Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032246.1 Gossypioides kirkii chromosome KI_03
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: 42061019
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 2000 characters in sequence are not A, C, G, or T
File 134 of 135
Found at i:41411018 original size:27 final size:29
Alignment explanation
Indices: 41410957--41411019 Score: 69
Period size: 27 Copynumber: 2.2 Consensus size: 29
41410947 ATTAATTTTT
*
41410957 TATTTTTAAAATAATAAAATATATAAAAA
1 TATTTTTAAAATAATAAAATAGATAAAAA
* *
41410986 TGTTTTTATAAAT-A-AAAATAGAT-AATA
1 TATTTTTA-AAATAATAAAATAGATAAAAA
41411013 TATTTTT
1 TATTTTT
41411020 TTATTATTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
27 9 0.31
28 8 0.28
29 8 0.28
30 4 0.14
ACGTcount: A:0.52, C:0.00, G:0.03, T:0.44
Consensus pattern (29 bp):
TATTTTTAAAATAATAAAATAGATAAAAA
Found at i:41418972 original size:31 final size:31
Alignment explanation
Indices: 41418944--41419058 Score: 106
Period size: 31 Copynumber: 3.7 Consensus size: 31
41418934 ATGTTTTGGG
* *
41418944 AGGTTTAATTAAAACTTTTAAAAATTTTGAG
1 AGGTTTAATTAAAACTTTTAAAACTTTTGAA
* * * *
41418975 AGGATTAATTAGAACTCTCAAAACTTTTGAA
1 AGGTTTAATTAAAACTTTTAAAACTTTTGAA
* * ** *
41419006 AGGTCTAATCAAATTTTTTAAAACTTTTGGA
1 AGGTTTAATTAAAACTTTTAAAACTTTTGAA
*
41419037 AGGTTCAATTGAAAA-TTTTAAA
1 AGGTTTAATT-AAAACTTTTAAA
41419059 GGGTATAATG
Statistics
Matches: 64, Mismatches: 19, Indels: 2
0.75 0.22 0.02
Matches are distributed among these distances:
31 61 0.95
32 3 0.05
ACGTcount: A:0.41, C:0.08, G:0.13, T:0.38
Consensus pattern (31 bp):
AGGTTTAATTAAAACTTTTAAAACTTTTGAA
Found at i:41427548 original size:31 final size:31
Alignment explanation
Indices: 41427513--41427571 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
41427503 GTTATTAAAC
*
41427513 TATTCAAAAATTTTCATTTATATAATTGAAT
1 TATTCAAAAATTTTCATTTAAATAATTGAAT
* *
41427544 TATTCAAAAGTTTTTATTTAAATAATTG
1 TATTCAAAAATTTTCATTTAAATAATTG
41427572 GTCTATTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (31 bp):
TATTCAAAAATTTTCATTTAAATAATTGAAT
Found at i:41428076 original size:29 final size:28
Alignment explanation
Indices: 41428044--41428135 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 28
41428034 ACAATTTGAT
41428044 ACATGAACTTTAATTTGGTGCAATTATAC
1 ACATGAACTTTAATTTGGTGCAATTAT-C
* ** *
41428073 ACATGAAACTTAAATGCGGTTCACATGTAT-
1 ACATG-AACTTTAATTTGGTGCA-AT-TATC
* *
41428103 ACATGAACTTTGATTTAGTGCAATTATGC
1 ACATGAACTTTAATTTGGTGCAATTAT-C
41428132 ACAT
1 ACAT
41428136 TAAACTTGGA
Statistics
Matches: 48, Mismatches: 10, Indels: 10
0.71 0.15 0.15
Matches are distributed among these distances:
27 3 0.06
28 2 0.04
29 20 0.42
30 18 0.38
31 2 0.04
32 3 0.06
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (28 bp):
ACATGAACTTTAATTTGGTGCAATTATC
Found at i:41428107 original size:59 final size:59
Alignment explanation
Indices: 41428042--41428173 Score: 174
Period size: 59 Copynumber: 2.2 Consensus size: 59
41428032 TTACAATTTG
* *
41428042 ATACATGAACTTTAATTTGGTGCAATTATACACATGAAACTTAAATGCGGTTCACATGT
1 ATACATGAACTTTAATTTAGTGCAATTATACACATGAAACTTAAATGCGATTCACATGT
* * * ** * *
41428101 ATACATGAACTTTGATTTAGTGCAATTATGCACATTAAACTTGGATGTGATTCATATGT
1 ATACATGAACTTTAATTTAGTGCAATTATACACATGAAACTTAAATGCGATTCACATGT
41428160 ATACATGAAACTTT
1 ATACATG-AACTTT
41428174 TGTTTTTGAT
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
59 57 0.90
60 6 0.10
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (59 bp):
ATACATGAACTTTAATTTAGTGCAATTATACACATGAAACTTAAATGCGATTCACATGT
Found at i:41441402 original size:29 final size:29
Alignment explanation
Indices: 41441360--41441419 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
41441350 ATCTCATCTA
41441360 TTCGATAAAATATCATTTGGAGTATTAGT
1 TTCGATAAAATATCATTTGGAGTATTAGT
41441389 TTCGATAAAATATCATTTGGAGTATTAGT
1 TTCGATAAAATATCATTTGGAGTATTAGT
41441418 TT
1 TT
41441420 AGAGAAGGAT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.43
Consensus pattern (29 bp):
TTCGATAAAATATCATTTGGAGTATTAGT
Found at i:41442492 original size:3 final size:3
Alignment explanation
Indices: 41442484--41442518 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
41442474 TACTTTATTT
* *
41442484 TAA TAA TAA TAA TAA TAA TAA TAT TAA TAT TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
41442519 TTAAATTTGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:41442519 original size:6 final size:6
Alignment explanation
Indices: 41442483--41442522 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
41442473 GTACTTTATT
* * *
41442483 TTAATA ATAATA ATAATA ATAATA TTAATA TTAATA TTAA
1 TTAATA TTAATA TTAATA TTAATA TTAATA TTAATA TTAA
41442523 ATTTGTGTTA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (6 bp):
TTAATA
Found at i:41442519 original size:12 final size:12
Alignment explanation
Indices: 41442483--41442522 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
41442473 GTACTTTATT
41442483 TTAATAATAATA
1 TTAATAATAATA
*
41442495 ATAATAATAATA
1 TTAATAATAATA
*
41442507 TTAATATTAATA
1 TTAATAATAATA
41442519 TTAA
1 TTAA
41442523 ATTTGTGTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
TTAATAATAATA
Found at i:41448077 original size:15 final size:15
Alignment explanation
Indices: 41448057--41448090 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
41448047 TAAATAAAAG
41448057 TAAAATGCAATTCAT
1 TAAAATGCAATTCAT
41448072 TAAAATGCAATTCAT
1 TAAAATGCAATTCAT
41448087 TAAA
1 TAAA
41448091 TTGATGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.32
Consensus pattern (15 bp):
TAAAATGCAATTCAT
Found at i:41453990 original size:60 final size:60
Alignment explanation
Indices: 41453894--41454012 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
41453884 TTAAGTTAAC
*
41453894 TTATAGATTATTTGCTACACACTCTTCGTTGAGACCACCAATGCACAACCACCTCAAACT
1 TTATAGACTATTTGCTACACACTCTTCGTTGAGACCACCAATGCACAACCACCTCAAACT
* * *
41453954 TTATAGACTATTTGCTACACATTCTTTGTTGGGACCACCAATGCACAACCACCTCAAAC
1 TTATAGACTATTTGCTACACACTCTTCGTTGAGACCACCAATGCACAACCACCTCAAAC
41454013 GACCTAAAGT
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 55 1.00
ACGTcount: A:0.31, C:0.29, G:0.11, T:0.29
Consensus pattern (60 bp):
TTATAGACTATTTGCTACACACTCTTCGTTGAGACCACCAATGCACAACCACCTCAAACT
Found at i:41454969 original size:18 final size:18
Alignment explanation
Indices: 41454946--41454981 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
41454936 CAATGTGTGT
*
41454946 TTTTTGTTTTTTGAATTG
1 TTTTTGTTTTTGGAATTG
41454964 TTTTTGTTTTTGGAATTG
1 TTTTTGTTTTTGGAATTG
41454982 GAATCAGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.11, C:0.00, G:0.19, T:0.69
Consensus pattern (18 bp):
TTTTTGTTTTTGGAATTG
Found at i:41466125 original size:7 final size:7
Alignment explanation
Indices: 41466113--41466142 Score: 60
Period size: 7 Copynumber: 4.3 Consensus size: 7
41466103 TTATTTTCCT
41466113 GAGTTCA
1 GAGTTCA
41466120 GAGTTCA
1 GAGTTCA
41466127 GAGTTCA
1 GAGTTCA
41466134 GAGTTCA
1 GAGTTCA
41466141 GA
1 GA
41466143 CAGCAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.30, C:0.13, G:0.30, T:0.27
Consensus pattern (7 bp):
GAGTTCA
Found at i:41466595 original size:104 final size:104
Alignment explanation
Indices: 41466415--41466609 Score: 372
Period size: 104 Copynumber: 1.9 Consensus size: 104
41466405 AGCAGCCACC
41466415 GACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAACATGGTTAACAACA
1 GACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAACATGGTTAACAACA
41466480 TAAGCTTATAATTTGAAAGCAATGGACCGCCAACAGACG
66 TAAGCTTATAATTTGAAAGCAATGGACCGCCAACAGACG
*
41466519 GACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAACATGGTTAATAACA
1 GACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAACATGGTTAACAACA
*
41466584 TAAGCTTATAATTTGAAAGGAATGGA
66 TAAGCTTATAATTTGAAAGCAATGGA
41466610 TGATATTAAT
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
104 89 1.00
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.25
Consensus pattern (104 bp):
GACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAACATGGTTAACAACA
TAAGCTTATAATTTGAAAGCAATGGACCGCCAACAGACG
Found at i:41466740 original size:132 final size:125
Alignment explanation
Indices: 41466505--41466741 Score: 366
Period size: 132 Copynumber: 1.8 Consensus size: 125
41466495 AAAGCAATGG
41466505 ACCGCCAACAGACGGACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAA
1 ACCGCCAACAGACGGACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAA
