Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008526.1 Hibiscus syriacus cultivar Beakdansim tig00111398_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: 3043201
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 9 of 12
Found at i:2138249 original size:20 final size:20
Alignment explanation
Indices: 2138224--2138276 Score: 88
Period size: 20 Copynumber: 2.6 Consensus size: 20
2138214 ACGCTATGTA
2138224 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
2138244 AATCGCGTTGCGAAAGTCAG
1 AATCGCGTTGCGAAAGTCAG
* *
2138264 TATCTCGTTGCGA
1 AATCGCGTTGCGA
2138277 TTTTGTATTA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.26, C:0.21, G:0.28, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGAAAGTCAG
Found at i:2138337 original size:41 final size:41
Alignment explanation
Indices: 2138245--2138339 Score: 102
Period size: 41 Copynumber: 2.3 Consensus size: 41
2138235 GAAAGTCAGA
* * * * ** *
2138245 ATCGCGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAT
*
2138286 ATCGCATTGCGATAGTCAGTATCGCATTGCAATTTTCCCAAT
1 ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTT-CCAAT
2138328 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
2138340 TTACTTATTC
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
41 42 0.95
42 2 0.05
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATAGTCAGTATCGCATTGCAATTTTCCAAT
Found at i:2147410 original size:2 final size:2
Alignment explanation
Indices: 2147403--2147435 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2147393 CTATTTTAAA
2147403 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
2147436 ACTGATCATT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2147577 original size:32 final size:31
Alignment explanation
Indices: 2147494--2147618 Score: 115
Period size: 32 Copynumber: 4.0 Consensus size: 31
2147484 TATAACAATG
* * *
2147494 ATAAAAGTTTAATAAATTTAATAACTATTTT
1 ATAACAGTTTCATAAATTTAATAATTATTTT
* * * *
2147525 GTAATAGTTTGATTATATTTAATAATTATTTT
1 ATAACAGTTTCA-TAAATTTAATAATTATTTT
* * * *
2147557 ATAACAATTTTATAAAATTTAATGATCATTTT
1 ATAACAGTTTCAT-AAATTTAATAATTATTTT
**
2147589 ATAACAGTTTCATAAATTTAACGATTATTT
1 ATAACAGTTTCATAAATTTAATAATTATTT
2147619 AATATTTTTT
Statistics
Matches: 76, Mismatches: 16, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
31 25 0.33
32 51 0.67
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.48
Consensus pattern (31 bp):
ATAACAGTTTCATAAATTTAATAATTATTTT
Found at i:2149262 original size:16 final size:16
Alignment explanation
Indices: 2149241--2149271 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2149231 GACGAGCACG
*
2149241 GATGAATATCATTAAT
1 GATGAACATCATTAAT
2149257 GATGAACATCATTAA
1 GATGAACATCATTAA
2149272 ATTAATTTAT
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:0.45, C:0.10, G:0.13, T:0.32
Consensus pattern (16 bp):
GATGAACATCATTAAT
Found at i:2150516 original size:6 final size:6
Alignment explanation
Indices: 2150507--2150606 Score: 182
Period size: 6 Copynumber: 16.7 Consensus size: 6
2150497 GCGCATGCGC
*
2150507 ATGTGC ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
*
2150555 ATGTGT ATGTGT ATGTGT ATGTGT ACGTGT ATGTGT ATGTGT ATGTGT
1 ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT ATGTGT
2150603 ATGT
1 ATGT
2150607 ATATTATCGT
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 91 1.00
ACGTcount: A:0.17, C:0.02, G:0.33, T:0.48
Consensus pattern (6 bp):
ATGTGT
Found at i:2171123 original size:3 final size:3
Alignment explanation
Indices: 2171115--2171139 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2171105 GAATTGGGTT
2171115 TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG T
2171140 ATATTTTAAG
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:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:2176430 original size:20 final size:20
Alignment explanation
Indices: 2176401--2176439 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2176391 ACTTCCTCAT
*
2176401 TGTTTTGATCTAC-AAAAATG
1 TGTTTCGATC-ACTAAAAATG
2176421 TGTTTCGATCACTAAAAAT
1 TGTTTCGATCACTAAAAAT
2176440 AACCCTTGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 2 0.12
20 15 0.88
ACGTcount: A:0.36, C:0.13, G:0.13, T:0.38
Consensus pattern (20 bp):
TGTTTCGATCACTAAAAATG
Found at i:2177803 original size:9 final size:10
Alignment explanation
Indices: 2177745--2177805 Score: 67
Period size: 10 Copynumber: 6.3 Consensus size: 10
2177735 TAATTTTTCA
2177745 AAAAATATTT
1 AAAAATATTT
2177755 AAAAATATTT
1 AAAAATATTT
2177765 AAAAATATATCT
1 AAAAATAT-T-T
*
2177777 -AAAATATAT
1 AAAAATATTT
2177786 -AAAA-ATTT
1 AAAAATATTT
2177794 AAAAAT-TTT
1 AAAAATATTT
2177803 AAA
1 AAA
2177806 GGGCGATAGC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
8 3 0.07
9 15 0.33
10 18 0.40
11 8 0.18
12 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (10 bp):
AAAAATATTT
Found at i:2185229 original size:50 final size:48
Alignment explanation
Indices: 2185167--2185283 Score: 119
Period size: 50 Copynumber: 2.4 Consensus size: 48
2185157 AAAAGTGCGT
* * *
2185167 CCCCT-ACACCGCGCTATATGCTGATTTGACGCCACGTGGGTATAGCGAGC
1 CCCCTGAC-CCGCGCTATACGCTAATCTGACGCCACGTGGGTATA--GAGC
* * * * *
2185217 CCCCTGCCCCGCGATATACGGTAATCTGGCGCCACGTGGGTATAGTGC
1 CCCCTGACCCGCGCTATACGCTAATCTGACGCCACGTGGGTATAGAGC
*
2185265 CCCCTGATCCGCGCTATAC
1 CCCCTGACCCGCGCTATAC
2185284 CTAGATATTT
Statistics
Matches: 55, Mismatches: 11, Indels: 4
0.79 0.16 0.06
Matches are distributed among these distances:
48 19 0.35
50 35 0.64
51 1 0.02
ACGTcount: A:0.18, C:0.35, G:0.26, T:0.21
Consensus pattern (48 bp):
CCCCTGACCCGCGCTATACGCTAATCTGACGCCACGTGGGTATAGAGC
Found at i:2185753 original size:111 final size:111
Alignment explanation
Indices: 2185559--2185780 Score: 363
Period size: 111 Copynumber: 2.0 Consensus size: 111
2185549 TGTAAATCAT
* * * * *
2185559 ATATCTCTATACTTTGTTGATACGATAACATTTTAACGTTTTAATTTAATTTGAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
* *
2185624 TATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
*
2185670 ATATCTCGACACTTTGCTAATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
2185735 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAATAATTAA
66 TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
2185781 TTTTTGTAAT
Statistics
Matches: 102, Mismatches: 9, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTAATACGATAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTCATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:2203675 original size:21 final size:22
Alignment explanation
Indices: 2203651--2203700 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 22
2203641 TATGTCATAA
2203651 TAATAATAATAAAT-TATAAAT
1 TAATAATAATAAATATATAAAT
**
2203672 TAAT-ATTGTAAATATATAAAT
1 TAATAATAATAAATATATAAAT
*
2203693 AAATAATA
1 TAATAATA
2203701 TAAGAATTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
20 7 0.30
21 14 0.61
22 2 0.09
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (22 bp):
TAATAATAATAAATATATAAAT
Found at i:2204618 original size:23 final size:22
Alignment explanation
Indices: 2204578--2204633 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
2204568 AGCGAAAATA
* *
2204578 TGTCATAAAAACAGAGAAGATTG
1 TGTCATAAAAACAAAGAA-ATCG
* *
2204601 TGTCATAAAGATAAAGAAATCG
1 TGTCATAAAAACAAAGAAATCG
*
2204623 TGCCATAAAAA
1 TGTCATAAAAA
2204634 TATAGTTATT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
22 12 0.44
23 15 0.56
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.21
Consensus pattern (22 bp):
TGTCATAAAAACAAAGAAATCG
Found at i:2211917 original size:12 final size:13
Alignment explanation
Indices: 2211881--2211924 Score: 72
Period size: 13 Copynumber: 3.5 Consensus size: 13
2211871 GCCCCGATTA
2211881 CCCGATTACCCGC
1 CCCGATTACCCGC
2211894 CCCGATTACCCGC
1 CCCGATTACCCGC
*
2211907 CCCGA-TACCCGA
1 CCCGATTACCCGC
2211919 CCCGAT
1 CCCGAT
2211925 AAATATTAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.18, C:0.52, G:0.16, T:0.14
Consensus pattern (13 bp):
CCCGATTACCCGC
Found at i:2212004 original size:19 final size:19
Alignment explanation
Indices: 2211980--2212019 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
2211970 AATAAATTTA
2211980 ATTTAAATAAAAAATATAT
1 ATTTAAATAAAAAATATAT
* * *
2211999 ATTTAATTTAAATATATAT
1 ATTTAAATAAAAAATATAT
2212018 AT
1 AT
2212020 ATATACCCGG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (19 bp):
ATTTAAATAAAAAATATAT
Found at i:2213522 original size:55 final size:55
Alignment explanation
Indices: 2213421--2213644 Score: 412
Period size: 55 Copynumber: 4.1 Consensus size: 55
2213411 ATAATATGTC
*
2213421 TGACGATAAATCTAGTCTTAAGGGGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
1 TGACGATAAATCTAGTCTTAA-GAGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
*
2213477 TGACGATAAATCTAGTCTTAAGAGGTAATTATGTTAAAGGATTGCTAGTAGTGAT
1 TGACGATAAATCTAGTCTTAAGAGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
2213532 TGACGATAAATCTAGTCTTAAGAGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
1 TGACGATAAATCTAGTCTTAAGAGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
*
2213587 TGACGATAAATCTAGTCTTAAGAGGTAATTATGTTAAAGGATTGCTAGTAGTGAT
1 TGACGATAAATCTAGTCTTAAGAGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
2213642 TGA
1 TGA
2213645 TTACAAATAT
Statistics
Matches: 164, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
55 143 0.87
56 21 0.13
ACGTcount: A:0.34, C:0.08, G:0.25, T:0.33
Consensus pattern (55 bp):
TGACGATAAATCTAGTCTTAAGAGGTAATTATGCTAAAGGATTGCTAGTAGTGAT
Found at i:2213953 original size:30 final size:31
Alignment explanation
Indices: 2213901--2213966 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 31
2213891 ATTTGTACAT
* *
2213901 ATATACATATGAAAATTTAATTTTAGTTCAA
1 ATATACATATGAAAAATTAATTTTAATTCAA
2213932 ATATACATAT-AAAAATTAATTTTAATTCAA
1 ATATACATATGAAAAATTAATTTTAATTCAA
*
2213962 TTATA
1 ATATA
2213967 ATTGTAAATG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 22 0.69
31 10 0.31
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (31 bp):
ATATACATATGAAAAATTAATTTTAATTCAA
Found at i:2217484 original size:2 final size:2
Alignment explanation
