Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006345.1 Hibiscus syriacus cultivar Beakdansim tig00015175_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: 144561
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.34
Found at i:5303 original size:71 final size:73
Alignment explanation
Indices: 5197--5348 Score: 265
Period size: 71 Copynumber: 2.1 Consensus size: 73
5187 TTAATGCAAG
5197 GTTTAAAAATAAAAATGAGTTTAAAATTTTATATTTTAAAATTAAACTA-TTTTATATGATTA-T
1 GTTT-AAAATAAAAATGAGTTTAAAATTTTATATTTTAAAATTAAACTATTTTTATATGATTATT
5260 TTTAAACAA
65 TTTAAACAA
5269 GTTTAAAAT-AAAATGAGTTTAAAATTTTTATATTTTAAAATTAAACTATTTTTATATGATTATT
1 GTTTAAAATAAAAATGAGTTTAAAA-TTTTATATTTTAAAATTAAACTATTTTTATATGATTATT
5333 TTTAAACAA
65 TTTAAACAA
5342 GTTTAAA
1 GTTTAAA
5349 TTAGACATGT
Statistics
Matches: 77, Mismatches: 0, Indels: 5
0.94 0.00 0.06
Matches are distributed among these distances:
70 15 0.19
71 28 0.36
72 17 0.22
73 17 0.22
ACGTcount: A:0.45, C:0.03, G:0.06, T:0.46
Consensus pattern (73 bp):
GTTTAAAATAAAAATGAGTTTAAAATTTTATATTTTAAAATTAAACTATTTTTATATGATTATTT
TTAAACAA
Found at i:5551 original size:88 final size:85
Alignment explanation
Indices: 5327--5619 Score: 317
Period size: 86 Copynumber: 3.4 Consensus size: 85
5317 TTTTTATATG
* * * * * *
5327 ATTATTTTTAAACAAGTTTAAATTAGACATGTTTTTTCTTTCTTACAATATTT-TTATTGATTTA
1 ATTATTTTAAAACAAATTTAAATTATATAT-TATTTTCTTTCTTACAATATTTGTTATTCATTTA
*
5391 TCATTT---AATTTTAGAATA
65 TCATTTAAAAATTTTAAAATA
* * ** *
5409 ATTATTTTAAAAAAAAATTAAATTATATATTATTTT-TTTCTTACAACGTTTGTTATACATTTAT
1 ATTATTTTAAAACAAATTTAAATTATATATTATTTTCTTTCTTACAATATTTGTTATTCATTTAT
5473 CATTTAAGAAATTTATAAAATA
66 CATTTAA-AAATTT-TAAAATA
* *
5495 ATTATTTTAAAACAAATTTATATTATATATTATATTTCTTTTTTACAATATTTGTTATTCATTTA
1 ATTATTTTAAAACAAATTTAAATTATATATTAT-TTTCTTTCTTACAATATTTGTTATTCATTTA
*
5560 TCATTTAAAAATAATTGTAAAACA
65 TCATTTAAAAAT--TT-TAAAATA
* * * *
5584 ACTATTTTTAAACAAGTTTAAATCATATATTATTTT
1 ATTATTTTAAAACAAATTTAAATTATATATTATTTT
5620 TAATTGATAA
Statistics
Matches: 175, Mismatches: 26, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
80 13 0.07
81 20 0.11
82 24 0.14
85 5 0.03
86 36 0.21
87 7 0.04
88 34 0.19
89 36 0.21
ACGTcount: A:0.39, C:0.07, G:0.04, T:0.51
Consensus pattern (85 bp):
ATTATTTTAAAACAAATTTAAATTATATATTATTTTCTTTCTTACAATATTTGTTATTCATTTAT
CATTTAAAAATTTTAAAATA
Found at i:9540 original size:36 final size:36
Alignment explanation
Indices: 9488--9557 Score: 131
Period size: 36 Copynumber: 1.9 Consensus size: 36
9478 TTTATGATTT
*
9488 CATCTACACTTCCGATTCAAGTCGAACGGAAGGAAG
1 CATCGACACTTCCGATTCAAGTCGAACGGAAGGAAG
9524 CATCGACACTTCCGATTCAAGTCGAACGGAAGGA
1 CATCGACACTTCCGATTCAAGTCGAACGGAAGGA
9558 TGTAGCGCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.19
Consensus pattern (36 bp):
CATCGACACTTCCGATTCAAGTCGAACGGAAGGAAG
Found at i:9700 original size:3 final size:3
Alignment explanation
Indices: 9692--9717 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
9682 TCAGAAGAGC
9692 AGA AGA AGA AGA AGA AGA AGA AGA AG
1 AGA AGA AGA AGA AGA AGA AGA AGA AG
9718 TAGAGGGAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:20242 original size:30 final size:29
Alignment explanation
Indices: 20203--20338 Score: 123
Period size: 30 Copynumber: 4.6 Consensus size: 29
20193 CATCTTAGCA
* *
20203 TTAAAAATATATTTTGTTTTTATTTTAAC
1 TTAAAAATATATTTTATTCTTATTTTAAC
* * *
20232 TTATTAAATATATTTTATTCTTGTTCTAACC
1 TTA-AAAATATATTTTATTCTTATTTTAA-C
* *
20263 TAAAAAACATATTTTATTCTTATTTTAAC
1 TTAAAAATATATTTTATTCTTATTTTAAC
* * *
20292 TTAGAAATATATTTCAGTCTT-TCTCTTAAC
1 TTAAAAATATATTTTATTCTTAT-T-TTAAC
*
20322 TTAAAAA-ATATTGTATT
1 TTAAAAATATATTTTATT
20339 ATGTTGAGTT
Statistics
Matches: 84, Mismatches: 19, Indels: 8
0.76 0.17 0.07
Matches are distributed among these distances:
28 1 0.01
29 28 0.33
30 52 0.62
31 3 0.04
ACGTcount: A:0.35, C:0.10, G:0.04, T:0.51
Consensus pattern (29 bp):
TTAAAAATATATTTTATTCTTATTTTAAC
Found at i:20327 original size:60 final size:60
Alignment explanation
Indices: 20205--20329 Score: 155
Period size: 60 Copynumber: 2.1 Consensus size: 60
20195 TCTTAGCATT
* * * * * *
20205 AAAAATATATTTTGTTTTTATTTTAACTTATTAAATATATTTTATTCTTGTTCTAACCTA
1 AAAAACATATTTTATTCTTATTTTAACTTATGAAATATATTTCAGTCTTGTTCTAACCTA
*
20265 AAAAACATATTTTATTCTTATTTTAACTTA-GAAATATATTTCAGTCTT-TCTCTTAACTTA
1 AAAAACATATTTTATTCTTATTTTAACTTATGAAATATATTTCAGTCTTGT-TC-TAACCTA
20325 AAAAA
1 AAAAA
20330 TATTGTATTA
Statistics
Matches: 56, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
58 1 0.02
59 17 0.30
60 38 0.68
ACGTcount: A:0.37, C:0.10, G:0.03, T:0.50
Consensus pattern (60 bp):
AAAAACATATTTTATTCTTATTTTAACTTATGAAATATATTTCAGTCTTGTTCTAACCTA
Found at i:21095 original size:18 final size:17
Alignment explanation
Indices: 21041--21089 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 17
21031 TTGGACCCTT
* *
21041 AGTGCATCGGTGCACTAA
1 AGTGCATCGATGCA-TCA
21059 GAGTGCATCGATGCATCA
1 -AGTGCATCGATGCATCA
21077 AGTGCATTCGATG
1 AGTGCA-TCGATG
21090 TTTCAAAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 6 0.22
18 8 0.30
19 13 0.48
ACGTcount: A:0.27, C:0.20, G:0.29, T:0.24
Consensus pattern (17 bp):
AGTGCATCGATGCATCA
Found at i:21259 original size:65 final size:64
Alignment explanation
Indices: 21061--21270 Score: 198
Period size: 65 Copynumber: 3.2 Consensus size: 64
21051 TGCACTAAGA
* ** ** *
21061 GTGCATCGATGCATCAAGTGCATTCGATGTTTCAAAAT-AGCCA-GAGTGCATCGATGCATGACT
1 GTGCATCGATGCATCAAATGCATTCGATG-TTCAATTTAAATCATG-GTGCATCGATGCATGATT
21124 G
64 G
* * *
21125 GTGCATCGATGCATCAAATGCATTCGATGTT---TTCATAACATCATTGGTGCATTGGTGCATGG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAATT--TAA-ATCA-TGGTGCATCGATGCATGA
21187 TAT-
62 T-TG
* *
21190 GTGCATCGATGCATGAAATGCATTCGATGTTCAATTTAATTCATGGTGCATCGATGCATGAATTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTAAATCATGGTGCATCGATGCATG-ATTG
