Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008527.1 Hibiscus syriacus cultivar Beakdansim tig00111402_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 9057482
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 23 of 37
Found at i:5471104 original size:7 final size:8
Alignment explanation
Indices: 5471086--5471111 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5471076 TTTTTCCTTC
5471086 TTTTTCAT
1 TTTTTCAT
5471094 TTTTTCAT
1 TTTTTCAT
5471102 TTTTTCAT
1 TTTTTCAT
5471110 TT
1 TT
5471112 CCTTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.00, T:0.77
Consensus pattern (8 bp):
TTTTTCAT
Found at i:5471118 original size:1 final size:1
Alignment explanation
Indices: 5471114--5471139 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
5471104 TTTCATTTCC
5471114 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
5471140 AGGTGTAATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5482790 original size:15 final size:16
Alignment explanation
Indices: 5482772--5482805 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
5482762 TATGAACATC
*
5482772 AAATAAATTAACAA-A
1 AAATAAAATAACAATA
5482787 AAATAAAATAACAATA
1 AAATAAAATAACAATA
5482803 AAA
1 AAA
5482806 ATAATTTCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
AAATAAAATAACAATA
Found at i:5484437 original size:25 final size:25
Alignment explanation
Indices: 5484399--5484547 Score: 264
Period size: 25 Copynumber: 6.0 Consensus size: 25
5484389 TGGAAGGGGA
*
5484399 TTAGGG-TTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
5484423 TTAGGGTTTGAAACCCTAAATTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5484448 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5484473 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5484498 TTAGGGTTTGAAACCCTAAACTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
*
5484523 TTAGGGTTTGAAACCCTAATCTGAT
1 TTAGGGTTTGAAACCCTAAACTGAT
5484548 GGGTTATTGG
Statistics
Matches: 122, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
24 6 0.05
25 116 0.95
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.34
Consensus pattern (25 bp):
TTAGGGTTTGAAACCCTAAACTGAT
Found at i:5484685 original size:3 final size:3
Alignment explanation
Indices: 5484677--5484740 Score: 89
Period size: 3 Copynumber: 22.0 Consensus size: 3
5484667 GCAAAAATTG
*
5484677 TAA TAA TAAA TAA TAA TAA -AA TAA TAA T-A TAA TGA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5484721 TAA TAA TAA TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA
5484741 CGGAAAAAAA
Statistics
Matches: 55, Mismatches: 2, Indels: 8
0.85 0.03 0.12
Matches are distributed among these distances:
2 6 0.11
3 46 0.84
4 3 0.05
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:5491799 original size:16 final size:16
Alignment explanation
Indices: 5491774--5491806 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
5491764 TTCAGAATGG
5491774 TTAAACGCTGAATGAT
1 TTAAACGCTGAATGAT
*
5491790 TTAAATGCTGAATGAT
1 TTAAACGCTGAATGAT
5491806 T
1 T
5491807 CAGATGCTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.36, C:0.09, G:0.18, T:0.36
Consensus pattern (16 bp):
TTAAACGCTGAATGAT
Found at i:5491813 original size:16 final size:16
Alignment explanation
Indices: 5491780--5491814 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5491770 ATGGTTAAAC
*
5491780 GCTGAATGATTTAAAT
1 GCTGAATGATTCAAAT
*
5491796 GCTGAATGATTCAGAT
1 GCTGAATGATTCAAAT
5491812 GCT
1 GCT
5491815 CCGTATGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.31, C:0.11, G:0.23, T:0.34
Consensus pattern (16 bp):
GCTGAATGATTCAAAT
Found at i:5491992 original size:22 final size:22
Alignment explanation
Indices: 5491964--5492013 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
5491954 CGCTAAATGT
*
5491964 TGAATGGTTCAGCATTCAACGC
1 TGAATGGTTCAACATTCAACGC
5491986 TGAATGGTTCAACATTCAACGC
1 TGAATGGTTCAACATTCAACGC
*
5492008 TAAATG
1 TGAATG
5492014 ATTCCATTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.28
Consensus pattern (22 bp):
TGAATGGTTCAACATTCAACGC
Found at i:5504955 original size:2 final size:2
Alignment explanation
Indices: 5504948--5504982 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
5504938 TTCCATATTT
5504948 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5504983 TGAAATAAGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5510228 original size:22 final size:22
Alignment explanation
Indices: 5510203--5510244 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
5510193 TTCAATCTTA
5510203 AAAT-TTGAGAAATTAAGATTTT
1 AAATCTTGAG-AATTAAGATTTT
*
5510225 AAATCTTGAGATTTAAGATT
1 AAATCTTGAGAATTAAGATT
5510245 AAAATATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 13 0.72
23 5 0.28
ACGTcount: A:0.43, C:0.02, G:0.14, T:0.40
Consensus pattern (22 bp):
AAATCTTGAGAATTAAGATTTT
Found at i:5516474 original size:15 final size:15
Alignment explanation
Indices: 5516454--5516486 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5516444 TGAGACATTA
*
5516454 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
5516469 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
5516484 CCC
1 CCC
5516487 ACCCAACTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.09, C:0.70, G:0.15, T:0.06
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:5517747 original size:20 final size:20
Alignment explanation
Indices: 5517724--5517783 Score: 102
Period size: 20 Copynumber: 3.0 Consensus size: 20
5517714 CACACTATTC
5517724 AGTGTTTAGTGGACTATTTT
1 AGTGTTTAGTGGACTATTTT
*
5517744 AGTGTTTAGTGGACTATTAT
1 AGTGTTTAGTGGACTATTTT
5517764 AGTGTTTAGTGGACTGATTT
1 AGTGTTTAGTGGACT-ATTT
5517784 CGACGGTGTA
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
20 34 0.92
21 3 0.08
ACGTcount: A:0.22, C:0.05, G:0.27, T:0.47
Consensus pattern (20 bp):
AGTGTTTAGTGGACTATTTT
Found at i:5520898 original size:20 final size:20
Alignment explanation
Indices: 5520875--5520912 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5520865 AATAATTAAA
5520875 TAATTTAATTAATA-AAATTT
1 TAATTTAA-TAATATAAATTT
5520895 TAATTTAATAATATAAAT
1 TAATTTAATAATATAAAT
5520913 AAAATATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (20 bp):
TAATTTAATAATATAAATTT
Found at i:5526713 original size:2 final size:2
Alignment explanation
Indices: 5526706--5526743 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
5526696 TGTTAAAGGA
5526706 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5526744 TGGAGAATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5527999 original size:3 final size:3
Alignment explanation
Indices: 5527991--5528036 Score: 65
Period size: 3 Copynumber: 15.3 Consensus size: 3
5527981 TTTAATCATT
* * *
5527991 TTA TTA TTA TTA TTC TTA TTC TTA TTC TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5528037 GTGAATACTT
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:5529453 original size:14 final size:14
Alignment explanation
Indices: 5529434--5529463 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
5529424 TATGTTGTTG
5529434 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
5529448 ACTTGTTCTTTCTC
1 ACTTGTTCTTTCTC
5529462 AC
1 AC
5529464 AATCAACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.10, C:0.30, G:0.07, T:0.53
Consensus pattern (14 bp):
ACTTGTTCTTTCTC
Found at i:5531469 original size:13 final size:14
Alignment explanation
Indices: 5531451--5531481 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
5531441 TATATAAAAA
5531451 AAAATCT-AAATAG
1 AAAATCTGAAATAG
5531464 AAAATCTGAAATAG
1 AAAATCTGAAATAG
5531478 AAAA
1 AAAA
5531482 AAAATTCACT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.41
14 10 0.59
ACGTcount: A:0.65, C:0.06, G:0.10, T:0.19
Consensus pattern (14 bp):
AAAATCTGAAATAG
Found at i:5540228 original size:20 final size:23
Alignment explanation
Indices: 5540174--5540228 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 23
5540164 TTTATTAAAA
*
5540174 TATTAAATTATTAAATAATGAGT
1 TATTAAAATATTAAATAATGAGT
*
5540197 TATTAAAA-ATTAAA-AAT-ATT
1 TATTAAAATATTAAATAATGAGT
5540217 TA-TAAAATATTA
1 TATTAAAATATTA
5540229 TTTTTTCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
19 5 0.17
20 8 0.28
21 3 0.10
22 6 0.21
23 7 0.24
ACGTcount: A:0.55, C:0.00, G:0.04, T:0.42
Consensus pattern (23 bp):
TATTAAAATATTAAATAATGAGT
Found at i:5542034 original size:2 final size:2
Alignment explanation
Indices: 5542029--5542062 Score: 59
Period size: 2 Copynumber: 16.5 Consensus size: 2
5542019 TGTGTGTGTG
5542029 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TCA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA T
5542063 TATCGTATTA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 29 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5542265 original size:20 final size:20
Alignment explanation
Indices: 5542240--5542292 Score: 79
Period size: 20 Copynumber: 2.6 Consensus size: 20
5542230 CAGCAGCAGA
**
5542240 TATTGATTTTATTTATTTTT
1 TATTGATTCAATTTATTTTT
5542260 TATTGATTCAATTTATTTTT
1 TATTGATTCAATTTATTTTT
*
5542280 TATTCATTCAATT
1 TATTGATTCAATT
5542293 GGTGATATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.25, C:0.06, G:0.04, T:0.66
Consensus pattern (20 bp):
TATTGATTCAATTTATTTTT
Found at i:5542728 original size:22 final size:24
Alignment explanation
Indices: 5542672--5542728 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 24
5542662 TTAAATTACC
5542672 TTTAGATTTTTAACTAATTTATAA
1 TTTAGATTTTTAACTAATTTATAA
* * *
5542696 -TTATATATTTAA-TATTTTATAA
1 TTTAGATTTTTAACTAATTTATAA
5542718 TTTA-ATTTTTA
1 TTTAGATTTTTA
5542729 TAAATTAATT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
