Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007716.1 Hibiscus syriacus cultivar Beakdansim tig00109945_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: 4364108
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 13 of 17
Found at i:3295219 original size:52 final size:52
Alignment explanation
Indices: 3295161--3295308 Score: 224
Period size: 52 Copynumber: 2.8 Consensus size: 52
3295151 GTTCGAGAAA
*
3295161 TGATTAGATGTGGAGACATAAAAGGAATTAGGATAAATCATTTTATGAAATC
1 TGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCATTTTATGAAATC
* * *
3295213 TGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCCTTTTATTAAATT
1 TGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCATTTTATGAAATC
* * * *
3295265 TGATTAGATGAGAAGACATGAAAGGGATTAGGATAAATCTTTTT
1 TGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCATTTT
3295309 TGTAAAGTGT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 88 1.00
ACGTcount: A:0.40, C:0.05, G:0.22, T:0.32
Consensus pattern (52 bp):
TGATTAGATGTGGAGACATGAAAGGAATTAGGATAAATCATTTTATGAAATC
Found at i:3296272 original size:42 final size:42
Alignment explanation
Indices: 3296202--3296285 Score: 123
Period size: 42 Copynumber: 2.0 Consensus size: 42
3296192 ATCACGAATT
* * *
3296202 TTTAAATCCTTCGGGTCATCTGTAAGTCTTTCGAGCATGATG
1 TTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATG
* *
3296244 TTTAAATCCTTCAGGTTATCTATCAGTCTTTCGAGCAAGATG
1 TTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATG
3296286 AGAAGTCCTT
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 37 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.38
Consensus pattern (42 bp):
TTTAAATCCTTCAGGTCATCTATAAGTCTTTCGAGCAAGATG
Found at i:3296550 original size:17 final size:16
Alignment explanation
Indices: 3296508--3296559 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 16
3296498 TATAATAATA
3296508 TATTATTA-TATATAT
1 TATTATTATTATATAT
*
3296523 TATAATGTTATTAGTATAT
1 TAT--TATTATTA-TATAT
3296542 TATTATTATTAT-TAT
1 TATTATTATTATATAT
3296557 TAT
1 TAT
3296560 AAATAATACA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 9 0.29
16 1 0.03
17 11 0.35
18 2 0.06
19 8 0.26
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.60
Consensus pattern (16 bp):
TATTATTATTATATAT
Found at i:3297218 original size:7 final size:7
Alignment explanation
Indices: 3297206--3297258 Score: 97
Period size: 7 Copynumber: 7.6 Consensus size: 7
3297196 ACGAAGGAAA
3297206 GAAAAGG
1 GAAAAGG
3297213 GAAAAGG
1 GAAAAGG
3297220 GAAAAGG
1 GAAAAGG
3297227 GAAAAGG
1 GAAAAGG
3297234 GAAAAGG
1 GAAAAGG
*
3297241 GAAAAGC
1 GAAAAGG
3297248 GAAAAGG
1 GAAAAGG
3297255 GAAA
1 GAAA
3297259 CTTATCGAGG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 44 1.00
ACGTcount: A:0.58, C:0.02, G:0.40, T:0.00
Consensus pattern (7 bp):
GAAAAGG
Found at i:3300482 original size:54 final size:54
Alignment explanation
Indices: 3300432--3300685 Score: 271
Period size: 54 Copynumber: 4.7 Consensus size: 54
3300422 CGTAGTGTCG
* * * * *
3300432 ATACAGTCGTTTATAAACATATTATGAATTCTTTGGGTTGGACACTTAGTGCCG
1 ATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGGACACTTAGTGCCT
* * * * * * *
3300486 ATATGGTCGTTCATCAATATATGATGAATTATGTGGGTTGTACACATAGTGTCT
1 ATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGGACACTTAGTGCCT
* * * * *
3300540 ATATGGTCGTTCATAAACACATAATGAATT-TCATGGGTT-GTCACTTAGTGCCT
1 ATACGGTCGTTCATAAACATATGATGAATTCT-GTGGGTTGGACACTTAGTGCCT
* * * * *
3300593 ATACGGTCGTTCATAAA-AAATTACGACTTCTGTGGGTTGCACACTTAGTGCCT
1 ATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGGACACTTAGTGCCT
*
3300646 ATACGGTCGTTCATCAACATATGATGAATTCTGTGGGTTG
1 ATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTG
3300686 CAAATCGCTT
Statistics
Matches: 162, Mismatches: 34, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
52 14 0.09
53 56 0.35
54 92 0.57
ACGTcount: A:0.27, C:0.16, G:0.21, T:0.36
Consensus pattern (54 bp):
ATACGGTCGTTCATAAACATATGATGAATTCTGTGGGTTGGACACTTAGTGCCT
Found at i:3302671 original size:2 final size:2
Alignment explanation
Indices: 3302664--3302711 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
3302654 CTCTTTATTC
3302664 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
3302706 AT AT AT
1 AT AT AT
3302712 CATGGGAATT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3312936 original size:54 final size:54
Alignment explanation
Indices: 3312756--3312938 Score: 206
Period size: 54 Copynumber: 3.4 Consensus size: 54
3312746 GGAGTTATCA
* * * * * *
3312756 GTTGAACACTTAGTTCCTATACGGTCATTCATAAATACATTATAAATTCCGTGG
1 GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACAAATTATGAATTCCGTGG
* * * *
3312810 GTTTCACACTTAGTGTCTATATGGTCGTTCATAAACAAATTATGAATTCCAT-G
1 GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACAAATTATGAATTCCGTGG
* * * * **
3312863 GTTGCACACTTAGTGCCTATACGGCCGTTCATCAACATATGATGAATTTTGTGG
1 GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACAAATTATGAATTCCGTGG
*
3312917 GTTGCACACTTAGTACCTATAC
1 GTTGCACACTTAGTGCCTATAC
3312939 TACACATAGT
Statistics
Matches: 107, Mismatches: 21, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
53 43 0.40
54 64 0.60
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (54 bp):
GTTGCACACTTAGTGCCTATACGGTCGTTCATAAACAAATTATGAATTCCGTGG
Found at i:3323400 original size:46 final size:46
Alignment explanation
Indices: 3323348--3323740 Score: 481
Period size: 46 Copynumber: 8.6 Consensus size: 46
3323338 TACATTACGT
** * * * * *
3323348 ATTTTCATTGGTGGCATCCTTTCATGCCAATTATTCACCGTTAAGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
* **
3323394 ATTTTCATTTATGG---CCTTTCATGCCTATAATGTATTGA-TATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCA-CCATTATGC
* * * *
3323437 ATTTTCATTTAGGGTATCCTTTCATGCCGATAATGCACCAATATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
* * *
3323483 ATTTTCATTTATGGCATCCATTCATGCCTATAATGCACCGTTATGG
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
* *
3323529 ATTTTCATTTATGGCATCCTTTCATGCCGATAATGCACCCTTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
3323575 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
** * * *
3323621 ATTTTCATTTATGATATCCTTTCATG-TTGATAATACACCATTATAC
1 ATTTTCATTTATGGCATCCTTTCATGCCT-ATAATGCACCATTATGC
* * *
3323667 ATTTTAATTTATGGCATCCTTTCATGCCTATAATGGACCATTATGT
1 ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
*
3323713 ATTTTCATTTATGGCATCTTTTCATGCC
1 ATTTTCATTTATGGCATCCTTTCATGCC
3323741 AAAGGCATTT
Statistics
Matches: 297, Mismatches: 43, Indels: 14
0.84 0.12 0.04
Matches are distributed among these distances:
43 33 0.11
45 2 0.01
46 261 0.88
47 1 0.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (46 bp):
ATTTTCATTTATGGCATCCTTTCATGCCTATAATGCACCATTATGC
Found at i:3323906 original size:81 final size:81
Alignment explanation
Indices: 3323740--3324222 Score: 698
Period size: 81 Copynumber: 6.0 Consensus size: 81
3323730 CTTTTCATGC
* * * * * * * * *
3323740 CAAAGGCATTTAACATTTTATCGAACTTGCATTATTGGCACCTTTCTGCCAAATGAACAA-TAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
**
3323804 CAATTAATAATTTACT
66 CAATTAATCTTTTACT
* *
3323820 CAAAGGTATTTAACCTTTCATCTAACTGACATGATTGACATCTTTCTGTCAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
* *
3323885 AAATTAATATTTTACT
66 CAATTAATCTTTTACT
* *
3323901 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACATCTTTCTGTCAAATGCACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
3323966 CAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* * *
3323982 CAAAGGTATTTAACCTTTCGTCTAACTGGCATGATTGACACCTTTCTGTAAAATGCACAATTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
3324047 CAATTAATCTTTTAGT
66 CAATTAATCTTTTACT
* ** *
3324063 CAAAGGTATTTAACCTTTCATCTAAATGGCATGATTGACATGTTTCTGTCAAATGCACAGCTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
*
3324128 TAATTAATCTTTTACT
66 CAATTAATCTTTTACT
* * *
3324144 CAAAGGTATTTAACCTTTCATCTAACTGACGTGATTGACACCTTTCTGTTAAATGCACAACTAGG
1 CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
3324209 CAATTAATCTTTTA
66 CAATTAATCTTTTA
3324223 TTTTAAAAGA
Statistics
Matches: 362, Mismatches: 40, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
80 49 0.14
81 313 0.86
ACGTcount: A:0.32, C:0.19, G:0.13, T:0.36
Consensus pattern (81 bp):
CAAAGGTATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAACTAGG
CAATTAATCTTTTACT
Found at i:3329407 original size:46 final size:46
Alignment explanation
Indices: 3329324--3329781 Score: 592
Period size: 46 Copynumber: 10.0 Consensus size: 46
3329314 TATATCCTGT
* * * ** *
3329324 TAATACACCATTATGTATTTTCATTGGTGGCATCCTTTCATGCCAA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * * ** * *
3329370 TTATTCACTGTTAAACATTTTCCTTTATAGCATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * * *
3329416 TAATGTACCATTATGCATTTTCATTTAGGGCATCCTTTCATGCCTT
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
3329462 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * * *
3329508 TAATGCACCGTTCTGCATTTTCATTTATGGCATCCTTTCGTGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* *
3329554 TAATGCATCGTTATGCACTTTCATTTATGGCATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * *
3329600 TAATGCACTGTTATGTATTTTCATTTATAGCATCCTTTCATGCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * *
3329646 TAATGCACCGTTATGCATTTTCATTTATGACATCCTTTCATGTCGA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * * *
3329692 TAAGGCACTGTTATGCATTTTCATTTATAGCATCCTTTCATTCCTA
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
* * *
3329738 TAATACAACGTTATGCATTTTCATTTATGGCATTCTTTCATGCC
1 TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCC
3329782 AAAGTCATTT
Statistics
Matches: 350, Mismatches: 62, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 350 1.00
ACGTcount: A:0.23, C:0.22, G:0.12, T:0.43
Consensus pattern (46 bp):
TAATGCACCGTTATGCATTTTCATTTATGGCATCCTTTCATGCCTA
Found at i:3329916 original size:81 final size:81
Alignment explanation
Indices: 3329788--3330122 Score: 454
Period size: 81 Copynumber: 4.1 Consensus size: 81
3329778 TGCCAAAGTC
* * * * * * * * *
