Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008893.1 Hibiscus syriacus cultivar Beakdansim tig00112159_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 2797279
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 12 of 13
Found at i:2328004 original size:63 final size:63
Alignment explanation
Indices: 2327905--2328041 Score: 247
Period size: 63 Copynumber: 2.2 Consensus size: 63
2327895 TATGGTCACC
* *
2327905 AAAATCGAACGGGAGTTAATAGTTGAGGGACTAAAATCAAATGGATTAATAATGTTAGGGATT
1 AAAATCGAACGAGAGTTAATAGCTGAGGGACTAAAATCAAATGGATTAATAATGTTAGGGATT
*
2327968 AAAATCGAACGAGAGTTAATAGCTGAGGGACTAAAATCGAATGGATTAATAATGTTAGGGATT
1 AAAATCGAACGAGAGTTAATAGCTGAGGGACTAAAATCAAATGGATTAATAATGTTAGGGATT
2328031 AAAATCGAACG
1 AAAATCGAACG
2328042 GATCAATAAC
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
63 71 1.00
ACGTcount: A:0.42, C:0.08, G:0.25, T:0.25
Consensus pattern (63 bp):
AAAATCGAACGAGAGTTAATAGCTGAGGGACTAAAATCAAATGGATTAATAATGTTAGGGATT
Found at i:2328613 original size:14 final size:14
Alignment explanation
Indices: 2328596--2328626 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
2328586 CCTTAACTTA
2328596 AAACCCTAAATTAT
1 AAACCCTAAATTAT
2328610 AAACCCTAAATTAT
1 AAACCCTAAATTAT
2328624 AAA
1 AAA
2328627 TCATAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (14 bp):
AAACCCTAAATTAT
Found at i:2341032 original size:20 final size:18
Alignment explanation
Indices: 2341004--2341048 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
2340994 TGGTTCACGT
*
2341004 AATATAAGATTATCAATGGG
1 AATAAAAGATTA-CAA-GGG
*
2341024 AATAAAAGATTACCAGGG
1 AATAAAAGATTACAAGGG
2341042 AATAAAA
1 AATAAAA
2341049 TTACTGGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 10 0.43
19 2 0.09
20 11 0.48
ACGTcount: A:0.53, C:0.07, G:0.18, T:0.22
Consensus pattern (18 bp):
AATAAAAGATTACAAGGG
Found at i:2347865 original size:34 final size:34
Alignment explanation
Indices: 2347820--2347904 Score: 86
Period size: 34 Copynumber: 2.4 Consensus size: 34
2347810 AGTATTTTTT
*
2347820 TAAATAGTTATTATTTT-TTATATAAT-ATATTTATG
1 TAAATA-TTATTATTTTATTA-A-AATAATATTTATA
2347855 TAAATATTATT-TTATTATTAAAATAATATTTATA
1 TAAATATTATTATT-TTATTAAAATAATATTTATA
*
2347889 TAATTATTATTTATTT
1 TAAATATTA-TTATTT
2347905 AGAATTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 10
0.78 0.04 0.18
Matches are distributed among these distances:
33 5 0.12
34 24 0.56
35 12 0.28
36 2 0.05
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (34 bp):
TAAATATTATTATTTTATTAAAATAATATTTATA
Found at i:2349658 original size:21 final size:21
Alignment explanation
Indices: 2349628--2349675 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
2349618 GCAGGGGTAC
* *
2349628 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
2349649 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
2349670 ATGCCA
1 ATGCCA
2349676 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:2349705 original size:21 final size:21
Alignment explanation
Indices: 2349679--2349772 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
2349669 TATGCCATCT
* *
2349679 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
2349700 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
2349721 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2349742 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
2349763 CCGCAGGGTT
1 CCGCAGGGTT
2349773 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:2350354 original size:33 final size:34
Alignment explanation
Indices: 2350295--2350367 Score: 94
Period size: 34 Copynumber: 2.2 Consensus size: 34
2350285 AAATGTTTTT
* * *
2350295 AAAATACAAATTATATTTTTCGAAATTTAAAATA
1 AAAATAAAAATAATATTATTCGAAATTTAAAATA
* *
2350329 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATAATATTATTCGAAATTTAAAATA
2350362 AAAATA
1 AAAATA
2350368 TACTAGAATA
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
33 16 0.47
34 18 0.53
ACGTcount: A:0.58, C:0.04, G:0.01, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATAATATTATTCGAAATTTAAAATA
Found at i:2350653 original size:12 final size:13
Alignment explanation
Indices: 2350621--2350660 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
2350611 TACATAAATA
*
2350621 TATTTAATATATT
1 TATTTAATATAAT
2350634 TATTTAATATAAT
1 TATTTAATATAAT
*
2350647 T-TTTAATATTAT
1 TATTTAATATAAT
2350659 TA
1 TA
2350661 GTTATAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 11 0.46
13 13 0.54
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (13 bp):
TATTTAATATAAT
Found at i:2357990 original size:5 final size:5
Alignment explanation
Indices: 2357980--2358010 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
2357970 TTTTTTATAC
2357980 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
1 ATAAT ATAAT ATAAT ATAAT ATAAT ATAAT A
2358011 CCAATTACAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
ATAAT
Found at i:2359262 original size:63 final size:63
Alignment explanation
Indices: 2359143--2359266 Score: 162
Period size: 63 Copynumber: 2.0 Consensus size: 63
2359133 ATCCTAGCCA
* * * *
2359143 GAAATGTGAGTTCTTTTCGATTAGTTATTTATTTTAACAATGATGTCTAACCTAAAATTTTTC
1 GAAATCTGAGTTCTTTTCGATTAATTACTTATTTTAACAATGATGTCTAACATAAAATTTTTC
* *
2359206 GAAATCTGAGTTCTTTTCGATTAATTACTTATTTT-ACGAATGTTGTCCT-TCATAAAATTTT
1 GAAATCTGAGTTCTTTTCGATTAATTACTTATTTTAAC-AATGATGT-CTAACATAAAATTTT
2359267 ATTTATACTG
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.92
64 2 0.04
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.47
Consensus pattern (63 bp):
GAAATCTGAGTTCTTTTCGATTAATTACTTATTTTAACAATGATGTCTAACATAAAATTTTTC
Found at i:2366636 original size:3 final size:3
Alignment explanation
Indices: 2366630--2366707 Score: 83
Period size: 3 Copynumber: 27.0 Consensus size: 3
2366620 ATCCATTTTT
* * *
2366630 TTA TTA TTA -TG TTA TTA TTG TTA TTA TTA TT- TTA TTTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
*
2366674 TTA TTA TT- TTA -TA TTA TTA ATA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2366708 CATTTCAGGC
Statistics
Matches: 62, Mismatches: 8, Indels: 10
0.77 0.10 0.12
Matches are distributed among these distances:
2 7 0.11
3 52 0.84
4 3 0.05
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:2368023 original size:42 final size:37
Alignment explanation
Indices: 2367977--2368056 Score: 97
Period size: 37 Copynumber: 2.0 Consensus size: 37
2367967 TATGTTCTAA
*
2367977 TTTAGTCACTAATTTTAATACTATAGTTTTAATTTTATTTAT
1 TTTAGTCACT-A-TTT-AT-CTATA-TTTTAATTTAATTTAT
*
2368019 TTTAGTCACTATTTATTTATATTTTAATTTAATTTAT
1 TTTAGTCACTATTTATCTATATTTTAATTTAATTTAT
2368056 T
1 T
2368057 ATTTAAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 16 0.44
38 4 0.11
39 2 0.06
40 3 0.08
41 1 0.03
42 10 0.28
ACGTcount: A:0.30, C:0.06, G:0.04, T:0.60
Consensus pattern (37 bp):
TTTAGTCACTATTTATCTATATTTTAATTTAATTTAT
Found at i:2368055 original size:17 final size:17
Alignment explanation
Indices: 2368029--2368066 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 17
2368019 TTTAGTCACT
*
2368029 ATTTATTTA-TATTTTA
1 ATTTATTTATTATTTAA
2368045 ATTTAATTTATTATTTAA
1 ATTT-ATTTATTATTTAA
2368063 ATTT
1 ATTT
2368067 CAATATGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 5 0.26
18 10 0.53
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
ATTTATTTATTATTTAA
Found at i:2368084 original size:14 final size:14
Alignment explanation
Indices: 2368065--2368094 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
2368055 TTATTTAAAT
2368065 TTCAATATGTTTAA
1 TTCAATATGTTTAA
2368079 TTCAATATGTTTAA
1 TTCAATATGTTTAA
2368093 TT
1 TT
2368095 ATTATTTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.53
Consensus pattern (14 bp):
TTCAATATGTTTAA
Found at i:2368530 original size:2 final size:2
Alignment explanation
Indices: 2368485--2368520 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
2368475 ATATCTTATT
*
2368485 TA TA AA 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
2368521 GTTAATATAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2371681 original size:14 final size:15
Alignment explanation
Indices: 2371656--2371684 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
2371646 TTATAAATAT
2371656 AATAATATTTTAAAA
1 AATAATATTTTAAAA
2371671 AATAA-ATTTTAAAA
1 AATAATATTTTAAAA
2371685 TCACCAGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATAATATTTTAAAA
Found at i:2375205 original size:2 final size:2
Alignment explanation
Indices: 2375198--2375224 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2375188 CTCGCTTTTG
2375198 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2375225 CACGTCAAAC
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2376168 original size:63 final size:63
Alignment explanation
Indices: 2376077--2376216 Score: 174
Period size: 63 Copynumber: 2.2 Consensus size: 63
2376067 AGAATCCATT
* *
2376077 CCCGTGGATGCCGGGGTCAAGCACCCGAATCAAGAAGCAAGTGACAGGTTTGTCGAAGAACAA
1 CCCGTGGATGCCGGGGTCAAGCAACCGAATCAAGAAGCAAGTGACAGGGTTGTCGAAGAACAA
** * * * *
2376140 CCCGTGGATG-CGGGGATTGAGCAACCGAATCAAGATGTAGGTGACGGGGTTGTCGAAGAACAA
1 CCCGTGGATGCCGGGG-TCAAGCAACCGAATCAAGAAGCAAGTGACAGGGTTGTCGAAGAACAA
* *
2376203 CCTGTGGATCCCGG
1 CCCGTGGATGCCGG
2376217 AAATGCTCAT
Statistics
Matches: 65, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 5 0.08
63 57 0.88
64 3 0.05
ACGTcount: A:0.28, C:0.22, G:0.34, T:0.16
Consensus pattern (63 bp):
CCCGTGGATGCCGGGGTCAAGCAACCGAATCAAGAAGCAAGTGACAGGGTTGTCGAAGAACAA
Found at i:2382654 original size:102 final size:102
Alignment explanation
Indices: 2382498--2382731 Score: 258
Period size: 102 Copynumber: 2.3 Consensus size: 102
2382488 TCCCTTGCAT
* * * *
