Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 180 of 313
Found at i:55802600 original size:16 final size:16
Alignment explanation
Indices: 55802575--55802605 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55802565 TTTATTTTTA
55802575 GATTTCTTTTAAAATT
1 GATTTCTTTTAAAATT
*
55802591 GATTTTTTTTAAAAT
1 GATTTCTTTTAAAAT
55802606 ACAATAAAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.58
Consensus pattern (16 bp):
GATTTCTTTTAAAATT
Found at i:55806960 original size:2 final size:2
Alignment explanation
Indices: 55806953--55806996 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
55806943 TGGGGACTGG
55806953 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
55806995 GA
1 GA
55806997 AAGGGGAGGG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:55811836 original size:23 final size:23
Alignment explanation
Indices: 55811804--55811849 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
55811794 TTTCTCACAA
*
55811804 ACGCCGCTAAAGACCAAGACCTT
1 ACGCCACTAAAGACCAAGACCTT
55811827 ACGCCACTAAAGACCAAGACCTT
1 ACGCCACTAAAGACCAAGACCTT
55811850 TAGTGGCGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.37, C:0.35, G:0.15, T:0.13
Consensus pattern (23 bp):
ACGCCACTAAAGACCAAGACCTT
Found at i:55812272 original size:42 final size:41
Alignment explanation
Indices: 55812203--55812290 Score: 115
Period size: 42 Copynumber: 2.1 Consensus size: 41
55812193 ACATATGCAA
* * * *
55812203 GGTAATAATATACAATGCATTTTCTTAATCAAGTAAATCTT
1 GGTAATAAGATACAATACATTTACTTAATCAAGGAAATCTT
*
55812244 GGTAATAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAAT-AAGATACAATACATTTACTTAATCAAGGAAATCTT
55812286 -GTAAT
1 GGTAAT
55812291 GAACTCAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
41 11 0.27
42 30 0.73
ACGTcount: A:0.42, C:0.10, G:0.11, T:0.36
Consensus pattern (41 bp):
GGTAATAAGATACAATACATTTACTTAATCAAGGAAATCTT
Found at i:55815497 original size:9 final size:9
Alignment explanation
Indices: 55815483--55815509 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
55815473 TTATATATCC
55815483 ATATCAAAT
1 ATATCAAAT
55815492 ATATCAAAT
1 ATATCAAAT
55815501 ATATCAAAT
1 ATATCAAAT
55815510 GATTTAGATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.11, G:0.00, T:0.33
Consensus pattern (9 bp):
ATATCAAAT
Found at i:55815814 original size:21 final size:21
Alignment explanation
Indices: 55815790--55815829 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
55815780 TGAAACCCTA
* *
55815790 AATCCTTAACTCTTAACCCAT
1 AATCCCTAACTCCTAACCCAT
55815811 AATCCCTAACTCCTAACCC
1 AATCCCTAACTCCTAACCC
55815830 CTAAATCTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.28
Consensus pattern (21 bp):
AATCCCTAACTCCTAACCCAT
Found at i:55815887 original size:15 final size:15
Alignment explanation
Indices: 55815852--55815889 Score: 62
Period size: 14 Copynumber: 2.7 Consensus size: 15
55815842 TCACAAACCT
55815852 TAAA-CCATAATCCC
1 TAAATCCATAATCCC
55815866 T-AATCCATAATCCC
1 TAAATCCATAATCCC
55815880 TAAATCCATA
1 TAAATCCATA
55815890 TATAATCCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 2 0.09
14 12 0.55
15 8 0.36
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAATCCATAATCCC
Found at i:55816072 original size:24 final size:24
Alignment explanation
Indices: 55816041--55816100 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
55816031 ATTATATATG
55816041 AAAT-TATTTAATATATAAATTAA
1 AAATATATTTAATATATAAATTAA
*
55816064 AAATATATTTAAAATATAAATTAA
1 AAATATATTTAATATATAAATTAA
* *
55816088 AAAAATAATTAAT
1 AAATATATTTAAT
55816101 CTAAACCCAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
23 4 0.12
24 28 0.88
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (24 bp):
AAATATATTTAATATATAAATTAA
Found at i:55816088 original size:12 final size:12
Alignment explanation
Indices: 55816048--55816089 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
55816038 ATGAAATTAT
*
55816048 TTAATATATAAA
1 TTAAAATATAAA
*
55816060 TTAAAA-ATATAT
1 TTAAAATATA-AA
55816072 TTAAAATATAAA
1 TTAAAATATAAA
55816084 TTAAAA
1 TTAAAA
55816090 AAATAATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
11 3 0.12
12 19 0.76
13 3 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
TTAAAATATAAA
Found at i:55816097 original size:12 final size:12
Alignment explanation
Indices: 55816053--55816099 Score: 51
Period size: 13 Copynumber: 3.8 Consensus size: 12
55816043 ATTATTTAAT
55816053 ATATAAATTAAAA
1 ATAT-AATTAAAA
*
55816066 ATAT-ATTTAAA
1 ATATAATTAAAA
55816077 ATATAAATTAAAA
1 ATAT-AATTAAAA
*
55816090 AAATAATTAA
1 ATATAATTAA
55816100 TCTAAACCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
11 10 0.34
12 6 0.21
13 13 0.45
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (12 bp):
ATATAATTAAAA
Found at i:55816640 original size:41 final size:41
Alignment explanation
Indices: 55816583--55816827 Score: 312
Period size: 41 Copynumber: 5.8 Consensus size: 41
55816573 AAAATGTTTC
*
55816583 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCCAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAAGCAT
*
55816624 TAGCGGCGCTTTTCCAAAAACGCCACTAAAGCCCGCTAAAGCCCCAAGCAA
1 TAGCGGCGCTTTTCC-AAAA----AC----G-CCGCTAAAGCCCCAAGCAT
* *
55816675 TAGCGGCGCTTTCCCAAAAACGCCGCTAAAGACCCAAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAAGCAT
* * *
55816716 TAGCGGCGCTTATCCAAAAACGCCGCTAAATCCCCCAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAAGCAT
55816757 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAG-CCCAAGCAT
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAAGCAT
**
55816797 TAGCGGCGCTTTTTTAAAAACGCCGCTAAAG
1 TAGCGGCGCTTTTCCAAAAACGCCGCTAAAG
55816828 ACCCGAAAGG
Statistics
Matches: 179, Mismatches: 15, Indels: 21
0.83 0.07 0.10
Matches are distributed among these distances:
40 37 0.21
41 97 0.54
42 5 0.03
46 4 0.02
50 5 0.03
51 31 0.17
ACGTcount: A:0.30, C:0.33, G:0.19, T:0.17
Consensus pattern (41 bp):
TAGCGGCGCTTTTCCAAAAACGCCGCTAAAGCCCCAAGCAT
Found at i:55816681 original size:51 final size:51
Alignment explanation
Indices: 55816605--55816705 Score: 166
Period size: 51 Copynumber: 2.0 Consensus size: 51
55816595 TCCAAAAACG
* * *
55816605 CCGCTAAAGCCCCCAGCATTAGCGGCGCTTTTCCAAAAACGCCACTAAAGC
1 CCGCTAAAGCCCCAAGCAATAGCGGCGCTTTCCCAAAAACGCCACTAAAGC
*
55816656 CCGCTAAAGCCCCAAGCAATAGCGGCGCTTTCCCAAAAACGCCGCTAAAG
1 CCGCTAAAGCCCCAAGCAATAGCGGCGCTTTCCCAAAAACGCCACTAAAG
55816706 ACCCAAGCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.31, C:0.37, G:0.19, T:0.14
Consensus pattern (51 bp):
CCGCTAAAGCCCCAAGCAATAGCGGCGCTTTCCCAAAAACGCCACTAAAGC
Found at i:55816922 original size:39 final size:39
Alignment explanation
Indices: 55816879--55816990 Score: 111
Period size: 40 Copynumber: 2.8 Consensus size: 39
55816869 TTGTGGCGTT
*
55816879 TTTTCCATAAACGCCGCTAATGCTCATTTTTAGCGGCAA
1 TTTTCCATAAACGCCGCTAATGCTCATTTTTAGCGACAA
* * * *
55816918 TTTT-CAAAAGACGCCGCTAATGCTCCATCTTTAGTGACGA
1 TTTTCCATAA-ACGCCGCTAATGCT-CATTTTTAGCGACAA
* *
55816958 -TTTCCGTAAAACGCTGCTAATGCTCGATTTTTA
1 TTTTCCAT-AAACGCCGCTAATGCTC-ATTTTTA
55816991 CTGACGTTTT
Statistics
Matches: 59, Mismatches: 9, Indels: 9
0.77 0.12 0.12
Matches are distributed among these distances:
38 4 0.07
39 22 0.37
40 31 0.53
41 2 0.03
ACGTcount: A:0.26, C:0.24, G:0.16, T:0.34
Consensus pattern (39 bp):
TTTTCCATAAACGCCGCTAATGCTCATTTTTAGCGACAA
Found at i:55824812 original size:18 final size:17
Alignment explanation
Indices: 55824789--55824841 Score: 79
Period size: 18 Copynumber: 3.0 Consensus size: 17
55824779 ATATATTATG
*
55824789 ATTTTAGTAAATTCATAT
1 ATTTTATTAAATT-ATAT
55824807 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
55824824 ATTTTTATTAAATTATAT
1 A-TTTTATTAAATTATAT
55824842 TTAATAATAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
17 5 0.15
18 28 0.85
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:55825068 original size:44 final size:46
Alignment explanation
Indices: 55825001--55825093 Score: 154
Period size: 44 Copynumber: 2.1 Consensus size: 46
55824991 TTACACATCT
*
55825001 ATTCCATTCAACCAAACACAAGAA-TA-CAATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCAATTACGCCTCTATTCC
*
55825045 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCAATTACGCCTCTATTCC
55825091 ATT
1 ATT
55825094 ACGCATCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
44 23 0.51
45 2 0.04
46 20 0.44
ACGTcount: A:0.38, C:0.30, G:0.04, T:0.28
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCAATTACGCCTCTATTCC
Found at i:55825096 original size:16 final size:16
Alignment explanation
Indices: 55825075--55825127 Score: 88
Period size: 16 Copynumber: 3.3 Consensus size: 16
55825065 AGAATTACCT
55825075 ATTACGCCTCTATTCC
1 ATTACGCCTCTATTCC
*
55825091 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
55825107 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
55825123 ATTAC
1 ATTAC
55825128 AGCGAACCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.25, C:0.34, G:0.04, T:0.38
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:55829520 original size:13 final size:14
Alignment explanation
Indices: 55829494--55829521 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
55829484 NNNNNNNNNN
55829494 AAAATCACTAAAAA
1 AAAATCACTAAAAA
55829508 AAAATCACTAAAAA
1 AAAATCACTAAAAA
55829522 TAGTAGGATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.71, C:0.14, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATCACTAAAAA
Found at i:55832602 original size:12 final size:11
Alignment explanation
Indices: 55832587--55832631 Score: 54
Period size: 12 Copynumber: 3.8 Consensus size: 11
55832577 AAGTAAAACC
*
55832587 TAATGTAAATAA
1 TAATATAAAT-A
55832599 TAATATAAATA
1 TAATATAAATA
55832610 TAATAATAAATA
1 TAAT-ATAAATA
55832622 TAATAATAAA
1 TAAT-ATAAA
55832632 CCAATTAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
11 5 0.16
12 26 0.84
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.33
Consensus pattern (11 bp):
TAATATAAATA
Found at i:55833046 original size:88 final size:87
Alignment explanation
Indices: 55832950--55833121 Score: 211
Period size: 88 Copynumber: 2.0 Consensus size: 87
55832940 AGGATTATTG
* * * * * *
55832950 GCTTCGATCTGCTTCATTGCCAATACAAGAAAG-CAAGATCTGCTATTTTCAACCTGCTCCGCTG
1 GCTTCGATCTGCTTCACTGCCAATAC-AGAAAGACAAGATCTACAATCTTCAACCTACTCCACTG
55833014 CTGCTCAGGGAGATAAGGCTGGT
65 CTGCTCAGGGAGATAAGGCTGGT
* * ** *
55833037 GCTTCCGATCTGCTTCACTGCCAGTACAGGAAGACAAGATCTACAATCTTGGACCTACTCCATTG
1 GCTT-CGATCTGCTTCACTGCCAATACAGAAAGACAAGATCTACAATCTTCAACCTACTCCACTG
*
55833102 TTGCTCAGGGAGATAAGGCT
65 CTGCTCAGGGAGATAAGGCT
55833122 AGTGGCTTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
87 9 0.13
88 62 0.87
ACGTcount: A:0.25, C:0.26, G:0.23, T:0.27
Consensus pattern (87 bp):
GCTTCGATCTGCTTCACTGCCAATACAGAAAGACAAGATCTACAATCTTCAACCTACTCCACTGC
TGCTCAGGGAGATAAGGCTGGT
Found at i:55833229 original size:132 final size:132
Alignment explanation
Indices: 55833089--55833779 Score: 999
Period size: 132 Copynumber: 5.2 Consensus size: 132
55833079 ACAATCTTGG
* * * * * *
55833089 ACCTACTCCATTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTGCTGTCTTAG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* *
55833154 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
55833219 CA
131 CA
* * * * *
55833221 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTTCGTACTACCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * *
55833286 GAAGATAAAA-TCGCTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
55833350 CA
131 CA
* * * * *
55833352 ACCTACTCCACTGCTGCTCAAGGAGATAAGGCTGGTGGCCTAAATCTGCTTCTCTATTGCCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * *
55833417 GAAGATAAAATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
55833482 CA
131 CA
* * *
55833484 ACCTACTCCACTACTACTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGTCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * * *
55833549 GAAGATAAAATTTGCCATTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
55833614 CA
131 CA
* * *
55833616 ACCTACTCTAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * *
55833681 GAAGAT-AAGTTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
55833745 CA
131 CA
* * * *
55833747 GCCTACTCCAGTGTTGCTCAAGGAGATAAGGCT
1 ACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
55833780 GGAATCTTCG
Statistics
Matches: 496, Mismatches: 62, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
131 198 0.40
132 298 0.60
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (132 bp):
ACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT
CA
Found at i:55833362 original size:44 final size:44
Alignment explanation
Indices: 55833177--55833645 Score: 167
Period size: 44 Copynumber: 10.7 Consensus size: 44
55833167 GCCGTCTTCG
* *
55833177 ATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATTTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCA
* * * * * * * *
55833221 ACCTACTCCACTGCTGCTCAGGGAGATAAG-GCTAATGA-CTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATTTTCA
* * ** * *
55833264 ATCTGCTTTCGTACTAC--CTT-GGGAAGATAAAATCGCT-GTCTTT-G
1 ATCTGC--TC-CACTACTGCTTAGGG-AGATAAGATCTATAAT-TTTCA
55833308 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCA
* * * * * * * **** *
55833352 ACCTACTCCACTGCTGCTCAAGGAGATAAG-GCTGGT-GGCCTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCT-ATAATTTTCA
* * * * ** * *
55833395 ATCTGCTTCTCTATTGCCTT-GGGAAGATAAAAT-TCACCATCTTCG
1 ATCTGCTCCACTACTG-CTTAGGG-AGATAAGATCT-ATAATTTTCA
*
55833440 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCA
* * * * * *** *
55833484 ACCTACTCCACTACTACTCAGGGAGATAAG-GCTAGT-GGCTTAA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTA-TAATTTTCA
* * *** *
55833527 ATCTGCTTCC-CTACTGTCTT-GGGAAGATAAAATTTGCCATTTTCG
1 ATCTGC-TCCACTACTG-CTTAGGG-AGATAAGATCTATAATTTTCA
* *
55833572 ATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCA
1 ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCA
* * * * * *
55833616 ACCTACTCTAATGCTGCTCAGGGAGATAAG
1 ATCTGCTCCACTACTGCTTAGGGAGATAAG
55833646 GCTGGTGGCT
Statistics
Matches: 293, Mismatches: 104, Indels: 56
0.65 0.23 0.12
Matches are distributed among these distances:
41 5 0.02
42 2 0.01
43 61 0.21
44 180 0.61
45 41 0.14
46 4 0.01
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (44 bp):
ATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCA
Found at i:55833550 original size:263 final size:264
Alignment explanation
Indices: 55833089--55833779 Score: 1003
Period size: 263 Copynumber: 2.6 Consensus size: 264
55833079 ACAATCTTGG
* * * * * * *
55833089 ACCTACTCCATTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTGCTGTCTTAG
1 ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * *
55833154 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTT
* *
55833219 CAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTTCGTACTACCTT
131 CAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTT
** *
55833284 GGGAAGATAAAA-TCGCTGTCTTT-GATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAAT
196 GGGAAGATAAAATTCGCCAT-TTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTATAAT
55833347 TTTCA
260 TTTCA
* * * * *
55833352 ACCTACTCCACTGCTGCTCAAGGAGATAAGGCTGGTGGCCTAAATCTGCTTCTCTATTGCCTTGG
1 ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* *
55833417 GAAGATAAAATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTT
* * * * **
55833482 CAACCTACTCCACTACTACTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGTCTT
131 CAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTT
* *
55833547 GGGAAGATAAAATTTGCCATTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATT
196 GGGAAGATAAAATTCGCCATTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTATAATT
55833612 TTCA
261 TTCA
*
55833616 ACCTACTCTAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
1 ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* *
55833681 GAAGAT-AAGTTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TTGTAATTT
66 GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTT-TAATTT
* * * *
55833744 TCAGCCTACTCCAGTGTTGCTCAAGGAGATAAGGCT
130 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCT
55833780 GGAATCTTCG
Statistics
Matches: 380, Mismatches: 45, Indels: 6
0.88 0.10 0.01
Matches are distributed among these distances:
262 2 0.01
263 266 0.70
264 112 0.29
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (264 bp):
ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
GAAGATAAAATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTT
CAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTT
GGGAAGATAAAATTCGCCATTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTATAATT
TTCA
Found at i:55833846 original size:395 final size:394
Alignment explanation
Indices: 55833105--55833864 Score: 1058
Period size: 395 Copynumber: 1.9 Consensus size: 394
55833095 TCCATTGTTG
* *
55833105 CTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTGCTGTCTTAGGAAGATAAGATTCGCC
1 CTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTACTGTCTTAGGAAGATAAAATTCGCC
* * *
55833170 GTCTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATTTTCAACCTACTCCACTGC
66 ATCTTCGATCTGCTCCACTACTGCCTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCAATGC
* *
55833235 TGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTTCGTACTACCTTGGGAAGATAAAATCGC
131 TGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAAATCGC
*
55833300 TGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTACTCCACTG
196 CGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTACTCCACTG
** * * * ** *
55833365 CTGCTCAAGGAGATAAGGCTGGTGGCCTAAATCTGCTTCTCTATTGCCTTGGGAAGATAAAATTC
261 CTGCTCAAGGAGATAAGGCTGGAAGCCTAAATCTACTTCTCTAGTGAC-TAAGAAGACAAAATTC
* * * *
55833430 ACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTTTAATTTTCAACCTACTCCAC
325 ACCATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGATCTTTAATTTTCAACCTACTCCAC
55833495 TACTA
390 TACTA
* * *
55833500 CTCAGGGAGATAAGGCTAGTGGCTTAAATCTGCTTCCCTACTGTCTTGGGAAGATAAAATTTGCC
1 CTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTACTGTCTTAGGAAGATAAAATTCGCC
* * *
55833565 ATTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTAATTTTCAACCTACTCTAATGC
66 ATCTTCGATCTGCTCCACTACTGCCTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCAATGC
** * * **
55833630 TGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGGGAAGATAAGTTCGC
131 TGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAAATCGC
* * * *
55833695 CGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAGCCTACTCCAGTG
196 CGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTACTCCACTG
* * * ** *
55833760 TTGCTCAAGGAGATAAGGCTGGAATCTTCGATCTACTTCGCTGCTAGT-AC-AAGAAGACAAGA-
261 CTGCTCAAGGAGATAAGGCTGGAAGCCTAAATCTACTT--CT-CTAGTGACTAAGAAGACAAAAT
* *
55833822 TCTGCTATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAG
323 TC-ACCATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAG
55833865 GCTGATTATC
Statistics
Matches: 317, Mismatches: 44, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
394 2 0.01
395 308 0.97
397 3 0.01
398 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (394 bp):
CTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTACTGTCTTAGGAAGATAAAATTCGCC
ATCTTCGATCTGCTCCACTACTGCCTAGAGAGATAAGATCTGTAATTTTCAACCTACTCCAATGC
TGCTCAGGGAGATAAGGCTAATGACTTAAATCTGCTTCCCTACTACCTTGGGAAGATAAAATCGC
CGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTCAACCTACTCCACTG
CTGCTCAAGGAGATAAGGCTGGAAGCCTAAATCTACTTCTCTAGTGACTAAGAAGACAAAATTCA
CCATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAGATCTTTAATTTTCAACCTACTCCACT
ACTA
Found at i:55833864 original size:263 final size:261
Alignment explanation
Indices: 55833089--55833864 Score: 961
Period size: 263 Copynumber: 2.9 Consensus size: 261
55833079 ACAATCTTGG
* * * * * * *
55833089 ACCTACTCCATTGTTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTGATTCCCTGCTGTCTTAG
1 ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* *
55833154 GAAGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCCTAGGGAGATAAGATCTGTAATTTT
66 GAAGATAAG-TTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTT
*
55833219 CAACCTACTCCACTGCTGCTCAGGGAGATAAGGCT-AATGACTTAAATCTGCTTTCG-TACTACC
130 CAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGAAT--CTTAAATCTGC-TTCGCTACTA-G
* * *
55833282 TTGGGAAGATAAAATC-GCTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAA
191 TCGGGAAGATAAAATCTGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAA
55833346 TTTTCA
256 TTTTCA
* * * * *
55833352 ACCTACTCCACTGCTGCTCAAGGAGATAAGGCTGGTGGCCTAAATCTGCTTCTCTATTGCCTTGG
1 ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
* * *
55833417 GAAGATAAAATTCACCATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTT-TAATTT
66 GAAGAT-AAGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGAT-TTGTAATTT
* * * *
55833481 TCAACCTACTCCACTACTACTCAGGGAGATAAGGCT-AGTGGCTTAAATCTGCTTCCCTACT-GT
129 TCAACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGAAT--CTTAAATCTGCTTCGCTACTAGT
* * * * *
55833544 CTTGGGAAGATAAAATTTGCCATTTTCGATCTGCTCCACTACTGCTTAGAGAGATAAGATCTGTA
192 C--GGGAAGATAAAATCTGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATA
55833609 ATTTTCA
255 ATTTTCA
*
55833616 ACCTACTCTAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
1 ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
*
55833681 GAAGATAAGTTCGCCGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTC
66 GAAGATAAGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTC
* * * * ** * * *
55833746 AGCCTACTCCAGTGTTGCTCAAGGAGATAAGGCTGGAATCTTCGATCTACTTCGCTGCTAGTACA
131 AACCTACTCCACTGCTGCTCAGGGAGATAAGGCT-GAATCTTAAATCTGCTTCGCTACTAGT-CG
* * * * * * *
55833811 AGAAGACAAGATCTGCTATCTTCAACCTACTCCACTACTGCTCAGGGAGATAAG
194 GGAAGATAAAATCTGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAG
55833865 GCTGATTATC
Statistics
Matches: 438, Mismatches: 64, Indels: 22
0.84 0.12 0.04
Matches are distributed among these distances:
261 1 0.00
262 5 0.01
263 311 0.71
264 118 0.27
265 3 0.01
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (261 bp):
ACCTACTCCAATGCTGCTCAGGGAGATAAGGCTGGTGGCTTAAATCTGCTTCCCTACTGCCTTGG
GAAGATAAGTTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTC
AACCTACTCCACTGCTGCTCAGGGAGATAAGGCTGAATCTTAAATCTGCTTCGCTACTAGTCGGG
AAGATAAAATCTGCTATCTTCGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTATAATTTTC
A
Found at i:55842898 original size:50 final size:50
Alignment explanation
Indices: 55842720--55842963 Score: 256
Period size: 50 Copynumber: 4.8 Consensus size: 50
55842710 GATCATAACA
* ** * *
55842720 TGCCAAAC-CCATGTCCCAGACATGGTCTTACGTGGGATGTTCTTATATCGG
1 TGCC-AACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* ** * ** * *
55842771 TGCCCATACCATGTCCCAGACATAGTCTTACATGGGATGTTCTTATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* * **
55842822 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* ***
55842872 TGCCAACGCCGTGTCCCAGGTGTGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
55842922 TGCCAACTCCATGTCCCAGACATGGTCTTACATGGGACCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
55842964 TTACCCAAAT
Statistics
Matches: 167, Mismatches: 25, Indels: 3
0.86 0.13 0.02
Matches are distributed among these distances:
50 89 0.53
51 78 0.47
ACGTcount: A:0.19, C:0.30, G:0.23, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:55851155 original size:16 final size:16
Alignment explanation
Indices: 55851131--55851200 Score: 122
Period size: 16 Copynumber: 4.4 Consensus size: 16
55851121 TTTGGTTCGC
*
55851131 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
55851147 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
55851163 TGTAATGGATTAGAGG
1 TGTAATGGATTAGAGG
*
55851179 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
