Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007321.1 Hibiscus syriacus cultivar Beakdansim tig00019539_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: 88857
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:3914 original size:15 final size:15
Alignment explanation
Indices: 3894--3923 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
3884 ATCTAAACAT
3894 GAAATGACCCGACCC
1 GAAATGACCCGACCC
3909 GAAATGACCCGACCC
1 GAAATGACCCGACCC
3924 AAACCCGATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.40, G:0.20, T:0.07
Consensus pattern (15 bp):
GAAATGACCCGACCC
Found at i:13519 original size:24 final size:22
Alignment explanation
Indices: 13461--13534 Score: 87
Period size: 21 Copynumber: 3.3 Consensus size: 22
13451 AGTCGAGGGT
13461 TTCATAGGTCCTTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
13482 CTCATAGGTCCTTCGGGACATATA
1 TTCATAGGTCCTTCGGGACA-A-A
* *
13506 TTCACAGGTCCTTCGAGACAAA
1 TTCATAGGTCCTTCGGGACAAA
13528 TCTCATA
1 T-TCATA
13535 TGTCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
21 18 0.41
22 2 0.05
23 6 0.14
24 18 0.41
ACGTcount: A:0.27, C:0.26, G:0.19, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:17135 original size:25 final size:25
Alignment explanation
Indices: 17107--17161 Score: 67
Period size: 25 Copynumber: 2.2 Consensus size: 25
17097 AATATTTTAT
17107 ATATAAT-TAATATAAAAAATATAAA
1 ATATAATAT-ATATAAAAAATATAAA
* **
17132 ATATTATATATATAATTAATATAAA
1 ATATAATATATATAAAAAATATAAA
17157 ATATA
1 ATATA
17162 TAAAATATTA
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 24 0.96
26 1 0.04
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (25 bp):
ATATAATATATATAAAAAATATAAA
Found at i:17142 original size:34 final size:34
Alignment explanation
Indices: 17095--17179 Score: 152
Period size: 34 Copynumber: 2.5 Consensus size: 34
17085 CCCGAACCCG
*
17095 AAAATATTTTATATATAATTAATATAAAAAATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
*
17129 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAAAATAT
17163 AAAATATTATATATATA
1 AAAATATTATATATATA
17180 TAATCGGGGC
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 49 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAAAATAT
Found at i:17178 original size:18 final size:18
Alignment explanation
Indices: 17125--17182 Score: 68
Period size: 18 Copynumber: 3.3 Consensus size: 18
17115 AATATAAAAA
17125 ATATAAAATATTATATAT
1 ATATAAAATATTATATAT
* *
17143 ATA-ATTAATA-TA-AAAT
1 ATATA-AAATATTATATAT
17159 ATATAAAATATTATATAT
1 ATATAAAATATTATATAT
17177 ATATAA
1 ATATAA
17183 TCGGGGCGGG
Statistics
Matches: 32, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
16 10 0.31
17 6 0.19
18 16 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
ATATAAAATATTATATAT
Found at i:17242 original size:5 final size:5
Alignment explanation
Indices: 17232--17257 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
17222 AATCCCCGAT
17232 ACCCG ACCCG ACCCG ACCCG ACCCG A
1 ACCCG ACCCG ACCCG ACCCG ACCCG A
17258 TATCATTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.23, C:0.58, G:0.19, T:0.00
Consensus pattern (5 bp):
ACCCG
Found at i:18434 original size:25 final size:26
Alignment explanation
Indices: 18400--18456 Score: 71
Period size: 27 Copynumber: 2.2 Consensus size: 26
18390 ATACTTTTAA
* * *
18400 TAAATTAAAAT-AAATTATATATTTT
1 TAAATGAAAATAAAATGAAATATTTT
18425 TAAATGAAAATAAAAATGAAATATTTT
1 TAAATGAAAAT-AAAATGAAATATTTT
18452 TAAAT
1 TAAAT
18457 TAAGTTAATA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 10 0.37
27 17 0.63
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (26 bp):
TAAATGAAAATAAAATGAAATATTTT
Found at i:18473 original size:27 final size:25
Alignment explanation
Indices: 18443--18503 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
18433 AATAAAAATG
*
18443 AAATATTTTTAAATTAAGTTAATAGT-A
1 AAATATTTTT-AA-TAAGTTAACA-TAA
*
18470 AAATATATTTAATAAGTTAACATAA
1 AAATATTTTTAATAAGTTAACATAA
18495 AAATATTTT
1 AAATATTTT
18504 AAGTTAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
24 1 0.03
25 18 0.60
26 2 0.07
27 9 0.30
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.43
Consensus pattern (25 bp):
AAATATTTTTAATAAGTTAACATAA
Found at i:18497 original size:25 final size:25
Alignment explanation
Indices: 18443--18510 Score: 68
Period size: 25 Copynumber: 2.6 Consensus size: 25
18433 AATAAAAATG
*
18443 AAATATTTTTAAATTAAGTTAATAGTA
1 AAATA-TTTT-AATTAAGTTAACAGTA
18470 AAATATATTTAA-TAAGTTAACA-TAA
1 AAATAT-TTTAATTAAGTTAACAGT-A
18495 AAATATTTTAAGTTAA
1 AAATATTTTAA-TTAA
18511 AATATATATT
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
24 6 0.17
25 16 0.44
26 6 0.17
27 8 0.22
ACGTcount: A:0.51, C:0.01, G:0.06, T:0.41
Consensus pattern (25 bp):
AAATATTTTAATTAAGTTAACAGTA
Found at i:18912 original size:6 final size:6
Alignment explanation
Indices: 18903--18934 Score: 55
Period size: 6 Copynumber: 5.2 Consensus size: 6
18893 AAAATTTAAT
18903 ATAAAA ATAAAA ATGAAAA ATAAAA ATAAAA A
1 ATAAAA ATAAAA AT-AAAA ATAAAA ATAAAA A
18935 ATATATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 19 0.76
7 6 0.24
ACGTcount: A:0.81, C:0.00, G:0.03, T:0.16
Consensus pattern (6 bp):
ATAAAA
Found at i:18921 original size:13 final size:13
Alignment explanation
