Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009616.1 Hibiscus syriacus cultivar Beakdansim tig00117002_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: 692457
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 4
Found at i:398350 original size:22 final size:22
Alignment explanation
Indices: 398320--398364 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
398310 CCCAATAGCT
398320 AATACAAAAAATT-CAAACTTGA
1 AATAC-AAAAATTGCAAACTTGA
* *
398342 AATATAAAAATTGTAAACTTGA
1 AATACAAAAATTGCAAACTTGA
398364 A
1 A
398365 CCTAGTTTGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.58, C:0.09, G:0.07, T:0.27
Consensus pattern (22 bp):
AATACAAAAATTGCAAACTTGA
Found at i:400730 original size:155 final size:152
Alignment explanation
Indices: 400352--400778 Score: 443
Period size: 151 Copynumber: 2.8 Consensus size: 152
400342 AGATAGTTAA
* * * * * * * *
400352 AAAAATAGCAATT-AAAGTTACATATGTATTCTATTGTGGTATATGAGCATGTGATTCAAATTTG
1 AAAAATAGGAATTGAAA-ATACACATGTATTCTAATATGGTTTAGGAGCATGTGGTTCAAATTTG
* * * * ** * * *
400416 ATAAAAAAAAATTGATTTAAAATAAATCACAAATTGAA-AGAACGAGGAGATTATGAAAAATTGA
65 AT--AAAAAAATAGACTTAAAATAAATGACGAATTGAAGA-AATAATGAAATCATGAAAAATTGA
400480 AGGACTAAATTAAAAAAATTGTTATC
127 AGGACTAAATTAAAAAAATTGTTATC
* * * * *
400506 AAAAATAGGAATTGAAAGTACACGTGTATTCTACTATGGTTTAGGAGCAAGTGGCTCAAATTTGA
1 AAAAATAGGAATTGAAAATACACATGTATTCTAATATGGTTTAGGAGCATGTGGTTCAAATTTGA
* *
400571 T-AAAAAATGGACTTAAAATAAATGACGAATTGAAGAAATAATGAAATCATGAAAAATTGAATGA
66 TAAAAAAATAGACTTAAAATAAATGACGAATTGAAGAAATAATGAAATCATGAAAAATTGAAGGA
400635 CTAAATTGAAAAATAAAAATTTTGTTAT-
131 CTAAATT----AA-AAAAA--TTGTTATC
* *
400663 AAAAA-A-GAATTGAAAATACACATGTATTCTAATATGGTTTAGGAGTATGTGGTTCAAATTTGG
1 AAAAATAGGAATTGAAAATACACATGTATTCTAATATGGTTTAGGAGCATGTGGTTCAAATTTGA
* * *
400726 TAAAAAAAATAGACTTAAAATGAAGGATGAATTGAAGAAATAATGAAATCATG
66 T-AAAAAAATAGACTTAAAATAAATGACGAATTGAAGAAATAATGAAATCATG
400779 GACTAAATCG
Statistics
Matches: 230, Mismatches: 32, Indels: 19
0.82 0.11 0.07
Matches are distributed among these distances:
151 58 0.25
152 1 0.00
154 51 0.22
155 56 0.24
156 6 0.03
157 51 0.22
158 7 0.03
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (152 bp):
AAAAATAGGAATTGAAAATACACATGTATTCTAATATGGTTTAGGAGCATGTGGTTCAAATTTGA
TAAAAAAATAGACTTAAAATAAATGACGAATTGAAGAAATAATGAAATCATGAAAAATTGAAGGA
CTAAATTAAAAAAATTGTTATC
Found at i:400778 original size:157 final size:151
Alignment explanation
Indices: 400468--400778 Score: 412
Period size: 157 Copynumber: 2.0 Consensus size: 151
400458 CGAGGAGATT
* *
400468 ATGAAAAATTGAAGGACTAAATTAAAAAAATTGTTATCAAAAATAGGAATTGAAAGTACACGTGT
1 ATGAAAAATTGAAGGACTAAATTAAAAAAATTGTTATCAAAAATAGGAATTGAAAATACACATGT
* * * *
400533 ATTCTACTATGGTTTAGGAGCAAGTGGCTCAAATTTGATAAAAAATGGACTTAAAATAAATGACG
66 ATTCTAATATGGTTTAGGAGCAAGTGGCTCAAATTTGAAAAAAAATAGACTTAAAATAAAGGACG
400598 AATTGAAGAAATAATGAAATC
131 AATTGAAGAAATAATGAAATC
*
400619 ATGAAAAATTGAATGACTAAATTGAAAAATAAAAATTTTGTTAT-AAAAA-A-GAATTGAAAATA
1 ATGAAAAATTGAAGGACTAAATT----AA-AAAAA--TTGTTATCAAAAATAGGAATTGAAAATA
* * *
400681 CACATGTATTCTAATATGGTTTAGGAGTATGTGGTTCAAATTTGGTAAAAAAAATAGACTTAAAA
59 CACATGTATTCTAATATGGTTTAGGAGCAAGTGGCTCAAATTT-G-AAAAAAAATAGACTTAAAA
* *
400746 TGAAGGATGAATTGAAGAAATAATGAAATC
122 TAAAGGACGAATTGAAGAAATAATGAAATC
400776 ATG
1 ATG
400779 GACTAAATCG
Statistics
Matches: 139, Mismatches: 12, Indels: 12
0.85 0.07 0.07
Matches are distributed among these distances:
151 22 0.16
155 51 0.37
156 7 0.05
157 52 0.37
158 7 0.05
ACGTcount: A:0.48, C:0.06, G:0.17, T:0.29
Consensus pattern (151 bp):
ATGAAAAATTGAAGGACTAAATTAAAAAAATTGTTATCAAAAATAGGAATTGAAAATACACATGT
ATTCTAATATGGTTTAGGAGCAAGTGGCTCAAATTTGAAAAAAAATAGACTTAAAATAAAGGACG
AATTGAAGAAATAATGAAATC
Found at i:401874 original size:22 final size:22
Alignment explanation
Indices: 401846--401894 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
401836 GTGTTTTTCT
401846 GCTTTCGAATACAAAAATAATA
1 GCTTTCGAATACAAAAATAATA
** *
401868 GCTTTCGAATATGATAATAATA
1 GCTTTCGAATACAAAAATAATA
401890 GCTTT
1 GCTTT
401895 TCAAAACGTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (22 bp):
GCTTTCGAATACAAAAATAATA
Found at i:405300 original size:24 final size:26
Alignment explanation
Indices: 405248--405308 Score: 81
Period size: 24 Copynumber: 2.4 Consensus size: 26
405238 GAAGTGTTGT
**
405248 TTTTAAGAGACAAATAATGAAGTGTTG
1 TTTTAAGAGAC-AATAATGAAGTAATG
405275 TTTTAAGAGAC-A-AATGAAGTAATG
1 TTTTAAGAGACAATAATGAAGTAATG
405299 TTTTAAGAGA
1 TTTTAAGAGA
405309 TAAACTTATT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
24 20 0.62
25 1 0.03
27 11 0.34
ACGTcount: A:0.43, C:0.03, G:0.21, T:0.33
Consensus pattern (26 bp):
TTTTAAGAGACAATAATGAAGTAATG
Found at i:405300 original size:27 final size:28
Alignment explanation
Indices: 405236--405289 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 28
405226 CATAGGATGC
405236 ATGAAGTGTTGTTTTTAAGAGACAAATA
1 ATGAAGTGTTGTTTTTAAGAGACAAATA
405264 ATGAAGTGTTG-TTTTAAGAGACAAAT
1 ATGAAGTGTTGTTTTTAAGAGACAAAT
405290 GAAGTAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
27 15 0.58
28 11 0.42
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (28 bp):
ATGAAGTGTTGTTTTTAAGAGACAAATA
Found at i:405485 original size:18 final size:18
Alignment explanation
Indices: 405462--405496 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
405452 TAGCAAATAA
*
405462 ATGTGAATTTAAATTATT
1 ATGTGAAATTAAATTATT
405480 ATGTGAAATTAAATTAT
1 ATGTGAAATTAAATTAT
405497 GTGTGCTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.43, C:0.00, G:0.11, T:0.46
Consensus pattern (18 bp):
ATGTGAAATTAAATTATT
Found at i:406782 original size:15 final size:15
Alignment explanation
Indices: 406758--406791 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
406748 CCGTAGGACC
406758 ACTACATCCCAAAAG
1 ACTACATCCCAAAAG
* *
406773 ACTACGTCCCGAAAG
1 ACTACATCCCAAAAG
406788 ACTA
1 ACTA
406792 TTATACCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.32, G:0.12, T:0.15
Consensus pattern (15 bp):
ACTACATCCCAAAAG
Found at i:406917 original size:29 final size:29
Alignment explanation
Indices: 406878--406978 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
406868 TCATATGTTA
406878 ATGTA-CTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
* *
406906 ATGTAGTTCATGTCATTTCTCTTGTGATG
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
406935 ATGTAGCTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
406964 ATGTAGCTCATGTCA
1 ATGTAGCTCATGTCA
406979 CGTTCTCATA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
28 5 0.07
29 63 0.93
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.45
Consensus pattern (29 bp):
ATGTAGCTCATGTCATTTCTCTTGTGATC
Found at i:407448 original size:45 final size:45
Alignment explanation
Indices: 407381--407486 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 45
407371 TGCACTACTT
* * *
407381 GTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATT-AATGG
1 GTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAAAAGA
* *
407425 GATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAGA
1 G-TGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
407471 GTGCATCGATGCACTA
1 GTGCATCGATGCACTA
407487 CCAGTGCATC
Statistics
Matches: 53, Mismatches: 5, Indels: 7
0.82 0.08 0.11
Matches are distributed among these distances:
44 1 0.02
45 40 0.75
46 12 0.23
ACGTcount: A:0.28, C:0.15, G:0.20, T:0.37
Consensus pattern (45 bp):
GTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAGA
Found at i:413858 original size:29 final size:29
Alignment explanation
Indices: 413819--413919 Score: 177
Period size: 29 Copynumber: 3.5 Consensus size: 29
413809 TCATATGTTA
413819 ATGTA-CTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
*
413847 ATGTAGTTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
*
413876 ATATAGCTCATGTCATTTCTCTTGTGATC
1 ATGTAGCTCATGTCATTTCTCTTGTGATC
413905 ATGTAGCTCATGTCA
1 ATGTAGCTCATGTCA
413920 CGTTCTCATA
Statistics
Matches: 68, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
28 5 0.07
29 63 0.93
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.45
Consensus pattern (29 bp):
ATGTAGCTCATGTCATTTCTCTTGTGATC
Found at i:414371 original size:64 final size:63
Alignment explanation
Indices: 414302--414458 Score: 158
Period size: 64 Copynumber: 2.5 Consensus size: 63
414292 TAATGAAGGT
* **
414302 ATGCATCGATGCACTACTTGTGCATCGGTGCA-TAAAATGCATTCGAT-GTTTTATTATTAATGG
1 ATGCATCGATGCACTACTTGTGCATCGATGCACT-AAATGCATTCGATCGTTTTATT-TTAA-AA
414365 G
63 G
* * * * *
414366 ATGCATCGATACA-TGCCTTATGCATCGATGCACTAATTGCATTCGATCTTTTTATTTTAAAAG
1 ATGCATCGATGCACT-ACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
**
414429 AGTGCATCGATGCACTACCAGTGCATCGAT
1 A-TGCATCGATGCACTACTTGTGCATCGAT
414459 ACACCTTCAA
Statistics
Matches: 75, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
63 3 0.04
64 63 0.84
65 9 0.12
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTGTGCATCGATGCACTAAATGCATTCGATCGTTTTATTTTAAAAG
Found at i:420621 original size:44 final size:44
Alignment explanation
Indices: 420558--420778 Score: 268
Period size: 44 Copynumber: 5.1 Consensus size: 44
420548 ACAAACACCA
* * * *
420558 CTATATATCA-ACCTTTAGCGACGTTTGTATACTAAAAACGCTG
1 CTATATACCAGACATTTAGCGGCGTTTGTATACTAAAAACGCCG
* * * *
420601 TTATATACCAGACTTTTAGCGACGTTTGTAT-CATAAAAACGTCG
1 CTATATACCAGACATTTAGCGGCGTTTGTATAC-TAAAAACGCCG
* * *
420645 CTATATACCAGACATTTAGTGGCGTTTGTATCCTAAAAACGCCA
1 CTATATACCAGACATTTAGCGGCGTTTGTATACTAAAAACGCCG
* *
420689 CTATATACCAGACATTTAGCGGTGTTTGTATCCTAAAAACGCCG
1 CTATATACCAGACATTTAGCGGCGTTTGTATACTAAAAACGCCG
* * *
420733 CTATATACCAGACATTTGGCGGCGTTTGTATA-AAAAAATGCCG
1 CTATATACCAGACATTTAGCGGCGTTTGTATACTAAAAACGCCG
420776 CTA
1 CTA
420779 AATCTCAAAA
Statistics
Matches: 156, Mismatches: 19, Indels: 6
0.86 0.10 0.03
Matches are distributed among these distances:
43 21 0.13
44 134 0.86
45 1 0.01
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (44 bp):
CTATATACCAGACATTTAGCGGCGTTTGTATACTAAAAACGCCG
Found at i:420816 original size:42 final size:41
Alignment explanation
Indices: 420763--420843 Score: 126
Period size: 42 Copynumber: 2.0 Consensus size: 41
420753 GGCGTTTGTA
*
420763 TAAAAAAATGCCGCTAAATCTCAAAACCTATTGCAGCGTAT
1 TAAAAAAATGCCGCTAAATATCAAAACCTATTGCAGCGTAT
* *
420804 TAAAACAAATGCCGCTAAATATCAGAACCTATTGCGGCGT
1 TAAAA-AAATGCCGCTAAATATCAAAACCTATTGCAGCGT
420844 TTGTTCAACA
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
41 5 0.14
42 31 0.86