22 15 0.54
23 13 0.46
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (24 bp):
TTTAGATTTTTAACTAATTTATAA
Found at i:5542731 original size:14 final size:14
Alignment explanation
Indices: 5542696--5542739 Score: 61
Period size: 14 Copynumber: 3.0 Consensus size: 14
5542686 TAATTTATAA
5542696 TTATATATTTAATATT
1 TTATA-ATTTAAT-TT
5542712 TTATAATTTAATTT
1 TTATAATTTAATTT
*
5542726 TTATAAATTAATTT
1 TTATAATTTAATTT
5542740 AATAATATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
14 15 0.56
15 7 0.26
16 5 0.19
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
TTATAATTTAATTT
Found at i:5573385 original size:73 final size:73
Alignment explanation
Indices: 5573266--5573412 Score: 276
Period size: 73 Copynumber: 2.0 Consensus size: 73
5573256 TTATTATAAC
* *
5573266 CATTATCAATCGTAATAATATAATATGTAGCGCTTATTTAATCAAAATATTCTCTCATTCTTTCT
1 CATTATCAATCGTAATAACATAATATGTAGCGCTTATTTAATCAAAATATTCTCTCATTCCTTCT
5573331 TAGAATGT
66 TAGAATGT
5573339 CATTATCAATCGTAATAACATAATATGTAGCGCTTATTTAATCAAAATATTCTCTCATTCCTTCT
1 CATTATCAATCGTAATAACATAATATGTAGCGCTTATTTAATCAAAATATTCTCTCATTCCTTCT
5573404 TAGAATGT
66 TAGAATGT
5573412 C
1 C
5573413 GTTTGCTTTG
Statistics
Matches: 72, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
73 72 1.00
ACGTcount: A:0.34, C:0.17, G:0.08, T:0.41
Consensus pattern (73 bp):
CATTATCAATCGTAATAACATAATATGTAGCGCTTATTTAATCAAAATATTCTCTCATTCCTTCT
TAGAATGT
Found at i:5574656 original size:4 final size:4
Alignment explanation
Indices: 5574655--5574712 Score: 80
Period size: 4 Copynumber: 14.5 Consensus size: 4
5574645 TATATGTGTG
* * *
5574655 TGTA TGTA TGTA TGTA TGTG TGTA TGTA TGTA TGTA TGTG TGTG TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
*
5574703 TATA TGTA TG
1 TGTA TGTA TG
5574713 CAAATTGTTT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
4 48 1.00
ACGTcount: A:0.21, C:0.00, G:0.29, T:0.50
Consensus pattern (4 bp):
TGTA
Found at i:5574659 original size:24 final size:24
Alignment explanation
Indices: 5574632--5574707 Score: 61
Period size: 22 Copynumber: 3.3 Consensus size: 24
5574622 TGTTTCGAAA
5574632 GTATATATATATATATATGTGTGT
1 GTATATATATATATATATGTGTGT
* * *
5574656 G--TATGTATGTATGTA--TGTGT
1 GTATATATATATATATATGTGTGT
* * * *
5574676 GTATGTATGTATGTATGTGTGTGT
1 GTATATATATATATATATGTGTGT
5574700 GTATATAT
1 GTATATAT
5574708 GTATGCAAAT
Statistics
Matches: 37, Mismatches: 11, Indels: 8
0.66 0.20 0.14
Matches are distributed among these distances:
20 6 0.16
22 18 0.49
24 13 0.35
ACGTcount: A:0.25, C:0.00, G:0.25, T:0.50
Consensus pattern (24 bp):
GTATATATATATATATATGTGTGT
Found at i:5574676 original size:20 final size:20
Alignment explanation
Indices: 5574651--5574712 Score: 106
Period size: 20 Copynumber: 3.1 Consensus size: 20
5574641 TATATATATG
5574651 TGTGTGTATGTATGTATGTA
1 TGTGTGTATGTATGTATGTA
5574671 TGTGTGTATGTATGTATGTA
1 TGTGTGTATGTATGTATGTA
* *
5574691 TGTGTGTGTGTATATATGTA
1 TGTGTGTATGTATGTATGTA
5574711 TG
1 TG
5574713 CAAATTGTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.19, C:0.00, G:0.31, T:0.50
Consensus pattern (20 bp):
TGTGTGTATGTATGTATGTA
Found at i:5574970 original size:143 final size:144
Alignment explanation
Indices: 5574737--5575041 Score: 418
Period size: 143 Copynumber: 2.1 Consensus size: 144
5574727 ATCATATTGG
*
5574737 AATAAAAGTATCGATACGAGCATCACAAGTATCGATACTTGGACATTTCAAATATTGCATATATT
1 AATAAAAGTATCGATACGAGCATAACAAGTATCGATACTTGGACATTTCAAATATTGCATATATT
* * * **
5574802 GTTTCGAAATTATATATATCGATAC-TT-TATATGTGTATTAATATATTTTGTGTGCAAATTGTT
66 GTTTCGAAATTATATATATCAATACTTTATATATGTGTATCAATACATTTTACGTGCAAATTGTT
5574865 TGAAAAATATACCTT
131 T-AAAAATATACCTT
* * * *
5574880 AATAAAAGTATCGATATGGGCTTAACAAGTATCGATACTTGGACATTTCAGATATTGCATATATT
1 AATAAAAGTATCGATACGAGCATAACAAGTATCGATACTTGGACATTTCAAATATTGCATATATT
* * *
5574945 GTTTTGAAATTATATGTATCAATACTTTATATATGTGTATCAATACATTTTACGTGTAAATTGTT
66 GTTTCGAAATTATATATATCAATACTTTATATATGTGTATCAATACATTTTACGTGCAAATTGTT
* *
5575010 TAAAAACCATA-CTAA
131 TAAAAA-TATACCT-T
*
5575025 AATAAAAGTATCAATAC
1 AATAAAAGTATCGATAC
5575042 AGAAATAATA
Statistics
Matches: 141, Mismatches: 17, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
143 82 0.58
144 9 0.06
145 50 0.35
ACGTcount: A:0.38, C:0.11, G:0.13, T:0.38
Consensus pattern (144 bp):
AATAAAAGTATCGATACGAGCATAACAAGTATCGATACTTGGACATTTCAAATATTGCATATATT
GTTTCGAAATTATATATATCAATACTTTATATATGTGTATCAATACATTTTACGTGCAAATTGTT
TAAAAATATACCTT
Found at i:5583784 original size:2 final size:2
Alignment explanation
Indices: 5583773--5583805 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5583763 CTTTCACATT
*
5583773 TA TA TA -A TA TA TA TA TA TA TA TA TA TA AA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5583806 ATTACTAAGG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:5590589 original size:31 final size:31
Alignment explanation
Indices: 5590548--5590628 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 31
5590538 CCTGCATCCG
*
5590548 ACCTAAACCCGAATTGAACCGAA-AATATGA
1 ACCTGAACCCGAATTGAACCGAATAATATGA
* * *
5590578 TACCTGAACCCGAACTGCATCCGAATGATATGA
1 -ACCTGAACCCGAATTG-AACCGAATAATATGA
*
5590611 ACCCGAACCCGAGATTGA
1 ACCTGAACCCGA-ATTGA
5590629 CCTGGTAAAT
Statistics
Matches: 41, Mismatches: 6, Indels: 5
0.79 0.12 0.10
Matches are distributed among these distances:
31 14 0.34
32 18 0.44
33 9 0.22
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.17
Consensus pattern (31 bp):
ACCTGAACCCGAATTGAACCGAATAATATGA
Found at i:5590972 original size:14 final size:14
Alignment explanation
Indices: 5590950--5590996 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
5590940 TGCAAAGAAA
*
5590950 AATTAATATAGTTT
1 AATTTATATAGTTT
5590964 AATTTATATA----
1 AATTTATATAGTTT
5590974 AA-TTATATAGTTT
1 AATTTATATAGTTT
5590987 AATTTATATA
1 AATTTATATA
5590997 AAGAAAAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 7 0.26
10 2 0.07
13 2 0.07
14 16 0.59
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (14 bp):
AATTTATATAGTTT
Found at i:5590983 original size:23 final size:24
Alignment explanation
Indices: 5590949--5590998 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
5590939 ATGCAAAGAA
5590949 AAATTAATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
5590973 AAATT-ATATAGTTTAATTTATAT
1 AAATTAATATAGTTTAATTTATAT
5590996 AAA
1 AAA
5590999 GAAAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 21 0.81
24 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.04, T:0.48
Consensus pattern (24 bp):
AAATTAATATAGTTTAATTTATAT
Found at i:5594259 original size:102 final size:102
Alignment explanation
Indices: 5594083--5594413 Score: 488
Period size: 102 Copynumber: 3.3 Consensus size: 102
5594073 AATGAACAAC
* * *
5594083 CAACAATAGCAACAAATTAAACAGTTCATTTAAATTGTAAATAAAGGAAGCTAACAACCTTATAA
1 CAACAATAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
*
5594148 AAGCAATCCGAATGAACAACCAACAACACAAACAAAT
66 AAGTAATCCGAATGAACAACCAACAACACAAACAAAT
* * *
5594185 CAACAATAGCAACAAATTGAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAAACTTATAG
1 CAACAATAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
*
5594250 AAGTAATCCGAATGAA-AA--ACCAACACAAACAAAT
66 AAGTAATCCGAATGAACAACCAACAACACAAACAAAT
* * * *
5594284 CAACAATAGCTACAAATTAAATAGTTTATTTGAACTATAAATAAAGGCAGCTAACAACCTTATAA
1 CAACAATAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
*
5594349 AAGTAATCTGAATGAACAACCAACAACACAAACAAAT
66 AAGTAATCCGAATGAACAACCAACAACACAAACAAAT
* * * *
5594386 CAGCAGTAGCTACAAATTAAACAATTTA
1 CAACAATAGCAACAAATTAAACAGTTTA
5594414 GTTACCTCTT
Statistics
Matches: 205, Mismatches: 21, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
99 88 0.43
100 2 0.01
101 2 0.01
102 113 0.55
ACGTcount: A:0.51, C:0.18, G:0.10, T:0.21
Consensus pattern (102 bp):
CAACAATAGCAACAAATTAAACAGTTTATTTAAACTGTAAATAAAGGCAGCTAACAACCTTATAA
AAGTAATCCGAATGAACAACCAACAACACAAACAAAT
Found at i:5596993 original size:102 final size:102
Alignment explanation
Indices: 5596704--5597033 Score: 481
Period size: 102 Copynumber: 3.3 Consensus size: 102
5596694 AAGAGGTAAC
*
5596704 TAAACTGTTTAATTTGTAGTTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGATTAC-T
1 TAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGATTACTT
* * *
5596768 TTATAAGGTTGTTACCTGCCTTTATTTATAGTTCAAA
66 TTATAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAA
* *
5596805 TAAACTGTTTAATTTGTAGTTACTGTTGATTTG-TT-TG-TGTTGGTTTTTCATTCAGATTACTT
1 TAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGATTACTT
* *
5596867 CTATAAGGTTGTTAGCTGTCTTTATTTACAGTTTAAA
66 TTATAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAA
* * * *
5596904 TAATA-TGTTCAATTTGTTGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCGGATTGCT
1 TAA-ACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGATTACT
*
5596968 TTTATAAGGTTGTTAGCTGCCTTTATTTAGAGTTTAAA
65 TTTATAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAA
* *
5597006 TAAACTGTTTATTTTGTTGCTACTGTTG
1 TAAACTGTTTAATTTGTAGCTACTGTTG
5597034 GTTGTTCATT
Statistics
Matches: 206, Mismatches: 17, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
98 22 0.11
99 63 0.31
100 5 0.02
101 36 0.17
102 80 0.39
ACGTcount: A:0.21, C:0.09, G:0.19, T:0.51
Consensus pattern (102 bp):
TAAACTGTTTAATTTGTAGCTACTGTTGATTTGTTTGTGTTGTTGGTTGTTCATTCAGATTACTT
TTATAAGGTTGTTAGCTGCCTTTATTTACAGTTTAAA
Found at i:5600171 original size:23 final size:24
Alignment explanation
Indices: 5600143--5600189 Score: 87
Period size: 23 Copynumber: 2.0 Consensus size: 24
5600133 TTTTTCTTTA
5600143 TATAAATTAAACTATA-TAATTTT
1 TATAAATTAAACTATATTAATTTT