** * *
41466570 CATGGTTAATAACATAAGCTTATAATTTGAAAGGAATGGATGATATTAATGGTGTAAGAC
66 CATAATCAATAACATAAGCTTATAATTTGAAAGCAATGGATGATATTAATGGTGTAAGAC
41466630 ACCGCCAACAGACGGACTACGCGCCACCTTTTACGGCGGGTTTTTTAAGTATGAAAAGAAAACTG
1 ACCGCCAACAGACGGACTACGCGCCACCTTTTACGGCGGG---TTT---TA-GAAAAGAAAACTG
*
41466695 GGTTTAACATAATCAATAACGTAAGCTTATAATTTGAAAGCAATGGA
59 GGTTTAACATAATCAATAACATAAGCTTATAATTTGAAAGCAATGGA
41466742 GAATAATAAT
Statistics
Matches: 100, Mismatches: 5, Indels: 7
0.89 0.04 0.06
Matches are distributed among these distances:
125 40 0.40
128 3 0.03
131 2 0.02
132 55 0.55
ACGTcount: A:0.35, C:0.17, G:0.22, T:0.25
Consensus pattern (125 bp):
ACCGCCAACAGACGGACTACGCGCCACCTTTTACGGCGGGTTTTAGAAAAGAAAACTGGGTTTAA
CATAATCAATAACATAAGCTTATAATTTGAAAGCAATGGATGATATTAATGGTGTAAGAC
Found at i:41473603 original size:18 final size:18
Alignment explanation
Indices: 41473580--41473617 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
41473570 ACAGACTTCA
41473580 CAGAACAGATTCAGAGAC
1 CAGAACAGATTCAGAGAC
41473598 CAGAACAGATTCAGAGAC
1 CAGAACAGATTCAGAGAC
41473616 CA
1 CA
41473618 TGATCTTGTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.45, C:0.24, G:0.21, T:0.11
Consensus pattern (18 bp):
CAGAACAGATTCAGAGAC
Found at i:41475815 original size:43 final size:45
Alignment explanation
Indices: 41475728--41475819 Score: 116
Period size: 43 Copynumber: 2.1 Consensus size: 45
41475718 ATTAACCGAC
* * *
41475728 TTTGTTTGGATTTTTTTAACTCTCAATCCGTTTATGCTTTAATAA
1 TTTGTTTGGAATTTTTTAACTCTCAATCCATTTATGCTATAATAA
* * *
41475773 TTTGTTT-GAATTTTTTAATTCTTAAT-CATTTGTGCTATAATAA
1 TTTGTTTGGAATTTTTTAACTCTCAATCCATTTATGCTATAATAA
41475816 TTTG
1 TTTG
41475820 ATTCTACTTA
Statistics
Matches: 41, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
43 18 0.44
44 16 0.39
45 7 0.17
ACGTcount: A:0.24, C:0.10, G:0.11, T:0.55
Consensus pattern (45 bp):
TTTGTTTGGAATTTTTTAACTCTCAATCCATTTATGCTATAATAA
Found at i:41481151 original size:69 final size:69
Alignment explanation
Indices: 41481027--41481160 Score: 178
Period size: 69 Copynumber: 1.9 Consensus size: 69
41481017 TGTCACTTCT
* * * *
41481027 AAAAACGAAATCTCCAATTATAAATCAACGACACAGTTTCTTTACGGAGATGGAAACCTAAACTT
1 AAAAACGAAATCTCCAATTATAAATCAACAACACAGTATCTTCACGGAGACGGAAACCTAAACTT
41481092 GCAA
66 GCAA
* * * ** *
41481096 AAAAACGAAATTTCCGATTATAAATCAACAACATAGTATCTTCGTGGGGACGGAAACCTAAACTT
1 AAAAACGAAATCTCCAATTATAAATCAACAACACAGTATCTTCACGGAGACGGAAACCTAAACTT
41481161 ACAATGCTGC
Statistics
Matches: 55, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
69 55 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (69 bp):
AAAAACGAAATCTCCAATTATAAATCAACAACACAGTATCTTCACGGAGACGGAAACCTAAACTT
GCAA
Found at i:41485272 original size:16 final size:15
Alignment explanation
Indices: 41485235--41485276 Score: 59
Period size: 14 Copynumber: 2.8 Consensus size: 15
41485225 TAATTTACAA
*
41485235 TTTTAAATA-ATAAT
1 TTTTAAATATTTAAT
41485249 TTTTAAATATTTAAT
1 TTTTAAATATTTAAT
41485264 TTTTAAAATATTT
1 TTTT-AAATATTT
41485277 TGAAAGGTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 9 0.36
15 8 0.32
16 8 0.32
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTTTAAATATTTAAT
Found at i:41494061 original size:30 final size:31
Alignment explanation
Indices: 41494012--41494071 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
41494002 AAAATTAAAA
* * *
41494012 AATTACTTTAAGAATATTTAAAATTTATATT
1 AATTACTTTAAAAACATTTAAAAATTATATT
41494043 AATTA-TTTAAAAACATTTAAAAATTATAT
1 AATTACTTTAAAAACATTTAAAAATTATAT
41494072 ATTATGTATC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 21 0.81
31 5 0.19
ACGTcount: A:0.50, C:0.03, G:0.02, T:0.45
Consensus pattern (31 bp):
AATTACTTTAAAAACATTTAAAAATTATATT
Found at i:41505468 original size:4 final size:4
Alignment explanation
Indices: 41505459--41505500 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
41505449 AACCTCATCA
* * *
41505459 GTAT GTAT GTAT GTAT GTAC GTAT GAAT GTCT GTAT GTAT GT
1 GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GTAT GT
41505501 TGCATTACCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.24, C:0.05, G:0.26, T:0.45
Consensus pattern (4 bp):
GTAT
Found at i:41509677 original size:15 final size:15
Alignment explanation
Indices: 41509659--41509702 Score: 58
Period size: 15 Copynumber: 3.1 Consensus size: 15
41509649 CATCAAAATA
*
41509659 ATCATCATCATCTCC
1 ATCATCATCACCTCC
41509674 ATCATCATCACCTCC
1 ATCATCATCACCTCC
41509689 ATC-TC--CACCTCC
1 ATCATCATCACCTCC
41509701 AT
1 AT
41509703 GATTAATTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
12 9 0.32
14 2 0.07
15 17 0.61
ACGTcount: A:0.25, C:0.45, G:0.00, T:0.30
Consensus pattern (15 bp):
ATCATCATCACCTCC
Found at i:41522553 original size:16 final size:17
Alignment explanation
Indices: 41522533--41522573 Score: 57
Period size: 18 Copynumber: 2.4 Consensus size: 17
41522523 TAATCCCTTC
41522533 AAAATT-TATAAAAGTA
1 AAAATTATATAAAAGTA
*
41522549 TAAATTAATATAAAAGTA
1 AAAATT-ATATAAAAGTA
41522567 AAAATTA
1 AAAATTA
41522574 CACTTTATTC
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
16 5 0.24
17 1 0.05
18 15 0.71
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.32
Consensus pattern (17 bp):
AAAATTATATAAAAGTA
Found at i:41522562 original size:18 final size:18
Alignment explanation
Indices: 41522539--41522573 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
41522529 CTTCAAAATT
*
41522539 TATAAAAGTATAAATTAA
1 TATAAAAGTAAAAATTAA
41522557 TATAAAAGTAAAAATTA
1 TATAAAAGTAAAAATTA
41522574 CACTTTATTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (18 bp):
TATAAAAGTAAAAATTAA
Found at i:41523094 original size:18 final size:17
Alignment explanation
Indices: 41523073--41523115 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
41523063 CCATGTTAGC
* *
41523073 AAAAAAAATTTAAACTT
1 AAAAAAAAATTAAAATT
*
41523090 AAAAACATAATTAAAATT
1 AAAAA-AAAATTAAAATT
41523108 AAAAAAAA
1 AAAAAAAA
41523116 CCTTTAAAAC
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (17 bp):
AAAAAAAAATTAAAATT
Found at i:41523644 original size:30 final size:30
Alignment explanation
Indices: 41523600--41523657 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
41523590 AATTTGGAGA
*
41523600 TTTTAGGTTGTTGAATTGGGGGATTTTGGG
1 TTTTAGGTGGTTGAATTGGGGGATTTTGGG
* *
41523630 TTTTGGGTGGTTGAATTTGGGGATTTTG
1 TTTTAGGTGGTTGAATTGGGGGATTTTG
41523658 AGTAAGAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.12, C:0.00, G:0.40, T:0.48
Consensus pattern (30 bp):
TTTTAGGTGGTTGAATTGGGGGATTTTGGG
Found at i:41524308 original size:19 final size:18
Alignment explanation
Indices: 41524284--41524335 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
41524274 TCATTAAATT
41524284 TTTTAACTATTTTTTTTAA
1 TTTTAA-TATTTTTTTTAA
*
41524303 TTTTAAT-TATGTTTTTAA
1 TTTTAATAT-TTTTTTTAA
*
41524321 GTTTAA-ATTTTTTTT
1 TTTTAATATTTTTTTT
41524336 GTTGACGTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
17 7 0.25
18 15 0.54
19 6 0.21
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (18 bp):
TTTTAATATTTTTTTTAA
Found at i:41524842 original size:29 final size:29
Alignment explanation
Indices: 41524810--41524881 Score: 69
Period size: 29 Copynumber: 2.5 Consensus size: 29
41524800 TTTTTTTAAA
41524810 ATTTAAAAATTTTAAAAA-AATAAAAATTT
1 ATTTAAAAATTTTAAAAATAAT-AAAATTT
* *
41524839 ATTTTTAAAAA--TTAAAAATAATTACATTT
1 A--TTTAAAAATTTTAAAAATAATAAAATTT
*
41524868 TTTTAAAAATTTTA
1 ATTTAAAAATTTTA
41524882 TTTATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 10
0.73 0.06 0.21
Matches are distributed among these distances:
27 8 0.23
29 16 0.46
30 3 0.09
31 8 0.23
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.44
Consensus pattern (29 bp):
ATTTAAAAATTTTAAAAATAATAAAATTT
Found at i:41524848 original size:21 final size:21
Alignment explanation
Indices: 41524818--41524857 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
41524808 AAATTTAAAA
41524818 ATTTTAAAAAAATAAAAATTT
1 ATTTTAAAAAAATAAAAATTT
* *
41524839 ATTTTTAAAAATTAAAAAT
1 ATTTTAAAAAAATAAAAAT
41524858 AATTACATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
ATTTTAAAAAAATAAAAATTT
Found at i:41532549 original size:39 final size:39
Alignment explanation
Indices: 41532475--41532549 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
41532465 AATATAACAT
* *
41532475 AATAATTATAAAAAATATATTATTTAACGTTAAAAATAC
1 AATAATTATAAAAAATATATTATTTAACATAAAAAATAC
**
41532514 AATAATTATAAATCATATATTATTTAACATAAAAAA
1 AATAATTATAAAAAATATATTATTTAACATAAAAAA
41532550 CCCGTTAACA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.57, C:0.05, G:0.01, T:0.36
