Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008143.1 Hibiscus syriacus cultivar Beakdansim tig00110705_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: 1142845
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 5
Found at i:482549 original size:21 final size:21
Alignment explanation
Indices: 482510--482550 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
482500 TTTATATTAG
* **
482510 GATTTAGGGTTTATTGTTTAT
1 GATTTAGAGTTTAGGGTTTAT
482531 GATTTAGAGTTTAGGGTTTA
1 GATTTAGAGTTTAGGGTTTA
482551 GAGTTTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.27, T:0.51
Consensus pattern (21 bp):
GATTTAGAGTTTAGGGTTTAT
Found at i:483033 original size:332 final size:332
Alignment explanation
Indices: 482427--483194 Score: 1252
Period size: 332 Copynumber: 2.3 Consensus size: 332
482417 ATTTTGACAA
* * *
482427 TACATTAGTTACATA-GACTCAATACATAAGCCCACTCTTTTATTACAAATATATATGCATTAGT
1 TACATTAGTTACATAGGTC-CAATACACAAGGCCACTCTTTTATTACAAATATATATGCATTAGT
* * * * * * *
482491 GCTGGTCTATTTATATTAGGATTTAGGGTTTATTGTTTATGATTTAGAGTTTAGGGTTTAGAGTT
65 GCTAGTCTATTTATATTAGGGTTTAGGGTTTATAGTTTAAGATTTAAAATTTAAGGTTTAGAGTT
*
482556 TATATATATTAATACATTAGTTTACATAGACCCAATACATAAGCCTACTCTTTTATTACAAATAT
130 TATATATATTAATACATTAGTTTACATAGACCCAATACATAAGCCCACTCTTTTATTACAAATAT
*
482621 ATATTAATTTCATTTGCATAATTAGTATTTTAGTTGTATGTTAGGTTAATTCACATTAATAACTC
195 ATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAACTC
* * *
482686 ATTTATTTTGTTGTTATGAATAAGTAATAATAAAACGAAAAAATAAGTCTATTTGCAACGGTGCT
260 ATTTATTTTGTTGTTATGAATAAGTAATAATAAAACGAAAAAACAAGTCCATTTGCAACAGTGCT
482751 TATCCATT
325 TATCCATT
*
482759 TACATTAGTTACATAGGTCCAATACACAAGGTCACTCTTTTATTACAAATATATATGCATTAGTG
1 TACATTAGTTACATAGGTCCAATACACAAGGCCACTCTTTTATTACAAATATATATGCATTAGTG
482824 CTAGTCTATTTATATTAGGGTTTAGGGTTTATAGTTTAAGATTTAAAATTTAAGGTTTAGAGTTT
66 CTAGTCTATTTATATTAGGGTTTAGGGTTTATAGTTTAAGATTTAAAATTTAAGGTTTAGAGTTT
* *
482889 ATATATATTAATACATTAGTTTACATATG-CCTAATACATAAGCCCACTCTTTTATTATAAATAT
131 ATATATATTAATACATTAGTTTACATA-GACCCAATACATAAGCCCACTCTTTTATTACAAATAT
482953 ATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAACTC
195 ATATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAACTC
* *
483018 ATTTATTTTGTTGTTATGAATAAGTAATAATAAAACGCAAAAACAAGTCCATTTGCAATAGTGCT
260 ATTTATTTTGTTGTTATGAATAAGTAATAATAAAACGAAAAAACAAGTCCATTTGCAACAGTGCT
*
483083 TGTCCATT
325 TATCCATT
*
483091 TACATTAGTTACATAGGTCCAATACACAAAGCCACTCTTTTATTACAAATATATATGCATTAGTG
1 TACATTAGTTACATAGGTCCAATACACAAGGCCACTCTTTTATTACAAATATATATGCATTAGTG
* * ** * *
483156 CTAGTCCATTTACATTAAAGTTTATGGTTTATGGTTTAA
66 CTAGTCTATTTATATTAGGGTTTAGGGTTTATAGTTTAA
483195 TGTTTATGGT
Statistics
Matches: 405, Mismatches: 29, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
332 402 0.99
333 3 0.01
ACGTcount: A:0.34, C:0.12, G:0.12, T:0.41
Consensus pattern (332 bp):
TACATTAGTTACATAGGTCCAATACACAAGGCCACTCTTTTATTACAAATATATATGCATTAGTG
CTAGTCTATTTATATTAGGGTTTAGGGTTTATAGTTTAAGATTTAAAATTTAAGGTTTAGAGTTT
ATATATATTAATACATTAGTTTACATAGACCCAATACATAAGCCCACTCTTTTATTACAAATATA
TATTAATTTCATTTGCATAATTAGTATTTTAGTTGCATGTTAGGTTAATTCACATTAATAACTCA
TTTATTTTGTTGTTATGAATAAGTAATAATAAAACGAAAAAACAAGTCCATTTGCAACAGTGCTT
ATCCATT
Found at i:483199 original size:14 final size:14
Alignment explanation
Indices: 483182--483235 Score: 63
Period size: 14 Copynumber: 3.9 Consensus size: 14
483172 AAAGTTTATG
*
483182 GTTTATGGTTTAAT
1 GTTTATGGTTTAAA
483196 GTTTATGGTTTAAA
1 GTTTATGGTTTAAA
* * *
483210 GTTTAGGGTGTATA
1 GTTTATGGTTTAAA
*
483224 GTTTATGATTTA
1 GTTTATGGTTTA
483236 GGGTTTAGAA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
14 33 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (14 bp):
GTTTATGGTTTAAA
Found at i:483213 original size:21 final size:21
Alignment explanation
Indices: 483170--483214 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
483160 TCCATTTACA
**
483170 TTAAAGTTTATGGTTTATGGT
1 TTAAAGTTTATGGTTTAAAGT
*
483191 TTAATGTTTATGGTTTAAAGT
1 TTAAAGTTTATGGTTTAAAGT
483212 TTA
1 TTA
483215 GGGTGTATAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.27, C:0.00, G:0.20, T:0.53
Consensus pattern (21 bp):
TTAAAGTTTATGGTTTAAAGT
Found at i:483243 original size:7 final size:7
Alignment explanation
Indices: 483175--483242 Score: 57
Period size: 7 Copynumber: 9.7 Consensus size: 7
483165 TTACATTAAA
483175 GTTTATG
1 GTTTATG
483182 GTTTATG
1 GTTTATG
483189 GTTTAAT-
1 GTTT-ATG
483196 GTTTATG
1 GTTTATG
**
483203 GTTTAAA
1 GTTTATG
*
483210 GTTTAGG
1 GTTTATG
* *
483217 GTGTATA
1 GTTTATG
483224 GTTTATG
1 GTTTATG
* *
483231 ATTTAGG
1 GTTTATG
483238 GTTTA
1 GTTTA
483243 GAATTTCTAT
Statistics
Matches: 47, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
6 2 0.04
7 43 0.91
8 2 0.04
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.51
Consensus pattern (7 bp):
GTTTATG
Found at i:483761 original size:7 final size:7
Alignment explanation
Indices: 483714--483770 Score: 51
Period size: 7 Copynumber: 8.1 Consensus size: 7
483704 TATGGTTCAT
483714 GGTTTAG
1 GGTTTAG
*
483721 GATTTAG
1 GGTTTAG
*
483728 GGTTTAA
1 GGTTTAG
* * *
483735 TGTGTAT
1 GGTTTAG
483742 GGTTTAG
1 GGTTTAG
**
483749 TATTTAG
1 GGTTTAG
483756 GGTTTAG
1 GGTTTAG
483763 GGTTTAG
1 GGTTTAG
483770 G
1 G
483771 TTTTTTTTTA
Statistics
Matches: 37, Mismatches: 13, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.19, C:0.00, G:0.35, T:0.46
Consensus pattern (7 bp):
GGTTTAG
Found at i:484227 original size:19 final size:20
Alignment explanation
Indices: 484195--484235 Score: 75
Period size: 19 Copynumber: 2.1 Consensus size: 20
484185 TTTCTATTAT
484195 CTCTAAATTTCTCAATTTCC
1 CTCTAAATTTCTCAATTTCC
484215 CTCTAAA-TTCTCAATTTCC
1 CTCTAAATTTCTCAATTTCC
484234 CT
1 CT
484236 ATATTCTCAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.67
20 7 0.33
ACGTcount: A:0.24, C:0.32, G:0.00, T:0.44
Consensus pattern (20 bp):
CTCTAAATTTCTCAATTTCC
Found at i:484535 original size:17 final size:16
Alignment explanation
Indices: 484513--484547 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
484503 ATATAAAAAT
484513 TTATATATAAACTTATA
1 TTATATATAAA-TTATA
*
484530 TTATATATATATTATA
1 TTATATATAAATTATA
484546 TT
1 TT
484548 TTTCAATTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATATAAATTATA
Found at i:488485 original size:17 final size:17
Alignment explanation
Indices: 488459--488499 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
488449 CAAATACAAA
*
488459 GAGGAGAGGGAGGACTG
1 GAGGAAAGGGAGGACTG
488476 GAGGAAAGGGAGGACTG
1 GAGGAAAGGGAGGACTG
488493 GAGGAAA
1 GAGGAAA
488500 AGCGGAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.54, T:0.05
Consensus pattern (17 bp):
GAGGAAAGGGAGGACTG
Found at i:504161 original size:6 final size:6
Alignment explanation
Indices: 504150--504176 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
504140 GGGTACAACC
504150 GAAAAT GAAAAT GAAAAT GAAAAT GAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAA
504177 GAATAAGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.67, C:0.00, G:0.19, T:0.15
Consensus pattern (6 bp):
GAAAAT
Found at i:504480 original size:21 final size:20
Alignment explanation
Indices: 504394--504551 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
504384 AAATGACCAA
**
504394 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
504413 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
504433 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
504453 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
504474 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
504495 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
504515 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
504536 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
504552 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:504580 original size:20 final size:20
Alignment explanation
Indices: 504518--504711 Score: 212
Period size: 20 Copynumber: 9.7 Consensus size: 20
504508 CGATTTTCCA
* ** *
504518 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
504538 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
504558 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
504578 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
504598 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
504618 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
504638 ATATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
504658 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
504678 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
504699 AAATCGCAACGCG
1 AAATCGCAACGCG
504712 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:504602 original size:60 final size:60
Alignment explanation
Indices: 504518--504711 Score: 244
Period size: 60 Copynumber: 3.2 Consensus size: 60
504508 CGATTTTCCA
* ** * *
504518 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
504578 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * **
504638 ATATCGCAATGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
504699 AAATCGCAACGCG
1 AAATCGCAACGCG
504712 ATATTTAAAG
Statistics
Matches: 110, Mismatches: 23, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
60 80 0.73
61 30 0.27
ACGTcount: A:0.36, C:0.25, G:0.20, T:0.20
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:505133 original size:33 final size:33
Alignment explanation
Indices: 505094--505164 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
505084 TTCACTTAGA
* *
505094 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
* *
505127 TTTCATTTCGCGTTGCTATTATCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
