Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002454.1 Hibiscus syriacus cultivar Beakdansim tig00005027_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: 55814
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.33
Found at i:372 original size:16 final size:15
Alignment explanation
Indices: 351--418 Score: 73
Period size: 15 Copynumber: 4.3 Consensus size: 15
341 TTTTTGTCCC
*
351 TTTTCTTTTTTATTT
1 TTTTCTTTTTTGTTT
366 TTATTCTTTTTTTTGTTT
1 TT-TTC--TTTTTTGTTT
*
384 TCTTCTTTTTTGTTCT
1 TTTTCTTTTTTGTT-T
*
400 TTTTTTTTTTTGTTT
1 TTTTCTTTTTTGTTT
415 TTTT
1 TTTT
419 TTGCCCTTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
15 16 0.36
16 16 0.36
17 3 0.07
18 10 0.22
ACGTcount: A:0.03, C:0.07, G:0.04, T:0.85
Consensus pattern (15 bp):
TTTTCTTTTTTGTTT
Found at i:376 original size:17 final size:17
Alignment explanation
Indices: 353--415 Score: 64
Period size: 16 Copynumber: 3.9 Consensus size: 17
343 TTTGTCCCTT
*
353 TTCTTTTTTAT-TTTTA
1 TTCTTTTTTTTGTTTTA
*
369 TTCTTTTTTTTGTTTTC
1 TTCTTTTTTTTGTTTTA
386 TTC--TTTTTTGTTCTT-
1 TTCTTTTTTTTGTT-TTA
401 TT-TTTTTTTTGTTTT
1 TTCTTTTTTTTGTTTT
416 TTTTTGCCCT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 13 0.32
16 21 0.51
17 7 0.17
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (17 bp):
TTCTTTTTTTTGTTTTA
Found at i:379 original size:13 final size:13
Alignment explanation
Indices: 351--420 Score: 77
Period size: 13 Copynumber: 5.1 Consensus size: 13
341 TTTTTGTCCC
351 TTTTCTTTTTTATTT
1 TTTTC-TTTTT-TTT
366 TTATTCTTTTTTTT
1 TT-TTCTTTTTTTT
*
380 GTTTTCTTCTTTTT
1 -TTTTCTTTTTTTT
*
394 TGTTCTTTTTTTT
1 TTTTCTTTTTTTT
*
407 TTTTGTTTTTTTT
1 TTTTCTTTTTTTT
420 T
1 T
421 GCCCTTTTTG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
13 23 0.48
14 13 0.27
15 9 0.19
16 3 0.06
ACGTcount: A:0.03, C:0.07, G:0.04, T:0.86
Consensus pattern (13 bp):
TTTTCTTTTTTTT
Found at i:390 original size:33 final size:31
Alignment explanation
Indices: 353--415 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
343 TTTGTCCCTT
*
353 TTCTTTTTTATTTTTATTCTTTTTTTTGTTTTC
1 TTCTTTTTTATTCTT-TT-TTTTTTTTGTTTTC
*
386 TTCTTTTTTGTTCTTTTTTTTTTTTGTTTT
1 TTCTTTTTTATTCTTTTTTTTTTTTGTTTT
416 TTTTTGCCCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 13 0.46
32 2 0.07
33 13 0.46
ACGTcount: A:0.03, C:0.08, G:0.05, T:0.84
Consensus pattern (31 bp):
TTCTTTTTTATTCTTTTTTTTTTTTGTTTTC
Found at i:401 original size:27 final size:26
Alignment explanation
Indices: 363--421 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
353 TTCTTTTTTA
*
363 TTTTTATTCTTTTTTTTGTTTTCTTCT
1 TTTTTGTTCTTTTTTTT-TTTTCTTCT
* *
390 TTTTTGTTCTTTTTTTTTTTTGTTTT
1 TTTTTGTTCTTTTTTTTTTTTCTTCT
416 TTTTTG
1 TTTTTG
422 CCCTTTTTGT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.85
Consensus pattern (26 bp):
TTTTTGTTCTTTTTTTTTTTTCTTCT
Found at i:427 original size:26 final size:27
Alignment explanation
Indices: 371--429 Score: 75
Period size: 26 Copynumber: 2.2 Consensus size: 27
361 TATTTTTATT
**
371 CTTTTTTTTGTTTTCTTCTTTTTTGTT
1 CTTTTTTTTGTTTTCTTCTTTTTTGCC
* *
398 CTTTTTTTT-TTTTGTTTTTTTTTGCC
1 CTTTTTTTTGTTTTCTTCTTTTTTGCC
424 CTTTTT
1 CTTTTT
430 GTTCTGATTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
26 19 0.68
27 9 0.32
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (27 bp):
CTTTTTTTTGTTTTCTTCTTTTTTGCC
Found at i:429 original size:1 final size:1
Alignment explanation
Indices: 351--420 Score: 50
Period size: 1 Copynumber: 70.0 Consensus size: 1
341 TTTTTGTCCC
* * * * * * * * * *
351 TTTTCTTTTTTATTTTTATTCTTTTTTTTGTTTTCTTCTTTTTTGTTCTTTTTTTTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
416 TTTTT
1 TTTTT
421 GCCCTTTTTG
Statistics
Matches: 49, Mismatches: 20, Indels: 0
0.71 0.29 0.00
Matches are distributed among these distances:
1 49 1.00
ACGTcount: A:0.03, C:0.07, G:0.04, T:0.86
Consensus pattern (1 bp):
T
Found at i:4923 original size:18 final size:17
Alignment explanation
Indices: 4839--4946 Score: 62
Period size: 18 Copynumber: 6.2 Consensus size: 17
4829 ATGAAAATAA
*
4839 ATAATAAAATAATATAT
1 ATAATAAAATAATAAAT
*
4856 ATATATATATATATATAAAT
1 ATA-ATA-AAATA-ATAAAT
* *
4876 ATAA-AAATGTATGTATAAT
1 ATAATAAA-ATA-ATA-AAT
*
4895 ATAATAAAATACTAAAT
1 ATAATAAAATAATAAAT
*
4912 AGTAATATAATAATAAAT
1 A-TAATAAAATAATAAAT
*
4930 A-AATGAAA-AA-AAAT
1 ATAATAAAATAATAAAT
4944 ATA
1 ATA
4947 CATATAATAT
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
14 5 0.07
15 3 0.04
16 5 0.07
17 8 0.11
18 26 0.36
19 14 0.19
20 11 0.15
ACGTcount: A:0.62, C:0.01, G:0.04, T:0.33
Consensus pattern (17 bp):
ATAATAAAATAATAAAT
Found at i:5668 original size:37 final size:37
Alignment explanation
Indices: 5575--5672 Score: 133
Period size: 37 Copynumber: 2.6 Consensus size: 37
5565 ATGCTTGTGG
* * * * *
5575 ATCATATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
5612 ATCATATTTTTAGGAGTTTGAATCATAGCAAAATTCT
1 ATCATATTTTTAGGAGTTTGAATCATAGCAAAACTCT
*
5649 ATCATATTTTTAAGAGTTTGAATC
1 ATCATATTTTTAGGAGTTTGAATC
5673 CTAGTAGGAC
Statistics
Matches: 54, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 54 1.00
ACGTcount: A:0.36, C:0.10, G:0.13, T:0.41
Consensus pattern (37 bp):
ATCATATTTTTAGGAGTTTGAATCATAGCAAAACTCT
Found at i:7682 original size:29 final size:31
Alignment explanation
Indices: 7650--7722 Score: 89
Period size: 33 Copynumber: 2.4 Consensus size: 31
7640 TACTATTATT
7650 AAAATATTATA-T-CTATAATTTTA-TAAATA
1 AAAATATTATATTACTAT-ATTTTATTAAATA
7679 AAAATATTATGATTACTATATTTTATTTAAATA
1 AAAATATTAT-ATTACTATATTTTA-TTAAATA
*
7712 AAATTATTATA
1 AAAATATTATA
7723 AATTATAGTA
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
