Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007729.1 Hibiscus syriacus cultivar Beakdansim tig00109980_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: 1111098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:283295 original size:6 final size:6
Alignment explanation
Indices: 283284--283346 Score: 108
Period size: 6 Copynumber: 10.5 Consensus size: 6
283274 GACACGTATT
* *
283284 ACCACG ACCACG ACCACG ACCACG ACCACG ATCACG ACCACA ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
283332 ACCACG ACCACG ACC
1 ACCACG ACCACG ACC
283347 CGAGACGAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.35, C:0.49, G:0.14, T:0.02
Consensus pattern (6 bp):
ACCACG
Found at i:284069 original size:21 final size:21
Alignment explanation
Indices: 284043--284248 Score: 137
Period size: 21 Copynumber: 9.9 Consensus size: 21
284033 GAATATGTAA
*
284043 ATCGCAATGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
* *
284064 ATCGCAATGCGA-ACTTCGACT
1 ATCGCATTGCGATA-GTCGACT
* *
284085 ATCGCAATGCGA-ACTTCGACT
1 ATCGCATTGCGATA-GTCGACT
*
284106 ATCGCATTGCGAT--T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
284125 ATTCGCATTGCGATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
* *
284148 -TCGCATTGCGATAGTCCAAGT
1 ATCGCATTGCGATAGT-CGACT
284169 -TCGCATTGCGATAGTCGACT
1 ATCGCATTGCGATAGTCGACT
*
284189 ATCGCATTGCGA-A-T-TACAT
1 ATCGCATTGCGATAGTCGAC-T
* *
284208 ATTCGCATTGCGATAGTCCAAGT
1 A-TCGCATTGCGATAGT-CGACT
284231 -TCGCATTGCGATAGTCGA
1 ATCGCATTGCGATAGTCGA
284249 AGTTCGCGTT
Statistics
Matches: 159, Mismatches: 11, Indels: 31
0.79 0.05 0.15
Matches are distributed among these distances:
18 4 0.03
19 6 0.04
20 30 0.19
21 113 0.71
22 2 0.01
23 2 0.01
24 2 0.01
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (21 bp):
ATCGCATTGCGATAGTCGACT
Found at i:284173 original size:62 final size:62
Alignment explanation
Indices: 284127--284248 Score: 201
Period size: 62 Copynumber: 2.0 Consensus size: 62
284117 ATTTACATAT
*
284127 TCGCATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
1 TCGCATTGCGA-AGTACATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
*
284190 TCGCATTGCGAATTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
1 TCGCATTGCGAAGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGA
284249 AGTTCGCGTT
Statistics
Matches: 56, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
62 44 0.79
63 12 0.21
ACGTcount: A:0.25, C:0.23, G:0.23, T:0.30
Consensus pattern (62 bp):
TCGCATTGCGAAGTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTA
Found at i:284244 original size:83 final size:83
Alignment explanation
Indices: 284100--284262 Score: 299
Period size: 83 Copynumber: 2.0 Consensus size: 83
284090 AATGCGAACT
*
284100 TCGACTATCGCATTGCGATTTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCC
1 TCGACTATCGCATTGCGAATTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCC
284165 AAGTTCGCATTGCGATAG
66 AAGTTCGCATTGCGATAG
*
284183 TCGACTATCGCATTGCGAATTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCG
1 TCGACTATCGCATTGCGAATTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCC
*
284248 AAGTTCGCGTTGCGA
66 AAGTTCGCATTGCGA
284263 ATCTGAAAAC
Statistics
Matches: 77, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
83 77 1.00
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.31
Consensus pattern (83 bp):
TCGACTATCGCATTGCGAATTACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCC
AAGTTCGCATTGCGATAG
Found at i:284251 original size:21 final size:21
Alignment explanation
Indices: 284126--284262 Score: 181
Period size: 21 Copynumber: 6.6 Consensus size: 21
284116 GATTTACATA
284126 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
284147 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
* *
284168 TTCGCATTGCGATAGT-CGAC
1 TTCGCATTGCGATAGTCCAAG
* *
284188 TATCGCATTGCGA-ATTACATA-
1 T-TCGCATTGCGATAGTCCA-AG
284209 TTCGCATTGCGATAGTCCAAG
1 TTCGCATTGCGATAGTCCAAG
*
284230 TTCGCATTGCGATAGTCGAAG
1 TTCGCATTGCGATAGTCCAAG
*
284251 TTCGCGTTGCGA
1 TTCGCATTGCGA
284263 ATCTGAAAAC
Statistics
Matches: 103, Mismatches: 8, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
20 17 0.17
21 85 0.83
22 1 0.01
ACGTcount: A:0.23, C:0.23, G:0.24, T:0.30
Consensus pattern (21 bp):
TTCGCATTGCGATAGTCCAAG
Found at i:284490 original size:21 final size:21
Alignment explanation
Indices: 284461--284520 Score: 70
Period size: 20 Copynumber: 2.9 Consensus size: 21
284451 GTCAATATAT
284461 ATATAAATAATATTTATTTAGC
1 ATATAAATAATATTTATTTA-C
* * *
284483 ATA-AAATAA-ATATATATAT
1 ATATAAATAATATTTATTTAC
284502 ATATAAATAATATTTATTT
1 ATATAAATAATATTTATTT
284521 TATGAAAATA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
19 3 0.10
20 13 0.42
21 12 0.39
22 3 0.10
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (21 bp):
ATATAAATAATATTTATTTAC
Found at i:286539 original size:20 final size:20
Alignment explanation
Indices: 286514--286561 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
286504 AACATTGCCA
286514 GTAATCTTTTATTCTCACTG
1 GTAATCTTTTATTCTCACTG
286534 GTAATCTTTTATTCTCACTG
1 GTAATCTTTTATTCTCACTG
*
286554 ATAATCTT
1 GTAATCTT
286562 ACATTCCGTG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.23, C:0.19, G:0.08, T:0.50
Consensus pattern (20 bp):
GTAATCTTTTATTCTCACTG
Found at i:286567 original size:20 final size:20
Alignment explanation
Indices: 286524--286567 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
286514 GTAATCTTTT
* **
286524 ATTCTCACTGGTAATCTTTT
1 ATTCTCACTGATAATCTTAC
286544 ATTCTCACTGATAATCTTAC
1 ATTCTCACTGATAATCTTAC
286564 ATTC
1 ATTC
286568 CGTGAACCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.25, C:0.23, G:0.07, T:0.45
Consensus pattern (20 bp):
ATTCTCACTGATAATCTTAC
Found at i:286674 original size:18 final size:18
Alignment explanation
Indices: 286632--286673 Score: 77
Period size: 18 Copynumber: 2.4 Consensus size: 18
286622 GCACCTTCGC
286632 ATGTTTTAAAAAATTCAT
1 ATGTTTTAAAAAATTCAT
286650 ATGTTTTAAAAAATTCAT
1 ATGTTTTAAAAAATTCAT
286668 AT-TTTT
1 ATGTTTT
286674 TTTGAAATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 4 0.17
18 20 0.83
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (18 bp):
ATGTTTTAAAAAATTCAT
Found at i:287390 original size:3 final size:3
Alignment explanation
Indices: 287382--287407 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
287372 ATTGATTGCT
287382 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
287408 TCCTTCTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:290578 original size:230 final size:227
Alignment explanation
Indices: 290149--290584 Score: 614
Period size: 230 Copynumber: 1.9 Consensus size: 227
290139 TTATTTCGGG
* *
290149 TCGGGTCGAGTTCGGGTTTAGGGTAAGAAATACCCGACCCAAAAATATATATAATTTTACTTTAT
1 TCGGGTCGAGTTCGGGTTTAGGGTAAGAAATACCCGACCCAAAAAAATATATAATTTTACCTTAT
* *
290214 ATATTTAGGAATAATTACAAAAATACCCCTCTATATATAATTTTTTTCAATTAAGTCATTGTTTT
66 ATATTTAGGAATAATTACAAAAATACCCCTCTATATATAATTTTTTTCAATTAAGCCACTGTTTT
* * * * **
290279 TATTGAATAAAAATAATTTTTTTATTATTTTGGGTCGGGTCGAGTCAGGTGAAACTTTATTTTGG
131 TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTCGAGTCAGCTGAAACTATATTCAGG
290344 TCGGGTCAGGTCGGTTTTTTTAAGTGTGATAT
196 TCGGGTCAGGTCGGTTTTTTTAAGTGTGATAT
290376 TCGGGTCG-GTTCGGGTTTAGGGTGAA-AAATACCCGACCCGACCCGAAAAAATATATAATTTTA
1 TCGGGTCGAGTTCGGGTTTAGGGT-AAGAAATACCCGACCC-A----AAAAAATATATAATTTTA
* *
290439 CCTTATATA-TTAGGAATAATTATAATAATACCCCTCTATATATAAATTTTTTTCAATTAAGCCA
60 CCTTATATATTTAGGAATAATTACAAAAATACCCCTCTATATAT-AATTTTTTTCAATTAAGCCA
** *
290503 CTGTTTTT-TTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTCGAGT-TTCT-AATTCAT
124 CTGTTTTTATTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTCGAGTCAGCTGAA-AC-T
290565 ATATTCAGGTCGGGTCAGGT
187 ATATTCAGGTCGGGTCAGGT
290585 GAAACTTTAT
Statistics
Matches: 185, Mismatches: 15, Indels: 15
0.86 0.07 0.07
Matches are distributed among these distances:
226 28 0.15
227 11 0.06
228 2 0.01
229 2 0.01
230 91 0.49
231 51 0.28
ACGTcount: A:0.31, C:0.13, G:0.17, T:0.39
Consensus pattern (227 bp):
TCGGGTCGAGTTCGGGTTTAGGGTAAGAAATACCCGACCCAAAAAAATATATAATTTTACCTTAT
ATATTTAGGAATAATTACAAAAATACCCCTCTATATATAATTTTTTTCAATTAAGCCACTGTTTT
TATTGAATAAAAATAATTTTTTTATTATTTCGGGTCAGGTCGAGTCAGCTGAAACTATATTCAGG
TCGGGTCAGGTCGGTTTTTTTAAGTGTGATAT
Found at i:290782 original size:16 final size:16
Alignment explanation
Indices: 290763--290805 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
290753 ATAAATAAAA
290763 TTAAA-ATTTAATATTT
1 TTAAATATTTAA-ATTT
*