505160 TTTCA
1 TTTCA
505165 AGTTAGTATT
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:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
Found at i:505363 original size:40 final size:41
Alignment explanation
Indices: 505302--505385 Score: 125
Period size: 41 Copynumber: 2.1 Consensus size: 41
505292 CGCGTTGCGA
***
505302 TTCTCTCGTTGCGATTTTCATT-TCGCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTCTCGCGTTGCGATTTTCAT
*
505342 TTCTCTCGTTGCGACAGTCATTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGACAGTCATTCTCGCGTTGCGATTTTCAT
505383 TTC
1 TTC
505386 AACCAAAAGA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
40 19 0.49
41 20 0.51
ACGTcount: A:0.11, C:0.25, G:0.17, T:0.48
Consensus pattern (41 bp):
TTCTCTCGTTGCGACAGTCATTCTCGCGTTGCGATTTTCAT
Found at i:505367 original size:20 final size:20
Alignment explanation
Indices: 505301--505383 Score: 114
Period size: 20 Copynumber: 4.2 Consensus size: 20
505291 TCGCGTTGCG
505301 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
505321 ATT-TCGCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
***
505340 ATTTCTCTCGTTGCGACAGTC
1 A-TTCTCTCGTTGCGATTTTC
505361 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
505381 ATT
1 ATT
505384 TCAACCAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
19 16 0.30
20 24 0.45
21 13 0.25
ACGTcount: A:0.12, C:0.24, G:0.17, T:0.47
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:507243 original size:93 final size:93
Alignment explanation
Indices: 507084--507549 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
507074 TAGATTGCTT
*
507084 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
507149 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507177 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
507242 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507270 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
507335 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507363 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
507426 TTTGTC-TTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507453 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
507518 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
507545 AGTAA
1 AGTAA
507550 TGCAATCCAT
Statistics
Matches: 369, Mismatches: 1, Indels: 7
0.98 0.00 0.02
Matches are distributed among these distances:
90 74 0.20
91 16 0.04
92 22 0.06
93 257 0.70
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:507637 original size:19 final size:19
Alignment explanation
Indices: 507597--507695 Score: 109
Period size: 19 Copynumber: 5.4 Consensus size: 19
507587 TAGTTTACTT
* *
507597 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
507617 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
507636 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
507655 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
507669 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
507688 TCGCAACG
1 TCGCAACG
507696 ACAAGATCGC
Statistics
Matches: 67, Mismatches: 7, Indels: 11
0.79 0.08 0.13
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.58
20 13 0.19
ACGTcount: A:0.45, C:0.28, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:507676 original size:33 final size:32
Alignment explanation
Indices: 507633--507716 Score: 132
Period size: 33 Copynumber: 2.6 Consensus size: 32
507623 CGCGAAACCA
**
507633 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
507665 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
507698 AAGATCGCAACGCGAAACC
1 AA-ATCGCAACGCGAAACC
507717 CCAATAGTGC
Statistics
Matches: 48, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
32 2 0.04
33 46 0.96
ACGTcount: A:0.45, C:0.29, G:0.19, T:0.07
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:509430 original size:19 final size:19
Alignment explanation
Indices: 509414--509514 Score: 149
Period size: 19 Copynumber: 5.5 Consensus size: 19
509404 AAAAATGACT
509414 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
509433 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
509452 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
509466 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
509485 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
509505 ATCGCAATGC
1 ATCGCAATGC
509515 CGATTTTCAT
Statistics
Matches: 74, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.53
20 19 0.26
ACGTcount: A:0.45, C:0.18, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:509529 original size:20 final size:18
Alignment explanation
Indices: 509506--509628 Score: 73
Period size: 14 Copynumber: 7.0 Consensus size: 18
509496 GAAATGAAAA
509506 TCGCAATGCCGATTTTCATT
1 TCGCAATG-CGATTTTCA-T
*
509526 TCGCATTGCGATTTTCAT
1 TCGCAATGCGATTTTCAT
* *
509544 TCGCATTGCGATTCTC--
1 TCGCAATGCGATTTTCAT
*
509560 TCG--TTGCGATTTTCATT
1 TCGCAATGCGATTTTCA-T
* *
509577 TCGCATTGCGATTCTC--
1 TCGCAATGCGATTTTCAT
*
509593 TCG--TTGCGATTTTCATT
1 TCGCAATGCGATTTTCA-T
*
509610 TCCGCATTGCGATTTTCAT
1 T-CGCAATGCGATTTTCAT
509629 GTTGGGATTT
Statistics
Matches: 87, Mismatches: 5, Indels: 23
0.76 0.04 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 4 0.05
18 18 0.21
19 20 0.23
20 19 0.22
ACGTcount: A:0.15, C:0.24, G:0.17, T:0.44
Consensus pattern (18 bp):
TCGCAATGCGATTTTCAT
Found at i:509638 original size:67 final size:67
Alignment explanation
Indices: 509531--509689 Score: 234
Period size: 67 Copynumber: 2.4 Consensus size: 67
509521 TCATTTCGCA
509531 TTGCGATTTTCA-TT-CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
509594 CG
66 CG
* *
509596 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCATTTCGCATTGCGATTCTC
1 TTGCGATTTTCATTTCCGCATTGCGATTCTC-TCGTTGCGATTTTCATTTCGCATTGCGATTCTC
509660 TCG
65 TCG
* * **
509663 TTGCGATTGTAATTTCCGTGTTGCGAT
1 TTGCGATTTTCATTTCCGCATTGCGAT
509690 AGTCAAATGC
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
65 12 0.14
66 2 0.02
67 70 0.82
68 1 0.01
ACGTcount: A:0.13, C:0.21, G:0.20, T:0.45
Consensus pattern (67 bp):
TTGCGATTTTCATTTCCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTCTCT
CG
Found at i:509678 original size:33 final size:33
Alignment explanation
Indices: 509531--509670 Score: 230
Period size: 33 Copynumber: 4.2 Consensus size: 33
509521 TCATTTCGCA
509531 TTGCGATTTTCA-TTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
509563 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
*
509596 TTGCGATTTTCATTTCCGCATTGCGATTTTCAT-G
1 TTGCGATTTTCATTT-CGCATTGCGATTCTC-TCG
*
509630 TTGGGATTTTCATTTCGCATTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
509663 TTGCGATT
1 TTGCGATT
509671 GTAATTTCCG
Statistics
Matches: 100, Mismatches: 4, Indels: 7
0.90 0.04 0.06
Matches are distributed among these distances:
32 13 0.13
33 57 0.57
34 29 0.29
35 1 0.01
ACGTcount: A:0.13, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCG
Found at i:512196 original size:24 final size:24
Alignment explanation
Indices: 512156--512210 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 24
512146 AAAATCCGTG
* * *
512156 TATTGACCAATATCAAAGTTCGGA
1 TATTGACCAAGACCAAAGTTCGAA
*
512180 TATTGACCAAGACCAAATTTCGAA
1 TATTGACCAAGACCAAAGTTCGAA
*
512204 TACTGAC
1 TATTGAC
512211 TAGTACTCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.27
Consensus pattern (24 bp):
TATTGACCAAGACCAAAGTTCGAA
Found at i:512899 original size:20 final size:20
Alignment explanation
Indices: 512871--513100 Score: 237
Period size: 20 Copynumber: 11.5 Consensus size: 20
512861 AAATTTCAGT
* * *
512871 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
512891 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
* *
512911 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCGC
**
512931 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCGC
*
512951 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
* *
512971 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCGC
* ** *
512991 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATTCGC
* *
513011 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATTCGC
*
513031 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCGC
*
513051 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCGC
* **
513071 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCGC
513091 GTTGCGATTT
1 GTTGCGATTT
513101 TGGAAAATCG
Statistics
Matches: 182, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 181 0.99
21 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.25, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCGC
Found at i:513117 original size:21 final size:21
Alignment explanation
Indices: 513087--513169 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
513077 ATTTTCATAT
*
513087 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
513108 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
513129 TCGCATTGCGATTTT-TAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
513150 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
513170 CTGATTTGCG
Statistics
Matches: 48, Mismatches: 12, Indels: 4
0.75 0.19 0.06
Matches are distributed among these distances:
20 2 0.04
21 44 0.92
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:513160 original size:42 final size:43
Alignment explanation
Indices: 513067--513165 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
513057 ATTTATGTGT
*
513067 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
** *
513108 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-TAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGGAA-AA
