Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008016.1 Hibiscus syriacus cultivar Beakdansim tig00110482_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: 5469637
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 25
Found at i:1264978 original size:112 final size:112
Alignment explanation
Indices: 1264487--1264950 Score: 748
Period size: 112 Copynumber: 4.1 Consensus size: 112
1264477 TTGTCGGTTT
* ** * *
1264487 GTGTCGATACTTTATAAAAATATATTAATCCATAACAATATAACATGTAAAAAAAATGATAAAAC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGT-AAAAAAATGACAAAAC
* *
1264552 CGGTTTATAAATGACAAAACAGGTAAAGCGCTACTGGATATATTGAAA
65 CGGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* *
1264600 GTGTCGATACTTTATAAAAATGTATCTATCTATAACAATATAACAGGTAAAAAAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
1264665 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
*
1264712 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAACAATGACAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
*
1264777 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCAGATATATTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
* * * *
1264824 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATTTAACATGTAAAAATATGATAAAACC
1 GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
** * *
1264889 GGTCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAA
66 GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
1264936 GTGTCGATACTTTAT
1 GTGTCGATACTTTAT
1264951 TATAAGCATC
Statistics
Matches: 329, Mismatches: 22, Indels: 1
0.93 0.06 0.00
Matches are distributed among these distances:
112 286 0.87
113 43 0.13
ACGTcount: A:0.44, C:0.14, G:0.15, T:0.26
Consensus pattern (112 bp):
GTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAAAATGACAAAACC
GGTCTATAAATGACAAAACAGGTAAAGCGCTACCGGATATATTGAAA
Found at i:1265128 original size:182 final size:182
Alignment explanation
Indices: 1264821--1265819 Score: 1646
Period size: 182 Copynumber: 5.5 Consensus size: 182
1264811 AGATATATTG
* *
1264821 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATTTAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * *
1264886 ACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* *
1264951 TATAAGCATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* *
1265003 AAAGTGTTGATACTTTATAAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* *
1265068 ATCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* * *
1265133 TATAAGCATCGACACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGTTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* * *
1265185 AAAGTATCGATACTTTATAAAAATGTATCGATCAATAACAATATAACAGGTACAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
*
1265250 ATCGGTCTCGAAATGGCAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
1265315 TATAAGTATCGACACTTTTGGAATTT---AGAGAAGAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* * *
1265364 AAAGTGTCGATATTTTATAAAAATATATCGATCCATAAAAATATAACAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* *
1265429 ATCGGTCTCGAAATGACAAAACCGATAAAGAGCTATCGGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
*
1265494 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAATAAGTTATAGCGCTAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* *
1265546 AAAGTGTAGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* *
1265611 ATCGGTCTCAAAATGACAAAATCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* * *
1265676 TATAAGTATCGAAACTTTTGGAATTTAAAAGA-ATAGAAGTTATAGTGCCAAT
131 TATAAGTATCGACACTTTTGGAATTTAAAAGAGA-AGAAGTTATAGCGCTAAT
* *
1265728 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* *
1265793 ATCGATATCGAAATGACAAAACCGGTA
66 ATCGGTCTCGAAATGACAAAACCGGTA
1265820 GTAAAAAAAT
Statistics
Matches: 767, Mismatches: 46, Indels: 8
0.93 0.06 0.01
Matches are distributed among these distances:
179 169 0.22
181 1 0.00
182 597 0.78
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (182 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:1265499 original size:361 final size:362
Alignment explanation
Indices: 1264821--1265816 Score: 1625
Period size: 361 Copynumber: 2.7 Consensus size: 362
1264811 AGATATATTG
* *
1264821 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATTTAACATGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* * *
1264886 ACCGGTCTCGAAATGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* * *
1264951 TATAAGCATCGACACTTTTAGAATTTAAAAGAGAAGAAGTTATAGCGCTAATAAAGTGTTGATAC
131 TATAAGTATCGACACTTTTGGAATTT--AAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATAC
*
1265016 TTTATAAAAATGTATCGATCAATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAA
194 TTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAA
* *
1265081 TGACAAAACCGGTAAAGCGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGCATCGAC
259 TGACAAAACCGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGCATCGAC
*
1265146 ACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGTTAAT
324 ACTTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* * *
1265185 AAAGTATCGATACTTTATAAAAATGTATCGATCAATAACAATATAACAGGTACAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
*
1265250 ATCGGTCTCGAAATGGCAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
*
1265315 TATAAGTATCGACACTTTTGGAATTT-AGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATATTT
131 TATAAGTATCGACACTTTTGGAATTTAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTT
* *
1265379 TATAAAAATATATCGATCCATAAAAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
196 TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
* * *
1265444 ACAAAACCGATAAAGAGCTATCGGATATGTTGATAGTGTCGATACTTTATTATAAGTATCGACAC
261 ACAAAACCGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGCATCGACAC
* *
1265509 TTTTGGAATTTAAAAGAGAATAAGTTATAGCGCTAAT
326 TTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
* *
1265546 AAAGTGTAGATACTTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGATAAA
1 AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
* *
1265611 ATCGGTCTCAAAATGACAAAATCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
66 ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
* * * *
1265676 TATAAGTATCGAAACTTTTGGAATTTAAAAGAATAGAAGTTATAGTGCCAATAAAGTGTCGATAC
131 TATAAGTATCGACACTTTTGGAATTTAAGAG-A-AGAAGTTATAGCGCTAATAAAGTGTCGATAC
* * * *
1265741 TTTATAAAAATGTATCGATCCATAACAATATAATAGGTAAAAATATGACAAAATCGATATCGAAA
194 TTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAA
1265806 TGACAAAACCG
259 TGACAAAACCG
1265817 GTAGTAAAAA
Statistics
Matches: 586, Mismatches: 43, Indels: 6
0.92 0.07 0.01
Matches are distributed among these distances:
361 339 0.58
362 3 0.01
363 1 0.00
364 243 0.41
ACGTcount: A:0.42, C:0.12, G:0.17, T:0.29
Consensus pattern (362 bp):
AAAGTGTCGATACTTTATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAA
ATCGGTCTCGAAATGACAAAACCGGTAAAGAGCTACCGGATATGTTGATAGTGTCGATACTTTAT
TATAAGTATCGACACTTTTGGAATTTAAGAGAAGAAGTTATAGCGCTAATAAAGTGTCGATACTT
TATAAAAATGTATCGATCCATAACAATATAACAGGTAAAAATATGATAAAATCGGTCTCGAAATG
ACAAAACCGATAAAGAGCTACCGGATATGTTGAAAGTGTCGATACTTTATTATAAGCATCGACAC
TTTTGAAATTTAAAAGAGAAGAAGTTATAGCGCTAAT
Found at i:1266034 original size:23 final size:23
Alignment explanation
Indices: 1266008--1266055 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
1265998 AAATAGGTCA
*
1266008 ATATAAGCGCTACCTATTACATT
1 ATATAAGCGCTACCTAATACATT
*
1266031 ATATAAGCGCTACCTAATATATT
1 ATATAAGCGCTACCTAATACATT
1266054 AT
1 AT
1266056 TATACTTGAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.38, C:0.19, G:0.08, T:0.35
Consensus pattern (23 bp):
ATATAAGCGCTACCTAATACATT
Found at i:1270054 original size:21 final size:18
Alignment explanation
Indices: 1270030--1270074 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 18
1270020 AAGTCTTTTA
1270030 ATTATTAAAAGTTATAAAAT
1 ATTATT-AAA-TTATAAAAT
*
1270050 GATTATTTAATTATAAAAT
1 -ATTATTAAATTATAAAAT
1270069 ATTATT
1 ATTATT
1270075 TTATTAAGCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 6 0.26
19 9 0.39
20 2 0.09
21 6 0.26
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (18 bp):
ATTATTAAATTATAAAAT
Found at i:1270072 original size:18 final size:19
Alignment explanation
Indices: 1270041--1270080 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
1270031 TTATTAAAAG
1270041 TTATAAAATGATTATTTAA
1 TTATAAAATGATTATTTAA
*
1270060 TTATAAAAT-ATTATTTTA
1 TTATAAAATGATTATTTAA
1270078 TTA
1 TTA
1270081 AGCCCCTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (19 bp):
TTATAAAATGATTATTTAA
Found at i:1275160 original size:30 final size:30
Alignment explanation
Indices: 1275108--1275387 Score: 126
Period size: 30 Copynumber: 9.8 Consensus size: 30
1275098 TAACATTAAA
1275108 AAATATATTTTGTATT-TT-TCTTAATTTATT
1 AAATATA-TTT-TATTCTTATCTTAATTTATT
* **
1275138 AAATATATTTTATTCTTATCTTAA-CTAAA
1 AAATATATTTTATTCTTATCTTAATTTATT
*
1275167 AAATATATTTTA-----ATC-TAATCTA--
1 AAATATATTTTATTCTTATCTTAATTTATT
* * * *
1275189 AAATTTATTTTATTTTTATCTTAACTTGTT
1 AAATATATTTTATTCTTATCTTAATTTATT
** * * * * *
1275219 ACCTACACTATATTCTTAACTTAAATTATT
1 AAATATATTTTATTCTTATCTTAATTTATT
* * *
1275249 AAATATATTATATTCTTACCTTAAATTATT
1 AAATATATTTTATTCTTATCTTAATTTATT
* * *
1275279 AAATAT-TATTTATTCTTAACTTTACTTA--
1 AAATATAT-TTTATTCTTATCTTAATTTATT
* * **
1275307 AAATATA---TATTTTTATTTTAATTTAAA
1 AAATATATTTTATTCTTATCTTAATTTATT
* * * *
1275334 AAATATTTTTTATTTTTATTTTAATTTAAT
1 AAATATATTTTATTCTTATCTTAATTTATT
* * *
1275364 AAATACATTTTATTTTTATTTTAA
1 AAATATATTTTATTCTTATCTTAA
1275388 CTATAAAAAA
Statistics
Matches: 197, Mismatches: 35, Indels: 36
0.74 0.13 0.13
Matches are distributed among these distances:
22 11 0.06
23 3 0.02
24 6 0.03
25 13 0.07
27 9 0.05
28 14 0.07
29 20 0.10
30 121 0.61
ACGTcount: A:0.37, C:0.07, G:0.01, T:0.55
Consensus pattern (30 bp):
AAATATATTTTATTCTTATCTTAATTTATT
Found at i:1275178 original size:29 final size:29
Alignment explanation
Indices: 1275094--1275187 Score: 84
Period size: 29 Copynumber: 3.1 Consensus size: 29
1275084 TTAAAATCAC
1275094 ATCTTAACATTAAAAAATATATTTTGTATT-TT
1 ATCTTAAC--TAAAAAATATA-TTT-TATTCTT
* **
1275126 -TCTTAATTTATTAAATATATTTTATTCTT
1 ATCTTAA-CTAAAAAATATATTTTATTCTT
* *
1275155 ATCTTAACTAAAAAATATATTTTAATCTA
1 ATCTTAACTAAAAAATATATTTTATTCTT
1275184 ATCT
1 ATCT
1275188 AAAATTTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
28 4 0.08
29 26 0.51
30 15 0.29
31 6 0.12
ACGTcount: A:0.39, C:0.09, G:0.01, T:0.51
Consensus pattern (29 bp):
ATCTTAACTAAAAAATATATTTTATTCTT
Found at i:1275357 original size:25 final size:25
Alignment explanation
Indices: 1275304--1275354 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
1275294 TTAACTTTAC
*
1275304 TTAAAATATATATTTTTATTTTAAT
1 TTAAAAAATATATTTTTATTTTAAT
*
1275329 TTAAAAAATAT-TTTTTATTTTTAT
1 TTAAAAAATATATTTTTATTTTAAT
1275353 TT
1 TT
1275355 TAATTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (25 bp):
TTAAAAAATATATTTTTATTTTAAT
Found at i:1275405 original size:30 final size:30
Alignment explanation
Indices: 1275314--1275406 Score: 134
Period size: 30 Copynumber: 3.1 Consensus size: 30
1275304 TTAAAATATA
*
1275314 TATTTTTATTTTAATTTAAAAAATATTTTT
