Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009067.1 Hibiscus syriacus cultivar Beakdansim tig00112491_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: 2329927
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 10
Found at i:5537 original size:31 final size:33
Alignment explanation
Indices: 5475--5537 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 33
5465 GCCATGGTAC
**
5475 GTGGCTTAAAAAGGAGTATTATAATTTATTTTT
1 GTGGCTTAAAAAGGAGTATTATAATACATTTTT
5508 GTGGCTTAAAAA-G-GTATTATAATACATTTT
1 GTGGCTTAAAAAGGAGTATTATAATACATTTT
5538 ATCTTGAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 15 0.54
32 1 0.04
33 12 0.43
ACGTcount: A:0.35, C:0.05, G:0.17, T:0.43
Consensus pattern (33 bp):
GTGGCTTAAAAAGGAGTATTATAATACATTTTT
Found at i:5644 original size:78 final size:76
Alignment explanation
Indices: 5556--5700 Score: 166
Period size: 76 Copynumber: 1.9 Consensus size: 76
5546 TTAGAATTGA
* *
5556 TTTTTATTGTGCATTCAAAATAAGATTTTATAGTGTAAATATCATA-TTTCCTGTCTTAAATTAG
1 TTTTTATTGTGCATTCAAAATAAGA--TTACAGTGTAAATATCATACTTT-ATGTCTTAAATTAG
5620 AATTGGTTTGTCTT
63 AATTGGTTTGTCTT
* * * * * * * *
5634 TTTTTCTTGTGTATTTAATATAGGATTACAGTTTAAGTATCGTACTTTATGTCTTAAATTAGAAT
1 TTTTTATTGTGCATTCAAAATAAGATTACAGTGTAAATATCATACTTTATGTCTTAAATTAGAAT
5699 TG
66 TG
5701 ATTTCTTAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
76 33 0.59
77 3 0.05
78 20 0.36
ACGTcount: A:0.29, C:0.08, G:0.14, T:0.49
Consensus pattern (76 bp):
TTTTTATTGTGCATTCAAAATAAGATTACAGTGTAAATATCATACTTTATGTCTTAAATTAGAAT
TGGTTTGTCTT
Found at i:26742 original size:16 final size:16
Alignment explanation
Indices: 26721--26751 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
26711 TTAATTTTTT
26721 TTTTATATTTTAAATA
1 TTTTATATTTTAAATA
*
26737 TTTTATTTTTTAAAT
1 TTTTATATTTTAAAT
26752 TTTAGAAATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (16 bp):
TTTTATATTTTAAATA
Found at i:47551 original size:30 final size:30
Alignment explanation
Indices: 47517--47579 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
47507 TAGTGAACGT
*
47517 TGAAAGACT-GCCAAAGCATATATCGTCTTC
1 TGAAAGA-TAGCCAAAGCACATATCGTCTTC
** *
47547 TGAAAGATAGCTGAAGCACATGTCGTCTTC
1 TGAAAGATAGCCAAAGCACATATCGTCTTC
47577 TGA
1 TGA
47580 CTCTTCGCCT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 1 0.04
30 27 0.96
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.27
Consensus pattern (30 bp):
TGAAAGATAGCCAAAGCACATATCGTCTTC
Found at i:49469 original size:18 final size:18
Alignment explanation
Indices: 49420--49520 Score: 77
Period size: 18 Copynumber: 5.7 Consensus size: 18
49410 AAATTAATAA
*
49420 ATAATATAA-ATTTTATT
1 ATAATATAATATATTATT
*
49437 AATAATTTATTATATATTATT
1 -ATAA--TATAATATATTATT
49458 ATAATATAATATA--A-T
1 ATAATATAATATATTATT
**
49473 ATAATATCTTATATTATT
1 ATAATATAATATATTATT
49491 ATAATATAAT-TGATTATT
1 ATAATATAATAT-ATTATT
* *
49509 TTATTATAATAT
1 ATAATATAATAT
49521 TAAAAATATA
Statistics
Matches: 66, Mismatches: 9, Indels: 15
0.73 0.10 0.17
Matches are distributed among these distances:
15 12 0.18
16 1 0.02
17 2 0.03
18 35 0.53
19 1 0.02
20 8 0.12
21 7 0.11
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.52
Consensus pattern (18 bp):
ATAATATAATATATTATT
Found at i:49474 original size:23 final size:24
Alignment explanation
Indices: 49416--49507 Score: 68
Period size: 23 Copynumber: 3.9 Consensus size: 24
49406 TATGAAATTA
*
49416 ATAA-ATAATATAAATT-TTATTA-
1 ATAATATAATAT-AATTATTATAAT
* *
49438 ATAATTTATTATATATTATTATAAT
1 ATAATATAATATA-ATTATTATAAT
*
49463 ATAATATAATATAATATCTTAT-AT
1 ATAATATAATATAAT-TATTATAAT
*
49487 -TATTATAATATAATTGATTAT
1 ATAATATAATATAATT-ATTAT
49508 TTTATTATAA
Statistics
Matches: 56, Mismatches: 8, Indels: 11
0.75 0.11 0.15
Matches are distributed among these distances:
22 6 0.11
23 25 0.45
24 9 0.16
25 16 0.29
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.50
Consensus pattern (24 bp):
ATAATATAATATAATTATTATAAT
Found at i:49512 original size:23 final size:23
Alignment explanation
Indices: 49443--49520 Score: 74
Period size: 23 Copynumber: 3.5 Consensus size: 23
49433 TATTAATAAT
* *
49443 TTATTAT-ATATTAT-TATAATA
1 TTATTATAATATAATATATTATA
* *
49464 -TAATATAATATAATATCTTATA
1 TTATTATAATATAATATATTATA
*
49486 TTATTATAATATAAT-TGATTATT
1 TTATTATAATATAATAT-ATTATA
49509 TTATTATAATAT
1 TTATTATAATAT
49521 TAAAAATATA
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
20 5 0.11
21 6 0.13
22 6 0.13
23 29 0.63
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.54
Consensus pattern (23 bp):
TTATTATAATATAATATATTATA
Found at i:49538 original size:22 final size:23
Alignment explanation
Indices: 49510--49556 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 23
49500 TTGATTATTT
49510 TATTATAATATTAAAAATA-TAA
1 TATTATAATATTAAAAATATTAA
* *
49532 TATTATATTATTGAAAATATTAA
1 TATTATAATATTAAAAATATTAA
49555 TA
1 TA
49557 AATATATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (23 bp):
TATTATAATATTAAAAATATTAA
Found at i:49561 original size:22 final size:22
Alignment explanation
Indices: 49518--49561 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
49508 TTTATTATAA
*
49518 TATTAAAAATATAATATTATAT
1 TATTAAAAATATAATATAATAT
*
49540 TATTGAAAATATTAATA-AATAT
1 TATTAAAAATA-TAATATAATAT
49562 ATTTTAAATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
TATTAAAAATATAATATAATAT
Found at i:51677 original size:2 final size:2
Alignment explanation
Indices: 51670--51730 Score: 79
Period size: 2 Copynumber: 30.5 Consensus size: 2
51660 TATGTTTAAT
* * *
51670 TA TA TA TA TA TA TA TA TA TA TT TA TG TA TA TA CT- TT 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
51712 TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA T
51731 TATTCAAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
1 1 0.02
2 50 0.96
3 1 0.02
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.54
Consensus pattern (2 bp):
TA
Found at i:52379 original size:14 final size:14
Alignment explanation
Indices: 52360--52406 Score: 50
Period size: 14 Copynumber: 3.7 Consensus size: 14
52350 ATTTTTTCTT
52360 TATATAAATTAAAC
1 TATATAAATTAAAC
52374 TATAT-AATT----
1 TATATAAATTAAAC
52383 TATATAAATTAAAC
1 TATATAAATTAAAC
*
52397 TATATTAATT
1 TATATAAATT
52407 TTCCTTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 10
0.71 0.03 0.26
Matches are distributed among these distances:
9 5 0.19
10 4 0.15
13 4 0.15
14 14 0.52
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TATATAAATTAAAC
Found at i:52384 original size:23 final size:24
Alignment explanation
Indices: 52358--52407 Score: 93
Period size: 23 Copynumber: 2.1 Consensus size: 24
52348 TTATTTTTTC
52358 TTTATATAAATTAAACTATA-TAA
1 TTTATATAAATTAAACTATATTAA
52381 TTTATATAAATTAAACTATATTAA
1 TTTATATAAATTAAACTATATTAA
52405 TTT
1 TTT
52408 TCCTTTGCAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 20 0.77
24 6 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (24 bp):
TTTATATAAATTAAACTATATTAA
Found at i:52478 original size:13 final size:13
Alignment explanation
Indices: 52446--52472 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
52436 TAATTTACAT
52446 TTAAATAATTTTA
1 TTAAATAATTTTA
52459 TTAAATAATTTTA
1 TTAAATAATTTTA
52472 T
1 T
52473 ATAATAGGTC
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:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTAAATAATTTTA
Found at i:52681 original size:16 final size:16
Alignment explanation
Indices: 52660--52708 Score: 80
Period size: 16 Copynumber: 3.1 Consensus size: 16
52650 CATTTACAAG
*
52660 CAGGTTAAAAACATGT
1 CAGGTTAAAAACAGGT
52676 CAGGTTAAAAACAGGT
1 CAGGTTAAAAACAGGT
*
52692 CAGGTTGAAAACAGGT
1 CAGGTTAAAAACAGGT
52708 C
1 C
52709 GGGTAATACC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.41, C:0.14, G:0.24, T:0.20
Consensus pattern (16 bp):
CAGGTTAAAAACAGGT
Found at i:66747 original size:48 final size:49
Alignment explanation
Indices: 66680--66775 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
66670 ATATACCAAT
* *
66680 TTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTTTTTTCA
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
*
66729 TTTTTTATTAAAAC-ACCAAAAGATTAATGTAATGATTATGTTTTTTC
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTC
66776 TTTATATGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 32 0.73
49 12 0.27
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (49 bp):
TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
Found at i:67110 original size:48 final size:49
Alignment explanation
Indices: 67043--67138 Score: 158
Period size: 48 Copynumber: 2.0 Consensus size: 49
67033 ATATACCAAT
* *
67043 TTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTTTTTTCA
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
*
67092 TTTTTTATTAAAAC-ACCAAAAGATTAATGTAATGATTATGTTTTTTC
1 TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTC
67139 TTTATATGTA
Statistics
Matches: 44, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
48 32 0.73
49 12 0.27
ACGTcount: A:0.34, C:0.10, G:0.09, T:0.46
Consensus pattern (49 bp):
TTTTTTACTAAAACTACCAAAAGATTAATGTAATGATTATGTTTTTTCA
Found at i:67323 original size:363 final size:363
Alignment explanation
Indices: 66658--67383 Score: 1452
Period size: 363 Copynumber: 2.0 Consensus size: 363
66648 TTTTGTCTTA
66658 GGGTTAGTCTAAATATACCAATTTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTT
1 GGGTTAGTCTAAATATACCAATTTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTT
66723 TTTTCATTTTTTATTAAAACACCAAAAGATTAATGTAATGATTATGTTTTTTCTTTATATGTATT
66 TTTTCATTTTTTATTAAAACACCAAAAGATTAATGTAATGATTATGTTTTTTCTTTATATGTATT
66788 AAAATTTTTATCATTATGTAATAATGATGTATTTTTATATTTTATTAAAATTTTATCTTTTTCAT
131 AAAATTTTTATCATTATGTAATAATGATGTATTTTTATATTTTATTAAAATTTTATCTTTTTCAT
66853 TATTAAAGTTTTTAATTAAAGTATTTTTCATTTATTTCTTTAACTTAAAAAAAATCTTATTTAAC
196 TATTAAAGTTTTTAATTAAAGTATTTTTCATTTATTTCTTTAACTTAAAAAAAATCTTATTTAAC
66918 CATTTAACAATTTTCAACATCTTGACAGTAAAAATTCTGACAGCAAAAAAATGTTATTTCCAACA
261 CATTTAACAATTTTCAACATCTTGACAGTAAAAATTCTGACAGCAAAAAAATGTTATTTCCAACA
66983 TGTTTGACTAATTGTTATTTCCAACATGATTAATTTTT
326 TGTTTGACTAATTGTTATTTCCAACATGATTAATTTTT
67021 GGGTTAGTCTAAATATACCAATTTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTT
1 GGGTTAGTCTAAATATACCAATTTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTT
67086 TTTTCATTTTTTATTAAAACACCAAAAGATTAATGTAATGATTATGTTTTTTCTTTATATGTATT
66 TTTTCATTTTTTATTAAAACACCAAAAGATTAATGTAATGATTATGTTTTTTCTTTATATGTATT
67151 AAAATTTTTATCATTATGTAATAATGATGTATTTTTATATTTTATTAAAATTTTATCTTTTTCAT
131 AAAATTTTTATCATTATGTAATAATGATGTATTTTTATATTTTATTAAAATTTTATCTTTTTCAT
67216 TATTAAAGTTTTTAATTAAAGTATTTTTCATTTATTTCTTTAACTTAAAAAAAATCTTATTTAAC
196 TATTAAAGTTTTTAATTAAAGTATTTTTCATTTATTTCTTTAACTTAAAAAAAATCTTATTTAAC
67281 CATTTAACAATTTTCAACATCTTGACAGTAAAAATTCTGACAGCAAAAAAATGTTATTTCCAACA
261 CATTTAACAATTTTCAACATCTTGACAGTAAAAATTCTGACAGCAAAAAAATGTTATTTCCAACA
67346 TGTTTGACTAATTGTTATTTCCAACATGATTAATTTTT
326 TGTTTGACTAATTGTTATTTCCAACATGATTAATTTTT
67384 TATTATTTTC
Statistics
Matches: 363, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
363 363 1.00
ACGTcount: A:0.36, C:0.10, G:0.08, T:0.47
Consensus pattern (363 bp):
GGGTTAGTCTAAATATACCAATTTTTTTACTAAACCTACCAAAAGATTAGTGTAATGATTATGTT
TTTTCATTTTTTATTAAAACACCAAAAGATTAATGTAATGATTATGTTTTTTCTTTATATGTATT
AAAATTTTTATCATTATGTAATAATGATGTATTTTTATATTTTATTAAAATTTTATCTTTTTCAT
TATTAAAGTTTTTAATTAAAGTATTTTTCATTTATTTCTTTAACTTAAAAAAAATCTTATTTAAC
CATTTAACAATTTTCAACATCTTGACAGTAAAAATTCTGACAGCAAAAAAATGTTATTTCCAACA
TGTTTGACTAATTGTTATTTCCAACATGATTAATTTTT
Found at i:70396 original size:20 final size:21
Alignment explanation
Indices: 70371--70409 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
70361 AGAAAATTCC
*