5600166 TATAAATTAAACTATATTAATTTT
1 TATAAATTAAACTATATTAATTTT
5600190 CCTTTGCATT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.70
24 7 0.30
ACGTcount: A:0.47, C:0.04, G:0.00, T:0.49
Consensus pattern (24 bp):
TATAAATTAAACTATATTAATTTT
Found at i:5600470 original size:32 final size:32
Alignment explanation
Indices: 5600429--5600504 Score: 107
Period size: 32 Copynumber: 2.4 Consensus size: 32
5600419 TTTACAGGTA
*
5600429 AGGTTAAAAACATGTCAGATTAAAAACAGATC
1 AGGTTAAAAACATGTCAGATTAAAAACAAATC
* * *
5600461 AGGTTAAAAACATGTTAGGTTGAAAACAAATC
1 AGGTTAAAAACATGTCAGATTAAAAACAAATC
*
5600493 AGGTTGAAAACA
1 AGGTTAAAAACA
5600505 GGTCGGATAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 39 1.00
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (32 bp):
AGGTTAAAAACATGTCAGATTAAAAACAAATC
Found at i:5600480 original size:16 final size:16
Alignment explanation
Indices: 5600429--5600504 Score: 82
Period size: 16 Copynumber: 4.8 Consensus size: 16
5600419 TTTACAGGTA
5600429 AGGTTAAAAACATGTC
1 AGGTTAAAAACATGTC
*
5600445 AGATTAAAAACA-GATC
1 AGGTTAAAAACATG-TC
*
5600461 AGGTTAAAAACATGTT
1 AGGTTAAAAACATGTC
* **
5600477 AGGTTGAAAACAAATC
1 AGGTTAAAAACATGTC
*
5600493 AGGTTGAAAACA
1 AGGTTAAAAACA
5600505 GGTCGGATAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
15 1 0.02
16 49 0.96
17 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.22
Consensus pattern (16 bp):
AGGTTAAAAACATGTC
Found at i:5600985 original size:39 final size:39
Alignment explanation
Indices: 5600941--5601037 Score: 185
Period size: 39 Copynumber: 2.5 Consensus size: 39
5600931 TTTAATGAAA
*
5600941 GTGCTCCACTTTGCATATAATTTCCAAGCAAACTGATCT
1 GTGCTCCACTTTGCATATAATTTCCAAGCAAACTAATCT
5600980 GTGCTCCACTTTGCATATAATTTCCAAGCAAACTAATCT
1 GTGCTCCACTTTGCATATAATTTCCAAGCAAACTAATCT
5601019 GTGCTCCACTTTGCATATA
1 GTGCTCCACTTTGCATATA
5601038 TGTAGTTTCA
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 57 1.00
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.34
Consensus pattern (39 bp):
GTGCTCCACTTTGCATATAATTTCCAAGCAAACTAATCT
Found at i:5604309 original size:15 final size:16
Alignment explanation
Indices: 5604279--5604311 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
5604269 TTCAAATCCC
5604279 AAAACAAAAGCAAATA
1 AAAACAAAAGCAAATA
*
5604295 AAAACAATAGC-AATA
1 AAAACAAAAGCAAATA
5604310 AA
1 AA
5604312 CTGGGAACAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.73, C:0.12, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAACAAAAGCAAATA
Found at i:5605118 original size:3 final size:3
Alignment explanation
Indices: 5605110--5605137 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5605100 TCCTGCATTT
5605110 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA G
5605138 GGAAGAATCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.36, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:5608944 original size:12 final size:12
Alignment explanation
Indices: 5608927--5608955 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
5608917 GGGCGACCTA
5608927 CGACGTGGCTTC
1 CGACGTGGCTTC
5608939 CGACGTGGCTTC
1 CGACGTGGCTTC
5608951 CGACG
1 CGACG
5608956 AGGGTCGTGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.10, C:0.34, G:0.34, T:0.21
Consensus pattern (12 bp):
CGACGTGGCTTC
Found at i:5609079 original size:29 final size:29
Alignment explanation
Indices: 5608994--5609063 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
5608984 CCAACCATAA
* * ****
5608994 GTCGCCATGCACTCCCAGCGACCTCCTAG
1 GTCGCCATGCACGCCCGGCGACCAAGGAG
5609023 GTCGCCATGCACGCCCGGCGACCAAGGAG
1 GTCGCCATGCACGCCCGGCGACCAAGGAG
5609052 GTCGCCATGCAC
1 GTCGCCATGCAC
5609064 TCGGGACGAC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.19, C:0.41, G:0.27, T:0.13
Consensus pattern (29 bp):
GTCGCCATGCACGCCCGGCGACCAAGGAG
Found at i:5615443 original size:96 final size:100
Alignment explanation
Indices: 5615256--5615456 Score: 277
Period size: 96 Copynumber: 2.0 Consensus size: 100
5615246 CTAGGGTTTT
*
5615256 TATAGGATAGAGTTGTTAGCAATTGTTAGGAATTTACATACATAACGCAGACCTAGTTGAAATGA
1 TATAGAATAGAGTTGTTAGCAATTGTTAGGAATTTACATACATAACGCAGACCTAGTTGAAATGA
* *
5615321 CTTGGTAAAAGGGGCAGAAATAAATAAATGAATAA
66 CTTAGTAAAAGGGGAAGAAATAAATAAATGAATAA
* * * *
5615356 TATAGAAT-GAGTTGTTA-C-A-TGTTAGGTATTTACATGCATTAA-GTAGACCTAGTTTAAATG
1 TATAGAATAGAGTTGTTAGCAATTGTTAGGAATTTACATACA-TAACGCAGACCTAGTTGAAATG
* *
5615416 ACTTAGTGAAAGGGGAAGAACTAAATAAATGAATAA
65 ACTTAGTAAAAGGGGAAGAAATAAATAAATGAATAA
5615452 TATAG
1 TATAG
5615457 GGATTGCATT
Statistics
Matches: 91, Mismatches: 9, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
96 70 0.77
97 4 0.04
98 1 0.01
99 9 0.10
100 7 0.08
ACGTcount: A:0.41, C:0.08, G:0.21, T:0.29
Consensus pattern (100 bp):
TATAGAATAGAGTTGTTAGCAATTGTTAGGAATTTACATACATAACGCAGACCTAGTTGAAATGA
CTTAGTAAAAGGGGAAGAAATAAATAAATGAATAA
Found at i:5619090 original size:30 final size:32
Alignment explanation
Indices: 5619033--5619091 Score: 86
Period size: 30 Copynumber: 1.9 Consensus size: 32
5619023 TCGTCGACTT
* *
5619033 TTATATTTCTTATTTTCTTTTATTTTTTATTG
1 TTATATCTCTTATTTTCTTTTAATTTTTATTG
5619065 TTATATCT-TTATTTT-TTTTAATTTTTA
1 TTATATCTCTTATTTTCTTTTAATTTTTA
5619092 ATAATTTTGA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
30 11 0.44
31 7 0.28
32 7 0.28
ACGTcount: A:0.19, C:0.05, G:0.02, T:0.75
Consensus pattern (32 bp):
TTATATCTCTTATTTTCTTTTAATTTTTATTG
Found at i:5619148 original size:21 final size:20
Alignment explanation
Indices: 5619102--5619149 Score: 53
Period size: 21 Copynumber: 2.3 Consensus size: 20
5619092 ATAATTTTGA
5619102 TTTTATGACAATTTTTTACAT
1 TTTTATGACAATTTTTTA-AT
*
5619123 ATTTATGACACATTTTTCT-AT
1 TTTTATGACA-ATTTTT-TAAT
5619144 TTTTAT
1 TTTTAT
5619150 TTTTTTGTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
21 16 0.70
22 6 0.26
23 1 0.04
ACGTcount: A:0.27, C:0.10, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTATGACAATTTTTTAAT
Found at i:5625894 original size:789 final size:789
Alignment explanation
Indices: 5624375--5625953 Score: 3149
Period size: 789 Copynumber: 2.0 Consensus size: 789
5624365 CTCCTTGGTA
5624375 ATCCTGCAAGTGTGAGCTTAATAGACTGCTGAGAAGCTTCATTGGGTGCTAATAGATCAACAGGG
1 ATCCTGCAAGTGTGAGCTTAATAGACTGCTGAGAAGCTTCATTGGGTGCTAATAGATCAACAGGG
*
5624440 CGATGAAGTTTGCATCTCTCTCCGAATTTACATTTGCCAGTTTTCACATAGTTCTGCAATGTAAA
66 CGATGAAGTTTGCATCTCTCTCCGAATTTACATTTGCCAGTTTTCACATAGTACTGCAATGTAAA
5624505 GAAATAAAACGGGGGGAAAGTCATCAATAAGCATAGGGATTCCTGCAATGCTTGACATTACAAAG
131 GAAATAAAACGGGGGGAAAGTCATCAATAAGCATAGGGATTCCTGCAATGCTTGACATTACAAAG
5624570 TGAGCCAACAGTATGTCCAAGGTAATTTGGATGCTTGATATGAAAACTGTGGCACAAAAGAATTG
196 TGAGCCAACAGTATGTCCAAGGTAATTTGGATGCTTGATATGAAAACTGTGGCACAAAAGAATTG
5624635 TGCAGCACTAATCCAAGCTCAATAATGTGTACCATCTTGATAGTCATAAGAAAATTGGGTGGCAA
261 TGCAGCACTAATCCAAGCTCAATAATGTGTACCATCTTGATAGTCATAAGAAAATTGGGTGGCAA
5624700 GGAATTCAAAATAACAATTAAAAACAAACATATATCAAAACGACACAGAATGGATTGATTTGCAC
326 GGAATTCAAAATAACAATTAAAAACAAACATATATCAAAACGACACAGAATGGATTGATTTGCAC
5624765 ATCTCATTCAGTTTGTCCTGGTCTCTGAGGATACACAGTCTGACTGCCTGCCAGCTGCAATAGGT
391 ATCTCATTCAGTTTGTCCTGGTCTCTGAGGATACACAGTCTGACTGCCTGCCAGCTGCAATAGGT
5624830 AAATAAATAATATACATCAGCCCTTAGGGAAACAAAAAAAATTCAGAAACATCAAGCAAAATACC
456 AAATAAATAATATACATCAGCCCTTAGGGAAACAAAAAAAATTCAGAAACATCAAGCAAAATACC
5624895 TCCACAGAGAAAGTTCTTGCATTATTGTACAGAAATTTTGGCAAACGTAGGAGGCAAGATTGAAG
521 TCCACAGAGAAAGTTCTTGCATTATTGTACAGAAATTTTGGCAAACGTAGGAGGCAAGATTGAAG
5624960 CTAAAGAGTAAAGATTACTCTAAATTTTGCAAACTGGTATATATTATAAAGGCAGCCAATGCAAT
586 CTAAAGAGTAAAGATTACTCTAAATTTTGCAAACTGGTATATATTATAAAGGCAGCCAATGCAAT
5625025 CAAAGTAGCCACAGGAACTCAAAACCATAGAAGACTGAGCGAAACTTGGGTGATATGAAGTAGAA
651 CAAAGTAGCCACAGGAACTCAAAACCATAGAAGACTGAGCGAAACTTGGGTGATATGAAGTAGAA
5625090 CTTGAACAAAAGAACGTAGCAGATGAATGACTAAACAAGTAATAGCCCTTGGAAGAGATAGTGAC
716 CTTGAACAAAAGAACGTAGCAGATGAATGACTAAACAAGTAATAGCCCTTGGAAGAGATAGTGAC
5625155 CTAGTCCCT
781 CTAGTCCCT
5625164 ATCCTGCAAGTGTGAGCTTAATAGACTGCTGAGAAGCTTCATTGGGTGCTAATAGATCAACAGGG
1 ATCCTGCAAGTGTGAGCTTAATAGACTGCTGAGAAGCTTCATTGGGTGCTAATAGATCAACAGGG
5625229 CGATGAAGTTTGCATCTCTCTCCGAATTTACATTTGCCAGTTTTCACATAGTACTGCAATGTAAA
66 CGATGAAGTTTGCATCTCTCTCCGAATTTACATTTGCCAGTTTTCACATAGTACTGCAATGTAAA
5625294 GAAATAAAACGGGGGGAAAGTCATCAATAAGCATAGGGATTCCTGCAATGCTTGACATTACAAAG
131 GAAATAAAACGGGGGGAAAGTCATCAATAAGCATAGGGATTCCTGCAATGCTTGACATTACAAAG
5625359 TGAGCCAACAGTATGTCCAAGGTAATTTGGATGCTTGATATGAAAACTGTGGCACAAAAGAATTG
196 TGAGCCAACAGTATGTCCAAGGTAATTTGGATGCTTGATATGAAAACTGTGGCACAAAAGAATTG
5625424 TGCAGCACTAATCCAAGCTCAATAATGTGTACCATCTTGATAGTCATAAGAAAATTGGGTGGCAA
261 TGCAGCACTAATCCAAGCTCAATAATGTGTACCATCTTGATAGTCATAAGAAAATTGGGTGGCAA
5625489 GGAATTCAAAATAACAATTAAAAACAAACATATATCAAAACGACACAGAATGGATTGATTTGCAC
326 GGAATTCAAAATAACAATTAAAAACAAACATATATCAAAACGACACAGAATGGATTGATTTGCAC
5625554 ATCTCATTCAGTTTGTCCTGGTCTCTGAGGATACACAGTCTGACTGCCTGCCAGCTGCAATAGGT
391 ATCTCATTCAGTTTGTCCTGGTCTCTGAGGATACACAGTCTGACTGCCTGCCAGCTGCAATAGGT
5625619 AAATAAATAATATACATCAGCCCTTAGGGAAACAAAAAAAATTCAGAAACATCAAGCAAAATACC
456 AAATAAATAATATACATCAGCCCTTAGGGAAACAAAAAAAATTCAGAAACATCAAGCAAAATACC
5625684 TCCACAGAGAAAGTTCTTGCATTATTGTACAGAAATTTTGGCAAACGTAGGAGGCAAGATTGAAG
521 TCCACAGAGAAAGTTCTTGCATTATTGTACAGAAATTTTGGCAAACGTAGGAGGCAAGATTGAAG
5625749 CTAAAGAGTAAAGATTACTCTAAATTTTGCAAACTGGTATATATTATAAAGGCAGCCAATGCAAT
586 CTAAAGAGTAAAGATTACTCTAAATTTTGCAAACTGGTATATATTATAAAGGCAGCCAATGCAAT
5625814 CAAAGTAGCCACAGGAACTCAAAACCATAGAAGACTGAGCGAAACTTGGGTGATATGAAGTAGAA
651 CAAAGTAGCCACAGGAACTCAAAACCATAGAAGACTGAGCGAAACTTGGGTGATATGAAGTAGAA
5625879 CTTGAACAAAAGAACGTAGCAGATGAATGACTAAACAAGTAATAGCCCTTGGAAGAGATAGTGAC
