Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007772.1 Hibiscus syriacus cultivar Beakdansim tig00110053_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1636317
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 8 of 9
Found at i:1345422 original size:22 final size:25
Alignment explanation
Indices: 1345382--1345428 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
1345372 AAAAAAAATT
1345382 AAAATATATTACTAATTT-ATAAAA
1 AAAATATATTACTAATTTAATAAAA
*
1345406 AAAAT-TATTA-TACTTTAATAAAA
1 AAAATATATTACTAATTTAATAAAA
1345429 TTTGTCACAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 11 0.52
24 5 0.24
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.38
Consensus pattern (25 bp):
AAAATATATTACTAATTTAATAAAA
Found at i:1348445 original size:39 final size:39
Alignment explanation
Indices: 1348388--1348479 Score: 166
Period size: 39 Copynumber: 2.4 Consensus size: 39
1348378 ACATTGAACT
*
1348388 TAAGTTTATCAATGGAGGATGCTTCCCATGAGCCAATAA
1 TAAGTTTATCAATGGAGGATGCTGCCCATGAGCCAATAA
*
1348427 TAGGTTTATCAATGGAGGATGCTGCCCATGAGCCAATAA
1 TAAGTTTATCAATGGAGGATGCTGCCCATGAGCCAATAA
1348466 TAAGTTTATCAATG
1 TAAGTTTATCAATG
1348480 AAATCGCTAA
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
39 50 1.00
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (39 bp):
TAAGTTTATCAATGGAGGATGCTGCCCATGAGCCAATAA
Found at i:1352186 original size:73 final size:73
Alignment explanation
Indices: 1352067--1352212 Score: 292
Period size: 73 Copynumber: 2.0 Consensus size: 73
1352057 TTGTCAGATT
1352067 GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACACTCATCTGACGTATCAAACTCAAC
1 GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACACTCATCTGACGTATCAAACTCAAC
1352132 ACCTATAA
66 ACCTATAA
1352140 GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACACTCATCTGACGTATCAAACTCAAC
1 GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACACTCATCTGACGTATCAAACTCAAC
1352205 ACCTATAA
66 ACCTATAA
1352213 TTCTATTGGT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
73 73 1.00
ACGTcount: A:0.29, C:0.33, G:0.11, T:0.27
Consensus pattern (73 bp):
GCATTCTCTTCCTCTAACTCCCTGATGTACTGGAGCACACACTCATCTGACGTATCAAACTCAAC
ACCTATAA
Found at i:1353937 original size:39 final size:39
Alignment explanation
Indices: 1353883--1354012 Score: 156
Period size: 39 Copynumber: 3.3 Consensus size: 39
1353873 AAGGGCCTAG
* *
1353883 GGTAAGGACTTACCCTATGCACAAAGCAGAGGA-TATTGC
1 GGTAAGGACTTACCCTATGCACAAAGTAGAGGAGT-CTGC
*
1353922 GGTAA-GAGCTTACCCTATGCACAAAGTAGAGGAGTCTGT
1 GGTAAGGA-CTTACCCTATGCACAAAGTAGAGGAGTCTGC
* * **
1353961 GGTAAGGACTTACCCTATGAACAAAGTAGAGGAGCCTAT
1 GGTAAGGACTTACCCTATGCACAAAGTAGAGGAGTCTGC
*
1354000 GGTAAGGTCTTAC
1 GGTAAGGACTTAC
1354013 AAGTCATAAA
Statistics
Matches: 81, Mismatches: 7, Indels: 6
0.86 0.07 0.06
Matches are distributed among these distances:
38 2 0.02
39 76 0.94
40 3 0.04
ACGTcount: A:0.32, C:0.18, G:0.27, T:0.22
Consensus pattern (39 bp):
GGTAAGGACTTACCCTATGCACAAAGTAGAGGAGTCTGC
Found at i:1354961 original size:27 final size:26
Alignment explanation
Indices: 1354931--1355009 Score: 61
Period size: 27 Copynumber: 2.9 Consensus size: 26
1354921 CATTCTAGAA
1354931 CTCGCAGGTATTTCAATCATTTTAAAG
1 CTCG-AGGTATTTCAATCATTTTAAAG
* ** *
1354958 CTCGATGGTACTAT-GGTCATTTTGAAG
1 CTCGA-GGTA-TTTCAATCATTTTAAAG
* *
1354985 CTTGGGGGTATTTCAATCATTTTAA
1 C-TCGAGGTATTTCAATCATTTTAA
1355010 TCAATTAAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 8
0.68 0.18 0.14
Matches are distributed among these distances:
26 3 0.08
27 31 0.82
28 4 0.11
ACGTcount: A:0.25, C:0.15, G:0.20, T:0.39
Consensus pattern (26 bp):
CTCGAGGTATTTCAATCATTTTAAAG
Found at i:1357225 original size:21 final size:21
Alignment explanation
Indices: 1357201--1357269 Score: 70
Period size: 21 Copynumber: 3.2 Consensus size: 21
1357191 ATACATGTGA
1357201 GGTGGAGGTGGGTGATATATT
1 GGTGGAGGTGGGTGATATATT
* * *
1357222 GGTGGCGGAGGGT-ACAT-TT
1 GGTGGAGGTGGGTGATATATT
1357241 GAGGGTGGAGGTGGGTGATATATT
1 ---GGTGGAGGTGGGTGATATATT
1357265 GGTGG
1 GGTGG
1357270 CGGAGGGTAC
Statistics
Matches: 37, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
19 2 0.05
20 3 0.08
21 16 0.43
22 11 0.30
23 3 0.08
24 2 0.05
ACGTcount: A:0.17, C:0.03, G:0.51, T:0.29
Consensus pattern (21 bp):
GGTGGAGGTGGGTGATATATT
Found at i:1357248 original size:22 final size:22
Alignment explanation
Indices: 1357222--1357287 Score: 66
Period size: 22 Copynumber: 3.0 Consensus size: 22
1357212 GTGATATATT
1357222 GGTGGCGGAGGGTACATTTGAG
1 GGTGGCGGAGGGTACATTTGAG
* * *
1357244 GGTGGAGGTGGGTGATATATT---
1 GGTGGCGGAGGGT-ACAT-TTGAG
1357265 GGTGGCGGAGGGTACATTTGAG
1 GGTGGCGGAGGGTACATTTGAG
1357287 G
1 G
1357288 CTGATATGGT
Statistics
Matches: 33, Mismatches: 6, Indels: 10
0.67 0.12 0.20
Matches are distributed among these distances:
19 2 0.06
20 3 0.09
21 11 0.33
22 12 0.36
23 3 0.09
24 2 0.06
ACGTcount: A:0.18, C:0.06, G:0.50, T:0.26
Consensus pattern (22 bp):
GGTGGCGGAGGGTACATTTGAG
Found at i:1357261 original size:43 final size:43
Alignment explanation
Indices: 1357186--1357287 Score: 179
Period size: 43 Copynumber: 2.4 Consensus size: 43
1357176 TACTCGAGGA
* *
1357186 GGAGGATACATGTGA-GGTGGAGGTGGGTGATATATTGGTGGC
1 GGAGGGTACATTTGAGGGTGGAGGTGGGTGATATATTGGTGGC
1357228 GGAGGGTACATTTGAGGGTGGAGGTGGGTGATATATTGGTGGC
1 GGAGGGTACATTTGAGGGTGGAGGTGGGTGATATATTGGTGGC
1357271 GGAGGGTACATTTGAGG
1 GGAGGGTACATTTGAGG
1357288 CTGATATGGT
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
42 13 0.23
43 44 0.77
ACGTcount: A:0.21, C:0.05, G:0.48, T:0.26
Consensus pattern (43 bp):
GGAGGGTACATTTGAGGGTGGAGGTGGGTGATATATTGGTGGC
Found at i:1357277 original size:21 final size:21
Alignment explanation
Indices: 1357201--1357277 Score: 68
Period size: 21 Copynumber: 3.6 Consensus size: 21
1357191 ATACATGTGA
*
1357201 GGTGGAGGTGGGTGATATATT
1 GGTGGAGGAGGGTGATATATT
* *
1357222 GGTGGCGGAGGGT-ACAT-TT
1 GGTGGAGGAGGGTGATATATT
*
1357241 GAGGGTGGAGGTGGGTGATATATT
1 ---GGTGGAGGAGGGTGATATATT
*
1357265 GGTGGCGGAGGGT
1 GGTGGAGGAGGGT
1357278 ACATTTGAGG
Statistics
Matches: 43, Mismatches: 8, Indels: 10
0.70 0.13 0.16
Matches are distributed among these distances:
19 2 0.05
20 3 0.07
21 22 0.51
22 11 0.26
23 3 0.07
24 2 0.05
ACGTcount: A:0.17, C:0.04, G:0.52, T:0.27
Consensus pattern (21 bp):
GGTGGAGGAGGGTGATATATT
Found at i:1361779 original size:30 final size:30
Alignment explanation
Indices: 1361743--1361809 Score: 125
Period size: 30 Copynumber: 2.2 Consensus size: 30
1361733 TCAACAGTCA
1361743 AAATCAATGTTGGTCAACGGTGATTGACGG
1 AAATCAATGTTGGTCAACGGTGATTGACGG
1361773 AAATCAATGTTGGTCAACGGTGATTGACGG
1 AAATCAATGTTGGTCAACGGTGATTGACGG
*
1361803 CAATCAA
1 AAATCAA
1361810 CGGTCAATAG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (30 bp):
AAATCAATGTTGGTCAACGGTGATTGACGG
Found at i:1367156 original size:8 final size:8
Alignment explanation
Indices: 1367143--1367183 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
1367133 CTCATTTTCA
1367143 GAGAATTT
1 GAGAATTT
1367151 GAGAATTT
1 GAGAATTT
*
1367159 -AGAGTTT
1 GAGAATTT
*
1367166 GGGAATTT
1 GAGAATTT
1367174 GAGAATTT
1 GAGAATTT
1367182 GA
1 GA
1367184 AAGCTTGTGA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (8 bp):
GAGAATTT
Found at i:1367492 original size:128 final size:128
Alignment explanation
Indices: 1367264--1367731 Score: 789
Period size: 118 Copynumber: 3.7 Consensus size: 128
1367254 ACTATTCACA
*
1367264 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1367329 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
*
1367392 TGAAGGCGCATTCCCGGGGGCGCGTCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
*
1367457 TTATGTCACTCATGTCCCTCGGGGACAC---T-AT-TC---A--TATTATTTCTTAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
* * *
1367510 TGAAGGCGCGTTCCCGGGGGCGCGCCTTCTATTATTTTGTCAGAGAATATGTTATCATTTCCCTA
1 TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
1367575 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTA-TTCTCAGGGGACT
66 TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
1367637 TGAAGGCG-AGTTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1 TGAAGGCGCA-TTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCT
1367701 ATTATGTCACTCATGTCCCTCGGGGACACTA
65 ATTATGTCACTCATGTCCCTCGGGGACACTA
1367732 GATGGATTGT
Statistics
Matches: 318, Mismatches: 11, Indels: 23
0.90 0.03 0.07
Matches are distributed among these distances:
118 107 0.34
120 1 0.00
121 1 0.00
122 2 0.01
123 4 0.01
124 2 0.01
125 1 0.00
126 1 0.00
127 103 0.32
128 96 0.30
ACGTcount: A:0.20, C:0.24, G:0.22, T:0.33
Consensus pattern (128 bp):
TGAAGGCGCATTCCCGGGGGCGCGCCTTCCATTATTTTGTCAGAGAATATGTTATCATTGCCCTA
TTATGTCACTCATGTCCCTCGGGGACACTATTCATATCAGTACCTATTATTTCTCAGGGGACT
Found at i:1368228 original size:33 final size:33
Alignment explanation
Indices: 1368126--1368231 Score: 122
Period size: 33 Copynumber: 3.2 Consensus size: 33
1368116 TAAGTTGAAA
* *
1368126 TTTAATGTTAAATTTTGAATACTATAATTTATAT
1 TTTAAT-TTAAATTTCGAATAATATAATTTATAT
* ** *
1368160 TTTAAATTTAAATTTCAAATAATATTTTTTTTAT
1 TTT-AATTTAAATTTCGAATAATATAATTTATAT
* *
1368194 TTTATTTTAAATTTCGAATAATATAATTTGTAT
1 TTTAATTTAAATTTCGAATAATATAATTTATAT
1368227 TTTAA
1 TTTAA
1368232 AAACATTTAT
Statistics
Matches: 59, Mismatches: 12, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
33 29 0.49
34 27 0.46
35 3 0.05
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.56
Consensus pattern (33 bp):
TTTAATTTAAATTTCGAATAATATAATTTATAT
Found at i:1368855 original size:63 final size:63
Alignment explanation
Indices: 1368756--1368878 Score: 228
Period size: 63 Copynumber: 2.0 Consensus size: 63
1368746 ATAAAACCCT
*
1368756 GCGGGCTAGGCATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGAAATGTAACATG
1 GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGAAATGTAACATG
*
1368819 GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGGAATGTAAC
1 GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGAAATGTAAC
1368879 CCTGCGGAGA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
63 58 1.00
ACGTcount: A:0.24, C:0.22, G:0.36, T:0.19
Consensus pattern (63 bp):
GCGGGCTAGGAATGTAACCTGGCGGGCTAGGAATGTAACCCTGCGGGCTCGAAATGTAACATG
Found at i:1368880 original size:21 final size:21
Alignment explanation
Indices: 1368750--1368885 Score: 179
Period size: 21 Copynumber: 6.5 Consensus size: 21