Consensus pattern (39 bp):
AATAATTATAAAAAATATATTATTTAACATAAAAAATAC
Found at i:41536824 original size:13 final size:13
Alignment explanation
Indices: 41536795--41536834 Score: 53
Period size: 13 Copynumber: 3.1 Consensus size: 13
41536785 CTTAAACAAA
* *
41536795 ACTTTTCAAATGT
1 ACTTTTCAAAAGC
41536808 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
41536821 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
41536834 A
1 A
41536835 ATGCTAAACT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.38, C:0.23, G:0.07, T:0.33
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:41538941 original size:33 final size:30
Alignment explanation
Indices: 41538866--41538948 Score: 94
Period size: 31 Copynumber: 2.6 Consensus size: 30
41538856 TCTTCCAAAA
* *
41538866 TTTTTAAAATTTTCATTAAGCCTTTTAATT
1 TTTTTAAAATTTTCATTAAGCCCTCTAATT
* *
41538896 TCTTTAAAAATTTTAATTAAGCTCCTCTAATTT
1 T-TTTTAAAATTTTCATTAAGC-CCTCTAA-TT
41538929 TTTTTGAAAATTTTCATTAA
1 TTTTT-AAAATTTTCATTAA
41538949 TATAAAAATC
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 1 0.02
31 18 0.42
32 8 0.19
33 16 0.37
ACGTcount: A:0.33, C:0.11, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTTTAAAATTTTCATTAAGCCCTCTAATT
Found at i:41539738 original size:18 final size:17
Alignment explanation
Indices: 41539724--41539757 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
41539714 GTTTTTTTTG
41539724 AATTTTGAATATTTTTAT
1 AATTTTGAA-ATTTTTAT
*
41539742 AATTTTTAAATTTTTA
1 AATTTTGAAATTTTTA
41539758 GTTGACTTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (17 bp):
AATTTTGAAATTTTTAT
Found at i:41542834 original size:28 final size:30
Alignment explanation
Indices: 41542793--41542859 Score: 102
Period size: 29 Copynumber: 2.3 Consensus size: 30
41542783 AATAATGATT
*
41542793 AAATTATATTTTAACT-TTTAAAAATTATA
1 AAATTATAATTTAACTGTTTAAAAATTATA
41542822 AAATT-TAATTTAACTGTTTAAAAATTATA
1 AAATTATAATTTAACTGTTTAAAAATTATA
*
41542851 AAGTTATAA
1 AAATTATAA
41542860 ACTATTAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
28 9 0.26
29 22 0.65
30 3 0.09
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.45
Consensus pattern (30 bp):
AAATTATAATTTAACTGTTTAAAAATTATA
Found at i:41546484 original size:16 final size:16
Alignment explanation
Indices: 41546453--41546486 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
41546443 TTGCTGTATA
*
41546453 TACGTACATAGGTACG
1 TACGTACATAGATACG
*
41546469 TACGTACATATATACG
1 TACGTACATAGATACG
41546485 TA
1 TA
41546487 TGCGTCTTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (16 bp):
TACGTACATAGATACG
Found at i:41551497 original size:28 final size:28
Alignment explanation
Indices: 41551457--41551520 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
41551447 GAGCCAGTTT
41551457 ATGCAGCAACCAAAGGGCTCATATCTTG
1 ATGCAGCAACCAAAGGGCTCATATCTTG
41551485 ATGCAGCAACCAAAGGGCTCATATCTTG
1 ATGCAGCAACCAAAGGGCTCATATCTTG
41551513 ATGCAGCA
1 ATGCAGCA
41551521 TTAAGGGTTG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.33, C:0.25, G:0.22, T:0.20
Consensus pattern (28 bp):
ATGCAGCAACCAAAGGGCTCATATCTTG
Found at i:41563344 original size:21 final size:20
Alignment explanation
Indices: 41563315--41563354 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
41563305 ATTTTAGAAG
41563315 TTAAAATTTAATTTTATTATT
1 TTAAAATTTAATTTT-TTATT
* *
41563336 TTAATATTTTATTTTTTAT
1 TTAAAATTTAATTTTTTAT
41563355 AATTTTTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TTAAAATTTAATTTTTTATT
Found at i:41567772 original size:2 final size:2
Alignment explanation
Indices: 41567765--41567823 Score: 118
Period size: 2 Copynumber: 29.5 Consensus size: 2
41567755 AAGCTAAAGT
41567765 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41567807 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
41567824 TCTTTTTGAA
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 57 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41569878 original size:15 final size:17
Alignment explanation
Indices: 41569847--41569878 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
41569837 TTTGCTTCTC
41569847 GTTCTATCTTCCTTGCT
1 GTTCTATCTTCCTTGCT
41569864 GTTCT-TCTT-CTTGCT
1 GTTCTATCTTCCTTGCT
41569879 TTCATGGTAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 4 0.27
17 5 0.33
ACGTcount: A:0.03, C:0.28, G:0.12, T:0.56
Consensus pattern (17 bp):
GTTCTATCTTCCTTGCT
Found at i:41571655 original size:30 final size:32
Alignment explanation
Indices: 41571614--41571672 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
41571604 TTAATAAAGT
41571614 ATTTAAAAATATATT-TTATAA-TTAAATTTAA
1 ATTTAAAAATAT-TTATTATAATTTAAATTTAA
41571645 ATTT-AAAATATTTATTATAATTTAAATT
1 ATTTAAAAATATTTATTATAATTTAAATT
41571673 GAATTCAAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 2 0.08
30 13 0.50
31 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
ATTTAAAAATATTTATTATAATTTAAATTTAA
Found at i:41573279 original size:52 final size:53
Alignment explanation
Indices: 41573221--41573335 Score: 135
Period size: 52 Copynumber: 2.2 Consensus size: 53
41573211 CATATGGTGA
* *
41573221 AAAAAAAATTGAATAGTTGAATGATTATTTTGTAATTTTTCATAGTT-AGGTGA-C
1 AAAAAAAA-T-AATAATTGAATGATTATTTTGTAACTTTTCATAGTTGA-GTGATC
* ** *
41573275 AAAAAAAATCATAATTGGGTGGTTATTTTGTAACTTTTCATAGTTGAGTGATC
1 AAAAAAAATAATAATTGAATGATTATTTTGTAACTTTTCATAGTTGAGTGATC
41573328 AAAAAAAA
1 AAAAAAAA
41573336 AAAAAAAACC
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
52 34 0.64
53 11 0.21
54 8 0.15
ACGTcount: A:0.41, C:0.05, G:0.17, T:0.37
Consensus pattern (53 bp):
AAAAAAAATAATAATTGAATGATTATTTTGTAACTTTTCATAGTTGAGTGATC
Found at i:41596168 original size:31 final size:30
Alignment explanation
Indices: 41596133--41596269 Score: 93
Period size: 31 Copynumber: 4.6 Consensus size: 30
41596123 ATTTTTCAGT
*
41596133 TTTTAAGGAACCCAAAAAAATTTTTACCAAC
1 TTTTAAGGAACCCAAAAAAAATTTT-CCAAC
***
41596164 TTTTAAGGGGGTCCAAAAAAAATTTT--AAC
1 TTTTAA-GGAACCCAAAAAAAATTTTCCAAC
* ****
41596193 TTTTAAGG-GCCC-AAATGTTTTTTACCAAC
1 TTTTAAGGAACCCAAAAAAAATTTT-CCAAC
* *
41596222 TTTTAAGGAAGCTAAAAAAAATTTTCTCAAC
1 TTTTAAGGAACCCAAAAAAAATTTTC-CAAC
* *
41596253 TTTTAAGAAACCTAAAA
1 TTTTAAGGAACCCAAAA
41596270 TTCCATTTTA
Statistics
Matches: 81, Mismatches: 18, Indels: 14
0.72 0.16 0.12
Matches are distributed among these distances:
26 7 0.09
27 3 0.04
28 2 0.02
29 20 0.25
30 2 0.02
31 32 0.40
32 15 0.19
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.32
Consensus pattern (30 bp):
TTTTAAGGAACCCAAAAAAAATTTTCCAAC
Found at i:41609903 original size:13 final size:13
Alignment explanation
Indices: 41609885--41609910 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41609875 AATCAAACTG
41609885 TTTTAAAATACTT
1 TTTTAAAATACTT
41609898 TTTTAAAATACTT
1 TTTTAAAATACTT
41609911 CTCAAAAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTTAAAATACTT
Found at i:41610950 original size:28 final size:29
Alignment explanation
Indices: 41610905--41610959 Score: 76
Period size: 28 Copynumber: 1.9 Consensus size: 29
41610895 ATTCCAAACT
*
41610905 CTCAAAATTTATAAAATTATAATTTAACC
1 CTCAAAATTAATAAAATTATAATTTAACC
* *
41610934 CTCAAAA-TAATAAAATTTTGATTTAA
1 CTCAAAATTAATAAAATTATAATTTAA
41610960 ACATTTTGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
28 16 0.70
29 7 0.30
ACGTcount: A:0.49, C:0.11, G:0.02, T:0.38
Consensus pattern (29 bp):
CTCAAAATTAATAAAATTATAATTTAACC
Found at i:41612631 original size:3 final size:3
Alignment explanation
Indices: 41612623--41612668 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
41612613 CCTAAACCAT
41612623 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
41612669 AAAAATGTGT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:41615861 original size:33 final size:32
Alignment explanation
Indices: 41615824--41615934 Score: 116
Period size: 33 Copynumber: 3.4 Consensus size: 32
41615814 TAAGAGGCTA
* * *
41615824 GAAGAAGAGGAGCATGG-AGGAGCAATAAAACAC
1 GAAGAAGAGGAGC-GGGAAGAAGGAAT-AAACAC
* * * *
41615857 GAAGAGGAGGAACGGGTAGAAGGAAGCAAACAC
1 GAAGAAGAGGAGCGGGAAGAAGGAA-TAAACAC
41615890 GAAGAAGAGGAGCGGGAAGAAGGAAGTAAACAC
1 GAAGAAGAGGAGCGGGAAGAAGGAA-TAAACAC
41615923 GAAGAAGAGGAG
1 GAAGAAGAGGAG
41615935 GAAGAAGAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
32 2 0.03
33 64 0.97
ACGTcount: A:0.48, C:0.10, G:0.39, T:0.04
Consensus pattern (32 bp):
GAAGAAGAGGAGCGGGAAGAAGGAATAAACAC
Found at i:41615936 original size:36 final size:36
Alignment explanation
