Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 102 of 226
Found at i:35084457 original size:18 final size:18
Alignment explanation
Indices: 35084417--35084458 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
35084407 TATAAAACTA
35084417 AAAGAAGAATGCAAAGAT
1 AAAGAAGAATGCAAAGAT
* *
35084435 TAAGAGAGAATG-AAAGGT
1 AAAGA-AGAATGCAAAGAT
35084453 AAAGAA
1 AAAGAA
35084459 ATGAAATGAT
Statistics
Matches: 20, Mismatches: 3, Indels: 3
0.77 0.12 0.12
Matches are distributed among these distances:
17 1 0.05
18 13 0.65
19 6 0.30
ACGTcount: A:0.60, C:0.02, G:0.26, T:0.12
Consensus pattern (18 bp):
AAAGAAGAATGCAAAGAT
Found at i:35084601 original size:19 final size:19
Alignment explanation
Indices: 35084577--35084616 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
35084567 GGTACCTTAA
35084577 AAATGATTTAGGGTTTATG
1 AAATGATTTAGGGTTTATG
35084596 AAATGATTTAGGGTTTATG
1 AAATGATTTAGGGTTTATG
35084615 AA
1 AA
35084617 CATTCATTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (19 bp):
AAATGATTTAGGGTTTATG
Found at i:35087151 original size:50 final size:50
Alignment explanation
Indices: 35087027--35087323 Score: 310
Period size: 50 Copynumber: 5.8 Consensus size: 50
35087017 GATAAGAACA
* ** * *
35087027 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTTCATGTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * ** *
35087076 TGCCAATGCCATATCCCAGATATGGTCTTTCATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
35087126 TGCCCATGCCATGCCCCAGACATGGTCTTACAGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
35087176 TGCCAACGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCGTCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
35087226 TGCCAACGCCATGTCCCAGACATGGCCTTACATGGGACCTCTCATGATCTCAAGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC--GG
* * * *
35087281 ACGCCAATGCCATGTCCCAGACATGGTCCTACATGGGATCTCT
1 -TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
35087324 TACCCTAAAT
Statistics
Matches: 209, Mismatches: 31, Indels: 9
0.84 0.12 0.04
Matches are distributed among these distances:
48 1 0.00
49 39 0.19
50 126 0.60
53 4 0.02
55 2 0.01
56 37 0.18
ACGTcount: A:0.22, C:0.30, G:0.23, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:35090003 original size:53 final size:54
Alignment explanation
Indices: 35089858--35090006 Score: 160
Period size: 54 Copynumber: 2.8 Consensus size: 54
35089848 CATAGTAAGA
** * ** *
35089858 AGACCATATAGTGTAAGACCTAGCCTGGGACTATGGGATCATATGGGGATACGG
1 AGACCATATAGTGTAAGACCTAGTTTGGGACTATGGCATCATATGGCAAGACGG
** * *
35089912 AGACCATATAGTGTAAGGTCTAGTAGTT-TG-CTAAGGCATCATATGGCAAGA-GG
1 AGACCATATAGTGTAAGACCTAGT--TTGGGACTATGGCATCATATGGCAAGACGG
*
35089965 AGACCACATAGTGTAAGACCTAGTTTGGGACTATGGCATCAT
1 AGACCATATAGTGTAAGACCTAGTTTGGGACTATGGCATCAT
35090007 GTAGAGAAAG
Statistics
Matches: 76, Mismatches: 15, Indels: 9
0.76 0.15 0.09
Matches are distributed among these distances:
51 2 0.03
52 1 0.01
53 34 0.45
54 37 0.49
55 1 0.01
56 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.28, T:0.25
Consensus pattern (54 bp):
AGACCATATAGTGTAAGACCTAGTTTGGGACTATGGCATCATATGGCAAGACGG
Found at i:35091150 original size:19 final size:19
Alignment explanation
Indices: 35091126--35091167 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
35091116 TTCTAAATGG
35091126 AATACTTGAGGTAATTCAA
1 AATACTTGAGGTAATTCAA
*
35091145 AATACTTGAGGTAATTCAG
1 AATACTTGAGGTAATTCAA
35091164 AATA
1 AATA
35091168 AGAGTTAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.31
Consensus pattern (19 bp):
AATACTTGAGGTAATTCAA
Found at i:35104019 original size:16 final size:17
Alignment explanation
Indices: 35104000--35104032 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
35103990 ATTTAGAGGT
35104000 TAATTAATT-TAATTTA
1 TAATTAATTCTAATTTA
*
35104016 TAATTATTTCTAATTTA
1 TAATTAATTCTAATTTA
35104033 GGCTCGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.39, C:0.03, G:0.00, T:0.58
Consensus pattern (17 bp):
TAATTAATTCTAATTTA
Found at i:35113953 original size:19 final size:19
Alignment explanation
Indices: 35113925--35113969 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
35113915 GCAGTGACAA
*
35113925 CCACAGCTATAAAGATTGT
1 CCACAACTATAAAGATTGT
35113944 CCACAACTATAAAGATTGT
1 CCACAACTATAAAGATTGT
35113963 CCACAAC
1 CCACAAC
35113970 ATGCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.40, C:0.27, G:0.11, T:0.22
Consensus pattern (19 bp):
CCACAACTATAAAGATTGT
Found at i:35122562 original size:73 final size:73
Alignment explanation
Indices: 35122438--35122655 Score: 373
Period size: 73 Copynumber: 3.0 Consensus size: 73
35122428 AACTAAGTCG
* * * * *
35122438 AAATAACGTATTCACGTTTCATTAAATCATAAAACTATCATATATTTTTACATGCAATTACACTC
1 AAATAACATATTCACGTTTCATTAAATCATACAACTAGCATATACTCTTACATGCAATTACACTC
35122503 AACTCGCA
66 AACTCGCA
35122511 AAATAACATATTCACGTTTCATTAAATCATACAACTAGCATATACTCTTACATGCAATTACACTC
1 AAATAACATATTCACGTTTCATTAAATCATACAACTAGCATATACTCTTACATGCAATTACACTC
*
35122576 AACTCACA
66 AACTCGCA
*
35122584 AAATAACATATTCATGTTTCATTAAATCATACAACTAGCATATACTCTTACATGCAATTACACTC
1 AAATAACATATTCACGTTTCATTAAATCATACAACTAGCATATACTCTTACATGCAATTACACTC
35122649 AACTCGC
66 AACTCGC
35122656 TTATATATAT
Statistics
Matches: 137, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
73 137 1.00
ACGTcount: A:0.40, C:0.23, G:0.05, T:0.32
Consensus pattern (73 bp):
AAATAACATATTCACGTTTCATTAAATCATACAACTAGCATATACTCTTACATGCAATTACACTC
AACTCGCA
Found at i:35138760 original size:20 final size:20
Alignment explanation
Indices: 35138732--35138770 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
35138722 GTTTAAGTGA
* *
35138732 AATATAATGTTATTTAATTT
1 AATAAAATGTTATTAAATTT
35138752 AATAAAATGTTATTAAATT
1 AATAAAATGTTATTAAATT
35138771 AATTAATTTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (20 bp):
AATAAAATGTTATTAAATTT
Found at i:35140540 original size:7 final size:7
Alignment explanation
Indices: 35140527--35140581 Score: 83
Period size: 7 Copynumber: 7.6 Consensus size: 7
35140517 TGGGATTTTC
35140527 TTTTGGA
1 TTTTGGA
*
35140534 CTTTGGA
1 TTTTGGA
35140541 TTATTTGGA
1 -T-TTTGGA
35140550 TTTTGGA
1 TTTTGGA
35140557 TTTTGGA
1 TTTTGGA
35140564 TTTTGGA
1 TTTTGGA
35140571 TTTTGGA
1 TTTTGGA
35140578 TTTT
1 TTTT
35140582 TCTGCATGAT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
7 37 0.84
8 1 0.02
9 6 0.14
ACGTcount: A:0.15, C:0.02, G:0.25, T:0.58
Consensus pattern (7 bp):
TTTTGGA
Found at i:35141702 original size:129 final size:129
Alignment explanation
Indices: 35141465--35141703 Score: 311
Period size: 129 Copynumber: 1.9 Consensus size: 129
35141455 AGAAAGGCTT
* * * *
35141465 CTTATGCTTCTGCAATAGGAAGCCTCATGTGTGCTATGTTATGCACACGCCCAGATATATGTTTC
1 CTTATGCTTCTACAATAGAAAGCCTCATGTATGCTATGTTATGCACACACCCAGATATATGTTTC
* * * *
35141530 GTAGTAGGGTTGGTGAGTCGATATCAAGCAAATCCAAGACCAAGAGAAAACATGAGAATGTTTC
66 ATAGTAGGGTTGGTGAATCAATATCAAACAAATCCAAGACCAAGAGAAAACATGAGAATGTTTC
* * *
35141594 CTTATGCTTCTACAGTAGAAAGTCC-CATGTATG-TCATGTTATGCACACATCCAGATATTTGTT
1 CTTATGCTTCTACAATAGAAAG-CCTCATGTATGCT-ATGTTATGCACACACCCAGATATATGTT
* * * *
35141657 TCATAGTGGGGTTGGTGAATCAATATCAAACGAATCCAGGGCCAAGA
64 TCATAGTAGGGTTGGTGAATCAATATCAAACAAATCCAAGACCAAGA
35141704 CATTGGTAAG
Statistics
Matches: 93, Mismatches: 15, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
128 1 0.01
129 90 0.97
130 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (129 bp):
CTTATGCTTCTACAATAGAAAGCCTCATGTATGCTATGTTATGCACACACCCAGATATATGTTTC
ATAGTAGGGTTGGTGAATCAATATCAAACAAATCCAAGACCAAGAGAAAACATGAGAATGTTTC
Found at i:35156783 original size:6 final size:6
Alignment explanation
Indices: 35156772--35156832 Score: 104
Period size: 6 Copynumber: 10.2 Consensus size: 6
35156762 TTGTTTTATG
* *
35156772 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTC TTATTC TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT TTATTT
35156820 TTATTT TTATTT T
1 TTATTT TTATTT T
35156833 CTTTTTCCCA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 53 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:35160123 original size:20 final size:20
Alignment explanation
Indices: 35160072--35160123 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
35160062 TTTATGTTGA
*
35160072 TAAATGGAATGCAAAGTAAG
1 TAAATGGAATGGAAAGTAAG
35160092 TAAATGGAATGGAAAGTAAG
1 TAAATGGAATGGAAAGTAAG
*
35160112 TAGATGGAATGG
1 TAAATGGAATGG
35160124 TTCATAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.46, C:0.02, G:0.31, T:0.21
Consensus pattern (20 bp):
TAAATGGAATGGAAAGTAAG
Found at i:35175869 original size:20 final size:20
Alignment explanation
Indices: 35175844--35175882 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35175834 AACATTCAAA
35175844 ATACCATAATCACAA-CCAAT
1 ATACCATAA-CACAAGCCAAT
35175864 ATACCATAACACAAGCCAA
1 ATACCATAACACAAGCCAA
35175883 ACCATATGGC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.51, C:0.31, G:0.03, T:0.15
Consensus pattern (20 bp):
ATACCATAACACAAGCCAAT
Found at i:35203886 original size:51 final size:51
Alignment explanation
Indices: 35203770--35204005 Score: 212
Period size: 51 Copynumber: 4.7 Consensus size: 51
35203760 CAATACACGC
* * * * * * * *
35203770 AGTAGCCTTCATATAGTGCTACACACGTGATCA--AACTTTTCGGTTCACGT
1 AGTAGCCTACACATAGTACTACACACGTGACCATTAA-TATCCGGTACACAT
*
35203820 AGTAGCCTACACATAGTACTACACACGTGACCATTAATATCCGATACACAT
1 AGTAGCCTACACATAGTACTACACACGTGACCATTAATATCCGGTACACAT
* * * *
35203871 AGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGGTACGCAT
1 AGTAGCCTACACATAGTACTACACACGTGA-CCATTA-ATATCCGGTACACAT
* * * * * * * * *
35203922 AGTAGCTTGCACACAGTACTACAAATGCGACCTTTCAT-TCCGGTACACGT
1 AGTAGCCTACACATAGTACTACACACGTGACCATTAATATCCGGTACACAT
35203972 AGTAGCCTACACATAGTACTACACACGTGACCAT
1 AGTAGCCTACACATAGTACTACACACGTGACCAT
35204006 CACTTTCACT
Statistics
Matches: 148, Mismatches: 32, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
50 68 0.46
51 76 0.51
52 4 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (51 bp):
AGTAGCCTACACATAGTACTACACACGTGACCATTAATATCCGGTACACAT
Found at i:35203969 original size:101 final size:101
Alignment explanation
Indices: 35203770--35204001 Score: 268
Period size: 101 Copynumber: 2.3 Consensus size: 101
35203760 CAATACACGC
* * * * * * * *
35203770 AGTAGCCTTCATATAGTGCTACACACGTGATCAAACTTTTCGGTTCACGTAGTAGCCTACACATA
1 AGTAGCCTACACATAGTACTACACACGTGATCAAACTATCCGGTACACATAGTAGCCTACACACA
* *
35203835 GTACTACACACGTGACCATTAATATCCGATACACAT
66 GTACTACAAACGCGACCATTAATATCCGATACACAT
* * * * *
35203871 AGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGCTTGCACAC
