Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002365.1 Hibiscus syriacus cultivar Beakdansim tig00004834_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: 166549
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.34
Found at i:3584 original size:2 final size:2
Alignment explanation
Indices: 3577--3610 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
3567 CAAACGATCC
3577 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
3611 TCTTTCCAGT
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):
AT
Found at i:5123 original size:12 final size:12
Alignment explanation
Indices: 5106--5147 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
5096 ATTATACGGT
5106 ATGAACAGTACC
1 ATGAACAGTACC
*
5118 ATGAACAATA--
1 ATGAACAGTACC
5128 ATGAACAGTACC
1 ATGAACAGTACC
*
5140 GTGAACAG
1 ATGAACAG
5148 AGAAATATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
10 9 0.36
12 16 0.64
ACGTcount: A:0.45, C:0.19, G:0.19, T:0.17
Consensus pattern (12 bp):
ATGAACAGTACC
Found at i:5215 original size:21 final size:19
Alignment explanation
Indices: 5187--5228 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 19
5177 AATGCACTAC
5187 TACAAT-AACTTTCGTAAAAA
1 TACAATAAAC-TT-GTAAAAA
5207 TACATATAAACTTGTAAAAA
1 TACA-ATAAACTTGTAAAAA
5227 TA
1 TA
5229 TAAACTTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 13 0.65
21 4 0.20
22 3 0.15
ACGTcount: A:0.52, C:0.12, G:0.05, T:0.31
Consensus pattern (19 bp):
TACAATAAACTTGTAAAAA
Found at i:7191 original size:23 final size:23
Alignment explanation
Indices: 7157--7223 Score: 82
Period size: 23 Copynumber: 2.9 Consensus size: 23
7147 CACCACAGCT
* *
7157 CGTATAAATGCACCGAAGTG-TCA
1 CGTAGAAATGCACCGTAGTGCT-A
* *
7180 CGTAGAATTGCACCGTAGTGCTG
1 CGTAGAAATGCACCGTAGTGCTA
7203 CGTAGAAATGCACCGTAGTGC
1 CGTAGAAATGCACCGTAGTGC
7224 CATATAATAT
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
23 37 0.97
24 1 0.03
ACGTcount: A:0.28, C:0.22, G:0.27, T:0.22
Consensus pattern (23 bp):
CGTAGAAATGCACCGTAGTGCTA
Found at i:8331 original size:16 final size:17
Alignment explanation
Indices: 8312--8348 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
8302 CTTACATCAT
8312 ATATCAA-ATACAAAAC
1 ATATCAACATACAAAAC
*
8328 ATATCAACATACAACAC
1 ATATCAACATACAAAAC
8345 ATAT
1 ATAT
8349 ACTCATATAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 7 0.37
17 12 0.63
ACGTcount: A:0.57, C:0.22, G:0.00, T:0.22
Consensus pattern (17 bp):
ATATCAACATACAAAAC
Found at i:12221 original size:5 final size:5
Alignment explanation
Indices: 12213--12241 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
12203 TTCACTTCAT
12213 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
12242 CATATCATTC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:15097 original size:31 final size:32
Alignment explanation
Indices: 15050--15131 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
15040 TCTTCCAATT
* *
15050 ATTATAAAATAATCATTAACCTTT-TCAAATG
1 ATTACAAAATAATCATTAACATTTATCAAATG
* *
15081 ATTACAAAATAGTCATTAACATTTATCAAATT
1 ATTACAAAATAATCATTAACATTTATCAAATG
* *
15113 ATTACAAAATTATCTTTAA
1 ATTACAAAATAATCATTAA
15132 ACATATCAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
31 21 0.49
32 22 0.51
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (32 bp):
ATTACAAAATAATCATTAACATTTATCAAATG
Found at i:15117 original size:32 final size:31
Alignment explanation
Indices: 15046--15162 Score: 112
Period size: 31 Copynumber: 3.7 Consensus size: 31
15036 ACAATCTTCC
* *
15046 AATTATTATAAAATAATCATTAACCTTTTCA
1 AATTATTACAAAATAATCATTAACATTTTCA
* *
15077 AATGATTACAAAATAGTCATTAACATTTATCA
1 AATTATTACAAAATAATCATTAACATTT-TCA
* * *
15109 AATTATTACAAAATTATCTTTAAACA-TATCA
1 AATTATTACAAAATAATCATT-AACATTTTCA
* *
15140 AACTT-TTACAAAACAATCCTTAA
1 AA-TTATTACAAAATAATCATTAA
15163 GTTGGTCTAA
Statistics
Matches: 71, Mismatches: 12, Indels: 7
0.79 0.13 0.08
Matches are distributed among these distances:
30 2 0.03
31 42 0.59
32 23 0.32
33 4 0.06
ACGTcount: A:0.47, C:0.15, G:0.02, T:0.37
Consensus pattern (31 bp):
AATTATTACAAAATAATCATTAACATTTTCA
Found at i:16016 original size:2 final size:2
Alignment explanation
Indices: 16009--16045 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
15999 TCTTTCTTAA
16009 AT AT 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 AT AT A
16046 GTTTAGTTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:21704 original size:2 final size:2
Alignment explanation
Indices: 21699--21768 Score: 140
Period size: 2 Copynumber: 35.0 Consensus size: 2
21689 ACACACACAA
21699 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
21741 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
21769 TTAATGAAAA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 68 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24520 original size:29 final size:30
Alignment explanation
Indices: 24469--24525 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
24459 ATTTAAGGCA
24469 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
*
24499 AAAATGTTTTTGGA-TTTAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
24526 ATTTAAAGTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.04, G:0.18, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:24632 original size:21 final size:21
Alignment explanation
Indices: 24606--24655 Score: 82
Period size: 21 Copynumber: 2.4 Consensus size: 21
24596 AGGATGTCAA
24606 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCACCCCTGC
* *
24627 AGTGCATCCATGCATCCTTGC
1 AGTGCATCCATGCACCCCTGC
24648 AGTGCATC
1 AGTGCATC
24656 TGCACTAATG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.20, C:0.36, G:0.20, T:0.24
Consensus pattern (21 bp):
AGTGCATCCATGCACCCCTGC
Found at i:24687 original size:20 final size:20
Alignment explanation
Indices: 24662--24812 Score: 93
Period size: 20 Copynumber: 7.8 Consensus size: 20
24652 CATCTGCACT
24662 AATGCATCGATGCATCATGC
1 AATGCATCGATGCATCATGC
*
24682 AATGCATCCATGCATC---C
1 AATGCATCGATGCATCATGC
* *
24699 AA-ACATCGAATGCA--AT-T
1 AATGCATCG-ATGCATCATGC
* * *
24716 AGTGCATCTATGCATCTTGC
1 AATGCATCGATGCATCATGC
* *
24736 TATGCATCGATGCATCCTTGC
1 AATGCATCGATGCAT-CATGC
* *
24757 TATGCATCGATGCTTC-TGC
1 AATGCATCGATGCATCATGC
* * *
24776 GATGCATCCATGCATCCTGC
1 AATGCATCGATGCATCATGC
* *
24796 GATGCATCCATGCATCA
1 AATGCATCGATGCATCA
24813 AGGCTGCAAC
Statistics
Matches: 105, Mismatches: 17, Indels: 18
0.75 0.12 0.13
Matches are distributed among these distances:
16 4 0.04
17 14 0.13
18 4 0.04
19 17 0.16
20 47 0.45
21 19 0.18
ACGTcount: A:0.26, C:0.28, G:0.18, T:0.28
Consensus pattern (20 bp):
AATGCATCGATGCATCATGC
Found at i:26462 original size:29 final size:30
Alignment explanation
Indices: 26394--26450 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
26384 ATTTAAGGCA
26394 AAAATGTTTTTGGACTTGAATTGAATTTGC
1 AAAATGTTTTTGGACTTGAATTGAATTTGC
26424 AAAATGTTTTTGGACTT-AATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
26451 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
29 10 0.37
30 17 0.63
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.46
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGC
Found at i:26587 original size:21 final size:21
Alignment explanation
Indices: 26531--26588 Score: 107
Period size: 21 Copynumber: 2.8 Consensus size: 21
26521 AGGGTGTCAA
*
26531 AGTGCATCCATGCACCCCTGC
1 AGTGCATCCATGCATCCCTGC
26552 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
26573 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
26589 TGCACTAATG
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 36 1.00
ACGTcount: A:0.21, C:0.38, G:0.19, T:0.22
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:28165 original size:20 final size:19