55851195 TGTAAT
1 TGTAAT
55851201 AGCAAATCAA
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 52 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:55851245 original size:45 final size:44
Alignment explanation
Indices: 55851186--55851276 Score: 119
Period size: 44 Copynumber: 2.0 Consensus size: 44
55851176 AGGTGTAATG
*
55851186 GAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAATGCAATA
1 GAATAGAGGCGTAATAG-AAATCAACTGTTTGGTTGAATGCAATA
* *** *
55851231 GAATAGAGGCGTAATAGTAATCTTGTGTTTGGTTGAATGGAATA
1 GAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAATGCAATA
55851275 GA
1 GA
55851277 GGTGCAATAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 24 0.60
45 16 0.40
ACGTcount: A:0.35, C:0.07, G:0.27, T:0.31
Consensus pattern (44 bp):
GAATAGAGGCGTAATAGAAATCAACTGTTTGGTTGAATGCAATA
Found at i:55851451 original size:16 final size:16
Alignment explanation
Indices: 55851414--55851455 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
55851404 TTAATCATAT
*
55851414 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
55851430 TT-AAATATATTATAA
1 TTAAAATATATTATAA
55851445 TTAAAATATAT
1 TTAAAATATAT
55851456 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:55851462 original size:14 final size:15
Alignment explanation
Indices: 55851423--55851464 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
55851413 TTTAAACATA
*
55851423 ATTATTATTAAATAT
1 ATTATAATTAAATAT
55851438 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
55851452 A-TATAATTTAATA
1 ATTATAATTAAATA
55851465 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:55851556 original size:120 final size:120
Alignment explanation
Indices: 55851412--55851772 Score: 625
Period size: 120 Copynumber: 3.0 Consensus size: 120
55851402 ATTTAATCAT
*
55851412 ATTTAAACATAATTATTATTAAATAT-ATTATAATTAAAATATATAATTTAATAAAATTCTTAAT
1 ATTT-AACATAATTATTATTAAATATAATT-TAATAAAAATATATAATTTAATAAAATTCTTAAT
* * * * * *
55851476 AATCAATATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATA
64 ATTAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
55851533 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
55851598 TAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
66 TAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
*
55851653 ATTTAAAATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
1 ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
55851718 TAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
66 TAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
55851773 GATTAATAAT
Statistics
Matches: 231, Mismatches: 8, Indels: 3
0.95 0.03 0.01
Matches are distributed among these distances:
120 224 0.97
121 7 0.03
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (120 bp):
ATTTAACATAATTATTATTAAATATAATTTAATAAAAATATATAATTTAATAAAATTCTTAATAT
TAAATATTCTTATATGAATTTAATAAAATCATAATATATAATACTATATAATATA
Found at i:55851618 original size:38 final size:37
Alignment explanation
Indices: 55851571--55851754 Score: 140
Period size: 37 Copynumber: 4.7 Consensus size: 37
55851561 TTAATAAAAA
*
55851571 TATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAATAAAATTCTTAATATTAAATATTAT
*
55851608 TATATGAATTTAATAAAA-TCATAATA-TATAATACTATAT
1 TATAT-AATTTAATAAAATTCTTAATATTA-AATA-T-TAT
* * * * ** *
55851647 AATATAATTTAAAATAATTATTATTAAATATAATTTAATAAAAA
1 TATATAATTT--AATAA-AATTCTT--A-AT-ATTAAATATTAT
*
55851691 TATATAATTTAATAAAATTCTTAATATTAAATATTCT
1 TATATAATTTAATAAAATTCTTAATATTAAATATTAT
*
55851728 TATATGAATTTAATAAAA-TCATAATAT
1 TATAT-AATTTAATAAAATTCTTAATAT
55851755 ATAATACTAT
Statistics
Matches: 114, Mismatches: 19, Indels: 28
0.71 0.12 0.17
Matches are distributed among these distances:
36 2 0.02
37 36 0.32
38 32 0.28
39 7 0.06
40 5 0.04
41 6 0.05
42 7 0.06
44 11 0.10
45 2 0.02
46 5 0.04
47 1 0.01
ACGTcount: A:0.51, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
TATATAATTTAATAAAATTCTTAATATTAAATATTAT
Found at i:55851720 original size:18 final size:18
Alignment explanation
Indices: 55851554--55851707 Score: 76
Period size: 18 Copynumber: 8.9 Consensus size: 18
55851544 TTATTATTAA
55851554 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
*
55851572 ATATAATTTAATAAAATT
1 ATATAATTTAATAAAAAT
* ****
55851590 CT-TAATATTAAATATTCTT
1 ATATAAT-TT-AATAAAAAT
55851609 ATATGAATTTAAT-AAAAT
1 ATAT-AATTTAATAAAAAT
* * * *
55851627 -CATAATAT-ATAATACT
1 ATATAATTTAATAAAAAT
* *
55851643 ATATAATATAATTTAAAAT
1 ATATAATTTAA-TAAAAAT
* *
55851662 A-ATTA-TT-AT--TAA-
1 ATATAATTTAATAAAAAT
55851674 ATATAATTTAATAAAAAT
1 ATATAATTTAATAAAAAT
55851692 ATATAATTTAATAAAA
1 ATATAATTTAATAAAA
55851708 TTCTTAATAT
Statistics
Matches: 99, Mismatches: 23, Indels: 28
0.66 0.15 0.19
Matches are distributed among these distances:
12 1 0.01
13 5 0.05
14 2 0.02
15 5 0.05
16 8 0.08
17 16 0.16
18 41 0.41
19 15 0.15
20 3 0.03
21 3 0.03
ACGTcount: A:0.55, C:0.03, G:0.01, T:0.42
Consensus pattern (18 bp):
ATATAATTTAATAAAAAT
Found at i:55868008 original size:12 final size:11
Alignment explanation
Indices: 55867993--55868032 Score: 53
Period size: 12 Copynumber: 3.5 Consensus size: 11
55867983 AAGTAAAACC
*
55867993 TAATGTAAATAA
1 TAATATAAAT-A
55868005 TAATATAAATA
1 TAATATAAATA
55868016 TAATAATAAATA
1 TAAT-ATAAATA
55868028 TAATA
1 TAATA
55868033 ATAATAAACC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 6 0.23
12 20 0.77
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (11 bp):
TAATATAAATA
Found at i:55868033 original size:12 final size:12
Alignment explanation
Indices: 55867998--55868036 Score: 62
Period size: 12 Copynumber: 3.2 Consensus size: 12
55867988 AAACCTAATG
55867998 TAAATAATAAT-A
1 TAAAT-ATAATAA
55868010 TAAATATAATAA
1 TAAATATAATAA
55868022 TAAATATAATAA
1 TAAATATAATAA
55868034 TAA
1 TAA
55868037 TAAACCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
11 5 0.19
12 21 0.81
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAATATAATAA
Found at i:55873043 original size:34 final size:33
Alignment explanation
Indices: 55873000--55873080 Score: 101
Period size: 33 Copynumber: 2.4 Consensus size: 33
55872990 TTCTGATATG
*
55873000 ATATGACATTTTGATATT-ATATACGTTCCTGAAA
1 ATATGACATTCTGAT-TTGATATACGTT-CTGAAA
* * *
55873034 ATATGACATTCTGATTTGGTATATGTTTTGAAA
1 ATATGACATTCTGATTTGATATACGTTCTGAAA
55873067 ATATGACATTCTGA
1 ATATGACATTCTGA
55873081 CCTGACATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
33 21 0.50
34 21 0.50
ACGTcount: A:0.33, C:0.10, G:0.15, T:0.42
Consensus pattern (33 bp):
ATATGACATTCTGATTTGATATACGTTCTGAAA
Found at i:55873091 original size:33 final size:33
Alignment explanation
Indices: 55873029--55873094 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
55873019 TATACGTTCC
** **
55873029 TGAAAATATGACATTCTGATTTGGTATATGTTT
1 TGAAAATATGACATTCTGACCTGACATATGTTT
55873062 TGAAAATATGACATTCTGACCTGACATATGTTT
1 TGAAAATATGACATTCTGACCTGACATATGTTT
55873095 CTGTTAATGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.32, C:0.11, G:0.17, T:0.41
Consensus pattern (33 bp):
TGAAAATATGACATTCTGACCTGACATATGTTT
Found at i:55875263 original size:43 final size:43
Alignment explanation
Indices: 55875186--55875275 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
55875176 TAGATGCCGT
* *
55875186 TAAAGAACATGACCTTTAGTGGCTCTTTTATCACAAACGTC-GC
1 TAAAGAACATGACCTTTAGCGACTCTTTTATCACAAACG-CAGC
*
55875229 TAAAGAACATGACCTTTAGCGACGT-TTTTTTCACAAACGCAGC
1 TAAAGAACATGACCTTTAGCGAC-TCTTTTATCACAAACGCAGC
55875272 TAAA
1 TAAA
55875276 AATACCGTTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
42 1 0.02
43 40 0.95
44 1 0.02
ACGTcount: A:0.33, C:0.22, G:0.16, T:0.29
Consensus pattern (43 bp):
TAAAGAACATGACCTTTAGCGACTCTTTTATCACAAACGCAGC
Found at i:55877327 original size:9 final size:9
Alignment explanation
Indices: 55877313--55877403 Score: 71
Period size: 9 Copynumber: 10.1 Consensus size: 9
55877303 GACCAAGATT
55877313 TAAGTTATG
1 TAAGTTATG
55877322 TAAGTTATG
1 TAAGTTATG
55877331 TGAA-TTATG
1 T-AAGTTATG
55877340 TAAGTTGAAT-
1 TAAGTT--ATG
* * *
55877350 TATGATATA
1 TAAGTTATG
55877359 TAAGTTAT-
1 TAAGTTATG
*
55877367 AAAGTTATG
1 TAAGTTATG
*
55877376 TATGTTATG
1 TAAGTTATG
*
55877385 TGAGTTATG
1 TAAGTTATG
*
55877394 TATGTTATG
1 TAAGTTATG
55877403 T
1 T
55877404 GGAAATTAGT
Statistics
Matches: 65, Mismatches: 11, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
8 11 0.17
9 46 0.71
10 6 0.09
11 2 0.03
ACGTcount: A:0.33, C:0.00, G:0.21, T:0.46
Consensus pattern (9 bp):
TAAGTTATG
Found at i:55877585 original size:111 final size:118
Alignment explanation
Indices: 55877460--55877959 Score: 488
Period size: 122 Copynumber: 4.2 Consensus size: 118
55877450 AAATTGAGTA
* * *
55877460 ATTAGTAATGAATTTGAAATATAGGTATTTCA-A-CAT-CT-ATA-A-TTATGTA-TAAAATTTA
1 ATTAGTAATGAATTTGAAATATA-G-ATTACATACCATACTAATATAGTTATATATTAAAATATA
* ** *
55877518 -GATTT-GTATTTAGTATTTCAACATTTATAATTATGTATAAAATTT-AAAAAGTT
64 GGATTTAATATTTAAAATAT-AACATTTATAATTATGTATAAAATTTAAAAAAGTT
55877571 ATTAGTAATGAATTTGAAATATAGATTACATATCCATACTAATATAGGTTATATATTTAAAATAT
1 ATTAGTAATGAATTTGAAATATAGATTACATA-CCATACTAATATA-GTTATATA-TTAAAATAT
* * *
55877636 AGGTTTTAATATTTAAAATATAATATTTATAATTATGTTTAAAATTTAAAAAAAGTT
63 AGGATTTAATATTTAAAATATAACATTTATAATTATGTATAAAATTT-AAAAAAGTT
* * * * *
55877693 ATTAGTAATGAATTTGAAATATATG-TAATATATCCAGACTAATATAGGTGATATATTTAAAAAA
1 ATTAGTAATGAATTTGAAATATA-GATTACATA-CCATACTAATATA-GTTATATA-TTAAAATA
* * ** *
55877757 TAGGTTTTAATATTTAAAAATATAAAATAAATAATTATGTTTAAAATTT-AAAAAGTT
62 TAGGATTTAATATTT-AAAATATAACATTTATAATTATGTATAAAATTTAAAAAAGTT
* * *
55877814 ATTAGTAATGAATTTGAAATACAGGTTATATATCCATACTAATATAGGTTATATATTAAAAATAT
1 ATTAGTAATGAATTTGAAATATAGATTACATA-CCATACTAATATA-GTTATATATT-AAAATAT
* * * * *
55877879 AGG-TTTAAAGTTATTTAAAATATAATAATTATAATTATTTTTAAAATTT-AAAAACTT
63 AGGATTT-AA--TATTTAAAATATAACATTTATAATTATGTATAAAATTTAAAAAAGTT
55877936 ATTAGTAATGAATTTGAAATATAG
1 ATTAGTAATGAATTTGAAATATAG
55877960 GTTATTTATT
Statistics
Matches: 338, Mismatches: 30, Indels: 31
0.85 0.08 0.08
Matches are distributed among these distances:
109 5 0.01
110 2 0.01
111 23 0.07
112 3 0.01
113 2 0.01
114 3 0.01
115 1 0.00
117 6 0.02
119 8 0.02
120 34 0.10
121 77 0.23
122 138 0.41
123 36 0.11
ACGTcount: A:0.46, C:0.03, G:0.09, T:0.42
Consensus pattern (118 bp):
ATTAGTAATGAATTTGAAATATAGATTACATACCATACTAATATAGTTATATATTAAAATATAGG
ATTTAATATTTAAAATATAACATTTATAATTATGTATAAAATTTAAAAAAGTT
Found at i:55877636 original size:20 final size:21
Alignment explanation
Indices: 55877611--55877657 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
55877601 TATCCATACT
55877611 AATATAGGTTAT-ATATTTAA
1 AATATAGGTTATAATATTTAA
*
55877631 AATATAGGTTTTAATATTTAA
1 AATATAGGTTATAATATTTAA
55877652 AATATA
1 AATATA
55877658 ATATTTATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
20 11 0.44
21 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.45
Consensus pattern (21 bp):
AATATAGGTTATAATATTTAA
Found at i:55877761 original size:20 final size:21
Alignment explanation
Indices: 55877736--55877776 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
55877726 CCAGACTAAT
55877736 ATAGGTGAT-ATATTTAAAAA
1 ATAGGTGATAATATTTAAAAA
**
55877756 ATAGGTTTTAATATTTAAAAA
1 ATAGGTGATAATATTTAAAAA
55877777 TATAAAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 7 0.39
21 11 0.61
ACGTcount: A:0.49, C:0.00, G:0.12, T:0.39
Consensus pattern (21 bp):
ATAGGTGATAATATTTAAAAA
Found at i:55877861 original size:121 final size:119
Alignment explanation
Indices: 55877542--55877964 Score: 632
Period size: 122 Copynumber: 3.5 Consensus size: 119
55877532 ATTTCAACAT
* * *
55877542 TTATAATTATGTATAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGATTACATATCCA
1 TTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCA
* *
55877607 TACTAATATAGGTTATATATTTAAAATATAGGTTTTAATATTTAAAATATAATAT
66 TACTAATATAGGTTATATATTTAAAAAATAGGTTTTAATATTTAAAATATAA-AA
* *
