Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007113.1 Hibiscus syriacus cultivar Beakdansim tig00018586_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: 836039
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 5
Found at i:456977 original size:20 final size:20
Alignment explanation
Indices: 456952--457018 Score: 68
Period size: 20 Copynumber: 3.4 Consensus size: 20
456942 CAACGCGGAA
456952 ATCGCAACGCGAATATGACT
1 ATCGCAACGCGAATATGACT
* *
456972 ATCGCAACACGGAA-ATAACT
1 ATCGCAACGC-GAATATGACT
456992 ATCGCAATACG-GAAT-TGACT
1 ATCGC-A-ACGCGAATATGACT
457012 ATCGCAA
1 ATCGCAA
457019 TAAGAGAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 31 0.79
21 4 0.10
22 2 0.05
ACGTcount: A:0.39, C:0.24, G:0.18, T:0.19
Consensus pattern (20 bp):
ATCGCAACGCGAATATGACT
Found at i:457019 original size:20 final size:20
Alignment explanation
Indices: 456962--457020 Score: 82
Period size: 20 Copynumber: 2.9 Consensus size: 20
456952 ATCGCAACGC
*
456962 GAATATGACTATCGCAACACG
1 GAAT-TGACTATCGCAATACG
* *
456983 GAAATAACTATCGCAATACG
1 GAATTGACTATCGCAATACG
457003 GAATTGACTATCGCAATA
1 GAATTGACTATCGCAATA
457021 AGAGAATCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
20 30 0.91
21 3 0.09
ACGTcount: A:0.41, C:0.20, G:0.17, T:0.22
Consensus pattern (20 bp):
GAATTGACTATCGCAATACG
Found at i:457049 original size:19 final size:19
Alignment explanation
Indices: 457025--457112 Score: 105
Period size: 19 Copynumber: 4.8 Consensus size: 19
457015 GCAATAAGAG
457025 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
457044 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
457063 AATCGCAA--CG-AGTG--
1 AATCGCAATGCGAAATGAA
*
457077 AATTGCAATGCGAAAATGAA
1 AATCGCAATGCG-AAATGAA
*
457097 AATCGCAACGCGAAAT
1 AATCGCAATGCGAAAT
457113 CATTTCGCAT
Statistics
Matches: 58, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
14 7 0.12
16 5 0.09
17 2 0.03
18 3 0.05
19 31 0.53
20 10 0.17
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:457283 original size:14 final size:14
Alignment explanation
Indices: 457264--457300 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
457254 CATCAATTAA
457264 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
457278 ACAAATCATCTTTT
1 ACAAATCAACATTT
457292 ACAAATCAA
1 ACAAATCAA
457301 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:458740 original size:21 final size:21
Alignment explanation
Indices: 458659--458745 Score: 84
Period size: 21 Copynumber: 4.1 Consensus size: 21
458649 GAATGTTGGG
* *
458659 AGGGACCTCTTCAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
* * **
458680 AGTGGCCTCTTGAACGGTGGG
1 AGGGGCCTCTTGAACGATGAC
* ** *
458701 AGGGGACTCTTGAGGGATGAT
1 AGGGGCCTCTTGAACGATGAC
458722 AGGGGCCTCTTGAACGATGAC
1 AGGGGCCTCTTGAACGATGAC
458743 AGG
1 AGG
458746 TGAGTCAGGC
Statistics
Matches: 49, Mismatches: 17, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
21 49 1.00
ACGTcount: A:0.23, C:0.20, G:0.37, T:0.21
Consensus pattern (21 bp):
AGGGGCCTCTTGAACGATGAC
Found at i:459429 original size:20 final size:20
Alignment explanation
Indices: 459404--459527 Score: 152
Period size: 20 Copynumber: 6.5 Consensus size: 20
459394 GATTCTTTCG
**
459404 TTGCGATAGTCAAATTCGCA
1 TTGCGATAGTCATTTTCGCA
*
459424 TTGCGATAGTTATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
*
459444 TTGCGAT--TC--TCTCG--
1 TTGCGATAGTCATTTTCGCA
*
459458 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
*
459478 TTGCGATAGTCATTTTCGCG
1 TTGCGATAGTCATTTTCGCA
459498 TTGCGATAGTCATTTTCGCA
1 TTGCGATAGTCATTTTCGCA
459518 TTGCGATAGT
1 TTGCGATAGT
459528 AAACTATTCT
Statistics
Matches: 91, Mismatches: 7, Indels: 12
0.83 0.06 0.11
Matches are distributed among these distances:
14 7 0.08
16 6 0.07
18 5 0.05
20 73 0.80
ACGTcount: A:0.19, C:0.19, G:0.23, T:0.40
Consensus pattern (20 bp):
TTGCGATAGTCATTTTCGCA
Found at i:459452 original size:54 final size:54
Alignment explanation
Indices: 459366--459504 Score: 181
Period size: 54 Copynumber: 2.6 Consensus size: 54
459356 AACGAGAGAA
* ** * *
459366 TCGCAATGCGATTTTCA-TTTCACATTGCGATTCTTTCGTTGCGATAGTCAAAT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
* **
459419 TCGCATTGCGATAGTTATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCATTT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
* *
459473 TCGCGTTGCGATAGTCATTTTCGCGTTGCGAT
1 TCGCATTGCGATAGTCATTTTCGCATTGCGAT
459505 AGTCATTTTC
Statistics
Matches: 74, Mismatches: 11, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
53 13 0.18
54 61 0.82
ACGTcount: A:0.18, C:0.21, G:0.21, T:0.40
Consensus pattern (54 bp):
TCGCATTGCGATAGTCATTTTCGCATTGCGATTCTCTCGTTGCGATAGTCAAAT
Found at i:461456 original size:20 final size:20
Alignment explanation
Indices: 461398--461467 Score: 86
Period size: 20 Copynumber: 3.5 Consensus size: 20
461388 GAAACTTTAA
* **
461398 ATCGCAACACGAAAATGAAA
1 ATCGCAACGCGAAAATGACT
*
461418 ATCGCAACACGAAAATGACT
1 ATCGCAACGCGAAAATGACT
**
461438 ATCGCAACGCGAATTTGACT
1 ATCGCAACGCGAAAATGACT
461458 ATCGCAACGC
1 ATCGCAACGC
461468 AAGAATCGCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 45 1.00
ACGTcount: A:0.41, C:0.26, G:0.17, T:0.16
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGACT
Found at i:462166 original size:20 final size:20
Alignment explanation
Indices: 462143--462295 Score: 234
Period size: 20 Copynumber: 7.7 Consensus size: 20
462133 CAATAGTCAG
*
462143 ATTCACATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
462163 ATTCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
462183 AATCGCATTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
* *
462203 ATTCGTATTGCGATTTATGT
1 ATTCGCATTGCGATTTACGT
* *
462223 AATCGCATTGTGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
462243 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
*
462263 ATTCGCGTTGCGATTTACGT
1 ATTCGCATTGCGATTTACGT
462283 ATTCGCATTGCGA
1 ATTCGCATTGCGA
462296 ATTAGGAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 120 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.40
Consensus pattern (20 bp):
ATTCGCATTGCGATTTACGT
Found at i:462377 original size:20 final size:20
Alignment explanation
Indices: 462325--462370 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
462315 AAATTTGGGA
462325 AATCGCAATGCGATAGTCAG
1 AATCGCAATGCGATAGTCAG
462345 AATCGCAATGCGATAGTCAG
1 AATCGCAATGCGATAGTCAG
462365 AATCGC
1 AATCGC
462371 GTTGCGAATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.22, G:0.24, T:0.20
Consensus pattern (20 bp):
AATCGCAATGCGATAGTCAG
Found at i:462429 original size:19 final size:19
Alignment explanation
Indices: 462405--462451 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
462395 CGATACCGGA
*
462405 GATCGCGTTGCGAATTATC
1 GATCGCATTGCGAATTATC
462424 GATCGCATTGCGAATTATC
1 GATCGCATTGCGAATTATC
462443 GATCGCATT
1 GATCGCATT
462452 TCGATTTAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.32
Consensus pattern (19 bp):
GATCGCATTGCGAATTATC
Found at i:463187 original size:2 final size:2
Alignment explanation
Indices: 463180--463221 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
463170 TTTGAACTTA
463180 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
463222 TCAATTAGTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:465936 original size:11 final size:11
Alignment explanation
Indices: 465915--466014 Score: 61
Period size: 12 Copynumber: 9.2 Consensus size: 11
465905 TGAAAAAAGA
465915 AATAA-AAAAT
1 AATAATAAAAT
* *
465925 ATTAATATAAT
1 AATAATAAAAT
465936 AATAATAAAAT
1 AATAATAAAAT
465947 -A-AATAAAAT
1 AATAATAAAAT
465956 ATATGAATAAAGAT
1 A-AT-AATAAA-AT
*
465970 -A-AATGAAAT
1 AATAATAAAAT
*
465979 --TGAGTAAAAT
1 AAT-AATAAAAT
465989 AATAATAATAAT
1 AATAATAA-AAT
466001 AATAATAATAAT
1 AATAATAA-AAT
466013 AA
1 AA
466015 GAGAAAAAAC
Statistics
Matches: 71, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
9 10 0.14
10 16 0.23
11 18 0.25
12 19 0.27
13 6 0.08
14 2 0.03
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (11 bp):
AATAATAAAAT
Found at i:465994 original size:3 final size:3
Alignment explanation
Indices: 465986--466014 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
465976 AATTGAGTAA
465986 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
466015 GAGAAAAAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:466053 original size:26 final size:28
Alignment explanation
Indices: 465995--466076 Score: 87
Period size: 28 Copynumber: 2.9 Consensus size: 28
465985 AAATAATAAT
*
465995 AATAATAATAATAATAATAAGAGAAAAAACAA
1 AATAAAAAT-ATAA-AA-AAGAG-AAAAACAA
* *
466027 AA-CAAAAT-TAAAAAATAGAAAAACAA
1 AATAAAAATATAAAAAAGAGAAAAACAA
466053 AATAAAAATATAAAAAAGAGAAAA
1 AATAAAAATATAAAAAAGAGAAAA
466077 CGTCTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
26 10 0.23
27 9 0.21
28 15 0.35
29 3 0.07
31 4 0.09
32 2 0.05
ACGTcount: A:0.76, C:0.04, G:0.06, T:0.15
Consensus pattern (28 bp):
AATAAAAATATAAAAAAGAGAAAAACAA
Found at i:466068 original size:20 final size:21
Alignment explanation
Indices: 466025--466069 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
466015 GAGAAAAAAC
466025 AAAACAAAATTAAAAAATAGA
1 AAAACAAAATTAAAAAATAGA
466046 AAAACAAAA-TAAAAATATA-A
1 AAAACAAAATTAAAAA-ATAGA
466066 AAAA
1 AAAA
466070 GAGAAAACGT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 11 0.48
21 12 0.52
ACGTcount: A:0.80, C:0.04, G:0.02, T:0.13
Consensus pattern (21 bp):
AAAACAAAATTAAAAAATAGA
Found at i:466841 original size:35 final size:36
Alignment explanation
Indices: 466795--466869 Score: 125
Period size: 35 Copynumber: 2.1 Consensus size: 36
466785 TATGTACTTT
*
466795 TTTGTTTCGGTTGTTTTCTGGTAGTTTTT-CGTTGC
1 TTTGTTTCGGTTGTTTTCTGGTAGTTTTTGCGTGGC
*
466830 TTTGTTTCGGTTGTTTTGTGGTAGTTTTTGCGTGGC
1 TTTGTTTCGGTTGTTTTCTGGTAGTTTTTGCGTGGC
466866 TTTG
1 TTTG
466870 ATGTTGATTT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
35 28 0.76
36 9 0.24
ACGTcount: A:0.03, C:0.09, G:0.29, T:0.59
Consensus pattern (36 bp):
TTTGTTTCGGTTGTTTTCTGGTAGTTTTTGCGTGGC
Found at i:467339 original size:4 final size:4
Alignment explanation
Indices: 467326--467387 Score: 58
Period size: 4 Copynumber: 15.2 Consensus size: 4
467316 AAATATTAAC
*
467326 AAAT -AAT AAAT AAAT -AAT AAAT AATATT AATAT AATAT ATAT AAA-
1 AAAT AAAT AAAT AAAT AAAT AAAT AA-A-T AA-AT AA-AT AAAT AAAT
467371 AAAT AAAT AAAT AAAT A
1 AAAT AAAT AAAT AAAT A
467388 CAAATCATTT
Statistics
Matches: 51, Mismatches: 2, Indels: 10
0.81 0.03 0.16
Matches are distributed among these distances:
3 9 0.18
4 29 0.57
5 8 0.16
6 5 0.10
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (4 bp):
AAAT
Found at i:467342 original size:11 final size:11
Alignment explanation
Indices: 467326--467387 Score: 65
Period size: 11 Copynumber: 5.5 Consensus size: 11
467316 AAATATTAAC
467326 AAATAATAAAT