1 AGTAGCCTACACATAGTACTACACACGTGATC-AAACTATCCGGTACACATAGTAGCCTACACAC
* * * * *
35203936 AGTACTACAAATGCGACCTTTCAT-TCCGGTACACGT
65 AGTACTACAAACGCGACCATTAATATCCGATACACAT
35203972 AGTAGCCTACACATAGTACTACACACGTGA
1 AGTAGCCTACACATAGTACTACACACGTGA
35204002 CCATCACTTT
Statistics
Matches: 110, Mismatches: 20, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 68 0.62
102 42 0.38
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (101 bp):
AGTAGCCTACACATAGTACTACACACGTGATCAAACTATCCGGTACACATAGTAGCCTACACACA
GTACTACAAACGCGACCATTAATATCCGATACACAT
Found at i:35204024 original size:101 final size:99
Alignment explanation
Indices: 35203762--35204039 Score: 254
Period size: 101 Copynumber: 2.7 Consensus size: 99
35203752 TTATCATTCA
* * * * * * *
35203762 ATACACGCAGTAGCCTTCATATAGTGCTACACACGTGATCAAACTTTTCGGTTCACGTAGTAGCC
1 ATACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCAAC-TTTCCGTTCACATAGTAGCC
* * *
35203827 TACACATAGTACTACACACGTGACCATTAATATCCG
64 TACACACAGTACTACAAACGCGACCATTAATATCCG
* * * * * *
35203863 ATACACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTACGCATAGTAGC
1 ATACACGTAGTAGCCTACACATAGTACTACACACGTGA-CCAA-CTTTCC-GTTCACATAGTAGC
* * * * *
35203928 TTGCACACAGTACTACAAATGCGACCTTTCAT-TCCG
63 CTACACACAGTACTACAAACGCGACCATTAATATCCG
* *
35203964 GTACACGTAGTAGCCTACACATAGTACTACACACGTGACCATCACTTTCACTTTCACATAGT-GA
1 ATACACGTAGTAGCCTACACATAGTACTACACACGTGACCA--ACTTTC-CGTTCACATAGTAG-
35204028 CCTACACACAGT
62 CCTACACACAGT
35204040 CCATGTCACA
Statistics
Matches: 142, Mismatches: 29, Indels: 12
0.78 0.16 0.07
Matches are distributed among these distances:
100 3 0.02
101 101 0.71
102 38 0.27
ACGTcount: A:0.31, C:0.28, G:0.16, T:0.25
Consensus pattern (99 bp):
ATACACGTAGTAGCCTACACATAGTACTACACACGTGACCAACTTTCCGTTCACATAGTAGCCTA
CACACAGTACTACAAACGCGACCATTAATATCCG
Found at i:35204447 original size:13 final size:14
Alignment explanation
Indices: 35204416--35204446 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
35204406 GTTTTCGCTG
*
35204416 AAAATCGTTTAGCA
1 AAAATCGTTTAACA
35204430 AAAATCGTTTAACA
1 AAAATCGTTTAACA
35204444 AAA
1 AAA
35204447 TTCTAAGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (14 bp):
AAAATCGTTTAACA
Found at i:35205920 original size:22 final size:19
Alignment explanation
Indices: 35205895--35205936 Score: 57
Period size: 22 Copynumber: 2.1 Consensus size: 19
35205885 TGATAATAAT
35205895 TAATATATAATTATATCTATTA
1 TAATATAT-ATTA-AT-TATTA
35205917 TAATATATATTAATTATTA
1 TAATATATATTAATTATTA
35205936 T
1 T
35205937 CAACTCTGCA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 6 0.30
20 2 0.10
21 4 0.20
22 8 0.40
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATATATTAATTATTA
Found at i:35207477 original size:3 final size:3
Alignment explanation
Indices: 35207469--35207515 Score: 85
Period size: 3 Copynumber: 15.7 Consensus size: 3
35207459 GGATCCCGAG
*
35207469 GAA GAA GAA GAA GAA GAA GAA AAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
35207516 TCTCATAGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:35215677 original size:20 final size:20
Alignment explanation
Indices: 35215652--35215729 Score: 120
Period size: 20 Copynumber: 3.9 Consensus size: 20
35215642 GATGTGTAAT
*
35215652 AGAGGCACCGAAGTGCAATC
1 AGAGGCACCGAAGTGCAAAC
* *
35215672 AGAGGCACTGAAGAGCAAAC
1 AGAGGCACCGAAGTGCAAAC
*
35215692 AGAGGCACCAAAGTGCAAAC
1 AGAGGCACCGAAGTGCAAAC
35215712 AGAGGCACCGAAGTGCAA
1 AGAGGCACCGAAGTGCAA
35215730 TCCCGTACAA
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.41, C:0.23, G:0.29, T:0.06
Consensus pattern (20 bp):
AGAGGCACCGAAGTGCAAAC
Found at i:35226925 original size:27 final size:27
Alignment explanation
Indices: 35226878--35227174 Score: 234
Period size: 27 Copynumber: 11.1 Consensus size: 27
35226868 TCGATATCTG
* * *
35226878 GACTGAAACA-CCCTCGAAGGGTAAAGT
1 GACTGAAATACCCCT-GTAGGGTAAAAT
* *
35226905 GACTGAAATGCCCCTATAGGGTAAAAT
1 GACTGAAATACCCCTGTAGGGTAAAAT
* *
35226932 GA-TCGAAATACCCCCGTAGGGTAGAAT
1 GACT-GAAATACCCCTGTAGGGTAAAAT
* ** *
35226959 -ACTGAAATATCCCAATAGTGTAAAA-
1 GACTGAAATACCCCTGTAGGGTAAAAT
* *
35226984 GAC-CATAATACCCCTGTAGGTTAAAAT
1 GACTGA-AATACCCCTGTAGGGTAAAAT
* * *
35227011 GACCGTAATGCCCCTGTAGGGTAAAAT
1 GACTGAAATACCCCTGTAGGGTAAAAT
* **
35227038 GACTGTAATGTCCCTGTAGGGTAAAAT
1 GACTGAAATACCCCTGTAGGGTAAAAT
*
35227065 GAC-CATAATA-CCCTGTAGGGTAAAAT
1 GACTGA-AATACCCCTGTAGGGTAAAAT
* *
35227091 GAC-CATAATACCCCTGTTGGGTAAAAT
1 GACTGA-AATACCCCTGTAGGGTAAAAT
*
35227118 GAC-CATAATACCCCTGTAGGGTAAAAT
1 GACTGA-AATACCCCTGTAGGGTAAAAT
* * * *
35227145 GACCGTAATACCCTTGTAAGGTAAAAT
1 GACTGAAATACCCCTGTAGGGTAAAAT
35227172 GAC
1 GAC
35227175 CGTAATGCCT
Statistics
Matches: 225, Mismatches: 35, Indels: 20
0.80 0.12 0.07
Matches are distributed among these distances:
25 1 0.00
26 62 0.28
27 158 0.70
28 4 0.02
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.23
Consensus pattern (27 bp):
GACTGAAATACCCCTGTAGGGTAAAAT
Found at i:35227054 original size:54 final size:53
Alignment explanation
Indices: 35226911--35227183 Score: 266
Period size: 53 Copynumber: 5.1 Consensus size: 53
35226901 AAGTGACTGA
* * * * * *
35226911 AATGCCCCTATAGGGTAAAATGATCGAAATACCCCCGTAGGGTAGAAT-ACTGA-
1 AATGCCCCTGTAGGGTAAAATGACCGTAATA-CCCTGTAGGGTAAAATGAC-CAT
** ** * * * *
35226964 AATATCCCAATAGTGTAAAA-GACCATAATACCCCTGTAGGTTAAAATGACCGT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATA-CCCTGTAGGGTAAAATGACCAT
* *
35227017 AATGCCCCTGTAGGGTAAAATGACTGTAATGTCCCTGTAGGGTAAAATGACCAT
1 AATGCCCCTGTAGGGTAAAATGACCGTAAT-ACCCTGTAGGGTAAAATGACCAT
* * *
35227071 AAT-ACCCTGTAGGGTAAAATGACCATAATACCCCTGTTGGGTAAAATGACCAT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATA-CCCTGTAGGGTAAAATGACCAT
* * *
35227124 AATACCCCTGTAGGGTAAAATGACCGTAATACCCTTGTAAGGTAAAATGACCGT
1 AATGCCCCTGTAGGGTAAAATGACCGTAATACCC-TGTAGGGTAAAATGACCAT
35227178 AATGCC
1 AATGCC
35227184 TTGGTGGGTA
Statistics
Matches: 180, Mismatches: 33, Indels: 13
0.80 0.15 0.06
Matches are distributed among these distances:
52 21 0.12
53 83 0.46
54 76 0.42
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (53 bp):
AATGCCCCTGTAGGGTAAAATGACCGTAATACCCTGTAGGGTAAAATGACCAT
Found at i:35227089 original size:80 final size:80
Alignment explanation
Indices: 35226916--35227180 Score: 327
Period size: 80 Copynumber: 3.3 Consensus size: 80
35226906 ACTGAAATGC
* * * * * * ** *
35226916 CCCTATAGGGTAAAATGATCGAAATACCCCCGTAGGGTAGAAT-ACTGAAATATCCCAATAGTGT
1 CCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATATCCCTGTAGGGT
35226980 AAAA-GACCATAATA
66 AAAATGACCATAATA
* * *
35226994 CCCCTGTAGGTTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACTGTAATGTCCCTGTAGGG
1 -CCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATATCCCTGTAGGG
35227059 TAAAATGACCATAATA
65 TAAAATGACCATAATA
* * ** *
35227075 CCCTGTAGGGTAAAATGACCATAATACCCCTGTTGGGTAAAATGACCATAATACCCCTGTAGGGT
1 CCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATATCCCTGTAGGGT
*
35227140 AAAATGACCGTAATA
66 AAAATGACCATAATA
*
35227155 CCCTTGTAAGGTAAAATGACCGTAAT
1 CCC-TGTAGGGTAAAATGACCGTAAT
35227181 GCCTTGGTGG
Statistics
Matches: 160, Mismatches: 23, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
79 36 0.22
80 94 0.59
81 30 0.19
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (80 bp):
CCCTGTAGGGTAAAATGACCGTAATACCCCTGTAGGGTAAAATGACTGTAATATCCCTGTAGGGT
AAAATGACCATAATA
Found at i:35227175 original size:27 final size:27
Alignment explanation
Indices: 35226915--35227180 Score: 290
Period size: 27 Copynumber: 10.0 Consensus size: 27
35226905 GACTGAAATG
* *
35226915 CCCCTATAGGGTAAAATGATCGA-AATA
1 CCCCTGTAGGGTAAAATGA-CCATAATA
* * *
35226942 CCCCCGTAGGGTAGAAT-ACTGA-AATA
1 CCCCTGTAGGGTAAAATGAC-CATAATA
* ** *
35226968 TCCCAATAGTGTAAAA-GACCATAATA
1 CCCCTGTAGGGTAAAATGACCATAATA
* * *
35226994 CCCCTGTAGGTTAAAATGACCGTAATG
1 CCCCTGTAGGGTAAAATGACCATAATA
** *
35227021 CCCCTGTAGGGTAAAATGACTGTAATG
1 CCCCTGTAGGGTAAAATGACCATAATA
*
35227048 TCCCTGTAGGGTAAAATGACCATAATA
1 CCCCTGTAGGGTAAAATGACCATAATA
35227075 -CCCTGTAGGGTAAAATGACCATAATA
1 CCCCTGTAGGGTAAAATGACCATAATA
*
35227101 CCCCTGTTGGGTAAAATGACCATAATA
1 CCCCTGTAGGGTAAAATGACCATAATA
*
35227128 CCCCTGTAGGGTAAAATGACCGTAATA
1 CCCCTGTAGGGTAAAATGACCATAATA
* * *
35227155 CCCTTGTAAGGTAAAATGACCGTAAT
1 CCCCTGTAGGGTAAAATGACCATAAT
35227181 GCCTTGGTGG
Statistics
Matches: 207, Mismatches: 27, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
25 2 0.01
26 61 0.29
27 144 0.70
ACGTcount: A:0.36, C:0.20, G:0.20, T:0.24
Consensus pattern (27 bp):
CCCCTGTAGGGTAAAATGACCATAATA
Found at i:35227195 original size:107 final size:107
Alignment explanation
Indices: 35226978--35227180 Score: 311
Period size: 107 Copynumber: 1.9 Consensus size: 107
35226968 TCCCAATAGT
* * * *
35226978 GTAAAA-GACCATAATACCCCTGTAGGTTAAAATGACCGTAATGCCCCTGTAGGGTAAAATGACT
1 GTAAAATGACCATAATACCCCTGTAGGGTAAAATGACCATAATACCCCTGTAGGGTAAAATGACC
* *
35227042 GTAATGTCCCTGTAGGGTAAAATGACCATAATACCCTGTAGG
66 GTAATGACCCTGTAAGGTAAAATGACCATAATACCCTGTAGG
*
35227084 GTAAAATGACCATAATACCCCTGTTGGGTAAAATGACCATAATACCCCTGTAGGGTAAAATGACC
1 GTAAAATGACCATAATACCCCTGTAGGGTAAAATGACCATAATACCCCTGTAGGGTAAAATGACC
*
35227149 GTAAT-ACCCTTGTAAGGTAAAATGACCGTAAT
66 GTAATGACCC-TGTAAGGTAAAATGACCATAAT
35227181 GCCTTGGTGG
Statistics
Matches: 87, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
106 9 0.10
107 78 0.90
ACGTcount: A:0.35, C:0.20, G:0.20, T:0.25
Consensus pattern (107 bp):
GTAAAATGACCATAATACCCCTGTAGGGTAAAATGACCATAATACCCCTGTAGGGTAAAATGACC
GTAATGACCCTGTAAGGTAAAATGACCATAATACCCTGTAGG
Found at i:35227422 original size:27 final size:26
Alignment explanation
Indices: 35227361--35227425 Score: 71
Period size: 27 Copynumber: 2.5 Consensus size: 26
35227351 ATGGAGGAAG
*
35227361 TACTA-TACTGGTGGCTCTGCCAGAA
1 TACTATTACTGGTGGCTCTGCCACAA
*
35227386 TCACTGTTACTGGTGGCT-TAGCCACATA
1 T-ACTATTACTGGTGGCTCT-GCCACA-A
35227414 TACTATTACTGG
1 TACTATTACTGG
35227426 CAGCTTTGCT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
25 1 0.03
26 4 0.12
27 26 0.79
28 2 0.06
ACGTcount: A:0.23, C:0.23, G:0.22, T:0.32
Consensus pattern (26 bp):
TACTATTACTGGTGGCTCTGCCACAA
Found at i:35227510 original size:32 final size:32
Alignment explanation
Indices: 35227466--35227683 Score: 240
Period size: 32 Copynumber: 6.8 Consensus size: 32
35227456 TTTGCTGCGA
*
35227466 TGCTACTGATGGCTTTGTGCAGATCATAGT-AC
1 TGCTACTGATGGCTTTGTGCCGATCATA-TCAC
* * * *
35227498 CGTTACTGATGGCTGTGTGCCGAGCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATCAC
* * *