Indices: 41615857--41615937 Score: 123
Period size: 33 Copynumber: 2.3 Consensus size: 36
41615847 AATAAAACAC
*
41615857 GAAGAGGAGGAACGGGTAGAAGGAAGCAAACACGAA
1 GAAGAGGAGGAACGGGAAGAAGGAAGCAAACACGAA
*
41615893 GAAGAGGA-G--CGGGAAGAAGGAAGTAAACACGAA
1 GAAGAGGAGGAACGGGAAGAAGGAAGCAAACACGAA
41615926 GAAGAGGAGGAA
1 GAAGAGGAGGAA
41615938 GAAGAAACAA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
33 30 0.75
34 1 0.03
35 1 0.03
36 8 0.20
ACGTcount: A:0.48, C:0.09, G:0.41, T:0.02
Consensus pattern (36 bp):
GAAGAGGAGGAACGGGAAGAAGGAAGCAAACACGAA
Found at i:41615942 original size:33 final size:33
Alignment explanation
Indices: 41615851--41615963 Score: 120
Period size: 33 Copynumber: 3.4 Consensus size: 33
41615841 AGGAGCAATA
* * * *
41615851 AAACACGAAGAGGAGGAACGGGTAGAAGGAAGC
1 AAACACGAAGAAGAGGAGCGAGAAGAAGGAAGC
* *
41615884 AAACACGAAGAAGAGGAGCGGGAAGAAGGAAGT
1 AAACACGAAGAAGAGGAGCGAGAAGAAGGAAGC
** *
41615917 AAACACGAAGAAGAGGAG-GAAGAAGAAACAAAC
1 AAACACGAAGAAGAGGAGCG-AGAAGAAGGAAGC
*
41615950 AAACATGAAGAAGA
1 AAACACGAAGAAGA
41615964 AGAAGAGGCT
Statistics
Matches: 69, Mismatches: 10, Indels: 2
0.85 0.12 0.02
Matches are distributed among these distances:
32 1 0.01
33 68 0.99
ACGTcount: A:0.53, C:0.11, G:0.34, T:0.03
Consensus pattern (33 bp):
AAACACGAAGAAGAGGAGCGAGAAGAAGGAAGC
Found at i:41619754 original size:84 final size:84
Alignment explanation
Indices: 41619626--41619824 Score: 328
Period size: 84 Copynumber: 2.4 Consensus size: 84
41619616 TAAGTTTAGC
* * *
41619626 TTCAATATTCAATTTGGTACCTAATATTTTTCTAATTTGATACTTGAGTTTCTATTTTTTAACAG
1 TTCAATGTTCAATTTGGTACCTAAGATTTTTCTAATTTGATACTTGAGTTTCTATTTTTTAACAA
41619691 TTAAGCACCTAAATTTGGT
66 TTAAGCACCTAAATTTGGT
* *
41619710 TTCAATGTTCAATTTGGTACCTGAGGTTTTTCTAATTTGATACTTGAGTTTCTATTTTTTAACAA
1 TTCAATGTTCAATTTGGTACCTAAGATTTTTCTAATTTGATACTTGAGTTTCTATTTTTTAACAA
41619775 TTAAGCACCTAAATTTGGT
66 TTAAGCACCTAAATTTGGT
*
41619794 TTCAATGTTCAATTTGGCACCTATA-ATTTTT
1 TTCAATGTTCAATTTGGTACCTA-AGATTTTT
41619825 TTTACTAGAA
Statistics
Matches: 106, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
84 105 0.99
85 1 0.01
ACGTcount: A:0.27, C:0.14, G:0.12, T:0.47
Consensus pattern (84 bp):
TTCAATGTTCAATTTGGTACCTAAGATTTTTCTAATTTGATACTTGAGTTTCTATTTTTTAACAA
TTAAGCACCTAAATTTGGT
Found at i:41620975 original size:18 final size:18
Alignment explanation
Indices: 41620929--41620978 Score: 55
Period size: 18 Copynumber: 2.8 Consensus size: 18
41620919 AACCCGAAAT
* *
41620929 CTGATCCTGATCCGGACC
1 CTGATCCTGACCCGGAAC
* *
41620947 CTGGTCTTGACCCGGAAC
1 CTGATCCTGACCCGGAAC
*
41620965 GTGATCCTGACCCG
1 CTGATCCTGACCCG
41620979 AAATCACCAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.16, C:0.36, G:0.26, T:0.22
Consensus pattern (18 bp):
CTGATCCTGACCCGGAAC
Found at i:41623740 original size:4 final size:4
Alignment explanation
Indices: 41623731--41623759 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
41623721 CGACAAGTAG
41623731 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC A
41623760 ATAAACAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAC
Found at i:41626162 original size:21 final size:21
Alignment explanation
Indices: 41626124--41626163 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
41626114 GGTGGCCGAA
** *
41626124 AGAGAAGACTTTGTTGCCGGG
1 AGAGAAGACGATGATGCCGGG
41626145 AGAGAAGACGATGATGCCG
1 AGAGAAGACGATGATGCCG
41626164 ATTTCAACAC
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.15, G:0.38, T:0.17
Consensus pattern (21 bp):
AGAGAAGACGATGATGCCGGG
Found at i:41630318 original size:16 final size:17
Alignment explanation
Indices: 41630287--41630320 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
41630277 ATTTTTCACA
41630287 TTAAAAAATGTAATATTT
1 TTAAAAAATG-AATATTT
41630305 TTAAAAAATG-ATATTT
1 TTAAAAAATGAATATTT
41630321 AAATAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (17 bp):
TTAAAAAATGAATATTT
Found at i:41634452 original size:107 final size:107
Alignment explanation
Indices: 41634332--41634537 Score: 394
Period size: 107 Copynumber: 1.9 Consensus size: 107
41634322 GGAACTTTGA
*
41634332 TACATAAGCCATATGGTCATTTTATTAAAATTTTTATTCATTTTTATTATTAAAAATTGATCCTT
1 TACATAAGCCATATGGTCATTTTATTAAAAATTTTATTCATTTTTATTATTAAAAATTGATCCTT
41634397 AGGTCAACACAGGTCAACATGAGGTATAGGTGCTTTGAACCG
66 AGGTCAACACAGGTCAACATGAGGTATAGGTGCTTTGAACCG
*
41634439 TACATAAGCCATATGGTCATTTTATTAAAAATTTTATTCATTTTTATTGTTAAAAATTGATCCTT
1 TACATAAGCCATATGGTCATTTTATTAAAAATTTTATTCATTTTTATTATTAAAAATTGATCCTT
41634504 AGGTCAACACAGGTCAACATGAGGTATAGGTGCT
66 AGGTCAACACAGGTCAACATGAGGTATAGGTGCT
41634538 GCGTTATGTA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
107 97 1.00
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.38
Consensus pattern (107 bp):
TACATAAGCCATATGGTCATTTTATTAAAAATTTTATTCATTTTTATTATTAAAAATTGATCCTT
AGGTCAACACAGGTCAACATGAGGTATAGGTGCTTTGAACCG
Found at i:41643600 original size:22 final size:22
Alignment explanation
Indices: 41643570--41643611 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
41643560 AATTTGGAAT
* *
41643570 TTTTCATTAAATCTTTCAAAAA
1 TTTTAATTAAATCTTCCAAAAA
*
41643592 TTTTAATTAGATCTTCCAAA
1 TTTTAATTAAATCTTCCAAA
41643612 TCTTTTGCCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.38, C:0.14, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTTAATTAAATCTTCCAAAAA
Found at i:41653979 original size:78 final size:78
Alignment explanation
Indices: 41653850--41654007 Score: 316
Period size: 78 Copynumber: 2.0 Consensus size: 78
41653840 AATATCTTTT
41653850 AACTTTCAATTAGTTCTAGGAAATATACTCGCCCTGCCCTAACCATATATAATTACCAAAAAACC
1 AACTTTCAATTAGTTCTAGGAAATATACTCGCCCTGCCCTAACCATATATAATTACCAAAAAACC
41653915 ACTCAACTCATTG
66 ACTCAACTCATTG
41653928 AACTTTCAATTAGTTCTAGGAAATATACTCGCCCTGCCCTAACCATATATAATTACCAAAAAACC
1 AACTTTCAATTAGTTCTAGGAAATATACTCGCCCTGCCCTAACCATATATAATTACCAAAAAACC
41653993 ACTCAACTCATTG
66 ACTCAACTCATTG
41654006 AA
1 AA
41654008 GGCTTTTGAG
Statistics
Matches: 80, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
78 80 1.00
ACGTcount: A:0.38, C:0.27, G:0.08, T:0.28
Consensus pattern (78 bp):
AACTTTCAATTAGTTCTAGGAAATATACTCGCCCTGCCCTAACCATATATAATTACCAAAAAACC
ACTCAACTCATTG
Found at i:41669749 original size:17 final size:17
Alignment explanation
Indices: 41669722--41669762 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41669712 TTTATTGATT
*
41669722 TTAAAATTAAAATTAAA
1 TTAATATTAAAATTAAA
* *
41669739 TTGATATTAAAATTTAA
1 TTAATATTAAAATTAAA
41669756 TTAATAT
1 TTAATAT
41669763 AATTAAGCAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (17 bp):
TTAATATTAAAATTAAA
Found at i:41670728 original size:13 final size:13
Alignment explanation
Indices: 41670710--41670735 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
41670700 TTTTTTTTTA
41670710 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
41670723 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
41670736 TAATAATAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAAAAG
Found at i:41672904 original size:6 final size:6
Alignment explanation
Indices: 41672895--41672922 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
41672885 TAAAATTAAA
41672895 TTGGAG TTGGAG TTGGAG TTGGAG TTGG
1 TTGGAG TTGGAG TTGGAG TTGGAG TTGG
41672923 GTGGTACATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.14, C:0.00, G:0.50, T:0.36
Consensus pattern (6 bp):
TTGGAG
Found at i:41673978 original size:13 final size:13
Alignment explanation
Indices: 41673960--41673984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
41673950 TTTTTTTTAC
41673960 AAAAAGAAAAAGA
1 AAAAAGAAAAAGA
41673973 AAAAAGAAAAAG
1 AAAAAGAAAAAG
41673985 TAATAATAAC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAGAAAAAGA
Found at i:41676999 original size:41 final size:41
Alignment explanation
Indices: 41676942--41677019 Score: 156
Period size: 41 Copynumber: 1.9 Consensus size: 41
41676932 GAATACATCT
41676942 TTATATATATACATATAAAGTGTTATGTTGTAATCTGTGTC
1 TTATATATATACATATAAAGTGTTATGTTGTAATCTGTGTC
41676983 TTATATATATACATATAAAGTGTTATGTTGTAATCTG
1 TTATATATATACATATAAAGTGTTATGTTGTAATCTG
41677020 CATCGGCAAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.33, C:0.06, G:0.14, T:0.46
Consensus pattern (41 bp):
TTATATATATACATATAAAGTGTTATGTTGTAATCTGTGTC
Found at i:41677247 original size:13 final size:12
Alignment explanation
Indices: 41677220--41677253 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
41677210 GAATAAAACT
*
41677220 AAATATAAATTA
1 AAATAAAAATTA
41677232 AAATAAAAACTTA
1 AAATAAAAA-TTA
