Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008824.1 Hibiscus syriacus cultivar Beakdansim tig00111996_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: 4603428
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 19
Found at i:179240 original size:20 final size:20
Alignment explanation
Indices: 179194--179287 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
179184 GTTTATGCAA
* *
179194 TCGCAACGCAATTTTCAAAAT
1 TCGCAACACGATTTTC-AAAT
179215 T-GCAACACGATTTTCAAAT
1 TCGCAACACGATTTTCAAAT
* * *
179234 TCACAACGCGATTTCCAAAT
1 TCGCAACACGATTTTCAAAT
* * *
179254 TCGTAACAGGAATTTCAAAT
1 TCGCAACACGATTTTCAAAT
* *
179274 TCGTAACTCGATTT
1 TCGCAACACGATTT
179288 CTGAATTCTC
Statistics
Matches: 58, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
19 5 0.09
20 52 0.90
21 1 0.02
ACGTcount: A:0.35, C:0.22, G:0.12, T:0.31
Consensus pattern (20 bp):
TCGCAACACGATTTTCAAAT
Found at i:179241 original size:40 final size:40
Alignment explanation
Indices: 179197--179275 Score: 97
Period size: 40 Copynumber: 2.0 Consensus size: 40
179187 TATGCAATCG
*
179197 CAACGCAATTTTCAAAATT-GCAACACGATTTTCAAATTCA
1 CAACGCAA-TTTCAAAATTCGCAACACGAATTTCAAATTCA
* * * *
179237 CAACGCGATTTCCAAATTCGTAACAGGAATTTCAAATTC
1 CAACGCAATTTCAAAATTCGCAACACGAATTTCAAATTC
179276 GTAACTCGAT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
39 9 0.27
40 24 0.73
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (40 bp):
CAACGCAATTTCAAAATTCGCAACACGAATTTCAAATTCA
Found at i:179362 original size:40 final size:40
Alignment explanation
Indices: 179318--179396 Score: 104
Period size: 40 Copynumber: 2.0 Consensus size: 40
179308 ACAAGTTTCC
* *
179318 TTTTCACAACAATATTTTCTAAATCGCAACACGAATTTTG
1 TTTTCACAACAAGATTTTCGAAATCGCAACACGAATTTTG
* ** *
179358 TTTTCGCAACTCGATTTTCGAATTCGCAACACGAATTTT
1 TTTTCACAACAAGATTTTCGAAATCGCAACACGAATTTT
179397 AATTTCGTAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 33 1.00
ACGTcount: A:0.30, C:0.22, G:0.10, T:0.38
Consensus pattern (40 bp):
TTTTCACAACAAGATTTTCGAAATCGCAACACGAATTTTG
Found at i:179364 original size:20 final size:21
Alignment explanation
Indices: 179331--179396 Score: 73
Period size: 20 Copynumber: 3.2 Consensus size: 21
179321 TCACAACAAT
* *
179331 ATTTTCTAAATCGCAACACGA
1 ATTTTCGAATTCGCAACACGA
** *
179352 ATTTT-GTTTTCGCAACTCG-
1 ATTTTCGAATTCGCAACACGA
179371 ATTTTCGAATTCGCAACACGA
1 ATTTTCGAATTCGCAACACGA
179392 ATTTT
1 ATTTT
179397 AATTTCGTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
19 5 0.14
20 20 0.57
21 10 0.29
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (21 bp):
ATTTTCGAATTCGCAACACGA
Found at i:179403 original size:20 final size:20
Alignment explanation
Indices: 179341--179408 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
179331 ATTTTCTAAA
**
179341 TCGCAACACGAATTTTGTTT
1 TCGCAACACGAATTTTAATT
*
179361 TCGCAACTCG-ATTTTCGAA-T
1 TCGCAACACGAATTTT--AATT
179381 TCGCAACACGAATTTTAATT
1 TCGCAACACGAATTTTAATT
*
179401 TCGTAACA
1 TCGCAACA
179409 GCTTTTATTT
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
19 7 0.18
20 27 0.69
21 5 0.13
ACGTcount: A:0.29, C:0.22, G:0.13, T:0.35
Consensus pattern (20 bp):
TCGCAACACGAATTTTAATT
Found at i:180398 original size:24 final size:24
Alignment explanation
Indices: 180347--180400 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
180337 GTATTCGAAA
**
180347 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCAAGAC
* *
180371 TTTGATCTTGGTCAATACTAAGAT
1 TTTGATCTTGGTCAATACCAAGAC
180395 TTTGAT
1 TTTGAT
180401 GATGTTTCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCAAGAC
Found at i:182332 original size:6 final size:6
Alignment explanation
Indices: 182323--182364 Score: 66
Period size: 6 Copynumber: 7.0 Consensus size: 6
182313 CAAGAAAAAG
**
182323 AAAATC AAAATC AAAATC GCAATC AAAATC AAAATC AAAATC
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC
182365 TCAATCACAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.62, C:0.19, G:0.02, T:0.17
Consensus pattern (6 bp):
AAAATC
Found at i:182355 original size:24 final size:24
Alignment explanation
Indices: 182323--182371 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
182313 CAAGAAAAAG
182323 AAAATCAAAATCAAAATCGCAATC
1 AAAATCAAAATCAAAATCGCAATC
*
182347 AAAATCAAAATCAAAATCTCAATC
1 AAAATCAAAATCAAAATCGCAATC
182371 A
1 A
182372 CAAACGGCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (24 bp):
AAAATCAAAATCAAAATCGCAATC
Found at i:182370 original size:12 final size:12
Alignment explanation
Indices: 182323--182371 Score: 62
Period size: 12 Copynumber: 4.1 Consensus size: 12
182313 CAAGAAAAAG
*
182323 AAAATCAAAATC
1 AAAATCACAATC
*
182335 AAAATCGCAATC
1 AAAATCACAATC
*
182347 AAAATCAAAATC
1 AAAATCACAATC
*
182359 AAAATCTCAATC
1 AAAATCACAATC
182371 A
1 A
182372 CAAACGGCTT
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 31 1.00
ACGTcount: A:0.59, C:0.20, G:0.02, T:0.18
Consensus pattern (12 bp):
AAAATCACAATC
Found at i:182650 original size:29 final size:29
Alignment explanation
Indices: 182608--182667 Score: 95
Period size: 29 Copynumber: 2.1 Consensus size: 29
182598 TGTTGCGATT
182608 TTCGCATTGCGATTGTTG-TGAAAGTCAAA
1 TTCGCATTGCGATTGTTGCT-AAAGTCAAA
*
182637 TTCGCGTTGCGATTGTTGCTAAAGTCAAA
1 TTCGCATTGCGATTGTTGCTAAAGTCAAA
182666 TT
1 TT
182668 TGAAATGCGA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.37
Consensus pattern (29 bp):
TTCGCATTGCGATTGTTGCTAAAGTCAAA
Found at i:182676 original size:29 final size:29
Alignment explanation
Indices: 182615--182677 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
182605 ATTTTCGCAT
***
182615 TGCGATTGTTGTGAAAGTCAAATTCGCGT
1 TGCGATTGTTGTGAAAGTCAAATTCGAAA
*
182644 TGCGATTGTTGCT-AAAGTCAAATTTGAAA
1 TGCGATTGTTG-TGAAAGTCAAATTCGAAA
182673 TGCGA
1 TGCGA
182678 AAGTAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 28 0.97
30 1 0.03
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (29 bp):
TGCGATTGTTGTGAAAGTCAAATTCGAAA
Found at i:182765 original size:20 final size:20
Alignment explanation
Indices: 182740--182781 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
182730 TCGCAATGCA
*
182740 AATTTGACTTTCACGTTGCG
1 AATTTGACTTTCACATTGCG
* *
182760 AATTTGATTTTCGCATTGCG
1 AATTTGACTTTCACATTGCG
182780 AA
1 AA
182782 AGTGTACCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.17, G:0.19, T:0.40
Consensus pattern (20 bp):
AATTTGACTTTCACATTGCG
Found at i:184283 original size:21 final size:21
Alignment explanation
Indices: 184259--184333 Score: 125
Period size: 21 Copynumber: 3.6 Consensus size: 21
184249 GTGAATTGGG
184259 CTCTTGAACGATGAGAGGGGC
1 CTCTTGAACGATGAGAGGGGC
*
184280 CTCTTGAACGATGAGAAGGGC
1 CTCTTGAACGATGAGAGGGGC
184301 CTCTTGAACGAT-AGGAGGGGC
1 CTCTTGAACGATGA-GAGGGGC
184322 CTCTTGAACGAT
1 CTCTTGAACGAT
184334 TACAGGTGAA
Statistics
Matches: 51, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
20 1 0.02
21 50 0.98
ACGTcount: A:0.25, C:0.20, G:0.33, T:0.21
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGGC
Found at i:184681 original size:42 final size:41
Alignment explanation
Indices: 184635--184715 Score: 101
Period size: 42 Copynumber: 2.0 Consensus size: 41
184625 AGCGGCTACC
**
184635 TCATCACGTAAAGTAGA-TACCTCACCACGTAAAGCACCATTG
1 TCATCACGTAAAACA-ACTACCTCACCACGTAAAG-ACCATTG
* *
184677 TCATCGCGTAAAACAACTACCTCATCACGTAAAGACCAT
1 TCATCACGTAAAACAACTACCTCACCACGTAAAGACCAT
184716 ACTTAATCAC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
41 6 0.18
42 28 0.82
ACGTcount: A:0.37, C:0.30, G:0.12, T:0.21
Consensus pattern (41 bp):
TCATCACGTAAAACAACTACCTCACCACGTAAAGACCATTG
Found at i:184767 original size:21 final size:21
Alignment explanation
Indices: 184743--184792 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
184733 ACCATTGTCG
*
184743 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
** *
184764 TCACACAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
184785 TCACGTAA
1 TCACGTAA
184793 CTCCCCTAAC
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.36, C:0.34, G:0.12, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:186519 original size:19 final size:20
Alignment explanation
Indices: 186459--186521 Score: 83
Period size: 20 Copynumber: 3.2 Consensus size: 20
186449 AAACTTAAAT
* *
186459 TCGCAACACAAAAATGAAAT
1 TCGCAACACGAAAATGAAAA
*
186479 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
186499 TCGCAACACGAAACT-AAAA
1 TCGCAACACGAAAATGAAAA
186518 TCGC
1 TCGC
186522 GTTGCGATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
19 8 0.21
20 30 0.79
ACGTcount: A:0.49, C:0.24, G:0.14, T:0.13
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:186553 original size:20 final size:20
Alignment explanation
