Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397260.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_51.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 10072460
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Warning! 70252 characters in sequence are not A, C, G, or T
File 18 of 20
Found at i:8213779 original size:15 final size:14
Alignment explanation
Indices: 8213717--8213776 Score: 52
Period size: 15 Copynumber: 4.2 Consensus size: 14
8213707 TAATTAATAT
*
8213717 GTTATAAAAACTAAA
1 GTTATATAAA-TAAA
* *
8213732 GTGATAATTAATAAA
1 GTTAT-ATAAATAAA
8213747 GTTAT-TAAATATAA
1 GTTATATAAATA-AA
8213761 -TTATATAAATAAA
1 GTTATATAAATAAA
8213774 GTT
1 GTT
8213777 TATCATAAGT
Statistics
Matches: 36, Mismatches: 5, Indels: 9
0.72 0.10 0.18
Matches are distributed among these distances:
13 11 0.31
14 10 0.28
15 12 0.33
16 3 0.08
ACGTcount: A:0.53, C:0.02, G:0.08, T:0.37
Consensus pattern (14 bp):
GTTATATAAATAAA
Found at i:8215377 original size:2 final size:2
Alignment explanation
Indices: 8215370--8215397 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8215360 TGTCTACGAG
8215370 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8215398 ACAAAGTTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8228384 original size:21 final size:19
Alignment explanation
Indices: 8228358--8228408 Score: 52
Period size: 18 Copynumber: 2.7 Consensus size: 19
8228348 TATGATATAA
8228358 AATAATATATAAATTTTAATT
1 AATAATATATAAA--TTAATT
*
8228379 AATAATA-ATTAATTAATT
1 AATAATATATAAATTAATT
*
8228397 ATTAAT-TATAAA
1 AATAATATATAAA
8228409 AATTTATATA
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 15 0.58
20 4 0.15
21 7 0.27
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
AATAATATATAAATTAATT
Found at i:8228420 original size:25 final size:25
Alignment explanation
Indices: 8228363--8228433 Score: 71
Period size: 24 Copynumber: 3.0 Consensus size: 25
8228353 TATAAAATAA
*
8228363 TATATAAATTTTAATTAATAATAATT
1 TATAT-AATTTTAATTAATAAAAATT
*
8228389 AAT-TAATTATTAATT-ATAAAAATT
1 TATATAATT-TTAATTAATAAAAATT
8228413 TATATAA-TTTAA--AATAAAAAT
1 TATATAATTTTAATTAATAAAAAT
8228434 ATGATGATTA
Statistics
Matches: 39, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
22 8 0.21
23 4 0.10
24 15 0.38
25 10 0.26
26 2 0.05
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (25 bp):
TATATAATTTTAATTAATAAAAATT
Found at i:8252946 original size:13 final size:14
Alignment explanation
Indices: 8252922--8252950 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
8252912 TTGGTTATTT
8252922 TTTTAGTATTTATC
1 TTTTAGTATTTATC
8252936 TTTTA-TATTTATC
1 TTTTAGTATTTATC
8252949 TT
1 TT
8252951 AAATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.21, C:0.07, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTTAGTATTTATC
Found at i:8282090 original size:3 final size:3
Alignment explanation
Indices: 8282084--8282121 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
8282074 ATCATCACTG
8282084 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
8282122 CAGGATTTGC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:8293451 original size:15 final size:15
Alignment explanation
Indices: 8293431--8293464 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
8293421 TTTAAATTTA
8293431 AATTAATTATATATT
1 AATTAATTATATATT
8293446 AATTAATTATATATT
1 AATTAATTATATATT
8293461 AATT
1 AATT
8293465 GTATCGATAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
AATTAATTATATATT
Found at i:8294247 original size:378 final size:374
Alignment explanation
Indices: 8293646--8294397 Score: 1378
Period size: 378 Copynumber: 2.0 Consensus size: 374
8293636 ATATAAATAG
8293646 TAATATTTTTATGATAATTAAGATTTATCAATATTAAATTTTATCATATTTGCTAAATATTATTA
1 TAATATTTTTATGATAATTAAGATTTATCAATATTAAATTTTATCATATTTGCTAAATATTATTA
* *
8293711 TGTTTATAATTTCTTATTCTAAATTTGAATAATAAAATTATATTTTATTTATACATATTCTAATT
66 TGTTTATAATTGCTTATTCTAAATTTGAATAATAAAACTATATTTTATTTATACATATTCTAATT
*
8293776 TTATTGTATTAATCATGTAAATAGTTTATAAATTGTATAAATTTTAATCATATTAATTTTATCAT
131 TTATTGTATCAATCATGTAAATAGTTTATAAATTGTATAAATTTTAATCATATTAATTTTATCAT
**
8293841 TTCATATAAAATTTAATATGTCATGTTTAATAAATGTATTTTTTTGAAAAATACGTTTAATAAAT
196 TTCATATAAAATTTAATATGTCATGTTTAATAAATGT-TTTTTTT---AAATACACTTAATAAAT
8293906 ATATTAATTATGTCATATAGTGTTACATGTTTATTAAATATATATGTATATGTGTTTAAGATTCA
257 ATATTAATTATGTCATATAGTGTTACATGTTTATTAAATATATATGTATATGTGTTTAAGATTCA
*
8293971 GACAAAAATTAATTAATTATGTCATGTCCATTTTTTCTTATATAACTATTAAT
322 GACAAAAATTAATTAATTATGTCATGTCCATTTTTTCTCATATAACTATTAAT
8294024 TAATATTTTTATGATAATTAAGATTTATCAATATTAAATTTTATCATATTTGCTAAATATTATTA
1 TAATATTTTTATGATAATTAAGATTTATCAATATTAAATTTTATCATATTTGCTAAATATTATTA
8294089 TGTTTATAATTGCTTATTCTAAATTTGAATAATAAAACTATATTTTATTTATACATATTCTAATT
66 TGTTTATAATTGCTTATTCTAAATTTGAATAATAAAACTATATTTTATTTATACATATTCTAATT
8294154 TTATTGTATCAATCATGTAAATAGTTTATAAATTGTATAAATTTTAATCATATTAATTTTATCAT
131 TTATTGTATCAATCATGTAAATAGTTTATAAATTGTATAAATTTTAATCATATTAATTTTATCAT
*
8294219 TTCATATAAAATTTAATATGTCATGTTTAATAAATGTTTTTTTTAAATACACTTAATAAATGTAT
196 TTCATATAAAATTTAATATGTCATGTTTAATAAATGTTTTTTTTAAATACACTTAATAAATATAT
*
8294284 TAATTATGTCATATAGTGTTACATGTTTATTAAATATATATGTGTATGTGTTTAAGATTCAGACA
261 TAATTATGTCATATAGTGTTACATGTTTATTAAATATATATGTATATGTGTTTAAGATTCAGACA
* *
8294349 GAAATTAATTAATTATGTCATGTCCGTTTTTTCTCATATAACTATTAAT
326 AAAATTAATTAATTATGTCATGTCCATTTTTTCTCATATAACTATTAAT
8294398 ACTCTATATT
Statistics
Matches: 364, Mismatches: 10, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
374 128 0.35
377 7 0.02
378 229 0.63
ACGTcount: A:0.38, C:0.06, G:0.07, T:0.49
Consensus pattern (374 bp):
TAATATTTTTATGATAATTAAGATTTATCAATATTAAATTTTATCATATTTGCTAAATATTATTA
TGTTTATAATTGCTTATTCTAAATTTGAATAATAAAACTATATTTTATTTATACATATTCTAATT
TTATTGTATCAATCATGTAAATAGTTTATAAATTGTATAAATTTTAATCATATTAATTTTATCAT
TTCATATAAAATTTAATATGTCATGTTTAATAAATGTTTTTTTTAAATACACTTAATAAATATAT
TAATTATGTCATATAGTGTTACATGTTTATTAAATATATATGTATATGTGTTTAAGATTCAGACA
AAAATTAATTAATTATGTCATGTCCATTTTTTCTCATATAACTATTAAT
Found at i:8294900 original size:32 final size:32
Alignment explanation
Indices: 8294850--8294922 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 32
8294840 TAATTTAGTG
* *
8294850 TATTTTCATTCATATTTGTT-GAAACATTTTAA
1 TATTTTTAATCATATTTGTTAG-AACATTTTAA
* *
8294882 TATTTTTAATCATGTTTGTTAGAATATTTTAA
1 TATTTTTAATCATATTTGTTAGAACATTTTAA
8294914 TATTATTTA
1 TATT-TTTA
8294923 CTTTAGGGTG
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
32 30 0.86
33 5 0.14
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (32 bp):
TATTTTTAATCATATTTGTTAGAACATTTTAA
Found at i:8299273 original size:24 final size:24
Alignment explanation
Indices: 8299241--8299290 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
8299231 AATTAGGGTT
8299241 CTTAAATCC-TGTATCTTCAGTAAG
1 CTTAAATCCGTG-ATCTTCAGTAAG
* *
8299265 CTTAAATCCGTGATTTTGAGTAAG
1 CTTAAATCCGTGATCTTCAGTAAG
8299289 CT
1 CT
8299291 AGCTAATCAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
24 21 0.91
25 2 0.09
ACGTcount: A:0.28, C:0.18, G:0.16, T:0.38
Consensus pattern (24 bp):
CTTAAATCCGTGATCTTCAGTAAG
Found at i:8312891 original size:49 final size:49
Alignment explanation
Indices: 8312720--8312974 Score: 353
Period size: 49 Copynumber: 5.2 Consensus size: 49
8312710 CCAGCCCGGC
* *
8312720 GGGCCGCA-GAGGGAATCGGGACTCGTGGGAGCCGGA-GGGGGCGGGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
* *
8312767 GCGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGTA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
*
8312816 GGG--GCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGAGGGGC-GACA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGG-GGGGCGGGCA
8312863 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGAGGGGC-GGCA
1 GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGG-GGGGCGGGCA
*
8312912 GGGCTGCAGGGGGGAACCGGGACTCGGCCGTGGGAGCCGGAGGGGGGCGGGCA
1 GGGCCGCAGGGGGGAACCGGGACT----CGTGGGAGCCGGAGGGGGGCGGGCA
8312965 GGG-CGCAGGG
1 GGGCCGCAGGG
8312975 CGAAAGGCGT
Statistics
Matches: 188, Mismatches: 10, Indels: 15
0.88 0.05 0.07
Matches are distributed among these distances:
47 46 0.24
48 31 0.16
49 78 0.41
52 11 0.06
53 22 0.12
ACGTcount: A:0.16, C:0.22, G:0.58, T:0.05
Consensus pattern (49 bp):
GGGCCGCAGGGGGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCA
Found at i:8312896 original size:96 final size:97
Alignment explanation
Indices: 8312730--8312974 Score: 356
Period size: 96 Copynumber: 2.5 Consensus size: 97
8312720 GGGCCGCAGA
* *
8312730 GGGAATCGGGACTCGTGGGAGCCGGA-GGGGGCGGGCAGCGCCGCAGGGGGGAACCGGGACTCGT
