Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007838.1 Hibiscus syriacus cultivar Beakdansim tig00110187_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: 3429202
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:407219 original size:70 final size:70
Alignment explanation
Indices: 406965--407209 Score: 368
Period size: 70 Copynumber: 3.5 Consensus size: 70
406955 GTTTGATACG
*
406965 AGTATATCTACACATGACCTATTGTGCTCGAACTCATAAGTGAATGCTGGATACGAATGTGTTCT
1 AGTATATCTACACATGACCTATTGTACTCGAACTCATAAGTGAATGCTGGATACGAATGTGTTCT
407030 ACACA
66 ACACA
* * *
407035 AGTATATTTACACATGACCTATT-TGACTCAAACTCGTAAGTGAATGCTGGATACGAATGTGTT-
1 AGTATATCTACACATGACCTATTGT-ACTCGAACTCATAAGTGAATGCTGGATACGAATGTGTTC
* *
407098 TGATACG
65 T-ACACA
*
407105 AGTATTATCTACACATGACCTATTGTACTCGAACTCATAAGTGAATGCTGTATACGAATGTGTTC
1 AGTA-TATCTACACATGACCTATTGTACTCGAACTCATAAGTGAATGCTGGATACGAATGTGTTC
407170 TACACA
65 TACACA
* *
407176 AGTATATCTACATATGACCTATTTTACTCGAACT
1 AGTATATCTACACATGACCTATTGTACTCGAACT
407210 TGGGTGTGAA
Statistics
Matches: 156, Mismatches: 14, Indels: 10
0.87 0.08 0.06
Matches are distributed among these distances:
69 2 0.01
70 92 0.59
71 60 0.38
72 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.33
Consensus pattern (70 bp):
AGTATATCTACACATGACCTATTGTACTCGAACTCATAAGTGAATGCTGGATACGAATGTGTTCT
ACACA
Found at i:417636 original size:40 final size:40
Alignment explanation
Indices: 417581--417660 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
417571 TGTAATGCTT
417581 CCTTTTAGAATTTTTAATATGGAAATTACATATGATGCCA
1 CCTTTTAGAATTTTTAATATGGAAATTACATATGATGCCA
417621 CCTTTTAGAATTTTTAATATGGAAATTACATATGATGCCA
1 CCTTTTAGAATTTTTAATATGGAAATTACATATGATGCCA
417661 AAAGTAAATG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.40
Consensus pattern (40 bp):
CCTTTTAGAATTTTTAATATGGAAATTACATATGATGCCA
Found at i:425823 original size:24 final size:22
Alignment explanation
Indices: 425787--425832 Score: 56
Period size: 24 Copynumber: 2.0 Consensus size: 22
425777 AAGTGAATAT
425787 GAGAAAGGACAAAAGAAGAAAGAG
1 GAGAAAGGAC-AAAGAA-AAAGAG
**
425811 GAGAAAGTTCAAAGAAAAAGAG
1 GAGAAAGGACAAAGAAAAAGAG
425833 AAAAGAGACG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 6 0.30
23 6 0.30
24 8 0.40
ACGTcount: A:0.61, C:0.04, G:0.30, T:0.04
Consensus pattern (22 bp):
GAGAAAGGACAAAGAAAAAGAG
Found at i:426065 original size:61 final size:60
Alignment explanation
Indices: 425949--426123 Score: 178
Period size: 61 Copynumber: 2.9 Consensus size: 60
425939 TTATAATTCC
* * * * *
425949 CATTTTAAATTAGTCTCT--AACTTTATAAACATTCCAATTTCATCCTCAAATTATGA-TTGT
1 CATTCTAAATTAGTCTCTAAAACTTT-TAAAAATTTCAATTTCATCC-CAAACTATGACAT-T
* * * * *
426009 CGTTCTAAATTAGTC-CTTCAAACTTTTGAATATTTTAATTTCATCTCCAAACTATGACATT
1 CATTCTAAATTAGTCTC-TAAAACTTTTAAAAATTTCAATTTCATC-CCAAACTATGACATT
*
426070 CATTCTAAATTAGTCTCTAAAATTTTTAAAAATTTCAATTTCATCCCAAACTAT
1 CATTCTAAATTAGTCTCTAAAACTTTTAAAAATTTCAATTTCATCCCAAACTAT
426124 ATACAATAAC
Statistics
Matches: 95, Mismatches: 14, Indels: 12
0.79 0.12 0.10
Matches are distributed among these distances:
59 1 0.01
60 23 0.24
61 62 0.65
62 9 0.09
ACGTcount: A:0.34, C:0.19, G:0.05, T:0.42
Consensus pattern (60 bp):
CATTCTAAATTAGTCTCTAAAACTTTTAAAAATTTCAATTTCATCCCAAACTATGACATT
Found at i:430684 original size:16 final size:17
Alignment explanation
Indices: 430659--430709 Score: 52
Period size: 16 Copynumber: 3.1 Consensus size: 17
430649 CCTCTCAATT
*
430659 TTTTTGATTTAAT-TAA
1 TTTTTAATTTAATGTAA
* *
430675 TTTTTAATTTTATGTTA
1 TTTTTAATTTAATGTAA
*
430692 TTTTTAA-TTAATGAAA
1 TTTTTAATTTAATGTAA
430708 TT
1 TT
430710 AAACACTATT
Statistics
Matches: 28, Mismatches: 6, Indels: 2
0.78 0.17 0.06
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
TTTTTAATTTAATGTAA
Found at i:439549 original size:21 final size:21
Alignment explanation
Indices: 439525--439670 Score: 136
Period size: 21 Copynumber: 7.1 Consensus size: 21
439515 GCAAATTCGT
439525 GTTGCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
439546 GTTGAAAATCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* **
439567 GTTGAAAATCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
439587 TTTCCATTTCGCGTTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
439607 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
* * *
439628 GTTGAAATTCGCATTGCGAT-
1 GTTGCATTTCGCGTTGCGATA
* *
439648 TTTCCATTTCGCGTTGCGATA
1 GTTGCATTTCGCGTTGCGATA
439669 GT
1 GT
439671 CTACAGTTGT
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
20 50 0.48
21 54 0.52
ACGTcount: A:0.18, C:0.19, G:0.25, T:0.38
Consensus pattern (21 bp):
GTTGCATTTCGCGTTGCGATA
Found at i:439600 original size:20 final size:20
Alignment explanation
Indices: 439575--439667 Score: 132
Period size: 20 Copynumber: 4.6 Consensus size: 20
439565 TAGTTGAAAA
439575 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
439595 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** *
439615 TCGCGTTGCGATAGTTGAAAT
1 TCGCGTTGCGAT-TTTCCATT
*
439636 TCGCATTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
439656 TCGCGTTGCGAT
1 TCGCGTTGCGAT
439668 AGTCTACAGT
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
20 47 0.76
21 15 0.24
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.41
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:439639 original size:41 final size:41
Alignment explanation
Indices: 439529--439695 Score: 169
Period size: 41 Copynumber: 4.0 Consensus size: 41
439519 ATTCGTGTTG
* * *
439529 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATAGTTG
1 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGAT-TTTC
* ** * ** *
439571 AAAATCGCGTTGCGAT-TTTCCATTTCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
*
439611 CATTTCGCGTTGCGATAGTTGAAATTCGCATTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
*
439652 CATTTCGCGTTGCGATAGTCT-ACAGTT-GTCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGT-TGA-AATTCG-CGTTGCGATTTTC
439694 CA
1 CA
439696 AATTCGTTTC
Statistics
Matches: 101, Mismatches: 20, Indels: 8
0.78 0.16 0.06
Matches are distributed among these distances:
40 15 0.15
41 55 0.54
42 31 0.31
ACGTcount: A:0.19, C:0.20, G:0.23, T:0.38
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAATTCGCGTTGCGATTTTC
Found at i:439687 original size:22 final size:22
Alignment explanation
Indices: 439659--439730 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
439649 TTCCATTTCG
439659 CGTTGCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
* * **
439681 CGTTGCGAT--TTTCCAAAT-T
1 CGTTGCGATAGTCTACAGTTGT
*
439700 CGTTTCGATAGTCTACAGTTGT
1 CGTTGCGATAGTCTACAGTTGT
439722 CGTTGCGAT
1 CGTTGCGAT
439731 TTTCCAAATT
Statistics
Matches: 37, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
19 9 0.24
20 5 0.14
21 5 0.14
22 18 0.49
ACGTcount: A:0.18, C:0.19, G:0.24, T:0.39
Consensus pattern (22 bp):
CGTTGCGATAGTCTACAGTTGT
Found at i:439709 original size:41 final size:41
Alignment explanation
Indices: 439641--439750 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
439631 GAAATTCGCA
*
439641 TTGCGATTTTCC-ATTTCGCGTTGCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCCAAATT--CGTTGCGATAGTCTACAGTTGTCG
*
439683 TTGCGATTTTCCAAATTCGTTTCGATAGTCTACAGTTGTCG
1 TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCG
*
439724 TTGCGATTTTCCAAATTCGTTGTGATA
1 TTGCGATTTTCCAAATTCGTTGCGATA
439751 ATTAAAAAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
41 48 0.76
42 12 0.19
43 3 0.05
ACGTcount: A:0.18, C:0.19, G:0.21, T:0.42
Consensus pattern (41 bp):
TTGCGATTTTCCAAATTCGTTGCGATAGTCTACAGTTGTCG
Found at i:439745 original size:19 final size:19
Alignment explanation
Indices: 439680--439745 Score: 60
Period size: 19 Copynumber: 3.3 Consensus size: 19
439670 TCTACAGTTG
439680 TCGTTGCGATTTTCCAAAT
1 TCGTTGCGATTTTCCAAAT
* * * **
439699 TCGTTTCGATAGTCTACAGTT
1 TCGTTGCGAT--TTTCCAAAT
439720 GTCGTTGCGATTTTCCAAAT
1 -TCGTTGCGATTTTCCAAAT
439740 TCGTTG
1 TCGTTG
439746 TGATAATTAA
Statistics
Matches: 34, Mismatches: 10, Indels: 6
0.68 0.20 0.12
Matches are distributed among these distances:
19 15 0.44
20 5 0.15
21 5 0.15
22 9 0.26
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.42
Consensus pattern (19 bp):
TCGTTGCGATTTTCCAAAT
Found at i:439840 original size:6 final size:6
Alignment explanation
Indices: 439829--439904 Score: 117
Period size: 6 Copynumber: 13.5 Consensus size: 6
439819 GACACGTATT
439829 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
439877 ACC-CG ACC-CG ACC-CG ACC-CG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
439905 CGAATAATCA
Statistics
Matches: 70, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 25 0.36
6 45 0.64
ACGTcount: A:0.29, C:0.54, G:0.17, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:440094 original size:6 final size:6
Alignment explanation
Indices: 440073--440133 Score: 90
Period size: 6 Copynumber: 10.5 Consensus size: 6
440063 TCTCGTCTCG
* *
440073 GGTCG- GGTCG- GGTCGT GGTCGT GGTCGT GGTCAT GGTCAT GGTCGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT
440119 GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGT
440134 GTCTTCGACA
Statistics
Matches: 53, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
5 10 0.19
6 43 0.81
ACGTcount: A:0.03, C:0.16, G:0.49, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:440264 original size:20 final size:20
Alignment explanation
Indices: 440239--440311 Score: 74
Period size: 20 Copynumber: 3.6 Consensus size: 20
440229 ACTGTAGACT
440239 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
** ** *
440259 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGAAATGGAA-A
440280 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGGAAA
* *
440300 ACCACAACGCGA
1 ATCGCAACGCGA
440312 TTTTCAACTA
Statistics
Matches: 40, Mismatches: 12, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
20 25 0.62
21 15 0.38
ACGTcount: A:0.40, C:0.26, G:0.21, T:0.14
Consensus pattern (20 bp):
ATCGCAACGCGAAATGGAAA
Found at i:440281 original size:41 final size:41
Alignment explanation
Indices: 440236--440336 Score: 184
