Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005676.1 Hibiscus syriacus cultivar Beakdansim tig00013275_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: 284150
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
File 2 of 2
Found at i:264100 original size:20 final size:20
Alignment explanation
Indices: 264077--264163 Score: 138
Period size: 20 Copynumber: 4.3 Consensus size: 20
264067 GAAACTTAAA
*
264077 ATCGCAACGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
264097 ATCGCAATGCGAAAATGACT
1 ATCGCAATGCGAAAATGACT
*
264117 ATCGCAATGTGAAAATGACT
1 ATCGCAATGCGAAAATGACT
**
264137 ATCGCAATGCGAATTTGACT
1 ATCGCAATGCGAAAATGACT
264157 ATCGCAA
1 ATCGCAA
264164 CGAGAGAATC
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 62 1.00
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.22
Consensus pattern (20 bp):
ATCGCAATGCGAAAATGACT
Found at i:264242 original size:19 final size:19
Alignment explanation
Indices: 264191--264273 Score: 79
Period size: 19 Copynumber: 4.7 Consensus size: 19
264181 GAAATGAAAA
* * *
264191 TCGCAATGCGATTATAGTT
1 TCGCATTGCGATTTTGGTT
*
264210 TCGCGTTGCGATTTTGGTT
1 TCGCATTGCGATTTTGGTT
264229 TCGCATTGCGA--TT--TT
1 TCGCATTGCGATTTTGGTT
264244 TCG--TTGCGATTTTGGTT
1 TCGCATTGCGATTTTGGTT
*
264261 TCGCGTTGCGATT
1 TCGCATTGCGATT
264274 CTCTCGTTGT
Statistics
Matches: 53, Mismatches: 5, Indels: 12
0.76 0.07 0.17
Matches are distributed among these distances:
13 6 0.11
15 7 0.13
17 7 0.13
19 33 0.62
ACGTcount: A:0.12, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTGGTT
Found at i:264287 original size:14 final size:14
Alignment explanation
Indices: 264264--264321 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 14
264254 TTTGGTTTCG
264264 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
264278 CGTTGTGATTTTCATTTCT
1 CGTTGCGA--TTC---TCT
264297 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
264311 CGTTGCGATTC
1 CGTTGCGATTC
264322 ATTTCGCGTT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 21 0.57
16 3 0.08
17 3 0.08
19 10 0.27
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:264288 original size:33 final size:33
Alignment explanation
Indices: 264213--264336 Score: 155
Period size: 33 Copynumber: 3.8 Consensus size: 33
264203 TATAGTTTCG
** * *
264213 CGTTGCGATTTTGGTTTCGCATTGCGATT-TTT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
**
264245 CGTTGCGATTTTGGTTTCGCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
* *
264278 CGTTGTGATTTTCATTTCTCGTTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
264311 CGTTGCGA--TTCATTTCGCGTTGCGAT
1 CGTTGCGATTTTCATTTCGCGTTGCGAT
264337 AGTCATTTTT
Statistics
Matches: 83, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
31 17 0.20
32 28 0.34
33 38 0.46
ACGTcount: A:0.09, C:0.20, G:0.24, T:0.47
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCGTTGCGATTCTCT
Found at i:264802 original size:94 final size:93
Alignment explanation
Indices: 264424--264803 Score: 580
Period size: 94 Copynumber: 4.1 Consensus size: 93
264414 ATGGATTGCA
* * * *
264424 TTACTTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAATT
1 TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
264489 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
* * * *
264517 TTATTTTCAACCAAAAGACAAAACAAAGACAAATATTAACTTCACATTGTTAAAGAATATACAGT
1 TTA-CTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
*
264582 TTAGCAGAATTTGCAGCAACCGAACAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
264611 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
1 TTAC-TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* *
264676 TTAGCATAATTGGCAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
* * *
264705 TTACTTAAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAGAATAAATAGT
1 TTACTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGT
* * *
264770 TTAGCAGTATTGGTAGCAACCGAATAAAT
65 TTAGCAGAATTGGCAGCAACCGAACAAAT
264799 TTACT
1 TTACT
264804 AAGCAATCTA
Statistics
Matches: 262, Mismatches: 22, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
93 21 0.08
94 241 0.92
ACGTcount: A:0.48, C:0.17, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:265425 original size:13 final size:13
Alignment explanation
Indices: 265407--265433 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
265397 GTCTACTATT
265407 AATAGCCCTAGGA
1 AATAGCCCTAGGA
265420 AATAGCCCTAGGA
1 AATAGCCCTAGGA
265433 A
1 A
265434 TATCATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.15
Consensus pattern (13 bp):
AATAGCCCTAGGA
Found at i:267265 original size:18 final size:19
Alignment explanation
Indices: 267230--267269 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
