Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold29
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: 5511024
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 57772 characters in sequence are not A, C, G, or T
File 31 of 34
Found at i:4872792 original size:35 final size:35
Alignment explanation
Indices: 4872705--4872836 Score: 177
Period size: 35 Copynumber: 3.9 Consensus size: 35
4872695 CCTTACAACA
4872705 CTATC-TTTC-AAGGCTAAGATAGAAACCTC-CT--
1 CTATCTTTTCAAAGGCTAAGATAG-AACCTCTCTCC
*
4872736 -TATCTTTTCATAGGCTAAGATAGAACCTCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
* * *
4872770 CTATATTTTTAAAGGCTAAGATAGAACCCCTCTCC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
4872805 CTATCTTTTCAAAGGCTAAGATAGAACCTCTC
1 CTATCTTTTCAAAGGCTAAGATAGAACCTCTC
4872837 AATCACTTAG
Statistics
Matches: 87, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.05
31 10 0.11
32 14 0.16
35 59 0.68
ACGTcount: A:0.30, C:0.26, G:0.12, T:0.32
Consensus pattern (35 bp):
CTATCTTTTCAAAGGCTAAGATAGAACCTCTCTCC
Found at i:4873384 original size:20 final size:19
Alignment explanation
Indices: 4873355--4873410 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4873345 TATTGCTAGT
*
4873355 TTCATATATCGATACAATTG
1 TTCATGTATCGATACAA-TG
*
4873375 TTCATGTATCGATGCAATG
1 TTCATGTATCGATACAATG
**
4873394 AGCATGTATCGATACAA
1 TTCATGTATCGATACAA
4873411 AGCAATATGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:4876719 original size:21 final size:21
Alignment explanation
Indices: 4876695--4876751 Score: 73
Period size: 21 Copynumber: 2.7 Consensus size: 21
4876685 TTTATTAGTT
*
4876695 AACTCA-TCATTTTCATTTTGC
1 AACTCATTCATTTTCA-TTTCC
4876716 AACTCATTTC-TTTTCATTTCC
1 AACTCA-TTCATTTTCATTTCC
4876737 AACTCATTCATTTTC
1 AACTCATTCATTTTC
4876752 TTCTCTAGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
20 3 0.09
21 21 0.66
22 6 0.19
23 2 0.06
ACGTcount: A:0.23, C:0.26, G:0.02, T:0.49
Consensus pattern (21 bp):
AACTCATTCATTTTCATTTCC
Found at i:4878686 original size:21 final size:21
Alignment explanation
Indices: 4878660--4878707 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
4878650 TGAATAAGCA
4878660 TGATTTTGCACTACTTGTTCT
1 TGATTTTGCACTACTTGTTCT
4878681 TGATTTTGCACTACTTGTTCT
1 TGATTTTGCACTACTTGTTCT
4878702 TGATTT
1 TGATTT
4878708 CTTGCTTGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.15, C:0.17, G:0.15, T:0.54
Consensus pattern (21 bp):
TGATTTTGCACTACTTGTTCT
Found at i:4878974 original size:20 final size:19
Alignment explanation
Indices: 4878949--4879004 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
4878939 TACTGCCAGT
*
4878949 TTCATGTATCAATACAATTG
1 TTCATGTATCGATACAA-TG
4878969 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
**
4878988 AGCATGTATCGATACAA
1 TTCATGTATCGATACAA
4879005 AGCAATATGT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 17 0.52
20 16 0.48
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.34
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:4879016 original size:20 final size:19
Alignment explanation
Indices: 4878971--4879022 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 19
4878961 TACAATTGTT
* *
4878971 CATGTATCGATACAATGAG
1 CATGTATCGATACAAAGAA
4878990 CATGTATCGATACAAAGCAA
1 CATGTATCGATACAAAG-AA
* *
4879010 TATGTATTGATAC
1 CATGTATCGATAC
4879023 TTCTGGGCTT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
19 16 0.57
20 12 0.43
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.29
Consensus pattern (19 bp):
CATGTATCGATACAAAGAA
Found at i:4881156 original size:16 final size:16
Alignment explanation
Indices: 4881137--4881167 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
4881127 TTTTTTGGGT
*
4881137 TTCTTTTTTGTTTTTG
1 TTCTTTTTTCTTTTTG
4881153 TTCTTTTTTCTTTTT
1 TTCTTTTTTCTTTTT
4881168 TTTTTGTTTA
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:0.00, C:0.10, G:0.06, T:0.84
Consensus pattern (16 bp):
TTCTTTTTTCTTTTTG
Found at i:4882614 original size:52 final size:52
Alignment explanation
Indices: 4882549--4883094 Score: 437
Period size: 52 Copynumber: 10.5 Consensus size: 52
4882539 AAGTCTGATA
* * * * *
4882549 TCGCTAGACTTGAATTAGCATATTAGCATCTTTATCATCTTTAAATCCAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
* * * * *
4882601 TTGCTAGCCTTGAATCAGCACATTAGCA-CTCTTCTCATCTTTACGTCAAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCT-TTATCATCTTTAAGTCCAATG
* * * * *
4882653 TCGCTGGCCTTGAATTAGCACATTAGCA-CTCTTGTCATCTTTAA-TCCAATA
1 TCGCTAGCCTTGAATCAGCACATTGGCATCT-TTATCATCTTTAAGTCCAATG
* * * * * * * *
4882704 TTGTTGGCCTTGAATCAGCATATTGGCACCTTTATCATATTTAACTCTAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
* * *
4882756 TCGC-GGCCTTGAATCAGCACATTGGCACTCTTT-TCAACTTTAAGTCCAATA
1 TCGCTAGCCTTGAATCAGCACATTGGCA-TCTTTATCATCTTTAAGTCCAATG
** * * *
4882807 TCAATAGCCTTGAATCAACATATTGGCATCTTTATCATCTTTAAGTTCAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
** * *
4882859 TCAATAGCCTTGAATTAGTACATTGGCA-CTTT-TCTTATCTTTAAGTCCAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCTTTATC--ATCTTTAAGTCCAATG
* * *
4882911 TCGCTAGCCTTGAATCAACATATTGGCAT-TCTTATTATCTTTAAGTCCAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCT-TTATCATCTTTAAGTCCAATG
*** * * ** * *
4882963 TTATTGGCCTTGAATAAATACATTGGCA-CTCTTATCATTTTTAAGTCTAATG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCT-TTATCATCTTTAAGTCCAATG
* * * * * ****
4883015 TCGTTGGCCTTGAATCAGTACATTGGCATCCTTATCATATTTAAGTTTGGTG
1 TCGCTAGCCTTGAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
*
4883067 TCG-TAGGCCTTGAATCTGCACATTGGCA
1 TCGCTA-GCCTTGAATCAGCACATTGGCA
4883095 CATTTTGTTA
Statistics
Matches: 405, Mismatches: 75, Indels: 28
0.80 0.15 0.06
Matches are distributed among these distances:
50 2 0.00
51 88 0.22
52 311 0.77
53 3 0.01
54 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (52 bp):
TCGCTAGCCTTGAATCAGCACATTGGCATCTTTATCATCTTTAAGTCCAATG
Found at i:4883058 original size:156 final size:154
Alignment explanation
Indices: 4882580--4883095 Score: 504
Period size: 156 Copynumber: 3.3 Consensus size: 154
4882570 ATTAGCATCT
* * * * * *
4882580 TTATCATCTTTAAATCCAATGTTGCTAGCCTTGAATCAGCACATTAGCACTCTTCTCATCTTTAC
1 TTATCATATTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACTCTT-TTATCTTTAA
* ** * * * * * * *
4882645 GTCAAATGTCGCTGGCCTTGAATTAGCACATTAGCACTCTTGTCATCTTTAA-TCCAATATTGTT
65 GTCCAATGTCAATGGCCTTGAATAAACACATTGGCACTCTTATCATCTTTAAGTCTAATGTCGTT
* *
4882709 GGCCTTGAATCAGCATATTGGCACC
130 GGCCTTGAATCAGTACATTGGCACC
* * * *
4882734 TTTATCATATTTAACTCTAATGTCGC-GGCCTTGAATCAGCACATTGGCACTCTTTTCAACTTTA
1 -TTATCATATTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACTCTTTT-ATCTTTA
* * * *
4882798 AGTCCAATATCAATAGCCTTGAATCAACATATTGGCA-TCTTTATCATCTTTAAGT-TCAATGTC
64 AGTCCAATGTCAATGGCCTTGAATAAACACATTGGCACTC-TTATCATCTTTAAGTCT-AATGTC
** * *
4882861 AATAGCCTTGAATTAGTACATTGGCA-C
127 GTTGGCCTTGAATCAGTACATTGGCACC
* * * * *
4882888 TTTTCTTATCTTTAAGTCCAATGTCGCTAGCCTTGAATCAACATATTGGCATTCTTATTATCTTT
1 TTATC--ATATTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACTCTT-TTATCTTT
* * * *
4882953 AAGTCCAATGTTATTGGCCTTGAATAAATACATTGGCACTCTTATCATTTTTAAGTCTAATGTCG
63 AAGTCCAATGTCAATGGCCTTGAATAAACACATTGGCACTCTTATCATCTTTAAGTCTAATGTCG
4883018 TTGGCCTTGAATCAGTACATTGGCATCC
128 TTGGCCTTGAATCAGTACATTGGCA-CC
**** *
4883046 TTATCATATTTAAGTTTGGTGTCG-TAGGCCTTGAATCTGCACATTGGCAC
1 TTATCATATTTAAGTCCAATGTCGCTA-GCCTTGAATCAGCACATTGGCAC
4883096 ATTTTGTTAA
Statistics
Matches: 289, Mismatches: 59, Indels: 25
0.77 0.16 0.07
Matches are distributed among these distances:
153 7 0.02
154 72 0.25
155 65 0.22
156 135 0.47
157 5 0.02
158 5 0.02
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.38
Consensus pattern (154 bp):
TTATCATATTTAAGTCCAATGTCGCTAGCCTTGAATCAGCACATTGGCACTCTTTTATCTTTAAG
TCCAATGTCAATGGCCTTGAATAAACACATTGGCACTCTTATCATCTTTAAGTCTAATGTCGTTG
GCCTTGAATCAGTACATTGGCACC
Found at i:4885158 original size:16 final size:17
Alignment explanation
Indices: 4885134--4885166 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4885124 CTCAAATATC
*
4885134 CAAACTAAATTT-TTAT
1 CAAAATAAATTTATTAT
4885150 CAAAATAAATTTATTAT
1 CAAAATAAATTTATTAT
4885167 TAAGTGTAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.48, C:0.09, G:0.00, T:0.42
Consensus pattern (17 bp):
CAAAATAAATTTATTAT
Found at i:4887433 original size:11 final size:11
Alignment explanation
Indices: 4887417--4887470 Score: 58
Period size: 11 Copynumber: 5.0 Consensus size: 11
4887407 AGCAAATTTA
4887417 TTTTTCTCTCT
1 TTTTTCTCTCT
*
4887428 TTTTTCTCTTT
1 TTTTTCTCTCT
4887439 TTCTTTC-CT-T
1 TT-TTTCTCTCT
* *
4887449 TTTTTCTTTTT
1 TTTTTCTCTCT
4887460 TTTTTCTCTCT
1 TTTTTCTCTCT
4887471 CTACTTTCTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
9 4 0.11
10 4 0.11
11 24 0.67
12 4 0.11
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTCTCT
Found at i:4887441 original size:19 final size:19
Alignment explanation
Indices: 4887417--4887459 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
4887407 AGCAAATTTA
4887417 TTTTTCTCT-CTTTTTTCTC
1 TTTTTCTCTCCTTTTTT-TC
*
4887436 TTTTTCTTTCCTTTTTTTC
1 TTTTTCTCTCCTTTTTTTC
4887455 TTTTT
1 TTTTT
4887460 TTTTTCTCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 15 0.68
20 7 0.32
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTTCTCTCCTTTTTTTC
Found at i:4887460 original size:20 final size:21
Alignment explanation
Indices: 4887427--4887465 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
4887417 TTTTTCTCTC
4887427 TTTTTTCTCTTTTTCTTTCCT
1 TTTTTTCTCTTTTTCTTTCCT
*
4887448 TTTTTTCT-TTTTTTTTTC
1 TTTTTTCTCTTTTTCTTTC
4887466 TCTCTCTACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (21 bp):
TTTTTTCTCTTTTTCTTTCCT
Found at i:4888344 original size:165 final size:161
Alignment explanation
Indices: 4887846--4888520 Score: 617
Period size: 166 Copynumber: 4.1 Consensus size: 161
4887836 ATGGGAGTAT
* * ** * * * *
4887846 AATAACAATATTAGATGAATTTTAAAAATTTTAAACTAAGAAAAATCATCCCGAAAAATTTATGG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATC-CCCCAAAAAATTTACGG
* * * * * * * *
4887911 AATAGAAAACTTGATTTTTCAAAAACTGGA-AAATTTTA-AAGAAAAATTAAAAACTAATGAAAA
65 AGTAGAAAACTCG-TATTTCAAAAA-TAGAGAAATTTGAGGA-AAAAATGAAAAACTCATGAAAA
*
4887974 T-ATAGGAATTTTTGAAAACTG------AT---TTA
127 TGA-ATGAATTTTTGAAAACTGTTTAATATGAATTA
*
4888000 AATAATAATATTTTATGAATTTTAAAAATT-AAAACCAAGAAAAATCCCCTCGAAAAAATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCC-C-AAAAAATTTACG
* ** * * * * *** *
4888064 GAGTAGAAAACGCCAAAGTTT-AGAAATAGTGAAATTTCAAGGAAAAAATTGAGATTTTAATGAA
64 GAGTAGAAAAC-TCGTA-TTTCAAAAATAGAGAAATTT-GAGGAAAAAA-TGAAAAACTCATGAA
4888128 AATGAAT-ATATTTTTGAAAACTGATTTAATATGAATTA
125 AATGAATGA-ATTTTTGAAAACTG-TTTAATATGAATTA
* * **
4888166 ACTAATAATATTTGATGAATTTTGAAAATTAAAAACCAAGAAAAATCCCCCAAAAACATTTACAA
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCAAAAA-ATTTACGG
* *
4888231 AGTAGAAAACTTCGTATTTCAAAAATAGAAAAATTTGATGGAAAAAATGAAAAAGTCATGAAAAT
65 AGTAGAAAAC-TCGTATTTCAAAAATAGAGAAATTTGA-GGAAAAAATGAAAAACTCATGAAAAT
*
4888296 GAATGAATTTTTGAAAAATGTTGTAATATGAATTA
128 GAATGAATTTTTGAAAACTGTT-TAATATGAATTA
* * *
4888331 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAATAAAAAGCCCTTCAAAAATATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCC-CCAAAAA-ATTTACG
* *
4888396 GAGTAGAAAACTCTGTATTTCAAAAACAAGAGAAATTTGAGAGAAAAAATGAAAAACTCTTGAAA
64 GAGTAGAAAACTC-GTATTTCAAAAA-TAGAGAAATTTGAG-GAAAAAATGAAAAACTCATGAAA
* *
4888461 ATGAATGAATTTTTGAAAACTAATTTAATA-CAAGTTA
126 ATGAATGAATTTTTGAAAACT-GTTTAATATGAA-TTA
* *
4888498 AATAATAATATTTAAAGAATTTT
1 AATAATAATATTTGATGAATTTT
4888521 GAAGTTAAAA
Statistics
Matches: 428, Mismatches: 61, Indels: 51
0.79 0.11 0.09
Matches are distributed among these distances:
152 2 0.00
153 17 0.04
154 57 0.13
155 10 0.02
156 29 0.07
157 1 0.00
163 2 0.00
164 2 0.00
165 98 0.23
166 108 0.25
167 100 0.23
168 2 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (161 bp):
AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCCCAAAAAATTTACGGA
GTAGAAAACTCGTATTTCAAAAATAGAGAAATTTGAGGAAAAAATGAAAAACTCATGAAAATGAA
