Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002646.1 Hibiscus syriacus cultivar Beakdansim tig00005401_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: 155397
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:3738 original size:8 final size:8
Alignment explanation
Indices: 3718--3796 Score: 76
Period size: 9 Copynumber: 9.8 Consensus size: 8
3708 CTTAAAGATA
3718 AAAAAATG
1 AAAAAATG
3726 -AAAAATG
1 AAAAAATG
3733 AGAAAAATG
1 A-AAAAATG
3742 AAAAAAAATG
1 --AAAAAATG
3752 AAAAAATG
1 AAAAAATG
3760 AAAAAATG
1 AAAAAATG
*
3768 -AAATA-G
1 AAAAAATG
3774 -AAAAATAG
1 AAAAAAT-G
3782 AAAAAATGG
1 AAAAAAT-G
3791 AAAAAA
1 AAAAAA
3797 ATAAAAAAAA
Statistics
Matches: 61, Mismatches: 3, Indels: 13
0.79 0.04 0.17
Matches are distributed among these distances:
6 5 0.08
7 11 0.18
8 17 0.28
9 20 0.33
10 7 0.11
11 1 0.02
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (8 bp):
AAAAAATG
Found at i:3765 original size:16 final size:16
Alignment explanation
Indices: 3718--3796 Score: 76
Period size: 16 Copynumber: 4.9 Consensus size: 16
3708 CTTAAAGATA
3718 AAAAAATG-AAAAATG
1 AAAAAATGAAAAAATG
3733 AGAAAAATGAAAAAAAATG
1 A-AAAAATG--AAAAAATG
3752 AAAAAATGAAAAAATG
1 AAAAAATGAAAAAATG
*
3768 -AAATA-G-AAAAATAG
1 AAAAAATGAAAAAAT-G
3782 AAAAAATGGAAAAAA
1 AAAAAAT-GAAAAAA
3797 ATAAAAAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 15
0.76 0.03 0.21
Matches are distributed among these distances:
13 6 0.11
14 2 0.04
15 9 0.17
16 15 0.28
17 1 0.02
18 12 0.23
19 8 0.15
ACGTcount: A:0.75, C:0.00, G:0.14, T:0.11
Consensus pattern (16 bp):
AAAAAATGAAAAAATG
Found at i:3802 original size:8 final size:8
Alignment explanation
Indices: 3715--3841 Score: 59
Period size: 8 Copynumber: 15.8 Consensus size: 8
3705 TTGCTTAAAG
3715 ATAAAAAA
1 ATAAAAAA
*
3723 AT-GAAAA
1 ATAAAAAA
*
3730 ATGAGAAAA
1 AT-AAAAAA
3739 ATGAAAAAAA
1 AT--AAAAAA
*
3749 ATGAAAAA
1 ATAAAAAA
*
3757 ATGAAAAA
1 ATAAAAAA
*
3765 AT---GAA
1 ATAAAAAA
*
3770 ATAGAAAA
1 ATAAAAAA
3778 ATAGAAAAA
1 ATA-AAAAA
3787 ATGGAAAAAA
1 AT--AAAAAA
3797 ATAAAAAA
1 ATAAAAAA
3805 A-AAGAAAA
1 ATAA-AAAA
* *
3813 A-AGAAGA
1 ATAAAAAA
*
3820 AGAAAAAA
1 ATAAAAAA
*
3828 ACAAAAAA
1 ATAAAAAA
3836 ATAAAA
1 ATAAAA
3842 GGGGGGGTTC
Statistics
Matches: 95, Mismatches: 13, Indels: 22
0.73 0.10 0.17
Matches are distributed among these distances:
5 4 0.04
7 12 0.13
8 51 0.54
9 13 0.14
10 14 0.15
11 1 0.01
ACGTcount: A:0.78, C:0.01, G:0.12, T:0.09
Consensus pattern (8 bp):
ATAAAAAA
Found at i:5251 original size:53 final size:55
Alignment explanation
Indices: 5105--5381 Score: 420
Period size: 55 Copynumber: 5.1 Consensus size: 55
5095 TGAAGCAAAA
* *
5105 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGGGCAGGCGCGATCGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* * *
5160 GAAGATTATTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATTGAT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
5215 GAAGATTG-TGGA-TCTTATACTCTCTAAAGAAATAGGGGGCAGACGCGATCG-T
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
* *
5267 GAAGATTGTTCGAGTCTTATA--CTCTGAATAAATAGGGGGCAGACGCGATTGTT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
5320 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCATT
1 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
*
5375 GGAGATT
1 GAAGATT
5382 ATTGTTCGAG
Statistics
Matches: 200, Mismatches: 17, Indels: 10
0.88 0.07 0.04
Matches are distributed among these distances:
52 36 0.18
53 62 0.31
54 10 0.05
55 92 0.46
ACGTcount: A:0.29, C:0.15, G:0.29, T:0.27
Consensus pattern (55 bp):
GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCGTT
Found at i:5433 original size:160 final size:158
Alignment explanation
Indices: 5105--6054 Score: 479
Period size: 156 Copynumber: 6.0 Consensus size: 158
5095 TGAAGCAAAA
* * *
5105 GAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGAGGGCAGGCGCGATCGTTGAAGATTATT
1 GAAGATTGTTCGAGTCTTATA--CTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAGATTGTT
** * * *
5170 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT-T-GATGAAGATTG-TGGATCTTA
64 CGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATATGGA-GATTATTGTTCGA-GTTC
* * * ** * *
5232 TACTCTCTAAAGAAATAGGGGGCAGACGCGATCG
127 TAGTCCCTGAAGAAA-ATTGGGCAGACCCG-TAG
* * *
5266 TGAAGATTGTTCGAGTCTTATACTCTGAATAAATAGGGGGCAGACGCGATTGTTGAAGATTGTTC
1 -GAAGATTGTTCGAGTCTTATACTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAGATTGTTC
5331 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATCATTGGAGATTATTGTTCGAGTTCT
65 GAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGAT-A-TGGAGATTATTGTTCGAGTTCT
5396 AGTCCCTGAAGAAAATTGGGCAGACCCGTAG
128 AGTCCCTGAAGAAAATTGGGCAGACCCGTAG
* * * *
5427 GAAGATTATTGTTCGAGT-TCTAGT-CCCTGAAGAAAT--TGGGCAGTCTCG-TAG--GAAGATT
1 GAAG---ATTGTTCGAGTCT-TA-TACTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAG---
* * * ** *
5485 ATTGTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGGCAGACCCG-TA-GGAAGATTATTGTTCG
58 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATATGG-AGATTATTGTTCG
* *
5545 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAG
122 AGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAG
* * ** *
5582 GAAGATTATTGCTCGAGT-TCTAGT-CCCTGAAGAAA-ATTGGGCAGACCCG-TAG--GAAGATT
1 GAAG---ATTGTTCGAGTCT-TA-TACTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAG---
* * * ** * *
5641 ATTGTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGGCAGTCTCG-TA-GGAAGATTATTGTTCG
58 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATATGG-AGATTATTGTTCG
* *
5701 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAG
122 AGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAG
* ** * *
5738 GAAGATTATTGTTCGAGT-TCTAGT-CCCTGAAGAAA-ATTGGGCAGTCTCG-TAG--GAAGATT
1 GAAG---ATTGTTCGAGTCT-TA-TACTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAG---
* * * ** * *
5797 ATTGTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGACAGACCCG-TA-GGAAGATTATTGTTCG
58 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATATGG-AGATTATTGTTCG
* * *
5857 AGTTCTAGTCCCTGAAG-AAATTGGACAGTCTCGTA-
122 AGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAG
* ** * *
5892 GAAGATTATTGTTCGAGT-TCTAGT-CCCTGAAGAAA-ATTGGGCAGTCTCG-TAG--GAAGATT
1 GAAG---ATTGTTCGAGTCT-TA-TACTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAG---
* * * ** ** *
5951 ATTGTTCGAG--TTCTAGTCCCTGAAGAAA-ATTGGATAGACCCG-TA-GGAAGATTATTGTTCG
58 ATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATATGG-AGATTATTGTTCG
* *
6011 AGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAG
122 AGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAG
6048 GAAGATT
1 GAAGATT
6055 ATCGTTCGAG
Statistics
Matches: 725, Mismatches: 45, Indels: 45
0.89 0.06 0.06
Matches are distributed among these distances:
153 3 0.00
154 137 0.19
155 116 0.16
156 250 0.34
157 1 0.00
158 15 0.02
159 15 0.02
160 84 0.12
161 21 0.03
162 33 0.05
163 44 0.06
164 6 0.01
ACGTcount: A:0.28, C:0.16, G:0.27, T:0.29
Consensus pattern (158 bp):
GAAGATTGTTCGAGTCTTATACTCTGAAGAAATAGAGGGCAGACGCGATAGTTGAAGATTGTTCG
AGTCTTATACTCTCTGAAGAAATAGGGGGCAGACGCGATATGGAGATTATTGTTCGAGTTCTAGT
CCCTGAAGAAAATTGGGCAGACCCGTAG
Found at i:5437 original size:52 final size:52
Alignment explanation
Indices: 5377--6082 Score: 1238
Period size: 52 Copynumber: 13.6 Consensus size: 52
5367 CGATCATTGG
* *
5377 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5429 AGATTATTGTTCGAGTTCTAGTCCCTGAAG-AAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