*
21255 GTGCATCGGTGCATCA
1 GTGCATCGATGCATCA
21271 CTCTGAAAAT
Statistics
Matches: 118, Mismatches: 16, Indels: 23
0.75 0.10 0.15
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 46 0.39
65 61 0.52
66 5 0.04
68 2 0.02
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.31
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTCAATTTAAATCATGGTGCATCGATGCATGATTG
Found at i:29921 original size:65 final size:64
Alignment explanation
Indices: 29784--29943 Score: 173
Period size: 65 Copynumber: 2.5 Consensus size: 64
29774 TGCACTAAGA
* * *
29784 GTGCAACGATGCATCAAGTGCATTCGATGTTTCAAAATAGCCAGAGTGCATCGATGCATGACTG
1 GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAACAGCCAGAGTGCATCGATGCATGACTG
* * * *
29848 GTGCATCGATGCATCAAATGCATTCGATGATTTCATAACATCCTTG-GTGCATCGGTGCATGGTA
1 GTGCATCGATGCATCAAATGCATTCGATG-TTTCAAAACAGCC-AGAGTGCATCGATGCAT-G-A
29912 -T-
62 CTG
* * *
29913 GTGGATCGATGCATGAAATGCATTTGATGTT
1 GTGCATCGATGCATCAAATGCATTCGATGTT
29944 CAATTTAATT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
64 29 0.35
65 49 0.60
66 3 0.04
67 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.25, T:0.30
Consensus pattern (64 bp):
GTGCATCGATGCATCAAATGCATTCGATGTTTCAAAACAGCCAGAGTGCATCGATGCATGACTG
Found at i:30305 original size:30 final size:30
Alignment explanation
Indices: 30271--30327 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
30261 GCATAAATTA
30271 TATTCTTTA-ATTAAATTATTAAATATATTC
1 TATTC-TTACATTAAATTATTAAATATATTC
*
30301 TATTCTTACCTTAAATTATTAAATATA
1 TATTCTTACATTAAATTATTAAATATA
30328 ATTAATTCTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.40, C:0.09, G:0.00, T:0.51
Consensus pattern (30 bp):
TATTCTTACATTAAATTATTAAATATATTC
Found at i:30320 original size:60 final size:60
Alignment explanation
Indices: 30241--30374 Score: 148
Period size: 60 Copynumber: 2.2 Consensus size: 60
30231 GTTTTCAACA
* * **
30241 TATTATTATCTTAACTTATTGCATA-AATTATATTCTTTAATTAAATTATT-AA-ATATATTC
1 TATTCTTATCTTAAATTATTAAATATAATTA-ATTC-TTAATTAAATT-TTAAACATATATTC
* * * *
30301 TATTCTTACCTTAAATTATTAAATATAATTAATTCTTATTTTAATTTTAAACATATATTT
1 TATTCTTATCTTAAATTATTAAATATAATTAATTCTTAATTAAATTTTAAACATATATTC
30361 TATTCTTATCTTAA
1 TATTCTTATCTTAA
30375 CTTAAAAATA
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
58 2 0.03
59 11 0.18
60 44 0.71
61 5 0.08
ACGTcount: A:0.37, C:0.09, G:0.01, T:0.53
Consensus pattern (60 bp):
TATTCTTATCTTAAATTATTAAATATAATTAATTCTTAATTAAATTTTAAACATATATTC
Found at i:30336 original size:30 final size:30
Alignment explanation
Indices: 30281--30338 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
30271 TATTCTTTAA
*
30281 TTAAATTATTAAATATATTCTATTCTTACC
1 TTAAATTATTAAATATATTCAATTCTTACC
30311 TTAAATTATTAAATATAATT-AATTCTTA
1 TTAAATTATTAAATAT-ATTCAATTCTTA
30339 TTTTAATTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (30 bp):
TTAAATTATTAAATATATTCAATTCTTACC
Found at i:30363 original size:24 final size:24
Alignment explanation
Indices: 30336--30420 Score: 71
Period size: 24 Copynumber: 3.3 Consensus size: 24
30326 TAATTAATTC
*
30336 TTATTTTAATTTTAAACATATATT
1 TTATTTTAATTTTAAAAATATATT
*
30360 TTATTCTTATCTTAACTTAAAAATATATTT
1 TTATT-TTA-ATT---TTAAAAATATA-TT
* **
30390 TTATTTTAACTACAAAAATATATT
1 TTATTTTAATTTTAAAAATATATT
30414 TTATTTT
1 TTATTTT
30421 TATCTTAACT
Statistics
Matches: 49, Mismatches: 6, Indels: 12
0.73 0.09 0.18
Matches are distributed among these distances:
24 14 0.29
25 12 0.24
26 2 0.04
28 1 0.02
29 13 0.27
30 7 0.14
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.55
Consensus pattern (24 bp):
TTATTTTAATTTTAAAAATATATT
Found at i:30392 original size:30 final size:29
Alignment explanation
Indices: 30291--30470 Score: 136
Period size: 30 Copynumber: 6.2 Consensus size: 29
30281 TTAAATTATT
* * * *
30291 AAATATATTCTATTCTTACCTTAAATTATT
1 AAATATATTTTATTCTTATCTTAACTTA-A
* * * *
30321 AAATATAATTAATTCTTATTTTAATTTTAA
1 AAATATATTTTATTCTTATCTTAA-CTTAA
*
30351 ACATATATTTTATTCTTATCTTAACTTAA
1 AAATATATTTTATTCTTATCTTAACTTAA
*
30380 AAATATATTTTTATT-TTAAC-T-AC--AA
1 AAATATA-TTTTATTCTTATCTTAACTTAA
* *
30405 AAATATATTTTATTTTTATCTTAACTACAAA
1 AAATATATTTTATTCTTATCTTAACT--TAA
* * * *
30436 AAATATATTATATTTTTATCTTAAATTCA
1 AAATATATTTTATTCTTATCTTAACTTAA
30465 AAATAT
1 AAATAT
30471 TATCATAATA
Statistics
Matches: 122, Mismatches: 19, Indels: 19
0.76 0.12 0.12
Matches are distributed among these distances:
24 7 0.06
25 13 0.11
26 1 0.01
27 4 0.03
28 1 0.01
29 21 0.17
30 46 0.38
31 29 0.24
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (29 bp):
AAATATATTTTATTCTTATCTTAACTTAA
Found at i:30412 original size:25 final size:24
Alignment explanation
Indices: 30361--30420 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
30351 ACATATATTT
* * *
30361 TATTCTTATCTTAACTTAAAAATA
1 TATTTTTATTTTAACTCAAAAATA
30385 TATTTTTATTTTAACTACAAAAATA
1 TATTTTTATTTTAACT-CAAAAATA
30410 TA-TTTTATTTT
1 TATTTTTATTTT
30421 TATCTTAACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 23 0.72
25 9 0.28
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTTTTATTTTAACTCAAAAATA
Found at i:30467 original size:31 final size:31
Alignment explanation
Indices: 30383--30459 Score: 129
Period size: 31 Copynumber: 2.5 Consensus size: 31
30373 AACTTAAAAA
*
30383 TATATTTTTATTTTAACTAC-AAAAATATAT
1 TATATTTTTATCTTAACTACAAAAAATATAT
*
30413 TTTATTTTTATCTTAACTACAAAAAATATAT
1 TATATTTTTATCTTAACTACAAAAAATATAT
30444 TATATTTTTATCTTAA
1 TATATTTTTATCTTAA
30460 ATTCAAAATA
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
30 18 0.42
31 25 0.58
ACGTcount: A:0.40, C:0.08, G:0.00, T:0.52
Consensus pattern (31 bp):
TATATTTTTATCTTAACTACAAAAAATATAT
Found at i:30671 original size:18 final size:18
Alignment explanation
Indices: 30644--30690 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
30634 AGTTTTTGAT
30644 GTTAAGATGTAAAATTAA
1 GTTAAGATGTAAAATTAA