3329788 ATTTAATCTTTTATCTAACTTGCATTATTGGCACCTTTCAGCCAAATGCACAGTTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGCAATTAA
*
3329853 TATTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
*
3329869 ATTTAACCTTTCATCTAACTGGCATGATTGACACCTTTCTGTCAAATGCACAGCTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGCAATTAA
*
3329934 TCTTTTATTCAAAGGT
66 TCTTTTACTCAAAGGT
* * * ** *
3329950 ATTTAACCTTTGATCTAACTGGCATGATTGACACATTTCTATCAAATACGTAGCTAGGCAATCAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGCAATTAA
3330015 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* * **
3330031 ATTTAACCTTTCATCTAATTGGCATGATTGACATATTTCTGTCAAATGCACATTTAGGCAATTAA
1 ATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGCAATTAA
3330096 TCTTTTACTCAAAGGT
66 TCTTTTACTCAAAGGT
* *
3330112 AATTAATCTTT
1 ATTTAACCTTT
3330123 TACTCAAATG
Statistics
Matches: 224, Mismatches: 30, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
81 224 1.00
ACGTcount: A:0.31, C:0.19, G:0.13, T:0.38
Consensus pattern (81 bp):
ATTTAACCTTTCATCTAACTGGCATGATTGACACATTTCTGTCAAATGCACAGCTAGGCAATTAA
TCTTTTACTCAAAGGT
Found at i:3330118 original size:22 final size:22
Alignment explanation
Indices: 3330090--3330144 Score: 92
Period size: 22 Copynumber: 2.5 Consensus size: 22
3330080 ACATTTAGGC
3330090 AATTAATCTTTTACTCAAAGGT
1 AATTAATCTTTTACTCAAAGGT
*
3330112 AATTAATCTTTTACTCAAATGT
1 AATTAATCTTTTACTCAAAGGT
*
3330134 ATTTAATCTTT
1 AATTAATCTTT
3330145 CATCTAACTG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.35, C:0.13, G:0.05, T:0.47
Consensus pattern (22 bp):
AATTAATCTTTTACTCAAAGGT
Found at i:3330192 original size:103 final size:103
Alignment explanation
Indices: 3330013--3330205 Score: 316
Period size: 103 Copynumber: 1.9 Consensus size: 103
3330003 CTAGGCAATC
* *
3330013 AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAATTGGCATGATTGACATATTTCTGTCAAAT
1 AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATCGACATATTTCTGTCAAAT
**
3330078 GCACATTTAGGCAATTAATCTTTTACTCAAAGGTAATT
66 GCACAACTAGGCAATTAATCTTTTACTCAAAGGTAATT
* *
3330116 AATCTTTTACTCAAATGTATTTAATCTTTCATCTAACTGGCATGATCGACACT-TTTCTGTCAAA
1 AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATCGACA-TATTTCTGTCAAA
3330180 TGCACAACTAGGCAATTAATCTTTTA
65 TGCACAACTAGGCAATTAATCTTTTA
3330206 TTTTAAAACA
Statistics
Matches: 83, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
103 82 0.99
104 1 0.01
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (103 bp):
AATCTTTTACTCAAAGGTATTTAACCTTTCATCTAACTGGCATGATCGACATATTTCTGTCAAAT
GCACAACTAGGCAATTAATCTTTTACTCAAAGGTAATT
Found at i:3330689 original size:21 final size:19
Alignment explanation
Indices: 3330663--3330707 Score: 63
Period size: 21 Copynumber: 2.3 Consensus size: 19
3330653 TCGATACCCA
*
3330663 CATCAGTATCGATACTAATT
1 CATCAGTATCAATACT-ATT
3330683 GCATCAGTATCAATACTATT
1 -CATCAGTATCAATACTATT
3330703 CATCA
1 CATCA
3330708 TAATTCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 3 0.13
21 15 0.65
ACGTcount: A:0.36, C:0.22, G:0.09, T:0.33
Consensus pattern (19 bp):
CATCAGTATCAATACTATT
Found at i:3334557 original size:18 final size:18
Alignment explanation
Indices: 3334534--3334568 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3334524 TAAGAAAATA
3334534 AATTTT-AAATAGCTTTTG
1 AATTTTGAAATAG-TTTTG
3334552 AATTTTGAAATAGTTTT
1 AATTTTGAAATAGTTTT
3334569 AGAAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
AATTTTGAAATAGTTTTG
Found at i:3336569 original size:18 final size:18
Alignment explanation
Indices: 3336546--3336580 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
3336536 TAAGAAAATA
3336546 AATTTT-AAATAGCTTTTG
1 AATTTTGAAATAG-TTTTG
3336564 AATTTTGAAATAGTTTT
1 AATTTTGAAATAGTTTT
3336581 AGAAAATACG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.51
Consensus pattern (18 bp):
AATTTTGAAATAGTTTTG
Found at i:3338811 original size:6 final size:6
Alignment explanation
Indices: 3338802--3338915 Score: 74
Period size: 6 Copynumber: 18.3 Consensus size: 6
3338792 TATATATTAT
* *
3338802 AAGAAA AAGAAA AA-ACAG AAGAAA AACAAA AA-AAA ACAGAAGA AA-AAA
1 AAGAAA AAGAAA AAGA-AA AAGAAA AAGAAA AAGAAA A-AGAA-A AAGAAA
* * * *
3338850 ATAGAAA AAGAAA AAGAAA ACGAAG AAGTAAAA AATGAAA ACGAGA AAG-AA
1 A-AGAAA AAGAAA AAGAAA AAGAAA AAG--AAA AA-GAAA AAGAAA AAGAAA
3338901 AAGAAA AAGAGAA AA
1 AAGAAA AAGA-AA AA
3338916 AAATGAGAGA
Statistics
Matches: 85, Mismatches: 11, Indels: 23
0.71 0.09 0.19
Matches are distributed among these distances:
5 11 0.13
6 51 0.60
7 16 0.19
8 6 0.07
9 1 0.01
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.03
Consensus pattern (6 bp):
AAGAAA
Found at i:3338825 original size:12 final size:12
Alignment explanation
Indices: 3338808--3338849 Score: 63
Period size: 10 Copynumber: 3.8 Consensus size: 12
3338798 TTATAAGAAA
3338808 AAGAAAAAACAG
1 AAGAAAAAACAG
3338820 AAG-AAAAACA-
1 AAGAAAAAACAG
3338830 AA-AAAAAACAG
1 AAGAAAAAACAG
3338841 AAGAAAAAA
1 AAGAAAAAA
3338850 ATAGAAAAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
10 9 0.33
11 9 0.33
12 9 0.33
ACGTcount: A:0.81, C:0.07, G:0.12, T:0.00
Consensus pattern (12 bp):
AAGAAAAAACAG
Found at i:3338828 original size:11 final size:11
Alignment explanation
Indices: 3338812--3338848 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3338802 AAGAAAAAGA
3338812 AAAAACAGAAG
1 AAAAACAGAAG
*
3338823 AAAAACA-AAA
1 AAAAACAGAAG
3338833 AAAAACAGAAG
1 AAAAACAGAAG
3338844 AAAAA
1 AAAAA
3338849 AATAGAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.81, C:0.08, G:0.11, T:0.00
Consensus pattern (11 bp):
AAAAACAGAAG
Found at i:3338876 original size:21 final size:22
Alignment explanation
Indices: 3338852--3338910 Score: 59
Period size: 21 Copynumber: 2.7 Consensus size: 22
3338842 AGAAAAAAAT
3338852 AGAAAAAGAAAAAGAAAACGA-
1 AGAAAAAGAAAAAGAAAACGAG
* *
3338873 AGAAGTAA-AAAATGAAAACGAG
1 AGAA-AAAGAAAAAGAAAACGAG
*
3338895 AAAGAAAAGAAAAAGA
1 AGA-AAAAGAAAAAGA
3338911 GAAAAAAATG
Statistics
Matches: 29, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
21 16 0.55
22 6 0.21
23 7 0.24
ACGTcount: A:0.73, C:0.03, G:0.20, T:0.03
Consensus pattern (22 bp):
AGAAAAAGAAAAAGAAAACGAG
Found at i:3338916 original size:33 final size:34
Alignment explanation
Indices: 3338804--3338917 Score: 103
Period size: 33 Copynumber: 3.4 Consensus size: 34
3338794 TATATTATAA
* *
3338804 GAAAAAGAAAAAACAGAAGAAAAACAAAAA-AAAAC
1 GAAAAAGAAAAAA-A-TAGAAAAAGAAAAAGAAAAC
*
3338839 --AGAAGAAAAAAATAGAAAAAGAAAAAGAAAAC
1 GAAAAAGAAAAAAATAGAAAAAGAAAAAGAAAAC
* * * *
3338871 GAAGAAGTAAAAAAT-GAAAACGAGAAAGAAAA-
1 GAAAAAGAAAAAAATAGAAAAAGAAAAAGAAAAC
3338903 GAAAAAGAGAAAAAA
1 GAAAAAGA-AAAAAA
3338918 ATGAGAGATG
Statistics
Matches: 67, Mismatches: 8, Indels: 10
0.79 0.09 0.12
Matches are distributed among these distances:
31 12 0.18
32 12 0.18
33 31 0.46
34 12 0.18
ACGTcount: A:0.76, C:0.04, G:0.17, T:0.03
Consensus pattern (34 bp):
GAAAAAGAAAAAAATAGAAAAAGAAAAAGAAAAC
Found at i:3346178 original size:78 final size:78
Alignment explanation
Indices: 3346081--3346229 Score: 178
Period size: 77 Copynumber: 1.9 Consensus size: 78
3346071 ATATAATAAG
* *
3346081 TAAACATTAAAAGAATGTAATTTTA-ATTACAACTCTTTTAATCGTTATTTAATTCGGAA-TAAT
1 TAAACATTAAAAGAATGTAA-TTCAGATTACAACTC-TTTAATCGATATTTAATT-GGAATTAAT
3346144 TAAATAAGAGTTTACA
63 TAAATAAGAGTTTACA
* * * * * *
3346160 TAAACGTT-AAAGATTGTAATTCAGATTATAAGTCTTTAATGGATATTTAATTTGAATTAATTAA
1 TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATCGATATTTAATTGGAATTAATTAA
3346224 ATAAGA
66 ATAAGA
3346230 TTTTTAATTA
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
76 3 0.05
77 32 0.53
78 18 0.30
79 7 0.12
ACGTcount: A:0.43, C:0.07, G:0.11, T:0.40
Consensus pattern (78 bp):
TAAACATTAAAAGAATGTAATTCAGATTACAACTCTTTAATCGATATTTAATTGGAATTAATTAA
ATAAGAGTTTACA
Found at i:3347642 original size:21 final size:21
Alignment explanation
Indices: 3347612--3347657 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
3347602 CCTCGAAGCT
* *
3347612 TCAATGAAAGATTTTATGGCG
1 TCAATAAAAGATTTCATGGCG
*
3347633 TCAATAAAAGATTTCATGGCT
1 TCAATAAAAGATTTCATGGCG
3347654 TCAA
1 TCAA
3347658 CAAAGGCCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.13, G:0.17, T:0.33
Consensus pattern (21 bp):
TCAATAAAAGATTTCATGGCG
Found at i:3362763 original size:12 final size:12
Alignment explanation
Indices: 3362746--3362774 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3362736 TTAAAGATTC
3362746 TTCATTTAAGTT
1 TTCATTTAAGTT
3362758 TTCATTTAAGTT
1 TTCATTTAAGTT
3362770 TTCAT
1 TTCAT
3362775 AATATATTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.24, C:0.10, G:0.07, T:0.59
Consensus pattern (12 bp):
TTCATTTAAGTT
Found at i:3363709 original size:24 final size:25
Alignment explanation
Indices: 3363671--3363721 Score: 95
Period size: 24 Copynumber: 2.1 Consensus size: 25
3363661 GCATTATTGG
3363671 AACATCAAATAAGTGAAGGAAAATA
1 AACATCAAATAAGTGAAGGAAAATA
3363696 AACATC-AATAAGTGAAGGAAAATA
1 AACATCAAATAAGTGAAGGAAAATA
3363720 AA
1 AA
3363722 ATTAGAGGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 20 0.77
25 6 0.23
ACGTcount: A:0.61, C:0.08, G:0.16, T:0.16
Consensus pattern (25 bp):
AACATCAAATAAGTGAAGGAAAATA
Found at i:3365359 original size:30 final size:30
Alignment explanation
Indices: 3365325--3365392 Score: 75
Period size: 30 Copynumber: 2.3 Consensus size: 30
3365315 TACAAGGATC
3365325 AAATAATAAAAACATA-AACTTAAAGCACCA
1 AAATAATAAAAACA-AGAACTTAAAGCACCA
* * * * *
3365355 AAATAGTACAAACAAGAATTTAAAGGACTA
1 AAATAATAAAAACAAGAACTTAAAGCACCA
3365385 AAATAATA
1 AAATAATA
3365393 TAAATAGAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
29 1 0.03
30 30 0.97
ACGTcount: A:0.62, C:0.12, G:0.07, T:0.19
Consensus pattern (30 bp):
AAATAATAAAAACAAGAACTTAAAGCACCA
Found at i:3367122 original size:75 final size:75
Alignment explanation
Indices: 3366999--3367149 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
3366989 TTTCATCCCA
3366999 TCAGTATCCATCATCTTCTCTGTCGGTCGCCGAAAATCTATGTAGCGGTCGTCAGAATCCAATGC
1 TCAGTATCCATCATCTTCTCTGTCGGTCGCCGAAAATCTATGTAGCGGTCGTCAGAATCCAATGC