Indices: 2217477--2217525 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
2217467 ACTCTATGTT
*
2217477 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2217519 TA TA TA T
1 TA TA TA T
2217526 GATTATAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2220141 original size:9 final size:9
Alignment explanation
Indices: 2220129--2220156 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
2220119 ATCTTATGAT
2220129 TTTAATTTA
1 TTTAATTTA
2220138 TTTAATTTA
1 TTTAATTTA
2220147 TTTAATTTA
1 TTTAATTTA
2220156 T
1 T
2220157 AGTAAAAGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTAATTTA
Found at i:2221839 original size:23 final size:23
Alignment explanation
Indices: 2221796--2221870 Score: 87
Period size: 23 Copynumber: 3.3 Consensus size: 23
2221786 GTACTCGCTT
* * *
2221796 GTTTAACGTTCACGAATATGTTT
1 GTTTAACGTTCATGAACATGTTC
*
2221819 GTTTAACGTTCGTGAACATGTTC
1 GTTTAACGTTCATGAACATGTTC
* * *
2221842 ATTTACCATTCATGAACATGTTC
1 GTTTAACGTTCATGAACATGTTC
2221865 GTTTAA
1 GTTTAA
2221871 TATTCATTTA
Statistics
Matches: 42, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
23 42 1.00
ACGTcount: A:0.27, C:0.16, G:0.16, T:0.41
Consensus pattern (23 bp):
GTTTAACGTTCATGAACATGTTC
Found at i:2222695 original size:24 final size:24
Alignment explanation
Indices: 2222667--2222757 Score: 112
Period size: 24 Copynumber: 3.6 Consensus size: 24
2222657 TATATTATAG
2222667 ATATTAATTTTTTAAATAAATTAA
1 ATATTAATTTTTTAAATAAATTAA
*
2222691 ATATTAATTTTTTAATATTATATTATA
1 ATATTAATTTTTTAA-A-TAAATTA-A
*
2222718 GATATTATTTTTTTTAAATAAATTAA
1 -ATATTA-ATTTTTTAAATAAATTAA
2222744 ATATT-ATTTTTTAA
1 ATATTAATTTTTTAA
2222758 TATTATATTA
Statistics
Matches: 58, Mismatches: 4, Indels: 11
0.79 0.05 0.15
Matches are distributed among these distances:
23 8 0.14
24 15 0.26
25 6 0.10
26 7 0.12
27 7 0.12
28 7 0.12
29 8 0.14
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.56
Consensus pattern (24 bp):
ATATTAATTTTTTAAATAAATTAA
Found at i:2222715 original size:52 final size:51
Alignment explanation
Indices: 2222649--2222782 Score: 223
Period size: 52 Copynumber: 2.6 Consensus size: 51
2222639 AAGTTTTATA
*
2222649 TTTAATTTTATATTATAGATATTAATTTTTTAAATAAATTAAATATTAATTT
1 TTTAATATTATATTATAGATATTAATTTTTTAAATAAATTAAATATT-ATTT
*
2222701 TTTAATATTATATTATAGATATTATTTTTTTTAAATAAATTAAATATTATTT
1 TTTAATATTATATTATAGATATTA-ATTTTTTAAATAAATTAAATATTATTT
2222753 TTTAATATTATATTATAGATATATAATTTT
1 TTTAATATTATATTATAGATAT-TAATTTT
2222783 ATATCATATA
Statistics
Matches: 77, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
52 53 0.69
53 24 0.31
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (51 bp):
TTTAATATTATATTATAGATATTAATTTTTTAAATAAATTAAATATTATTT
Found at i:2222747 original size:25 final size:25
Alignment explanation
Indices: 2222674--2222755 Score: 103
Period size: 25 Copynumber: 3.2 Consensus size: 25
2222664 TAGATATTAA
*
2222674 TTTTTTAAATAAATTAAATATTA-A
1 TTTTTTAAATAAATTAAATATTATT
*
2222698 TTTTTTAATATTATATTATAGATATTATT
1 TTTTTTAA-A-TAAATTA-A-ATATTATT
2222727 TTTTTTAAATAAATTAAATATTATT
1 TTTTTTAAATAAATTAAATATTATT
2222752 TTTT
1 TTTT
2222756 AATATTATAT
Statistics
Matches: 50, Mismatches: 3, Indels: 9
0.81 0.05 0.15
Matches are distributed among these distances:
24 8 0.16
25 13 0.26
26 7 0.14
27 7 0.14
28 7 0.14
29 8 0.16
ACGTcount: A:0.40, C:0.00, G:0.01, T:0.59
Consensus pattern (25 bp):
TTTTTTAAATAAATTAAATATTATT
Found at i:2222843 original size:19 final size:20
Alignment explanation
Indices: 2222793--2222845 Score: 58
Period size: 19 Copynumber: 2.8 Consensus size: 20
2222783 ATATCATATA
*
2222793 AATTA-TTTTATATATTATT
1 AATTATTTTTATTTATTATT
*
2222812 AA-AATTTTATATTTATT-TT
1 AATTATTTT-TATTTATTATT
2222831 AATTATTTTTATTTA
1 AATTATTTTTATTTA
2222846 AGTTTAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
18 1 0.04
19 15 0.54
20 12 0.43
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (20 bp):
AATTATTTTTATTTATTATT
Found at i:2222851 original size:20 final size:20
Alignment explanation
Indices: 2222793--2222852 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 20
2222783 ATATCATATA
2222793 AATTATTTTATATATTA--TT
1 AATTATTTTATAT-TTAGTTT
* *
2222812 AA-AATTTTATATTTATTTT
1 AATTATTTTATATTTAGTTT
2222831 AATTATTTT-TATTTAAGTTT
1 AATTATTTTATATTT-AGTTT
2222851 AA
1 AA
2222853 ATATAATATT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
17 3 0.09
18 9 0.26
19 11 0.32
20 11 0.32
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.62
Consensus pattern (20 bp):
AATTATTTTATATTTAGTTT
Found at i:2223105 original size:25 final size:25
Alignment explanation
Indices: 2223079--2223126 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2223069 ATATTTTCTA
2223079 AAAATAT-AATATA-ATTATAAAAAT
1 AAAATATGAATATATATT-TAAAAAT
*
2223103 AAATTATGAATATATATTTAAAAA
1 AAAATATGAATATATATTTAAAAA
2223127 AATTAAAAGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 12 0.57
26 3 0.14
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.35
Consensus pattern (25 bp):
AAAATATGAATATATATTTAAAAAT
Found at i:2223492 original size:31 final size:31
Alignment explanation
Indices: 2223455--2223514 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
2223445 TAGTTGTATG
* *
2223455 AATTATTTAAATTTCAGTATTGTAAAACTAA
1 AATTATTTAAATCTCAATATTGTAAAACTAA
2223486 AATTATTTAAATCTCAATATTGTAAAACT
1 AATTATTTAAATCTCAATATTGTAAAACT
2223515 CTTTTAAGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.45, C:0.08, G:0.05, T:0.42
Consensus pattern (31 bp):
AATTATTTAAATCTCAATATTGTAAAACTAA
Found at i:2223864 original size:12 final size:12
Alignment explanation
Indices: 2223847--2223879 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
2223837 ATGTAAAAAT
2223847 ATAAACGAGCTC
1 ATAAACGAGCTC
*
2223859 ATAAACGAGCTT
1 ATAAACGAGCTC
2223871 ATAAACGAG
1 ATAAACGAG
2223880 TTTGTTCGTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (12 bp):
ATAAACGAGCTC
Found at i:2225924 original size:25 final size:25
Alignment explanation
Indices: 2225890--2225946 Score: 96
Period size: 25 Copynumber: 2.3 Consensus size: 25
2225880 AGGTTTGTTT
*
2225890 CTTGAAGTTGAAGCGAAGTATGATA
1 CTTGAAGTTGAAGCAAAGTATGATA
2225915 CTTGAAGTTGAAGCAAAGTATGATA
1 CTTGAAGTTGAAGCAAAGTATGATA
*
2225940 CTCGAAG
1 CTTGAAG
2225947 ATAAATATGC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
25 30 1.00
ACGTcount: A:0.37, C:0.11, G:0.26, T:0.26
Consensus pattern (25 bp):
CTTGAAGTTGAAGCAAAGTATGATA
Found at i:2231762 original size:31 final size:30
Alignment explanation
Indices: 2231718--2231799 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 30
2231708 TAAAAACTAC
* *
2231718 AAAATAATTAAATTTATCAAATTATTATAA
1 AAAATTATTAAATTTATCAAATTATTACAA
*
2231748 AATAATTATTAAATTTATCAAATTGTTACAA
1 AA-AATTATTAAATTTATCAAATTATTACAA
* * *
2231779 AAGATTATTATATCTATCAAA
1 AAAATTATTAAATTTATCAAA
2231800 CTTTATTAGT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
30 18 0.40
31 27 0.60
ACGTcount: A:0.51, C:0.06, G:0.02, T:0.40
Consensus pattern (30 bp):
AAAATTATTAAATTTATCAAATTATTACAA
Found at i:2234776 original size:2 final size:2
Alignment explanation
Indices: 2234769--2234813 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
2234759 AATAAATAAT
2234769 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2234811 TA T
1 TA T
2234814 GGGTACAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2239264 original size:3 final size:3
Alignment explanation
Indices: 2239218--2239252 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
2239208 AATAAATCAA
*
2239218 AAT AAT AAT AAT AAT AAT AAT ACT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2239253 AAGTAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.66, C:0.03, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2240648 original size:26 final size:25
Alignment explanation
Indices: 2240604--2240652 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
2240594 AATAATAATA
2240604 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
*
2240630 ATATAATATATAAA-TTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
2240653 TGTTTTTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:2240718 original size:42 final size:42
Alignment explanation
Indices: 2240624--2240707 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
2240614 AAACGTTTTC
* *
2240624 AAAAAC-ATATAATATATAAATTTTTAAAATGTTTTTTTAAA
1 AAAAACTATATAATATATAAATTTTCAAAATGTGTTTTTAAA
* *
2240665 AAAAACTATATATTATATATATTTTCAAAATG-GTTTTTAAA
1 AAAAACTATATAATATATAAATTTTCAAAATGTGTTTTTAAA
2240706 AA
1 AA
2240708 TTATATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
41 16 0.42
42 22 0.58
ACGTcount: A:0.50, C:0.04, G:0.04, T:0.43
Consensus pattern (42 bp):
AAAAACTATATAATATATAAATTTTCAAAATGTGTTTTTAAA
Found at i:2240748 original size:33 final size:32
Alignment explanation
Indices: 2240711--2240774 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2240701 TTAAAAATTA
* *
2240711 TATATATAAATGTTTTCATAACGTTTTCAAAAG
1 TATATATAAATATTTT-AAAACGTTTTCAAAAG
*
2240744 TATATATATATATTTTAAAACGTTTTCAAAA
1 TATATATAAATATTTTAAAACGTTTTCAAAA
2240775 ACTATATTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 14 0.50
33 14 0.50
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.44
Consensus pattern (32 bp):
TATATATAAATATTTTAAAACGTTTTCAAAAG
Found at i:2240748 original size:35 final size:34
Alignment explanation
Indices: 2240666--2240788 Score: 106
Period size: 35 Copynumber: 3.5 Consensus size: 34
2240656 TTTTTTAAAA
* * *
2240666 AAAACTATATATTATATATATTTTCAAAATGGTTTTTA
1 AAAACTATATA-TATAAATATTTT-AAAA-CG-TTTTC
* * *
2240704 AAAATTATATATATAAATGTTTTCATAACGTTTTC
1 AAAACTATATATATAAATATTTT-AAAACGTTTTC
*
2240739 AAAAGTATATATAT--ATATTTTAAAACGTTTTC
1 AAAACTATATATATAAATATTTTAAAACGTTTTC
2240771 AAAAACTATATTATATAA
1 -AAAACTATA-TATATAA
2240789 TTTTCAAAAA
Statistics
Matches: 71, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
32 10 0.14
33 14 0.20
34 5 0.07
35 17 0.24
36 1 0.01
37 14 0.20
38 10 0.14
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.44
Consensus pattern (34 bp):
AAAACTATATATATAAATATTTTAAAACGTTTTC
Found at i:2240750 original size:37 final size:38
