Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008926.1 Hibiscus syriacus cultivar Beakdansim tig00112231_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: 4069050
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 20
Found at i:545056 original size:3 final size:3
Alignment explanation
Indices: 545032--545119 Score: 101
Period size: 3 Copynumber: 29.7 Consensus size: 3
545022 CTACAAAAAC
* *
545032 ATT A-T ATT A-T ATT ATT ACT ATT ATT ATT ATT ATC ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* *
545078 ATT ATT ATT ATT ATTT ATT AAT -TT ATAT ATT ATA ATT ATT AT
1 ATT ATT ATT ATT A-TT ATT ATT ATT AT-T ATT ATT ATT ATT AT
545120 ATAGGCCCCC
Statistics
Matches: 72, Mismatches: 8, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
2 5 0.07
3 61 0.85
4 6 0.08
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.61
Consensus pattern (3 bp):
ATT
Found at i:552041 original size:20 final size:20
Alignment explanation
Indices: 551992--552074 Score: 112
Period size: 20 Copynumber: 4.1 Consensus size: 20
551982 AATCAGATTG
*
551992 CCCAGGGGGTATAGATTCCCC
1 CCCAGGGGGTACAGATT-CCC
*
552013 CCCAAGGGGTACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
* *
552033 CCTAGGGGGAACAGATTCCC
1 CCCAGGGGGTACAGATTCCC
*
552053 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGTACAGATTCCC
552073 CC
1 CC
552075 TGTCTAACGG
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
20 39 0.72
21 15 0.28
ACGTcount: A:0.20, C:0.36, G:0.28, T:0.16
Consensus pattern (20 bp):
CCCAGGGGGTACAGATTCCC
Found at i:555498 original size:21 final size:20
Alignment explanation
Indices: 555455--555557 Score: 134
Period size: 20 Copynumber: 5.1 Consensus size: 20
555445 AATCAGATTG
*
555455 CCCAGGGGGTACAGATTCCC
1 CCCAGGGGGAACAGATTCCC
* *
555475 CCCACGGGAAACAGATTCCCC
1 CCCAGGGGGAACAGATT-CCC
* *
555496 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGAACAGATTCCC
555516 CCCAGGGGGAACAGATTCCC
1 CCCAGGGGGAACAGATTCCC
* *
555536 CCCAGGGGGTACCGATTCCC
1 CCCAGGGGGAACAGATTCCC
555556 CC
1 CC
555558 TGGCTAACGG
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 55 0.77
21 16 0.23
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (20 bp):
CCCAGGGGGAACAGATTCCC
Found at i:555537 original size:40 final size:41
Alignment explanation
Indices: 555455--555557 Score: 172
Period size: 41 Copynumber: 2.5 Consensus size: 41
555445 AATCAGATTG
*
555455 CCCAGGGGGTACAGATTCCCCCCACGGGAAACAGATTCCCC
1 CCCAGGGGGTACCGATTCCCCCCACGGGAAACAGATTCCCC
* *
555496 CCCAGGGGGTACCGATTCCCCCCAGGGGGAACAGATT-CCC
1 CCCAGGGGGTACCGATTCCCCCCACGGGAAACAGATTCCCC
555536 CCCAGGGGGTACCGATTCCCCC
1 CCCAGGGGGTACCGATTCCCCC
555558 TGGCTAACGG
Statistics
Matches: 59, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
40 25 0.42
41 34 0.58
ACGTcount: A:0.20, C:0.40, G:0.27, T:0.13
Consensus pattern (41 bp):
CCCAGGGGGTACCGATTCCCCCCACGGGAAACAGATTCCCC
Found at i:556939 original size:85 final size:85
Alignment explanation
Indices: 556794--557067 Score: 282
Period size: 85 Copynumber: 3.2 Consensus size: 85
556784 AGATCCTCAG
* * *
556794 TTCGA-TCACATTCAGCTCTAAGACATATCAAAATTTACAGCATAACTCAAGGCGAGAAGGGTTA
1 TTCGATTC-CATTCAGCTCAAAGGCATATC-AAATTTACAGCATAACTCAAGGCGAGAAGGGCTA
* *
556858 TCTGTTAGCAAAGACATTCGAC
64 TCTGTCAACAAAGACATTCGAC
** * *
556880 TTCGATTCCATTCAGCTCAAAGGCATATCAAATTTGTAGCATAGCTCAAGGCGATAAGGGCTATC
1 TTCGATTCCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCTATC
* * *
556945 TGTCAACAAATACCTTCGAG
66 TGTCAACAAAGACATTCGAC
* * * * * * ** * *
556965 TTTGATTTCATTCAGCTCAAGGGCATGTCAAATTTACAGCATAACTTAAGTCGAGAAAAGATATA
1 TTCGATTCCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCTATC
* *
557030 TGTCAACAGAA-ACTTTCGAG
66 TGTCAACA-AAGACATTCGAC
*
557050 TTCGATTCTATTCAGCTC
1 TTCGATTCCATTCAGCTC
557068 GATGACACAT
Statistics
Matches: 156, Mismatches: 30, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
85 128 0.82
86 26 0.17
87 2 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (85 bp):
TTCGATTCCATTCAGCTCAAAGGCATATCAAATTTACAGCATAACTCAAGGCGAGAAGGGCTATC
TGTCAACAAAGACATTCGAC
Found at i:564470 original size:26 final size:24
Alignment explanation
Indices: 564408--564470 Score: 60
Period size: 23 Copynumber: 2.6 Consensus size: 24
564398 CATTTTCATC
564408 AAAATAT-TAATTATTAAAATATTT
1 AAAATATAT-ATTATTAAAATATTT
*
564432 AAAATATAT-TTATTAATAT-TTAT
1 AAAATATATATTATTAAAATATT-T
564455 AATAATATAATATTAT
1 AA-AATAT-ATATTAT
564471 ATTTTTAATA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
22 2 0.06
23 12 0.36
24 12 0.36
25 3 0.09
26 4 0.12
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AAAATATATATTATTAAAATATTT
Found at i:564472 original size:22 final size:23
Alignment explanation
Indices: 564425--564485 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 23
564415 TAATTATTAA
* *
564425 AATATTTAAAAT-ATAT-TTATT
1 AATATTTATAATAATATAATATT
564446 AATATTTATAATAATATAATATT
1 AATATTTATAATAATATAATATT
* *
564469 -ATATTTTTAATATTATA
1 AATATTTATAATAATATA
564486 TAAAATAATC
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.32
22 19 0.56
23 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
AATATTTATAATAATATAATATT
Found at i:564492 original size:26 final size:26
Alignment explanation
Indices: 564408--564525 Score: 70
Period size: 24 Copynumber: 4.5 Consensus size: 26
564398 CATTTTCATC
* *
564408 AAAATATTA-ATTATTAA-AATATTT
1 AAAATATTATATTATTAATATTATAT
564432 AAAATA-TAT-TTATTAATATTTATAAT
1 AAAATATTATATTATTAATA-TTAT-AT
*
564458 AATATAATATTATATTTTTAATATTATAT
1 -A-A-AATATTATATTATTAATATTATAT
* *
564487 AAAATAATCA-ATTA-T-ATATAATAAT
1 AAAAT-ATTATATTATTAATATTAT-AT
564512 AAAGATATTATATT
1 AAA-ATATTATATT
564526 TTTATTTTAA
Statistics
Matches: 74, Mismatches: 7, Indels: 24
0.70 0.07 0.23
Matches are distributed among these distances:
23 9 0.12
24 13 0.18
25 12 0.16
26 12 0.16
27 5 0.07
28 2 0.03
29 6 0.08
30 7 0.09
31 8 0.11
ACGTcount: A:0.52, C:0.01, G:0.01, T:0.47
Consensus pattern (26 bp):
AAAATATTATATTATTAATATTATAT
Found at i:564845 original size:20 final size:20
Alignment explanation
Indices: 564768--564836 Score: 138
Period size: 20 Copynumber: 3.5 Consensus size: 20
564758 TTCCATATGA
564768 TTTCCAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCAT
564788 TTTCCAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCAT
564808 TTTCCAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCAT
564828 TTTCCAGAA
1 TTTCCAGAA
564837 TTCAAATTCC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (20 bp):
TTTCCAGAAATGTAATTCAT
Found at i:564845 original size:40 final size:40
Alignment explanation
Indices: 564768--564845 Score: 129
Period size: 40 Copynumber: 1.9 Consensus size: 40
564758 TTCCATATGA
**
564768 TTTCCAGAAATGTAATTCATTTTCCAGAAATGTAATTCAT
1 TTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTCAT
*
564808 TTTCCAGAAATGTAATTCATTTTCCAGAATTCAAATTC
1 TTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTC
564846 CAGTAATTCA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.35, C:0.17, G:0.09, T:0.40
Consensus pattern (40 bp):
TTTCCAGAAATGTAATTCATTTTCCAGAAATCAAATTCAT
Found at i:564855 original size:15 final size:15
Alignment explanation
Indices: 564819--564885 Score: 91
Period size: 15 Copynumber: 4.5 Consensus size: 15
564809 TTCCAGAAAT
**
564819 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
564834 G-AATTCAAATTCCA
1 GTAATTCAAATTCCA
**
564848 GTAATTCATTTTCCA
1 GTAATTCAAATTCCA
564863 GTAATTCAAATTCCA
1 GTAATTCAAATTCCA
564878 GTAATTCA
1 GTAATTCA
564886 TTTTCTGGAA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
14 12 0.27
15 33 0.73
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.39
Consensus pattern (15 bp):
GTAATTCAAATTCCA
Found at i:564861 original size:29 final size:30
Alignment explanation
Indices: 564819--564890 Score: 137
Period size: 30 Copynumber: 2.4 Consensus size: 30
564809 TTCCAGAAAT
564819 GTAATTCATTTTCCAG-AATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
564848 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
564878 GTAATTCATTTTC
1 GTAATTCATTTTC
564891 TGGAAAACCA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
29 16 0.38
30 26 0.62
ACGTcount: A:0.32, C:0.19, G:0.07, T:0.42
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:566849 original size:17 final size:17
Alignment explanation
Indices: 566824--566859 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
566814 CCTTTTTAAA
566824 ATTTAAAATTATTATAT
1 ATTTAAAATTATTATAT
* *
566841 ATTTTAAATTTTTATAT
1 ATTTAAAATTATTATAT
566858 AT
1 AT
566860 ATTTTTTATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
ATTTAAAATTATTATAT
Found at i:566936 original size:20 final size:20
Alignment explanation
Indices: 566889--566926 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
566879 TTTAACTACT
*
566889 TAAAATTTTACTTCATCCTC
1 TAAAATTTTAATTCATCCTC
566909 TAAAATTTTAATTCATCC
1 TAAAATTTTAATTCATCC
566927 ATTTAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.34, C:0.21, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAAATTTTAATTCATCCTC
Found at i:571488 original size:20 final size:20
Alignment explanation
Indices: 571463--571555 Score: 87
Period size: 21 Copynumber: 4.5 Consensus size: 20
571453 TTTTCCCAAT
*
571463 TCGCAATACGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
571483 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
571504 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* ** *
571524 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
571545 TCGCAATGCGA
1 TCGCAATGCGA
571556 TACTGACTAT
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
20 26 0.46
21 31 0.54
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:571506 original size:21 final size:21
Alignment explanation
Indices: 571480--571555 Score: 100
Period size: 21 Copynumber: 3.7 Consensus size: 21
571470 ACGAATAAGT
571480 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* ** *
571501 AAATCGCAATGCGAA-TAAGT
1 AAATCGCAACGCGAATTGGGA
571521 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
571542 AAATCGCAATGCGA
1 AAATCGCAACGCGA
571556 TACTGACTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
20 16 0.36
21 29 0.64
ACGTcount: A:0.41, C:0.18, G:0.25, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:571520 original size:41 final size:41
Alignment explanation
Indices: 571463--571555 Score: 177
Period size: 41 Copynumber: 2.3 Consensus size: 41
571453 TTTTCCCAAT
*
571463 TCGCAATACGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
571504 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
571545 TCGCAATGCGA
1 TCGCAATGCGA
571556 TACTGACTAT
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.41, C:0.18, G:0.24, T:0.17
Consensus pattern (41 bp):
TCGCAATGCGAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:571568 original size:41 final size:41
Alignment explanation
Indices: 571482--571616 Score: 132
Period size: 41 Copynumber: 3.3 Consensus size: 41
571472 GAATAAGTAA
* *
571482 ATCGCAACGCGAATTGGGAAAATCGCAATGCGAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCG-ATACTG-ACT
571523 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
571564 ATCGCAATGCGATAAT-AAAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
571605 TTCGCAACGCGA
1 ATCGCAACGCGA
571617 TACTGACTTT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
40 4 0.05
41 74 0.93
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:571569 original size:20 final size:20
Alignment explanation
Indices: 571544--571638 Score: 91
Period size: 20 Copynumber: 4.7 Consensus size: 20
571534 AATTGGGAAA
*
571544 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * * **
571564 ATCGCAATGCGATAATAAAAA
1 ATCGCAACGCGATACT-GACT
* *
571585 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATACTGACT
*
571605 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACTGACT
*
571625 TTCGCAACGCGATA
1 ATCGCAACGCGATA
571639 ATACATAATC
Statistics
Matches: 61, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 47 0.77
21 14 0.23
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:571854 original size:22 final size:22
Alignment explanation
Indices: 571826--571869 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
571816 CACTCTCTCA
571826 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
571848 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
571870 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:572171 original size:20 final size:20
Alignment explanation
Indices: 572148--572190 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
572138 GATAGTCGAA
572148 TTCGCGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
*
572168 TTCGTGTTGCGATTTTCATT
1 TTCGCGTTGCGATTTTCATT
572188 TTC
1 TTC
572191 AGAAACTATT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.09, C:0.19, G:0.19, T:0.53
Consensus pattern (20 bp):
TTCGCGTTGCGATTTTCATT
Found at i:573531 original size:18 final size:18
Alignment explanation
Indices: 573510--573554 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 18
573500 TCCACTTCGG
*
573510 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
* *
573528 GAGCTATAACCTCACCCA
1 GAGCCATCACCTCACCCA
573546 GAGCCATCA
1 GAGCCATCA
573555 TCTGATCGAC
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.29, C:0.42, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:574090 original size:19 final size:20
Alignment explanation
Indices: 574036--574102 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
574026 TAGTTTACTT
* *
574036 TCGCAACACGAAAATGACTA
1 TCGCAACGCGGAAATGACTA
*
574056 TCGCAACGCGGAAATGGCTA
1 TCGCAACGCGGAAATGACTA
* **
574076 TCGCAATGC-GAAATGAAAA
1 TCGCAACGCGGAAATGACTA
574095 TCGCAACG
1 TCGCAACG
574103 ACAAAATCGC
Statistics
Matches: 39, Mismatches: 8, Indels: 1
0.81 0.17 0.02
Matches are distributed among these distances:
19 14 0.36
20 25 0.64
ACGTcount: A:0.39, C:0.24, G:0.22, T:0.15
Consensus pattern (20 bp):
TCGCAACGCGGAAATGACTA
Found at i:574110 original size:14 final size:14
Alignment explanation
Indices: 574091--574180 Score: 90
Period size: 14 Copynumber: 5.9 Consensus size: 14
574081 ATGCGAAATG
574091 AAAATCGCAACGAC
1 AAAATCGCAACGAC
*
574105 AAAATCGCAACACGAA
1 AAAATCGC-A-ACGAC
574121 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
*
574137 AAAATCGCAACGCGAA
1 AAAATCGCAA--CGAC
574153 ATGAAATCGCAACGAC
1 A--AAATCGCAACGAC
574169 AAAATCGCAACG
1 AAAATCGCAACG
574181 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 16
0.76 0.05 0.19
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 18 0.28
17 1 0.02
18 16 0.25
ACGTcount: A:0.49, C:0.26, G:0.17, T:0.09
Consensus pattern (14 bp):
AAAATCGCAACGAC
Found at i:574133 original size:32 final size:33
Alignment explanation
Indices: 574075--574197 Score: 214
Period size: 32 Copynumber: 3.8 Consensus size: 33
574065 GGAAATGGCT
*
574075 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
*
574108 ATCGCAACACGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
574140 ATCGCAACGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGACAAA
574172 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAACGCGAAATGAAAATCGCAA
574198 TGCGATTTGT
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 63 0.73
33 23 0.27
ACGTcount: A:0.48, C:0.24, G:0.18, T:0.11
Consensus pattern (33 bp):
ATCGCAACGCGAAATGAAAATCGCAACGACAAA
Found at i:574233 original size:14 final size:14
Alignment explanation
Indices: 574214--574271 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
574204 TTGTGTTTCG
574214 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
574228 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
574244 CGCGTTGCGATTTTGT
1 --CGTTGCGATTTTGT
574260 CGTTGCGATTTT
1 CGTTGCGATTTT
574272 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 23 0.61
16 4 0.11
18 11 0.29
ACGTcount: A:0.09, C:0.17, G:0.26, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:574248 original size:32 final size:33
Alignment explanation
Indices: 574209--574287 Score: 142
Period size: 32 Copynumber: 2.4 Consensus size: 33
574199 GCGATTTGTG
574209 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
574241 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
*
574274 TTTCGCATTGCGAT
1 TTTCGCGTTGCGAT
574288 AGCCATTTCC
Statistics
Matches: 45, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
32 27 0.60
33 18 0.40
ACGTcount: A:0.10, C:0.19, G:0.24, T:0.47
Consensus pattern (33 bp):
TTTCGCGTTGCGATTTTGTCGTTGCGATTTTCA
Found at i:574286 original size:19 final size:19
Alignment explanation
Indices: 574228--574345 Score: 95
Period size: 20 Copynumber: 6.4 Consensus size: 19
574218 GCGATTTTGT
574228 CGTTGCGA-TTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
574246 CGTTGCGA-TTT--TGT--
1 CGTTGCGATTTTCATTTCG
574260 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
* ***
574279 CATTGCGATAGCCATTTCCG
1 CGTTGCGATTTTCATTT-CG
**
574299 CGTTGCGATAGTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
574318 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTCA-TTTCG
*
574338 TGTTGCGA
1 CGTTGCGA
574346 AAGTAAACTA
Statistics
Matches: 81, Mismatches: 12, Indels: 12
0.77 0.11 0.11
Matches are distributed among these distances:
14 8 0.10
15 3 0.04
16 2 0.02
17 2 0.02
18 11 0.14
19 26 0.32
20 29 0.36
ACGTcount: A:0.14, C:0.20, G:0.25, T:0.42
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:576214 original size:14 final size:14
Alignment explanation
Indices: 576195--576230 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
576185 ATTGTTTAAT
576195 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
576209 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
576223 TGATTTGT
1 TGATTTGT
576231 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:576369 original size:19 final size:19
Alignment explanation
Indices: 576347--576428 Score: 129
Period size: 19 Copynumber: 4.6 Consensus size: 19
576337 ATCGCAACGA
576347 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