1 AAATAATAAAT
467337 AAATAATAAAT
1 AAATAATAAAT
*
467348 -AATATTAATAT
1 AAATAATAA-AT
467359 AATATATATAAA-
1 AA-ATA-ATAAAT
467371 AAATAAATAAAT
1 AAAT-AATAAAT
467383 AAATA
1 AAATA
467388 CAAATCATTT
Statistics
Matches: 43, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
10 7 0.16
11 21 0.49
12 8 0.19
13 4 0.09
14 3 0.07
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
AAATAATAAAT
Found at i:467352 original size:31 final size:31
Alignment explanation
Indices: 467317--467380 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
467307 GAAAAAAGAA
*
467317 AATATTAACA-AATAATAAATAAATAATAAAT
1 AATATTAACATAAT-ATAAATAAAAAATAAAT
* *
467348 AATATTAATATAATATATATAAAAAATAAAT
1 AATATTAACATAATATAAATAAAAAATAAAT
467379 AA
1 AA
467381 ATAAATACAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 26 0.90
32 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (31 bp):
AATATTAACATAATATAAATAAAAAATAAAT
Found at i:467365 original size:13 final size:13
Alignment explanation
Indices: 467329--467387 Score: 54
Period size: 13 Copynumber: 4.7 Consensus size: 13
467319 TATTAACAAA
467329 TAATAAATAA-A-
1 TAATAAATAATAT
467340 TAATAAATAATAT
1 TAATAAATAATAT
467353 TAATATAAT-ATAT
1 TAATA-AATAATAT
*
467366 ATAAAAAATAA-AT
1 -TAATAAATAATAT
*
467379 AAATAAATA
1 TAATAAATA
467388 CAAATCATTT
Statistics
Matches: 40, Mismatches: 3, Indels: 9
0.77 0.06 0.17
Matches are distributed among these distances:
11 10 0.25
12 8 0.20
13 14 0.35
14 8 0.20
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
TAATAAATAATAT
Found at i:467558 original size:38 final size:38
Alignment explanation
Indices: 467516--467882 Score: 211
Period size: 40 Copynumber: 9.5 Consensus size: 38
467506 TTTCAAAACT
*
467516 ATATATTATATACATATTTTCAAAATATTTTTTAAAAAA
1 ATATATTATATATATATTTTCAAAATATTTTTT-AAAAA
* * *
467555 TATATATTATATATATTTTTTCAAAAT-GTTTTTAAAATCT
1 -ATATATTATATATATATTTTCAAAATATTTTTTAAAA--A
* * *
467595 ATATATTATATATATCTTTTCAAAATGTTTTTAAAAACTA
1 ATATATTATATATATATTTTCAAAATATTTTTTAAAA--A
* *
467635 TATATTATATATATATATATTTTTTC-AAA-ATGTTTTCAAAA
1 -ATA-TAT-TATATATATA--TTTTCAAAATATTTTTTAAAAA
* * * * * * **
467676 CTATATAATATTTATGTTTT-AAAAAATGTTTCCAAAA
1 ATATATTATATATATATTTTCAAAATATTTTTTAAAAA
* *
467713 CTATA-TA-ATATATATTTTCAAAA-ATGTTTTCAAAAA
1 ATATATTATATATATATTTTCAAAATAT-TTTTTAAAAA
* **
467749 CTATATATTATATATATATTTTAAAAATA-TTTTCCAAAA
1 --ATATATTATATATATATTTTCAAAATATTTTTTAAAAA
* * * *
467788 CTATATAATATATATATTTTCGAAAACCA--TTTTCAAAA
1 ATATATTATATATATATTTTC-AAAA-TATTTTTTAAAAA
* * * *
467826 CTATATGATATATATATTTTCGAAATCCATTTTCTAAAAA
1 ATATATTATATATATATTTTCAAAAT--ATTTTTTAAAAA
467866 AT-TA-TATAT-TATATTTT
1 ATATATTATATATATATTTT
467883 TTTAAAATAA
Statistics
Matches: 264, Mismatches: 40, Indels: 49
0.75 0.11 0.14
Matches are distributed among these distances:
35 11 0.04
36 20 0.08
37 45 0.17
38 52 0.20
39 47 0.18
40 57 0.22
41 5 0.02
42 3 0.01
43 16 0.06
44 3 0.01
45 5 0.02
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (38 bp):
ATATATTATATATATATTTTCAAAATATTTTTTAAAAA
Found at i:467598 original size:39 final size:38
Alignment explanation
Indices: 467505--467845 Score: 304
Period size: 39 Copynumber: 8.8 Consensus size: 38
467495 TCCAAAAGCA
* * *
467505 TTTTCAAAACTATATATTATATACATATTTTCAAAATATT
1 TTTTCAAAACTATATATTATATATATTTTTTC-AAA-ATG
* *
467545 TTTTAAAAAATATATATTATATATATTTTTTCAAAATG
1 TTTTCAAAACTATATATTATATATATTTTTTCAAAATG
* *
467583 TTTTTAAAATCTATATATTATATATATCTTTTCAAAATG
1 TTTTCAAAA-CTATATATTATATATATTTTTTCAAAATG
*
467622 TTTTTAAAAACTATATATTATATATATATATATTTTTTCAAAATG
1 -TTTTCAAAAC----TA-TATAT-TATATATATTTTTTCAAAATG
* **
467667 TTTTCAAAACTATATA--ATATTTATGTTTTAAAAAATG
1 TTTTCAAAACTATATATTATATATAT-TTTTTCAAAATG
*
467704 TTTCCAAAACTATATA--ATATATA--TTTTCAAAAATG
1 TTTTCAAAACTATATATTATATATATTTTTTC-AAAATG
* * *
467739 TTTTCAAAAACTATATATTATATATATATTTTAAAAATA
1 TTTTC-AAAACTATATATTATATATATTTTTTCAAAATG
* **
467778 TTTTCCAAAACTATATA--ATATATATATTTTCGAAAACCA
1 TTTT-CAAAACTATATATTATATATATTTTTTC-AAAA-TG
467817 TTTTCAAAACTATATGA-TATATATATTTT
1 TTTTCAAAACTATAT-ATTATATATATTTT
467846 CGAAATCCAT
Statistics
Matches: 257, Mismatches: 24, Indels: 40
0.80 0.07 0.12
Matches are distributed among these distances:
34 3 0.01
35 10 0.04
36 18 0.07
37 44 0.17
38 32 0.12
39 61 0.24
40 53 0.21
43 2 0.01
44 14 0.05
45 20 0.08
ACGTcount: A:0.43, C:0.08, G:0.02, T:0.47
Consensus pattern (38 bp):
TTTTCAAAACTATATATTATATATATTTTTTCAAAATG
Found at i:467783 original size:75 final size:74
Alignment explanation
Indices: 467642--467842 Score: 266
Period size: 75 Copynumber: 2.7 Consensus size: 74
467632 CTATATATTA
* * *
467642 TATATATATATATTTTTTC-AAAATGTTTTCAAAACTATATA-ATATTTATGTTTTAAAAAATGT
1 TATATATATATATATTTTCAAAAATGTTTTCAAAACTATATATATATATATATTTTAAAAAATGT
467705 TTCCAAAAC
66 TTCCAAAAC
467714 TATATA-ATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATATTTTAAAAATA
1 TATATATATATATATTTTCAAAAATGTTTTC-AAAACTATATA-TATATATATATTTTAAAAA-A
467778 T-TTTCCAAAAC
63 TGTTTCCAAAAC
***
467789 TATATAATATATATATTTTCGAAAACCATTTTCAAAACTATATGATATATATAT
1 TATAT-ATATATATATTTTC-AAAAATGTTTTCAAAACTATAT-ATATATATAT
467843 TTTCGAAATC
Statistics
Matches: 114, Mismatches: 6, Indels: 13
0.86 0.05 0.10
Matches are distributed among these distances:
71 11 0.10
72 17 0.15
73 11 0.10
75 31 0.27
76 3 0.03
77 31 0.27
78 10 0.09
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.44
Consensus pattern (74 bp):
TATATATATATATATTTTCAAAAATGTTTTCAAAACTATATATATATATATATTTTAAAAAATGT
TTCCAAAAC
Found at i:467879 original size:77 final size:74
Alignment explanation
Indices: 467642--467889 Score: 202
Period size: 75 Copynumber: 3.3 Consensus size: 74
467632 CTATATATTA
* ** * * *
467642 TATATATATATATTTTTTC-AAAATGTTTTC-AAAAC-TATATAATATTTATGTTTTAAAAA-AT
1 TATATAT-TATATATTTTCAAAAACATTTTCAAAAACATATATGATATATATATTTTAAAAATAT
*
467703 GTTTCCAAAAC
65 -TTTCAAAAAC
* ** *
467714 TATATAATATATATTTTCAAAAATGTTTTCAAAAACTATATATTATATATATATTTTAAAAATAT
1 TATATATTATATATTTTCAAAAACATTTTCAAAAAC-ATATATGATATATATATTTTAAAAATAT
*
467779 TTTCCAAAAC
65 TTTCAAAAAC
* **
467789 TATATAATATATATATTTTCGAAAACCATTTTC-AAAAC-TATATGATATATATATTTTCGAAAT
1 TATAT-AT-TATATATTTTC-AAAAACATTTTCAAAAACATATATGATATATATATTTTAAAAAT
*
467852 CCATTTTCTAAAAAAT
63 --ATTTTC--AAAAAC
* *
467868 TATATATTATATTTTTTTAAAA
1 TATATATTATATATTTTCAAAA
467890 TAAAAAATTA
Statistics
Matches: 148, Mismatches: 16, Indels: 20
0.80 0.09 0.11
Matches are distributed among these distances:
71 10 0.07
72 17 0.11
73 5 0.03
75 58 0.39
76 7 0.05
77 31 0.21
78 11 0.07
79 9 0.06
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (74 bp):
TATATATTATATATTTTCAAAAACATTTTCAAAAACATATATGATATATATATTTTAAAAATATT
TTCAAAAAC
Found at i:468721 original size:85 final size:85
Alignment explanation
Indices: 468539--468776 Score: 291
Period size: 85 Copynumber: 2.8 Consensus size: 85
468529 GGTTGATACA
* * * * * *
468539 CCCTCGAGCTGAATGGAATCGAACTCGATA-GTTTTTGTTGACAGAT-AGCTTTCTCGACTTAAG
1 CCCTTGAGCTGAATGTAATCGAACTCGA-AGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAG
*
468602 CTATATTGTAAATTTGATATG
65 CTATACTGTAAATTTGATATG
* *
468623 CCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTATTGACAGATAACCCTTCTCGCCTTGAGT
1 CCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGC
*
468688 TATGCTGTAAATTTGATATG
66 TATACTGTAAATTTGATATG
* * * * * ** *
468708 TCCTTGAGTTGAATATAATCGAACTCGAAGGTTTTGGTTGAAAGATAGTCCTTATCGCCTTGAGC
1 CCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGC
468773 TATA
66 TATA
468777 TTGTGATAGG
Statistics
Matches: 131, Mismatches: 21, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
83 1 0.01
84 41 0.31
85 89 0.68
ACGTcount: A:0.27, C:0.17, G:0.21, T:0.35
Consensus pattern (85 bp):
CCCTTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAACCCTTCTCGCCTTGAGC
TATACTGTAAATTTGATATG
Found at i:470415 original size:99 final size:99
Alignment explanation
Indices: 470242--470436 Score: 318
Period size: 99 Copynumber: 2.0 Consensus size: 99
470232 GGACAACTCA
*
470242 ATATTATAATCACCTTTATCAGGCTAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATT
1 ATATTATAATCACCTTTATCAGGATAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATT
** **
470307 TTTTTAGAGGGAAAACTCAAGCTTTATTGTATAG
66 GCTCAAGAGGGAAAACTCAAGCTTTATTGTATAG
* *
470341 ATATTATAATCACCTTTATCAGGATAGTTGAATCTTATCCATAAAGTCGGGGCGTTTAATCAATT
1 ATATTATAATCACCTTTATCAGGATAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATT
*
470406 GCTCAAGAGGGACAACTCAAGCTTTATTGTA
66 GCTCAAGAGGGAAAACTCAAGCTTTATTGTA
470437 CACATATAAT
Statistics
Matches: 88, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
99 88 1.00
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.34
Consensus pattern (99 bp):
ATATTATAATCACCTTTATCAGGATAGCTGAATCTTATCCATAAAGTCGGGGCGTTTAACCAATT
GCTCAAGAGGGAAAACTCAAGCTTTATTGTATAG
Found at i:474582 original size:23 final size:22
Alignment explanation
Indices: 474546--474619 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 22
474536 GAAATTGAGT
*
474546 AAAAAATAATAATAAAAATAAGAG
1 AAAAAACAATAATAAAAA-AA-AG
474570 AAAAAACAA-AATAAAAAAAAG
1 AAAAAACAATAATAAAAAAAAG
* *
474591 AAAAAGAAAAT-ATAATAAAAAAT
1 AAAAA-ACAATAATAA-AAAAAAG
474614 AAAAAA
1 AAAAAA
474620 GAGAAAACGT
Statistics
Matches: 44, Mismatches: 3, Indels: 8
0.80 0.05 0.15
Matches are distributed among these distances:
21 7 0.16
22 10 0.23
23 19 0.43
24 8 0.18
ACGTcount: A:0.81, C:0.01, G:0.05, T:0.12
Consensus pattern (22 bp):
AAAAAACAATAATAAAAAAAAG
Found at i:474582 original size:26 final size:24
Alignment explanation
Indices: 474548--474626 Score: 67
Period size: 24 Copynumber: 3.2 Consensus size: 24
474538 AATTGAGTAA
474548 AAAATAATAATAAAAATAAGAGAAAA-
1 AAAA-AATAATAAAAA-AAGA-AAAAG
474574 AACAAAAT-A-AAAAAAAGAAAAAG
1 AA-AAAATAATAAAAAAAGAAAAAG
*
474597 AAAATATAATAAAAAATA-AAAAAG
1 AAAAAATAATAAAAAA-AGAAAAAG
*
474621 AGAAAA
1 AAAAAA
474627 CGTCTAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
22 8 0.18
23 7 0.16
24 21 0.47
25 2 0.04
26 5 0.11
27 2 0.04
ACGTcount: A:0.80, C:0.01, G:0.08, T:0.11
Consensus pattern (24 bp):
AAAAAATAATAAAAAAAGAAAAAG
Found at i:476078 original size:7 final size:7
Alignment explanation
Indices: 476068--476116 Score: 53
Period size: 7 Copynumber: 6.3 Consensus size: 7
476058 AGAAAAATAT
476068 TAATAAA
1 TAATAAA
476075 TAATAAA
1 TAATAAA
476082 TAATATTAA
1 TAATA--AA
476091 TAATATATA
1 TAATA-A-A
476100 TAATAAA
1 TAATAAA
476107 TAAATAAA
1 T-AATAAA
476115 TA
1 TA
476117 CAAATCATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
7 15 0.39
8 10 0.26
9 13 0.34
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (7 bp):
TAATAAA
Found at i:476088 original size:20 final size:22
Alignment explanation
Indices: 476063--476116 Score: 71
Period size: 20 Copynumber: 2.6 Consensus size: 22
476053 AAAAAAGAAA
