Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr08 ID=Chr08-JGI_221_v2.0
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: 57128820
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 677448 characters in sequence are not A, C, G, or T
File 21 of 190
Found at i:5950646 original size:13 final size:14
Alignment explanation
Indices: 5950628--5950662 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
5950618 AATAAGTAAG
5950628 TTATTATATTA-TA
1 TTATTATATTATTA
5950641 TTATTATATTATTA
1 TTATTATATTATTA
5950655 TT-TTATAT
1 TTATTATAT
5950663 ATAAAACAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 17 0.81
14 4 0.19
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (14 bp):
TTATTATATTATTA
Found at i:5951907 original size:24 final size:24
Alignment explanation
Indices: 5951832--5951957 Score: 127
Period size: 22 Copynumber: 5.3 Consensus size: 24
5951822 ACTTTAGCGC
5951832 GCTCTCTGATTATTAGCACGTTAGT
1 GCTCTCTGATT-TTAGCACGTTAGT
** *
5951857 GCTCTCTGACTACTAGCACGTTGGT
1 GCTCTCTGA-TTTTAGCACGTTAGT
*
5951882 GCTCTCTGATTTTAGCACGTCAGT
1 GCTCTCTGATTTTAGCACGTTAGT
*
5951906 GCTCTCTG--TTTAGCACATCT-GT
1 GCTCTCTGATTTTAGCACGT-TAGT
* *
5951928 GCTCTCTG--TATAGCACTTTAGT
1 GCTCTCTGATTTTAGCACGTTAGT
5951950 GCTCTCTG
1 GCTCTCTG
5951958 TTCATTAGTG
Statistics
Matches: 87, Mismatches: 11, Indels: 9
0.81 0.10 0.08
Matches are distributed among these distances:
21 1 0.01
22 37 0.43
24 19 0.22
25 29 0.33
26 1 0.01
ACGTcount: A:0.16, C:0.25, G:0.21, T:0.38
Consensus pattern (24 bp):
GCTCTCTGATTTTAGCACGTTAGT
Found at i:5952674 original size:39 final size:37
Alignment explanation
Indices: 5952607--5952699 Score: 89
Period size: 39 Copynumber: 2.5 Consensus size: 37
5952597 TCCAGTATGG
* *
5952607 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
5952646 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* * *
5952683 TACCTAGTACCTCATCG
1 CACCCAGTGCCTCATCG
5952700 AATCTATCCT
Statistics
Matches: 45, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
37 18 0.40
38 2 0.04
39 22 0.49
40 3 0.07
ACGTcount: A:0.28, C:0.28, G:0.23, T:0.22
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:5952905 original size:23 final size:26
Alignment explanation
Indices: 5952858--5952906 Score: 77
Period size: 23 Copynumber: 2.0 Consensus size: 26
5952848 TCAATCACAA
5952858 TTTCTCACATTTTCAATTCAATAATT
1 TTTCTCACATTTTCAATTCAATAATT
5952884 TTTC-CAC-TTTTCAA-TCAATAATT
1 TTTCTCACATTTTCAATTCAATAATT
5952907 AATCCACAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 9 0.39
24 7 0.30
25 3 0.13
26 4 0.17
ACGTcount: A:0.31, C:0.20, G:0.00, T:0.49
Consensus pattern (26 bp):
TTTCTCACATTTTCAATTCAATAATT
Found at i:5952912 original size:23 final size:24
Alignment explanation
Indices: 5952867--5952913 Score: 69
Period size: 23 Copynumber: 2.0 Consensus size: 24
5952857 ATTTCTCACA
**
5952867 TTTTCAATTCAATAATTTTTCCAC
1 TTTTCAATTCAATAATTAATCCAC
5952891 TTTTCAA-TCAATAATTAATCCAC
1 TTTTCAATTCAATAATTAATCCAC
5952914 AAATTTACAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 14 0.67
24 7 0.33
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTTCAATTCAATAATTAATCCAC
Found at i:5953067 original size:3 final size:3
Alignment explanation
Indices: 5953059--5953117 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
5953049 CCACTCATCT
5953059 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5953107 TAA TAA TAA TA
1 TAA TAA TAA TA
5953118 CTTACCTCAC
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:5954007 original size:3 final size:3
Alignment explanation
Indices: 5953999--5954048 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
5953989 ATTTCACAAT
5953999 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5954047 AT
1 AT
5954049 TTAATAACAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:5954523 original size:28 final size:29
Alignment explanation
Indices: 5954473--5954533 Score: 72
Period size: 28 Copynumber: 2.1 Consensus size: 29
5954463 TGTCAGGTAG
*
5954473 CACCCAAGTGGAGGAGCATTGTC-GACGA
1 CACCCAAGTGGAGGAGCACTGTCTGACGA
* *
5954501 CACCCAGGTGGAGG-GACACTGTCTGGCGA
1 CACCCAAGTGGAGGAG-CACTGTCTGACGA
5954530 CACC
1 CACC
5954534 ATTTGGGGGG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 1 0.04
28 19 0.68
29 8 0.29
ACGTcount: A:0.25, C:0.30, G:0.33, T:0.13
Consensus pattern (29 bp):
CACCCAAGTGGAGGAGCACTGTCTGACGA
Found at i:5955940 original size:24 final size:23
Alignment explanation
Indices: 5955913--5955967 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 23
5955903 CCATTTCCTC
* *
5955913 TTTAGTTTTATTTTCTATTTGTAA
1 TTTAGTTTTATATTC-AGTTGTAA
* *
5955937 TTTAGATTTCTATTCAGTTGTAA
1 TTTAGTTTTATATTCAGTTGTAA
5955960 TTCTAGTT
1 TT-TAGTT
5955968 AGTTTATTTC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.22, C:0.07, G:0.11, T:0.60
Consensus pattern (23 bp):
TTTAGTTTTATATTCAGTTGTAA
Found at i:5959454 original size:13 final size:13
Alignment explanation
Indices: 5959436--5959460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5959426 TTTTTTCTAA
5959436 TTTTAATTTTAAT
1 TTTTAATTTTAAT
5959449 TTTTAATTTTAA
1 TTTTAATTTTAA
5959461 ACCCCCTTTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTTTAATTTTAAT
Found at i:5963843 original size:50 final size:50
Alignment explanation
Indices: 5963728--5963976 Score: 291
Period size: 50 Copynumber: 4.8 Consensus size: 50
5963718 GATAATAACA
* * ** * *
5963728 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATTTTCTCATGTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGA-CCTCTCATCTCGG
* *
5963779 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5963829 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
* * *
5963879 TGCCCATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTC---TCATC-T-CGG
* *
5963934 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 -TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCT
5963977 TTACCCAAAT
Statistics
Matches: 170, Mismatches: 22, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
50 92 0.54
51 33 0.19
53 4 0.02
54 1 0.01
55 2 0.01
56 38 0.22
ACGTcount: A:0.20, C:0.29, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
Found at i:5963914 original size:100 final size:104
Alignment explanation
Indices: 5963727--5963976 Score: 355
Period size: 100 Copynumber: 2.4 Consensus size: 104
5963717 TGATAATAAC
* * *
5963727 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATTTTCTCATGTTGGTGCCCATGCCATG
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA-TCTCTCATCTCGGTGCCCATGCCATG
* *
5963792 TCCCAGACATGGTCTTATAGGGGACCTC-TCATC-T-CGG
65 TCCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
* * *
5963829 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGGTGCCCATGCCATGT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCCATGCCATGT
*
5963893 CCCAGACATGGTCTTACAGGGGACCTCTTATGATCTTAAGG
66 CCCAGACATGGTCTTACAGGGGACCTC-T-TCATCTTAAGG
*
5963934 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
5963977 TTACCCAAAT
Statistics
Matches: 131, Mismatches: 11, Indels: 8
0.87 0.07 0.05
Matches are distributed among these distances:
100 48 0.37
101 36 0.27
103 4 0.03
104 1 0.01
105 2 0.02
106 40 0.31
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.27
Consensus pattern (104 bp):
ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATCTCTCATCTCGGTGCCCATGCCATGT
CCCAGACATGGTCTTACAGGGGACCTCTTCATCTTAAGG
Found at i:5964092 original size:13 final size:13
Alignment explanation
Indices: 5964071--5964101 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5964061 GCTTAGATCA
*
5964071 TCATCAAATAAAT
1 TCATAAAATAAAT
5964084 TCATAAAATAAAT
1 TCATAAAATAAAT
5964097 TCATA
1 TCATA
5964102 GTTTCTGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.13, G:0.00, T:0.32
Consensus pattern (13 bp):
TCATAAAATAAAT
Found at i:5964349 original size:30 final size:30
Alignment explanation
Indices: 5964314--5964371 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
5964304 CCTCGACTGT
* *
5964314 AACTTTTTCAAAATTATAATTTTGCCCCTA
1 AACTTTTACAAAATTACAATTTTGCCCCTA
* *
5964344 AACTTTTACATAATTACATTTTTGCCCC
1 AACTTTTACAAAATTACAATTTTGCCCC
5964372 AAGGCTCGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.03, T:0.43
Consensus pattern (30 bp):
AACTTTTACAAAATTACAATTTTGCCCCTA
Found at i:5966474 original size:16 final size:16
Alignment explanation
Indices: 5966450--5966499 Score: 73
Period size: 16 Copynumber: 3.1 Consensus size: 16
5966440 TGGTTCGCTA
5966450 TATTGGATTAGAGGTG
1 TATTGGATTAGAGGTG
*
5966466 TATTAGATTAGAGGTG
1 TATTGGATTAGAGGTG
* *
5966482 TAATGGAATAGAGGTG
1 TATTGGATTAGAGGTG
5966498 TA
1 TA
5966500 ATAGCAAATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 30 1.00
