Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007186.1 Hibiscus syriacus cultivar Beakdansim tig00018924_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: 156055
ACGTcount: A:0.34, C:0.18, G:0.16, T:0.32
Found at i:1492 original size:6 final size:6
Alignment explanation
Indices: 1475--1513 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
1465 AATGAATGTT
*
1475 ATGCATA ATGCAA ATGCAG ATGCCAA ATGCAA ATGCAA A
1 ATGCA-A ATGCAA ATGCAA ATG-CAA ATGCAA ATGCAA A
1514 AGGTGTCATT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
6 19 0.66
7 10 0.34
ACGTcount: A:0.46, C:0.18, G:0.18, T:0.18
Consensus pattern (6 bp):
ATGCAA
Found at i:3296 original size:19 final size:21
Alignment explanation
Indices: 3268--3307 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3258 CAACAATATC
*
3268 AAAATAAATAA-GCCAATGCA
1 AAAATAAATAATGCAAATGCA
3288 AAAAT-AATAATGCAAATGCA
1 AAAATAAATAATGCAAATGCA
3308 CGAGGTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.60, C:0.12, G:0.10, T:0.17
Consensus pattern (21 bp):
AAAATAAATAATGCAAATGCA
Found at i:7161 original size:3 final size:3
Alignment explanation
Indices: 7153--7199 Score: 51
Period size: 3 Copynumber: 15.7 Consensus size: 3
7143 AATATTGTAA
* * *
7153 AAT AAT AAT AAT AAT AAT AAT AAT CAT ACT -AT AGT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
7198 AA
1 AA
7200 ATATAATATA
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
2 1 0.03
3 33 0.92
4 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:8494 original size:13 final size:13
Alignment explanation
Indices: 8476--8505 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
8466 AACAACACAA
*
8476 CACATTCACATTT
1 CACATTCACATTC
8489 CACATTCACATTC
1 CACATTCACATTC
8502 CACA
1 CACA
8506 ATTCCGATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (13 bp):
CACATTCACATTC
Found at i:15751 original size:111 final size:111
Alignment explanation
Indices: 15542--15770 Score: 327
Period size: 111 Copynumber: 2.1 Consensus size: 111
15532 ATTGAAGTGC
* *
15542 CGAAATGGTAATTCACATCATTATGAATACCATGGGTGGCACATTTTATGCCAAAATGCCCCGTT
1 CGAAATGGTAATTCACATCATTATGAATACAATGGGTGGCACATTTTATGCCAAAATGCACCGTT
* * **
15607 ACGCATTAAGCAAAATCGATCGATAACTTTCATAAATGAAGTATGT
66 ACGCATTAAACAAAATCGATCGATAACTATCATAAACAAAGTATGT
* *
15653 CGAAATGGTAATTCA-ACTTATTATGAATACAATGGGTGGCACCTTTTATGCCAAAAATGCACCG
1 CGAAATGGTAATTCACA-TCATTATGAATACAATGGGTGGCACATTTTATGCC-AAAATGCACCG
* * *
15717 TTATGCATTAAACAAAATCGATCGAT-ACTATCATACACAAAGTATTT
64 TTACGCATTAAACAAAATCGATCGATAACTATCATAAACAAAGTATGT
15764 CGAAATG
1 CGAAATG
15771 CACCTATGGC
Statistics
Matches: 105, Mismatches: 11, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
110 1 0.01
111 70 0.67
112 34 0.32
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (111 bp):
CGAAATGGTAATTCACATCATTATGAATACAATGGGTGGCACATTTTATGCCAAAATGCACCGTT
ACGCATTAAACAAAATCGATCGATAACTATCATAAACAAAGTATGT
Found at i:16277 original size:11 final size:11
Alignment explanation
Indices: 16263--16300 Score: 51
Period size: 11 Copynumber: 3.4 Consensus size: 11
16253 AAATGTACTA
16263 TTATTATAAAT
1 TTATTATAAAT
16274 TTATTATAAATT
1 TTATTATAAA-T
16286 TCTATTA-AAAT
1 T-TATTATAAAT
16297 TTAT
1 TTAT
16301 CCTATCTTAA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
10 3 0.12
11 12 0.48
12 5 0.20
13 5 0.20
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (11 bp):
TTATTATAAAT
Found at i:21943 original size:45 final size:45
Alignment explanation
Indices: 21886--22243 Score: 425
Period size: 45 Copynumber: 8.0 Consensus size: 45
21876 CACTTTAAAT
* * * **
21886 TATAACAT-CTTTTGTGTTGATAATGCACCCATATGTATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
**
21930 TATAATATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
21975 CATAGTATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * *
22020 CATAGTATACTTTTCTGTTGATAATGTACCGATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * *
22065 TCTAGCATGCTCTTT-TGTTGATAATGAACCCATATGCATTTCAAC
1 TATAGCATACT-TTTCTGTTGATAATGTACCCATATACATTTCAAC
* * * *
22110 TCTAGCATACATTTCTGTTGATAATGCACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* *
22155 TATAACATA-TTTTTTGTTGATAATGTACCCATATACATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
* ** * * * *
22199 CATATTATACTTTTATGTTCATAATCTACCCATATGCATTTCAAC
1 TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
22244 AATGGCATTA
Statistics
Matches: 279, Mismatches: 31, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
44 47 0.17
45 229 0.82
46 3 0.01
ACGTcount: A:0.31, C:0.20, G:0.09, T:0.40
Consensus pattern (45 bp):
TATAGCATACTTTTCTGTTGATAATGTACCCATATACATTTCAAC