476063 AATATTAATAAATA-ATA-AAT
1 AATATTAATAAATATATATAAT
476083 AATATTAAT-AATATATATAAT
1 AATATTAATAAATATATATAAT
*
476104 AA-ATAAATAAATA
1 AATATTAATAAATA
476117 CAAATCATTT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
19 4 0.13
20 17 0.57
21 9 0.30
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
AATATTAATAAATATATATAAT
Found at i:476326 original size:37 final size:37
Alignment explanation
Indices: 476247--476610 Score: 255
Period size: 38 Copynumber: 9.6 Consensus size: 37
476237 TTCAAAACTA
* * * *
476247 TATATTATATACATATTTTTAAAATATTTTTTAAAAAC
1 TATATTATATATATATTTTCAAAAT-GTTTTTAAAAAT
*
476285 TATATTATATATATGTTTTCAAAATGTTTTTAAAAATT
1 TATATTATATATATATTTTCAAAATGTTTTTAAAAA-T
* *
476323 ATATATTATATATATGTTTTCAAAATG-TTTT-AAAAC
1 -TATATTATATATATATTTTCAAAATGTTTTTAAAAAT
* * ** *
476359 TATATAATATATATGTTTTCAAAAATG-TTTCCAAAAC
1 TATATTATATATATATTTTC-AAAATGTTTTTAAAAAT
*
476396 TATA-TA-ATATATATTTTCAAAAATGTTTTCAAAAACT
1 TATATTATATATATATTTTC-AAAATGTTTTTAAAAA-T
* * * *
476433 ATATATTATATATATA--TTAAAAATATTTTCCAAAACT
1 -TATATTATATATATATTTTCAAAATGTTTT-TAAAAAT
* * *
476470 ATATATTATATATATACTTTCAAAATGTTTTCAAAACT
1 -TATATTATATATATATTTTCAAAATGTTTTTAAAAAT
* * * *
476508 ATATAATATATATATATATATTTGAAAACCG-TTTTCAAAAC
1 -TAT-AT-TATATATATAT-TTTCAAAA-TGTTTTTAAAAAT
*
476549 TATATGATATATATATTTTCAAAATTCGTTTTCTAAAAAAT
1 TATATTATATATATATTTTCAAAA-T-GTTTT-T-AAAAAT
*
476590 TATA-TAT-TTTAT-TTTTCAAAA
1 TATATTATATATATATTTTCAAAA
476611 AAATATTTTC
Statistics
Matches: 274, Mismatches: 32, Indels: 40
0.79 0.09 0.12
Matches are distributed among these distances:
35 37 0.14
36 18 0.07
37 56 0.20
38 68 0.25
39 50 0.18
40 23 0.08
41 21 0.08
42 1 0.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.46
Consensus pattern (37 bp):
TATATTATATATATATTTTCAAAATGTTTTTAAAAAT
Found at i:476523 original size:38 final size:37
Alignment explanation
Indices: 476235--476573 Score: 307
Period size: 37 Copynumber: 9.0 Consensus size: 37
476225 TTCAAAAGCA
* * * *
476235 TTTTCAAAACTATATATTATATACATATTTTTAAAATATT
1 TTTTCAAAACTATATA--ATATATATATATTTCAAA-ATG
* * *
476275 TTTTAAAAACTATATTATATATATGT-TTTCAAAATG
1 TTTTCAAAACTATATAATATATATATATTTCAAAATG
* * * *
476311 TTTTTAAAAATTATATATTATATATATGTTTTCAAAATG
1 -TTTTCAAAACTATATAATATATATAT-ATTTCAAAATG
*
476350 TTTT-AAAACTATATAATATATATGT-TTTCAAAAATG
1 TTTTCAAAACTATATAATATATATATATTTC-AAAATG
*
476386 TTTCCAAAACTATAT-A-ATATATAT-TTTCAAAAATG
1 TTTTCAAAACTATATAATATATATATATTTC-AAAATG
* * *
476421 TTTTCAAAAACTATATATTATATATATA-TTAAAAATA
1 TTTTC-AAAACTATATAATATATATATATTTCAAAATG
*
476458 TTTTCCAAAACTATATATTATATATATACTTTCAAAATG
1 TTTT-CAAAACTATATAATATATATATA-TTTCAAAATG
* *
476497 TTTTCAAAACTATATAATATATATATATATATTTGAAAACCG
1 TTTTCAAAAC--TAT-ATA-ATATATATATATTTCAAAA-TG
*
476539 TTTTCAAAACTATATGATATATATAT-TTTCAAAAT
1 TTTTCAAAACTATATAATATATATATATTTCAAAAT
476574 TCGTTTTCTA
Statistics
Matches: 255, Mismatches: 27, Indels: 38
0.80 0.08 0.12
Matches are distributed among these distances:
35 26 0.10
36 22 0.09
37 94 0.37
38 39 0.15
39 23 0.09
40 20 0.08
41 10 0.04
42 21 0.08
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.45
Consensus pattern (37 bp):
TTTTCAAAACTATATAATATATATATATTTCAAAATG
Found at i:476802 original size:23 final size:23
Alignment explanation
Indices: 476758--476799 Score: 70
Period size: 21 Copynumber: 1.9 Consensus size: 23
476748 ATTTGAATTA
476758 AAATAAATATATATATAAATAAC
1 AAATAAATATATATATAAATAAC
476781 AAATAAA-AT-TATATAAATA
1 AAATAAATATATATATAAATA
476800 TAAAAACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
22 2 0.11
23 7 0.37
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (23 bp):
AAATAAATATATATATAAATAAC
Found at i:476811 original size:23 final size:21
Alignment explanation
Indices: 476769--476812 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
476759 AATAAATATA
* *
476769 TATATAAATAACAAATAAAAT
1 TATATAAATAAAAAACAAAAT
476790 TATATAAATATAAAAACCAAAAT
1 TATATAAATA-AAAAA-CAAAAT
476813 GACATAGGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 10 0.53
22 4 0.21
23 5 0.26
ACGTcount: A:0.66, C:0.07, G:0.00, T:0.27
Consensus pattern (21 bp):
TATATAAATAAAAAACAAAAT
Found at i:477843 original size:13 final size:13
Alignment explanation
Indices: 477825--477851 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
477815 TGGGATCTAC
477825 GGATCAATGAACT
1 GGATCAATGAACT
477838 GGATCAATGAACT
1 GGATCAATGAACT
477851 G
1 G
477852 TATACAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.15, G:0.26, T:0.22
Consensus pattern (13 bp):
GGATCAATGAACT
Found at i:482275 original size:26 final size:27
Alignment explanation
Indices: 482239--482291 Score: 81
Period size: 29 Copynumber: 1.9 Consensus size: 27
482229 TGCCTACCTT
482239 TCTCTTTAC-TTGTTCAAGAATGATTG
1 TCTCTTTACTTTGTTCAAGAATGATTG
482265 TCTCTTTACTTATTGTTCAAGAATGAT
1 TCTCTTTAC-T-TTGTTCAAGAATGAT
482292 AATCTTTTAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 9 0.38
29 15 0.62
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (27 bp):
TCTCTTTACTTTGTTCAAGAATGATTG
Found at i:483378 original size:24 final size:24
Alignment explanation
Indices: 483350--483398 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
483340 TAAAATATAA
*
483350 TTTTGCGAGTCTTAAAGATGTTAT
1 TTTTGCGAGTCTTAAAAATGTTAT
483374 TTTTGCGAGTCTTAAAAATGTTAT
1 TTTTGCGAGTCTTAAAAATGTTAT
483398 T
1 T
483399 CTATAAAGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.27, C:0.08, G:0.18, T:0.47
Consensus pattern (24 bp):
TTTTGCGAGTCTTAAAAATGTTAT
Found at i:485298 original size:60 final size:60
Alignment explanation
Indices: 485166--485301 Score: 157
Period size: 60 Copynumber: 2.3 Consensus size: 60
485156 ATATATGAAA
**
485166 AGTTGGGTGACCATTTTGTAACTTTTAAAAGTTGAAAGACTCAACAAATCAACACTATAT
1 AGTTGGGTGACCATTTTGTAACTTTTAAAAGTTGAAAGACTCAACAAAAAAACACTATAT
* * * * *** *
485226 AGTCGGATGACCATTTTGTAATTTTTAATAGTTGGGGGACTCAACAAAAAAACACCT-TGT
1 AGTTGGGTGACCATTTTGTAACTTTTAAAAGTTGAAAGACTCAACAAAAAAACA-CTATAT
*
485286 AGTTGGGGGACCATTT
1 AGTTGGGTGACCATTT
485302 GATGTACTTT
Statistics
Matches: 62, Mismatches: 13, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
60 60 0.97
61 2 0.03
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.32
Consensus pattern (60 bp):
AGTTGGGTGACCATTTTGTAACTTTTAAAAGTTGAAAGACTCAACAAAAAAACACTATAT
Found at i:490013 original size:4 final size:4
Alignment explanation
Indices: 490006--490038 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
489996 TATTATTATT
490006 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
1 ATTA ATTA ATTA ATTA ATTA ATTA ATTA ATTA A
490039 ATTTTATGTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
ATTA
Found at i:492334 original size:131 final size:132
Alignment explanation
Indices: 492135--492491 Score: 391
Period size: 131 Copynumber: 2.7 Consensus size: 132
492125 CGATATTGAG
* * * * * *
492135 AATAGTAATATCTTTTCATTTTGGTCGGAGTAATAAATGAATGCTTTAAGGCATGAGAGGTCATT
1 AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
* * * *
492200 TATTCTCGATTGGAAATAATTTA-ATATTGTCGTTTTCTCTCGAATTAATA-CCAATTTTTAAGA
66 TATTCTCGATTGGAAATAATTTAGATATTATCGTCTTCACTCGAATCAATATCCAA-TTTTAAGA
* *
492263 TGG
130 CGA
* * *
492266 AATAATGATATCTCTTCATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGGTCATT
1 AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
* * * * **
492331 TATTCTCGATTGGAAATCA-TTAGATGTTATCGTCTTCACTTGAATCGATATTGAATTTTAAGAC
66 TATTCTCGATTGGAAATAATTTAGATATTATCGTCTTCACTCGAATCAATATCCAATTTTAAGAC
492395 GA
131 GA
* * * * * * *
492397 AATAGTAATATCTCTTTATTTCAATTGGGGTAATAAATGATT-CTTTTAATGCACGAAAGGTCAT
1 AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGC-TTTAAGGCATGAGAGGTCAT
* *
492461 TTATTATCGATTGAAAATAA-TTAGATATTAT
65 TTATTCTCGATTGGAAATAATTTAGATATTAT
492492 TGTTTTGACT
Statistics
Matches: 188, Mismatches: 35, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
130 4 0.02
131 182 0.97
132 2 0.01
ACGTcount: A:0.33, C:0.11, G:0.17, T:0.40
Consensus pattern (132 bp):
AATAATAATATCTCTTCATTTCGATTGGAGTAATAAATGATTGCTTTAAGGCATGAGAGGTCATT
TATTCTCGATTGGAAATAATTTAGATATTATCGTCTTCACTCGAATCAATATCCAATTTTAAGAC
GA
Found at i:493899 original size:23 final size:23
Alignment explanation
Indices: 493830--493899 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 23
493820 ACCATTTATC
493830 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
* *
493853 ACCAATATA-CTTGTCA--TTA--TT
1 -CC-ATA-AGCTCGTAAGCTTATTTT
493874 CCATAAGCTCGTAAGCTTATTTT
1 CCATAAGCTCGTAAGCTTATTTT
493897 CCA
1 CCA
493900 ATTTATCATT
Statistics
Matches: 35, Mismatches: 4, Indels: 15
0.65 0.07 0.28
Matches are distributed among these distances:
18 1 0.03
19 8 0.23
20 2 0.06
21 5 0.14
23 8 0.23
24 2 0.06
25 8 0.23
26 1 0.03
ACGTcount: A:0.29, C:0.23, G:0.10, T:0.39
Consensus pattern (23 bp):
CCATAAGCTCGTAAGCTTATTTT
Found at i:494056 original size:40 final size:40
Alignment explanation
Indices: 493977--494057 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
493967 ATAGGAGTCA
* * * * *
493977 AATATTGCACCGAAGTGCTGAGGTCGAGCTTTGCTCACCT
1 AATAATGCACCGAAGTGCTGAAGTCGAGATTTACCCACCT
* *
494017 AATAATGCACCGTAGTGCTGAAGTCGGGATTTACCCACCT
1 AATAATGCACCGAAGTGCTGAAGTCGAGATTTACCCACCT
494057 A
1 A
494058 GTAAATCGTA
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.26, C:0.25, G:0.23, T:0.26
Consensus pattern (40 bp):
AATAATGCACCGAAGTGCTGAAGTCGAGATTTACCCACCT
Found at i:494769 original size:34 final size:34
Alignment explanation
Indices: 494731--494798 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
494721 CACTTATTAA
*
494731 TTCTTTTTAATATTGAAACAAACTTTTCCAATTT
1 TTCTTTTTAACATTGAAACAAACTTTTCCAATTT
494765 TTCTTTTTAACATTGAAACAAACTTTTCCAATTT
1 TTCTTTTTAACATTGAAACAAACTTTTCCAATTT
494799 ACTCAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.32, C:0.16, G:0.03, T:0.49
Consensus pattern (34 bp):
TTCTTTTTAACATTGAAACAAACTTTTCCAATTT
Found at i:495505 original size:41 final size:41
Alignment explanation
Indices: 495438--495840 Score: 355
Period size: 41 Copynumber: 9.7 Consensus size: 41
495428 CAAAATACTA
* * * *
495438 TACTTTAGTGACGTTTGTATAAAAACGCCGCTAAATAATCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCG
* * * * *
495479 TAATGTAGTGGCGTTTTTATATAAACGCCGCTATAA-ACTAG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTA-AAGAATCG
* * *
495520 TATTTTAGTGGCGTTTTTATACAAACGCCGCTATAGACA-CA
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA-ATCG
* * * *
495561 TACTTTTGTGGCGTTTTAATACCAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCGCTAAAGAATCG
* * * *
495603 TACTTTAGTGGCATTTTTACATAAACGCCGCTATAGACAT-G
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA-ATCG
* * * * **
495644 TACTTTTGTGGCGTTTTAATACCAAACGCCACTATAGACCCG
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCGCTAAAGAATCG
* * *
