Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007859.1 Hibiscus syriacus cultivar Beakdansim tig00110221_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: 3538007
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 18
Found at i:1364826 original size:36 final size:36
Alignment explanation
Indices: 1364762--1364883 Score: 219
Period size: 37 Copynumber: 3.4 Consensus size: 36
1364752 GCTCGAAAAT
1364762 ATAAT-ATATTAAGATTTTATTTAAAAAAATAAATTA
1 ATAATAATATTAAGATTTTATTT-AAAAAATAAATTA
1364798 ATAATAATATTAAGATTTTATTTTAAAAAATAAATTA
1 ATAATAATATTAAGATTTTA-TTTAAAAAATAAATTA
1364835 ATAATAATATTAAGATTTTATTTAAAAAATAAATTA
1 ATAATAATATTAAGATTTTATTTAAAAAATAAATTA
1364871 ATAATAATATTAA
1 ATAATAATATTAA
1364884 TTTTTATGTA
Statistics
Matches: 84, Mismatches: 0, Indels: 4
0.95 0.00 0.05
Matches are distributed among these distances:
36 34 0.40
37 47 0.56
38 3 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (36 bp):
ATAATAATATTAAGATTTTATTTAAAAAATAAATTA
Found at i:1365343 original size:29 final size:29
Alignment explanation
Indices: 1365311--1365375 Score: 121
Period size: 29 Copynumber: 2.2 Consensus size: 29
1365301 GCTGCTTGAA
*
1365311 GTGAGTTTTCAGTGATATTGAATATTTTT
1 GTGAGTTTTAAGTGATATTGAATATTTTT
1365340 GTGAGTTTTAAGTGATATTGAATATTTTT
1 GTGAGTTTTAAGTGATATTGAATATTTTT
1365369 GTGAGTT
1 GTGAGTT
1365376 CGATAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.25, C:0.02, G:0.23, T:0.51
Consensus pattern (29 bp):
GTGAGTTTTAAGTGATATTGAATATTTTT
Found at i:1373571 original size:29 final size:28
Alignment explanation
Indices: 1373536--1373592 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 28
1373526 TAATTAAAAA
1373536 TAAAATTACAA-AACAA-AATAAATAAATAC
1 TAAAATTA-AACAA-AATAATAAA-AAATAC
1373565 TAAAATTAAACAAAATAATAAAAAATAC
1 TAAAATTAAACAAAATAATAAAAAATAC
1373593 AAATAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
28 10 0.38
29 16 0.62
ACGTcount: A:0.70, C:0.09, G:0.00, T:0.21
Consensus pattern (28 bp):
TAAAATTAAACAAAATAATAAAAAATAC
Found at i:1373596 original size:26 final size:26
Alignment explanation
Indices: 1373531--1373596 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 26
1373521 AATCCTAATT
1373531 AAAAATAAAATTACAAAACAAAATAAATA
1 AAAAATAAAATT---AAACAAAATAAATA
* *
1373560 AATACTAAAATTAAACAAAAT-AATA
1 AAAAATAAAATTAAACAAAATAAATA
1373585 AAAAATACAAAT
1 AAAAATA-AAAT
1373597 AATAAAGAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
25 9 0.28
26 13 0.41
29 10 0.31
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.20
Consensus pattern (26 bp):
AAAAATAAAATTAAACAAAATAAATA
Found at i:1373670 original size:30 final size:32
Alignment explanation
Indices: 1373597--1373659 Score: 80
Period size: 32 Copynumber: 2.1 Consensus size: 32
1373587 AAATACAAAT
1373597 AATA-AAGAAAATTAAAATATACAAGGATCTA
1 AATATAAGAAAATTAAAATATACAAGGATCTA
* *
1373628 AATATAATAAAATTTAAATA-A-AAGGA-CTA
1 AATATAAGAAAATTAAAATATACAAGGATCTA
1373657 AAT
1 AAT
1373660 TACGAGAAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
29 6 0.21
30 5 0.17
31 5 0.17
32 13 0.45
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.25
Consensus pattern (32 bp):
AATATAAGAAAATTAAAATATACAAGGATCTA
Found at i:1375182 original size:26 final size:26
Alignment explanation
Indices: 1375133--1375182 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
1375123 ATTTAAAATT
* *
1375133 AGAAAATTCAAGTTTGATTGTTATAC
1 AGAAAATTCAAGTTTGAGTATTATAC
*
1375159 AGAAAATTTAAGTTTGAGTATTAT
1 AGAAAATTCAAGTTTGAGTATTAT
1375183 TGTTAATTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.16, T:0.40
Consensus pattern (26 bp):
AGAAAATTCAAGTTTGAGTATTATAC
Found at i:1376819 original size:26 final size:26
Alignment explanation
Indices: 1376790--1376843 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
1376780 AATAGGGGTT
1376790 CATACTTGCCAACGCTCACTCCCATA
1 CATACTTGCCAACGCTCACTCCCATA
1376816 CATACTTGCCAACGCTCACTCCCATA
1 CATACTTGCCAACGCTCACTCCCATA
1376842 CA
1 CA
1376844 AGCGTATGAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.28, C:0.43, G:0.07, T:0.22
Consensus pattern (26 bp):
CATACTTGCCAACGCTCACTCCCATA
Found at i:1377574 original size:33 final size:33
Alignment explanation
Indices: 1377537--1377639 Score: 147
Period size: 33 Copynumber: 3.1 Consensus size: 33
1377527 GTACAATGAA
*
1377537 ATTTATATTTAAATATTGAAATAAAAATTAAAT
1 ATTTATATTTAAATATTAAAATAAAAATTAAAT
*
1377570 ATTTA-ATTTAAATATTAAAATATAAAATTCAAT
1 ATTTATATTTAAATATTAAAATA-AAAATTAAAT
1377603 ATTT-TATTTAAATATTAAAATAAAAATATTAAAT
1 ATTTATATTTAAATATTAAAAT-AAAA-ATTAAAT
1377637 ATT
1 ATT
1377640 ATTCACGGGA
Statistics
Matches: 63, Mismatches: 3, Indels: 7
0.86 0.04 0.10
Matches are distributed among these distances:
32 16 0.25
33 37 0.59
34 10 0.16
ACGTcount: A:0.54, C:0.01, G:0.01, T:0.44
Consensus pattern (33 bp):
ATTTATATTTAAATATTAAAATAAAAATTAAAT
Found at i:1377586 original size:20 final size:20
Alignment explanation
Indices: 1377536--1377588 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 20
1377526 GGTACAATGA
*
1377536 AATTTATAT-TTAAATATTG
1 AATTTAAATATTAAATATTG
* * *
1377555 AA-ATAAAAATTAAATATTT
1 AATTTAAATATTAAATATTG
1377574 AATTTAAATATTAAA
1 AATTTAAATATTAAA
1377589 ATATAAAATT
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
18 3 0.12
19 13 0.50
20 10 0.38
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
AATTTAAATATTAAATATTG
Found at i:1377587 original size:7 final size:7
Alignment explanation
Indices: 1377545--1377640 Score: 64
Period size: 7 Copynumber: 14.4 Consensus size: 7
1377535 AAATTTATAT
1377545 TTAAATA
1 TTAAATA
1377552 TTGAAATA
1 TT-AAATA
1377560 --AAA-A
1 TTAAATA
1377564 TTAAATA
1 TTAAATA
*
1377571 TTTAAT-
1 TTAAATA
1377577 TTAAATA
1 TTAAATA
1377584 TTAAA-A
1 TTAAATA
1377590 TATAAA-A
1 T-TAAATA
*
1377597 TTCAATA
1 TTAAATA
**
1377604 TTTTAT-
1 TTAAATA
1377610 TTAAATA
1 TTAAATA
1377617 TTAAA-A
1 TTAAATA
*
1377623 TAAAAATA
1 T-TAAATA
1377631 TTAAATA
1 TTAAATA
1377638 TTA
1 TTA
1377641 TTCACGGGAA
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
4 1 0.01
5 3 0.04
6 19 0.27
7 40 0.57
8 7 0.10
ACGTcount: A:0.56, C:0.01, G:0.01, T:0.42
Consensus pattern (7 bp):
TTAAATA
Found at i:1377695 original size:25 final size:25
Alignment explanation
Indices: 1377661--1377710 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
1377651 TGTGAATAAT
1377661 CATTGCCTTAAATAATCATTATTAA
1 CATTGCCTTAAATAATCATTATTAA
1377686 CATTGCCTTAAATAATCATTATTAA
1 CATTGCCTTAAATAATCATTATTAA
1377711 ATCATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.40, C:0.16, G:0.04, T:0.40
Consensus pattern (25 bp):
CATTGCCTTAAATAATCATTATTAA
Found at i:1377728 original size:13 final size:13
Alignment explanation
Indices: 1377698--1377746 Score: 84
Period size: 13 Copynumber: 3.9 Consensus size: 13
1377688 TTGCCTTAAA
1377698 TAATCATTATTA-
1 TAATCATTATTAG
1377710 -AATCATTATTAG
1 TAATCATTATTAG
1377722 TAATCATTATTAG
1 TAATCATTATTAG
1377735 TAATCATTATTA
1 TAATCATTATTA
1377747 AATCATTGAT
Statistics
Matches: 35, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
11 11 0.31
13 24 0.69
ACGTcount: A:0.41, C:0.08, G:0.04, T:0.47
Consensus pattern (13 bp):
TAATCATTATTAG
Found at i:1377730 original size:24 final size:24
Alignment explanation
Indices: 1377697--1377753 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
1377687 ATTGCCTTAA
1377697 ATAATCATTATTA-AATCATTATT
1 ATAATCATTATTAGAATCATTATT
1377720 AGTAATCATTATTAGTAATCATTATT
1 A-TAATCATTATTAG-AATCATTATT
1377746 A-AATCATT
1 ATAATCATT
1377754 GATCAAATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
23 1 0.03
24 19 0.61
26 11 0.35
ACGTcount: A:0.42, C:0.09, G:0.04, T:0.46
Consensus pattern (24 bp):
ATAATCATTATTAGAATCATTATT
Found at i:1380714 original size:45 final size:45
Alignment explanation
Indices: 1380644--1380737 Score: 143
Period size: 45 Copynumber: 2.1 Consensus size: 45
1380634 CTTTCCTGTG
* *
1380644 CAACCACCAACCTACCCAAGATATTAATGGATAATTAATAACCAC
1 CAACAACCAACCTACCCAAGATATTAAAGGATAATTAATAACCAC
* * *
1380689 CAACAACCAACCTACCCGAGTTATTAAAGGATAATTATTAACCAC
1 CAACAACCAACCTACCCAAGATATTAAAGGATAATTAATAACCAC
1380734 CAAC
1 CAAC
1380738 CTATCGATAT
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.44, C:0.29, G:0.07, T:0.20
Consensus pattern (45 bp):
CAACAACCAACCTACCCAAGATATTAAAGGATAATTAATAACCAC
Found at i:1387527 original size:17 final size:17
Alignment explanation
Indices: 1387505--1387537 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
1387495 CAACGTCAGC
1387505 GCGTCACTAAAAATGCT
1 GCGTCACTAAAAATGCT
1387522 GCGTCACTAAAAATGC
1 GCGTCACTAAAAATGC
1387538 CATTTTCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.36, C:0.24, G:0.18, T:0.21
Consensus pattern (17 bp):
GCGTCACTAAAAATGCT
Found at i:1389592 original size:2 final size:2
Alignment explanation
Indices: 1389585--1389634 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
1389575 AAGATATAAA
1389585 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
1389627 AT AT AT AT
1 AT AT AT AT
1389635 GTTTTTGAGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1397543 original size:35 final size:35
Alignment explanation
Indices: 1397490--1397627 Score: 163
Period size: 35 Copynumber: 3.9 Consensus size: 35
1397480 ATTAGATCTG
1397490 TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
** * * * *
1397525 TAAGGAATTTTCAATTTGATCAAGT-TGAACCTGCTG
1 TAAGGAATTACCAGTTTGATC-GGTCTGAACCT-ATA
*
1397561 TAAGGAATTACCAGTTCGATCGGTCTGAACCTATA
1 TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
*
1397596 TAAGGAATTACCACTTTGATCGAG-CTGAACCT
1 TAAGGAATTACCAGTTTGATCG-GTCTGAACCT
1397628 GCAGAGACTT
Statistics
Matches: 84, Mismatches: 15, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