Found at i:22842 original size:95 final size:96
Alignment explanation
Indices: 22712--22915 Score: 263
Period size: 95 Copynumber: 2.2 Consensus size: 96
22702 TACTACCCTA
* *
22712 CTATGGTATCGATA-CCCCCTTCCAGTATCGATACCAAATTTAGCTTCGATGTAGCCTGGTATCG
1 CTATGGTACCGATACCCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTAGCCTGGTATCG
*
22776 ATACTCTTACCATGATATCGATACTAC-TATG
66 ATACCCTTACCATGATATCGATACTACAT-TG
* * **
22807 CTATGGTACCGATACCCCCCTT-CGGTATCGATACCAAAATTAGGTTCGATGTTTCCTGGTATCG
1 CTATGGTACCGATACCCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTAGCCTGGTATCG
** * *
22871 ATACCCTTACTGTGGTATCGATATTACATTG
66 ATACCCTTACCATGATATCGATACTACATTG
*
22902 -TTTGGTACCGATAC
1 CTATGGTACCGATAC
22916 TATTTGAATC
Statistics
Matches: 95, Mismatches: 12, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
94 13 0.14
95 74 0.78
96 8 0.08
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.33
Consensus pattern (96 bp):
CTATGGTACCGATACCCCCCTTCCAGTATCGATACCAAAATTAGCTTCGATGTAGCCTGGTATCG
ATACCCTTACCATGATATCGATACTACATTG
Found at i:36070 original size:112 final size:111
Alignment explanation
Indices: 35873--36102 Score: 352
Period size: 112 Copynumber: 2.1 Consensus size: 111
35863 ATGGAAGTGC
* * *
35873 CGAAATGGTAATTCACCTCATTATAAATACCATGGGTGGCACCTTTTATGCCGAAAATGCACTAT
1 CGAAATGGTAATTCACCTCATTATAAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCAA
* * * * *
35938 TATGCATTAAGCAAAATCGATTGATAACTTTTATACACGAAGTATGT
66 TATGCATTAAACAAAATCGATCGAT-ACTATCATACACAAAGTATGT
*
35985 CGAAATGGTAATTCACCTCATTATGAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCAA
1 CGAAATGGTAATTCACCTCATTATAAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCAA
*
36050 TATGCATTAAACAAAATCGATCGATACTATCATAGACAAAGTATGT
66 TATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGT
*
36096 TGAAATG
1 CGAAATG
36103 CACCCATGAC
Statistics
Matches: 107, Mismatches: 11, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
111 23 0.21
112 84 0.79
ACGTcount: A:0.37, C:0.18, G:0.16, T:0.29
Consensus pattern (111 bp):
CGAAATGGTAATTCACCTCATTATAAATACCATGGGTGGCACCTTTTATGCCAAAAATGCACCAA
TATGCATTAAACAAAATCGATCGATACTATCATACACAAAGTATGT
Found at i:36703 original size:20 final size:19
Alignment explanation
Indices: 36671--36709 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
36661 ACCGATACTC
*
36671 TTTTCATTATCGATTCCAT
1 TTTTCATTATCGAATCCAT
*
36690 TTTTGCATTCTCGAATCCAT
1 TTTT-CATTATCGAATCCAT
36710 AGTATCGATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.21, C:0.23, G:0.08, T:0.49
Consensus pattern (19 bp):
TTTTCATTATCGAATCCAT
Found at i:42678 original size:21 final size:20
Alignment explanation
Indices: 42650--42689 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
42640 TATTGCAGGA
*
42650 ATTTATGGCCTCGACAAAAG
1 ATTTATGGCCTCAACAAAAG
*
42670 ATTTCATGGCTTCAACAAAA
1 ATTT-ATGGCCTCAACAAAA
42690 ACCTTGATGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.38, C:0.20, G:0.15, T:0.28
Consensus pattern (20 bp):
ATTTATGGCCTCAACAAAAG
Found at i:57505 original size:101 final size:100
Alignment explanation
Indices: 57337--57518 Score: 310
Period size: 101 Copynumber: 1.8 Consensus size: 100
57327 ACTCTACTTG
*
57337 ACTAGCTCGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTGCGATGAGCTG
1 ACTAGCTCGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTGCGATGAGATG
57402 ACTCCCCTTAAAGTATGCTTAAAAAACTCTACCGA
66 ACTCCCCTTAAAGTATGCTTAAAAAACTCTACCGA
* * *
57437 ACTAGCTCGGGGGTGGAAGGTATGCTTCCTTTTACTTAGAGTGTGGGATGGTAGTGTGATGAGAT
1 ACTAGCTC-GGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTGCGATGAGAT
*
57502 GACTCCCCTTGAAGTAT
65 GACTCCCCTTAAAGTAT
57519 AAAAAAAGGA
Statistics
Matches: 76, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
100 8 0.11
101 68 0.89
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (100 bp):
ACTAGCTCGGGGTGGAAGGTATGCTCCCTTTCACTTAGAGTGTGGGATGGTAGTGCGATGAGATG
ACTCCCCTTAAAGTATGCTTAAAAAACTCTACCGA
Found at i:63324 original size:112 final size:111
Alignment explanation
Indices: 63141--63352 Score: 289
Period size: 112 Copynumber: 1.9 Consensus size: 111
63131 TAATTCACCA
* * * * * *
63141 CATTATGAATACCTTGGGTGGCACCTTTTATGCCGAAAATGCATCGTTATGCATTCAACAAAATA
1 CATTATGAATACCATAGGTGCCACCTTTTATACCGAAAATGCACCGTTATGCATTAAACAAAATA
* *
63206 AATCGATAACTTTCATACACTAAGTATGTCAAAATGGTAATTTAAAT
66 AATCGAT-ACTGTCATACACAAAGTATGTCAAAATGGTAATTTAAAT
* * * *
63253 CATTATGAATACCATAGGTGCCACCTTTTATATCGAAAATGTACCGTTATTCATTAAACAAAATT
1 CATTATGAATACCATAGGTGCCACCTTTTATACCGAAAATGCACCGTTATGCATTAAACAAAATA
**
63318 GGTCGATACTGTCATACACAAAGTATGTCAAAATG
66 AATCGATACTGTCATACACAAAGTATGTCAAAATG
63353 CACCCATGAC