3367064 CAAAACCACG
66 CAAAACCACG
3367074 TCAGTATCCATCATCTTCTCTGTCGGTCGCCGAAAATCTATGTAGCGGTCGTCAGAATCCAATGC
1 TCAGTATCCATCATCTTCTCTGTCGGTCGCCGAAAATCTATGTAGCGGTCGTCAGAATCCAATGC
3367139 CAAAACCACG
66 CAAAACCACG
3367149 T
1 T
3367150 TATTCTCGAA
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.26
Consensus pattern (75 bp):
TCAGTATCCATCATCTTCTCTGTCGGTCGCCGAAAATCTATGTAGCGGTCGTCAGAATCCAATGC
CAAAACCACG
Found at i:3369920 original size:30 final size:30
Alignment explanation
Indices: 3369851--3369908 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
3369841 AATTTAAGGC
3369851 AAAATGTTTTTGGACTTGAATTGAATTTGA
1 AAAATGTTTTTGGACTTGAATTGAATTTGA
*
3369881 AAAATGTTTTTGGATTTGAATTGAATTT
1 AAAATGTTTTTGGACTTGAATTGAATTT
3369909 ATTCAAAGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.33, C:0.02, G:0.19, T:0.47
Consensus pattern (30 bp):
AAAATGTTTTTGGACTTGAATTGAATTTGA
Found at i:3370016 original size:21 final size:21
Alignment explanation
Indices: 3369990--3370068 Score: 149
Period size: 21 Copynumber: 3.8 Consensus size: 21
3369980 AGGGTGTCAA
*
3369990 AGTGCATCCATGCATCCCTGT
1 AGTGCATCCATGCATCCCTGC
3370011 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
3370032 AGTGCATCCATGCATCCCTGC
1 AGTGCATCCATGCATCCCTGC
3370053 AGTGCATCCATGCATC
1 AGTGCATCCATGCATC
3370069 TGCACTAATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
21 57 1.00
ACGTcount: A:0.20, C:0.35, G:0.19, T:0.25
Consensus pattern (21 bp):
AGTGCATCCATGCATCCCTGC
Found at i:3370157 original size:21 final size:21
Alignment explanation
Indices: 3370131--3370198 Score: 102
Period size: 21 Copynumber: 3.3 Consensus size: 21
3370121 ATGCAATTAC
3370131 TGCATCGATGCATCCTTGCCA
1 TGCATCGATGCATCCTTGCCA
* *
3370152 TGCATCCATGCATCCTTTCCA
1 TGCATCGATGCATCCTTGCCA
*
3370173 TGCATCGATGCAT-CATGCCA
1 TGCATCGATGCATCCTTGCCA
3370193 TGCATC
1 TGCATC
3370199 CAAGCATCAA
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
20 11 0.26
21 31 0.74
ACGTcount: A:0.21, C:0.34, G:0.16, T:0.29
Consensus pattern (21 bp):
TGCATCGATGCATCCTTGCCA
Found at i:3373589 original size:53 final size:53
Alignment explanation
Indices: 3373500--3373608 Score: 202
Period size: 53 Copynumber: 2.1 Consensus size: 53
3373490 TTAAGGGGGA
3373500 GTTTTGCCAAAAACAATTTTTCAAATGTTTTGTTATATCAAAAAGGGGGATATT
1 GTTTTGCCAAAAACAATTTTTCAAATGTTTTGTTATATC-AAAAGGGGGATATT
3373554 GTTTTGCCAAAAACAA-TTTTCAAATGTTTTGTTATATCAAAAGGGGGATATT
1 GTTTTGCCAAAAACAATTTTTCAAATGTTTTGTTATATCAAAAGGGGGATATT
3373606 GTT
1 GTT
3373609 GAACTATGTT
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
52 17 0.31
53 22 0.40
54 16 0.29
ACGTcount: A:0.34, C:0.09, G:0.17, T:0.39
Consensus pattern (53 bp):
GTTTTGCCAAAAACAATTTTTCAAATGTTTTGTTATATCAAAAGGGGGATATT
Found at i:3373708 original size:30 final size:30
Alignment explanation
Indices: 3373637--3373696 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3373627 ACAATTTAAG
3373637 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
3373667 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
3373697 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:3373876 original size:18 final size:17
Alignment explanation
Indices: 3373853--3373914 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
3373843 TGCATCCAAA
3373853 CATCGAATGCAATTAGTG
1 CATCG-ATGCAATTAGTG
* **
3373871 CATCGATG-AATCCA-AA
1 CATCGATGCAAT-TAGTG
3373887 CATCGAATGCAATTAGTG
1 CATCG-ATGCAATTAGTG
3373905 CATCGATGCA
1 CATCGATGCA
3373915 TCCTTGCCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 9
0.69 0.12 0.18
Matches are distributed among these distances:
16 8 0.24
17 13 0.38
18 13 0.38
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.24
Consensus pattern (17 bp):
CATCGATGCAATTAGTG
Found at i:3373885 original size:34 final size:34
Alignment explanation
Indices: 3373846--3373917 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
3373836 CAGGCAATGC
3373846 ATCCAAACATCGAATGCAATTAGTGCATCGATGA
1 ATCCAAACATCGAATGCAATTAGTGCATCGATGA
*
3373880 ATCCAAACATCGAATGCAATTAGTGCATCGATGC
1 ATCCAAACATCGAATGCAATTAGTGCATCGATGA
3373914 ATCC
1 ATCC
3373918 TTGCCATGCA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.24
Consensus pattern (34 bp):
ATCCAAACATCGAATGCAATTAGTGCATCGATGA
Found at i:3373929 original size:21 final size:21
Alignment explanation
Indices: 3373903--3373978 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
3373893 ATGCAATTAG
*
3373903 TGCATCGATGCATCCTTGCCA
1 TGCATCCATGCATCCTTGCCA
3373924 TGCATCCATGCATCCTTGCCA
1 TGCATCCATGCATCCTTGCCA
* * *
3373945 TGCATCGATGAAT-CATGCCA
1 TGCATCCATGCATCCTTGCCA
3373965 TGCATCCATGCATC
1 TGCATCCATGCATC
3373979 AAGGCTGCAA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
20 17 0.35
21 31 0.65
ACGTcount: A:0.22, C:0.33, G:0.17, T:0.28
Consensus pattern (21 bp):
TGCATCCATGCATCCTTGCCA
Found at i:3375567 original size:18 final size:18
Alignment explanation
Indices: 3375544--3375602 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
3375534 AAATGAAATG
3375544 AAAAGGAATAGTACAGGA
1 AAAAGGAATAGTACAGGA
* *
3375562 AAAAGGAACAATACAGG-
1 AAAAGGAATAGTACAGGA
*
3375579 AAAAGAAATAGTACAGGA
1 AAAAGGAATAGTACAGGA
3375597 ATAAAG
1 A-AAAG
3375603 AACAATACAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
17 14 0.41
18 16 0.47
19 4 0.12
ACGTcount: A:0.59, C:0.07, G:0.24, T:0.10
Consensus pattern (18 bp):
AAAAGGAATAGTACAGGA
Found at i:3375582 original size:17 final size:17
Alignment explanation
Indices: 3375543--3375611 Score: 66
Period size: 18 Copynumber: 3.9 Consensus size: 17
3375533 AAAATGAAAT
* *
3375543 GAAAAGGAATAGTACAG
1 GAAAAGGAACAATACAG
3375560 GAAAAAGGAACAATACAG
1 G-AAAAGGAACAATACAG
* * *
3375578 GAAAAGAAATAGTACAG
1 GAAAAGGAACAATACAG
*
3375595 GAATAAAGAACAATACA
1 GAA-AAGGAACAATACA
3375612 TGTTTGATTT
Statistics
Matches: 41, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
17 17 0.41
18 24 0.59
ACGTcount: A:0.59, C:0.09, G:0.22, T:0.10
Consensus pattern (17 bp):
GAAAAGGAACAATACAG
Found at i:3375589 original size:35 final size:35
Alignment explanation
Indices: 3375543--3375611 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
3375533 AAAATGAAAT
*
3375543 GAAAAGGAATAGTACAGGAA-AAAGGAACAATACAG
1 GAAAAGAAATAGTACAGGAATAAA-GAACAATACAG
3375578 GAAAAGAAATAGTACAGGAATAAAGAACAATACA
1 GAAAAGAAATAGTACAGGAATAAAGAACAATACA
3375612 TGTTTGATTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 29 0.91
36 3 0.09
ACGTcount: A:0.59, C:0.09, G:0.22, T:0.10
Consensus pattern (35 bp):
GAAAAGAAATAGTACAGGAATAAAGAACAATACAG
Found at i:3376671 original size:2 final size:2
Alignment explanation
Indices: 3376664--3376694 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
3376654 ATAATTCAAT
3376664 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3376695 AAAATCTAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3376924 original size:15 final size:15
Alignment explanation
Indices: 3376901--3376946 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
3376891 ATTTTTTACA
* *
3376901 TAATATTTTAAAAGT
1 TAATTTTTTAAAAAT
3376916 TAATTTTTTAAAAAT
1 TAATTTTTTAAAAAT
*
3376931 TAACCTTTTTAAAAAT
1 TAA-TTTTTTAAAAAT
3376947 ATATAATATC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
15 16 0.59
16 11 0.41
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.48
Consensus pattern (15 bp):
TAATTTTTTAAAAAT
Found at i:3378005 original size:5 final size:5
Alignment explanation
Indices: 3377995--3378022 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3377985 AACAAACAAT
3377995 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
1 AAAGA AAAGA AAAGA AAAGA AAAGA AAA
3378023 CTTACAAAAA
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:0.18, T:0.00
Consensus pattern (5 bp):
AAAGA
Found at i:3378917 original size:18 final size:18
Alignment explanation
Indices: 3378891--3378931 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
3378881 ATCCTTCTAA
3378891 AAAAATTGACTAAACTCG
1 AAAAATTGACTAAACTCG
* **
3378909 AAAATTTGACTTGACTCG
1 AAAAATTGACTAAACTCG
3378927 AAAAA
1 AAAAA
3378932 ATTTCAAATC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.15, G:0.12, T:0.24
Consensus pattern (18 bp):
AAAAATTGACTAAACTCG
Found at i:3379258 original size:31 final size:31
Alignment explanation
Indices: 3379187--3379250 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
3379177 AATACAATCT
*
3379187 CCCAACATTTAGTCCGTTTTCAATATGGTCC
1 CCCAACATTTAGTCCGTTTGCAATATGGTCC
*
3379218 CCCAACATTTAGTCTGTTTGCAATATGGTCC
1 CCCAACATTTAGTCCGTTTGCAATATGGTCC
3379249 CC
1 CC
3379251 GACCATTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.22, C:0.30, G:0.14, T:0.34
Consensus pattern (31 bp):
CCCAACATTTAGTCCGTTTGCAATATGGTCC
Found at i:3381006 original size:31 final size:31
Alignment explanation
Indices: 3380968--3381044 Score: 100
Period size: 31 Copynumber: 2.5 Consensus size: 31
3380958 CAAACGGTCA
*
3380968 GGGACCATATTGTAAACAAACTAAATGTTGG
1 GGGACCATATTGCAAACAAACTAAATGTTGG
**
3380999 GGGACCATATTGCAAACGGACTAAATGTTGG
1 GGGACCATATTGCAAACAAACTAAATGTTGG
* **
3381030 GTGACTGTATTGCAA
1 GGGACCATATTGCAA
3381045 GTTTTAAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 40 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (31 bp):
GGGACCATATTGCAAACAAACTAAATGTTGG
Found at i:3381472 original size:2 final size:2
Alignment explanation
Indices: 3381465--3381570 Score: 51
Period size: 2 Copynumber: 53.5 Consensus size: 2
3381455 ACTAACATTA
* * * * * *
3381465 AT AT AT AT AT AT AT AT AT AT AC AC AC AC ACT AT AT TT AT AGT AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT AT A-T AT
* *
3381509 AT AT AT GT -T AT AT A- AT AT A- AT AT A- AT AT TT AT AT AGT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT
* *
3381548 GT AGT AT AT GT AT AT AT -T AT AT A
1 AT A-T AT AT AT AT AT AT AT AT AT A
3381571 GTATTTATTA
Statistics
Matches: 82, Mismatches: 13, Indels: 18
0.73 0.12 0.16
Matches are distributed among these distances:
1 5 0.06
2 70 0.85
3 7 0.09
ACGTcount: A:0.44, C:0.06, G:0.06, T:0.44
Consensus pattern (2 bp):
AT