Alignment explanation
Indices: 2240617--2240788 Score: 116
Period size: 40 Copynumber: 4.7 Consensus size: 38
2240607 TATATATAAA
*
2240617 CGTTTTCAAAAACATATAATATATAAAT-TTTT-AAAAT
1 CGTTTTCAAAAATATAT-ATATATAAATATTTTCAAAAT
* * *
2240654 -GTTTTTTTAAAAAAAACTATATATTATATATATTTTCAAAAT
1 CG---TTTTCAAAAATA-TATATA-TATAAATATTTTCAAAAT
* * * *
2240696 GGTTTTTAAAAAT-TATATATATAAATGTTTTCATAA-
1 CGTTTTCAAAAATATATATATATAAATATTTTCAAAAT
*
2240732 CGTTTTC-AAAA-GTATATATAT--ATATTTT-AAAA-
1 CGTTTTCAAAAATATATATATATAAATATTTTCAAAAT
2240764 CGTTTTCAAAAACTATAT-TATATAA
1 CGTTTTCAAAAA-TATATATATATAA
2240789 TTTTCAAAAA
Statistics
Matches: 108, Mismatches: 13, Indels: 29
0.72 0.09 0.19
Matches are distributed among these distances:
32 10 0.09
33 10 0.09
34 5 0.05
35 16 0.15
36 6 0.06
37 14 0.13
38 6 0.06
39 13 0.12
40 18 0.17
41 4 0.04
42 5 0.05
43 1 0.01
ACGTcount: A:0.45, C:0.06, G:0.05, T:0.44
Consensus pattern (38 bp):
CGTTTTCAAAAATATATATATATAAATATTTTCAAAAT
Found at i:2240812 original size:119 final size:124
Alignment explanation
Indices: 2240681--2240925 Score: 428
Period size: 119 Copynumber: 2.0 Consensus size: 124
2240671 TATATATTAT
2240681 ATATATTTTCAAAATGGTTTTTAAAAATTATA-TATATAAATGTTTTCATAACGTTTTCAAAAG-
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGA
2240744 TATA-TATATATATTTT-AAAACGTTTTCAAAAACTATAT-TATATAATTTTCAAAAAA
66 TATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATATATAATTTTCAAAAAA
*
2240800 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAGTGTTTTCATAACGTTTTCAAAAGT
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAG-
2240865 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATAATTTTCAAAAAA
65 ATATATTATATATATTTTAAAAACGTTTTCAAAAACTATAT-ATATATAATTTTCAAAAAA
2240926 TATTTTAAAA
Statistics
Matches: 118, Mismatches: 1, Indels: 7
0.94 0.01 0.06
Matches are distributed among these distances:
119 32 0.27
120 30 0.25
122 4 0.03
123 12 0.10
124 22 0.19
126 18 0.15
ACGTcount: A:0.44, C:0.07, G:0.05, T:0.44
Consensus pattern (124 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATTATATAAATGTTTTCATAACGTTTTCAAAAGA
TATATTATATATATTTTAAAAACGTTTTCAAAAACTATATATATATAATTTTCAAAAAA
Found at i:2240956 original size:38 final size:39
Alignment explanation
Indices: 2240854--2241026 Score: 175
Period size: 37 Copynumber: 4.6 Consensus size: 39
2240844 TTTCATAACG
* * * *
2240854 TTTTCAAAAGTATATATTATATATATTTT-AAAAACGT-
1 TTTTAAAAACTATATAATATATATATTTTCAAAAACATA
*
2240891 TTTCAAAAACTATATAATATATA-ATTTTCAAAAA-ATA
1 TTTTAAAAACTATATAATATATATATTTTCAAAAACATA
* *
2240928 TTTTAAAAACTATATAATATACATATTTTCAAAAA-ATG
1 TTTTAAAAACTATATAATATATATATTTTCAAAAACATA
*
2240966 TTTT--AAACTATATATTATATATGTATTTTCAAAAACA-A
1 TTTTAAAAACTATATA--ATATATATATTTTCAAAAACATA
**
2241004 -TTTGCAAACTATATAATATATAT
1 TTTTAAAAACTATATAATATATAT
2241027 GTGTATATAT
Statistics
Matches: 116, Mismatches: 12, Indels: 16
0.81 0.08 0.11
Matches are distributed among these distances:
36 16 0.14
37 55 0.47
38 34 0.29
39 11 0.09
ACGTcount: A:0.47, C:0.08, G:0.03, T:0.42
Consensus pattern (39 bp):
TTTTAAAAACTATATAATATATATATTTTCAAAAACATA
Found at i:2241727 original size:80 final size:81
Alignment explanation
Indices: 2241629--2242239 Score: 552
Period size: 83 Copynumber: 7.5 Consensus size: 81
2241619 AAGTTGAATA
* *
2241629 TAATCGAACTCGAAGGTCTT-TAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
1 TAATCGAACTCAAAGGTCTTGTAGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
2241693 GCCTTGGAGCTGAGCG
66 GCCTTGGAGCTGAGCG
* * * * * * * *
2241709 GATTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCAAAGGTC-TTG-TAGCAGATAACCCTTCTCA-ACTTAAGCTATGCTGCAAATGA
* * *
2241773 TATGCCCTTGAAGCTGAGTG
63 TGTG-CCTTGGAGCTGAGCG
*** * * *
2241793 TAATCGAACTCGGGGGTCTT-TGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGT
1 TAATCGAACTCAAAGGTCTTGTAGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
2241857 GCCTTGGAGCTGAGCG
66 GCCTTGGAGCTGAGCG
* * * * * *
2241873 TAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGA
1 TAATCGAACTCAAAGGTC-TTG-TAGCAGATAACCCTTCTCA-ACTTAAGCTATGCTGCAAATGA
* * *
2241937 TGTGCCCTCGAAGCTGAGTG
63 TGTG-CCTTGGAGCTGAGCG
*** * * * *
2241957 TAATCGAACTCGGGGGTCTT-TGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGT
1 TAATCGAACTCAAAGGTCTTGTAGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
*
2242021 GCCTAGGAGCTGAGCG
66 GCCTTGGAGCTGAGCG
* * * * * * *
2242037 TAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCT-AGCCTTGAGTTATGCTGTAAATGT
1 TAATCGAACTCAAAGGTC-TTG-TAGCAGATAACCCTTCTCA-ACTTAAGCTATGCTGCAAATGA
* * *
2242101 TATGCCCTTGAAGCTGAGTG
63 TGTG-CCTTGGAGCTGAGCG
* * * * *
2242121 TAATCGAACTTAAGGGTCTT-TGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGT
1 TAATCGAACTCAAAGGTCTTGTAGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
2242185 GCCTTGGAGCTGAGCG
66 GCCTTGGAGCTGAGCG
* * * * *
2242201 TAGTCGAACTCGAAGGTCTTGGTGGCAGGTAGCCCTTCT
1 TAATCGAACTCAAAGGTCTT-GTAGCAGATAACCCTTCT
2242240 GGCCTTGAGC
Statistics
Matches: 411, Mismatches: 100, Indels: 38
0.75 0.18 0.07
Matches are distributed among these distances:
80 97 0.24
81 109 0.27
82 16 0.04
83 110 0.27
84 79 0.19
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (81 bp):
TAATCGAACTCAAAGGTCTTGTAGCAGATAACCCTTCTCAACTTAAGCTATGCTGCAAATGATGT
GCCTTGGAGCTGAGCG
Found at i:2241813 original size:164 final size:164
Alignment explanation
Indices: 2241629--2242220 Score: 1031
Period size: 164 Copynumber: 3.6 Consensus size: 164
2241619 AAGTTGAATA
* * *
2241629 TAATCGAACTCGAAGGTCTTTAGCAGATAGCCCTTCTCAACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
* *
2241694 CCTTGGAGCTGAGCGGATTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
2241759 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
*
2241793 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
2241858 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
* * *
2241923 TATGCTGTAAATGATGTGCCCTCGAAGCTGAGTG
131 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
* *
2241957 TAATCGAACTCGGGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
2242022 CCTAGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
2242087 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
131 TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
** * *
2242121 TAATCGAACTTAAGGGTCTTTGGCAGATAACCCTTCTCGACTTAAGCTATTCTGCAAATGATGTG
1 TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
*
2242186 CCTTGGAGCTGAGCGTAGTCGAACTCGAAGGTCTT
66 CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTT
2242221 GGTGGCAGGT
Statistics
Matches: 408, Mismatches: 20, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
164 408 1.00
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
TAATCGAACTCGAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATGTG
CCTTGGAGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTAACAGATAACCCTTCTAGCCTTGAGT
TATGCTGTAAATGTTATGCCCTTGAAGCTGAGTG
Found at i:2245668 original size:18 final size:19
Alignment explanation
Indices: 2245627--2245671 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
2245617 AGTTAATGTG
2245627 AATGCAAAGAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
2245646 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
2245664 AATGCAAA
1 AATGCAAA
2245672 ATGTCTAAAT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.67, C:0.09, G:0.13, T:0.11
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:2247385 original size:10 final size:9
Alignment explanation
Indices: 2247370--2247479 Score: 63
Period size: 10 Copynumber: 12.1 Consensus size: 9
2247360 AAAAGATATT
2247370 AAATAAATCA
1 AAATAAAT-A
2247380 AAATAAATA
1 AAATAAATA
2247389 ATAAT-AATA
1 A-AATAAATA
2247398 AAAGTAAATA
1 AAA-TAAATA
*
2247408 ATATAAA-A
1 AAATAAATA
*
2247416 AAA-CAAT-
1 AAATAAATA
*
2247423 AAATCAAAGA
1 AAAT-AAATA
*
2247433 AATTAAATTA
1 AAATAAA-TA
2247443 AAATTAAAT-
1 AAA-TAAATA
2247452 AAAT-AAT-
1 AAATAAATA
2247459 AAATAAATA
1 AAATAAATA
2247468 CTAAATAAATA
1 --AAATAAATA
2247479 A
1 A
2247480 GAAAAAATAT
Statistics
Matches: 79, Mismatches: 8, Indels: 27
0.69 0.07 0.24
Matches are distributed among these distances:
7 12 0.15
8 9 0.11
9 21 0.27
10 24 0.30
11 13 0.16
ACGTcount: A:0.70, C:0.04, G:0.02, T:0.25
Consensus pattern (9 bp):
AAATAAATA
Found at i:2247387 original size:4 final size:4
Alignment explanation
Indices: 2247369--2247479 Score: 58
Period size: 4 Copynumber: 27.8 Consensus size: 4
2247359 AAAAAGATAT
2247369 TAAA TAAA TCAAAA TAAA T-AA T-AA T-AA TAAAA GTAAA TAATA TAAA
1 TAAA TAAA T--AAA TAAA TAAA TAAA TAAA T-AAA -TAAA TAA-A TAAA
* * *
2247415 -AAA -ACAA TAAA TCAAA GAAA TTAAA TTAA -AAT TAAA TAAA T-AA TAAA
1 TAAA TA-AA TAAA T-AAA TAAA -TAAA TAAA TAAA TAAA TAAA TAAA TAAA
*
2247462 TAAA T-AC TAAA TAAA TAA
1 TAAA TAAA TAAA TAAA TAA
2247480 GAAAAAATAT
Statistics
Matches: 86, Mismatches: 8, Indels: 26
0.72 0.07 0.22
Matches are distributed among these distances:
3 19 0.22
4 46 0.53
5 16 0.19
6 5 0.06
ACGTcount: A:0.69, C:0.04, G:0.02, T:0.25
Consensus pattern (4 bp):
TAAA
Found at i:2247461 original size:11 final size:11
Alignment explanation
Indices: 2247369--2247488 Score: 72
Period size: 11 Copynumber: 10.9 Consensus size: 11
2247359 AAAAAGATAT
*
2247369 TAAATAAATCA
1 TAAATAAATAA
2247380 -AAATAAATAA
1 TAAATAAATAA
2247390 T-AAT-AATAA
1 TAAATAAATAA
*
2247399 -AAGTAAATAATA
1 TAAATAAAT-A-A
* *
2247411 TAAAAAAACAA
1 TAAATAAATAA
*
2247422 TAAATCAAAGAAA
1 TAAAT-AAA-TAA
*
2247435 TTAAATTAAA-AT
1 -TAAA-TAAATAA
2247447 TAAATAAATAA
1 TAAATAAATAA
*
2247458 TAAATAAATAC
1 TAAATAAATAA
2247469 TAAATAAATAA
1 TAAATAAATAA
*
2247480 GAAA-AAATA
1 TAAATAAATA
2247489 TTATTTTAAA
Statistics
Matches: 86, Mismatches: 12, Indels: 23
0.71 0.10 0.19
Matches are distributed among these distances:
9 7 0.08
10 24 0.28
11 34 0.40
12 6 0.07
13 7 0.08
14 7 0.08
15 1 0.01
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (11 bp):
TAAATAAATAA
Found at i:2248799 original size:26 final size:25
Alignment explanation
Indices: 2248755--2248803 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
2248745 TAATAATATA
2248755 ATATATATATAAACGTTTTCAAAAAC
1 ATATATATATAAACGTTTT-AAAAAC