Indices: 18900--18937 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
18890 ATTAAAATTT
18900 AATATAAAAATAAA
1 AATA-AAAAATAAA
*
18914 AATGAAAAATAAA
1 AATAAAAAATAAA
18927 AATAAAAAATA
1 AATAAAAAATA
18938 TATAATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 19 0.86
14 3 0.14
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (13 bp):
AATAAAAAATAAA
Found at i:19090 original size:22 final size:23
Alignment explanation
Indices: 19042--19091 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
19032 AAAAATCATT
* *
19042 TTTTTAATTACAAATACATGATC
1 TTTTTAATTACAAATACACGATA
* *
19065 TTTTT-ATTATAAATACCCGATA
1 TTTTTAATTACAAATACACGATA
19087 TTTTT
1 TTTTT
19092 TAACTGGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.34, C:0.12, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTTTAATTACAAATACACGATA
Found at i:19320 original size:31 final size:31
Alignment explanation
Indices: 19285--19350 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
19275 TTAACTTGGG
*
19285 GTGACCACAAATTAATTAAATAAAAACGAAA
1 GTGACCACAAATTAATTAAATAAAAACAAAA
* **
19316 GTGACCATATCTTAATTAAATAAAAACAAAA
1 GTGACCACAAATTAATTAAATAAAAACAAAA
19347 GTGA
1 GTGA
19351 TCATATCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.55, C:0.12, G:0.11, T:0.23
Consensus pattern (31 bp):
GTGACCACAAATTAATTAAATAAAAACAAAA
Found at i:19356 original size:31 final size:31
Alignment explanation
Indices: 19296--19360 Score: 112
Period size: 31 Copynumber: 2.1 Consensus size: 31
19286 TGACCACAAA
*
19296 TTAATTAAATAAAAACGAAAGTGACCATATC
1 TTAATTAAATAAAAACAAAAGTGACCATATC
*
19327 TTAATTAAATAAAAACAAAAGTGATCATATC
1 TTAATTAAATAAAAACAAAAGTGACCATATC
19358 TTA
1 TTA
19361 TGTTTTTTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.52, C:0.11, G:0.08, T:0.29
Consensus pattern (31 bp):
TTAATTAAATAAAAACAAAAGTGACCATATC
Found at i:20073 original size:4 final size:4
Alignment explanation
Indices: 20064--20089 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
20054 AGTTTACTTT
20064 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
20090 ATTTTAAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:20750 original size:20 final size:20
Alignment explanation
Indices: 20727--20773 Score: 85
Period size: 20 Copynumber: 2.4 Consensus size: 20
20717 AAATTCGCGT
20727 TGCGAATACGTAAATCGCAA
1 TGCGAATACGTAAATCGCAA
*
20747 TGCGAATACGTAAATCTCAA
1 TGCGAATACGTAAATCGCAA
20767 TGCGAAT
1 TGCGAAT
20774 CTGACTATCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.23
Consensus pattern (20 bp):
TGCGAATACGTAAATCGCAA
Found at i:20994 original size:22 final size:22
Alignment explanation
Indices: 20969--21030 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 22
20959 GGCGACATCC
20969 GTCCCCATCTCCGACGAAATCA
1 GTCCCCATCTCCGACGAAATCA
20991 GTCCCCA----CGACGATAA-CA
1 GTCCCCATCTCCGACGA-AATCA
* *
21009 GTCTCCATCTCCGGCGAAATCA
1 GTCCCCATCTCCGACGAAATCA
21031 TTCACTGTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
18 14 0.44
19 2 0.06
21 2 0.06
22 14 0.44
ACGTcount: A:0.27, C:0.39, G:0.16, T:0.18
Consensus pattern (22 bp):
GTCCCCATCTCCGACGAAATCA
Found at i:21387 original size:20 final size:20
Alignment explanation
Indices: 21362--21410 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
21352 CAACGAGTGA
*
21362 ATCGCAACGCGAAAATGACT
1 ATCGCAACGCGAAAATAACT
* **
21382 ATCGCAATGCGAATTTAACT
1 ATCGCAACGCGAAAATAACT
21402 ATCGCAACG
1 ATCGCAACG
21411 AGAGAATTGC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.37, C:0.24, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGCGAAAATAACT
Found at i:21492 original size:20 final size:20
Alignment explanation
Indices: 21452--21512 Score: 68
Period size: 20 Copynumber: 3.0 Consensus size: 20
21442 TGCGATTCTT
**
21452 GCGTTGCGATAGTCAAATTC
1 GCGTTGCGATAGTCATTTTC
*
21472 GCGTTACGATAGTCATTTTC
1 GCGTTGCGATAGTCATTTTC
* **
21492 GTGTTGCGATTTTCATTTTC
1 GCGTTGCGATAGTCATTTTC
21512 G
1 G
21513 TGTTTCGATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.18, C:0.18, G:0.23, T:0.41
Consensus pattern (20 bp):
GCGTTGCGATAGTCATTTTC
Found at i:21513 original size:20 final size:20
Alignment explanation
Indices: 21484--21523 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
21474 GTTACGATAG
21484 TCATTTTCGTGTTGCGATTT
1 TCATTTTCGTGTTGCGATTT
*
21504 TCATTTTCGTGTTTCGATTT
1 TCATTTTCGTGTTGCGATTT
21524 AAAGTTTCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.10, C:0.15, G:0.17, T:0.57
Consensus pattern (20 bp):
TCATTTTCGTGTTGCGATTT
Found at i:21531 original size:20 final size:20
Alignment explanation
Indices: 21488--21531 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
21478 CGATAGTCAT
** *
21488 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
*
21508 TTTCGTGTTTCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
21528 TTTC
1 TTTC
21532 AGAAACTATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.14, C:0.14, G:0.18, T:0.55
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:23410 original size:20 final size:20
Alignment explanation
Indices: 23385--23528 Score: 167
Period size: 20 Copynumber: 7.5 Consensus size: 20
23375 AGAATAGTTT
23385 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
* *
23405 ACTATCGTAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
