: 66
1096246 AGAATCAGTA
1096256 GAGACTAGTGAGGCCAGGTGAGTGCATCATATTTTAATATAGGATTATATGGAAATTGGACTTGC
1 GAGACTAGTGAGGCCAGGTGAGTGCATCATATTTTAATATAGGATTATATGGAAATTGGACTTGC
1096321 G
66 G
*
1096322 GAGACTAGTGAGGCCAGGTGAGTGCATCTTATTTTAATATAGGATTATATGGAAATTGGACTTGC
1 GAGACTAGTGAGGCCAGGTGAGTGCATCATATTTTAATATAGGATTATATGGAAATTGGACTTGC
1096387 G
66 G
1096388 ATAAGTTTAA
Statistics
Matches: 65, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.31
Consensus pattern (66 bp):
GAGACTAGTGAGGCCAGGTGAGTGCATCATATTTTAATATAGGATTATATGGAAATTGGACTTGC
G
Found at i:1097026 original size:2 final size:2
Alignment explanation
Indices: 1097019--1097051 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
1097009 GATTAGATTA
1097019 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
1097052 AGTAAAATGA
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:1097232 original size:2 final size:2
Alignment explanation
Indices: 1097225--1097252 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1097215 AGGTAAAAGG
1097225 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
1097253 GACTATGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1105238 original size:43 final size:43
Alignment explanation
Indices: 1105177--1105392 Score: 317
Period size: 43 Copynumber: 5.0 Consensus size: 43
1105167 TGCCATGCCC
* *
1105177 CAGGTCCGGTCCTGCTATTTATTTTCCCAGCAAAAGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
*
1105220 CAGGTCCGGTCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
*
1105263 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAATGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
* *
1105306 CAGGTCCGGGCCTGCTATTAATTCTCCCACCAAACA-CAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAA-AGCAAGACT
* * * * *
1105349 CAGGTCGGGGCCTGCTATTAATTCTACCACCAAACGCAAGACT
1 CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
1105392 C
1 C
1105393 TGTAAAACAA
Statistics
Matches: 162, Mismatches: 9, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
43 162 1.00
ACGTcount: A:0.26, C:0.31, G:0.18, T:0.25
Consensus pattern (43 bp):
CAGGTCCGGGCCTGCTATTTATTTTCCCACCAAAAGCAAGACT
Found at i:1108850 original size:18 final size:19
Alignment explanation
Indices: 1108815--1108851 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1108805 AAGAGAATGC
1108815 AAGATTATTAGTGAGAATAA
1 AAGATTATTAG-GAGAATAA
1108835 AAGATTATTA-GAGAATA
1 AAGATTATTAGGAGAATA
1108852 TAATTACTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.51, C:0.00, G:0.19, T:0.30
Consensus pattern (19 bp):
AAGATTATTAGGAGAATAA
Found at i:1111381 original size:18 final size:19
Alignment explanation
Indices: 1111339--1111381 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1111329 ACCAAGATTA
* *
1111339 AATTTAATTCTTAATTTTT
1 AATTTAAGTCTTAATTTTC
1111358 AA-TTAAGTCTTAA-TTTC
1 AATTTAAGTCTTAATTTTC
1111375 AATTTAA
1 AATTTAA
1111382 TATAACAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 5 0.24
18 14 0.67
19 2 0.10
ACGTcount: A:0.37, C:0.07, G:0.02, T:0.53
Consensus pattern (19 bp):
AATTTAAGTCTTAATTTTC
Found at i:1111594 original size:39 final size:39
Alignment explanation
Indices: 1111482--1111595 Score: 135
Period size: 39 Copynumber: 2.9 Consensus size: 39
1111472 TTATTTATAA
* * **
1111482 TTCTCAAATTATTTCA-TTCTAACATTCTAAATTCCTAAT
1 TTCTTAAATTATTTCACAT-TAACATTCTAAATTATTAAT
*
1111521 TTCTTAAATT-TTTCCACCA-TAACATTTTAAATTATTAAT
1 TTCTTAAATTATTT-CA-CATTAACATTCTAAATTATTAAT
1111560 TTCTTAAATTATTTCACATTAACATTCTAAATTATT
1 TTCTTAAATTATTTCACATTAACATTCTAAATTATT
1111596 TTTTAAAATA
Statistics
Matches: 64, Mismatches: 6, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
38 5 0.08
39 56 0.88
40 3 0.05
ACGTcount: A:0.35, C:0.17, G:0.00, T:0.48
Consensus pattern (39 bp):
TTCTTAAATTATTTCACATTAACATTCTAAATTATTAAT
Found at i:1115507 original size:44 final size:44
Alignment explanation
Indices: 1115437--1115528 Score: 139
Period size: 44 Copynumber: 2.1 Consensus size: 44
1115427 CACCAATAAT
* * * * *
1115437 AGTACATAAAACTTAAAAGCATCCCCTGGCATAAAATCCTTTAC
1 AGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTCAC
1115481 AGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTCAC
1 AGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTCAC
1115525 AGTA
1 AGTA
1115529 GAATAGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.43, C:0.27, G:0.08, T:0.22
Consensus pattern (44 bp):
AGTACATAAAACTTAAAAACACCCCCTGCCATAAAAACCTTCAC
Found at i:1124546 original size:4 final size:4
Alignment explanation
Indices: 1124537--1124561 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
1124527 CATTTTTGCT
1124537 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
1124562 GTATGTCAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:1125423 original size:13 final size:12
Alignment explanation
Indices: 1125405--1125439 Score: 54
Period size: 11 Copynumber: 2.9 Consensus size: 12
1125395 ATGTTTTTTT
1125405 AAATAATTATATA
1 AAATAATT-TATA
1125418 AAATAA-TTATA
1 AAATAATTTATA
1125429 AAATAATTTAT
1 AAATAATTTAT
1125440 GTTCAGTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 10 0.48
12 5 0.24
13 6 0.29
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (12 bp):
AAATAATTTATA
Found at i:1126238 original size:128 final size:128
Alignment explanation
Indices: 1126073--1126312 Score: 399
Period size: 128 Copynumber: 1.9 Consensus size: 128
1126063 CTCGACGAAC
* *
1126073 AGTAGTGAGCATAACTAATGATGAGCACCGCTGAACACTATTAATTTAATTTATAAAAATTTAAA
1 AGTAGTGAGCACAACTAATGATGAGCACCGCTAAACACTATTAATTTAATTTATAAAAATTTAAA
*
1126138 ATTATAAGTTACTCAACACATAATCATAGATTAGTTAAAAGTTAAAAAATAAATTATTTATTT
66 ATTATAAGTTACTCAACACATAATCATAAATTAGTTAAAAGTTAAAAAATAAATTATTTATTT
* * * *
1126201 AGTAGTGATCACAACTAATGATGAGTACCGCTAAACACTATTAGTTTAATTTCTAAAAATTTAAA
1 AGTAGTGAGCACAACTAATGATGAGCACCGCTAAACACTATTAATTTAATTTATAAAAATTTAAA
* *