576366 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
576385 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
576399 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
576418 GAAAATCGCAA
1 GAAAATCGCAA
576429 CGAGAGAATC
Statistics
Matches: 58, Mismatches: 0, Indels: 10
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.19
15 1 0.02
16 2 0.03
17 2 0.03
18 1 0.02
19 41 0.71
ACGTcount: A:0.49, C:0.17, G:0.21, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:576396 original size:52 final size:52
Alignment explanation
Indices: 576318--576430 Score: 190
Period size: 52 Copynumber: 2.2 Consensus size: 52
576308 AAAACAGACT
***
576318 ATCGCAACGCGAAATGGCTATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
*
576370 ATCGCAATGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
576422 ATCGCAACG
1 ATCGCAACG
576431 AGAGAATCGC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
52 56 1.00
ACGTcount: A:0.44, C:0.20, G:0.22, T:0.13
Consensus pattern (52 bp):
ATCGCAACGCGAAATGAAAATCGCAACGAGAAAATCGCAATGCGAAATGAAA
Found at i:576403 original size:33 final size:33
Alignment explanation
Indices: 576366--576445 Score: 151
Period size: 33 Copynumber: 2.4 Consensus size: 33
576356 AATGCGAAAT
576366 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
576399 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
1 GAAAATCGCAATGCGAAATGAAAATCGCAACGA
*
576432 GAGAATCGCAATGC
1 GAAAATCGCAATGC
576446 AATTTTCATT
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (33 bp):
GAAAATCGCAATGCGAAATGAAAATCGCAACGA
Found at i:576491 original size:20 final size:20
Alignment explanation
Indices: 576466--576523 Score: 107
Period size: 20 Copynumber: 2.9 Consensus size: 20
576456 TCGCATTGTG
*
576466 ATTTTCTCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
576486 ATTTTCGCGTTGCGATAGCC
1 ATTTTCGCGTTGCGATAGCC
576506 ATTTTCGCGTTGCGATAG
1 ATTTTCGCGTTGCGATAG
576524 TCAAATGAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 37 1.00
ACGTcount: A:0.16, C:0.22, G:0.24, T:0.38
Consensus pattern (20 bp):
ATTTTCGCGTTGCGATAGCC
Found at i:577593 original size:24 final size:24
Alignment explanation
Indices: 577566--577619 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
577556 GTATTCGAAA
* *
577566 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACACGGAC
*
577590 TTTGATATTGGTCAATACACGGAT
1 TTTGATATTGGTCAATACACGGAC
577614 TTTGAT
1 TTTGAT
577620 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.24, C:0.17, G:0.20, T:0.39
Consensus pattern (24 bp):
TTTGATATTGGTCAATACACGGAC
Found at i:577811 original size:12 final size:12
Alignment explanation
Indices: 577794--577818 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
577784 ATATAATCCT
577794 GAAGAAGAAAAA
1 GAAGAAGAAAAA
577806 GAAGAAGAAAAA
1 GAAGAAGAAAAA
577818 G
1 G
577819 TCCCCGAAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:580133 original size:19 final size:19
Alignment explanation
Indices: 580111--580208 Score: 90
Period size: 19 Copynumber: 5.7 Consensus size: 19
580101 GGAAATTACT
580111 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
580130 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
580144 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
580163 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
580177 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
580196 ATCGCAACGCGAA
1 ATCGCAATGCGAA
580209 TTTAATTTCG
Statistics
Matches: 62, Mismatches: 7, Indels: 20
0.70 0.08 0.22
Matches are distributed among these distances:
14 19 0.31
15 2 0.03
16 4 0.06
17 4 0.06
18 2 0.03
19 31 0.50
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.12
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:580153 original size:33 final size:33
Alignment explanation
Indices: 580111--580204 Score: 179
Period size: 33 Copynumber: 2.8 Consensus size: 33
580101 GGAAATTACT
580111 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
580144 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
580177 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
580205 CGAATTTAAT
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 60 1.00
ACGTcount: A:0.44, C:0.19, G:0.24, T:0.13
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:580226 original size:19 final size:20
Alignment explanation
Indices: 580204--580246 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
580194 AAATCGCAAC
580204 GCGAATTT-AATTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
* *
580223 GCGATTTTCATTTTCGCGTT
1 GCGAATTTCAATTTCGCGTT
580243 GCGA
1 GCGA
580247 TTCTCTCGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.33
20 14 0.67
ACGTcount: A:0.16, C:0.19, G:0.23, T:0.42
Consensus pattern (20 bp):
GCGAATTTCAATTTCGCGTT
Found at i:580231 original size:14 final size:14
Alignment explanation
Indices: 580232--580265 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
580222 TGCGATTTTC
580232 ATTTTCGCGTTGCG
1 ATTTTCGCGTTGCG
* *
580246 ATTCTCTCGTTGCG
1 ATTTTCGCGTTGCG
580260 ATTTTC
1 ATTTTC
580266 ATTTCGCATT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.09, C:0.24, G:0.21, T:0.47
Consensus pattern (14 bp):
ATTTTCGCGTTGCG
Found at i:580406 original size:14 final size:14
Alignment explanation
Indices: 580387--580423 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
580377 CATCAATTAA
580387 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
580401 ACAAATCACCTTTT
1 ACAAATCAACTTTT
580415 ACAAATCAA
1 ACAAATCAA
580424 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:581847 original size:21 final size:21
Alignment explanation
Indices: 581781--581847 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
581771 GTGAATCGGG
*
581781 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
581801 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
581823 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
581844 CTCT
1 CTCT
581848 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:581866 original size:42 final size:41
Alignment explanation
Indices: 581781--581903 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
581771 GTGAATCGGG
* * * * *
581781 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGATAGGGGC
581823 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGATAGGGGC
* * * * *
581865 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGATAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGATAGG
581904 CGAGTCGGGC
Statistics
Matches: 68, Mismatches: 10, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
41 4 0.06
42 58 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.18, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGATAGGGGC
Found at i:583977 original size:33 final size:33
Alignment explanation
Indices: 583920--584018 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
583910 ACGAGATAAT
**
583920 GAGAATCGCAACGCGGAAATGACTATCGCAATGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
*
583954 GAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
583987 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
584019 GCGAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
33 44 0.76
34 14 0.24
ACGTcount: A:0.39, C:0.25, G:0.23, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:584012 original size:19 final size:19
Alignment explanation
Indices: 583990--584079 Score: 135
Period size: 19 Copynumber: 4.7 Consensus size: 19
583980 GCGACCAGAC
*
583990 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAAATAAA
584009 AATCGCAACCGCGAAATAAA
1 AATCGCAA-CGCGAAATAAA
* *
584029 AATCGCAACGCTAAATGAA
1 AATCGCAACGCGAAATAAA
584048 AATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATAAA
*
584067 AATCGCAATGCGA
1 AATCGCAACGCGA
584080 TTTTTGTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 46 0.72
20 18 0.28
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (19 bp):
AATCGCAACGCGAAATAAA
Found at i:584033 original size:39 final size:38
Alignment explanation
Indices: 583990--584079 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
583980 GCGACCAGAC
583990 AATCGCAACGCGAAATGAAAATCGCAACCGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAA-CGCGAAATAAA
*
584029 AATCGCAACGCTAAATGAAAATCGCAACGCGAAATAAA
1 AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
*
584067 AATCGCAATGCGA
1 AATCGCAACGCGA
584080 TTTTTGTTTC
Statistics
Matches: 48, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
38 22 0.46
39 26 0.54
ACGTcount: A:0.48, C:0.22, G:0.18, T:0.12
Consensus pattern (38 bp):
AATCGCAACGCGAAATGAAAATCGCAACGCGAAATAAA
Found at i:584701 original size:20 final size:20
Alignment explanation
Indices: 584673--584725 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
584663 GCGCTATGTA
*
584673 AATCGCGTTGCGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
*
584693 AATCACGTTGTGAAAGTCAG
1 AATCACGTTGCGAAAGTCAG
* *
584713 TATCTCGTTGCGA
1 AATCACGTTGCGA
584726 TTTTGTATTA
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCACGTTGCGAAAGTCAG
Found at i:584759 original size:20 final size:20
Alignment explanation
Indices: 584734--584787 Score: 81
Period size: 20 Copynumber: 2.7 Consensus size: 20
584724 GATTTTGTAT
584734 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
* * *
584754 TATCGCATTGTGGTAGTCAG
1 TATCGCATTGCGATAGTAAG
584774 TATCGCATTGCGAT
1 TATCGCATTGCGAT
584788 TTTCCCAATT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:584898 original size:21 final size:21
Alignment explanation
Indices: 584858--584898 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
584848 ATTGTATACC
**
584858 ATCGCAACGCGATTTCCAACT
1 ATCGCAACGCGAAATCCAACT
*
584879 ATCGCAACGCGAAATGCAAC
1 ATCGCAACGCGAAATCCAAC
584899 GCGAATTTGC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.34, C:0.32, G:0.17, T:0.17
Consensus pattern (21 bp):
ATCGCAACGCGAAATCCAACT
Found at i:590063 original size:36 final size:36
Alignment explanation
Indices: 590022--590093 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
590012 AACAAGCGAT
590022 GGTTGTGTCGGCCATCCCTGTACAACGACAACAAAC
1 GGTTGTGTCGGCCATCCCTGTACAACGACAACAAAC
590058 GGTTGTGTCGGCCATCCCTGTACAACGACAACAAAC
1 GGTTGTGTCGGCCATCCCTGTACAACGACAACAAAC
590094 CCTCGATATT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.28, C:0.31, G:0.22, T:0.19
Consensus pattern (36 bp):
GGTTGTGTCGGCCATCCCTGTACAACGACAACAAAC
Found at i:591113 original size:29 final size:29
Alignment explanation
Indices: 591071--591129 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
591061 ATTTTCACCT
591071 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
591100 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
591129 A
1 A
591130 TTAATTTAGG
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:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:600871 original size:18 final size:18
Alignment explanation
Indices: 600848--600894 Score: 76
Period size: 18 Copynumber: 2.6 Consensus size: 18
600838 GTTAGTTTGA
600848 TTAATGAACTAACATTAT
1 TTAATGAACTAACATTAT
*
600866 TTAATGAACTAACTTTAT
1 TTAATGAACTAACATTAT
*
600884 TCAATGAACTA
1 TTAATGAACTA
600895 GATGCATGAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.43, C:0.13, G:0.06, T:0.38
Consensus pattern (18 bp):
TTAATGAACTAACATTAT
Found at i:614220 original size:21 final size:23
Alignment explanation
Indices: 614190--614241 Score: 72
Period size: 21 Copynumber: 2.3 Consensus size: 23
614180 GTACTAATAT
*
614190 TTTTTTAAAAAA-TTATATT-AA
1 TTTTTAAAAAAATTTATATTAAA
614211 TTTTTAAAAAAATTTATATTAAA
1 TTTTTAAAAAAATTTATATTAAA
*
614234 TTTATAAA
1 TTTTTAAA
614242 TAAACTTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
21 11 0.41
22 7 0.26
23 9 0.33
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
TTTTTAAAAAAATTTATATTAAA
Found at i:614221 original size:22 final size:23
Alignment explanation
Indices: 614196--614241 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
614186 ATATTTTTTT
*
614196 AAAAAATTATATT-AATTTTTAA
1 AAAAAATTATATTAAATTTATAA
*
614218 AAAAATTTATATTAAATTTATAA
1 AAAAAATTATATTAAATTTATAA
614241 A
1 A
614242 TAAACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 12 0.57
23 9 0.43
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (23 bp):
AAAAAATTATATTAAATTTATAA
Found at i:614253 original size:23 final size:22
Alignment explanation
Indices: 614196--614241 Score: 67
Period size: 23 Copynumber: 2.1 Consensus size: 22
614186 ATATTTTTTT
*
614196 AAAAAA-TTATATTAATTTTTA
1 AAAAAATTTATATTAATTTATA
614217 AAAAAATTTATATTAAATTTATA
1 AAAAAATTTATATT-AATTTATA
614240 AA
1 AA
614242 TAAACTTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 6 0.27
22 7 0.32
23 9 0.41
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
AAAAAATTTATATTAATTTATA
Found at i:614627 original size:22 final size:21
Alignment explanation
Indices: 614587--614627 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
614577 AATAAGAATA
*
614587 TTATTATGTAAATATTAGTAC
1 TTATTATGTAAATAATAGTAC
*
614608 TTATTATTTAAAATAATAGT
1 TTATTATGT-AAATAATAGT
614628 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.49
Consensus pattern (21 bp):
TTATTATGTAAATAATAGTAC
Found at i:617596 original size:26 final size:27
Alignment explanation
Indices: 617531--617583 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
617521 TAAACAAATG
**
617531 TGTAAACAAACTTTTAATTAAACTAAA
1 TGTAAACAATTTTTTAATTAAACTAAA
617558 TGTAAACAATTTTTTAATTAAACTAA
1 TGTAAACAATTTTTTAATTAAACTAA
617584 CTTTGAAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (27 bp):
TGTAAACAATTTTTTAATTAAACTAAA
Found at i:617790 original size:81 final size:82
Alignment explanation
Indices: 617681--617986 Score: 418
Period size: 82 Copynumber: 3.7 Consensus size: 82
617671 GAAATTATTG
* *
617681 CAGTTTATCTGAGTTGATGTGAAATGTCAATGAAAAGAAAAAGATGTGAATAGTATAGATTCCCT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGCAAAAGATGTGAATAGTATAGATTCCCT
*
617746 GATTCTC-AAAATATTT
66 GATTCTCTAAAACATTT
* *
617762 CAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGC-AAAGAATGTGAATAGTATAAATTCCT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGCAAAAG-ATGTGAATAGTATAGATTCCC
*
617826 TGATTTTCTAAAACATTT
65 TGATTCTCTAAAACATTT
* * * * * *
617844 CAATTTATTTGAGTTGATGTGAAATGTCAATGACAAGCAAATGATGTAAATAGTGTAGATTCCTT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGCAAAAGATGTGAATAGTATAGATTCCCT
* *
617909 GTTTCTCTAAAGCATTT
66 GATTCTCTAAAACATTT
* * * * *
617926 CGGTTTATCTGAATTGATGTGAAATGTCAATGACAAGCAAAGGATGTGAATATTGTAGATT
1 CAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGCAAAAGATGTGAATAGTATAGATT
617987 GTCTACAAGG
Statistics
Matches: 200, Mismatches: 22, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
80 4 0.02
81 62 0.31
82 131 0.65
83 3 0.01
ACGTcount: A:0.36, C:0.10, G:0.19, T:0.35
Consensus pattern (82 bp):
CAGTTTATCTGAGTTGATGTGAAATGTCAATGACAAGCAAAAGATGTGAATAGTATAGATTCCCT
GATTCTCTAAAACATTT
Found at i:621597 original size:2 final size:2
Alignment explanation
Indices: 621590--621633 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
621580 ATGATCATTA
621590 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
621632 AT
1 AT
621634 TAAAAATTCT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:621916 original size:13 final size:13
Alignment explanation
Indices: 621895--621994 Score: 81
Period size: 13 Copynumber: 8.3 Consensus size: 13
621885 ATTGAAATTA
*
621895 ATAAAAAATAAAT
1 ATAATAAATAAAT
621908 ATAATAAATAAAT
1 ATAATAAATAAAT
621921 ATAATAAATAAAT
1 ATAATAAATAAAT
*
621934 AAAAT-AAT-AAT
1 ATAATAAATAAAT
621945 -TAAT-AAT--AT
1 ATAATAAATAAAT
* *
621954 -TAATTATTAAAT
1 ATAATAAATAAAT
*
621966 ATAATAAATACAT
1 ATAATAAATAAAT
* *
621979 ATAGTAATTAAA-
1 ATAATAAATAAAT
621991 ATAA
1 ATAA
621995 ATATTTTATA
Statistics
Matches: 72, Mismatches: 11, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
9 6 0.08
10 8 0.11
11 3 0.04
12 8 0.11
13 47 0.65
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (13 bp):
ATAATAAATAAAT
Found at i:621940 original size:29 final size:30
Alignment explanation
Indices: 621889--621998 Score: 104
Period size: 28 Copynumber: 3.8 Consensus size: 30
621879 TTTCAAATTG
621889 AAAT-TAATAAA-AAATAAATATAATAAAT
1 AAATATAATAAATAAATAAATATAATAAAT
621917 AAATATAATAAATAAATAAA-ATAAT-AAT
1 AAATATAATAAATAAATAAATATAATAAAT
* * * *
621945 TAATA-ATATTAATTATTAAATATAATAAAT
1 AAATATA-ATAAATAAATAAATATAATAAAT
* * *
621975 ACATATAGTAATTAAAATAAATAT
1 AAATATAATAAAT-AAATAAATAT
621999 TTTATAAATA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
27 1 0.02
28 21 0.33
29 17 0.27
30 16 0.25
31 9 0.14
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.34
Consensus pattern (30 bp):
AAATATAATAAATAAATAAATATAATAAAT
Found at i:621957 original size:16 final size:15
Alignment explanation
Indices: 621889--621997 Score: 73
Period size: 17 Copynumber: 7.1 Consensus size: 15
621879 TTTCAAATTG
*
621889 AAATTAATAAAAAAT
1 AAATTAATAATAAAT
621904 AAA-T-ATAATAAAT
1 AAATTAATAATAAAT
621917 AAATATAATAAATAAAT
1 AAAT-TAAT-AATAAAT
* *
621934 AAAATAATAATTAAT
1 AAATTAATAATAAAT
*
621949 AATATTAATTATTAAAT
1 AA-ATTAA-TAATAAAT
* *
621966 ATAATAAATACATATAGT
1 A-AATTAATA-ATA-AAT
621984 -AATTAA-AATAAAT
1 AAATTAATAATAAAT
621997 A
1 A
621998 TTTTATAAAT
Statistics
Matches: 73, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
13 13 0.18
14 4 0.05
15 13 0.18
16 17 0.23
17 23 0.32
18 3 0.04
ACGTcount: A:0.65, C:0.01, G:0.01, T:0.33
Consensus pattern (15 bp):
AAATTAATAATAAAT
Found at i:621998 original size:45 final size:44
Alignment explanation
Indices: 621894--622009 Score: 121
Period size: 45 Copynumber: 2.6 Consensus size: 44
621884 AATTGAAATT
621894 AATAA-AAAATAAATA-TAATAAATAAATATAATAAATAAATAA
1 AATAATAAAATAAATATTAATAAATAAATATAATAAATAAATAA
* * * *
621936 AATAATAATTAAT-AATATTAATTATTAAATATAATAAATACATAT
1 AATAATAA--AATAAATATTAATAAATAAATATAATAAATAAATAA
* *
621981 AGTAATTAAAATAAATATTTTATAAATAA
1 AATAA-TAAAATAAATA-TTAATAAATAA
622010 TAATTATAAT
Statistics
Matches: 59, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
42 5 0.08
43 2 0.03