23425 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
23441 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
23459 ACTATCGCAATGCGAAAATA
1 ACTATCGCAATGCGAAAATG
23479 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
** *
23499 ACTATCTTAATGC-AAATTTG
1 ACTATCGCAATGCGAAA-ATG
23519 ACTATCGCAA
1 ACTATCGCAA
23529 CGAAAAAATC
Statistics
Matches: 105, Mismatches: 12, Indels: 14
0.80 0.09 0.11
Matches are distributed among these distances:
14 7 0.07
16 4 0.04
17 4 0.04
18 4 0.04
19 3 0.03
20 83 0.79
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:23617 original size:19 final size:20
Alignment explanation
Indices: 23573--23620 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
23563 GCGATTCTCT
23573 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* *
23593 CATTGCGATAGTC-ATTTCG
1 CGTTGCGATAGTCAAATTCG
*
23612 TGTTGCGAT
1 CGTTGCGAT
23621 TTTGTTGTTG
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:23686 original size:20 final size:20
Alignment explanation
Indices: 23661--23736 Score: 134
Period size: 20 Copynumber: 3.8 Consensus size: 20
23651 GATTCTCTCG
**
23661 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
23681 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
23701 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
23721 TTGCGATAGTCATTTT
1 TTGCGATAGTCATTTT
23737 TGCGTTGTGA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.22, C:0.18, G:0.20, T:0.39
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:23824 original size:11 final size:11
Alignment explanation
Indices: 23808--23832 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
23798 TGCATTACTT
23808 CAACCAAAAGA
1 CAACCAAAAGA
23819 CAACCAAAAGA
1 CAACCAAAAGA
23830 CAA
1 CAA
23833 ATACTAACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.64, C:0.28, G:0.08, T:0.00
Consensus pattern (11 bp):
CAACCAAAAGA
Found at i:24083 original size:12 final size:12
Alignment explanation
Indices: 24068--24098 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
24058 ATCATGTTTG
24068 TTTATTTATTAA
1 TTTATTTATTAA
*
24080 TTTATGTATTAA
1 TTTATTTATTAA
24092 TTTATTT
1 TTTATTT
24099 TTAGCGGCCC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTATTTATTAA
Found at i:24333 original size:21 final size:21
Alignment explanation
Indices: 24242--24349 Score: 92
Period size: 21 Copynumber: 5.1 Consensus size: 21
24232 GACTTACCTG
* *
24242 TCATCGTTCAATAGGCCTCCCC
1 TCATCGTTCAAGAGGCC-CCTC
*
24264 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTC
** *
24284 TCATCCCTCAAGAGTCCCCTC
1 TCATCGTTCAAGAGGCCCCTC
* * * *
24305 CCACCGTTCAAGAGGCCACTG
1 TCATCGTTCAAGAGGCCCCTC
* *
24326 TCATCGTTGAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTC
24347 TCA
1 TCA
24350 ACATTCTAGA
Statistics
Matches: 65, Mismatches: 20, Indels: 3
0.74 0.23 0.03
Matches are distributed among these distances:
20 3 0.05
21 61 0.94
22 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTC
Found at i:30255 original size:2 final size:2
Alignment explanation
Indices: 30248--30280 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
30238 CCCGATTTAT
30248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
30281 TTATTTTATA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30371 original size:39 final size:39
Alignment explanation
Indices: 30305--30421 Score: 125
Period size: 39 Copynumber: 3.0 Consensus size: 39
30295 ATTTTATTTA
* * *
30305 TAATT-CTCAAATTATATCAC-TCTAACATTCTAAATTCT
1 TAATTCCTTAAATTATTTCACAT-TAACATTCTAAATTAT
* *
30343 TAATTTCTTAAA-TATTGTCACCA-TAACATTCCAAATTAT
1 TAATTCCTTAAATTATT-TCA-CATTAACATTCTAAATTAT
*
30382 TAATTCCTTAAATTATTTCACATTAACACTCTAAATTAT
1 TAATTCCTTAAATTATTTCACATTAACATTCTAAATTAT
30421 T
1 T
30422 TTTTAGAATA
Statistics
Matches: 66, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
38 10 0.15
39 51 0.77
40 5 0.08
ACGTcount: A:0.38, C:0.19, G:0.01, T:0.43
Consensus pattern (39 bp):
TAATTCCTTAAATTATTTCACATTAACATTCTAAATTAT
Found at i:33147 original size:22 final size:22
Alignment explanation
Indices: 33119--33171 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
33109 ACTTTTGGTA
33119 GCCTTAAGGGGGCATAAAAGAG
1 GCCTTAAGGGGGCATAAAAGAG
* *
33141 GCCTTAAGGGGGCTTAAGAGAG
1 GCCTTAAGGGGGCATAAAAGAG
* *
33163 ACTTTAAGG
1 GCCTTAAGG
33172 AGCCATCTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.32, C:0.13, G:0.36, T:0.19
Consensus pattern (22 bp):
GCCTTAAGGGGGCATAAAAGAG
Found at i:36311 original size:12 final size:12
Alignment explanation
Indices: 36290--36333 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
36280 ATAGTATTGA
*
36290 TTCATATTGCAT
1 TTCATGTTGCAT
36302 TTCATGTTGCAT
1 TTCATGTTGCAT
* *
36314 TTCATGATCCAT
1 TTCATGTTGCAT
*
36326 TTAATGTT
1 TTCATGTT
36334 AAATAGTTAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 27 1.00
ACGTcount: A:0.23, C:0.16, G:0.11, T:0.50
Consensus pattern (12 bp):
TTCATGTTGCAT
Found at i:38379 original size:34 final size:32
Alignment explanation
Indices: 38313--38382 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
38303 ACCTTACAAC
* * *
38313 TCCCTAGTTTTTCAGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACAGGGATAAACTAAAACCTT
*
38345 TCCCTAGCTTTTACACGGGATAAGCTAAAACCTT
1 TCCCTAG-TTTTACA-GGGATAAACTAAAACCTT