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
111 26 0.30
112 60 0.70
ACGTcount: A:0.37, C:0.17, G:0.14, T:0.32
Consensus pattern (111 bp):
CATTATGAATACCATAGGTGCCACCTTTTATACCGAAAATGCACCGTTATGCATTAAACAAAATA
AATCGATACTGTCATACACAAAGTATGTCAAAATGGTAATTTAAAT
Found at i:66036 original size:596 final size:596
Alignment explanation
Indices: 64904--66063 Score: 2104
Period size: 596 Copynumber: 1.9 Consensus size: 596
64894 TGCTAAAATC
*
64904 CGCATTGGTTCTTCTTCGTAAGTCAGTTCTGATCGGATATCTTTTTCATCTTGTGTGATAATATG
1 CGCATTGGTTCTTCTTCGTAAGTCAGTTCTGATCGAATATCTTTTTCATCTTGTGTGATAATATG
64969 GGAAGGATCTAATCGGTACTTTCTAAGCATCGACATGTGAAAAATATTGTGGATCTTGTCCATAT
66 GGAAGGATCTAATCGGTACTTTCTAAGCATCGACATGTGAAAAATATTGTGGATCTTGTCCATAT
* * * * *
65034 CATGAGGCAAAGATAACTTATAAGCTATGTGTTTGACCCTTTTCAAAATCTCATAAGGTCCAATG
131 AAGGAGGCAAAGATAACATATAAGCTATGGGTCTGACCCTTTTCAAAATCTCATAAGGTCCAATG
* * *
65099 AATCTCGGACTCAGCTTTCCTTTGCGCCCAAATCTCAATATTTTCTTTCAAGGTGATACTTTCAG
196 AATCTCAGACTCAGCTTTCCTTTACGCCCAAATCTCAATACTTTCTTTCAAGGTGATACTTTCAG
65164 AAATACCTTGTCTCCCACTTGAAATTCAATCTATTTTCTTTTCAAATAAGCATAAGACTTTTGTC
261 AAATACCTTGTCTCCCACTTGAAATTCAATCTATTTTCTTTTCAAATAAGCATAAGACTTTTGTC
65229 GATCGGAGGCTATCTTAAGATTATCCTTGATAACTTTCACTTTCTCTTCCATTACTTTCTTCAAA
326 GATCGGAGGCTATCTTAAGATTATCCTTGATAACTTTCACTTTCTCTTCCATTACTTTCTTCAAA
*
65294 TCTGGGCCAACTAGGTCTCGATATTTTAGTTCAAACCAATTTAATGGTGTTTGACACTTCCTCCC
391 TCTGGGCCAACTAGGTCTCGATATTTTAGATCAAACCAATTTAATGGTGTTTGACACTTCCTCCC
* * * * *
65359 ATACAAAGCTTTATACGGGGCCATCTTAATACTCAATTGGTAACTATTATTATAAGAAAATTTTG
456 ATACAAAGCTTCATACGGGGCAATCTTAATACTCAACTGGTAACTATTATTATAAGAAAACTTCG
65424 CTAAAGGAAAATACCTTTCCCATGATCCTTTAAACTCAATCACATATGTGAAAAATATGGAAAGG
521 CTAAAGGAAAATACCTTTCCCATGATCCTTTAAACTCAATCACATATGTGAAAAATATGGAAAGG
65489 CAAATACCTTT
586 CAAATACCTTT
*
65500 CGCATTGGTTCTTCTTCTTAAGTCAGTTCTGATCGAATATCTTTTTCATCTTGTGTGATAATATG
1 CGCATTGGTTCTTCTTCGTAAGTCAGTTCTGATCGAATATCTTTTTCATCTTGTGTGATAATATG
65565 GGAAGGATCTAATCGGTACTTTCTAAGCATCGACATGTGAAAAATATTGTGGATCTTGTCCATAT
66 GGAAGGATCTAATCGGTACTTTCTAAGCATCGACATGTGAAAAATATTGTGGATCTTGTCCATAT
65630 AAGGAGGCAAAGATAACATATAAGCTATGGGTCTGACCCTTTTCAAAATCTCATAAGGTCCAATG
131 AAGGAGGCAAAGATAACATATAAGCTATGGGTCTGACCCTTTTCAAAATCTCATAAGGTCCAATG
*
65695 AATCTCAGACTCAGCTTTCCTTTACGCCCAAATCTCAATACTTTCTTTCAATGTGATACTTTCAG
196 AATCTCAGACTCAGCTTTCCTTTACGCCCAAATCTCAATACTTTCTTTCAAGGTGATACTTTCAG
*
65760 AAATACCTTGTCTCCCACTTGAAATTCAATCTTTTTTCTTTTCAAATAAGCATAAGACTTTTGTC
261 AAATACCTTGTCTCCCACTTGAAATTCAATCTATTTTCTTTTCAAATAAGCATAAGACTTTTGTC
*
65825 GATCGGAGGCTATCTTAAGATTATCCTTGATAACTTTCACTTTCTCTTCCATTACTTTTTTCAAA
326 GATCGGAGGCTATCTTAAGATTATCCTTGATAACTTTCACTTTCTCTTCCATTACTTTCTTCAAA
* *
65890 TTTGGGCCAACTAGGTCTTGATATTTTAGATCAAACCAATTTAATGGTGTTTGACACTTCCTCCC
391 TCTGGGCCAACTAGGTCTCGATATTTTAGATCAAACCAATTTAATGGTGTTTGACACTTCCTCCC
*
65955 ATACAAAGCTTCATACGGGGCAATCTTAATACTCAACTGGTAACTATTATTATAAGCAAACTTCG
456 ATACAAAGCTTCATACGGGGCAATCTTAATACTCAACTGGTAACTATTATTATAAGAAAACTTCG
* *
66020 CTAAAGGCAAATACCTTTCCCATGATCCTTTGAACTCAATCACA
521 CTAAAGGAAAATACCTTTCCCATGATCCTTTAAACTCAATCACA
66064 CATGCCCTTA
Statistics
Matches: 540, Mismatches: 24, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
596 540 1.00
ACGTcount: A:0.29, C:0.21, G:0.14, T:0.36
Consensus pattern (596 bp):
CGCATTGGTTCTTCTTCGTAAGTCAGTTCTGATCGAATATCTTTTTCATCTTGTGTGATAATATG
GGAAGGATCTAATCGGTACTTTCTAAGCATCGACATGTGAAAAATATTGTGGATCTTGTCCATAT
AAGGAGGCAAAGATAACATATAAGCTATGGGTCTGACCCTTTTCAAAATCTCATAAGGTCCAATG
AATCTCAGACTCAGCTTTCCTTTACGCCCAAATCTCAATACTTTCTTTCAAGGTGATACTTTCAG
AAATACCTTGTCTCCCACTTGAAATTCAATCTATTTTCTTTTCAAATAAGCATAAGACTTTTGTC
GATCGGAGGCTATCTTAAGATTATCCTTGATAACTTTCACTTTCTCTTCCATTACTTTCTTCAAA
TCTGGGCCAACTAGGTCTCGATATTTTAGATCAAACCAATTTAATGGTGTTTGACACTTCCTCCC
ATACAAAGCTTCATACGGGGCAATCTTAATACTCAACTGGTAACTATTATTATAAGAAAACTTCG
CTAAAGGAAAATACCTTTCCCATGATCCTTTAAACTCAATCACATATGTGAAAAATATGGAAAGG
CAAATACCTTT
Found at i:69342 original size:112 final size:111
Alignment explanation
Indices: 69140--69371 Score: 313
Period size: 112 Copynumber: 2.1 Consensus size: 111
69130 GCACCAAAGT
*
69140 GTCGAAATGGTAATTCACCACATTATGAAGACCATGGGTGCCACCTTTTATGCCGAAAATGCATC
1 GTCGAAATGGTAATTCACCACATTATGAAGACCATGGGTGCCACCTTTTATGCCGAAAATGCACC
* * *
69205 GATATGCATTAAACAAAATCAATCGATAACTCTCATACACGAAGTAC
66 GATATGCATTAAACAAAACCAATCGAT-ACTATCATACACAAAGTAC
* * * *
69252 GTCGAAATGGTAGTTCA-CATCATTATGAATACCATGGGTGGCACCTTTTATGGCGAAAATGCAC
1 GTCGAAATGGTAATTCACCA-CATTATGAAGACCATGGGTGCCACCTTTTATGCCGAAAATGCAC
* * * * *
69316 CGTTATTCATTAAACAAAACCGATCGATACTATCATATACAAAGTAT
65 CGATATGCATTAAACAAAACCAATCGATACTATCATACACAAAGTAC
*
69363 GTCAAAATG
1 GTCGAAATG