35227530 TGCTACTGATGGCTTTGTGCCGGTCATGTTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATCAC
* * * *
35227562 AGTTACTGATGGCTGTGTGCCGGTCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATCAC
* * *
35227594 TGCTGCTGATGGCTTTGTGCCGATCATGTTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATCAC
* * * *
35227626 CGTTACTGATGGCTGTGTGCCGATTATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATCAC
*
35227658 TGCTACTGATGGCTTTGTGCCAATCA
1 TGCTACTGATGGCTTTGTGCCGATCA
35227684 CATTACTGTA
Statistics
Matches: 149, Mismatches: 36, Indels: 2
0.80 0.19 0.01
Matches are distributed among these distances:
31 1 0.01
32 148 0.99
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (32 bp):
TGCTACTGATGGCTTTGTGCCGATCATATCAC
Found at i:35227567 original size:64 final size:64
Alignment explanation
Indices: 35227466--35227683 Score: 341
Period size: 64 Copynumber: 3.4 Consensus size: 64
35227456 TTTGCTGCGA
*
35227466 TGCTACTGATGGCTTTGTGCAGATCATAG-TACCGTTACTGATGGCTGTGTGCCGAGCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCAT-GTTACCGTTACTGATGGCTGTGTGCCGAGCATATCAC
* *
35227530 TGCTACTGATGGCTTTGTGCCGGTCATGTTACAGTTACTGATGGCTGTGTGCCG-GTCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGAG-CATATCAC
* **
35227594 TGCTGCTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGATTATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGAGCATATCAC
*
35227658 TGCTACTGATGGCTTTGTGCCAATCA
1 TGCTACTGATGGCTTTGTGCCGATCA
35227684 CATTACTGTA
Statistics
Matches: 141, Mismatches: 10, Indels: 6
0.90 0.06 0.04
Matches are distributed among these distances:
63 2 0.01
64 139 0.99
ACGTcount: A:0.17, C:0.22, G:0.27, T:0.34
Consensus pattern (64 bp):
TGCTACTGATGGCTTTGTGCCGATCATGTTACCGTTACTGATGGCTGTGTGCCGAGCATATCAC
Found at i:35237918 original size:19 final size:18
Alignment explanation
Indices: 35237894--35237931 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35237884 TGGAAATGAA
35237894 TCATTTCTCATTTTCATTT
1 TCATTTC-CATTTTCATTT
*
35237913 TCATTTCCATTTTTATTT
1 TCATTTCCATTTTCATTT
35237931 T
1 T
35237932 GAGAAAACCA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (18 bp):
TCATTTCCATTTTCATTT
Found at i:35254951 original size:19 final size:19
Alignment explanation
Indices: 35254919--35254957 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
35254909 TCATCTTTCA
35254919 CTCTTCACTCTTCTCTCTT
1 CTCTTCACTCTTCTCTCTT
*
35254938 CTCTCTCACT-TTCTTTCTT
1 CTCT-TCACTCTTCTCTCTT
35254957 C
1 C
35254958 AAAACCCTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (19 bp):
CTCTTCACTCTTCTCTCTT
Found at i:35258811 original size:19 final size:19
Alignment explanation
Indices: 35258787--35258823 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
35258777 AGGAAAGCGA
*
35258787 GTTTTATTCGGTCACTGAT
1 GTTTTATGCGGTCACTGAT
35258806 GTTTTATGCGGTCACTGA
1 GTTTTATGCGGTCACTGA
35258824 CCCTAGTGAT
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:0.16, C:0.16, G:0.24, T:0.43
Consensus pattern (19 bp):
GTTTTATGCGGTCACTGAT
Found at i:35260992 original size:22 final size:23
Alignment explanation
Indices: 35260962--35261006 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
35260952 TCAGATATAA
* *
35260962 AATAGTGCGATACAATCGCCAAT
1 AATAGTGCGATAAAATCACCAAT
35260985 AATA-TGCGATAAAATCACCAAT
1 AATAGTGCGATAAAATCACCAAT
35261007 CCCCTCGGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 16 0.80
23 4 0.20
ACGTcount: A:0.44, C:0.20, G:0.13, T:0.22
Consensus pattern (23 bp):
AATAGTGCGATAAAATCACCAAT
Found at i:35262672 original size:8 final size:8
Alignment explanation
Indices: 35262659--35262689 Score: 62
Period size: 8 Copynumber: 3.9 Consensus size: 8
35262649 ATATGCATTA
35262659 AAAATTTT
1 AAAATTTT
35262667 AAAATTTT
1 AAAATTTT
35262675 AAAATTTT
1 AAAATTTT
35262683 AAAATTT
1 AAAATTT
35262690 ATTCCTTCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (8 bp):
AAAATTTT
Found at i:35267733 original size:6 final size:6
Alignment explanation
Indices: 35267701--35267774 Score: 55
Period size: 6 Copynumber: 12.2 Consensus size: 6
35267691 CGAAGATCGC
* * * *
35267701 TTATTT TTTTCTT TTCTTT TCAATT TTATTT TTATTT TTATTT TT-TGTT
1 TTATTT TTAT-TT TTATTT TTATTT TTATTT TTATTT TTATTT TTAT-TT
35267750 TT-TTT AGTTA-TT TTATTT TTATTT T
1 TTATTT --TTATTT TTATTT TTATTT T
35267775 CTTAGACCTC
Statistics
Matches: 55, Mismatches: 7, Indels: 12
0.74 0.09 0.16
Matches are distributed among these distances:
5 6 0.11
6 40 0.73
7 9 0.16
ACGTcount: A:0.14, C:0.04, G:0.03, T:0.80
Consensus pattern (6 bp):
TTATTT
Found at i:35267793 original size:23 final size:23
Alignment explanation
Indices: 35267767--35267820 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
35267757 TTATTTTATT
*
35267767 TTTATTTTC-TTAGACCTCATTCG
1 TTTATTTTCTTTAGAACT-ATTCG
* *
35267790 TTTATTATCTTTAGAACTATTCT
1 TTTATTTTCTTTAGAACTATTCG
35267813 TTTATTTT
1 TTTATTTT
35267821 TATGGTTGTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
23 19 0.73
24 7 0.27
ACGTcount: A:0.20, C:0.15, G:0.06, T:0.59
Consensus pattern (23 bp):
TTTATTTTCTTTAGAACTATTCG
Found at i:35270267 original size:39 final size:39
Alignment explanation
Indices: 35270222--35270298 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 39
35270212 TTAATTAGAA
35270222 AGAAATTTCAATTAATCAACCTAAAGTCAATTGCTCTTT
1 AGAAATTTCAATTAATCAACCTAAAGTCAATTGCTCTTT
* *
35270261 AGAAATTTCAATTAATCAACCTAAAGTCAGTTGGTCTT
1 AGAAATTTCAATTAATCAACCTAAAGTCAATTGCTCTT
35270299 ACTCTCGAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 36 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (39 bp):
AGAAATTTCAATTAATCAACCTAAAGTCAATTGCTCTTT
Found at i:35271794 original size:21 final size:22
Alignment explanation
Indices: 35271754--35271800 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
35271744 CACATAGCAC
*
35271754 ATTGTGGATAAACCACCACATA
1 ATTGTCGATAAACCACCACATA
*
35271776 ATTGTCGAT-AACGACCACATA
1 ATTGTCGATAAACCACCACATA
35271797 ATTG
1 ATTG
35271801 CTAGTTAAAC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 15 0.65
22 8 0.35
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (22 bp):
ATTGTCGATAAACCACCACATA
Found at i:35289128 original size:14 final size:15
Alignment explanation
Indices: 35289091--35289128 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
35289081 AACATAACTT
*
35289091 AAAATCATTCATTTC
1 AAAATCATTCATTTA
35289106 AAAATCATTCA-TTA
1 AAAATCATTCATTTA
*
35289120 AAAAACATT
1 AAAATCATT
35289129 TCATAAATCA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 10 0.48
15 11 0.52
ACGTcount: A:0.50, C:0.16, G:0.00, T:0.34
Consensus pattern (15 bp):
AAAATCATTCATTTA
Found at i:35292204 original size:18 final size:19
Alignment explanation
Indices: 35292183--35292235 Score: 63
Period size: 18 Copynumber: 2.7 Consensus size: 19
35292173 TTGCACTTGT
35292183 AGAAGAAGAAGTTGTTGC-
1 AGAAGAAGAAGTTGTTGCA
* *
35292201 AGAAGAGGAGGTTGTTGCTAA
1 AGAAGAAGAAGTTGTTGC--A
35292222 AGAAGAAGAAGTTG
1 AGAAGAAGAAGTTG
35292236 ATGAAAATGA
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
18 16 0.57
21 12 0.43
ACGTcount: A:0.40, C:0.04, G:0.36, T:0.21
Consensus pattern (19 bp):
AGAAGAAGAAGTTGTTGCA
Found at i:35302043 original size:42 final size:42
Alignment explanation
Indices: 35301966--35302091 Score: 146
Period size: 42 Copynumber: 2.9 Consensus size: 42
35301956 TCCCAGATGT
* * * *
35301966 GGTCTTATATGTAATCAAATATCGATGCCACTGTCCTAGACAG
1 GGTCTTACATGAAATCAAATA-CGATGCCAATGTCCCAGACAG
* *
35302009 GGTCTTACATGAAATCATATACGATGCCAATGTCCCAGACAT
1 GGTCTTACATGAAATCAAATACGATGCCAATGTCCCAGACAG
*
35302051 GGTCTTACACATAAATATCAAAT-CGATGCCAATGTCCCAGA
1 GGTCTT--ACATGAA-ATCAAATACGATGCCAATGTCCCAGA
35302092 TGTGGTCTTA
Statistics
Matches: 72, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
42 24 0.33
43 18 0.25
44 24 0.33
45 6 0.08
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (42 bp):
GGTCTTACATGAAATCAAATACGATGCCAATGTCCCAGACAG
Found at i:35302087 original size:44 final size:43
Alignment explanation
Indices: 35301986--35302104 Score: 143
Period size: 44 Copynumber: 2.8 Consensus size: 43
35301976 GTAATCAAAT
* * * * *
35301986 ATCGATGCCACTGTCCTAGACAGGGTCTT--ACATGAAATCAT
1 ATCGATGCCAATGTCCCAGACATGGTCTTACACATAAAATCAA
35302027 ATACGATGCCAATGTCCCAGACATGGTCTTACACATAAATATCAA
1 AT-CGATGCCAATGTCCCAGACATGGTCTTACACATAAA-ATCAA
**
35302072 ATCGATGCCAATGTCCCAGATGTGGTCTTACAC
1 ATCGATGCCAATGTCCCAGACATGGTCTTACAC
35302105 GTAATTACAT
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 2 0.03
42 24 0.36
44 35 0.52
45 6 0.09
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.26
Consensus pattern (43 bp):
ATCGATGCCAATGTCCCAGACATGGTCTTACACATAAAATCAA
Found at i:35303230 original size:13 final size:13
Alignment explanation
Indices: 35303212--35303238 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35303202 CACAAACGAT
35303212 AAAACTTTCACAC
1 AAAACTTTCACAC
35303225 AAAACTTTCACAC
1 AAAACTTTCACAC
35303238 A
1 A
35303239 TATTAATTCA
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:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (13 bp):
AAAACTTTCACAC
Found at i:35327174 original size:25 final size:25
Alignment explanation
Indices: 35327096--35327175 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
35327086 ACATGTATTA
*
35327096 TCATACGAGCT-ATGAATCGGTATGC
1 TCATACGAGCTGA-GAATCGGTAAGC
** * * *
35327121 TCCCACAAGCTGTGAATCGATAAGC
1 TCATACGAGCTGAGAATCGGTAAGC
35327146 TCATACGAGCTGAGAATCGGTAAGC
1 TCATACGAGCTGAGAATCGGTAAGC
35327171 TCATA
1 TCATA
35327176 AAAGTTGTGG
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.24
Consensus pattern (25 bp):
TCATACGAGCTGAGAATCGGTAAGC
Found at i:35329046 original size:16 final size:17
Alignment explanation
Indices: 35329020--35329064 Score: 53
Period size: 16 Copynumber: 2.8 Consensus size: 17
35329010 TTGATCAATT
35329020 TCCATATACATATATCA
1 TCCATATACATATATCA
35329037 TCCA-ATACAT-T-T-A
1 TCCATATACATATATCA
35329050 TCCATATATCATATA
1 TCCATATA-CATATA
35329065 ACAACATTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 8
0.75 0.00 0.25
Matches are distributed among these distances:
13 5 0.21
14 4 0.17
15 4 0.17
16 7 0.29
17 4 0.17
ACGTcount: A:0.40, C:0.22, G:0.00, T:0.38
Consensus pattern (17 bp):
TCCATATACATATATCA
Found at i:35329275 original size:25 final size:25
Alignment explanation
Indices: 35329242--35329312 Score: 88
Period size: 25 Copynumber: 2.8 Consensus size: 25
35329232 CAAGCTGTAG
* *
35329242 ATCGATATGCTCTCACAAGTTACAA
1 ATCGGTATGCTCTCACGAGTTACAA
* * * *
35329267 ATTGGTATGCTCTTACGAGCTATAA
1 ATCGGTATGCTCTCACGAGTTACAA