55877662 TTATAATTATGTTTAAAATTTAAAAAAAGTTATTAGTAATGAATTTGAAATATATGTAATATATC
1 TTATAATTATGTTTAAAATTT--AAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATC
* *
55877727 CAGACTAATATAGGTGATATATTTAAAAAATAGGTTTTAATATTTAAAAATATAAAA
64 CATACTAATATAGGTTATATATTTAAAAAATAGGTTTTAATATTT-AAAATATAAAA
* *
55877784 TAAATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATACAGGTTATATATCC
1 T-TATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCC
*
55877849 ATACTAATATAGGTTATATA-TTAAAAATATAGGTTTAAAGTTATTTAAAATATAATAA
65 ATACTAATATAGGTTATATATTTAAAAA-ATAGGTTTTAA--TATTTAAAATATAA-AA
* *
55877907 TTATAATTATTTTTAAAATTTAAAAACTTATTAGTAATGAATTTGAAATATAGGTTAT
1 TTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTAT
55877965 TTATTAATAA
Statistics
Matches: 275, Mismatches: 20, Indels: 14
0.89 0.06 0.05
Matches are distributed among these distances:
120 27 0.10
121 68 0.25
122 144 0.52
123 36 0.13
ACGTcount: A:0.47, C:0.03, G:0.09, T:0.41
Consensus pattern (119 bp):
TTATAATTATGTTTAAAATTTAAAAAGTTATTAGTAATGAATTTGAAATATAGGTTATATATCCA
TACTAATATAGGTTATATATTTAAAAAATAGGTTTTAATATTTAAAATATAAAA
Found at i:55878032 original size:100 final size:99
Alignment explanation
Indices: 55877854--55878085 Score: 383
Period size: 100 Copynumber: 2.3 Consensus size: 99
55877844 TATCCATACT
*
55877854 AATATAGGTTATATATTAAAAATATAGGTTTAAAGTTATTTAAAATATAATAATTATAATTATTT
1 AATATAGGTTATATATTAATAATATAGGTTTAAAGTTATTTAAAATATAATAATTATAATTATTT
55877919 TTAAAATTTAAAAACTTATTAGTAATGAATTTGA
66 TTAAAATTTAAAAACTTATTAGTAATGAATTTGA
* * *
55877953 AATATAGGTTATTTATTAATAATATAGGTTTTAAGTTATTTAAAAATATAATATTTATAATTATT
1 AATATAGGTTATATATTAATAATATAGGTTTAAAGTTATTT-AAAATATAATAATTATAATTATT
*
55878018 TTTAAAATTTAAAAATTTATTAGTAATGAATTTGA
65 TTTAAAATTTAAAAACTTATTAGTAATGAATTTGA
55878053 AATATAGGTTATATATTCATACTAATATAGGTT
1 AATATAGGTTATATATT-A-A-TAATATAGGTT
55878086 ACATATTAAT
Statistics
Matches: 123, Mismatches: 6, Indels: 4
0.92 0.05 0.03
Matches are distributed among these distances:
99 38 0.31
100 72 0.59
101 1 0.01
102 1 0.01
103 11 0.09
ACGTcount: A:0.45, C:0.01, G:0.09, T:0.45
Consensus pattern (99 bp):
AATATAGGTTATATATTAATAATATAGGTTTAAAGTTATTTAAAATATAATAATTATAATTATTT
TTAAAATTTAAAAACTTATTAGTAATGAATTTGA
Found at i:55879908 original size:125 final size:124
Alignment explanation
Indices: 55879749--55880147 Score: 559
Period size: 125 Copynumber: 3.2 Consensus size: 124
55879739 AATTTTATAA
* * * * *
55879749 CTTTTGCAGCGTTT-TCAGCAAAAACGCCACTAAAAAATTAATTTCCTATAACGAAACAGCACCA
1 CTTTTGCGGCGTTTCTGAG-AAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAGCACCG
*** * *
55879813 TTTTGCACAATTTTTAATACACAATTGCGGCGTTTTTAGACCAAACGGCACTATTGCTTAC
65 TTTTG-ACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
* * * * *
55879874 CTTTTGCGGCATTTCTGAGAAAAACGCCACTAAAAATTTAATTTCCTGGAACTAAACAACACCGT
1 CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAGCACCGT
55879939 TTTGTACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
66 TTTG-ACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
* * * *
55879999 CTTTTGCGGCGTTTTTGAGAAAAATGCCACTAAAAAATTAAATTCCTGTAACCAAACGGCACCGT
1 CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAGCACCGT
* *
55880064 CTTT-ACAATTTTTAATACATTGTTGCGGCGTTTTTTGTCCAAACGCCGCTATTGCTTAC
66 -TTTGACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
55880123 CTTTTGCGGCGTTTCTGAGAAAAAC
1 CTTTTGCGGCGTTTCTGAGAAAAAC
55880148 ACCGCAAACG
Statistics
Matches: 244, Mismatches: 28, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
124 76 0.31
125 162 0.66
126 6 0.02
ACGTcount: A:0.30, C:0.22, G:0.15, T:0.33
Consensus pattern (124 bp):
CTTTTGCGGCGTTTCTGAGAAAAACGCCACTAAAAAATTAATTTCCTGTAACCAAACAGCACCGT
TTTGACAATTTTTAATACATTGTTGCGGCGTTTTTAGACCAAACGCCGCTATTGCTTAC
Found at i:55881141 original size:31 final size:30
Alignment explanation
Indices: 55881106--55881165 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
55881096 GGAGGTGGGA
*
55881106 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
55881137 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
55881166 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:55881393 original size:9 final size:9
Alignment explanation
Indices: 55881379--55881415 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
55881369 TATAGTTTGA
55881379 TATTCGAAT
1 TATTCGAAT
55881388 TATTCGAAT
1 TATTCGAAT
*
55881397 TATTCGAGT
1 TATTCGAAT
55881406 TATTCGAAT
1 TATTCGAAT
55881415 T
1 T
55881416 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:55881491 original size:18 final size:18
Alignment explanation
Indices: 55881468--55881502 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
55881458 ATTCGAGTTG
55881468 ATTCGAATAACTCGATTA
1 ATTCGAATAACTCGATTA
55881486 ATTCGAATAACTCGATT
1 ATTCGAATAACTCGATT
55881503 CGTTTAACTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.34
Consensus pattern (18 bp):
ATTCGAATAACTCGATTA
Found at i:55881537 original size:9 final size:10
Alignment explanation
Indices: 55881517--55881541 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
55881507 TAACTCGAAA
55881517 TTCGATTTTT
1 TTCGATTTTT
55881527 TTCGATTTTT
1 TTCGATTTTT
55881537 TTCGA
1 TTCGA
55881542 GTCGAATCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.64
Consensus pattern (10 bp):
TTCGATTTTT
Found at i:55881651 original size:7 final size:7
Alignment explanation
Indices: 55881639--55881752 Score: 97
Period size: 7 Copynumber: 16.6 Consensus size: 7
55881629 AAAAACCTCT
55881639 TAAACCC
1 TAAACCC
55881646 TAAA-CC
1 TAAACCC
*
55881652 TAAACCG
1 TAAACCC
*
55881659 TAAACAC
1 TAAACCC
*
55881666 TAAACTC
1 TAAACCC
* *
55881673 TTAACAC
1 TAAACCC
* *
55881680 TAAATCA
1 TAAACCC
55881687 TAAACCC
1 TAAACCC
55881694 TAAACCC
1 TAAACCC
55881701 TAAACCC
1 TAAACCC
*
55881708 TAAACCT
1 TAAACCC
55881715 TAAACCC
1 TAAACCC
* *
55881722 CAAACCT
1 TAAACCC
*
55881729 TAAA-CA
1 TAAACCC
*
55881735 TACACCC
1 TAAACCC
*
55881742 TAAACCT
1 TAAACCC
55881749 TAAA
1 TAAA
55881753 TATATATATT
Statistics
Matches: 83, Mismatches: 22, Indels: 4
0.76 0.20 0.04
Matches are distributed among these distances:
6 10 0.12
7 73 0.88
ACGTcount: A:0.46, C:0.33, G:0.01, T:0.19
Consensus pattern (7 bp):
TAAACCC
Found at i:55882002 original size:19 final size:19
Alignment explanation
Indices: 55881980--55882017 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
55881970 AAAAGTCTAA
55881980 AATAAAATTATTTTCTTGC
1 AATAAAATTATTTTCTTGC
55881999 AATAAAATTATTTTCTTGC
1 AATAAAATTATTTTCTTGC
55882018 GGCGTTTCTT
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:0.11, G:0.05, T:0.47
Consensus pattern (19 bp):
AATAAAATTATTTTCTTGC
Found at i:55882154 original size:76 final size:76
Alignment explanation
Indices: 55882040--55882197 Score: 192
Period size: 76 Copynumber: 2.1 Consensus size: 76
55882030 AAACCGCCAT
* * * * *
55882040 TAATGCCGCTAAAGCTCAACAAAAAAATGACATCGTTTTGCTCAACTTTTTTATGGTGTTTTCCA
1 TAATGCCGCCAAAGCTCAACAAAAAAACGACATCGTTTTGCTCAAATTTTTTACGGCGTTTTCCA
*
55882105 AAAAGTGCCGC
66 AAAAGCGCCGC
* * * *
55882116 TAATGCCGCCAAAGCTCACCAAGAGAACGACGAT-GTTTTGCTCAAATTTTTTGCGGCGTTTTCC
1 TAATGCCGCCAAAGCTCAACAAAAAAACGAC-ATCGTTTTGCTCAAATTTTTTACGGCGTTTTCC
* *
55882180 AAGACGCGCCGC
65 AAAAAGCGCCGC
55882192 TAATGC
1 TAATGC
55882198 TTGACCTATA
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
76 67 0.97
77 2 0.03
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.28
Consensus pattern (76 bp):
TAATGCCGCCAAAGCTCAACAAAAAAACGACATCGTTTTGCTCAAATTTTTTACGGCGTTTTCCA
AAAAGCGCCGC
Found at i:55883634 original size:6 final size:6
Alignment explanation
Indices: 55883623--55883652 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
55883613 TTTGATAGAT
55883623 TTAATA TTAATA TTAATA TTAATA TTAATA
1 TTAATA TTAATA TTAATA TTAATA TTAATA
55883653 CTTATCTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (6 bp):
TTAATA
Found at i:55883768 original size:21 final size:23
Alignment explanation
Indices: 55883744--55883786 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
55883734 ATAAATATTC
55883744 TATT-AATTAA-ATAAGATTTAA
1 TATTAAATTAATATAAGATTTAA
*
55883765 TATTAAATTAATATAATATTTA
1 TATTAAATTAATATAAGATTTA
55883787 TCAAGTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (23 bp):
TATTAAATTAATATAAGATTTAA
Found at i:55888771 original size:23 final size:23
Alignment explanation
Indices: 55888741--55888786 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
55888731 CAACCAATTT
55888741 CTAGCTATGAACTAGTTATAGTC
1 CTAGCTATGAACTAGTTATAGTC
55888764 CTAGCTATGAACTAGTTATAGTC
1 CTAGCTATGAACTAGTTATAGTC
55888787 TTTTTGTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.35
Consensus pattern (23 bp):
CTAGCTATGAACTAGTTATAGTC
Found at i:55889135 original size:4 final size:4
Alignment explanation
Indices: 55889126--55889172 Score: 58
Period size: 4 Copynumber: 11.0 Consensus size: 4
55889116 TATGCATTGA
*
55889126 CTTT CTTT CTTT CTTT CTTT CTTT TTATT GACTTT CTTT CTTT CTTT
1 CTTT CTTT CTTT CTTT CTTT CTTT CT-TT --CTTT CTTT CTTT CTTT
55889173 TTTAATGAAG
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
4 33 0.87
5 2 0.05
6 2 0.05
7 1 0.03
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.72
Consensus pattern (4 bp):
CTTT
Found at i:55896005 original size:19 final size:20
Alignment explanation
Indices: 55895965--55896009 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
55895955 ATCAACCTTT
55895965 AATCAAGTTAAAATGGTTTC
1 AATCAAGTTAAAATGGTTTC
* *
55895985 AATCAAGTTAGAAT-TTTTC
1 AATCAAGTTAAAATGGTTTC
55896004 AATCAA
1 AATCAA
55896010 AATTAAATTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 10 0.43
20 13 0.57
ACGTcount: A:0.42, C:0.11, G:0.11, T:0.36
Consensus pattern (20 bp):
AATCAAGTTAAAATGGTTTC
Found at i:55896809 original size:20 final size:20
Alignment explanation
Indices: 55896784--55896823 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
55896774 ACTTTAAATT
55896784 CAAGTTAAAATAATTTTAAC
1 CAAGTTAAAATAATTTTAAC
*
55896804 CAAGTTAAAATGATTTTAAC
1 CAAGTTAAAATAATTTTAAC
55896824 AAATCAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.47, C:0.10, G:0.07, T:0.35
Consensus pattern (20 bp):
CAAGTTAAAATAATTTTAAC
Found at i:55898316 original size:15 final size:17
Alignment explanation
Indices: 55898296--55898332 Score: 51
Period size: 15 Copynumber: 2.3 Consensus size: 17
55898286 TATAAAATCA
55898296 ATAATATA-ATATAA-T
1 ATAATATATATATAATT
*
55898311 ATAATATATTTATAATT
1 ATAATATATATATAATT
55898328 ATAAT
1 ATAAT
55898333 TATTTTCTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 5 0.26
17 6 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATAATATATATATAATT
Found at i:55903712 original size:31 final size:30
Alignment explanation
Indices: 55903639--55903702 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
55903629 GGCTCGATCA
*
55903639 AAATTTAATTTAAAATATAAAAATATTTTT
1 AAATTTAAATTAAAATATAAAAATATTTTT
*
55903669 AAATTTAAATTAAATTATAAAAA-ATATTTT
1 AAATTTAAATTAAAATATAAAAATAT-TTTT
55903699 AAAT
1 AAAT
55903703 ATTTTATTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 2 0.06
30 29 0.94
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (30 bp):
AAATTTAAATTAAAATATAAAAATATTTTT
Found at i:55905878 original size:20 final size:19
Alignment explanation
Indices: 55905848--55905885 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
55905838 TATTATCCAT
*
55905848 ATAGAATGTTGTTATATAA
1 ATAGAATGTTGGTATATAA
55905867 ATAGATATGTTGGTATATA
1 ATAGA-ATGTTGGTATATA
55905886 TTATAGATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (19 bp):
ATAGAATGTTGGTATATAA
Found at i:55905930 original size:58 final size:56
Alignment explanation
Indices: 55905810--55906004 Score: 187
Period size: 58 Copynumber: 3.4 Consensus size: 56
55905800 TGGAAGATGT
* * ** *
55905810 TAGATATGTTGCTATATATTATAAATTTTATTATCCATATAGAATGTTGTTATATAAA
1 TAGATATGTTG-TATATATTATAGATTTTAGTAT-TTTATAAAATGTTGTTATATAAA
* * * *