38379 TCCC
1 TCCC
38383 CATTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 7 0.22
33 6 0.19
34 19 0.59
ACGTcount: A:0.26, C:0.29, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACAGGGATAAACTAAAACCTT
Found at i:38622 original size:20 final size:22
Alignment explanation
Indices: 38597--38636 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
38587 TGTTTTATAT
38597 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
38617 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
38637 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:38741 original size:21 final size:21
Alignment explanation
Indices: 38715--38772 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
38705 TGCACAGCAG
38715 GATGCATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
38736 GATGCATCGATGCACAACCTT
1 GATGCATCGATGCACAACCTT
38757 GATGCATCGATGCACA
1 GATGCATCGATGCACA
38773 GAAGTATGCA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (21 bp):
GATGCATCGATGCACAACCTT
Found at i:38980 original size:29 final size:31
Alignment explanation
Indices: 38948--39007 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 31
38938 AAACTTTGAA
38948 TAAATTCAATT-AAGTCCAAAAA-CATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
38977 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATTCAAGTCCAAAAACCATTTTG
39008 CCTTAAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (31 bp):
TAAATTCAATTCAAGTCCAAAAACCATTTTG
Found at i:42683 original size:33 final size:33
Alignment explanation
Indices: 42612--42684 Score: 78
Period size: 33 Copynumber: 2.2 Consensus size: 33
42602 TTAGATTTTT
* **
42612 AATTAAGCCTTAGATTTTAGGTTCTTTTGTTATT
1 AATTAAGCCTTAGA-TTTAGGTTCTCTTGTTAGA
42646 AATTAATGCCTTAG-TTTAGGTTC-CTTGATTAGA
1 AATTAA-GCCTTAGATTTAGGTTCTCTTG-TTAGA
42679 AATTAA
1 AATTAA
42685 ATAAGTTTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 3 0.09
33 18 0.53
34 6 0.18
35 7 0.21
ACGTcount: A:0.29, C:0.10, G:0.15, T:0.47
Consensus pattern (33 bp):
AATTAAGCCTTAGATTTAGGTTCTCTTGTTAGA
Found at i:43558 original size:21 final size:20
Alignment explanation
Indices: 43472--43629 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
43462 AAATGACCAA
**
43472 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
43491 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
43511 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
43531 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
43552 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
43573 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
43593 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
43614 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
43630 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:43661 original size:20 final size:20
Alignment explanation
Indices: 43596--43825 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
43586 CGATTTTCCA
** *
43596 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
43616 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
* *
43636 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
43656 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
43676 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
43696 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
**
43716 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
43736 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
43756 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
43776 AAATCGCAAGGAGAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
43796 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
43816 AAATCACAAC
1 AAATCGCAAC
43826 ACTGAAATTT
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:44546 original size:24 final size:24
Alignment explanation
Indices: 44507--44553 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44497 AAATTTGGTC
44507 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
44531 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
44554 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:44745 original size:12 final size:12
Alignment explanation
Indices: 44728--44752 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44718 ATATAATCCT
44728 GAAGAAGAAAAA
1 GAAGAAGAAAAA
44740 GAAGAAGAAAAA
1 GAAGAAGAAAAA
44752 G
1 G
44753 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:47126 original size:19 final size:19
Alignment explanation
Indices: 47086--47183 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
47076 GATTCTCTCG
47086 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
47106 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
47125 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
47139 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47158 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
47177 TTGCGAT
1 TTGCGAT
47184 AGTCAATTTT
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 6 0.08
16 7 0.10
17 7 0.10
19 36 0.51
20 15 0.21
ACGTcount: A:0.14, C:0.22, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:47180 original size:52 final size:53
Alignment explanation
Indices: 47067--47183 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
47057 GAAATGAAAA