35329292 ATCGGTATGCTCTCACGAGTT
1 ATCGGTATGCTCTCACGAGTT
35329313 GTTGAGTTTC
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.32
Consensus pattern (25 bp):
ATCGGTATGCTCTCACGAGTTACAA
Found at i:35337817 original size:17 final size:17
Alignment explanation
Indices: 35337795--35337827 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
35337785 GGCTAACATG
35337795 TTGGTGAATATGTGCTA
1 TTGGTGAATATGTGCTA
35337812 TTGGTGAATATGTGCT
1 TTGGTGAATATGTGCT
35337828 TAGGCATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.21, C:0.06, G:0.30, T:0.42
Consensus pattern (17 bp):
TTGGTGAATATGTGCTA
Found at i:35343845 original size:9 final size:9
Alignment explanation
Indices: 35343831--35343856 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35343821 ATATATAACA
35343831 TTTATTTTT
1 TTTATTTTT
35343840 TTTATTTTT
1 TTTATTTTT
35343849 TTTATTTT
1 TTTATTTT
35343857 GCTTTGGAAT
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:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (9 bp):
TTTATTTTT
Found at i:35355135 original size:52 final size:50
Alignment explanation
Indices: 35355048--35355183 Score: 163
Period size: 52 Copynumber: 2.7 Consensus size: 50
35355038 GTATTAAAAA
* *
35355048 AAAACTCTTTTAAATAATAAT-TTAAATTCTATTTAATTATCT-TTTATTT
1 AAAACTCTTTTAAATAATAATATTAAATTATATTTAATTAT-TATTTATCT
* * *
35355097 AAAATTGTTTTAAATAATAATAATTAAATTATGTTTTAATTATTATTTATCT
1 AAAACTCTTTTAAATAATAAT-ATTAAATTAT-ATTTAATTATTATTTATCT
35355149 AAAACTCTTTTAAATAATAATA-T-AATTACTATTTA
1 AAAACTCTTTTAAATAATAATATTAAATTA-TATTTA
35355184 TCTAAATCTC
Statistics
Matches: 74, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
49 28 0.38
50 2 0.03
51 10 0.14
52 34 0.46
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (50 bp):
AAAACTCTTTTAAATAATAATATTAAATTATATTTAATTATTATTTATCT
Found at i:35355175 original size:38 final size:38
Alignment explanation
Indices: 35355133--35355207 Score: 132
Period size: 38 Copynumber: 2.0 Consensus size: 38
35355123 AATTATGTTT
*
35355133 TAATTATTATTTATCTAAAACTCTTTTAAATAATAATA
1 TAATTACTATTTATCTAAAACTCTTTTAAATAATAATA
*
35355171 TAATTACTATTTATCTAAATCTCTTTTAAATAATAAT
1 TAATTACTATTTATCTAAAACTCTTTTAAATAATAAT
35355208 TAAAATCTAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 35 1.00
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.48
Consensus pattern (38 bp):
TAATTACTATTTATCTAAAACTCTTTTAAATAATAATA
Found at i:35369089 original size:50 final size:54
Alignment explanation
Indices: 35368988--35369130 Score: 168
Period size: 50 Copynumber: 2.7 Consensus size: 54
35368978 GGGAATGAGA
**
35368988 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATT-AGA-TATGAGAAC
* * *
35369044 TTCCATGTAAAACCATGTCTGGGACATGGCATGGGCA-C-TT-G-TATGAGAAC
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTAGATATGAGAAC
* * *
35369094 TCCCATGTAAGACCATATCTAGGATATGGCATTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
35369131 GTACAGAAAA
Statistics
Matches: 76, Mismatches: 11, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
50 38 0.50
52 1 0.01
54 2 0.03
55 1 0.01
56 34 0.45
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.27
Consensus pattern (54 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATCATTAGATATGAGAAC
Found at i:35381322 original size:46 final size:46
Alignment explanation
Indices: 35381258--35381346 Score: 178
Period size: 46 Copynumber: 1.9 Consensus size: 46
35381248 AAAAACCTAA
35381258 TTTTTTTTACTTTCAAGGGAATTTCGTCCAAGGCCTTTAATGGATT
1 TTTTTTTTACTTTCAAGGGAATTTCGTCCAAGGCCTTTAATGGATT
35381304 TTTTTTTTACTTTCAAGGGAATTTCGTCCAAGGCCTTTAATGG
1 TTTTTTTTACTTTCAAGGGAATTTCGTCCAAGGCCTTTAATGG
35381347 GCCTCTTTGG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (46 bp):
TTTTTTTTACTTTCAAGGGAATTTCGTCCAAGGCCTTTAATGGATT
Found at i:35383360 original size:27 final size:27
Alignment explanation
Indices: 35383341--35383783 Score: 571
Period size: 27 Copynumber: 16.4 Consensus size: 27
35383331 GGGTATAATA
35383341 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
**
35383368 GTCATTTTACCCTATGGCAGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
35383395 GTCATTCTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
35383422 GTCATTCTACCTTATGGGGGTAATTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
35383449 GTTATTCTACCCTATGAGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
35383476 CTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * * *
35383503 ATTATTCTACCTTATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
*
35383530 GTCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
35383557 ATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
35383584 ATCATTTTACCCCATGGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
35383611 GTCATTCTACCCTATAGGGGTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
35383638 GTCATTCTACCCTATGGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
35383665 GTCATTTTACCCTATAGGGGTATTTTG
1 GTCATTTTACCCTATGGGGGTATTTCG
* *
35383692 GTCATTTTACCCTATAGGGTTATTTCG
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
35383719 ATCATTCTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
* * *
35383746 ATCATTTTACCCTATGAGGGTATTTCA
1 GTCATTTTACCCTATGGGGGTATTTCG
35383773 GTCATTTTACC
1 GTCATTTTACC
35383784 TATTTTGGAG
Statistics
Matches: 367, Mismatches: 49, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 367 1.00
ACGTcount: A:0.19, C:0.19, G:0.21, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTATGGGGGTATTTCG
Found at i:35389793 original size:19 final size:20
Alignment explanation
Indices: 35389751--35389793 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
35389741 TCATGCTTTC
*
35389751 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
35389771 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
35389789 TATTC
1 TATTC
35389794 CACTTAGTCA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:35390002 original size:51 final size:50
Alignment explanation
Indices: 35389926--35390061 Score: 195
Period size: 50 Copynumber: 2.7 Consensus size: 50
35389916 CTGGTTCACA
*
35389926 TAGTAGCCTACACATAGTACTACACATGTGACCATTTCCA-TCCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCA-TT-CATTCCGATACACG
* *
35389977 TAGTAGCCTGCACATAGTACTACACATGCGACCCA-TCATTCCTATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGA-CCATTCATTCCGATACACG
*
35390027 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACATGTGACCAT
35390062 CACTTTCACT
Statistics
Matches: 77, Mismatches: 5, Indels: 7
0.87 0.06 0.08
Matches are distributed among these distances:
49 5 0.06
50 40 0.52
51 29 0.38
52 3 0.04
ACGTcount: A:0.31, C:0.30, G:0.15, T:0.24
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCATTCATTCCGATACACG
Found at i:35396439 original size:50 final size:50
Alignment explanation
Indices: 35396329--35396576 Score: 277
Period size: 50 Copynumber: 4.9 Consensus size: 50
35396319 ACATTAAGAG
*
35396329 GATGAGA--TCCCATGTAAAACCATGTCTGGGACATGGCATTGGCATCATTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA-C--TGA
* * *
35396380 GATTATGAGAGGTCCCATGTAAGACCATGTATGGGACATGGCGTTGGCACCGA
1 G---ATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA
* *
35396433 GATGAGAGGTCCCATGTAAGACCATGTCTCGGACATGGCGTTGGCACTGA
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA
** *
35396483 GATGAGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACAT-A
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCAC-TGA
* ** * * *
35396533 TATGAGAACTCCCATGTAAGACCATATCTAGGATATGGCATTGG
1 GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGG
35396577 AAGTATAAGA
Statistics
Matches: 170, Mismatches: 21, Indels: 13
0.83 0.10 0.06
Matches are distributed among these distances:
50 124 0.73
51 2 0.01
53 3 0.02
54 6 0.04
55 1 0.01
56 34 0.20
ACGTcount: A:0.27, C:0.21, G:0.29, T:0.23
Consensus pattern (50 bp):
GATGAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACTGA
Found at i:35411642 original size:268 final size:261
Alignment explanation
Indices: 35411171--35411702 Score: 843
Period size: 268 Copynumber: 2.0 Consensus size: 261
35411161 TTCGCTATGC
** *
35411171 GTCACCAATCATTTCATGACAGGAATGGAAATTTTTGAAATAAAATATTTGTTTAGAACTAAAGT
1 GTCACCAATCATTTCATGACAGGAATGGAAATTAATGAAATAAAATATTTGGTTAGAACTAAAGT
*
35411236 TGCGTAATTAATTAAAAATTTTAACAATCGCGAGACCATTTAGTTTCTATAAATTTTTGTATGTC
66 TGCG-AATTAATTAAAAATTTTAACAATCGCGAGACCATTTAGCTTCTATAAATTTTTGTATGTC
*
35411301 CCAACTTACATATTCACGTACTTAGTCATTTGTCAAAACACATCAAAGTAAGAAAAGAAAGAAAC
130 CCAACTTACATATTCACGTACTCAGTCATTTGTCAAAACACATCAAAGTAAGAAAAGAAAGAAAC
35411366 AAGAATCATGAGCGTTCCTCATATAGTAATATTCGGAATAATGCAATCGCAACGGTGATTCCACC
195 AAGAATCATGAGCGTTCCTCATATAGTAATATTCGGAATAATGCAATCGCAACGGTGATTCCACC
35411431 AG
260 AG
35411433 GTCACCAATCATTTCATGACAGGAATGGAAATTAATGAAATAAAATATTTGGTTAGAACTAAAGT
1 GTCACCAATCATTTCATGACAGGAATGGAAATTAATGAAATAAAATATTTGGTTAGAACTAAAGT
* * * *
35411498 TGC-ATTTAGTTTAGAATTCTCTATGTGTCACCAATCGCGAGACCATTTAGCTTCTATAAA-TTT
66 TGCGAATTAATTAAAAATT-T-TA------A-CAATCGCGAGACCATTTAGCTTCTATAAATTTT
** * *
35411561 TGTATGTCCCAACTTACATATTCGGGTACTCAGTCATTTGTCAAAACACTTCAAAGTGAGAAAAG
122 TGTATGTCCCAACTTACATATTCACGTACTCAGTCATTTGTCAAAACACATCAAAGTAAGAAAAG
35411626 AAAGAAACAAGAATCATGAGCGTTCCTCATATAGTAATATTCGGAATAATGCAATCGCAACGGTG
187 AAAGAAACAAGAATCATGAGCGTTCCTCATATAGTAATATTCGGAATAATGCAATCGCAACGGTG
35411691 ATTCCACCAG
252 ATTCCACCAG
35411701 GT
1 GT
35411703 GTTCTTGGAT
Statistics
Matches: 248, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
260 11 0.04
261 1 0.00
262 67 0.27
268 141 0.57
269 28 0.11
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.30
Consensus pattern (261 bp):
GTCACCAATCATTTCATGACAGGAATGGAAATTAATGAAATAAAATATTTGGTTAGAACTAAAGT
TGCGAATTAATTAAAAATTTTAACAATCGCGAGACCATTTAGCTTCTATAAATTTTTGTATGTCC
CAACTTACATATTCACGTACTCAGTCATTTGTCAAAACACATCAAAGTAAGAAAAGAAAGAAACA
AGAATCATGAGCGTTCCTCATATAGTAATATTCGGAATAATGCAATCGCAACGGTGATTCCACCA
G
Found at i:35425950 original size:30 final size:30
Alignment explanation
Indices: 35425914--35426089 Score: 253
Period size: 30 Copynumber: 5.9 Consensus size: 30
35425904 AGAATCAGTC
* *
35425914 TGGGCCTGAGCCCTATATAGTAACAGAGTG
1 TGGGCCTTAGCCCAATATAGTAACAGAGTG
* *
35425944 TGGGCCTTAGCCCAATAGAGTATCAGAGTG
1 TGGGCCTTAGCCCAATATAGTAACAGAGTG
* * * *
35425974 TGGGGCTTAGCCTAATACAGTTACAGAGTG
1 TGGGCCTTAGCCCAATATAGTAACAGAGTG
35426004 TGGGCCTTAGCCCAATATAGTAACAGAGTG
1 TGGGCCTTAGCCCAATATAGTAACAGAGTG
35426034 TGGGCCTTAGCCCAATATAGTAACAGAGTG
1 TGGGCCTTAGCCCAATATAGTAACAGAGTG
* * *
35426064 TGGACCTTAGCCTAATAGAGTAACAG
1 TGGGCCTTAGCCCAATATAGTAACAG