Alignment explanation
Indices: 28126--28177 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
28116 TTTCTTTGAT
28126 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
28145 ATTAAAATAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
28165 ATTTATAAAATAA
1 A-TTAAAAAATAA
28178 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:28278 original size:120 final size:120
Alignment explanation
Indices: 28030--28294 Score: 285
Period size: 120 Copynumber: 2.2 Consensus size: 120
28020 TATGAAAAAT
* * *
28030 ATATATTAATTTATATATTTAT-AAATAAAATATTTATTTATTTAGAAATATCAGAAAAGGACTT
1 ATATATTAATATATA-ATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACAT
* * * * * *
28094 CTAGGTGCCTTAAGACAATTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAA
65 CCAGGTACCTTAAGAC-ATCCCTTTCTCTAATATTAAAAAATAAATAAATAATTAAA
*
28151 ATA-ATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACAT
1 ATATATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAA-GGACAT
* ** **
28215 CCAGTTATTTTAAGAC-TGCCCTTTC-CTAATATTGGAAAATAAATAAAT-ATTAAA
65 CCAGGTACCTTAAGACAT-CCCTTTCTCTAATATTAAAAAATAAATAAATAATTAAA
*
28269 ATATGATTAA-A-ATAAGTTA-AAAATAA
1 ATAT-ATTAATATATAATTTATAAAATAA
28295 TTAGCTAAGA
Statistics
Matches: 123, Mismatches: 16, Indels: 14
0.80 0.10 0.09
Matches are distributed among these distances:
117 7 0.06
118 16 0.13
119 27 0.22
120 54 0.44
121 19 0.15
ACGTcount: A:0.48, C:0.07, G:0.08, T:0.38
Consensus pattern (120 bp):
ATATATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAGGACATC
CAGGTACCTTAAGACATCCCTTTCTCTAATATTAAAAAATAAATAAATAATTAAA
Found at i:29680 original size:3 final size:3
Alignment explanation
Indices: 29662--29732 Score: 88
Period size: 3 Copynumber: 22.7 Consensus size: 3
29652 TTTGGGCCTG
* *
29662 TAA TATA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA TAA AAA TAAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA
*
29710 TAA TAA TAA AAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TA
29733 TAAAAAAACC
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
3 50 0.85
4 9 0.15
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
TAA
Found at i:29709 original size:34 final size:33
Alignment explanation
Indices: 29662--29738 Score: 111
Period size: 34 Copynumber: 2.3 Consensus size: 33
29652 TTTGGGCCTG
* **
29662 TAATAT-ATAATAAATAATAATATTAATAATAA
1 TAATATAAAAATAAATAATAATAAAAATAATAA
29694 TAATAATAAAAATAAATAATAATAAAAATAATAA
1 TAAT-ATAAAAATAAATAATAATAAAAATAATAA
29728 TAATATAAAAA
1 TAATATAAAAA
29739 AACCAAATGT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
32 4 0.10
33 9 0.22
34 27 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (33 bp):
TAATATAAAAATAAATAATAATAAAAATAATAA
Found at i:29739 original size:34 final size:34
Alignment explanation
Indices: 29670--29738 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
29660 TGTAATATAT
**
29670 AATAAATAATAATATTAATAATAATAATAATAAA
1 AATAAATAATAATAAAAATAATAATAATAATAAA
29704 AATAAATAATAATAAAAATAATAATAAT-ATAAA
1 AATAAATAATAATAAAAATAATAATAATAATAAA
29737 AA
1 AA
29739 AACCAAATGT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 7 0.21
34 26 0.79
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (34 bp):
AATAAATAATAATAAAAATAATAATAATAATAAA
Found at i:30183 original size:113 final size:113
Alignment explanation
Indices: 30000--30665 Score: 1027
Period size: 113 Copynumber: 5.9 Consensus size: 113
29990 AGAATCATGC
*
30000 AAAAGATTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTTAGATGAGTTCTTCTCAT
1 AAAAG-TTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCAT
* * * * * * *
30065 TATGAACTC-TCTCTGGAAAAGTTGATCCATCGAGTGATGAATTCGAGCA
65 TATGAACTCGAC-CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
* * *
30114 AAAAGTTGAACAAATTCTTCTCATTATGAACTTATTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
30179 ATGAACTCG-CTCTGGCAATGCTGATCCATCAAATGATGAATTCAAGCG
66 ATGAACTCGAC-CTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
* **
30227 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTATTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
30292 ATGAACTCGACCTGGCAATGCTGATCCATTGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
30340 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTATTCTTCTTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
*
30405 ATGAACTCGACCTGGCAATGCTGATCCATTGAATGATGAATTCAAGCG
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
30453 AAAAGTTGAACAAGTTCTTCTCATTATGAA---CTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
30515 ATGAACTCGACCTGGCAATACTGATCTATCGAATGATGAATTCAAGCA
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
* *
30563 AAAATTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAAATGAGTTCTTCTCATT
1 AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
* * *
30628 ATGAACTTGACCTGGCAATGTTGATCAATCGAATGATG
66 ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATG
30666 GATTTGAATC
Statistics
Matches: 515, Mismatches: 32, Indels: 11
0.92 0.06 0.02
Matches are distributed among these distances:
110 103 0.20
113 406 0.79
114 6 0.01
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.37
Consensus pattern (113 bp):
AAAAGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTTCTTCAGATGAGTTCTTCTCATT
ATGAACTCGACCTGGCAATGCTGATCCATCGAATGATGAATTCAAGCG
Found at i:31107 original size:22 final size:22
Alignment explanation
Indices: 31076--31124 Score: 89
Period size: 22 Copynumber: 2.2 Consensus size: 22
31066 AAAGCTTTCG
*
31076 TCTTTGAAAAGAGAATCTATCA
1 TCTTTAAAAAGAGAATCTATCA
31098 TCTTTAAAAAGAGAATCTATCA
1 TCTTTAAAAAGAGAATCTATCA
31120 TCTTT
1 TCTTT
31125 GAAGAGTGTA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.39, C:0.14, G:0.10, T:0.37
Consensus pattern (22 bp):
TCTTTAAAAAGAGAATCTATCA
Found at i:31690 original size:54 final size:54
Alignment explanation
Indices: 31494--31676 Score: 276
Period size: 54 Copynumber: 3.4 Consensus size: 54
31484 CGTAAAACAT
* * * ***
31494 TTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGATGTTTACAAAGTTT
1 TTGACAACACATTCATCCTTTCCTGTAGCTTCTGCTCAGATGTTTGCAAAGCAC
* * *
31548 TTGACAATACATTCATCCTTTCCTGTAGCTTTTTCTCAGATGTTTGCAAAGCAC
1 TTGACAACACATTCATCCTTTCCTGTAGCTTCTGCTCAGATGTTTGCAAAGCAC
31602 TTGACAACACATTCATCCTTTCCTGTAGCTTCTGCTCAGATGTTTGCAAAGCAC
1 TTGACAACACATTCATCCTTTCCTGTAGCTTCTGCTCAGATGTTTGCAAAGCAC
*
31656 TTGACAACACCTTCATCCTTT
1 TTGACAACACATTCATCCTTT
31677 TATGTGTCTT
Statistics
Matches: 116, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
54 116 1.00
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (54 bp):
TTGACAACACATTCATCCTTTCCTGTAGCTTCTGCTCAGATGTTTGCAAAGCAC
Found at i:32797 original size:36 final size:35
Alignment explanation
Indices: 32757--32825 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 35
32747 CAACATTTCT
32757 TATTGAGATGAGCCTTCAAAAATGC-CCAAATATTTA
1 TATTGAGATGAGCCTTC-AAAATGCTCC-AATATTTA
***
32793 TATTGTTCTGAGCCTTCAAAATGCTCCAATATT
1 TATTGAGATGAGCCTTCAAAATGCTCCAATATT
32826 CTATTTCTGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.33, C:0.19, G:0.13, T:0.35
Consensus pattern (35 bp):
TATTGAGATGAGCCTTCAAAATGCTCCAATATTTA
Found at i:33946 original size:114 final size:114
Alignment explanation
Indices: 33746--33969 Score: 342
Period size: 114 Copynumber: 2.0 Consensus size: 114
33736 GATCATGCAG
* * * *
33746 TTCATCTTTCAATTCCACTGATTGGTTCTGGGGTTCTTACCGAACCAGATCAGATAATTCAAAGA
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAATTCAAAGA
*
33811 ACACTTCCAGAAGATGCTATTGGGTTTCCTTATTTCTACTATGAGCAAA
66 ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
* * *
33860 TTCATCTTTCAAATCCAATGATTGGTTTTGGGGTTCATACCAAATCGGATCAGATAACTT-AAAG
1 TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAA-TTCAAAG
* *