44 7 0.12
45 34 0.58
46 11 0.19
ACGTcount: A:0.64, C:0.01, G:0.01, T:0.34
Consensus pattern (44 bp):
AATAATAAAATAAATATTAATAAATAAATATAATAAATAAATAA
Found at i:622013 original size:27 final size:24
Alignment explanation
Indices: 621983--622031 Score: 62
Period size: 27 Copynumber: 1.9 Consensus size: 24
621973 ATACATATAG
621983 TAATTAAAATAAATATTTTATAAATAA
1 TAATTAAAAT--ATATTTT-TAAATAA
*
622010 TAATTATAATATATTTTTAAAT
1 TAATTAAAATATATTTTTAAAT
622032 TTTGAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 7 0.33
27 9 0.43
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (24 bp):
TAATTAAAATATATTTTTAAATAA
Found at i:622018 original size:13 final size:13
Alignment explanation
Indices: 621890--622018 Score: 54
Period size: 13 Copynumber: 9.6 Consensus size: 13
621880 TTCAAATTGA
*
621890 AATTAATAAAAAAT
1 AATT-ATAAATAAT
*
621904 AAATAT-AATAAAT
1 AATTATAAAT-AAT
*
621917 AAATAT-AATAAAT
1 AATTATAAAT-AAT
*
621930 AAATA-AAATAAT
1 AATTATAAATAAT
*
621942 AATTA-ATAATATT
1 AATTATA-AATAAT
621955 AATTATTAAAT-AT
1 AATTA-TAAATAAT
* *
621968 AATAAATACATATAGT
1 AAT-TATA-A-ATAAT
621984 AATTA-AAATAAAT
1 AATTATAAAT-AAT
*
621997 ATTTTATAAATAAT
1 A-ATTATAAATAAT
622011 AATTATAA
1 AATTATAA
622019 TATATTTTTA
Statistics
Matches: 92, Mismatches: 11, Indels: 25
0.72 0.09 0.20
Matches are distributed among these distances:
12 12 0.13
13 52 0.57
14 16 0.17
15 8 0.09
16 4 0.04
ACGTcount: A:0.63, C:0.01, G:0.01, T:0.36
Consensus pattern (13 bp):
AATTATAAATAAT
Found at i:622081 original size:21 final size:21
Alignment explanation
Indices: 622057--622097 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
622047 AATTATATGT
622057 ATAATA-TATTAAATATAATAA
1 ATAATATTA-TAAATATAATAA
*
622078 ATAATATTATAATTATAATA
1 ATAATATTATAAATATAATA
622098 TATTTTGAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATAATATTATAAATATAATAA
Found at i:622495 original size:13 final size:12
Alignment explanation
Indices: 622470--622503 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
622460 TTATTTTTAG
622470 TATTTATTTGTT
1 TATTTATTTGTT
*
622482 TATTTGTTTAGTT
1 TATTTATTT-GTT
622495 TATTTATTT
1 TATTTATTT
622504 TGGTATTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
12 8 0.42
13 11 0.58
ACGTcount: A:0.18, C:0.00, G:0.09, T:0.74
Consensus pattern (12 bp):
TATTTATTTGTT
Found at i:623752 original size:19 final size:21
Alignment explanation
Indices: 623702--623753 Score: 54
Period size: 19 Copynumber: 2.5 Consensus size: 21
623692 ATCTTAACAA
*
623702 CTCATCAACAACTTGACAGTAG
1 CTCAGCAACAACTTGACA-TAG
* *
623724 CTTAGTAACAACTTG-C-TAG
1 CTCAGCAACAACTTGACATAG
623743 CTCAGCAACAA
1 CTCAGCAACAA
623754 TGTAACCCCC
Statistics
Matches: 25, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 12 0.48
21 1 0.04
22 12 0.48
ACGTcount: A:0.37, C:0.27, G:0.13, T:0.23
Consensus pattern (21 bp):
CTCAGCAACAACTTGACATAG
Found at i:624513 original size:16 final size:17
Alignment explanation
Indices: 624492--624524 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
624482 TAAAATCTAA
624492 AATATATTA-TAATTAT
1 AATATATTATTAATTAT
624508 AATATATTATTAATTAT
1 AATATATTATTAATTAT
624525 TTATTATATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (17 bp):
AATATATTATTAATTAT
Found at i:624601 original size:13 final size:13
Alignment explanation
Indices: 624585--624701 Score: 52
Period size: 13 Copynumber: 9.0 Consensus size: 13
624575 ACAAAATATA
624585 TTATAATTATTAT
1 TTATAATTATTAT
* *
624598 TTATAAAATATCTAG
1 TTAT-AATTAT-TAT
624613 TT-TAATTACTATAT
1 TTATAATTA-T-TAT
624627 TTAT--TTATTA-
1 TTATAATTATTAT
*
624637 TTATATTTTAATTAT
1 TTATA-ATT-ATTAT
624652 TT-T-ATTA-TAT
1 TTATAATTATTAT
*
624662 TTAATAATTAATA-
1 TT-ATAATTATTAT
624675 TTATTAATTATTAT
1 TTA-TAATTATTAT
* *
624689 TTTTATTTATTAT
1 TTATAATTATTAT
624702 ATTTATTTGT
Statistics
Matches: 80, Mismatches: 9, Indels: 30
0.67 0.08 0.25
Matches are distributed among these distances:
10 9 0.11
11 3 0.04
12 5 0.06
13 36 0.45
14 20 0.25
15 7 0.09
ACGTcount: A:0.37, C:0.02, G:0.01, T:0.61
Consensus pattern (13 bp):
TTATAATTATTAT
Found at i:624641 original size:16 final size:16
Alignment explanation
Indices: 624617--624720 Score: 69
Period size: 16 Copynumber: 6.8 Consensus size: 16
624607 ATCTAGTTTA
*
624617 ATTACTATATTTATTT
1 ATTATTATATTTATTT
*
624633 ATTATTATATTTTAATT
1 ATTATTATA-TTTATTT
*
624650 ATT-TTAT-TATATTT
1 ATTATTATATTTATTT
* *
624664 AATAATTA-ATATTATTA
1 -ATTATTATAT-TTATTT
*
624681 ATTATTAT-TTT-TAT
1 ATTATTATATTTATTT
624695 -TTATTATATTTATTT
1 ATTATTATATTTATTT
*
624710 GTTATTA-ATTT
1 ATTATTATATTT
624721 CAATTTGAAA
Statistics
Matches: 68, Mismatches: 11, Indels: 19
0.69 0.11 0.19
Matches are distributed among these distances:
13 7 0.10
14 9 0.13
15 10 0.15
16 29 0.43
17 13 0.19
ACGTcount: A:0.34, C:0.01, G:0.01, T:0.64
Consensus pattern (16 bp):
ATTATTATATTTATTT
Found at i:624656 original size:19 final size:19
Alignment explanation
Indices: 624634--624705 Score: 65
Period size: 19 Copynumber: 3.6 Consensus size: 19
624624 TATTTATTTA
624634 TTATTATATTTTAATTATT
1 TTATTATATTTTAATTATT
*
624653 TTATTATATTTAATAATTAATA
1 TTATTATATTT--TAATT-ATT
* *
624675 TTATTA-ATTATTATTTTTAT
1 TTATTATATT-TTAATTAT-T
624695 TTATTATATTT
1 TTATTATATTT
624706 ATTTGTTATT
Statistics
Matches: 43, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
19 12 0.28
20 11 0.26
21 11 0.26
22 9 0.21
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (19 bp):
TTATTATATTTTAATTATT
Found at i:624706 original size:13 final size:13
Alignment explanation
Indices: 624622--624714 Score: 61
Period size: 13 Copynumber: 7.2 Consensus size: 13
624612 GTTTAATTAC
624622 TATATTTATTTAT
1 TATATTTATTTAT
*
624635 TAT-TATA-TT-T
1 TATATTTATTTAT
624645 TA-A-TTATTTTAT
1 TATATTTA-TTTAT
* *
624657 TATATTTAATAAT
1 TATATTTATTTAT
*
624670 TAATATTATTAATTAT
1 T-ATA-T-TTATTTAT
*
624686 TATTTTTATTTAT
1 TATATTTATTTAT
*
624699 TATATTTATTTGT
1 TATATTTATTTAT
624712 TAT
1 TAT
624715 TAATTTCAAT
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
9 2 0.03
10 3 0.05
11 4 0.06
12 6 0.10
13 29 0.47
14 7 0.11
15 3 0.05
16 8 0.13
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (13 bp):
TATATTTATTTAT
Found at i:626220 original size:21 final size:21
Alignment explanation
Indices: 626158--626220 Score: 108
Period size: 21 Copynumber: 3.0 Consensus size: 21
626148 AGATTAGAGC
* *
626158 CTCTCTAAATATAATAAAAAC
1 CTCTCTAAGTATAATAAAAAG
626179 CTCTCTAAGTATAATAAAAAG
1 CTCTCTAAGTATAATAAAAAG
626200 CTCTCTAAGTATAATAAAAAG
1 CTCTCTAAGTATAATAAAAAG
626221 AATGTCCTGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.49, C:0.16, G:0.06, T:0.29
Consensus pattern (21 bp):
CTCTCTAAGTATAATAAAAAG
Found at i:627832 original size:23 final size:23
Alignment explanation
Indices: 627806--627855 Score: 82
Period size: 23 Copynumber: 2.2 Consensus size: 23
627796 ATTCGGTAAT
**
627806 GAAAAGAAATTGAAAAGGGTAGA
1 GAAAAGAAATTGAAAAACGTAGA
627829 GAAAAGAAATTGAAAAACGTAGA
1 GAAAAGAAATTGAAAAACGTAGA
627852 GAAA
1 GAAA
627856 TGGAGAACTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.60, C:0.02, G:0.26, T:0.12
Consensus pattern (23 bp):
GAAAAGAAATTGAAAAACGTAGA
Found at i:629263 original size:50 final size:50
Alignment explanation
Indices: 629183--629357 Score: 273
Period size: 50 Copynumber: 3.5 Consensus size: 50
629173 CAATTAGAAA
629183 AATTGATATA-ATT-ATTAAATATTTACGTGATAATTAACAAAGTTTATAT
1 AATT-ATATATATTGATTAAATATTTACGTGATAATTAACAAAGTTTATAT
* *
629232 AATTACATATATTGATTATATATTTACGTGATAATTAACAAAGTTTATAT
1 AATTATATATATTGATTAAATATTTACGTGATAATTAACAAAGTTTATAT
* * * *
629282 AATTATATATATTGGTTAAATATTTACATGATAATTAACAAAATTGATAT
1 AATTATATATATTGATTAAATATTTACGTGATAATTAACAAAGTTTATAT
629332 AATTATATATATTGATTAAATATTTA
1 AATTATATATATTGATTAAATATTTA
629358 GCTACTTTGA
Statistics
Matches: 115, Mismatches: 9, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
48 4 0.03
49 7 0.06
50 104 0.90
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (50 bp):
AATTATATATATTGATTAAATATTTACGTGATAATTAACAAAGTTTATAT
Found at i:630150 original size:36 final size:39
Alignment explanation
Indices: 630077--630154 Score: 126
Period size: 39 Copynumber: 2.1 Consensus size: 39
630067 TATATTAAGC
*
630077 ATTTATATGCATTTATCTCTTATTTGTTTCTTTTTGTTG
1 ATTTATATGCATATATCTCTTATTTGTTTCTTTTTGTTG
630116 ATTTATATGCATATATCT-TT-TTT-TTTCTTTTTGTTG
1 ATTTATATGCATATATCTCTTATTTGTTTCTTTTTGTTG
630152 ATT
1 ATT
630155 ATTATATTGT
Statistics
Matches: 38, Mismatches: 1, Indels: 3
0.90 0.02 0.07
Matches are distributed among these distances:
36 16 0.42
37 3 0.08
38 2 0.05
39 17 0.45
ACGTcount: A:0.17, C:0.09, G:0.09, T:0.65
Consensus pattern (39 bp):
ATTTATATGCATATATCTCTTATTTGTTTCTTTTTGTTG
Found at i:632464 original size:19 final size:20
Alignment explanation
Indices: 632426--632477 Score: 79
Period size: 19 Copynumber: 2.6 Consensus size: 20
632416 GAAACCCCTT
632426 TGAAAATACATGATTTTTTAA
1 TGAAAATACATGA-TTTTTAA
632447 TGAAAATACATG-TTTTTAA
1 TGAAAATACATGATTTTTAA
*
632466 TGAAGATACATG