2382498 TTCAAGAGGAAAATATTCATCTGTCAACTTCTTCGACCTTAACATAGAATTACCATCGACACAAC
1 TTCAAGACGAAGACATTCATCTGCCAACTTCTTCGACCTTAACATAGAATTACCATCGACACAAC
* * *
2382563 AGTT-TTTTCAAAACCCATATGACATTATACATTCAAG
66 A-TTCTGTACAAAACCCATATGACACTATACATTCAAG
* * * * * *
2382600 TTTAATG-CGAAGGCATTCATCTGCCAACTTCTTGGACCTTAATATCGAGA-TACCATTGACACA
1 TTCAA-GACGAAGACATTCATCTGCCAACTTCTTCGACCTTAACATAGA-ATTACCATCGACACA
* * * *
2382663 ACATTCTGTACAAAACTCATATGTCACTATGCCTTCAAG
64 ACATTCTGTACAAAACCCATATGACACTATACATTCAAG
*
2382702 TTCAAGAGGAAGACATTCATCTGCCAACTT
1 TTCAAGACGAAGACATTCATCTGCCAACTT
2382732 GTTCAACTTG
Statistics
Matches: 108, Mismatches: 20, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
101 3 0.03
102 103 0.95
103 2 0.02
ACGTcount: A:0.34, C:0.24, G:0.12, T:0.30
Consensus pattern (102 bp):
TTCAAGACGAAGACATTCATCTGCCAACTTCTTCGACCTTAACATAGAATTACCATCGACACAAC
ATTCTGTACAAAACCCATATGACACTATACATTCAAG
Found at i:2396010 original size:14 final size:14
Alignment explanation
Indices: 2395991--2396020 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2395981 TTAAATGATA
2395991 AACGAACACAAATG
1 AACGAACACAAATG
*
2396005 AACGAACATAAATG
1 AACGAACACAAATG
2396019 AA
1 AA
2396021 AGGATGTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.60, C:0.17, G:0.13, T:0.10
Consensus pattern (14 bp):
AACGAACACAAATG
Found at i:2396480 original size:23 final size:23
Alignment explanation
Indices: 2396450--2396494 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
2396440 TTTGCTTGAC
2396450 TGTATGGTAAAGGGGAGAGCCCT
1 TGTATGGTAAAGGGGAGAGCCCT
2396473 TGTATGGTAAAGGGGAGAGCCC
1 TGTATGGTAAAGGGGAGAGCCC
2396495 ACCATGAGCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.27, C:0.13, G:0.40, T:0.20
Consensus pattern (23 bp):
TGTATGGTAAAGGGGAGAGCCCT
Found at i:2400983 original size:2 final size:2
Alignment explanation
Indices: 2400976--2401024 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
2400966 ATCCTAATTC
2400976 AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2401017 AT AT AT AT
1 AT AT AT AT
2401025 TCTTTTGCTA
Statistics
Matches: 46, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 45 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:2402817 original size:7 final size:7
Alignment explanation
Indices: 2402805--2402854 Score: 50
Period size: 7 Copynumber: 7.3 Consensus size: 7
2402795 CCTACTTTTA
2402805 AAACCCT
1 AAACCCT
2402812 AAACCCT
1 AAACCCT
2402819 -AACCCT
1 AAACCCT
*
2402825 AAACCAT
1 AAACCCT
2402832 -AACCTCT
1 AAACC-CT
*
2402839 AAACCTT
1 AAACCCT
*
2402846 AAACTCT
1 AAACCCT
2402853 AA
1 AA
2402855 TTTAAAGTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
6 10 0.29
7 21 0.60
8 4 0.11
ACGTcount: A:0.44, C:0.36, G:0.00, T:0.20
Consensus pattern (7 bp):
AAACCCT
Found at i:2402824 original size:13 final size:13
Alignment explanation
Indices: 2402806--2402843 Score: 58
Period size: 13 Copynumber: 2.8 Consensus size: 13
2402796 CTACTTTTAA
*
2402806 AACCCTAAACCCT
1 AACCCTAAACCAT
2402819 AACCCTAAACCAT
1 AACCCTAAACCAT
2402832 AACCTCTAAACC
1 AACC-CTAAACC
2402844 TTAAACTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 16 0.70
14 7 0.30
ACGTcount: A:0.42, C:0.42, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCTAAACCAT
Found at i:2403004 original size:2 final size:2
Alignment explanation
Indices: 2402999--2403084 Score: 133
Period size: 2 Copynumber: 44.5 Consensus size: 2
2402989 TTTTTTATTC
*
2402999 AT AT AT AT AT AT AT AT AT AG AT AT AT AT -T AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
2403040 AT AT AT AT A- AT AT AT A- AT AT AT AT AT AT CT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2403080 AT AT A
1 AT AT A
2403085 ATTGGATAAA
Statistics
Matches: 77, Mismatches: 4, Indels: 6
0.89 0.05 0.07
Matches are distributed among these distances:
1 3 0.04
2 74 0.96
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2405208 original size:13 final size:15
Alignment explanation
Indices: 2405190--2405222 Score: 52
Period size: 13 Copynumber: 2.3 Consensus size: 15
2405180 ACTGAACTTT
2405190 TTTTACT-ATCATA-
1 TTTTACTCATCATAC
2405203 TTTTACTCATCATAC
1 TTTTACTCATCATAC
2405218 TTTTA
1 TTTTA
2405223 ATTTTTTCAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 7 0.39
14 6 0.33
15 5 0.28
ACGTcount: A:0.27, C:0.18, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTTACTCATCATAC
Found at i:2405404 original size:39 final size:39
Alignment explanation
Indices: 2405350--2405427 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
2405340 GTGCATATTT
*
2405350 AATATTATTAATATCAAGAACTTTCACGTCTACTATAAA
1 AATATTATTAATATCAAGAACATTCACGTCTACTATAAA
*
2405389 AATATTATTAATATCAAGAACATTCACGTCTATTATAAA
1 AATATTATTAATATCAAGAACATTCACGTCTACTATAAA
2405428 TCTTTATTTT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.45, C:0.14, G:0.05, T:0.36
Consensus pattern (39 bp):
AATATTATTAATATCAAGAACATTCACGTCTACTATAAA
Found at i:2406277 original size:15 final size:16
Alignment explanation
Indices: 2406245--2406284 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
2406235 TCAATAAAAA
2406245 TAAATAAAAAATATAT
1 TAAATAAAAAATATAT
*
2406261 TAAATAAAATATA-AT
1 TAAATAAAAAATATAT
2406276 TAAAATAAA
1 T-AAATAAA
2406285 CCCATTGACT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 3 0.14
16 19 0.86
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (16 bp):
TAAATAAAAAATATAT
Found at i:2410690 original size:24 final size:24
Alignment explanation
Indices: 2410663--2410719 Score: 96
Period size: 24 Copynumber: 2.4 Consensus size: 24
2410653 GATTAAATCG
* *
2410663 AGTTGAGTTAATAAACATATCTAA
1 AGTTTAGTTAAGAAACATATCTAA
2410687 AGTTTAGTTAAGAAACATATCTAA
1 AGTTTAGTTAAGAAACATATCTAA
2410711 AGTTTAGTT
1 AGTTTAGTT
2410720 TTTGTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.42, C:0.07, G:0.14, T:0.37
Consensus pattern (24 bp):
AGTTTAGTTAAGAAACATATCTAA
Found at i:2411509 original size:19 final size:18
Alignment explanation
Indices: 2411482--2411517 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
2411472 TTAATTTCTG
*
2411482 TTTTTTTTTTTTTTGTAA
1 TTTTTTTTTTATTTGTAA
2411500 TTTTTATTTTTATTTGTA
1 TTTTT-TTTTTATTTGTA
2411518 GTATGACTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.14, C:0.00, G:0.06, T:0.81
Consensus pattern (18 bp):
TTTTTTTTTTATTTGTAA
Found at i:2413784 original size:107 final size:106
Alignment explanation
Indices: 2413567--2414068 Score: 507
Period size: 107 Copynumber: 4.7 Consensus size: 106
2413557 TTGTTTGCTT
* *
2413567 TAATTTTTATGAGTG-AATATCGATATCGACTGACAATATATAATTTTATGC-TCTATCAGTGAA
1 TAATTTTTATCAGTGAAATATCGATATCGACTGACAGTATATAATTTTATGCATC-ATCAGTGAA
* * * * *
2413630 TAAGATGATCACTCGCTTTGTTAGAATAGATTTAGTGATACG
65 CAAGATGATCACGCTCTCTATTAGAATAGATTTAGTGATACG
* * * * * *
2413672 AAATTGTTTATCAGTGAAATACCGATATCGACTGTCGGTATATGATTTTATGCATCATCGGTGAA
1 TAATT-TTTATCAGTGAAATATCGATATCGACTGACAGTATATAATTTTATGCATCATCAGTGAA
* * *
2413737 CGAGATGATCACGCTCTCTATTAGAATAGATTTAGCGATATG
65 CAAGATGATCACGCTCTCTATTAGAATAGATTTAGTGATACG
* * *
2413779 TAATTGTTTATGAGTGAAATATCGATA-CGGACTGGCTGTATATAA-TTTATGCATCATCAGTGA
1 TAATT-TTTATCAGTGAAATATCGATATC-GACTGACAGTATATAATTTTATGCATCATCAGTGA
* * * * *
2413842 ATAAGATGATCACACACGCTATTAGAATTGATTTAGTGATACG
64 ACAAGATGATCACGCTCTCTATTAGAATAGATTTAGTGATACG
* * * *
2413885 TAATTTTTCA-CGAGTGAAATATCGATATGGACTGACATTATATAAGTTTATGCA-CTATCAGCG
1 TAATTTTT-ATC-AGTGAAATATCGATATCGACTGACAGTATATAATTTTATGCATC-ATCAGTG
* * * * *
2413948 AACAAGATGATCATGCGTGT-TATTAGAATGGATTTAGTGATGCA
63 AACAAGATGATCACGC-TCTCTATTAGAATAGATTTAGTGATACG
* * * * **
2413992 TAATTATTTA-CGAGTGAAATACCGATATGGACTAACTGTATATAATTTTATGCCCCATCAGTGA
1 TAATT-TTTATC-AGTGAAATATCGATATCGACTGACAGTATATAATTTTATGCATCATCAGTGA
2414056 ACAAGATGATCAC
64 ACAAGATGATCAC
2414069 CCGCTTTTAT
Statistics
Matches: 331, Mismatches: 54, Indels: 22
0.81 0.13 0.05
Matches are distributed among these distances:
105 7 0.02
106 97 0.29
107 221 0.67
108 6 0.02
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (106 bp):
TAATTTTTATCAGTGAAATATCGATATCGACTGACAGTATATAATTTTATGCATCATCAGTGAAC
AAGATGATCACGCTCTCTATTAGAATAGATTTAGTGATACG
Found at i:2413958 original size:213 final size:212
Alignment explanation
Indices: 2413567--2414068 Score: 568
Period size: 213 Copynumber: 2.4 Consensus size: 212
2413557 TTGTTTGCTT
**
2413567 TAATTTTTATGAGTG-AATATCGATATC-GACTGACAATATATAATTTTATGCTCTATCAGTGAA
1 TAATTTTTATGAGTGAAATATCGATA-CGGACTGACTGTATATAATTTTATGCTC-ATCAGTGAA
* * ** *
2413630 TAAGATGATCACTCGCTTTGTTAGAATAGATTTAGTGATACGAAATTGTTTATCAGTGAAATACC
64 TAAGATGATCACACACGCTATTAGAATAGATTTAGTGATACGAAATTGTTTATCAGTGAAATACC
* * * * * * *
2413695 GATATCGACTGTCGGTATATGATTTTATGCATCATCGGTGAACGAGATGATCACGC-TCTCTATT
129 GATATCGACTGACAGTATATAAGTTTATGCATCATCAGCGAACAAGATGATCACGCGTCT-TATT
**
2413759 AGAATAGATTTAGCGATATG
193 AGAATAGATTTAGCGATACA
*
2413779 TAATTGTTTATGAGTGAAATATCGATACGGACTGGCTGTATATAA-TTTATGCATCATCAGTGAA
1 TAATT-TTTATGAGTGAAATATCGATACGGACTGACTGTATATAATTTTATGC-TCATCAGTGAA
* *
2413843 TAAGATGATCACACACGCTATTAGAATTGATTTAGTGATACGTAATT-TTTCA-CGAGTGAAATA
64 TAAGATGATCACACACGCTATTAGAATAGATTTAGTGATACGAAATTGTTT-ATC-AGTGAAATA
* * * * *
2413906 TCGATATGGACTGACATTATATAAGTTTATGCA-CTATCAGCGAACAAGATGATCATGCGTGTTA
127 CCGATATCGACTGACAGTATATAAGTTTATGCATC-ATCAGCGAACAAGATGATCACGCGTCTTA
* * *
2413970 TTAGAATGGATTTAGTGATGCA
191 TTAGAATAGATTTAGCGATACA
* * * * *
2413992 TAATTATTTACGAGTGAAATACCGATATGGACTAACTGTATATAATTTTATGCCCCATCAGTGAA
1 TAATT-TTTATGAGTGAAATATCGATACGGACTGACTGTATATAATTTTATG-CTCATCAGTGAA
*
2414057 CAAGATGATCAC
64 TAAGATGATCAC
2414069 CCGCTTTTAT
Statistics
Matches: 245, Mismatches: 35, Indels: 18
0.82 0.12 0.06