29 10 0.26
30 1 0.03
31 7 0.18
32 5 0.13
33 15 0.39
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (31 bp):
AAAATATTATATTACTATATTTTATTAAATA
Found at i:7762 original size:42 final size:42
Alignment explanation
Indices: 7716--7796 Score: 126
Period size: 42 Copynumber: 1.9 Consensus size: 42
7706 TAAATAAAAT
*
7716 TATTATAAATTATAGTAATTATTTATTGAAATAAGAATAATA
1 TATTATAAATTATAGTAATTATTTATTAAAATAAGAATAATA
* * *
7758 TATTATTAATTATATTAATTATTTATTAAAATAATAATA
1 TATTATAAATTATAGTAATTATTTATTAAAATAAGAATA
7797 CTATTTAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (42 bp):
TATTATAAATTATAGTAATTATTTATTAAAATAAGAATAATA
Found at i:7967 original size:23 final size:23
Alignment explanation
Indices: 7924--7967 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
7914 TGATTTTATT
* *
7924 AATAATTTATTATATATTATTAA
1 AATAATTTAATATATAATATTAA
*
7947 AATAATTTAATATTTAATATT
1 AATAATTTAATATATAATATT
7968 TTTATTAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATAATTTAATATATAATATTAA
Found at i:8021 original size:19 final size:18
Alignment explanation
Indices: 7973--8023 Score: 59
Period size: 19 Copynumber: 2.7 Consensus size: 18
7963 ATATTTTTAT
7973 TAAAATTATACTAAAATA
1 TAAAATTATACTAAAATA
*
7991 -ATATATTAATACTAAACATA
1 TA-AAATT-ATACTAAA-ATA
8011 TAAAATTATACTA
1 TAAAATTATACTA
8024 TTAAAATTAT
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 1 0.04
18 4 0.15
19 14 0.52
20 7 0.26
21 1 0.04
ACGTcount: A:0.57, C:0.08, G:0.00, T:0.35
Consensus pattern (18 bp):
TAAAATTATACTAAAATA
Found at i:8103 original size:36 final size:33
Alignment explanation
Indices: 8031--8103 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 33
8021 CTATTAAAAT
* **
8031 TATTTTTATGAAATTATATAATTTAATAATTAA
1 TATTTTTATAAAATTATATAAAATAATAATTAA
8064 TATTTTTATTAAAATTATACTAAAATAATATATTAA
1 TATTTTTA-TAAAATTATA-TAAAATAATA-ATTAA
8100 TATT
1 TATT
8104 AAACATATAA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
33 8 0.24
34 9 0.26
35 8 0.24
36 9 0.26
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (33 bp):
TATTTTTATAAAATTATATAAAATAATAATTAA
Found at i:13532 original size:34 final size:34
Alignment explanation
Indices: 13459--13549 Score: 148
Period size: 34 Copynumber: 2.7 Consensus size: 34
13449 TTTTTTTTTT
*
13459 TTTTTTTGTTGTTTCAAGAGAACCGATTTCAAAGG
1 TTTTTTTG-TGTTTCAAGAGAAACGATTTCAAAGG
13494 -TTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
1 TTTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
*
13527 TTTTTTTATGTTTCAAGAGAAAC
1 TTTTTTTGTGTTTCAAGAGAAAC
13550 TGTCTTAAGA
Statistics
Matches: 53, Mismatches: 2, Indels: 3
0.91 0.03 0.05
Matches are distributed among these distances:
33 25 0.47
34 28 0.53
ACGTcount: A:0.29, C:0.10, G:0.19, T:0.43
Consensus pattern (34 bp):
TTTTTTTGTGTTTCAAGAGAAACGATTTCAAAGG
Found at i:13622 original size:36 final size:36
Alignment explanation
Indices: 13535--13823 Score: 335
Period size: 36 Copynumber: 8.1 Consensus size: 36
13525 GGTTTTTTTA
*
13535 TGTTTCAAGAGAAACTGTCTTAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
*
13572 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
13608 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
* * * * * **
13645 AGTTCCAAAAGAAACTGTCCCAAGGGAGATGAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* * *
13681 TGTTCCAAG-GAAAACATAT-TC-A-A-AG----ATTT
1 TGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAATT
*
13710 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
* *
13746 TATTTCAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
13782 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TT
13819 TGTTT
1 TGTTT
13824 TGAGTAAATT
Statistics
Matches: 217, Mismatches: 22, Indels: 26
0.82 0.08 0.10
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 2 0.01
31 1 0.00
32 2 0.01
33 2 0.01
35 2 0.01
36 119 0.55
37 70 0.32
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:13724 original size:102 final size:102
Alignment explanation
Indices: 13606--13795 Score: 274
Period size: 102 Copynumber: 1.9 Consensus size: 102
13596 AGAGACAAAA
*
13606 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCCAAAAGAAACTGTCCCAAGGG
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTA-TTCCAAAAGAAACTGTCCCAAGAG
**
13671 AGATGAAATTTGTTCCAAG-GAAAACATATTCAAAGAT
65 AGACAAAATTTGTTCCAAGAGAAAACATATTCAAAGAT
* * * ** *
13708 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCCCAAGAGA
*
13773 GACAAAATTTGTTTCAAGAGAAA
66 GACAAAATTTGTTCCAAGAGAAA
13796 CTGTCTCAAG
Statistics
Matches: 77, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
101 35 0.45
102 42 0.55
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (102 bp):
TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTATTCCAAAAGAAACTGTCCCAAGAGA
GACAAAATTTGTTCCAAGAGAAAACATATTCAAAGAT
Found at i:13791 original size:21 final size:21
Alignment explanation
Indices: 13729--13793 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
13719 GGAAACTGTC
*
13729 TCAAGAGAGACAAAATTTATT
1 TCAAGAGAGACAAAATTTGTT
* *
13750 TCAAG-G-G---AAA-CTGTC
1 TCAAGAGAGACAAAATTTGTT
13765 TCAAGAGAGACAAAATTTGTT
1 TCAAGAGAGACAAAATTTGTT
13786 TCAAGAGA
1 TCAAGAGA
13794 AACTGTCTCA
Statistics
Matches: 33, Mismatches: 5, Indels: 12
0.66 0.10 0.24
Matches are distributed among these distances:
15 7 0.21
16 4 0.12
17 1 0.03
19 1 0.03
20 4 0.12
21 16 0.48
ACGTcount: A:0.43, C:0.12, G:0.20, T:0.25
Consensus pattern (21 bp):
TCAAGAGAGACAAAATTTGTT
Found at i:13821 original size:138 final size:138
Alignment explanation
Indices: 13570--13822 Score: 409
Period size: 138 Copynumber: 1.8 Consensus size: 138
13560 GAGACAAAAC
*