70371 TCATAATATTTAA-ATTATTT
1 TCATAAAATTTAATATTATTT
70391 TCATAAAATTTAATATTAT
1 TCATAAAATTTAATATTAT
70410 ACATGTATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (21 bp):
TCATAAAATTTAATATTATTT
Found at i:72129 original size:6 final size:6
Alignment explanation
Indices: 72118--72144 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
72108 ATGTGGGGAT
72118 GAATCA GAATCA GAATCA GAATCA GAA
1 GAATCA GAATCA GAATCA GAATCA GAA
72145 CATGATCTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.19, T:0.15
Consensus pattern (6 bp):
GAATCA
Found at i:72567 original size:24 final size:24
Alignment explanation
Indices: 72540--72585 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
72530 TCGTGAACGC
*
72540 TCGGTTGTGTTCGTTTATGTTCGT
1 TCGGTTATGTTCGTTTATGTTCGT
72564 TCGGTTATGTTCGTTTATGTTC
1 TCGGTTATGTTCGTTTATGTTC
72586 ATTCATTTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.07, C:0.13, G:0.26, T:0.54
Consensus pattern (24 bp):
TCGGTTATGTTCGTTTATGTTCGT
Found at i:72571 original size:14 final size:14
Alignment explanation
Indices: 72548--72578 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
72538 GCTCGGTTGT
*
72548 GTTCGTTTATGTTC
1 GTTCGGTTATGTTC
72562 GTTCGGTTATGTTC
1 GTTCGGTTATGTTC
72576 GTT
1 GTT
72579 TATGTTCATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.13, G:0.26, T:0.55
Consensus pattern (14 bp):
GTTCGGTTATGTTC
Found at i:72595 original size:24 final size:24
Alignment explanation
Indices: 72547--72598 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
72537 CGCTCGGTTG
* *
72547 TGTTCGTTTATGTTCGTTCGGTTA
1 TGTTCGTTTATGTTCATTCAGTTA
*
72571 TGTTCGTTTATGTTCATTCATTTA
1 TGTTCGTTTATGTTCATTCAGTTA
72595 TGTT
1 TGTT
72599 TAACCCAATC
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.19, T:0.58
Consensus pattern (24 bp):
TGTTCGTTTATGTTCATTCAGTTA
Found at i:73693 original size:16 final size:16
Alignment explanation
Indices: 73672--73722 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
73662 GTCTCCAACG
73672 TTTATG-TCTGTGTTCA
1 TTTATGTTC-GTGTTCA
*
73688 TTTATGTTCGTGTTCG
1 TTTATGTTCGTGTTCA
73704 TTTATGTTCGT-TT-A
1 TTTATGTTCGTGTTCA
73718 TTTAT
1 TTTAT
73723 TAAATGAACG
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 5 0.16
15 2 0.06
16 23 0.72
17 2 0.06
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.61
Consensus pattern (16 bp):
TTTATGTTCGTGTTCA
Found at i:75230 original size:25 final size:25
Alignment explanation
Indices: 75171--75233 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 25
75161 TATTTTAAAC
*
75171 AATAATTTTATACTTTTTTTATTGAT
1 AATAATTTTATAC-TTTTTTATTAAT
75197 AGATAATTTTATA-TTTTTTATTAAT
1 A-ATAATTTTATACTTTTTTATTAAT
75222 AATATATTTTAT
1 AATA-ATTTTAT
75234 TTTCTAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
24 3 0.09
25 19 0.56
26 1 0.03
27 11 0.32
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (25 bp):
AATAATTTTATACTTTTTTATTAAT
Found at i:78741 original size:29 final size:29
Alignment explanation
Indices: 78654--78724 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
78644 ACCCAACCAT
* * ****
78654 AGGTCGCCATGCACTCCCAGCGACCTCCT
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
78683 AGGTCGCCATGCACGCCCGGCGACCAAGG
1 AGGTCGCCATGCACGCCCGGCGACCAAGG
78712 AGGTCGCCATGCA
1 AGGTCGCCATGCA
78725 TTCGGGGCGA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.20, C:0.39, G:0.28, T:0.13
Consensus pattern (29 bp):
AGGTCGCCATGCACGCCCGGCGACCAAGG
Found at i:78989 original size:29 final size:29
Alignment explanation
Indices: 78956--79041 Score: 109
Period size: 29 Copynumber: 3.0 Consensus size: 29
78946 AGCAGGGGAT
* * **
78956 GTCGCCGCGAGTGCATGGCGACCTCCTTG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
* *
78985 GTCGCCGGGCGTGCATGGCGACCTAGGAG
1 GTCGCCGGGAGTGCATGGCGACCTACGAG
*
79014 GTCGCTGGGAGTGCATGGCGACCTACGA
1 GTCGCCGGGAGTGCATGGCGACCTACGA
79042 CCACTGTTGA
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 48 1.00
ACGTcount: A:0.14, C:0.29, G:0.40, T:0.17
Consensus pattern (29 bp):
GTCGCCGGGAGTGCATGGCGACCTACGAG
Found at i:87687 original size:16 final size:16
Alignment explanation
Indices: 87663--87694 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
87653 TATCGCCGAC
*
87663 CAAATTTCACTATTCA
1 CAAAATTCACTATTCA
87679 CAAAATTCACTATTCA
1 CAAAATTCACTATTCA
87695 TGTTAATAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.25, G:0.00, T:0.34
Consensus pattern (16 bp):
CAAAATTCACTATTCA
Found at i:91810 original size:15 final size:16
Alignment explanation
Indices: 91790--91819 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
91780 ATAACAACGG
91790 TGAT-AACTGACACAT
1 TGATAAACTGACACAT
91805 TGATAAACTGACACA
1 TGATAAACTGACACA
91820 ACACAATCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.43, C:0.20, G:0.13, T:0.23
Consensus pattern (16 bp):
TGATAAACTGACACAT
Found at i:92585 original size:21 final size:22
Alignment explanation
Indices: 92546--92586 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
92536 ATTTTTTTAT
**
92546 AAAGTTTTTAAAATATAATATC
1 AAAGTTTAAAAAATATAATATC
92568 AAAGTTTAAAAAAT-TAATA
1 AAAGTTTAAAAAATATAATA
92587 CATAATATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (22 bp):
AAAGTTTAAAAAATATAATATC
Found at i:93144 original size:2 final size:2
Alignment explanation
Indices: 93139--93168 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
93129 CCCTATAAAT
93139 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
93169 AGGAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:93227 original size:22 final size:23
Alignment explanation
Indices: 93180--93228 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
93170 GGAAAAAAGA
**
93180 TGACACGCCTTTAAGAAAGATTT
1 TGACACGCCTTTAAGAAAGAAAT
93203 TGACAC-CCTTTGAA-AAAGAAAT
1 TGACACGCCTTT-AAGAAAGAAAT
93225 TGAC
1 TGAC
93229 TCTATATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
22 15 0.65
23 8 0.35
ACGTcount: A:0.39, C:0.18, G:0.16, T:0.27
Consensus pattern (23 bp):
TGACACGCCTTTAAGAAAGAAAT
Found at i:97157 original size:25 final size:25
Alignment explanation
Indices: 97122--97183 Score: 115
Period size: 25 Copynumber: 2.5 Consensus size: 25
97112 AAAATAAATA
*
97122 AATAATAATTTTAATAATGGAATGG
1 AATAATTATTTTAATAATGGAATGG
97147 AATAATTATTTTAATAATGGAATGG
1 AATAATTATTTTAATAATGGAATGG
97172 AATAATTATTTT
1 AATAATTATTTT
97184 TCCGATGTGT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (25 bp):
AATAATTATTTTAATAATGGAATGG
Found at i:98358 original size:415 final size:412
Alignment explanation
Indices: 97527--98359 Score: 1458
Period size: 416 Copynumber: 2.0 Consensus size: 412
97517 GTTTCTCAGA
* * *
97527 TTTAACCCAATTCTATGTCCTTTCTCCGCTCCTTAATTTTCTTCGATTAGGGAAAAAAACGAATA
1 TTTAACCCAATTCTATGTCCTTTATCCGCTCCTTAATTTTCTTCGATTAGGAAAAAAAACGAAGA
*
97592 AATTTTCCAAATCCTCAATTCGTCGGCTCTGTCAATTTTCTTGGCAGAGATTCTTCATAGCCAGG
66 AATTTTCCAAATCCTCAATTCGTCGGCTCTGTCAATTTTCTCGGCAGAGATTCTTCATAGCCAGG
*
97657 TATTTTCTTTCCTCAATTTATTTTCATTCTTCTATATTTTATTTTATTTTATTTGTTTTTATGCT
131 TATTTTCTTTCCTCAATTTAATTTCATTCTTC-ATA--TTATTTTATTTTATTTGTTTTTATGCT
97722 GTTATTTATTTATTTATTTCAAGTCTTGAGAATTTCTTTTATTTACTTGTTTCTGTTAGGGCTTT
193 GTTATTTATTTATTTATTTCAAGTCTTGAGAATTTCTTTTATTTACTTGTTTCTGTTAGGGCTTT
* *
97787 GATATTGGCGCTATATTCCTAAACGCTGAAAATATATATTTTTTATAAATATTTAGTTGAATTGA
258 GATATTGGCGCTATATTCCTAAACGCTGAAAACATATATTTTTTATAAACATTTAGTTGAATTGA
97852 GGATTAGATTTTTGTTTGTTTATGTGGTGTTTTATATTATGATGGCGATTGAGAAGAATAACTTC
323 GGATTAGATTTTTGTTTGTTTATGTGGTGTTTTATATTATGATGGCGATTGAGAAGAATAACTTC
97917 AAGGTTTCACGGTTTGATTCGGAGT
388 AAGGTTTCACGGTTTGATTCGGAGT
97942 TTTAACCCCAATTCTATGTCCTTTATCCGCTCCTTAATTTTCTTCGATTAGGAAAAAAAACGAAG
1 TTTAA-CCCAATTCTATGTCCTTTATCCGCTCCTTAATTTTCTTCGATTAGGAAAAAAAACGAAG
*
98007 AAATTTTCCAAATCCTCAATTCGTCGGCTCTGTCAATTTTCTCGGCAGCGATTCTTCATAGCCAG
65 AAATTTTCCAAATCCTCAATTCGTCGGCTCTGTCAATTTTCTCGGCAGAGATTCTTCATAGCCAG
98072 GTATTTTCTTTCCTCAATTTAATTTCATTCTTC-TA-TA-TTTATTTTATTTGTTTTTATGCTGT
130 GTATTTTCTTTCCTCAATTTAATTTCATTCTTCATATTATTTTATTTTATTTGTTTTTATGCTG-
98134 TATTTATTTATTTATTTATTTCAAGTCTTGAGAATTTCTTTTATTTACTTGTTTCTGTTAGGGCT
194 ---TTATTTATTTATTTATTTCAAGTCTTGAGAATTTCTTTTATTTACTTGTTTCTGTTAGGGCT
* *
98199 TTGATGAATTGGCGCTATATTCCTAAACGCTGAAAACATA-GTTTTTTATAAACATTTGGTTGAA
256 TTGAT--ATTGGCGCTATATTCCTAAACGCTGAAAACATATATTTTTTATAAACATTTAGTTGAA
98263 TTGAGGATTAGATTTTTGTTTGTTTATGTGGTGTTTTATATTATGATGGCGATTGAGAAGAATAA
319 TTGAGGATTAGATTTTTGTTTGTTTATGTGGTGTTTTATATTATGATGGCGATTGAGAAGAATAA
98328 CTTCAAGGTTTCACGGTTTGATTCGGAGT
384 CTTCAAGGTTTCACGGTTTGATTCGGAGT
98357 TTT
1 TTT
98360 CGCCTGGTAG
Statistics
Matches: 401, Mismatches: 10, Indels: 14
0.94 0.02 0.03
Matches are distributed among these distances:
410 24 0.06
411 2 0.00
414 69 0.17
415 123 0.31
416 183 0.46
ACGTcount: A:0.24, C:0.14, G:0.15, T:0.46
Consensus pattern (412 bp):
TTTAACCCAATTCTATGTCCTTTATCCGCTCCTTAATTTTCTTCGATTAGGAAAAAAAACGAAGA
AATTTTCCAAATCCTCAATTCGTCGGCTCTGTCAATTTTCTCGGCAGAGATTCTTCATAGCCAGG
TATTTTCTTTCCTCAATTTAATTTCATTCTTCATATTATTTTATTTTATTTGTTTTTATGCTGTT
ATTTATTTATTTATTTCAAGTCTTGAGAATTTCTTTTATTTACTTGTTTCTGTTAGGGCTTTGAT
ATTGGCGCTATATTCCTAAACGCTGAAAACATATATTTTTTATAAACATTTAGTTGAATTGAGGA
TTAGATTTTTGTTTGTTTATGTGGTGTTTTATATTATGATGGCGATTGAGAAGAATAACTTCAAG
GTTTCACGGTTTGATTCGGAGT
Found at i:109809 original size:26 final size:26
Alignment explanation
Indices: 109760--109884 Score: 71
Period size: 26 Copynumber: 4.7 Consensus size: 26
109750 AGAAATAAAT
*
109760 AAATAAATAAAATTAAAATGAAGAAA
1 AAATAAATAAAATAAAAATGAAGAAA
* *
109786 AAATAAATTAAATAAAAGAT-AAG-AT
1 AAATAAATAAAATAAAA-ATGAAGAAA
* *
109811 AAAGAAACAAAGAT-AAAATAGTAAGTAAAA
1 AAATAAATAAA-ATAAAAAT-G-AAG--AAA
*
109841 TAAATATAAAAAAATAAAAA-GAAAGAAA
1 -AAATA-AATAAAATAAAAATG-AAGAAA
*
109869 AAATATAT-AAATAAAA
1 AAATAAATAAAATAAAA
109885 CAAATAAATA
Statistics
Matches: 76, Mismatches: 12, Indels: 23
0.68 0.11 0.21
Matches are distributed among these distances:
24 2 0.03
25 20 0.26
26 21 0.28
27 10 0.13
28 3 0.04
30 5 0.07
31 6 0.08
32 9 0.12
ACGTcount: A:0.73, C:0.01, G:0.08, T:0.18
Consensus pattern (26 bp):
AAATAAATAAAATAAAAATGAAGAAA
Found at i:109866 original size:43 final size:43
Alignment explanation
Indices: 109819--109946 Score: 107
Period size: 49 Copynumber: 2.8 Consensus size: 43
109809 ATAAAGAAAC
* * * *
109819 AAAGATAAAATA-GTAAGTAAAATAAATATAAAAAAATAAAAAG
1 AAAGAAAAAATATATAAATAAAACAAATA-AAAAAAATAAAAAG
109862 AAAGAAAAAATATATAAATAAAACAAATAAATAAAATAATAATAAA-
1 AAAGAAAAAATATATAAATAAAACAAAT-AA-AAAA-AATAA-AAAG
* * *
109908 AAAGTAAAAATAATATATATATATAATAAATAAAAAAAA
1 AAAG--AAAA-AATATATAAATAAAACAAATAAAAAAAA
109947 AACAATAGTA
Statistics
Matches: 70, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
43 11 0.16
44 13 0.19
45 5 0.07
46 11 0.16
47 7 0.10
48 6 0.09
49 17 0.24
ACGTcount: A:0.73, C:0.01, G:0.05, T:0.21
Consensus pattern (43 bp):
AAAGAAAAAATATATAAATAAAACAAATAAAAAAAATAAAAAG
Found at i:109909 original size:25 final size:25
Alignment explanation
Indices: 109838--109909 Score: 64
Period size: 24 Copynumber: 3.0 Consensus size: 25
109828 ATAGTAAGTA
*
109838 AAATAAATATAAA-AA-AATAAAAAG
1 AAATAAATA-AAATAATAATAAAAAC
*
109862 AAA-GAA-AAAATATATAA-ATAAAAC
1 AAATAAATAAAATA-ATAATA-AAAAC
109886 AAATAAATAAAATAATAATAAAAA
1 AAATAAATAAAATAATAATAAAAA
109910 AGTAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
21 3 0.08
22 2 0.05
23 4 0.11
24 12 0.32
25 10 0.26
26 7 0.18
ACGTcount: A:0.78, C:0.01, G:0.03, T:0.18
Consensus pattern (25 bp):
AAATAAATAAAATAATAATAAAAAC
Found at i:109925 original size:49 final size:47
Alignment explanation
Indices: 109838--109948 Score: 127
Period size: 49 Copynumber: 2.3 Consensus size: 47
109828 ATAGTAAGTA
109838 AAATAAATATAAAAAAATAAAAAGAAAGAAAAAATATATAAATAAAAC
1 AAATAAATA-AAAAAAATAAAAAGAAAGAAAAAATATATAAATAAAAC
