Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008360.1 Hibiscus syriacus cultivar Beakdansim tig00111099_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: 1563863
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 7
Found at i:484086 original size:20 final size:19
Alignment explanation
Indices: 484040--484086 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
484030 TCCGGTATCG
*
484040 TTTTATCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
484059 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
484080 TTTTACC
1 TTTTACC
484087 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.15, G:0.11, T:0.55
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:484266 original size:20 final size:19
Alignment explanation
Indices: 484220--484266 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
484210 TCCGGTAACG
*
484220 TTTTACCGGTTTTATCATT
1 TTTTACCGATTTTATCATT
*
484239 TTGATACCGATTTTATCATAT
1 TT-TTACCGATTTTATCAT-T
484260 TTTTACC
1 TTTTACC
484267 TGGTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (19 bp):
TTTTACCGATTTTATCATT
Found at i:484465 original size:182 final size:181
Alignment explanation
Indices: 484007--484478 Score: 685
Period size: 180 Copynumber: 2.6 Consensus size: 181
483997 CGTACTTACG
* *
484007 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
484072 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATA-TTTTTTTTAAAGTATCGACACATTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
*
484136 AGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
484187 CAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
484252 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
** * *
484317 AGGATTTAAAACTGCTTTTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
131 AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * * * * **
484369 AAAGTACCGACACTTTAAATGTATCTGATAGCGCTTTACCAGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
484434 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTT
484479 AATTTAGATC
Statistics
Matches: 260, Mismatches: 30, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
180 97 0.37
181 68 0.26
182 95 0.37
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.43
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGATACATTTTTTAAAAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:484492 original size:182 final size:181
Alignment explanation
Indices: 484007--484493 Score: 644
Period size: 182 Copynumber: 2.7 Consensus size: 181
483997 CGTACTTACG
* *
484007 AAAGTATCGACACTTTCAATATATCCGGTATCGTTTTATCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
484072 TATCATATTTTTACCTGTTATATCGTTGTGGATCG-ATATTTTT--TTTAAAGTATCGACACATT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGAACATTTTTAATTT--AGTATCGACACATT
*
484134 ATAGGCGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
129 ATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
* *
484187 CAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGATTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* * *
484252 TATCATATTTTTACCTGGTATATCGTTTTGGATCGATACATTTTTTAA--AAGTATCGACACTTT
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGA-ACA-TTTTTAATTTAGTATCGACACATT
** * *
484315 ATAGGATTTAAAACTGCTTTTCTTTTAAATTCACGAAGTGTCGATCCTTATATT
129 ATAGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
* * * * * * * * **
484369 AAAGTACCGACACTTTAAATGTATCTGATAGCGCTTTACCAGTTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
484434 TGTCATAGTTTTACCTGTTATATCGTTTTGGATCGACACATTTTTAATTTAG-ATCGACAC
66 TATCATATTTTTACCTGTTATATCGTTTTGGATCGA-ACATTTTTAATTTAGTATCGACAC
484494 GAACCGACAA
Statistics
Matches: 268, Mismatches: 31, Indels: 14
0.86 0.10 0.04
Matches are distributed among these distances:
180 94 0.35
181 67 0.25
182 100 0.37
183 7 0.03
ACGTcount: A:0.27, C:0.17, G:0.14, T:0.42
Consensus pattern (181 bp):
AAAGTATCGACACTTTCAATATATCCGGTAACGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTTTGGATCGAACATTTTTAATTTAGTATCGACACATTAT
AGGAGCTAAAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATAT
Found at i:489237 original size:15 final size:15
Alignment explanation
Indices: 489217--489246 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
489207 GGGGATGTCC
489217 CCAAGAGTAATTTTG
1 CCAAGAGTAATTTTG
489232 CCAAGAGTAATTTTG
1 CCAAGAGTAATTTTG
489247 GTGATGTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (15 bp):
CCAAGAGTAATTTTG
Found at i:490434 original size:25 final size:25
Alignment explanation
Indices: 490400--490448 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
490390 TCTAAAGTCA
490400 CCTGGAGGTGACCTTTTAACTGTCG
1 CCTGGAGGTGACCTTTTAACTGTCG
490425 CCTGGAGGTGACCTTTTAACTGTC
1 CCTGGAGGTGACCTTTTAACTGTC
490449 ACCAGCCGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.16, C:0.24, G:0.27, T:0.33
Consensus pattern (25 bp):
CCTGGAGGTGACCTTTTAACTGTCG
Found at i:493762 original size:23 final size:20
Alignment explanation
Indices: 493710--493762 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 20
493700 TTTCTCTAAT
*
493710 TAAATAAATAATATATAAAC
1 TAAATAAATAATATATAAAA
*
493730 TAAAATATAACTAATA-CTAAAA
1 T-AAATA-AA-TAATATATAAAA
493752 TAAATAAATAA
1 TAAATAAATAA
493763 AACATTCATA
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
19 3 0.11
20 3 0.11
21 10 0.36
22 7 0.25
23 5 0.18
ACGTcount: A:0.66, C:0.06, G:0.00, T:0.28
Consensus pattern (20 bp):
TAAATAAATAATATATAAAA
Found at i:502552 original size:39 final size:38
Alignment explanation
Indices: 502503--502747 Score: 231
Period size: 36 Copynumber: 6.5 Consensus size: 38
502493 TCGCAAATGG
*
502503 TTTTTGAAAATACATATAATATATAGGTTTTTTAAAAGCA
1 TTTTTGAAAATATATATAATATATA-GTTTTTTAAAA-CA
* *
502543 -TTTTGAAAATGTATATAATATATAG-TTTTTAAGACA
1 TTTTTGAAAATATATATAATATATAGTTTTTTAAAACA
* * * *
502579 CTTTTGAAAA-CTATATAATATATA-ATTTTTAAAATA
1 TTTTTGAAAATATATATAATATATAGTTTTTTAAAACA
* *
502615 TTTTAGAAAA-ATATATAATATAT-GCTTTTTAAAATCA
1 TTTTTGAAAATATATATAATATATAGTTTTTTAAAA-CA
*
502652 TTTTTTGAAAACT-TATATAATATATAGTTTTTGAAAACA
1 -TTTTTGAAAA-TATATATAATATATAGTTTTTTAAAACA
*
502691 TTTTTTGAAAACTTATATATAATATATA-ATTTTTAAAAC-
1 -TTTTTGAAAA--TATATATAATATATAGTTTTTTAAAACA
*
502730 TCTTTTGGAAAT-TATATA
1 T-TTTTGAAAATATATATA
502748 GTTTTTTAAA
Statistics
Matches: 176, Mismatches: 18, Indels: 26
0.80 0.08 0.12
Matches are distributed among these distances:
36 59 0.34
37 19 0.11
38 11 0.06
39 55 0.31
40 19 0.11
41 13 0.07
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (38 bp):
TTTTTGAAAATATATATAATATATAGTTTTTTAAAACA
Found at i:502747 original size:111 final size:106
Alignment explanation
Indices: 502516--502780 Score: 288
Period size: 111 Copynumber: 2.4 Consensus size: 106
502506 TTGAAAATAC
* *
502516 ATATAATATATAGGTTTTTTAAAAGCA-TTTTGAAAATGTATATAATATATAGTTTTTAAGACAC
1 ATAT-ATATATA-GTTTTTTAAAAACATTTTTGAAAAT-TATATAATATATAGTTTTTAAAACAC
502580 TTTTGAAAACTATATAATATATAATTTTTAAAATATTTTAGAAAA
63 TTTTGAAAACTATATAATATATAATTTTTAAAATATTTTAG-AAA
* *
502625 ATATATAATATATGCTTTTTAAAATCATTTTTTGAAAACTTATATAATATATAGTTTTTGAAAAC
1 ATATAT-ATATA-GTTTTTTAAAAACA-TTTTTGAAAA-TTATATAATATATAGTTTTT-AAAAC
* * *
502690 ATTTTTTGAAAACTTATATATAATATATAATTTTTAAAACTCTTTT-G-GA
61 A-CTTTTGAAAAC---TATATAATATATAATTTTTAAAA-TATTTTAGAAA
502739 A-AT-TATATAGTTTTTTAAAAAAACATTTTTGAAAATTATATA
1 ATATATATATAGTTTTTT--AAAAACATTTTTGAAAATTATATA
502781 GTTTTTTAAA
Statistics
Matches: 135, Mismatches: 9, Indels: 23
0.81 0.05 0.14
Matches are distributed among these distances:
108 2 0.01
109 21 0.16
110 13 0.10
111 43 0.32
112 13 0.10
113 12 0.09
114 2 0.01
116 24 0.18
117 5 0.04
ACGTcount: A:0.43, C:0.05, G:0.07, T:0.45
Consensus pattern (106 bp):
ATATATATATAGTTTTTTAAAAACATTTTTGAAAATTATATAATATATAGTTTTTAAAACACTTT
TGAAAACTATATAATATATAATTTTTAAAATATTTTAGAAA
Found at i:502792 original size:32 final size:33
Alignment explanation
Indices: 502732--502813 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
502722 TTTAAAACTC
*
502732 TTTTGGAAATTATATAGTTTTTTAAAAAAACAT
1 TTTTGAAAATTATATAGTTTTTTAAAAAAACAT
502765 TTTTGAAAATTATATAGTTTTTT-AAAAAACAT
1 TTTTGAAAATTATATAGTTTTTTAAAAAAACAT
*
502797 TTTTAAAAATTTATATA
1 TTTTGAAAA-TTATATA
502814 TAATATGTAG
Statistics
Matches: 46, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 17 0.37
33 29 0.63
ACGTcount: A:0.44, C:0.02, G:0.06, T:0.48
Consensus pattern (33 bp):
TTTTGAAAATTATATAGTTTTTTAAAAAAACAT
Found at i:502906 original size:15 final size:16
Alignment explanation
Indices: 502879--502908 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
502869 TTAAAATAAT
502879 TATTTACTTATTATTG
1 TATTTACTTATTATTG
502895 TATTTA-TTATTATT
1 TATTTACTTATTATT
502909 ATTACTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (16 bp):
TATTTACTTATTATTG
Found at i:502923 original size:19 final size:18
Alignment explanation
Indices: 502877--502945 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 18
502867 TTTTAAAATA
*
502877 ATTATTTACTTATTATTGT
1 ATTATTTA-TTATTATTCT
502896 ATT-TATTATTATTATTACT
1 ATTAT-TTATTATTATT-CT
502915 ATTATTTATTATTATTCCTT
1 ATTATTTATTATTATT-C-T
502935 ATTCATTTATT
1 ATT-ATTTATT
502946 TTTCTGTCTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
18 9 0.21
19 22 0.51
20 5 0.12
21 7 0.16
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (18 bp):
ATTATTTATTATTATTCT
Found at i:506813 original size:20 final size:21
Alignment explanation
Indices: 506777--506815 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
506767 CAGACCGGTC
506777 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
506798 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