47067 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
47120 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
47172 TCGCATTGCGAT
1 TCGCATTGCGAT
47184 AGTCAATTTT
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 30 0.47
53 34 0.53
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:47294 original size:33 final size:33
Alignment explanation
Indices: 47242--47403 Score: 150
Period size: 33 Copynumber: 4.7 Consensus size: 33
47232 CCATTACATT
47242 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
* *
47276 TCGCAATGCGAAATGAAAATCGCAATGCGA-AA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* * * *
47308 T-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAGAA
47347 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
* *
47380 TCGCAACGCGAAATTAAAATCGCA
1 TCGCAATGCGAAATGAAAATCGCA
47404 TTGCGATTAT
Statistics
Matches: 104, Mismatches: 13, Indels: 23
0.74 0.09 0.16
Matches are distributed among these distances:
31 7 0.07
32 7 0.07
33 53 0.51
34 10 0.10
35 1 0.01
36 2 0.02
38 10 0.10
39 7 0.07
40 7 0.07
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.14
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:47298 original size:19 final size:19
Alignment explanation
Indices: 47242--47409 Score: 168
Period size: 19 Copynumber: 9.6 Consensus size: 19
47232 CCATTACATT
47242 TCGCAATGCGGAAATGAAAA
1 TCGCAATGC-GAAATGAAAA
*
47262 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
47276 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
47295 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
47314 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
47328 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
47347 TCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAA
*
47366 TCGCAA--CG--A-GAGAA
1 TCGCAATGCGAAATGAAAA
* *
47380 TCGCAACGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAA
*
47399 TCGCATTGCGA
1 TCGCAATGCGA
47410 TTATCCCATT
Statistics
Matches: 124, Mismatches: 9, Indels: 31
0.76 0.05 0.19
Matches are distributed among these distances:
14 30 0.24
15 3 0.02
16 6 0.05
17 5 0.04
18 4 0.03
19 70 0.56
20 6 0.05
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (19 bp):
TCGCAATGCGAAATGAAAA
Found at i:47321 original size:52 final size:52
Alignment explanation
Indices: 47242--47409 Score: 300
Period size: 52 Copynumber: 3.2 Consensus size: 52
47232 CCATTACATT
47242 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
47295 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
* *
47347 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATTAAAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
*
47399 TCGCATTGCGA
1 TCGCAATGCGA
47410 TTATCCCATT
Statistics
Matches: 112, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
52 103 0.92
53 9 0.08
ACGTcount: A:0.44, C:0.18, G:0.23, T:0.14
Consensus pattern (52 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAA
Found at i:47458 original size:19 final size:19
Alignment explanation
Indices: 47416--47496 Score: 109
Period size: 19 Copynumber: 4.5 Consensus size: 19
47406 GCGATTATCC
47416 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
47436 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
47455 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
47471 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
47488 CATTGCGAT
1 CATTGCGAT
47497 AGTCAATTTT
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.13
17 7 0.13
19 17 0.31
20 17 0.31
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.44
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:47622 original size:14 final size:14
Alignment explanation
Indices: 47603--47639 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
47593 CATCAATTAC
47603 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
47617 ACAAATCATCTTTT
1 ACAAATCAACTTTT
47631 ACAAATCAA
1 ACAAATCAA
47640 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:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:49637 original size:14 final size:14
Alignment explanation
Indices: 49618--49674 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
49608 GCGAAATGAA
*
49618 AATCGCAACGACAG
1 AATCGCAACGAAAG
49632 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
49649 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
49665 AATCGCAACG
1 AATCGCAACG
49675 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:49645 original size:33 final size:33
Alignment explanation
Indices: 49599--49691 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
49589 GCGAAACCAA
*
49599 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
49632 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
49665 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
49692 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:49656 original size:19 final size:19
Alignment explanation
Indices: 49562--49696 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
49552 TAGTTTACTT
* *
49562 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
49582 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
49601 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49620 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
49634 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