* * * * *
109886 AAATAAATAAAATAATAATAAAAAAGTAA-AAATAATATATATATATAAT
1 AAATAAATAAAA-AA-AAT-AAAAAGAAAGAAAAAATATATAAATAAAAC
109935 AAATAAA-AAAAAAA
1 AAATAAATAAAAAAA
109949 CAATAGTAAA
Statistics
Matches: 55, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
46 1 0.02
47 5 0.09
48 15 0.27
49 26 0.47
50 8 0.15
ACGTcount: A:0.76, C:0.01, G:0.03, T:0.21
Consensus pattern (47 bp):
AAATAAATAAAAAAAATAAAAAGAAAGAAAAAATATATAAATAAAAC
Found at i:109947 original size:38 final size:37
Alignment explanation
Indices: 109895--110015 Score: 111
Period size: 37 Copynumber: 3.1 Consensus size: 37
109885 CAAATAAATA
109895 AAATAATAATAAAAAAGTAAAAATAATATATATATATAAT
1 AAATAA-AATAAAAAA--AAAAATAATATATATATATAAT
* *
109935 AAATAAAA-AAAAAACAATAGTAA-ATATATATATAAAT
1 AAATAAAATAAAAAA-AAAAATAATATATATATAT-AAT
*
109972 TAATAAAACTGATAATAAAAAAAATAATATATATATATATAT
1 AAATAAAA-T-A-AA-AAAAAAAATAATATATATATATA-AT
110014 AA
1 AA
110016 TCTAAAAAAT
Statistics
Matches: 66, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
36 10 0.15
37 16 0.24
38 6 0.09
39 2 0.03
40 7 0.11
41 9 0.14
42 16 0.24
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (37 bp):
AAATAAAATAAAAAAAAAAATAATATATATATATAAT
Found at i:109962 original size:34 final size:34
Alignment explanation
Indices: 109881--109971 Score: 95
Period size: 34 Copynumber: 2.8 Consensus size: 34
109871 ATATATAAAT
*
109881 AAAACAA-ATAAATA-AAATAAT-AATAAAAAAG
1 AAAACAATATAAATATATATAATAAATAAAAAAG
* *
109912 TAAA-AATAATATATATATATAATAAATAAAAAA-
1 AAAACAAT-ATAAATATATATAATAAATAAAAAAG
109945 AAAACAATAGTAAATATATAT-ATAAAT
1 AAAACAATA-TAAATATATATAATAAAT
109972 TAATAAAACT
Statistics
Matches: 49, Mismatches: 5, Indels: 10
0.77 0.08 0.16
Matches are distributed among these distances:
30 2 0.04
31 3 0.06
32 6 0.12
33 16 0.33
34 22 0.45
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.25
Consensus pattern (34 bp):
AAAACAATATAAATATATATAATAAATAAAAAAG
Found at i:110027 original size:38 final size:36
Alignment explanation
Indices: 109913--110031 Score: 107
Period size: 42 Copynumber: 3.1 Consensus size: 36
109903 ATAAAAAAGT
*
109913 AAAAATAATATATATATATAATAAATAAAAAA-AAA
1 AAAAATAATATATATATATAATAATTAAAAAATAAA
* *
109948 ACAATAGTAA-ATATATATATAAATTAATAAAACTGATAATAAA
1 A-AA-AATAATATATATATAT-AA-TAATTAAA---A-AATAAA
109991 AAAAATAATATATATATATATATAATCTAAAAAATAAA
1 AAAAATAATATATATATATA-ATAAT-TAAAAAATAAA
110029 AAA
1 AAA
110032 TATACTAAAA
Statistics
Matches: 67, Mismatches: 5, Indels: 21
0.72 0.05 0.23
Matches are distributed among these distances:
35 1 0.01
36 12 0.18
37 6 0.09
38 15 0.22
39 1 0.01
41 10 0.15
42 18 0.27
43 4 0.06
ACGTcount: A:0.67, C:0.03, G:0.02, T:0.29
Consensus pattern (36 bp):
AAAAATAATATATATATATAATAATTAAAAAATAAA
Found at i:111211 original size:38 final size:36
Alignment explanation
Indices: 111165--111255 Score: 110
Period size: 38 Copynumber: 2.4 Consensus size: 36
111155 CGAGGTTTTG
111165 GTGTTTCAAGAGAAACATTTTCAAAGGTTTTTTGTGT
1 GTGTTTCAAGAGAAACATTTTCAAA-GTTTTTTGTGT
* * * * *
111202 GTGTTTTCAAGAGAAATAATTTTGAGAGTTTTTTTTTT
1 GTG-TTTCAAGAGAAA-CATTTTCAAAGTTTTTTGTGT
111240 GTGTTTCAAGAGAAAC
1 GTGTTTCAAGAGAAAC
111256 TGTCTCAAGA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
37 15 0.33
38 24 0.52
39 7 0.15
ACGTcount: A:0.29, C:0.07, G:0.21, T:0.44
Consensus pattern (36 bp):
GTGTTTCAAGAGAAACATTTTCAAAGTTTTTTGTGT
Found at i:111329 original size:36 final size:36
Alignment explanation
Indices: 111241--111335 Score: 111
Period size: 36 Copynumber: 2.6 Consensus size: 36
111231 TTTTTTTTTG
* *
111241 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
111277 TGTTTCAAAAGAAACTGTCTCAAGAGAGCCAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAA-AATT
* * *
111314 TGTTT-TAAGGGAACTGTCTCAA
1 TGTTTCAAAAGAAACTGTCTCAA
111336 AACTCGTTTT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 43 0.84
37 8 0.16
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:111417 original size:37 final size:37
Alignment explanation
Indices: 111371--111443 Score: 119
Period size: 37 Copynumber: 2.0 Consensus size: 37
111361 AAATATTTTG
* * *
111371 TGTTTCAAGGGAAACTTTTTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
111408 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATT
111444 CATTTCAAAG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (37 bp):
TGTTTCAAGGGAAACTATCTCAAGAGAGACAAAATTT
Found at i:111568 original size:102 final size:102
Alignment explanation
Indices: 111356--111590 Score: 249
Period size: 102 Copynumber: 2.3 Consensus size: 102
111346 AAGGGGAACT
* * * * * **
111356 TATTTAAATATTTTGTGTTTCAAGGGAAACTTTTTCAAGGGAGACAAAATTTTGTTTCAAGGGAA
1 TATTCAAATA-TTT-TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAA
* * **
111421 ACTATCTCAAGAGAGACAAAATTCATTTCAAAGGAAATG
64 AATATCTCAAGAGAGACAAAATTCATTTCAAAGAAAACA
* * * *
111460 TTTTC-AATGTTTATGTTTCAAGAGAAACTGTCTCATGGGAGACAAAATTTAGTTCCAAAAGAAA
1 TATTCAAATATTT-TGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAA
* * * *
111524 ATGTCTCAAGGGAGACGAAATT-AGTTTCAATGAAAACA
65 ATATCTCAAGAGAGACAAAATTCA-TTTCAAAGAAAACA
111562 TATTCAAATATTTTGTTTCAAGGGAAACT
1 TATTCAAATATTTTGTTTCAAGGGAAACT
111591 TGGAATCTGT
Statistics
Matches: 106, Mismatches: 23, Indels: 6
0.79 0.17 0.04
Matches are distributed among these distances:
101 1 0.01
102 93 0.88
103 9 0.08
104 3 0.03
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.32
Consensus pattern (102 bp):
TATTCAAATATTTTGTTTCAAGGGAAACTGTCTCAAGGGAGACAAAATTTAGTTCCAAAAGAAAA
TATCTCAAGAGAGACAAAATTCATTTCAAAGAAAACA
Found at i:111923 original size:106 final size:106
Alignment explanation
Indices: 111738--112057 Score: 441
Period size: 106 Copynumber: 3.0 Consensus size: 106
111728 TGTATTGTTC
* * * * * *
111738 CGAGTCCAATATCC-TCTGCCGTAAAGTTAAAATTGGCTCTGGAACTAAGAAATTGTTTGTTGAC
1 CGAGTCCAATATCCTTC-GCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGAC
* * * * *
111802 AGCCAGCCGCCCCTTCGCTGTGAAGTTGAGCTTGTGATGTCT
65 AACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
*
111844 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCCGAAATTGAGAAATTGTTTGTTGACA
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
* *
111909 ACCAACCGTCCCTTCGTTGTGAAGTTGAACTTTTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
* * *
111950 CGAGTCCAATATCATTCGCTGTGAAATTGAAATTGGCTCTGAAATTGGGAAATTGTTTGTTGAC-
1 CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
*
112014 A--AGCCGTCCCTTCGTTGTGGAGTTGAACTTGTGTTGTCT
66 ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
112053 CGAGT
1 CGAGT
112058 GGCACGATAT
Statistics
Matches: 192, Mismatches: 21, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
103 40 0.21
105 1 0.01
106 149 0.78
107 2 0.01
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (106 bp):
CGAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATTGTTTGTTGACA
ACCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCT
Found at i:112676 original size:32 final size:32
Alignment explanation
Indices: 112635--112739 Score: 124
Period size: 32 Copynumber: 3.3 Consensus size: 32
112625 TTTGCATCAG
* * *
112635 GATGTTGAATTCCCAAAGATGCCCCAATATTC
1 GATGTTGAATTCCAAAAAATGCCCCAATATTT
112667 GATGTTGAA-TCTCAAAAAATGCCCCAATATTT
1 GATGTTGAATTC-CAAAAAATGCCCCAATATTT
* * * *
112699 GATGTT-AAATCTAAAAAAAGCCCCAACATTT
1 GATGTTGAATTCCAAAAAATGCCCCAATATTT
112730 GATGTTGAAT
1 GATGTTGAAT
112740 CTTCAAAGAT
Statistics
Matches: 63, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
31 27 0.43
32 36 0.57
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (32 bp):
GATGTTGAATTCCAAAAAATGCCCCAATATTT
Found at i:112722 original size:31 final size:32
Alignment explanation
Indices: 112655--112746 Score: 132
Period size: 31 Copynumber: 2.9 Consensus size: 32
112645 TCCCAAAGAT
* *
112655 GCCCCAATATTCGATGTTGAATCTCAAAAAAT
1 GCCCCAATATTTGATGTTGAATCTCAAAAAAA
*
112687 GCCCCAATATTTGATGTTAAATCT-AAAAAAA
1 GCCCCAATATTTGATGTTGAATCTCAAAAAAA
*
112718 GCCCCAACATTTGATGTTGAATCTTCAAA
1 GCCCCAATATTTGATGTTGAATC-TCAAA
112747 GATGCTCTCA
Statistics
Matches: 53, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
31 27 0.51
32 23 0.43
33 3 0.06
ACGTcount: A:0.38, C:0.21, G:0.12, T:0.29
Consensus pattern (32 bp):
GCCCCAATATTTGATGTTGAATCTCAAAAAAA
Found at i:113829 original size:14 final size:13
Alignment explanation
Indices: 113801--113858 Score: 55
Period size: 14 Copynumber: 4.2 Consensus size: 13
113791 TCTTGTCTTC
113801 TTTTTTCT-TTATT
1 TTTTTTCTCTT-TT
113814 TTTGTTTCTCTTTT
1 TTT-TTTCTCTTTT
*
113828 TTATTTTCTCTTTG
1 TT-TTTTCTCTTTT
*
113842 CTTTTTCTTCTTTT
1 TTTTTTC-TCTTTT
113856 TTT
1 TTT
113859 CTTTTTTTCC
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
13 8 0.22
14 26 0.70
15 3 0.08
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.79
Consensus pattern (13 bp):
TTTTTTCTCTTTT
Found at i:113856 original size:9 final size:8
Alignment explanation
Indices: 113801--113878 Score: 52
Period size: 9 Copynumber: 9.0 Consensus size: 8
113791 TCTTGTCTTC
113801 TTTTTTCT
1 TTTTTTCT
113809 TTATTTT-T
1 TT-TTTTCT
* *
113817 GTTTCTCT
1 TTTTTTCT
113825 TTTTTAT-T
1 TTTTT-TCT
113833 TTCTCTTTGCT
1 TT-T-TTT-CT
113844 TTTTCTTCT
1 TTTT-TTCT
113853 TTTTTTCT
1 TTTTTTCT
113861 TTTTTTCCT
1 TTTTTT-CT
113870 TTTTGTTCT
1 TTTT-TTCT
113879 GATTGCATCT
Statistics
Matches: 56, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
7 3 0.05
8 21 0.38
9 22 0.39
10 7 0.12
11 3 0.05
ACGTcount: A:0.03, C:0.15, G:0.04, T:0.78
Consensus pattern (8 bp):
TTTTTTCT
Found at i:116926 original size:4 final size:4
Alignment explanation
Indices: 116917--117091 Score: 57
Period size: 4 Copynumber: 43.8 Consensus size: 4
116907 AAAAGGTAAG
* *
116917 AAAT AAAT AAAT AAAT AAAATT AAAAT GAAG AAA- AAAT AAATT AAAT
1 AAAT AAAT AAAT AAAT -AAA-T -AAAT AAAT AAAT AAAT AAA-T AAAT
* * * *
116964 AAA- AGAT AAGAT AAAG AAA- ACAA- AAAT AAA- ATAGT AAGT AAAAT
1 AAAT AAAT AA-AT AAAT AAAT A-AAT AAAT AAAT A-AAT AAAT -AAAT
* * * * * *
117008 AAAT --AT AAAA AAAT AAA- AAAT AAAG AAAA AGAAG AAAA AAAT ATAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT
*
117054 AAAT AAAAC AAAT AAAT AAA- ATAAT -AAT AAA- AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT A-AAT AAAT AAAT AAAT AAA
117092 AATAATATAT
Statistics
Matches: 132, Mismatches: 19, Indels: 40
0.69 0.10 0.21
Matches are distributed among these distances:
2 2 0.02
3 19 0.14
4 84 0.64
5 22 0.17
6 5 0.04
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (4 bp):
AAAT
Found at i:116974 original size:26 final size:26
Alignment explanation
Indices: 116925--117077 Score: 68
Period size: 26 Copynumber: 5.6 Consensus size: 26
116915 AGAAATAAAT
*
116925 AAATAAATAAAATTAAAATGAAGAAA
1 AAATAAATAAAATAAAAATGAAGAAA
*
116951 AAATAAATTAAATAAAAGAT-AAGATAA
1 AAATAAATAAAATAAAA-ATGAAGA-AA
116978 AGAA-AACA-AAAAT-AAAATAGTAAGTAAAA
1 A-AATAA-ATAAAATAAAAAT-G-AAG--AAA
* *
117007 TAAATATAAAAAAATAAAAAATAAAGAAA
1 -AAATA-AATAAAAT-AAAAATGAAGAAA
* *
117036 AAGA-AGAAAAAAATATATAAAT-AA-AAC
1 AA-ATA-AATAAAATA-A-AAATGAAGAAA
117063 AAATAAATAAAATAA
1 AAATAAATAAAATAA
117078 TAATAAAAAA
Statistics
Matches: 101, Mismatches: 7, Indels: 39
0.69 0.05 0.27
Matches are distributed among these distances:
25 3 0.03
26 31 0.31
27 17 0.17
28 20 0.20
29 12 0.12
30 4 0.04
31 9 0.09
33 5 0.05
ACGTcount: A:0.75, C:0.01, G:0.07, T:0.18
Consensus pattern (26 bp):
AAATAAATAAAATAAAAATGAAGAAA
Found at i:117010 original size:32 final size:31
Alignment explanation
Indices: 116914--117061 Score: 108
Period size: 31 Copynumber: 4.7 Consensus size: 31
116904 ATAAAAAGGT
* *
116914 AAGAAATAAATAAAT-AAATAAAA-TTAAAATG
1 AAGAAA-AAA-AAATAAAATAAAAGATAAAATA
* *
116945 AAGAAAAAATAAATTAAATAAAAGATAAGATA
1 AAGAAAAAA-AAATAAAATAAAAGATAAAATA
*