1368740 TATGGTATAA
*
1368750 AACCCTGCGGGCTAGGCATGT
1 AACCCTGCGGGCTAGGAATGT
1368771 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
* *
1368792 AACCCTGCGGGCTCGAAATGT
1 AACCCTGCGGGCTAGGAATGT
*
1368813 AA-CATGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
1368834 AA-CCTGGCGGGCTAGGAATGT
1 AACCCT-GCGGGCTAGGAATGT
*
1368855 AACCCTGCGGGCTCGGAATGT
1 AACCCTGCGGGCTAGGAATGT
1368876 AACCCTGCGG
1 AACCCTGCGG
1368886 AGATGGCATA
Statistics
Matches: 103, Mismatches: 8, Indels: 8
0.87 0.07 0.07
Matches are distributed among these distances:
20 5 0.05
21 92 0.89
22 6 0.06
ACGTcount: A:0.23, C:0.24, G:0.35, T:0.18
Consensus pattern (21 bp):
AACCCTGCGGGCTAGGAATGT
Found at i:1368934 original size:20 final size:21
Alignment explanation
Indices: 1368890--1368935 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
1368880 CTGCGGAGAT
* *
1368890 GGCATATGAACTGGTGGGCTT
1 GGCATATGAACTGGAGGGCTG
*
1368911 GGCATATGAAGT-GAGGGCTG
1 GGCATATGAACTGGAGGGCTG
1368931 GGCAT
1 GGCAT
1368936 GTACCCTTGC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 11 0.50
21 11 0.50
ACGTcount: A:0.22, C:0.13, G:0.41, T:0.24
Consensus pattern (21 bp):
GGCATATGAACTGGAGGGCTG
Found at i:1370718 original size:30 final size:32
Alignment explanation
Indices: 1370654--1370732 Score: 90
Period size: 33 Copynumber: 2.4 Consensus size: 32
1370644 TTAATAATTC
*
1370654 TAAATAAATAATAATTATATAAATATTATTTTAA
1 TAAA-AAATAATAATTACATAAATATTA-TTTAA
*
1370688 TAAAAAATAATATTTACATAAATA-TA-TTAA
1 TAAAAAATAATAATTACATAAATATTATTTAA
1370718 TATAAAATATAATAA
1 TA-AAAA-ATAATAA
1370733 CTATTTAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 6 0.15
31 4 0.10
32 8 0.20
33 18 0.45
34 4 0.10
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.39
Consensus pattern (32 bp):
TAAAAAATAATAATTACATAAATATTATTTAA
Found at i:1375580 original size:21 final size:22
Alignment explanation
Indices: 1375537--1375580 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
1375527 ATTCAATTAA
* *
1375537 ACATGTTTAACATGTGAATTCC
1 ACATGTTTAAAATGCGAATTCC
1375559 ACATGTTTAAAATGCG-ATTCC
1 ACATGTTTAAAATGCGAATTCC
1375580 A
1 A
1375581 TGGAGAGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (22 bp):
ACATGTTTAAAATGCGAATTCC
Found at i:1376049 original size:21 final size:21
Alignment explanation
Indices: 1376016--1376055 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
1376006 AGTCTAAATG
* *
1376016 TACCAAATGTTTTACTAAACA
1 TACCAAATCTTTTAATAAACA
*
1376037 TACCAATTCTTTTAATAAA
1 TACCAAATCTTTTAATAAA
1376056 ATAATAGAAA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (21 bp):
TACCAAATCTTTTAATAAACA
Found at i:1376457 original size:17 final size:18
Alignment explanation
Indices: 1376435--1376477 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 18
1376425 GCGACATATA
1376435 AAAATA-TATTATTAACT
1 AAAATATTATTATTAACT
* *
1376452 AAAATATTCTTATTAAGT
1 AAAATATTATTATTAACT
1376470 -AAATATTA
1 AAAATATTA
1376478 AATAATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 13 0.59
18 9 0.41
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (18 bp):
AAAATATTATTATTAACT
Found at i:1376464 original size:18 final size:17
Alignment explanation
Indices: 1376443--1376476 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
1376433 TAAAAATATA
1376443 TTATTAACTAAAATATTC
1 TTATTAACT-AAATATTC
*
1376461 TTATTAAGTAAATATT
1 TTATTAACTAAATATT
1376477 AAATAATAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.06, G:0.03, T:0.47
Consensus pattern (17 bp):
TTATTAACTAAATATTC
Found at i:1378508 original size:13 final size:13
Alignment explanation
Indices: 1378492--1378519 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1378482 TTTGATATGA
1378492 AATATTAAAAAAT
1 AATATTAAAAAAT
1378505 AATATTAAAAAAT
1 AATATTAAAAAAT
1378518 AA
1 AA
1378520 AAATATGTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AATATTAAAAAAT
Found at i:1387090 original size:94 final size:94
Alignment explanation
Indices: 1386929--1387118 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
1386919 TAATGCGTTA
1386929 TGTCGGATGTTAAAGCAGCTTGCTCGGTTAAAACAAATTCTGTCAGATGTAGGTTGATGCTATTT
1 TGTCGGATGTTAAAGCAGCTTGCTCGGTTAAAACAAATTCTGTCAGATGTAGGTTGATGCTATTT
1386994 TAGCATTTACAAAATTATTGGACTTGACT
66 TAGCATTTACAAAATTATTGGACTTGACT
1387023 TGTCGGATGTTAAAGCAGCTTGCTCGGTTAAAACAAATTCTGTCAGATGTAGGTTGATGCTATTT
1 TGTCGGATGTTAAAGCAGCTTGCTCGGTTAAAACAAATTCTGTCAGATGTAGGTTGATGCTATTT
1387088 TAGCATTTACAAAATTATTGGACTTGACT
66 TAGCATTTACAAAATTATTGGACTTGACT
1387117 TG
1 TG
1387119 ACATGACTTT
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.28, C:0.14, G:0.22, T:0.36
Consensus pattern (94 bp):
TGTCGGATGTTAAAGCAGCTTGCTCGGTTAAAACAAATTCTGTCAGATGTAGGTTGATGCTATTT
TAGCATTTACAAAATTATTGGACTTGACT
Found at i:1387859 original size:13 final size:13
Alignment explanation
Indices: 1387841--1387875 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
1387831 AAAATTTATG
*
1387841 AAAATAAATGAAT
1 AAAATAAATAAAT
1387854 AAAATAAATAAAT
1 AAAATAAATAAAT
1387867 -AAATAAATA
1 AAAATAAATA
1387876 TTGAATAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
12 9 0.43
13 12 0.57
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (13 bp):
AAAATAAATAAAT
Found at i:1387862 original size:4 final size:4
Alignment explanation
Indices: 1387842--1387875 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
1387832 AAATTTATGA
*
1387842 AAAT AAAT GAAT AAAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT -AAAT AAAT AAAT AAAT AAAT A
1387876 TTGAATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1390501 original size:14 final size:15
Alignment explanation
Indices: 1390482--1390546 Score: 73
Period size: 14 Copynumber: 4.4 Consensus size: 15
1390472 TTACATGAAA
1390482 ATGTGATATAAGT-T
1 ATGTGATATAAGTCT
*
1390496 ATGTGATA-ATGATCT
1 ATGTGATATAAG-TCT
*
1390511 ATGTGATTATATGTCT
1 ATGTGA-TATAAGTCT
1390527 ATGTGATATAA-TCT
1 ATGTGATATAAGTCT
1390541 ATGTGA
1 ATGTGA
1390547 AATGTTATAA
Statistics
Matches: 45, Mismatches: 2, Indels: 8
0.82 0.04 0.15
Matches are distributed among these distances:
13 2 0.04
14 18 0.40
15 11 0.24
16 11 0.24
17 3 0.07
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (15 bp):
ATGTGATATAAGTCT
Found at i:1390513 original size:45 final size:45
Alignment explanation
Indices: 1390409--1390550 Score: 157
Period size: 45 Copynumber: 3.2 Consensus size: 45
1390399 GTATGCTATA
* * *
1390409 TGATATTGACCTATGTGATTACATGAAAATGAGATATAAGCTATG
1 TGATAATGACCTATGTGATTACATGAAAATGTGATATAAGTTATG
1390454 TAGCAT--TGACCTATGTGATTACATGAAAATGTGATATAAGTTATG
1 T-G-ATAATGACCTATGTGATTACATGAAAATGTGATATAAGTTATG
* * ***
1390499 TGATAATGATCTATGTGATTATATGTCTATGTGATATAA-TCTATG
1 TGATAATGACCTATGTGATTACATGAAAATGTGATATAAGT-TATG
1390544 TGA-AATG
1 TGATAATG
1390551 TTATAAATGA
Statistics
Matches: 85, Mismatches: 7, Indels: 11
0.83 0.07 0.11
Matches are distributed among these distances:
43 2 0.02
44 6 0.07
45 74 0.87
46 1 0.01
47 2 0.02
ACGTcount: A:0.35, C:0.08, G:0.20, T:0.37
Consensus pattern (45 bp):
TGATAATGACCTATGTGATTACATGAAAATGTGATATAAGTTATG
Found at i:1390543 original size:30 final size:29
Alignment explanation
Indices: 1390482--1390546 Score: 87
Period size: 30 Copynumber: 2.2 Consensus size: 29
1390472 TTACATGAAA
*
1390482 ATGTGATATAAGTTATGTGATAATGATCT
1 ATGTGATATAAGTTATGTGATAATAATCT
*
1390511 ATGTGATTATATGTCTATGTGAT-ATAATCT
1 ATGTGA-TATAAGT-TATGTGATAATAATCT
1390541 ATGTGA
1 ATGTGA
1390547 AATGTTATAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
29 6 0.19
30 18 0.56
31 8 0.25
ACGTcount: A:0.32, C:0.05, G:0.20, T:0.43
Consensus pattern (29 bp):
ATGTGATATAAGTTATGTGATAATAATCT
Found at i:1390686 original size:23 final size:23
Alignment explanation
Indices: 1390623--1390723 Score: 130
Period size: 23 Copynumber: 4.4 Consensus size: 23
1390613 GAGTCGAGGG
* * *
1390623 TTCTACGCGGTCCTTCGAGACAA
1 TTCTACGTGGTCCTTCGGGACAT
1390646 TTCTACGTGGTCCTTCGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
*
1390669 TTCTACGTGGTCCTTCGGGCCAT
1 TTCTACGTGGTCCTTCGGGACAT
* * * *
1390692 ATCTATGTGGTCTTTCGGAACAT
1 TTCTACGTGGTCCTTCGGGACAT
1390715 TTCTACGTG
1 TTCTACGTG
1390724 ACACTTCGGT
Statistics
Matches: 67, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 67 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.35
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:1390731 original size:46 final size:47
Alignment explanation
Indices: 1390645--1390756 Score: 131
Period size: 46 Copynumber: 2.4 Consensus size: 47
1390635 CTTCGAGACA
* * *
1390645 ATTCTACGTGGTCCTTCGGGACATTTCTACGTGGTCCTTCGG-GCCAT
1 ATTCTATGTGGTCCTTCGGAACATTTCTACGTGGACCTTCGGTG-CAT
*
1390692 A-TCTATGTGGTCTTTCGGAACATTTCTACGT-GACACTTCGGTGCAT
1 ATTCTATGTGGTCCTTCGGAACATTTCTACGTGGAC-CTTCGGTGCAT
* *
1390738 ATTCTATGCGGTACTTCGG
1 ATTCTATGTGGTCCTTCGG
1390757 TGCAATTTAT
Statistics
Matches: 55, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
45 2 0.04
46 37 0.67
47 16 0.29
ACGTcount: A:0.16, C:0.24, G:0.24, T:0.36
Consensus pattern (47 bp):
ATTCTATGTGGTCCTTCGGAACATTTCTACGTGGACCTTCGGTGCAT
Found at i:1391696 original size:27 final size:27
Alignment explanation
Indices: 1391638--1391696 Score: 91
Period size: 27 Copynumber: 2.2 Consensus size: 27
1391628 ATTGGGCAGA
*
1391638 CTGATGTTGAAGCTAAGGGCTACTCGG
1 CTGATGTTGAAGCTAAGGGCTACTCAG
* *
1391665 GTGATGTTGAAGCTAAGGTCTACTCAG
1 CTGATGTTGAAGCTAAGGGCTACTCAG
1391692 CTGAT
1 CTGAT
1391697 AATCTTAGGG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.17, G:0.31, T:0.29
Consensus pattern (27 bp):
CTGATGTTGAAGCTAAGGGCTACTCAG
Found at i:1396136 original size:19 final size:19
Alignment explanation
Indices: 1396112--1396156 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
1396102 CTCAACCCCT
*
1396112 TTATCTTGAAATCGAGTAA
1 TTATCTTGAAATCAAGTAA
1396131 TTATCTTGAAATCAAGTAA
1 TTATCTTGAAATCAAGTAA
1396150 TTATCTT
1 TTATCTT
1396157 CTCGTTTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.36, C:0.11, G:0.11, T:0.42
Consensus pattern (19 bp):
TTATCTTGAAATCAAGTAA
Found at i:1405667 original size:21 final size:21
Alignment explanation
Indices: 1405620--1405667 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 21
1405610 TTACAAAAAG
* *
1405620 TATCAATACAAATATACATAG
1 TATCAAAACAAATATACATAA
*
1405641 TGTCAAAACAAATATA-ATAAA
1 TATCAAAACAAATATACAT-AA
1405662 TATCAA
1 TATCAA