495686 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACA-CG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGA-ATCG
** * * *
495727 TACTTTTTTGGCGTTTTAATACCAAACGCCGCTATAGATTCG
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCGCTAAAGAATCG
* * * *
495769 TACTTTAGTGGCATTTTTACACAAACGCCGCTATAGACTCG
1 TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCG
*
495810 TACTTTAGTGGCGTTTTAATACCAAACGCCG
1 TACTTTAGTGGCGTTTTTATA-CAAACGCCG
495841 TAATTGTCAT
Statistics
Matches: 296, Mismatches: 54, Indels: 23
0.79 0.14 0.06
Matches are distributed among these distances:
40 1 0.00
41 183 0.62
42 112 0.38
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.33
Consensus pattern (41 bp):
TACTTTAGTGGCGTTTTTATACAAACGCCGCTAAAGAATCG
Found at i:495863 original size:83 final size:83
Alignment explanation
Indices: 495486--495840 Score: 559
Period size: 83 Copynumber: 4.3 Consensus size: 83
495476 TCGTAATGTA
* * * * * * *
495486 GTGGCGTTTTTATA-TAAACGCCGCTATAAACTAGTATTTTAGTGGCGTTTTTATACAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCG
*
495550 CTATAGACACATACTTTT
66 CTATAGACACGTACTTTT
*
495568 GTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACATAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCG
*
495633 CTATAGACATGTACTTTT
66 CTATAGACACGTACTTTT
* *
495651 GTGGCGTTTTAATACCAAACGCCACTATAGACCCGTACTTTAGTGGCATTTTTACACAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCG
495716 CTATAGACACGTACTTTT
66 CTATAGACACGTACTTTT
* *
495734 TTGGCGTTTTAATACCAAACGCCGCTATAGATTCGTACTTTAGTGGCATTTTTACACAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCG
* *
495799 CTATAGACTCGTACTTTA
66 CTATAGACACGTACTTTT
495817 GTGGCGTTTTAATACCAAACGCCG
1 GTGGCGTTTTAATACCAAACGCCG
495841 TAATTGTCAT
Statistics
Matches: 251, Mismatches: 21, Indels: 1
0.92 0.08 0.00
Matches are distributed among these distances:
82 13 0.05
83 238 0.95
ACGTcount: A:0.27, C:0.22, G:0.18, T:0.33
Consensus pattern (83 bp):
GTGGCGTTTTAATACCAAACGCCGCTATAGACTCGTACTTTAGTGGCATTTTTACACAAACGCCG
CTATAGACACGTACTTTT
Found at i:499317 original size:43 final size:43
Alignment explanation
Indices: 499248--499568 Score: 328
Period size: 43 Copynumber: 7.5 Consensus size: 43
499238 TAATTAGCGA
* * *
499248 CGTTTGTATCCAAAAATGCCGCTATAGGTCTGACTTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
** * * * *
499291 CGTTTGTGTTTAAAAACACTGTTATAGGTCTGACCTTTTGCAG
1 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
*
499334 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCTG
1 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
* *
499377 CGTTTGT-TCTAAAAACGCCAG-TATAGGCCTG-CTCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCC-GCTATAGGTCTGAC-CTTTTGCGG
* * *
499419 CGTTTGTATCCAAAAACGCCGCTATAGATCTAACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
* * * * ** * * *
499462 CGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTACGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGGTC-TGACCTTTTGCGG
* *
499506 CGTTTGT-TCCAAAAACGCCGCTATAGATATCGACCTTTTGCGG
1 CGTTTGTGTCCAAAAACGCCGCTATAGGTCT-GACCTTTTGCGG
*
499549 CGTTTGT-TCAAAAAACGCCG
1 CGTTTGTGTCCAAAAACGCCG
499569 TAATATATAT
Statistics
Matches: 233, Mismatches: 38, Indels: 14
0.82 0.13 0.05
Matches are distributed among these distances:
41 1 0.00
42 37 0.16
43 177 0.76
44 18 0.08
ACGTcount: A:0.23, C:0.23, G:0.21, T:0.34
Consensus pattern (43 bp):
CGTTTGTGTCCAAAAACGCCGCTATAGGTCTGACCTTTTGCGG
Found at i:499434 original size:128 final size:129
Alignment explanation
Indices: 499248--499564 Score: 327
Period size: 128 Copynumber: 2.5 Consensus size: 129
499238 TAATTAGCGA
* * * ** * *
499248 CGTTTGTATCCAAAAATGCCGCTATAGGTCTGACTTTTTGCGGCGTTTGTGTTTAAAAACACTGT
1 CGTTTGT-TCCAAAAACGCCGCTATAGGCCTGACTTTTTGCGGCGTTTGTATCCAAAAACACCGC
* * * * * *
499313 TATAGGTCTGACCTTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGGTC-TGACCTTTTGCTG
65 TATAGATCTAACCTTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGATCATAACCTTTTACGG
* *
499377 CGTTTGTTCTAAAAACGCCAG-TATAGGCCTG-CTCTTTTGCGGCGTTTGTATCCAAAAACGCCG
1 CGTTTGTTCCAAAAACGCC-GCTATAGGCCTGACT-TTTTGCGGCGTTTGTATCCAAAAACACCG
* * * * * * *
499440 CTATAGATCTAACCTTTTGCGGCGTTTTTTTCTAGAAACGCCGCTATATATCATAACTTTTTACG
64 CTATAGATCTAACCTTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGATCATAACCTTTTACG
499505 G
129 G
*** * *
499506 CGTTTGTTCCAAAAACGCCGCTATAGATATCGACCTTTTGCGGCGTTTGT-TCAAAAAAC
1 CGTTTGTTCCAAAAACGCCGCTATAGGCCT-GACTTTTTGCGGCGTTTGTATCCAAAAAC
499565 GCCGTAATAT
Statistics
Matches: 154, Mismatches: 28, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
127 2 0.01
128 86 0.56
129 49 0.32
130 16 0.10
131 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.20, T:0.34
Consensus pattern (129 bp):
CGTTTGTTCCAAAAACGCCGCTATAGGCCTGACTTTTTGCGGCGTTTGTATCCAAAAACACCGCT
ATAGATCTAACCTTTTGCAGCGTTTGTGTCCAAAAACGCCGCTATAGATCATAACCTTTTACGG
Found at i:512400 original size:408 final size:404
Alignment explanation
Indices: 511635--512605 Score: 1224
Period size: 408 Copynumber: 2.4 Consensus size: 404
511625 AATCAAACAT
* * * * *
511635 GATTCAATCTTCCTTGAGTGACAGTGGAATGAATCAACGTCATTATATCTGATTTTACCTCAAGA
1 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATC-CTAGATCTGATTTTCCCTCAAGA
* *
511700 ATAAGCAGAACATATCCCTATCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTCTC
65 ATAAGCAGAACATATCCCTATCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT-TT
* * * *
511765 CCTTGATTCAATCTTTCCT-AAG-CA--ACAATGGAATGAATCAACATCCCCATATCTGATGTTT
129 CCTCGATTCAATC-TTCCTGATGACAGTACAATAGAATGAATCAACATCCCCATATATGATGTTT
* * *
511826 CCCTTAAGAAGAAGTGGAACAGATACCTCTCTTTCAAGATTTAATATTCCCTGAGTAACAGTGGA
193 CCCTCAAGAAGAAGAGGAACAGATACCTCTCTTTCAAGATTTAATATTCCCTGAGTAACAATGGA
* * *
511891 ACAAGTTTACCTCGATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAAAATCCCCAGATCTGA
258 AAAAGTTTACCTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAAAATCCCCAGATCTAA
* *
511956 TTTTCCCTCAGGAAGAAGCAGAACAAATCATTCTCTTTCAAGATTTAATATTCCCTGAGTAACAG
323 TTTTCCCTCAAGAAGAAGCAGAACAAATCATTCTCTTTCAAGATTTAACATTCCCTGAGTAACAG
512021 TGGAACAAGTC-GAACC-C
388 TGGAACAAGTCTG--CCTC
* *
512038 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCTCAGGTCTAATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCT-AGATCTGATTTTCCCTCAAGA
* * * * * * *
512103 AGAAGCAAAACAAATCCATTTCTTTCAAGATTTAATATTCCCTAAGTAACAGTGGAACAAGTTTG
65 ATAAGCAGAACATATCCCTATCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTT-
* ** **
512168 CCTCGATTCAATCTTACCTGATTGACAGTGACAGTAGAATGAATCAATGTTTCCATATATGAT-T
129 CCTCGATTCAATCTT-CCTGA-TGACAGT-ACAATAGAATGAATCAACATCCCCATATATGATGT
* * * * *
512232 TTCCCTCAAGAAGAAGAGGATCATATCCCTCTGC-TTCAAGATTTGATATTCTCTGAGTAACAAT
191 TTCCCTCAAGAAGAAGAGGAACAGATACCTCT-CTTTCAAGATTTAATATTCCCTGAGTAACAAT
** ** * *
512296 GGAAAAAGTCTT-CCTCGATTCAATCTTCTTTAAGTGACAGTGGAATGAATCAACGTCCTCGGAT
255 GGAAAAAGT-TTACCTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAAAATCCCCAGAT
* * * *
512360 CTAATTTTCCCTCAAGAAGAA-CTGGAACAAATCCTTCTCTTTCAAGATTTGACATTCTCTGAGT
319 CTAATTTTCCCTCAAGAAGAAGC-AGAACAAATCATTCTCTTTCAAGATTTAACATTCCCTGAGT
*
512424 AATAGTGGAACAAGTCTGCCTC
383 AACAGTGGAACAAGTCTGCCTC
* * *
512446 GATTCAATCTTCCCTGAGTGAAAGTTGAATGAATCAACGTTCCTAGATCTGATTTTCCCTCAAGA
1 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAAC-ATCCTAGATCTGATTTTCCCTCAAGA
** *
512511 ATAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTT
65 ATAAGCAGAACATATCCCTATCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGT-TT
512576 CCTCGATTCAATCTTCTCTGAGTGACAGTA
129 CCTCGATTCAATCTTC-CTGA-TGACAGTA
512606 GAACAAATTA
Statistics
Matches: 487, Mismatches: 64, Indels: 30
0.84 0.11 0.05
Matches are distributed among these distances:
402 4 0.01
403 125 0.26
404 1 0.00
405 1 0.00
406 2 0.00
407 5 0.01
408 313 0.64
409 36 0.07
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (404 bp):
GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATCCTAGATCTGATTTTCCCTCAAGAA
TAAGCAGAACATATCCCTATCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTTTCC
TCGATTCAATCTTCCTGATGACAGTACAATAGAATGAATCAACATCCCCATATATGATGTTTCCC
TCAAGAAGAAGAGGAACAGATACCTCTCTTTCAAGATTTAATATTCCCTGAGTAACAATGGAAAA
AGTTTACCTCGATTCAATCTTCCCTAAGTGACAGTGGAATGAATCAAAATCCCCAGATCTAATTT
TCCCTCAAGAAGAAGCAGAACAAATCATTCTCTTTCAAGATTTAACATTCCCTGAGTAACAGTGG
AACAAGTCTGCCTC
Found at i:512653 original size:134 final size:134
Alignment explanation
Indices: 511635--512664 Score: 1108
Period size: 134 Copynumber: 7.6 Consensus size: 134
511625 AATCAAACAT
* *
511635 GATTCAATCTTC-CTTGAGTGACAGTGGAATGAATCAACGTCAT-TATATCTGATTTTACCTCAA
1 GATTCAATCTTCTC-TGAGTGACAGTGGAATGAATCAACGTC-TCTAGATCTGATTTTCCCTCAA
* ** * * *
511698 GAATAAGCAGAACATATCCCTATCTTTCAAGATTTGATATTCCCTGAGTAACAATGGAACAAGTC
64 GAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
* *
511763 TCCCTT
129 TTCCTC
* ** * * * * * *
511769 GATTCAATCTT-TCCTAAGCAACAATGGAATGAATCAACATCCCCATATCTGATGTTTCCCTTAA
1 GATTCAATCTTCT-CTGAGTGACAGTGGAATGAATCAACGTCTCTAGATCTGAT-TTTCCCTCAA
* * *
511833 GAAGAAGTGGAACAGATACCTCTCTTTCAAGATTTAATATTCCCTGAGTAACAGTGGAACAAGT-
64 GAAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC
511897 TTACCTC
129 TT-CCTC
* ** * * *
511904 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAAAATCCCCAGATCTGATTTTCCCTCAGGA
1 GATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACGTCTCTAGATCTGATTTTCCCTCAAGA
** ** * *
511969 AGAAGCAGAACAAATCATTCTCTTTCAAGATTTAATATTCCCTGAGTAACAGTGGAACAAGTCGA
66 AGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTC-T
*
512034 ACC-C
130 TCCTC
* * * *
512038 GATTCAATCTTCCCTGAGTGACAGTGGAATGAATCAACATC-CTCAGGTCTAATTTTCCCTCAAG
1 GATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACGTCTCT-AGATCTGATTTTCCCTCAAG
*** * * * *
512102 AAGAAGCAAAACAAATCCATTTCTTTCAAGATTTAATATTCCCTAAGTAACAGTGGAACAAGT-T
65 AAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
512166 TGCCTC
130 T-CCTC
* * * * * * *
512172 GATTCAATCTTACCTGATTGACAGTGACAGTAGAATGAATCAATGTTTCCATATATGATTTTCCC
1 GATTCAATCTT--CT--CTG--AGTGACAGTGGAATGAATCAACGTCTCTAGATCTGATTTTCCC
* * * * * *
512237 TCAAGAAGAAGAGGATCATATCCCTCTGC-TTCAAGATTTGATATTCTCTGAGTAACAATGGAAA
60 TCAAGAAGAAGTGGAACAAATCCCTCT-CTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAAC
512301 AAGTCTTCCTC
124 AAGTCTTCCTC
* * * *
512312 GATTCAATCTTCTTTAAGTGACAGTGGAATGAATCAACGTC-CTCGGATCTAATTTTCCCTCAAG
1 GATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACGTCTCT-AGATCTGATTTTCCCTCAAG
* * * * *
512376 AAGAACTGGAACAAATCCTTCTCTTTCAAGATTTGACATTCTCTGAGTAATAGTGGAACAAGTCT
65 AAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
*
512441 GCCTC
130 TCCTC
* * *
512446 GATTCAATCTTCCCTGAGTGAAAGTTGAATGAATCAACGT-TCCTAGATCTGATTTTCCCTCAAG
1 GATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACGTCT-CTAGATCTGATTTTCCCTCAAG
* *
512510 AATAAGTGGAACATATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