290779 TTAAATTTTTAAATTT
1 TTAAATATTTAAATTT
*
290795 TTAAATTTTTA
1 TTAAATATTTA
290806 TAATATATTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
16 20 0.80
17 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (16 bp):
TTAAATATTTAAATTT
Found at i:290788 original size:8 final size:8
Alignment explanation
Indices: 290769--290805 Score: 65
Period size: 8 Copynumber: 4.5 Consensus size: 8
290759 AAAATTAAAA
290769 TTTAATATT
1 TTTAA-ATT
290778 TTTAAATT
1 TTTAAATT
290786 TTTAAATT
1 TTTAAATT
290794 TTTAAATT
1 TTTAAATT
290802 TTTA
1 TTTA
290806 TAATATATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
8 23 0.82
9 5 0.18
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (8 bp):
TTTAAATT
Found at i:290974 original size:43 final size:43
Alignment explanation
Indices: 290913--290995 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
290903 ATCTGACATG
* * *
290913 TCTGCGAACCAAACAGAATATGGAATTGGATTCTAATTCAATT
1 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCAATT
290956 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCA
1 TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCA
290996 TGACAGGTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (43 bp):
TCTGCCAACCAAACAGAATATGAAATTGGATTCCAATTCAATT
Found at i:296976 original size:17 final size:17
Alignment explanation
Indices: 296956--296993 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
296946 AATTTAATTT
*
296956 TATATCTTGAAATTTTA
1 TATATCTTAAAATTTTA
*
296973 TATATTTTAAAATTTTA
1 TATATCTTAAAATTTTA
296990 -ATAT
1 TATAT
296994 AATTTCTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (17 bp):
TATATCTTAAAATTTTA
Found at i:299912 original size:60 final size:58
Alignment explanation
Indices: 299827--299962 Score: 170
Period size: 60 Copynumber: 2.3 Consensus size: 58
299817 TTTCCATGAA
* * *
299827 TTTGGGAATGAAGTTGGAATATTCAAAAGTTCAAGGA-TCAATTTAGAATGATACTCATAG
1 TTTGGGGATGAAATTAGAATATTCAAAAGTTCAAGGACT-AATTTAGAATG--ACTCATAG
* * *
299887 TTTGGGGATGAAATTAGAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAGTCATAG
1 TTTGGGGATGAAATTAGAATATTCAAAAGTTCAAGGACTAATTTAGAATGACTCATAG
299945 -TT-GGGATGAAATTAGAAT
1 TTTGGGGATGAAATTAGAAT
299963 CTCAAATTAC
Statistics
Matches: 69, Mismatches: 6, Indels: 6
0.85 0.07 0.07
Matches are distributed among these distances:
56 16 0.23
57 2 0.03
58 7 0.10
60 43 0.62
61 1 0.01
ACGTcount: A:0.38, C:0.06, G:0.24, T:0.32
Consensus pattern (58 bp):
TTTGGGGATGAAATTAGAATATTCAAAAGTTCAAGGACTAATTTAGAATGACTCATAG
Found at i:302347 original size:3 final size:3
Alignment explanation
Indices: 302334--302379 Score: 83
Period size: 3 Copynumber: 15.0 Consensus size: 3
302324 GATCCCATAT
302334 TAA TCAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
302380 AGTAACAAAT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:306020 original size:22 final size:20
Alignment explanation
Indices: 305988--306040 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
305978 CCATGAGGAG
*
305988 GTATCGATACCCTTGAAGGGTA
1 GTATCGATACCATT--AGGGTA
*
306010 GTATCGGTACCATTAGGGTA
1 GTATCGATACCATTAGGGTA
*
306030 GTACCGATACC
1 GTATCGATACC
306041 TCTAAGTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 15 0.56
22 12 0.44
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
GTATCGATACCATTAGGGTA
Found at i:306415 original size:21 final size:21
Alignment explanation
Indices: 306389--306439 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
306379 ATATTATGGA
306389 AATGTGAACTATGAATAAGTG
1 AATGTGAACTATGAATAAGTG
* * *
306410 AATGTGAACTTTGAATCATTG
1 AATGTGAACTATGAATAAGTG
306431 AATGTGAAC
1 AATGTGAAC
306440 AAACTCTATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.39, C:0.08, G:0.22, T:0.31
Consensus pattern (21 bp):
AATGTGAACTATGAATAAGTG
Found at i:309303 original size:12 final size:12
Alignment explanation
Indices: 309281--309315 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
309271 TTAACATTCG
*
309281 GGTATTGTTCAC
1 GGTACTGTTCAC
*
309293 GTTACTGTTCAC
1 GGTACTGTTCAC
309305 GGTACTGTTCA
1 GGTACTGTTCA
309316 TTAATGTTCA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.17, C:0.20, G:0.23, T:0.40
Consensus pattern (12 bp):
GGTACTGTTCAC
Found at i:309569 original size:21 final size:21
Alignment explanation
Indices: 309527--309575 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
309517 TCGAGGGTCT
**
309527 TATGTGGTCCTTTGAGACAAA
1 TATGTGGTCCTCCGAGACAAA
* *
309548 TATGTGGTCCTCCGGGATAAA
1 TATGTGGTCCTCCGAGACAAA
309569 TATGTGG
1 TATGTGG
309576 CACTTCGGTG
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.24, C:0.14, G:0.29, T:0.33
Consensus pattern (21 bp):
TATGTGGTCCTCCGAGACAAA
Found at i:309590 original size:21 final size:22
Alignment explanation
Indices: 309569--309636 Score: 79
Period size: 21 Copynumber: 3.1 Consensus size: 22
309559 CCGGGATAAA
309569 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
*
309591 CTATATGGTCA-TTCGG-G-ATAAT
1 -TATGTGG-CACTTCGGTGCA-AAT
309613 TATGTGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGCAAAT
309635 TA
1 TA
309637 CGAGCTGTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
20 2 0.05
21 12 0.32
22 10 0.26
23 12 0.32
24 2 0.05
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.34
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGCAAAT
Found at i:309921 original size:65 final size:65
Alignment explanation
Indices: 309813--309947 Score: 254
Period size: 65 Copynumber: 2.1 Consensus size: 65
309803 CTAAATAAGA
309813 TTTT-TGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTT
1 TTTTCTGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTT
*
309877 TTTTCTGTTAATAAGTTAGCACTATTAGTATTGCTTCACTAAGTCATCGACTTAGCGTGTGTGTT
1 TTTTCTGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTT
309942 TTTTCT
1 TTTTCT
309948 TGCGTAGGTT
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
64 4 0.06
65 65 0.94
ACGTcount: A:0.22, C:0.16, G:0.18, T:0.44
Consensus pattern (65 bp):
TTTTCTGTTAATAAGTTAGCACTATTAGTATTGCCTCACTAAGTCATCGACTTAGCGTGTGTGTT
Found at i:315879 original size:20 final size:21
Alignment explanation
Indices: 315816--315888 Score: 78
Period size: 20 Copynumber: 3.5 Consensus size: 21
315806 TATAAGGGTT
* *
315816 GTATCGATACCTGTTGATGATG
1 GTATCGATACCTG-TAATGATA
* *
315838 GTATCGATACC-GTAAGGGTA
1 GTATCGATACCTGTAATGATA
315858 GTATCGATACCTG-AATGATA
1 GTATCGATACCTGTAATGATA
*
315878 GTATTGATACC
1 GTATCGATACC
315889 CTTGAAACAT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 30 0.70
21 2 0.05
22 11 0.26
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.32
Consensus pattern (21 bp):
GTATCGATACCTGTAATGATA
Found at i:315887 original size:40 final size:41
Alignment explanation
Indices: 315808--315888 Score: 110
Period size: 42 Copynumber: 2.0 Consensus size: 41
315798 GAGTATTTTA
* * *
315808 TAAGGGTTGTATCGATACCTGTTGATGATGGTATCGATACCG
1 TAAGGGTAGTATCGATACCTG-TAATGATAGTATCGATACCG
*
315850 TAAGGGTAGTATCGATACCTG-AATGATAGTATTGATACC
1 TAAGGGTAGTATCGATACCTGTAATGATAGTATCGATACC
315889 CTTGAAACAT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
40 15 0.43
42 20 0.57
ACGTcount: A:0.28, C:0.14, G:0.26, T:0.32
Consensus pattern (41 bp):
TAAGGGTAGTATCGATACCTGTAATGATAGTATCGATACCG
Found at i:315973 original size:20 final size:20
Alignment explanation
Indices: 315912--315976 Score: 62
Period size: 22 Copynumber: 3.2 Consensus size: 20
315902 ATGTTATTTC
*
315912 AGTATCGGTACCATGA-GG-
1 AGTATCGGTACCATTAGGGT
* *
315930 AGGTATCGATACCCTTGAAGGGT
1 A-GTATCGGTACCATT--AGGGT
315953 AGTATCGGTACCATTAGGGT
1 AGTATCGGTACCATTAGGGT
315973 AGTA
1 AGTA
315977 CTGATACCTC
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
18 1 0.03
19 11 0.30
20 9 0.24
21 1 0.03
22 14 0.38
23 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.31, T:0.26
Consensus pattern (20 bp):
AGTATCGGTACCATTAGGGT
Found at i:316358 original size:21 final size:21
Alignment explanation
Indices: 316332--316382 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
316322 ATATTATGGA
316332 AATGTGAACTCTGAATAAGTG
1 AATGTGAACTCTGAATAAGTG
* * *
316353 AATGTGAACTTTGAATCATTG
1 AATGTGAACTCTGAATAAGTG
*
316374 AATATGAAC
1 AATGTGAAC
316383 AAACTCTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (21 bp):
AATGTGAACTCTGAATAAGTG
Found at i:316542 original size:21 final size:21
Alignment explanation
Indices: 316516--316593 Score: 95
Period size: 21 Copynumber: 3.7 Consensus size: 21
316506 TCGAGGGTCT
316516 TATGTGGTCCTTCGGGACAAA
1 TATGTGGTCCTTCGGGACAAA
* *
316537 TATGTGGTCTTTCGAGACAAA
1 TATGTGGTCCTTCGGGACAAA
* * *