13570 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGAGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
* **
13635 GACAAAACTTAGTTCCAAAAGAAACTGTCCCAAGGGAGATGAAATTTGTTCCAAGGAAAACATAT
66 GACAAAACTTAGTTCCAAAAGAAACTGTCCCAAGAGAGACAAAATTTGTTCCAAGGAAAACATAT
13700 TCAAAGAT
131 TCAAAGAT
*
13708 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGAGA
1 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
* * * *
13773 GACAAAA-TTTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTTGTT
66 GACAAAACTTAGTTCCAAAAGAAACTGTCCCAAGAGAGACAAAA-TTTGTT
13823 TTGAGTAAAT
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
137 29 0.28
138 76 0.72
ACGTcount: A:0.40, C:0.15, G:0.20, T:0.26
Consensus pattern (138 bp):
TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGA
GACAAAACTTAGTTCCAAAAGAAACTGTCCCAAGAGAGACAAAATTTGTTCCAAGGAAAACATAT
TCAAAGAT
Found at i:15356 original size:95 final size:96
Alignment explanation
Indices: 15181--15380 Score: 294
Period size: 95 Copynumber: 2.1 Consensus size: 96
15171 GGACATCTCA
* * ** * *
15181 ATATGTAAACACCTTTATCAGGTTAGCGGAATCTTATCCATAAAGTCGGGGCGTCTAACCAATTG
1 ATATATAATCACCTTTATCAGACTAGCGGAATATTATCCATAAAATCGGGGCGTCTAACCAATTG
* *
15246 CTTTAGAGGGACAACTCAAGCTTTATTGTAT
66 CTCTAGAGGGACAACTAAAGCTTTATTGTAT
* *
15277 A-ATATAATCACCTTTATCAGACTAGCTGAATATTATCCATAAAATCGGGGCGTTTAACCAATTG
1 ATATATAATCACCTTTATCAGACTAGCGGAATATTATCCATAAAATCGGGGCGTCTAACCAATTG
*
15341 CTCTAGAGGGGCAACTAAAGCTTTATTGTAT
66 CTCTAGAGGGACAACTAAAGCTTTATTGTAT
15372 ATATATAAT
1 ATATATAAT
15381 ATTATAATAT
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
95 84 0.91
96 8 0.09
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Consensus pattern (96 bp):
ATATATAATCACCTTTATCAGACTAGCGGAATATTATCCATAAAATCGGGGCGTCTAACCAATTG
CTCTAGAGGGACAACTAAAGCTTTATTGTAT
Found at i:19332 original size:31 final size:30
Alignment explanation
Indices: 19264--19333 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
19254 AAGAGTTAGT
*
19264 ATTAAAAATAAAAAAAAATAAAAGGAAAGA
1 ATTAAAATTAAAAAAAAATAAAAGGAAAGA
** * * *
19294 AAGAAAATTAAAAAAGATTAAATTGGAAAGA
1 ATTAAAATTAAAAAAAAATAAA-AGGAAAGA
19325 ATTAAAATT
1 ATTAAAATT
19334 CATGGATCAA
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
30 17 0.55
31 14 0.45
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.20
Consensus pattern (30 bp):
ATTAAAATTAAAAAAAAATAAAAGGAAAGA
Found at i:19777 original size:5 final size:5
Alignment explanation
Indices: 19767--19791 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
19757 ATAAAGCGCC
19767 TAAAA TAAAA TAAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA
19792 GCGTAGATGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
TAAAA
Found at i:26975 original size:19 final size:19
Alignment explanation
Indices: 26951--26987 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
26941 CTTGATACCA
26951 TGTAGAAAACAGACTGTAT
1 TGTAGAAAACAGACTGTAT
*
26970 TGTAGAAAATAGACTGTA
1 TGTAGAAAACAGACTGTA
26988 GGAAACAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.43, C:0.08, G:0.22, T:0.27
Consensus pattern (19 bp):
TGTAGAAAACAGACTGTAT
Found at i:27207 original size:19 final size:19
Alignment explanation
Indices: 27183--27219 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
27173 CCTGATACCA
27183 TGTAGAAAACAGACTGTAT
1 TGTAGAAAACAGACTGTAT
27202 TGTAGAAAACAGACTGTA
1 TGTAGAAAACAGACTGTA
27220 GGAAACAGAC
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:0.43, C:0.11, G:0.22, T:0.24
Consensus pattern (19 bp):
TGTAGAAAACAGACTGTAT
Found at i:27337 original size:232 final size:232
Alignment explanation
Indices: 26931--27394 Score: 901
Period size: 232 Copynumber: 2.0 Consensus size: 232
26921 AATCGAATTG
* *
26931 ATCGCTCTAACTTGATACCATGTAGAAAACAGACTGTATTGTAGAAAATAGACTGTAGGAAACAG
1 ATCGCTCTAACCTGATACCATGTAGAAAACAGACTGTATTGTAGAAAACAGACTGTAGGAAACAG
26996 ACAAGTCTGTTATTTTATTCTTGCATACTTTCAGTAGAAACATATTACATATTTATATACAAATT
66 ACAAGTCTGTTATTTTATTCTTGCATACTTTCAGTAGAAACATATTACATATTTATATACAAATT
*
27061 ATTCCTCTAAACTAGGAAACTCTAAGTTAGGAAAGATACTAATCCTAGGAGATGTAATCCCTTGA
131 ATACCTCTAAACTAGGAAACTCTAAGTTAGGAAAGATACTAATCCTAGGAGATGTAATCCCTTGA
27126 AATAAGGGATTGAAAAACAGAAAATAATTACAGAATC
196 AATAAGGGATTGAAAAACAGAAAATAATTACAGAATC
27163 ATCGCTCTAACCTGATACCATGTAGAAAACAGACTGTATTGTAGAAAACAGACTGTAGGAAACAG
1 ATCGCTCTAACCTGATACCATGTAGAAAACAGACTGTATTGTAGAAAACAGACTGTAGGAAACAG
27228 ACAAGTCTGTTATTTTATTCTTGCATACTTTCAGTAGAAACATATTACATATTTATATACAAATT
66 ACAAGTCTGTTATTTTATTCTTGCATACTTTCAGTAGAAACATATTACATATTTATATACAAATT
27293 ATACCTCTAAACTAGGAAACTCTAAGTTAGGAAAGATACTAATCCTAGGAGATGTAATCCCTTGA
131 ATACCTCTAAACTAGGAAACTCTAAGTTAGGAAAGATACTAATCCTAGGAGATGTAATCCCTTGA
27358 AATAAGGGATTGAAAAACAGAAAATAATTACAGAATC
196 AATAAGGGATTGAAAAACAGAAAATAATTACAGAATC
27395 TCTTGACATC
Statistics
Matches: 229, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
232 229 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.29
Consensus pattern (232 bp):
ATCGCTCTAACCTGATACCATGTAGAAAACAGACTGTATTGTAGAAAACAGACTGTAGGAAACAG
ACAAGTCTGTTATTTTATTCTTGCATACTTTCAGTAGAAACATATTACATATTTATATACAAATT
ATACCTCTAAACTAGGAAACTCTAAGTTAGGAAAGATACTAATCCTAGGAGATGTAATCCCTTGA
AATAAGGGATTGAAAAACAGAAAATAATTACAGAATC
Found at i:35468 original size:14 final size:13
Alignment explanation
Indices: 35442--35467 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35432 TTCTCGCACG
35442 TCAATAAAAAAAA
1 TCAATAAAAAAAA
35455 TCAATAAAAAAAA
1 TCAATAAAAAAAA
35468 AATCCTCTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
TCAATAAAAAAAA
Found at i:36146 original size:21 final size:20
Alignment explanation
Indices: 36098--36156 Score: 109
Period size: 20 Copynumber: 2.9 Consensus size: 20
