Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001582.1 Hibiscus syriacus cultivar Beakdansim tig00003151_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: 1162828
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 6
Found at i:201349 original size:14 final size:14
Alignment explanation
Indices: 201330--201370 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
201320 AAACTTTATA
201330 TATATATATATAAG
1 TATATATATATAAG
201344 TATATA-ATATAAAG
1 TATATATATAT-AAG
201358 TATATATATATAA
1 TATATATATATAA
201371 AGTTTTAGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
13 4 0.16
14 17 0.68
15 4 0.16
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (14 bp):
TATATATATATAAG
Found at i:201362 original size:30 final size:28
Alignment explanation
Indices: 201328--201390 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
201318 TAAAACTTTA
201328 TATATATATATATAAGTATATAATATAAAG
1 TATATATATATA-AAGT-TATAATATAAAG
* *
201358 TATATATATATAAAGTTTTAGTATAAAG
1 TATATATATATAAAGTTATAATATAAAG
201386 TATAT
1 TATAT
201391 TACTTTATAG
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
28 15 0.48
29 4 0.13
30 12 0.39
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.43
Consensus pattern (28 bp):
TATATATATATAAAGTTATAATATAAAG
Found at i:201419 original size:21 final size:21
Alignment explanation
Indices: 201386--201454 Score: 58
Period size: 21 Copynumber: 3.4 Consensus size: 21
201376 TAGTATAAAG
201386 TATAT-TACTTTATAGTTTATA
1 TATATATAC-TTATAGTTTATA
*
201407 TATATATACTTATA--ATATA
1 TATATATACTTATAGTTTATA
*
201426 CT-TATAT-TTTATAGTTTTATA
1 -TATATATACTTATAG-TTTATA
201447 TATATATA
1 TATATATA
201455 TATATATACA
Statistics
Matches: 38, Mismatches: 3, Indels: 13
0.70 0.06 0.24
Matches are distributed among these distances:
18 5 0.13
19 9 0.24
20 2 0.05
21 19 0.50
22 3 0.08
ACGTcount: A:0.38, C:0.04, G:0.03, T:0.55
Consensus pattern (21 bp):
TATATATACTTATAGTTTATA
Found at i:201424 original size:11 final size:12
Alignment explanation
Indices: 201405--201611 Score: 61
Period size: 12 Copynumber: 16.3 Consensus size: 12
201395 TTATAGTTTA
201405 TATATATATACT
1 TATATATATACT
201417 TATA-ATATACT
1 TATATATATACT
* *
201428 TATATTTTATAGTTT
1 TATA-TATATA--CT
201443 TATATATATA-T
1 TATATATATACT
*
201454 ATATATATACACTT
1 -TATATATATAC-T
* * *
201468 TATACTTTAAAGT
1 TATA-TATATACT
*
201481 ATATATACCTTATAGTT
1 -TATATA---TATA-CT
*
201498 TTTATATATACTT
1 TATATATATAC-T
* *
201511 TATAGTTTAAACTT
1 TATA-TATATAC-T
201525 TATATATATACT
1 TATATATATACT
* *
201537 TATACTCT-T-TT
1 TATA-TATATACT
*
201548 TATATATGTATATT
1 TATATA--TATACT
*
201562 TAAATATATA-T
1 TATATATATACT
201573 ATATATATATA-T
1 -TATATATATACT
201585 ATATATATATA-T
1 -TATATATATACT
201597 T-TATATATACT
1 TATATATATACT
201608 TATA
1 TATA
201612 ATGTATTAAT
Statistics
Matches: 150, Mismatches: 22, Indels: 46
0.69 0.10 0.21
Matches are distributed among these distances:
10 9 0.06
11 21 0.14
12 48 0.32
13 26 0.17
14 32 0.21
15 5 0.03
16 8 0.05
17 1 0.01
ACGTcount: A:0.39, C:0.06, G:0.02, T:0.52
Consensus pattern (12 bp):
TATATATATACT
Found at i:201471 original size:40 final size:39
Alignment explanation
Indices: 201391--201487 Score: 117
Period size: 39 Copynumber: 2.5 Consensus size: 39
201381 TAAAGTATAT
*
201391 TACTTTATAGTTTATATATATATACTTATAATATACTTA
1 TACTTTATAGTTTATATATATATACTTATAATACACTTA
*
201430 TATTTTATAGTTT-TATATATATA-TATATATATACACTTTA
1 TACTTTATAGTTTATATATATATACT-TATA-ATACAC-TTA
* *
201470 TACTTTAAAGTATATATA
1 TACTTTATAGTTTATATA
201488 CCTTATAGTT
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
37 1 0.02
38 14 0.29
39 17 0.35
40 13 0.27
41 4 0.08
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (39 bp):
TACTTTATAGTTTATATATATATACTTATAATACACTTA
Found at i:201505 original size:20 final size:20
Alignment explanation
Indices: 201480--201518 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
201470 TACTTTAAAG
201480 TATATATACCTTATAGTTTT
1 TATATATACCTTATAGTTTT
*
201500 TATATATACTTTATAGTTT
1 TATATATACCTTATAGTTT
201519 AAACTTTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.31, C:0.08, G:0.05, T:0.56
Consensus pattern (20 bp):
TATATATACCTTATAGTTTT
Found at i:201511 original size:43 final size:43
Alignment explanation
Indices: 201457--201575 Score: 120
Period size: 43 Copynumber: 2.7 Consensus size: 43
201447 TATATATATA
* * *
201457 TATATACACTTTATACTTTAAAGTATATATA-CCTTATAGT-TTT
1 TATATATACTTTATA-TTTAAA-TATATATATACTTATACTCTTT
201500 TATATATACTTTATAGTTTAAACTTTATATATATACTTATACTCTTT
1 TATATATACTTTATA-TTTAAA---TATATATATACTTATACTCTTT
*
201547 T-TATATA-TGTATATTTAAATATATATATA
1 TATATATACTTTATATTTAAATATATATATA
201576 TATATATATA
Statistics
Matches: 66, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
41 10 0.15
43 20 0.30
44 6 0.09
45 13 0.20
46 13 0.20
47 4 0.06
ACGTcount: A:0.37, C:0.08, G:0.03, T:0.51
Consensus pattern (43 bp):
TATATATACTTTATATTTAAATATATATATACTTATACTCTTT
Found at i:201553 original size:2 final size:2
Alignment explanation
Indices: 201548--201738 Score: 86
Period size: 2 Copynumber: 100.0 Consensus size: 2
201538 ATACTCTTTT
* * *
201548 TA TA TA TG TA TA TT TA AA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * *
201590 TA TA TA TT TA TA TA TA CT- TA TA -A TG TA T- TA -A TT TA TG TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
* * * * * *
201629 TA -A GTA TA -A TG TA CA T- TA TA TA TA CA TG CA TCA TA T- TA TC