716 CTTGAACAAAAGAACGTAGCAGATGAATGACTAAACAAGTAATAGCCCTTGGAAGAGATAGTGAC
5625944 CTAGTCCCT
781 CTAGTCCCT
5625953 A
1 A
5625954 ATGGTATTGC
Statistics
Matches: 789, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
789 789 1.00
ACGTcount: A:0.38, C:0.17, G:0.20, T:0.25
Consensus pattern (789 bp):
ATCCTGCAAGTGTGAGCTTAATAGACTGCTGAGAAGCTTCATTGGGTGCTAATAGATCAACAGGG
CGATGAAGTTTGCATCTCTCTCCGAATTTACATTTGCCAGTTTTCACATAGTACTGCAATGTAAA
GAAATAAAACGGGGGGAAAGTCATCAATAAGCATAGGGATTCCTGCAATGCTTGACATTACAAAG
TGAGCCAACAGTATGTCCAAGGTAATTTGGATGCTTGATATGAAAACTGTGGCACAAAAGAATTG
TGCAGCACTAATCCAAGCTCAATAATGTGTACCATCTTGATAGTCATAAGAAAATTGGGTGGCAA
GGAATTCAAAATAACAATTAAAAACAAACATATATCAAAACGACACAGAATGGATTGATTTGCAC
ATCTCATTCAGTTTGTCCTGGTCTCTGAGGATACACAGTCTGACTGCCTGCCAGCTGCAATAGGT
AAATAAATAATATACATCAGCCCTTAGGGAAACAAAAAAAATTCAGAAACATCAAGCAAAATACC
TCCACAGAGAAAGTTCTTGCATTATTGTACAGAAATTTTGGCAAACGTAGGAGGCAAGATTGAAG
CTAAAGAGTAAAGATTACTCTAAATTTTGCAAACTGGTATATATTATAAAGGCAGCCAATGCAAT
CAAAGTAGCCACAGGAACTCAAAACCATAGAAGACTGAGCGAAACTTGGGTGATATGAAGTAGAA
CTTGAACAAAAGAACGTAGCAGATGAATGACTAAACAAGTAATAGCCCTTGGAAGAGATAGTGAC
CTAGTCCCT
Found at i:5627271 original size:18 final size:18
Alignment explanation
Indices: 5627248--5627288 Score: 82
Period size: 18 Copynumber: 2.3 Consensus size: 18
5627238 AAATCTATAT
5627248 CAACCTCTCTCAGGAAAG
1 CAACCTCTCTCAGGAAAG
5627266 CAACCTCTCTCAGGAAAG
1 CAACCTCTCTCAGGAAAG
5627284 CAACC
1 CAACC
5627289 AGAGGGCATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.34, C:0.37, G:0.15, T:0.15
Consensus pattern (18 bp):
CAACCTCTCTCAGGAAAG
Found at i:5635282 original size:18 final size:18
Alignment explanation
Indices: 5635256--5635290 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5635246 ACACCAAATT
5635256 TCAAGAATACTTTTAATC
1 TCAAGAATACTTTTAATC
*
5635274 TCAATAATACTTTTAAT
1 TCAAGAATACTTTTAAT
5635291 AGACAATACT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.40, C:0.14, G:0.03, T:0.43
Consensus pattern (18 bp):
TCAAGAATACTTTTAATC
Found at i:5642055 original size:53 final size:54
Alignment explanation
Indices: 5641977--5642086 Score: 195
Period size: 53 Copynumber: 2.0 Consensus size: 54
5641967 TTATCTTTCC
*
5641977 TTTTGTAGGCTATATAAACGTGGGAAATGGTAGAAAGTTTCCAGAGAACTCTCCA
1 TTTTGTAGGC-ATATAAACGTGGGAAATGGGAGAAAGTTTCCAGAGAACTCTCCA
5642032 TTTTGTAGGC-TATAAACGTGGGAAATGGGAGAAAGTTTCCAGAGAACTCTCCA
1 TTTTGTAGGCATATAAACGTGGGAAATGGGAGAAAGTTTCCAGAGAACTCTCCA
5642085 TT
1 TT
5642087 CTTTTTTTTC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
53 44 0.81
55 10 0.19
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.29
Consensus pattern (54 bp):
TTTTGTAGGCATATAAACGTGGGAAATGGGAGAAAGTTTCCAGAGAACTCTCCA
Found at i:5643545 original size:23 final size:23
Alignment explanation
Indices: 5643515--5643567 Score: 79
Period size: 23 Copynumber: 2.3 Consensus size: 23
5643505 AATAGAACAA
*
5643515 CGGTGCAATTCTACGCGGCACTT
1 CGGTGCAATTCTACGCGACACTT
* *
5643538 CGGTGCAATTCTATGTGACACTT
1 CGGTGCAATTCTACGCGACACTT
5643561 CGGTGCA
1 CGGTGCA
5643568 TTTATACGAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.19, C:0.26, G:0.26, T:0.28
Consensus pattern (23 bp):
CGGTGCAATTCTACGCGACACTT
Found at i:5648817 original size:23 final size:23
Alignment explanation
Indices: 5648791--5648837 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
5648781 ACTACGGTGT
5648791 AATTCTAAGCGGCACTTCAGTGC
1 AATTCTAAGCGGCACTTCAGTGC
* * *
5648814 AATTCTACGTGGCACTTCGGTGC
1 AATTCTAAGCGGCACTTCAGTGC
5648837 A
1 A
5648838 TTTATACGAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (23 bp):
AATTCTAAGCGGCACTTCAGTGC
Found at i:5648845 original size:23 final size:23
Alignment explanation
Indices: 5648801--5648845 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
5648791 AATTCTAAGC
*
5648801 GGCACTTCAGTGCAATTCTACGT
1 GGCACTTCAGTGCAATTATACGT
* *
5648824 GGCACTTCGGTGCATTTATACG
1 GGCACTTCAGTGCAATTATACG
5648846 AGCTGTGGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.31
Consensus pattern (23 bp):
GGCACTTCAGTGCAATTATACGT
Found at i:5651838 original size:18 final size:18
Alignment explanation
Indices: 5651811--5651856 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
5651801 AAACTAAGAA
*
5651811 ATACTGGCATAAGTTATT
1 ATACTAGCATAAGTTATT
5651829 ATACTAGCATAAGTTATT
1 ATACTAGCATAAGTTATT
5651847 ATACTAGCAT
1 ATACTAGCAT
5651857 TTAATAATAG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.37, C:0.13, G:0.13, T:0.37
Consensus pattern (18 bp):
ATACTAGCATAAGTTATT
Found at i:5665021 original size:30 final size:30
Alignment explanation
Indices: 5664987--5665046 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5664977 CAAGAAAGCT
5664987 GTTTAAAGAAAGATGATGACTGGACAGGTG
1 GTTTAAAGAAAGATGATGACTGGACAGGTG
*
5665017 GTTTAAAGAAAGATGATGACTGGACGGGTG
1 GTTTAAAGAAAGATGATGACTGGACAGGTG
5665047 CCAGAATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.35, C:0.07, G:0.35, T:0.23
Consensus pattern (30 bp):
GTTTAAAGAAAGATGATGACTGGACAGGTG
Found at i:5666516 original size:16 final size:17
Alignment explanation
Indices: 5666495--5666527 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5666485 TAAATGCAAG
*
5666495 ATGAAA-AGGTAAAAAA
1 ATGAAAGAGGGAAAAAA
5666511 ATGAAAGAGGGAAAAAA
1 ATGAAAGAGGGAAAAAA
5666528 TTGTCACCGG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (17 bp):
ATGAAAGAGGGAAAAAA
Found at i:5672752 original size:45 final size:45
Alignment explanation
Indices: 5672688--5672778 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
5672678 CATAGGTCAC
5672688 TAAGGTTTTGCCTTTTCTTTTTCTTTTTTTGATTTTCCTGTTAGA
1 TAAGGTTTTGCCTTTTCTTTTTCTTTTTTTGATTTTCCTGTTAGA
5672733 TAAGGTTTTGCCTTTTCTTTTTCTTTTTTTGATTTTCCTGTTAGA
1 TAAGGTTTTGCCTTTTCTTTTTCTTTTTTTGATTTTCCTGTTAGA
5672778 T
1 T
5672779 TTCGCTTCCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.63
Consensus pattern (45 bp):
TAAGGTTTTGCCTTTTCTTTTTCTTTTTTTGATTTTCCTGTTAGA
Found at i:5674716 original size:3 final size:3
Alignment explanation
Indices: 5674710--5674754 Score: 54
Period size: 3 Copynumber: 15.0 Consensus size: 3
5674700 AAAAAAATAT
* * * *
5674710 TTA TTA TTA TTA TTA TTA TTA GTA GTA GTA GTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5674755 ACATACAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:5681743 original size:24 final size:24
Alignment explanation
Indices: 5681716--5681823 Score: 74
Period size: 24 Copynumber: 4.5 Consensus size: 24
5681706 AAATATTTTA
*
5681716 TCTGATTTCTGACTTGAATTATGT
1 TCTGATTTCTGACCTGAATTATGT
* *
5681740 TCTGA-TACATGACCTGAATTCTGT
1 TCTGATTTC-TGACCTGAATTATGT
* ** * *
5681764 TCTGATTTCTTATATGGATTCTGT
1 TCTGATTTCTGACCTGAATTATGT
* * ** *
5681788 TCTTATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGACCTGAATTATGT
*
5681812 TTTGATTTCTGA
1 TCTGATTTCTGA
5681824 TATCTCATTT
Statistics
Matches: 64, Mismatches: 18, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
23 2 0.03
24 60 0.94
25 2 0.03
ACGTcount: A:0.19, C:0.15, G:0.16, T:0.50
Consensus pattern (24 bp):
TCTGATTTCTGACCTGAATTATGT
Found at i:5681768 original size:12 final size:12
Alignment explanation
Indices: 5681753--5681822 Score: 54
Period size: 12 Copynumber: 5.8 Consensus size: 12
5681743 GATACATGAC
5681753 CTGAATTCTGTT
1 CTGAATTCTGTT
*
5681765 CTGATTTCT-TAT
1 CTGAATTCTGT-T
* *
5681777 ATGGATTCTGTT
1 CTGAATTCTGTT
*
5681789 CT-TATATCTGTT
1 CTGAAT-TCTGTT
5681801 CTGAATTCTGTT
1 CTGAATTCTGTT
* *
5681813 TTGATTTCTG
1 CTGAATTCTG
5681823 ATATCTCATT
Statistics
Matches: 45, Mismatches: 9, Indels: 8
0.73 0.15 0.13
Matches are distributed among these distances:
11 3 0.07
12 39 0.87
13 3 0.07
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.54
Consensus pattern (12 bp):
CTGAATTCTGTT
Found at i:5681772 original size:48 final size:48
Alignment explanation
Indices: 5681716--5681826 Score: 127
Period size: 48 Copynumber: 2.3 Consensus size: 48
5681706 AAATATTTTA
5681716 TCTGATTTCTGACT-TGAATTATGTTCTGATA-CATGACCTGAATTCTGT
1 TCTGATTTCTGA-TATGAATTATGTTCTGATATC-TGACCTGAATTCTGT
* * * * **
5681764 TCTGATTTCTTATATGGATTCTGTTCTTATATCTGTTCTGAATTCTGT
1 TCTGATTTCTGATATGAATTATGTTCTGATATCTGACCTGAATTCTGT
*
5681812 TTTGATTTCTGATAT
1 TCTGATTTCTGATAT
5681827 CTCATTTTAA
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
47 1 0.02
48 51 0.96
49 1 0.02
ACGTcount: A:0.20, C:0.14, G:0.15, T:0.50
Consensus pattern (48 bp):
TCTGATTTCTGATATGAATTATGTTCTGATATCTGACCTGAATTCTGT
Found at i:5681802 original size:17 final size:18
Alignment explanation
Indices: 5681759--5681809 Score: 52
Period size: 17 Copynumber: 2.8 Consensus size: 18
5681749 TGACCTGAAT
5681759 TCTGTTCTGATTTCTTATA
1 TCTGTTCTGA-TTCTTATA
*
5681778 T-GGATTCTG-TTCTTATA
1 TCTG-TTCTGATTCTTATA
5681795 TCTGTTCTGAATTCT
1 TCTGTTCTG-ATTCT
5681810 GTTTTGATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 8
0.72 0.06 0.22
Matches are distributed among these distances:
17 14 0.54
18 2 0.08
19 10 0.38
ACGTcount: A:0.16, C:0.16, G:0.14, T:0.55
Consensus pattern (18 bp):
TCTGTTCTGATTCTTATA
Found at i:5684176 original size:30 final size:30
Alignment explanation
Indices: 5684136--5684306 Score: 150
Period size: 30 Copynumber: 5.7 Consensus size: 30
5684126 TTTATTTGTA
* *
5684136 TTTG-TATTTTAGTCCCTTAAGTTTTTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
* * *
5684165 TTTGATATTTTAGTCTTTTAACTTTCTATTT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTA-TT
* * *
5684196 TTTGCTATTTTAATCTTTTAAGTTTCTGTT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
* * *
5684226 TTTGCTATTTTGGTCTTTTAAAGTTT-TGTTT
1 TTTGCTATTTTAGTCCTTT-AAGTTTCT-ATT
* *
5684257 TTTTCTA-TTTAATCCTTTAAGTTTCTATT