1 TATTTTTATTTTAATTTAAAAAATACTTTT
* *
1275344 TATTTTTATTTTAATTTAATAAATACATTT
1 TATTTTTATTTTAATTTAAAAAATACTTTT
*
1275374 TATTTTTATTTTAACTATAAAAAATA-TTTT
1 TATTTTTATTTTAA-TTTAAAAAATACTTTT
1275404 TAT
1 TAT
1275407 CTTAATTAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 47 0.84
31 9 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (30 bp):
TATTTTTATTTTAATTTAAAAAATACTTTT
Found at i:1275419 original size:21 final size:24
Alignment explanation
Indices: 1275374--1275422 Score: 68
Period size: 24 Copynumber: 2.2 Consensus size: 24
1275364 AAATACATTT
*
1275374 TATTTTTATTTTAACTATAAAAAA
1 TATTTTTATCTTAACTATAAAAAA
1275398 TATTTTTATCTTAA-T-T-AAAAA
1 TATTTTTATCTTAACTATAAAAAA
1275419 TATT
1 TATT
1275423 ATAAGAATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 9 0.38
22 1 0.04
23 1 0.04
24 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.00, T:0.53
Consensus pattern (24 bp):
TATTTTTATCTTAACTATAAAAAA
Found at i:1277661 original size:17 final size:17
Alignment explanation
Indices: 1277641--1277673 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1277631 AGTAAAATAA
1277641 TAAATAAATTAAATACT
1 TAAATAAATTAAATACT
1277658 TAAATAAATTAAATAC
1 TAAATAAATTAAATAC
1277674 AAAATATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAATAAATTAAATACT
Found at i:1279385 original size:31 final size:31
Alignment explanation
Indices: 1279347--1279422 Score: 116
Period size: 31 Copynumber: 2.5 Consensus size: 31
1279337 ATAGTCAGGG
1279347 ACTCAAGAAAGCAACATCTTATAGACGAAGA
1 ACTCAAGAAAGCAACATCTTATAGACGAAGA
* * *
1279378 ACTCAAGAAAACAACGTCTTATAGTCGAAGA
1 ACTCAAGAAAGCAACATCTTATAGACGAAGA
*
1279409 ACTCAATAAAGCAA
1 ACTCAAGAAAGCAA
1279423 GACTCTATGG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.49, C:0.20, G:0.14, T:0.17
Consensus pattern (31 bp):
ACTCAAGAAAGCAACATCTTATAGACGAAGA
Found at i:1279436 original size:31 final size:31
Alignment explanation
Indices: 1279347--1279436 Score: 94
Period size: 31 Copynumber: 2.9 Consensus size: 31
1279337 ATAGTCAGGG
* *
1279347 ACTCAAGAAAGCAAC-ATCTTATAGACGAAGA
1 ACTCAAGAAAACAACGA-CTTATAGTCGAAGA
*
1279378 ACTCAAGAAAACAACGTCTTATAGTCGAAGA
1 ACTCAAGAAAACAACGACTTATAGTCGAAGA
* * *
1279409 ACTCAATAAAGCAA-GACTCTATGGTCGA
1 ACTCAAGAAAACAACGACT-TATAGTCGA
1279437 GGGGTCATTT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
30 3 0.06
31 47 0.94
ACGTcount: A:0.44, C:0.20, G:0.17, T:0.19
Consensus pattern (31 bp):
ACTCAAGAAAACAACGACTTATAGTCGAAGA
Found at i:1284258 original size:23 final size:24
Alignment explanation
Indices: 1284232--1284276 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
1284222 TTAACGACTG
1284232 TATCAAGATAA-T-AAAATATTTAT
1 TATCAA-ATAATTAAAAATATTTAT
1284255 TATCAAATAATTAAAAATATTT
1 TATCAAATAATTAAAAATATTT
1284277 TAAACAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 4 0.20
23 7 0.35
24 9 0.45
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.40
Consensus pattern (24 bp):
TATCAAATAATTAAAAATATTTAT
Found at i:1284571 original size:23 final size:23
Alignment explanation
Indices: 1284544--1284587 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
1284534 ATCTCCCTCT
*
1284544 GATTTTATAACAACGTCTCTGGA
1 GATTTTATAACAACGGCTCTGGA
1284567 GATTTTATAACAACGGCTCTG
1 GATTTTATAACAACGGCTCTG
1284588 CTGGTTATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (23 bp):
GATTTTATAACAACGGCTCTGGA
Found at i:1287220 original size:55 final size:55
Alignment explanation
Indices: 1287160--1287270 Score: 204
Period size: 55 Copynumber: 2.0 Consensus size: 55
1287150 ATAGTTTACC
1287160 TCAAATGTGTTGCCGTCGAATGTGACTGTTAGCTCCTGGCCAACTCTCCATTCTT
1 TCAAATGTGTTGCCGTCGAATGTGACTGTTAGCTCCTGGCCAACTCTCCATTCTT
* *
1287215 TCAAATGTGTTGCCTTCGAATGTGACTGTTAGCTCCTGGCTAACTCTCCATTCTT
1 TCAAATGTGTTGCCGTCGAATGTGACTGTTAGCTCCTGGCCAACTCTCCATTCTT
1287270 T
1 T
1287271 ATGTGATTTA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
55 54 1.00
ACGTcount: A:0.18, C:0.26, G:0.19, T:0.37
Consensus pattern (55 bp):
TCAAATGTGTTGCCGTCGAATGTGACTGTTAGCTCCTGGCCAACTCTCCATTCTT
Found at i:1290176 original size:2 final size:2
Alignment explanation
Indices: 1290169--1290208 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
1290159 ATTTCAAGAG
1290169 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
1290209 GGGGGCATGC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1291129 original size:28 final size:29
Alignment explanation
Indices: 1291096--1291162 Score: 109
Period size: 29 Copynumber: 2.3 Consensus size: 29
1291086 GAATGATATT
*
1291096 ACATACAAATGGA-AACACACATGGATAA
1 ACATACAAATGGATAACACACATGAATAA
*
1291124 ATATACAAATGGATAACACACATGAATAA
1 ACATACAAATGGATAACACACATGAATAA
1291153 ACATACAAAT
1 ACATACAAAT
1291163 CATAAGGGCG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
28 12 0.34
29 23 0.66
ACGTcount: A:0.55, C:0.16, G:0.10, T:0.18
Consensus pattern (29 bp):
ACATACAAATGGATAACACACATGAATAA
Found at i:1292355 original size:21 final size:22
Alignment explanation
Indices: 1292325--1292373 Score: 73
Period size: 21 Copynumber: 2.3 Consensus size: 22
1292315 TTCTAATAAA
*
1292325 TTTTAACTAAAACATT-ATTTT
1 TTTTAACTAAAACATTAATGTT
*
1292346 TTTTATCTAAAACATTAATGTT
1 TTTTAACTAAAACATTAATGTT
1292368 TTTTAA
1 TTTTAA
1292374 TATTTTCGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.37, C:0.08, G:0.02, T:0.53
Consensus pattern (22 bp):
TTTTAACTAAAACATTAATGTT
Found at i:1292422 original size:27 final size:27
Alignment explanation
Indices: 1292370--1292422 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
1292360 TTAATGTTTT
***
1292370 TTAATATTTTCGGTGAAATGTCTAATA
1 TTAATATTTTCGGTGAAATAAATAATA
1292397 TTAATATTTTCGGTAGAAA-AAATAAT
1 TTAATATTTTCGGT-GAAATAAATAAT
1292423 GTTTTAGGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 18 0.82
28 4 0.18
ACGTcount: A:0.40, C:0.06, G:0.13, T:0.42
Consensus pattern (27 bp):
TTAATATTTTCGGTGAAATAAATAATA
Found at i:1297208 original size:4 final size:4
Alignment explanation
Indices: 1297199--1297227 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
1297189 GAAGGTGGCG
1297199 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT A
1297228 GCATATGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
AAAT
Found at i:1297707 original size:50 final size:50
Alignment explanation
Indices: 1297632--1297735 Score: 199
Period size: 50 Copynumber: 2.1 Consensus size: 50
1297622 ATACGAGTGT
1297632 GGTTGCTATGAGGGCAAATCTCATCTTTCATGCTCATTCTAAACATGCGG
1 GGTTGCTATGAGGGCAAATCTCATCTTTCATGCTCATTCTAAACATGCGG
*
1297682 GGTTGCTATGAGGGCAAATCTCATCTTTCATGCTCGTTCTAAACATGCGG
1 GGTTGCTATGAGGGCAAATCTCATCTTTCATGCTCATTCTAAACATGCGG
1297732 GGTT
1 GGTT
1297736 AGATGTTTAC
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (50 bp):
GGTTGCTATGAGGGCAAATCTCATCTTTCATGCTCATTCTAAACATGCGG
Found at i:1300966 original size:21 final size:21
Alignment explanation
Indices: 1300940--1300997 Score: 116
Period size: 21 Copynumber: 2.8 Consensus size: 21
1300930 GTGATTAATT
1300940 TAATAAATACTTTTACTGATG
1 TAATAAATACTTTTACTGATG
1300961 TAATAAATACTTTTACTGATG
1 TAATAAATACTTTTACTGATG
1300982 TAATAAATACTTTTAC
1 TAATAAATACTTTTAC
1300998 CGGGAAAAGT
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:0.40, C:0.10, G:0.07, T:0.43
Consensus pattern (21 bp):
TAATAAATACTTTTACTGATG
Found at i:1302586 original size:64 final size:64
Alignment explanation
Indices: 1302381--1302590 Score: 219
Period size: 65 Copynumber: 3.2 Consensus size: 64
1302371 TTTTTCAGAG
* * ** *
1302381 TGATGCACCGATGCACCAATCCATGCATCGATGCAC-CATGAATTAAATTG-AACATTGAATGCA
1 TGATGCATCGATGCACCAA-CCATGCATCGATGCACTC-TGGA-TATTTTGAAACATCGAATGCA
1302444 TT
63 TT
* * ** * **
1302446 TCATGCATCGACGCACTTACCATGCACCGATGCACTGAGGAT-TTTATGAAAACATCGAATGCAT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTT-TG-AAACATCGAATGCAT
1302510 T
64 T
* * *
1302511 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGCTATTTTGAAACATCGAATACACT
1 TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
1302575 TGATGCATCGATGCAC
1 TGATGCATCGATGCAC
1302591 TCTTAGTGCA
Statistics
Matches: 118, Mismatches: 22, Indels: 11
0.78 0.15 0.07
Matches are distributed among these distances:
62 1 0.01
63 3 0.03
64 47 0.40
65 64 0.54
66 3 0.03
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (64 bp):
TGATGCATCGATGCACCAACCATGCATCGATGCACTCTGGATATTTTGAAACATCGAATGCATT
Found at i:1308427 original size:24 final size:24
Alignment explanation
Indices: 1308400--1308480 Score: 75
Period size: 24 Copynumber: 3.5 Consensus size: 24
1308390 ACACTTAACA
1308400 GTGCATCGATGCATCCCTTTGAAT
1 GTGCATCGATGCATCCCTTTGAAT
* *
1308424 GTGCATCGATTCAT-CATGTTG-A-
1 GTGCATCGATGCATCCCT-TTGAAT
*
1308446 -TGCACCGATGCA-CTCC-TTGAAT
1 GTGCATCGATGCATC-CCTTTGAAT
1308468 GTGCATCGATGCA
1 GTGCATCGATGCA
1308481 CAGGGTCATG
Statistics
Matches: 45, Mismatches: 6, Indels: 13
0.70 0.09 0.20
Matches are distributed among these distances:
20 3 0.07
21 11 0.24
22 1 0.02
23 14 0.31
24 16 0.36
ACGTcount: A:0.22, C:0.25, G:0.22, T:0.31
Consensus pattern (24 bp):
GTGCATCGATGCATCCCTTTGAAT
Found at i:1312414 original size:2 final size:2
Alignment explanation
Indices: 1312407--1312454 Score: 78
Period size: 2 Copynumber: 23.5 Consensus size: 2
1312397 GAGTACTTGA
1312407 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
*
1312450 GT AT A
1 AT AT A
1312455 AATACATGTT
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
2 41 0.95
3 2 0.05
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1312850 original size:31 final size:31
Alignment explanation
Indices: 1312815--1312905 Score: 128
Period size: 31 Copynumber: 2.9 Consensus size: 31
1312805 AGTTAAGAGC
***
1312815 TACCTATGTACTTTAAGACATATGGACAGTT
1 TACCTATGTACTTCGGGACATATGGACAGTT
* *
1312846 TACCTATGTCCTTCGGGACATATGGACATTT
1 TACCTATGTACTTCGGGACATATGGACAGTT
*
1312877 TACCTATGTTCTTCGGGACATATGGACAG
1 TACCTATGTACTTCGGGACATATGGACAG
1312906 GTCATTCGGG
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.26, C:0.20, G:0.20, T:0.34
Consensus pattern (31 bp):
TACCTATGTACTTCGGGACATATGGACAGTT
Found at i:1317014 original size:19 final size:19
Alignment explanation
Indices: 1316992--1317035 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
1316982 TCCTAAAATC
1316992 TTTAAACAATAGTAAATAT
1 TTTAAACAATAGTAAATAT
1317011 TTTAAACAATAGTAAATAT
1 TTTAAACAATAGTAAATAT
*
1317030 TGTAAA
1 TTTAAA
1317036 ATCATCTATA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.52, C:0.05, G:0.07, T:0.36
Consensus pattern (19 bp):
TTTAAACAATAGTAAATAT
Found at i:1317111 original size:19 final size:19
Alignment explanation
Indices: 1317087--1317141 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
1317077 AACCTAAAAC
1317087 TTTAAACAATAGTAAATAT
1 TTTAAACAATAGTAAATAT
1317106 TTTAAACAATAGTAAATAT
1 TTTAAACAATAGTAAATAT
1317125 TTTAAACAATAGTAAAT
1 TTTAAACAATAGTAAAT
1317142 TTAATCAATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 36 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (19 bp):
TTTAAACAATAGTAAATAT
Found at i:1322756 original size:84 final size:85
Alignment explanation
Indices: 1322659--1322847 Score: 319
Period size: 85 Copynumber: 2.2 Consensus size: 85
1322649 TTTATTATAT
*