5480 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5532 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * *
5584 AGATTATTGCTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5636 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5688 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5740 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* * *
5792 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGACAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
*
5844 AGATTATTGTTCGAGTTCTAGTCCCTGAAG-AAATTGGACAGTCTCGTA-GA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5894 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
** * *
5946 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGATAGACCCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
5998 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
* *
6050 AGATTATCGTTCGAGTTCTACTCCCTGAAGAAA
1 AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAA
6083 TAGAGAGCGA
Statistics
Matches: 623, Mismatches: 28, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
50 32 0.05
51 82 0.13
52 509 0.82
ACGTcount: A:0.28, C:0.16, G:0.26, T:0.29
Consensus pattern (52 bp):
AGATTATTGTTCGAGTTCTAGTCCCTGAAGAAAATTGGGCAGTCTCGTAGGA
Found at i:5689 original size:24 final size:24
Alignment explanation
Indices: 5662--5794 Score: 68
Period size: 24 Copynumber: 5.2 Consensus size: 24
5652 TCTAGTCCCT
5662 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
** ** * **
5686 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGAAAATTGGGC-AG-TCTCGT--AG
5714 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
** ** * **
5738 GAAGATTATTGTTCGAGTTCTAGTCCCT
1 GAAGAAAATTGGGC-AG-TCTCGT--AG
5766 GAAGAAAATTGGGCAGTCTCGTAG
1 GAAGAAAATTGGGCAGTCTCGTAG
5790 GAAGA
1 GAAGA
5795 TTATTGTTCG
Statistics
Matches: 73, Mismatches: 28, Indels: 16
0.62 0.24 0.14
Matches are distributed among these distances:
24 25 0.34
25 4 0.05
26 20 0.27
27 4 0.05
28 20 0.27
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (24 bp):
GAAGAAAATTGGGCAGTCTCGTAG
Found at i:6349 original size:3 final size:3
Alignment explanation
Indices: 6341--6372 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
6331 GGATACTATC
6341 ATT ATT ATT ATT A-T ATT ATT ATT -TT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
6373 ATAATAATGT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
2 4 0.15
3 23 0.85
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:6359 original size:11 final size:11
Alignment explanation
Indices: 6343--6372 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
6333 ATACTATCAT
6343 TATTATTATTA
1 TATTATTATTA
*
6354 TATTATTATTT
1 TATTATTATTA
6365 TATTATTA
1 TATTATTA
6373 ATAATAATGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (11 bp):
TATTATTATTA
Found at i:7065 original size:20 final size:20
Alignment explanation
Indices: 7042--7096 Score: 76
Period size: 20 Copynumber: 2.8 Consensus size: 20
7032 GCACTAACTC
7042 TATTATACT-GCCACCACTAA
1 TATT-TACTGGCCACCACTAA
*
7062 TATTTGCTGGCCACCACTAA
1 TATTTACTGGCCACCACTAA
*
7082 TATTTGCTGGCCACC
1 TATTTACTGGCCACC
7097 CATGTTTTGT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
19 3 0.09
20 30 0.91
ACGTcount: A:0.25, C:0.31, G:0.13, T:0.31
Consensus pattern (20 bp):
TATTTACTGGCCACCACTAA
Found at i:9491 original size:9 final size:10
Alignment explanation
Indices: 9471--9501 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
9461 GAATATATAA
9471 TTAAAAATAT
1 TTAAAAATAT
9481 TTAAAAA-AT
1 TTAAAAATAT
9490 TTAAAAATAT
1 TTAAAAATAT
9500 TT
1 TT
9502 TTATAAATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
TTAAAAATAT
Found at i:13925 original size:21 final size:21
Alignment explanation
Indices: 13901--13941 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13891 TCTTTGAATG
13901 AAATATA-AATTTATAAAATTA
1 AAATATACAA-TTATAAAATTA
*
13922 AAATATACAATTATACAATT
1 AAATATACAATTATAAAATT
13942 TATCAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (21 bp):
AAATATACAATTATAAAATTA
Found at i:13999 original size:21 final size:20
Alignment explanation
Indices: 13953--14004 Score: 52
Period size: 22 Copynumber: 2.5 Consensus size: 20
13943 ATCAAAATTT
13953 ATATAAATTAAATTATTATC
1 ATATAAATTAAATTATTATC
*
13973 AT-TATAATATAAATATATTATG
1 ATATA-AAT-TAAAT-TATTATC
*
13995 ATATAGATTA
1 ATATAAATTA
14005 GATTTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 7
0.74 0.06 0.20
Matches are distributed among these distances:
19 2 0.08
20 5 0.19
21 7 0.27
22 10 0.38
23 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (20 bp):
ATATAAATTAAATTATTATC
Found at i:14243 original size:14 final size:14
Alignment explanation
Indices: 14224--14256 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
14214 AATTGACAGT
14224 GATGAGGGATGGCC
1 GATGAGGGATGGCC
14238 GATGAGGGATGGCC
1 GATGAGGGATGGCC
14252 GATGA
1 GATGA
14257 CGGGGACTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.24, C:0.12, G:0.48, T:0.15
Consensus pattern (14 bp):
GATGAGGGATGGCC
Found at i:21994 original size:60 final size:60
Alignment explanation
Indices: 21877--22128 Score: 198
Period size: 60 Copynumber: 4.2 Consensus size: 60
21867 ATACATATAG
* * * * *
21877 TTTGGGATAAAATTGGAATGTTCAAAAAGTTTAGGGACT-ATTTAGAA-CAAAATTCATAA
1 TTTGGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAATC-ATAGTCATAA
* * *
21936 TTTGGGTATGAAATTGAAATGTTC-AAAAGTTTGAGGACTAATTTAGAGTCATAGTCATAG
1 TTTGGG-ATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAATCATAGTCATAA
* * * * * * * *
21996 TGTAGGGATGCAATTAAAATATT-TAAAAGTTTAAAGA-TCAATTTAAAAT-AT-GT-AAAA
1 T-TTGGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACT-AATTTAGAATCATAGTCATAA
* * *
22053 GTTTAGGGATGAAATTGAAATGTTCTAAAA-TTTAAGGATTAATTTAGAATCATAATCATAA
1 -TTT-GGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAATCATAGTCATAA
*
22114 TTTAGGGATGTAATT
1 TTT-GGGATGAAATT
22129 TTTTTTTTTA
Statistics
Matches: 153, Mismatches: 27, Indels: 25
0.75 0.13 0.12
Matches are distributed among these distances:
57 3 0.02
58 35 0.23
59 30 0.20
60 77 0.50
61 8 0.05
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.35
Consensus pattern (60 bp):
TTTGGGATGAAATTGAAATGTTCAAAAAGTTTAAGGACTAATTTAGAATCATAGTCATAA
Found at i:22073 original size:29 final size:29
Alignment explanation
Indices: 21998--22073 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
21988 AGTCATAGTG
* *
21998 TAGGGATGCAATTAAAATATTTAAAAGTT
1 TAGGGATGAAATTAAAATATGTAAAAGTT
** * *
22027 TAAAGATCAATTTAAAATATGTAAAAGTT
1 TAGGGATGAAATTAAAATATGTAAAAGTT
*
22056 TAGGGATGAAATTGAAAT
1 TAGGGATGAAATTAAAAT
22074 GTTCTAAAAT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.47, C:0.03, G:0.17, T:0.33
Consensus pattern (29 bp):
TAGGGATGAAATTAAAATATGTAAAAGTT
Found at i:29474 original size:24 final size:22
Alignment explanation
Indices: 29431--29484 Score: 63
Period size: 24 Copynumber: 2.4 Consensus size: 22
29421 AGGCATTTAG
*
29431 TTTTCTTTACTCTACTTTCTTC
1 TTTTCTTTACTCTACATTCTTC
* *
29453 TCTTTCTTATATTCTACATTCTTG
1 T-TTTCTT-TACTCTACATTCTTC
29477 TTTTCTTT
1 TTTTCTTT
29485 GACTTTCTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 2 0.07
23 12 0.44
24 13 0.48
ACGTcount: A:0.11, C:0.22, G:0.02, T:0.65
Consensus pattern (22 bp):
TTTTCTTTACTCTACATTCTTC
Found at i:31299 original size:56 final size:55
Alignment explanation
Indices: 31239--31432 Score: 271
Period size: 56 Copynumber: 3.5 Consensus size: 55
31229 CTATACGGTA
* * * *
31239 ATTCATCAACTCATGAATGAATTCCGTGGATTGGCACACATAGGGCCTGTACGGCT
1 ATTCATCAACTCATG-ATGAATTTCGTGGATTTGCACACATAGTGCCTGTACGACT