TGAATTTTTGAAAACTGTTTAATATGAATTA
Found at i:4888501 original size:167 final size:163
Alignment explanation
Indices: 4887846--4888520 Score: 611
Period size: 165 Copynumber: 4.1 Consensus size: 163
4887836 ATGGGAGTAT
* * ** * * *
4887846 AATAACAATATTAGATGAATTTTAAAAATTTTAAACTAAGAAAAATCATCC-CGAAAAATTTATG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATC--CCTCAAAAAATTTACG
* * * * * * *
4887910 GAATAGAAAACT-TGATTTTTCAAAAACTGGA-AAATTTTAAAG-AAAAATTAAAAACTAATGAA
64 GAGTAGAAAACTCTG-TATTTCAAAAA-TAGAGAAATTTGAGAGAAAAAATGAAAAACTCATGAA
*
4887972 AAT-ATAGGAATTTTTGAAAACTGA-TT--TA--AA-T-
127 AATGA-ATGAATTTTTGAAAACT-ATTTAATATGAATTA
4888003 AATAAT-AT-TTT-ATGAATTTTAAAAATT-AAAACCAAGAAAAATCCCCTCGAAAAAATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAAT-CCCTC-AAAAAATTTACG
* *** * * * * *** *
4888064 GAGTAGAAAACGCCAAAGTTT-AGAAATAGTGAAATTTCA-AGGAAAAAATTGAGATTTTAATGA
64 GAGTAGAAAACTCTGTA-TTTCAAAAATAGAGAAATTTGAGA-GAAAAAA-TGAAAAACTCATGA
4888127 AAATGAAT-ATATTTTTGAAAACTGATTTAATATGAATTA
126 AAATGAATGA-ATTTTTGAAAACT-ATTTAATATGAATTA
* * * **
4888166 ACTAATAATATTTGATGAATTTTGAAAATTAAAAACCAAGAAAAATCCCCCAAAAACATTTACAA
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCAAAAA-ATTTACGG
* *
4888231 AGTAGAAAACT-TCGTATTTCAAAAATAGAAAAATTTGATG-GAAAAAATGAAAAAGTCATGAAA
65 AGTAGAAAACTCT-GTATTTCAAAAATAGAGAAATTTGA-GAGAAAAAATGAAAAACTCATGAAA
* *
4888294 ATGAATGAATTTTTGAAAAATGTTGTAATATGAATTA
128 ATGAATGAATTTTTGAAAACTATT-TAATATGAATTA
* *
4888331 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAATAAAAAGCCCTTCAAAAATATTTACG
1 AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCC-TCAAAAA-ATTTACG
* *
4888396 GAGTAGAAAACTCTGTATTTCAAAAACAAGAGAAATTTGAGAGAAAAAATGAAAAACTCTTGAAA
64 GAGTAGAAAACTCTGTATTTCAAAAA-TAGAGAAATTTGAGAGAAAAAATGAAAAACTCATGAAA
*
4888461 ATGAATGAATTTTTGAAAACTAATTTAATA-CAAGTTA
128 ATGAATGAATTTTTGAAAACT-ATTTAATATGAA-TTA
* *
4888498 AATAATAATATTTAAAGAATTTT
1 AATAATAATATTTGATGAATTTT
4888521 GAAGTTAAAA
Statistics
Matches: 424, Mismatches: 59, Indels: 60
0.78 0.11 0.11
Matches are distributed among these distances:
152 2 0.00
153 17 0.04
154 49 0.12
155 11 0.03
156 31 0.07
157 8 0.02
159 2 0.00
161 2 0.00
162 1 0.00
163 5 0.01
164 4 0.01
165 97 0.23
166 96 0.23
167 97 0.23
168 2 0.00
ACGTcount: A:0.51, C:0.08, G:0.11, T:0.30
Consensus pattern (163 bp):
AATAATAATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATCCCTCAAAAAATTTACGGA
GTAGAAAACTCTGTATTTCAAAAATAGAGAAATTTGAGAGAAAAAATGAAAAACTCATGAAAATG
AATGAATTTTTGAAAACTATTTAATATGAATTA
Found at i:4892456 original size:16 final size:16
Alignment explanation
Indices: 4892431--4892462 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
4892421 CCCCAGTTTA
4892431 TGATTATGGGCAAATT
1 TGATTATGGGCAAATT
*
4892447 TGATTGTGGGCAAATT
1 TGATTATGGGCAAATT
4892463 CGGAAAGTGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.06, G:0.28, T:0.38
Consensus pattern (16 bp):
TGATTATGGGCAAATT
Found at i:4893618 original size:27 final size:27
Alignment explanation
Indices: 4893580--4893677 Score: 135
Period size: 27 Copynumber: 3.6 Consensus size: 27
4893570 TATTCACACG
*
4893580 GATACTCTAACCCCATTCTTCCAAGGA
1 GATACTCTAACCCCATTCTTTCAAGGA
**
4893607 GATACTAC-AACCCCATTCTTTTGAGGA
1 GATACT-CTAACCCCATTCTTTCAAGGA
*
4893634 GATACTCTAACCCCATTCTTTCAAGGG
1 GATACTCTAACCCCATTCTTTCAAGGA
*
4893661 GATACTCCAACCCCATT
1 GATACTCTAACCCCATT
4893678 TTTAAACTTG
Statistics
Matches: 62, Mismatches: 7, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
26 1 0.02
27 60 0.97
28 1 0.02
ACGTcount: A:0.29, C:0.32, G:0.12, T:0.28
Consensus pattern (27 bp):
GATACTCTAACCCCATTCTTTCAAGGA
Found at i:4899453 original size:141 final size:141
Alignment explanation
Indices: 4899195--4899596 Score: 563
Period size: 142 Copynumber: 2.8 Consensus size: 141
4899185 TGTAAATTTT
* * *
4899195 AAAAATCTCATTTCGTACCTTAATGGAGAACTGAAAATATATGAAAAGTTTTAAAGATTTCTATA
1 AAAAATC-CATTTCGTACCTTAATGGAGAACTGAAAATATACGAAAAGTTTTGAAGATTTTTATA
* * *
4899260 CCCCTATGGATAACCATAGGAATATTAGAAACCTTGAAAAATTAACATAATAATTTTTGTTTAA-
65 CCCCTATGGATAACCATAGAAATATTAGAAAACTTGAAAAA-TAAGATAATAATTTTTGTTTAAT
4899324 TTTTTTATTTCCA
129 TTTTTTATTTCCA
* *
4899337 AAAAATCCATTTCGTACCTTAATGGAGAACCGAAAAGATACGAAAAGTTTTGAAGATTTTTATAC
1 AAAAATCCATTTCGTACCTTAATGGAGAACTGAAAATATACGAAAAGTTTTGAAGATTTTTATAC
* *
4899402 CCCTATGGATAACCATAGAAAAATTAGAAAACTTGAAAAATAAAGAGAATAATTTTTGTTTAATT
66 CCCTATGGATAACCATAGAAATATTAGAAAACTTGAAAAAT-AAGATAATAATTTTTGTTTAATT
*
4899467 TTTTTATTTTCA
130 TTTTTATTTCCA
* ** * * * *
4899479 TAAAATTTATTTCGTACCTTCATGGAAAACTGAAAATATACAAAAAGTTTTGAAGATTTTAATAC
1 AAAAATCCATTTCGTACCTTAATGGAGAACTGAAAATATACGAAAAGTTTTGAAGATTTTTATAC
** * *
4899544 CGTTACGGATAACCATAGAAATATTAGAAATCTTGAAAAACTAAGATAATAAT
66 CCCTATGGATAACCATAGAAATATTAGAAAACTTGAAAAA-TAAGATAATAAT
4899597 CTTAATTTAG
Statistics
Matches: 231, Mismatches: 26, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
140 1 0.00
141 109 0.47
142 120 0.52
143 1 0.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.34
Consensus pattern (141 bp):
AAAAATCCATTTCGTACCTTAATGGAGAACTGAAAATATACGAAAAGTTTTGAAGATTTTTATAC
CCCTATGGATAACCATAGAAATATTAGAAAACTTGAAAAATAAGATAATAATTTTTGTTTAATTT
TTTTATTTCCA
Found at i:4900787 original size:15 final size:15
Alignment explanation
Indices: 4900763--4900793 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4900753 ACTAGTTTAG
*
4900763 TAAAAGTAAATAAAA
1 TAAAAATAAATAAAA
4900778 TAAAAATAAATAAAA
1 TAAAAATAAATAAAA
4900793 T
1 T
4900794 TTCAAAATGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
TAAAAATAAATAAAA
Found at i:4901204 original size:167 final size:164
Alignment explanation
Indices: 4900918--4901265 Score: 425
Period size: 167 Copynumber: 2.1 Consensus size: 164
4900908 AATTAGAATT
* *
4900918 TTTTCAAAACTAATTT-AATGTGAAAT-TAATGACAATATTAGATGAATTTAAAAATTTTAAACC
1 TTTTCAAAACTAATTTAAAAG-G-AGTCTAATGACAATATTAGATGAATTTAAAAATTTTAAACC
** * * *
4900981 AAAAAAAATCTTCCTCGAAAATATTTATGGAATACAAAACTCGATTTTTTGAAAAT-AGAAAAAT
64 AAAAAAAATCCACCTCGAAAACATTTATGGAATACAAAACTCAATTTTTGGAAAATAAG-AAAAT
* * *
4901045 TTCAAAGAAAAAAATGAAAACCTTATGAAAATAAATGAAT
128 TTC--A-AAAAAAATGAAAAACTCATGAAAATAAATGAAA
* * * * *
4901085 TTTTCAAAACTGATTTAAAAGGAGTCTAATGACAATGTTATATGAATTTTAAAAATTTTAAATCG
1 TTTTCAAAACTAATTTAAAAGGAGTCTAATGACAATATTAGATGAA-TTTAAAAATTTTAAACCA
* * * *
4901150 AGAAAAATCCACC-CGAAAACGTTTATGGAATAGAAAACTCAATTTTTGGAAAATAAGAGAATTT
65 AAAAAAATCCACCTCGAAAACATTTATGGAATACAAAACTCAATTTTTGGAAAATAAGAAAATTT
*
4901214 CAAAAAAATTGAAAAACTCATGAAAATAAATGAAA
130 CAAAAAAAATGAAAAACTCATGAAAATAAATGAAA
4901249 TTTTCAAAACTAATTTA
1 TTTTCAAAACTAATTTA
4901266 CTATGAATTA
Statistics
Matches: 156, Mismatches: 21, Indels: 11
0.83 0.11 0.06
Matches are distributed among these distances:
164 45 0.29
165 1 0.01
166 2 0.01
167 77 0.49
168 31 0.20
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (164 bp):
TTTTCAAAACTAATTTAAAAGGAGTCTAATGACAATATTAGATGAATTTAAAAATTTTAAACCAA
AAAAAATCCACCTCGAAAACATTTATGGAATACAAAACTCAATTTTTGGAAAATAAGAAAATTTC
AAAAAAAATGAAAAACTCATGAAAATAAATGAAA
Found at i:4901300 original size:164 final size:163
Alignment explanation
Indices: 4900894--4901430 Score: 482
Period size: 164 Copynumber: 3.2 Consensus size: 163
4900884 TACAAAATAC
* * * *
4900894 AAAATTCATG-AAATAATTAGAATTTTTTCAAAACTAATTTAATGTGAAATTAATGACAATATTA
1 AAAACTCATGAAAATAAAT-GAA-TTTTTCAAAACTAATTTAATATGAAATTAATGACAATATTT
* * * *
4900958 GATGAA-TTTAAAAATTTTAAACCAAAAAAAATCTTCCTCGAAAATATTTATGGAATACAAAACT
64 GATGAATTTTAAAAATTTTAAA-CAAGAAAAATCCTCC-CGAAAAAATTTATGGAATAGAAAACT
* *
4901022 CGATTTTTTGAAAAT-AGAAAAATTTCAAAGAAAAAAATGA
127 C-AATTTTTGAAAATAAG-AGAATTTC-AA-AAAAAAATGA
* * * * * * *
4901062 AAACCTTATGAAAATAAATGAATTTTTCAAAACTGATTTAA-AAGGAGTCTAATGACAATGTTAT
1 AAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTAATATGAAAT-TAATGACAATATT-T
* * **
4901126 -ATGAATTTTAAAAATTTTAAATCGAGAAAAATCCACCCGAAAACGTTTATGGAATAGAAAACTC
64 GATGAATTTTAAAAATTTTAAA-CAAGAAAAATCCTCCCGAAAAAATTTATGGAATAGAAAACTC
*
4901190 AATTTTTGGAAAATAAGAGAATTTC-AAAAAAATTGA
128 AATTTTT-GAAAATAAGAGAATTTCAAAAAAAAATGA
* * **
4901226 AAAACTCATGAAAATAAATGAAATTTTCAAAACTAATTTACTATG-AATTAAATGATGATATTTG
1 AAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTAATATGAAATT-AATGACAATATTTG
* * * * *
4901290 ATGAATTTT-AAAATTTATAAACCAGTGAAAATCGTCCTGAAAAAATTTACGGAGA-AGAAAACT
65 ATGAATTTTAAAAATTT-TAAACAAG-AAAAATCCTCCCGAAAAAATTTATGGA-ATAGAAAACT
* * * * * *
4901353 TAATATTTCAAAAGTAGGAGGAATTCCAAAAAAAAATCA
127 CAATTTTTGAAAA-TAAGA-GAATTTCAAAAAAAAATGA
* *
4901392 ATAACTCATG-AAATAAAAGGAATTTTTCAAAACTAATTT
1 AAAACTCATGAAAAT-AAATGAATTTTTCAAAACTAATTT
4901431 GACAGTAATT
Statistics
Matches: 303, Mismatches: 50, Indels: 34
0.78 0.13 0.09
Matches are distributed among these distances:
163 16 0.05
164 107 0.35
165 14 0.05
166 49 0.16
167 72 0.24
168 38 0.13
169 7 0.02
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.31
Consensus pattern (163 bp):
AAAACTCATGAAAATAAATGAATTTTTCAAAACTAATTTAATATGAAATTAATGACAATATTTGA
TGAATTTTAAAAATTTTAAACAAGAAAAATCCTCCCGAAAAAATTTATGGAATAGAAAACTCAAT
TTTTGAAAATAAGAGAATTTCAAAAAAAAATGA
Found at i:4902744 original size:21 final size:21
Alignment explanation
Indices: 4902720--4902764 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
4902710 GTGTATTGAC
4902720 ACATTTAAGAAATGTATCAAT
1 ACATTTAAGAAATGTATCAAT
*
4902741 ACATTTAAGAAATGTATCGAT
1 ACATTTAAGAAATGTATCAAT
4902762 ACA
1 ACA
4902765 AAGTCCTGAC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (21 bp):
ACATTTAAGAAATGTATCAAT
Found at i:4902846 original size:20 final size:21
Alignment explanation
Indices: 4902802--4902849 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
4902792 TTTTATAACT
4902802 TGTATCGATAGAAATAGTAAA
1 TGTATCGATAGAAATAGTAAA
* * *
4902823 TGTATCGATATATA-AGTGAA
1 TGTATCGATAGAAATAGTAAA
4902843 TGTATCG
1 TGTATCG
4902850 TTACATGCCT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.40, C:0.06, G:0.21, T:0.33
Consensus pattern (21 bp):
TGTATCGATAGAAATAGTAAA
Found at i:4902990 original size:32 final size:32
Alignment explanation
Indices: 4902954--4903025 Score: 101
Period size: 32 Copynumber: 2.2 Consensus size: 32
4902944 TTATATCGAC
4902954 ACATT-TTGGGTTTTCGACCCAAATGTATAGAT
1 ACATTCTT-GGTTTTCGACCCAAATGTATAGAT
* *
4902986 ACATTCTTGGTTTTTGACCCAAATGTATCGAT
1 ACATTCTTGGTTTTCGACCCAAATGTATAGAT
*
4903018 ACACTCTT
1 ACATTCTT
4903026 CAATGCATCG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
32 34 0.94
33 2 0.06
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (32 bp):
ACATTCTTGGTTTTCGACCCAAATGTATAGAT
Found at i:4906787 original size:40 final size:41
Alignment explanation
Indices: 4906742--4906833 Score: 116
Period size: 40 Copynumber: 2.3 Consensus size: 41
4906732 CACTCAAAAC
*
4906742 CAGCAGCTCCAACAAGCAGCAACTTCCACAGA-AGGAACG-A
1 CAGCAGCTCCAACAAGCAGCAACTTCCACA-ACAAGAACGAA
* * * *
4906782 CAGCAGCTCTAATAAGCAGCAGCTTCCACAACAAGCACGAA
1 CAGCAGCTCCAACAAGCAGCAACTTCCACAACAAGAACGAA
4906823 CAGCAGCTCCA
1 CAGCAGCTCCA
4906834 CAAAACACTT
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
39 1 0.02
40 32 0.73
41 11 0.25
ACGTcount: A:0.38, C:0.34, G:0.18, T:0.10
Consensus pattern (41 bp):
CAGCAGCTCCAACAAGCAGCAACTTCCACAACAAGAACGAA
Found at i:4906790 original size:107 final size:107
Alignment explanation
Indices: 4906597--4906896 Score: 447
Period size: 107 Copynumber: 2.8 Consensus size: 107
4906587 CGAAAGCTCT
* * * * * * *
4906597 AACAAGCATGAATAGCAGCTCCACAAAGCACCCAAAACTAGTAGCTCCAATAAGCAGCAGCTTCC
1 AACAAGCACGAACAGCAGCTCCACAAAACACTCAAAACCAGCAGCTCCAACAAGCAGCAGCTTCC
* * *
4906662 ACGGTAGCAACGAGAGTAGCTCCAATAAGTAGCAGCTTCCAC
66 ACGGTAGCAACGACAGCAGCTCCAATAAGCAGCAGCTTCCAC
*
4906704 AACAAGCACGAACAGCAGCTCCACAAAACACTCAAAACCAGCAGCTCCAACAAGCAGCAACTTCC
1 AACAAGCACGAACAGCAGCTCCACAAAACACTCAAAACCAGCAGCTCCAACAAGCAGCAGCTTCC
* * * *
4906769 ACAGAAGGAACGACAGCAGCTCTAATAAGCAGCAGCTTCCAC
66 ACGGTAGCAACGACAGCAGCTCCAATAAGCAGCAGCTTCCAC
*
4906811 AACAAGCACGAACAGCAGCTCCACAAAACACTTAAAACCAGCAGCTCCAACAAGCAGCAGCTTCC
1 AACAAGCACGAACAGCAGCTCCACAAAACACTCAAAACCAGCAGCTCCAACAAGCAGCAGCTTCC