49653 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
49667 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
49686 TCGCAATGCGA
1 TCGCAACGCGA
49697 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:49714 original size:19 final size:19
Alignment explanation
Indices: 49692--49820 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
49682 AAAATCGCAA
49692 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
49711 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
49725 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
49744 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
49758 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
49777 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
49796 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
49816 TGCGA
1 TGCGA
49821 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:49734 original size:33 final size:33
Alignment explanation
Indices: 49692--49783 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
49682 AAAATCGCAA
49692 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
49725 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
49758 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
49784 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:50158 original size:93 final size:93
Alignment explanation
Indices: 49864--50335 Score: 903
Period size: 93 Copynumber: 5.1 Consensus size: 93
49854 TTGAATGGAT
49864 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
49929 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
49957 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTA-TTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50021 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
50049 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50114 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50142 AAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50206 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50234 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
50299 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
50327 AAATTTACT
1 AAATTTACT
50336 AAGCAATCTA
Statistics
Matches: 374, Mismatches: 3, Indels: 4
0.98 0.01 0.01
Matches are distributed among these distances:
92 182 0.49
93 192 0.51
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:50190 original size:185 final size:185
Alignment explanation
Indices: 49864--50335 Score: 901
Period size: 185 Copynumber: 2.6 Consensus size: 185
49854 TTGAATGGAT
49864 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
49929 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
49994 TACTATTCACAGTGTTATAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
50049 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTATAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
50114 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGAC-AAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
50178 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTA-TTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
50234 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
50299 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
50336 AAGCAATCTA
Statistics
Matches: 282, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 18 0.06
185 264 0.94
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:52061 original size:14 final size:14
Alignment explanation
Indices: 52042--52131 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
52032 TTGAAATGAA
52042 AATCGCAACGAGAG
1 AATCGCAACGAGAG
52056 AATCGCAACGAGAGATG
1 AATCGCAAC--GAGA-G
52073 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
52089 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
52108 AATCGCAACGAGAG
1 AATCGCAACGAGAG
52122 AATCGCAACG
1 AATCGCAACG
52132 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 29 0.45
15 1 0.02
16 7 0.11
17 7 0.11
18 1 0.02
19 19 0.30
ACGTcount: A:0.43, C:0.22, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:52079 original size:33 final size:33
Alignment explanation
Indices: 52034--52148 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
52024 TCTTTTGGTT
*
52034 GAAATGAAAATCGCAACGAGAGAATCGCAACGA
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
52067 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
52100 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
52133 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
52149 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 77 1.00
ACGTcount: A:0.46, C:0.20, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:52080 original size:19 final size:18
Alignment explanation
Indices: 52041--52122 Score: 72
Period size: 19 Copynumber: 4.9 Consensus size: 18
52031 GTTGAAATGA
52041 AAATCGCAAC--GAGA-G
1 AAATCGCAACGAGAGATG
52056 -AATCGCAACGAGAGATG
1 AAATCGCAACGAGAGATG
52073 ACAATCGCAAC--GAGA-G
1 A-AATCGCAACGAGAGATG
* *
52089 -AATCGCAACGCGAAATG
1 AAATCGCAACGAGAGATG
52106 AAAATCGCAACGAGAGA
1 -AAATCGCAACGAGAGA
52123 ATCGCAACGC
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.33
16 8 0.15
17 6 0.11
19 22 0.41
ACGTcount: A:0.45, C:0.21, G:0.26, T:0.09
Consensus pattern (18 bp):
AAATCGCAACGAGAGATG