69372 CACCTATGAC
Statistics
Matches: 105, Mismatches: 14, Indels: 3
0.86 0.11 0.02
Matches are distributed among these distances:
111 25 0.24
112 80 0.76
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.27
Consensus pattern (111 bp):
GTCGAAATGGTAATTCACCACATTATGAAGACCATGGGTGCCACCTTTTATGCCGAAAATGCACC
GATATGCATTAAACAAAACCAATCGATACTATCATACACAAAGTAC
Found at i:74369 original size:14 final size:14
Alignment explanation
Indices: 74350--74389 Score: 73
Period size: 14 Copynumber: 2.9 Consensus size: 14
74340 TGCATAAAGG
74350 AAGAAAAAGAAAAT
1 AAGAAAAAGAAAAT
74364 AAGAAAAAGAAAAT
1 AAGAAAAAGAAAAT
74378 AAG-AAAAGAAAA
1 AAGAAAAAGAAAA
74390 GAAAGAAAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 9 0.35
14 17 0.65
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (14 bp):
AAGAAAAAGAAAAT
Found at i:74396 original size:4 final size:4
Alignment explanation
Indices: 74369--74433 Score: 96
Period size: 4 Copynumber: 15.8 Consensus size: 4
74359 AAAATAAGAA
74369 AAAG AAA- ATAAG AAAAG AAAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
1 AAAG AAAG A-AAG -AAAG -AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
74419 AAAG AAAG AAAG AAA
1 AAAG AAAG AAAG AAA
74434 AATAATGACT
Statistics
Matches: 58, Mismatches: 0, Indels: 6
0.91 0.00 0.09
Matches are distributed among these distances:
3 1 0.02
4 48 0.83
5 8 0.14
6 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.02
Consensus pattern (4 bp):
AAAG
Found at i:79345 original size:21 final size:20
Alignment explanation
Indices: 79321--79359 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
79311 AATTAATCAA
*
79321 ATAATTTAATATAAAAAATAT
1 ATAATATAATA-AAAAAATAT
79342 ATAATATAATAAAAAAAT
1 ATAATATAATAAAAAAAT
79360 TACCTTCTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAATATAATAAAAAAATAT
Found at i:80490 original size:20 final size:19
Alignment explanation
Indices: 80461--80499 Score: 60
Period size: 20 Copynumber: 2.0 Consensus size: 19
80451 ATTTAATCAA
*
80461 ATAATTTAATATAAAAAAAT
1 ATAATATAATA-AAAAAAAT
80481 ATAATATAATAAAAAAAAT
1 ATAATATAATAAAAAAAAT
80500 TACCTTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 8 0.44
20 10 0.56
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (19 bp):
ATAATATAATAAAAAAAAT
Found at i:85017 original size:29 final size:29
Alignment explanation
Indices: 84984--85067 Score: 141
Period size: 29 Copynumber: 2.9 Consensus size: 29
84974 TTTACTTTTC
* *
84984 TCCTTTAAAATTAAGCTTTTACATTTCAG
1 TCCTTTAAATTTCAGCTTTTACATTTCAG
*
85013 TCCTTTAAATTTCAGCTTTTACATTTCTG
1 TCCTTTAAATTTCAGCTTTTACATTTCAG
85042 TCCTTTAAATTTCAGCTTTTACATTT
1 TCCTTTAAATTTCAGCTTTTACATTT
85068 TATGCATTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 52 1.00
ACGTcount: A:0.25, C:0.19, G:0.06, T:0.50
Consensus pattern (29 bp):
TCCTTTAAATTTCAGCTTTTACATTTCAG
Found at i:85038 original size:14 final size:14
Alignment explanation
Indices: 84997--85067 Score: 79
Period size: 15 Copynumber: 4.9 Consensus size: 14
84987 TTTAAAATTA
84997 AGCTTTTACATTTC
1 AGCTTTTACATTTC
* *
85011 AGTCCTTTAAATTTC
1 AG-CTTTTACATTTC
85026 AGCTTTTACATTTC
1 AGCTTTTACATTTC
* * *
85040 TGTCCTTTAAATTTC
1 AG-CTTTTACATTTC
85055 AGCTTTTACATTT
1 AGCTTTTACATTT
85068 TATGCATTTT
Statistics
Matches: 45, Mismatches: 10, Indels: 4
0.76 0.17 0.07
Matches are distributed among these distances:
14 22 0.49
15 23 0.51
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.51
Consensus pattern (14 bp):
AGCTTTTACATTTC
Found at i:85591 original size:62 final size:62
Alignment explanation
Indices: 85515--85639 Score: 214
Period size: 62 Copynumber: 2.0 Consensus size: 62
85505 ACTCAATGAG
* *
85515 AAAGGATAGTTAGAACGCATAAAAGGTTTGATATCGATGTCTTTAAATAATCGAACATTCTT
1 AAAGGATAGTTAGAACGCATAAAAGGTTCGATATCGATATCTTTAAATAATCGAACATTCTT
* *
85577 AAAGGATAGTTAGAACGCATAAAAGGTTCGATCTCGATATCTTTAAATAATCGTACATTCTT
1 AAAGGATAGTTAGAACGCATAAAAGGTTCGATATCGATATCTTTAAATAATCGAACATTCTT
85639 A
1 A
85640 TTCTTTCTTA
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.38, C:0.13, G:0.17, T:0.32
Consensus pattern (62 bp):
AAAGGATAGTTAGAACGCATAAAAGGTTCGATATCGATATCTTTAAATAATCGAACATTCTT
Found at i:86358 original size:2 final size:2
Alignment explanation
Indices: 86351--86397 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
86341 TAAATTGATA
86351 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
86393 AT AT A
1 AT AT A
86398 AAATAAACAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:87217 original size:16 final size:17
Alignment explanation
Indices: 87188--87224 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
87178 TATCATCCAT
87188 ATTAAAAGCAGTAGCAA