506816 TCCAGCAGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.18
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:513985 original size:17 final size:17
Alignment explanation
Indices: 513963--514007 Score: 90
Period size: 17 Copynumber: 2.6 Consensus size: 17
513953 AGAAAGTCAA
513963 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
513980 CGGGTCGGGTCAACGGT
1 CGGGTCGGGTCAACGGT
513997 CGGGTCGGGTC
1 CGGGTCGGGTC
514008 GGGTCAGACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 28 1.00
ACGTcount: A:0.09, C:0.24, G:0.49, T:0.18
Consensus pattern (17 bp):
CGGGTCGGGTCAACGGT
Found at i:514033 original size:19 final size:18
Alignment explanation
Indices: 514009--514077 Score: 102
Period size: 19 Copynumber: 3.7 Consensus size: 18
513999 GGTCGGGTCG
514009 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
*
514027 GATTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
514046 GGTCAGAACCGGTCAAACC
1 GGTCAG-ACCGGTCAAACC
514065 GGTCAGAACCGGT
1 GGTCAG-ACCGGT
514078 TGAAAACCGG
Statistics
Matches: 47, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
18 5 0.11
19 42 0.89
ACGTcount: A:0.29, C:0.30, G:0.28, T:0.13
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:514046 original size:28 final size:28
Alignment explanation
Indices: 514010--514077 Score: 77
Period size: 28 Copynumber: 2.4 Consensus size: 28
514000 GTCGGGTCGG
* *
514010 GTCAGACCGGTCAAACCGATTCAG-ACCG
1 GTCAAACCGGTCAAACCG-GTCAGAACCG
514038 GTCAAACCGGTCAGAACCGGTCA-AACCG
1 GTCAAACCGGTCA-AACCGGTCAGAACCG
514066 GTCAGAACCGGT
1 GTCA-AACCGGT
514078 TGAAAACCGG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
28 23 0.66
29 12 0.34
ACGTcount: A:0.29, C:0.31, G:0.26, T:0.13
Consensus pattern (28 bp):
GTCAAACCGGTCAAACCGGTCAGAACCG
Found at i:514096 original size:20 final size:21
Alignment explanation
Indices: 514041--514098 Score: 77
Period size: 19 Copynumber: 2.9 Consensus size: 21
514031 CAGACCGGTC
*
514041 AAACCGGTCAGAACCGG-T-C
1 AAACCGGTCAGAACCGGTTGA
514060 AAACCGGTCAGAACCGGTTGA
1 AAACCGGTCAGAACCGGTTGA
*
514081 AAACCGGTTA-AACCGGTT
1 AAACCGGTCAGAACCGGTT
514099 TCCAGCAGCC
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 17 0.49
20 9 0.26
21 9 0.26
ACGTcount: A:0.33, C:0.26, G:0.26, T:0.16
Consensus pattern (21 bp):
AAACCGGTCAGAACCGGTTGA
Found at i:514098 original size:9 final size:9
Alignment explanation
Indices: 514009--514097 Score: 88
Period size: 9 Copynumber: 9.3 Consensus size: 9
513999 GGTCGGGTCG
*
514009 GGTCAGACC
1 GGTCAAACC
514018 GGTCAAACC
1 GGTCAAACC
* *
514027 GATTCAGACC
1 G-GTCAAACC
514037 GGTCAAACC
1 GGTCAAACC
514046 GGTCAGAACC
1 GGTCA-AACC
514056 GGTCAAACC
1 GGTCAAACC
514065 GGTCAGAACC
1 GGTCA-AACC
*
514075 GGTTGAAAACC
1 GG-T-CAAACC
*
514086 GGTTAAACC
1 GGTCAAACC
514095 GGT
1 GGT
514098 TTCCAGCAGC
Statistics
Matches: 68, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
9 37 0.54
10 23 0.34
11 7 0.10
12 1 0.01
ACGTcount: A:0.30, C:0.28, G:0.27, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:515391 original size:23 final size:22
Alignment explanation
Indices: 515342--515392 Score: 57
Period size: 23 Copynumber: 2.3 Consensus size: 22
515332 ATTAAGTTAG
* * *
515342 TTTATTTAATTTGAGTTGATTA
1 TTTATTTAATTGGAGATAATTA
*
515364 ATTATTTAAGTTGGAGATAATTA
1 TTTATTTAA-TTGGAGATAATTA
515387 TTTATT
1 TTTATT
515393 ATACTTCTGG
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.55
Consensus pattern (22 bp):
TTTATTTAATTGGAGATAATTA
Found at i:521722 original size:33 final size:35
Alignment explanation
Indices: 521660--521730 Score: 94
Period size: 33 Copynumber: 2.1 Consensus size: 35
521650 CAAAACAATC
* *
521660 AATTATTCTGATTAATTTATTTATTTTTTTTA-TA
1 AATTATTCTCATTAATTTATTTATATTTTTTATTA
521694 AATTATTCTCA-TAATTT-TATTATATTTTTTATTA
1 AATTATTCTCATTAATTTAT-TTATATTTTTTATTA
521728 AAT
1 AAT
521731 GGCTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
32 1 0.03
33 17 0.52
34 15 0.45
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (35 bp):
AATTATTCTCATTAATTTATTTATATTTTTTATTA
Found at i:521730 original size:34 final size:34
Alignment explanation
Indices: 521660--521730 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 34
521650 CAAAACAATC
* *
521660 AATTATTCTGATTAATTTATTTATTTTTTTTATA
1 AATTATTCTCATTAATTTATTTATTTTTTATATA
521694 AATTATTCTCA-TAATTTTATTATATTTTTTAT-TA
1 AATTATTCTCATTAA-TTTATT-TATTTTTTATATA
521728 AAT
1 AAT
521731 GGCTTTTATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
33 3 0.09
34 21 0.64
35 9 0.27
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (34 bp):
AATTATTCTCATTAATTTATTTATTTTTTATATA
Found at i:522479 original size:4 final size:4
Alignment explanation
Indices: 522470--522496 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
522460 ACTGTTCAAC
522470 TATT TATT TATT TATT TATT TATT TAT
1 TATT TATT TATT TATT TATT TATT TAT
522497 ACATGTATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (4 bp):
TATT
Found at i:531790 original size:255 final size:251
Alignment explanation
Indices: 531320--531958 Score: 972
Period size: 255 Copynumber: 2.5 Consensus size: 251
531310 CTTATTCATA
* *
531320 TATTGAATAAAAATATTTTTTTATTATTTCGGGTCGAGTCAGG-TTTCTAATTCATATATTCGGG
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTC-GGATTTCTAATTCATATATTCGGG
*
531384 TCGGGTCGGGTGAAACTTTATTTTGGTCGGGTCGGGTTTTTTTAAGTGTGATATTCGGGTCGGGT
65 TCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGG-TTTTTTAAGTGTGATA-T----TCGGGT
*
531449 CGGGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATAT
124 CGAGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATAT
* * *
531514 ATTTAGGAATTATTACAATAATACCCCTCTTTATATATATTTTTTCAATTAAGTCACTGTTTT
189 ATTTAGAAATAATTACAATAATACCCCTCTCTATATATATTTTTTCAATTAAGTCACTGTTTT
531577 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGCCGGGTCGGATTTCTAATTCATATATT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGT-----CGGGTCGGATTTCTAATTCATATATT
* *
531642 CGGGTCGGGTCGGGTGAAACTTTATTTTGTTTGGGTCAGGTTTTTTAAGTGTGATATTCGGGTCG
61 CGGGTCGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCG
* *
531707 AGTTCGGGTTTAGGGT-AAAAAAACTGGACCGACCCGAAAATATATATAATTTTACCTTATATAT
126 AGTTCGGGTTTAGGGTGAAAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATATAT
531771 TTAGAAATAATTACAATAATACCCCTCTCTATATATATTTTTTCAATTAAGTCACTGTTTT
191 TTAGAAATAATTACAATAATACCCCTCTCTATATATATTTTTTCAATTAAGTCACTGTTTT
* *
531832 TATTAAATAAAAACAATTTTTT-TTA-TT----TCGGGTCGGATTTCTAATTCATATATTCGGGT
1 TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
* *
531891 TGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGATTTTTAAGTGTGATATTCGGGTCGAG-TC
66 CGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTTC
531955 GGGT
131 GGGT
531959 CGAATTTTTT
Statistics
Matches: 359, Mismatches: 17, Indels: 26
0.89 0.04 0.06
Matches are distributed among these distances:
243 6 0.02
244 89 0.25
249 1 0.00
253 2 0.01
254 3 0.01
255 124 0.35
256 23 0.06
257 33 0.09
260 1 0.00
261 18 0.05
262 59 0.16
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.40
Consensus pattern (251 bp):
TATTAAATAAAAATATTTTTTTATTATTTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGT
CGGGTCGGGTGAAACTTTATTTTGTTCGGGTCGGGTTTTTTAAGTGTGATATTCGGGTCGAGTTC
GGGTTTAGGGTGAAAAAAACCGGACCGACCCAAAAATATATATAATTTTACCTTATATATTTAGA
AATAATTACAATAATACCCCTCTCTATATATATTTTTTCAATTAAGTCACTGTTTT
Found at i:533398 original size:23 final size:23
Alignment explanation
Indices: 533342--533426 Score: 102
Period size: 23 Copynumber: 3.8 Consensus size: 23
533332 TGCCATATAT
*
533342 AATGTCCCAAAGGACCAC--ATA
1 AATGTCCCAAAGGACCACGTAGA
* *
533363 TATGTCCCGAAGGACCACGTAGA
1 AATGTCCCAAAGGACCACGTAGA
*
533386 AATGTCCCAAAGGACCAAGTAGA
1 AATGTCCCAAAGGACCACGTAGA
* *
533409 ATTGTCCCGAAGGACCAC
1 AATGTCCCAAAGGACCAC
533427 ATATATGTGT
Statistics
Matches: 53, Mismatches: 9, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
21 16 0.30
23 37 0.70
ACGTcount: A:0.36, C:0.27, G:0.21, T:0.15
Consensus pattern (23 bp):
AATGTCCCAAAGGACCACGTAGA
Found at i:533437 original size:23 final size:22
Alignment explanation
Indices: 533338--533447 Score: 89
Period size: 23 Copynumber: 4.9 Consensus size: 22
533328 TGAGTGCCAT
*
533338 ATATAATGTCCCAAAGGACCAC
1 ATATATTGTCCCAAAGGACCAC
*
533360 ATATA-TGTCCCGAAGGACCAC
1 ATATATTGTCCCAAAGGACCAC
* * *
533381 GTAGAAATGTCCCAAAGGACCA-
1 ATA-TATTGTCCCAAAGGACCAC
* *
533403 AGTAGAATTGTCCCGAAGGACCAC
1 A-TA-TATTGTCCCAAAGGACCAC
* *
533427 ATATATGTGTCCTAAATGACC
1 ATATAT-TGTCCCAAAGGACC
533448 GTGTAGAACC
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
21 17 0.24
22 8 0.11
23 46 0.64
24 1 0.01
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (22 bp):
ATATATTGTCCCAAAGGACCAC
Found at i:533438 original size:46 final size:44
Alignment explanation
Indices: 533335--533447 Score: 120
Period size: 46 Copynumber: 2.5 Consensus size: 44
533325 AATTGAGTGC
*
533335 CATATATAATGTCCCAAAGGACCACATATATGTCCCGAAGGACCA
1 CATATAT-ATGTCCCAAAGGACCACATAAATGTCCCGAAGGACCA
* * *
533380 CGTAGAAATGTCCCAAAGGACCA-AGTAGAATTGTCCCGAAGGACCA
1 CATATATATGTCCCAAAGGACCACA-TA-AA-TGTCCCGAAGGACCA
* * *
533426 CATATATGTGTCCTAAATGACC
1 CATATATATGTCCCAAAGGACC
533448 GTGTAGAACC
Statistics
Matches: 55, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
43 1 0.02
44 18 0.33
45 5 0.09
46 31 0.56
ACGTcount: A:0.36, C:0.25, G:0.19, T:0.20
Consensus pattern (44 bp):
CATATATATGTCCCAAAGGACCACATAAATGTCCCGAAGGACCA
Found at i:533455 original size:46 final size:46
Alignment explanation
Indices: 533342--533429 Score: 128
Period size: 44 Copynumber: 2.0 Consensus size: 46
533332 TGCCATATAT
* *
533342 AATGTCCCAAAGGACCACA-TA-TA-TGTCCCGAAGGACCACGTAGA