1 TTTGCTATTTTAGTCCTTTAAGTTTCTATT
* * *
5684286 TTTGTTAGTTTAGCCCTTTAA
1 TTTGCTATTTTAGTCCTTTAA
5684307 ATTTATGTTA
Statistics
Matches: 116, Mismatches: 20, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
29 17 0.15
30 59 0.51
31 40 0.34
ACGTcount: A:0.18, C:0.11, G:0.10, T:0.62
Consensus pattern (30 bp):
TTTGCTATTTTAGTCCTTTAAGTTTCTATT
Found at i:5684205 original size:31 final size:31
Alignment explanation
Indices: 5684136--5684288 Score: 154
Period size: 30 Copynumber: 5.1 Consensus size: 31
5684126 TTTATTTGTA
** *
5684136 TTTG-TATTTTAGTCCCTTAAGTTTTTA-TT
1 TTTGCTATTTTAGTCTTTTAAGTTTCTATTT
* *
5684165 TTTGATATTTTAGTCTTTTAACTTTCTATTT
1 TTTGCTATTTTAGTCTTTTAAGTTTCTATTT
* *
5684196 TTTGCTATTTTAATCTTTTAAGTTTCT-GTT
1 TTTGCTATTTTAGTCTTTTAAGTTTCTATTT
* *
5684226 TTTGCTATTTTGGTCTTTTAAAGTTT-TGTTT
1 TTTGCTATTTTAGTCTTTT-AAGTTTCTATTT
* * *
5684257 TTTTCTA-TTTAATCCTTTAAGTTTCTATTT
1 TTTGCTATTTTAGTCTTTTAAGTTTCTATTT
5684287 TT
1 TT
5684289 GTTAGTTTAG
Statistics
Matches: 103, Mismatches: 16, Indels: 9
0.80 0.12 0.07
Matches are distributed among these distances:
29 10 0.10
30 53 0.51
31 40 0.39
ACGTcount: A:0.17, C:0.10, G:0.09, T:0.64
Consensus pattern (31 bp):
TTTGCTATTTTAGTCTTTTAAGTTTCTATTT
Found at i:5684217 original size:61 final size:60
Alignment explanation
Indices: 5684143--5684307 Score: 179
Period size: 61 Copynumber: 2.7 Consensus size: 60
5684133 GTATTTGTAT
* * *
5684143 TTTAGTCCCTTAAGTTTTTATTTTTGATATTTTAGTCTTTT-AACTTTCTATTTTTTGCTA
1 TTTAATCCTTTAAGTTTCTATTTTTGATATTTTAGTCTTTTAAACTTT-TATTTTTTGCTA
* * * * * * *
5684203 TTTTAATCTTTTAAGTTTCTGTTTTTGCTATTTTGGTCTTTTAAAGTTTTGTTTTTTTCTA
1 -TTTAATCCTTTAAGTTTCTATTTTTGATATTTTAGTCTTTTAAACTTTTATTTTTTGCTA
* * * *
5684264 TTTAATCCTTTAAGTTTCTATTTTTGTTAGTTTAGCCCTTTAAA
1 TTTAATCCTTTAAGTTTCTATTTTTGATATTTTAGTCTTTTAAA
5684308 TTTATGTTAA
Statistics
Matches: 86, Mismatches: 17, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
60 37 0.43
61 44 0.51
62 5 0.06
ACGTcount: A:0.18, C:0.11, G:0.10, T:0.61
Consensus pattern (60 bp):
TTTAATCCTTTAAGTTTCTATTTTTGATATTTTAGTCTTTTAAACTTTTATTTTTTGCTA
Found at i:5687482 original size:12 final size:12
Alignment explanation
Indices: 5687467--5687494 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
5687457 AATATAAAAA
5687467 TATTTGTACTTT
1 TATTTGTACTTT
5687479 TATTTGTACTTT
1 TATTTGTACTTT
5687491 TATT
1 TATT
5687495 GAATGATCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.07, G:0.07, T:0.68
Consensus pattern (12 bp):
TATTTGTACTTT
Found at i:5691495 original size:23 final size:24
Alignment explanation
Indices: 5691444--5691503 Score: 60
Period size: 21 Copynumber: 2.8 Consensus size: 24
5691434 TTCAAGATAA
* *
5691444 ATATAATATATAATTAATATGATT
1 ATATAATATATAATTAAAATAATT
5691468 A-ATAATATA-AA-TAAAATAATT
1 ATATAATATATAATTAAAATAATT
5691489 -TAT-ATA-ATAATTAAA
1 ATATAATATATAATTAAA
5691504 TCCTTCTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
19 1 0.03
20 5 0.16
21 14 0.45
22 2 0.06
23 8 0.26
24 1 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (24 bp):
ATATAATATATAATTAAAATAATT
Found at i:5698258 original size:17 final size:18
Alignment explanation
Indices: 5698236--5698269 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5698226 TTGAAAGGTA
*
5698236 TGGAA-TAAATGATAAGT
1 TGGAATTAAATAATAAGT
5698253 TGGAATTAAATAATAAG
1 TGGAATTAAATAATAAG
5698270 ACAGAATTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.50, C:0.00, G:0.21, T:0.29
Consensus pattern (18 bp):
TGGAATTAAATAATAAGT
Found at i:5703699 original size:2 final size:2
Alignment explanation
Indices: 5703692--5703716 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5703682 CGTCTAAATG
5703692 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
5703717 GTGAATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5708543 original size:397 final size:398
Alignment explanation
Indices: 5707808--5708606 Score: 1237
Period size: 397 Copynumber: 2.0 Consensus size: 398
5707798 ACATTTTAGA
* * *
5707808 GGTATATTTGTTCAATACCTACCACGAAACTTATCACGTAACGGAATAATTTATTTAATTTTTTT
1 GGTATATCTGTTCAATACCTACCACGAAACTTATCACGGAACAGAATAATTTATTTAATTTTTTT
*
5707873 ATTAAACTAAAGTGTTTATAAAGTAATATATATTCTACATATTTTTATTATTATTTGACAATAAA
66 ATTAAACTAAAGTGTTTATAAAGTAATATATATTCTAAATATTTTTATTATTATTTGACAATAAA
* * *
5707938 CATTCAATCACTATTAAAGTTGCAGGTGTTCGAACACATAACTTCTAAGAACACAATTCCTTTAA
131 CATTCAATCACCATTAAAGTCGCACGTGTTCGAACACATAACTTCTAAGAACACAATTCCTTTAA
* *
5708003 CCAAAAAAGTAAGTTTATCACAACCATAAATAGTAATAAATTAAAAATTTTAAGTTAATTTAATT
196 CCAAAAAAGTAAGTTTATCACAACCATAAATAATAATAAAATAAAAATTTTAAGTTAATTTAATT
* * * * * * *
5708068 TAAATTAGGGACCAAATTGTAAGTTTTTAGAACTTACAACTCGTTTTAGAAAGTTGCATGAAGTT
261 TAAATTAGGGACAAAATTGTAAGGTTTCAGAACATACAACCCGTTTTAGAAAATTGCATGAAGTC
* *
5708133 TAGGGACTTAACCCTGAATTTCTC-TTTTTTGTCGATAGAGAAAAAATAAAATATGAAGTTGGTG
326 TAGGGACTTAACCCTGAATTTCTCTTTTTTTGTCGACAGAGAAAAAATAAAATATAAAGTTGGTG
5708197 GCTACAAG
391 GCTACAAG
*
5708205 GGTATATCTGTTCAATACCTACCACGAAACTTATCATGGAACAGAATAATTTATTTAATTTTTTT
1 GGTATATCTGTTCAATACCTACCACGAAACTTATCACGGAACAGAATAATTTATTTAA-TTTTTT
* * *
5708270 TATTAAGA-TGAGGTGTTTATAAAGTAATATATATTCTAAATATTTTT-TTATTATTTGATAATA
65 TATTAA-ACTAAAGTGTTTATAAAGTAATATATATTCTAAATATTTTTATTATTATTTGACAATA
* * * * * * *
5708333 AACGTTCAATCACCATTACAGTCGCACGTGTTTGAACACTTAACTTCTAAGAATACGATTCTTTT
129 AACATTCAATCACCATTAAAGTCGCACGTGTTCGAACACATAACTTCTAAGAACACAATTCCTTT
*
5708398 AACCAATAAAGTAAGTTTATCACAACCATAAATAATAATAAAATAAAAATTTTAAGTTAATTTAA
194 AACCAAAAAAGTAAGTTTATCACAACCATAAATAATAATAAAATAAAAATTTTAAGTTAATTTAA
*
5708463 TTTAAATTAGGGACAAAATTGTAAGGTTTCAGAACATACAACCCGTTTTAGAAAATTGTATGAAG
259 TTTAAATTAGGGACAAAATTGTAAGGTTTCAGAACATACAACCCGTTTTAGAAAATTGCATGAAG
* *
5708528 -CTCGTGGATTTAACCCTGAATTTCTCTTTTTTTTGTCGACAGAGAAAAAATAAAATATAAAGTT
324 TCTAG-GGACTTAACCCTGAATTTCTC-TTTTTTTGTCGACAGAGAAAAAATAAAATATAAAGTT
5708592 GGTGGCTACAAG
387 GGTGGCTACAAG
5708604 GGT
1 GGT
5708607 TCAAACTTGT
Statistics
Matches: 364, Mismatches: 33, Indels: 8
0.90 0.08 0.02
Matches are distributed among these distances:
396 2 0.01
397 264 0.73
398 48 0.13
399 50 0.14
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (398 bp):
GGTATATCTGTTCAATACCTACCACGAAACTTATCACGGAACAGAATAATTTATTTAATTTTTTT
ATTAAACTAAAGTGTTTATAAAGTAATATATATTCTAAATATTTTTATTATTATTTGACAATAAA
CATTCAATCACCATTAAAGTCGCACGTGTTCGAACACATAACTTCTAAGAACACAATTCCTTTAA
CCAAAAAAGTAAGTTTATCACAACCATAAATAATAATAAAATAAAAATTTTAAGTTAATTTAATT
TAAATTAGGGACAAAATTGTAAGGTTTCAGAACATACAACCCGTTTTAGAAAATTGCATGAAGTC
TAGGGACTTAACCCTGAATTTCTCTTTTTTTGTCGACAGAGAAAAAATAAAATATAAAGTTGGTG
GCTACAAG
Found at i:5709408 original size:17 final size:17
Alignment explanation
Indices: 5709382--5709415 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
5709372 TTAACTTTGA
*
5709382 CCAAATAGTCAAATTTT
1 CCAAAAAGTCAAATTTT
*
5709399 CCAAAAAGTCATATTTT
1 CCAAAAAGTCAAATTTT
5709416 ATGTTTTTCA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.41, C:0.18, G:0.06, T:0.35
Consensus pattern (17 bp):
CCAAAAAGTCAAATTTT
Found at i:5711967 original size:20 final size:21
Alignment explanation
Indices: 5711936--5711977 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
5711926 AAGAAATAAT
5711936 AAAACAACATAAACA-AAAACA
1 AAAACAACATAAA-ATAAAACA
5711957 AAAACAA-ATAAAATAAAACA
1 AAAACAACATAAAATAAAACA
5711977 A
1 A
5711978 TGAGGATCAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 1 0.05
20 12 0.60
21 7 0.35
ACGTcount: A:0.79, C:0.14, G:0.00, T:0.07
Consensus pattern (21 bp):
AAAACAACATAAAATAAAACA
Found at i:5714202 original size:2 final size:2
Alignment explanation
Indices: 5714197--5714259 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
5714187 TTTATCTCTC
5714197 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5714239 AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT A
5714260 AAAGTTAAAA
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5714567 original size:2 final size:2
Alignment explanation
Indices: 5714560--5714589 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5714550 ATGCATTAAT
*
5714560 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5714590 AAAGGATGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:5718287 original size:15 final size:15
Alignment explanation
Indices: 5718256--5718289 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
5718246 TTGTCTTGGA
*
5718256 TTTTCTCTTTTCCTC
1 TTTTCTCTTTGCCTC
*
5718271 TTTTCTCTTTGCTTC
1 TTTTCTCTTTGCCTC
5718286 TTTT
1 TTTT
5718290 GATTACACTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.26, G:0.03, T:0.71
Consensus pattern (15 bp):
TTTTCTCTTTGCCTC
Found at i:5723264 original size:2 final size:2
Alignment explanation
Indices: 5723259--5723288 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5723249 TTTTAAAAAT
5723259 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5723289 ATTTCTTACC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5723456 original size:57 final size:57
Alignment explanation
Indices: 5723395--5723505 Score: 213
Period size: 57 Copynumber: 1.9 Consensus size: 57
5723385 TGTTTTGAGA
5723395 GTTTAAAATTATTTTTATATATACTTTAAACTTATATTTTGTGTACCAAATACTCGT
1 GTTTAAAATTATTTTTATATATACTTTAAACTTATATTTTGTGTACCAAATACTCGT
*
5723452 GTTTAAACTTATTTTTATATATACTTTAAACTTATATTTTGTGTACCAAATACT
1 GTTTAAAATTATTTTTATATATACTTTAAACTTATATTTTGTGTACCAAATACT
5723506 TCCTTGAATG
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
57 53 1.00
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (57 bp):
GTTTAAAATTATTTTTATATATACTTTAAACTTATATTTTGTGTACCAAATACTCGT
Found at i:5723880 original size:30 final size:30
Alignment explanation