316558 TATGTGGTTCTCCGGAACAAA
1 TATGTGGTCCTTCGGGACAAA
316579 TATGTGG-CACTTCGG
1 TATGTGGTC-CTTCGG
316594 TGTAAATCTA
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
21 47 1.00
ACGTcount: A:0.24, C:0.18, G:0.27, T:0.31
Consensus pattern (21 bp):
TATGTGGTCCTTCGGGACAAA
Found at i:316606 original size:23 final size:22
Alignment explanation
Indices: 316579--316646 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 22
316569 CCGGAACAAA
*
316579 TATGTGGCACTTCGGTGTAAAT
1 TATGTGGCACTTCGGTGAAAAT
*
316601 CTATGTGGTC-TTTCGG-GAAAAT
1 -TATGTGG-CACTTCGGTGAAAAT
* *
316623 TATATGGCACTTCGGTGCAAAT
1 TATGTGGCACTTCGGTGAAAAT
316645 TA
1 TA
316647 CGAGCTGTAG
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
20 1 0.03
21 11 0.30
22 12 0.32
23 12 0.32
24 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (22 bp):
TATGTGGCACTTCGGTGAAAAT
Found at i:321383 original size:16 final size:16
Alignment explanation
Indices: 321364--321394 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
321354 ATATAATATA
321364 ATATAATGAATTATTT
1 ATATAATGAATTATTT
*
321380 ATATTATGAATTATT
1 ATATAATGAATTATT
321395 AGATTTTGTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (16 bp):
ATATAATGAATTATTT
Found at i:323777 original size:21 final size:21
Alignment explanation
Indices: 323735--323777 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
323725 TTTCTGGGCT
* *
323735 AGGGGAATCGGTACCCATTCA
1 AGGGGAATCGATACCCACTCA
* *
323756 AGGGGAATCGATTCCCCCTCA
1 AGGGGAATCGATACCCACTCA
323777 A
1 A
323778 ACGAATATGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.28, C:0.28, G:0.26, T:0.19
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:328695 original size:32 final size:32
Alignment explanation
Indices: 328654--328750 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
328644 GAGTCGAGGG
*
328654 TTTACCTATGTTCTACGGAACATATAGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
*
328686 TTTACCTATG-TCTTTC-GAGACATATGGACAG-
1 TTTACCTATGTTC-TACGGA-ACATATGGACAGT
* *
328717 TATACCTATGTTCTAAGGAACATATGGACAGT
1 TTTACCTATGTTCTACGGAACATATGGACAGT
328749 TT
1 TT
328751 ACCGAGGATC
Statistics
Matches: 54, Mismatches: 6, Indels: 10
0.77 0.09 0.14
Matches are distributed among these distances:
31 26 0.48
32 28 0.52
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (32 bp):
TTTACCTATGTTCTACGGAACATATGGACAGT
Found at i:328726 original size:31 final size:31
Alignment explanation
Indices: 328653--328753 Score: 116
Period size: 31 Copynumber: 3.2 Consensus size: 31
328643 AGAGTCGAGG
*
328653 GTTTACCTATGTTCT-ACGGAACATATAGACA
1 GTTTACCTATGTTCTAAC-GAACATATGGACA
**
328684 GTTTTACCTATG-TCTTTCGAGACATATGGACA
1 G-TTTACCTATGTTCTAACGA-ACATATGGACA
* *
328716 GTATACCTATGTTCTAAGGAACATATGGACA
1 GTTTACCTATGTTCTAACGAACATATGGACA
328747 GTTTACC
1 GTTTACC
328754 GAGGATCTTT
Statistics
Matches: 59, Mismatches: 7, Indels: 8
0.80 0.09 0.11
Matches are distributed among these distances:
31 32 0.54
32 27 0.46
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (31 bp):
GTTTACCTATGTTCTAACGAACATATGGACA
Found at i:328785 original size:30 final size:30
Alignment explanation
Indices: 328741--328834 Score: 127
Period size: 30 Copynumber: 3.1 Consensus size: 30
328731 AAGGAACATA
328741 TGGACAGTTTACCGAGGATCTTTATGACCTC
1 TGGACAG-TTACCGAGGATCTTTATGACCTC
328772 TGGACAGTTACCGAGGATCTTTATGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
* * * * *
328802 TGAATAGTTACCG-GGGTCTGTGTGACCTC
1 TGGACAGTTACCGAGGATCTTTATGACCTC
328831 TGGA
1 TGGA
328835 TAGGTCCTTC
Statistics
Matches: 57, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
29 16 0.28
30 34 0.60
31 7 0.12
ACGTcount: A:0.21, C:0.21, G:0.27, T:0.31
Consensus pattern (30 bp):
TGGACAGTTACCGAGGATCTTTATGACCTC
Found at i:331450 original size:29 final size:29
Alignment explanation
Indices: 331408--331467 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
331398 AAACCCTAAT
331408 TTCAATTATTATATATATAAAAATCATTG
1 TTCAATTATTATATATATAAAAATCATTG
*
331437 TTCAATTATTATATATATAAAGATCATTG
1 TTCAATTATTATATATATAAAAATCATTG
331466 TT
1 TT
331468 TTATTTTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.42, C:0.07, G:0.05, T:0.47
Consensus pattern (29 bp):
TTCAATTATTATATATATAAAAATCATTG
Found at i:332165 original size:21 final size:21
Alignment explanation
Indices: 332139--332186 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
332129 GCCCTGCAAA
*
332139 TAACGGAATTAA-TGGATTTTC
1 TAACGGAAGTAACT-GATTTTC
*
332160 TAACGGAAGTAACTGATTTTG
1 TAACGGAAGTAACTGATTTTC
332181 TAACGG
1 TAACGG
332187 GATTTTGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 23 0.96
22 1 0.04
ACGTcount: A:0.33, C:0.10, G:0.23, T:0.33
Consensus pattern (21 bp):
TAACGGAAGTAACTGATTTTC
Found at i:337661 original size:60 final size:60
Alignment explanation
Indices: 337562--337719 Score: 167
Period size: 60 Copynumber: 2.6 Consensus size: 60
337552 TTTTAAATTG
* * * *
337562 GTCCTTAAACTTTTAAATATTTCAATTTTAT-TCTTAAACTATGA-CTATCATTCTAACGTA
1 GTCCTCAAACTTTTAAATATTTCAATTTCATCTC-AAAACTATGACCT-TCATTCTAAAGTA
* * *
337622 GTCCTCAAACTTTTAAATATTTCAATTTCATCTCAAAACTGTGACCTTCATTCTAAATTG
1 GTCCTCAAACTTTTAAATATTTCAATTTCATCTCAAAACTATGACCTTCATTCTAAAGTA
* * * * *
337682 GTCCCCAAACTTTTTGAACATTCCAATTTCATCCCAAA
1 GTCCTCAAAC-TTTTAAATATTTCAATTTCATCTCAAA
337720 CAATACATAT
Statistics
Matches: 83, Mismatches: 12, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
60 56 0.67
61 27 0.33
ACGTcount: A:0.32, C:0.22, G:0.06, T:0.40
Consensus pattern (60 bp):
GTCCTCAAACTTTTAAATATTTCAATTTCATCTCAAAACTATGACCTTCATTCTAAAGTA
Found at i:337966 original size:58 final size:60
Alignment explanation
Indices: 337839--338015 Score: 196
Period size: 58 Copynumber: 3.0 Consensus size: 60
337829 GATGAATTTG
* **
337839 AGGATGAAAGTAGAATATTAAAAAGTTTGGGGACAAATTTAGAAAGAGAGTCATAGTTTA
1 AGGATGAAATTAGAATATTAAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTTA
* * * * *
337899 AGGATGAAATTAGAATGTTTAAAAGTTTAAGGACTACTTTA-AAA-TGAGTCATAGTTTA
1 AGGATGAAATTAGAATATTAAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTTA
* * * * * * * *
337957 AGGATGAAATTATAATATTCAAAATTTTAAGGGCCAATTTAGAATGAAAGTTATAGTTT
1 AGGATGAAATTAGAATATTAAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTT
338016 GGGGATATAT
Statistics
Matches: 96, Mismatches: 19, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
58 47 0.49
59 5 0.05
60 44 0.46
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (60 bp):
AGGATGAAATTAGAATATTAAAAAGTTTAAGGACAAATTTAGAAAGAGAGTCATAGTTTA
Found at i:340637 original size:76 final size:76
Alignment explanation
Indices: 340547--340699 Score: 306
Period size: 76 Copynumber: 2.0 Consensus size: 76
340537 AAAACATATA
340547 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAGAAATAATACTTATACATACTTAC
1 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAGAAATAATACTTATACATACTTAC
340612 ATTAGTGTAAG
66 ATTAGTGTAAG
340623 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAGAAATAATACTTATACATACTTAC
1 TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAGAAATAATACTTATACATACTTAC
340688 ATTAGTGTAAG
66 ATTAGTGTAAG
340699 T
1 T
340700 ATGATAAAAG
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 77 1.00
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (76 bp):
TTTACATTGATATAAGTATATTTTTGAAGAAATAAAAAATAGAAATAATACTTATACATACTTAC
ATTAGTGTAAG
Found at i:340792 original size:2 final size:2
Alignment explanation
Indices: 340785--340826 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
340775 GACGCGTGAA
340785 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
340827 TAAGTTTCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:349002 original size:2 final size:2
Alignment explanation
Indices: 348995--349019 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
348985 GGAAACTATG
348995 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
349020 ATTGAAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:353667 original size:35 final size:34
Alignment explanation
Indices: 353628--353740 Score: 120
Period size: 35 Copynumber: 3.2 Consensus size: 34
353618 TCAATCGGTC
353628 TGAACCTATATAAGGAATTACAAGTTTGATCAAGT
1 TGAACCTATATAAGGAATTACAAGTTTGATC-AGT
** * * *
353663 TGAACCTACCGTAAGGAATTACCAGTTCGATCGGT
1 TGAACCTA-TATAAGGAATTACAAGTTTGATCAGT
*
353698 CTGAACCTATATAAGGAATTACCAA-TTTGATCGAGC
1 -TGAACCTATATAAGGAATTA-CAAGTTTGATC-AGT
353734 TGAACCT
1 TGAACCT
353741 GTAGAGACTT
Statistics
Matches: 63, Mismatches: 11, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
35 33 0.52
36 30 0.48