35 56 0.67
36 28 0.33
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Consensus pattern (35 bp):
TAAGGAATTACCAGTTTGATCGGTCTGAACCTATA
Found at i:1397603 original size:71 final size:71
Alignment explanation
Indices: 1397487--1397629 Score: 232
Period size: 71 Copynumber: 2.0 Consensus size: 71
1397477 CACATTAGAT
* ** *
1397487 CTGTAAGGAATTACCAGTTTGATCGGTCTGAACCTATATAAGGAATTTTCAATTTGATCAAGTTG
1 CTGTAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
1397552 AACCTG
66 AACCTG
* *
1397558 CTGTAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCACTTTGATCGAGCTG
1 CTGTAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
1397623 AACCTG
66 AACCTG
1397629 C
1 C
1397630 AGAGACTTCA
Statistics
Matches: 66, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 66 1.00
ACGTcount: A:0.30, C:0.19, G:0.20, T:0.31
Consensus pattern (71 bp):
CTGTAAGGAATTACCAGTTCGATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCAAGCTG
AACCTG
Found at i:1401777 original size:35 final size:34
Alignment explanation
Indices: 1401731--1401865 Score: 162
Period size: 35 Copynumber: 3.8 Consensus size: 34
1401721 CCTTAGATCC
*
1401731 ATAAGGAATTACTAGTTTGATCGGTCTGAACCTAT
1 ATAAGGAATTACCAGTTTGATCGG-CTGAACCTAT
* * *
1401766 ATAAGGAATTACCAATTTGATCGAGCTAAACCTAC
1 ATAAGGAATTACCAGTTTGATCG-GCTGAACCTAT
* * *
1401801 AGTAAGGAATTACCAGTTGGATCAGACTGAATCTAT
1 A-TAAGGAATTACCAGTTTGATC-GGCTGAACCTAT
1401837 ATAAGGAATTACCAGTTTGATCGAGCTGA
1 ATAAGGAATTACCAGTTTGATCG-GCTGA
1401866 CTGCAAAGAC
Statistics
Matches: 84, Mismatches: 12, Indels: 8
0.81 0.12 0.08
Matches are distributed among these distances:
34 1 0.01
35 54 0.64
36 28 0.33
37 1 0.01
ACGTcount: A:0.36, C:0.16, G:0.20, T:0.29
Consensus pattern (34 bp):
ATAAGGAATTACCAGTTTGATCGGCTGAACCTAT
Found at i:1401848 original size:71 final size:71
Alignment explanation
Indices: 1401732--1401863 Score: 210
Period size: 71 Copynumber: 1.9 Consensus size: 71
1401722 CTTAGATCCA
* * * *
1401732 TAAGGAATTACTAGTTTGATCGGTCTGAACCTATATAAGGAATTACCAATTTGATCGAGCTAAAC
1 TAAGGAATTACCAGTTGGATCAGACTGAACCTATATAAGGAATTACCAATTTGATCGAGCTAAAC
1401797 CTACAG
66 CTACAG
* *
1401803 TAAGGAATTACCAGTTGGATCAGACTGAATCTATATAAGGAATTACCAGTTTGATCGAGCT
1 TAAGGAATTACCAGTTGGATCAGACTGAACCTATATAAGGAATTACCAATTTGATCGAGCT
1401864 GACTGCAAAG
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
71 55 1.00
ACGTcount: A:0.35, C:0.16, G:0.20, T:0.30
Consensus pattern (71 bp):
TAAGGAATTACCAGTTGGATCAGACTGAACCTATATAAGGAATTACCAATTTGATCGAGCTAAAC
CTACAG
Found at i:1403651 original size:20 final size:20
Alignment explanation
Indices: 1403594--1403642 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
1403584 AACCGGTCGA
* **
1403594 GTCAAGTTGACTTGGTTCAG
1 GTCAGGTTGACTCAGTTCAG
*
1403614 GTCAGGTTGACTCAGTTCGG
1 GTCAGGTTGACTCAGTTCAG
1403634 GTCAGGTTG
1 GTCAGGTTG
1403643 GTCCAGTTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.16, C:0.16, G:0.35, T:0.33
Consensus pattern (20 bp):
GTCAGGTTGACTCAGTTCAG
Found at i:1410332 original size:2 final size:2
Alignment explanation
Indices: 1410325--1410378 Score: 62
Period size: 2 Copynumber: 28.0 Consensus size: 2
1410315 ATTTTCGAAA
1410325 AT AT AT AT GAT AT AT AT AT AT AT AT AT -T AT A- AT AT AT AGT -T
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
1410366 AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT
1410379 TAGATATTTG
Statistics
Matches: 46, Mismatches: 0, Indels: 12
0.79 0.00 0.21
Matches are distributed among these distances:
1 4 0.09
2 39 0.85
3 3 0.07
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1410385 original size:24 final size:24
Alignment explanation
Indices: 1410324--1410385 Score: 65
Period size: 24 Copynumber: 2.5 Consensus size: 24
1410314 GATTTTCGAA
1410324 AATATATATGATATATATATATATAT
1 AATAT-TA-GATATATATATATATAT
*
1410350 ATTA-TA-ATATATAGTTATATATAT
1 AATATTAGATATATA--TATATATAT
1410374 AATATTAGATAT
1 AATATTAGATAT
1410386 TTGATATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
22 7 0.23
24 14 0.47
25 2 0.07
26 7 0.23
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.47
Consensus pattern (24 bp):
AATATTAGATATATATATATATAT
Found at i:1410491 original size:29 final size:26
Alignment explanation
Indices: 1410459--1410512 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
1410449 AATTTTTAAA
1410459 ATTATACGAGTTTTGAAAATATAATATAT
1 ATTATA-GAGTTTT-AAAATAT-ATATAT
*
1410488 ATTATATAGTTTTAAAATATATATA
1 ATTATAGAGTTTTAAAATATATATA
1410513 GTTTTTAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 5 0.21
27 7 0.29
28 6 0.25
29 6 0.25
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (26 bp):
ATTATAGAGTTTTAAAATATATATAT
Found at i:1410535 original size:3 final size:3
Alignment explanation
Indices: 1410527--1410565 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
1410517 TTAAAGGAAT
1410527 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1410566 GTATTTTCTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:1414072 original size:65 final size:64
Alignment explanation
Indices: 1413924--1414080 Score: 212
Period size: 65 Copynumber: 2.4 Consensus size: 64
1413914 TGCACTAAGA
*
1413924 GTGCATCGATGCATAAAATGCATTCGATATTTTAAAATAGCCTGAGTGCATCGATGCATGGCTT
1 GTGCATCGATGCATAAAATGCATTCGATATTTTAAAATAGCCTAAGTGCATCGATGCATGGCTT
**
1413988 GTGCATCGATGCATAAAATGCATTCGATATTTTCGTAAAA-A-CCTAAGTGCATCGATGTGTGG-
1 GTGCATCGATGCATAAAATGCATTCGATA-TTT--TAAAATAGCCTAAGTGCATCGATGCATGGC
1414050 TAT
63 T-T
* *
1414053 GTGTATCGATGCATAAAATGTATTCGAT
1 GTGCATCGATGCATAAAATGCATTCGAT
1414081 GTCCAATTTA
Statistics
Matches: 84, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
64 30 0.36
65 48 0.57
66 1 0.01
67 5 0.06
ACGTcount: A:0.31, C:0.15, G:0.22, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATAAAATGCATTCGATATTTTAAAATAGCCTAAGTGCATCGATGCATGGCTT
Found at i:1416875 original size:45 final size:44
Alignment explanation
Indices: 1416788--1416882 Score: 115
Period size: 45 Copynumber: 2.1 Consensus size: 44
1416778 CTTGTGCATT
*
1416788 GATGCAAATTCAAGGCGTGCATCGGTGCATCTTTATGATGTATC
1 GATGCAAATTCAAGGCGTGCATCGATGCATCTTTATGATGTATC
*
1416832 GATGCACATTCAAAGG-GATGCATCGATGCA-CTTTCAT-AGTGTATC
1 GATGCAAATTC-AAGGCG-TGCATCGATGCATCTTT-ATGA-TGTATC
1416877 GATGCA
1 GATGCA
1416883 TTATGCACAA
Statistics
Matches: 45, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
44 16 0.36
45 29 0.64
ACGTcount: A:0.27, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
GATGCAAATTCAAGGCGTGCATCGATGCATCTTTATGATGTATC
Found at i:1416879 original size:21 final size:23
Alignment explanation
Indices: 1416824--1416882 Score: 68
Period size: 24 Copynumber: 2.6 Consensus size: 23
1416814 GCATCTTTAT
1416824 GATGTATCGATGCACATTCAAAGG
1 GATGTATCGATGCACATTCAAA-G
* * *
1416848 GATGCATCGATGCACTTTCATA-
1 GATGTATCGATGCACATTCAAAG
1416870 G-TGTATCGATGCA
1 GATGTATCGATGCA
1416883 TTATGCACAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 11 0.35
22 1 0.03
24 19 0.61
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (23 bp):
GATGTATCGATGCACATTCAAAG
Found at i:1422397 original size:65 final size:64
Alignment explanation
Indices: 1422271--1422423 Score: 238
Period size: 65 Copynumber: 2.4 Consensus size: 64
1422261 AGAGTGCACG
* * *
1422271 GATGCATAAAATGCATTCGATGTTTTAAAATAGCCTGAGTGCATCGATGCATGGCTTGTGCATT
1 GATGCATAAAATGCATTCGATGTTTTAAAATAACCTGAGTGCATCGATCCATGGCTTGTGCATC
1422335 GATGCATAAAATGCATTCGATGTTTTCATAAA-AACCTGAGTGCATCGATCCATGG-TATGTGCA
1 GATGCATAAAATGCATTCGATGTTTT-A-AAATAACCTGAGTGCATCGATCCATGGCT-TGTGCA
1422398 TC
63 TC
1422400 GATGCATAAAATGCATTCGATGTT
1 GATGCATAAAATGCATTCGATGTT
1422424 AAATTTATTC
Statistics
Matches: 83, Mismatches: 3, Indels: 5
0.91 0.03 0.05
Matches are distributed among these distances:
64 27 0.33
65 53 0.64
66 3 0.04
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (64 bp):
GATGCATAAAATGCATTCGATGTTTTAAAATAACCTGAGTGCATCGATCCATGGCTTGTGCATC
Found at i:1422462 original size:65 final size:64
Alignment explanation
Indices: 1422271--1422464 Score: 179
Period size: 65 Copynumber: 3.0 Consensus size: 64
1422261 AGAGTGCACG
*
1422271 GATGCATAAAATGCATTCGATGTTTTAAA---ATAGC-CTGAGTGCATCGATGCATGGCTTGTGC
1 GATGCATAAAATGCATTCGATG--TTAAATTTATA-CAATGAGTGCATCGATGCATGG-TTGTGC
*
1422332 ATT
62 ATC
* * *
1422335 GATGCATAAAATGCATTCGATGTT---TTCATAAAAACCTGAGTGCATCGATCCATGGTATGTGC
1 GATGCATAAAATGCATTCGATGTTAAATTTAT-ACAA--TGAGTGCATCGATGCATGGT-TGTGC
1422397 ATC
62 ATC
* *
1422400 GATGCATAAAATGCATTCGATGTTAAATTTATTCAATG-GTGTATCGATGCATGGATTGGTGCAT
1 GATGCATAAAATGCATTCGATGTTAAATTTATACAATGAGTGCATCGATGCATGG-TT-GTGCAT
1422464 C
64 C
1422465 AGTACACTCT
Statistics
Matches: 108, Mismatches: 9, Indels: 25
0.76 0.06 0.18
Matches are distributed among these distances:
62 4 0.04
63 1 0.01
64 38 0.35
65 59 0.55
67 2 0.02
68 4 0.04
ACGTcount: A:0.29, C:0.15, G:0.22, T:0.33
Consensus pattern (64 bp):
GATGCATAAAATGCATTCGATGTTAAATTTATACAATGAGTGCATCGATGCATGGTTGTGCATC
Found at i:1423703 original size:62 final size:62
Alignment explanation
Indices: 1423633--1423752 Score: 195
Period size: 62 Copynumber: 1.9 Consensus size: 62
1423623 ATGGAGATAG
*
1423633 TCCACCACTATATTTCGTGTTGGATTGATTCAGAGTAGTCTCTCCTAAAAAGGAAAGCATAA
1 TCCACCACTATATTTCGTGTTGGATTAATTCAGAGTAGTCTCTCCTAAAAAGGAAAGCATAA
* * * *
1423695 TCCACCACTATATTTTGTTTTGGATTAATTTAGAGTAGTCTCTCCTAAAAAGGCAAGC
1 TCCACCACTATATTTCGTGTTGGATTAATTCAGAGTAGTCTCTCCTAAAAAGGAAAGC
1423753 TCAATAGTGG
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 53 1.00
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Consensus pattern (62 bp):
TCCACCACTATATTTCGTGTTGGATTAATTCAGAGTAGTCTCTCCTAAAAAGGAAAGCATAA
Found at i:1430655 original size:2 final size:2
Alignment explanation