1 TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
* * * *
201669 TA -A CA T- TCA T- TA TA CA TA T- TA TA TA TT TA AA TA -A GTA TA
1 TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA
201708 TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
201739 ATTGTTTTAA
Statistics
Matches: 137, Mismatches: 33, Indels: 38
0.66 0.16 0.18
Matches are distributed among these distances:
1 14 0.10
2 117 0.85
3 6 0.04
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.48
Consensus pattern (2 bp):
TA
Found at i:203739 original size:12 final size:12
Alignment explanation
Indices: 203718--203752 Score: 61
Period size: 12 Copynumber: 2.9 Consensus size: 12
203708 AATAATTTTT
*
203718 AGGAAATTTTCC
1 AGGAATTTTTCC
203730 AGGAATTTTTCC
1 AGGAATTTTTCC
203742 AGGAATTTTTC
1 AGGAATTTTTC
203753 GACACCGTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (12 bp):
AGGAATTTTTCC
Found at i:206489 original size:24 final size:24
Alignment explanation
Indices: 206458--206573 Score: 135
Period size: 24 Copynumber: 4.8 Consensus size: 24
206448 TTCGATTTGA
*
206458 ATTCTGATCTGATACTTGACATGG
1 ATTCTGATATGATACTTGACATGG
* *
206482 ATTATGATATGATA-TCTGACATAG
1 ATTCTGATATGATACT-TGACATGG
*
206506 ATTCTGATATGATACTTGACTTGG
1 ATTCTGATATGATACTTGACATGG
* *
206530 ATTCTGATCTGATACTTGACCTGG
1 ATTCTGATATGATACTTGACATGG
* * *
206554 ATTTTAATATGACACTTGAC
1 ATTCTGATATGATACTTGAC
206574 CTGATTTATG
Statistics
Matches: 78, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
23 1 0.01
24 76 0.97
25 1 0.01
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.39
Consensus pattern (24 bp):
ATTCTGATATGATACTTGACATGG
Found at i:208098 original size:7 final size:7
Alignment explanation
Indices: 208084--208127 Score: 65
Period size: 7 Copynumber: 6.6 Consensus size: 7
208074 GGGTTACATA
208084 AATA-AT
1 AATATAT
208090 AATATAT
1 AATATAT
208097 AATATAT
1 AATATAT
208104 AATATAT
1 AATATAT
208111 AATA-AT
1 AATATAT
*
208117 TATATAT
1 AATATAT
208124 AATA
1 AATA
208128 ATGTACATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
6 9 0.26
7 25 0.74
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
AATATAT
Found at i:208121 original size:20 final size:20
Alignment explanation
Indices: 208084--208129 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
208074 GGGTTACATA
208084 AATAATAATATATAATATAT
1 AATAATAATATATAATATAT
*
208104 AATATATAATA-ATTATATAT
1 AATA-ATAATATATAATATAT
208124 AATAAT
1 AATAAT
208130 GTACATAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 2 0.08
20 16 0.67
21 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
AATAATAATATATAATATAT
Found at i:208669 original size:83 final size:83
Alignment explanation
Indices: 208567--209062 Score: 746
Period size: 83 Copynumber: 6.0 Consensus size: 83
208557 GTGGAGTCTG
* * * *
208567 ATACTTTGTTGAAAAATCCGTTCCACTACTCTTTCGTGGAGTTCGAAA-TTTATTTTGCTTCATT
1 ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTC-AAATTTTACTTTGCTTCACT
***
208631 ACTCTTTAATGAAGATTTC
65 ACTCTTCCGTGAAGATTTC
* * *
208650 ATACTTTGTTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTCGAATTTTACTCTGCTTCACTA
1 ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTCAAATTTTACTTTGCTTCACTA
208715 CTCTTCCGTGAAGATTTC
66 CTCTTCCGTGAAGATTTC
* * * * *
208733 ATACTTTACTGAAAAATCCTTTCCACTACTCTTCCGTGGACTTCGAATTTTACTTTGCTTCATTA
1 ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTCAAATTTTACTTTGCTTCACTA
208798 CTCTTCCGTGAAGATTTC
66 CTCTTCCGTGAAGATTTC
* *
208816 ATATTTTGCTGAAAAATCCGTTCCACTACTCTTCCATGGAGTTCAAATTTTACTTTGCTTCACTA
1 ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTCAAATTTTACTTTGCTTCACTA
*
208881 CTCTTCCGTGAATATTTC
66 CTCTTCCGTGAAGATTTC
* * *
208899 ATACTTTGCTAAAAAATCCGTTTCACTACTCTTCCATGGAGTTCAAATTTTACTTTGCTTCACTA
1 ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTCAAATTTTACTTTGCTTCACTA
*
208964 CTCTTCCGTGAAGATTTT
66 CTCTTCCGTGAAGATTTC
*
208982 ATACTTTGCTGAAAATAT--GTTCCACTACTCTTCCGTTGAGTTCAAATTTTACTTTGCTTCACT
1 ATACTTTGCTGAAAA-ATCCGTTCCACTACTCTTCCGTGGAGTTCAAATTTTACTTTGCTTCACT
209045 ACTCTTCCGTGAAGATTT
65 ACTCTTCCGTGAAGATTT
209063 ATCTGGCTTG
Statistics
Matches: 380, Mismatches: 31, Indels: 5
0.91 0.07 0.01
Matches are distributed among these distances:
82 62 0.16
83 316 0.83
84 2 0.01
ACGTcount: A:0.24, C:0.23, G:0.12, T:0.41
Consensus pattern (83 bp):
ATACTTTGCTGAAAAATCCGTTCCACTACTCTTCCGTGGAGTTCAAATTTTACTTTGCTTCACTA
CTCTTCCGTGAAGATTTC
Found at i:218491 original size:21 final size:21
Alignment explanation
Indices: 218461--218505 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
218451 ATCTGAACCA
* *
218461 GGCCTGTGTGCTTTGTAATTG
1 GGCCTGTGTGCCTTGTAATCG
*
218482 GGCCTTTGTGCCTTGTAATCG
1 GGCCTGTGTGCCTTGTAATCG
218503 GGC
1 GGC
218506 TCCTGAGTTA
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:0.09, C:0.20, G:0.33, T:0.38
Consensus pattern (21 bp):
GGCCTGTGTGCCTTGTAATCG
Found at i:218594 original size:13 final size:12
Alignment explanation
Indices: 218576--218609 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
218566 AATATATAAC
218576 ATATAATAATTAT
1 ATATAATAA-TAT
218589 ATATAATAATAT
1 ATATAATAATAT
*
218601 ACATAATAA
1 ATATAATAA
218610 ACGTCACTCG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
12 11 0.55
13 9 0.45
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (12 bp):
ATATAATAATAT
Found at i:218894 original size:21 final size:22
Alignment explanation