267220 ATTTAAAAAT
*
267230 TAAATTAATATGAATGAAA
1 TAAAATAATATGAATGAAA
267249 TAAAATAATAT-AATGAAA
1 TAAAATAATATGAATGAAA
267267 TAA
1 TAA
267270 GCAATATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 10 0.50
19 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (19 bp):
TAAAATAATATGAATGAAA
Found at i:267325 original size:2 final size:2
Alignment explanation
Indices: 267320--267366 Score: 67
Period size: 2 Copynumber: 23.5 Consensus size: 2
267310 ACACACATAA
* * *
267320 AT AT AT AT AT AC AT AA AT AT AT AT AT AT AT AC AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
267362 AT AT A
1 AT AT A
267367 ATAAAACATC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:267335 original size:16 final size:16
Alignment explanation
Indices: 267314--267367 Score: 81
Period size: 16 Copynumber: 3.4 Consensus size: 16
267304 AATTAAACAC
267314 ACATAAATATATATAT
1 ACATAAATATATATAT
267330 ACATAAATATATATAT
1 ACATAAATATATATAT
* *
267346 ATATACATATATATAT
1 ACATAAATATATATAT
*
267362 ATATAA
1 ACATAA
267368 TAAAACATCT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 35 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ACATAAATATATATAT
Found at i:267464 original size:16 final size:16
Alignment explanation
Indices: 267445--267479 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
267435 TTTAAAAAAC
* *
267445 AAAAGGACTAAATTAT
1 AAAAGGACAAAATGAT
267461 AAAAGGACAAAATGAT
1 AAAAGGACAAAATGAT
267477 AAA
1 AAA
267480 GCATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATGAT
Found at i:269171 original size:91 final size:93
Alignment explanation
Indices: 269014--269182 Score: 279
Period size: 91 Copynumber: 1.8 Consensus size: 93
269004 TGTTGAAGAC
*
269014 GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACATGGTTCCA
1 GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACACGGTTCCA
*
269079 CTCTGCTGGGGACATCTGGCCGAGGGAT
66 CTCTGCTGCGGACATCTGGCCGAGGGAT
* * *
269107 GACACTGCTCATCCGCGATGAAGAG-TTC-TGGCCATCTTTAGGAATGATGCTAACACGGTTCCA
1 GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACACGGTTCCA
269170 CTCTGCTGCGGAC
66 CTCTGCTGCGGAC
269183 GGCTGGTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
91 44 0.62
92 2 0.03
93 25 0.35
ACGTcount: A:0.24, C:0.25, G:0.27, T:0.24
Consensus pattern (93 bp):
GACACTGCTCATCCGCGATGAAGAGAATCTTGGCCATCTTTAGGAAAGATGATAACACGGTTCCA
CTCTGCTGCGGACATCTGGCCGAGGGAT
Found at i:269386 original size:40 final size:42
Alignment explanation
Indices: 269200--269525 Score: 193
Period size: 40 Copynumber: 7.6 Consensus size: 42
269190 TATCTGATGT
* * *
269200 TGACACGGCTCATACGTGATGAAGAGTTCTGG-TCAG-GGGA
1 TGACACGGCTCATACGTGATGAAGAGGTCTGGATCTGAGGAA
*** * * * *
269240 TGACATTACTCATACATGATGAAGAGTTCTTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGGTC-TGG--ATCT-GAGG-AA
* * * * * * * *
269287 TAACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGG-G
1 TGACACGGCTCATACGTGATGAAGAGGTCTGG--ATCTGAGGAA
*
269330 TGACACGGCTCCTACGTGATGAAGAGGTCTGG-TC-GAGGAA
1 TGACACGGCTCATACGTGATGAAGAGGTCTGGATCTGAGGAA
* * *
269370 TGACACGGTTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTAA
1 TGACACGGCTCATACGTGATGAAGAGGTCTGG--ATCT-GAGG-AA
* * * * *
269416 TAACACGGTTCCTACGTGATGAGGACGG-CTGGTTATCT-ATGG-T
1 TGACACGGCTCATACGTGATGAAGA-GGTCTGG--ATCTGA-GGAA
* *
269459 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGAA
1 TGACACGGCTCATACGTGATGAAGAGGTCTGGATCTGAGGAA
269500 TGACACGGCTCATACGTGATGAAGAG
1 TGACACGGCTCATACGTGATGAAGAG
269526 TTATGGCCAT
Statistics
Matches: 222, Mismatches: 45, Indels: 37
0.73 0.15 0.12
Matches are distributed among these distances:
39 3 0.01
40 61 0.27
41 29 0.13
42 1 0.00
43 54 0.24
44 3 0.01
45 9 0.04
46 41 0.18
47 21 0.09
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (42 bp):
TGACACGGCTCATACGTGATGAAGAGGTCTGGATCTGAGGAA
Found at i:269463 original size:129 final size:129
Alignment explanation
Indices: 269092--269577 Score: 636
Period size: 130 Copynumber: 3.7 Consensus size: 129
269082 TGCTGGGGAC
* * * * * * *
269092 ATCTGGCCGAGGGATGACACTGCTCATCCGCGATGAAGAGTTCTGGCCATCTTTAGGAATGATGC
1 ATCTGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATC--TA--AA-GGTGA
* * *
269157 TAACACGGTTCC-ACTCTGCTGCGGACGGCTGGTTATCTGAT-GTTGACACGGCTCATACGTGAT
61 TAACACGGTTCCTAC-GTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCATACGTGAT
269220 GAAGAG
124 GAAGAG
* * *** *
269226 TTCTGGTC-AGGGGATGACATTACTCATACATGATGAAGAGTTCTTGGCCATCTAAAGGTGATAA
1 ATCTGGTCGA-GGAATGACACGGCTCATACGTGATGAAGAGTTC-TGGCCATCTAAAGGTGATAA
* * * *
269290 CACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGA
64 CACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGA
269355 G
129 G
* * *