35426090 TGCAAATGCA
Statistics
Matches: 130, Mismatches: 16, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 130 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (30 bp):
TGGGCCTTAGCCCAATATAGTAACAGAGTG
Found at i:35426073 original size:90 final size:90
Alignment explanation
Indices: 35425914--35426089 Score: 280
Period size: 90 Copynumber: 2.0 Consensus size: 90
35425904 AGAATCAGTC
* * **
35425914 TGGGCCTGAGCCCTATATAGTAACAGAGTGTGGGCCTTAGCCCAATAGAGTATCAGAGTGTGGGG
1 TGGGCCTGAGCCCAATATAGTAACAGAGTGTGGGCCTTAGCCCAATAGAGTAACAGAGTGTGGAC
*
35425979 CTTAGCCTAATACAGTTACAGAGTG
66 CTTAGCCTAATACAGTAACAGAGTG
* *
35426004 TGGGCCTTAGCCCAATATAGTAACAGAGTGTGGGCCTTAGCCCAATATAGTAACAGAGTGTGGAC
1 TGGGCCTGAGCCCAATATAGTAACAGAGTGTGGGCCTTAGCCCAATAGAGTAACAGAGTGTGGAC
*
35426069 CTTAGCCTAATAGAGTAACAG
66 CTTAGCCTAATACAGTAACAG
35426090 TGCAAATGCA
Statistics
Matches: 78, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 78 1.00
ACGTcount: A:0.29, C:0.19, G:0.28, T:0.24
Consensus pattern (90 bp):
TGGGCCTGAGCCCAATATAGTAACAGAGTGTGGGCCTTAGCCCAATAGAGTAACAGAGTGTGGAC
CTTAGCCTAATACAGTAACAGAGTG
Found at i:35426453 original size:27 final size:27
Alignment explanation
Indices: 35426422--35426511 Score: 146
Period size: 27 Copynumber: 3.3 Consensus size: 27
35426412 GGGTATAACA
*
35426422 GTCATTTTACCCTAT-GGGGATATTTCG
1 GTCATTTTACCCT-TCGGGGGTATTTCG
*
35426449 ATCATTTTACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGGGGGTATTTCG
35426476 GTCATTTTACCCTTCGGGGGTATTTCG
1 GTCATTTTACCCTTCGGGGGTATTTCG
35426503 GTCATTTTA
1 GTCATTTTA
35426512 GAGGCCTATT
Statistics
Matches: 59, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
26 1 0.02
27 58 0.98
ACGTcount: A:0.16, C:0.20, G:0.22, T:0.42
Consensus pattern (27 bp):
GTCATTTTACCCTTCGGGGGTATTTCG
Found at i:35440874 original size:27 final size:27
Alignment explanation
Indices: 35440804--35440932 Score: 161
Period size: 27 Copynumber: 4.8 Consensus size: 27
35440794 TTGCATCGAG
* * *
35440804 ACCCCCACAGGGTAAAATTACTGAAA-T
1 ACCCCCATAGGGTAAAATGAC-CAAATT
* ** *
35440831 ACCCCCGTAGGACAAAATGACCGAATT
1 ACCCCCATAGGGTAAAATGACCAAATT
* *
35440858 ACCCCTATAGCGTAAAATGACCAAATT
1 ACCCCCATAGGGTAAAATGACCAAATT
35440885 ACCCCCATAGGGTAAAATGACCAAATT
1 ACCCCCATAGGGTAAAATGACCAAATT
35440912 ACCCCCATAGGGTAAAATGAC
1 ACCCCCATAGGGTAAAATGAC
35440933 TGAAATACCT
Statistics
Matches: 86, Mismatches: 15, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
26 2 0.02
27 84 0.98
ACGTcount: A:0.40, C:0.27, G:0.16, T:0.18
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACCAAATT
Found at i:35440941 original size:27 final size:27
Alignment explanation
Indices: 35440804--35440970 Score: 151
Period size: 27 Copynumber: 6.2 Consensus size: 27
35440794 TTGCATCGAG
* *
35440804 ACCCCCACAGGGTAAAATTACTGAAAT
1 ACCCCCATAGGGTAAAATGACTGAAAT
* ** * *
35440831 ACCCCCGTAGGACAAAATGACCGAATT
1 ACCCCCATAGGGTAAAATGACTGAAAT
* * *
35440858 ACCCCTATAGCGTAAAATGAC-CAAATT
1 ACCCCCATAGGGTAAAATGACTGAAA-T
*
35440885 ACCCCCATAGGGTAAAATGAC-CAAATT
1 ACCCCCATAGGGTAAAATGACTGAAA-T
35440912 ACCCCCATAGGGTAAAATGACTGAAAT
1 ACCCCCATAGGGTAAAATGACTGAAAT
* * **
35440939 ACCTCTATTA-GGTAAAATGACTGTTAT
1 ACCCCCA-TAGGGTAAAATGACTGAAAT
35440966 ACCCC
1 ACCCC
35440971 TAGGAGATGA
Statistics
Matches: 115, Mismatches: 22, Indels: 6
0.80 0.15 0.04
Matches are distributed among these distances:
26 2 0.02
27 108 0.94
28 5 0.04
ACGTcount: A:0.38, C:0.26, G:0.15, T:0.21
Consensus pattern (27 bp):
ACCCCCATAGGGTAAAATGACTGAAAT
Found at i:35440970 original size:81 final size:81
Alignment explanation
Indices: 35440804--35440959 Score: 199
Period size: 81 Copynumber: 1.9 Consensus size: 81
35440794 TTGCATCGAG
* * * *
35440804 ACCCCCACAGGGTAAAATTACTGAAATACCCCCGTAGGACAAAATGACCGAATTACCCCTATAGC
1 ACCCCCACAGGGTAAAATGACTCAAATACCCCCATAGGACAAAATGACCGAAATACCCCTATAGC
35440869 GTAAAATGACCAAATT
66 GTAAAATGACCAAATT
* ** * *
35440885 ACCCCCATAGGGTAAAATGAC-CAAATTACCCCCATAGGGTAAAATGACTGAAATACCTCTATTA
1 ACCCCCACAGGGTAAAATGACTCAAA-TACCCCCATAGGACAAAATGACCGAAATACCCCTA-TA
35440949 G-GTAAAATGAC
64 GCGTAAAATGAC
35440960 TGTTATACCC
Statistics
Matches: 64, Mismatches: 9, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 3 0.05
81 58 0.91
82 3 0.05
ACGTcount: A:0.40, C:0.25, G:0.15, T:0.20
Consensus pattern (81 bp):
ACCCCCACAGGGTAAAATGACTCAAATACCCCCATAGGACAAAATGACCGAAATACCCCTATAGC
GTAAAATGACCAAATT
Found at i:35441394 original size:28 final size:28
Alignment explanation
Indices: 35441287--35441393 Score: 151
Period size: 28 Copynumber: 3.8 Consensus size: 28
35441277 CTGTACCGAC
35441287 ACTGTATTGGGCTAAGGCCCACACTGTT
1 ACTGTATTGGGCTAAGGCCCACACTGTT
* * *
35441315 ACTGTATTAGGTTAAGGCCCACACTATT
1 ACTGTATTGGGCTAAGGCCCACACTGTT
** * *
35441343 ACTGTATTGGGGAAAGGCCTACATTGTT
1 ACTGTATTGGGCTAAGGCCCACACTGTT
35441371 ACTGTATTGGGCTAAGGCCCACA
1 ACTGTATTGGGCTAAGGCCCACA
35441394 TCGTACTATT
Statistics
Matches: 67, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 67 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.29
Consensus pattern (28 bp):
ACTGTATTGGGCTAAGGCCCACACTGTT
Found at i:35443965 original size:107 final size:107
Alignment explanation
Indices: 35443693--35443983 Score: 297
Period size: 107 Copynumber: 2.7 Consensus size: 107
35443683 CTGCACCGAG
* * * * ** * * *
35443693 ACCCCCATAGGGTAAAAAGACCGAAATACTCCC-ATAGGGTAAAATGACCAAATTACCCCCATAG
1 ACCCCTATAGGATAAAATGACCGAAATAC-CCCTATAAGGTAAAATGACCGTATTACCCCTAGAA
* ** * *
35443757 GGTAAAATGACCAAATTACTTCC-ATAGGGTAAAATGACCGAATT
65 GATAAAATGACTGAATTAC-CCCTATA-GGTAAAATGACCAAATT
* * *
35443801 ACCCCTATAGGATAAAATGACCGAATTACCCCTATAAGGTAAAATGACCGTATTACCCTTATAAG
1 ACCCCTATAGGATAAAATGACCGAAATACCCCTATAAGGTAAAATGACCGTATTACCCCTAGAAG
35443866 ATAAAATGACTGAATTACCCCTATAGGTAAAATGACCAAATT
66 ATAAAATGACTGAATTACCCCTATAGGTAAAATGACCAAATT
*
35443908 A-CCCTCATAGCG-TAAAATGACCGAAATACCCCTAT-AGGATAAAATGACTGT-TATACCCCTA
1 ACCCCT-ATAG-GATAAAATGACCGAAATACCCCTATAAGG-TAAAATGACCGTAT-TACCCCTA
* *
35443969 GGAGATGAAATGACT
62 GAAGATAAAATGACT
35443984 ATTATGGCCT
Statistics
Matches: 156, Mismatches: 21, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
106 8 0.05
107 78 0.50
108 70 0.45
ACGTcount: A:0.40, C:0.22, G:0.15, T:0.22
Consensus pattern (107 bp):
ACCCCTATAGGATAAAATGACCGAAATACCCCTATAAGGTAAAATGACCGTATTACCCCTAGAAG
ATAAAATGACTGAATTACCCCTATAGGTAAAATGACCAAATT
Found at i:35443968 original size:27 final size:26
Alignment explanation
Indices: 35443693--35443955 Score: 280
Period size: 27 Copynumber: 9.8 Consensus size: 26
35443683 CTGCACCGAG
* * *
35443693 ACCCCCATAGGGTAAAAAGACCGAAAT
1 ACCCCTATA-GGTAAAATGACCGAATT
*
35443720 ACTCCC-ATAGGGTAAAATGACCAAATT
1 AC-CCCTATA-GGTAAAATGACCGAATT
* *
35443747 ACCCCCATAGGGTAAAATGACCAAATT
1 ACCCCTATA-GGTAAAATGACCGAATT
*
35443774 ACTTCC-ATAGGGTAAAATGACCGAATT
1 AC-CCCTATA-GGTAAAATGACCGAATT
35443801 ACCCCTATAGGATAAAATGACCGAATT
1 ACCCCTATAGG-TAAAATGACCGAATT
*
35443828 ACCCCTATAAGGTAAAATGACCGTATT
1 ACCCCTAT-AGGTAAAATGACCGAATT
* * *
35443855 ACCCTTATAAGATAAAATGACTGAATT
1 ACCCCTAT-AGGTAAAATGACCGAATT
*
35443882 ACCCCTATAGGTAAAATGACCAAATT
1 ACCCCTATAGGTAAAATGACCGAATT
*
35443908 A-CCCTCATAGCGTAAAATGACCGAAAT
1 ACCCCT-ATAG-GTAAAATGACCGAATT
35443935 ACCCCTATAGGATAAAATGAC
1 ACCCCTATAGG-TAAAATGAC
35443956 TGTTATACCC
Statistics
Matches: 209, Mismatches: 17, Indels: 20
0.85 0.07 0.08
Matches are distributed among these distances:
25 4 0.02
26 28 0.13
27 165 0.79
28 12 0.06
ACGTcount: A:0.41, C:0.22, G:0.15, T:0.22
Consensus pattern (26 bp):
ACCCCTATAGGTAAAATGACCGAATT
Found at i:35443996 original size:134 final size:135
Alignment explanation
Indices: 35443732--35443982 Score: 355
Period size: 134 Copynumber: 1.9 Consensus size: 135
35443722 TCCCATAGGG
* *
35443732 TAAAATGACCAAATTACCCCCATAGGGTAAAATGACCAAATTACTTCCATAGGGTAAAATGACCG
1 TAAAATGACCAAATTACCCCCATAGGGTAAAATGACCAAATTACCTCCATAGCGTAAAATGACCG
* * *
35443797 AATTACCCCTATAGGATAAAATGACCGAATTACCCCTATAAGGTAAAATGACCGTATTACCCTTA
66 AAATACCCCTATAGGATAAAATGACCGAATTACCCCTAGAAGATAAAATGACCGTATTACCCTTA
35443862 TAAGA
131 TAAGA
** *
35443867 TAAAATGACTGAATTACCCCTATA-GGTAAAATGACCAAATTACC-CTCATAGCGTAAAATGACC
1 TAAAATGACCAAATTACCCCCATAGGGTAAAATGACCAAATTACCTC-CATAGCGTAAAATGACC
* * * *
35443930 GAAATACCCCTATAGGATAAAATGACTG-TTATACCCCTAGGAGATGAAATGAC
65 GAAATACCCCTATAGGATAAAATGACCGAAT-TACCCCTAGAAGATAAAATGAC
35443983 TATTATGGCC
Statistics
Matches: 102, Mismatches: 12, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
133 2 0.02
134 79 0.77
135 21 0.21
ACGTcount: A:0.41, C:0.21, G:0.15, T:0.24
Consensus pattern (135 bp):
TAAAATGACCAAATTACCCCCATAGGGTAAAATGACCAAATTACCTCCATAGCGTAAAATGACCG
AAATACCCCTATAGGATAAAATGACCGAATTACCCCTAGAAGATAAAATGACCGTATTACCCTTA
TAAGA
Found at i:35444306 original size:28 final size:28
Alignment explanation
Indices: 35444262--35444350 Score: 135
Period size: 28 Copynumber: 3.2 Consensus size: 28
35444252 ACTGTACGGA
35444262 TACTGTATTGGGCTAAGGCCCACACTGT
1 TACTGTATTGGGCTAAGGCCCACACTGT
* * * *
35444290 TACTGTAATGGGGTAAGGTCCACATTGT
1 TACTGTATTGGGCTAAGGCCCACACTGT
35444318 TACTGTATTGGGCTAAGGCCCACACTG-
1 TACTGTATTGGGCTAAGGCCCACACTGT
35444345 TACTGT
1 TACTGT
35444351 TACTGAATAG
Statistics
Matches: 53, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 6 0.11
28 47 0.89
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.30
Consensus pattern (28 bp):
TACTGTATTGGGCTAAGGCCCACACTGT
Found at i:35451769 original size:21 final size:20
Alignment explanation
Indices: 35451741--35451785 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
35451731 CAGGACTAAA
*
35451741 TCAAAAAATGAT-AAAATTTT
1 TCAAAAAAAGATGAAAA-TTT
*
35451761 TCAAAAAAAGGTGAAAATTT
1 TCAAAAAAAGATGAAAATTT
35451781 TCAAA
1 TCAAA
35451786 CAATAGGGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 18 0.82
21 4 0.18
ACGTcount: A:0.56, C:0.07, G:0.09, T:0.29
Consensus pattern (20 bp):
TCAAAAAAAGATGAAAATTT
Found at i:35453813 original size:25 final size:25
Alignment explanation
Indices: 35453772--35453865 Score: 86
Period size: 25 Copynumber: 3.8 Consensus size: 25
35453762 CTCGTGTAAA
* *
35453772 CATACTGATTTATAGCTC-ATGAGAG
1 CATACTGATCTACAGCTCGA-GAGAG
*
35453797 CATACTGATCTACAGCTCGAGTGAG
1 CATACTGATCTACAGCTCGAGAGAG
* *
35453822 CATA-TCGATCTACAGCTTGAGTGAG
1 CATACT-GATCTACAGCTCGAGAGAG
*
35453847 CATACCGAT-TCACAGCTCG
1 CATACTGATCT-ACAGCTCG
35453866 TATGAGCATC
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
24 2 0.03
25 56 0.95
26 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.27
Consensus pattern (25 bp):
CATACTGATCTACAGCTCGAGAGAG