Indices: 218853--218909 Score: 62
Period size: 21 Copynumber: 2.5 Consensus size: 22
218843 TATATATATA
*
218853 TATATAAACTATAAACTATAA-G
1 TATATATA-TATAAACTATAATG
*
218875 TATATATATATAAAGTATAATG
1 TATATATATATAAACTATAATG
*
218897 TACATTATATATA
1 TATA-TATATATA
218910 CATGCATCAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.37
22 11 0.37
23 8 0.27
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.39
Consensus pattern (22 bp):
TATATATATATAAACTATAATG
Found at i:219285 original size:24 final size:24
Alignment explanation
Indices: 219256--219301 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
219246 TTTAGTCCAT
219256 TTTTAT-ATTAATATCAACTTCACA
1 TTTTATAATTAAT-TCAACTTCACA
*
219280 TTTTATAATTAATTCAATTTCA
1 TTTTATAATTAATTCAACTTCA
219302 TCCCTCATCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTTATAATTAATTCAACTTCACA
Found at i:219409 original size:7 final size:8
Alignment explanation
Indices: 219390--219606 Score: 90
Period size: 7 Copynumber: 29.6 Consensus size: 8
219380 CAAACACATA
219390 TATATAAGG
1 TATATAA-G
219399 TATATAA-
1 TATATAAG
219406 TATA-AAG
1 TATATAAG
219413 TAT-TAAAG
1 TATAT-AAG
219421 TATATAA-
1 TATATAAG
219428 TATA-AAG
1 TATATAAG
219435 TA-ATAA-
1 TATATAAG
* * **
219441 AATGTTTG
1 TATATAAG
*
219449 GATATAAG
1 TATATAAG
219457 TAT-TAAAG
1 TATAT-AAG
219465 TATATAA-
1 TATATAAG
219472 -ATATAAG
1 TATATAAG
*
219479 TAT-TAAA
1 TATATAAG
219486 TATA-AAG
1 TATATAAG
*
219493 TATATAAA
1 TATATAAG
219501 TATATAAG
1 TATATAAG
219509 TACTA-AAG
1 TA-TATAAG
219517 TATATAA-
1 TATATAAG
219524 TATA-AAG
1 TATATAAG
*
219531 TAT-TAAAC
1 TATAT-AAG
*
219539 TTTAT-A-
1 TATATAAG
219545 -ATATAAG
1 TATATAAG
*
219552 TAT-TAAA
1 TATATAAG
219559 TATA-AAG
1 TATATAAG
*
219566 TAT-TAAAA
1 TATAT-AAG
219574 TATATAA-
1 TATATAAG
219581 -ATATAAG
1 TATATAAG
*
219588 TAT-TAAA
1 TATATAAG
219595 TATA-AAG
1 TATATAAG
219602 TATAT
1 TATAT
219607 TAATTATCAT
Statistics
Matches: 156, Mismatches: 21, Indels: 63
0.65 0.09 0.26
Matches are distributed among these distances:
5 3 0.02
6 21 0.13
7 62 0.40
8 57 0.37
9 13 0.08
ACGTcount: A:0.53, C:0.01, G:0.09, T:0.37
Consensus pattern (8 bp):
TATATAAG
Found at i:219426 original size:22 final size:23
Alignment explanation
Indices: 219398--219606 Score: 132
Period size: 22 Copynumber: 9.6 Consensus size: 23
219388 TATATATAAG
219398 GTATATAATATA-AAGTATTAAA
1 GTATATAATATATAAGTATTAAA
*
219420 GTATATAATATA-AAGTAATAAA
1 GTATATAATATATAAGTATTAAA
* * ***
219442 ATGT-TTGGATATAAGTATTAAA
1 GTATATAATATATAAGTATTAAA
219464 GTATATAA-ATATAAGTATTAAA
1 GTATATAATATATAAGTATTAAA
*
219486 -TATA-AAGTATATAAATA-TATAA
1 GTATATAA-TATATAAGTATTA-AA
219508 GTACTA-AAGTATATAA-TA-TAAA
1 GTA-TATAA-TATATAAGTATTAAA
*
219530 GTAT-TAAACTTTATAA-TA-T-AA
1 GTATAT-AA-TATATAAGTATTAAA
219551 GTAT-TAA-ATATAAAGTATTAAA
1 GTATATAATATAT-AAGTATTAAA
*
219573 ATATATAA-ATATAAGTATTAAA
1 GTATATAATATATAAGTATTAAA
219595 -TATA-AAGTATAT
1 GTATATAA-TATAT
219607 TAATTATCAT
Statistics
Matches: 155, Mismatches: 16, Indels: 32
0.76 0.08 0.16
Matches are distributed among these distances:
18 3 0.02
19 2 0.01
20 8 0.05
21 23 0.15
22 93 0.60
23 14 0.09
24 12 0.08
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.37
Consensus pattern (23 bp):
GTATATAATATATAAGTATTAAA
Found at i:219432 original size:36 final size:35
Alignment explanation
Indices: 219387--219604 Score: 210
Period size: 36 Copynumber: 5.8 Consensus size: 35
219377 ACACAAACAC
219387 ATAT-ATATAAGGTA-TATAATATAAAGTATTAAAGT
1 ATATAATATAA-GTATTA-AATATAAAGTATTAAAGT
*
219422 ATATAATATAAAGTAATAAAATGTTTGGATATAAGTATTAAAGT
1 ATATAATAT-AAGT-ATTAAA----T--ATA-AAGTATTAAAGT
219466 ATATAAATATAAGTATTAAATATAAAGTATATAAA-T
1 ATAT-AATATAAGTATTAAATATAAAGTAT-TAAAGT
*
219502 ATATAAGTACTAAAGTA-TATAATATAAAGTATTAAACT
1 ATATAA-TA-T-AAGTATTA-AATATAAAGTATTAAAGT
* *
219540 TTATAATATAAGTATTAAATATAAAGTATTAAAAT
1 ATATAATATAAGTATTAAATATAAAGTATTAAAGT
219575 ATATAAATATAAGTATTAAATATAAAGTAT
1 ATAT-AATATAAGTATTAAATATAAAGTAT
219605 ATTAATTATC
Statistics
Matches: 158, Mismatches: 5, Indels: 39
0.78 0.02 0.19
Matches are distributed among these distances:
35 31 0.20
36 47 0.30
37 21 0.13
38 24 0.15
39 1 0.01
41 1 0.01
43 8 0.05
44 20 0.13
45 5 0.03
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.37
Consensus pattern (35 bp):
ATATAATATAAGTATTAAATATAAAGTATTAAAGT
Found at i:219440 original size:8 final size:7
Alignment explanation
Indices: 219392--219605 Score: 83
Period size: 8 Copynumber: 29.6 Consensus size: 7
219382 AACACATATA
*
219392 TATAAGG
1 TATAAAG
219399 TATATAA-
1 TATA-AAG
219406 TATAAAG
1 TATAAAG
219413 TATTAAAG
1 TA-TAAAG
219421 TATATAA-
1 TATA-AAG
219428 TATAAAG
1 TATAAAG
219435 TAATAAAATG
1 T-AT-AAA-G
* **
219445 TTTGGA-
1 TATAAAG
219451 TAT-AAG
1 TATAAAG
219457 TATTAAAG
1 TA-TAAAG
*
219465 TATATAAA
1 TATA-AAG
219473 TAT-AAG
1 TATAAAG
219479 TATTAAA-
1 TA-TAAAG
219486 TATAAAG
1 TATAAAG
*
219493 TATATAAA
1 TATA-AAG
219501 TATATAAG
1 TATA-AAG
219509 TACTAAAG
1 TA-TAAAG
219517 TATATAA-
1 TATA-AAG
219524 TATAAAG
1 TATAAAG
*
219531 TATTAAAC
1 TA-TAAAG
*
219539 TTTATAA-
1 TATA-AAG
219546 TAT-AAG
1 TATAAAG
219552 TATTAAA-
1 TA-TAAAG
219559 TATAAAG
1 TATAAAG
*
219566 TATTAAAA
1 TA-TAAAG
*
219574 TATATAAA
1 TATA-AAG
219582 TAT-AAG
1 TATAAAG
219588 TATTAAA-
1 TA-TAAAG
219595 TATAAAG
1 TATAAAG
219602 TATA
1 TATA
219606 TTAATTATCA
Statistics
Matches: 162, Mismatches: 15, Indels: 60
0.68 0.06 0.25