269356 GTCTGGTCGAGGAATGACACGGTTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTAATAACA
1 ATCTGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACA
269421 CGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAG
66 CGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAG
* *
269485 ATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTTATGGCCATCTAAAGGTGATAAC
1 ATCTGGTC-GAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAAC
269550 ACGGTTCCTACGTGATGAGGACGGCTGG
65 ACGGTTCCTACGTGATGAGGACGGCTGG
269578 CCATCTTTAG
Statistics
Matches: 313, Mismatches: 33, Indels: 16
0.86 0.09 0.04
Matches are distributed among these distances:
129 89 0.28
130 174 0.56
131 5 0.02
133 3 0.01
134 34 0.11
135 8 0.03
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (129 bp):
ATCTGGTCGAGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATAACA
CGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATACGTGATGAAGAG
Found at i:269569 original size:259 final size:262
Alignment explanation
Indices: 269093--269577 Score: 703
Period size: 259 Copynumber: 1.9 Consensus size: 262
269083 GCTGGGGACA
* * * **
269093 TCTGGCCGAGGGATGACACTGCTCATCCGCGATGAAGAGTTCTGGCCATCTTTAGGAATGATGCT
1 TCTGGCCGAGGAATGACACGGCTCATACGCGATGAAGAGTTCTGGCCATC-TTA-GAATGATAAT
* *
269158 AACACGGTTCCACTCTGCTGCGGACGGCTGGTTATCTGATGTTGACACGGCTCATACGTGATGAA
64 AACACGGTTCCACTCTGATGAGGACGGCTGGTTATCTGATGTTGACACGGCTCATACGTGATGAA
* ** *
269223 GAGTTCTGGTCAGGGGATGACATTACTCATACATGATGAAGAGTTCTTGGCCATCTAAAGGTGAT
129 GAGATCTGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCATGGCCATCTAAAGGTGAT
269288 AACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAA
194 AACACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAA
269353 GAGG
259 GAGG
* * * *
269357 TCTGGTCGAGGAATGACACGGTTCATACGTGATGAAGAGTTCTGGCCATC-TA-AA-GGTAATAA
1 TCTGGCCGAGGAATGACACGGCTCATACGCGATGAAGAGTTCTGGCCATCTTAGAATGATAATAA
*
269419 CACGGTTCCTAC-GTGATGAGGACGGCTGGTTATCT-ATGGTTGACACGGCTCATACGTGATGAA
66 CACGGTTCC-ACTCTGATGAGGACGGCTGGTTATCTGAT-GTTGACACGGCTCATACGTGATGAA
* * *
269482 GAGATCTGGTCTGGGGAATGACACGGCTCATACGTGATGAAGAGTT-ATGGCCATCTAAAGGTGA
129 GAGATCTGGTCAGGGG-ATGACACGACTCATACATGATGAAGAGTTCATGGCCATCTAAAGGTGA
*
269546 TAACACGGTTCCTACGTGATGAGGACGGCTGG
193 TAACACGGTTCCTACGTGATGAGGACGACTGG
269578 CCATCTTTAG
Statistics
Matches: 198, Mismatches: 20, Indels: 11
0.86 0.09 0.05
Matches are distributed among these distances:
258 2 0.01
259 121 0.61
260 29 0.15
262 2 0.01
264 44 0.22
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (262 bp):
TCTGGCCGAGGAATGACACGGCTCATACGCGATGAAGAGTTCTGGCCATCTTAGAATGATAATAA
CACGGTTCCACTCTGATGAGGACGGCTGGTTATCTGATGTTGACACGGCTCATACGTGATGAAGA
GATCTGGTCAGGGGATGACACGACTCATACATGATGAAGAGTTCATGGCCATCTAAAGGTGATAA
CACGGTTCCTACGTGATGAGGACGACTGGTTATCTAAGGGTGACACGGCTCCTACGTGATGAAGA
GG
Found at i:269579 original size:46 final size:44
Alignment explanation
Indices: 269256--269583 Score: 198
Period size: 46 Copynumber: 7.5 Consensus size: 44
269246 TACTCATACA
* *
269256 TGATGAAGAGTTCTTGGCCATCTAAAGGTGATAACACGGTTCCTACG
1 TGATGAAGAG-GC-TGGCCATCT-AAGGTGATGACACGGTTCCTACG
* * ** *
269303 TGATGAGGACGACTGGTTATCTAAGG-G-TGACACGGCTCCTACG
1 TGATGAAGA-GGCTGGCCATCTAAGGTGATGACACGGTTCCTACG
* * *
269346 TGATGAAGAGGTCTGG---TC-GAGG-AATGACACGGTTCATACG
1 TGATGAAGAGG-CTGGCCATCTAAGGTGATGACACGGTTCCTACG
* * *
269386 TGATGAAGAGTTCTGGCCATCTAAAGGTAATAACACGGTTCCTACG
1 TGATGAAGAG-GCTGGCCATCT-AAGGTGATGACACGGTTCCTACG
* ** * * *
269432 TGATGAGGACGGCTGGTTATCTATGGT--TGACACGGCTCATACG
1 TGATGAAGA-GGCTGGCCATCTAAGGTGATGACACGGTTCCTACG
* * * *
269475 TGATGAAGAGATCTGG---TCT--GGGGAATGACACGGCTCATACG
1 TGATGAAGAG-GCTGGCCATCTAAGGTG-ATGACACGGTTCCTACG
** *
269516 TGATGAAGAGTTATGGCCATCTAAAGGTGATAACACGGTTCCTACG
1 TGATGAAGAG-GCTGGCCATCT-AAGGTGATGACACGGTTCCTACG
*
269562 TGATGAGGACGGCTGGCCATCT
1 TGATGAAGA-GGCTGGCCATCT
269584 TTAGGAGTTA
Statistics
Matches: 223, Mismatches: 36, Indels: 45
0.73 0.12 0.15
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 33 0.15
41 30 0.13
42 2 0.01
43 53 0.24
44 4 0.02
45 11 0.05
46 70 0.31
47 14 0.06
48 1 0.00
ACGTcount: A:0.26, C:0.19, G:0.30, T:0.25
Consensus pattern (44 bp):
TGATGAAGAGGCTGGCCATCTAAGGTGATGACACGGTTCCTACG
Found at i:269636 original size:28 final size:28
Alignment explanation
Indices: 269616--269684 Score: 95
Period size: 28 Copynumber: 2.4 Consensus size: 28
269606 AAACCAAATT
269616 AAAGATTTGTTTCAAAAGAAACAAACCC
1 AAAGATTTGTTTCAAAAGAAACAAACCC
* *
269644 AAAGATTTGTTTCAAGAA-AAACATACTC
1 AAAGATTTGTTTCAA-AAGAAACAAACCC
269672 AAAGACTTTGTTT
1 AAAGA-TTTGTTT
269685 GTTTTGTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
28 28 0.76
29 9 0.24
ACGTcount: A:0.45, C:0.14, G:0.12, T:0.29