55905868 TAGATATGTTGGTATATATTATAGATTTTAGTATTTGTATAAAATATTGTCATTTAAG
1 TAGATATGTT-GTATATATTATAGATTTTAGTATTT-TATAAAATGTTGTTATATAAA
* * **
55905926 TAGATATGTTGT-TATAATA-AGATTTTGGTAGTTATTATAAAAATGTTGTTATATATT
1 TAGATATGTTGTATATATTATAGATTTTAGTA-TT-TTAT-AAAATGTTGTTATATAAA
*
55905983 TAGATATGTTATATATATTATA
1 TAGATATGTTGTATATATTATA
55906005 TAAATAGATT
Statistics
Matches: 112, Mismatches: 18, Indels: 13
0.78 0.13 0.09
Matches are distributed among these distances:
55 10 0.09
56 11 0.10
57 27 0.24
58 62 0.55
59 2 0.02
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.48
Consensus pattern (56 bp):
TAGATATGTTGTATATATTATAGATTTTAGTATTTTATAAAATGTTGTTATATAAA
Found at i:55906151 original size:43 final size:39
Alignment explanation
Indices: 55906101--55906202 Score: 116
Period size: 40 Copynumber: 2.5 Consensus size: 39
55906091 TATTGAAATT
* *
55906101 CCAACTTTGTAACTAAATACT-TTGTAATTGTGCGTAGGTGTAC
1 CCAACTTTGTAACCAAATACTATT-T-A-TATGCG-A-GTGTAC
*
55906144 CCAACTTTATAACCAAATACTCATTTATATGCGAGTGTAC
1 CCAACTTTGTAACCAAATACT-ATTTATATGCGAGTGTAC
55906184 CCAACTTTGTAACCAAATA
1 CCAACTTTGTAACCAAATA
55906203 GTAAAATTTC
Statistics
Matches: 53, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
40 24 0.45
41 1 0.02
42 5 0.09
43 20 0.38
44 1 0.02
45 2 0.04
ACGTcount: A:0.33, C:0.21, G:0.13, T:0.33
Consensus pattern (39 bp):
CCAACTTTGTAACCAAATACTATTTATATGCGAGTGTAC
Found at i:55906278 original size:39 final size:38
Alignment explanation
Indices: 55906182--55906279 Score: 117
Period size: 38 Copynumber: 2.6 Consensus size: 38
55906172 ATGCGAGTGT
55906182 ACCCAACTTTGTAACCAAATAGTAAAATTTCTACTGAA
1 ACCCAACTTTGTAACCAAATAGTAAAATTTCTACTGAA
** * *
55906220 ATTCAACTTTGTAACCAAATATTAAAA-TTCTTATTGAAA
1 ACCCAACTTTGTAACCAAATAGTAAAATTTC-TACTG-AA
* *
55906259 ACCCAATTTTGTAATCAAATA
1 ACCCAACTTTGTAACCAAATA
55906280 CTTAGTAAAA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
37 3 0.06
38 28 0.56
39 19 0.38
ACGTcount: A:0.43, C:0.17, G:0.06, T:0.34
Consensus pattern (38 bp):
ACCCAACTTTGTAACCAAATAGTAAAATTTCTACTGAA
Found at i:55906920 original size:80 final size:81
Alignment explanation
Indices: 55906810--55907009 Score: 258
Period size: 80 Copynumber: 2.5 Consensus size: 81
55906800 CAAAGTTAAG
* * *
55906810 TTTCCAATAGAAATTTTAGTTTTTGGTTACAAAGTTGGACACAGTCACACACAATTACAAAGTAT
1 TTTCCAATA-AAAATTTAGTTTTTCGTTACAAAGTTGGACACACTCACACACAATTACAAAGTAT
** *
55906875 TTGGTTACAAACTT-GA
65 TTAATTACAAAATTGGA
* *
55906891 TTTCCAATAAAAATTTAGTTTTTCGTTACAAAGTTGGATACACTCACGCACAATTACAAAGTATT
1 TTTCCAATAAAAATTTAGTTTTTCGTTACAAAGTTGGACACACTCACACACAATTACAAAGTATT
*
55906956 TAATTACAAAATTGGG
66 TAATTACAAAATTGGA
* * * *
55906972 TCTCCAATAGAAACTTAGTTTTTTTGTTACAAAGTTGG
1 TTTCCAATAAAAATTTAG-TTTTTCGTTACAAAGTTGG
55907010 GTTTCCAATA
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
80 61 0.59
81 25 0.24
82 18 0.17
ACGTcount: A:0.35, C:0.14, G:0.14, T:0.36
Consensus pattern (81 bp):
TTTCCAATAAAAATTTAGTTTTTCGTTACAAAGTTGGACACACTCACACACAATTACAAAGTATT
TAATTACAAAATTGGA
Found at i:55908180 original size:13 final size:13
Alignment explanation
Indices: 55908162--55908186 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55908152 TAGGTGATAT
55908162 GTGTGAAAATTTC
1 GTGTGAAAATTTC
55908175 GTGTGAAAATTT
1 GTGTGAAAATTT
55908187 TATCGTTTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:55912044 original size:41 final size:42
Alignment explanation
Indices: 55911985--55912114 Score: 151
Period size: 41 Copynumber: 3.2 Consensus size: 42
55911975 CTGATACGCT
** * *
55911985 TATAGTCTAATTCCGTTCACCGGCACTTAGCCTGCTAGG-CT
1 TATAGTCCGATTCAGTTCACCGGCACTTAGCCTGCTAGGACG
* *
55912026 TGTAG-CCTGATTTAGTTCACCGGCACTTAGCCTGCT-GGACG
1 TATAGTCC-GATTCAGTTCACCGGCACTTAGCCTGCTAGGACG
* *
55912067 TATAGTCCGATTCAATTCACCAGCACTTAGCCTGCTA-GACG
1 TATAGTCCGATTCAGTTCACCGGCACTTAGCCTGCTAGGACG
55912108 TATAGTC
1 TATAGTC
55912115 TGAACAATTT
Statistics
Matches: 75, Mismatches: 10, Indels: 8
0.81 0.11 0.09
Matches are distributed among these distances:
40 3 0.04
41 70 0.93
42 2 0.03
ACGTcount: A:0.22, C:0.28, G:0.21, T:0.30
Consensus pattern (42 bp):
TATAGTCCGATTCAGTTCACCGGCACTTAGCCTGCTAGGACG
Found at i:55912127 original size:41 final size:40
Alignment explanation
Indices: 55912000--55912132 Score: 140
Period size: 41 Copynumber: 3.2 Consensus size: 40
55911990 TCTAATTCCG
* * * * * *
55912000 TTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTTAG
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA-TCAA
* *
55912041 TTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA-TCAA
* *
55912082 TTCACCAGCACTTAGCCTGCTAGACGTATAGTCTGAACAA
1 TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATCAA
*
55912122 TTTCACTGGCA
1 -TTCACCGGCA
55912133 ATAAATCCGA
Statistics
Matches: 77, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
40 3 0.04
41 74 0.96
ACGTcount: A:0.23, C:0.28, G:0.21, T:0.29
Consensus pattern (40 bp):
TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATCAA
Found at i:55920275 original size:45 final size:44
Alignment explanation
Indices: 55920203--55920345 Score: 146
Period size: 44 Copynumber: 3.2 Consensus size: 44
55920193 NNNNNNNCTT
* * * * *
55920203 CGATCTACTTCACGCCAATACATGAAGACAAGATCTGCTTTCTG
1 CGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTG
*
55920247 CGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGC-ATC-G
1 CGATCTACTTC-CCACCAATATAGGAAGACAAGATCTGCTATCTG
* * * * * *
55920290 TCGATCCACTTCCTACCAATATAGGAAGATAGGATCAGCTATCTT
1 -CGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTG
55920335 CGATCTACTTC
1 CGATCTACTTC
55920346 TTGCCCCGGG
Statistics
Matches: 81, Mismatches: 14, Indels: 8
0.79 0.14 0.08
Matches are distributed among these distances:
43 23 0.28
44 36 0.44
45 22 0.27
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (44 bp):
CGATCTACTTCCCACCAATATAGGAAGACAAGATCTGCTATCTG
Found at i:55920609 original size:46 final size:46
Alignment explanation
Indices: 55920523--55921026 Score: 277
Period size: 46 Copynumber: 11.1 Consensus size: 46
55920513 CCACTGTAGT
* * ** * *
55920523 CAGGGAGGTAAAATCTGCCATCTTTGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCAAATA
* * *
55920569 CAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATG
1 CAGGGAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
* * * ** * * *
55920615 CAGGGAGATAGAGTTAT-C-GGCTTCAATCTACTCCACTG--TAGTCA
1 CAGGGAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCAAAT-A
* * * * * *
55920659 CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCTAATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCAAATA
* * *
55920705 CAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAGATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
* * * * * * * *
55920751 CAGGGAGAT-AGAGT-TACCAGCTTCAATGTACTCCACTG--TAGTCA
1 CAGGGAGGTAAGA-TCTGCAATCTTCAATCTATTCCACTGCCAAAT-A
* * * * * *
55920795 CAGGGCGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCAAATA
*
55920841 CAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
* * * ** * * * *
55920887 CAGGGAGATAGAGTTAT-C-GGCTTCAATGTACTCCACTG--TAGT-
1 CAGGGAGGTA-AGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
* * * * *
55920929 CAGGGAGGTAAAATCTGCCATCTTCGATCTGCTT-CGCTGCCAAATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCT-ATTCCACTGCCAAATA
* * * *
55920975 CAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAATA
1 CAGGGAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
55921021 CAGGGA
1 CAGGGA
55921027 CAAGATCTGC
Statistics
Matches: 330, Mismatches: 103, Indels: 50
0.68 0.21 0.10
Matches are distributed among these distances:
41 3 0.01
42 10 0.03
43 19 0.06
44 20 0.06
45 94 0.28
46 171 0.52
47 13 0.04
ACGTcount: A:0.29, C:0.25, G:0.21, T:0.26
Consensus pattern (46 bp):
CAGGGAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCAAATA
Found at i:55920695 original size:136 final size:134
Alignment explanation
Indices: 55920353--55921026 Score: 924
Period size: 136 Copynumber: 5.0 Consensus size: 134
55920343 TTCTTGCCCC
** * * * *
55920353 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
* * * ****** * ** * * ***
55920418 GACCTGCTCCACTATTGCTTAGA-G-AGATAAGATCTGTAATCTTCGATCTATTCCACTG--TTG
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
**
55920479 CCCA
131 TACA
** *
55920483 GGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTT
1 GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
55920548 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
*
55920613 TGCA
131 TACA
* * *
55920617 GGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCT
*
55920682 TCGATCTGCTTCGCTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
64 TCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
*
55920747 GATACA
129 AATACA
*
55920753 GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGTCACAGGGCGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCT
*
55920818 TCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCACTGCCA
64 TCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
55920883 AATACA
129 AATACA
* *
55920889 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
1 GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
* *
55920954 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
55921019 TACA
131 TACA
55921023 GGGA
1 GGGA
55921027 CAAGATCTGC
Statistics
Matches: 492, Mismatches: 46, Indels: 8
0.90 0.08 0.01
Matches are distributed among these distances:
130 73 0.15
131 1 0.00
132 30 0.06
134 131 0.27
136 257 0.52
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (134 bp):
GGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCAAA
TACA
Found at i:55920786 original size:45 final size:46
Alignment explanation
Indices: 55920590--55920924 Score: 159
Period size: 45 Copynumber: 7.4 Consensus size: 46
55920580 GATCTGCAAT
* * * *
55920590 CTTCAATCTATTCCACTGCCAAATGCAGGGAGATAGAGT-TATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTCTACCAG
* * * * * * *
55920635 CTTCAATCTACTCCACTG--TAGTCACAGGGAGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGCCAAAT-ACAGGGAGATAGAGTCTACCAG
* * * * * * * * *
55920680 CTTCGATCTGCTTCGCTGCCTAATACAGGAAGGCA-AGA-TCTGCAAT
1 CTTCAATCTACTCCACTGCCAAATACAGGGA-G-ATAGAGTCTACCAG
* *
55920726 CTTCAATCTATTCCACTGCCAGATACAGGGAGATAGAGT-TACCAG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTCTACCAG
* * * * * * * * *
55920771 CTTCAATGTACTCCACTG--TAGTCACAGGGCGGTAAAATCTGCCAT
1 CTTCAATCTACTCCACTGCCAAAT-ACAGGGAGATAGAGTCTACCAG
* * * * * * * * *
55920816 CTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTA-AGATCTGCAAT
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAG-TCTACCAG
* * *
55920862 CTTCAATCTATTCCACTGCCAAATACAGGGAGATAGAGT-TATCGG
1 CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTCTACCAG
*
55920907 CTTCAATGTACTCCACTG
1 CTTCAATCTACTCCACTG
55920925 TAGTCAGGGA
Statistics
Matches: 209, Mismatches: 67, Indels: 28
0.69 0.22 0.09
Matches are distributed among these distances:
43 3 0.01
44 23 0.11
45 91 0.44
46 82 0.39
47 10 0.05
ACGTcount: A:0.28, C:0.25, G:0.20, T:0.27
Consensus pattern (46 bp):
CTTCAATCTACTCCACTGCCAAATACAGGGAGATAGAGTCTACCAG
Found at i:55920977 original size:270 final size:267
Alignment explanation
Indices: 55920353--55921026 Score: 967
Period size: 270 Copynumber: 2.5 Consensus size: 267
55920343 TTCTTGCCCC
** * * * *
55920353 GGGAGATAGAACTATCAGCTTCAATGTACTCCACTGTAATCAGGGAGGTAAAATCCGCCGTCTTC
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
* * * ****** * ** * * ** *
55920418 GACCTGCTCCACTATTGCTTAGA-G-AGATAAGATCTGTAATCTTCGATCTATTCCACTGTTG-C
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCAGAT
*
55920480 CCAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATC
131 ACAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATC
*
55920545 TTTGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC
196 TTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC
*
55920610 AAATGCA
261 AAATACA
*
55920617 GGGAGATAGAGTTATCGGCTTCAATCTACTCCACTGTAGTCACAGGGAGGTAAAATCTGCCATCT
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTGCCATCT
*
55920682 TCGATCTGCTTCGCTGCCTAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCCA
64 TCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG-CA
** *
55920747 GATACAGGGAGATAGAGTTACCAGCTTCAATGTACTCCACTGTAGTCACAGGGCGGTAAAATCTG
128 GATACAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAGT--CAGGGAGGTAAAATCTG
*
55920812 CCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGTAAGATCTGCAATCTTCAATCTATTCCA
191 CCATCTTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCA
55920877 CTGCCAAATACA
256 CTGCCAAATACA
55920889 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
1 GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
* *
55920954 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCCTCAATCTATTCCACTGTCAAA
66 GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTG-CAGA
55921019 TACAGGGA
130 TACAGGGA
55921027 CAAGATCTGC
Statistics
Matches: 366, Mismatches: 36, Indels: 10
0.89 0.09 0.02
Matches are distributed among these distances:
264 35 0.10
266 36 0.10
267 1 0.00
268 30 0.08
269 1 0.00
270 134 0.37
272 129 0.35
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (267 bp):
GGGAGATAGAGTTATCGGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATCTTC
GATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCAGAT
ACAGGGAGATAGAACTACCAGCTTCAATGTACTCCACTGTAGTCAGGGAGGTAAAATCTGCCATC
TTCGATCTGCTTCGCTGCCAAATACAGGAAGGCAAGATCTGCAATCTTCAATCTATTCCACTGCC
AAATACA
Found at i:55921218 original size:132 final size:132
Alignment explanation
Indices: 55921025--55922227 Score: 2325
Period size: 132 Copynumber: 9.1 Consensus size: 132
55921015 CAAATACAGG
* * * * *
55921025 GACAAGATCTGCTTTCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTATCTTGGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
* *
55921090 TCCACTTCCTATCAATATAGGAAGATAGGACCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921155 AA
131 AA
55921157 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55921222 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921287 AA
131 AA
55921289 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55921354 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921419 AA
131 AA
55921421 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55921486 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921551 AA
131 AA
55921553 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55921618 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921683 AA
131 AA
55921685 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55921750 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921815 AA
131 AA
55921817 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55921882 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55921947 AA
131 AA
*
55921949 GACAAGATCTGCTTTCTTCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
55922014 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55922079 AA
131 AA
55922081 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
1 GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
*
55922146 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTACCTTCGATCTACTTCACGCCAATACATG
66 TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
55922211 AA
131 AA
55922213 GACAAGATCTGCTTT
1 GACAAGATCTGCTTT
55922228 AATGACTTCA
Statistics
Matches: 1061, Mismatches: 10, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
132 1061 1.00
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.28
Consensus pattern (132 bp):
GACAAGATCTGCTTTCTGCGATCTACTTCGCCACCAATATGGGAAGACAAGATCTGCATCTTCGA
TCCACTTCCTACCAATATAGGAAGATAGGATCTGCTATCTTCGATCTACTTCACGCCAATACATG
AA
Found at i:55923721 original size:22 final size:23
Alignment explanation
Indices: 55923692--55923740 Score: 66
Period size: 24 Copynumber: 2.2 Consensus size: 23
55923682 AGTAGAGGTC
*
55923692 TTTTC-TTTTATTTT-TGGTTTT
1 TTTTCTTTTTATTTTCTAGTTTT
55923713 TTTTGCTTTTTATTTTCTAGTTTT
1 TTTT-CTTTTTATTTTCTAGTTTT
55923737 TTTT
1 TTTT
55923741 TTGCTTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 4 0.17
22 1 0.04
23 9 0.38
24 10 0.42
ACGTcount: A:0.06, C:0.06, G:0.08, T:0.80
Consensus pattern (23 bp):
TTTTCTTTTTATTTTCTAGTTTT
Found at i:55925130 original size:62 final size:62
Alignment explanation
Indices: 55925048--55925172 Score: 205
Period size: 62 Copynumber: 2.0 Consensus size: 62
55925038 CTAAACTCGA
* *
55925048 CGTACTTTTGGATTTTAGGAAATTTATTATATAAAATGAAATGTAATGTTGATGCATGAATG
1 CGTACTTTTGAATTTTAGGAAATTTATTATATAAAATGAAATGTAACGTTGATGCATGAATG
* **
55925110 CGTATTTTTGAATTTTAGGAAATTTATTATATGCAATGAAATGTAACGTTGATGCATGAATG
1 CGTACTTTTGAATTTTAGGAAATTTATTATATAAAATGAAATGTAACGTTGATGCATGAATG
55925172 C
1 C
55925173 AAAAAAAAGA
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.40
Consensus pattern (62 bp):
CGTACTTTTGAATTTTAGGAAATTTATTATATAAAATGAAATGTAACGTTGATGCATGAATG
Found at i:55927101 original size:16 final size:16
Alignment explanation
Indices: 55927077--55927107 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
55927067 TATGTACCGA
*
55927077 AAATTTAAATAAATAT
1 AAATATAAATAAATAT
55927093 AAATATAAATAAATA
1 AAATATAAATAAATA
55927108 GATAACAATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATAAATAAATAT
Found at i:55928545 original size:31 final size:31
Alignment explanation
Indices: 55928504--55928565 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
55928494 CATATTCACT
55928504 TATACCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
*
55928535 TATATCCACCTATGCCGAATGCATACATATA
1 TATACCCACCTATGCCGAATGCATACATATA
55928566 CACACTTAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.35, C:0.27, G:0.10, T:0.27
Consensus pattern (31 bp):
TATACCCACCTATGCCGAATGCATACATATA
Found at i:55929033 original size:82 final size:82
Alignment explanation
Indices: 55928792--55929047 Score: 365
Period size: 82 Copynumber: 3.1 Consensus size: 82
55928782 TCTAATTCCG
* * *
55928792 TTCACCGGCACTTTGCCTGCTAGG-CCTATAG-CCTGATTCAGTTCACCGGCACTTAGCCTGCTA
1 TTCACCGGCACTTAGCCTGCT-GGACGTATAGTCC-GATTCAATTCACCGGCACTTAGCCTGCTA
* * * * * *
55928855 GGCTTGTAGCCTGATTC-AG
64 GACGTATAGTCTGA-ACAAT
55928874 TTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCAATTCACCGGCACTTAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCAATTCACCGGCACTTAGCCTGCTAGA
55928939 CGTATAGTCTGAACAAT
66 CGTATAGTCTGAACAAT
*
55928956 TTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCAATTCACCGGCACATAGCCTGCTAGA
1 TTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCAATTCACCGGCACTTAGCCTGCTAGA
55929021 CGTATAGTCTGAACAAT
66 CGTATAGTCTGAACAAT
*
55929038 TTCACTGGCA
1 TTCACCGGCA
55929048 ATAAATCCGA
Statistics
Matches: 160, Mismatches: 11, Indels: 6
0.90 0.06 0.03
Matches are distributed among these distances:
81 3 0.02
82 155 0.97
83 2 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.27
Consensus pattern (82 bp):
TTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCAATTCACCGGCACTTAGCCTGCTAGA
CGTATAGTCTGAACAAT
Found at i:55929042 original size:41 final size:41
Alignment explanation
Indices: 55928750--55929032 Score: 327
Period size: 41 Copynumber: 6.9 Consensus size: 41
55928740 ATTTAAACAG
* * * * * *
55928750 ATTCACTGGCACTTCA-CCTGATAGGCTTATAGTCTAATTCC
1 ATTCACCGGCACTT-AGCCTGCTAGACGTATAGTCTGATTCA
* * * * *
55928791 GTTCACCGGCACTTTGCCTGCTAGGCCTATAGCCTGATTCA
1 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTCA
* * * * *
55928832 GTTCACCGGCACTTAGCCTGCTAGGCTTGTAGCCTGATTCA
1 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTCA
* * *
55928873 GTTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCA
1 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTCA
*
55928914 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA-ACA
1 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTCA
* *
55928954 ATTTCACCGGCACTTAGCCTGCTGGACGTATAGTCCGATTCA
1 A-TTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTCA
*
55928996 ATTCACCGGCACATAGCCTGCTAGACGTATAGTCTGA
1 ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGA
55929033 ACAATTTCAC
Statistics
Matches: 212, Mismatches: 27, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
40 3 0.01
41 206 0.97
42 3 0.01
ACGTcount: A:0.22, C:0.29, G:0.21, T:0.28
Consensus pattern (41 bp):
ATTCACCGGCACTTAGCCTGCTAGACGTATAGTCTGATTCA
Found at i:55936070 original size:17 final size:16
Alignment explanation
Indices: 55936048--55936080 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
55936038 GGAAGTCGTG
55936048 ATAATTATACATTTAAA
1 ATAATTATA-ATTTAAA
55936065 ATAATTATAATTTAAA
1 ATAATTATAATTTAAA
55936081 TTTATAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.44
17 9 0.56
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (16 bp):
ATAATTATAATTTAAA
Found at i:55936093 original size:22 final size:23
Alignment explanation
Indices: 55936048--55936093 Score: 58
Period size: 22 Copynumber: 2.0 Consensus size: 23
55936038 GGAAGTCGTG
*
55936048 ATAATTATACATTTAAAATAATT
1 ATAATTATAAATTTAAAATAATT
* *
55936071 ATAATT-TAAATTTATAATTATT
1 ATAATTATAAATTTAAAATAATT
55936093 A
1 A
55936094 GCTAAAAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 14 0.70
23 6 0.30
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAATTATAAATTTAAAATAATT
Found at i:55936204 original size:19 final size:18
Alignment explanation
Indices: 55936162--55936204 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 18
55936152 AAAATATAAG
55936162 AAAA-AATTATAATTTAA
1 AAAATAATTATAATTTAA
**
55936179 ATTATAATTATTAATTTAA
1 AAAATAATTA-TAATTTAA
55936198 AAAATAA
1 AAAATAA
55936205 GTTGTGCTAA
Statistics
Matches: 20, Mismatches: 4, Indels: 2
0.77 0.15 0.08
Matches are distributed among these distances:
17 2 0.10
18 5 0.25
19 13 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (18 bp):
AAAATAATTATAATTTAA
Found at i:55942229 original size:12 final size:14
Alignment explanation
Indices: 55942207--55942245 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
55942197 AGGAAAATTT
*
55942207 TAATAATAATATAAA
1 TAATAAT-ATATACA
*
55942222 TGATAATATATACA
1 TAATAATATATACA
55942236 TAATAATATA
1 TAATAATATA
55942246 CAAAAGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATATATACA
Found at i:55944207 original size:12 final size:14
Alignment explanation
Indices: 55944185--55944223 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
55944175 AGGAAAATTT
*
55944185 TAATAATAATATAAA
1 TAATAAT-ATATACA
*
55944200 TGATAATATATACA
1 TAATAATATATACA
55944214 TAATAATATA
1 TAATAATATA
55944224 CAAAAGTTGA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (14 bp):
TAATAATATATACA
Found at i:55946639 original size:39 final size:39
Alignment explanation
Indices: 55946596--55946673 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
55946586 ACTATAGAGT
55946596 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
1 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
55946635 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
1 ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
55946674 GTTGTAGAGT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.31
Consensus pattern (39 bp):
ACCATCCCGATAAGGCTAATATTGTGGCTGATGCTCTTA
Found at i:55949347 original size:29 final size:29
Alignment explanation
Indices: 55949305--55949369 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
55949295 ATGTGATGAG
* * *
55949305 CCACACGGCTGTGTGCCAGGTCTTGTGGA
1 CCACACGACCGTGTGCCAGGTCTTGTGAA
*
55949334 CCACACGACCGTGTGCTAGGTCTTGTGAA
1 CCACACGACCGTGTGCCAGGTCTTGTGAA
*
55949363 CTACACG
1 CCACACG
55949370 GGCCAGCCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.29, G:0.29, T:0.23
Consensus pattern (29 bp):
CCACACGACCGTGTGCCAGGTCTTGTGAA
Found at i:55950858 original size:23 final size:25
Alignment explanation