Matches are distributed among these distances:
212 10 0.04
213 180 0.73
214 54 0.22
215 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.34
Consensus pattern (212 bp):
TAATTTTTATGAGTGAAATATCGATACGGACTGACTGTATATAATTTTATGCTCATCAGTGAATA
AGATGATCACACACGCTATTAGAATAGATTTAGTGATACGAAATTGTTTATCAGTGAAATACCGA
TATCGACTGACAGTATATAAGTTTATGCATCATCAGCGAACAAGATGATCACGCGTCTTATTAGA
ATAGATTTAGCGATACA
Found at i:2414371 original size:426 final size:413
Alignment explanation
Indices: 2413835--2414663 Score: 967
Period size: 426 Copynumber: 2.0 Consensus size: 413
2413825 TTATGCATCA
* *
2413835 TCAGTGAATAAGATGATCACACACGCTATTAGAATTGATTTAGTGATACGTAATTTTTCACGAGT
1 TCAGTGAACAAGATGATCACACACGCTATTAGAATAGATTTAGTGATACGTAATTTTTCACGAGT
** *
2413900 GAAATATCGATATGGACTGACATTATATAAGTTTATGCACTATCAGCGAACAAGATGATCA-TGC
66 GAAATATCGATATGGACTGACAGCATATAAGTTAATGCACTATCAGCGAACAAGATGATCACTG-
* *
2413964 GTGTTATTAGAATGGATTTAGTGAT-GCATAATTATTTACGAGTGAAATACCGATATGGACTAAC
130 GCGTTATTAGAATAGATTTAGTGATAG-ATAATTATTTACGAGTGAAATACCGATATGGACTAA-
* * *
2414028 T-GTATATAATTTTATGCCCCATCAGTGAACAAGATGAT-C-ACCCGCTTTTATTAGAAACTTAG
193 TGGTATATAATGTTATGCACCATCAGTGAACAAGATGATCCTACACG---TTATTAG-AA--TAG
** **
2414090 AATAGATATAGTGATAAGTAACTGTTTGGTTCACC-GATAGTGTATAGA-A-ATTTACGCATCAA
252 -AT---T-TAGTGATAACAAACTGTTTGGTTCACCAG-TAGTGTATAGAGAGAGATACGCATCAA
* * * *
2414152 ATATAAATCCGAGTGAAATATATGGCGTATTGATCATGAAATAGTTGGTTATGGCCAATTTTCTT
311 ACATAAATCCGAGTGAAATATATGACGTATTGATCATGAAATAATTGGTTATAGCCAATTTT-TT
* *
2414217 TTTTTTCTCGTATGTCGATTGATTTGGGTTAATTTTATGCTCTT
375 GTTTGT-T-GTA--T-GATTGATTTGGGTTAATTTTATGCTCTT
*** * * * * *
2414261 TCAGTGAACAAGATGATCACTGGCGTTATTAGAATAGATTTAGTGGTAGGTAGTTGTTT-ATGAG
1 TCAGTGAACAAGATGATCACACACGCTATTAGAATAGATTTAGTGATACGTAATT-TTTCACGAG
* ** *
2414325 TGAAATATCGATCTGGACTGATGGCATATAA-TGTAATGCACTATCAGTGAACAAGATGATCACT
65 TGAAATATCGATATGGACTGACAGCATATAAGT-TAATGCACTATCAGCGAACAAGATGATCACT
* * * * ** *
2414389 GGCGTTATTAGAATAGATTTAGTGATAGGTAGTTGTTTATGAGTGAAATATTGATATGGACTGAT
129 GGCGTTATTAGAATAGATTTAGTGATAGATAATTATTTACGAGTGAAATACCGATATGGACTAAT
* *
2414454 GGTATATAATGTTATGCACTATCAGTGAACAAGATGATCCTACACGTTATTAGAATAGATTTATT
194 GGTATATAATGTTATGCACCATCAGTGAACAAGATGATCCTACACGTTATTAGAATAGATTTAGT
* *
2414519 GATACCAAATTGTTTGGTTCACCAGTAGTGTATAGAGAGAGATACGCATCAAACATAAATCCGAG
259 GATAACAAACTGTTTGGTTCACCAGTAGTGTATAGAGAGAGATACGCATCAAACATAAATCCGAG
* * *
2414584 TGAAATATATGATGTATTGATCTTGGAATAATTGGTTATAGCCAATTTTTTGTTTGTTGTATGAT
324 TGAAATATATGACGTATTGATCATGAAATAATTGGTTATAGCCAATTTTTTGTTTGTTGTATGAT
2414649 TGATTTGGGTTAATT
389 TGATTTGGGTTAATT
2414664 GCTTTTGTTT
Statistics
Matches: 347, Mismatches: 46, Indels: 33
0.81 0.11 0.08
Matches are distributed among these distances:
413 18 0.05
414 1 0.00
416 3 0.01
417 34 0.10
418 9 0.03
419 66 0.19
421 2 0.01
422 3 0.01
424 2 0.01
425 9 0.03
426 189 0.54
427 7 0.02
428 4 0.01
ACGTcount: A:0.32, C:0.11, G:0.21, T:0.36
Consensus pattern (413 bp):
TCAGTGAACAAGATGATCACACACGCTATTAGAATAGATTTAGTGATACGTAATTTTTCACGAGT
GAAATATCGATATGGACTGACAGCATATAAGTTAATGCACTATCAGCGAACAAGATGATCACTGG
CGTTATTAGAATAGATTTAGTGATAGATAATTATTTACGAGTGAAATACCGATATGGACTAATGG
TATATAATGTTATGCACCATCAGTGAACAAGATGATCCTACACGTTATTAGAATAGATTTAGTGA
TAACAAACTGTTTGGTTCACCAGTAGTGTATAGAGAGAGATACGCATCAAACATAAATCCGAGTG
AAATATATGACGTATTGATCATGAAATAATTGGTTATAGCCAATTTTTTGTTTGTTGTATGATTG
ATTTGGGTTAATTTTATGCTCTT
Found at i:2414533 original size:107 final size:107
Alignment explanation
Indices: 2414246--2414522 Score: 439
Period size: 107 Copynumber: 2.6 Consensus size: 107
2414236 TGATTTGGGT
* * * *
2414246 TAATTTTATGCTCTTTCAGTGAACAAGATGATCACTGGCGTTATTAGAATAGATTTAGTGGTAGG
1 TAATGTTATGCACTATCAGTGAACAAGATGATCACTGGCGTTATTAGAATAGATTTAGTGATAGG
*
2414311 TAGTTGTTTATGAGTGAAATATCGATCTGGACTGATGGCATA
66 TAGTTGTTTATGAGTGAAATATCGATATGGACTGATGGCATA
*
2414353 TAATGTAATGCACTATCAGTGAACAAGATGATCACTGGCGTTATTAGAATAGATTTAGTGATAGG
1 TAATGTTATGCACTATCAGTGAACAAGATGATCACTGGCGTTATTAGAATAGATTTAGTGATAGG
* *
2414418 TAGTTGTTTATGAGTGAAATATTGATATGGACTGATGGTATA
66 TAGTTGTTTATGAGTGAAATATCGATATGGACTGATGGCATA
** *
2414460 TAATGTTATGCACTATCAGTGAACAAGATGATC-CTACACGTTATTAGAATAGATTTATTGATA
1 TAATGTTATGCACTATCAGTGAACAAGATGATCACT-GGCGTTATTAGAATAGATTTAGTGATA
2414523 CCAAATTGTT
Statistics
Matches: 157, Mismatches: 12, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
106 2 0.01
107 155 0.99
ACGTcount: A:0.32, C:0.10, G:0.22, T:0.35
Consensus pattern (107 bp):
TAATGTTATGCACTATCAGTGAACAAGATGATCACTGGCGTTATTAGAATAGATTTAGTGATAGG
TAGTTGTTTATGAGTGAAATATCGATATGGACTGATGGCATA
Found at i:2417614 original size:19 final size:20
Alignment explanation
Indices: 2417592--2417630 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
2417582 ATCATTAATC
2417592 TTAAATATAATTATT-TTTT
1 TTAAATATAATTATTATTTT
*
2417611 TTAAATTTAATTATTATTTT
1 TTAAATATAATTATTATTTT
2417631 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
TTAAATATAATTATTATTTT
Found at i:2417778 original size:21 final size:21
Alignment explanation
Indices: 2417754--2417802 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
2417744 AGTACAGTAG
*
2417754 TTAAATAAATGATTATTATTT
1 TTAAATAAATAATTATTATTT
2417775 TTAAATAAATAATTATTATTT
1 TTAAATAAATAATTATTATTT
2417796 TTAAATA
1 TTAAATA
2417803 TTTCGGATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (21 bp):
TTAAATAAATAATTATTATTT
Found at i:2422880 original size:29 final size:29
Alignment explanation
Indices: 2422843--2422898 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
2422833 TAATTATTTA
* *
2422843 TATTATGAATTATTAGATTTTGTATTTTG
1 TATTATGAATTATTAAATTTTATATTTTG
* *
2422872 TATTTTGAATTTTTAAATTTTATATTT
1 TATTATGAATTATTAAATTTTATATTT
2422899 AGATATTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.29, C:0.00, G:0.09, T:0.62
Consensus pattern (29 bp):
TATTATGAATTATTAAATTTTATATTTTG
Found at i:2429724 original size:65 final size:66
Alignment explanation
Indices: 2429601--2429733 Score: 250
Period size: 66 Copynumber: 2.0 Consensus size: 66
2429591 TACCGTCCAA
2429601 CATATTAGTTGAAAACTTATTCCTGTTTAAGAACAAGTGGTTCTTTTCTTTTCTTTTTTTCAATG
1 CATATTAGTTGAAAACTTATTCCTGTTTAAGAACAAGTGGTTCTTTTCTTTTCTTTTTTTCAATG
2429666 T
66 T
2429667 CATATTAGTTG-AAACTTATTCCTGTTTAAGAACAAAGTGGTTCTTTTCTTTTCTTTTTTTCAAT
1 CATATTAGTTGAAAACTTATTCCTGTTTAAGAAC-AAGTGGTTCTTTTCTTTTCTTTTTTTCAAT
2429731 GT
65 GT
2429733 C
1 C
2429734 TTCTACATAA
Statistics
Matches: 66, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
65 22 0.33
66 44 0.67
ACGTcount: A:0.24, C:0.14, G:0.12, T:0.50
Consensus pattern (66 bp):
CATATTAGTTGAAAACTTATTCCTGTTTAAGAACAAGTGGTTCTTTTCTTTTCTTTTTTTCAATG
T
Found at i:2431500 original size:2 final size:2
Alignment explanation
Indices: 2431495--2431526 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2431485 ATATATATAT
*
2431495 AG AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2431527 GGGGGAAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.53, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2434555 original size:13 final size:13
Alignment explanation
Indices: 2434537--2434563 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2434527 CCAGACATCT
2434537 GGAGGTGATCGTG
1 GGAGGTGATCGTG
2434550 GGAGGTGATCGTG
1 GGAGGTGATCGTG
2434563 G
1 G
2434564 TGCACTTATT
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:0.15, C:0.07, G:0.56, T:0.22
Consensus pattern (13 bp):
GGAGGTGATCGTG
Found at i:2443177 original size:15 final size:16
Alignment explanation
Indices: 2443141--2443179 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
2443131 AGAGCCTTTA
2443141 AATCATTCAGCATTTG
1 AATCATTCAGCATTTG
*
2443157 AATCATTCAGCGTTT-
1 AATCATTCAGCATTTG
2443172 AATCATTC
1 AATCATTC
2443180 TGAAGTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 8 0.36
16 14 0.64
ACGTcount: A:0.31, C:0.21, G:0.10, T:0.38
Consensus pattern (16 bp):
AATCATTCAGCATTTG
Found at i:2446500 original size:16 final size:18
Alignment explanation
Indices: 2446468--2446500 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
2446458 TATTAATGTA
2446468 TGAATCATTTATATTTTT
1 TGAATCATTTATATTTTT
2446486 TGAAT-ATTT-TATTTT
1 TGAATCATTTATATTTT
2446501 AATAAGAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 4 0.27
18 5 0.33
ACGTcount: A:0.27, C:0.03, G:0.06, T:0.64
Consensus pattern (18 bp):
TGAATCATTTATATTTTT
Found at i:2447031 original size:13 final size:13
Alignment explanation
Indices: 2447013--2447038 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2447003 AAATTGATAG
2447013 CATATATAAATAA
1 CATATATAAATAA
2447026 CATATATAAATAA
1 CATATATAAATAA
2447039 TTAGGTGGTG
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:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (13 bp):
CATATATAAATAA
Found at i:2447140 original size:140 final size:139
Alignment explanation
Indices: 2446898--2447151 Score: 379
Period size: 141 Copynumber: 1.8 Consensus size: 139
2446888 AATTTTCTTC
* * *
2446898 TAATTAGGTGGTGACATGTGTCACCATAACATATCATGATCATGTGTTAACATATGTCAGATCCT
1 TAATTAGGTGGTGACATGCGTCACCATAACATATCATGATCATGTGATAACACATGTCAGATCCT
**
2446963 GGTTAAATGATTAATTATTAAATTTTATTTAATTTAGG-CCAAATTGATAGCATATATAAATAAC
66 AATTAAATGATTAATTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAAC
2447027 ATATATAAA
131 ATATATAAA
* * *
2447036 TAATTAGGTGGTGACATGCGTCACCAATGACACGTGTCATGATCATGTGATAACACATGTC-TAT
1 TAATTAGGTGGTGACATGCGTCACC-AT-A-ACATATCATGATCATGTGATAACACATGTCAGAT
2447100 CCTAATTAAATGATTAATTTATTAAA-TTTATTTAATTTAGGACCAAATTGAT
63 CCTAATTAAATGATTAA-TTATTAAATTTTATTTAATTTAGGACCAAATTGAT
2447152 TATATAAATA
Statistics
Matches: 103, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
138 24 0.23
139 2 0.02
140 33 0.32