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (34 bp):
TGAACCTATATAAGGAATTACAAGTTTGATCAGT
Found at i:353690 original size:71 final size:71
Alignment explanation
Indices: 353600--353740 Score: 230
Period size: 71 Copynumber: 2.0 Consensus size: 71
353590 CCACTTAGAT
* *
353600 CCGTAAGGAATTATCAGTTCAATCGGTCTGAACCTATATAAGGAATTA-CAAGTTTGATCAAGTT
1 CCGTAAGGAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATTACCAA-TTTGATCAAGCT
353664 GAACCTA
65 GAACCTA
* *
353671 CCGTAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCGAGCTG
1 CCGTAAGGAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
353736 AACCT
66 AACCT
353741 GTAGAGACTT
Statistics
Matches: 65, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
71 62 0.95
72 3 0.05
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.28
Consensus pattern (71 bp):
CCGTAAGGAATTACCAGTTCAATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
AACCTA
Found at i:355246 original size:18 final size:18
Alignment explanation
Indices: 355223--355257 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
355213 AAATCCCATT
355223 GTATGTGCATTGAGAGTC
1 GTATGTGCATTGAGAGTC
355241 GTATGTGCATTGAGAGT
1 GTATGTGCATTGAGAGT
355258 AATAAGTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.09, G:0.34, T:0.34
Consensus pattern (18 bp):
GTATGTGCATTGAGAGTC
Found at i:355266 original size:18 final size:18
Alignment explanation
Indices: 355227--355269 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
355217 CCCATTGTAT
** *
355227 GTGCATTGAGAGTCGTAT
1 GTGCATTGAGAGTAATAA
355245 GTGCATTGAGAGTAATAA
1 GTGCATTGAGAGTAATAA
355263 GTGCATT
1 GTGCATT
355270 TCGACATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.09, G:0.30, T:0.33
Consensus pattern (18 bp):
GTGCATTGAGAGTAATAA
Found at i:355473 original size:136 final size:137
Alignment explanation
Indices: 355266--355543 Score: 382
Period size: 136 Copynumber: 2.0 Consensus size: 137
355256 GTAATAAGTG
*
355266 CATTTCGACATAAATTGTATATAAAAGTTATCGATCAATTTTTTTTAATGCATAATGATGTATTT
1 CATTTCGACATAAATTATATATAAAAGTTATCGATCAATTTTTTTTAATGCATAATGATGTATTT
* ** * *
355331 TCGTATCAGTACTATGTGTTCTTTCGGCACTA-GATGTGCAAATATGGTATTCATAATGAGTTTG
66 TCGTATCAGTACTATATGTAATTTCGGCACTATG-TGTGCAAACATGGAATTCATAATGAGTTTG
355395 TGAATTAC
130 TGAATTAC
* * * *
355403 CATTTCGATATACAATTATGTATAAAAG-TATCGATCGA-TTTTTTTAATGCATAATGGTGTATT
1 CATTTCGACATA-AATTATATATAAAAGTTATCGATCAATTTTTTTTAATGCATAATGATGTATT
* ** *
355466 TTTGTATCAGTACTATATGTAATTTCGGCACTATGTGTGCATCCATGGAATTCATAATGGGTTTG
65 TTCGTATCAGTACTATATGTAATTTCGGCACTATGTGTGCAAACATGGAATTCATAATGAGTTTG
*
355531 TGAATTTC
130 TGAATTAC
355539 CATTT
1 CATTT
355544 TGGCACTTAG
Statistics
Matches: 124, Mismatches: 15, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
136 90 0.73
137 21 0.17
138 13 0.10
ACGTcount: A:0.29, C:0.12, G:0.17, T:0.42
Consensus pattern (137 bp):
CATTTCGACATAAATTATATATAAAAGTTATCGATCAATTTTTTTTAATGCATAATGATGTATTT
TCGTATCAGTACTATATGTAATTTCGGCACTATGTGTGCAAACATGGAATTCATAATGAGTTTGT
GAATTAC
Found at i:365355 original size:19 final size:19
Alignment explanation
Indices: 365293--365374 Score: 74
Period size: 19 Copynumber: 4.3 Consensus size: 19
365283 ATAAATAGAA
* *
365293 ATATCAGAAATCATACCAG
1 ATATCAGAGATCATAACAG
* * *
365312 ATATTAGAGATAATAAAAG
1 ATATCAGAGATCATAACAG
* *
365331 AAATCAGAGATCATAACAT
1 ATATCAGAGATCATAACAG
* *
365350 ATATCAAAGTTCATAACAG
1 ATATCAGAGATCATAACAG
*
365369 AAATCA
1 ATATCA
365375 AAGGTCAGAC
Statistics
Matches: 48, Mismatches: 15, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
19 48 1.00
ACGTcount: A:0.52, C:0.13, G:0.11, T:0.23
Consensus pattern (19 bp):
ATATCAGAGATCATAACAG
Found at i:368016 original size:23 final size:23
Alignment explanation
Indices: 367989--368056 Score: 84
Period size: 23 Copynumber: 2.9 Consensus size: 23
367979 CCACATAGAA
367989 TATCCCGAGGACCGCGTAGAAAT
1 TATCCCGAGGACCGCGTAGAAAT
* *
368012 TATCCCCAAGGACCACGTA-AAAT
1 TAT-CCCGAGGACCGCGTAGAAAT
*
368035 TATCCCGAAGGACCGCATAGAA
1 TATCCCG-AGGACCGCGTAGAA
368057 CCCTCGACTC
Statistics
Matches: 37, Mismatches: 5, Indels: 5
0.79 0.11 0.11
Matches are distributed among these distances:
22 3 0.08
23 19 0.51
24 15 0.41
ACGTcount: A:0.35, C:0.28, G:0.21, T:0.16
Consensus pattern (23 bp):
TATCCCGAGGACCGCGTAGAAAT
Found at i:368025 original size:24 final size:24
Alignment explanation
Indices: 367996--368056 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
367986 GAATATCCCG
367996 AGGACCGCGTAGAAATTATCCCCA
1 AGGACCGCGTAGAAATTATCCCCA
* *
368020 AGGACCACGTA-AAATTATCCCGA
1 AGGACCGCGTAGAAATTATCCCCA
*
368043 AGGACCGCATAGAA
1 AGGACCGCGTAGAA
368057 CCCTCGACTC
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.38, C:0.26, G:0.21, T:0.15
Consensus pattern (24 bp):
AGGACCGCGTAGAAATTATCCCCA
Found at i:374536 original size:24 final size:25
Alignment explanation
Indices: 374498--374546 Score: 66
Period size: 24 Copynumber: 2.0 Consensus size: 25
374488 AAACTTTCAT
*
374498 TAAATAAAACTAAAATA-ATTTACA
1 TAAATAAAACTAAAAAAGATTTACA
374522 TAAATAAAA-TAAAAAAAGATTTACA
1 TAAATAAAACT-AAAAAAGATTTACA
374547 AAACCAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 14 0.64
25 7 0.32
ACGTcount: A:0.65, C:0.06, G:0.02, T:0.27
Consensus pattern (25 bp):
TAAATAAAACTAAAAAAGATTTACA
Found at i:375056 original size:24 final size:23
Alignment explanation
Indices: 375028--375094 Score: 66
Period size: 21 Copynumber: 2.9 Consensus size: 23
375018 ACCACATATA
375028 TGTCCCGAAGGATCGCGTAGAAAT
1 TGTCCCGAAGGA-CGCGTAGAAAT
* *
375052 TGTCCCGAATGAC-CTTAG-AAT
1 TGTCCCGAAGGACGCGTAGAAAT
* *
375073 TGTCTCAAAGGACCGCGTAGAA
1 TGTCCCGAAGGA-CGCGTAGAA
375095 CCCTTGACTC
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
21 12 0.35
22 5 0.15
23 5 0.15
24 12 0.35
ACGTcount: A:0.30, C:0.22, G:0.25, T:0.22
Consensus pattern (23 bp):
TGTCCCGAAGGACGCGTAGAAAT
Found at i:378706 original size:16 final size:15
Alignment explanation
Indices: 378681--378710 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
378671 ACTGAATGAA
378681 TTTATGATTTATTGT
1 TTTATGATTTATTGT
378696 TTTACTGATTTATTG
1 TTTA-TGATTTATTG
378711 GTTCATGGCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.03, G:0.13, T:0.63
Consensus pattern (15 bp):
TTTATGATTTATTGT
Found at i:381561 original size:20 final size:21
Alignment explanation
Indices: 381523--381561 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
381513 TCTTTTTCGT
381523 AACGCGATTTTCTAAATTCAC
1 AACGCGATTTTCTAAATTCAC
381544 AACGCGATTTTC-AAATTC
1 AACGCGATTTTCTAAATTC
381562 GTAACTCGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.23, G:0.10, T:0.33
Consensus pattern (21 bp):
AACGCGATTTTCTAAATTCAC
Found at i:381582 original size:61 final size:60
Alignment explanation
Indices: 381434--381585 Score: 153
Period size: 61 Copynumber: 2.5 Consensus size: 60
381424 AAATAACTAA
* * *
381434 CAAATTCGCAACGCGAACTCCAATTTCGCAACACAATTTCAAAATTCGCAACTCAGTTTT
1 CAAATTCGCAACTCGAACTCCAATTTCGCAACACAATTTCAAAATTCACAACGCAGTTTT
* * * * ** * * * *
381494 GAAATTCACAACTCGAATTTCTTTTTCGTAACGCGATTTTCTAAATTCACAACGC-GATTTT
1 CAAATTCGCAACTCGAACTCCAATTTCGCAACAC-AATTTCAAAATTCACAACGCAG-TTTT
*
381555 CAAATTCGTAACTCGAACTCCAATTTCGCAA
1 CAAATTCGCAACTCGAACTCCAATTTCGCAA
381586 ATGCAATTTC
Statistics
Matches: 69, Mismatches: 21, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
60 26 0.38
61 43 0.62
ACGTcount: A:0.33, C:0.26, G:0.11, T:0.31
Consensus pattern (60 bp):
CAAATTCGCAACTCGAACTCCAATTTCGCAACACAATTTCAAAATTCACAACGCAGTTTT
Found at i:381711 original size:21 final size:21
Alignment explanation
Indices: 381613--381711 Score: 100
Period size: 20 Copynumber: 4.9 Consensus size: 21
381603 CGAATTTGGT
*
381613 ATTCGCAACACGGAATTT-TAA
1 ATTCGCAACGC-GAATTTCTAA
*
381634 ATTCGCAACTCG-ATTTCTAA
1 ATTCGCAACGCGAATTTCTAA
*
381654 ATTCGCAACGCGAATTT-T-T
1 ATTCGCAACGCGAATTTCTAA
* * *
381673 TTTCGCAACTCG-ATTTCTGA
1 ATTCGCAACGCGAATTTCTAA
381693 ATTCGCAACGCGAATTTCT
1 ATTCGCAACGCGAATTTCT
381712 TTTTAACAAC
Statistics
Matches: 65, Mismatches: 8, Indels: 10
0.78 0.10 0.12
Matches are distributed among these distances:
18 4 0.06
19 15 0.23
20 26 0.40
21 20 0.31
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (21 bp):
ATTCGCAACGCGAATTTCTAA
Found at i:381728 original size:79 final size:79
Alignment explanation
Indices: 381639--381788 Score: 189
Period size: 79 Copynumber: 1.9 Consensus size: 79
381629 TTTAAATTCG
* * * **
381639 CAACTCGATTTCTAAATTCGCAACGCGAA-TTT-TTTTTCGCAACTCGATTT-CTGAATTCGCAA
1 CAACGCGATTTCTAAATTCG-AACAC-AAGTTTCCTTTTCGCAACAAGATTTCCT-AATTCGCAA