ACGTcount: A:0.32, C:0.00, G:0.34, T:0.34
Consensus pattern (16 bp):
TATTGGATTAGAGGTG
Found at i:5966752 original size:16 final size:16
Alignment explanation
Indices: 5966715--5966758 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
5966705 TTAATCATAT
*
5966715 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
5966731 TT-AAATATATTATAA
1 TTAAAATATATTATAA
5966746 TTAAAATATATTA
1 TTAAAATATATTA
5966759 ATAAAATTCT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
14 3 0.12
15 10 0.40
16 12 0.48
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:5966858 original size:15 final size:15
Alignment explanation
Indices: 5966830--5966876 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
5966820 GTAAAATATA
5966830 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
5966845 TATTAAATATATTAT
1 AATTAAATATATTAT
5966860 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
5966873 AATT
1 AATT
5966877 NNNNNNNNNN
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
13 7 0.24
14 6 0.21
15 16 0.55
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:5968653 original size:11 final size:11
Alignment explanation
Indices: 5968637--5968663 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
5968627 AAAACTCAAT
5968637 ACAAAAGTTTC
1 ACAAAAGTTTC
5968648 ACAAAAGTTTC
1 ACAAAAGTTTC
5968659 ACAAA
1 ACAAA
5968664 CTAATTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.52, C:0.19, G:0.07, T:0.22
Consensus pattern (11 bp):
ACAAAAGTTTC
Found at i:5970185 original size:15 final size:15
Alignment explanation
Indices: 5970140--5970185 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
5970130 TTACTGCAAC
5970140 ATTTAGAACACAC-A
1 ATTTAGAACACACGA
*
5970154 TAGTTTA-AACTCACGA
1 -A-TTTAGAACACACGA
5970170 ATTTAGAACACACGA
1 ATTTAGAACACACGA
5970185 A
1 A
5970186 GCAAAGAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
14 4 0.15
15 17 0.65
16 5 0.19
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.24
Consensus pattern (15 bp):
ATTTAGAACACACGA
Found at i:5976495 original size:28 final size:29
Alignment explanation
Indices: 5976462--5976516 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
5976452 ACTATACTAG
5976462 TTTTATCA-AATTGGTACATAAACTTTTT
1 TTTTATCAGAATTGGTACATAAACTTTTT
*
5976490 TTTTATCAGAATTGGTACCTAAACTTT
1 TTTTATCAGAATTGGTACATAAACTTT
5976517 AAACTGTTAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
28 8 0.32
29 17 0.68
ACGTcount: A:0.31, C:0.13, G:0.09, T:0.47
Consensus pattern (29 bp):
TTTTATCAGAATTGGTACATAAACTTTTT
Found at i:5978413 original size:14 final size:15
Alignment explanation
Indices: 5978394--5978428 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5978384 ATATTTATTG
5978394 TATAAA-TACTTAAA
1 TATAAAGTACTTAAA
5978408 TATAAAGTACTTAAA
1 TATAAAGTACTTAAA
5978423 TATAAA
1 TATAAA
5978429 AATATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATAAAGTACTTAAA
Found at i:5979113 original size:7 final size:7
Alignment explanation
Indices: 5979097--5979130 Score: 54
Period size: 7 Copynumber: 5.1 Consensus size: 7
5979087 ATCAAAAATT
5979097 AAAT-AA
1 AAATAAA
5979103 AAATAAA
1 AAATAAA
5979110 AAATAAA
1 AAATAAA
5979117 AAATAAA
1 AAATAAA
5979124 AAA-AAA
1 AAATAAA
5979130 A
1 A
5979131 CTTTGAGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 8 0.30
7 19 0.70
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAATAAA
Found at i:5979946 original size:44 final size:44
Alignment explanation
Indices: 5979848--5980001 Score: 131
Period size: 44 Copynumber: 3.6 Consensus size: 44
5979838 TATTTAGTCT
* * * * * *
5979848 GCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC-GT--TCT
1 GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTTAATCC
* *
5979889 GCT-CTCTGCAACTTCAGAGAGATAAGATTCA-AGGTTTTAATCC
1 GCTCCACTGCAACTTCAGAGAGATAAGATT-ATAGGCTTTAATCC
* * * *
5979932 GCTTCACTGCAACTTCA-AGGAGATAGGATTATCGGCTTTAATCT
1 GCTCCACTGCAACTTCAGA-GAGATAAGATTATAGGCTTTAATCC
*
5979976 GCTCCACTGCAACTTCAGGGAGATAA
1 GCTCCACTGCAACTTCAGAGAGATAA
5980002 AATTTGCCAT
Statistics
Matches: 90, Mismatches: 15, Indels: 13
0.76 0.13 0.11
Matches are distributed among these distances:
40 25 0.28
41 5 0.06
43 7 0.08
44 53 0.59
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (44 bp):
GCTCCACTGCAACTTCAGAGAGATAAGATTATAGGCTTTAATCC
Found at i:5979954 original size:128 final size:129
Alignment explanation
Indices: 5979750--5980001 Score: 305
Period size: 128 Copynumber: 2.0 Consensus size: 129
5979740 AGATGAATTT
* * * *
5979750 GATGCGATCTGCTCTACTGTAATTTCAGAGAGATAAGATCCATCATTCTAATCCACTCCGCTACA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
* * *
5979815 ACCTTAGGGAGATAGGATT-T-GTTTATTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
66 ACCTTAAGGAGATAGGATTATCG--GATTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
5979878 A
129 A
* * ** * * * *
5979879 GATGCGTTCTGCTCT-CTGCAACTTCAGAGAGATAAGATTCAAGGTTTTAATCCGCTTCACTGCA
1 GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
*
5979943 A-CTTCAAGGAGATAGGATTATCGGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
66 ACCTT-AAGGAGATAGGATTATCGGATTTAATCTGCTCCACTGCAACTTCAGGGAGATAA
5980002 AATTTGCCAT
Statistics
Matches: 104, Mismatches: 16, Indels: 7
0.82 0.13 0.06
Matches are distributed among these distances:
127 3 0.03
128 85 0.82
129 15 0.14
130 1 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (129 bp):
GATGCGATCTGCTCTACTGCAACTTCAGAGAGATAAGATCCAACATTCTAATCCACTCCACTACA
ACCTTAAGGAGATAGGATTATCGGATTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTA
Found at i:5980362 original size:44 final size:44
Alignment explanation
Indices: 5980308--5980727 Score: 525
Period size: 44 Copynumber: 9.7 Consensus size: 44
5980298 GTTATTTTCC
* *
5980308 ACCTACTCCACTGCTG-CTCAGGGAGATAGGGTTCACAATCTTCA
1 ACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCA
* *
5980352 ACCTATTCCACTGTTGACCAGGGAGATAGGA-CCTACAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * * *
5980396 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
5980440 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
5980484 ACCTATTCCACTGCTGTCCAGGGAGATAGGATT--C--T-TT-A
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* * * *
5980522 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
*
5980566 ACCTATTCCACTGCTGACCAGGGAGATAGGA-TCTACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTCA
* * * ** * *
5980610 ATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
* *
5980654 ACCTATTCCACTGCTGACCAGGGAGATGGGATTCACAATCTTTA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
5980698 ACCTATTCCACTGCTGACCAGGGAGATAGG
1 ACCTATTCCACTGCTGACCAGGGAGATAGG
5980728 GTTGGGATCA
Statistics
Matches: 325, Mismatches: 40, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
38 31 0.10
39 2 0.01
40 2 0.01
42 2 0.01
43 5 0.02
44 279 0.86
45 4 0.01
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.28
Consensus pattern (44 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCA
Found at i:5980688 original size:214 final size:214
Alignment explanation
Indices: 5980314--5980727 Score: 729
Period size: 214 Copynumber: 1.9 Consensus size: 214
5980304 TTCCACCTAC
* ** *
5980314 TCCACTGCTGCTCAGGGAGATAGGGTTCACAATCTTCAACCTATTCCACTGTTGACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
5980379 AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
66 AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
*
5980444 ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAG
131 ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGACCAGGGAG
5980509 ATAGGATTCTTTAATCTAT
196 ATAGGATTCTTTAATCTAT
*
5980528 TCCACTGCTGCCCAGGGAGATAGAATTCTCAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
1 TCCACTGCTGCCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
* * * *
5980593 AGGATCTACAATCTTTAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTTAATTTTTAACCT
66 AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
*
5980658 ATTCCACTGCTGACCAGGGAGATGGGATTCACAATCTTTAACCTATTCCACTGCTGACCAGGGAG
131 ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGACCAGGGAG
5980723 ATAGG
196 ATAGG
5980728 GTTGGGATCA
Statistics
Matches: 189, Mismatches: 11, Indels: 0
0.94 0.05 0.00
Matches are distributed among these distances:
214 189 1.00
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (214 bp):
TCCACTGCTGCCCAGGGAGATAGAATTCACAATCTTCAACCTATTCCACTGCTGACCAGGGAGAT
AGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGGGAGATAGAATTCTCAATTTTCAACCT
ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTGCTGACCAGGGAG
ATAGGATTCTTTAATCTAT
Found at i:5980788 original size:88 final size:88
Alignment explanation
Indices: 5980730--5981314 Score: 870
Period size: 88 Copynumber: 6.6 Consensus size: 88