116977 AAGAAAACAAAAATAAAATAGTAAG-TAAAATA
1 AAGAAAA-AAAAATAAAATA-AAAGATAAAATA
* * * *
117009 AATATAAAAAAATAAAAAATAAAGA-AAAA-G
1 AAGAAAAAAAAATAAAATA-AAAGATAAAATA
*
117039 AAGAAAAAAATATATAAATAAAA
1 AAGAAAAAAAAATA-AAATAAAA
117062 CAAATAAATA
Statistics
Matches: 95, Mismatches: 16, Indels: 13
0.77 0.13 0.10
Matches are distributed among these distances:
30 22 0.23
31 36 0.38
32 32 0.34
33 5 0.05
ACGTcount: A:0.74, C:0.01, G:0.07, T:0.18
Consensus pattern (31 bp):
AAGAAAAAAAAATAAAATAAAAGATAAAATA
Found at i:117027 original size:21 final size:21
Alignment explanation
Indices: 117003--117096 Score: 72
Period size: 20 Copynumber: 4.6 Consensus size: 21
116993 AATAGTAAGT
117003 AAAATAAATATAAAAAAATAA
1 AAAATAAATATAAAAAAATAA
* * *
117024 AAAATAAAGA-AAAAGAAGAA
1 AAAATAAATATAAAAAAATAA
* *
117044 AAAA-ATATATAAATAAAACAA
1 AAAATAAATATAAA-AAAATAA
*
117065 ATAAATAAA-AT--AATAATAA
1 A-AAATAAATATAAAAAAATAA
*
117084 AAAATAAAAATAA
1 AAAATAAATATAA
117097 TATATATATA
Statistics
Matches: 56, Mismatches: 10, Indels: 14
0.70 0.12 0.17
Matches are distributed among these distances:
18 7 0.12
19 11 0.20
20 16 0.29
21 15 0.27
22 5 0.09
23 2 0.04
ACGTcount: A:0.79, C:0.01, G:0.03, T:0.17
Consensus pattern (21 bp):
AAAATAAATATAAAAAAATAA
Found at i:117077 original size:18 final size:17
Alignment explanation
Indices: 116917--117092 Score: 65
Period size: 20 Copynumber: 9.5 Consensus size: 17
116907 AAAAGGTAAG
*
116917 AAAT-AAATAAATAAAT
1 AAATAAAATAAAAAAAT
116933 AAAATTAAAATGAAGAAAAAAT
1 -AAA-TAAAAT--A-AAAAAAT
* *
116955 AAATTAAAT-AAAAGAT
1 AAATAAAATAAAAAAAT
*
116971 AAGATAAAGAAAACAAAAAT
1 AA-ATAAA-ATAA-AAAAAT
*
116991 AAAATAGTAAGTAAAATAAAT
1 -AAATA--AAATAAAA-AAAT
*
117012 ATAAAAAAAT-AAAAAAT
1 A-AATAAAATAAAAAAAT
* *
117029 AAAGAAAA-AGAAGAAAAA
1 AAATAAAATA-AA-AAAAT
117047 AATATATAAATAAAACAAAT
1 AA-ATA-AAATAAAA-AAAT
117067 AAATAAAATAATAATAAA-
1 AAATAAAATAA-AA-AAAT
117085 AAATAAAA
1 AAATAAAA
117093 ATAATATATA
Statistics
Matches: 122, Mismatches: 15, Indels: 43
0.68 0.08 0.24
Matches are distributed among these distances:
16 14 0.11
17 14 0.11
18 25 0.20
19 19 0.16
20 26 0.21
21 16 0.13
22 8 0.07
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATAAAATAAAAAAAT
Found at i:117086 original size:38 final size:37
Alignment explanation
Indices: 116974--117096 Score: 90
Period size: 37 Copynumber: 3.2 Consensus size: 37
116964 AAAAGATAAG
* *
116974 ATAAAGAAAAC-AA-AAATAAAATAGTAAGTAAAATAAAT
1 ATAAATAAAACAAATAAATAAAATAATAA-T-AAA-AAAT
* * * * *
117012 ATAAAAAAATAAAAAATAAAGAAAAAGAAGAA-AAAAATAT
1 AT-AAATAA-AACAAATAAA-TAAAATAATAATAAAAA-AT
117052 ATAAATAAAACAAATAAATAAAATAATAATAAAAAAT
1 ATAAATAAAACAAATAAATAAAATAATAATAAAAAAT
*
117089 AAAAATAA
1 ATAAATAA
117097 TATATATATA
Statistics
Matches: 66, Mismatches: 12, Indels: 15
0.71 0.13 0.16
Matches are distributed among these distances:
37 17 0.26
38 16 0.24
39 12 0.18
40 9 0.14
41 2 0.03
42 3 0.05
43 7 0.11
ACGTcount: A:0.76, C:0.02, G:0.05, T:0.17
Consensus pattern (37 bp):
ATAAATAAAACAAATAAATAAAATAATAATAAAAAAT
Found at i:117087 original size:13 final size:13
Alignment explanation
Indices: 117043--117119 Score: 50
Period size: 13 Copynumber: 5.6 Consensus size: 13
117033 AAAAAGAAGA
117043 AAAAAATATATAAAT
1 AAAAAATA-AT-AAT
*
117058 AAAACA-AATAA-
1 AAAAAATAATAAT
*
117069 ATAAAATAATAAT
1 AAAAAATAATAAT
*
117082 AAAAAATAAAAAT
1 AAAAAATAATAAT
*
117095 AATATATATATATATAT
1 AA-A-AAATA-ATA-AT
117112 AAAAAATA
1 AAAAAATA
117120 GTAAATATAT
Statistics
Matches: 48, Mismatches: 8, Indels: 12
0.71 0.12 0.18
Matches are distributed among these distances:
11 4 0.08
12 7 0.15
13 15 0.31
14 2 0.04
15 13 0.27
16 3 0.06
17 4 0.08
ACGTcount: A:0.73, C:0.01, G:0.00, T:0.26
Consensus pattern (13 bp):
AAAAAATAATAAT
Found at i:117087 original size:50 final size:50
Alignment explanation
Indices: 116974--117117 Score: 127
Period size: 50 Copynumber: 2.8 Consensus size: 50
116964 AAAAGATAAG
* *
116974 ATAAAG-AAAACAAAAATAAAATAGTAAGTAAAATAAATATAAAAAAATAAAAA
1 ATAAAGAAAAAGAAAAATAAAATA-T-A-T-AAATAAATACAAAAAAATAAAAA
*
117027 ATAAAGAAAAAGAAGAAA-AAAATATATAAATAAA-ACAAATAAATAAAATA
1 ATAAAGAAAAAGAA-AAATAAAATATATAAATAAATACAAAAAAATAAAA-A
* * * *
117077 ATAATA-AAAAATAAAAATAATATATATATATATATA-AAAAA
1 ATAA-AGAAAAAGAAAAATAAAATATATAAATAAATACAAAAA
117118 TAGTAAATAT
Statistics
Matches: 77, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
49 15 0.19
50 36 0.47
51 3 0.04
52 1 0.01
53 7 0.09
54 12 0.16
55 3 0.04
ACGTcount: A:0.74, C:0.01, G:0.04, T:0.20
Consensus pattern (50 bp):
ATAAAGAAAAAGAAAAATAAAATATATAAATAAATACAAAAAAATAAAAA
Found at i:117189 original size:23 final size:21
Alignment explanation
Indices: 117163--117220 Score: 62
Period size: 23 Copynumber: 2.7 Consensus size: 21
117153 TGATAATAAA
* *
117163 AAAATAATATATATATATAATCT
1 AAAATAATAAAAATATAT-A-CT
*
117186 AAAAAAATAAAAATATATACT
1 AAAATAATAAAAATATATACT
*
117207 AAAATAAAAAAAAT
1 AAAATAATAAAAAT
117221 GCATAAAATG
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
21 14 0.47
22 1 0.03
23 15 0.50
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAATAATAAAAATATATACT
Found at i:117201 original size:21 final size:21
Alignment explanation
Indices: 117175--117220 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 21
117165 AATAATATAT
117175 ATATATAATCTAAAA-AAATAAAA
1 ATATAT-A-CTAAAATAAA-AAAA
117198 ATATATACTAAAATAAAAAAA
1 ATATATACTAAAATAAAAAAA
117219 AT
1 AT
117221 GCATAAAATG
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
21 12 0.55
22 4 0.18
23 6 0.27
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.26
Consensus pattern (21 bp):
ATATATACTAAAATAAAAAAA
Found at i:117210 original size:47 final size:48
Alignment explanation
Indices: 117104--117210 Score: 123
Period size: 45 Copynumber: 2.2 Consensus size: 48
117094 TAATATATAT
**
117104 ATATATATAAAAAATAGTAAATATATATATATATATAAATTAATAAAA
1 ATATATATAAAAAATAGTAAATATATATATATATATAAAAAAATAAAA
* *
117152 CTGATA-ATAAAAAA-A-T-AATATATATATATAATCTAAAAAAATAAAA
1 AT-ATATATAAAAAATAGTAAATATATATATAT-ATATAAAAAAATAAAA
117198 ATATATACTAAAA
1 ATATATA-TAAAA
117211 TAAAAAAAAT
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
45 16 0.32
46 16 0.32
47 6 0.12
48 9 0.18
49 3 0.06
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.32
Consensus pattern (48 bp):
ATATATATAAAAAATAGTAAATATATATATATATATAAAAAAATAAAA
Found at i:117214 original size:26 final size:26
Alignment explanation
Indices: 117048--117218 Score: 103
Period size: 26 Copynumber: 6.7 Consensus size: 26
117038 GAAGAAAAAA
117048 ATATAT-AAATAAAACAAATAAATAAA-
1 ATATATAAAATAAAA-AAAT-AATAAAT
*
117074 ATAATAATAAAA-AATAAAAATAATATAT
1 AT-AT-ATAAAATAA-AAAAATAATAAAT
* *
117102 ATATAT-ATAT-AAAAAATAGTAAAT
1 ATATATAAAATAAAAAAATAATAAAT
* * *
117126 ATATAT-ATATATATAAATTAATAAA-
1 ATATATAAAATA-AAAAAATAATAAAT
* *
117151 ACT-GAT--AATAAAAAAATAATATAT
1 A-TATATAAAATAAAAAAATAATAAAT
**
117175 ATATATAATCTAAAAAAATAA-AAAT
1 ATATATAAAATAAAAAAATAATAAAT
117200 ATATACTAAAATAAAAAAA
1 ATATA-TAAAATAAAAAAA
117219 ATGCATAAAA
Statistics
Matches: 113, Mismatches: 18, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
23 11 0.10
24 27 0.24
25 14 0.12
26 37 0.33
27 9 0.08
28 10 0.09
29 5 0.04
ACGTcount: A:0.67, C:0.02, G:0.01, T:0.29
Consensus pattern (26 bp):
ATATATAAAATAAAAAAATAATAAAT
Found at i:117216 original size:27 final size:26
Alignment explanation
Indices: 117160--117220 Score: 70
Period size: 27 Copynumber: 2.3 Consensus size: 26
117150 AACTGATAAT
* * *
117160 AAAAAAATAATATATATATATAATCT
1 AAAAAAATAAAATATATATAAAATCA
117186 AAAAAAATAAAAATATATACTAAAAT-A
1 AAAAAAAT-AAAATATATA-TAAAATCA
117213 AAAAAAAT
1 AAAAAAAT
117221 GCATAAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
26 8 0.27
27 17 0.57
28 5 0.17
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (26 bp):
AAAAAAATAAAATATATATAAAATCA
Found at i:124421 original size:19 final size:19
Alignment explanation
Indices: 124401--124436 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
124391 TTTAACTTTA
124401 AAATAA-ATTATAAATTAT
1 AAATAATATTATAAATTAT
*
124419 AAATAATATTATTAATTA
1 AAATAATATTATAAATTA
124437 ATCACGTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
AAATAATATTATAAATTAT
Found at i:125317 original size:14 final size:14
Alignment explanation
Indices: 125275--125318 Score: 70
Period size: 14 Copynumber: 3.1 Consensus size: 14
125265 TTCGATTATA
*
125275 TGTTCGTTTATGTT
1 TGTTCATTTATGTT
*
125289 CGTTCATTTATGTT
1 TGTTCATTTATGTT
125303 TGTTCATTTATGTT
1 TGTTCATTTATGTT
125317 TG
1 TG
125319 ATTAGAGGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 27 1.00
ACGTcount: A:0.11, C:0.09, G:0.18, T:0.61
Consensus pattern (14 bp):
TGTTCATTTATGTT
Found at i:125618 original size:14 final size:15
Alignment explanation
Indices: 125591--125628 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
125581 GTTGTTTATT
125591 GTTTCGTTTATGTTC
1 GTTTCGTTTATGTTC
*
125606 GTTT-GTTTGTGTTC
1 GTTTCGTTTATGTTC
125620 GTTTACGTT
1 GTTT-CGTT
125629 CATTTATTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
14 13 0.65
15 4 0.20
16 3 0.15
ACGTcount: A:0.05, C:0.11, G:0.24, T:0.61
Consensus pattern (15 bp):
GTTTCGTTTATGTTC
Found at i:132935 original size:24 final size:24
Alignment explanation
Indices: 132906--132954 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
132896 AAGTTCAAAC
132906 CGTGCATTCTTCTCATTTAGGAAA
1 CGTGCATTCTTCTCATTTAGGAAA
132930 CGTGCATTCTTCTCATTTAGGAAA
1 CGTGCATTCTTCTCATTTAGGAAA
132954 C
1 C
132955 AAAGCTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.24, C:0.22, G:0.16, T:0.37
Consensus pattern (24 bp):
CGTGCATTCTTCTCATTTAGGAAA
Found at i:148941 original size:28 final size:28
Alignment explanation
Indices: 148909--148966 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
148899 TCTCAATTCC
148909 CTATTTATTCTCTCGACTCTCATCGTCT
1 CTATTTATTCTCTCGACTCTCATCGTCT
148937 CTATTTATTCTCTCGACTCTCATCGTCT
1 CTATTTATTCTCTCGACTCTCATCGTCT
148965 CT
1 CT
148967 TAACTCTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.33, G:0.07, T:0.47
Consensus pattern (28 bp):
CTATTTATTCTCTCGACTCTCATCGTCT
Found at i:152355 original size:11 final size:12
Alignment explanation
Indices: 152339--152367 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
152329 GACACTTTAA
152339 TATTAT-GATTT
1 TATTATGGATTT
152350 TATTATGGATTT
1 TATTATGGATTT
152362 TATTAT
1 TATTAT
152368 TCTAGAGTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 6 0.35
12 11 0.65
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (12 bp):
TATTATGGATTT
Found at i:152413 original size:75 final size:75
Alignment explanation
Indices: 152286--152481 Score: 234
Period size: 75 Copynumber: 2.6 Consensus size: 75
152276 TTGATTTGGG
*
152286 TTATTTTTCTAGACTTAATATTATGGTTTGAGTCTT-AAGATTTGACACTTTAATATTAT-GATT
1 TTATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAA-ATTTGACACTTTAATATTATGGATT
*
152349 TTATTATGGATT
65 GT-TTATGGATT
* * * * * *
152361 TTATTATTCTAGAGTTAATATTATGGTTTGAATCTTGAAATTTGATATTTTAATATTGTGGCTTG
1 TTATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACACTTTAATATTATGGATTG
152426 TTTATGGATT
66 TTTATGGATT
* * * * * *
152436 TTATTGTTCTAAACTTAATATTGTTGTTTGAGTCATGATATTTGAC
1 TTATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGAC
152482 TTTATTTATG
Statistics
Matches: 102, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
75 96 0.94
76 6 0.06
ACGTcount: A:0.27, C:0.06, G:0.15, T:0.52
Consensus pattern (75 bp):
TTATTATTCTAGACTTAATATTATGGTTTGAGTCTTGAAATTTGACACTTTAATATTATGGATTG
TTTATGGATT
Found at i:157811 original size:54 final size:54
Alignment explanation
Indices: 157728--157845 Score: 191
Period size: 54 Copynumber: 2.2 Consensus size: 54
157718 ACCCGTCATA
*
157728 GGGAATCAGTTCCCTAAGTGTAAAATTCAAATATTTCGACCGTTAAACAGTGGG