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.23
Consensus pattern (41 bp):
TAAAAAAATGCCGCTAAATATCAAAACCTATTGCAGCGTAT
Found at i:420869 original size:43 final size:43
Alignment explanation
Indices: 420807--420888 Score: 112
Period size: 43 Copynumber: 1.9 Consensus size: 43
420797 AGCGTATTAA
* *
420807 AACAAATGCCGCTAAATATCAG-AACCTATTGCGGCGTTTGTTC
1 AACAAACGCCGATAAATATC-GTAACCTATTGCGGCGTTTGTTC
* *
420850 AACAAACGCCGATATATATCGTTACCTATTGCGGCGTTT
1 AACAAACGCCGATAAATATCGTAACCTATTGCGGCGTTT
420889 TTTTGTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
42 1 0.03
43 33 0.97
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (43 bp):
AACAAACGCCGATAAATATCGTAACCTATTGCGGCGTTTGTTC
Found at i:422480 original size:20 final size:21
Alignment explanation
Indices: 422455--422495 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
422445 ATCAAAATTC
* *
422455 AAATATGTAAA-AAATAAAAA
1 AAATATGGAAAGAAAGAAAAA
422475 AAATATGGAAAGAAAGAAAAA
1 AAATATGGAAAGAAAGAAAAA
422496 GAAGAAGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.15
Consensus pattern (21 bp):
AAATATGGAAAGAAAGAAAAA
Found at i:423387 original size:16 final size:16
Alignment explanation
Indices: 423366--423396 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
423356 AAAACATTCC
423366 AATGAGAATGACGACA
1 AATGAGAATGACGACA
423382 AATGAGAATGACGAC
1 AATGAGAATGACGAC
423397 CAACATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.48, C:0.13, G:0.26, T:0.13
Consensus pattern (16 bp):
AATGAGAATGACGACA
Found at i:424077 original size:21 final size:23
Alignment explanation
Indices: 424038--424087 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
424028 AATGTAGTTA
*
424038 ATATTT-AATTTATTAATTAAAT
1 ATATTTAAATTAATTAATTAAAT
*
424060 A-ATTTAAATTAATT-ATTATAT
1 ATATTTAAATTAATTAATTAAAT
424081 ATATTTA
1 ATATTTA
424088 TTAAGAAGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
ATATTTAAATTAATTAATTAAAT
Found at i:424961 original size:28 final size:28
Alignment explanation
Indices: 424924--424985 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
424914 TCCCAAATTT
* *
424924 CAAAGTAATTCAATTTCATTCTAAACCC
1 CAAATTAATTCAATTACATTCTAAACCC
*
424952 TAAATTAATTCAATTACATTCTAAACCC
1 CAAATTAATTCAATTACATTCTAAACCC
424980 CAAATT
1 CAAATT
424986 CTAAAATATT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.42, C:0.23, G:0.02, T:0.34
Consensus pattern (28 bp):
CAAATTAATTCAATTACATTCTAAACCC
Found at i:426082 original size:35 final size:34
Alignment explanation
Indices: 426013--426124 Score: 170
Period size: 35 Copynumber: 3.2 Consensus size: 34
426003 AAAAAAGACA
* *
426013 GAAATTGAAGTATTTTAGAATTTGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
*
426047 GTAATTGAATTATTTTGGAATTTAGGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTT-GGGTTTAGAAT
*
426082 GAAATTGAATTACTTTGGAATTTGTGGTTTAGAAT
1 GAAATTGAATTATTTTGGAATTTG-GGTTTAGAAT
426117 GAAATTGA
1 GAAATTGA
426125 GAATTGTTTT
Statistics
Matches: 71, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
34 21 0.30
35 50 0.70
ACGTcount: A:0.34, C:0.01, G:0.23, T:0.42
Consensus pattern (34 bp):
GAAATTGAATTATTTTGGAATTTGGGTTTAGAAT
Found at i:426424 original size:21 final size:21
Alignment explanation
Indices: 426395--426436 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
426385 AGTAAAAAAA
* *
426395 ATTACTTAAAATATTATTATT
1 ATTACTTAAAACATCATTATT
*
426416 ATTATTTAAAACATCATTATT
1 ATTACTTAAAACATCATTATT
426437 TTAATATTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (21 bp):
ATTACTTAAAACATCATTATT
Found at i:429008 original size:20 final size:21
Alignment explanation
Indices: 428985--429034 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
428975 TTGTTCTACG
428985 TTTGTTCTT-TAGTTTCTTTC
1 TTTGTTCTTCTAGTTTCTTTC
*
429005 TTTGTT-TTCTATTTTCTTTC
1 TTTGTTCTTCTAGTTTCTTTC
*
429025 GTTGTTCTTC
1 TTTGTTCTTC
429035 AATTTTCCTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 2 0.08
20 21 0.81
21 3 0.12
ACGTcount: A:0.04, C:0.16, G:0.10, T:0.70
Consensus pattern (21 bp):
TTTGTTCTTCTAGTTTCTTTC
Found at i:429041 original size:21 final size:20
Alignment explanation
Indices: 428997--429041 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
428987 TGTTCTTTAG
* *
428997 TTTCTTTCTTTGTTTTCTAT
1 TTTCTTTCGTTGTTTTCAAT
429017 TTTCTTTCGTTGTTCTTCAAT
1 TTTCTTTCGTTGTT-TTCAAT
429038 TTTC
1 TTTC
429042 CTTTGCTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.07, C:0.18, G:0.07, T:0.69
Consensus pattern (20 bp):
TTTCTTTCGTTGTTTTCAAT
Found at i:429984 original size:58 final size:58
Alignment explanation
Indices: 429894--430010 Score: 198
Period size: 58 Copynumber: 2.0 Consensus size: 58
429884 TGAAAGATAT
*
429894 TAAAAGTAAATCTAAATTCGTCTCAAAAATTACAACATATGCTTTGGACTGCATATAC
1 TAAAAGTAAATCTAAATTCGTCTCAAAAATTACAACACATGCTTTGGACTGCATATAC
* * *
429952 TAAAAGTAAATCTAAATTTGTCTTAAAAATTACAACACATGCTTTGGATTGCATATAC
1 TAAAAGTAAATCTAAATTCGTCTCAAAAATTACAACACATGCTTTGGACTGCATATAC
430010 T
1 T
430011 TAGGGTCCAC
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
58 55 1.00
ACGTcount: A:0.41, C:0.15, G:0.10, T:0.33
Consensus pattern (58 bp):
TAAAAGTAAATCTAAATTCGTCTCAAAAATTACAACACATGCTTTGGACTGCATATAC
Found at i:433850 original size:21 final size:20
Alignment explanation
Indices: 433764--433962 Score: 96
Period size: 21 Copynumber: 9.8 Consensus size: 20
433754 AAATGACCAA
**
433764 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
433783 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
433803 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
433823 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
433844 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* * **
433865 CAAATTTGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
433885 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
* **
433906 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* * *
433926 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
433947 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
433963 ACACATAAAT
Statistics
Matches: 130, Mismatches: 43, Indels: 13
0.70 0.23 0.07
Matches are distributed among these distances:
19 16 0.12
20 55 0.42
21 59 0.45
ACGTcount: A:0.38, C:0.24, G:0.18, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:433912 original size:20 final size:20
Alignment explanation
Indices: 433886--433981 Score: 95
Period size: 20 Copynumber: 4.8 Consensus size: 20
433876 TGCGATTTTC
433886 CAAAATCGCAACGCGAATAT
1 CAAAATCGCAACGCGAATAT
* ** * *
433906 GAAAATCGCATTGCGATTTT
1 CAAAATCGCAACGCGAATAT
*
433926 CCAGAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGAATAT
* *
433947 GAAAATCGCAACGCGAACA-
1 CAAAATCGCAACGCGAATAT
433966 CATAAATCGCAACGCG
1 CA-AAATCGCAACGCG
433982 TATCCGTAAA
Statistics
Matches: 59, Mismatches: 15, Indels: 4
0.76 0.19 0.05
Matches are distributed among these distances:
19 1 0.02
20 44 0.75
21 14 0.24
ACGTcount: A:0.40, C:0.25, G:0.19, T:0.17
Consensus pattern (20 bp):
CAAAATCGCAACGCGAATAT
Found at i:433924 original size:41 final size:41
Alignment explanation
Indices: 433872--433956 Score: 161
Period size: 41 Copynumber: 2.1 Consensus size: 41
433862 GTACAAATTT
433872 GCATTGCGATTTTCCAAAATCGCAACGCGAATATGAAAATC
1 GCATTGCGATTTTCCAAAATCGCAACGCGAATATGAAAATC
*
433913 GCATTGCGATTTTCCAGAATCGCAACGCGAATATGAAAATC
1 GCATTGCGATTTTCCAAAATCGCAACGCGAATATGAAAATC
433954 GCA
1 GCA
433957 ACGCGAACAC
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.35, C:0.22, G:0.19, T:0.24
Consensus pattern (41 bp):
GCATTGCGATTTTCCAAAATCGCAACGCGAATATGAAAATC
Found at i:433991 original size:20 final size:20
Alignment explanation
Indices: 433930--434137 Score: 205
Period size: 20 Copynumber: 10.6 Consensus size: 20
433920 GATTTTCCAG
* ** *
433930 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
433950 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
433970 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
433990 AAT-----CGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
434005 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
434025 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
* *
434045 AATCGCAATGCGTATCTGTA
1 AATCGCAACGCGTATCCGTA
*
434065 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
434085 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
434106 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
434126 AATCGCAACGCG
1 AATCGCAACGCG
434138 ATATTTAAAG
Statistics
Matches: 154, Mismatches: 24, Indels: 20
0.78 0.12 0.10
Matches are distributed among these distances:
15 15 0.10
19 2 0.01
20 119 0.77
21 17 0.11
22 1 0.01
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:433998 original size:15 final size:15
Alignment explanation
Indices: 433978--434010 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
433968 TAAATCGCAA
433978 CGCGTATCCGTAAAT
1 CGCGTATCCGTAAAT
433993 CGCGTATCCGTAAAT
1 CGCGTATCCGTAAAT
434008 CGC
1 CGC
434011 AACGTGTATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.30, G:0.21, T:0.24
Consensus pattern (15 bp):
CGCGTATCCGTAAAT
Found at i:434583 original size:31 final size:32
Alignment explanation
Indices: 434519--434587 Score: 95
Period size: 33 Copynumber: 2.2 Consensus size: 32
434509 TTCACTTAGA
*
434519 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTC-GTCGTTCCGAT
* *
434552 TTTCATTTCGCGTTGCTATTC-TCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCGTCGTTCCGAT
434583 TTTCA
1 TTTCA
434588 AGTTAGTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 14 0.42
33 19 0.58
ACGTcount: A:0.12, C:0.23, G:0.17, T:0.48
Consensus pattern (32 bp):
TTTCATTTCGCGTTACGATTCGTCGTTCCGAT
Found at i:434693 original size:21 final size:20
Alignment explanation
Indices: 434667--434771 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
434657 TGCAGAAGAG
434667 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* ***
434688 TCGCAACGAGAGAATGACTG
1 TCGCAACGAGAAAATGAAAA
434708 TCGCAACGAGAGAAATG-AAA
1 TCGCAACGAGA-AAATGAAAA
*
434728 GCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
434742 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
434761 TCGCAACGAGA
1 TCGCAACGAGA
434772 GAATCGCAAC
Statistics
Matches: 65, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.15
15 1 0.02
16 2 0.03
17 1 0.02
19 11 0.17
20 25 0.38
21 15 0.23
ACGTcount: A:0.45, C:0.19, G:0.26, T:0.10
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:434711 original size:20 final size:20
Alignment explanation