1126266 ATTATAAGTTACTCAATATATAATCATAAATTAGTTAAAAGTTAAAA
66 ATTATAAGTTACTCAACACATAATCATAAATTAGTTAAAAGTTAAAA
1126313 TAAAATATTT
Statistics
Matches: 103, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
128 103 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (128 bp):
AGTAGTGAGCACAACTAATGATGAGCACCGCTAAACACTATTAATTTAATTTATAAAAATTTAAA
ATTATAAGTTACTCAACACATAATCATAAATTAGTTAAAAGTTAAAAAATAAATTATTTATTT
Found at i:1126315 original size:21 final size:19
Alignment explanation
Indices: 1126291--1126333 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
1126281 ATATATAATC
*
1126291 ATAAATTAGTTAAAAGTTAAA
1 ATAAAATAGTTAAAA--TAAA
*
1126312 ATAAAATATTTAAAATAAA
1 ATAAAATAGTTAAAATAAA
1126331 ATA
1 ATA
1126334 TTAATTACAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 7 0.35
21 13 0.65
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAAAATAGTTAAAATAAA
Found at i:1126326 original size:14 final size:14
Alignment explanation
Indices: 1126307--1126335 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
1126297 TAGTTAAAAG
1126307 TTAAAATAAAATAT
1 TTAAAATAAAATAT
1126321 TTAAAATAAAATAT
1 TTAAAATAAAATAT
1126335 T
1 T
1126336 AATTACATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (14 bp):
TTAAAATAAAATAT
Found at i:1126471 original size:15 final size:14
Alignment explanation
Indices: 1126431--1126486 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
1126421 AAATTATGAA
1126431 AAATAATTTA--TT
1 AAATAATTTATTTT
1126443 -AATAATTTATTTT
1 AAATAATTTATTTT
1126456 AAATAATTTATCTTT
1 AAATAATTTAT-TTT
*
1126471 AAA-ATTTTAATTTT
1 AAATAATTT-ATTTT
1126485 AA
1 AA
1126487 TCTTTTAAAA
Statistics
Matches: 38, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
11 9 0.24
13 2 0.05
14 19 0.50
15 8 0.21
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.54
Consensus pattern (14 bp):
AAATAATTTATTTT
Found at i:1127148 original size:21 final size:22
Alignment explanation
Indices: 1127096--1127154 Score: 84
Period size: 21 Copynumber: 2.6 Consensus size: 22
1127086 TATTTTTACA
1127096 TTAAGTTAATAGTAAAATATATT
1 TTAAGTTAATA-TAAAATATATT
1127119 TAATAAGTTAATATAAAA-ATATT
1 T--TAAGTTAATATAAAATATATT
1127142 TTAAGTTAATATA
1 TTAAGTTAATATA
1127155 TATATATAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.35
23 7 0.21
24 5 0.15
25 10 0.29
ACGTcount: A:0.51, C:0.00, G:0.07, T:0.42
Consensus pattern (22 bp):
TTAAGTTAATATAAAATATATT
Found at i:1127161 original size:21 final size:21
Alignment explanation
Indices: 1127096--1127161 Score: 78
Period size: 21 Copynumber: 3.0 Consensus size: 21
1127086 TATTTTTACA
1127096 TTAAGTTAATAGTAAAATATATT
1 TTAAGTTAATA-T-AAATATATT
*
1127119 TAATAAGTTAATATAAAAATATT
1 T--TAAGTTAATATAAATATATT
*
1127142 TTAAGTTAATATATATATAT
1 TTAAGTTAATATAAATATAT
1127162 AATTCGAGTC
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
21 17 0.45
23 10 0.26
24 1 0.03
25 10 0.26
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (21 bp):
TTAAGTTAATATAAATATATT
Found at i:1127240 original size:7 final size:8
Alignment explanation
Indices: 1127213--1127244 Score: 57
Period size: 8 Copynumber: 4.1 Consensus size: 8
1127203 AATTATATAA
1127213 AAAATTCT
1 AAAATTCT
1127221 AAAATTCT
1 AAAATTCT
1127229 AAAATT-T
1 AAAATTCT
1127236 AAAATTCT
1 AAAATTCT
1127244 A
1 A
1127245 TAATATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (8 bp):
AAAATTCT
Found at i:1127240 original size:15 final size:16
Alignment explanation
Indices: 1127213--1127244 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
1127203 AATTATATAA
1127213 AAAATTCTAAAATTCT
1 AAAATTCTAAAATTCT
1127229 AAAATT-TAAAATTCT
1 AAAATTCTAAAATTCT
1127244 A
1 A
1127245 TAATATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.53, C:0.09, G:0.00, T:0.38
Consensus pattern (16 bp):
AAAATTCTAAAATTCT
Found at i:1128237 original size:20 final size:20
Alignment explanation
Indices: 1128212--1128265 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
1128202 AAATTTGAAG
1128212 GTGCATCGATGCATTAAGGA
1 GTGCATCGATGCATTAAGGA
1128232 GTGCATCGATGCATTAAGGA
1 GTGCATCGATGCATTAAGGA
1128252 GTGCATCGATGCAT
1 GTGCATCGATGCAT
1128266 AGGAATTTCG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.26
Consensus pattern (20 bp):
GTGCATCGATGCATTAAGGA
Found at i:1131185 original size:22 final size:23
Alignment explanation
Indices: 1131144--1131190 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
1131134 CGCATTGATG
*
1131144 CACTGTTCATTGGTACTGTTCAT
1 CACTGTTCATCGGTACTGTTCAT
*
1131167 CACTGTTCA-CGGTATTGTTCAT
1 CACTGTTCATCGGTACTGTTCAT
1131189 CA
1 CA
1131191 TTATTCATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 13 0.59
23 9 0.41
ACGTcount: A:0.19, C:0.23, G:0.17, T:0.40
Consensus pattern (23 bp):
CACTGTTCATCGGTACTGTTCAT
Found at i:1131197 original size:22 final size:22
Alignment explanation
Indices: 1131155--1131197 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
1131145 ACTGTTCATT
*
1131155 GGTACTGTTCATCACTGTTCAC
1 GGTACTGTTCATCACTATTCAC
* *
1131177 GGTATTGTTCATCATTATTCA
1 GGTACTGTTCATCACTATTCA
1131198 TAAAAAAATC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.21, G:0.16, T:0.42
Consensus pattern (22 bp):
GGTACTGTTCATCACTATTCAC
Found at i:1132388 original size:22 final size:23
Alignment explanation
Indices: 1132348--1132400 Score: 81
Period size: 22 Copynumber: 2.3 Consensus size: 23
1132338 ATACTCTGCA
1132348 ACTGTTCACGGGTACTGTTCATC
1 ACTGTTCACGGGTACTGTTCATC
*
1132371 ACTGTTCAC-GGTATTGTTCATC
1 ACTGTTCACGGGTACTGTTCATC
*
1132393 ACTATTCA
1 ACTGTTCA
1132401 TAAAAAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.38
Consensus pattern (23 bp):
ACTGTTCACGGGTACTGTTCATC
Found at i:1132697 original size:25 final size:25
Alignment explanation
Indices: 1132639--1132700 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
1132629 ATAAGTCTAG
* *
1132639 ATTCAATATTTTGATACATGATCAC