1322659 TTTAAGTTGATATATTTCATGAT-AAAAATATTAAATATTATTTAAATATAT-TTTTAAATTTTA
1 TTTAAATTGATATATTTCATGATAAAAAATATTAAATATTATTTAAATATATATTTT-AATTTTA
1322722 TTTGATGTATTTTCATCATGC
65 TTTGATGTATTTTCATCATGC
* *
1322743 TTTAAATTAATATATTTCATGATAAAAAATATTAAATATTATTTAAATGTATATTTTAATTTTAT
1 TTTAAATTGATATATTTCATGATAAAAAATATTAAATATTATTTAAATATATATTTTAATTTTAT
*
1322808 TTGATGTATTTTCATCTTGC
66 TTGATGTATTTTCATCATGC
1322828 TTTAAATTGATATATTTCAT
1 TTTAAATTGATATATTTCAT
1322848 AGTTGTCGAA
Statistics
Matches: 98, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
84 21 0.21
85 73 0.74
86 4 0.04
ACGTcount: A:0.37, C:0.05, G:0.06, T:0.52
Consensus pattern (85 bp):
TTTAAATTGATATATTTCATGATAAAAAATATTAAATATTATTTAAATATATATTTTAATTTTAT
TTGATGTATTTTCATCATGC
Found at i:1323632 original size:40 final size:38
Alignment explanation
Indices: 1323573--1323667 Score: 129
Period size: 40 Copynumber: 2.4 Consensus size: 38
1323563 TAATTTTTGA
1323573 AAATATTATATATATTATATAGTAT-GATTTTTGAAAAC
1 AAATATTATATATATTATATAGTATAGA-TTTTGAAAAC
1323611 AAATATTATGCATATATTATATAGTATAGATTTTGAAAAC
1 AAATATTAT--ATATATTATATAGTATAGATTTTGAAAAC
*
1323651 AAACAATTATTATATAT
1 AAA-TATTA-TATATAT
1323668 ATTAAAATAA
Statistics
Matches: 51, Mismatches: 1, Indels: 8
0.85 0.02 0.13
Matches are distributed among these distances:
38 9 0.18
40 35 0.69
41 6 0.12
42 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.07, T:0.42
Consensus pattern (38 bp):
AAATATTATATATATTATATAGTATAGATTTTGAAAAC
Found at i:1332773 original size:38 final size:38
Alignment explanation
Indices: 1332722--1332794 Score: 137
Period size: 38 Copynumber: 1.9 Consensus size: 38
1332712 CTGGGAAAGC
1332722 ACGCGAGAGTAGATGATGTTTCTATGGAAATTGACTGT
1 ACGCGAGAGTAGATGATGTTTCTATGGAAATTGACTGT
*
1332760 ACGCGAGAGTAGATGATGTTTCTGTGGAAATTGAC
1 ACGCGAGAGTAGATGATGTTTCTATGGAAATTGAC
1332795 CATCTTCTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (38 bp):
ACGCGAGAGTAGATGATGTTTCTATGGAAATTGACTGT
Found at i:1340879 original size:18 final size:18
Alignment explanation
Indices: 1340848--1340898 Score: 75
Period size: 18 Copynumber: 2.8 Consensus size: 18
1340838 ACTGAATATT
* *
1340848 TGTCCTGAATGACCACTA
1 TGTCCCGAAGGACCACTA
1340866 TGTCCCGAAGGACCACTA
1 TGTCCCGAAGGACCACTA
*
1340884 TGTCTCGAAGGACCA
1 TGTCCCGAAGGACCA
1340899 TTGATATGTC
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.22
Consensus pattern (18 bp):
TGTCCCGAAGGACCACTA
Found at i:1340908 original size:21 final size:21
Alignment explanation
Indices: 1340848--1340925 Score: 62
Period size: 18 Copynumber: 4.0 Consensus size: 21
1340838 ACTGAATATT
*
1340848 TGTCCTGAATGACCAC---TA
1 TGTCCTGAAGGACCACTGATA
*
1340866 TGTCCCGAAGGACCAC---TA
1 TGTCCTGAAGGACCACTGATA
*
1340884 TGT-CTCGAAGGACCATTGATA
1 TGTCCT-GAAGGACCACTGATA
*
1340905 TGTCCTGAATGACCACTGATA
1 TGTCCTGAAGGACCACTGATA
1340926 ATCCCTCGAC
Statistics
Matches: 49, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
17 1 0.02
18 28 0.57
21 18 0.37
22 2 0.04
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (21 bp):
TGTCCTGAAGGACCACTGATA
Found at i:1342518 original size:24 final size:23
Alignment explanation
Indices: 1342459--1342523 Score: 75
Period size: 20 Copynumber: 3.0 Consensus size: 23
1342449 TTTATATTTC
*
1342459 CCTTTAA-AGTGCATCGATACAT
1 CCTTTAACAGTGCATCGATGCAT
*
1342481 --TTT-ACAGTGTATCGATGCAT
1 CCTTTAACAGTGCATCGATGCAT
1342501 CCTTTAACATGTGCATCGATGCA
1 CCTTTAACA-GTGCATCGATGCA
1342524 CTACCCCATG
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
19 1 0.03
20 16 0.46
22 3 0.09
23 3 0.09
24 12 0.34
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (23 bp):
CCTTTAACAGTGCATCGATGCAT
Found at i:1346007 original size:21 final size:21
Alignment explanation
Indices: 1345962--1346066 Score: 153
Period size: 21 Copynumber: 5.1 Consensus size: 21
1345952 GGAGCTGAAT
1345962 ATATGTCCCGAAGGACCA-T-
1 ATATGTCCCGAAGGACCACTG
*
1345981 -TATGTCCCGAAGGACAACTG
1 ATATGTCCCGAAGGACCACTG
*
1346001 ATATGTCCCGAATGACCACTG
1 ATATGTCCCGAAGGACCACTG
*
1346022 ATATGTCCTGAAGGACCACTG
1 ATATGTCCCGAAGGACCACTG
*
1346043 ATATGTCCCGAAGAACCACTG
1 ATATGTCCCGAAGGACCACTG
1346064 ATA
1 ATA
1346067 ATCCCTCGAC
Statistics
Matches: 76, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
18 16 0.21
19 1 0.01
21 59 0.78
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.22
Consensus pattern (21 bp):
ATATGTCCCGAAGGACCACTG
Found at i:1347742 original size:19 final size:17
Alignment explanation
Indices: 1347718--1347761 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
1347708 TAATGGGTGT
1347718 ATCGATGCACTCCCTATGC
1 ATCGATGCACT-CCT-TGC
*
1347737 ATCGATACACTCCTTGC
1 ATCGATGCACTCCTTGC
1347754 ATTCGATG
1 A-TCGATG
1347762 TTCATTTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
17 4 0.18
18 8 0.36
19 10 0.45
ACGTcount: A:0.23, C:0.32, G:0.16, T:0.30
Consensus pattern (17 bp):
ATCGATGCACTCCTTGC
Found at i:1349054 original size:23 final size:23
Alignment explanation
Indices: 1349028--1349085 Score: 98
Period size: 23 Copynumber: 2.5 Consensus size: 23
1349018 CTTTTGAAAA
1349028 TTTACATTTTTAGTCTTTAAACT
1 TTTACATTTTTAGTCTTTAAACT
*
1349051 TTTACATTTTGAGTCTTTAAACT
1 TTTACATTTTTAGTCTTTAAACT
*
1349074 TTTACATCTTTA
1 TTTACATTTTTA
1349086 CATTTTGGTT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 32 1.00
ACGTcount: A:0.26, C:0.14, G:0.05, T:0.55
Consensus pattern (23 bp):
TTTACATTTTTAGTCTTTAAACT
Found at i:1352579 original size:11 final size:11
Alignment explanation
Indices: 1352550--1352579 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
1352540 GTGATCCTAC
1352550 AAAAAAAATTT
1 AAAAAAAATTT
*
1352561 TAAAAAAATTT
1 AAAAAAAATTT
1352572 AAAAAAAA
1 AAAAAAAA
1352580 ATTGTAACCA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (11 bp):
AAAAAAAATTT
Found at i:1361761 original size:21 final size:20
Alignment explanation
Indices: 1361675--1361832 Score: 77
Period size: 21 Copynumber: 7.8 Consensus size: 20
1361665 AAATGACCAA
**
1361675 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
1361694 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
1361714 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
1361734 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
1361755 GAAAATCGCAATGTGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
1361776 CAAATTCGCATTGCGATTTTT
1 CAAAATCGCAACGCGA-TTTT
* *
1361797 CAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGATTTT
*
1361817 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
1361833 ACACATAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 16 0.16
20 42 0.41
21 43 0.42
22 1 0.01
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:1361823 original size:20 final size:20
Alignment explanation
Indices: 1361799--1362048 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
1361789 CGATTTTTCA
** *
1361799 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGAATCCGT
*
1361819 AAATCGCAACGCGAA-CACAT
1 AAATCGCAACGCGAATC-CGT
*
1361839 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
*
1361859 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* **
1361879 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGAATCCGT
* *
1361899 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1361919 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1361939 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1361959 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1361979 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
**
1361999 AAATCGCAACGATAATCCGT
1 AAATCGCAACGCGAATCCGT
* *
1362019 AAATCGCAACGAGAATCTGT
1 AAATCGCAACGCGAATCCGT
*
1362039 AAATCACAAC
1 AAATCGCAAC
1362049 ACTGAAATTT
Statistics
Matches: 202, Mismatches: 26, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 201 1.00
21 1 0.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGAATCCGT
Found at i:1362770 original size:24 final size:24
Alignment explanation
Indices: 1362731--1362777 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1362721 AAATTTGGTC
1362731 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1362755 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1362778 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:1365352 original size:19 final size:19
Alignment explanation
Indices: 1365312--1365409 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
1365302 GATTCTCTCG
1365312 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
1365332 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
1365351 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
1365365 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1365384 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
1365403 TTGCGAT
1 TTGCGAT
1365410 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:1365406 original size:52 final size:53
Alignment explanation
Indices: 1365293--1365409 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
1365283 GAAATGAAAA
1365293 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1365346 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1365398 TCGCATTGCGAT
1 TCGCATTGCGAT
1365410 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:1365505 original size:14 final size:14
Alignment explanation
Indices: 1365486--1365540 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1365476 CGGAAATGAA
1365486 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
1365500 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1365519 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1365533 AATCGCAA
1 AATCGCAA
1365541 TGCGAAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.45, C:0.20, G:0.24, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1365520 original size:33 final size:33
Alignment explanation
Indices: 1365468--1365559 Score: 175
Period size: 33 Copynumber: 2.8 Consensus size: 33
1365458 CAATTACATT
1365468 TCGCAATGCGGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGC-GAAATGAAAATCGCAACGAGAGAA
1365502 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
1365535 TCGCAATGCGAAATGAAAATCGCAA
1 TCGCAATGCGAAATGAAAATCGCAA
1365560 TGCGAAATGA
Statistics
Matches: 58, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 49 0.84
34 9 0.16
ACGTcount: A:0.45, C:0.18, G:0.24, T:0.13
Consensus pattern (33 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAA
Found at i:1365559 original size:52 final size:52
Alignment explanation
Indices: 1365500--1365610 Score: 204
Period size: 52 Copynumber: 2.1 Consensus size: 52
1365490 GCAACGAGAG
1365500 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
* *
1365552 AATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
1365604 AATCGCA
1 AATCGCA
1365611 TTGTGATTCT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 57 1.00
ACGTcount: A:0.46, C:0.18, G:0.21, T:0.15
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAA
Found at i:1365665 original size:19 final size:19
Alignment explanation
Indices: 1365623--1365722 Score: 147
Period size: 19 Copynumber: 5.5 Consensus size: 19
1365613 GTGATTCTCC
1365623 CATTGCGATTTTCATTTCCG
1 CATTGCGATTTTCATTT-CG
1365643 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
*
1365662 CATTGCGA--TTC-TCTCG
1 CATTGCGATTTTCATTTCG