Period size: 41 Copynumber: 2.5 Consensus size: 41
440226 ACAACTGTAG
* *
440236 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
440277 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
440318 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
440337 CAACGCGAAT
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 58 1.00
ACGTcount: A:0.38, C:0.26, G:0.19, T:0.18
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAACCACAACGCGATTTTCA
Found at i:440340 original size:21 final size:21
Alignment explanation
Indices: 440236--440340 Score: 88
Period size: 21 Copynumber: 5.1 Consensus size: 21
440226 ACAACTGTAG
*
440236 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* ** *
440257 A-AATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
*
440277 ACTATCGCAACGCGAAATGGA
1 ACTATCGCAACGCGAAATGCA
* * * ** *
440298 A-AACCACAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGCA
440318 ACTATCGCAACGCGAAATGCA
1 ACTATCGCAACGCGAAATGCA
440339 AC
1 AC
440341 GCGAATTTTC
Statistics
Matches: 59, Mismatches: 23, Indels: 4
0.69 0.27 0.05
Matches are distributed among these distances:
20 28 0.47
21 31 0.53
ACGTcount: A:0.38, C:0.27, G:0.18, T:0.17
Consensus pattern (21 bp):
ACTATCGCAACGCGAAATGCA
Found at i:440428 original size:43 final size:41
Alignment explanation
Indices: 440369--440480 Score: 172
Period size: 43 Copynumber: 2.7 Consensus size: 41
440359 AGATCGCGTT
*
440369 GCGATTT-CAACTATCGCAACGCGAAATGGAAAATCGCAAC
1 GCGATTTCCAACTATCGCAACGCGAAATGGAAAAACGCAAC
440409 GCGATCTCTCCAACTATCGCAACGCGAAATGGAAAAACGCAAC
1 GCGAT-T-TCCAACTATCGCAACGCGAAATGGAAAAACGCAAC
* *
440452 GCGATTTTCAACTATCGCAATGCGAAATG
1 GCGATTTCCAACTATCGCAACGCGAAATG
440481 CAACGTGAAT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
40 5 0.08
41 22 0.33
42 2 0.03
43 37 0.56
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (41 bp):
GCGATTTCCAACTATCGCAACGCGAAATGGAAAAACGCAAC
Found at i:440477 original size:144 final size:142
Alignment explanation
Indices: 440236--440509 Score: 460
Period size: 144 Copynumber: 1.9 Consensus size: 142
440226 ACAACTGTAG
*
440236 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCAACTATCGCAACGCGAAATGGAAAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAA
* *
440301 CCACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTTCGAT-GATGGAGATCG
66 ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAG-TGGAGATCG
440365 CGTTGCGATTTCA
130 CGTTGCGATTTCA
440378 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATCTCTCCAACTATCGCAACGCGAAATGGAA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGAT-T-TCCAACTATCGCAACGCGAAATGGAA
* * *
440443 AAACGCAACGCGATTTTCAACTATCGCAATGCGAAATGCAACGTGAATTTGCGATAGTGGAGATC
64 AAACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATC
440508 GC
129 GC
440510 AATGCGAATT
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
142 36 0.29
143 1 0.01
144 85 0.69
145 1 0.01
ACGTcount: A:0.34, C:0.24, G:0.22, T:0.20
Consensus pattern (142 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTCCAACTATCGCAACGCGAAATGGAAAA
ACACAACGCGATTTTCAACTATCGCAACGCGAAATGCAACGCGAATTTGCGATAGTGGAGATCGC
GTTGCGATTTCA
Found at i:440484 original size:21 final size:21
Alignment explanation
Indices: 440376--440484 Score: 78
Period size: 20 Copynumber: 5.2 Consensus size: 21
440366 GTTGCGATTT
440376 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * ** *
440397 GAA-AATCGCAACGCGATCTCTC
1 CAACTATCGCAACGCGA--AATG
440419 CAACTATCGCAACGCGAAATG
1 CAACTATCGCAACGCGAAATG
* * * ** *
440440 GAA-AAACGCAACGCGATTTT
1 CAACTATCGCAACGCGAAATG
*
440460 CAACTATCGCAATGCGAAATG
1 CAACTATCGCAACGCGAAATG
440481 CAAC
1 CAAC
440485 GTGAATTTGC
Statistics
Matches: 61, Mismatches: 23, Indels: 8
0.66 0.25 0.09
Matches are distributed among these distances:
20 26 0.43
21 20 0.33
22 3 0.05
23 12 0.20
ACGTcount: A:0.38, C:0.28, G:0.18, T:0.17
Consensus pattern (21 bp):
CAACTATCGCAACGCGAAATG
Found at i:441808 original size:21 final size:24
Alignment explanation
Indices: 441783--441842 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 24
441773 TATTTTTAAT
441783 TATATT-TTTTTATTTA-TT-TAC
1 TATATTCTTTTTATTTATTTATAC
*
441804 TATATTCCTTTTT-TTTATTTATAT
1 TATATT-CTTTTTATTTATTTATAC
*
441828 TATATTATTTTTATT
1 TATATTCTTTTTATT
441843 ATATAAATCT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
21 6 0.19
22 4 0.12
23 12 0.38
24 10 0.31
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (24 bp):
TATATTCTTTTTATTTATTTATAC
Found at i:441838 original size:22 final size:23
Alignment explanation
Indices: 441785--441844 Score: 59
Period size: 26 Copynumber: 2.5 Consensus size: 23
441775 TTTTTAATTA
441785 TATTTTTTTATTTATTTACTATAT
1 TATTTTTTTATTTA-TTACTATAT
* *
441809 TCCTTTTTTTTATTTA-TATTATAT
1 T--ATTTTTTTATTTATTACTATAT
441833 TATTTTTATTAT
1 TATTTTT-TTAT
441845 ATAAATCTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 7
0.75 0.08 0.17
Matches are distributed among these distances:
22 5 0.17
23 4 0.13
24 9 0.30
26 12 0.40
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (23 bp):
TATTTTTTTATTTATTACTATAT
Found at i:441947 original size:39 final size:38
Alignment explanation
Indices: 441904--441995 Score: 121
Period size: 39 Copynumber: 2.4 Consensus size: 38
441894 ATTTGGTATG
441904 TATATATATTTTTTATTAATATTATATTTTATACATTTA
1 TATATATATTTTTTATTAATATTATATTTT-TACATTTA
* * * **
441943 TATATATATATTTTCTTAATATTCTATTTTTTTATTTA
1 TATATATATTTTTTATTAATATTATATTTTTACATTTA
441981 TATATATATTATTTT
1 TATATATATT-TTTT
441996 TACTTTATTT
Statistics
Matches: 46, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 15 0.33
39 31 0.67
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (38 bp):
TATATATATTTTTTATTAATATTATATTTTTACATTTA
Found at i:442012 original size:38 final size:37
Alignment explanation
Indices: 441904--442014 Score: 107
Period size: 39 Copynumber: 2.9 Consensus size: 37
441894 ATTTGGTATG
* * * **
441904 TATATATATTTTTTATTAATATTATATTTTATACATTTA
1 TATATATATATTTTCTT-ATATTCTATTTT-TTTATTTA
441943 TATATATATATTTTCTTAATATTCTATTTTTTTATTTA
1 TATATATATATTTTCTT-ATATTCTATTTTTTTATTTA
*
441981 TATATATATTATTTTTACTT-TATTTTATTTTTTT
1 TATATATA-TA-TTTT-CTTATATTCTATTTTTTT
442015 TCTATTTTTT
Statistics
Matches: 63, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
38 14 0.22
39 42 0.67
40 4 0.06
41 3 0.05
ACGTcount: A:0.30, C:0.04, G:0.00, T:0.67
Consensus pattern (37 bp):
TATATATATATTTTCTTATATTCTATTTTTTTATTTA
Found at i:442022 original size:10 final size:10
Alignment explanation
Indices: 442009--442037 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
441999 TTTATTTTAT
442009 TTTTTTTCTA
1 TTTTTTTCTA
442019 TTTTTTTCTA
1 TTTTTTTCTA
442029 TTTTTTTCT
1 TTTTTTTCT
442038 TAATATCATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.07, C:0.10, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTTTCTA
Found at i:445371 original size:13 final size:13
Alignment explanation
Indices: 445337--445396 Score: 65
Period size: 13 Copynumber: 4.8 Consensus size: 13
445327 ATCAGAACAA
*
445337 AAAGAGAAAAAAG
1 AAAGAGAAAAAAC
445350 ATAA-A-AAAAAAC
1 A-AAGAGAAAAAAC
445362 AAAGAGAAAATAA-
1 AAAGAGAAAA-AAC
445375 AAAGAGAAAAAAC
1 AAAGAGAAAAAAC
445388 AAAG-GAAAA
1 AAAGAGAAAA
445397 TTGAAGAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
11 2 0.05
12 15 0.37
13 20 0.49
14 4 0.10
ACGTcount: A:0.78, C:0.03, G:0.15, T:0.03
Consensus pattern (13 bp):
AAAGAGAAAAAAC
Found at i:447101 original size:37 final size:37
Alignment explanation
Indices: 447049--447119 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 37
447039 TAAAAAGAAG
* *
447049 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACCAA
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACCAA
* *
447086 ATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC
1 ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAAC
447120 ATAAACATTG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 30 1.00
ACGTcount: A:0.24, C:0.23, G:0.14, T:0.39
Consensus pattern (37 bp):
ATTTTATCTCCCTTGAGACAGTTTCCCTTGAAACCAA
Found at i:447189 original size:36 final size:36
Alignment explanation
Indices: 447136--447361 Score: 193
Period size: 36 Copynumber: 6.4 Consensus size: 36
447126 ATTGAAAACA
* *
447136 TTTCCCTTGAAATAAATTTCATCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAG
**
447172 TTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAG
*
447208 TTT-TCCTTGAAACAAA-TT-A----T-TTGA-ATATG
1 TTTCT-CTTGAAACAAATTTCATCTCTCTTGAGACA-G
* * * * *
447237 TTT-TATTTGAAACAAATTTCATCTCCCTTAAGAAAT
1 TTTCT-CTTGAAACAAATTTCATCTCTCTTGAGACAG
* * * **
447273 TTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAG
1 TTTCTCTTGAAAC-AAATTTCATCTCTCTTGAGACAG
*
447310 TTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAG
1 TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAG
*
447346 TTTCCCTTGAAACAAA
1 TTTCTCTTGAAACAAA
447362 ATCTTTGAAT
Statistics
Matches: 153, Mismatches: 25, Indels: 24
0.76 0.12 0.12
Matches are distributed among these distances:
28 2 0.01
29 19 0.12
30 3 0.02
31 1 0.01
35 3 0.02
36 95 0.62
37 30 0.20
ACGTcount: A:0.28, C:0.19, G:0.12, T:0.41
Consensus pattern (36 bp):
TTTCTCTTGAAACAAATTTCATCTCTCTTGAGACAG
Found at i:447232 original size:101 final size:100
Alignment explanation
Indices: 447049--447327 Score: 317
Period size: 101 Copynumber: 2.8 Consensus size: 100
447039 TAAAAAGAAG
* * * * *
447049 ATTTTATCTCGCTTGAGATAGTTTCCCTTGAAACCAAATTTTGTCTCCCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTGAGAAAGTTTCTCTTGAAA-CAAATTTTGTCTCTCTTGAGACAGTTTCTCT
** * *
447114 TGAAACATAAACATTGAAAACATTTCCCTTGAAATAA
65 TGAAACA-AATTATTGAAAACATTTCACTTGAAACAA
* *
447151 ATTTCATCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTT-TCCT
1 ATTTCATCTCCCTTGAGAAAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCT-CT
* ** * *
447215 TGAAACAAATTATTTGAATATGTTTTATTTGAAACAA
65 TGAAACAAATTA-TTGAAAACATTTCACTTGAAACAA
* * * * *
447252 ATTTCATCTCCCTTAAGAAATTTTCTTTTGGAACTAAGTTTTGTCTCTCTTGAGACAGTTTCTCT
1 ATTTCATCTCCCTTGAGAAAGTTTCTCTTGAAAC-AAATTTTGTCTCTCTTGAGACAGTTTCTCT
447317 TGAAACAAATT
65 TGAAACAAATT
