Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008759.1 Hibiscus syriacus cultivar Beakdansim tig00111851_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: 899239
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 4
Found at i:346486 original size:19 final size:18
Alignment explanation
Indices: 346462--346500 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 18
346452 CGATTAATTA
346462 ACTAATAAGATTATTTGAT
1 ACTAAT-AGATTATTTGAT
*
346481 ACTAATATATTATTTGAT
1 ACTAATAGATTATTTGAT
346499 AC
1 AC
346501 ATCATACTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 13 0.68
19 6 0.32
ACGTcount: A:0.41, C:0.08, G:0.08, T:0.44
Consensus pattern (18 bp):
ACTAATAGATTATTTGAT
Found at i:349214 original size:2 final size:2
Alignment explanation
Indices: 349178--349206 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
349168 GCTTTTTTAA
349178 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
349207 AAATATATTT
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:352088 original size:2 final size:2
Alignment explanation
Indices: 352081--352105 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
352071 AAGTGCTCCA
352081 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 A
352106 AAGTCAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:354198 original size:29 final size:29
Alignment explanation
Indices: 354156--354230 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
354146 AACCCAACCA
**
354156 TAGGTCGCCATGCACTCCCAGCGACCTCC
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
* * *
354185 TAGGTCGCCATGCACGCCCGGCGACCAAG
1 TAGGTCGCCATGCACTCCCAGCGACCAAC
*
354214 GAGGTCGCCATGCACTC
1 TAGGTCGCCATGCACTC
354231 GGGGCGACCA
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 39 1.00
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.15
Consensus pattern (29 bp):
TAGGTCGCCATGCACTCCCAGCGACCAAC
Found at i:354236 original size:29 final size:29
Alignment explanation
Indices: 354157--354244 Score: 95
Period size: 29 Copynumber: 3.0 Consensus size: 29
354147 ACCCAACCAT
* * ****
354157 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
354186 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
* **
354215 AGGTCGCCATGCACTCGGGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
354244 A
1 A
354245 TTCATGCATG
Statistics
Matches: 50, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 50 1.00
ACGTcount: A:0.20, C:0.38, G:0.31, T:0.11
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:354498 original size:10 final size:10
Alignment explanation
Indices: 354483--354508 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
354473 CTTTGGCGAG
354483 ATGGGCGTGC
1 ATGGGCGTGC
354493 ATGGGCGTGC
1 ATGGGCGTGC
354503 ATGGGC
1 ATGGGC
354509 ATGGAGGTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.12, C:0.19, G:0.50, T:0.19
Consensus pattern (10 bp):
ATGGGCGTGC
Found at i:354563 original size:29 final size:29
Alignment explanation
Indices: 354528--354614 Score: 120
Period size: 29 Copynumber: 3.0 Consensus size: 29
354518 GTTGGCTGGT
*
354528 AGGTCGCAGGGCATGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
* ***
354557 AGGTCGCTGGGCGTGCATGGCGACCTGGT
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
*
354586 AGGTCGCCGGGCGTGCATGGCGACCTACC
1 AGGTCGCAGGGCGTGCATGGCGACCTACC
354615 CCCGGTACTG
Statistics
Matches: 49, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 49 1.00
ACGTcount: A:0.15, C:0.30, G:0.39, T:0.16
Consensus pattern (29 bp):
AGGTCGCAGGGCGTGCATGGCGACCTACC
Found at i:357352 original size:60 final size:60
Alignment explanation
Indices: 357234--357366 Score: 146
Period size: 60 Copynumber: 2.2 Consensus size: 60
357224 ATAGTCAAGT
* *
357234 GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAGTCGGAG
1 GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAATCGGAA
* * * * *
357294 GATCATTTTGTAACTTTTAATAGTC-AGATGACTTAATAAAGTAGTAC-CT-TATAATCGGAA
1 GACCATTTTGTAACTTTTAATAGTCGAG-GGACTCAACAAAGCA--ACACTCTATAATCGGAA
357354 GACCATTTATGTA
1 GACCATTT-TGTA
357367 CTTGACCCTA
Statistics
Matches: 61, Mismatches: 8, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
59 2 0.03
60 51 0.84
61 6 0.10
62 2 0.03
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.32
Consensus pattern (60 bp):
GACCATTTTGTAACTTTTAATAGTCGAGGGACTCAACAAAGCAACACTCTATAATCGGAA
Found at i:357462 original size:16 final size:17
Alignment explanation
Indices: 357441--357476 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
357431 AATTTCTGAC
*
357441 TTTTATGA-ATATAAAT
1 TTTTATGATATAAAAAT
357457 TTTTATGATATAAAAAT
1 TTTTATGATATAAAAAT
357474 TTT
1 TTT
357477 ATTTTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (17 bp):
TTTTATGATATAAAAAT
Found at i:357477 original size:16 final size:16
Alignment explanation
Indices: 357441--357478 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
357431 AATTTCTGAC
*
357441 TTTTATGAATATAAAT
1 TTTTATGAATATAAAA
357457 TTTTATG-ATATAAAAA
1 TTTTATGAATAT-AAAA
357473 TTTTAT
1 TTTTAT
357479 TTTAAAATCT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 4 0.20
16 16 0.80
ACGTcount: A:0.42, C:0.00, G:0.05, T:0.53
Consensus pattern (16 bp):
TTTTATGAATATAAAA
Found at i:357911 original size:20 final size:20
Alignment explanation
Indices: 357886--357934 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
357876 ATATTATTAA
357886 AATTATAAAATAATTCAAAT
1 AATTATAAAATAATTCAAAT
*
357906 AATTATAAAATAATTTAAAT
1 AATTATAAAATAATTCAAAT
357926 AATTATAAA
1 AATTATAAA
357935 CAAATATTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
AATTATAAAATAATTCAAAT
Found at i:360860 original size:21 final size:21
Alignment explanation
Indices: 360834--360874 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
360824 ATTTGAAATT
* *
360834 TTAAAATTTTAGAGGATAAAC
1 TTAAAATTTCAGAAGATAAAC
360855 TTAAAATTTCAGAAGATAAA
1 TTAAAATTTCAGAAGATAAA
360875 ATCAAACTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.51, C:0.05, G:0.12, T:0.32
Consensus pattern (21 bp):
TTAAAATTTCAGAAGATAAAC
Found at i:363780 original size:43 final size:44
Alignment explanation
Indices: 363703--363801 Score: 175
Period size: 43 Copynumber: 2.3 Consensus size: 44
363693 TTTCACCATA
*
363703 AATCT-AATTTTACTCACATCCTTAAAAATTTTGATATATCTCG
1 AATCTAAATTTTACTCACATCCTTAAAAATATTGATATATCTCG
363746 AATCTAAATTTTACTCACATCCTTAAAAA-ATTGATATATCTCG
1 AATCTAAATTTTACTCACATCCTTAAAAATATTGATATATCTCG
363789 AATCTAAATTTTA
1 AATCTAAATTTTA
363802 GATGAAAAAT
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
43 31 0.57
44 23 0.43
ACGTcount: A:0.38, C:0.17, G:0.04, T:0.40
Consensus pattern (44 bp):
AATCTAAATTTTACTCACATCCTTAAAAATATTGATATATCTCG
Found at i:364166 original size:20 final size:21
Alignment explanation
Indices: 364141--364181 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
364131 AGGTTGTACT
*
364141 AAAAT-GTTATACATGGTAAG
1 AAAATAGTTATAAATGGTAAG
364161 AAAATGAGTTATAAATGGTAA
1 AAAAT-AGTTATAAATGGTAA
364182 ATGTTAGGAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.49, C:0.02, G:0.20, T:0.29
Consensus pattern (21 bp):
AAAATAGTTATAAATGGTAAG
Found at i:365913 original size:15 final size:15
Alignment explanation
Indices: 365893--365924 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
365883 CACCCAACAA
365893 GATGGTGATGGTGAT
1 GATGGTGATGGTGAT
365908 GATGGTGATGGTGAT
1 GATGGTGATGGTGAT
365923 GA
1 GA
365925 AGGGAGTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.00, G:0.47, T:0.31
Consensus pattern (15 bp):
GATGGTGATGGTGAT
Found at i:367390 original size:62 final size:63
Alignment explanation
Indices: 367285--367410 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 63
367275 TAGTGGTCAG
367285 ATCAAGATATCAAATGGTAAAAAAAAGTCAGTAAGAAGAGTAATATATCTCAAAACCATGATGA
1 ATCAAGATATCAAATGGT-AAAAAAAGTCAGTAAGAAGAGTAATATATCTCAAAACCATGATGA
367349 ATCAAGATATCAAATGGT-AAAAAAGTCAGTAAGAAGAGTAATATATCTCAAAACCATGATGA
1 ATCAAGATATCAAATGGTAAAAAAAGTCAGTAAGAAGAGTAATATATCTCAAAACCATGATGA
367411 TCTAATAGTC
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
62 44 0.71
64 18 0.29
ACGTcount: A:0.51, C:0.11, G:0.16, T:0.22
Consensus pattern (63 bp):
ATCAAGATATCAAATGGTAAAAAAAGTCAGTAAGAAGAGTAATATATCTCAAAACCATGATGA
Found at i:368740 original size:10 final size:9
Alignment explanation
Indices: 368705--368802 Score: 72
Period size: 10 Copynumber: 10.3 Consensus size: 9
368695 GCTGCTGGAA
*
368705 ACCGGTTTA
1 ACCGGTTTG
*
368714 ACCGGTTTTCA
1 ACCGG-TTT-G
368725 ACCGGTTCTG
1 ACCGGTT-TG
368735 ACCGGTTT-
1 ACCGGTTTG
*
368743 ACCGGTTTCA
1 ACCGGTTT-G
*
368753 ACCGGTTCG
1 ACCGGTTTG
368762 AACCGGTTTG
1 -ACCGGTTTG
*
368772 ACCGGTCTG
1 ACCGGTTTG
*
368781 AATCGGTTTG
1 -ACCGGTTTG
*
368791 ACCGGTCTG
1 ACCGGTTTG
368800 ACC
1 ACC
368803 CGACCCGACC
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
8 8 0.11
9 24 0.33
10 34 0.47
11 7 0.10
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.30
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:368756 original size:28 final size:29
Alignment explanation
Indices: 368705--368796 Score: 109
Period size: 28 Copynumber: 3.2 Consensus size: 29
368695 GCTGCTGGAA
368705 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTAACCGG-TTTCAACCGGTTCTG
368735 ACCGGTTT-ACCGGTTTCAACCGGTTC-G