1 AATGTCCCAAAGGACCA-AGTAGAATTGTCCCGAAGGACCACATAGA
533386 AATGTCCCAAAGGACCAAGTAGAATTGTCCCGAAGGACCACATA
1 AATGTCCCAAAGGACCAAGTAGAATTGTCCCGAAGGACCACATA
533430 TATGTGTCCT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
43 1 0.03
44 19 0.49
45 1 0.03
46 18 0.46
ACGTcount: A:0.38, C:0.26, G:0.20, T:0.16
Consensus pattern (46 bp):
AATGTCCCAAAGGACCAAGTAGAATTGTCCCGAAGGACCACATAGA
Found at i:534730 original size:21 final size:21
Alignment explanation
Indices: 534706--534749 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
534696 CTAACTGATG
534706 ACAAGTCAAATTTAACCTCAA
1 ACAAGTCAAATTTAACCTCAA
534727 ACAAGTCAAATTTAACCTCAA
1 ACAAGTCAAATTTAACCTCAA
534748 AC
1 AC
534750 TTCCCTTACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.48, C:0.25, G:0.05, T:0.23
Consensus pattern (21 bp):
ACAAGTCAAATTTAACCTCAA
Found at i:536572 original size:23 final size:21
Alignment explanation
Indices: 536546--536593 Score: 51
Period size: 23 Copynumber: 2.1 Consensus size: 21
536536 CATTTTAATA
536546 TAAATAGTAATTATTAAGATATT
1 TAAATA-TAATTATTAAGAT-TT
* *
536569 TAAAATATATTTATTAATATTT
1 T-AAATATAATTATTAAGATTT
536591 TAA
1 TAA
536594 TATTTTAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 2 0.09
22 3 0.14
23 12 0.55
24 5 0.23
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (21 bp):
TAAATATAATTATTAAGATTT
Found at i:536611 original size:13 final size:14
Alignment explanation
Indices: 536567--536622 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
536557 TATTAAGATA
536567 TTTAA-AATATATT
1 TTTAATAATATATT
* *
536580 TATTAATATTTTAATAT
1 T-TTAATAATAT-AT-T
536597 TTTAATAATATATT
1 TTTAATAATATATT
*
536611 TTTAATATTATA
1 TTTAATAATATA
536623 ACAATATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
13 1 0.03
14 16 0.47
15 5 0.15
16 10 0.29
17 2 0.06
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (14 bp):
TTTAATAATATATT
Found at i:536613 original size:22 final size:22
Alignment explanation
Indices: 536588--536630 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
536578 TTTATTAATA
* *
536588 TTTTAATATTTTAATAATATAT
1 TTTTAATATTATAACAATATAT
536610 TTTTAATATTATAACAATATA
1 TTTTAATATTATAACAATATA
536631 AACAATTATA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.53
Consensus pattern (22 bp):
TTTTAATATTATAACAATATAT
Found at i:536616 original size:11 final size:12
Alignment explanation
Indices: 536556--536618 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 12
536546 TAAATAGTAA
*
536556 TTATTAAGATAT
1 TTATTAATATAT
*
536568 TTA-AAATATAT
1 TTATTAATATAT
536579 TTATT-A-ATA-
1 TTATTAATATAT
536588 TT-TTAATAT-T
1 TTATTAATATAT
*
536598 TTAATAATATAT
1 TTATTAATATAT
536610 TT-TTAATAT
1 TTATTAATAT
536619 TATAACAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 13
0.69 0.09 0.22
Matches are distributed among these distances:
8 2 0.05
9 3 0.08
10 7 0.17
11 22 0.55
12 6 0.15
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.56
Consensus pattern (12 bp):
TTATTAATATAT
Found at i:536622 original size:14 final size:14
Alignment explanation
Indices: 536574--536622 Score: 53
Period size: 14 Copynumber: 3.3 Consensus size: 14
536564 ATATTTAAAA
536574 TATATTTATTAATAT
1 TATATTT-TTAATAT
* *
536589 TTTAATATTTTAATAA
1 TAT-AT-TTTTAATAT
536605 TATATTTTTAATAT
1 TATATTTTTAATAT
536619 TATA
1 TATA
536623 ACAATATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
14 12 0.43
15 4 0.14
16 10 0.36
17 2 0.07
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (14 bp):
TATATTTTTAATAT
Found at i:536694 original size:16 final size:19
Alignment explanation
Indices: 536673--536711 Score: 57
Period size: 16 Copynumber: 2.2 Consensus size: 19
536663 ATTTTTTTAA
536673 AATAAAATA-A-ATTA-TT
1 AATAAAATATATATTATTT
536689 AATAAAATATATATTATTT
1 AATAAAATATATATTATTT
536708 AATA
1 AATA
536712 TTTTCATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 9 0.45
17 1 0.05
18 4 0.20
19 6 0.30
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (19 bp):
AATAAAATATATATTATTT
Found at i:536721 original size:27 final size:27
Alignment explanation
Indices: 536687--536772 Score: 83
Period size: 27 Copynumber: 3.2 Consensus size: 27
536677 AAATAAATTA
536687 TTAATAAAATATATATTATTTAATATT
1 TTAATAAAATATATATTATTTAATATT
*
536714 TTCATAAAA-ATAATATTA-TTAA-ATT
1 TTAATAAAATAT-ATATTATTTAATATT
*
536739 ATTAATATTAATA-ATATTATTT-ATATAT
1 -TTAATA-AAATATATATTATTTAATAT-T
536767 TTAATA
1 TTAATA
536773 CTACTATAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 14
0.74 0.05 0.21
Matches are distributed among these distances:
25 3 0.06
26 18 0.37
27 26 0.53
28 2 0.04
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (27 bp):
TTAATAAAATATATATTATTTAATATT
Found at i:536751 original size:26 final size:25
Alignment explanation
Indices: 536680--536759 Score: 90
Period size: 26 Copynumber: 3.0 Consensus size: 25
536670 TAAAATAAAA
536680 TAAATTATTAATAAAATATATATTATT
1 TAAATTATTAATAAAATA-ATATTA-T
*
536707 TAATATT-TTCATAAAAATAATATTAT
1 TAA-ATTATTAAT-AAAATAATATTAT
*
536733 TAAATTATTAATATTAATAATATTAT
1 TAAATTATTAATA-AAATAATATTAT
536759 T
1 T
536760 TATATATTTA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
25 4 0.09
26 20 0.43
27 13 0.28
28 9 0.20
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (25 bp):
TAAATTATTAATAAAATAATATTAT
Found at i:536850 original size:21 final size:20
Alignment explanation
Indices: 536826--536872 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
536816 ATATATTTAT
536826 TAATAATTTTCAAATATAATA
1 TAATAATTTT-AAATATAATA
* *
536847 TAAT-ATTTTTAATTTAATA
1 TAATAATTTTAAATATAATA
536866 -AATAATT
1 TAATAATT
536873 AATATAATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 3 0.13
19 11 0.48
20 5 0.22
21 4 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (20 bp):
TAATAATTTTAAATATAATA
Found at i:537536 original size:23 final size:23
Alignment explanation
Indices: 537510--537576 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
537500 AACATAAATG
* *
537510 AACACAATAAACTAACGTTAACA
1 AACACAATAAACGAACGTAAACA
*
537533 AACACAA-AGAACGAACGTAAACG
1 AACACAATA-AACGAACGTAAACA
* * *
537556 AATACAATAAATGAACATAAA
1 AACACAATAAACGAACGTAAA
537577 TGAAAAAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
22 1 0.03
23 34 0.94
24 1 0.03
ACGTcount: A:0.60, C:0.18, G:0.09, T:0.13
Consensus pattern (23 bp):
AACACAATAAACGAACGTAAACA
Found at i:537793 original size:16 final size:14
Alignment explanation
Indices: 537740--537783 Score: 51
Period size: 14 Copynumber: 3.4 Consensus size: 14
537730 GATTGGTCTA
537740 AACATAAATGAACG
1 AACATAAATGAACG
*
537754 --CAT--ATAAACG
1 AACATAAATGAACG
537764 AACATAAATGAACG
1 AACATAAATGAACG
537778 AACATA
1 AACATA
537784 TTACTGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 8
0.71 0.06 0.24
Matches are distributed among these distances:
10 6 0.25
12 6 0.25
14 12 0.50
ACGTcount: A:0.57, C:0.16, G:0.11, T:0.16
Consensus pattern (14 bp):
AACATAAATGAACG
Found at i:538838 original size:19 final size:19
Alignment explanation
Indices: 538816--538882 Score: 52
Period size: 19 Copynumber: 3.5 Consensus size: 19
538806 AAACATAATG
538816 AAAATAAATAAATAGTATA
1 AAAATAAATAAATAGTATA
*
538835 AAAA-ATACTAAATAGTA-A
1 AAAATA-AATAAATAGTATA
*
538853 CAATAAT-AATAAATA-AATGA
1 -AA-AATAAATAAATAGTAT-A
538873 AAAATAAATA
1 AAAATAAATA
538883 TACATATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 14
0.69 0.05 0.25
Matches are distributed among these distances:
18 6 0.16
19 29 0.76
20 3 0.08
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (19 bp):
AAAATAAATAAATAGTATA
Found at i:538869 original size:23 final size:20
Alignment explanation
Indices: 538816--538870 Score: 58
Period size: 19 Copynumber: 2.6 Consensus size: 20
538806 AAACATAATG
*
538816 AAAATAAATAAATAGTATAA
1 AAAATAAATAAATAGTACAA
*
538836 AAAAT-ACTAAATAGTAACAA
1 AAAATAAATAAATAGT-ACAA
538856 TAATAATAAATAAAT
1 -AA-AATAAATAAAT
538871 GAAAAATAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
19 9 0.32
20 8 0.29
21 2 0.07
22 3 0.11
23 6 0.21
ACGTcount: A:0.67, C:0.04, G:0.04, T:0.25
Consensus pattern (20 bp):
AAAATAAATAAATAGTACAA
Found at i:538995 original size:13 final size:13
Alignment explanation
Indices: 538977--539002 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
538967 TAACATTAGG
538977 AAAATATAGTAAA
1 AAAATATAGTAAA
538990 AAAATATAGTAAA
1 AAAATATAGTAAA
539003 TAAGTAAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:539037 original size:2 final size:2
Alignment explanation
Indices: 539032--539060 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
539022 AATAATAATA
539032 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
539061 ATAGGAAAAT
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:539079 original size:8 final size:9
Alignment explanation
Indices: 539029--539063 Score: 52
Period size: 10 Copynumber: 3.7 Consensus size: 9
539019 AAAAATAATA
539029 ATAATATAT
1 ATAATATAT
539038 ATATATATAT
1 ATA-ATATAT
539048 ATATATATAT
1 ATA-ATATAT
539058 ATAATA
1 ATAATA
539064 GGAAAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 6 0.24
10 19 0.76
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (9 bp):
ATAATATAT
Found at i:539115 original size:10 final size:9
Alignment explanation
Indices: 539102--539139 Score: 51
Period size: 10 Copynumber: 4.1 Consensus size: 9
539092 AAATGAAAAA
539102 AAATTATAAT
1 AAATTA-AAT
539112 AAA-TAAAT
1 AAATTAAAT
539120 AAATTAAAT
1 AAATTAAAT
539129 ATAATTAAAT
1 A-AATTAAAT
539139 A
1 A
539140 TATATATATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
8 6 0.23
9 8 0.31
10 12 0.46
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATTAAAT
Found at i:539137 original size:19 final size:18
Alignment explanation
Indices: 539102--539139 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
539092 AAATGAAAAA
539102 AAATTATAATAAATAAAT
1 AAATTATAATAAATAAAT
539120 AAATTA-AATATAATTAAAT
1 AAATTATAATA-AA-TAAAT
539139 A
1 A
539140 TATATATATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 4 0.22
18 8 0.44
19 6 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (18 bp):
AAATTATAATAAATAAAT
Found at i:539644 original size:37 final size:37
Alignment explanation
Indices: 539551--539648 Score: 124
Period size: 37 Copynumber: 2.6 Consensus size: 37
539541 ATGCTTGTTG
* * * * * *
539551 ATCCTATCTTTAGGAGTTTAAATAATAGTAGAACTCT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTAT
* *
539588 ATCCTATTTTTAGGAGTTTGAATCTTAGCAAAATTAT
1 ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTAT
539625 ATCCTATTTTTAGGAGTTTGAATC
1 ATCCTATTTTTAGGAGTTTGAATC
539649 CTAGTAGGAC
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
37 53 1.00
ACGTcount: A:0.32, C:0.12, G:0.14, T:0.42
Consensus pattern (37 bp):
ATCCTATTTTTAGGAGTTTGAATCATAGCAAAACTAT
Found at i:540596 original size:106 final size:106
Alignment explanation
Indices: 540404--541679 Score: 2054
Period size: 106 Copynumber: 12.0 Consensus size: 106
540394 GCATTGTTCC
* * * *
540404 GAGTCCAATAT-CTTC-CGTCGTGAAGTTAAAATTGGCTCTGGAATCGGGAAATTGTTTGTTGAC
1 GAGTCCAATATCCTTCGC-T-GTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGAC
* * *
540467 AACCAGTC-GTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
64 AACCAG-CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
540510 GAATCTAATATCCTTTGTTGTGAAGTTGAAATTGGCTTTGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
540575 CCAACGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
540616 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTATGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
540681 CCAGCGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
540722 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
540787 CCAGCGGTTCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
540828 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
540893 CCAGCGGTCTCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
540934 GAGTCCAATATCTTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTAACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
540999 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
541040 GAGTCCAATATCCTTTGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
541105 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
541146 GAGTCTAATATCCTTCGTTATGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
541211 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTACGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
541252 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTATTGATAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* *
541317 CCAGCGGTCCCTTCGTCATGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
541358 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTATTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
541423 CCAGCGGTCCCTTCGTCGTAAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
541464 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
541529 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
541570 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * *
541635 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
541676 GAGT
1 GAGT
541680 GGCACGATAT
Statistics
Matches: 1092, Mismatches: 75, Indels: 6
0.93 0.06 0.01
Matches are distributed among these distances:
105 1 0.00
106 1087 1.00
107 4 0.00
ACGTcount: A:0.22, C:0.18, G:0.25, T:0.34
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:542651 original size:22 final size:22
Alignment explanation
Indices: 542625--542680 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
542615 TTGTGTTTGG
542625 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
*
542647 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
542669 TCAAAGGTTTGA
1 TCAAAGGTTTGA
542681 TGGGATAGCT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:543310 original size:13 final size:14
Alignment explanation
Indices: 543281--543318 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
543271 CTTTTTGTCC
543281 TTTT-TTCTTTCGAT
1 TTTTGTTCTTTC-AT
543295 TTTTGTTCTTTC-T
1 TTTTGTTCTTTCAT
543308 TTTTGTTCTTT
1 TTTTGTTCTTT
543319 TGTTTTTCCT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 12 0.52
14 4 0.17
15 7 0.30
ACGTcount: A:0.03, C:0.13, G:0.08, T:0.76
Consensus pattern (14 bp):
TTTTGTTCTTTCAT
Found at i:543310 original size:35 final size:35
Alignment explanation
Indices: 543271--543355 Score: 95
Period size: 35 Copynumber: 2.4 Consensus size: 35
543261 TTTGCATGTG
*
543271 CTTTTTGTCCTTTTTTCTTTCGATTTTTG-TTC-TTT
1 CTTTTTGT-CTTTTTT-TTTCCATTTTTGCTTCTTTT
*
543306 CTTTTTGTTCTTTTGTTTTTCCTTTTTTGCTTCTTTT
1 CTTTTTG-TCTTTT-TTTTTCCATTTTTGCTTCTTTT
543343 CTTTTT-TCTTTTT
1 CTTTTTGTCTTTTT
543356 GCTCTTTTTG
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
34 1 0.02
35 28 0.64
36 6 0.14
37 9 0.20
ACGTcount: A:0.01, C:0.16, G:0.07, T:0.75
Consensus pattern (35 bp):
CTTTTTGTCTTTTTTTTTCCATTTTTGCTTCTTTT
Found at i:543319 original size:22 final size:21
Alignment explanation
Indices: 543294--543367 Score: 80
Period size: 21 Copynumber: 3.4 Consensus size: 21
543284 TTTCTTTCGA
543294 TTTTTGTTCTTTCTTTTTGTTC
1 TTTTTGTT-TTTCTTTTTGTTC
543316 -TTTTGTTTTTCCTTTTTTGCTTC
1 TTTTTGTTTTT-C-TTTTTG-TTC
*
543339 TTTTCT-TTTTTCTTTTTGCTC
1 TTTT-TGTTTTTCTTTTTGTTC
543360 TTTTTGTT
1 TTTTTGTT
543368 CTGATTGAAT
Statistics
Matches: 45, Mismatches: 1, Indels: 13
0.76 0.02 0.22
Matches are distributed among these distances:
20 4 0.09
21 16 0.36
22 12 0.27
23 4 0.09
24 8 0.18
25 1 0.02
ACGTcount: A:0.00, C:0.15, G:0.08, T:0.77
Consensus pattern (21 bp):
TTTTTGTTTTTCTTTTTGTTC
Found at i:546742 original size:19 final size:19
Alignment explanation
Indices: 546709--546745 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
546699 TGCAGATGAT
546709 GGAAATAAAATAAAAGAGA
1 GGAAATAAAATAAAAGAGA
546728 GGAAA-AAAATGAAAAGAG
1 GGAAATAAAAT-AAAAGAG
546746 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (19 bp):
GGAAATAAAATAAAAGAGA
Found at i:548112 original size:31 final size:29
Alignment explanation
Indices: 548043--548113 Score: 74
Period size: 31 Copynumber: 2.3 Consensus size: 29
548033 TAATGAAAAT
548043 AAATAAATAGTATAAATAAAATAAAATAA
1 AAATAAATAGTATAAATAAAATAAAATAA
548072 AATACTAAATAGTA-ACAATAATAA-ATAAATGAA
1 AA-A-TAAATAGTATA-AATAA-AATA-AAAT-AA
548105 AAATAAATA
1 AAATAAATA
548114 TACATATAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
29 2 0.06
30 2 0.06
31 21 0.58
32 7 0.19
33 4 0.11
ACGTcount: A:0.69, C:0.03, G:0.04, T:0.24
Consensus pattern (29 bp):
AAATAAATAGTATAAATAAAATAAAATAA
Found at i:548216 original size:13 final size:13
Alignment explanation
Indices: 548198--548223 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
548188 TAACGTTAGG
548198 AAAATATAGTAAA
1 AAAATATAGTAAA
548211 AAAATATAGTAAA
1 AAAATATAGTAAA
548224 TAAGTTAACA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.69, C:0.00, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAATATAGTAAA
Found at i:548285 original size:21 final size:21
Alignment explanation
Indices: 548244--548292 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 21
548234 TAGATAAAAA
* *
548244 ATAATAATATAATATATATAT
1 ATAATAATAGAAAATATATAT
548265 ATAATAATAGGAAAATAATATAAT
1 ATAATAATA-GAAAAT-ATAT-AT
548289 ATAA
1 ATAA
548293 CACAAAGAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 9 0.39
22 4 0.17
23 4 0.17
24 6 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
ATAATAATAGAAAATATATAT
Found at i:548336 original size:22 final size:24
Alignment explanation
Indices: 548302--548348 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
548292 ACACAAAGAA
548302 AAATGAAAAAAAATATAA-TAAAT
1 AAATGAAAAAAAATATAATTAAAT
*
548325 AAAT-AAATAAAATATAATTAAAT
1 AAATGAAAAAAAATATAATTAAAT
548348 A
1 A
548349 TATATATATA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (24 bp):
AAATGAAAAAAAATATAATTAAAT
Found at i:554127 original size:28 final size:28
Alignment explanation
Indices: 554095--554157 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 28
554085 CGTTAAACAT
*
554095 ATATATTTATTCTTATCTTAACTTTAAA
1 ATATATTTATTCTTATCTTAACTTAAAA
* *
554123 ATATATTTTGTTCTTATTTTAACTTAAAA
1 ATATA-TTTATTCTTATCTTAACTTAAAA
*
554152 AGATAT
1 ATATAT
554158 ATTTTATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 6 0.20
29 24 0.80
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.52
Consensus pattern (28 bp):
ATATATTTATTCTTATCTTAACTTAAAA
Found at i:554144 original size:29 final size:30
Alignment explanation
Indices: 554078--554164 Score: 95
Period size: 31 Copynumber: 2.9 Consensus size: 30
554068 TTAAATTAAC
* *
554078 ATCTAAACGTTAAACATATATATTTATTCTT
1 ATCTTAACTTTAAACATATAT-TTTATTCTT
*
554109 ATCTTAACTTTAAA-ATATATTTTGTTCTT
1 ATCTTAACTTTAAACATATATTTTATTCTT
* * *
554138 ATTTTAACTTAAAAAGATATATTTTAT
1 ATCTTAACTT-TAAACATATATTTTAT
554165 ATATCTTATA
Statistics
Matches: 48, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
29 17 0.35
30 9 0.19
31 22 0.46
ACGTcount: A:0.38, C:0.09, G:0.03, T:0.49
Consensus pattern (30 bp):
ATCTTAACTTTAAACATATATTTTATTCTT
Found at i:554301 original size:31 final size:31
Alignment explanation
Indices: 554263--554324 Score: 97
Period size: 31 Copynumber: 2.0 Consensus size: 31
554253 TTATCATAAC
*
554263 TTAAAAATACATTTTATTTTTATCTTAACTT
1 TTAAAAATACATCTTATTTTTATCTTAACTT