*
4906876 ACGGTAGCAACGATAGCAGCT
66 ACGGTAGCAACGACAGCAGCT
4906897 TTAACAACCA
Statistics
Matches: 172, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
107 172 1.00
ACGTcount: A:0.39, C:0.32, G:0.17, T:0.12
Consensus pattern (107 bp):
AACAAGCACGAACAGCAGCTCCACAAAACACTCAAAACCAGCAGCTCCAACAAGCAGCAGCTTCC
ACGGTAGCAACGACAGCAGCTCCAATAAGCAGCAGCTTCCAC
Found at i:4907826 original size:13 final size:13
Alignment explanation
Indices: 4907808--4907832 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
4907798 CATTTTGGGA
4907808 TGTATCGATACAT
1 TGTATCGATACAT
4907821 TGTATCGATACA
1 TGTATCGATACA
4907833 AACAGTTAAG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4910315 original size:13 final size:13
Alignment explanation
Indices: 4910297--4910322 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4910287 CAATTTTTTA
4910297 TGTATCGATACAT
1 TGTATCGATACAT
4910310 TGTATCGATACAT
1 TGTATCGATACAT
4910323 ACTTTGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:4910338 original size:32 final size:33
Alignment explanation
Indices: 4910277--4910340 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
4910267 TACAAGCCAA
**
4910277 TGTATCGATACAATTTTTTATGTATCGATACAT
1 TGTATCGATACAATACTTTATGTATCGATACAT
*
4910310 TGTATCGATAC-ATACTTTGTGTATCGATACA
1 TGTATCGATACAATACTTTATGTATCGATACA
4910341 AGTTTGGCTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 17 0.61
33 11 0.39
ACGTcount: A:0.30, C:0.14, G:0.14, T:0.42
Consensus pattern (33 bp):
TGTATCGATACAATACTTTATGTATCGATACAT
Found at i:4910682 original size:22 final size:22
Alignment explanation
Indices: 4910638--4910683 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
4910628 TTAATTGAAT
*
4910638 AAAATATATTTTTGGCTTTTTC
1 AAAATATATTTTCGGCTTTTTC
*
4910660 AAAATA-ATTTTCGGTTTTATTC
1 AAAATATATTTTCGGCTTT-TTC
4910682 AA
1 AA
4910684 TCCTTTGTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 10 0.48
22 11 0.52
ACGTcount: A:0.33, C:0.09, G:0.09, T:0.50
Consensus pattern (22 bp):
AAAATATATTTTCGGCTTTTTC
Found at i:4913307 original size:13 final size:13
Alignment explanation
Indices: 4913289--4913314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4913279 TACACAAAGT
4913289 ATGTATCGATACA
1 ATGTATCGATACA
4913302 ATGTATCGATACA
1 ATGTATCGATACA
4913315 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:4913312 original size:32 final size:33
Alignment explanation
Indices: 4913271--4913332 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 33
4913261 TAGCCAAACT
**
4913271 TGTATCGATACACAAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
4913303 TGTATCGATACACAAAAAATTGTATCGATA
1 TGTATCGATACACAAAAAATTGTATCGATA
4913333 AATTGGCTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
32 17 0.63
33 10 0.37
ACGTcount: A:0.42, C:0.15, G:0.15, T:0.29
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:4917412 original size:15 final size:15
Alignment explanation
Indices: 4917392--4917422 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4917382 TAAAAATGTC
*
4917392 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
4917407 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
4917422 C
1 C
4917423 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:4919524 original size:13 final size:13
Alignment explanation
Indices: 4919506--4919543 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
4919496 CATTTTTCTT
4919506 TGTATCGATACAA
1 TGTATCGATACAA
*
4919519 TGTATCGATACAC
1 TGTATCGATACAA
4919532 TGTATCGATACA
1 TGTATCGATACA
4919544 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:4919698 original size:20 final size:20
Alignment explanation
Indices: 4919660--4919699 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 20
4919650 TTTTGCGAAA
4919660 TACTTGTTTTTCACTTCAAAT
1 TACTTGTTTTTCAC-TCAAAT
4919681 TACTTCGTTTTTCA-TCAAA
1 TACTT-GTTTTTCACTCAAA
4919700 ACCAGCATCA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 5 0.28
22 8 0.44
ACGTcount: A:0.25, C:0.20, G:0.05, T:0.50
Consensus pattern (20 bp):
TACTTGTTTTTCACTCAAAT
Found at i:4934712 original size:43 final size:42
Alignment explanation
Indices: 4934545--4934891 Score: 165
Period size: 42 Copynumber: 8.2 Consensus size: 42
4934535 CATTAAACTT
* * * * *
4934545 CTAGAGACTTTTCTACCCTCAATCTGCTTGTC-GACTTTGACC
1 CTAGAGACTTTCCTACCCTTAGTCTACCTGTCAG-CTTTGACC
* * * * * * *
4934587 CTAGAGACTCT-CT-CGTCTAAAGTTTACCTTTCGGCTTTAACC
1 CTAGAGACTTTCCTAC-CCT-TAGTCTACCTGTCAGCTTTGACC
* * * *
4934629 CTAGAGACTTTCTTCT-CCCTTAGTTTGCTTGTC-GATTTTGACC
1 CTAGAGACTTTC--CTACCCTTAGTCTACCTGTCAG-CTTTGACC
* *
4934672 CTAGAGACTTTCCTATCCCTTAGTCTACCTATCGGCTTTGACC
1 CTAGAGACTTTCCTA-CCCTTAGTCTACCTGTCAGCTTTGACC
* * * * *
4934715 CTGGAGACTTT-TTCACCCTTGGTCTGCCTGTTAGCTTTGACC
1 CTAGAGACTTTCCT-ACCCTTAGTCTACCTGTCAGCTTTGACC
* * * * *
4934757 TTGGAGACTTTTCTA-CCTTAGTTTGA-CTATCAGCTTTGACC
1 CTAGAGACTTTCCTACCCTTAGTCT-ACCTGTCAGCTTTGACC
* * * * *
4934798 TTGGAGA-TTGCCTTA-CCTAAAGTCTGCCTGTCAGCTTTGACC
1 CTAGAGACTTTCC-TACCCT-TAGTCTACCTGTCAGCTTTGACC
* * * *
4934840 CTAGAGACTTTCCTACCCTTCGGTTTGCTTGTCAGCTTTGACC
1 CTAGAGACTTTCCTACCCTT-AGTCTACCTGTCAGCTTTGACC
* *
4934883 TTGGAGACT
1 CTAGAGACT
4934892 GCCTCATCTA
Statistics
Matches: 235, Mismatches: 51, Indels: 37
0.73 0.16 0.11
Matches are distributed among these distances:
40 4 0.02
41 38 0.16
42 94 0.40
43 93 0.40
44 3 0.01
45 3 0.01
ACGTcount: A:0.17, C:0.28, G:0.18, T:0.37
Consensus pattern (42 bp):
CTAGAGACTTTCCTACCCTTAGTCTACCTGTCAGCTTTGACC
Found at i:4934734 original size:85 final size:85
Alignment explanation
Indices: 4934569--4934734 Score: 203
Period size: 85 Copynumber: 2.0 Consensus size: 85
4934559 ACCCTCAATC
* * * *
4934569 TGCTTGTCGACTTTGACCCTAGAGACTCTCTCGTCTAAAGTTTACCTTTCGGCTTTAACCCTAGA
1 TGCTTGTCGACTTTGACCCTAGAGACTCTATCGCCTAAAGTCTACCTATCGGCTTTAACCCTAGA
*
4934634 GACTTTCTTCTCCCTTAGTT
66 GACTTTCTTCACCCTTAGTT
* * *
4934654 TGCTTGTCGATTTTGACCCTAGAGACTTTCCTATC-CCT-TAGTCTACCTATCGGCTTTGACCCT
1 TGCTTGTCGACTTTGACCCTAGAGAC--T-CTATCGCCTAAAGTCTACCTATCGGCTTTAACCCT
*
4934717 GGAGACTTT-TTCACCCTT
63 AGAGACTTTCTTCACCCTT
4934735 GGTCTGCCTG
Statistics
Matches: 69, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
85 33 0.48
86 29 0.42
87 3 0.04
88 4 0.06
ACGTcount: A:0.17, C:0.29, G:0.16, T:0.39
Consensus pattern (85 bp):
TGCTTGTCGACTTTGACCCTAGAGACTCTATCGCCTAAAGTCTACCTATCGGCTTTAACCCTAGA
GACTTTCTTCACCCTTAGTT
Found at i:4934753 original size:42 final size:42
Alignment explanation
Indices: 4934632--4934935 Score: 165
Period size: 42 Copynumber: 7.2 Consensus size: 42
4934622 TTTAACCCTA
* * * * * *
4934632 GAGACTTTCTTCTCCCTTAGTTTGCTTGTC-GATTTTGACCCTA
1 GAGACTTT-TTCTACCTTAGTCTGCCTGTCAG-CTTTGACCTTG
* * * * *
4934675 GAGAC-TTTCCTATCCCTTAGTCTACCTATCGGCTTTGACCCTG
1 GAGACTTTTTCTA--CCTTAGTCTGCCTGTCAGCTTTGACCTTG
* *
4934718 GAGACTTTTTC-ACCCTTGGTCTGCCTGTTAGCTTTGACCTTG
1 GAGACTTTTTCTA-CCTTAGTCTGCCTGTCAGCTTTGACCTTG
* * *
4934760 GAGAC-TTTTCTACCTTAGTTTGACTATCAGCTTTGACCTTG
1 GAGACTTTTTCTACCTTAGTCTGCCTGTCAGCTTTGACCTTG
** * * *
4934801 GAGA--TTGCCTTACCTAAAGTCTGCCTGTCAGCTTTGACCCTA
1 GAGACTTTTTC-TACCT-TAGTCTGCCTGTCAGCTTTGACCTTG
* * * *
4934843 GAGAC-TTTCCTACCCTTCGGTTTGCTTGTCAGCTTTGACCTTG
1 GAGACTTTTTCTA-CCTT-AGTCTGCCTGTCAGCTTTGACCTTG
*** * * * * *
4934886 GAGACTGCCTC-ATCTAAAGTTTGCTTGTTAGCTTTGACCTTG
1 GAGACTTTTTCTACCT-TAGTCTGCCTGTCAGCTTTGACCTTG
4934928 GAGACTTT
1 GAGACTTT
4934936 CCTATCCTTC
Statistics
Matches: 204, Mismatches: 45, Indels: 25
0.74 0.16 0.09
Matches are distributed among these distances:
40 3 0.01
41 41 0.20
42 89 0.44
43 65 0.32
44 6 0.03
ACGTcount: A:0.16, C:0.26, G:0.19, T:0.38
Consensus pattern (42 bp):
GAGACTTTTTCTACCTTAGTCTGCCTGTCAGCTTTGACCTTG
Found at i:4935133 original size:42 final size:42
Alignment explanation
Indices: 4934665--4935481 Score: 245
Period size: 42 Copynumber: 19.4 Consensus size: 42
4934655 GCTTGTCGAT
* * * * *
4934665 TTTGACCCTAGAGACTTTCCTATCCCTT-AGTCTACCTATCGGC
1 TTTGACCTTGGAGACTTTCCTA--CCTTAAATCTGCCTGTCGGC
* * ** **
4934708 TTTGACCCTGGAGACTTT-TTCACCCTT-GGTCTGCCTGTTAGC
1 TTTGACCTTGGAGACTTTCCT-A-CCTTAAATCTGCCTGTCGGC
* * * * * *
4934750 TTTGACCTTGGAGACTTTTCTACCTT-AGTTTGACTATCAGC
1 TTTGACCTTGGAGACTTTCCTACCTTAAATCTGCCTGTCGGC
* *
4934791 TTTGACCTTGGAGA-TTGCCTTACC-TAAAGTCTGCCTGTCAGC
1 TTTGACCTTGGAGACTTTCC-TACCTTAAA-TCTGCCTGTCGGC
* * *** * * *
4934833 TTTGACCCTAGAGACTTTCCTACCCTTCGGTTTGCTTGTCAGC
1 TTTGACCTTGGAGACTTTCCTA-CCTTAAATCTGCCTGTCGGC
* * * * **
4934876 TTTGACCTTGGAGAC-TGCCT-CATCTAAAGTTTGCTTGTTAGC
1 TTTGACCTTGGAGACTTTCCTACCT-TAAA-TCTGCCTGTCGGC
* * * *
4934918 TTTGACCTTGGAGACTTTCCTATCCTTCAATCTGCCTATTGAC
1 TTTGACCTTGGAGACTTTCCTA-CCTTAAATCTGCCTGTCGGC
* * * * *
4934961 TTTGACCTTGGATACTGTTTC-A-TTTAAAGTCTGCTTGTCAGC
1 TTTGACCTTGGAGACT-TTCCTACCTTAAA-TCTGCCTGTCGGC
* * * * * * * *
4935003 TTTAACCATAGAGACTTTCCGATCCCTCAATCTGCTTGTCAGC
1 TTTGACCTTGGAGACTTTCCTA-CCTTAAATCTGCCTGTCGGC
* * * * *
4935046 TTTGACCCTT-GAGAC-TGCCT-CTTCTAAAGTTTGCTTGTCGAC
1 TTTGA-CCTTGGAGACTTTCCTACCT-TAAA-TCTGCCTGTCGGC
* * *
4935088 TTTGACCTTGGAGACTTTTCTACCTTAAATCTGCCTATTGGC
1 TTTGACCTTGGAGACTTTCCTACCTTAAATCTGCCTGTCGGC
* * * * * * *
4935130 TTTGACCCTAGAGAC-TGCCT-CATCTAAACTCTACCTATTGGC
1 TTTGACCTTGGAGACTTTCCTACCT-TAAA-TCTGCCTGTCGGC
* ** * * * * *
4935172 TTTGACCCTGGAGACTTTTATACCCTCAGTCTGCCTATCGTC
1 TTTGACCTTGGAGACTTTCCTACCTTAAATCTGCCTGTCGGC
* * * * * *
4935214 TTTGACATTGGAGGCTGT-CT-CATCTAAATTCTACCTATCGGC
1 TTTGACCTTGGAGACTTTCCTACCT-TAAA-TCTGCCTGTCGGC
* * * * * *
4935256 TTTGACCTTGGAG-GTTCTTCTACCCTCAGTCTGCCTGTCGAC
1 TTTGACCTTGGAGACTT-TCCTACCTTAAATCTGCCTGTCGGC
* * * * * * *
4935298 TTTAACCTTGGAGAC-TACCT-CATCTAAAGTTTGCCTATTGAC
1 TTTGACCTTGGAGACTTTCCTACCT-TAAA-TCTGCCTGTCGGC
** * * * * * **
4935340 TTTGACCTTGGAGACTTTTTTACCCTCAGTCTTCTTGTTAGC
1 TTTGACCTTGGAGACTTTCCTACCTTAAATCTGCCTGTCGGC
* * * * * **
4935382 TTTGACCCTGGAGAC-TGCCTCATCTAAAAGCTGCCTGTCGAT
1 TTTGACCTTGGAGACTTTCCT-ACCTTAAATCTGCCTGTCGGC
* * * * *
4935424 TTTGACCCTGGAGACTTTTCTACCCTCAATCTACCTGTCGGC
1 TTTGACCTTGGAGACTTTCCTACCTTAAATCTGCCTGTCGGC
*
4935466 TTTGACCCTGGAGACT
1 TTTGACCTTGGAGACT
4935482 GACTCATCTA
Statistics
Matches: 566, Mismatches: 168, Indels: 81
0.69 0.21 0.10
Matches are distributed among these distances:
40 11 0.02
41 65 0.11
42 349 0.62
43 121 0.21
44 18 0.03
45 2 0.00
ACGTcount: A:0.18, C:0.27, G:0.18, T:0.37
Consensus pattern (42 bp):
TTTGACCTTGGAGACTTTCCTACCTTAAATCTGCCTGTCGGC
Found at i:4935144 original size:84 final size:84
Alignment explanation
Indices: 4934650--4935642 Score: 757
Period size: 84 Copynumber: 11.8 Consensus size: 84
4934640 CTTCTCCCTT
* * * * * * *
4934650 AGTTTGCTTGTCGATTTTGACCCTAGAGACTTTCCTATCCCTTAGTCTACCTATCGGCTTTGACC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTA-CCCTCAGTCTGCCTATCGGCTTTGACC
*** * *
4934715 CTGGAGACTTTTTCACCCT-T
65 CTGGAGACTGCCTCA-TCTAA
* * * * * * *
4934735 GGTCTGCCTGT-TAGCTTTGACCTTGGAGACTTTTCTA-CCTTAGTTTGACTATCAGCTTTGACC
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACC
* * * *
4934798 TTGGAGATTGCCTTACCTAA
65 CTGGAGACTGCCTCATCTAA
* * * * * * * * *
4934818 AGTCTGCCTGTC-AGCTTTGACCCTAGAGACTTTCCTACCCTTCGGTTTGCTTGTCAGCTTTGAC
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTTCTACCC-TCAGTCTGCCTATCGGCTTTGAC
*
4934882 CTTGGAGACTGCCTCATCTAA
64 CCTGGAGACTGCCTCATCTAA
* * * * * * *
4934903 AGTTTGCTTGT-TAGCTTTGACCTTGGAGACTTTCCTATCCTTCAATCTGCCTATTGACTTTGAC
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTTCTA-CCCTCAGTCTGCCTATCGGCTTTGAC
* * ** *
4934967 CTTGGATACTGTTTCATTTAA
64 CCTGGAGACTGCCTCATCTAA
* * * * * * * * * * *
4934988 AGTCTGCTTGTC-AGCTTTAACCATAGAGACTTTCCGATCCCTCAATCTGCTTGTCAGCTTTGAC
1 AGTTTGCCTGTCGA-CTTTGACCTTGGAGACTTTTCTA-CCCTCAGTCTGCCTATCGGCTTTGAC
* *
4935052 CCTTGAGACTGCCTCTTCTAA
64 CCTGGAGACTGCCTCATCTAA
* * * * *
4935073 AGTTTGCTTGTCGACTTTGACCTTGGAGACTTTTCTACCTTAAATCTGCCTATTGGCTTTGACCC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACCC
*
4935138 TAGAGACTGCCTCATCTAA
66 TGGAGACTGCCTCATCTAA
* * * * * * * * * **
4935157 ACTCTACCTATTGGCTTTGACCCTGGAGACTTTTATACCCTCAGTCTGCCTATCGTCTTTGACAT