Consensus pattern (28 bp):
AAAGATTTGTTTCAAAAGAAACAAACCC
Found at i:270500 original size:66 final size:66
Alignment explanation
Indices: 270430--270555 Score: 175
Period size: 67 Copynumber: 1.9 Consensus size: 66
270420 AAACGGTTTC
* * *
270430 AAGAGATACAAAATTCAT-TTT-AAGAGAAACAGATTCAAAGATTTTTGTTTCAAAAGAAATTAT
1 AAGAGAGACAAAATT-ATGTTTCAA-AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTAT
270493 CTT
64 CTT
*
270496 AAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
1 AAGAGAGACAAAATTATGTTT-CAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAA
270556 CACTCTCAAA
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
65 1 0.02
66 17 0.32
67 33 0.62
68 2 0.04
ACGTcount: A:0.47, C:0.10, G:0.13, T:0.30
Consensus pattern (66 bp):
AAGAGAGACAAAATTATGTTTCAAAGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAATTATCT
T
Found at i:270543 original size:30 final size:30
Alignment explanation
Indices: 270509--270572 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 30
270499 AGAGACAAAA
*
270509 TTTTGTTTCCAAAGAAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
**
270539 TTTTGTTTCAAAAGAAACACTCTCAAAGAT
1 TTTTGTTTCAAAAGAAACAAACTCAAAGAT
270569 TTTT
1 TTTT
270573 TCACAAAATT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACAAACTCAAAGAT
Found at i:270634 original size:52 final size:53
Alignment explanation
Indices: 270560--270662 Score: 181
Period size: 52 Copynumber: 2.0 Consensus size: 53
270550 AAGAAACACT
*
270560 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAACACTTTGTTTCAGA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
270613 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
270663 AAATAAATAG
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
52 40 0.83
53 8 0.17
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:270719 original size:28 final size:29
Alignment explanation
Indices: 270659--270782 Score: 132
Period size: 29 Copynumber: 4.4 Consensus size: 29
270649 AAAACTTTGT
* *
270659 TTCAAAATAAATAGACTCAAAGAT-TTT-
1 TTCAAAAGAAACAGACTCAAAGATATTTA
270686 TTCAAAAGAAACA-ACTCAAAGATATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
* * * *
270714 TTCAAAAGGAACAAACTCCAAGATTTTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
270743 TTCAAAAGGAACAGACTCAAAG--ATTTA
1 TTCAAAAGAAACAGACTCAAAGATATTTA
*
270770 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
270783 TGTCTCCAGA
Statistics
Matches: 83, Mismatches: 10, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
26 10 0.12
27 19 0.23
28 21 0.25
29 33 0.40
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (29 bp):
TTCAAAAGAAACAGACTCAAAGATATTTA
Found at i:270742 original size:29 final size:29
Alignment explanation
Indices: 270673--270768 Score: 135
Period size: 29 Copynumber: 3.4 Consensus size: 29
270663 AAATAAATAG
*
270673 ACTCAAAGA-TTTT-TTCAAAAGAAAC-A
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
*
270699 ACTCAAAGATATTTATTCAAAAGGAACAA
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
* *
270728 ACTCCAAGATTTTTATTCAAAAGGAACAG
1 ACTCAAAGATTTTTATTCAAAAGGAACAA
270757 ACTCAAAGATTT
1 ACTCAAAGATTT
270769 ATCTCAAGAG
Statistics
Matches: 61, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
26 9 0.15
27 3 0.05
28 11 0.18
29 38 0.62
ACGTcount: A:0.47, C:0.16, G:0.10, T:0.27
Consensus pattern (29 bp):
ACTCAAAGATTTTTATTCAAAAGGAACAA
Found at i:270790 original size:57 final size:54
Alignment explanation
Indices: 270659--270782 Score: 133
Period size: 57 Copynumber: 2.2 Consensus size: 54
270649 AAAACTTTGT
* * * *
270659 TTCAAAATAAATAGACTCAAAGATTTTTTCAAAAGAAACAACTCAAAGATATTTA
1 TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGA-ATTTA
* *
270714 TTCAAAAGGAACAAACTCCAAGATTTTTATTCAAAAGGAACAGACTCAAAG-ATTTA
1 TTCAAAAGAAACAAACTCCAAGA-TTTT-TTCAAAAGAAACA-ACTCAAAGAATTTA
*
270770 TCTCAAGAGAAAC
1 T-TCAAAAGAAAC
270783 TGTCTCCAGA
Statistics
Matches: 57, Mismatches: 8, Indels: 6
0.80 0.11 0.08
Matches are distributed among these distances:
55 18 0.32
56 10 0.18
57 21 0.37
58 8 0.14
ACGTcount: A:0.48, C:0.15, G:0.10, T:0.26
Consensus pattern (54 bp):
TTCAAAAGAAACAAACTCCAAGATTTTTTCAAAAGAAACAACTCAAAGAATTTA
Found at i:271166 original size:36 final size:36
Alignment explanation
Indices: 271082--271185 Score: 124
Period size: 36 Copynumber: 3.0 Consensus size: 36
271072 AAAGGAAAAA
* * *
271082 TGTCTCAAGCGAGACGAAATTTG-CTTTA-AGATAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
* **
271116 AGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAAT
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
*
271152 TGTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAA
1 TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAA
271186 ACGATCTCAA
Statistics
Matches: 58, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
34 19 0.33
35 10 0.17
36 29 0.50
ACGTcount: A:0.36, C:0.12, G:0.20, T:0.33
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAAATTTGTTTTTAGAGAAAT
Found at i:271213 original size:36 final size:36
Alignment explanation
Indices: 271078--271201 Score: 112
Period size: 36 Copynumber: 3.5 Consensus size: 36
271068 TCTCAAAGGA
* * * *
271078 AAAATGTCTCAAGCGAGACGAAATTTG-CTTTA-AG
1 AAAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
* *
271112 ATATA-GTCTCAAATGAGACAAAATTTGTTTTTAGAG
1 A-AAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
** * *
271148 AAATTGTCTCAAGCGAGACAAAGTTTGTTTTT-GAG
1 AAAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
271183 AAAACGATCTCAAGTGAGA
1 AAAACG-TCTCAAGTGAGA
271202 TCAACTTTGT
Statistics
Matches: 72, Mismatches: 13, Indels: 8
0.77 0.14 0.09
Matches are distributed among these distances:
34 20 0.28
35 14 0.19
36 38 0.53
ACGTcount: A:0.38, C:0.12, G:0.20, T:0.30
Consensus pattern (36 bp):
AAAACGTCTCAAGTGAGACAAAATTTGTTTTTAGAG
Found at i:271332 original size:105 final size:101
Alignment explanation
Indices: 271153--271385 Score: 292
Period size: 105 Copynumber: 2.3 Consensus size: 101
271143 TAGAGAAATT
*
271153 GTCTCAAGCGAGAC-AAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAAT
1 GTCTCAAGCGAGACGAAA-TTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAAT
* *
271217 GTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
64 GTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
* *
271255 GTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACGAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* * *
271319 TAA-GTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
*
271360 GTCTCAAGCGAGACGAAGTTTGTTTT
1 GTCTCAAGCGAGACGAAATTTGTTTT
271386 AAGAGAATTT
Statistics
Matches: 115, Mismatches: 9, Indels: 11
0.85 0.07 0.08
Matches are distributed among these distances:
101 5 0.04
102 18 0.16
103 5 0.04
104 4 0.03
105 78 0.68
106 5 0.04
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.30
Consensus pattern (101 bp):
GTCTCAAGCGAGACGAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGGATCTCAAAGGAAAAAG
Found at i:271399 original size:36 final size:36
Alignment explanation
Indices: 271359--271440 Score: 94
Period size: 36 Copynumber: 2.3 Consensus size: 36
271349 AAAGGAAAAA
* * *
271359 TGTCTCAAGCGAGACGAAGTTTG-TTTTAAGAGAATT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAA-AGAAAT
* * *
271395 TGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAAT
1 TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
271431 TGTCTCAAGC
1 TGTCTCAAGC
271441 AAAACAAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
36 31 0.84
37 6 0.16
ACGTcount: A:0.32, C:0.12, G:0.20, T:0.37
Consensus pattern (36 bp):
TGTCTCAAGCGAGACAAACTTTGTTTTTAAAGAAAT
Found at i:271448 original size:36 final size:36
Alignment explanation
Indices: 271359--271453 Score: 93
Period size: 36 Copynumber: 2.6 Consensus size: 36
271349 AAAGGAAAAA
* * * *
271359 TGTCTCAAGCGAGACGAAGTTTGTTTTAAGAGAATT
1 TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
* * * *
271395 TGTCTTAAGTGATACAAACTTTGTTTTTAA-AGAAAT
1 TGTCTCAAGCGAAACAAAATTTG-TTTTAAGAGAAAT
*
271431 TGTCTCAAGCAAAACAAAATTTG
1 TGTCTCAAGCGAAACAAAATTTG
271454 AGAAAACGAT
Statistics
Matches: 47, Mismatches: 11, Indels: 2
0.78 0.18 0.03
Matches are distributed among these distances:
36 41 0.87
37 6 0.13
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.35
Consensus pattern (36 bp):
TGTCTCAAGCGAAACAAAATTTGTTTTAAGAGAAAT
Found at i:271479 original size:273 final size:268
Alignment explanation
Indices: 270920--271552 Score: 821
Period size: 273 Copynumber: 2.3 Consensus size: 268
270910 TTTTGAAAAA
* * * * *
270920 CTCAAGTGATATTAATTTTGTTTCAA-GT-ACAACAAATT-TAAATTTGTATCTCAGA-GAAAAA
1 CTCAAGTGAGATCAACTTTGTTT-AATGTGA-AACAAATTCGAAATTTGTATCTCAAAGGAAAAA
* * *
270981 TGTCTCAAGCGAAACGAAATTTGTTTCGAAATAAACAACAATATCAAGTGAGATTTTGTTTTAAG
64 TGTCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATATCAAGTGAGATTTTGTTTTAAG
271046 TGAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAA
129 TGAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAA
* * * *
271111 GATATAGTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATTGTCTCAAGCGAGACAAAGTTTGT
194 GAAATAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-----T
*
271176 TTTTGAGAAAACGAT
254 ATTTGAGAAAACGAT
* * *
271191 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAGG
1 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAGGAAAAATG
*
271256 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTTT
66 TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATATCAA-GTGAG----ATTTTGTTTT
* * * *
271320 AAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAGTTTGTTT
126 AAGTGAAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTT
* * * * *
271385 TAAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAA-
191 TAAGA-AA-TAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAAT
271449 ATTTGAGAAAACGAT
254 ATTTGAGAAAACGAT
*
271464 CTCAAGTGAGATCAACTTTGTTTAATGTGAATCAAATTCGAAATTTGTATCTC-AAGGAAAAATG
1 CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAGGAAAAATG
* * *
271528 TCTCCAGTGAGACGGAATTTGTTTT
66 TCTCAAGCGAGACGAAATTTGTTTT
271553 TCAAGAAATT
Statistics
Matches: 318, Mismatches: 33, Indels: 21
0.85 0.09 0.06
Matches are distributed among these distances:
270 2 0.01
271 30 0.09
272 48 0.15
273 114 0.36
277 76 0.24
278 1 0.00
279 47 0.15
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (268 bp):
CTCAAGTGAGATCAACTTTGTTTAATGTGAAACAAATTCGAAATTTGTATCTCAAAGGAAAAATG
TCTCAAGCGAGACGAAATTTGTTTTGAAAGAAACAACAATATCAAGTGAGATTTTGTTTTAAGTG
AAACAAATTCAAAATTAGTATCTCAAAGGAAAAATGTCTCAAGCGAGACGAAATTTGCTTTAAGA
AATAGTCTCAAATGAGACAAAATTTGTTTTTAAAGAAATTGTCTCAAGCAAAACAAATATTTGAG
AAAACGAT
Found at i:271496 original size:168 final size:166
Alignment explanation
Indices: 271301--271619 Score: 441
Period size: 167 Copynumber: 1.9 Consensus size: 166
271291 ACAATCTAAG
* *
271301 GTGAGATTAATTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAAGGAAAAATGTCTCA
1 GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTC-AAGGAAAAATGTCTCA
* * * *
271366 AGCGAGAC-GAAGTTTG-TTTT-AAGAGAATTTGTCTTAAGTGATACAAACTTTGTTTTTAAAGA
65 AGCGAGACGGAA-TTTGTTTTTCAAGA-AA-TTGTCTCAAATGAGACAAAATTTGTTTTT--AGA
271428 AA-TTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
125 AAGTTGTCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
* *
271469 GTGAGATCAACTTTG-TTTAATGTGAATCAAATTCGAAATTTGTATCTCAAGGAAAAATGTCTCC
1 GTGAGATCAACTTTGTTTTAA-GTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCA
*
271533 AGTGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAATGAGACAAAATTTGTTTTTAGAAAGTT
65 AGCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAATGAGACAAAATTTGTTTTTAGAAAGTT
* *
271598 GTCTCAAGCGAGACAAAATTTG
130 GTCTCAAGCAAAACAAAATTTG
271620 CTTTGAAAGA
Statistics
Matches: 135, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
165 5 0.04
166 22 0.16
167 56 0.41
168 48 0.36
169 4 0.03
ACGTcount: A:0.37, C:0.11, G:0.18, T:0.34
Consensus pattern (166 bp):
GTGAGATCAACTTTGTTTTAAGTGAATCAAATTCAAAATTTGTATCTCAAGGAAAAATGTCTCAA
GCGAGACGGAATTTGTTTTTCAAGAAATTGTCTCAAATGAGACAAAATTTGTTTTTAGAAAGTTG
TCTCAAGCAAAACAAAATTTGAGAAAACGATCTCAA
Found at i:271557 original size:38 final size:36
Alignment explanation
Indices: 271504--271660 Score: 120
Period size: 36 Copynumber: 4.3 Consensus size: 36
271494 ATCAAATTCG
* * * * *
271504 AAATTTGTATCTCAAGGAAAAATGTCTCCAGTGAGACG
1 AAATTTGTTTTTCAA-G-AAAATGTCTCAAATGAGACA
* *
271542 GAATTTGTTTTTCAAGAAATTGTCTCAAATGAGACA
1 AAATTTGTTTTTCAAGAAAATGTCTCAAATGAGACA
* **
271578 AAATTTGTTTTT--AGAAAGTTGTCTCAAGCGAGACA
1 AAATTTGTTTTTCAAGAAA-ATGTCTCAAATGAGACA
* ** * **
271613 AAATTTGCTTTGAAAGAAATTGTCTCAAGCGAGACAA
1 AAATTTGTTTTTCAAGAAAATGTCTCAAATGAGAC-A
271650 AAATTTGTTTT
1 AAATTTGTTTT
271661 AAAATTCTCA
Statistics
Matches: 102, Mismatches: 13, Indels: 9
0.82 0.10 0.07
Matches are distributed among these distances:
34 5 0.05
35 25 0.25
36 43 0.42
37 17 0.17
38 12 0.12
ACGTcount: A:0.36, C:0.12, G:0.18, T:0.33
Consensus pattern (36 bp):
AAATTTGTTTTTCAAGAAAATGTCTCAAATGAGACA
Found at i:271575 original size:36 final size:35
Alignment explanation
Indices: 271526--271660 Score: 155
Period size: 36 Copynumber: 3.8 Consensus size: 35
271516 CAAGGAAAAA
* **
271526 TGTCTCCAGTGAGACGGAATTTGTTTTTCAAGAAAT
1 TGTCTCAAGTGAGACAAAATTTGTTTTT-AAGAAAT
*
271562 TGTCTCAAATGAGACAAAATTTGTTTTT-AGAAAGT
1 TGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAA-T
* **
271597 TGTCTCAAGCGAGACAAAATTTGCTTTGAAAGAAAT
1 TGTCTCAAGTGAGACAAAATTTG-TTTTTAAGAAAT
*
271633 TGTCTCAAGCGAGACAAAAATTTGTTTT
1 TGTCTCAAGTGAGAC-AAAATTTGTTTT
271661 AAAATTCTCA
Statistics
Matches: 86, Mismatches: 9, Indels: 8
0.83 0.09 0.08
Matches are distributed among these distances:
34 5 0.06
35 22 0.26
36 46 0.53
37 13 0.15
ACGTcount: A:0.34, C:0.13, G:0.19, T:0.34
Consensus pattern (35 bp):
TGTCTCAAGTGAGACAAAATTTGTTTTTAAGAAAT
Found at i:272255 original size:4 final size:4
Alignment explanation
Indices: 272206--272243 Score: 53
Period size: 4 Copynumber: 10.0 Consensus size: 4
272196 TTTATGTATC
*
272206 ATGT ATGT ATG- -TGT ATGT ATGT ATAT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