447328 TCGTCTCTCT
Statistics
Matches: 152, Mismatches: 21, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
100 4 0.03
101 80 0.53
102 67 0.44
103 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (100 bp):
ATTTCATCTCCCTTGAGAAAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCTCTT
GAAACAAATTATTGAAAACATTTCACTTGAAACAA
Found at i:447415 original size:138 final size:138
Alignment explanation
Indices: 447157--447415 Score: 374
Period size: 138 Copynumber: 1.9 Consensus size: 138
447147 ATAAATTTCA
* *
447157 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTTCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* * * ** * *
447222 AATTATTTGAATATGTTTTATTTGAAACAAATTTCATCTCCCTTAAGAAATTTTCTTTTGGAACT
66 AAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGAAAGTTTCTTTTGGAACT
447287 AAGTTTTG
131 AAGTTTTG
447295 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
1 TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
* * * ** * *
447360 AAATCTTTGAATTTATTTCCCCTAAAACAAATTTTGTCTCCCTTGAGACAGTTTCT
66 AAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGAAAGTTTCT
447416 CTTAAAACAC
Statistics
Matches: 105, Mismatches: 16, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
138 105 1.00
ACGTcount: A:0.27, C:0.19, G:0.12, T:0.41
Consensus pattern (138 bp):
TCTCTCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTTGAAACA
AAATATTTGAATATATTTCACCTAAAACAAATTTCATCTCCCTTAAGAAAGTTTCTTTTGGAACT
AAGTTTTG
Found at i:447424 original size:65 final size:67
Alignment explanation
Indices: 447319--447476 Score: 221
Period size: 65 Copynumber: 2.4 Consensus size: 67
447309 GTTTCTCTTG
* * * **
447319 AAACAAATTTCGTCTCTCTTGAGACAGTTTCCCTT-GAA-ACAAAATCTTTGAATTTATTTCCCC
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACACAAAATCTTCAAATTTATTTCCCC
447382 TA
66 TA
* *
447384 AAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTAAAACACAAAATCTTCAAATTTATTTCCCT
1 AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACACAAAATCTTCAAATTTATTTCCCC
447449 TA
66 TA
*
447451 AAACAAAATTTTGTTTCCCTTGAGAC
1 AAAC-AAATTTTGTCTCCCTTGAGAC
447477 CTTTTTCAAG
Statistics
Matches: 82, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
65 32 0.39
66 2 0.02
67 28 0.34
68 20 0.24
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
AAACAAATTTTGTCTCCCTTGAGACAGTTTCCCTTAAAACACAAAATCTTCAAATTTATTTCCCC
TA
Found at i:448353 original size:110 final size:110
Alignment explanation
Indices: 448155--448412 Score: 285
Period size: 110 Copynumber: 2.4 Consensus size: 110
448145 GCTTCCCAGT
* * * *
448155 TTCAGAGCCAATTTCATCTTCACAGCGAGGGATATTGGACTCAAAACAACACATACTCAACTTCA
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAAACAACACATACTCAACTTCA
* *
448220 CAACGAAGGGGCGACTGATTGTCAACAAACAACTTT-TCAGTTTCA
66 CAACGAAGAGGCGACTGACTGTCAACAAACAA-TTTCTCAGTTTCA
* * * * * *
448265 TTCAGAGTCAATTTTAACTTCACAACGAATGATATTGAACTCGAGACAACATA-AGCTCAACTTC
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAAACAACACATA-CTCAACTTC
* * *
448329 ACAGCGAAGAGGCGGCTGGCTGTCAACAAACAATTTCTCAG-TTC-
65 ACAACGAAGAGGCGACTGACTGTCAACAAACAATTTCTCAGTTTCA
* * * *
448373 --CAGAGCCAATTTCAACTTCACGATGGAGGATATTGGACTC
1 TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTC
448413 GGAACAATAC
Statistics
Matches: 124, Mismatches: 22, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
106 33 0.27
109 7 0.06
110 84 0.68
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.25
Consensus pattern (110 bp):
TTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGAACTCAAAACAACACATACTCAACTTCA
CAACGAAGAGGCGACTGACTGTCAACAAACAATTTCTCAGTTTCA
Found at i:449537 original size:23 final size:23
Alignment explanation
Indices: 449511--449575 Score: 76
Period size: 23 Copynumber: 2.8 Consensus size: 23
449501 CAGCTCATAT
449511 AATTGCACCGAAGTGCCATGTAG
1 AATTGCACCGAAGTGCCATGTAG
* * **
449534 AATTGCATCGGAGTGCCGCGTAG
1 AATTGCACCGAAGTGCCATGTAG
* *
449557 AATTACACCGTAGTGCCAT
1 AATTGCACCGAAGTGCCAT
449576 ATAATAATGT
Statistics
Matches: 33, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.28, C:0.23, G:0.26, T:0.23
Consensus pattern (23 bp):
AATTGCACCGAAGTGCCATGTAG
Found at i:450550 original size:64 final size:64
Alignment explanation
Indices: 450442--450666 Score: 244
Period size: 64 Copynumber: 3.5 Consensus size: 64
450432 TAATGAAGGT
* * * * *
450442 ATGCATCGATGCACTACTGATGCATCGGTGCA-TAAAATGTATTCGATGTTGT-ATTATTACTGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACT-AATTGCATTCGATGTT-TCATTATTAATGG
450505 G
64 G
* * *
450506 TTGCATCGATGCA-TGCCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCTTATTAATGGG
1 ATGCATCGATGCACT-ACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
* * **
450570 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTATTTATT-TTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGT-TTCATTATTAATGGG
**
450633 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
450667 CTTCAAATAA
Statistics
Matches: 138, Mismatches: 17, Indels: 12
0.83 0.10 0.07
Matches are distributed among these distances:
63 4 0.03
64 128 0.93
65 6 0.04
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACTAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:452445 original size:20 final size:19
Alignment explanation
Indices: 452422--452545 Score: 87
Period size: 20 Copynumber: 6.5 Consensus size: 19
452412 TTTCATCCCC
452422 TATATATATATATTTTTAAT
1 TATATATATATATTTTT-AT
*
452442 TATATATATATTTTTTTAT
1 TATATATATATATTTTTAT
* *
452461 T-TTTTTACTATATTCCTTT-T
1 TATATATA-TATATT--TTTAT
452481 T-TATATATACTATTTTTAT
1 TATATATATA-TATTTTTAT
* * *
452500 TATATATCTCTCATTATTA-
1 TATATATATAT-ATTTTTAT
* *
452519 TATATATATATATATATA-
1 TATATATATATATTTTTAT
452537 TATATATAT
1 TATATATAT
452546 GTATAGATGT
Statistics
Matches: 83, Mismatches: 14, Indels: 16
0.73 0.12 0.14
Matches are distributed among these distances:
18 20 0.24
19 22 0.27
20 38 0.46
21 3 0.04
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (19 bp):
TATATATATATATTTTTAT
Found at i:452503 original size:16 final size:15
Alignment explanation
Indices: 452426--452541 Score: 64
Period size: 16 Copynumber: 7.6 Consensus size: 15
452416 ATCCCCTATA
452426 TATATATATTTTTAAT
1 TATATATATTTTT-AT
452442 TATATATATATTTT-T
1 TATATATAT-TTTTAT
*
452457 T-TAT-T-TTTTTAC
1 TATATATATTTTTAT
*
452469 TATAT-TCCTTTTT-T
1 TATATAT-ATTTTTAT
452483 ATATATACTATTTTTAT
1 -TATATA-TATTTTTAT
* *
452500 TATATATCTCTCATTAT
1 TATATATAT-T-TTTAT
* *
452517 TATATATATATATAT
1 TATATATATTTTTAT
452532 ATATATATAT
1 -TATATATAT
452542 ATATGTATAG
Statistics
Matches: 79, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
11 4 0.05
12 2 0.03
13 5 0.06
14 3 0.04
15 17 0.22
16 30 0.38
17 18 0.23
ACGTcount: A:0.33, C:0.06, G:0.00, T:0.61
Consensus pattern (15 bp):
TATATATATTTTTAT
Found at i:452522 original size:2 final size:2
Alignment explanation
Indices: 452517--452550 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
452507 CTCTCATTAT
*
452517 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
452551 GATGTATTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:452625 original size:41 final size:38
Alignment explanation
Indices: 452580--452690 Score: 114
Period size: 39 Copynumber: 2.8 Consensus size: 38
452570 ATTTGCTATG
*
452580 TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTTTCTTAATATTATATTTT-TACGTTAT
* **
452619 TATATATATTTTTTCTTAATATTCTATTTTTTTGTTTAT
1 TATATATATTTTTTCTTAATATTATATTTTTACG-TTAT
* * * *
452658 ATATATATTATTTTTACTTTATTTTATTTTTTT
1 -TATATA-TATTTTTTCTTAATATTATATTTTT
452691 CTATTTTTTT
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
38 2 0.03
39 32 0.53
40 6 0.10
41 20 0.33
ACGTcount: A:0.25, C:0.05, G:0.02, T:0.68
Consensus pattern (38 bp):
TATATATATTTTTTCTTAATATTATATTTTTACGTTAT
Found at i:452631 original size:38 final size:38
Alignment explanation
Indices: 452580--452671 Score: 130
Period size: 39 Copynumber: 2.4 Consensus size: 38
452570 ATTTGCTATG
*
452580 TATATATATTTTTTCTTAATATTATATTTTATACGTTTT
1 TATATATATTTTTTCTTAATATTATATTTT-TACGTTTA
* **
452619 TATATATATTTTTTCTTAATATTCTATTTTTTTGTTTA
1 TATATATATTTTTTCTTAATATTATATTTTTACGTTTA
452657 TATATATATTATTTT
1 TATATATATT-TTTT
452672 TACTTTATTT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
38 15 0.31
39 33 0.69
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.66
Consensus pattern (38 bp):
TATATATATTTTTTCTTAATATTATATTTTTACGTTTA
Found at i:452651 original size:19 final size:18
Alignment explanation
Indices: 452582--452692 Score: 66
Period size: 19 Copynumber: 5.7 Consensus size: 18
452572 TTGCTATGTA
452582 TATATATTTTTTCTTAATAT
1 TATAT-TTTTTTCTT-ATAT
*
452602 TATATTTTATACGTTTTTATA-
1 TATATTTT-T---TTCTTATAT
452623 TATA-TTTTTTCTTAATAT
1 TATATTTTTTTCTT-ATAT
* *
452641 TCTATTTTTTTGTTTATAT
1 TATATTTTTTT-CTTATAT
452660 ATATATTATTTTTACTT-TAT
1 -TATATT-TTTTT-CTTATAT
*
452680 TTTATTTTTTTCT
1 TATATTTTTTTCT
452693 ATTTTTTTCT
Statistics
Matches: 73, Mismatches: 8, Indels: 23
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.05
17 5 0.07
18 8 0.11
19 19 0.26
20 19 0.26
21 11 0.15
22 3 0.04
23 4 0.05
ACGTcount: A:0.24, C:0.05, G:0.02, T:0.68
Consensus pattern (18 bp):
TATATTTTTTTCTTATAT
Found at i:453798 original size:2 final size:2
Alignment explanation
Indices: 453786--453823 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
453776 AATTAAATAC
453786 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
453824 ACTCAGCCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:453894 original size:18 final size:18
Alignment explanation
Indices: 453871--453906 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
453861 AACCCACTGT
453871 CCATTTAAATTTTAAAAC
1 CCATTTAAATTTTAAAAC
453889 CCATTTAAATTTTAAAAC
1 CCATTTAAATTTTAAAAC
453907 TAAATAAATA
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:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (18 bp):
CCATTTAAATTTTAAAAC
Found at i:456380 original size:18 final size:18
Alignment explanation
Indices: 456357--456392 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
456347 ACTTTTAAGG
456357 GATGTTCAATTAAGTGTT