1405668 TATTTTGTAC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 2 0.09
21 20 0.91
ACGTcount: A:0.56, C:0.12, G:0.04, T:0.27
Consensus pattern (21 bp):
TATCAAAACAAATATACATAA
Found at i:1408970 original size:19 final size:20
Alignment explanation
Indices: 1408934--1408984 Score: 54
Period size: 19 Copynumber: 2.6 Consensus size: 20
1408924 TTTTAAATGA
*
1408934 TTTA-TATTTAATTATTAT-
1 TTTATTATTTTATTATTATC
*
1408952 TTTATTATTTTATTCTTATC
1 TTTATTATTTTATTATTATC
1408972 TTT-TTATCTTTAT
1 TTTATTAT-TTTAT
1408985 CAGAAATTCT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
18 4 0.14
19 16 0.57
20 8 0.29
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.71
Consensus pattern (20 bp):
TTTATTATTTTATTATTATC
Found at i:1416722 original size:30 final size:29
Alignment explanation
Indices: 1416662--1416722 Score: 86
Period size: 30 Copynumber: 2.1 Consensus size: 29
1416652 CTTGTTCTAT
*
1416662 AAAAAATATTCATTGTTTCGAACATCAAAA
1 AAAAAATATTCATTGTTTCGAACA-GAAAA
* *
1416692 AAAAATTGTTCATTGTTTCGAACAGAAAA
1 AAAAAATATTCATTGTTTCGAACAGAAAA
1416721 AA
1 AA
1416723 GAAGGAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.49, C:0.11, G:0.10, T:0.30
Consensus pattern (29 bp):
AAAAAATATTCATTGTTTCGAACAGAAAA
Found at i:1418605 original size:12 final size:12
Alignment explanation
Indices: 1418588--1418613 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1418578 AAACGATTTA
1418588 TATTTAATTATT
1 TATTTAATTATT
1418600 TATTTAATTATT
1 TATTTAATTATT
1418612 TA
1 TA
1418614 ATTATTATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:1420628 original size:13 final size:13
Alignment explanation
Indices: 1420612--1420636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1420602 TAATGCTTCA
1420612 AAATAATAATAAT
1 AAATAATAATAAT
1420625 AAATAATAATAA
1 AAATAATAATAA
1420637 CAATACTATC
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:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAATAATAATAAT
Found at i:1420658 original size:24 final size:24
Alignment explanation
Indices: 1420631--1420689 Score: 109
Period size: 24 Copynumber: 2.5 Consensus size: 24
1420621 TAATAAATAA
*
1420631 TAATAACAATACTATCCTATTTCC
1 TAATAACAATACTATCATATTTCC
1420655 TAATAACAATACTATCATATTTCC
1 TAATAACAATACTATCATATTTCC
1420679 TAATAACAATA
1 TAATAACAATA
1420690 AAATAAATAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 34 1.00
ACGTcount: A:0.44, C:0.20, G:0.00, T:0.36
Consensus pattern (24 bp):
TAATAACAATACTATCATATTTCC
Found at i:1422171 original size:20 final size:19
Alignment explanation
Indices: 1422148--1422203 Score: 64
Period size: 18 Copynumber: 3.1 Consensus size: 19
1422138 AACTTTCTAT
1422148 TATTTTTATTATAAATCTAA
1 TATTTTTATTATAAAT-TAA
*
1422168 TATTTTTA--ATAAATTAT
1 TATTTTTATTATAAATTAA
*
1422185 TAATTTTATT-TAAATTAA
1 TATTTTTATTATAAATTAA
1422203 T
1 T
1422204 TTATTATTCA
Statistics
Matches: 31, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
17 9 0.29
18 14 0.45
20 8 0.26
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTTTTATTATAAATTAA
Found at i:1422302 original size:21 final size:21
Alignment explanation
Indices: 1422263--1422304 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1422253 TTTCTTTCGG
**
1422263 TTCGGGTTAATTTTGGTTTCA
1 TTCGGGTTAATTTCAGTTTCA
*
1422284 TTCGGGTTACTTTCAGTTTCA
1 TTCGGGTTAATTTCAGTTTCA
1422305 CTAAATTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.14, C:0.14, G:0.21, T:0.50
Consensus pattern (21 bp):
TTCGGGTTAATTTCAGTTTCA
Found at i:1435829 original size:13 final size:14
Alignment explanation
Indices: 1435804--1435837 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
1435794 TTTGGACCCT
1435804 GAAAA-AATAAAAA
1 GAAAATAATAAAAA
1435817 GAAAATAAT-AAAA
1 GAAAATAATAAAAA
1435830 GAAAATAA
1 GAAAATAA
1435838 ATAATAATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.85
14 3 0.15
ACGTcount: A:0.79, C:0.00, G:0.09, T:0.12
Consensus pattern (14 bp):
GAAAATAATAAAAA
Found at i:1435840 original size:14 final size:14
Alignment explanation
Indices: 1435808--1435841 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1435798 GACCCTGAAA
1435808 AAATAAAAAGAAAAT
1 AAAT-AAAAGAAAAT
1435823 -AATAAAAGAAAAT
1 AAATAAAAGAAAAT
1435836 AAATAA
1 AAATAA
1435842 TAATACTGAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.79, C:0.00, G:0.06, T:0.15
Consensus pattern (14 bp):
AAATAAAAGAAAAT
Found at i:1435911 original size:32 final size:32
Alignment explanation
Indices: 1435873--1436043 Score: 111
Period size: 31 Copynumber: 5.2 Consensus size: 32
1435863 TATATATACA
*
1435873 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTTCAAAAATATTTTTAAAACTATATAT
*
1435905 TATATTT-AAAAA-AGTTTTCAAAACTATAT-T
1 TATATTTCAAAAATA-TTTTTAAAACTATATAT
* *
1435935 ATATAGTTTTC-AAAAT-GTTTTAAAAATATTATAT
1 -TATA--TTTCAAAAATATTTTTAAAACTA-TATAT
* * **
1435969 AAGT-TTTAAAAAACGTTTTTAAAACTATATATT
1 TA-TATTTCAAAAATATTTTTAAAACTATATA-T
*
1436002 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-A--T-TTCAAAAATATTTTTAAAACTATATAT
1436039 TATAT
1 TATAT
1436044 AAGTTTTTAA
Statistics
Matches: 108, Mismatches: 13, Indels: 35
0.69 0.08 0.22
Matches are distributed among these distances:
30 2 0.02
31 25 0.23
32 24 0.22
33 24 0.22
34 3 0.03
35 1 0.01
36 3 0.03
37 2 0.02
38 24 0.22
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTCAAAAATATTTTTAAAACTATATAT
Found at i:1435929 original size:31 final size:32
Alignment explanation
Indices: 1435873--1436043 Score: 125
Period size: 32 Copynumber: 5.2 Consensus size: 32
1435863 TATATATACA
* ** *
1435873 TATATTTCAAAAATATTTTTTAAACTATATAT
1 TATATTTAAAAAACGTTTTTAAAACTATATAT
*
1435905 TATATTTAAAAAA-GTTTTCAAAACTATAT-T
1 TATATTTAAAAAACGTTTTTAAAACTATATAT
** * *
1435935 ATATAGTTTTCAAAATG-TTTTAAAAATATTATAT
1 -TATA-TTTAAAAAACGTTTTTAAAACTA-TATAT
*
1435969 AAGT-TTTAAAAAACGTTTTTAAAACTATATATT
1 TA-TATTTAAAAAACGTTTTTAAAACTATATA-T
*
1436002 ATATAATTTATTCAAAAATGTTTTTAAAACTATATAT
1 -TAT-ATTTA---AAAAACGTTTTTAAAACTATATAT
1436039 TATAT
1 TATAT
1436044 AAGTTTTTAA
Statistics
Matches: 110, Mismatches: 15, Indels: 25
0.73 0.10 0.17
Matches are distributed among these distances:
30 1 0.01
31 17 0.15
32 40 0.36
33 17 0.15
34 3 0.03
35 6 0.05
36 3 0.03
37 1 0.01
38 22 0.20
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (32 bp):
TATATTTAAAAAACGTTTTTAAAACTATATAT
Found at i:1436004 original size:37 final size:37
Alignment explanation
Indices: 1435877--1436139 Score: 247
Period size: 36 Copynumber: 7.5 Consensus size: 37
1435867 TATACATATA
* *
1435877 TTTCAAAAATATTTTTTAAACTATATA-T-TAT-A--
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
1435909 TTT-AAAAAAGTTTTCAAAACTATA--TTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
1435942 TTTC-AAAATG-TTTT-AAA--A-ATATTATATAAGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* * *
1435973 TTTAAAAAACGTTTTTAAAACTATATATTATATAATT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
1436010 TATTCAAAAATGTTTTTAAAACTATATATTATATAAGT
1 T-TTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* * *
1436048 TTT-TAAAATGATTTTAAAACTATATGTTATATATA-T
1 TTTCAAAAATGTTTTTAAAACTATATATTATATA-AGT
* * *
1436084 TTTCTAAAATGTTTTAAAAACTATATGTTATAT-AGT
1 TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
* *
1436120 TTTCAAAAATATTTTAAAAA
1 TTTCAAAAATGTTTTTAAAA
1436140 AAACTATATA
Statistics
Matches: 194, Mismatches: 19, Indels: 32
0.79 0.08 0.13
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 7 0.04
31 30 0.15
32 11 0.06
33 12 0.06
34 3 0.02
35 1 0.01
36 51 0.26
37 43 0.22
38 34 0.18
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (37 bp):
TTTCAAAAATGTTTTTAAAACTATATATTATATAAGT
Found at i:1436056 original size:36 final size:36
Alignment explanation
Indices: 1435882--1436127 Score: 209
Period size: 37 Copynumber: 7.1 Consensus size: 36
1435872 ATATATTTCA
* * *
1435882 AAAATATTTTTTAAACTATATA-T-TAT-A--TTTA
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTT
* * *
1435913 AAAAAGTTTTCAAAACTATA--TTATAT-AGTTTTC
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTT
*
1435946 AAAATG-TTTT-AAA--A-ATATTATATAAGTTTTAA
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTT-T
*
1435978 AAAACGTTTTTAAAACTATATATTATATAA-TTTATT
1 AAAATGTTTTTAAAACTATATATTATATAAGTTT-TT
1436014 CAAAAATGTTTTTAAAACTATATATTATATAAGTTTTT
1 --AAAATGTTTTTAAAACTATATATTATATAAGTTTTT
* *
1436052 AAAATGATTTTAAAACTATATGTTATATATA-TTTTCT
1 AAAATGTTTTTAAAACTATATATTATATA-AGTTTT-T
* * *
1436089 AAAATGTTTTAAAAACTATATGTTATAT-AGTTTTC
1 AAAATGTTTTTAAAACTATATATTATATAAGTTTTT
1436124 AAAA
1 AAAA
1436128 ATATTTTAAA
Statistics
Matches: 179, Mismatches: 16, Indels: 36
0.77 0.07 0.16
Matches are distributed among these distances:
28 1 0.01
29 1 0.01
30 7 0.04
31 29 0.16
32 8 0.04
33 12 0.07
34 3 0.02
35 5 0.03
36 39 0.22
37 40 0.22
38 31 0.17
39 3 0.02
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (36 bp):
AAAATGTTTTTAAAACTATATATTATATAAGTTTTT
Found at i:1437096 original size:81 final size:82
Alignment explanation
Indices: 1436871--1437509 Score: 673
Period size: 81 Copynumber: 7.7 Consensus size: 82
1436861 AAGTTGAATA
* * *
1436871 TAATCGAACTCGAAGGTC-TTTAG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAATGAT
1 TAATCGAACTCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGC-AAATGAT
1436934 GTGCCTTGGAGCTGAGCG
65 GTGCCTTGGAGCTGAGCG
* * * * * * * *
1436952 GAGTCGAGCTCGAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCGAAGGTCTTTTGG--ACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGA
* * *
1437017 TGTGCCCTCGAAGCTGAGTG
64 TGTG-CCTTGGAGCTGAGCG
** * *
1437037 TAATCGAACTCGGGGGTC-TTTGG-CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGACG
1 TAATCGAACTCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
1437100 TGCCTTGGAGCTGAGCG
66 TGCCTTGGAGCTGAGCG
* * * * * * *
1437117 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAGTTATTCTGTAAATGA
1 TAATCGAACTCGAAGGTCTTTTGG--ACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGA
* * *
1437182 TGTGCCCTCGAAGCTGAGTG
64 TGTG-CCTTGGAGCTGAGCG
** * *
1437202 TAATCGAACTCGGGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TAATCGAACTCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
*
1437265 TGCCTTGGAGTTGAGCG
66 TGCCTTGGAGCTGAGCG
* * * * *
1437282 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCGAAGGTCTTTTGG--ACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGA
* * *
1437347 TGTGCCCTCGAAGCTGAGTG
64 TGTG-CCTTGGAGCTGAGCG
** * *
1437367 TAATCGAACTCGGGGGTC-TTTGG-CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TAATCGAACTCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
1437430 TGCCTTGGAGCTGAGCG
66 TGCCTTGGAGCTGAGCG
* * * *
1437447 TAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TAATCGAACTCGAAGGTCTTTTGG--ACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAAT
1437510 AGTTTGTTTA
Statistics
Matches: 448, Mismatches: 91, Indels: 35
0.78 0.16 0.06
Matches are distributed among these distances:
80 80 0.18
81 135 0.30
82 4 0.01
84 126 0.28
85 103 0.23
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (82 bp):
TAATCGAACTCGAAGGTCTTTTGGACAGATAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
TGCCTTGGAGCTGAGCG
Found at i:1437160 original size:165 final size:165
Alignment explanation
Indices: 1436871--1437509 Score: 1161
Period size: 165 Copynumber: 3.9 Consensus size: 165
1436861 AAGTTGAATA
** *
1436871 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAATGATGT
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGC-AAATGATGT
* * *
1436936 GCCTTGGAGCTGAGCGGAGTCGAGCTCGAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGA
65 GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGA
1437001 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
130 GTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
* *
1437037 TAATCGAACTCGGGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGACGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
1437102 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTTTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
*
1437167 TTATTCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
1437202 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
1437267 CCTTGGAGTTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
1437332 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
1437367 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1437432 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
66 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
*
1437497 TTATGCTGCAAAT
131 TTATGCTGTAAAT
1437510 AGTTTGTTTA
Statistics
Matches: 458, Mismatches: 15, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
165 407 0.89
166 51 0.11
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (165 bp):
TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTTGGTCACAGATAACCCTTCTAGCCTTGAG
TTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
Found at i:1437187 original size:84 final size:84
Alignment explanation
Indices: 1436894--1437509 Score: 689
Period size: 84 Copynumber: 7.4 Consensus size: 84
1436884 AGGTCTTTAG
* * * * * *
1436894 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAAATGATGTGCCTTGGAGCTGAGCGGAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGC-AAATGATGTGCCTTGGAGCTGAGCGTAGTCGA
*
1436959 GCTCGAAGGTCTTTTGGTCA
65 ACTCGAAGGTCTTTTGGTCA
* * * * * *
1436979 CAGATAACCCTTTTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
**
1437044 ACTCGGGGGTC-TTTGG---
65 ACTCGAAGGTCTTTTGGTCA
* * * * *
1437060 CAGATAACCCTTCTCGACTTAAGCTATGCTGCAAATGACGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1437125 CTCGAAGGTCTTTTGGTCA
66 CTCGAAGGTCTTTTGGTCA
* * * * * * *
1437144 CAGATAACCCTTTTAGCCTTGAGTTATTCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
**
1437209 ACTCGGGGGTC-TTTGG---
65 ACTCGAAGGTCTTTTGGTCA
* * * * * *
1437225 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGTTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1437290 CTCGAAGGTCTTTTGGTCA
66 CTCGAAGGTCTTTTGGTCA
* * * * *
1437309 CAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGA
**
1437374 ACTCGGGGGTC-TTTGG---
65 ACTCGAAGGTCTTTTGGTCA
* * * * *
1437390 CAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
1437455 CTCGAAGGTCTTTTGGTCA
66 CTCGAAGGTCTTTTGGTCA
1437474 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
1437510 AGTTTGTTTA
Statistics
Matches: 429, Mismatches: 87, Indels: 31
0.78 0.16 0.06
Matches are distributed among these distances:
80 80 0.19
81 120 0.28
84 126 0.29
85 103 0.24
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (84 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTTGGTCA
Found at i:1443964 original size:14 final size:14
Alignment explanation
Indices: 1443940--1443974 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1443930 TTTGGACCCT
1443940 GAAAA-AATAAAAA
1 GAAAATAATAAAAA
1443953 GAAAATAATAAAAA
1 GAAAATAATAAAAA
1443967 GAAAATAA
1 GAAAATAA
1443975 ATAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 5 0.24
14 16 0.76
ACGTcount: A:0.80, C:0.00, G:0.09, T:0.11
Consensus pattern (14 bp):
GAAAATAATAAAAA
Found at i:1444069 original size:30 final size:30
Alignment explanation
Indices: 1444013--1444181 Score: 112
Period size: 30 Copynumber: 5.2 Consensus size: 30
1444003 TATATAATAC
*
1444013 ATATATTTCAAAAATA-TTTTTTAAACTATAT
1 ATATATTT-AAAAA-AGTTTTTAAAACTATAT
*
1444044 ATATATTTAAAAAAGTTTTCAAAACTATAT
1 ATATATTTAAAAAAGTTTTTAAAACTATAT
** *
1444074 -TATAGTTTTCAAAA-TGTTTTAAAAATAT-T
1 ATATA-TTTAAAAAAGT-TTTTAAAACTATAT
1444103 ATATAAGTTTTAAAAAACGTTTTTAAAACTATATATT
1 ATAT-A--TTTAAAAAA-GTTTTTAAAAC--TATA-T
1444140 ATATAATTTATTCAAAAATGTTTTTAAAACTATAT
1 ATAT-ATTTA---AAAAA-GTTTTTAAAACTATAT
1444175 ATTATAT
1 A-TATAT
1444182 AAGTTTTTAA
Statistics
Matches: 111, Mismatches: 11, Indels: 28
0.74 0.07 0.19
Matches are distributed among these distances:
29 7 0.06
30 38 0.34
31 9 0.08
32 7 0.06
33 8 0.07
34 1 0.01
35 11 0.10
36 7 0.06
37 7 0.06
38 16 0.14
ACGTcount: A:0.46, C:0.05, G:0.04, T:0.46
Consensus pattern (30 bp):
ATATATTTAAAAAAGTTTTTAAAACTATAT
Found at i:1444164 original size:38 final size:37
Alignment explanation
Indices: 1444098--1444276 Score: 190
Period size: 36 Copynumber: 4.9 Consensus size: 37
1444088 TGTTTTAAAA
* * *
1444098 ATATTATATAAGTTTTAAAAAACGTTTTTAAAACTAT
1 ATATTATATAATTTTTCAAAAATGTTTTTAAAACTAT
1444135 ATATTATATAATTTATTCAAAAATGTTTTTAAAACTAT
1 ATATTATATAATTT-TTCAAAAATGTTTTTAAAACTAT
*
1444173 ATATTATATAAGTTTTT--AAAATGATTTTAAAACTAT
1 ATATTATATAA-TTTTTCAAAAATGTTTTTAAAACTAT
* *
1444209 ATGTTATAT-ATATTTTC-TAAATG-TTTTAAAAGCTAT
1 ATATTATATAAT-TTTTCAAAAATGTTTTTAAAA-CTAT
* * * *
1444245 ATGTTATAT-AGTTTTCAAAAATATTTTAAAAA
1 ATATTATATAATTTTTCAAAAATGTTTTTAAAA
1444277 AAACTATATA
Statistics
Matches: 125, Mismatches: 10, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
34 1 0.01
35 18 0.14
36 49 0.39
37 20 0.16
38 34 0.27
39 3 0.02
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (37 bp):
ATATTATATAATTTTTCAAAAATGTTTTTAAAACTAT
Found at i:1444252 original size:72 final size:72
Alignment explanation
Indices: 1444069--1444275 Score: 232
Period size: 71 Copynumber: 2.9 Consensus size: 72
1444059 TTTTCAAAAC
* *
1444069 TATATTATAGTTTTCAAAATGTTTTAAAA--ATA-TTATATAAGTTTTAAAAAACGTTTTTAAAA
1 TATA-TATAGTTTTCAAAATGTTTTAAAACTATATTTATATAAGTTTTAAAAAATGATTTTAAAA
1444131 CTATATAT
65 CTATATAT
* *
1444139 TATATA-ATTTATTCAAAAATGTTTTTAAAACTATATATTATATAAGTTTT-TAAAATGATTTTA
1 TATATATAGTT-TTC-AAAATG-TTTTAAAACTATAT-TTATATAAGTTTTAAAAAATGATTTTA
*
1444202 AAACTATATGT
62 AAACTATATAT
* *
1444213 TATATATA-TTTTCTAAATGTTTTAAAAGCTATATGTTATAT-AGTTTTCAAAAAT-ATTTTAAA
1 TATATATAGTTTTCAAAATGTTTTAAAA-CTATAT-TTATATAAGTTTTAAAAAATGATTTTAAA
1444275 A
64 A
1444276 AAAACTATAT
Statistics
Matches: 119, Mismatches: 8, Indels: 19
0.82 0.05 0.13
Matches are distributed among these distances:
68 3 0.03
69 5 0.04
70 10 0.08
71 31 0.26
72 22 0.18
73 6 0.05
74 28 0.24
75 14 0.12
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (72 bp):
TATATATAGTTTTCAAAATGTTTTAAAACTATATTTATATAAGTTTTAAAAAATGATTTTAAAAC
TATATAT
Found at i:1450549 original size:26 final size:26
Alignment explanation
Indices: 1450520--1450602 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
1450510 TGTGTTTCTT
1450520 TTAGATAAGATTGATTAGTGTTCAAA
1 TTAGATAAGATTGATTAGTGTTCAAA
* * * * **
1450546 TTAGTTAATATTTCATT-GTTAATTC-TT
1 TTAGATAAGA-TTGATTAG-T-GTTCAAA
1450573 TTAGATAAGATTGATTAGTGTTCAAA
1 TTAGATAAGATTGATTAGTGTTCAAA
1450599 TTAG
1 TTAG
1450603 TTAATATTTC
Statistics
Matches: 40, Mismatches: 12, Indels: 10
0.65 0.19 0.16
Matches are distributed among these distances:
25 3 0.08
26 19 0.47
27 15 0.38
28 3 0.08
ACGTcount: A:0.34, C:0.05, G:0.16, T:0.46
Consensus pattern (26 bp):
TTAGATAAGATTGATTAGTGTTCAAA
Found at i:1450595 original size:53 final size:53
Alignment explanation
Indices: 1450515--1450622 Score: 216
Period size: 53 Copynumber: 2.0 Consensus size: 53
1450505 TTATATGTGT
1450515 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
1 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
1450568 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
1 TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
1450621 TT
1 TT
1450623 ACTCCTTGAT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 55 1.00
ACGTcount: A:0.31, C:0.06, G:0.13, T:0.50
Consensus pattern (53 bp):
TTCTTTTAGATAAGATTGATTAGTGTTCAAATTAGTTAATATTTCATTGTTAA
Found at i:1454601 original size:18 final size:18
Alignment explanation
Indices: 1454578--1454614 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
1454568 ATGGAAGATC
*
1454578 ATCGACGTTAAGGTTCTT
1 ATCGACATTAAGGTTCTT
1454596 ATCGACATTAAGGTTCTT
1 ATCGACATTAAGGTTCTT
1454614 A
1 A
1454615 ATCCCTCGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (18 bp):
ATCGACATTAAGGTTCTT
Found at i:1455339 original size:98 final size:98
Alignment explanation
Indices: 1455164--1455345 Score: 319
Period size: 98 Copynumber: 1.9 Consensus size: 98
1455154 TAGAGAAAGG
* *
1455164 TATTAAGGTCTTTATGGATGATTTCATGATCTACGATAACTCTTTCGACGAATGCCTTCTCAATT
1 TATTAAGGTCTTTATGGATGATTTCACGATCTACGATAACTCTTTCGAAGAATGCCTTCTCAATT
1455229 TAACCAAAATATTGAAGCAGTGCCTAGAATACA
66 TAACCAAAATATTGAAGCAGTGCCTAGAATACA
* *
1455262 TATTGAGGTCTTTATGGATGATTTCGCGATCTACGATAACTCTTTCGAAGAATGCCTTCTCAATT
1 TATTAAGGTCTTTATGGATGATTTCACGATCTACGATAACTCTTTCGAAGAATGCCTTCTCAATT
*
1455327 TAACCAAGATATTGAAGCA
66 TAACCAAAATATTGAAGCA
1455346 ATGTTGTTAG
Statistics
Matches: 79, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
98 79 1.00
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.34
Consensus pattern (98 bp):
TATTAAGGTCTTTATGGATGATTTCACGATCTACGATAACTCTTTCGAAGAATGCCTTCTCAATT