1365678 --TTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1365695 CATTGCGATTTTCATTTCG
1 CATTGCGATTTTCATTTCG
1365714 CATTGCGAT
1 CATTGCGAT
1365723 AGTCAATTTT
Statistics
Matches: 73, 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 0.49
20 17 0.23
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.45
Consensus pattern (19 bp):
CATTGCGATTTTCATTTCG
Found at i:1365719 original size:52 final size:53
Alignment explanation
Indices: 1365606--1365722 Score: 200
Period size: 53 Copynumber: 2.2 Consensus size: 53
1365596 GAAATTAAAA
*
1365606 TCGCATTGTGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
* *
1365659 TCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCATTGCGATTTTCATT
1 TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
1365711 TCGCATTGCGAT
1 TCGCATTGCGAT
1365723 AGTCAATTTT
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
52 30 0.49
53 31 0.51
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (53 bp):
TCGCATTGCGATTCTCCCATTGCGATTTTCATTTCCGCATTGCGATTTTCATT
Found at i:1365848 original size:14 final size:14
Alignment explanation
Indices: 1365829--1365865 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
1365819 CATCAATTAC
1365829 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
1365843 ACAAATCATCTTTT
1 ACAAATCAACTTTT
1365857 ACAAATCAA
1 ACAAATCAA
1365866 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:1367834 original size:33 final size:33
Alignment explanation
Indices: 1367797--1367889 Score: 177
Period size: 33 Copynumber: 2.8 Consensus size: 33
1367787 GCGAAACCAA
1367797 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1367830 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1367863 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1367890 TGCGATTTTG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.48, C:0.20, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1367835 original size:14 final size:14
Alignment explanation
Indices: 1367816--1367872 Score: 69
Period size: 14 Copynumber: 3.7 Consensus size: 14
1367806 GCGAAATGAA
1367816 AATCGCAACGAAAG
1 AATCGCAACGAAAG
1367830 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1367847 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1367863 AATCGCAACG
1 AATCGCAACG
1367873 CGAAATGAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 10
0.79 0.00 0.21
Matches are distributed among these distances:
14 18 0.47
16 6 0.16
17 6 0.16
19 8 0.21
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1367854 original size:19 final size:19
Alignment explanation
Indices: 1367760--1367894 Score: 137
Period size: 19 Copynumber: 7.6 Consensus size: 19
1367750 TAGTTTACTT
* *
1367760 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1367780 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1367799 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1367818 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1367832 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1367851 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1367865 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1367884 TCGCAATGCGA
1 TCGCAACGCGA
1367895 TTTTGGTTTC
Statistics
Matches: 99, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
14 16 0.16
16 12 0.12
17 12 0.12
19 47 0.47
20 12 0.12
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1367886 original size:52 final size:54
Alignment explanation
Indices: 1367760--1367894 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 54
1367750 TAGTTTACTT
* *
1367760 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAATGAAAA
1 TCGCAAC-CGAAA-TGAAAATCGCAATGCGAAACCAAAATCGCAAC-CGAAATG-AAA
**
1367818 TCGCAA-CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAA-CGAAA-G-AA
1 TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
1367865 TCGCAACGCGAAATGAAAATCGCAATGCGA
1 TCGCAAC-CGAAATGAAAATCGCAATGCGA
1367895 TTTTGGTTTC
Statistics
Matches: 68, Mismatches: 4, Indels: 16
0.77 0.05 0.18
Matches are distributed among these distances:
47 8 0.12
49 6 0.09
50 6 0.09
52 37 0.54
56 5 0.07
58 6 0.09
ACGTcount: A:0.47, C:0.23, G:0.19, T:0.11
Consensus pattern (54 bp):
TCGCAACCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACCGAAATGAAA
Found at i:1367912 original size:19 final size:19
Alignment explanation
Indices: 1367890--1368018 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1367880 AAAATCGCAA
1367890 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1367909 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1367923 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1367942 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1367956 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1367975 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1367994 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1368014 TGCGA
1 TGCGA
1368019 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:1367932 original size:33 final size:33
Alignment explanation
Indices: 1367890--1367981 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1367880 AAAATCGCAA
1367890 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1367923 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1367956 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1367982 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:1368269 original size:93 final size:93
Alignment explanation
Indices: 1368172--1368524 Score: 679
Period size: 93 Copynumber: 3.8 Consensus size: 93
1368162 CTTTCAACCA
* *
1368172 AAAGACAAATACTATTTCACAGTGTTATAGAATACACAGTTTAGCATAATTGGCAGCAACCGAAC
1 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1368237 AAATTTACTTTCAACCAAAAGACAAAAC
66 AAATTTACTTTCAACCAAAAGACAAAAC
1368265 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1368330 AAATTTACTTTCAACCAAAAGACAAAAC
66 AAATTTACTTTCAACCAAAAGACAAAAC
1368358 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1368423 AAATTTACTTTCAACCAAAAGACAAAAC
66 AAATTTACTTTCAACCAAAAGACAAAAC
*
1368451 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
1 AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1368516 AAATTTACT
66 AAATTTACT
1368525 AAGCAATCTA
Statistics
Matches: 257, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 257 1.00
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (93 bp):
AAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
AAATTTACTTTCAACCAAAAGACAAAAC
Found at i:1368353 original size:175 final size:179
Alignment explanation
Indices: 1368062--1368524 Score: 808
Period size: 186 Copynumber: 2.6 Consensus size: 179
1368052 TTGAATGGAT
1368062 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1368127 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAA-C-C-A-AAAGACAAATACTATT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCACAACAAAGACAAATACTATT
* *
1368188 TCACAGTGTTATAGAATACACAGTTTAGCATAATTGGCAGCAACCGAAC
131 TCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1368237 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1368302 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACC-----AC--AACAAAGACAAA
1368367 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
124 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1368423 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
1368488 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1368525 AAGCAATCTA
Statistics
Matches: 274, Mismatches: 3, Indels: 11
0.95 0.01 0.04
Matches are distributed among these distances:
175 107 0.39
176 1 0.00
182 1 0.00
185 1 0.00
186 164 0.60
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.23
Consensus pattern (179 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCACAACAAAGACAAATACTATT
TCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1370250 original size:14 final size:14
Alignment explanation
Indices: 1370231--1370306 Score: 53
Period size: 14 Copynumber: 4.7 Consensus size: 14
1370221 TTGAAATGAA
1370231 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1370245 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
*
1370262 ACAATCGCAACGCGAAATGAA
1 --AATCGCAA--CG--A-GAG
1370283 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1370297 AATCGCAACG
1 AATCGCAACG
1370307 CGAAATGAAA
Statistics
Matches: 52, Mismatches: 2, Indels: 16
0.74 0.03 0.23
Matches are distributed among these distances:
14 20 0.38
15 1 0.02
16 5 0.10
17 3 0.06
19 20 0.38
21 1 0.02
22 2 0.04
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1370269 original size:19 final size:19
Alignment explanation
Indices: 1370245--1370328 Score: 97
Period size: 19 Copynumber: 4.7 Consensus size: 19
1370235 GCAACGAGAG
* *
1370245 AATCGCAACGCGAGATGAC
1 AATCGCAACGCGAAATGAA
1370264 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1370283 AATCGCAA--CG--A-GAG
1 AATCGCAACGCGAAATGAA
1370297 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATGAA
*
1370316 AATCGCAATGCGA
1 AATCGCAACGCGA
1370329 TTTTGGTTTC
Statistics
Matches: 55, Mismatches: 5, Indels: 10
0.79 0.07 0.14
Matches are distributed among these distances:
14 10 0.18
15 1 0.02
16 2 0.04
17 2 0.04
18 1 0.02
19 39 0.71
ACGTcount: A:0.43, C:0.23, G:0.24, T:0.11
Consensus pattern (19 bp):
AATCGCAACGCGAAATGAA
Found at i:1370285 original size:52 final size:52
Alignment explanation
Indices: 1370223--1370328 Score: 185
Period size: 52 Copynumber: 2.0 Consensus size: 52
1370213 TCTTTTGGTT
* *
1370223 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAGATGACAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
*
1370275 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
1370327 GA
1 GA
1370329 TTTTGGTTTC
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.44, C:0.21, G:0.25, T:0.10
Consensus pattern (52 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGCGAAATGAAAATCGCAACGC
Found at i:1370359 original size:14 final size:14
Alignment explanation
Indices: 1370340--1370393 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
1370330 TTTGGTTTCG
1370340 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1370354 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
1370373 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1370387 CGTTGCG
1 CGTTGCG
1370394 CTTTTCATTT
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
16 3 0.09
17 3 0.09
19 10 0.30
ACGTcount: A:0.07, C:0.26, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1370372 original size:33 final size:33
Alignment explanation
Indices: 1370324--1370404 Score: 135
Period size: 33 Copynumber: 2.5 Consensus size: 33
1370314 AAAATCGCAA
**
1370324 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1370357 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
*
1370390 TGCGCTTTTCATTTC
1 TGCGATTTTCATTTC
1370405 TCTCGTTGCG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.07, C:0.23, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:1370440 original size:41 final size:41
Alignment explanation
Indices: 1370380--1370457 Score: 138
Period size: 41 Copynumber: 1.9 Consensus size: 41
1370370 TCGCGTTGCG
* *
1370380 ATTCTCTCGTTGCGCTTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