1 GGGAATCGGTTCCCTAAGTGTAAAATTCAAATATTTCGACCGTTAAACAGTGGG
* * *
157782 GGGAATCGGTTCCCTAGGTGTAAATTTCAAATATTTCGACCGTTGAACAGTGGG
1 GGGAATCGGTTCCCTAAGTGTAAAATTCAAATATTTCGACCGTTAAACAGTGGG
*
157836 GAGAATCGGT
1 GGGAATCGGT
157846 ACCCCCTGGG
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
54 59 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (54 bp):
GGGAATCGGTTCCCTAAGTGTAAAATTCAAATATTTCGACCGTTAAACAGTGGG
Found at i:158124 original size:41 final size:40
Alignment explanation
Indices: 158038--158126 Score: 117
Period size: 41 Copynumber: 2.1 Consensus size: 40
158028 AATTTTACAC
*
158038 TTGAGTAAGGATTAAAAATGACTTTTAAAATTAGAGTAATTT
1 TTGA-TAAGGATTAAAAATGACTTTTAAAATTAGAGT-ATGT
*
158080 TTGATAAGGATTAAAAATGACTTTTGAAGATTTAGAGT-TGT
1 TTGATAAGGATTAAAAATGACTTTT-AA-AATTAGAGTATGT
158121 TTGATA
1 TTGATA
158127 TTCGAATATT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
41 29 0.67
42 6 0.14
43 8 0.19
ACGTcount: A:0.39, C:0.02, G:0.19, T:0.39
Consensus pattern (40 bp):
TTGATAAGGATTAAAAATGACTTTTAAAATTAGAGTATGT
Found at i:160644 original size:20 final size:20
Alignment explanation
Indices: 160565--160644 Score: 70
Period size: 20 Copynumber: 3.9 Consensus size: 20
160555 AGAACCCCAG
* * *
160565 GGGGGTATCGATTCCCCTGT
1 GGGGGAATCGATTCCCTTAT
* *
160585 GGGGGAATCGGTTCCCCTTCAAA
1 GGGGGAATCGATT-CCCTT--AT
*
160608 GGGGGAATCGGTTCCCTTAT
1 GGGGGAATCGATTCCCTTAT
*
160628 GGGGGTATCGATTCCCT
1 GGGGGAATCGATTCCCT
160645 CTGCACCAAA
Statistics
Matches: 49, Mismatches: 8, Indels: 6
0.78 0.13 0.10
Matches are distributed among these distances:
20 27 0.55
21 4 0.08
22 5 0.10
23 13 0.27
ACGTcount: A:0.15, C:0.24, G:0.34, T:0.28
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTTAT
Found at i:166445 original size:74 final size:74
Alignment explanation
Indices: 166338--166494 Score: 226
Period size: 74 Copynumber: 2.1 Consensus size: 74
166328 GGAGCGTGGA
* * * *
166338 GGAATAGGTACCCCTCATAGGGAATCGGATCCCTAAGTGTAAAATTTAAATATTTCG-GCAGTTA
1 GGAATCGGTACCCCTAATAGGGAATCGGATCCCTAAGTGTAAAATTCAAATATTTCGACCA-TTA
166402 AACAGTGGGG
65 AACAGTGGGG
* * * *
166412 GGAATCGGTACCCCTAATGGGGAATCGGTTCCCTAGGTGTAAAATTCAAATATTTCGACCATTGA
1 GGAATCGGTACCCCTAATAGGGAATCGGATCCCTAAGTGTAAAATTCAAATATTTCGACCATTAA
166477 ACAGTGGGG
66 ACAGTGGGG
166486 GGAATCGGT
1 GGAATCGGT
166495 TCCCTCCGAG
Statistics
Matches: 74, Mismatches: 8, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
74 72 0.97
75 2 0.03
ACGTcount: A:0.30, C:0.17, G:0.27, T:0.25
Consensus pattern (74 bp):
GGAATCGGTACCCCTAATAGGGAATCGGATCCCTAAGTGTAAAATTCAAATATTTCGACCATTAA
ACAGTGGGG
Found at i:182691 original size:6 final size:6
Alignment explanation
Indices: 182682--182711 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
182672 TTTAATCAAT
182682 GAATTA GAATTA GAATTA GAATTA GAATTA
1 GAATTA GAATTA GAATTA GAATTA GAATTA
182712 TAGATTTCCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.17, T:0.33
Consensus pattern (6 bp):
GAATTA
Found at i:183361 original size:2 final size:2
Alignment explanation
Indices: 183354--183383 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
183344 ACCATATACA
183354 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
183384 GTTTCATGTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:185047 original size:36 final size:36
Alignment explanation
Indices: 185000--185138 Score: 233
Period size: 36 Copynumber: 3.9 Consensus size: 36
184990 ACAGAGCTGG
* * *
185000 ACATTGATACACGAATGTACTAAAGTTGATATAATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
185036 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
185072 ACATTGATACACGAATGTACCAAAGCTGATATGATA
1 ACATTGATACACGAATGTACCAAAGCTGATATGATA
* *
185108 ACATTGATACACGAATGTATCAAAGTTGATA
1 ACATTGATACACGAATGTACCAAAGCTGATA
185139 ATACTCAACT
Statistics
Matches: 98, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 98 1.00
ACGTcount: A:0.42, C:0.14, G:0.16, T:0.27
Consensus pattern (36 bp):
ACATTGATACACGAATGTACCAAAGCTGATATGATA
Found at i:185373 original size:12 final size:12
Alignment explanation
Indices: 185356--185380 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
185346 GCAAGTCGTC
185356 ATCGATCAAAAT
1 ATCGATCAAAAT
185368 ATCGATCAAAAT
1 ATCGATCAAAAT
185380 A
1 A
185381 ATTAAATAAA
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:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (12 bp):
ATCGATCAAAAT
Found at i:185552 original size:16 final size:16
Alignment explanation
Indices: 185531--185562 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
185521 AAATGTTCGA
185531 ACTACATATTAGTATC
1 ACTACATATTAGTATC
185547 ACTACATATTAGTATC
1 ACTACATATTAGTATC
185563 GTACTAATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.19, G:0.06, T:0.38
Consensus pattern (16 bp):
ACTACATATTAGTATC
Found at i:187282 original size:29 final size:29
Alignment explanation
Indices: 187194--187282 Score: 85
Period size: 29 Copynumber: 3.0 Consensus size: 29
187184 TAAAATATAT
*
187194 AACTTTTCAAAATTATAATTTTGGTC-CTTA
1 AACTTTTCAAAATTAT-ATTTTAGTCAC-TA
* *
187224 AACTTTTCAAAATTTATACTTTA-ACTACTA
1 AACTTTTCAAAA-TTATATTTTAGTC-ACTA
187254 AAC-TTTCAAAACTTATATTTTAGTCACTA
1 AACTTTTCAAAA-TTATATTTTAGTCACTA
187283 GAAAAAATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
29 22 0.45
30 22 0.45
31 5 0.10
ACGTcount: A:0.37, C:0.16, G:0.03, T:0.44
Consensus pattern (29 bp):
AACTTTTCAAAATTATATTTTAGTCACTA
Found at i:190502 original size:36 final size:38
Alignment explanation
Indices: 190457--190545 Score: 114
Period size: 36 Copynumber: 2.4 Consensus size: 38
190447 TTTGTATAAT
190457 ATTACAAATTATAAAATATTTATAT-ATTTTTTTAAAAA
1 ATTA-AAATTATAAAATATTTATATAATTTTTTTAAAAA
*
190495 ATT-AAATTCAT--AATATTTATATAATTTTTTTACAAA
1 ATTAAAATT-ATAAAATATTTATATAATTTTTTTAAAAA
*
190531 ATTAAAAATATAAAA
1 ATTAAAATTATAAAA
190546 AAGGTTTAAT
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
35 11 0.25
36 22 0.50
37 6 0.14
38 5 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (38 bp):
ATTAAAATTATAAAATATTTATATAATTTTTTTAAAAA
Found at i:196043 original size:18 final size:18
Alignment explanation
Indices: 196000--196035 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
195990 AAAAATTGGG
196000 TGATTTTAATAAAATATT
1 TGATTTTAATAAAATATT
*
196018 TTATTTTAATAAAATATT
1 TGATTTTAATAAAATATT
196036 GAGTTTTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.03, T:0.53
Consensus pattern (18 bp):
TGATTTTAATAAAATATT
Found at i:197152 original size:22 final size:21
Alignment explanation
Indices: 197114--197205 Score: 55
Period size: 20 Copynumber: 4.1 Consensus size: 21
197104 AAGTTAATAA
* *
197114 AAACATTAAA-AATATAAAAT
1 AAACATAAAATAAAATAAAAT
197134 AAACATAAACATAAAATAAAGACCT
1 AAACATAAA-ATAAAATAAA-A--T
197159 AATTACATAAATATAAAATAATAAT
1 AA--ACATAAA-ATAAAATAA-AAT
* *
197184 -GAC-TAAAATACAATAAAAT
1 AAACATAAAATAAAATAAAAT
197203 AAA
1 AAA
197206 AGTTAGTAAC
Statistics
Matches: 57, Mismatches: 6, Indels: 18
0.70 0.07 0.22
Matches are distributed among these distances:
19 3 0.05
20 17 0.30
21 5 0.09
22 9 0.16
23 1 0.02
25 4 0.07
27 17 0.30
28 1 0.02
ACGTcount: A:0.66, C:0.09, G:0.02, T:0.23
Consensus pattern (21 bp):
AAACATAAAATAAAATAAAAT
Found at i:197228 original size:50 final size:50
Alignment explanation
Indices: 197166--197302 Score: 118
Period size: 51 Copynumber: 2.7 Consensus size: 50
197156 CCTAATTACA
*
197166 TAAATATA-AAATAATAATGACTAAAATACAATAAAATAAAAGT-TAGTAAC
1 TAAATA-AGAAATAAAAATGACTAAAATACAATAAAATAAAA-TATAGTAAC
* * * * *
197216 TAAATAAGAAATAAAAAGTGACCAAAATGCAA-AAATTAAAATAATATTAGC
1 TAAATAAGAAATAAAAA-TGACTAAAATACAATAAAATAAAAT-ATAGTAAC
* * * * *
197267 TAAATAAGAAATTACAGTGACTAAATTAAAATAAAA
1 TAAATAAGAAATAAAAATGACTAAAATACAATAAAA
197303 CAACATCAGC
Statistics
Matches: 68, Mismatches: 14, Indels: 9
0.75 0.15 0.10
Matches are distributed among these distances:
49 2 0.03
50 32 0.47
51 34 0.50
ACGTcount: A:0.61, C:0.07, G:0.08, T:0.24
Consensus pattern (50 bp):
TAAATAAGAAATAAAAATGACTAAAATACAATAAAATAAAATATAGTAAC
Found at i:198579 original size:44 final size:44
Alignment explanation
Indices: 198526--198903 Score: 165
Period size: 44 Copynumber: 8.5 Consensus size: 44
198516 TAAAAATGTG
* * * *
198526 GATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGCTACT
1 GATCCACCTCCTTCTGTGATGGAATCGAACAAAAAGTTGATACT
* * *
198570 GGTCTACCTCCTTCTGTGATAGAATCGAACAAAAAGTTGATACT
1 GATCCACCTCCTTCTGTGATGGAATCGAACAAAAAGTTGATACT
* * * * * * ** * *
198614 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAAA-TAAAAATGT
1 GATCCACCTCCTTCTGTGATGGAATCGAACAAAAAGTTGATA-CT
* * *** * * *
198658 CGAACCACCTCCTTCTATGATGGAATCGAACGGGATGTTGGTGCT
1 -GATCCACCTCCTTCTGTGATGGAATCGAACAAAAAGTTGATACT
* * * * **
198703 GATCTACCTCCTTCTGTGATAGAATC-AAGCTAAAAGTTAACGCT
1 GATCCACCTCCTTCTGTGATGGAATCGAA-CAAAAAGTTGATACT
* * * * * * ** * *
198747 GATCCAACTCCTTCTGCGATAGATTTGAGCAAAAA-TAAAAATGT
1 GATCCACCTCCTTCTGTGATGGAATCGAACAAAAAGTTGATA-CT
* * * * **
198791 CGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCGATGTT
1 -GATCCACCTCCTTCTGTGATGG-AATCGAACAAAAAGTTGATACT
* * *
198837 GATCTACCTCCTTCTGTGATAGAATC-AAGCTAAAAGTT--TACGTT
1 GATCCACCTCCTTCTGTGATGGAATCGAA-CAAAAAGTTGATAC--T
* *
198881 GATCCAACTCCTTCTGCGATGGA
1 GATCCACCTCCTTCTGTGATGGA
198904 TTTGAGCGAA
Statistics
Matches: 238, Mismatches: 84, Indels: 24
0.69 0.24 0.07
Matches are distributed among these distances:
42 1 0.00
43 10 0.04
44 150 0.63
45 66 0.28
46 9 0.04
47 2 0.01
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.29
Consensus pattern (44 bp):
GATCCACCTCCTTCTGTGATGGAATCGAACAAAAAGTTGATACT
Found at i:198803 original size:45 final size:45
Alignment explanation
Indices: 198747--198941 Score: 117
Period size: 45 Copynumber: 4.4 Consensus size: 45
198737 AGTTAACGCT
* * *
198747 GATCCAACTCCTTCTGCGATAGATTTGAGCAAAAATAAAAATGTC
1 GATCCACCTCCTTCTGCGATAGAATCGAGCAAAAATAAAAATGTC
* * * * * **** *
198792 GATCCACCTCCTTCTGTGATGGAAATCGAAC-GATATGTCGATGTT
1 GATCCACCTCCTTCTGCGATAG-AATCGAGCAAAAATAAAAATGTC
* * * * ** * *
198837 GATCTACCTCCTTCTGTGATAGAATCAAGCTAAAAGT--TTACGTT
1 GATCCACCTCCTTCTGCGATAGAATCGAGC-AAAAATAAAAATGTC
* * * * *
198881 GATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAAATGTC
1 GATCCACCTCCTTCTGCGATAGAATCGAGCAAAAATAAAAATGTC
198926 GATCCACCTCCTTCTG
1 GATCCACCTCCTTCTG
198942 TGATGTAAAT
Statistics
Matches: 108, Mismatches: 37, Indels: 10
0.70 0.24 0.06
Matches are distributed among these distances:
43 4 0.04
44 33 0.31
45 64 0.59
46 7 0.06
ACGTcount: A:0.30, C:0.23, G:0.18, T:0.30
Consensus pattern (45 bp):
GATCCACCTCCTTCTGCGATAGAATCGAGCAAAAATAAAAATGTC
Found at i:198898 original size:134 final size:133
Alignment explanation
Indices: 198393--198980 Score: 844
Period size: 133 Copynumber: 4.4 Consensus size: 133
198383 AATGAAAACA
* * * *
198393 TCGATCC-TCTCCTTCTGTGATGGAATCGAACGAGATGTCGGTACTGATCTACCTCCTTCTATGA
1 TCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
* * *
198457 TAGAATCGAGCTAAAAGTTGACGTTGATCCAACTCCTTCTGCGAT-GATTTGAGTGAAAATAAAA
66 TAGAATCAAGCTAAAAGTTTACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAA
198521 ATG
131 ATG
* * * * *
198524 TGGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTTGCTACTGGTCTACCTCCTTCTGTGA
1 TCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
*
198589 TAGAATCGAA-CAAAAAGTTGATAC--TGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
66 TAGAATC-AAGCTAAAAGTT--TACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATA
198651 AAAATG
128 AAAATG
* * * * *
198657 TCGAACCACCTCCTTCTATGATGGAATCGAACGGGATGTTGGTGCTGATCTACCTCCTTCTGTGA
1 TCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
* * * *
198722 TAGAATCAAGCTAAAAGTTAACGCTGATCCAACTCCTTCTGCGATAGATTTGAGCAAAAATAAAA