*
513150 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
513166 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.38
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGGAAAA
Found at i:514492 original size:13 final size:13
Alignment explanation
Indices: 514474--514499 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
514464 ATGTAGTCTT
514474 GGATCGCACCACC
1 GGATCGCACCACC
514487 GGATCGCACCACC
1 GGATCGCACCACC
514500 TCTATAAGGC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.46, G:0.23, T:0.08
Consensus pattern (13 bp):
GGATCGCACCACC
Found at i:517647 original size:13 final size:14
Alignment explanation
Indices: 517629--517666 Score: 60
Period size: 13 Copynumber: 2.8 Consensus size: 14
517619 CACATAATTG
517629 GGTTTTGGGTTT-A
1 GGTTTTGGGTTTAA
517642 GGTTTTGGGTTTAA
1 GGTTTTGGGTTTAA
*
517656 GGTTTAGGGTT
1 GGTTTTGGGTT
517667 CATTACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.50
Consensus pattern (14 bp):
GGTTTTGGGTTTAA
Found at i:517651 original size:20 final size:20
Alignment explanation
Indices: 517626--517663 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
517616 TATCACATAA
**
517626 TTGGGTTTTGGGTTTAGGTT
1 TTGGGTTTAAGGTTTAGGTT
517646 TTGGGTTTAAGGTTTAGG
1 TTGGGTTTAAGGTTTAGG
517664 GTTCATTACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.11, C:0.00, G:0.39, T:0.50
Consensus pattern (20 bp):
TTGGGTTTAAGGTTTAGGTT
Found at i:517858 original size:25 final size:26
Alignment explanation
Indices: 517813--517867 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
517803 AAAAATTAGT
517813 TATTAAAAATATTATCATTAGA-AATA
1 TATTAAAAATATTATCATTAGATAA-A
* *
517839 TATTAAATAT-TTTTCATTAGATAAA
1 TATTAAAAATATTATCATTAGATAAA
517864 TATT
1 TATT
517868 TTTTTTTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 15 0.58
26 11 0.42
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (26 bp):
TATTAAAAATATTATCATTAGATAAA
Found at i:518684 original size:23 final size:23
Alignment explanation
Indices: 518658--518702 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
518648 CACCACAGCT
*
518658 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
518681 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
518703 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:519080 original size:151 final size:149
Alignment explanation
Indices: 518670--519135 Score: 862
Period size: 149 Copynumber: 3.1 Consensus size: 149
518660 TATAATTGCA
518670 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
518734 TTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
518799 CCATAGAATATATATATATC
130 CCATAGAATATATATATATC
518819 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
518884 TCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
518949 CATAGAATATATATATATATC
131 CATAG-A-ATATATATATATC
518970 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
*
519035 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
* * *
519100 CAAAGAATATACATATGTC
131 CATAGAATATATATATATC
519119 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
519136 CCCTCGGCTC
Statistics
Matches: 310, Mismatches: 4, Indels: 6
0.97 0.01 0.02
Matches are distributed among these distances:
148 1 0.00
149 161 0.52
150 2 0.01
151 146 0.47
ACGTcount: A:0.35, C:0.21, G:0.16, T:0.29
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGAGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CATAGAATATATATATATC
Found at i:520624 original size:21 final size:21
Alignment explanation
Indices: 520600--520644 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
520590 TTTTGTTCGT
* *
520600 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
520621 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
520642 TTG
1 TTG
520645 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:523902 original size:23 final size:23
Alignment explanation
Indices: 523876--523920 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
523866 CACCACAGCT
*
523876 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCG
*
523899 CGTAGAATTGCACCGTAGTGCC
1 CGTAGAATTGCACCGAAGTGCC
523921 ATATAATAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.24, C:0.27, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCG
Found at i:524138 original size:149 final size:149
Alignment explanation
Indices: 523888--524202 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
523878 TATAATTGCA
523888 CCGAAGTG-CCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
523952 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
* *
524017 CCACAGAATATATATATATC
130 CCAAAGAATATACATATATC
*
524037 CCGAAGGACTGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
524102 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
*
524167 CAAAGAATATACATATGTC
131 CAAAGAATATACATATATC
524186 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
524203 CCCTCGACTC
Statistics
Matches: 160, Mismatches: 5, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
148 1 0.01
149 159 0.99
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATATC
Found at i:524589 original size:2 final size:2
Alignment explanation
Indices: 524582--524612 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
524572 ACCTGATGAC
524582 AT AT AT AT AT AT AT AT AT AT AT AT AT CAT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT -AT AT
524613 TATCTACCTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:525696 original size:21 final size:21
Alignment explanation
Indices: 525657--525701 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
525647 TTTTATTCGT
* * *
525657 TTGAAGGGGTATCGGTTCCTC
1 TTGAAGGGGTACCGATTCCCC
*
525678 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
525699 TTG
1 TTG
525702 CCCAGAAATC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.22, G:0.29, T:0.33
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:528087 original size:13 final size:13
Alignment explanation
Indices: 528069--528094 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
528059 ACATTTTTGC
528069 TTATGTTATCATA
1 TTATGTTATCATA
528082 TTATGTTATCATA
1 TTATGTTATCATA
528095 GGTATAATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.08, G:0.08, T:0.54
Consensus pattern (13 bp):
TTATGTTATCATA
Found at i:528712 original size:14 final size:15
Alignment explanation
Indices: 528682--528712 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
528672 AAATAAAAGT
528682 AAGAATGAGATAGAA
1 AAGAATGAGATAGAA
528697 AAGAATGAGA-AGAA
1 AAGAATGAGATAGAA
528711 AA
1 AA
528713 TGAAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.38
15 10 0.62
ACGTcount: A:0.65, C:0.00, G:0.26, T:0.10
Consensus pattern (15 bp):
AAGAATGAGATAGAA
Found at i:528832 original size:21 final size:20
Alignment explanation
Indices: 528792--528836 Score: 63
Period size: 21 Copynumber: 2.2 Consensus size: 20
528782 AGAATGAAAA
528792 ATTTGAGATTAAGGTTAGAG
1 ATTTGAGATTAAGGTTAGAG
* *
528812 ATTTGAGTATTTAGTTTAGAG
1 ATTTGAG-ATTAAGGTTAGAG
528833 ATTT
1 ATTT
528837 AATTTAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 7 0.32
21 15 0.68
ACGTcount: A:0.31, C:0.00, G:0.24, T:0.44
Consensus pattern (20 bp):
ATTTGAGATTAAGGTTAGAG
Found at i:529076 original size:17 final size:17
Alignment explanation
Indices: 529054--529088 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
529044 TATTAATCTT
529054 TTTTAAAAAATAAAAAA
1 TTTTAAAAAATAAAAAA
* *
529071 TTTTAAAATATATAAAA
1 TTTTAAAAAATAAAAAA
529088 T
1 T
529089 GACATGTGTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
TTTTAAAAAATAAAAAA
Found at i:529371 original size:31 final size:31
Alignment explanation
Indices: 529307--529371 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
529297 ACGTAGACAT
*
529307 CTAAAAGTGTAACATAGAAAATGCCAGACAC
1 CTAAAAGTGTAACATAGAAAATGCCAGAAAC
**
529338 CTAAAAGTGTAACATCAG-AAATGTTAGAAAC
1 CTAAAAGTGTAACAT-AGAAAATGCCAGAAAC
529369 CTA
1 CTA
529372 TTTTTAACGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.48, C:0.17, G:0.15, T:0.20
Consensus pattern (31 bp):
CTAAAAGTGTAACATAGAAAATGCCAGAAAC
Found at i:535449 original size:2 final size:2
Alignment explanation
Indices: 535442--535489 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
535432 AAATCCATGC
535442 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
535484 AT AT AT
1 AT AT AT
535490 TACCTGAGGG
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:548607 original size:15 final size:15
Alignment explanation
Indices: 548587--548615 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
548577 TAACGAATCT
548587 ATAAAATTTTATTAG
1 ATAAAATTTTATTAG
548602 ATAAAATTTTATTA
1 ATAAAATTTTATTA
548616 TCAATAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
ATAAAATTTTATTAG
Found at i:549963 original size:20 final size:20
Alignment explanation
Indices: 549927--549964 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
549917 ATCATATTCC
**
549927 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
549947 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
549965 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:551960 original size:20 final size:22
Alignment explanation
Indices: 551935--551974 Score: 66
Period size: 20 Copynumber: 1.9 Consensus size: 22
551925 TTATATTTAT
551935 ATTTGTT-TATATT-TATAAAG
1 ATTTGTTATATATTATATAAAG
551955 ATTTGTTATATATTATATAA
1 ATTTGTTATATATTATATAA
551975 CATATTACCT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 7 0.39
21 6 0.33
22 5 0.28
ACGTcount: A:0.38, C:0.00, G:0.07, T:0.55
Consensus pattern (22 bp):
ATTTGTTATATATTATATAAAG