*
381701 CGCGAATTTCTTTTTAA
63 CACGAATTTCTTTTTAA
*
381718 CAACGCGATTTTTAAATTCGAACACAAGTTTCCTTTTCGCAACAAGATTTCCTAATTCGCAACAC
1 CAACGCGATTTCTAAATTCGAACACAAGTTTCCTTTTCGCAACAAGATTTCCTAATTCGCAACAC
381783 GAATTT
66 GAATTT
381789 TGTTTTCGCA
Statistics
Matches: 61, Mismatches: 7, Indels: 6
0.82 0.09 0.08
Matches are distributed among these distances:
77 2 0.03
78 7 0.11
79 50 0.82
80 2 0.03
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (79 bp):
CAACGCGATTTCTAAATTCGAACACAAGTTTCCTTTTCGCAACAAGATTTCCTAATTCGCAACAC
GAATTTCTTTTTAA
Found at i:381776 original size:20 final size:18
Alignment explanation
Indices: 381741--381781 Score: 55
Period size: 20 Copynumber: 2.2 Consensus size: 18
381731 AAATTCGAAC
*
381741 ACAAGTTTCCTTTTCGCA
1 ACAAGTTTCCTATTCGCA
381759 ACAAGATTTCCTAATTCGCA
1 ACAAG-TTTCCT-ATTCGCA
381779 ACA
1 ACA
381782 CGAATTTTGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 5 0.25
19 6 0.30
20 9 0.45
ACGTcount: A:0.32, C:0.27, G:0.10, T:0.32
Consensus pattern (18 bp):
ACAAGTTTCCTATTCGCA
Found at i:381795 original size:40 final size:39
Alignment explanation
Indices: 381613--381829 Score: 190
Period size: 40 Copynumber: 5.5 Consensus size: 39
381603 CGAATTTGGT
**
381613 ATTCGCAACACGGAATTTTAAATTCGCAACTCGATTTCTAA
1 ATTCGCAACAC-GAATTTT-TTTTCGCAACTCGATTTCTAA
* *
381654 ATTCGCAACGCGAATTTTTTTTCGCAACTCGATTTCTGA
1 ATTCGCAACACGAATTTTTTTTCGCAACTCGATTTCTAA
* ** * *
381693 ATTCGCAACGCGAATTTCTTTTTAACAACGCGATTTTTAA
1 ATTCGCAACACGAATTT-TTTTTCGCAACTCGATTTCTAA
* **
381733 ATTCG-AACAC-AAGTTTCCTTTTCGCAACAAGATTTCCT-A
1 ATTCGCAACACGAA-TTT-TTTTTCGCAACTCGATTT-CTAA
**
381772 ATTCGCAACACGAATTTTGTTTTCGCAACTC-AGTTTCCGA
1 ATTCGCAACACGAATTTT-TTTTCGCAACTCGA-TTTCTAA
**
381812 ATTCGCAATTCGAATTTT
1 ATTCGCAACACGAATTTT
381830 AATTTAGCAA
Statistics
Matches: 146, Mismatches: 22, Indels: 17
0.79 0.12 0.09
Matches are distributed among these distances:
38 2 0.01
39 64 0.44
40 68 0.47
41 12 0.08
ACGTcount: A:0.29, C:0.23, G:0.13, T:0.36
Consensus pattern (39 bp):
ATTCGCAACACGAATTTTTTTTCGCAACTCGATTTCTAA
Found at i:381997 original size:14 final size:15
Alignment explanation
Indices: 381978--382015 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
381968 TTCCCCATCC
381978 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
381992 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
382008 TAATTTTT
1 TAATTTTT
382016 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:382779 original size:24 final size:24
Alignment explanation
Indices: 382752--382805 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
382742 GTATTCAAAA
382752 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
382776 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
382800 TTTGAT
1 TTTGAT
382806 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:385099 original size:19 final size:20
Alignment explanation
Indices: 385077--385114 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
385067 ATATTCGTGT
385077 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
385096 TTCGTGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
385115 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.11, G:0.16, T:0.29
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:385228 original size:22 final size:21
Alignment explanation
Indices: 385200--385253 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
385190 TCAAAACTGA
*
385200 GTTGCGAATTTGGGAAATTTGC
1 GTTGCGAATTTGGG-AATTCGC
* *
385222 GTTGCGAAATT-GGAGTTCGC
1 GTTGCGAATTTGGGAATTCGC
385242 GTTGCGAATTTG
1 GTTGCGAATTTG
385254 TTGGTTATTT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
20 15 0.56
21 2 0.07
22 10 0.37
ACGTcount: A:0.20, C:0.11, G:0.33, T:0.35
Consensus pattern (21 bp):
GTTGCGAATTTGGGAATTCGC
Found at i:393365 original size:23 final size:24
Alignment explanation
Indices: 393318--393367 Score: 68
Period size: 23 Copynumber: 2.1 Consensus size: 24
393308 AAAATTCAGG
393318 AAAACAAAAGAAAGCAAAAATAAT
1 AAAACAAAAGAAAGCAAAAATAAT
*
393342 AAAACAAAA-CAAG-AAAAATAAAT
1 AAAACAAAAGAAAGCAAAAAT-AAT
393365 AAA
1 AAA
393368 TTAAAAAACC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 6 0.25
23 9 0.38
24 9 0.38
ACGTcount: A:0.78, C:0.08, G:0.06, T:0.08
Consensus pattern (24 bp):
AAAACAAAAGAAAGCAAAAATAAT
Found at i:393813 original size:74 final size:77
Alignment explanation
Indices: 393722--393874 Score: 215
Period size: 74 Copynumber: 2.0 Consensus size: 77
393712 ATTAATATTT
* *
393722 TTTAATAATTTTAGTAAAATGTTATTTAAA-A-TATTATTTT-ATCAAAAATATTAATATTG-AT
1 TTTAATAATTTTAGTAAAATGTTACTTAAATATTATTATTTTAAT-AAAAATATTAATATTGAAA
393783 GTTATTTAAAATA
65 GTTATTTAAAATA
* * * *
393796 TTTAATATTTTTTGTAAAGTGTTACTTAAATATTATTTTTTTAATAAAAATATTAATATTGAAAG
1 TTTAATAATTTTAGTAAAATGTTACTTAAATATTATTATTTTAATAAAAATATTAATATTGAAAG
393861 TTATTTAAAATA
66 TTATTTAAAATA
393873 TT
1 TT
393875 ATTTTTTATC
Statistics
Matches: 69, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
74 26 0.38
75 1 0.01
76 24 0.35
77 18 0.26
ACGTcount: A:0.42, C:0.01, G:0.06, T:0.50
Consensus pattern (77 bp):
TTTAATAATTTTAGTAAAATGTTACTTAAATATTATTATTTTAATAAAAATATTAATATTGAAAG
TTATTTAAAATA
Found at i:393869 original size:44 final size:42
Alignment explanation
Indices: 393816--393897 Score: 112
Period size: 44 Copynumber: 1.9 Consensus size: 42
393806 TTTGTAAAGT
393816 GTTACTT-AAATATTATTTTTTTAATAAAAATATTAATATTGAAA
1 GTTACTTAAAATATTA-TTTTTT-ATAAAAA-ATTAATATTGAAA
* *
393860 GTTATTTAAAATATTATTTTTTATCAAAAATTAATATT
1 GTTACTTAAAATATTATTTTTTATAAAAAATTAATATT
393898 TTTGGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 9 0.26
43 6 0.17
44 12 0.34
45 8 0.23
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (42 bp):
GTTACTTAAAATATTATTTTTTATAAAAAATTAATATTGAAA
Found at i:393878 original size:73 final size:72
Alignment explanation
Indices: 393730--393881 Score: 191
Period size: 76 Copynumber: 2.1 Consensus size: 72
393720 TTTTTAATAA
* * *
393730 TTTTAGTAAAATGTTATTTAAAATATTATTTTATCAAAAATATTAATATTGATGTTATTTAAAAT
1 TTTTTGTAAAATGTTACTTAAAATATTATTTTATCAAAAATATTAATATTGAAGTTATTTAAAAT
393795 ATTTAATAT
66 A-TT-ATAT
* *
393804 TTTTTGTAAAGTGTTACTTAAATATTATTTTTTTAAT-AAAAATATTAATATTGAAAGTTATTTA
1 TTTTTGTAAAATGTTACTTAAA-A-TATTATTTT-ATCAAAAATATTAATATTG-AAGTTATTTA
393868 AAATATTAT-T
62 AAATATTATAT
393878 TTTT
1 TTTT
393882 ATCAAAAATT
Statistics
Matches: 69, Mismatches: 5, Indels: 8
0.84 0.06 0.10
Matches are distributed among these distances:
74 24 0.35
75 3 0.04
76 26 0.38
77 16 0.23
ACGTcount: A:0.41, C:0.01, G:0.06, T:0.52
Consensus pattern (72 bp):
TTTTTGTAAAATGTTACTTAAAATATTATTTTATCAAAAATATTAATATTGAAGTTATTTAAAAT
ATTATAT
Found at i:394301 original size:21 final size:22
Alignment explanation
Indices: 394277--394317 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
394267 CTATTTCTAG
* *
394277 AAAATATTTATTTAT-TTAAAT
1 AAAATAATTATATATATTAAAT
394298 AAAATAATTATATATATTAA
1 AAAATAATTATATATATTAA
394318 CAATTTAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (22 bp):
AAAATAATTATATATATTAAAT
Found at i:395007 original size:94 final size:94
Alignment explanation
Indices: 394788--395053 Score: 344
Period size: 94 Copynumber: 2.8 Consensus size: 94
394778 AATTACGGAG
* *
394788 TAATTAAGTATTCATTGTTAAATGATTGAGAATA-TTATCAACAAATAATATTTTATAATCACCT
1 TAATTAAGTGTTCATTGTTAAATGATTGAGAATACTT-TAAACAAATAATATTTTATAATCACCT
*
394852 TT-GCTTAATAAAAACAATGATTGCAAGAA
65 TTAGCTTAATAAAAACAATGATTACAAGAA
* * * * *
394881 TGATTGAGTGTAT-ATTGTCAAATGATTAAGAATACTTTGAACAAATAATATTTTATAATCA-CT
1 TAATTAAGTGT-TCATTGTTAAATGATTGAGAATACTTTAAACAAATAATATTTTATAATCACCT
394944 GTTAGCTTAATAAAAACAATGATTACAAGAA
65 -TTAGCTTAATAAAAACAATGATTACAAGAA
* * *
394975 TAATTAAATGTTCATTATTAAAT-AGTTGAGAATACTTTAAACAAATAATATTTTATAATCATCT
1 TAATTAAGTGTTCATTGTTAAATGA-TTGAGAATACTTTAAACAAATAATATTTTATAATCACCT
* *
395039 TTAACTTAAAAAAAA
65 TTAGCTTAATAAAAA
395054 TGATATCAAT
Statistics
Matches: 150, Mismatches: 16, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
92 2 0.01
93 54 0.36
94 92 0.61
95 2 0.01
ACGTcount: A:0.45, C:0.09, G:0.09, T:0.37
Consensus pattern (94 bp):
TAATTAAGTGTTCATTGTTAAATGATTGAGAATACTTTAAACAAATAATATTTTATAATCACCTT
TAGCTTAATAAAAACAATGATTACAAGAA
Found at i:395385 original size:24 final size:24
Alignment explanation
Indices: 395323--395414 Score: 114
Period size: 24 Copynumber: 3.9 Consensus size: 24
395313 ATCTATGTAT
* * *
395323 TTGTGACAC-ATTTTTCTCTACTC
1 TTGTGACACGCTTTTTCTCTGCTA
* * * *
395346 TTATGGCATGCATTTTCTCTGCTA
1 TTGTGACACGCTTTTTCTCTGCTA
395370 TTGTGACACGCTTTTTCTCTGCTA