41677245 AAATAAAAA
1 AAATAAAAA
41677254 AAATTAAGGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 8 0.40
13 12 0.60
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (12 bp):
AAATAAAAATTA
Found at i:41691258 original size:7 final size:7
Alignment explanation
Indices: 41691240--41691271 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
41691230 TTGAAGTGAT
41691240 CAGAGCAG
1 CAGAG-AG
41691248 CAGAGAG
1 CAGAGAG
41691255 CAGAGAG
1 CAGAGAG
41691262 CAGAGAG
1 CAGAGAG
41691269 CAG
1 CAG
41691272 CGGAGAGCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 19 0.79
8 5 0.21
ACGTcount: A:0.41, C:0.19, G:0.41, T:0.00
Consensus pattern (7 bp):
CAGAGAG
Found at i:41691263 original size:17 final size:17
Alignment explanation
Indices: 41691241--41691280 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
41691231 TGAAGTGATC
41691241 AGAGCAGCAGAG-AGCAG
1 AGAGCAG-AGAGCAGCAG
*
41691258 AGAGCAGAGAGCAGCGG
1 AGAGCAGAGAGCAGCAG
41691275 AGAGCA
1 AGAGCA
41691281 AGATAGATGA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 4 0.19
17 17 0.81
ACGTcount: A:0.40, C:0.17, G:0.42, T:0.00
Consensus pattern (17 bp):
AGAGCAGAGAGCAGCAG
Found at i:41691306 original size:2 final size:2
Alignment explanation
Indices: 41691299--41691323 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41691289 GAATTGGAAG
41691299 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
41691324 CTATGCTATC
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:41693183 original size:18 final size:18
Alignment explanation
Indices: 41693162--41693204 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
41693152 GTTTATATTT
41693162 TATTTTTAAAAGTTTT-TA
1 TATTTTT-AAAGTTTTGTA
*
41693180 TATTTTTAAATTTTTGTA
1 TATTTTTAAAGTTTTGTA
41693198 TATTTTT
1 TATTTTT
41693205 TATTTAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.30
18 16 0.70
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.67
Consensus pattern (18 bp):
TATTTTTAAAGTTTTGTA
Found at i:41693206 original size:43 final size:40
Alignment explanation
Indices: 41693145--41693223 Score: 113
Period size: 43 Copynumber: 1.9 Consensus size: 40
41693135 CTCTCTATAC
*
41693145 AATTTTTGTTTATATTTTATTTTTAAAAGTTTTTATATTTTTA
1 AATTTTTGTATATATTTTA--TTTAAAA-TTTTTATATTTTTA
*
41693188 AATTTTTGTATATTTTTTATTTAAAATTTTTATATT
1 AATTTTTGTATATATTTTATTTAAAATTTTTATATT
41693224 CTTCGAAGGA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
40 10 0.29
41 7 0.21
43 17 0.50
ACGTcount: A:0.29, C:0.00, G:0.04, T:0.67
Consensus pattern (40 bp):
AATTTTTGTATATATTTTATTTAAAATTTTTATATTTTTA
Found at i:41719655 original size:23 final size:24
Alignment explanation
Indices: 41719601--41719658 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 24
41719591 AATTTAATAA
*
41719601 TTATAAATTAATATATCATAAAAT
1 TTATAATTTAATATATCATAAAAT
* * *
41719625 CTAT-ATTTAATATCTCA-AAATT
1 TTATAATTTAATATATCATAAAAT
41719647 TTATAATTTAAT
1 TTATAATTTAAT
41719659 TTTGACTAAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
22 7 0.25
23 18 0.64
24 3 0.11
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.47
Consensus pattern (24 bp):
TTATAATTTAATATATCATAAAAT
Found at i:41720829 original size:25 final size:25
Alignment explanation
Indices: 41720801--41720861 Score: 122
Period size: 25 Copynumber: 2.4 Consensus size: 25
41720791 CAGACACACT
41720801 AATTTTTAACAGTAAAAATTGATGA
1 AATTTTTAACAGTAAAAATTGATGA
41720826 AATTTTTAACAGTAAAAATTGATGA
1 AATTTTTAACAGTAAAAATTGATGA
41720851 AATTTTTAACA
1 AATTTTTAACA
41720862 AAAACAGATC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.48, C:0.05, G:0.10, T:0.38
Consensus pattern (25 bp):
AATTTTTAACAGTAAAAATTGATGA
Found at i:41737982 original size:6 final size:6
Alignment explanation
Indices: 41737971--41738011 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
41737961 GAAGTGTCTA
* *
41737971 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG AGAGAG AGAGA
1 GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGAG GGAGA
41738012 TTGAGTGAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
GGAGAG
Found at i:41742391 original size:20 final size:21
Alignment explanation
Indices: 41742363--41742401 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
41742353 TCATGAATAA
41742363 AAAGCAAAAGAT-TCTTTTCT
1 AAAGCAAAAGATATCTTTTCT
*
41742383 AAAGTAAAAGATATCTTTT
1 AAAGCAAAAGATATCTTTT
41742402 TTTTATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.36
Consensus pattern (21 bp):
AAAGCAAAAGATATCTTTTCT
Found at i:41746349 original size:6 final size:6
Alignment explanation
Indices: 41746338--41746366 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
41746328 CAAAAGGGAA
41746338 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
1 GAAGAT GAAGAT GAAGAT GAAGAT GAAGA
41746367 AGAGAGGTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.34, T:0.14
Consensus pattern (6 bp):
GAAGAT
Found at i:41748921 original size:24 final size:24
Alignment explanation
Indices: 41748894--41748944 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
41748884 TGAGAAAGGC
41748894 TATGGATTTCCAAAATAAAAAGTT
1 TATGGATTTCCAAAATAAAAAGTT
41748918 TATGGATTTCCAAAATAAAAAGTT
1 TATGGATTTCCAAAATAAAAAGTT
41748942 TAT
1 TAT
41748945 AATTTAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (24 bp):
TATGGATTTCCAAAATAAAAAGTT
Found at i:41749695 original size:31 final size:31
Alignment explanation
Indices: 41749659--41749720 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
41749649 ATGACCTCTT
41749659 ATCCATTTCATAGTCATACCATTCAACCAAA
1 ATCCATTTCATAGTCATACCATTCAACCAAA
41749690 ATCCATTTCATAGTCATACCATTCAACCAAA
1 ATCCATTTCATAGTCATACCATTCAACCAAA
41749721 CTTACTACTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.39, C:0.29, G:0.03, T:0.29
Consensus pattern (31 bp):
ATCCATTTCATAGTCATACCATTCAACCAAA
Found at i:41767609 original size:6 final size:6
Alignment explanation
Indices: 41767598--41767627 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
41767588 TTTATTTGCT
41767598 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
1 CCTCTC CCTCTC CCTCTC CCTCTC CCTCTC
41767628 TCTTCTTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.00, C:0.67, G:0.00, T:0.33
Consensus pattern (6 bp):
CCTCTC
Found at i:41767875 original size:8 final size:8
Alignment explanation
Indices: 41767835--41767877 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
41767825 TCAGTCAAAT
41767835 AATAATAA
1 AATAATAA
41767843 AATAA-AA
1 AATAATAA
41767850 AATATATAA
1 AATA-ATAA
* *
41767859 ATTATTAA
1 AATAATAA
41767867 AATAATAA
1 AATAATAA
41767875 AAT
1 AAT
41767878 TGTATTTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
7 6 0.21
8 18 0.62
9 5 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (8 bp):
AATAATAA
Found at i:41773327 original size:21 final size:23
Alignment explanation
Indices: 41773288--41773346 Score: 68
Period size: 21 Copynumber: 2.7 Consensus size: 23
41773278 ACTTGAATAG
** *
41773288 AGTTAACATTTACTGTTTAA-AA
1 AGTTAACATTTTTTATTTAACAA
41773310 A-TTAACATTTTTTATTTAACAA
1 AGTTAACATTTTTTATTTAACAA
*
41773332 AGTTAATATTTTTTA
1 AGTTAACATTTTTTA
41773347 AGTTTTTATG
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
21 15 0.48
22 4 0.13
23 12 0.39
ACGTcount: A:0.39, C:0.07, G:0.05, T:0.49
Consensus pattern (23 bp):
AGTTAACATTTTTTATTTAACAA
Found at i:41773342 original size:23 final size:21
Alignment explanation
Indices: 41773303--41773346 Score: 61
Period size: 23 Copynumber: 2.0 Consensus size: 21
41773293 ACATTTACTG
41773303 TTTAAAAATTAACATTTTTTA
1 TTTAAAAATTAACATTTTTTA
*
41773324 TTTAACAAAGTTAATATTTTTTA
1 TTTAA-AAA-TTAACATTTTTTA
41773347 AGTTTTTATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 3 0.15
23 12 0.60
ACGTcount: A:0.41, C:0.05, G:0.02, T:0.52
Consensus pattern (21 bp):
TTTAAAAATTAACATTTTTTA
Found at i:41781778 original size:2 final size:2
Alignment explanation
Indices: 41781771--41781823 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
41781761 TTCTGAATTT
41781771 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41781813 TA TA TA TA TA T
1 TA TA TA TA TA T
41781824 TGGTATTTTT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41782855 original size:6 final size:6
Alignment explanation
Indices: 41782844--41782876 Score: 66
Period size: 6 Copynumber: 5.5 Consensus size: 6
41782834 CTAAATCACT
41782844 CCAATC CCAATC CCAATC CCAATC CCAATC CCA
1 CCAATC CCAATC CCAATC CCAATC CCAATC CCA
41782877 TAAAACAGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.33, C:0.52, G:0.00, T:0.15