1 TGAAAATACATG
632478 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 18 0.60
21 12 0.40
ACGTcount: A:0.42, C:0.06, G:0.13, T:0.38
Consensus pattern (20 bp):
TGAAAATACATGATTTTTAA
Found at i:636242 original size:35 final size:36
Alignment explanation
Indices: 636196--636298 Score: 117
Period size: 35 Copynumber: 3.0 Consensus size: 36
636186 TAATCTGTTT
*
636196 CTGATAACTGTAAAAT-ATATGATATATGTAAATAC
1 CTGATAACTGTAAAATCATCTGATATATGTAAATAC
* *
636231 CTGATAACTGT--AATCATCTGATATCTGTAAATAT
1 CTGATAACTGTAAAATCATCTGATATATGTAAATAC
* *
636265 CTTATAACT-AAAAATCATCTGATA-AGTGTAAATA
1 CTGATAACTGTAAAATCATCTGATATA-TGTAAATA
636299 TTTAGAATTC
Statistics
Matches: 58, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
33 3 0.05
34 24 0.41
35 31 0.53
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (36 bp):
CTGATAACTGTAAAATCATCTGATATATGTAAATAC
Found at i:636266 original size:17 final size:17
Alignment explanation
Indices: 636195--636299 Score: 97
Period size: 17 Copynumber: 6.1 Consensus size: 17
636185 TTAATCTGTT
636195 TCTGATAACTGTAAAATA
1 TCTGATAACTGT-AAATA
*
636213 TATGATATA-TGTAAATA
1 TCTGATA-ACTGTAAATA
*
636230 CCTGATAACTGT-AATCA
1 TCTGATAACTGTAAAT-A
*
636247 TCTGATATCTGTAAATA
1 TCTGATAACTGTAAATA
* **
636264 TCTTATAACTAAAAATCA
1 TCTGATAACTGTAAAT-A
*
636282 TCTGATAAGTGTAAATA
1 TCTGATAACTGTAAATA
636299 T
1 T
636300 TTAGAATTCA
Statistics
Matches: 69, Mismatches: 13, Indels: 11
0.74 0.14 0.12
Matches are distributed among these distances:
16 4 0.06
17 39 0.57
18 25 0.36
19 1 0.01
ACGTcount: A:0.42, C:0.11, G:0.10, T:0.36
Consensus pattern (17 bp):
TCTGATAACTGTAAATA
Found at i:640336 original size:21 final size:21
Alignment explanation
Indices: 640296--640336 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
640286 TAGTGATGTC
*
640296 ACAACAGCAATAATATCAACT
1 ACAACAGCAATAATAACAACT
640317 ACAACAGCAACT-ATAACAAC
1 ACAACAGCAA-TAATAACAAC
640337 AATCGCAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 17 0.94
22 1 0.06
ACGTcount: A:0.54, C:0.27, G:0.05, T:0.15
Consensus pattern (21 bp):
ACAACAGCAATAATAACAACT
Found at i:641214 original size:14 final size:14
Alignment explanation
Indices: 641191--641226 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
641181 AATACTCATT
641191 TTTC-TCTCATTTC
1 TTTCTTCTCATTTC
641204 TTTCTTCTCATTTC
1 TTTCTTCTCATTTC
641218 TTCTCTTCT
1 TT-TCTTCT
641227 TATTATCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
13 4 0.19
14 11 0.52
15 6 0.29
ACGTcount: A:0.06, C:0.31, G:0.00, T:0.64
Consensus pattern (14 bp):
TTTCTTCTCATTTC
Found at i:643680 original size:12 final size:12
Alignment explanation
Indices: 643663--643692 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
643653 AAGCTTGGTT
643663 TGCTAGTATTCG
1 TGCTAGTATTCG
643675 TGCTAGTATTCG
1 TGCTAGTATTCG
643687 TGCTAG
1 TGCTAG
643693 CTGAAGAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.17, G:0.27, T:0.40
Consensus pattern (12 bp):
TGCTAGTATTCG
Found at i:647460 original size:37 final size:37
Alignment explanation
Indices: 647401--647507 Score: 124
Period size: 37 Copynumber: 2.9 Consensus size: 37
647391 CACCTTTTCG
* *
647401 TTCTATTAAGATTCAAACTCCTAAAAATAGGATAAAA
1 TTCTACTAGGATTCAAACTCCTAAAAATAGGATAAAA
* * * *
647438 TTTTGCTAGGATTCAAACTCCTAAAAATAGGATAGAG
1 TTCTACTAGGATTCAAACTCCTAAAAATAGGATAAAA
** * *
647475 TTCTACTATTATTTAAACTCCTAAAGATAGGAT
1 TTCTACTAGGATTCAAACTCCTAAAAATAGGAT
647508 CCACAAGCAT
Statistics
Matches: 58, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.41, C:0.14, G:0.12, T:0.33
Consensus pattern (37 bp):
TTCTACTAGGATTCAAACTCCTAAAAATAGGATAAAA
Found at i:647947 original size:18 final size:19
Alignment explanation
Indices: 647903--647970 Score: 57
Period size: 21 Copynumber: 3.3 Consensus size: 19
647893 TTAACCCTTA
*
647903 TTATTTATATGTATATATGTAT
1 TTATTTATAT-TATAT-T-TTT
*
647925 ATATTTA-ATTATATTTTT
1 TTATTTATATTATATTTTT
647943 TTATTTATTTATTATATTTTT
1 TTATTTA--TATTATATTTTT
647964 TTCATTT
1 TT-ATTT
647971 TTCTTTGCGT
Statistics
Matches: 39, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
18 8 0.21
19 1 0.03
20 5 0.13
21 15 0.38
22 10 0.26
ACGTcount: A:0.28, C:0.01, G:0.03, T:0.68
Consensus pattern (19 bp):
TTATTTATATTATATTTTT
Found at i:647958 original size:21 final size:23
Alignment explanation
Indices: 647926--647970 Score: 76
Period size: 21 Copynumber: 2.0 Consensus size: 23
647916 TATATGTATA
647926 TATTTAATTATATTTTTTT-ATT
1 TATTTAATTATATTTTTTTCATT
647948 TATTT-ATTATATTTTTTTCATT
1 TATTTAATTATATTTTTTTCATT
647970 T
1 T
647971 TTCTTTGCGT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.59
22 9 0.41
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (23 bp):
TATTTAATTATATTTTTTTCATT
Found at i:648388 original size:20 final size:19
Alignment explanation
Indices: 648361--648416 Score: 62
Period size: 19 Copynumber: 2.9 Consensus size: 19
648351 TTTTATCTTC
648361 ATTTATTTTATTTTATTCA
1 ATTTATTTTATTTTATTCA
*
648380 ATTTCATTTT-TTTTCATCCA
1 ATTT-ATTTTATTTT-ATTCA
648400 A-TTATTTTATGTTTATT
1 ATTTATTTTAT-TTTATT
648417 ATTATTGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
18 5 0.16
19 13 0.42
20 13 0.42
ACGTcount: A:0.23, C:0.09, G:0.02, T:0.66
Consensus pattern (19 bp):
ATTTATTTTATTTTATTCA
Found at i:652723 original size:16 final size:15
Alignment explanation
Indices: 652702--652754 Score: 74
Period size: 16 Copynumber: 3.5 Consensus size: 15
652692 AAAGGGCAAA
652702 AACAAAAAAGAAAAG
1 AACAAAAAAGAAAAG
652717 AAGCAAAAAAGAAGAA-
1 AA-CAAAAAAGAA-AAG
652733 AACAAAAAAG-AAAG
1 AACAAAAAAGAAAAG
652747 AACAAAAA
1 AACAAAAA
652755 TCAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
13 2 0.06
14 9 0.26
15 10 0.29
16 12 0.34
17 2 0.06
ACGTcount: A:0.79, C:0.08, G:0.13, T:0.00
Consensus pattern (15 bp):
AACAAAAAAGAAAAG
Found at i:654667 original size:106 final size:106
Alignment explanation
Indices: 654150--654673 Score: 694
Period size: 106 Copynumber: 4.9 Consensus size: 106
654140 GAGAGTGGAT
* * * * * *
654150 TTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAACTTCCCAAATTCAGAGCCAATGT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCAATTT
** *
654215 CAACTTCACTGCGAAGGATATTGGACTCCAGACAACGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
* *
654256 TTCAACTTCACGACAAAGGGACCGCTGGTTGTCAACAAACAACTT-CTCAATTTCAGAGCCAATT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCT-AATTTCAGAGCCAATT
*
654320 TCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAG
65 TCAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
* * * *
654362 TTCAACTTCACGACAAAGGGACCGTTGGTTGTCAACAAACAACTTCCTTATTTCAGAGCCAATTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCAATTT
* *
654427 AAACTTCACAACGAAGGATATTGGACTCGAGACAATGCAAG
66 CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
* * * *
654468 TTCAACTTCACGATGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCATTTT
1 TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCAATTT
** * * *
654533 CAAAGTCACAACAAAGGATATTAGACTCGAGACAACACAAG
66 CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
* * * *
654574 TTCAACTTCA-GAACGAAGGGACGGTTGGTTGTCAACAAATAATTTCCTGA-TTCTAGAGCCAAT
1 TTCAACTTCACG-ACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTTC-AGAGCCAAT
* * *
654637 TTCAACTTCACGACGGAGGATATTGGACTCGAAACAA
64 TTCAACTTCACAACGAAGGATATTGGACTCGAGACAA
654674 TGCTACTTAC
Statistics
Matches: 371, Mismatches: 43, Indels: 8
0.88 0.10 0.02
Matches are distributed among these distances:
105 5 0.01
106 364 0.98
107 2 0.01
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.23
Consensus pattern (106 bp):
TTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCTAATTTCAGAGCCAATTT
CAACTTCACAACGAAGGATATTGGACTCGAGACAACGCAAG
Found at i:655506 original size:37 final size:37
Alignment explanation
Indices: 655417--655520 Score: 131
Period size: 37 Copynumber: 2.8 Consensus size: 37
655407 CTTTTCGTCC
655417 TACT-AGGATTCAAACTCCTAAAAATAGGATAGAATT
1 TACTAAGGATTCAAACTCCTAAAAATAGGATAGAATT
**
655453 TTGTAAGGATTCAAACTCCTAAAAATAGGATAGAATT
1 TACTAAGGATTCAAACTCCTAAAAATAGGATAGAATT
** * *
655490 CTACT-ATTATTTAAACTCCTAAAGATAGGAT
1 -TACTAAGGATTCAAACTCCTAAAAATAGGAT
655521 CCACAAACAT
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
36 2 0.03
37 54 0.93
38 2 0.03
ACGTcount: A:0.42, C:0.13, G:0.13, T:0.31
Consensus pattern (37 bp):
TACTAAGGATTCAAACTCCTAAAAATAGGATAGAATT
Found at i:656071 original size:13 final size:13
Alignment explanation
Indices: 656053--656078 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
656043 TGTTTACTTA
656053 TTTACTATATTTT
1 TTTACTATATTTT
656066 TTTACTATATTTT
1 TTTACTATATTTT
656079 CCTAACATTA
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:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTACTATATTTT
Found at i:656178 original size:29 final size:28
Alignment explanation
Indices: 656146--656221 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 28
656136 TGATTACTAT
*
656146 TTTTTTAGTTAATATTATATGTATATTTA-
1 TTTTTTA-TTAATATTATAT-TAAATTTAG
* *