1 TTGTGACACGCTTTTTCTCTGCTA
395394 TTGTGACACGCTTTTTCTCTG
1 TTGTGACACGCTTTTTCTCTG
395415 TTGTATGATC
Statistics
Matches: 57, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
23 6 0.11
24 51 0.89
ACGTcount: A:0.14, C:0.24, G:0.15, T:0.47
Consensus pattern (24 bp):
TTGTGACACGCTTTTTCTCTGCTA
Found at i:395894 original size:2 final size:2
Alignment explanation
Indices: 395887--395921 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
395877 TTAGATCTAA
395887 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
395922 GACTCGTTGA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:397154 original size:20 final size:20
Alignment explanation
Indices: 397129--397195 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
397119 TTTTCCCAAT
*
397129 TCGCAATACGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
397149 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
397170 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
397190 TCGCAA
1 TCGCAA
397196 CGCAAATTGG
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
20 21 0.57
21 16 0.43
ACGTcount: A:0.43, C:0.18, G:0.21, T:0.18
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:397172 original size:21 final size:21
Alignment explanation
Indices: 397146--397221 Score: 82
Period size: 21 Copynumber: 3.7 Consensus size: 21
397136 ACGAATAAGT
397146 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
397167 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
*
397187 AAATCGCAACGCAAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* *
397208 AAATTGCAATGCGA
1 AAATCGCAACGCGA
397222 TACTGACTAT
Statistics
Matches: 42, Mismatches: 12, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 15 0.36
21 27 0.64
ACGTcount: A:0.42, C:0.17, G:0.24, T:0.17
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:397236 original size:41 final size:41
Alignment explanation
Indices: 397129--397221 Score: 159
Period size: 41 Copynumber: 2.3 Consensus size: 41
397119 TTTTCCCAAT
* *
397129 TCGCAATACGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGAAAA
397170 TCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGAAAA
*
397211 TTGCAATGCGA
1 TCGCAATGCGA
397222 TACTGACTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 49 1.00
ACGTcount: A:0.42, C:0.17, G:0.23, T:0.18
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCAAATTGGGAAAA
Found at i:397238 original size:20 final size:20
Alignment explanation
Indices: 397213--397304 Score: 76
Period size: 20 Copynumber: 4.5 Consensus size: 20
397203 TGGGAAAATT
*
397213 GCAATGCGATACTGACTATC
1 GCAACGCGATACTGACTATC
* * * **
397233 GCAATGCGATAATAAAAAATC
1 GCAACGCGATACT-GACTATC
* * * *
397254 ACAACGAGATACTTACTTTC
1 GCAACGCGATACTGACTATC
*
397274 GCAACGCGATACTGACTTTC
1 GCAACGCGATACTGACTATC
397294 GCAACGCGATA
1 GCAACGCGATA
397305 ATACATAATC
Statistics
Matches: 56, Mismatches: 15, Indels: 2
0.77 0.21 0.03
Matches are distributed among these distances:
20 43 0.77
21 13 0.23
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.23
Consensus pattern (20 bp):
GCAACGCGATACTGACTATC
Found at i:397520 original size:22 final size:22
Alignment explanation
Indices: 397493--397536 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
397483 CACTCTCTCA
397493 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
397515 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
397537 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:397825 original size:20 final size:20
Alignment explanation
Indices: 397800--397837 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
397790 CGATTCTCTC
397800 GTTGCGATAGTCATTTTCGT
1 GTTGCGATAGTCATTTTCGT
**
397820 GTTGCGATTTTCATTTTC
1 GTTGCGATAGTCATTTTC
397838 AGAAACTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.16, G:0.21, T:0.50
Consensus pattern (20 bp):
GTTGCGATAGTCATTTTCGT
Found at i:399178 original size:18 final size:18
Alignment explanation
Indices: 399157--399201 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
399147 TCCACTTCGG
*
399157 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
399175 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
399193 GAGCCATCA
1 GAGCCATCA
399202 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:399737 original size:19 final size:20
Alignment explanation
Indices: 399683--399738 Score: 69
Period size: 20 Copynumber: 2.9 Consensus size: 20
399673 TAGTTTACTT
* *
399683 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
399703 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
*
399723 TCGCAATGC-GAAATGA
1 TCGCAACGCGGAAATGA
399739 AAATCGTAAC
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
19 6 0.19
20 25 0.81
ACGTcount: A:0.38, C:0.23, G:0.23, T:0.16
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:399757 original size:14 final size:14
Alignment explanation
Indices: 399738--399795 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
399728 ATGCGAAATG
*
399738 AAAATCGTAACGAC
1 AAAATCGCAACGAC
*
399752 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAC
399768 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
399784 AAAATCGCAACG
1 AAAATCGCAACG
399796 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
14 20 0.54
16 8 0.22
18 9 0.24
ACGTcount: A:0.48, C:0.22, G:0.17, T:0.12
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:399782 original size:32 final size:33
Alignment explanation
Indices: 399722--399812 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
399712 GGAAATGGCT
*
399722 ATCGCAATGCGAAATGAAAATCGTAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
399755 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
*
399787 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
399813 TGCGATTTGT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:399848 original size:14 final size:14
Alignment explanation
Indices: 399829--399886 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
399819 TTGTGTTTCG
399829 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
399843 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
399859 CACGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
399875 CGTTGCGATTTT
1 CGTTGCGATTTT
399887 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:399868 original size:32 final size:33
Alignment explanation
Indices: 399824--399902 Score: 133
Period size: 32 Copynumber: 2.4 Consensus size: 33
399814 GCGATTTGTG
399824 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
399856 TTTCACGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
399889 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
399903 AGCCATTTCC
Statistics
Matches: 43, Mismatches: 3, Indels: 1
0.91 0.06 0.02
Matches are distributed among these distances:
32 26 0.60
33 17 0.40
ACGTcount: A:0.11, C:0.19, G:0.23, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:399901 original size:19 final size:19
Alignment explanation
Indices: 399875--399941 Score: 89
Period size: 19 Copynumber: 3.5 Consensus size: 19
399865 GCGATTTTGT
**
399875 CGTTGCGATTTTCATTTCG
1 CGTTGCGATAGTCATTTCG
* *
399894 CATTGCGATAGCCATTTCCG
1 CGTTGCGATAGTCATTT-CG
399914 CGTTGCGATAGTCATTTCG
1 CGTTGCGATAGTCATTTCG
399933 CGTTGCGAT
1 CGTTGCGAT
399942 TTTAAGTTTC
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
19 24 0.59
20 17 0.41
ACGTcount: A:0.15, C:0.24, G:0.24, T:0.37
Consensus pattern (19 bp):
CGTTGCGATAGTCATTTCG
Found at i:399921 original size:20 final size:19
Alignment explanation
Indices: 399887--399941 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
399877 TTGCGATTTT
*
399887 CATTTCGCATTGCGATAGC
1 CATTTCGCGTTGCGATAGC
*
399906 CATTTCCGCGTTGCGATAGT
1 CATTT-CGCGTTGCGATAGC
399926 CATTTCGCGTTGCGAT
1 CATTTCGCGTTGCGAT
399942 TTTAAGTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.16, C:0.25, G:0.24, T:0.35
Consensus pattern (19 bp):
CATTTCGCGTTGCGATAGC
Found at i:401830 original size:14 final size:14
Alignment explanation
Indices: 401811--401846 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
401801 ATTGTTTAAT
401811 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
401825 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
401839 TGATTTGT
1 TGATTTGT
401847 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:401972 original size:14 final size:14
Alignment explanation
Indices: 401953--402002 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 14
401943 CGAAATGGCT
401953 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
401967 ATCGCAATGCGAAATGAAA