141 44 0.43
ACGTcount: A:0.37, C:0.12, G:0.15, T:0.37
Consensus pattern (139 bp):
TAATTAGGTGGTGACATGCGTCACCATAACATATCATGATCATGTGATAACACATGTCAGATCCT
AATTAAATGATTAATTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAATAAC
ATATATAAA
Found at i:2449524 original size:31 final size:32
Alignment explanation
Indices: 2449453--2449524 Score: 94
Period size: 31 Copynumber: 2.3 Consensus size: 32
2449443 GTGATAAAGC
*
2449453 TGGATAAGTTTAAGGACCATTTTGTAATAGTT
1 TGGATAAGTTTAAGGACAATTTTGTAATAGTT
* * *
2449485 T-GATAAGTTTAATGATAATTTTGTAATTGTT
1 TGGATAAGTTTAAGGACAATTTTGTAATAGTT
2449516 TGGA-AAGTT
1 TGGATAAGTT
2449525 CAATAATCAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
31 32 0.91
32 3 0.09
ACGTcount: A:0.32, C:0.03, G:0.21, T:0.44
Consensus pattern (32 bp):
TGGATAAGTTTAAGGACAATTTTGTAATAGTT
Found at i:2449537 original size:31 final size:31
Alignment explanation
Indices: 2449470--2449537 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
2449460 GTTTAAGGAC
* *
2449470 CATTTTGTAATAGTTTGATAAGTTTAATGAT
1 CATTTTGTAATAGTTTGATAAGTTCAATAAT
* *
2449501 AATTTTGTAATTGTTTGGA-AAGTTCAATAAT
1 CATTTTGTAATAGTTT-GATAAGTTCAATAAT
2449532 CATTTT
1 CATTTT
2449538 TTATGTGAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
31 29 0.94
32 2 0.06
ACGTcount: A:0.32, C:0.04, G:0.15, T:0.49
Consensus pattern (31 bp):
CATTTTGTAATAGTTTGATAAGTTCAATAAT
Found at i:2449844 original size:21 final size:21
Alignment explanation
Indices: 2449818--2449868 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
2449808 ATAATATAAC
2449818 ATTTAGTCCCTAAATTTATCA
1 ATTTAGTCCCTAAATTTATCA
* *
2449839 ATTTAGTCCCTAGATTTGTCA
1 ATTTAGTCCCTAAATTTATCA
2449860 ATTT-GTCCC
1 ATTTAGTCCC
2449869 AACTGAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 5 0.18
21 23 0.82
ACGTcount: A:0.25, C:0.22, G:0.10, T:0.43
Consensus pattern (21 bp):
ATTTAGTCCCTAAATTTATCA
Found at i:2451296 original size:11 final size:11
Alignment explanation
Indices: 2451280--2451306 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
2451270 AATCCGTGTT
2451280 ATGTCGCGTTA
1 ATGTCGCGTTA
2451291 ATGTCGCGTTA
1 ATGTCGCGTTA
2451302 ATGTC
1 ATGTC
2451307 ATTAACCGTG
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:0.19, C:0.19, G:0.26, T:0.37
Consensus pattern (11 bp):
ATGTCGCGTTA
Found at i:2454390 original size:55 final size:55
Alignment explanation
Indices: 2454324--2454435 Score: 179
Period size: 55 Copynumber: 2.0 Consensus size: 55
2454314 TTACAGAGAG
**
2454324 CATATCAAGCGAAAGTGCAGTGACATTTGCAGCTCAGGCATGCTAAATAGAAAAA
1 CATATCAAGCGAAAGTGCAGTGACATTTGCAGCTCAGGCACACTAAATAGAAAAA
** *
2454379 CATATCAAGCGAAAGTGCAGTGACATTTTTAGCTCAGGCACACTAAATAGAAGAA
1 CATATCAAGCGAAAGTGCAGTGACATTTGCAGCTCAGGCACACTAAATAGAAAAA
2454434 CA
1 CA
2454436 ATGGGAGCAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
55 52 1.00
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (55 bp):
CATATCAAGCGAAAGTGCAGTGACATTTGCAGCTCAGGCACACTAAATAGAAAAA
Found at i:2458252 original size:25 final size:26
Alignment explanation
Indices: 2458191--2458262 Score: 92
Period size: 25 Copynumber: 2.7 Consensus size: 26
2458181 TATACCAAAG
*
2458191 AAAAAGACTCAAATTAGCAAAAAGGAAA
1 AAAAAGGCTCAAATTAGC-AAAAGG-AA
* *
2458219 AAAAAGGCTCACATTAGCAAAATG-A
1 AAAAAGGCTCAAATTAGCAAAAGGAA
2458244 AAAAAGGCTCAAATTAGCA
1 AAAAAGGCTCAAATTAGCA
2458263 GTAAGAAGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
25 19 0.47
27 5 0.12
28 16 0.40
ACGTcount: A:0.57, C:0.14, G:0.15, T:0.14
Consensus pattern (26 bp):
AAAAAGGCTCAAATTAGCAAAAGGAA
Found at i:2461725 original size:18 final size:18
Alignment explanation
Indices: 2461702--2461743 Score: 84
Period size: 18 Copynumber: 2.3 Consensus size: 18
2461692 GATCACTCCA
2461702 ATCAGCATCTTGGAACCC
1 ATCAGCATCTTGGAACCC
2461720 ATCAGCATCTTGGAACCC
1 ATCAGCATCTTGGAACCC
2461738 ATCAGC
1 ATCAGC
2461744 TTCTAGCTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.17, T:0.21
Consensus pattern (18 bp):
ATCAGCATCTTGGAACCC
Found at i:2464439 original size:44 final size:45
Alignment explanation
Indices: 2464390--2464484 Score: 156
Period size: 45 Copynumber: 2.1 Consensus size: 45
2464380 TCATATCTAA
*
2464390 ATTTTAAAA-TTTTCAAATCATACCTAAAATTCAAATTTTGTTTC
1 ATTTTAAAATTTTTAAAATCATACCTAAAATTCAAATTTTGTTTC
* *
2464434 ATTTTAAAATTTTTAAAATCATACCTAAAATTTAATTTTTGTTTC
1 ATTTTAAAATTTTTAAAATCATACCTAAAATTCAAATTTTGTTTC
2464479 ATTTTA
1 ATTTTA
2464485 GTATATGTTC
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
44 9 0.19
45 38 0.81
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (45 bp):
ATTTTAAAATTTTTAAAATCATACCTAAAATTCAAATTTTGTTTC
Found at i:2464605 original size:22 final size:22
Alignment explanation
Indices: 2464580--2464649 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
2464570 TTAACACGTT
*
2464580 AAATATTTTACGATAAATACTA
1 AAATATTTTAAGATAAATACTA
** * * *
2464602 AAATA-AATAAAACTAAAT-GTT
1 AAATATTTTAAGA-TAAATACTA
*
2464623 AAATATTTTAGGATAAATACTA
1 AAATATTTTAAGATAAATACTA
2464645 AAATA
1 AAATA
2464650 AATAAAAATT
Statistics
Matches: 33, Mismatches: 12, Indels: 6
0.65 0.24 0.12
Matches are distributed among these distances:
21 14 0.42
22 19 0.58
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (22 bp):
AAATATTTTAAGATAAATACTA
Found at i:2464691 original size:24 final size:23
Alignment explanation
Indices: 2464656--2464702 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
2464646 AATAAATAAA
* * *
2464656 AATTAAACTTTAAGTATTGAAAC
1 AATTAAAATTTAAATATTAAAAC
2464679 AATTGAAAATTTAAATATTAAAAC
1 AATT-AAAATTTAAATATTAAAAC
2464703 GGATCAAAAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.53, C:0.06, G:0.06, T:0.34
Consensus pattern (23 bp):
AATTAAAATTTAAATATTAAAAC
Found at i:2464972 original size:45 final size:45
Alignment explanation
Indices: 2464907--2465043 Score: 157
Period size: 45 Copynumber: 3.0 Consensus size: 45
2464897 TGGAATATCA
* * * * *
2464907 GGAGGGAATCCGGGTGTTGGAATTTCTGGCGGTACCGATGGTGGC
1 GGAGGGATTCCCGGCGTTGGAAGTTCTGGCGGTACAGATGGTGGC
* * * * * *
2464952 GGTGGGATTCCCGGCGTTGGAAGTACCGGCGGTTCAGACGGTGAC
1 GGAGGGATTCCCGGCGTTGGAAGTTCTGGCGGTACAGATGGTGGC
* *
2464997 GGAGGGATTCCTGGCGTGGGAAGTTCTGGCGGTACAGATGGTGGC
1 GGAGGGATTCCCGGCGTTGGAAGTTCTGGCGGTACAGATGGTGGC
2465042 GG
1 GG
2465044 CACATAATCC
Statistics
Matches: 73, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
45 73 1.00
ACGTcount: A:0.15, C:0.18, G:0.45, T:0.22
Consensus pattern (45 bp):
GGAGGGATTCCCGGCGTTGGAAGTTCTGGCGGTACAGATGGTGGC
Found at i:2467725 original size:2 final size:2
Alignment explanation
Indices: 2467718--2467748 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2467708 AGAGAAGGTT
2467718 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2467749 GTAATAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2470443 original size:77 final size:77
Alignment explanation
Indices: 2470316--2470459 Score: 234
Period size: 77 Copynumber: 1.9 Consensus size: 77
2470306 TTTTTTTAAT
* * * * *
2470316 TTCATCCTTAAACTACAATTTTCATTTTAAATTAGTCCTTAAACTTTTGAACATTCAGATTTTAT
1 TTCATCCTTAAACTACAACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCAT
2470381 CCAAAAAATTGA
66 CCAAAAAATTGA
*
2470393 TTCATCCTTAAACTACGACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCAT
1 TTCATCCTTAAACTACAACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCAT
2470458 CC
66 CC
2470460 CCAAACTATG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
77 61 1.00
ACGTcount: A:0.34, C:0.21, G:0.05, T:0.40
Consensus pattern (77 bp):
TTCATCCTTAAACTACAACTCTCATTCTAAATTAGTCCTTAAACTTTTGAACATTCAAATTTCAT
CCAAAAAATTGA
Found at i:2470491 original size:60 final size:60
Alignment explanation
Indices: 2470393--2470524 Score: 185
Period size: 60 Copynumber: 2.2 Consensus size: 60
2470383 AAAAAATTGA
** *
2470393 TTCATCCTTAAACTACGACTCTCATTCTAAATTAGTCCTTAAACTTTT-GAACATTCAAAT
1 TTCATCCCCAAACTACGAATCTCATTCTAAATTAGTCCTTAAACTTTTAGAACATTC-AAT
* * * *
2470453 TTCATCCCCAAACTATGAATCTCATTCTAAATTGGTCCTTAAACTTTTAGATCTTTCAAT
1 TTCATCCCCAAACTACGAATCTCATTCTAAATTAGTCCTTAAACTTTTAGAACATTCAAT
2470513 TTCATCCCCAAA
1 TTCATCCCCAAA
2470525 TTCATTGAAA
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
60 58 0.91
61 6 0.09
ACGTcount: A:0.32, C:0.25, G:0.05, T:0.38
Consensus pattern (60 bp):
TTCATCCCCAAACTACGAATCTCATTCTAAATTAGTCCTTAAACTTTTAGAACATTCAAT
Found at i:2470497 original size:31 final size:31
Alignment explanation
Indices: 2470397--2470497 Score: 86
Period size: 31 Copynumber: 3.3 Consensus size: 31
2470387 AATTGATTCA
* *
2470397 TCCTTAAACTACGACTCTCATTCTAAATTAG
1 TCCTTAAACTATGAATCTCATTCTAAATTAG
*
2470428 TCCTTAAACTTTTGAA---CATTC-AAATTTCA-
1 TCCTTAAAC-TATGAATCTCATTCTAAA-TT-AG
** *
2470457 TCCCCAAACTATGAATCTCATTCTAAATTGG
1 TCCTTAAACTATGAATCTCATTCTAAATTAG
2470488 TCCTTAAACT
1 TCCTTAAACT
2470498 TTTAGATCTT
Statistics
Matches: 53, Mismatches: 9, Indels: 16
0.68 0.12 0.21
Matches are distributed among these distances:
28 8 0.15
29 14 0.26
30 1 0.02
31 24 0.45
32 6 0.11
ACGTcount: A:0.33, C:0.25, G:0.06, T:0.37
Consensus pattern (31 bp):
TCCTTAAACTATGAATCTCATTCTAAATTAG
Found at i:2472840 original size:7 final size:7
Alignment explanation
Indices: 2472823--2472868 Score: 51
Period size: 7 Copynumber: 6.7 Consensus size: 7
2472813 GGTGTAATAA
2472823 AATTA-T
1 AATTATT
2472829 AATTATT
1 AATTATT
2472836 AATTATT
1 AATTATT
2472843 AATTTATT
1 AA-TTATT
*
2472851 -ATTTTT
1 AATTATT
2472857 AATTATT
1 AATTATT
*
2472864 TATTA
1 AATTA
2472869 AAAATTAATA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
6 9 0.26
7 20 0.59
8 5 0.15
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
AATTATT