1 ATTAAAAGCAGTAGCAA
*
87205 ATTAAAA-CAGTAGTAA
1 ATTAAAAGCAGTAGCAA
87221 ATTA
1 ATTA
87225 TTACTACAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.54, C:0.08, G:0.14, T:0.24
Consensus pattern (17 bp):
ATTAAAAGCAGTAGCAA
Found at i:93683 original size:20 final size:20
Alignment explanation
Indices: 93650--93699 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
93640 ACTAGTCGTG
* *
93650 GTATCAATATTAAACCTTCA
1 GTATCGATACTAAACCTTCA
**
93670 GTATCGATACTAAACCTTTG
1 GTATCGATACTAAACCTTCA
93690 GTATCGATAC
1 GTATCGATAC
93700 CCACTTGTTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (20 bp):
GTATCGATACTAAACCTTCA
Found at i:96048 original size:4 final size:4
Alignment explanation
Indices: 96039--99364 Score: 5485
Period size: 4 Copynumber: 832.8 Consensus size: 4
96029 CAGTGTTGCT
96039 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96087 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96135 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96183 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96231 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96279 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96327 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96375 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96423 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96471 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* ** * * * * * * *
96519 TACA TACA TACA TACCA T-CG T-GT TTCT TGCA TTA-T TCCGA GTCCG
1 TACA TACA TACA TA-CA TACA TACA TACA TACA -TACA TAC-A -TACA
* * * *** * * * * * * * * **
96564 T-CGGTG TCCT TTGT TTC- TCCA T-CG T-CA T-CGG CACG TAGA GAGG
1 TAC---A TACA TACA TACA TACA TACA TACA TAC-A TACA TACA TACA
* * * ** * *** ** *
96607 TGAGA AAGTCA AAGTT TTCGA TGTTT TGGA -ACT TACA TACA TACA TACA
1 T-ACA TA--CA TA-CA TAC-A T-ACA TACA TACA TACA TACA TACA TACA
96656 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96704 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96752 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96800 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96848 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96896 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96944 TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
96990 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97038 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97086 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
* ** * * * * * * * * * * ***
97134 TACCA T-CG T-GT TTCT TGCA TTA-T TCCGA GTCCG T-CGGTG TCCT TTGT
1 TA-CA TACA TACA TACA TACA -TACA TAC-A -TACA TAC---A TACA TACA
* * * * * * * * ** * * * **
97181 TTC- TCCA T-CG T-CA T-CGG CACG TAGA GAGG TGAGA AAGTCA AAGTT
1 TACA TACA TACA TACA TAC-A TACA TACA TACA T-ACA TA--CA TA-CA
* *** ** *
97226 TTCGA TGTTT TGGA -ACT TACA TACA TACA TACA TACA TACA TACA TACA
1 TAC-A T-ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97275 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97323 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97371 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97419 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97467 TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97513 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97561 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97609 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97657 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97705 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97753 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97800 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97848 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97896 TACA TACA TACA TACA TACA TACA TACA TACA T--A TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97942 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
97990 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98038 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98086 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98134 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98182 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98230 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98278 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98326 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98374 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98422 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98470 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98518 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98566 TACA TAC- -ACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98612 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA T--A