Indices: 434665--434742 Score: 95
Period size: 20 Copynumber: 3.9 Consensus size: 20
434655 TTTGCAGAAG
*
434665 AGTCGCAACGAGATAAATGAA
1 AGTCGCAACGAGA-GAATGAA
* *
434686 AATCGCAACGAGAGAATGAC
1 AGTCGCAACGAGAGAATGAA
*
434706 TGTCGCAACGAGAGAAATGAA
1 AGTCGCAACGAGAG-AATGAA
434727 AG-CGCAACGAGAGAAT
1 AGTCGCAACGAGAGAAT
434743 CGCAACGCGA
Statistics
Matches: 49, Mismatches: 7, Indels: 4
0.82 0.12 0.07
Matches are distributed among these distances:
19 3 0.06
20 28 0.57
21 18 0.37
ACGTcount: A:0.45, C:0.17, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTCGCAACGAGAGAATGAA
Found at i:434724 original size:41 final size:38
Alignment explanation
Indices: 434660--434775 Score: 127
Period size: 41 Copynumber: 3.1 Consensus size: 38
434650 TTCAATTTGC
* *
434660 AGAAGAGTCGCAACGAGATAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
434698 AGAATGACTGTCGCAACGAGAGAAATG-AAAGCGCAACGAG
1 AGAAT-A--GTCGCAACGAGAGAAATGAAAATCGCAACGAG
*
434738 AG-A-A-TCGCAAC--GCGAAATGAAAATCGCAACGAG
1 AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
434771 AGAAT
1 AGAAT
434776 CGCAACGCGG
Statistics
Matches: 67, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
32 7 0.10
33 14 0.21
34 8 0.12
37 1 0.01
38 4 0.06
39 2 0.03
40 14 0.21
41 17 0.25
ACGTcount: A:0.46, C:0.17, G:0.27, T:0.10
Consensus pattern (38 bp):
AGAATAGTCGCAACGAGAGAAATGAAAATCGCAACGAG
Found at i:434748 original size:14 final size:14
Alignment explanation
Indices: 434729--434782 Score: 54
Period size: 14 Copynumber: 3.5 Consensus size: 14
434719 GAAATGAAAG
434729 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
*
434743 CGCAACGCGAAATGAAAAT
1 CGCAA--CG--A-GAGAAT
434762 CGCAACGAGAGAAT
1 CGCAACGAGAGAAT
434776 CGCAACG
1 CGCAACG
434783 CGGAACCAAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
14 17 0.52
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.30
ACGTcount: A:0.43, C:0.24, G:0.26, T:0.07
Consensus pattern (14 bp):
CGCAACGAGAGAAT
Found at i:434770 original size:33 final size:33
Alignment explanation
Indices: 434719--434798 Score: 117
Period size: 33 Copynumber: 2.5 Consensus size: 33
434709 CGCAACGAGA
*
434719 GAAATG-AAAGCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
434751 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* **
434784 GGAACCAAAATCGCA
1 GAAATGAAAATCGCA
434799 TTGCGATTTT
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
32 6 0.14
33 37 0.86
ACGTcount: A:0.45, C:0.23, G:0.25, T:0.07
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:434816 original size:19 final size:19
Alignment explanation
Indices: 434794--434891 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
434784 GGAACCAAAA
*
434794 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
434813 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
434827 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
434846 TTGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
434860 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
434879 TCGCGTTGCGATT
1 TCGCGTTGCGATT
434892 CTCTCGTTGC
Statistics
Matches: 61, Mismatches: 8, Indels: 20
0.69 0.09 0.22
Matches are distributed among these distances:
14 19 0.31
16 5 0.08
17 6 0.10
19 31 0.51
ACGTcount: A:0.10, C:0.23, G:0.22, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:434835 original size:14 final size:14
Alignment explanation
Indices: 434816--434905 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
434806 TTTCATTTCG
434816 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
434830 CGTTGCGATTTTCATTTT
1 CGTTGCGA--TTC--TCT
434848 GCGTTGCGATTCTCT
1 -CGTTGCGATTCTCT
434863 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
434880 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
434896 CGTTGCGATT
1 CGTTGCGATT
434906 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 26 0.41
15 3 0.05
16 8 0.12
17 8 0.12
18 3 0.05
19 16 0.25
ACGTcount: A:0.09, C:0.24, G:0.23, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:434841 original size:33 final size:33
Alignment explanation
Indices: 434799--434913 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
434789 CAAAATCGCA
434799 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
434832 TTGCGATTTTCATTTTGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
434865 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
434898 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
434914 AACCAAAAGA
Statistics
Matches: 76, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
33 76 1.00
ACGTcount: A:0.10, C:0.23, G:0.21, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:436920 original size:184 final size:184
Alignment explanation
Indices: 436611--436990 Score: 717
Period size: 184 Copynumber: 2.1 Consensus size: 184
436601 TAGATTGCTT
*
436611 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
436676 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
436741 GTGTATTCTTTAACAC-TGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTG-TTTGTCTTTTGGTTGAA
*
436795 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
436860 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
436925 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACAC-GTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
436980 AGTAAATTTAT
1 AGTAAATTTAT
436991 CCATTCAAGT
Statistics
Matches: 191, Mismatches: 3, Indels: 3
0.97 0.02 0.02
Matches are distributed among these distances:
184 144 0.75
185 27 0.14
186 20 0.10
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (184 bp):
AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACGTGAAATAGTATTTGTCTTTGTTTGTCTTTTGGTTGAA
Found at i:437007 original size:93 final size:93
Alignment explanation
Indices: 436611--436988 Score: 717
Period size: 93 Copynumber: 4.1 Consensus size: 93
436601 TAGATTGCTT
*
436611 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
436676 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
436704 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACAC--TGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
436767 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
436795 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
436860 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
436888 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
436953 TTTGTCTTTG-TTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
436980 AGTAAATTT
1 AGTAAATTT
436989 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 3, Indels: 5
0.97 0.01 0.02
Matches are distributed among these distances:
91 90 0.32
92 26 0.09
93 164 0.59
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:437072 original size:19 final size:19
Alignment explanation
Indices: 437032--437160 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
437022 TAGTTTACTT
* *
437032 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
437052 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
437071 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
437090 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
437104 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
437123 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
437137 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
437156 TCGCA
1 TCGCA
437161 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:437111 original size:33 final size:32
Alignment explanation
Indices: 437068--437160 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
437058 CGCGAAACCA
**
437068 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
437100 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
437133 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
437161 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:437158 original size:52 final size:52
Alignment explanation
Indices: 437032--437160 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
437022 TAGTTTACTT
**
437032 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
437084 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
437137 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
437161 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:437178 original size:19 final size:19
Alignment explanation
Indices: 437156--437271 Score: 117
Period size: 19 Copynumber: 6.6 Consensus size: 19
437146 GAAACCAAAA
*
437156 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
437175 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
437191 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
437208 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
437224 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
437241 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
437261 TCGCGTTGCGA
1 TCGCGTTGCGA
437272 AAGTAAACTA
Statistics
Matches: 80, Mismatches: 6, Indels: 21
0.75 0.06 0.20
Matches are distributed among these distances:
14 15 0.19
16 11 0.14
17 11 0.14
19 30 0.38
20 13 0.16
ACGTcount: A:0.12, C:0.21, G:0.22, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:437197 original size:14 final size:14
Alignment explanation
Indices: 437178--437234 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
437168 TTTCATTTCG
437178 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
437192 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
437209 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
437225 CGTTGCGATT
1 CGTTGCGATT
437235 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:437203 original size:33 final size:33
Alignment explanation
Indices: 437161--437253 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
437151 CAAAATCGCA
*
437161 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
437194 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
437227 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
437254 TTAAGTTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:439214 original size:14 final size:14
Alignment explanation
Indices: 439195--439230 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
439185 ATTGTTTAAT
439195 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
439209 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
439223 TGATTTGT
1 TGATTTGT
439231 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:439361 original size:19 final size:19
Alignment explanation
Indices: 439337--439434 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
439327 AAAATTGACT