33924 AATACTTCCAGAAGATGTTATTGGGTCTCCTTATTTCTACTATGAG
65 AACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAG
33970 AACGTGGCAC
Statistics
Matches: 99, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
114 97 0.98
115 2 0.02
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (114 bp):
TTCATCTTTCAAATCCAATGATTGGTTCTGGGGTTCATACCAAACCAGATCAGATAATTCAAAGA
ACACTTCCAGAAGATGCTATTGGGTCTCCTTATTTCTACTATGAGCAAA
Found at i:36047 original size:7 final size:6
Alignment explanation
Indices: 36032--36128 Score: 53
Period size: 6 Copynumber: 16.5 Consensus size: 6
36022 ATTTCTCCTA
* * *
36032 TTTTTC TTTTTC CTTTTC TCTTTT- TTTTTC TCTTT- TTTTTC -ATTT-
1 TTTTTC TTTTTC TTTTTC T-TTTTC TTTTTC TTTTTC TTTTTC TTTTTC
* * * *
36077 TTTTTC TTTCTC ATTTTTTC TTTTTC ATCTTT- TTTTTC ATCTT- TTTTTC
1 TTTTTC TTTTTC --TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
36126 TTT
1 TTT
36129 CTTTGCTGGA
Statistics
Matches: 67, Mismatches: 14, Indels: 20
0.66 0.14 0.20
Matches are distributed among these distances:
5 21 0.31
6 33 0.49
7 8 0.12
8 5 0.07
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (6 bp):
TTTTTC
Found at i:36058 original size:23 final size:22
Alignment explanation
Indices: 36023--36128 Score: 69
Period size: 23 Copynumber: 4.8 Consensus size: 22
36013 CTTGATTCAA
* *
36023 TTTCTCCTATTTTTCTTTTTCCT
1 TTTCTCTTTTTTTTCTTTTT-CT
36046 TTTCTCTTTTTTTTTCTCTTTT-T
1 TTTCTC-TTTTTTTTCT-TTTTCT
* *
36069 TTTC-ATTTTTTTTCTTTCTCAT
1 TTTCTCTTTTTTTTCTTTTTC-T
* **
36091 TTTTTCTTTTTCATC-TTTT-T
1 TTTCTCTTTTTTTTCTTTTTCT
36111 TTTCATC-TTTTTTTCTTT
1 TTTC-TCTTTTTTTTCTTT
36129 CTTTGCTGGA
Statistics
Matches: 64, Mismatches: 12, Indels: 16
0.70 0.13 0.17
Matches are distributed among these distances:
20 13 0.20
21 14 0.22
22 7 0.11
23 18 0.28
24 8 0.12
25 4 0.06
ACGTcount: A:0.05, C:0.19, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTCTCTTTTTTTTCTTTTTCT
Found at i:36060 original size:12 final size:12
Alignment explanation
Indices: 36032--36124 Score: 73
Period size: 14 Copynumber: 7.2 Consensus size: 12
36022 ATTTCTCCTA
36032 TTTTTCT-TTTT
1 TTTTTCTCTTTT
*
36043 CCTTTTCTCTTTT
1 -TTTTTCTCTTTT
36056 TTTTTCTC-TTT
1 TTTTTCTCTTTT
*
36067 TTTTTCATTTTTT
1 TTTTTC-TCTTTT
36080 TTCTTTCTCATTTT
1 TT-TTTCTC-TTTT
*
36094 TTCTTTTTCATCTTT
1 TT-TTTCTC-T-TTT
36109 TTTTTCATCTTTT
1 TTTTTC-TCTTTT
36122 TTT
1 TTT
36125 CTTTCTTTGC
Statistics
Matches: 68, Mismatches: 6, Indels: 13
0.78 0.07 0.15
Matches are distributed among these distances:
11 9 0.13
12 14 0.21
13 16 0.24
14 22 0.32
15 7 0.10
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.78
Consensus pattern (12 bp):
TTTTTCTCTTTT
Found at i:36071 original size:16 final size:16
Alignment explanation
Indices: 36064--36113 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
36054 TTTTTTTCTC
36064 TTTTTTT-TCATTTTT
1 TTTTTTTCTCATTTTT
*
36079 TTTCTTTCTCATTTTT
1 TTTTTTTCTCATTTTT
*
36095 TCTTTTTCATC-TTTTT
1 TTTTTTTC-TCATTTTT
36111 TTT
1 TTT
36114 CATCTTTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
15 6 0.21
16 21 0.72
17 2 0.07
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTTCTCATTTTT
Found at i:36071 original size:35 final size:39
Alignment explanation
Indices: 36023--36114 Score: 93
Period size: 35 Copynumber: 2.4 Consensus size: 39
36013 CTTGATTCAA
* *
36023 TTTCTCCTATTTTTC-TTTTTCCTTT-TC-TCTTTT-TT
1 TTTCTCTTTTTTTTCTTTTTTCCTTTCTCATCTTTTCTT
* *
36058 TTTCTCTTTTTTTTCATTTTTTTTCTTTCTCATTTTTTCTT
1 TTTCTCTTTTTTTTC--TTTTTTCCTTTCTCATCTTTTCTT
36099 TTTCATCTTTTTTTTC
1 TTTC-TCTTTTTTTTC
36115 ATCTTTTTTT
Statistics
Matches: 46, Mismatches: 4, Indels: 7
0.81 0.07 0.12
Matches are distributed among these distances:
35 13 0.28
38 9 0.20
39 2 0.04
40 5 0.11
41 6 0.13
42 11 0.24
ACGTcount: A:0.04, C:0.20, G:0.00, T:0.76
Consensus pattern (39 bp):
TTTCTCTTTTTTTTCTTTTTTCCTTTCTCATCTTTTCTT
Found at i:36111 original size:43 final size:41
Alignment explanation
Indices: 36052--36130 Score: 133
Period size: 42 Copynumber: 1.9 Consensus size: 41
36042 TCCTTTTCTC
36052 TTTTTTTTTCTCTTTTTTTTCAT-TTTTTTTCTTTCTCATT
1 TTTTTTTTTCTCTTTTTTTTCATCTTTTTTTCTTTCTCATT
36092 TTTTCTTTTTCATCTTTTTTTTCATCTTTTTTTCTTTCT
1 TTTT-TTTTTC-TCTTTTTTTTCATCTTTTTTTCTTTCT
36131 TTGCTGGATG
Statistics
Matches: 36, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
40 4 0.11
41 6 0.17
42 13 0.36
43 13 0.36
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (41 bp):
TTTTTTTTTCTCTTTTTTTTCATCTTTTTTTCTTTCTCATT
Found at i:36125 original size:11 final size:12
Alignment explanation
Indices: 36053--36124 Score: 65
Period size: 12 Copynumber: 5.6 Consensus size: 12
36043 CCTTTTCTCT
36053 TTTTTTTTC-TC
1 TTTTTTTTCATC
*
36064 TTTTTTTTCATTTT
1 TTTTTTTTCA--TC
*
36078 TTTTCTTTCTCATTT
1 TTTT-TTT-TCA-TC
36093 TTTCTTTTTCATC
1 TTT-TTTTTCATC
36106 TTTTTTTTCATC
1 TTTTTTTTCATC
36118 TTTTTTT
1 TTTTTTT
36125 CTTTCTTTGC
Statistics
Matches: 53, Mismatches: 2, Indels: 11
0.80 0.03 0.17
Matches are distributed among these distances:
11 9 0.17
12 16 0.30
13 4 0.08
14 8 0.15
15 12 0.23
16 4 0.08
ACGTcount: A:0.06, C:0.15, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTTTTTTCATC
Found at i:36125 original size:29 final size:30
Alignment explanation
Indices: 36067--36128 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
36057 TTTTCTCTTT
*
36067 TTTTTCATTTTTTTTCTTTCTCATTTTTTC
1 TTTTTCATTCTTTTTCTTTCTCATTTTTTC
*
36097 TTTTTCA-TCTTTTT-TTTCATCTTTTTTTC
1 TTTTTCATTCTTTTTCTTTC-TCATTTTTTC
36126 TTT
1 TTT
36129 CTTTGCTGGA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
28 4 0.14
29 18 0.62
30 7 0.24
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.77
Consensus pattern (30 bp):
TTTTTCATTCTTTTTCTTTCTCATTTTTTC
Found at i:36131 original size:12 final size:11
Alignment explanation
Indices: 36032--36132 Score: 64
Period size: 12 Copynumber: 8.8 Consensus size: 11
36022 ATTTCTCCTA
36032 TTTTTCTTTTT
1 TTTTTCTTTTT
*
36043 CCTTTTCTCTTTT
1 -TTTTTCT-TTTT
*
36056 TTTTTCTCTTT
1 TTTTTCTTTTT
*
36067 TTTTTC-ATTT
1 TTTTTCTTTTT
36077 TTTTTCTTTCTCAT
1 TTTTTCTTT-T--T
36091 TTTTTC--TTT
1 TTTTTCTTTTT
**
36100 TTCATCTTTTT
1 TTTTTCTTTTT
*
36111 TTTCATCTTTTT
1 TTT-TTCTTTTT
36123 TTCTTTCTTT
1 TT-TTTCTTT
36133 GCTGGATGGG
Statistics
Matches: 71, Mismatches: 9, Indels: 18
0.72 0.09 0.18
Matches are distributed among these distances:
9 5 0.07
10 9 0.13
11 16 0.23
12 29 0.41
13 5 0.07
14 7 0.10
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:36183 original size:7 final size:7
Alignment explanation
Indices: 36171--36229 Score: 55
Period size: 7 Copynumber: 7.4 Consensus size: 7
36161 TTGAATATCT
36171 CTTTTTC
1 CTTTTTC
36178 CTTTTTTGTC
1 C--TTTT-TC
36188 CTTTTTC
1 CTTTTTC
36195 CTTCTTGTC
1 CTT-TT-TC
36204 CTTTTTC
1 CTTTTTC
36211 CTTCTTGTC
1 CTT-TT-TC
36220 CTTTTTC
1 CTTTTTC
36227 CTT
1 CTT
36230 CTTCAAGTAT
Statistics
Matches: 45, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
7 16 0.36
8 12 0.27
9 14 0.31
10 3 0.07
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.66
Consensus pattern (7 bp):
CTTTTTC
Found at i:36202 original size:16 final size:16
Alignment explanation
Indices: 36171--36232 Score: 106
Period size: 16 Copynumber: 3.8 Consensus size: 16
36161 TTGAATATCT
*
36171 CTTTTTCCTTTTTTGTC
1 CTTTTTCC-TTCTTGTC
36188 CTTTTTCCTTCTTGTC
1 CTTTTTCCTTCTTGTC
36204 CTTTTTCCTTCTTGTC
1 CTTTTTCCTTCTTGTC
36220 CTTTTTCCTTCTT
1 CTTTTTCCTTCTT
36233 CAAGTATAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
16 36 0.82
17 8 0.18
ACGTcount: A:0.00, C:0.29, G:0.05, T:0.66
Consensus pattern (16 bp):
CTTTTTCCTTCTTGTC
Found at i:38941 original size:14 final size:14
Alignment explanation
Indices: 38922--39003 Score: 73
Period size: 14 Copynumber: 6.1 Consensus size: 14
38912 AAATGTAATT
*