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98658 TACA TACA TACA TACA TACA TACA TACA TAC- TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98705 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98753 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98801 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98849 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98897 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC-
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98944 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
98992 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99040 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99088 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99136 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99184 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99232 TACA TACA TACA TACA TACA TAC- -ACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99278 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA TACA
99326 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
1 TACA TACA TACA TACA TACA TACA TACA TACA TACA TAC
99365 CATCGTGTTT
Statistics
Matches: 3179, Mismatches: 90, Indels: 106
0.94 0.03 0.03
Matches are distributed among these distances:
2 12 0.00
3 33 0.01
4 3096 0.97
5 18 0.01
6 18 0.01
7 2 0.00
ACGTcount: A:0.48, C:0.25, G:0.02, T:0.26
Consensus pattern (4 bp):
TACA
Found at i:102239 original size:24 final size:24
Alignment explanation
Indices: 102218--102291 Score: 121
Period size: 24 Copynumber: 3.1 Consensus size: 24
102208 ATTTTTGATT
102218 TGGATTTTGATATGATACTTGACC
1 TGGATTTTGATATGATACTTGACC
102242 TGGATTTTGATATGATACTTGACC
1 TGGATTTTGATATGATACTTGACC
* * *
102266 TGGATTCTGATCTGCTACTTGACC
1 TGGATTTTGATATGATACTTGACC
102290 TG
1 TG
102292 AATTATGTTT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 47 1.00
ACGTcount: A:0.22, C:0.16, G:0.22, T:0.41
Consensus pattern (24 bp):
TGGATTTTGATATGATACTTGACC
Found at i:102318 original size:2 final size:2
Alignment explanation
Indices: 102311--102342 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
102301 TTGATTTTTG
102311 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
102343 GTTGCGAACG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:103595 original size:17 final size:17
Alignment explanation
Indices: 103575--103632 Score: 59
Period size: 17 Copynumber: 3.5 Consensus size: 17
103565 AAAGATATGG
103575 TACAATAAAAGATACAA
1 TACAATAAAAGATACAA
*
103592 TAC-ATAAAAGTTATAGAA
1 TACAATAAAAG--ATACAA
*
103610 T--ATTAAAAGATACAA
1 TACAATAAAAGATACAA
103625 TACAATAA
1 TACAATAA
103633 GAGAAATAGT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 6 0.19
16 7 0.22
17 13 0.41
18 6 0.19
ACGTcount: A:0.60, C:0.09, G:0.07, T:0.24
Consensus pattern (17 bp):
TACAATAAAAGATACAA
Found at i:103600 original size:16 final size:16
Alignment explanation
Indices: 103579--103628 Score: 57
Period size: 15 Copynumber: 3.1 Consensus size: 16
103569 ATATGGTACA
103579 ATAAAAGATACAATAC
1 ATAAAAGATACAATAC
*
103595 ATAAAAGTTATAGAATA-
1 ATAAAAG--ATACAATAC
*
103612 TTAAAAGATACAATAC
1 ATAAAAGATACAATAC
103628 A
1 A
103629 ATAAGAGAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
15 7 0.26
16 7 0.26
17 6 0.22
18 7 0.26
ACGTcount: A:0.60, C:0.08, G:0.08, T:0.24
Consensus pattern (16 bp):
ATAAAAGATACAATAC
Found at i:114631 original size:42 final size:42
Alignment explanation
Indices: 114550--114633 Score: 114
Period size: 42 Copynumber: 2.0 Consensus size: 42
114540 TTTGCTACAA
* * ** *
114550 CATTTTGGGGTGTTCTTCCTCCATTGGCTCTGCAGGCTGTGG
1 CATTTTGGGGTGTTCCTCCTCCAGTGGCTCAACAAGCTGTGG
*
114592 CATTTTGGGGTGTTCCTCCTCCAGTGGCTCAATAAGCTGTGG
1 CATTTTGGGGTGTTCCTCCTCCAGTGGCTCAACAAGCTGTGG
114634 GGGTTCTGGT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.30, T:0.36
Consensus pattern (42 bp):
CATTTTGGGGTGTTCCTCCTCCAGTGGCTCAACAAGCTGTGG
Found at i:126486 original size:5 final size:5
Alignment explanation
Indices: 126476--126503 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
126466 TAAAGGAATG
126476 AAATA AAATA AAATA AAATA AAATA AAA
1 AAATA AAATA AAATA AAATA AAATA AAA
126504 ATTTAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.82, C:0.00, G:0.00, T:0.18
Consensus pattern (5 bp):
AAATA
Found at i:128052 original size:15 final size:15
Alignment explanation
Indices: 128034--128068 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
128024 AAAAATACAT
* *
128034 AAAATAGAAGGAAAG
1 AAAATACAAGAAAAG