1 ATCGCAA--CG--A-GAAA
401986 ATCGCAACGAGAAA
1 ATCGCAACGAGAAA
402000 ATC
1 ATC
402003 ACAATGCGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 10
0.76 0.00 0.24
Matches are distributed among these distances:
14 14 0.45
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 11 0.35
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.12
Consensus pattern (14 bp):
ATCGCAACGAGAAA
Found at i:401979 original size:33 final size:33
Alignment explanation
Indices: 401934--402011 Score: 111
Period size: 33 Copynumber: 2.4 Consensus size: 33
401924 AAAACAGACT
* ***
401934 ATCGCAACGCGAAATGGCTATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
401967 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
*
402000 ATCACAATGCGA
1 ATCGCAATGCGA
402012 TTTTCATTTC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 40 1.00
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAAA
Found at i:401999 original size:19 final size:19
Alignment explanation
Indices: 401963--401999 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
401953 ATCGCAACGA
* *
401963 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAACGAGAAAT
401982 GAAAATCGCAACGAGAAA
1 GAAAATCGCAACGAGAAA
402000 ATCACAATGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.51, C:0.16, G:0.22, T:0.11
Consensus pattern (19 bp):
GAAAATCGCAACGAGAAAT
Found at i:402087 original size:20 final size:20
Alignment explanation
Indices: 402030--402087 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
402020 TCGCATTGCG
* *
402030 ATTTTCTCGTTGCGATAACC
1 ATTTTCGCGTTGCGATAGCC
402050 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
402070 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
402088 TCAAATGAAT
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:0.17, C:0.22, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:403195 original size:24 final size:24
Alignment explanation
Indices: 403152--403197 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
403142 AAATTTGATC
*
403152 TGGTCAATACCCGGACTTTGATAT
1 TGGTCAATACACGGACTTTGATAT
* *
403176 TGGTCAATACATGGATTTTGAT
1 TGGTCAATACACGGACTTTGAT
403198 GATGTTTCAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.15, G:0.22, T:0.37
Consensus pattern (24 bp):
TGGTCAATACACGGACTTTGATAT
Found at i:403389 original size:12 final size:12
Alignment explanation
Indices: 403372--403396 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
403362 ATATAATCCT
403372 GAAGAAGAAAAA
1 GAAGAAGAAAAA
403384 GAAGAAGAAAAA
1 GAAGAAGAAAAA
403396 G
1 G
403397 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:405708 original size:19 final size:19
Alignment explanation
Indices: 405686--405783 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
405676 GGAAATTACT
405686 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
405705 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
405719 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
405738 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
405752 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
405771 ATCGCAACGCGAA
1 ATCGCAATGCGAA
405784 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:405728 original size:33 final size:33
Alignment explanation
Indices: 405686--405779 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
405676 GGAAATTACT
405686 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
405719 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
405752 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
405780 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:405801 original size:19 final size:20
Alignment explanation
Indices: 405779--405821 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
405769 AAATCGCAAC
405779 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
405798 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
405818 GCGA
1 GCGA
405822 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:405981 original size:14 final size:14
Alignment explanation
Indices: 405962--405998 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
405952 CATCAATTAA
405962 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
405976 ACAAATCACCTTTT
1 ACAAATCAACTTTT
405990 ACAAATCAA
1 ACAAATCAA
405999 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:408752 original size:20 final size:19
Alignment explanation
Indices: 408721--408781 Score: 68
Period size: 20 Copynumber: 3.1 Consensus size: 19
408711 TCTTTTGGTT
408721 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGA
* *
408740 GATAATGAGAATCGCAACGCG
1 GA-AATGAAAATCGCAACG-A
**
408761 GAAATGACTATCGCAACGA
1 GAAATGAAAATCGCAACGA
408780 GA
1 GA
408782 GAATCGCAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGA
Found at i:408803 original size:33 final size:33
Alignment explanation
Indices: 408746--408865 Score: 152
Period size: 33 Copynumber: 3.6 Consensus size: 33
408736 ACGAGATAAT
408746 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACGA
* * *
408780 GAGAATCGCAACGCGAAATGACTATCACGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
* * ** *
408813 GACAATCGCAACGCGAAATAAAAATCGCAACGC
1 GAGAATCGCAACGCGAAATGACTATCGCAACGA
408846 GA-AATCGCAACGCGAAATGA
1 GAGAATCGCAACGCGAAATGA
408866 AAATTGCAAT
Statistics
Matches: 74, Mismatches: 12, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
32 17 0.23
33 43 0.58
34 14 0.19
ACGTcount: A:0.42, C:0.25, G:0.23, T:0.11
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACGA
Found at i:408852 original size:13 final size:13
Alignment explanation
Indices: 408834--408863 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
408824 CGCGAAATAA
408834 AAATCGCAACGCG
1 AAATCGCAACGCG
408847 AAATCGCAACGCG
1 AAATCGCAACGCG
408860 AAAT
1 AAAT
408864 GAAAATTGCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.27, G:0.20, T:0.10
Consensus pattern (13 bp):
AAATCGCAACGCG
Found at i:408857 original size:32 final size:33
Alignment explanation
Indices: 408749--408879 Score: 131
Period size: 33 Copynumber: 4.0 Consensus size: 33
408739 AGATAATGAG
** * *
408749 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGCGAC
** * *
408783 AATCGCAACGCGAAATGACTATCACGAC-CAGAC
1 AATCGCAACGCGAAATGAAAATCGCAACGC-GAC
*
408816 AATCGCAACGCGAAATAAAAATCGCAACGCGA-
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAC
* *
408848 AATCGCAACGCGAAATGAAAATTGCAATGCGA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGA
408880 TTTTGGTTTC
Statistics
Matches: 83, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
32 29 0.35
33 42 0.51
34 12 0.14
ACGTcount: A:0.42, C:0.24, G:0.21, T:0.12
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAC
Found at i:409479 original size:20 final size:20
Alignment explanation
Indices: 409454--409506 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
409444 GCGCTATGTA
*
409454 AATCGCGTTGCGAAAGTTAG
1 AATCGCGTTGCGAAAGTCAG
409474 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
409494 TATCTCGTTGCGA
1 AATCGCGTTGCGA
409507 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:409540 original size:20 final size:20
Alignment explanation
Indices: 409515--409568 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
409505 GATTTTGTAT
409515 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
409535 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
409555 TATCGCATTGCGAT
1 TATCGCATTGCGAT
409569 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:409553 original size:61 final size:61
Alignment explanation
Indices: 409455--409571 Score: 162
Period size: 61 Copynumber: 1.9 Consensus size: 61
409445 CGCTATGTAA
* * * * *
409455 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
* * *
409516 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
409572 CCCAATTCGC
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 48 1.00
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTGTATT
Found at i:409587 original size:61 final size:61
Alignment explanation
Indices: 409455--409589 Score: 155
Period size: 61 Copynumber: 2.2 Consensus size: 61
409445 CGCTATGTAA
* * * * * ** *
409455 ATCGCGTTGCGAAAGTTAGAATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
409516 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
409578 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
409590 TTACTTATTC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:409921 original size:2 final size:2
Alignment explanation
Indices: 409914--409948 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
409904 AATAAAATAA