TAACCAAAATATTGAAGCAGTGCCTAGAATACA
Found at i:1467464 original size:2 final size:2
Alignment explanation
Indices: 1467457--1467507 Score: 102
Period size: 2 Copynumber: 25.5 Consensus size: 2
1467447 GGTGTAAAAC
1467457 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1467499 TA TA TA TA T
1 TA TA TA TA T
1467508 TAGGAATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 49 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1468727 original size:43 final size:43
Alignment explanation
Indices: 1468680--1468882 Score: 177
Period size: 43 Copynumber: 4.7 Consensus size: 43
1468670 TAGAGACCTT
*
1468680 AATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGGCCTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
** * *
1468723 AATTAGGAAGTTAGAAAGTGAGATT-AAAAAAATTTAAGGGCCTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAA--TAGGGGCCTC
* *
1468767 AATTATAAAGTTCA-ATAAGTGAGATT--AAAAATTAGGGGCCTC
1 AATTATAAAGGT-AGA-AAGTGAGATTGAAAAAAATAGGGGCCTC
* * ** *
1468809 AATTATAAAGATAGAAATTGAGATTGAAAAACTTA-GAG-CTC
1 AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
*
1468850 GAGATTGA-AAAGGTAGAAACTGAGATTGAAAAA
1 -A-ATT-ATAAAGGTAGAAAGTGAGATTGAAAAA
1468883 TTTTAAAAGC
Statistics
Matches: 135, Mismatches: 15, Indels: 20
0.79 0.09 0.12
Matches are distributed among these distances:
41 13 0.10
42 31 0.23
43 54 0.40
44 26 0.19
45 11 0.08
ACGTcount: A:0.47, C:0.07, G:0.22, T:0.25
Consensus pattern (43 bp):
AATTATAAAGGTAGAAAGTGAGATTGAAAAAAATAGGGGCCTC
Found at i:1468816 original size:42 final size:42
Alignment explanation
Indices: 1468662--1468844 Score: 190
Period size: 43 Copynumber: 4.3 Consensus size: 42
1468652 TATGAAATTG
* * * * *
1468662 TAAAAAATTAGAGACCTTAATTATAAAGGTAGAAATTGAGAT
1 TAAAAAATTAGGGGCCTCAATTATAAAGTTAGAAAGTGAGAT
* **
1468704 TGAAAAAAATAGGGGCCTCAATTAGGAAGTTAGAAAGTGAGAT
1 T-AAAAAATTAGGGGCCTCAATTATAAAGTTAGAAAGTGAGAT
*
1468747 TAAAAAAATTTAAGGGCCTCAATTATAAAGTTCA-ATAAGTGAGAT
1 T-AAAAAA-TTAGGGGCCTCAATTATAAAGTT-AGA-AAGTGAGAT
* *
1468792 T-AAAAATTAGGGGCCTCAATTATAAAGATAGAAATTGAGAT
1 TAAAAAATTAGGGGCCTCAATTATAAAGTTAGAAAGTGAGAT
*
1468833 TGAAAAACTTAG
1 T-AAAAAATTAG
1468845 AGCTCGAGAT
Statistics
Matches: 117, Mismatches: 17, Indels: 13
0.80 0.12 0.09
Matches are distributed among these distances:
41 10 0.09
42 23 0.20
43 53 0.45
44 20 0.17
45 11 0.09
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.26
Consensus pattern (42 bp):
TAAAAAATTAGGGGCCTCAATTATAAAGTTAGAAAGTGAGAT
Found at i:1468866 original size:21 final size:21
Alignment explanation
Indices: 1468820--1468881 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
1468810 ATTATAAAGA
* *
1468820 TAGAAATTGAGATTGAAAAACT
1 TAGAAACTGAGATTG-AAAACG
* *
1468842 TAG-AGCTCGAGATTGAAAAGG
1 TAGAAACT-GAGATTGAAAACG
1468863 TAGAAACTGAGATTGAAAA
1 TAGAAACTGAGATTGAAAA
1468882 ATTTTAAAAG
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
21 20 0.61
22 13 0.39
ACGTcount: A:0.47, C:0.06, G:0.24, T:0.23
Consensus pattern (21 bp):
TAGAAACTGAGATTGAAAACG
Found at i:1468898 original size:129 final size:125
Alignment explanation
Indices: 1468664--1468941 Score: 301
Period size: 129 Copynumber: 2.2 Consensus size: 125
1468654 TGAAATTGTA
* * * * *
1468664 AAAAATTAGAGACCTTAATTATAAAGGTAGAAATTGAGATTGAAAAAAATAGGGGCCTCAATTAG
1 AAAAATTAGGGGCCTCAATTATAAAGATAGAAATTGAGATTGAAAAAAATAGGAGCCTCAATTAG
* * * ** *
1468729 GAAGTTAGAAAGTGAGATTAAAAAAATTTAAGGGCCTCAATTATAAAGTTCAATAAGTGAGATT
66 AAAGGTAGAAACTGAGATTAAAAAAATTTAAAAGCCTCAATTATAAA----AAAAAGTGAGATT
**
1468793 AAAAATTAGGGGCCTCAATTATAAAGATAGAAATTGAGATTGAAAAACTTA-GAG-CTCGAGATT
1 AAAAATTAGGGGCCTCAATTATAAAGATAGAAATTGAGATTGAAAAAAATAGGAGCCTC-A-ATT
* * *
1468856 -GAAAAGGTAGAAACTGAGATTGAAAAATTTTAAAAGCTTCAATTATAAAAAAAAGTGAGATT
64 AG-AAAGGTAGAAACTGAGATTAAAAAAATTTAAAAGCCTCAATTATAAAAAAAAGTGAGATT
* *
1468918 ACAAAATTAGGAGTCTCAATTATA
1 A-AAAATTAGGGGCCTCAATTATA
1468942 TAGGTAAAAA
Statistics
Matches: 127, Mismatches: 18, Indels: 11
0.81 0.12 0.07
Matches are distributed among these distances:
125 13 0.10
126 20 0.16
127 3 0.02
128 4 0.03
129 87 0.69
ACGTcount: A:0.47, C:0.08, G:0.19, T:0.26
Consensus pattern (125 bp):
AAAAATTAGGGGCCTCAATTATAAAGATAGAAATTGAGATTGAAAAAAATAGGAGCCTCAATTAG
AAAGGTAGAAACTGAGATTAAAAAAATTTAAAAGCCTCAATTATAAAAAAAAGTGAGATT
Found at i:1471364 original size:23 final size:23
Alignment explanation
Indices: 1471337--1471382 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
1471327 CTGATTGGAT
*
1471337 CTTCTAGAAGCTGTTGACTGGGC
1 CTTCTAGAAGCTGCTGACTGGGC
*
1471360 CTTCTAGAAGTTGCTGACTGGGC
1 CTTCTAGAAGCTGCTGACTGGGC
1471383 ACCATGTCAC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.17, C:0.22, G:0.30, T:0.30
Consensus pattern (23 bp):
CTTCTAGAAGCTGCTGACTGGGC
Found at i:1474069 original size:29 final size:29
Alignment explanation
Indices: 1474029--1474198 Score: 245
Period size: 29 Copynumber: 5.9 Consensus size: 29
1474019 CAACCAGCAT
*
1474029 AGGTCGCTATGCACGCCCGGCGTCCT-TA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
1474057 TAGGTCGCCATGCACGCCCGGCGTCCT-TA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
* **
1474086 TAGGTCGCCATGCATGCCTAGCGTCCTATA
1 -AGGTCGCCATGCACGCCCGGCGTCCTATA
*
1474116 AGGTTGCCATGCACGCCCGGCGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
* *
1474145 AGGTTGCCATGCACGCCTGGCGTCCTATA
1 AGGTCGCCATGCACGCCCGGCGTCCTATA
1474174 AGGTCGCCATGCACGCCCGGCGTCC
1 AGGTCGCCATGCACGCCCGGCGTCC
1474199 AACGTTCTTT
Statistics
Matches: 129, Mismatches: 11, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
29 127 0.98
30 2 0.02
ACGTcount: A:0.16, C:0.35, G:0.28, T:0.21
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGTCCTATA
Found at i:1474244 original size:28 final size:28
Alignment explanation
Indices: 1474202--1474259 Score: 98
Period size: 28 Copynumber: 2.1 Consensus size: 28
1474192 GGCGTCCAAC
*
1474202 GTTCTTTGCCCGCTGCTGCTCTGCTTTG
1 GTTCTTTGCCCGCTGATGCTCTGCTTTG
*
1474230 GTTCTTTGCCTGCTGATGCTCTGCTTTG
1 GTTCTTTGCCCGCTGATGCTCTGCTTTG
1474258 GT
1 GT
1474260 GCTATGCATG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.02, C:0.28, G:0.26, T:0.45
Consensus pattern (28 bp):
GTTCTTTGCCCGCTGATGCTCTGCTTTG
Found at i:1474847 original size:35 final size:31
Alignment explanation
Indices: 1474784--1474876 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 31
1474774 TGAATTTATA
1474784 TTATATAAAAAAATTAGTTAATTAGTTTAAG
1 TTATATAAAAAAATTAGTTAATTAGTTTAAG
*
1474815 TTATATAAAAGAATAATTATTTAAATTAGTTT-A-
1 TTATAT-AAA-AA-AATTAGTT-AATTAGTTTAAG
* **
1474848 TTGT-TATAAATTATTAGTTAATTAGTTTA
1 TTATATA-AAAAAATTAGTTAATTAGTTTA
1474877 TTATTATAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
29 9 0.18
30 6 0.12
31 8 0.16
32 6 0.12
33 5 0.10
34 8 0.16
35 9 0.18
ACGTcount: A:0.44, C:0.00, G:0.09, T:0.47
Consensus pattern (31 bp):
TTATATAAAAAAATTAGTTAATTAGTTTAAG
Found at i:1474859 original size:18 final size:18
Alignment explanation
Indices: 1474836--1474890 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
1474826 AATAATTATT
1474836 TAAATTAGTTTATTGTTA
1 TAAATTAGTTTATTGTTA
1474854 TAAATTA--TTA--G-T-
1 TAAATTAGTTTATTGTTA
*
1474866 T-AATTAGTTTATTATTA
1 TAAATTAGTTTATTGTTA
1474883 TAAATTAG
1 TAAATTAG
1474891 GGTAAAACAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
11 5 0.17
12 1 0.03
13 4 0.14
14 1 0.03
16 4 0.14
17 1 0.03
18 13 0.45
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (18 bp):
TAAATTAGTTTATTGTTA
Found at i:1475173 original size:22 final size:22
Alignment explanation
Indices: 1475147--1475194 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
1475137 ATAGTTTATT
*
1475147 AGTTAACGTTATATTAAAGAAC
1 AGTTAAAGTTATATTAAAGAAC
*
1475169 AGTTAAAGTTATATTAAAGAAT
1 AGTTAAAGTTATATTAAAGAAC
1475191 AGTT
1 AGTT
1475195 TATTAGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.46, C:0.04, G:0.15, T:0.35
Consensus pattern (22 bp):
AGTTAAAGTTATATTAAAGAAC
Found at i:1476508 original size:23 final size:23
Alignment explanation
Indices: 1476480--1476524 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1476470 TTTAATTATT
*
1476480 ATTTAAATTAACTATATTATTTG
1 ATTTAAATAAACTATATTATTTG
* *
1476503 ATTTAAATAAATTTTATTATTT
1 ATTTAAATAAACTATATTATTT
1476525 TGTAATTTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATAAACTATATTATTTG
Found at i:1476524 original size:18 final size:20
Alignment explanation
Indices: 1476474--1476524 Score: 52
Period size: 23 Copynumber: 2.5 Consensus size: 20
1476464 GTTATTTTTA
1476474 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATTAAC-AT
1476495 ATTATTTGATTTAAA-TAA-AT
1 ATTA-TT-ATTTAAATTAACAT
*
1476515 TTTATTATTT
1 ATTATTATTT
1476525 TGTAATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
18 4 0.15
19 2 0.07
20 5 0.19
21 4 0.15
22 5 0.19
23 7 0.26
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (20 bp):
ATTATTATTTAAATTAACAT
Found at i:1477480 original size:60 final size:60
Alignment explanation
Indices: 1477411--1477525 Score: 212
Period size: 60 Copynumber: 1.9 Consensus size: 60
1477401 AATCATTACT
1477411 AAATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTAATATC
1 AAATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTAATATC
* *
1477471 AAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTATTAAATCATTA
1 AAATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTA
1477526 TTATAATTTC
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 53 1.00
ACGTcount: A:0.47, C:0.10, G:0.01, T:0.42
Consensus pattern (60 bp):
AAATCATTAAATATTAATAATAATTTCATTAGTACTAATCATTACTAAATCATTAATATC
Found at i:1477514 original size:13 final size:12
Alignment explanation
Indices: 1477496--1477532 Score: 58
Period size: 11 Copynumber: 3.1 Consensus size: 12
1477486 AATAATAATT
1477496 TCATTATTACTAA
1 TCATTATTA-TAA
1477509 TCATTATTA-AA
1 TCATTATTATAA
1477520 TCATTATTATAA
1 TCATTATTATAA
1477532 T
1 T
1477533 TTCGTAAGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.48
12 3 0.13
13 9 0.39
ACGTcount: A:0.41, C:0.11, G:0.00, T:0.49
Consensus pattern (12 bp):
TCATTATTATAA
Found at i:1477525 original size:21 final size:21
Alignment explanation
Indices: 1477446--1477525 Score: 53
Period size: 21 Copynumber: 4.0 Consensus size: 21
1477436 TCATTAGTAC
*
1477446 TAATCATTACTAAATCATTAA
1 TAATCATTATTAAATCATTAA
*
1477467 T-ATCAAATCATTAAAT-ATTAA
1 TAATC--ATTATTAAATCATTAA