Matches are distributed among these distances:
5 3 0.02
6 32 0.20
7 53 0.33
8 66 0.41
9 6 0.04
10 2 0.01
ACGTcount: A:0.54, C:0.01, G:0.09, T:0.36
Consensus pattern (7 bp):
TATAAAG
Found at i:219551 original size:73 final size:73
Alignment explanation
Indices: 219400--219604 Score: 223
Period size: 73 Copynumber: 2.8 Consensus size: 73
219390 TATATAAGGT
**
219400 ATATAA-TA-TAAAGTATTAAAGTATAT-AATATA-AAGTAATAAAATGT-TTGGATAT-AAGTA
1 ATATAAGTATTAAA-TA-TAAAGTATATAAATATATAAGT-AT-AAA-GTATTAAATATAAAGTA
*
219459 TTAAAGTATATAA
61 TTAAACTATATAA
219472 ATATAAGTATTAAATATAAAGTATATAAATATATAAGTACTAAAGTA-TATAATATAAAGTATTA
1 ATATAAGTATTAAATATAAAGTATATAAATATATAAGTA-TAAAGTATTA-AATATAAAGTATTA
*
219536 AACTTTAT-A
64 AACTATATAA
*
219545 ATATAAGTATTAAATATAAAGTAT-TAAAATATATAAATAT-AAGTATTAAATATAAAGTAT
1 ATATAAGTATTAAATATAAAGTATAT-AAATATATAAGTATAAAGTATTAAATATAAAGTAT
219605 ATTAATTATC
Statistics
Matches: 118, Mismatches: 5, Indels: 21
0.82 0.03 0.15
Matches are distributed among these distances:
71 17 0.14
72 23 0.19
73 55 0.47
74 23 0.19
ACGTcount: A:0.54, C:0.01, G:0.08, T:0.37
Consensus pattern (73 bp):
ATATAAGTATTAAATATAAAGTATATAAATATATAAGTATAAAGTATTAAATATAAAGTATTAAA
CTATATAA
Found at i:219578 original size:57 final size:60
Alignment explanation
Indices: 219484--219594 Score: 167
Period size: 57 Copynumber: 1.9 Consensus size: 60
219474 ATAAGTATTA
*
219484 AATATAAAGTATATAAATATATAAGTACTAAAGTATAT-AATATAAAGTATTAAACTTTAT
1 AATATAAAGTATATAAATATATAAGTACTAAAATATATAAATAT-AAGTATTAAACTTTAT
*
219544 AATAT-AAGTAT-TAAATATA-AAGTATTAAAATATATAAATATAAGTATTAAA
1 AATATAAAGTATATAAATATATAAGTACTAAAATATATAAATATAAGTATTAAA
219595 TATAAAGTAT
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
57 24 0.50
58 13 0.27
59 6 0.12
60 5 0.10
ACGTcount: A:0.56, C:0.02, G:0.06, T:0.36
Consensus pattern (60 bp):
AATATAAAGTATATAAATATATAAGTACTAAAATATATAAATATAAGTATTAAACTTTAT
Found at i:219628 original size:21 final size:21
Alignment explanation
Indices: 219602--219664 Score: 80
Period size: 21 Copynumber: 3.1 Consensus size: 21
219592 AAATATAAAG
219602 TATATTAATTATCATAATTAA
1 TATATTAATTATCATAATTAA
*
219623 TATATTAATTAT-AT--TTAT
1 TATATTAATTATCATAATTAA
219641 TA-ATTTAATTATCATAATTAA
1 TATA-TTAATTATCATAATTAA
219662 TAT
1 TAT
219665 TTTATTTACA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
17 1 0.03
18 13 0.37
19 2 0.06
20 2 0.06
21 17 0.49
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (21 bp):
TATATTAATTATCATAATTAA
Found at i:219660 original size:18 final size:19
Alignment explanation
Indices: 219603--219665 Score: 76
Period size: 18 Copynumber: 3.3 Consensus size: 19
219593 AATATAAAGT
219603 ATATTAATTATCATAATTAA
1 ATATTAATTATCATAATT-A
*
219623 TATATTAATTAT-ATTTATTA
1 -ATATTAATTATCA-TAATTA
219643 AT-TTAATTATCATAATTA
1 ATATTAATTATCATAATTA
219661 ATATT
1 ATATT
219666 TTATTTACAT
Statistics
Matches: 37, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
18 15 0.41
19 5 0.14
20 2 0.05
21 15 0.41
ACGTcount: A:0.44, C:0.03, G:0.00, T:0.52
Consensus pattern (19 bp):
ATATTAATTATCATAATTA
Found at i:221135 original size:9 final size:9
Alignment explanation
Indices: 221113--221149 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
221103 TTTGGGGAAG
221113 ATTTTT-AA
1 ATTTTTGAA
221121 ATTTTTTGAA
1 A-TTTTTGAA
221131 ATTTTTG-A
1 ATTTTTGAA
221139 ATTTTTGAA
1 ATTTTTGAA
221148 AT
1 AT
221150 ATAATTTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 9 0.35
9 14 0.54
10 3 0.12
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (9 bp):
ATTTTTGAA
Found at i:221136 original size:18 final size:17
Alignment explanation
Indices: 221113--221149 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 17
221103 TTTGGGGAAG
221113 ATTTTTAAATTTTTTGAA
1 ATTTTTAAA-TTTTTGAA
*
221131 ATTTTTGAATTTTTGAA
1 ATTTTTAAATTTTTGAA
221148 AT
1 AT
221150 ATAATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.59
Consensus pattern (17 bp):
ATTTTTAAATTTTTGAA
Found at i:222707 original size:31 final size:31
Alignment explanation
Indices: 222672--222741 Score: 140
Period size: 31 Copynumber: 2.3 Consensus size: 31
222662 TGATTATTTA
222672 TTTATTTTACTAATGATGTTCACCTTAAAAT
1 TTTATTTTACTAATGATGTTCACCTTAAAAT
222703 TTTATTTTACTAATGATGTTCACCTTAAAAT
1 TTTATTTTACTAATGATGTTCACCTTAAAAT
222734 TTTATTTT
1 TTTATTTT
222742 TACGCATTCC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.30, C:0.11, G:0.06, T:0.53
Consensus pattern (31 bp):
TTTATTTTACTAATGATGTTCACCTTAAAAT
Found at i:223046 original size:2 final size:2
Alignment explanation
Indices: 223039--223078 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
223029 ACATAACAGA
223039 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
223079 GGATCCTAAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:227671 original size:31 final size:31
Alignment explanation
Indices: 227630--227733 Score: 118
Period size: 31 Copynumber: 3.4 Consensus size: 31
227620 GGTCTGAGAA
* ** * *
227630 CCTACACAAGAAAGTTCCCAGGGCCACGGGG
1 CCTACCCAAGAAAAATCTCAGGGCCACAGGG
* *
227661 CCTACCCAAGAAAAATATTAGGGCCACAGGG
1 CCTACCCAAGAAAAATCTCAGGGCCACAGGG
* * *
227692 CCTACCCTAGAAAAATCTCAAGGCCACAGAG
1 CCTACCCAAGAAAAATCTCAGGGCCACAGGG
227723 CCTACCCAAGA
1 CCTACCCAAGA
227734 GCCACATTAG
Statistics
Matches: 60, Mismatches: 13, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
31 60 1.00
ACGTcount: A:0.36, C:0.32, G:0.21, T:0.12
Consensus pattern (31 bp):