Indices: 1430644--1430673 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
1430634 TATACATTAG
1430644 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1430674 TATGTTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1431686 original size:226 final size:225
Alignment explanation
Indices: 1431242--1431836 Score: 680
Period size: 226 Copynumber: 2.6 Consensus size: 225
1431232 GACAGTCGAC
* * * * * *
1431242 TCAGAATCGACTGCAGTCTAGCTTAACTCTGCGACGAGGAACTAGTTTCCAATTGAAGTTTTTAG
1 TCAGACTCAACTGCAGTCTAGCTTAACTCAGCGACGAGGAGCAAGTTTCCAGTTGAAGTTTTTAG
* * * * * * *
1431307 GCTAAGTTTCAACTTCATGACGAAGGATTCATGAC-CCAAAAGCACA-TCCAAAATCGAATGCAT
66 GCCAAGTTTCAACTTCA-CATGGAGGATTCTTGACTCCAAAA-CACATTCAAAAATCGATTGCA-
* * * * **
1431370 TTTTGT-TTAAATCAACAGGGAGGAGTCATCTTTTAGTCAAATATTTTTGAAGTCAATTTCAACT
128 ATTTGTCTTAACTCAACAGGGAGGAGCCATCTTCTAGTCAAATATTTTCAAAGTCAATTTCAACT
* *
1431434 CTACAATGGAGGATATTGAGTTCAAGAGCCAAT
193 CCACAATGGAGGATATAGAGTTCAAGAGCCAAT
* * * * *
1431467 TCAGACTCAATTGCAATCTAGCTTAACTCAACAACGAGGAGCAATTTTCCAGTTGAAGTTTTTAG
1 TCAGACTCAACTGCAGTCTAGCTTAACTCAGCGACGAGGAGCAAGTTTCCAGTTGAAGTTTTTAG
* *
1431532 GCCAAGTTTCAACTTCACAATGGAGGATTCTTGACTCTAAAACACATTCAAAAACCGATTGCAAT
66 GCCAAGTTTCAACTTCAC-ATGGAGGATTCTTGACTCCAAAACACATTCAAAAATCGATTGCAAT
*
1431597 TTGTCTTAACTCAACAGTGAGGAGCCATCTTCTAGTCAAATATTTTCAAAGTCAATTTCAACTCC
130 TTGTCTTAACTCAACAGGGAGGAGCCATCTTCTAGTCAAATATTTTCAAAGTCAATTTCAACTCC
1431662 AC-ATAGGAGGATATAGAGTTCAAGAGCCAAT
195 ACAAT-GGAGGATATAGAGTTCAAGAGCCAAT
* * * * * ** * *
1431693 TCATAGTCGACTGTAGTCTAGCTTAACTCAGTGGTGAGGAG-ATAGTTTCCAG-AGTATGTTTTT
1 TCAGACTCAACTGCAGTCTAGCTTAACTCAGCGACGAGGAGCA-AGTTTCCAGTTG-AAG-TTTT
* * * *
1431756 TTGGCCAAGTTTCAACTTCACATCGGAGGATTCTTGACTCGAAAACACATCCAAAAATTGATTGC
63 TAGGCCAAGTTTCAACTTCACAT-GGAGGATTCTTGACTCCAAAACACATTCAAAAATCGATTGC
*
1431821 AATTTGGCTTAACTCA
127 AATTTGTCTTAACTCA
1431837 GTGATGAGAA
Statistics
Matches: 312, Mismatches: 49, Indels: 16
0.83 0.13 0.04
Matches are distributed among these distances:
225 96 0.31
226 140 0.45
227 76 0.24
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.30
Consensus pattern (225 bp):
TCAGACTCAACTGCAGTCTAGCTTAACTCAGCGACGAGGAGCAAGTTTCCAGTTGAAGTTTTTAG
GCCAAGTTTCAACTTCACATGGAGGATTCTTGACTCCAAAACACATTCAAAAATCGATTGCAATT
TGTCTTAACTCAACAGGGAGGAGCCATCTTCTAGTCAAATATTTTCAAAGTCAATTTCAACTCCA
CAATGGAGGATATAGAGTTCAAGAGCCAAT
Found at i:1432281 original size:2 final size:2
Alignment explanation
Indices: 1432185--1432268 Score: 63
Period size: 2 Copynumber: 44.0 Consensus size: 2
1432175 TTTTCAAAAA
* * * *
1432185 AT AT AT AT GGT AT AT AT AT -T AT A- AT AT AT AGT TT TT AG A- AT
1 AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT
*
1432226 AT AT AT AT AT AT AT AT AT AT AT A- AT AT -T AT AT AT -T AG AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1432265 AT AT
1 AT AT
1432269 TTGAAAATAT
Statistics
Matches: 67, Mismatches: 7, Indels: 16
0.74 0.08 0.18
Matches are distributed among these distances:
1 6 0.09
2 59 0.88
3 2 0.03
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1432306 original size:28 final size:29
Alignment explanation
Indices: 1432265--1432324 Score: 86
Period size: 28 Copynumber: 2.1 Consensus size: 29
1432255 TATATTAGAT
*
1432265 ATATTTGAAAATATATAGTTTTTGAAAAC
1 ATATTTGAAAATATATAATTTTTGAAAAC
* *
1432294 ATATTTG-ATATATATAATTTTTGAAATC
1 ATATTTGAAAATATATAATTTTTGAAAAC
1432322 ATA
1 ATA
1432325 CGATTTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
28 21 0.75
29 7 0.25
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.45
Consensus pattern (29 bp):
ATATTTGAAAATATATAATTTTTGAAAAC
Found at i:1434075 original size:65 final size:65
Alignment explanation
Indices: 1433998--1434133 Score: 184
Period size: 65 Copynumber: 2.1 Consensus size: 65
1433988 CATTAATTGT
* * *
1433998 ATTCCATGTTTCAAAATAGCCAGGAGTGCATCGAAGCAT-GTTATGTGCATCGGTACACAAAATC
1 ATTCGATGTTTCAAAATAGCCAAGAGTGCATCGAAGCATGGCT-TGTGCATCGGTACACAAAATC
1434062 A
65 A
*** * *
1434063 ATTCGATGTTTCAAAATATTTAAGAGTGCATCGATGCATGGCTTGTGCATCGGTACACAAAATGA
1 ATTCGATGTTTCAAAATAGCCAAGAGTGCATCGAAGCATGGCTTGTGCATCGGTACACAAAATCA
1434128 ATTCGA
1 ATTCGA
1434134 AATAGGTATG
Statistics
Matches: 62, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
65 60 0.97
66 2 0.03
ACGTcount: A:0.33, C:0.18, G:0.21, T:0.29
Consensus pattern (65 bp):
ATTCGATGTTTCAAAATAGCCAAGAGTGCATCGAAGCATGGCTTGTGCATCGGTACACAAAATCA
Found at i:1440726 original size:56 final size:55
Alignment explanation
Indices: 1440640--1440839 Score: 258
Period size: 56 Copynumber: 3.6 Consensus size: 55
1440630 CAGGGCCCCA
* * *
1440640 AAAAATTAGGGCCCCAAAATCGAGTATATCTATCAGTTGTTGTCATTAATAAGCAT
1 AAAAA-TAGGGGCCCGAAATCGAGTATATCTATCAGTTGTTGTCATTAAGAAGCAT
1440696 AAAAATAGGGGCCCTGAAATCGAGTATATCTATCAGTTGTT-TCCATTAAGAAGCAT
1 AAAAATAGGGGCCC-GAAATCGAGTATATCTATCAGTTGTTGT-CATTAAGAAGCAT
* * * * *
1440752 AAAAATAAAGGCCCCGAAATCGAGTACATATATCAGTTGTTGCCATTAAGAAGCAT
1 AAAAAT-AGGGGCCCGAAATCGAGTATATCTATCAGTTGTTGTCATTAAGAAGCAT
* *
1440808 AAAAATAGGGGGCCCGAAATTGAATATATCTA
1 AAAAATA-GGGGCCCGAAATCGAGTATATCTA
1440840 GAAAATAAGA
Statistics
Matches: 125, Mismatches: 14, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
55 10 0.08
56 109 0.87
57 6 0.05
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (55 bp):
AAAAATAGGGGCCCGAAATCGAGTATATCTATCAGTTGTTGTCATTAAGAAGCAT
Found at i:1441550 original size:18 final size:18
Alignment explanation
Indices: 1441522--1441563 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
1441512 TTAAATGAAG
*
1441522 AAAAAGGAATTTAAT-TA
1 AAAAAGGAATTGAATGTA
*
1441539 AATAAAGTAATTGAATGTA
1 AA-AAAGGAATTGAATGTA
1441558 AAAAAG
1 AAAAAG
1441564 AGTTTTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 2 0.10
18 15 0.71
19 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.14, T:0.26
Consensus pattern (18 bp):
AAAAAGGAATTGAATGTA
Found at i:1453416 original size:23 final size:22
Alignment explanation
Indices: 1453366--1453421 Score: 67
Period size: 23 Copynumber: 2.5 Consensus size: 22
1453356 TCATAAAATA
* * *
1453366 AATATAATTTTGATATATATAT
1 AATATAGTTTTGAAATATAGAT
*
1453388 AGTATAGTTTTGAAAATATAGAT
1 AATATAGTTTTG-AAATATAGAT
1453411 AATATAGTTTT
1 AATATAGTTTT
1453422 ATAAAATAAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
22 10 0.36
23 18 0.64
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (22 bp):
AATATAGTTTTGAAATATAGAT
Found at i:1453531 original size:16 final size:15
Alignment explanation
Indices: 1453487--1453541 Score: 58
Period size: 14 Copynumber: 3.5 Consensus size: 15
1453477 GTTTAAAAAT
*
1453487 AAAATATAATAGTAA
1 AAAATATAATAATAA
*
1453502 AAAATATAA-GATAA
1 AAAATATAATAATAA
1453516 AAAATATATATAATAA
1 AAAATATA-ATAATAA
1453532 TAATAATATA
1 -AA-AATATA
1453542 GTTTTTGAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
14 11 0.33
15 10 0.30
16 4 0.12
17 2 0.06
18 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (15 bp):
AAAATATAATAATAA
Found at i:1454486 original size:30 final size:30
Alignment explanation
Indices: 1454427--1454515 Score: 144
Period size: 30 Copynumber: 3.0 Consensus size: 30
1454417 CCCGAAGGAC
* *
1454427 CTATCCAGAGGTCATACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1454456 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1454486 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1454516 ACTGTCCATA
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
29 19 0.34
30 37 0.66
ACGTcount: A:0.31, C:0.26, G:0.21, T:0.21
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1454551 original size:31 final size:31
Alignment explanation
Indices: 1454511--1454611 Score: 105
Period size: 31 Copynumber: 3.2 Consensus size: 31
1454501 AAAGATCCTC
*
1454511 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
1454542 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
* * * *
1454573 GTTAAAACTGTCCATATGTTTCGTAAAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
1454605 GGTAAAC
1 GGTAAAC
1454612 CCTCGACTCT
Statistics
Matches: 55, Mismatches: 12, Indels: 6
0.75 0.16 0.08
Matches are distributed among these distances:
31 30 0.55
32 25 0.45
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.31
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:1454588 original size:32 final size:32
Alignment explanation
Indices: 1454514--1454610 Score: 110
Period size: 32 Copynumber: 3.1 Consensus size: 32
1454504 GATCCTCGGT
* *
1454514 AAACTGTCCATATGT-TCCTTAGAACATAGGT-
1 AAACTGTCCATATGTCT-CGTAAAACATAGGTA
* *
1454545 ATACTGTCCATATGTCTCG-AAAGACATAGTTA
1 AAACTGTCCATATGTCTCGTAAA-ACATAGGTA
*
1454577 AAACTGTCCATATGTTTCGTAAAACATAGGTA
1 AAACTGTCCATATGTCTCGTAAAACATAGGTA
1454609 AA
1 AA
1454611 CCCTCGACTC
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
30 2 0.04
31 22 0.40
32 28 0.51
33 3 0.05
ACGTcount: A:0.36, C:0.18, G:0.15, T:0.31
Consensus pattern (32 bp):
AAACTGTCCATATGTCTCGTAAAACATAGGTA
Found at i:1455456 original size:2 final size:2
Alignment explanation
Indices: 1455449--1455508 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
1455439 ATACAATTCC
1455449 TA TA TA TA 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
1455491 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
1455509 CTCATGTAAT
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1455591 original size:29 final size:29
Alignment explanation
Indices: 1455537--1455592 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1455527 TTTCTCTTGT
* *
1455537 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
1455566 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
1455593 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:1456005 original size:21 final size:21
Alignment explanation