36088 ATCCTATTCC
36098 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
36118 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
36138 CTGGGTAATCTTACATTCC
1 CT-GGTAATCTTACATTCC
36157 GTGAACCAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 22 0.58
21 16 0.42
ACGTcount: A:0.24, C:0.29, G:0.12, T:0.36
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:37323 original size:10 final size:10
Alignment explanation
Indices: 37274--37303 Score: 60
Period size: 10 Copynumber: 3.0 Consensus size: 10
37264 GAAAGATATT
37274 TAAAAGAAAA
1 TAAAAGAAAA
37284 TAAAAGAAAA
1 TAAAAGAAAA
37294 TAAAAGAAAA
1 TAAAAGAAAA
37304 ACCTAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.10, T:0.10
Consensus pattern (10 bp):
TAAAAGAAAA
Found at i:38639 original size:28 final size:27
Alignment explanation
Indices: 38597--38659 Score: 81
Period size: 28 Copynumber: 2.3 Consensus size: 27
38587 GGACCTGGAA
** *
38597 AAAATAAAATTAAAAGAAAATAATTAAT
1 AAAATAAAAAGAAAAG-AAATAAATAAT
38625 AAAATAAAAAGAAAAGAAATAAATAAT
1 AAAATAAAAAGAAAAGAAATAAATAAT
38652 AATAATAA
1 AA-AATAA
38660 TAATAATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
27 12 0.39
28 19 0.61
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.21
Consensus pattern (27 bp):
AAAATAAAAAGAAAAGAAATAAATAAT
Found at i:38654 original size:3 final size:3
Alignment explanation
Indices: 38646--38678 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
38636 AAAAGAAATA
*
38646 AAT AAT AAT AAT AAT AAT AAT AA- AAT AAA AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
38679 TTTTCCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (3 bp):
AAT
Found at i:38678 original size:23 final size:22
Alignment explanation
Indices: 38599--38676 Score: 81
Period size: 23 Copynumber: 3.6 Consensus size: 22
38589 ACCTGGAAAA
*
38599 AATAAAATTAAAAGAAAATAATT
1 AATAAAATAAAAAGAAAATAA-T
*
38622 AATAAAATAAAAAGAAAA-GA-
1 AATAAAATAAAAAGAAAATAAT
* *
38642 AAT-AAATAATAATAATAATAAT
1 AATAAAATAAAAAGAA-AATAAT
38664 AATAAAATAAAAA
1 AATAAAATAAAAA
38677 TATTTTCCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 10 0.22
20 5 0.11
21 1 0.02
22 4 0.09
23 25 0.56
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (22 bp):
AATAAAATAAAAAGAAAATAAT
Found at i:38739 original size:34 final size:32
Alignment explanation
Indices: 38692--39017 Score: 169
Period size: 36 Copynumber: 9.4 Consensus size: 32
38682 TCCAAAAACC
38692 TATATAATATATATTTTCAAAAAATATTTTAAAATT
1 TATAT-ATATATATTTTC--AAAATATTTTAAAA-T
* *
38728 ATATATATATATATTTTTTAAAATATTTTCAAA-
1 -TATATATATATA-TTTTCAAAATATTTTAAAAT
* * *
38761 -A-CTATATA-GTTTTCAAAAATGTTTTAAAAT
1 TATATATATATATTTTC-AAAATATTTTAAAAT
* * *
38791 TATATATTATATGTTTTCAAAATGATTTAAAAAC
1 TATATA-TATATATTTTCAAAAT-ATTTTAAAAT
*
38825 TATATAT-TATATATTTCAAAATGTTTTAAAAACT
1 TATATATATATAT-TTTCAAAATATTTT-AAAA-T
*
38859 ATAATATATATATATATTCAAAAATATTTTAAACACT
1 -T-ATATATATATATTTTC-AAAATATTTTAAA-A-T
* *
38896 ATATATTATATTTATTTTCAAAATGTTTTAAAAACT
1 -TATA-TATATATATTTTCAAAATATTTT-AAAA-T
* * *
38932 ATATAATATATAAATGTTTTCACAATGTTTTCAAAACT
1 -TAT-ATATAT--ATATTTTCAAAATATTTT-AAAA-T
* * *
38970 ATATATTATATATATTTTAAAAATGTTTTCAAAAAC
1 -TATA-TATATATATTTTCAAAATATTTT--AAAAT
39006 TATATA-ATATAT
1 TATATATATATAT
39018 GAATTTTCGA
Statistics
Matches: 237, Mismatches: 29, Indels: 50
0.75 0.09 0.16
Matches are distributed among these distances:
28 4 0.02
29 12 0.05
30 6 0.03
31 2 0.01
32 9 0.04
33 29 0.12
34 21 0.09
35 18 0.08
36 58 0.24
37 48 0.20
38 30 0.13
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (32 bp):
TATATATATATATTTTCAAAATATTTTAAAAT
Found at i:38767 original size:36 final size:36
Alignment explanation
Indices: 38671--38768 Score: 119
Period size: 36 Copynumber: 2.7 Consensus size: 36
38661 AATAATAAAA
38671 TAAAAATATTTTCCAAAAACCTATATA-ATATATATTTT
1 TAAAAATATTTT-C-AAAA-CTATATATATATATATTTT
* *
38709 CAAAAAATATTTT-AAAATTATATATATATATATTTT
1 -TAAAAATATTTTCAAAACTATATATATATATATTTT
*
38745 TTAAAATATTTTCAAAACTATATA
1 TAAAAATATTTTCAAAACTATATA
38769 GTTTTCAAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 7
0.81 0.08 0.11
Matches are distributed among these distances:
35 16 0.31
36 25 0.48
39 11 0.21
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (36 bp):
TAAAAATATTTTCAAAACTATATATATATATATTTT
Found at i:38773 original size:28 final size:28
Alignment explanation
Indices: 38735--38796 Score: 72
Period size: 28 Copynumber: 2.2 Consensus size: 28
38725 ATTATATATA
* *
38735 TATATATTTTTTAAAATAT-TTTCAAAAC
1 TATATAGTTTTCAAAA-ATGTTTCAAAAC
* *
38763 TATATAGTTTTCAAAAATGTTTTAAAAT
1 TATATAGTTTTCAAAAATGTTTCAAAAC
38791 TATATA
1 TATATA
38797 TTATATGTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
27 2 0.07
28 27 0.93
ACGTcount: A:0.44, C:0.05, G:0.03, T:0.48
Consensus pattern (28 bp):
TATATAGTTTTCAAAAATGTTTCAAAAC
Found at i:38824 original size:62 final size:64
Alignment explanation
Indices: 38699--38902 Score: 195
Period size: 64 Copynumber: 3.1 Consensus size: 64
38689 ACCTATATAA
* * *
38699 TATATATTTTCAAAAAATATTTTAAAATTATATATATATATATTTTTTAAAATATTTTCAAAAC
1 TATATATTTTCAAAAAATATTTTAAAATTATATATATATATAGTTTTCAAAATATTTTAAAAAC
*
38763 TATATAGTTTTC-AAAAATGTTTTAAAATTATATAT-TATAT-GTTTTCAAAATGA-TTTAAAAA
1 TATATA-TTTTCAAAAAATATTTTAAAATTATATATATATATAGTTTTCAAAAT-ATTTTAAAAA
38824 C
64 C
* * * *
38825 TATATATTATAT-ATTTCAAAATGTTTTAAAAACTATAATATATATATA-TATTCAAAAATATTT
1 TATATATT-T-TCA---AAAAATATTTT-AAAATTAT-ATATATATATAGTTTTC-AAAATATTT
*
38888 TAAACAC
58 TAAAAAC
38895 TATATATT
1 TATATATT
38903 ATATTTATTT
Statistics
Matches: 118, Mismatches: 8, Indels: 22
0.80 0.05 0.15