* *
31295 ATTCATCAACTCATGATGAATTTCATGGAATTTGCACACATAGTGCCTATACGACT
1 ATTCATCAACTCATGATGAATTTCGTGG-ATTTGCACACATAGTGCCTGTACGACT
* * *
31351 ATTCATCAACTCATGATGAATTTTGTGGATTTTCCACACATAGTGCCTGTATGACT
1 ATTCATCAACTCATGATGAATTTCGTGGA-TTTGCACACATAGTGCCTGTACGACT
*
31407 ATTCATCAACTCATGGTGAATTTCGT
1 ATTCATCAACTCATGATGAATTTCGT
31433 AGAATTTTAC
Statistics
Matches: 123, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
55 12 0.10
56 111 0.90
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (55 bp):
ATTCATCAACTCATGATGAATTTCGTGGATTTGCACACATAGTGCCTGTACGACT
Found at i:31412 original size:112 final size:113
Alignment explanation
Indices: 31239--31449 Score: 300
Period size: 112 Copynumber: 1.9 Consensus size: 113
31229 CTATACGGTA
* *
31239 ATTCATCAACTCATGAATGAATTCCGTGGATTGGCACACATAGGGCCTGTACGGCTATTCATCAA
1 ATTCATCAACTCATGAATGAATTCCGTGGATTGCCACACATAGGGCCTGTACGACTATTCATCAA
* *
31304 CTCATGATGAATTTCATGGAA-TTTGCACACATAGTGCCTATACGACT
66 CTCATGATGAATTTCATAGAATTTTACACACATAGTGCCTATACGACT
** * * *
31351 ATTCATCAACTCATG-ATGAATTTTGTGGATTTTCCACACATAGTGCCTGTATGACTATTCATCA
1 ATTCATCAACTCATGAATGAATTCCGTGGA-TTGCCACACATAGGGCCTGTACGACTATTCATCA
* *
31415 ACTCATGGTGAATTTCGTAGAATTTTACACACATA
65 ACTCATGATGAATTTCATAGAATTTTACACACATA
31450 TTGCTTGTAG
Statistics
Matches: 86, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
111 12 0.14
112 63 0.73
113 11 0.13
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.33
Consensus pattern (113 bp):
ATTCATCAACTCATGAATGAATTCCGTGGATTGCCACACATAGGGCCTGTACGACTATTCATCAA
CTCATGATGAATTTCATAGAATTTTACACACATAGTGCCTATACGACT
Found at i:35831 original size:23 final size:22
Alignment explanation
Indices: 35804--35856 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 22
35794 CGAGGGTTCT
*
35804 ATGTGGTCCTTC-GAGACAAACTA
1 ATGTGGTCATTCGGAGA-AAAC-A
35827 ATGTGGTCATTCGGGAGAAAACA
1 ATGTGGTCATTC-GGAGAAAACA
35850 ATGTGGT
1 ATGTGGT
35857 TTTCGGTACA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 19 0.70
24 4 0.15
25 4 0.15
ACGTcount: A:0.30, C:0.15, G:0.28, T:0.26
Consensus pattern (22 bp):
ATGTGGTCATTCGGAGAAAACA
Found at i:42219 original size:23 final size:23
Alignment explanation
Indices: 42168--42219 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
42158 AGCATCCTTG
* * *
42168 CATCACTGTATCAATTCAGCAAG
1 CATCATTGAATCAATTCAGCAAA
*
42191 CATCATTGAATCAATTTAGCAAA
1 CATCATTGAATCAATTCAGCAAA
42214 CATCAT
1 CATCAT
42220 GCATTCAGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.23, G:0.10, T:0.29
Consensus pattern (23 bp):
CATCATTGAATCAATTCAGCAAA
Found at i:42335 original size:20 final size:20
Alignment explanation
Indices: 42310--42387 Score: 84
Period size: 20 Copynumber: 3.9 Consensus size: 20
42300 AATCTTTACA
*
42310 AATATCAAGCAGAATCAAGC
1 AATATCAAACAGAATCAAGC
* *
42330 AATATCAAACAGAAGCAAAC
1 AATATCAAACAGAATCAAGC
* * * *
42350 AATATAAAATAAAATCATGC
1 AATATCAAACAGAATCAAGC
*
42370 AATATCAAGCAGAATCAA
1 AATATCAAACAGAATCAA
42388 ACATCAGCTA
Statistics
Matches: 44, Mismatches: 14, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 44 1.00
ACGTcount: A:0.56, C:0.17, G:0.10, T:0.17
Consensus pattern (20 bp):
AATATCAAACAGAATCAAGC
Found at i:46593 original size:14 final size:14
Alignment explanation
Indices: 46576--46604 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
46566 ATCTCTTGTG
46576 TTTGATTTCTTGGA
1 TTTGATTTCTTGGA
46590 TTTGATTTCTTGGA
1 TTTGATTTCTTGGA
46604 T
1 T
46605 AGGTGTTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.07, G:0.21, T:0.59
Consensus pattern (14 bp):
TTTGATTTCTTGGA
Found at i:46883 original size:7 final size:7
Alignment explanation
Indices: 46873--46945 Score: 63
Period size: 7 Copynumber: 11.6 Consensus size: 7
46863 ATATTTTATA
46873 TATACTT
1 TATACTT
46880 TATACTT
1 TATACTT
46887 TATACTT
1 TATACTT
*
46894 TATA-TA
1 TATACTT
*
46900 AATAC-T
1 TATACTT
*
46906 TATA-TA
1 TATACTT
46912 TATACTT
1 TATACTT
46919 TATA---
1 TATACTT
46923 TATAC-T
1 TATACTT
46929 TATAC-T
1 TATACTT
46935 TATACTT
1 TATACTT
46942 TATA
1 TATA
46946 TATATATATA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
4 4 0.07
6 22 0.41
7 28 0.52
ACGTcount: A:0.37, C:0.11, G:0.00, T:0.52
Consensus pattern (7 bp):
TATACTT
Found at i:46890 original size:25 final size:24
Alignment explanation
Indices: 46842--46949 Score: 121
Period size: 23 Copynumber: 4.3 Consensus size: 24
46832 CTATGTAAAG
* *
46842 TATATATATTATATACCTTATATATTT
1 TATATATACT-TATA-CTT-TATACTT
46869 TATATATACTTTATACTTTATACTT
1 TATATATAC-TTATACTTTATACTT
*
46894 TATATAAATACTTATA-TATATACTT
1 TATAT--ATACTTATACTTTATACTT
46919 TATATATACTTATAC-TTATACTT
1 TATATATACTTATACTTTATACTT
46942 TATATATA
1 TATATATA
46950 TATATATAAA
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
23 24 0.33
25 24 0.33
26 8 0.11
27 16 0.22
28 1 0.01
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (24 bp):
TATATATACTTATACTTTATACTT
Found at i:46950 original size:25 final size:25
Alignment explanation
Indices: 46842--46951 Score: 111
Period size: 27 Copynumber: 4.3 Consensus size: 25
46832 CTATGTAAAG
* *
46842 TATATATATTATATACCTTATA-TATTT
1 TATATATACT-TATA-CTTATACT-TTA
46869 TATATATACTTTATACTTTATACTTTA
1 TATATATAC-TTATAC-TTATACTTTA
*
46896 TATAAATACTTATA-TATATAC-TT-
1 TATATATACTTATACT-TATACTTTA
46919 TATATATACTTATACTTATACTTTA
1 TATATATACTTATACTTATACTTTA
46944 TATATATA
1 TATATATA
46952 TATATAAATA
Statistics
Matches: 72, Mismatches: 4, Indels: 16
0.78 0.04 0.17
Matches are distributed among these distances:
23 18 0.25
24 6 0.08
25 13 0.18
26 6 0.08
27 27 0.38
28 2 0.03
ACGTcount: A:0.38, C:0.09, G:0.00, T:0.53
Consensus pattern (25 bp):
TATATATACTTATACTTATACTTTA
Found at i:46955 original size:23 final size:26
Alignment explanation
Indices: 46842--46985 Score: 119
Period size: 23 Copynumber: 5.7 Consensus size: 26
46832 CTATGTAAAG
* *
46842 TATATATATTATATACCTTATATATTT
1 TATATATACTATATA-CTTATATACTT
*
46869 TATATATACTTTATACTT-TATACTT
1 TATATATACTATATACTTATATACTT
46894 TATATAAATACT-TATA--TATATACTT
1 TATAT--ATACTATATACTTATATACTT
46919 TATATATACT-TATAC-T-TATACTT
1 TATATATACTATATACTTATATACTT
* * *
46942 TATATATA-TATATA--TAAATAAGTA
1 TATATATACTATATACTTATAT-ACTT
46966 TATATATAACTATATACTTA
1 TATATAT-ACTATATACTTA
46986 CAATGTATTA
Statistics
Matches: 100, Mismatches: 6, Indels: 21
0.79 0.05 0.17
Matches are distributed among these distances:
22 2 0.02
23 30 0.30
24 11 0.11
25 24 0.24
26 13 0.13
27 18 0.18
28 2 0.02
ACGTcount: A:0.41, C:0.08, G:0.01, T:0.50
Consensus pattern (26 bp):
TATATATACTATATACTTATATACTT
Found at i:46957 original size:25 final size:24
Alignment explanation
Indices: 46862--46957 Score: 99
Period size: 25 Copynumber: 3.9 Consensus size: 24
46852 ATATACCTTA
*
46862 TATATTTTATATATACT-TTATACTT
1 TATACTTTATATATA-TATTATAC-T
*
46887 TATACTTTATATAAATACTTATA-T
1 TATACTTTATATATATA-TTATACT
*
46911 ATATACTTTATATATA-CTTATACT
1 -TATACTTTATATATATATTATACT
46935 TATACTTTATATATATATATATA
1 TATACTTTATATATATAT-TATA
46958 AATAAGTATA
Statistics
Matches: 60, Mismatches: 5, Indels: 12
0.78 0.06 0.16
Matches are distributed among these distances:
23 20 0.33
24 4 0.07
25 31 0.52
26 5 0.08
ACGTcount: A:0.39, C:0.08, G:0.00, T:0.53
Consensus pattern (24 bp):
TATACTTTATATATATATTATACT
Found at i:47273 original size:22 final size:22
Alignment explanation
Indices: 47243--47321 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
47233 CGATTTGAAC
* *
47243 TCAATCTGTATCTGATAAAGAT
1 TCAACCTGTATTTGATAAAGAT
47265 TCAACCTGTATTTGATAAAGAT
1 TCAACCTGTATTTGATAAAGAT
47287 TCAACCTGTATTTGATAAAGAT