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACCC
* *
4935222 TGGAGGCTGTCTCATCTAA
66 TGGAGACTGCCTCATCTAA
* * * * * * *
4935241 A-TTCTACCTATCGGCTTTGACCTTGGAG-GTTCTTCTACCCTCAGTCTGCCTGTCGACTTTAAC
1 AGTT-TGCCTGTCGACTTTGACCTTGGAGACTT-TTCTACCCTCAGTCTGCCTATCGGCTTTGAC
* *
4935304 CTTGGAGACTACCTCATCTAA
64 CCTGGAGACTGCCTCATCTAA
* * * * * * **
4935325 AGTTTGCCTATTGACTTTGACCTTGGAGACTTTTTTACCCTCAGTCTTCTTGTTAGCTTTGACCC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACCC
4935390 TGGAGACTGCCTCATCTAAA
66 TGGAGACTGCCTCATCT-AA
* * * * * *
4935410 AG-CTGCCTGTCGATTTTGACCCTGGAGACTTTTCTACCCTCAATCTACCTGTCGGCTTTGACCC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACCC
*
4935474 TGGAGACTGACTCATCTAA
66 TGGAGACTGCCTCATCTAA
* * * * * *
4935493 AGTTTGCCTATCAACTTTGACCCTAGAGACTTTTCTACCCTCAGTTTGCCTATCGGCTTTGGCCC
1 AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACCC
*
4935558 TAGAGACTGCCTCATCTAA
66 TGGAGACTGCCTCATCTAA
* * * * *
4935577 AGTTTACCTGTCAACTTTGACCCTT-GAGACTTTT-TCACTCTTAAGTCTGCCTATTGGCTTTGA
1 AGTTTGCCTGTCGACTTTGA-CCTTGGAGACTTTTCT-AC-CCTCAGTCTGCCTATCGGCTTTGA
4935640 CCC
63 CCC
4935643 GAGGACCTTT
Statistics
Matches: 734, Mismatches: 156, Indels: 36
0.79 0.17 0.04
Matches are distributed among these distances:
82 3 0.00
83 71 0.10
84 402 0.55
85 255 0.35
86 3 0.00
ACGTcount: A:0.19, C:0.27, G:0.18, T:0.37
Consensus pattern (84 bp):
AGTTTGCCTGTCGACTTTGACCTTGGAGACTTTTCTACCCTCAGTCTGCCTATCGGCTTTGACCC
TGGAGACTGCCTCATCTAA
Found at i:4935511 original size:42 final size:42
Alignment explanation
Indices: 4935465--4935607 Score: 146
Period size: 42 Copynumber: 3.4 Consensus size: 42
4935455 TACCTGTCGG
*
4935465 CTTTGACCCTGGAGACTGACTCATCTAAAGTTTGCCTATCAA
1 CTTTGACCCTAGAGACTGACTCATCTAAAGTTTGCCTATCAA
** * * **
4935507 CTTTGACCCTAGAGACT-TTTCTACCCT-CAGTTTGCCTATCGG
1 CTTTGACCCTAGAGACTGACTC-A-TCTAAAGTTTGCCTATCAA
* * * *
4935549 CTTTGGCCCTAGAGACTGCCTCATCTAAAGTTTACCTGTCAA
1 CTTTGACCCTAGAGACTGACTCATCTAAAGTTTGCCTATCAA
*
4935591 CTTTGACCCTTGAGACT
1 CTTTGACCCTAGAGACT
4935608 TTTTCACTCT
Statistics
Matches: 79, Mismatches: 18, Indels: 8
0.75 0.17 0.08
Matches are distributed among these distances:
41 4 0.05
42 71 0.90
43 4 0.05
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.33
Consensus pattern (42 bp):
CTTTGACCCTAGAGACTGACTCATCTAAAGTTTGCCTATCAA
Found at i:4936551 original size:7 final size:7
Alignment explanation
Indices: 4936536--4936583 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
4936526 TAATAAGTAG
*
4936536 AAATCAA
1 AAATAAA
4936543 AAATAAAA
1 AAAT-AAA
4936551 AAATAAA
1 AAATAAA
4936558 AAATAAA
1 AAATAAA
* *
4936565 TAA-AAT
1 AAATAAA
4936571 AAATAAA
1 AAATAAA
4936578 AAATAA
1 AAATAA
4936584 TCGTGAAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
6 4 0.12
7 24 0.71
8 6 0.18
ACGTcount: A:0.81, C:0.02, G:0.00, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:4936554 original size:8 final size:8
Alignment explanation
Indices: 4936541--4936578 Score: 51
Period size: 9 Copynumber: 4.6 Consensus size: 8
4936531 AGTAGAAATC
4936541 AAAAATAA
1 AAAAATAA
4936549 AAAAAT-A
1 AAAAATAA
4936556 AAAAATAA
1 AAAAATAA
4936564 ATAAAATAA
1 A-AAAATAA
4936573 ATAAAA
1 A-AAAA
4936579 AATAATCGTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
7 7 0.25
8 8 0.29
9 13 0.46
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (8 bp):
AAAAATAA
Found at i:4936559 original size:15 final size:16
Alignment explanation
Indices: 4936515--4936583 Score: 70
Period size: 16 Copynumber: 4.2 Consensus size: 16
4936505 TTTATTCGAT
*
4936515 ATAAAATATAATAATAA
1 ATAAAATA-AAAAATAA
* *
4936532 GTAGAAATCAAAAATAA
1 ATA-AAATAAAAAATAA
4936549 A-AAAATAAAAAATAA
1 ATAAAATAAAAAATAA
4936564 ATAAAATAAATAAA-AA
1 ATAAAATAAA-AAATAA
4936580 ATAA
1 ATAA
4936584 TCGTGAAATG
Statistics
Matches: 44, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
15 13 0.30
16 15 0.34
17 12 0.27
18 4 0.09
ACGTcount: A:0.75, C:0.01, G:0.03, T:0.20
Consensus pattern (16 bp):
ATAAAATAAAAAATAA
Found at i:4936567 original size:4 final size:4
Alignment explanation
Indices: 4936543--4936583 Score: 50
Period size: 4 Copynumber: 10.5 Consensus size: 4
4936533 TAGAAATCAA
*
4936543 AAAT AAAA AAAT AAA- AAAT AAAT AAAAT AAAT AAA- AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AA
4936584 TCGTGAAATG
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
3 6 0.19
4 22 0.69
5 4 0.12
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (4 bp):
AAAT
Found at i:4936576 original size:20 final size:19
Alignment explanation
Indices: 4936543--4936583 Score: 73
Period size: 20 Copynumber: 2.1 Consensus size: 19
4936533 TAGAAATCAA
4936543 AAATAAAAAAATAAAAAAT
1 AAATAAAAAAATAAAAAAT
4936562 AAATAAAATAAATAAAAAAT
1 AAATAAAA-AAATAAAAAAT
4936582 AA
1 AA
4936584 TCGTGAAATG
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (19 bp):
AAATAAAAAAATAAAAAAT
Found at i:4937415 original size:107 final size:107
Alignment explanation
Indices: 4937226--4937429 Score: 302
Period size: 107 Copynumber: 1.9 Consensus size: 107
4937216 TCCAAAGCTC
* * *
4937226 CAACAAGCATGAATAGCAGCTTCACAAAGCACTCGAAACTACTAGCTCCAATAAGCAACAGCTTC
1 CAACAAGCATGAACAGCAGCTTCACAAAACACTCGAAACTACTAGCTCCAACAAGCAACAGCTTC
* *
4937291 CACGGTAGCAACAATAGCAGCTCCAACAAGCAGTAGCTTCCA
66 CACAGCAGCAACAATAGCAGCTCCAACAAGCAGTAGCTTCCA
* *
4937333 CAACAAGCATGAACAGTAGCTTCACAAAACACTCGAAACTAGC-AGCTCCAACAAGCAGCAGCTT
1 CAACAAGCATGAACAGCAGCTTCACAAAACACTCGAAACTA-CTAGCTCCAACAAGCAACAGCTT
** *
4937397 CCACAGCAGCAATGATAGCAGTTCCAACAAGCA
65 CCACAGCAGCAACAATAGCAGCTCCAACAAGCA
4937430 CGAACAGCAA
Statistics
Matches: 86, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
107 85 0.99
108 1 0.01
ACGTcount: A:0.39, C:0.30, G:0.16, T:0.15
Consensus pattern (107 bp):
CAACAAGCATGAACAGCAGCTTCACAAAACACTCGAAACTACTAGCTCCAACAAGCAACAGCTTC
CACAGCAGCAACAATAGCAGCTCCAACAAGCAGTAGCTTCCA
Found at i:4941374 original size:24 final size:24
Alignment explanation
Indices: 4941337--4941385 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
4941327 AAGCAAAAGT
* *
4941337 ACAAAAATAAGAAACACAAAAGAA
1 ACAAAAATAAGAAAAAAAAAAGAA
4941361 ACAAAAA-AATGAAAAAAAAAAGAA
1 ACAAAAATAA-GAAAAAAAAAAGAA
4941385 A
1 A
4941386 AGGCAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
23 2 0.09
24 20 0.91
ACGTcount: A:0.80, C:0.08, G:0.08, T:0.04
Consensus pattern (24 bp):
ACAAAAATAAGAAAAAAAAAAGAA
Found at i:4941386 original size:11 final size:11
Alignment explanation
Indices: 4941339--4941386 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
4941329 GCAAAAGTAC
*
4941339 AAAAATAAGAA
1 AAAAAAAAGAA
* *
4941350 ACACAAAAGAA
1 AAAAAAAAGAA
4941361 ACAAAAAAATGAA
1 A-AAAAAAA-GAA
4941374 AAAAAAAAGAA
1 AAAAAAAAGAA
4941385 AA
1 AA
4941387 GGCAAAATAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
11 14 0.47
12 12 0.40
13 4 0.13
ACGTcount: A:0.81, C:0.06, G:0.08, T:0.04
Consensus pattern (11 bp):
AAAAAAAAGAA
Found at i:4942429 original size:20 final size:21
Alignment explanation
Indices: 4942406--4942453 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
4942396 GACATTTATT
*
4942406 GATACATTCACTT-ATATATC
1 GATACAATCACTTAATATATC
*
4942426 GATACAATCACTTAATGTATC
1 GATACAATCACTTAATATATC
4942447 GATACAA
1 GATACAA
4942454 ATTGTGGAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.40, C:0.19, G:0.08, T:0.33
Consensus pattern (21 bp):
GATACAATCACTTAATATATC
Found at i:4943641 original size:23 final size:22
Alignment explanation
Indices: 4943606--4943662 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 22
4943596 AGATTTGACA
* *
4943606 AAGGAGGAGAAATGCCTTGATT
1 AAGGGGGAGAAATGCCTTAATT
* *
4943628 AAGGGGGGAGAAATTCTTTAATT
1 AA-GGGGGAGAAATGCCTTAATT
4943651 AAGGGGGAGAAA
1 AAGGGGGAGAAA
4943663 AAAGTAAACT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 12 0.40
23 18 0.60
ACGTcount: A:0.39, C:0.05, G:0.35, T:0.21
Consensus pattern (22 bp):
AAGGGGGAGAAATGCCTTAATT
Found at i:4949043 original size:20 final size:20
Alignment explanation
Indices: 4949005--4949044 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
4948995 TTTCAAATTT
4949005 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
4949026 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
4949045 TATCAACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:4951219 original size:21 final size:21
Alignment explanation
Indices: 4951195--4951245 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 21
4951185 TATATCAATG
4951195 AATGTTTTAGAA-TTATAAACA
1 AATGTTTTAGAACTT-TAAACA
* *
4951216 AATGTTTTTGAACCTTTAATCA
1 AATGTTTTAGAA-CTTTAAACA
4951238 AATGTTTT
1 AATGTTTT
4951246 TAAGTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 11 0.42
22 13 0.50
23 2 0.08
ACGTcount: A:0.37, C:0.08, G:0.10, T:0.45
Consensus pattern (21 bp):
AATGTTTTAGAACTTTAAACA
Found at i:4955436 original size:12 final size:12
Alignment explanation
Indices: 4955419--4955457 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
4955409 CTTGATTTTC
4955419 CTTTTTTTCTCT
1 CTTTTTTTCTCT
4955431 CTTTTTTTCTCT
1 CTTTTTTTCTCT
4955443 -TTTTTTT-T-T
1 CTTTTTTTCTCT
4955452 CTTTTT
1 CTTTTT
4955458 GTTCCCACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
9 1 0.04
10 6 0.23
11 7 0.27
12 12 0.46
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (12 bp):
CTTTTTTTCTCT
Found at i:4956399 original size:167 final size:166
Alignment explanation
Indices: 4955905--4956472 Score: 601
Period size: 167 Copynumber: 3.4 Consensus size: 166
4955895 AAAAGTCATG
* * * * *
4955905 AAATAAATTGAATTTTTTAAAACTGAA-TTAATAGGAGTTCAATGATAATATTAGATGAATTTTA
1 AAATAAATT-AATTTTTCAAAACT-AATTTAATAGGAATTAAATTATAATATTTGATGAATTTTA
** * * * * ** * *
4955969 AAAATTTTAAATTTGAGAAAAACCCCCCCGAAAACCTTTGTGGAATAGAAAATTCAAT-TTTTCA
64 AAAA--TTAAAACTAAGAAAAATCCCCTCGAAAACATTTACGGAGTAGAAAATTCAGTATTTT-A
*
4956033 GAAAAAA-AGAATTTCAAGG-AGAAAATTCAAAAACTAATGA
126 GAAAAAAGAGAATTTC-AGGAAAAAAATTCAAAAACTAATGA
* * * * * *
4956073 AGATAAATTAATTTTTTAAAACTAATTTAATATGAAATAGATTATAATATTTGATGAATTTTCAA
1 AAATAAATTAATTTTTCAAAACTAATTTAATAGGAATTAAATTATAATATTTGATGAATTTTAAA
* * * * * *
4956138 AATTAAAACCAAGAAAAATCCCTTTGAAAACAATTACGGAGTAGAAAACTCCGTA-TTTAGAAAA
66 AATTAAAACTAAGAAAAATCCCCTCGAAAACATTTACGGAGTAGAAAATTCAGTATTTTAG-AAA
* * * * *
4956202 AAAGAGAATTTTAAGAAAGAAATTCAAAAACTTATTA
130 AAAGAGAATTTCAGGAAAAAAATTCAAAAACTAATGA
* * *
4956239 AAATAAATTAATATTTCAAAACTGATTTAATAGGAATTAAATTATAATATTTTATGAATTTTAAA
1 AAATAAATTAATTTTTCAAAACTAATTTAATAGGAATTAAATTATAATATTTGATGAATTTTAAA
**
4956304 AATTAAAAGCTAAGAAAAATCCCCTCGAAAACATTTACGGAGTAGAAAATTTTGTATTTTAGAAA
66 AATTAAAA-CTAAGAAAAATCCCCTCGAAAACATTTACGGAGTAGAAAATTCAGTATTTTAGAAA
* *
4956369 AAAGAAAATTTCAGGAAAAAAATTCAAAAACTCATGA
130 AAAGAGAATTTCAGGAAAAAAATTCAAAAACTAATGA
* * * * * *
4956406 AAATGATTTAATTTTTCAAAAGTAATTT--TATGAATTAAATAATAATATTTGATGAATTTTCAA
1 AAATAAATTAATTTTTCAAAACTAATTTAATAGGAATTAAATTATAATATTTGATGAATTTTAAA
4956469 AATT
66 AATT
4956473 TTAAACCCAT
Statistics
Matches: 331, Mismatches: 62, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
164 2 0.01
165 82 0.25
166 90 0.27
167 144 0.44
168 13 0.04
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.33
Consensus pattern (166 bp):
AAATAAATTAATTTTTCAAAACTAATTTAATAGGAATTAAATTATAATATTTGATGAATTTTAAA
AATTAAAACTAAGAAAAATCCCCTCGAAAACATTTACGGAGTAGAAAATTCAGTATTTTAGAAAA
AAGAGAATTTCAGGAAAAAAATTCAAAAACTAATGA
Found at i:4958187 original size:47 final size:47
Alignment explanation
Indices: 4958133--4958703 Score: 244
Period size: 47 Copynumber: 12.8 Consensus size: 47
4958123 CAAAACCAAT
* * *
4958133 GCCAATATAGTGAAACGAGAGTAGAAAGAGTTTGACCAGGTCCTCAC
1 GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* * * *
4958180 GCTAATATAGTCAAATGAGGGTAAAAAGAGTTTGACCAGGTCCTAAT
1 GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* *
4958227 GCCAATATAATCAAACGAGGGTGGAAAGAAGTTT-A--A----CT-A-
1 GCCAATATAGTCAAACGAGGGTAGAAAG-AGTTTGACCAGGTCCTAAC
* * * * * *
4958266 G---ATATAGTCAAACGATGATGGAAATGAGTTGGACTAGGTCTTAAC
1 GCCAATATAGTCAAACGAGGGTAGAAA-GAGTTTGACCAGGTCCTAAC
* * ** *