Matches are distributed among these distances:
61 2 0.02
62 24 0.20
63 7 0.06
64 28 0.24
65 5 0.04
66 10 0.08
67 7 0.06
68 4 0.03
69 10 0.08
70 21 0.18
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (64 bp):
TATATATTTTCAAAAAATATTTTAAAATTATATATATATATAGTTTTCAAAATATTTTAAAAAC
Found at i:38838 original size:36 final size:36
Alignment explanation
Indices: 38763--39030 Score: 282
Period size: 37 Copynumber: 7.4 Consensus size: 36
38753 TTTTCAAAAC
*
38763 TATATAGTTTTCAAAAATGTTTT-AAAATTATATA-T-
1 TATATA-TTTTC-AAAATGTTTTAAAAACTATATATTA
* *
38798 TATATGTTTTCAAAATGATTTAAAAACTATATA-T-
1 TATATATTTTCAAAATGTTTTAAAAACTATATATTA
38832 TATATA-TTTCAAAATGTTTTAAAAACTATA-ATATA
1 TATATATTTTCAAAATGTTTTAAAAACTATATAT-TA
* * *
38867 TATATATATTCAAAAATATTTTAAACACTATATATTA
1 TATATATTTTC-AAAATGTTTTAAAAACTATATATTA
*
38904 TATTTATTTTCAAAATGTTTTAAAAACTATATAATATA
1 TATATATTTTCAAAATGTTTTAAAAACTATAT-AT-TA
* * * *
38942 TAAATGTTTTCACAATGTTTTCAAAACTATATATTA
1 TATATATTTTCAAAATGTTTTAAAAACTATATATTA
* *
38978 TATATATTTTAAAAATGTTTTCAAAAACTATATAATA
1 TATATATTTTCAAAATGTTTT-AAAAACTATATATTA
39015 TATGA-ATTTTCGAAAA
1 TAT-ATATTTTC-AAAA
39031 CCATTTTCTG
Statistics
Matches: 197, Mismatches: 24, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
32 1 0.01
33 32 0.16
34 22 0.11
35 11 0.06
36 41 0.21
37 54 0.27
38 36 0.18
ACGTcount: A:0.45, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
TATATATTTTCAAAATGTTTTAAAAACTATATATTA
Found at i:40016 original size:84 final size:83
Alignment explanation
Indices: 39680--40486 Score: 793
Period size: 84 Copynumber: 9.8 Consensus size: 83
39670 TGCCTTGGGC
* *
39680 TATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTC--T-TTGGCAGATA
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATA
* * * *
39742 ACCCTTCTAGCCTTGAGC
66 ACCCTTCTCGACTTAAGT
* * * * * *
39760 TATACCGCAAATGATGTGCCGTT-GAGCTGATCATAATCGAACTCAAAGGTCTTTGTTGGCAGAT
1 TATGCTGCAAATGATGTGCC-TTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGAT
* * *
39824 AACCCTTCTAGCCTTGAGT
65 AACCCTTCTCGACTTAAGT
* *** * *
39843 TATGCCGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGAACTCGAAGG--TTT-TTGGCAGAT
1 TATGCTGCAAATGATGTG-CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGAT
*
39905 AA-CCTTCTCGACTTAAGC
65 AACCCTTCTCGACTTAAGT
* * * *
39923 TATGCTGCAAATGATGTGCCTTGGAGATGAACATAGTCGAACTCGAAGATCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGAT
39988 AACCCTTCTCGACTTAAGT
65 AACCCTTCTCGACTTAAGT
* * * * *
40007 TATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTTGAAGGTCTTTTGGTGACAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTC-TTTGTTGGCAGAT
* * * *
40072 AACTCTTCTAGCCTTGAGT
65 AACCCTTCTCGACTTAAGT
* * * * * * *
40091 TATGCTGTAAATGATGTTCCCTCGAAGTTGAGTGTAATCGAACTC-AAGGGTC--T-TTGGCAGA
1 TATGCTGCAAATGATG-TGCCTTGGAGCTGAGCGTAGTCGAACTCGAA-GGTCTTTGTTGGCAGA
*
40152 TAGCCCTTCTCGACTTAAGT
64 TAACCCTTCTCGACTTAAGT
*
40172 TATGCTGCAAATGATGTGCCTTGGAGCTGAGGGTAGTCGAACTCGAAGGTCTTTGGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAGAT
40237 AACCCTTCTCGACTTAAGT
65 AACCCTTCTCGACTTAAGT
* * * * *
40256 TATGTTGTAAATGATATGCCTTAGAGTTGAGCGTAGTCGAACTCGAAGGT-TTT-TTAGTGACAG
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTT-G-G-CAG
* * *
40319 ATAACCCTTCTAGCCTTGAGT
63 ATAACCCTTCTCGACTTAAGT
* * * * * * * * *
40340 TATGTTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCGAACTCGAGGGTC--T-TTGACAGAT
1 TATGCTGCAAATGATGT-GCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGAT
* * *
40402 AGCCCTTCTCAACTTAAGC
65 AACCCTTCTCGACTTAAGT
* *
40421 TATGCTGCAAATGATGTGTCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCCTTTGTTGGCAGAT
1 TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGTTGGCAGAT
40486 A
65 A
40487 TGCTGCAAAT
Statistics
Matches: 594, Mismatches: 105, Indels: 52
0.79 0.14 0.07
Matches are distributed among these distances:
79 22 0.04
80 120 0.20
81 90 0.15
82 7 0.01
83 62 0.10
84 241 0.41
85 52 0.09
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (83 bp):
TATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGATA
ACCCTTCTCGACTTAAGT
Found at i:40229 original size:249 final size:248
Alignment explanation
Indices: 39678--40486 Score: 1146
Period size: 249 Copynumber: 3.3 Consensus size: 248
39668 TTTGCCTTGG
* *
39678 GCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAACTCGAAGGTC--T-TTGGCAGA
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGA
* * * * * * * * * *
39740 TAACCCTTCTAGCCTTGAGCTATACCGCAAATGATGTGCCGTT-GAGCTGATCATAATCGAACTC
66 TAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCC-TTAGAGCTGAGCGTAGTCGAACTC
* * * * * * *
39804 AAAGGTC-TTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCCGCAAATGATGTGCCCTCAA
130 GAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGA
* *
39868 AGCTGAGTGTAATCGAACTCGAA-GGTTTTTGGCAGATA-ACCTTCTCGACTTAA
195 AGCTGAGTGTAATCGAACTC-AAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
* * * *
39921 GCTATGCTGCAAATGATGTGCCTTGGAGATGAACATAGTCGAACTCGAAGATCTTTGGTTGGCAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAG
*
39986 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTT
65 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
* *
40051 GAAGGTCTTTTGGTGACAGATAACTCTTCTAGCCTTGAGTTATGCTGTAAATGATGTTCCCTCGA
130 GAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGA
*
40116 AGTTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
195 AGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
* *
40170 GTTATGCTGCAAATGATGTGCCTTGGAGCTGAGGGTAGTCGAACTCGAAGGTCTTTGGTTGGCAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GTTGGCAG
* * *