1 TCAACCTGTATTTGATAAAGAT
*
47309 TCAACCTGGATTT
1 TCAACCTGTATTT
47322 TATCTGCCAA
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.34, C:0.15, G:0.14, T:0.37
Consensus pattern (22 bp):
TCAACCTGTATTTGATAAAGAT
Found at i:48355 original size:22 final size:21
Alignment explanation
Indices: 48321--48361 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
48311 ATAATTATTT
48321 AAAAAATTAAATAAAAATACC
1 AAAAAATTAAATAAAAATACC
*
48342 AAAAATATTTAATAAAAATA
1 AAAAA-ATTAAATAAAAATA
48362 AATTTATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.71, C:0.05, G:0.00, T:0.24
Consensus pattern (21 bp):
AAAAAATTAAATAAAAATACC
Found at i:50897 original size:32 final size:33
Alignment explanation
Indices: 50820--50897 Score: 79
Period size: 32 Copynumber: 2.4 Consensus size: 33
50810 ATTAAAAATA
* * *
50820 AAAAATATAAATTTGAAAGTTAGAGTGATTAAAT
1 AAAAA-ATAAATTTGAAAGTTAGAGTAACTAAAC
* * *
50854 TAAGAGT-AATTTGAAAGTTA-AGTAACTAAAC
1 AAAAAATAAATTTGAAAGTTAGAGTAACTAAAC
50885 AAAAAATAAATTT
1 AAAAAATAAATTT
50898 TAGTGATCAA
Statistics
Matches: 34, Mismatches: 9, Indels: 4
0.72 0.19 0.09
Matches are distributed among these distances:
31 12 0.35
32 18 0.53
33 1 0.03
34 3 0.09
ACGTcount: A:0.54, C:0.03, G:0.13, T:0.31
Consensus pattern (33 bp):
AAAAAATAAATTTGAAAGTTAGAGTAACTAAAC
Found at i:52763 original size:60 final size:60
Alignment explanation
Indices: 52699--52890 Score: 216
Period size: 60 Copynumber: 3.2 Consensus size: 60
52689 ACTAGGCCTA
*
52699 GGGTAAGACCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATT
1 GGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATT
* ** * * *** *
52759 GGGTAAGTCCTTAT--AGCCTAGGGGTACTCCCCTCA-GGTGGGCTCCTGC-GC-TTCAAC-TA
1 GGGTAAGTCCTTATGGAGCCTA-AGGTACT-TTCTTAGGGTGGG-TCCT-CTTCTTTGTGCATT
52817 GGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATT
1 GGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATT
52877 GGGTAAGTCCTTAT
1 GGGTAAGTCCTTAT
52891 AGCCTAGGGG
Statistics
Matches: 103, Mismatches: 19, Indels: 20
0.73 0.13 0.14
Matches are distributed among these distances:
57 1 0.01
58 29 0.28
59 30 0.29
60 42 0.41
61 1 0.01
ACGTcount: A:0.17, C:0.21, G:0.28, T:0.34
Consensus pattern (60 bp):
GGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATT
Found at i:52823 original size:58 final size:58
Alignment explanation
Indices: 52759--52948 Score: 217
Period size: 58 Copynumber: 3.2 Consensus size: 58
52749 TTTGTGCATT
* *
52759 GGGTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAACTA
1 GGGTAAGTCCTTATAGCCTAGGGGTACTCCTCTCAGGTGGGCTCCTGCGCTTCAGCTA
* * * * ** *
52817 GGGTAAGTCCTTATGGAGCCTA-AGGTACT-TTCTTAGGGTGGG-TCCT-CTTCTTTGTGCATT
1 GGGTAAGTCCTTAT--AGCCTAGGGGTACTCCTCTCA-GGTGGGCTCCTGC-GC-TTCAGC-TA
52877 GGGTAAGTCCTTATAGCCTAGGGGTACTCCTCTCAGGTGGGCTCCTGCGCTTCAGCTA
1 GGGTAAGTCCTTATAGCCTAGGGGTACTCCTCTCAGGTGGGCTCCTGCGCTTCAGCTA
52935 GGGTAAGTCCTTAT
1 GGGTAAGTCCTTAT
52949 GGTCCATGGT
Statistics
Matches: 106, Mismatches: 16, Indels: 20
0.75 0.11 0.14
Matches are distributed among these distances:
57 1 0.01
58 43 0.41
59 31 0.29
60 30 0.28
61 1 0.01
ACGTcount: A:0.16, C:0.24, G:0.28, T:0.31
Consensus pattern (58 bp):
GGGTAAGTCCTTATAGCCTAGGGGTACTCCTCTCAGGTGGGCTCCTGCGCTTCAGCTA
Found at i:52850 original size:118 final size:118
Alignment explanation
Indices: 52696--52950 Score: 483
Period size: 118 Copynumber: 2.2 Consensus size: 118
52686 CATACTAGGC
*
52696 CTAGGGTAAGACCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
1 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
52761 GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
66 GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
52814 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
1 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
* *
52879 GTAAGTCCTTATAGCCTAGGGGTACTCCTCTCAGGTGGGCTCCTGCGCTTCAG
66 GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
52932 CTAGGGTAAGTCCTTATGG
1 CTAGGGTAAGTCCTTATGG
52951 TCCATGGTGC
Statistics
Matches: 134, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
118 134 1.00
ACGTcount: A:0.16, C:0.23, G:0.29, T:0.32
Consensus pattern (118 bp):
CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
Found at i:52999 original size:118 final size:118
Alignment explanation
Indices: 52696--53008 Score: 342
Period size: 118 Copynumber: 2.7 Consensus size: 118
52686 CATACTAGGC
* ** * * * * * * *
52696 CTAGGGTAAGACCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
1 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTCCCTTAGGGTAGGTACTATCCTATGGGCATAGG
52761 GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
66 GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
** * * * * * * *
52814 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTTTCTTAGGGTGGGTCCTCTTCTTTGTGCATTGG
1 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTCCCTTAGGGTAGGTACTATCCTATGGGCATAGG
* *
52879 GTAAGTCCTTATAGCCTAGGGGTACTCCTCTCAGGTGGGCTCCTGCGCTTCAG
66 GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
* * * * * * *
52932 CTAGGGTAAGTCCTTATGG-TCC-ATGGTGCTCCCTTAGGTTAGTTATTATACCTAATGGGTATA
1 CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTCCCTTAGGGTAGGTACTAT-CCT-ATGGGCATA
52995 GGGTAAGTCCTTAT
64 GGGTAAGTCCTTAT
53009 TAATGCAGTT
Statistics
Matches: 174, Mismatches: 19, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
116 17 0.10
117 4 0.02
118 153 0.88
ACGTcount: A:0.18, C:0.22, G:0.27, T:0.33
Consensus pattern (118 bp):
CTAGGGTAAGTCCTTATGGAGCCTAAGGTACTCCCTTAGGGTAGGTACTATCCTATGGGCATAGG
GTAAGTCCTTATAGCCTAGGGGTACTCCCCTCAGGTGGGCTCCTGCGCTTCAA
Found at i:55279 original size:27 final size:27
Alignment explanation
Indices: 55249--55305 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
55239 AAAAACAACC
55249 TCATTGAAGGCTAGAAAACGAAGGAAA
1 TCATTGAAGGCTAGAAAACGAAGGAAA
55276 TCATTGAAGGCTAGAAAACGAAGGAAA
1 TCATTGAAGGCTAGAAAACGAAGGAAA
55303 TCA
1 TCA
55306 GATGCGACCG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.47, C:0.12, G:0.25, T:0.16
Consensus pattern (27 bp):
TCATTGAAGGCTAGAAAACGAAGGAAA
Found at i:56726 original size:3 final size:3
Alignment explanation
Indices: 56718--56756 Score: 69
Period size: 3 Copynumber: 13.0 Consensus size: 3
56708 AGATATAAAC
*
56718 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAG TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56757 ATTAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:57344 original size:27 final size:29
Alignment explanation
Indices: 57310--57367 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
57300 AATTAATGTT
*
57310 AAATAAATGA-AAGG-AAAAAGAAAAAAA
1 AAATAAATCAGAAGGAAAAAAGAAAAAAA
57337 AAATAAATCAGAAGGAAAAAAGAAAAAAA
1 AAATAAATCAGAAGGAAAAAAGAAAAAAA
57366 AA
1 AA
57368 TAATAATAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
27 9 0.32
28 4 0.14
29 15 0.54
ACGTcount: A:0.78, C:0.02, G:0.14, T:0.07
Consensus pattern (29 bp):
AAATAAATCAGAAGGAAAAAAGAAAAAAA
Found at i:58043 original size:30 final size:30
Alignment explanation
Indices: 57987--58044 Score: 73
Period size: 31 Copynumber: 1.9 Consensus size: 30
57977 TATTTTTTTT
*
57987 ATGATTTTTTTGCTGCTTTGTATGTTTCGAA
1 ATGATTTTTTTGCT-CTTAGTATGTTTCGAA
*
58018 ATGATTTTTTTGCT-TTGAGTTTGTTTC
1 ATGATTTTTTTGCTCTT-AGTATGTTTC
58045 CTTTGTGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
29 2 0.08
30 8 0.33
31 14 0.58
ACGTcount: A:0.14, C:0.09, G:0.19, T:0.59
Consensus pattern (30 bp):
ATGATTTTTTTGCTCTTAGTATGTTTCGAA
Found at i:64035 original size:28 final size:28
Alignment explanation