* * *
30662 TTTAATATGTAAATTTAA
1 GTTAAGATGTAAAATTAA
30680 GTTAAGATGTA
1 GTTAAGATGTA
30691 TAAAATATTA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (18 bp):
GTTAAGATGTAAAATTAA
Found at i:35926 original size:31 final size:30
Alignment explanation
Indices: 35862--35928 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 30
35852 TAAAATATAT
* *
35862 AACTTTTTAAAATTATATTTTTAGTCTCTA
1 AACTTTTTAAAATTATATCTTTAGTATCTA
35892 AACTTTTATAAAATTGATA-CTTTAGCTATC-A
1 AACTTTT-TAAAATT-ATATCTTTAG-TATCTA
35923 AACTTT
1 AACTTT
35929 CAAAACTTAC
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
30 7 0.22
31 19 0.59
32 6 0.19
ACGTcount: A:0.36, C:0.12, G:0.04, T:0.48
Consensus pattern (30 bp):
AACTTTTTAAAATTATATCTTTAGTATCTA
Found at i:39591 original size:18 final size:18
Alignment explanation
Indices: 39547--39594 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
39537 AGCAGAAGAC
39547 ACCTAAAGGATCGACCAA
1 ACCTAAAGGATCGACCAA
* * * **
39565 ATCTCAAGGATCGGCTGA
1 ACCTAAAGGATCGACCAA
39583 ACCTAAAGGATC
1 ACCTAAAGGATC
39595 AGCCAAGCCT
Statistics
Matches: 23, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.38, C:0.25, G:0.21, T:0.17
Consensus pattern (18 bp):
ACCTAAAGGATCGACCAA
Found at i:41516 original size:13 final size:13
Alignment explanation
Indices: 41493--41531 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 13
41483 AGATTATAAA
41493 TTTATACTTTTTAT
1 TTTATA-TTTTTAT
*
41507 TTTATATTTTAAT
1 TTTATATTTTTAT
41520 TTTATGATTTTT
1 TTTAT-ATTTTT
41532 TTTATTTATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (13 bp):
TTTATATTTTTAT
Found at i:44260 original size:72 final size:73
Alignment explanation
Indices: 44161--44355 Score: 189
Period size: 74 Copynumber: 2.7 Consensus size: 73
44151 ACAACTCCAT
* * * * * *
44161 TTCATGATTTAAGTC-GATCTTGATTCTTCAGATAACTCCCCTTCGCGGG-AAAGCCATATGAGA
1 TTCATGATTTAAGTCAG-TTTTGGTTCTTTAGATGACTCCCCTTCGCGGGCAAAGCCAAATAAGA
* * *
44224 TGACTCTCA
65 CGACCCCCA
* * ** * * * *
44233 TTCATGGTTTAAGTCAGTTTTGGTTCTTTGGGCGACTCCTCTTCGTGGGTCTAAGTCAAATAAGA
1 TTCATGATTTAAGTCAGTTTTGGTTCTTTAGATGACTCCCCTTCGCGGG-CAAAGCCAAATAAGA
44298 CGACCCCCA
65 CGACCCCCA
44307 TTC-TCGATTTAAGTCAGTTTTGGTTCTTTAGATGACTCCCCTTCGCGGG
1 TTCAT-GATTTAAGTCAGTTTTGGTTCTTTAGATGACTCCCCTTCGCGGG
44356 TCTAAGTCAA
Statistics
Matches: 96, Mismatches: 23, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
72 37 0.39
73 2 0.02
74 57 0.59
ACGTcount: A:0.21, C:0.23, G:0.21, T:0.35
Consensus pattern (73 bp):
TTCATGATTTAAGTCAGTTTTGGTTCTTTAGATGACTCCCCTTCGCGGGCAAAGCCAAATAAGAC
GACCCCCA
Found at i:45879 original size:21 final size:21
Alignment explanation
Indices: 45855--45894 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
45845 TTCCTACACA
45855 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
45876 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
45895 TCCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:46310 original size:21 final size:20
Alignment explanation
Indices: 46285--46344 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
46275 GGGCACTATA
46285 TATTTGTCCCGAAGGACCAC
1 TATTTGTCCCGAAGGACCAC
*
46305 TGATTTGTCCCAAAGGACCAC
1 T-ATTTGTCCCGAAGGACCAC
*
46326 TA--TGTCCCGAAGAACCAC
1 TATTTGTCCCGAAGGACCAC
46344 T
1 T
46345 CCTTAAGAAC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 15 0.42
20 2 0.06
21 19 0.53
ACGTcount: A:0.28, C:0.30, G:0.18, T:0.23
Consensus pattern (20 bp):
TATTTGTCCCGAAGGACCAC
Found at i:51199 original size:21 final size:21
Alignment explanation
Indices: 51175--51214 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
51165 TTCCTACACA
51175 ACTTATCTAATAT-CCTTTTAT
1 ACTTAT-TAATATACCTTTTAT
*
51196 ACTTATTTATATACCTTTT
1 ACTTATTAATATACCTTTT
51215 TCCTCAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.28, C:0.17, G:0.00, T:0.55
Consensus pattern (21 bp):
ACTTATTAATATACCTTTTAT
Found at i:51631 original size:18 final size:18
Alignment explanation
Indices: 51608--51660 Score: 97
Period size: 18 Copynumber: 2.9 Consensus size: 18
51598 ACTGTATATT
51608 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
51626 TGTCCCGAATGACCACTA
1 TGTCCCGAATGACCACTA
*
51644 TGTCCCGAAGGACCACT
1 TGTCCCGAATGACCACT
51661 CCTTAAGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (18 bp):
TGTCCCGAATGACCACTA
Found at i:59969 original size:6 final size:6
Alignment explanation
Indices: 59960--59991 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
59950 AAATAAAAAT
59960 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AA
59992 AATACTAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:60046 original size:27 final size:29
Alignment explanation
Indices: 60010--60069 Score: 97
Period size: 29 Copynumber: 2.1 Consensus size: 29
60000 TAATAATATG
*
60010 TATACTATAT-TTATATTTT-AAAAACTA
1 TATAATATATATTATATTTTCAAAAACTA
60037 TATAATATATATTATATTTTCAAAAACTA
1 TATAATATATATTATATTTTCAAAAACTA
60066 TATA
1 TATA
60070 TTATGTTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 9 0.30
28 9 0.30
29 12 0.40
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (29 bp):
TATAATATATATTATATTTTCAAAAACTA
Found at i:60069 original size:22 final size:22
Alignment explanation
Indices: 60042--60140 Score: 116
Period size: 22 Copynumber: 4.5 Consensus size: 22
60032 AACTATATAA
60042 TATATATTATATTTTCAAAAAC
1 TATATATTATATTTTCAAAAAC
*
60064 TATATATTATGTTTTC-AAAAC
1 TATATATTATATTTTCAAAAAC
* *
60085 TATATAATATGTTTTCAAAAAC
1 TATATATTATATTTTCAAAAAC
60107 TATATA-T-TATTTTCAATCAAAAC
1 TATATATTATATTTTC-A--AAAAC
60130 TATAT-TTATAT
1 TATATATTATAT
60141 ATTATATATT
Statistics
Matches: 68, Mismatches: 3, Indels: 10
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.09
21 22 0.32
22 26 0.38
23 11 0.16
24 3 0.04
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.46
Consensus pattern (22 bp):
TATATATTATATTTTCAAAAAC
Found at i:60085 original size:21 final size:22