65 AAGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCT
512575 TCCTC
130 TCCTC
* ** * *
512580 GATTCAATCTTCTCTGAGTGACAGTAGAACAAATTAACGTCTCTAGATCTGATTTTCCCTCAAAA
1 GATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACGTCTCTAGATCTGATTTTCCCTCAAGA
* *
512645 AGATGTGGAACAGATCCCTC
66 AGAAGTGGAACAAATCCCTC
512665 ATCATATTTC
Statistics
Matches: 756, Mismatches: 115, Indels: 50
0.82 0.12 0.05
Matches are distributed among these distances:
133 5 0.01
134 521 0.69
135 118 0.16
136 3 0.00
138 4 0.01
140 101 0.13
141 4 0.01
ACGTcount: A:0.32, C:0.22, G:0.16, T:0.30
Consensus pattern (134 bp):
GATTCAATCTTCTCTGAGTGACAGTGGAATGAATCAACGTCTCTAGATCTGATTTTCCCTCAAGA
AGAAGTGGAACAAATCCCTCTCTTTCAAGATTTGATATTCCCTGAGTAACAGTGGAACAAGTCTT
CCTC
Found at i:515125 original size:131 final size:131
Alignment explanation
Indices: 514869--515142 Score: 323
Period size: 131 Copynumber: 2.1 Consensus size: 131
514859 TCGCTATTGA
* * * * *
514869 GAATAGTAATATCTTTTCATTTCGGTCGGAGTAATAAACGATTGCTTTAAGGCATGAGAGGTCAT
1 GAATAGTAATATCTCTTAATTTCGATCGGAGCAATAAACGATTGCTTTAAGGCATGAGAGATCAT
* * * * * ** *
514934 TTATTCTCGATTAGAAATAATTTGATATTGTCATTTTCTCTCGAATTAATACTGTTTTTTAAGAT
66 TTATTCTCGATTAGAAATAATTAGATATTATCATATTCACTCGAATCAATACTGAATTTTAAGAC
514999 G
131 G
* * * *
515000 GAATAGTGATATCTCTTAATTTCGATTGGAGCAATAAATGATTGCTTTAAGGTATGAGAGATCAT
1 GAATAGTAATATCTCTTAATTTCGATCGGAGCAATAAACGATTGCTTTAAGGCATGAGAGATCAT
* * * * * * *
515065 TTATTCTCGATTGGAAATCATTAGATGTTATCGTATTCACTTGAATCGATATTGAATTTTAAGAC
66 TTATTCTCGATTAGAAATAATTAGATATTATCATATTCACTCGAATCAATACTGAATTTTAAGAC
515130 G
131 G
*
515131 AAATAGTAATAT
1 GAATAGTAATAT
515143 TTTTTTTTGA
Statistics
Matches: 117, Mismatches: 26, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
131 117 1.00
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (131 bp):
GAATAGTAATATCTCTTAATTTCGATCGGAGCAATAAACGATTGCTTTAAGGCATGAGAGATCAT
TTATTCTCGATTAGAAATAATTAGATATTATCATATTCACTCGAATCAATACTGAATTTTAAGAC
G
Found at i:517841 original size:59 final size:59
Alignment explanation
Indices: 517778--517905 Score: 222
Period size: 59 Copynumber: 2.2 Consensus size: 59
517768 TCAGATGACC
*
517778 ATTTTATAACTTTTAATAGT-GGAAGACTCAATAAAATAACGTCATATTGTCAGAGGAAT
1 ATTTTGTAACTTTTAATAGTAGG-AGACTCAATAAAATAACGTCATATTGTCAGAGGAAT
*
517837 ATTTTGTAACTTTTAATAGTAGGAGACTCAATAAAATAACGTCATATTGTTAGAGGAAT
1 ATTTTGTAACTTTTAATAGTAGGAGACTCAATAAAATAACGTCATATTGTCAGAGGAAT
517896 ATTTTGTAAC
1 ATTTTGTAAC
517906 GTCATATAAT
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
59 64 0.97
60 2 0.03
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (59 bp):
ATTTTGTAACTTTTAATAGTAGGAGACTCAATAAAATAACGTCATATTGTCAGAGGAAT
Found at i:519542 original size:21 final size:21
Alignment explanation
Indices: 519518--519591 Score: 87
Period size: 21 Copynumber: 3.6 Consensus size: 21
519508 GCGTTGCATT
*
519518 TCGCATTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
* ** **
519539 TCGCGTTGCGAT-TTTCCATT
1 TCGCGTTGCGATAGTTGAAAA
519559 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGATAGTTGAAAA
519580 TCGCGTTGCGAT
1 TCGCGTTGCGAT
519592 TTTCCTGTTC
Statistics
Matches: 41, Mismatches: 11, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
20 15 0.37
21 26 0.63
ACGTcount: A:0.22, C:0.19, G:0.26, T:0.34
Consensus pattern (21 bp):
TCGCGTTGCGATAGTTGAAAA
Found at i:519559 original size:41 final size:41
Alignment explanation
Indices: 519514--519614 Score: 177
Period size: 41 Copynumber: 2.5 Consensus size: 41
519504 ATTCGCGTTG
*
519514 CATTTCGCATTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
519555 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
1 CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
519596 C-TGTTCGCGTTGCGATAGT
1 CAT-TTCGCGTTGCGATAGT
519615 CTACAGTTGT
Statistics
Matches: 58, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
40 1 0.02
41 57 0.98
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.37
Consensus pattern (41 bp):
CATTTCGCGTTGCGATAGTTGAAAATCGCGTTGCGATTTTC
Found at i:519564 original size:20 final size:20
Alignment explanation
Indices: 519539--519611 Score: 76
Period size: 20 Copynumber: 3.6 Consensus size: 20
519529 TAGTTGAAAA
519539 TCGCGTTGCGATTTTCCATT
1 TCGCGTTGCGATTTTCCATT
* ** **
519559 TCGCGTTGCGATAGTTGAAAA
1 TCGCGTTGCGAT-TTTCCATT
519580 TCGCGTTGCGATTTTCC-TGT
1 TCGCGTTGCGATTTTCCAT-T
519600 TCGCGTTGCGAT
1 TCGCGTTGCGAT
519612 AGTCTACAGT
Statistics
Matches: 41, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
20 26 0.63
21 15 0.37
ACGTcount: A:0.14, C:0.22, G:0.26, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCCATT
Found at i:520269 original size:6 final size:6
Alignment explanation
Indices: 520260--520313 Score: 108
Period size: 6 Copynumber: 9.0 Consensus size: 6
520250 CGCCGCCGTC
520260 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
1 CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT CGTGGT
520308 CGTGGT
1 CGTGGT
520314 AATACGTGTC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 48 1.00
ACGTcount: A:0.00, C:0.17, G:0.50, T:0.33
Consensus pattern (6 bp):
CGTGGT
Found at i:520427 original size:20 final size:20
Alignment explanation
Indices: 520402--520515 Score: 84
Period size: 20 Copynumber: 5.6 Consensus size: 20
520392 ACTGTAGACT
520402 ATCGCAACGCGAAATGAAAA
1 ATCGCAACGCGAAATGAAAA
** * **
520422 ATCGCAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
* *
520443 ATCGCAATGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
* ** * **
520463 ATCGTAACGCGATTTTCAACT
1 ATCGCAACGCGA-AATGAAAA
*
520484 ATCGCAACGCGAAATGGAAA
1 ATCGCAACGCGAAATGAAAA
520504 ATCGCAACGCGA
1 ATCGCAACGCGA
520516 TTTTCAACTA
Statistics
Matches: 65, Mismatches: 27, Indels: 4
0.68 0.28 0.04
Matches are distributed among these distances:
20 38 0.58
21 27 0.42
ACGTcount: A:0.39, C:0.23, G:0.20, T:0.18
Consensus pattern (20 bp):
ATCGCAACGCGAAATGAAAA
Found at i:520448 original size:41 final size:41
Alignment explanation
Indices: 520399--520540 Score: 257
Period size: 41 Copynumber: 3.5 Consensus size: 41
520389 AGAACTGTAG
*
520399 ACTATCGCAACGCGAAATGAAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
* *
520440 ACTATCGCAATGCGAAATGGAAAATCGTAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
520481 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
1 ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
520522 ACTATCGCAACGCGAAATG
1 ACTATCGCAACGCGAAATG
520541 CAACGCGAAT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
41 96 1.00
ACGTcount: A:0.37, C:0.23, G:0.19, T:0.20
Consensus pattern (41 bp):
ACTATCGCAACGCGAAATGGAAAATCGCAACGCGATTTTCA
Found at i:520544 original size:21 final size:21
Alignment explanation
Indices: 520376--520544 Score: 128
Period size: 21 Copynumber: 8.1 Consensus size: 21
520366 ATCTTTTTTT
* * *
520376 AACTATCGCAACGAGAACTGT
1 AACTATCGCAACGCGAAATGC
520397 AGACTATCGCAACGCGAAATG-
1 A-ACTATCGCAACGCGAAATGC
** ** *
520418 AAAAATCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGC
* *
520439 AACTATCGCAATGCGAAATGG
1 AACTATCGCAACGCGAAATGC
* * ** *
520460 AA-AATCGTAACGCGATTTTC
1 AACTATCGCAACGCGAAATGC
*
520480 AACTATCGCAACGCGAAATGG
1 AACTATCGCAACGCGAAATGC
* ** *
520501 AA-AATCGCAACGCGATTTTC
1 AACTATCGCAACGCGAAATGC
520521 AACTATCGCAACGCGAAATGC
1 AACTATCGCAACGCGAAATGC
520542 AAC
1 AAC
520545 GCGAATTTGC
Statistics
Matches: 108, Mismatches: 36, Indels: 8
0.71 0.24 0.05
Matches are distributed among these distances:
20 42 0.39
21 49 0.45
22 17 0.16
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.20
Consensus pattern (21 bp):
AACTATCGCAACGCGAAATGC
Found at i:521871 original size:30 final size:30
Alignment explanation
Indices: 521835--521892 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
521825 TAACCACATA
521835 TTAATTAAATAAAAAC-AAAATGATCAAATC
1 TTAATTAAATAAAAACGAAAATGA-CAAATC
*
521865 TTAATTAATTAAAAACGAAAATGACAAA
1 TTAATTAAATAAAAACGAAAATGACAAA
521893 ATAATATATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (30 bp):
TTAATTAAATAAAAACGAAAATGACAAATC
Found at i:522656 original size:9 final size:9
Alignment explanation
Indices: 522642--522670 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
522632 CCCTAACACT
522642 TAAAATTGA
1 TAAAATTGA
522651 TAAAATTGA
1 TAAAATTGA
522660 TAAAATTGA
1 TAAAATTGA
522669 TA
1 TA
522671 GAGTTTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.55, C:0.00, G:0.10, T:0.34
Consensus pattern (9 bp):
TAAAATTGA
Found at i:525438 original size:28 final size:28
Alignment explanation
Indices: 525407--525473 Score: 91
Period size: 28 Copynumber: 2.4 Consensus size: 28
525397 CTGTCAAGCT
* *
525407 AGTGCTTGAAACATTATGCCATCGAA-TC
1 AGTGCTTGAAACACTATACCATC-AAGTC
*
525435 AGTGCTTAAAACACTATACCATCAAGTC
1 AGTGCTTGAAACACTATACCATCAAGTC
525463 AGTGCTTGAAA
1 AGTGCTTGAAA
525474 GCAACGGTGA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
27 2 0.06
28 32 0.94
ACGTcount: A:0.36, C:0.21, G:0.16, T:0.27
Consensus pattern (28 bp):
AGTGCTTGAAACACTATACCATCAAGTC
Found at i:527467 original size:23 final size:23
Alignment explanation
Indices: 527432--527505 Score: 85
Period size: 23 Copynumber: 3.2 Consensus size: 23
527422 GAGTCAAGGG
** *
527432 TTCTACGCAGTCCTTCGGGACAA
1 TTCTACGTGGTCCTTCGGGACAT
*
527455 TTCTACGTGGTCCTTTGGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
* * *
527478 TTCTAAGTGGTCTTTCAGGACAT
1 TTCTACGTGGTCCTTCGGGACAT
527501 TTCTA
1 TTCTA
527506 TGTAGAACTT
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 43 1.00
ACGTcount: A:0.19, C:0.23, G:0.22, T:0.36
Consensus pattern (23 bp):
TTCTACGTGGTCCTTCGGGACAT
Found at i:528337 original size:3 final size:3
Alignment explanation
Indices: 528324--528365 Score: 75
Period size: 3 Copynumber: 13.7 Consensus size: 3
528314 TAAATGCCCA
528324 AAT ATAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
528366 ATAAAGCCAA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 35 0.92
4 3 0.08
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:529219 original size:29 final size:30
Alignment explanation
Indices: 529187--529245 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
529177 TATACCGTCA
* *
529187 AACTTTTAATTTTG-TCAATTATAGCACTG
1 AACTTTGAATTTTGTTCAATTATACCACTG
*
529216 AACTTTGATTTTTGTTTCAATTATACCACT
1 AACTTTGAATTTTG-TTCAATTATACCACT
529246 AGGCCATTAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 12 0.48
31 13 0.52
ACGTcount: A:0.29, C:0.15, G:0.08, T:0.47
Consensus pattern (30 bp):
AACTTTGAATTTTGTTCAATTATACCACTG
Found at i:530085 original size:37 final size:37
Alignment explanation
Indices: 530010--530085 Score: 84
Period size: 37 Copynumber: 2.1 Consensus size: 37
530000 AATTTTGTAA
** * *
530010 AAAATATATAAATTTTATGAATATAAATTTTTTAAAG
1 AAAATATATAAATTAAATGAATATAAATATTATAAAG