Found at i:52146 original size:19 final size:19
Alignment explanation
Indices: 52089--52153 Score: 77
Period size: 19 Copynumber: 3.7 Consensus size: 19
52079 GCAACGAGAG
52089 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
52108 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
52122 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
52141 AATCGCAATGCGA
1 AATCGCAACGCGA
52154 TTTTGGTTTC
Statistics
Matches: 38, Mismatches: 3, Indels: 10
0.75 0.06 0.20
Matches are distributed among these distances:
14 10 0.26
15 1 0.03
16 2 0.05
17 2 0.05
18 1 0.03
19 22 0.58
ACGTcount: A:0.45, C:0.22, G:0.23, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:52184 original size:14 final size:14
Alignment explanation
Indices: 52165--52221 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
52155 TTTGGTTTCG
52165 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
52179 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
52198 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
52212 CGTTGCGATT
1 CGTTGCGATT
52222 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:52197 original size:33 final size:33
Alignment explanation
Indices: 52149--52229 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
52139 AAAATCGCAA
**
52149 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
52182 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
52215 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
52230 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:52232 original size:21 final size:21
Alignment explanation
Indices: 52206--52281 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
52196 CGCGTTGCGA
52206 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
52227 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
52247 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
52268 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
52282 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:52262 original size:41 final size:41
Alignment explanation
Indices: 52205--52282 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
52195 TCGCGTTGCG
*
52205 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
52246 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
52283 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:52408 original size:33 final size:33
Alignment explanation
Indices: 52361--52431 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
52351 AATACTAACT
* *
52361 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
52394 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
52427 TGAAA
1 TGAAA
52432 TCTAAGTGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.48, C:0.17, G:0.24, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:52665 original size:22 final size:22
Alignment explanation
Indices: 52613--52667 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
52603 TGGTTGTGAG
**
52613 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
52635 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
52657 GGATTTCTTCG
1 GGATTTCTTCG
52668 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:52838 original size:20 final size:20
Alignment explanation
Indices: 52813--53006 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
52803 CTTTAAATAT
52813 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
52833 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
52855 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52874 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
52894 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
52914 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
52934 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
52954 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
52974 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
52994 CGCGTTGCGATTT
1 CGCGTTGCGATTT
53007 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:53000 original size:60 final size:60
Alignment explanation
Indices: 52813--53006 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
52803 CTTTAAATAT
**
52813 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
52874 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
52934 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
52994 CGCGTTGCGATTT
1 CGCGTTGCGATTT
53007 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:53023 original size:21 final size:21
Alignment explanation
Indices: 52993--53075 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
52983 ATTTTCATAT
*
52993 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
53014 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
53035 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
53056 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
53076 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:53066 original size:42 final size:43
Alignment explanation
Indices: 52973--53071 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
52963 ATTTATGTGT
* *
52973 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
53014 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
53056 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