Indices: 63995--64051 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
63985 TTTCTTTGAG
63995 TTAATGCTGGGAAAGTCGACGAATAACT
1 TTAATGCTGGGAAAGTCGACGAATAACT
64023 TTAATGCTGGGAAAGTCGACGAATAACT
1 TTAATGCTGGGAAAGTCGACGAATAACT
64051 T
1 T
64052 CAAGGATCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (28 bp):
TTAATGCTGGGAAAGTCGACGAATAACT
Found at i:67587 original size:42 final size:42
Alignment explanation
Indices: 67525--67616 Score: 130
Period size: 42 Copynumber: 2.2 Consensus size: 42
67515 ACTTAGTAAG
* * *
67525 TCCTTCGGGCCATCAATAAGTCTTTTGAGCATGATGCTTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTAGAGCATGATGATTAAA
* *
67567 TCCTTAGGGCCATTAGTAAGTCTTTAGAGCATGATGATTAAA
1 TCCTTAGGGCCATCAATAAGTCTTTAGAGCATGATGATTAAA
*
67609 TCTTTAGG
1 TCCTTAGG
67617 CTAATTTGTA
Statistics
Matches: 44, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (42 bp):
TCCTTAGGGCCATCAATAAGTCTTTAGAGCATGATGATTAAA
Found at i:67612 original size:22 final size:22
Alignment explanation
Indices: 67545--67615 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
67535 CATCAATAAG
* *
67545 TCTTTTGAGCATGATGCTTAAA
1 TCTTTAGAGCATGATGATTAAA
* * * *
67567 TCCTTAGGGCCAT--T-AGTAAG
1 TCTTTAGAG-CATGATGATTAAA
67587 TCTTTAGAGCATGATGATTAAA
1 TCTTTAGAGCATGATGATTAAA
67609 TCTTTAG
1 TCTTTAG
67616 GCTAATTTGT
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 2 0.06
22 17 0.49
23 3 0.09
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (22 bp):
TCTTTAGAGCATGATGATTAAA
Found at i:67735 original size:93 final size:93
Alignment explanation
Indices: 67575--67760 Score: 272
Period size: 93 Copynumber: 2.0 Consensus size: 93
67565 AATCCTTAGG
*
67575 GCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCTTTAGGCTAATTTGTAAGCCTTCACGAAA
1 GCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCTTCAGGCTAATTTGTAAGCCTTCACGAAA
*
67640 GAGTAGTGAAGCAAA-CCAATCAGTAAGT
66 GAGTAATGAAGCAAATCC-ATCAGTAAGT
*
67668 GCCATTAGTAAGTCTTTCA-AGCATGATGATTAAATACTTCAGG-TAATTTGTAATCCTTCACCG
1 GCCATTAGTAAGTCTTT-AGAGCATGATGATTAAAT-CTTCAGGCTAATTTGTAAGCCTTCA-CG
*
67731 -AAGAGTAATGAAGCAAATTCATCAGTAAGT
63 AAAGAGTAATGAAGCAAATCCATCAGTAAGT
67761 CTTTCGAGCA
Statistics
Matches: 85, Mismatches: 4, Indels: 8
0.88 0.04 0.08
Matches are distributed among these distances:
93 75 0.88
94 10 0.12
ACGTcount: A:0.35, C:0.16, G:0.19, T:0.30
Consensus pattern (93 bp):
GCCATTAGTAAGTCTTTAGAGCATGATGATTAAATCTTCAGGCTAATTTGTAAGCCTTCACGAAA
GAGTAATGAAGCAAATCCATCAGTAAGT
Found at i:68331 original size:53 final size:53
Alignment explanation
Indices: 68214--68580 Score: 429
Period size: 53 Copynumber: 7.0 Consensus size: 53
68204 AGAATCACAC
* * * *
68214 CAGAAGATTGTTCGAGTTTTACTTCCTGAAGCAAGATGGAG-G-A-CTGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* *
68264 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGTAAGAGGGAGCGAACCCGTAGA
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
68317 CAGAAGATTGTTCGAGTTCTACTTCCTGAAGCAAGAGGGAGCGAACTCATAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
68370 CAGAAGATTGTTCGAGTTCTACTCCTTGAAGCAAGAGAGAGTGAACCCGTAGG
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * *
68423 CAGAAGATTGTTCGAGTTCTAC-CCTCTCAAGCAAGAGGGAGCGAACTCATAAG
1 CAGAAGATTGTTCGAGTTCTACTCC-CTGAAGCAAGAGGGAGCGAACCCGTAGG
* * * * * ***
68476 CAAAAGATTATTCGAGTTCTACTCCTTGAAGCAATAGGGAGCGGACCCGTTTT
1 CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
* * *
68529 TAGAAGATTGTTCGAGTTCCTTAATCCCTGAA-CAAGAGGGAGCGGACCCGTA
1 CAGAAGATTGTTCGAGTT-C-TACTCCCTGAAGCAAGAGGGAGCGAACCCGTA
68581 ATTTGAAGAT
Statistics
Matches: 268, Mismatches: 42, Indels: 10
0.84 0.13 0.03
Matches are distributed among these distances:
50 37 0.14
51 1 0.00
52 3 0.01
53 197 0.74
54 21 0.08
55 9 0.03
ACGTcount: A:0.30, C:0.20, G:0.27, T:0.24
Consensus pattern (53 bp):
CAGAAGATTGTTCGAGTTCTACTCCCTGAAGCAAGAGGGAGCGAACCCGTAGG
Found at i:88795 original size:14 final size:14
Alignment explanation
Indices: 88776--88809 Score: 61
Period size: 13 Copynumber: 2.5 Consensus size: 14
88766 GTGGGGTAAG
88776 GCGCGCCCCCTGCA
1 GCGCGCCCCCTGCA
88790 GCGCG-CCCCTGCA
1 GCGCGCCCCCTGCA
88803 GCGCGCC
1 GCGCGCC
88810 TTATGCTGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 13 0.68
14 6 0.32
ACGTcount: A:0.06, C:0.56, G:0.32, T:0.06
Consensus pattern (14 bp):
GCGCGCCCCCTGCA
Found at i:94837 original size:24 final size:24
Alignment explanation
Indices: 94802--94848 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
94792 TATCTGCAAA
*
94802 AAAAAAAATTAATTAAATAAATAT
1 AAAAAAAATTAAATAAATAAATAT
* *
94826 AAAAAAATTTAAATAATTAAATA
1 AAAAAAAATTAAATAAATAAATA
94849 AATTACTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAAAAATTAAATAAATAAATAT
Found at i:94852 original size:9 final size:9
Alignment explanation
Indices: 94807--94853 Score: 51
Period size: 9 Copynumber: 5.1 Consensus size: 9
94797 GCAAAAAAAA
*
94807 AAATTAATT
1 AAATAAATT
94816 AAATAAATAT
1 AAATAAAT-T
*
94826 AAAAAAATTT
1 AAATAAA-TT
94836 AAAT-AATT
1 AAATAAATT
94844 AAATAAATT
1 AAATAAATT
94853 A
1 A
94854 CTAAAAAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
8 6 0.19
9 14 0.44
10 11 0.34
11 1 0.03
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (9 bp):
AAATAAATT
Found at i:94864 original size:24 final size:25
Alignment explanation
Indices: 94800--94862 Score: 72
Period size: 28 Copynumber: 2.3 Consensus size: 25
94790 TATATCTGCA
94800 AAAAAAAAAATTAATTAAATAAATAT
1 AAAAAAAAAA-TAATTAAATAAATAT
94826 AAAAAAATTTAAATAATTAAATAAATTACT
1 AAAAAAA---AAATAATTAAATAAA-TA-T
94856 AAAAAAA
1 AAAAAAA
94863 TACTAAATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
26 7 0.22
28 12 0.38
29 5 0.16
30 8 0.25
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (25 bp):
AAAAAAAAAATAATTAAATAAATAT
Found at i:95685 original size:36 final size:35
Alignment explanation
Indices: 95645--95861 Score: 259
Period size: 36 Copynumber: 6.2 Consensus size: 35
95635 GTAGTATATT
95645 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATATATAT-ATATATAGTTTTTAAAACA
95681 TTTTGAAAACT-TATATAATATATAGTTTTTAAAACA
1 TTTTGAAAA-TATATAT-ATATATAGTTTTTAAAACA
* *
95717 TTTTGAATATATATATATAATATAG-TTTTCAAACA
1 TTTTGAAAATATATATAT-ATATAGTTTTTAAAACA
* *
95752 -TTTG-AAATATATATA-ATATAGTTTTCAAATCA
1 TTTTGAAAATATATATATATATAGTTTTTAAAACA
95784 TTTTG-AAA-ATATATATATATAGTTTTTAAAACA
1 TTTTGAAAATATATATATATATAGTTTTTAAAACA
* **
95817 TTTTGAAAAAATATATATAATATATAATTTTCGAAACA
1 TTTTG--AAAATATATAT-ATATATAGTTTTTAAAACA
95855 TTTTGAA
1 TTTTGAA
95862 TATTTTTTAA
Statistics
Matches: 159, Mismatches: 11, Indels: 22
0.83 0.06 0.11
Matches are distributed among these distances:
31 6 0.04
32 14 0.09
33 37 0.23
34 4 0.03
35 12 0.08
36 58 0.36
37 7 0.04
38 21 0.13
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (35 bp):
TTTTGAAAATATATATATATATAGTTTTTAAAACA
Found at i:95848 original size:71 final size:70
Alignment explanation
Indices: 95645--95861 Score: 270
Period size: 71 Copynumber: 3.1 Consensus size: 70
95635 GTAGTATATT
*
95645 TTTTGAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAACT-TATATAATATATAGTTT
1 TTTTG-AAATATATAT-ATATATAGTTTTTAAAACATTTTGAAAAATATATATAATATATAG-TT
*
95709 TTAAAACA
63 TTCAAACA
*
95717 TTTTGAATATATATATATAATATAG-TTTTCAAACA-TTTG--AAATATATAT-A-ATATAGTTT
1 TTTTGAA-ATATATATAT-ATATAGTTTTTAAAACATTTTGAAAAATATATATAATATATAGTTT
95776 TCAAATCA
64 TCAAA-CA
*
95784 TTTTGAAA-ATATATATATATAGTTTTTAAAACATTTTGAAAAAATATATATAATATATAATTTT
1 TTTTGAAATATATATATATATAGTTTTTAAAACATTTTG-AAAAATATATATAATATATAGTTTT
95848 CGAAACA
65 C-AAACA
95855 TTTTGAA