4958311 ACCAATACAGTCAAATAAGGGTAAAAAGAGTTTGACCAGGTCCTAAC
1 GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* * * * *
4958358 GCCAATATAGTGAAACAAGGGTAAAAAGTGTTTGACCAGGTCCTAAT
1 GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* * ** * *
4958405 GCCAATACAATCAAATAAGGGTGGAAAAAGTTTG---A---CC--A-
1 GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* * * * * * *
4958443 ---AATACAGTCAAACAATGATGGAAATGAGTTTGACCAAGTCCCAAC
1 GCCAATATAGTCAAACGAGGGTAGAAA-GAGTTTGACCAGGTCCTAAC
* * * * * * ** *
4958488 TCTAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAAGTTTTAAT
1 GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* * * * *
4958535 GCCAACACAATCAAA-GAAGGGTGGAAAAAAGTTTG---A----CT-A-
1 GCCAATATAGTCAAACG-AGGGTAG-AAAGAGTTTGACCAGGTCCTAAC
* * * * *
4958574 G---ATATAGTCAAACGATGATGGAAACGAGTTTGACTAGGTCCTAAT
1 GCCAATATAGTCAAACGAGGGTAGAAA-GAGTTTGACCAGGTCCTAAC
* * *
4958619 GCCAAATAGAGTCAAACGAGGGTAAAAAGAGTTTGACCAAGTCCTAAC
1 GCC-AATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
* * *
4958667 GCTAATCTAGTCAAACGAGGGTGGAAAGAAGTTTGAC
1 GCCAATATAGTCAAACGAGGGTAGAAAG-AGTTTGAC
4958704 TAGATACAGT
Statistics
Matches: 396, Mismatches: 83, Indels: 89
0.70 0.15 0.16
Matches are distributed among these distances:
35 23 0.06
36 49 0.12
37 3 0.01
39 6 0.02
40 2 0.01
41 5 0.01
42 2 0.01
43 3 0.01
44 4 0.01
45 3 0.01
47 201 0.51
48 77 0.19
49 18 0.05
ACGTcount: A:0.40, C:0.15, G:0.23, T:0.22
Consensus pattern (47 bp):
GCCAATATAGTCAAACGAGGGTAGAAAGAGTTTGACCAGGTCCTAAC
Found at i:4958302 original size:36 final size:36
Alignment explanation
Indices: 4958231--4958302 Score: 83
Period size: 36 Copynumber: 2.0 Consensus size: 36
4958221 CCTAATGCCA
* *
4958231 ATATAATCAAACGAGGGTGGAAAGAAGTTTAACTAG
1 ATATAATCAAACGAGGATGGAAAGAAGTTGAACTAG
* * *
4958267 ATATAGTCAAACGATGATGGAAATG-AGTTGGACTAG
1 ATATAATCAAACGAGGATGGAAA-GAAGTTGAACTAG
4958303 GTCTTAACAC
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
36 29 0.97
37 1 0.03
ACGTcount: A:0.42, C:0.08, G:0.26, T:0.24
Consensus pattern (36 bp):
ATATAATCAAACGAGGATGGAAAGAAGTTGAACTAG
Found at i:4958454 original size:35 final size:36
Alignment explanation
Indices: 4958408--4958479 Score: 92
Period size: 35 Copynumber: 2.0 Consensus size: 36
4958398 TCCTAATGCC
* *
4958408 AATACAATCAAATAAGGGTGGAAA-AAGTTTGACCA
1 AATACAATCAAACAAGGATGGAAATAAGTTTGACCA
* * *
4958443 AATACAGTCAAACAATGATGGAAATGAGTTTGACCA
1 AATACAATCAAACAAGGATGGAAATAAGTTTGACCA
4958479 A
1 A
4958480 GTCCCAACTC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
35 20 0.65
36 11 0.35
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.21
Consensus pattern (36 bp):
AATACAATCAAACAAGGATGGAAATAAGTTTGACCA
Found at i:4958663 original size:48 final size:47
Alignment explanation
Indices: 4958599--4958703 Score: 120
Period size: 48 Copynumber: 2.2 Consensus size: 47
4958589 TGATGGAAAC
* * *
4958599 GAGTTTGACTAGGTCCTAATGCCAAATAGAGTCAAACGAGGGTAAAAA
1 GAGTTTGACCAAGTCCTAACG-CAAATAGAGTCAAACGAGGGTAAAAA
* ** **
4958647 GAGTTTGACCAAGTCCTAACGCTAATCTAGTCAAACGAGGGTGGAAA
1 GAGTTTGACCAAGTCCTAACGCAAATAGAGTCAAACGAGGGTAAAAA
4958694 GAAGTTTGAC
1 G-AGTTTGAC
4958704 TAGATACAGT
Statistics
Matches: 48, Mismatches: 8, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
47 22 0.46
48 26 0.54
ACGTcount: A:0.36, C:0.16, G:0.26, T:0.22
Consensus pattern (47 bp):
GAGTTTGACCAAGTCCTAACGCAAATAGAGTCAAACGAGGGTAAAAA
Found at i:4958832 original size:132 final size:131
Alignment explanation
Indices: 4958338--4958835 Score: 581
Period size: 132 Copynumber: 3.8 Consensus size: 131
4958328 AGGGTAAAAA
* * * *
4958338 GAGTTTGACCAGGTCCTAACGCCAATATAGTGAAACAAGGGTAAAAAGTGTTTGACCAGGTCCTA
1 GAGTTTGACCAGGTCCTAACGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAAGTCCTA
* * * *
4958403 ATGCCAATACAATCAAATAAGGGTGGAAAA-AGTTTGACCAAATACAGTCAAACAATGATGGAAA
66 ATGCCAATACAATCAAACAAGGGTGGAAAAGAGTTTGACTAGATACAGTCAAACGATGATGGAAA
*
4958467 T
131 C
* * * * **
4958468 GAGTTTGACCAAGTCCCAACTCTAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAAGTTTTA
1 GAGTTTGACCAGGTCCTAACGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAAGTCCTA
* * * *
4958533 ATGCCAACACAATCAAAGAAGGGTGGAAAAAAGTTTGACTAGATATAGTCAAACGATGATGGAAA
66 ATGCCAATACAATCAAACAAGGGTGGAAAAGAGTTTGACTAGATACAGTCAAACGATGATGGAAA
4958598 C
131 C
* * * *
4958599 GAGTTTGACTAGGTCCTAATGCCAAATAGAGTCAAACGAGGGTAAAAAGAGTTTGACCAAGTCCT
1 GAGTTTGACCAGGTCCTAACGCC-AATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAAGTCCT
* * * *
4958664 AACGCTAAT-CTAGTCAAACGAGGGTGG-AAAGAAGTTTGACTAGATACAGTCAAACGATGATGG
65 AATGCCAATAC-AATCAAACAAGGGTGGAAAAG-AGTTTGACTAGATACAGTCAAACGATGATGG
4958727 AAAC
128 AAAC
* * * ** * *
4958731 GAGTTTGATCACGTCTTAACGCCAATACAGTCAAACAAGGGTAGAATTTGACTTTGACCAGGTCC
1 GAGTTTGACCAGGTCCTAACGCCAATACAGTCAAACAAGGGTA-AA-AAGAGTTTGACCAAGTCC
* * **
4958796 TAATGCTAATACAGTCAAACAAGAAT-GAAAAGAGTTTGAC
64 TAATGCCAATACAATCAAACAAGGGTGGAAAAGAGTTTGAC
4958836 CTAGTGCTAT
Statistics
Matches: 310, Mismatches: 50, Indels: 14
0.83 0.13 0.04
Matches are distributed among these distances:
130 83 0.27
131 69 0.22
132 119 0.38
133 38 0.12
134 1 0.00
ACGTcount: A:0.40, C:0.16, G:0.22, T:0.22
Consensus pattern (131 bp):
GAGTTTGACCAGGTCCTAACGCCAATACAGTCAAACAAGGGTAAAAAGAGTTTGACCAAGTCCTA
ATGCCAATACAATCAAACAAGGGTGGAAAAGAGTTTGACTAGATACAGTCAAACGATGATGGAAA
C
Found at i:4965300 original size:10 final size:10
Alignment explanation
Indices: 4965286--4965321 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
4965276 ATTTTCCGTT
4965286 TTTTTCTTCTC
1 TTTTT-TTCTC
4965297 TTTTTTTCTC
1 TTTTTTTCTC
*
4965307 TTTTTTTTTC
1 TTTTTTTCTC
4965317 TTTTT
1 TTTTT
4965322 GTTCCCACTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 19 0.79
11 5 0.21
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTC
Found at i:4965302 original size:12 final size:11
Alignment explanation
Indices: 4965284--4965321 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 11
4965274 TAATTTTCCG
4965284 TTTTTTTCTTCT
1 TTTTTTTC-TCT
4965296 CTTTTTTTCTCT
1 -TTTTTTTCTCT
4965308 TTTTTTT-TCT
1 TTTTTTTCTCT
4965318 TTTT
1 TTTT
4965322 GTTCCCACTT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 7 0.28
11 7 0.28
12 3 0.12
13 8 0.32
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (11 bp):
TTTTTTTCTCT
Found at i:4968470 original size:21 final size:22
Alignment explanation
Indices: 4968445--4968502 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 22
4968435 GAACTAGTGG
*
4968445 AGAAAATGAATGAGTTGGAA-A
1 AGAAAATGAATGAGTTGCAAGA
*
4968466 GGAAAA-GAAATGAGTTGCAAGA
1 AGAAAATG-AATGAGTTGCAAGA
4968488 AGAAAATG-ATGAGTT
1 AGAAAATGAATGAGTT
4968503 AACAAAGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
20 1 0.03
21 23 0.74
22 6 0.19
23 1 0.03
ACGTcount: A:0.50, C:0.02, G:0.29, T:0.19
Consensus pattern (22 bp):
AGAAAATGAATGAGTTGCAAGA
Found at i:4970196 original size:18 final size:18
Alignment explanation
Indices: 4970169--4970224 Score: 60
Period size: 18 Copynumber: 3.0 Consensus size: 18
4970159 CTCATTAATC
*
4970169 TTTCAACAATTGGTATCA
1 TTTCATCAATTGGTATCA
*
4970187 TTTCATCAATTGGTAACAA
1 TTTCATCAATTGGTATC-A
4970206 TTGGT-ATCAATTGGTATCA
1 TT--TCATCAATTGGTATCA
4970225 ATCTCATTCA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 15 0.47
19 4 0.12
20 12 0.38
21 1 0.03
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.39
Consensus pattern (18 bp):
TTTCATCAATTGGTATCA
Found at i:4970208 original size:10 final size:10
Alignment explanation
Indices: 4970175--4970226 Score: 65
Period size: 10 Copynumber: 5.4 Consensus size: 10
4970165 AATCTTTCAA
4970175 CAATTGGTAT
1 CAATTGGTAT
4970185 C-ATT--TCAT
1 CAATTGGT-AT
*
4970193 CAATTGGTAA
1 CAATTGGTAT
4970203 CAATTGGTAT
1 CAATTGGTAT
4970213 CAATTGGTAT
1 CAATTGGTAT
4970223 CAAT
1 CAAT
4970227 CTCATTCATC
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
7 1 0.03
8 3 0.08
9 6 0.17
10 25 0.69
11 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.38
Consensus pattern (10 bp):
CAATTGGTAT
Found at i:4970953 original size:20 final size:21
Alignment explanation
Indices: 4970915--4970957 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
4970905 GAGTTTCCAT
4970915 AAAATTTGTATTAAAGGGGAG
1 AAAATTTGTATTAAAGGGGAG
*
4970936 AAAATTTGTATTAAGGGGGAG
1 AAAATTTGTATTAAAGGGGAG
4970957 A
1 A
4970958 GCTTGCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.30, T:0.28
Consensus pattern (21 bp):
AAAATTTGTATTAAAGGGGAG
Found at i:4973019 original size:165 final size:166
Alignment explanation
Indices: 4972755--4973210 Score: 611
Period size: 165 Copynumber: 2.8 Consensus size: 166
4972745 CTTTGTGGAA
* * * *
4972755 TAGAAAACTC-G-ATTTTTCGAAAATAA-AATTTCAA-GAAAAAATTCAAAAACTCAAGAAGATG
1 TAGAAAACTCTGTA-TTTTCGAAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATA
* * *
4972816 AATTAATTTTTCAAAACTTATTTAATTTAAAATAAATTATAATATTTGATGAATTTTAAAAATTA
65 AATTAATTTTTCAAAACTAATTTAATATAAATTAAATTATAATATTTGATGAATTTTAAAAATTA
* *
4972881 AAAACCAACAAAAATCCCTTTGAAAATATTTATAGAG
130 AAAACCAACAAAAATCCCTTTGAAAACATTTATAAAG
* * *
4972918 TAGAAAACTCTGTATTTTAGAAAAAAAGAATTTCAAGGAAAAACTTAAAAAACTCATGAAAATAA
1 TAGAAAACTCTGTATTTTCGAAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATAA
* *
4972983 ATTAATTTTT-AAAACTAATTTAATATGAATTAAATTATAATATTTTATGAATTTTAAAAATTAA
66 ATTAATTTTTCAAAACTAATTTAATATAAATTAAATTATAATATTTGATGAATTTTAAAAATTAA
* *
4973047 AAACTAAGAAAAATCCCTTTGAAAACATTTATAAAG
131 AAACCAACAAAAATCCCTTTGAAAACATTTATAAAG
* ** * *
4973083 TAGAAAACTCTATA-TTTCGTAAAAAAAGAATTTTGAGGAAAAAATTCAAAAACTCATAAAAATC
1 TAGAAAACTCTGTATTTTCG-AAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATA
* * * *
4973147 AATTAATTTTTCAAGAA-TGATTTAATATCAATTAAATAATAATATTTGATGAATTTTTAAAATT
65 AATTAATTTTTCAA-AACTAATTTAATATAAATTAAATTATAATATTTGATGAATTTTAAAAATT
4973211 TTAAACCTAT
Statistics
Matches: 257, Mismatches: 29, Indels: 11
0.87 0.10 0.04
Matches are distributed among these distances:
163 10 0.04
164 16 0.06
165 152 0.59
166 77 0.30
167 2 0.01
ACGTcount: A:0.51, C:0.08, G:0.07, T:0.34
Consensus pattern (166 bp):
TAGAAAACTCTGTATTTTCGAAAAAAAGAATTTCAAGGAAAAAATTCAAAAACTCATGAAAATAA
ATTAATTTTTCAAAACTAATTTAATATAAATTAAATTATAATATTTGATGAATTTTAAAAATTAA
AAACCAACAAAAATCCCTTTGAAAACATTTATAAAG
Found at i:4975621 original size:164 final size:161
Alignment explanation
Indices: 4975190--4975621 Score: 458
Period size: 164 Copynumber: 2.6 Consensus size: 161
4975180 TTTGGGAGGA
* * * *
4975190 TTTTCATCAAATTAAAATTTTTAAAATTCATCAAATATTATTATCTAGTTACCA-TACAATCAAT
1 TTTTC-TCAATTTAAAATTTTTAAAATTCATCAAATATTATCAT-TAATT-CCAGTA-AATCAGT
* * * *
4975254 TTTGAAAAATTCATTTATTTTTATGAGTTTTTTATTTTTTCTTTGAAATTCTTTTGTTTTTAAAA
62 TTTG-AAAATTCATTTA-TTTTATGAGTTTTTAATTTTTTCTTTGAAATTCCTTTATTTTCAAAA
* *
4975319 AACTATGTTTTCTATTCTATAAATGTTTTTGGGGAGT
125 AACTATGTTCTCTATTCTATAAATGTTTTCGGGGAGT
* * ** * *
4975356 TTTTCTCAATTAAAAATTTTTAATATTCATCAAATACCATCATTTAAATCATAGTAAATCAGTTT
1 TTTTCTCAATTTAAAATTTTTAAAATTCATCAAATATTATCA-TTAATTC-CAGTAAATCAGTTT
* * * *
4975421 TGAAAATTCATTTATTTTCATAAGTTTTTCATTTTTTC-TTGAAATTCCTTTATTTTCGAAAAGC
64 TGAAAATTCATTTATTTT-ATGAGTTTTTAATTTTTTCTTTGAAATTCCTTTATTTTCAAAAAAC
*
4975485 TGA-GTTCTCTATT-TCATAAATGTTTTCGGGGGGCT
128 T-ATGTTCTCTATTCT-ATAAATGTTTTCGGGGAG-T
* * **
4975520 TTTTCTCAGTTTAAAATTTTTAAAATTCATCTAATATTGCCATTGAATTCCAGTAAATCAGTTTT
1 TTTTCTCAATTTAAAATTTTTAAAATTCATCAAATATTATCATT-AATTCCAGTAAATCAGTTTT
* *
4975585 GAAAATTTTAATTTATTTTATGAGTTTTGAATTTTTT
65 GAAAA--TTCATTTATTTTATGAGTTTTTAATTTTTT
4975622 TGTATTTATT
Statistics
Matches: 222, Mismatches: 34, Indels: 22
0.80 0.12 0.08
Matches are distributed among these distances:
162 1 0.00
163 72 0.32
164 85 0.38
165 56 0.25
166 8 0.04
ACGTcount: A:0.31, C:0.11, G:0.09, T:0.49
Consensus pattern (161 bp):
TTTTCTCAATTTAAAATTTTTAAAATTCATCAAATATTATCATTAATTCCAGTAAATCAGTTTTG
AAAATTCATTTATTTTATGAGTTTTTAATTTTTTCTTTGAAATTCCTTTATTTTCAAAAAACTAT
GTTCTCTATTCTATAAATGTTTTCGGGGAGT
Found at i:4976131 original size:12 final size:12
Alignment explanation
Indices: 4976114--4976159 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
4976104 TTTGGCAAGT
4976114 GAGAAAAAAAGA