Alignment explanation
Indices: 60042--60116 Score: 125
Period size: 22 Copynumber: 3.5 Consensus size: 22
60032 AACTATATAA
*
60042 TATATATTATATTTTCAAAAAC
1 TATATATTATGTTTTCAAAAAC
60064 TATATATTATGTTTTC-AAAAC
1 TATATATTATGTTTTCAAAAAC
*
60085 TATATAATATGTTTTCAAAAAC
1 TATATATTATGTTTTCAAAAAC
60107 TATATATTAT
1 TATATATTAT
60117 TTTCAATCAA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
21 20 0.41
22 29 0.59
ACGTcount: A:0.43, C:0.08, G:0.03, T:0.47
Consensus pattern (22 bp):
TATATATTATGTTTTCAAAAAC
Found at i:60089 original size:43 final size:43
Alignment explanation
Indices: 60042--60140 Score: 139
Period size: 43 Copynumber: 2.3 Consensus size: 43
60032 AACTATATAA
60042 TATATATTATATTTTCAAAAACTATATATTATGTTT-TCAAAAC
1 TATATATTATATTTTCAAAAACTATATATTAT-TTTATCAAAAC
* *
60085 TATATAATATGTTTTCAAAAACTATATATTATTTTCAATCAAAAC
1 TATATATTATATTTTCAAAAACTATATATTATTTT--ATCAAAAC
60130 TATAT-TTATAT
1 TATATATTATAT
60141 ATTATATATT
Statistics
Matches: 49, Mismatches: 4, Indels: 5
0.84 0.07 0.09
Matches are distributed among these distances:
42 3 0.06
43 30 0.61
44 4 0.08
45 12 0.24
ACGTcount: A:0.42, C:0.09, G:0.02, T:0.46
Consensus pattern (43 bp):
TATATATTATATTTTCAAAAACTATATATTATTTTATCAAAAC
Found at i:60871 original size:72 final size:72
Alignment explanation
Indices: 60649--60872 Score: 209
Period size: 72 Copynumber: 3.1 Consensus size: 72
60639 GCAAGACGAA
* * * * *
60649 TCCCCTTCGCAAGAAAGCCAGGTGAAACGACTCCCCTTCACGGTTTAAGTCGGA-CTTGATTCTT
1 TCCCCTTCACAGGAAAGTCAAGTGAGACGACTCCCCTTCACGGTTTAAGTC-GATCTTGATTCTT
*
60713 TGGGTAAC
65 TGGGTGAC
* * * * * * * ** *
60721 TCCCATTCA-TGGGAATTCCAAGTTAGATGATTCCCCTTCAAAGTTTAAGTCGATCATGATTCTT
1 TCCCCTTCACAGGAAAGT-CAAGTGAGACGACTCCCCTTCACGGTTTAAGTCGATCTTGATTCTT
* * *
60785 CGGATGAA
65 TGGGTGAC
* * * *
60793 TTCCCTTCACAGGAAAGTCATGTGAGACGACTCCCCTTCACGGTTTAAGTCAATCTTGGTTCTTT
1 TCCCCTTCACAGGAAAGTCAAGTGAGACGACTCCCCTTCACGGTTTAAGTCGATCTTGATTCTTT
60858 GGGTGAC
66 GGGTGAC
60865 TCCCCTTC
1 TCCCCTTC
60873 GCGGGTCTAA
Statistics
Matches: 112, Mismatches: 37, Indels: 6
0.72 0.24 0.04
Matches are distributed among these distances:
71 5 0.04
72 102 0.91
73 5 0.04
ACGTcount: A:0.23, C:0.26, G:0.20, T:0.31
Consensus pattern (72 bp):
TCCCCTTCACAGGAAAGTCAAGTGAGACGACTCCCCTTCACGGTTTAAGTCGATCTTGATTCTTT
GGGTGAC
Found at i:60913 original size:74 final size:74
Alignment explanation
Indices: 60824--60963 Score: 210
Period size: 74 Copynumber: 1.9 Consensus size: 74
60814 GTGAGACGAC
*
60824 TCCCCTTCACGGTTTAAGTCAATCTTGGTTCTTT-GGGTGACTCCCCTTCGCGGGTCTAAGTCAA
1 TCCCCTTCACGGTTTAAGTCAATCTAGGTT-TTTGGGGTGACTCCCCTTCGCGGGTCTAAGTCAA
60888 ATAAGTCGAA
65 ATAAGTCGAA
** * * *
60898 TCCCCTTCGTGGTTTAAGTCAGTCTAGGTTTTTGGGGTGACTCTCCTTTGCGGGTCTAAGTCAAA
1 TCCCCTTCACGGTTTAAGTCAATCTAGGTTTTTGGGGTGACTCCCCTTCGCGGGTCTAAGTCAAA
60963 T
66 T
60964 GAGACGATTC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
73 3 0.05
74 56 0.95
ACGTcount: A:0.18, C:0.24, G:0.24, T:0.35
Consensus pattern (74 bp):
TCCCCTTCACGGTTTAAGTCAATCTAGGTTTTTGGGGTGACTCCCCTTCGCGGGTCTAAGTCAAA
TAAGTCGAA
Found at i:70611 original size:33 final size:34
Alignment explanation
Indices: 70569--70638 Score: 81
Period size: 33 Copynumber: 2.1 Consensus size: 34
70559 GTTTAGGTTA
*
70569 AATTTTTTTTAATTAGATTT-GAGATAATAAT-AT
1 AATTATTTTTAA-TAGATTTAGAGATAATAATAAT
* * *
70602 AATTATTTTTTATATATTTAGAGATAATTATAAT
1 AATTATTTTTAATAGATTTAGAGATAATAATAAT
70636 AAT
1 AAT
70639 ATGCTTTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
32 6 0.19
33 20 0.65
34 5 0.16
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.51
Consensus pattern (34 bp):
AATTATTTTTAATAGATTTAGAGATAATAATAAT
Found at i:70647 original size:33 final size:32
Alignment explanation
Indices: 70585--70647 Score: 74
Period size: 33 Copynumber: 1.9 Consensus size: 32
70575 TTTTAATTAG
**
70585 ATTTGAGATAATAATATAATTATTTTTTATAT
1 ATTTGAGATAATAATATAATTATGCTTTATAT
*
70617 ATTTAGAGATAATTATAATAA-TATGCTTTAT
1 ATTT-GAGATAATAAT-ATAATTATGCTTTAT
70648 TTATATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 4 0.15
33 18 0.69
34 4 0.15
ACGTcount: A:0.41, C:0.02, G:0.08, T:0.49
Consensus pattern (32 bp):
ATTTGAGATAATAATATAATTATGCTTTATAT
Found at i:71149 original size:24 final size:23
Alignment explanation
Indices: 71096--71146 Score: 57
Period size: 24 Copynumber: 2.1 Consensus size: 23
71086 CGATTAAATC
* *
71096 TTTAAAATTTGAATATAAAATAT
1 TTTAAAATTAGAAAATAAAATAT
71119 TCTTAAAATTAGATAAATAATAATAT
1 T-TTAAAATTAGA-AAATAA-AATAT
71145 TT
1 TT
71147 AAATAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
23 1 0.04
24 10 0.43
25 6 0.26
26 6 0.26
ACGTcount: A:0.51, C:0.02, G:0.04, T:0.43
Consensus pattern (23 bp):
TTTAAAATTAGAAAATAAAATAT
Found at i:71160 original size:20 final size:19
Alignment explanation
Indices: 71135--71181 Score: 60
Period size: 20 Copynumber: 2.5 Consensus size: 19
71125 AATTAGATAA
*
71135 ATAATAATATTTAAATAAAT
1 ATAATAAAATTTAAA-AAAT
*
71155 ATAATAAAATTTGAAAAAT
1 ATAATAAAATTTAAAAAAT
71174 A-AATAAAA
1 ATAATAAAA
71182 AGTAATAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 7 0.28
19 5 0.20
20 13 0.52
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (19 bp):
ATAATAAAATTTAAAAAAT
Found at i:80042 original size:35 final size:35
Alignment explanation
Indices: 80003--80069 Score: 107
Period size: 35 Copynumber: 1.9 Consensus size: 35
79993 CCAAACACGA
* *
80003 TAATCTTACATTCCTGCTAAATCAACCAAACATAG
1 TAATCTTACAGTCCTGCTAAACCAACCAAACATAG
*
80038 TAATCTTACAGTCCTGCTAAACCAACCGAACA
1 TAATCTTACAGTCCTGCTAAACCAACCAAACA
80070 CAAAATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.25
Consensus pattern (35 bp):
TAATCTTACAGTCCTGCTAAACCAACCAAACATAG
Found at i:80586 original size:13 final size:13
Alignment explanation
Indices: 80568--80603 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
80558 TGGGTTTGAG