*
2248781 ATATAATATATAAA-TTTTTAAAA
1 ATAT-ATATATAAACGTTTTAAAA
2248804 TGTTTTTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 4 0.19
26 8 0.38
27 9 0.43
ACGTcount: A:0.53, C:0.06, G:0.02, T:0.39
Consensus pattern (25 bp):
ATATATATATAAACGTTTTAAAAAC
Found at i:2248809 original size:36 final size:36
Alignment explanation
Indices: 2248765--2248956 Score: 154
Period size: 38 Copynumber: 5.1 Consensus size: 36
2248755 ATATATATAT
*
2248765 AAACGTTTTCAAAAACATATAATATATAAATTTTTA
1 AAACGTTTTCAAAAACATATATTATATAAATTTTTA
* * * *
2248801 AAATGTTTTTTAAAAAAAAACTATATATTATATATATTTTCA
1 AAACG--TTTT---CAAAAAC-ATATATTATATAAATTTTTA
* * *
2248843 AAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCA
1 AAA-CGTTTTCAAAAA-CATATATTATATAAAT-TTTT-A
* ** *
2248883 TAACGTTTTCAAAAGTATATATTATATATA-TTTTA
1 AAACGTTTTCAAAAACATATATTATATAAATTTTTA
*
2248918 AAACGTTTTCAAAAACTATATATTATAT-AATTTTCA
1 AAACGTTTTCAAAAAC-ATATATTATATAAATTTTTA
2248954 AAA
1 AAA
2248957 AAATATATTT
Statistics
Matches: 124, Mismatches: 20, Indels: 24
0.74 0.12 0.14
Matches are distributed among these distances:
35 15 0.12
36 26 0.21
38 37 0.30
39 12 0.10
40 3 0.02
41 10 0.08
42 20 0.16
43 1 0.01
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (36 bp):
AAACGTTTTCAAAAACATATATTATATAAATTTTTA
Found at i:2248827 original size:42 final size:41
Alignment explanation
Indices: 2248775--2248858 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 41
2248765 AAACGTTTTC
* *
2248775 AAAAACATATAATATATAAATTTTTAAAATGTTTTTTAAAA
1 AAAAACATATAATATATAAATTTTCAAAATGGTTTTTAAAA
* *
2248816 AAAAACTATATATTATATATATTTTCAAAATGGTTTTTAAAA
1 AAAAAC-ATATAATATATAAATTTTCAAAATGGTTTTTAAAA
2248858 A
1 A
2248859 TTATATATTA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
41 6 0.16
42 32 0.84
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.42
Consensus pattern (41 bp):
AAAAACATATAATATATAAATTTTCAAAATGGTTTTTAAAA
Found at i:2248937 original size:25 final size:24
Alignment explanation
Indices: 2248908--2248991 Score: 62
Period size: 27 Copynumber: 3.2 Consensus size: 24
2248898 TATATATTAT
2248908 ATATATTTTAAAACGTTTTCAAAAA
1 ATATATTTTAAAA-GTTTTCAAAAA
* *
2248933 CTATATATTATATAA-TTTTCAAAAAA
1 --ATATATTTTAAAAGTTTTC-AAAAA
*
2248959 ATATATTTTCAAAATGGTTTTTAAAAA
1 ATATATTTT-AAAA--GTTTTCAAAAA
*
2248986 TTATAT
1 ATATAT
2248992 ATTATATAAG
Statistics
Matches: 46, Mismatches: 6, Indels: 10
0.74 0.10 0.16
Matches are distributed among these distances:
24 8 0.17
25 8 0.17
26 5 0.11
27 21 0.46
28 4 0.09
ACGTcount: A:0.46, C:0.06, G:0.04, T:0.44
Consensus pattern (24 bp):
ATATATTTTAAAAGTTTTCAAAAA
Found at i:2248941 original size:27 final size:25
Alignment explanation
Indices: 2248906--2248994 Score: 81
Period size: 25 Copynumber: 3.4 Consensus size: 25
2248896 AGTATATATT
2248906 ATATATATTTTAAAACGTTTTCAAAA
1 ATATATATTTTAAAA-GTTTTCAAAA
* *
2248932 ACTATATATTATATAA-TTTTCAAAA
1 A-TATATATTTTAAAAGTTTTCAAAA
* *
2248957 AAATATATTTTCAAAATGGTTTTTAAAA
1 ATATATATTTT-AAAA--GTTTTCAAAA
2248985 ATTATATATT
1 A-TATATATT
2248995 ATATAAGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 9
0.76 0.11 0.14
Matches are distributed among these distances:
24 8 0.16
25 13 0.26
26 1 0.02
27 12 0.24
28 9 0.18
29 7 0.14
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (25 bp):
ATATATATTTTAAAAGTTTTCAAAA
Found at i:2248969 original size:127 final size:128
Alignment explanation
Indices: 2248832--2249086 Score: 485
Period size: 127 Copynumber: 2.0 Consensus size: 128
2248822 TATATATTAT
2248832 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
*
2248897 GTATATATTATATATATTTT-AAAACGTTTTCAAAAACTATATATTATATAATTTTCAAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATAATTTTCAAAAAA
*
2248959 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAGTGTTTTCATAACGTTTTCAAAA
1 ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
2249024 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATAATTTTCAAAAAA
66 GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATAATTTTCAAAAAA
2249087 TATTTTAAAA
Statistics
Matches: 125, Mismatches: 2, Indels: 1
0.98 0.02 0.01
Matches are distributed among these distances:
127 84 0.67
128 41 0.33
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.44
Consensus pattern (128 bp):
ATATATTTTCAAAATGGTTTTTAAAAATTATATATTATATAAATGTTTTCATAACGTTTTCAAAA
GTATATATTATATATATTTTAAAAACGTTTTCAAAAACTATATAATATATAATTTTCAAAAAA
Found at i:2249035 original size:38 final size:37
Alignment explanation
Indices: 2248977--2249186 Score: 146
Period size: 38 Copynumber: 5.6 Consensus size: 37
2248967 TCAAAATGGT
* * * * *
2248977 TTTTAAAAATTATATATTATATAAGTGTTTTCATAACG
1 TTTTCAAAACTATATATTATATAA-TATTTTAAAAACG
*
2249015 TTTTCAAAAGTATATATTATAT-ATATTTTAAAAACG
1 TTTTCAAAACTATATATTATATAATATTTTAAAAACG
* * **
2249051 TTTTCAAAAACTATATAATATATAAT-TTTCAAAAAATA
1 TTTTC-AAAACTATATATTATATAATATTT-TAAAAACG
* *
2249089 TTTTAAAAACTATATA--ATATACATATTTTCAAAAAATG
1 TTTTCAAAACTATATATTATATA-ATATTTT--AAAAACG
* *
2249127 TTTT--AAACTATATATTATATATGTATTTTCAAAAACAA
1 TTTTCAAAACTATATATTATATA-ATATTTT-AAAAAC-G
* *
2249165 TTTGC-AAACTATATAATATATA
1 TTTTCAAAACTATATATTATATA
2249187 TGTGTATATA
Statistics
Matches: 141, Mismatches: 20, Indels: 21
0.77 0.11 0.12
Matches are distributed among these distances:
35 5 0.04
36 27 0.19
37 38 0.27
38 55 0.39
39 16 0.11
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (37 bp):
TTTTCAAAACTATATATTATATAATATTTTAAAAACG
Found at i:2249189 original size:39 final size:36
Alignment explanation
Indices: 2249020--2249187 Score: 153
Period size: 37 Copynumber: 4.5 Consensus size: 36
2249010 TAACGTTTTC
* * **
2249020 AAAAGTATATATTATATATATTTT-AAAAACGTTTTCA
1 AAAACTATATAATATATATATTTTCAAAAA-AATTT-A
2249057 AAAACTATATAATATATA-ATTTTCAAAAAATATTTTA
1 AAAACTATATAATATATATATTTTCAAAAAA-A-TTTA
* *
2249094 AAAACTATATAATATACATATTTTC-AAAAAATGTTT
1 AAAACTATATAATATATATATTTTCAAAAAAAT-TTA
* * *
2249130 TAAACTATATATTATATATGTATTTTCAAAAACAATTTG
1 AAAACTATATA--ATATATATATTTTCAAAAA-AATTTA
*
2249169 CAAACTATATAATATATAT
1 AAAACTATATAATATATAT
2249188 GTGTATATAT
Statistics
Matches: 110, Mismatches: 12, Indels: 18
0.79 0.09 0.13
Matches are distributed among these distances:
35 1 0.01
36 18 0.16
37 51 0.46
38 21 0.19
39 16 0.15
40 3 0.03
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (36 bp):
AAAACTATATAATATATATATTTTCAAAAAAATTTA
Found at i:2254252 original size:37 final size:37
Alignment explanation
Indices: 2254202--2254275 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
2254192 AATCTCTTAC
2254202 AGAAACTACTTACCAGCTCATGAATGCATACTAGGAA
1 AGAAACTACTTACCAGCTCATGAATGCATACTAGGAA
2254239 AGAAACTACTTACCAGCTCATGAATGCATACTAGGAA
1 AGAAACTACTTACCAGCTCATGAATGCATACTAGGAA
2254276 CTTGTTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.22
Consensus pattern (37 bp):
AGAAACTACTTACCAGCTCATGAATGCATACTAGGAA
Found at i:2261631 original size:13 final size:13
Alignment explanation
Indices: 2261613--2261649 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
2261603 ATTTTGAGTC
2261613 AATTTGAATTTTT
1 AATTTGAATTTTT
*
2261626 AATTTGCATTTTT
1 AATTTGAATTTTT
*
2261639 AGTTTGAATTT
1 AATTTGAATTT
2261650 ATAAAGTTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.27, C:0.03, G:0.11, T:0.59
Consensus pattern (13 bp):
AATTTGAATTTTT
Found at i:2261914 original size:31 final size:31
Alignment explanation
Indices: 2261876--2261935 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
2261866 TTCCCCACGA
* *
2261876 TCTTGTGGCAGCTTTGGAAATGCAGAAATGC
1 TCTTGTGGCAGCCTTGGAAACGCAGAAATGC
*
2261907 TCTTGTGGCAGCCTTGGAAACGCCGAAAT
1 TCTTGTGGCAGCCTTGGAAACGCAGAAAT
2261936 AGTTACGTTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (31 bp):
TCTTGTGGCAGCCTTGGAAACGCAGAAATGC
Found at i:2269208 original size:39 final size:39
Alignment explanation
Indices: 2269158--2269319 Score: 243
Period size: 39 Copynumber: 4.1 Consensus size: 39
2269148 AATCTTCATT
2269158 ATGTATCTTATTGATAATTACAAGTTCATTATGATTATG
1 ATGTATCTTATTGATAATTACAAGTTCATTATGATTATG
* *
2269197 ATGTATTTTATTGATAATTACAAGTTCGTTATGATTATG
1 ATGTATCTTATTGATAATTACAAGTTCATTATGATTATG
* ** **
2269236 ATGTATTTTATTGATAATTACAAGTTCATTACAAATTGACA
1 ATGTATCTTATTGATAATTACAAGTTCATTA-TGATT-ATG
2269277 ATGTATCTTATTGATAATTACAAGTTCATTATGATTATG
1 ATGTATCTTATTGATAATTACAAGTTCATTATGATTATG
2269316 ATGT
1 ATGT
2269320 TGGTGTATTC
Statistics
Matches: 109, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
39 72 0.66
40 6 0.06
41 31 0.28
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (39 bp):
ATGTATCTTATTGATAATTACAAGTTCATTATGATTATG
Found at i:2269309 original size:80 final size:78
Alignment explanation
Indices: 2269158--2269319 Score: 243
Period size: 80 Copynumber: 2.1 Consensus size: 78
2269148 AATCTTCATT
** ** *
2269158 ATGTATCTTATTGATAATTACAAGTTCATTATGATTATGATGTATTTTATTGATAATTACAAGTT
1 ATGTATCTTATTGATAATTACAAGTTCATTAAAATTACAATGTATCTTATTGATAATTACAAGTT
*
2269223 CGTTATGATTATG
66 CATTATGATTATG
*
2269236 ATGTATTTTATTGATAATTACAAGTTCATTACAAATTGACAATGTATCTTATTGATAATTACAAG
1 ATGTATCTTATTGATAATTACAAGTTCATTA-AAATT-ACAATGTATCTTATTGATAATTACAAG
2269301 TTCATTATGATTATG
64 TTCATTATGATTATG
2269316 ATGT
1 ATGT
2269320 TGGTGTATTC
Statistics
Matches: 75, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
78 30 0.40
79 3 0.04
80 42 0.56
ACGTcount: A:0.34, C:0.07, G:0.13, T:0.46
Consensus pattern (78 bp):
ATGTATCTTATTGATAATTACAAGTTCATTAAAATTACAATGTATCTTATTGATAATTACAAGTT
CATTATGATTATG
Found at i:2272110 original size:13 final size:13
Alignment explanation
Indices: 2272092--2272117 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2272082 TTTTTGGTTC
2272092 AAATTGATACTTA
1 AAATTGATACTTA
2272105 AAATTGATACTTA
1 AAATTGATACTTA
2272118 TGGTAAATAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.08, G:0.08, T:0.38
Consensus pattern (13 bp):
AAATTGATACTTA
Found at i:2274321 original size:2 final size:2
Alignment explanation
Indices: 2274314--2274354 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2274304 CTAGTTAGTT
2274314 TA TA TA 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 TA TA TA T