1 TTTTGAA
95862 TATTTTTTAA
Statistics
Matches: 128, Mismatches: 5, Indels: 25
0.81 0.03 0.16
Matches are distributed among these distances:
64 6 0.05
65 17 0.13
66 12 0.09
67 15 0.12
68 4 0.03
69 15 0.12
70 5 0.04
71 32 0.25
72 22 0.17
ACGTcount: A:0.45, C:0.05, G:0.06, T:0.44
Consensus pattern (70 bp):
TTTTGAAATATATATATATATAGTTTTTAAAACATTTTGAAAAATATATATAATATATAGTTTTC
AAACA
Found at i:95879 original size:59 final size:55
Alignment explanation
Indices: 95806--95916 Score: 141
Period size: 57 Copynumber: 1.9 Consensus size: 55
95796 ATATATATAG
*
95806 TTTTTAAAACATTTTGAAAAAATATATATAATATATAATTTTCGAAACATTTTGAATAT
1 TTTTTAAAACATTTTG--AAAATATATATAAGATATAATTTT-G-AACATTTTGAATAT
* * * *
95865 TTTTTAAAATATTTTGAATATATATATAAGATATAGTTTTGAATATTTTGAA
1 TTTTTAAAACATTTTGAAAATATATATAAGATATAATTTTGAACATTTTGAA
95917 AATATATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
55 10 0.21
56 1 0.02
57 21 0.45
59 15 0.32
ACGTcount: A:0.43, C:0.03, G:0.07, T:0.47
Consensus pattern (55 bp):
TTTTTAAAACATTTTGAAAATATATATAAGATATAATTTTGAACATTTTGAATAT
Found at i:95940 original size:34 final size:34
Alignment explanation
Indices: 95872--95941 Score: 88
Period size: 34 Copynumber: 2.1 Consensus size: 34
95862 TATTTTTTAA
* *
95872 AATATTTTGAATATATATATAAGATATAGTTTTG
1 AATATTTTGAAAATATATATAAGATATAGATTTG
**
95906 AATATTTTGAAAATATATTATATTATAT-GATTTG
1 AATATTTTGAAAATATA-TATAAGATATAGATTTG
95940 AA
1 AA
95942 AATAATTATT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
34 23 0.74
35 8 0.26
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (34 bp):
AATATTTTGAAAATATATATAAGATATAGATTTG
Found at i:96000 original size:24 final size:24
Alignment explanation
Indices: 95973--96033 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 24
95963 TATATGAATA
95973 TAATTTTTTTATTATA-TATTATAT
1 TAATTTTTTTATTATATTATTAT-T
*
95997 TAATATTTTTA-TATATTATTATT
1 TAATTTTTTTATTATATTATTATT
96020 TAATTTTATTTATT
1 TAATTTT-TTTATT
96034 TACTTTTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
23 11 0.34
24 20 0.62
25 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TAATTTTTTTATTATATTATTATT
Found at i:96004 original size:26 final size:24
Alignment explanation
Indices: 95975--96033 Score: 68
Period size: 26 Copynumber: 2.5 Consensus size: 24
95965 TATGAATATA
95975 ATTTTTTTATTATATATTATATTAAT
1 ATTTTTTTATTAT-TATTAT-TTAAT
*
96001 ATTTTTATA-TATTATTATTTAAT
1 ATTTTTTTATTATTATTATTTAAT
*
96024 -TTTATTTATT
1 ATTTTTTTATT
96034 TACTTTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 6 0.21
23 6 0.21
24 6 0.21
25 3 0.10
26 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (24 bp):
ATTTTTTTATTATTATTATTTAAT
Found at i:96005 original size:23 final size:23
Alignment explanation
Indices: 95979--96029 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 23
95969 AATATAATTT
95979 TTTTATTATATATTA-TATT-AA
1 TTTTATTATATATTATTATTAAA
*
96000 TATTT-TTATATATTATTATTTAA
1 T-TTTATTATATATTATTATTAAA
96023 TTTTATT
1 TTTTATT
96030 TATTTACTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 11 0.42
22 10 0.38
23 5 0.19
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (23 bp):
TTTTATTATATATTATTATTAAA
Found at i:99280 original size:30 final size:30
Alignment explanation
Indices: 99241--99309 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
99231 ATTTTATTTT
*
99241 TACTGTTTT-AGCCTCTTAACTTTCTGTTTA
1 TACTATTTTAAGCCT-TTAACTTTCTGTTTA
* * *
99271 TACTATTTTAATCCTTTAATTTTCTGTTTG
1 TACTATTTTAAGCCTTTAACTTTCTGTTTA
*
99301 TGCTATTTT
1 TACTATTTT
99310 GGTACTTTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
30 29 0.88
31 4 0.12
ACGTcount: A:0.17, C:0.16, G:0.09, T:0.58
Consensus pattern (30 bp):
TACTATTTTAAGCCTTTAACTTTCTGTTTA
Found at i:99318 original size:30 final size:30
Alignment explanation
Indices: 99256--99325 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
99246 TTTTAGCCTC
* *
99256 TTAACTTTCTGTTTATACTATTTTAATCCT
1 TTAAATTTCTGTTTATACTATTTTAATACT
* * * **
99286 TTAATTTTCTGTTTGTGCTATTTTGGTACT
1 TTAAATTTCTGTTTATACTATTTTAATACT
99316 TTAAATTTCT
1 TTAAATTTCT
99326 TTTCTTTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.59
Consensus pattern (30 bp):
TTAAATTTCTGTTTATACTATTTTAATACT
Found at i:104368 original size:156 final size:156
Alignment explanation
Indices: 104163--104449 Score: 405
Period size: 156 Copynumber: 1.8 Consensus size: 156
104153 AAAAGCTGTC
* * * *
104163 TGTCAACAAACAACTTTCCAGTTTCATTTAGAGTCAATTTTAACTTCACAGTGAAGGATATTGGA
1 TGTCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
* * ** * *
104228 TTCGAAACAACACAACTTACACAAGATTGGATTTCAACTTCACAACT-AATGATATCCAATTCAA
66 CTCGAAACAACACAACTTACAAAAGATTAAATTTCAACTTCACAA-TGAAGGATATCCAACTCAA
104292 AGTTTAACTTCATAGTGAATTAGCGTA
130 AGTTTAACTTCATAGTGAATTAGCGTA
* *
104319 TGTCAACAAATAACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
1 TGTCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
* * * * *
104384 CTCGAATCGACACAATTTATAAAATATTAAATTTCAACTTCACAATGAAGGATATCCAACTCAAA
66 CTCGAAACAACACAACTTACAAAAGATTAAATTTCAACTTCACAATGAAGGATATCCAACTCAAA
104449 G
131 G
104450 CAAAACAATA
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
155 1 0.01
156 112 0.99
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (156 bp):
TGTCAACAAACAACTTTCCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGAA
CTCGAAACAACACAACTTACAAAAGATTAAATTTCAACTTCACAATGAAGGATATCCAACTCAAA
GTTTAACTTCATAGTGAATTAGCGTA
Found at i:104458 original size:59 final size:57
Alignment explanation
Indices: 104354--104564 Score: 187
Period size: 57 Copynumber: 3.6 Consensus size: 57
104344 ATTCAGAGTC
** ** * * *
104354 AATTTCAACTTCACAGCGAAGGATATTGAACTCGAATCGACACAATTTATAAAATATTA
1 AATTTCAACTTCACAATGAAGGATATCCAACTCAAAGC-A-ACAATTTATAAAATATTG
** *
104413 AATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCAAAACAA--TATTCAAGATTG
1 AATTTCAACTTCACAATGAAGGATATCCAACTCAAAGC--AACAATTTATAAAATATTG
* * *
104470 GATTTCAACTTCACAATGAACGATATCCAACTCAAAGC--CAATTTGGTGAAACAATACTTG
1 AATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCAACAATTT-AT--AA-AATA-TTG
*
104530 GATTTCAACTTCACAATGAAGGATATCCAACTCAA
1 AATTTCAACTTCACAATGAAGGATATCCAACTCAA
104565 TGCTCAACGA
Statistics
Matches: 126, Mismatches: 18, Indels: 15
0.79 0.11 0.09
Matches are distributed among these distances:
53 3 0.02
55 1 0.01
56 1 0.01
57 44 0.35
59 39 0.31
60 38 0.30
ACGTcount: A:0.42, C:0.20, G:0.12, T:0.27
Consensus pattern (57 bp):
AATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCAACAATTTATAAAATATTG
Found at i:104489 original size:57 final size:60
Alignment explanation
Indices: 104414--104564 Score: 200
Period size: 60 Copynumber: 2.6 Consensus size: 60
104404 AAAATATTAA
**
104414 ATTTCAACTTCACAATGAAGGATATCCAACTCAAAG-CAAAACAAT-ATTCAAGA-TTGG
1 ATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCCAAAACAATGAAACAAGACTTGG
* ***** *
104471 ATTTCAACTTCACAATGAACGATATCCAACTCAAAGCCAATTTGGTGAAACAATACTTGG
1 ATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCCAAAACAATGAAACAAGACTTGG
104531 ATTTCAACTTCACAATGAAGGATATCCAACTCAA
1 ATTTCAACTTCACAATGAAGGATATCCAACTCAA
104565 TGCTCAACGA
Statistics
Matches: 81, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
57 35 0.43
58 4 0.05
59 5 0.06
60 37 0.46
ACGTcount: A:0.41, C:0.21, G:0.12, T:0.26
Consensus pattern (60 bp):
ATTTCAACTTCACAATGAAGGATATCCAACTCAAAGCCAAAACAATGAAACAAGACTTGG
Found at i:105027 original size:85 final size:84
Alignment explanation
Indices: 104679--105037 Score: 403
Period size: 85 Copynumber: 4.2 Consensus size: 84
104669 CCCAGTGCAG
* * * *