38922 ATGTAAAAATGAAA
1 ATGTAAAAATGCAA
*
38936 ATGT--AAATACAA
1 ATGTAAAAATGCAA
*
38948 ACGTAAAAATGCAA
1 ATGTAAAAATGCAA
38962 ATGT--AAATGCAA
1 ATGTAAAAATGCAA
* **
38974 ATGTAAATATGTGA
1 ATGTAAAAATGCAA
*
38988 ATGTAACAATGCAA
1 ATGTAAAAATGCAA
39002 AT
1 AT
39004 TGTATAGTAC
Statistics
Matches: 52, Mismatches: 12, Indels: 8
0.72 0.17 0.11
Matches are distributed among these distances:
12 21 0.40
14 31 0.60
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (14 bp):
ATGTAAAAATGCAA
Found at i:38953 original size:12 final size:12
Alignment explanation
Indices: 38934--38982 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
38924 GTAAAAATGA
38934 AAATGTAAATAC
1 AAATGTAAATAC
* *
38946 AAACGTAAAAATGC
1 AAATGT--AAATAC
*
38960 AAATGTAAATGC
1 AAATGTAAATAC
38972 AAATGTAAATA
1 AAATGTAAATA
38983 TGTGAATGTA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.57, C:0.08, G:0.12, T:0.22
Consensus pattern (12 bp):
AAATGTAAATAC
Found at i:38990 original size:26 final size:26
Alignment explanation
Indices: 38922--39003 Score: 92
Period size: 26 Copynumber: 3.1 Consensus size: 26
38912 AAATGTAATT
* *
38922 ATGTAAAAATGAAAATGTAAATACAA
1 ATGTAAAAATGCAAATGTAAATGCAA
*
38948 ACGTAAAAATGCAAATGTAAATGCAA
1 ATGTAAAAATGCAAATGTAAATGCAA
* **
38974 ATGTAAATATGTGAATGTAACAATGCAA
1 ATGTAAAAATGCAAATGT-A-AATGCAA
39002 AT
1 AT
39004 TGTATAGTAC
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
26 37 0.79
27 1 0.02
28 9 0.19
ACGTcount: A:0.54, C:0.07, G:0.15, T:0.24
Consensus pattern (26 bp):
ATGTAAAAATGCAAATGTAAATGCAA
Found at i:39065 original size:15 final size:15
Alignment explanation
Indices: 39042--39071 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39032 ATAAATGCAC
39042 AATGAAAAATGCAAA
1 AATGAAAAATGCAAA
*
39057 AATGCAAAATGCAAA
1 AATGAAAAATGCAAA
39072 TGTATGTATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.63, C:0.10, G:0.13, T:0.13
Consensus pattern (15 bp):
AATGAAAAATGCAAA
Found at i:41231 original size:20 final size:19
Alignment explanation
Indices: 41192--41243 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
41182 TTTCTTTGAT
41192 ATTAAAAAATAAATAAATA
1 ATTAAAAAATAAATAAATA
* *
41211 ATTAAAACAATTAATATATA
1 ATTAAAA-AATAAATAAATA
*
41231 ATTTATAAAATAA
1 A-TTAAAAAATAA
41244 GATATTTATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 7 0.26
20 15 0.56
21 5 0.19
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAAAAATAAATAAATA
Found at i:41344 original size:120 final size:121
Alignment explanation
Indices: 41096--41360 Score: 276
Period size: 120 Copynumber: 2.2 Consensus size: 121
41086 TATGAAAAAT
* * * *
41096 ATATATTAATTTAT-ATTTTTATAAATAAAATATTTATTTATTTAGAAATATCAGAAAATGACTT
1 ATATATTAATATATAATTTATA-AAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACAT
* * * * *
41160 CTAGGTGCCTTAAGACAACTCTTTTCTTTGATATTAAAAAATAAATAAATAATTAAA
65 CCAGGTACCTTAAGACAACTCCTTTCTCTAATATTAAAAAATAAATAAATAATTAAA
* *
41217 ACA-ATTAATATATAATTTATAAAATAAGATATTTATTTATTTAAAAATATCAGAAAATGGACAT
1 ATATATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAAT-GACAT
* ** ** **
41281 CCAGTTATTTTAAGACTGC-CCTTTC-CTAATATTGGAAAATAAATAAAT-ATTAAA
65 CCAGGTACCTTAAGACAACTCCTTTCTCTAATATTAAAAAATAAATAAATAATTAAA
*
41335 ATATGATTAA-A-ATAAGTTA-AAAATAA
1 ATAT-ATTAATATATAATTTATAAAATAA
41361 TTAGCTAAGA
Statistics
Matches: 120, Mismatches: 20, Indels: 12
0.79 0.13 0.08
Matches are distributed among these distances:
117 7 0.06
118 15 0.12
119 20 0.17
120 54 0.45
121 24 0.20
ACGTcount: A:0.47, C:0.08, G:0.07, T:0.38
Consensus pattern (121 bp):
ATATATTAATATATAATTTATAAAATAAAATATTTATTTATTTAAAAATATCAGAAAATGACATC
CAGGTACCTTAAGACAACTCCTTTCTCTAATATTAAAAAATAAATAAATAATTAAA
Found at i:42748 original size:3 final size:3
Alignment explanation
Indices: 42730--42791 Score: 88
Period size: 3 Copynumber: 19.7 Consensus size: 3
42720 TTTGGGCTTG
*
42730 TAA TATA TAA TAAA TAA TAA TAT TAA TAA TAA TAA TAA TAAA TAA TAA
1 TAA TA-A TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
42778 TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TA
42792 TAAAAAAACC
Statistics
Matches: 54, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
3 45 0.83
4 9 0.17
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42770 original size:28 final size:29
Alignment explanation
Indices: 42730--42793 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 29
42720 TTTGGGCTTG
*
42730 TAATATATAATAAATAATAATATTAATAA
1 TAATATATAATAAATAATAATAATAATAA
42759 TAATA-ATAATAAATAATAATAATAATAA
1 TAATATATAATAAATAATAATAATAATAA
42787 TAATATA
1 TAATATA
42794 AAAAAACCAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
28 27 0.82
29 6 0.18
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (29 bp):
TAATATATAATAAATAATAATAATAATAA
Found at i:44096 original size:5 final size:5
Alignment explanation
Indices: 44086--44133 Score: 51
Period size: 5 Copynumber: 9.4 Consensus size: 5
44076 AAATCTTTAA
* * * *
44086 ATTTT ATTTT ATATT ATATT ATTTA ATTTA ATATTT ATTTT ATTTT AT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATTTT AT-TTT ATTTT ATTTT AT
44134 ATATGTTATT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
5 34 0.89
6 4 0.11
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (5 bp):
ATTTT
Found at i:44110 original size:26 final size:26
Alignment explanation
Indices: 44085--44133 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
44075 TAAATCTTTA
*
44085 AATTTTAT-TTTATATTATATTATTT
1 AATTTAATATTTATATTATATTATTT
* *
44110 AATTTAATATTTATTTTATTTTAT
1 AATTTAATATTTATATTATATTAT
44134 ATATGTTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
25 7 0.35
26 13 0.65
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (26 bp):
AATTTAATATTTATATTATATTATTT
Found at i:54361 original size:22 final size:23
Alignment explanation
Indices: 54336--54382 Score: 78
Period size: 23 Copynumber: 2.1 Consensus size: 23
54326 AAAGCAGCTC
*
54336 GAAAAGGAAA-AAAACATAAAAA
1 GAAAAGAAAAGAAAACATAAAAA
54358 GAAAAGAAAAGAAAACATAAAAA
1 GAAAAGAAAAGAAAACATAAAAA
54381 GA
1 GA
54383 CATGAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.77, C:0.04, G:0.15, T:0.04
Consensus pattern (23 bp):
GAAAAGAAAAGAAAACATAAAAA
Found at i:54374 original size:23 final size:22
Alignment explanation
Indices: 54336--54391 Score: 76
Period size: 23 Copynumber: 2.5 Consensus size: 22
54326 AAAGCAGCTC
*
54336 GAAAAGGAAAAAAACATAAAAA
1 GAAAAGAAAAAAAACATAAAAA
54358 GAAAAGAAAAGAAAACATAAAAA
1 GAAAAGAAAA-AAAACATAAAAA
* *
54381 GACATGAAAAA
1 GAAAAGAAAAA
54392 CAATGGAAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
22 10 0.33
23 20 0.67
ACGTcount: A:0.75, C:0.05, G:0.14, T:0.05
Consensus pattern (22 bp):
GAAAAGAAAAAAAACATAAAAA
Found at i:70741 original size:20 final size:20
Alignment explanation
Indices: 70716--70757 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
70706 AAAATATGAC
70716 TTTGTAAAACAGAGAGTATG
1 TTTGTAAAACAGAGAGTATG
*
70736 TTTGTAAAACAGAGGGTATG
1 TTTGTAAAACAGAGAGTATG
70756 TT
1 TT
70758 CCTTATGGAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.36, C:0.05, G:0.26, T:0.33
Consensus pattern (20 bp):
TTTGTAAAACAGAGAGTATG
Found at i:80303 original size:3 final size:3
Alignment explanation
Indices: 80295--80339 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
80285 TTTAGAATTA
*
80295 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT ATT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
80340 CATCATTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
AAT
Found at i:82988 original size:22 final size:21
Alignment explanation
Indices: 82946--82987 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
82936 TTTCGTATAC
82946 ATAATAATAAAATAATAAAAT
1 ATAATAATAAAATAATAAAAT
*
82967 ATAATTAATATAAATATTAAA
1 ATAA-TAATA-AAATAATAAA