1 GGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGGCCGCAGGGGGGAACCGGGACTCGT
*
8312794 GGGAGCCGGAGG-GGGGCGGGTAGGG-GCAGGG
66 GGGAGCCGGAGGAGGGGC-GGCAGGGCGCAGGG
*
8312825 GGGAACCGGGACTCGTGGGAGCCGGAGGAGGGGC-GACAGGGCCGCAGGGGGGAACCGGGACTCG
1 GGGAACCGGGACTCGTGGGAGCCGGAGG-GGGGCGGGCAGGGCCGCAGGGGGGAACCGGGACTCG
8312889 TGGGAGCCGGAGGAGGGGCGGCAGGGCTGCAGGG
65 TGGGAGCCGGAGGAGGGGCGGCAGGGC-GCAGGG
8312923 GGGAACCGGGACTCGGCCGTGGGAGCCGGAGGGGGGCGGGCAGGG-CGCAGGG
1 GGGAACCGGGACT----CGTGGGAGCCGGAGGGGGGCGGGCAGGGCCGCAGGG
8312975 CGAAAGGCGT
Statistics
Matches: 135, Mismatches: 5, Indels: 14
0.88 0.03 0.09
Matches are distributed among these distances:
95 25 0.19
96 48 0.36
97 10 0.07
98 19 0.14
101 12 0.09
102 21 0.16
ACGTcount: A:0.16, C:0.21, G:0.58, T:0.05
Consensus pattern (97 bp):
GGGAACCGGGACTCGTGGGAGCCGGAGGGGGGCGGGCAGGGCCGCAGGGGGGAACCGGGACTCGT
GGGAGCCGGAGGAGGGGCGGCAGGGCGCAGGG
Found at i:8317147 original size:14 final size:14
Alignment explanation
Indices: 8317128--8317154 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
8317118 TTCTTTTAAT
8317128 AATATATTGTCAAC
1 AATATATTGTCAAC
8317142 AATATATTGTCAA
1 AATATATTGTCAA
8317155 AGACACTGAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.07, T:0.37
Consensus pattern (14 bp):
AATATATTGTCAAC
Found at i:8348839 original size:5 final size:5
Alignment explanation
Indices: 8348829--8348854 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
8348819 GAGAGATTTC
8348829 AGGCA AGGCA AGGCA AGGCA AGGCA A
1 AGGCA AGGCA AGGCA AGGCA AGGCA A
8348855 CTAATTTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.38, T:0.00
Consensus pattern (5 bp):
AGGCA
Found at i:8349971 original size:3 final size:3
Alignment explanation
Indices: 8349963--8349994 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
8349953 AGGAACGGTC
8349963 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
8349995 AAATGTACAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:8363680 original size:20 final size:21
Alignment explanation
Indices: 8363643--8363681 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
8363633 TAGAATTCGA
* *
8363643 TTTAATTTATTTTGTTATGAT
1 TTTAATTGATGTTGTTATGAT
8363664 TTTAATTGATGTT-TTATG
1 TTTAATTGATGTTGTTATG
8363682 TAAAAGATCT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.00, G:0.13, T:0.64
Consensus pattern (21 bp):
TTTAATTGATGTTGTTATGAT
Found at i:8366670 original size:18 final size:18
Alignment explanation
Indices: 8366616--8366677 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
8366606 CAAGAACTAC
*
8366616 AATTAAATCAATCAA-AAA
1 AATTAAATTAAT-AATAAA
* *
8366634 AATATAATTGTATTAATAAA
1 AAT-TAAAT-TAATAATAAA
8366654 AATTAAATTAATAATAAA
1 AATTAAATTAATAATAAA
8366672 ATATTA
1 A-ATTA
8366678 TTAATATATC
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
18 13 0.37
19 14 0.40
20 8 0.23
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTAAATTAATAATAAA
Found at i:8366708 original size:15 final size:15
Alignment explanation
Indices: 8366678--8366725 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
8366668 TAAAATATTA
*
8366678 TTAA-TATATCAATT
1 TTAATTATATTAATT
8366692 TTAACTTA-ATTAATT
1 TTAA-TTATATTAATT
*
8366707 TTAATTATTTTAATT
1 TTAATTATATTAATT
8366722 TTAA
1 TTAA
8366726 ATAGAATTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
14 7 0.24
15 20 0.69
16 2 0.07
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (15 bp):
TTAATTATATTAATT
Found at i:8366924 original size:19 final size:18
Alignment explanation
Indices: 8366885--8366945 Score: 61
Period size: 18 Copynumber: 3.3 Consensus size: 18
8366875 AAAGAACTAC
*
8366885 AATTAAATCAATCAA-AAA
1 AATTAAATTAAT-AATAAA
* *
8366903 AATTAATTGTATTAATAAA
1 AATTAAAT-TAATAATAAA
8366922 AATTAAATTAATAATAAA
1 AATTAAATTAATAATAAA
8366940 ATATTA
1 A-ATTA
8366946 TTAATATATC
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 19 0.54
19 16 0.46
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (18 bp):
AATTAAATTAATAATAAA
Found at i:8366948 original size:17 final size:17
Alignment explanation
Indices: 8366900--8366951 Score: 52
Period size: 19 Copynumber: 2.9 Consensus size: 17
8366890 AATCAATCAA
*
8366900 AAAAATTAATTGTATTAAT
1 AAAAATTAA-T-TAATAAT
8366919 AAAAATTAAATTAATAAT
1 AAAAATT-AATTAATAAT
8366937 AAAATATT-ATTAATA
1 AAAA-ATTAATTAATA
8366952 TATCAATTTT
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 7 0.23
18 10 0.33
19 11 0.37
20 2 0.07
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (17 bp):
AAAAATTAATTAATAAT
Found at i:8367990 original size:34 final size:34
Alignment explanation
Indices: 8367947--8368018 Score: 110
Period size: 34 Copynumber: 2.1 Consensus size: 34
8367937 CTGGATATAA
*
8367947 CTGGATATGAAT-TCTTTTTAATAGAACCTTAGAG
1 CTGGATATGAATGT-TTTTTAATAGAACCTAAGAG
*
8367981 CTGGATATGACTGTTTTTTAATAGAACCTAAGAG
1 CTGGATATGAATGTTTTTTAATAGAACCTAAGAG
8368015 CTGG
1 CTGG
8368019 TACTGTTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
34 34 0.97
35 1 0.03
ACGTcount: A:0.31, C:0.12, G:0.21, T:0.36
Consensus pattern (34 bp):
CTGGATATGAATGTTTTTTAATAGAACCTAAGAG
Found at i:8368024 original size:30 final size:32
Alignment explanation
Indices: 8367961--8368026 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 32
8367951 ATATGAATTC
*
8367961 TTTTTAATAGAACCTTAGAGCTGGATATGACTGT
1 TTTTTAATAGAACCTAAGAGCTGG--ATGACTGT
8367995 TTTTTAATAGAACCTAAGAGCTGG-T-ACTGT
1 TTTTTAATAGAACCTAAGAGCTGGATGACTGT
8368025 TT
1 TT
8368027 AGGATTTTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
30 7 0.23
31 1 0.03
34 23 0.74
ACGTcount: A:0.29, C:0.12, G:0.20, T:0.39
Consensus pattern (32 bp):
TTTTTAATAGAACCTAAGAGCTGGATGACTGT
Found at i:8380219 original size:16 final size:18
Alignment explanation
Indices: 8380188--8380222 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
8380178 GATAGATTTA
8380188 AAAATTAATCAAATCTAT
1 AAAATTAATCAAATCTAT
8380206 AAAATT-AT-AAATCTAT
1 AAAATTAATCAAATCTAT
8380222 A
1 A
8380223 TCAAATTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 2 0.12
18 6 0.35
ACGTcount: A:0.57, C:0.09, G:0.00, T:0.34
Consensus pattern (18 bp):
AAAATTAATCAAATCTAT
Found at i:8382174 original size:30 final size:29
Alignment explanation
Indices: 8382141--8382256 Score: 153
Period size: 30 Copynumber: 3.9 Consensus size: 29
8382131 TTGTATATGG
*
8382141 ACTATAGATCTCGAGTTGATATTGATTTGG
1 ACTATAGATCTCGA-TTGATATTGATTTGA
* *
8382171 ACTATAGATC-GGGTTGATATTGATTTGA
1 ACTATAGATCTCGATTGATATTGATTTGA
*
8382199 ACTATAAATCTCTGATTGATATTGATTTGA
1 ACTATAGATCTC-GATTGATATTGATTTGA
*
8382229 ACTATAGATCTTTGATTGATATTGATTT
1 ACTATAGATC-TCGATTGATATTGATTT
8382257 TATCTTGGAT
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
28 23 0.31
29 1 0.01
30 50 0.67
31 1 0.01
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (29 bp):
ACTATAGATCTCGATTGATATTGATTTGA
Found at i:8382233 original size:58 final size:59
Alignment explanation
Indices: 8382141--8382256 Score: 164
Period size: 58 Copynumber: 2.0 Consensus size: 59
8382131 TTGTATATGG
* * *
8382141 ACTATAGATCTCGAGTTGATATTGATTTGGACTATAGATC-GGGTTGATATTGATTTGA
1 ACTATAAATCTCGAGTTGATATTGATTTGAACTATAGATCTGGATTGATATTGATTTGA
*
8382199 ACTATAAATCTCTGA-TTGATATTGATTTGAACTATAGATCTTTGATTGATATTGATTT
1 ACTATAAATCTC-GAGTTGATATTGATTTGAACTATAGATC-TGGATTGATATTGATTT
8382257 TATCTTGGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
58 35 0.69
59 2 0.04
60 14 0.27
ACGTcount: A:0.29, C:0.09, G:0.19, T:0.43
Consensus pattern (59 bp):
ACTATAAATCTCGAGTTGATATTGATTTGAACTATAGATCTGGATTGATATTGATTTGA
Found at i:8382710 original size:44 final size:45
Alignment explanation
Indices: 8382632--8382722 Score: 157
Period size: 44 Copynumber: 2.0 Consensus size: 45
8382622 GTTGGTGACA
*
8382632 GTGACATCAAGCTCAGGGGTTGCTTTGGACGCTAATAGTGTGGAT
1 GTGACATCAAGCTCAGAGGTTGCTTTGGACGCTAATAGTGTGGAT
*
8382677 GTGACATCAAGCTCA-AGGTTGCTTTGGATGCTAATAGTGTGGAT
1 GTGACATCAAGCTCAGAGGTTGCTTTGGACGCTAATAGTGTGGAT
8382721 GT
1 GT
8382723 TCAAATTGTT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
44 29 0.66
45 15 0.34
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.31
Consensus pattern (45 bp):
GTGACATCAAGCTCAGAGGTTGCTTTGGACGCTAATAGTGTGGAT
Found at i:8383452 original size:36 final size:36
Alignment explanation
Indices: 8383412--8383485 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
8383402 TCTTAACCAT
8383412 GTAGTTGGGTAGTGGGCATAAGTTTTGAGTAATAGA
1 GTAGTTGGGTAGTGGGCATAAGTTTTGAGTAATAGA
* *
8383448 GTAGTTGGGTAGTGTGCATAAGTTTTGAGTGATAGA
1 GTAGTTGGGTAGTGGGCATAAGTTTTGAGTAATAGA
8383484 GT
1 GT