104679 CATAACTAAAGGCGAGAAGGGTTATCTGTCATCAAAGACCTTCGAGTTCGATTATACTCAGCTCA
1 CATAACTCAAGGCGAGAA-GGTTATATGTCATCAAAGACCTTCGAGTTCAATTACACTCAGCTCA
*
104744 AAGGCATATTAAATTTACAA
65 AAGGCATATCAAATTTACAA
* ** * * * *
104764 CATAGCTCAAGGCGAGAAGGGCATATATCAACCAAGACCTTCGAGTTCAATTACACTCAGCTTAA
1 CATAACTCAAGGCGAGAAGGTTATATGTCATCAAAGACCTTCGAGTTCAATTACACTCAGCTCAA
*
104829 AGGCATATTAAATTTACAA
66 AGGCATATCAAATTTACAA
* * * * ** * *
104848 CATAACTCAAAGCGAGAAGTGTTTTTTGTCATCAAAGTCCTTTTAGTTCAATTATATTCAGCTCA
1 CATAACTCAAGGCGAGAAG-GTTATATGTCATCAAAGACCTTCGAGTTCAATTACACTCAGCTCA
* *
104913 AATGCATATCAAATTTATAA
65 AAGGCATATCAAATTTACAA
* * * *
104933 CATAACTCAAGGCAAGAAGAGTTATATGTCATTAAAGACCTTCGAGTTCGATTACATTCAGCTCA
1 CATAACTCAAGGCGAGAAG-GTTATATGTCATCAAAGACCTTCGAGTTCAATTACACTCAGCTCA
* *
104998 GAGGCATATCAAATTTACAG
65 AAGGCATATCAAATTTACAA
* * *
105018 TATAGCTCAAGGCAAGAAGG
1 CATAACTCAAGGCGAGAAGG
105038 GCTATCTATT
Statistics
Matches: 227, Mismatches: 46, Indels: 3
0.82 0.17 0.01
Matches are distributed among these distances:
84 75 0.33
85 152 0.67
ACGTcount: A:0.37, C:0.19, G:0.17, T:0.28
Consensus pattern (84 bp):
CATAACTCAAGGCGAGAAGGTTATATGTCATCAAAGACCTTCGAGTTCAATTACACTCAGCTCAA
AGGCATATCAAATTTACAA
Found at i:107040 original size:30 final size:30
Alignment explanation
Indices: 106978--107047 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
106968 TTTCAGCCTC
* *
106978 TTAACTTTCTGTTTATACTATTTTAATCCT
1 TTAAATTTCTGTTTATACTATTTTAATACT
* * * **
107008 TTAATTTTCTGTTTGTGCTATTTTGGTACT
1 TTAAATTTCTGTTTATACTATTTTAATACT
107038 TTAAATTTCT
1 TTAAATTTCT
107048 TATTTTATAT
Statistics
Matches: 33, Mismatches: 7, Indels: 0
0.82 0.17 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.20, C:0.13, G:0.09, T:0.59
Consensus pattern (30 bp):
TTAAATTTCTGTTTATACTATTTTAATACT
Found at i:107075 original size:21 final size:21
Alignment explanation
Indices: 107049--107089 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
107039 TAAATTTCTT
107049 ATTTTATATT-TTCTTTTATTC
1 ATTTTAT-TTATTCTTTTATTC
*
107070 ATTTTATTTATTTTTTTATT
1 ATTTTATTTATTCTTTTATT
107090 TTGATCTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 2 0.11
21 16 0.89
ACGTcount: A:0.20, C:0.05, G:0.00, T:0.76
Consensus pattern (21 bp):
ATTTTATTTATTCTTTTATTC
Found at i:109627 original size:85 final size:85
Alignment explanation
Indices: 109455--110039 Score: 762
Period size: 85 Copynumber: 6.9 Consensus size: 85
109445 CTCCCAGCCT
* * * *
109455 ATTTACAGAATAGCTCAAGGCGAGAAGGGCTATCT-TCCAGCAACAAACCTTCGAGTTCTATTAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGT-CAACAA-AAACCTTCGAGTTCGATTAC
109519 ATTCAGCTCAAGGGCATATCAA
64 ATTCAGCTCAAGGGCATATCAA
* ** * *
109541 ATTTACAGCATAACTCAAGGTAAGAAGGGCTATCTGTCAACAAAAACCTTCGATTTTGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
109606 TCCA-CTCAAGGGCATATCAA
66 T-CAGCTCAAGGGCATATCAA
* * * * * *
109626 ATTTACAACATAGCTCAAGACGAGAAGGGTTATTTGTCAACAAAGACCTTTGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
*
109691 TCAGCTCAATGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* * *
109711 ATTTACAGCATAGCTCAAGGTGAGAA-GGCTTATCTGTCAACAAAGACCTTCGAGTTTGATTACA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGC-TATCTGTCAACAAAAACCTTCGAGTTCGATTACA
*
109775 TTCAGCTCAAAGGCATATCAA
65 TTCAGCTCAAGGGCATATCAA
* * * *
109796 ATTTACAGCATAGCTCAAGGCGAGAAGGGTTATCTGTCAACAAATACCTTTGAGTTCGATTACAA
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
* *
109861 TCAACTCAAAGGCATATCAA
66 TCAGCTCAAGGGCATATCAA
* *
109881 ATTTACAGCATAGCTCAAGGTGAGAAGGGCTATCTGTCATCAAAAACCTTCGAGTTCGATTACAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
*
109946 TCAGCTCAAGGACATATCAA
66 TCAGCTCAAGGGCATATCAA
* * * * * * * * *
109966 ATTTACATCATAACTCAAGGAGAGAAGGGTTATGTGTCAATAAATACCTTTGAGTTCGATTTCAT
1 ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
*
110031 TCAACTCAA
66 TCAGCTCAA
110040 TGAGACATCA
Statistics
Matches: 438, Mismatches: 56, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
84 4 0.01
85 393 0.90
86 40 0.09
87 1 0.00
ACGTcount: A:0.35, C:0.20, G:0.18, T:0.27
Consensus pattern (85 bp):
ATTTACAGCATAGCTCAAGGCGAGAAGGGCTATCTGTCAACAAAAACCTTCGAGTTCGATTACAT
TCAGCTCAAGGGCATATCAA
Found at i:110866 original size:38 final size:36
Alignment explanation
Indices: 110815--111090 Score: 374
Period size: 36 Copynumber: 7.5 Consensus size: 36
110805 GTAGTATGAT
*
110815 TTTTGAAAATATATATAATATATAGATTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
110851 TTTTGAAAACT-TATATAATATATAGTTTTTAAAACA
1 TTTTGAAAA-TATATATAATATATAGTTTTTAAAACA
110887 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACA
1 TTTTGAAAATA--TATATAATATATAGTTTTTAAAACA
* *
110925 TTTTAAAAATATATATAATATTTAGTTTTTAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
*
110961 TTTTGAAAAAATATATATAATATATAGTTTTCAAAACA
1 TTTTG--AAAATATATATAATATATAGTTTTTAAAACA
* *
110999 TTTTTAAAATATATATAATATATAGTTTTCAAAACA
1 TTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * * *
111035 TTTTGATTATATATATATAATATATAATTTATGAAACA
1 TTTTGA--AAATATATATAATATATAGTTTTTAAAACA
*
111073 TTTTGAATATATAATATA
1 TTTTGAAAATAT-ATATA
111091 TGAGATATAA
Statistics
Matches: 218, Mismatches: 13, Indels: 17
0.88 0.05 0.07
Matches are distributed among these distances:
35 1 0.00
36 112 0.51
37 6 0.03
38 99 0.45
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (36 bp):
TTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:110905 original size:74 final size:74
Alignment explanation
Indices: 110815--111090 Score: 382
Period size: 74 Copynumber: 3.7 Consensus size: 74
110805 GTAGTATGAT
110815 TTTTG-AAA-ATATATATAATATATAGATTTTAAAACATTTTGAAAACT-TATATAATATATAGT
1 TTTTGAAAATATATATATAATATATAGATTTTAAAACATTTTGAAAA-TATATATAATATATAGT
110877 TTTTAAAACA
65 TTTTAAAACA
* * * *
110887 TTTTGAAAATATGTATATAATATATAGTTTTTAAAACATTTTAAAAATATATATAATATTTAGTT
1 TTTTGAAAATATATATATAATATATAGATTTTAAAACATTTTGAAAATATATATAATATATAGTT
110952 TTTAAAACA
66 TTTAAAACA
* *
110961 TTTTGAAAAAATATATATAATATATAG-TTTTCAAAACATTTTTAAAATATATATAATATATAGT
1 TTTTGAAAATATATATATAATATATAGATTTT-AAAACATTTTGAAAATATATATAATATATAGT
*
111025 TTTCAAAACA
65 TTTTAAAACA
** * *
111035 TTTTGATTATATATATATAATATATA-ATTTATGAAACATTTTGAATATATAATATA
1 TTTTGAAAATATATATATAATATATAGATTT-TAAAACATTTTGAAAATAT-ATATA
111091 TGAGATATAA
Statistics
Matches: 182, Mismatches: 15, Indels: 11
0.88 0.07 0.05
Matches are distributed among these distances:
72 5 0.03
73 8 0.04
74 163 0.90
75 6 0.03
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.45
Consensus pattern (74 bp):
TTTTGAAAATATATATATAATATATAGATTTTAAAACATTTTGAAAATATATATAATATATAGTT
TTTAAAACA
Found at i:111145 original size:15 final size:16
Alignment explanation
Indices: 111125--111158 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
111115 GTATTATATA
111125 TTATATTAATATTT-T
1 TTATATTAATATTTAT
*
111140 TTATATTATTATTTAT
1 TTATATTAATATTTAT
111156 TTA
1 TTA
111159 CTTATTTTTC
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTATATTAATATTTAT
Found at i:112464 original size:24 final size:23
Alignment explanation
Indices: 112437--112522 Score: 59
Period size: 26 Copynumber: 3.5 Consensus size: 23
112427 TTTTTGTTCA
112437 ATTTATCTTTTTTATTCATTTTTT
1 ATTTATCTTTTTTATT-ATTTTTT
112461 ATTTTTATCTTTTTTTATT-TTTTTT
1 A--TTTATC-TTTTTTATTATTTTTT
* *
112486 CTTTGATTTGTTTTTATTTATTTTATT
1 ATTT-ATCT-TTTTTA-TTATTTT-TT
*
112513 -TTTTTCTTTT
1 ATTTATCTTTT
112523 GATTTATTCT
Statistics
Matches: 50, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
23 4 0.08
24 12 0.24
25 10 0.20
26 13 0.26
27 11 0.22