Found at i:3381561 original size:20 final size:19
Alignment explanation
Indices: 3381495--3381587 Score: 68
Period size: 20 Copynumber: 4.8 Consensus size: 19
3381485 ACACACACAC
*
3381495 TATATT-TATAGTACATA-
1 TATATTATATAGTATATAG
* *
3381512 TATGTTATATAATATAATA-
1 TATATTATATAGTAT-ATAG
*
3381531 TAATATTTATATAGTATGTAG
1 T-ATA-TTATATAGTATATAG
*
3381552 TATATGTATATATTATATAG
1 TATAT-TATATAGTATATAG
3381572 TAT-TTATTATAGTATA
1 TATATTA-TATAGTATA
3381588 GCATTAGTGT
Statistics
Matches: 60, Mismatches: 9, Indels: 12
0.74 0.11 0.15
Matches are distributed among these distances:
17 5 0.08
18 8 0.13
19 14 0.23
20 22 0.37
21 11 0.18
ACGTcount: A:0.41, C:0.01, G:0.09, T:0.49
Consensus pattern (19 bp):
TATATTATATAGTATATAG
Found at i:3381572 original size:27 final size:25
Alignment explanation
Indices: 3381533--3381587 Score: 74
Period size: 27 Copynumber: 2.1 Consensus size: 25
3381523 ATATAATATA
3381533 ATATTTATATAGTATGTAGTATATGT
1 ATATTTATATAGTATGTAGTATA-GT
* *
3381559 ATATATTATATAGTATTTATTATAGT
1 ATAT-TTATATAGTATGTAGTATAGT
3381585 ATA
1 ATA
3381588 GCATTAGTGT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
26 9 0.35
27 17 0.65
ACGTcount: A:0.38, C:0.00, G:0.11, T:0.51
Consensus pattern (25 bp):
ATATTTATATAGTATGTAGTATAGT
Found at i:3381593 original size:27 final size:27
Alignment explanation
Indices: 3381537--3381593 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
3381527 AATATAATAT
*
3381537 TTATATAGTATGTAGTATATGTATATA
1 TTATATAGTATGTAGTATATGTATACA
* *
3381564 TTATATAGTATTTATTATA-GTATAGCA
1 TTATATAGTATGTAGTATATGTATA-CA
3381591 TTA
1 TTA
3381594 GTGTTTATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
26 5 0.19
27 21 0.81
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (27 bp):
TTATATAGTATGTAGTATATGTATACA
Found at i:3383615 original size:37 final size:37
Alignment explanation
Indices: 3383565--3383635 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
3383555 ACTATACAAG
* *
3383565 TTGAATTAGAAAGAGTGTTTTATATGGTTAGATTCAA
1 TTGAATTAGAAAGAATGCTTTATATGGTTAGATTCAA
3383602 TTGAATTAGAAAGAATGCTTTATATGGTTAGATT
1 TTGAATTAGAAAGAATGCTTTATATGGTTAGATT
3383636 TATATTCGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.35, C:0.03, G:0.21, T:0.41
Consensus pattern (37 bp):
TTGAATTAGAAAGAATGCTTTATATGGTTAGATTCAA
Found at i:3384147 original size:23 final size:23
Alignment explanation
Indices: 3384111--3384160 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
3384101 CATATTTGTA
3384111 CATTCTACGAGGCACTACATGTG
1 CATTCTACGAGGCACTACATGTG
* * *
3384134 CATTCTATGTGGCACTATATGTG
1 CATTCTACGAGGCACTACATGTG
3384157 CATT
1 CATT
3384161 ATGGAAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (23 bp):
CATTCTACGAGGCACTACATGTG
Found at i:3386998 original size:83 final size:83
Alignment explanation
Indices: 3386854--3387024 Score: 324
Period size: 83 Copynumber: 2.1 Consensus size: 83
3386844 TAACATAATA
*
3386854 TATGGAATATATGCAAAATTGGACTTGCACACAGGTAAGCCTTCATAAAATTACCTATATAAGAT
1 TATGAAATATATGCAAAATTGGACTTGCACACAGGTAAGCCTTCATAAAATTACCTATATAAGAT
3386919 GTATTATGAATATATATG
66 GTATTATGAATATATATG
*
3386937 TATGAAATATATGCAAAATTGGACTTGCACACAGGTAAGCCTTTATAAAATTACCTATATAAGAT
1 TATGAAATATATGCAAAATTGGACTTGCACACAGGTAAGCCTTCATAAAATTACCTATATAAGAT
3387002 GTATTATGAATATATATG
66 GTATTATGAATATATATG
3387020 TATGA
1 TATGA
3387025 CATAAGCATG
Statistics
Matches: 86, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
83 86 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.33
Consensus pattern (83 bp):
TATGAAATATATGCAAAATTGGACTTGCACACAGGTAAGCCTTCATAAAATTACCTATATAAGAT
GTATTATGAATATATATG
Found at i:3395083 original size:90 final size:90
Alignment explanation
Indices: 3394970--3395147 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 90
3394960 TAATCCCGAA
* * * * * *
3394970 TATTTAATTTTAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAATCCCTGATATGAT
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
3395035 TAAGGTAACTTGGATATAAAAGGAT
66 TAAGGTAACTTGGATATAAAAGGAT
3395060 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
1 TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
* *
3395125 TAGGGTAACTTGGCTATAAAAGG
66 TAAGGTAACTTGGATATAAAAGG
3395148 GTGTGTTAGG
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
90 80 1.00
ACGTcount: A:0.46, C:0.06, G:0.11, T:0.38
Consensus pattern (90 bp):
TATTAAATTCTAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAAACCCTAATATGAC
TAAGGTAACTTGGATATAAAAGGAT
Found at i:3400530 original size:10 final size:10
Alignment explanation
Indices: 3400515--3400570 Score: 62
Period size: 10 Copynumber: 5.7 Consensus size: 10
3400505 CTATTTATTT
3400515 AAAAAAAACA
1 AAAAAAAACA
3400525 AAAAAAAACA
1 AAAAAAAACA
**
3400535 AAAAAAGGCA
1 AAAAAAAACA
*
3400545 AAAAAAAGGC-
1 AAAAAAA-ACA
3400555 -AAAAAAACA
1 AAAAAAAACA
3400564 AAAAAAA
1 AAAAAAA
3400571 GCCAAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
8 1 0.03
9 6 0.15
10 30 0.77
11 2 0.05
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (10 bp):
AAAAAAAACA
Found at i:3400571 original size:19 final size:19
Alignment explanation
Indices: 3400516--3400577 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
3400506 TATTTATTTA
3400516 AAAAAAACAAAAAAAA-AC
1 AAAAAAACAAAAAAAAGAC
*
3400534 AAAAAAAGGCAAAAAAAAGGC
1 AAAAAAA--CAAAAAAAAGAC
*
3400555 AAAAAAACAAAAAAAAGCC
1 AAAAAAACAAAAAAAAGAC
3400574 AAAA
1 AAAA
3400578 TTTCAGAAAA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
18 7 0.18
19 15 0.38
20 9 0.23
21 8 0.21
ACGTcount: A:0.81, C:0.11, G:0.08, T:0.00
Consensus pattern (19 bp):
AAAAAAACAAAAAAAAGAC
Found at i:3406528 original size:29 final size:29
Alignment explanation
Indices: 3406496--3406554 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
3406486 AAAGATGAAA
3406496 AGAATTCATCCTTGAATTGCTTTGAATAG
1 AGAATTCATCCTTGAATTGCTTTGAATAG
3406525 AGAATTCATCCTTGAATTGCTTTGAATAG
1 AGAATTCATCCTTGAATTGCTTTGAATAG
3406554 A
1 A
3406555 AGCATTAAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.32, C:0.14, G:0.17, T:0.37
Consensus pattern (29 bp):
AGAATTCATCCTTGAATTGCTTTGAATAG
Found at i:3407013 original size:33 final size:35
Alignment explanation
Indices: 3406948--3407021 Score: 98
Period size: 33 Copynumber: 2.2 Consensus size: 35
3406938 TAGTTTGATT
* *
3406948 AATGAAATAGTATTATTCAATGAACTAAATGCATG
1 AATGAAATAGTATTATTAAATGAACTAAATGCATA
* *
3406983 AATGAATTAGT-TTATTAAAT-AACTAGATGCATA
1 AATGAAATAGTATTATTAAATGAACTAAATGCATA
3407016 AATGAA
1 AATGAA
3407022 CTACTTCCCT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
33 17 0.49
34 8 0.23
35 10 0.29
ACGTcount: A:0.47, C:0.07, G:0.14, T:0.32
Consensus pattern (35 bp):
AATGAAATAGTATTATTAAATGAACTAAATGCATA
Found at i:3407051 original size:17 final size:17
Alignment explanation
Indices: 3407031--3407072 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
3407021 ACTACTTCCC
3407031 TAAATGAAATACATGCT
1 TAAATGAAATACATGCT
* *
3407048 TAAATGCAATGCATGCT
1 TAAATGAAATACATGCT
*
3407065 TTAATGAA
1 TAAATGAA
3407073 CAACATACTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.14, T:0.31
Consensus pattern (17 bp):
TAAATGAAATACATGCT
Found at i:3408174 original size:21 final size:21
Alignment explanation
Indices: 3408148--3408187 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
3408138 CTCATTTTCA
3408148 CTCTCAAT-TCTCTTTTCAATG
1 CTCTCAATGTCT-TTTTCAATG
3408169 CTCTCAATGTCTTTTTCAA
1 CTCTCAATGTCTTTTTCAA
3408188 CTCTTGTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.20, C:0.28, G:0.05, T:0.47
Consensus pattern (21 bp):
CTCTCAATGTCTTTTTCAATG
Found at i:3409768 original size:27 final size:27
Alignment explanation
Indices: 3409737--3409792 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
3409727 ATTAAAAGAA
3409737 AACAATCACCTAAATGCAATTGAATTC
1 AACAATCACCTAAATGCAATTGAATTC
3409764 AACAATCACCTAAATGCAATTGAATTC
1 AACAATCACCTAAATGCAATTGAATTC
3409791 AA
1 AA
3409793 TTAAATGACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.21, G:0.07, T:0.25
Consensus pattern (27 bp):
AACAATCACCTAAATGCAATTGAATTC
Found at i:3410645 original size:18 final size:18
Alignment explanation
Indices: 3410597--3410648 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
3410587 AAGAGTTAGT
*
3410597 TTTATT-AATGAAATAAC
1 TTTATTCAATGAACTAAC
*
3410614 ATTATTCAATGAACTAAC
1 TTTATTCAATGAACTAAC
3410632 TTTATTCAATGAACTAA
1 TTTATTCAATGAACTAA
3410649 ATGCATGAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
17 5 0.16
18 26 0.84
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (18 bp):
TTTATTCAATGAACTAAC
Found at i:3410724 original size:17 final size:18
Alignment explanation
Indices: 3410704--3410745 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
3410694 ACTACTTCCC
3410704 TAAATGAAATACATG-TT
1 TAAATGAAATACATGCTT
* *
3410721 TAAATGCAATGCATGCTT
1 TAAATGAAATACATGCTT
3410739 T-AATGAA
1 TAAATGAA
3410746 CAACATACTT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 18 0.86
18 3 0.14
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (18 bp):
TAAATGAAATACATGCTT
Found at i:3411674 original size:13 final size:13
Alignment explanation
Indices: 3411656--3411681 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3411646 TCCATAATAC
3411656 ATCAATTTCCTAA
1 ATCAATTTCCTAA
3411669 ATCAATTTCCTAA
1 ATCAATTTCCTAA
3411682 CTCGACGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.23, G:0.00, T:0.38
Consensus pattern (13 bp):
ATCAATTTCCTAA
Found at i:3411885 original size:3 final size:3
Alignment explanation
Indices: 3411879--3411952 Score: 71
Period size: 3 Copynumber: 24.7 Consensus size: 3
3411869 GTAACCTTTA
* * * *
3411879 AAT AAT AAT AAA AAT AAT -AT TAT CAAT AAT AAC AAT AAT AAT GAT
1 AAT AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT
*
3411924 AAT AAT AAT AAA AATT AA- AAT AAT AAT AA
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AA
3411953 ACCCCGAGAA
Statistics
Matches: 58, Mismatches: 9, Indels: 8
0.77 0.12 0.11
Matches are distributed among these distances:
2 4 0.07
3 50 0.86
4 4 0.07