Consensus pattern (6 bp):
CCAATC
Found at i:41789130 original size:23 final size:22
Alignment explanation
Indices: 41789104--41789164 Score: 68
Period size: 23 Copynumber: 2.7 Consensus size: 22
41789094 CTTTAGTAAA
* *
41789104 ATTTTATTTTTATATTTTTATAC
1 ATTTTATTTTTAT-TATATATAC
*
41789127 ATTTTAATTTTATTATATATAC
1 ATTTTATTTTTATTATATATAC
*
41789149 TTTATTATTTTTATTA
1 ATT-TTATTTTTATTA
41789165 ATTGTATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
22 9 0.28
23 23 0.72
ACGTcount: A:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (22 bp):
ATTTTATTTTTATTATATATAC
Found at i:41791070 original size:16 final size:16
Alignment explanation
Indices: 41791022--41791073 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
41791012 AAAATATATA
* *
41791022 TTCTTTCTTTCTATTT
1 TTCTATCTTTCTAATT
* *
41791038 TTCTACTCATTC-GATT
1 TTCTA-TCTTTCTAATT
41791054 TTCTATCTTTCTAATT
1 TTCTATCTTTCTAATT
41791070 TTCT
1 TTCT
41791074 TTAATGTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 4
0.74 0.16 0.11
Matches are distributed among these distances:
15 5 0.18
16 18 0.64
17 5 0.18
ACGTcount: A:0.13, C:0.21, G:0.02, T:0.63
Consensus pattern (16 bp):
TTCTATCTTTCTAATT
Found at i:41793450 original size:20 final size:22
Alignment explanation
Indices: 41793415--41793457 Score: 72
Period size: 20 Copynumber: 2.0 Consensus size: 22
41793405 TGTCCCTTCG
41793415 TTTATTCAATAAAAACTAAAAT
1 TTTATTCAATAAAAACTAAAAT
41793437 TTTATT-AA-AAAAACTAAAAT
1 TTTATTCAATAAAAACTAAAAT
41793457 T
1 T
41793458 AAAATTACTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 13 0.62
21 2 0.10
22 6 0.29
ACGTcount: A:0.56, C:0.07, G:0.00, T:0.37
Consensus pattern (22 bp):
TTTATTCAATAAAAACTAAAAT
Found at i:41793511 original size:15 final size:15
Alignment explanation
Indices: 41793487--41793516 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
41793477 CTAACGTTTT
*
41793487 AATTATTTTTATTTG
1 AATTAATTTTATTTG
41793502 AATTAATTTTATTTG
1 AATTAATTTTATTTG
41793517 TTAAAAATTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (15 bp):
AATTAATTTTATTTG
Found at i:41794573 original size:19 final size:18
Alignment explanation
Indices: 41794549--41794593 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
41794539 ATCATTAATT
* *
41794549 ATTCAATTTTAATATAAGA
1 ATTCAATATTAATA-AAAA
*
41794568 ATTCAATATTATTAAAAA
1 ATTCAATATTAATAAAAA
41794586 ATTCAATA
1 ATTCAATA
41794594 ATATAAATAG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
18 11 0.48
19 12 0.52
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
ATTCAATATTAATAAAAA
Found at i:41795051 original size:20 final size:22
Alignment explanation
Indices: 41795018--41795058 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
41795008 GGGAGGAGGT
*
41795018 AAAAGTTTTGGGAA-AAAAATA
1 AAAAGGTTTGGGAATAAAAATA
41795039 AAAAGGTTT-GGAATAAAAAT
1 AAAAGGTTTGGGAATAAAAAT
41795059 GTAAAATATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.56, C:0.00, G:0.20, T:0.24
Consensus pattern (22 bp):
AAAAGGTTTGGGAATAAAAATA
Found at i:41795064 original size:22 final size:22
Alignment explanation
Indices: 41795016--41795064 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 22
41795006 ATGGGAGGAG
*
41795016 GTAAAAGTTTTGGGAAAAAAAT
1 GTAAAAGGTTTGGGAAAAAAAT
*
41795038 -AAAAAGGTTT-GGAATAAAAAT
1 GTAAAAGGTTTGGGAA-AAAAAT
41795059 GTAAAA
1 GTAAAA
41795065 TATTATAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
20 4 0.18
21 14 0.64
22 4 0.18
ACGTcount: A:0.55, C:0.00, G:0.20, T:0.24
Consensus pattern (22 bp):
GTAAAAGGTTTGGGAAAAAAAT
Found at i:41795714 original size:30 final size:32
Alignment explanation
Indices: 41795678--41795745 Score: 90
Period size: 31 Copynumber: 2.2 Consensus size: 32
41795668 TTTACATTTT
*
41795678 AGTCACTTAAC-TT-T-GAAAATGTGACAAAAC
1 AGTCACTTAACGTTATCGAAAA-GTAACAAAAC
41795708 AGTCAC-TAACGTTATCGAAAAGTAACAAAAC
1 AGTCACTTAACGTTATCGAAAAGTAACAAAAC
41795739 AGTCACT
1 AGTCACT
41795746 GATTAACAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
29 4 0.12
30 8 0.24
31 16 0.48
32 5 0.15
ACGTcount: A:0.44, C:0.19, G:0.13, T:0.24
Consensus pattern (32 bp):
AGTCACTTAACGTTATCGAAAAGTAACAAAAC
Found at i:41797406 original size:30 final size:31
Alignment explanation
Indices: 41797347--41797413 Score: 93
Period size: 30 Copynumber: 2.2 Consensus size: 31
41797337 AAGAGGATTA
* *
41797347 TTTTGTCACTTTTCGATAGCTTTAGTGACTG
1 TTTTGTCACTTTTCGAAAGCTTGAGTGACTG
41797378 TTTTGTCACATTTTC-AAAG-TTGAGTGACTG
1 TTTTGTCAC-TTTTCGAAAGCTTGAGTGACTG
41797408 TTTTGT
1 TTTTGT
41797414 TAAATGTAAC
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 16 0.48
31 12 0.36
32 5 0.15
ACGTcount: A:0.18, C:0.13, G:0.19, T:0.49
Consensus pattern (31 bp):
TTTTGTCACTTTTCGAAAGCTTGAGTGACTG
Found at i:41802712 original size:168 final size:168
Alignment explanation
Indices: 41802434--41802769 Score: 672
Period size: 168 Copynumber: 2.0 Consensus size: 168
41802424 CAACTCCTCG
41802434 ATCAGTGGCACAAATAAACACTTCTTTCGTGGTGTATCAAAACTGAAGCTATGCAAGCTATAGCT
1 ATCAGTGGCACAAATAAACACTTCTTTCGTGGTGTATCAAAACTGAAGCTATGCAAGCTATAGCT
41802499 CCCTAGCAAACTGATAAAAAGGATTCCCTTTTCTCAATCATTATAAAACCCATCTATAAAGCAAA
66 CCCTAGCAAACTGATAAAAAGGATTCCCTTTTCTCAATCATTATAAAACCCATCTATAAAGCAAA
41802564 GAAAGAAACATTAATAGACAATAGCCACAAAGCTAGAA
131 GAAAGAAACATTAATAGACAATAGCCACAAAGCTAGAA
41802602 ATCAGTGGCACAAATAAACACTTCTTTCGTGGTGTATCAAAACTGAAGCTATGCAAGCTATAGCT
1 ATCAGTGGCACAAATAAACACTTCTTTCGTGGTGTATCAAAACTGAAGCTATGCAAGCTATAGCT
41802667 CCCTAGCAAACTGATAAAAAGGATTCCCTTTTCTCAATCATTATAAAACCCATCTATAAAGCAAA
66 CCCTAGCAAACTGATAAAAAGGATTCCCTTTTCTCAATCATTATAAAACCCATCTATAAAGCAAA
41802732 GAAAGAAACATTAATAGACAATAGCCACAAAGCTAGAA
131 GAAAGAAACATTAATAGACAATAGCCACAAAGCTAGAA
41802770 GATAATAAGA
Statistics
Matches: 168, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
168 168 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.24
Consensus pattern (168 bp):
ATCAGTGGCACAAATAAACACTTCTTTCGTGGTGTATCAAAACTGAAGCTATGCAAGCTATAGCT
CCCTAGCAAACTGATAAAAAGGATTCCCTTTTCTCAATCATTATAAAACCCATCTATAAAGCAAA
GAAAGAAACATTAATAGACAATAGCCACAAAGCTAGAA
Found at i:41805753 original size:23 final size:23
Alignment explanation
Indices: 41805727--41805770 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
41805717 ATAAATATCT
41805727 GTTTAAAAATAATAAATAATATA
1 GTTTAAAAATAATAAATAATATA
* * *
41805750 GTTTGAAATTAATTAATAATA
1 GTTTAAAAATAATAAATAATA
41805771 ATATATAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.07, T:0.39
Consensus pattern (23 bp):
GTTTAAAAATAATAAATAATATA
Found at i:41806294 original size:21 final size:21
Alignment explanation
Indices: 41806268--41806309 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
41806258 CAAACAATGA
41806268 CAAAAAGTATCGATACATTTT
1 CAAAAAGTATCGATACATTTT
*
41806289 CAAAAAGTATCGATACCTTTT
1 CAAAAAGTATCGATACATTTT
41806310 ATTAGGTATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.40, C:0.17, G:0.10, T:0.33
Consensus pattern (21 bp):
CAAAAAGTATCGATACATTTT
Found at i:41807218 original size:17 final size:15
Alignment explanation
Indices: 41807195--41807233 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
41807185 AACACAATTA
41807195 AAATTTTTATTAATAT
1 AAATTTTTATTAA-AT
41807211 AAATTTTTATTAAA-
1 AAATTTTTATTAAAT
41807225 AACATTTTT
1 AA-ATTTTT
41807234 TATAATTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 2 0.09
15 7 0.32
16 13 0.59
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.54
Consensus pattern (15 bp):
AAATTTTTATTAAAT
Found at i:41816626 original size:94 final size:96
Alignment explanation
Indices: 41816446--41816640 Score: 288
Period size: 94 Copynumber: 2.0 Consensus size: 96
41816436 TAGAGCATAT
* *
41816446 ATTAACTCATATATTGTTCAATCGTTTCAATTGTAATTACAATTCATTTTTTAACCTTATTCTTT
1 ATTAACTCATATATTGTTCAATCGTTTCAATTGTAATTACAATTCA-TTTTTAACCTTACTCTTA
*
41816511 TTAGTATATGAAGTTGTAGGACTATATGCTTC
65 TTAGTATATGAAGTTGTAGGACTATATGATTC
* * * *
41816543 ATTAACTCATAT-TT-TTCATTTGTTTCAATTGTAATTGCAATTGC-TTTTTAACGTTACTCTTA
1 ATTAACTCATATATTGTTCAATCGTTTCAATTGTAATTACAATT-CATTTTTAACCTTACTCTTA
41816605 TTAGTATATGAAGTTGTAGGACTATATGATTC
65 TTAGTATATGAAGTTGTAGGACTATATGATTC
41816637 ATTA
1 ATTA
41816641 GAGAAGAGAA
Statistics
Matches: 90, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
94 50 0.56
95 25 0.28
96 3 0.03
97 12 0.13
ACGTcount: A:0.29, C:0.12, G:0.11, T:0.48
Consensus pattern (96 bp):
ATTAACTCATATATTGTTCAATCGTTTCAATTGTAATTACAATTCATTTTTAACCTTACTCTTAT
TAGTATATGAAGTTGTAGGACTATATGATTC