* *
554294 TTAAAAATATATCTTATTTTTATTTTAACTT
1 TTAAAAATACATCTTATTTTTATCTTAACTT
554325 ATTACATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.35, C:0.08, G:0.00, T:0.56
Consensus pattern (31 bp):
TTAAAAATACATCTTATTTTTATCTTAACTT
Found at i:554357 original size:30 final size:30
Alignment explanation
Indices: 554318--554393 Score: 98
Period size: 30 Copynumber: 2.5 Consensus size: 30
554308 TATTTTTATT
* * * *
554318 TTAACTTATTACATATATTATATTCTTAAC
1 TTAAATTATTAAATATATTACAATCTTAAC
* *
554348 TTAAATTATTAAATATATTCCAATCTTACC
1 TTAAATTATTAAATATATTACAATCTTAAC
554378 TTAAATTATTAAATAT
1 TTAAATTATTAAATAT
554394 GATTTATCCT
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.47
Consensus pattern (30 bp):
TTAAATTATTAAATATATTACAATCTTAAC
Found at i:554542 original size:29 final size:27
Alignment explanation
Indices: 554454--554542 Score: 92
Period size: 28 Copynumber: 3.1 Consensus size: 27
554444 TTAACATGTA
554454 TATTTTATTTT-TTTATTTAAAAATATT
1 TATTTTATTTTATTTATTTAAAAATA-T
*
554481 TATATTAATTTTATTTTCATTTAAAAATA-
1 TAT-TTTATTTTA-TTT-ATTTAAAAATAT
*
554510 TATTTTATTTTATCTTAATTTTAAAATAT
1 TATTTTATTTTAT-TT-ATTTAAAAATAT
554539 TATT
1 TATT
554543 ATAATAAAAT
Statistics
Matches: 52, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
27 4 0.08
28 27 0.52
29 7 0.13
30 3 0.06
31 11 0.21
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (27 bp):
TATTTTATTTTATTTATTTAAAAATAT
Found at i:554634 original size:29 final size:29
Alignment explanation
Indices: 554545--554727 Score: 234
Period size: 29 Copynumber: 6.4 Consensus size: 29
554535 ATATTATTAT
*
554545 AATAAAATATAATATTT-AAGTTAAGGTAAG
1 AATAAAATAT-AT-TTTAAAGTTAAGATAAG
*
554575 AAT-AAAT-TA-TTTAAAGTT-A-ATAAA
1 AATAAAATATATTTTAAAGTTAAGATAAG
* * *
554599 AATTAAAATATATTTTTATGTTAAAATAAG
1 AA-TAAAATATATTTTAAAGTTAAGATAAG
**
554629 AATAAAATGGATTTTAAAGTTAAGATAAG
1 AATAAAATATATTTTAAAGTTAAGATAAG
554658 AATAAAATATATTTTAAAGTTAAGATAAG
1 AATAAAATATATTTTAAAGTTAAGATAAG
554687 AATAAAATATATTTTAAAGTTAAGATAAG
1 AATAAAATATATTTTAAAGTTAAGATAAG
554716 AATAAAATATAT
1 AATAAAATATAT
554728 ATTTTTAATG
Statistics
Matches: 134, Mismatches: 12, Indels: 15
0.83 0.07 0.09
Matches are distributed among these distances:
24 5 0.04
25 5 0.04
26 9 0.07
27 3 0.02
28 8 0.06
29 95 0.71
30 9 0.07
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.36
Consensus pattern (29 bp):
AATAAAATATATTTTAAAGTTAAGATAAG
Found at i:570256 original size:25 final size:25
Alignment explanation
Indices: 570228--570277 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
570218 TGTTTTTCAT
570228 TTTATTAATTATATATAATATAAAA
1 TTTATTAATTATATATAATATAAAA
*
570253 TTTATTAATTATATATAATTTAAAA
1 TTTATTAATTATATATAATATAAAA
570278 AAATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (25 bp):
TTTATTAATTATATATAATATAAAA
Found at i:570288 original size:27 final size:25
Alignment explanation
Indices: 570230--570284 Score: 74
Period size: 25 Copynumber: 2.2 Consensus size: 25
570220 TTTTTCATTT
**
570230 TATTAATTATATATAATATAAAATT
1 TATTAATTATATATAATATAAAAAA
*
570255 TATTAATTATATATAATTTAAAAAAA
1 TATTAATTATATATAATAT-AAAAAA
570281 TATT
1 TATT
570285 TAATCATAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
25 18 0.69
26 8 0.31
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
TATTAATTATATATAATATAAAAAA
Found at i:571738 original size:45 final size:45
Alignment explanation
Indices: 571644--571766 Score: 138
Period size: 45 Copynumber: 2.7 Consensus size: 45
571634 TTGATATATG
* * * **
571644 TGATTACATGAAAAAGTGATATAAGATATGTGTCATTGACCTATG
1 TGATTACATGAAAATGTGATATAAGATATGTGACAATGACCTAAA
* *
571689 TGATTACATGAAAATGTGATATAAGCTATGTGACAATGAGCTAAA
1 TGATTACATGAAAATGTGATATAAGATATGTGACAATGACCTAAA
* * * * *
571734 TGATTATATGTATATGTGATACAAGTTATGTGA
1 TGATTACATGAAAATGTGATATAAGATATGTGA
571767 ATATGTAAAC
Statistics
Matches: 66, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
45 66 1.00
ACGTcount: A:0.38, C:0.07, G:0.20, T:0.34
Consensus pattern (45 bp):
TGATTACATGAAAATGTGATATAAGATATGTGACAATGACCTAAA
Found at i:571914 original size:23 final size:24
Alignment explanation
Indices: 571841--571932 Score: 73
Period size: 23 Copynumber: 4.0 Consensus size: 24
571831 GAGTTGAGGG
* * *
571841 TTCTACGCGGTCCTTTGAGACA-A
1 TTCTACGCGGTCCTTCGGGATATA
* * *
571864 TTCTATGTGGTCTTTCGGGATA-A
1 TTCTACGCGGTCCTTCGGGATATA
*
571887 TTCTACGCGGTTCTTCGGGATATA
1 TTCTACGCGGTCCTTCGGGATATA
* * *
571911 -TCTATGTGGTCCTTTGGGATAT
1 TTCTACGCGGTCCTTCGGGATAT
571933 TTTTACGTGA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
23 53 0.98
24 1 0.02
ACGTcount: A:0.17, C:0.18, G:0.25, T:0.39
Consensus pattern (24 bp):
TTCTACGCGGTCCTTCGGGATATA
Found at i:581518 original size:33 final size:33
Alignment explanation
Indices: 581471--581551 Score: 126
Period size: 33 Copynumber: 2.4 Consensus size: 33
581461 TTCGGGTCAA
* *
581471 GTCGGGTCGAGTTTTTTTAAGTATGATATTCGG
1 GTCGGGTCGGGTTTTTGTAAGTATGATATTCGG
*
581504 GTTGGGTCGGGTTTTTGTAAGTATGATATTCGG
1 GTCGGGTCGGGTTTTTGTAAGTATGATATTCGG
581537 GTCGGGTTCGGGTTT
1 GTCGGG-TCGGGTTT
581552 ATGGTGAAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 35 0.81
34 8 0.19
ACGTcount: A:0.14, C:0.09, G:0.36, T:0.42
Consensus pattern (33 bp):
GTCGGGTCGGGTTTTTGTAAGTATGATATTCGG
Found at i:581989 original size:15 final size:15
Alignment explanation
Indices: 581969--582002 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
581959 TGTAAGTTGT
**
581969 AAAATAAACTAAAAC
1 AAAATAAAAAAAAAC
581984 AAAATAAAAAAAAAC
1 AAAATAAAAAAAAAC
581999 AAAA
1 AAAA
582003 AGGACACTTC
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:0.82, C:0.09, G:0.00, T:0.09
Consensus pattern (15 bp):
AAAATAAAAAAAAAC
Found at i:582175 original size:18 final size:17
Alignment explanation
Indices: 582124--582176 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
582114 TATAGAATTG
* *
582124 GATTTCAATTCCTGATA
1 GATTCCAATTCCTCATA
*
582141 GATTCCAATTTCTTCATA
1 GATTCCAA-TTCCTCATA
*
582159 GGTTCCAATTCCCTCATA
1 GATTCCAATT-CCTCATA
582177 AACATTCCAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 9 0.31
18 20 0.69
ACGTcount: A:0.26, C:0.25, G:0.09, T:0.40
Consensus pattern (17 bp):
GATTCCAATTCCTCATA
Found at i:583030 original size:54 final size:54
Alignment explanation
Indices: 582943--583053 Score: 186
Period size: 54 Copynumber: 2.1 Consensus size: 54
582933 TTTCAGGTTC
* * *
582943 GAGCATCAAGAATATCAAGGGTGTAGAGGTGTGACCGTTCAATGTCAAATAATT
1 GAGCATCAAGAATATAAAGGCTGTAGAGATGTGACCGTTCAATGTCAAATAATT
*
582997 GAGCATCAAGAATATAAAGGCTGTAGAGATGTGATCGTTCAATGTCAAATAATT
1 GAGCATCAAGAATATAAAGGCTGTAGAGATGTGACCGTTCAATGTCAAATAATT
583051 GAG
1 GAG
583054 AGTTAACTTT
Statistics
Matches: 53, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.37, C:0.12, G:0.25, T:0.26
Consensus pattern (54 bp):
GAGCATCAAGAATATAAAGGCTGTAGAGATGTGACCGTTCAATGTCAAATAATT
Found at i:583372 original size:2 final size:2
Alignment explanation
Indices: 583361--583394 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
583351 TCATTGAAAT
583361 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
583395 AAAGCAATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:583961 original size:12 final size:12
Alignment explanation
Indices: 583903--583961 Score: 57
Period size: 12 Copynumber: 5.0 Consensus size: 12
583893 TCATTAAAAT
*
583903 TTTTATTATTCA
1 TTTTATTATTTA
* * *
583915 TGTAATTAATTA
1 TTTTATTATTTA
583927 TTTTATTA-TTA
1 TTTTATTATTTA
*
583938 TTTTATTTTTTA
1 TTTTATTATTTA
*
583950 TTTGATTATTTA
1 TTTTATTATTTA
583962 ACAGTAAACT
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
11 10 0.27
12 27 0.73
ACGTcount: A:0.27, C:0.02, G:0.03, T:0.68
Consensus pattern (12 bp):
TTTTATTATTTA
Found at i:584932 original size:2 final size:2
Alignment explanation
Indices: 584925--584979 Score: 103
Period size: 2 Copynumber: 28.0 Consensus size: 2
584915 ATAGAATGAC
584925 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
584967 AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT
584980 TAAATATGTG
Statistics
Matches: 52, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 51 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:589523 original size:15 final size:15
Alignment explanation
Indices: 589505--589535 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
589495 ACATAAACCT
*
589505 TAAATACATGAAATC
1 TAAATACATAAAATC
589520 TAAATACATAAAATC
1 TAAATACATAAAATC
589535 T
1 T
589536 TACTGTATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.13, G:0.03, T:0.29
Consensus pattern (15 bp):
TAAATACATAAAATC
Found at i:591730 original size:18 final size:19
Alignment explanation
Indices: 591695--591731 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
591685 CACGGAATGT
591695 AAGATTACCAGTGGGAATAA
1 AAGATTACCAG-GGGAATAA
591715 AAGATTACCA-GGGAATA
1 AAGATTACCAGGGGAATA
591732 GGATTACTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 7 0.41
20 10 0.59
ACGTcount: A:0.46, C:0.11, G:0.24, T:0.19
Consensus pattern (19 bp):
AAGATTACCAGGGGAATAA
Found at i:592628 original size:37 final size:36
Alignment explanation
Indices: 592557--592628 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
592547 TATATTTTTT
*
592557 ATTTTGTAAAAAAATTATATAAATATTATGAATTTA
1 ATTTTGTAAAAAAATTATATAAATATTATCAATTTA
* *
592593 ATTTTTTAAAGAAAA-TATATAAATATTTTACAATTT
1 ATTTTGTAAA-AAAATTATATAAATATTAT-CAATTT
592629 TTAATATTAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 22 0.71
37 9 0.29
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.46
Consensus pattern (36 bp):
ATTTTGTAAAAAAATTATATAAATATTATCAATTTA
Found at i:600746 original size:12 final size:12
Alignment explanation