272244 GTTGATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
2 2 0.07
4 28 0.93
ACGTcount: A:0.26, C:0.00, G:0.24, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:274107 original size:26 final size:23
Alignment explanation
Indices: 274076--274146 Score: 76
Period size: 20 Copynumber: 3.1 Consensus size: 23
274066 TCAAGGTGGA
274076 AAGAATATTTCAAGGTCTCAAAG
1 AAGAATATTTCAAGGTCTCAAAG
* *
274099 AGAGGGAATGTTTCAAGG--TCGAA-
1 A-A--GAATATTTCAAGGTCTCAAAG
274122 AAGAATATTTCAAGGTCTCAAAG
1 AAGAATATTTCAAGGTCTCAAAG
274145 AA
1 AA
274147 ATAGAATGTC
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
20 12 0.32
22 5 0.13
23 4 0.11
24 5 0.13
26 12 0.32
ACGTcount: A:0.42, C:0.11, G:0.23, T:0.24
Consensus pattern (23 bp):
AAGAATATTTCAAGGTCTCAAAG
Found at i:274132 original size:20 final size:20
Alignment explanation
Indices: 274064--274138 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
274054 AAATGCAATG
*
274064 TTTCAAGGT-GGAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
* *
274083 TTTCAAGGTCTCAAAGAGAGGGAATG
1 TTTCAAGG--TCGAA-A-A--GAATA
274109 TTTCAAGGTCGAAAAGAATA
1 TTTCAAGGTCGAAAAGAATA
274129 TTTCAAGGTC
1 TTTCAAGGTC
274139 TCAAAGAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 8 0.18
20 14 0.32
21 1 0.02
22 2 0.05
23 2 0.05
24 5 0.11
26 12 0.27
ACGTcount: A:0.37, C:0.11, G:0.25, T:0.27
Consensus pattern (20 bp):
TTTCAAGGTCGAAAAGAATA
Found at i:274152 original size:26 final size:25
Alignment explanation
Indices: 274075--274153 Score: 78
Period size: 26 Copynumber: 3.3 Consensus size: 25
274065 TTCAAGGTGG
274075 AAAGAATATTTCAAGGTCTCAAAGA
1 AAAGAATATTTCAAGGTCTCAAAGA
** *
274100 GAGGGAATGTTTCAAGG--TC---GA
1 -AAAGAATATTTCAAGGTCTCAAAGA
274121 AAAGAATATTTCAAGGTCTCAAAGA
1 AAAGAATATTTCAAGGTCTCAAAGA
274146 AATAGAAT
1 AA-AGAAT
274154 GTCAAAAATT
Statistics
Matches: 41, Mismatches: 6, Indels: 12
0.69 0.10 0.20
Matches are distributed among these distances:
20 13 0.32
21 2 0.05
22 2 0.05
24 2 0.05
25 4 0.10
26 18 0.44
ACGTcount: A:0.44, C:0.10, G:0.22, T:0.24
Consensus pattern (25 bp):
AAAGAATATTTCAAGGTCTCAAAGA
Found at i:274154 original size:46 final size:45
Alignment explanation
Indices: 274060--274155 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 45
274050 AAATAAATGC
* * *
274060 AATGTTTCAAGGTGGAAAGAATATTTCAAGGTCTCAAAGAGAGGG
1 AATGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAAAGAG
*
274105 AATGTTTCAAGGTCGAAAAGAATATTTCAAGGTCTCAAAGAAATAG
1 AATGTTTCAAGGT-GAAAAGAATATTTCAAGGTCTCAAAGAAAGAG
274151 AATGT
1 AATGT
274156 CAAAAATTGG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
45 13 0.28
46 33 0.72
ACGTcount: A:0.41, C:0.09, G:0.24, T:0.26
Consensus pattern (45 bp):
AATGTTTCAAGGTGAAAAGAATATTTCAAGGTCTCAAAGAAAGAG
Found at i:276767 original size:48 final size:49
Alignment explanation
Indices: 276699--276824 Score: 161
Period size: 50 Copynumber: 2.6 Consensus size: 49
276689 GAATATAACA
* * *
276699 CCTACCC-GACATGATATCTACCCTAACA-TGCTTT-AA-AAGATAACGAT
1 CCTACCCGGACATGCTATCTACCC-AAAATTGCTTTCAATAA-ATAACAAT
*
276746 CCTACCCGGACATGCTTTCTACCCAAAATTGCTTTCAATTAAATAACAAT
1 CCTACCCGGACATGCTATCTACCCAAAATTGCTTTCAA-TAAATAACAAT
276796 CCTACCCGGACATGCTATCTACCCAAAAT
1 CCTACCCGGACATGCTATCTACCCAAAAT
276825 GATCTATTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
47 10 0.14
48 20 0.29
49 2 0.03
50 35 0.51
51 2 0.03
ACGTcount: A:0.34, C:0.30, G:0.10, T:0.26
Consensus pattern (49 bp):
CCTACCCGGACATGCTATCTACCCAAAATTGCTTTCAATAAATAACAAT
Found at i:278467 original size:2 final size:2
Alignment explanation
Indices: 278462--278512 Score: 75
Period size: 2 Copynumber: 25.5 Consensus size: 2
278452 ACACACATAA
* * *
278462 AT AT AT AC AT AA AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
278504 AT AT AT AT A
1 AT AT AT AT A
278513 AAACATCTAA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:278473 original size:12 final size:12
Alignment explanation
Indices: 278456--278506 Score: 66
Period size: 12 Copynumber: 4.1 Consensus size: 12
278446 AATTAAACAC
278456 ACATAAATATAT
1 ACATAAATATAT
278468 ACATAAATATAT
1 ACATAAATATAT
*
278480 ATATATATATATAT
1 ACATA-A-ATATAT
*
278494 ACATATATATAT
1 ACATAAATATAT
278506 A
1 A
278507 TATATAAAAC
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
12 23 0.68
13 1 0.03
14 10 0.29
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (12 bp):
ACATAAATATAT
Found at i:278606 original size:16 final size:16
Alignment explanation
Indices: 278587--278621 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
278577 TTTAAAAAAC
* *
278587 AAAAGGACTAAATTAT
1 AAAAGGACAAAATGAT
278603 AAAAGGACAAAATGAT
1 AAAAGGACAAAATGAT
278619 AAA
1 AAA