656175 TTTTTCATTTATTATTATTATTAAATTTAG
1 TTTTTTA-TTAATATTA-TATTAAATTTAG
*
656205 TATTTTATT-ATATTATA
1 TTTTTTATTAATATTATA
656222 CATACATTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
27 2 0.05
28 5 0.13
29 23 0.61
30 8 0.21
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (28 bp):
TTTTTTATTAATATTATATTAAATTTAG
Found at i:656242 original size:9 final size:9
Alignment explanation
Indices: 656228--656281 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 9
656218 TATACATACA
656228 TTTTTATAT
1 TTTTTATAT
656237 TTTTTATTAT
1 TTTTTA-TAT
656247 TTTTTATAT
1 TTTTTATAT
*
656256 TATTTATTTAT
1 T-TTT-TATAT
656267 TTTCATTATAT
1 TTT--TTATAT
656278 TTTT
1 TTTT
656282 AGTTTCTTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
9 11 0.29
10 14 0.37
11 12 0.32
12 1 0.03
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTTTATAT
Found at i:656250 original size:19 final size:20
Alignment explanation
Indices: 656228--656281 Score: 74
Period size: 19 Copynumber: 2.6 Consensus size: 20
656218 TATACATACA
656228 TTTTTATATTTTTTA-TTAT
1 TTTTTATATTTTTTATTTAT
*
656247 TTTTTATATTATTTATTTAT
1 TTTTTATATTTTTTATTTAT
656267 TTTCATTATATTTTT
1 TTT--TTATATTTTT
656282 AGTTTCTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
19 14 0.47
20 7 0.23
22 9 0.30
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (20 bp):
TTTTTATATTTTTTATTTAT
Found at i:656503 original size:18 final size:18
Alignment explanation
Indices: 656468--656506 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
656458 GTTTTGTTAC
*
656468 TTTCTTTTATATTATTAT
1 TTTCTTTTAAATTATTAT
656486 TTTCTTTTAAAATT-TTAT
1 TTTCTTTT-AAATTATTAT
656504 TTT
1 TTT
656507 TTAAGGATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.23, C:0.05, G:0.00, T:0.72
Consensus pattern (18 bp):
TTTCTTTTAAATTATTAT
Found at i:665158 original size:14 final size:14
Alignment explanation
Indices: 665141--665167 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
665131 GGGTTAAAGA
665141 TTTAGAGTTTATGG
1 TTTAGAGTTTATGG
665155 TTTAGAGTTTATG
1 TTTAGAGTTTATG
665168 AGATTATGGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTAGAGTTTATGG
Found at i:665180 original size:21 final size:20
Alignment explanation
Indices: 665141--665185 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
665131 GGGTTAAAGA
*
665141 TTTAGAGTTTATGGTTTAGAG
1 TTTAGAGATTATGG-TTAGAG
*
665162 TTTATGAGATTATGGTTAGGG
1 TTTA-GAGATTATGGTTAGAG
665183 TTT
1 TTT
665186 GAGGTTTATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.22, C:0.00, G:0.29, T:0.49
Consensus pattern (20 bp):
TTTAGAGATTATGGTTAGAG
Found at i:668121 original size:19 final size:19
Alignment explanation
Indices: 668097--668133 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
668087 AGGCACGTGA
668097 TGGTGGTAGCA-GGCATGGT
1 TGGTGGT-GCAGGGCATGGT
668116 TGGTGGTGCAGGGCATGG
1 TGGTGGTGCAGGGCATGG
668134 GCACTCGGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 3 0.18
19 14 0.82
ACGTcount: A:0.14, C:0.11, G:0.51, T:0.24
Consensus pattern (19 bp):
TGGTGGTGCAGGGCATGGT
Found at i:672904 original size:19 final size:20
Alignment explanation
Indices: 672864--672904 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
672854 TGTCTAATTG
*
672864 ATCAAATTAAAACATCAATA
1 ATCAAAATAAAACATCAATA
*
672884 ATCAAAATAAAA-ATGAATA
1 ATCAAAATAAAACATCAATA
672903 AT
1 AT
672905 AGTTTAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 8 0.42
20 11 0.58
ACGTcount: A:0.63, C:0.10, G:0.02, T:0.24
Consensus pattern (20 bp):
ATCAAAATAAAACATCAATA
Found at i:673035 original size:20 final size:20
Alignment explanation
Indices: 673012--673082 Score: 124
Period size: 20 Copynumber: 3.5 Consensus size: 20
673002 TACAGAATGT
*
673012 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGAGAATAA
673032 AAGATTACCAGTGAGAATAA
1 AAGATTACCAGTGAGAATAA
*
673052 AAGATTACCAGTGCGAATAA
1 AAGATTACCAGTGAGAATAA
673072 AAGATTACCAG
1 AAGATTACCAG
673083 GGAATAGGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 49 1.00
ACGTcount: A:0.46, C:0.13, G:0.21, T:0.20
Consensus pattern (20 bp):
AAGATTACCAGTGAGAATAA
Found at i:673254 original size:15 final size:15
Alignment explanation
Indices: 673236--673266 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
673226 AAATTCTAAA
673236 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
673251 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
673266 T
1 T
673267 CTATCTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:675201 original size:20 final size:20
Alignment explanation
Indices: 675176--675229 Score: 108
Period size: 20 Copynumber: 2.7 Consensus size: 20
675166 GGAGCGTGGG
675176 GGGAATCGGTTCCCCTCATA
1 GGGAATCGGTTCCCCTCATA
675196 GGGAATCGGTTCCCCTCATA
1 GGGAATCGGTTCCCCTCATA
675216 GGGAATCGGTTCCC
1 GGGAATCGGTTCCC
675230 TAAGTGTAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.19, C:0.30, G:0.28, T:0.24
Consensus pattern (20 bp):
GGGAATCGGTTCCCCTCATA
Found at i:676020 original size:118 final size:118
Alignment explanation
Indices: 675870--676086 Score: 380
Period size: 118 Copynumber: 1.8 Consensus size: 118
675860 ATTATGTGGA
*
675870 TCAACAAATTTCAACAAAAACAACGAATTCCCTTTCAAAATAATACTCGCATGGAATTATGAAAA
1 TCAACAAATTTCAACAAAAACAACGAATTCCCTTTCAAAATAATACTCGCATGGAACTATGAAAA
* * *
675935 TTCTATCACAAATCCAGGAAAATAAGTGAAAATTTTACCTTCTGGATGAAATT
66 CTCTATCACAAATCCAGAAAAAGAAGTGAAAATTTTACCTTCTGGATGAAATT
*
675988 TCAATAAATTTCAACAAAAACAACGAATTCCCTTTCAAAATAATACTCGCATGGAACTATGAAAA
1 TCAACAAATTTCAACAAAAACAACGAATTCCCTTTCAAAATAATACTCGCATGGAACTATGAAAA
*
676053 CTCTATCACAAATCTAGAAAAAGAAGTGAAAATT
66 CTCTATCACAAATCCAGAAAAAGAAGTGAAAATT
676087 CTATCACAAA
Statistics
Matches: 93, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
118 93 1.00
ACGTcount: A:0.46, C:0.18, G:0.10, T:0.26
Consensus pattern (118 bp):
TCAACAAATTTCAACAAAAACAACGAATTCCCTTTCAAAATAATACTCGCATGGAACTATGAAAA
CTCTATCACAAATCCAGAAAAAGAAGTGAAAATTTTACCTTCTGGATGAAATT
Found at i:680105 original size:27 final size:28
Alignment explanation
Indices: 680067--680128 Score: 99
Period size: 27 Copynumber: 2.2 Consensus size: 28
680057 TGAAAGCTTA
680067 AGGAGAAGATGTGGCCGTTGTAGCAT-T
1 AGGAGAAGATGTGGCCGTTGTAGCATGT
*
680094 AGGAGAAGATGTGGTCGTTGTAGCATGT
1 AGGAGAAGATGTGGCCGTTGTAGCATGT
*
680122 TGGAGAA
1 AGGAGAA
680129 ATTTCTACTA
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
27 25 0.78
28 7 0.22
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.26
Consensus pattern (28 bp):
AGGAGAAGATGTGGCCGTTGTAGCATGT
Found at i:701204 original size:62 final size:62
Alignment explanation
Indices: 701107--701235 Score: 258
Period size: 62 Copynumber: 2.1 Consensus size: 62
701097 AAAGGCATAA
701107 GTACCATACAAGCAAATAAAGGTTTTCTCCACTTGCTCTTCTAGTGCTATGGCAATCTGATT
1 GTACCATACAAGCAAATAAAGGTTTTCTCCACTTGCTCTTCTAGTGCTATGGCAATCTGATT
701169 GTACCATACAAGCAAATAAAGGTTTTCTCCACTTGCTCTTCTAGTGCTATGGCAATCTGATT
1 GTACCATACAAGCAAATAAAGGTTTTCTCCACTTGCTCTTCTAGTGCTATGGCAATCTGATT
701231 GTACC
1 GTACC
701236 CTTATCAAGG
Statistics
Matches: 67, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
62 67 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (62 bp):
GTACCATACAAGCAAATAAAGGTTTTCTCCACTTGCTCTTCTAGTGCTATGGCAATCTGATT
Found at i:717116 original size:29 final size:31
Alignment explanation
Indices: 717054--717123 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
717044 TTATTTTAAC
717054 TTAAAAATATATTTTATTCTTTTCTTAAATT
1 TTAAAAATATATTTTATTCTTTTCTTAAATT
* *
717085 TTAAAGATATATTTTATT-TTTATCTT-TA-T
1 TTAAAAATATATTTTATTCTTT-TCTTAAATT
717114 TTAAAAATAT
1 TTAAAAATAT
717124 TTAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.29
30 4 0.11
31 21 0.60
ACGTcount: A:0.37, C:0.04, G:0.01, T:0.57
Consensus pattern (31 bp):
TTAAAAATATATTTTATTCTTTTCTTAAATT
Found at i:717165 original size:30 final size:30
Alignment explanation
Indices: 717131--717196 Score: 98
Period size: 30 Copynumber: 2.2 Consensus size: 30
717121 TATTTAAAAT
* *
717131 ATATATTTTATTTTTA-TATTAATTTATTAA
1 ATATATTTTATTCTTACT-TTAACTTATTAA
717161 ATATATTTTATTCTTACTTTAACTTATTAA
1 ATATATTTTATTCTTACTTTAACTTATTAA
717191 ATATAT
1 ATATAT
717197 ATTAAAAATA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
30 32 0.97
31 1 0.03
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (30 bp):
ATATATTTTATTCTTACTTTAACTTATTAA
Found at i:717244 original size:26 final size:25
Alignment explanation
Indices: 717210--717261 Score: 68
Period size: 26 Copynumber: 2.0 Consensus size: 25
717200 AAAAATATTT
717210 TTAAATTAAGGTAAAAATAATATATA
1 TTAAATTAAGGTAAAAATAA-ATATA
* * *
717236 TTAAGTTAAGTTAAGAATAAATATA
1 TTAAATTAAGGTAAAAATAAATATA
717261 T
1 T
717262 GTTTTTAAGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 6 0.26
26 17 0.74
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.37
Consensus pattern (25 bp):
TTAAATTAAGGTAAAAATAAATATA
Found at i:717270 original size:30 final size:30
Alignment explanation
Indices: 717236--717343 Score: 107
Period size: 30 Copynumber: 3.7 Consensus size: 30