1370421 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1370458 TCTTCTGCAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 35 1.00
ACGTcount: A:0.12, C:0.27, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:1370456 original size:21 final size:21
Alignment explanation
Indices: 1370381--1370456 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
1370371 CGCGTTGCGA
*
1370381 TTCTCTCGTTGCGCTTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
1370402 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
1370422 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
1370443 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
1370457 CTCTTCTGCA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 17 0.37
21 29 0.63
ACGTcount: A:0.11, C:0.26, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:1370583 original size:33 final size:33
Alignment explanation
Indices: 1370536--1370606 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
1370526 AATACTAACT
* *
1370536 TGAAAATCGGAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1370569 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1370602 TGAAA
1 TGAAA
1370607 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:1370840 original size:22 final size:22
Alignment explanation
Indices: 1370788--1370842 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1370778 TGGTTGTGAG
**
1370788 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1370810 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1370832 GGATTTCTTCG
1 GGATTTCTTCG
1370843 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:1371013 original size:20 final size:20
Alignment explanation
Indices: 1370988--1371181 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1370978 CTTTAAATAT
1370988 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1371008 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1371030 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1371049 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1371069 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1371089 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1371109 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1371129 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1371149 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1371169 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1371182 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:1371175 original size:60 final size:60
Alignment explanation
Indices: 1370988--1371181 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1370978 CTTTAAATAT
**
1370988 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1371049 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1371109 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1371169 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1371182 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:1371198 original size:21 final size:21
Alignment explanation
Indices: 1371168--1371250 Score: 69
Period size: 21 Copynumber: 4.0 Consensus size: 21
1371158 ATTTTCATAT
*
1371168 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
1371189 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
* *
1371210 TCGTATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
1371231 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
1371251 CTGATTTGCG
Statistics
Matches: 45, Mismatches: 15, Indels: 4
0.70 0.23 0.06
Matches are distributed among these distances:
20 1 0.02
21 42 0.93
22 2 0.04
ACGTcount: A:0.25, C:0.16, G:0.24, T:0.35
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:1375365 original size:2 final size:2
Alignment explanation
Indices: 1375358--1375459 Score: 204
Period size: 2 Copynumber: 51.0 Consensus size: 2
1375348 AAGAGAAAAG
1375358 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
1375400 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
1375442 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
1375460 TGTAGAAAAC
Statistics
Matches: 100, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 100 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1375624 original size:10 final size:10
Alignment explanation
Indices: 1375609--1375638 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
1375599 AGACCTTTAA
1375609 ATTTTGATTT
1 ATTTTGATTT
1375619 ATTTTGATTT
1 ATTTTGATTT
*
1375629 CTTTTGATTT
1 ATTTTGATTT
1375639 TGCCCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.03, G:0.10, T:0.70
Consensus pattern (10 bp):
ATTTTGATTT
Found at i:1379437 original size:3 final size:3
Alignment explanation
Indices: 1379429--1379462 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
1379419 ATGTAAATTA
* *
1379429 AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1379463 TACAAAAAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:1379771 original size:43 final size:43
Alignment explanation
Indices: 1379710--1380041 Score: 243
Period size: 43 Copynumber: 7.7 Consensus size: 43
1379700 AAAGGTGATA
* * * *
1379710 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCATACGTGATGAAGA-GATCTGGTTATCTATGGTTG
* ** *
1379753 ACACGGCTCCTACGTGATGAAGAGATCTGG---TC-GGGGAATG
1 ACACGGCTCATACGTGATGAAGAGATCTGGTTATCTATGG-TTG
* ** * *
1379793 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGATCTGGTTATCT-ATGGT--TG
* * * *
1379839 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCATACGTGATGAAGA-GATCTGGTTATCTATGGTTG
** *
1379882 ACACGGCTCATACGTGATGAAGAGATCTGG---TCTGGGGATG
1 ACACGGCTCATACGTGATGAAGAGATCTGGTTATCTATGGTTG
* ** * *
1379922 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGATCTGGTTATCT-ATGGT--TG
* * * *
1379968 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTATGGTTG
1 ACACGGCTCATACGTGATGAAGA-GATCTGGTTATCTATGGTTG
1380011 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCATACGTGATGAAGAGATCTGGT
1380042 CTGGGGATGA
Statistics
Matches: 226, Mismatches: 44, Indels: 38
0.73 0.14 0.12
Matches are distributed among these distances:
39 2 0.01
40 68 0.30
42 3 0.01
43 81 0.36
44 2 0.01
45 10 0.04
46 58 0.26
47 2 0.01
ACGTcount: A:0.24, C:0.19, G:0.31, T:0.26
Consensus pattern (43 bp):
ACACGGCTCATACGTGATGAAGAGATCTGGTTATCTATGGTTG
Found at i:1379807 original size:40 final size:41
Alignment explanation
Indices: 1379751--1380070 Score: 197
Period size: 40 Copynumber: 7.5 Consensus size: 41
1379741 TATCTATGGT
*
1379751 TGACACGGCTCCTACGTGATGAAGAGATCTGG-TC-GGGGAA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGG-A
* *
1379791 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * * * *
1379837 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA-TGGT
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-AGGGGA
*
1379880 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGGA
* *
1379920 TGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGG--ATC---AGGGGA
* * * * * * *
1379966 TAACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCTA-TGGT
1 TGACACGGCTCATACGTGATGAAGA-GATCTGG--ATC-AGGGGA
*
1380009 TGACACGGCTCATACGTGATGAAGAGATCTGG-TCTGGGGA
1 TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGGA
* * *
1380049 TGACACGGTTCCTACATGATGA
1 TGACACGGCTCATACGTGATGA
1380071 GGACGACTGG
Statistics
Matches: 214, Mismatches: 47, Indels: 38
0.72 0.16 0.13
Matches are distributed among these distances:
40 88 0.41
42 2 0.01
43 56 0.26
44 2 0.01
46 61 0.29
47 5 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (41 bp):
TGACACGGCTCATACGTGATGAAGAGATCTGGATCAGGGGA
Found at i:1379875 original size:46 final size:46
Alignment explanation
Indices: 1379793--1380041 Score: 184
Period size: 46 Copynumber: 5.7 Consensus size: 46
1379783 TCGGGGAATG
** **
1379793 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAAGGTGATA
* * * * *
1379839 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAAAGGTGATA
* * *
1379882 ACACGGCTCATACGTGATGAAGAGATCTGG---TCT---GGGGATG
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAAGGTGATA
** **
1379922 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTAAAGGTGATA
1 ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAAGGTGATA
* * * * *
1379968 ACACGGTTCCTACGTGATGAGGACG-GCTGGTTATCT-ATGGT--TG
1 ACACGGCTCATACGTGATGAAGA-GAGCTGGTTATCTAAAGGTGATA
*
1380011 ACACGGCTCATACGTGATGAAGAGATCTGGT
1 ACACGGCTCATACGTGATGAAGAGAGCTGGT
1380042 CTGGGGATGA
Statistics
Matches: 163, Mismatches: 28, Indels: 27
0.75 0.13 0.12
Matches are distributed among these distances:
38 2 0.01
40 34 0.21
42 2 0.01
43 54 0.33
45 8 0.05
46 61 0.37
47 2 0.01
ACGTcount: A:0.25, C:0.19, G:0.30, T:0.26
Consensus pattern (46 bp):
ACACGGCTCATACGTGATGAAGAGAGCTGGTTATCTAAAGGTGATA
Found at i:1380086 original size:129 final size:129
Alignment explanation
Indices: 1379700--1380070 Score: 690
Period size: 129 Copynumber: 2.9 Consensus size: 129
1379690 TGGTCAGGAG
*
1379700 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCCTA
1 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATA
1379765 CGTGATGAAGAGATCTGGTC-GGGGAATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
66 CGTGATGAAGAGATCTGGTCTGGGG-ATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
1379829 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATA
1 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATA
1379894 CGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
66 CGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
1379958 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATA
1 AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATA
* * *
1380023 CGTGATGAAGAGATCTGGTCTGGGGATGACACGGTTCCTACATGATGA
66 CGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGA
1380071 GGACGACTGG
Statistics
Matches: 237, Mismatches: 4, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
129 233 0.98
130 4 0.02
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (129 bp):
AAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTGACACGGCTCATA
CGTGATGAAGAGATCTGGTCTGGGGATGACACGGCTCATACGTGATGAAGAGTTCTGGCCATCT
Found at i:1380512 original size:15 final size:15
Alignment explanation
Indices: 1380488--1380531 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
1380478 AAGATGATCT
*
1380488 TGTTTTAAGAGAAAA
1 TGTTTCAAGAGAAAA
1380503 TGTTTCAAGAGAAAA
1 TGTTTCAAGAGAAAA
*
1380518 TGTTTCAAGTGAAA
1 TGTTTCAAGAGAAA
1380532 CGACTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 27 1.00
ACGTcount: A:0.43, C:0.05, G:0.20, T:0.32
Consensus pattern (15 bp):
TGTTTCAAGAGAAAA
Found at i:1380790 original size:64 final size:64
Alignment explanation
Indices: 1380688--1381010 Score: 434
Period size: 64 Copynumber: 5.0 Consensus size: 64
1380678 AAGGTTGGTA
* ** * * *
1380688 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
* *
1380751 TTTTCAAAAGAAATGGTCTTTAATAGATAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
*
1380814 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGA-TTT
* * * ** * * *
1380879 TGTTTTAAAAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCCAAAGAAACAAACTCAAAGATT
1 T-TTTCAAAAGAAATTGTCTTTA-ATAGATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATT
1380944 T
64 T
* *