82988 TCCATAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 5 0.28
23 9 0.50
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (21 bp):
ATAATAATAAAATAATAAAAT
Found at i:84929 original size:29 final size:30
Alignment explanation
Indices: 84890--84957 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
84880 AAATAGGGAT
* * *
84890 GGGATGGGGAAAAGCCAAATGTTTTAAACG
1 GGGACGGGAAAAAACCAAATGTTTTAAACG
* *
84920 GGGACGGGAAAAAATCGAATGTTTTAAACG
1 GGGACGGGAAAAAACCAAATGTTTTAAACG
84950 GGGACGGG
1 GGGACGGG
84958 TTTGATAATC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.35, C:0.10, G:0.37, T:0.18
Consensus pattern (30 bp):
GGGACGGGAAAAAACCAAATGTTTTAAACG
Found at i:88765 original size:26 final size:26
Alignment explanation
Indices: 88712--88765 Score: 81
Period size: 26 Copynumber: 2.1 Consensus size: 26
88702 ACCGAAGTGC
*
88712 TAATACACATAAGGTCGTGCTCACCA
1 TAATACACATAAGGTCGTGCCCACCA
* *
88738 TAATACACATAAGTTCGTGCCCATCA
1 TAATACACATAAGGTCGTGCCCACCA
88764 TA
1 TA
88766 TGCACTAAGT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (26 bp):
TAATACACATAAGGTCGTGCCCACCA
Found at i:91056 original size:59 final size:58
Alignment explanation
Indices: 90969--91090 Score: 158
Period size: 59 Copynumber: 2.1 Consensus size: 58
90959 TACTACTTTT
* * * *
90969 TTTTTAATTTTCTAATTTTATCCCTAAACTAT-ATCTATCATTTTAAATTAGTCTTTAGA
1 TTTTTAATTTTCTAATTTCATCCCTAAACTATGATCT-TCATTCTAAATTAATCCTTA-A
*
91028 TTTTTAATATTT-TAGTTTCATCCCTAAACTATGATCTTCATTCTAAATTAATCCTTAA
1 TTTTTAAT-TTTCTAATTTCATCCCTAAACTATGATCTTCATTCTAAATTAATCCTTAA
91086 TTTTT
1 TTTTT
91091 TTAAATACTT
Statistics
Matches: 56, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
58 6 0.11
59 43 0.77
60 7 0.12
ACGTcount: A:0.30, C:0.15, G:0.03, T:0.52
Consensus pattern (58 bp):
TTTTTAATTTTCTAATTTCATCCCTAAACTATGATCTTCATTCTAAATTAATCCTTAA
Found at i:91554 original size:59 final size:60
Alignment explanation
Indices: 91478--91604 Score: 150
Period size: 59 Copynumber: 2.1 Consensus size: 60
91468 TAAAGAACAC
* * *
91478 AAATGGTCCCCTAACTATAGGATGTTGCTTTGTT-GAGTCCCCA-ACTATTAAAAGCTATA
1 AAATGGTCCCCTAACTATAGGATATTGCTTT-TTCAAGTCCCCAGACTATTAAAAGCTACA
* * * * * *
91537 AAATGGTCCTCTGACTATATGATATTGCTTTTTCAAGTCCCTAGATTATTAAAAGTTACA
1 AAATGGTCCCCTAACTATAGGATATTGCTTTTTCAAGTCCCCAGACTATTAAAAGCTACA
91597 AAATGGTC
1 AAATGGTC
91605 ACATGACTAT
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
58 2 0.04
59 34 0.60
60 21 0.37
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (60 bp):
AAATGGTCCCCTAACTATAGGATATTGCTTTTTCAAGTCCCCAGACTATTAAAAGCTACA
Found at i:97245 original size:16 final size:16
Alignment explanation
Indices: 97224--97264 Score: 73
Period size: 16 Copynumber: 2.6 Consensus size: 16
97214 GATTAAGCGC
*
97224 TGAATGATTTTAATGT
1 TGAATGATTTAAATGT
97240 TGAATGATTTAAATGT
1 TGAATGATTTAAATGT
97256 TGAATGATT
1 TGAATGATT
97265 CAGAGGCTCT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.34, C:0.00, G:0.20, T:0.46
Consensus pattern (16 bp):
TGAATGATTTAAATGT
Found at i:97424 original size:22 final size:22
Alignment explanation
Indices: 97399--97459 Score: 99
Period size: 22 Copynumber: 2.9 Consensus size: 22
97389 GCCTGAATGA
97399 TGAACGGTTCAACATTCAGCAC
1 TGAACGGTTCAACATTCAGCAC
*
97421 TGAACGGTTCAACATTCAGCGC
1 TGAACGGTTCAACATTCAGCAC
97443 TGAACGGTT--ACATTCAG
1 TGAACGGTTCAACATTCAG
97460 AGCCAAACAA
Statistics
Matches: 38, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
20 8 0.21
22 30 0.79
ACGTcount: A:0.30, C:0.25, G:0.21, T:0.25
Consensus pattern (22 bp):
TGAACGGTTCAACATTCAGCAC
Found at i:97599 original size:25 final size:26
Alignment explanation
Indices: 97570--97624 Score: 69
Period size: 25 Copynumber: 2.2 Consensus size: 26
97560 ACTCAATCAT
*
97570 TTTTTTCTCA-AATATTGACTTGATG
1 TTTTTTATCACAATATTGACTTGATG
* *
97595 -TTTTTATGACGATATTGACTTGATG
1 TTTTTTATCACAATATTGACTTGATG
97620 TTTTT
1 TTTTT
97625 ATTATTATTT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
24 7 0.28
25 14 0.56
26 4 0.16
ACGTcount: A:0.22, C:0.09, G:0.15, T:0.55
Consensus pattern (26 bp):
TTTTTTATCACAATATTGACTTGATG
Found at i:101393 original size:32 final size:31
Alignment explanation
Indices: 101317--101405 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
101307 ACCTAAAGGA
* *
101317 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAT
1 ACATCTTAGGGCCGTG-GGGCCTACCCAAGAC
* *
101348 AGAT-TTCAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTT-AGGGCCGTGGGGCCTACCCAAG-AC
**
101380 ACATCTTAGGGCCGCAGGGCCTACCC
1 ACATCTTAGGGCCGTGGGGCCTACCC
101406 GAGAATGATC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
30 2 0.04
31 20 0.43
32 22 0.48
33 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (31 bp):
ACATCTTAGGGCCGTGGGGCCTACCCAAGAC
Found at i:101420 original size:63 final size:63
Alignment explanation
Indices: 101317--101439 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
101307 ACCTAAAGGA
* ** *
101317 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
101380 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
101440 TGTCACATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:102947 original size:18 final size:18
Alignment explanation
Indices: 102924--102958 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
102914 TTCCATCCGG
*
102924 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
102942 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
102959 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:104250 original size:7 final size:7
Alignment explanation
Indices: 104238--104274 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
104228 GTCAACAGTA
104238 GTCAACG
1 GTCAACG
104245 GTCAACGG
1 GTCAAC-G
104253 GTCAACG
1 GTCAACG
104260 GTCAACG
1 GTCAACG
104267 GTCAACG
1 GTCAACG
104274 G
1 G
104275 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (7 bp):
GTCAACG
Found at i:104277 original size:15 final size:14
Alignment explanation
Indices: 104238--104274 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
104228 GTCAACAGTA
104238 GTCAACGGTCAACGG
1 GTCAACGGTCAAC-G
104253 GTCAACGGTCAACG
1 GTCAACGGTCAACG
104267 GTCAACGG
1 GTCAACGG
104275 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:104284 original size:13 final size:13
Alignment explanation
Indices: 104266--104326 Score: 50
Period size: 13 Copynumber: 4.3 Consensus size: 13
104256 AACGGTCAAC
104266 GGTCAACGGGTCG
1 GGTCAACGGGTCG
104279 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
*
104297 GGTAAACGGGTCG
1 GGTCAACGGGTCG
* *
104310 GGTAAATGGGTCG
1 GGTCAACGGGTCG
104323 GGTC
1 GGTC
104327 GGGTAAACGG
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 26 0.65
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 10 0.25
ACGTcount: A:0.20, C:0.18, G:0.44, T:0.18
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:104298 original size:18 final size:18
Alignment explanation
Indices: 104275--104309 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
104265 CGGTCAACGG
*
104275 GTCGGGTCAACGAGTCGA
1 GTCGGGTAAACGAGTCGA
*
104293 GTCGGGTAAACGGGTCG
1 GTCGGGTAAACGAGTCG
104310 GGTAAATGGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.20, C:0.20, G:0.43, T:0.17
Consensus pattern (18 bp):
GTCGGGTAAACGAGTCGA
Found at i:104308 original size:31 final size:31
Alignment explanation
Indices: 104270--104344 Score: 105
Period size: 31 Copynumber: 2.4 Consensus size: 31
104260 GTCAACGGTC
104270 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
1 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
* * * *
104301 AACGGGTCGGGTAAATGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
*
104332 AACGGGTTGGGTC
1 AACGGGTCGGGTC
104345 GGGTTGTGAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.20, C:0.16, G:0.45, T:0.19