CCTACCCAAGAAAAATCTCAGGGCCACAGGG
Found at i:232868 original size:31 final size:30
Alignment explanation
Indices: 232829--232888 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
232819 TAAGGGAGTA
**
232829 TTTTGGGGCCTGAGAGCCTACCCAAGAAAG
1 TTTTGGGGCCACAGAGCCTACCCAAGAAAG
* *
232859 TTTTAGGGGCCACAGATCCTACCTAAGAAA
1 TTTT-GGGGCCACAGAGCCTACCCAAGAAA
232889 AATCTCAGGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 4 0.16
31 21 0.84
ACGTcount: A:0.30, C:0.23, G:0.25, T:0.22
Consensus pattern (30 bp):
TTTTGGGGCCACAGAGCCTACCCAAGAAAG
Found at i:232941 original size:31 final size:30
Alignment explanation
Indices: 232841--232948 Score: 83
Period size: 31 Copynumber: 3.5 Consensus size: 30
232831 TTGGGGCCTG
* **
232841 AGAGCCTACCCAAGAAAGTT-TTAGGGGCCAC
1 AGAGCCTACCCAAGAAAATTCTTA--GGCTGC
* * * * *
232872 AGATCCTACCTAAGAAAAATCTCAGGGTCGC
1 AGAGCCTACCCAAGAAAATTCTTAGGCT-GC
*
232903 AGGGCCTACCCAAGAAAATTCTTATGGCTGC
1 AGAGCCTACCCAAGAAAATTCTTA-GGCTGC
*
232934 AGAGCCTACCGAAGA
1 AGAGCCTACCCAAGA
232949 GCCACATTAG
Statistics
Matches: 58, Mismatches: 16, Indels: 6
0.73 0.20 0.08
Matches are distributed among these distances:
30 2 0.03
31 51 0.88
32 5 0.09
ACGTcount: A:0.33, C:0.26, G:0.23, T:0.18
Consensus pattern (30 bp):
AGAGCCTACCCAAGAAAATTCTTAGGCTGC
Found at i:233998 original size:31 final size:31
Alignment explanation
Indices: 233963--234033 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
233953 AGGGGCCACG
* *
233963 GGGCCTACCCAAGAAAATTCTC-AGGGTCGTA
1 GGGCCTACCCAAGAAAAATCTCAAGGAT-GTA
233994 GGGCCTACCCAAGAAAAATCTCAAGGATGTA
1 GGGCCTACCCAAGAAAAATCTCAAGGATGTA
*
234025 GAGCCTACC
1 GGGCCTACC
234034 GAACTGTCAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
31 32 0.89
32 4 0.11
ACGTcount: A:0.32, C:0.27, G:0.24, T:0.17
Consensus pattern (31 bp):
GGGCCTACCCAAGAAAAATCTCAAGGATGTA
Found at i:247959 original size:24 final size:23
Alignment explanation
Indices: 247932--247978 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
247922 TCTTTAATGT
247932 ATATTTAATTGAATTAATTAAAAA
1 ATATTTAATT-AATTAATTAAAAA
* * *
247956 ATATTTTATTTATTAATTCAAAA
1 ATATTTAATTAATTAATTAAAAA
247979 TAACTTTAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (23 bp):
ATATTTAATTAATTAATTAAAAA
Found at i:251420 original size:15 final size:15
Alignment explanation
Indices: 251402--251451 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
251392 AAGGCTGCAA
251402 CATCACAAGCACCAT
1 CATCACAAGCACCAT
** *
251417 CATCACAAGCTGCAA
1 CATCACAAGCACCAT
*
251432 CATCACAACCACCAT
1 CATCACAAGCACCAT
251447 CATCA
1 CATCA
251452 TCACAAGCTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.40, C:0.40, G:0.06, T:0.14
Consensus pattern (15 bp):
CATCACAAGCACCAT
Found at i:251461 original size:33 final size:30
Alignment explanation
Indices: 251381--251451 Score: 117
Period size: 30 Copynumber: 2.4 Consensus size: 30
251371 ACAAGGATTA
*
251381 CACCATCATCA-AAGGCTGCAACATCACAAG
1 CACCATCATCACAA-GCTGCAACATCACAAC
251411 CACCATCATCACAAGCTGCAACATCACAAC
1 CACCATCATCACAAGCTGCAACATCACAAC
251441 CACCATCATCA
1 CACCATCATCA
251452 TCACAAGCTG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
30 37 0.95
31 2 0.05
ACGTcount: A:0.39, C:0.38, G:0.08, T:0.14
Consensus pattern (30 bp):
CACCATCATCACAAGCTGCAACATCACAAC
Found at i:254189 original size:25 final size:26
Alignment explanation
Indices: 254148--254203 Score: 96
Period size: 25 Copynumber: 2.2 Consensus size: 26
254138 TGTTGTTACC
254148 TTGACATTATTTCATGTGTCCAATTG
1 TTGACATTATTTCATGTGTCCAATTG
*
254174 TTGACATT-TTTCATGTGTCCAGTTG
1 TTGACATTATTTCATGTGTCCAATTG
254199 TTGAC
1 TTGAC
254204 GTAACATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
25 21 0.72
26 8 0.28
ACGTcount: A:0.20, C:0.16, G:0.18, T:0.46
Consensus pattern (26 bp):
TTGACATTATTTCATGTGTCCAATTG
Found at i:258058 original size:163 final size:158
Alignment explanation
Indices: 257781--258369 Score: 588
Period size: 163 Copynumber: 3.6 Consensus size: 158
257771 TTCCCGAGCT
* * * * *
257781 ACAAGTTCTTCTCTTTATGAACTTCTTTTCCCTCTTCGAACGACTTCTTCTCATTATGAA-TCCT
1 ACAAGTTCTTCTCATTATGAAC-T-TTCT-CC-CTTCGGATGAGTTCTTCTCATTATGAACT-C-
* * ** *
257845 TCTATTGGAAATGATAATCCACCTCCTTCTGCGATGGAATCGAACAAAATGTTGATGCTTGATCT
60 TCCATTGGAAATGATGATCCACCTCCTTCTATGATGAAATCGAACAAAATGTTGATGCTTGATCT
* **
257910 ATCTCCTTTTGTGATAGAATCTAGCAAAATGGTGA
125 ATCTCCTTCTACGATAGAATCTAGCAAAA-GGTGA
* * *
257945 ACACGATCTTCTCATTATGAACCTTTTCTGCCACTTCGGATGAGTTCTTCTCTTTATGAACTCTC
1 ACAAGTTCTTCTCATTATGAA-C-TTTCT-CC-CTTCGGATGAGTTCTTCTCATTATGAACTCTC
* * * *
258010 CATTGGAAATGCTGACCCATCTCCTTCTATGATGAAATCGAACAAAATGTTGATGCTTGATTTAT
62 CATTGGAAATGATGATCCACCTCCTTCTATGATGAAATCGAACAAAATGTTGATGCTTGATCTAT
*
258075 CTCCTTCTACGATAGAATATAGCAAAAGGGTGA
127 CTCCTTCTACGATAGAATCTAGCAAAA-GGTGA
* * *
258108 ATAAGTTCTTCTCATTATGAACTTTCTCTCCTTCTGTTGATAAATTCTTCTCATTATGAACTCTC
1 ACAAGTTCTTCTCATTATGAACTTTCTC-CCTTC-G--GATGAGTTCTTCTCATTATGAACTCTC
* * * * * * * *
258173 CATTGGAAATTATGATCCACCTCCTTTTGTGATGTATTTGAGCAAAAATGTGGATGC-TGATCTA
62 CATTGGAAATGATGATCCACCTCCTTCTATGATGAAATCGAAC-AAAATGTTGATGCTTGATCTA
* * *
258237 TCTCCTTCTACGATATAGTCGAGCAAAAGGTTGA
126 TCTCCTTCTACGATAGAATCTAGCAAAAGG-TGA
* * *
258271 ACAAGTTCTTCTCATTATGAACTTCCTATCCTTCTTTGGATGAGTTATTCTCATTATGAACTCTC
1 ACAAGTTCTTCTCATTATGAACTT--TCTCC--CTTCGGATGAGTTCTTCTCATTATGAACTCTC
* * * *
258336 CCTTGGAAATGTTGATTCACATCCTTCTATGATG
62 CATTGGAAATGATGATCCACCTCCTTCTATGATG