1380945 TTTTCAAGAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
1381009 TT
1 TT
1381011 GTTTTAAAAG
Statistics
Matches: 227, Mismatches: 28, Indels: 9
0.86 0.11 0.03
Matches are distributed among these distances:
63 76 0.33
64 78 0.34
65 18 0.08
66 20 0.09
67 35 0.15
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (64 bp):
TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTT
Found at i:1380793 original size:36 final size:34
Alignment explanation
Indices: 1380747--1380862 Score: 97
Period size: 36 Copynumber: 3.5 Consensus size: 34
1380737 AAACTCAAAG
1380747 ATTTTTTTCAAAAGAAATGGTCTTTAATAGATAAA
1 ATTTTTTTCAAAAGAAAT-GTCTTTAATAGATAAA
* *
1380782 ATTTTGTTTCAAAGGAAA---C---AA-A-CTCAAA
1 ATTTT-TTTCAAAAGAAATGTCTTTAATAGAT-AAA
1380810 GA-TTTTTTCAAAAGAAATTGTCTTTAATAGATAAA
1 -ATTTTTTTCAAAAGAAA-TGTCTTTAATAGATAAA
1380845 ATTTTGTTTCAAAAGAAA
1 ATTTT-TTTCAAAAGAAA
1380863 CATACTCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 27
0.67 0.04 0.29
Matches are distributed among these distances:
27 12 0.19
28 7 0.11
29 3 0.05
31 1 0.02
32 1 0.02
34 3 0.05
35 12 0.19
36 24 0.38
ACGTcount: A:0.44, C:0.08, G:0.11, T:0.37
Consensus pattern (34 bp):
ATTTTTTTCAAAAGAAATGTCTTTAATAGATAAA
Found at i:1380903 original size:29 final size:30
Alignment explanation
Indices: 1380846--1381098 Score: 171
Period size: 30 Copynumber: 8.1 Consensus size: 30
1380836 ATAGATAAAA
1380846 TTTTGTTTCAAAAGAAACATACTCAAAGAT
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
* *
1380876 TTTTGTTTTAAAAGAAAC-TATCTCAAGAGAGACAAAA
1 TTTTGTTTCAAAAGAAACATA-CTC-A-A-AG----AT
* *
1380913 TTTTGTTTCCAAAGAAACAAACTCAAAGA-
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
* * * *
1380942 TTTT-TTTCAAGAGAAA-TTGTCTTTAATAGAT
1 TTTTGTTTCAAAAGAAACAT-AC-TCAA-AGAT
1380973 AAAATTTTGTTTCAAAAGAAACATACTCAAAGAT
1 ----TTTTGTTTCAAAAGAAACATACTCAAAGAT
*
1381007 TTTTGTTTTAAAAGAAAC-TATCTCAAAGAT
1 TTTTGTTTCAAAAGAAACATA-CTCAAAGAT
* * *
1381037 TTTT-TTTTAAAAGGAACAAACTCAAAGAT
1 TTTTGTTTCAAAAGAAACATACTCAAAGAT
* *
1381066 TTTTATTT-AAAAGGAACCA-ACTCAAAGAT
1 TTTTGTTTCAAAA-GAAACATACTCAAAGAT
1381095 TTTT
1 TTTT
1381099 TAAGAGAAAT
Statistics
Matches: 180, Mismatches: 20, Indels: 47
0.73 0.08 0.19
Matches are distributed among these distances:
28 11 0.06
29 54 0.30
30 62 0.34
31 1 0.01
32 1 0.01
33 2 0.01
34 6 0.03
35 8 0.04
36 13 0.07
37 21 0.12
38 1 0.01
ACGTcount: A:0.43, C:0.11, G:0.11, T:0.35
Consensus pattern (30 bp):
TTTTGTTTCAAAAGAAACATACTCAAAGAT
Found at i:1380974 original size:131 final size:129
Alignment explanation
Indices: 1380688--1381035 Score: 499
Period size: 131 Copynumber: 2.7 Consensus size: 129
1380678 AAGGTTGGTA
* ** * * * *
1380688 TTTTCAAAAGAAGTTGTC-TCGAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGA-TTT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
* * ** * *
1380751 T-TTTCAAAAGAAA-TGGTCTTTAATAGATAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
66 TGTTTTAAAAGAAACT-ATCTCAAAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
1380814 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
1380879 TGTTTTAAAAGAAACTATCTCAAGAGAGACAAAATTTTGTTTCCAAA-GAAACAAACTCAAAGAT
66 TGTTTTAAAAGAAACTATCTCAA-AGAGACAAAATTTTGTTT-CAAAGGAAACAAACTCAAAGA-
1380943 TT
128 TT
*
1380945 TTTTCAAGAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
1 TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
1381010 TGTTTTAAAAGAAACTATCTCAAAGA
66 TGTTTTAAAAGAAACTATCTCAAAGA
1381036 TTTTTTTTTA
Statistics
Matches: 201, Mismatches: 14, Indels: 10
0.89 0.06 0.04
Matches are distributed among these distances:
126 17 0.08
127 36 0.18
128 4 0.02
129 15 0.07
130 36 0.18
131 93 0.46
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (129 bp):
TTTTCAAAAGAAATTGTCTTTAATAGATAAAATTTTGTTTCAAAAGAAACATACTCAAAGATTTT
TGTTTTAAAAGAAACTATCTCAAAGAGACAAAATTTTGTTTCAAAGGAAACAAACTCAAAGATT
Found at i:1381060 original size:59 final size:58
Alignment explanation
Indices: 1380976--1381099 Score: 167
Period size: 59 Copynumber: 2.1 Consensus size: 58
1380966 AATAGATAAA
* * * * *
1380976 ATTTTGTTTCAAAAGAAACATACTCAAAGATTTTTGTTTTAAAAGAAACTATCTCAAAG
1 ATTTTTTTTCAAAAGAAACAAACTCAAAGATTTTT-ATTTAAAAGAAACCAACTCAAAG
* * *
1381035 ATTTTTTTTTAAAAGGAACAAACTCAAAGATTTTTATTTAAAAGGAACCAACTCAAAG
1 ATTTTTTTTCAAAAGAAACAAACTCAAAGATTTTTATTTAAAAGAAACCAACTCAAAG
1381093 ATTTTTT
1 ATTTTTT
1381100 AAGAGAAATT
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
58 26 0.46
59 31 0.54
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.37
Consensus pattern (58 bp):
ATTTTTTTTCAAAAGAAACAAACTCAAAGATTTTTATTTAAAAGAAACCAACTCAAAG
Found at i:1381772 original size:4 final size:4
Alignment explanation
Indices: 1381756--1381805 Score: 70
Period size: 4 Copynumber: 13.2 Consensus size: 4
1381746 ATACAAATTT
*
1381756 TATG TAT- TATG TATG TATG --TG TATT TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1381801 TATG T
1 TATG T
1381806 TTTCTCGATC
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 3 0.07
4 36 0.88
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (4 bp):
TATG
Found at i:1389725 original size:3 final size:3
Alignment explanation
Indices: 1389717--1389753 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
1389707 ATGTAAATTA
* *
1389717 AAT AAT AAT AAT AAT AAT AAT AAT AAC GAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1389754 TACAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:1393296 original size:22 final size:21
Alignment explanation
Indices: 1393271--1393313 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
1393261 TAGTTTGGTT
1393271 TTAAAAAATAAACATATAAATA
1 TTAAAAAATAAACATA-AAATA
* **
1393293 TTAAGATTTAAACATAAAATA
1 TTAAAAAATAAACATAAAATA
1393314 ATACCAAGTG
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.63, C:0.05, G:0.02, T:0.30
Consensus pattern (21 bp):
TTAAAAAATAAACATAAAATA
Found at i:1393656 original size:41 final size:41
Alignment explanation
Indices: 1393566--1393742 Score: 105
Period size: 40 Copynumber: 4.3 Consensus size: 41
1393556 AATTTGACAT
* * **
1393566 TTAGCGGCGTTTTTACAAAAAAACGCCGCAATAGGGTGGTTTA
1 TTAGCGGCGTTTTT--AAAAAAACGCAGCAATAGAGTGGTAAA
*
1393609 TT-GCGGCGTTTGTT-AAAAAATGCAGCAATAGAGTGGTAAA
1 TTAGCGGCGTTT-TTAAAAAAACGCAGCAATAGAGTGGTAAA
* * * * * *
1393649 TTAGCGGCGTTTATACCACAAACGCCGTAATA-A-T-TTAACA
1 TTAGCGGCGTTTTTA-AAAAAACGCAGCAATAGAGTGGTAA-A
* ** * *
1393689 TATAGTGGCG-TTTTAGCTAAAACGCCGCAATAGATTGGTAAA
1 T-TAGCGGCGTTTTTA-AAAAAACGCAGCAATAGAGTGGTAAA
1393731 TTAGCGGCGTTT
1 TTAGCGGCGTTT
1393743 ATACCATAAA
Statistics
Matches: 104, Mismatches: 20, Indels: 21
0.72 0.14 0.14
Matches are distributed among these distances:
39 3 0.03
40 44 0.42
41 25 0.24
42 25 0.24
43 7 0.07
ACGTcount: A:0.32, C:0.16, G:0.24, T:0.29
Consensus pattern (41 bp):
TTAGCGGCGTTTTTAAAAAAACGCAGCAATAGAGTGGTAAA
Found at i:1393699 original size:82 final size:82
Alignment explanation
Indices: 1393624--1393780 Score: 219
Period size: 82 Copynumber: 1.9 Consensus size: 82
1393614 GCGTTTGTTA
* * *
1393624 AAAAATGCAGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGTAATA-ATTTA-A
1 AAAAACGCAGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAAAGCCATAATAGA-TTACA
1393687 CATATAGTGGCGTTTTAGC
65 CATATAGTGGCGTTTTA-C
* * * *
1393706 TAAAACGCCGCAATAGATTGGTAAATTAGCGGCGTTTATACCATAAAAGCCATAATAGATTACAC
1 AAAAACGCAGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAAAGCCATAATAGATTACAC
1393771 ATATAGTGGC
66 ATATAGTGGC
1393781 ATTTATTCTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
82 53 0.80
83 13 0.20
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.26
Consensus pattern (82 bp):
AAAAACGCAGCAATAGAGTGGTAAATTAGCGGCGTTTATACCACAAAAGCCATAATAGATTACAC
ATATAGTGGCGTTTTAC
Found at i:1393714 original size:40 final size:43
Alignment explanation
Indices: 1393654--1393805 Score: 133
Period size: 42 Copynumber: 3.7 Consensus size: 43
1393644 GTAAATTAGC
*
1393654 GGCGTTTATACCA-CAAACGCCGTAATA-ATTTAACATATAGT
1 GGCGTTTATACCATAAAACGCCGTAATAGATTTAACATATAGT
* * *
1393695 GGCGTTT-TAGC-TAAAACGCCGCAATAGATTGGTAA-AT-TAGC
1 GGCGTTTATACCATAAAACGCCGTAATAGATT--TAACATATAGT
*
1393736 GGCGTTTATACCATAAAA-GCCATAATAGA-TTACACATATAGT
1 GGCGTTTATACCATAAAACGCCGTAATAGATTTA-ACATATAGT
* * * *
1393778 GGCATTTAT-TCTTAAAATGCCGTAATAG
1 GGCGTTTATACCATAAAACGCCGTAATAG
1393806 TGATAATAAA
Statistics
Matches: 89, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
39 2 0.02
40 16 0.18
41 29 0.33
42 34 0.38
43 8 0.09
ACGTcount: A:0.36, C:0.17, G:0.18, T:0.30
Consensus pattern (43 bp):
GGCGTTTATACCATAAAACGCCGTAATAGATTTAACATATAGT
Found at i:1393765 original size:42 final size:42
Alignment explanation
Indices: 1393635--1393766 Score: 139
Period size: 41 Copynumber: 3.2 Consensus size: 42
1393625 AAAATGCAGC
* * *
1393635 AATAGAGTGGTAAATTAGCGGCGTTTATACCACAAACGCCGT
1 AATAGATTGGTAAATTAGCGGCGTTTATACCATAAAAGCCGT
* * *
1393677 AATA-ATT--TAACATATAGTGGCGTTT-TAGC-TAAAACGCCGC
1 AATAGATTGGTAA-AT-TAGCGGCGTTTATACCATAAAA-GCCGT
*
1393717 AATAGATTGGTAAATTAGCGGCGTTTATACCATAAAAGCCAT
1 AATAGATTGGTAAATTAGCGGCGTTTATACCATAAAAGCCGT
1393759 AATAGATT
1 AATAGATT
1393767 ACACATATAG
Statistics
Matches: 72, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
39 6 0.08
40 13 0.18
41 25 0.35
42 20 0.28
43 8 0.11
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.28
Consensus pattern (42 bp):
AATAGATTGGTAAATTAGCGGCGTTTATACCATAAAAGCCGT
Found at i:1393859 original size:41 final size:41
Alignment explanation
Indices: 1393791--1393910 Score: 134
Period size: 41 Copynumber: 2.9 Consensus size: 41
1393781 ATTTATTCTT
* * * * *
1393791 AAAATGCCGTAATAGTGATAATAAATAGTGGCATTTTTA-A
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
*
1393831 ATAAACGCCGCAATAGTGTTAATCAATAGTGGCGCTTTTAGA
1 A-AAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
*** *
1393873 AAAACGTTACAATAGTTTTAATCAATAGTGGCGTTTTT
1 AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTT
1393911 TTTGTATAAA
Statistics
Matches: 67, Mismatches: 11, Indels: 3
0.83 0.14 0.04
Matches are distributed among these distances:
40 1 0.01
41 64 0.96
42 2 0.03
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (41 bp):
AAAACGCCGCAATAGTGTTAATCAATAGTGGCGTTTTTAGA
Found at i:1395484 original size:41 final size:41
Alignment explanation
Indices: 1395200--1395508 Score: 282
Period size: 41 Copynumber: 7.5 Consensus size: 41
1395190 TATAGGTACG
* * *
1395200 TACTTTAGTGGCGTTTTTATACAAACGTCGCTATAGAATCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCA
* * *
1395241 TACATTAGTGGCGTTTTTATACAAACGCCGTTATATACT-A
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCA
* *
1395281 GTACTTTAGTGGCGTTTCTATACAAACGCCGCTATATACTCA
1 -TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCA
* * ** * *
1395323 TACTTTAGTGGTGTTTTGA-ATCTAAACGATGCTATAAACTCG
1 TACTTTAGTGGCGTTTTTATA-C-AAACGCCGCTATAGACTCA
* * * * * *
1395365 TACTTTAGTGGCGTTTTGAATGA-AAATGCCGCTAAATAATCG
1 TACTTTAGTGGCGTTTT-TAT-ACAAACGCCGCTATAGACTCA
** * * *
1395407 TACTTTAGCAGTGTTTTTATATAAACGCCGCTATAGACTTA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCA
* *
1395448 TACTTTAGTGGCGTTTTTATACAAACGCTGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCA
* *