1 ATTCAATATTATGATACATGATCAA
*
1132664 ATTCTATATTATGATACATGA-CATGA
1 ATTCAATATTATGATACATGATCA--A
1132690 ATTC-ATATTAT
1 ATTCAATATTAT
1132701 ATGCATTATG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
24 2 0.06
25 26 0.81
26 4 0.12
ACGTcount: A:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (25 bp):
ATTCAATATTATGATACATGATCAA
Found at i:1132804 original size:29 final size:31
Alignment explanation
Indices: 1132742--1132811 Score: 108
Period size: 29 Copynumber: 2.3 Consensus size: 31
1132732 GTTATATGAG
*
1132742 CTATGTGATAAAGGTATGGAAAATGATATGT
1 CTATGTGATAAAGGTATGGAAAATGATAAGT
1132773 CTATGTGA-AAAGGTATGG-AAATGATAAGT
1 CTATGTGATAAAGGTATGGAAAATGATAAGT
*
1132802 CTACGTGATA
1 CTATGTGATA
1132812 TAAACTATGT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
29 17 0.47
30 11 0.31
31 8 0.22
ACGTcount: A:0.39, C:0.06, G:0.26, T:0.30
Consensus pattern (31 bp):
CTATGTGATAAAGGTATGGAAAATGATAAGT
Found at i:1133080 original size:23 final size:25
Alignment explanation
Indices: 1133047--1133095 Score: 75
Period size: 23 Copynumber: 2.0 Consensus size: 25
1133037 CATATTATAT
1133047 GGCACTACGGTGC-AA-TTCTACGC
1 GGCACTACGGTGCAAATTTCTACGC
*
1133070 GGCACTTCGGTGCAAATTTCTACGC
1 GGCACTACGGTGCAAATTTCTACGC
1133095 G
1 G
1133096 ATCCTTCGGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.52
24 2 0.09
25 9 0.39
ACGTcount: A:0.20, C:0.29, G:0.27, T:0.24
Consensus pattern (25 bp):
GGCACTACGGTGCAAATTTCTACGC
Found at i:1133102 original size:25 final size:25
Alignment explanation
Indices: 1133047--1133142 Score: 76
Period size: 25 Copynumber: 4.0 Consensus size: 25
1133037 CATATTATAT
*
1133047 GGCACTACGGTGC-AA-TTCTACGC
1 GGCACTTCGGTGCAAATTTCTACGC
1133070 GGCACTTCGGTGCAAATTTCTACGC
1 GGCACTTCGGTGCAAATTTCTACGC
* * *
1133095 GATC-CTTCGG-GACAAA-TTCTAAGT
1 G-GCACTTCGGTG-CAAATTTCTACGC
* * *
1133119 GGCACTTCGATGAAAATTTATACG
1 GGCACTTCGGTGCAAATTTCTACG
1133143 AGTTGTGGTG
Statistics
Matches: 57, Mismatches: 9, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
23 13 0.23
24 18 0.32
25 25 0.44
26 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.23, T:0.27
Consensus pattern (25 bp):
GGCACTTCGGTGCAAATTTCTACGC
Found at i:1134028 original size:19 final size:19
Alignment explanation
Indices: 1134004--1134042 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
1133994 GATTATGAAT
*
1134004 AAAAATTTA-ATATAAATAA
1 AAAAATATATATAT-AATAA
1134023 AAAAATATATATATAATAA
1 AAAAATATATATATAATAA
1134042 A
1 A
1134043 TCGAGTATCG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
AAAAATATATATATAATAA
Found at i:1134403 original size:31 final size:31
Alignment explanation
Indices: 1134365--1134432 Score: 118
Period size: 31 Copynumber: 2.2 Consensus size: 31
1134355 GGGTGACCAC
*
1134365 ATCTTAATTAAATAAAAACAAAAGTGATCAT
1 ATCTTAATTAAATAAAAACAAAAGTCATCAT
*
1134396 ATCTTAATTAAATAAAAACAAAATTCATCAT
1 ATCTTAATTAAATAAAAACAAAAGTCATCAT
1134427 ATCTTA
1 ATCTTA
1134433 TGTTTTTTGA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.53, C:0.12, G:0.03, T:0.32
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAACAAAAGTCATCAT
Found at i:1141311 original size:20 final size:20
Alignment explanation
Indices: 1141260--1141311 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1141250 AATTCAATGG
*
1141260 TATCGATACCAAGAGGGGAA
1 TATCGATACCATGAGGGGAA
*
1141280 TATCGATACCATGAGGATG-A
1 TATCGATACCATGAGG-GGAA
1141300 TATCGATACCAT
1 TATCGATACCAT
1141312 TGATCATAGA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 28 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.17, G:0.23, T:0.23
Consensus pattern (20 bp):
TATCGATACCATGAGGGGAA
Found at i:1142173 original size:68 final size:68
Alignment explanation
Indices: 1142093--1142277 Score: 280
Period size: 68 Copynumber: 2.7 Consensus size: 68
1142083 AGATAAATAG
* * * *
1142093 CCTAACTATGCATTTGATAGAAATGTGTCAATTATACCAGTTAGATGAAAGTCTAAGTCCCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
1142158 AAA
66 AAA
* *
1142161 CCTAACTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTGCCTTTG
1 CCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
**
1142226 ATG
66 AAA
* *
1142229 GCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
1 CCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAA
1142278 CGATTAAAGA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
68 106 1.00
ACGTcount: A:0.32, C:0.16, G:0.22, T:0.31
Consensus pattern (68 bp):
CCTAACTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAGGCTAAGTCCCTTTG
AAA
Found at i:1142366 original size:81 final size:80
Alignment explanation
Indices: 1142226--1142439 Score: 243
Period size: 81 Copynumber: 2.6 Consensus size: 80
1142216 AGTGCCTTTG
* * *
1142226 ATGG-CTAGCTGTGCATTT-GACAGAAATGTGTCAATTATGCCAGTTAGATGAACGATTAAAGAC
1 ATGGCCTAGCTGTGCATTTGGA-AGAAAAGTGTCAATCATG-CAATTAGATGAACGATTAAAGAC
1142289 CGTTGAGTAAAAGATAA
64 CGTTGAGTAAAAGATAA
* * * * * * *
1142306 ATGGCCTAGCTGTGTATTTGGTAGAAAGGTGTCAATGATGTCAATTAGATGAATGGTTAAAGACT
1 ATGGCCTAGCTGTGCATTTGGAAGAAAAGTGTCAATCATG-CAATTAGATGAACGATTAAAGACC
1142371 GTTGAGTAAAAGATAA
65 GTTGAGTAAAAGATAA
* * ** *
1142387 ATAGCCTAACCATGCATTTAGAAGAAAAGTGTCAATCATGCAAGTTAGATGAA
1 ATGGCCTAGCTGTGCATTTGGAAGAAAAGTGTCAATCATGCAA-TTAGATGAA
1142440 AAGTAAATGC
Statistics
Matches: 113, Mismatches: 18, Indels: 5
0.83 0.13 0.04
Matches are distributed among these distances:
80 7 0.06
81 105 0.93
82 1 0.01
ACGTcount: A:0.37, C:0.11, G:0.24, T:0.28
Consensus pattern (80 bp):
ATGGCCTAGCTGTGCATTTGGAAGAAAAGTGTCAATCATGCAATTAGATGAACGATTAAAGACCG
TTGAGTAAAAGATAA
Found at i:1146123 original size:147 final size:151
Alignment explanation
Indices: 1145869--1146172 Score: 440
Period size: 147 Copynumber: 2.0 Consensus size: 151
1145859 TACTTAGGTC
*
1145869 ATTTAGTATTCAAGTTTATCCCGGTCATTTCGGAGTTTCCAGAGTAATTCGATCGTTTCAATAAT