40235 ATAACCCTTCTCGACTTAAGTTATGTTGTAAATGATATGCCTTAGAGTTGAGCGTAGTCGAACTC
65 ATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTC
* * *
40300 GAAGGTTTTTTAGTGACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTACCCTCGA
130 GAAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGA
* * *
40365 AGCTGAGTGTAATCGAACTCGAGGGTCTTTGACAGATAGCCCTTCTCAACTTAA
195 AGCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
* *
40419 GCTATGCTGCAAATGATGTGTCTTGGAGCTGAGCGGAGTCGAACTCGAAGGTCCTTTGTTGGCAG
1 GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGT-CTTTGTTGGCAG
40484 ATA
65 ATA
40487 TGCTGCAAAT
Statistics
Matches: 506, Mismatches: 51, Indels: 12
0.89 0.09 0.02
Matches are distributed among these distances:
243 47 0.09
245 1 0.00
246 2 0.00
247 66 0.13
248 83 0.16
249 303 0.60
250 4 0.01
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.30
Consensus pattern (248 bp):
GCTATGCTGCAAATGATGTGCCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTTTGTTGGCAGA
TAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCTTAGAGCTGAGCGTAGTCGAACTCG
AAGGTCTTTTGGTGACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTACCCTCGAA
GCTGAGTGTAATCGAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAA
Found at i:40461 original size:165 final size:162
Alignment explanation
Indices: 39656--40470 Score: 730
Period size: 165 Copynumber: 5.0 Consensus size: 162
39646 ATTTTATTGA
* * * * * * * * *
39656 CAGATAACCCTTTTTGCCTTGGGCTATGCTGTAAATGATGTGCCTTGGAGCTGAGCGTAGTTGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTCCCTCGAAGCTGAGCGTAGTCGAA
* * * *
39721 CTCGAAGGTCTTTGGCAGATAACCCTTCT-AGCCTTGAGCTATACCGCAAATGATGTGCCGTT-G
66 CTCGAAGGTCTTTGGCAGATAACCCTTCTCA-ACTTAAGCTATGCTGCAAATGATGTGCC-TTGG
* * * *
39784 AGCTGATCATAATCGAACTCAAAGGTCTTTGTTG-G
129 AGCTGAGCGTAGTCGAACTCGAAGGT-TTT-TTGTG
* * * *
39819 CAGATAACCCTTCTAGCCTTGAGTTATGCCGCAAATGATGTGCCCTCAAAGCTGAGTGTAATCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT-CCCTCGAAGCTGAGCGTAGTCGA
* *
39884 ACTCGAAGGTTTTTGGCAGATAA-CCTTCTCGACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
65 ACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGGA
* * * *
39948 GATGAACATAGTCGAACTCGAAGATCTTTGGTTG-G
130 GCTGAGCGTAGTCGAACTCGAAGGT-TTT--TTGTG
* * * * * *
39983 CAGATAACCCTTCTCGACTTAAGTTATGCTGCAAATGATATGCCT-TAGAGCTGAGCGTAGTCGA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTCCCTCGA-AGCTGAGCGTAGTCGA
* * * * * * *
40047 ACTTGAAGGTCTTTTGGTGACAGATAACTCTTCT-AGCCTTGAGTTATGCTGTAAATGATGTTCC
65 ACTCGAAGGTC-TTT-G-G-CAGATAACCCTTCTCA-ACTTAAGCTATGCTGCAAATGATG-TGC
* * * * * * *
40111 CTCGAAGTTGAGTGTAATCGAACTC-AAGGGTCTTTG-G
124 CTTGGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTTGTG
* * * * * * * *
40148 CAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGGAGCTGAGGGTAGTCGAA
1 CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTCCCTCGAAGCTGAGCGTAGTCGAA
* * * * *
40213 CTCGAAGGTCTTTGGTTGGCAGATAACCCTTCTCGACTTAAGTTATGTTGTAAATGATATGCCTT
66 CTCGAAGGTC--T--TTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTT
* *
40278 AGAGTTGAGCGTAGTCGAACTCGAAGGTTTTTTAGTG
127 GGAGCTGAGCGTAGTCGAACTCGAAGGTTTTTT-GTG
* * * *
40315 ACAGATAACCCTTCTAGCCTTGAGTTATGTTGTAAATGATGTACCCTCGAAGCTGAGTGTAATCG
1 -CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGT-CCCTCGAAGCTGAGCGTAGTCG
* * * *
40380 AACTCGAGGGTCTTTGACAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGTCTTGG
64 AACTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGG
*
40445 AGCTGAGCGGAGTCGAACTCGAAGGT
129 AGCTGAGCGTAGTCGAACTCGAAGGT
40471 CCTTTGTTGG
Statistics
Matches: 535, Mismatches: 95, Indels: 42
0.80 0.14 0.06
Matches are distributed among these distances:
162 3 0.01
163 117 0.22
164 104 0.19
165 181 0.34
166 5 0.01
167 12 0.02
168 65 0.12
169 48 0.09
ACGTcount: A:0.25, C:0.20, G:0.25, T:0.30
Consensus pattern (162 bp):
CAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAATGATGTCCCTCGAAGCTGAGCGTAGTCGAA
CTCGAAGGTCTTTGGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGTGCCTTGGAG
CTGAGCGTAGTCGAACTCGAAGGTTTTTTGTG
Found at i:41823 original size:93 final size:95
Alignment explanation
Indices: 41651--41830 Score: 249
Period size: 93 Copynumber: 1.9 Consensus size: 95
41641 ATATGTAAAC
* * * *
41651 ACCTTTATCAGGTTAGCTGAATCTTATCTATAAAGCCGGGGCGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTGCCTTAGAGGG
*
41716 ACAACTCAATCTTTAGTGTATAGTAAAATT
66 ACAACTCAAGCTTTAGTGTATAGTAAAATT
* * *
41746 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAG-C-ATGCGTTTAACCATTTG-CTCTGGAGG
1 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTGCCT-TAGAGG
*
41808 GACAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTAGTGTATA
41831 TATATAATAT
Statistics
Matches: 75, Mismatches: 9, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
92 2 0.03
93 40 0.53
94 1 0.01
95 32 0.43
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.33
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGAGGCGTTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTAGTGTATAGTAAAATT
Found at i:46826 original size:5 final size:5
Alignment explanation
Indices: 46816--46894 Score: 70
Period size: 5 Copynumber: 14.8 Consensus size: 5
46806 GGACCTGGAA
* *
46816 AAAAT AAAAT AAAAAG AAAAT AATTAAT AAAAT AAAAT AAAAA AGAAAT
1 AAAAT AAAAT -AAAAT AAAAT AA--AAT AAAAT AAAAT AAAAT A-AAAT
*
46865 -AATT AATAAT AATAAT AAAAT AAAAT AAAA
1 AAAAT AA-AAT AA-AAT AAAAT AAAAT AAAA
46895 ATATTTTCCA
Statistics
Matches: 62, Mismatches: 6, Indels: 12
0.77 0.08 0.15
Matches are distributed among these distances:
4 3 0.05
5 37 0.60
6 17 0.27
7 5 0.08
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (5 bp):
AAAAT