1 GATGTTCAATTAAGTGTT
* *
456375 GATGTTGAATTTAGTGTT
1 GATGTTCAATTAAGTGTT
456393 ATGGCCATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.03, G:0.25, T:0.47
Consensus pattern (18 bp):
GATGTTCAATTAAGTGTT
Found at i:458053 original size:30 final size:30
Alignment explanation
Indices: 457995--458054 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
457985 ACCGAAATTT
** ** *
457995 GTTCGGTTCGGTTAATTTTTTCATAAAAAA
1 GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
458025 GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
1 GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
458055 AAATTTAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.08, G:0.22, T:0.37
Consensus pattern (30 bp):
GTTCGGTTCGGTTAATGGTTAAAGAAAAAA
Found at i:458117 original size:2 final size:2
Alignment explanation
Indices: 458110--458196 Score: 165
Period size: 2 Copynumber: 43.5 Consensus size: 2
458100 AACACCCCTA
458110 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
*
458152 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TA TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
458194 TC T
1 TC T
458197 ATATAATATA
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 83 1.00
ACGTcount: A:0.01, C:0.48, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:458201 original size:2 final size:2
Alignment explanation
Indices: 458196--458244 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
458186 TCTCTATCTC
458196 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
458237 TA TA -A TA T
1 TA TA TA TA T
458245 TAGTGTGTGT
Statistics
Matches: 45, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 43 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:463713 original size:5 final size:5
Alignment explanation
Indices: 463703--463731 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
463693 TAATTATTAA
463703 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AAAAG AAAA
463732 ATAATAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:463772 original size:19 final size:19
Alignment explanation
Indices: 463745--463787 Score: 68
Period size: 20 Copynumber: 2.2 Consensus size: 19
463735 ATAATATAAT
463745 ATAATATAAAAAATAAAGAAA
1 ATAATA-AAAAAATAAA-AAA
463766 ATAATAAAAAAATAAAAAA
1 ATAATAAAAAAATAAAAAA
463785 ATA
1 ATA
463788 TCGACAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.27
20 10 0.45
21 6 0.27
ACGTcount: A:0.79, C:0.00, G:0.02, T:0.19
Consensus pattern (19 bp):
ATAATAAAAAAATAAAAAA
Found at i:464205 original size:15 final size:15
Alignment explanation
Indices: 464185--464214 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
464175 TTGCTTTTTT
464185 TTTTCTTCACAAAAC
1 TTTTCTTCACAAAAC
*
464200 TTTTCTTCATAAAAC
1 TTTTCTTCACAAAAC
464215 ATTAACATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.43
Consensus pattern (15 bp):
TTTTCTTCACAAAAC
Found at i:465801 original size:4 final size:4
Alignment explanation
Indices: 465764--465841 Score: 102
Period size: 4 Copynumber: 19.2 Consensus size: 4
465754 CAACAACAAA
* * * * *
465764 ACAT CACAT ACGT ACTT ACAT GCAT GCAT GCAT ACAT ACAT ACAT ACAT
1 ACAT -ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
465813 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT A
465842 GAGCTAATGG
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
4 64 0.94
5 4 0.06
ACGTcount: A:0.44, C:0.26, G:0.05, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:467322 original size:18 final size:17
Alignment explanation
Indices: 467299--467333 Score: 61
Period size: 17 Copynumber: 2.0 Consensus size: 17
467289 TAAACTTTCA
467299 AATTTTAATTTTAATTTT
1 AATTTTAA-TTTAATTTT
467317 AATTTTAATTTAATTTT
1 AATTTTAATTTAATTTT
467334 GTTTTGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
AATTTTAATTTAATTTT
Found at i:467330 original size:5 final size:6
Alignment explanation
Indices: 467299--467333 Score: 63
Period size: 6 Copynumber: 6.0 Consensus size: 6
467289 TAAACTTTCA
467299 AATTTT AATTTT AATTTT AATTTT AA-TTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
467334 GTTTTGTTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
AATTTT
Found at i:467426 original size:9 final size:10
Alignment explanation
Indices: 467403--467427 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
467393 CATGCTGATT
467403 TTTTTGAAAG
1 TTTTTGAAAG
467413 TTTTTGAAAG
1 TTTTTGAAAG
467423 TTTTT
1 TTTTT
467428 AACTCATGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.00, G:0.16, T:0.60
Consensus pattern (10 bp):
TTTTTGAAAG
Found at i:474366 original size:152 final size:152
Alignment explanation
Indices: 474084--474370 Score: 412
Period size: 152 Copynumber: 1.9 Consensus size: 152
474074 GGGTCGTCGG
* * * *
474084 AAATATTTATATTGAACATGTATTTGATACTCGCACATAGAGAATATTTTTATATCTGACACTCA
1 AAATATTTATATCGAACATGTATTTGATACTCGCAAATAGAGAATATTCTTATATCCGACACTCA
*
474149 CATCAAATGATGTAGACATTTAGAACTTCGAAACTTCCTTTGAGACTAGGGATACATCGAAAATA
66 CATCAAATAATGTAGACATTTAGAACTTCGAAACTTCCTTTGAGACTAGGGATACATCGAAAATA
474214 TTTGTCACTAGGGATTCATCGA
131 TTTGTCACTAGGGATTCATCGA
* * * *
474236 AAATATTTATATCGAACATGTATTTTATACTCGCAAATAGAGTATATTCTTATATCCGGCACTCG
1 AAATATTTATATCGAACATGTATTTGATACTCGCAAATAGAGAATATTCTTATATCCGACACTCA
* * * * * * * **
474301 CATCGAATAATGTAGTCGTTTGGAACTTTGAAACTTCCTTTGAGATTAGGGATTCATCGGGAATA
66 CATCAAATAATGTAGACATTTAGAACTTCGAAACTTCCTTTGAGACTAGGGATACATCGAAAATA
474366 TTTGT
131 TTTGT
474371 GATTTGGCTA
Statistics
Matches: 117, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
152 117 1.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (152 bp):
AAATATTTATATCGAACATGTATTTGATACTCGCAAATAGAGAATATTCTTATATCCGACACTCA
CATCAAATAATGTAGACATTTAGAACTTCGAAACTTCCTTTGAGACTAGGGATACATCGAAAATA
TTTGTCACTAGGGATTCATCGA
Found at i:478269 original size:26 final size:25
Alignment explanation
Indices: 478240--478313 Score: 77
Period size: 27 Copynumber: 3.1 Consensus size: 25
478230 AAAATAAGTT
478240 TAAAGTTTAAATTGTATTAATATAAA
1 TAAAGTTTAAATTGTATTAATA-AAA
**
478266 TAAAACATTAAA-TGT-TT--TAAAA
1 T-AAAGTTTAAATTGTATTAATAAAA
478288 T-AAGTTTAAATTGTATTAATAAAA
1 TAAAGTTTAAATTGTATTAATAAAA
478312 TA
1 TA
478314 TATATGATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 13
0.69 0.07 0.24
Matches are distributed among these distances:
20 7 0.18
21 3 0.08
22 6 0.16
23 2 0.05
24 6 0.16
25 2 0.05
26 4 0.11
27 8 0.21
ACGTcount: A:0.51, C:0.01, G:0.07, T:0.41
Consensus pattern (25 bp):
TAAAGTTTAAATTGTATTAATAAAA
Found at i:478297 original size:28 final size:28
Alignment explanation
Indices: 478211--478297 Score: 81
Period size: 28 Copynumber: 3.1 Consensus size: 28
478201 TTTAATGAAA
*
478211 TAAAACATTAAATCTTTTAAAAATAAGTT
1 TAAAACATTAAATGTTTT-AAAATAAGTT
** * * *
478240 T-AAAGTTTAAATTGTATTAATATAA--A
1 TAAAACATTAAA-TGTTTTAAAATAAGTT
478266 TAAAACATTAAATGTTTTAAAATAAGTT
1 TAAAACATTAAATGTTTTAAAATAAGTT
478294 TAAA
1 TAAA
478298 TTGTATTAAT
Statistics
Matches: 43, Mismatches: 11, Indels: 9
0.68 0.17 0.14
Matches are distributed among these distances:
26 12 0.28
27 8 0.19
28 18 0.42
29 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.06, T:0.39
Consensus pattern (28 bp):
TAAAACATTAAATGTTTTAAAATAAGTT
Found at i:481949 original size:21 final size:20
Alignment explanation
Indices: 481923--481972 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
481913 ACGAAATAAT
*
481923 AAAAAATATTATTTTTATTCA
1 AAAAAATATTA-TTTAATTCA
* *
481944 AAAAAACAATTATTTAATTGA
1 AAAAAA-TATTATTTAATTCA
481965 AAAAAATA
1 AAAAAATA
481973 ATATATAGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 1 0.04
21 19 0.79
22 4 0.17
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (20 bp):
AAAAAATATTATTTAATTCA
Found at i:483717 original size:2 final size:2
Alignment explanation
Indices: 483710--483735 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
483700 TTATCTTGTC
483710 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
483736 GTGTGTGTGT
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:490978 original size:20 final size:20
Alignment explanation
Indices: 490955--491005 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
490945 ACGCGATCTT
490955 CAGAATCGCAAATCAGTTCC
1 CAGAATCGCAAATCAGTTCC
490975 CAGAATCGCAAATCAGTTCC
1 CAGAATCGCAAATCAGTTCC
490995 CAGAATCGCAA
1 CAGAATCGCAA
491006 CGCGATTATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.37, C:0.29, G:0.16, T:0.18
Consensus pattern (20 bp):
CAGAATCGCAAATCAGTTCC
Found at i:491022 original size:21 final size:21
Alignment explanation
Indices: 490996--491093 Score: 60
Period size: 21 Copynumber: 4.7 Consensus size: 21
490986 ATCAGTTCCC
490996 AGAATCGCAACGCGATTATGA
1 AGAATCGCAACGCGATTATGA
* *
491017 AGAATCACAATGCGA-TA-GTA
1 AGAATCGCAACGCGATTATG-A
* ** * **
491037 CA-AATTAGCATTGCGATTTTCC
1 -AGAA-TCGCAACGCGATTATGA
*
491059 AGAATCGCAACGCGAATATGA
1 AGAATCGCAACGCGATTATGA
491080 A-AATCGCAACGCGA
1 AGAATCGCAACGCGA
491094 ACATATAAAT
Statistics
Matches: 56, Mismatches: 15, Indels: 13
0.67 0.18 0.15
Matches are distributed among these distances:
19 1 0.02
20 18 0.32
21 34 0.61
22 3 0.05
ACGTcount: A:0.39, C:0.20, G:0.20, T:0.20
Consensus pattern (21 bp):
AGAATCGCAACGCGATTATGA
Found at i:491086 original size:20 final size:20
Alignment explanation
Indices: 491061--491336 Score: 177
Period size: 20 Copynumber: 13.7 Consensus size: 20
491051 GATTTTCCAG
*
491061 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGAATACGAA
* *
491081 AATCGCAACGCGAACA-TATA
1 AATCGCAACGCGAATACGA-A
* * *
491101 AATCGCAACACG-ATTCTGAC
1 AATCGCAACGCGAATAC-GAA
* * * *
491121 TATCGCAACGAGTATCCGTAA
1 AATCGCAACGCGAATACG-AA
* * *
491142 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
491162 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* * *
491183 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
* *
491203 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* *
491223 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GAA
* *
491243 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGAA
* * * *
491263 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGAA
491283 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACG-AA
* *
491304 AATCGCAACGCGTAT-CCATA
1 AATCGCAACGCGAATACGA-A
491324 AATCGCAACGCGA
1 AATCGCAACGCGA
491337 TTTTTAAAGC
Statistics
Matches: 203, Mismatches: 39, Indels: 28
0.75 0.14 0.10
Matches are distributed among these distances:
19 4 0.02
20 147 0.72
21 52 0.26
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGAA
Found at i:491165 original size:81 final size:81
Alignment explanation
Indices: 491061--491336 Score: 317
Period size: 81 Copynumber: 3.4 Consensus size: 81
491051 GATTTTCCAG
* ** * * * *
491061 AATCGCAACGCGAATATGAAAATCGCAACGCGAACATATAAATCGCAACACG-ATTC-TGACTAT
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGT-A-AAT
* *
491124 CGCAACGAGTATCCGTAA
64 CGCAACGAGAATACGTAA
* *
491142 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTA-AAATCGCAACGCGTATCCGTAAAT
1 AATCGCAACGCGTATCCGTAAATCGCAACG-CGA-ACATATAAATCGCAACGCGTATCCGTAAAT
491206 CGCAACGAGAATACGT-A
64 CGCAACGAGAATACGTAA
* * * ** *
491223 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGTAAATCGCAATGCGTATCCGTAAATCG
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
*
491288 CAACGACAATACGTAA
66 CAACGAGAATACGTAA
*
491304 AATCGCAACGCGTATCCATAAATCGCAACGCGA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGA
491337 TTTTTAAAGC
Statistics
Matches: 166, Mismatches: 23, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
79 1 0.01
80 39 0.23
81 87 0.52
82 30 0.18
83 8 0.05
84 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (81 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAACATATAAATCGCAACGCGTATCCGTAAATCG
CAACGAGAATACGTAA
Found at i:491237 original size:40 final size:41
Alignment explanation
Indices: 491122--491333 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
491112 GATTCTGACT
* *
491122 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
491163 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
491204 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
491244 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
491284 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
491325 ATCGCAACG
1 ATCGCAACG
491334 CGATTTTTAA
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 76 0.47
41 84 0.52
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:491740 original size:20 final size:20
Alignment explanation
Indices: 491715--491789 Score: 123
Period size: 20 Copynumber: 3.8 Consensus size: 20
491705 AATAAATCAT
*
491715 ATGACTATCGCAACACGGAA
1 ATGACTATCGCAACGCGGAA
*
491735 ATGACTATCGCAATGCGGAA
1 ATGACTATCGCAACGCGGAA
*
491755 TTGACTATCGCAACGCGGAA
1 ATGACTATCGCAACGCGGAA
491775 ATGACTATCGCAACG
1 ATGACTATCGCAACG
491790 AGAGAATCGC
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 50 1.00
ACGTcount: A:0.35, C:0.24, G:0.23, T:0.19
Consensus pattern (20 bp):
ATGACTATCGCAACGCGGAA
Found at i:491849 original size:34 final size:33
Alignment explanation
Indices: 491761--491856 Score: 129
Period size: 33 Copynumber: 2.8 Consensus size: 33
491751 GGAATTGACT
* **
491761 ATCGCAACGCGGAAATGACTATCGCAACGAGAGA
1 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
* *
491795 ATCGCAATGCGAAATGAAAATCGCATCGAGTGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
491828 ATCGCAATGCGAAAATGAAAATCGCAACG
1 ATCGCAATGCG-AAATGAAAATCGCAACG
491857 CGAAATTAGT
Statistics
Matches: 55, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
33 30 0.55
34 25 0.45
ACGTcount: A:0.41, C:0.21, G:0.24, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:491852 original size:20 final size:19
Alignment explanation
Indices: 491794--491862 Score: 76
Period size: 20 Copynumber: 3.8 Consensus size: 19
491784 GCAACGAGAG
491794 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
491813 AATCGC-AT-CG-AGTG--
1 AATCGCAATGCGAAATGAA
491827 AATCGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
491847 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
491863 TAGTTTCGCG
Statistics
Matches: 41, Mismatches: 3, Indels: 12
0.73 0.05 0.21
Matches are distributed among these distances:
14 6 0.15
15 2 0.05
16 5 0.12
17 2 0.05
18 5 0.12
19 10 0.24
20 11 0.27
ACGTcount: A:0.43, C:0.19, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:491928 original size:33 final size:33
Alignment explanation
Indices: 491871--491955 Score: 134
Period size: 33 Copynumber: 2.5 Consensus size: 33
491861 ATTAGTTTCG
491871 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
*
491905 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
491938 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
491956 CGTGTTGCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
33 34 0.71
34 14 0.29
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:492087 original size:14 final size:14
Alignment explanation
Indices: 492068--492104 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
492058 CATCAATTAA
492068 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
492082 ACAAATCATCTTTT
1 ACAAATCAACATTT
492096 ACAAATCAA
1 ACAAATCAA
492105 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:493554 original size:42 final size:42
Alignment explanation
Indices: 493475--493567 Score: 107
Period size: 42 Copynumber: 2.2 Consensus size: 42
493465 CCTCTTCAAC
* * *
493475 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
493517 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAC
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
493559 GATGACAGG
1 GATGACAGG
493568 TGAGTCGGGC
Statistics
Matches: 42, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
42 39 0.93
43 3 0.07
ACGTcount: A:0.23, C:0.17, G:0.40, T:0.20
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:494113 original size:95 final size:94
Alignment explanation
Indices: 493951--494143 Score: 289
Period size: 95 Copynumber: 2.1 Consensus size: 94
493941 ATGGATTGTA
* * * *
493951 TTAC-TTCAACCAAAAGATAAAACAAAGACAAATACTAACTTCAGAGTATTAAAGAATACACAAT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAAAATAAACAAT
*
494015 TTAGCAGAATTGGCAGCAACCGAACAAAT
66 TTAGCAGAATTGGCAGCAACCAAACAAAT
* *
494044 TTACTTTCAACCAAAAGACAAAACAAAAGACAAATACTAACTTCACAGTGTTAAAAAATAAACAG
1 TTACTTTCAACCAAAAGACAAAAC-AAAGACAAATACTAACTTCACAGTATTAAAAAATAAACAA
* *
494109 TTTAGCAGTATTGGCAGCAACCAAATAAAT
65 TTTAGCAGAATTGGCAGCAACCAAACAAAT
494139 TTACT
1 TTACT
494144 AAGCAATCTA
Statistics
Matches: 89, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 4 0.04
94 18 0.20
95 67 0.75
ACGTcount: A:0.49, C:0.18, G:0.11, T:0.22
Consensus pattern (94 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTATTAAAAAATAAACAAT
TTAGCAGAATTGGCAGCAACCAAACAAAT
Found at i:495877 original size:40 final size:39
Alignment explanation
Indices: 495833--495944 Score: 110
Period size: 33 Copynumber: 3.0 Consensus size: 39
495823 TCTTTTGGTT
**
495833 GAAATGAAAATCGCAACGAGAGAATGACTATCGCAATGCG
1 GAAATGAAAATCGCAACGAGA-AATGAAAATCGCAATGCG
** *
495873 GAAATGACTATCGCAACGCGAAATGAAAATCGCAA--C-
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAATGCG
* *
495909 --AA-GAGAATCGCAACGCGAAATGAAAATCGCAATGCG
1 GAAATGAAAATCGCAACGAGAAATGAAAATCGCAATGCG
495945 ATTTTGGTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
33 28 0.45
34 2 0.03
35 1 0.02
37 1 0.02
39 12 0.19
40 18 0.29
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (39 bp):
GAAATGAAAATCGCAACGAGAAATGAAAATCGCAATGCG
Found at i:495897 original size:19 final size:19
Alignment explanation
Indices: 495842--495908 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
495832 TGAAATGAAA
*
495842 ATCGCAACGAGAGAATGACT
1 ATCGCAACGCGA-AATGACT
*
495862 ATCGCAATGCGGAAATGACT
1 ATCGCAACGC-GAAATGACT
**
495882 ATCGCAACGCGAAATGAAA
1 ATCGCAACGCGAAATGACT
495901 ATCGCAAC
1 ATCGCAAC
495909 AAGAGAATCG
Statistics
Matches: 41, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
19 15 0.37
20 24 0.59
21 2 0.05
ACGTcount: A:0.40, C:0.22, G:0.22, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGACT
Found at i:495938 original size:19 final size:19
Alignment explanation
Indices: 495833--495945 Score: 101
Period size: 19 Copynumber: 6.1 Consensus size: 19
495823 TCTTTTGGTT
*
495833 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
** *
495852 GAGAATGACTATCGCAATGC
1 GA-AATGAAAATCGCAACGC
**
495872 GGAAATGACTATCGCAACGC
1 -GAAATGAAAATCGCAACGC
495892 GAAATGAAAATCGCAA--C
1 GAAATGAAAATCGCAACGC
*
495909 --AA-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
*
495925 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
495944 GA
1 GA
495946 TTTTGGTTTC
Statistics
Matches: 77, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
14 10 0.13
15 2 0.03
16 1 0.01
17 1 0.01
18 2 0.03
19 30 0.39
20 29 0.38
21 2 0.03
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.13
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:495991 original size:21 final size:20
Alignment explanation
Indices: 495972--496043 Score: 83
Period size: 20 Copynumber: 3.5 Consensus size: 20
495962 CGATTCTCTC
495972 GTTGCGATTTTCATTTCTC-T
1 GTTGCGATTTTCATTT-TCAT
** *
495992 CGTTGCGATAGTCATTTTCGT
1 -GTTGCGATTTTCATTTTCAT
*
496013 GTTGTGATTTTCATTTTCAT
1 GTTGCGATTTTCATTTTCAT
496033 GTTGCGATTTT
1 GTTGCGATTTT
496044 AAGTTTAGAA
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
20 28 0.65
21 15 0.35
ACGTcount: A:0.12, C:0.15, G:0.19, T:0.53
Consensus pattern (20 bp):
GTTGCGATTTTCATTTTCAT
Found at i:496902 original size:20 final size:20
Alignment explanation
Indices: 496877--497069 Score: 192
Period size: 20 Copynumber: 9.6 Consensus size: 20
496867 CTTTAAAAAT
*
496877 CGCGTTGCGATTTATGGATA
1 CGCGTTGCGATTTACGGATA
*
496897 CGCGTTGCGATTTTACGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
496919 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* * *
496938 CGCATTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
* *
496958 CTCGTTGCGATTTACAGATA
1 CGCGTTGCGATTTACGGATA
* *
496978 CGCGTTGCGATTTACGTATT
1 CGCGTTGCGATTTACGGATA
*
496998 CTCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
497018 CACGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
* *
497038 TGTCGTTGCGATTTACGAATA