66 TAGAATCAAGCTAAAAGTTTACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAA
198787 ATG
131 ATG
* *
198790 TCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCGATGTTGATCTACCTCCTTCTGTG
1 TCGATCCACCTCCTTCTGTGATGG-AATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTG
198855 ATAGAATCAAGCTAAAAGTTTACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAA
65 ATAGAATCAAGCTAAAAGTTTACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAA
198920 AATG
130 AATG
* * * *
198924 TCGATCCACCTCCTTCTGTGATGTAAATCGAACGATATGTCAATGTTGATCTACCTC
1 TCGATCCACCTCCTTCTGTGATG-GAATCGAACGAGATGTCGATGCTGATCTACCTC
198981 ATTGTAACAC
Statistics
Matches: 413, Mismatches: 34, Indels: 17
0.89 0.07 0.04
Matches are distributed among these distances:
131 8 0.02
132 90 0.22
133 159 0.38
134 156 0.38
ACGTcount: A:0.29, C:0.22, G:0.20, T:0.30
Consensus pattern (133 bp):
TCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGCTGATCTACCTCCTTCTGTGA
TAGAATCAAGCTAAAAGTTTACGTTGATCCAACTCCTTCTGCGATGGATTTGAGCGAAAATAAAA
ATG
Found at i:198969 original size:45 final size:45
Alignment explanation
Indices: 198786--198980 Score: 137
Period size: 45 Copynumber: 4.4 Consensus size: 45
198776 CAAAAATAAA
* * *
198786 AATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTC
1 AATGTTGATCCACCTCCTTCTGTGATGTAAATCGAACGAAATGTC
* * * * *
198831 GATGTTGATCTACCTCCTTCTGTGA--TAGAATC-AAGCTAAAAGTT
1 AATGTTGATCCACCTCCTTCTGTGATGTA-AATCGAA-CGAAATGTC
* * * * * * * * ***
198875 TACGTTGATCCAACTCCTTCTGCGATG-GATTTGAGCGAAAATAAA
1 AATGTTGATCCACCTCCTTCTGTGATGTAAATCGAACG-AAATGTC
* *
198920 AATGTCGATCCACCTCCTTCTGTGATGTAAATCGAACGATATGTC
1 AATGTTGATCCACCTCCTTCTGTGATGTAAATCGAACGAAATGTC
*
198965 AATGTTGATCTACCTC
1 AATGTTGATCCACCTC
198981 ATTGTAACAC
Statistics
Matches: 106, Mismatches: 37, Indels: 14
0.68 0.24 0.09
Matches are distributed among these distances:
43 3 0.03
44 32 0.30
45 65 0.61
46 6 0.06
ACGTcount: A:0.28, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
AATGTTGATCCACCTCCTTCTGTGATGTAAATCGAACGAAATGTC
Found at i:199683 original size:23 final size:23
Alignment explanation
Indices: 199657--199701 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
199647 CACCACAGCT
* *
199657 CGTATAATTGCACCGAAGTGCCG
1 CGTAGAATTACACCGAAGTGCCG
*
199680 CGTAGAATTACACCGTAGTGCC
1 CGTAGAATTACACCGAAGTGCC
199702 ATATAATAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (23 bp):
CGTAGAATTACACCGAAGTGCCG
Found at i:199939 original size:149 final size:149
Alignment explanation
Indices: 199669--199983 Score: 578
Period size: 149 Copynumber: 2.1 Consensus size: 149
199659 TATAATTGCA
*
199669 CCGAAGTG-CCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTA
1 CCGAAG-GACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAAGACCACATATTA
199733 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
65 TTCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTT
*
199798 CCAAAGAATATATATATGTC
130 CCAAAGAATATACATATGTC
* *
199818 CCGAAGGACCGCGTAGAATTGCACCGTAGTGTCATATAATAATGTCCATAAAGACCACATATTAT
1 CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAAGACCACATATTAT
199883 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
66 TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
199948 CAAAGAATATACATATGTC
131 CAAAGAATATACATATGTC
199967 CCGAAGGACCGCGTAGA
1 CCGAAGGACCGCGTAGA
199984 CCCTCGACTC
Statistics
Matches: 161, Mismatches: 4, Indels: 2
0.96 0.02 0.01
Matches are distributed among these distances:
148 1 0.01
149 160 0.99
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.28
Consensus pattern (149 bp):
CCGAAGGACCGCGTAGAATTACACCGTAGTGCCATATAATAATGTCCATAAAGACCACATATTAT
TCCTTAAGAATCATATACATATACTAGGGATCAAGTATGTGTCTTTCAAGACTTCACACATGTTC
CAAAGAATATACATATGTC
Found at i:201472 original size:21 final size:21
Alignment explanation
Indices: 201448--201492 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
201438 TGTTGTTCGT
* *
201448 TTGAAGGGGTATCGGTTCCCC
1 TTGAAGGGGTACCGATTCCCC
*
201469 TTGAATGGGTACCGATTCCCC
1 TTGAAGGGGTACCGATTCCCC
201490 TTG
1 TTG
201493 CCCAGAAATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.24, G:0.29, T:0.31
Consensus pattern (21 bp):
TTGAAGGGGTACCGATTCCCC
Found at i:202334 original size:44 final size:44
Alignment explanation
Indices: 202275--203270 Score: 361
Period size: 44 Copynumber: 22.6 Consensus size: 44
202265 AAATGTCGAC
* * * *
202275 CCACCTCCTTTTGTGATGGAATCGAGCGAAATGTTGGTGATGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * ** * *
202319 CTACCTCATTATGTGATAGAATCGAGTAAAAAGTTGAAGTTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * ****
202363 CCAACTCATTCTGCGATGGATTTGAGCGAAAATAAAAATGTTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCG-AAATGTTGATGTTGAT
* * * * * *
202408 CCATCTTATTCTGTAATGGAATCGAGCGAGATGTTGGTGATGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * *
202452 CTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * **** *
202496 CCAACTCATTCTGTGATGGATTTGAGCGAAAATAAAAATGTCGAT
1 CCACCTCATTCTGTGATGGAATCGAGCG-AAATGTTGATGTTGAT
* * * **
202541 CCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGTTGAT
1 CCACCTCATTCTGTGATGG-AATCGAGCGAAATGTTGATGTTGAT
* * * * * * *
202586 CTACCTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * ** * * * *
202630 CCAACTCCTTCTGCGATGGATTTTAGTGAACA----AATGTCGAC
1 CCACCTCATTCTGTGATGGAATCGAGCGAA-ATGTTGATGTTGAT
* * * * * *
202671 CCACCTCCTTTTGTGATTGAATCAAGCGAAATGTTGGTGATGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * *
202715 CTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * * ****
202759 CCAACACATTCTGCGATGGATTTGAGCGAAAATAAAAAATGTTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCG-AAAT-GTTGATGTTGAT
* * * * * *
202805 CCATCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * * * * *
202849 CTACCTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACGCTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * * * **** *
202893 CCAACTCCTTCTGCGATGGATTTGAGCAAAAATAAAAATGTCGAT
1 CCACCTCATTCTGTGATGGAATCGAGC-GAAATGTTGATGTTGAT
* * * * * **
202938 CCACCTCCTTCTGTGATGTAATCGAACGAGATGTCGATACTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
** * * * * **
202982 TTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCAGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * ** * * **** * *
203026 CCAACTCCTTCTACGATGGATTTGAGCGAAAATAAAAATATCGAT
1 CCACCTCATTCTGTGATGGAATCGAGCG-AAATGTTGATGTTGAT
* * * * * * * *
203071 CAATCTCCTTCTATGATGGAATCGAACGAGATGTCGATGCTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * * * ***
203115 CTACCTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACACTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * * * * * *
203159 CCAACTCCTTCTGCGATGGATTTGAGCGAACA----AATGTCGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAA-ATGTTGATGTTGAT
* * ** * * *
203200 CCACCTCCTTCTATGATGGAATTAAACGAAATGTTGGTGCTGAT
1 CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
* * *
203244 CTACCTCATTTTGTGATAGAATCGAGC
1 CCACCTCATTCTGTGATGGAATCGAGC
203271 AAACAATTTA
Statistics
Matches: 656, Mismatches: 279, Indels: 34
0.68 0.29 0.04
Matches are distributed among these distances:
40 2 0.00
41 54 0.08
44 414 0.63
45 152 0.23
46 34 0.05
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Consensus pattern (44 bp):
CCACCTCATTCTGTGATGGAATCGAGCGAAATGTTGATGTTGAT
Found at i:202467 original size:133 final size:133
Alignment explanation
Indices: 202194--203273 Score: 1396
Period size: 133 Copynumber: 8.2 Consensus size: 133
202184 GGATGTTACA
* * *
202194 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTATGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * * * * *
202259 GTG---A-ACAAATGTCGACCCACCTCCTTTTGTGATGGAATCGAGCGAAATGTTGGTGATGATC
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATC
202320 TAC
131 TAC
* * * * *
202323 CTCATTATGTGATAGAATCGAGTAAAAAGTTGAAGTTGATCCAACTCATTCTGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * ** * * * *
202388 GCGAAAATAAAAATGTTGATCCATCTTATTCTGTAATGGAATCGAGCGAGATGTTGGTGATGATC
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATC
202453 TAC
131 TAC
* * *
202456 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCATTCTGTGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * *
202521 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGTTGAT
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGG-AATCGAACGAGATGTCGATGATGAT
202586 CTAC
130 CTAC
* * *
202590 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTTA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * * * * *
202655 GTG---A-ACAAATGTCGACCCACCTCCTTTTGTGATTGAATC-AAGCGAAATGTTGGTGATGAT
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAA-CGAGATGTCGATGATGAT
202715 CTAC
130 CTAC
* * *
202719 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACACATTCTGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* *
202784 GCGAAAATAAAAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGAT
66 GCGAAAAT-AAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGAT
202849 CTAC
130 CTAC
* *
202853 CTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* *
202918 GCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGTAATCGAACGAGATGTCGAT-ACTGAT
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGA-TGAT
*
202982 TTAC
130 CTAC
* *
202986 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCAGATCCAACTCCTTCTACGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * *
203051 GCGAAAATAAAAATATCGATCAATCTCCTTCTATGATGGAATCGAACGAGATGTCGATGCTGATC
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATC
203116 TAC
131 TAC
* * *
203119 CTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * ** * * * *
203184 GCG---A-ACAAATGTCGATCCACCTCCTTCTATGATGGAATTAAACGAAATGTTGGTGCTGATC
66 GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATC
203245 TAC
131 TAC
*
203248 CTCATTTTGTGATAGAATCGAGCAAA
1 CTCATTCTGTGATAGAATCGAGCAAA
203274 CAATTTATCA
Statistics
Matches: 833, Mismatches: 104, Indels: 28
0.86 0.11 0.03
Matches are distributed among these distances:
128 2 0.00
129 215 0.26
130 28 0.03
131 1 0.00
132 3 0.00
133 383 0.46
134 199 0.24
135 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (133 bp):
CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
GCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATC
TAC
Found at i:202963 original size:396 final size:397
Alignment explanation
Indices: 202194--203273 Score: 1555
Period size: 396 Copynumber: 2.7 Consensus size: 397
202184 GGATGTTACA
*
202194 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTATGCGATGGATTTGA
1 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
*
202259 GTGAACAAATGTCGACCCACCTCCTTTTGTGATGGAATCGAGCGAAATGTTGGTGATGATCTACC
66 GTGAACAAATGTCGACCCACCTCCTTTTGTGATGGAATCAAGCGAAATGTTGGTGATGATCTACC
* * *
202324 TCATTATGTGATAGAATCGAGTAAAAAGTTGAAGTTGATCCAACTCATTCTGCGATGGATTTGAG
131 TCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCATTCTGCGATGGATTTGAG
** * *
202389 CGAAAAT-AAAAATGTTGATCCATCTTATTCTGTAATGGAATCGAGCGAGATGTTGGTGATGATC
196 CGAAAATAAAAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGATGATC
* *
202453 TACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCATTCTGTGATGGATT
261 TACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCATTCTGCGATGGATT
* * **
202518 TGAGCGAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGATATGTCAATGTT
326 TGAGCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGAGATGTCAATACT
202583 GATCTAC
391 GATCTAC
*
202590 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTTA
1 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
*
202655 GTGAACAAATGTCGACCCACCTCCTTTTGTGATTGAATCAAGCGAAATGTTGGTGATGATCTACC
66 GTGAACAAATGTCGACCCACCTCCTTTTGTGATGGAATCAAGCGAAATGTTGGTGATGATCTACC
*
202720 TCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACACATTCTGCGATGGATTTGAG
131 TCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCATTCTGCGATGGATTTGAG
* *
202785 CGAAAATAAAAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACGAGATGTCGATGATGATC
196 CGAAAATAAAAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGATGATC
* * *
202850 TACCTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATT
261 TACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCATTCTGCGATGGATT
* *
202915 TGAGCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGAT-GTAATCGAACGAGATGTCGATACT
326 TGAGCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGAGATGTCAATACT
*
202979 GATTTAC
391 GATCTAC
* * * *
202986 CTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCAGATCCAACTCCTTCTACGATGGATTTGA
1 CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
* * * * * * * * * * * *
203051 GCGAAAATAAAAATATCGATCAATCTCCTTCTATGATGGAATCGAA-CGAGATGTCGATGCTGAT
66 GTG---A-ACAAATGTCGACCCACCTCCTTTTGTGATGGAATC-AAGCGAAATGTTGGTGATGAT
* * ** *
203115 CTACCTCCTTCTGTGATAGAATCTAGCAAAAAGTTGACACTGATCCAACTCCTTCTGCGATGGAT
126 CTACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCATTCTGCGATGGAT
* * * * ** * *
203180 TTGAGCG-----AACAAATGTCGATCCACCTCCTTCTATGATGGAATTAAACGAAATGTTGGTGC
191 TTGAGCGAAAATAAAAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGA
*
203240 TGATCTACCTCATTTTGTGATAGAATCGAGCAAA
256 TGATCTACCTCATTCTGTGATAGAATCGAGCAAA
203274 CAATTTATCA
Statistics
Matches: 615, Mismatches: 63, Indels: 13
0.89 0.09 0.02
Matches are distributed among these distances:
395 74 0.12
396 281 0.46
397 150 0.24
399 1 0.00
400 107 0.17
401 2 0.00
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.30
Consensus pattern (397 bp):
CTCATTCTGTGATAGAATCAAGCTAAAAGTTGACGCTGATCCAACTCCTTCTGCGATGGATTTGA
GTGAACAAATGTCGACCCACCTCCTTTTGTGATGGAATCAAGCGAAATGTTGGTGATGATCTACC
TCATTCTGTGATAGAATCGAGCAAAAAGTTGACGTTGATCCAACTCATTCTGCGATGGATTTGAG
CGAAAATAAAAAATGTTGATCCATCTCCTTCTGTGATGGAATCGAACGAGATGTTGGTGATGATC
TACCTCATTCTGTGATAGAATCGAGCAAAAAGTTGACGCTGATCCAACTCATTCTGCGATGGATT
TGAGCAAAAATAAAAATGTCGATCCACCTCCTTCTGTGATGGAAATCGAACGAGATGTCAATACT
GATCTAC
Found at i:203649 original size:40 final size:38
Alignment explanation
Indices: 203573--203673 Score: 109
Period size: 40 Copynumber: 2.7 Consensus size: 38
203563 GAATAAGAAA
* * *
203573 CTTGTTTTAAGAGAAACT-ATCTCGAGTGAGATAAAATTT
1 CTTGTTTTAAGAGAAACTGA-CTCAAGAGAGACAAAA-TT
*
203612 CTTGTTTCAAGAGAAAACTGACTCAAGAGAGACAAAATT
1 CTTGTTTTAAGAG-AAACTGACTCAAGAGAGACAAAATT
*
203651 C--GTTTTAAGAGAAACTGTCTCAA
1 CTTGTTTTAAGAGAAACTGACTCAA
203674 AGGTTGGTGC
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
36 11 0.20
37 9 0.17
39 15 0.28
40 18 0.33
41 1 0.02
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (38 bp):
CTTGTTTTAAGAGAAACTGACTCAAGAGAGACAAAATT
Found at i:203813 original size:67 final size:65
Alignment explanation
Indices: 203614--203852 Score: 191
Period size: 65 Copynumber: 3.6 Consensus size: 65
203604 TAAAATTTCT
* * * * *
203614 TGTTTCAAGAGAAAACTGA-CTCAAGAGAGACAAAA-TTCGTTTTAAGAGAAACTGTCTCAAAGG
1 TGTTTCAAGAG-AAACT-ATCTCAAGAGAGACAAAACTT-GTTTCAAGAGAAACAGACTCAGA-T
*
203677 TTGG
62 TTTG
* * * ** * * **
203681 TGCTTCAAGAG-AACTGTCTCAGGAGAGACAAAACAAGTTTCAAGGGAAACCATCACAAAGATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGAGAAA-CA-GACTCAGATTT
203745 TG
64 TG
203747 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTTGTTTCAAGAGAAACAGACTCAGACTTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAAC-TTGTTTCAAGAGAAACAGACTCAGA-TTT
203812 TG
64 TG
* * * * *
203814 T-TTT-GAGAAAAACTGTCTCAAAAGATACAAAACTTGTTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTT
203853 TGAGTAAAAA
Statistics
Matches: 136, Mismatches: 29, Indels: 17
0.75 0.16 0.09
Matches are distributed among these distances:
64 6 0.04
65 54 0.40
66 22 0.16
67 42 0.31
68 12 0.09
ACGTcount: A:0.39, C:0.15, G:0.19, T:0.26
Consensus pattern (65 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAACTTGTTTCAAGAGAAACAGACTCAGATTTTG
Found at i:203881 original size:37 final size:36
Alignment explanation
Indices: 203811--203882 Score: 90
Period size: 37 Copynumber: 2.0 Consensus size: 36
203801 ACTCAGACTT
* *
203811 TTGTTTTGAGAAAAACTGTCTCAAAAGATACAAAAC
1 TTGTTTTGAGAAAAACTATCTCAAAAGAGACAAAAC
* **
203847 TTGTTTTGAGTAAAAATTATCTCAAGTGAGACAAAA
1 TTGTTTTGAG-AAAAACTATCTCAAAAGAGACAAAA
203883 TTCATTTTTT
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 10 0.33
37 20 0.67
ACGTcount: A:0.43, C:0.11, G:0.15, T:0.31
Consensus pattern (36 bp):
TTGTTTTGAGAAAAACTATCTCAAAAGAGACAAAAC
Found at i:204085 original size:90 final size:90
Alignment explanation
Indices: 203925--204299 Score: 574
Period size: 90 Copynumber: 4.2 Consensus size: 90
203915 TGAAAATCAT
* *
203925 GCTTAGTTTCTAAAAACTCATTTGAAAACATCCAGCACT-AAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAAGA
*
203989 CTTACAAATCAAGAAACCCCTGAAG
66 CTTACAAATCAAGAAACCCCTAAAG
* * *
204014 GCTCAATTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAGGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAAGA
204079 CTTACAAATCAAGAAACCCCTAAAG
66 CTTACAAATCAAGAAACCCCTAAAG
* *
204104 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCTGCACTGAAGGTCTTATGGATGGCCTGAAAGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAAGA
*
204169 CTTATAAATCAAGAAACCTCC-AAAG
66 CTTACAAATCAAGAAACC-CCTAAAG
* * *
204194 GCTTAGTTTCTAAAATATCATTTGAAAACATCCTGCACTAAAGGTCTTATGGATGGCCCGAAAGA
1 GCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAAGA
** **
204259 CTTACAAATTGAGAAACCCCCGAAG
66 CTTACAAATCAAGAAACCCCTAAAG
204284 GCTTAGTTTCTTAAAA
1 GCTTAGTTTC-TAAAA
204300 AATCTTTTGA
Statistics
Matches: 265, Mismatches: 17, Indels: 6
0.92 0.06 0.02
Matches are distributed among these distances:
89 38 0.14
90 220 0.83
91 7 0.03
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (90 bp):
GCTTAGTTTCTAAAATCTCATTTGAAAACATCCAGCACTGAAGGTCTTATGGATGGCCCGAAAGA
CTTACAAATCAAGAAACCCCTAAAG
Found at i:206304 original size:17 final size:16
Alignment explanation
Indices: 206283--206325 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
206273 TTCGTCTCTC
206283 TTTTCTTTTCTT-TTTT
1 TTTTCTTTT-TTGTTTT
206299 TGTTTCTTTTTTGTTTT
1 T-TTTCTTTTTTGTTTT
206316 TTTATCTTTT
1 TTT-TCTTTT
206326 ATCTTCTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 5 0.21
17 19 0.79
ACGTcount: A:0.02, C:0.09, G:0.05, T:0.84
Consensus pattern (16 bp):
TTTTCTTTTTTGTTTT
Found at i:207558 original size:20 final size:20
Alignment explanation
Indices: 207529--207566 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
207519 GATACAAAAA
207529 ATGCACATGCAAATGCAAAG
1 ATGCACATGCAAATGCAAAG
*
207549 ATGCATATGCAAATGCAA
1 ATGCACATGCAAATGCAA
207567 CCCGATATTG
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:0.45, C:0.18, G:0.18, T:0.18
Consensus pattern (20 bp):
ATGCACATGCAAATGCAAAG
Found at i:209025 original size:30 final size:30
Alignment explanation
Indices: 208989--209052 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
208979 GAAGGACCTG
* *
208989 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
209019 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
209049 TCCA
1 TCCA
209053 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:209882 original size:64 final size:64
Alignment explanation
Indices: 209732--209884 Score: 161
Period size: 64 Copynumber: 2.4 Consensus size: 64
209722 CAATGAAAGT
* * * ** *
209732 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCT-ATGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * *
209796 ATGCATCGATGCA-TTCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
209859 AG
63 AG
209861 -TGCATCGATGCACTACCTATGCAT
1 ATGCATCGATGCACTACCTATGCAT
209885 TGATACACCT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
63 1 0.01
64 58 0.78
65 15 0.20
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTATGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:210884 original size:3 final size:3
Alignment explanation
Indices: 210876--210900 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
210866 TTGTACTTGG
210876 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
210901 TTCTTCCTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:213809 original size:30 final size:30
Alignment explanation
Indices: 213773--213836 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
213763 GAAGGACCTG
* *
213773 TCCAGAGGTTACAAAGAACCCCGGTAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
* * *
213803 TCCAGAGGTCATAAAGATCCTCGGCAACTA
1 TCCAGAGGTCACAAAGAACCCCGGCAACTA
213833 TCCA
1 TCCA
213837 TATGTTCCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.34, C:0.28, G:0.19, T:0.19
Consensus pattern (30 bp):
TCCAGAGGTCACAAAGAACCCCGGCAACTA
Found at i:214666 original size:64 final size:64
Alignment explanation
Indices: 214516--214668 Score: 161
Period size: 64 Copynumber: 2.4 Consensus size: 64
214506 CAATGAAAGT
* * * ** *
214516 ATGCATCGATGCACTA-CTGATGCATCGGTGCATAAAATGCATTCGATGTTGTATTATCACTGGG
1 ATGCATCGATGCACTACCT-ATGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
* * *
214580 ATGCATCGATGCA-TTCCTTATGCATCGATGCACT-AATTGCATTCGATGTTTCTATTTTAAAAG
1 ATGCATCGATGCACTACC-TATGCATCGATGCA-TAAAATGCATTCGATG-TTCTATTATAAAAG
214643 AG
63 AG
214645 -TGCATCGATGCACTACCTATGCAT
1 ATGCATCGATGCACTACCTATGCAT
214669 TGATACACCT
Statistics
Matches: 74, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
63 1 0.01
64 58 0.78
65 15 0.20
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACCTATGCATCGATGCATAAAATGCATTCGATGTTCTATTATAAAAGAG
Found at i:217717 original size:50 final size:49
Alignment explanation
Indices: 217663--217799 Score: 125
Period size: 51 Copynumber: 2.7 Consensus size: 49
217653 CCTAATTACA
*
217663 TAAATATAAAATAATAATGACTAAAATACAATAAAATAAAAGT-TAGTAAC
1 TAAATA-AAAATAAAAATGACTAAAATACAATAAAATAAAA-TATAGTAAC
* * * *
217713 TAAATAAGAAATAAAAAGTGACCAAAATGCAA-AAATTAAAATAATAGTAGC
1 TAAATAA-AAATAAAAA-TGACTAAAATACAATAAAATAAAAT-ATAGTAAC
* * * *
217764 TAAATCAAAAATTACAATGACTAAATTAAAATAAAA
1 TAAAT-AAAAATAAAAATGACTAAAATACAATAAAA
217800 CAACATCAGC
Statistics
Matches: 69, Mismatches: 12, Indels: 11
0.75 0.13 0.12
Matches are distributed among these distances:
49 2 0.03
50 32 0.46
51 33 0.48
52 2 0.03
ACGTcount: A:0.62, C:0.07, G:0.07, T:0.23
Consensus pattern (49 bp):
TAAATAAAAATAAAAATGACTAAAATACAATAAAATAAAATATAGTAAC
Found at i:217937 original size:61 final size:60
Alignment explanation
Indices: 217863--217993 Score: 158
Period size: 60 Copynumber: 2.2 Consensus size: 60
217853 CTAGGGATTT
* * *
217863 ATGCGTGATTTACCCATTAATA-TA-TAACTAAACGTGTAATACACTAAATAGGGAGGACTTG
1 ATGCGTGATTTACCC-TTAA-ACTAGTAACT-AACGTGAAACACACTAAACAGGGAGGACTTG
* * * *
217924 ATGTGTGATTTACCCTTAAACTAGTAACTAACGTGAAACATACTAGACATGGAGGACTTG
1 ATGCGTGATTTACCCTTAAACTAGTAACTAACGTGAAACACACTAAACAGGGAGGACTTG
217984 ATGCGTGATT
1 ATGCGTGATT
217994 AGCCCAAAAC
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
59 1 0.02
60 40 0.67
61 19 0.32
ACGTcount: A:0.35, C:0.15, G:0.20, T:0.30
Consensus pattern (60 bp):
ATGCGTGATTTACCCTTAAACTAGTAACTAACGTGAAACACACTAAACAGGGAGGACTTG
Found at i:220267 original size:31 final size:30
Alignment explanation
Indices: 220225--220319 Score: 109
Period size: 31 Copynumber: 3.1 Consensus size: 30
220215 GATCACACCA
* *
220225 ATAGCGGCGGATCACGATCGTAATTTAACGG
1 ATAGCGACGGATCGCGA-CGTAATTTAACGG
* *
220256 ATAGCGACGGATCGCGGCCGTAATTTAACGA
1 ATAGCGACGGATCGC-GACGTAATTTAACGG
* *
220287 ATAGCGATGAATCGCGACTGTAATTTAACGG
1 ATAGCGACGGATCGCGAC-GTAATTTAACGG
220318 AT
1 AT
220320 GGTGGCCAAT
Statistics
Matches: 54, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
30 2 0.04
31 51 0.94
32 1 0.02
ACGTcount: A:0.31, C:0.19, G:0.27, T:0.23
Consensus pattern (30 bp):