530047 AAAATATATAAATTAAAT--ATAATAAATATTATAGAAG
1 AAAATATATAAATTAAATGAAT-ATAAATATTATA-AAG
530084 AA
1 AA
530086 TTCAACTTGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
35 2 0.06
36 10 0.30
37 21 0.64
ACGTcount: A:0.58, C:0.00, G:0.05, T:0.37
Consensus pattern (37 bp):
AAAATATATAAATTAAATGAATATAAATATTATAAAG
Found at i:530766 original size:21 final size:21
Alignment explanation
Indices: 530742--530782 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
530732 CATTTCAATG
530742 AAAGGACT-TAACATTTTGATT
1 AAAGGA-TATAACATTTTGATT
530763 AAAGGATATAACATTTTGAT
1 AAAGGATATAACATTTTGAT
530783 GAACGAGCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 1 0.05
21 18 0.95
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (21 bp):
AAAGGATATAACATTTTGATT
Found at i:532677 original size:22 final size:21
Alignment explanation
Indices: 532649--532691 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
532639 TTATGTATTT
532649 TTAATTAAAATAATATTTATAA
1 TTAATTAAAATAAT-TTTATAA
* *
532671 TTAATTATATTAATTTTATAA
1 TTAATTAAAATAATTTTATAA
532692 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
TTAATTAAAATAATTTTATAA
Found at i:533505 original size:23 final size:23
Alignment explanation
Indices: 533475--533521 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
533465 AAATCCCTAA
533475 AATTCTAACACTAACCCACCGCC
1 AATTCTAACACTAACCCACCGCC
*
533498 AATTCTAACACTAACCCACTGCC
1 AATTCTAACACTAACCCACCGCC
533521 A
1 A
533522 TTACTCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.36, C:0.40, G:0.04, T:0.19
Consensus pattern (23 bp):
AATTCTAACACTAACCCACCGCC
Found at i:534676 original size:3 final size:3
Alignment explanation
Indices: 534658--534742 Score: 88
Period size: 3 Copynumber: 29.3 Consensus size: 3
534648 GGATTATAAA
* * *
534658 TAT TA- TAT TAAT TAT TAT TGT TA- TAT AAT AAT TA- TAT TAT TAT
1 TAT TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
534701 TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT TAT AAT AAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
534743 GGTAATAGTA
Statistics
Matches: 71, Mismatches: 6, Indels: 10
0.82 0.07 0.11
Matches are distributed among these distances:
2 8 0.11
3 60 0.85
4 3 0.04
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:534902 original size:13 final size:13
Alignment explanation
Indices: 534884--534908 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
534874 GCTACAGTCC
534884 AACCCTAAATCAA
1 AACCCTAAATCAA
534897 AACCCTAAATCA
1 AACCCTAAATCA
534909 TTAGGGTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.32, G:0.00, T:0.16
Consensus pattern (13 bp):
AACCCTAAATCAA
Found at i:548056 original size:12 final size:12
Alignment explanation
Indices: 548041--548084 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
548031 AAGAAGAAGG
548041 AAAAATGAATGAA
1 AAAAATGAATG-A
*
548054 AAAAAT-AA-AA
1 AAAAATGAATGA
548064 AAAAATGAATGA
1 AAAAATGAATGA
548076 AAAAATGAA
1 AAAAATGAA
548085 AAGAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
10 7 0.26
11 2 0.07
12 12 0.44
13 6 0.22
ACGTcount: A:0.75, C:0.00, G:0.11, T:0.14
Consensus pattern (12 bp):
AAAAATGAATGA
Found at i:548065 original size:10 final size:11
Alignment explanation
Indices: 548041--548092 Score: 52
Period size: 12 Copynumber: 4.5 Consensus size: 11
548031 AAGAAGAAGG
548041 AAAAATGAATGAA
1 AAAAATGAA--AA
548054 AAAAAT-AAAA
1 AAAAATGAAAA
*
548064 AAAAATGAATGA
1 AAAAATGAA-AA
548076 AAAAATGAAAA
1 AAAAATGAAAA
548087 GAAAAA
1 -AAAAA
548093 AAAAGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
10 8 0.24
11 3 0.09
12 17 0.50
13 6 0.18
ACGTcount: A:0.77, C:0.00, G:0.12, T:0.12
Consensus pattern (11 bp):
AAAAATGAAAA
Found at i:548086 original size:23 final size:24
Alignment explanation
Indices: 548021--548092 Score: 87
Period size: 23 Copynumber: 3.0 Consensus size: 24
548011 GTATTTTGCT
*
548021 TGAA-GAAAAAAAGAAGAAGGAAAAA
1 TGAATGAAAAAAATAA-AA-GAAAAA
548046 TGAATGAAAAAAATAAAA-AAAAA
1 TGAATGAAAAAAATAAAAGAAAAA
548069 TGAATG-AAAAAATGAAAAGAAAAA
1 TGAATGAAAAAAAT-AAAAGAAAAA
548093 AAAAGAAAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
22 7 0.16
23 15 0.35
24 5 0.12
25 6 0.14
26 10 0.23
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (24 bp):
TGAATGAAAAAAATAAAAGAAAAA
Found at i:548092 original size:14 final size:13
Alignment explanation
Indices: 548023--548094 Score: 57
Period size: 13 Copynumber: 5.8 Consensus size: 13
548013 ATTTTGCTTG
548023 AAGAAAAAAA-G-
1 AAGAAAAAAATGA
548034 AAGAAGGAAAAATGA
1 AAGAA--AAAAATGA
*
548049 ATGAAAAAAAT--
1 AAGAAAAAAATGA
548060 AA-AAAAAAATGA
1 AAGAAAAAAATGA
*
548072 ATG-AAAAAATGAA
1 AAGAAAAAAATG-A
548085 AAGAAAAAAA
1 AAGAAAAAAA
548095 AAGAAAAAAA
Statistics
Matches: 48, Mismatches: 4, Indels: 15
0.72 0.06 0.22
Matches are distributed among these distances:
10 8 0.17
11 6 0.12
12 9 0.19
13 14 0.29
14 7 0.15
15 4 0.08
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.08
Consensus pattern (13 bp):
AAGAAAAAAATGA
Found at i:549176 original size:55 final size:55
Alignment explanation
Indices: 549110--549486 Score: 449
Period size: 55 Copynumber: 6.9 Consensus size: 55
549100 TTCCCCAACA
*
549110 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGTAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
549165 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGG-GACAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAG-CAGACACG
549220 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
1 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
* *
549275 AGTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACATG
1 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
* * * * * *
549330 ATTATTGATGATTGTTCGAGT-TCTATACTCCCTGAAGAAAGAGGGAGCAAACCCG
1 ATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGAAGAAATAGGGAGCAGACACG
* ** * * * * * * * *
549385 TTTGCAGATGATTGTTCAAGTTTTATACTCCCTGAAGGAAGAGGGAAC-GAACCCG
1 ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAG-ACACG
** * * *
549440 ATTAATGAAGATTGTCCGAGT-TCTATACTCCCT-ATAGAAAGAGGGAG
1 ATTGTTGAAGATTGTTCGAGTCT-TATACTCTCTGA-AGAAATAGGGAG
549487 TGAACCCGTT
Statistics
Matches: 287, Mismatches: 28, Indels: 14
0.87 0.09 0.04
Matches are distributed among these distances:
54 4 0.01
55 281 0.98
56 2 0.01
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (55 bp):
ATTGTTGAAGATTGTTCGAGTCTTATACTCTCTGAAGAAATAGGGAGCAGACACG
Found at i:549533 original size:110 final size:110
Alignment explanation
Indices: 549329--549537 Score: 262
Period size: 110 Copynumber: 1.9 Consensus size: 110
549319 GAGCAGACAT
* * * * *
549329 GATTATTGATGATTGTTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTTGCAGAT
1 GATTAATGAAGATTGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTGGCAGAA
* * *
549394 GATTGTTCAAGTTTTATACTCCCTGAAGGAAGAGGGAACGAACCC
66 GATTGTTCAAGTTCTACACTCCCTAAAGGAAGAGGGAACGAACCC
** *
549439 GATTAATGAAGATTGTCCGAGTTCTATACTCCCT-ATAGAAAGAGGGAGTGAACCCGTTGGCTGA
1 GATTAATGAAGATTGTCCGAGTTCTATACTCCCTGA-AGAAAGAGGGAGCAAACCCGTTGGCAGA
*
549503 AGATTTTTCAAG-TCT-CACTCACCTTAAAGGAAGAG
65 AGATTGTTCAAGTTCTACACTC-CC-TAAAGGAAGAG
549538 TGGAGCAAAT
Statistics
Matches: 84, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
108 4 0.05
109 5 0.06
110 75 0.89
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (110 bp):
GATTAATGAAGATTGTCCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCAAACCCGTTGGCAGAA
GATTGTTCAAGTTCTACACTCCCTAAAGGAAGAGGGAACGAACCC
Found at i:549718 original size:11 final size:11
Alignment explanation
Indices: 549702--549747 Score: 56
Period size: 11 Copynumber: 4.1 Consensus size: 11
549692 ATTATTATTG
549702 TTATATAATAA
1 TTATATAATAA
549713 TTATATAATAA
1 TTATATAATAA
* *
549724 TTATTATTATTA
1 TTA-TATAATAA
*
549736 TTATATTATAA
1 TTATATAATAA
549747 T
1 T
549748 AATTATTGCT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
11 22 0.71
12 9 0.29
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (11 bp):
TTATATAATAA
Found at i:549912 original size:13 final size:13
Alignment explanation
Indices: 549896--549920 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
549886 GCTACAGTCC
549896 AACCTTAAATCAA
1 AACCTTAAATCAA
549909 AACCTTAAATCA
1 AACCTTAAATCA
549921 TTAGGGTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.24, G:0.00, T:0.24
Consensus pattern (13 bp):
AACCTTAAATCAA
Found at i:561495 original size:2 final size:2
Alignment explanation
Indices: 561488--561535 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
561478 ATAATTAAAG
561488 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
561530 TA TA TA
1 TA TA TA
561536 CTTAGAGTTT
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):
TA
Found at i:561828 original size:11 final size:11
Alignment explanation
Indices: 561812--561836 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
561802 TATATGACTA
561812 AAATAATAATT
1 AAATAATAATT
561823 AAATAATAATT
1 AAATAATAATT
561834 AAA
1 AAA
561837 GTACTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (11 bp):
AAATAATAATT
Found at i:563257 original size:3 final size:3
Alignment explanation
Indices: 563251--563296 Score: 62
Period size: 3 Copynumber: 16.3 Consensus size: 3
563241 AAATATTATT
*
563251 TAA TAA TAA TAA TAA T-A TAA TAA -AA TAA AAA TAA TAA -AA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
563296 T
1 T
563297 TAAAAACTAT
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.16
3 32 0.84
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:563272 original size:14 final size:13
Alignment explanation
Indices: 563253--563294 Score: 57
Period size: 14 Copynumber: 3.1 Consensus size: 13
563243 ATATTATTTA
563253 ATAATAATAATAAT
1 ATAATAA-AATAAT
*
563267 ATAATAAAATAAAA
1 ATAATAAAAT-AAT
563281 ATAATAAAATAAT
1 ATAATAAAATAAT
563294 A
1 A
563295 ATTAAAAACT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 6 0.24
14 19 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
ATAATAAAATAAT
Found at i:563277 original size:19 final size:19
Alignment explanation
Indices: 563255--563302 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 19
563245 ATTATTTAAT
* *
563255 AATAATAATAATATAATAA
1 AATAAAAATAATAAAATAA
563274 AATAAAAATAATAAAATAA
1 AATAAAAATAATAAAATAA
563293 TAATTAAAAA
1 -AA-TAAAAA
563303 CTATGACAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 17 0.68
20 2 0.08
21 6 0.24
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (19 bp):
AATAAAAATAATAAAATAA
Found at i:563302 original size:22 final size:22
Alignment explanation
Indices: 563252--563295 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
563242 AATATTATTT
* *
563252 AATAATAATAATAATATAATAA
1 AATAAAAATAATAAAATAATAA
563274 AATAAAAATAATAAAATAATAA
1 AATAAAAATAATAAAATAATAA
563296 TTAAAAACTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (22 bp):
AATAAAAATAATAAAATAATAA