8383486 GATGATACTT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.26, C:0.03, G:0.36, T:0.35
Consensus pattern (36 bp):
GTAGTTGGGTAGTGGGCATAAGTTTTGAGTAATAGA
Found at i:8400817 original size:29 final size:28
Alignment explanation
Indices: 8400776--8400831 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
8400766 GAACTATATC
*
8400776 TATTTATGTAATTAAGTTATTAATTTTT
1 TATTTATGTAATTAAATTATTAATTTTT
* *
8400804 TATTATATTTAATTAAATTTTTAATTTT
1 TATT-TATGTAATTAAATTATTAATTTT
8400832 AATTAATAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.34, C:0.00, G:0.04, T:0.62
Consensus pattern (28 bp):
TATTTATGTAATTAAATTATTAATTTTT
Found at i:8400837 original size:22 final size:22
Alignment explanation
Indices: 8400797--8400838 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
8400787 TTAAGTTATT
* *
8400797 AATTTTTTATTATATTTAATTA
1 AATTTTTAATTATAATTAATTA
*
8400819 AATTTTTAATTTTAATTAAT
1 AATTTTTAATTATAATTAAT
8400839 AATTAATATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (22 bp):
AATTTTTAATTATAATTAATTA
Found at i:8400844 original size:29 final size:29
Alignment explanation
Indices: 8400784--8400845 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
8400774 TCTATTTATG
* * *
8400784 TAATTAAGTTATTAATTTTTTATTATATT
1 TAATTAAATTATTAATTTTTAATTATAAT
*
8400813 TAATTAAATTTTTAA-TTTTAATTAATAAT
1 TAATTAAATTATTAATTTTTAATT-ATAAT
8400842 TAAT
1 TAAT
8400846 ATTTATCAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 7 0.25
29 21 0.75
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (29 bp):
TAATTAAATTATTAATTTTTAATTATAAT
Found at i:8400850 original size:18 final size:19
Alignment explanation
Indices: 8400808--8400850 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
8400798 ATTTTTTATT
**
8400808 ATATTTAATTAAATTTTTA
1 ATATTTAATTAAATAATTA
8400827 AT-TTTAATT-AATAATTA
1 ATATTTAATTAAATAATTA
8400844 ATATTTA
1 ATATTTA
8400851 TCAAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 8 0.38
18 11 0.52
19 2 0.10
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
ATATTTAATTAAATAATTA
Found at i:8401551 original size:17 final size:17
Alignment explanation
Indices: 8401529--8401577 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
8401519 ATTTTGATTT
8401529 ATTTTATATAATTTAAA
1 ATTTTATATAATTTAAA
* *
8401546 ATTTTAGAT-ATCTAAA
1 ATTTTATATAATTTAAA
*
8401562 ATTTTAATATATTTTA
1 ATTTT-ATATAATTTA
8401578 TGACATTCAA
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
16 11 0.44
17 11 0.44
18 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (17 bp):
ATTTTATATAATTTAAA
Found at i:8412616 original size:3 final size:3
Alignment explanation
Indices: 8412608--8412637 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
8412598 GGTCAAAAAG
8412608 TCA TCA TCA TCA TCA TCA TCA TCAA TCA TC
1 TCA TCA TCA TCA TCA TCA TCA TC-A TCA TC
8412638 GAGGGCGGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.33, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:8421425 original size:23 final size:23
Alignment explanation
Indices: 8421382--8421425 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
8421372 TTTGGAGTAT
**
8421382 AATATTTGCATATCAATATTCAA
1 AATATTTGCATAAAAATATTCAA
8421405 AATATTT-CATAAAAATCATTC
1 AATATTTGCATAAAAAT-ATTC
8421426 CCAAACAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.45, C:0.14, G:0.02, T:0.39
Consensus pattern (23 bp):
AATATTTGCATAAAAATATTCAA
Found at i:8421945 original size:12 final size:12
Alignment explanation
Indices: 8421928--8421952 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
8421918 CCTGCTTTTG
8421928 TTTTATTTTATT
1 TTTTATTTTATT
8421940 TTTTATTTTATT
1 TTTTATTTTATT
8421952 T
1 T
8421953 ATTTCAAGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTTATTTTATT
Found at i:8421948 original size:17 final size:16
Alignment explanation
Indices: 8421923--8421956 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
8421913 TTTGCCCTGC
*
8421923 TTTTGTTTTATTTTATT
1 TTTTATTTTA-TTTATT
8421940 TTTTATTTTATTTATT
1 TTTTATTTTATTTATT
8421956 T
1 T
8421957 CAAGTCTCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.15, C:0.00, G:0.03, T:0.82
Consensus pattern (16 bp):
TTTTATTTTATTTATT
Found at i:8436504 original size:2 final size:2
Alignment explanation
Indices: 8436497--8436521 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8436487 TTTTAAAGGA
8436497 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8436522 CTTTTCCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8442316 original size:2 final size:2
Alignment explanation
Indices: 8442311--8442338 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8442301 GACTCTCTGA
8442311 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8442339 AACAGTGTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:8444688 original size:3 final size:3
Alignment explanation
Indices: 8444680--8444716 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
8444670 GCAACTAGGG
8444680 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
8444717 CAATGAAAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:8452736 original size:15 final size:15
Alignment explanation
Indices: 8452697--8452737 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
8452687 AGCCAAAGTA
*
8452697 GCAGCAGCAGCATCT
1 GCAGCAGCAGCAGCT
* *
8452712 GCTGCAGCAGCCGCT
1 GCAGCAGCAGCAGCT
8452727 GCAGCAGCAGC
1 GCAGCAGCAGC
8452738 TTTATCACCT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.22, C:0.37, G:0.32, T:0.10
Consensus pattern (15 bp):
GCAGCAGCAGCAGCT
Found at i:8471015 original size:2 final size:2
Alignment explanation
Indices: 8471008--8471034 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
8470998 TAATCCGTAC
8471008 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
8471035 CCTTTTCGTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8471655 original size:2 final size:2
Alignment explanation
Indices: 8471650--8471675 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8471640 TTTTTTATTT
8471650 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
8471676 GCGATGATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:8479075 original size:25 final size:25
Alignment explanation
Indices: 8479016--8479077 Score: 65
Period size: 25 Copynumber: 2.5 Consensus size: 25
8479006 AGTACTTAAA
*
8479016 TTATTTTAAA-AAATTTATATTTTT
1 TTATTTTAAATAAATTTATATTATT
** *
8479040 TTAAGTCAAATAAA-TTATTATTATT
1 TTATTTTAAATAAATTTA-TATTATT
8479065 TTATTTTAAATAA
1 TTATTTTAAATAA
8479078 GTCCTTATGT
Statistics
Matches: 29, Mismatches: 7, Indels: 3
0.74 0.18 0.08
Matches are distributed among these distances:
24 10 0.34
25 19 0.66
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (25 bp):
TTATTTTAAATAAATTTATATTATT
Found at i:8492964 original size:9 final size:9
Alignment explanation
Indices: 8492947--8492977 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
8492937 TGGATTTGTG
*
8492947 AAGTGGAGC
1 AAGTAGAGC
8492956 AAGTAGAGC
1 AAGTAGAGC
8492965 AAGTAGAGC
1 AAGTAGAGC
8492974 AAGT
1 AAGT
8492978 GGAGATTTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.42, C:0.10, G:0.35, T:0.13
Consensus pattern (9 bp):
AAGTAGAGC
Found at i:8495008 original size:48 final size:50
Alignment explanation
Indices: 8494933--8495030 Score: 173
Period size: 49 Copynumber: 2.0 Consensus size: 50
8494923 TACATCTACT
8494933 AGTGAACAAAACAAAATTCAAACAGATGAAA-AGACAGATCAAGGAAGTC
1 AGTGAACAAAACAAAATTCAAACAGATGAAAGAGACAGATCAAGGAAGTC
*
8494982 AGTGAACAAAAC-AAATTCAAACAGATGAAAGAGAGAGATCAAGGAAGTC
1 AGTGAACAAAACAAAATTCAAACAGATGAAAGAGACAGATCAAGGAAGTC
8495031 CGGCTTCTTG
Statistics
Matches: 47, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
48 18 0.38
49 29 0.62
ACGTcount: A:0.54, C:0.13, G:0.20, T:0.12
Consensus pattern (50 bp):
AGTGAACAAAACAAAATTCAAACAGATGAAAGAGACAGATCAAGGAAGTC
Found at i:8498297 original size:33 final size:30
Alignment explanation
Indices: 8498238--8498312 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 30
8498228 ACTCTTTATA
* *
8498238 TCTATCTCTATGCCTACTCCTGTCTCTGTC
1 TCTATCTCTATCCCTACTCCTATCTCTGTC
8498268 TCTATCTCTATCCCTATCCCTCCTATCTCTGTC
1 TCTATCTCTATCCCTA---CTCCTATCTCTGTC
*
8498301 TCTGTCTCTATC
1 TCTATCTCTATC
8498313 TTCTTCTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 15 0.38
33 24 0.62
ACGTcount: A:0.11, C:0.39, G:0.07, T:0.44
Consensus pattern (30 bp):
TCTATCTCTATCCCTACTCCTATCTCTGTC
Found at i:8500604 original size:35 final size:35
Alignment explanation
Indices: 8500564--8500633 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
8500554 TCCACTCATT
8500564 AGATATTGTGATTTATCTTCTTGAATGTATTGCTG
1 AGATATTGTGATTTATCTTCTTGAATGTATTGCTG