ACGTcount: A:0.66, C:0.03, G:0.01, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:3413371 original size:26 final size:26
Alignment explanation
Indices: 3413333--3413594 Score: 187
Period size: 26 Copynumber: 11.0 Consensus size: 26
3413323 CGCATTAACA
* * * *
3413333 CATCCATTGATGCAATTTAACTATGG
1 CATCCTTTCATGCATTTTAATTATGG
*
3413359 CATCCTTTCATGCATTTTAATTTTGG
1 CATCCTTTCATGCATTTTAATTATGG
* *
3413385 CATCCTTTCGTGCATTTTAATTATGT
1 CATCCTTTCATGCATTTTAATTATGG
*
3413411 CATCCTTAT-ATGC--CTT-A--AT-G
1 CATCCTT-TCATGCATTTTAATTATGG
* *
3413431 CATCATTTCATGCATTTTAATTATGA
1 CATCCTTTCATGCATTTTAATTATGG
*
3413457 CATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
3413477 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
* * *
3413503 CATCATTTGATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
*
3413523 CATCCTTTTATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
* *
3413549 AATCCTTTCATGC--CTT-A--AT-G
1 CATCCTTTCATGCATTTTAATTATGG
3413569 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
3413595 ATTCAATTTA
Statistics
Matches: 181, Mismatches: 29, Indels: 52
0.69 0.11 0.20
Matches are distributed among these distances:
19 1 0.01
20 48 0.27
21 8 0.04
22 8 0.04
23 8 0.04
24 8 0.04
25 8 0.04
26 91 0.50
27 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (26 bp):
CATCCTTTCATGCATTTTAATTATGG
Found at i:3413374 original size:46 final size:46
Alignment explanation
Indices: 3413333--3413594 Score: 337
Period size: 46 Copynumber: 5.6 Consensus size: 46
3413323 CGCATTAACA
* * * * *
3413333 CATCCATTGATGCAATTTAACTATGGCATCCTTTCATGCATTTTAATTTTGG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGC--CTTAA---T-G
* *
3413385 CATCCTTTCGTGCATTTTAATTATGTCATCCTTAT-ATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTT-TCATGCCTTAATG
* *
3413431 CATCATTTCATGCATTTTAATTATGACATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
* *
3413477 CATCCTTTCATGCATTTTAATTATGGCATCATTTGATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
* *
3413523 CATCCTTTTATGCATTTTAATTATGGAATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
3413569 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGCATTTTAATTATGG
3413595 ATTCAATTTA
Statistics
Matches: 189, Mismatches: 19, Indels: 10
0.87 0.09 0.05
Matches are distributed among these distances:
45 1 0.01
46 151 0.80
47 1 0.01
50 4 0.02
52 31 0.16
53 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.11, T:0.44
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGGCATCCTTTCATGCCTTAATG
Found at i:3413443 original size:20 final size:20
Alignment explanation
Indices: 3413411--3413581 Score: 92
Period size: 20 Copynumber: 7.7 Consensus size: 20
3413401 TTAATTATGT
3413411 CATCCTTAT-ATGCCTTAATG
1 CATCCTT-TCATGCCTTAATG
* *
3413431 CATCATTTCATGCATTTTAATTATG
1 CATCCTTTCATGC--CTT-A--ATG
3413456 ACATCCTTTCATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
*
3413477 CATCCTTTCATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
* *
3413503 CATCATTTGATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
3413523 CATCCTTTTATGCATTTTAATTATGG
1 CATCCTTTCATGC--CTT-A--AT-G
*
3413549 AATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
3413569 CATCCTTTCATGC
1 CATCCTTTCATGC
3413582 ATTTTAATTA
Statistics
Matches: 117, Mismatches: 15, Indels: 38
0.69 0.09 0.22
Matches are distributed among these distances:
19 1 0.01
20 48 0.41
21 7 0.06
22 6 0.05
23 6 0.05
24 6 0.05
25 7 0.06
26 36 0.31
ACGTcount: A:0.24, C:0.22, G:0.11, T:0.43
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:3414336 original size:45 final size:45
Alignment explanation
Indices: 3414233--3414339 Score: 160
Period size: 45 Copynumber: 2.4 Consensus size: 45
3414223 TGCATTTTAA
* * * * *
3414233 TTATGTCATCCTTACATGTCTTTTATACACTATTATACCTTTCAT
1 TTATGACATCCTTTCATGCCTTTGATACACTATTATACATTTCAT
3414278 TTATGACATCCTTTCATGCCTTTGATACACTATTATACATTTCAT
1 TTATGACATCCTTTCATGCCTTTGATACACTATTATACATTTCAT
*
3414323 TTATGGCATCCTTTCAT
1 TTATGACATCCTTTCAT
3414340 ACAATTATGC
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.24, C:0.22, G:0.07, T:0.47
Consensus pattern (45 bp):
TTATGACATCCTTTCATGCCTTTGATACACTATTATACATTTCAT
Found at i:3415243 original size:57 final size:57
Alignment explanation
Indices: 3415074--3415674 Score: 817
Period size: 57 Copynumber: 10.5 Consensus size: 57
3415064 GTCCAATAAA
* * ** * **
3415074 GAAATTCATACACTTAGTATGAATTTCTTATCATGTTAGCACATGAAGTGCCCTATCT
1 GAAATTCATACACTTAGTATG-ATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
3415132 GGAAATTCATACACTTAGTATGATTTCCTTATCATTTTAGCGTACGAAATGCCCTATCT
1 -GAAATTCATACACTTAGTATGATTT-CTTAACATTTTAGCGTACGAAACGCCCTATCT
* *
3415191 GAAATTCATACACTTAGTATGATGTCTTAACATTTTAGCGTACGAAATGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * * *
3415248 AAAATTCATACACTTAGTACGATTTCTTAACATTTTAGCGTACGAAACACCATATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * * *
3415305 GAAATTCATACATTTAGTATTATTTCTTAACATTTTAGCATACGAAACACCCTATAT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3415362 GAAATTCATACACTTAGTTTCATTTCTTAACATTTTAGCGTACGAAATGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * * *
3415419 GAAATTCATACACGTAGTATGTTTTCTTAATATTTTAGTGTACGAAACGCCCTATTT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * * ** *
3415476 GAAATTCATACCCTTGGTATAATTTCTTAACATTTTAGTATACGAAACGCCCTATTT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
3415533 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
* * *
3415590 GAAATTCATACACTTAGTATGATTTCTTAACATTGTAACGTACGAAACTCCCTATCT
1 GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
*
3415647 GAAATTTATACAC-TAGTATGATTTCTTA
1 GAAATTCATACACTTAGTATGATTTCTTA
3415675 TATTTTGCAC
Statistics
Matches: 489, Mismatches: 52, Indels: 5
0.90 0.10 0.01
Matches are distributed among these distances:
56 15 0.03
57 398 0.81
58 28 0.06
59 48 0.10
ACGTcount: A:0.32, C:0.19, G:0.11, T:0.37
Consensus pattern (57 bp):
GAAATTCATACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCT
Found at i:3415742 original size:84 final size:85
Alignment explanation
Indices: 3415599--3415759 Score: 254
Period size: 84 Copynumber: 1.9 Consensus size: 85
3415589 TGAAATTCAT
* *
3415599 ACACTTAGTATGATTTCTTAACATTGTAACGTACGAAACTCCCTATCTGAAATTTATACAC-TAG
1 ACACTTAGTATGATTTCTTAACATTGTAACGTACGAAACTCCCTATCTAAAATTCATACACTTAG
3415663 TATGATTTCTTATATTTTGC
66 TATGATTTCTTATATTTTGC
* * *
3415683 ACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAA-TGCCCTATCTAAAATTCATACACTTA
1 ACACTTAGTATGATTTCTTAACATTGTAACGTACGAAACT-CCCTATCTAAAATTCATACACTTA
3415747 GTATGATTTCTTA
65 GTATGATTTCTTA
3415760 AAATTTTAGC
Statistics
Matches: 70, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
83 1 0.01
84 54 0.77
85 15 0.21
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.40
Consensus pattern (85 bp):
ACACTTAGTATGATTTCTTAACATTGTAACGTACGAAACTCCCTATCTAAAATTCATACACTTAG
TATGATTTCTTATATTTTGC
Found at i:3415771 original size:57 final size:57
Alignment explanation
Indices: 3415683--3415816 Score: 214
Period size: 57 Copynumber: 2.4 Consensus size: 57
3415673 TATATTTTGC
* * *
3415683 ACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAATGCCCTATCTAAAATTCAT
1 ACACTTAGTATGATTTCTTAAAATTTTAGCGTACGAAACGCCCTATCTAAAATTCAT
* *
3415740 ACACTTAGTATGATTTCTTAAAATTTTAGCGTACGAAACGTCCTATCTGAAATTCAT
1 ACACTTAGTATGATTTCTTAAAATTTTAGCGTACGAAACGCCCTATCTAAAATTCAT
*
3415797 ACACTTAATATGATTTCTTA
1 ACACTTAGTATGATTTCTTA
3415817 TATTTTGCAC
Statistics
Matches: 71, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
57 71 1.00
ACGTcount: A:0.34, C:0.17, G:0.10, T:0.39
Consensus pattern (57 bp):
ACACTTAGTATGATTTCTTAAAATTTTAGCGTACGAAACGCCCTATCTAAAATTCAT
Found at i:3415799 original size:141 final size:142
Alignment explanation
Indices: 3415542--3415833 Score: 489
Period size: 141 Copynumber: 2.1 Consensus size: 142
3415532 TGAAATTCAT
*
3415542 ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTGAAATTCATACACTTAG
1 ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTAAAATTCATACACTTAG
* * *
3415607 TATGATTTCTTAACATTGTAACGTACGAAACTCCCTATCTGAAATTTATACAC-TAGTATGATTT
66 TATGATTTCTTAAAATTGTAACGTACGAAACTCCCTATCTGAAATTCATACACTTAATATGATTT
3415671 CTTATATTTTGC
131 CTTATATTTTGC
* *
3415683 ACACTTAGTATGATTTCTTAACATTTTAGCGTATGAAATGCCCTATCTAAAATTCATACACTTAG
1 ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTAAAATTCATACACTTAG
* *
3415748 TATGATTTCTTAAAATTTTAGCGTACGAAACGT-CCTATCTGAAATTCATACACTTAATATGATT
66 TATGATTTCTTAAAATTGTAACGTACGAAAC-TCCCTATCTGAAATTCATACACTTAATATGATT
3415812 TCTTATATTTTGC
130 TCTTATATTTTGC
3415825 ACACTTAGT
1 ACACTTAGT
3415834 GCCCTTTGGA
Statistics
Matches: 141, Mismatches: 8, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
141 109 0.77
142 32 0.23
ACGTcount: A:0.32, C:0.18, G:0.11, T:0.39
Consensus pattern (142 bp):
ACACTTAGTATGATTTCTTAACATTTTAGCGTACGAAACGCCCTATCTAAAATTCATACACTTAG
TATGATTTCTTAAAATTGTAACGTACGAAACTCCCTATCTGAAATTCATACACTTAATATGATTT
CTTATATTTTGC
Found at i:3423794 original size:46 final size:45
Alignment explanation
Indices: 3423735--3423838 Score: 102
Period size: 46 Copynumber: 2.3 Consensus size: 45
3423725 TAATTTTAGT
* *
3423735 TATGTC-TCTTTTCACGCATTAACACATCCATTGATGCAATTTAA
1 TATGTCATCCTTTCACGCATTAACACATCCATTCATGCAATTTAA
* * ** * *
3423779 CTATGTCATCCTTTCATGCCTTAATGCATCCTTTCATGCATTTTAA
1 -TATGTCATCCTTTCACGCATTAACACATCCATTCATGCAATTTAA
*
3423825 TGATGGCATCCTTT
1 T-ATGTCATCCTTT
3423839 TATGCCTTAA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
45 7 0.15
46 41 0.85
ACGTcount: A:0.24, C:0.24, G:0.11, T:0.41
Consensus pattern (45 bp):
TATGTCATCCTTTCACGCATTAACACATCCATTCATGCAATTTAA
Found at i:3423810 original size:20 final size:20
Alignment explanation
Indices: 3423785--3423973 Score: 83
Period size: 20 Copynumber: 8.6 Consensus size: 20
3423775 TTAACTATGT
3423785 CATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
*
3423805 CATCCTTTCATGCATTTTAATGATGG
1 CATCCTTTCATGC--CTT-A--AT-G
*
3423831 CATCCTTTTATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
** * * *
3423851 CATTATTTCATTCATTTTAATTATAA
1 CATCCTTTCATGC--CTT-A--AT-G
*