2274355 GATTGTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2277803 original size:35 final size:35
Alignment explanation
Indices: 2277685--2277824 Score: 181
Period size: 36 Copynumber: 3.9 Consensus size: 35
2277675 TGAATAAGAA
* *
2277685 GAACGAAATGAAGCATCAGCACTTTCGATTCAAAGT
1 GAACGAAAGGAAGCATCCGCACTTTCGATTC-AAGT
* *
2277721 GAACGGAAGGAAGCATCCGCACTTTCGATTCAAGAA
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAAG-T
* * *
2277757 GAACGAAAGGAAGTATCGGCACTTTCTATTCAAGT
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAAGT
* *
2277792 GAACGGAAGGAAACATCCGCACTTTCGATTCAA
1 GAACGAAAGGAAGCATCCGCACTTTCGATTCAA
2277825 TTGTCCATCT
Statistics
Matches: 89, Mismatches: 14, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
35 31 0.35
36 58 0.65
ACGTcount: A:0.36, C:0.21, G:0.22, T:0.21
Consensus pattern (35 bp):
GAACGAAAGGAAGCATCCGCACTTTCGATTCAAGT
Found at i:2277815 original size:71 final size:72
Alignment explanation
Indices: 2277680--2277824 Score: 238
Period size: 71 Copynumber: 2.0 Consensus size: 72
2277670 GAAAGTGAAT
* *
2277680 AAGAAGAACGAAATGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAGCATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCCGCACTT
2277745 TCGATTC
66 TCGATTC
* * *
2277752 AAGAAGAACGAAAGGAAGTATCGGCACTTTCTATTC-AAGTGAACGGAAGGAAACATCCGCACTT
1 AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCCGCACTT
2277816 TCGATTC
66 TCGATTC
2277823 AA
1 AA
2277825 TTGTCCATCT
Statistics
Matches: 68, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
71 36 0.53
72 32 0.47
ACGTcount: A:0.38, C:0.20, G:0.22, T:0.20
Consensus pattern (72 bp):
AAGAAGAACGAAAGGAAGCATCAGCACTTTCGATTCAAAGTGAACGGAAGGAAACATCCGCACTT
TCGATTC
Found at i:2281338 original size:131 final size:123
Alignment explanation
Indices: 2281118--2281453 Score: 365
Period size: 122 Copynumber: 2.7 Consensus size: 123
2281108 ATATTTAATT
* * * *
2281118 ATTTCCAATCGATAATAAATGACCTCTCATGCCTTAAAACAATCATTTATCACTCCAATCGAAAT
1 ATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAAT
* * * * *
2281183 GAAGAGATATCGCTA-TTCTGTCTTAAAATTCAAAATCGATTCGAGTGGAAAC-GATAATATCTA
66 GAAGAGATATCACTATTTCTATCTT--AATT----A---ATTCGAGAGAAAACAG-TAATATCGA
2281246 ATG
121 ATG
* * * * * *
2281249 ATTTTCAA-CTGAGAATAAATGACCTATCATACCTTAAAGCAGTCATTTATTGCTTCAATCGAAA
1 ATTTCCAATC-GAAAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAA
*
2281313 TGAAGAGATATCACTATTTC-ATCTTAATTAATTCGAGAGAAAACAGTAATATCGAATT
65 TGAAGAGATATCACTATTTCTATCTTAATTAATTCGAGAGAAAACAGTAATATCGAATG
*
2281371 ATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAACCGAAAT
1 ATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAAT
* * *
2281436 GAAAATATATTACTATTT
66 GAAGAGATATCACTATTT
2281454 TCAATATCGA
Statistics
Matches: 176, Mismatches: 25, Indels: 17
0.81 0.11 0.08
Matches are distributed among these distances:
122 93 0.53
123 2 0.01
125 1 0.01
129 4 0.02
130 1 0.01
131 72 0.41
132 3 0.02
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (123 bp):
ATTTCCAATCGAAAATAAATGACCTCTCATGCCTTAAAGCAGTCATTTATTACTCCAATCGAAAT
GAAGAGATATCACTATTTCTATCTTAATTAATTCGAGAGAAAACAGTAATATCGAATG
Found at i:2282092 original size:29 final size:26
Alignment explanation
Indices: 2282052--2282121 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 26
2282042 ACAAAGAATA
2282052 AAAATAAATAAAA-CATGGGGACTAAATT
1 AAAATAAATAAAACCAT--GG-CTAAATT
2282080 AAAATAAACTAAAATCGCATGGCTAAATT
1 AAAATAAA-TAAAA-C-CATGGCTAAATT
2282109 AAAATAAATAAAA
1 AAAATAAATAAAA
2282122 AGATAGATTC
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
28 13 0.34
29 20 0.53
30 2 0.05
32 3 0.08
ACGTcount: A:0.60, C:0.09, G:0.10, T:0.21
Consensus pattern (26 bp):
AAAATAAATAAAACCATGGCTAAATT
Found at i:2283957 original size:2 final size:2
Alignment explanation
Indices: 2283950--2283974 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2283940 AATCTTGCTA
2283950 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
2283975 AATTGTTGTG
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:2284650 original size:38 final size:38
Alignment explanation
Indices: 2284607--2284685 Score: 106
Period size: 38 Copynumber: 2.1 Consensus size: 38
2284597 TAAAAGAAAT
2284607 AATTTAGAAT-CTAGGGTAAAATAATTTGAGAAATTTGA
1 AATTTAGAATGCTAGGGTAAAATAATTTGA-AAATTTGA
* * * *
2284645 AATTTAGAATGTTATGGTGAAATATTTTGAAAATTTGA
1 AATTTAGAATGCTAGGGTAAAATAATTTGAAAATTTGA
2284683 AAT
1 AAT
2284686 GAAAAATTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
38 21 0.58
39 15 0.42
ACGTcount: A:0.43, C:0.01, G:0.18, T:0.38
Consensus pattern (38 bp):
AATTTAGAATGCTAGGGTAAAATAATTTGAAAATTTGA
Found at i:2289313 original size:2 final size:2
Alignment explanation
Indices: 2289306--2289333 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2289296 AGTAGTACAA
2289306 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT
2289334 ATATATATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2289338 original size:2 final size:2
Alignment explanation
Indices: 2289333--2289366 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2289323 TCTCTCTCTC
2289333 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2289367 ATGAGTAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2289658 original size:26 final size:26
Alignment explanation
Indices: 2289622--2289675 Score: 108
Period size: 26 Copynumber: 2.1 Consensus size: 26
2289612 TGTAAACAAA
2289622 CTGAGTCGAGCTCGAGTATTGCTGAG
1 CTGAGTCGAGCTCGAGTATTGCTGAG
2289648 CTGAGTCGAGCTCGAGTATTGCTGAG
1 CTGAGTCGAGCTCGAGTATTGCTGAG
2289674 CT
1 CT
2289676 CGAACTCGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.19, C:0.20, G:0.33, T:0.28
Consensus pattern (26 bp):
CTGAGTCGAGCTCGAGTATTGCTGAG
Found at i:2289676 original size:16 final size:16
Alignment explanation
Indices: 2289629--2289678 Score: 58
Period size: 16 Copynumber: 3.5 Consensus size: 16
2289619 AAACTGAGTC
2289629 GAGCTCGAGTATTGCT
1 GAGCTCGAGTATTGCT
2289645 GAGCT-GAG---T-C-
1 GAGCTCGAGTATTGCT
2289655 GAGCTCGAGTATTGCT
1 GAGCTCGAGTATTGCT
2289671 GAGCTCGA
1 GAGCTCGA
2289679 ACTCGAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 12
0.70 0.00 0.30
Matches are distributed among these distances:
10 5 0.18
11 4 0.14
12 1 0.04
14 1 0.04
15 4 0.14
16 13 0.46
ACGTcount: A:0.20, C:0.20, G:0.34, T:0.26
Consensus pattern (16 bp):
GAGCTCGAGTATTGCT
Found at i:2291973 original size:14 final size:14
Alignment explanation
Indices: 2291953--2291994 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
2291943 GAAAAATTCT
2291953 ATTAAAACAATATA
1 ATTAAAACAATATA
*
2291967 TTTAAAAACAATA-A
1 ATT-AAAACAATATA
2291981 ATTAAAAC-ATATA
1 ATTAAAACAATATA
2291994 A
1 A
2291995 AATAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 7 0.29
14 5 0.21
15 9 0.38
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAAACAATATA
Found at i:2291995 original size:14 final size:13
Alignment explanation
Indices: 2291953--2292000 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2291943 GAAAAATTCT
2291953 ATTAAAACAATATA
1 ATTAAAACAATA-A
*
2291967 TTTAAAAACAATAA
1 ATT-AAAACAATAA
2291981 ATTAAAACATATAA
1 ATTAAAACA-ATAA
*
2291995 AATAAA
1 ATTAAA
2292001 TGACTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.21
14 14 0.48
15 9 0.31
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (13 bp):
ATTAAAACAATAA
Found at i:2293395 original size:3 final size:3
Alignment explanation
Indices: 2293387--2293439 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
2293377 TTAATATATT
*
2293387 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2293435 TAA TA
1 TAA TA
2293440 TGGATAAAAA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2293881 original size:113 final size:113
Alignment explanation
Indices: 2293683--2294194 Score: 936
Period size: 113 Copynumber: 4.5 Consensus size: 113
2293673 ATAAGCTCTT
* * *
2293683 GATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGATGATCCATCAAATGATGAATTCAGGTA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
2293748 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
2293796 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
*
2293861 AAAGGTTGAACAAATTCTTCTCATTATGAATTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
2293909 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
2293974 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
2294022 GATGAGTTCTTCTCATTATGAACTTTCTTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
1 GATGAGTTCTTCTCATTATGAACTTTC-TCTGGAAAAGATGATCCACCAAATGATGGATTCAGGT
*
2294087 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCG
65 AAAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
* *
2294136 GATGAGTTCTTCTCATTATGAACTCTT-TCTGGAAAAGCTGATCCATCAAATGATGGATT
1 GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCACCAAATGATGGATT
2294195 TGAATCTTTG
Statistics
Matches: 389, Mismatches: 8, Indels: 4
0.97 0.02 0.01
Matches are distributed among these distances:
113 278 0.71
114 109 0.28
115 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (113 bp):
GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCA
Found at i:2294169 original size:227 final size:226
Alignment explanation
Indices: 2293683--2294194 Score: 945
Period size: 227 Copynumber: 2.3 Consensus size: 226
2293673 ATAAGCTCTT
* *
2293683 GATGAGTTCTTCTCATTATGAACTTTCTCTAGAAAAGATGATCCATCAAATGATGAATTCAGGTA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTA
2293748 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2293813 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
131 ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
*
2293878 TTCTCATTATGAATTTCTTCTTCCTTCTTCA
196 TTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
2293909 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTA
1 GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTA
2293974 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
66 AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
2294039 ATGAACTTTCTTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
131 ATGAACTTTC-TCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATT
*
2294104 CTTCTCATTATGAACTTCTTCTTCCTTCTTCG
195 CTTCTCATTATGAACTTCTTCTTCCTTCTTCA
*