8500599 AGATATTGTGATTTATCTTCTTGAATGTATTGCTG
1 AGATATTGTGATTTATCTTCTTGAATGTATTGCTG
8500634 GTTAAAGTAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.23, C:0.09, G:0.20, T:0.49
Consensus pattern (35 bp):
AGATATTGTGATTTATCTTCTTGAATGTATTGCTG
Found at i:8503402 original size:40 final size:40
Alignment explanation
Indices: 8503347--8503429 Score: 157
Period size: 40 Copynumber: 2.1 Consensus size: 40
8503337 TTGCTTCCTT
8503347 TTTGTCTTTGTTGCAGTCTTGTTTCTTCACTCCACTGGGA
1 TTTGTCTTTGTTGCAGTCTTGTTTCTTCACTCCACTGGGA
*
8503387 TTTGTCTTTGTTGCAGTCTTGTTTTTTCACTCCACTGGGA
1 TTTGTCTTTGTTGCAGTCTTGTTTCTTCACTCCACTGGGA
8503427 TTT
1 TTT
8503430 ACTCGCTCAT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.10, C:0.20, G:0.19, T:0.51
Consensus pattern (40 bp):
TTTGTCTTTGTTGCAGTCTTGTTTCTTCACTCCACTGGGA
Found at i:8503539 original size:45 final size:45
Alignment explanation
Indices: 8503462--8503564 Score: 127
Period size: 45 Copynumber: 2.3 Consensus size: 45
8503452 AAAAGTGCCA
* *
8503462 ACTCATCTGTTTTGTGGTTCATATATGCGCTTTTGGGCCCT-GCCTT
1 ACTCATCT-TTTTGTGGTTCATACATGCGCTTTTAGG-CCTGGCCTT
* * *
8503508 ACTCATCTTTTTGTGTTTTATACATGGGCTTTTAGGCCTGGCCTT
1 ACTCATCTTTTTGTGGTTCATACATGCGCTTTTAGGCCTGGCCTT
*
8503553 ACTCATCCTTTT
1 ACTCATCTTTTT
8503565 ACGTTTCATA
Statistics
Matches: 50, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
44 3 0.06
45 39 0.78
46 8 0.16
ACGTcount: A:0.13, C:0.23, G:0.18, T:0.46
Consensus pattern (45 bp):
ACTCATCTTTTTGTGGTTCATACATGCGCTTTTAGGCCTGGCCTT
Found at i:8507178 original size:30 final size:30
Alignment explanation
Indices: 8507144--8507203 Score: 120
Period size: 30 Copynumber: 2.0 Consensus size: 30
8507134 AAATGGACTA
8507144 AATTAACCACCAGAAATGTTCAAATGCAAC
1 AATTAACCACCAGAAATGTTCAAATGCAAC
8507174 AATTAACCACCAGAAATGTTCAAATGCAAC
1 AATTAACCACCAGAAATGTTCAAATGCAAC
8507204 TCATCACACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.47, C:0.23, G:0.10, T:0.20
Consensus pattern (30 bp):
AATTAACCACCAGAAATGTTCAAATGCAAC
Found at i:8512779 original size:39 final size:39
Alignment explanation
Indices: 8512720--8512904 Score: 210
Period size: 39 Copynumber: 4.7 Consensus size: 39
8512710 GTCCTCTGGG
* * * *
8512720 GTCAACAACTGAGATTTTTCTTCAGTGTATTCTATTGGT
1 GTCAGCAACTGAGATTTTTCTTCAGTATACTCTTTTGGT
* *
8512759 GTCAGCAACTGAGATTTTTCTTCTGCATACTCTTTTGGT
1 GTCAGCAACTGAGATTTTTCTTCAGTATACTCTTTTGGT
* * *
8512798 GCCAGCAACTCAGATTTTTCTTCAGTGTACTCTTTTGGT
1 GTCAGCAACTGAGATTTTTCTTCAGTATACTCTTTTGGT
* * * * *
8512837 GCCAGCAACTCAGATTTTACTTCAAT-TAACTCTTTCGGT
1 GTCAGCAACTGAGATTTTTCTTCAGTAT-ACTCTTTTGGT
* *
8512876 GTCAGCAACTGAGGTTTCTCTTCAGTATA
1 GTCAGCAACTGAGATTTTTCTTCAGTATA
8512905 TTCAATGGTG
Statistics
Matches: 124, Mismatches: 20, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
38 1 0.01
39 122 0.98
40 1 0.01
ACGTcount: A:0.22, C:0.21, G:0.17, T:0.40
Consensus pattern (39 bp):
GTCAGCAACTGAGATTTTTCTTCAGTATACTCTTTTGGT
Found at i:8516068 original size:20 final size:21
Alignment explanation
Indices: 8516043--8516082 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
8516033 TCAAATATTT
*
8516043 AATATT-ATTTTTATATTAAA
1 AATATTCACTTTTATATTAAA
8516063 AATATTGCACTTTTATATTA
1 AATATT-CACTTTTATATTA
8516083 TAATTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.40, C:0.05, G:0.03, T:0.53
Consensus pattern (21 bp):
AATATTCACTTTTATATTAAA
Found at i:8516368 original size:2 final size:2
Alignment explanation
Indices: 8516361--8516388 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
8516351 TAACGGTGGC
8516361 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8516389 GCGTATTATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8516718 original size:8 final size:8
Alignment explanation
Indices: 8516705--8516751 Score: 51
Period size: 8 Copynumber: 5.9 Consensus size: 8
8516695 AGTACAAACC
8516705 AAAAAAAG
1 AAAAAAAG
8516713 AAAAAAAG
1 AAAAAAAG
* *
8516721 AGAACAAG
1 AAAAAAAG
8516729 AAAACAAAG
1 AAAA-AAAG
*
8516738 -AAAGAAG
1 AAAAAAAG
8516745 AAAAAAA
1 AAAAAAA
8516752 CCACTTATAA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
7 3 0.10
8 25 0.81
9 3 0.10
ACGTcount: A:0.81, C:0.04, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:8516731 original size:16 final size:15
Alignment explanation
Indices: 8516710--8516751 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
8516700 AAACCAAAAA
8516710 AAGAAAAAAAGAGAAC
1 AAGAAAAAAAGA-AAC
*
8516726 AAGAAAACAAAGAAAG
1 AAGAAAA-AAAGAAAC
8516742 AAGAAAAAAA
1 AAGAAAAAAA
8516752 CCACTTATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 3 0.12
16 16 0.67
17 5 0.21
ACGTcount: A:0.79, C:0.05, G:0.17, T:0.00
Consensus pattern (15 bp):
AAGAAAAAAAGAAAC
Found at i:8520211 original size:19 final size:19
Alignment explanation
Indices: 8520187--8520225 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
8520177 ACCTCTTTTC
8520187 TTTTAAAAAATTTATCAAT
1 TTTTAAAAAATTTATCAAT
*
8520206 TTTTAAAAAATTTGTCAAT
1 TTTTAAAAAATTTATCAAT
8520225 T
1 T
8520226 GTCTTCAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.49
Consensus pattern (19 bp):
TTTTAAAAAATTTATCAAT
Found at i:8520348 original size:22 final size:21
Alignment explanation
Indices: 8520305--8520349 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
8520295 ATTTATATTT
8520305 AAACTTAAAAAATAAAACATA
1 AAACTTAAAAAATAAAACATA
* * *
8520326 AAACTATAAGAAATTAAATATA
1 AAACT-TAAAAAATAAAACATA
8520348 AA
1 AA
8520350 TAATTAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 5 0.25
22 15 0.75
ACGTcount: A:0.69, C:0.07, G:0.02, T:0.22
Consensus pattern (21 bp):
AAACTTAAAAAATAAAACATA
Found at i:8520598 original size:12 final size:12
Alignment explanation
Indices: 8520542--8520598 Score: 51
Period size: 12 Copynumber: 4.4 Consensus size: 12
8520532 TGAGTTACTA
*
8520542 AAAAAGAGAAAT
1 AAAAAGAGAAAG
* *
8520554 AAAAATAAAAAG
1 AAAAAGAGAAAG
8520566 ACAGAAAAGAGAAGAG
1 --A-AAAAGAGAA-AG
8520582 AAAAAGAGAAAG
1 AAAAAGAGAAAG
8520594 AAAAA
1 AAAAA
8520599 AAAAGAGGTG
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
12 16 0.44
13 9 0.25
14 2 0.06
15 7 0.19
16 2 0.06
ACGTcount: A:0.75, C:0.02, G:0.19, T:0.04
Consensus pattern (12 bp):
AAAAAGAGAAAG
Found at i:8520599 original size:13 final size:13
Alignment explanation
Indices: 8520541--8520599 Score: 52
Period size: 13 Copynumber: 4.5 Consensus size: 13
8520531 GTGAGTTACT
*
8520541 AAAAAAGAGAAAT
1 AAAAAAGAGAAAG
8520554 AAAAATA-A-AAAG
1 AAAAA-AGAGAAAG
8520566 ACAGAAAAGAG-AAG
1 A-A-AAAAGAGAAAG
8520580 AGAAAAAGAGAAAG
1 A-AAAAAGAGAAAG
8520594 AAAAAA
1 AAAAAA
8520600 AAAGAGGTGT
Statistics
Matches: 38, Mismatches: 2, Indels: 12
0.73 0.04 0.23
Matches are distributed among these distances:
12 4 0.11
13 20 0.53
14 14 0.37
ACGTcount: A:0.76, C:0.02, G:0.19, T:0.03
Consensus pattern (13 bp):
AAAAAAGAGAAAG
Found at i:8520600 original size:27 final size:27
Alignment explanation
Indices: 8520541--8520601 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
8520531 GTGAGTTACT
* *
8520541 AAAAAAGAGAAATAAAAATAAAAAGAC
1 AAAAAAGAGAAAGAAAAAGAAAAAGAC
* * *
8520568 AGAAAAGAGAAGAGAAAAAGAGAAAGAA
1 AAAAAAGAGAA-AGAAAAAGAAAAAGAC
8520596 AAAAAA
1 AAAAAA
8520602 AGAGGTGTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
27 10 0.37
28 17 0.63
ACGTcount: A:0.77, C:0.02, G:0.18, T:0.03
Consensus pattern (27 bp):
AAAAAAGAGAAAGAAAAAGAAAAAGAC
Found at i:8520604 original size:24 final size:23
Alignment explanation
Indices: 8520560--8520605 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 23
8520550 AAATAAAAAT
* * *
8520560 AAAAAGACAGAAAAGAGAAGAGA
1 AAAAAGAAAGAAAAAAAAAGAGA
8520583 AAAAGAGAAAGAAAAAAAAAGAG
1 AAAA-AGAAAGAAAAAAAAAGAG
8520606 GTGTAGAGAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 4 0.21
24 15 0.79
ACGTcount: A:0.74, C:0.02, G:0.24, T:0.00
Consensus pattern (23 bp):
AAAAAGAAAGAAAAAAAAAGAGA
Found at i:8536197 original size:41 final size:41
Alignment explanation
Indices: 8536151--8536233 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
8536141 TCAAGAAGTT
8536151 ATTGATGAACATCTTGATCCAAATATATCAAAATTTGAGCA
1 ATTGATGAACATCTTGATCCAAATATATCAAAATTTGAGCA
8536192 ATTGATGAACATCTTGATCCAAATATATCAAAATTTGAGCA
1 ATTGATGAACATCTTGATCCAAATATATCAAAATTTGAGCA
8536233 A
1 A
8536234 GATGATATAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (41 bp):
ATTGATGAACATCTTGATCCAAATATATCAAAATTTGAGCA
Found at i:8547689 original size:30 final size:30
Alignment explanation
Indices: 8547653--8547741 Score: 133
Period size: 30 Copynumber: 3.0 Consensus size: 30
8547643 TTACTAGAAG
*
8547653 AAATATATCTAATAGATGTAGAAACCTCTT