ATAGCGACGGATCGCGACGTAATTTAACGG
Found at i:225985 original size:3 final size:3
Alignment explanation
Indices: 225967--226031 Score: 71
Period size: 3 Copynumber: 21.0 Consensus size: 3
225957 GTTTGGTTAG
*
225967 TAA TATA TATA TAA TAA TAA T-A TATA TAA TAA TAA TAT TAA TAA TAA
1 TAA TA-A TA-A TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TAA
226014 TAA T-A TAAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA
226032 AGAGAAGAAT
Statistics
Matches: 55, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
2 4 0.07
3 39 0.71
4 12 0.22
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:225991 original size:15 final size:15
Alignment explanation
Indices: 225967--226031 Score: 98
Period size: 15 Copynumber: 4.4 Consensus size: 15
225957 GTTTGGTTAG
225967 TAAT-ATATATATAA
1 TAATAATATATATAA
225981 TAATAATATATATAA
1 TAATAATATATATAA
225996 TAATAATAT-TAATAA
1 TAATAATATAT-ATAA
*
226011 TAATAATATAAATAA
1 TAATAATATATATAA
226026 TAATAA
1 TAATAA
226032 AGAGAAGAAT
Statistics
Matches: 47, Mismatches: 1, Indels: 5
0.89 0.02 0.09
Matches are distributed among these distances:
14 5 0.11
15 42 0.89
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
TAATAATATATATAA
Found at i:228197 original size:105 final size:105
Alignment explanation
Indices: 227881--228973 Score: 1837
Period size: 105 Copynumber: 10.4 Consensus size: 105
227871 GTATTGCTCC
* * * * * *
227881 GAGTCCAATATCCTCCGCTGTGAAGTTGAAACTGGTTCTGGAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAA
* * * *
227946 CTAACGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCCG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * **
227987 GAGTCCAGTATCATTCGTTGTGAAGTTGAAATTGGCTCTTGAAATTGAGAAGTTGTCGGTTGACA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC-TGAAATTGAGAA-ATGTTTGTTGACA
** * *** *
228052 GTCAGCGGTCCCTTCGTCATGAAGTTGAACTTGTACTGTCTT
64 ACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
228094 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
228159 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
228199 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGACATTGAGAAATATTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
228264 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
228304 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
228369 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
228409 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTATTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
228474 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
228514 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
228579 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
228619 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAAT-TTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
228683 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
228723 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGAAATCGAGAAATGTTTGTTGACAAC
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
*
228788 CAGCGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTG
66 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* *
228828 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGACTCTGGAATTTGAGAAATGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCT-GAAATTGAGAAATGTTTGTTGACAA
228893 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
65 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
228934 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTG
228974 GGTAAAACCT
Statistics
Matches: 934, Mismatches: 49, Indels: 9
0.94 0.05 0.01
Matches are distributed among these distances:
104 104 0.11
105 596 0.64
106 145 0.16
107 89 0.10
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.34
Consensus pattern (105 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAAC
CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:236420 original size:20 final size:21
Alignment explanation
Indices: 236395--236433 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
236385 TCTTCTAATA
*
236395 TTTTTTATCTTT-TCTTCCAT
1 TTTTTTAGCTTTATCTTCCAT
236415 TTTTTTAGCTTTATCTTCC
1 TTTTTTAGCTTTATCTTCC
236434 TCGTCAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (21 bp):
TTTTTTAGCTTTATCTTCCAT
Found at i:240717 original size:3 final size:3
Alignment explanation
Indices: 240699--240754 Score: 62
Period size: 3 Copynumber: 18.0 Consensus size: 3
240689 GTTTGGTTAG
240699 TAA TATA TATA TAA TAA TAA TAA TAA T-A TAAA TAA TAA TAA T-A TAAA
1 TAA TA-A TA-A TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA T-AA
240746 TAA TAA TAA
1 TAA TAA TAA
240755 AGAGAAGAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
2 4 0.08
3 33 0.69
4 11 0.23
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:240734 original size:15 final size:15
Alignment explanation
Indices: 240714--240754 Score: 82
Period size: 15 Copynumber: 2.7 Consensus size: 15
240704 TATATATAAT
240714 AATAATAATAATATA
1 AATAATAATAATATA
240729 AATAATAATAATATA
1 AATAATAATAATATA
240744 AATAATAATAA
1 AATAATAATAA
240755 AGAGAAGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (15 bp):
AATAATAATAATATA
Found at i:242099 original size:15 final size:15
Alignment explanation
Indices: 242079--242111 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
242069 TGGAAACATG
242079 AAATAA-AAAATAAAT
1 AAATAATAAAAT-AAT
242094 AAATAATAAAATAAT
1 AAATAATAAAATAAT
242109 AAA
1 AAA
242112 ATATGTGTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (15 bp):
AAATAATAAAATAAT
Found at i:252149 original size:74 final size:73
Alignment explanation
Indices: 251742--252390 Score: 789
Period size: 73 Copynumber: 8.9 Consensus size: 73
251732 GGTTAAAACG
** * *
251742 GCTAATAATGTAAACGGTAAAAAAAATAAACGCTACATATTACATTACACA-ACCTATCGGTTTT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTA-AAATACCTATCGGTTTT
*
251806 TTTAATGTT
65 TTTAAAGTT
* * * * *
251815 ACTAATAATGTAAACGGTAAAAAAAATAGGTGCTACCTATTATATTAAAATA-CTA-CCGTTTGT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTTT
251878 TTAAAGATT
66 TTAAAG-TT
* *
251887 ACTAATAA--TAAACGGT-AAAAAAATAGGCACTACCTATTACATTAAAATACCTA-CTGGTTTT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATC-GGTTTT
251948 TTTGAAAGTT
65 TTT-AAAGTT
* * * *
251958 GCTAATAATGTAAACGGT-AAAAAAATAGCCGTTACCTATTACATTGAAATATCTA-CTGGTTTT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATC-GGTTTT
* *
252021 TTGAAGGTT
65 TTTAAAGTT
* * * *
252030 GTTAATAATGT-AACGAT-AAAAAAATAGACGCTACCTATTACATTAAAATACCTATCGATTTTT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTTT
252093 TTGAAAGTT
66 TT-AAAGTT
* *
252102 GCTAATAATGTAAACGGTAAAAAAAATAGGCACTACCTATTACATTAAAATACCTATCGATTTTT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTTT
*
252167 TTGAAGGTT
66 TT-AAAGTT
* * *
252176 GCTAATAATGTAAACGGTAAAAAAAAATAAGCGCTACCTATTACATTAAAATACCTACCGGTTTG
1 GCTAATAATGTAAACGGT-AAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTT
252241 TTTAAAGATT
65 TTTAAAG-TT
* * * * *
252251 GTTAATAATGTAAACGATAAAATAAAATAAGCACTACCTATTATATTAAAATACCTATCGGTTTT
1 GCTAATAATGTAAACGGTAAAA-AAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTT
*
252316 TTTAAGGTT
65 TTTAAAGTT
* * * *
252325 GTTAATAATGTAAACGGTAAAAAAAATAGGCGCTACATATTACATTAAAATACCTACCGGATTTT
1 GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTTT
252390 T
66 T
252391 GAAATGTATC
Statistics
Matches: 505, Mismatches: 57, Indels: 28
0.86 0.10 0.05
Matches are distributed among these distances:
69 30 0.06
70 12 0.02
71 72 0.14
72 50 0.10
73 135 0.27
74 100 0.20
75 106 0.21
ACGTcount: A:0.41, C:0.13, G:0.13, T:0.33
Consensus pattern (73 bp):
GCTAATAATGTAAACGGTAAAAAAAATAGGCGCTACCTATTACATTAAAATACCTATCGGTTTTT
TTAAAGTT
Found at i:254436 original size:32 final size:32
Alignment explanation
Indices: 254395--254480 Score: 147
Period size: 32 Copynumber: 2.7 Consensus size: 32
254385 AGTCGAGTCG
254395 AGCTCGACTCGAACTCGAAAACTTTAAATGTA
1 AGCTCGACTCGAACTCGAAAACTTTAAATGTA
*
254427 AGCTCGACTCGAATTCGAAAACTTTAAATGTA
1 AGCTCGACTCGAACTCGAAAACTTTAAATGTA
*
254459 AGCTCGACTCG-ACTCAAAAACT
1 AGCTCGACTCGAACTCGAAAACT
254481 CGCGAGCCTA
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
31 9 0.18
32 42 0.82
ACGTcount: A:0.37, C:0.23, G:0.15, T:0.24
Consensus pattern (32 bp):
AGCTCGACTCGAACTCGAAAACTTTAAATGTA
Found at i:259820 original size:13 final size:13
Alignment explanation
Indices: 259802--259826 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
259792 TTCATCTGCC
259802 AATGCTAGATGAT
1 AATGCTAGATGAT
259815 AATGCTAGATGA
1 AATGCTAGATGA
259827 AAGTTTGCCA
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:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (13 bp):
AATGCTAGATGAT
Found at i:262922 original size:258 final size:247
Alignment explanation
Indices: 262544--263113 Score: 786
Period size: 258 Copynumber: 2.2 Consensus size: 247
262534 ATTTTTATTC
*
262544 AATATATGAATTAGAAACCCGACCCGACATGACACAAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAA-CCGACCCGAC----C-CGAAATAATAAAAAATTATTTTTATTCAATA
* *
262609 AAAACATTGTCTTAATTGAAAAAAAAATATAGAGGGGTATTATTGTAATTATTCCTAAATATATA
60 AAAACAGTGACTTAATTGAAAAAAAAATATAGAGGGGTATTATTGTAATTATTCCTAAATATATA
* *
262674 AGGTAAAATTATATAT-TTTTTGGGTCGATCCGGT-TTATTTCACCCTAAACCCGAACCCGACCC
125 AAGTAAAATTATATATATTTTCGGGTCG----GGTATT-TTTCACCCTAAACCCGAACCCGACCC
* **
262737 GACCCGAATATCACACTTAAAAAACCCGACCCGACCTTAACAAAATAAAATTTCACCCGACCCGA
185 GACCCGAATATCACACTTAAAAAA-ACGACCCGACCCGAACAAAATAAAATTT----C-ACCCGA
262802 CCCG
244 CCCG
* *
262806 AATATATGAATTAGAAATACGACCCGACCCGAAATAATAAAAAATTA-TTTTATTCAATAAAAAT
1 AATATATGAATTAGAAA-CCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAAC
262870 AGTGACTTAATTGAAAAAAAAATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAAG
65 AGTGACTTAATTG-AAAAAAAA-ATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAAG
* * *
262935 TAAAATTATATATATTTTCGGGTCGGGTATTTTTCACCTTAAACCCGAACTCGACCTGACCCGAA
128 TAAAATTATATATATTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAA
* *
263000 TATCACACTTAAAAAAACGACCCGACCCGACCAAAATAAAGTTTCACCCGACCCG
193 TATCACACTTAAAAAAACGACCCGACCCGAACAAAATAAAATTTCACCCGACCCG
* *
263055 AATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAAATATTTTTATTTAATA
1 AATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
263114 TATAAATAAG
Statistics
Matches: 284, Mismatches: 19, Indels: 23
0.87 0.06 0.07
Matches are distributed among these distances:
248 27 0.10
249 38 0.13
250 1 0.00
254 23 0.08
255 50 0.18
256 29 0.10
257 25 0.09
258 55 0.19
259 10 0.04
262 26 0.09
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (247 bp):
AATATATGAATTAGAAACCGACCCGACCCGAAATAATAAAAAATTATTTTTATTCAATAAAAACA
GTGACTTAATTGAAAAAAAAATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAAGTAA
AATTATATATATTTTCGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGACCCGAATAT
CACACTTAAAAAAACGACCCGACCCGAACAAAATAAAATTTCACCCGACCCG
Found at i:276434 original size:28 final size:27
Alignment explanation
Indices: 276387--276440 Score: 74
Period size: 27 Copynumber: 1.9 Consensus size: 27
276377 AATTTATTTG
276387 AAAAAAAACTCAACTTTCTTTAAAATCAC
1 AAAAAAAACTCAAC-TTC-TTAAAATCAC
276416 AAAAAAAATCTCAAC-TCTTAAAATC
1 AAAAAAAA-CTCAACTTCTTAAAATC
276441 TTGATTTCAA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
27 8 0.33
28 2 0.08
29 8 0.33
30 6 0.25
ACGTcount: A:0.54, C:0.20, G:0.00, T:0.26
Consensus pattern (27 bp):
AAAAAAAACTCAACTTCTTAAAATCAC
Found at i:291537 original size:2 final size:2
Alignment explanation
Indices: 291530--291561 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
291520 CATAGCATAA
291530 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
291562 GAATATGCAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.