80568 TTTAAAATATGTA
1 TTTAAAATATGTA
80581 TTTAAAATATGTA
1 TTTAAAATATGTA
*
80594 TTTAATATAT
1 TTTAAAATAT
80604 ATAATATATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (13 bp):
TTTAAAATATGTA
Found at i:81099 original size:27 final size:28
Alignment explanation
Indices: 81062--81129 Score: 102
Period size: 27 Copynumber: 2.5 Consensus size: 28
81052 TTAGTGAGTA
*
81062 AAACTCTACTCGAAAAATCGA-TTTTTT
1 AAACTCGACTCGAAAAATCGATTTTTTT
81089 AAACTCGACTCGAAAAATCGATTTTTTT
1 AAACTCGACTCGAAAAATCGATTTTTTT
* *
81117 GAACTCGAATCGA
1 AAACTCGACTCGA
81130 TTTGAAAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
27 20 0.54
28 17 0.46
ACGTcount: A:0.37, C:0.19, G:0.12, T:0.32
Consensus pattern (28 bp):
AAACTCGACTCGAAAAATCGATTTTTTT
Found at i:82378 original size:3 final size:3
Alignment explanation
Indices: 82370--82403 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
82360 TTCACTGTTA
82370 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
82404 TATCAATCTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:93544 original size:55 final size:55
Alignment explanation
Indices: 93481--93934 Score: 402
Period size: 55 Copynumber: 8.5 Consensus size: 55
93471 ATGATGGGTC
**
93481 CGCTCCCTATTCCTTCATG-GAGTATAAGACTCGAGTAATCTTCAACAAACATGTT
1 CGCTCCCTATTCCTTCA-GAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
* * * *
93536 CGCACCCTATTCCTTCAGAGATTATATGACTCGAACAATCTTCAACAAACGTG-T
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
* * * * * *
93590 CTGCTCCCTATTTCTTTAGAGAGTATAGGACTTGAACCATATTCAACAAACATG-T
1 C-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
* * * * * * *
93645 CTGCTCCATTTTTCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAATATGTT
1 C-GCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
* * * * *
93701 TGTTCCCTATTCCTTCAGAGAGTATAAGACTCG----ATCTTCAACAAACGTATC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
* * *
93752 CGCTCCCTATTTCTTCAGAGAGTATAGGACTTGAACAATCTTCAA-AAA-ATGTGT
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGT-T
** * * * * * *
93806 CCGCTCTTTATTCATTCAGAGAGTATAATACTCG----GTCTTCAATAAACGTGTC
1 -CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
* * *
93858 CTCTCCCTATTCCTTCAGAGAGTATAAGACTCG----ATCTTCAACAAACGTGTC
1 CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
93909 CGCTCCCTATTCCTTCAGAGAGTATA
1 CGCTCCCTATTCCTTCAGAGAGTATA
93935 GGAATCGATC
Statistics
Matches: 328, Mismatches: 60, Indels: 26
0.79 0.14 0.06
Matches are distributed among these distances:
51 117 0.36
52 3 0.01
53 5 0.02
54 6 0.02
55 196 0.60
56 1 0.00
ACGTcount: A:0.30, C:0.24, G:0.15, T:0.32
Consensus pattern (55 bp):
CGCTCCCTATTCCTTCAGAGAGTATAAGACTCGAACAATCTTCAACAAACATGTT
Found at i:93776 original size:106 final size:106
Alignment explanation
Indices: 93478--93948 Score: 484
Period size: 106 Copynumber: 4.4 Consensus size: 106
93468 CGAATGATGG
* *
93478 GTCCGCTCCCTATTCCTTCATG-GAGTATAAGACTCGAGTAATCTTCAACAAACATGTTCGCACC
1 GTCCGCTCCCTATTCCTTCA-GAGAGTATAAGACTC--G--ATCTTCAACAAACATGTCCGCTCC
* * * *
93542 CTATTCCTTCAGAGATTATATGACTCGAACAATCTTCAACAAACGT
61 CTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAACGT
* * * * * * * *
93588 GTCTGCTCCCTATTTCTTTAGAGAGTATAGGACTTGAACCATATTCAACAAACATGTCTGCTCCA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGAC-T---CGATCTTCAACAAACATGTCCGCTCCC
* * **
93653 TTTTTCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAATAT
62 TATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAACGT
** * * *
93698 GTTTGTTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACGTATCCGCTCCCTATT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCGCTCCCTATT
* *
93763 TCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAATGT
66 CCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAACGT
** * * * * * *
93804 GTCCGCTCTTTATTCATTCAGAGAGTATAATACTCGGTCTTCAATAAACGTGTCCTCTCCCTATT
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCGCTCCCTATT
* * *
93869 CCTTCAGAGAGTATAAGAC-T---CGATCTTCAACAAACGT
66 CCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAACGT
* *
93906 GTCCGCTCCCTATTCCTTCAGAGAGTATAGGAATCGATCTTCA
1 GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCA
93949 TAAAATGAGT
Statistics
Matches: 302, Mismatches: 54, Indels: 18
0.81 0.14 0.05
Matches are distributed among these distances:
102 50 0.17
105 1 0.00
106 135 0.45
109 2 0.01
110 112 0.37
111 1 0.00
114 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.15, T:0.32
Consensus pattern (106 bp):
GTCCGCTCCCTATTCCTTCAGAGAGTATAAGACTCGATCTTCAACAAACATGTCCGCTCCCTATT
CCTTCAGAGAGTATAGGACTTGAACAATCTTCAAAAAACGT
Found at i:93999 original size:37 final size:37
Alignment explanation
Indices: 93959--94109 Score: 198
Period size: 37 Copynumber: 4.1 Consensus size: 37
93949 TAAAATGAGT
*
93959 TTGCTTCACTACTCTTCCGTGAA-GAGTTATAGA-TGAT
1 TTGCTTCACTACTCTTCCGTGAAGGA-TTA-AGATTGAA
*
93996 TTGCTTCAGTACTCTTCCGTGAAGGATTAAGATTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGATTAAGATTGAA
* * *
94033 TTGCTTCACTACTCTTTCATGAAGGCTTAAGATTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGATTAAGATTGAA
* * *
94070 TTGCTTCACTGCTCTTTCGTGAAGGCTTAAGATTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGATTAAGATTGAA
94107 TTG
1 TTG
94110 TTTCGAAGGT
Statistics
Matches: 104, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
36 3 0.03
37 99 0.95
38 2 0.02
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.38
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGATTAAGATTGAA
Found at i:95396 original size:65 final size:64
Alignment explanation
Indices: 95284--95484 Score: 207
Period size: 65 Copynumber: 3.1 Consensus size: 64
95274 GTGATGCACT
** **
95284 GATGCACCAATCCATGCATCGATGCAC-CATAGAATAAATTG-AACATCGAATGCATTTCATGCA
1 GATGCACCAA-CCATGCATCGATGCACTC--AGGCTATTTTGAAACATCGAATGCATTTCATGCA
*
95347 CC
63 TC
* * *