Consensus pattern (31 bp):
AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
Found at i:104324 original size:18 final size:18
Alignment explanation
Indices: 104303--104348 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
104293 GTCGGGTAAA
*
104303 CGGGTCGGGTAAATGGGT
1 CGGGTCGGGTAAACGGGT
104321 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
104339 TGGGTCGGGT
1 CGGGTCGGGT
104349 TGTGACCGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.13, C:0.13, G:0.52, T:0.22
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:104338 original size:13 final size:13
Alignment explanation
Indices: 104293--104325 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
104283 AACGAGTCGA
104293 GTCGGGTAAACGG
1 GTCGGGTAAACGG
*
104306 GTCGGGTAAATGG
1 GTCGGGTAAACGG
104319 GTCGGGT
1 GTCGGGT
104326 CGGGTAAACG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.12, G:0.48, T:0.21
Consensus pattern (13 bp):
GTCGGGTAAACGG
Found at i:106405 original size:32 final size:31
Alignment explanation
Indices: 106329--106417 Score: 83
Period size: 32 Copynumber: 2.8 Consensus size: 31
106319 ACCTAAGGGA
* *
106329 ACATCTTAGGGCC-TGAGAGCCTACCCAAGAT
1 ACATCTTAGGGCCGTG-GGGCCTACCCAAGAC
* *
106360 AGAT-TTCAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTT-AGGGCCGTGGGGCCTACCCAAG-AC
**
106392 ACATCTTAGGGCCGCAGGGCCTACCC
1 ACATCTTAGGGCCGTGGGGCCTACCC
106418 GAGAATGATC
Statistics
Matches: 46, Mismatches: 8, Indels: 7
0.75 0.13 0.11
Matches are distributed among these distances:
30 2 0.04
31 20 0.43
32 22 0.48
33 2 0.04
ACGTcount: A:0.25, C:0.30, G:0.27, T:0.18
Consensus pattern (31 bp):
ACATCTTAGGGCCGTGGGGCCTACCCAAGAC
Found at i:106432 original size:63 final size:63
Alignment explanation
Indices: 106329--106451 Score: 160
Period size: 63 Copynumber: 2.0 Consensus size: 63
106319 ACCTAAGGGA
* ** *
106329 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCAGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
106392 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
106452 TGTCACATTA
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
62 2 0.04
63 50 0.96
ACGTcount: A:0.26, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:107960 original size:18 final size:18
Alignment explanation
Indices: 107937--107971 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
107927 TTCCATCCGG
*
107937 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
107955 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
107972 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:109261 original size:7 final size:7
Alignment explanation
Indices: 109249--109285 Score: 65
Period size: 7 Copynumber: 5.1 Consensus size: 7
109239 GTCAACAGTA
109249 GTCAACG
1 GTCAACG
109256 GTCAACGG
1 GTCAAC-G
109264 GTCAACG
1 GTCAACG
109271 GTCAACG
1 GTCAACG
109278 GTCAACG
1 GTCAACG
109285 G
1 G
109286 GTCGGGTCAA
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
7 22 0.76
8 7 0.24
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (7 bp):
GTCAACG
Found at i:109288 original size:15 final size:14
Alignment explanation
Indices: 109249--109285 Score: 65
Period size: 15 Copynumber: 2.6 Consensus size: 14
109239 GTCAACAGTA
109249 GTCAACGGTCAACGG
1 GTCAACGGTCAAC-G
109264 GTCAACGGTCAACG
1 GTCAACGGTCAACG
109278 GTCAACGG
1 GTCAACGG
109286 GTCGGGTCAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.27, C:0.27, G:0.32, T:0.14
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:109295 original size:13 final size:13
Alignment explanation
Indices: 109277--109337 Score: 59
Period size: 13 Copynumber: 4.3 Consensus size: 13
109267 AACGGTCAAC
109277 GGTCAACGGGTCG
1 GGTCAACGGGTCG
109290 GGTCAACGAGTCGAGTCG
1 GGTCAAC--G--G-GTCG
*
109308 GGTAAACGGGTCG
1 GGTCAACGGGTCG
*
109321 GGTAAACGGGTCG
1 GGTCAACGGGTCG
109334 GGTC
1 GGTC
109338 GGGTAAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
13 27 0.66
14 1 0.02
15 1 0.02
16 1 0.02
17 1 0.02
18 10 0.24
ACGTcount: A:0.20, C:0.20, G:0.44, T:0.16
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:109309 original size:18 final size:18
Alignment explanation
Indices: 109286--109346 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 18
109276 CGGTCAACGG
*
109286 GTCGGGTCAACGAGTCGA
1 GTCGGGTAAACGAGTCGA
109304 GTCGGGTAAAC--G--G-
1 GTCGGGTAAACGAGTCGA
* *
109317 GTCGGGTAAACGGGTCGG
1 GTCGGGTAAACGAGTCGA
109335 GTCGGGTAAACG
1 GTCGGGTAAACG
109347 GGTTGGGTCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 11 0.30
14 1 0.03
15 1 0.03
16 1 0.03
17 1 0.03
18 22 0.59
ACGTcount: A:0.21, C:0.18, G:0.44, T:0.16
Consensus pattern (18 bp):
GTCGGGTAAACGAGTCGA
Found at i:109319 original size:31 final size:31
Alignment explanation
Indices: 109281--109355 Score: 114
Period size: 31 Copynumber: 2.4 Consensus size: 31
109271 GTCAACGGTC
109281 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
1 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
* * *
109312 AACGGGTCGGGTAAACGGGTCGGGTCGGGTA
1 AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
*
109343 AACGGGTTGGGTC
1 AACGGGTCGGGTC
109356 GGGTTGTGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.20, C:0.17, G:0.45, T:0.17
Consensus pattern (31 bp):
AACGGGTCGGGTCAACGAGTCGAGTCGGGTA
Found at i:109347 original size:18 final size:18
Alignment explanation
Indices: 109314--109359 Score: 83
Period size: 18 Copynumber: 2.6 Consensus size: 18
109304 GTCGGGTAAA
109314 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
109332 CGGGTCGGGTAAACGGGT
1 CGGGTCGGGTAAACGGGT
*
109350 TGGGTCGGGT
1 CGGGTCGGGT
109360 TGTGACCGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.13, C:0.15, G:0.52, T:0.20
Consensus pattern (18 bp):
CGGGTCGGGTAAACGGGT
Found at i:109354 original size:13 final size:13
Alignment explanation
Indices: 109304--109336 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
109294 AACGAGTCGA
109304 GTCGGGTAAACGG
1 GTCGGGTAAACGG
109317 GTCGGGTAAACGG
1 GTCGGGTAAACGG
109330 GTCGGGT
1 GTCGGGT
109337 CGGGTAAACG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.48, T:0.18
Consensus pattern (13 bp):
GTCGGGTAAACGG
Found at i:109378 original size:9 final size:9
Alignment explanation
Indices: 109364--109409 Score: 56
Period size: 9 Copynumber: 4.9 Consensus size: 9
109354 TCGGGTTGTG
109364 ACCGGTCAA
1 ACCGGTCAA
109373 ACCGGTCAA
1 ACCGGTCAA
* *
109382 ACAGTTCCAAA
1 ACCGGT-C-AA
109393 ACCGGTCAA
1 ACCGGTCAA
109402 ACCGGTCA
1 ACCGGTCA
109410 CTTTTCCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
9 23 0.74
10 2 0.06
11 6 0.19
ACGTcount: A:0.35, C:0.33, G:0.20, T:0.13
Consensus pattern (9 bp):
ACCGGTCAA
Found at i:114380 original size:14 final size:14
Alignment explanation
Indices: 114345--114380 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
114335 AAAAAAAAAT
114345 AAAAAATATTAATA
1 AAAAAATATTAATA
* *
114359 TAATAATATTAATA
1 AAAAAATATTAATA
114373 AAAAAATA
1 AAAAAATA
114381 AATATATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (14 bp):
AAAAAATATTAATA
Found at i:114838 original size:22 final size:22
Alignment explanation
Indices: 114813--114857 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 22
114803 CAGTTTACAA
*
114813 ATAGGGAATCGATTCCCCTGCT
1 ATAGGGAACCGATTCCCCTGCT
114835 ATAGGGAACCGATTCCCCTGCT
1 ATAGGGAACCGATTCCCCTGCT
114857 A
1 A
114858 CAGTACCGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.24, C:0.29, G:0.22, T:0.24
Consensus pattern (22 bp):
ATAGGGAACCGATTCCCCTGCT
Found at i:114870 original size:11 final size:11
Alignment explanation
Indices: 114854--114896 Score: 77
Period size: 11 Copynumber: 3.9 Consensus size: 11
114844 CGATTCCCCT
114854 GCTACAGTACC
1 GCTACAGTACC
114865 GCTACAGTACC
1 GCTACAGTACC
*