5980720 GAGATAGGGT
* * *
5980730 TGGGATCATCAATCTGCTTCGCTGCCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCC
1 TGGGATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCC
* *
5980795 GCTGCAACCTAGGAAGGCAAGGC
66 GCTGCAACCCAGGGAGGCAAGGC
* * * *
5980818 TGGTG-TCTTCAATCTGCTTCGCTGCCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTACTC
1 TGG-GATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
* *
5980882 CACTGCAACCCAGGGAGGCAAAGC
65 CGCTGCAACCCAGGGAGGCAAGGC
* *
5980906 AGGGTATCTTCGATCTGCTTCGCTGTTGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
1 TGGG-ATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
* *
5980971 CGCTGCAACCCAGTGAGGCAAGGT
65 CGCTGCAACCCAGGGAGGCAAGGC
* *
5980995 TGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTACTCC
1 TGGGATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCC
5981060 GCTGCAACCCAGGGAGGCAAGGC
66 GCTGCAACCCAGGGAGGCAAGGC
* * * * *
5981083 TAGTG-TCTTTGATCTGCTTCGCTGTCAGTACAGAAAGGCAAGATCTGCTATTTTTAACCTGCTC
1 T-GGGATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
5981147 CGCTGCAACCCAGGGAGGCAAGGC
65 CGCTGCAACCCAGGGAGGCAAGGC
* * *
5981171 TGGTG-TCTTTGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTACTATTTTTAACCTGTTC
1 TGG-GATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTC
5981235 CGCTGCAACCCAGGGAGGCAAGGC
65 CGCTGCAACCCAGGGAGGCAAGGC
* *
5981259 TGGTATCTTCGATCTGCTTCGCTGTCGGTGCAGTAAGGCAAGATCTGCTATTTTTA
1 TGGGATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTA
5981315 CTGATCTGCT
Statistics
Matches: 451, Mismatches: 40, Indels: 12
0.90 0.08 0.02
Matches are distributed among these distances:
87 2 0.00
88 371 0.82
89 78 0.17
ACGTcount: A:0.21, C:0.25, G:0.27, T:0.28
Consensus pattern (88 bp):
TGGGATCTTCGATCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGCTCC
GCTGCAACCCAGGGAGGCAAGGC
Found at i:5987959 original size:2 final size:2
Alignment explanation
Indices: 5987952--5987991 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5987942 ACATAAAATA
5987952 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
5987992 TTAAATCAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5988254 original size:14 final size:15
Alignment explanation
Indices: 5988235--5988269 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
5988225 ATATTTATTG
5988235 TATAAA-TACTTAAA
1 TATAAAGTACTTAAA
5988249 TATAAAGTACTTAAA
1 TATAAAGTACTTAAA
5988264 TATAAA
1 TATAAA
5988270 AATGGATTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (15 bp):
TATAAAGTACTTAAA
Found at i:5988977 original size:17 final size:16
Alignment explanation
Indices: 5988955--5988986 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
5988945 AGAACAGATC
5988955 AAAAAATAAATAAAAAT
1 AAAAAATAAA-AAAAAT
5988972 AAAAAATAAAAAAAA
1 AAAAAATAAAAAAAA
5988987 CTTTGAGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.33
17 10 0.67
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (16 bp):
AAAAAATAAAAAAAAT
Found at i:5992646 original size:9 final size:9
Alignment explanation
Indices: 5992632--5992668 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
5992622 TATAGTTTGA
5992632 TATTCGAAT
1 TATTCGAAT
5992641 TATTCGAAT
1 TATTCGAAT
*
5992650 TATTCGAGT
1 TATTCGAAT
5992659 TATTCGAAT
1 TATTCGAAT
5992668 T
1 T
5992669 CGAAAAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:5992708 original size:9 final size:9
Alignment explanation
Indices: 5992691--5992721 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5992681 TCGAGTTGAT
5992691 TCGAATAAC
1 TCGAATAAC
*
5992700 TCGATTAAC
1 TCGAATAAC
5992709 TCGAATAAC
1 TCGAATAAC
5992718 TCGA
1 TCGA
5992722 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:5993070 original size:19 final size:19
Alignment explanation
Indices: 5993035--5993074 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
5993025 TTACAGTAAC
*
5993035 AATTAAATAAATTTTTTTAA
1 AATTAAATAAA-TATTTTAA
5993055 AATTAAA-AAATATTTTAA
1 AATTAAATAAATATTTTAA
5993073 AA
1 AA
5993075 GATATATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 9 0.47
19 3 0.16
20 7 0.37
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AATTAAATAAATATTTTAA
Found at i:6004071 original size:13 final size:13
Alignment explanation
Indices: 6004053--6004079 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
6004043 GCCAAAATAC
6004053 ACCATGTGATCAA
1 ACCATGTGATCAA
6004066 ACCATGTGATCAA
1 ACCATGTGATCAA
6004079 A
1 A
6004080 ACACATATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (13 bp):
ACCATGTGATCAA
Found at i:6004589 original size:67 final size:67
Alignment explanation
Indices: 6004443--6004574 Score: 201
Period size: 67 Copynumber: 2.0 Consensus size: 67
6004433 ATTTGAACCA
* * * * *
6004443 TTCAAACATGAATTCGTTTATATGCCAATTTCACATCTTTCATTTCTATACATACATGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATTGCACAGCTTTCATTTCTATACACACACGTTTCAAA
6004508 GG
66 GG
* *
6004510 TTCAAACATGAATTCATTTATATGCTAATTGCACAGCTTTCGTTTCTATACACACACGTTTCAAA
1 TTCAAACATGAATTCATTTATATGCCAATTGCACAGCTTTCATTTCTATACACACACGTTTCAAA
6004575 TGTTAGCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
67 58 1.00
ACGTcount: A:0.32, C:0.20, G:0.09, T:0.39
Consensus pattern (67 bp):
TTCAAACATGAATTCATTTATATGCCAATTGCACAGCTTTCATTTCTATACACACACGTTTCAAA
GG
Found at i:6007405 original size:11 final size:11
Alignment explanation
Indices: 6007389--6007415 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
6007379 CTATATAATG
6007389 CCATAGCTTTT
1 CCATAGCTTTT
6007400 CCATAGCTTTT
1 CCATAGCTTTT
6007411 CCATA
1 CCATA
6007416 CCATATATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.22, C:0.30, G:0.07, T:0.41
Consensus pattern (11 bp):
CCATAGCTTTT
Found at i:6008905 original size:26 final size:26
Alignment explanation
Indices: 6008876--6008925 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
6008866 TTATTTAAAC
6008876 CTATGAATTTTAA-ATTGTATTAATTA
1 CTAT-AATTTTAATATTGTATTAATTA
* *
6008902 CTATACTTTTAATTTTGTATTAAT
1 CTATAATTTTAATATTGTATTAAT
6008926 CATGAATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 7 0.33
26 14 0.67
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.54
Consensus pattern (26 bp):
CTATAATTTTAATATTGTATTAATTA
Found at i:6009483 original size:20 final size:21
Alignment explanation
Indices: 6009458--6009498 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
6009448 TTAATCATTC
*
6009458 TTTTAAAATTAT-TTATATTT
1 TTTTAAAAATATATTATATTT
6009478 TTTTAAAAATATATTATATTT
1 TTTTAAAAATATATTATATTT
6009499 AAAATTTATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (21 bp):
TTTTAAAAATATATTATATTT
Found at i:6010080 original size:18 final size:18
Alignment explanation
Indices: 6010057--6010133 Score: 55
Period size: 18 Copynumber: 3.9 Consensus size: 18
6010047 TGTTAGTTAA
6010057 TTTTTCTTTCTTTCTTTC
1 TTTTTCTTTCTTTCTTTC
6010075 TTTTTCCTATTCTTTTCTTTTTAC
1 TTTTT-CT-TTC-TTTC--TTT-C
* * *
6010099 GTTTTCTATCCTTCTTTC
1 TTTTTCTTTCTTTCTTTC
* *
6010117 TTTTTCTCTGTTTCTTT
1 TTTTTCTTTCTTTCTTT
6010134 TTATTATTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 12
0.71 0.11 0.18
Matches are distributed among these distances:
18 19 0.41
19 5 0.11
20 3 0.07
21 7 0.15
22 2 0.04
23 5 0.11
24 5 0.11
ACGTcount: A:0.04, C:0.22, G:0.03, T:0.71
Consensus pattern (18 bp):
TTTTTCTTTCTTTCTTTC
Found at i:6010827 original size:63 final size:63
Alignment explanation
Indices: 6010690--6010836 Score: 177
Period size: 63 Copynumber: 2.3 Consensus size: 63
6010680 CCGTGTGATT
* * ** * * *
6010690 GGCCGTGTAACCCACTATTTGTGAATTAAGGTCACATGGGCTAGGGACACGAGCGTGTGTCTA
1 GGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGCGTGTGTCCA
* * *
6010753 GGCCGTGTAACTCACTGTTTGTGAATTAGGGTCACACAGGCCAAGGACACGGGTGTGTGTCCA
1 GGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGCGTGTGTCCA
* * *
6010816 GGCCATGTAACTTATTGTTTG
1 GGCCGTGTAACTCACTGTTTG
6010837 CTAATGTCAC
Statistics
Matches: 71, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.22, C:0.20, G:0.30, T:0.27
Consensus pattern (63 bp):
GGCCGTGTAACTCACTGTTTGTGAATTAAGGTCACACAGGCCAAGGACACGAGCGTGTGTCCA
Found at i:6012347 original size:17 final size:17
Alignment explanation
Indices: 6012325--6012366 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
6012315 GGCCCGAAGT
*
6012325 GGCCCAAACCTAACTA-A
1 GGCCCAAACCAAAC-AGA
6012342 GGCCCAAACCAAACAGA
1 GGCCCAAACCAAACAGA
6012359 GGCCCAAA
1 GGCCCAAA
6012367 GCAGATTCGG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.43, C:0.36, G:0.17, T:0.05
Consensus pattern (17 bp):
GGCCCAAACCAAACAGA
Found at i:6013560 original size:23 final size:23
Alignment explanation
Indices: 6013534--6013581 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
6013524 TTAAAATCTA
* *