Indices: 1455981--1456025 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1455971 TGTTGTTCGT
* *
1455981 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1456002 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1456023 TTG
1 TTG
1456026 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:1458934 original size:30 final size:30
Alignment explanation
Indices: 1458875--1458963 Score: 135
Period size: 30 Copynumber: 3.0 Consensus size: 30
1458865 CCCGAAGGAT
* * *
1458875 CTATCCAGAGGTCACACAGA-CCCCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1458904 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
*
1458934 CTGTCCAGAGGTCATAAAGATCCTCGGTAA
1 CTATCCAGAGGTCATAAAGATCCTCGGTAA
1458964 ACTGTCCATA
Statistics
Matches: 55, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
29 18 0.33
30 37 0.67
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.20
Consensus pattern (30 bp):
CTATCCAGAGGTCATAAAGATCCTCGGTAA
Found at i:1458999 original size:31 final size:31
Alignment explanation
Indices: 1458959--1459059 Score: 114
Period size: 31 Copynumber: 3.2 Consensus size: 31
1458949 AAAGATCCTC
*
1458959 GGTAAACTGTCCATATGTTCCTTAGAACATA
1 GGTAAACTGTCCATATGTTCCATAGAACATA
* * *
1458990 GGTATACTGTCCATATGTCTCGAAAG-ACATA
1 GGTAAACTGTCCATATGT-TCCATAGAACATA
* * *
1459021 GGTAAAACTGTCCATATGTTTCGTAAAACATA
1 GGT-AAACTGTCCATATGTTCCATAGAACATA
1459053 GGTAAAC
1 GGTAAAC
1459060 CCTCGACTCT
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
31 31 0.54
32 26 0.46
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.30
Consensus pattern (31 bp):
GGTAAACTGTCCATATGTTCCATAGAACATA
Found at i:1459036 original size:32 final size:31
Alignment explanation
Indices: 1458962--1459058 Score: 108
Period size: 32 Copynumber: 3.1 Consensus size: 31
1458952 GATCCTCGGT
***
1458962 AAACTGTCCATATGTTCCTTAGAACATAGGT-
1 AAACTGTCCATATGTTCGAAAG-ACATAGGTA
*
1458993 ATACTGTCCATATGTCTCGAAAGACATAGGTA
1 AAACTGTCCATATGT-TCGAAAGACATAGGTA
1459025 AAACTGTCCATATGTTTCGTAAA-ACATAGGTA
1 AAACTGTCCATATG-TTCG-AAAGACATAGGTA
1459057 AA
1 AA
1459059 CCCTCGACTC
Statistics
Matches: 57, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
31 22 0.39
32 31 0.54
33 4 0.07
ACGTcount: A:0.36, C:0.18, G:0.16, T:0.30
Consensus pattern (31 bp):
AAACTGTCCATATGTTCGAAAGACATAGGTA
Found at i:1460004 original size:29 final size:29
Alignment explanation
Indices: 1459950--1460005 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
1459940 TTTCTCTTGT
* *
1459950 TATCATATAAATCATTGCCATATAACACA
1 TATCATATAAATCATTACCACATAACACA
*
1459979 TATCATATAAATTCA-TACCACCTAACA
1 TATCATATAAA-TCATTACCACATAACA
1460006 TGTAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.45, C:0.23, G:0.02, T:0.30
Consensus pattern (29 bp):
TATCATATAAATCATTACCACATAACACA
Found at i:1460418 original size:21 final size:21
Alignment explanation
Indices: 1460394--1460438 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
1460384 TGTTGTTCGT
* *
1460394 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
1460415 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
1460436 TTG
1 TTG
1460439 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:1463726 original size:2 final size:2
Alignment explanation
Indices: 1463719--1463746 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1463709 TAATTTTAAC
1463719 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
1463747 GCTCGCGCGC
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:1472760 original size:2 final size:2
Alignment explanation
Indices: 1472747--1472806 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
1472737 TAATGACATG
*
1472747 AT AT AA 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
1472789 AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT A
1472807 ATTATAGTAC
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 54 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1473304 original size:33 final size:33
Alignment explanation
Indices: 1473219--1473333 Score: 151
Period size: 33 Copynumber: 3.4 Consensus size: 33
1473209 TTGAAAGGCC
*
1473219 TTTGTGTTTCAAGAGAAA-CATTTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAATGA-TTTCAAAGGTTT
* *
1473252 TTCTTTTTTCTCAAGAGAAATGATTTCAAAGGTTT
1 TT-TGTGTT-TCAAGAGAAATGATTTCAAAGGTTT
*
1473287 TTTGGGTTTCAAGAGAAATGATTTCAAAGGTTT
1 TTTGTGTTTCAAGAGAAATGATTTCAAAGGTTT
*
1473320 TTTATGTTTCAAGA
1 TTTGTGTTTCAAGA
1473334 AAACTATCTC
Statistics
Matches: 71, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
33 39 0.55
34 7 0.10
35 24 0.34
36 1 0.01
ACGTcount: A:0.30, C:0.09, G:0.18, T:0.43
Consensus pattern (33 bp):
TTTGTGTTTCAAGAGAAATGATTTCAAAGGTTT
Found at i:1473513 original size:65 final size:66
Alignment explanation
Indices: 1473353--1473504 Score: 200
Period size: 65 Copynumber: 2.3 Consensus size: 66
1473343 CAATGGAGGT
* * * *
1473353 AAAATTTTGTTT-CAAGAGAAACATATTCAAAGATTGTTGTTTTAAGAGAAACTGTCTCAAGAGA
1 AAAA-TTTGTTTAAAAGA-AAACAGATTCAAAGATTGTTGTTTCAAGAGAAACCGTCTCAAGAGA
1473417 GAC
64 GAC
* * *
1473420 GAAATTTGTTTAAAGGAAAACAGATTCAAAGATT-TTGTTTCAAGGGAAACCGTCTCAAGAGAGA
1 AAAATTTGTTTAAAAGAAAACAGATTCAAAGATTGTTGTTTCAAGAGAAACCGTCTCAAGAGAGA
1473484 C
66 C
1473485 AAAATTTGTTTTAAAAGAAA
1 AAAATTTG-TTTAAAAGAAA
1473505 TTGTTTCAAG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
65 35 0.47
66 33 0.45
67 6 0.08
ACGTcount: A:0.42, C:0.10, G:0.18, T:0.30
Consensus pattern (66 bp):
AAAATTTGTTTAAAAGAAAACAGATTCAAAGATTGTTGTTTCAAGAGAAACCGTCTCAAGAGAGA
C
Found at i:1473568 original size:29 final size:29
Alignment explanation
Indices: 1473521--1473634 Score: 72
Period size: 29 Copynumber: 3.7 Consensus size: 29
1473511 CAAGGGAGAC
* *
1473521 GATTTT-TTTTAAGGAAAACAGATTCAAA
1 GATTTTGTTTCAAGGGAAACAGATTCAAA
*
1473549 GATTTTGTTTCAAGGGAAACTG-TCTCAAGAGA
1 GATTTTGTTTCAAGGGAAACAGAT-TC-A-A-A
* *
1473581 GACAAAATTTGTTT-TAGGAGAAAACAGATTCAAA
1 G----ATTTTGTTTCAAGG-G-AAACAGATTCAAA
1473615 GATTTTGTTTCAAGGGAAAC
1 GATTTTGTTTCAAGGGAAAC
1473635 CGTCTCATGA
Statistics
Matches: 65, Mismatches: 8, Indels: 25
0.66 0.08 0.26
Matches are distributed among these distances:
28 7 0.11
29 18 0.28
30 10 0.15
31 4 0.06
32 2 0.03
34 2 0.03
35 4 0.06
36 10 0.15
37 7 0.11
38 1 0.02
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.32
Consensus pattern (29 bp):
GATTTTGTTTCAAGGGAAACAGATTCAAA
Found at i:1473603 original size:99 final size:100
Alignment explanation
Indices: 1473389--1473603 Score: 342
Period size: 99 Copynumber: 2.1 Consensus size: 100
1473379 TCAAAGATTG
1473389 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACGAAATTTGTTTAAAGGAAAACAGATTCAAAGATT
1 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACG-AATTTGTTTAAAGGAAAACAGATTCAAAGATT
1473454 TTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAT
65 TTGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAT
* * * * * *
1473490 TTGTTTTAAAAGAAATTGTTTCAAGGGAGACG-ATTTTTTTTAAGGAAAACAGATTCAAAGATTT
1 TTGTTTTAAGAGAAACTGTCTCAAGAGAGACGAATTTGTTTAAAGGAAAACAGATTCAAAGATTT
*
1473554 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAAT
66 TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAT
*
1473589 TTGTTTTAGGAGAAA
1 TTGTTTTAAGAGAAA
1473604 ACAGATTCAA
Statistics
Matches: 105, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
99 77 0.73
101 28 0.27
ACGTcount: A:0.39, C:0.10, G:0.21, T:0.30
Consensus pattern (100 bp):
TTGTTTTAAGAGAAACTGTCTCAAGAGAGACGAATTTGTTTAAAGGAAAACAGATTCAAAGATTT
TGTTTCAAGGGAAACCGTCTCAAGAGAGACAAAAT
Found at i:1473616 original size:66 final size:64
Alignment explanation
Indices: 1473534--1473660 Score: 218
Period size: 66 Copynumber: 2.0 Consensus size: 64
1473524 TTTTTTTAAG
*
1473534 GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAGG
1 GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAG--AAAATTTGTTTTAGG
1473599 A
64 A
*
1473600 GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCATGAGAGAAAATTTGTTTTA
1 GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGAAAATTTGTTTTA
1473661 AAAGAAACTG
Statistics
Matches: 59, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
64 13 0.22
66 46 0.78
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (64 bp):
GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGAAAATTTGTTTTAGGA
Found at i:1473626 original size:165 final size:163
Alignment explanation
Indices: 1473358--1473761 Score: 614
Period size: 165 Copynumber: 2.4 Consensus size: 163
1473348 GAGGTAAAAT
* * * * *
1473358 TTTGTTTCAA-GAGAAACATATTCAAAGATTGTTGTTTTAAGAGAAACTGTCTCAAGAGAGACGA
1 TTTGTTTTAAGGA-AAACAGATTCAAAGATT-TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAA
*
1473422 AATTTGTTTAAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGACAA
64 AATTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAG--AA
* * *
1473487 AATTTGTTTTAAAAGAAATTGTTTCAAGGGAGAC-GA
127 AATTTGTTTTAAAAGAAACTGTCTCAAGGGAGACAAA
*
1473523 TTTTTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
* *
1473588 TTTGTTTTAGGAGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCATGAGAGAAAAT
66 TTTGTTTTAAG-GAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGAAAAT
1473653 TTGTTTTAAAAGAAACTGTCTCAAGGGAGACAAAA
130 TTGTTTTAAAAGAAACTGTCTCAAGGGAGAC-AAA
*
1473688 TTTGTTTTAAGGAAAATAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1473753 TTTTGTTTT
66 -TTTGTTTT
1473762 GAGTAAATTA
Statistics
Matches: 220, Mismatches: 14, Indels: 9
0.91 0.06 0.04
Matches are distributed among these distances:
163 34 0.15
164 41 0.19
165 135 0.61
166 10 0.05
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (163 bp):
TTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
TTTGTTTTAAGGAAAACAGATTCAAAGATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGAAAATT
TGTTTTAAAAGAAACTGTCTCAAGGGAGACAAA
Found at i:1473668 original size:34 final size:36
Alignment explanation
Indices: 1473630--1473697 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
1473620 TGTTTCAAGG
* *
1473630 GAAACCGTCTC-A-TGAGAGAAAATTTGTTTTAAAA
1 GAAACCGTCTCAAGGGAGACAAAATTTGTTTTAAAA
*
1473664 GAAACTGTCTCAAGGGAGACAAAATTTGTTTTAA
1 GAAACCGTCTCAAGGGAGACAAAATTTGTTTTAA
1473698 GGAAAATAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
34 10 0.34
35 1 0.03
36 18 0.62
ACGTcount: A:0.40, C:0.12, G:0.19, T:0.29
Consensus pattern (36 bp):
GAAACCGTCTCAAGGGAGACAAAATTTGTTTTAAAA
Found at i:1473739 original size:99 final size:102
Alignment explanation
Indices: 1473550--1473761 Score: 322
Period size: 99 Copynumber: 2.1 Consensus size: 102
1473540 AGATTCAAAG
* ** *
1473550 ATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAGGAGAAAACAGATTCAAA
1 ATTTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAACAGATTCAAA
*
1473615 GATTTTGTTTCAAGGGAAACCGTCTCATGAGAG-AAA
66 GATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGAAAA
* *
1473651 A-TTTGTTTTAAAAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAG-GAAAATAGATTCAAA
1 ATTTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAACAGATTCAAA
*
1473714 GATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAA
66 GATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGA-AAA
1473752 ATTTTGTTTT
1 ATTTTGTTTT
1473762 GAGTAAATTA
Statistics
Matches: 100, Mismatches: 8, Indels: 5
0.88 0.07 0.04
Matches are distributed among these distances:
99 45 0.45
100 42 0.42
101 5 0.05
102 8 0.08
ACGTcount: A:0.38, C:0.10, G:0.20, T:0.32
Consensus pattern (102 bp):
ATTTTGTTTTAAAAGAAACTGTCTCAAGAGAGACAAAATTTGTTTTAAGAGAAAACAGATTCAAA
GATTTTGTTTCAAGGGAAACCGTCTCAAGAGAGAAAA
Found at i:1475305 original size:95 final size:95
Alignment explanation
Indices: 1475137--1475318 Score: 294
Period size: 95 Copynumber: 1.9 Consensus size: 95
1475127 ATGTGTAAAT
* * **
1475137 ACCTTTATCAGGTTAGCTGAATCTTACCCATAAAGCCGGGGTGTTTAACCAATTGCCTTAGAGGG
1 ACCTTTATCAGGCTAGCTGAATATTACCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
*
1475202 ACAGCTCAAGCTTTATTGTATAGTATAATC
66 ACAACTCAAGCTTTATTGTATAGTATAATC
*
1475232 ACCTTTATCAGGCTAGCTGAATATTATCCATAAAGCCGGGGCATTTAACCAATTG-CTCTAGAGG
1 ACCTTTATCAGGCTAGCTGAATATTACCCATAAAGCCGGGGCATTTAACCAATTGCCT-TAGAGG
1475296 GACAACTCAAGCTTTATTGTATA
65 GACAACTCAAGCTTTATTGTATA
1475319 TAAATAATAT
Statistics
Matches: 80, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
94 2 0.03
95 78 0.98
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.31
Consensus pattern (95 bp):
ACCTTTATCAGGCTAGCTGAATATTACCCATAAAGCCGGGGCATTTAACCAATTGCCTTAGAGGG
ACAACTCAAGCTTTATTGTATAGTATAATC
Found at i:1479369 original size:11 final size:11
Alignment explanation
Indices: 1479349--1479378 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
1479339 AAATGTTAGA
1479349 TAAA-AAATAT
1 TAAATAAATAT
1479359 TAAATAAATAT
1 TAAATAAATAT
1479370 TAAATAAAT
1 TAAATAAAT
1479379 TAAAGAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 4 0.21
11 15 0.79
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAATAAATAT
Found at i:1479394 original size:18 final size:17
Alignment explanation
Indices: 1479372--1479438 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
1479362 ATAAATATTA
*
1479372 AATAAATTAAAGAAAAA
1 AATAAATTAAAGAAAAT
*
1479389 ACATAAA--AATGAAAAT
1 A-ATAAATTAAAGAAAAT
*
1479405 AATAAATTATAATAAAAT
1 AATAAATTA-AAGAAAAT
1479423 AATAAATTAAATGAAA
1 AATAAATTAAA-GAAA
1479439 TCAAAAGAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 9
0.74 0.09 0.17
Matches are distributed among these distances:
15 5 0.12
16 8 0.20
17 4 0.10
18 23 0.57
ACGTcount: A:0.70, C:0.01, G:0.04, T:0.24
Consensus pattern (17 bp):
AATAAATTAAAGAAAAT
Found at i:1480851 original size:5 final size:5
Alignment explanation
Indices: 1480838--1480944 Score: 65
Period size: 5 Copynumber: 20.2 Consensus size: 5
1480828 TTACTAAAAG
* *
1480838 AAATG AAATA AAATAA AAATA TAAA-A AAACCTA AAATA TAAAAA AATATA
1 AAATA AAATA AAAT-A AAATA -AAATA AAA--TA AAATA -AAATA AA-ATA
* * * * *
1480888 AAATA AAATA AAAT- AAATA AAACA TAATA AATTA AAGTAA AAATA AACTA
1 AAATA AAATA AAATA AAATA AAATA AAATA AAATA AAAT-A AAATA AAATA
1480938 CAAATA A
1 -AAATA A
1480945 GGAAGAAGAA
Statistics
Matches: 80, Mismatches: 12, Indels: 20
0.71 0.11 0.18
Matches are distributed among these distances:
4 7 0.09
5 45 0.56
6 24 0.30
7 4 0.05
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (5 bp):
AAATA
Found at i:1480889 original size:17 final size:17
Alignment explanation
Indices: 1480847--1480902 Score: 71
Period size: 17 Copynumber: 3.4 Consensus size: 17
1480837 GAAATGAAAT
1480847 AAAATA-AAAATATAAA
1 AAAATATAAAATATAAA
**
1480863 AAAACCTAAAATATAAA
1 AAAATATAAAATATAAA
1480880 AAAATATAAAATA-AAA
1 AAAATATAAAATATAAA
1480896 TAAAATA
1 -AAAATA
1480903 AATAAAACAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
16 7 0.21
17 27 0.79
ACGTcount: A:0.77, C:0.04, G:0.00, T:0.20
Consensus pattern (17 bp):
AAAATATAAAATATAAA
Found at i:1480934 original size:45 final size:43
Alignment explanation
Indices: 1480832--1480914 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
1480822 AACCACTTAC
* * *
1480832 TAAAAGAAATGAAATAAAATAAAAATATAAAAAAACCTAAAATA
1 TAAAAAAAATAAAATAAAAT-AAAATATAAAAAAACATAAAATA
*
1480876 TAAAAAAATATAAAATAAAATAAAATA-AATAAAACATAA
1 TAAAAAAA-ATAAAATAAAATAAAATATAAAAAAACATAA
1480915 TAAATTAAAG
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 10 0.29
44 13 0.38
45 11 0.32
ACGTcount: A:0.75, C:0.04, G:0.02, T:0.19
Consensus pattern (43 bp):
TAAAAAAAATAAAATAAAATAAAATATAAAAAAACATAAAATA
Found at i:1480972 original size:10 final size:10
Alignment explanation
Indices: 1480843--1481026 Score: 87
Period size: 10 Copynumber: 17.4 Consensus size: 10
1480833 AAAAGAAATG
1480843 AAATAAAATAA
1 AAAT-AAATAA
1480854 AAATATAA-AA
1 AAATA-AATAA
1480864 AAACCTAAAATATA
1 AAA--T-AAATA-A
1480878 AAA-AAATATA
1 AAATAAATA-A
1480888 AAATAAA-ATA
1 AAATAAATA-A
1480898 AAATAAATAA
1 AAATAAATAA
1480908 AACAT-AAT-A
1 AA-ATAAATAA
*
1480917 AATTAAAGTAA
1 AAATAAA-TAA
*
1480928 AAATAAACTAC
1 AAATAAA-TAA
*
1480939 AAATAAGGAAGAA
1 AAAT-A--AATAA
*
1480952 GAAAGAAATAA
1 -AAATAAATAA
1480963 AAATAAATAAA
1 AAATAAAT-AA
* *
1480974 TAAATATAGAA
1 -AAATAAATAA
1480985 AAATAAA-ACA
1 AAATAAATA-A
*
1480995 AAGT-AA-AA
1 AAATAAATAA
1481003 AAATAAATAA
1 AAATAAATAA
1481013 AAATAAATAA
1 AAATAAATAA
1481023 AAAT
1 AAAT
1481027 GAAAGTCGAA
Statistics
Matches: 138, Mismatches: 14, Indels: 43
0.71 0.07 0.22
Matches are distributed among these distances:
8 5 0.04
9 11 0.08
10 66 0.48
11 33 0.24
12 10 0.07
13 4 0.03
14 9 0.07
ACGTcount: A:0.74, C:0.03, G:0.04, T:0.18
Consensus pattern (10 bp):
AAATAAATAA
Found at i:1480988 original size:28 final size:28
Alignment explanation
Indices: 1480957--1481019 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
1480947 AAGAAGAAAG
* *
1480957 AAATAAAA-ATAAATAAATAAATATAGAA
1 AAATAAAACA-AAATAAAAAAATAAAGAA
* *
1480985 AAATAAAACAAAGTAAAAAAATAAATAA
1 AAATAAAACAAAATAAAAAAATAAAGAA
1481013 AAATAAA
1 AAATAAA
1481020 TAAAAATGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.78, C:0.02, G:0.03, T:0.17
Consensus pattern (28 bp):
AAATAAAACAAAATAAAAAAATAAAGAA
Found at i:1481129 original size:2 final size:2
Alignment explanation
Indices: 1481122--1481150 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
1481112 TAATGAACTC
1481122 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 A
1481151 CACATAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1496758 original size:31 final size:31
Alignment explanation
Indices: 1496691--1496750 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1496681 AAATTTAAGG
*
1496691 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1496722 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1496751 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1496842 original size:19 final size:19
Alignment explanation
Indices: 1496826--1496877 Score: 86
Period size: 19 Copynumber: 2.7 Consensus size: 19
1496816 GAATAGTAGT
1496826 TTACTATTTGAACAGTAAA
1 TTACTATTTGAACAGTAAA
1496845 TTACTATTTGAACAGTAAA
1 TTACTATTTGAACAGTAAA
* *
1496864 TCACTGTTTGAACA
1 TTACTATTTGAACA
1496878 ATAACCCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 31 1.00
ACGTcount: A:0.38, C:0.13, G:0.12, T:0.37
Consensus pattern (19 bp):
TTACTATTTGAACAGTAAA
Found at i:1497013 original size:21 final size:21
Alignment explanation
Indices: 1496987--1497028 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
1496977 ATTTGAATAT
*
1496987 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1497008 TATGAAGGGGTACCGATTCCC
1 TATGAAGGGGTACCGATTCCC
1497029 CCCCCATTCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.24, C:0.21, G:0.29, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCGATTCCC
Found at i:1498284 original size:20 final size:19
Alignment explanation
Indices: 1498243--1498289 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
1498233 AATGATTTTC
*
1498243 TTTTGAAAACAAAAATAGA
1 TTTTGAAAACAAAAATAAA
* *
1498262 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAAT-AAA
1498282 TTTT-AAAA
1 TTTTGAAAA
1498290 AAGGATTTAG
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
19 17 0.74
20 6 0.26
ACGTcount: A:0.53, C:0.06, G:0.11, T:0.30
Consensus pattern (19 bp):
TTTTGAAAACAAAAATAAA
Found at i:1499578 original size:31 final size:31
Alignment explanation
Indices: 1499511--1499570 Score: 97
Period size: 29 Copynumber: 2.0 Consensus size: 31
1499501 CAATTTAAGG
*
1499511 CAAAATGGTTTTTGGACTTGAATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1499542 CAAAAT-GTATTTGGACTT-AATTGAATTTA