1 GAGAAAAAAAGA
*
4976126 GAGAAAAAAAAA
1 GAGAAAAAAAGA
*
4976138 GAAAAAGAAAAGA
1 GAGAAA-AAAAGA
*
4976151 AAGAAAAAA
1 GAGAAAAAA
4976160 GAAAAATTAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
12 19 0.68
13 9 0.32
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (12 bp):
GAGAAAAAAAGA
Found at i:4976146 original size:16 final size:17
Alignment explanation
Indices: 4976127--4976165 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
4976117 AAAAAAAGAG
4976127 AGAAAAAAAAAG-AAAA
1 AGAAAAAAAAAGAAAAA
*
4976143 AG-AAAAGAAAGAAAAA
1 AGAAAAAAAAAGAAAAA
4976159 AGAAAAA
1 AGAAAAA
4976166 TTAAGCCAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 8 0.40
16 8 0.40
17 4 0.20
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (17 bp):
AGAAAAAAAAAGAAAAA
Found at i:4976148 original size:11 final size:10
Alignment explanation
Indices: 4976115--4976165 Score: 66
Period size: 11 Copynumber: 4.7 Consensus size: 10
4976105 TTGGCAAGTG
4976115 AGAAAAAAAGA
1 AGAAAAAAA-A
4976126 GAGAAAAAAAA
1 -AGAAAAAAAA
4976137 AGAAAAAGAAA
1 AGAAAAA-AAA
4976148 AGAAAGAAAAA
1 AGAAA-AAAAA
4976159 AGAAAAA
1 AGAAAAA
4976166 TTAAGCCAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
10 9 0.24
11 17 0.46
12 11 0.30
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (10 bp):
AGAAAAAAAA
Found at i:4977036 original size:16 final size:16
Alignment explanation
Indices: 4977015--4977051 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
4977005 AAATTTTTGA
4977015 AAATAAAA-AATAAAAT
1 AAATAAAATAAT-AAAT
4977031 AAATAAAATAATAAAT
1 AAATAAAATAATAAAT
4977047 AAATA
1 AAATA
4977052 TTATTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 17 0.85
17 3 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (16 bp):
AAATAAAATAATAAAT
Found at i:4977244 original size:134 final size:133
Alignment explanation
Indices: 4977086--4977591 Score: 373
Period size: 134 Copynumber: 3.7 Consensus size: 133
4977076 ATTATCTTAA
*
4977086 TTTTTCAAAACTTCTAATATTCCTATAGTTTTCTGCG-A-GGCTATAGAAACCTTCAAAATGTTT
1 TTTTTCAAAACTTCTAATATTCCTATAGTTTT-T-CGTAGGGCTATAGAAACCTTCAAAACGTTT
* * *
4977149 CGTATCTTTTCAGTTTTTCTTTAAGGTGCGAAATGAATTTTCTTATAAAAAATAAAAATTATTCT
64 CGTATCTTTTCAGTTCTCCATTAAGGTGCGAAATGAATTTTCTTA-AAAAAATAAAAATTATTCT
4977214 TAATTT
128 TAATTT
* * * * * **
4977220 TTTTTCAATATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATAGAAATCTTCAAAACGTTTTT
1 TTTTTCAAAACTTCTAATATTCCTATAGTTTTTCGTAGGGCTATAGAAACCTTCAAAACGTTTCG
**
4977285 TATCTTTTTTGTTCTCCATTAAGGTGCGAAATGAATTTTCTTAAAAAAATAAAAATGAAATAAAA
66 TATCTTTTCAGTTCTCCATTAAGGTGCGAAATGAATTTTCTTAAAAAAATAAAAAT----T----
*
4977350 ATT-TATTATTAAT
123 ATTCT-TAATT--T
* * * * * * * *
4977363 TTTTTCAAGATTTCTAATATTCCTATTA-TTTTCCGTAAGGG-TACAAAAATCTTAAAAACTTTT
1 TTTTTCAAAACTTCTAATATTCCTA-TAGTTTTTCGT-AGGGCTATAGAAACCTTCAAAACGTTT
* * *** *
4977426 GGTATCTTTTCGGTTCTCCATTAAGGTATAAAATGAATTTTTTAGAAATAAAAAATTAAATAAAA
64 CGTATCTTTTCAGTTCTCCATTAAGGTGCGAAATGAATTTTCT-----T--AAAA--AAATAAAA
4977491 ATTATTCTTAA--T
120 ATTATTCTTAATTT
* * * * * * *
4977503 TTTTT-AATATTTCTAATATTCCTATGGTTTTTTGTAGGGGTATATAAATCTTCAAAAC-TTCTC
1 TTTTTCAAAACTTCTAATATTCCTATAGTTTTTCGTAGGGCTATAGAAACCTTCAAAACGTT-TC
** *
4977566 GTATCTTTTTGGTTCTCTATTAAGGT
65 GTATCTTTTCAGTTCTCCATTAAGGT
4977592 ACAAAATAAG
Statistics
Matches: 304, Mismatches: 40, Indels: 51
0.77 0.10 0.13
Matches are distributed among these distances:
132 2 0.01
133 15 0.05
134 89 0.29
137 1 0.00
138 7 0.02
139 64 0.21
140 7 0.02
141 7 0.02
143 85 0.28
144 10 0.03
145 1 0.00
148 2 0.01
150 4 0.01
152 10 0.03
ACGTcount: A:0.33, C:0.11, G:0.11, T:0.45
Consensus pattern (133 bp):
TTTTTCAAAACTTCTAATATTCCTATAGTTTTTCGTAGGGCTATAGAAACCTTCAAAACGTTTCG
TATCTTTTCAGTTCTCCATTAAGGTGCGAAATGAATTTTCTTAAAAAAATAAAAATTATTCTTAA
TTT
Found at i:4977560 original size:139 final size:141
Alignment explanation
Indices: 4977198--4977607 Score: 529
Period size: 143 Copynumber: 2.9 Consensus size: 141
4977188 TTCTTATAAA
4977198 AAATAAAAATTATTCTTAATTTTTTTTCAATATTTCTAATATTCCTATGGTTTTTCGTAGGGGTA
1 AAATAAAAATTATTCTTAA--TTTTTTCAATATTTCTAATATTCCTATGGTTTTTCGTAGGGGTA
* * * * *
4977263 TAGAAATCTTCAAAACGTTTTTTATCTTTTTTGTTCTCCATTAAGGTGCGAAATGAATTTTCTTA
64 TAAAAATCTTCAAAAC-TTTTGTATCTTTTTGGTTCTCCATTAAGGTACAAAATGAATTTTCTTA
4977328 AAAAAATAAAAATG
128 AAAAAATAAAAATG
* * ** * * *
4977342 AAATAAAAATTTATTATTAATTTTTTCAAGATTTCTAATATTCCTATTATTTTCCGTAAGGGTAC
1 AAATAAAAA-TTATTCTTAATTTTTTCAATATTTCTAATATTCCTATGGTTTTTCGTAGGGGTAT
* * * *
4977407 AAAAATCTTAAAAACTTTTGGTATCTTTTCGGTTCTCCATTAAGGTATAAAATGAATTTT-TTAG
65 AAAAATCTTCAAAACTTTT-GTATCTTTTTGGTTCTCCATTAAGGTACAAAATGAATTTTCTTAA
* *
4977471 AAATA-AAAAATT
129 AAAAATAAAAATG
*
4977483 AAATAAAAATTATTCTTAATTTTTT-AATATTTCTAATATTCCTATGGTTTTTTGTAGGGGTATA
1 AAATAAAAATTATTCTTAATTTTTTCAATATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATA
* * * *
4977547 TAAATCTTCAAAACTTCTCGTATCTTTTTGGTTCTCTATTAAGGTACAAAATAAGATTTTC
66 AAAATCTTCAAAACTT-TTGTATCTTTTTGGTTCTCCATTAAGGTACAAAATGA-ATTTTC
4977608 GAAATTTATA
Statistics
Matches: 228, Mismatches: 33, Indels: 13
0.83 0.12 0.05
Matches are distributed among these distances:
139 77 0.34
140 21 0.09
141 15 0.07
142 11 0.05
143 86 0.38
144 9 0.04
145 9 0.04
ACGTcount: A:0.35, C:0.10, G:0.10, T:0.44
Consensus pattern (141 bp):
AAATAAAAATTATTCTTAATTTTTTCAATATTTCTAATATTCCTATGGTTTTTCGTAGGGGTATA
AAAATCTTCAAAACTTTTGTATCTTTTTGGTTCTCCATTAAGGTACAAAATGAATTTTCTTAAAA
AAATAAAAATG
Found at i:4982066 original size:20 final size:20
Alignment explanation
Indices: 4982037--4982075 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4982027 ATCAATACAA
* *
4982037 TAAGTTAATGTATTGATACG
1 TAAGTGAATGTATCGATACG
4982057 TAAGTGAATGTATCGATAC
1 TAAGTGAATGTATCGATAC
4982076 ATGCTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.36, C:0.08, G:0.21, T:0.36
Consensus pattern (20 bp):
TAAGTGAATGTATCGATACG
Found at i:4988469 original size:28 final size:26
Alignment explanation
Indices: 4988417--4988469 Score: 61
Period size: 28 Copynumber: 2.0 Consensus size: 26
4988407 CTGAATTCTT
* * *
4988417 CATCTTTAGGGATAGTTCAATCCCAC
1 CATCTTTAGGGATACTCCAACCCCAC
4988443 CATCTTTGAAGGGATACTCCAACCCCA
1 CATCTTT--AGGGATACTCCAACCCCA
4988470 TTTTTACTTC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
26 7 0.32
28 15 0.68
ACGTcount: A:0.28, C:0.30, G:0.15, T:0.26
Consensus pattern (26 bp):
CATCTTTAGGGATACTCCAACCCCAC
Found at i:4988496 original size:134 final size:134
Alignment explanation
Indices: 4988276--4988517 Score: 351
Period size: 134 Copynumber: 1.8 Consensus size: 134
4988266 TAAAACATCA
* * * * *
4988276 AATTTTTCATCTCTCGGGATACTTTAACCCCACTATCTCTAAAGGGATACTCCAACCCTATTTTT
1 AATTCTTCATCTCTAGGGATACTTCAACCCCACCATCTCTAAAGGGATACTCCAACCCCATTTTT
* *
4988341 ACTTCTGAAACATCAAATTTTTCATCTCTGGGGATACTCCAACCTCATTTTTTTACTTCCATAAT
66 ACTTCTAAAACATCAAATTTTTCATCTCTGGGGAAACTCCAACCTCATTTTTTTACTTCCATAAT
4988406 ACTG
131 ACTG
* * * * *
4988410 AATTCTTCATCTTTAGGGATAGTTCAATCCCACCATCTTTGAAGGGATACTCCAACCCCATTTTT
1 AATTCTTCATCTCTAGGGATACTTCAACCCCACCATCTCTAAAGGGATACTCCAACCCCATTTTT
*
4988475 ACTTCTAAAACA-CTGAATTTTTCATCTCTGGGGAAACTCCAAC
66 ACTTCTAAAACATC-AAATTTTTCATCTCTGGGGAAACTCCAAC
4988518 TCCACCATCT
Statistics
Matches: 94, Mismatches: 13, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
133 1 0.01
134 93 0.99
ACGTcount: A:0.28, C:0.26, G:0.10, T:0.36
Consensus pattern (134 bp):
AATTCTTCATCTCTAGGGATACTTCAACCCCACCATCTCTAAAGGGATACTCCAACCCCATTTTT
ACTTCTAAAACATCAAATTTTTCATCTCTGGGGAAACTCCAACCTCATTTTTTTACTTCCATAAT
ACTG
Found at i:4988523 original size:80 final size:80
Alignment explanation
Indices: 4988371--4988598 Score: 226
Period size: 80 Copynumber: 2.8 Consensus size: 80
4988361 TTCATCTCTG
* * * * * * *
4988371 GGGATACTCCAACCTCATTTTTTTACTTCCATAATACTGAATTCTTCATCTTTAGGGATAGTTCA
1 GGGATACTCCAACCCCA--TTTTTACTTCCAAAACACTGAATTCTTCATCTCTAGGGAAACTCCA
*
4988436 ATCCCACCATCTTTGAA
64 ATCCCACCATCTTCGAA
* * *
4988453 GGGATACTCCAACCCCATTTTTACTTCTAAAACACTGAATTTTTCATCTCTGGGGAAACTCCAA-
1 GGGATACTCCAACCCCATTTTTACTTCCAAAACACTGAATTCTTCATCTCTAGGGAAACTCCAAT
4988517 CTCCACCATCTTCGAA
66 C-CCACCATCTTCGAA
* * * * * * * * *
4988533 GGGATACTCTAACCCTATTTTTATTTTCAAAACA-TCAAATTTTTGATCTCTAGGGATACTCTAA
1 GGGATACTCCAACCCCATTTTTACTTCCAAAACACT-GAATTCTTCATCTCTAGGGAAACTCCAA
4988597 TC
65 TC
4988599 GCATTTTTTA
Statistics
Matches: 122, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
79 2 0.02
80 103 0.84
81 1 0.01
82 16 0.13
ACGTcount: A:0.29, C:0.25, G:0.11, T:0.36
Consensus pattern (80 bp):
GGGATACTCCAACCCCATTTTTACTTCCAAAACACTGAATTCTTCATCTCTAGGGAAACTCCAAT
CCCACCATCTTCGAA
Found at i:4989620 original size:20 final size:19
Alignment explanation
Indices: 4989577--4989627 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
4989567 ACCCTTGAAA
*
4989577 GTATCAATACACACTAGAT
1 GTATCAATACATACTAGAT
* *
4989596 GTATCAATACATATTAGTTT
1 GTATCAATACATACTAG-AT
*
4989616 GTATCGATACAT
1 GTATCAATACAT
4989628 TGTATCGATA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (19 bp):
GTATCAATACATACTAGAT
Found at i:4989632 original size:13 final size:13
Alignment explanation
Indices: 4989614--4989640 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4989604 ACATATTAGT
4989614 TTGTATCGATACA
1 TTGTATCGATACA
4989627 TTGTATCGATACA
1 TTGTATCGATACA
4989640 T
1 T
4989641 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:4997652 original size:20 final size:20
Alignment explanation
Indices: 4997627--4997667 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4997617 TGATACAATA
4997627 AGTGAATGTATCAATACATG
1 AGTGAATGTATCAATACATG
*
4997647 AGTGAATGTATCGATACATG
1 AGTGAATGTATCAATACATG
4997667 A
1 A
4997668 TCGATACAAG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.39, C:0.10, G:0.22, T:0.29
Consensus pattern (20 bp):
AGTGAATGTATCAATACATG
Found at i:4997814 original size:51 final size:51
Alignment explanation
Indices: 4997734--4997892 Score: 273
Period size: 51 Copynumber: 3.1 Consensus size: 51
4997724 ACATTTCTAT
* *
4997734 TGTATCGATACATTCTGAGTTTTTGACCCAAATGTATGGATACATTATTCAA
1 TGTATCGATACATTCTG-GGTTTTGACCCAAATGTATCGATACATTATTCAA
*
4997786 TGTATCGATACATTCTGGGTTTTGACCCAAATGTATCGATACATTATTCAG
1 TGTATCGATACATTCTGGGTTTTGACCCAAATGTATCGATACATTATTCAA
*
4997837 TGTATCGATACATTCTGGGTTTTGACCCAAATGTATCGATACATTCTTCAA
1 TGTATCGATACATTCTGGGTTTTGACCCAAATGTATCGATACATTATTCAA
4997888 TGTAT
1 TGTAT
4997893 TAATAAATGT
Statistics
Matches: 102, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
51 85 0.83
52 17 0.17
ACGTcount: A:0.28, C:0.17, G:0.16, T:0.38
Consensus pattern (51 bp):
TGTATCGATACATTCTGGGTTTTGACCCAAATGTATCGATACATTATTCAA
Found at i:5000409 original size:82 final size:82
Alignment explanation
Indices: 5000267--5000670 Score: 340
Period size: 81 Copynumber: 5.0 Consensus size: 82
5000257 ACATTAAAGG
** * * * * * * * *
5000267 GGGATACTTTAACCCTTCTATTTCCGATGGGATACTCCAACCTCGTCTTCACTTCGAAAAAACTT
1 GGGATACTTTAACCCCACCATTTCCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAAACAT
*
5000332 TAAATTTTCCATCTTTA
66 CAAATTTTCCATCTTTA
* * **
5000349 GGGATACTTTAGCCCCACCATTTCCAAAGGGATACTCCAACCTTATCTTTATTTCC-AAAAACAT
1 GGGATACTTTAACCCCACCATTTCCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAAACAT
* *
5000413 CGAATTTTCCATCTTCA
66 CAAATTTTCCATCTTTA
* * * * * *
5000430 AGGATA-TTCTAACCTCACCAGTACTGAGGGGATACTCCAACCCCATCTTTATTTCCAAAAAA-A
1 GGGATACTT-TAACCCCACCATTTCCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAAACA
* *
5000493 TCAAAATTTCCAT-TTTCG
65 TCAAATTTTCCATCTTT-A
** * * * *
5000511 GGGATACTCCAACCCCACTATTTTC-AAGGGAATACTCTAACCCCATTTTTATTT-CAAAAAACA
1 GGGATACTTTAACCCCACCATTTCCGAAGGG-ATACTCCAACCCCATCTTTATTTCCAAAAAACA
* *
5000574 TCAAATTTTTCAGCTTTA
65 TCAAATTTTCCATCTTTA
* * * ** *
5000592 GGGATACTTCAATCCCACGATTTTTG-AGAGGATACTCCAACCCCATTTTTATTTCC--AAAACA
1 GGGATACTTTAACCCCACCATTTCCGAAG-GGATACTCCAACCCCATCTTTATTTCCAAAAAACA
* *
5000654 TCGAGTTTTCCATCTTT
65 TCAAATTTTCCATCTTT
5000671 GTGGTACTCC
Statistics
Matches: 258, Mismatches: 54, Indels: 22
0.77 0.16 0.07
Matches are distributed among these distances:
80 34 0.13
81 167 0.65
82 57 0.22
ACGTcount: A:0.30, C:0.26, G:0.11, T:0.33
Consensus pattern (82 bp):
GGGATACTTTAACCCCACCATTTCCGAAGGGATACTCCAACCCCATCTTTATTTCCAAAAAACAT
CAAATTTTCCATCTTTA
Found at i:5000715 original size:51 final size:53
Alignment explanation
Indices: 5000621--5000738 Score: 125
Period size: 52 Copynumber: 2.3 Consensus size: 53
5000611 ATTTTTGAGA
* * * ** *
5000621 GGATACTCCAACCCCATTTTTATTTCCAAAACATCG-AGTTTTCCATCTTTGT
1 GGATACTCCAACCCCATTTTTATTTCAAAAACATCGAAATTTCCCATCTACGG
* * *
5000673 GG-TACTCCAACCCCGTTTTTACTTTTAAAAATATC-AAATTTCCCATCTACGG
1 GGATACTCCAACCCCATTTTTA-TTTCAAAAACATCGAAATTTCCCATCTACGG
5000725 GGATACTCCAACCC
1 GGATACTCCAACCC
5000739 TACCATCTCC
Statistics
Matches: 54, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
51 18 0.33
52 25 0.46
53 11 0.20
ACGTcount: A:0.27, C:0.29, G:0.10, T:0.34
Consensus pattern (53 bp):
GGATACTCCAACCCCATTTTTATTTCAAAAACATCGAAATTTCCCATCTACGG
Found at i:5004351 original size:49 final size:49
Alignment explanation
Indices: 5004086--5004805 Score: 932
Period size: 49 Copynumber: 14.9 Consensus size: 49
5004076 AGATGAGAAA
*
5004086 AAGGATGCCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGG
1 AAGG-TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
5004137 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--
1 --AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
5004182 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
5004231 -GGGTGCCAATGTGCTGATTCAAGGCCAACTACATTGGACTTAAAGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
5004279 -AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
5004327 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * * *
5004376 AAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGGCTTAATGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
5004425 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGATTTAAAGATA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * * *
5004474 AAGGTGCCAATATGCTGATTCAAGGCTAGCTATATTGGACTTAATGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
*
5004523 AAGGTGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G
* *
5004573 AAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--
1 --AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* *
5004618 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * *
5004667 -GGGTGCCAATGTGCTGATTCAAGGCCAGCTACGTTGGACTTAAAGGTG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
5004715 -AGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
* * * * *
5004763 AAGGTGCTAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
5004806 GAAGGGTTGC
Statistics
Matches: 589, Mismatches: 61, Indels: 38
0.86 0.09 0.06
Matches are distributed among these distances:
43 78 0.13
48 184 0.31
49 248 0.42
50 1 0.00
52 74 0.13
53 4 0.01
ACGTcount: A:0.29, C:0.18, G:0.28, T:0.26
Consensus pattern (49 bp):
AAGGTGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATG
Found at i:5004849 original size:33 final size:33
Alignment explanation
Indices: 5004805--5004876 Score: 110
Period size: 33 Copynumber: 2.2 Consensus size: 33
5004795 TATTGGGCTT
*
5004805 AGAAGGGTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
* *
5004838 AGAATGGTTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
5004871 A-AAGGG
1 AGAAGGG
5004877 AAAAAGAGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
32 4 0.11
33 31 0.89
ACGTcount: A:0.21, C:0.17, G:0.36, T:0.26
Consensus pattern (33 bp):
AGAAGGGTTGCCACCAACTTGTGTGGGCTTTAG
Found at i:5004959 original size:34 final size:34
Alignment explanation
Indices: 5004859--5005009 Score: 207
Period size: 32 Copynumber: 4.4 Consensus size: 34
5004849 CACCAACTTG
* *
5004859 TGTGGGCTTTGGAAAGGGAAAAAGAGTGCCACAGAGT
1 TGTGGGCTTT-GAAA-AGAAAAAG-GTGCCACGGAGT
*
5004896 TGTGGGCTTTAAAAAGAAAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAG-AAAAAGGTGCCACGGAGT
*
5004931 TGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
*
5004965 TGTGGGCTTT--AAAGGAAAAGGTGCCACGGAGT
1 TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
5004997 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
5005010 GAAAAAATGC
Statistics
Matches: 104, Mismatches: 7, Indels: 9
0.87 0.06 0.08
Matches are distributed among these distances:
32 30 0.29
34 28 0.27
35 27 0.26
36 9 0.09
37 10 0.10
ACGTcount: A:0.30, C:0.11, G:0.36, T:0.22
Consensus pattern (34 bp):
TGTGGGCTTTGAAAAGAAAAAGGTGCCACGGAGT
Found at i:5005003 original size:66 final size:70
Alignment explanation
Indices: 5004859--5005016 Score: 220
Period size: 66 Copynumber: 2.3 Consensus size: 70
5004849 CACCAACTTG
*
5004859 TGTGGGCTTTGGAAAGGGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCC
1 TGTGGGCTTT-GAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAAGGTGCC
5004924 ACGGAGT
64 ACGGAGT
* * *
5004931 TGTGGGCTTTGAAA-AGAAGAAG-GTGCCACGGAGTTGTGGGCTTT-AAAG-GAAAAGGTGCCAC
1 TGTGGGCTTTGAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGGTGCCAC
5004992 GGAGT
66 GGAGT
5004997 TGTGGGCTTTG-AAGA-AAAAA
1 TGTGGGCTTTGAAAGAGAAAAA
5005017 TGCCACTGAG
Statistics
Matches: 80, Mismatches: 5, Indels: 9
0.85 0.05 0.10
Matches are distributed among these distances:
65 6 0.08
66 29 0.36
67 4 0.05
69 21 0.26
70 6 0.08
71 4 0.05
72 10 0.12
ACGTcount: A:0.33, C:0.11, G:0.35, T:0.21
Consensus pattern (70 bp):
TGTGGGCTTTGAAAGAGAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAAGGTGCCAC
GGAGT
Found at i:5005077 original size:93 final size:93
Alignment explanation
Indices: 5004876--5005164 Score: 294
Period size: 93 Copynumber: 3.0 Consensus size: 93
5004866 TTTGGAAAGG
* * * *
5004876 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAAGGTGCCACGGAGTTGTGGGCTTT
1 GAAAAAG-GTGCCACAGAGTTGTGGGCTTT--GAAGAAAAAA--TGCCACTGAGTCGTGGACTTT
* * * *
5004941 GAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
61 G-AGA-AAGAA--TGCCACTGAGTCGTGGACTTTAAA
* * *
5004978 GGAAAAGGTGCCACGGAGTTGTGGGCTTTGAAGAAAAAATGCCACTGAGTCGTGGATTTTGAGAC
1 GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGAGA-
5005043 AA-AATGCCACTGAGTCGTGGACTTTAAA
65 AAGAATGCCACTGAGTCGTGGACTTTAAA
* * * * * *
5005071 GAAAAAGATGCCACTGAGTCGTGGACTTTG-AGAAGAGATTGCCACTGAGTCGTGGACTTTGAGA
1 GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAA-AAAATGCCACTGAGTCGTGGACTTTGAGA
*
5005135 AGAGATTGCCACTGAGTCGTGGACTTTAAA
65 A-AGAATGCCACTGAGTCGTGGACTTTAAA
5005165 AAGGTATTTG
Statistics
Matches: 163, Mismatches: 21, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
92 5 0.03
93 73 0.45
94 25 0.15
95 2 0.01
96 4 0.02
97 18 0.11
99 9 0.06
101 21 0.13
102 6 0.04
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (93 bp):
GAAAAAGGTGCCACAGAGTTGTGGGCTTTGAAGAAAAAATGCCACTGAGTCGTGGACTTTGAGAA
AGAATGCCACTGAGTCGTGGACTTTAAA
Found at i:5005087 original size:32 final size:32
Alignment explanation
Indices: 5004876--5005164 Score: 232
Period size: 31 Copynumber: 9.0 Consensus size: 32
5004866 TTTGGAAAGG
* * *
5004876 GAAAAAGAGTGCCACAGAGTTGTGGGCTTTAAAAA
1 GAAAAAGA-TGCCACTGAGTCGTGGACTTT--AAA
* * * *
5004911 GAAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 G-AAAAAGATGCCACTGAGTCGTGGACTTT--AAA
* * * * *
5004946 GAAGAAGGTGCCACGGAGTTGTGGGCTTTAAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAAA
* * * * * *
5004978 GGAAAAGGTGCCACGGAGTTGTGGGCTTTGAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAAA
**
5005010 GAAAAA-ATGCCACTGAGTCGTGGA-TTTTGA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAAA
*
5005040 GACAAA-ATGCCACTGAGTCGTGGACTTTAAA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAAA
*
5005071 GAAAAAGATGCCACTGAGTCGTGGACTTT-GA
1 GAAAAAGATGCCACTGAGTCGTGGACTTTAAA
* *
5005102 G-AAGAGATTGCCACTGAGTCGTGGACTTT-GA
1 GAAAAAGA-TGCCACTGAGTCGTGGACTTTAAA
*
5005133 G-AAGAGATTGCCACTGAGTCGTGGACTTTAAA
1 GAAAAAGA-TGCCACTGAGTCGTGGACTTTAAA
5005165 AAGGTATTTG
Statistics
Matches: 228, Mismatches: 21, Indels: 13
0.87 0.08 0.05
Matches are distributed among these distances:
30 32 0.14
31 77 0.34
32 60 0.26
34 27 0.12
35 26 0.11
36 6 0.03
ACGTcount: A:0.32, C:0.14, G:0.31, T:0.23
Consensus pattern (32 bp):
GAAAAAGATGCCACTGAGTCGTGGACTTTAAA
Found at i:5005297 original size:16 final size:17
Alignment explanation
Indices: 5005266--5005303 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
5005256 GATGCAAATA
* *
5005266 ATGATGTTATTGATGTT
1 ATGATGTCATTGATGTC
5005283 ATGATGTCA-TGATGTC
1 ATGATGTCATTGATGTC
5005299 ATGAT
1 ATGAT
5005304 TATAGCACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 11 0.58
17 8 0.42
ACGTcount: A:0.26, C:0.05, G:0.24, T:0.45
Consensus pattern (17 bp):
ATGATGTCATTGATGTC
Found at i:5006465 original size:1 final size:1
Alignment explanation
Indices: 5006459--5006538 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
5006449 ACCTTTGCAC
* * * * * * * * * * *
5006459 TTTTTTTTGTGTTTTTTTTGTTTTTTGTTTTTTGTGTTTTTTGTTTTTTTTGTGTGTTTTTTTTG
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
*
5006524 TTTGTTTTTTTTTTT
1 TTTTTTTTTTTTTTT
5006539 CATCACTTCT
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (1 bp):
T
Found at i:5006475 original size:9 final size:9
Alignment explanation
Indices: 5006461--5006519 Score: 77
Period size: 9 Copynumber: 6.7 Consensus size: 9
5006451 CTTTGCACTT
5006461 TTTTTTGTG
1 TTTTTTGTG
*
5006470 TTTTTTTTG
1 TTTTTTGTG
5006479 -TTTTT-TG
1 TTTTTTGTG
5006486 TTTTTTGTG
1 TTTTTTGTG
*
5006495 TTTTTTGTT
1 TTTTTTGTG
5006504 TTTTTTGTG
1 TTTTTTGTG
5006513 TGTTTTT
1 T-TTTTT
5006520 TTTGTTTGTT
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
7 2 0.05
8 10 0.23
9 27 0.61
10 5 0.11
ACGTcount: A:0.00, C:0.00, G:0.17, T:0.83
Consensus pattern (9 bp):
TTTTTTGTG
Found at i:5006525 original size:9 final size:9
Alignment explanation
Indices: 5006459--5006538 Score: 76
Period size: 9 Copynumber: 8.7 Consensus size: 9
5006449 ACCTTTGCAC
5006459 TTTTTTTTG
1 TTTTTTTTG
5006468 TGTTTTTTT-
1 T-TTTTTTTG
*
5006477 TGTTTTTTG
1 TTTTTTTTG
*
5006486 TTTTTTGTG
1 TTTTTTTTG
5006495 TTTTTTGTT-
1 TTTTTT-TTG
5006504 TTTTTTGTGTG
1 TTTTTT-T-TG
5006515 TTTTTTTTG
1 TTTTTTTTG
5006524 TTTGTTTTT-
1 TTT-TTTTTG
5006533 TTTTTT
1 TTTTTT
5006539 CATCACTTCT
Statistics
Matches: 61, Mismatches: 4, Indels: 13
0.78 0.05 0.17
Matches are distributed among these distances:
8 9 0.15
9 31 0.51
10 15 0.25
11 6 0.10
ACGTcount: A:0.00, C:0.00, G:0.15, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:5006537 original size:16 final size:16
Alignment explanation
Indices: 5006462--5006538 Score: 95
Period size: 16 Copynumber: 4.8 Consensus size: 16
5006452 TTTGCACTTT
5006462 TTTTTGTGTTTTTTTTG
1 TTTTT-TGTTTTTTTTG
*
5006479 TTTTTTGTTTTTTGTG
1 TTTTTTGTTTTTTTTG
5006495 TTTTTTGTTTTTTTTG
1 TTTTTTGTTTTTTTTG
*
5006511 TGTGTTTT-TTTTGTTTG
1 T-T-TTTTGTTTTTTTTG
5006528 TTTTTT-TTTTT
1 TTTTTTGTTTTT
5006539 CATCACTTCT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
15 8 0.15
16 27 0.50
17 15 0.28
18 4 0.07
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (16 bp):
TTTTTTGTTTTTTTTG
Found at i:5013533 original size:52 final size:52
Alignment explanation
Indices: 5013453--5013572 Score: 213
Period size: 52 Copynumber: 2.3 Consensus size: 52
5013443 AAAAGTTACT
* *
5013453 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
*
5013505 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
5013557 TGCATGTATCGATACA
1 TGCATGTATCGATACA
5013573 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.35
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGCC
Found at i:5013585 original size:52 final size:52
Alignment explanation
Indices: 5013453--5013592 Score: 185
Period size: 52 Copynumber: 2.7 Consensus size: 52
5013443 AAAAGTTACT
* *
5013453 TGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAGATTTGCC
1 TGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*** *
5013505 TGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
*
5013557 TGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 TGCATGTATCGATACATAAGAT-AGTGTATCGATACA
5013593 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.29, C:0.17, G:0.20, T:0.34