1 ACCGGTTTAACCGGTTTCAACCGGTTCTG
* * * *
368762 AACCGGTTTGACCGGTCTGAATCGGTT-TG
1 -ACCGGTTTAACCGGTTTCAACCGGTTCTG
368791 ACCGGT
1 ACCGGT
368797 CTGACCCGAC
Statistics
Matches: 56, Mismatches: 3, Indels: 8
0.84 0.04 0.12
Matches are distributed among these distances:
27 1 0.02
28 27 0.48
29 20 0.36
30 8 0.14
ACGTcount: A:0.16, C:0.26, G:0.27, T:0.30
Consensus pattern (29 bp):
ACCGGTTTAACCGGTTTCAACCGGTTCTG
Found at i:368766 original size:38 final size:36
Alignment explanation
Indices: 368705--368777 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 36
368695 GCTGCTGGAA
368705 ACCGGTTTAACCGGTTTTCAACCGGTTCTGACCGGTTT
1 ACCGGTTTAACCGG-TTTCAACCGGTT-TGACCGGTTT
368743 ACCGGTTTCAACCGG-TTCGAACCGGTTTGACCGGT
1 ACCGGTTT-AACCGGTTTC-AACCGGTTTGACCGGT
368778 CTGAATCGGT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
37 11 0.33
38 16 0.48
39 6 0.18
ACGTcount: A:0.16, C:0.27, G:0.26, T:0.30
Consensus pattern (36 bp):
ACCGGTTTAACCGGTTTCAACCGGTTTGACCGGTTT
Found at i:368777 original size:19 final size:18
Alignment explanation
Indices: 368704--368796 Score: 80
Period size: 19 Copynumber: 4.9 Consensus size: 18
368694 GGCTGCTGGA
*
368704 AACCGGTTTAACCGGTTTTC
1 AACCGGTTTGACCGG--TTC
368724 AACCGGTTCTGACCGGTT-
1 AACCGGTT-TGACCGGTTC
* *
368742 TACCGGTTTCAACCGGTTC
1 AACCGGTTT-GACCGGTTC
*
368761 GAACCGGTTTGACCGGTCTG
1 -AACCGGTTTGACCGGT-TC
*
368781 AATCGGTTTGACCGGT
1 AACCGGTTTGACCGGT
368797 CTGACCCGAC
Statistics
Matches: 61, Mismatches: 7, Indels: 11
0.77 0.09 0.14
Matches are distributed among these distances:
17 1 0.02
18 14 0.23
19 23 0.38
20 17 0.28
21 6 0.10
ACGTcount: A:0.17, C:0.26, G:0.27, T:0.30
Consensus pattern (18 bp):
AACCGGTTTGACCGGTTC
Found at i:368821 original size:12 final size:12
Alignment explanation
Indices: 368804--368857 Score: 56
Period size: 12 Copynumber: 4.3 Consensus size: 12
368794 GGTCTGACCC
368804 GACCCGACCGTT
1 GACCCGACCGTT
*
368816 GACCCGACCCG-A
1 GACCCGA-CCGTT
368828 GACCCGACCGTT
1 GACCCGACCGTT
*
368840 GACCGTTGACCGTT
1 GACC--CGACCGTT
368854 GACC
1 GACC
368858 GTTGACTTTC
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
11 3 0.09
12 18 0.51
13 3 0.09
14 11 0.31
ACGTcount: A:0.19, C:0.41, G:0.26, T:0.15
Consensus pattern (12 bp):
GACCCGACCGTT
Found at i:368843 original size:7 final size:7
Alignment explanation
Indices: 368833--368863 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
368823 CCCGAGACCC
368833 GACCGTT
1 GACCGTT
368840 GACCGTT
1 GACCGTT
368847 GACCGTT
1 GACCGTT
368854 GACCGTT
1 GACCGTT
368861 GAC
1 GAC
368864 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:369800 original size:63 final size:63
Alignment explanation
Indices: 369732--369855 Score: 153
Period size: 63 Copynumber: 2.0 Consensus size: 63
369722 CTAATGTGAC
* ** * *
369732 TCTTAGGTAGGCTTTGCGGCCCTGAGATC-ATTCTCGGGTAGGCCCTGC-GGCCCTAAGATGTGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTA-TCTCGGGTAGGCCCT-CAGGCCCTAAGATGTGT
* *
369795 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTTGGGTAGGCTCTCAGGCCCTAAGATGT
1 TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGT
369856 TCCCTTAGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
62 1 0.02
63 50 0.96
64 1 0.02
ACGTcount: A:0.17, C:0.27, G:0.29, T:0.27
Consensus pattern (63 bp):
TCTTAGGTAGGCCTCACGGCCCCGAAATCTATCTCGGGTAGGCCCTCAGGCCCTAAGATGTGT
Found at i:369815 original size:32 final size:32
Alignment explanation
Indices: 369779--369855 Score: 79
Period size: 31 Copynumber: 2.4 Consensus size: 32
369769 GTAGGCCCTG
*
369779 CGGCCCTAAGATGTGTTCTTAGGTAGGC-CTCA
1 CGGCCCTAAGATGT-ATCTTAGGTAGGCTCTCA
* * *
369811 CGGCCCCGAA-ATCTATCTTGGGTAGGCTCTCA
1 CGG-CCCTAAGATGTATCTTAGGTAGGCTCTCA
369843 -GGCCCTAAGATGT
1 CGGCCCTAAGATGT
369856 TCCCTTAGGG
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
30 5 0.14
31 16 0.44
32 10 0.28
33 5 0.14
ACGTcount: A:0.19, C:0.27, G:0.27, T:0.26
Consensus pattern (32 bp):
CGGCCCTAAGATGTATCTTAGGTAGGCTCTCA
Found at i:376065 original size:9 final size:9
Alignment explanation
Indices: 376051--376133 Score: 58
Period size: 9 Copynumber: 8.8 Consensus size: 9
376041 GGCTGCTGGA
376051 AACCGGTTT
1 AACCGGTTT
376060 AACCGGTTCT
1 AACCGGTT-T
*
376070 GACCGGTTT
1 AACCGGTTT
*
376079 GACCGGTTT
1 AACCGGTTT
* *
376088 CAACCGATTCG
1 -AACCGGTT-T
376099 AACCGGTTT
1 AACCGGTTT
* *
376108 GACCGGTCTG
1 AACCGGT-TT
*
376118 AATCGGTTT
1 AACCGGTTT
*
376127 GACCGGT
1 AACCGGT
376134 CTGACCCGAC
Statistics
Matches: 57, Mismatches: 13, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
9 30 0.53
10 27 0.47
ACGTcount: A:0.18, C:0.25, G:0.28, T:0.29
Consensus pattern (9 bp):
AACCGGTTT
Found at i:376076 original size:19 final size:18
Alignment explanation
Indices: 376052--376133 Score: 76
Period size: 19 Copynumber: 4.3 Consensus size: 18
376042 GCTGCTGGAA
*
376052 ACCGGTTTAACCGGTTCTG
1 ACCGGTTGAACCGGTT-TG
*
376071 ACCGGTTTG-ACCGGTTTCA
1 ACCGG-TTGAACCGGTTT-G
*
376090 ACCGATTCGAACCGGTTTG
1 ACCGGTT-GAACCGGTTTG
*
376109 ACCGGTCTGAATCGGTTTG
1 ACCGGT-TGAACCGGTTTG
376128 ACCGGT
1 ACCGGT
376134 CTGACCCGAC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
18 3 0.06
19 38 0.73
20 11 0.21
ACGTcount: A:0.17, C:0.26, G:0.28, T:0.29
Consensus pattern (18 bp):
ACCGGTTGAACCGGTTTG
Found at i:376103 original size:29 final size:28
Alignment explanation
Indices: 376052--376114 Score: 92
Period size: 29 Copynumber: 2.2 Consensus size: 28
376042 GCTGCTGGAA
*
376052 ACCGGTTTAACCGGTTCTGACCGGTTTG
1 ACCGGTTTAACCGATTCTGACCGGTTTG
376080 ACCGGTTTCAACCGATTC-GAACCGGTTTG
1 ACCGGTTT-AACCGATTCTG-ACCGGTTTG
376109 ACCGGT
1 ACCGGT
376115 CTGAATCGGT
Statistics
Matches: 32, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
28 9 0.28
29 23 0.72
ACGTcount: A:0.17, C:0.27, G:0.27, T:0.29
Consensus pattern (28 bp):
ACCGGTTTAACCGATTCTGACCGGTTTG
Found at i:376146 original size:5 final size:5
Alignment explanation
Indices: 376136--376193 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
376126 TGACCGGTCT
* *
376136 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
376185 GACCC GACC
1 GACCC GACC
376194 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:376162 original size:22 final size:22
Alignment explanation
Indices: 376136--376200 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
376126 TGACCGGTCT
376136 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
376158 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
376180 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
376201 GTTGACTTTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:378034 original size:14 final size:14
Alignment explanation
Indices: 378015--378070 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
378005 CGTTCGTGAA
378015 CGTTCGATTATGTT
1 CGTTCGATTATGTT
*
378029 CGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
378042 --TT-GTTTATGTT
1 CGTTCGATTATGTT
378053 CGTTCGATTATGTT
1 CGTTCGATTATGTT
378067 CGTT
1 CGTT
378071 TATGTTCATT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
10 6 0.17
11 3 0.09
13 3 0.09
14 23 0.66
ACGTcount: A:0.11, C:0.12, G:0.23, T:0.54
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:378049 original size:24 final size:24
Alignment explanation
Indices: 378022--378091 Score: 97
Period size: 24 Copynumber: 2.9 Consensus size: 24
378012 GAACGTTCGA
*
378022 TTATGTTCGTTCGGTTATGTTTGT
1 TTATGTTCGTTCGATTATGTTTGT
*
378046 TTATGTTCGTTCGATTATGTTCGT
1 TTATGTTCGTTCGATTATGTTTGT
*
378070 TTATGTTCATTC-ATTTATGTTT
1 TTATGTTCGTTCGA-TTATGTTT
378092 AACTCAATCT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 40 0.98
ACGTcount: A:0.13, C:0.10, G:0.19, T:0.59
Consensus pattern (24 bp):
TTATGTTCGTTCGATTATGTTTGT
Found at i:378816 original size:10 final size:10
Alignment explanation
Indices: 378801--378875 Score: 61
Period size: 10 Copynumber: 7.7 Consensus size: 10
378791 GGGTCTCCAA
378801 CGTTTATGTT
1 CGTTTATGTT
378811 CGTTTATGTT
1 CGTTTATGTT
378821 CGTGTTCAT-TT
1 CGT-TT-ATGTT
* **
378832 ATGTTCGTGTT
1 -CGTTTATGTT
378843 CGTTTATGTT
1 CGTTTATGTT
378853 CG----TGTT
1 CGTTTATGTT
378859 CGTTTATGTT
1 CGTTTATGTT
378869 CGTTTAT
1 CGTTTAT
378876 TTATTAAATG
Statistics
Matches: 51, Mismatches: 6, Indels: 16
0.70 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
10 34 0.67
11 7 0.14
12 4 0.08
ACGTcount: A:0.09, C:0.12, G:0.21, T:0.57
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:378832 original size:16 final size:16
Alignment explanation
Indices: 378807--378871 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
378797 CCAACGTTTA
378807 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
*
378823 TGTTCATTTATGTTCG
1 TGTTCGTTTATGTTCG
378839 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
378855 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
378871 T
1 T
378872 TTATTTATTA
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.08, C:0.12, G:0.23, T:0.57
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:378962 original size:16 final size:16
Alignment explanation
Indices: 378941--378973 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
378931 AAAAAAATTT
378941 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
378957 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
378973 T
1 T