3423877 CATCTTTTCATGCCTTAATG
1 CATCCTTTCATGCCTTAATG
* *
3423897 CATCATTTCATGCATTTTAATTATG
1 CATCCTTTCATGC--CTT-A--ATG
* * *
3423922 ACCTTCTTTTATGCCTTAATG
1 -CATCCTTTCATGCCTTAATG
*
3423943 CATCCTTTCATGCCTTAATA
1 CATCCTTTCATGCCTTAATG
3423963 CATCC-TTCATG
1 CATCCTTTCATG
3423974 TATTTTAATT
Statistics
Matches: 126, Mismatches: 25, Indels: 37
0.67 0.13 0.20
Matches are distributed among these distances:
19 6 0.05
20 56 0.44
21 7 0.06
22 6 0.05
23 6 0.05
24 6 0.05
25 7 0.06
26 32 0.25
ACGTcount: A:0.24, C:0.23, G:0.08, T:0.45
Consensus pattern (20 bp):
CATCCTTTCATGCCTTAATG
Found at i:3423844 original size:46 final size:46
Alignment explanation
Indices: 3423759--3423955 Score: 243
Period size: 46 Copynumber: 4.3 Consensus size: 46
3423749 CGCATTAACA
* * * * * *
3423759 CATCCATTGATGCAATTTAACTATGTCATCCTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTTATGCCTTAATG
* *
3423805 CATCCTTTCATGCATTTTAATGATGGCATCCTTTTATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTTATGCCTTAATG
** * *
3423851 CATTATTTCATTCATTTTAATTATAACAT-CTTTTCATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTT-ATGCCTTAATG
* * *
3423897 CATCATTTCATGCATTTTAATTATGACCTTCTTTTATGCCTTAATG
1 CATCCTTTCATGCATTTTAATTATGACATCCTTTTATGCCTTAATG
3423943 CATCCTTTCATGC
1 CATCCTTTCATGC
3423956 CTTAATACAT
Statistics
Matches: 131, Mismatches: 18, Indels: 4
0.86 0.12 0.03
Matches are distributed among these distances:
45 5 0.04
46 121 0.92
47 5 0.04
ACGTcount: A:0.24, C:0.22, G:0.09, T:0.45
Consensus pattern (46 bp):
CATCCTTTCATGCATTTTAATTATGACATCCTTTTATGCCTTAATG
Found at i:3424076 original size:2 final size:2
Alignment explanation
Indices: 3424064--3424115 Score: 97
Period size: 2 Copynumber: 26.5 Consensus size: 2
3424054 ATAATCAACA
3424064 AT AT A- 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
3424105 AT AT AT AT AT A
1 AT AT AT AT AT A
3424116 AATAGCATTC
Statistics
Matches: 49, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 48 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3424530 original size:19 final size:20
Alignment explanation
Indices: 3424506--3424555 Score: 93
Period size: 20 Copynumber: 2.5 Consensus size: 20
3424496 GTTTTAAAAT
3424506 GGTATTGATACCTT-CCTTC
1 GGTATTGATACCTTCCCTTC
3424525 GGTATTGATACCTTCCCTTC
1 GGTATTGATACCTTCCCTTC
3424545 GGTATTGATAC
1 GGTATTGATAC
3424556 TACTTGGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.18, C:0.24, G:0.18, T:0.40
Consensus pattern (20 bp):
GGTATTGATACCTTCCCTTC
Found at i:3427828 original size:12 final size:11
Alignment explanation
Indices: 3427781--3427824 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
3427771 AAAAGATCAA
*
3427781 TTAAAAGAATT
1 TTAAAAAAATT
*
3427792 TTGAAAAAATT
1 TTAAAAAAATT
*
3427803 TTAATAAAAAAT
1 TTAA-AAAAATT
3427815 TTAAAAAAAT
1 TTAAAAAAAT
3427825 ATTTCCCTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 17 0.63
12 10 0.37
ACGTcount: A:0.61, C:0.00, G:0.05, T:0.34
Consensus pattern (11 bp):
TTAAAAAAATT
Found at i:3428701 original size:10 final size:10
Alignment explanation
Indices: 3428677--3428753 Score: 67
Period size: 10 Copynumber: 8.0 Consensus size: 10
3428667 ACTTAATATG
*
3428677 TTCTCTTTC-
1 TTCTTTTTCT
3428686 TTCTTTTTCT
1 TTCTTTTTCT
3428696 TTCTTTTTC-
1 TTCTTTTTCT
3428705 -TCTTTTT-T
1 TTCTTTTTCT
3428713 ATTCTTTTTCT
1 -TTCTTTTTCT
3428724 TT-TCTTTTCT
1 TTCT-TTTTCT
*
3428734 TTTTTTCTTCT
1 TTCTTT-TTCT
3428745 TT-TTTTTCT
1 TTCTTTTTCT
3428754 CTTTATTTTT
Statistics
Matches: 59, Mismatches: 1, Indels: 16
0.78 0.01 0.21
Matches are distributed among these distances:
8 7 0.12
9 13 0.22
10 31 0.53
11 8 0.14
ACGTcount: A:0.01, C:0.19, G:0.00, T:0.79
Consensus pattern (10 bp):
TTCTTTTTCT
Found at i:3428710 original size:18 final size:17
Alignment explanation
Indices: 3428680--3428781 Score: 72
Period size: 18 Copynumber: 5.9 Consensus size: 17
3428670 TAATATGTTC
3428680 TCTTTCTTC-TTTTTCTT
1 TCTTT-TTCTTTTTTCTT
3428697 TCTTTTTCTCTTTTT-TAT
1 TCTTTTTCT-TTTTTCT-T
*
3428715 TCTTTTTCTTTTCT-TT
1 TCTTTTTCTTTTTTCTT
*
3428731 TC-TTTT-TTTCTTCTT
1 TCTTTTTCTTTTTTCTT
*
3428746 T-TTTTTCTCTTTATTTTT
1 TCTTTTTCT-TTT-TTCTT
3428764 TCATTTTTCATTTTTTCT
1 TC-TTTTTC-TTTTTTCT
3428782 CTATCCTCAC
Statistics
Matches: 68, Mismatches: 6, Indels: 20
0.72 0.06 0.21
Matches are distributed among these distances:
14 4 0.06
15 11 0.16
16 7 0.10
17 13 0.19
18 20 0.29
19 3 0.04
20 9 0.13
21 1 0.01
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (17 bp):
TCTTTTTCTTTTTTCTT
Found at i:3428721 original size:28 final size:28
Alignment explanation
Indices: 3428686--3428757 Score: 105
Period size: 27 Copynumber: 2.6 Consensus size: 28
3428676 GTTCTCTTTC
3428686 TTCTTTTTCTTTCT-TTTTCTCTTTTTTA
1 TTCTTTTTCTTTCTCTTTTCT-TTTTTTA
*
3428714 TTCTTTTTCTTT-TCTTTTCTTTTTTTC
1 TTCTTTTTCTTTCTCTTTTCTTTTTTTA
3428741 TTCTTTTT-TTTCTCTTT
1 TTCTTTTTCTTTCTCTTT
3428758 ATTTTTTCAT
Statistics
Matches: 41, Mismatches: 1, Indels: 5
0.87 0.02 0.11
Matches are distributed among these distances:
26 3 0.07
27 20 0.49
28 18 0.44
ACGTcount: A:0.01, C:0.18, G:0.00, T:0.81
Consensus pattern (28 bp):
TTCTTTTTCTTTCTCTTTTCTTTTTTTA
Found at i:3428744 original size:16 final size:16
Alignment explanation
Indices: 3428695--3428751 Score: 55
Period size: 16 Copynumber: 3.5 Consensus size: 16
3428685 CTTCTTTTTC
*
3428695 TTTCTTTTTCTCTT-T
1 TTTCTTTTTTTCTTCT
*
3428710 TTTATTCTTTTTCTTTTCT
1 TTTCTT-TTTTTC--TTCT
3428729 TTTCTTTTTTTCTTCT
1 TTTCTTTTTTTCTTCT
3428745 TTT-TTTT
1 TTTCTTTT
3428752 CTCTTTATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 8
0.76 0.07 0.17
Matches are distributed among these distances:
15 9 0.26
16 12 0.34
18 8 0.23
19 6 0.17
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (16 bp):
TTTCTTTTTTTCTTCT
Found at i:3428749 original size:46 final size:52
Alignment explanation
Indices: 3428677--3428777 Score: 133
Period size: 48 Copynumber: 2.0 Consensus size: 52
3428667 ACTTAATATG
3428677 TTCTCTTTCTTCTTTTTCTTTC-TTTTTCTCTTT-TTTATTC-TTTTTC-TT
1 TTCTCTTTCTTCTTTTTCTTTCTTTTTTCTCTTTATTTATTCATTTTTCATT
* *
3428725 TTCT-TTTCTT-TTTTTCTTCTTTTTTTTCTCTTTATTTTTTCATTTTTCATT
1 TTCTCTTTCTTCTTTTTCTT-TCTTTTTTCTCTTTATTTATTCATTTTTCATT
3428776 TT
1 TT
3428778 TTCTCTATCC
Statistics
Matches: 46, Mismatches: 2, Indels: 7
0.84 0.04 0.13
Matches are distributed among these distances:
46 8 0.17
47 7 0.15
48 15 0.33
49 6 0.13
50 6 0.13
51 4 0.09
ACGTcount: A:0.04, C:0.18, G:0.00, T:0.78
Consensus pattern (52 bp):
TTCTCTTTCTTCTTTTTCTTTCTTTTTTCTCTTTATTTATTCATTTTTCATT
Found at i:3428764 original size:28 final size:28
Alignment explanation
Indices: 3428682--3428764 Score: 100
Period size: 27 Copynumber: 3.0 Consensus size: 28
3428672 ATATGTTCTC
*
3428682 TTTCTTCTTTTTCTTTCT-TTTTCTCTTT
1 TTTCTTCTTTTTCTTTCTCTTTT-TTTTT
* *
3428710 TTTATTCTTTTTCTTT-TCTTTTCTTTT
1 TTTCTTCTTTTTCTTTCTCTTTTTTTTT
*
3428737 TTTCTTCTTTTT-TTTCTCTTTATTTTT
1 TTTCTTCTTTTTCTTTCTCTTTTTTTTT
3428764 T
1 T
3428765 CATTTTTCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 5
0.81 0.10 0.09
Matches are distributed among these distances:
26 3 0.06
27 25 0.53
28 19 0.40
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (28 bp):
TTTCTTCTTTTTCTTTCTCTTTTTTTTT
Found at i:3428776 original size:15 final size:13
Alignment explanation
Indices: 3428677--3428783 Score: 66
Period size: 13 Copynumber: 8.5 Consensus size: 13
3428667 ACTTAATATG
*
3428677 TTCTCTTTCTTCTT
1 TTCTCTTTATT-TT
*
3428691 TT-TCTTT-CTTT
1 TTCTCTTTATTTT
*
3428702 TTCTCTTT-TTTA
1 TTCTCTTTATTTT
*
3428714 TTCT-TTT-TCTT
1 TTCTCTTTATTTT
*
3428725 TTCT-TTTCTTTT
1 TTCTCTTTATTTT
*
3428737 TT-TCTTCTTTTTT
1 TTCTCTT-TATTTT
3428750 TTCTCTTTATTTT
1 TTCTCTTTATTTT
*
3428763 TTCATTTTTCATTTT
1 TTC-TCTTT-ATTTT
3428778 TTCTCT
1 TTCTCT
3428784 ATCCTCACCT
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
11 17 0.22
12 19 0.25
13 20 0.26
14 12 0.16
15 8 0.11
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.78
Consensus pattern (13 bp):
TTCTCTTTATTTT
Found at i:3432694 original size:17 final size:17
Alignment explanation
Indices: 3432652--3432694 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3432642 AAGAAAAATC
* *
3432652 AAGAAAAAATAAAAATA
1 AAGAAAATATAAAAAGA
3432669 AA-AATAATATAAAAAGA
1 AAGAA-AATATAAAAAGA
3432686 AAGAAAATA
1 AAGAAAATA
3432695 GAAATTTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 2 0.09
17 18 0.82
18 2 0.09
ACGTcount: A:0.79, C:0.00, G:0.07, T:0.14
Consensus pattern (17 bp):
AAGAAAATATAAAAAGA
Found at i:3438169 original size:37 final size:37
Alignment explanation
Indices: 3438112--3438185 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
3438102 ACCTTTGGAT
*
3438112 TAGGTAGATCGAATATCTAAAAACGTCTTTTAAAACA
1 TAGGTAGATCGAATACCTAAAAACGTCTTTTAAAACA
* *
3438149 TAGGTAGATCGAGTACCTAAAAGCGTCTTTTAAAACA
1 TAGGTAGATCGAATACCTAAAAACGTCTTTTAAAACA
3438186 AATTGAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.41, C:0.15, G:0.16, T:0.28
Consensus pattern (37 bp):
TAGGTAGATCGAATACCTAAAAACGTCTTTTAAAACA
Found at i:3438622 original size:9 final size:9
Alignment explanation
Indices: 3438608--3438640 Score: 66
Period size: 9 Copynumber: 3.7 Consensus size: 9
3438598 AAATGAGGAA
3438608 ATAATTATT
1 ATAATTATT
3438617 ATAATTATT
1 ATAATTATT
3438626 ATAATTATT
1 ATAATTATT
3438635 ATAATT
1 ATAATT
3438641 CATCCCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
ATAATTATT
Found at i:3440309 original size:3 final size:3
Alignment explanation
Indices: 3440301--3440353 Score: 63
Period size: 3 Copynumber: 17.7 Consensus size: 3
3440291 ACATCATGTA
* * *
3440301 AAT AAT AAT AAA AAT AAT ATT AGT AAT AAT AAT AAT AATT AA- AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT AAT
3440346 AAT AAT AA
1 AAT AAT AA
3440354 ACTCCGGACA
Statistics
Matches: 43, Mismatches: 5, Indels: 4
0.83 0.10 0.08
Matches are distributed among these distances:
2 2 0.05
3 38 0.88
4 3 0.07
ACGTcount: A:0.66, C:0.00, G:0.02, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:3442792 original size:19 final size:19
Alignment explanation
Indices: 3442756--3442827 Score: 90