** * *
1477488 TAAT-A--ATTTCATTATTAC
1 TAATCATTATTAAATCATTAA
1477506 TAATCATTATTAAATCATTA
1 TAATCATTATTAAATCATTA
1477526 TTATAATTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 14
0.67 0.12 0.21
Matches are distributed among these distances:
17 5 0.11
18 8 0.18
19 2 0.05
20 3 0.07
21 16 0.36
22 10 0.23
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (21 bp):
TAATCATTATTAAATCATTAA
Found at i:1477616 original size:21 final size:22
Alignment explanation
Indices: 1477586--1477664 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
1477576 GTTCAAGTCG
1477586 TAAATCATTACTATCAAATCAT
1 TAAATCATTACTATCAAATCAT
* * *
1477608 TAAAT-ATTAATAATAAATTATTAT
1 TAAATCATTACT-ATCAA--ATCAT
1477632 TACTAATCATTACTATCAAATCAT
1 TA--AATCATTACTATCAAATCAT
1477656 TAAAT-ATTA
1 TAAATCATTA
1477665 ATAATAATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
21 9 0.20
22 12 0.27
24 12 0.27
26 7 0.16
27 5 0.11
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (22 bp):
TAAATCATTACTATCAAATCAT
Found at i:1477752 original size:60 final size:59
Alignment explanation
Indices: 1477679--1477803 Score: 216
Period size: 60 Copynumber: 2.1 Consensus size: 59
1477669 TAATTTCATT
*
1477679 ATTACT-AATCATTAATATCAAATCATTAAATATTAATAATAATTTTATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAA-ATTATTATTACTAATC
*
1477738 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATC
1477797 ATTACTA
1 ATTACTA
1477804 TCAAATCATT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 28 0.44
60 35 0.56
ACGTcount: A:0.46, C:0.11, G:0.00, T:0.42
Consensus pattern (59 bp):
ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAAATTATTATTACTAATC
Found at i:1477760 original size:157 final size:156
Alignment explanation
Indices: 1477586--1477971 Score: 682
Period size: 157 Copynumber: 2.5 Consensus size: 156
1477576 GTTCAAGTCG
1477586 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
1 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
* *
1477651 ATCATTAAATATTAATAATAATTTCATTATTACTAATCATTAATATCAAATCATTAAATATTAAT
66 ATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTAATATCAAATCATTAAAAATTAAT
*
1477716 AATAATTTTATTATTACTAATCATTAC
130 AATAATTTCATTATTACTAATCATTAC
1477743 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
1 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
*
1477808 ATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAAATCATTAAAAATTAATA
66 ATCATTAAATATTAATAATAAATTATTATTACTAATCATTAATATCAAATCATTAAAAATTAATA
1477873 ATAATTTCATTATTACTAATCATTAC
131 ATAATTTCATTATTACTAATCATTAC
* * *
1477899 TAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATCATTACTATTA
1 TAAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATTATTACTAATCATTACTATCA
*
1477964 AATTATTA
65 AATCATTA
1477972 TTATTAAATC
Statistics
Matches: 220, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
156 103 0.47
157 117 0.53
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (156 bp):
TAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATTATTACTAATCATTACTATCAA
ATCATTAAATATTAATAATAAATTATTATTACTAATCATTAATATCAAATCATTAAAAATTAATA
ATAATTTCATTATTACTAATCATTAC
Found at i:1477800 original size:48 final size:48
Alignment explanation
Indices: 1477738--1478049 Score: 292
Period size: 48 Copynumber: 6.6 Consensus size: 48
1477728 ATTACTAATC
1477738 ATTACTAAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACT-AATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1477787 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* *
1477835 ATTACTAATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATT
1 ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATT-ATT
* *
1477884 ATTACTAATCATTAC--T-AAATCATT-AATATCAAATCATTAAA-TATT
1 ATTACTAATCATTACTATCAAATCATTAAATAT-TAAT-AATAAATTATT
* * * * * *
1477929 AATAATAATTTCATTATTA-CTAATCATT-ACTATT-A-AAT-TATTATT
1 ATTACTAA--TCATTACTATCAAATCATTAAATATTAATAATAAATTATT
* * * *
1477974 ATTA--AATCATTATTAT-AATGATTATTATAATGATTATTATTAAATTATT
1 ATTACTAATCATTACTATCAA--ATCATTA-AAT-ATTAATAATAAATTATT
* *
1478023 ATTA-TAATGATTATTATCAAATCATTA
1 ATTACTAATCATTACTATCAAATCATTA
1478050 CTAAATCATC
Statistics
Matches: 220, Mismatches: 23, Indels: 40
0.78 0.08 0.14
Matches are distributed among these distances:
41 10 0.05
43 7 0.03
44 1 0.00
45 24 0.11
46 15 0.07
47 12 0.05
48 87 0.40
49 51 0.23
50 11 0.05
51 2 0.01
ACGTcount: A:0.46, C:0.09, G:0.01, T:0.44
Consensus pattern (48 bp):
ATTACTAATCATTACTATCAAATCATTAAATATTAATAATAAATTATT
Found at i:1477964 original size:41 final size:40
Alignment explanation
Indices: 1477919--1478049 Score: 106
Period size: 38 Copynumber: 3.3 Consensus size: 40
1477909 ATATCAAATC
*
1477919 ATTAAA-TATTAATAATAATTTCATTATTACTAATCATTACT
1 ATTAAATTATTAATAATAA-ATCATTATTA-TAATCATTACT
* * * *
1477960 ATTAAATTATTATTATTAAATCATTATTATAATGATTATT
1 ATTAAATTATTAATAATAAATCATTATTATAATCATTACT
* * * * * *
1478000 A-T-AATGATTATTATTAAATTATTATTATAATGATTATT
1 ATTAAATTATTAATAATAAATCATTATTATAATCATTACT
* *
1478038 ATCAAATCATTA
1 ATTAAATTATTA
1478050 CTAAATCATC
Statistics
Matches: 78, Mismatches: 9, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
38 35 0.45
39 1 0.01
40 17 0.22
41 15 0.19
42 10 0.13
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (40 bp):
ATTAAATTATTAATAATAAATCATTATTATAATCATTACT
Found at i:1477973 original size:3 final size:3
Alignment explanation
Indices: 1477965--1478039 Score: 55
Period size: 3 Copynumber: 25.7 Consensus size: 3
1477955 TTACTATTAA
* * * * * *
1477965 ATT ATT ATT ATT A-A ATC ATT ATT ATA ATG ATT ATT ATA ATG ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
1478012 ATT A-A ATT ATT ATT ATA ATG ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1478040 CAAATCATTA
Statistics
Matches: 56, Mismatches: 14, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
2 2 0.04
3 54 0.96
ACGTcount: A:0.41, C:0.01, G:0.04, T:0.53
Consensus pattern (3 bp):
ATT
Found at i:1477985 original size:63 final size:60
Alignment explanation
Indices: 1477835--1477960 Score: 227
Period size: 60 Copynumber: 2.1 Consensus size: 60
1477825 ATAAATTATT
*
1477835 ATTACT-AATCATTACTATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
*
1477894 ATTACTAAATCATTAATATCAAATCATTAAATATTAATAATAATTTCATTATTACTAATC
1 ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
1477954 ATTACTA
1 ATTACTA
1477961 TTAAATTATT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
59 6 0.09
60 58 0.91
ACGTcount: A:0.46, C:0.13, G:0.00, T:0.41
Consensus pattern (60 bp):
ATTACTAAATCATTAATATCAAATCATTAAAAATTAATAATAATTTCATTATTACTAATC
Found at i:1477998 original size:26 final size:25
Alignment explanation
Indices: 1477703--1478258 Score: 137
Period size: 26 Copynumber: 22.6 Consensus size: 25
1477693 ATATCAAATC
* *
1477703 ATTAAAT-ATTAATAATAATTTTATT
1 ATTAAATCATT-ATTATAATATTATT
* *
1477728 ATTACTAATCATTACTA-AATCATTACT
1 ATTA--AATCATTATTATAAT-ATTATT
* *
1477755 ATCAAATC---ATTA-AATATTAAT
1 ATTAAATCATTATTATAATATTATT
* * *
1477776 AATAAATTATTATTACTAATCATTACT
1 ATTAAATCATTATTA-TAAT-ATTATT
* *
1477803 ATCAAATC---ATTA-AATATTAAT
1 ATTAAATCATTATTATAATATTATT
* * *
1477824 AATAAATTATTATTACTAATCATTACT
1 ATTAAATCATTATTA-TAAT-ATTATT
* *
1477851 ATCAAATCATTA--A-AA-ATTAAT
1 ATTAAATCATTATTATAATATTATT
* * *
1477872 AATAATTTCATTATTACT-A-ATCATT
1 ATTAA-ATCATTATTA-TAATATTATT
* * * *
1477897 ACTAAATCATTAATATCA-A--ATC
1 ATTAAATCATTATTATAATATTATT
*
1477919 ATTAAAT-ATTAATAATAAT-TTCATT
1 ATTAAATCATT-ATTATAATATT-ATT
*
1477944 ATTACTAATCATTACTATTAAATTATTATT
1 ATTA--AATCATTATTA-T-AA-TATTATT
1477974 ATTAAATCATTATTATAATGATTATT
1 ATTAAATCATTATTATAAT-ATTATT
*
1478000 A-T-AATGATTATTATTAA-ATTATT
1 ATTAAATCATTATTA-TAATATTATT
* *
1478023 ATTATAATGATTATTATCAA-ATCATT
1 ATTA-AATCATTATTAT-AATATTATT
* * * * * *
1478049 ACTAAATCATCA-AATCAT-TAAAT
1 ATTAAATCATTATTATAATATTATT
1478072 ATTTAAATCATTATTA-AATCATTATT
1 A-TTAAATCATTATTATAAT-ATTATT
* *
1478098 A-T-AATGATTATTACTAA-ATCATT
1 ATTAAATCATTATTA-TAATATTATT
*
1478121 ATTATAATGATTATTATCAA-ATTATT
1 ATTA-AATCATTATTAT-AATATTATT
* * *
1478147 ATTATAATGATTATTATCATATCATT
1 ATTA-AATCATTATTATAATATTATT
* * * * * *
1478173 ACTAAATCATCA-AATCAT-TAAAT
1 ATTAAATCATTATTATAATATTATT
*
1478196 ATTAAATTCATTATTA-AAT-TCATT
1 ATTAAA-TCATTATTATAATATTATT
1478220 ATTAAATC---ATTATAATGATTATT
1 ATTAAATCATTATTATAAT-ATTATT
* *
1478243 ATCAAATCATTTTTAT
1 ATTAAATCATTATTAT
1478259 GGTTAATTTA
Statistics
Matches: 396, Mismatches: 75, Indels: 119
0.67 0.13 0.20
Matches are distributed among these distances:
20 4 0.01
21 34 0.09
22 27 0.07
23 52 0.13
24 70 0.18
25 48 0.12
26 90 0.23
27 42 0.11
28 17 0.04
29 2 0.01
30 8 0.02
31 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.01, T:0.45
Consensus pattern (25 bp):
ATTAAATCATTATTATAATATTATT
Found at i:1478131 original size:124 final size:122
Alignment explanation
Indices: 1477959--1478232 Score: 435
Period size: 124 Copynumber: 2.2 Consensus size: 122
1477949 TAATCATTAC
* * *
1477959 TATTAAATTATTATTATTAAATCATTATTATAATGATTATTATAATGATTATTATTAAATTATTA
1 TATTAAATCATTATTA-T-AATCATTATTATAATCATTATTATAATGATTATTATCAAATTATTA
1478024 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAA-TCAT
64 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATA-TTAAATTCAT
*
1478083 TATTAAATCATTATTATAATGATTATTACTAAATCATTATTATAATGATTATTATCAAATTATTA
1 TATTAAATCATTATTATAATCATTATTA-T-AATCATTATTATAATGATTATTATCAAATTATTA
*
1478148 TTATAATGATTATTATCATATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
64 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
1478207 TATTAAATTCATTATTA-AATCATTAT
1 TATTAAA-TCATTATTATAATCATTAT
1478233 AATGATTATT
Statistics
Matches: 140, Mismatches: 6, Indels: 8
0.91 0.04 0.05
Matches are distributed among these distances:
122 10 0.07
123 7 0.05
124 114 0.81
125 9 0.06
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.46
Consensus pattern (122 bp):
TATTAAATCATTATTATAATCATTATTATAATCATTATTATAATGATTATTATCAAATTATTATT
ATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAATTCAT
Found at i:1478212 original size:12 final size:12
Alignment explanation
Indices: 1478195--1478232 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
1478185 AATCATTAAA
1478195 TATTAAATTCAT
1 TATTAAATTCAT
1478207 TATTAAATTCAT
1 TATTAAATTCAT
1478219 TATTAAA-TCAT
1 TATTAAATTCAT
1478230 TAT
1 TAT
1478233 AATGATTATT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