1 CAAAATGGTATTTGGACTTGAATTGAATTTA
1499571 TTCAAAATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 11 0.39
30 11 0.39
31 6 0.21
ACGTcount: A:0.35, C:0.07, G:0.17, T:0.42
Consensus pattern (31 bp):
CAAAATGGTATTTGGACTTGAATTGAATTTA
Found at i:1499659 original size:19 final size:19
Alignment explanation
Indices: 1499635--1499697 Score: 90
Period size: 19 Copynumber: 3.3 Consensus size: 19
1499625 AATGTTTTTA
**
1499635 TGAACAGTAGTTTACTATT
1 TGAACAGTAAATTACTATT
1499654 TGAACAGTAAATTACTATT
1 TGAACAGTAAATTACTATT
* *
1499673 TGAACAGTAAATCACTGTT
1 TGAACAGTAAATTACTATT
1499692 TGAACA
1 TGAACA
1499698 ATAACCGAGG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 40 1.00
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (19 bp):
TGAACAGTAAATTACTATT
Found at i:1499831 original size:21 final size:21
Alignment explanation
Indices: 1499806--1499847 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
1499796 ATTTGACTAT
1499806 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
1499827 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTATCGATTCCC
1499848 CCCATTCTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.19, G:0.29, T:0.29
Consensus pattern (21 bp):
TATGAAGGGGTATCGATTCCC
Found at i:1500171 original size:34 final size:32
Alignment explanation
Indices: 1500132--1500201 Score: 104
Period size: 34 Copynumber: 2.1 Consensus size: 32
1500122 TTTTGTAAAG
*
1500132 GGGAAAGGTTCTAGCTTAGCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
1500166 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
1500198 GGGA
1 GGGA
1500202 GTTTGTAAGG
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 11 0.32
33 1 0.03
34 22 0.65
ACGTcount: A:0.31, C:0.16, G:0.31, T:0.21
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:1502244 original size:22 final size:22
Alignment explanation
Indices: 1502210--1502264 Score: 76
Period size: 22 Copynumber: 2.5 Consensus size: 22
1502200 ATTTTTCCTA
1502210 AAAGG-CCTCATGTATATGTCCC
1 AAAGGACCT-ATGTATATGTCCC
1502232 AAAGGACCTATGTATATGTCCC
1 AAAGGACCTATGTATATGTCCC
* *
1502254 GAATGACCTAT
1 AAAGGACCTAT
1502265 TTACCCTCGA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 27 0.90
23 3 0.10
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (22 bp):
AAAGGACCTATGTATATGTCCC
Found at i:1509215 original size:23 final size:22
Alignment explanation
Indices: 1509189--1509231 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
1509179 ATGTGAAATT
* *
1509189 TGTCCTGAATGACCTCATGTATA
1 TGTCCCGAAGGACCT-ATGTATA
1509212 TGTCCCGAAGGACCTATGTA
1 TGTCCCGAAGGACCTATGTA
1509232 ACCATCGACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (22 bp):
TGTCCCGAAGGACCTATGTATA
Found at i:1525846 original size:3 final size:3
Alignment explanation
Indices: 1525838--1525894 Score: 89
Period size: 3 Copynumber: 19.0 Consensus size: 3
1525828 ATTTATTTAT
*
1525838 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA TTA -TA TATA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
1525883 TTA TTA TTA TTA
1 TTA TTA TTA TTA
1525895 AAAAATAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 2 0.04
3 45 0.90
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1525894 original size:21 final size:21
Alignment explanation
Indices: 1525830--1525894 Score: 98
Period size: 21 Copynumber: 3.1 Consensus size: 21
1525820 TTTTACTTAT
*
1525830 TTATTTAT-TTATTATTATTA
1 TTATATATATTATTATTATTA
1525850 TTATA-ATTATTATTATTATTA
1 TTATATA-TATTATTATTATTA
1525871 TTATATATATTATTATTATTA
1 TTATATATATTATTATTATTA
1525892 TTA
1 TTA
1525895 AAAAATAATT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
19 1 0.02
20 5 0.12
21 34 0.83
22 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (21 bp):
TTATATATATTATTATTATTA
Found at i:1528126 original size:17 final size:17
Alignment explanation
Indices: 1528104--1528140 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1528094 CTTTTCAAAT
1528104 TTTTTATA-TACTTTATA
1 TTTTTATATTA-TTTATA
1528121 TTTTTATATTATTTATA
1 TTTTTATATTATTTATA
1528138 TTT
1 TTT
1528141 CATTTTACTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.27, C:0.03, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTATATTATTTATA
Found at i:1531438 original size:15 final size:15
Alignment explanation
Indices: 1531418--1531449 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
1531408 GATCAATACC
1531418 TTTTGCATACATGCA
1 TTTTGCATACATGCA
*
1531433 TTTTGCATACATTCA
1 TTTTGCATACATGCA
1531448 TT
1 TT
1531450 ATTTATTGCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.19, G:0.09, T:0.47
Consensus pattern (15 bp):
TTTTGCATACATGCA
Found at i:1538794 original size:11 final size:11
Alignment explanation
Indices: 1538778--1538850 Score: 80
Period size: 11 Copynumber: 6.6 Consensus size: 11
1538768 GCTTGAAGAA
1538778 AAAAAGAAAAG
1 AAAAAGAAAAG
1538789 AAAAAGAAAA-
1 AAAAAGAAAAG
1538799 AAAAGAGAAAAAG
1 AAAA-AG-AAAAG
1538812 AAAAAGAAAAG
1 AAAAAGAAAAG
*
1538823 AAAAAAAAGAAG
1 AAAAAGAA-AAG
*
1538835 -AAAAGAAGA-
1 AAAAAGAAAAG
1538844 AAAAAGA
1 AAAAAGA
1538851 GGGGGTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
10 11 0.20
11 30 0.56
12 9 0.17
13 4 0.07
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:1538807 original size:17 final size:17
Alignment explanation
Indices: 1538777--1538847 Score: 72
Period size: 17 Copynumber: 3.9 Consensus size: 17
1538767 TGCTTGAAGA
*
1538777 AAAAAAGAAAAGAAAAAG
1 AAAAAA-AAGAGAAAAAG
1538795 AAAAAAAAGAGAAAAAG
1 AAAAAAAAGAGAAAAAG
*
1538812 AAAAAGAAA-AGAAAAAA
1 AAAAA-AAAGAGAAAAAG
1538829 AAGAAGAAAAGAAGAAAAA
1 AA-AA-AAAAG-AGAAAAA
1538848 AGAGGGGGTC
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
17 24 0.52
18 14 0.30
19 1 0.02
20 7 0.15
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAGAGAAAAAG
Found at i:1538813 original size:28 final size:26
Alignment explanation
Indices: 1538777--1538850 Score: 103
Period size: 28 Copynumber: 2.7 Consensus size: 26
1538767 TGCTTGAAGA
1538777 AAAAAAGAAAAGAAAAAGAAAAAAAAG
1 AAAAAAGAAAA-AAAAAGAAAAAAAAG
1538804 AGAAAAAGAAAAAGAAAAGAAAAAAAAG
1 A-AAAAAGAAAAA-AAAAGAAAAAAAAG
*
1538832 AAGAAAAGAAGAAAAAAGA
1 AA-AAAAGAAAAAAAAAGA
1538851 GGGGGTCAAG
Statistics
Matches: 43, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
27 9 0.21
28 34 0.79
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (26 bp):
AAAAAAGAAAAAAAAAGAAAAAAAAG
Found at i:1539745 original size:114 final size:114
Alignment explanation
Indices: 1539546--1539882 Score: 505
Period size: 114 Copynumber: 3.0 Consensus size: 114
1539536 GTGCTACGTT
*
1539546 CTCATAGTAGAAATAAGAAGA-CCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCCGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
*
1539610 ATTTGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTG
66 ATTCGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTG
*
1539659 CTCATAGTAGAAATACGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * *
1539724 ATTCGGTATGAACCCCAAAATCAATCATTAGATTTGAAAGATAAATTTG
66 ATTCGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTG
* * * * * *
1539773 CTCATAGTAGACATAAGAAGACCTAATAGCATCTTCTAGAAGTTTTCTTTGAGTCATCTGATATG
1 CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
* * * * * *
1539838 GTTCGGTAGGAACCACAGAACCAATCATTGGAATTAAAAGATGAA
66 ATTCGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAA
1539883 CTGCATGATC
Statistics
Matches: 201, Mismatches: 22, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
113 20 0.10
114 181 0.90
ACGTcount: A:0.35, C:0.16, G:0.18, T:0.31
Consensus pattern (114 bp):
CTCATAGTAGAAATAAGAAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTG
ATTCGGTATGAACCCCAAAATCAATCATTGGATTTAAAAGATGAATTTG
Found at i:1541226 original size:24 final size:23
Alignment explanation
Indices: 1541183--1541227 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
1541173 GTTCATAATG
*
1541183 AGAAGAACTCATCTGAAGAAGGA
1 AGAAGAACTCATATGAAGAAGGA
1541206 AGAAGAAGCTCATAATG-AGAAG
1 AGAAGAA-CTCAT-ATGAAGAAG
1541228 AATTTGTTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 7 0.37
24 10 0.53
25 2 0.11
ACGTcount: A:0.49, C:0.11, G:0.27, T:0.13
Consensus pattern (23 bp):
AGAAGAACTCATATGAAGAAGGA
Found at i:1541359 original size:113 final size:113
Alignment explanation
Indices: 1540576--1541357 Score: 1375
Period size: 113 Copynumber: 6.9 Consensus size: 113
1540566 GATTAAAATC
1540576 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1540641 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1540689 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
*
1540754 AGAAGAAGTTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1540802 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
* *
1540867 AGAAGAAGTTCATAATAAGAAGAACTTGTTTAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
1540915 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1540980 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * * *
1541028 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1541093 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * * *
1541141 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
* *
1541206 AGAAGAAGCTCATAATGAGAAGAATTTGTTCAACTTTTTGCTTGAATT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
* * * * *
1541254 CATCATTCAATGGATCAGCATTACCAGGTCGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGA
1 CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
1541319 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAATCTTTT
66 AGAAGAAGTTCATAATGAGAAGAACTTGTTCAA-CTTTT
1541358 GCATGATTCT
Statistics
Matches: 653, Mismatches: 15, Indels: 1
0.98 0.02 0.00
Matches are distributed among these distances:
113 648 0.99
114 5 0.01
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (113 bp):
CATCATTCAATGGATCAACATTTCCAGTTAGAGTTCATAATGAGAAGAACTCATTTGAAGAAGGA
AGAAGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGCTTGAATT
Found at i:1541638 original size:3 final size:3
Alignment explanation
Indices: 1541630--1541683 Score: 83
Period size: 3 Copynumber: 18.0 Consensus size: 3
1541620 ACTTATTTAT
*
1541630 TTA TTA TTA TTA TTA TAA TTA TTA TTA TTA TTA -TA TATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
1541675 TTA TTA TTA
1 TTA TTA TTA
1541684 AAAATAATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:1554458 original size:21 final size:21
Alignment explanation
Indices: 1554433--1554487 Score: 57
Period size: 16 Copynumber: 2.9 Consensus size: 21
1554423 TGTAAATGAT
1554433 AAAAATAAAATGAAAGAGAAC
1 AAAAATAAAATGAAAGAGAAC
1554454 ----A-AAAATGAAAGAGAAC
1 AAAAATAAAATGAAAGAGAAC
* *
1554470 AAAAATGAAAGGAAAGAG
1 AAAAATAAAATGAAAGAG
1554488 TTAGTGAGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
16 15 0.56
17 1 0.04
20 1 0.04
21 10 0.37
ACGTcount: A:0.69, C:0.04, G:0.20, T:0.07
Consensus pattern (21 bp):
AAAAATAAAATGAAAGAGAAC
Found at i:1554460 original size:16 final size:16
Alignment explanation
Indices: 1554439--1554480 Score: 84
Period size: 16 Copynumber: 2.6 Consensus size: 16
1554429 TGATAAAAAT
1554439 AAAATGAAAGAGAACA
1 AAAATGAAAGAGAACA
1554455 AAAATGAAAGAGAACA
1 AAAATGAAAGAGAACA
1554471 AAAATGAAAG
1 AAAATGAAAG
1554481 GAAAGAGTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.69, C:0.05, G:0.19, T:0.07
Consensus pattern (16 bp):
AAAATGAAAGAGAACA
Found at i:1555635 original size:18 final size:19
Alignment explanation
Indices: 1555549--1555635 Score: 60
Period size: 19 Copynumber: 4.7 Consensus size: 19
1555539 TTTCAAGGGG
1555549 AAAAAATAAAACAAAA--TA
1 AAAAAATAAAA-AAAATGTA
*
1555567 AAAAAAT--AAAAAATGTT
1 AAAAAATAAAAAAAATGTA
* *
1555584 AAAAGAGAAAAAAAATGGTA
1 AAAAAATAAAAAAAAT-GTA
* *
1555604 AAATAA-AAATAAAATG-A
1 AAAAAATAAAAAAAATGTA
1555621 AAAAAATAATAAAAA
1 AAAAAATAA-AAAAA
1555636 GAGTGTTAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 13
0.71 0.12 0.17
Matches are distributed among these distances:
15 4 0.08
16 2 0.04
17 12 0.23
18 10 0.19
19 19 0.36
20 6 0.11
ACGTcount: A:0.77, C:0.01, G:0.07, T:0.15
Consensus pattern (19 bp):
AAAAAATAAAAAAAATGTA
Found at i:1556846 original size:12 final size:11
Alignment explanation
Indices: 1556825--1556867 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 11
1556815 AATACATATA
1556825 ATAT-TATAAT
1 ATATATATAAT
1556835 ATATGATATAAT
1 ATAT-ATATAAT
1556847 ATAATATATAAT
1 AT-ATATATAAT
1556859 ATA-ATATAA
1 ATATATATAA
1556868 CTTTTTTGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
10 10 0.33
11 1 0.03
12 17 0.57
13 2 0.07
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (11 bp):
ATATATATAAT
Found at i:1556849 original size:17 final size:17
Alignment explanation
Indices: 1556820--1556867 Score: 73
Period size: 17 Copynumber: 2.9 Consensus size: 17
1556810 TAAAAAATAC
1556820 ATATAATAT--TATAAT
1 ATATAATATAATATAAT
*
1556835 ATATGATATAATATAAT
1 ATATAATATAATATAAT
1556852 ATATAATATAATATAA
1 ATATAATATAATATAA
1556868 CTTTTTTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 8 0.28
17 21 0.72
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (17 bp):
ATATAATATAATATAAT
Found at i:1556941 original size:35 final size:35
Alignment explanation
Indices: 1556890--1557119 Score: 193
Period size: 35 Copynumber: 6.5 Consensus size: 35
1556880 TATATAAAAG
* *
1556890 ATATGTTTTCAAAAATTAATTTTCAAAACTATATA-
1 ATATATTTTTAAAAA-TAATTTTCAAAACTATATAT
*
1556925 ATATATTTTTAAAAATTGATTTTCAAAACTATATAT
1 ATATATTTTTAAAAA-TAATTTTCAAAACTATATAT
* * **
1556961 -TATATTTTCAAAAATATTTTTTTAAACTATATA-
1 ATATATTTTTAAAAATAATTTTCAAAACTATATAT
* *
1556994 ATATATTTTCAAAAAT-ATTTTTAAAACTATATAGT
1 ATATATTTTTAAAAATAATTTTCAAAACTATATA-T
* * *
1557029 ATATATATTTT-TAAATCATTTTAAAAACTATATATT
1 ATATAT-TTTTAAAAATAATTTTCAAAACTATATA-T
* *
1557065 ATATATATTTTCAAAAT-GTTTTCAAAGAACTATATATT
1 ATATAT-TTTTAAAAATAATTTTC-AA-AACTATATA-T
*
1557103 ATATATGTTTTCAAAAT
1 ATATAT-TTTTAAAAAT
1557120 TATATAATAT
Statistics
Matches: 168, Mismatches: 18, Indels: 15
0.84 0.09 0.07
Matches are distributed among these distances:
33 15 0.09
34 30 0.18
35 55 0.33
36 35 0.21
37 6 0.04
38 27 0.16
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (35 bp):
ATATATTTTTAAAAATAATTTTCAAAACTATATAT
Found at i:1557057 original size:36 final size:36
Alignment explanation
Indices: 1556890--1557119 Score: 178
Period size: 36 Copynumber: 6.4 Consensus size: 36
1556880 TATATAAAAG
* *
1556890 ATATGTTTTCAAAAATTAATTTTCAAAACTATATA--AT
1 ATATATTTTC-AAAA-T-ATTTTAAAAACTATATATTAT
* *
1556927 ATAT-TTTTAAAAATTGATTTTCAAAAC--TATA-TAT
1 ATATATTTTCAAAA-T-ATTTTAAAAACTATATATTAT
**
1556961 -TATATTTTCAAAAATATTTTTTTAAAC--TATA-TA-
1 ATATATTTTC-AAAATA-TTTTAAAAACTATATATTAT
* *
1556994 ATATATTTTCAAAAATATTTTTAAAACTATATAGTAT
1 ATATATTTTC-AAAATATTTTAAAAACTATATATTAT
*
1557031 ATATATTTT-TAAATCATTTTAAAAACTATATATTAT
1 ATATATTTTCAAAAT-ATTTTAAAAACTATATATTAT
*
1557067 ATATATTTTCAAAATGTTTTCAAAGAACTATATATTAT
1 ATATATTTTCAAAATATTTT-AAA-AACTATATATTAT
*
1557105 ATATGTTTTCAAAAT
1 ATATATTTTCAAAAT
1557120 TATATAATAT
Statistics
Matches: 168, Mismatches: 12, Indels: 25
0.82 0.06 0.12
Matches are distributed among these distances:
33 17 0.10
34 37 0.22
35 29 0.17
36 38 0.23
37 20 0.12
38 27 0.16
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.47
Consensus pattern (36 bp):
ATATATTTTCAAAATATTTTAAAAACTATATATTAT
Found at i:1557130 original size:25 final size:27
Alignment explanation
Indices: 1557080--1557131 Score: 72
Period size: 25 Copynumber: 2.0 Consensus size: 27
1557070 TATTTTCAAA
*
1557080 ATGTTTTCAAAGAACTATATATTATAT
1 ATGTTTTCAAAGAACTATATAATATAT
*
1557107 ATGTTTTC-AA-AATTATATAATATAT
1 ATGTTTTCAAAGAACTATATAATATAT
1557132 GTTTTTAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 13 0.57
26 2 0.09
27 8 0.35
ACGTcount: A:0.42, C:0.06, G:0.06, T:0.46
Consensus pattern (27 bp):
ATGTTTTCAAAGAACTATATAATATAT
Found at i:1558437 original size:38 final size:38
Alignment explanation
Indices: 1558395--1558470 Score: 143
Period size: 38 Copynumber: 2.0 Consensus size: 38
1558385 AATTTTTTAA
*
1558395 CAAAAAATTACAAGTTTAGAACACATGAGTAGTTGGGT
1 CAAAAAATTACAAGTTTAGAACAAATGAGTAGTTGGGT
1558433 CAAAAAATTACAAGTTTAGAACAAATGAGTAGTTGGGT
1 CAAAAAATTACAAGTTTAGAACAAATGAGTAGTTGGGT
1558471 GATAATTTTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 37 1.00
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.26
Consensus pattern (38 bp):
CAAAAAATTACAAGTTTAGAACAAATGAGTAGTTGGGT
Found at i:1559110 original size:3 final size:3
Alignment explanation
Indices: 1559104--1559148 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
1559094 CCCATTTTAT
1559104 TTA TTA TTA TTA TTA TTA TTA TTA -TA TATA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA
1559149 AAAAAATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1559160 original size:21 final size:21
Alignment explanation
Indices: 1559115--1559160 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
1559105 TATTATTATT
* * * *
1559115 ATTATTATTATTATATATATT
1 ATTATTATTATTAAAAAAATA
1559136 ATTATTATTATTAAAAAAATA
1 ATTATTATTATTAAAAAAATA
1559157 ATTA
1 ATTA
1559161 CAGGCCCAAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
ATTATTATTATTAAAAAAATA
Found at i:1560557 original size:27 final size:27
Alignment explanation
Indices: 1560485--1560557 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 27
1560475 AGTTCTAATT
** *
1560485 TTATTTTTATTATTGAT-TATTTATGTT
1 TTATTTTTATTATT-ATATATTTAAATA
*
1560512 TTAATTTTACTTATT-TATATTTAAATA
1 TTATTTTTA-TTATTATATATTTAAATA
1560539 TTATTTTTATTATTATATA
1 TTATTTTTATTATTATATA
1560558 GTCATATAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
26 6 0.16
27 27 0.71
28 5 0.13
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (27 bp):
TTATTTTTATTATTATATATTTAAATA
Found at i:1561522 original size:25 final size:25
Alignment explanation
Indices: 1561494--1561547 Score: 108
Period size: 25 Copynumber: 2.2 Consensus size: 25
1561484 TCTTGGTAAT
1561494 AGCTTCCCTGCTTGTTTCATGTTTA
1 AGCTTCCCTGCTTGTTTCATGTTTA
1561519 AGCTTCCCTGCTTGTTTCATGTTTA
1 AGCTTCCCTGCTTGTTTCATGTTTA
1561544 AGCT
1 AGCT
1561548 CTTCTTTCGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.13, C:0.24, G:0.17, T:0.46
Consensus pattern (25 bp):
AGCTTCCCTGCTTGTTTCATGTTTA
Found at i:1562320 original size:20 final size:20
Alignment explanation
Indices: 1562295--1562333 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1562285 GAAAAGAAAA
1562295 ATAGACAAAGAAGAGAAGAG
1 ATAGACAAAGAAGAGAAGAG
1562315 ATAGACAAAGAAGAGAAGA
1 ATAGACAAAGAAGAGAAGA
1562334 ACAAGATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.62, C:0.05, G:0.28, T:0.05
Consensus pattern (20 bp):
ATAGACAAAGAAGAGAAGAG
Found at i:1576154 original size:2 final size:2
Alignment explanation
Indices: 1576147--1576189 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1576137 TGCTAAATTA
1576147 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1576189 A
1 A
1576190 CTGCTAGAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:1584031 original size:2 final size:2
Alignment explanation
Indices: 1584024--1584050 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
1584014 TTGGATGCCG
1584024 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1584051 GATGAAGTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:1584965 original size:31 final size:31
Alignment explanation
Indices: 1584930--1585008 Score: 95
Period size: 31 Copynumber: 2.5 Consensus size: 31