Found at i:2472849 original size:21 final size:21
Alignment explanation
Indices: 2472825--2472892 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
2472815 TGTAATAAAA
2472825 TTATAATTATTAATTATTAAT
1 TTATAATTATTAATTATTAAT
* * *
2472846 TTATTATTTTTAATTATTTAT
1 TTATAATTATTAATTATTAAT
* * * *
2472867 TAAAAATTAATAGATTAGTAAT
1 TTATAATTATTA-ATTATTAAT
2472889 TTAT
1 TTAT
2472893 TATTTGTTTT
Statistics
Matches: 34, Mismatches: 12, Indels: 1
0.72 0.26 0.02
Matches are distributed among these distances:
21 25 0.74
22 9 0.26
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (21 bp):
TTATAATTATTAATTATTAAT
Found at i:2473602 original size:31 final size:31
Alignment explanation
Indices: 2473567--2473626 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2473557 CATTTAGTCT
2473567 GTTTGCAATATGGCCCCCAAAGTAATCGACC
1 GTTTGCAATATGGCCCCCAAAGTAATCGACC
* * *
2473598 GTTTGCAATATGGTCCCCGACGTAATCGA
1 GTTTGCAATATGGCCCCCAAAGTAATCGA
2473627 TCATTTGATG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.25
Consensus pattern (31 bp):
GTTTGCAATATGGCCCCCAAAGTAATCGACC
Found at i:2480047 original size:31 final size:31
Alignment explanation
Indices: 2480009--2480081 Score: 101
Period size: 31 Copynumber: 2.4 Consensus size: 31
2479999 AAATAATAGT
*
2480009 ATATGATCATTTTCATTTATATTTAATTAAG
1 ATATGATCACTTTCATTTATATTTAATTAAG
* *
2480040 ATATGATCACTTTCATTTTTATTTATTTAAG
1 ATATGATCACTTTCATTTATATTTAATTAAG
* *
2480071 ATGTGGTCACT
1 ATATGATCACT
2480082 ACGAGTTAAC
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 37 1.00
ACGTcount: A:0.30, C:0.10, G:0.10, T:0.51
Consensus pattern (31 bp):
ATATGATCACTTTCATTTATATTTAATTAAG
Found at i:2484577 original size:14 final size:15
Alignment explanation
Indices: 2484558--2484590 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
2484548 TACAATGCAT
2484558 AAAT-AAATATATTA
1 AAATAAAATATATTA
*
2484572 AAATAAAATATATTC
1 AAATAAAATATATTA
2484587 AAAT
1 AAAT
2484591 TTATAATAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
AAATAAAATATATTA
Found at i:2485948 original size:31 final size:32
Alignment explanation
Indices: 2485898--2485957 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
2485888 AACAATTGTA
*
2485898 AAAATAATAATAAATTTAATTATT-ATTTTATG
1 AAAATAATAATAAAATTAA-TATTCATTTTATG
*
2485930 AAAAT-ATGATAAAATTAATATTCATTTT
1 AAAATAATAATAAAATTAATATTCATTTT
2485958 GCAACATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 4 0.16
31 16 0.64
32 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.03, T:0.45
Consensus pattern (32 bp):
AAAATAATAATAAAATTAATATTCATTTTATG
Found at i:2489582 original size:29 final size:29
Alignment explanation
Indices: 2489546--2489606 Score: 95
Period size: 30 Copynumber: 2.1 Consensus size: 29
2489536 TTATAATCAA
* *
2489546 TATAAAAATTGATAAATTTAATTAATATTT
1 TATAAAAAGTGATAAATTTAA-TAATAATT
2489576 TATAAAAAGTGATAAATTTAATAATAATT
1 TATAAAAAGTGATAAATTTAATAATAATT
2489605 TA
1 TA
2489607 ATTTTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
29 9 0.31
30 20 0.69
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (29 bp):
TATAAAAAGTGATAAATTTAATAATAATT
Found at i:2490024 original size:4 final size:4
Alignment explanation
Indices: 2490015--2490132 Score: 191
Period size: 4 Copynumber: 29.5 Consensus size: 4
2490005 TATTGAATAT
* * * *
2490015 TACA TACA TACA TACA TACA TACA TGCA TGCA TGCA TGCA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
*
2490063 TGCA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
2490111 TACA TACA TACA TACA TACA TA
1 TACA TACA TACA TACA TACA TA
2490133 TGTCTATATA
Statistics
Matches: 110, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
4 110 1.00
ACGTcount: A:0.46, C:0.25, G:0.04, T:0.25
Consensus pattern (4 bp):
TACA
Found at i:2490144 original size:2 final size:2
Alignment explanation
Indices: 2490137--2490192 Score: 76
Period size: 2 Copynumber: 28.0 Consensus size: 2
2490127 TACATATGTC
* * * *
2490137 TA TA TA TA TA TA TA TA CA TA CA TA TG TC 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
2490179 TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA
2490193 GAGAGAGAGA
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.46
Consensus pattern (2 bp):
TA
Found at i:2490153 original size:28 final size:28
Alignment explanation
Indices: 2490122--2490189 Score: 118
Period size: 28 Copynumber: 2.4 Consensus size: 28
2490112 ACATACATAC
2490122 ATACATACATATGTCTATATATATATAT
1 ATACATACATATGTCTATATATATATAT
2490150 ATACATACATATGTCTATATATATATAT
1 ATACATACATATGTCTATATATATATAT
* *
2490178 ATATATATATAT
1 ATACATACATAT
2490190 ATAGAGAGAG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.44, C:0.09, G:0.03, T:0.44
Consensus pattern (28 bp):
ATACATACATATGTCTATATATATATAT
Found at i:2490297 original size:2 final size:2
Alignment explanation
Indices: 2490290--2490466 Score: 302
Period size: 2 Copynumber: 89.0 Consensus size: 2
2490280 TACATATGTC
* * *
2490290 TA TA TA TA TA TA TA CA TA CA TA TG 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
2490332 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
* *
2490374 TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA GA CA 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
2490415 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
2490457 TA TA TA TA TA
1 TA TA TA TA TA
2490467 GAGAGAGAGA
Statistics
Matches: 165, Mismatches: 9, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
1 1 0.01
2 164 0.99
ACGTcount: A:0.49, C:0.02, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2498601 original size:25 final size:25
Alignment explanation
Indices: 2498560--2498631 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
2498550 CATTAGGGGA
* *
2498560 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
2498584 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
2498609 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
2498632 ATGGGTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:2498741 original size:3 final size:3
Alignment explanation
Indices: 2498729--2498770 Score: 63
Period size: 3 Copynumber: 15.0 Consensus size: 3
2498719 AATATGTAAT
2498729 TAA T-A TAA TAA TAA TAA TAA TAA T-A TAA TAA TAA T-A TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2498771 ATTAAAATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
2 6 0.17
3 30 0.83
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:2498743 original size:11 final size:11
Alignment explanation
Indices: 2498729--2498770 Score: 70
Period size: 11 Copynumber: 4.0 Consensus size: 11
2498719 AATATGTAAT
2498729 TAATATAATAA
1 TAATATAATAA
2498740 T-A-ATAATAA
1 TAATATAATAA
2498749 TAATATAATAA
1 TAATATAATAA
2498760 TAATATAATAA
1 TAATATAATAA
2498771 ATTAAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
9 8 0.28
10 2 0.07
11 19 0.66
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (11 bp):
TAATATAATAA
Found at i:2498756 original size:14 final size:14
Alignment explanation
Indices: 2498729--2498770 Score: 57
Period size: 17 Copynumber: 2.8 Consensus size: 14
2498719 AATATGTAAT
2498729 TAATATAATAATAA
1 TAATATAATAATAA
2498743 TAATAATAATATAATAA
1 TAAT-AT-A-ATAATAA
2498760 TAATATAATAA
1 TAATATAATAA
2498771 ATTAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
14 8 0.32
15 3 0.12
16 3 0.12
17 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
TAATATAATAATAA
Found at i:2499129 original size:43 final size:40
Alignment explanation
Indices: 2499071--2499310 Score: 155
Period size: 43 Copynumber: 5.7 Consensus size: 40
2499061 TAAAGGTGAA
* *
2499071 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GGCTGG--ATCTAGGGTTG
* * *
2499114 ACACGGCTCCTACGTGATAAGGAGATCTGG-TCT-GGGAATG
1 ACACGGCTCCTACGTGATGAGGAG-GCTGGATCTAGGG-TTG
* * * * *
2499154 ACACGGCTCATACGTGATGAAGAGTTCTGGCCATCTTAAGGTGATA
1 ACACGGCTCCTACGTGATGAGGAG-GCTGG--ATC-T-AGG-GTTG
* *
2499200 ACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGTTG
1 ACACGGCTCCTACGTGATGAGGA-GGCTGG--ATCTAGGGTTG
* * * *
2499243 ACACGGCTCCTACGTGATAAGGA-GATGG-TCTGGGGATG
1 ACACGGCTCCTACGTGATGAGGAGGCTGGATCTAGGGTTG
* *
2499281 ACACGGTTCCTACATGATGAGGACGGCTGG
1 ACACGGCTCCTACGTGATGAGGA-GGCTGG
2499311 CCATCTTTAG
Statistics
Matches: 156, Mismatches: 29, Indels: 27
0.74 0.14 0.13
Matches are distributed among these distances:
38 27 0.17
39 2 0.01
40 35 0.22
41 4 0.03
42 1 0.01
43 50 0.32
44 3 0.02
45 1 0.01
46 31 0.20
47 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.32, T:0.25
Consensus pattern (40 bp):
ACACGGCTCCTACGTGATGAGGAGGCTGGATCTAGGGTTG
Found at i:2499185 original size:128 final size:127
Alignment explanation
Indices: 2498985--2499300 Score: 499
Period size: 129 Copynumber: 2.5 Consensus size: 127
2498975 CGTCTAAAAG
* * * * * *
2498985 TGACAAGGTTCCTACATGATGAGGACTATGGTCGGGGAATGACACGGCTCATACGTGATGAAGAG
1 TGACACGGCTCCTACGTGATAAGGA-GATGGTCTGGGAATGACACGGCTCATACGTGATGAAGAG
2499050 TTCTGGCCATCTAAAGGTGA-AACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
65 TTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
2499112 TGACACGGCTCCTACGTGATAAGGAGATCTGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
1 TGACACGGCTCCTACGTGATAAGGAGA--TGGTCTGGGAATGACACGGCTCATACGTGATGAAGA
*
2499177 GTTCTGGCCATCTTAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
64 GTTCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
* * * *
2499241 TGACACGGCTCCTACGTGATAAGGAGATGGTCTGGGGATGACACGGTTCCTACATGATGA
1 TGACACGGCTCCTACGTGATAAGGAGATGGTCTGGGAATGACACGGCTCATACGTGATGA
2499301 GGACGGCTGG
Statistics
Matches: 175, Mismatches: 11, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
126 1 0.01
127 50 0.29
128 55 0.31
129 69 0.39