Indices: 600729--600753 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
600719 ACAAAGCATC
600729 ATTTGGTGCCTA
1 ATTTGGTGCCTA
600741 ATTTGGTGCCTA
1 ATTTGGTGCCTA
600753 A
1 A
600754 CATTATTTGA
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:0.20, C:0.16, G:0.24, T:0.40
Consensus pattern (12 bp):
ATTTGGTGCCTA
Found at i:608908 original size:17 final size:18
Alignment explanation
Indices: 608886--608923 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
608876 TTAATTATTT
*
608886 TTTATTTGTTTAT-AATA
1 TTTATTTATTTATAAATA
*
608903 TTTATTTATTTTTAAATA
1 TTTATTTATTTATAAATA
608921 TTT
1 TTT
608924 TAGATGGAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 11 0.61
18 7 0.39
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (18 bp):
TTTATTTATTTATAAATA
Found at i:608922 original size:18 final size:19
Alignment explanation
Indices: 608875--608924 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
608865 ATTTCATAAA
*
608875 TTTAATTATTTTTTATTTG
1 TTTAAATATTTTTTATTTG
608894 TTTATAATATTTATTTA-TT-
1 TTTA-AATATTT-TTTATTTG
608913 TTTAAATATTTT
1 TTTAAATATTTT
608925 AGATGGAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
17 1 0.04
18 7 0.25
19 8 0.29
20 8 0.29
21 4 0.14
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (19 bp):
TTTAAATATTTTTTATTTG
Found at i:611022 original size:21 final size:21
Alignment explanation
Indices: 610970--611026 Score: 87
Period size: 21 Copynumber: 2.7 Consensus size: 21
610960 TTTTACACTT
610970 AGGGAACCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
* *
610991 AGGAAATCGATTCCCTATGAG
1 AGGGAACCGATTCCCTATGAG
*
611012 AGGGTACCGATTCCC
1 AGGGAACCGATTCCC
611027 CCACGCTCCA
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (21 bp):
AGGGAACCGATTCCCTATGAG
Found at i:611243 original size:13 final size:13
Alignment explanation
Indices: 611222--611276 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
611212 AAGTTCGATA
*
611222 AATTCAAATACTT
1 AATTGAAATACTT
611235 AATTGAAATACTT
1 AATTGAAATACTT
* *
611248 AATT-AACTCAACAT
1 AATTGAAAT--ACTT
611262 AATTGAAATACTT
1 AATTGAAATACTT
611275 AA
1 AA
611277 ATACTTCCAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.35
Consensus pattern (13 bp):
AATTGAAATACTT
Found at i:611307 original size:33 final size:32
Alignment explanation
Indices: 611262--611359 Score: 137
Period size: 33 Copynumber: 3.0 Consensus size: 32
611252 AACTCAACAT
*
611262 AATTGAAATACTTAAATACTTCCAAGTTTGATA
1 AATTCAAATACTTAAA-ACTTCCAAGTTTGATA
611295 AATTCAAATACTTAAAAACTTCCAA-TTTCGATA
1 AATTCAAATACTT-AAAACTTCCAAGTTT-GATA
*
611328 AATTCAAATACTTAAAACTT-CAAGTTCGATA
1 AATTCAAATACTTAAAACTTCCAAGTTTGATA
611359 A
1 A
611360 TTGAAACAAA
Statistics
Matches: 60, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.13
32 12 0.20
33 37 0.62
34 3 0.05
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (32 bp):
AATTCAAATACTTAAAACTTCCAAGTTTGATA
Found at i:617405 original size:2 final size:2
Alignment explanation
Indices: 617398--617434 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
617388 TGAGAAGTGA
617398 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
617435 AATTCTCCAC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:617903 original size:38 final size:39
Alignment explanation
Indices: 617825--617906 Score: 103
Period size: 38 Copynumber: 2.1 Consensus size: 39
617815 AGCTAAACAT
* *
617825 AAGACTCCACGACTATATGGAGTCTTCAGGCAAACCAAG
1 AAGACTCCACGACTACACGGAGTCTTCAGGCAAACCAAG
* * **
617864 AAGACTCCATGACTACACGGTG-CTTCAGGCAAATGAAG
1 AAGACTCCACGACTACACGGAGTCTTCAGGCAAACCAAG
617902 AAGAC
1 AAGAC
617907 ACGAGAGTGC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
38 19 0.51
39 18 0.49
ACGTcount: A:0.37, C:0.24, G:0.22, T:0.17
Consensus pattern (39 bp):
AAGACTCCACGACTACACGGAGTCTTCAGGCAAACCAAG
Found at i:620281 original size:30 final size:31
Alignment explanation
Indices: 620229--620316 Score: 124
Period size: 30 Copynumber: 2.9 Consensus size: 31
620219 GAGTCGAGGG
**
620229 TTACCTATGTTCTTCGAAACATATGGATTGA
1 TTACCTATGTTCTTCGGGACATATGGATTGA
620260 TTACCTATG-TCTTCGGGACATATGGATTGA
1 TTACCTATGTTCTTCGGGACATATGGATTGA
* * *
620290 TTACCTAGGTTCTTTGGGACCTATGGA
1 TTACCTATGTTCTTCGGGACATATGGA
620317 CTGGTCCTTC
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
30 27 0.53
31 24 0.47
ACGTcount: A:0.24, C:0.17, G:0.22, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGATTGA
Found at i:622657 original size:2 final size:2
Alignment explanation
Indices: 622650--622680 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
622640 TGATAATTTA
622650 AT AT AT AT AT AT AT AT AT A- AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
622681 TTCTAAGTTG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:624668 original size:55 final size:55
Alignment explanation
Indices: 624394--624846 Score: 550
Period size: 55 Copynumber: 8.4 Consensus size: 55
624384 TTTATAAAGA
* * *
624394 TGCACACGTAGTGCCTATACGG-TAGTTCATCAACTCATGATGAATT-TCGTGG-GT
1 TGCACACATAGTGCCTGTACGGTTA-TTCATCAACTCATGATGAATTCT-GTGGATT
* * *
624448 TGCACACATAGTGCTTGTACGGTTATTCATCAACTCATTATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * * * * *
624503 TGTACATATAGTG-CTCTATGGTTATTCATCAACTTATGGTGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
624557 TGCAAACATAGTGCATGTACGGTTATTCATCAA---ATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
624609 TGCACATATAGTGCCTGTACGATTATTTATCAACTCATGATGAATTCTGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* *
624664 TGCACACATAGTGCATGTACGGTTATTCATCAACTCATGATGAATTCCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
* * *
624719 TGCACACATAGTACCTGTACGGTTATTCATTAACTCATGATAAATT-TCGTGGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATT
* * * *
624774 TGCACACATAATGCCTGTATGGTTATTCATCAACACATGATGAATT-TCGTCGATT
1 TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCT-GTGGATT
624829 TG--CACATAGTGCCTGTAC
1 TGCACACATAGTGCCTGTAC
624847 ACTATTGCAA
Statistics
Matches: 343, Mismatches: 48, Indels: 17
0.84 0.12 0.04
Matches are distributed among these distances:
52 45 0.13
53 14 0.04
54 87 0.25
55 197 0.57
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.35
Consensus pattern (55 bp):
TGCACACATAGTGCCTGTACGGTTATTCATCAACTCATGATGAATTCTGTGGATT
Found at i:625195 original size:18 final size:19
Alignment explanation
Indices: 625169--625208 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
625159 GTATCGATAC
*
625169 TACTATATTATGGTA-CGA
1 TACTATATTACGGTATCGA
*
625187 TACTCTATTACGGTATCGA
1 TACTATATTACGGTATCGA
625206 TAC
1 TAC
625209 CTTTTTGCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (19 bp):
TACTATATTACGGTATCGA
Found at i:633598 original size:99 final size:101
Alignment explanation
Indices: 633424--633626 Score: 335
Period size: 99 Copynumber: 2.0 Consensus size: 101
633414 GCCAACCATC
633424 GATAAACCAAATGTCATTCTTCCACACAGTGGCACTGCATCCAAGCTCTACCCGTCCCTACCAGT
1 GATAAACCAAATGTCATTCTTCCACACAGTGG-ACTGCATCCAAGCTCTACCCGTCCCTACCAGT
633489 TAATCAACCACGCGAGTACGTTTGACGGGAAGCAACT
65 TAATCAACCACGCGAGTACGTTTGACGGGAAGCAACT
633526 GATAAACCAAATGTCCA-T-TTCCACACAGTTGG-C-GC-TCCAAGCTCTACCCCGTCCCTACCA
1 GATAAACCAAATGT-CATTCTTCCACACAG-TGGACTGCATCCAAGCTCTA-CCCGTCCCTACCA
633586 GTTAATCAACCACGCGAGTACGTTTGACGGGAAGCAACT
63 GTTAATCAACCACGCGAGTACGTTTGACGGGAAGCAACT
633625 GA
1 GA
633627 CATCTTTATT
Statistics
Matches: 98, Mismatches: 0, Indels: 9
0.92 0.00 0.08
Matches are distributed among these distances:
98 11 0.11
99 56 0.57
100 1 0.01
101 10 0.10
102 18 0.18
103 2 0.02
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (101 bp):
GATAAACCAAATGTCATTCTTCCACACAGTGGACTGCATCCAAGCTCTACCCGTCCCTACCAGTT
AATCAACCACGCGAGTACGTTTGACGGGAAGCAACT
Found at i:641877 original size:20 final size:20
Alignment explanation
Indices: 641852--641892 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
641842 TTTGCACTAC
641852 TCTTGCTCATCTTTATTCCT
1 TCTTGCTCATCTTTATTCCT
641872 TCTTGCTCATCTTTATTCCT
1 TCTTGCTCATCTTTATTCCT
641892 T
1 T
641893 TTGTATATCC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.10, C:0.29, G:0.05, T:0.56
Consensus pattern (20 bp):
TCTTGCTCATCTTTATTCCT
Found at i:647118 original size:33 final size:30
Alignment explanation
Indices: 647059--647118 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 30
647049 ACAAGGATTG
* *
647059 TGTCCCCCCTTACACTGTTTTTTCATTCGA
1 TGTCCCCCCTCACACTATTTTTTCATTCGA
647089 TGTCCTCCCCTCACACTTATTTTTCTCATT
1 TGTCC-CCCCTCACAC-TATTTTT-TCATT
647119 TATTTATACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 9 0.36
32 6 0.24
33 5 0.20
ACGTcount: A:0.13, C:0.35, G:0.07, T:0.45
Consensus pattern (30 bp):
TGTCCCCCCTCACACTATTTTTTCATTCGA
Found at i:647427 original size:16 final size:18
Alignment explanation
Indices: 647396--647441 Score: 69
Period size: 16 Copynumber: 2.6 Consensus size: 18
647386 TGCAAACATG
647396 TAATATATATAATAATAA
1 TAATATATATAATAATAA
647414 TAATA-ATA-AATAATAA
1 TAATATATATAATAATAA
647430 TATATATATATA
1 TA-ATATATATA
647442 TATATATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 10 0.40
17 6 0.24
18 8 0.32
19 1 0.04
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
TAATATATATAATAATAA
Found at i:650143 original size:2 final size:2
Alignment explanation
Indices: 650136--650182 Score: 62
Period size: 2 Copynumber: 24.5 Consensus size: 2
650126 GATTTAATCC
* *
650136 AT AT AT AT AT -T AT AT AT AT AT AT AT AT AT AT AA AT AT A- AA
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
650176 AT AT AT A
1 AT AT AT A
650183 GATTATTTTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
1 2 0.05
2 38 0.95