1395489 TACCCTTAGTGGCATTTTTA
1 TA-CTTTAGTGGCGTTTTTA
1395509 AGATAAACAC
Statistics
Matches: 216, Mismatches: 43, Indels: 17
0.78 0.16 0.06
Matches are distributed among these distances:
40 2 0.01
41 138 0.64
42 74 0.34
43 1 0.00
45 1 0.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACTCA
Found at i:1401400 original size:15 final size:15
Alignment explanation
Indices: 1401380--1401419 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
1401370 TGGATCCAGT
*
1401380 TCATCACTGTACATG
1 TCATCACAGTACATG
1401395 TCATCACAGTACATG
1 TCATCACAGTACATG
1401410 TCATCACAGT
1 TCATCACAGT
1401420 CTCAATCTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.12, T:0.30
Consensus pattern (15 bp):
TCATCACAGTACATG
Found at i:1401532 original size:21 final size:21
Alignment explanation
Indices: 1401508--1401566 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
1401498 CGGAAAATGA
1401508 AGCAAGGGAAGCAGAGAGAGC
1 AGCAAGGGAAGCAGAGAGAGC
** *
1401529 AGCAACAGAAGCA-ACCAGAGC
1 AGCAAGGGAAGCAGA-GAGAGC
1401550 AGC-AGCGGAAGCAGAGA
1 AGCAAG-GGAAGCAGAGA
1401567 AAGAAGCAGC
Statistics
Matches: 29, Mismatches: 6, Indels: 6
0.71 0.15 0.15
Matches are distributed among these distances:
20 2 0.07
21 26 0.90
22 1 0.03
ACGTcount: A:0.44, C:0.20, G:0.36, T:0.00
Consensus pattern (21 bp):
AGCAAGGGAAGCAGAGAGAGC
Found at i:1401574 original size:21 final size:21
Alignment explanation
Indices: 1401550--1401597 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
1401540 CAACCAGAGC
*
1401550 AGCAGCGGAAGCAGAGAAAGA
1 AGCAGCGGAAGCACAGAAAGA
* *
1401571 AGCAGCGGCAGCACAGAGAGA
1 AGCAGCGGAAGCACAGAAAGA
1401592 AGCAGC
1 AGCAGC
1401598 ATATCAGCAG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.21, G:0.38, T:0.00
Consensus pattern (21 bp):
AGCAGCGGAAGCACAGAAAGA
Found at i:1402069 original size:43 final size:43
Alignment explanation
Indices: 1402023--1402306 Score: 234
Period size: 43 Copynumber: 6.5 Consensus size: 43
1402013 ATCGCAAAAC
* * *
1402023 ATCAACACCTACTGCAGCGTTTTAACAAAAAACGCCGCTAAAC
1 ATCAACACCTATTGCGGCGTTTTAACAAAAAACGCCGCTAAAT
* ** * * *
1402066 ATCATA-ACATATTGCGGCG-TTTGCCTGAGAAACGCTGCTAAAT
1 ATCA-ACACCTATTGCGGCGTTTTAAC-AAAAAACGCCGCTAAAT
* * ** *
1402109 ATTAACACCTATTGCGGCGTTTTTATGACAAACGCCGCTAAAT
1 ATCAACACCTATTGCGGCGTTTTAACAAAAAACGCCGCTAAAT
* * * *
1402152 ATCAACACCTTTTGCGGCGTTTTTATATAAAAAAAATGCCACTAAAT
1 ATCAACACCTATTGCGGCG--TTT-TA-ACAAAAAACGCCGCTAAAT
** *
1402199 ATCAACACCTATTGCGGCGTTTGT-TGAAAAAA-GACGCTAAAT
1 ATCAACACCTATTGCGGCGTTT-TAACAAAAAACGCCGCTAAAT
* * * * *
1402241 ATCAACACCTATTGCGGCGTTTTTATAACAAACACCACTAAAT
1 ATCAACACCTATTGCGGCGTTTTAACAAAAAACGCCGCTAAAT
*
1402284 ATCAACACCTATTGCGACGTTTT
1 ATCAACACCTATTGCGGCGTTTT
1402307 TCACACAAAC
Statistics
Matches: 194, Mismatches: 37, Indels: 20
0.77 0.15 0.08
Matches are distributed among these distances:
41 1 0.01
42 40 0.21
43 109 0.56
44 4 0.02
45 7 0.04
46 1 0.01
47 32 0.16
ACGTcount: A:0.35, C:0.23, G:0.14, T:0.28
Consensus pattern (43 bp):
ATCAACACCTATTGCGGCGTTTTAACAAAAAACGCCGCTAAAT
Found at i:1402253 original size:132 final size:133
Alignment explanation
Indices: 1402049--1402307 Score: 362
Period size: 132 Copynumber: 2.0 Consensus size: 133
1402039 GCGTTTTAAC
* * * *
1402049 AAAAAACGCCGCTAAACATCATAACATATTGCGGCGTTTGCCTGAGAAACGCTGCTAAATATTAA
1 AAAAAACGCCACTAAACATCATAACATATTGCGGCGTTTGCCTGAAAAAAGCTGCTAAATATCAA
* * * * *
1402114 CACCTATTGCGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTTTTGCGGCGTTTTTATA
66 CACCTATTGCGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTGCGACGTTTTTATA
1402179 TAA
131 TAA
* * * *
1402182 AAAAAATGCCACTAAATATCA-ACACCTATTGCGGCGTTTG-TTGAAAAAAGAC-GCTAAATATC
1 AAAAAACGCCACTAAACATCATA-ACATATTGCGGCGTTTGCCTGAAAAAAG-CTGCTAAATATC
1402244 AACACCTATTGCGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTGCGACGTTTTT
64 AACACCTATTGCGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTGCGACGTTTTT
1402308 CACACAAACG
Statistics
Matches: 111, Mismatches: 13, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
132 76 0.68
133 35 0.32
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (133 bp):
AAAAAACGCCACTAAACATCATAACATATTGCGGCGTTTGCCTGAAAAAAGCTGCTAAATATCAA
CACCTATTGCGGCGTTTTTATAACAAACACCACTAAATATCAACACCTATTGCGACGTTTTTATA
TAA
Found at i:1402260 original size:89 final size:86
Alignment explanation
Indices: 1402103--1402305 Score: 282
Period size: 89 Copynumber: 2.3 Consensus size: 86
1402093 AGAAACGCTG
* * * * * *
1402103 CTAAATATTAACACCTATTGCGGCGTTTTTATGACAAACGCCGCTAAATATCAACACCTTTTGCG
1 CTAAATATCAACACCTATTGCGGCGTTTGTATGAAAAAAGACGCTAAATATCAACACCTATTGCG
1402168 GCGTTTTTATATAAAAAAAATGCCA
66 GCG-TTTT-TATAAAAAAAA--CCA
1402193 CTAAATATCAACACCTATTGCGGCGTTTGT-TGAAAAAAGACGCTAAATATCAACACCTATTGCG
1 CTAAATATCAACACCTATTGCGGCGTTTGTATGAAAAAAGACGCTAAATATCAACACCTATTGCG
* *
1402257 GCGTTTTTATAACAAACACCA
66 GCGTTTTTATAAAAAAAACCA
*
1402278 CTAAATATCAACACCTATTGCGACGTTT
1 CTAAATATCAACACCTATTGCGGCGTTT
1402306 TTCACACAAA
Statistics
Matches: 104, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
85 30 0.29
87 9 0.09
88 4 0.04
89 33 0.32
90 28 0.27
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (86 bp):
CTAAATATCAACACCTATTGCGGCGTTTGTATGAAAAAAGACGCTAAATATCAACACCTATTGCG
GCGTTTTTATAAAAAAAACCA
Found at i:1402316 original size:43 final size:43
Alignment explanation
Indices: 1402103--1402307 Score: 245
Period size: 43 Copynumber: 4.7 Consensus size: 43
1402093 AGAAACGCTG
* * * *
1402103 CTAAATATTAACACCTATTGCGGCGTTTTTATGACAAACGCCG
1 CTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCA
* * *
1402146 CTAAATATCAACACCTTTTGCGGCGTTTTTATATAAAAAAAATGCCA
1 CTAAATATCAACACCTATTGCGGCG-TTTT-TATAACAAACA--CCA
* *
1402193 CTAAATATCAACACCTATTGCGGCGTTTGTTGA-AA-AAAGA-CG
1 CTAAATATCAACACCTATTGCGGCGTTT-TT-ATAACAAACACCA
1402235 CTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCA
1 CTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCA
*
1402278 CTAAATATCAACACCTATTGCGACGTTTTT
1 CTAAATATCAACACCTATTGCGGCGTTTTT
1402308 CACACAAACG
Statistics
Matches: 140, Mismatches: 13, Indels: 18
0.82 0.08 0.11
Matches are distributed among these distances:
40 1 0.01
41 4 0.03
42 33 0.24
43 53 0.38
44 4 0.03
45 11 0.08
46 6 0.04
47 28 0.20
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (43 bp):
CTAAATATCAACACCTATTGCGGCGTTTTTATAACAAACACCA
Found at i:1412872 original size:2 final size:2
Alignment explanation
Indices: 1412865--1412889 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1412855 TTTCATTTTG
1412865 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1412890 ACAAAAAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1430250 original size:74 final size:74
Alignment explanation
Indices: 1430166--1430313 Score: 296
Period size: 74 Copynumber: 2.0 Consensus size: 74
1430156 TTCCATTCTT
1430166 TTTTTGATCTTGTAATTAAATTCTATGATTTGATTTGCTCATGTAACTACTGTTCCTTCAGGTTT
1 TTTTTGATCTTGTAATTAAATTCTATGATTTGATTTGCTCATGTAACTACTGTTCCTTCAGGTTT
1430231 TAACTACGG
66 TAACTACGG
1430240 TTTTTGATCTTGTAATTAAATTCTATGATTTGATTTGCTCATGTAACTACTGTTCCTTCAGGTTT
1 TTTTTGATCTTGTAATTAAATTCTATGATTTGATTTGCTCATGTAACTACTGTTCCTTCAGGTTT
1430305 TAACTACGG
66 TAACTACGG
1430314 AAGGGTTTGA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
74 74 1.00
ACGTcount: A:0.23, C:0.15, G:0.15, T:0.47
Consensus pattern (74 bp):
TTTTTGATCTTGTAATTAAATTCTATGATTTGATTTGCTCATGTAACTACTGTTCCTTCAGGTTT
TAACTACGG
Found at i:1436210 original size:30 final size:26
Alignment explanation
Indices: 1436145--1436207 Score: 117
Period size: 26 Copynumber: 2.4 Consensus size: 26
1436135 TTTGTGTTTT
1436145 TTTATTTATTTTTGAATGCATTCATA
1 TTTATTTATTTTTGAATGCATTCATA
*
1436171 TTTATTTATTTTTGAATGTATTCATA
1 TTTATTTATTTTTGAATGCATTCATA
1436197 TTTATTTATTT
1 TTTATTTATTT
1436208 ATTGTTCGCC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 36 1.00
ACGTcount: A:0.25, C:0.05, G:0.06, T:0.63
Consensus pattern (26 bp):
TTTATTTATTTTTGAATGCATTCATA
Found at i:1436470 original size:12 final size:12
Alignment explanation
Indices: 1436455--1436490 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
1436445 AAATATGTTG
*
1436455 ATAAATGAGTTT
1 ATAAACGAGTTT
*
1436467 ATAAACGAATTT
1 ATAAACGAGTTT
1436479 ATAAACGAGTTT
1 ATAAACGAGTTT
1436491 GTTTATGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.36
Consensus pattern (12 bp):
ATAAACGAGTTT
Found at i:1436999 original size:193 final size:193
Alignment explanation
Indices: 1436670--1437056 Score: 774
Period size: 193 Copynumber: 2.0 Consensus size: 193
1436660 CTTTATTTAA
1436670 AATTAAATTATAACTTTGTTCTATGACTTGAGGACTTTTTCTATAATTAATCCAATAAAAGGTAA
1 AATTAAATTATAACTTTGTTCTATGACTTGAGGACTTTTTCTATAATTAATCCAATAAAAGGTAA
1436735 AGGTCAAAAATAGACACCTGACACTGAAATTGAACCCATGCCAGCAAGAGAGTCTACTCGGGAAC
66 AGGTCAAAAATAGACACCTGACACTGAAATTGAACCCATGCCAGCAAGAGAGTCTACTCGGGAAC
1436800 TTTTGTCTGTCACTTAAAATGTGAAATAAAAAATAATAAAAAGGAAAAAGGAAATGGAATTTG
131 TTTTGTCTGTCACTTAAAATGTGAAATAAAAAATAATAAAAAGGAAAAAGGAAATGGAATTTG
1436863 AATTAAATTATAACTTTGTTCTATGACTTGAGGACTTTTTCTATAATTAATCCAATAAAAGGTAA
1 AATTAAATTATAACTTTGTTCTATGACTTGAGGACTTTTTCTATAATTAATCCAATAAAAGGTAA
1436928 AGGTCAAAAATAGACACCTGACACTGAAATTGAACCCATGCCAGCAAGAGAGTCTACTCGGGAAC
66 AGGTCAAAAATAGACACCTGACACTGAAATTGAACCCATGCCAGCAAGAGAGTCTACTCGGGAAC
1436993 TTTTGTCTGTCACTTAAAATGTGAAATAAAAAATAATAAAAAGGAAAAAGGAAATGGAATTTG
131 TTTTGTCTGTCACTTAAAATGTGAAATAAAAAATAATAAAAAGGAAAAAGGAAATGGAATTTG
1437056 A
1 A
1437057 CAGTTGCCTT
Statistics
Matches: 194, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
193 194 1.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.28
Consensus pattern (193 bp):
AATTAAATTATAACTTTGTTCTATGACTTGAGGACTTTTTCTATAATTAATCCAATAAAAGGTAA
AGGTCAAAAATAGACACCTGACACTGAAATTGAACCCATGCCAGCAAGAGAGTCTACTCGGGAAC
TTTTGTCTGTCACTTAAAATGTGAAATAAAAAATAATAAAAAGGAAAAAGGAAATGGAATTTG
Found at i:1437444 original size:41 final size:42
Alignment explanation
Indices: 1437109--1437432 Score: 532
Period size: 41 Copynumber: 7.8 Consensus size: 42
1437099 CAGTGACCAA
* *
1437109 CTATCACAACGAATTTGGAATGAATCGCAACGCGAACTTCAC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
1437151 CTATCTCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* **
1437193 CTGTCGCAACGAA-TTGGAATGAATCGCAATACGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1437234 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
*
1437275 CTATCGCAACGAA-TTGGAATGAATCGCAACGTGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
* *
1437316 CTATCGCAACG-ATTTGGAATAAATCGCAACGCGAACTTCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1437357 CTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGC
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
1437398 CTATCGCAACGAATTTGGAATGAATCGCAACGCGA
1 CTATCGCAACGAATTTGGAATGAATCGCAACGCGA
1437433 TCTCCGGTAT
Statistics
Matches: 263, Mismatches: 15, Indels: 8
0.92 0.05 0.03
Matches are distributed among these distances:
40 2 0.01
41 186 0.71
42 75 0.29
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.22
Consensus pattern (42 bp):
CTATCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGC
Found at i:1437487 original size:123 final size:121
Alignment explanation
Indices: 1437108--1437472 Score: 448