95349 GATGTA-CATACTATGCATTGATGCACTCAGAG-T-TTTATGAAAACATCGAATGCA-TTCGATG
1 GATGCACCA-ACCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATCGAATGCATTTC-ATG
95410 CATC
61 CATC
*
95414 GATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTTATGCATC
1 GATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATC
95478 GATGCAC
1 GATGCAC
95485 TAAGGGTCCA
Statistics
Matches: 114, Mismatches: 11, Indels: 23
0.77 0.07 0.16
Matches are distributed among these distances:
62 1 0.01
63 5 0.04
64 48 0.42
65 55 0.48
66 5 0.04
ACGTcount: A:0.32, C:0.23, G:0.17, T:0.27
Consensus pattern (64 bp):
GATGCACCAACCATGCATCGATGCACTCAGGCTATTTTGAAACATCGAATGCATTTCATGCATC
Found at i:100949 original size:21 final size:21
Alignment explanation
Indices: 100925--100979 Score: 65
Period size: 23 Copynumber: 2.5 Consensus size: 21
100915 GTGCATTATA
*
100925 CATCGATGCACCATGAAGGTG
1 CATCGATGCACCATAAAGGTG
* *
100946 CATCGATGCACACCTTAAATGTG
1 CATCGATG--CACCATAAAGGTG
100969 CATCGATGCAC
1 CATCGATGCAC
100980 AAGGCCATGC
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
21 11 0.38
23 18 0.62
ACGTcount: A:0.29, C:0.27, G:0.22, T:0.22
Consensus pattern (21 bp):
CATCGATGCACCATAAAGGTG
Found at i:103335 original size:33 final size:33
Alignment explanation
Indices: 103296--103376 Score: 162
Period size: 33 Copynumber: 2.5 Consensus size: 33
103286 TAACAAAAAG
103296 GGGGAGAAGTGTTAAGTGTTAAAATGTTTTAAA
1 GGGGAGAAGTGTTAAGTGTTAAAATGTTTTAAA
103329 GGGGAGAAGTGTTAAGTGTTAAAATGTTTTAAA
1 GGGGAGAAGTGTTAAGTGTTAAAATGTTTTAAA
103362 GGGGAGAAGTGTTAA
1 GGGGAGAAGTGTTAA
103377 AGTAAGGGGG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 48 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.31
Consensus pattern (33 bp):
GGGGAGAAGTGTTAAGTGTTAAAATGTTTTAAA
Found at i:103819 original size:19 final size:19
Alignment explanation
Indices: 103791--103842 Score: 95
Period size: 19 Copynumber: 2.7 Consensus size: 19
103781 AATGTATTTC
*
103791 ATGCACCGATGCACATACT
1 ATGCATCGATGCACATACT
103810 ATGCATCGATGCACATACT
1 ATGCATCGATGCACATACT
103829 ATGCATCGATGCAC
1 ATGCATCGATGCAC
103843 TCAGAGTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (19 bp):
ATGCATCGATGCACATACT
Found at i:103923 original size:65 final size:65
Alignment explanation
Indices: 103810--103952 Score: 195
Period size: 65 Copynumber: 2.2 Consensus size: 65
103800 TGCACATACT
* *
103810 ATGCATCGATGCA-CATACTATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAAAGCATTT
1 ATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATG-AAACATAGAAAGCATTT
103874 A
65 A
*
103875 ATGCATCGATGCACCAT-CCATGCATCGATGCACTCAG-GCTATTT-TGAAACATAGAATGCATT
1 ATGCATCGATGCACCATACCATGCATCGATGCACTCAGAG-T-TTTATGAAACATAGAAAGCATT
*
103937 TT
64 TA
103939 ATGCATCGATGCAC
1 ATGCATCGATGCAC
103953 TCTTAGTGCA
Statistics
Matches: 71, Mismatches: 4, Indels: 7
0.87 0.05 0.09
Matches are distributed among these distances:
64 30 0.42
65 35 0.49
66 6 0.08
ACGTcount: A:0.32, C:0.22, G:0.17, T:0.28
Consensus pattern (65 bp):
ATGCATCGATGCACCATACCATGCATCGATGCACTCAGAGTTTTATGAAACATAGAAAGCATTTA
Found at i:103968 original size:64 final size:64
Alignment explanation
Indices: 103809--103969 Score: 179
Period size: 64 Copynumber: 2.5 Consensus size: 64
103799 ATGCACATAC
*
103809 TATGCATCGATGCACATAC-TATGCATCGATGCACTCAGAGTTTTATGAAAACATCGAAAGCATT
1 TATGCATCGATGCAC-T-CTTATGCATCGATGCACTCAGAGTTTTATGAAAACATAGAAAGCATT
103873 T
64 T
* * *
103874 AATGCATCGATGCAC-CATCCATGCATCGATGCACTCAG-GCTATTT-TG-AAACATAGAATGCA
1 TATGCATCGATGCACTC-T-TATGCATCGATGCACTCAGAG-T-TTTATGAAAACATAGAAAGCA
103935 TTT
62 TTT
*
103938 TATGCATCGATGCACTCTTAGTGCACCGATGC
1 TATGCATCGATGCACTCTTA-TGCATCGATGC
103970 TCTAAGGGTC
Statistics
Matches: 82, Mismatches: 7, Indels: 15
0.79 0.07 0.14
Matches are distributed among these distances:
62 1 0.01
63 1 0.01
64 41 0.50
65 36 0.44
66 3 0.04
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (64 bp):
TATGCATCGATGCACTCTTATGCATCGATGCACTCAGAGTTTTATGAAAACATAGAAAGCATTT
Found at i:105072 original size:18 final size:17
Alignment explanation
Indices: 105030--105068 Score: 60
Period size: 17 Copynumber: 2.3 Consensus size: 17
105020 TTTTATTTCC
105030 TTTTTCTTTTTTCATCA
1 TTTTTCTTTTTTCATCA
**
105047 TTTTTCTTTTTTTTTCA
1 TTTTTCTTTTTTCATCA
105064 TTTTT
1 TTTTT
105069 TCTTCCATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.79
Consensus pattern (17 bp):
TTTTTCTTTTTTCATCA
Found at i:105135 original size:19 final size:20
Alignment explanation
Indices: 105113--105166 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
105103 TTTTTCATCA
105113 TTCTTTAAT-TTTTTTCCTT
1 TTCTTTAATATTTTTTCCTT
**
105132 TTCTTTTTTATTTTTTCCTT
1 TTCTTTAATATTTTTTCCTT
* *
105152 TCCTTT-TTATTTTTT
1 TTCTTTAATATTTTTT
105167 ATTTCTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.07, C:0.15, G:0.00, T:0.78
Consensus pattern (20 bp):
TTCTTTAATATTTTTTCCTT
Found at i:105145 original size:20 final size:18
Alignment explanation
Indices: 105122--105183 Score: 81
Period size: 19 Copynumber: 3.3 Consensus size: 18
105112 ATTCTTTAAT
105122 TTTTTTCCTTTTCTTTTTTA
1 TTTTTTCC-TTTC-TTTTTA
105142 TTTTTTCCTTTCCTTTTTA
1 TTTTTTCCTTT-CTTTTTA
*
105161 TTTTTT-ATTTCTTTTTA
1 TTTTTTCCTTTCTTTTTA
105178 TTTTTT
1 TTTTTT
105184 TCATTTATTC
Statistics
Matches: 40, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
17 13 0.32
18 3 0.08
19 15 0.38
20 9 0.22
ACGTcount: A:0.06, C:0.13, G:0.00, T:0.81
Consensus pattern (18 bp):
TTTTTTCCTTTCTTTTTA
Found at i:105183 original size:19 final size:19
Alignment explanation
Indices: 105131--105189 Score: 52
Period size: 19 Copynumber: 3.2 Consensus size: 19
105121 TTTTTTTCCT
*
105131 TTTCTTTTTTATTTTTTCCT-
1 TTTC-TTTTTATTTTTT-TTA
*
105151 TTCCTTTTTA--TTTTTTA
1 TTTCTTTTTATTTTTTTTA
*
105168 TTTCTTTTTATTTTTTTCA
1 TTTCTTTTTATTTTTTTTA
105187 TTT
1 TTT
105190 ATTCTTCAAG
Statistics
Matches: 32, Mismatches: 4, Indels: 7