2294136 GATGAGTTCTTCTCATTATGAACTCTT-TCTGGAAAAGCTGATCCATCAAATGATGGATT
1 GATGAGTTCTTCTCATTATGAACT-TTCTCTGGAAAAGATGATCCATCAAATGATGGATT
2294195 TGAATCTTTG
Statistics
Matches: 277, Mismatches: 7, Indels: 3
0.97 0.02 0.01
Matches are distributed among these distances:
226 137 0.49
227 138 0.50
228 2 0.01
ACGTcount: A:0.29, C:0.19, G:0.15, T:0.37
Consensus pattern (226 bp):
GATGAGTTCTTCTCATTATGAACTTTCTCTGGAAAAGATGATCCATCAAATGATGGATTCAGGTA
AAAGGTTGAACAAATTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTTTCTCTGGAAAAGATGATCCACCAAATGATGGATTCAGGTAAAAGGTTGAACAAATTC
TTCTCATTATGAACTTCTTCTTCCTTCTTCA
Found at i:2295063 original size:81 final size:82
Alignment explanation
Indices: 2294928--2295703 Score: 1161
Period size: 81 Copynumber: 9.5 Consensus size: 82
2294918 CCTACTGAAT
* *
2294928 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTA-TGGACATTCATCTTCCAAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
* * * *
2294992 GATTGGTTTTATCAAAC
66 GCTTGGTTCTGTCCAAC
*
2295009 CAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTA-TGAACATTCATCTTCCAAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
2295073 GCTTGGTTCTGTCCAAC
66 GCTTGGTTCTGTCCAAC
*
2295090 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACATTCATCTTCCTAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
2295154 GCTTGGTTCTGTCCAAC
66 GCTTGGTTCTGTCCAAC
* **
2295171 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAGCCATTCATCTTATAAATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-ACATTCATCTTCCAAATTCAA
* * *
2295236 TGCTTGGTTTTATCAAAC
65 TGCTTGGTTCTGTCCAAC
* *
2295254 CAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTA-TGAACATTCATCTTCTAAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
2295318 GCTTGGTTCTGTCCAAC
66 GCTTGGTTCTGTCCAAC
* *
2295335 CAGCTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACATTCATCTTCCTAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
* *
2295399 GATTGGTTCTGTCTAAC
66 GCTTGGTTCTGTCCAAC
* *
2295416 CAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGGACATTCATCTTCCAAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
2295480 GCTTGGTTCTGTCCAAC
66 GCTTGGTTCTGTCCAAC
*
2295497 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACATTCATCTTCCTAATTCAAT
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
* * * *
2295561 GATTGGTTTTATCAAAC
66 GCTTGGTTCTGTCCAAC
* * * ** *
2295578 CATATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGAGCCATTCATCTTATATATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA-ACATTCATCTTCCAAATTCAA
* *
2295643 TGATTGGTTCTGTCTAAC
65 TGCTTGGTTCTGTCCAAC
*
2295661 CAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
2295704 GCCCATATAA
Statistics
Matches: 635, Mismatches: 52, Indels: 14
0.91 0.07 0.02
Matches are distributed among these distances:
80 2 0.00
81 483 0.76
82 9 0.01
83 141 0.22
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (82 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGAACATTCATCTTCCAAATTCAAT
GCTTGGTTCTGTCCAAC
Found at i:2295521 original size:326 final size:324
Alignment explanation
Indices: 2294928--2295703 Score: 1259
Period size: 326 Copynumber: 2.4 Consensus size: 324
2294918 CCTACTGAAT
* * *
2294928 CAGATCAAATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCTAAATTCAATG
* * *
2294993 ATTGGTTTTATCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTA-TGAACATTC
66 ATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTG-ACATTC
*
2295057 ATCTTCCAAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
130 ATCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAA
* *
2295122 GATGCTATTGACATTCATCTTCCTAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCA
195 GATGCTATGGACATTCATCTTCCAAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCA
*
2295187 AAGAACACTTCCAGAAGATGCTATTGAGCCATTCATCTT-ATAAATTCAATGCTTGGTTTTATCA
260 AAGAACACTTCCAGAAGATGCTATTGA--CATTCATCTTCAT-AATTCAATGATTGGTTTTATCA
2295251 AAC
322 AAC
*
2295254 CAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATGAACATTCATCTTCTAAATTCAATG
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCTAAATTCAATG
* * *
2295319 CTTGGTTCTGTCCAACCAGCTCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACATTCA
66 ATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACATTCA
* * *
2295384 TCTTCCTAATTCAATGATTGGTTCTGTCTAACCAGATTAGATAACTCAAAGAACACTTCCAGAAG
131 TCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
2295449 ATGCTATGGACATTCATCTTCCAAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAA
196 ATGCTATGGACATTCATCTTCCAAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAA
*
2295514 AGAACACTTCCAGAAGATGCTATTGACATTCATCTTCCTAATTCAATGATTGGTTTTATCAAAC
261 AGAACACTTCCAGAAGATGCTATTGACATTCATCTTCATAATTCAATGATTGGTTTTATCAAAC
* * * * *
2295578 CATATCAGATAACTCAAAGAACACTTCCAGAAGATGTTATTGAGCCATTCATCTTATATATTCAA
1 CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTA-TGA-ACATTCATCTTCTAAATTCAA
* *
2295643 TGATTGGTTCTGTCTAACCAGATCAGATAACTCAAAGAACACTTCCAGAAAATGCTATTGA
64 TGATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGA
2295704 GCCCATATAA
Statistics
Matches: 418, Mismatches: 28, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
324 70 0.17
325 4 0.01
326 342 0.82
327 2 0.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (324 bp):
CAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCTAAATTCAATG
ATTGGTTCTGTCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATTGACATTCA
TCTTCCAAATTCAATGATTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAG
ATGCTATGGACATTCATCTTCCAAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAA
AGAACACTTCCAGAAGATGCTATTGACATTCATCTTCATAATTCAATGATTGGTTTTATCAAAC
Found at i:2295691 original size:407 final size:407
Alignment explanation
Indices: 2294936--2295700 Score: 1341
Period size: 407 Copynumber: 1.9 Consensus size: 407
2294926 ATCAGATCAA
*
2294936 ATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATGATTGGTTT
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATGATTGGTTC
*
2295001 TATCAAACCAGATCAGATAACTCAAAGAATACTTCCAGAAGATGCTATGAACATTCATCTTCCAA
66 TATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAA
2295066 ATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
131 ATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
* * *
2295131 GACATTCATCTTCCTAATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACT
196 GACATTCATCTTCCTAATTCAATGATTGGTTCTATCAAACCAGATCAGATAACTCAAAGAACACT
* *
2295196 TCCAGAAGATGCTATTGAGCCATTCATCTTATAAATTCAATGCTTGGTTTTATCAAACCAGATCA
261 TCCAGAAGATGCTATTGAGCCATTCATCTTATAAATTCAATGATTGGTTCTATCAAACCAGATCA
* *
2295261 GATAACTCAAAGAATACTTCCAGAAGATGCTATGAACATTCATCTTCTAAATTCAATGCTTGGTT
326 GATAACTCAAAGAACACTTCCAGAAAATGCTATGAACATTCATCTTCTAAATTCAATGCTTGGTT
2295326 CTGTCCAACCAGCTCAG
391 CTGTCCAACCAGCTCAG
* *
2295343 ATAACTCAAAGAACACTTCCAGAAGATGCTATTGACATTCATCTTCCTAATTCAATGATTGGTTC
1 ATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATGATTGGTTC
* * * *
2295408 TGTCTAACCAGATTAGATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAA
66 TATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAA
2295473 ATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
131 ATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
* *
2295538 GACATTCATCTTCCTAATTCAATGATTGGTTTTATCAAACCATATCAGATAACTCAAAGAACACT
196 GACATTCATCTTCCTAATTCAATGATTGGTTCTATCAAACCAGATCAGATAACTCAAAGAACACT
* * * *
2295603 TCCAGAAGATGTTATTGAGCCATTCATCTTATATATTCAATGATTGGTTCTGTCTAACCAGATCA
261 TCCAGAAGATGCTATTGAGCCATTCATCTTATAAATTCAATGATTGGTTCTATCAAACCAGATCA
2295668 GATAACTCAAAGAACACTTCCAGAAAATGCTAT
326 GATAACTCAAAGAACACTTCCAGAAAATGCTAT
2295701 TGAGCCCATA
Statistics
Matches: 337, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
407 337 1.00
ACGTcount: A:0.35, C:0.22, G:0.13, T:0.30
Consensus pattern (407 bp):
ATAACTCAAAGAACACTTCCAGAAGATGCTATGGACATTCATCTTCCAAATTCAATGATTGGTTC
TATCAAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATGAACATTCATCTTCCAA
ATTCAATGCTTGGTTCTGTCCAACCAGATCAGATAACTCAAAGAACACTTCCAGAAGATGCTATT
GACATTCATCTTCCTAATTCAATGATTGGTTCTATCAAACCAGATCAGATAACTCAAAGAACACT
TCCAGAAGATGCTATTGAGCCATTCATCTTATAAATTCAATGATTGGTTCTATCAAACCAGATCA
GATAACTCAAAGAACACTTCCAGAAAATGCTATGAACATTCATCTTCTAAATTCAATGCTTGGTT
CTGTCCAACCAGCTCAG
Found at i:2296293 original size:19 final size:20
Alignment explanation
Indices: 2296269--2296310 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
2296259 AATAGAAAAG
*
2296269 AATAAATTGAATTTCCAA-A
1 AATAAATTGAATCTCCAATA
2296288 AATAAATTGAATCTCCAATA
1 AATAAATTGAATCTCCAATA
2296308 AAT
1 AAT
2296311 TGAACTTGAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 17 0.81
20 4 0.19
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (20 bp):
AATAAATTGAATCTCCAATA
Found at i:2296650 original size:7 final size:7
Alignment explanation
Indices: 2296638--2296677 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
2296628 ACCTTGACCC
2296638 TCTTTTT
1 TCTTTTT
2296645 TC-TTTT
1 TCTTTTT
2296651 TCTTTTT
1 TCTTTTT
2296658 TCTTTTT
1 TCTTTTT
*
2296665 TCCTTTT
1 TCTTTTT
2296672 T-TTTTT
1 TCTTTTT
2296678 AATTAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
6 10 0.33
7 20 0.67
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (7 bp):
TCTTTTT
Found at i:2296656 original size:13 final size:13
Alignment explanation
Indices: 2296638--2296677 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
2296628 ACCTTGACCC
2296638 TCTTTTTTCTTTT
1 TCTTTTTTCTTTT
2296651 TCTTTTTTCTTTTT
1 TCTTTTTTC-TTTT
2296665 TCCTTTTTT-TTTT
1 T-CTTTTTTCTTTT
2296678 AATTAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 13 0.52
14 5 0.20
15 7 0.28
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (13 bp):
TCTTTTTTCTTTT
Found at i:2296663 original size:20 final size:20
Alignment explanation
Indices: 2296638--2296677 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
2296628 ACCTTGACCC
2296638 TCTTTTTT-CTTTTTCTTTTT
1 TCTTTTTTCCTTTTT-TTTTT
2296658 TCTTTTTTCCTTTTTTTTTT
1 TCTTTTTTCCTTTTTTTTTT
2296678 AATTAATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (20 bp):
TCTTTTTTCCTTTTTTTTTT
Found at i:2308087 original size:14 final size:14