6013534 TATATACATATATATTTATTTTT
1 TATACACATACATATTTATTTTT
**
6013557 TATACATGTACATATTTATTTTT
1 TATACACATACATATTTATTTTT
6013580 TA
1 TA
6013582 ACTAATATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.58
Consensus pattern (23 bp):
TATACACATACATATTTATTTTT
Found at i:6014039 original size:19 final size:20
Alignment explanation
Indices: 6013998--6014039 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
6013988 ATTTCTATGC
* *
6013998 CATTGTAATATTTATTATTG
1 CATTGTAATATTTAATATAG
*
6014018 CATTGT-ATATTTAATGTAG
1 CATTGTAATATTTAATATAG
6014037 CAT
1 CAT
6014040 CACATCATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.31, C:0.07, G:0.12, T:0.50
Consensus pattern (20 bp):
CATTGTAATATTTAATATAG
Found at i:6015623 original size:11 final size:11
Alignment explanation
Indices: 6015609--6015675 Score: 56
Period size: 11 Copynumber: 6.6 Consensus size: 11
6015599 CGGCCCGAAT
6015609 TATATATTAAA
1 TATATATTAAA
6015620 TATATATT---
1 TATATATTAAA
**
6015628 TATATATTATT
1 TATATATTAAA
* *
6015639 TTTA-ATCAAA
1 TATATATTAAA
6015649 TATATATT--A
1 TATATATTAAA
6015658 TATATATTAAA
1 TATATATTAAA
6015669 TATATAT
1 TATATAT
6015676 AATATGGGCC
Statistics
Matches: 44, Mismatches: 6, Indels: 12
0.71 0.10 0.19
Matches are distributed among these distances:
8 8 0.18
9 9 0.20
10 6 0.14
11 21 0.48
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (11 bp):
TATATATTAAA
Found at i:6018249 original size:17 final size:18
Alignment explanation
Indices: 6018214--6018251 Score: 53
Period size: 17 Copynumber: 2.2 Consensus size: 18
6018204 CCCGGCGCAG
6018214 AGGAACAAAACACGAACA
1 AGGAACAAAACACGAACA
6018232 AGGAAGCAAAA-A-GAACA
1 AGGAA-CAAAACACGAACA
6018249 AGG
1 AGG
6018252 CTAACAGTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 6 0.32
19 5 0.26
ACGTcount: A:0.61, C:0.16, G:0.24, T:0.00
Consensus pattern (18 bp):
AGGAACAAAACACGAACA
Found at i:6018771 original size:26 final size:26
Alignment explanation
Indices: 6018735--6018785 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
6018725 AGATTAAACA
*
6018735 CTTAATTTGTTCTTTCCATCAAAGAT
1 CTTAACTTGTTCTTTCCATCAAAGAT
*
6018761 CTTAACTTGTTCTTTCCATTAAAGA
1 CTTAACTTGTTCTTTCCATCAAAGA
6018786 AAATTTTAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.27, C:0.20, G:0.08, T:0.45
Consensus pattern (26 bp):
CTTAACTTGTTCTTTCCATCAAAGAT
Found at i:6020601 original size:35 final size:35
Alignment explanation
Indices: 6020512--6020601 Score: 85
Period size: 35 Copynumber: 2.6 Consensus size: 35
6020502 GTATATTCTA
* *
6020512 TTTTGTCGATTTCTTAATCATATATATATCATTCT
1 TTTTGTCGATTTCTTAATCATATATATATCAATAT
* * * * *
6020547 TTTTGTCG-TAATATAAATCAT-TAATGTATTAATAT
1 TTTTGTCGAT-TTCTTAATCATAT-ATATATCAATAT
6020582 TTTTGTCGATTTCTTAATCA
1 TTTTGTCGATTTCTTAATCA
6020602 CACATTTAAC
Statistics
Matches: 42, Mismatches: 10, Indels: 6
0.72 0.17 0.10
Matches are distributed among these distances:
34 2 0.05
35 39 0.93
36 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.08, T:0.52
Consensus pattern (35 bp):
TTTTGTCGATTTCTTAATCATATATATATCAATAT
Found at i:6020754 original size:20 final size:21
Alignment explanation
Indices: 6020729--6020774 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 21
6020719 TTTTTCATAA
*
6020729 TTAAGTATTTAATTTA-GTGG
1 TTAAGTATTTAATTTATGTGC
* *
6020749 TTAAGTGTTTTATTTATGTGC
1 TTAAGTATTTAATTTATGTGC
6020770 TTAAG
1 TTAAG
6020775 GTTTGGGGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 14 0.64
21 8 0.36
ACGTcount: A:0.26, C:0.02, G:0.20, T:0.52
Consensus pattern (21 bp):
TTAAGTATTTAATTTATGTGC
Found at i:6021270 original size:273 final size:273
Alignment explanation
Indices: 6020783--6021323 Score: 922
Period size: 273 Copynumber: 2.0 Consensus size: 273
6020773 AGGTTTGGGG
* *
6020783 TTCAAGTCCCATTTTTGGAAATTTTGCTTTTTGTTTTGAATCAACCCTCACTTTCAAACTTTTGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
** **
6020848 CTTAAGATTAATTTTGTGTAAACTTATATTAAGAATGAGCTTGTTGGTTTAATAGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
* * * *
6020913 GTATACCCTTTGGTCTTATGTTCGAGTTTCTGCAAAAGCTATGAGAAAATATCTTATGCTAGTTT
131 GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
*
6020978 ATAAAAATTAGTTTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAAATTT-TTTCACGTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTT-AAAATTTCTTTCACGTT
6021042 TTATTTCTTTCACA
260 TTATTTCTTTCACA
*
6021056 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTTAAACTTTCGA
1 TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
* * *
6021121 CTTAAGATTAATTTTGCATAAACTTGTGTTAAGAATGAGCTTACTGGTTTAATGGTTAAACTTTT
66 CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
*
6021186 GTATACCCTTTGCTCTTGTGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
131 GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
6021251 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
196 ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
6021316 TATTTCTT
261 TATTTCTT
6021324 CCTTTATCCT
Statistics
Matches: 251, Mismatches: 16, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
272 7 0.03
273 244 0.97
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.46
Consensus pattern (273 bp):
TTCAAGTCCCATTTTTGGAAATTTTGCTATTTGTTTTGAATCAACCCTCACTTTCAAACTTTCGA
CTTAAGATTAATTTTGCATAAACTTATATTAAGAATGAGCTTACTGGTTTAATAGTTAAACTTTT
GTATACCCTTTGCTCTTATGTTCAAGTTTCTGCAAAAGCTATGAGAAAACATCTTATACTAGTTT
ATAAAAATTAGTCTATTTTAAGGTAATTAAATTCCTTTATTTTTGTTAAAATTTCTTTCACGTTT
TATTTCTTTCACA
Found at i:6022060 original size:42 final size:43
Alignment explanation
Indices: 6021971--6022061 Score: 105
Period size: 42 Copynumber: 2.1 Consensus size: 43
6021961 ATGACATGGG
* * * * *
6021971 TGTGTATCTAGACCGTGTGACTCTCTAACTTGAGTAACATGGT
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
*
6022014 TGTGTGTC-AGACCGTATAACTCTCTAACTT-AGGTCACACGGC
1 TGTGTGTCTAGACCGTATAACTCTCTAACTTGA-GTAACACGGC
6022056 TGTGTG
1 TGTGTG
6022062 CCAGGTCGTG
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
41 1 0.02
42 33 0.80
43 7 0.17
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (43 bp):
TGTGTGTCTAGACCGTATAACTCTCTAACTTGAGTAACACGGC
Found at i:6024004 original size:20 final size:20
Alignment explanation
Indices: 6023965--6024010 Score: 58
Period size: 20 Copynumber: 2.2 Consensus size: 20
6023955 CCAATATGAT
*
6023965 GTTCTTCAGGATTTCTTCAA
1 GTTCTTCAGAATTTCTTCAA
6023985 GTTCTTCAGAAATTTC-TCAA
1 GTTCTTCAG-AATTTCTTCAA
6024005 GATTCT
1 G-TTCT
6024011 AAAAAGAGCT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 14 0.61
21 9 0.39
ACGTcount: A:0.24, C:0.20, G:0.13, T:0.43
Consensus pattern (20 bp):
GTTCTTCAGAATTTCTTCAA
Found at i:6030720 original size:12 final size:12
Alignment explanation
Indices: 6030703--6030727 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
6030693 ACATCAATTC
6030703 AATAATATACCA
1 AATAATATACCA
6030715 AATAATATACCA
1 AATAATATACCA
6030727 A
1 A
6030728 TTGCATTCAA
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:0.60, C:0.16, G:0.00, T:0.24
Consensus pattern (12 bp):
AATAATATACCA
Found at i:6031658 original size:19 final size:19
Alignment explanation
Indices: 6031630--6031687 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
6031620 TACTAGCGTG
*
6031630 CAAAACGCATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
* *
6031649 -AAAAGTGCATACTGGCACA
1 CAAAA-TGCATCCTGGCGCA
*
6031668 CAAAATACATCCTGGCGCA
1 CAAAATGCATCCTGGCGCA
6031687 C
1 C
6031688 GAAGCGCATA
Statistics
Matches: 31, Mismatches: 6, Indels: 4
0.76 0.15 0.10
Matches are distributed among these distances:
18 4 0.13
19 23 0.74
20 4 0.13
ACGTcount: A:0.36, C:0.31, G:0.19, T:0.14
Consensus pattern (19 bp):
CAAAATGCATCCTGGCGCA
Found at i:6031728 original size:19 final size:19
Alignment explanation
Indices: 6031651--6031812 Score: 85
Period size: 19 Copynumber: 8.4 Consensus size: 19
6031641 CTGGCGCAAA
*
6031651 AAGTGCATAC-TGGCACACA
1 AAGTGCAT-CTTGGCACACG
* * * *
6031670 AAATACATCCTGGCGCACG
1 AAGTGCATCTTGGCACACG
* * *
6031689 AAGCGCATATCTGGAACACG
1 AAGTGCATCT-TGGCACACG
*
6031709 ATGTGCATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
* *
6031728 AAGTGCATAC-TGGCATACA
1 AAGTGCAT-CTTGGCACACG
* * **
6031747 AAGTGCATCCTAGTGCACG
1 AAGTGCATCTTGGCACACG
* * * *
6031766 AAGCGTATATCTGGCACATG
1 AAGTGCATCT-TGGCACACG
* *
6031786 ATGTGTATCTTGGCACACG
1 AAGTGCATCTTGGCACACG
6031805 AAGTGCAT
1 AAGTGCAT
6031813 TATGAAGAAT
Statistics
Matches: 101, Mismatches: 37, Indels: 10
0.68 0.25 0.07
Matches are distributed among these distances:
18 2 0.02
19 72 0.71
20 27 0.27
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (19 bp):
AAGTGCATCTTGGCACACG
Found at i:6031732 original size:77 final size:77
Alignment explanation