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (127 bp):
TGACACGGCTCCTACGTGATAAGGAGATGGTCTGGGAATGACACGGCTCATACGTGATGAAGAGT
TCTGGCCATCTAAAGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGTTATCTATGGT
Found at i:2500202 original size:63 final size:63
Alignment explanation
Indices: 2499868--2500223 Score: 208
Period size: 62 Copynumber: 5.6 Consensus size: 63
2499858 GTATCTTAGT
* * * * *
2499868 GAGACAAAA-TTTGTTTCCAAAGAAACAGACTC--AGATTTTTCTTCAAAAGAAACTGTTTTAA
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTT-TTCAAAAGAAATTGTCTCAA
* * ** * * * * *
2499929 GGGATAAAACCTTGTTTCCAGAGAAACAAACTCAAAGATGATCTTATTT-AAGAGAAAATGTTTC
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT--T-TT-TTTCAAAAGAAATTGTCTC
2499993 AA
62 AA
* * ** * * ** * * * *
2499995 GAGACAAAA-TTCGTTTGAAGGGAAAC-GACTCAAAGATGTCATTGAAAGGAAACTGT-TCATGC
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTCA--A
* * * * * * * *
2500057 GAGACAAAA-TTGGTTTTAATAGAAACAATCTCAAAGGTGGGTATTTTCAAAAGAAGTTGTCTCG
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT---TTTTTTCAAAAGAAATTGTCTCA
2500121 A
63 A
* *
2500122 GAGACAAAATTTTGTTTC-AAAGGAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTTTAA
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTC-TCAA
* *
2500185 GAGATAAAATTTTGTTTCAAAAGAAACTAACTCAAAGAT
1 GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGAT
2500224 GGATCTCATC
Statistics
Matches: 224, Mismatches: 53, Indels: 33
0.72 0.17 0.11
Matches are distributed among these distances:
60 5 0.02
61 17 0.08
62 60 0.27
63 27 0.12
64 32 0.14
65 37 0.17
66 39 0.17
67 6 0.03
68 1 0.00
ACGTcount: A:0.42, C:0.13, G:0.17, T:0.29
Consensus pattern (63 bp):
GAGACAAAATTTTGTTTCAAAAGAAACAAACTCAAAGATTTTTTTCAAAAGAAATTGTCTCAA
Found at i:2500489 original size:65 final size:66
Alignment explanation
Indices: 2500406--2500615 Score: 237
Period size: 67 Copynumber: 3.2 Consensus size: 66
2500396 GATTTACTTC
** * * * * * *
2500406 AAAGAAACGGTCTCAAGAGATACAAAATTCATTTTAAGAGAAACAGATTCAAAGATTTTTGTTTC
1 AAAGAAACTATCTTAAGAGAGACAAAATTCATTTCAAAAGAAACAAACTCAAAGATTTTTGTTTC
2500471 -
66 A
* **
2500471 AAAGAAATTATCTTAAGAGAGACAAAAATTTGTTTCAAAAGAAACAAACTCAAAGATTTTTGTTT
1 AAAGAAACTATCTTAAGAGAGAC-AAAATTCATTTCAAAAGAAACAAACTCAAAGATTTTTGTTT
2500536 CA
65 CA
* ** *
2500538 AAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCCAAAGAAACAAACTCAAAGA-TTTT-TTT
1 AAAGAAACTATCTTAAGAGAGACAAAA-TTCATTTCAAAAGAAACAAACTCAAAGATTTTTGTTT
2500601 CA
65 CA
*
2500603 AAAGAAACAATCT
1 AAAGAAACTATCT
2500616 CAAAGATTTT
Statistics
Matches: 127, Mismatches: 15, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
65 35 0.28
66 44 0.35
67 48 0.38
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.29
Consensus pattern (66 bp):
AAAGAAACTATCTTAAGAGAGACAAAATTCATTTCAAAAGAAACAAACTCAAAGATTTTTGTTTC
A
Found at i:2500556 original size:67 final size:67
Alignment explanation
Indices: 2500444--2500615 Score: 262
Period size: 67 Copynumber: 2.6 Consensus size: 67
2500434 TCATTTTAAG
* * *
2500444 AGAAACAGATTCAAAGATTTTTGTTTC-AAAGAAATTATCTTAAGAGAGACAAAAA-TTTGTTTC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGA-AAAAATTTTGTTTC
2500507 AAA
65 AAA
*
2500510 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCC
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
2500575 AA
66 AA
*
2500577 AGAAACAAACTCAAAGA-TTTT-TTTCAAAAGAAACAATCT
1 AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCT
2500616 CAAAGATTTT
Statistics
Matches: 99, Mismatches: 5, Indels: 5
0.91 0.05 0.05
Matches are distributed among these distances:
65 17 0.17
66 34 0.34
67 48 0.48
ACGTcount: A:0.47, C:0.12, G:0.12, T:0.30
Consensus pattern (67 bp):
AGAAACAAACTCAAAGATTTTTGTTTCAAAAGAAACTATCTTAAGAGAGAAAAAATTTTGTTTCA
AA
Found at i:2500644 original size:26 final size:28
Alignment explanation
Indices: 2500564--2500630 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
2500554 GAGAGAAAAA
* *
2500564 ATTTTGTTTCCAAAGAAACAAACTCAAAG
1 ATTTT-TTTCAAAAGAAACAATCTCAAAG
2500593 ATTTTTTTCAAAAGAAACAATCTCAAAG
1 ATTTTTTTCAAAAGAAACAATCTCAAAG
2500621 ATTTTTTTCA
1 ATTTTTTTCA
2500631 CAAAATTGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
28 31 0.86
29 5 0.14
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (28 bp):
ATTTTTTTCAAAAGAAACAATCTCAAAG
Found at i:2500694 original size:52 final size:53
Alignment explanation
Indices: 2500614--2500717 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
2500604 AAGAAACAAT
2500614 CTCAAAGATTTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
1 CTCAAAGA-TTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
*
2500668 CTCAAAGA-TTTTTCACGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
1 CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCA
2500718 AAAAAATAGA
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 41 0.84
54 8 0.16
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (53 bp):
CTCAAAGATTTTTTCACAAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAGA
Found at i:2500741 original size:25 final size:25
Alignment explanation
Indices: 2500713--2500831 Score: 91
Period size: 29 Copynumber: 4.5 Consensus size: 25
2500703 CAAAACTTTG
2500713 TTTCAAAA-AAATAGACTCAAAGATT
1 TTTCAAAAGAAA-AGACTCAAAGATT
* *
2500738 TTTCAAAAGAAACGACTCAAATATT
1 TTTCAAAAGAAAAGACTCAAAGATT
*
2500763 TATTCAAAAGGAACAA-ACTCCAAGATTTT
1 T-TTCAAAA-GAA-AAGACTCAAAGA--TT
2500792 TATTCAAAAGGAACAA-ACTCAAAGATT
1 T-TTCAAAA-GAA-AAGACTCAAAGATT
*
2500819 TTTACAAGAGAAA
1 TTT-CAAAAGAAA
2500832 CTGTCTCAAG
Statistics
Matches: 80, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
25 21 0.26
26 15 0.19
27 17 0.21
28 1 0.01
29 26 0.32
ACGTcount: A:0.50, C:0.14, G:0.10, T:0.26
Consensus pattern (25 bp):
TTTCAAAAGAAAAGACTCAAAGATT
Found at i:2500797 original size:29 final size:29
Alignment explanation
Indices: 2500761--2500965 Score: 158
Period size: 29 Copynumber: 7.1 Consensus size: 29
2500751 GACTCAAATA
*
2500761 TTTATTCAAAAGGAACAAACTCCAAGATT
1 TTTATTCAAAAGGAACAAACTCAAAGATT
2500790 TTTATTCAAAAGGAACAAACTCAAAGATT
1 TTTATTCAAAAGGAACAAACTCAAAGATT
* * ***
2500819 TTTA--CAAGAGAAACTGTCTCAAGAGACAAAACTT
1 TTTATTCAAAAGGAACAAACTCAA-AG-----A-TT
** * *
2500853 TGTT-TT-AAAATAAATAGACTCAAAGA--
1 T-TTATTCAAAAGGAACAAACTCAAAGATT
* *
2500879 TTT-TTCAAAA-GAA-ACACTCAAAGATA
1 TTTATTCAAAAGGAACAAACTCAAAGATT
*
2500905 TTTATTCAAAAGGAACAAACTCCAAGATT
1 TTTATTCAAAAGGAACAAACTCAAAGATT
2500934 TTTATTCAAAAGGAACAAACTCAAAGATT
1 TTTATTCAAAAGGAACAAACTCAAAGATT
2500963 TTT
1 TTT
2500966 TCAAGAGAAA
Statistics
Matches: 143, Mismatches: 17, Indels: 32
0.74 0.09 0.17
Matches are distributed among these distances:
24 10 0.07
25 6 0.04
26 8 0.06
27 20 0.14
28 5 0.03
29 74 0.52
33 1 0.01
34 5 0.03
35 14 0.10
ACGTcount: A:0.46, C:0.15, G:0.11, T:0.28
Consensus pattern (29 bp):
TTTATTCAAAAGGAACAAACTCAAAGATT
Found at i:2500919 original size:144 final size:141
Alignment explanation
Indices: 2500667--2500993 Score: 543
Period size: 144 Copynumber: 2.3 Consensus size: 141
2500657 TTTGTTTCAG
* *
2500667 ACTCAAAGATTTTTC-A-CGAAATTGTCTCAAGAGAGACAAAACTTTGTTTCAAAAAAATAGACT
1 ACTCAAAGATTTTTCAAGAGAAACTGTCTC-A-AGAGACAAAACTTTGTTTCAAAAAAATAGACT
2500730 CAAAGATTTTTCAAAAGAAACGACTCAAATATTTATTCAAAAGGAACAAACTCCAAGATTTTTAT
64 CAAAGATTTTTCAAAAGAAACGACTCAAATATTTATTCAAAAGGAACAAACTCCAAGATTTTTAT
2500795 TCAAAAGGAACAA
129 TCAAAAGGAACAA
*
2500808 ACTCAAAGATTTTTACAAGAGAAACTGTCTCAAGAGACAAAACTTTGTTTTAAAATAAATAGACT
1 ACTCAAAGATTTTT-CAAGAGAAACTGTCTCAAGAGACAAAACTTTGTTTCAAAA-AAATAGACT
2500873 CAAAGATTTTTCAAAAGAAAC-ACTCAAAGATATTTATTCAAAAGGAACAAACTCCAAGATTTTT
64 CAAAGATTTTTCAAAAGAAACGACTC-AA-ATATTTATTCAAAAGGAACAAACTCCAAGATTTTT
2500937 ATTCAAAAGGAACAA
127 ATTCAAAAGGAACAA
2500952 ACTCAAAGATTTTTTCAAGAGAAACTGTCTCAAGAGACAAAA
1 ACTCAAAGA-TTTTTCAAGAGAAACTGTCTCAAGAGACAAAA
2500994 ATCGTTTTAA
Statistics
Matches: 176, Mismatches: 3, Indels: 11
0.93 0.02 0.06
Matches are distributed among these distances:
141 14 0.08
142 27 0.15
143 34 0.19
144 96 0.55
145 5 0.03
ACGTcount: A:0.46, C:0.15, G:0.12, T:0.27
Consensus pattern (141 bp):
ACTCAAAGATTTTTCAAGAGAAACTGTCTCAAGAGACAAAACTTTGTTTCAAAAAAATAGACTCA
AAGATTTTTCAAAAGAAACGACTCAAATATTTATTCAAAAGGAACAAACTCCAAGATTTTTATTC
AAAAGGAACAA
Found at i:2501342 original size:36 final size:36
Alignment explanation
Indices: 2501246--2501330 Score: 109
Period size: 36 Copynumber: 2.4 Consensus size: 36
2501236 TTAAGATATA
* **
2501246 GTCTCAAATGAGACAAAATTTGTTTTTAGAGAAATT
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
* *
2501282 GTCTCAAGCGAGACAAAGTTTGTTTTT-GAGAAAAC
1 GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
2501317 GATCTCAAGTGAGA
1 G-TCTCAAGTGAGA
2501331 TCAACTTTGT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
35 7 0.17
36 35 0.83
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (36 bp):
GTCTCAAGTGAGACAAAATTTGTTTTTAGAGAAAAC
Found at i:2501462 original size:105 final size:99
Alignment explanation
Indices: 2501282--2501512 Score: 268
Period size: 103 Copynumber: 2.3 Consensus size: 99
2501272 TAGAGAAATT
* *
2501282 GTCTCAAGCGAGACAAAGTTTGTTTTTGAGAAAACGATCTCAAGTGAGATCAACTTTGTTTAATG
1 GTCTCAAGCGAGACAAAATTTG-TTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATG
* * *
2501347 TGAAACAAATTCGAAATTTGGATCTCAAAGGGAAAAG
65 TGAAACAAATTCAAAATTT-G-TATCAAAGGAAAAAG
* *
2501384 GTCTCAAGCGAGACAAAATTTGTTTTGAAAGAAACAACAATCT-AAGGTGAGATTAATTTTGTTT
1 GTCTCAAGCGAGACAAAATTTGTTTTG--AG-AA-AACAATCTCAA-GTGAGATCAACTTTG-TT
* *
2501448 TAA-GTGAATCAAATTCAAAATTTGTATCAAAGGAAAAAT
60 TAATGTGAAACAAATTCAAAATTTGTATCAAAGGAAAAAG
**
2501487 GTCTCAAGCGAGACGCAATTTGTTTT
1 GTCTCAAGCGAGACAAAATTTGTTTT
2501513 AAAATTCTCA