1 CG-CGTTGCGATTTACGGATA
*
497059 CTCGTTGCGAT
1 CGCGTTGCGAT
497070 AGTCAGAATC
Statistics
Matches: 140, Mismatches: 27, Indels: 12
0.78 0.15 0.07
Matches are distributed among these distances:
19 2 0.01
20 106 0.76
21 30 0.21
22 2 0.01
ACGTcount: A:0.20, C:0.19, G:0.24, T:0.38
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:496963 original size:40 final size:40
Alignment explanation
Indices: 496879--497069 Score: 292
Period size: 40 Copynumber: 4.7 Consensus size: 40
496869 TTAAAAATCG
* *
496879 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTAT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
*
496920 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
*
496960 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
* *
497000 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGT
1 CGTTGCGATTTACGGATACGCGTTGCGA-TTTACGTATTCT
* *
497041 CGTTGCGATTTACGAATACTCGTTGCGAT
1 CGTTGCGATTTACGGATACGCGTTGCGAT
497070 AGTCAGAATC
Statistics
Matches: 139, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
40 76 0.55
41 63 0.45
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (40 bp):
CGTTGCGATTTACGGATACGCGTTGCGATTTACGTATTCT
Found at i:497006 original size:60 final size:61
Alignment explanation
Indices: 496879--497069 Score: 226
Period size: 61 Copynumber: 3.1 Consensus size: 61
496869 TTAAAAATCG
* * ** * *
496879 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTATCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATCGTCGTTGCGATTTACGAATACT
* * * * * *
496940 CATTGCGATTTACGTATTCTCGTTGCGA-TTTACAG-ATACG-CGTTGCGATTTACGTATTCT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTAC-GTAT-CGTCGTTGCGATTTACGAATACT
*
497000 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATCGTCGTTGCGATTTACGAATACT
497061 CGTTGCGAT
1 CGTTGCGAT
497070 AGTCAGAATC
Statistics
Matches: 108, Mismatches: 17, Indels: 10
0.80 0.13 0.07
Matches are distributed among these distances:
60 50 0.46
61 58 0.54
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (61 bp):
CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATCGTCGTTGCGATTTACGAATACT
Found at i:497033 original size:81 final size:79
Alignment explanation
Indices: 496879--497069 Score: 283
Period size: 81 Copynumber: 2.4 Consensus size: 79
496869 TTAAAAATCG
* *
496879 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTATCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTA-CGATACGCGTTGCGA-TTTACGTATTATCGTTGCGATTTACGGATACACATT
496944 GCGATTTACGTATTCT
64 GCGATTTACGTATTCT
* *
496960 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACACGTTG
1 CGTTGCGATTTAC-GATACGCGTTGCGATTTACGTATTATCGTTGCGATTTACGGATACACATTG
*
497025 CGATTTTACGTATTGT
65 CGA-TTTACGTATTCT
*
497041 CGTTGCGATTTACGAATACTCGTTGCGAT
1 CGTTGCGATTTACG-ATACGCGTTGCGAT
497070 AGTCAGAATC
Statistics
Matches: 101, Mismatches: 6, Indels: 6
0.89 0.05 0.05
Matches are distributed among these distances:
80 38 0.38
81 63 0.62
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (79 bp):
CGTTGCGATTTACGATACGCGTTGCGATTTACGTATTATCGTTGCGATTTACGGATACACATTGC
GATTTACGTATTCT
Found at i:497085 original size:81 final size:80
Alignment explanation
Indices: 496879--497092 Score: 245
Period size: 81 Copynumber: 2.6 Consensus size: 80
496869 TTAAAAATCG
** * * ** *
496879 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTATCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACAGATACGCGTTGCGA-TTCACGTAATCGCGTTGCGATTTACGGATACACATT
496944 GCGATTTACGTATTCT
65 GCGATTTACGTATTCT
* * * *
496960 CGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCTCGTTGCGATTTACGGATACACGTTG
1 CGTTGCGATTTACAGATACGCGTTGCGATTCACGTAATCGCGTTGCGATTTACGGATACACATTG
*
497025 CGATTTTACGTATTGT
66 CGA-TTTACGTATTCT
*
497041 CGTTGCGATTTAC-GAATACTCGTTGCGATAGTCA-G-AATCGCGTTGCGATTTA
1 CGTTGCGATTTACAG-ATACGCGTTGCGAT--TCACGTAATCGCGTTGCGATTTA
497093 TATGTTCGCG
Statistics
Matches: 119, Mismatches: 10, Indels: 8
0.87 0.07 0.06
Matches are distributed among these distances:
80 38 0.32
81 78 0.66
82 1 0.01
83 2 0.02
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (80 bp):
CGTTGCGATTTACAGATACGCGTTGCGATTCACGTAATCGCGTTGCGATTTACGGATACACATTG
CGATTTACGTATTCT
Found at i:497103 original size:121 final size:121
Alignment explanation
Indices: 496879--497110 Score: 317
Period size: 121 Copynumber: 1.9 Consensus size: 121
496869 TTAAAAATCG
* * *
496879 CGTTGCGATTTATGGATACGCGTTGCGATTTTACGTATTATCGTTGCGATTTACGGATACGCATT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTATCGTTGCGATTTACGAATACGCATT
* * *
496944 GCGATTTACGTATTCTCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
66 GCGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
* * *
497000 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTGTCGTTGCGATTTACGAATACTCGTT
1 CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTATCGTTGCGATTTACGAATACGCATT
* *
497065 GCGATAGTCA-G-AATCGCGTTGCGATTTATATG-TTCGCGTTGCGATT
66 GCGAT--TCACGTAATCGCGTTGCGATTTACA-GATACGCGTTGCGATT
497111 CTGGAAAATC
Statistics
Matches: 97, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
121 93 0.96
122 2 0.02
123 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (121 bp):
CGTTGCGATTTACGGATACACGTTGCGATTTTACGTATTATCGTTGCGATTTACGAATACGCATT
GCGATTCACGTAATCGCGTTGCGATTTACAGATACGCGTTGCGATTTACGTATTCT
Found at i:497171 original size:42 final size:42
Alignment explanation
Indices: 497076--497171 Score: 97
Period size: 42 Copynumber: 2.3 Consensus size: 42
497066 CGATAGTCAG
* * *
497076 AATCGCGTTGCG-ATTTATATGTTCGCGTTGCGATTCTGGAA
1 AATCGCGTTGCGAATTTATATGATCGCATTGCGATTCTGCAA
** * * *
497117 AATCGCAATGCGAATTTGTACT-ATCGCATTGCGATTCTTCAT
1 AATCGCGTTGCGAATTTATA-TGATCGCATTGCGATTCTGCAA
497159 AATCGCGTTGCGA
1 AATCGCGTTGCGA
497172 TTCTGAGAAC
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
41 10 0.23
42 32 0.74
43 1 0.02
ACGTcount: A:0.23, C:0.20, G:0.23, T:0.34
Consensus pattern (42 bp):
AATCGCGTTGCGAATTTATATGATCGCATTGCGATTCTGCAA
Found at i:497209 original size:20 final size:19
Alignment explanation
Indices: 497160--497213 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
497150 ATTCTTCATA
497160 ATCGCGTTGCGATTCTGAG
1 ATCGCGTTGCGATTCTGAG
* **
497179 AACTGATTTGCGATTCTGGAG
1 ATC-GCGTTGCGATTCT-GAG
497200 ATCGCGTTGCGATT
1 ATCGCGTTGCGATT
497214 TTTATTTCGC
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 2 0.07
20 20 0.74
21 5 0.19
ACGTcount: A:0.19, C:0.19, G:0.30, T:0.33
Consensus pattern (19 bp):
ATCGCGTTGCGATTCTGAG
Found at i:498708 original size:2 final size:2
Alignment explanation
Indices: 498701--498729 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
498691 TAAAAACATC
498701 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
498730 TCCATCAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:520371 original size:16 final size:16
Alignment explanation
Indices: 520347--520377 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
520337 ATAAATAAAC
*
520347 GAACTTAAACGAACAT
1 GAACATAAACGAACAT
520363 GAACATAAACGAACA
1 GAACATAAACGAACA
520378 AATTTTTTTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.55, C:0.19, G:0.13, T:0.13
Consensus pattern (16 bp):
GAACATAAACGAACAT
Found at i:520459 original size:16 final size:16
Alignment explanation
Indices: 520438--520493 Score: 94
Period size: 16 Copynumber: 3.5 Consensus size: 16
520428 TTGTTCATTT
520438 AACGAACACGAACATA
1 AACGAACACGAACATA
*
520454 AACGAATACGAACATA
1 AACGAACACGAACATA
*
520470 AATGAACACGAACATA
1 AACGAACACGAACATA
520486 AACGAACA
1 AACGAACA
520494 TAAACGTTGG
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 36 1.00
ACGTcount: A:0.57, C:0.21, G:0.12, T:0.09
Consensus pattern (16 bp):
AACGAACACGAACATA
Found at i:528090 original size:20 final size:20
Alignment explanation
Indices: 528057--528101 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
528047 AAATTGATCG
*
528057 ACTG-TTTTCTTTCTCTATC
1 ACTGTTTTTCCTTCTCTATC
*
528076 ACTGTTTTTCCTTCTCTTTC
1 ACTGTTTTTCCTTCTCTATC
528096 ACTGTT
1 ACTGTT
528102 CTCAATCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 4 0.17
20 19 0.83
ACGTcount: A:0.09, C:0.27, G:0.07, T:0.58
Consensus pattern (20 bp):
ACTGTTTTTCCTTCTCTATC
Found at i:528296 original size:20 final size:19
Alignment explanation
Indices: 528271--528315 Score: 63
Period size: 20 Copynumber: 2.3 Consensus size: 19
528261 AGTGATTGAG
528271 AACAGTGAAAGAGAAGAAAA
1 AACAGTGAAAGAGAA-AAAA
* *
528291 AACAGTGATAGAGAAAGAA
1 AACAGTGAAAGAGAAAAAA
528310 AACAGT
1 AACAGT
528316 CGATCGATGT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 9 0.39
20 14 0.61
ACGTcount: A:0.60, C:0.07, G:0.24, T:0.09
Consensus pattern (19 bp):
AACAGTGAAAGAGAAAAAA
Found at i:533566 original size:73 final size:73
Alignment explanation
Indices: 533447--533583 Score: 238
Period size: 73 Copynumber: 1.9 Consensus size: 73
533437 GGTAATTCAC
* * * *
533447 ATTGGTATTATCAACTTCCTGTCTGGAGGTATTGTTTATGAGTTGTAGCTTATCTGAAGATTAAT
1 ATTGGTATTATCAACGTCCTGTCTAGAAGTATTGTCTATGAGTTGTAGCTTATCTGAAGATTAAT
533512 GACACTAT
66 GACACTAT
533520 ATTGGTATTATCAACGTCCTGTCTAGAAGTATTGTCTATGAGTTGTAGCTTATCTGAAGATTAA
1 ATTGGTATTATCAACGTCCTGTCTAGAAGTATTGTCTATGAGTTGTAGCTTATCTGAAGATTAA
533584 CGATGCTTTC
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 60 1.00
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.40
Consensus pattern (73 bp):
ATTGGTATTATCAACGTCCTGTCTAGAAGTATTGTCTATGAGTTGTAGCTTATCTGAAGATTAAT
GACACTAT
Found at i:534006 original size:26 final size:28
Alignment explanation
Indices: 533944--534006 Score: 67
Period size: 31 Copynumber: 2.2 Consensus size: 28
533934 CGAGTATTGT
*
533944 TGAGCTTGACTCGACTCGAAAACTCTGAAA
1 TGAGCTCGACTCGACTCGAAAACTCTG--A
*
533974 TGAAGCTCGAGTCGACTCGAAAACTC-G-
1 TG-AGCTCGACTCGACTCGAAAACTCTGA
534001 TGAGCT
1 TGAGCT
534007 TAAAATTTTC
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
26 4 0.13
27 2 0.07
30 3 0.10
31 21 0.70
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (28 bp):
TGAGCTCGACTCGACTCGAAAACTCTGA
Found at i:548302 original size:112 final size:111
Alignment explanation
Indices: 548081--548302 Score: 304