278622 GCATAAATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.63, C:0.06, G:0.14, T:0.17
Consensus pattern (16 bp):
AAAAGGACAAAATGAT
Found at i:279895 original size:14 final size:14
Alignment explanation
Indices: 279876--279936 Score: 50
Period size: 14 Copynumber: 4.0 Consensus size: 14
279866 CGTAATGACT
*
279876 ATCGCAACGAGAGA
1 ATCGCAACGAGAAA
279890 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
*
279909 ATCGCAACGAGATA
1 ATCGCAACGAGAAA
*
279923 ATCGCAACGTGAAA
1 ATCGCAACGAGAAA
279937 CCAAAATCGC
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
14 22 0.58
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 10 0.26
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:279906 original size:33 final size:33
Alignment explanation
Indices: 279857--279947 Score: 110
Period size: 33 Copynumber: 2.8 Consensus size: 33
279847 AAGAATGACT
* * **
279857 ATCGCAATGCGTAATGACTATCGCAACGAGAGA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
*
279890 ATCGCAACGCGAAATGAAAATCGCAACGAGATA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
* **
279923 ATCGCAACGTGAAACCAAAATCGCA
1 ATCGCAACGCGAAATGAAAATCGCA
279948 TTGCGATTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 50 1.00
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAGA
Found at i:279980 original size:21 final size:21
Alignment explanation
Indices: 279954--280032 Score: 85
Period size: 20 Copynumber: 3.9 Consensus size: 21
279944 CGCATTGCGA
*
279954 TTCTCTCGTTACGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
**
279975 TTCTCTCGTTGCGATAGTCAT
1 TTCTCTCGTTGCGATTTTCAT
279996 TT-TCGT-GTTGCGATTTTCAT
1 TTCTC-TCGTTGCGATTTTCAT
280016 TT-TCAT-GTTGCGATTTT
1 TTCTC-TCGTTGCGATTTT
280033 AAGTTTAGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
20 30 0.59
21 21 0.41
ACGTcount: A:0.13, C:0.19, G:0.16, T:0.52
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:280798 original size:21 final size:21
Alignment explanation
Indices: 280598--280801 Score: 154
Period size: 20 Copynumber: 10.0 Consensus size: 21
280588 CGAGTTGTGA
* *
280598 TTTACGAAAACGCGTTGCGAT
1 TTTACGGATACGCGTTGCGAT
* *
280619 TTTACGTAT-TGTCGTTGCGA-
1 TTTACGGATACG-CGTTGCGAT
**
280639 TTTACGGATACGTATTGCGA-
1 TTTACGGATACGCGTTGCGAT
* * *
280659 TTTACGTATTCTCGTTGCGA-
1 TTTACGGATACGCGTTGCGAT
*
280679 TTTACAGATACGCGTTGCGA-
1 TTTACGGATACGCGTTGCGAT
** * *
280699 TTTACATATTCTCGTTGCGA-
1 TTTACGGATACGCGTTGCGAT
280719 TTTACGGATACGCGTTGCGAT
1 TTTACGGATACGCGTTGCGAT
* *
280740 TTTACGTAT-TGTCGTTGCGA-
1 TTTACGGATACG-CGTTGCGAT
* *
280760 TTTACGGATAAGCGTTGCAAT
1 TTTACGGATACGCGTTGCGAT
* *
280781 TTTACGGATACTCATTGCGAT
1 TTTACGGATACGCGTTGCGAT
280802 AGTCAGAATC
Statistics
Matches: 145, Mismatches: 32, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
20 95 0.66
21 50 0.34
ACGTcount: A:0.22, C:0.18, G:0.23, T:0.38
Consensus pattern (21 bp):
TTTACGGATACGCGTTGCGAT
Found at i:280799 original size:41 final size:41
Alignment explanation
Indices: 280591--280801 Score: 282
Period size: 41 Copynumber: 5.2 Consensus size: 41
280581 TAAAAATCGA
* * * *
280591 GTTGTGATTTACGAAAACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
**
280632 GTTGCGATTTACGGATACGTATTGCGA-TTTACGTATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* *
280672 GTTGCGATTTACAGATACGCGTTGCGA-TTTACATATTCTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
280712 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTGTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
* * * *
280753 GTTGCGATTTACGGATAAGCGTTGCAATTTTACGGATACTC
1 GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
*
280794 ATTGCGAT
1 GTTGCGAT
280802 AGTCAGAATC
Statistics
Matches: 150, Mismatches: 19, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
40 74 0.49
41 76 0.51
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (41 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTTACGTATTCTC
Found at i:281804 original size:80 final size:80
Alignment explanation
Indices: 281666--281825 Score: 259
Period size: 80 Copynumber: 2.0 Consensus size: 80
281656 TAAGCTCTGT
** *
281666 TATGCATGGTGAGATAGAATTTGTAGAGTATTTAGAGAATGCGATGAAAATTTTTTAAAAACGGA
1 TATGCATGGTGAGATAGAATTTGTAGAGTATTTAGAGAATGCGATGAAAAAATGTTAAAAACGGA
281731 ATAACATTGTTTTTG
66 ATAACATTGTTTTTG
* *
281746 TATGCATGGTGAGATCGAATTTGTAGAGTATTTAGAGAATG-TACTGAAAAAATGTTAAAAACGG
1 TATGCATGGTGAGATAGAATTTGTAGAGTATTTAGAGAATGCGA-TGAAAAAATGTTAAAAACGG
281810 AATAACATTGTTTTTG
65 AATAACATTGTTTTTG
281826 CTAATAAAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
79 1 0.01
80 73 0.99
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.35
Consensus pattern (80 bp):
TATGCATGGTGAGATAGAATTTGTAGAGTATTTAGAGAATGCGATGAAAAAATGTTAAAAACGGA
ATAACATTGTTTTTG
Done.