1 ATTTAGTATTCAAGTTTATCCCGGTCATTTCGGAGTTTCCAGAGTAATTCGATCGTTTCAACAAT
* * *
1145934 TCAAATATGTATAATACTTCCATTCAGTTCAACTTTGTCATATATGTAGTCA-TTCGAATAATTC
66 TCAAATACGTATAATACTTCCATTCAGTTCAACTTTGTCATATATATAAT-ATTTCGAATAATTC
1145998 AGATGTGTAAAGTACTTTCGCTA
130 AGATGTGTAAAGTA-TTTCGCTA
**
1146021 ATTTAGTATTCAAG-TTATCCTTGTCA-TTCGGAGTTTCCAGAGTAATT-GATCGTTTCAACAAT
1 ATTTAGTATTCAAGTTTATCCCGGTCATTTCGGAGTTTCCAGAGTAATTCGATCGTTTCAACAAT
** * * *
1146083 TCGGATACGTA-CAT-CTTCTATTCAGTTCAACTTTGTCATATATATAATATTTCGAATAATTTA
66 TCAAATACGTATAATACTTCCATTCAGTTCAACTTTGTCATATATATAATATTTCGAATAATTCA
*
1146146 GATGTGTAAAGTATTTCGTTA
131 GATGTGTAAAGTATTTCGCTA
1146167 ATTTAG
1 ATTTAG
1146173 CCTTCGGGAG
Statistics
Matches: 139, Mismatches: 12, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
146 14 0.10
147 56 0.40
148 2 0.01
149 22 0.16
150 21 0.15
151 10 0.07
152 14 0.10
ACGTcount: A:0.30, C:0.15, G:0.14, T:0.41
Consensus pattern (151 bp):
ATTTAGTATTCAAGTTTATCCCGGTCATTTCGGAGTTTCCAGAGTAATTCGATCGTTTCAACAAT
TCAAATACGTATAATACTTCCATTCAGTTCAACTTTGTCATATATATAATATTTCGAATAATTCA
GATGTGTAAAGTATTTCGCTA
Found at i:1147761 original size:2 final size:2
Alignment explanation
Indices: 1147754--1147821 Score: 108
Period size: 2 Copynumber: 36.0 Consensus size: 2
1147744 TCAAAGAACC
1147754 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1147794 AT AT AT AT AT AT AT AT AT -T AT AT -T AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1147822 TAAAATAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 8
0.89 0.00 0.11
Matches are distributed among these distances:
1 4 0.06
2 58 0.94
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:1149629 original size:5 final size:5
Alignment explanation
Indices: 1149615--1149914 Score: 84
Period size: 5 Copynumber: 60.8 Consensus size: 5
1149605 AGGTAATGAA
* * * * * *
1149615 AAAAT AAAAAT AAAAA ATAAAT GAAAT -AAAG AAAAT GAGAT AAAA- AAAAA
1 AAAAT -AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * *
1149665 AAAAT AAAGAGA AAAAG AAACGAT AAAGT AAAGAT AAAA- AAAGT -AAA-
1 AAAAT AAA-A-T AAAAT AAA--AT AAAAT AAA-AT AAAAT AAAAT AAAAT
* * *
1149712 AAAAT -AAAT AAAAT AAAGAT -AAA- GAAAT AAAA- GAAA- AAAAT AAGAT
1 AAAAT AAAAT AAAAT AAA-AT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* * * * * *
1149758 AAAAAG AAAAT -AAAT AAAAT -GAAG AAAGT AATAAT -ATAT ATAAT -AAAT
1 -AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AA-AAT AAAAT AAAAT AAAAT
*
1149806 -AAAT -AAAT AGAAACA AAAAT AAAAT -AAAT ATAAAT AAAAT AAAAT
1 AAAAT AAAAT A-AAA-T AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT
* * *
1149851 AAAAT AAATAT AAAAG AAATAA AAAAT AAAGAT -AAAT AATAA- ACAAT
1 AAAAT AAA-AT AAAAT AAA-AT AAAAT AAA-AT AAAAT AA-AAT AAAAT
*
1149898 -AAAT AATA- AAAAT AAAA
1 AAAAT AAAAT AAAAT AAAA
1149915 AATAGAAAGA
Statistics
Matches: 217, Mismatches: 43, Indels: 69
0.66 0.13 0.21
Matches are distributed among these distances:
4 62 0.29
5 102 0.47
6 45 0.21
7 8 0.04
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.17
Consensus pattern (5 bp):
AAAAT
Found at i:1149719 original size:23 final size:24
Alignment explanation
Indices: 1149662--1149762 Score: 75
Period size: 23 Copynumber: 4.2 Consensus size: 24
1149652 AGATAAAAAA
* *
1149662 AAAAAAATAAAGAGAAAAAGAA-AC
1 AAAAAAATAAAGATAAAAA-AAGAT
* * *
1149686 GATAAAGTAAAGATAAAAAAAG-T
1 AAAAAAATAAAGATAAAAAAAGAT
1149709 AAAAAAAT-AA-ATAAAATAAAGAT
1 AAAAAAATAAAGATAAAA-AAAGAT
* *
1149732 AAAGAAATAAAAGAAAAAAATAAGAT
1 AAAAAAAT-AAAGATAAAAA-AAGAT
1149758 AAAAA
1 AAAAA
1149763 GAAAATAAAT
Statistics
Matches: 59, Mismatches: 11, Indels: 12
0.72 0.13 0.15
Matches are distributed among these distances:
21 6 0.10
22 6 0.10
23 15 0.25
24 15 0.25
25 3 0.05
26 14 0.24
ACGTcount: A:0.76, C:0.01, G:0.11, T:0.12
Consensus pattern (24 bp):
AAAAAAATAAAGATAAAAAAAGAT
Found at i:1149722 original size:4 final size:4
Alignment explanation
Indices: 1149698--1149918 Score: 72
Period size: 4 Copynumber: 53.8 Consensus size: 4
1149688 TAAAGTAAAG
* * * *
1149698 ATAA AAAA AGTAA AAAA ATAA ATAAA ATAAA GATAA AGAA ATAAA AGAA
1 ATAA ATAA A-TAA ATAA ATAA AT-AA AT-AA -ATAA ATAA AT-AA ATAA
* * *
1149747 AAAA ATAA GATAA A-AA GA-AA ATAA ATAAA ATGA AGAA AGT-A AT-A
1 ATAA ATAA -ATAA ATAA -ATAA ATAA AT-AA ATAA ATAA A-TAA ATAA
*
1149791 ATAT ATATA ATAA ATAA ATAA ATAGA A-ACA A-AA ATAAA ATAA AT--
1 ATAA ATA-A ATAA ATAA ATAA ATA-A ATA-A ATAA AT-AA ATAA ATAA
* *
1149835 ATAA ATAAA ATAAA ATAAA ATAA ATAT A-AA AGAA ATAA A-AA ATAAA
1 ATAA AT-AA AT-AA AT-AA ATAA ATAA ATAA ATAA ATAA ATAA AT-AA
* *
1149881 GATAA AT-A ATAA A-CA ATAA ATAA TAAAA ATAA A-AA ATA
1 -ATAA ATAA ATAA ATAA ATAA ATAA -ATAA ATAA ATAA ATA
1149919 GAAAGAAAAA
Statistics
Matches: 169, Mismatches: 23, Indels: 50
0.70 0.10 0.21
Matches are distributed among these distances:
2 2 0.01
3 22 0.13
4 88 0.52
5 53 0.31
6 4 0.02
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (4 bp):
ATAA
Found at i:1149724 original size:20 final size:20
Alignment explanation
Indices: 1149701--1149916 Score: 66
Period size: 19 Copynumber: 10.7 Consensus size: 20
1149691 AGTAAAGATA
1149701 AAAAAAGTAAAAAAATAAAT
1 AAAAAAGTAAAAAAATAAAT
*
1149721 --AAAA-TAAAGATAAAGAAAT
1 AAAAAAGTAAA-A-AAATAAAT
1149740 --AAAAG-AAAAAAATAAGAT
1 AAAAAAGTAAAAAAATAA-AT
1149758 -AAAAAG-AAAATAAATAAAAT
1 AAAAAAGTAAAA-AAAT-AAAT
* * * *
1149778 GAAGAAAGTAATAATATATAT
1 -AAAAAAGTAAAAAAATAAAT
* *
1149799 AATAAA-TAAATAAATAGAA-
1 AAAAAAGTAAAAAAATA-AAT
1149818 ACAAAAA-TAAAATAAATATAAAT
1 A-AAAAAGT-AAA-AAA-ATAAAT
*
1149841 AAAATAA--AATAAAATAAAT
1 AAAA-AAGTAAAAAAATAAAT
* *
1149860 ATAAAAG-AAATAAA-AAAT
1 AAAAAAGTAAAAAAATAAAT
*
1149878 AAAGATAAATAATAAACAATAAAT
1 AAA-A-AAGTAA-AAA-AATAAAT
*
1149902 AATAAAAATAAAAAA
1 AA-AAAAGTAAAAAA
1149917 TAGAAAGAAA
Statistics
Matches: 151, Mismatches: 20, Indels: 49
0.69 0.09 0.22