Found at i:35453871 original size:25 final size:25
Alignment explanation
Indices: 35453794--35453874 Score: 103
Period size: 25 Copynumber: 3.2 Consensus size: 25
35453784 TAGCTCATGA
*
35453794 GAGCATACTGATCTACAGCTCGAGT
1 GAGCATACCGATCTACAGCTCGAGT
* *
35453819 GAGCATATCGATCTACAGCTTGAGT
1 GAGCATACCGATCTACAGCTCGAGT
35453844 GAGCATACCGAT-TCACAGCTCGTA-T
1 GAGCATACCGATCT-ACAGCTCG-AGT
35453869 GAGCAT
1 GAGCAT
35453875 CCATGTACAT
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
24 1 0.02
25 47 0.96
26 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.25
Consensus pattern (25 bp):
GAGCATACCGATCTACAGCTCGAGT
Found at i:35455674 original size:16 final size:16
Alignment explanation
Indices: 35455632--35455674 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
35455622 ACTCGGATCT
* *
35455632 TTACTTTCTTCTTTAC
1 TTACTTACTTGTTTAC
*
35455648 TTACTCACTTGTTTAC
1 TTACTTACTTGTTTAC
*
35455664 TTACTTGCTTG
1 TTACTTACTTG
35455675 CTTAAATAAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.14, C:0.23, G:0.07, T:0.56
Consensus pattern (16 bp):
TTACTTACTTGTTTAC
Found at i:35456010 original size:50 final size:50
Alignment explanation
Indices: 35455931--35456128 Score: 155
Period size: 50 Copynumber: 3.8 Consensus size: 50
35455921 TTTCCTGTAC
* * * * ** *
35455931 TGCCAATGCCATATCCTAGATATGGTCTTACATGAGATTTCTTATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
* ** * *
35455981 TGCCCATTCCATGTCCCAGACATGGTCTTACGA-GGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTAC-ATGAGACCTCTCATATCGG
* * * *
35456031 TTCCAACGCCATGTCCCAGACATGTTCTTACATGGGACCTCTCATAATCTCAATGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--TC---GG
* * *
35456087 TGCCAATGCCATGTCCAAGACATGGTCTTACATGAGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCT
35456129 TTACCCAAAT
Statistics
Matches: 117, Mismatches: 23, Indels: 10
0.78 0.15 0.07
Matches are distributed among these distances:
49 1 0.01
50 76 0.65
51 1 0.01
53 2 0.02
56 37 0.32
ACGTcount: A:0.24, C:0.28, G:0.18, T:0.30
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATCGG
Found at i:35464725 original size:12 final size:12
Alignment explanation
Indices: 35464706--35464738 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
35464696 TTTCAATACG
35464706 AATTTTTTTT--
1 AATTTTTTTTCA
35464716 AATTTTTTTTCA
1 AATTTTTTTTCA
35464728 AATTTTTTTTC
1 AATTTTTTTTC
35464739 TTGTCGAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.48
12 11 0.52
ACGTcount: A:0.21, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
AATTTTTTTTCA
Found at i:35466879 original size:30 final size:30
Alignment explanation
Indices: 35466798--35466883 Score: 93
Period size: 30 Copynumber: 2.9 Consensus size: 30
35466788 TTTACCAATA
* * *
35466798 GATAACTGAAGCTAACTCA-TTTCATAATTC
1 GATAGCTGAAGCTATC-CATTTTCATAATCC
* * **
35466828 GATAGCCGAAGCTTTATATTTTCATAATCC
1 GATAGCTGAAGCTATCCATTTTCATAATCC
35466858 GATAGCTGAAGCTATCCATTTTCATA
1 GATAGCTGAAGCTATCCATTTTCATA
35466884 GTTTGATGGT
Statistics
Matches: 44, Mismatches: 11, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 1 0.02
30 43 0.98
ACGTcount: A:0.33, C:0.20, G:0.13, T:0.35
Consensus pattern (30 bp):
GATAGCTGAAGCTATCCATTTTCATAATCC
Found at i:35466916 original size:29 final size:29
Alignment explanation
Indices: 35466877--35466937 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
35466867 AGCTATCCAT
35466877 TTTCATAGTTTGATGGTCGTCACCATCCC
1 TTTCATAGTTTGATGGTCGTCACCATCCC
*
35466906 TTTCATTGTTTGATGGTCGTCACCATCCC
1 TTTCATAGTTTGATGGTCGTCACCATCCC
35466935 TTT
1 TTT
35466938 TTATAATTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.15, C:0.26, G:0.16, T:0.43
Consensus pattern (29 bp):
TTTCATAGTTTGATGGTCGTCACCATCCC
Found at i:35470810 original size:6 final size:6
Alignment explanation
Indices: 35470801--35470855 Score: 51
Period size: 6 Copynumber: 9.3 Consensus size: 6
35470791 AAAAACAACT
* * * *
35470801 AAAATA AAAATA AAAATA AACATA AAAGA-A AAAAGA AAACTA AAAA-G
1 AAAATA AAAATA AAAATA AAAATA AAA-ATA AAAATA AAAATA AAAATA
35470848 AAAATA AA
1 AAAATA AA
35470856 TACACTTAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 6
0.75 0.13 0.12
Matches are distributed among these distances:
5 5 0.13
6 33 0.85
7 1 0.03
ACGTcount: A:0.80, C:0.04, G:0.05, T:0.11
Consensus pattern (6 bp):
AAAATA
Found at i:35470833 original size:18 final size:16
Alignment explanation
Indices: 35470780--35470855 Score: 64
Period size: 18 Copynumber: 4.5 Consensus size: 16
35470770 TAAGTCTAAG
35470780 AAAATAACAAT-AAAAA
1 AAAATAA-AATAAAAAA
* *
35470796 CAACTAAAATAAAAATA
1 AAAATAAAATAAAAA-A
35470813 AAAATAAACATAAAAGAA
1 AAAATAAA-ATAAAA-AA
* *
35470831 AAAAGAAAACTAAAAAG
1 AAAATAAAA-TAAAAAA
35470848 AAAATAAA
1 AAAATAAA
35470856 TACACTTAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
15 3 0.06
16 9 0.19
17 16 0.33
18 19 0.40
19 1 0.02
ACGTcount: A:0.78, C:0.07, G:0.04, T:0.12
Consensus pattern (16 bp):
AAAATAAAATAAAAAA
Found at i:35477841 original size:30 final size:30
Alignment explanation
Indices: 35477805--35477878 Score: 87
Period size: 30 Copynumber: 2.5 Consensus size: 30
35477795 TTTTTACCAA
*
35477805 TCGATAGCCAAAGCAAACTCA-TTTCATAAT
1 TCGATAGCCGAAGCAAACT-ATTTTCATAAT
* * *
35477835 TCGATAGTCGAAGCTATCTATTTTCATAAT
1 TCGATAGCCGAAGCAAACTATTTTCATAAT
*
35477865 TTGATAGCCGAAGC
1 TCGATAGCCGAAGC
35477879 TATCCCTTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 1 0.03
30 36 0.97
ACGTcount: A:0.34, C:0.20, G:0.15, T:0.31
Consensus pattern (30 bp):
TCGATAGCCGAAGCAAACTATTTTCATAAT
Found at i:35477879 original size:30 final size:30
Alignment explanation
Indices: 35477826--35478007 Score: 197
Period size: 30 Copynumber: 6.1 Consensus size: 30
35477816 AGCAAACTCA
* **
35477826 TTTCATAATTCGATAGTCGAAGCTATCTAT
1 TTTCATAATTTGATAGTCGAAGCTATCCCT
*
35477856 TTTCATAATTTGATAGCCGAAGCTATCCCT
1 TTTCATAATTTGATAGTCGAAGCTATCCCT
* * * * * *
35477886 TTACATAGTTTGATGGTCGTCA-CCATCTCT
1 TTTCATAATTTGATAGTCG-AAGCTATCCCT
35477916 TTTCATAATTTGATAGTCGAAGCTATCCCT
1 TTTCATAATTTGATAGTCGAAGCTATCCCT
** * * *
35477946 TTTCATTGTTTGATGGTCGTCA-CCATCCCT
1 TTTCATAATTTGATAGTCG-AAGCTATCCCT
35477976 TTTCATAATTTGATAGTCGAAGCTATCCCT
1 TTTCATAATTTGATAGTCGAAGCTATCCCT
35478006 TT
1 TT
35478008 CCAGTAGTCG
Statistics
Matches: 121, Mismatches: 27, Indels: 8
0.78 0.17 0.05
Matches are distributed among these distances:
29 2 0.02
30 117 0.97
31 2 0.02
ACGTcount: A:0.24, C:0.21, G:0.14, T:0.41
Consensus pattern (30 bp):
TTTCATAATTTGATAGTCGAAGCTATCCCT
Found at i:35477926 original size:60 final size:60
Alignment explanation
Indices: 35477850--35478007 Score: 271
Period size: 60 Copynumber: 2.6 Consensus size: 60
35477840 AGTCGAAGCT
* *
35477850 ATCTATTTTCATAATTTGATAGCCGAAGCTATCCCTTTACATAGTTTGATGGTCGTCACC
1 ATCTCTTTTCATAATTTGATAGTCGAAGCTATCCCTTTACATAGTTTGATGGTCGTCACC
* *
35477910 ATCTCTTTTCATAATTTGATAGTCGAAGCTATCCCTTTTCATTGTTTGATGGTCGTCACC
1 ATCTCTTTTCATAATTTGATAGTCGAAGCTATCCCTTTACATAGTTTGATGGTCGTCACC
*
35477970 ATCCCTTTTCATAATTTGATAGTCGAAGCTATCCCTTT
1 ATCTCTTTTCATAATTTGATAGTCGAAGCTATCCCTTT
35478008 CCAGTAGTCG
Statistics
Matches: 93, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
60 93 1.00
ACGTcount: A:0.23, C:0.22, G:0.14, T:0.41
Consensus pattern (60 bp):
ATCTCTTTTCATAATTTGATAGTCGAAGCTATCCCTTTACATAGTTTGATGGTCGTCACC
Found at i:35479947 original size:25 final size:25
Alignment explanation
Indices: 35479890--35479948 Score: 100
Period size: 25 Copynumber: 2.4 Consensus size: 25
35479880 ACGAGGTCCC
35479890 CTCGAGCTCCCCATTGGACCAATTA
1 CTCGAGCTCCCCATTGGACCAATTA
*
35479915 CTCAAGCTCCCCATTGGACCAATTA
1 CTCGAGCTCCCCATTGGACCAATTA
*
35479940 CTTGAGCTC
1 CTCGAGCTC
35479949 GAGCTAAACA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.24, C:0.36, G:0.15, T:0.25
Consensus pattern (25 bp):
CTCGAGCTCCCCATTGGACCAATTA
Found at i:35480127 original size:18 final size:19
Alignment explanation
Indices: 35480104--35480139 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
35480094 CTTGAACATC
35480104 TTAATTAT-TTTAGCTCAT
1 TTAATTATGTTTAGCTCAT
*
35480122 TTAATTTTGTTTAGCTCA
1 TTAATTATGTTTAGCTCA
35480140 ATACAGCTTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.25, C:0.11, G:0.08, T:0.56
Consensus pattern (19 bp):
TTAATTATGTTTAGCTCAT
Found at i:35492299 original size:28 final size:28
Alignment explanation
Indices: 35492267--35492321 Score: 92
Period size: 28 Copynumber: 2.0 Consensus size: 28
35492257 CTAAAGAATG
*
35492267 TATTAACCGAAATTTATTCTGAATTGGT
1 TATTAACAGAAATTTATTCTGAATTGGT
*
35492295 TATTAACAGGAATTTATTCTGAATTGG
1 TATTAACAGAAATTTATTCTGAATTGG
35492322 CTTCTTTAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.33, C:0.09, G:0.16, T:0.42
Consensus pattern (28 bp):
TATTAACAGAAATTTATTCTGAATTGGT
Found at i:35495648 original size:25 final size:25
Alignment explanation
Indices: 35495620--35495763 Score: 173
Period size: 25 Copynumber: 5.8 Consensus size: 25
35495610 TTTCCGACCC
*
35495620 ACAGCTCGTGAGAGAATACCGATTT
1 ACAGCTCGTGAGAGCATACCGATTT
* * *
35495645 ACAGCTCATGAGAGCATACCAATCT
1 ACAGCTCGTGAGAGCATACCGATTT
*
35495670 ACAGCTCGTGTGAGCATACCGATTT
1 ACAGCTCGTGAGAGCATACCGATTT
* * *
35495695 ATAGCTCATGAGAGCATACCGATCT
1 ACAGCTCGTGAGAGCATACCGATTT
* * *
35495720 ACAGCTCGGGTGAGCATACCGATTC
1 ACAGCTCGTGAGAGCATACCGATTT
35495745 ACAGCTCGT-ATGAGCATAC
1 ACAGCTCGTGA-GAGCATAC
35495764 ATGTACATGA
Statistics
Matches: 98, Mismatches: 20, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
25 98 1.00
ACGTcount: A:0.30, C:0.25, G:0.22, T:0.23
Consensus pattern (25 bp):
ACAGCTCGTGAGAGCATACCGATTT
Found at i:35495749 original size:75 final size:75
Alignment explanation
Indices: 35495622--35495763 Score: 196
Period size: 75 Copynumber: 1.9 Consensus size: 75
35495612 TCCGACCCAC
* * * *
35495622 AGCTCGTGAGAGAATACCGATTTACAGCTCATGAGAGCATACCAATCTACAGCTCGTGTGAGCAT
1 AGCTCATGAGAGAATACCGATCTACAGCTCAGGAGAGCATACCAATCTACAGCTCGTATGAGCAT
35495687 ACCGATTTAT
66 ACCGATTTAT
* * * *
35495697 AGCTCATGAGAGCATACCGATCTACAGCTCGGGTGAGCATACCGAT-TCACAGCTCGTATGAGCA
1 AGCTCATGAGAGAATACCGATCTACAGCTCAGGAGAGCATACCAATCT-ACAGCTCGTATGAGCA
35495761 TAC
65 TAC
35495764 ATGTACATGA
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
74 1 0.02
75 57 0.98
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (75 bp):
AGCTCATGAGAGAATACCGATCTACAGCTCAGGAGAGCATACCAATCTACAGCTCGTATGAGCAT
ACCGATTTAT
Found at i:35495763 original size:50 final size:50
Alignment explanation
Indices: 35495620--35495751 Score: 210
Period size: 50 Copynumber: 2.6 Consensus size: 50
35495610 TTTCCGACCC