258370 GATTTAAATC
Statistics
Matches: 354, Mismatches: 59, Indels: 25
0.81 0.13 0.06
Matches are distributed among these distances:
160 5 0.01
161 7 0.02
162 3 0.01
163 268 0.76
164 60 0.17
165 8 0.02
166 3 0.01
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (158 bp):
ACAAGTTCTTCTCATTATGAACTTTCTCCCTTCGGATGAGTTCTTCTCATTATGAACTCTCCATT
GGAAATGATGATCCACCTCCTTCTATGATGAAATCGAACAAAATGTTGATGCTTGATCTATCTCC
TTCTACGATAGAATCTAGCAAAAGGTGA
Found at i:264490 original size:25 final size:25
Alignment explanation
Indices: 264461--264524 Score: 119
Period size: 25 Copynumber: 2.6 Consensus size: 25
264451 ATGCATCTCG
264461 AGTTGTAGCTTATGCAAGAAGATAA
1 AGTTGTAGCTTATGCAAGAAGATAA
*
264486 AGTTGTAGCTTATGCAAGAAGGTAA
1 AGTTGTAGCTTATGCAAGAAGATAA
264511 AGTTGTAGCTTATG
1 AGTTGTAGCTTATG
264525 ATACCCGATA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 38 1.00
ACGTcount: A:0.34, C:0.08, G:0.27, T:0.31
Consensus pattern (25 bp):
AGTTGTAGCTTATGCAAGAAGATAA
Found at i:267363 original size:23 final size:23
Alignment explanation
Indices: 267333--267378 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
267323 ATGTTGTAAT
267333 GTTGGATGGAGGTTGATTTCATG
1 GTTGGATGGAGGTTGATTTCATG
267356 GTTGGATGGAGGTTGATTTCATG
1 GTTGGATGGAGGTTGATTTCATG
267379 CTTGAATAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.04, G:0.39, T:0.39
Consensus pattern (23 bp):
GTTGGATGGAGGTTGATTTCATG
Found at i:278400 original size:22 final size:22
Alignment explanation
Indices: 278370--278422 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
278360 TTTCTTGCTT
278370 TGAACGGCGTGAATGGTGGCGAC
1 TGAA-GGCGTGAATGGTGGCGAC
278393 TGAAGGCGTGAATGGTGGCGAC
1 TGAAGGCGTGAATGGTGGCGAC
278415 TGAAGGCG
1 TGAAGGCG
278423 CGACGCAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.23, C:0.15, G:0.45, T:0.17
Consensus pattern (22 bp):
TGAAGGCGTGAATGGTGGCGAC
Found at i:302022 original size:15 final size:15
Alignment explanation
Indices: 301998--302028 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
301988 ATTCACACGG
*
301998 TTTCTTTTAATTTTC
1 TTTCTCTTAATTTTC
302013 TTTCTCTTAATTTTC
1 TTTCTCTTAATTTTC
302028 T
1 T
302029 AATTTATTAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.16, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTCTCTTAATTTTC
Found at i:310162 original size:17 final size:18
Alignment explanation
Indices: 310133--310167 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
310123 GAGGGTCTTG
310133 GTAAAATGAGATTAAATA
1 GTAAAATGAGATTAAATA
*
310151 GTAAAA-GAGATTTAATA
1 GTAAAATGAGATTAAATA
310168 AAAGGTAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 10 0.62
18 6 0.38
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
GTAAAATGAGATTAAATA
Found at i:333068 original size:15 final size:16
Alignment explanation
Indices: 333037--333070 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
333027 GCTCAATAAC
333037 TTTATTATCAGCTTCA
1 TTTATTATCAGCTTCA
*
333053 TTTATTTTCA-CTTCA
1 TTTATTATCAGCTTCA
333068 TTT
1 TTT
333071 GTATTAGTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 8 0.47
16 9 0.53
ACGTcount: A:0.21, C:0.18, G:0.03, T:0.59
Consensus pattern (16 bp):
TTTATTATCAGCTTCA
Found at i:333973 original size:101 final size:101
Alignment explanation
Indices: 333804--333985 Score: 310
Period size: 101 Copynumber: 1.8 Consensus size: 101
333794 GAGTCACTTT
**
333804 CTTTCTTTCTTTCTTTCTTTGCATTTGCCTCAACACCCAAATATTGTTACCTTAAAGGCTACTTA
1 CTTTCTTTCTTTCTTTCTTTGCATTTGCCTCAACACCCAAATATTGACACCTTAAAGGCTACTTA
333869 TGAGGATGACAATGCGTACGTGAAGGTGGTGAGTCA
66 TGAGGATGACAATGCGTACGTGAAGGTGGTGAGTCA
* * * *
333905 CTTTCTTTCTTTCTTTCTTTGCATTTGCCTCAGCACGCGAATATTGACACCTTGAAGGCTACTTA
1 CTTTCTTTCTTTCTTTCTTTGCATTTGCCTCAACACCCAAATATTGACACCTTAAAGGCTACTTA
333970 TGAGGATGACAATGCG
66 TGAGGATGACAATGCG
333986 GTCCATTTTG
Statistics
Matches: 75, Mismatches: 6, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
101 75 1.00
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.37
Consensus pattern (101 bp):
CTTTCTTTCTTTCTTTCTTTGCATTTGCCTCAACACCCAAATATTGACACCTTAAAGGCTACTTA
TGAGGATGACAATGCGTACGTGAAGGTGGTGAGTCA
Found at i:334118 original size:4 final size:4
Alignment explanation
Indices: 334109--334135 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
334099 TATTCAATAT
334109 TTTC TTTC TTTC TTTC TTTC TTTC TTT
1 TTTC TTTC TTTC TTTC TTTC TTTC TTT
334136 ATTCATTTGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.22, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTC
Found at i:334919 original size:29 final size:29
Alignment explanation
Indices: 334887--334954 Score: 127
Period size: 29 Copynumber: 2.3 Consensus size: 29
334877 AAAAAGATGA
*
334887 AATAAAAATGTAAGAGGGAAGTGAACAAT
1 AATATAAATGTAAGAGGGAAGTGAACAAT
334916 AATATAAATGTAAGAGGGAAGTGAACAAT
1 AATATAAATGTAAGAGGGAAGTGAACAAT
334945 AATATAAATG
1 AATATAAATG
334955 AAACAAGCAT
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 38 1.00
ACGTcount: A:0.54, C:0.03, G:0.22, T:0.21
Consensus pattern (29 bp):
AATATAAATGTAAGAGGGAAGTGAACAAT
Found at i:336060 original size:22 final size:24
Alignment explanation
Indices: 336034--336077 Score: 65
Period size: 22 Copynumber: 1.9 Consensus size: 24
336024 GAGCTAAACC
336034 AGAAAGGT-GGGGAAGG-GGAGGA
1 AGAAAGGTCGGGGAAGGAGGAGGA
*
336056 AGAAAGGTCGGGGTAGGAGGAG
1 AGAAAGGTCGGGGAAGGAGGAG
336078 AGGTGATTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 7 0.37