439337 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
439356 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
439375 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
439389 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
439408 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
439428 ATCGCAA
1 ATCGCAA
439435 CGAGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:439466 original size:53 final size:53
Alignment explanation
Indices: 439337--439453 Score: 227
Period size: 53 Copynumber: 2.2 Consensus size: 53
439327 AAAATTGACT
439337 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
439389 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
439442 ATCGCAATGCGA
1 ATCGCAATGCGA
439454 TTTTCATTTC
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
52 29 0.45
53 35 0.55
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:441786 original size:12 final size:12
Alignment explanation
Indices: 441769--441793 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
441759 TCTTCGGGGA
441769 CTTTTTCTTCTT
1 CTTTTTCTTCTT
441781 CTTTTTCTTCTT
1 CTTTTTCTTCTT
441793 C
1 C
441794 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:442002 original size:24 final size:24
Alignment explanation
Indices: 441968--442014 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
441958 CTGAAACATC
441968 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
441992 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
442015 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:442724 original size:20 final size:20
Alignment explanation
Indices: 442696--442945 Score: 268
Period size: 20 Copynumber: 12.5 Consensus size: 20
442686 AAATTTCAGT
* *
442696 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
442716 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
442736 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
442756 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
442776 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
442796 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
442816 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
442836 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
442856 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
442876 GTTGCGATATACGGATACAC
1 GTTGCGATTTACGGATTCTC
* *
442896 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATTCTC
* ** *
442916 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATTCTC
442936 GTTGCGATTT
1 GTTGCGATTT
442946 TGGAAAATCG
Statistics
Matches: 200, Mismatches: 28, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
20 199 1.00
21 1 0.00
ACGTcount: A:0.20, C:0.18, G:0.25, T:0.38
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:442962 original size:21 final size:21
Alignment explanation
Indices: 442932--443014 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
442922 ATTTTCATAT
*
442932 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
442953 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
442974 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
442995 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
443015 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:443005 original size:42 final size:43
Alignment explanation
Indices: 442912--443010 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
442902 ATTTATGTGT
* *
442912 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
442953 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
442995 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
443011 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:447664 original size:13 final size:13
Alignment explanation
Indices: 447646--447672 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
447636 AATAATTTAG
447646 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
447659 AAAAGAAAAAAAA
1 AAAAGAAAAAAAA
447672 A
1 A
447673 GAAAAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (13 bp):
AAAAGAAAAAAAA
Found at i:447667 original size:10 final size:10
Alignment explanation
Indices: 447654--447678 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
447644 AGAAAAGAAA
447654 AAAAAAAAAG
1 AAAAAAAAAG
447664 AAAAAAAAAG
1 AAAAAAAAAG
447674 AAAAA
1 AAAAA
447679 GAAATGGTGT
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:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:447672 original size:16 final size:16
Alignment explanation
Indices: 447651--447682 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
447641 TTTAGAAAAG
447651 AAAAAAAAAAAAGAAA
1 AAAAAAAAAAAAGAAA
*
447667 AAAAAAGAAAAAGAAA
1 AAAAAAAAAAAAGAAA
447683 TGGTGTTCCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.91, C:0.00, G:0.09, T:0.00
Consensus pattern (16 bp):
AAAAAAAAAAAAGAAA
Found at i:465361 original size:18 final size:18
Alignment explanation
Indices: 465335--465374 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 18
465325 GAATATTTTT
*
465335 TTAATAAAAATAT-TAAAA
1 TTAAAAAAAAT-TGTAAAA
465353 TTAAAAAAAATTGTAAAA
1 TTAAAAAAAATTGTAAAA
465371 TTAA
1 TTAA
465375 TAATATATAC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.65, C:0.00, G:0.03, T:0.33
Consensus pattern (18 bp):
TTAAAAAAAATTGTAAAA
Found at i:465644 original size:38 final size:38
Alignment explanation
Indices: 465588--465664 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
465578 AACCGATATA
*
465588 TATATGAGTGCGTAATACCTTATGCCAAAACTGGGGCT
1 TATACGAGTGCGTAATACCTTATGCCAAAACTGGGGCT
465626 TATACGAGTGCGTAATACCTTATGCCAAAACTGGGGCT
1 TATACGAGTGCGTAATACCTTATGCCAAAACTGGGGCT
465664 T
1 T
465665 CAAATGCTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (38 bp):
TATACGAGTGCGTAATACCTTATGCCAAAACTGGGGCT
Found at i:470487 original size:23 final size:23
Alignment explanation
Indices: 470457--470516 Score: 93
Period size: 23 Copynumber: 2.6 Consensus size: 23
470447 ACATTTATAT
*
470457 GGCACTTCGGTGTAATTCTACGC
1 GGCACTTCGGTGCAATTCTACGC
*
470480 GGCACTTCGGTGCAATTCTACGT
1 GGCACTTCGGTGCAATTCTACGC
*
470503 AGCACTTCGGTGCA
1 GGCACTTCGGTGCA
470517 TTTATACGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 34 1.00
ACGTcount: A:0.18, C:0.27, G:0.27, T:0.28
Consensus pattern (23 bp):
GGCACTTCGGTGCAATTCTACGC
Found at i:473826 original size:63 final size:62
Alignment explanation
Indices: 473754--473893 Score: 160
Period size: 64 Copynumber: 2.2 Consensus size: 62
473744 CATATTCAAT
* * *
473754 GTGCATCGATGCACTC-TCAAATAAATGAACATCGATTGCAATTGGTGCATCGATGCATAAGG-A
1 GTGCATCGATGCACCCTTAAAATAAA--AACATCGAATGCAATTGGTGCATCGATGCAT-AGGTA
* * *
473817 GTGCATCGATGCATCCCCTTAAAATAAAAACATCGAATGTAATTGGTGTATCGATGCATGGGTA
1 GTGCATCGATGCA--CCCTTAAAATAAAAACATCGAATGCAATTGGTGCATCGATGCATAGGTA
473881 -TGCATCGATGCAC
1 GTGCATCGATGCAC
473894 ATGTTAAAGA
Statistics
Matches: 67, Mismatches: 6, Indels: 10
0.81 0.07 0.12
Matches are distributed among these distances:
61 1 0.01
63 27 0.40
64 29 0.43
65 2 0.03
66 8 0.12
ACGTcount: A:0.32, C:0.19, G:0.22, T:0.26
Consensus pattern (62 bp):
GTGCATCGATGCACCCTTAAAATAAAAACATCGAATGCAATTGGTGCATCGATGCATAGGTA
Found at i:473863 original size:64 final size:64
Alignment explanation
Indices: 473772--473892 Score: 165
Period size: 64 Copynumber: 1.9 Consensus size: 64
473762 ATGCACTCTC
*
473772 AAATAAATGAACATCGATTGCAATTGGTGCATCGATGCATAAGG-AGTGCATCGATGCATCCCCT
1 AAATAAA-GAACATCGAATGCAATTGGTGCATCGATGCAT-AGGTA-TGCATCGATGCATCCCCT
473836 TA
63 TA
* * *
473838 AAATAAA-AACATCGAATGTAATTGGTGTATCGATGCATGGGTATGCATCGATGCA
1 AAATAAAGAACATCGAATGCAATTGGTGCATCGATGCATAGGTATGCATCGATGCA
473893 CATGTTAAAG
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
63 14 0.28
64 29 0.58
66 7 0.14
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.26
Consensus pattern (64 bp):
AAATAAAGAACATCGAATGCAATTGGTGCATCGATGCATAGGTATGCATCGATGCATCCCCTTA
Found at i:473926 original size:20 final size:20
Alignment explanation
Indices: 473901--473938 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
473891 CACATGTTAA
473901 AGAATGCATCGATGCACTAT
1 AGAATGCATCGATGCACTAT
473921 AGAATGCATCGATGCACT
1 AGAATGCATCGATGCACT
473939 TCAAGGGGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (20 bp):
AGAATGCATCGATGCACTAT
Found at i:475861 original size:24 final size:23
Alignment explanation
Indices: 475834--475879 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
475824 CAAACCATTT
475834 CATATAACA-TAATGCATACTTATA
1 CATATAACATTAAT--ATACTTATA
*
475858 CATATATCATTAATATACTTAT
1 CATATAACATTAATATACTTAT
475880 CAGTACTCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 8 0.40
24 8 0.40
25 4 0.20
ACGTcount: A:0.43, C:0.15, G:0.02, T:0.39
Consensus pattern (23 bp):
CATATAACATTAATATACTTATA
Found at i:476197 original size:31 final size:31
Alignment explanation
Indices: 476159--476283 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
476149 CCCGAAGGAC
*
476159 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
476190 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
476221 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
**
476252 CAGTTTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
476283 C
1 C
476284 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:477069 original size:64 final size:64
Alignment explanation
Indices: 476936--477092 Score: 162
Period size: 64 Copynumber: 2.5 Consensus size: 64
476926 TAATGAAGGT
* * *
476936 ATGCATCGATGCACTA-TTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATTACTGGG
1 ATGCATCGATGCACTACTT-ATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAATGAG
* *
477000 ATGCATCGATGCACTACTTATGCATCGATGCA-AGAATTGCATTCGATGTATTTATT-TTAAAAT
1 ATGCATCGATGCACTACTTATGCATCGATGCATA-AAATGCATTCGATGT-TGTATTATT--AAT
477063 -AG
62 GAG
* * *
477065 -TGCATCGATGCACTTCCTGTGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
477093 ACACCTTCAA
Statistics
Matches: 80, Mismatches: 8, Indels: 10
0.82 0.08 0.10
Matches are distributed among these distances:
63 1 0.01
64 69 0.86
65 8 0.10
66 2 0.03
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAAATGCATTCGATGTTGTATTATTAATGAG
Found at i:481067 original size:31 final size:31
Alignment explanation
Indices: 481028--481152 Score: 180
Period size: 31 Copynumber: 4.0 Consensus size: 31
481018 TCCGAAGGAC
*
481028 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
481059 CAATCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
481090 CAGTTCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* * *
481121 CAGTCCATATGTCTCAAAAAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
481152 C
1 C
481153 CCTCGACCCT
Statistics
Matches: 85, Mismatches: 8, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
31 84 0.99
32 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:487980 original size:2 final size:2
Alignment explanation
Indices: 487973--488010 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
487963 GTAAGCCAAG
*
487973 TC TC TC TC TT 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
488011 CTATGACATA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:493122 original size:24 final size:24
Alignment explanation
Indices: 493090--493176 Score: 95
Period size: 24 Copynumber: 3.7 Consensus size: 24
493080 CATTTAAATG
* *
493090 ATAAACGAACACAAATGATCGAAC
1 ATAAACGAACACAAATAAACGAAC
** **
493114 ATAAACGAACGGATGTAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
*
493138 ATAAAAGAACAC-AATAAACGAAC
1 ATAAACGAACACAAATAAACGAAC
*
493161 GTAAACGAACACAAAT
1 ATAAACGAACACAAAT
493177 GAACAAATAC
Statistics
Matches: 49, Mismatches: 13, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 19 0.39
24 30 0.61
ACGTcount: A:0.56, C:0.18, G:0.14, T:0.11
Consensus pattern (24 bp):
ATAAACGAACACAAATAAACGAAC
Found at i:493142 original size:10 final size:10
Alignment explanation
Indices: 493109--493222 Score: 56
Period size: 10 Copynumber: 11.0 Consensus size: 10
493099 CACAAATGAT
493109 CGAACATAAA
1 CGAACATAAA
493119 CGAACGGATGTAAA
1 CGAAC--A--TAAA
493133 CGAACATAAA
1 CGAACATAAA
*
493143 AGAACACAATAAA
1 CG-A-AC-ATAAA
*
493156 CGAACGTAAA
1 CGAACATAAA
*
493166 CGAACACAAA
1 CGAACATAAA
*
493176 TGAACA-AATA
1 CGAACATAA-A
493186 C--A-ATAAA
1 CGAACATAAA
**
493193 TTAACATAAA
1 CGAACATAAA
* *
493203 TGAACGTAAA
1 CGAACATAAA
493213 CGAACATAAA
1 CGAACATAAA
493223 TGAAAATAGA
Statistics
Matches: 80, Mismatches: 12, Indels: 24
0.69 0.10 0.21
Matches are distributed among these distances:
7 2 0.03
8 3 0.04
9 3 0.04
10 49 0.61
11 3 0.04
12 5 0.06
13 6 0.08
14 9 0.11
ACGTcount: A:0.58, C:0.17, G:0.12, T:0.13
Consensus pattern (10 bp):
CGAACATAAA
Found at i:493159 original size:23 final size:23
Alignment explanation
Indices: 493129--493174 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
493119 CGAACGGATG
493129 TAAACGAACATAAAAGAACACAA
1 TAAACGAACATAAAAGAACACAA
* *
493152 TAAACGAACGTAAACGAACACAA
1 TAAACGAACATAAAAGAACACAA
493175 ATGAACAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.61, C:0.20, G:0.11, T:0.09
Consensus pattern (23 bp):
TAAACGAACATAAAAGAACACAA
Found at i:495338 original size:229 final size:229
Alignment explanation
Indices: 494937--495399 Score: 899
Period size: 229 Copynumber: 2.0 Consensus size: 229
494927 TTAGGGTTGT
*
494937 AACGAGTTGAGTCGGGCCCGAATATCTGTGTTTGACTCGATTTGAAACTCTAAAATAGAGTTCGA
1 AACGAGTTGAGTCGGGCCCGAATATATGTGTTTGACTCGATTTGAAACTCTAAAATAGAGTTCGA
*
495002 CATGATTTGAAAATCCGTGAGCCTGAAACTTTTAAATTCGATTTGAACTCAAAACTATAAATTAA
66 CATGATTTGAAAATCCGTGAGCCTGAAACTTTCAAATTCGATTTGAACTCAAAACTATAAATTAA
495067 AATTTGAAAAAACTCGAAATAAAAACAATCTTAAATTTAACTTGATTGATGGTCAGTTTGGCATT
131 AATTTGAAAAAACTCGAAATAAAAACAATCTTAAATTTAACTTGATTGATGGTCAGTTTGGCATT
495132 GCTTTTAAACAATGATTTTTAAAAATGATGTAGA
196 GCTTTTAAACAATGATTTTTAAAAATGATGTAGA
*
495166 AACGAGTTGAGTCGGGCCCGAATATATGTGTTTGACTCGATTTGAAACTCTAAAATCGAGTTCGA
1 AACGAGTTGAGTCGGGCCCGAATATATGTGTTTGACTCGATTTGAAACTCTAAAATAGAGTTCGA
495231 CATGATTTGAAAATCCGTGAGCCTGAAACTTTCAAATTCGATTTGAACTCAAAACTATAAATTAA
66 CATGATTTGAAAATCCGTGAGCCTGAAACTTTCAAATTCGATTTGAACTCAAAACTATAAATTAA
495296 AATTTGAAAAAACTCGAAATAAAAACAATCTTAAATTTAACTTGATTGATGGTCAGTTTGGCATT
131 AATTTGAAAAAACTCGAAATAAAAACAATCTTAAATTTAACTTGATTGATGGTCAGTTTGGCATT
495361 GCTTTTAAACAATGATTTTTAAAAATGATGTAGA
196 GCTTTTAAACAATGATTTTTAAAAATGATGTAGA
495395 AACGA
1 AACGA
495400 ACTTTTAAAA
Statistics
Matches: 231, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
229 231 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (229 bp):
AACGAGTTGAGTCGGGCCCGAATATATGTGTTTGACTCGATTTGAAACTCTAAAATAGAGTTCGA
CATGATTTGAAAATCCGTGAGCCTGAAACTTTCAAATTCGATTTGAACTCAAAACTATAAATTAA
AATTTGAAAAAACTCGAAATAAAAACAATCTTAAATTTAACTTGATTGATGGTCAGTTTGGCATT
GCTTTTAAACAATGATTTTTAAAAATGATGTAGA
Found at i:502231 original size:17 final size:17
Alignment explanation
Indices: 502209--502254 Score: 67
Period size: 17 Copynumber: 2.7 Consensus size: 17
502199 TGTTTATGAG
502209 GGAATT-GAATCTGTGAA
1 GGAATTGGAATCTGT-AA
*
502226 GGAATTGGAATCTGTCA
1 GGAATTGGAATCTGTAA
502243 GGAATTGGAATC
1 GGAATTGGAATC
502255 CAATTCCATA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
17 19 0.70
18 8 0.30
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (17 bp):
GGAATTGGAATCTGTAA
Found at i:502955 original size:263 final size:265
Alignment explanation
Indices: 502635--503198 Score: 855
Period size: 263 Copynumber: 2.2 Consensus size: 265
502625 ATGAATTAGA
* * * *
502635 AACCCGACCCAAAAAAAT-AAAAAATTATTTTTATTCAATAAAAGCATTGACTTAATTG-AAAAA
1 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAA
502698 A-TATATATGGAGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT-TTT
66 ATTATATAT--AGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
*
502761 TTGGGTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCAAATATCACACTTTA
129 TTGGGTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCAAATATAACAC-TTA
* * *
502826 AAAAAA-A-TCGACCAGACCAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAA
193 AAAAAACACCCGACCAGACCAAAACAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAA
502889 CCCGACTC
258 CCCGACTC
502897 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAA
1 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAA
*
502962 ATTATATATAGAGGGTATTATTGTAATTATTTCTAAATATATAAGGTAAAATTATATATATTTTT
66 ATTATATATAGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTT
* * * *
503027 TGGTCGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGAATATAACACTTAAAA
131 GGGTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCAAATATAACACTTAAAA
** *
503092 AAACCGACCCGACCCTACCAAAACAAAGTTTCACCCGACCCGATCCGAATATATGAATTAGAAAC
196 AAA-C-ACCCGACCAGACCAAAACAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAAC
503157 CCGACTC
259 CCGACTC
503164 -A----ACCCGAAATAATAAAAAAA-TATTTTTATTCAATA
1 AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATA
503199 TATGAATAAG
Statistics
Matches: 278, Mismatches: 16, Indels: 17
0.89 0.05 0.05
Matches are distributed among these distances:
261 15 0.05
262 35 0.13
263 96 0.35
264 65 0.23
265 7 0.03
266 2 0.01
267 58 0.21
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (265 bp):
AACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAATGACTTAATTGAAAAAA
ATTATATATAGAGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTT
GGGTCGGGTCGGGTATTTTTCACCCTAAACCCAAACCCGACCCGACCCAAATATAACACTTAAAA
AAACACCCGACCAGACCAAAACAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAACCC
GACTC
Found at i:504772 original size:2 final size:2
Alignment explanation
Indices: 504765--504799 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
504755 TGCAGCTGTG
504765 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
504800 ATTAATCAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:510176 original size:21 final size:21
Alignment explanation
Indices: 510132--510192 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 21
510122 CCATCAGAGA
* *
510132 ATCAAGCAAGAACAGAAAAACC
1 ATCAA-CAACAACATAAAAACC
* * *
510154 ATCAACAGCTACATAAAAGCC
1 ATCAACAACAACATAAAAACC
*
510175 ATCAGCAACAACATAAAA
1 ATCAACAACAACATAAAA
510193 CAATTTTAAC
Statistics
Matches: 31, Mismatches: 8, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
21 26 0.84
22 5 0.16
ACGTcount: A:0.56, C:0.25, G:0.10, T:0.10
Consensus pattern (21 bp):
ATCAACAACAACATAAAAACC
Found at i:514572 original size:22 final size:22
Alignment explanation
Indices: 514525--514585 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
514515 GGATCTACGC
* *
514525 GGTCCTTCGGGACATATATAGT
1 GGTCCTTCGGGACAAATACAGT
*
514547 GGTCCTTCGGGATAAATACA-T
1 GGTCCTTCGGGACAAATACAGT
*
514568 AGGTCATTCGGGACAAAT
1 -GGTCCTTCGGGACAAAT
514586 TTCATATGCC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
21 1 0.03
22 32 0.97
ACGTcount: A:0.28, C:0.18, G:0.26, T:0.28
Consensus pattern (22 bp):
GGTCCTTCGGGACAAATACAGT
Found at i:514878 original size:36 final size:36
Alignment explanation
Indices: 514838--514927 Score: 137
Period size: 39 Copynumber: 2.4 Consensus size: 36
514828 AATGTTCAAC
*
514838 ATATGCTTATATGATATAAAGGAATTAGTGATAATA
1 ATATGATTATATGATATAAAGGAATTAGTGATAATA
514874 ATATGATTATTATATGATATAAAGGAATTAGTGATAATA
1 ATATG---ATTATATGATATAAAGGAATTAGTGATAATA
514913 ATATGATTAT-TGATA
1 ATATGATTATATGATA
514928 AATATGTTCA
Statistics
Matches: 50, Mismatches: 1, Indels: 7
0.86 0.02 0.12
Matches are distributed among these distances:
35 5 0.10
36 10 0.20
39 35 0.70
ACGTcount: A:0.44, C:0.01, G:0.16, T:0.39
Consensus pattern (36 bp):
ATATGATTATATGATATAAAGGAATTAGTGATAATA
Found at i:514882 original size:18 final size:18
Alignment explanation
Indices: 514861--514928 Score: 57
Period size: 18 Copynumber: 3.6 Consensus size: 18
514851 ATATAAAGGA
514861 ATTAGTGATAATAATATG
1 ATTAGTGATAATAATATG
* * *
514879 ATTA-TTATATGATATAAAGG
1 ATTAGTGATA--ATA-ATATG
514899 AATTAGTGATAATAATATG
1 -ATTAGTGATAATAATATG
*
514918 ATTATTGATAA
1 ATTAGTGATAA
514929 ATATGTTCAT
Statistics
Matches: 38, Mismatches: 7, Indels: 10
0.69 0.13 0.18
Matches are distributed among these distances:
17 4 0.11
18 14 0.37
19 6 0.16
20 6 0.16
21 4 0.11
22 4 0.11
ACGTcount: A:0.46, C:0.00, G:0.15, T:0.40
Consensus pattern (18 bp):
ATTAGTGATAATAATATG
Found at i:514888 original size:39 final size:39
Alignment explanation
Indices: 514844--514923 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
514834 CAACATATGC
514844 TTATATGATATAAAGGAATTAGTGATAATAATATGATTA
1 TTATATGATATAAAGGAATTAGTGATAATAATATGATTA
514883 TTATATGATATAAAGGAATTAGTGATAATAATATGATTA
1 TTATATGATATAAAGGAATTAGTGATAATAATATGATTA
514922 TT
1 TT
514924 GATAAATATG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.45, C:0.00, G:0.15, T:0.40
Consensus pattern (39 bp):
TTATATGATATAAAGGAATTAGTGATAATAATATGATTA
Found at i:516841 original size:12 final size:12
Alignment explanation
Indices: 516824--516862 Score: 69
Period size: 12 Copynumber: 3.2 Consensus size: 12
516814 TCTTGCGATT
516824 TTTCGTTATAAA
1 TTTCGTTATAAA
516836 TTTCGTTATAAA
1 TTTCGTTATAAA
*
516848 TTTTGTTATAAA
1 TTTCGTTATAAA
516860 TTT