Statistics
Matches: 112, Mismatches: 11, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
101 5 0.04
102 21 0.19
103 38 0.34
104 5 0.04
105 38 0.34
106 5 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.30
Consensus pattern (99 bp):
GTCTCAAGCGAGACAAAATTTGTTTTGAGAAAACAATCTCAAGTGAGATCAACTTTGTTTAATGT
GAAACAAATTCAAAATTTGTATCAAAGGAAAAAG
Found at i:2501978 original size:4 final size:4
Alignment explanation
Indices: 2501969--2502008 Score: 57
Period size: 4 Copynumber: 10.5 Consensus size: 4
2501959 TGTATCATGG
*
2501969 ATGT ATGT ATGT ATGT ATGT ATG- -TGT GTGT ATGT ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
2502009 ATACTTTTCT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
2 2 0.06
4 31 0.94
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.50
Consensus pattern (4 bp):
ATGT
Found at i:2503209 original size:12 final size:11
Alignment explanation
Indices: 2503181--2503216 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
2503171 TCCTCTTTTG
*
2503181 TTCTTTGCTTT
1 TTCTTTGATTT
2503192 TTCTTTGATTT
1 TTCTTTGATTT
2503203 TTGCTTTGATTT
1 TT-CTTTGATTT
2503215 TT
1 TT
2503217 TTCTTTGGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 12 0.52
12 11 0.48
ACGTcount: A:0.06, C:0.11, G:0.11, T:0.72
Consensus pattern (11 bp):
TTCTTTGATTT
Found at i:2508780 original size:25 final size:25
Alignment explanation
Indices: 2508739--2508810 Score: 119
Period size: 25 Copynumber: 2.9 Consensus size: 25
2508729 CATTAGGGGA
* *
2508739 TTAGGG-TTAAAACCCTAATTTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
2508763 TTAGGGTTTGAAACCCTAATCTGTT
1 TTAGGGTTTGAAACCCTAATCTGTT
2508788 TTAGGGTTTGAAACCCTAATCTG
1 TTAGGGTTTGAAACCCTAATCTG
2508811 ATGGGTTGGT
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
24 6 0.13
25 39 0.87
ACGTcount: A:0.26, C:0.15, G:0.19, T:0.39
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAATCTGTT
Found at i:2508920 original size:3 final size:3
Alignment explanation
Indices: 2508908--2508952 Score: 74
Period size: 3 Copynumber: 15.0 Consensus size: 3
2508898 AATATGTAAT
2508908 TAA T-A TAA TAA TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA
2508953 AATTAAAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 2 0.05
3 35 0.88
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:2511429 original size:2 final size:2
Alignment explanation
Indices: 2511424--2511449 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2511414 AAAATCATAA
2511424 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
2511450 TAAATTATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2512925 original size:2 final size:2
Alignment explanation
Indices: 2512920--2512946 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2512910 TTAATCATTA
2512920 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
2512947 ATGATATAAT
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:2516874 original size:2 final size:2
Alignment explanation
Indices: 2516867--2516898 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
2516857 TTTAATTTAT
2516867 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
2516899 GAGAGAGAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2516903 original size:2 final size:2
Alignment explanation
Indices: 2516898--2516928 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2516888 ATATATATAT
2516898 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2516929 CCTAATTTCT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2523091 original size:23 final size:20
Alignment explanation
Indices: 2523063--2523111 Score: 55
Period size: 19 Copynumber: 2.4 Consensus size: 20
2523053 GAAAAAAGAA
2523063 AAGAAAAATCATACATGTAATAT
1 AAGAAAAAT-A-A-ATGTAATAT
*
2523086 AAG-AAAATAAATGTGATAT
1 AAGAAAAATAAATGTAATAT
2523105 AAGAAAA
1 AAGAAAA
2523112 CAAAATAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
19 11 0.46
20 4 0.17
21 1 0.04
22 5 0.21
23 3 0.12
ACGTcount: A:0.61, C:0.04, G:0.12, T:0.22
Consensus pattern (20 bp):
AAGAAAAATAAATGTAATAT
Found at i:2523313 original size:16 final size:16
Alignment explanation
Indices: 2523292--2523331 Score: 71
Period size: 16 Copynumber: 2.5 Consensus size: 16
2523282 CGCAGACCAC
2523292 GCGCAGACATTGGGCT
1 GCGCAGACATTGGGCT
2523308 GCGCAGACATTGGGCT
1 GCGCAGACATTGGGCT
*
2523324 TCGCAGAC
1 GCGCAGAC
2523332 CGTTTGTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.20, C:0.28, G:0.35, T:0.17
Consensus pattern (16 bp):
GCGCAGACATTGGGCT
Found at i:2523469 original size:12 final size:12
Alignment explanation
Indices: 2523437--2523476 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
2523427 TTCAAATAAA
2523437 TTAAAA-TTA-T
1 TTAAAATTTATT
*
2523447 TT-AAATCTATT
1 TTAAAATTTATT
2523458 TTAAAATTTATT
1 TTAAAATTTATT
2523470 TTAAAAT
1 TTAAAAT
2523477 ATAGATTGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 3 0.12
10 4 0.16
11 3 0.12
12 15 0.60
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (12 bp):
TTAAAATTTATT
Found at i:2523488 original size:22 final size:22
Alignment explanation
Indices: 2523463--2523750 Score: 231
Period size: 22 Copynumber: 12.6 Consensus size: 22
2523453 CTATTTTAAA
*
2523463 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
2523485 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2523507 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* * * **
2523529 ATTTATTTTTTATTTATTTTAAAATATGG
1 ATTTA--TTTTA--AAATAT-GGAT-T-G
** *** **
2523558 AAAT-TTTTATTTTA-AAATATGG
1 ATTTATTTTAAAATATGGAT-T-G
***
2523580 ATTGATTTATTTTAAAATATGGAAAA
1 ATT---T-ATTTTAAAATATGGATTG
*
2523606 ATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTG
2523628 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
2523650 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
* ***
2523672 GTTTATTTTAAAATAT-GAAAA
1 ATTTATTTTAAAATATGGATTG
2523693 ATTATATTTTAAAATATGGATTG
1 ATT-TATTTTAAAATATGGATTG
*
2523716 ATTTATTTTAAAATATTGATTG
1 ATTTATTTTAAAATATGGATTG
2523738 ATTTATTTTAAAA
1 ATTTATTTTAAAA
2523751 AATTTATTAT
Statistics
Matches: 217, Mismatches: 34, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
21 4 0.02
22 173 0.80
23 6 0.03
24 8 0.04
25 1 0.00
26 11 0.05
27 9 0.04
28 2 0.01
29 3 0.01
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.50
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:2523511 original size:44 final size:44
Alignment explanation
Indices: 2523463--2523750 Score: 361
Period size: 44 Copynumber: 6.8 Consensus size: 44
2523453 CTATTTTAAA
*
2523463 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2523507 ATTTATTTTAAAATATGGATTGATTTA--TT----T-T---TT-
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2523540 ATTTATTTTAAAATATGGAAATT--TTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGG--ATTGATTTATTTTAAAATATGGATTG
*** *
2523584 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
2523628 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
* ***
2523672 GTTTATTTTAAAATAT-GAAAAATTATATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTGATT-TATTTTAAAATATGGATTG
*
2523716 ATTTATTTTAAAATATTGATTGATTTATTTTAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAA
2523751 AATTTATTAT
Statistics
Matches: 211, Mismatches: 16, Indels: 34
0.81 0.06 0.13
Matches are distributed among these distances:
33 22 0.10
34 2 0.01
35 5 0.02
37 1 0.00
38 1 0.00
39 1 0.00
40 1 0.00
42 3 0.01
43 7 0.03
44 163 0.77
45 5 0.02
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.50
Consensus pattern (44 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTG
Found at i:2523533 original size:66 final size:66
Alignment explanation
Indices: 2523463--2523750 Score: 361
Period size: 66 Copynumber: 4.5 Consensus size: 66
2523453 CTATTTTAAA
*
2523463 ATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
2523528 G
66 G
2523529 ATTTA--TT----T-T---TT-ATTTATTTTAAAATATGGAAATT--TTTATTTTAAAATATGGA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGG--ATTGATTTATTTTAAAATATGGA
2523581 TTG
64 TTG
*** *
2523584 ATTTATTTTAAAATATGGAAAAATTTATTTTAAAATATAGATTGATTTATTTTAAAATATGGATT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
2523649 G
66 G
* ***
2523650 ATTTATTTTAAAATATGGATTGGTTTATTTTAAAATAT-GAAAAATTATATTTTAAAATATGGAT
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATT-TATTTTAAAATATGGAT
2523714 TG
65 TG
*
2523716 ATTTATTTTAAAATATTGATTGATTTATTTTAAAA
1 ATTTATTTTAAAATATGGATTGATTTATTTTAAAA
2523751 AATTTATTAT
Statistics
Matches: 194, Mismatches: 12, Indels: 32
0.82 0.05 0.13
Matches are distributed among these distances:
55 44 0.23
56 2 0.01
57 5 0.03
59 1 0.01
60 1 0.01
61 1 0.01
62 1 0.01
64 5 0.03
65 5 0.03
66 129 0.66
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.50
Consensus pattern (66 bp):
ATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAAATATGGATT
G
Found at i:2523809 original size:31 final size:31
Alignment explanation
Indices: 2523774--2523832 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2523764 AGTTATATGG
* *
2523774 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
2523805 ATTATTTAAATTTCAGTATTACAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
2523833 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:2524795 original size:12 final size:12
Alignment explanation
Indices: 2524767--2524801 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2524757 TTTAGTTTGA
*
2524767 TTATTCTATTA-
1 TTATTTTATTAG
2524778 TTATTTTATTAG
1 TTATTTTATTAG
2524790 TTATTTTATTAG
1 TTATTTTATTAG
2524802 AACTATTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.26, C:0.03, G:0.06, T:0.66
Consensus pattern (12 bp):
TTATTTTATTAG