1584920 ATGACGATCG
*
1584930 AGTGATTATTTTATTACAAATCAATAACATT
1 AGTGACTATTTTATTACAAATCAATAACATT
* * * *
1584961 AGTGACCATTTTGTTACAAATCGATAATATT
1 AGTGACTATTTTATTACAAATCAATAACATT
* *
1584992 AATGACTAATTTATTAC
1 AGTGACTATTTTATTAC
1585009 TTTTGAAACT
Statistics
Matches: 39, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.41
Consensus pattern (31 bp):
AGTGACTATTTTATTACAAATCAATAACATT
Found at i:1585788 original size:23 final size:23
Alignment explanation
Indices: 1585762--1585815 Score: 90
Period size: 23 Copynumber: 2.3 Consensus size: 23
1585752 AAATGTACCA
*
1585762 AAGTGCCACGTAGAGTTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
*
1585785 AAGTGCCGCGTAGAATTGCACCG
1 AAGTGCCACGTAGAATTGCACCG
1585808 AAGTGCCA
1 AAGTGCCA
1585816 TATAAAATGT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.28, C:0.26, G:0.30, T:0.17
Consensus pattern (23 bp):
AAGTGCCACGTAGAATTGCACCG
Found at i:1588669 original size:29 final size:27
Alignment explanation
Indices: 1588637--1588717 Score: 65
Period size: 29 Copynumber: 2.8 Consensus size: 27
1588627 AAAACCCATG
1588637 AAATTATTAAAATTCTCAAAAAACACCTT
1 AAATTATTAAAA-TCTCAAAAAACACC-T
* *
1588666 AAATTCCA-GAAAATCTCAAAAAACTCCT
1 AAATT--ATTAAAATCTCAAAAAACACCT
* *
1588694 AAGTTTTTAAAAATCTCAACAAAA
1 AAATTATT-AAAATCTCAA-AAAA
1588718 AAAACATAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 10
0.74 0.09 0.18
Matches are distributed among these distances:
28 15 0.36
29 22 0.52
30 4 0.10
31 1 0.02
ACGTcount: A:0.52, C:0.19, G:0.02, T:0.27
Consensus pattern (27 bp):
AAATTATTAAAATCTCAAAAAACACCT
Found at i:1588844 original size:157 final size:158
Alignment explanation
Indices: 1588626--1588912 Score: 429
Period size: 157 Copynumber: 1.8 Consensus size: 158
1588616 GTTACTTTCT
*
1588626 AAAAACCCATGAAATTATTAAAATTCTCAAAAAACACCTTAAATTCCAGAAAATCTCAAAAAACT
1 AAAAACCCATGAAATTATTAAAATTCTCAAAAAACACCTTAAATTCCAGAAAATCTAAAAAAACT
* * * *
1588691 CCTAAGTTTTTAAAAA-TCTCAACAAAAAAAACATAAACTCTAAATCGTAATCCCTAAAAATCAT
66 CCTAAATTTCTAAAAATTC-CAA-AAAAAAAACATAAACTCTAAACCATAATCCCTAAAAATCAT
1588755 AAGGTTATTTTTTAGGGAGTTTATTTCTAA
129 AAGGTTATTTTTTAGGGAGTTTATTTCTAA
* * *
1588785 AAAAACCCCATGAAATTATTAAAATTC-CCAAAAA-A-GTTAAATTCTAGAAAATCTAAAAAAAC
1 AAAAA-CCCATGAAATTATTAAAATTCTCAAAAAACACCTTAAATTCCAGAAAATCTAAAAAAAC
**
1588847 TCCTAAATTTCTAAAAATTCCAAAAAAAAATTATAAACTCTAAACCATAATCCCTAAAAATCATA
65 TCCTAAATTTCTAAAAATTCCAAAAAAAAAACATAAACTCTAAACCATAATCCCTAAAAATCATA
1588912 A
130 A
1588913 TTGCATGTGC
Statistics
Matches: 116, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
156 39 0.34
157 42 0.36
158 3 0.03
159 11 0.09
160 21 0.18
ACGTcount: A:0.51, C:0.17, G:0.05, T:0.28
Consensus pattern (158 bp):
AAAAACCCATGAAATTATTAAAATTCTCAAAAAACACCTTAAATTCCAGAAAATCTAAAAAAACT
CCTAAATTTCTAAAAATTCCAAAAAAAAAACATAAACTCTAAACCATAATCCCTAAAAATCATAA
GGTTATTTTTTAGGGAGTTTATTTCTAA
Found at i:1589716 original size:153 final size:154
Alignment explanation
Indices: 1589471--1589749 Score: 411
Period size: 153 Copynumber: 1.8 Consensus size: 154
1589461 TCACAATAAA
* * ** *
1589471 TTTTAGGGATTATGATTTAGAGTTTATGATTTTTTTTGGAATTTTTAGGAATTTAGGAGTTTTTT
1 TTTTAGGGATTATGATTTAGAATTTATGATTTTTTTTAGAATTTTTAAAAACTTAGGAGTTTTTT
* *
1589536 AATATTTTCTAGAATTTAAGGTATTTTTGGGAATTTTAATAATTTCATGGGGTTTTTAGAAATAA
66 AAGATTTTCTAGAATTTAAGGTATTTTTGAGAATTTTAATAATTTCAT-GGGTTTTTAGAAATAA
1589601 ACTCCCTAAAAATGAATCTTATGAT
130 ACTCCCTAAAAATGAATCTTATGAT
1589626 TTTTAGGGATTATGATTTAGAATTTATG-TTTTTTTTA-AGATTTTTAAAAACTTAGGAG-TTTT
1 TTTTAGGGATTATGATTTAGAATTTATGATTTTTTTTAGA-ATTTTTAAAAACTTAGGAGTTTTT
* * * * *
1589688 TGAGATTTTCTGGAATTTAAGGTGTTTTTTATAATTTTAATAATTTCATGGGTTTTTAGAAA
65 TAAGATTTTCTAGAATTTAAGGTATTTTTGAGAATTTTAATAATTTCATGGGTTTTTAGAAA
1589750 GTAACTTTTG
Statistics
Matches: 111, Mismatches: 12, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
152 13 0.12
153 47 0.42
154 24 0.22
155 27 0.24
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.49
Consensus pattern (154 bp):
TTTTAGGGATTATGATTTAGAATTTATGATTTTTTTTAGAATTTTTAAAAACTTAGGAGTTTTTT
AAGATTTTCTAGAATTTAAGGTATTTTTGAGAATTTTAATAATTTCATGGGTTTTTAGAAATAAA
CTCCCTAAAAATGAATCTTATGAT
Found at i:1590262 original size:14 final size:14
Alignment explanation
Indices: 1590243--1590275 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
1590233 TTTGGCCGCT
1590243 TTAATCTTAATTTA
1 TTAATCTTAATTTA
1590257 TTAATCTTAATTTA
1 TTAATCTTAATTTA
1590271 TTAAT
1 TTAAT
1590276 ATGTGATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.00, T:0.58
Consensus pattern (14 bp):
TTAATCTTAATTTA
Found at i:1590486 original size:3 final size:3
Alignment explanation
Indices: 1590478--1590514 Score: 51
Period size: 3 Copynumber: 12.7 Consensus size: 3
1590468 TTTGTTCGAG
1590478 TAT TAT TAT TAT TAGT TAT TAT T-T TAT TA- TAT TAT TA
1 TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TAT TAT TA
1590515 CTAATATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
2 4 0.13
3 24 0.77
4 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:1590510 original size:10 final size:12
Alignment explanation
Indices: 1590478--1590514 Score: 51
Period size: 13 Copynumber: 3.2 Consensus size: 12
1590468 TTTGTTCGAG
1590478 TATTATTATTAT
1 TATTATTATTAT
1590490 TAGTTATTATT-T
1 TA-TTATTATTAT
1590502 TATTA-TATTAT
1 TATTATTATTAT
1590513 TA
1 TA
1590515 CTAATATTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
10 4 0.17
11 6 0.26
12 5 0.22
13 8 0.35
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (12 bp):
TATTATTATTAT
Found at i:1596857 original size:15 final size:15
Alignment explanation
Indices: 1596837--1596869 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
1596827 AATGAGAGGT
1596837 AAAAAATAA-AAAATA
1 AAAAAATAATAAAA-A
1596852 AAAAAATAATAAAAA
1 AAAAAATAATAAAAA
1596867 AAA
1 AAA
1596870 GAAAAGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (15 bp):
AAAAAATAATAAAAA
Found at i:1596895 original size:6 final size:6
Alignment explanation
Indices: 1596886--1596925 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
1596876 GAAAGGAAAG
*
1596886 GAAAAT GAAAAT GAAAAT AAAAAT G-AAAT GAAAAT GAAAA
1 GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAAT GAAAA
1596926 AAATGAATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (6 bp):
GAAAAT
Found at i:1596907 original size:17 final size:16
Alignment explanation
Indices: 1596888--1596946 Score: 57
Period size: 17 Copynumber: 3.5 Consensus size: 16
1596878 AAGGAAAGGA
*
1596888 AAATGAAAATGAAAATAA
1 AAAT-AAAATGAAAAT-G
*
1596906 AAATGAAATGAAAATG
1 AAATAAAATGAAAATG
1596922 AAA-AAAATGAATGAATG
1 AAATAAAATGAA--AATG
1596939 AAATAAAA
1 AAATAAAA
1596947 GAGTTTAGGT
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
15 7 0.20
16 3 0.09
17 17 0.49
18 8 0.23
ACGTcount: A:0.69, C:0.00, G:0.14, T:0.17
Consensus pattern (16 bp):
AAATAAAATGAAAATG
Found at i:1596918 original size:23 final size:23
Alignment explanation
Indices: 1596888--1596941 Score: 76
Period size: 23 Copynumber: 2.3 Consensus size: 23
1596878 AAGGAAAGGA
1596888 AAATGAAAATGAAAATAAA-AATG
1 AAATGAAAATGAAAA-AAAGAATG
1596911 AAATGAAAATGAAAAAAATGAATG
1 AAATGAAAATGAAAAAAA-GAATG
1596935 -AATGAAA
1 AAATGAAA
1596942 TAAAAGAGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
22 3 0.10
23 22 0.76
24 4 0.14
ACGTcount: A:0.69, C:0.00, G:0.15, T:0.17
Consensus pattern (23 bp):
AAATGAAAATGAAAAAAAGAATG
Found at i:1599479 original size:45 final size:45
Alignment explanation
Indices: 1599409--1600064 Score: 397
Period size: 45 Copynumber: 14.9 Consensus size: 45
1599399 AAAACCTCAA
* * ** * * *
1599409 CTTGACTTTTTCGTGAAGATTAGTTAATCTTTTAGTGATGCCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* ** *
1599454 CTTGACTTTCTAGCGAAGAAAAGTTAATATTTTAGTGATGTCTTT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* * * * *
1599499 CTCGACTTTCTTGCGAAGAGGAGTCAATATTTTAGTAATGCCATT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* *
1599544 CTTGACATTCTCGCAAAGAGGA-TTCAATATTTTAGTGATGT-ATTT
1 CTTGACTTTCTCGCGAAGAGGAGTT-AATATTTTAGTGATGTCA-TT
* **
1599589 CTTGAATTTCTCGCGAAGAGGA-TTCAACCTTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTT-AATATTTTAGTGATGTCATT
* * * * * * *
1599634 CTTGATTTTCTCGCGAAGAAGCGTCAATCTTTTAATGATGTCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* * * * ** *
1599679 ATTGACTTTCTCACAAAGAGGA-TCCAACCTTTTAGTGATTTCATT
1 CTTGACTTTCTCGCGAAGAGGAGT-TAATATTTTAGTGATGTCATT
* * * *
1599724 CTTGACTTTCTTGAGAAGA-GAG---------T-G-A-TGTCTTT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* * *
1599756 CTTGACTTTCTCGCGAAAAGAAGTCAACT-TTTTAGTGATGTCATT
1 CTTGACTTTCTCGCGAAGAGGAGTTAA-TATTTTAGTGATGTCATT
* * * * * * ** *
1599801 ATTGACTTTCTTG-TAGAGATGAGTCAATCTTTTAGTTTTTTCCA-T
1 CTTGACTTTCTCGCGA-AGAGGAGTTAATATTTTAGTGATGT-CATT
* * ** *
1599846 CTTGACTTTCTCGCGAAGATGAGTCAACCTTTTAGTGATGTTATT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* * *
1599891 CTTAACTTTCTCGCGAAGAGGAGTCAATATTTTAGTGATGTCCTT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* * * *
1599936 CTTGACTTTCTCGCAAAGAGGAG-TCATAATTTAGTGATGCCATT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
* * * * * *
1599980 ATTGACTTTCTCGTGGAGAGGAGTCAATCTTTTAGTGTTGTTC-TT
1 CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATG-TCATT
* * * *
1600025 CTTAAATTTCTCGCGGAA-AGTAGTGAACT-TTTTAGTGATG
1 CTTGACTTTCTCGC-GAAGAGGAGTTAA-TATTTTAGTGATG
1600065 CCCTTCTTCA
Statistics
Matches: 476, Mismatches: 107, Indels: 56
0.74 0.17 0.09
Matches are distributed among these distances:
32 21 0.04
33 2 0.00
34 1 0.00
35 1 0.00
42 1 0.00
43 1 0.00
44 43 0.09
45 397 0.83
46 9 0.02
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (45 bp):
CTTGACTTTCTCGCGAAGAGGAGTTAATATTTTAGTGATGTCATT
Done.