Consensus pattern (52 bp):
TGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGCC
Found at i:5013599 original size:13 final size:13
Alignment explanation
Indices: 5013581--5013605 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5013571 CAAAGATCGG
5013581 TGTATCGATACAA
1 TGTATCGATACAA
5013594 TGTATCGATACA
1 TGTATCGATACA
5013606 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5013683 original size:33 final size:33
Alignment explanation
Indices: 5013646--5013712 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
5013636 AGTAGCTTAA
5013646 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
5013679 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
5013712 A
1 A
5013713 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:5013686 original size:13 final size:13
Alignment explanation
Indices: 5013668--5013692 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5013658 CAAAAAAATA
5013668 TGTATCGATACAT
1 TGTATCGATACAT
5013681 TGTATCGATACA
1 TGTATCGATACA
5013693 ACATTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5014704 original size:13 final size:13
Alignment explanation
Indices: 5014686--5014711 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5014676 ATATTTTGGG
5014686 ATGTATCGATACA
1 ATGTATCGATACA
5014699 ATGTATCGATACA
1 ATGTATCGATACA
5014712 TATTGTGTAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5014828 original size:13 final size:13
Alignment explanation
Indices: 5014810--5014834 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5014800 ACATTTGGTC
5014810 ATGTATCGATACA
1 ATGTATCGATACA
5014823 ATGTATCGATAC
1 ATGTATCGATAC
5014835 TGTGCAATCT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:5015423 original size:22 final size:22
Alignment explanation
Indices: 5015396--5015440 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 22
5015386 TTTTCTTTTC
*
5015396 TCTCCCCTTTAATCAAAA-AATT
1 TCTCCCCCTTAAT-AAAATAATT
5015418 TCTCCCCCTTAATAAAATAATT
1 TCTCCCCCTTAATAAAATAATT
5015440 T
1 T
5015441 AACAATTTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 17 0.81
ACGTcount: A:0.36, C:0.27, G:0.00, T:0.38
Consensus pattern (22 bp):
TCTCCCCCTTAATAAAATAATT
Found at i:5017317 original size:13 final size:13
Alignment explanation
Indices: 5017299--5017337 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
5017289 ATAAACCCTT
*
5017299 TGTATCGATACAC
1 TGTATCGATACAA
*
5017312 TGTATCAATACAA
1 TGTATCGATACAA
5017325 TGTATCGATACAA
1 TGTATCGATACAA
5017338 AGAATGCTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.38, C:0.18, G:0.13, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5031966 original size:20 final size:22
Alignment explanation
Indices: 5031926--5031967 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
5031916 ATTTTGGAAA
*
5031926 TAAAAAGAGGGAGAGATATTTT
1 TAAAAAGAGGGAGAGAAATTTT
5031948 TAAAAAG-GGGA-AGAAATTTT
1 TAAAAAGAGGGAGAGAAATTTT
5031968 ATTAAGAGGG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 8 0.42
21 4 0.21
22 7 0.37
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.26
Consensus pattern (22 bp):
TAAAAAGAGGGAGAGAAATTTT
Found at i:5031972 original size:22 final size:22
Alignment explanation
Indices: 5031926--5031972 Score: 53
Period size: 22 Copynumber: 2.1 Consensus size: 22
5031916 ATTTTGGAAA
*
5031926 TAAAAAGAGGGAGAGATATTTT
1 TAAAAAGAGGGAGAAATATTTT
5031948 TAAAAAG-GGGAAGAAAT-TTTAT
1 TAAAAAGAGGG-AGAAATATTT-T
5031970 TAA
1 TAA
5031973 GAGGGACAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 6 0.27
22 16 0.73
ACGTcount: A:0.49, C:0.00, G:0.23, T:0.28
Consensus pattern (22 bp):
TAAAAAGAGGGAGAAATATTTT
Found at i:5039954 original size:20 final size:19
Alignment explanation
Indices: 5039884--5039964 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 19
5039874 TGAAAAAACC
* * *
5039884 AGAAGGTATCGATACAATG
1 AGAATGTATCGATACATTT
*
5039903 AGAAATGTATTGATACAATTGT
1 AG-AATGTATCGATAC-ATT-T
*
5039925 AAGCATGTATCGATACATTT
1 -AGAATGTATCGATACATTT
5039945 AGTAATGTATCGATACATTT
1 AG-AATGTATCGATACATTT
5039965 TCTTGGTAGT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
19 4 0.08
20 28 0.56
21 5 0.10
22 11 0.22
23 2 0.04
ACGTcount: A:0.38, C:0.10, G:0.19, T:0.33
Consensus pattern (19 bp):
AGAATGTATCGATACATTT
Found at i:5047234 original size:51 final size:52
Alignment explanation
Indices: 5047128--5047254 Score: 175
Period size: 51 Copynumber: 2.5 Consensus size: 52
5047118 AAAATATGAC
* **
5047128 AATTTTCCTGCATGTATTAATACATTTTATAGTGTATCGATAAATCTAGGCA
1 AATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATAAATCTAGGCA
* ** * *
5047180 AATTTGCCTGCACGTATCGATACATTTTA-AGTGTATTTATACATCTGGGCA
1 AATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATAAATCTAGGCA
5047231 AATTTGCCTGCATGTATCGATACA
1 AATTTGCCTGCATGTATCGATACA
5047255 AAGATTAGTG
Statistics
Matches: 66, Mismatches: 9, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
51 41 0.62
52 25 0.38
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.38
Consensus pattern (52 bp):
AATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATAAATCTAGGCA
Found at i:5047281 original size:13 final size:13
Alignment explanation
Indices: 5047263--5047287 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5047253 CAAAGATTAG
5047263 TGTATCGATACAA
1 TGTATCGATACAA
5047276 TGTATCGATACA
1 TGTATCGATACA
5047288 TTTGAGTAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:5047355 original size:19 final size:18
Alignment explanation
Indices: 5047331--5047428 Score: 81
Period size: 19 Copynumber: 5.8 Consensus size: 18
5047321 TAGCTTAAAT
5047331 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
5047350 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
5047363 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
*
5047382 TGTATCAATAC--A--T-
1 TGTATCGATACAAACTTA
5047395 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
5047415 TGTATCGATACAAA
1 TGTATCGATACAAA
5047429 TCGTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 26
0.70 0.02 0.28
Matches are distributed among these distances:
13 21 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 23 0.36
20 13 0.20
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:5047368 original size:13 final size:13
Alignment explanation
Indices: 5047350--5047406 Score: 51
Period size: 13 Copynumber: 3.9 Consensus size: 13
5047340 ACAAAACTTA
5047350 TGTATCGATACAT
1 TGTATCGATACAT
5047363 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
*
5047381 ATGTATCAATACAT
1 -TGTATCGATACAT
5047395 TGTATCGATACA
1 TGTATCGATACA
5047407 ACACTTTATG
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
13 20 0.56
14 1 0.03
16 6 0.17
18 1 0.03
19 8 0.22
ACGTcount: A:0.35, C:0.18, G:0.12, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:5047370 original size:32 final size:32
Alignment explanation
Indices: 5047329--5047426 Score: 169
Period size: 32 Copynumber: 3.0 Consensus size: 32
5047319 AGTAGCTTAA
*
5047329 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
*
5047361 ATTGTATCGATACAACACTTATGTATCAATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
5047393 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
5047426 A
1 A
5047427 AATCGTTGAA
Statistics
Matches: 62, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
32 48 0.77
33 14 0.23
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:5056399 original size:20 final size:20
Alignment explanation
Indices: 5056373--5056427 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
5056363 ATTTTTTTTA
5056373 CAATGTATCGATACATGTAT
1 CAATGTATCGATACATGTAT
* * *
5056393 GAATGTATCGATACATTTTT
1 CAATGTATCGATACATGTAT
5056413 CAATGTATC-ATACAT
1 CAATGTATCGATACAT
5056428 TTTGTTTTTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.38
Consensus pattern (20 bp):
CAATGTATCGATACATGTAT
Found at i:5057384 original size:19 final size:19
Alignment explanation
Indices: 5057352--5057388 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5057342 TAGCCTTTTG
5057352 TCATGAATTCTAATATGTT
1 TCATGAATTCTAATATGTT
* *
5057371 TCATGCATTTTAATATGT
1 TCATGAATTCTAATATGT
5057389 CCAACATCTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.49
Consensus pattern (19 bp):
TCATGAATTCTAATATGTT
Found at i:5076953 original size:19 final size:19
Alignment explanation
Indices: 5076931--5076967 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5076921 GAGATGTTGG
*
5076931 ACATATTAAAATGCATGAA
1 ACATAGTAAAATGCATGAA
*
5076950 ACATAGTAGAATGCATGA
1 ACATAGTAAAATGCATGA
5076968 TCAAAGGCTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.49, C:0.11, G:0.16, T:0.24
Consensus pattern (19 bp):
ACATAGTAAAATGCATGAA
Found at i:5079305 original size:65 final size:63
Alignment explanation
Indices: 5079231--5079454 Score: 193
Period size: 62 Copynumber: 3.5 Consensus size: 63
5079221 TGATGCTTTT
* * * * * *
5079231 TTTTCTAAAGCCCACAAAAGTTGGTAGCACCTTTTAGTCCTCAAAGAGTAGGATACCTTTTTCTT
1 TTTT-TAAAGCCCACACAAGTTGGTGGCACCTTTTAATCCTAAAAGAGCAGGAT--CTATTTCTT
5079296 C
63 C
* * * * * *
5079297 TTTTTAAAGCTCATACAAGTTGGTGGTACCTTTTAATCCAAAAAAAGCAAGATGC-ATTT-TTC
1 TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAATCCTAAAAGAGCAGGAT-CTATTTCTTC
* * * * * *
5079359 TTTTTAAAGCCTACACAAGCTGGTGGCACCTTTTACTCCTTAAAGAGCAGGATGTCTTTC-TC
1 TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAATCCTAAAAGAGCAGGATCTATTTCTTC
* * **
5079421 TTTTCAAAGCCCACACAAGCTACTGGCACCTTTT
1 TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTT
5079455 TCCCTTTTCT
Statistics
Matches: 127, Mismatches: 29, Indels: 8
0.77 0.18 0.05
Matches are distributed among these distances:
62 81 0.64
63 3 0.02
64 1 0.01
65 38 0.30
66 4 0.03
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (63 bp):
TTTTTAAAGCCCACACAAGTTGGTGGCACCTTTTAATCCTAAAAGAGCAGGATCTATTTCTTC
Found at i:5080159 original size:21 final size:21
Alignment explanation
Indices: 5080135--5080229 Score: 129
Period size: 21 Copynumber: 4.6 Consensus size: 21
5080125 TTCTAGAATT
5080135 TGTATCGATACAATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
5080156 TGTATCGATGCAATAAGTGAA
1 TGTATCGATACAATAAGTGAA
*
5080177 TGTATCGATGCAATAAGTGAA
1 TGTATCGATACAATAAGTGAA
* * *
5080198 TATATCGATAC-ATGAGTGGA
1 TGTATCGATACAATAAGTGAA
*
5080218 TGTATCAATACA
1 TGTATCGATACA
5080230 TGTCTAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.24
21 50 0.76
ACGTcount: A:0.39, C:0.11, G:0.21, T:0.29
Consensus pattern (21 bp):
TGTATCGATACAATAAGTGAA
Found at i:5080342 original size:51 final size:50
Alignment explanation
Indices: 5080287--5080406 Score: 159
Period size: 51 Copynumber: 2.4 Consensus size: 50
5080277 TCTGGAAGGA
*
5080287 AAATGTATCGATACATTTCTATTATATCAATACATTATGGGTTTTTGACCC
1 AAATGTATCGATACATTTCCATTATATCAATACATTATGGG-TTTTGACCC
* * * * *
5080338 AAATGTATCAATACATGATCCATTGTATCGATACATTTTGGGTTTTGACCC
1 AAATGTATCGATACAT-TTCCATTATATCAATACATTATGGGTTTTGACCC
*
5080389 AAATGTATCGATGCATTT
1 AAATGTATCGATACATTT
5080407 TCAATGTATC
Statistics
Matches: 59, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
50 1 0.02
51 38 0.64
52 20 0.34
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (50 bp):
AAATGTATCGATACATTTCCATTATATCAATACATTATGGGTTTTGACCC
Found at i:5083143 original size:20 final size:21
Alignment explanation
Indices: 5083118--5083168 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
5083108 CGATACATTT
**
5083118 TATCGATACATGACCAA-ATG
1 TATCGATACATGAAAAAGATG
*
5083138 TATCGATACTTGAAAAAGATG
1 TATCGATACATGAAAAAGATG
5083159 TATCGATACA
1 TATCGATACA
5083169 GGTCATTGGC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 14 0.54
21 12 0.46
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.27
Consensus pattern (21 bp):
TATCGATACATGAAAAAGATG
Found at i:5083238 original size:13 final size:13
Alignment explanation
Indices: 5083220--5083244 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5083210 ACACACAATC
5083220 TGTATCGATACAT
1 TGTATCGATACAT
5083233 TGTATCGATACA
1 TGTATCGATACA
5083245 CCACAAAATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Done.