Indices: 6031651--6031812 Score: 243
Period size: 77 Copynumber: 2.1 Consensus size: 77
6031641 CTGGCGCAAA
*
6031651 AAGTGCATACTGGCACACAAAATACATCCTGGCGCACGAAGCGCATATCTGGAACACGATGTGCA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
6031716 TCTTGGCACACG
66 TCTTGGCACACG
* * * * * * * *
6031728 AAGTGCATACTGGCATACAAAGTGCATCCTAGTGCACGAAGCGTATATCTGGCACATGATGTGTA
1 AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
6031793 TCTTGGCACACG
66 TCTTGGCACACG
6031805 AAGTGCAT
1 AAGTGCAT
6031813 TATGAAGAAT
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
77 76 1.00
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (77 bp):
AAGTGCATACTGGCACACAAAATACATCCTAGCGCACGAAGCGCATATCTGGAACACGATGTGCA
TCTTGGCACACG
Found at i:6032382 original size:2 final size:2
Alignment explanation
Indices: 6032375--6032401 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6032365 CATATAATTA
6032375 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 A
6032402 GGCTTACAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6034710 original size:2 final size:2
Alignment explanation
Indices: 6034703--6034738 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
6034693 TTCTAAGAAC
6034703 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6034739 GAAAATGCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:6035075 original size:19 final size:18
Alignment explanation
Indices: 6035051--6035087 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
6035041 AACTTAAAAA
*
6035051 AAATATATATTAAATATGC
1 AAATATATA-AAAATATGC
6035070 AAATATATAAAAATATGC
1 AAATATATAAAAATATGC
6035088 GAATGTAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.32
Consensus pattern (18 bp):
AAATATATAAAAATATGC
Found at i:6035603 original size:11 final size:11
Alignment explanation
Indices: 6035583--6035624 Score: 59
Period size: 11 Copynumber: 3.9 Consensus size: 11
6035573 AAATTGCAAC
6035583 AGAAAGAAAAA
1 AGAAAGAAAAA
6035594 AGAAA-AAAAA
1 AGAAAGAAAAA
*
6035604 TGAAAGAAAAA
1 AGAAAGAAAAA
*
6035615 AGATAGAAAA
1 AGAAAGAAAA
6035625 CTCTCTGTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.05
Consensus pattern (11 bp):
AGAAAGAAAAA
Found at i:6036845 original size:45 final size:45
Alignment explanation
Indices: 6036777--6036975 Score: 165
Period size: 45 Copynumber: 4.5 Consensus size: 45
6036767 TCACGCCAAT
* * *
6036777 GAAGACAAGGTCT-GTTCTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTACTT-TCTTCGATCTACTTCACCACCAGTATGG
* * * **
6036822 GGATACAAGATCTA-TTGTCTTCGATCTACTTCA-CGCCAGTATAT
1 GAAGACAAGATCTACTT-TCTTCGATCTACTTCACCACCAGTATGG
* * *
6036866 GAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGG
** * * ***
6036911 GAAGACAAGATCTGGTATC-TCTGATCTACTTCA-CGCCAGTACAT
1 GAAGACAAGATCTACTTTCTTC-GATCTACTTCACCACCAGTATGG
*
6036955 GAAGACAAGATCTGCTTTCTT
1 GAAGACAAGATCTACTTTCTT
6036976 TGAACCTGCT
Statistics
Matches: 121, Mismatches: 28, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
44 58 0.48
45 63 0.52
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.30
Consensus pattern (45 bp):
GAAGACAAGATCTACTTTCTTCGATCTACTTCACCACCAGTATGG
Found at i:6036903 original size:89 final size:88
Alignment explanation
Indices: 6036775--6036978 Score: 257
Period size: 89 Copynumber: 2.3 Consensus size: 88
6036765 CCTCACGCCA
* * * * * * *
6036775 ATGAAGACAAGGTCTGTTCTCTTCGATCTACTCCACCACCAGTATGGGGATACAAGATCTATTGT
1 ATGAAGACAAGATCTCTT-TCTTTGATCTACTCCACCACCAGTATGGGAAGACAAGATCTAGTAT
*
6036840 CT-TCGATCTACTTCACGCCAGTAT
65 CTCT-GATCTACTTCACGCCAGTAC
* * * *
6036864 ATGAAGACAAGATCTACTTTCTTTGATCTGCTTCGCCACCAGTATGGGAAGACAAGATCTGGTAT
1 ATGAAGACAAGATCT-CTTTCTTTGATCTACTCCACCACCAGTATGGGAAGACAAGATCTAGTAT
6036929 CTCTGATCTACTTCACGCCAGTAC
65 CTCTGATCTACTTCACGCCAGTAC
6036953 ATGAAGACAAGATCTGCTTTCTTTGA
1 ATGAAGACAAGATCT-CTTTCTTTGA
6036979 ACCTGCTCCA
Statistics
Matches: 100, Mismatches: 13, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
89 97 0.97
90 3 0.03
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (88 bp):
ATGAAGACAAGATCTCTTTCTTTGATCTACTCCACCACCAGTATGGGAAGACAAGATCTAGTATC
TCTGATCTACTTCACGCCAGTAC
Found at i:6038279 original size:13 final size:14
Alignment explanation
Indices: 6038261--6038309 Score: 57
Period size: 13 Copynumber: 3.6 Consensus size: 14
6038251 CCTTAGTCTC
6038261 TCCATTTT-ACTTT
1 TCCATTTTCACTTT
*
6038274 TCCATTTTTCAGTTT
1 TCCA-TTTTCACTTT
6038289 T-CATTTTCACTTT
1 TCCATTTTCACTTT
*
6038302 TTCATTTT
1 TCCATTTT
6038310 TCATCTCGTC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
13 14 0.45
14 12 0.39
15 5 0.16
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.63
Consensus pattern (14 bp):
TCCATTTTCACTTT
Found at i:6038289 original size:7 final size:7
Alignment explanation
Indices: 6038271--6038313 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
6038261 TCCATTTTAC
*
6038271 TTTTCCA
1 TTTTTCA
6038278 TTTTTCA
1 TTTTTCA
*
6038285 GTTTTCA
1 TTTTTCA
6038292 -TTTTCA
1 TTTTTCA
6038298 CTTTTTCA
1 -TTTTTCA
6038306 TTTTTCA
1 TTTTTCA
6038313 T
1 T
6038314 CTCGTCATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 6 0.19
7 20 0.62
8 6 0.19
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.65
Consensus pattern (7 bp):
TTTTTCA
Found at i:6038293 original size:14 final size:15
Alignment explanation
Indices: 6038271--6038312 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
6038261 TCCATTTTAC
6038271 TTTTCCATTTTTCA-G
1 TTTT-CATTTTTCACG
*
6038286 TTTTCA-TTTTCACT
1 TTTTCATTTTTCACG
6038300 TTTTCATTTTTCA
1 TTTTCATTTTTCA
6038313 TCTCGTCATT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
13 6 0.25
14 8 0.33
15 10 0.42
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.64
Consensus pattern (15 bp):
TTTTCATTTTTCACG
Found at i:6041200 original size:19 final size:19
Alignment explanation
Indices: 6041160--6041201 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6041150 ATAATCTTTG
* *
6041160 ATGCATATGATGTAATGTA
1 ATGCAAATGATGAAATGTA
6041179 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
6041198 ATGC
1 ATGC
6041202 GAAAAGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.10, G:0.21, T:0.29
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Found at i:6044704 original size:43 final size:43
Alignment explanation
Indices: 6044644--6044791 Score: 215
Period size: 43 Copynumber: 3.4 Consensus size: 43
6044634 TGTCCCAAAC
* ***
6044644 ATGGTCTTACATGGAAATCTTGTATCGATGCCAATAGCCCAGCT
1 ATGGTCTTACA-CGAAATCTCAAATCGATGCCAATAGCCCAGCT
* * *
6044688 ATAGTCTTACATGAAATCTCAAATCGATGCCAATAGCCCAGTT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
*
6044731 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCGCAGCT
1 ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
6044774 ATGGTCTTACACGAAATC
1 ATGGTCTTACACGAAATC
6044792 ACACCTCGGA
Statistics
Matches: 94, Mismatches: 10, Indels: 1
0.90 0.10 0.01
Matches are distributed among these distances:
43 84 0.89
44 10 0.11
ACGTcount: A:0.32, C:0.24, G:0.18, T:0.27
Consensus pattern (43 bp):
ATGGTCTTACACGAAATCTCAAATCGATGCCAATAGCCCAGCT
Found at i:6045006 original size:31 final size:31
Alignment explanation
Indices: 6044901--6045009 Score: 166
Period size: 31 Copynumber: 3.5 Consensus size: 31
6044891 AACTAGTCTC
* * *
6044901 AATTCGGCAATATATATCCATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
*
6044932 AATTCGACAATGAATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
6044963 AATTCGACAATGTATATCTATATACAAATCA
1 AATTCGACAATGTATATCTATATACAAATCA
6044994 AATTCGGA-AATGTATA
1 AATTC-GACAATGTATA
6045010 AAACATATAC
Statistics
Matches: 72, Mismatches: 5, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
31 70 0.97
32 2 0.03
ACGTcount: A:0.46, C:0.16, G:0.08, T:0.30
Consensus pattern (31 bp):
AATTCGACAATGTATATCTATATACAAATCA
Found at i:6049235 original size:6 final size:6
Alignment explanation
Indices: 6049226--6049296 Score: 76
Period size: 6 Copynumber: 12.3 Consensus size: 6
6049216 CTAAGAAAAT
* * * * *
6049226 AATAAA AAT--A ACTAAA AATAAC AATAAA CATAAT CAT-AA AATAAA
1 AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA AATAAA
6049271 AATAAA AATAAA AATAAA AATAAA AA
1 AATAAA AATAAA AATAAA AATAAA AA
6049297 AACTTAATGG
Statistics
Matches: 54, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
4 3 0.06
5 3 0.06
6 48 0.89
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (6 bp):
AATAAA
Found at i:6049274 original size:23 final size:24
Alignment explanation
Indices: 6049226--6049296 Score: 76
Period size: 23 Copynumber: 3.1 Consensus size: 24
6049216 CTAAGAAAAT
* *
6049226 AATAAAAAT--AACTAAAAATAAC
1 AATAAAAATAAAAATAAAAATAAA
* **
6049248 AATAAACATAATCAT-AAAATAAA
1 AATAAAAATAAAAATAAAAATAAA
6049271 AATAAAAATAAAAATAAAAATAAA