0.74 0.09 0.16
Matches are distributed among these distances:
16 1 0.03
17 13 0.41
19 15 0.47
20 3 0.09
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.80
Consensus pattern (19 bp):
TTTCTTTTTATTTTTTTTA
Found at i:109215 original size:6 final size:6
Alignment explanation
Indices: 109204--109233 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
109194 ATGCATTGCA
109204 AAAAAT AAAAAT AAAAAT -AAAAT AAAAAT A
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT A
109234 CATATACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAAAT
Found at i:109225 original size:11 final size:11
Alignment explanation
Indices: 109204--109233 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
109194 ATGCATTGCA
109204 AAAAATAAAAAT
1 AAAAAT-AAAAT
109216 AAAAATAAAAT
1 AAAAATAAAAT
109227 AAAAATA
1 AAAAATA
109234 CATATACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 12 0.67
12 6 0.33
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:111654 original size:30 final size:30
Alignment explanation
Indices: 111615--111927 Score: 554
Period size: 30 Copynumber: 10.4 Consensus size: 30
111605 TCCGAATGAC
111615 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
111645 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
111675 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
111705 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
111735 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
111765 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
111795 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
111825 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
111855 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
111885 ATATCCAGAGGTCATAAAGATCCTCAGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
111915 CTGTCCATAGGTC
1 CTATCCAGAGGTC
111928 CCGAAGAACC
Statistics
Matches: 274, Mismatches: 9, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 274 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:112188 original size:4 final size:4
Alignment explanation
Indices: 112179--112203 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
112169 ATATAACCAT
112179 TACA TACA TACA TACA TACA TACA T
1 TACA TACA TACA TACA TACA TACA T
112204 GTCATCCCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.28
Consensus pattern (4 bp):
TACA
Found at i:112372 original size:2 final size:2
Alignment explanation
Indices: 112360--112394 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
112350 TACACAACTC
112360 AT AT A- 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
112395 GTAACATGTC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:112898 original size:20 final size:20
Alignment explanation
Indices: 112873--112930 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
112863 TTTTTCATTA
*
112873 TGGGGGAATCGGTTCCCCCC
1 TGGGGGTATCGGTTCCCCCC
112893 TGGGGGTATCGGTTCCCCCC
1 TGGGGGTATCGGTTCCCCCC
*
112913 TGGGGGTATCGATTCCCC
1 TGGGGGTATCGGTTCCCC
112931 TCTAGCATTC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.09, C:0.33, G:0.34, T:0.24
Consensus pattern (20 bp):
TGGGGGTATCGGTTCCCCCC
Found at i:116750 original size:30 final size:30
Alignment explanation
Indices: 116331--116733 Score: 743
Period size: 30 Copynumber: 13.4 Consensus size: 30
116321 TCCGAAGGAC
116331 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116361 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116391 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116421 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116451 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116481 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116511 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
116541 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116571 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116601 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116631 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116661 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
116691 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
* *
116721 CTGTCCATAGGTC
1 CTATCCAGAGGTC
116734 CCGAAGAACC
Statistics
Matches: 367, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 367 1.00
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.24
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:116807 original size:31 final size:30
Alignment explanation
Indices: 116716--116811 Score: 88
Period size: 31 Copynumber: 3.1 Consensus size: 30
116706 AAAGATCCTC
* * *
116716 GGTAACTGTCCATAGGTCCCGAAGAACCTA
1 GGTAACTGTCCATATGTCTCGAAGAACATA
* **
116746 GGTAAACTATCCATATGT-TCCTTAGAACATA
1 GGT-AACTGTCCATATGTCT-CGAAGAACATA
116777 GGTATACTGTCCATATGTCTCGAA-AGACATA
1 GGTA-ACTGTCCATATGTCTCGAAGA-ACATA
116808 GGTA
1 GGTA
116812 GTTCTTTGAC
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
30 5 0.10
31 46 0.88
32 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.27
Consensus pattern (30 bp):
GGTAACTGTCCATATGTCTCGAAGAACATA
Found at i:130178 original size:23 final size:23
Alignment explanation
Indices: 130110--130187 Score: 90
Period size: 23 Copynumber: 3.5 Consensus size: 23
130100 CACCTAACAC
*
130110 TGCATCGATGCA-TCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
* *
130132 TGCATCGAT--ACACCATGAAGG
1 TGCATCGATGCACACCTTGAATG
* *
130153 TGCACCGATGCACGCCTTGAATG
1 TGCATCGATGCACACCTTGAATG
130176 TGCATCGATGCA
1 TGCATCGATGCA
130188 TCCGTCGGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 5
0.78 0.14 0.09
Matches are distributed among these distances:
20 1 0.02
21 15 0.33
22 9 0.20
23 20 0.44
ACGTcount: A:0.26, C:0.26, G:0.24, T:0.24
Consensus pattern (23 bp):
TGCATCGATGCACACCTTGAATG
Found at i:131852 original size:23 final size:23
Alignment explanation
Indices: 131826--131909 Score: 123