1 AAATATATCTAATAGGTGTAGAAACCTCTT
* *
8547683 AAATATATTTGATAGGTGTAGAAACCTCTT
1 AAATATATCTAATAGGTGTAGAAACCTCTT
* *
8547713 AAATATATCTTATAGGTATAGAAACCTCT
1 AAATATATCTAATAGGTGTAGAAACCTCT
8547742 ATTTGATCAC
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 53 1.00
ACGTcount: A:0.40, C:0.12, G:0.12, T:0.35
Consensus pattern (30 bp):
AAATATATCTAATAGGTGTAGAAACCTCTT
Found at i:8555268 original size:21 final size:21
Alignment explanation
Indices: 8555244--8555303 Score: 52
Period size: 21 Copynumber: 2.9 Consensus size: 21
8555234 TAGCACTATT
8555244 TCGCTCAGCAATTGCTGCATC
1 TCGCTCAGCAATTGCTGCATC
***
8555265 TCGCTGCAAG-AA-TGCCATATC
1 TCGCT-C-AGCAATTGCTGCATC
*
8555286 TCTCTCAGCAATTGCTGC
1 TCGCTCAGCAATTGCTGC
8555304 CTTCTTCTCA
Statistics
Matches: 28, Mismatches: 7, Indels: 8
0.65 0.16 0.19
Matches are distributed among these distances:
19 2 0.07
20 3 0.11
21 18 0.64
22 3 0.11
23 2 0.07
ACGTcount: A:0.22, C:0.32, G:0.18, T:0.28
Consensus pattern (21 bp):
TCGCTCAGCAATTGCTGCATC
Found at i:8558027 original size:15 final size:15
Alignment explanation
Indices: 8558007--8558075 Score: 65
Period size: 15 Copynumber: 4.8 Consensus size: 15
8557997 TATAATCTAT
8558007 TATTTTTTATTTTAA
1 TATTTTTTATTTTAA
*
8558022 TATTTTTTATTTCAA
1 TATTTTTTATTTTAA
***
8558037 T-TATAAATATTTT-A
1 TAT-TTTTTATTTTAA
8558051 TA--TTTTATTTTAA
1 TATTTTTTATTTTAA
8558064 TATTTTTTATTT
1 TATTTTTTATTT
8558076 CAATTATAAC
Statistics
Matches: 41, Mismatches: 8, Indels: 10
0.69 0.14 0.17
Matches are distributed among these distances:
12 6 0.15
13 3 0.07
14 3 0.07
15 29 0.71
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.70
Consensus pattern (15 bp):
TATTTTTTATTTTAA
Found at i:8558045 original size:22 final size:22
Alignment explanation
Indices: 8558020--8558084 Score: 89
Period size: 22 Copynumber: 3.0 Consensus size: 22
8558010 TTTTTATTTT
8558020 AATATTTTTTATTTCAATTATA
1 AATATTTTTTATTTCAATTATA
* * *
8558042 AATATTTTATATTT-TATT-TT
1 AATATTTTTTATTTCAATTATA
8558062 AATATTTTTTATTTCAATTATA
1 AATATTTTTTATTTCAATTATA
8558084 A
1 A
8558085 CATTACAAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
20 14 0.40
21 6 0.17
22 15 0.43
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (22 bp):
AATATTTTTTATTTCAATTATA
Found at i:8558051 original size:20 final size:21
Alignment explanation
Indices: 8558019--8558084 Score: 71
Period size: 21 Copynumber: 3.1 Consensus size: 21
8558009 TTTTTTATTT
*
8558019 TAATATTTTTTATTTCAATTA
1 TAATATATTTTATTTCAATTA
** *
8558040 TAA-ATATTTTATATTTTATTT
1 TAATATATTTTAT-TTCAATTA
*
8558061 TAATATTTTTTATTTCAATTA
1 TAATATATTTTATTTCAATTA
8558082 TAA
1 TAA
8558085 CATTACAAAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
20 8 0.23
21 19 0.54
22 8 0.23
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (21 bp):
TAATATATTTTATTTCAATTA
Found at i:8562675 original size:203 final size:200
Alignment explanation
Indices: 8562306--8562756 Score: 694
Period size: 203 Copynumber: 2.2 Consensus size: 200
8562296 CCTAGTCCCG
*
8562306 AAAATTTTTAAAATA--TTTTATATTATATATTTGAAACATTAATTCATACCAATTTTTTTGAAA
1 AAAATTTTTAAAATATTTTTTATATTATATATTTAAAACATTAATTCATACCAATTTTTTTGAAA
8562369 AGTAACATTAATTCATATCATAGATAAGGAAAATATTTAGCTTCAAAAATTTTTAAAATATTTTA
66 AGTAACATTAATTCATATCATAGATAAGGAAAATATTTAGCTTCAAAAATTTTTAAAATATTTTA
*
8562434 TGTATTATACATGTAAAGCATTAATCAATACAATCATTATGAGAATAGATAAGGAAAATATTTAA
131 TGTATTATACATGTAAAACATTAATCAATACAATCATTATGAGAATAGATAAGGAAAATATTTAA
8562499 -T-CT
196 TTCCT
* *
8562502 CAAATTTTTTAAAATATTTTTTATATTATATATTTAAAACATTAATTCATACCAATTTTTTTTGG
1 -AAAATTTTTAAAATATTTTTTATATTATATATTTAAAACATTAATTCATACCAA-TTTTTTTGA
* * *
8562567 AAAGTAATATTAATTCATATCATAATAGATAAGGAAAATATTTAGCTTTAAAATTTTTTAAAATA
64 AAAGTAACATTAATTCATATC---ATAGATAAGGAAAATATTTAGCTTCAAAAATTTTTAAAATA
* * ** *
8562632 TTTTATGTATTATACATTTAAAACATTAATTAATATTATCATTATGAGAATAGATAGGGAAAATA
126 TTTTATGTATTATACATGTAAAACATTAATCAATACAATCATTATGAGAATAGATAAGGAAAATA
8562697 TTTAATTCCT
191 TTTAATTCCT
* * *
8562707 AAAAATTTTAAAATATTTTATACATTATATATTTAAAACATTAATTCATA
1 AAAATTTTTAAAATATTTTTTATATTATATATTTAAAACATTAATTCATA
8562757 TCATTATTAT
Statistics
Matches: 230, Mismatches: 16, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
197 14 0.06
199 36 0.16
200 28 0.12
203 103 0.45
204 47 0.20
205 2 0.01
ACGTcount: A:0.44, C:0.07, G:0.06, T:0.42
Consensus pattern (200 bp):
AAAATTTTTAAAATATTTTTTATATTATATATTTAAAACATTAATTCATACCAATTTTTTTGAAA
AGTAACATTAATTCATATCATAGATAAGGAAAATATTTAGCTTCAAAAATTTTTAAAATATTTTA
TGTATTATACATGTAAAACATTAATCAATACAATCATTATGAGAATAGATAAGGAAAATATTTAA
TTCCT
Found at i:8562696 original size:90 final size:89
Alignment explanation
Indices: 8562590--8562773 Score: 244
Period size: 90 Copynumber: 2.0 Consensus size: 89
8562580 TTCATATCAT
* * **
8562590 AATAGATAAGGAAAATATTTAGCTT-TAAAATTTTTTAAAATATTTTATGTATTATACATTTAAA
1 AATAGATAAGGAAAATATTTA-ATTCTAAAA-ATTTTAAAATATTTTATACATTATACATTTAAA
* *
8562654 ACATTAATTAATATTATCATTATGAG
64 ACATTAATTAATATCATCATTATAAG
* *
8562680 AATAGATAGGGAAAATATTTAATTCCTAAAAATTTTAAAATATTTTATACATTATATATTTAAAA
1 AATAGATAAGGAAAATATTTAATT-CTAAAAATTTTAAAATATTTTATACATTATACATTTAAAA
* *
8562745 CATTAATTCATATCATTATTATAAG
65 CATTAATTAATATCATCATTATAAG
8562770 AATA
1 AATA
8562774 CGAATTGTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
89 2 0.02
90 75 0.91
91 5 0.06
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (89 bp):
AATAGATAAGGAAAATATTTAATTCTAAAAATTTTAAAATATTTTATACATTATACATTTAAAAC
ATTAATTAATATCATCATTATAAG
Found at i:8570197 original size:2 final size:2
Alignment explanation
Indices: 8570192--8570227 Score: 58
Period size: 2 Copynumber: 19.0 Consensus size: 2
8570182 ATATGACAGA
8570192 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T A- AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8570228 GCCATTCATG
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 2 0.06
2 30 0.94
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8578504 original size:2 final size:2
Alignment explanation
Indices: 8578497--8578526 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
8578487 TAACATAGGA
8578497 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8578527 GAAATGTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:8599870 original size:26 final size:26
Alignment explanation
Indices: 8599834--8599885 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
8599824 TGTACTAGTC
8599834 ATAACTTCAAGTTATTAGGTTGTTAG
1 ATAACTTCAAGTTATTAGGTTGTTAG
*
8599860 ATAACTTCAAGTTGTTAGGTTGTTAG
1 ATAACTTCAAGTTATTAGGTTGTTAG
8599886 GTTCGTGTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.29, C:0.08, G:0.21, T:0.42
Consensus pattern (26 bp):
ATAACTTCAAGTTATTAGGTTGTTAG
Found at i:8634635 original size:27 final size:27
Alignment explanation
Indices: 8634605--8634666 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
8634595 TGGAGGTGGT
8634605 GGTGGTGGAGGGGGAAGACGAGGAGGA
1 GGTGGTGGAGGGGGAAGACGAGGAGGA
* * * **
8634632 GGTGGGGGATGGGGATGGGGAGGAGGA
1 GGTGGTGGAGGGGGAAGACGAGGAGGA
8634659 GGTGGTGG
1 GGTGGTGG
8634667 TTGGTATAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.19, C:0.02, G:0.68, T:0.11
Consensus pattern (27 bp):
GGTGGTGGAGGGGGAAGACGAGGAGGA
Found at i:8635176 original size:15 final size:16
Alignment explanation
Indices: 8635147--8635176 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
8635137 TCAATTATCT
8635147 AGCCTTTTTTATGGAA
1 AGCCTTTTTTATGGAA
8635163 AGCCTTTTTT-TGGA
1 AGCCTTTTTTATGGA
8635177 CAAATATTGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.13, G:0.20, T:0.47
Consensus pattern (16 bp):
AGCCTTTTTTATGGAA
Found at i:8636223 original size:13 final size:13
Alignment explanation
Indices: 8636205--8636235 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
8636195 AAACAGAAGT
8636205 GTTATCTTTCTGA
1 GTTATCTTTCTGA
8636218 GTTATCTTTCTGA
1 GTTATCTTTCTGA
8636231 GTTAT
1 GTTAT
8636236 GTCTGTAAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.16, C:0.13, G:0.16, T:0.55
Consensus pattern (13 bp):
GTTATCTTTCTGA
Found at i:8640210 original size:61 final size:62
Alignment explanation
Indices: 8640084--8640211 Score: 161
Period size: 61 Copynumber: 2.1 Consensus size: 62
8640074 CTCGAGACGG
* * ** *
8640084 GCAAAAGTATCTCGTCGGACCTTTTATCTCTCAACGACTTTCTTTGTAATACTGTACACCGAA
1 GCAAAAGTATCTCGTCCGACCTTTTA-CTCTCAACAACTTTCGATGTAATACTGTACACAGAA
* *
8640147 GCAAAAGTATCTCGTCCGCCCTTTTA-TCTCAACAACTTTCGATGTAA-AGTGTACACAGAAA
1 GCAAAAGTATCTCGTCCGACCTTTTACTCTCAACAACTTTCGATGTAATACTGTACACAG-AA
8640208 GCAA
1 GCAA
8640212 GCATGGGGCA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