378974 CTATTTATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:379445 original size:25 final size:24
Alignment explanation
Indices: 379411--379458 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
379401 AATGTTTGGA
379411 AAATATA-TTTAATATAAAATAATT
1 AAATATATTTTAAT-TAAAATAATT
*
379435 AAATATGATTTTAATTAAATTAAT
1 AAATAT-ATTTTAATTAAAATAAT
379459 ATCGGCATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 9 0.43
26 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATATATTTTAATTAAAATAATT
Found at i:379573 original size:25 final size:24
Alignment explanation
Indices: 379539--379586 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
379529 AATGTTTGGA
379539 AAATATA-TTTAATATAAAATAATT
1 AAATATATTTTAAT-TAAAATAATT
*
379563 AAATATGATTTTAATTAAATTAAT
1 AAATAT-ATTTTAATTAAAATAAT
379587 ATCGGCATCC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 9 0.43
26 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (24 bp):
AAATATATTTTAATTAAAATAATT
Found at i:379609 original size:128 final size:128
Alignment explanation
Indices: 379381--379638 Score: 498
Period size: 128 Copynumber: 2.0 Consensus size: 128
379371 TCCAAGTTCG
379381 ATTTCTTGAAAATGAAATATAATGTTTGGAAAATATATTTAATATAAAATAATTAAATATGATTT
1 ATTTCTTGAAAATGAAATATAATGTTTGGAAAATATATTTAATATAAAATAATTAAATATGATTT
*
379446 TAATTAAATTAATATCGGCATCCTTATGATATTTCAAAGGTCATGGATTTAATATACTGACTA
66 TAATTAAATTAATATCGGCATCCTTATGATATTTCAAAGGTCATGGATATAATATACTGACTA
379509 ATTTCTTGAAAATGAAATATAATGTTTGGAAAATATATTTAATATAAAATAATTAAATATGATTT
1 ATTTCTTGAAAATGAAATATAATGTTTGGAAAATATATTTAATATAAAATAATTAAATATGATTT
*
379574 TAATTAAATTAATATCGGCATCCTTATGATATTTCAAAGGTCGTGGATATAATATACTGACTA
66 TAATTAAATTAATATCGGCATCCTTATGATATTTCAAAGGTCATGGATATAATATACTGACTA
379637 AT
1 AT
379639 CTAAATTGGA
Statistics
Matches: 128, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
128 128 1.00
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (128 bp):
ATTTCTTGAAAATGAAATATAATGTTTGGAAAATATATTTAATATAAAATAATTAAATATGATTT
TAATTAAATTAATATCGGCATCCTTATGATATTTCAAAGGTCATGGATATAATATACTGACTA
Found at i:381251 original size:4 final size:4
Alignment explanation
Indices: 381242--381329 Score: 53
Period size: 4 Copynumber: 23.5 Consensus size: 4
381232 ATAATTATTT
* * * * *
381242 TATA TATA TATA TACA -ATA T-TA -ATA AATT TAAA T-TA AATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
381286 TATA TATA TATA TAT- TATT TATA TATT TA-A TTTA AATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
381330 CTCGGCCCGA
Statistics
Matches: 62, Mismatches: 16, Indels: 12
0.69 0.18 0.13
Matches are distributed among these distances:
3 11 0.18
4 51 0.82
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (4 bp):
TATA
Found at i:381253 original size:6 final size:6
Alignment explanation
Indices: 381242--381329 Score: 53
Period size: 6 Copynumber: 15.7 Consensus size: 6
381232 ATAATTATTT
* * * * *
381242 TATATA TATATA TACA-A TAT-TA -ATAAA TTTAAA T-TAAA TATATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATATA
* * * *
381286 TATATA TATATA TAT-TA TTTATA TATTTA -ATTTA AATATA TATA
1 TATATA TATATA TATATA TATATA TATATA TATATA TATATA TATA
381330 CTCGGCCCGA
Statistics
Matches: 66, Mismatches: 10, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
4 2 0.03
5 19 0.29
6 45 0.68
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATA
Found at i:381314 original size:42 final size:42
Alignment explanation
Indices: 381242--381329 Score: 131
Period size: 42 Copynumber: 2.1 Consensus size: 42
381232 ATAATTATTT
381242 TATATATATATATACAATATTAATAAATTTAAATTAAATATA
1 TATATATATATATACAATATTAATAAATTTAAATTAAATATA
* * * * *
381284 TATATATATATATATATTATTTATATATTTAATTTAAATATA
1 TATATATATATATACAATATTAATAAATTTAAATTAAATATA
381326 TATA
1 TATA
381330 CTCGGCCCGA
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 41 1.00
ACGTcount: A:0.50, C:0.01, G:0.00, T:0.49
Consensus pattern (42 bp):
TATATATATATATACAATATTAATAAATTTAAATTAAATATA
Found at i:381589 original size:26 final size:26
Alignment explanation
Indices: 381553--381605 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
381543 CAATATAAAC
*
381553 AAATTATATATTAG-GGGTAGGAATGG
1 AAATTACATATT-GCGGGTAGGAATGG
*
381579 AAATTACATATTGCGGGTGGGAATGG
1 AAATTACATATTGCGGGTAGGAATGG
381605 A
1 A
381606 CATTCGATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 1 0.04
26 23 0.96
ACGTcount: A:0.36, C:0.04, G:0.32, T:0.28
Consensus pattern (26 bp):
AAATTACATATTGCGGGTAGGAATGG
Found at i:381771 original size:36 final size:36
Alignment explanation
Indices: 381704--381773 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
381694 TTAACCCAAG
381704 CATAATTGTATAATTTACCTATCAATATATATTTAAA
1 CATAATTGTATAA-TTACCTATCAATATATATTTAAA
* * *
381741 CATAATTGCTATAA-TACCTCTCTATTTATATTT
1 CATAATTG-TATAATTACCTATCAATATATATTT
381774 TTTTAACCGG
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
36 16 0.55
37 8 0.28
38 5 0.17
ACGTcount: A:0.37, C:0.14, G:0.03, T:0.46
Consensus pattern (36 bp):
CATAATTGTATAATTACCTATCAATATATATTTAAA
Found at i:381815 original size:10 final size:10
Alignment explanation
Indices: 381800--381831 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
381790 ATTTTATCTA
381800 ATAAATATAT
1 ATAAATATAT
381810 ATAAATATAT
1 ATAAATATAT
*
381820 ATATATATAT
1 ATAAATATAT
381830 AT
1 AT
381832 GTCAAATCGA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (10 bp):
ATAAATATAT
Found at i:383671 original size:21 final size:20
Alignment explanation
Indices: 383631--383672 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
383621 ATATTTTATA
*
383631 ATTTAAATTTATTTAAAAAT
1 ATTTAAATTAATTTAAAAAT
*
383651 ATTTAAATTAAATTTATAAAT
1 ATTTAAATT-AATTTAAAAAT
383672 A
1 A
383673 AATTATTCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
ATTTAAATTAATTTAAAAAT
Found at i:384674 original size:60 final size:60
Alignment explanation
Indices: 384610--384728 Score: 152
Period size: 60 Copynumber: 2.0 Consensus size: 60
384600 TAAATTATCT
* *
384610 TCGATTATA-AGATATTATTTAATCGAA-TCATTTGATTATTAAAAGTTATAAAATAGTCAA
1 TCGATTATAGAGA-ATTATTTAAT-GAAGTCATTTAACTATTAAAAGTTATAAAATAGTCAA
* ** *
384670 TCGATTATAGAGAGTTATTTTGTTAAGTCATTTAACTATTAAAAGTTATAAAATAGTCA
1 TCGATTATAGAGAATTATTTAATGAAGTCATTTAACTATTAAAAGTTATAAAATAGTCA
384729 TCTGACTATT
Statistics
Matches: 51, Mismatches: 6, Indels: 4
0.84 0.10 0.07
Matches are distributed among these distances:
59 2 0.04
60 46 0.90
61 3 0.06
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (60 bp):
TCGATTATAGAGAATTATTTAATGAAGTCATTTAACTATTAAAAGTTATAAAATAGTCAA
Found at i:388750 original size:2 final size:2
Alignment explanation
Indices: 388743--388773 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
388733 TGCACGCTTT
388743 TA TA TA TA TA TA T- TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
388774 ACTGAGCGTG
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:390840 original size:189 final size:182
Alignment explanation
Indices: 390521--390917 Score: 731
Period size: 189 Copynumber: 2.1 Consensus size: 182
390511 TATGAGACTG
390521 GTGTGTTGGATTAATGGATAAAAATAAGAACAAAAGGATGCTAAGTCTTTGATGGATTCAATGTT
1 GTGTGTTGGATTAATGGATAAAAATAAGAACAAAAGGATGCTAAGTCTTTGATGGATTCAATGTT
390586 GTTTTGATCTTTCTTAACGCCAATAGGGGGACCGAGTTGTTGATTTTGCCTTTTTCGTGTGTTGG
66 GTTTTGATCTTTCTTAACGCCAATAGGGGGACCGAGTTGTTGATTTTGCCTTTTTCGTGTGTTGG
390651 ATTAGTCTTTTTTCAATGCCAATAGGATGGCAGATGTTGATTTTTCCCATTTGT
131 ATTAGTCTTTTTTCAATGCCAATAGGATGGCAGATGTTGATTTTTCCCA-TT-T
390705 GTGTGTTGGATTAATGGATAAAAATAAGAACAAAAGGATGCTAAGTCTTTTACTGATGGATTCAA
1 GTGTGTTGGATTAATGGATAAAAATAAGAACAAAAGGATGCTAAGTC--TT--TGATGGATTCAA
390770 TGTTGTTTTGATCTTTTCTTAACGCCAATAGGGGGACCGAGTTGTTGATTTTGCCTTTTTCGTGT
62 TGTTGTTTTGATC-TTTCTTAACGCCAATAGGGGGACCGAGTTGTTGATTTTGCCTTTTTCGTGT
390835 GTTGGATTAGTCTTTTTTCAATGCCAATAGGATGGCAGATGTTGATTTTTCCCATTT
126 GTTGGATTAGTCTTTTTTCAATGCCAATAGGATGGCAGATGTTGATTTTTCCCATTT
390892 GTGTGTTGGATTAATGGATAAAAATA
1 GTGTGTTGGATTAATGGATAAAAATA
390918 GTGATAACAT
Statistics
Matches: 208, Mismatches: 0, Indels: 7
0.97 0.00 0.03
Matches are distributed among these distances:
184 47 0.23
186 2 0.01
187 27 0.13
188 27 0.13
189 105 0.50
ACGTcount: A:0.25, C:0.11, G:0.24, T:0.40
Consensus pattern (182 bp):
GTGTGTTGGATTAATGGATAAAAATAAGAACAAAAGGATGCTAAGTCTTTGATGGATTCAATGTT
GTTTTGATCTTTCTTAACGCCAATAGGGGGACCGAGTTGTTGATTTTGCCTTTTTCGTGTGTTGG
ATTAGTCTTTTTTCAATGCCAATAGGATGGCAGATGTTGATTTTTCCCATTT
Found at i:393379 original size:35 final size:35
Alignment explanation
Indices: 393333--393399 Score: 134
Period size: 35 Copynumber: 1.9 Consensus size: 35
393323 AATCGAAGCA
393333 TTGTGATTGAGGGATATCTTCAACATAAGTGAGCG
1 TTGTGATTGAGGGATATCTTCAACATAAGTGAGCG
393368 TTGTGATTGAGGGATATCTTCAACATAAGTGA
1 TTGTGATTGAGGGATATCTTCAACATAAGTGA
393400 TTATGATCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.33
Consensus pattern (35 bp):
TTGTGATTGAGGGATATCTTCAACATAAGTGAGCG
Found at i:393437 original size:16 final size:16
Alignment explanation
Indices: 393413--393445 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
393403 TGATCTCATC
*
393413 GGCGGCCACCATGTTT
1 GGCGACCACCATGTTT
393429 GGCGACCACCATGTTT
1 GGCGACCACCATGTTT
393445 G
1 G
393446 TATGATAGGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.15, C:0.30, G:0.30, T:0.24
Consensus pattern (16 bp):