24 4 0.21
ACGTcount: A:0.34, C:0.02, G:0.57, T:0.07
Consensus pattern (24 bp):
AGAAAGGTCGGGGAAGGAGGAGGA
Found at i:336446 original size:13 final size:13
Alignment explanation
Indices: 336428--336454 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
336418 TTTAAAACCC
336428 TGTAACACACAAA
1 TGTAACACACAAA
336441 TGTAACACACAAA
1 TGTAACACACAAA
336454 T
1 T
336455 AAAGCATTGA
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:0.52, C:0.22, G:0.07, T:0.19
Consensus pattern (13 bp):
TGTAACACACAAA
Found at i:344147 original size:4 final size:4
Alignment explanation
Indices: 344138--344163 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
344128 TGACCAAATG
344138 AAGA AAGA AAGA AAGA AAGA AAGA AA
1 AAGA AAGA AAGA AAGA AAGA AAGA AA
344164 ATATTGAACA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (4 bp):
AAGA
Found at i:344455 original size:115 final size:116
Alignment explanation
Indices: 344248--344478 Score: 340
Period size: 115 Copynumber: 2.0 Consensus size: 116
344238 TCCTGTCAAA
* *
344248 TAACTCCCCACCTTCACACAACTCCATAACAAAATGGACCACATTTTCATCCTCAAAAGTAGCCT
1 TAACTCACCACCTTCACACAACTCCATAACAAAATGGACCACATTGTCATCCTCAAAAGTAGCCT
* *
344313 TCAAGGTATCAATATTTGCGTGCTGAGGCAAATGC-AAGAAATAAAGAAAG
66 TCAAGGTAACAATATTTGCGTGCTGAGGCAAATGCAAAGAAAGAAAGAAAG
* * * * *
344363 TAACTCACCACCTTCACACAATTCCATAACCAAATGGACCGCGTTGTCATCCTCATAAGTAGCCT
1 TAACTCACCACCTTCACACAACTCCATAACAAAATGGACCACATTGTCATCCTCAAAAGTAGCCT
* *
344428 TCAAGGTAACATTATTTAG-GTGTTGAGGCAAATGCAAAGAAAGAAAGAAAG
66 TCAAGGTAACAATATTT-GCGTGCTGAGGCAAATGCAAAGAAAGAAAGAAAG
344479 AAAGTGACTC
Statistics
Matches: 103, Mismatches: 11, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
115 88 0.85
116 15 0.15
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.23
Consensus pattern (116 bp):
TAACTCACCACCTTCACACAACTCCATAACAAAATGGACCACATTGTCATCCTCAAAAGTAGCCT
TCAAGGTAACAATATTTGCGTGCTGAGGCAAATGCAAAGAAAGAAAGAAAG
Found at i:345436 original size:24 final size:25
Alignment explanation
Indices: 345388--345436 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
345378 TCGGGAGATA
* *
345388 AATTATATTTTAAAAATACATTAGT
1 AATTATATTTTAAAAATAAACTAGT
345413 AATTATATTTT-AAAATAAACTAGT
1 AATTATATTTTAAAAATAAACTAGT
345437 GGTAAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.43
Consensus pattern (25 bp):
AATTATATTTTAAAAATAAACTAGT
Found at i:350778 original size:20 final size:21
Alignment explanation
Indices: 350753--350797 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
350743 AACTGGATCT
350753 GGTTGT-AACATGGGCATTCG
1 GGTTGTGAACATGGGCATTCG
* * *
350773 GGTTGTGTATATGGGCCTTCG
1 GGTTGTGAACATGGGCATTCG
350794 GGTT
1 GGTT
350798 TAATGTGCGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.13, C:0.13, G:0.38, T:0.36
Consensus pattern (21 bp):
GGTTGTGAACATGGGCATTCG
Found at i:350841 original size:13 final size:13
Alignment explanation
Indices: 350825--350871 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
350815 TATAAAATTG
*
350825 TAATAATTAATTA
1 TAATAATTAATAA
350838 TAATAATATAATAA
1 TAATAAT-TAATAA
*
350852 CAATAA-TATATAA
1 TAATAATTA-ATAA
350865 TAATAAT
1 TAATAAT
350872 ATTATAACAC
Statistics
Matches: 28, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
12 2 0.07
13 16 0.57
14 10 0.36
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATTAATAA
Found at i:350843 original size:3 final size:3
Alignment explanation
Indices: 350825--350872 Score: 53
Period size: 3 Copynumber: 15.7 Consensus size: 3
350815 TATAAAATTG
* *
350825 TAA TAA TTAA TTA TAA TAA T-A TAA TAA CAA TAA TATA TAA TAA TAA
1 TAA TAA -TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
350871 TA
1 TA
350873 TTATAACACT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
2 2 0.05
3 30 0.79
4 6 0.16
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:350862 original size:16 final size:16
Alignment explanation
Indices: 350837--350877 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
350827 ATAATTAATT
350837 ATAATAATATAATAACA
1 ATAAT-ATATAATAACA
*
350854 ATAATATATAATAATA
1 ATAATATATAATAACA
*
350870 ATATTATA
1 ATAATATA
350878 ACACTTATAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.77
17 5 0.23
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAATATATAATAACA
Found at i:351257 original size:89 final size:89
Alignment explanation
Indices: 351127--351293 Score: 289
Period size: 89 Copynumber: 1.9 Consensus size: 89
351117 GTGAAGGCTA
* * *
351127 GATTGACTTGAAAAGAATCTGTTTCACTACTCTTTCGTGAAGATCAGATTCAAGGTTGATTTGCT
1 GATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCAGATTCAAGGTTGATTTGCT
*
351192 TGCACTACTCTTCCGTAGAGGTTG
66 TCCACTACTCTTCCGTAGAGGTTG
*
351216 GATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCATATTCAAGGTTGATTTGCT
1 GATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCAGATTCAAGGTTGATTTGCT
351281 TCCACTACTCTTC
66 TCCACTACTCTTC
351294 TGTGGAGACC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
89 73 1.00
ACGTcount: A:0.26, C:0.20, G:0.17, T:0.37
Consensus pattern (89 bp):
GATTGACTTGAAAAGAATCTATTTCACTACTCTTCCATGAAGATCAGATTCAAGGTTGATTTGCT
TCCACTACTCTTCCGTAGAGGTTG
Found at i:363962 original size:21 final size:21
Alignment explanation
Indices: 363938--363993 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
363928 TGTAACATAG
* *
363938 GCATTCGGGTTGTGTATATGA
1 GCATTCAGGTTGTATATATGA
363959 GCATTCAGGTTGTATATATGA
1 GCATTCAGGTTGTATATATGA