1 TTT
516863 TTTTATTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 26 1.00
ACGTcount: A:0.31, C:0.05, G:0.08, T:0.56
Consensus pattern (12 bp):
TTTCGTTATAAA
Found at i:516863 original size:12 final size:12
Alignment explanation
Indices: 516823--516868 Score: 65
Period size: 12 Copynumber: 3.8 Consensus size: 12
516813 TTCTTGCGAT
516823 TTTTCGTTATAAA
1 TTTT-GTTATAAA
*
516836 TTTCGTTATAAA
1 TTTTGTTATAAA
516848 TTTTGTTATAAA
1 TTTTGTTATAAA
*
516860 TTTTTTTAT
1 TTTTGTTAT
516869 TATACTTATT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
12 27 0.90
13 3 0.10
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (12 bp):
TTTTGTTATAAA
Found at i:529208 original size:6 final size:6
Alignment explanation
Indices: 529197--529224 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
529187 AAATTAGTTT
529197 GTGTTG GTGTTG GTGTTG GTGTTG GTGT
1 GTGTTG GTGTTG GTGTTG GTGTTG GTGT
529225 CGGCTGAGTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.00, G:0.50, T:0.50
Consensus pattern (6 bp):
GTGTTG
Found at i:529656 original size:26 final size:27
Alignment explanation
Indices: 529625--529692 Score: 75
Period size: 28 Copynumber: 2.5 Consensus size: 27
529615 TTAACGTTTA
*
529625 AAAATACACATAT-TAGATATTTTATC
1 AAAATACAAATATATAGATATTTTATC
* * *
529651 AGAATAGAAATATCATATATATTTTATC
1 AAAATACAAATAT-ATAGATATTTTATC
*
529679 AAAATAGAAATATA
1 AAAATACAAATATA
529693 AAATTAAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 10 0.29
27 1 0.03
28 24 0.69
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.35
Consensus pattern (27 bp):
AAAATACAAATATATAGATATTTTATC
Found at i:529929 original size:21 final size:20
Alignment explanation
Indices: 529902--530000 Score: 81
Period size: 21 Copynumber: 4.8 Consensus size: 20
529892 AATCAGTTTC
529902 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
529923 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
529944 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
529964 CAAGAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
529985 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
530001 ACACATAAAT
Statistics
Matches: 61, Mismatches: 15, Indels: 5
0.75 0.19 0.06
Matches are distributed among these distances:
20 17 0.28
21 44 0.72
ACGTcount: A:0.37, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:530029 original size:20 final size:20
Alignment explanation
Indices: 529968--530216 Score: 261
Period size: 20 Copynumber: 12.4 Consensus size: 20
529958 GATTTTCAAG
* ** *
529968 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
529988 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
530008 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
530028 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
530048 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
530068 AATAGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
530088 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
530108 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
530128 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
530148 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
530168 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
530188 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
530208 AATCACAAC
1 AATCGCAAC
530217 ACTGAAATTT
Statistics
Matches: 195, Mismatches: 28, Indels: 12
0.83 0.12 0.05
Matches are distributed among these distances:
19 2 0.01
20 191 0.98
21 2 0.01
ACGTcount: A:0.37, C:0.26, G:0.18, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:530948 original size:24 final size:24
Alignment explanation
Indices: 530909--530955 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
530899 AAATTTGGTC
530909 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
530933 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
530956 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:531147 original size:12 final size:12
Alignment explanation
Indices: 531130--531154 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
531120 ATATAATCCT
531130 GAAGAAGAAAAA
1 GAAGAAGAAAAA
531142 GAAGAAGAAAAA
1 GAAGAAGAAAAA
531154 G
1 G
531155 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:533505 original size:34 final size:34
Alignment explanation
Indices: 533418--533650 Score: 219
Period size: 34 Copynumber: 6.8 Consensus size: 34
533408 GCATTTGACT
** * * * *
533418 ATCGCAACACGGAAATTACAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACAAGAAA
*
533452 ATCGCAATGC-GAAATGAAAATCCCAACAAGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAACAAGAAA
533485 ATCGCAATGCGGAAATGAAAATCGCAATGCGAAATGAAA
1 ATCGCAATGCGGAAATGAAAATCGCAA--C--AA-GAAA
*
533524 ATCGCAA--CGAGAGAATCG-CAAT-GCGAA-AATGAAA
1 ATCGCAATGCG-GA-AAT-GAAAATCGC-AACAA-GAAA
* *
533558 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACAAGAAA
* *
533591 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGGAAATGAAAATCGCAACAAGAAA
533625 ATCGCAATGCGGAAATGAAAATCGCA
1 ATCGCAATGCGGAAATGAAAATCGCA
533651 TTGCGATTTT
Statistics
Matches: 171, Mismatches: 12, Indels: 32
0.80 0.06 0.15
Matches are distributed among these distances:
32 1 0.01
33 49 0.29
34 91 0.53
36 2 0.01
37 2 0.01
38 6 0.04
39 19 0.11
40 1 0.01
ACGTcount: A:0.46, C:0.19, G:0.22, T:0.13
Consensus pattern (34 bp):
ATCGCAATGCGGAAATGAAAATCGCAACAAGAAA
Found at i:533514 original size:53 final size:53
Alignment explanation
Indices: 533451--533617 Score: 298
Period size: 53 Copynumber: 3.2 Consensus size: 53
533441 GCAACGAGAG
* * *
533451 AATCGCAATGCGAAATGAAAATCCCAACAAGAAAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
*
533504 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
533557 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
1 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
533610 AATCGCAA
1 AATCGCAA
533618 CGAGAGAATC
Statistics
Matches: 109, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 109 1.00
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (53 bp):
AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAA
Found at i:533622 original size:87 final size:89
Alignment explanation
Indices: 533418--533656 Score: 307
Period size: 87 Copynumber: 2.7 Consensus size: 89
533408 GCATTTGACT
** * * *
533418 ATCGCAACACGGAAATTACAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C--
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
533479 AAGAAAATCGCAATGCGGAAATGAAA
66 AAGAAAATCGCAA-GCGG-AATGAAA
533505 ATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAAATGAAAATCGCAATGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCG-AAATGAAAATCGCAATGCG
*
533569 AAATGAAAATCGCAA-C-G-A-GAGA
65 AAA-GAAAATCGCAAGCGGAATGAAA
*
533591 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGGAAATGAAAATCGCATTGCG
1 ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGC-GAAATGAAAATCGCAATGCG
533656 A
65 A
533657 TTTTCATTTC
Statistics
Matches: 137, Mismatches: 7, Indels: 16
0.86 0.04 0.10
Matches are distributed among these distances:
86 45 0.33
87 75 0.55
88 1 0.01
89 2 0.01
90 1 0.01
91 2 0.01
92 11 0.08
ACGTcount: A:0.45, C:0.19, G:0.23, T:0.13
Consensus pattern (89 bp):
ATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAATGCGA
AAGAAAATCGCAAGCGGAATGAAA
Found at i:533776 original size:14 final size:14
Alignment explanation
Indices: 533757--533793 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
533747 CATCAATTAC
533757 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
533771 ACAAATCATCTTTT
1 ACAAATCAACTTTT
533785 ACAAATCAA
1 ACAAATCAA
533794 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:535754 original size:19 final size:19
Alignment explanation
Indices: 535712--535884 Score: 150
Period size: 19 Copynumber: 9.6 Consensus size: 19
535702 TAGTTTACTT
* *
535712 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
*
535732 TCGCAACGCGAAATGAGAA
1 TCGCAACGCGAAATGAAAA
* **
535751 TCGCAACGAGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
**
535770 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
535789 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
* *
535808 TCGCAA--TGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
535822 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
535841 TCGCAA--C--AA-GAGAA
1 TCGCAACGCGAAATGAAAA
535855 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
535874 TCGCAATGCGA
1 TCGCAACGCGA
535885 TTTTAGTTTC
Statistics
Matches: 126, Mismatches: 17, Indels: 21
0.77 0.10 0.13
Matches are distributed among these distances:
14 18 0.14
15 2 0.02
16 5 0.04
17 5 0.04
18 2 0.02
19 82 0.65
20 12 0.10
ACGTcount: A:0.46, C:0.23, G:0.20, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:535833 original size:33 final size:33
Alignment explanation
Indices: 535787--535881 Score: 154
Period size: 33 Copynumber: 2.9 Consensus size: 33
535777 GCGAAACCAA
535787 AATCGCAACGCGAAATGAAAATCGCAATGACAG
1 AATCGCAACGCGAAATGAAAATCGCAATGACAG
* ** *
535820 AATCGCAATGCGAAATGAAAATCGCAACAAGAG
1 AATCGCAACGCGAAATGAAAATCGCAATGACAG
535853 AATCGCAACGCGAAATGAAAATCGCAATG
1 AATCGCAACGCGAAATGAAAATCGCAATG
535882 CGATTTTAGT
Statistics
Matches: 55, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 55 1.00
ACGTcount: A:0.46, C:0.20, G:0.21, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAATGACAG
Found at i:535876 original size:52 final size:52
Alignment explanation
Indices: 535746--535884 Score: 138
Period size: 52 Copynumber: 2.7 Consensus size: 52
535736 AACGCGAAAT
* ** * **
535746 GAGAATCGCAACGAGAAACCAAAATCGCAACGCGAAACCAAAATCGCAACGC
1 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACAA
* ** * **
535798 GA-AAT-GAAAATCGCAATGACAGAATCGCAATGCGAAATGAAAATCGCAACAA
1 GAGAATCGCAACGCGAAATGA-A-AATCGCAATGCGAAACCAAAATCGCAACAA
535850 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
1 GAGAATCGCAACGCGAAATGAAAATCGCAATGCGA
535885 TTTTAGTTTC
Statistics
Matches: 67, Mismatches: 16, Indels: 8
0.74 0.18 0.09
Matches are distributed among these distances:
50 7 0.10
51 4 0.06
52 42 0.63
53 4 0.06
54 10 0.15
ACGTcount: A:0.47, C:0.22, G:0.21, T:0.10
Consensus pattern (52 bp):
GAGAATCGCAACGCGAAATGAAAATCGCAATGCGAAACCAAAATCGCAACAA
Found at i:535902 original size:19 final size:19
Alignment explanation
Indices: 535880--535938 Score: 58
Period size: 19 Copynumber: 3.4 Consensus size: 19
535870 AAAATCGCAA
535880 TGCGATTTTAGTTTCGCGT
1 TGCGATTTTAGTTTCGCGT
*
535899 TGCGATTCT-G--T--CGT
1 TGCGATTTTAGTTTCGCGT