GGCGACCACCATGTTT
Found at i:394687 original size:13 final size:14
Alignment explanation
Indices: 394662--394688 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
394652 ACGAAAGAAT
394662 TGAAATAAAAAAAA
1 TGAAATAAAAAAAA
394676 TGAAATAAAAAAA
1 TGAAATAAAAAAA
394689 GTAATAAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.78, C:0.00, G:0.07, T:0.15
Consensus pattern (14 bp):
TGAAATAAAAAAAA
Found at i:394934 original size:20 final size:20
Alignment explanation
Indices: 394909--394978 Score: 104
Period size: 20 Copynumber: 3.5 Consensus size: 20
394899 TTTCCAATTT
394909 GCAATGCGAATAAGTAAATC
1 GCAATGCGAATAAGTAAATC
394929 GCAATGCGAATAAGTAAATC
1 GCAATGCGAATAAGTAAATC
** *
394949 GCAATGCGAATTTGGAAAATC
1 GCAATGCGAA-TAAGTAAATC
394970 GCAATGCGA
1 GCAATGCGA
394979 TACTGACTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 30 0.65
21 16 0.35
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (20 bp):
GCAATGCGAATAAGTAAATC
Found at i:394993 original size:20 final size:20
Alignment explanation
Indices: 394977--395020 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
394967 ATCGCAATGC
*
394977 GATACTGACTTTCGCAACGA
1 GATACTAACTTTCGCAACGA
*
394997 TATACTAACTTTCGCAACGA
1 GATACTAACTTTCGCAACGA
395017 GATA
1 GATA
395021 ATACATAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.34, C:0.23, G:0.16, T:0.27
Consensus pattern (20 bp):
GATACTAACTTTCGCAACGA
Found at i:395244 original size:20 final size:21
Alignment explanation
Indices: 395205--395244 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
395195 CACTCTCTCA
395205 CCCATCTCCGACGAAATCCGT
1 CCCATCTCCGACGAAATCCGT
*
395226 CCCATCTCCGGCG-AATCCG
1 CCCATCTCCGACGAAATCCG
395245 CTATCTCCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.20, C:0.45, G:0.17, T:0.17
Consensus pattern (21 bp):
CCCATCTCCGACGAAATCCGT
Found at i:395575 original size:20 final size:20
Alignment explanation
Indices: 395506--395574 Score: 102
Period size: 20 Copynumber: 3.5 Consensus size: 20
395496 TTTATTCTCT
395506 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
395526 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCAAATTCG
* **
395546 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATAGTCAAATTCG
*
395566 TGTTGCGAT
1 CGTTGCGAT
395575 TTTCATTTTC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.19, C:0.19, G:0.26, T:0.36
Consensus pattern (20 bp):
CGTTGCGATAGTCAAATTCG
Found at i:395580 original size:20 final size:20
Alignment explanation
Indices: 395506--395584 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 20
395496 TTTATTCTCT
* **
395506 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
* **
395526 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATTGTCATTTTCG
395546 CGTTGCGATTGTCATTTTCG
1 CGTTGCGATTGTCATTTTCG
* *
395566 TGTTGCGATTTTCATTTTC
1 CGTTGCGATTGTCATTTTC
395585 AGAAATTGTT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 54 1.00
ACGTcount: A:0.18, C:0.19, G:0.23, T:0.41
Consensus pattern (20 bp):
CGTTGCGATTGTCATTTTCG
Found at i:399314 original size:28 final size:28
Alignment explanation
Indices: 399274--399333 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
399264 CATAAACTGA
** *
399274 TATTTTTTGTCAAAATAGATACCTAAAT
1 TATTTTTAATCAAAATAGATACCTAAAG
* *
399302 TATTTTTAATCAAAATAGGTACTTAAAG
1 TATTTTTAATCAAAATAGATACCTAAAG
399330 TATT
1 TATT
399334 CAATTTTTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.43
Consensus pattern (28 bp):
TATTTTTAATCAAAATAGATACCTAAAG
Found at i:402812 original size:16 final size:16
Alignment explanation
Indices: 402791--402823 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
402781 TAATAAATAA
402791 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
402807 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
402823 A
1 A
402824 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:402903 original size:10 final size:10
Alignment explanation
Indices: 402888--402961 Score: 59
Period size: 10 Copynumber: 7.6 Consensus size: 10
402878 CATTTAATAA
402888 ATAAACGAAC
1 ATAAACGAAC
402898 ATAAACGAAC
1 ATAAACGAAC
402908 ----ACGAAC
1 ATAAACGAAC
402914 ATAAACGAAC
1 ATAAACGAAC
** *
402924 ACGAAC-ATAA
1 ATAAACGA-AC
402934 ATGAACACGAAC
1 AT-AA-ACGAAC
402946 ATAAACGAAC
1 ATAAACGAAC
402956 ATAAAC
1 ATAAAC
402962 ATTGGAGGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 16
0.69 0.08 0.22
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.68
11 3 0.06
12 5 0.10
13 1 0.02
ACGTcount: A:0.58, C:0.22, G:0.11, T:0.09
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:402963 original size:16 final size:16
Alignment explanation
Indices: 402892--402956 Score: 121
Period size: 16 Copynumber: 4.1 Consensus size: 16
402882 TAATAAATAA
402892 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
402908 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
402924 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
402940 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
402956 A
1 A
402957 TAAACATTGG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 47 1.00
ACGTcount: A:0.57, C:0.23, G:0.12, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:402963 original size:32 final size:32
Alignment explanation
Indices: 402895--402963 Score: 111
Period size: 32 Copynumber: 2.2 Consensus size: 32
402885 TAAATAAACG
*
402895 AACATAAACGAACACGAACATAAACGAACACG
1 AACATAAACGAACACGAACATAAACGAACACA
* *
402927 AACATAAATGAACACGAACATAAACGAACATA
1 AACATAAACGAACACGAACATAAACGAACACA
402959 AACAT
1 AACAT
402964 TGGAGGCCCT
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.58, C:0.22, G:0.10, T:0.10
Consensus pattern (32 bp):
AACATAAACGAACACGAACATAAACGAACACA
Found at i:403722 original size:14 final size:14
Alignment explanation
Indices: 403705--403737 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
403695 GAATGAACAT
403705 AAACGAACATAACC
1 AAACGAACATAACC
403719 AAACGAACATAACC
1 AAACGAACATAACC
*
403733 GAACG
1 AAACG
403738 TTCACGAACG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.55, C:0.27, G:0.12, T:0.06
Consensus pattern (14 bp):
AAACGAACATAACC
Found at i:410352 original size:21 final size:22
Alignment explanation
Indices: 410326--410375 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 22
410316 AGTACTGATG
410326 TGACAGTTC-ACAAT-CATAACA
1 TGACAGTTCTACAATGC-TAACA
*
410347 TGACAG-TCTACAATGCTAATA
1 TGACAGTTCTACAATGCTAACA
410368 TGACAGTT
1 TGACAGTT
410376 TAGGGTGACA
Statistics
Matches: 25, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
20 2 0.08
21 21 0.84
22 2 0.08
ACGTcount: A:0.38, C:0.20, G:0.14, T:0.28
Consensus pattern (22 bp):
TGACAGTTCTACAATGCTAACA
Found at i:410869 original size:32 final size:32
Alignment explanation
Indices: 410833--410894 Score: 90
Period size: 32 Copynumber: 1.9 Consensus size: 32
410823 TTTTTTTATT
*
410833 TTTTATAATA-TTTAGATAAAATTTAATGATCA
1 TTTTATAACAGTTTAGAT-AAATTTAATGATCA
*
410865 TTTTATAACAGTTTTGATAAATTTAATGAT
1 TTTTATAACAGTTTAGATAAATTTAATGAT
410895 TTCATTGTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
32 21 0.78
33 6 0.22
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.48
Consensus pattern (32 bp):
TTTTATAACAGTTTAGATAAATTTAATGATCA
Found at i:411416 original size:36 final size:38
Alignment explanation
Indices: 411366--411442 Score: 97
Period size: 37 Copynumber: 2.1 Consensus size: 38
411356 GATTTTATAT
* **
411366 TAATGTTACAAATA-TTAAAATGTATATAA-TAATATTA
1 TAATGTTAAAAATATTTAAAAAAT-TATAATTAATATTA
411403 TAAT-TTAAAAATATTTAAAAAATTATAATTAATATTA
1 TAATGTTAAAAATATTTAAAAAATTATAATTAATATTA
411440 TAA
1 TAA
411443 ACATAAAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
36 13 0.37
37 22 0.63
ACGTcount: A:0.55, C:0.01, G:0.03, T:0.42
Consensus pattern (38 bp):
TAATGTTAAAAATATTTAAAAAATTATAATTAATATTA
Found at i:412013 original size:25 final size:26
Alignment explanation
Indices: 411985--412037 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
411975 ATTAAAATTT
411985 AATAAATTGAT-ATATAAATAATAAA
1 AATAAATTGATAATATAAATAATAAA
412010 AATAAATTGATAATATAAATAATAAA
1 AATAAATTGATAATATAAATAATAAA
412036 AA
1 AA
412038 CCTAACTTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 11 0.41
26 16 0.59
ACGTcount: A:0.66, C:0.00, G:0.04, T:0.30
Consensus pattern (26 bp):
AATAAATTGATAATATAAATAATAAA
Found at i:426004 original size:158 final size:154
Alignment explanation
Indices: 425762--426074 Score: 574
Period size: 158 Copynumber: 2.0 Consensus size: 154
425752 ATTTCATAGT
425762 TCAATGATTTATGTCTTTGTAGTTCATCTGTTAAACTGCTTCATCTTCTAATATTTCCTTATTAG
1 TCAATGATTTATGTCTTTGTAGTTCATCTGTTAAACTGCTTCATCTTCTAATATTTCCTTATTAG
425827 CCAGAAGGTCTTCCTGGG-TTCTAACCTATAGCATGGACATGCGACAAATCTTAGTCCTGATTGT
66 CCAGAAGGTCTTCCTGGGTTTCTAACCTATAGCATGGACATGCGAC-AATCTTAGTCCTGATTGT
425891 AATTATTAACTTTTATGAACATTGC
130 AATTATTAACTTTTATGAACATTGC
425916 TCAATGATTTATGTCTTTATGTAGTTCTCATCTGTTAAACTGCTTCATCTTCTAATATTTCCTTA
1 TCAATGATTTATGTC-TT-TGTAG-T-TCATCTGTTAAACTGCTTCATCTTCTAATATTTCCTTA
425981 TTAGCCAGAAGGTCTTCCTGGGTTTCTAACCTATAGCATGGACATGCGACAATCTTAGTCCTGAT
62 TTAGCCAGAAGGTCTTCCTGGGTTTCTAACCTATAGCATGGACATGCGACAATCTTAGTCCTGAT
426046 TGTAATTATTAACTTTTATGAACATTGC
127 TGTAATTATTAACTTTTATGAACATTGC
426074 T
1 T
426075 TTGACTTTCT
Statistics