Period size: 112 Copynumber: 2.0 Consensus size: 111
548071 GATGTTGGGA
* * * *
548081 GAGTTTTCCCACTTCAGAGGGTCAATCTAACTCGACTCCGAAATAGTTGGACCCAATGTGACCAA
1 GAGTCTTCCCACTTCAGAGGGTCAACCTAACTCAACTCCGAAATAGTTGGACCCAATGCGACCAA
* * *
548146 AAAAGAGTATAAGCTAGTCGAAAATTGCGGCGAATGCGAGGACAAT
66 AAAAGAGTATAAGCTAGTCGAAAATAGCGGCGAATACGAAGACAAT
* *
548192 GAGTCTTCCCACTTCGGAGGGTCAACCTAACTCAACTCC-AATATAGTTGGAGCCCAATGCGA-T
1 GAGTCTTCCCACTTCAGAGGGTCAACCTAACTCAACTCCGAA-ATAGTTGGA-CCCAATGCGACC
* *
548255 AGAAAAAGAGTATAAGCTAGTTGAAAATAGTGGCGAATACGAAGACAA
64 A-AAAAAGAGTATAAGCTAGTCGAAAATAGCGGCGAATACGAAGACAA
548303 AGTTATAGAT
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
110 2 0.02
111 45 0.46
112 50 0.52
ACGTcount: A:0.36, C:0.20, G:0.23, T:0.21
Consensus pattern (111 bp):
GAGTCTTCCCACTTCAGAGGGTCAACCTAACTCAACTCCGAAATAGTTGGACCCAATGCGACCAA
AAAAGAGTATAAGCTAGTCGAAAATAGCGGCGAATACGAAGACAAT
Found at i:556545 original size:30 final size:30
Alignment explanation
Indices: 556494--556574 Score: 119
Period size: 30 Copynumber: 2.7 Consensus size: 30
556484 CTGATTTTTC
556494 ATTTAAAATTTAAAGATTAAATTAAAATGTT
1 ATTTAAAATTTAAA-ATTAAATTAAAATGTT
* *
556525 ATTTAAAATTTAAAATTAAATTAATATTTT
1 ATTTAAAATTTAAAATTAAATTAAAATGTT
*
556555 GTTTAAAATTTAAAA-TAAAT
1 ATTTAAAATTTAAAATTAAAT
556575 ATTAACTTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
29 5 0.11
30 28 0.60
31 14 0.30
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (30 bp):
ATTTAAAATTTAAAATTAAATTAAAATGTT
Found at i:559301 original size:19 final size:19
Alignment explanation
Indices: 559277--559316 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
559267 ATGACCAACA
*
559277 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
*
559296 AAATCGCAACGTGATCTCT
1 AAATCGCAACGCGATCTCT
559315 AA
1 AA
559317 TATCACAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.35, C:0.25, G:0.15, T:0.25
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:559371 original size:20 final size:22
Alignment explanation
Indices: 559346--559393 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 22
559336 GATTTGCAAC
559346 GCGATTTTTAC-TA-TCACATT
1 GCGATTTTTACATATTCACATT
*
559366 GCGA--TTTACATATTCGCATT
1 GCGATTTTTACATATTCACATT
559386 GCGATTTT
1 GCGATTTT
559394 CTAAAATCGC
Statistics
Matches: 23, Mismatches: 1, Indels: 6
0.77 0.03 0.20
Matches are distributed among these distances:
18 5 0.22
19 2 0.09
20 14 0.61
22 2 0.09
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.44
Consensus pattern (22 bp):
GCGATTTTTACATATTCACATT
Found at i:559439 original size:20 final size:20
Alignment explanation
Indices: 559379--559440 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
559369 ATTTACATAT
*
559379 TCGCATTGCGATTTTCTAAAA
1 TCGCAATGCGATTTTCT-AAA
* * * *
559400 TCGCAATGCAAATATGTAAA
1 TCGCAATGCGATTTTCTAAA
*
559420 TCGCAATTCGATTTTCTAAA
1 TCGCAATGCGATTTTCTAAA
559440 T
1 T
559441 TTACGTTAGT
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
20 19 0.61
21 12 0.39
ACGTcount: A:0.34, C:0.18, G:0.13, T:0.35
Consensus pattern (20 bp):
TCGCAATGCGATTTTCTAAA
Found at i:559884 original size:19 final size:20
Alignment explanation
Indices: 559859--559947 Score: 83
Period size: 19 Copynumber: 4.3 Consensus size: 20
559849 CTTATTTTGG
559859 ATTTTTCACTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
*
559879 -TTTTTCACTATCACAACAAC
1 ATTTTTCACTATCGCAAC-AC
*
559899 ACGTTTTTCAAACTCTCGCAACAC
1 A--TTTTTC--ACTATCGCAACAC
* *
559923 A-TTTTAATTATCGCAACAC
1 ATTTTTCACTATCGCAACAC
559942 ATTTTT
1 ATTTTT
559948 TAAAATCGCA
Statistics
Matches: 56, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
19 28 0.50
20 6 0.11
21 4 0.07
23 6 0.11
24 3 0.05
25 9 0.16
ACGTcount: A:0.31, C:0.27, G:0.04, T:0.37
Consensus pattern (20 bp):
ATTTTTCACTATCGCAACAC
Found at i:566621 original size:35 final size:35
Alignment explanation
Indices: 566551--566638 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
566541 TTTCCATGAA
*
566551 TTTTTAAATTAAAATTTATATTAAAATTTTAATTATT
1 TTTTTAAAATAAAA--TATATTAAAATTTTAATTATT
*
566588 TTTTTAAAATAAAATATGTTAATAATTTT-ATTATT
1 TTTTTAAAATAAAATATATTAA-AATTTTAATTATT
* * *
566623 ATATTAAAATTAAATA
1 TTTTTAAAATAAAATA
566639 ATAAGTTCAA
Statistics
Matches: 45, Mismatches: 5, Indels: 4
0.83 0.09 0.07
Matches are distributed among these distances:
35 26 0.58
36 6 0.13
37 13 0.29
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (35 bp):
TTTTTAAAATAAAATATATTAAAATTTTAATTATT
Found at i:572368 original size:265 final size:261
Alignment explanation
Indices: 571895--572424 Score: 961
Period size: 265 Copynumber: 2.0 Consensus size: 261
571885 ACCATTCATC
571895 ACTTTTACTTAATTTGATAATTCCAAATTTAATAAAGAAGGAAAATCAACCAAAATTGGGAAGTT
1 ACTTTTACTTAATTTGATAATTCCAAATTTAATAAAGAAGGAAAATCAACCAAAATTGGGAAGTT
*
571960 CCTAGAGATTAATTACATTGCAAATGAAGATGAATGACGGATCCAGGGTATATAAATATATGATA
66 CCTAGAGATTAATTACATTGCAAATGAAGATGAATGACGGATCCAGGGCATATAAATATATGATA
* *
572025 AATTAGAGACCACATATCAATCAGAATTGAATTACCTTATAGCACAAGGGTGAAAATTAGTTCCT
131 AATTAGAGACCACATATCAATCAGAATTGAATTACATTATAGCACAAGGGTGAAAATGAGTTCCT
* *
572090 TTTTTGTTTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGTATACC
196 TGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGTATACC
572155 A
261 A
572156 ACTTTTACTTAATTTGATAATTCCAAATTTAATAAAGAAAGAAGGAAAATCAACCAAAATTGGGA
1 ACTTTTACTTAATTTGATAATTCCAAATTTAAT----AAAGAAGGAAAATCAACCAAAATTGGGA
*
572221 AGTTTCTAGAGATTAATTACATTGCAAATGAAGATGAATGACGGATCCAGGGCATATAAATATAT
62 AGTTCCTAGAGATTAATTACATTGCAAATGAAGATGAATGACGGATCCAGGGCATATAAATATAT
*
572286 GATAAATTAGAGACCTCATATCAATCAGAATTGAATTACATTATAGCACAAGGGTGAAAATGAGT
127 GATAAATTAGAGACCACATATCAATCAGAATTGAATTACATTATAGCACAAGGGTGAAAATGAGT
572351 TCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGTA
192 TCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGTA
572416 TACCA
257 TACCA
572421 ACTT
1 ACTT
572425 CCGATGGCTC
Statistics
Matches: 258, Mismatches: 7, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
261 33 0.13
265 225 0.87
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.29
Consensus pattern (261 bp):
ACTTTTACTTAATTTGATAATTCCAAATTTAATAAAGAAGGAAAATCAACCAAAATTGGGAAGTT
CCTAGAGATTAATTACATTGCAAATGAAGATGAATGACGGATCCAGGGCATATAAATATATGATA
AATTAGAGACCACATATCAATCAGAATTGAATTACATTATAGCACAAGGGTGAAAATGAGTTCCT
TGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGTATACC
A
Found at i:572654 original size:181 final size:180
Alignment explanation
Indices: 572350--572710 Score: 697
Period size: 181 Copynumber: 2.0 Consensus size: 180
572340 TGAAAATGAG
572350 TTCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGT
1 TTCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGT
572415 ATACCAACTTCCGATGGCTCAAAGTGCTGGAAATTTCATGGAAACAAATGAAATTATAAACACAC
66 ATACCAACTTCCGATGGCTCAAAGTGCTGGAAATTTCATGGAAACAAATGAAATTATAAACACAC
572480 AC-AAAACTACTAATACATTAACAATATTTTCAGATTAGACATATATCAATT
131 ACAAAAACTAC--ATACATTAACAATATTTTCAGATTAGACATATATCAATT
572531 TTCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGT
1 TTCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGT
572596 ATACCAACTTCCGATGGCTCAAAGTGCTGGAAATTTCATGGAAACAAATGAAATTATAAACACAC
66 ATACCAACTTCCGATGGCTCAAAGTGCTGGAAATTTCATGGAAACAAATGAAATTATAAACACAC
572661 ACAAAAACTACATACATTAACAATATTTTCAGATTAGACATATATCAATT
131 ACAAAAACTACATACATTAACAATATTTTCAGATTAGACATATATCAATT
572711 GAAATTCCAA
Statistics
Matches: 179, Mismatches: 0, Indels: 3
0.98 0.00 0.02
Matches are distributed among these distances:
180 39 0.22
181 132 0.74
182 8 0.04
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (180 bp):
TTCCTTGTTTGATTATCTTCCCTACTCGAACTGAAACCAAAGGTATGCAAAAACACCTCCCCAGT
ATACCAACTTCCGATGGCTCAAAGTGCTGGAAATTTCATGGAAACAAATGAAATTATAAACACAC
ACAAAAACTACATACATTAACAATATTTTCAGATTAGACATATATCAATT
Found at i:575044 original size:74 final size:74
Alignment explanation
Indices: 574883--575097 Score: 378
Period size: 74 Copynumber: 2.9 Consensus size: 74
574873 TAATTTTTTT
* * * * *
574883 GATTATTTATTTATTTCTATTGATGATATTTACCTTTTAATTTTATTTAT-ATTATTCTATTAAA
1 GATTATTTATTTATTTTTATTAATGATATATACCTTTTAATTTTATTTATGATCAGTCTATTAAA
574947 AAACTTGAC
66 AAACTTGAC
574956 GATTATTTATTTATTTTTATTAATGATATATACCTTTTAATTTTATTTATGATCAGTCTATTAAA
1 GATTATTTATTTATTTTTATTAATGATATATACCTTTTAATTTTATTTATGATCAGTCTATTAAA
575021 AAACTTGAC
66 AAACTTGAC
575030 GATTATTTATTTATTTTTATTAATGATATATACCTTTTAATTTTATTTATGATCAGTCTATTAAA
1 GATTATTTATTTATTTTTATTAATGATATATACCTTTTAATTTTATTTATGATCAGTCTATTAAA
575095 AAA
66 AAA
575098 AATGTGTGAA
Statistics
Matches: 136, Mismatches: 5, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
73 47 0.35
74 89 0.65
ACGTcount: A:0.33, C:0.07, G:0.06, T:0.53
Consensus pattern (74 bp):
GATTATTTATTTATTTTTATTAATGATATATACCTTTTAATTTTATTTATGATCAGTCTATTAAA
AAACTTGAC
Found at i:576865 original size:5 final size:5
Alignment explanation
Indices: 576847--576882 Score: 54
Period size: 5 Copynumber: 7.0 Consensus size: 5
576837 AGAAAGAGAT
*
576847 CGGAGG CGGGG CGGAG CGGAG CGGAG CGGAG CGGAG
1 CGGA-G CGGAG CGGAG CGGAG CGGAG CGGAG CGGAG
576883 AGCAAAAGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
5 25 0.89
6 3 0.11
ACGTcount: A:0.17, C:0.19, G:0.64, T:0.00
Consensus pattern (5 bp):
CGGAG
Found at i:579828 original size:51 final size:51
Alignment explanation
Indices: 579752--579850 Score: 180
Period size: 51 Copynumber: 1.9 Consensus size: 51
579742 ATAACTTGAA
579752 TTCACGAAACAATGTAGTTAAGCAACTCTAAAACAGCTCCATAGAGGTGAG
1 TTCACGAAACAATGTAGTTAAGCAACTCTAAAACAGCTCCATAGAGGTGAG
* *
579803 TTCACGAAACAATGTAGTTAAGCAACTTTAAAATAGCTCCATAGAGGT
1 TTCACGAAACAATGTAGTTAAGCAACTCTAAAACAGCTCCATAGAGGT
579851 CAGAAGATCC
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (51 bp):
TTCACGAAACAATGTAGTTAAGCAACTCTAAAACAGCTCCATAGAGGTGAG
Found at i:584843 original size:14 final size:14
Alignment explanation
Indices: 584812--584909 Score: 57
Period size: 14 Copynumber: 7.3 Consensus size: 14
584802 AATATTAAAA
*
584812 AAAAAATTATTTATTT
1 AAAAAATTA-ATA-TT
*
584828 AAAAAACTAATATT
1 AAAAAATTAATATT
584842 --AAAATTAATATCT
1 AAAAAATTAATAT-T
* *
584855 ATAATA-TAATATT