114876 GCTACAGTACT
1 GCTACAGTACC
114887 GCTACAGTAC
1 GCTACAGTAC
114897 TTCCGTAAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
11 31 1.00
ACGTcount: A:0.28, C:0.33, G:0.19, T:0.21
Consensus pattern (11 bp):
GCTACAGTACC
Found at i:115422 original size:22 final size:21
Alignment explanation
Indices: 115396--115459 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
115386 CATATGAAAT
*
115396 TTGTCCCGAAGGACCTGTGAA
1 TTGTCCCGAAGGACCTATGAA
*
115417 TATGTCCCGAAGGACCTATGAG
1 T-TGTCCCGAAGGACCTATGAA
*
115439 TTATCCCGAAGGACCTATGAA
1 TTGTCCCGAAGGACCTATGAA
115460 ACCCTCGACT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
21 19 0.50
22 19 0.50
ACGTcount: A:0.28, C:0.23, G:0.25, T:0.23
Consensus pattern (21 bp):
TTGTCCCGAAGGACCTATGAA
Found at i:116971 original size:33 final size:33
Alignment explanation
Indices: 116891--116971 Score: 112
Period size: 33 Copynumber: 2.5 Consensus size: 33
116881 GTCCTACTTG
* *
116891 GACTCAAATAC-TTCAGTTTTAAGGTTTCAATAT
1 GACTCAAATACGTT-GGTTTTAAGGTTTCAATAA
116924 GACTCAAATACGTTGGTTTT-AGTGTTTCAATAA
1 GACTCAAATACGTTGGTTTTAAG-GTTTCAATAA
116957 GACTCAAATACGTTG
1 GACTCAAATACGTTG
116972 ATTTATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
32 2 0.05
33 40 0.91
34 2 0.05
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (33 bp):
GACTCAAATACGTTGGTTTTAAGGTTTCAATAA
Found at i:117078 original size:25 final size:23
Alignment explanation
Indices: 117024--117092 Score: 61
Period size: 25 Copynumber: 2.9 Consensus size: 23
117014 GGGCCTACAA
* *
117024 AAATAATAAAATTAAAAAATATT
1 AAATAATAATATTAAAAAATAAT
117047 AGTAATAATAATATTAAATAAATAAAT
1 A--AATAATAATATTAAA-AAAT-AAT
117074 AAAT-ATAATA-TAATAAAAT
1 AAATAATAATATTAA-AAAAT
117093 GTTTTTGTAG
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
23 8 0.21
24 7 0.18
25 17 0.44
26 4 0.10
27 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.32
Consensus pattern (23 bp):
AAATAATAATATTAAAAAATAAT
Found at i:117613 original size:83 final size:81
Alignment explanation
Indices: 117438--117695 Score: 313
Period size: 83 Copynumber: 3.1 Consensus size: 81
117428 AATAAAATCA
* * * * * *
117438 AACTCGAAGGTC-TTTGGCAGATAGCCCTTCTTGCCTTGAGCTATACTGCAAATAATGGTGCCTT
1 AACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGAT-GTG-CTT
* *
117502 T-GAGCTGAGTGGAGTCG
64 TGGAGCTGAGCGTAGTCG
* * *
117519 AACTCGGAGGTCTTCATTGACAGATAACCCTTCTAGCCTTGAGTTATGCTATAAATGATGTGCTT
1 AACTCGAAGGTCTT--TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCTT
*
117584 TGGAGCTGAACGTAGTCG
64 TGGAGCTGAGCGTAGTCG
*
117602 AACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCCT
1 AACTCGAAGGTC-TT-TTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCTT
* *
117667 TGAAGTTGAGCGTAGTCG
64 TGGAGCTGAGCGTAGTCG
117685 AACTCGAAGGT
1 AACTCGAAGGT
117696 TTGATGTTTC
Statistics
Matches: 152, Mismatches: 20, Indels: 8
0.84 0.11 0.04
Matches are distributed among these distances:
81 11 0.07
82 5 0.03
83 99 0.65
84 37 0.24
ACGTcount: A:0.24, C:0.19, G:0.26, T:0.31
Consensus pattern (81 bp):
AACTCGAAGGTCTTTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGATGTGCTTTG
GAGCTGAGCGTAGTCG
Found at i:117814 original size:36 final size:36
Alignment explanation
Indices: 117763--118002 Score: 154
Period size: 36 Copynumber: 6.9 Consensus size: 36
117753 AGTTTTTTTG
*
117763 TGTTTCAAGAA-AAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAA-AAGAAACTGTCTCAAGAGAGACAAAATT
**
117799 TGTTTCAAAAGAAACTGTCTC-A-AGA-A-AATCTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
* * *
117831 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACGAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
117867 TGTTTCAAGGAA-AAGA-TAT-TC-A-A-AG----ATTT
1 TGTTTCAA--AAGAA-ACTGTCTCAAGAGAGACAAAATT
* * **
117896 TATTTTAAGGGAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
117932 TGTTTC-AAGGAAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAAAG-AAACTGTCTCAAGAGAGACAA-AATT
**
117969 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA
118003 CTTGGAAACT
Statistics
Matches: 157, Mismatches: 24, Indels: 46
0.69 0.11 0.20
Matches are distributed among these distances:
27 1 0.01
28 4 0.03
29 11 0.07
30 1 0.01
31 4 0.03
32 22 0.14
33 4 0.03
34 4 0.03
35 8 0.05
36 55 0.35
37 37 0.24
38 6 0.04
ACGTcount: A:0.41, C:0.13, G:0.20, T:0.27
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:117971 original size:37 final size:37
Alignment explanation
Indices: 117889--118000 Score: 181
Period size: 37 Copynumber: 3.1 Consensus size: 37
117879 AAGATATTCA
* *
117889 AAGATTTTATTTTAAGGGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
* *
117926 AA-AATTTGTTTCAAGGAAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
117962 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
1 AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
117999 AA
1 AA
118001 AACTTGGAAA
Statistics
Matches: 68, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
36 32 0.47
37 36 0.53
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.27
Consensus pattern (37 bp):
AAGATTTTGTTTCAAGGGAAACTGTCTCAAGAGAGAC
Found at i:122251 original size:15 final size:15
Alignment explanation
Indices: 122228--122275 Score: 87
Period size: 15 Copynumber: 3.2 Consensus size: 15
122218 CGTAGGACTC
122228 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
122243 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
122258 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
122273 CTA
1 CTA
122276 TTATACCCTC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 31 1.00
ACGTcount: A:0.31, C:0.33, G:0.21, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:122402 original size:29 final size:29
Alignment explanation
Indices: 122360--122433 Score: 141
Period size: 29 Copynumber: 2.6 Consensus size: 29
122350 TTTCATATGT
122360 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
122388 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
122417 TCATGTAGCTCATGTCA
1 TCATGTAGCTCATGTCA
122434 CTTCATATCA
Statistics
Matches: 45, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.16
29 38 0.84
ACGTcount: A:0.19, C:0.22, G:0.16, T:0.43
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:122466 original size:12 final size:12
Alignment explanation
Indices: 122449--122483 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
122439 TATCATGTTC
122449 TCATATCACATA
1 TCATATCACATA
122461 TCATATCACATA
1 TCATATCACATA
122473 TCATATCACAT
1 TCATATCACAT
122484 GAACATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (12 bp):
TCATATCACATA
Found at i:122899 original size:64 final size:65
Alignment explanation
Indices: 122791--123015 Score: 217
Period size: 64 Copynumber: 3.5 Consensus size: 65
122781 TAATGAAGGT
* * ** **** * ** *
122791 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAAGGTATTCGATGTATT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTATTCACTATTAATAGG
* *
122855 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGT-TTCACTATTAATAG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTACATTCGATGTATTCACTATTAATAG
122918 G
65 G
* * * *
122919 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTACATTCGATGTATTTA-TTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTATTCACTATTAATAGG
**
122982 AGTGCATCGATGCACTACCAATGCATCGATGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
123016 ATTCAAACAA
Statistics
Matches: 135, Mismatches: 21, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
63 6 0.04
64 126 0.93
65 3 0.02
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (65 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTATTCACTATTAATAGG
Found at i:129024 original size:29 final size:29
Alignment explanation
Indices: 128973--129051 Score: 124