11 7 0.27
12 19 0.73
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (12 bp):
TATTAAATTCAT
Found at i:1478448 original size:17 final size:18
Alignment explanation
Indices: 1478428--1478462 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
1478418 TATTAGTAAA
1478428 TCATTATTATT-ATAATT
1 TCATTATTATTAATAATT
1478445 TCATTATTATTAATAATT
1 TCATTATTATTAATAATT
1478463 ACTAATCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.37, C:0.06, G:0.00, T:0.57
Consensus pattern (18 bp):
TCATTATTATTAATAATT
Found at i:1481541 original size:26 final size:24
Alignment explanation
Indices: 1481481--1481541 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
1481471 TACTAATATT
*
1481481 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
1481505 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
1481532 ATTTAATAAT
1 A-TTAATAAT
1481542 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:1481828 original size:17 final size:17
Alignment explanation
Indices: 1481775--1481834 Score: 57
Period size: 17 Copynumber: 3.3 Consensus size: 17
1481765 AATATAAATA
*
1481775 AAACAAAATATTTTTTT
1 AAACACAATATTTTTTT
* *
1481792 AAAACAACACTAAATATTTTT
1 -AAAC-ACA--ATATTTTTTT
1481813 AAACACAATATTTTTTT
1 AAACACAATATTTTTTT
1481830 AAACA
1 AAACA
1481835 AAAATTATCT
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
17 13 0.38
18 4 0.12
19 5 0.15
20 4 0.12
21 8 0.24
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (17 bp):
AAACACAATATTTTTTT
Found at i:1481925 original size:16 final size:16
Alignment explanation
Indices: 1481904--1481945 Score: 56
Period size: 13 Copynumber: 2.9 Consensus size: 16
1481894 TTACACATAC
1481904 ACAACACAAAAAATGG
1 ACAACACAAAAAATGG
1481920 AC-A-AC-AAAAATGG
1 ACAACACAAAAAATGG
1481933 ACAACA-AAAAAAT
1 ACAACACAAAAAAT
1481946 AAATTACTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
13 10 0.43
14 3 0.13
15 8 0.35
16 2 0.09
ACGTcount: A:0.67, C:0.17, G:0.10, T:0.07
Consensus pattern (16 bp):
ACAACACAAAAAATGG
Found at i:1481928 original size:14 final size:14
Alignment explanation
Indices: 1481909--1481943 Score: 63
Period size: 13 Copynumber: 2.6 Consensus size: 14
1481899 CATACACAAC
1481909 ACAAAAAATGGACA
1 ACAAAAAATGGACA
1481923 AC-AAAAATGGACA
1 ACAAAAAATGGACA
1481936 ACAAAAAA
1 ACAAAAAA
1481944 ATAAATTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.69, C:0.14, G:0.11, T:0.06
Consensus pattern (14 bp):
ACAAAAAATGGACA
Found at i:1482889 original size:17 final size:17
Alignment explanation
Indices: 1482867--1482900 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
1482857 ATGGATGCAT
1482867 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
1482884 GATGAGGGATAGGGTTA
1 GATGAGGGATAGGGTTA
1482901 AAGTTTGGGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.47, T:0.24
Consensus pattern (17 bp):
GATGAGGGATAGGGTTA
Found at i:1483059 original size:35 final size:36
Alignment explanation
Indices: 1483013--1483084 Score: 137
Period size: 36 Copynumber: 2.0 Consensus size: 36
1483003 TCCCCAATCT
1483013 CCCCATGCATGAA-CGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1483048 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1 CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
1483084 C
1 C
1483085 ATGGCACGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
35 13 0.36
36 23 0.64
ACGTcount: A:0.17, C:0.39, G:0.25, T:0.19
Consensus pattern (36 bp):
CCCCATGCATGAACCGATCCTTGGTCGCCCCGAGTG
Found at i:1483087 original size:29 final size:29
Alignment explanation
Indices: 1483053--1483145 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 29
1483043 GAGTGCCCCA
1483053 TGCATGAACCGATCCTTGGTCGCCCCGAG
1 TGCATGAACCGATCCTTGGTCGCCCCGAG
* **** *
1483082 TGCATG-GCACGATCTCCCCAATCTCCCC-A-
1 TGCATGAAC-CGA--TCCTTGGTCGCCCCGAG
1483111 TGCATGAACCGATCCTTGGTCGCCCCGAG
1 TGCATGAACCGATCCTTGGTCGCCCCGAG
1483140 TGCATG
1 TGCATG
1483146 GCGACCTCCT
Statistics
Matches: 46, Mismatches: 12, Indels: 12
0.66 0.17 0.17
Matches are distributed among these distances:
27 9 0.20
28 2 0.04
29 24 0.52
30 2 0.04
31 9 0.20
ACGTcount: A:0.18, C:0.37, G:0.24, T:0.22
Consensus pattern (29 bp):
TGCATGAACCGATCCTTGGTCGCCCCGAG
Found at i:1491714 original size:7 final size:7
Alignment explanation
Indices: 1491702--1491733 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1491692 AAATAATTCC
1491702 AATTTTT
1 AATTTTT
1491709 AATTTTT
1 AATTTTT
1491716 AATTTTT
1 AATTTTT
1491723 AATTTTT
1 AATTTTT
1491730 AATT
1 AATT
1491734 CAACTAGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
AATTTTT
Found at i:1492083 original size:16 final size:17
Alignment explanation
Indices: 1492053--1492091 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
1492043 GAGAATCATT
1492053 AATTT-AATTTATAAAA
1 AATTTAAATTTATAAAA
*
1492069 ATTTTAAATTT-TAAAA
1 AATTTAAATTTATAAAA
1492085 AATTTAA
1 AATTTAA
1492092 CGTAAAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 15 0.75
17 5 0.25
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
AATTTAAATTTATAAAA
Found at i:1493605 original size:167 final size:163
Alignment explanation
Indices: 1493309--1493637 Score: 622
Period size: 167 Copynumber: 2.0 Consensus size: 163
1493299 CACAAATATA
1493309 AAAAATACGAAAAACATAAAATTCTTAAATTGAGCTCATTATTTAAAGAACAAGTACAAAAATAA
1 AAAAATACGAAAAACATAAAATTCTTAAATTGAGCTCATTATTTAAAGAACAAGTACAAAAATAA
1493374 AATATTTACGACATGACTAAAAAGAATTATAACATCTACATACTCATTTAAATAATCATTGTTGT
66 AATATTTACGACATGACTAAAAAGAATTATAACATCTACATACTCATTTAAATAATCATTGTTGT
1493439 ATTTTGGTACTCTCACTTAGATTCTTTCGAGAT
131 ATTTTGGTACTCTCACTTAGATTCTTTCGAGAT
1493472 AAAAATACGAAAAACATAAAATTCTTAAATTGAGCTCATTATTTTAAAGAACAAGTACAAAAATA
1 AAAAATACGAAAAACATAAAATTCTTAAATTGAGCTCATTA-TTTAAAGAACAAGTACAAAAATA
1493537 AAATATTTTACGACATGACTAAAATAAGAATTATAACATCTACATACTCATTTAAATAATCATTG
65 AAATA-TTTACGACATGACT-AAA-AAGAATTATAACATCTACATACTCATTTAAATAATCATTG
1493602 TTGTATTTTGGTACTCTCACTTAGATTCTTTCGAGA
127 TTGTATTTTGGTACTCTCACTTAGATTCTTTCGAGA
1493638 GTATTGTTAT
Statistics
Matches: 162, Mismatches: 0, Indels: 4
0.98 0.00 0.02
Matches are distributed among these distances:
163 41 0.25
164 28 0.17
165 14 0.09
166 3 0.02
167 76 0.47
ACGTcount: A:0.44, C:0.13, G:0.09, T:0.33
Consensus pattern (163 bp):
AAAAATACGAAAAACATAAAATTCTTAAATTGAGCTCATTATTTAAAGAACAAGTACAAAAATAA
AATATTTACGACATGACTAAAAAGAATTATAACATCTACATACTCATTTAAATAATCATTGTTGT
ATTTTGGTACTCTCACTTAGATTCTTTCGAGAT
Found at i:1495149 original size:14 final size:14
Alignment explanation
Indices: 1495125--1495159 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
1495115 TTAATCAATT
1495125 ATCGA-ATCGAATA
1 ATCGAGATCGAATA
1495138 ATCGAGATCGAATA
1 ATCGAGATCGAATA
*
1495152 ATCAAGAT
1 ATCGAGAT
1495160 GGTCCCTCAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 5 0.25
14 15 0.75
ACGTcount: A:0.46, C:0.14, G:0.17, T:0.23
Consensus pattern (14 bp):
ATCGAGATCGAATA
Found at i:1495424 original size:22 final size:22
Alignment explanation
Indices: 1495399--1495445 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
1495389 TAATCTTAAT
1495399 TAATTATGTCAATAAAAAGTTC
1 TAATTATGTCAATAAAAAGTTC
*
1495421 TAA-TCTGTCAATAAAAAGTTC
1 TAATTATGTCAATAAAAAGTTC
1495442 TAAT
1 TAAT
1495446 CGAAGTTTGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.45, C:0.11, G:0.09, T:0.36
Consensus pattern (22 bp):
TAATTATGTCAATAAAAAGTTC
Found at i:1495429 original size:21 final size:21
Alignment explanation
Indices: 1495405--1495446 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1495395 TAATTAATTA
1495405 TGTCAATAAAAAGTTCTAATC
1 TGTCAATAAAAAGTTCTAATC
1495426 TGTCAATAAAAAGTTCTAATC
1 TGTCAATAAAAAGTTCTAATC
1495447 GAAGTTTGGG
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:0.10, T:0.33
Consensus pattern (21 bp):
TGTCAATAAAAAGTTCTAATC
Found at i:1496257 original size:15 final size:14
Alignment explanation
Indices: 1496231--1496265 Score: 52
Period size: 15 Copynumber: 2.4 Consensus size: 14
1496221 ATATTCTAAA
*
1496231 AAAATATTAAAATT
1 AAAATATTAAAATG
1496245 AAAATATTAAAAATG
1 AAAATATT-AAAATG
1496260 AAAATA
1 AAAATA
1496266 CTCTAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.42
15 11 0.58
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAAATATTAAAATG
Found at i:1503675 original size:21 final size:22
Alignment explanation
Indices: 1503631--1503687 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
1503621 CTTAGCATTT
* *
1503631 TAAAAATAAAGAAAACTTTGAA
1 TAAAAATAAAGAAAACTGTAAA
*
1503653 TAAAAATAAAGAAAGC-GTAAA
1 TAAAAATAAAGAAAACTGTAAA
1503674 TAAAGAA-AAAGAAA
1 TAAA-AATAAAGAAA
1503688 TAACTTTTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 14 0.45
22 17 0.55
ACGTcount: A:0.68, C:0.04, G:0.12, T:0.16
Consensus pattern (22 bp):
TAAAAATAAAGAAAACTGTAAA
Found at i:1506730 original size:14 final size:14
Alignment explanation
Indices: 1506713--1506744 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
1506703 GTTTGGTTAT
*
1506713 GTTCGTTTATGTTC
1 GTTCGGTTATGTTC
1506727 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
1506741 GTTC
1 GTTC
1506745 ATTTGTGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.06, C:0.16, G:0.25, T:0.53
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:1507860 original size:16 final size:16
Alignment explanation
Indices: 1507839--1507879 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
1507829 ATTTATGTTT
*
1507839 GTTTATGTTCGTGTCC
1 GTTTATGTTCGTATCC
*
1507855 GTTTATGTTCGTATTC
1 GTTTATGTTCGTATCC
1507871 GTTTATGTT
1 GTTTATGTT
1507880 TGTTTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.10, C:0.12, G:0.22, T:0.56
Consensus pattern (16 bp):
GTTTATGTTCGTATCC
Found at i:1507972 original size:16 final size:16
Alignment explanation
Indices: 1507951--1507983 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1507941 AAAAATATTT
1507951 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1507967 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
1507983 T
1 T
1507984 TTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:1508207 original size:25 final size:25
Alignment explanation
Indices: 1508173--1508223 Score: 84
Period size: 25 Copynumber: 2.0 Consensus size: 25
1508163 GGATGGTCAT
1508173 CGATCCCGACGGGTTCCGACCCGAC
1 CGATCCCGACGGGTTCCGACCCGAC
* *
1508198 CGATCCCGACGGGTTCTGACTCGAC
1 CGATCCCGACGGGTTCCGACCCGAC
1508223 C