Indices: 186528--186566 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
186518 TCGCGTTGCG
186528 ATTTTCGTGTTACGAATTTT
1 ATTTTCGTGTTACGAATTTT
*
186548 ATTTTCGTGTTGCGAATTT
1 ATTTTCGTGTTACGAATTT
186567 AAGTTTCAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.10, G:0.18, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTACGAATTTT
Found at i:186573 original size:20 final size:20
Alignment explanation
Indices: 186530--186573 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
186520 GCGTTGCGAT
* *
186530 TTTCGTGTTACGAATTTTAT
1 TTTCGTGTTACGAATTTAAG
*
186550 TTTCGTGTTGCGAATTTAAG
1 TTTCGTGTTACGAATTTAAG
186570 TTTC
1 TTTC
186574 AAAAACTATT
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:0.18, C:0.11, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTACGAATTTAAG
Found at i:187075 original size:19 final size:19
Alignment explanation
Indices: 187037--187075 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
187027 GTTTCGAATT
**
187037 CGAAAATAAATTCGCGTTG
1 CGAAAATAAACGCGCGTTG
*
187056 CGAAAATAAACGCGCTTTG
1 CGAAAATAAACGCGCGTTG
187075 C
1 C
187076 AAATTTGACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.36, C:0.21, G:0.21, T:0.23
Consensus pattern (19 bp):
CGAAAATAAACGCGCGTTG
Found at i:187114 original size:20 final size:20
Alignment explanation
Indices: 187091--187160 Score: 122
Period size: 20 Copynumber: 3.5 Consensus size: 20
187081 TGACTTCTGT
*
187091 GTTGCGAATTACAAATTCGC
1 GTTGCGAATTACATATTCGC
*
187111 GTTGCGATTTACATATTCGC
1 GTTGCGAATTACATATTCGC
187131 GTTGCGAATTACATATTCGC
1 GTTGCGAATTACATATTCGC
187151 GTTGCGAATT
1 GTTGCGAATT
187161 TGGAAAATCG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGAATTACATATTCGC
Found at i:187256 original size:20 final size:20
Alignment explanation
Indices: 187194--187250 Score: 96
Period size: 20 Copynumber: 2.9 Consensus size: 20
187184 AAATTCGAGA
**
187194 TGCGAATTTCAAAACTGAGT
1 TGCGAATTTGGAAACTGAGT
187214 TGCGAATTTGGAAACTGAGT
1 TGCGAATTTGGAAACTGAGT
187234 TGCGAATTTGGAAACTG
1 TGCGAATTTGGAAACTG
187251 CATTGCAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (20 bp):
TGCGAATTTGGAAACTGAGT
Found at i:187264 original size:20 final size:20
Alignment explanation
Indices: 187205--187265 Score: 70
Period size: 20 Copynumber: 3.0 Consensus size: 20
187195 GCGAATTTCA
* *
187205 AAACTGAGTTGCGAATTTGG
1 AAACTGAGTTGCAAAATTGG
* *
187225 AAACTGAGTTGCGAATTTGG
1 AAACTGAGTTGCAAAATTGG
187245 AAACTGCA-TTGCAAAATTGG
1 AAACTG-AGTTGCAAAATTGG
187265 A
1 A
187266 GTTCGCGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
20 37 0.97
21 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.26, T:0.28
Consensus pattern (20 bp):
AAACTGAGTTGCAAAATTGG
Found at i:187433 original size:25 final size:24
Alignment explanation
Indices: 187381--187429 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 24
187371 ATAACATAGT
*
187381 ATATATAATAAATATAGTTTTTGAA
1 ATATATAAT-AATATAGTTTTTAAA
187406 ATATATAAT-ATATAGTTTTTAAA
1 ATATATAATAATATAGTTTTTAAA
187429 A
1 A
187430 AATAGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 14 0.61
25 9 0.39
ACGTcount: A:0.49, C:0.00, G:0.06, T:0.45
Consensus pattern (24 bp):
ATATATAATAATATAGTTTTTAAA
Found at i:187461 original size:35 final size:33
Alignment explanation
Indices: 187415--187566 Score: 166
Period size: 35 Copynumber: 4.5 Consensus size: 33
187405 AATATATAAT
187415 ATATAGTTTTTAAAAAATAGTTTTGAAAACGTATA
1 ATATAGTTTTT--AAAATAGTTTTGAAAACGTATA
*
187450 ATATAGTTTTTAAAATAATTTTGAAAACG--T-
1 ATATAGTTTTTAAAATAGTTTTGAAAACGTATA
*
187480 ATATAGTTTTTAAAATAGTTTTGAAAGCGTATAA
1 ATATAGTTTTTAAAATAGTTTTGAAAACGTAT-A
** *
187514 TATATAGTTTTTAAAACGGTTTTGAAAACCTATATATA
1 -ATATAGTTTTTAAAATAGTTTTGAAAA-C---GTATA
187552 ATATAGTTTTTAAAA
1 ATATAGTTTTTAAAA
187567 ATAATTTTTT
Statistics
Matches: 101, Mismatches: 7, Indels: 16
0.81 0.06 0.13
Matches are distributed among these distances:
30 27 0.27
31 1 0.01
32 1 0.01
33 17 0.17
35 35 0.35
36 1 0.01
37 15 0.15
38 1 0.01
39 3 0.03
ACGTcount: A:0.43, C:0.04, G:0.11, T:0.42
Consensus pattern (33 bp):
ATATAGTTTTTAAAATAGTTTTGAAAACGTATA
Found at i:187511 original size:63 final size:66
Alignment explanation
Indices: 187414--187549 Score: 197
Period size: 65 Copynumber: 2.1 Consensus size: 66
187404 AAATATATAA
*
187414 TATATAGTTTTTAAAAAATAGTTTTGAAAACGTAT-A-ATATAGTTTTTAAAATAATTTTGAAAA
1 TATATAGTTTTT-AAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACAATTTTGAAAA
*
187477 CG
65 CC
* **
187479 TATATAGTTTTT-AAAATAGTTTTGAAAGCGTATAATATATAGTTTTTAAAACGGTTTTGAAAAC
1 TATATAGTTTTTAAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACAATTTTGAAAAC
187543 C
66 C
187544 TATATA
1 TATATA
187550 TAATATAGTT
Statistics
Matches: 64, Mismatches: 5, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
63 20 0.31
64 1 0.02
65 43 0.67
ACGTcount: A:0.42, C:0.04, G:0.12, T:0.42
Consensus pattern (66 bp):
TATATAGTTTTTAAAAATAGTTTTGAAAACGTATAATATATAGTTTTTAAAACAATTTTGAAAAC
C
Found at i:187649 original size:30 final size:30
Alignment explanation
Indices: 187585--187648 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
187575 TTGAAAATGG
*
187585 TTTTTGAAAATATATTAATATATTATATAA
1 TTTTTGAAAATATAATAATATATTATATAA
* * *
187615 TTTTTGGAAATATAAT-ATATGTTATATAG
1 TTTTTGAAAATATAATAATATATTATATAA
187644 TTTTT
1 TTTTT
187649 TATTATTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 16 0.53
30 14 0.47
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (30 bp):
TTTTTGAAAATATAATAATATATTATATAA
Found at i:187692 original size:18 final size:17
Alignment explanation
Indices: 187648--187694 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 17
187638 ATATAGTTTT
187648 TTATTATT-TATTATTA
1 TTATTATTATATTATTA
187664 TT-TTAGGTTATATTATTA
1 TTATTA--TTATATTATTA
187682 TTATTATT-TATTA
1 TTATTATTATATTA
187695 AATTTTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 8
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.11
16 7 0.26
17 4 0.15
18 10 0.37
19 3 0.11
ACGTcount: A:0.30, C:0.00, G:0.04, T:0.66
Consensus pattern (17 bp):
TTATTATTATATTATTA
Found at i:202107 original size:2 final size:2
Alignment explanation
Indices: 202100--202131 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
202090 AATTTTGATA
202100 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
202132 TTGTTTTAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:208646 original size:19 final size:20
Alignment explanation
Indices: 208596--208647 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
208586 GAAAGAAAGA
*
208596 GAAAAGGTAAAAGTTAAAAT
1 GAAAAGATAAAAGTTAAAAT
208616 GAAATAGA-AAAA-TTAATAAT
1 GAAA-AGATAAAAGTTAA-AAT
208636 G-AAAGATAAAAG
1 GAAAAGATAAAAG
208648 AAAAAGTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
18 3 0.11
19 10 0.37
20 12 0.44
21 2 0.07
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.19
Consensus pattern (20 bp):
GAAAAGATAAAAGTTAAAAT
Found at i:223862 original size:23 final size:23
Alignment explanation
Indices: 223832--223883 Score: 74
Period size: 20 Copynumber: 2.4 Consensus size: 23
223822 CAGTACCATA
223832 AAAGGGTATTATCGATACCATGT
1 AAAGGGTATTATCGATACCATGT
*
223855 AAAGGG---TATCGATATCATGT
1 AAAGGGTATTATCGATACCATGT
223875 AAAGGGTAT
1 AAAGGGTAT
223884 CGATACCATG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 19 0.76
23 6 0.24
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (23 bp):
AAAGGGTATTATCGATACCATGT
Found at i:223866 original size:20 final size:20
Alignment explanation
Indices: 223841--223893 Score: 97
Period size: 20 Copynumber: 2.6 Consensus size: 20
223831 AAAAGGGTAT
223841 TATCGATACCATGTAAAGGG
1 TATCGATACCATGTAAAGGG
*
223861 TATCGATATCATGTAAAGGG
1 TATCGATACCATGTAAAGGG
223881 TATCGATACCATG
1 TATCGATACCATG
223894 AAACATCAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.34, C:0.15, G:0.23, T:0.28
Consensus pattern (20 bp):
TATCGATACCATGTAAAGGG
Found at i:223972 original size:20 final size:21
Alignment explanation
Indices: 223933--223978 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
223923 CCAGAAAAGG
*
223933 GTATCGGTACCCTAGTGTAGAA
1 GTATCGGTA-CCTAGGGTAGAA
*
223955 GTATCGGTA-CTAGGGTAGTA
1 GTATCGGTACCTAGGGTAGAA
223975 GTAT
1 GTAT
223979 TGATACTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 13 0.59
22 9 0.41
ACGTcount: A:0.26, C:0.13, G:0.30, T:0.30
Consensus pattern (21 bp):
GTATCGGTACCTAGGGTAGAA
Found at i:224526 original size:79 final size:79
Alignment explanation
Indices: 224395--224633 Score: 352
Period size: 79 Copynumber: 3.0 Consensus size: 79
224385 GAAAAAAATA
* * * * **
224395 ATGCCATAGCTAAAATATATATAGGTACATTGTCATCACAAAAGAATAATGCATACAGGTGCATT
1 ATGCCATAGCTGAAATATATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATT
224460 ATTGGCATGAAAGG
66 ATTGGCATGAAAGG
* * *
224474 ATGCCATAGCTGAAATGTATATGGGTACATTGTCAGCTTAAAATAATAATGCATATGGGTGCATT
1 ATGCCATAGCTGAAATATATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATT
* *
224539 GTTGTCATGAAAGG
66 ATTGGCATGAAAGG
* * *
224553 ATGTCATAGCTTAAATATATATGGGTATATTGTCAGCATAAAAGAATAATGCATATGGGTGCATT
1 ATGCCATAGCTGAAATATATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATT
224618 ATTGGCATGAAAGG
66 ATTGGCATGAAAGG
224632 AT
1 AT
224634 ACTATCACTG
Statistics
Matches: 141, Mismatches: 19, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 141 1.00
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (79 bp):
ATGCCATAGCTGAAATATATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATT
ATTGGCATGAAAGG
Found at i:224654 original size:79 final size:78
Alignment explanation
Indices: 224400--224662 Score: 321
Period size: 79 Copynumber: 3.3 Consensus size: 78
224390 AAATAATGCC
* * * * * **
224400 ATAGCTAAAATATATATAGGTACATTGTCATCACAAAAGAATAATGCATACAGGTGCATTATTGG
1 ATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATTATTGG
*
224465 CATGAAAGGATGCC
66 CATGAAAGGAT-CT
* * * *
224479 ATAGCTGAAATGTATATGGGTACATTGTCAGCTTAAAATAATAATGCATATGGGTGCATTGTTGT
1 ATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATTATTGG
*
224544 CATGAAAGGATGT
66 CATGAAAGGATCT
* * *
224557 CATAGCTTAAATATATATGGGTATATTGTCAGCATAAAAGAATAATGCATATGGGTGCATTATTG
1 -ATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATTATTG
224622 GCATGAAAGGATACT
65 GCATGAAAGGAT-CT
* *
224637 ATCA-CTGAAATGCATATGGGTGCATT
1 AT-AGCTGAAATGTATATGGGTACATT
224663 ATCATTATAA
Statistics
Matches: 155, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
79 153 0.99
80 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.22, T:0.30
Consensus pattern (78 bp):
ATAGCTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGCATTATTGG
CATGAAAGGATCT
Found at i:230828 original size:20 final size:20
Alignment explanation
Indices: 230803--230840 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
230793 CTGATTCACT
*
230803 CAGTATCGATACCGTTGATG
1 CAGTATCGATACCATTGATG
230823 CAGTATCGATACCATTGA
1 CAGTATCGATACCATTGA
230841 AAGGGTATCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.29
Consensus pattern (20 bp):
CAGTATCGATACCATTGATG
Found at i:231574 original size:45 final size:45
Alignment explanation
Indices: 231505--231604 Score: 146
Period size: 45 Copynumber: 2.2 Consensus size: 45
231495 ATAAAAGAAT
* * * *
231505 AATGCATATGGGTGTATTGTTGGCATGAAAGGATGTCATAGCTAA
1 AATGTATATGCGTGCATTGTTGGCATGAAAGGATGCCATAGCTAA
*
231550 AATGTATATGCGTGCATTGTTGGCATGAAAGGATGCCATAGCTTA
1 AATGTATATGCGTGCATTGTTGGCATGAAAGGATGCCATAGCTAA
*
231595 AATCTATATG
1 AATGTATATG
231605 GGTACATCGT
Statistics
Matches: 49, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.31, C:0.11, G:0.26, T:0.32
Consensus pattern (45 bp):
AATGTATATGCGTGCATTGTTGGCATGAAAGGATGCCATAGCTAA
Found at i:231683 original size:124 final size:124
Alignment explanation
Indices: 231458--231691 Score: 346
Period size: 124 Copynumber: 1.9 Consensus size: 124
231448 GAAAAAAATA
* * * *
231458 ATGCCATAGTTGAAATGTATATGGGTACATTGTCAGCATAAAAGAATAATGCATATGGGTGTATT
1 ATGCCATAGTTGAAATCTATATGGGTACATCGTCAGCATAAAAGAATAATGCATATGGGAGCATT
* * *
231523 GTTGGCATGAAAGGATGTCATAGCTAAAATGTATATGCGTGCATTGTTGGCATGAAAGG
66 ATTGGCATGAAAGAATGTCATAGCTAAAATGCATATGCGTGCATTGTTGGCATGAAAGG
*
231582 ATGCCATAGCTT-AAATCTATATGGGTACATCGTTAGCATAAAAGAATAATGCATATGGGAGCAT
1 ATGCCATAG-TTGAAATCTATATGGGTACATCGTCAGCATAAAAGAATAATGCATATGGGAGCAT
* *
231646 TATTGGCATGAAAGAATGTCATTA-CTGAAATGCATATGGGTGCATT
65 TATTGGCATGAAAGAATGTCA-TAGCTAAAATGCATATGCGTGCATT
231692 ATCAGAATAA
Statistics
Matches: 98, Mismatches: 10, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
124 94 0.96
125 4 0.04
ACGTcount: A:0.34, C:0.11, G:0.24, T:0.30
Consensus pattern (124 bp):
ATGCCATAGTTGAAATCTATATGGGTACATCGTCAGCATAAAAGAATAATGCATATGGGAGCATT
ATTGGCATGAAAGAATGTCATAGCTAAAATGCATATGCGTGCATTGTTGGCATGAAAGG
Found at i:236885 original size:90 final size:88
Alignment explanation
Indices: 236777--236950 Score: 294
Period size: 89 Copynumber: 2.0 Consensus size: 88
236767 TCCCGAATAT
*
236777 TTAATTTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAATCCCTAATATGATTAG
1 TTAAATTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAA-CCCTAATATGATTAG
*
236842 GGTAACTTGGATATAAAAGGATTA
65 GGTAACTTAGATATAAAAGGATTA
*
236866 TTAAATTCTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
1 TTAAATTC-AATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAG
*
236931 GGTAACTTAGCTATAAAAGG
65 GGTAACTTAGATATAAAAGG
236951 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
89 40 0.50
90 40 0.50
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.37
Consensus pattern (88 bp):
TTAAATTCAATTAATTAAATATAAATTTAATTAATTTGAAATAATAAAACCCTAATATGATTAGG
GTAACTTAGATATAAAAGGATTA
Found at i:243815 original size:90 final size:89
Alignment explanation
Indices: 243701--243877 Score: 291
Period size: 90 Copynumber: 2.0 Consensus size: 89
243691 TAATCCCGAA
* *
243701 TATTTAATTTTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCCCTAATATGAT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAATATGAT
243766 TAGGGTAACTTAGATATAAAAGGAT
65 TAGGGTAACTTAGATATAAAAGGAT
* *
243791 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCTTAATATGATT
1 TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
* *
243856 AGGGTAACTTGGCTATAAAAGG
66 AGGGTAACTTAGATATAAAAGG
243878 GTGTGTTAGG
Statistics
Matches: 81, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
89 32 0.40
90 49 0.60
ACGTcount: A:0.46, C:0.05, G:0.10, T:0.39
Consensus pattern (89 bp):
TATTAAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAATATGATT
AGGGTAACTTAGATATAAAAGGAT
Found at i:245359 original size:2 final size:2
Alignment explanation
Indices: 245352--245392 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
245342 CTATTTGACA
245352 AT AT AT AT AT AT AT AT AT AT AT -T 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
245393 GGAGGGGTTA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:247103 original size:1 final size:1
Alignment explanation
Indices: 247097--247126 Score: 60
Period size: 1 Copynumber: 30.0 Consensus size: 1
247087 CAACCATCTA
247097 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
247127 GCATTTCCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 29 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:250752 original size:18 final size:19
Alignment explanation
Indices: 250729--250766 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
250719 GAACAATGCA
250729 AATTTATTTA-AATAAACT
1 AATTTATTTAGAATAAACT
*
250747 AATTTATTTAGAGTAAACT
1 AATTTATTTAGAATAAACT
250766 A
1 A
250767 TACAAATGAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (19 bp):
AATTTATTTAGAATAAACT
Found at i:253119 original size:19 final size:19
Alignment explanation
Indices: 253095--253159 Score: 121
Period size: 19 Copynumber: 3.4 Consensus size: 19
253085 TTAAGGATTT
253095 GGGTTTTGAGCATATTTGA
1 GGGTTTTGAGCATATTTGA
*
253114 GGGTTTTGAGCATATCTGA
1 GGGTTTTGAGCATATTTGA
253133 GGGTTTTGAGCATATTTGA
1 GGGTTTTGAGCATATTTGA
253152 GGGTTTTG
1 GGGTTTTG
253160 CTTGATTTAT
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 44 1.00
ACGTcount: A:0.18, C:0.06, G:0.34, T:0.42
Consensus pattern (19 bp):
GGGTTTTGAGCATATTTGA
Found at i:258142 original size:24 final size:24
Alignment explanation
Indices: 258108--258174 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
258098 GAGATATCAT
*
258108 AAATCAAAACAGAATTCAGAACA-
1 AAATCAGAACAGAATTCAGAACAG
* * *
258131 AATTTCAGAACAGAATCCAGATCAG
1 AA-ATCAGAACAGAATTCAGAACAG
*
258156 AAATCAGAACATAATTCAG
1 AAATCAGAACAGAATTCAG
258175 GTCATGTATC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGAACAG
Found at i:258151 original size:12 final size:12
Alignment explanation
Indices: 258115--258174 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
258105 CATAAATCAA
258115 AACAGAATTCAG
1 AACAGAATTCAG
258127 AACA-AATTTCAG
1 AACAGAA-TTCAG
*
258139 AACAGAATCCAG
1 AACAGAATTCAG
* *
258151 ATCAGAAATCAG
1 AACAGAATTCAG
*
258163 AACATAATTCAG
1 AACAGAATTCAG
258175 GTCATGTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:258209 original size:24 final size:25
Alignment explanation
Indices: 258155--258209 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
258145 ATCCAGATCA
* *
258155 GAAATCAGAACATAATTCAGGTCAT
1 GAAATCAGAACATAATTCAAGTCAG
* *
258180 G-TATCAGAACTTAATTCAAGTC-G
1 GAAATCAGAACATAATTCAAGTCAG
258203 GAAATCA
1 GAAATCA
258210 AATAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 22 0.92
25 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (25 bp):