128049 AAAATACAAGAAAAG
1 AAAATACAAGAAAAG
128064 AAAAT
1 AAAAT
128069 CACATAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.71, C:0.03, G:0.17, T:0.09
Consensus pattern (15 bp):
AAAATACAAGAAAAG
Found at i:130471 original size:102 final size:102
Alignment explanation
Indices: 130295--130515 Score: 273
Period size: 102 Copynumber: 2.2 Consensus size: 102
130285 TTCCCCTTAA
* * *
130295 CCCCTTGAACTTGAAGGCATAGTTTCATATGGGTTTTGAACAGACTGTTATGTTGAAGGCATATC
1 CCCCTTGAACTTGAAGGCATAGTGTCATATGGGTTTTAAACAGACTGTTATGTCGAAGGCATATC
* * *
130360 GATATTGAGGTCCAAA-AAGTTGGCAGATGAATGCCTT
66 CATATTGAGGT-CAAATAAATTGGCAAATGAATGCCTT
* * * * * * *
130397 CCCCTTGAGCTTGAAGGTATAGTGTCATATGGGTTTTAAACATATTGTTGTGTCGATGGCATTTC
1 CCCCTTGAACTTGAAGGCATAGTGTCATATGGGTTTTAAACAGACTGTTATGTCGAAGGCATATC
* *
130462 CATATTGAGGTCAAATAAATTGGTAAATGAATGTCTT
66 CATATTGAGGTCAAATAAATTGGCAAATGAATGCCTT
* *
130499 CCCCTTTAACTGGAAGG
1 CCCCTTGAACTTGAAGG
130516 GATGTTTGCT
Statistics
Matches: 100, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
101 4 0.04
102 96 0.96
ACGTcount: A:0.28, C:0.15, G:0.24, T:0.33
Consensus pattern (102 bp):
CCCCTTGAACTTGAAGGCATAGTGTCATATGGGTTTTAAACAGACTGTTATGTCGAAGGCATATC
CATATTGAGGTCAAATAAATTGGCAAATGAATGCCTT
Found at i:131245 original size:67 final size:68
Alignment explanation
Indices: 131129--131263 Score: 254
Period size: 67 Copynumber: 2.0 Consensus size: 68
131119 TCGGGAAACT
*
131129 ATTCATCATGGATATCACAATATTTTTTGTTTTTGATGACCACCTATTTAATATAAAAATATCTT
1 ATTCATCATGGATATCACAATATTTTTTGTTTTTGATGACCACCTATTTAATATAAAAATATATT
131194 TTA
66 TTA
131197 ATTCATCATGGATATCACAATA-TTTTTGTTTTTGATGACCACCTATTTAATATAAAAATATATT
1 ATTCATCATGGATATCACAATATTTTTTGTTTTTGATGACCACCTATTTAATATAAAAATATATT
131261 TTA
66 TTA
131264 CTTTATTGTA
Statistics
Matches: 66, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
67 44 0.67
68 22 0.33
ACGTcount: A:0.35, C:0.13, G:0.07, T:0.45
Consensus pattern (68 bp):
ATTCATCATGGATATCACAATATTTTTTGTTTTTGATGACCACCTATTTAATATAAAAATATATT
TTA
Found at i:137625 original size:27 final size:24
Alignment explanation
Indices: 137587--137647 Score: 79
Period size: 27 Copynumber: 2.5 Consensus size: 24
137577 GACAATGGAG
*
137587 AAAATATTTTTAAATTAAGTTAATCAT
1 AAAATATATTT-AA-TAAGTTAAT-AT
137614 AAAATATATTTAATAAGTTAATAT
1 AAAATATATTTAATAAGTTAATAT
137638 AAAA-ATATTT
1 AAAATATATTT
137648 TTTTATAGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
23 6 0.18
24 6 0.18
25 9 0.27
26 2 0.06
27 10 0.30
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (24 bp):
AAAATATATTTAATAAGTTAATAT
Found at i:137652 original size:27 final size:26
Alignment explanation
Indices: 137587--137663 Score: 88
Period size: 25 Copynumber: 3.0 Consensus size: 26
137577 GACAATGGAG
*
137587 AAAATATTTTTAAATTAAGTTAATCAT-
1 AAAATATTTTTTAA-TAAGTTAAT-ATA
*
137614 AAAATA-TATTTAATAAGTTAATATA
1 AAAATATTTTTTAATAAGTTAATATA
*
137639 AAAATATTTTTTTAT-AGTTAATATA
1 AAAATATTTTTTAATAAGTTAATATA
137664 TATAAAAATA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
24 2 0.05
25 25 0.57
26 11 0.25
27 6 0.14
ACGTcount: A:0.49, C:0.01, G:0.04, T:0.45
Consensus pattern (26 bp):
AAAATATTTTTTAATAAGTTAATATA
Found at i:138299 original size:2 final size:2
Alignment explanation
Indices: 138292--138321 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
138282 ATTGCCCCGA
138292 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
138322 ATATATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:138326 original size:2 final size:2
Alignment explanation
Indices: 138321--138361 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
138311 TCTCTCTCTC
138321 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
138362 TTGCATTACA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:143086 original size:24 final size:26
Alignment explanation
Indices: 143056--143111 Score: 82
Period size: 24 Copynumber: 2.2 Consensus size: 26
143046 AGTTACCCAC
143056 ACATTAGAAACATTACAC-C-TACATT
1 ACATTAGAAACATTA-ACTCTTACATT
143081 A-ATTAGAAACATTAACTCTTACATT
1 ACATTAGAAACATTAACTCTTACATT
143106 ACATTA
1 ACATTA
143112 CAATTCAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
23 2 0.07
24 14 0.50
25 8 0.29
26 4 0.14
ACGTcount: A:0.45, C:0.20, G:0.04, T:0.32
Consensus pattern (26 bp):
ACATTAGAAACATTAACTCTTACATT
Found at i:143987 original size:156 final size:157
Alignment explanation
Indices: 143666--144014 Score: 517
Period size: 156 Copynumber: 2.2 Consensus size: 157
143656 AAATATGGTT
* * *
143666 AAAAACATCATTCAATTGTCTGATATTTCAATGAAATGAAGTAATACATCATTGAAAAGTTTCTA
1 AAAAACATCATTCAATTGTCTGATATATCACTGAAATGAAGTAATACATCACTGAAAAGTTTCTA
* *