Found at i:552079 original size:26 final size:29
Alignment explanation
Indices: 552031--552091 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 29
552021 GATATTAGGA
*
552031 TATATTAAAATAATATGATAATA-ATTTT
1 TATATTAAAATAATATGAAAATATATTTT
* *
552059 TATATTAATATAAT-T-AAAATATTTTTT
1 TATATTAAAATAATATGAAAATATATTTT
552086 TATATT
1 TATATT
552092 TACATTCGTC
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 5 0.17
27 11 0.38
28 13 0.45
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (29 bp):
TATATTAAAATAATATGAAAATATATTTT
Found at i:552959 original size:136 final size:134
Alignment explanation
Indices: 552717--552986 Score: 522
Period size: 136 Copynumber: 2.0 Consensus size: 134
552707 TATACATTAT
552717 CAATGACCAAGATTCTATATAAGCATTACCTCGTAAGACTTTTCAATATATATACACATTCACTG
1 CAATGACCAAGATTCTATATAAGCATTACCTCGTAAGACTTTTCAATATATATACACATTCACTG
552782 CACTACTTTACAGACATAATTAACCGTCTTTTTTAACCATTTTTTTCATTTCTTTTTACCCTACG
66 CACTACTTTACAGACATAATTAACCGTCTTTTTTAACCATTTTTTTCATTTCTTTTTACCCTACG
552847 TTAC
131 TTAC
552851 CAATGACCAAGATTCTATATAAGCATTACCTCGTAAGACTTTTCAATATATATAGACACATTCAC
1 CAATGACCAAGATTCTATATAAGCATTACCTCGTAAGACTTTTCAATATATAT--ACACATTCAC
552916 TGCACTACTTTACAGACATAATTAACCGTCTTTTTTAACCATTTTTTTCATTTCTTTTTACCCTA
64 TGCACTACTTTACAGACATAATTAACCGTCTTTTTTAACCATTTTTTTCATTTCTTTTTACCCTA
552981 CGTTAC
129 CGTTAC
552987 ATGATTATTT
Statistics
Matches: 134, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
134 53 0.40
136 81 0.60
ACGTcount: A:0.31, C:0.23, G:0.07, T:0.39
Consensus pattern (134 bp):
CAATGACCAAGATTCTATATAAGCATTACCTCGTAAGACTTTTCAATATATATACACATTCACTG
CACTACTTTACAGACATAATTAACCGTCTTTTTTAACCATTTTTTTCATTTCTTTTTACCCTACG
TTAC
Found at i:557579 original size:21 final size:21
Alignment explanation
Indices: 557553--557615 Score: 90
Period size: 21 Copynumber: 3.0 Consensus size: 21
557543 GTCGAGGGTT
*
557553 TCATAGGTCATTCGGGACAAC
1 TCATAGGTCCTTCGGGACAAC
*
557574 TCATAGGTCCTTCGGGACAAAT
1 TCATAGGTCCTTCGGGAC-AAC
*
557596 TCACAGGTCCTTCGGGACAA
1 TCATAGGTCCTTCGGGACAA
557616 ATTTCATATG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.27, C:0.25, G:0.24, T:0.24
Consensus pattern (21 bp):
TCATAGGTCCTTCGGGACAAC
Found at i:557606 original size:22 final size:22
Alignment explanation
Indices: 557552--557623 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
557542 AGTCGAGGGT
*
557552 TTCATAGGTCATTCGGGAC-AA
1 TTCATAGGTCCTTCGGGACAAA
*
557573 CTCATAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
*
557595 TTCACAGGTCCTTCGGGACAAA
1 TTCATAGGTCCTTCGGGACAAA
557617 TTTCATA
1 -TTCATA
557624 TGCCACTCAG
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
21 17 0.39
22 22 0.50
23 5 0.11
ACGTcount: A:0.28, C:0.24, G:0.21, T:0.28
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACAAA
Found at i:560072 original size:20 final size:20
Alignment explanation
Indices: 560047--560084 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
560037 CACCTGTTAA
*
560047 AGAATGCATCGATGCACTAT
1 AGAATGCACCGATGCACTAT
560067 AGAATGCACCGATGCACT
1 AGAATGCACCGATGCACT
560085 TCAATGGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.24, G:0.21, T:0.21
Consensus pattern (20 bp):
AGAATGCACCGATGCACTAT
Found at i:560929 original size:18 final size:18
Alignment explanation
Indices: 560906--560941 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
560896 GAGGGTCTAC
560906 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
560924 GTGGTCCTTCGGGACATA
1 GTGGTCCTTCGGGACATA
560942 TGTGTTATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.17, C:0.22, G:0.33, T:0.28
Consensus pattern (18 bp):
GTGGTCCTTCGGGACATA
Found at i:564848 original size:25 final size:24
Alignment explanation
Indices: 564805--564857 Score: 79
Period size: 25 Copynumber: 2.2 Consensus size: 24
564795 TTAACAAAAA
*
564805 ATATTTTTTAAAATCAAAATTTAT
1 ATATTTTTTAAAATCAAAATTTAG
*
564829 ATATTTTATTTAAATCAAAATTTAG
1 ATATTTT-TTAAAATCAAAATTTAG
564854 ATAT
1 ATAT
564858 AATATGTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (24 bp):
ATATTTTTTAAAATCAAAATTTAG
Found at i:564867 original size:25 final size:25
Alignment explanation
Indices: 564815--564867 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
564805 ATATTTTTTA
* ** *
564815 AAATCAAAATTTATATATTTTATTT
1 AAATCAAAATTTAGATATAATATGT
564840 AAATCAAAATTTAGATATAATATGT
1 AAATCAAAATTTAGATATAATATGT
564865 AAA
1 AAA
564868 AATTTATAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (25 bp):
AAATCAAAATTTAGATATAATATGT
Found at i:577114 original size:18 final size:19
Alignment explanation
Indices: 577074--577117 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
577064 TTTCGCAATT
*
577074 TTTATTAATTAATATAAAA
1 TTTATTAATAAATATAAAA
*
577093 -TTATTTATAAAT-TAAAA
1 TTTATTAATAAATATAAAA
577110 TTTATTAA
1 TTTATTAA
577118 GTTAATTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTTATTAATAAATATAAAA
Found at i:579030 original size:17 final size:17
Alignment explanation
Indices: 579010--579049 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
579000 CGCACAAATT
579010 TAAT-TTATATAAATAAA
1 TAATATTATA-AAATAAA
*
579027 TAATATTATAACATAAA
1 TAATATTATAAAATAAA
579044 TAATAT
1 TAATAT
579050 ATTAATTTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 16 0.76
18 5 0.24
ACGTcount: A:0.57, C:0.03, G:0.00, T:0.40
Consensus pattern (17 bp):
TAATATTATAAAATAAA
Found at i:583390 original size:15 final size:15
Alignment explanation
Indices: 583370--583416 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
583360 TCAGCATTCG
583370 AATCATTCAACGCTT
1 AATCATTCAACGCTT
*
583385 AATCATTCAACGTTT
1 AATCATTCAACGCTT
*
583400 AATCATTCAGCGCTT
1 AATCATTCAACGCTT
583415 AA
1 AA
583417 CCAACTCAAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (15 bp):
AATCATTCAACGCTT
Found at i:584905 original size:22 final size:21
Alignment explanation
Indices: 584850--584905 Score: 51
Period size: 22 Copynumber: 2.5 Consensus size: 21
584840 AAAATTTCAC
584850 ATAATTTTATCTCTTCTTATTA
1 ATAATTTTAT-TCTTCTTATTA
* *
584872 ATAACTTGTATTTTATCTT-TTAA
1 ATAA-TTTTATTCT-TCTTATT-A
584895 ATAATTTTATT
1 ATAATTTTATT
584906 GAAACTAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
22 14 0.50
23 14 0.50
ACGTcount: A:0.30, C:0.09, G:0.02, T:0.59
Consensus pattern (21 bp):
ATAATTTTATTCTTCTTATTA
Found at i:585023 original size:17 final size:18
Alignment explanation
Indices: 584998--585034 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
584988 ATTAGTGATG
*
584998 ATTTTATAA-AAAAAATA
1 ATTTGATAATAAAAAATA
585015 ATTTGATAATAAAAAATA
1 ATTTGATAATAAAAAATA
585033 AT
1 AT
585035 AATAAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 8 0.44
18 10 0.56
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (18 bp):
ATTTGATAATAAAAAATA
Found at i:585038 original size:13 final size:13
Alignment explanation
Indices: 585020--585044 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
585010 AAATAATTTG
585020 ATAATAAAAAATA
1 ATAATAAAAAATA
585033 ATAATAAAAAAT
1 ATAATAAAAAAT
585045 TAACAACTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
ATAATAAAAAATA
Found at i:585306 original size:20 final size:20
Alignment explanation
Indices: 585281--585374 Score: 116
Period size: 20 Copynumber: 4.7 Consensus size: 20
585271 TTTTCTTAAT
*
585281 TCGCAATGCTAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* ** *
585301 TCGCAACGCGAATTTGGAAAA
1 TCGCAATGCGAA-TACGTAAA
* *
585322 TCGTAATGCGATTACGTAAA
1 TCGCAATGCGAATACGTAAA
585342 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
585362 TCGCAATGCGAAT
1 TCGCAATGCGAAT
585375 CTGACTATCG
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 46 0.77
21 14 0.23
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.23
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:585593 original size:22 final size:21
Alignment explanation
Indices: 585571--585629 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 21
585561 GACATCCGTC
585571 CCCATCTCCGACGAAATCAGT
1 CCCATCTCCGACGAAATCAGT
* *
585592 -CC-TC-ACGACGATATCAGT
1 CCCATCTCCGACGAAATCAGT
*
585610 CTCCATCTCCGGCGAAATCA
1 C-CCATCTCCGACGAAATCA
585630 TTCACGGTCA
Statistics
Matches: 29, Mismatches: 5, Indels: 7
0.71 0.12 0.17
Matches are distributed among these distances:
18 12 0.41
19 2 0.07
20 4 0.14
21 2 0.07
22 9 0.31
ACGTcount: A:0.27, C:0.37, G:0.15, T:0.20
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCAGT
Found at i:586037 original size:20 final size:20
Alignment explanation
Indices: 585966--586053 Score: 97
Period size: 20 Copynumber: 4.5 Consensus size: 20
585956 GATTCTGTCA
585966 TTGCGATTTTCA-TTTCGCG
1 TTGCGATTTTCATTTTCGCG
** **
585985 TTGCGATAGTCAAATTCGCG
1 TTGCGATTTTCATTTTCGCG
** *
586005 TTGCGATAGTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
*
586025 TTGCGATTTTCATTTTCGTG
1 TTGCGATTTTCATTTTCGCG
586045 TTGCGATTT
1 TTGCGATTT
586054 AAAGTTTCAG
Statistics
Matches: 60, Mismatches: 8, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
19 10 0.17
20 50 0.83
ACGTcount: A:0.15, C:0.17, G:0.23, T:0.45
Consensus pattern (20 bp):
TTGCGATTTTCATTTTCGCG
Found at i:586061 original size:20 final size:20
Alignment explanation
Indices: 586018--586061 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
586008 CGATAGTCAT
** *
586018 TTTCGTGTTGCGATTTTCAT
1 TTTCGTGTTGCGATTTAAAG
586038 TTTCGTGTTGCGATTTAAAG
1 TTTCGTGTTGCGATTTAAAG
586058 TTTC
1 TTTC
586062 AGAAACTATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.14, C:0.14, G:0.20, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGATTTAAAG
Found at i:587869 original size:20 final size:20
Alignment explanation