GAAATCAGAACATAATTCAAGTCAG
Found at i:260713 original size:18 final size:18
Alignment explanation
Indices: 260690--260727 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
260680 CTGGTCAACA
260690 GTCAACGGGT-TGGGTCGG
1 GTCAACGGGTCT-GGTCGG
260708 GTCAACGGGTCTGGTCGG
1 GTCAACGGGTCTGGTCGG
260726 GT
1 GT
260728 TGAAATCGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 18 0.95
19 1 0.05
ACGTcount: A:0.11, C:0.18, G:0.47, T:0.24
Consensus pattern (18 bp):
GTCAACGGGTCTGGTCGG
Found at i:262517 original size:24 final size:24
Alignment explanation
Indices: 262483--262549 Score: 73
Period size: 24 Copynumber: 2.8 Consensus size: 24
262473 GAGATATCAT
*
262483 AAATCAAAACAGAATTCAGAACA-
1 AAATCAGAACAGAATTCAGAACAG
* * *
262506 AATTTCAGAACAGAATCCAGATCAG
1 AA-ATCAGAACAGAATTCAGAACAG
*
262531 AAATCAGAACATAATTCAG
1 AAATCAGAACAGAATTCAG
262550 GTCATGTATC
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
23 2 0.06
24 31 0.89
25 2 0.06
ACGTcount: A:0.52, C:0.18, G:0.12, T:0.18
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAGAACAG
Found at i:262526 original size:12 final size:12
Alignment explanation
Indices: 262490--262549 Score: 68
Period size: 12 Copynumber: 5.0 Consensus size: 12
262480 CATAAATCAA
262490 AACAGAATTCAG
1 AACAGAATTCAG
262502 AACA-AATTTCAG
1 AACAGAA-TTCAG
*
262514 AACAGAATCCAG
1 AACAGAATTCAG
* *
262526 ATCAGAAATCAG
1 AACAGAATTCAG
*
262538 AACATAATTCAG
1 AACAGAATTCAG
262550 GTCATGTATC
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
11 2 0.05
12 35 0.90
13 2 0.05
ACGTcount: A:0.50, C:0.18, G:0.13, T:0.18
Consensus pattern (12 bp):
AACAGAATTCAG
Found at i:262584 original size:24 final size:25
Alignment explanation
Indices: 262530--262584 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 25
262520 ATCCAGATCA
* *
262530 GAAATCAGAACATAATTCAGGTCAT
1 GAAATCAGAACATAATTCAAGTCAG
* *
262555 G-TATCAGAACTTAATTCAAGTC-G
1 GAAATCAGAACATAATTCAAGTCAG
262578 GAAATCA
1 GAAATCA
262585 AATAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
23 1 0.04
24 22 0.92
25 1 0.04
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.25
Consensus pattern (25 bp):
GAAATCAGAACATAATTCAAGTCAG
Found at i:263511 original size:160 final size:160
Alignment explanation
Indices: 263247--263568 Score: 644
Period size: 160 Copynumber: 2.0 Consensus size: 160
263237 AGCGTTATTG
263247 AATTTCGGATACATGTTGTACTTTCGTTCTATTCAATTTGGTCTTCGTGGTTGATTTGTCGAACA
1 AATTTCGGATACATGTTGTACTTTCGTTCTATTCAATTTGGTCTTCGTGGTTGATTTGTCGAACA
263312 AACGTCCAATTCTTAGTACTGAATGCGATCTAAAGTTGAGCTAAATACTTCCAAAATTATCATCG
66 AACGTCCAATTCTTAGTACTGAATGCGATCTAAAGTTGAGCTAAATACTTCCAAAATTATCATCG
263377 ATCCAAACTTGAGAAGACAAACATGCGTTC
131 ATCCAAACTTGAGAAGACAAACATGCGTTC
263407 AATTTCGGATACATGTTGTACTTTCGTTCTATTCAATTTGGTCTTCGTGGTTGATTTGTCGAACA
1 AATTTCGGATACATGTTGTACTTTCGTTCTATTCAATTTGGTCTTCGTGGTTGATTTGTCGAACA
263472 AACGTCCAATTCTTAGTACTGAATGCGATCTAAAGTTGAGCTAAATACTTCCAAAATTATCATCG
66 AACGTCCAATTCTTAGTACTGAATGCGATCTAAAGTTGAGCTAAATACTTCCAAAATTATCATCG
263537 ATCCAAACTTGAGAAGACAAACATGCGTTC
131 ATCCAAACTTGAGAAGACAAACATGCGTTC
263567 AA
1 AA
263569 ATAATATCTA
Statistics
Matches: 162, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
160 162 1.00
ACGTcount: A:0.30, C:0.19, G:0.17, T:0.34
Consensus pattern (160 bp):
AATTTCGGATACATGTTGTACTTTCGTTCTATTCAATTTGGTCTTCGTGGTTGATTTGTCGAACA
AACGTCCAATTCTTAGTACTGAATGCGATCTAAAGTTGAGCTAAATACTTCCAAAATTATCATCG
ATCCAAACTTGAGAAGACAAACATGCGTTC
Found at i:265098 original size:23 final size:23
Alignment explanation
Indices: 265072--265128 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
265062 ACACCGGTTA
265072 ACGGGTCGGGTC-GTGTAAAAGGG
1 ACGGGTCGGGTCAG-GTAAAAGGG
* *
265095 ACGGGTTGGGTCAGGTAAACGGG
1 ACGGGTCGGGTCAGGTAAAAGGG
*
265118 TCGGGTCGGGT
1 ACGGGTCGGGT
265129 TGGAATTGGT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
23 28 0.97
24 1 0.03
ACGTcount: A:0.18, C:0.14, G:0.49, T:0.19
Consensus pattern (23 bp):
ACGGGTCGGGTCAGGTAAAAGGG
Found at i:267325 original size:24 final size:25
Alignment explanation
Indices: 267270--267327 Score: 84
Period size: 24 Copynumber: 2.4 Consensus size: 25
267260 AATCTGGATC
*
267270 TGAAATCAGAACAGAATTCAGGTCA
1 TGAAATCAGAACAGAATTCAAGTCA
*
267295 TG-TATCAGAACAGAATTCAAGTCA
1 TGAAATCAGAACAGAATTCAAGTCA
267319 -GAAATCAGA
1 TGAAATCAGA
267328 TAAAATATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
23 1 0.03
24 26 0.90
25 2 0.07
ACGTcount: A:0.45, C:0.16, G:0.19, T:0.21
Consensus pattern (25 bp):
TGAAATCAGAACAGAATTCAAGTCA
Found at i:271623 original size:2 final size:2
Alignment explanation
Indices: 271616--271662 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
271606 TTTTTAAAAC
271616 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
271658 AT AT A
1 AT AT A
271663 CCCCCATCCC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:274426 original size:18 final size:18
Alignment explanation
Indices: 274403--274437 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
274393 AACACCGGTC
274403 AACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCGGGTA
274421 AACGGGTCGGGTCGGGT
1 AACGGGTCGGGTCGGGT
274438 TGGAATCTGT
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:0.14, C:0.17, G:0.51, T:0.17
Consensus pattern (18 bp):
AACGGGTCGGGTCGGGTA
Found at i:276272 original size:2 final size:2
Alignment explanation
Indices: 276267--276307 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
276257 AAACACACAC
276267 AT AT AT 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 AT AT AT A
276308 CCCCCATCCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:276519 original size:24 final size:24
Alignment explanation
Indices: 276468--276534 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
276458 ACGGAGATAT
* *
276468 CAGAAAACAAAACAGAATTAAGAA
1 CAGAAATCAGAACAGAATTAAGAA
* * *
276492 CAGATATCATAACAGAATCT-AGAT
1 CAGAAATCAGAACAGAAT-TAAGAA
*
276516 CAGAAATCAGAATAGAATT
1 CAGAAATCAGAACAGAATT
276535 CAGGTCATGT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
23 1 0.03
24 33 0.94
25 1 0.03
ACGTcount: A:0.55, C:0.13, G:0.13, T:0.18
Consensus pattern (24 bp):
CAGAAATCAGAACAGAATTAAGAA
Found at i:280161 original size:94 final size:94
Alignment explanation
Indices: 280000--280189 Score: 380
Period size: 94 Copynumber: 2.0 Consensus size: 94
279990 AATAACTCTA
280000 ACATGGCTCGTGAGGTACTTTACATTGTTTAGACAGATGTTACTGGTATTCATTTTTGTACAAGT
1 ACATGGCTCGTGAGGTACTTTACATTGTTTAGACAGATGTTACTGGTATTCATTTTTGTACAAGT
280065 ATAGCCTTAACAAATTGAAACTTCGGTTT
66 ATAGCCTTAACAAATTGAAACTTCGGTTT
280094 ACATGGCTCGTGAGGTACTTTACATTGTTTAGACAGATGTTACTGGTATTCATTTTTGTACAAGT
1 ACATGGCTCGTGAGGTACTTTACATTGTTTAGACAGATGTTACTGGTATTCATTTTTGTACAAGT
280159 ATAGCCTTAACAAATTGAAACTTCGGTTT
66 ATAGCCTTAACAAATTGAAACTTCGGTTT
280188 AC
1 AC
280190 TCATTACAGA
Statistics
Matches: 96, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 96 1.00
ACGTcount: A:0.28, C:0.15, G:0.19, T:0.38
Consensus pattern (94 bp):
ACATGGCTCGTGAGGTACTTTACATTGTTTAGACAGATGTTACTGGTATTCATTTTTGTACAAGT
ATAGCCTTAACAAATTGAAACTTCGGTTT
Found at i:280962 original size:12 final size:12
Alignment explanation
Indices: 280937--281005 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
280927 ACGGAGATAT
* *
280937 CAGAAATCAAAA
1 CAGAATTCAGAA
280949 CAGAATTCAGAA
1 CAGAATTCAGAA
280961 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
280973 CAGAA-TCTAGATA
1 CAGAATTC-AGA-A
*
280986 -AGAAATCAGAA
1 CAGAATTCAGAA
*
280997 TAGAATTCA
1 CAGAATTCA
281006 AGTCATGTAT
Statistics
Matches: 48, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
11 5 0.10
12 39 0.81
13 4 0.08
ACGTcount: A:0.54, C:0.14, G:0.14, T:0.17
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:280964 original size:24 final size:25
Alignment explanation
Indices: 280931--281005 Score: 84
Period size: 24 Copynumber: 3.0 Consensus size: 25
280921 CATTAAACGG
*
280931 AGATATCAGAAATCAAAACAGAATTC
1 AGATA-CAGAAATCAGAACAGAATTC
*
280957 AGA-ACAGATATCAGAACAGAA-TC
1 AGATACAGAAATCAGAACAGAATTC
*
280980 TAGATA-AGAAATCAGAATAGAATTC
1 -AGATACAGAAATCAGAACAGAATTC
281005 A
1 A
281006 AGTCATGTAT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
23 2 0.05
24 33 0.79
25 4 0.10
26 3 0.07
ACGTcount: A:0.53, C:0.13, G:0.15, T:0.19
Consensus pattern (25 bp):
AGATACAGAAATCAGAACAGAATTC
Found at i:282670 original size:19 final size:18
Alignment explanation
Indices: 282648--282686 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
282638 TAAAACTAAC
282648 ATTTCTTATACACATCAAT
1 ATTTCTTAT-CACATCAAT
* *
282667 ATTTTTTATCAGATCAAT
1 ATTTCTTATCACATCAAT
282685 AT
1 AT
282687 GTCTGTAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 10 0.56
19 8 0.44