Indices: 5723824--5723881 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
5723814 ATATATTTTA
* *
5723824 TTTAAAAATGGTATAATTTTTGTTTAATCC
1 TTTAAAAATGATATAATTTTTATTTAATCC
*
5723854 TTTAAAAAT-ATATATTTTTTAATTTAAT
1 TTTAAAAATGATATAATTTTT-ATTTAAT
5723882 ACAATGATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 9 0.38
30 15 0.62
ACGTcount: A:0.38, C:0.03, G:0.05, T:0.53
Consensus pattern (30 bp):
TTTAAAAATGATATAATTTTTATTTAATCC
Found at i:5724970 original size:18 final size:20
Alignment explanation
Indices: 5724933--5724970 Score: 53
Period size: 18 Copynumber: 2.0 Consensus size: 20
5724923 TAGTGTTTTG
5724933 ATTAAGAAATTGAAAAACAT
1 ATTAAGAAATTGAAAAACAT
*
5724953 ATTAA-AAA-TGAAACACAT
1 ATTAAGAAATTGAAAAACAT
5724971 GATCACTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 9 0.53
19 3 0.18
20 5 0.29
ACGTcount: A:0.61, C:0.08, G:0.08, T:0.24
Consensus pattern (20 bp):
ATTAAGAAATTGAAAAACAT
Found at i:5726633 original size:15 final size:16
Alignment explanation
Indices: 5726613--5726646 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5726603 AATCTCTTAA
*
5726613 AAATT-AGAAAATTAT
1 AAATTAAGAAAATAAT
5726628 AAATTAAGAAAATAAT
1 AAATTAAGAAAATAAT
5726644 AAA
1 AAA
5726647 GTTGTTCCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (16 bp):
AAATTAAGAAAATAAT
Found at i:5727815 original size:3 final size:3
Alignment explanation
Indices: 5727807--5727831 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
5727797 TAATACCAGT
5727807 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
5727832 AATTCTATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:5729291 original size:26 final size:26
Alignment explanation
Indices: 5729259--5729309 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
5729249 CTTTCCTGTT
5729259 TGGCCCATCTCTCGCTGAATTTTTTG
1 TGGCCCATCTCTCGCTGAATTTTTTG
*
5729285 TGGCCCATCTCTCGCTGAGTTTTTT
1 TGGCCCATCTCTCGCTGAATTTTTT
5729310 TTAGATTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.10, C:0.27, G:0.20, T:0.43
Consensus pattern (26 bp):
TGGCCCATCTCTCGCTGAATTTTTTG
Found at i:5732939 original size:21 final size:21
Alignment explanation
Indices: 5732897--5732939 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
5732887 TTTCTGGGCT
*
5732897 AGGGGAATCGATACCCATTCA
1 AGGGGAATCGATACCCACTCA
*
5732918 AGGGGAATCGATACCCCCTCA
1 AGGGGAATCGATACCCACTCA
5732939 A
1 A
5732940 ACGAACATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.28, G:0.23, T:0.16
Consensus pattern (21 bp):
AGGGGAATCGATACCCACTCA
Found at i:5733831 original size:2 final size:2
Alignment explanation
Indices: 5733824--5733865 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5733814 AATAGAAGTA
5733824 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5733866 TATCAGTATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5733969 original size:13 final size:15
Alignment explanation
Indices: 5733942--5733973 Score: 50
Period size: 13 Copynumber: 2.3 Consensus size: 15
5733932 CGATGTAAAT
5733942 TATATGAATTAGTGA
1 TATATGAATTAGTGA
5733957 TATATGAA-T-GTGA
1 TATATGAATTAGTGA
5733970 TATA
1 TATA
5733974 AGTATGTAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
13 8 0.47
14 1 0.06
15 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.19, T:0.41
Consensus pattern (15 bp):
TATATGAATTAGTGA
Found at i:5734785 original size:103 final size:103
Alignment explanation
Indices: 5734560--5734777 Score: 382
Period size: 103 Copynumber: 2.1 Consensus size: 103
5734550 GTCGAGGGTC
5734560 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* *
5734625 TTGATCCTTGGCATATGTATATGATTCTTAAAGAATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
*
5734663 TATGTGGTCATTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
1 TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
* * *
5734728 TTGATCCCTAGTATATGTATATGATTCTTAAGGTATGA
66 TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
5734766 TATGTGGTCCTT
1 TATGTGGTCCTT
5734778 ATGGACATTA
Statistics
Matches: 108, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 108 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.37
Consensus pattern (103 bp):
TATGTGGTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATAC
TTGATCCCTAGCATATGTATATGATTCTTAAAGAATGA
Found at i:5734820 original size:23 final size:23
Alignment explanation
Indices: 5734787--5734861 Score: 100
Period size: 23 Copynumber: 3.3 Consensus size: 23
5734777 TATGGACATT
5734787 ATTATAT--GGCACTACGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
5734808 ATTCTATGCGGCACTCCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
* *
5734831 ATTATATGTGGCACTTCGGTGCA
1 ATTATATGCGGCACTACGGTGCA
5734854 ATTATATG
1 ATTATATG
5734862 AGATGTGGTG
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.13
23 41 0.87
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (23 bp):
ATTATATGCGGCACTACGGTGCA
Found at i:5742887 original size:21 final size:21
Alignment explanation
Indices: 5742861--5742900 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
5742851 CATCGCACTA
5742861 TATCTGACAAATGGAGATCAT
1 TATCTGACAAATGGAGATCAT
5742882 TATCTGACAAATGGAGATC
1 TATCTGACAAATGGAGATC
5742901 CTTCTTTATG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.28
Consensus pattern (21 bp):
TATCTGACAAATGGAGATCAT
Found at i:5744285 original size:60 final size:60
Alignment explanation
Indices: 5744156--5744286 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
5744146 ATTGTTCTTT
* * ** *
5744156 AAACTTTTGAATATTCTAATTTGATCCCTAAACTATGACTTTCATTCTAAATTAATCCTT
1 AAACTTTTGAACATTCTAATTTGATCCCTAAACCATGACCCTCATTCTAAATTAATCCTC
*
5744216 AAA-TATTTGAACATTCTAA-TTGCATCCCTAAACCATGACCCT-ATTTCTAAATTAGTGCC-C
1 AAACT-TTTGAACATTCTAATTTG-ATCCCTAAACCATGACCCTCA-TTCTAAATTAAT-CCTC
5744276 AAACTTTTGAA
1 AAACTTTTGAA
5744287 TATTTCAATT
Statistics
Matches: 60, Mismatches: 6, Indels: 10
0.79 0.08 0.13
Matches are distributed among these distances:
59 5 0.08
60 52 0.87
61 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.07, T:0.38
Consensus pattern (60 bp):
AAACTTTTGAACATTCTAATTTGATCCCTAAACCATGACCCTCATTCTAAATTAATCCTC
Found at i:5744506 original size:60 final size:59
Alignment explanation
Indices: 5744429--5744586 Score: 176
Period size: 60 Copynumber: 2.6 Consensus size: 59
5744419 GTATATACAT
* ** *
5744429 ATAGTTTGGGATGAAATTGGAATGTTCAAAAAGTTTGGGGAC-ACTTTAGAATGA-ATGTC
1 ATAGTTTGGGATGAAATTGAAATGTT-AAAAAGTTTAAGGACTAATTTAGAATGATA-GTC
* * *
5744488 ATAGTTTGGGGATGAAATTGAAATGTTAGAAATTTTAATGACTAATTTAGAATGATAGTC
1 ATAGTTT-GGGATGAAATTGAAATGTTAAAAAGTTTAAGGACTAATTTAGAATGATAGTC
* * *
5744548 ATAGTTTAGAGATGAAATTGAAATATTTAAAAGTTTAAG
1 ATAGTTT-GGGATGAAATTGAAATGTTAAAAAGTTTAAG
5744587 AACAAAATTG
Statistics
Matches: 82, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
59 17 0.21
60 64 0.78
61 1 0.01
ACGTcount: A:0.39, C:0.04, G:0.23, T:0.35
Consensus pattern (59 bp):
ATAGTTTGGGATGAAATTGAAATGTTAAAAAGTTTAAGGACTAATTTAGAATGATAGTC
Found at i:5745156 original size:14 final size:15
Alignment explanation
Indices: 5745137--5745173 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5745127 TTAATCTAAT
5745137 TATTATTAAAAA-AA
1 TATTATTAAAAATAA
5745151 TATTA-TAAAAATAA
1 TATTATTAAAAATAA
*
5745165 TATAATTAA
1 TATTATTAA
5745174 TATTTTATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 6 0.30
14 11 0.55
15 3 0.15
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TATTATTAAAAATAA
Found at i:5745191 original size:14 final size:15
Alignment explanation
Indices: 5745172--5745208 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
5745162 TAATATAATT
*
5745172 AATATTTTA-TTTTA
1 AATATTTTAGCTTTA
5745186 AATATTTTAGCTTTA
1 AATATTTTAGCTTTA
5745201 AA-ATTTTA
1 AATATTTTA
5745209 ACTAAATTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (15 bp):
AATATTTTAGCTTTA
Found at i:5749789 original size:40 final size:40
Alignment explanation
Indices: 5749741--5749821 Score: 108
Period size: 40 Copynumber: 2.0 Consensus size: 40
5749731 AAATAGTAAT
*
5749741 TGATATTTCCTAAACAATAAATATTAAACCCGTAAAAATC
1 TGATATTTCCTAAACAATAAATATTAAACCCGCAAAAATC
* * * * *
5749781 TGATATTTCCTATACCATAAATGTTAAGCCTGCAAAAATC
1 TGATATTTCCTAAACAATAAATATTAAACCCGCAAAAATC
5749821 T
1 T
5749822 ACTCATTTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.42, C:0.19, G:0.07, T:0.32
Consensus pattern (40 bp):
TGATATTTCCTAAACAATAAATATTAAACCCGCAAAAATC
Found at i:5750712 original size:30 final size:30
Alignment explanation
Indices: 5750676--5750868 Score: 289
Period size: 30 Copynumber: 6.2 Consensus size: 30
5750666 TAATAAGGTT
5750676 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
5750706 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
5750736 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
5750766 ATTTATTTTAAAATAATTTATTATAAAATA
1 ATTTATTTTAAAATAATTTATTATAAAATA
* *
5750796 ATTTATTTTAGAATAAATTATTATAAAATATGGA
1 ATTTATTTTAAAATAATTTATTAT-AAA-AT--A
*
5750830 TTGATTTATTTTAAAATAATTTATT-TTAAATA
1 ---ATTTATTTTAAAATAATTTATTATAAAATA
5750862 ATTTATT
1 ATTTATT
5750869 AGTATGTATT
Statistics
Matches: 151, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
29 7 0.05
30 112 0.74
31 3 0.02
32 3 0.02
34 3 0.02
35 2 0.01
36 1 0.01
37 20 0.13
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (30 bp):
ATTTATTTTAAAATAATTTATTATAAAATA
Found at i:5750838 original size:22 final size:22
Alignment explanation
Indices: 5750813--5750935 Score: 104
Period size: 22 Copynumber: 5.5 Consensus size: 22
5750803 TTAGAATAAA
5750813 TTATTATAAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
* ** * *
5750835 TTATTTTAAAATAATTTATTTTAAA