409914 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
409949 CATAAATAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:410177 original size:21 final size:21
Alignment explanation
Indices: 410139--410196 Score: 62
Period size: 21 Copynumber: 2.6 Consensus size: 21
410129 AAACAAATAA
410139 AATAATATATATATATATAAACAAT
1 AATAATAT-TA-ATAT-TAAA-AAT
*
410164 AATAATATTAATATTGAAAAT
1 AATAATATTAATATTAAAAAT
*
410185 AATAATAATAAT
1 AATAATATTAAT
410197 GGTTTAAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
21 14 0.45
22 3 0.10
23 4 0.13
24 2 0.06
25 8 0.26
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (21 bp):
AATAATATTAATATTAAAAAT
Found at i:410844 original size:20 final size:21
Alignment explanation
Indices: 410807--410846 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
410797 AAATTAAGTT
410807 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
410828 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
410847 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:411132 original size:65 final size:64
Alignment explanation
Indices: 411014--411225 Score: 234
Period size: 65 Copynumber: 3.3 Consensus size: 64
411004 TAATCAAAGG
* * *
411014 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCA-CACTCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGCA
*
411076 TTC
62 TTT
411079 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * ** * **
411144 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
411208 CATGCATCGATGCACACT
1 CATGCACCGATGCACACT
411226 TGGTGCACCG
Statistics
Matches: 128, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 7 0.05
64 55 0.43
65 66 0.52
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (64 bp):
CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:413193 original size:20 final size:21
Alignment explanation
Indices: 413170--413210 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
413160 TGAGAAATTG
413170 TTTTT-AAAATATAAAAATGA
1 TTTTTCAAAATATAAAAATGA
*
413190 TTTTTCAAAATTTAAAAATGA
1 TTTTTCAAAATATAAAAATGA
413211 AAACAAACTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.41
Consensus pattern (21 bp):
TTTTTCAAAATATAAAAATGA
Found at i:418428 original size:20 final size:21
Alignment explanation
Indices: 418391--418430 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
418381 AAATTAAGTT
418391 AAATGAATTTTAAGATTTTAC
1 AAATGAATTTTAAGATTTTAC
418412 AAATG-ATTTTACA-ATTTTA
1 AAATGAATTTTA-AGATTTTA
418431 TATTCGATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.42, C:0.05, G:0.07, T:0.45
Consensus pattern (21 bp):
AAATGAATTTTAAGATTTTAC
Found at i:418716 original size:65 final size:64
Alignment explanation
Indices: 418598--418809 Score: 234
Period size: 65 Copynumber: 3.3 Consensus size: 64
418588 TATTCAAAGG
* * *
418598 CATGCACCGATGCATCAGTCCATGCATCGATGCA-TCGATGAAT-TAATT-GAACATCGAATGCA
1 CATGCACCGATGCA-CACTCCATGCATCGATGCACTC--TGAATAT-TTTCAAACATCGAATGCA
*
418660 TTC
62 TTT
418663 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTC-AAACATCGAATGCATTT
* * ** * **
418728 GATGCATCGATGCACAAGCCATGCATCGATGCAC-CAGGCTATTTTTCAAACATCGAATGCATTT
1 CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATA-TTTTCAAACATCGAATGCATTT
*
418792 CATGCATCGATGCACACT
1 CATGCACCGATGCACACT
418810 TGGTGCACCG
Statistics
Matches: 128, Mismatches: 14, Indels: 11
0.84 0.09 0.07
Matches are distributed among these distances:
63 7 0.05
64 55 0.43
65 66 0.52
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.26
Consensus pattern (64 bp):
CATGCACCGATGCACACTCCATGCATCGATGCACTCTGAATATTTTCAAACATCGAATGCATTT
Found at i:420171 original size:2 final size:2
Alignment explanation
Indices: 420166--420200 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
420156 TATATTTTGT
420166 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
420201 ATTTAAACGG
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:422247 original size:6 final size:6
Alignment explanation
Indices: 422224--422289 Score: 73
Period size: 6 Copynumber: 10.8 Consensus size: 6
422214 ACCCACCTTA
* *
422224 TTTTTC TTTTATC TTTTTTC TTTTT- TTCTT- TTGTTC TTTTTTC TTTTTC
1 TTTTTC TTTT-TC -TTTTTC TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC
422273 TTTTTC TTTTTC TTTTT
1 TTTTTC TTTTTC TTTTT
422290 TTCAATTTAG
Statistics
Matches: 53, Mismatches: 3, Indels: 8
0.83 0.05 0.12
Matches are distributed among these distances:
5 8 0.15
6 32 0.60
7 9 0.17
8 4 0.08
ACGTcount: A:0.02, C:0.14, G:0.02, T:0.83
Consensus pattern (6 bp):
TTTTTC
Found at i:422290 original size:7 final size:7
Alignment explanation
Indices: 422224--422290 Score: 86
Period size: 7 Copynumber: 9.7 Consensus size: 7
422214 ACCCACCTTA
422224 TTTTTCT
1 TTTTTCT
*
422231 TTTATCT
1 TTTTTCT
422238 TTTTTCTT
1 TTTTTC-T
422246 TTTTTCT
1 TTTTTCT
422253 TTTGTTCT
1 TTT-TTCT
422261 TTTTTC-
1 TTTTTCT
422267 TTTTTC-
1 TTTTTCT
422273 TTTTTC-
1 TTTTTCT
422279 TTTTTCT
1 TTTTTCT
422286 TTTTT
1 TTTTT
422291 TCAATTTAGG
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
6 18 0.33
7 23 0.42
8 14 0.25
ACGTcount: A:0.01, C:0.13, G:0.01, T:0.84
Consensus pattern (7 bp):
TTTTTCT
Found at i:428946 original size:23 final size:23
Alignment explanation
Indices: 428919--428972 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
428909 AGTGAATATT
*
428919 TAAAAACGAA-AAAAAAATAAAAA
1 TAAAAAC-AAGAAAAAAACAAAAA
* *
428942 TAAAAACAAGAACAAAACAAGAA
1 TAAAAACAAGAAAAAAACAAAAA
428965 TAAAAACA
1 TAAAAACA
428973 CAGAGAAGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
22 2 0.07
23 25 0.93
ACGTcount: A:0.78, C:0.09, G:0.06, T:0.07
Consensus pattern (23 bp):
TAAAAACAAGAAAAAAACAAAAA
Found at i:428984 original size:23 final size:22
Alignment explanation
Indices: 428938--428992 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
428928 AAAAAAAATA
428938 AAAATAAAAACAAGAACAAAAC
1 AAAATAAAAACAAGAACAAAAC
* *
428960 AAGAATAAAAACACAG-AGAAGAC
1 AA-AATAAAAACA-AGAACAAAAC
428983 AAAATAAAAA
1 AAAATAAAAA
428993 AGAATAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 10 0.34
23 17 0.59
24 2 0.07
ACGTcount: A:0.75, C:0.11, G:0.09, T:0.05
Consensus pattern (22 bp):
AAAATAAAAACAAGAACAAAAC
Found at i:429238 original size:27 final size:28
Alignment explanation
Indices: 429195--429249 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
429185 TAATAATTTG
*
429195 TAAATAAAAAAAGTAATA-AAATAAAAA
1 TAAACAAAAAAAGTAATATAAATAAAAA
*
429222 TAAACAAATAAAA-TAATATATATAAAAA
1 TAAACAAA-AAAAGTAATATAAATAAAAA
429250 ACAATAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.75, C:0.02, G:0.02, T:0.22
Consensus pattern (28 bp):
TAAACAAAAAAAGTAATATAAATAAAAA
Found at i:429246 original size:22 final size:20
Alignment explanation
Indices: 429209--429267 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 20
429199 TAAAAAAAGT
429209 AATAAAATAA-A-AATAAACA
1 AATAAAATAATATAATAAA-A
429228 AATAAAATAATATATATAAAA
1 AATAAAATAATATA-ATAAAA
*
429249 AACAATAATAATATTAATA
1 AATAA-AATAATA-TAATA
429268 TTGAAAATAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
19 10 0.29
20 1 0.03
21 6 0.18
22 15 0.44
23 2 0.06
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.25
Consensus pattern (20 bp):
AATAAAATAATATAATAAAA
Found at i:429255 original size:24 final size:24
Alignment explanation
Indices: 429208--429287 Score: 74
Period size: 24 Copynumber: 3.3 Consensus size: 24
429198 ATAAAAAAAG
*
429208 TAATAA-AATAAAAATAAACAAATAA
1 TAATAATAATATAAA-AAAC-AATAA
429233 -AATAATATATATAAAAAACAATAA
1 TAATAATA-ATATAAAAAACAATAA
* ** *
429257 TAATATTAATATTGAAAATAATAA
1 TAATAATAATATAAAAAACAATAA
429281 TAATAAT
1 TAATAAT
429288 GGTTTAAAAA
Statistics
Matches: 46, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
24 29 0.63
25 11 0.24
26 6 0.13
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.29
Consensus pattern (24 bp):
TAATAATAATATAAAAAACAATAA
Found at i:450465 original size:3 final size:3
Alignment explanation
Indices: 450457--450500 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
450447 GGAAGCAGGT
450457 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
450501 GCGTTTATCC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:456240 original size:19 final size:20
Alignment explanation
Indices: 456216--456256 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
456206 TGATTTAATC
* *
456216 TATATATG-TTAGTTTTTAT
1 TATATATGAATAGTATTTAT
456235 TATATATGAATAGTATTTAT
1 TATATATGAATAGTATTTAT
456255 TA
1 TA
456257 AATCATATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
TATATATGAATAGTATTTAT
Done.