60 9 0.16
61 24 0.42
63 24 0.42
ACGTcount: A:0.30, C:0.25, G:0.15, T:0.30
Consensus pattern (62 bp):
GCAAAAGTATCTCGTCCGACCTTTTACTCTCAACAACTTTCGATGTAATACTGTACACAGAA
Found at i:8652341 original size:3 final size:3
Alignment explanation
Indices: 8652333--8652358 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
8652323 GCATTGGCAG
8652333 CTT CTT CTT CTT CTT CTT CTT CTT CT
1 CTT CTT CTT CTT CTT CTT CTT CTT CT
8652359 GTCCTCGCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (3 bp):
CTT
Found at i:8655710 original size:2 final size:2
Alignment explanation
Indices: 8655703--8655741 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
8655693 AGGGTTTTAA
8655703 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8655742 TACGAGGTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8666486 original size:17 final size:17
Alignment explanation
Indices: 8666436--8666486 Score: 66
Period size: 17 Copynumber: 3.0 Consensus size: 17
8666426 TCATGAACTT
*
8666436 CTTGATCACGAAGTATG
1 CTTGATCACGAAGTTTG
* *
8666453 CTTCATCACGAACTTTG
1 CTTGATCACGAAGTTTG
*
8666470 CTTGATCACAAAGTTTG
1 CTTGATCACGAAGTTTG
8666487 ATCATGAAGT
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (17 bp):
CTTGATCACGAAGTTTG
Found at i:8666521 original size:17 final size:17
Alignment explanation
Indices: 8666421--8666522 Score: 51
Period size: 17 Copynumber: 6.5 Consensus size: 17
8666411 CTTAGAAAAC
*
8666421 TTTGATCATGAACTTC-
1 TTTGATCACGAACTTCG
*
8666437 -TTGATCACGAAGTAT-G
1 TTTGATCACGAACT-TCG
* * *
8666453 CTTCATCACGAACTTTG
1 TTTGATCACGAACTTCG
* *
8666470 CTTGATCAC-AA---AG
1 TTTGATCACGAACTTCG
* *
8666483 TTTGATCATGAAGTTC-
1 TTTGATCACGAACTTCG
8666499 -TTGATCACGAACTTCG
1 TTTGATCACGAACTTCG
8666515 TTTGATCA
1 TTTGATCA
8666523 TAAACTTTAT
Statistics
Matches: 65, Mismatches: 11, Indels: 19
0.68 0.12 0.20
Matches are distributed among these distances:
13 8 0.12
14 2 0.03
15 24 0.37
16 4 0.06
17 27 0.42
ACGTcount: A:0.27, C:0.20, G:0.17, T:0.36
Consensus pattern (17 bp):
TTTGATCACGAACTTCG
Found at i:8666528 original size:17 final size:17
Alignment explanation
Indices: 8666482--8666529 Score: 55
Period size: 15 Copynumber: 2.9 Consensus size: 17
8666472 TGATCACAAA
*
8666482 GTTTGATCATGAAGTTC
1 GTTTGATCATGAACTTC
*
8666499 --TTGATCACGAACTTC
1 GTTTGATCATGAACTTC
*
8666514 GTTTGATCATAAACTT
1 GTTTGATCATGAACTT
8666530 TATTTGATGA
Statistics
Matches: 25, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
15 13 0.52
17 12 0.48
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.40
Consensus pattern (17 bp):
GTTTGATCATGAACTTC
Found at i:8666537 original size:62 final size:62
Alignment explanation
Indices: 8666421--8666537 Score: 146
Period size: 62 Copynumber: 1.9 Consensus size: 62
8666411 CTTAGAAAAC
* * *
8666421 TTTGATCATGAACTTCTTGATCACGAAGTATGCTTCATCACGAACTTTGCTTGATCACAAAG
1 TTTGATCATGAACTTCTTGATCACGAACTATGCTTCATCACAAACTTTACTTGATCACAAAG
* * * * *
8666483 TTTGATCATGAAGTTCTTGATCACGAACT-TCGTTTGATCATAAACTTTATTTGAT
1 TTTGATCATGAACTTCTTGATCACGAACTAT-GCTTCATCACAAACTTTACTTGAT
8666538 GAGTTGATCT
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
61 1 0.02
62 45 0.98
ACGTcount: A:0.28, C:0.18, G:0.15, T:0.38
Consensus pattern (62 bp):
TTTGATCATGAACTTCTTGATCACGAACTATGCTTCATCACAAACTTTACTTGATCACAAAG
Found at i:8666560 original size:48 final size:48
Alignment explanation
Indices: 8666497--8666706 Score: 219
Period size: 48 Copynumber: 4.4 Consensus size: 48
8666487 ATCATGAAGT
* * *
8666497 TCTTGATCACGAACTTCGTTTGATCATAAACTTTATTTGATGAGTTGA
1 TCTTGATCACGAACTTCGCTTGATCATAAACTTTATTTAATGACTTGA
* *
8666545 TCTTGATTACAAACTTCGCTTGATCATAAACTTTATTTAATGACTTGA
1 TCTTGATCACGAACTTCGCTTGATCATAAACTTTATTTAATGACTTGA
* * ** * *
8666593 TCTTGATCACGAACTTCGCTTGATCACAAAC-TT-TTTGACCAC-AGT
1 TCTTGATCACGAACTTCGCTTGATCATAAACTTTATTTAATGACTTGA
* * * * ** * *
8666638 TCTTGATCACGAGCTTCACTAGATCATGAACTTCGTTTGATGACTCGA
1 TCTTGATCACGAACTTCGCTTGATCATAAACTTTATTTAATGACTTGA
*
8666686 TCTTGATCAAGAACTTCGCTT
1 TCTTGATCACGAACTTCGCTT
8666707 AATAACTTTG
Statistics
Matches: 132, Mismatches: 27, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
45 27 0.20
46 7 0.05
47 9 0.07
48 89 0.67
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (48 bp):
TCTTGATCACGAACTTCGCTTGATCATAAACTTTATTTAATGACTTGA
Found at i:8666616 original size:17 final size:17
Alignment explanation
Indices: 8666594--8666809 Score: 67
Period size: 17 Copynumber: 13.4 Consensus size: 17
8666584 ATGACTTGAT
8666594 CTTGATCACGAACTTCG
1 CTTGATCACGAACTTCG
*
8666611 CTTGATCACAAACTT--
1 CTTGATCACGAACTTCG
* * *
8666626 TTTGACCAC--AGTT--
1 CTTGATCACGAACTTCG
* *
8666639 CTTGATCACGAGCTTCA
1 CTTGATCACGAACTTCG
* *
8666656 CTAGATCATGAACTTCG
1 CTTGATCACGAACTTCG
*
8666673 TTTGAT---G-AC-TCG
1 CTTGATCACGAACTTCG
*
8666685 ATCTTGATCAAGAACTTCG
1 --CTTGATCACGAACTTCG
* *
8666704 CTT-A--A-TAACTTTG
1 CTTGATCACGAACTTCG
8666717 --TGATCACGAACTTCG
1 CTTGATCACGAACTTCG
* *
8666732 CTTAAAGATTATGAACTTCG
1 CTT---GATCACGAACTTCG
8666752 -TGTGATCACGAACTTCG
1 CT-TGATCACGAACTTCG
* *
8666769 CTTCAAGATCACAAAGTT--
1 CTT---GATCACGAACTTCG
8666787 CTTGATCACGAACTTCG
1 CTTGATCACGAACTTCG
8666804 CTTGAT
1 CTTGAT
8666810 GACTTGATCT
Statistics
Matches: 145, Mismatches: 27, Indels: 54
0.64 0.12 0.24
Matches are distributed among these distances:
11 1 0.01
12 4 0.03
13 18 0.12
14 8 0.06
15 25 0.17
16 1 0.01
17 55 0.38
18 6 0.04
19 4 0.03
20 23 0.16
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.33
Consensus pattern (17 bp):
CTTGATCACGAACTTCG
Found at i:8666691 original size:93 final size:96
Alignment explanation
Indices: 8666497--8666706 Score: 237
Period size: 93 Copynumber: 2.2 Consensus size: 96
8666487 ATCATGAAGT
* * ** ** *
8666497 TCTTGATCACGAACTTCGTTTGATCATAAACTTTATTTGATGAGTTGATCTTGATTACAAACTTC
1 TCTTGATCACGAACTTCGCTTGATCACAAACTTTATTTGACCAGCAGATCTTGATCACAAACTTC
* * * *
8666562 GCTTGATCATAAACTTTATTTAATGACTTGA
66 ACTAGATCATAAACTTCATTTAATGACTCGA
* * *
8666593 TCTTGATCACGAACTTCGCTTGATCACAAAC-TT-TTTGACCA-CAGTTCTTGATCACGAGCTTC
1 TCTTGATCACGAACTTCGCTTGATCACAAACTTTATTTGACCAGCAGATCTTGATCACAAACTTC
* * *
8666655 ACTAGATCATGAACTTCGTTTGATGACTCGA
66 ACTAGATCATAAACTTCATTTAATGACTCGA
*
8666686 TCTTGATCAAGAACTTCGCTT
1 TCTTGATCACGAACTTCGCTT
8666707 AATAACTTTG
Statistics
Matches: 96, Mismatches: 18, Indels: 3
0.82 0.15 0.03
Matches are distributed among these distances:
93 59 0.61
94 6 0.06
95 2 0.02
96 29 0.30
ACGTcount: A:0.27, C:0.20, G:0.15, T:0.38
Consensus pattern (96 bp):
TCTTGATCACGAACTTCGCTTGATCACAAACTTTATTTGACCAGCAGATCTTGATCACAAACTTC
ACTAGATCATAAACTTCATTTAATGACTCGA
Found at i:8666758 original size:37 final size:36
Alignment explanation
Indices: 8666710--8666806 Score: 126
Period size: 37 Copynumber: 2.7 Consensus size: 36
8666700 TTCGCTTAAT
* **
8666710 AACTT-TGTGATCACGAACTTCGCTTAAAGATTATG
1 AACTTCTGTGATCACGAACTTCGCTTAAAGATCACA
*
8666745 AACTTCGTGTGATCACGAACTTCGCTTCAAGATCACA
1 AACTTC-TGTGATCACGAACTTCGCTTAAAGATCACA
*
8666782 AAGTTCT-TGATCACGAACTTCGCTT
1 AACTTCTGTGATCACGAACTTCGCTT
8666807 GATGACTTGA
Statistics
Matches: 55, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 23 0.42
36 1 0.02
37 31 0.56
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (36 bp):
AACTTCTGTGATCACGAACTTCGCTTAAAGATCACA
Found at i:8666780 original size:20 final size:19
Alignment explanation
Indices: 8666718--8666806 Score: 66
Period size: 20 Copynumber: 4.9 Consensus size: 19
8666708 ATAACTTTGT
8666718 GATCACGAACTTCGCTTAAA
1 GATCACGAACTTCGCTT-AA
* *
8666738 GATTATGAACTTCG-TGT--
1 GATCACGAACTTCGCT-TAA
8666755 GATCACGAACTTCGCTTCAA
1 GATCACGAACTTCGCTT-AA
* *
8666775 GATCACAAAGTT--CTT--
1 GATCACGAACTTCGCTTAA
8666790 GATCACGAACTTCGCTT
1 GATCACGAACTTCGCTT
8666807 GATGACTTGA
Statistics
Matches: 54, Mismatches: 8, Indels: 17
0.68 0.10 0.22
Matches are distributed among these distances:
15 10 0.19
17 16 0.30
18 4 0.07
19 1 0.02
20 23 0.43
ACGTcount: A:0.29, C:0.24, G:0.17, T:0.30
Consensus pattern (19 bp):
GATCACGAACTTCGCTTAA
Found at i:8666826 original size:16 final size:16
Alignment explanation
Indices: 8666805--8666836 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
8666795 CGAACTTCGC
8666805 TTGATGACTTGATCTT
1 TTGATGACTTGATCTT
8666821 TTGATGACTTGATCTT
1 TTGATGACTTGATCTT
8666837 GATCAAGAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (16 bp):
TTGATGACTTGATCTT
Found at i:8666847 original size:147 final size:138
Alignment explanation
Indices: 8666594--8666972 Score: 417
Period size: 147 Copynumber: 2.7 Consensus size: 138
8666584 ATGACTTGAT
* * * * *
8666594 CTTGATCACGAACTTCGCTTGATCACAAACTT--TTTGACCAC-AGTTCTTGATCACGAGCTTCA