Period size: 29 Copynumber: 2.8 Consensus size: 29
128963 TTATATTTCA
*
128973 TATGTTCATGTA-CTCATGTCATTTCTCG
1 TATGATCATGTAGCTCATGTCATTTCTCG
*
129001 TATGATCATGTAGCTCATGTCATTTCTCT
1 TATGATCATGTAGCTCATGTCATTTCTCG
*
129030 TGTGATCATGTAGCTCATGTCA
1 TATGATCATGTAGCTCATGTCA
129052 CTTCATATCA
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
28 11 0.23
29 36 0.77
ACGTcount: A:0.20, C:0.20, G:0.16, T:0.43
Consensus pattern (29 bp):
TATGATCATGTAGCTCATGTCATTTCTCG
Found at i:129506 original size:64 final size:64
Alignment explanation
Indices: 129398--129622 Score: 213
Period size: 64 Copynumber: 3.5 Consensus size: 64
129388 TAATGAAGGT
* * ** **** * ** *
129398 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTATTATTATTGCTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTCCATTCGATGTATTACTATTAATAGG
* * *
129462 ATGCATCGATGCACTCCTTATGCATCGATGCACCG-ATTGCATTCGATGTTTTACTATTAATAGG
1 ATGCATCGATGCACTACTTATGCATCGATGCA-CGAATTCCATTCGATGTATTACTATTAATAGG
* * *
129526 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTCCATTCGATGTATTTA-TTTTAA-AAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTCCATTCGATGTA-TTACTATTAATAGG
** *
129589 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
129623 ATTCAAACAA
Statistics
Matches: 134, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
63 4 0.03
64 127 0.95
65 3 0.02
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTCCATTCGATGTATTACTATTAATAGG
Found at i:131600 original size:37 final size:32
Alignment explanation
Indices: 131538--131628 Score: 103
Period size: 35 Copynumber: 2.7 Consensus size: 32
131528 AAACATAAGA
*
131538 AAAAAATAATAAAAAATATTAATATAATAATATT
1 AAAAAA-AATAAAAAATATTAATATAACAATA-T
131572 AATAAAAAATAAATAAATATATATATATAACAATAT
1 AA-AAAAAATAAA-AAATAT-TA-ATATAACAATAT
131608 AAAAAGAAAT-AAAAATATTAA
1 AAAAA-AAATAAAAAATATTAA
131629 AATTATGAGA
Statistics
Matches: 51, Mismatches: 1, Indels: 12
0.80 0.02 0.19
Matches are distributed among these distances:
32 1 0.02
33 2 0.04
34 14 0.27
35 15 0.29
36 9 0.18
37 10 0.20
ACGTcount: A:0.69, C:0.01, G:0.01, T:0.29
Consensus pattern (32 bp):
AAAAAAAATAAAAAATATTAATATAACAATAT
Found at i:132121 original size:15 final size:15
Alignment explanation
Indices: 132056--132123 Score: 52
Period size: 15 Copynumber: 4.5 Consensus size: 15
132046 TGGAGCCTGC
*
132056 AAAA-ATAATAAAAT
1 AAAATATAATATAAT
* *
132070 AAAAAATATTAGTAAT
1 AAAATATAATA-TAAT
132086 AATAATA-ATATATAA-
1 AA-AATATA-ATATAAT
132101 ATAAATATAATATAAT
1 A-AAATATAATATAAT
132117 AAAATAT
1 AAAATAT
132124 TTTTGTAGAT
Statistics
Matches: 43, Mismatches: 4, Indels: 13
0.72 0.07 0.22
Matches are distributed among these distances:
14 4 0.09
15 22 0.51
16 12 0.28
17 5 0.12
ACGTcount: A:0.68, C:0.00, G:0.01, T:0.31
Consensus pattern (15 bp):
AAAATATAATATAAT
Found at i:133654 original size:20 final size:20
Alignment explanation
Indices: 133631--133674 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
133621 AACGCGATTT
* *
133631 AGAAAATTGCAACGTTAAAA
1 AGAAAATCGCAACGGTAAAA
*
133651 AGAAAATCGCAACGGTCAAA
1 AGAAAATCGCAACGGTAAAA
133671 AGAA
1 AGAA
133675 TAGTTAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.55, C:0.14, G:0.18, T:0.14
Consensus pattern (20 bp):
AGAAAATCGCAACGGTAAAA
Found at i:133763 original size:6 final size:6
Alignment explanation
Indices: 133752--133933 Score: 357
Period size: 6 Copynumber: 30.5 Consensus size: 6
133742 GACACGTATT
133752 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
133800 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
133848 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG
133896 ACCACG ACCACG ACCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
133934 CGAGACGAGA
Statistics
Matches: 176, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
5 5 0.03
6 171 0.97
ACGTcount: A:0.33, C:0.51, G:0.16, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:134627 original size:5 final size:5
Alignment explanation
Indices: 134619--134664 Score: 56
Period size: 5 Copynumber: 8.6 Consensus size: 5
134609 CCATCTCGTC
*
134619 TCGGG TCGGG TCGGG TTGGG TCGGG TCGTGG TCGTGG TCGTGG TCG
1 TCGGG TCGGG TCGGG TCGGG TCGGG TCG-GG TCG-GG TCG-GG TCG
134665 TGGTAATACG
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
5 21 0.55
6 17 0.45
ACGTcount: A:0.00, C:0.17, G:0.54, T:0.28
Consensus pattern (5 bp):
TCGGG
Found at i:134653 original size:6 final size:6
Alignment explanation
Indices: 134637--134668 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
134627 GGTCGGGTTG
134637 GGTCG- GGTCGT GGTCGT GGTCGT GGTCGT GGT
1 GGTCGT GGTCGT GGTCGT GGTCGT GGTCGT GGT
134669 AATACGTGTC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.16, G:0.53, T:0.31
Consensus pattern (6 bp):
GGTCGT
Found at i:134769 original size:20 final size:20
Alignment explanation
Indices: 134744--134787 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
134734 TTTTTAACTA
*
134744 TTCTTTTGACCGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
*
134764 TTCTTTTTAACGTTGCGATT
1 TTCTTTTGAACGTTGCGATT
134784 TTCT
1 TTCT
134788 AAATCGCGTT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.11, C:0.18, G:0.16, T:0.55
Consensus pattern (20 bp):
TTCTTTTGAACGTTGCGATT
Found at i:134797 original size:20 final size:20
Alignment explanation
Indices: 134776--134906 Score: 154
Period size: 20 Copynumber: 6.4 Consensus size: 20
134766 CTTTTTAACG
* *
134776 TTGCGATTTTCTAAATCGCG
1 TTGCGATTCTCTAAATCGCA
*
134796 TTGCGATTCTCTCAATCGCA
1 TTGCGATTCTCTAAATCGCA
*
134816 TTGCGATTCTATAAATCGCA
1 TTGCGATTCTCTAAATCGCA
* *
134836 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
* *
134856 TTGCGATTCTCTCAGTCGCA
1 TTGCGATTCTCTAAATCGCA
*
134876 TTGCGATTTTCTTCTAAATCGCG
1 TTGCGA--TTC-TCTAAATCGCA
134899 TTGCGATT
1 TTGCGATT
134907 TTATTGGTCA
Statistics
Matches: 97, Mismatches: 11, Indels: 5
0.86 0.10 0.04
Matches are distributed among these distances:
20 78 0.80
21 2 0.02
22 3 0.03
23 14 0.14
ACGTcount: A:0.19, C:0.24, G:0.18, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTCTAAATCGCA
Found at i:134823 original size:60 final size:62
Alignment explanation
Indices: 134756--134906 Score: 168
Period size: 60 Copynumber: 2.5 Consensus size: 62
134746 CTTTTGACCG
* * * *
134756 TTGCGATTTTCTTTTTAA-CG-TTGCGATTTTCTAAATCGCGTTGCGATTCTCTCAATCGCA
1 TTGCGATTTTCTTATAAATCGATTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* * *
134816 TTGCGA--TTC-TATAAATCGCATTGCGATTCTCTCAGTCGCATTGCGATTCTCTCAGTCGCA
1 TTGCGATTTTCTTATAAATCG-ATTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
* *
134876 TTGCGATTTTCTTCTAAATCGCGTTGCGATT
1 TTGCGATTTTCTTATAAATCG-ATTGCGATT
134907 TTATTGGTCA
Statistics
Matches: 76, Mismatches: 9, Indels: 9
0.81 0.10 0.10
Matches are distributed among these distances:
57 4 0.05
58 5 0.07
60 47 0.62
62 3 0.04
63 17 0.22
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (62 bp):
TTGCGATTTTCTTATAAATCGATTGCGATTCTCTAAATCGCATTGCGATTCTCTCAATCGCA
Found at i:151803 original size:36 final size:35
Alignment explanation
Indices: 151743--151859 Score: 180
Period size: 35 Copynumber: 3.3 Consensus size: 35
151733 AAAGGAAACA
*
151743 TTTCGATTCAAGTGAACGGAAGGAAGCATCGGCAC
1 TTTCGATTCAAGTGAACGGAAGGAAGCATCGACAC
* *
151778 TTTCGATTCAAGAAGAACGAAAGGAAGCATCGACAC
1 TTTCGATTCAAG-TGAACGGAAGGAAGCATCGACAC
*
151814 TTTCGATTCAAGTGAACGGAAGGAAGCATCAACAC
1 TTTCGATTCAAGTGAACGGAAGGAAGCATCGACAC
*
151849 TTTCAATTCAA
1 TTTCGATTCAA
151860 TTGTTCATCT
Statistics
Matches: 74, Mismatches: 7, Indels: 2
0.89 0.08 0.02
Matches are distributed among these distances:
35 42 0.57
36 32 0.43
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.21
Consensus pattern (35 bp):
TTTCGATTCAAGTGAACGGAAGGAAGCATCGACAC
Done.