53072 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:53313 original size:15 final size:14
Alignment explanation
Indices: 53293--53324 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
53283 ATTTCAAATC
53293 TTTTCTAAAATTTGA
1 TTTTCTAAAATTT-A
53308 TTTTCTAAAATTTA
1 TTTTCTAAAATTTA
53322 TTT
1 TTT
53325 CGATTTTTGC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.31, C:0.06, G:0.03, T:0.59
Consensus pattern (14 bp):
TTTTCTAAAATTTA
Found at i:57493 original size:23 final size:23
Alignment explanation
Indices: 57463--57509 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
57453 TTTGAGACAC
57463 AGTGAGTATAGTATAGTGGAGCA
1 AGTGAGTATAGTATAGTGGAGCA
57486 AGTGAGTATAGTATAGTGGAGCA
1 AGTGAGTATAGTATAGTGGAGCA
57509 A
1 A
57510 CTACACAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.36, C:0.04, G:0.34, T:0.26
Consensus pattern (23 bp):
AGTGAGTATAGTATAGTGGAGCA
Found at i:62198 original size:6 final size:6
Alignment explanation
Indices: 62187--62270 Score: 98
Period size: 6 Copynumber: 13.5 Consensus size: 6
62177 ATTATGCTTG
* *
62187 AAAAGA AAAAGA AAAAGAA AAAAGA AAAATA AAAAGA AAATGA AAAAGA
1 AAAAGA AAAAGA AAAAG-A AAAAGA AAAAGA AAAAGA AAAAGA AAAAGA
*
62236 AAATGA AAAAGA AAATA-A AAGGAAGA AAAAGA AAA
1 AAAAGA AAAAGA AAA-AGA AA--AAGA AAAAGA AAA
62271 GGAGGGTTCA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
6 55 0.82
7 8 0.12
8 4 0.06
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (6 bp):
AAAAGA
Found at i:65015 original size:18 final size:19
Alignment explanation
Indices: 64982--65021 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
64972 GTATGTTACA
*
64982 TATTTCATATTATATAGTT
1 TATTTCATACTATATAGTT
65001 TATTT-ATACTATATAGTT
1 TATTTCATACTATATAGTT
65019 TAT
1 TAT
65022 AAATAATAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 15 0.75
19 5 0.25
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (19 bp):
TATTTCATACTATATAGTT
Found at i:67753 original size:19 final size:19
Alignment explanation
Indices: 67684--67751 Score: 82
Period size: 19 Copynumber: 3.5 Consensus size: 19
67674 ACCATATCGA
*
67684 TAGATTCATAACTATACTTT
1 TAGATTCATAACTTTAC-TT
*
67704 TAGATTCACAACTTTACTT
1 TAGATTCATAACTTTACTT
* *
67723 TAGATTCGTAGCTTTACTT
1 TAGATTCATAACTTTACTT
*
67742 TATATTCATA
1 TAGATTCATA
67752 GCCCAATGTA
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
19 26 0.63
20 15 0.37
ACGTcount: A:0.31, C:0.16, G:0.07, T:0.46
Consensus pattern (19 bp):
TAGATTCATAACTTTACTT
Found at i:76306 original size:74 final size:75
Alignment explanation
Indices: 76101--76304 Score: 270
Period size: 74 Copynumber: 2.7 Consensus size: 75
76091 CAAAGCCAAA
* * * * **
76101 AATTACAGATTGCTCAGAGGGAACTGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGTT
1 AATTCCAGAATGCTCGGAGGGAACCGA-TCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
76166 TTGGCCTCGAG
65 TTGGCCTCGAG
* *
76177 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
76242 T-G-CTCCGAG
66 TGGCCT-CGAG
* * *
76251 AATTCCAGTATGCTCGGAGGGAACCGATCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCC
76305 CTTGTACAAC
Statistics
Matches: 114, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
73 19 0.17
74 37 0.32
75 36 0.32
76 22 0.19
ACGTcount: A:0.25, C:0.30, G:0.24, T:0.21
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTT
TGGCCTCGAG
Found at i:84297 original size:29 final size:30
Alignment explanation
Indices: 84254--84324 Score: 117
Period size: 29 Copynumber: 2.3 Consensus size: 30
84244 GGGGGAAGAT
84254 AGGTGTTAAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
84284 AGGTG-TAAATGTTTTACATAATAAATTGA
1 AGGTGTTAAATGTTTTACATAATAAATTGA
84313 AGAAGTGTTAAA
1 AG--GTGTTAAA
84325 GTAAGGGGAG
Statistics
Matches: 38, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
29 26 0.68
30 5 0.13
31 3 0.08
32 4 0.11
ACGTcount: A:0.42, C:0.03, G:0.18, T:0.37
Consensus pattern (30 bp):
AGGTGTTAAATGTTTTACATAATAAATTGA
Found at i:84758 original size:75 final size:75
Alignment explanation
Indices: 84624--84828 Score: 288
Period size: 75 Copynumber: 2.7 Consensus size: 75
84614 CAAAGCCAAA
* * * **
84624 AATTACAGATTGCTCAGAGGGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGT
1 AATTCCAGAATGCTCGGAGGGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGT
*
84689 TTGGCTCTGAG
65 TTGGCTCCGAG
*
84700 ATTTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
*
84765 TTGCTCCGAG
66 TGGCTCCGAG
* * *
84775 AATTCCAGTATGCTCGGAGGGAACCGA-TCCCCCCA-AGGGGGTACCGATTCCCCC
1 AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCC
84829 CTTGTACAAC
Statistics
Matches: 117, Mismatches: 12, Indels: 3
0.89 0.09 0.02
Matches are distributed among these distances:
73 17 0.15
74 8 0.07
75 67 0.57
76 25 0.21
ACGTcount: A:0.25, C:0.31, G:0.24, T:0.20
Consensus pattern (75 bp):
AATTCCAGAATGCTCGGAGGGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTT
TGGCTCCGAG
Found at i:87070 original size:21 final size:21
Alignment explanation
Indices: 87037--87077 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
87027 GATTATAAAA
87037 ATTACTCCTAGTATCGATACT
1 ATTACTCCTAGTATCGATACT
*
87058 ATTAC-CCTCAGTATTGATAC
1 ATTACTCCT-AGTATCGATAC
87078 CCATGCTACA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (21 bp):
ATTACTCCTAGTATCGATACT
Done.