* *
35495620 ACAGCTCGTGAGAGAATACCGATTTACAGCTCATGAGAGCATACCAATCT
1 ACAGCTCGTGTGAGCATACCGATTTACAGCTCATGAGAGCATACCAATCT
* *
35495670 ACAGCTCGTGTGAGCATACCGATTTATAGCTCATGAGAGCATACCGATCT
1 ACAGCTCGTGTGAGCATACCGATTTACAGCTCATGAGAGCATACCAATCT
* *
35495720 ACAGCTCGGGTGAGCATACCGATTCACAGCTC
1 ACAGCTCGTGTGAGCATACCGATTTACAGCTC
35495752 GTATGAGCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 75 1.00
ACGTcount: A:0.30, C:0.26, G:0.22, T:0.23
Consensus pattern (50 bp):
ACAGCTCGTGTGAGCATACCGATTTACAGCTCATGAGAGCATACCAATCT
Found at i:35498005 original size:3 final size:3
Alignment explanation
Indices: 35497993--35498028 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
35497983 TTCAACATAA
35497993 TAT T-T TAT TAT TAT T-T TAT TAT TAT T-T TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
35498029 CATAATAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.20
3 24 0.80
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (3 bp):
TAT
Found at i:35498007 original size:11 final size:11
Alignment explanation
Indices: 35497993--35498028 Score: 72
Period size: 11 Copynumber: 3.3 Consensus size: 11
35497983 TTCAACATAA
35497993 TATTTTATTAT
1 TATTTTATTAT
35498004 TATTTTATTAT
1 TATTTTATTAT
35498015 TATTTTATTAT
1 TATTTTATTAT
35498026 TAT
1 TAT
35498029 CATAATAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:35500931 original size:19 final size:19
Alignment explanation
Indices: 35500907--35500944 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
35500897 TCCATTGCAA
35500907 ATGTGTTTTGAAAACTAAG
1 ATGTGTTTTGAAAACTAAG
35500926 ATGTGTTTTGAAAACTAAG
1 ATGTGTTTTGAAAACTAAG
35500945 TTATAATACA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.37, C:0.05, G:0.21, T:0.37
Consensus pattern (19 bp):
ATGTGTTTTGAAAACTAAG
Found at i:35502923 original size:20 final size:19
Alignment explanation
Indices: 35502894--35502967 Score: 87
Period size: 20 Copynumber: 3.7 Consensus size: 19
35502884 AGCTAATAAC
35502894 GAGCTCAATGAGCTGAATT
1 GAGCTCAATGAGCTGAATT
35502913 GAGCTCGAATGAGCTGACA-T
1 GAGCTC-AATGAGCTGA-ATT
* *
35502933 GAGCTTGAATGAGCTGACTT
1 GAGC-TCAATGAGCTGAATT
35502953 GAGCTCAAGTGAGCT
1 GAGCTCAA-TGAGCT
35502968 AAACCAAGGA
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
19 9 0.19
20 36 0.77
21 2 0.04
ACGTcount: A:0.28, C:0.18, G:0.30, T:0.24
Consensus pattern (19 bp):
GAGCTCAATGAGCTGAATT
Found at i:35502957 original size:10 final size:9
Alignment explanation
Indices: 35502894--35502949 Score: 67
Period size: 10 Copynumber: 5.8 Consensus size: 9
35502884 AGCTAATAAC
*
35502894 GAGCTCAAT
1 GAGCTGAAT
35502903 GAGCTGAATT
1 GAGCTGAA-T
35502913 GAGCTCGAAT
1 GAGCT-GAAT
35502923 GAGCTGACAT
1 GAGCTGA-AT
35502933 GAGCTTGAAT
1 GAGC-TGAAT
35502943 GAGCTGA
1 GAGCTGA
35502950 CTTGAGCTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
9 12 0.29
10 24 0.57
11 6 0.14
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.23
Consensus pattern (9 bp):
GAGCTGAAT
Found at i:35505633 original size:30 final size:30
Alignment explanation
Indices: 35505593--35505653 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
35505583 GCCTTCCCTT
*
35505593 CCCATTATTGGTGCTTAAAGGGAAGGATAA
1 CCCATGATTGGTGCTTAAAGGGAAGGATAA
35505623 CCCATGATTGGTGCTTAAAGGGAAGGATAA
1 CCCATGATTGGTGCTTAAAGGGAAGGATAA
35505653 C
1 C
35505654 GACTTGTGTA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.15, G:0.28, T:0.25
Consensus pattern (30 bp):
CCCATGATTGGTGCTTAAAGGGAAGGATAA
Found at i:35507627 original size:39 final size:39
Alignment explanation
Indices: 35507584--35507691 Score: 144
Period size: 39 Copynumber: 2.8 Consensus size: 39
35507574 ACAGAGGTAT
*
35507584 ATTTTGCTGAAAACTGCTTGAGCGAGAATAGGGAGATGG
1 ATTTTGCTGAAAACTGCTTGAGCGAGAATACGGAGATGG
* ** **
35507623 ATTTTGCTTAAAACTGCCGGATTGAGAATACGGAGATGG
1 ATTTTGCTGAAAACTGCTTGAGCGAGAATACGGAGATGG
**
35507662 ATCCTGCTGAAAACTGCTTGAGCGAGAATA
1 ATTTTGCTGAAAACTGCTTGAGCGAGAATA
35507692 AGACTTCGGG
Statistics
Matches: 56, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
39 56 1.00
ACGTcount: A:0.31, C:0.14, G:0.29, T:0.26
Consensus pattern (39 bp):
ATTTTGCTGAAAACTGCTTGAGCGAGAATACGGAGATGG
Found at i:35517893 original size:13 final size:13
Alignment explanation
Indices: 35517875--35517927 Score: 61
Period size: 13 Copynumber: 4.1 Consensus size: 13
35517865 AGTTCTTCAT
35517875 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
*
35517888 TGCTTTTGAAAAA
1 TGCTTTTGAAAAG
* ** *
35517901 TACGGTGGAAAAG
1 TGCTTTTGAAAAG
35517914 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
35517927 T
1 T
35517928 TTGGTTTAAA
Statistics
Matches: 30, Mismatches: 10, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.34
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:35525680 original size:17 final size:17
Alignment explanation
Indices: 35525654--35525687 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
35525644 GCCATATGGG
35525654 ATACTGCTCATTTTGGT
1 ATACTGCTCATTTTGGT
*
35525671 ATACTTCTCATTTTGGT
1 ATACTGCTCATTTTGGT
35525688 TTTGGGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (17 bp):
ATACTGCTCATTTTGGT
Found at i:35527164 original size:26 final size:26
Alignment explanation
Indices: 35527123--35527208 Score: 100
Period size: 26 Copynumber: 3.3 Consensus size: 26
35527113 TGTAGTTGTG
* *
35527123 GCTTTGCCACATATACTGTTACTGGTA
1 GCTTTGCCACA-ATACTATTACTGGCA
* *
35527150 GCTTTGCTACAATACTAATACTGGCA
1 GCTTTGCCACAATACTATTACTGGCA
* * *
35527176 GCTTCGCCGCGATACTATTACTGGCA
1 GCTTTGCCACAATACTATTACTGGCA
35527202 GCTTTGC
1 GCTTTGC
35527209 TGCGATATTG
Statistics
Matches: 49, Mismatches: 10, Indels: 1
0.82 0.17 0.02
Matches are distributed among these distances:
26 39 0.80
27 10 0.20
ACGTcount: A:0.22, C:0.26, G:0.20, T:0.33
Consensus pattern (26 bp):
GCTTTGCCACAATACTATTACTGGCA
Found at i:35527338 original size:33 final size:33
Alignment explanation
Indices: 35527289--35527373 Score: 125
Period size: 33 Copynumber: 2.6 Consensus size: 33
35527279 GTTGTATTAT
* *
35527289 CACACTGTACTATTACTGTATTGGGCTAAGGCC
1 CACACTGTACTGTTACTGTATAGGGCTAAGGCC
* * *
35527322 CATACTGTACTGTTACTGAATAGGGCTCAGGCC
1 CACACTGTACTGTTACTGTATAGGGCTAAGGCC
35527355 CACACTGTACTGTTACTGT
1 CACACTGTACTGTTACTGT
35527374 TACTGATAGG
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.21, T:0.31
Consensus pattern (33 bp):
CACACTGTACTGTTACTGTATAGGGCTAAGGCC
Found at i:35535062 original size:9 final size:9
Alignment explanation
Indices: 35535048--35535073 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
35535038 TAAAAATATT
35535048 CTATTTCAC
1 CTATTTCAC
35535057 CTATTTCAC
1 CTATTTCAC
35535066 CTATTTCA
1 CTATTTCA
35535074 TGTCCATTTT
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:0.23, C:0.31, G:0.00, T:0.46
Consensus pattern (9 bp):
CTATTTCAC
Found at i:35549264 original size:16 final size:16
Alignment explanation
Indices: 35549243--35549276 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
35549233 AACCTCCTTC
35549243 GGCTTGTGTGTTCATT
1 GGCTTGTGTGTTCATT
35549259 GGCTTGTGTGTTCATT
1 GGCTTGTGTGTTCATT
35549275 GG
1 GG
35549277 TTTTGGGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.06, C:0.12, G:0.35, T:0.47
Consensus pattern (16 bp):
GGCTTGTGTGTTCATT
Found at i:35549761 original size:13 final size:13
Alignment explanation
Indices: 35549743--35549768 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35549733 AACTTAGCCG
35549743 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
35549756 TTCCTTCTGTTTC
1 TTCCTTCTGTTTC
35549769 AGTTTAGCTG
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:0.00, C:0.31, G:0.08, T:0.62
Consensus pattern (13 bp):
TTCCTTCTGTTTC
Found at i:35557050 original size:18 final size:17
Alignment explanation
Indices: 35557022--35557056 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
35557012 ATTATTAAGA
*
35557022 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
35557039 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
35557057 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:35557301 original size:45 final size:40
Alignment explanation
Indices: 35557202--35557311 Score: 105
Period size: 45 Copynumber: 2.6 Consensus size: 40
35557192 TTTTCCATTA
35557202 TGCTATTACACCTCTATTCCATT-CAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACAACCAAACACAAGAT
* * ***
35557241 TACTATTACGCCTCTATTCCATTACATTCAGCCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACA---A-CCAAACACAAGA-T
* *
35557286 TGCTATTACACCTCTAATCCAATACA
1 TGCTATTACACCTCTATTCCATTACA
35557312 CCTCTAATCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 21 0.38
40 2 0.04
43 1 0.02
44 9 0.16
45 23 0.41
ACGTcount: A:0.33, C:0.29, G:0.06, T:0.32
Consensus pattern (40 bp):
TGCTATTACACCTCTATTCCATTACAACCAAACACAAGAT
Found at i:35557313 original size:16 final size:16
Alignment explanation
Indices: 35557292--35557327 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
35557282 GATTTGCTAT
35557292 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35557308 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
35557324 TACA
1 TACA
35557328 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.39, C:0.36, G:0.00, T:0.25
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:35563284 original size:13 final size:13
Alignment explanation
Indices: 35563266--35563307 Score: 57
Period size: 13 Copynumber: 3.0 Consensus size: 13
35563256 TATTCTGCAT
35563266 TTAAACAACAGCA
1 TTAAACAACAGCA
35563279 TTAAACAACAGCAGCA
1 TTAAAC-A-A-CAGCA
35563295 TTAAACAACAGCA
1 TTAAACAACAGCA
35563308 GCAAAACACA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
13 11 0.42
14 2 0.08
15 2 0.08
16 11 0.42
ACGTcount: A:0.52, C:0.24, G:0.10, T:0.14
Consensus pattern (13 bp):
TTAAACAACAGCA
Found at i:35563293 original size:16 final size:16
Alignment explanation
Indices: 35563269--35563310 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
35563259 TCTGCATTTA
*
35563269 AACAACAGCATTAAAC
1 AACAGCAGCATTAAAC
35563285 AACAGCAGCATTAAAC
1 AACAGCAGCATTAAAC
35563301 AACAGCAGCA
1 AACAGCAGCA
35563311 AAACACATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.52, C:0.26, G:0.12, T:0.10
Consensus pattern (16 bp):
AACAGCAGCATTAAAC
Found at i:35566501 original size:43 final size:43
Alignment explanation
Indices: 35566421--35566504 Score: 105
Period size: 43 Copynumber: 2.0 Consensus size: 43
35566411 CTGGATAATC
* * * *
35566421 ATACTGGCACATACCGTGCATCACCGGGTATACCGAAGCATCT
1 ATACTGGCACACACAGTGCATCACCGGATAAACCGAAGCATCT
* * *
35566464 ATACTGGCACACACAGTGTATCATCGGATAAATCGAAGCAT