Matches are distributed among these distances:
17 9 0.06
18 16 0.11
19 46 0.30
20 22 0.15
21 13 0.09
22 20 0.13
23 17 0.11
24 7 0.05
25 1 0.01
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.19
Consensus pattern (20 bp):
AAAAAAGTAAAAAAATAAAT
Found at i:1149728 original size:37 final size:37
Alignment explanation
Indices: 1149687--1149761 Score: 109
Period size: 37 Copynumber: 2.0 Consensus size: 37
1149677 AAAAGAAACG
1149687 ATAAAG-TAAAGATAAAAAAAGTAAAAAAATAA-ATAAA
1 ATAAAGATAAAGA-AAAAAAAG-AAAAAAATAAGATAAA
*
1149724 ATAAAGATAAAGAAATAAAAGAAAAAAATAAGATAAA
1 ATAAAGATAAAGAAAAAAAAGAAAAAAATAAGATAAA
1149761 A
1 A
1149762 AGAAAATAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
36 10 0.29
37 19 0.54
38 6 0.17
ACGTcount: A:0.76, C:0.00, G:0.09, T:0.15
Consensus pattern (37 bp):
ATAAAGATAAAGAAAAAAAAGAAAAAAATAAGATAAA
Found at i:1149771 original size:37 final size:38
Alignment explanation
Indices: 1149693--1149893 Score: 103
Period size: 41 Copynumber: 5.1 Consensus size: 38
1149683 AACGATAAAG
*
1149693 TAAAGATAAAAAAAGTAAAAAAATAAATAAAATAAAGA
1 TAAAGATAAAAAAAGTAAAAAAATAAATAAAATAAAAA
*
1149731 TAAAGA-AATAAAAG-AAAAAAATAAGATAAAA-AGAAAA
1 TAAAGATAAAAAAAGTAAAAAAATAA-ATAAAATA-AAAA
* * * * * *
1149768 TAAATAAAATGAAGAAAGTAATAATATATATAATAA-ATAAA
1 TAAAGATAA--AA-AAAGTAAAAAAATAAATAA-AATAAAAA
* * *
1149809 TAAATAGAAACAAAAATAAAATAAATATAAATAAAAT-AAAA
1 TAAAGATAAA-AAAAGT-AAA-AAA-ATAAATAAAATAAAAA
*
1149850 TAAA-ATAAATATAAAAG-AAATAAA-AAATAAAGATAAATAA
1 TAAAGAT-AA-A-AAAAGTAAAAAAATAAATAAA-ATAAA-AA
1149890 TAAA
1 TAAA
1149894 CAATAAATAA
Statistics
Matches: 127, Mismatches: 18, Indels: 34
0.71 0.10 0.19
Matches are distributed among these distances:
36 11 0.09
37 28 0.22
38 11 0.09
39 9 0.07
40 14 0.11
41 32 0.25
42 22 0.17
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (38 bp):
TAAAGATAAAAAAAGTAAAAAAATAAATAAAATAAAAA
Found at i:1149898 original size:27 final size:25
Alignment explanation
Indices: 1149709--1149913 Score: 109
Period size: 25 Copynumber: 7.8 Consensus size: 25
1149699 TAAAAAAAGT
* *
1149709 AAAAA-AATAAATAAAATAAAGATA
1 AAAAATAAAAAATAAAATAAATATA
*
1149733 AAGAAATAAAAGAAAAAAATAAGATA-A
1 AA-AAATAAAA-AATAAAATAA-ATATA
* *
1149760 AAAGAA-AATAAATAAAATGAAGAAAGTA
1 AAA-AATAAAAAATAAAAT-AA-ATA-TA
* * *
1149788 ATAATATATATAAT-AAATAAATA-A
1 A-AAAATAAAAAATAAAATAAATATA
*
1149812 ATAGAAA-CAAAAATAAAATAAATATA
1 A-A-AAATAAAAAATAAAATAAATATA
*
1149838 AATAAA-ATAAAATAAAATAAATATAA
1 AA-AAATAAAAAATAAAATAAATAT-A
1149864 AAGAAATAAAAAATAAAGATAAATAATA
1 AA-AAATAAAAAATAAA-ATAAAT-ATA
* *
1149892 AACAATAAATAATAAAAATAAA
1 AAAAATAAAAAAT-AAAATAAA
1149914 AAATAGAAAG
Statistics
Matches: 141, Mismatches: 22, Indels: 33
0.72 0.11 0.17
Matches are distributed among these distances:
24 10 0.07
25 41 0.29
26 22 0.16
27 39 0.28
28 21 0.15
29 8 0.06
ACGTcount: A:0.75, C:0.01, G:0.05, T:0.19
Consensus pattern (25 bp):
AAAAATAAAAAATAAAATAAATATA
Found at i:1149992 original size:12 final size:12
Alignment explanation
Indices: 1149975--1150003 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
1149965 AACAAATAAT
1149975 ACAAAAAAAAAA
1 ACAAAAAAAAAA
1149987 AC-AAAAAAAAA
1 ACAAAAAAAAAA
1149998 ACAAAA
1 ACAAAA
1150004 TAGTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.69
12 5 0.31
ACGTcount: A:0.90, C:0.10, G:0.00, T:0.00
Consensus pattern (12 bp):
ACAAAAAAAAAA
Found at i:1149994 original size:11 final size:11
Alignment explanation
Indices: 1149978--1150003 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1149968 AAATAATACA
1149978 AAAAAAAAAAC
1 AAAAAAAAAAC
1149989 AAAAAAAAAAC
1 AAAAAAAAAAC
1150000 AAAA
1 AAAA
1150004 TAGTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAAAAAC
Found at i:1150075 original size:2 final size:2
Alignment explanation
Indices: 1150068--1150101 Score: 50
Period size: 2 Copynumber: 16.5 Consensus size: 2
1150058 TAATAAACAA
*
1150068 AT AT AT AT AT AT AT AT AG AT AT AT AT AT CAT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT A
1150102 AAATACTACG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 27 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:1150223 original size:20 final size:19
Alignment explanation
Indices: 1150188--1150225 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
1150178 AAAAAAATAA
1150188 AAATAATAAAATTAACAAT
1 AAATAATAAAATTAACAAT
1150207 AAATAAATAATAA-TAACAA
1 AAAT-AATAA-AATTAACAA
1150226 AAGGACTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 11 0.65
21 2 0.12
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (19 bp):
AAATAATAAAATTAACAAT
Found at i:1151221 original size:10 final size:11
Alignment explanation
Indices: 1151199--1151249 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
1151189 TATGTAAATG
1151199 ATATATATATA
1 ATATATATATA
1151210 ATATAT-TATA
1 ATATATATATA
* *
1151220 ATATATACATT
1 ATATATATATA
1151231 ATATAATCATATA
1 ATAT-AT-ATATA
1151244 AT-TATA
1 ATATATA
1151250 ACATAGGAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
10 11 0.33
11 14 0.42
12 3 0.09
13 5 0.15
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (11 bp):
ATATATATATA
Found at i:1151223 original size:17 final size:15
Alignment explanation
Indices: 1151199--1151249 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
1151189 TATGTAAATG
1151199 ATAT-ATATATAATAT
1 ATATAATATATAAT-T
1151214 ATTATAATATATACATT
1 A-TATAATATATA-ATT
1151231 ATATAATCATATAATT
1 ATATAAT-ATATAATT
1151247 ATA
1 ATA
1151250 ACATAGGAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
15 1 0.03
16 15 0.47
17 14 0.44
18 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (15 bp):
ATATAATATATAATT
Found at i:1151242 original size:19 final size:19
Alignment explanation
Indices: 1151201--1151243 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
1151191 TGTAAATGAT
* *
1151201 ATATATATAATATATTATA
1 ATATATACAATATATAATA