Found at i:46856 original size:28 final size:28
Alignment explanation
Indices: 46816--46879 Score: 103
Period size: 28 Copynumber: 2.2 Consensus size: 28
46806 GGACCTGGAA
46816 AAAATAAAAT-AAAAAGAAAATAATTAAT
1 AAAATAAAATAAAAAAG-AAATAATTAAT
46844 AAAATAAAATAAAAAAGAAATAATTAAT
1 AAAATAAAATAAAAAAGAAATAATTAAT
46872 AATAATAA
1 AA-AATAA
46880 TAAAATAAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
28 23 0.68
29 11 0.32
ACGTcount: A:0.75, C:0.00, G:0.03, T:0.22
Consensus pattern (28 bp):
AAAATAAAATAAAAAAGAAATAATTAAT
Found at i:46864 original size:11 final size:10
Alignment explanation
Indices: 46814--46897 Score: 51
Period size: 11 Copynumber: 7.8 Consensus size: 10
46804 TTGGACCTGG
46814 AAAAAATAAA
1 AAAAAATAAA
*
46824 ATAAAAAGAAA
1 A-AAAAATAAA
*
46835 ATAATTAATAAA
1 A-AA-AAATAAA
*
46847 ATAAAATAAA
1 AAAAAATAAA
*
46857 AAAGAAATAAT
1 AAA-AAATAAA
* *
46868 TAATAATAATA
1 AAAAAATAA-A
*
46879 ATAAAATAAA
1 AAAAAATAAA
46889 ATAAAAATA
1 A-AAAAATA
46898 TTTTCCAAAA
Statistics
Matches: 55, Mismatches: 14, Indels: 9
0.71 0.18 0.12
Matches are distributed among these distances:
10 16 0.29
11 33 0.60
12 6 0.11
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.21
Consensus pattern (10 bp):
AAAAAATAAA
Found at i:46986 original size:36 final size:36
Alignment explanation
Indices: 46890--47240 Score: 160
Period size: 36 Copynumber: 9.8 Consensus size: 36
46880 TAAAATAAAA
* * *
46890 TAAAAATATTTTCCAAAAACCTATCTAATATATATTTTC
1 TAAAAATATTTT--AAAAA-CTATATATTATATATTTTT
* *
46929 AAAAAATATTTT-AAAATTATATATTATATATTTTT
1 TAAAAATATTTTAAAAACTATATATTATATATTTTT
* *
46964 TAAAAATATTTTCAAAAC-------TATATAGTTTT
1 TAAAAATATTTTAAAAACTATATATTATATATTTTT
* * * * * *
46993 CAAAAATATTTTAAAAT--TATATACTATATGTTTTC
1 TAAAAATA-TTTTAAAAACTATATATTATATATTTTT
* * ** *
47028 AAAATGAT-TTAAAAAC--TATATATTATATA-T--T
1 TAAA-AATATTTTAAAAACTATATATTATATATTTTT
* *
47059 TCAAAATGTTTTAAAAACTATATAATATATATATATATATT
1 TAAAAATATTTTAAAAACTATAT-AT-TATATAT-T-T-TT
* *
47100 CAAAAATATTTTAAACACTATATATTATAT-TTATTT
1 TAAAAATATTTTAAAAACTATATATTATATATT-TTT
* * * *
47136 TCAAAATGTTTTAAAAACTATATAATATATAAATGTTT
1 TAAAAATATTTTAAAAACTATAT-AT-TATATATTTTT
* * * * *
47174 TCACAATGTTTTCAAAACTATATATTATATATATTT
1 TAAAAATATTTTAAAAACTATATATTATATATTTTT
* *
47210 TAAAAATGTTTTCAAAAACTATATAATATAT
1 TAAAAATATTTT-AAAAACTATATATTATAT
47241 GAATTTTCGA
Statistics
Matches: 241, Mismatches: 46, Indels: 52
0.71 0.14 0.15
Matches are distributed among these distances:
29 17 0.07
30 7 0.03
31 7 0.03
33 6 0.02
34 19 0.08
35 43 0.18
36 50 0.21
37 24 0.10
38 29 0.12
39 17 0.07
40 2 0.01
41 20 0.08
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (36 bp):
TAAAAATATTTTAAAAACTATATATTATATATTTTT
Found at i:47008 original size:28 final size:29
Alignment explanation
Indices: 46953--47015 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 29
46943 AATTATATAT
* *
46953 TATATATTTTTTAAAAATATTTTCAAAAC
1 TATATAGTTTTCAAAAATATTTTCAAAAC
*
46982 TATATAGTTTTCAAAAATATTTT-AAAAT
1 TATATAGTTTTCAAAAATATTTTCAAAAC
47010 TATATA
1 TATATA
47016 CTATATGTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
28 10 0.32
29 21 0.68
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.48
Consensus pattern (29 bp):
TATATAGTTTTCAAAAATATTTTCAAAAC
Found at i:47032 original size:62 final size:63
Alignment explanation
Indices: 46918--47051 Score: 184
Period size: 62 Copynumber: 2.1 Consensus size: 63
46908 ACCTATCTAA
* *
46918 TATATATTTTCAAAAAATATTTTAAAATTATATATTATATATTTTTTAAAAAT-ATTTTCAAAAC
1 TATATATTTTCAAAAAATATTTTAAAATTATATA-TATATATGTTTTAAAAATGA-TTTAAAAAC
* *
46982 TATATAGTTTTC-AAAAATATTTTAAAATTATATA-CTATATGTTTTCAAAATGATTTAAAAAC
1 TATATA-TTTTCAAAAAATATTTTAAAATTATATATATATATGTTTTAAAAATGATTTAAAAAC
47044 TATATATT
1 TATATATT
47052 ATATATTTCA
Statistics
Matches: 64, Mismatches: 4, Indels: 7
0.85 0.05 0.09
Matches are distributed among these distances:
61 2 0.03
62 28 0.44
63 1 0.02
64 28 0.44
65 5 0.08
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (63 bp):
TATATATTTTCAAAAAATATTTTAAAATTATATATATATATGTTTTAAAAATGATTTAAAAAC
Found at i:47039 original size:33 final size:34
Alignment explanation
Indices: 46980--47241 Score: 152
Period size: 38 Copynumber: 7.2 Consensus size: 34
46970 TATTTTCAAA
* *
46980 ACTATATAGTTTTCAAAAAT-ATTTTAAAATTATAT
1 ACTATAT-GTTTTC-AAAATGATTTAAAAACTATAT
47015 ACTATATGTTTTCAAAATGATTTAAAAACTATAT
1 ACTATATGTTTTCAAAATGATTTAAAAACTATAT
* * *
47049 ATTATAT-ATTTCAAAATGTTTTAAAAACTATATAAT
1 ACTATATGTTTTCAAAATGATTTAAAAAC--TAT-AT
* * *
47085 ATATATATATATATTCAAAAAT-ATTTTAAACACTATAT
1 A-CTATATGT-T-TTC-AAAATGA-TTTAAAAACTATAT
* * *
47123 ATTATATTTATTTTCAAAATGTTTTAAAAACTATAT
1 ACTATA--TGTTTTCAAAATGATTTAAAAACTATAT
* * * *
47159 AATATATAAATGTTTTCACAATGTTTTCAAAACTATAT
1 -A-CTAT--ATGTTTTCAAAATGATTTAAAAACTATAT
* * * *
47197 ATTATATATATTTTAAAAATGTTTTCAAAAACTATAT
1 A--CTATATGTTTTCAAAATGATTT-AAAAACTATAT
*
47234 AATATATG
1 ACTATATG
47242 AATTTTCGAA
Statistics
Matches: 187, Mismatches: 21, Indels: 38
0.76 0.09 0.15
Matches are distributed among these distances:
33 24 0.13
34 25 0.13
35 16 0.09
36 36 0.19
37 25 0.13
38 37 0.20
39 7 0.04
40 4 0.02
41 13 0.07
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.44
Consensus pattern (34 bp):
ACTATATGTTTTCAAAATGATTTAAAAACTATAT
Found at i:47087 original size:31 final size:32
Alignment explanation
Indices: 46982--47090 Score: 114
Period size: 33 Copynumber: 3.3 Consensus size: 32
46972 TTTTCAAAAC
* *
46982 TATATAGT-TTTCAAAAAT-ATTTTAAAATTATA
1 TATATA-TATTTC-AAAATGATTTAAAAACTATA
*
47014 TACTATATGTTTTCAAAATGATTTAAAAACTATA
1 TA-TATAT-ATTTCAAAATGATTTAAAAACTATA
*