1 CTTGATCACGAACTT--CTTGATCACAAACTTCACTTGATCACAAGATCTTGATCACGAACTTCG
* * *
8666656 CTAGAT--CATGAACTTCGTTTGATGACTCGATCTTGATCAAGAACTTCGCTTAATAACTTTGTG
64 CTTGATGACTTGAAC-T--TTTGATGACTTGATCTTGATCAAGAACTTCGCTTAATAACTTTGTG
* *
8666719 ATCACGAACTTCG
126 ATCACAAACTTCA
* * * * *
8666732 CTTAAAGATTATGAACTTCGTGTGATCACGAACTTCGCTTCAAGATCACAAAGTTCTTGATCACG
1 CTT---GATCACGAACTTC-T-TGATCACAAACTTCACTT---GATCAC-AAGATCTTGATCACG
*
8666797 AACTTCGCTTGATGACTTGATCTTTTGATGACTTGATCTTGATCAAGAACTTCGCTTAATAACTT
57 AACTTCGCTTGATGACTTGAACTTTTGATGACTTGATCTTGATCAAGAACTTCGCTTAATAACTT
8666862 TGTGATCACAAACTTCA
122 TGTGATCACAAACTTCA
* * **
8666879 CTTGATCACGAAGTTCTTGATCACAAACTTCACTTGATGACTTGATCTTGATCACGAACTTCGCT
1 CTTGATCACGAACTTCTTGATCACAAACTTCACTTGATCACAAGATCTTGATCACGAACTTCGCT
8666944 TGATGACTTGAACTTTTGATGACTTGATC
66 TGATGACTTGAACTTTTGATGACTTGATC
8666973 ATGAGCTTCA
Statistics
Matches: 204, Mismatches: 23, Indels: 28
0.80 0.09 0.11
Matches are distributed among these distances:
138 52 0.25
139 6 0.03
140 1 0.00
141 22 0.11
142 16 0.08
143 3 0.01
144 10 0.05
146 5 0.02
147 59 0.29
148 24 0.12
149 1 0.00
150 5 0.02
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.35
Consensus pattern (138 bp):
CTTGATCACGAACTTCTTGATCACAAACTTCACTTGATCACAAGATCTTGATCACGAACTTCGCT
TGATGACTTGAACTTTTGATGACTTGATCTTGATCAAGAACTTCGCTTAATAACTTTGTGATCAC
AAACTTCA
Found at i:8666886 original size:17 final size:17
Alignment explanation
Indices: 8666864--8666916 Score: 74
Period size: 17 Copynumber: 3.2 Consensus size: 17
8666854 AATAACTTTG
8666864 TGATCACAAACTTCACT
1 TGATCACAAACTTCACT
* *
8666881 TGATCACGAAGTT--CT
1 TGATCACAAACTTCACT
8666896 TGATCACAAACTTCACT
1 TGATCACAAACTTCACT
8666913 TGAT
1 TGAT
8666917 GACTTGATCT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
15 13 0.43
17 17 0.57
ACGTcount: A:0.32, C:0.25, G:0.11, T:0.32
Consensus pattern (17 bp):
TGATCACAAACTTCACT
Found at i:8666931 original size:31 final size:31
Alignment explanation
Indices: 8666821--8666954 Score: 132
Period size: 31 Copynumber: 4.4 Consensus size: 31
8666811 ACTTGATCTT
*
8666821 TTGATGACTTGATCTTGATCA-AGAACTTCGC
1 TTGATGACTTGATCTTGATCACA-AACTTCAC
* * *
8666852 TTAATAACTT--T-GTGATCACAAACTTCAC
1 TTGATGACTTGATCTTGATCACAAACTTCAC
* ** *
8666880 TTGATCACGAAGTTCTTGATCACAAACTTCAC
1 TTGATGAC-TTGATCTTGATCACAAACTTCAC
* *
8666912 TTGATGACTTGATCTTGATCACGAACTTCGC
1 TTGATGACTTGATCTTGATCACAAACTTCAC
8666943 TTGATGACTTGA
1 TTGATGACTTGA
8666955 ACTTTTGATG
Statistics
Matches: 83, Mismatches: 15, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
28 19 0.23
29 2 0.02
31 39 0.47
32 23 0.28
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (31 bp):
TTGATGACTTGATCTTGATCACAAACTTCAC
Found at i:8666947 original size:17 final size:17
Alignment explanation
Indices: 8666864--8666947 Score: 72
Period size: 17 Copynumber: 5.2 Consensus size: 17
8666854 AATAACTTTG
*
8666864 TGATCACAAACTTCACT
1 TGATCACGAACTTCACT
*
8666881 TGATCACGAAGTT--CT
1 TGATCACGAACTTCACT
*
8666896 TGATCACAAACTTCACT
1 TGATCACGAACTTCACT
*
8666913 TGAT---G-ACTTGATCT
1 TGATCACGAACTTCA-CT
*
8666927 TGATCACGAACTTCGCT
1 TGATCACGAACTTCACT
8666944 TGAT
1 TGAT
8666948 GACTTGAACT
Statistics
Matches: 52, Mismatches: 8, Indels: 14
0.70 0.11 0.19
Matches are distributed among these distances:
13 5 0.10
14 6 0.12
15 13 0.25
17 24 0.46
18 4 0.08
ACGTcount: A:0.29, C:0.24, G:0.14, T:0.33
Consensus pattern (17 bp):
TGATCACGAACTTCACT
Found at i:8666970 original size:47 final size:46
Alignment explanation
Indices: 8666786--8666972 Score: 158
Period size: 47 Copynumber: 4.0 Consensus size: 46
8666776 ATCACAAAGT
*
8666786 TCTTGATCACGAACTTCGCTTGATGACTTGATCTTTTGATGACTTGA
1 TCTTGATCACGAACTTCGCTTGATGAC-TGAACTTTTGATGACTTGA
* * *
8666833 TCTTGATCAAGAACTTCGCTT-A--A-T-AACTTTGTGATCACAAACTTCA
1 TCTTGATCACGAACTTCGCTTGATGACTGAACTTT-TGAT----GACTTGA
* * *
8666879 -CTTGATCACGAAGTT--CTTGATCAC-AAACTTCACTTGATGACTTGA
1 TCTTGATCACGAACTTCGCTTGATGACTGAACTT---TTGATGACTTGA
8666924 TCTTGATCACGAACTTCGCTTGATGACTTGAACTTTTGATGACTTGA
1 TCTTGATCACGAACTTCGCTTGATGAC-TGAACTTTTGATGACTTGA
8666971 TC
1 TC
8666973 ATGAGCTTCA
Statistics
Matches: 111, Mismatches: 11, Indels: 36
0.70 0.07 0.23
Matches are distributed among these distances:
41 5 0.05
42 5 0.05
43 3 0.03
44 2 0.02
45 18 0.16
46 21 0.19
47 39 0.35
48 8 0.07
49 4 0.04
50 6 0.05
ACGTcount: A:0.26, C:0.21, G:0.16, T:0.37
Consensus pattern (46 bp):
TCTTGATCACGAACTTCGCTTGATGACTGAACTTTTGATGACTTGA
Found at i:8667117 original size:11 final size:11
Alignment explanation
Indices: 8667101--8667135 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
8667091 CATAATGTAA
8667101 TATCTTTAAAT
1 TATCTTTAAAT
8667112 TATCTTTAAAT
1 TATCTTTAAAT
*
8667123 TAT-TTTAATT
1 TATCTTTAAAT
8667133 TAT
1 TAT
8667136 TTAGAGATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (11 bp):
TATCTTTAAAT
Found at i:8676864 original size:2 final size:2
Alignment explanation
Indices: 8676857--8676881 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8676847 AAATATTGGA
8676857 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8676882 AAGAAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8692741 original size:5 final size:5
Alignment explanation
Indices: 8692731--8692756 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
8692721 CTCTTTAGGA
8692731 TAATT TAATT TAATT TAATT TAATT T
1 TAATT TAATT TAATT TAATT TAATT T
8692757 TAATGGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
TAATT
Found at i:8697595 original size:14 final size:14
Alignment explanation
Indices: 8697573--8697606 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
8697563 AGTGATTGAA
8697573 GGTACAATCAAACC
1 GGTACAATCAAACC
* *
8697587 GGTATAATCAAACT
1 GGTACAATCAAACC
8697601 GGTACA
1 GGTACA
8697607 TATTTCAACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.41, C:0.21, G:0.18, T:0.21
Consensus pattern (14 bp):
GGTACAATCAAACC
Found at i:8731471 original size:15 final size:15
Alignment explanation
Indices: 8731431--8731468 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
8731421 TTTCTTCAAT
8731431 ATAAAATTTATATGA
1 ATAAAATTTATATGA
* *
8731446 TTAAAAATTATA-GA
1 ATAAAATTTATATGA
8731460 ATAAAATTT
1 ATAAAATTT
8731469 TATTTAAATA
Statistics
Matches: 19, Mismatches: 4, Indels: 1
0.79 0.17 0.04
Matches are distributed among these distances:
14 9 0.47
15 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (15 bp):
ATAAAATTTATATGA
Found at i:8741677 original size:99 final size:99
Alignment explanation
Indices: 8741555--8741752 Score: 342
Period size: 99 Copynumber: 2.0 Consensus size: 99
8741545 TGACAACTTC
* *
8741555 TACATGTAAAATGATTTAAACTGTAGATACCAAATATCGAGTGGCGGTTGGCTATGGATTATCTC
1 TACATGTAAAATGATTCAAACTGTAGATACCAAATATCGAGTGGCGGTTGGCTATGGATTATCTA
*
8741620 TAGTTTCCTCCTCTCTCTGTCTAGTTCAGTCTCA
66 TAGTTTCCTCCTCTCTCTGTCCAGTTCAGTCTCA
* *
8741654 TACATGTAAAATGATTCAAACTGTAGATATCAAATATCTAGTGGCGGTTGGCTATGGATTATCTA
1 TACATGTAAAATGATTCAAACTGTAGATACCAAATATCGAGTGGCGGTTGGCTATGGATTATCTA
*
8741719 TGGTTTCCTCCTCTCTCTGTCCAGTTCAGTCTCA
66 TAGTTTCCTCCTCTCTCTGTCCAGTTCAGTCTCA
8741753 AGATCCCCAG
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
99 93 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (99 bp):
TACATGTAAAATGATTCAAACTGTAGATACCAAATATCGAGTGGCGGTTGGCTATGGATTATCTA
TAGTTTCCTCCTCTCTCTGTCCAGTTCAGTCTCA
Found at i:8751610 original size:2 final size:2
Alignment explanation
Indices: 8751605--8751640 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
8751595 TGTATATCTT
* *
8751605 TA TA TA TA TA TA TA TG TA TA TA TT TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8751641 ATTTGTTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:8751630 original size:24 final size:24
Alignment explanation
Indices: 8751595--8751640 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
8751585 ATAAAAAAAT
*
8751595 TGTATATCTTTATATATATATATA
1 TGTATATATTTATATATATATATA
8751619 TGTATATATTTATATATATATA
1 TGTATATATTTATATATATATA
8751641 ATTTGTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TGTATATATTTATATATATATATA
Found at i:8755932 original size:16 final size:17
Alignment explanation
Indices: 8755899--8755935 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8755889 ATAAAAATAC
*
8755899 TTAAATTTGATCTTAAA
1 TTAAATTTAATCTTAAA
8755916 TTAAATTTAAT-TTAAA
1 TTAAATTTAATCTTAAA
8755932 TTAA
1 TTAA
8755936 TTAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.47
17 10 0.53
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (17 bp):
TTAAATTTAATCTTAAA
Found at i:8778559 original size:18 final size:19