Period size: 19 Copynumber: 3.6 Consensus size: 19
3442746 ACCCAGTTTC
3442756 CAAATTCGCAACACTGAATTT
1 CAAATTCGC-A-ACTGAATTT
*
3442777 CAAATTCGTAACTGAATTT
1 CAAATTCGCAACTGAATTT
*
3442796 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACT-GAATTT
*
3442816 CGAATTCGCAAC
1 CAAATTCGCAAC
3442828 AGGTTTTAGT
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
19 21 0.46
20 17 0.37
21 8 0.17
ACGTcount: A:0.35, C:0.24, G:0.11, T:0.31
Consensus pattern (19 bp):
CAAATTCGCAACTGAATTT
Found at i:3442821 original size:20 final size:20
Alignment explanation
Indices: 3442716--3442827 Score: 93
Period size: 20 Copynumber: 5.6 Consensus size: 20
3442706 AAATGACCAA
* * * *
3442716 CAAATTTGCAACGCGAACTC
1 CAAATTCGCAACTCGAATTT
* * *
3442736 CAATTTCGCAAC-CCAGTTT
1 CAAATTCGCAACTCGAATTT
*
3442755 CCAAATTCGCAACACTGAATTT
1 -CAAATTCGCAACTC-GAATTT
*
3442777 CAAATTCGTAACT-GAATTT
1 CAAATTCGCAACTCGAATTT
*
3442796 CAAATTCGCAACTCGATTTT
1 CAAATTCGCAACTCGAATTT
*
3442816 CGAATTCGCAAC
1 CAAATTCGCAAC
3442828 AGGTTTTAGT
Statistics
Matches: 74, Mismatches: 14, Indels: 8
0.77 0.15 0.08
Matches are distributed among these distances:
19 21 0.28
20 37 0.50
21 12 0.16
22 4 0.05
ACGTcount: A:0.33, C:0.27, G:0.12, T:0.29
Consensus pattern (20 bp):
CAAATTCGCAACTCGAATTT
Found at i:3443003 original size:14 final size:15
Alignment explanation
Indices: 3442984--3443021 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
3442974 TCCCCATCTC
3442984 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
3442998 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
3443014 TAATTTTT
1 TAATTTTT
3443022 AAATGATTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:3443809 original size:24 final size:24
Alignment explanation
Indices: 3443749--3443816 Score: 91
Period size: 24 Copynumber: 2.8 Consensus size: 24
3443739 ATGAGTACTA
* *
3443749 GTCAATATTCGAAATTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
* *
3443773 GTCAATACCCGGACTTTGATCTTG
1 GTCAATACTCGGAATTTGATCTTG
*
3443797 GTCAATACTCGGATTTTGAT
1 GTCAATACTCGGAATTTGAT
3443817 GATGTTTCAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.25, C:0.18, G:0.19, T:0.38
Consensus pattern (24 bp):
GTCAATACTCGGAATTTGATCTTG
Found at i:3444007 original size:20 final size:21
Alignment explanation
Indices: 3443970--3444010 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3443960 TGAACATTCA
*
3443970 TCCCTGAAGAAGAAAAAGAAG
1 TCCCCGAAGAAGAAAAAGAAG
3443991 TCCCCGAAGAA-AAAAAGAAG
1 TCCCCGAAGAAGAAAAAGAAG
3444011 AAGAAAATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.54, C:0.17, G:0.22, T:0.07
Consensus pattern (21 bp):
TCCCCGAAGAAGAAAAAGAAG
Found at i:3446070 original size:12 final size:12
Alignment explanation
Indices: 3446053--3446093 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
3446043 AGCAAAAAGA
*
3446053 AATCAAAATCGC
1 AATCAAAATCAC
*
3446065 AATCAAAATCAA
1 AATCAAAATCAC
*
3446077 AATCAAAATCCC
1 AATCAAAATCAC
3446089 AATCA
1 AATCA
3446094 CAACCGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (12 bp):
AATCAAAATCAC
Found at i:3446074 original size:6 final size:6
Alignment explanation
Indices: 3446052--3446086 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
3446042 AAGCAAAAAG
* *
3446052 AAATCA AAATCG CAATCA AAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
3446087 CCAATCACAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (6 bp):
AAATCA
Found at i:3446369 original size:42 final size:43
Alignment explanation
Indices: 3446305--3446385 Score: 128
Period size: 42 Copynumber: 1.9 Consensus size: 43
3446295 AATTCGCAAC
* * *
3446305 GCGAAATTCAAATTCACGTTGCGATTTTT-TGTTGCGATTGAT
1 GCGAAAGTCAAATTCACATTGCGATTTTTGCGTTGCGATTGAT
3446347 GCGAAAGTCAAATTCACATTGCGATTTTTGCGTTGCGAT
1 GCGAAAGTCAAATTCACATTGCGATTTTTGCGTTGCGAT
3446386 AGTCAAATTC
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
42 27 0.77
43 8 0.23
ACGTcount: A:0.25, C:0.16, G:0.22, T:0.37
Consensus pattern (43 bp):
GCGAAAGTCAAATTCACATTGCGATTTTTGCGTTGCGATTGAT
Found at i:3446409 original size:20 final size:20
Alignment explanation
Indices: 3446381--3446424 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
3446371 TTTTTGCGTT
*
3446381 GCGATAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
* *
3446401 GCGAAAGTCAAATTTGCAAT
1 GCGAAAGTCAAATTCGCAAC
3446421 GCGA
1 GCGA
3446425 TTATCGCGTT
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:0.36, C:0.20, G:0.23, T:0.20
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:3446537 original size:20 final size:20
Alignment explanation
Indices: 3446491--3446542 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
3446481 AAATCGCAAC
**
3446491 GCGAATTTGACTTTCGCATT
1 GCGAATTTGACTTTAACATT
* * *
3446511 ACAAATTTGACTTTAACGTT
1 GCGAATTTGACTTTAACATT
3446531 GCGAATTTGACT
1 GCGAATTTGACT
3446543 ATCGCAACGA
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.27, C:0.17, G:0.17, T:0.38
Consensus pattern (20 bp):
GCGAATTTGACTTTAACATT
Found at i:3446685 original size:64 final size:64
Alignment explanation
Indices: 3446608--3446762 Score: 274
Period size: 64 Copynumber: 2.4 Consensus size: 64
3446598 AATAAATAAT
3446608 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAAC
* * *
3446672 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTTTTATTTCCTCATCAATTAAAC
1 AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAAC
3446736 AAATCAACTTTTACAAATCAATGTAAA
1 AAATCAACTTTTACAAATCAAT-TAAA
3446763 ATTCAATTAA
Statistics
Matches: 87, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
64 83 0.95
65 4 0.05
ACGTcount: A:0.50, C:0.17, G:0.02, T:0.31
Consensus pattern (64 bp):
AAATCAACTTTTACAAATCAATTAAACAAGCAAAAAATAATTCTTATTTACACATCAATTAAAC
Found at i:3448189 original size:42 final size:42
Alignment explanation
Indices: 3448130--3448248 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
3448120 GTGAATCGAG
* *
3448130 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGAGAGGGGA
* * *
3448172 CTCTTGAACGGTGGGAGGGGCCTCCTGAACGATGAGAGTGGA
1 CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGAGAGGGGA
* *
3448214 CTCTTGAA-GGATAGGAGGTACCTCTTGAACGATGA
1 CTCTTGAACGG-TGGGAGGGACCTCTTGAACGATGA
3448249 CAGGTGCATC
Statistics
Matches: 67, Mismatches: 9, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
41 2 0.03
42 65 0.97
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (42 bp):
CTCTTGAACGGTGGGAGGGACCTCTTGAACGATGAGAGGGGA
Found at i:3448253 original size:21 final size:21
Alignment explanation
Indices: 3448130--3448248 Score: 116
Period size: 21 Copynumber: 5.7 Consensus size: 21
3448120 GTGAATCGAG
* *
3448130 CTCTTGAACGGTGGGAGGGAC
1 CTCTTGAACGATGAGAGGGAC
* *
3448151 CTCTTGAACGATGATAGGGGC
1 CTCTTGAACGATGAGAGGGAC
* * *
3448172 CTCTTGAACGGTGGGAGGGGC
1 CTCTTGAACGATGAGAGGGAC
*
3448193 CTCCTGAACGATGAGAGTGGA-
1 CTCTTGAACGATGAGAG-GGAC
* *
3448214 CTCTTGAAGGAT-AGGAGGTAC
1 CTCTTGAACGATGA-GAGGGAC
3448235 CTCTTGAACGATGA
1 CTCTTGAACGATGA
3448249 CAGGTGCATC
Statistics
Matches: 79, Mismatches: 15, Indels: 7
0.78 0.15 0.07
Matches are distributed among these distances:
20 3 0.04
21 73 0.92
22 3 0.04
ACGTcount: A:0.24, C:0.18, G:0.36, T:0.22
Consensus pattern (21 bp):
CTCTTGAACGATGAGAGGGAC
Found at i:3448557 original size:21 final size:21
Alignment explanation
Indices: 3448519--3448560 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3448509 TAAAACAATC
* *
3448519 TCACGTAAAGCGGCTACCTCA
1 TCACGTAAAGCAGATACCTCA
*
3448540 TCACGTAAAGTAGATACCTCA
1 TCACGTAAAGCAGATACCTCA
3448561 CCACATAGCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.29, G:0.17, T:0.21
Consensus pattern (21 bp):
TCACGTAAAGCAGATACCTCA
Found at i:3450832 original size:22 final size:22
Alignment explanation
Indices: 3450773--3450842 Score: 72
Period size: 22 Copynumber: 3.3 Consensus size: 22
3450763 TATGAGAGAT
3450773 GGAGATA--GACGGATTTCGTC
1 GGAGATAGGGACGGATTTCGTC
* * * *
3450793 GAAGATGGGGAAGAATTTCGTC
1 GGAGATAGGGACGGATTTCGTC
* *
3450815 GGAGATAGGGACGGATTTTGTT
1 GGAGATAGGGACGGATTTCGTC
3450837 GGAGAT
1 GGAGAT
3450843 GAGAACGGAT
Statistics
Matches: 38, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 5 0.13
22 33 0.87
ACGTcount: A:0.27, C:0.09, G:0.39, T:0.26
Consensus pattern (22 bp):
GGAGATAGGGACGGATTTCGTC
Found at i:3451000 original size:20 final size:20
Alignment explanation
Indices: 3450975--3451013 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
3450965 ATAAATGCGC
*
3450975 TTTGACTTTTGTGTTGCGAA
1 TTTGACTTCTGTGTTGCGAA
3450995 TTTGACTTCTGTGTTGCGA
1 TTTGACTTCTGTGTTGCGA
3451014 TTTACAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.13, C:0.13, G:0.26, T:0.49
Consensus pattern (20 bp):
TTTGACTTCTGTGTTGCGAA
Found at i:3451030 original size:20 final size:20
Alignment explanation
Indices: 3451007--3451114 Score: 135
Period size: 20 Copynumber: 5.3 Consensus size: 20
3450997 TGACTTCTGT
*
3451007 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACATATTCGC
3451027 GTTGCGATTTACATATTCGC
1 GTTGCGATTTACATATTCGC
*
3451047 GTTGCGATTTACATATTCGT
1 GTTGCGATTTACATATTCGC
* * *
3451067 GTTGCGATTTTAGAAAATCGC
1 GTTGCGA-TTTACATATTCGC
** *
3451088 AATGCGATTCACATATTCGC
1 GTTGCGATTTACATATTCGC
3451108 GTTGCGA
1 GTTGCGA
3451115 ATTTGTTGGT
Statistics
Matches: 73, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
20 59 0.81
21 14 0.19
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACATATTCGC
Found at i:3451105 original size:41 final size:40
Alignment explanation
Indices: 3451009--3451114 Score: 131
Period size: 41 Copynumber: 2.6 Consensus size: 40
3450999 ACTTCTGTGT
* * * **
3451009 TGCGATTTACAAATTCGCGTTGCGATTTACATATTCGCGT
1 TGCGATTTACATATTCGCGTTGCGATTTACAAAATCGCAA
* *
3451049 TGCGATTTACATATTCGTGTTGCGATTTTAGAAAATCGCAA
1 TGCGATTTACATATTCGCGTTGCGA-TTTACAAAATCGCAA
*
3451090 TGCGATTCACATATTCGCGTTGCGA
1 TGCGATTTACATATTCGCGTTGCGA
3451115 ATTTGTTGGT
Statistics
Matches: 56, Mismatches: 9, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
40 23 0.41
41 33 0.59
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.36