ACGTcount: A:0.36, C:0.15, G:0.03, T:0.46
Consensus pattern (18 bp):
ATTTCTTATCACATCAAT
Found at i:285660 original size:24 final size:24
Alignment explanation
Indices: 285631--285686 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
285621 TCCAGATCAA
* * *
285631 AAATCAGAACATAATTCAGGTCAT
1 AAATCAGAACAGAATTCAAGTCAG
*
285655 ATATCAGAACAGAATTCAAGTCAG
1 AAATCAGAACAGAATTCAAGTCAG
285679 AAATCAGA
1 AAATCAGA
285687 TAAAATATTT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.48, C:0.16, G:0.14, T:0.21
Consensus pattern (24 bp):
AAATCAGAACAGAATTCAAGTCAG
Found at i:292398 original size:25 final size:23
Alignment explanation
Indices: 292362--292409 Score: 78
Period size: 25 Copynumber: 2.0 Consensus size: 23
292352 TAGTAAATTA
292362 TTACCTTGATTGCACTCGATCTT
1 TTACCTTGATTGCACTCGATCTT
292385 TTACCATTAGATTGCACTCGATCTT
1 TTACC-TT-GATTGCACTCGATCTT
292410 GAAATCATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 5 0.22
24 2 0.09
25 16 0.70
ACGTcount: A:0.21, C:0.25, G:0.12, T:0.42
Consensus pattern (23 bp):
TTACCTTGATTGCACTCGATCTT
Found at i:294562 original size:2 final size:2
Alignment explanation
Indices: 294555--294581 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
294545 TTTTTAAAAC
294555 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 A
294582 CCCCTATCCC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:294775 original size:12 final size:12
Alignment explanation
Indices: 294760--294815 Score: 51
Period size: 12 Copynumber: 4.7 Consensus size: 12
294750 AAAATAGAAT
294760 TCAGAACAGATA
1 TCAGAACAGATA
*
294772 TCAGAACATATA
1 TCAGAACAGATA
*
294784 TCATAACAGA-A
1 TCAGAACAGATA
* * *
294795 TCCAGATCAAAAA
1 T-CAGAACAGATA
294808 TCAGAACA
1 TCAGAACA
294816 TAATTCAGGT
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
11 2 0.06
12 31 0.89
13 2 0.06
ACGTcount: A:0.52, C:0.20, G:0.11, T:0.18
Consensus pattern (12 bp):
TCAGAACAGATA
Found at i:294858 original size:24 final size:24
Alignment explanation
Indices: 294783--294860 Score: 70
Period size: 24 Copynumber: 3.2 Consensus size: 24
294773 CAGAACATAT
* * *
294783 ATCATAACAGAA-TCCAGATCAAAA
1 ATCAGAACAGAATTCAAG-TCAGAA
* * *
294807 ATCAGAACATAATTCAGGTCATG-T
1 ATCAGAACAGAATTCAAGTCA-GAA
294831 ATCAGAACAGAATTCAAGTCAGAA
1 ATCAGAACAGAATTCAAGTCAGAA
294855 ATCAGA
1 ATCAGA
294861 TAAAATATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 6
0.74 0.16 0.11
Matches are distributed among these distances:
23 1 0.02
24 38 0.90
25 3 0.07
ACGTcount: A:0.47, C:0.18, G:0.14, T:0.21
Consensus pattern (24 bp):
ATCAGAACAGAATTCAAGTCAGAA
Found at i:298619 original size:20 final size:20
Alignment explanation
Indices: 298596--298644 Score: 71
Period size: 20 Copynumber: 2.5 Consensus size: 20
298586 ACCACTAAAT
*
298596 GTAACCCTAGACCATTACAG
1 GTAACCCGAGACCATTACAG
* *
298616 GTAACTCGAGACCATTACGG
1 GTAACCCGAGACCATTACAG
298636 GTAACCCGA
1 GTAACCCGA
298645 TCCGATCTAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.33, C:0.29, G:0.20, T:0.18
Consensus pattern (20 bp):
GTAACCCGAGACCATTACAG
Found at i:299418 original size:12 final size:12
Alignment explanation
Indices: 299393--299461 Score: 59
Period size: 12 Copynumber: 5.8 Consensus size: 12
299383 ACAGAGATAT
* *
299393 CAGAAATCAAAA
1 CAGAATTCAGAA
299405 CAGAATTCAGAA
1 CAGAATTCAGAA
299417 CAG-ATATCAGAA
1 CAGAAT-TCAGAA
* *
299429 CAGAATCCAGAT
1 CAGAATTCAGAA
* * *
299441 CAAAAATCAGAG
1 CAGAATTCAGAA
299453 CAGAATTCA
1 CAGAATTCA
299462 AGTCGGAAAT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
11 2 0.04
12 41 0.91
13 2 0.04
ACGTcount: A:0.52, C:0.19, G:0.14, T:0.14
Consensus pattern (12 bp):
CAGAATTCAGAA
Found at i:299425 original size:24 final size:24
Alignment explanation
Indices: 299393--299458 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 24
299383 ACAGAGATAT
*
299393 CAGAAATCAAAACAGAATTCAGAA
1 CAGAAATCAAAACAGAATCCAGAA
* * *
299417 CAGATATCAGAACAGAATCCAGAT
1 CAGAAATCAAAACAGAATCCAGAA
* * *
299441 CAAAAATCAGAGCAGAAT
1 CAGAAATCAAAACAGAAT
299459 TCAAGTCGGA
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 35 1.00
ACGTcount: A:0.53, C:0.18, G:0.15, T:0.14
Consensus pattern (24 bp):
CAGAAATCAAAACAGAATCCAGAA
Found at i:301973 original size:18 final size:18
Alignment explanation
Indices: 301951--302007 Score: 87
Period size: 18 Copynumber: 3.2 Consensus size: 18
301941 GGTCAACACC
301951 GGTCAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
* *
301969 TGTCAACGGGTCAGGTCA
1 GGTCAACGGGTCGGGTCA
*
301987 GGTAAACGGGTCGGGTCA
1 GGTCAACGGGTCGGGTCA
302005 GGT
1 GGT
302008 TGGAATCGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.19, C:0.19, G:0.42, T:0.19
Consensus pattern (18 bp):
GGTCAACGGGTCGGGTCA
Found at i:305667 original size:45 final size:45
Alignment explanation
Indices: 305603--305692 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
305593 GAAGGTGCGC
305603 CCAAGAGTATCCCATAAAGGAGATCTCATGCTAAATAAGATTTGG
1 CCAAGAGTATCCCATAAAGGAGATCTCATGCTAAATAAGATTTGG
*
305648 CCAAGAGTATTCCATAAAGGAGATCTCATGCTAAATAAGATTTGG
1 CCAAGAGTATCCCATAAAGGAGATCTCATGCTAAATAAGATTTGG
305693 TCAATTCAAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (45 bp):
CCAAGAGTATCCCATAAAGGAGATCTCATGCTAAATAAGATTTGG
Found at i:307315 original size:82 final size:81
Alignment explanation
Indices: 307197--307417 Score: 279
Period size: 82 Copynumber: 2.7 Consensus size: 81
307187 CAACTCACAG
* * * *
307197 CAAAAGATATCATGCTCGAAGAA--TCAAAGATTGACTCGACTTCACAACGAATGAGTCAACCAC
1 CAAAGGATATCATGCTCAAAGAATCTCAAAGATTGACTCAACTTCACAACGAAAGAGTCAACCAC
307260 GATTTCAACTTCATGA
66 GATTTCAACTTCATGA
* *
307276 CAAAGGATATCATGCTCAAAGATATCTCAAAGATTGACTCAATTTCACAACGAAAGAGTTAACCA
1 CAAAGGATATCATGCTCAAAGA-ATCTCAAAGATTGACTCAACTTCACAACGAAAGAGTCAACCA
*
307341 TGATTTCAACTTCATGA
65 CGATTTCAACTTCATGA
* * * * *
307358 CGAAGGATATCGTGCTCAAAGACATCTC-AAGATTGATTCAACATCACGAC-AAAGAAGTCA
1 CAAAGGATATCATGCTCAAAGA-ATCTCAAAGATTGACTCAACTTCACAACGAAAG-AGTCA
307418 TATGTAATTC
Statistics
Matches: 123, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
79 20 0.16
80 5 0.04
81 22 0.18
82 76 0.62
ACGTcount: A:0.40, C:0.21, G:0.15, T:0.24
Consensus pattern (81 bp):
CAAAGGATATCATGCTCAAAGAATCTCAAAGATTGACTCAACTTCACAACGAAAGAGTCAACCAC
GATTTCAACTTCATGA
Found at i:307797 original size:16 final size:17
Alignment explanation
Indices: 307763--307802 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
307753 AAAGGTATAT
307763 AATATATGGTTTATGAA
1 AATATATGGTTTATGAA
*
307780 AATATGTGGTTT-TGAA
1 AATATATGGTTTATGAA
*
307796 AACATAT
1 AATATAT
307803 AATATATATG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.40, C:0.03, G:0.17, T:0.40
Consensus pattern (17 bp):
AATATATGGTTTATGAA
Found at i:307848 original size:43 final size:41
Alignment explanation
Indices: 307764--307852 Score: 103
Period size: 43 Copynumber: 2.1 Consensus size: 41
307754 AAGGTATATA
307764 ATATATGGTTTATGAAAATATGTGGTTTTGAAAACATATAAT
1 ATATATGGTTTATGAAAATATGT-GTTTTGAAAACATATAAT
307806 ATATATGGCTTCT-TGAAAATA-GT-TTTTGAAAAACATAGATAAT
1 ATATATGG-TT-TATGAAAATATGTGTTTTG-AAAACAT--ATAAT
307849 ATAT
1 ATAT
307853 TTAATTTTTG
Statistics
Matches: 42, Mismatches: 0, Indels: 9
0.82 0.00 0.18
Matches are distributed among these distances:
40 5 0.12
41 7 0.17
42 10 0.24
43 19 0.45
44 1 0.02
ACGTcount: A:0.42, C:0.04, G:0.15, T:0.39
Consensus pattern (41 bp):
ATATATGGTTTATGAAAATATGTGTTTTGAAAACATATAAT
Found at i:307889 original size:29 final size:28
Alignment explanation
Indices: 307824--307902 Score: 76
Period size: 28 Copynumber: 2.8 Consensus size: 28
307814 CTTCTTGAAA
307824 ATAGTTTTTGAAAAACATAGATAATATATTT
1 ATAGTTTTTG-AAAACATA-AT-ATATATTT
*
307855 A-A-TTTTTGAAAACATAATATATGTTAT
1 ATAGTTTTTGAAAACATAATATATATT-T
*
307882 ATAGTTTTT-AAAATA-AATATA
1 ATAGTTTTTGAAAACATAATATA
307903 GTGTGCATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
26 6 0.14
27 10 0.23
28 14 0.33
29 11 0.26
30 1 0.02
31 1 0.02
ACGTcount: A:0.47, C:0.03, G:0.08, T:0.43
Consensus pattern (28 bp):
ATAGTTTTTGAAAACATAATATATATTT
Found at i:307956 original size:19 final size:18
Alignment explanation
Indices: 307913--307960 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
307903 GTGTGCATAT
307913 TATTTATTATA-TATAGA
1 TATTTATTATATTATAGA
* *
307930 TATATATTATATTATTATA
1 TATTTATTATATTA-TAGA
307949 TATTTATTATAT
1 TATTTATTATAT
307961 GTTTATTAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 10 0.38
18 2 0.08
19 14 0.54
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (18 bp):
TATTTATTATATTATAGA
Found at i:307957 original size:11 final size:11
Alignment explanation
Indices: 307913--307987 Score: 66
Period size: 11 Copynumber: 6.7 Consensus size: 11
307903 GTGTGCATAT
307913 TATTTATTATA
1 TATTTATTATA