535913 TGCGATTTTCA-TTTCGCGT
1 TGCGATTTT-AGTTTCGCGT
535932 TGCGATT
1 TGCGATT
535939 CTCTCGTTGC
Statistics
Matches: 32, Mismatches: 2, Indels: 12
0.70 0.04 0.26
Matches are distributed among these distances:
14 11 0.34
16 1 0.03
17 1 0.03
18 1 0.03
19 18 0.56
ACGTcount: A:0.10, C:0.19, G:0.25, T:0.46
Consensus pattern (19 bp):
TGCGATTTTAGTTTCGCGT
Found at i:535915 original size:14 final size:14
Alignment explanation
Indices: 535896--535952 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
535886 TTTAGTTTCG
*
535896 CGTTGCGATTCTGT
1 CGTTGCGATTCTCT
*
535910 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
535929 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
535943 CGTTGCGATT
1 CGTTGCGATT
535953 TTAAGTTTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
14 20 0.57
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.25, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:535928 original size:33 final size:33
Alignment explanation
Indices: 535880--535970 Score: 139
Period size: 33 Copynumber: 2.7 Consensus size: 33
535870 AAAATCGCAA
*
535880 TGCGATTTTAGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTAGTTTCGCGTTGCGATTCTCTCGT
535913 TGCGATTTTCA-TTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTT-AGTTTCGCGTTGCGATTCTCTCGT
*
535946 TGCGATTTTAAGTTTCGTGTTGCGA
1 TGCGATTTT-AGTTTCGCGTTGCGA
535971 AAGTAAACTA
Statistics
Matches: 53, Mismatches: 3, Indels: 3
0.90 0.05 0.05
Matches are distributed among these distances:
33 40 0.75
34 13 0.25
ACGTcount: A:0.11, C:0.19, G:0.25, T:0.45
Consensus pattern (33 bp):
TGCGATTTTAGTTTCGCGTTGCGATTCTCTCGT
Found at i:536227 original size:93 final size:93
Alignment explanation
Indices: 536068--536381 Score: 596
Period size: 93 Copynumber: 3.4 Consensus size: 93
536058 TCAGGGTATT
536068 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
536133 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
536161 AGTTTAGCAGAATTGGCAACAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
536226 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
536254 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGAC--A
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
536317 TACTATTTCACAGTGTTAAAGAATACAC
66 TACTATTTCACAGTGTTAAAGAATACAC
*
536345 AGTTTAGCAGAATTGGCAGCAACCGAATAAATTTACT
1 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
536382 AAGCAATCTA
Statistics
Matches: 218, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
91 65 0.30
93 153 0.70
ACGTcount: A:0.45, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACAC
Found at i:538117 original size:14 final size:14
Alignment explanation
Indices: 538100--538156 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
538090 TTTGGTTTCG
538100 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
538114 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
538133 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
538147 CGTTGCGATT
1 CGTTGCGATT
538157 TTCATTTTTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:538132 original size:33 final size:33
Alignment explanation
Indices: 538085--538163 Score: 140
Period size: 33 Copynumber: 2.4 Consensus size: 33
538075 AAATCGCAAC
**
538085 GCGATTTTGGTTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
538118 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
538151 GCGATTTTCATTT
1 GCGATTTTCATTT
538164 TTCTCGTTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 44 1.00
ACGTcount: A:0.09, C:0.22, G:0.23, T:0.47
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:538169 original size:21 final size:21
Alignment explanation
Indices: 538144--538217 Score: 96
Period size: 21 Copynumber: 3.5 Consensus size: 21
538134 GTTGCGATTC
538144 TCTCGTTGCGATTTTCATTTT
1 TCTCGTTGCGATTTTCATTTT
**
538165 TCTCGTTGCAGATAGTCA-TTT
1 TCTCGTTGC-GATTTTCATTTT
* *
538186 TCACGTTGCGATTTTCATTTA
1 TCTCGTTGCGATTTTCATTTT
538207 TCTCGTTGCGA
1 TCTCGTTGCGA
538218 CTCTTCTGCA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 6 0.14
21 32 0.73
22 6 0.14
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (21 bp):
TCTCGTTGCGATTTTCATTTT
Found at i:538338 original size:33 final size:33
Alignment explanation
Indices: 538299--538366 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
538289 TACTAACTTG
538299 AAATCGCAACGAGAGAATAGCAACGCGAAATGA
1 AAATCGCAACGAGAGAATAGCAACGCGAAATGA
* *
538332 AAATCGCAACGAGAGAATCGTAACGCGAAATGA
1 AAATCGCAACGAGAGAATAGCAACGCGAAATGA
538365 AA
1 AA
538367 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.18, G:0.24, T:0.10
Consensus pattern (33 bp):
AAATCGCAACGAGAGAATAGCAACGCGAAATGA
Found at i:538769 original size:20 final size:20
Alignment explanation
Indices: 538744--538936 Score: 246
Period size: 20 Copynumber: 9.6 Consensus size: 20
538734 CTTTAAAAAT
538744 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
538764 CGCGTTGCGATTTTACGTAT-
1 CGCGTTGCGA-TTTACGGATA
*
538784 TGTCGTTGCGATTTACGGATA
1 CG-CGTTGCGATTTACGGATA
*
538805 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
*
538825 CGCATTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
538845 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
538865 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
538885 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
538905 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
538925 CGCGTTGCGATT
1 CGCGTTGCGATT
538937 CTGGAAAATC
Statistics
Matches: 152, Mismatches: 16, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
20 134 0.88
21 18 0.12
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:539170 original size:20 final size:20
Alignment explanation
Indices: 539145--539195 Score: 102
Period size: 20 Copynumber: 2.5 Consensus size: 20
539135 ATTTTCTCAA
539145 TATAAAATCATCCATGTTAT
1 TATAAAATCATCCATGTTAT
539165 TATAAAATCATCCATGTTAT
1 TATAAAATCATCCATGTTAT
539185 TATAAAATCAT
1 TATAAAATCAT
539196 TATTCCCTTG
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:0.43, C:0.14, G:0.04, T:0.39
Consensus pattern (20 bp):
TATAAAATCATCCATGTTAT
Found at i:540549 original size:182 final size:182
Alignment explanation
Indices: 540250--540723 Score: 727
Period size: 182 Copynumber: 2.6 Consensus size: 182
540240 GATCCAAATT
* * * * * **
540250 AAAAATGTGTCGATCCAAAATGATATAACAGGTAAAACTATGACAAAACTGGTATTGAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
* * * *
540315 AAACCGGTAAAGCGTTACCGGATACATTTAAAGTGTCGGTACTTTAATATAAGGATCGACAC-TT
66 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACATT
* *
540379 CGTGAATTTAAAAGAGAAGCAGTTTTAAATCCTATAAAGTGTCGATACTTTTA
131 -GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
*
540432 AAAAATGTATCGATCCAAAACGATATACCAGGTAAAAATATGATAAAACCGGTATCAAAAATGAT
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATC-AAAATGAT
*
540497 AAAACCAGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT-ATATAAGGATCGACACAT
65 AAAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACAT
** *
540561 TGTGAATTTAAAAGAGAAGCAGTTTTAGCGCCTATAATGTGTCGATACTTTAA
130 TGTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
* *
540614 AAAAATATATCGATCCACAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
1 AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
*
540679 AAACCGGTAAAACGATACCGGATATATTGAAAGTGTCGATACTTT
66 AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTT
540724 CGTAAGTACG
Statistics
Matches: 267, Mismatches: 23, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
181 52 0.19
182 165 0.62
183 50 0.19
ACGTcount: A:0.42, C:0.14, G:0.17, T:0.27
Consensus pattern (182 bp):
AAAAATGTATCGATCCAAAACGATATAACAGGTAAAAATATGATAAAACCGGTATCAAAATGATA
AAACCGGTAAAACGTTACCGGATATATTGAAAGTGTCGATACTTTAATATAAGGATCGACACATT
GTGAATTTAAAAGAGAAGCAGTTTTAAAGCCTATAAAGTGTCGATACTTTAA
Found at i:540667 original size:20 final size:19
Alignment explanation
Indices: 540644--540690 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
540634 CGATATAACA
540644 GGTAAAAATATGATAAAACC
1 GGTAAAAA-ATGATAAAACC
*
540664 GGTATCAAAATGATAAAACC
1 GGTA-AAAAATGATAAAACC
540684 GGTAAAA
1 GGTAAAA
540691 CGATACCGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.53, C:0.11, G:0.17, T:0.19
Consensus pattern (19 bp):
GGTAAAAAATGATAAAACC
Found at i:540695 original size:17 final size:19
Alignment explanation
Indices: 540655--540695 Score: 50
Period size: 20 Copynumber: 2.2 Consensus size: 19
540645 GTAAAAATAT
*
540655 GATAAAACCGGTATCAAAAT
1 GATAAAACCGG-ATCAAAAC
540675 GATAAAACCGG-T-AAAAC
1 GATAAAACCGGATCAAAAC
540692 GATA
1 GATA
540696 CCGGATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
17 8 0.40
18 1 0.05
20 11 0.55
ACGTcount: A:0.51, C:0.15, G:0.17, T:0.17
Consensus pattern (19 bp):
GATAAAACCGGATCAAAAC
Found at i:542917 original size:21 final size:21
Alignment explanation
Indices: 542893--542936 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
542883 AAGACAATCA
542893 AGAGTCGAAGAGAAACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
* *
542914 AGAGTCGAAGATACACTTGAG
1 AGAGTCGAAGAGAAACTTGAG
542935 AG
1 AG
542937 GCATAAGGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.41, C:0.11, G:0.32, T:0.16
Consensus pattern (21 bp):
AGAGTCGAAGAGAAACTTGAG
Found at i:543007 original size:33 final size:33
Alignment explanation
Indices: 542970--543035 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
542960 AAATAGATGG
*
542970 AGTGGTGAAAGAA-GTAGAGGTGTTGAGGGGTGA
1 AGTGGTGAAAGAAGGT-GAGGTGTTAAGGGGTGA
*
543003 AGTGGTGAAAGAAGGTGGGGTGTTAAGGGGTGA
1 AGTGGTGAAAGAAGGTGAGGTGTTAAGGGGTGA
543036 TATTAAGATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.29, C:0.00, G:0.50, T:0.21
Consensus pattern (33 bp):
AGTGGTGAAAGAAGGTGAGGTGTTAAGGGGTGA
Found at i:544842 original size:19 final size:19
Alignment explanation
Indices: 544818--544866 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
544808 AATGTAGGGT
544818 TAATTTTGTATAAGATTTA
1 TAATTTTGTATAAGATTTA
*
544837 TAATTTTGTATACGATTTA
1 TAATTTTGTATAAGATTTA
544856 TAATTTTGTAT
1 TAATTTTGTAT
544867 GTGAATATAA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.33, C:0.02, G:0.10, T:0.55
Consensus pattern (19 bp):
TAATTTTGTATAAGATTTA
Found at i:545076 original size:20 final size:20
Alignment explanation
Indices: 545051--545093 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
545041 TCTAAGAGCC
*
545051 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
545071 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
545091 CAT
1 CAT