47048 TATTATATATTTCAAAATGTTTTAAAAACTATA
1 TA-TATATATTTCAAAATGATTTAAAAACTATA
47081 TAATATATAT
1 T-ATATATAT
47091 ATATATATTC
Statistics
Matches: 67, Mismatches: 5, Indels: 9
0.83 0.06 0.11
Matches are distributed among these distances:
32 3 0.04
33 40 0.60
34 24 0.36
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.45
Consensus pattern (32 bp):
TATATATATTTCAAAATGATTTAAAAACTATA
Found at i:47120 original size:74 final size:73
Alignment explanation
Indices: 47010--47240 Score: 297
Period size: 74 Copynumber: 3.1 Consensus size: 73
47000 ATTTTAAAAT
*
47010 TATATACTATATGTTTTCAAAATGATTTAAAAACTATATATTATATA-TTTCAAAATGTTTTAAA
1 TATATA-TATATGTTTTCAAAAT-ATTTTAAAACTATATATTATATATTTTCAAAATGTTTTAAA
47074 AACTATATAA
64 AACTATATAA
* *
47084 TATATATATATATATTCAAAAATATTTTAAACACTATATATTATATTTATTTTCAAAATGTTTTA
1 TATATATATATGTTTTC-AAAATATTTTAAA-ACTATATATTATA--TATTTTCAAAATGTTTTA
47149 AAAACTATATAA
62 AAAACTATATAA
* * *
47161 TATATA-A-ATGTTTTCACAATGTTTTCAAAACTATATATTATATATATTTTAAAAATGTTTTCA
1 TATATATATATGTTTTCAAAATATTTT-AAAACTATATA-T-TATATATTTTCAAAATGTTTT-A
47224 AAAACTATATAA
62 AAAACTATATAA
47236 TATAT
1 TATAT
47241 GAATTTTCGA
Statistics
Matches: 140, Mismatches: 8, Indels: 17
0.85 0.05 0.10
Matches are distributed among these distances:
73 16 0.11
74 56 0.40
75 28 0.20
76 7 0.05
77 33 0.24
ACGTcount: A:0.45, C:0.07, G:0.03, T:0.45
Consensus pattern (73 bp):
TATATATATATGTTTTCAAAATATTTTAAAACTATATATTATATATTTTCAAAATGTTTTAAAAA
CTATATAA
Found at i:47273 original size:75 final size:73
Alignment explanation
Indices: 46982--47277 Score: 261
Period size: 77 Copynumber: 4.0 Consensus size: 73
46972 TTTTCAAAAC
* * * * * *
46982 TATATAGTTTTCAAAAATATTTT-AAAATTATATACTATAT---GTTTTCAAAATGATTTAAAAA
1 TATATA-TTTT-AAAAATGTTTTAAAAACTATATAATATATAAAGTTTTCAAAACGTTTTCAAAA
47043 CTATATA-T-
64 CTATATATTA
* * *
47051 TATATA-TTTCAAAATGTTTTAAAAACTATATAATATATATATA-TATATTCAAAA-ATATTTTA
1 TATATATTTTAAAAATGTTTTAAAAACTATATAATATATA-A-AGT-T-TTCAAAACGT-TTTCA
47113 AACACTATATATTA
61 AA-ACTATATATTA
* * * *
47127 TATTTATTTTCAAAATGTTTTAAAAACTATATAATATATAAATGTTTTCACAATGTTTTCAAAAC
1 TATATATTTTAAAAATGTTTTAAAAACTATATAATATATAAA-GTTTTCAAAACGTTTTCAAAAC
47192 TATATATTA
65 TATATATTA
*
47201 TATATATTTTAAAAATGTTTTCAAAAACTATATAATATATGAA-TTTTCGAAAACCGTTTTCTGA
1 TATATATTTTAAAAATGTTTT-AAAAACTATATAATATATAAAGTTTTC-AAAA-CGTTTTC--A
*
47265 AAATTATATATTA
61 AAACTATATATTA
47278 ATTTTTTCAA
Statistics
Matches: 189, Mismatches: 17, Indels: 34
0.79 0.07 0.14
Matches are distributed among these distances:
66 9 0.05
67 18 0.10
69 6 0.03
71 1 0.01
72 1 0.01
73 18 0.10
74 41 0.22
75 40 0.21
76 8 0.04
77 47 0.25
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (73 bp):
TATATATTTTAAAAATGTTTTAAAAACTATATAATATATAAAGTTTTCAAAACGTTTTCAAAACT
ATATATTA
Found at i:47290 original size:75 final size:74
Alignment explanation
Indices: 46989--47305 Score: 263
Period size: 75 Copynumber: 4.3 Consensus size: 74
46979 AACTATATAG
* * * * * *
46989 TTTTCAAAAATATTTT--AAAATTATATACTATAT---GTTTTCAAAATGATTTAAAAACTATAT
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATAAAGTTTTCAAAACGTTTTCAAAACTATAT
47049 ATTATA-TA
66 ATTATATTA
* *
47057 -TTTC-AAAATGTTTT-AAAAACTATATAATATATATATA-TATATTCAAAA-ATATTTTAAACA
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATA-A-AGT-T-TTCAAAACGT-TTTCAAA-A
47117 CTATATATTATATTTA
60 CTATATATTATA-TTA
* *
47133 TTTTC-AAAATGTTTT-AAAAACTATATAATATATAAATGTTTTCACAATGTTTTCAAAACTATA
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATAAA-GTTTTCAAAACGTTTTCAAAACTATA
47196 TATTATATATA
65 TATTATAT-TA
* *
47207 TTTT-AAAAATGTTTTCAAAAACTATATAATATATGAA-TTTTCGAAAACCGTTTTCTGAAAATT
1 TTTTCAAAAATGTTTTCAAAAACTATATAATATATAAAGTTTTC-AAAA-CGTTTTC--AAAACT
47270 ATATATTA-ATT-
62 ATATATTATATTA
** *
47281 TTTTCAAAAACATTTTCAGAAACTA
1 TTTTCAAAAATGTTTTCAAAAACTA
47306 CATTACTATA
Statistics
Matches: 209, Mismatches: 16, Indels: 41
0.79 0.06 0.15
Matches are distributed among these distances:
66 9 0.04
67 19 0.09
71 1 0.00
72 1 0.00
73 19 0.09
74 49 0.23
75 57 0.27
76 7 0.03
77 47 0.22
ACGTcount: A:0.44, C:0.08, G:0.04, T:0.44
Consensus pattern (74 bp):
TTTTCAAAAATGTTTTCAAAAACTATATAATATATAAAGTTTTCAAAACGTTTTCAAAACTATAT
ATTATATTA
Found at i:47560 original size:17 final size:18
Alignment explanation
Indices: 47538--47571 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
47528 CAATTTTTTT
47538 ATTTGA-AAATATATAAA
1 ATTTGAGAAATATATAAA
*
47555 ATTTGAGAAATTTATAA
1 ATTTGAGAAATATATAA
47572 CAATAAGCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.53, C:0.00, G:0.09, T:0.38
Consensus pattern (18 bp):
ATTTGAGAAATATATAAA
Found at i:54216 original size:20 final size:20
Alignment explanation
Indices: 54179--54220 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
54169 TGCAAACCAA
*
54179 CGGTCTCGAAACTAAGCATC
1 CGGTCTCGAAACCAAGCATC
* *
54199 CGGTCTCGATACCGAGCATC
1 CGGTCTCGAAACCAAGCATC
54219 CG
1 CG
54221 ATATCAATAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.33, G:0.24, T:0.19
Consensus pattern (20 bp):
CGGTCTCGAAACCAAGCATC
Found at i:55462 original size:27 final size:27
Alignment explanation
Indices: 55427--55501 Score: 107
Period size: 27 Copynumber: 2.8 Consensus size: 27
55417 TTATATACTG
* *
55427 AATTTTTTAATAATTATATTCTAATTT
1 AATTATTTAATAATTATATTATAATTT
*
55454 AATTATTTAATGATTATATTATAATTT
1 AATTATTTAATAATTATATTATAATTT
*
55481 AATTATTTAATAACTAT-TTAT
1 AATTATTTAATAATTATATTAT
55502 TCACCTCTAT
Statistics
Matches: 43, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
26 4 0.09
27 39 0.91
ACGTcount: A:0.40, C:0.03, G:0.01, T:0.56
Consensus pattern (27 bp):
AATTATTTAATAATTATATTATAATTT
Done.