Indices: 587844--587967 Score: 179
Period size: 20 Copynumber: 6.5 Consensus size: 20
587834 ATAATAGTTT
587844 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
587864 ACTATCGCAACGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
587884 ACTATCGCAA--CG-AGA-G
1 ACTATCGCAATGCGAAAATG
587900 A--ATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
*
587918 ACTATCGCAATGTGAAAATG
1 ACTATCGCAATGCGAAAATG
587938 ACTATCGCAATGCGAAAATG
1 ACTATCGCAATGCGAAAATG
587958 ACTATCGCAA
1 ACTATCGCAA
587968 CGAAAGAATC
Statistics
Matches: 93, Mismatches: 5, Indels: 12
0.85 0.05 0.11
Matches are distributed among these distances:
14 7 0.08
16 4 0.04
17 4 0.04
18 4 0.04
20 74 0.80
ACGTcount: A:0.40, C:0.21, G:0.20, T:0.19
Consensus pattern (20 bp):
ACTATCGCAATGCGAAAATG
Found at i:587913 original size:34 final size:34
Alignment explanation
Indices: 587867--587988 Score: 163
Period size: 34 Copynumber: 3.4 Consensus size: 34
587857 GAAAATGACT
* *
587867 ATCGCAACGCGAAAATGACTATCGCAACGAGAGA
1 ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
*
587901 ATCGCAATGCGAAAATGACTATCGCAATGTGAAAATGA
1 ATCGCAATGCGAAAATGACTATCGCAA--CG-AAA-GA
587939 CTATCGCAATGCGAAAATGACTATCGCAACGAAAGA
1 --ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
587975 ATCGCAATGCGAAA
1 ATCGCAATGCGAAA
587989 TGAAAATCGC
Statistics
Matches: 78, Mismatches: 4, Indels: 12
0.83 0.04 0.13
Matches are distributed among these distances:
34 40 0.51
36 3 0.04
37 5 0.06
38 3 0.04
40 27 0.35
ACGTcount: A:0.42, C:0.20, G:0.21, T:0.16
Consensus pattern (34 bp):
ATCGCAATGCGAAAATGACTATCGCAACGAAAGA
Found at i:587965 original size:74 final size:74
Alignment explanation
Indices: 587844--587988 Score: 263
Period size: 74 Copynumber: 2.0 Consensus size: 74
587834 ATAATAGTTT
*
587844 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAGAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
587909 GCGAAAATG
66 GCGAAAATG
* *
587918 ACTATCGCAATGTGAAAATGACTATCGCAATGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
1 ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
587983 GCGAAA
66 GCGAAA
587989 TGAAAATCGC
Statistics
Matches: 68, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
74 68 1.00
ACGTcount: A:0.41, C:0.21, G:0.21, T:0.17
Consensus pattern (74 bp):
ACTATCGCAATGCGAAAATGACTATCGCAACGCGAAAATGACTATCGCAACGAAAGAATCGCAAT
GCGAAAATG
Found at i:588039 original size:20 final size:20
Alignment explanation
Indices: 588014--588078 Score: 112
Period size: 20 Copynumber: 3.2 Consensus size: 20
588004 GATTCTCTCG
**
588014 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
588034 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
588054 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
588074 TTGCG
1 TTGCG
588079 CTTTTGTTGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 43 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.37
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:588109 original size:33 final size:33
Alignment explanation
Indices: 587995--588130 Score: 92
Period size: 33 Copynumber: 3.9 Consensus size: 33
587985 GAAATGAAAA
* * ** *
587995 TCGCATTACGATTCTCTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATTGTCTCGTTGCGATTTTC-ATT
* **
588029 TCGCATTGCGATAGTCATTTTCGCATTGCGATAGTCATTT
1 TCGCATTGCGATTGTC----TCG--TTGCGATTTTCA-TT
* * * *
588069 TCGCATTGCGCTTTTGTTGTTGCGATTTTCATT
1 TCGCATTGCGATTGTCTCGTTGCGATTTTCATT
588102 TCGCATTGCGATTGTCTCGTTGCGATTTT
1 TCGCATTGCGATTGTCTCGTTGCGATTTT
588131 AAGTTTCAGA
Statistics
Matches: 80, Mismatches: 15, Indels: 15
0.73 0.14 0.14
Matches are distributed among these distances:
33 27 0.34
34 23 0.29
36 2 0.03
38 3 0.04
39 1 0.01
40 24 0.30
ACGTcount: A:0.16, C:0.21, G:0.21, T:0.43
Consensus pattern (33 bp):
TCGCATTGCGATTGTCTCGTTGCGATTTTCATT
Found at i:588652 original size:18 final size:19
Alignment explanation
Indices: 588613--588654 Score: 59
Period size: 21 Copynumber: 2.2 Consensus size: 19
588603 CTCACCTGTC
588613 ATCGTTCAAGAGGCCTCCCCT
1 ATCGTTCAAGAGG-C-CCCCT
588634 ATCGTTCAAGAGG-CCCCT
1 ATCGTTCAAGAGGCCCCCT
588652 ATC
1 ATC
588655 ATCCCTCAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
21 13 0.62
ACGTcount: A:0.21, C:0.36, G:0.19, T:0.24
Consensus pattern (19 bp):
ATCGTTCAAGAGGCCCCCT
Found at i:590093 original size:14 final size:14
Alignment explanation
Indices: 590074--590109 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
590064 ATTGTTTAAT
590074 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
590088 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
590102 TGATTTGT
1 TGATTTGT
590110 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:590355 original size:33 final size:33
Alignment explanation
Indices: 590294--590377 Score: 105
Period size: 33 Copynumber: 2.5 Consensus size: 33
590284 CTAATTTCGC
* *
590294 GTTGTGATTTTCATTTTCGCATTGCGATTCACTA
1 GTTGCGATTTTCA-TTTCACATTGCGATTCACTA
* *
590328 GTTGCGATTTTCATTTCACATTGCGATTCTCTC
1 GTTGCGATTTTCATTTCACATTGCGATTCACTA
**
590361 GTTGCGATAGTCATTTC
1 GTTGCGATTTTCATTTC
590378 CGCGTTGCGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.17, C:0.20, G:0.18, T:0.45
Consensus pattern (33 bp):
GTTGCGATTTTCATTTCACATTGCGATTCACTA
Found at i:590385 original size:20 final size:20
Alignment explanation
Indices: 590360--590454 Score: 147
Period size: 20 Copynumber: 4.8 Consensus size: 20
590350 GCGATTCTCT
*
590360 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATAGTCAATTCCG
*
590380 CGTTGCGATAGTCAATTCCA
1 CGTTGCGATAGTCAATTCCG
590400 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCG
*
590420 TGTTGCGATAGTCATATT-CG
1 CGTTGCGATAGTCA-ATTCCG
590440 CGTTGCGATAGTCAA
1 CGTTGCGATAGTCAA
590455 ATGAATGTCT
Statistics
Matches: 69, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
19 1 0.01
20 65 0.94
21 3 0.04
ACGTcount: A:0.21, C:0.22, G:0.24, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCG
Found at i:592900 original size:24 final size:24
Alignment explanation
Indices: 592866--592919 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
592856 CTGAAAAATC
592866 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* * *
592890 ATCAAAGTCCGGGTATTGACCAAT
1 ATCAAAATCCGAGTATTGACCAAG
592914 ATCAAA
1 ATCAAA
592920 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:593969 original size:31 final size:31
Alignment explanation
Indices: 593931--594024 Score: 145
Period size: 31 Copynumber: 3.0 Consensus size: 31
593921 CCCGAAGGAC
* * *
593931 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
593962 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
593993 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
594024 C
1 C
594025 CCTCGACCCT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
31 58 0.98
32 1 0.02
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:594638 original size:19 final size:19
Alignment explanation
Indices: 594614--594668 Score: 110
Period size: 19 Copynumber: 2.9 Consensus size: 19
594604 TTTCATTTAG
594614 GGGGAATCGATACCCCCCA
1 GGGGAATCGATACCCCCCA
594633 GGGGAATCGATACCCCCCA
1 GGGGAATCGATACCCCCCA
594652 GGGGAATCGATACCCCC
1 GGGGAATCGATACCCCC
594669 TGAACATACT
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:0.25, C:0.36, G:0.27, T:0.11
Consensus pattern (19 bp):
GGGGAATCGATACCCCCCA
Found at i:595367 original size:8 final size:8
Alignment explanation
Indices: 595354--595380 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
595344 CGAACAAATC
595354 ATTAAACT
1 ATTAAACT
595362 ATTAAACT
1 ATTAAACT
595370 ATTAAACT
1 ATTAAACT
595378 ATT
1 ATT
595381 CTACTTTAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.48, C:0.11, G:0.00, T:0.41
Consensus pattern (8 bp):
ATTAAACT
Found at i:596619 original size:22 final size:22
Alignment explanation
Indices: 596578--596658 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
596568 CTCGTATAAA
*
596578 TGCACCGAAGTACCCCGTAGAAT
1 TGCACCGAAGT-GCCCGTAGAAT
596601 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
596623 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
596645 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
596659 ATATAATGAT
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
22 45 0.80
23 11 0.20
ACGTcount: A:0.26, C:0.30, G:0.26, T:0.19
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:596654 original size:13 final size:13
Alignment explanation
Indices: 596592--596654 Score: 52
Period size: 10 Copynumber: 5.5 Consensus size: 13
596582 CCGAAGTACC
596592 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
596605 CC---GAAGTGC-
1 CCGTAGAATTGCA
596614 CCGTAGAATTGCA
1 CCGTAGAATTGCA
*
596627 CC---GAAGTGC-
1 CCGTAGAATTGCA
596636 CCGTAGAATTGCA
1 CCGTAGAATTGCA
596649 CCGTAG
1 CCGTAG
596655 TGCCATATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 16
0.66 0.07 0.28
Matches are distributed among these distances:
9 4 0.11
10 12 0.32
12 12 0.32
13 10 0.26
ACGTcount: A:0.27, C:0.27, G:0.27, T:0.19
Consensus pattern (13 bp):
CCGTAGAATTGCA
Found at i:596991 original size:29 final size:29
Alignment explanation
Indices: 596958--597029 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
596948 TTTTCTGCAT
**
596958 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
596987 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
597016 ATTCATGTCATGTA
1 ATTCATGTCATGTA
597030 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:597492 original size:21 final size:21
Alignment explanation
Indices: 597462--597504 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
597452 ATCATATTCG
* *
597462 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