1 C
1508224 CGACCCAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.41, G:0.27, T:0.16
Consensus pattern (25 bp):
CGATCCCGACGGGTTCCGACCCGAC
Found at i:1514594 original size:18 final size:18
Alignment explanation
Indices: 1514548--1514590 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
1514538 TTTTCTTATT
*
1514548 TTTACTTTAATTGCTTTTA
1 TTTA-TTTAATCGCTTTTA
1514567 TTTATTTAATCGCTTTTA
1 TTTATTTAATCGCTTTTA
1514585 -TTATTT
1 TTTATTT
1514591 TAATATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 6 0.26
18 13 0.57
19 4 0.17
ACGTcount: A:0.21, C:0.09, G:0.05, T:0.65
Consensus pattern (18 bp):
TTTATTTAATCGCTTTTA
Found at i:1517488 original size:13 final size:13
Alignment explanation
Indices: 1517472--1517496 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1517462 TTCCGTTAAA
1517472 TTTTTATTTTTAC
1 TTTTTATTTTTAC
1517485 TTTTTATTTTTA
1 TTTTTATTTTTA
1517497 TTCGATCAAG
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:0.16, C:0.04, G:0.00, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAC
Found at i:1518875 original size:18 final size:17
Alignment explanation
Indices: 1518852--1518894 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
1518842 CTTGTTAAAT
**
1518852 ATTGTTTGGAATGCTATG
1 ATTGTTTGGAACAC-ATG
1518870 ATTGTTTTGGAACACATG
1 ATTG-TTTGGAACACATG
1518888 ATTGTTT
1 ATTGTTT
1518895 AGGTTAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 3 0.14
18 11 0.50
19 8 0.36
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.47
Consensus pattern (17 bp):
ATTGTTTGGAACACATG
Found at i:1532483 original size:3 final size:3
Alignment explanation
Indices: 1532475--1532508 Score: 59
Period size: 3 Copynumber: 11.3 Consensus size: 3
1532465 TTTATCATAA
*
1532475 ATT ATT ATT ATT ATT ATT ATT AGT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1532509 ATCTTTTTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1544453 original size:120 final size:126
Alignment explanation
Indices: 1544314--1544562 Score: 384
Period size: 130 Copynumber: 2.0 Consensus size: 126
1544304 CCCAATGGAC
*
1544314 CAGCCATGTCTATGAATATTCCCTCCCCTTGCT-CTC-CC-TC-TC-CATCTT-CTTCTTCTCCT
1 CAGCCATGTCTATGAATATTCCCTCCCCTTGCTCCTCTCCTTCTTCTCATCTTCCTTCTCCTCCT
1544373 TTCCCTCCAATCTCCACTGGATTTCACCCCTTCCTCCGCTGCCTTCTTCTCCGCCTTCAAG
66 TTCCCTCCAATCTCCACTGGATTTCACCCCTTCCTCCGCTGCCTTCTTCTCCGCCTTCAAG
* *
1544434 CAGCCATGTCTATGAATATTCCTTCCCCTTGCTCACCCTCTCCTTCTTCTTCTTCTTCCTTCTCC
1 CAGCCATGTCTATGAATATTCCCTCCCCTTGCT---CCTCTCCTTCTTC-TCATCTTCCTTCTCC
*
1544499 TCCTTTCCCTCCACTCTCCACTGGATTTCACCCCTTCCTCCGCTGCCTTCTTCTCCGCCTTCAA
62 TCCTTTCCCTCCAATCTCCACTGGATTTCACCCCTTCCTCCGCTGCCTTCTTCTCCGCCTTCAA
1544563 CCACCACCTC
Statistics
Matches: 115, Mismatches: 4, Indels: 10
0.89 0.03 0.08
Matches are distributed among these distances:
120 32 0.28
124 3 0.03
125 2 0.02
126 2 0.02
127 2 0.02
129 5 0.04
130 69 0.60
ACGTcount: A:0.11, C:0.45, G:0.08, T:0.37
Consensus pattern (126 bp):
CAGCCATGTCTATGAATATTCCCTCCCCTTGCTCCTCTCCTTCTTCTCATCTTCCTTCTCCTCCT
TTCCCTCCAATCTCCACTGGATTTCACCCCTTCCTCCGCTGCCTTCTTCTCCGCCTTCAAG
Found at i:1548393 original size:3 final size:3
Alignment explanation
Indices: 1548385--1548409 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1548375 TGAGGTTGAT
1548385 GGA GGA GGA GGA GGA GGA GGA GGA G
1 GGA GGA GGA GGA GGA GGA GGA GGA G
1548410 CTGGAGCTGG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (3 bp):
GGA
Found at i:1555489 original size:2 final size:2
Alignment explanation
Indices: 1555484--1555556 Score: 105
Period size: 2 Copynumber: 37.5 Consensus size: 2
1555474 ATGCATAAGC
1555484 AT AT AT AT AT AT 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 AT AT AT AT AT AT
* * *
1555526 AT AT AT AC AT AC AT AA AT AT -T AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1555557 AGTATAATGG
Statistics
Matches: 63, Mismatches: 6, Indels: 4
0.86 0.08 0.05
Matches are distributed among these distances:
1 2 0.03
2 61 0.97
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:1555647 original size:22 final size:21
Alignment explanation
Indices: 1555613--1555654 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
1555603 TAATATTCAT
1555613 TATACATATATTATATTTAATA
1 TATACATATATTAT-TTTAATA
1555635 TATAC-TATAATTATTTTAAT
1 TATACATAT-ATTATTTTAAT
1555655 TGAATCTTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (21 bp):
TATACATATATTATTTTAATA
Found at i:1557999 original size:21 final size:21
Alignment explanation
Indices: 1557975--1558021 Score: 51
Period size: 21 Copynumber: 2.3 Consensus size: 21
1557965 ATTACATGAA
*
1557975 TATACAATATGTGATACATGT
1 TATACAATATGAGATACATGT
** *
1557996 TATATGATATGAGATAGATGT
1 TATACAATATGAGATACATGT
1558017 T-TACA
1 TATACA
1558022 CATACATGTG
Statistics
Matches: 20, Mismatches: 6, Indels: 1
0.74 0.22 0.04
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (21 bp):
TATACAATATGAGATACATGT
Found at i:1558251 original size:33 final size:32
Alignment explanation
Indices: 1558152--1558277 Score: 175
Period size: 32 Copynumber: 3.9 Consensus size: 32
1558142 GAGTCGAGGG
*
1558152 TTACCTATGTCTTTCGGGATATATGGACA-AGA
1 TTACCTATGTCTTTCGGGACATATGGACAGA-A
* *
1558184 TTGCCTATGTCTTT-GGGACATATGGACAGTA
1 TTACCTATGTCTTTCGGGACATATGGACAGAA
* *
1558215 TTACCTATGTCTTTTCGGTACATATGGATAGAA
1 TTACCTATGTC-TTTCGGGACATATGGACAGAA
1558248 TTACCTATGTCTTTCGGGACATATGGACAG
1 TTACCTATGTCTTTCGGGACATATGGACAG
1558278 TTATTTATGT
Statistics
Matches: 82, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
31 24 0.29
32 33 0.40
33 25 0.30
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (32 bp):
TTACCTATGTCTTTCGGGACATATGGACAGAA
Found at i:1558531 original size:3 final size:3
Alignment explanation
Indices: 1558523--1558563 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
1558513 TATGAAATGC
* *
1558523 ATT ATT ATT ATT AGT ATT AGT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1558564 GCCTCACTAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:1559389 original size:23 final size:23
Alignment explanation
Indices: 1559341--1559399 Score: 75
Period size: 23 Copynumber: 2.6 Consensus size: 23
1559331 GAACGTTTAT
*
1559341 ACGAACATTAAA-AAATATATTG
1 ACGAACATTAAACAAATATATTC
* * *
1559363 ACGAATATTAAACGAATATGTTC
1 ACGAACATTAAACAAATATATTC
1559386 ACGAACATTAAACA
1 ACGAACATTAAACA
1559400 GCAATGGCAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 11 0.37
23 19 0.63
ACGTcount: A:0.51, C:0.14, G:0.10, T:0.25
Consensus pattern (23 bp):
ACGAACATTAAACAAATATATTC
Found at i:1560602 original size:17 final size:18
Alignment explanation
Indices: 1560570--1560603 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1560560 AAGCTGCTTA
1560570 CTTTACGCTGTATTTCAT
1 CTTTACGCTGTATTTCAT
*
1560588 CTTTTCGCT-TATTTCA
1 CTTTACGCTGTATTTCA
1560604 ACCGCTGCCG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.15, C:0.24, G:0.09, T:0.53
Consensus pattern (18 bp):
CTTTACGCTGTATTTCAT
Found at i:1572864 original size:20 final size:20
Alignment explanation
Indices: 1572839--1572911 Score: 137
Period size: 20 Copynumber: 3.6 Consensus size: 20
1572829 AATTTTAGAT
1572839 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
1572859 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
1572879 AATCGCAATGCGAATATGTA
1 AATCGCAATGCGAATATGTA
*
1572899 AATCGCAACGCGA
1 AATCGCAATGCGA
1572912 TAACACGTGA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
20 52 1.00
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (20 bp):
AATCGCAATGCGAATATGTA
Found at i:1572945 original size:61 final size:61
Alignment explanation
Indices: 1572900--1573095 Score: 322
Period size: 61 Copynumber: 3.2 Consensus size: 61
1572890 GAATATGTAA
*
1572900 ATCGCAACGCGATAACACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTCA-GACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATT-ATGACT
* * * *
1572961 ATCGCAACGCGATAATACGTGATCGCAACGTGATTCAGACTATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTATGACT
*
1573022 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTATGACT
1573083 ATCGCAACGCGAT
1 ATCGCAACGCGAT
1573096 TCTGACTAAC
Statistics
Matches: 126, Mismatches: 8, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
61 126 1.00
ACGTcount: A:0.30, C:0.28, G:0.21, T:0.21
Consensus pattern (61 bp):
ATCGCAACGCGATAATACGTGATCGCAACGCGATTCTGACTATCGCAACGCGATTATGACT
Found at i:1572946 original size:20 final size:20
Alignment explanation
Indices: 1572921--1573108 Score: 245
Period size: 20 Copynumber: 9.3 Consensus size: 20
1572911 ATAACACGTG
1572921 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1572941 ATCGCAACGCGATTCAGACT
1 ATCGCAACGCGATTCTGACT
**
1572961 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
* *
1572981 GATCGCAACGTGATTCAGACT
1 -ATCGCAACGCGATTCTGACT
*
1573002 ATCGCAACGAGATTCTGACT
1 ATCGCAACGCGATTCTGACT
**
1573022 ATCGCAACGCGATAAT-ACGT
1 ATCGCAACGCGATTCTGAC-T
1573042 GATCGCAACGCGATTCTGACT
1 -ATCGCAACGCGATTCTGACT
1573063 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
1573083 ATCGCAACGCGATTCTGACT
1 ATCGCAACGCGATTCTGACT
*
1573103 AACGCA
1 ATCGCA
1573109 TCACTGAATT
Statistics
Matches: 146, Mismatches: 16, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
19 4 0.03
20 110 0.75
21 28 0.19
22 4 0.03
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (20 bp):
ATCGCAACGCGATTCTGACT
Found at i:1573067 original size:81 final size:81
Alignment explanation
Indices: 1572921--1573108 Score: 256
Period size: 81 Copynumber: 2.3 Consensus size: 81
1572911 ATAACACGTG
*
1572921 ATCGCAACGCGATTCTGACTATCGCAACGCGATTCAGACTATCGCAACGCGATAATACGTGATCG
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATTAAGACTATCGCAACGCGATAATACGTGATCG
*
1572986 CAACGTGATTCAGACT
66 CAACGCGATTCAGACT
* * **
1573002 ATCGCAACGAGATTCTGACTATCGCAACGCGA-TAATACGTGATCGCAACGCGATTCTGAC-T-A
1 ATCGCAACGCGATTCTGACTATCGCAACGCGATTAAGAC-T-ATCGCAACGCGATAAT-ACGTGA
*
1573064 TCGCAACGCGATTCTGACT
63 TCGCAACGCGATTCAGACT
*
1573083 ATCGCAACGCGATTCTGACTAACGCA
1 ATCGCAACGCGATTCTGACTATCGCA
1573109 TCACTGAATT
Statistics
Matches: 95, Mismatches: 9, Indels: 6
0.86 0.08 0.05
Matches are distributed among these distances:
80 4 0.04
81 74 0.78
82 15 0.16
83 2 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (81 bp):
ATCGCAACGCGATTCTGACTATCGCAACGCGATTAAGACTATCGCAACGCGATAATACGTGATCG
CAACGCGATTCAGACT
Done.