Matches: 154, Mismatches: 0, Indels: 6
0.96 0.00 0.04
Matches are distributed among these distances:
154 15 0.10
155 2 0.01
156 5 0.03
157 1 0.01
158 104 0.68
159 27 0.18
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.41
Consensus pattern (154 bp):
TCAATGATTTATGTCTTTGTAGTTCATCTGTTAAACTGCTTCATCTTCTAATATTTCCTTATTAG
CCAGAAGGTCTTCCTGGGTTTCTAACCTATAGCATGGACATGCGACAATCTTAGTCCTGATTGTA
ATTATTAACTTTTATGAACATTGC
Found at i:444918 original size:15 final size:15
Alignment explanation
Indices: 444898--444927 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
444888 CGTCCGTCTC
444898 GTCTCGTCTCGTGGT
1 GTCTCGTCTCGTGGT
444913 GTCTCGTCTCGTGGT
1 GTCTCGTCTCGTGGT
444928 CGTGGTAATA
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:0.00, C:0.27, G:0.33, T:0.40
Consensus pattern (15 bp):
GTCTCGTCTCGTGGT
Found at i:447815 original size:32 final size:34
Alignment explanation
Indices: 447765--447866 Score: 106
Period size: 32 Copynumber: 3.1 Consensus size: 34
447755 TTTTTTAAAA
*
447765 ATTAAATATTAATTTTTTAATATTGTATTATAGAT
1 ATTAAATATTAATGTTTTAATATT-TATTATAGAT
* * *
447800 ATT-AATATT-A-GTTTTAAT-TTT-TTAAATAA
1 ATTAAATATTAATGTTTTAATATTTATTATAGAT
*
447829 ATTAAATATTAATTTTTTAATATTATATTATAGAT
1 ATTAAATATTAATGTTTTAATATT-TATTATAGAT
447864 ATT
1 ATT
447867 TAATTTTATA
Statistics
Matches: 53, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
29 8 0.15
30 7 0.13
31 3 0.06
32 14 0.26
33 3 0.06
34 7 0.13
35 11 0.21
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (34 bp):
ATTAAATATTAATGTTTTAATATTTATTATAGAT
Found at i:448392 original size:31 final size:31
Alignment explanation
Indices: 448355--448414 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
448345 TAGTTGTATG
* *
448355 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATATCAGTATTGCAAAACTAA
448386 AATTATTTAAATATCAGTATTGCAAAACT
1 AATTATTTAAATATCAGTATTGCAAAACT
448415 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.07, T:0.40
Consensus pattern (31 bp):
AATTATTTAAATATCAGTATTGCAAAACTAA
Found at i:449762 original size:24 final size:24
Alignment explanation
Indices: 449718--449773 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
449708 ATATTATCAT
449718 TATTATTATAATAATAATAAT-AA
1 TATTATTATAATAATAATAATAAA
* * *
449741 TAATTATTATTATATTATTAATAAA
1 T-ATTATTATAATAATAATAATAAA
449766 TATTATTA
1 TATTATTA
449774 CAGACCCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
23 1 0.04
24 24 0.86
25 3 0.11
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TATTATTATAATAATAATAATAAA
Found at i:451079 original size:117 final size:115
Alignment explanation
Indices: 450991--451219 Score: 284
Period size: 117 Copynumber: 2.0 Consensus size: 115
450981 GTTTTAATAT
* * * * *
450991 TTATTTATTTTTTAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTGGATGTCCATTTTCTGATA
1 TTATATATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAG-CCATTTTCTGATA
*
451054 TTTTTAAATAAATAAATATTTTATTTTTTTAAATCATATATTAATTATTTTAA
65 TTTCTAAATAAATAAATATTTTA--TTTTTAAATCATATATTAATTATTTTAA
* ** **
451107 TTATATATTTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCGCCTAGAAGCCATTTTCTGATAT
1 TTATATATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCATTTTCTGATAT
* *
451172 TTCTAAATAAATAAATATTTTATTTATAAATATATATATTAA-TATTTT
66 TTCTAAATAAATAAATATTTTATTTTTAAAT-CATATATTAATTATTTT
451220 TCATAATTAT
Statistics
Matches: 97, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
115 14 0.14
116 26 0.27
117 38 0.39
118 19 0.20
ACGTcount: A:0.38, C:0.08, G:0.09, T:0.46
Consensus pattern (115 bp):
TTATATATTTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGCCATTTTCTGATAT
TTCTAAATAAATAAATATTTTATTTTTAAATCATATATTAATTATTTTAA
Found at i:451094 original size:22 final size:21
Alignment explanation
Indices: 451069--451117 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
451059 AAATAAATAA
*
451069 ATATTTTATTTTTTTAAATCAT
1 ATATTTTATTATTTT-AATCAT
* *
451091 ATA-TTAATTATTTTAATTAT
1 ATATTTTATTATTTTAATCAT
451111 ATATTTT
1 ATATTTT
451118 TTAATATCGA
Statistics
Matches: 22, Mismatches: 4, Indels: 3
0.76 0.14 0.10
Matches are distributed among these distances:
20 8 0.36
21 11 0.50
22 3 0.14
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (21 bp):
ATATTTTATTATTTTAATCAT
Found at i:452481 original size:27 final size:28
Alignment explanation
Indices: 452451--452504 Score: 67
Period size: 30 Copynumber: 1.9 Consensus size: 28
452441 CATATTCTAT
452451 TAGAA-GT-CCTTATACTATATGTTTTTA
1 TAGAATGTCCCTTATACTATA-GTTTTTA
*
452478 TAGAATTGTCCCTTATATTATAGTTTT
1 TAGAA-TGTCCCTTATACTATAGTTTT
452505 ATTATTTCAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
29 7 0.30
30 11 0.48
ACGTcount: A:0.28, C:0.11, G:0.11, T:0.50
Consensus pattern (28 bp):
TAGAATGTCCCTTATACTATAGTTTTTA
Found at i:465277 original size:23 final size:23
Alignment explanation
Indices: 465210--465296 Score: 79
Period size: 23 Copynumber: 3.7 Consensus size: 23
465200 TCATATAAAT
*
465210 TTGCACCGTAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
*
465233 TTTTGTC-CCGAAG-GACCGCGTAGAA
1 --TTG-CACCGAAGTG-CCACGTAGAA
*
465258 ATGCACCGAAGTGCCACGTAGAA
1 TTGCACCGAAGTGCCACGTAGAA
* *
465281 TTGAACCGTAGTGCCA
1 TTGCACCGAAGTGCCA
465297 TATAATATGT
Statistics
Matches: 51, Mismatches: 7, Indels: 10
0.75 0.10 0.15
Matches are distributed among these distances:
22 1 0.02
23 30 0.59
24 2 0.04
25 17 0.33
26 1 0.02
ACGTcount: A:0.28, C:0.25, G:0.26, T:0.21
Consensus pattern (23 bp):
TTGCACCGAAGTGCCACGTAGAA
Found at i:471568 original size:64 final size:64
Alignment explanation
Indices: 471451--471571 Score: 149
Period size: 65 Copynumber: 1.9 Consensus size: 64
471441 AACTGGTGTT
* * *
471451 GACCTGAACCCGATTTGGACCTGGAAATTATGGATCCGAACCCGACTTGCATCCGACCTGAGAAC
1 GACCTGAACCCGAATTGAACC-GGAAAATATGGATCCGAACCCGACTTGCATCCGACCTGAGAAC
*
471516 GACCTGAACCCGAATTGAACC-GAAAATAT-GATACCCGAACTCGAAC-TGCATCCGAC
1 GACCTGAACCCGAATTGAACCGGAAAATATGGAT--CCGAACCCG-ACTTGCATCCGAC
471572 TGATATGAAC
Statistics
Matches: 49, Mismatches: 4, Indels: 7
0.82 0.07 0.12
Matches are distributed among these distances:
62 3 0.06
63 7 0.14
64 18 0.37
65 21 0.43
ACGTcount: A:0.31, C:0.30, G:0.21, T:0.18
Consensus pattern (64 bp):
GACCTGAACCCGAATTGAACCGGAAAATATGGATCCGAACCCGACTTGCATCCGACCTGAGAAC
Found at i:471639 original size:16 final size:16
Alignment explanation
Indices: 471622--471708 Score: 120
Period size: 16 Copynumber: 5.4 Consensus size: 16
471612 GGTATTACCC
*
471622 GACCTGTTTTCAACCC
1 GACCTGTTTTCAACCT
*
471638 GACTTGTTTTCAACCT
1 GACCTGTTTTCAACCT
471654 GACCTGTTTTCAACCT
1 GACCTGTTTTCAACCT
* *
471670 GACATGTTTTTAACCT
1 GACCTGTTTTCAACCT
* *
471686 GACCTGTTTTTAACCG
1 GACCTGTTTTCAACCT
471702 GACCTGT
1 GACCTGT
471709 AAATGATCCG
Statistics
Matches: 64, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 64 1.00
ACGTcount: A:0.20, C:0.28, G:0.15, T:0.38
Consensus pattern (16 bp):
GACCTGTTTTCAACCT
Found at i:471981 original size:14 final size:14
Alignment explanation
Indices: 471959--472005 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
471949 TGTGAAGGAA
*
471959 AATTAATATAGTTT
1 AATTTATATAGTTT
471973 AATTTATATA----
1 AATTTATATAGTTT
471983 AA-TTATATAGTTT
1 AATTTATATAGTTT
471996 AATTTATATA
1 AATTTATATA
472006 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:471992 original size:23 final size:24
Alignment explanation
Indices: 471958--472007 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
471948 ATGTGAAGGA
471958 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
471982 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
472005 AAA
1 AAA
472008 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:475289 original size:102 final size:99
Alignment explanation
Indices: 475113--475340 Score: 348
Period size: 102 Copynumber: 2.3 Consensus size: 99
475103 ATAAACAACG
*
475113 AACAGTAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGACAGCTAACAACCTTATAAA
1 AACAGTAGCAACAAATTAAACAGTTTATTTAAACTCTAAATAAAGACAGCTAACAACCTTATAAA
475178 AACAATCCGAATGAACAACCAACAACACAAACAAATC
66 AACAATCCGAATGAA-AA--AACAACACAAACAAATC
* * * *
475215 AACAGTAGCAACAAATTGAACAGTTTATTTAAACTCTAAATAAAGGCATCTAACAACCTTATAGA
1 AACAGTAGCAACAAATTAAACAGTTTATTTAAACTCTAAATAAAGACAGCTAACAACCTTATAAA
** *
475280 AGTAATCCGAATGAAAAACCAACACAAACAAATC
66 AACAATCCGAATGAAAAAACAACACAAACAAATC
*
475314 AACAGTAGCAACAAATTAAACATTTTA
1 AACAGTAGCAACAAATTAAACAGTTTA
475341 GTTACCTCTT
Statistics
Matches: 116, Mismatches: 10, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
99 41 0.35
101 2 0.02
102 73 0.63
ACGTcount: A:0.51, C:0.19, G:0.09, T:0.21
Consensus pattern (99 bp):
AACAGTAGCAACAAATTAAACAGTTTATTTAAACTCTAAATAAAGACAGCTAACAACCTTATAAA
AACAATCCGAATGAAAAAACAACACAAACAAATC
Found at i:475580 original size:32 final size:32
Alignment explanation
Indices: 475512--475614 Score: 136
Period size: 33 Copynumber: 3.1 Consensus size: 32
475502 TGAAACCCTT
* *
475512 GAAAGAAAGGATTCAAATATCAACCAAAAAACAGA
1 GAAA-AAACGATTC-AATATCAACC-AAAAATAGA
475547 GAAAAAA-GATTCGAATATCAACCAAAAATAGA
1 GAAAAAACGATTC-AATATCAACCAAAAATAGA
475579 GAAAAAACGATTCAATTATCAACCAAAAATAGA
1 GAAAAAACGATTCAA-TATCAACCAAAAATAGA
475612 GAA
1 GAA
475615 TTTGAGAGAA
Statistics
Matches: 64, Mismatches: 2, Indels: 6
0.89 0.03 0.08
Matches are distributed among these distances:
32 17 0.27
33 40 0.62
34 3 0.05
35 4 0.06
ACGTcount: A:0.59, C:0.14, G:0.13, T:0.15
Consensus pattern (32 bp):
GAAAAAACGATTCAATATCAACCAAAAATAGA
Found at i:475664 original size:22 final size:22
Alignment explanation
Indices: 475638--475686 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
475628 GAGAGCTAGT
475638 GAGATCAAAATGAGAGAAATGA
1 GAGATCAAAATGAGAGAAATGA
*
475660 GAGATCAAAATGAGATAAATGA
1 GAGATCAAAATGAGAGAAATGA
475682 GAGAT
1 GAGAT
475687 AACCAGTGTG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.53, C:0.04, G:0.27, T:0.16
Consensus pattern (22 bp):
GAGATCAAAATGAGAGAAATGA
Found at i:477435 original size:20 final size:21
Alignment explanation
Indices: 477410--477458 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 21
477400 GTAAGGGTTA
477410 AGGTTTAGGATT-TAAAGTTT
1 AGGTTTAGGATTATAAAGTTT
*
477430 AGGTTTA-GATTATCAAGTTT
1 AGGTTTAGGATTATAAAGTTT
477450 AGGGTTTAG
1 A-GGTTTAG
477459 AGTTTTTATA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
19 4 0.16
20 15 0.60
21 6 0.24
ACGTcount: A:0.29, C:0.02, G:0.27, T:0.43
Consensus pattern (21 bp):
AGGTTTAGGATTATAAAGTTT
Found at i:477611 original size:18 final size:18
Alignment explanation
Indices: 477588--477658 Score: 52
Period size: 18 Copynumber: 3.6 Consensus size: 18
477578 GTACTATAAG
477588 TTACATATATAGTTTACA
1 TTACATATATAGTTTACA
* * *
477606 TTACATGTATACATATACTATAA
1 TTACATATATA-GT-T--TA-CA
477629 GTTACATATATAGTTTACA
1 -TTACATATATAGTTTACA
*
477648 TTACATGTATA
1 TTACATATATA
477659 CACATACTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 12
0.68 0.12 0.20
Matches are distributed among these distances:
18 20 0.50
19 2 0.05
20 3 0.08
22 3 0.08
23 2 0.05
24 10 0.25
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.42
Consensus pattern (18 bp):
TTACATATATAGTTTACA
Found at i:477618 original size:42 final size:42
Alignment explanation
Indices: 477572--477681 Score: 202
Period size: 42 Copynumber: 2.6 Consensus size: 42
477562 TAGTTTATAC
*
477572 ATACATGTACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
477614 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
1 ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
*
477656 ATACACATACTATAAGTTACATATAT
1 ATACATATACTATAAGTTACATATAT
477682 TAACTATTGT
Statistics
Matches: 66, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 66 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (42 bp):
ATACATATACTATAAGTTACATATATAGTTTACATTACATGT
Found at i:477633 original size:24 final size:24
Alignment explanation
Indices: 477606--477677 Score: 66
Period size: 24 Copynumber: 3.2 Consensus size: 24
477596 ATAGTTTACA
477606 TTACATGTATACATATACTATAAG
1 TTACATGTATACATATACTATAAG
* * *
477630 TTACATATATA-GT-T--TA-CA-
1 TTACATGTATACATATACTATAAG
*
477648 TTACATGTATACACATACTATAAG
1 TTACATGTATACATATACTATAAG
477672 TTACAT
1 TTACAT
477678 ATATTAACTA
Statistics
Matches: 35, Mismatches: 7, Indels: 12
0.65 0.13 0.22
Matches are distributed among these distances:
18 10 0.29
19 1 0.03
20 3 0.09
22 3 0.09
23 2 0.06
24 16 0.46
ACGTcount: A:0.40, C:0.14, G:0.07, T:0.39
Consensus pattern (24 bp):
TTACATGTATACATATACTATAAG
Found at i:477993 original size:77 final size:75
Alignment explanation
Indices: 477904--478093 Score: 179
Period size: 77 Copynumber: 2.5 Consensus size: 75
477894 AATATATATA
*
477904 TATATATCTATATA--T-TACTTATATTAGTTATGCATACATATATATACTATATTAATATAAAT
1 TATATATCTATATAGTTATACATATA-TAGTT-T--ATACATATATATACTATATTAATATAAAT
*
477966 TATAACATATAAAC
62 AATAACATATAAAC
* * * *
477980 TATATAGTTTATATAGTTTATACATATATAGTTTATATATATATATAGTATATTAATATATATAA
1 TATATA-TCTATATAG-TTATACATATATAGTTTATACATATATATACTATATTAATATAAATAA
***
478045 TATTTTATAAAC
64 TAACATATAAAC
* * *
478057 TATATATTTTTTGTAGTTTATACATATATAGTTTATA
1 TATATA-TCTATATAG-TTATACATATATAGTTTATA
478094 TACATAGTTT
Statistics
Matches: 97, Mismatches: 12, Indels: 9
0.82 0.10 0.08
Matches are distributed among these distances:
76 6 0.06
77 77 0.79
79 1 0.01
80 6 0.06
81 7 0.07
ACGTcount: A:0.42, C:0.05, G:0.05, T:0.48
Consensus pattern (75 bp):
TATATATCTATATAGTTATACATATATAGTTTATACATATATATACTATATTAATATAAATAATA
ACATATAAAC
Found at i:478009 original size:15 final size:15
Alignment explanation
Indices: 477989--478024 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
477979 CTATATAGTT
477989 TATATAGTTTATACA
1 TATATAGTTTATACA
*
478004 TATATAGTTTATATA
1 TATATAGTTTATACA
478019 TATATA
1 TATATA
478025 TAGTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.42, C:0.03, G:0.06, T:0.50
Consensus pattern (15 bp):
TATATAGTTTATACA
Found at i:478019 original size:13 final size:13
Alignment explanation
Indices: 477989--478294 Score: 121
Period size: 13 Copynumber: 22.5 Consensus size: 13
477979 CTATATAGTT
477989 TATATAGTTTATACA
1 TATATAGTTTAT--A
478004 TATATAGTTTATA
1 TATATAGTTTATA
*
478017 TATATA-TATAGTA
1 TATATAGTTTA-TA
* *
478030 TAT-TAATATATA
1 TATATAGTTTATA
*
478042 TA-ATATTTTATAAA
1 TATATAGTTTAT--A
478056 CTATATA-TTT-T-
1 -TATATAGTTTATA
*
478067 T-TGTAGTTTATACA
1 TATATAGTTTAT--A
478081 TATATAGTTTATA
1 TATATAGTTTATA
*
478094 TACATAGTTTATA
1 TATATAGTTTATA
*
478107 TATATAGTTCACATA
1 TATATAGTT--TATA
* * *
478122 AACATAATTTATA
1 TATATAGTTTATA
478135 TATATAGCTTATAATAA
1 TATATAG-TT-T-AT-A
478152 TTATATAGTTTATA
1 -TATATAGTTTATA
**
478166 -ATATA-AATATA
1 TATATAGTTTATA
* *
478177 GTTTATAATTTTATA
1 -TATAT-AGTTTATA
*
478192 TACATAGTTTATA
1 TATATAGTTTATA
**
478205 TATATAGTGCACATA
1 TATATAGT--TTATA
* *
478220 AATATAATTTATA
1 TATATAGTTTATA
478233 TATATAGTTTATAATAA
1 TATATAG-TT-T-AT-A
478250 TTATATAGTTTATA
1 -TATATAGTTTATA
*
478264 TATA-ATTTTATA
1 TATATAGTTTATA
*
478276 TTATATA-TATATA
1 -TATATAGTTTATA
478289 TATATA
1 TATATA
478295 TATTTTTTTC
Statistics
Matches: 224, Mismatches: 34, Indels: 69
0.69 0.10 0.21
Matches are distributed among these distances:
9 3 0.01
10 4 0.02
11 5 0.02
12 33 0.15
13 82 0.37
14 14 0.06
15 54 0.24
16 9 0.04
17 6 0.03
18 14 0.06
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (13 bp):
TATATAGTTTATA
Found at i:478062 original size:2 final size:2
Alignment explanation
Indices: 477895--478047 Score: 58
Period size: 2 Copynumber: 78.0 Consensus size: 2
477885 TATTTCTTTA
*
477895 AT AT AT AT AT AT AT AT CT AT AT AT -T ACT -T AT AT -T AGT -T AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT AT
** * * *
477935 GC AT AC AT AT AT AT ACT AT AT -T A- AT AT AA AT -T AT A- AC AT
1 AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * *
477974 AT AA ACT AT AT AGT TT AT AT AGT TT AT AC AT AT AT AGT TT AT AT
1 AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT AT A-T AT AT AT
478018 AT AT AT AT AGT AT AT -T A- AT AT AT AT A- AT AT
1 AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
478048 TTTATAAACT
Statistics
Matches: 111, Mismatches: 21, Indels: 38
0.65 0.12 0.22
Matches are distributed among these distances:
1 11 0.10
2 90 0.81
3 10 0.09
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.46
Consensus pattern (2 bp):
AT
Found at i:478094 original size:77 final size:77
Alignment explanation
Indices: 477941--478095 Score: 229
Period size: 77 Copynumber: 2.0 Consensus size: 77
477931 TTATGCATAC
*
477941 ATATATATACTATATTAATATAAATTATAACATATAAACTATATAGTTTATATAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATAGTTTATATAGTTTATACATA
478006 TATAGTTTATAT
66 TATAGTTTATAT
* * *** * * *
478018 ATATATATAGTATATTAATATATATAATATTTTATAAACTATATATTTTTTGTAGTTTATACATA
1 ATATATATACTATATTAATATAAATAATAACATATAAACTATATAGTTTATATAGTTTATACATA
478083 TATAGTTTATAT
66 TATAGTTTATAT
478095 A
1 A
478096 CATAGTTTAT
Statistics
Matches: 69, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.43, C:0.04, G:0.05, T:0.48
Consensus pattern (77 bp):
ATATATATACTATATTAATATAAATAATAACATATAAACTATATAGTTTATATAGTTTATACATA
TATAGTTTATAT
Found at i:478097 original size:17 final size:17
Alignment explanation
Indices: 477989--478099 Score: 64
Period size: 17 Copynumber: 6.1 Consensus size: 17
477979 CTATATAGTT
477989 TATATAG-TT-TATACA
1 TATATAGTTTATATACA
*
478004 TATATAGTTTATATATA
1 TATATAGTTTATATACA
* *
478021 TATATAGTATATTAATATA
1 TATATAGTTTA-T-ATACA
* *
478040 TATAATATTTTATAAACTA
1 TAT-ATAGTTTATATAC-A
**
478059 TATATTTTTTGTAGTTTATACA
1 TATA-TAGTT-TA---TATACA
478081 TATATAGTTTATATACA
1 TATATAGTTTATATACA
478098 TA
1 TA
478100 GTTTATATAT
Statistics
Matches: 75, Mismatches: 10, Indels: 20
0.71 0.10 0.19
Matches are distributed among these distances:
15 7 0.09
16 2 0.03
17 23 0.31
18 4 0.05
19 17 0.23
20 10 0.13
21 3 0.04
22 5 0.07
23 4 0.05
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (17 bp):
TATATAGTTTATATACA
Found at i:478126 original size:28 final size:26
Alignment explanation
Indices: 478070--478246 Score: 88
Period size: 28 Copynumber: 6.9 Consensus size: 26
478060 ATATTTTTTG
* *
478070 TAGTTTATACATATATAGTTTATATACA
1 TAGTTTAT--ATATATAGTTCATAAACA
478098 TAGTTTATATATATAGTTCACATAAACA
1 TAGTTTATATATATAGTT--CATAAACA
*
478126 TAATTTATATATATAGCTT-ATAATA-A
1 TAGTTTATATATATAG-TTCATAA-ACA
* * * *
478152 T--TATATAGTTTATA-AT-ATAAATA
1 TAGTTTATA-TATATAGTTCATAAACA
*
478175 TAGTTTATA-AT-T--TT-ATATACA
1 TAGTTTATATATATAGTTCATAAACA
* *
478196 TAGTTTATATATATAGTGCACATAAATA
1 TAGTTTATATATATAGT--TCATAAACA
* *
478224 TAATTTATATATATAGTTTATAA