1 AATAAAAATAAAAATAAAAATAAA
6049295 AA
1 AA
6049297 AACTTAATGG
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
22 8 0.21
23 19 0.50
24 11 0.29
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (24 bp):
AATAAAAATAAAAATAAAAATAAA
Found at i:6049293 original size:29 final size:29
Alignment explanation
Indices: 6049226--6049295 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
6049216 CTAAGAAAAT
* *
6049226 AATAAAAAT-AACTAAAAATAACAATAAA
1 AATAAAAATAAAATAAAAATAAAAATAAA
* **
6049254 CATAATCATAAAATAAAAATAAAAATAAA
1 AATAAAAATAAAATAAAAATAAAAATAAA
6049283 AATAAAAATAAAA
1 AATAAAAATAAAA
6049296 AAACTTAATG
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
28 6 0.18
29 27 0.82
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.19
Consensus pattern (29 bp):
AATAAAAATAAAATAAAAATAAAAATAAA
Found at i:6051149 original size:15 final size:16
Alignment explanation
Indices: 6051124--6051153 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
6051114 GTTGACCTCT
6051124 AAAAGACAAAAAAAGA
1 AAAAGACAAAAAAAGA
6051140 AAAAGA-AAAAAAAG
1 AAAAGACAAAAAAAG
6051154 CTGAAGATGC
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:0.83, C:0.03, G:0.13, T:0.00
Consensus pattern (16 bp):
AAAAGACAAAAAAAGA
Found at i:6055149 original size:14 final size:15
Alignment explanation
Indices: 6055115--6055149 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
6055105 TAAATCCATT
6055115 TTTATATTTAAGTAC
1 TTTATATTTAAGTAC
6055130 TTTATATTTAAGTA-
1 TTTATATTTAAGTAC
6055144 TTTATA
1 TTTATA
6055150 CAATAAATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 6 0.30
15 14 0.70
ACGTcount: A:0.34, C:0.03, G:0.06, T:0.57
Consensus pattern (15 bp):
TTTATATTTAAGTAC
Found at i:6055180 original size:13 final size:13
Alignment explanation
Indices: 6055162--6055186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
6055152 ATAAATATTC
6055162 TTAAATATTTTTT
1 TTAAATATTTTTT
6055175 TTAAATATTTTT
1 TTAAATATTTTT
6055187 ATACGGGTAC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTAAATATTTTTT
Found at i:6058322 original size:31 final size:32
Alignment explanation
Indices: 6058263--6058327 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
6058253 GGCAAATTAC
6058263 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6058295 AAGAGTAATTGAATCCTAAT-AAAACTCTTTA
1 AAGAGTAATTGAATCCTAATAAAAACTCTTTA
6058326 AA
1 AA
6058328 ATTATCTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
31 13 0.39
32 20 0.61
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (32 bp):
AAGAGTAATTGAATCCTAATAAAAACTCTTTA
Found at i:6059121 original size:15 final size:15
Alignment explanation
Indices: 6059090--6059144 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 15
6059080 CATCATCATC
*
6059090 ATAATAATAAATGAA
1 ATAATAATAAATAAA
6059105 ATAATTAATAAA-AAA
1 ATAA-TAATAAATAAA
*
6059120 ATATAGTATTAAATAAA
1 ATA-A-TAATAAATAAA
6059137 ATAA-AATA
1 ATAATAATA
6059145 CAATGAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
14 3 0.09
15 9 0.27
16 15 0.45
17 6 0.18
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (15 bp):
ATAATAATAAATAAA
Found at i:6063859 original size:22 final size:22
Alignment explanation
Indices: 6063830--6063883 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
6063820 GATATGCAAG
6063830 GGTT-GAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
6063851 GGTTCGAATGCCCTAATGTTTT
1 GGTTCGAATGCCCTAATGTTTT
*
6063873 GGGTCGAATGC
1 GGTTCGAATGC
6063884 TCGATTTGAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
21 4 0.13
22 27 0.87
ACGTcount: A:0.19, C:0.17, G:0.28, T:0.37
Consensus pattern (22 bp):
GGTTCGAATGCCCTAATGTTTT
Found at i:6064311 original size:26 final size:26
Alignment explanation
Indices: 6064275--6064357 Score: 96
Period size: 26 Copynumber: 3.1 Consensus size: 26
6064265 TATGCGTTAA
6064275 TCTGTGTCAAGAATGAGCCTGTTGGT
1 TCTGTGTCAAGAATGAGCCTGTTGGT
6064301 TCTGTGTCAAGAATGAGCCTG-TGCGTT
1 TCTGTGTCAAGAATGAGCCTGTTG-G-T
* * *
6064328 AATCTGTGTCAAGAGTGGGCTTGTTGGT
1 --TCTGTGTCAAGAATGAGCCTGTTGGT
6064356 TC
1 TC
6064358 AATGGATAAG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
25 2 0.04
26 24 0.49
27 1 0.02
28 1 0.02
29 19 0.39
30 2 0.04
ACGTcount: A:0.18, C:0.16, G:0.31, T:0.35
Consensus pattern (26 bp):
TCTGTGTCAAGAATGAGCCTGTTGGT
Found at i:6068690 original size:23 final size:23
Alignment explanation
Indices: 6068664--6068707 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
6068654 TAATTAGTAA
6068664 TTTAAT-ATTTAATATTTTTTATT
1 TTTAATAATTT-ATATTTTTTATT
*
6068687 TTTAATAATTTATTTTTTTTA
1 TTTAATAATTTATATTTTTTA
6068708 AATTGATCAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 15 0.79
24 4 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTAATAATTTATATTTTTTATT
Found at i:6068692 original size:16 final size:17
Alignment explanation
Indices: 6068671--6068708 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
6068661 TAATTTAATA
6068671 TTTAAT-ATTT-TTTATT
1 TTTAATAATTTATTT-TT
6068687 TTTAATAATTTATTTTT
1 TTTAATAATTTATTTTT
6068704 TTTAA
1 TTTAA
6068709 ATTGATCAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 6 0.30
17 11 0.55
18 3 0.15
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TTTAATAATTTATTTTT
Found at i:6068813 original size:27 final size:27
Alignment explanation
Indices: 6068764--6068822 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
6068754 AGTGAATTCA
* * *
6068764 AAATATATTTTAATTAGGAAATTGATT
1 AAATTTATTTTAATTAGAAAATTAATT
6068791 AAATTTATTTTAATTA-AACAATTAATT
1 AAATTTATTTTAATTAGAA-AATTAATT
*
6068818 TAATT
1 AAATT
6068823 AAAATATTAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 26 0.96
ACGTcount: A:0.46, C:0.02, G:0.05, T:0.47
Consensus pattern (27 bp):
AAATTTATTTTAATTAGAAAATTAATT
Found at i:6068821 original size:17 final size:17
Alignment explanation
Indices: 6068799--6068838 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
6068789 TTAAATTTAT
6068799 TTTAATTAAACA-ATTAA
1 TTTAATTAAA-ATATTAA
6068816 TTTAATTAAAATATTAA
1 TTTAATTAAAATATTAA
6068833 -TTAATT
1 TTTAATT
6068839 GGATTAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 7 0.32
17 15 0.68
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTAATTAAAATATTAA
Found at i:6069868 original size:17 final size:17
Alignment explanation
Indices: 6069848--6069884 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
6069838 AATTTTTGAA
6069848 TTAGTGAATTCTGTGAT
1 TTAGTGAATTCTGTGAT
*
6069865 TTAGTGAATTTTGTGAT
1 TTAGTGAATTCTGTGAT
6069882 TTA
1 TTA
6069885 AAAAGAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.24, C:0.03, G:0.22, T:0.51
Consensus pattern (17 bp):
TTAGTGAATTCTGTGAT
Found at i:6071164 original size:46 final size:46
Alignment explanation
Indices: 6071111--6071250 Score: 253
Period size: 46 Copynumber: 3.0 Consensus size: 46
6071101 CCATTGCAAA
*
6071111 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAATCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
6071157 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
* *
6071203 TTGTGAAAAGTATGTATGGTATTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
6071249 TT
1 TT
6071251 ATAGCATTGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
46 91 1.00
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
Found at i:6072189 original size:23 final size:23
Alignment explanation
Indices: 6072163--6072213 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
6072153 ACCAAAAATT
*
6072163 ATGA-AAATTAAATTAGAAGCTGA
1 ATGAGAAATGAAATTA-AAGCTGA
* *
6072186 ATGAGATATGAAATTAAAGTTGA
1 ATGAGAAATGAAATTAAAGCTGA
6072209 ATGAG
1 ATGAG
6072214 TCTATTTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.49, C:0.02, G:0.22, T:0.27
Consensus pattern (23 bp):
ATGAGAAATGAAATTAAAGCTGA
Found at i:6078407 original size:17 final size:17
Alignment explanation
Indices: 6078378--6078410 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6078368 ATGAATAAAA
6078378 AATAATAATTTTTTTTG
1 AATAATAATTTTTTTTG
6078395 AATAA-AATATTTTTTT
1 AATAATAAT-TTTTTTT
6078411 ATATTTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.20
17 12 0.80
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (17 bp):
AATAATAATTTTTTTTG
Found at i:6078625 original size:8 final size:8
Alignment explanation
Indices: 6078612--6078701 Score: 56
Period size: 8 Copynumber: 10.4 Consensus size: 8
6078602 ATTTTGTATG
6078612 AATATTGT
1 AATATTGT
*
6078620 AATATTAT
1 AATATTGT
*
6078628 AATTTTGTAT
1 AATATTG--T
6078638 GAATATTGT
1 -AATATTGT
6078647 AATATTGT
1 AATATTGT
6078655 AAT-TTGTAT
1 AATATTG--T
6078664 GAATATTGT
1 -AATATTGT
* * *
6078673 AATGTCGGG
1 AATAT-TGT
6078682 ATATATTGT
1 A-ATATTGT
6078691 AATATTGT
1 AATATTGT
6078699 AAT
1 AAT
6078702 TTTTTGTATG
Statistics