Found at i:41827241 original size:286 final size:286
Alignment explanation
Indices: 41826729--41827300 Score: 1144
Period size: 286 Copynumber: 2.0 Consensus size: 286
41826719 TTTCAAAATG
41826729 AACCTAACCAGTGCAAAGGAAACAAAATGTCAAAAACAGTACACAAACTTGATTCTCGATTGAAT
1 AACCTAACCAGTGCAAAGGAAACAAAATGTCAAAAACAGTACACAAACTTGATTCTCGATTGAAT
41826794 TATTATACCTTAAGAAATGGAAACTAGGAAAGTTTTTTCTTTGTTTTTCTCCTTTATGCAGTAAA
66 TATTATACCTTAAGAAATGGAAACTAGGAAAGTTTTTTCTTTGTTTTTCTCCTTTATGCAGTAAA
41826859 GAAGCAACAAATTGTCGTCAATAGGAAATAGAAATAGAATGGATTAAGAGAACGAATGTTATGTC
131 GAAGCAACAAATTGTCGTCAATAGGAAATAGAAATAGAATGGATTAAGAGAACGAATGTTATGTC
41826924 ACACTTTTTTTTACTACAAGAAAGAAGGGTAAAAAGCACCTATATGAACAGTAAACACAAATTAC
196 ACACTTTTTTTTACTACAAGAAAGAAGGGTAAAAAGCACCTATATGAACAGTAAACACAAATTAC
41826989 AGTGATGATATAAATATAAATATATA
261 AGTGATGATATAAATATAAATATATA
41827015 AACCTAACCAGTGCAAAGGAAACAAAATGTCAAAAACAGTACACAAACTTGATTCTCGATTGAAT
1 AACCTAACCAGTGCAAAGGAAACAAAATGTCAAAAACAGTACACAAACTTGATTCTCGATTGAAT
41827080 TATTATACCTTAAGAAATGGAAACTAGGAAAGTTTTTTCTTTGTTTTTCTCCTTTATGCAGTAAA
66 TATTATACCTTAAGAAATGGAAACTAGGAAAGTTTTTTCTTTGTTTTTCTCCTTTATGCAGTAAA
41827145 GAAGCAACAAATTGTCGTCAATAGGAAATAGAAATAGAATGGATTAAGAGAACGAATGTTATGTC
131 GAAGCAACAAATTGTCGTCAATAGGAAATAGAAATAGAATGGATTAAGAGAACGAATGTTATGTC
41827210 ACACTTTTTTTTACTACAAGAAAGAAGGGTAAAAAGCACCTATATGAACAGTAAACACAAATTAC
196 ACACTTTTTTTTACTACAAGAAAGAAGGGTAAAAAGCACCTATATGAACAGTAAACACAAATTAC
41827275 AGTGATGATATAAATATAAATATATA
261 AGTGATGATATAAATATAAATATATA
41827301 TAATCCTGGG
Statistics
Matches: 286, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
286 286 1.00
ACGTcount: A:0.43, C:0.13, G:0.15, T:0.28
Consensus pattern (286 bp):
AACCTAACCAGTGCAAAGGAAACAAAATGTCAAAAACAGTACACAAACTTGATTCTCGATTGAAT
TATTATACCTTAAGAAATGGAAACTAGGAAAGTTTTTTCTTTGTTTTTCTCCTTTATGCAGTAAA
GAAGCAACAAATTGTCGTCAATAGGAAATAGAAATAGAATGGATTAAGAGAACGAATGTTATGTC
ACACTTTTTTTTACTACAAGAAAGAAGGGTAAAAAGCACCTATATGAACAGTAAACACAAATTAC
AGTGATGATATAAATATAAATATATA
Found at i:41830283 original size:2 final size:2
Alignment explanation
Indices: 41830278--41830302 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
41830268 GTGTGTGTGT
41830278 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
41830303 GGCAAAAAGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:41833995 original size:4 final size:4
Alignment explanation
Indices: 41833986--41834012 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
41833976 TAACACTATG
41833986 AATA AATA AATA AATA AATA AATA AAT
1 AATA AATA AATA AATA AATA AATA AAT
41834013 GGGAACGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (4 bp):
AATA
Found at i:41853525 original size:16 final size:16
Alignment explanation
Indices: 41853504--41853535 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
41853494 GCTAAACAGA
41853504 GAGAACACAAAGTACT
1 GAGAACACAAAGTACT
41853520 GAGAACACAAAGTACT
1 GAGAACACAAAGTACT
41853536 AATCAGAGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.50, C:0.19, G:0.19, T:0.12
Consensus pattern (16 bp):
GAGAACACAAAGTACT
Found at i:41853526 original size:25 final size:24
Alignment explanation
Indices: 41853449--41853526 Score: 81
Period size: 23 Copynumber: 3.2 Consensus size: 24
41853439 CCGGAGTACT
*
41853449 GAACAGAGAG-CACATAAGTGCTGG
1 GAACAGAGAGACACA-AAGTGCTGA
41853473 GCAACAGAGAGCACACAAAGTGCT-A
1 G-AACAGAGAG-ACACAAAGTGCTGA
*
41853498 -AACAGAGAGAACACAAAGTACTGA
1 GAACAGAGAG-ACACAAAGTGCTGA
41853522 GAACA
1 GAACA
41853527 CAAAGTACTA
Statistics
Matches: 46, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
23 20 0.43
24 2 0.04
25 13 0.28
26 7 0.15
27 4 0.09
ACGTcount: A:0.46, C:0.19, G:0.26, T:0.09
Consensus pattern (24 bp):
GAACAGAGAGACACAAAGTGCTGA
Found at i:41853555 original size:23 final size:22
Alignment explanation
Indices: 41853477--41853665 Score: 163
Period size: 23 Copynumber: 8.5 Consensus size: 22
41853467 TGCTGGGCAA
*
41853477 CAGAGAGCACACAAAGTGCTAAA
1 CAGAGAGCACAC-AAGTGCTAAT
* *
41853500 CAGAGAGAACACAA-AG-T-A-
1 CAGAGAGCACACAAGTGCTAAT
* * *
41853518 CTGAGAACACA-AAGTACTAAT
1 CAGAGAGCACACAAGTGCTAAT
41853539 CAGAGAGCACACGAAGTGCTAAT
1 CAGAGAGCACAC-AAGTGCTAAT
*
41853562 CGGAGAGCACACAAAGTGCTAAT
1 CAGAGAGCACAC-AAGTGCTAAT
* *
41853585 CGGAGAGCAAACACAGTGCTAAT
1 CAGAGAGCACACA-AGTGCTAAT
* * *
41853608 AACAGAGAGCACGAGACGTGCTAAA
1 --CAGAGAGCAC-ACAAGTGCTAAT
41853633 CAGAGAGCACACACAGTGCTAAT
1 CAGAGAGCACACA-AGTGCTAAT
41853656 CAGAGAGCAC
1 CAGAGAGCAC
41853666 GCTAGTGTTC
Statistics
Matches: 134, Mismatches: 21, Indels: 22
0.76 0.12 0.12
Matches are distributed among these distances:
17 2 0.01
18 8 0.06
19 2 0.01
20 2 0.01
21 10 0.07
22 5 0.04
23 88 0.66
25 15 0.11
26 2 0.01
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.11
Consensus pattern (22 bp):
CAGAGAGCACACAAGTGCTAAT
Found at i:41853639 original size:48 final size:46
Alignment explanation
Indices: 41853534--41853666 Score: 144
Period size: 48 Copynumber: 2.8 Consensus size: 46
41853524 ACACAAAGTA
* * * * *
41853534 CTAATCAGAGAGCACACGA-AGTGCTAATCGGAGAGCAC-ACAAAGTG
1 CTAAACAGAGAGCAAAC-ACAGTGCTAATCAGAGAGCACGA-GACGTG
* *
41853580 CTAATCGGAGAGCAAACACAGTGCTAATAACAGAGAGCACGAGACGTG
1 CTAAACAGAGAGCAAACACAGTGCTAAT--CAGAGAGCACGAGACGTG
*
41853628 CTAAACAGAGAGCACACACAGTGCTAATCAGAGAGCACG
1 CTAAACAGAGAGCAAACACAGTGCTAATCAGAGAGCACG
41853667 CTAGTGTTCC
Statistics
Matches: 75, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
45 1 0.01
46 35 0.47
48 38 0.51
49 1 0.01
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.12
Consensus pattern (46 bp):
CTAAACAGAGAGCAAACACAGTGCTAATCAGAGAGCACGAGACGTG
Found at i:41860916 original size:9 final size:9
Alignment explanation
Indices: 41860904--41860929 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
41860894 GGTTTAAAAA
41860904 ATTTAATTT
1 ATTTAATTT
41860913 ATTTAATTT
1 ATTTAATTT
41860922 ATTTAATT
1 ATTTAATT
41860930 AAATATTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (9 bp):
ATTTAATTT
Found at i:41866686 original size:2 final size:2
Alignment explanation
Indices: 41866679--41866707 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
41866669 TGGATTCTTT
41866679 TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
41866708 ATTTGGTAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:41882167 original size:3 final size:3
Alignment explanation
Indices: 41882159--41882196 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
41882149 GGAAGGAGGT
41882159 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
41882197 GGATCCCCTT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:41888579 original size:31 final size:31
Alignment explanation
Indices: 41888532--41888604 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
41888522 AAAATAGTAA
* *
41888532 ATTAATAAATTAAAAAATAAATTGATTCTTTTT
1 ATTAAT-AA-TAAAAAACAAATTGATTCTTATT
*
41888565 TTTAATAATAAAAAACAAATTGATTCTTATT
1 ATTAATAATAAAAAACAAATTGATTCTTATT
41888596 ATTAATAAT
1 ATTAATAAT
41888605 GTTATTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 29 0.81
32 2 0.06
33 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTAATAATAAAAAACAAATTGATTCTTATT
Found at i:41898376 original size:229 final size:229
Alignment explanation
Indices: 41897975--41898438 Score: 928
Period size: 229 Copynumber: 2.0 Consensus size: 229
41897965 ACTCCCTCAC
41897975 ACTTATCCCGCTCCTCAAGTATGTGTTTGTTGTGTGTAAAGCAAATGACTACGGTCAAGGTGAGC
1 ACTTATCCCGCTCCTCAAGTATGTGTTTGTTGTGTGTAAAGCAAATGACTACGGTCAAGGTGAGC
41898040 TGATATTAGTGAATGAGGATGCATACCTTGTAATCTGAGACATGATGATGATGATGATCCTGTTT
66 TGATATTAGTGAATGAGGATGCATACCTTGTAATCTGAGACATGATGATGATGATGATCCTGTTT
41898105 GTCGTGCAGGTGGAACATTTGCTCTATATTCTTTGCTTTGTACACATGCAAATGTAAAAATCATT
131 GTCGTGCAGGTGGAACATTTGCTCTATATTCTTTGCTTTGTACACATGCAAATGTAAAAATCATT
41898170 CCTAATCAAACACAGGACCGATGAGGAGCTTACA
196 CCTAATCAAACACAGGACCGATGAGGAGCTTACA
41898204 ACTTATCCCGCTCCTCAAGTATGTGTTTGTTGTGTGTAAAGCAAATGACTACGGTCAAGGTGAGC
1 ACTTATCCCGCTCCTCAAGTATGTGTTTGTTGTGTGTAAAGCAAATGACTACGGTCAAGGTGAGC
41898269 TGATATTAGTGAATGAGGATGCATACCTTGTAATCTGAGACATGATGATGATGATGATCCTGTTT
66 TGATATTAGTGAATGAGGATGCATACCTTGTAATCTGAGACATGATGATGATGATGATCCTGTTT
41898334 GTCGTGCAGGTGGAACATTTGCTCTATATTCTTTGCTTTGTACACATGCAAATGTAAAAATCATT
131 GTCGTGCAGGTGGAACATTTGCTCTATATTCTTTGCTTTGTACACATGCAAATGTAAAAATCATT
41898399 CCTAATCAAACACAGGACCGATGAGGAGCTTACA
196 CCTAATCAAACACAGGACCGATGAGGAGCTTACA
41898433 ACTTAT
1 ACTTAT
41898439 AGTTGTTCTA
Statistics
Matches: 235, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
229 235 1.00