Found at i:2525570 original size:18 final size:19
Alignment explanation
Indices: 2525548--2525597 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
2525538 ATTCTTCTAC
*
2525548 TTTATTTATTT-TCTCATTA
1 TTTATTTATTTAT-TCAATA
2525567 -TTATTT-TTTATTCAATA
1 TTTATTTATTTATTCAATA
2525584 TTTATTTATTTATT
1 TTTATTTATTTATT
2525598 TATTTAATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.30
18 13 0.48
19 6 0.22
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTATTTATTCAATA
Found at i:2525591 original size:4 final size:4
Alignment explanation
Indices: 2525582--2525615 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
2525572 TTTTATTCAA
*
2525582 TATT TATT TATT TATT TATT TAATT CATT TATT T
1 TATT TATT TATT TATT TATT T-ATT TATT TATT T
2525616 TCATTAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:2525599 original size:12 final size:13
Alignment explanation
Indices: 2525582--2525615 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
2525572 TTTTATTCAA
2525582 TATTTATTT-ATT
1 TATTTATTTAATT
2525594 TATTTATTTAATT
1 TATTTATTTAATT
*
2525607 CATTTATTT
1 TATTTATTT
2525616 TCATTAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (13 bp):
TATTTATTTAATT
Found at i:2525766 original size:22 final size:22
Alignment explanation
Indices: 2525735--2525780 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
2525725 TTATTTATTT
2525735 AATATGGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
*
2525757 AATATTGATTGATTTATTTTAA
1 AATATGGATTGATTTATTTTAA
2525779 AA
1 AA
2525781 AATTTATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
AATATGGATTGATTTATTTTAA
Found at i:2525839 original size:31 final size:31
Alignment explanation
Indices: 2525804--2525862 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
2525794 AGTTATATGG
* *
2525804 ATTATTTAAATTTCATTATTATAAAACTAAA
1 ATTATTTAAATTTCAGTATTACAAAACTAAA
2525835 ATTATTTAAATTTCAGTATTACAAAACT
1 ATTATTTAAATTTCAGTATTACAAAACT
2525863 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (31 bp):
ATTATTTAAATTTCAGTATTACAAAACTAAA
Found at i:2526997 original size:13 final size:13
Alignment explanation
Indices: 2526981--2527011 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
2526971 TTCATATCCA
*
2526981 TCTTTCTTTATTT
1 TCTTTCATTATTT
2526994 TCTTTCATTATTT
1 TCTTTCATTATTT
2527007 TCTTT
1 TCTTT
2527012 TCACAATGCT
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:0.10, C:0.16, G:0.00, T:0.74
Consensus pattern (13 bp):
TCTTTCATTATTT
Found at i:2527625 original size:18 final size:19
Alignment explanation
Indices: 2527603--2527652 Score: 61
Period size: 18 Copynumber: 2.7 Consensus size: 19
2527593 ATTCTTCTAC
*
2527603 TTTATTTATTT-TCTCATTA
1 TTTATTTATTTAT-TCAATA
2527622 -TTATTT-TTTATTCAATA
1 TTTATTTATTTATTCAATA
2527639 TTTATTTATTTATT
1 TTTATTTATTTATT
2527653 TATTTCATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 8 0.30
18 13 0.48
19 6 0.22
ACGTcount: A:0.24, C:0.06, G:0.00, T:0.70
Consensus pattern (19 bp):
TTTATTTATTTATTCAATA
Found at i:2527646 original size:4 final size:4
Alignment explanation
Indices: 2527637--2527666 Score: 51
Period size: 4 Copynumber: 7.2 Consensus size: 4
2527627 TTTTATTCAA
2527637 TATT TATT TATT TATT TATT TCATT TATT T
1 TATT TATT TATT TATT TATT T-ATT TATT T
2527667 TCATTAATTT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 21 0.84
5 4 0.16
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (4 bp):
TATT
Found at i:2528491 original size:161 final size:160
Alignment explanation
Indices: 2528154--2528503 Score: 350
Period size: 161 Copynumber: 2.2 Consensus size: 160
2528144 TTAGAAGAAA
* * * * * * *
2528154 AAAAACAGACTCAAAAT-AAGGACGAATTGAAGAAATGAGAAAAATACAAAAAATTAAGGGATTA
1 AAAAACACACTTAAAATAAAGAATGAATTGAAGAAATAAGAAAAATAAAAAAAAATAAGGGATTA
* * *
2528218 AATTAAAAAATAGAAAATGTGTTAACGAAAAGAGTAATTGAAAACACATATGTATTATATATATG
66 AATTAAAAAATAAAAAATGTGTTAACAAAAAGAGAAATTGAAAACACATATGTA-TATATATATG
* * *
2528283 ATGTTTTAGGAGCATACAGTTCAAAGTTGGT
130 ATGTTCTAGGAACATACAGTTCAAAGTTGAT
* * * *
2528314 AAAAACACACTTAAAATAAATAATGAATTGAAGAAATAAGGAAATTATAAAAAAAAATGATGGAT
1 AAAAACACACTTAAAATAAAGAATGAATTGAAGAAATAA-GAAA-AATAAAAAAAAATAAGGGAT
* * ** *
2528379 TAAATTGAAAAAATAAAAAAATTTGTTATCAAAAAGAGAAATTGAAAGTACATATG-A-AT-TCT
64 TAAATT-AAAAAAT-AAAAAATGTGTTAACAAAAAGAGAAATTGAAAACACATATGTATATATAT
* *
2528441 ATGATGGTTCT-GGAACATGCAGTTCAAATTTGAT
127 ATGAT-GTTCTAGGAACATACAGTTCAAAGTTGAT
*** * *
2528475 AAAAATTGATTTAAAATAAAGGATGAATT
1 AAAAACACACTTAAAATAAAGAATGAATT
2528504 AAATGAATAA
Statistics
Matches: 154, Mismatches: 30, Indels: 11
0.79 0.15 0.06
Matches are distributed among these distances:
160 15 0.10
161 66 0.43
162 10 0.06
163 21 0.14
164 8 0.05
165 34 0.22
ACGTcount: A:0.52, C:0.06, G:0.16, T:0.27
Consensus pattern (160 bp):
AAAAACACACTTAAAATAAAGAATGAATTGAAGAAATAAGAAAAATAAAAAAAAATAAGGGATTA
AATTAAAAAATAAAAAATGTGTTAACAAAAAGAGAAATTGAAAACACATATGTATATATATATGA
TGTTCTAGGAACATACAGTTCAAAGTTGAT
Found at i:2529743 original size:25 final size:26
Alignment explanation
Indices: 2529689--2529747 Score: 68
Period size: 25 Copynumber: 2.2 Consensus size: 26
2529679 TAAGGATGGG
*
2529689 TATAAATTTTATGTAGGAGTAACGAACT
1 TATAAATTTTA--TAGGAGTAAAGAACT
2529717 TATAAATTTTA-AGGAG-AAAGAAGCT
1 TATAAATTTTATAGGAGTAAAGAA-CT
2529742 TATAAA
1 TATAAA
2529748 AAATTTAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 5 0.17
25 13 0.45
28 11 0.38
ACGTcount: A:0.46, C:0.05, G:0.17, T:0.32
Consensus pattern (26 bp):
TATAAATTTTATAGGAGTAAAGAACT
Found at i:2532890 original size:19 final size:19
Alignment explanation
Indices: 2532866--2532902 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
2532856 ATGACCAATA
*
2532866 AAATCGCAATGCGATCTCT
1 AAATCGCAACGCGATCTCT
2532885 AAATCGCAACGCGATCTC
1 AAATCGCAACGCGATCTC
2532903 CAGTATCGCA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.32, C:0.30, G:0.16, T:0.22
Consensus pattern (19 bp):
AAATCGCAACGCGATCTCT
Found at i:2533059 original size:21 final size:20
Alignment explanation
Indices: 2533035--2533101 Score: 73
Period size: 21 Copynumber: 3.3 Consensus size: 20
2533025 ATTATCGCAA
2533035 TGCGATAGTCGAAGTTCGCGT
1 TGCGATAGTCGAAGTTC-CGT
** * *
2533056 TGCGATTTTCCAAATT-CGT
1 TGCGATAGTCGAAGTTCCGT
2533075 TGCGATAGTCGAAGTTCACGT
1 TGCGATAGTCGAAGTTC-CGT
2533096 TGCGAT
1 TGCGAT
2533102 TTTCCTATTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 15 0.42
21 21 0.58
ACGTcount: A:0.21, C:0.19, G:0.27, T:0.33
Consensus pattern (20 bp):
TGCGATAGTCGAAGTTCCGT
Found at i:2533242 original size:21 final size:21
Alignment explanation
Indices: 2533218--2533257 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
2533208 ACATATTCGC
2533218 GTTGCGATTTTGTATTATCAT
1 GTTGCGATTTTGTATTATCAT
2533239 GTTGCGATTTTGTATTATC
1 GTTGCGATTTTGTATTATC
2533258 GCATTACGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.17, C:0.10, G:0.20, T:0.53
Consensus pattern (21 bp):
GTTGCGATTTTGTATTATCAT
Found at i:2533267 original size:21 final size:21
Alignment explanation
Indices: 2533222--2533267 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
2533212 ATTCGCGTTG
** *
2533222 CGATTTTGTATTATCATGTTG
1 CGATTTTGTATTATCACATTA
*
2533243 CGATTTTGTATTATCGCATTA
1 CGATTTTGTATTATCACATTA
2533264 CGAT
1 CGAT
2533268 AGTCAGAATC
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.22, C:0.13, G:0.17, T:0.48
Consensus pattern (21 bp):
CGATTTTGTATTATCACATTA
Found at i:2533308 original size:19 final size:20
Alignment explanation
Indices: 2533284--2533347 Score: 96
Period size: 19 Copynumber: 3.3 Consensus size: 20
2533274 AATCGCGTTG
2533284 CGATTTACATATTCGCATT-
1 CGATTTACATATTCGCATTA
*
2533303 CGATTTACATATTCGCGTTA
1 CGATTTACATATTCGCATTA
*
2533323 CGA-TTACATATTCGCATTG
1 CGATTTACATATTCGCATTA
2533342 CGATTT
1 CGATTT
2533348 TGAAAAAATC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
19 35 0.88
20 5 0.12
ACGTcount: A:0.25, C:0.20, G:0.14, T:0.41
Consensus pattern (20 bp):
CGATTTACATATTCGCATTA
Found at i:2534829 original size:26 final size:28
Alignment explanation
Indices: 2534799--2534860 Score: 74
Period size: 31 Copynumber: 2.2 Consensus size: 28
2534789 AAAAATTTTA
2534799 AGCTC-GC-GAGTTTTCGAGTCGAGTCG
1 AGCTCTGCAGAGTTTTCGAGTCGAGTCG
*
2534825 AGCTCCATTTCAGAGTTTTCGAGTCGAGTCG
1 AGCT-C--TGCAGAGTTTTCGAGTCGAGTCG
2534856 AGCTC
1 AGCTC
2534861 AACAATACTC
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
26 4 0.13
27 1 0.03
30 2 0.07
31 23 0.77
ACGTcount: A:0.18, C:0.24, G:0.29, T:0.29
Consensus pattern (28 bp):
AGCTCTGCAGAGTTTTCGAGTCGAGTCG
Found at i:2535395 original size:31 final size:29
Alignment explanation
Indices: 2535321--2535405 Score: 91
Period size: 31 Copynumber: 2.8 Consensus size: 29
2535311 TTCGATAATA
* *
2535321 TAATAATAATTTTATAGTATTTAGATAAATT
1 TAATAATAATTTTA-AATTTTTA-ATAAATT
*
2535352 TATTAATAATTTTATAATCTTTTAATAAATT
1 TAATAATAATTTTA-AAT-TTTTAATAAATT
2535383 TAATAAGT-ATTTTAAATTTTTAA
1 TAATAA-TAATTTTAAATTTTTAA
2535406 ATTTTATTGA
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
29 6 0.12
30 3 0.06
31 34 0.71
32 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (29 bp):
TAATAATAATTTTAAATTTTTAATAAATT
Found at i:2541441 original size:24 final size:24
Alignment explanation
Indices: 2541396--2541447 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
2541386 AAGCTACACG
*
2541396 TTTAGTAACTAATTATTATTTTAT
1 TTTAGTAACTAACTATTATTTTAT
*
2541420 TTTAGTCACTTAACTATT-TTTTAT
1 TTTAGTAAC-TAACTATTATTTTAT
2541444 TTTA
1 TTTA
2541448 AAATCATATA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
24 18 0.72
25 7 0.28
ACGTcount: A:0.29, C:0.08, G:0.04, T:0.60
Consensus pattern (24 bp):
TTTAGTAACTAACTATTATTTTAT
Done.