**
307924 TATAGATATATA
1 TATTTAT-TATA
307936 TTATATTATTATA
1 -TAT-TTATTATA
307949 TATTTATTATA
1 TATTTATTATA
*
307960 TGTTTATTA-A
1 TATTTATTATA
307970 TA-TTACTT-TA
1 TATTTA-TTATA
307980 TATTTATT
1 TATTTATT
307988 TAGGTCCAAT
Statistics
Matches: 52, Mismatches: 6, Indels: 13
0.73 0.08 0.18
Matches are distributed among these distances:
9 3 0.06
10 9 0.17
11 24 0.46
12 7 0.13
13 7 0.13
14 2 0.04
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.60
Consensus pattern (11 bp):
TATTTATTATA
Found at i:309909 original size:17 final size:16
Alignment explanation
Indices: 309887--309928 Score: 57
Period size: 17 Copynumber: 2.6 Consensus size: 16
309877 AGCCCAAGTT
*
309887 CAGATCCAGATTTGACC
1 CAGATCCAGATCT-ACC
*
309904 CAGATCCAGATCTACT
1 CAGATCCAGATCTACC
309920 CAGATCCAG
1 CAGATCCAG
309929 CCGGCTACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 11 0.48
17 12 0.52
ACGTcount: A:0.31, C:0.31, G:0.17, T:0.21
Consensus pattern (16 bp):
CAGATCCAGATCTACC
Found at i:311270 original size:2 final size:2
Alignment explanation
Indices: 311148--311258 Score: 133
Period size: 2 Copynumber: 57.5 Consensus size: 2
311138 ACACACACAC
*
311148 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT 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
* * * *
311190 AT AT AT AT -T AA AT AT AT -T TT TT AT -T CT ACT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
311229 AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
311259 AAATTAATAT
Statistics
Matches: 97, Mismatches: 6, Indels: 12
0.84 0.05 0.10
Matches are distributed among these distances:
1 5 0.05
2 90 0.93
3 2 0.02
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:317633 original size:41 final size:42
Alignment explanation
Indices: 317575--317668 Score: 113
Period size: 41 Copynumber: 2.3 Consensus size: 42
317565 AGGTTGAGAT
*
317575 ATTTTGAAAGTCCATTTCA-ACCAGAAAT-A-TAATGTTGGGGC
1 ATTTTGAAAGTCCATTTCAGA-CAAAAATGATTAATG-TGGGGC
* * *
317616 ATTTTGAAGGTCTATTTCAGACAAAAATGATTCATGTGGGGC
1 ATTTTGAAAGTCCATTTCAGACAAAAATGATTAATGTGGGGC
317658 ATTTTGAAAGT
1 ATTTTGAAAGT
317669 TCATGTTGAA
Statistics
Matches: 45, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
41 23 0.51
42 18 0.40
43 4 0.09
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.34
Consensus pattern (42 bp):
ATTTTGAAAGTCCATTTCAGACAAAAATGATTAATGTGGGGC
Found at i:318982 original size:40 final size:39
Alignment explanation
Indices: 318922--319039 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 39
318912 TTCATTTGAC
* *
318922 TCAAGATTGTTTTTCTTTGAAACAAAAGATATTATCTCGT
1 TCAAGATTGGTTTTCCTTGAAACAAAA-ATATTATCTCGT
*
318962 TCAAGATTGGTTTTCCTTGAAACAAAAAAATTTATCTCGGT
1 TCAAGATTGGTTTTCCTTGAAACAAAAATA-TTATCTC-GT
* * * * *
319003 T-GAGA-TAGTTTCCCTCGAAACAAAAAATTTTATCTCG
1 TCAAGATTGGTTTTCCTTGAAAC-AAAAATATTATCTCG
319040 CTTGAGATAG
Statistics
Matches: 66, Mismatches: 9, Indels: 8
0.80 0.11 0.10
Matches are distributed among these distances:
38 1 0.02
39 22 0.33
40 40 0.61
41 3 0.05
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (39 bp):
TCAAGATTGGTTTTCCTTGAAACAAAAATATTATCTCGT
Found at i:319028 original size:39 final size:39
Alignment explanation
Indices: 318971--319065 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
318961 TTCAAGATTG
* *
318971 GTTTTCCTTGAAACAAAAAAATTTATCTCGGTTGAGATA
1 GTTTCCCTTGAAACAAAAAAATTTATCTCGCTTGAGATA
* *
319010 GTTTCCCTCGAAACAAAAAATTTTATCTCGCTTGAGATA
1 GTTTCCCTTGAAACAAAAAAATTTATCTCGCTTGAGATA
319049 GTTTCCCTTGAAA-AAAA
1 GTTTCCCTTGAAACAAAA
319066 TTGAGACAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
38 4 0.08
39 47 0.92
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.34
Consensus pattern (39 bp):
GTTTCCCTTGAAACAAAAAAATTTATCTCGCTTGAGATA
Found at i:319076 original size:25 final size:25
Alignment explanation
Indices: 319041--319092 Score: 86
Period size: 25 Copynumber: 2.1 Consensus size: 25
319031 TTTATCTCGC
*
319041 TTGAGATAGTTTCCCTTGAAAAAAA
1 TTGAGACAGTTTCCCTTGAAAAAAA
*
319066 TTGAGACAGTTTCCCTTGAAACAAA
1 TTGAGACAGTTTCCCTTGAAAAAAA
319091 TT
1 TT
319093 TTGTCTCCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (25 bp):
TTGAGACAGTTTCCCTTGAAAAAAA
Found at i:319122 original size:61 final size:62
Alignment explanation
Indices: 319002--319122 Score: 154
Period size: 61 Copynumber: 1.9 Consensus size: 62
318992 TTTATCTCGG
* * * * *
319002 TTGAGATAGTTTCCCTCGAAACAAAAAATTTTATCTCGCTTGAGATAGTTTCCCTTGAAAAAAA
1 TTGAGACAGTTTCCCTCGAAAC--AAAATTTTATCTCCCTTGAGACAATTTCACTTGAAAAAAA
* *
319066 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCCTTGAGACAATTTCACTTGAAA
1 TTGAGACAGTTTCCCTCGAAACAAAATTTTATCTCCCTTGAGACAATTTCACTTGAAA
319123 CAGAAGATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
61 30 0.60
64 20 0.40
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (62 bp):
TTGAGACAGTTTCCCTCGAAACAAAATTTTATCTCCCTTGAGACAATTTCACTTGAAAAAAA
Found at i:319144 original size:39 final size:37
Alignment explanation
Indices: 319066--319191 Score: 146
Period size: 39 Copynumber: 3.3 Consensus size: 37
319056 TTGAAAAAAA
* * *
319066 TTGAGACAGTTTCCCTTGAAAC-AAATTTTGTCTCCC
1 TTGAGACAGTTTCACTTGAAACAAAATTTTATCTCGC
*
319102 TTGAGACAATTTCACTTGAAACAGAAGATTTTATCTCGC
1 TTGAGACAGTTTCACTTGAAACA-AA-ATTTTATCTCGC
**
319141 TTGAGATTGTTTCACTTGAAACAAAATATTTTATCTCGC
1 TTGAGACAGTTTCACTTGAAAC-AAA-ATTTTATCTCGC
*
319180 TTGAGATAGTTT
1 TTGAGACAGTTT
319192 TGCACGAAAC
Statistics
Matches: 77, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
36 20 0.26
38 2 0.03
39 54 0.70
40 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.15, T:0.38
Consensus pattern (37 bp):
TTGAGACAGTTTCACTTGAAACAAAATTTTATCTCGC
Found at i:319201 original size:39 final size:38
Alignment explanation
Indices: 319066--319211 Score: 129
Period size: 39 Copynumber: 3.8 Consensus size: 38
319056 TTGAAAAAAA
* * * *
319066 TTGAGACAGTTTCCCTTGAAAC--AA-ATTTTGTCTCCC
1 TTGAGATAGTTTCAC-TGAAACAAAATATTTTATCTCGC
* * * *
319102 TTGAGACAATTTCACTTGAAACAGAAGATTTTATCTCGC
1 TTGAGATAGTTTCAC-TGAAACAAAATATTTTATCTCGC
*
319141 TTGAGATTGTTTCACTTGAAACAAAATATTTTATCTCGC
1 TTGAGATAGTTTCAC-TGAAACAAAATATTTTATCTCGC
*
319180 TTGAGATAGTTTTGCAC-GAAACACAATATTTT
1 TTGAGATAG-TTT-CACTGAAACAAAATATTTT
319212 GAGAAACCAT
Statistics
Matches: 94, Mismatches: 11, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
36 20 0.21
38 2 0.02
39 66 0.70
40 3 0.03
41 3 0.03
ACGTcount: A:0.31, C:0.18, G:0.14, T:0.37
Consensus pattern (38 bp):
TTGAGATAGTTTCACTGAAACAAAATATTTTATCTCGC
Found at i:319271 original size:43 final size:42
Alignment explanation
Indices: 319210--319469 Score: 276
Period size: 43 Copynumber: 6.1 Consensus size: 42
319200 ACACAATATT
* * * *
319210 TTGAGAAACCATCATGATATCTAGAGGCTTCTTGATGAAAAGC
1 TTGAGAGACCATCGTGATATGTAG-GGGTTCTTGATGAAAAGC
* * * *
319253 TTGAGAGATCATCGTGATATGTA-GGTTTCTTGATGACAAGA
1 TTGAGAGACCATCGTGATATGTAGGGGTTCTTGATGAAAAGC
* *
319294 TTGA-AGGACCATCGTGATATGTAGGGGTTCCATGATGACAAGC
1 TTGAGA-GACCATCGTGATATGTAGGGGTT-CTTGATGAAAAGC
* *
319337 TTGA-AGGACCATAGTGATATGTAGGGGTTCTTTGATGACAAGC
1 TTGAGA-GACCATCGTGATATGTAGGGGTTC-TTGATGAAAAGC
* * *
319380 TTGAGAAAACATTGTGATATGTAGGGGTTTCTTGATGAAAAGC
1 TTGAGAGACCATCGTGATATGTAGGGG-TTCTTGATGAAAAGC
*
319423 TTGAGGGACCATCGTGATATGTAGGGGTTACTTGATGACAAA-C
1 TTGAGAGACCATCGTGATATGTAGGGGTT-CTTGATGA-AAAGC
319466 TTGA
1 TTGA
319470 TGAACACTTG
Statistics
Matches: 188, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
40 1 0.01
41 35 0.19
42 7 0.04
43 138 0.73
44 7 0.04
ACGTcount: A:0.30, C:0.12, G:0.28, T:0.30
Consensus pattern (42 bp):
TTGAGAGACCATCGTGATATGTAGGGGTTCTTGATGAAAAGC
Found at i:319459 original size:129 final size:127
Alignment explanation
Indices: 319224--319469 Score: 350
Period size: 129 Copynumber: 1.9 Consensus size: 127
319214 GAAACCATCA
* *
319224 TGATATCTAGAGGCTTCTTGATGAAAAGCTTGAGAGATCATCGTGATATGTAGGTTTCTTGATGA
1 TGATATCTAGAGGCTTCTTGATGAAAAGCTTGAGAAAACATCGTGATATGTAGGTTTCTTGATGA
* * *
319289 CAAGATTGAAGGACCATCGTGATATGTAGGGGTTCCATGATGACAAGCTTGAAGGACCATAG
66 AAAGATTGAAGGACCATCGTGATATGTAGGGGTTACATGATGACAAACTTGAAGGACCATAG
* * * *
319351 TGATATGTAG-GGGTTCTTTGATGACAAGCTTGAGAAAACATTGTGATATGTAGGGGTTTCTTGA
1 TGATATCTAGAGGCTTC-TTGATGAAAAGCTTGAGAAAACATCGTGATATGTA--GGTTTCTTGA
* * *
319415 TGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTACTTGATGACAAACTTGA
63 TGAAAAGATTGAAGGACCATCGTGATATGTAGGGGTTACATGATGACAAACTTGA
319470 TGAACACTTG
Statistics
Matches: 104, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
126 5 0.05
127 40 0.38
129 59 0.57
ACGTcount: A:0.29, C:0.12, G:0.28, T:0.30
Consensus pattern (127 bp):
TGATATCTAGAGGCTTCTTGATGAAAAGCTTGAGAAAACATCGTGATATGTAGGTTTCTTGATGA
AAAGATTGAAGGACCATCGTGATATGTAGGGGTTACATGATGACAAACTTGAAGGACCATAG