Alignment explanation
Indices: 8778521--8778561 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
8778511 ATAAAAAGTC
*
8778521 AAAAACATCAAACAAATAG
1 AAAAACAACAAACAAATAG
*
8778540 AAAAACAACAAAGAAA-AG
1 AAAAACAACAAACAAATAG
8778558 AAAA
1 AAAA
8778562 TCTGCCAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 6 0.30
19 14 0.70
ACGTcount: A:0.76, C:0.12, G:0.07, T:0.05
Consensus pattern (19 bp):
AAAAACAACAAACAAATAG
Found at i:8782968 original size:2 final size:2
Alignment explanation
Indices: 8782961--8782989 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
8782951 GTGCTGTCAT
8782961 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
8782990 CCAAAAAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:8793379 original size:2 final size:2
Alignment explanation
Indices: 8793374--8793399 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
8793364 CATTTTTATT
8793374 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
8793400 AAATCTATCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:8821693 original size:23 final size:23
Alignment explanation
Indices: 8821663--8821710 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
8821653 AACATTCCTC
8821663 TTTGCTCTACCTATGCTGATAAA
1 TTTGCTCTACCTATGCTGATAAA
8821686 TTTGCTCTACCTATGCTGATAAA
1 TTTGCTCTACCTATGCTGATAAA
8821709 TT
1 TT
8821711 ATGTACATTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.25, C:0.21, G:0.12, T:0.42
Consensus pattern (23 bp):
TTTGCTCTACCTATGCTGATAAA
Found at i:8822045 original size:21 final size:21
Alignment explanation
Indices: 8822019--8822060 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
8822009 GATCGTTTTT
8822019 ATATTAGGCTTATCAAAAAGC
1 ATATTAGGCTTATCAAAAAGC
8822040 ATATTAGGCTTATCAAAAAGC
1 ATATTAGGCTTATCAAAAAGC
8822061 TGAATGGCCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (21 bp):
ATATTAGGCTTATCAAAAAGC
Found at i:8827906 original size:3 final size:3
Alignment explanation
Indices: 8827898--8827934 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
8827888 CCATTTAGTA
* *
8827898 ATG ATG ATG ATG ATG ATG ATG ACG ATG ATG AGG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
8827935 AGATCAGTGT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.35, T:0.27
Consensus pattern (3 bp):
ATG
Found at i:8829876 original size:6 final size:6
Alignment explanation
Indices: 8829859--8829904 Score: 65
Period size: 6 Copynumber: 7.7 Consensus size: 6
8829849 AGAGGAAGTT
* * *
8829859 GGTTTG AGTTTG GATTTG GGTTTG GGTTTG GGTTGG GGTTTG GGTT
1 GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTTTG GGTT
8829905 GTTTTACCCT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.04, C:0.00, G:0.48, T:0.48
Consensus pattern (6 bp):
GGTTTG
Found at i:8834617 original size:16 final size:18
Alignment explanation
Indices: 8834587--8834628 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
8834577 GATTTTCACG
8834587 TCTTCTTCT-TT-C-TTT
1 TCTTCTTCTCTTCCTTTT
8834602 TCTT-TTCTCTTCCTTTT
1 TCTTCTTCTCTTCCTTTT
8834619 TCTTCTTCTC
1 TCTTCTTCTC
8834629 CCCAATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.17
15 6 0.26
16 1 0.04
17 7 0.30
18 5 0.22
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (18 bp):
TCTTCTTCTCTTCCTTTT
Found at i:8836399 original size:19 final size:19
Alignment explanation
Indices: 8836375--8836411 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
8836365 CCTTAACCAC
8836375 AATAATGATTTGCAGATCA
1 AATAATGATTTGCAGATCA
8836394 AATAATGATTTGCAGATC
1 AATAATGATTTGCAGATC
8836412 TCCTCTGTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (19 bp):
AATAATGATTTGCAGATCA
Found at i:8840858 original size:27 final size:26
Alignment explanation
Indices: 8840828--8840891 Score: 67
Period size: 28 Copynumber: 2.4 Consensus size: 26
8840818 CTATGGTTTA
* * *
8840828 TAAAATTTAATTTTATTATTAAAATAT
1 TAAAATTTAATATTATAATAAAAAT-T
8840855 TAAAATATCT-ATATTATAATAAAAATT
1 TAAAAT-T-TAATATTATAATAAAAATT
8840882 TAAAATTTAA
1 TAAAATTTAA
8840892 AATAAATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
25 1 0.03
26 2 0.06
27 13 0.42
28 14 0.45
29 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TAAAATTTAATATTATAATAAAAATT
Found at i:8840903 original size:35 final size:35
Alignment explanation
Indices: 8840846--8840912 Score: 84
Period size: 35 Copynumber: 1.9 Consensus size: 35
8840836 AATTTTATTA
* *
8840846 TTAAAATATTAAAATATCTATATTATAATAAAAAT
1 TTAAAATATTAAAATATCTATATCAAAATAAAAAT
8840881 TTAAAAT-TTAAAATAAAT-TATATCAAAATAAA
1 TTAAAATATTAAAAT--ATCTATATCAAAATAAA
8840913 CGCGAGTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
34 7 0.25
35 19 0.68
36 2 0.07
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (35 bp):
TTAAAATATTAAAATATCTATATCAAAATAAAAAT
Found at i:8849264 original size:2 final size:2
Alignment explanation
Indices: 8849231--8849255 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
8849221 ATAATTTCTA
8849231 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
8849256 AAAATATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:8860284 original size:162 final size:163
Alignment explanation
Indices: 8860082--8860397 Score: 472
Period size: 162 Copynumber: 1.9 Consensus size: 163
8860072 GAAGAATCTG
* *
8860082 ATCTGAACCCAAGCTTTAAGATTGTTTCAGTTCATAATACCTTTAGCAAGAGTGATGCTGACCAG
1 ATCTGAACCCAAGCTTTAAGATTGTTTCAGTTCATAATACCTTTAGCAAGAATGATGCTAACCAG
* * * * * **
8860147 TTTAGAGAGACCTTGAAGAGGAGGAGATGTGATAGGGCTGCCAATCGGAAGTGTGTTGGAGGCAT
66 ATTAGAGAGACCTTGAAGAGGAGAAGATGTGATAGAGCTGCAAATCGGAAGTATGTCCGAGGCAT
* * *
8860212 AGAAGATGAGGCAGACAGTGAAGCAACTGAGGA
131 AGAAGACGAGACAAACAGTGAAGCAACTGAGGA
* * * *
8860245 ATCTG-ACCGAAGCTTTAAGATTGTTTCAGTTCGTAATACCTTTAGTAAGAATGATGCTAACCGG
1 ATCTGAACCCAAGCTTTAAGATTGTTTCAGTTCATAATACCTTTAGCAAGAATGATGCTAACCAG
8860309 ATTAGAGAGACCTTGAAGAGGAGAAGATGTGATAGAGCTGCAAATCGGAAGTATGTCCGAGGCAT
66 ATTAGAGAGACCTTGAAGAGGAGAAGATGTGATAGAGCTGCAAATCGGAAGTATGTCCGAGGCAT
*
8860374 AGATGACGAGACAAACAGTGAAGC
131 AGAAGACGAGACAAACAGTGAAGC
8860398 CTGGATAGAG
Statistics
Matches: 136, Mismatches: 17, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
162 131 0.96
163 5 0.04
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.23
Consensus pattern (163 bp):
ATCTGAACCCAAGCTTTAAGATTGTTTCAGTTCATAATACCTTTAGCAAGAATGATGCTAACCAG
ATTAGAGAGACCTTGAAGAGGAGAAGATGTGATAGAGCTGCAAATCGGAAGTATGTCCGAGGCAT
AGAAGACGAGACAAACAGTGAAGCAACTGAGGA
Found at i:8866411 original size:15 final size:15
Alignment explanation
Indices: 8866388--8866417 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
8866378 CTTATGTATA
*
8866388 CATATTCAAAATTAT
1 CATACTCAAAATTAT
8866403 CATACTCAAAATTAT
1 CATACTCAAAATTAT
8866418 AAGAACGTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (15 bp):
CATACTCAAAATTAT
Found at i:8866738 original size:2 final size:2
Alignment explanation
Indices: 8866733--8866766 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
8866723 CTCTCCCACA
*
8866733 AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
8866767 TTCCCATGTC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:8868668 original size:2 final size:2
Alignment explanation
Indices: 8868656--8868714 Score: 97
Period size: 2 Copynumber: 31.0 Consensus size: 2
8868646 TGTAAGTCAC
8868656 CT CT C- CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C- CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
8868696 C- CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT
8868715 ATGCTTTCTA
Statistics
Matches: 54, Mismatches: 0, Indels: 6
0.90 0.00 0.10
Matches are distributed among these distances:
1 3 0.06
2 51 0.94
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (2 bp):
CT
Found at i:8874773 original size:25 final size:26
Alignment explanation
Indices: 8874723--8874774 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
8874713 AGGTATTTTT
*
8874723 TAATAAAATTAATTAAATTTAAATAA
1 TAATAAAATTAATTAAATTCAAATAA
*
8874749 TAAT-AAATT-ATATAAATTCATATAA
1 TAATAAAATTAAT-TAAATTCAAATAA
8874774 T
1 T
8874775 CAAACTTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 2 0.09
25 17 0.74
26 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (26 bp):
TAATAAAATTAATTAAATTCAAATAA
Found at i:8875470 original size:16 final size:17
Alignment explanation
Indices: 8875433--8875469 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
8875423 AATAATTAAA
**
8875433 TTTTAAAAGTAATTATT
1 TTTTAAAAAAAATTATT
8875450 TTTTAAAAAAAATTATT
1 TTTTAAAAAAAATTATT
8875467 TTT
1 TTT
8875470 ACTTGTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (17 bp):
TTTTAAAAAAAATTATT
Done.