Indices: 55950800--55950906 Score: 83
Period size: 23 Copynumber: 4.6 Consensus size: 25
55950790 CTGTAAAATC
55950800 ATTAAATATAATTTGATAA--A-TTA
1 ATTAAATATAATTT-ATAATTATTTA
*
55950823 A--AAATAATTAATTTTTAATT-TTTA
1 ATTAAAT-A-TAATTTATAATTATTTA
*
55950847 ATTAAATA-AA-TTATATTTATTTA
1 ATTAAATATAATTTATAATTATTTA
55950870 ATTAAATATAATTTAT--TTATTTA
1 ATTAAATATAATTTATAATTATTTA
*
55950893 A-TAAATATATTTTA
1 ATTAAATATAATTTA
55950907 AAAATCATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
21 4 0.06
22 22 0.31
23 29 0.41
24 6 0.09
25 5 0.07
26 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
ATTAAATATAATTTATAATTATTTA
Found at i:55950870 original size:19 final size:19
Alignment explanation
Indices: 55950843--55950888 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
55950833 ATTTTTAATT
*
55950843 TTTAATTAAATAAAT-TATA
1 TTTATTTAAATAAATATA-A
*
55950862 TTTATTTAATTAAATATAA
1 TTTATTTAAATAAATATAA
55950881 TTTATTTA
1 TTTATTTA
55950889 TTTAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTTAAATAAATATAA
Found at i:55951968 original size:23 final size:25
Alignment explanation
Indices: 55951910--55952016 Score: 83
Period size: 23 Copynumber: 4.6 Consensus size: 25
55951900 CTGTAAAATC
55951910 ATTAAATATAATTTGATAA--A-TTA
1 ATTAAATATAATTT-ATAATTATTTA
*
55951933 A--AAATAATTAATTTTTAATT-TTTA
1 ATTAAAT-A-TAATTTATAATTATTTA
*
55951957 ATTAAATA-AA-TTATATTTATTTA
1 ATTAAATATAATTTATAATTATTTA
55951980 ATTAAATATAATTTAT--TTATTTA
1 ATTAAATATAATTTATAATTATTTA
*
55952003 A-TAAATATATTTTA
1 ATTAAATATAATTTA
55952017 AAAATCATAA
Statistics
Matches: 70, Mismatches: 4, Indels: 21
0.74 0.04 0.22
Matches are distributed among these distances:
21 4 0.06
22 22 0.31
23 29 0.41
24 6 0.09
25 5 0.07
26 4 0.06
ACGTcount: A:0.48, C:0.00, G:0.01, T:0.51
Consensus pattern (25 bp):
ATTAAATATAATTTATAATTATTTA
Found at i:55951980 original size:19 final size:19
Alignment explanation
Indices: 55951953--55951998 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
55951943 ATTTTTAATT
*
55951953 TTTAATTAAATAAAT-TATA
1 TTTATTTAAATAAATATA-A
*
55951972 TTTATTTAATTAAATATAA
1 TTTATTTAAATAAATATAA
55951991 TTTATTTA
1 TTTATTTA
55951999 TTTAATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 22 0.92
20 2 0.08
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (19 bp):
TTTATTTAAATAAATATAA
Found at i:55954572 original size:19 final size:19
Alignment explanation
Indices: 55954548--55954586 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
55954538 TTCAAAATGA
55954548 AAACTCATATTTTAAAGTT
1 AAACTCATATTTTAAAGTT
55954567 AAACTCATATTTTAAAGTT
1 AAACTCATATTTTAAAGTT
55954586 A
1 A
55954587 TGGCAAATTC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.05, T:0.41
Consensus pattern (19 bp):
AAACTCATATTTTAAAGTT
Found at i:55960891 original size:6 final size:6
Alignment explanation
Indices: 55960880--55960929 Score: 50
Period size: 6 Copynumber: 8.2 Consensus size: 6
55960870 AACCCAATTA
*
55960880 TTATTT TTATTT TTATTT TTA-CT TTATTT ATTACTTT ATT-TTT TTATTT
1 TTATTT TTATTT TTATTT TTATTT TTATTT -TTA-TTT -TTATTT TTATTT
55960929 T
1 T
55960930 ACTTATTTGG
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
5 6 0.16
6 23 0.61
7 3 0.08
8 6 0.16
ACGTcount: A:0.18, C:0.04, G:0.00, T:0.78
Consensus pattern (6 bp):
TTATTT
Found at i:55969553 original size:416 final size:416
Alignment explanation
Indices: 55968782--55969613 Score: 1655
Period size: 416 Copynumber: 2.0 Consensus size: 416
55968772 CCAGGTGCAA
55968782 CAAAAATCGCCTTTGAAATTCTCCTCCTCTAGTTCCCCCCCCCCTTTCTTTCTGGATTCTGACGA
1 CAAAAATCGCCTTTGAAATTCTCCTCCTCTAGTTCCCCCCCCCCTTTCTTTCTGGATTCTGACGA
55968847 ACCATGACAATTCTTTATAACCCATTTTTTCTCTTGTTTATAACTTTCGTTTTCCTGTTTCTTTT
66 ACCATGACAATTCTTTATAACCCATTTTTTCTCTTGTTTATAACTTTCGTTTTCCTGTTTCTTTT
55968912 CCGGGTTGTTTTGATCAAGACCGGACTGATTTTTACTGTCAAGAAAAAGTGGCGTCTTTTTGAAG
131 CCGGGTTGTTTTGATCAAGACCGGACTGATTTTTACTGTCAAGAAAAAGTGGCGTCTTTTTGAAG
55968977 ATTGCTTTCATGTCTACCAGTTGTTCAAAGTCCCCAAATTCAATGAAAGCATGCAAAGAAACCAA
196 ATTGCTTTCATGTCTACCAGTTGTTCAAAGTCCCCAAATTCAATGAAAGCATGCAAAGAAACCAA
55969042 CTTTATCACAAAGTTTTTGTTTATCTCAATTCACTCACTTCCATTGAAGATTCCGATTTCACCAA
261 CTTTATCACAAAGTTTTTGTTTATCTCAATTCACTCACTTCCATTGAAGATTCCGATTTCACCAA
55969107 TCTCTTCACCGGCAAAAAACCAAATGAAATCCTTCTCCGCCTCGACCCCAACCAAATAATCGAAG
326 TCTCTTCACCGGCAAAAAACCAAATGAAATCCTTCTCCGCCTCGACCCCAACCAAATAATCGAAG
55969172 ACGATTTTCTGGGTGCCAAGATTCTC
391 ACGATTTTCTGGGTGCCAAGATTCTC
55969198 CAAAAATCGCCTTTGAAATTCTCCTCCTCTAGTTCCCCCCCCCCTTTCTTTCTGGATTCTGACGA
1 CAAAAATCGCCTTTGAAATTCTCCTCCTCTAGTTCCCCCCCCCCTTTCTTTCTGGATTCTGACGA
55969263 ACCATGACAATTCTTTATAACCCATTTTTTCTCTTGTTTATAACTTTCGTTTTCCTGTTTCTTTT
66 ACCATGACAATTCTTTATAACCCATTTTTTCTCTTGTTTATAACTTTCGTTTTCCTGTTTCTTTT
55969328 CCGGGTTGTTTTGATCAAGACCGGACTGATTTTTACTGTCAAGAAAAAGTGGCGTCTTTTTGAAG
131 CCGGGTTGTTTTGATCAAGACCGGACTGATTTTTACTGTCAAGAAAAAGTGGCGTCTTTTTGAAG
55969393 ATTGCTTTCATGTCTACCAGTTGTTCAAAGTCCCCAAATTCAATGAAAGCATGCAAAGAAACCAA
196 ATTGCTTTCATGTCTACCAGTTGTTCAAAGTCCCCAAATTCAATGAAAGCATGCAAAGAAACCAA
*
55969458 CTTTATCACAAAGTTTTTGTTTATCTCAATTCACTCACTTCCGTTGAAGATTCCGATTTCACCAA
261 CTTTATCACAAAGTTTTTGTTTATCTCAATTCACTCACTTCCATTGAAGATTCCGATTTCACCAA
55969523 TCTCTTCACCGGCAAAAAACCAAATGAAATCCTTCTCCGCCTCGACCCCAACCAAATAATCGAAG
326 TCTCTTCACCGGCAAAAAACCAAATGAAATCCTTCTCCGCCTCGACCCCAACCAAATAATCGAAG
55969588 ACGATTTTCTGGGTGCCAAGATTCTC
391 ACGATTTTCTGGGTGCCAAGATTCTC
55969614 TGGATCAACG
Statistics
Matches: 415, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
416 415 1.00
ACGTcount: A:0.26, C:0.26, G:0.13, T:0.34
Consensus pattern (416 bp):
CAAAAATCGCCTTTGAAATTCTCCTCCTCTAGTTCCCCCCCCCCTTTCTTTCTGGATTCTGACGA
ACCATGACAATTCTTTATAACCCATTTTTTCTCTTGTTTATAACTTTCGTTTTCCTGTTTCTTTT
CCGGGTTGTTTTGATCAAGACCGGACTGATTTTTACTGTCAAGAAAAAGTGGCGTCTTTTTGAAG
ATTGCTTTCATGTCTACCAGTTGTTCAAAGTCCCCAAATTCAATGAAAGCATGCAAAGAAACCAA
CTTTATCACAAAGTTTTTGTTTATCTCAATTCACTCACTTCCATTGAAGATTCCGATTTCACCAA
TCTCTTCACCGGCAAAAAACCAAATGAAATCCTTCTCCGCCTCGACCCCAACCAAATAATCGAAG
ACGATTTTCTGGGTGCCAAGATTCTC
Found at i:55971722 original size:57 final size:57
Alignment explanation
Indices: 55971652--55971772 Score: 179
Period size: 57 Copynumber: 2.1 Consensus size: 57
55971642 TAAACGCAAC
* * *
55971652 CACGATAAGTAAATAAAATATTTTCTAAATTCAGTCACTATAATAAATTACATAAAA
1 CACGATAAATAAATAAAATATTCTCTAAATTCAATCACTATAATAAATTACATAAAA
* * * *
55971709 CATGATAAATAAATAAAATGTTCTCTAAATTCAATCACTGTAATAAATTACTTAAAA
1 CACGATAAATAAATAAAATATTCTCTAAATTCAATCACTATAATAAATTACATAAAA
55971766 CACGATA
1 CACGATA
55971773 CGGTAAGAAA
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.50, C:0.13, G:0.06, T:0.31
Consensus pattern (57 bp):
CACGATAAATAAATAAAATATTCTCTAAATTCAATCACTATAATAAATTACATAAAA
Found at i:55972349 original size:19 final size:20
Alignment explanation
Indices: 55972311--55972349 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
55972301 AAAAAGAAAG
**
55972311 TTCAAAAAATTATGAGATAA
1 TTCAAAAAATTAACAGATAA
55972331 TTCAAAAAATTAACA-ATAA
1 TTCAAAAAATTAACAGATAA
55972350 AAAATGAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.59, C:0.08, G:0.05, T:0.28
Consensus pattern (20 bp):
TTCAAAAAATTAACAGATAA
Found at i:55972623 original size:24 final size:24
Alignment explanation
Indices: 55972593--55972641 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
55972583 ATAGTGATAA
*
55972593 AATCTTTCACCATCCTTAAAATAT
1 AATCTTTCACCATCCCTAAAATAT
55972617 AATCTTTCACCATCCCTAAAATAT
1 AATCTTTCACCATCCCTAAAATAT
55972641 A
1 A
55972642 GAAATAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.35
Consensus pattern (24 bp):
AATCTTTCACCATCCCTAAAATAT
Found at i:55975667 original size:46 final size:46
Alignment explanation
Indices: 55975601--55975808 Score: 323
Period size: 46 Copynumber: 4.6 Consensus size: 46
55975591 TTTGAGTACT
* * *
55975601 TCTGATC-AGTGGCAAAGTGATAAGTGTTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
55975646 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
55975692 TCTGATCAAATGACAAAGTAATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* *
55975738 TCTTATCAAGTGACAAAGTGATAAGTGGTAGCATTAGCTACACTTA
1 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
*
55975784 TCTGATC-AGGGAC-AAGTGATAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTG
55975809 ATCATACGTA
Statistics
Matches: 151, Mismatches: 11, Indels: 3
0.92 0.07 0.02
Matches are distributed among these distances:
44 12 0.08
45 12 0.08
46 127 0.84
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:55986192 original size:160 final size:161
Alignment explanation
Indices: 55985872--55986194 Score: 603
Period size: 160 Copynumber: 2.0 Consensus size: 161
55985862 AAAACAAGTG
55985872 AAATGACATAATCGGTAAAAATTATTATTGTTCATAAGTGCATGTTAGAGCAAGAATTTGATGTT
1 AAATGACATAATCGGTAAAAATTATTATTGTTCATAAGTGCATGTTAGAGCAAGAATTTGATGTT
*
55985937 GATATAGAAGGGAAAAATATTCAGCATGTTATAAATCATAAGAAAAAGGAATAAATTTTAATTTC
66 GATATAGAAGGGAAAAATATTCAACATGTTATAAATCATAAGAAAAAGGAATAAATTTTAATTTC
55986002 CGAACCTAGGGGAAAAATTGTAATTTTGTGA
131 CGAACCTAGGGGAAAAATTGTAATTTTGTGA
55986033 AAATGACATAATCGGTAAAAATTATTATTGTTCATAAGTGCATGTTAGAGCAAGAATTTGATGTT
1 AAATGACATAATCGGTAAAAATTATTATTGTTCATAAGTGCATGTTAGAGCAAGAATTTGATGTT
* *
55986098 GCTATAGAAGGG-AAAATATTCAACATGTTATAAATCATAAGAAAAAGGAATAAATTTTAATTTT
66 GATATAGAAGGGAAAAATATTCAACATGTTATAAATCATAAGAAAAAGGAATAAATTTTAATTTC
*
55986162 CGAACCTAGGGGAAAATTTGTAATTTTGTGA
131 CGAACCTAGGGGAAAAATTGTAATTTTGTGA
55986193 AA
1 AA
55986195 CTTTAGGGGC
Statistics
Matches: 158, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
160 82 0.52
161 76 0.48
ACGTcount: A:0.42, C:0.07, G:0.18, T:0.32
Consensus pattern (161 bp):
AAATGACATAATCGGTAAAAATTATTATTGTTCATAAGTGCATGTTAGAGCAAGAATTTGATGTT
GATATAGAAGGGAAAAATATTCAACATGTTATAAATCATAAGAAAAAGGAATAAATTTTAATTTC
CGAACCTAGGGGAAAAATTGTAATTTTGTGA
Found at i:55986482 original size:50 final size:51
Alignment explanation
Indices: 55986389--55986522 Score: 139
Period size: 50 Copynumber: 2.6 Consensus size: 51
55986379 GTGAAGTTGC
* **
55986389 TAGGTCACGTGTGTAGTACTATGTGC-AGACTACTACGTGTACCAGAAT-G-A
1 TAGGTCACGTGTGTAGTACTATGTGCAAG-CTACAACGCATACCA-AATAGCA
* * * *
55986439 TAGGTCGCATGTGTAGTACTATGTGCAAGCTACAATGCATACCAAATAGCT
1 TAGGTCACGTGTGTAGTACTATGTGCAAGCTACAACGCATACCAAATAGCA
* * *
55986490 TCGATCACGTGTGTAGTACTATGTGCAGGCTAC
1 TAGGTCACGTGTGTAGTACTATGTGCAAGCTAC
55986523 TATGTGAACC
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
49 3 0.04
50 36 0.52
51 30 0.43
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (51 bp):
TAGGTCACGTGTGTAGTACTATGTGCAAGCTACAACGCATACCAAATAGCA
Found at i:55987071 original size:95 final size:95
Alignment explanation
Indices: 55986955--55987141 Score: 338
Period size: 95 Copynumber: 2.0 Consensus size: 95
55986945 AGAAACAGAG
* *
55986955 CAAGTAAAAGAATTATATATTTTGAGATATTTGAATTTTAGTGAGGCAGAGTTGGATTGATTTTG
1 CAAGCAAAAGAATTATATATTTTGAGATATTTGAATTTTAGTGAGACAGAGTTGGATTGATTTTG
55987020 GAATCCCCTGTTCTGACTTTGGAAAATGAA
66 GAATCCCCTGTTCTGACTTTGGAAAATGAA
* *
55987050 CAAGCAAAAGAGTTATATATTTTGAGATATTTGAATTTTAGTGAGACAGGGTTGGATTGATTTTG
1 CAAGCAAAAGAATTATATATTTTGAGATATTTGAATTTTAGTGAGACAGAGTTGGATTGATTTTG
55987115 GAATCCCCTGTTCTGACTTTGGAAAAT
66 GAATCCCCTGTTCTGACTTTGGAAAAT
55987142 AATTAAAAAT
Statistics
Matches: 88, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
95 88 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.37
Consensus pattern (95 bp):
CAAGCAAAAGAATTATATATTTTGAGATATTTGAATTTTAGTGAGACAGAGTTGGATTGATTTTG
GAATCCCCTGTTCTGACTTTGGAAAATGAA
Found at i:55989591 original size:37 final size:37
Alignment explanation
Indices: 55989550--55989626 Score: 136
Period size: 37 Copynumber: 2.1 Consensus size: 37
55989540 GGAAAGCTTG
*
55989550 TTTTACAAATTCCAAAATCATTTTCATTTCCTTCTTC
1 TTTTACAAATTCCAAAATCATTTTCATTTCCTTCTCC
*
55989587 TTTTACAAATTCCAAAATCATTTTCTTTTCCTTCTCC
1 TTTTACAAATTCCAAAATCATTTTCATTTCCTTCTCC
55989624 TTT
1 TTT