Found at i:319493 original size:54 final size:55
Alignment explanation
Indices: 319410--319517 Score: 173
Period size: 54 Copynumber: 2.0 Consensus size: 55
319400 GTAGGGGTTT
319410 CTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTACTTGATGACAAA
1 CTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTACTTGATGACAAA
* * * *
319465 CTTGATGAACA-CTTGAGGGACTATCGTGATATGTAGGGGTTCCTTGGTGACAA
1 CTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTACTTGATGACAA
319518 TTAAGAAACT
Statistics
Matches: 49, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
54 39 0.80
55 10 0.20
ACGTcount: A:0.28, C:0.14, G:0.30, T:0.29
Consensus pattern (55 bp):
CTTGATGAAAAGCTTGAGGGACCATCGTGATATGTAGGGGTTACTTGATGACAAA
Found at i:319674 original size:90 final size:90
Alignment explanation
Indices: 319519--319761 Score: 409
Period size: 90 Copynumber: 2.7 Consensus size: 90
319509 TGGTGACAAT
**
319519 TAAGAAACTGAGCCTTCGGGGGTTTCTTGA-TGATAAGTCCTTCGGGCCATCCATAAGACCTTCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
319583 GTGCAGGATGTTTTCAAATGAGATC
66 GTGCAGGATGTTTTCAAATGAGATC
* *
319608 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCATTCGGGCCATCCATATGACCTTCA
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
*
319673 GTGCAGGATGTTTTCAAATGAGATT
66 GTGCAGGATGTTTTCAAATGAGATC
*
319698 TAAGAAACTGAGCCTTCGAGGGTTTCTTGATTTTTAAAGTCCTTCGGGCCA-CCATAAGACCTTC
1 TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTT-AAGTCCTTCGGGCCATCCATAAGACCTTC
319762 GGGCAAGATG
Statistics
Matches: 144, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
89 30 0.21
90 100 0.69
91 14 0.10
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (90 bp):
TAAGAAACTGAGCCTTCGGGGGTTTCTTGATTTTTAAGTCCTTCGGGCCATCCATAAGACCTTCA
GTGCAGGATGTTTTCAAATGAGATC
Found at i:320151 original size:16 final size:17
Alignment explanation
Indices: 320112--320151 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
320102 GAGCCCAAGT
320112 TCAGATCCAGATTTGAC
1 TCAGATCCAGATTTGAC
*
320129 CCAGATCCAGATTT-AC
1 TCAGATCCAGATTTGAC
320145 TCAGATC
1 TCAGATC
320152 TAGCCGGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 8 0.38
17 13 0.62
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (17 bp):
TCAGATCCAGATTTGAC
Found at i:321368 original size:2 final size:2
Alignment explanation
Indices: 321358--321434 Score: 58
Period size: 2 Copynumber: 41.0 Consensus size: 2
321348 TTTTTGGTGT
* * * * *
321358 TA TA CA TA TA TA TA TA TA TT TA -A TA TA T- TT TT TA T- TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
321397 CTA T- TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA -A TA TA
1 -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
321435 AATTAATATA
Statistics
Matches: 62, Mismatches: 6, Indels: 14
0.76 0.07 0.17
Matches are distributed among these distances:
1 6 0.10
2 54 0.87
3 2 0.03
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:321435 original size:10 final size:11
Alignment explanation
Indices: 321363--321435 Score: 53
Period size: 11 Copynumber: 6.7 Consensus size: 11
321353 GGTGTTATAC
321363 ATATAT-ATAT
1 ATATATAATAT
*
321373 ATATTTAATAT
1 ATATATAATAT
* * *
321384 ATTTTTTAT-T
1 ATATATAATAT
* *
321394 CTACTATTATAT
1 ATA-TATAATAT
321406 ATATATATATAT
1 ATATATA-ATAT
321418 ATATATAATAT
1 ATATATAATAT
321429 A-ATATAA
1 ATATATAA
321436 ATTAATATAT
Statistics
Matches: 51, Mismatches: 8, Indels: 8
0.76 0.12 0.12
Matches are distributed among these distances:
10 13 0.25
11 24 0.47
12 14 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (11 bp):
ATATATAATAT
Found at i:321441 original size:10 final size:12
Alignment explanation
Indices: 321404--321445 Score: 52
Period size: 10 Copynumber: 3.5 Consensus size: 12
321394 CTACTATTAT
321404 ATATATATATATA
1 ATATATA-ATATA
321417 TATATATAATATA
1 -ATATATAATATA
321430 ATATA-AAT-TA
1 ATATATAATATA
321440 ATATAT
1 ATATAT
321446 TTCAAGAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
10 7 0.26
11 3 0.11
12 5 0.19
13 5 0.19
14 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (12 bp):
ATATATAATATA
Found at i:324631 original size:2 final size:2
Alignment explanation
Indices: 324624--324662 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
324614 ACTTATTGAA
*
324624 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AG AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
324663 ATTATACATT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
1 2 0.06
2 32 0.94
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.44
Consensus pattern (2 bp):
AT
Found at i:327230 original size:21 final size:20
Alignment explanation
Indices: 327204--327242 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
327194 TAAGATGAGG
327204 GTATCGATATTGAGCCCTTCA
1 GTATCGATATTGA-CCCTTCA
327225 GTATCGATATTGACCCTT
1 GTATCGATATTGACCCTT
327243 GAGTTAGCGA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.23, C:0.23, G:0.18, T:0.36
Consensus pattern (20 bp):
GTATCGATATTGACCCTTCA
Found at i:327253 original size:21 final size:21
Alignment explanation
Indices: 327208--327254 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
327198 ATGAGGGTAT
*
327208 CGATATTGAGCCCTTCAGTAT
1 CGATATTGAGCCCTTCAGTAG
*
327229 CGATATTGA-CCCTTGAGTTAG
1 CGATATTGAGCCCTTCAG-TAG
327250 CGATA
1 CGATA
327255 CCCACTATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
21 16 0.70
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.32
Consensus pattern (21 bp):
CGATATTGAGCCCTTCAGTAG
Found at i:328260 original size:90 final size:90
Alignment explanation
Indices: 328107--328281 Score: 296
Period size: 90 Copynumber: 1.9 Consensus size: 90
328097 TGATTGATAG
* * *
328107 CCATCATACACCAAGTGTGCCAATTACATATATAGTGCTTCAGTACGCAAAGTAATACAACAATA
1 CCATCATACACCAAGTATGCCAATTACATACATAGTGCTTCAGTACACAAAGTAATACAACAATA
328172 CCACCTTATTTATGGTATTACAACA
66 CCACCTTATTTATGGTATTACAACA
* * *
328197 CCATCATACACCAAGTATGCCAATTATATACATAGTGCTTCAGTACACAAAGTACTACTACAATA
1 CCATCATACACCAAGTATGCCAATTACATACATAGTGCTTCAGTACACAAAGTAATACAACAATA
328262 CCACCTTATTTATGGTATTA
66 CCACCTTATTTATGGTATTA
328282 TAATTGCACC
Statistics
Matches: 79, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
90 79 1.00
ACGTcount: A:0.37, C:0.23, G:0.10, T:0.29
Consensus pattern (90 bp):
CCATCATACACCAAGTATGCCAATTACATACATAGTGCTTCAGTACACAAAGTAATACAACAATA
CCACCTTATTTATGGTATTACAACA
Found at i:337135 original size:13 final size:13
Alignment explanation
Indices: 337117--337142 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
337107 ACTCACTTGG
337117 TATGCCTTACTAT
1 TATGCCTTACTAT
337130 TATGCCTTACTAT
1 TATGCCTTACTAT
337143 CAATATCTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.23, G:0.08, T:0.46
Consensus pattern (13 bp):
TATGCCTTACTAT
Found at i:339631 original size:21 final size:21
Alignment explanation
Indices: 339586--339633 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
339576 AATGACAAAT
*
339586 TGAAG-AGAGAAAGGAATAGG
1 TGAAGAAGAGAAAGGAAGAGG
*
339606 AGAAGAAGAG-AAGGAAGATGG
1 TGAAGAAGAGAAAGGAAGA-GG
339627 TGAAGAA
1 TGAAGAA
339634 AAAAGAGATG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.52, C:0.00, G:0.40, T:0.08
Consensus pattern (21 bp):
TGAAGAAGAGAAAGGAAGAGG
Found at i:341732 original size:2 final size:2
Alignment explanation
Indices: 341725--341750 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
341715 ATTTATTTCA
341725 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
341751 TAACCAATAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:343283 original size:4 final size:4
Alignment explanation
Indices: 343276--343515 Score: 453
Period size: 4 Copynumber: 60.0 Consensus size: 4
343266 AAAATAATAA
* *
343276 ACAT ACAT ACAT ACAT ACAT ACCT ACAT ACAT ACAT ACAT ACAT ACCT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
*
343324 ACAT ACCT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
343372 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
343420 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
343468 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
343516 TTATATACAA
Statistics
Matches: 230, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
4 230 1.00
ACGTcount: A:0.49, C:0.26, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:345095 original size:14 final size:14
Alignment explanation
Indices: 345076--345111 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
345066 GTATCCAGTG
345076 TCAGAAACCAAAGA
1 TCAGAAACCAAAGA
* *
345090 TCAGAAACCATATA
1 TCAGAAACCAAAGA
345104 TCAGAAAC
1 TCAGAAAC
345112 TAGAGCTCAT
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:0.53, C:0.22, G:0.11, T:0.14
Consensus pattern (14 bp):
TCAGAAACCAAAGA