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:655802 original size:42 final size:41
Alignment explanation
Indices: 655705--656022 Score: 298
Period size: 42 Copynumber: 7.8 Consensus size: 41
655695 GAAAATAATA
* * * **
655705 TACTTTAGTGGCATTTTTATACAAACGCCGCTAA--AGGTCG
1 TACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACAT-G
655745 TACTTTAGTGGCGTTTTAAGCACAAACGCCGCTAATTACATG
1 TACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACATG
* *
655787 TTCTTTAGTGGCGTTTTACGCACAAACGCCGCT-ATTACATG
1 TACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACATG
* * * * * * * *
655828 CACTATAGTGGCGTTTTTATATAAACGCTGATAAATAC-TG
1 TACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACATG
**
655868 TACTTTAGTGGCGATTTT---ACAAACGCCGCTAA--AGGTCG
1 TACTTTAGTGGCG-TTTTAACACAAACGCCGCTAATTACAT-G
*
655906 TACTTTAGTGGCGTTTTAAGCAAAAACGCCGCTAATTACATG
1 TACTTTAGTGGCGTTTTAA-CACAAACGCCGCTAATTACATG
* *
655948 TTCTTTAGTGGCGTTTTATACACAAACGCCGCTAATTACACG
1 TACTTTAGTGGCGTTTTA-ACACAAACGCCGCTAATTACATG
*
655990 TACTTTAGTGGCATTTTTAA-A-AAACGCCGCTAA
1 TACTTTAGTGGC-GTTTTAACACAAACGCCGCTAA
656023 AGGTCGTCTT
Statistics
Matches: 231, Mismatches: 31, Indels: 32
0.79 0.11 0.11
Matches are distributed among these distances:
36 1 0.00
37 5 0.02
38 25 0.11
40 51 0.22
41 58 0.25
42 81 0.35
43 10 0.04
ACGTcount: A:0.28, C:0.20, G:0.19, T:0.32
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTAACACAAACGCCGCTAATTACATG
Found at i:656986 original size:53 final size:52
Alignment explanation
Indices: 656903--657008 Score: 187
Period size: 54 Copynumber: 2.0 Consensus size: 52
656893 TAAAGTCCTA
656903 TTTCTATTCTCAATAATGTGAAGTAGGGATAA-CATATAGAGATAATTTTCT
1 TTTCTATTCTCAATAATGTGAAGTAGGGATAACCATATAGAGATAATTTTCT
656954 TTTCTATTCTCAATTAATCGTGAAGTAGGGATAACCATATAGAGATAATTTTCT
1 TTTCTATTCTCAA-TAAT-GTGAAGTAGGGATAACCATATAGAGATAATTTTCT
657008 T
1 T
657009 GCTTTGAAAC
Statistics
Matches: 52, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
51 13 0.25
52 4 0.08
53 15 0.29
54 20 0.38
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (52 bp):
TTTCTATTCTCAATAATGTGAAGTAGGGATAACCATATAGAGATAATTTTCT
Found at i:660301 original size:43 final size:43
Alignment explanation
Indices: 660251--660603 Score: 564
Period size: 43 Copynumber: 8.2 Consensus size: 43
660241 ACGGTCATTA
* * * *
660251 GCGGCGTTTGTATCAAAAAACGCCGCTATAGATCT-AACCTTTT
1 GCGGCGTTTGT-CCCAAAAACGCCGCTATAGATCTCGACCTATT
* * * *
660294 GTGGCGTTTGTTCCAAAAACGCCGCTATAAATCTCGACATATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
* *
660337 GCGGCGTTTGTTCCAAAAACGTCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
660380 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
*
660423 GAGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
* *
660466 GAGGCGTTTATCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
660509 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
*
660552 GCGGCGTTTGTCCTAAAAACGCCGCTATAGATCTCGACCTATT
1 GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
660595 GCGGCGTTT
1 GCGGCGTTT
660604 TTTGTTCACA
Statistics
Matches: 292, Mismatches: 17, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
42 21 0.07
43 271 0.93
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.28
Consensus pattern (43 bp):
GCGGCGTTTGTCCCAAAAACGCCGCTATAGATCTCGACCTATT
Found at i:672667 original size:21 final size:21
Alignment explanation
Indices: 672617--672683 Score: 66
Period size: 21 Copynumber: 3.2 Consensus size: 21
672607 ATGCGGCGAT
672617 GATGGCATCGAATCCGGGG-A
1 GATGGCATCGAATCCGGGGAA
* *
672637 GTCAT-CCATCGAGTCCGGGGAA
1 G--ATGGCATCGAATCCGGGGAA
* *
672659 GATGGCATCAAATCCGGGGAC
1 GATGGCATCGAATCCGGGGAA
672680 GATG
1 GATG
672684 TCGATGATGG
Statistics
Matches: 37, Mismatches: 6, Indels: 7
0.74 0.12 0.14
Matches are distributed among these distances:
20 3 0.08
21 30 0.81
22 4 0.11
ACGTcount: A:0.25, C:0.22, G:0.36, T:0.16
Consensus pattern (21 bp):
GATGGCATCGAATCCGGGGAA
Found at i:673689 original size:2 final size:2
Alignment explanation
Indices: 673682--673707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
673672 TCTAATCATA
673682 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
673708 CTTTCATATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:674292 original size:154 final size:148
Alignment explanation
Indices: 674010--674453 Score: 419
Period size: 154 Copynumber: 2.9 Consensus size: 148
674000 TTTAGTATAA
* * * * *
674010 AAAAAAAAGACATAAAATAAATCACAAATTCAAGGAATAAGAAATTATGAAAAATTG-AAGACTA
1 AAAAAAATGACTTAAAATAAATGACAAATTCAAGAAATAAGAAATTATGAAAAATTGAAAGATTA
* * * *
674074 AATTGAAAAATAAAAATTTGTTATTAAAGAGAGAAATTGAAAGCACACATATATTTTACTATGGT
66 AATTG--AAA-AAAAA-TTGTTATCAAAAAGAG-AATTGAAAG--TACATATATTCTACTATGGT
674139 TTAGGAGCACATGACTCAAATTCGG
124 TTAGGAGCACATGACTCAAATTCGG
* * *
674164 CAAAAAAAAT-ATTTAAAATAAATGACGAATAT-AAGAAATAAGGAAATTATGAAAATTTGAAAG
1 --AAAAAAATGACTTAAAATAAATGACAAAT-TCAAGAAATAA-GAAATTATGAAAAATTGAAAG
674227 ATTAAATTGGAAAAAAAATTGTTATCAAAAAGATGAATTGAAAGTACATATGCATTCTACTATGG
62 ATTAAATT-GAAAAAAAATTGTTATCAAAAAGA-GAATTGAAAGTACATAT--ATTCTACTATGG
* ** * *
674292 TTTAGGATCATGTGGCTCAAATTTGG
123 TTTAGGAGCACATGACTCAAATTCGG
* * * * * *
674318 TAAAAATTGACTTAAAATAAACGACAAATTGAAGAAATAAAGAGATTATGAAAAATTGAAGGATT
1 AAAAAAATGACTTAAAATAAATGACAAATTCAAGAAAT-AAGAAATTATGAAAAATTGAAAGATT
*** * *
674383 AAATT-AAAAAATAAAAATTATCAAAAAGAGGAATTAAAAGTACGCATATATTCTAGTATGGTTT
65 AAATTGAAAAAA-AATTGTTATCAAAAAGA-GAATTGAAAGTA--CATATATTCTACTATGGTTT
*
674447 AAGAGCA
126 AGGAGCA
674454 TTTAGTTCAA
Statistics
Matches: 242, Mismatches: 33, Indels: 30
0.79 0.11 0.10
Matches are distributed among these distances:
151 6 0.02
152 57 0.24
153 50 0.21
154 61 0.25
155 30 0.12
156 27 0.11
157 10 0.04
158 1 0.00
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (148 bp):
AAAAAAATGACTTAAAATAAATGACAAATTCAAGAAATAAGAAATTATGAAAAATTGAAAGATTA
AATTGAAAAAAAATTGTTATCAAAAAGAGAATTGAAAGTACATATATTCTACTATGGTTTAGGAG
CACATGACTCAAATTCGG
Found at i:674446 original size:152 final size:149
Alignment explanation
Indices: 674010--674453 Score: 421
Period size: 152 Copynumber: 2.9 Consensus size: 149
674000 TTTAGTATAA
* * * *
674010 AAAAAAAAGACATAAAATAAATC-ACAAATTCAAGGAAT-AAGAAATTATGAAAAATTGAAGACT
1 AAAAAAAATACTTAAAATAAA-CGACAAATT-AAGAAATAAAGAAATTATGAAAAATTGAAGATT
* * * * * *
674073 AAATTGAAAAATAAAAATTTGTTATTAAAGAGAGAAATTGAAAGCACACATATATTTTACTATGG
64 AAATTAAAAAATAAAAA----TTATCAAAAAGAGGAATTGAAAGTAC-CATATATTCTACTATGG
674138 TTTAGGAGCACATGACTCAAATTCGG
124 TTTAGGAGCACATGACTCAAATTCGG
* * * * *
674164 CAAAAAAAATATTTAAAATAAATGACGAATATAAGAAATAAGGAAATTATGAAAATTTGAAAGAT
1 -AAAAAAAATACTTAAAATAAACGACAAAT-TAAGAAATAAAGAAATTATGAAAAATTG-AAGAT
*** *
674229 TAAATTGGAAAAAA-AATTGTTATCAAAAAGATGAATTGAAAGTA-CATATGCATTCTACTATGG
63 TAAATT--AAAAAATAAAAATTATCAAAAAGAGGAATTGAAAGTACCATAT--ATTCTACTATGG
* ** * *
674292 TTTAGGATCATGTGGCTCAAATTTGG
124 TTTAGGAGCACATGACTCAAATTCGG
* * *
674318 -TAAAAATTGACTTAAAATAAACGACAAATTGAAGAAATAAAGAGATTATGAAAAATTGAAGGAT
1 AAAAAAAAT-ACTTAAAATAAACGACAAATT-AAGAAATAAAGAAATTATGAAAAATTGAA-GAT
* *
674382 TAAATTAAAAAATAAAAATTATCAAAAAGAGGAATTAAAAGTACGCATATATTCTAGTATGGTTT
63 TAAATTAAAAAATAAAAATTATCAAAAAGAGGAATTGAAAGTAC-CATATATTCTACTATGGTTT
*
674447 AAGAGCA
127 AGGAGCA
674454 TTTAGTTCAA
Statistics
Matches: 235, Mismatches: 40, Indels: 31
0.77 0.13 0.10
Matches are distributed among these distances:
151 6 0.03
152 58 0.25
153 50 0.21
154 57 0.24
155 29 0.12
156 18 0.08
157 10 0.04
158 2 0.01
159 5 0.02
ACGTcount: A:0.51, C:0.07, G:0.15, T:0.27
Consensus pattern (149 bp):
AAAAAAAATACTTAAAATAAACGACAAATTAAGAAATAAAGAAATTATGAAAAATTGAAGATTAA
ATTAAAAAATAAAAATTATCAAAAAGAGGAATTGAAAGTACCATATATTCTACTATGGTTTAGGA
GCACATGACTCAAATTCGG
Found at i:675553 original size:28 final size:28
Alignment explanation
Indices: 675518--675590 Score: 121
Period size: 28 Copynumber: 2.6 Consensus size: 28
675508 ATTAGTAATA
*
675518 AATTTTGATTTTATTTTGTAATCTAAAC
1 AATTTTGATTTTATTTTGTAATCAAAAC
675546 AATTTTGATTTTATTTTGTAATCAAAAC
1 AATTTTGATTTTATTTTGTAATCAAAAC
675574 AATTTTGACTTTT-TTTT
1 AATTTTGA-TTTTATTTT
675591 CGTTTAAAAT
Statistics
Matches: 43, Mismatches: 1, Indels: 2
0.93 0.02 0.04
Matches are distributed among these distances:
28 39 0.91
29 4 0.09
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (28 bp):
AATTTTGATTTTATTTTGTAATCAAAAC
Found at i:675836 original size:16 final size:16
Alignment explanation
Indices: 675812--675843 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
675802 TGTGATTATA
675812 TATTCAACAGTTACAT
1 TATTCAACAGTTACAT
*
675828 TATTGAACAGTTACAT
1 TATTCAACAGTTACAT
675844 CATAAAATCA
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:0.38, C:0.16, G:0.09, T:0.38
Consensus pattern (16 bp):
TATTCAACAGTTACAT
Found at i:678503 original size:18 final size:18
Alignment explanation
Indices: 678480--678517 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
678470 TATTCGGGTC
*
678480 GGATCGAGTTTGGGTTTA
1 GGATCGAGTTCGGGTTTA
678498 GGATCGAGTTCGGGTTTA
1 GGATCGAGTTCGGGTTTA
678516 GG
1 GG
678518 GTGAAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.16, C:0.08, G:0.42, T:0.34
Consensus pattern (18 bp):
GGATCGAGTTCGGGTTTA
Found at i:678802 original size:239 final size:230
Alignment explanation
Indices: 678527--678964 Score: 666
Period size: 239 Copynumber: 1.9 Consensus size: 230
678517 GGTGAAAAAT
* * *
678527 ACCCGACTCGAAAATATATATAATTTTACCTTATATATTTAGGAATAATTACAATAAGACCCTTC
1 ACCCGACTCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAAGACCCCTC
678592 TATATATAATTTTTTTCAATTAAGTCACTA-TTTTTATTGAATAAAAATAATTTTTTATTATTTC
66 TATATAT-ATTTTTTTCAATTAAGTCAC-AGTTTTTATTGAATAAAAATAATTTTTTATTA-TT-