55989627 CTCTTCAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.25, C:0.25, G:0.00, T:0.51
Consensus pattern (37 bp):
TTTTACAAATTCCAAAATCATTTTCATTTCCTTCTCC
Found at i:55994279 original size:16 final size:17
Alignment explanation
Indices: 55994246--55994280 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55994236 TAAACATCTT
55994246 ATTAAAATAATATTTTA
1 ATTAAAATAATATTTTA
*
55994263 ATTAAGATAAT-TTTTA
1 ATTAAAATAATATTTTA
55994279 AT
1 AT
55994281 AAATTATAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (17 bp):
ATTAAAATAATATTTTA
Found at i:56000437 original size:19 final size:19
Alignment explanation
Indices: 56000415--56000451 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
56000405 CGAACGGATC
*
56000415 GCCTAAGGCCGAACAAATT
1 GCCTAAGCCCGAACAAATT
56000434 GCCTAAGCCCGAACAAAT
1 GCCTAAGCCCGAACAAAT
56000452 CGCAAGACGA
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:0.38, C:0.30, G:0.19, T:0.14
Consensus pattern (19 bp):
GCCTAAGCCCGAACAAATT
Found at i:56002853 original size:137 final size:137
Alignment explanation
Indices: 56002595--56002864 Score: 371
Period size: 137 Copynumber: 2.0 Consensus size: 137
56002585 TCAATTTAGG
* *
56002595 GATGAAATGTATGTGATTGAATGGTTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
1 GATGAAACGTATGTGATTGAATGATTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
* * * * * *
56002660 TATTTCTGATTGTATAGTAATACTCTGTAACCCTAATTCGACGATAGAGGCGGGTTAGGGGTGTT
66 TATTTCTGATTGTACAGTAATACTCCGTAACCCTAATTCGACGACAGAGACAGGTTAGAGGTGTT
56002725 ACATTTA
131 ACATTTA
* * *
56002732 GATGAAACGTATGTGATTGGATGATTTATGATATATTTAAATTATTGAGTGTTATGGTGTTTGAA
1 GATGAAACGTATGTGATTGAATGATTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
* * * * * *
56002797 TGTTTTTTATTGTACGGTAATACTCCGTAACCCTAATTTGGCGACAG-GTACAGGTTAGAGGTGT
66 TATTTCTGATTGTACAGTAATACTCCGTAACCCTAATTCGACGACAGAG-ACAGGTTAGAGGTGT
56002861 TACA
130 TACA
56002865 GTTCGAGTTT
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
136 1 0.01
137 114 0.99
ACGTcount: A:0.29, C:0.08, G:0.23, T:0.40
Consensus pattern (137 bp):
GATGAAACGTATGTGATTGAATGATTTATGATATATTTAAATTATTGAATGTTATGATGTTTGAA
TATTTCTGATTGTACAGTAATACTCCGTAACCCTAATTCGACGACAGAGACAGGTTAGAGGTGTT
ACATTTA
Found at i:56003381 original size:10 final size:10
Alignment explanation
Indices: 56003368--56003409 Score: 52
Period size: 10 Copynumber: 4.2 Consensus size: 10
56003358 CAAAAAGACA
56003368 AAGAGAAGAG
1 AAGAGAAGAG
56003378 AAGAGAAGAG
1 AAGAGAAGAG
56003388 -AGAG-AGAG
1 AAGAGAAGAG
56003396 AAAGAGAAAGAG
1 -AAGAG-AAGAG
56003408 AA
1 AA
56003410 TTGGAAATGA
Statistics
Matches: 28, Mismatches: 0, Indels: 7
0.80 0.00 0.20
Matches are distributed among these distances:
8 4 0.14
9 4 0.14
10 14 0.50
11 2 0.07
12 4 0.14
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (10 bp):
AAGAGAAGAG
Found at i:56003409 original size:6 final size:6
Alignment explanation
Indices: 56003361--56003409 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
56003351 AAAGAAACAA
* *
56003361 AAAGAC AAAGAG -AAGAG -AAGAG AAGAGAG AGAGAG AAAGAG AAAGAG
1 AAAGAG AAAGAG AAAGAG AAAGAG AA-AGAG AAAGAG AAAGAG AAAGAG
56003408 AA
1 AA
56003410 TTGGAAATGA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
5 10 0.26
6 23 0.61
7 5 0.13
ACGTcount: A:0.63, C:0.02, G:0.35, T:0.00
Consensus pattern (6 bp):
AAAGAG
Found at i:56003579 original size:23 final size:25
Alignment explanation
Indices: 56003547--56003610 Score: 78
Period size: 23 Copynumber: 2.6 Consensus size: 25
56003537 TATAAAAACC
* * *
56003547 AAAACGCACCGTTTAATTAAA-TC-
1 AAAACACACCGTTTAACTAAAGACA
*
56003570 AATACACACCGTTTAACTAAAGACA
1 AAAACACACCGTTTAACTAAAGACA
56003595 AAAACACACCGTTTAA
1 AAAACACACCGTTTAA
56003611 GCTAGCCAAC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
23 18 0.53
24 1 0.03
25 15 0.44
ACGTcount: A:0.47, C:0.23, G:0.08, T:0.22
Consensus pattern (25 bp):
AAAACACACCGTTTAACTAAAGACA
Found at i:56005445 original size:29 final size:28
Alignment explanation
Indices: 56005380--56005444 Score: 105
Period size: 28 Copynumber: 2.3 Consensus size: 28
56005370 AAATTAAAAA
*
56005380 TTACCAAAATGTTATAACTTTTTTTTAT
1 TTACCAAAATATTATAACTTTTTTTTAT
56005408 TTACCAAAATATATATAA-TTTTTTTTAT
1 TTACCAAAATAT-TATAACTTTTTTTTAT
56005436 TTACCAAAA
1 TTACCAAAA
56005445 AATAAAAAAA
Statistics
Matches: 35, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
28 30 0.86
29 5 0.14
ACGTcount: A:0.38, C:0.11, G:0.02, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATTATAACTTTTTTTTAT
Found at i:56005453 original size:9 final size:9
Alignment explanation
Indices: 56005440--56005484 Score: 65
Period size: 9 Copynumber: 5.0 Consensus size: 9
56005430 TTTTATTTAC
56005440 CAAAAAATAA
1 CAAAAAA-AA
56005450 -AAAAAAAA
1 CAAAAAAAA
56005458 CAAAAAAAA
1 CAAAAAAAA
*
56005467 CAGAAAAAA
1 CAAAAAAAA
56005476 CAAAAAAAA
1 CAAAAAAAA
56005485 ACCTGGACTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
8 2 0.06
9 30 0.94
ACGTcount: A:0.87, C:0.09, G:0.02, T:0.02
Consensus pattern (9 bp):
CAAAAAAAA
Found at i:56005555 original size:27 final size:27
Alignment explanation
Indices: 56005515--56005592 Score: 97
Period size: 27 Copynumber: 2.9 Consensus size: 27
56005505 TCCCTGGGTG
*
56005515 AAGGGAACACTGTTGGTGGCACCAAAC
1 AAGGGAACACTGTTGGCGGCACCAAAC
56005542 AAGGGAAC-CTTGTTGGCGGCACCAAAC
1 AAGGGAACAC-TGTTGGCGGCACCAAAC
* *
56005569 AA-GGATTCCCTGTTGGCGGCACCA
1 AAGGGA-ACACTGTTGGCGGCACCA
56005593 CCCTTGAATT
Statistics
Matches: 46, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
26 4 0.09
27 41 0.89
28 1 0.02
ACGTcount: A:0.28, C:0.26, G:0.29, T:0.17
Consensus pattern (27 bp):
AAGGGAACACTGTTGGCGGCACCAAAC
Found at i:56005662 original size:18 final size:17
Alignment explanation
Indices: 56005639--56005711 Score: 71
Period size: 19 Copynumber: 4.2 Consensus size: 17
56005629 GAAGGAGAGG
56005639 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
56005657 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
56005674 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
56005690 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
56005708 GGAA
1 GGAA
56005712 AGGAGAGGAA
Statistics
Matches: 46, Mismatches: 4, Indels: 11
0.75 0.07 0.18
Matches are distributed among these distances:
15 9 0.20
16 4 0.09
17 6 0.13
18 13 0.28
19 14 0.30
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:56005672 original size:10 final size:10
Alignment explanation
Indices: 56005641--56005712 Score: 54
Period size: 10 Copynumber: 6.6 Consensus size: 10
56005631 AGGAGAGGGG
*
56005641 AAGAAGAAGA
1 AAGAAAAAGA
56005651 AAGAAAGGAAGA
1 AAGAAA--AAGA
56005663 AAGAAAAAGA
1 AAGAAAAAGA
* *
56005673 AGGAAAAGGA
1 AAGAAAAAGA
56005683 AAGGAGAGGAAAGA
1 AA-GA-A--AAAGA
56005697 AAGAAAAAGA
1 AAGAAAAAGA
*
56005707 AGGAAA
1 AAGAAA
56005713 GGAGAGGAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
10 28 0.56
11 2 0.04
12 12 0.24
13 2 0.04
14 6 0.12
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (10 bp):
AAGAAAAAGA
Found at i:56005672 original size:22 final size:23
Alignment explanation
Indices: 56005641--56005727 Score: 61
Period size: 24 Copynumber: 3.7 Consensus size: 23
56005631 AGGAGAGGGG
*
56005641 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
56005663 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
56005685 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* * *
56005711 AAGGAGAGGAAAGAAAA
1 AAGAAAAAGAAAGAAAA
56005728 AAAAATAAGG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
22 12 0.24
23 10 0.20
24 24 0.49
25 2 0.04
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:56005684 original size:28 final size:28
Alignment explanation
Indices: 56005644--56005748 Score: 99
Period size: 28 Copynumber: 3.6 Consensus size: 28
56005634 AGAGGGGAAG
56005644 AAGAA-GAAA-GAAAGG-AAGAAAGAAA
1 AAGAAGGAAAGGAAAGGAAAGAAAGAAA
56005669 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAAGG--A--A-AGGAAAGAAAGAAA
* *
56005703 AAGAAGGAAAGGAGAGGAAAGAAAAAAA
1 AAGAAGGAAAGGAAAGGAAAGAAAGAAA
* *
56005731 AATAAGGAAAGAAAAGGA
1 AAGAAGGAAAGGAAAGGA
56005749 GAGGAGAAGA
Statistics
Matches: 66, Mismatches: 5, Indels: 15
0.77 0.06 0.17
Matches are distributed among these distances:
25 5 0.08
26 1 0.02
27 3 0.05
28 29 0.44
30 1 0.02
31 1 0.02
32 1 0.02
33 8 0.12
34 17 0.26
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.01
Consensus pattern (28 bp):
AAGAAGGAAAGGAAAGGAAAGAAAGAAA
Found at i:56005796 original size:30 final size:29
Alignment explanation
Indices: 56005738--56005804 Score: 84
Period size: 30 Copynumber: 2.3 Consensus size: 29
56005728 AAAAATAAGG
*
56005738 AAAGAAAAGGAGAGGAGAAGAGAAAAAAA
1 AAAGAAAAGAAGAGGAGAAGAGAAAAAAA
56005767 AAAGAAGAAGAAGAGG-GAAG-GAAGGAAAAA
1 AAAGAA-AAGAAGAGGAGAAGAGAA--AAAAA
56005797 AAAGAAAA
1 AAAGAAAA
56005805 TAAGGTAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
28 3 0.09
29 12 0.35
30 19 0.56
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (29 bp):
AAAGAAAAGAAGAGGAGAAGAGAAAAAAA
Found at i:56005797 original size:33 final size:32
Alignment explanation
Indices: 56005640--56005799 Score: 112
Period size: 33 Copynumber: 4.8 Consensus size: 32
56005630 AAGGAGAGGG
* * *
56005640 GAAGAAGAAGAAAGAAAGGAAGAAAGAAAAAGAA
1 GAAGAA-AAGGAAGGAAGGAA-AAAAAAAAAGAA
* *
56005674 G--GAAAAGGAAAGGAGAGGAAAGAAAGAAA-AA
1 GAAGAAAAGG-AAGGA-AGGAAAAAAAAAAAGAA
* * *
56005705 GAAGGAAAGGAGAGGAAAGAAAAAAAAATAAGGA
1 GAAGAAAAGGA-AGGAAGGAAAAAAAAA-AAGAA
*
56005739 -AAGAAAAGGAGAGGAGAAGAGAAAAAAAAAAGAA
1 GAAGAAAAGGA-AGGA-AGGA-AAAAAAAAAAGAA
*
56005773 GAAGAAGAGGGAAGGAAGGAAAAAAAA
1 GAAGAA-AAGGAAGGAAGGAAAAAAAA
56005800 GAAAATAAGG
Statistics
Matches: 101, Mismatches: 14, Indels: 23
0.73 0.10 0.17
Matches are distributed among these distances:
31 6 0.06
32 23 0.23
33 38 0.38
34 13 0.13
35 17 0.17
36 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.01
Consensus pattern (32 bp):
GAAGAAAAGGAAGGAAGGAAAAAAAAAAAGAA
Found at i:56006514 original size:18 final size:18
Alignment explanation
Indices: 56006482--56006517 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
56006472 AAAATATATA
*
56006482 TAATATTTTGGTATTTTT
1 TAATATTTTAGTATTTTT
*
56006500 TAATATTTTATTATTTTT
1 TAATATTTTAGTATTTTT
56006518 GTATAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.06, T:0.69
Consensus pattern (18 bp):
TAATATTTTAGTATTTTT
Found at i:56006588 original size:27 final size:27
Alignment explanation
Indices: 56006551--56006620 Score: 115
Period size: 27 Copynumber: 2.6 Consensus size: 27
56006541 AAATAAAAAA
56006551 TTACCAAAATATTATAAC-TTTTTTTAT
1 TTACCAAAATA-TATAACGTTTTTTTAT
*
56006578 TTACCAAAATATATATCGTTTTTTTAT
1 TTACCAAAATATATAACGTTTTTTTAT
56006605 TTACCAAAATATATAA
1 TTACCAAAATATATAA
56006621 AAAAGTAAAA
Statistics
Matches: 40, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 5 0.12
27 35 0.88
ACGTcount: A:0.40, C:0.11, G:0.01, T:0.47
Consensus pattern (27 bp):
TTACCAAAATATATAACGTTTTTTTAT
Found at i:56006639 original size:17 final size:18
Alignment explanation
Indices: 56006619--56006659 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
56006609 CAAAATATAT
*
56006619 AAAAAAGTAAAAAAACA-
1 AAAAAAATAAAAAAACAG
56006636 AAAAAAATAAAAAAACAG
1 AAAAAAATAAAAAAACAG
56006654 AAAAAA
1 AAAAAA
56006660 CACACTAAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.73
18 6 0.27
ACGTcount: A:0.85, C:0.05, G:0.05, T:0.05
Consensus pattern (18 bp):
AAAAAAATAAAAAAACAG
Found at i:56010053 original size:18 final size:18
Alignment explanation
Indices: 56010027--56010064 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
56010017 ATCCCAATGA
* *
56010027 TCGCCACCACCTTCTTCT
1 TCGCAACCACATTCTTCT
56010045 TCGCAACCACATTCTTCT
1 TCGCAACCACATTCTTCT
56010063 TC
1 TC
56010065 ACCACCAACC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.16, C:0.45, G:0.05, T:0.34
Consensus pattern (18 bp):
TCGCAACCACATTCTTCT
Done.