Found at i:346790 original size:22 final size:22
Alignment explanation
Indices: 346765--346819 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
346755 ACATTAGTGA
346765 ACCATTTAAACTCTGTTTGATC
1 ACCATTTAAACTCTGTTTGATC
346787 ACCATTTAAACTCTGTTTGATC
1 ACCATTTAAACTCTGTTTGATC
*
346809 ACC-CTTAAACT
1 ACCATTTAAACT
346820 TGTATTGGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.29, C:0.25, G:0.07, T:0.38
Consensus pattern (22 bp):
ACCATTTAAACTCTGTTTGATC
Found at i:348265 original size:36 final size:36
Alignment explanation
Indices: 348225--348340 Score: 214
Period size: 36 Copynumber: 3.2 Consensus size: 36
348215 TCAGAGTAAC
348225 ATTTTCTTACCTTTAGTGCAATATGCATATATAGCT
1 ATTTTCTTACCTTTAGTGCAATATGCATATATAGCT
348261 ATTTTCTTACCTTTAGTGCAATATGCATATATAGCT
1 ATTTTCTTACCTTTAGTGCAATATGCATATATAGCT
* *
348297 ATTTTCTTACCTTTAGTGCAACATACATATATAGCT
1 ATTTTCTTACCTTTAGTGCAATATGCATATATAGCT
348333 ATTTTCTT
1 ATTTTCTT
348341 TTAGATGTAG
Statistics
Matches: 78, Mismatches: 2, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 78 1.00
ACGTcount: A:0.28, C:0.17, G:0.09, T:0.46
Consensus pattern (36 bp):
ATTTTCTTACCTTTAGTGCAATATGCATATATAGCT
Found at i:359764 original size:16 final size:14
Alignment explanation
Indices: 359743--359778 Score: 54
Period size: 16 Copynumber: 2.4 Consensus size: 14
359733 TAAGTTATAA
359743 TAATTAATTATAATT
1 TAATTAATTAT-ATT
359758 TATATTAATTATATT
1 TA-ATTAATTATATT
359773 TAATTA
1 TAATTA
359779 TAATCTATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 9 0.45
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (14 bp):
TAATTAATTATATT
Found at i:359798 original size:26 final size:24
Alignment explanation
Indices: 359745--359802 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 24
359735 AGTTATAATA
*
359745 ATTAATTATAATTTATATTAATTAT
1 ATTAATTATAATCTATATT-ATTAT
359770 ATTTAATTATAATCTATTATT-TTATT
1 A-TTAATTATAATCTA-TATTATTA-T
359796 ATTAATT
1 ATTAATT
359803 TTATTATTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
25 10 0.34
26 15 0.52
27 4 0.14
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTAATTATAATCTATATTATTAT
Found at i:359805 original size:12 final size:12
Alignment explanation
Indices: 359784--359812 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
359774 AATTATAATC
359784 TATT-ATTTTAT
1 TATTAATTTTAT
359795 TATTAATTTTAT
1 TATTAATTTTAT
359807 TATTAA
1 TATTAA
359813 AATTTATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
TATTAATTTTAT
Found at i:359820 original size:13 final size:13
Alignment explanation
Indices: 359790--359831 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
359780 AATCTATTAT
*
359790 TTTATTATT-AAT
1 TTTATTATTAAAA
359802 TTTATTATTAAAA
1 TTTATTATTAAAA
*
359815 TTTATTTTTAAATA
1 TTTATTATTAAA-A
359829 TTT
1 TTT
359832 TAAAATTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
12 9 0.35
13 13 0.50
14 4 0.15
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TTTATTATTAAAA
Found at i:359903 original size:2 final size:2
Alignment explanation
Indices: 359896--359954 Score: 54
Period size: 2 Copynumber: 31.0 Consensus size: 2
359886 ATAAACTTAC
** *
359896 TA TA TA TA TA TA TA TA CC TA TA AA TA TA -A TA TA CT- TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA
359936 T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA
359955 ATAAGTATAA
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
1 4 0.09
2 41 0.89
3 1 0.02
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:359904 original size:40 final size:40
Alignment explanation
Indices: 359826--359910 Score: 95
Period size: 40 Copynumber: 2.1 Consensus size: 40
359816 TTATTTTTAA
* *
359826 ATATTTTAAAATTTAATTTAATTTAAATTTATATTATAT-T
1 ATATTTTAAAATTTAAATTAA-TTAAACTTATATTATATAT
359866 ATATTTCTAAAA-TTAAATTAA-TAAACTTACTATATATATAT
1 ATATTT-TAAAATTTAAATTAATTAAACTTA-TAT-TATATAT
359907 ATAT
1 ATAT
359911 ACCTATAAAT
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
38 7 0.18
39 3 0.08
40 19 0.49
41 10 0.26
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.51
Consensus pattern (40 bp):
ATATTTTAAAATTTAAATTAATTAAACTTATATTATATAT
Found at i:360049 original size:17 final size:17
Alignment explanation
Indices: 360027--360062 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
360017 TCACATGTAT
360027 TATATATATACT-TATTA
1 TATATATATA-TATATTA
360044 TATATATATATATATTA
1 TATATATATATATATTA
360061 TA
1 TA
360063 ATTGTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 1 0.06
17 17 0.94
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATTA
Found at i:360252 original size:18 final size:18
Alignment explanation
Indices: 360229--360263 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
360219 TTTTATATTA
360229 ATTTCAACTTCATATTTT
1 ATTTCAACTTCATATTTT
* *
360247 ATTTCAATTTTATATTT
1 ATTTCAACTTCATATTT
360264 GCATGTTGTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.11, G:0.00, T:0.60
Consensus pattern (18 bp):
ATTTCAACTTCATATTTT
Found at i:361825 original size:20 final size:20
Alignment explanation
Indices: 361798--361904 Score: 124
Period size: 20 Copynumber: 5.3 Consensus size: 20
361788 AATTTGTAAA
361798 TCGCAACACAAAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
361818 TCGAAACACATAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* * *
361838 TCGCAACGCGATAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
**
361858 TCGCAACACTGAAGTCAAAT
1 TCGCAACACAAAAGTCAAAT
* *
361878 TTGCAACACAAAAGTCATAT
1 TCGCAACACAAAAGTCAAAT
*
361898 TCACAAC
1 TCGCAAC
361905 GCGAATCTGT
Statistics
Matches: 70, Mismatches: 17, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 70 1.00
ACGTcount: A:0.44, C:0.24, G:0.12, T:0.20
Consensus pattern (20 bp):
TCGCAACACAAAAGTCAAAT
Found at i:361970 original size:20 final size:20
Alignment explanation
Indices: 361942--362021 Score: 72
Period size: 20 Copynumber: 4.0 Consensus size: 20
361932 TGTAAATGGC
361942 AACACAGAAGTCAAATTCGT
1 AACACAGAAGTCAAATTCGT
* *
361962 AACATAGAAGTCAAATTCGC
1 AACACAGAAGTCAAATTCGT
** *
361982 AATGC-GATAGTCAAATTCGC
1 AACACAGA-AGTCAAATTCGT
* *
362002 AACACTGAATTTCAAATTCG
1 AACACAGAA-GTCAAATTCG
362022 CAACTCAATT
Statistics
Matches: 49, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
19 2 0.04
20 36 0.73
21 11 0.22
ACGTcount: A:0.41, C:0.20, G:0.15, T:0.24
Consensus pattern (20 bp):
AACACAGAAGTCAAATTCGT
Found at i:362018 original size:21 final size:21
Alignment explanation
Indices: 361992--362065 Score: 75
Period size: 19 Copynumber: 3.7 Consensus size: 21
361982 AATGCGATAG
361992 TCAAATTCGCAACACTGAATT
1 TCAAATTCGCAACACTGAATT
*
362013 TCAAATTCGC-A-ACTCAATTT
1 TCAAATTCGCAACACTGAA-TT
**
362033 TTGAATTCGCAACAC-GAATT
1 TCAAATTCGCAACACTGAATT
*
362053 T-AATTTCGCAACA
1 TCAAATTCGCAACA
362066 GGTTTTAGTT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
19 15 0.34
20 14 0.32
21 13 0.30
22 2 0.05
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.31
Consensus pattern (21 bp):
TCAAATTCGCAACACTGAATT
Found at i:362062 original size:19 final size:20
Alignment explanation
Indices: 361992--362065 Score: 64
Period size: 21 Copynumber: 3.7 Consensus size: 20
361982 AATGCGATAG
*
361992 TCAAATTCGCAACACTGAATT
1 TCAATTTCGCAACAC-GAATT
* *
362013 TCAAATTCGCAACTC-AATTTT
1 TCAATTTCGCAACACGAA--TT
*
362034 TGAA-TTCGCAACACGAATT
1 TCAATTTCGCAACACGAATT
362053 T-AATTTCGCAACA
1 TCAATTTCGCAACA
362066 GGTTTTAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
18 2 0.04
19 14 0.30
20 9 0.20
21 21 0.46
ACGTcount: A:0.36, C:0.23, G:0.09, T:0.31
Consensus pattern (20 bp):
TCAATTTCGCAACACGAATT
Found at i:363033 original size:24 final size:24
Alignment explanation
Indices: 363015--363060 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
363005 AGTTAGTATT
363015 CGAAATTTGATCTTGGTTAATAAC
1 CGAAATTTGATCTTGGTTAATAAC
* *
363039 CGGACTTTGATCTTGGTTAATA
1 CGAAATTTGATCTTGGTTAATA
363061 CTCGGATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTTAATAAC
Found at i:363066 original size:24 final size:24
Alignment explanation
Indices: 363020--363073 Score: 83
Period size: 24 Copynumber: 2.2 Consensus size: 24
363010 GTATTCGAAA
363020 TTTGATCTTGGTTAATAACCGGAC
1 TTTGATCTTGGTTAATAACCGGAC
*
363044 TTTGATCTTGGTTAAT-ACTCGGAT
1 TTTGATCTTGGTTAATAAC-CGGAC
363068 TTTGAT
1 TTTGAT
363074 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.22, C:0.13, G:0.20, T:0.44
Consensus pattern (24 bp):
TTTGATCTTGGTTAATAACCGGAC
Found at i:365355 original size:6 final size:6
Alignment explanation
Indices: 365344--365378 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
365334 AAGCAAAAGG
* *
365344 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
365379 CCAATCAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Done.