Alignment explanation
Indices: 2308067--2308108 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
2308057 GAAAAATTCT
2308067 ATTAAAACAATATA
1 ATTAAAACAATATA
*
2308081 TTTAAAAACAATA-A
1 ATT-AAAACAATATA
2308095 ATTAAAAC-ATATA
1 ATTAAAACAATATA
2308108 A
1 A
2308109 AATAAATGAC
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 7 0.29
14 5 0.21
15 9 0.38
ACGTcount: A:0.64, C:0.07, G:0.00, T:0.29
Consensus pattern (14 bp):
ATTAAAACAATATA
Found at i:2308109 original size:14 final size:13
Alignment explanation
Indices: 2308067--2308114 Score: 51
Period size: 14 Copynumber: 3.5 Consensus size: 13
2308057 GAAAAATTCT
2308067 ATTAAAACAATATA
1 ATTAAAACAATA-A
*
2308081 TTTAAAAACAATAA
1 ATT-AAAACAATAA
2308095 ATTAAAACATATAA
1 ATTAAAACA-ATAA
*
2308109 AATAAA
1 ATTAAA
2308115 TGACTAAATT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
13 6 0.21
14 14 0.48
15 9 0.31
ACGTcount: A:0.67, C:0.06, G:0.00, T:0.27
Consensus pattern (13 bp):
ATTAAAACAATAA
Found at i:2309487 original size:20 final size:19
Alignment explanation
Indices: 2309464--2309508 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2309454 TTTTTTTTAT
* *
2309464 TATTTATTTATTTTTAATAA
1 TATTTATATATATTTAAT-A
*
2309484 TATTTATATGTATTTAATA
1 TATTTATATATATTTAATA
2309503 TATTTA
1 TATTTA
2309509 ATAATAATAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (19 bp):
TATTTATATATATTTAATA
Found at i:2309498 original size:26 final size:30
Alignment explanation
Indices: 2309459--2309514 Score: 75
Period size: 29 Copynumber: 2.0 Consensus size: 30
2309449 TTATATTTTT
*
2309459 TTTATTATTTATTT-AT-T-TTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
2309486 TTTA-TATGTATTTAATATATTTAATAATA
1 TTTATTATGTATTTAATATATTTAATAATA
2309515 ATAGTAATAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
26 8 0.32
27 6 0.24
28 1 0.04
29 10 0.40
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.61
Consensus pattern (30 bp):
TTTATTATGTATTTAATATATTTAATAATA
Found at i:2309515 original size:3 final size:3
Alignment explanation
Indices: 2309507--2309556 Score: 91
Period size: 3 Copynumber: 16.7 Consensus size: 3
2309497 TTAATATATT
*
2309507 TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2309555 TA
1 TA
2309557 TGGATAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2314389 original size:44 final size:44
Alignment explanation
Indices: 2314326--2314412 Score: 174
Period size: 44 Copynumber: 2.0 Consensus size: 44
2314316 AGAAAGGTAA
2314326 GTTCCCAAGAAATACATTGCTGCCATCTTATTGGGAAGACACTT
1 GTTCCCAAGAAATACATTGCTGCCATCTTATTGGGAAGACACTT
2314370 GTTCCCAAGAAATACATTGCTGCCATCTTATTGGGAAGACACT
1 GTTCCCAAGAAATACATTGCTGCCATCTTATTGGGAAGACACT
2314413 AAAGCAATTC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.29
Consensus pattern (44 bp):
GTTCCCAAGAAATACATTGCTGCCATCTTATTGGGAAGACACTT
Found at i:2317619 original size:18 final size:18
Alignment explanation
Indices: 2317596--2317630 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
2317586 TAAGATTAAA
2317596 AAAAAAAGGAATGAAGTG
1 AAAAAAAGGAATGAAGTG
*
2317614 AAAAAAAGGAGTGAAGT
1 AAAAAAAGGAATGAAGT
2317631 TTGACCAAAA
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:0.60, C:0.00, G:0.29, T:0.11
Consensus pattern (18 bp):
AAAAAAAGGAATGAAGTG
Found at i:2319393 original size:2 final size:2
Alignment explanation
Indices: 2319386--2319420 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
2319376 GGACGGTGAG
*
2319386 TA TA TA TA TA TA TA TA TG 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
2319421 TAATAACATA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2342310 original size:60 final size:60
Alignment explanation
Indices: 2342200--2342314 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
2342190 GTCATGTGAC
* ** *
2342200 CATTTTGTAACTTTTAATAGTAAGGAAACTCAACAAAACATCGTCTTATAATCGAAGAAT
1 CATTTTGTAACTTTTAATAATAAGGAAACTCAACAAAACATCAACCTATAATCGAAGAAT
* *
2342260 CATTTTGTAACTTTTAATAATCAA-GAGACTCAACAAAGCAAT-AACCTATAATCGA
1 CATTTTGTAACTTTTAATAAT-AAGGAAACTCAACAAAAC-ATCAACCTATAATCGA
2342315 GGGATTATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 43 0.91
61 4 0.09
ACGTcount: A:0.43, C:0.17, G:0.10, T:0.30
Consensus pattern (60 bp):
CATTTTGTAACTTTTAATAATAAGGAAACTCAACAAAACATCAACCTATAATCGAAGAAT
Found at i:2347087 original size:20 final size:20
Alignment explanation
Indices: 2347059--2347096 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
2347049 TTTTACAGAA
*
2347059 AAATTATCTCCAACGGCTCC
1 AAATCATCTCCAACGGCTCC
2347079 AAATCATCTCCAACGGCT
1 AAATCATCTCCAACGGCT
2347097 AGAAACTGCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.32, C:0.34, G:0.11, T:0.24
Consensus pattern (20 bp):
AAATCATCTCCAACGGCTCC
Found at i:2348952 original size:43 final size:43
Alignment explanation
Indices: 2348891--2348985 Score: 172
Period size: 43 Copynumber: 2.2 Consensus size: 43
2348881 CCTCCAACCG
* *
2348891 AACACATCATAATGTGTAGGTTTCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
2348934 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
1 AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
2348977 AACACACCA
1 AACACACCA
2348986 AGTAAGGCCC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 50 1.00
ACGTcount: A:0.37, C:0.36, G:0.11, T:0.17
Consensus pattern (43 bp):
AACACACCATAATGTGTAGGTTCCCCAGAACCATACACCCACC
Found at i:2349114 original size:24 final size:24
Alignment explanation
Indices: 2349101--2349195 Score: 136
Period size: 24 Copynumber: 4.0 Consensus size: 24
2349091 AAACATAATT
*
2349101 CATGTCAAGTATCATATCAAAATC
1 CATGTCAAGTATCATATCAGAATC
*
2349125 CAGGTCAAGTATCATATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* *
2349149 CAAGTCAAGTATCAGATCAGAATC
1 CATGTCAAGTATCATATCAGAATC
* *
2349173 CATGTCGAGTATCAGATCAGAAT
1 CATGTCAAGTATCATATCAGAAT
2349196 TCAAATCGAA
Statistics
Matches: 65, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 65 1.00
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.25
Consensus pattern (24 bp):
CATGTCAAGTATCATATCAGAATC
Found at i:2349210 original size:24 final size:24
Alignment explanation
Indices: 2349135--2349210 Score: 64
Period size: 24 Copynumber: 3.2 Consensus size: 24
2349125 CAGGTCAAGT
* * *
2349135 ATCATATCAGAATCCAAGTC-AAGT
1 ATCAGATCAGAATCCAAATCGAA-A
** **
2349159 ATCAGATCAGAATCCATGTCGAGT
1 ATCAGATCAGAATCCAAATCGAAA
*
2349183 ATCAGATCAGAATTCAAATCGAAA
1 ATCAGATCAGAATCCAAATCGAAA
2349207 ATCA
1 ATCA
2349211 AATAAAATAT
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
24 42 0.98
25 1 0.02
ACGTcount: A:0.42, C:0.20, G:0.14, T:0.24
Consensus pattern (24 bp):
ATCAGATCAGAATCCAAATCGAAA
Found at i:2353301 original size:15 final size:16
Alignment explanation
Indices: 2353274--2353303 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
2353264 TCGCTATATA
2353274 CCATCTCTACTCTAAG
1 CCATCTCTACTCTAAG
2353290 CCATCT-TACTCTAA
1 CCATCTCTACTCTAA
2353304 TTCGAACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.27, C:0.37, G:0.03, T:0.33
Consensus pattern (16 bp):
CCATCTCTACTCTAAG
Found at i:2359996 original size:22 final size:22
Alignment explanation
Indices: 2359971--2360049 Score: 92
Period size: 22 Copynumber: 3.7 Consensus size: 22
2359961 AAATTTACAT
*
2359971 TTTGCAACACGAATTTGCCAAA
1 TTTGCAACTCGAATTTGCCAAA
* *
2359993 TTTGCAACTC-AGTTT-TCAAA
1 TTTGCAACTCGAATTTGCCAAA
* *
2360013 TTCGCAACTCGAATTTGCCAAT
1 TTTGCAACTCGAATTTGCCAAA
2360035 TTTGCAACTC-AATTT
1 TTTGCAACTCGAATTT
2360050 TCGAATTCGT
Statistics
Matches: 47, Mismatches: 8, Indels: 5
0.78 0.13 0.08
Matches are distributed among these distances:
20 13 0.28
21 13 0.28
22 21 0.45
ACGTcount: A:0.30, C:0.23, G:0.11, T:0.35
Consensus pattern (22 bp):
TTTGCAACTCGAATTTGCCAAA
Found at i:2360014 original size:20 final size:20
Alignment explanation
Indices: 2359989--2360056 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
2359979 ACGAATTTGC
*
2359989 CAAATTTGCAACTCAGTTTT
1 CAAATTTGCAACTCAATTTT
* *
2360009 CAAATTCGCAACTCGAATTTGC
1 CAAATTTGCAACTC-AATTT-T
*
2360031 CAATTTTGCAACTCAATTTT
1 CAAATTTGCAACTCAATTTT
*
2360051 CGAATT
1 CAAATT
2360057 CGTAACTTGA
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 17 0.45
21 9 0.24
22 12 0.32
ACGTcount: A:0.31, C:0.22, G:0.10, T:0.37
Consensus pattern (20 bp):
CAAATTTGCAACTCAATTTT
Found at i:2360026 original size:42 final size:42
Alignment explanation
Indices: 2359974--2360068 Score: 136
Period size: 42 Copynumber: 2.3 Consensus size: 42
2359964 TTTACATTTT
* *
2359974 GCAACACGAATTTGCCAAATTTGCAACTCAGTTTTCAAATTC
1 GCAACTCGAATTTGCCAAATTTGCAACTCAATTTTCAAATTC
* *
2360016 GCAACTCGAATTTGCCAATTTTGCAACTCAATTTTCGAATTC
1 GCAACTCGAATTTGCCAAATTTGCAACTCAATTTTCAAATTC
* *
2360058 GTAACTTGAAT
1 GCAACTCGAAT
2360069 ATGGATTTCG
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.32, C:0.22, G:0.13, T:0.34
Consensus pattern (42 bp):
GCAACTCGAATTTGCCAAATTTGCAACTCAATTTTCAAATTC
Found at i:2360098 original size:20 final size:20
Alignment explanation
Indices: 2360050--2360187 Score: 132
Period size: 20 Copynumber: 6.9 Consensus size: 20
2360040 AACTCAATTT
* * *
2360050 TCGAATTCGTAACTTGAATA
1 TCGAATTCGCAACTCGAAAA
* *
2360070 TGGATTTCGCAACTCGAAAA
1 TCGAATTCGCAACTCGAAAA
*
2360090 TCGAATTCGCAACTCGAAAT
1 TCGAATTCGCAACTCGAAAA
* * * *
2360110 TCAAATTCACTACTCGAAAC
1 TCGAATTCGCAACTCGAAAA
* *
2360130 TCAAATTCGCAACTCGAAAT
1 TCGAATTCGCAACTCGAAAA
** *
2360150 TAAAATTCACAACTCGAAAA
1 TCGAATTCGCAACTCGAAAA
*
2360170 TTGAATTCGCAACTCGAA
1 TCGAATTCGCAACTCGAA
2360188 TTTCATTTGT
Statistics
Matches: 97, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 97 1.00
ACGTcount: A:0.39, C:0.22, G:0.12, T:0.26
Consensus pattern (20 bp):
TCGAATTCGCAACTCGAAAA
Found at i:2360125 original size:40 final size:40
Alignment explanation
Indices: 2360079--2360192 Score: 174
Period size: 40 Copynumber: 2.9 Consensus size: 40
2360069 ATGGATTTCG
2360079 CAACTCGAAAATCGAATTCGCAACTCGAAATTCAAATTCA
1 CAACTCGAAAATCGAATTCGCAACTCGAAATTCAAATTCA
* * * *
2360119 CTACTCGAAACTCAAATTCGCAACTCGAAATTAAAATTCA
1 CAACTCGAAAATCGAATTCGCAACTCGAAATTCAAATTCA
* *
2360159 CAACTCGAAAATTGAATTCGCAACTCGAATTTCA
1 CAACTCGAAAATCGAATTCGCAACTCGAAATTCA
2360193 TTTGTGTTGC