Period size: 123 Copynumber: 3.0 Consensus size: 121
1437098 TCAGTGACCA
* * *
1437108 ACTATCACAACGAATTTGGAATGAATCGCAACGCGAACTTCACCTATCTCAACGAATTTGGAATG
1 ACTATCGCAACG-ATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATG
* * ** * **
1437173 AATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATCGCAATACGAACTTCG
65 AATCGCAACGCGAACTTCGCCTATCGCAAC-AGTT-TTA-GATTCGCAACGCGAACTTCG
*
1437233 CCTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAA-TTGGAATGA
1 ACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
* * *
1437297 ATCGCAACGTGAACTTCGCCTATCGCAAC-GATTTGGAATAAATCGCAACGCGAACTTCG
66 ATCGCAACGCGAACTTCGCCTATCGCAACAGTTTTAG-AT---TCGCAACGCGAACTTCG
1437356 ACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
1 ACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
* * * *
1437421 ATCGCAACGCGATCTCCG-GTATCGTAAATCAGTTTTCAGATTCGCAACGCGA
66 ATCGCAACGCGAACTTCGCCTATCG-CAA-CAGTTTT-AGATTCGCAACGCGA
1437473 TAGTCGAAGT
Statistics
Matches: 209, Mismatches: 22, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
119 1 0.00
120 1 0.00
121 1 0.00
123 121 0.58
124 67 0.32
125 11 0.05
126 6 0.03
127 1 0.00
ACGTcount: A:0.32, C:0.25, G:0.21, T:0.23
Consensus pattern (121 bp):
ACTATCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCAACGAATTTGGAATGA
ATCGCAACGCGAACTTCGCCTATCGCAACAGTTTTAGATTCGCAACGCGAACTTCG
Found at i:1437515 original size:21 final size:21
Alignment explanation
Indices: 1437491--1437597 Score: 64
Period size: 21 Copynumber: 5.2 Consensus size: 21
1437481 GTTCGCATTA
1437491 CGATTTATTCCAAATTCGTTG
1 CGATTTATTCCAAATTCGTTG
** * *
1437512 CGA--TAGGCGAAGTTCGCGTTG
1 CGATTTATTCCAAATT--CGTTG
*
1437533 CGATTCATTCCAAA-TCGTTG
1 CGATTTATTCCAAATTCGTTG
* * *
1437553 CGA--TAGTCGAAGTTCGCGTTG
1 CGATTTATTCCAAATT--CGTTG
1437574 CGATTTATTCC-AATTCGTTG
1 CGATTTATTCCAAATTCGTTG
1437594 CGAT
1 CGAT
1437598 AGGCGAAGTT
Statistics
Matches: 61, Mismatches: 16, Indels: 19
0.64 0.17 0.20
Matches are distributed among these distances:
18 5 0.08
19 8 0.13
20 17 0.28
21 19 0.31
22 4 0.07
23 8 0.13
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (21 bp):
CGATTTATTCCAAATTCGTTG
Found at i:1437564 original size:41 final size:41
Alignment explanation
Indices: 1437469--1437806 Score: 514
Period size: 41 Copynumber: 8.2 Consensus size: 41
1437459 GATTCGCAAC
* * * *
1437469 GCGATAGTCGAAGTTCGCATTACGATTTATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
1437511 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* * *
1437552 GCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
* *
1437593 GCGATAGGCGAAGTTCACGTTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1437634 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
** *
1437675 GCGATAGGCGAAGTTCGTATTGCGATTCATTCCAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
*
1437716 GCGACAGGCGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
*
1437758 GCGATAGGTGAAGTTCGCGTTGCGATTCATTCCAAATTCGTT
1 GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTT
*
1437800 GTGATAG
1 GCGATAG
1437807 TCCAAATATT
Statistics
Matches: 273, Mismatches: 22, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
41 190 0.70
42 83 0.30
ACGTcount: A:0.22, C:0.20, G:0.25, T:0.32
Consensus pattern (41 bp):
GCGATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTT
Found at i:1437594 original size:20 final size:20
Alignment explanation
Indices: 1437528--1437638 Score: 68
Period size: 20 Copynumber: 5.5 Consensus size: 20
1437518 GCGAAGTTCG
* *
1437528 CGTTGCGATTCATTCCAAAT
1 CGTTGCGATTTATTCCAATT
* *
1437548 CGTTGCGA--TAGTCGAAGTT
1 CGTTGCGATTTATTCCAA-TT
1437567 CGCGTTGCGATTTATTCCAATT
1 --CGTTGCGATTTATTCCAATT
** *
1437589 CGTTGCGA--TAGGCGAAGTT
1 CGTTGCGATTTATTCCAA-TT
*
1437608 CACGTTGCGATTCATTCCAATT
1 --CGTTGCGATTTATTCCAATT
1437630 CGTTGCGAT
1 CGTTGCGAT
1437639 AGGCGAAGTT
Statistics
Matches: 68, Mismatches: 13, Indels: 20
0.67 0.13 0.20
Matches are distributed among these distances:
18 10 0.15
19 3 0.04
20 25 0.37
21 16 0.24
22 4 0.06
23 10 0.15
ACGTcount: A:0.21, C:0.22, G:0.23, T:0.34
Consensus pattern (20 bp):
CGTTGCGATTTATTCCAATT
Found at i:1437615 original size:21 final size:20
Alignment explanation
Indices: 1437507--1437659 Score: 75
Period size: 21 Copynumber: 7.5 Consensus size: 20
1437497 ATTCCAAATT
1437507 CGTTGCGATAGGCGAAGTTC
1 CGTTGCGATAGGCGAAGTTC
** * *
1437527 GCGTTGCGATTCATTCCAA-AT-
1 -CGTTGCGA-T-AGGCGAAGTTC
*
1437548 CGTTGCGATAGTCGAAGTTC
1 CGTTGCGATAGGCGAAGTTC
** *
1437568 GCGTTGCGATTTATTCCAA-TT-
1 -CGTTGCGA--TAGGCGAAGTTC
1437589 CGTTGCGATAGGCGAAGTTC
1 CGTTGCGATAGGCGAAGTTC
** *
1437609 ACGTTGCGATTCATTCCAA-TT-
1 -CGTTGCGA-T-AGGCGAAGTTC
1437630 CGTTGCGATAGGCGAAGTTC
1 CGTTGCGATAGGCGAAGTTC
1437650 GCGTTGCGAT
1 -CGTTGCGAT
1437660 TCATTCCAAA
Statistics
Matches: 99, Mismatches: 18, Indels: 30
0.67 0.12 0.20
Matches are distributed among these distances:
18 14 0.14
19 7 0.07
20 24 0.24
21 33 0.33
22 7 0.07
23 14 0.14
ACGTcount: A:0.20, C:0.21, G:0.27, T:0.31
Consensus pattern (20 bp):
CGTTGCGATAGGCGAAGTTC
Found at i:1437948 original size:21 final size:21
Alignment explanation
Indices: 1437924--1437995 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
1437914 TTTGGAATGA
1437924 ATCGCAACGCGAACTTCGCCT
1 ATCGCAACGCGAACTTCGCCT
* * * **
1437945 ATCGC--CCCGAATTTGGAAT
1 ATCGCAACGCGAACTTCGCCT
1437964 GAATCGCAACGCGAACTTCGCCT
1 --ATCGCAACGCGAACTTCGCCT
*
1437987 GTCGCAACG
1 ATCGCAACG
1437996 ATTTGGAATG
Statistics
Matches: 36, Mismatches: 11, Indels: 8
0.65 0.20 0.15
Matches are distributed among these distances:
19 9 0.25
21 18 0.50
23 9 0.25
ACGTcount: A:0.25, C:0.33, G:0.22, T:0.19
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGCCT
Found at i:1438012 original size:41 final size:41
Alignment explanation
Indices: 1437913--1438154 Score: 394
Period size: 41 Copynumber: 5.9 Consensus size: 41
1437903 CCCGACCCGA
* **
1437913 ATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCCCCG
1 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
* *
1437954 AATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACG
1 -ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
1437996 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
1 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
*
1438037 ATTTGGAATGAATCGTAACGCGAACTTCGACTATCGCAACG
1 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
*
1438078 ATTTGGAATGAATCGCAACGCAAACTTCGACTATCGCAACG
1 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
*
1438119 AATTTAGAATGAATCGCAACGCGAACTTCGACTATC
1 -ATTTGGAATGAATCGCAACGCGAACTTCGACTATC
1438155 ACGTTGCGAA
Statistics
Matches: 189, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
41 118 0.62
42 71 0.38
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (41 bp):
ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
Found at i:1438013 original size:20 final size:20
Alignment explanation
Indices: 1437988--1438097 Score: 75
Period size: 20 Copynumber: 5.4 Consensus size: 20
1437978 ACTTCGCCTG
1437988 TCGCAACGATTTGGAATGAA
1 TCGCAACGATTTGGAATGAA
* * *
1438008 TCGCAACGCGAACTTCGACT--A
1 TCGCAA--CG-ATTTGGAATGAA
1438029 TCGCAACGATTTGGAATGAA
1 TCGCAACGATTTGGAATGAA
* * * *
1438049 TCGTAACGCGAACTTCGACT--A
1 TCGCAA--CG-ATTTGGAATGAA
1438070 TCGCAACGATTTGGAATGAA
1 TCGCAACGATTTGGAATGAA
1438090 TCGCAACG
1 TCGCAACG
1438098 CAAACTTCGA
Statistics
Matches: 66, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
18 12 0.18
19 4 0.06
20 21 0.32
21 13 0.20
22 4 0.06
23 12 0.18
ACGTcount: A:0.32, C:0.23, G:0.23, T:0.23
Consensus pattern (20 bp):
TCGCAACGATTTGGAATGAA
Found at i:1438133 original size:124 final size:124
Alignment explanation
Indices: 1437913--1438154 Score: 396
Period size: 124 Copynumber: 2.0 Consensus size: 124
1437903 CCCGACCCGA
* ** *
1437913 ATTTGGAATGAATCGCAACGCGAACTTCGCCTATCGCCCCGAATTTGGAATGAATCGCAACGCGA
1 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGAATCGCAACGCAA
* * *
1437978 ACTTCGCCTGTCGCAACGATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
66 ACTTCGACTATCGCAACGATTTAGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
*
1438037 ATTTGGAATGAATCGTAACGCGAACTTCGACTATCGCAACG-ATTTGGAATGAATCGCAACGCAA
1 ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGAATCGCAACGCAA
1438101 ACTTCGACTATCGCAACGAATTTAGAATGAATCGCAACGCGAACTTCGACTATC
66 ACTTCGACTATCGCAACG-ATTTAGAATGAATCGCAACGCGAACTTCGACTATC
1438155 ACGTTGCGAA
Statistics
Matches: 109, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
123 38 0.35
124 71 0.65
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (124 bp):
ATTTGGAATGAATCGCAACGCGAACTTCGACTATCGCAACGAATTTGGAATGAATCGCAACGCAA
ACTTCGACTATCGCAACGATTTAGAATGAATCGCAACGCGAACTTCGACTATCGCAACG
Found at i:1439764 original size:31 final size:31
Alignment explanation
Indices: 1439723--1439788 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
1439713 AGAATGGTTC
* *
1439723 CTAACGTTATTTATCCGTTCGATTTTAATCT
1 CTAACATTATTGATCCGTTCGATTTTAATCT
* *
1439754 CTAACATTATTGATTCGTTCGATTTTAGTCT
1 CTAACATTATTGATCCGTTCGATTTTAATCT
1439785 CTAA
1 CTAA
1439789 GCCATGTTAA
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:0.24, C:0.18, G:0.11, T:0.47
Consensus pattern (31 bp):
CTAACATTATTGATCCGTTCGATTTTAATCT
Found at i:1443025 original size:20 final size:20
Alignment explanation
Indices: 1442980--1443028 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
1442970 CGTGATGAAA
1442980 AGGTTTTGGTAACTACAAAGT
1 AGGTTTT-GTAACTACAAAGT
*
1443001 A-GTTTTGTAACTGCAAACG-
1 AGGTTTTGTAACTACAAA-GT
1443020 AGGTTTTGT
1 AGGTTTTGT
1443029 GAAGAAAACT
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 11 0.44
20 13 0.52
21 1 0.04
ACGTcount: A:0.29, C:0.10, G:0.24, T:0.37
Consensus pattern (20 bp):
AGGTTTTGTAACTACAAAGT
Found at i:1445758 original size:2 final size:2
Alignment explanation
Indices: 1445751--1445791 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
1445741 ATTTTTAAAT
1445751 TA TA TA TA 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 TA TA TA TA T
1445792 TATTTGATGC
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1450010 original size:23 final size:23
Alignment explanation
Indices: 1449979--1450051 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
1449969 ATAGGTAAAA
*
1449979 ATATGATGTAATAGGTAGCGCTT
1 ATATAATGTAATAGGTAGCGCTT
*
1450002 ATATAATGTAATAGGTAGCGTTT
1 ATATAATGTAATAGGTAGCGCTT
* *
1450025 ATATAATATAATAGGTAGTGCTT
1 ATATAATGTAATAGGTAGCGCTT
1450048 ATAT
1 ATAT
1450052 TGTAAAGTAT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 45 1.00
ACGTcount: A:0.36, C:0.05, G:0.21, T:0.38
Consensus pattern (23 bp):
ATATAATGTAATAGGTAGCGCTT
Found at i:1450489 original size:23 final size:23
Alignment explanation
Indices: 1450463--1450530 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
1450453 TAAAAGTATG
*
1450463 ATGTAATAAGTAGCGCTTATATA
1 ATGTAATAGGTAGCGCTTATATA
*
1450486 ATGTAATAGGTAGCGTTTATATA
1 ATGTAATAGGTAGCGCTTATATA
**
1450509 ATGTAATAGGTAGTACTTATAT
1 ATGTAATAGGTAGCGCTTATAT
1450531 TGTAAAGTAT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.37, C:0.06, G:0.19, T:0.38
Consensus pattern (23 bp):
ATGTAATAGGTAGCGCTTATATA
Done.