* *
1151220 ATATATACATTATATAATC
1 ATATATACAATATATAATA
1151239 ATATA
1 ATATA
1151244 ATTATAACAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATATACAATATATAATA
Found at i:1153026 original size:80 final size:80
Alignment explanation
Indices: 1152911--1153071 Score: 306
Period size: 80 Copynumber: 2.0 Consensus size: 80
1152901 AATAAATAAT
1152911 TATAATATACAATAAACTTGTCGTAATGGTCTTTCGGTTGGGCCTGAAATTGGGTTTCGACTTAG
1 TATAATATACAATAAACTTGTCGTAATGGTCTTTCGGTTGGGCCTGAAATTGGGTTTCGACTTAG
1152976 AT-AAAACGTTAGAG
66 ATAAAAACGTTAGAG
1152990 TATATATATACAATAAACTTGTCGTAATGGTCTTTCGGTTGGGCCTGAAATTGGGTTTCGACTTA
1 TATA-ATATACAATAAACTTGTCGTAATGGTCTTTCGGTTGGGCCTGAAATTGGGTTTCGACTTA
1153055 GATAAAAACGTTAGAG
65 GATAAAAACGTTAGAG
1153071 T
1 T
1153072 CGCCACCGAT
Statistics
Matches: 80, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
79 4 0.05
80 63 0.79
81 13 0.16
ACGTcount: A:0.30, C:0.12, G:0.22, T:0.35
Consensus pattern (80 bp):
TATAATATACAATAAACTTGTCGTAATGGTCTTTCGGTTGGGCCTGAAATTGGGTTTCGACTTAG
ATAAAAACGTTAGAG
Found at i:1153363 original size:6 final size:6
Alignment explanation
Indices: 1153352--1153432 Score: 71
Period size: 6 Copynumber: 13.5 Consensus size: 6
1153342 ATAAATAAAT
* *
1153352 AAATAA AAATAA GAATAA AAATATA AAA-AA ATATAA AAA-ATA AAA-AA
1 AAATAA AAATAA AAATAA AAATA-A AAATAA AAATAA AAATA-A AAATAA
*
1153399 AAATAA AGATAA ATAA-AA AAATAAA AAATAA AAA
1 AAATAA AAATAA A-AATAA AAAT-AA AAATAA AAA
1153433 AAGAAAGAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
5 10 0.16
6 41 0.66
7 11 0.18
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (6 bp):
AAATAA
Found at i:1153366 original size:45 final size:41
Alignment explanation
Indices: 1153302--1153434 Score: 110
Period size: 45 Copynumber: 3.1 Consensus size: 41
1153292 GGATAAAAAG
* * * *
1153302 AAAATAAAT-AAAATGAAGAAAGTAATAATATATATATATAATAA
1 AAAATAAATAAAAAT-AAG-AA-TAAAAATATAAAAAAAT-ATAA
1153346 ATAAATAAATAAAAATAAGAATAAAAATATAAAAAAATATAA
1 A-AAATAAATAAAAATAAGAATAAAAATATAAAAAAATATAA
* *
1153388 AAAATAAAAAAAAATAAAGATAAATAAAAAAAT-AAAAAATA-AA
1 AAAATAAATAAAAAT-AAG---AATAAAAATATAAAAAAATATAA
1153431 AAAA
1 AAAA
1153435 GAAAGAAAGA
Statistics
Matches: 77, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
41 13 0.17
42 8 0.10
43 19 0.25
44 11 0.14
45 21 0.27
46 5 0.06
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (41 bp):
AAAATAAATAAAAATAAGAATAAAAATATAAAAAAATATAA
Found at i:1153376 original size:37 final size:36
Alignment explanation
Indices: 1153302--1153437 Score: 125
Period size: 37 Copynumber: 3.6 Consensus size: 36
1153292 GGATAAAAAG
* *
1153302 AAAATAAATAAAATGAAGAAAGTAATAATATATATATATAA
1 AAAATAAAT-AAATAAAAAAAG-AATAA-A-A-ATATATAA
*
1153343 TAAATAAATAAATAAAAATAAGAATAAAAATATA-AA
1 AAAATAAATAAATAAAAA-AAGAATAAAAATATATAA
* * *
1153379 AAAATATAAAAAATAAAAAAA-AATAAAGATAAATAAA
1 AAAATA-AATAAATAAAAAAAGAATAAAAATATAT-AA
1153416 AAAATAAA-AAATAAAAAAAGAA
1 AAAATAAATAAATAAAAAAAGAA
1153438 AGAAAGAAAA
Statistics
Matches: 83, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
35 21 0.25
36 13 0.16
37 24 0.29
38 1 0.01
39 1 0.01
40 12 0.14
41 11 0.13
ACGTcount: A:0.76, C:0.00, G:0.04, T:0.20
Consensus pattern (36 bp):
AAAATAAATAAATAAAAAAAGAATAAAAATATATAA
Found at i:1153376 original size:41 final size:36
Alignment explanation
Indices: 1153333--1153437 Score: 126
Period size: 35 Copynumber: 2.9 Consensus size: 36
1153323 GTAATAATAT
*
1153333 ATATATATAATAAATAAATAAATAAAAATAAGAATAAAA
1 ATATA-ATAAAAAATAAA-AAATAAAAA-AAGAATAAAA
*
1153372 ATATAA-AAAAATATAAAAAATAAAAAAA-AATAAAG
1 ATATAATAAAAA-ATAAAAAATAAAAAAAGAATAAAA
1153407 ATA-AATAAAAAAATAAAAAATAAAAAAAGAA
1 ATATAAT-AAAAAATAAAAAATAAAAAAAGAA
1153438 AGAAAGAAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 11
0.82 0.03 0.15
Matches are distributed among these distances:
34 2 0.03
35 25 0.42
36 9 0.15
37 13 0.22
38 6 0.10
39 5 0.08
ACGTcount: A:0.78, C:0.00, G:0.03, T:0.19
Consensus pattern (36 bp):
ATATAATAAAAAATAAAAAATAAAAAAAGAATAAAA
Found at i:1153390 original size:19 final size:17
Alignment explanation
Indices: 1153344--1153434 Score: 103
Period size: 17 Copynumber: 5.1 Consensus size: 17
1153334 TATATATAAT
1153344 AAATAAATAAATAAAAATA
1 AAATAAA-AAATAAAAA-A
1153363 AGAATAAAAATATAAAAAA
1 A-AATAAAAA-ATAAAAAA
*
1153382 ATATAAAAAATAAAAAA
1 AAATAAAAAATAAAAAA
*
1153399 AAATAAAGATAA-ATAAAA
1 AAATAAA-A-AATAAAAAA
1153417 AAATAAAAAATAAAAAA
1 AAATAAAAAATAAAAAA
1153434 A
1 A
1153435 GAAAGAAAGA
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
16 2 0.03
17 21 0.33
18 20 0.32
19 7 0.11
20 13 0.21
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (17 bp):
AAATAAAAAATAAAAAA
Found at i:1153404 original size:35 final size:36
Alignment explanation
Indices: 1153344--1153437 Score: 129
Period size: 35 Copynumber: 2.6 Consensus size: 36
1153334 TATATATAAT
1153344 AAATAAATAAATAAAAATAAGAATAAAAATATAA-AAAA
1 AAATAAA-AAATAAAAA-AAGAATAAAAATA-AATAAAA
* *
1153382 ATATAAAAAATAAAAAAA-AATAAAGATAAATAAAA
1 AAATAAAAAATAAAAAAAGAATAAAAATAAATAAAA
1153417 AAATAAAAAATAAAAAAAGAA
1 AAATAAAAAATAAAAAAAGAA
1153438 AGAAAGAAAA
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
34 2 0.04
35 30 0.59
36 4 0.08
37 9 0.18
38 6 0.12
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (36 bp):
AAATAAAAAATAAAAAAAGAATAAAAATAAATAAAA
Found at i:1153432 original size:8 final size:8
Alignment explanation
Indices: 1153341--1153434 Score: 84
Period size: 8 Copynumber: 11.2 Consensus size: 8
1153331 ATATATATAT
*
1153341 AATAAATA
1 AATAAAAA
1153349 AATAAATAA
1 AATAAA-AA
* *
1153358 AA-ATAAG
1 AATAAAAA
1153365 AATAAAAA
1 AATAAAAA
*
1153373 TATAAAAA
1 AATAAAAA
1153381 AATATAAAA
1 AATA-AAAA
1153390 AATAAAAAAA
1 AAT--AAAAA
1153400 AATAAAGATA
1 AATAAA-A-A
1153410 AATAAAAA
1 AATAAAAA
1153418 AAT-AAAA
1 AATAAAAA
1153425 AATAAAAA
1 AATAAAAA
1153433 AA