1 TTATTATAAAAT-ATGGA--TTGAT
* * * *
5750860 TAATT-TATTAGTATGTATTGAT
1 TTATTATA-AAATATGGATTGAT
*
5750882 TTATTATGAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
5750904 TTATTATAAAATATGGATTGAT
1 TTATTATAAAATATGGATTGAT
*
5750926 TTATTTTAAA
1 TTATTATAAA
5750936 TAATTTATTA
Statistics
Matches: 78, Mismatches: 18, Indels: 10
0.74 0.17 0.09
Matches are distributed among these distances:
22 59 0.76
23 4 0.05
24 6 0.08
25 9 0.12
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (22 bp):
TTATTATAAAATATGGATTGAT
Found at i:5750862 original size:14 final size:15
Alignment explanation
Indices: 5750676--5750868 Score: 253
Period size: 15 Copynumber: 12.5 Consensus size: 15
5750666 TAATAAGGTT
5750676 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5750691 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
5750706 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5750721 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
5750736 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5750751 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
5750766 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
5750781 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
5750796 ATTTATTTTAGAATA
1 ATTTATTTTAAAATA
* *
5750811 AATTATTATAAAATATGGA
1 ATTTATT-TTAAA-AT--A
5750830 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
5750848 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
5750862 ATTTATT
1 ATTTATT
5750869 AGTATGTATT
Statistics
Matches: 157, Mismatches: 14, Indels: 15
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.08
15 126 0.80
16 3 0.02
17 2 0.01
18 1 0.01
19 1 0.01
20 2 0.01
21 4 0.03
22 6 0.04
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:5750945 original size:36 final size:34
Alignment explanation
Indices: 5750902--5750999 Score: 123
Period size: 32 Copynumber: 2.9 Consensus size: 34
5750892 ATATGGATTG
5750902 ATTTATTATAAAATATGGATTGATTTATTTTAAATA
1 ATTTATTAT--AATATGGATTGATTTATTTTAAATA
*
5750938 ATTTA-T-TAGTATGGATTGATTTATTTTAAATA
1 ATTTATTATAATATGGATTGATTTATTTTAAATA
* *
5750970 ATTTA-T-TAGTATGGACTGATTTATTTTAAA
1 ATTTATTATAATATGGATTGATTTATTTTAAA
5751000 ATATGGATTG
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
32 53 0.88
34 1 0.02
35 1 0.02
36 5 0.08
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (34 bp):
ATTTATTATAATATGGATTGATTTATTTTAAATA
Found at i:5750954 original size:32 final size:32
Alignment explanation
Indices: 5750915--5750999 Score: 161
Period size: 32 Copynumber: 2.7 Consensus size: 32
5750905 TATTATAAAA
5750915 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
5750947 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAATTTATTAG
*
5750979 TATGGACTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5751000 ATATGGATTG
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 52 1.00
ACGTcount: A:0.34, C:0.01, G:0.13, T:0.52
Consensus pattern (32 bp):
TATGGATTGATTTATTTTAAATAATTTATTAG
Found at i:5750961 original size:18 final size:18
Alignment explanation
Indices: 5750862--5750962 Score: 57
Period size: 22 Copynumber: 5.4 Consensus size: 18
5750852 ATTTTAAATA
*
5750862 ATTTATTAGTATGTATTG
1 ATTTATTAGTATGGATTG
5750880 ATTTATTATGAAATATGGATTG
1 ATTTATTA-G---TATGGATTG
*
5750902 ATTTATTATAAAATATGGATTG
1 ATTTA-T-T--AGTATGGATTG
* * *
5750924 ATTTATT--T-T-AAATA
1 ATTTATTAGTATGGATTG
5750938 ATTTATTAGTATGGATTG
1 ATTTATTAGTATGGATTG
5750956 ATTTATT
1 ATTTATT
5750963 TTAAATAATT
Statistics
Matches: 63, Mismatches: 8, Indels: 24
0.66 0.08 0.25
Matches are distributed among these distances:
14 9 0.14
15 1 0.02
16 2 0.03
17 1 0.02
18 17 0.27
19 1 0.02
20 1 0.02
21 1 0.02
22 27 0.43
23 1 0.02
24 1 0.02
26 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (18 bp):
ATTTATTAGTATGGATTG
Found at i:5751068 original size:32 final size:31
Alignment explanation
Indices: 5751026--5751132 Score: 108
Period size: 32 Copynumber: 3.7 Consensus size: 31
5751016 TATTGTAGTT
5751026 GTATAGATTGATTTATTTTAAATAATTTATTA
1 GTAT-GATTGATTTATTTTAAATAATTTATTA
5751058 GTATGAATTGATTTATTTT-AA-AA--TA-T-
1 GTATG-ATTGATTTATTTTAAATAATTTATTA
*
5751084 G---GATTGGTTTATTTTAAATAATTTATTA
1 GTATGATTGATTTATTTTAAATAATTTATTA
5751112 GTATGGA-TGATTTATTTTAAA
1 GTAT-GATTGATTTATTTTAAA
5751133 ATATGGATTG
Statistics
Matches: 62, Mismatches: 2, Indels: 23
0.71 0.02 0.26
Matches are distributed among these distances:
22 12 0.19
23 3 0.05
24 2 0.03
26 3 0.05
27 2 0.03
28 3 0.05
30 2 0.03
31 16 0.26
32 19 0.31
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (31 bp):
GTATGATTGATTTATTTTAAATAATTTATTA
Found at i:5751070 original size:80 final size:80
Alignment explanation
Indices: 5750893--5751132 Score: 288
Period size: 80 Copynumber: 2.9 Consensus size: 80
5750883 TATTATGAAA
* *
5750893 TATGGATTGATTTATTATAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGAT
1 TATGGATTGATTTATTTTAAAATATGGATTG----A-TTT-AATAATTTATTAGTATAGATTGAT
5750958 TTATTTTAAATAATTTATTAG
60 TTATTTTAAATAATTTATTAG
*
5750979 TATGGACTGATTTATTTTAAAATATGGATTGATTTAAT-ATTGTAGTT-GTATAGATTGATTTAT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTAATAATT-TA-TTAGTATAGATTGATTTAT
5751042 TTTAAATAATTTATTAG
64 TTTAAATAATTTATTAG
* *
5751059 TATGAATTGATTTATTTTAAAATATGGATTGGTTTATTTTAAATAATTTATTAGTATGGA-TGAT
1 TATGGATTGATTTATTTTAAAATATGGATT-G---A-TTT-AATAATTTATTAGTATAGATTGAT
5751123 TTATTTTAAA
60 TTATTTTAAA
5751133 ATATGGATTG
Statistics
Matches: 138, Mismatches: 6, Indels: 21
0.84 0.04 0.13
Matches are distributed among these distances:
79 3 0.02
80 65 0.47
81 6 0.04
82 1 0.01
84 1 0.01
85 19 0.14
86 40 0.29
87 3 0.02
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (80 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTAATAATTTATTAGTATAGATTGATTTATTT
TAAATAATTTATTAG
Found at i:5751084 original size:22 final size:22
Alignment explanation
Indices: 5751059--5751101 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
5751049 AATTTATTAG
5751059 TATGAATTGATTTATTTTAAAA
1 TATGAATTGATTTATTTTAAAA
* *
5751081 TATGGATTGGTTTATTTTAAA
1 TATGAATTGATTTATTTTAAA
5751102 TAATTTATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGAATTGATTTATTTTAAAA
Found at i:5751117 original size:112 final size:111
Alignment explanation
Indices: 5750919--5751266 Score: 264
Period size: 112 Copynumber: 3.2 Consensus size: 111
5750909 ATAAAATATG
* **
5750919 GATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGG
1 GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATGGATTAGTATGG
** *
5750984 ACTGATTTATTTTAAAATATGGATTGATTTAATATTGTAGTTGTATA
66 ACTGAAATAATTTAAAATATGGA-TGATTTAATATTGTAGTTGTATA
*
5751031 GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAA-ATATGGATTGGT-T-
1 GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATA-ATGGATTAGTATG
* * * * * *** *
5751093 TATTTTAAATAATTTATTAGTATGGATGATTT-AT-TT-TA-AAATATG
65 GA-CTGAAATAATTTA-AAATATGGATGATTTAATATTGTAGTTGTATA
* **
5751138 GATTGATTTA--TT--AT--TGTAGTT-GTATGAATTGATTTATTTTAAATAATTTATTAGTATG
1 GATTGATTTATTTTAAATAATTTA-TTAGTATGAATTGATTTATTTTAAATAATGGATTAGTATG
* * ** * *** *
5751196 AATTGATTTATTTTAAAATATGGATTGATTT-AT-TT-TA-AAATATG
65 GACTGAAATAATTTAAAATATGGA-TGATTTAATATTGTAGTTGTATA
5751240 GATTGATTTATTTTAAATAATTTATTA
1 GATTGATTTATTTTAAATAATTTATTA
5751267 TTGTAGTTGT
Statistics
Matches: 193, Mismatches: 28, Indels: 34
0.76 0.11 0.13
Matches are distributed among these distances:
101 39 0.20
102 42 0.22
103 3 0.02
104 2 0.01
105 2 0.01
106 2 0.01
107 15 0.08
108 5 0.03
109 2 0.01
110 3 0.02
111 16 0.08
112 62 0.32
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (111 bp):
GATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTTAAATAATGGATTAGTATGG
ACTGAAATAATTTAAAATATGGATGATTTAATATTGTAGTTGTATA
Found at i:5751169 original size:133 final size:134
Alignment explanation
Indices: 5750947--5751234 Score: 535
Period size: 133 Copynumber: 2.2 Consensus size: 134
5750937 AATTTATTAG
5750947 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAAATATGGATTGAT
5751012 TTAATATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
66 TTAATATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
5751077 AAAA
131 AAAA
*
5751081 TATGGATTGGTTTATTTTAAATAATTTATTAGTATGGA-TGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAAATATGGATTGAT
*
5751145 TTATTATTGTAGTTGTAT-GAATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTT
66 TTAATATTGTAGTTGTATAG-ATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTT
5751209 TAAAA
130 TAAAA
5751214 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5751235 ATATGGATTG
Statistics
Matches: 150, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
132 1 0.01
133 112 0.75
134 37 0.25
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.51
Consensus pattern (134 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGACTGATTTATTTTAAAATATGGATTGAT
TTAATATTGTAGTTGTATAGATTGATTTATTTTAAATAATTTATTAGTATGAATTGATTTATTTT
AAAA
Found at i:5751204 original size:18 final size:17
Alignment explanation
Indices: 5751157--5751207 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 17
5751147 ATTATTGTAG
5751157 TTGTATGAATTGATTTA
1 TTGTATGAATTGATTTA
* *
5751174 TT-T-T-AAATAATTTA
1 TTGTATGAATTGATTTA
5751188 TTAGTATGAATTGATTTA
1 TT-GTATGAATTGATTTA
5751206 TT
1 TT
5751208 TTAAAATATG
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
14 10 0.38
15 1 0.04
16 2 0.08
17 3 0.12
18 10 0.38
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (17 bp):
TTGTATGAATTGATTTA
Found at i:5751217 original size:22 final size:22
Alignment explanation
Indices: 5751192--5751256 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