ACGTcount: A:0.29, C:0.17, G:0.22, T:0.32
Consensus pattern (229 bp):
ACTTATCCCGCTCCTCAAGTATGTGTTTGTTGTGTGTAAAGCAAATGACTACGGTCAAGGTGAGC
TGATATTAGTGAATGAGGATGCATACCTTGTAATCTGAGACATGATGATGATGATGATCCTGTTT
GTCGTGCAGGTGGAACATTTGCTCTATATTCTTTGCTTTGTACACATGCAAATGTAAAAATCATT
CCTAATCAAACACAGGACCGATGAGGAGCTTACA
Found at i:41902791 original size:31 final size:31
Alignment explanation
Indices: 41902744--41902816 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
41902734 AAAATAGTAA
* *
41902744 ATTAATAAATTAAAAAATAAATTGATTCTTTTT
1 ATTAAT-AA-TAAAAAACAAATTGATTCTTATT
*
41902777 TTTAATAATAAAAAACAAATTGATTCTTATT
1 ATTAATAATAAAAAACAAATTGATTCTTATT
41902808 ATTAATAAT
1 ATTAATAAT
41902817 GTTATTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 29 0.81
32 2 0.06
33 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTAATAATAAAAAACAAATTGATTCTTATT
Found at i:41916813 original size:31 final size:31
Alignment explanation
Indices: 41916766--41916838 Score: 101
Period size: 31 Copynumber: 2.3 Consensus size: 31
41916756 AAAATAGTAA
* *
41916766 ATTAATAAATTAAAAAATAAATTGATTCTTTTT
1 ATTAAT-AA-TAAAAAACAAATTGATTCTTATT
*
41916799 TTTAATAATAAAAAACAAATTGATTCTTATT
1 ATTAATAATAAAAAACAAATTGATTCTTATT
41916830 ATTAATAAT
1 ATTAATAAT
41916839 GTTATTTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 29 0.81
32 2 0.06
33 5 0.14
ACGTcount: A:0.49, C:0.04, G:0.03, T:0.44
Consensus pattern (31 bp):
ATTAATAATAAAAAACAAATTGATTCTTATT
Found at i:41920788 original size:3 final size:3
Alignment explanation
Indices: 41920780--41920805 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
41920770 AATCTGAGAC
41920780 ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG AT
41920806 CCTGTTTGTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.31, T:0.35
Consensus pattern (3 bp):
ATG
Found at i:41931973 original size:10 final size:10
Alignment explanation
Indices: 41931958--41932021 Score: 51
Period size: 10 Copynumber: 6.6 Consensus size: 10
41931948 TTATCATGCC
41931958 AAAAAATTAT
1 AAAAAATTAT
*
41931968 AAAAAAATAT
1 AAAAAATTAT
* *
41931978 TAAAAATTGT
1 AAAAAATTAT
* *
41931988 AAAAAGTTTT
1 AAAAAATTAT
*
41931998 AAAATA-TAT
1 AAAAAATTAT
*
41932007 -AAAAATTGT
1 AAAAAATTAT
41932016 AAAAAA
1 AAAAAA
41932022 ATATTTTGAA
Statistics
Matches: 40, Mismatches: 12, Indels: 4
0.71 0.21 0.07
Matches are distributed among these distances:
8 4 0.10
9 4 0.10
10 32 0.80
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.30
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:41932020 original size:19 final size:18
Alignment explanation
Indices: 41931959--41932025 Score: 55
Period size: 19 Copynumber: 3.6 Consensus size: 18
41931949 TATCATGCCA
*
41931959 AAAAATTATAAAAAAATATT
1 AAAAA-TATATAAAAAT-TT
*
41931979 AAAAAT-TGTAAAAAGTTT
1 AAAAATATATAAAAA-TTT
*
41931997 TAAAATATATAAAAATTGT
1 AAAAATATATAAAAATT-T
*
41932016 AAAAAAATAT
1 AAAAATATAT
41932026 TTTGAAAATA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
18 15 0.39
19 18 0.47
20 5 0.13
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.31
Consensus pattern (18 bp):
AAAAATATATAAAAATTT
Found at i:41932040 original size:15 final size:14
Alignment explanation
Indices: 41932005--41932051 Score: 53
Period size: 13 Copynumber: 3.4 Consensus size: 14
41931995 TTTAAAATAT
* *
41932005 ATAAAAATTGTAAA
1 ATAAATATTTTAAA
41932019 A-AAATATTTTGAAA
1 ATAAATATTTT-AAA
41932033 ATAAATATTTT-AA
1 ATAAATATTTTAAA
41932046 ATAAAT
1 ATAAAT
41932052 TTTAAATATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
13 15 0.52
14 5 0.17
15 9 0.31
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (14 bp):
ATAAATATTTTAAA
Found at i:41932047 original size:13 final size:13
Alignment explanation
Indices: 41932005--41932059 Score: 51
Period size: 13 Copynumber: 4.2 Consensus size: 13
41931995 TTTAAAATAT
* *
41932005 ATAAAAATTGTAA
1 ATAAATATTTTAA
*
41932018 AAAAATATTTTGAAA
1 ATAAATATTTT--AA
41932033 ATAAATATTTTAA
1 ATAAATATTTTAA
41932046 AT-AA-ATTTTAA
1 ATAAATATTTTAA
41932057 ATA
1 ATA
41932060 TTGTTAAAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
11 9 0.26
12 2 0.06
13 12 0.34
15 12 0.34
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (13 bp):
ATAAATATTTTAA
Found at i:41932077 original size:11 final size:11
Alignment explanation
Indices: 41932035--41932079 Score: 51
Period size: 11 Copynumber: 4.2 Consensus size: 11
41932025 TTTTGAAAAT
41932035 AAATATTTTAA
1 AAATATTTTAA
41932046 ATAA-ATTTT--
1 A-AATATTTTAA
41932055 AAATATTGTTAA
1 AAATATT-TTAA
41932067 AAATATTTTAA
1 AAATATTTTAA
41932078 AA
1 AA
41932080 TTGTAAAAAG
Statistics
Matches: 29, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
8 2 0.07
9 4 0.14
10 2 0.07
11 12 0.41
12 9 0.31
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (11 bp):
AAATATTTTAA
Found at i:41932094 original size:21 final size:21
Alignment explanation
Indices: 41932034--41932088 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
41932024 ATTTTGAAAA
41932034 TAAATATT-TTAAATAA-ATTT
1 TAAATATTGTTAAA-AATATTT
41932054 TAAATATTGTTAAAAATATTT
1 TAAATATTGTTAAAAATATTT
41932075 TAAA-ATTG-TAAAAA
1 TAAATATTGTTAAAAA
41932089 GTTATTAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.18
20 14 0.42
21 13 0.39
ACGTcount: A:0.53, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TAAATATTGTTAAAAATATTT
Found at i:41932131 original size:20 final size:20
Alignment explanation
Indices: 41932052--41932139 Score: 67
Period size: 19 Copynumber: 4.4 Consensus size: 20
41932042 TTAAATAAAT
*
41932052 TTTAAATATTGTTAAAAA-TA
1 TTTAAA-ATTTTTAAAAATTA
*
41932072 TTTTAAAA-TTGTAAAAAGTTA
1 -TTTAAAATTTTTAAAAA-TTA
**
41932093 -TT-AAATTAATAAAACATTA
1 TTTAAAATTTTTAAAA-ATTA
41932112 TTTAAAATTTTTAAAAATTA
1 TTTAAAATTTTTAAAAATTA
*
41932132 TTAAAAAT
1 TTTAAAAT
41932140 CATAAATAAT
Statistics
Matches: 54, Mismatches: 7, Indels: 13
0.73 0.09 0.18
Matches are distributed among these distances:
18 3 0.06
19 18 0.33
20 15 0.28
21 18 0.33
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.43
Consensus pattern (20 bp):
TTTAAAATTTTTAAAAATTA
Found at i:41932408 original size:21 final size:21
Alignment explanation
Indices: 41932383--41932431 Score: 80
Period size: 21 Copynumber: 2.3 Consensus size: 21
41932373 AAAAAATTTA
*
41932383 AATAATTATTTGTAATTTTCT
1 AATAATTATTTGCAATTTTCT
*
41932404 AATAATTATTTGCAATTTTTT
1 AATAATTATTTGCAATTTTCT
41932425 AATAATT
1 AATAATT
41932432 TTCCTAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.37, C:0.04, G:0.04, T:0.55
Consensus pattern (21 bp):
AATAATTATTTGCAATTTTCT
Found at i:41932433 original size:10 final size:10
Alignment explanation
Indices: 41932420--41932496 Score: 66
Period size: 10 Copynumber: 7.6 Consensus size: 10
41932410 TATTTGCAAT
41932420 TTTTTAATAA
1 TTTTTAATAA
**
41932430 -TTTTCCTAA
1 TTTTTAATAA
*
41932439 TTATTAATAA
1 TTTTTAATAA
*
41932449 TTTTTAAAAA
1 TTTTTAATAA
*
41932459 TTTTAAATAA
1 TTTTTAATAA
*
41932469 TTTTTTTATAA
1 -TTTTTAATAA
*
41932480 TATTTAATAA
1 TTTTTAATAA
41932490 CTTTTTA
1 -TTTTTA
41932497 CAATTTTAAA
Statistics
Matches: 50, Mismatches: 14, Indels: 5
0.72 0.20 0.07
Matches are distributed among these distances:
9 7 0.14
10 30 0.60
11 13 0.26
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (10 bp):
TTTTTAATAA
Found at i:41932502 original size:41 final size:40
Alignment explanation
Indices: 41932442--41932543 Score: 125
Period size: 41 Copynumber: 2.5 Consensus size: 40
41932432 TTCCTAATTA
* * * *
41932442 TTAATAATTTTTAAAAATTTTAAATAAT-TTTTTTATAATAT
1 TTAATAATTTTT-ACAATTTTAAA-AATGTTTTTAACAACAT
41932483 TTAATAACTTTTTACAATTTTAAAAATGTTTTTAACAACAT
1 TTAATAA-TTTTTACAATTTTAAAAATGTTTTTAACAACAT
41932524 TTAATAATTATTTACAATTT
1 TTAATAATT-TTTACAATTT
41932544 ATTTACAATT
Statistics
Matches: 54, Mismatches: 4, Indels: 6
0.84 0.06 0.09
Matches are distributed among these distances:
40 5 0.09
41 44 0.81
42 5 0.09
ACGTcount: A:0.42, C:0.05, G:0.01, T:0.52
Consensus pattern (40 bp):
TTAATAATTTTTACAATTTTAAAAATGTTTTTAACAACAT
Found at i:41932587 original size:22 final size:21
Alignment explanation
Indices: 41932552--41932597 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 21
41932542 TTATTTACAA
41932552 TTTTTATATATTTAA-AAATAT
1 TTTTTATATATTTAATAAA-AT
*
41932573 TTTTTATGATTTTTAATAAAAT
1 TTTTTAT-ATATTTAATAAAAT
41932595 TTT
1 TTT
41932598 CATAAAATTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
21 7 0.32
22 12 0.55
23 3 0.14
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTTATATATTTAATAAAAT
Done.