545094 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:545414 original size:18 final size:18
Alignment explanation
Indices: 545391--545464 Score: 130
Period size: 18 Copynumber: 4.1 Consensus size: 18
545381 ATGTCAGATG
545391 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
*
545409 CCCATGCTGGATCACTGC
1 CCCATGCTGGACCACTGC
*
545427 ACCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
545445 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
545463 CC
1 CC
545465 AATCCTCACG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 52 1.00
ACGTcount: A:0.18, C:0.43, G:0.22, T:0.18
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:549815 original size:20 final size:20
Alignment explanation
Indices: 549790--549832 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
549780 TCTAAGAGCC
*
549790 CATTTAGGACCATTTAGATG
1 CATTTAGGACCATATAGATG
* *
549810 CATTTAGGAGCATATAGTTG
1 CATTTAGGACCATATAGATG
549830 CAT
1 CAT
549833 GTGGTGGAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (20 bp):
CATTTAGGACCATATAGATG
Found at i:550153 original size:18 final size:18
Alignment explanation
Indices: 550130--550221 Score: 130
Period size: 18 Copynumber: 5.1 Consensus size: 18
550120 ATGTCAGATG
550130 CCCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
* *
550148 CCCATGCTGGATCACTGT
1 CCCATGCTGGACCACTGC
*
550166 ACCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
* *
550184 CCCATGCTGGATCACTAC
1 CCCATGCTGGACCACTGC
*
550202 ACCATGCTGGACCACTGC
1 CCCATGCTGGACCACTGC
550220 CC
1 CC
550222 AATCCTCACG
Statistics
Matches: 62, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 62 1.00
ACGTcount: A:0.20, C:0.40, G:0.21, T:0.20
Consensus pattern (18 bp):
CCCATGCTGGACCACTGC
Found at i:550174 original size:36 final size:36
Alignment explanation
Indices: 550131--550221 Score: 164
Period size: 36 Copynumber: 2.5 Consensus size: 36
550121 TGTCAGATGC
**
550131 CCATGCTGGACCACTGCCCCATGCTGGATCACTGTA
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTACA
550167 CCATGCTGGACCACTGCCCCATGCTGGATCACTACA
1 CCATGCTGGACCACTGCCCCATGCTGGATCACTACA
550203 CCATGCTGGACCACTGCCC
1 CCATGCTGGACCACTGCCC
550222 AATCCTCACG
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
36 53 1.00
ACGTcount: A:0.20, C:0.40, G:0.21, T:0.20
Consensus pattern (36 bp):
CCATGCTGGACCACTGCCCCATGCTGGATCACTACA
Found at i:551800 original size:200 final size:200
Alignment explanation
Indices: 551453--552188 Score: 1164
Period size: 200 Copynumber: 3.7 Consensus size: 200
551443 AAACAGGGCC
*
551453 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCTAAAAGTATAATG
1 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
* *
551518 TAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
66 GAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
551583 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
131 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
*
551648 CAATA
196 CAACA
* *
551653 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGAAACCCATAAGTATAATG
1 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
* **
551718 GAATAGGTAATTTTTCAATCTAACCGGTAAAAGTATACTGGTTTTATGAGAGAATAGGTCTAAAT
66 GAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
* *
551783 AATATATCGATACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
131 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
551848 CAACA
196 CAACA
*
551853 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATG
1 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
* *
551918 G--TA---ATTTTTTCAATCT-ATC-GTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
66 GAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
* *
551976 AATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTTCAGAATGAATGGCAAACAGGGTG
131 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
*
552041 CAACC
196 CAACA
* *
552046 ATAAGGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATAATG
1 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
* * * * * * * *
552111 TATTAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGTTTTATGGGAGAATTGGTATATAA
66 GAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTA-AA
552176 T-ATGTATCGACAC
130 TAATGTATCGACAC
552189 CGTTTAATGT
Statistics
Matches: 494, Mismatches: 34, Indels: 16
0.91 0.06 0.03
Matches are distributed among these distances:
193 163 0.33
194 2 0.00
195 14 0.03
198 14 0.03
199 2 0.00
200 296 0.60
201 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.31
Consensus pattern (200 bp):
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
GAATAGGTAATTTTTCAATCTAACCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
CAACA
Found at i:552207 original size:393 final size:398
Alignment explanation
Indices: 551453--552208 Score: 1197
Period size: 393 Copynumber: 1.9 Consensus size: 398
551443 AAACAGGGCC
*
551453 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCTAAAAGTATAATG
1 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
551518 TAATAGGTAATTTTTCAATCTAATCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
66 TAATA-GT-ATTTTTCAATCTAATCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAAT
551583 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
129 AATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTG
* * * *
551648 CAATAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCGATAAACATCGAAACCCATAAGTA
194 CAACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTA
* * *
551713 TAATGGAATAGGTAATTTTTCAATCTAACCGGTAAAAGTATACTGGTTTTATGAGAGAATAGGTC
259 TAATGGAATAGGTAATTTTTCAATCTAACCAGTAAAAGTATACCGGTTTTATGAGAGAATAGGTA
* **
551778 TAAATAATATATCGATACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACA
324 TAAATAATATATCGACACTTTAATAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACA
551843 GGGTGCAACA
389 GGGTGCAACA
*
551853 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCATAAGTATAATG
1 ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAAT-
551918 GT-A-A-T-TTTTTCAATCT-ATC-GTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATA
65 GTAATAGTATTTTTCAATCTAATCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATA
* *
551977 ATGTGTCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTTCAGAATGAATGGCAAACAGGGTGC
130 ATGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGC
* *
552042 AACCATAAGGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTAT
195 AACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTAT
* * * * *
552107 AATGTATTAGGTAATTTTTCAATCTAACCAGTATAAGTATACCGGTTTTATGGGAGAATTGGTAT
260 AATGGAATAGGTAATTTTTCAATCTAACCAGTAAAAGTATACCGGTTTTATGAGAGAATAGGTAT
*
552172 ATAAT-ATGTATCGACACCGTTTAAT-GTTT-TGTCGATA
325 A-AATAATATATCGACA-C-TTTAATAGTTTGTGTCGATA
552209 CTAATTTAAA
Statistics
Matches: 330, Mismatches: 22, Indels: 15
0.90 0.06 0.04
Matches are distributed among these distances:
393 237 0.72
394 11 0.03
395 15 0.05
397 1 0.00
399 1 0.00
400 63 0.19
401 2 0.01
ACGTcount: A:0.36, C:0.14, G:0.19, T:0.32
Consensus pattern (398 bp):
ATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAACCCAAAAGTATAATG
TAATAGTATTTTTCAATCTAATCGGTACAAGTATACCAGTTTTATGAGAGAATAGGTCTAAATAA
TGTATCGACACTTTTGTAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGGGTGCA
ACAATAAAGTGTCGATCCATATATAAAAAGTGTCGATCCCATAAACATCGAAAACCAAAAGTATA
ATGGAATAGGTAATTTTTCAATCTAACCAGTAAAAGTATACCGGTTTTATGAGAGAATAGGTATA
AATAATATATCGACACTTTAATAGTTTGTGTCGATATTTTTGGTCCAGAATGAATGGCAAACAGG
GTGCAACA
Found at i:554595 original size:183 final size:183
Alignment explanation
Indices: 554246--555013 Score: 1324
Period size: 183 Copynumber: 4.2 Consensus size: 183
554236 CAAAATTTTC
*
554246 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTTT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
* * * *
554311 CAAAAAGTGTTG--ATTGAAAAAATATCGGAACCCATAATTATAATGTAATAGATAATTTTATAA
66 CAAAAAGTGTCGACATT---TACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAA
* * *
554374 TATAATCGGTATAAATATACTGATTTTATGAGCGAATAGGTCTACAACCTATATCG
128 TATAACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
* *
554430 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATATGTCGATACCTTAT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
554495 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAATAT
* *
554560 AACCGGTATAAATATGCTGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
554613 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
554678 CAAAAAGTGTCGACATTTACACATCGGAACCCAAAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAATAT
**
554743 AACCGGTATAAATATACCGGTTTTATGAGCGAATAAATCTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
554796 ACACTTTTTAATATTGTGTCGGTACTTTATGCCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
*
554861 CAAAAAGTGTCGACATTTACACATCGGAACCCAGAATTATAATGTAATAGATAATTTTATAATAT
66 CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAATAT
*
554926 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTTTACAACCTATATCG
131 AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
*
554979 ACACTTTTTAATTTTGTGTCGGTACTTTATGTCCA
1 ACACTTTTTAATATTGTGTCGGTACTTTATGTCCA
555014 AAATTATAAT
Statistics
Matches: 559, Mismatches: 23, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
183 482 0.86
184 74 0.13
186 3 0.01
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (183 bp):
ACACTTTTTAATATTGTGTCGGTACTTTATGTCCAGAATGGAAGAAAAATGTGTCGATACCTTGT
CAAAAAGTGTCGACATTTACACATCGGAACCCATAATTATAATGTAATAGATAATTTTATAATAT
AACCGGTATAAATATACCGGTTTTATGAGCGAATAGGTCTACAACCTATATCG
Found at i:555108 original size:120 final size:120
Alignment explanation
Indices: 554895--555133 Score: 370
Period size: 120 Copynumber: 2.0 Consensus size: 120
554885 CGGAACCCAG
554895 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
* * *
554960 AGGTTTACAACCTATATCGACACTTTTTAATTTTGTGTCGGTACTTTATGTCCAA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGTCCAA
* * * * *
555015 AATTATAATGTACTAGATAATTTTGTAATATAACCGGTATAAGTATACCTGTTTTATTAGCGAAT
1 AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
* ** *
555080 AGGTCTACAACCTATGTCGACACTTTTTAATATTCTGTTTGTATTTTATGTCCA
66 AGGTCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGTCCA
555134 GAATAGAAGA
Statistics
Matches: 107, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
120 107 1.00
ACGTcount: A:0.33, C:0.13, G:0.14, T:0.41
Consensus pattern (120 bp):
AATTATAATGTAATAGATAATTTTATAATATAACCGGTATAAATATACCGGTTTTATGAGCGAAT
AGGTCTACAACCTATATCGACACTTTTTAATATTCTGTCGGTACTTTATGTCCAA
Done.