Consensus pattern (40 bp):
TGCGATTTACATATTCGCGTTGCGATTTACAAAATCGCAA
Found at i:3456800 original size:38 final size:39
Alignment explanation
Indices: 3456721--3456804 Score: 107
Period size: 38 Copynumber: 2.2 Consensus size: 39
3456711 TATCTAGGGG
* *
3456721 TGACATGGCTCCTACGTGATGAGGAGGCCTGGTCGTTGGA
1 TGACACGGCTCCTACGTGATGA-GAGGCCTGGTCGGTGGA
* * *
3456761 TGACACGGTTCCTATGTGATGA-AGGTCTGGTCGGTGGA
1 TGACACGGCTCCTACGTGATGAGAGGCCTGGTCGGTGGA
3456799 TGACAC
1 TGACAC
3456805 AGTTTCTACG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
38 20 0.51
40 19 0.49
ACGTcount: A:0.19, C:0.19, G:0.36, T:0.26
Consensus pattern (39 bp):
TGACACGGCTCCTACGTGATGAGAGGCCTGGTCGGTGGA
Found at i:3457115 original size:30 final size:30
Alignment explanation
Indices: 3457081--3457137 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
3457071 GAGACAAAGC
* *
3457081 TTTGTGTCAAGGGAAACAGA-CTCAAAGATT
1 TTTGTGTCAAAGAAAACA-ATCTCAAAGATT
*
3457111 TTTGTTTCAAAGAAAACAATCTCAAAG
1 TTTGTGTCAAAGAAAACAATCTCAAAG
3457138 TTTGGTGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 1 0.04
30 22 0.96
ACGTcount: A:0.40, C:0.14, G:0.18, T:0.28
Consensus pattern (30 bp):
TTTGTGTCAAAGAAAACAATCTCAAAGATT
Found at i:3457301 original size:36 final size:35
Alignment explanation
Indices: 3457244--3457385 Score: 153
Period size: 36 Copynumber: 3.9 Consensus size: 35
3457234 TCAGAATTTG
*
3457244 TGTTTTAAAGAAAAATT-TCTCAAGCGAGACGAAATT
1 TGTTTT-AAGAGAAATTGTCTCAAGCGAGAC-AAATT
* *
3457280 TGTTTTGAGAGAAATTATCTCAAGCGAGACAAAATT
1 TGTTTTAAGAGAAATTGTCTCAAGCGAGAC-AAATT
* *
3457316 TGTTTTTAGAGAAAATTGTCTCAAGCAAGACAAAGTTT
1 TGTTTTAAGAG-AAATTGTCTCAAGCGAGACAAA--TT
*
3457354 TCTTTTAAGA-AAACTTGTCTCAAGCGAGACAA
1 TGTTTTAAGAGAAA-TTGTCTCAAGCGAGACAA
3457386 CCCTTTGTTT
Statistics
Matches: 92, Mismatches: 9, Indels: 9
0.84 0.08 0.08
Matches are distributed among these distances:
35 8 0.09
36 40 0.43
37 34 0.37
38 10 0.11
ACGTcount: A:0.39, C:0.13, G:0.18, T:0.31
Consensus pattern (35 bp):
TGTTTTAAGAGAAATTGTCTCAAGCGAGACAAATT
Found at i:3457341 original size:37 final size:38
Alignment explanation
Indices: 3457238--3457385 Score: 173
Period size: 37 Copynumber: 4.0 Consensus size: 38
3457228 ACAACTTCAG
* * *
3457238 AATTTGTGTTTTAAAGAAAAATT-TCTCAAGCGAGACGA
1 AATTTGTCTTTTAGAG-AAAATTGTCTCAAGCGAGACAA
* *
3457276 AATTTGT-TTTGAGAG-AAATTATCTCAAGCGAGACAA
1 AATTTGTCTTTTAGAGAAAATTGTCTCAAGCGAGACAA
*
3457312 AATTTGT-TTTTAGAGAAAATTGTCTCAAGCAAGACAA
1 AATTTGTCTTTTAGAGAAAATTGTCTCAAGCGAGACAA
*
3457349 AGTTT-TCTTTTA-AGAAAACTTGTCTCAAGCGAGACAA
1 AATTTGTCTTTTAGAGAAAA-TTGTCTCAAGCGAGACAA
3457386 CCCTTTGTTT
Statistics
Matches: 98, Mismatches: 8, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
35 5 0.05
36 35 0.36
37 51 0.52
38 7 0.07
ACGTcount: A:0.39, C:0.12, G:0.18, T:0.32
Consensus pattern (38 bp):
AATTTGTCTTTTAGAGAAAATTGTCTCAAGCGAGACAA
Found at i:3458400 original size:22 final size:22
Alignment explanation
Indices: 3458355--3458415 Score: 81
Period size: 22 Copynumber: 2.8 Consensus size: 22
3458345 GTGAAATTTT
*
3458355 TCCCGAATGACCTCATG--TATG
1 TCCCGAAAGACCT-ATGTATATG
3458376 TCCCGAAAGACCTATGTATATG
1 TCCCGAAAGACCTATGTATATG
*
3458398 TCCCGAAGGACCTATGTA
1 TCCCGAAAGACCTATGTA
3458416 ACCCTCAACT
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
20 3 0.08
21 12 0.33
22 21 0.58
ACGTcount: A:0.28, C:0.26, G:0.20, T:0.26
Consensus pattern (22 bp):
TCCCGAAAGACCTATGTATATG
Found at i:3459081 original size:2 final size:2
Alignment explanation
Indices: 3459074--3459104 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
3459064 TCGCCTAAGC
*
3459074 AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3459105 ACTTATTATC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:3461702 original size:14 final size:14
Alignment explanation
Indices: 3461673--3461717 Score: 51
Period size: 13 Copynumber: 3.4 Consensus size: 14
3461663 TCCTTGCATG
*
3461673 TTCTTCTGA-TTTT
1 TTCTTTTGATTTTT
3461686 TTCTTTTG-TTCTTT
1 TTCTTTTGATT-TTT
3461700 TTC-TTTGATTTTT
1 TTCTTTTGATTTTT
3461713 TTCTT
1 TTCTT
3461718 CTTTGCTCTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
13 18 0.67
14 9 0.33
ACGTcount: A:0.04, C:0.13, G:0.07, T:0.76
Consensus pattern (14 bp):
TTCTTTTGATTTTT
Found at i:3461734 original size:23 final size:22
Alignment explanation
Indices: 3461684--3461735 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
3461674 TCTTCTGATT
* *
3461684 TTTTCTTTTGTTCTTTTTCTTTG
1 TTTT-TTTTCTTCTTTCTCTTTG
*
3461707 ATTTTTTTCTTCTTTGCTCTTTG
1 TTTTTTTTCTTCTTT-CTCTTTG
3461730 TTTTTT
1 TTTTTT
3461736 CTTTGCTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
22 10 0.42
23 14 0.58
ACGTcount: A:0.02, C:0.13, G:0.08, T:0.77
Consensus pattern (22 bp):
TTTTTTTTCTTCTTTCTCTTTG
Found at i:3461739 original size:18 final size:17
Alignment explanation
Indices: 3461697--3461748 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
3461687 TCTTTTGTTC
*
3461697 TTTTTCTTTGAT-TTTT
1 TTTTTCTTTGCTCTTTT
*
3461713 TTCTTCTTTGCTCTTTGT
1 TTTTTCTTTGCTCTTT-T
3461731 TTTTTCTTTGCTTCTTTT
1 TTTTTCTTTGC-TCTTTT
3461749 CTATTTGTTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
16 10 0.33
17 3 0.10
18 12 0.40
19 5 0.17
ACGTcount: A:0.02, C:0.15, G:0.08, T:0.75
Consensus pattern (17 bp):
TTTTTCTTTGCTCTTTT
Found at i:3461755 original size:26 final size:26
Alignment explanation
Indices: 3461682--3461757 Score: 81
Period size: 26 Copynumber: 3.1 Consensus size: 26
3461672 GTTCTTCTGA
3461682 TTTTTTCTTTTG-TTCTTTT-TCTTTG
1 TTTTTTC-TTTGCTTCTTTTCTCTTTG
* *
3461707 -ATTTT-TTT-CTTCTTTGCTCTTTG
1 TTTTTTCTTTGCTTCTTTTCTCTTTG
*
3461730 TTTTTTCTTTGCTTCTTTTCTATTTG
1 TTTTTTCTTTGCTTCTTTTCTCTTTG
3461756 TT
1 TT
3461758 ATGATTGGAT
Statistics
Matches: 41, Mismatches: 5, Indels: 9
0.75 0.09 0.16
Matches are distributed among these distances:
22 9 0.22
23 6 0.15
24 8 0.20
25 3 0.07
26 15 0.37
ACGTcount: A:0.03, C:0.14, G:0.08, T:0.75
Consensus pattern (26 bp):
TTTTTTCTTTGCTTCTTTTCTCTTTG
Found at i:3465416 original size:54 final size:54
Alignment explanation
Indices: 3465348--3465553 Score: 259
Period size: 54 Copynumber: 3.8 Consensus size: 54
3465338 GCCCATATGT
* ** * *
3465348 TTATTCATAAACATATTATAAATTCCGTGAAATGTACACTTAGTACCGAAATGG
1 TTATTCATCAACATAGGATAAATTCCGTGAAATGTACACTTAGTGCCGAAACGG
* *
3465402 TTATTCATCCACATAGGATAAATTCCGTGAAATGTACACTTAGTGCCAAAACGG
1 TTATTCATCAACATAGGATAAATTCCGTGAAATGTACACTTAGTGCCGAAACGG
* ** * * *
3465456 TTATTCATCCACATAGGATGGATTCCGTGAAATCTACACTTATTGTCGAAACGG
1 TTATTCATCAACATAGGATAAATTCCGTGAAATGTACACTTAGTGCCGAAACGG
* * * *
3465510 TTATTCATCAACATAGGATGAATTCCATGAAATGCACATTTAGT
1 TTATTCATCAACATAGGATAAATTCCGTGAAATGTACACTTAGT
3465554 TCCTATTGGG
Statistics
Matches: 132, Mismatches: 20, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 132 1.00
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Consensus pattern (54 bp):
TTATTCATCAACATAGGATAAATTCCGTGAAATGTACACTTAGTGCCGAAACGG
Found at i:3466030 original size:19 final size:19
Alignment explanation
Indices: 3465992--3466061 Score: 77
Period size: 19 Copynumber: 3.6 Consensus size: 19
3465982 TGTTTTGAAT
* *
3465992 GGTATCGATACCTTCCCTTC
1 GGTATCAATACC-CCCCTTC
*
3466012 GATATCAATACCCCCCTTC
1 GGTATCAATACCCCCCTTC
* *
3466031 GGTATCAATATCCCCATTC
1 GGTATCAATACCCCCCTTC
*
3466050 GGTATCGATACC
1 GGTATCAATACC
3466062 GATTGAATCA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
19 32 0.76
20 10 0.24
ACGTcount: A:0.23, C:0.34, G:0.13, T:0.30
Consensus pattern (19 bp):
GGTATCAATACCCCCCTTC
Found at i:3474146 original size:54 final size:54
Alignment explanation
Indices: 3474097--3474415 Score: 453
Period size: 54 Copynumber: 5.9 Consensus size: 54
3474087 TAGTGCCCAT
* ** * * * *
3474097 ACGGTTATTCATAAACATATTATAAATTCCTTGAAATGTACACTTAGTGCCGAA
1 ACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* *
3474151 ACGGATATTCATCCACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* *
3474205 ATGGTTATTCATCCAA-ATAGGATGAATTCTGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCAT-CAACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
*
3474259 ACGGTTTTTCATCCAA-ATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCAT-CAACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* *
3474313 ACGGTTATTCATCCACATAGGATGAATTTCGTGAAATGCACACTTAGTGTCGAA
1 ACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
* * *
3474367 ATGGTTATTCATCCACATATGATGAATTCCGTGAAATGCACACTTAGTG
1 ACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAGTG
3474416 CCTATTGGAT
Statistics
Matches: 241, Mismatches: 22, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
53 2 0.01
54 237 0.98
55 2 0.01
ACGTcount: A:0.33, C:0.18, G:0.19, T:0.30
Consensus pattern (54 bp):
ACGGTTATTCATCAACATAGGATGAATTCCGTGAAATGCACACTTAGTGTCGAA
Found at i:3474395 original size:162 final size:162
Alignment explanation
Indices: 3474121--3474415 Score: 518
Period size: 162 Copynumber: 1.8 Consensus size: 162
3474111 ACATATTATA
* *
3474121 AATTCCTTGAAATGTACACTTAGTGCCGAAACGGATATTCATCCACATAGGATGAATTCCGTGAA
1 AATTCCGTGAAATGCACACTTAGTGCCGAAACGGATATTCATCCACATAGGATGAATTCCGTGAA
*
3474186 ATGCACACTTAGTGTCGAAATGGTTATTCATCCAAATAGGATGAATTCTGTGAAATGCACACTTA
66 ATGCACACTTAGTGTCGAAATGGTTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACTTA
3474251 GTGTCGAAACGGTTTTTCATCCAAATAGGATG
131 GTGTCGAAACGGTTTTTCATCCAAATAGGATG
* * *
3474283 AATTCCGTGAAATGCACACTTAGTGTCGAAACGGTTATTCATCCACATAGGATGAATTTCGTGAA
1 AATTCCGTGAAATGCACACTTAGTGCCGAAACGGATATTCATCCACATAGGATGAATTCCGTGAA
* *
3474348 ATGCACACTTAGTGTCGAAATGGTTATTCATCCACATATGATGAATTCCGTGAAATGCACACTTA
66 ATGCACACTTAGTGTCGAAATGGTTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACTTA
3474413 GTG
131 GTG
3474416 CCTATTGGAT
Statistics
Matches: 125, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
162 125 1.00
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.30
Consensus pattern (162 bp):
AATTCCGTGAAATGCACACTTAGTGCCGAAACGGATATTCATCCACATAGGATGAATTCCGTGAA
ATGCACACTTAGTGTCGAAATGGTTATTCATCCAAATAGGATGAATTCCGTGAAATGCACACTTA
GTGTCGAAACGGTTTTTCATCCAAATAGGATG
Done.