ACGTcount: A:0.13, C:0.06, G:0.02, T:0.79
Consensus pattern (23 bp):
ATTTATCTTTTTTATTATTTTTT
Found at i:112465 original size:16 final size:16
Alignment explanation
Indices: 112445--112482 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
112435 CAATTTATCT
112445 TTTTTATTCATTTTTTA
1 TTTTTA-TCATTTTTTA
*
112462 TTTTTATCTTTTTTTA
1 TTTTTATCATTTTTTA
112478 TTTTT
1 TTTTT
112483 TTTCTTTGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTTTATCATTTTTTA
Found at i:112467 original size:6 final size:6
Alignment explanation
Indices: 112456--112571 Score: 53
Period size: 6 Copynumber: 18.8 Consensus size: 6
112446 TTTTATTCAT
* * *
112456 TTTTTA TTTTTA -TCTT- TTTTTA TTTTTT TTCTTTGA TTTGTTT TTATTTA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TT-TTT-A TTT-TTA TT-TTTA
* * * * *
112506 -TTTTA TTTTT- TTCTTT- TGATTTA TTCTTG TTATTA TTATTA TTTCTTA
1 TTTTTA TTTTTA TT-TTTA T-TTTTA TTTTTA TTTTTA TTTTTA TTT-TTA
112554 TTTTTA TTTTTA TGTTTT
1 TTTTTA TTTTTA T-TTTT
112572 TCTTTGATTT
Statistics
Matches: 85, Mismatches: 13, Indels: 23
0.70 0.11 0.19
Matches are distributed among these distances:
5 12 0.14
6 49 0.58
7 19 0.22
8 5 0.06
ACGTcount: A:0.14, C:0.04, G:0.04, T:0.78
Consensus pattern (6 bp):
TTTTTA
Found at i:112475 original size:10 final size:9
Alignment explanation
Indices: 112438--112517 Score: 56
Period size: 9 Copynumber: 8.2 Consensus size: 9
112428 TTTTGTTCAA
*
112438 TTTATCTTT
1 TTTATTTTT
112447 TTTATTCATTT
1 TTTATT--TTT
112458 TTTATTTTT
1 TTTATTTTT
112467 ATCTT-TTTTT
1 -T-TTATTTTT
112477 ATTT-TTTTT
1 -TTTATTTTT
112486 CTTTGATTTGTT
1 -TTT-ATTT-TT
*
112498 TTTATTTAT
1 TTTATTTTT
112507 TTTATTTTT
1 TTTATTTTT
112516 TT
1 TT
112518 CTTTTGATTT
Statistics
Matches: 60, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
9 29 0.48
10 12 0.20
11 17 0.28
12 2 0.03
ACGTcount: A:0.12, C:0.05, G:0.03, T:0.80
Consensus pattern (9 bp):
TTTATTTTT
Found at i:112510 original size:33 final size:34
Alignment explanation
Indices: 112462--112527 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 34
112452 TCATTTTTTA
*
112462 TTTTTATCTTTTTTTATTTTTTT-TCTTTGATTTG
1 TTTTTATCTTATTTTATTTTTTTCT-TTTGATTTG
112496 TTTTTAT-TTATTTTATTTTTTTCTTTTGATTT
1 TTTTTATCTTATTTTATTTTTTTCTTTTGATTT
112528 ATTCTTGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 22 0.73
34 8 0.27
ACGTcount: A:0.11, C:0.05, G:0.05, T:0.80
Consensus pattern (34 bp):
TTTTTATCTTATTTTATTTTTTTCTTTTGATTTG
Found at i:112539 original size:32 final size:33
Alignment explanation
Indices: 112473--112545 Score: 87
Period size: 33 Copynumber: 2.2 Consensus size: 33
112463 TTTTATCTTT
* * *
112473 TTTTATTTTTTTTCTTTGATTTGTTTTTATTTA
1 TTTTATTTTTTTTCTTTGATTTATTCTTAGTTA
112506 TTTTA-TTTTTTTCTTTTGATTTATTCTT-GTTA
1 TTTTATTTTTTTTC-TTTGATTTATTCTTAGTTA
112538 TTATTATT
1 TT-TTATT
112546 ATTTCTTATT
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
32 13 0.38
33 20 0.59
34 1 0.03
ACGTcount: A:0.14, C:0.04, G:0.05, T:0.77
Consensus pattern (33 bp):
TTTTATTTTTTTTCTTTGATTTATTCTTAGTTA
Found at i:112599 original size:54 final size:53
Alignment explanation
Indices: 112502--112607 Score: 119
Period size: 54 Copynumber: 2.0 Consensus size: 53
112492 TTTGTTTTTA
* **
112502 TTTATTTTATTTTTTTCTTTTGATTTATTCTTGTTATTATTATTATTTCTTATT
1 TTTATTTTATGTTTTTCTTTTGATTTATTCTAATTATTATTATTATTT-TTATT
*
112556 TTTATTTTTATGTTTTTC-TTTGATTTATT-TAA-TATTTATTTATTGTTTTTAT
1 TTTA-TTTTATGTTTTTCTTTTGATTTATTCTAATTA-TTA-TTATTATTTTTAT
112608 CTAACATTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
52 2 0.04
53 8 0.18
54 23 0.51
55 12 0.27
ACGTcount: A:0.18, C:0.04, G:0.05, T:0.74
Consensus pattern (53 bp):
TTTATTTTATGTTTTTCTTTTGATTTATTCTAATTATTATTATTATTTTTATT
Found at i:139402 original size:14 final size:14
Alignment explanation
Indices: 139383--139423 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
139373 TTTCTGTCTA
139383 TATGCAGAGATTAT
1 TATGCAGAGATTAT
139397 TATGCAGAGATTTAT
1 TATGCAGAGA-TTAT
*
139412 TA-GCAGGGATTA
1 TATGCAGAGATTA
139424 CTTCCCATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 3 0.12
14 16 0.64
15 6 0.24
ACGTcount: A:0.34, C:0.07, G:0.24, T:0.34
Consensus pattern (14 bp):
TATGCAGAGATTAT
Found at i:140556 original size:31 final size:29
Alignment explanation
Indices: 140488--140557 Score: 79
Period size: 29 Copynumber: 2.4 Consensus size: 29
140478 TTAAAAAATA
* *
140488 TATT-TAAAAAATAACTTAAAATTATTAT
1 TATTCTAAAAAAAAACTTAAAATAATTAT
* *
140516 TATTTTAAAAAAAAACTTAAAATAATTTT
1 TATTCTAAAAAAAAACTTAAAATAATTAT
140545 TAAATTCTAAAAA
1 T--ATTCTAAAAA
140558 TACTCCAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
28 4 0.11
29 22 0.63
31 9 0.26
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (29 bp):
TATTCTAAAAAAAAACTTAAAATAATTAT
Found at i:140861 original size:2 final size:2
Alignment explanation
Indices: 140856--140912 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
140846 ATATGAAGAA
140856 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
140898 AT AT AT AT AT -T AT AT
1 AT AT AT AT AT AT AT AT
140913 GATTAGAGAA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:142563 original size:24 final size:23
Alignment explanation
Indices: 142512--142559 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
142502 TAATTTAATT
142512 AATAATTTTACTTTTTATTAAAA
1 AATAATTTTACTTTTTATTAAAA
142535 AATAATTTTACTTTTTATTAAAA
1 AATAATTTTACTTTTTATTAAAA
142558 AA
1 AA
142560 ATAAAATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (23 bp):
AATAATTTTACTTTTTATTAAAA
Found at i:143132 original size:23 final size:23
Alignment explanation
Indices: 143098--143165 Score: 86
Period size: 23 Copynumber: 3.0 Consensus size: 23
143088 CCAAACAACC
143098 GAAAAT-GTGTCATAAAGGCAAA
1 GAAAATAGTGTCATAAAGGCAAA
*
143120 GAAAATAGTGTCATAAAGGAAGAA
1 GAAAATAGTGTCATAAAGGCA-AA
* *
143144 GAATATA-TGTCAAAAAGGCAAA
1 GAAAATAGTGTCATAAAGGCAAA
143166 ATTATTAAGA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
22 8 0.20
23 24 0.60
24 8 0.20
ACGTcount: A:0.53, C:0.07, G:0.22, T:0.18
Consensus pattern (23 bp):
GAAAATAGTGTCATAAAGGCAAA
Found at i:146153 original size:2 final size:2
Alignment explanation
Indices: 146146--146181 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
146136 TGGTAATAAT
146146 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
146182 GTTTGAATGG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:148039 original size:22 final size:22
Alignment explanation
Indices: 148011--148083 Score: 101
Period size: 22 Copynumber: 3.3 Consensus size: 22
148001 AGTCGAGGGT
*
148011 TTCATAGGTCATTCGGGATATA
1 TTCATAGGTCATTCGGGACATA
*
148033 TTCATAGGTCCTTCGGGACATA
1 TTCATAGGTCATTCGGGACATA
**
148055 TTCATAGGTTTTTCGGGACATA
1 TTCATAGGTCATTCGGGACATA
148077 TTTCATA
1 -TTCATA
148084 TGCCACTCAG
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
22 40 0.87
23 6 0.13
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (22 bp):
TTCATAGGTCATTCGGGACATA
Found at i:153241 original size:22 final size:22
Alignment explanation
Indices: 153213--153285 Score: 110
Period size: 22 Copynumber: 3.3 Consensus size: 22
153203 AGTCGAGGGT
*
153213 TTCATAGGTCCTTCGGGATATA
1 TTCATAGGTCCTTCGGGACATA
*
153235 TTCATAGGTCATTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
*
153257 ATCATAGGTCCTTCGGGACATA
1 TTCATAGGTCCTTCGGGACATA
153279 TTTCATA
1 -TTCATA
153286 TGCCACTCAG
Statistics
Matches: 45, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
22 40 0.89
23 5 0.11
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (22 bp):
TTCATAGGTCCTTCGGGACATA
Done.