1 TAGTTTATATATATAGTTCATAA
478247 TAATTATATA
Statistics
Matches: 117, Mismatches: 17, Indels: 32
0.70 0.10 0.19
Matches are distributed among these distances:
21 15 0.13
22 4 0.03
23 9 0.08
24 5 0.04
25 11 0.09
26 20 0.17
27 1 0.01
28 50 0.43
29 2 0.02
ACGTcount: A:0.43, C:0.05, G:0.06, T:0.46
Consensus pattern (26 bp):
TAGTTTATATATATAGTTCATAAACA
Found at i:478175 original size:18 final size:18
Alignment explanation
Indices: 478131--478294 Score: 95
Period size: 18 Copynumber: 8.6 Consensus size: 18
478121 AAACATAATT
*
478131 TATATATATAGCTTATAA
1 TATATATATAGTTTATAA
478149 TA-ATTATATAGTTTATAA
1 TATA-TATATAGTTTATAA
*
478167 TATAAATATAGTTTATAA
1 TATATATATAGTTTATAA
*
478185 TTTTATATACATAGTTTATATA
1 ---TATATATATAGTTTATA-A
* **
478207 TATAGTGCACATA-AATATAA
1 TATA-T--ATATAGTTTATAA
478227 TTTATATATATAGTTTATAA
1 --TATATATATAGTTTATAA
478247 TA-ATTATATAGTTTAT-A
1 TATA-TATATAGTTTATAA
*
478264 TATAATTTTATA-TTATATATA
1 TAT-A-TATATAGTT-TATA-A
478285 TATATATATA
1 TATATATATA
478295 TATTTTTTTC
Statistics
Matches: 117, Mismatches: 11, Indels: 35
0.72 0.07 0.21
Matches are distributed among these distances:
17 5 0.04
18 46 0.39
19 24 0.21
20 8 0.07
21 24 0.21
22 10 0.09
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.49
Consensus pattern (18 bp):
TATATATATAGTTTATAA
Found at i:478211 original size:98 final size:97
Alignment explanation
Indices: 478088--478268 Score: 326
Period size: 98 Copynumber: 1.9 Consensus size: 97
478078 ACATATATAG
*
478088 TTTATATACATAGTTTATATATATAGTTCACATAAACATAATTTATATATATAGCTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTGCACATAAACATAATTTATATATATAGCTTATAATAAT
478153 TATATAGTTTATAATATAAATATAGTTTATAAT
66 TATATAGTTTAT-ATATAAATATAGTTTATAAT
* *
478186 TTTATATACATAGTTTATATATATAGTGCACATAAATATAATTTATATATATAGTTTATAATAAT
1 TTTATATACATAGTTTATATATATAGTGCACATAAACATAATTTATATATATAGCTTATAATAAT
478251 TATATAGTTTATATATAA
66 TATATAGTTTATATATAA
478269 TTTTATATTA
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
97 6 0.08
98 74 0.93
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (97 bp):
TTTATATACATAGTTTATATATATAGTGCACATAAACATAATTTATATATATAGCTTATAATAAT
TATATAGTTTATATATAAATATAGTTTATAAT
Found at i:478236 original size:2 final size:2
Alignment explanation
Indices: 478229--478297 Score: 51
Period size: 2 Copynumber: 36.5 Consensus size: 2
478219 AAATATAATT
* *
478229 TA TA TA TA TA GTT TA TA -A TA -A T- TA TA TA GTT TA TA TA TA -A
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA
*
478269 T- TT TA TA T- TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
478298 TTTTTTCATT
Statistics
Matches: 54, Mismatches: 5, Indels: 16
0.72 0.07 0.21
Matches are distributed among these distances:
1 6 0.11
2 46 0.85
3 2 0.04
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (2 bp):
TA
Found at i:478263 original size:29 final size:25
Alignment explanation
Indices: 478230--478292 Score: 72
Period size: 29 Copynumber: 2.4 Consensus size: 25
478220 AATATAATTT
*
478230 ATATATATAGTTTATAATAATTATATAGT
1 ATATATATAATTT-T-AT-ATTATATA-T
*
478259 TTATATATAATTTTATATTATATAT
1 ATATATATAATTTTATATTATATAT
478284 ATATATATA
1 ATATATATA
478293 TATATTTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
25 9 0.29
26 8 0.26
27 2 0.06
28 1 0.03
29 11 0.35
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.52
Consensus pattern (25 bp):
ATATATATAATTTTATATTATATAT
Found at i:478281 original size:17 final size:18
Alignment explanation
Indices: 478233--478294 Score: 65
Period size: 19 Copynumber: 3.3 Consensus size: 18
478223 ATAATTTATA
478233 TATATAGTT-TATAATAAT
1 TATATAGTTATAT-ATAAT
478251 TATATAGTTTATATATAAT
1 TATATAG-TTATATATAAT
*
478270 TTTATA-TTATATATATAT
1 TATATAGTTATATATA-AT
478288 ATATATA
1 -TATATA
478295 TATTTTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.24
18 9 0.24
19 17 0.45
20 3 0.08
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TATATAGTTATATATAAT
Found at i:479813 original size:24 final size:24
Alignment explanation
Indices: 479763--479813 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
479753 ACTAAAAATA
* *
479763 TTATAAAAATTATAATATTTTATG
1 TTATAAAAATCATAATATTTTAGG
*
479787 TTATAAAAATCATAATATTTTCGG
1 TTATAAAAATCATAATATTTTAGG
479811 TTA
1 TTA
479814 GATATATTCT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TTATAAAAATCATAATATTTTAGG
Found at i:483250 original size:21 final size:20
Alignment explanation
Indices: 483226--483278 Score: 54
Period size: 21 Copynumber: 2.6 Consensus size: 20
483216 AAAATTAAAT
*
483226 TTATTTTTTTATTTTTTTCAA
1 TTATTTTTTTATTTTATTC-A
* *
483247 TTATATATTTATTTTATTCA
1 TTATTTTTTTATTTTATTCA
483267 TT-TTTTATTTAT
1 TTATTTT-TTTAT
483279 ATCGAGTCAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 2 0.08
20 8 0.31
21 16 0.62
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.74
Consensus pattern (20 bp):
TTATTTTTTTATTTTATTCA
Found at i:490243 original size:15 final size:15
Alignment explanation
Indices: 490223--490289 Score: 89
Period size: 15 Copynumber: 4.5 Consensus size: 15
490213 ATATTTAACT
* *
490223 GGGCGGGTGGATGTG
1 GGGCGGGCGGATGCG
490238 GGGCGGGCGGATGCG
1 GGGCGGGCGGATGCG
* *
490253 AGGCGGGAGGATGCG
1 GGGCGGGCGGATGCG
*
490268 GGACGGGCGGATGCG
1 GGGCGGGCGGATGCG
490283 GGGCGGG
1 GGGCGGG
490290 TAATGTCTCA
Statistics
Matches: 44, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 44 1.00
ACGTcount: A:0.10, C:0.15, G:0.66, T:0.09
Consensus pattern (15 bp):
GGGCGGGCGGATGCG
Found at i:491035 original size:40 final size:38
Alignment explanation
Indices: 490979--491108 Score: 167
Period size: 40 Copynumber: 3.4 Consensus size: 38
490969 GGATAATTCG
490979 GAGTTTTGGTCCCTACTTGGCACACAATCTCGGGAACTT
1 GAGTTTTGGTCCCTACTTGGCACACAATCTCGGGAA-TT
491018 GTAGTTTTGGTCCCTACTTGGCACACAATCTCGGGAA-T
1 G-AGTTTTGGTCCCTACTTGGCACACAATCTCGGGAATT
* * *
491056 G-GTTATT-GTCCCTGCTTAGCACACAATCTCCGGAATTT
1 GAGTT-TTGGTCCCTACTTGGCACACAATCTCGGGAA-TT
491094 GGAGTTTTGGTCCCT
1 -GAGTTTTGGTCCCT
491109 GCTTCGCAGT
Statistics
Matches: 81, Mismatches: 3, Indels: 13
0.84 0.03 0.13
Matches are distributed among these distances:
36 28 0.35
37 2 0.02
38 3 0.04
39 4 0.05
40 44 0.54
ACGTcount: A:0.19, C:0.25, G:0.23, T:0.33
Consensus pattern (38 bp):
GAGTTTTGGTCCCTACTTGGCACACAATCTCGGGAATT
Found at i:496351 original size:16 final size:16
Alignment explanation
Indices: 496310--496352 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
496300 AACTTTCTTT
496310 TTATTAAATTAATATAA
1 TTATTAAA-TAATATAA
*
496327 TTATAAAATAATATATA
1 TTATTAAATAATATA-A
496344 TT-TTAAATA
1 TTATTAAATA
496353 CTCTCAATCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 13 0.57
17 10 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATTAAATAATATAA
Found at i:496914 original size:2 final size:2
Alignment explanation
Indices: 496876--496906 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
496866 ATCCCAATTC
496876 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 A
496907 ACATATATGC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:504979 original size:20 final size:19
Alignment explanation
Indices: 504954--505023 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 19
504944 ATTTTTAAAC
504954 AAACTTTGACAGAAGTTTCG
1 AAACTTTGACA-AAGTTTCG
504974 AAACTTCT-ACAAGAGTTTCG
1 AAACTT-TGACAA-AGTTTCG
**
504994 AAACTTTCCCCAAAGTTTCG
1 AAACTTT-GACAAAGTTTCG
*
505014 ATACTTTGAC
1 AAACTTTGAC
505024 TCAACGATCA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
19 3 0.07
20 35 0.83
21 4 0.10
ACGTcount: A:0.33, C:0.21, G:0.14, T:0.31
Consensus pattern (19 bp):
AAACTTTGACAAAGTTTCG
Found at i:505686 original size:10 final size:10
Alignment explanation
Indices: 505671--505730 Score: 57
Period size: 10 Copynumber: 5.8 Consensus size: 10
505661 AAATTTTATA
*
505671 ATAATTCAAT
1 ATAATTTAAT
*
505681 ATAATTTTAT
1 ATAATTTAAT
505691 AATAATTTAAT
1 -ATAATTTAAT
*
505702 ATAATTTTAT
1 ATAATTTAAT
*
505712 AATAATTTGAT
1 -ATAATTTAAT
*
505723 AAAATTTA
1 ATAATTTA
505731 GTCATCTAAA
Statistics
Matches: 41, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
10 23 0.56
11 18 0.44
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (10 bp):
ATAATTTAAT
Found at i:505695 original size:11 final size:11
Alignment explanation
Indices: 505662--505729 Score: 79
Period size: 11 Copynumber: 6.5 Consensus size: 11
505652 AAAATAGATA
505662 AATTTTATAAT
1 AATTTTATAAT
**
505673 AATTCAAT-AT
1 AATTTTATAAT
505683 AATTTTATAAT
1 AATTTTATAAT
*
505694 AATTTAAT-AT
1 AATTTTATAAT
505704 AATTTTATAAT
1 AATTTTATAAT
*
505715 AATTTGATAA-
1 AATTTTATAAT
505725 AATTT
1 AATTT
505730 AGTCATCTAA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
10 22 0.46
11 26 0.54
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (11 bp):
AATTTTATAAT
Found at i:505719 original size:21 final size:21
Alignment explanation
Indices: 505662--505825 Score: 122
Period size: 21 Copynumber: 7.8 Consensus size: 21
505652 AAAATAGATA
*
505662 AATTTTATAATAATTCAATAT
1 AATTTTATAATAATTTAATAT
505683 AATTTTATAATAATTTAATAT
1 AATTTTATAATAATTTAATAT
*
505704 AATTTTATAATAATTTGATA-
1 AATTTTATAATAATTTAATAT
* * * *
505724 AA-ATT-TAGTCATCTAA-ACGT
1 AATTTTATAATAATTTAATA--T
* *
505744 AA-CTTATAGATAAATTTAATGGT
1 AATTTTATA-AT-AATTTAAT-AT
* *
505767 CATTTTATAATAATATAATAT