597483 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
597504 T
1 T
597505 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:597504 original size:67 final size:67
Alignment explanation
Indices: 597333--597482 Score: 230
Period size: 67 Copynumber: 2.2 Consensus size: 67
597323 TTTTCTCATG
* *
597333 GGGGAATCGGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGAT
1 GGGGTATCGGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGAT
*
597398 GAG
65 GAA
* * *
597401 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTG
1 GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGATG
597465 AA
66 AA
597467 GGGGTATCGGTTCCCC
1 GGGGTATCGGTTCCCC
597483 TTGAATGGGT
Statistics
Matches: 76, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
66 27 0.36
67 38 0.50
68 11 0.14
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (67 bp):
GGGGTATCGGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGATG
AA
Found at i:603589 original size:22 final size:22
Alignment explanation
Indices: 603548--603628 Score: 135
Period size: 22 Copynumber: 3.6 Consensus size: 22
603538 CTCGTATAAA
603548 TGCACCGAAGTGCCCCGTAGAAT
1 TGCACCGAAGTG-CCCGTAGAAT
603571 TGCACCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
603593 TGCATCGAAGTGCCCGTAGAAT
1 TGCACCGAAGTGCCCGTAGAAT
*
603615 TGCACCGTAGTGCC
1 TGCACCGAAGTGCC
603629 ATATAATGAT
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
22 43 0.78
23 12 0.22
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (22 bp):
TGCACCGAAGTGCCCGTAGAAT
Found at i:603963 original size:29 final size:29
Alignment explanation
Indices: 603930--604001 Score: 117
Period size: 29 Copynumber: 2.5 Consensus size: 29
603920 TTTTCTGCAT
**
603930 ATTCATGTCATGTAATACATATAATATGA
1 ATTCATGTCATGTAATACATATAATACAA
*
603959 ATTCATGTCATGTAATACATTTAATACAA
1 ATTCATGTCATGTAATACATATAATACAA
603988 ATTCATGTCATGTA
1 ATTCATGTCATGTA
604002 TCATAATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.39, C:0.12, G:0.10, T:0.39
Consensus pattern (29 bp):
ATTCATGTCATGTAATACATATAATACAA
Found at i:604463 original size:21 final size:21
Alignment explanation
Indices: 604433--604475 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
604423 ATCATATTCG
* *
604433 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
604454 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
604475 T
1 T
604476 AGCCCGAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.16, C:0.26, G:0.28, T:0.30
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:604475 original size:67 final size:67
Alignment explanation
Indices: 604312--604453 Score: 223
Period size: 67 Copynumber: 2.1 Consensus size: 67
604302 TGGGGGAATT
* *
604312 GGTTCCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATTTCATATACGATGAGGGGGT
1 GGTT-CCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGATGAAGGGGT
604377 ATC
65 ATC
* * *
604380 GGTTCCCCCCTGGGGGTATCGATTCCCCTCTAGCATTCTGGAA-ATCATATTCGTTGAAGGGGTA
1 GGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGATGAAGGGGTA
604444 TC
66 TC
604446 GGTTCCCC
1 GGTTCCCC
604454 TTGAATGGGT
Statistics
Matches: 69, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
66 27 0.39
67 38 0.55
68 4 0.06
ACGTcount: A:0.18, C:0.27, G:0.26, T:0.29
Consensus pattern (67 bp):
GGTTCCCCCCTGGGGGTATCGATTCCCCTCAAGCATTCTGGAATATCATATACGATGAAGGGGTA
TC
Found at i:607627 original size:31 final size:31
Alignment explanation
Indices: 607589--607713 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
607579 CCCGAAGGAC
* * *
607589 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
607620 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
607651 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
607682 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
607713 C
1 C
607714 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:609848 original size:20 final size:19
Alignment explanation
Indices: 609835--609981 Score: 141
Period size: 20 Copynumber: 7.3 Consensus size: 19
609825 CAGAATCTCG
*
609835 TTGCGATTTACAGATTCGCA
1 TTGCGATTTAC-GAATCGCA
*
609855 TTGCGATTTACGTATTCGCA
1 TTGCGATTTACG-AATCGCA
*
609875 TTGCGATTTATGTAATCGCA
1 TTGCGATTTACG-AATCGCA
609895 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACG-AATCGCA
609915 TTGCGATTTACGTAATCGCA
1 TTGCGATTTACG-AATCGCA
* * * *
609935 TTACGATTTTCCAAATTCGCG
1 TTGCGA-TTTACGAA-TCGCA
* *
609956 TTGAGATTTACGTATTCGCA
1 TTGCGATTTACG-AATCGCA
609976 TTGCGA
1 TTGCGA
609982 ATTAGGAAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
19 1 0.01
20 95 0.87
21 13 0.12
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (19 bp):
TTGCGATTTACGAATCGCA
Found at i:609879 original size:40 final size:40
Alignment explanation
Indices: 609835--609981 Score: 179
Period size: 40 Copynumber: 3.6 Consensus size: 40
609825 CAGAATCTCG
*
609835 TTGCGATTTACAG-ATTCGCATTGCGATTTACGTATTCGCA
1 TTGCGATTTAC-GTAATCGCATTGCGATTTACGTATTCGCA
* *
609875 TTGCGATTTATGTAATCGCATTGCGATTTACGTAATCGCA
1 TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
* * ** *
609915 TTGCGATTTACGTAATCGCATTACGATTTTCCAAATTCGCG
1 TTGCGATTTACGTAATCGCATTGCGA-TTTACGTATTCGCA
* *
609956 TTGAGATTTACGTATTCGCATTGCGA
1 TTGCGATTTACGTAATCGCATTGCGA
609982 ATTAGGAAAA
Statistics
Matches: 92, Mismatches: 13, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
39 1 0.01
40 59 0.64
41 32 0.35
ACGTcount: A:0.24, C:0.19, G:0.20, T:0.37
Consensus pattern (40 bp):
TTGCGATTTACGTAATCGCATTGCGATTTACGTATTCGCA
Found at i:616665 original size:22 final size:21
Alignment explanation
Indices: 616635--616680 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 21
616625 TTGAACGTCA
*
616635 TTTTTAATGGAATGTTTCATT
1 TTTTTAATGGAATATTTCATT
*
616656 TTTTTCAATGGAATATTTCGTT
1 TTTTT-AATGGAATATTTCATT
616678 TTT
1 TTT
616681 GTTTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 5 0.23
22 17 0.77
ACGTcount: A:0.22, C:0.07, G:0.13, T:0.59
Consensus pattern (21 bp):
TTTTTAATGGAATATTTCATT
Found at i:617000 original size:2 final size:2
Alignment explanation
Indices: 616993--617018 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
616983 AAACCAATTA
616993 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
617019 TTCTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:623764 original size:2 final size:2
Alignment explanation
Indices: 623757--623784 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
623747 TATTTGTATC
623757 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG
623785 ACAAAGGGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (2 bp):
TG
Found at i:626081 original size:58 final size:57
Alignment explanation
Indices: 625991--626106 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 57
625981 AAATAAGTTT
625991 AATTAAAATATTTATGGATATATCAGGTAATGTATCTAGAATTTGATTTCATTTTAAA
1 AATTAAAATATTTATGGATATATCAGGTAATGTATCTAGAATTTGATTTCA-TTTAAA
*
626049 AATTAAAATATTTATGGATATA-CAAGGTAATGTATCTAGACTTTGATTTCATTTAAA
1 AATTAAAATATTTATGGATATATC-AGGTAATGTATCTAGAATTTGATTTCATTTAAA
626106 A
1 A
626107 TATTTATGGA
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
57 8 0.14
58 48 0.86
ACGTcount: A:0.41, C:0.06, G:0.12, T:0.41
Consensus pattern (57 bp):
AATTAAAATATTTATGGATATATCAGGTAATGTATCTAGAATTTGATTTCATTTAAA
Found at i:628810 original size:24 final size:24
Alignment explanation
Indices: 628762--628816 Score: 62
Period size: 24 Copynumber: 2.3 Consensus size: 24
628752 TAATTAAACT
*
628762 TAATTTTAAAATTATATTCATTAA
1 TAATTTTAAAATTATAATCATTAA
628786 TAATTTTAATAA-TATAAT-ATGTAA
1 TAATTTTAA-AATTATAATCAT-TAA
628810 T-ATTTTA
1 TAATTTTA
628817 TTACATTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
23 8 0.29
24 18 0.64
25 2 0.07
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TAATTTTAAAATTATAATCATTAA
Found at i:629062 original size:14 final size:14
Alignment explanation
Indices: 629043--629081 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
629033 AAAACAATAT
629043 AATTTATTTTATAA
1 AATTTATTTTATAA
*
629057 AATTTATTTTCTAA
1 AATTTATTTTATAA
*
629071 GATTTATTTTA
1 AATTTATTTTA
629082 GTGCATAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.36, C:0.03, G:0.03, T:0.59
Consensus pattern (14 bp):
AATTTATTTTATAA
Found at i:634999 original size:24 final size:24
Alignment explanation
Indices: 634972--635017 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
634962 TAAATTTTGG
*
634972 TTAATTAATACCTGAACAAAATCT
1 TTAACTAATACCTGAACAAAATCT
*
634996 TTAACTAATACCTGACCAAAAT
1 TTAACTAATACCTGAACAAAAT
635018 TATTTTGGCC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.46, C:0.20, G:0.04, T:0.30
Consensus pattern (24 bp):
TTAACTAATACCTGAACAAAATCT
Found at i:639701 original size:20 final size:20
Alignment explanation
Indices: 639607--639975 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
639597 GATTTTCCAT
* ** *
639607 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
639627 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
639647 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
639667 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
639687 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
639707 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
639727 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
639747 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
639767 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
639787 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
639807 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
639827 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