Found at i:564854 original size:22 final size:22
Alignment explanation
Indices: 564768--564850 Score: 123
Period size: 22 Copynumber: 3.8 Consensus size: 22
564758 AAATCCAATA
*
564768 AATCTTTCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
564790 AATCTATCATCTTTGAAAAGAG
1 AATCTATCATCTTTGAAAAGAG
* *
564812 AATCTATCATCTTTTAAGAA-TG
1 AATCTATCATCTTTGAA-AAGAG
564834 AATCTATCATCTTTGAA
1 AATCTATCATCTTTGAA
564851 GAATATAGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
22 54 0.96
23 2 0.04
ACGTcount: A:0.37, C:0.14, G:0.11, T:0.37
Consensus pattern (22 bp):
AATCTATCATCTTTGAAAAGAG
Found at i:565756 original size:21 final size:21
Alignment explanation
Indices: 565732--565775 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
565722 TCAAAATAGG
565732 CCTCCAAGATGTCCCAAACTT
1 CCTCCAAGATGTCCCAAACTT
565753 CCTCCAAGATGTCCCAAACTT
1 CCTCCAAGATGTCCCAAACTT
565774 CC
1 CC
565776 ATGATGACGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.27, C:0.41, G:0.09, T:0.23
Consensus pattern (21 bp):
CCTCCAAGATGTCCCAAACTT
Found at i:571951 original size:2 final size:2
Alignment explanation
Indices: 571944--571982 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
571934 TTAAAACAAC
571944 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 T
571983 TTTTTATAAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:572000 original size:22 final size:23
Alignment explanation
Indices: 571975--572017 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
571965 ATATATATAT
*
571975 ATATATATTT-TTTATAAATAAG
1 ATATATATTTATTTAAAAATAAG
*
571997 ATATTTATTTATTTAAAAATA
1 ATATATATTTATTTAAAAATA
572018 TCAGAATATG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATATTTATTTAAAAATAAG
Found at i:573534 original size:3 final size:3
Alignment explanation
Indices: 573528--573601 Score: 83
Period size: 3 Copynumber: 27.3 Consensus size: 3
573518 ATTATTTATT
573528 TAA TAA TAA TAA TAA T-A TAA -AA TAA TAA -AA TAA -AA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
*
573571 -AA TAA TAA -AA TAA TAA TAA TTA -AA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
573602 TAAAAACTGT
Statistics
Matches: 61, Mismatches: 2, Indels: 16
0.77 0.03 0.20
Matches are distributed among these distances:
2 15 0.25
3 46 0.75
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (3 bp):
TAA
Found at i:573552 original size:5 final size:5
Alignment explanation
Indices: 573532--573589 Score: 61
Period size: 5 Copynumber: 12.0 Consensus size: 5
573522 TTTATTTAAT
*
573532 AATAA TAATAA TATAA AAT-- AATAA AATAA AATAA AATAA AAT-- AATAA
1 AATAA -AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA AATAA
573579 AATAA TAATAA
1 AATAA -AATAA
573590 TTAAATAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
3 6 0.13
5 29 0.64
6 10 0.22
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (5 bp):
AATAA
Found at i:573555 original size:8 final size:8
Alignment explanation
Indices: 573532--573600 Score: 76
Period size: 8 Copynumber: 9.0 Consensus size: 8
573522 TTTATTTAAT
573532 AATAATAA
1 AATAATAA
573540 TAAT-ATAA
1 -AATAATAA
573548 AATAATAA
1 AATAATAA
573556 AATAA-AA
1 AATAATAA
573563 TAA-AATAA
1 -AATAATAA
573571 AATAATAA
1 AATAATAA
573579 AATAAT--
1 AATAATAA
*
573585 AATAATTA
1 AATAATAA
573593 AATAATAA
1 AATAATAA
573601 TTAAAAACTG
Statistics
Matches: 53, Mismatches: 1, Indels: 13
0.79 0.01 0.19
Matches are distributed among these distances:
6 6 0.11
7 9 0.17
8 35 0.66
9 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (8 bp):
AATAATAA
Found at i:573570 original size:23 final size:24
Alignment explanation
Indices: 573532--573589 Score: 100
Period size: 23 Copynumber: 2.5 Consensus size: 24
573522 TTTATTTAAT
*
573532 AATAATAATAATATAAAATAATAA
1 AATAATAATAAAATAAAATAATAA
573556 AATAA-AATAAAATAAAATAATAA
1 AATAATAATAAAATAAAATAATAA
573579 AATAATAATAA
1 AATAATAATAA
573590 TTAAATAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 22 0.69
24 10 0.31
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (24 bp):
AATAATAATAAAATAAAATAATAA
Found at i:573594 original size:23 final size:23
Alignment explanation
Indices: 573532--573600 Score: 97
Period size: 23 Copynumber: 3.0 Consensus size: 23
573522 TTTATTTAAT
573532 AATAATAATAATATAAAATAATAA
1 AATAATAATAAT-TAAAATAATAA
*
573556 AATAA-AATAAAATAAAATAATAA
1 AATAATAAT-AATTAAAATAATAA
573579 AATAATAATAATT-AAATAATAA
1 AATAATAATAATTAAAATAATAA
573601 TTAAAAACTG
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
22 9 0.22
23 22 0.54
24 10 0.24
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (23 bp):
AATAATAATAATTAAAATAATAA
Found at i:576651 original size:40 final size:39
Alignment explanation
Indices: 576607--576722 Score: 117
Period size: 40 Copynumber: 2.9 Consensus size: 39
576597 GATTTCTGAA
* *
576607 TTCGCGACGCGATTTTTAAATTCGCAACAC-AAGTTTCCTT
1 TTCGCAACACGATTTTT-AATTCGCAACACGAA-TTTCCTT
* **
576647 TTCGCAACAAGATTTTCTAATTCGCAACACGAATTTTGTT
1 TTCGCAACACGATTTT-TAATTCGCAACACGAATTTCCTT
* **
576687 TTCGCAACTCGATTTCCGAATTCGCAACACGAATTT
1 TTCGCAACACGATTT-TTAATTCGCAACACGAATTT
576723 TAATTTCGCA
Statistics
Matches: 64, Mismatches: 9, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
40 61 0.95
41 3 0.05
ACGTcount: A:0.28, C:0.24, G:0.14, T:0.34
Consensus pattern (39 bp):
TTCGCAACACGATTTTTAATTCGCAACACGAATTTCCTT
Found at i:576663 original size:20 final size:19
Alignment explanation
Indices: 576635--576753 Score: 62
Period size: 20 Copynumber: 6.2 Consensus size: 19
576625 AATTCGCAAC
*
576635 ACAAG-TTTCCTTTTCGCA
1 ACAAGATTTTCTTTTCGCA
*
576653 ACAAGATTTTCTAATTCGCA
1 ACAAGATTTTCT-TTTCGCA
* *
576673 ACACGAATTTTGTTTTCGCA
1 ACAAG-ATTTTCTTTTCGCA
** * **
576693 ACTCGATTTCCGAATTCGCA
1 ACAAGATTTTC-TTTTCGCA
* **
576713 ACACGAATTTTAATTTCGCA
1 ACAAG-ATTTTCTTTTCGCA
* *
576733 AC-AGCTTTTATTTTCGCA
1 ACAAGATTTTCTTTTCGCA
576751 ACA
1 ACA
576754 CAAATGTTTT
Statistics
Matches: 78, Mismatches: 17, Indels: 11
0.74 0.16 0.10
Matches are distributed among these distances:
18 19 0.24
19 10 0.13
20 39 0.50
21 10 0.13
ACGTcount: A:0.29, C:0.24, G:0.12, T:0.36
Consensus pattern (19 bp):
ACAAGATTTTCTTTTCGCA
Found at i:576692 original size:60 final size:58
Alignment explanation
Indices: 576627--576756 Score: 138
Period size: 60 Copynumber: 2.2 Consensus size: 58
576617 GATTTTTAAA
** * *
576627 TTCGCAACACAAGTTTCC-TTTTCGCAACAAGATTTTCTAA-TTCGCAACACGAATTTTGTT
1 TTCGCAACACAA-TTTCCGAATTCGCAACAAGAATTT-TAATTTCGCAACA-G-ATTTTATT
* * * *
576687 TTCGCAACTCGATTTCCGAATTCGCAACACGAATTTTAATTTCGCAACAGCTTTTATT
1 TTCGCAACACAATTTCCGAATTCGCAACAAGAATTTTAATTTCGCAACAGATTTTATT
576745 TTCGCAACACAA
1 TTCGCAACACAA
576757 ATGTTTTAGG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
58 16 0.28
59 9 0.16
60 33 0.57
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.35
Consensus pattern (58 bp):
TTCGCAACACAATTTCCGAATTCGCAACAAGAATTTTAATTTCGCAACAGATTTTATT
Found at i:576723 original size:40 final size:40
Alignment explanation
Indices: 576625--576735 Score: 134
Period size: 40 Copynumber: 2.8 Consensus size: 40
576615 GCGATTTTTA
** * *
576625 AATTCGCAACAC-AAGTTTCCTTTTCGCAACAAGATTTTCT
1 AATTCGCAACACGAA-TTTTATTTTCGCAACAAGATTTCCG
* **
576665 AATTCGCAACACGAATTTTGTTTTCGCAACTCGATTTCCG
1 AATTCGCAACACGAATTTTATTTTCGCAACAAGATTTCCG
*
576705 AATTCGCAACACGAATTTTAATTTCGCAACA
1 AATTCGCAACACGAATTTTATTTTCGCAACA
576736 GCTTTTATTT
Statistics
Matches: 61, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 59 0.97
41 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.12, T:0.33
Consensus pattern (40 bp):
AATTCGCAACACGAATTTTATTTTCGCAACAAGATTTCCG
Found at i:577700 original size:24 final size:24
Alignment explanation
Indices: 577683--577740 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
577673 GTCAGTATTC
577683 GAAATTTGATCTTGGTCAATACTT
1 GAAATTTGATCTTGGTCAATACTT
* *
577707 GGACTTTGATCTTGGTCAATACTT
1 GAAATTTGATCTTGGTCAATACTT
* *
577731 GGATTTTGAT
1 GAAATTTGAT
577741 GATGTTTCAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.24, C:0.12, G:0.21, T:0.43
Consensus pattern (24 bp):
GAAATTTGATCTTGGTCAATACTT
Found at i:580018 original size:6 final size:6
Alignment explanation
Indices: 580007--580041 Score: 52
Period size: 6 Copynumber: 5.8 Consensus size: 6
579997 ACGAAAAAGG
* *
580007 AAATCA AAATCA AAATCG CAATCA AAATCA AAATC
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATC
580042 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:580029 original size:18 final size:18
Alignment explanation
Indices: 580008--580048 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
579998 CGAAAAAGGA
*
580008 AATCAAAATCAAAATCGC
1 AATCAAAATCAAAATCCC
580026 AATCAAAATCAAAATCCC
1 AATCAAAATCAAAATCCC
580044 AATCA
1 AATCA
580049 CAACCGCCTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.56, C:0.24, G:0.02, T:0.17
Consensus pattern (18 bp):
AATCAAAATCAAAATCCC
Found at i:580343 original size:20 final size:20
Alignment explanation
Indices: 580300--580378 Score: 86
Period size: 20 Copynumber: 4.0 Consensus size: 20
580290 TTCGCAACTC
* * * *
580300 AAATTCGCAACTCGATATTC
1 AAATTCGCAACGCGAAAATA
580320 AAATTCGCAACGCGAAAATA
1 AAATTCGCAACGCGAAAATA
* *
580340 AAATTTGTAACGCGAAAATA
1 AAATTCGCAACGCGAAAATA
* *
580360 AAATTTGCAATGCGAAAAT
1 AAATTCGCAACGCGAAAAT
580379 CGCAACTTGA
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 51 1.00
ACGTcount: A:0.46, C:0.16, G:0.14, T:0.24
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATA
Found at i:581943 original size:21 final size:21
Alignment explanation
Indices: 581917--582070 Score: 125
Period size: 21 Copynumber: 7.3 Consensus size: 21
581907 CGAATGCCAT
*
581917 GTGGATCCTGAACGGTGGGAG
1 GTGGATCCTGAACGATGGGAG
*
581938 GTGGATCATGAACGATGGGAG
1 GTGGATCCTGAACGATGGGAG
* *
581959 G-GGCCTCTTGAACGATGGGA-
1 GTGG-ATCCTGAACGATGGGAG
* * **
581979 -TAGGCCTCTTGAACGATGACAG
1 GT-GG-ATCCTGAACGATGGGAG
* *
582001 GTGAATCCTGAACAATGGGAG
1 GTGGATCCTGAACGATGGGAG
** *
582022 GTGGATCCTGAATAATGGTAG
1 GTGGATCCTGAACGATGGGAG
* *
582043 GTGGATCCTGAACAATGGTAG
1 GTGGATCCTGAACGATGGGAG
582064 GTGGATC
1 GTGGATC
582071 GGGCTTTTTT
Statistics
Matches: 112, Mismatches: 16, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
20 2 0.02
21 108 0.96
22 1 0.01
23 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.37, T:0.22
Consensus pattern (21 bp):
GTGGATCCTGAACGATGGGAG
Found at i:582392 original size:21 final size:21
Alignment explanation
Indices: 582368--582446 Score: 61
Period size: 21 Copynumber: 3.8 Consensus size: 21
582358 GTAGAGCAGC
*
582368 TACCTCATCACGTAAAACAGA
1 TACCTCACCACGTAAAACAGA
* * *
582389 TACCTCACCATGTAAAGCACCA
1 TACCTCACCACGTAAAACA-GA
** * * *
582411 T-TGTCATCACGTAAAATAGC
1 TACCTCACCACGTAAAACAGA
582431 TACCTCACCACGTAAA
1 TACCTCACCACGTAAA
582447 GACCCTACCT
Statistics