143731 AAATAAAGTGATTGGACATTGAAAAGTTGTTTGTCATTGTGTACTAAATGGTCTATGAGAAAATG
66 AAATAAAGTGATTGGACACTGAAAAGTTGTTTGTCAGTGTGTACTAAATGGTCTATGAGAAAATG
143796 ACGTTTTTCATTAAAGGGAAACAAGTC
131 ACGTTTTTCATTAAAGGGAAACAAGTC
* * * * *
143823 AAAGACATCATTCAATTGTTTGATATATCACTGAAATGAAGTGATATATCACTGAAAAGTTTCTG
1 AAAAACATCATTCAATTGTCTGATATATCACTGAAATGAAGTAATACATCACTGAAAAGTTTCTA
*
143888 AAATGAAA-TGATTGGGA-ACTGAAAAGATT-TTT-TCAGTGTGTATTAAATGGTCTATGAGAAA
66 AAAT-AAAGTGATT-GGACACTGAAAAG-TTGTTTGTCAGTGTGTACTAAATGGTCTATGAGAAA
* *
143949 ATGATGTTTTTCATTAAAGGGAAATAAGTC
128 ATGACGTTTTTCATTAAAGGGAAACAAGTC
*
143979 AAAAACATCATTCAATGGTCTGATATATCACTGAAA
1 AAAAACATCATTCAATTGTCTGATATATCACTGAAA
144015 AGTTTCTATC
Statistics
Matches: 173, Mismatches: 16, Indels: 7
0.88 0.08 0.04
Matches are distributed among these distances:
156 88 0.51
157 77 0.45
158 8 0.05
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (157 bp):
AAAAACATCATTCAATTGTCTGATATATCACTGAAATGAAGTAATACATCACTGAAAAGTTTCTA
AAATAAAGTGATTGGACACTGAAAAGTTGTTTGTCAGTGTGTACTAAATGGTCTATGAGAAAATG
ACGTTTTTCATTAAAGGGAAACAAGTC
Found at i:150033 original size:20 final size:21
Alignment explanation
Indices: 149993--150035 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
149983 TGTGTGTTGG
*
149993 GATTTAAAGATTTTGAGTTTA
1 GATTTAAAGATTTTAAGTTTA
*
150014 GATTTAAGGA-TTTAAGTTTA
1 GATTTAAAGATTTTAAGTTTA
150034 GA
1 GA
150036 GATTTGGGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.35, C:0.00, G:0.21, T:0.44
Consensus pattern (21 bp):
GATTTAAAGATTTTAAGTTTA
Found at i:153377 original size:2 final size:2
Alignment explanation
Indices: 153370--153396 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
153360 GTAAAACAAG
153370 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 A
153397 AGTTGTGAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:153615 original size:67 final size:65
Alignment explanation
Indices: 153541--153668 Score: 193
Period size: 67 Copynumber: 1.9 Consensus size: 65
153531 TCAATCATCT
*
153541 AAATCCACAACCAAAGTATGAAAAATCATCCAAAAAACATAAAATCATCCAAATATCCAAATAAT
1 AAATCCACAACCAAAGTATGAAAAATCATCC--AAAACATAAAATCATACAAATATCCAAATAAT
153606 CC
64 CC
* * * *
153608 AAATCCACAACCAAAGTATGAAAAATCATTCAAGAGATAAATTCATACAAATATCCAAATA
1 AAATCCACAACCAAAGTATGAAAAATCATCCAAAACATAAAATCATACAAATATCCAAATA
153669 TCTAAACCCC
Statistics
Matches: 56, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
65 26 0.46
67 30 0.54
ACGTcount: A:0.55, C:0.21, G:0.05, T:0.20
Consensus pattern (65 bp):
AAATCCACAACCAAAGTATGAAAAATCATCCAAAACATAAAATCATACAAATATCCAAATAATCC
Found at i:155292 original size:6 final size:6
Alignment explanation
Indices: 155281--155942 Score: 884
Period size: 6 Copynumber: 113.8 Consensus size: 6
155271 AAACTAAACA
155281 TATATG TATATG TATATG T-TATG TATA-G TATA-G TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155326 TATATG TATATG TATATGG TATATG TATATG TATATGTG TATATG TATATG
1 TATATG TATATG TATAT-G TATATG TATATG TATA--TG TATATG TATATG
* *
155377 TATATG TATATG TATATG TATATG TATA-G GATATG TATATG -GTATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155423 TATATG TATATG TATATG TATATG TATATG TAT-TG --TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155468 TATATG TATATG TA-ATG TATATG TATATG TATA-- T-TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
155512 TATATG TATCTG TATATG TATA-G TAT-T- TATATG T-TATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155556 TATATG TATATG TATATG TATAT- TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155603 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
*
155651 TATA-G TATATG TATATG TATATG TATATG TCTATG TATATG TATATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155698 TA-ATG TATATG TATATG --TA-G TATATG TATATG TATATG TA-ATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
* *
155741 TATATG TATATG TATATG TATATG TATATG TATGTG TATGTATG TGTATG
1 TATATG TATATG TATATG TATATG TATATG TATATG TA--TATG TATATG
* * * * *
155791 TGTATG TGTATG TAGTGTA TATTATG TATA-G TCTATG TATATG TATATG
1 TATATG TATATG TA-TATG TA-TATG TATATG TATATG TATATG TATATG
* *
155840 ATGTATTG TATATG TATATG --TATG TAATTTG ATATATG TATA-- T-TATG
1 -TATA-TG TATATG TATATG TATATG T-ATATG -TATATG TATATG TATATG
155887 TATATG TATATG TATA-G TATATG TATATG TATATG TATATG TATAT-
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
155933 TATAT- TATAT
1 TATATG TATAT
155943 AGTAATGTCT
Statistics
Matches: 594, Mismatches: 23, Indels: 79
0.85 0.03 0.11
Matches are distributed among these distances:
3 6 0.01
4 13 0.02
5 83 0.14
6 452 0.76
7 27 0.05
8 13 0.02
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (6 bp):
TATATG
Done.