Matches: 63, Mismatches: 10, Indels: 18
0.69 0.11 0.20
Matches are distributed among these distances:
7 3 0.05
8 37 0.59
9 7 0.11
10 7 0.11
11 9 0.14
ACGTcount: A:0.36, C:0.01, G:0.16, T:0.48
Consensus pattern (8 bp):
AATATTGT
Found at i:6078667 original size:26 final size:27
Alignment explanation
Indices: 6078602--6078675 Score: 132
Period size: 27 Copynumber: 2.8 Consensus size: 27
6078592 TTGGATTAGT
6078602 ATTTTGTATGAATATTGTAATATTATA
1 ATTTTGTATGAATATTGTAATATTATA
*
6078629 ATTTTGTATGAATATTGTAATATTGTA
1 ATTTTGTATGAATATTGTAATATTATA
6078656 A-TTTGTATGAATATTGTAAT
1 ATTTTGTATGAATATTGTAAT
6078676 GTCGGGATAT
Statistics
Matches: 46, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
26 19 0.41
27 27 0.59
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (27 bp):
ATTTTGTATGAATATTGTAATATTATA
Found at i:6078904 original size:16 final size:16
Alignment explanation
Indices: 6078861--6078904 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
6078851 AAAATCAAAT
*
6078861 AAAATTTAATTATATA
1 AAAATTAAATTATATA
* *
6078877 AAAGTTACATTATATA
1 AAAATTAAATTATATA
6078893 AAAATTAAATTA
1 AAAATTAAATTA
6078905 GTTAACAACA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (16 bp):
AAAATTAAATTATATA
Found at i:6078980 original size:38 final size:38
Alignment explanation
Indices: 6078937--6079018 Score: 155
Period size: 38 Copynumber: 2.2 Consensus size: 38
6078927 AAAAAGTCAG
6078937 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
*
6078975 TTATAATTAAACTTTTAATAAGATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
6079013 TTATAA
1 TTATAA
6079019 ACTTTATATG
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 43 1.00
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (38 bp):
TTATAATTAAACTTTTAATAAAATGATTTTTAATTTTT
Found at i:6079434 original size:27 final size:27
Alignment explanation
Indices: 6079396--6079462 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
6079386 NNNNNNNNNA
6079396 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
6079423 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
6079450 TTCATTGGCGCCT
1 TTCATTGGCGCCT
6079463 ACTTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:6084123 original size:2 final size:2
Alignment explanation
Indices: 6084116--6084142 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6084106 GAGAAGAACA
6084116 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 A
6084143 CACTGACCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:6085628 original size:16 final size:17
Alignment explanation
Indices: 6085603--6085635 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
6085593 TGTCTCCCCC
*
6085603 TCTTCCCCAT-ATTCCT
1 TCTTCACCATCATTCCT
6085619 TCTTCACCATCATTCCT
1 TCTTCACCATCATTCCT
6085636 CTCACCCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.15, C:0.42, G:0.00, T:0.42
Consensus pattern (17 bp):
TCTTCACCATCATTCCT
Found at i:6089181 original size:18 final size:18
Alignment explanation
Indices: 6089160--6089196 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
6089150 TGAGTTTTCG
6089160 AATTCGAATAATTTAAAT
1 AATTCGAATAATTTAAAT
*
6089178 AATTCGAATAATTTGAAT
1 AATTCGAATAATTTAAAT
6089196 A
1 A
6089197 TCAAACTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.05, G:0.08, T:0.38
Consensus pattern (18 bp):
AATTCGAATAATTTAAAT
Found at i:6093340 original size:14 final size:15
Alignment explanation
Indices: 6093321--6093352 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
6093311 TTTTGATCAC
6093321 ATAAAATT-AAATTA
1 ATAAAATTAAAATTA
6093335 ATAAAATTAAAATTA
1 ATAAAATTAAAATTA
6093350 ATA
1 ATA
6093353 TAATATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
ATAAAATTAAAATTA
Found at i:6093875 original size:17 final size:17
Alignment explanation
Indices: 6093829--6093879 Score: 57
Period size: 20 Copynumber: 2.8 Consensus size: 17
6093819 ATAGTATTTT
*
6093829 ATTAATTTGATATTAAA
1 ATTAATTTAATATTAAA
*
6093846 GTTATTATCTTAATATTAAA
1 ATTA--AT-TTAATATTAAA
6093866 ATTAATTTAATATT
1 ATTAATTTAATATT
6093880 TATCTTGTAG
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 11 0.39
18 2 0.07
19 2 0.07
20 13 0.46
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (17 bp):
ATTAATTTAATATTAAA
Found at i:6099255 original size:34 final size:34
Alignment explanation
Indices: 6099212--6099279 Score: 86
Period size: 34 Copynumber: 2.0 Consensus size: 34
6099202 GCATTTTTGA
* *
6099212 CACTGTACTGAGATGGGC-TAGGGCCCAA-ACTGT
1 CACTGTACTGAAAAGGGCTTA-GGCCCAAGACTGT
6099245 CACTGATACTGAAAAGGGCTTAGGCCCAAGACTGT
1 CACTG-TACTGAAAAGGGCTTAGGCCCAAGACTGT
6099280 TCAACTGTGC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
33 5 0.17
34 18 0.60
35 7 0.23
ACGTcount: A:0.28, C:0.24, G:0.28, T:0.21
Consensus pattern (34 bp):
CACTGTACTGAAAAGGGCTTAGGCCCAAGACTGT
Found at i:6102072 original size:17 final size:17
Alignment explanation
Indices: 6102046--6102144 Score: 59
Period size: 17 Copynumber: 5.8 Consensus size: 17
6102036 ATTTATCTAC
*
6102046 AAATTAAATATTAAATT
1 AAATTTAATATTAAATT
6102063 AAATTTAATATTAAGA-T
1 AAATTTAATATTAA-ATT
6102080 AACCACTTTAATATTAAATTT
1 AA--A-TTTAATATTAAA-TT
* *
6102101 AAA---AA-ATTACTATC
1 AAATTTAATATTA-AATT
6102115 AAA--TAAGTATTAAATT
1 AAATTTAA-TATTAAATT
6102131 AAATTTAATATTAA
1 AAATTTAATATTAA
6102145 TTTATTAAAA
Statistics
Matches: 65, Mismatches: 5, Indels: 24
0.69 0.05 0.26
Matches are distributed among these distances:
14 8 0.12
15 5 0.08
16 5 0.08
17 26 0.40
18 4 0.06
19 3 0.05
20 11 0.17
21 3 0.05
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (17 bp):
AAATTTAATATTAAATT
Found at i:6105364 original size:14 final size:14
Alignment explanation
Indices: 6105326--6105358 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
6105316 TACATGTATG
*
6105326 TAATTTAACAAATA
1 TAATCTAACAAATA
6105340 TAATCTAACAAATA
1 TAATCTAACAAATA
6105354 TAATC
1 TAATC
6105359 ATACAATTCA
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:0.12, G:0.00, T:0.33
Consensus pattern (14 bp):
TAATCTAACAAATA
Found at i:6107703 original size:27 final size:29
Alignment explanation
Indices: 6107673--6107728 Score: 71
Period size: 27 Copynumber: 2.0 Consensus size: 29
6107663 GCAAAGTCAC
*
6107673 ATGTGCATATTTG-AC-AATCAAAATTTT
1 ATGTGCATAATTGCACAAATCAAAATTTT
*
6107700 ATGTTCATAATTGCACAAAATCAAAATTT
1 ATGTGCATAATTGCAC-AAATCAAAATTT
6107729 ACAAATCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 11 0.46
28 2 0.08
30 11 0.46
ACGTcount: A:0.41, C:0.12, G:0.09, T:0.38
Consensus pattern (29 bp):
ATGTGCATAATTGCACAAATCAAAATTTT
Found at i:6120305 original size:6 final size:6
Alignment explanation
Indices: 6120294--6120318 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
6120284 AGATATGCCG
6120294 ATATGT ATATGT ATATGT ATATGT A
1 ATATGT ATATGT ATATGT ATATGT A
6120319 CGTATGTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.48
Consensus pattern (6 bp):
ATATGT
Found at i:6121682 original size:2 final size:2
Alignment explanation
Indices: 6121675--6121725 Score: 66
Period size: 2 Copynumber: 25.5 Consensus size: 2
6121665 ATACATACAT
* * *
6121675 AC AC AC AC AC GC AC GC AC GC AC AC AC AC AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
*
6121717 AC AC GC AC A
1 AC AC AC AC A
6121726 TACATACATG
Statistics
Matches: 41, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.43, C:0.49, G:0.08, T:0.00
Consensus pattern (2 bp):
AC
Found at i:6123443 original size:9 final size:9
Alignment explanation
Indices: 6123425--6123464 Score: 62
Period size: 9 Copynumber: 4.4 Consensus size: 9
6123415 TTTGGTTAAA
6123425 AATTAACCG
1 AATTAACCG
*
6123434 AATTACCCG
1 AATTAACCG
6123443 AATTAACCG
1 AATTAACCG
*
6123452 AATTACCCG
1 AATTAACCG
6123461 AATT
1 AATT
6123465 GAATCATTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 28 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (9 bp):
AATTAACCG
Found at i:6123448 original size:18 final size:18
Alignment explanation
Indices: 6123425--6123464 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
6123415 TTTGGTTAAA
6123425 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
6123443 AATTAACCGAATTACCCG
1 AATTAACCGAATTACCCG
6123461 AATT
1 AATT
6123465 GAATCATTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.40, C:0.25, G:0.10, T:0.25
Consensus pattern (18 bp):
AATTAACCGAATTACCCG
Found at i:6123712 original size:39 final size:39
Alignment explanation
Indices: 6123630--6123746 Score: 200
Period size: 39 Copynumber: 3.0 Consensus size: 39
6123620 ACTTAAGAGT
*
6123630 TAGACTTTAGTTTTATTTTTATTGGGTT-GGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
6123668 TAGACTTTAGTTTTAGTTTTATTGAGTTGGGTAATTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
*