1 AAAAAATTAATATT
584868 AAAAAATTAATATT
1 AAAAAATTAATATT
* * *
584882 ---TAATTTATTTT
1 AAAAAATTAATATT
584893 AAAAAA-TAATATT
1 AAAAAATTAATATT
584906 AAAA
1 AAAA
584910 TTAAAATCAA
Statistics
Matches: 63, Mismatches: 12, Indels: 17
0.68 0.13 0.18
Matches are distributed among these distances:
11 8 0.13
12 10 0.16
13 15 0.24
14 17 0.27
15 5 0.08
16 8 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
AAAAAATTAATATT
Found at i:584885 original size:26 final size:26
Alignment explanation
Indices: 584835--584913 Score: 85
Period size: 25 Copynumber: 3.1 Consensus size: 26
584825 TTTAAAAAAC
584835 TAATATT--AAAATTAATATCTATAAT
1 TAATATTAAAAAATTAATAT-TATAAT
584860 ATAATATTAAAAAATTAATATT-TAAT
1 -TAATATTAAAAAATTAATATTATAAT
* * *
584886 TTATTTTAAAAAA-TAATATTAAAAT
1 TAATATTAAAAAATTAATATTATAAT
584911 TAA
1 TAA
584914 AATCAAATAT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
24 7 0.15
25 16 0.35
26 11 0.24
27 1 0.02
28 11 0.24
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (26 bp):
TAATATTAAAAAATTAATATTATAAT
Found at i:584906 original size:64 final size:58
Alignment explanation
Indices: 584782--584913 Score: 167
Period size: 64 Copynumber: 2.2 Consensus size: 58
584772 TTATATGATA
584782 TAAAATTAAACATCTATAATAATATTAAAAAAAAAATTATTTATTTAAAAAACTAATAT
1 TAAAATT-AACATCTATAATAATATTAAAAAAAAAATTATTTATTTAAAAAACTAATAT
* *
584841 TAAAATTAATATCTATAATATAATATTAAAAAATTAATATTTAATTTATTTTAAAAAA-TAATAT
1 TAAAATTAACATCTAT-A-ATAATATTAAAAAA--AA-AATT-ATTTA-TTTAAAAAACTAATAT
584905 TAAAATTAA
1 TAAAATTAA
584914 AATCAAATAT
Statistics
Matches: 64, Mismatches: 2, Indels: 9
0.85 0.03 0.12
Matches are distributed among these distances:
58 8 0.12
59 8 0.12
60 14 0.22
62 2 0.03
63 3 0.05
64 20 0.31
65 9 0.14
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (58 bp):
TAAAATTAACATCTATAATAATATTAAAAAAAAAATTATTTATTTAAAAAACTAATAT
Found at i:586681 original size:77 final size:77
Alignment explanation
Indices: 586597--586740 Score: 261
Period size: 77 Copynumber: 1.9 Consensus size: 77
586587 GAGCCCTTAT
* *
586597 ATAAGAGAGATTCGTCCACGCCTCTATTTTTTTGGTATAATTAGTTTTTAGTCCCCTAACATTTT
1 ATAAGAGAGATTCGTCCACGCCACTATTTCTTTGGTATAATTAGTTTTTAGTCCCCTAACATTTT
586662 TTGAACCCCTAA
66 TTGAACCCCTAA
*
586674 ATAAGAGAGATTCGTCCACGCCACTATTTCTTTGGTATAATTAGTTTTTATTCCCCTAACATTTT
1 ATAAGAGAGATTCGTCCACGCCACTATTTCTTTGGTATAATTAGTTTTTAGTCCCCTAACATTTT
586739 TT
66 TT
586741 TAATTCAATC
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
77 64 1.00
ACGTcount: A:0.26, C:0.20, G:0.12, T:0.42
Consensus pattern (77 bp):
ATAAGAGAGATTCGTCCACGCCACTATTTCTTTGGTATAATTAGTTTTTAGTCCCCTAACATTTT
TTGAACCCCTAA
Found at i:587450 original size:3 final size:3
Alignment explanation
Indices: 587442--587480 Score: 53
Period size: 3 Copynumber: 13.0 Consensus size: 3
587432 AAACCCTCGG
*
587442 TCT TCT TCT TCC TCT T-T TCT TCTT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TC-T TCT TCT TCT TCT TCT
587481 CTCACACCCC
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
2 2 0.06
3 27 0.84
4 3 0.09
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TCT
Found at i:593345 original size:3 final size:3
Alignment explanation
Indices: 593337--593361 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
593327 ATCAATCTAG
593337 TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA T
593362 ATTTTTAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:596506 original size:47 final size:47
Alignment explanation
Indices: 596453--596548 Score: 183
Period size: 47 Copynumber: 2.0 Consensus size: 47
596443 TATTTGAAGC
*
596453 AGTAAATAGTTACTATTTCTCACACAAGTATGCCTATATGCAATGGA
1 AGTAAATAGTTACTATTTCTCACACAAGTATGCCCATATGCAATGGA
596500 AGTAAATAGTTACTATTTCTCACACAAGTATGCCCATATGCAATGGA
1 AGTAAATAGTTACTATTTCTCACACAAGTATGCCCATATGCAATGGA
596547 AG
1 AG
596549 AATGACGATA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 48 1.00
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (47 bp):
AGTAAATAGTTACTATTTCTCACACAAGTATGCCCATATGCAATGGA
Found at i:599535 original size:26 final size:26
Alignment explanation
Indices: 599483--599535 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
599473 AAATAAAATA
* *
599483 ATATAATATATTTTCTATGAATTTTT
1 ATATAATATATTTTCTATAAATATTT
*
599509 ATATAA-ATATTTTCATTTAAATATTT
1 ATATAATATATTTTC-TATAAATATTT
599535 A
1 A
599536 GAATACAACT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 15 0.65
ACGTcount: A:0.40, C:0.04, G:0.02, T:0.55
Consensus pattern (26 bp):
ATATAATATATTTTCTATAAATATTT
Found at i:605837 original size:17 final size:17
Alignment explanation
Indices: 605815--605848 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
605805 TATATTTATT
605815 ACATATGTAGATACGAG
1 ACATATGTAGATACGAG
605832 ACATATGTAGATACGAG
1 ACATATGTAGATACGAG
605849 TACAGAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.12, G:0.24, T:0.24
Consensus pattern (17 bp):
ACATATGTAGATACGAG
Found at i:609412 original size:14 final size:14
Alignment explanation
Indices: 609393--609445 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
609383 CAAGTCGAAT
609393 TTTTAATTTTTATA
1 TTTTAATTTTTATA
609407 TTTTAATTTAATTA-A
1 TTTTAATTT--TTATA
* *
609422 TTTTACTTTCTATA
1 TTTTAATTTTTATA
*
609436 TTTTTATTTT
1 TTTTAATTTT
609446 AAATTTAAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
13 2 0.06
14 17 0.55
15 9 0.29
16 3 0.10
ACGTcount: A:0.26, C:0.04, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTTAATTTTTATA
Found at i:625183 original size:29 final size:28
Alignment explanation
Indices: 625151--625223 Score: 71
Period size: 29 Copynumber: 2.5 Consensus size: 28
625141 TATATTTTCT
625151 AAATTAATAAAAATATTTAGATATTAT-AA
1 AAATTAATAAAAATATTTA-A-ATTATGAA
625180 AAATGTAA-AAAAATCTATTTAAATTATGAA
1 AAAT-TAATAAAAA--TATTTAAATTATGAA
*
625210 AAACT-ATAAAAATA
1 AAATTAATAAAAATA
625224 AATAATATGA
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
27 2 0.05
28 1 0.03
29 20 0.53
30 9 0.24
31 6 0.16
ACGTcount: A:0.60, C:0.03, G:0.04, T:0.33
Consensus pattern (28 bp):
AAATTAATAAAAATATTTAAATTATGAA
Found at i:625225 original size:23 final size:24
Alignment explanation
Indices: 625199--625245 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
625189 AAAATCTATT
*
625199 TAAAT-TATGAAAAACTATAAAAA
1 TAAATATATGAAAAAATATAAAAA
625222 TAAATAATATGAAAAAATATAAAA
1 TAAAT-ATATGAAAAAATATAAAA
625246 GAATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 5 0.24
25 16 0.76
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (24 bp):
TAAATATATGAAAAAATATAAAAA
Found at i:626782 original size:31 final size:31
Alignment explanation
Indices: 626747--626810 Score: 128
Period size: 31 Copynumber: 2.1 Consensus size: 31
626737 TTTTTCGATT
626747 GAAATGGGGGAATGTTGTGAAAGTTGATGCA
1 GAAATGGGGGAATGTTGTGAAAGTTGATGCA
626778 GAAATGGGGGAATGTTGTGAAAGTTGATGCA
1 GAAATGGGGGAATGTTGTGAAAGTTGATGCA
626809 GA
1 GA
626811 CACTTTGGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.33, C:0.03, G:0.39, T:0.25
Consensus pattern (31 bp):
GAAATGGGGGAATGTTGTGAAAGTTGATGCA
Found at i:628391 original size:33 final size:34
Alignment explanation
Indices: 628349--628414 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 34
628339 AGTTGACAAG
628349 TTGGAAATTTCATCTTGGTTGGTGG-CAAACTTA
1 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTA
*
628382 TTGGAAATTTCATTTTGGTTGGTGGCCAAACTT
1 TTGGAAATTTCATCTTGGTTGGTGGCCAAACTT
628415 TGAACATGTG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.23, C:0.12, G:0.24, T:0.41
Consensus pattern (34 bp):
TTGGAAATTTCATCTTGGTTGGTGGCCAAACTTA
Found at i:635977 original size:35 final size:35
Alignment explanation
Indices: 635931--636004 Score: 130
Period size: 35 Copynumber: 2.1 Consensus size: 35
635921 ATACGACAAG
*
635931 TACAACTATAGCTGACCATAATAATACCAGGAAAA
1 TACAACTATAGCTGACAATAATAATACCAGGAAAA
*
635966 TACAACTATAGCTGACAATAGTAATACCAGGAAAA
1 TACAACTATAGCTGACAATAATAATACCAGGAAAA
636001 TACA
1 TACA
636005 TGCATCCAAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
35 37 1.00
ACGTcount: A:0.49, C:0.19, G:0.12, T:0.20
Consensus pattern (35 bp):
TACAACTATAGCTGACAATAATAATACCAGGAAAA
Found at i:638463 original size:2 final size:2
Alignment explanation
Indices: 638456--638483 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
638446 CCCATCCTTT
638456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
638484 AACAATATGA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:642285 original size:24 final size:28
Alignment explanation
Indices: 642235--642289 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 28
642225 ATACTTTATT
642235 ATTTTATCTAATTATAAATATTAATTTA
1 ATTTTATCTAATTATAAATATTAATTTA
642263 ATTTT-TC-AATT-TAAA-ATTAATTTA
1 ATTTTATCTAATTATAAATATTAATTTA
642287 ATT
1 ATT
642290 ATCGTAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
24 12 0.44
25 4 0.15
26 4 0.15
27 2 0.07
28 5 0.19
ACGTcount: A:0.42, C:0.04, G:0.00, T:0.55
Consensus pattern (28 bp):
ATTTTATCTAATTATAAATATTAATTTA
Found at i:651138 original size:5 final size:6
Alignment explanation
Indices: 651111--651137 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
651101 TTTAAATATT
651111 AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAA
651138 TTTAGATATC
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:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:666619 original size:2 final size:2
Alignment explanation
Indices: 666612--666639 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
666602 TTTAGAGTGG
666612 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
666640 TAACACAATT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:668764 original size:18 final size:20
Alignment explanation
Indices: 668725--668765 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
668715 CATTTCAAAC
*
668725 AAACTCCTCAAATCTAGAAA
1 AAACTCCTCAAATATAGAAA
668745 AAAC-CCTCAAATAT-GAAA
1 AAACTCCTCAAATATAGAAA
668763 AAA
1 AAA
668766 AAAATCTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 7 0.35
19 9 0.45
20 4 0.20
ACGTcount: A:0.56, C:0.22, G:0.05, T:0.17
Consensus pattern (20 bp):
AAACTCCTCAAATATAGAAA
Done.