1 AA
1153435 GAAAGAAAGA
Statistics
Matches: 71, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
7 10 0.14
8 34 0.48
9 12 0.17
10 14 0.20
11 1 0.01
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.17
Consensus pattern (8 bp):
AATAAAAA
Found at i:1153434 original size:10 final size:10
Alignment explanation
Indices: 1153348--1153432 Score: 75
Period size: 10 Copynumber: 8.3 Consensus size: 10
1153338 TATAATAAAT
*
1153348 AAATAAATAA
1 AAATAAAAAA
1153358 AAATAAGAATAA
1 AAATAA-AA-AA
*
1153370 AAATATAAAA
1 AAATAAAAAA
*
1153380 AAAT-ATAAA
1 AAATAAAAAA
1153389 AAATAAAAAA
1 AAATAAAAAA
* *
1153399 AAATAAAGAT
1 AAATAAAAAA
1153409 AAATAAAAAA
1 AAATAAAAAA
1153419 ATAA-AAAATAA
1 A-AATAAAA-AA
1153430 AAA
1 AAA
1153433 AAGAAAGAAA
Statistics
Matches: 61, Mismatches: 9, Indels: 10
0.76 0.11 0.12
Matches are distributed among these distances:
9 7 0.11
10 39 0.64
11 8 0.13
12 7 0.11
ACGTcount: A:0.81, C:0.00, G:0.02, T:0.16
Consensus pattern (10 bp):
AAATAAAAAA
Found at i:1153435 original size:29 final size:29
Alignment explanation
Indices: 1153346--1153436 Score: 89
Period size: 29 Copynumber: 3.0 Consensus size: 29
1153336 TATATAATAA
*
1153346 ATAAATAAATAAAAATAAGAATAAAAATATAAA-
1 ATAAATATA-AAAAATAA-AA-AAAAA-A-AAAG
*
1153379 A-AAATATAAAAAATAAAAAAAAATAAAG
1 ATAAATATAAAAAATAAAAAAAAAAAAAG
1153407 ATAAATA-AAAAAATAAAAAATAAAAAAAG
1 ATAAATATAAAAAATAAAAAA-AAAAAAAG
1153436 A
1 A
1153437 AAGAAAGAAA
Statistics
Matches: 52, Mismatches: 3, Indels: 10
0.80 0.05 0.15
Matches are distributed among these distances:
27 3 0.06
28 14 0.27
29 18 0.35
30 2 0.04
31 8 0.15
32 6 0.12
33 1 0.02
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.16
Consensus pattern (29 bp):
ATAAATATAAAAAATAAAAAAAAAAAAAG
Found at i:1153447 original size:28 final size:28
Alignment explanation
Indices: 1153365--1153450 Score: 51
Period size: 25 Copynumber: 3.2 Consensus size: 28
1153355 TAAAAATAAG
*
1153365 AATAAAAATATAAAAAAATATAAAAA-ATA
1 AATAAAAAAATAAAAAAA-A-AAAAAGATA
* * *
1153394 AA-A-AAAAATAAAGATAAATAAA-A-A
1 AATAAAAAAATAAAAAAAAAAAAAGATA
1153418 AAT-AAAAAATAAAAAAAGAAAGAAAGA-A
1 AATAAAAAAATAAAAAAA-AAA-AAAGATA
1153446 AATAA
1 AATAA
1153451 TAGTAAATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 12
0.70 0.11 0.19
Matches are distributed among these distances:
24 3 0.07
25 16 0.36
26 3 0.07
27 13 0.30
28 6 0.14
29 3 0.07
ACGTcount: A:0.81, C:0.00, G:0.05, T:0.14
Consensus pattern (28 bp):
AATAAAAAAATAAAAAAAAAAAAAGATA
Found at i:1153512 original size:24 final size:24
Alignment explanation
Indices: 1153480--1153527 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
1153470 AAATGTTAAG
1153480 AAAACAAATA-CAAAAAAAAAAAC
1 AAAACAAATAGCAAAAAAAAAAAC
* *
1153503 AAAACAAAATAGTAAAAAATAAAAC
1 AAAAC-AAATAGCAAAAAAAAAAAC
1153528 GAATAAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 5 0.24
24 5 0.24
25 11 0.52
ACGTcount: A:0.79, C:0.10, G:0.02, T:0.08
Consensus pattern (24 bp):
AAAACAAATAGCAAAAAAAAAAAC
Found at i:1155659 original size:13 final size:13
Alignment explanation
Indices: 1155649--1155673 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1155639 CAAATAAATT
1155649 TAACCAATAAAAG
1 TAACCAATAAAAG
1155662 TAACCAATAAAA
1 TAACCAATAAAA
1155674 TAAGTCCAGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
TAACCAATAAAAG
Found at i:1155911 original size:2 final size:2
Alignment explanation
Indices: 1155904--1155941 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
1155894 ATATACAATA
*
1155904 AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1155942 TTCTTCATAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:1162118 original size:61 final size:61
Alignment explanation
Indices: 1162023--1162138 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
1162013 AGTGCGGGAA
* *
1162023 GGTGGATACGACCTTATGTATCATGTCCGAATTAGCACTATAGCGTAAGTTTAGTATAGGT
1 GGTGGACACGACCTTATGTATCATATCCGAATTAGCACTATAGCGTAAGTTTAGTATAGGT
* * *
1162084 GGTGGACACGACCTTATGTGTCATATCCGGATTAGCACTATGGCGTAAGTTTAGT
1 GGTGGACACGACCTTATGTATCATATCCGAATTAGCACTATAGCGTAAGTTTAGT
1162139 GCAGATTTAG
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (61 bp):
GGTGGACACGACCTTATGTATCATATCCGAATTAGCACTATAGCGTAAGTTTAGTATAGGT
Found at i:1162386 original size:88 final size:88
Alignment explanation
Indices: 1162257--1162468 Score: 322
Period size: 88 Copynumber: 2.4 Consensus size: 88
1162247 GATAACATAC
* * * *
1162257 AATAAGCTTACGAGCTCATGGAAT-AATGGTAAATATATTGGTAAAATAAGTTTACGAGC-TATG
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
1162320 GGATAAATGGCAAGTATATTGGT-A
66 GGATAAATGGCAAGT-TA-TGGTAA
*
1162344 AATAAGCTTACGAGCTTATGGGATAAATGGTATGTATATTGGTAAAATAAGCTTACGAGCTTATG
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
*
1162409 GGATAAATGGTAAGTTATGGTAA
66 GGATAAATGGCAAGTTATGGTAA
*
1162432 AATAAGCTTACGGGCTTATGGGATAAATGGTAAGTAT
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTAT
1162469 TGATAAGAAA
Statistics
Matches: 114, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
87 26 0.23
88 70 0.61
89 18 0.16
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (88 bp):
AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATG
GGATAAATGGCAAGTTATGGTAA
Found at i:1162449 original size:43 final size:45
Alignment explanation
Indices: 1162257--1162468 Score: 326
Period size: 43 Copynumber: 4.8 Consensus size: 45
1162247 GATAACATAC
* * *
1162257 AATAAGCTTACGAGCTCATGGAAT-AATGGTAAATATATTGGTAA
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
* *
1162301 AATAAGTTTACGAGC-TATGGGATAAATGGCAAGTATATTGGT-A
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
*
1162344 AATAAGCTTACGAGCTTATGGGATAAATGGTATGTATATTGGTAA
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
1162389 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGT-TA-TGGTAA
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