1 ATACTGGCACACACAGTGCATCACCGGATAAACCGAAGCAT
35566505 AACCTGTACA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
43 34 1.00
ACGTcount: A:0.32, C:0.26, G:0.20, T:0.21
Consensus pattern (43 bp):
ATACTGGCACACACAGTGCATCACCGGATAAACCGAAGCATCT
Found at i:35568037 original size:22 final size:22
Alignment explanation
Indices: 35568008--35568052 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
35567998 AAAATGGATT
35568008 AAAAAATA-ATTCAAAAAATTA
1 AAAAAATATATTCAAAAAATTA
*
35568029 AAAATAATATTTTCAAAAAATTA
1 AAAA-AATATATTCAAAAAATTA
35568052 A
1 A
35568053 TTTTAAAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 4 0.19
22 4 0.19
23 13 0.62
ACGTcount: A:0.67, C:0.04, G:0.00, T:0.29
Consensus pattern (22 bp):
AAAAAATATATTCAAAAAATTA
Found at i:35575490 original size:120 final size:120
Alignment explanation
Indices: 35575347--35575584 Score: 386
Period size: 120 Copynumber: 2.0 Consensus size: 120
35575337 TCTAACATCT
* * * *
35575347 TCCACTAACTCATATATGGGCTAATTACCATATAAGGACCTTCACTTTAAAGTTCTATAGCTATT
1 TCCACTAACTCATATATGGGCTAATTACAATAAAAGAACCTTCACTTTAAAGTTCTATAGCTATG
*
35575412 ATACACCTTTAACTATTAGAACCCAACTTTTGCACTTTACGCGATTTAGTCCTCC
66 AGACACCTTTAACTATTAGAACCCAACTTTTGCACTTTACGCGATTTAGTCCTCC
* * *
35575467 TCCACTGACTCATTTATGGGCTAATTACAATAAAAGAACCTTCACTTTAAAGTTCTATAGCTGTG
1 TCCACTAACTCATATATGGGCTAATTACAATAAAAGAACCTTCACTTTAAAGTTCTATAGCTATG
* *
35575532 AGACACCTTTAGCTATTAGAACCTAACTTTTGCACTTTACGCGATTTAGTCCT
66 AGACACCTTTAACTATTAGAACCCAACTTTTGCACTTTACGCGATTTAGTCCT
35575585 TTTATCAAAA
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
120 108 1.00
ACGTcount: A:0.30, C:0.24, G:0.12, T:0.35
Consensus pattern (120 bp):
TCCACTAACTCATATATGGGCTAATTACAATAAAAGAACCTTCACTTTAAAGTTCTATAGCTATG
AGACACCTTTAACTATTAGAACCCAACTTTTGCACTTTACGCGATTTAGTCCTCC
Found at i:35588069 original size:106 final size:106
Alignment explanation
Indices: 35587869--35588088 Score: 334
Period size: 106 Copynumber: 2.1 Consensus size: 106
35587859 ACGGTGAAGC
* * *
35587869 CACACACCCATGTGCTAGGCTGTGTGAGGTTACCTAAATGCTTGCTTTAGAAGTTACAGTGGACA
1 CACACGCCCATGTGCTAGGCCGTGTGAGGTTACCTAAATGCTTGCTTTAGAAGTTACAGGGGACA
* *
35587934 CTCAACCATGTCCCCTAGCAGTGTGTCACACAATG-CTGAGA
66 CGCAACCATGTCCCCTAGCAGTGTATCACAC-ATGACTGAGA
*
35587975 CACACGCCCATGTGCTAGGCCGTGTGAGGTTACCTATATGCTTGCTTTAGAAGTTACAGGGGACA
1 CACACGCCCATGTGCTAGGCCGTGTGAGGTTACCTAAATGCTTGCTTTAGAAGTTACAGGGGACA
* * * *
35588040 CGCGACCATGTCTCCTGGCCGTGTATCACACATGACTGAGA
66 CGCAACCATGTCCCCTAGCAGTGTATCACACATGACTGAGA
35588081 CACACGCC
1 CACACGCC
35588089 TGTGTCTCTG
Statistics
Matches: 103, Mismatches: 10, Indels: 2
0.90 0.09 0.02
Matches are distributed among these distances:
105 3 0.03
106 100 0.97
ACGTcount: A:0.25, C:0.27, G:0.24, T:0.24
Consensus pattern (106 bp):
CACACGCCCATGTGCTAGGCCGTGTGAGGTTACCTAAATGCTTGCTTTAGAAGTTACAGGGGACA
CGCAACCATGTCCCCTAGCAGTGTATCACACATGACTGAGA
Found at i:35588509 original size:76 final size:76
Alignment explanation
Indices: 35588383--35588610 Score: 456
Period size: 76 Copynumber: 3.0 Consensus size: 76
35588373 CATATCTCAA
35588383 TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
1 TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
35588448 AACATAAGGCC
66 AACATAAGGCC
35588459 TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
1 TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
35588524 AACATAAGGCC
66 AACATAAGGCC
35588535 TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
1 TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
35588600 AACATAAGGCC
66 AACATAAGGCC
35588611 AATTACACAT
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
76 152 1.00
ACGTcount: A:0.41, C:0.25, G:0.09, T:0.25
Consensus pattern (76 bp):
TTTCAACCATTTGGTCATCACAATAACAATTCACAAGGCATTCACATAGCAATATATCAACACAT
AACATAAGGCC
Found at i:35594819 original size:23 final size:22
Alignment explanation
Indices: 35594776--35594819 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 22
35594766 TTCTAAATCG
35594776 ATATTCAATTCAATTCCACACCT
1 ATATTCAATTCAATT-CACACCT
35594799 ATATTCATTATTCAATT-ACAC
1 ATATTCA--ATTCAATTCACAC
35594820 TTAGTCAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
23 11 0.58
25 8 0.42
ACGTcount: A:0.36, C:0.25, G:0.00, T:0.39
Consensus pattern (22 bp):
ATATTCAATTCAATTCACACCT
Found at i:35594928 original size:45 final size:45
Alignment explanation
Indices: 35594864--35594957 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
35594854 AACAGATACT
* *
35594864 CGGTGGAATCAGCACATAGCAACCACCTTATTAATCCATGATGTC
1 CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
* *
35594909 CGGTGGAA-CTAGCACATAGCAACCACTTTACTAATCAATGATGTT
1 CGGTGGAATC-AGCACATAGCAACCACCTTACTAATCAATGATGTC
35594954 CGGT
1 CGGT
35594958 TCACATAGTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
44 1 0.02
45 43 0.98
ACGTcount: A:0.31, C:0.24, G:0.19, T:0.26
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTC
Found at i:35595026 original size:51 final size:49
Alignment explanation
Indices: 35594963--35595096 Score: 162
Period size: 50 Copynumber: 2.7 Consensus size: 49
35594953 TCGGTTCACA
* *
35594963 TAGTAGCTTGCACATAGTACTACACATGTGATCATTACCA-TTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGA-C-CTACCATTTCG-TACACG
* *
35595014 TAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTTTCGTACACG
1 TAGTAGCCTGCACATAGTACTACACATGTGACCTACCA-TTTCGTACACG
* * *
35595064 TAGTAGCCTACACATAGTACTAAACACGTGACC
1 TAGTAGCCTGCACATAGTACTACACATGTGACC
35595097 ATCACTTTCA
Statistics
Matches: 73, Mismatches: 8, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
49 4 0.05
50 36 0.49
51 33 0.45
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (49 bp):
TAGTAGCCTGCACATAGTACTACACATGTGACCTACCATTTCGTACACG
Found at i:35595078 original size:50 final size:51
Alignment explanation
Indices: 35594963--35595085 Score: 162
Period size: 51 Copynumber: 2.4 Consensus size: 51
35594953 TCGGTTCACA
* * *
35594963 TAGTAGCTTGCACATAGTACTACACATGTGATCATTACCATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGATCACTACCATTCGATACACG
*
35595014 TAGTAGCCTGCACATAGTACTACACATGCGA-C-CTATCATTTTCG-TACACG
1 TAGTAGCCTGCACATAGTACTACACATGCGATCACTACCA--TTCGATACACG
*
35595064 TAGTAGCCTACACATAGTACTA
1 TAGTAGCCTGCACATAGTACTA
35595086 AACACGTGAC
Statistics
Matches: 65, Mismatches: 5, Indels: 5
0.87 0.07 0.07
Matches are distributed among these distances:
49 4 0.06
50 28 0.43
51 33 0.51
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (51 bp):
TAGTAGCCTGCACATAGTACTACACATGCGATCACTACCATTCGATACACG
Found at i:35605128 original size:22 final size:22
Alignment explanation
Indices: 35605103--35605244 Score: 203
Period size: 22 Copynumber: 6.5 Consensus size: 22
35605093 AGAACTTGCA
*
35605103 CTTAGTACGTGAAACATGAGAG
1 CTTAGTACGTTAAACATGAGAG
**
35605125 CTTAGTACGTTAGCCATGAGAG
1 CTTAGTACGTTAAACATGAGAG
** *
35605147 CTTAGTACGTTAGCCATGAGGG
1 CTTAGTACGTTAAACATGAGAG
* *
35605169 TTTAGTTCGTTAAACATGAGAG
1 CTTAGTACGTTAAACATGAGAG
35605191 CTTAGTACGTTAAACATGAGAG
1 CTTAGTACGTTAAACATGAGAG
*
35605213 CTTAGTACGTGAAACATGAGAG
1 CTTAGTACGTTAAACATGAGAG
35605235 CTTAGTACGT
1 CTTAGTACGT
35605245 ACTATCAAGA
Statistics
Matches: 108, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 108 1.00
ACGTcount: A:0.31, C:0.15, G:0.26, T:0.28
Consensus pattern (22 bp):
CTTAGTACGTTAAACATGAGAG
Found at i:35605812 original size:52 final size:52
Alignment explanation
Indices: 35605742--35605842 Score: 166
Period size: 52 Copynumber: 1.9 Consensus size: 52
35605732 CATGCACATA
* * * *
35605742 TTTGAGCTTTAACTGAGCTAGAAATGAGGTCTTAAGCTGCTGTCTATTATTG
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
35605794 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
1 TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTA
35605843 CGTTTCCTTA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 45 1.00
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.35
Consensus pattern (52 bp):
TTTGAGCTTCAACCGAGCTAGAAATGAGATCTTAAGCTGCTGTCCATTATTG
Found at i:35608641 original size:45 final size:45
Alignment explanation
Indices: 35608590--35608680 Score: 146
Period size: 45 Copynumber: 2.0 Consensus size: 45
35608580 TAATAGATAC
* *
35608590 TCGGTGGATTCAGCACATAGAAACCACCTTATTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGT
* *
35608635 TCGGTGGAATCAGCACATAGCAACCACTTTACTAATCAATGATGT
1 TCGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGT
35608680 T
1 T
35608681 TGGTTCACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.18, T:0.29
Consensus pattern (45 bp):
TCGGTGGAATCAGCACATAGAAACCACCTTACTAATCAATGATGT
Found at i:35608748 original size:51 final size:50
Alignment explanation
Indices: 35608690--35608876 Score: 232
Period size: 51 Copynumber: 3.7 Consensus size: 50
35608680 TTGGTTCACA
*
35608690 TAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCA-TACCATTCGATACACG
** * * * *
35608741 TAGTAGCCTGCACATAGTACTACACACGTGATTGAAACTATTCGATACGCA
1 TAGTAGCCTGCACATAGTACTACACACGTGA-CCATACCATTCGATACACG
* * * * *
35608792 TAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTTGGGTACACG
1 TAGTAGCCTGCACATAGTACTACACACGTGACCATACCA-TTCGATACACG
35608842 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 TAGTAGCCTGCACATAGTACTACACACGTGACCAT
35608877 CATTTTCACT
Statistics
Matches: 113, Mismatches: 20, Indels: 6
0.81 0.14 0.04
Matches are distributed among these distances:
49 2 0.02
50 38 0.34
51 72 0.64
52 1 0.01
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (50 bp):
TAGTAGCCTGCACATAGTACTACACACGTGACCATACCATTCGATACACG
Found at i:35608865 original size:101 final size:101
Alignment explanation
Indices: 35608688--35608872 Score: 309
Period size: 101 Copynumber: 1.8 Consensus size: 101
35608678 GTTTGGTTCA
*
35608688 CATAGTAGCCTGCACATAGTACTACACATGTGACCATTACCATTCGATACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCA-TACCATTCGATACACGTAGTAGCCTGCA
35608753 CATAGTACTACACACGTGATTGAAACTATTCGATACG
65 CATAGTACTACACACGTGATTGAAACTATTCGATACG
* * *
35608790 CATAGTAGCCTGCACATAGTACTACACATGCGACC-TATCATTTGGGTACACGTAGTAGCCTGCA
1 CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCA-TTCGATACACGTAGTAGCCTGCA
35608854 CATAGTACTACACACGTGA
65 CATAGTACTACACACGTGA
35608873 CCATCATTTT
Statistics
Matches: 78, Mismatches: 4, Indels: 3
0.92 0.05 0.04
Matches are distributed among these distances:
100 4 0.05
101 40 0.51
102 34 0.44
ACGTcount: A:0.31, C:0.26, G:0.18, T:0.25
Consensus pattern (101 bp):
CATAGTAGCCTGCACATAGTACTACACATGCGACCATACCATTCGATACACGTAGTAGCCTGCAC
ATAGTACTACACACGTGATTGAAACTATTCGATACG
Done.