639847 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
639867 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
639887 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
639907 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
639927 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
639947 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
639967 AATCACAAC
1 AATCGCAAC
639976 ACTGAAATTT
Statistics
Matches: 305, Mismatches: 36, Indels: 16
0.85 0.10 0.04
Matches are distributed among these distances:
19 3 0.01
20 299 0.98
21 3 0.01
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:640688 original size:24 final size:24
Alignment explanation
Indices: 640649--640695 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
640639 AAATTTGGTC
640649 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
640673 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
640696 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:640887 original size:12 final size:12
Alignment explanation
Indices: 640870--640894 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
640860 ATATAATCCT
640870 GAAGAAGAAAAA
1 GAAGAAGAAAAA
640882 GAAGAAGAAAAA
1 GAAGAAGAAAAA
640894 G
1 G
640895 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:643270 original size:14 final size:14
Alignment explanation
Indices: 643251--643305 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
643241 CGGAAATGAA
643251 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
643265 AATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-GAG
643284 AATCGCAACGAGAG
1 AATCGCAACGAGAG
643298 AATCGCAA
1 AATCGCAA
643306 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:643285 original size:33 final size:33
Alignment explanation
Indices: 643198--643501 Score: 276
Period size: 33 Copynumber: 8.8 Consensus size: 33
643188 CGGAAAATAC
* *
643198 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
643231 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
*
643265 AATCGCAATGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* *
643298 AATCGCAATGCGAAATGAAAATCGCAATGCG-A
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAA
* ** *
643330 AAT-GAAAAT-CGAACCGACATAATCGCAATGCGAAATTAA
1 AATCG-CAATGCGAAATGA-A-AATCGCAA--CG--A-GAA
* *
643369 AATCGCAATACGAAATGAAAATCGCAACACGGAAAATA
1 AATCGCAATGCGAAATGAAAATCGC-A-AC-G-AGA-A
* *
643407 CAATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 -AATCGCAATGCGAAATGAAAATCGCAACGA-GAA
*
643441 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCGCAACGAGAA
643475 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
643502 TGCGAAATGA
Statistics
Matches: 227, Mismatches: 23, Indels: 42
0.78 0.08 0.14
Matches are distributed among these distances:
31 7 0.03
32 7 0.03
33 95 0.42
34 60 0.26
35 4 0.02
37 3 0.01
38 11 0.05
39 32 0.14
40 8 0.04
ACGTcount: A:0.47, C:0.20, G:0.20, T:0.13
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAA
Found at i:643329 original size:52 final size:52
Alignment explanation
Indices: 643265--643605 Score: 278
Period size: 52 Copynumber: 6.5 Consensus size: 52
643255 GCAACGAGAG
643265 AATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGA-AATCGCAATGCGAAATGAA
* *
643317 AATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAAAATCGCAACCGAGA-AATCGCAATGCGAAATGAA
* * *
643369 AATCGCAATACGAAATGAAAATCGCAACACGGAAAATACAATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAAC-C-G---AGA-AATCGCAATGCGAAATGAA
* * * * *
643427 AATCCCAA--C---ATGAAAATCGCAATGCG-GAAAT-GAAAAT-CGCAACGAGA
1 AATCGCAATGCGAAATGAAAATCGCAA-CCGAGAAATCG-CAATGCGAAATGA-A
* * * * *
643474 GAATCGCAATGCGAAATGAAAATCGCAA-TGCGAAAT-GAAAAT-CGCAACGAGA
1 -AATCGCAATGCGAAATGAAAATCGCAACCGAGAAATCG-CAATGCGAAATGA-A
* *
643526 GAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAAATTAA
1 -AATCGCAATGCGAAATGAAAATCGCAACCGAGA-AATCGCAATGCGAAATGAA
*
643579 AATCGCAATACGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
643606 TGCGAAATTA
Statistics
Matches: 242, Mismatches: 25, Indels: 43
0.78 0.08 0.14
Matches are distributed among these distances:
46 7 0.03
47 6 0.02
48 8 0.03
50 1 0.00
51 5 0.02
52 141 0.58
53 39 0.16
54 7 0.03
55 1 0.00
56 1 0.00
58 26 0.11
ACGTcount: A:0.47, C:0.19, G:0.19, T:0.14
Consensus pattern (52 bp):
AATCGCAATGCGAAATGAAAATCGCAACCGAGAAATCGCAATGCGAAATGAA
Found at i:643488 original size:177 final size:177
Alignment explanation
Indices: 643231--643550 Score: 538
Period size: 177 Copynumber: 1.8 Consensus size: 177
643221 CCAACATGAA
* * *
643231 AATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAG
1 AATCGCAACGCGGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
*
643296 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATG
66 AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGACAGAATCGCAATG
*
643360 CGAAATTAAAATCGCAATACGAAATGAAAATCGCAACACGGAAAATAC
130 CGAAATGAAAATCGCAATACGAAATGAAAATCGCAACACGGAAAATAC
643408 AATCGCAACGC-GAAATGAAAATCCCAAC-ATGAAAATCGCAATGCGGAAATGAAAATCGCAACG
1 AATCGCAACGCGGAAATGAAAATCCCAACGA-GAAAATCGCAATGC-GAAATGAAAATCGCAACG
*
643471 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
64 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAAT
643536 GCGAAATGAAAATCG
129 GCGAAATGAAAATCG
643551 AACCGACATA
Statistics
Matches: 134, Mismatches: 6, Indels: 6
0.92 0.04 0.04
Matches are distributed among these distances:
175 1 0.01
176 29 0.22
177 102 0.76
178 2 0.01
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.14
Consensus pattern (177 bp):
AATCGCAACGCGGAAATGAAAATCCCAACGAGAAAATCGCAATGCGAAATGAAAATCGCAACGAG
AGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGACAGAATCGCAATGC
GAAATGAAAATCGCAATACGAAATGAAAATCGCAACACGGAAAATAC
Found at i:643531 original size:33 final size:33
Alignment explanation
Indices: 643491--643613 Score: 149
Period size: 33 Copynumber: 3.6 Consensus size: 33
643481 AATGCGAAAT
643491 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
*
643524 GAGAATCGCAATGCGAAATGAAAATCG-AACCGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAA-CGA
* * *
643557 CATAATCGCAATGCGAAATTAAAATCGCAATACGAAA
1 GAAAATCGCAATGCGAAATGAAAATCGC-A-ACG--A
643594 TGAAAATCGCAATGCGAAAT
1 -GAAAATCGCAATGCGAAAT
643614 TATAAACGCA
Statistics
Matches: 77, Mismatches: 6, Indels: 9
0.84 0.07 0.10
Matches are distributed among these distances:
32 2 0.03
33 53 0.69
35 3 0.04
36 1 0.01
37 1 0.01
38 17 0.22
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (33 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:643541 original size:210 final size:210
Alignment explanation
Indices: 643179--643605 Score: 761
Period size: 210 Copynumber: 2.0 Consensus size: 210
643169 GCATTTGACT
643179 ATCGCAACACGGAAAATACAATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGG
1 ATCGCAACACGGAAAATACAATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGG
*
643244 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGC
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGC
*
643309 GAAATGAAAATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCG
131 GAAACGAAAATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCG
643374 CAATACGAAATGAAA
196 CAATACGAAATGAAA
643389 ATCGCAACACGGAAAATACAATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGG
1 ATCGCAACACGGAAAATACAATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGG
* *
643454 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA-AAT-GAAAAT-
66 AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-AAATG
*
643516 CGCAACGAGAGAATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAA
130 CGAAACGA-A-AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAA
643581 TCGCAATACGAAATGAAA
193 TCGCAATACGAAATGAAA
643599 ATCGCAA
1 ATCGCAA
643606 TGCGAAATTA
Statistics
Matches: 209, Mismatches: 5, Indels: 6
0.95 0.02 0.03
Matches are distributed among these distances:
208 7 0.03
209 7 0.03
210 195 0.93
ACGTcount: A:0.47, C:0.20, G:0.19, T:0.14
Consensus pattern (210 bp):
ATCGCAACACGGAAAATACAATCGCAACGCGAAATGAAAATCCCAACATGAAAATCGCAATGCGG
AAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGAAATGC
GAAACGAAAATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCG
CAATACGAAATGAAA
Found at i:643623 original size:19 final size:19
Alignment explanation
Indices: 643229--643629 Score: 217
Period size: 19 Copynumber: 22.8 Consensus size: 19
643219 TCCCAACATG
*
643229 AAAATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATT
*
643249 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATT
* *
643263 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATT
*
643282 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATT
* *
643296 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATT
*
643315 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATT
* *
643334 AAAATCG-AA-CCGACA-T
1 AAAATCGCAATGCGAAATT
643350 --AATCGCAATGCGAAATT
1 AAAATCGCAATGCGAAATT
* *
643367 AAAATCGCAATACGAAATG
1 AAAATCGCAATGCGAAATT
** *
643386 AAAATCGCAACACGGAAAAT
1 AAAATCGCAATGC-GAAATT
* * *
643406 ACAATCGCAACGCGAAATG
1 AAAATCGCAATGCGAAATT
* *
643425 AAAATCCCAA--C---ATG
1 AAAATCGCAATGCGAAATT
*
643439 AAAATCGCAATGCGGAAATG
1 AAAATCGCAATGC-GAAATT
*
643459 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATT
* *
643473 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATT
*
643492 AAAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATT
*
643511 AAAATCGCAA--CG--A-G
1 AAAATCGCAATGCGAAATT
* *
643525 AGAATCGCAATGCGAAATG
1 AAAATCGCAATGCGAAATT
* *
643544 AAAATCG-AA-CCGACA-T
1 AAAATCGCAATGCGAAATT
643560 --AATCGCAATGCGAAATT