*
1162432 AATAAGCTTACGGGCTTATGGGATAAATGGTAAGTAT
1 AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTAT
1162469 TGATAAGAAA
Statistics
Matches: 154, Mismatches: 10, Indels: 8
0.90 0.06 0.05
Matches are distributed among these distances:
43 61 0.40
44 58 0.38
45 35 0.23
ACGTcount: A:0.37, C:0.08, G:0.25, T:0.31
Consensus pattern (45 bp):
AATAAGCTTACGAGCTTATGGGATAAATGGTAAGTATATTGGTAA
Found at i:1181525 original size:16 final size:16
Alignment explanation
Indices: 1181504--1181536 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
1181494 TAATAAATAA
*
1181504 ACGAACATAAAGGAAC
1 ACGAACATAAACGAAC
1181520 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
1181536 A
1 A
1181537 AAATGTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.58, C:0.21, G:0.15, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:1181631 original size:16 final size:15
Alignment explanation
Indices: 1181610--1181668 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
1181600 AAATAAACGG
*
1181610 ACATAAACGAATACAA
1 ACATAAACGAACAC-A
1181626 ACAT-AACGAACACGA
1 ACATAAACGAACAC-A
* *
1181641 ACATAAATGAACACG
1 ACATAAACGAACACA
1181656 ACATAAACGAACA
1 ACATAAACGAACA
1181669 TAAACATTGG
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
15 25 0.68
16 12 0.32
ACGTcount: A:0.58, C:0.22, G:0.10, T:0.10
Consensus pattern (15 bp):
ACATAAACGAACACA
Found at i:1181635 original size:15 final size:15
Alignment explanation
Indices: 1181610--1181675 Score: 53
Period size: 15 Copynumber: 4.3 Consensus size: 15
1181600 AAATAAACGG
*
1181610 ACATAAACGAATACAA
1 ACAT-AACGAACACAA
*
1181626 ACATAACGAACACGA
1 ACATAACGAACACAA
* *
1181641 ACATAAATGAACAC-G
1 ACAT-AACGAACACAA
*
1181656 ACATAAACGAACATAA
1 ACAT-AACGAACACAA
1181672 ACAT
1 ACAT
1181676 TGGAGACCCT
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
15 25 0.61
16 16 0.39
ACGTcount: A:0.58, C:0.21, G:0.09, T:0.12
Consensus pattern (15 bp):
ACATAACGAACACAA
Found at i:1182319 original size:14 final size:14
Alignment explanation
Indices: 1182300--1182326 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1182290 CAAACATAAC
1182300 GAACATAACTGAAT
1 GAACATAACTGAAT
1182314 GAACATAACTGAA
1 GAACATAACTGAA
1182327 CGTTCCACGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (14 bp):
GAACATAACTGAAT
Found at i:1188602 original size:25 final size:23
Alignment explanation
Indices: 1188574--1188624 Score: 57
Period size: 25 Copynumber: 2.1 Consensus size: 23
1188564 TATCAAAATG
* *
1188574 TATAAATATTTAAATTAATGTATTT
1 TATAAATATTCAAA--AATATATTT
*
1188599 TATATATATTCAAAAATATATTT
1 TATAAATATTCAAAAATATATTT
1188622 TAT
1 TAT
1188625 TTTATTATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 11 0.48
25 12 0.52
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
TATAAATATTCAAAAATATATTT
Found at i:1188656 original size:27 final size:27
Alignment explanation
Indices: 1188622--1188742 Score: 109
Period size: 27 Copynumber: 4.2 Consensus size: 27
1188612 AAATATATTT
*
1188622 TATTTTATTATTAATTTAATTTAAAAA
1 TATTTTATTATTATTTTAATTTAAAAA
* *
1188649 TATTTTATTAGTATTTTAATATAAAAA
1 TATTTTATTATTATTTTAATTTAAAAA
* *
1188676 TATATATT-TTATTCTTATAATAGTTAAAATA
1 TAT-T-TTATTATTATTTTAAT--TTAAAA-A
*
1188707 TATATTTATGATTATTTTAAATTTTAAAAA
1 TAT-TTTATTATTATTTT-AA-TTTAAAAA
1188737 TATTTT
1 TATTTT
1188743 TTTAAAAAAT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
27 27 0.36
28 11 0.14
29 5 0.07
30 11 0.14
31 19 0.25
32 2 0.03
33 1 0.01
ACGTcount: A:0.42, C:0.01, G:0.02, T:0.55
Consensus pattern (27 bp):
TATTTTATTATTATTTTAATTTAAAAA
Found at i:1190414 original size:30 final size:31
Alignment explanation
Indices: 1190347--1190414 Score: 102
Period size: 31 Copynumber: 2.2 Consensus size: 31
1190337 AGATTACATG
* *
1190347 ATTTATGTTATAAGCATGGTATAAAACCTTA
1 ATTTATGTTATAAACATGATATAAAACCTTA
*
1190378 ATTTATGTTATAAACATGATATAAAGCCTT-
1 ATTTATGTTATAAACATGATATAAAACCTTA
1190408 ATTTATG
1 ATTTATG
1190415 CTCCTTGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 7 0.21
31 27 0.79
ACGTcount: A:0.38, C:0.09, G:0.12, T:0.41
Consensus pattern (31 bp):
ATTTATGTTATAAACATGATATAAAACCTTA
Found at i:1198422 original size:22 final size:23
Alignment explanation
Indices: 1198369--1198428 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 23
1198359 GACAAGCTGT
* *
1198369 TAATATCAGGAGTTACATTGATT
1 TAATATCAGGAGTTACATTAATA
*
1198392 TAATTTCAGGAGTTACA-TAATA
1 TAATATCAGGAGTTACATTAATA
1198414 TAATATCAGGAGTTA
1 TAATATCAGGAGTTA
1198429 TAACAGCTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
22 17 0.52
23 16 0.48
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.37
Consensus pattern (23 bp):
TAATATCAGGAGTTACATTAATA
Found at i:1205752 original size:18 final size:17
Alignment explanation
Indices: 1205716--1205757 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
1205706 AATATTTTAT
1205716 ATATATTAACTTAAAAA
1 ATATATTAACTTAAAAA
**
1205733 ATTATATTAACTTATTAA
1 A-TATATTAACTTAAAAA
1205751 ATATATT
1 ATATATT
1205758 TTATTATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
17 7 0.32
18 15 0.68
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (17 bp):
ATATATTAACTTAAAAA
Found at i:1205772 original size:22 final size:22
Alignment explanation
Indices: 1205706--1205772 Score: 52
Period size: 22 Copynumber: 3.0 Consensus size: 22
1205696 TTAAATTCAT
1205706 AATAT-TTTATATATATTAACTTA
1 AATATATTT-TAT-TATTAACTTA
* *
1205729 AA-AAATTATATTAACTT-A-TTA
1 AATATATTTTATT-A-TTAACTTA
1205750 AATATATTTTATTATTAACTTA
1 AATATATTTTATTATTAACTTA
1205772 A
1 A
1205773 TTTAAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 13
0.67 0.08 0.25
Matches are distributed among these distances:
20 2 0.06
21 8 0.24
22 18 0.53
23 6 0.18
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.49
Consensus pattern (22 bp):
AATATATTTTATTATTAACTTA
Done.