Statistics
Matches: 64, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 64 1.00
ACGTcount: A:0.41, C:0.25, G:0.10, T:0.25
Consensus pattern (40 bp):
CAACTCGAAAATCGAATTCGCAACTCGAAATTCAAATTCA
Found at i:2360177 original size:60 final size:60
Alignment explanation
Indices: 2360075--2360187 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
2360065 GAATATGGAT
** * *
2360075 TTCGCAACTCGAAAATCGAATTCGCAACTCGAAATTCAAATTCACTACTCGAAACTCAAA
1 TTCGCAACTCGAAAATAAAATTCACAACTCGAAATTCAAATTCACAACTCGAAACTCAAA
* * *
2360135 TTCGCAACTCGAAATTAAAATTCACAACTCGAAAATT-GAATTCGCAACTCGAA
1 TTCGCAACTCGAAAATAAAATTCACAACTCG-AAATTCAAATTCACAACTCGAA
2360188 TTTCATTTGT
Statistics
Matches: 45, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
60 40 0.89
61 5 0.11
ACGTcount: A:0.41, C:0.25, G:0.11, T:0.24
Consensus pattern (60 bp):
TTCGCAACTCGAAAATAAAATTCACAACTCGAAATTCAAATTCACAACTCGAAACTCAAA
Found at i:2364088 original size:15 final size:15
Alignment explanation
Indices: 2364064--2364099 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2364054 GTATTATTAA
*
2364064 ATTAATTTATAAAAT
1 ATTAAATTATAAAAT
2364079 ATTAAATTATAAAAT
1 ATTAAATTATAAAAT
*
2364094 ACTAAA
1 ATTAAA
2364100 CATATAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (15 bp):
ATTAAATTATAAAAT
Found at i:2364425 original size:23 final size:23
Alignment explanation
Indices: 2364398--2364450 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
2364388 AAATATTGTA
*
2364398 TTTTAATTAAATTATATTTAGAT
1 TTTTAATTAAATTATAATTAGAT
* * *
2364421 TTTTAAGTAATTTATAATTATAT
1 TTTTAATTAAATTATAATTAGAT
*
2364444 GTTTAAT
1 TTTTAAT
2364451 ATTTTATAAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.57
Consensus pattern (23 bp):
TTTTAATTAAATTATAATTAGAT
Found at i:2364469 original size:22 final size:23
Alignment explanation
Indices: 2364422--2364469 Score: 55
Period size: 22 Copynumber: 2.1 Consensus size: 23
2364412 TATTTAGATT
*
2364422 TTTAAGTAATTTATAATTATATG
1 TTTAAGTAATTTATAATTATACG
*
2364445 TTTAA-TATTTTATAATT-TAACG
1 TTTAAGTAATTTATAATTAT-ACG
2364467 TTT
1 TTT
2364470 TATAAATTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
21 1 0.05
22 16 0.73
23 5 0.23
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (23 bp):
TTTAAGTAATTTATAATTATACG
Found at i:2365122 original size:30 final size:30
Alignment explanation
Indices: 2365086--2365148 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
2365076 CCTAGACATA
* **
2365086 TACTAACTTTTTTATACTCAGGAAATTGAG
1 TACTAACTTTTTTATACTAAAAAAATTGAG
2365116 TACTAACTTTTTTATACTAAAAAAATTGAG
1 TACTAACTTTTTTATACTAAAAAAATTGAG
2365146 TAC
1 TAC
2365149 CTGATACCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.38, C:0.13, G:0.10, T:0.40
Consensus pattern (30 bp):
TACTAACTTTTTTATACTAAAAAAATTGAG
Found at i:2371814 original size:22 final size:22
Alignment explanation
Indices: 2371763--2371814 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
2371753 TTCAAAAGCT
* *
2371763 TTCAAAAATTGTTGGAATATGA
1 TTCAAAATTTGCTGGAATATGA
2371785 TTCAAAATTTGCTGGAATATGA
1 TTCAAAATTTGCTGGAATATGA
2371807 TTCAAAAT
1 TTCAAAAT
2371815 ATACCATTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.08, G:0.15, T:0.37
Consensus pattern (22 bp):
TTCAAAATTTGCTGGAATATGA
Found at i:2382859 original size:30 final size:28
Alignment explanation
Indices: 2382782--2382859 Score: 68
Period size: 30 Copynumber: 2.7 Consensus size: 28
2382772 TGGGATTAAA
** *
2382782 TTATTTTTTTTTTGTCAAATTCGAGGGT
1 TTATTTTTTTTTTGAAAAATTAGAGGGT
* *
2382810 TAAATTGTTTTGTTT-AAAAAGTTAGAGGGT
1 T-TATT-TTTTTTTTGAAAAA-TTAGAGGGT
2382840 TTATTTATTTTTTTGAAAAA
1 TTATTT-TTTTTTTGAAAAA
2382860 ATAAAAAATT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
28 2 0.05
29 15 0.39
30 21 0.55
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.53
Consensus pattern (28 bp):
TTATTTTTTTTTTGAAAAATTAGAGGGT
Found at i:2390282 original size:10 final size:10
Alignment explanation
Indices: 2390267--2390295 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
2390257 TAGGACCATG
2390267 TAGTTGCATA
1 TAGTTGCATA
2390277 TAGTTGCATA
1 TAGTTGCATA
2390287 TAGTTGCAT
1 TAGTTGCAT
2390296 TTGTAGTGGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.28, C:0.10, G:0.21, T:0.41
Consensus pattern (10 bp):
TAGTTGCATA
Found at i:2391575 original size:16 final size:16
Alignment explanation
Indices: 2391539--2391572 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
2391529 CACGTGAGGA
2391539 TTATTTTCTTCTTATT
1 TTATTTTCTTCTTATT
*
2391555 TTATTTATCTTTTTATT
1 TTATTT-TCTTCTTATT
2391572 T
1 T
2391573 ATTGTCTTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.15, C:0.09, G:0.00, T:0.76
Consensus pattern (16 bp):
TTATTTTCTTCTTATT
Found at i:2396855 original size:85 final size:85
Alignment explanation
Indices: 2396712--2396883 Score: 317
Period size: 85 Copynumber: 2.0 Consensus size: 85
2396702 GTCGATGGAC
*
2396712 ATTATTCCATTAGCTAAGGAATCGTTTGGACTTAATCCGTATCAGAAAGTAAACATCCTTTAATG
1 ATTATTCCATTAGCTAAGGAATCGTTTGAACTTAATCCGTATCAGAAAGTAAACATCCTTTAATG
2396777 CAACTTATAAATCACAACAT
66 CAACTTATAAATCACAACAT
*
2396797 ATTATTCCATTAGCTAATGAATCGTTTGAACTTAATCCGTATCAGAAAGTAAACATCCTTTAATG
1 ATTATTCCATTAGCTAAGGAATCGTTTGAACTTAATCCGTATCAGAAAGTAAACATCCTTTAATG
*
2396862 TAACTTATAAATCACAACAT
66 CAACTTATAAATCACAACAT
2396882 AT
1 AT
2396884 AATTTTTAGA
Statistics
Matches: 84, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (85 bp):
ATTATTCCATTAGCTAAGGAATCGTTTGAACTTAATCCGTATCAGAAAGTAAACATCCTTTAATG
CAACTTATAAATCACAACAT
Found at i:2397089 original size:63 final size:63
Alignment explanation
Indices: 2396975--2397100 Score: 198
Period size: 63 Copynumber: 2.0 Consensus size: 63
2396965 ACTATTCCAC
* * * * *
2396975 ACTTCTAGGCCTAATTTTTGTTTGATTTCCCTCGTATATTAACTTTGTGCATTTTGTACATGT
1 ACTTCTAGGCCCAATTTTTGTTTGATTTCCCTCGTATATCAACTCTCTGCATTTTGCACATGT
*
2397038 ACTTTTAGGCCCAATTTTTGTTTGATTTCCCTCGTATATCAACTCTCTGCATTTTGCACATGT
1 ACTTCTAGGCCCAATTTTTGTTTGATTTCCCTCGTATATCAACTCTCTGCATTTTGCACATGT
2397101 TCATAACTGG
Statistics
Matches: 57, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.19, C:0.21, G:0.13, T:0.47
Consensus pattern (63 bp):
ACTTCTAGGCCCAATTTTTGTTTGATTTCCCTCGTATATCAACTCTCTGCATTTTGCACATGT
Found at i:2397623 original size:43 final size:43
Alignment explanation
Indices: 2397576--2397658 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
2397566 AAAGACATCA
*
2397576 AAATTATATTTAAAACAGAAAATTCTAATAATAATTAACACGT
1 AAATTATATTTAAAACAGAAAATTCTAATAATAATAAACACGT
* *
2397619 AAATTATATTTAAAACATAAAATTTTAATAATAATAAACA
1 AAATTATATTTAAAACAGAAAATTCTAATAATAATAAACA
2397659 TCCCCAAATA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.57, C:0.07, G:0.02, T:0.34
Consensus pattern (43 bp):
AAATTATATTTAAAACAGAAAATTCTAATAATAATAAACACGT
Found at i:2400871 original size:18 final size:19
Alignment explanation
Indices: 2400828--2400871 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
2400818 TTTGATTCAC
*
2400828 GGAATATAATATTATCAAT
1 GGAATAAAATATTATCAAT
*
2400847 GAAAATAAAATATTA-CAAT
1 G-GAATAAAATATTATCAAT
2400866 GGAATA
1 GGAATA
2400872 TGATTACTGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 4 0.19
19 6 0.29
20 11 0.52
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.30
Consensus pattern (19 bp):
GGAATAAAATATTATCAAT
Found at i:2401116 original size:37 final size:37
Alignment explanation
Indices: 2401044--2401118 Score: 91
Period size: 37 Copynumber: 2.0 Consensus size: 37
2401034 ACTATAGGAT
*
2401044 ATTTATATATTTTCTTTAAAAAAATTAAATTTATAAA
1 ATTTATATATTTTCTTTAAAAAAATTAAATATATAAA
* *
2401081 ATTTATATAATTTT-TTTTACAAAATTGAAA-ATATAAA
1 ATTTATAT-ATTTTCTTTAAAAAAATT-AAATATATAAA
2401118 A
1 A
2401119 ATGTTTAATG
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
37 25 0.76
38 8 0.24
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAAATTAAATATATAAA
Found at i:2402676 original size:16 final size:16
Alignment explanation
Indices: 2402655--2402687 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
2402645 ATTTATTGAC
2402655 TTTATATTTATATTTT
1 TTTATATTTATATTTT
*
2402671 TTTATATTTTTATTTT
1 TTTATATTTATATTTT
2402687 T
1 T
2402688 GCTCTTTTAA
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:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (16 bp):
TTTATATTTATATTTT
Found at i:2406185 original size:19 final size:19
Alignment explanation
Indices: 2406161--2406199 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
2406151 ATTTAGGAGA
2406161 TTACGTAGTGGAGTCTGTT
1 TTACGTAGTGGAGTCTGTT
*
2406180 TTACGTAGTGGAGTTTGTT
1 TTACGTAGTGGAGTCTGTT
2406199 T
1 T
2406200 CCTAGTTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.08, G:0.31, T:0.46
Consensus pattern (19 bp):
TTACGTAGTGGAGTCTGTT
Found at i:2406222 original size:32 final size:32
Alignment explanation
Indices: 2406181--2406245 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2406171 GAGTCTGTTT
*
2406181 TACGTAGTGGAGTTTGTTTCCTAGTTTCTAGC
1 TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
2406213 TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
1 TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
2406245 T
1 T
2406246 TGTTTATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (32 bp):
TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
Found at i:2410618 original size:32 final size:32
Alignment explanation
Indices: 2410577--2410641 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
2410567 GAGTCTGTTT
*
2410577 TACGTAGTGGAGTCTGTTTTCTAGTTTCTAGC
1 TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
2410609 TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
1 TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
2410641 T
1 T
2410642 TGTTTATGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (32 bp):
TACGTAGTGGAGTCTGTTTCCTAGTTTCTAGC
Found at i:2411978 original size:2 final size:2
Alignment explanation
Indices: 2411971--2412019 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
2411961 TATTTAATTT
2411971 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2412013 TA TA TA T
1 TA TA TA T
2412020 TACTCTCAGT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.