717226 ATAATATATA
*
717236 TTAAGTTAAGTTAAGAATAAATATATGTTT
1 TTAAGTTAAGATAAGAATAAATATATGTTT
* * *
717266 TTAAGTTAAAATAACAACAAAATATATGTTT
1 TTAAGTTAAGATAAGAA-TAAATATATGTTT
* *
717297 TTAAG-TAAGGTAAGAATAAA-GTAT-TTT
1 TTAAGTTAAGATAAGAATAAATATATGTTT
* *
717324 TTAATTTAAAATAAG-ATAAA
1 TTAAGTTAAGATAAGAATAAA
717344 AAAAATCTAA
Statistics
Matches: 64, Mismatches: 12, Indels: 7
0.77 0.14 0.08
Matches are distributed among these distances:
27 12 0.19
28 10 0.16
29 3 0.05
30 22 0.34
31 17 0.27
ACGTcount: A:0.49, C:0.02, G:0.11, T:0.38
Consensus pattern (30 bp):
TTAAGTTAAGATAAGAATAAATATATGTTT
Found at i:717457 original size:85 final size:85
Alignment explanation
Indices: 717352--717511 Score: 209
Period size: 85 Copynumber: 1.9 Consensus size: 85
717342 AAAAAAATCT
* * *
717352 AAGTTAATATAATAAAAAAATATTTAATAATTTAA-AG-TAATAACATAATATATTTAATAAATT
1 AAGTTAAAATAATAAAAAAATA--TAA-AATTTAATAGTTAAGAACAAAATATATTTAATAAATT
717415 -AAGATAAAATATATACTTTCAA
63 AAAGATAAAATATATACTTTCAA
* * *
717437 AAGTTAAAATAATAATAAAATATAAAATTTAATTAGTTAAGAATAAAATATATTTAATAAGTTAA
1 AAGTTAAAATAATAAAAAAATATAAAATTTAA-TAGTTAAGAACAAAATATATTTAATAAATTAA
717502 AGATAAAATA
65 AGATAAAATA
717512 AAATATTTTT
Statistics
Matches: 65, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
82 7 0.11
83 3 0.05
84 2 0.03
85 42 0.65
86 11 0.17
ACGTcount: A:0.58, C:0.02, G:0.05, T:0.35
Consensus pattern (85 bp):
AAGTTAAAATAATAAAAAAATATAAAATTTAATAGTTAAGAACAAAATATATTTAATAAATTAAA
GATAAAATATATACTTTCAA
Found at i:717491 original size:25 final size:25
Alignment explanation
Indices: 717463--717511 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
717453 AAAATATAAA
*
717463 ATTTAATTAGTT-AAGAATAAAATAT
1 ATTTAATAAGTTAAAG-ATAAAATAT
717488 ATTTAATAAGTTAAAGATAAAATA
1 ATTTAATAAGTTAAAGATAAAATA
717512 AAATATTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.55, C:0.00, G:0.08, T:0.37
Consensus pattern (25 bp):
ATTTAATAAGTTAAAGATAAAATAT
Found at i:720689 original size:2 final size:2
Alignment explanation
Indices: 720682--720739 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
720672 ATGGAAAAAC
720682 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
720724 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
720740 TAACAATACA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:725766 original size:182 final size:182
Alignment explanation
Indices: 725182--725843 Score: 917
Period size: 182 Copynumber: 3.7 Consensus size: 182
725172 TTGTCGGTAC
* * * *
725182 GTATCGATACTATTA-AAATATATATCGATACATAACAATATCATCAAGTAAAAATATGAGAAAA
1 GTATCGATACT-TTATAAACATGTATCGATACATAACAATAT-AACAAGTAAAAATATGACAAAA
** * * *
725246 CCGGGTTCAATATGACAAAACCAGTAAAGCGCTACCGATATGTTGAAGGTATCGATTCCATTCAA
64 CCGATTTCATTATGACAAAACCGGTAAAGCGATACCGATATGTTGAAGGTATCGATTCCATTCAA
* * * * * *
725311 ATAAGTATCAACACTTTTGGAATTTAAAAGAAAAGCAGTAATAGCGCTTATAAA
129 ATAAGTATCGATACATTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
* * * *
725365 GCATCGATACTTTATAATCATGTATCGATACATAACAATATAACATGT--AAA-A--A-AAAACT
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAAGTAAAAATATGACAAAACC
725424 GATTTCATTATGACAAAACCGGTAAAGCGATACCGAATATGTTGAAGGTATCGATTCCATTCAAA
66 GATTTCATTATGACAAAACCGGTAAAGCGATACCG-ATATGTTGAAGGTATCGATTCCATTCAAA
725489 TAAGTATCGATACATTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
130 TAAGTATCGATACATTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
* * * *
725542 GTATCGATACTTTATAAACATGTATCGATATATAATAATATAACAGGTAAAAATATGACAAAATC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAAGTAAAAATATGACAAAACC
* * * *
725607 GGTTTCATTATAACAAAACCGGTAAAGCGATACTTGATATGTTAAAGGTATCGATTCCATTCAAA
66 GATTTCATTATGACAAAACCGGTAAAGCGATAC-CGATATGTTGAAGGTATCGATTCCATTCAAA
* * * *
725672 TAAATATCGATGC-TTTGGAATTTAAAAGAAAATCAATAATAGAGCCTATAAA
130 TAAGTATCGATACATTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
725724 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAAGTAAAAATATGACAAAACC
1 GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAAGTAAAAATATGACAAAACC
* * *
725789 GATTTCATTATGACAAAACCGGTAAAGCGCTACTGGATATGTTGAATGTATCGAT
66 GATTTCATTATGACAAAACCGGTAAAGCGATAC-CGATATGTTGAAGGTATCGAT
725844 ACTTTAATAA
Statistics
Matches: 427, Mismatches: 43, Indels: 19
0.87 0.09 0.04
Matches are distributed among these distances:
176 35 0.08
177 120 0.28
179 4 0.01
180 4 0.01
182 156 0.37
183 107 0.25
184 1 0.00
ACGTcount: A:0.44, C:0.14, G:0.14, T:0.28
Consensus pattern (182 bp):
GTATCGATACTTTATAAACATGTATCGATACATAACAATATAACAAGTAAAAATATGACAAAACC
GATTTCATTATGACAAAACCGGTAAAGCGATACCGATATGTTGAAGGTATCGATTCCATTCAAAT
AAGTATCGATACATTTGGAATTTAAAAGAAAAACAATAATAGCGCCTATAAA
Found at i:728380 original size:17 final size:17
Alignment explanation
Indices: 728358--728400 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
728348 TACTCCCTTA
728358 CTCCCCCTTACTATATT
1 CTCCCCCTTACTATATT
728375 CTCCCCCTTACTATATT
1 CTCCCCCTTACTATATT
728392 CTCCCCCTT
1 CTCCCCCTT
728401 TTTGTTAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.14, C:0.47, G:0.00, T:0.40
Consensus pattern (17 bp):
CTCCCCCTTACTATATT
Found at i:732941 original size:24 final size:24
Alignment explanation
Indices: 732914--732967 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
732904 ATTACAAAAA
732914 TCAGTAAATCCAAGATTTTCAAAT
1 TCAGTAAATCCAAGATTTTCAAAT
732938 TCAGTAAATCCAAGATTTTCAAAT
1 TCAGTAAATCCAAGATTTTCAAAT
732962 TCAGTA
1 TCAGTA
732968 CCATGATCAC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (24 bp):
TCAGTAAATCCAAGATTTTCAAAT
Found at i:737519 original size:27 final size:27
Alignment explanation
Indices: 737488--737548 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 27
737478 AAGGTTTGGC
* *
737488 AAGGAGGTAG-AGAAGGAAGATGAGGTA
1 AAGGAGGCAGAAG-AGGAAGATAAGGTA
* *
737515 GAGGAGGCAGAAGAGGCAGATAAGGTA
1 AAGGAGGCAGAAGAGGAAGATAAGGTA
737542 AAGGAGG
1 AAGGAGG
737549 AAAAGGAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
27 26 0.93
28 2 0.07
ACGTcount: A:0.43, C:0.03, G:0.46, T:0.08
Consensus pattern (27 bp):
AAGGAGGCAGAAGAGGAAGATAAGGTA
Found at i:737530 original size:18 final size:18
Alignment explanation
Indices: 737491--737530 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
737481 GTTTGGCAAG
*
737491 GAGGTAGAGAAGGAAGAT
1 GAGGTAGAGAAGGAAGAA
* *
737509 GAGGTAGAGGAGGCAGAA
1 GAGGTAGAGAAGGAAGAA
737527 GAGG
1 GAGG
737531 CAGATAAGGT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.40, C:0.03, G:0.50, T:0.07
Consensus pattern (18 bp):
GAGGTAGAGAAGGAAGAA
Found at i:737857 original size:66 final size:66
Alignment explanation
Indices: 737733--737857 Score: 162
Period size: 66 Copynumber: 1.9 Consensus size: 66
737723 AAGTGGTTAG
* * * *
737733 AAAAATAGATGAAGTGGTGAAAGAATTTGTGAAGTTGAGGGGTGAATTTAAGATGGTGATGGGTG
1 AAAAATAGATGAAGTGGTGAAAGAAATTGTGAAATTGAGGGGTGAACTTAAGAGGGTGATGGGTG
737798 A
66 A
* * * *
737799 AAAAATTGATGGAA-TGGTGAAGGAAATTGTGAAATTGAGGGGTGAACTTACGGGGGTGA
1 AAAAATAGAT-GAAGTGGTGAAAGAAATTGTGAAATTGAGGGGTGAACTTAAGAGGGTGA
737858 AGGGAGTGGT
Statistics
Matches: 50, Mismatches: 8, Indels: 2
0.83 0.13 0.03
Matches are distributed among these distances:
66 47 0.94
67 3 0.06
ACGTcount: A:0.36, C:0.02, G:0.37, T:0.26
Consensus pattern (66 bp):
AAAAATAGATGAAGTGGTGAAAGAAATTGTGAAATTGAGGGGTGAACTTAAGAGGGTGATGGGTG
A
Found at i:742999 original size:9 final size:9
Alignment explanation
Indices: 742975--743084 Score: 53
Period size: 9 Copynumber: 11.7 Consensus size: 9
742965 AAATAGTAAG
*
742975 TAAAATAAA
1 TAAAAAAAA
*
742984 TATAAAAAA
1 TAAAAAAAA
742993 TAAAAAATAA
1 TAAAAAA-AA
743003 -AGAAAAAGAA
1 TA-AAAAA-AA
*
743013 GAAAAAATATA
1 TAAAAAA-A-A
*
743024 TAAATAAAA
1 TAAAAAAAA
743033 TAATAAAAAA
1 TAA-AAAAAA
*
743043 GTAAAAATAA
1 -TAAAAAAAA
* * *
743053 T-ATATATA
1 TAAAAAAAA
* *
743061 TATAATAAA
1 TAAAAAAAA
743070 TAAAAAAAA
1 TAAAAAAAA
743079 TAAAAA
1 TAAAAA
743085 CTAGTAAATA
Statistics
Matches: 76, Mismatches: 18, Indels: 14
0.70 0.17 0.13
Matches are distributed among these distances:
8 4 0.05
9 36 0.47
10 26 0.34
11 10 0.13
ACGTcount: A:0.75, C:0.00, G:0.04, T:0.21
Consensus pattern (9 bp):
TAAAAAAAA
Found at i:743051 original size:30 final size:34
Alignment explanation
Indices: 742996--743076 Score: 96
Period size: 33 Copynumber: 2.4 Consensus size: 34
742986 TAAAAAATAA
* *
742996 AAAATAAA-GAAAAAGAAGAAAA-AATATATAAAT
1 AAAATAAATAAAAAAGAA-AAAATAATATATATAT
*
743029 AAAAT-AATAAAAAAGTAAAAATAATATATATAT
1 AAAATAAATAAAAAAGAAAAAATAATATATATAT
*
743062 ATAATAAATAAAAAA
1 AAAATAAATAAAAAA
743077 AATAAAAACT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
32 6 0.15
33 26 0.63
34 9 0.22
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (34 bp):
AAAATAAATAAAAAAGAAAAAATAATATATATAT
Found at i:743097 original size:2 final size:2
Alignment explanation
Indices: 743092--743120 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
743082 AAACTAGTAA
743092 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
743121 AATTAATAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Done.