Matches: 41, Mismatches: 15, Indels: 4
0.68 0.25 0.07
Matches are distributed among these distances:
20 1 0.02
21 38 0.93
22 2 0.05
ACGTcount: A:0.38, C:0.30, G:0.10, T:0.22
Consensus pattern (21 bp):
TACCTCACCACGTAAAACAGA
Found at i:582423 original size:63 final size:62
Alignment explanation
Indices: 582356--582535 Score: 189
Period size: 63 Copynumber: 2.9 Consensus size: 62
582346 AAACAATCTT
* * *
582356 ACGTAGAGCAGCTACCTCATCACGTAAAACAGATACCTCACCATGTAAAGCACCATTGTCATC
1 ACGTAAAGCAGCTACCTCATCACGTAAAACA-CTACCTCATCATGTAAAGCACCATTGTCATC
** * * ** * * *
582419 ACGTAAAATAGCTACCTCACCACGTAAAGACCCTACCTCATCATGCCATGCACTATTGTCGTC
1 ACGTAAAGCAGCTACCTCATCACGTAAA-ACACTACCTCATCATGTAAAGCACCATTGTCATC
* * * *
582482 ACGTAAAGCACCGACCTCATCACGTAAAGCACTGACCTCATCACGTAAAGCACC
1 ACGTAAAGCAGCTACCTCATCACGTAAAACACT-ACCTCATCATGTAAAGCACC
582536 TAACTCATCT
Statistics
Matches: 91, Mismatches: 24, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
62 3 0.03
63 86 0.95
64 2 0.02
ACGTcount: A:0.33, C:0.33, G:0.14, T:0.20
Consensus pattern (62 bp):
ACGTAAAGCAGCTACCTCATCACGTAAAACACTACCTCATCATGTAAAGCACCATTGTCATC
Found at i:582460 original size:42 final size:43
Alignment explanation
Indices: 582367--582461 Score: 122
Period size: 42 Copynumber: 2.3 Consensus size: 43
582357 CGTAGAGCAG
*
582367 CTACCTCATCACGTAAAACAGATACCTCACCATGTAAAGCACC
1 CTACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACC
* ** * *
582410 AT-TGTCATCACGTAAAATAGCTACCTCACCACGTAAAG-ACC
1 CTACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACC
582451 CTACCTCATCA
1 CTACCTCATCA
582462 TGCCATGCAC
Statistics
Matches: 42, Mismatches: 9, Indels: 3
0.78 0.17 0.06
Matches are distributed among these distances:
41 4 0.10
42 37 0.88
43 1 0.02
ACGTcount: A:0.36, C:0.34, G:0.09, T:0.21
Consensus pattern (43 bp):
CTACCTCATCACGTAAAACAGATACCTCACCACGTAAAGCACC
Found at i:582504 original size:21 final size:21
Alignment explanation
Indices: 582480--582544 Score: 103
Period size: 21 Copynumber: 3.1 Consensus size: 21
582470 ACTATTGTCG
582480 TCACGTAAAGCACCGACCTCA
1 TCACGTAAAGCACCGACCTCA
*
582501 TCACGTAAAGCACTGACCTCA
1 TCACGTAAAGCACCGACCTCA
* *
582522 TCACGTAAAGCACCTAACTCA
1 TCACGTAAAGCACCGACCTCA
582543 TC
1 TC
582545 TTGTGGAGGT
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.34, C:0.35, G:0.12, T:0.18
Consensus pattern (21 bp):
TCACGTAAAGCACCGACCTCA
Found at i:582703 original size:42 final size:42
Alignment explanation
Indices: 582644--582788 Score: 184
Period size: 42 Copynumber: 3.5 Consensus size: 42
582634 GTGATGGAAT
* * *
582644 AGGTGATGGCTCTCGGTGTCAAGGTGTAGAATCGACTCGATC
1 AGGTGATGGATCTCGGTGTCAAGGTGTAGAATAGGCTCGATC
* * *
582686 AGGTGATGGCTCTCGGTGTCGAGGTGTAGAATTGGCTCGATC
1 AGGTGATGGATCTCGGTGTCAAGGTGTAGAATAGGCTCGATC
* * * *
582728 AGGTGATGGATCTTGGTGTCGAA-GTGGAGAAGAGGCTCGATG
1 AGGTGATGGATCTCGGTGTC-AAGGTGTAGAATAGGCTCGATC
582770 AGGTGATGGATCTCGGTGT
1 AGGTGATGGATCTCGGTGT
582789 TGAAGTGGGG
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
42 90 0.99
43 1 0.01
ACGTcount: A:0.20, C:0.14, G:0.39, T:0.27
Consensus pattern (42 bp):
AGGTGATGGATCTCGGTGTCAAGGTGTAGAATAGGCTCGATC
Found at i:584353 original size:14 final size:14
Alignment explanation
Indices: 584334--584367 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
584324 AGTGAATTTC
584334 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
*
584348 ATTTTCGTGTTGCG
1 ATTTTCGCGTTGCG
*
584362 AATTTC
1 ATTTTC
584368 ATTTTCTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.18, G:0.24, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:584371 original size:20 final size:20
Alignment explanation
Indices: 584348--584386 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
584338 TCGCGTTGCG
584348 ATTTTCGTGTTGCGAATTTC
1 ATTTTCGTGTTGCGAATTTC
*
584368 ATTTTCTTGTTGCGAATTT
1 ATTTTCGTGTTGCGAATTT
584387 AAGTTTCAAA
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:0.15, C:0.13, G:0.18, T:0.54
Consensus pattern (20 bp):
ATTTTCGTGTTGCGAATTTC
Found at i:584393 original size:20 final size:20
Alignment explanation
Indices: 584350--584393 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
584340 GCGTTGCGAT
* *
584350 TTTCGTGTTGCGAATTTCAT
1 TTTCGTGTTGCGAATTTAAG
*
584370 TTTCTTGTTGCGAATTTAAG
1 TTTCGTGTTGCGAATTTAAG
584390 TTTC
1 TTTC
584394 AAAAACTACT
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:0.16, C:0.14, G:0.18, T:0.52
Consensus pattern (20 bp):
TTTCGTGTTGCGAATTTAAG
Found at i:584870 original size:19 final size:20
Alignment explanation
Indices: 584848--584885 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
584838 ATATTCATGT
584848 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
*
584867 TTCGAGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
584886 CACGTTTTGC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:587990 original size:116 final size:116
Alignment explanation
Indices: 587797--588022 Score: 443
Period size: 116 Copynumber: 1.9 Consensus size: 116
587787 AACTTTTTTT
587797 CATAATTTAAATATGTTTCTTGTATTTTATTTAAATTATCTAATTTTGTATCTATTAAATTTTAT
1 CATAATTTAAATATGTTTCTTGTATTTTATTTAAATTATCTAATTTTGTATCTATTAAATTTTAT
587862 AATTTTACACTCCTAAATTTTTAATATAATTTCTTAAATTTATACATCTGA
66 AATTTTACACTCCTAAATTTTTAATATAATTTCTTAAATTTATACATCTGA
587913 CATAATTTAAATATGTTTCTTGTATTTTATTTAAATTATCTAATTTTGTATCTATTAAATTTTAT
1 CATAATTTAAATATGTTTCTTGTATTTTATTTAAATTATCTAATTTTGTATCTATTAAATTTTAT
*
587978 AATTTTATACTCCTAAATTTTTAATATAATTTCTTAAATTTATAC
66 AATTTTACACTCCTAAATTTTTAATATAATTTCTTAAATTTATAC
588023 GTTCATAAAT
Statistics
Matches: 109, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
116 109 1.00
ACGTcount: A:0.35, C:0.09, G:0.03, T:0.54
Consensus pattern (116 bp):
CATAATTTAAATATGTTTCTTGTATTTTATTTAAATTATCTAATTTTGTATCTATTAAATTTTAT
AATTTTACACTCCTAAATTTTTAATATAATTTCTTAAATTTATACATCTGA
Found at i:589307 original size:16 final size:16
Alignment explanation
Indices: 589270--589311 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 16
589260 TTTCAAACCT
589270 CTAAACCTT--AAATC
1 CTAAACCTTAAAAATC
* *
589284 ATATACCTTAAAAATC
1 CTAAACCTTAAAAATC
589300 CTAAACCTTAAA
1 CTAAACCTTAAA
589312 TTCTAAAACC
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
14 7 0.32
16 15 0.68
ACGTcount: A:0.48, C:0.24, G:0.00, T:0.29
Consensus pattern (16 bp):
CTAAACCTTAAAAATC
Found at i:589312 original size:14 final size:14
Alignment explanation
Indices: 589270--589318 Score: 53
Period size: 14 Copynumber: 3.4 Consensus size: 14
589260 TTTCAAACCT
589270 CTAAACCTTAAATC
1 CTAAACCTTAAATC
* *
589284 ATATACCTTAAAAATC
1 CTAAACCTT--AAATC
*
589300 CTAAACCTTAAATT
1 CTAAACCTTAAATC
589314 CTAAA
1 CTAAA
589319 ACCATATACC
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
14 16 0.57
16 12 0.43
ACGTcount: A:0.47, C:0.22, G:0.00, T:0.31
Consensus pattern (14 bp):
CTAAACCTTAAATC
Found at i:589586 original size:7 final size:7
Alignment explanation
Indices: 589576--589713 Score: 61
Period size: 7 Copynumber: 19.1 Consensus size: 7
589566 AAACCTATAT
589576 CTTAAAC
1 CTTAAAC
589583 CTTAAAC
1 CTTAAAC
589590 CTTAAAC
1 CTTAAAC
589597 CTTAAA-
1 CTTAAAC
589603 CTCTAAAC
1 CT-TAAAC
* *
589611 ATTGAAC
1 CTTAAAC
* *
589618 CCTAGATC
1 CTTA-AAC
*
589626 C-TAAAT
1 CTTAAAC
*
589632 CATAAAC
1 CTTAAAC
*
589639 CTTAAAA
1 CTTAAAC
*
589646 CTTAAAAAA
1 CTT--AAAC
**
589655 AATAAACC
1 CTTAAA-C
*
589663 CTAAAATC
1 CTTAAA-C
589671 C-TAAAC
1 CTTAAAC
589677 CTTAATA-
1 CTTAA-AC
589684 -TATAAAC
1 CT-TAAAC
589691 CTTAAAC
1 CTTAAAC
589698 TCTTAAAC
1 -CTTAAAC
589706 CTTAAAC
1 CTTAAAC
589713 C
1 C
589714 AAGAAACAAT
Statistics
Matches: 99, Mismatches: 19, Indels: 26
0.69 0.13 0.18
Matches are distributed among these distances:
6 8 0.08
7 68 0.69
8 18 0.18
9 5 0.05
ACGTcount: A:0.47, C:0.25, G:0.01, T:0.27
Consensus pattern (7 bp):
CTTAAAC
Found at i:589775 original size:15 final size:16
Alignment explanation
Indices: 589757--589786 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
589747 AACCATGAAT
589757 CTTAAAACC-TAAACA
1 CTTAAAACCATAAACA
589772 CTTAAAACCATAAAC
1 CTTAAAACCATAAAC
589787 CTTTGAACAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.53, C:0.27, G:0.00, T:0.20
Consensus pattern (16 bp):
CTTAAAACCATAAACA
Found at i:589914 original size:182 final size:180
Alignment explanation
Indices: 589657--589993 Score: 584
Period size: 182 Copynumber: 1.9 Consensus size: 180
589647 TTAAAAAAAA
589657 TAAACCCTAAAATCCTAAACCTTAATATATAAACCTTAAACTCTTAAACCTTAAACCAAGAAACA
1 TAAACCCTAAAATCCTAAACCTTAATATATAAACCTTAAACTCTTAAACCTTAAACCAAGAAACA
*
589722 ATAAACTCTAAGACCTTAAACCATGAACCATGAATCTTAAAACCTAAACACTTAAAACCATAAAC
66 ATAAACTCTAAGACCTTAAACCATGAACCATGAAGCTTAAAACCTAAAC-CTTAAAACCATAAAC
* *
589787 CTTTGAACACTAAATTTTAACCCTAAAACTTAAAGTTTAAACCCTAATTAT
130 CTTTGAACACTAAATCTTAAACCTAAAACTTAAAGTTTAAACCCTAATTAT
* * *
589838 TAAACCCTAAAATCCTAAACCTTAATATATTGAACCTTAAGCTCTTGAACCTTAAACCAAGAAAC
1 TAAACCCTAAAATCCTAAACCTTAATATA-TAAACCTTAAACTCTTAAACCTTAAACCAAGAAAC
* *
589903 AATAAACTCTAAGACCTTAAATCATGAACCATGAAGCTTAAAACCTAAACCTTAACACCATAAAC
65 AATAAACTCTAAGACCTTAAACCATGAACCATGAAGCTTAAAACCTAAACCTTAAAACCATAAAC
589968 CTTTGAACACTAAATCTTAAACCTAA
130 CTTTGAACACTAAATCTTAAACCTAA
589994 CACCAAAATT
Statistics
Matches: 147, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
181 67 0.46
182 80 0.54
ACGTcount: A:0.46, C:0.24, G:0.04, T:0.26
Consensus pattern (180 bp):
TAAACCCTAAAATCCTAAACCTTAATATATAAACCTTAAACTCTTAAACCTTAAACCAAGAAACA
ATAAACTCTAAGACCTTAAACCATGAACCATGAAGCTTAAAACCTAAACCTTAAAACCATAAACC
TTTGAACACTAAATCTTAAACCTAAAACTTAAAGTTTAAACCCTAATTAT
Found at i:590814 original size:35 final size:35
Alignment explanation
Indices: 590741--590815 Score: 114
Period size: 35 Copynumber: 2.1 Consensus size: 35
590731 CGTCACGTCC
* **
590741 AGTAAGGCCCTGAGCACACAGCCGAGGAGCCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
590776 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
590811 AGTAA
1 AGTAA
590816 TCTTCCTCCA
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.29, G:0.29, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:590903 original size:24 final size:24
Alignment explanation
Indices: 590876--590987 Score: 82
Period size: 24 Copynumber: 4.7 Consensus size: 24
590866 TATATCAAAA
*
590876 ATCAAAACATAATTCAAGTCAAGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
590900 ATCATATCAGAATTCAGGTCATGT
1 ATCAAAACAGAATTCAAGTCAAGT
* * * *
590924 ATCATATCAGAATCCATGTCAA-T
1 ATCAAAACAGAATTCAAGTCAAGT
* * * * *
590947 ATCAGATCAGAATCCAGGTCAGGT
1 ATCAAAACAGAATTCAAGTCAAGT
*
590971 ATCATAACAGAATTCAA
1 ATCAAAACAGAATTCAA
590988 ATTTGAAATC
Statistics
Matches: 72, Mismatches: 15, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
23 20 0.28
24 52 0.72
ACGTcount: A:0.41, C:0.19, G:0.13, T:0.27
Consensus pattern (24 bp):
ATCAAAACAGAATTCAAGTCAAGT
Done.