1 AATTTTATAATAATTTAATAT
* *
505788 TATTTTATAATAATTTAATAA
1 AATTTTATAATAATTTAATAT
*
505809 AATTTAATAATATATTT
1 AATTTTATAATA-ATTT
505826 CTAATATATT
Statistics
Matches: 112, Mismatches: 21, Indels: 19
0.74 0.14 0.12
Matches are distributed among these distances:
17 1 0.01
18 7 0.06
19 2 0.02
20 6 0.05
21 70 0.62
22 12 0.11
23 9 0.08
24 5 0.04
ACGTcount: A:0.46, C:0.04, G:0.04, T:0.47
Consensus pattern (21 bp):
AATTTTATAATAATTTAATAT
Found at i:505812 original size:10 final size:11
Alignment explanation
Indices: 505768--505839 Score: 60
Period size: 11 Copynumber: 6.6 Consensus size: 11
505758 TTTAATGGTC
*
505768 ATTTTATAATA
1 ATTTAATAATA
* *
505779 ATATAAT-ATT
1 ATTTAATAATA
*
505789 ATTTTATAATA
1 ATTTAATAATA
505800 ATTTAATAA-A
1 ATTTAATAATA
505810 ATTTAATAATA
1 ATTTAATAATA
*
505821 TATTT-CTAATA
1 -ATTTAATAATA
505832 TATTTAAT
1 -ATTTAAT
505840 CATATAAAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
10 17 0.35
11 26 0.54
12 5 0.10
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (11 bp):
ATTTAATAATA
Found at i:505844 original size:12 final size:12
Alignment explanation
Indices: 505781--505845 Score: 66
Period size: 11 Copynumber: 5.7 Consensus size: 12
505771 TTATAATAAT
*
505781 ATAATATTATTTT
1 ATAATA-TATTTA
505794 ATAATA-ATTTA
1 ATAATATATTTA
505805 ATAA-A-ATTTA
1 ATAATATATTTA
505815 ATAATATATTT-
1 ATAATATATTTA
*
505826 CTAATATATTTA
1 ATAATATATTTA
*
505838 ATCATATA
1 ATAATATA
505846 AAATTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
10 10 0.22
11 19 0.42
12 10 0.22
13 6 0.13
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (12 bp):
ATAATATATTTA
Found at i:511867 original size:25 final size:25
Alignment explanation
Indices: 511839--511892 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
511829 TTCTTCTTCT
511839 TTTTTCGATTCCTTTCAAACCCAAA
1 TTTTTCGATTCCTTTCAAACCCAAA
* * *
511864 TTTTTTGATTCTTTTCAAACCCAGA
1 TTTTTCGATTCCTTTCAAACCCAAA
511889 TTTT
1 TTTT
511893 CTTTTCACAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.22, G:0.06, T:0.48
Consensus pattern (25 bp):
TTTTTCGATTCCTTTCAAACCCAAA
Found at i:512522 original size:217 final size:220
Alignment explanation
Indices: 512141--512578 Score: 796
Period size: 217 Copynumber: 2.0 Consensus size: 220
512131 GCACTTATTG
512141 ATCCCAATTTGGTTTCAAGAAAAGAGCACATATTTGGGAAAAAGAGATTCTCAACAAATTTGGCT
1 ATCCCAATTTGGTTTCAAGAAAAGAGCACATATTTGGGAAAAAGAGATTCTCAACAAATTTGGCT
*
512206 CTTTTTGTGAAGTAGTCGATGGTAATAATCCTGATGTTCATTGCAATACGAGAATAAATTTGGGT
66 CTTTTTGTGAAGGAGTCGATGGTAATAATCCTGATGTTCATTGCAATACGAGAATAAATTTGGGT
*
512271 ATGGAATCTAGCTGAAGTTAAGCCATTTATCTATGTTGAAGG-TTTTGGCTC-TTTTG-T-TTTT
131 ATGGAATCCAGCTGAAGTTAAGCCATTTATCTATGTTGAAGGTTTTTGGCTCTTTTTGTTCTTTT
512332 TGGGTTTGGTAAACTAGTAGTGAGT
196 TGGGTTTGGTAAACTAGTAGTGAGT
*
512357 ATCCCATTTTGGTTTCAAGAAAAGAGCACATATTTGGGAAAAAGAGATTCTCAACAAATTTTGGC
1 ATCCCAATTTGGTTTCAAGAAAAGAGCACATATTTGGGAAAAAGAGATTCTCAACAAA-TTTGGC
512422 TCTTTTTGTGAAGGAGTCGATGGTAATAATCCTGATGTTCATTGCAATACGAGAATAAAATTT-G
65 TCTTTTTGTGAAGGAGTCGATGGTAATAATCCTGATGTTCATTGCAATACGAGAAT-AAATTTGG
512486 GTATGGAATCCAGCTGAAGTTAAGCCATTTATCTATGTTGAAGGTTTTTGGCTCTTTTTGTTCTT
129 GTATGGAATCCAGCTGAAGTTAAGCCATTTATCTATGTTGAAGGTTTTTGGCTCTTTTTGTTCTT
512551 TTTGGGTTTGGTAAACTAGTAGTGAGT
194 TTTGGGTTTGGTAAACTAGTAGTGAGT
512578 A
1 A
512579 AATAAGAGAA
Statistics
Matches: 213, Mismatches: 3, Indels: 7
0.96 0.01 0.03
Matches are distributed among these distances:
216 57 0.27
217 105 0.49
218 15 0.07
219 5 0.02
220 1 0.00
221 30 0.14
ACGTcount: A:0.29, C:0.12, G:0.22, T:0.37
Consensus pattern (220 bp):
ATCCCAATTTGGTTTCAAGAAAAGAGCACATATTTGGGAAAAAGAGATTCTCAACAAATTTGGCT
CTTTTTGTGAAGGAGTCGATGGTAATAATCCTGATGTTCATTGCAATACGAGAATAAATTTGGGT
ATGGAATCCAGCTGAAGTTAAGCCATTTATCTATGTTGAAGGTTTTTGGCTCTTTTTGTTCTTTT
TGGGTTTGGTAAACTAGTAGTGAGT
Found at i:518499 original size:30 final size:30
Alignment explanation
Indices: 518465--518522 Score: 116
Period size: 30 Copynumber: 1.9 Consensus size: 30
518455 CAAGTAAAAC
518465 AAAAATATATCGACTTTTTATTTTATTTGA
1 AAAAATATATCGACTTTTTATTTTATTTGA
518495 AAAAATATATCGACTTTTTATTTTATTT
1 AAAAATATATCGACTTTTTATTTTATTT
518523 TGATTATTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.36, C:0.07, G:0.05, T:0.52
Consensus pattern (30 bp):
AAAAATATATCGACTTTTTATTTTATTTGA
Found at i:524436 original size:41 final size:41
Alignment explanation
Indices: 524377--524457 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
524367 CACTATTCTC
* *
524377 TTTTAATTAAAATCGCTAGTCTTATTAAAAA-AGAAAATATA
1 TTTTAATTAAAATCGCTAGACTTAATAAAAATA-AAAATATA
*
524418 TTTTAATTAAAATTGCTAGACTTAATAAAAATAAAAATAT
1 TTTTAATTAAAATCGCTAGACTTAATAAAAATAAAAATAT
524458 TTAAAATTAT
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 35 0.97
42 1 0.03
ACGTcount: A:0.51, C:0.06, G:0.06, T:0.37
Consensus pattern (41 bp):
TTTTAATTAAAATCGCTAGACTTAATAAAAATAAAAATATA
Found at i:525235 original size:101 final size:101
Alignment explanation
Indices: 525060--525260 Score: 393
Period size: 101 Copynumber: 2.0 Consensus size: 101
525050 GATTACGTGG
525060 CACGGTAAATACATAAAATTAAAATCACATCATTTTCACGTAGATAATGTGTGGATTAAGTTTTG
1 CACGGTAAATACATAAAATTAAAATCACATCATTTTCACGTAGATAATGTGTGGATTAAGTTTTG
*
525125 ATCACTTTCATATTTGTGCACTTTTTGTCACTTACT
66 ATCACTTTCATATTTGTGCACTTTTGGTCACTTACT
525161 CACGGTAAATACATAAAATTAAAATCACATCATTTTCACGTAGATAATGTGTGGATTAAGTTTTG
1 CACGGTAAATACATAAAATTAAAATCACATCATTTTCACGTAGATAATGTGTGGATTAAGTTTTG
525226 ATCACTTTCATATTTGTGCACTTTTGGTCACTTAC
66 ATCACTTTCATATTTGTGCACTTTTGGTCACTTAC
525261 ATTATTGTTT
Statistics
Matches: 99, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 99 1.00
ACGTcount: A:0.32, C:0.16, G:0.13, T:0.39
Consensus pattern (101 bp):
CACGGTAAATACATAAAATTAAAATCACATCATTTTCACGTAGATAATGTGTGGATTAAGTTTTG
ATCACTTTCATATTTGTGCACTTTTGGTCACTTACT
Found at i:525304 original size:31 final size:31
Alignment explanation
Indices: 525247--525311 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
525237 ATTTGTGCAC
***
525247 TTTTGGTCACTTACATTATTGTTTTATTAAG
1 TTTTGGTCACTTACATTATCAATTTATTAAG
525278 TTTTGGTCACTTA-AGTTATCAATTTATTAAG
1 TTTTGGTCACTTACA-TTATCAATTTATTAAG
525309 TTT
1 TTT
525312 AATGGATGAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
30 1 0.03
31 29 0.97
ACGTcount: A:0.25, C:0.09, G:0.12, T:0.54
Consensus pattern (31 bp):
TTTTGGTCACTTACATTATCAATTTATTAAG
Found at i:527199 original size:31 final size:30
Alignment explanation
Indices: 527164--527238 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 30
527154 GATCACCTTC
*
527164 GACCAAAACTTATTAAATTGATAAAATAAGT
1 GACCAAAACTTATGAAA-TGATAAAATAAGT
**
527195 GACCAAAACTTAATGAAATGATAACGTAAGT
1 GACCAAAACTT-ATGAAATGATAAAATAAGT
527226 GACCAAAACTTAT
1 GACCAAAACTTAT
527239 ATTTTTTAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
30 2 0.05
31 33 0.82
32 5 0.12
ACGTcount: A:0.49, C:0.13, G:0.12, T:0.25
Consensus pattern (30 bp):
GACCAAAACTTATGAAATGATAAAATAAGT
Found at i:527953 original size:25 final size:25
Alignment explanation
Indices: 527925--527972 Score: 62
Period size: 25 Copynumber: 1.9 Consensus size: 25
527915 AATAAACTTA
527925 ACATCAAAGTTATT-AAATTATAATT
1 ACAT-AAAGTTATTAAAATTATAATT
* *
527950 ACATAAATTTTTTAAAATTATAA
1 ACATAAAGTTATTAAAATTATAA
527973 AATAATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 7 0.35
25 13 0.65
ACGTcount: A:0.50, C:0.06, G:0.02, T:0.42
Consensus pattern (25 bp):
ACATAAAGTTATTAAAATTATAATT
Found at i:528019 original size:2 final size:2
Alignment explanation
Indices: 528012--528041 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
528002 AATCGATTAA
528012 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
528042 TTTCGGTTTC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:531617 original size:87 final size:86
Alignment explanation
Indices: 531470--531649 Score: 283
Period size: 87 Copynumber: 2.1 Consensus size: 86
531460 GGAATTAGAG
* *
531470 TATAGGGATTAAAACCATAAAAACAGAATATTGGGACTTCAAACAAAATTAACCACAAAAAGGTT
1 TATAGGGATTAAAACCATAAAAACAGAATATAGGGACTTAAAACAAAATTAACCACAAAAAGGTT
*
531535 CATTTACAATCGACATG-TAATA
66 CATTTACAATC-A-ATGCAAATA
*
531557 TATAGGGATTAAAACCATAAAAACAGAATATAGGGACTTAAAACACAATTAACC-CGAAAAAGGT
1 TATAGGGATTAAAACCATAAAAACAGAATATAGGGACTTAAAACAAAATTAACCAC-AAAAAGGT
531621 TCATTTACAATCAATGCAAATA
65 TCATTTACAATCAATGCAAATA
531643 TATAGGG
1 TATAGGG
531650 TCCGTGTAAA
Statistics
Matches: 87, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
85 3 0.03
86 13 0.15
87 71 0.82
ACGTcount: A:0.48, C:0.14, G:0.14, T:0.23
Consensus pattern (86 bp):
TATAGGGATTAAAACCATAAAAACAGAATATAGGGACTTAAAACAAAATTAACCACAAAAAGGTT
CATTTACAATCAATGCAAATA
Found at i:531872 original size:20 final size:20
Alignment explanation
Indices: 531847--531936 Score: 108
Period size: 20 Copynumber: 4.5 Consensus size: 20
531837 ACATGTTCCA
* *
531847 AAATCGTAACGCGAATAGGT
1 AAATCGCAACGCGAATATGT
**
531867 AAATCGCAACGATAATATGT
1 AAATCGCAACGCGAATATGT
*
531887 AAATCGCATCGCGAATATGT
1 AAATCGCAACGCGAATATGT
* *
531907 AAATCGAAACGCGAATTTGT
1 AAATCGCAACGCGAATATGT
*
531927 AAATTGCAAC
1 AAATCGCAAC
531937 ACATAAGTCA
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 58 1.00
ACGTcount: A:0.41, C:0.17, G:0.19, T:0.23
Consensus pattern (20 bp):
AAATCGCAACGCGAATATGT
Done.