1 AAAATCGCAATGCGAAATT
* *
643577 AAAATCGCAATACGAAATG
1 AAAATCGCAATGCGAAATT
643596 AAAATCGCAATGCGAAATT
1 AAAATCGCAATGCGAAATT
*
643615 ATAAA-CGCATTGCGA
1 A-AAATCGCAATGCGA
643630 TTTTCATTTC
Statistics
Matches: 308, Mismatches: 35, Indels: 77
0.73 0.08 0.18
Matches are distributed among these distances:
14 62 0.20
15 8 0.03
16 17 0.06
17 17 0.06
18 10 0.03
19 153 0.50
20 41 0.13
ACGTcount: A:0.47, C:0.19, G:0.20, T:0.15
Consensus pattern (19 bp):
AAAATCGCAATGCGAAATT
Found at i:643710 original size:19 final size:19
Alignment explanation
Indices: 643620--643702 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
643610 AAATTATAAA
643620 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
643639 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
643659 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
643675 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
643692 CGCATTGCGAT
1 CGCATTGCGAT
643703 AGTCATTTTT
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:643944 original size:93 final size:93
Alignment explanation
Indices: 643785--644294 Score: 1006
Period size: 93 Copynumber: 5.5 Consensus size: 93
643775 AAGCACAAAT
643785 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
643850 CAAAGACAAATACTATTTCACAGTGTTA
66 CAAAGACAAATACTATTTCACAGTGTTA
643878 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
643943 CAAAGACAAATA-TATTTCACAGTGTTA
66 CAAAGACAAATACTATTTCACAGTGTTA
643970 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
644035 CAAAGACAAATACTATTTCACAGTGTTA
66 CAAAGACAAATACTATTTCACAGTGTTA
644063 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
644128 CAAAGACAAATACTATTTCACAGTGTTA
66 CAAAGACAAATACTATTTCACAGTGTTA
644156 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
644221 CAAAGACAAATA-TATTTCACAGTGTTA
66 CAAAGACAAATACTATTTCACAGTGTTA
644248 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
644295 AAGCAATCTA
Statistics
Matches: 416, Mismatches: 0, Indels: 3
0.99 0.00 0.01
Matches are distributed among these distances:
92 154 0.37
93 262 0.63
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
CAAAGACAAATACTATTTCACAGTGTTA
Found at i:644097 original size:185 final size:186
Alignment explanation
Indices: 643785--644294 Score: 1006
Period size: 185 Copynumber: 2.8 Consensus size: 186
643775 AAGCACAAAT
643785 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
643850 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
66 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
643915 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTA
131 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTA
643970 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
644035 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
66 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
644100 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTA
131 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTA
644156 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
644221 CAAAGACAAATA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
66 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
644285 CAAATTTACT
131 CAAATTTACT
644295 AAGCAATCTA
Statistics
Matches: 324, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
185 232 0.72
186 92 0.28
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTA
Found at i:644282 original size:278 final size:278
Alignment explanation
Indices: 643785--644294 Score: 1020
Period size: 278 Copynumber: 1.8 Consensus size: 278
643775 AAGCACAAAT
643785 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
643850 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
66 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
643915 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACAC
131 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACAC
643980 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
196 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
644045 TACTATTTCACAGTGTTA
261 TACTATTTCACAGTGTTA
644063 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
1 AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
644128 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
66 CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
644193 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACAC
131 CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACAC
644258 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
196 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
644295 AAGCAATCTA
Statistics
Matches: 232, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
278 232 1.00
ACGTcount: A:0.46, C:0.19, G:0.13, T:0.22
Consensus pattern (278 bp):
AAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAA
CAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAA
CAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATATATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTA
Found at i:646018 original size:14 final size:14
Alignment explanation
Indices: 645999--646088 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
645989 TTGAAATGAA
645999 AATCGCAACGAGAG
1 AATCGCAACGAGAG
646013 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
646030 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
646046 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
646065 AATCGCAACGAGAG
1 AATCGCAACGAGAG
646079 AATCGCAACG
1 AATCGCAACG
646089 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:646036 original size:33 final size:33
Alignment explanation
Indices: 645991--646105 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
645981 TCTTTTGGTT
645991 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
646024 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
646057 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
646090 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
646106 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:646037 original size:19 final size:18
Alignment explanation
Indices: 645998--646110 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
645988 GTTGAAATGA
645998 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
646013 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
646030 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
646046 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
646063 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
646079 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
646096 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
646111 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:646141 original size:14 final size:14
Alignment explanation
Indices: 646122--646176 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
646112 TTTGGTTTCG
646122 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
646136 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
646155 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
646169 CGTTGCGA
1 CGTTGCGA
646177 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:646339 original size:33 final size:33
Alignment explanation
Indices: 646297--646367 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
646287 AATACTAACT
*
646297 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
646330 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
646363 TGAAA
1 TGAAA
646368 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:646600 original size:22 final size:22
Alignment explanation
Indices: 646548--646602 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
646538 TGGTTGTGAG
**
646548 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
646570 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
646592 GGATTTCTTCG
1 GGATTTCTTCG
646603 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:646773 original size:20 final size:20
Alignment explanation
Indices: 646748--646941 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
646738 CTTTAAATAT
646748 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
646768 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
646790 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
646809 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
646829 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
646849 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
646869 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
646889 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
646909 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
646929 CGCGTTGCGATTT
1 CGCGTTGCGATTT
646942 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:646935 original size:60 final size:60
Alignment explanation
Indices: 646748--646941 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
646738 CTTTAAATAT
**
646748 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
646809 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
646869 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
646929 CGCGTTGCGATTT
1 CGCGTTGCGATTT
646942 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:646958 original size:21 final size:20
Alignment explanation
Indices: 646934--647010 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
646924 ATATTCGCGT
646934 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
646955 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
646975 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
646997 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
647011 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Done.