*
678656 GGGTCGGGTCGGGTCGGATTTCTAATTCATATATTCGGGTCGGGTCGGGTGAAACTTTATTTTGG
127 ---TCGGGTC--G--GG-TTTCTAATTCATATATTCGGGTCGGGTCGGGTAAAACTTTATTTTGG
678721 TCGGGTCGGGT-TCGGGTTTAGGGTGAAAAATACCCAACCTGACCCG
184 TCGGGTCGGGTCTCGGGTTTAGGGTGAAAAATACCCAACCTGACCCG
*
678767 ACCCGAC-CCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAATACCCCTC
1 ACCCGACTCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAAGACCCCTC
* *
678831 TATATATTTTTTTTTCAATTAAGTCACAGTTTTTATTGAATAAAAATATTTTTTTATTATTTCGG
66 TATATATATTTTTTTCAATTAAGTCACAGTTTTTATTGAATAAAAATAATTTTTTATTATTTCGG
* *
678896 GTCGGGTTTCTAATTCATATATTTGGGTTGGGTCGGGTAAAACTTTATTTTGGTCGGGTCGGGTC
131 GTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTAAAACTTTATTTTGGTCGGGTCGGGTC
678961 TCGG
196 TCGG
678965 ATGGAGGTTC
Statistics
Matches: 187, Mismatches: 9, Indels: 15
0.89 0.04 0.07
Matches are distributed among these distances:
228 55 0.29
229 6 0.03
231 1 0.01
233 7 0.04
237 3 0.02
238 48 0.26
239 60 0.32
240 7 0.04
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.39
Consensus pattern (230 bp):
ACCCGACTCCAAAAAATATATAATTTTACCTTATATATTTAGGAATAATTACAATAAGACCCCTC
TATATATATTTTTTTCAATTAAGTCACAGTTTTTATTGAATAAAAATAATTTTTTATTATTTCGG
GTCGGGTTTCTAATTCATATATTCGGGTCGGGTCGGGTAAAACTTTATTTTGGTCGGGTCGGGTC
TCGGGTTTAGGGTGAAAAATACCCAACCTGACCCG
Found at i:679287 original size:18 final size:18
Alignment explanation
Indices: 679264--679310 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
679254 ATGGAATTGG
679264 ATTCCAATTCCTTCACAA
1 ATTCCAATTCCTTCACAA
* *
679282 ATTCCAATTCATTCACAG
1 ATTCCAATTCCTTCACAA
679300 ATTCCAATTCC
1 ATTCCAATTCC
679311 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.32, C:0.32, G:0.02, T:0.34
Consensus pattern (18 bp):
ATTCCAATTCCTTCACAA
Found at i:684238 original size:20 final size:20
Alignment explanation
Indices: 684208--684262 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
684198 AAATCGGTTT
684208 TTTTAAAAATTGGATCGAATA
1 TTTT-AAAATTGGATCGAATA
* *
684229 TTTTAAAATTAGATCGGATA
1 TTTTAAAATTGGATCGAATA
*
684249 TTTTAAAATCGGAT
1 TTTTAAAATTGGAT
684263 AGTATAACCG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 26 0.87
21 4 0.13
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (20 bp):
TTTTAAAATTGGATCGAATA
Found at i:684820 original size:13 final size:13
Alignment explanation
Indices: 684802--684835 Score: 68
Period size: 13 Copynumber: 2.6 Consensus size: 13
684792 TAATTTTAGT
684802 AATTATTTTAAAA
1 AATTATTTTAAAA
684815 AATTATTTTAAAA
1 AATTATTTTAAAA
684828 AATTATTT
1 AATTATTT
684836 CATTCAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
AATTATTTTAAAA
Found at i:685077 original size:73 final size:72
Alignment explanation
Indices: 684978--685119 Score: 164
Period size: 73 Copynumber: 1.9 Consensus size: 72
684968 CTGAGCAATG
* * *
684978 ATTTTAACGAGCAACGAGCTTAACGAG-CATGAGTCGAGCAATAA-GTTTTTTTAACGAGCACAA
1 ATTTTAACGAGCAACGAGC-TAACGAGTC--GAATCGAGCAACAATGTTTTTTTAAAGAGCACAA
685041 ATCGAGTAAA
63 ATCGAGTAAA
* * *
685051 ATTTTAACGAGTTTAACGAGC-AACGAGTCGAATCGAGCAACAATTTTTTTTTAAAGAGCACAAG
1 ATTTTAACGAG--CAACGAGCTAACGAGTCGAATCGAGCAACAATGTTTTTTTAAAGAGCACAAA
685115 TCGAG
64 TCGAG
685120 CACTACCCAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
72 12 0.20
73 39 0.66
74 1 0.02
75 7 0.12
ACGTcount: A:0.37, C:0.16, G:0.20, T:0.26
Consensus pattern (72 bp):
ATTTTAACGAGCAACGAGCTAACGAGTCGAATCGAGCAACAATGTTTTTTTAAAGAGCACAAATC
GAGTAAA
Found at i:685607 original size:20 final size:20
Alignment explanation
Indices: 685584--685635 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
685574 AACGCGATCC
685584 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
685604 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
685624 CCAAAATCGCAA
1 CCAGAATCGCAA
685636 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:685652 original size:21 final size:20
Alignment explanation
Indices: 685625--685723 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
685615 AATCAGTTTC
685625 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
685646 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
685667 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
685687 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
685708 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
685724 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:685752 original size:20 final size:20
Alignment explanation
Indices: 685690--685883 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
685680 CGATTTTCCA
* ** *
685690 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
685710 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
685730 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
685750 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
685770 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
685790 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
685810 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
685830 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
685850 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
685871 AAATCGCAACGCG
1 AAATCGCAACGCG
685884 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:685774 original size:60 final size:60
Alignment explanation
Indices: 685690--685883 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
685680 CGATTTTCCA
* ** * *
685690 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
685750 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
685810 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
685871 AAATCGCAACGCG
1 AAATCGCAACGCG
685884 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:686304 original size:33 final size:33
Alignment explanation
Indices: 686265--686335 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
686255 TTCACTTAGA
*
686265 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* * *
686298 TTTCATTTCGTGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
686331 TTTCA
1 TTTCA
686336 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.21, G:0.18, T:0.49
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:686475 original size:14 final size:14
Alignment explanation
Indices: 686456--686510 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
686446 AGAATGACTG
686456 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
686470 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
686489 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
686503 TCGCAACG
1 TCGCAACG
686511 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:686523 original size:33 final size:33
Alignment explanation
Indices: 686456--686526 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
686446 AGAATGACTG
***
686456 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
686489 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
686522 TCGCA
1 TCGCA
686527 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:686544 original size:19 final size:19
Alignment explanation
Indices: 686522--686619 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
686512 GAAACCAAAA
*
686522 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
686541 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
686555 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
686574 TCGCGTTGCGA--TTC-TA
1 TCGCGTTGCGATTTTCATT
* *
686590 T--CGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
686607 TCGCGTTGCGATT
1 TCGCGTTGCGATT
686620 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 18 0.29
16 7 0.11
17 8 0.13
19 30 0.48
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:686563 original size:14 final size:14
Alignment explanation
Indices: 686544--686633 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
686534 TTTCATTTCG
686544 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
686558 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
*
686577 CGTTGCGATTCTAT
1 CGTTGCGATTCTCT
686591 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
686608 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
686624 CGTTGCGATT
1 CGTTGCGATT
686634 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 27 0.44
15 1 0.02
16 8 0.13
17 7 0.11
18 1 0.02
19 18 0.29
ACGTcount: A:0.10, C:0.24, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:686569 original size:33 final size:33
Alignment explanation
Indices: 686527--686641 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
686517 CAAAATCGCA
686527 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
686560 TTGCGATTTTCATTTCGCGTTGCGATTCTATCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
686593 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
686626 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
686642 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:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:688569 original size:185 final size:186
Alignment explanation
Indices: 688340--688719 Score: 753
Period size: 185 Copynumber: 2.0 Consensus size: 186
688330 TAGATTGCTT
688340 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
688405 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
688470 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
688525 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
688590 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
688655 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
688711 AGTAAATTT
1 AGTAAATTT
688720 ATCCATTCAA
Statistics
Matches: 194, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
185 155 0.80
186 39 0.20
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Done.