6123707 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTATTTGGG
1 TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
6123746 T
1 T
6123747 TGGGTTGGTA
Statistics
Matches: 74, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
38 26 0.35
39 48 0.65
ACGTcount: A:0.18, C:0.03, G:0.28, T:0.51
Consensus pattern (39 bp):
TAGACTTTAGTTTTAGTTTTATTGGGTTGGGTAATTGGG
Found at i:6123776 original size:18 final size:17
Alignment explanation
Indices: 6123728--6123777 Score: 64
Period size: 17 Copynumber: 2.8 Consensus size: 17
6123718 TTTAGTTTTA
*
6123728 TTGGGTTGGGTATTTGGG
1 TTGGGTT-GGTAATTGGG
6123746 TTGGGTTGGTAATTGGG
1 TTGGGTTGGTAATTGGG
*
6123763 TTTGGTTGGATAATT
1 TTGGGTTGG-TAATT
6123778 TTATTTATTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
17 17 0.59
18 12 0.41
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.46
Consensus pattern (17 bp):
TTGGGTTGGTAATTGGG
Found at i:6124407 original size:9 final size:9
Alignment explanation
Indices: 6124390--6124426 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
6124380 TGAGTTTTTG
6124390 AATTCGAAT
1 AATTCGAAT
*
6124399 AACTCGAAT
1 AATTCGAAT
6124408 AATTCGAAT
1 AATTCGAAT
6124417 AATTCGAAT
1 AATTCGAAT
6124426 A
1 A
6124427 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:6125470 original size:5 final size:5
Alignment explanation
Indices: 6125460--6125496 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
6125450 AAAATTTTTT
* *
6125460 ATTCG ATTCG ATTCG ATTTG ATTCG ATTTG ATTCG AT
1 ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG ATTCG AT
6125497 CGAATGCTCA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (5 bp):
ATTCG
Found at i:6125475 original size:10 final size:10
Alignment explanation
Indices: 6125460--6125496 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
6125450 AAAATTTTTT
*
6125460 ATTCGATTCG
1 ATTCGATTTG
6125470 ATTCGATTTG
1 ATTCGATTTG
6125480 ATTCGATTTG
1 ATTCGATTTG
6125490 ATTCGAT
1 ATTCGAT
6125497 CGAATGCTCA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 26 1.00
ACGTcount: A:0.22, C:0.14, G:0.19, T:0.46
Consensus pattern (10 bp):
ATTCGATTTG
Found at i:6126894 original size:19 final size:20
Alignment explanation
Indices: 6126866--6126915 Score: 61
Period size: 19 Copynumber: 2.6 Consensus size: 20
6126856 TTAAATTTTT
*
6126866 AAAA-ATTAAAAATCAT-TA
1 AAAATATTAAAAATAATATA
*
6126884 AAATTATT-AAAATAATATA
1 AAAATATTAAAAATAATATA
6126903 AAAATATTAAAAA
1 AAAATATTAAAAA
6126916 ATATCTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAATATTAAAAATAATATA
Found at i:6126919 original size:10 final size:9
Alignment explanation
Indices: 6126866--6126915 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
6126856 TTAAATTTTT
6126866 AAAA-ATTA
1 AAAATATTA
6126874 AAAATCATTA
1 AAAAT-ATTA
*
6126884 AAATTATT-
1 AAAATATTA
6126892 AAAATAATATA
1 AAAAT-AT-TA
6126903 AAAATATTA
1 AAAATATTA
6126912 AAAA
1 AAAA
6126916 ATATCTTTTC
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
8 8 0.23
9 11 0.31
10 11 0.31
11 5 0.14
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
AAAATATTA
Found at i:6131390 original size:124 final size:125
Alignment explanation
Indices: 6131225--6131485 Score: 427
Period size: 124 Copynumber: 2.1 Consensus size: 125
6131215 TGTTACACAG
*
6131225 TAGGTCCT-GAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGC
1 TAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * *
6131289 AGAATGCTGTTTGATAAGAATTTGTGAAATCGCGGCCTCGTGAACA-ACTTTTGCTACAA
66 AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACACACTTTTGCTACAA
*
6131348 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
* * * *
6131413 AGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACACGCTTTTGCTACAG
66 AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACACACTTTTGCTACAA
6131473 TAGGTCCTGGAAA
1 TAGGTCCTGGAAA
6131486 TTGAGAGGAA
Statistics
Matches: 126, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
123 8 0.06
124 95 0.75
125 23 0.18
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (125 bp):
TAGGTCCTGGAAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTCTAGC
AGAATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGAACACACTTTTGCTACAA
Found at i:6132516 original size:18 final size:19
Alignment explanation
Indices: 6132473--6132516 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
6132463 ATTTTATTTA
6132473 TGCATTTATTTTATTTTCT
1 TGCATTTATTTTATTTTCT
** *
6132492 TAAATTTA-TTTATTTTTT
1 TGCATTTATTTTATTTTCT
6132510 TGCATTT
1 TGCATTT
6132517 TTGAATCTGT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
18 14 0.70
19 6 0.30
ACGTcount: A:0.20, C:0.07, G:0.05, T:0.68
Consensus pattern (19 bp):
TGCATTTATTTTATTTTCT
Found at i:6138059 original size:16 final size:17
Alignment explanation
Indices: 6138040--6138076 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
6138030 TGCTTGATAG
6138040 AGAAAAGAAAA-TAAAA
1 AGAAAAGAAAAGTAAAA
6138056 AGAAAAGAAAAGTTAAAA
1 AGAAAAGAAAAG-TAAAA
6138074 AGA
1 AGA
6138077 GGGAGGCTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 11 0.58
18 8 0.42
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.08
Consensus pattern (17 bp):
AGAAAAGAAAAGTAAAA
Found at i:6143018 original size:5 final size:5
Alignment explanation
Indices: 6143008--6143032 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
6142998 GCTTTGCCTG
6143008 CTATT CTATT CTATT CTATT CTATT
1 CTATT CTATT CTATT CTATT CTATT
6143033 GTATCGGAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.20, G:0.00, T:0.60
Consensus pattern (5 bp):
CTATT
Found at i:6144112 original size:2 final size:2
Alignment explanation
Indices: 6144105--6144135 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6144095 AGTAATTATC
6144105 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
6144136 AATGTAACAC
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:6144709 original size:2 final size:2
Alignment explanation
Indices: 6144702--6144745 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
6144692 AATCCATTAC
*
6144702 TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
6144744 TA
1 TA
6144746 CACCTTACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (2 bp):
TA
Found at i:6148524 original size:26 final size:26
Alignment explanation
Indices: 6148490--6148539 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
6148480 AAATGTCAAA
*
6148490 TTTTTTTAATATTTATTGGATTAGAT
1 TTTTTTTAATATTTATAGGATTAGAT
*
6148516 TTTTTTTAATATTTGTAGGATTAG
1 TTTTTTTAATATTTATAGGATTAG
6148540 GTCAATTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.26, C:0.00, G:0.14, T:0.60
Consensus pattern (26 bp):
TTTTTTTAATATTTATAGGATTAGAT
Found at i:6151211 original size:18 final size:18
Alignment explanation
Indices: 6151171--6151211 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
6151161 ACGACATTCC
*
6151171 TGGAAAAAATTAAAAAAA
1 TGGACAAAATTAAAAAAA
* *
6151189 AGGACAAAATTAAAAATA
1 TGGACAAAATTAAAAAAA
6151207 TGGAC
1 TGGAC
6151212 GAATTGAAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.63, C:0.05, G:0.15, T:0.17
Consensus pattern (18 bp):
TGGACAAAATTAAAAAAA
Found at i:6152828 original size:113 final size:113
Alignment explanation
Indices: 6152620--6152829 Score: 303
Period size: 113 Copynumber: 1.9 Consensus size: 113
6152610 TCTTTTTCGT
* * * *
6152620 TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCGAAGAGAGATGACAACCAAGTACCCCAC
1 TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCAAAAAGAGATGAAAACCAAGCACCCCAC
* * *
6152685 ACTGGTTATTCAGCCCAACATACTCCTAATTTATTATATTTATATATG
66 ACCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
* *
6152733 TTTTCTTTTCTTAAGAATATATTGAACCTTTTGACGCAAAAAGAGATGAAAACCAAGCACCCCAC
1 TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCAAAAAGAGATGAAAACCAAGCACCCCAC
* * * *
6152798 CCCGGTTACTCATCCCAACACATTCTTAATTT
66 ACCGGTTACTCAGCCCAACACACTCCTAATTT
6152830 TTTTGTTTAA
Statistics
Matches: 84, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
113 84 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.33
Consensus pattern (113 bp):
TTTTCTTTTCTTAAGAATATATTAAACCTTTTGAAGCAAAAAGAGATGAAAACCAAGCACCCCAC
ACCGGTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATG
Found at i:6155048 original size:11 final size:13
Alignment explanation
Indices: 6155037--6155079 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
6155027 ATTATAATAT
6155037 ATAA-ATGTTATA
1 ATAATATGTTATA
*
6155049 ATAAGTATATTATA
1 ATAA-TATGTTATA
*
6155063 TTAATATGTTATA
1 ATAATATGTTATA
6155076 ATAA
1 ATAA
6155080 ACATTAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
12 4 0.16
13 11 0.44
14 10 0.40
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (13 bp):
ATAATATGTTATA
Done.