Period size: 23 Copynumber: 3.7 Consensus size: 23
131816 CACCACAGCT
* *
131826 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
131849 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
* *
131872 CGTAGAATTGCACCGGAGTACCG
1 CGTAGAATTGCACCGGAGTGCCA
*
131895 CGTAGAATTACACCG
1 CGTAGAATTGCACCG
131910 TTGTACCATA
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 56 1.00
ACGTcount: A:0.29, C:0.26, G:0.26, T:0.19
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:132058 original size:103 final size:103
Alignment explanation
Indices: 131924--132145 Score: 365
Period size: 103 Copynumber: 2.2 Consensus size: 103
131914 ACCATATAAT
* *
131924 AATGTCCAT-AAGGACCACATATCATTCCTTAAGAATCATATACATATACTAGGGATCAAGTATG
1 AATGTCC-TGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATG
*
131988 TGTCTCACAAGACTTCACACATGTTCCAAAGAATACATA
65 TGTCTCACAAGACTTCACACATATTCCAAAGAATACATA
* *
132027 TATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGT
1 AATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
*
132092 GTCTCACCAGACTTCACACATATTCCAAAGAATACATA
66 GTCTCACAAGACTTCACACATATTCCAAAGAATACATA
*
132130 AATGTCCCGAAGGACC
1 AATGTCCTGAAGGACC
132146 GCGTAGACCC
Statistics
Matches: 110, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
102 1 0.01
103 109 0.99
ACGTcount: A:0.37, C:0.23, G:0.14, T:0.26
Consensus pattern (103 bp):
AATGTCCTGAAGGACCACATATCATTCCTTAAGAATCATATACATATACCAAGGATCAAGTATGT
GTCTCACAAGACTTCACACATATTCCAAAGAATACATA
Found at i:133542 original size:22 final size:21
Alignment explanation
Indices: 133517--133576 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
133507 TTCGCTTGAG
133517 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
*
133539 GGGTACCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
133559 GGGTATCGATTCCCCTTG
1 GGGTATCGATTCCCCTTG
133577 CCCAGAAATC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
20 16 0.46
21 9 0.26
22 10 0.29
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:134504 original size:16 final size:16
Alignment explanation
Indices: 134465--134507 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
134455 AACATCAGTT
*
134465 CTTATCACTCAAAATC
1 CTTATCAATCAAAATC
* *
134481 ATTAATCAATCAAATTC
1 CTT-ATCAATCAAAATC
134498 CTTATCAATC
1 CTTATCAATC
134508 TTTAATTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
16 9 0.41
17 13 0.59
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.35
Consensus pattern (16 bp):
CTTATCAATCAAAATC
Found at i:137272 original size:23 final size:23
Alignment explanation
Indices: 137246--137335 Score: 126
Period size: 23 Copynumber: 3.9 Consensus size: 23
137236 CACCACAGCT
* *
137246 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
137269 CGTAGAATTGCACCGGAGTGCCA
1 CGTAGAATTGCACCGGAGTGCCA
* *
137292 CGTAGAATTGCATCGGAGTGCCG
1 CGTAGAATTGCACCGGAGTGCCA
* *
137315 CGTAGAATTACACCGTAGTGC
1 CGTAGAATTGCACCGGAGTGC
137336 TATATAATAA
Statistics
Matches: 60, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 60 1.00
ACGTcount: A:0.27, C:0.24, G:0.28, T:0.21
Consensus pattern (23 bp):
CGTAGAATTGCACCGGAGTGCCA
Found at i:137528 original size:103 final size:101
Alignment explanation
Indices: 137355--137554 Score: 328
Period size: 103 Copynumber: 2.0 Consensus size: 101
137345 ATGTCCATAA
* * *
137355 GGACCACATATCATTCCTTAAGAATCATACATATACTAGGGATCAAGTATGTGTCTCACCAGACT
1 GGACCACATATCATTCCTTAAGAATCATACATATACCAAGGATCAAGTATGTGTCTCACCAGACG
137420 TCACACATGTTCCAAAGAATACATATATGTCCCGAT
66 TCACACATGTTCCAAAGAATACATATATGTCCCGAT
* *
137456 GGACCACATATCATTCCTTAAGAATCATATACATATGCCAAGGATCAAGTATGTGTCTCACCTGA
1 GGACCACATATCATTCCTTAAGAATC--ATACATATACCAAGGATCAAGTATGTGTCTCACCAGA
*
137521 CGTCACACTTGTTCCAAAGAATACATATATGTCC
64 CGTCACACATGTTCCAAAGAATACATATATGTCC
137555 TGAAGGACTG
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
101 26 0.29
103 65 0.71
ACGTcount: A:0.34, C:0.24, G:0.14, T:0.28
Consensus pattern (101 bp):
GGACCACATATCATTCCTTAAGAATCATACATATACCAAGGATCAAGTATGTGTCTCACCAGACG
TCACACATGTTCCAAAGAATACATATATGTCCCGAT
Found at i:138956 original size:22 final size:21
Alignment explanation
Indices: 138931--138990 Score: 95
Period size: 20 Copynumber: 2.9 Consensus size: 21
138921 TTCGCTTGAG
138931 GGGTATCGATTCCCCATTGAAT
1 GGGTATCGATTCCCC-TTGAAT
138953 GGGTATCGATT-CCCTTGAAT
1 GGGTATCGATTCCCCTTGAAT
*
138973 GGGTACCGATTCCCCTTG
1 GGGTATCGATTCCCCTTG
138991 CCCAGAAATC
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
20 16 0.44
21 9 0.25
22 11 0.31
ACGTcount: A:0.18, C:0.25, G:0.25, T:0.32
Consensus pattern (21 bp):
GGGTATCGATTCCCCTTGAAT
Found at i:139243 original size:12 final size:12
Alignment explanation
Indices: 139226--139262 Score: 65
Period size: 12 Copynumber: 3.1 Consensus size: 12
139216 TATTGACAAG
139226 TCAAATTCAACT
1 TCAAATTCAACT
139238 TCAAATTCAACT
1 TCAAATTCAACT
*
139250 TAAAATTCAACT
1 TCAAATTCAACT
139262 T
1 T
139263 ATCAACTTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.43, C:0.22, G:0.00, T:0.35
Consensus pattern (12 bp):
TCAAATTCAACT
Found at i:140454 original size:21 final size:21
Alignment explanation
Indices: 140412--140455 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
140402 ACCCCGGGAG
* *
140412 CTAGCTCTTCATGAGCTGCTC
1 CTAGCTCTTCATCAGCTCCTC
140433 CTAGCTCTTC-TCATGCTCCTC
1 CTAGCTCTTCATCA-GCTCCTC
140454 CT
1 CT
140456 CCTCCTCTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.11, C:0.39, G:0.14, T:0.36
Consensus pattern (21 bp):
CTAGCTCTTCATCAGCTCCTC
Found at i:141666 original size:17 final size:19
Alignment explanation
Indices: 141638--141686 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
141628 TATTTTGAAA
141638 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
141656 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
141675 CACCGATGCACT
1 CATCGATGCACT
141687 AAGGATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Done.