5751182 AATTTATTAG
*
5751192 TATGAATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
5751214 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
5751236 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
5751257 TAATTTATTA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:5751224 original size:80 final size:75
Alignment explanation
Indices: 5751059--5751266 Score: 308
Period size: 79 Copynumber: 2.7 Consensus size: 75
5751049 AATTTATTAG
* * *
5751059 TATGAATTGATTTATTTTAAAATATGGATTGGTTTATTTTAAATAATTTATTAGTATGGATGATT
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATGATT
5751124 TATTTTAAAA
66 TATTTTAAAA
*** *
5751134 TATGGATTGATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGTATGAAT
1 TATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAA-
5751199 TGATTTATTTTAAAA
61 TGATTTATTTTAAAA
5751214 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
1 TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTA
5751267 TTGTAGTTGT
Statistics
Matches: 117, Mismatches: 11, Indels: 9
0.85 0.08 0.07
Matches are distributed among these distances:
75 13 0.11
76 31 0.26
77 4 0.03
78 4 0.03
79 36 0.31
80 29 0.25
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (75 bp):
TATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGAATGATT
TATTTTAAAA
Found at i:5751316 original size:31 final size:31
Alignment explanation
Indices: 5751281--5751339 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
5751271 AGTTGTATGG
* *
5751281 ATTATTTAAATTTCAGTATTGTAAAACTAAA
1 ATTATTTAAATCTCAGTATTGCAAAACTAAA
5751312 ATTATTTAAATCTCAGTATTGCAAAACT
1 ATTATTTAAATCTCAGTATTGCAAAACT
5751340 CTTTTAAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.42, C:0.10, G:0.07, T:0.41
Consensus pattern (31 bp):
ATTATTTAAATCTCAGTATTGCAAAACTAAA
Found at i:5751363 original size:19 final size:19
Alignment explanation
Indices: 5751341--5751383 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
5751331 TGCAAAACTC
5751341 TTTTAAGTTTAAAAAATCA
1 TTTTAAGTTTAAAAAATCA
5751360 TTTTAAGTTTAAAAAATCA
1 TTTTAAGTTTAAAAAATCA
*
5751379 GTTTA
1 TTTTA
5751384 TTTATATTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (19 bp):
TTTTAAGTTTAAAAAATCA
Found at i:5755332 original size:22 final size:22
Alignment explanation
Indices: 5755307--5755348 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 22
5755297 TATTTAAGAC
5755307 CTTAACTCTTAAAATT-TAAAGT
1 CTTAA-TCTTAAAATTCTAAAGT
*
5755329 CTTAATCTTTAAATTCTAAA
1 CTTAATCTTAAAATTCTAAA
5755349 TAAAATACGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (22 bp):
CTTAATCTTAAAATTCTAAAGT
Found at i:5757215 original size:172 final size:171
Alignment explanation
Indices: 5756923--5757265 Score: 560
Period size: 172 Copynumber: 2.0 Consensus size: 171
5756913 CAGTTTCGAC
5756923 AGGCGGTTTTAAAAGATTGGGTGTATGAGCACTCGAGCTAGCATCGTTCTGGGAAATATGGAGAT
1 AGGCGGTTTTAAAAGATTGGGTGTATGAGCACTCGAGCTAGCATCGTTCTGGGAAATATGGAGAT
* * *
5756988 TTTCGGAGATGGTGCTCTATCTTGTAGGGTCTCGCATGCTGTCCTTTTGTGGGATATGAGGCGGT
66 TGTCAGAGATGGTGCTCTATCTTGTAGGGTATCGCATGCTGTCCTTTTGTGGGATATGAGGCGGT
*
5757053 TTTCGGGTGAGTGCGTGTTCTAATATGAGTTTTAAGGCTTTT
131 TGTC-GGTGAGTGCGTGTTCTAATATGAGTTTTAAGGCTTTT
* * *
5757095 AGGCGGTTTTGAAAGATTGGGTGTATGGGCACTCGGGCTAGCATCGTTCTGGGAAATATGGAGAT
1 AGGCGGTTTTAAAAGATTGGGTGTATGAGCACTCGAGCTAGCATCGTTCTGGGAAATATGGAGAT
* * * * *
5757160 TGTCAGAGATGGTGCTCTGTCTTGTAGGGTATCGCGTGCTGTTCTTTTTTGGGATATGAGGTGGT
66 TGTCAGAGATGGTGCTCTATCTTGTAGGGTATCGCATGCTGTCCTTTTGTGGGATATGAGGCGGT
*
5757225 TGTCGGTTAGTGCGTGTTCTAATATGAGTTTTAAGGCTTTT
131 TGTCGGTGAGTGCGTGTTCTAATATGAGTTTTAAGGCTTTT
5757266 TTATTGGATT
Statistics
Matches: 158, Mismatches: 13, Indels: 1
0.92 0.08 0.01
Matches are distributed among these distances:
171 36 0.23
172 122 0.77
ACGTcount: A:0.18, C:0.13, G:0.33, T:0.36
Consensus pattern (171 bp):
AGGCGGTTTTAAAAGATTGGGTGTATGAGCACTCGAGCTAGCATCGTTCTGGGAAATATGGAGAT
TGTCAGAGATGGTGCTCTATCTTGTAGGGTATCGCATGCTGTCCTTTTGTGGGATATGAGGCGGT
TGTCGGTGAGTGCGTGTTCTAATATGAGTTTTAAGGCTTTT
Found at i:5758349 original size:9 final size:9
Alignment explanation
Indices: 5758337--5758370 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5758327 ATATATTCAT
5758337 CATATAACA
1 CATATAACA
*
5758346 CATATATCA
1 CATATAACA
5758355 TCATATAACA
1 -CATATAACA
5758365 CATATA
1 CATATA
5758371 TCATTATACT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
9 14 0.64
10 8 0.36
ACGTcount: A:0.50, C:0.21, G:0.00, T:0.29
Consensus pattern (9 bp):
CATATAACA
Found at i:5758357 original size:19 final size:19
Alignment explanation
Indices: 5758326--5758374 Score: 89
Period size: 19 Copynumber: 2.5 Consensus size: 19
5758316 TTTTACTTAC
5758326 CATATATTCATCATATAACA
1 CATATA-TCATCATATAACA
5758346 CATATATCATCATATAACA
1 CATATATCATCATATAACA
5758365 CATATATCAT
1 CATATATCAT
5758375 TATACTAAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 23 0.79
20 6 0.21
ACGTcount: A:0.45, C:0.20, G:0.00, T:0.35
Consensus pattern (19 bp):
CATATATCATCATATAACA
Found at i:5758741 original size:31 final size:31
Alignment explanation
Indices: 5758691--5758815 Score: 173
Period size: 31 Copynumber: 4.0 Consensus size: 31
5758681 CCCGAATGAC
* *
5758691 CAGTCCATA-GATTCCGAAGAACCTAGGTAATA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAA-A
* *
5758723 -AATCCATATGTCCAGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5758753 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
5758784 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
5758815 C
1 C
5758816 CCTCGACCCT
Statistics
Matches: 84, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
30 1 0.01
31 82 0.98
32 1 0.01
ACGTcount: A:0.41, C:0.22, G:0.18, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:5779937 original size:24 final size:25
Alignment explanation
Indices: 5779893--5779940 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
5779883 ATAAAAAACA
*
5779893 TTTTTATAATTTACATTATTAATTT
1 TTTTTATAATTTACATCATTAATTT
*
5779918 TTTTTATATTTTA-ATCATTAATT
1 TTTTTATAATTTACATCATTAATT
5779941 ATCAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.65
Consensus pattern (25 bp):
TTTTTATAATTTACATCATTAATTT
Found at i:5780989 original size:5 final size:5
Alignment explanation
Indices: 5780979--5781008 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
5780969 AAATTGGAAT
5780979 GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA
1 GTTGA GTTGA GTTGA GTTGA GTTGA GTTGA
5781009 ATTGGGCTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.20, C:0.00, G:0.40, T:0.40
Consensus pattern (5 bp):
GTTGA
Found at i:5791901 original size:14 final size:14
Alignment explanation
Indices: 5791884--5791918 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
5791874 AAAATGATTT
5791884 ATATTTTCTGAAAA
1 ATATTTTCTGAAAA
*
5791898 ATATTTTTTGAAAA
1 ATATTTTCTGAAAA
*
5791912 ATGTTTT
1 ATATTTT
5791919 ACGATGTTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.37, C:0.03, G:0.09, T:0.51
Consensus pattern (14 bp):
ATATTTTCTGAAAA
Found at i:5791913 original size:35 final size:34
Alignment explanation
Indices: 5791853--5791919 Score: 82
Period size: 35 Copynumber: 1.9 Consensus size: 34
5791843 TTAAAAACGT
*
5791853 TTTTCGAAAAATGATTTTCGTAAAATGATTTATA
1 TTTTCGAAAAATGATTTTCGAAAAATGATTTATA
* *
5791887 TTTTCTGAAAAAT-ATTTTTTGAAAAATGTTTTA
1 TTTTC-GAAAAATGA-TTTTCGAAAAATGATTTA
5791920 CGATGTTTGA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
34 6 0.21
35 22 0.79
ACGTcount: A:0.37, C:0.04, G:0.10, T:0.48
Consensus pattern (34 bp):
TTTTCGAAAAATGATTTTCGAAAAATGATTTATA
Found at i:5792087 original size:19 final size:20
Alignment explanation
Indices: 5792050--5792088 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
5792040 ATTTTTAAAA
5792050 TATTAAAATAATTTATTTAT
1 TATTAAAATAATTTATTTAT
*
5792070 TATTAAAAT-ATTTTTTTAT
1 TATTAAAATAATTTATTTAT
5792089 AATTTTATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTAAAATAATTTATTTAT
Found at i:5792284 original size:26 final size:24
Alignment explanation
Indices: 5792208--5792285 Score: 77
Period size: 23 Copynumber: 3.1 Consensus size: 24
5792198 TATTATATCT
**
5792208 TATATTATTATAATATAATTGAT-
1 TATATTATTATAATATAATAAATA
* *
5792231 TATTTTATTATAATATAAAAAATTTA
1 TATATTATTATAATATAATAAA--TA
5792257 TATATTATTATAAATATTAATAAATA
1 TATATTATTAT-AATA-TAATAAATA
5792283 TAT
1 TAT
5792286 TTTAATATTT
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
23 18 0.41
25 1 0.02
26 15 0.34
27 4 0.09
28 6 0.14
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (24 bp):
TATATTATTATAATATAATAAATA
Found at i:5800394 original size:30 final size:29
Alignment explanation
Indices: 5800326--5800400 Score: 116
Period size: 29 Copynumber: 2.6 Consensus size: 29
5800316 TATTAGATGA
*
5800326 AGTAGGTCGCCATGCACGCCCAGCGACCT
1 AGTAGGTCGCCATGCACGCCCAACGACCT
5800355 A-TCAGGTCGCCATGCACGCCCAACGACCT
1 AGT-AGGTCGCCATGCACGCCCAACGACCT
5800384 AGGTAGGTCGCCATGCA
1 A-GTAGGTCGCCATGCA
5800401 ATCCATGTCG
Statistics
Matches: 42, Mismatches: 1, Indels: 5
0.88 0.02 0.10
Matches are distributed among these distances:
28 1 0.02
29 27 0.64
30 13 0.31
31 1 0.02
ACGTcount: A:0.23, C:0.36, G:0.27, T:0.15
Consensus pattern (29 bp):
AGTAGGTCGCCATGCACGCCCAACGACCT
Found at i:5800412 original size:17 final size:17
Alignment explanation
Indices: 5800390--5800424 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
5800380 ACCTAGGTAG
5800390 GTCGCCATGCAATCCAT
1 GTCGCCATGCAATCCAT
5800407 GTCGCCATGCAATCCAT
1 GTCGCCATGCAATCCAT
5800424 G
1 G
5800425 CTTGACAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (17 bp):
GTCGCCATGCAATCCAT
Done.