* *
363980 GTATTTAGGTTGTA
1 GCATTCAGGTTGTA
363994 ATTGGGCCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.23, C:0.07, G:0.29, T:0.41
Consensus pattern (21 bp):
GCATTCAGGTTGTATATATGA
Found at i:364073 original size:16 final size:16
Alignment explanation
Indices: 364052--364086 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
364042 ATTAATTATA
364052 ATATAATAACAATAAT
1 ATATAATAACAATAAT
* *
364068 ATATAATAATAATATT
1 ATATAATAACAATAAT
364084 ATA
1 ATA
364087 ACACTTATAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (16 bp):
ATATAATAACAATAAT
Found at i:365412 original size:44 final size:44
Alignment explanation
Indices: 365349--365441 Score: 177
Period size: 44 Copynumber: 2.1 Consensus size: 44
365339 CCATACCCTA
365349 CCACCTCTACTGAAACCCCATACCCCAAGCCATCCCTGCTGCTG
1 CCACCTCTACTGAAACCCCATACCCCAAGCCATCCCTGCTGCTG
*
365393 CCACCTCTACTGCAACCCCATACCCCAAGCCATCCCTGCTGCTG
1 CCACCTCTACTGAAACCCCATACCCCAAGCCATCCCTGCTGCTG
365437 CCACC
1 CCACC
365442 ACCAAATCCC
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 48 1.00
ACGTcount: A:0.22, C:0.51, G:0.11, T:0.17
Consensus pattern (44 bp):
CCACCTCTACTGAAACCCCATACCCCAAGCCATCCCTGCTGCTG
Found at i:367155 original size:19 final size:19
Alignment explanation
Indices: 367114--367160 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
367104 ACTCCAATTA
*
367114 TTATTTTTATTCTATTTTT
1 TTATTTTTATTCTATTTTC
*
367133 TTATTTTTTTTC-ATTTATC
1 TTATTTTTATTCTATTT-TC
*
367152 TTATCTTTA
1 TTATTTTTA
367161 AATAGCTTTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (19 bp):
TTATTTTTATTCTATTTTC
Found at i:368296 original size:37 final size:38
Alignment explanation
Indices: 368243--368526 Score: 212
Period size: 37 Copynumber: 7.8 Consensus size: 38
368233 ATATATATTA
*
368243 AAAACT-TATATAATATATAGTTTTTAAAACATTTTAG
1 AAAACTATATATAATATATAGTTTTTAAAACATTTTTG
* *
368280 AAAA-TATATATAATATATGGTTTTCAAAATCA-TTTTG
1 AAAACTATATATAATATATAGTTTTTAAAA-CATTTTTG
* * ***
368317 AAAACTA-ATATAATTTATAGTTTTTGAATTTTTTTTG
1 AAAACTATATATAATATATAGTTTTTAAAACATTTTTG
* * *
368354 AAAACT-TATAAAATATATAGTTTATGAAAACATTTTTAAA
1 AAAACTATATATAATATATAGTTT-TTAAAACATTTTT--G
*
368394 AAAACTTATATATAATATATAATTTTTAAAACATTTTTG
1 AAAAC-TATATATAATATATAGTTTTTAAAACATTTTTG
*
368433 ---A--A-A-A-AATATATAGCTTTTAAAAACATTTTTG
1 AAAACTATATATAATATATAG-TTTTTAAAACATTTTTG
* *
368464 AAAA-T-TATAT-A-GT-T--TTTTAAAAACATTTTTTG
1 AAAACTATATATAATATATAGTTTTTAAAACA-TTTTTG
*
368496 AAAATTTATATATAATATATAGTTTTTAAAA
1 AAAA-CTATATATAATATATAGTTTTTAAAA
368527 GTAACAATTT
Statistics
Matches: 193, Mismatches: 27, Indels: 51
0.71 0.10 0.19
Matches are distributed among these distances:
30 8 0.04
31 28 0.15
32 11 0.06
33 1 0.01
34 3 0.02
35 7 0.04
36 5 0.03
37 76 0.39
38 13 0.07
40 13 0.07
41 13 0.07
42 15 0.08
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (38 bp):
AAAACTATATATAATATATAGTTTTTAAAACATTTTTG
Found at i:368398 original size:40 final size:41
Alignment explanation
Indices: 368354--368438 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
368344 ATTTTTTTTG
*
368354 AAAACTTATA-A-AATATATAGTTTATGAAAACATTTTTAAA
1 AAAACTTATATATAATATATAATTT-TGAAAACATTTTTAAA
* *
368394 AAAACTTATATATAATATATAATTTTTAAAACATTTTTGAA
1 AAAACTTATATATAATATATAATTTTGAAAACATTTTTAAA
368435 AAAA
1 AAAA
368439 TATATAGCTT
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
40 10 0.25
41 19 0.47
42 11 0.28
ACGTcount: A:0.53, C:0.05, G:0.04, T:0.39
Consensus pattern (41 bp):
AAAACTTATATATAATATATAATTTTGAAAACATTTTTAAA
Found at i:368441 original size:30 final size:31
Alignment explanation
Indices: 368407--368499 Score: 118
Period size: 30 Copynumber: 3.0 Consensus size: 31
368397 ACTTATATAT
368407 AATATATA-ATTTTTAAAACATTTTTGAAAA
1 AATATATAGATTTTTAAAACATTTTTGAAAA
* *
368437 AATATATAGCTTTTAAAAACATTTTTG-AAA
1 AATATATAGATTTTTAAAACATTTTTGAAAA
* *
368467 ATTATATAGTTTTTTAAAAACATTTTTTGAAAA
1 AATATATAGATTTTT-AAAACA-TTTTTGAAAA
368500 TTTATATATA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
30 23 0.43
31 22 0.41
32 6 0.11
33 3 0.06
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (31 bp):
AATATATAGATTTTTAAAACATTTTTGAAAA
Found at i:368459 original size:31 final size:31
Alignment explanation
Indices: 368407--368499 Score: 118
Period size: 31 Copynumber: 3.0 Consensus size: 31
368397 ACTTATATAT
*
368407 AATATATA-ATTTTTAAAACATTTTTGAAAA
1 AATATATAGATTTTAAAAACATTTTTGAAAA
*
368437 AATATATAGCTTTTAAAAACATTTTTG-AAA
1 AATATATAGATTTTAAAAACATTTTTGAAAA
* *
368467 ATTATATAGTTTTTTAAAAACATTTTTTGAAAA
1 AATATATAG-ATTTTAAAAACA-TTTTTGAAAA
368500 TTTATATATA
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
30 19 0.35
31 27 0.49
32 6 0.11
33 3 0.05
ACGTcount: A:0.46, C:0.04, G:0.05, T:0.44
Consensus pattern (31 bp):
AATATATAGATTTTAAAAACATTTTTGAAAA
Found at i:368558 original size:4 final size:4
Alignment explanation
Indices: 368549--368580 Score: 50
Period size: 4 Copynumber: 8.5 Consensus size: 4
368539 AAAATGTATA
368549 TTAT TTAT TTAT TTA- TTA- TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT TTAT TT
368581 TATTATTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 6 0.22
4 21 0.78
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:368568 original size:18 final size:18
Alignment explanation
Indices: 368547--368617 Score: 85
Period size: 18 Copynumber: 3.9 Consensus size: 18
368537 TAAAAATGTA
368547 TATTATTTATTTATTTAT
1 TATTATTTATTTATTTAT
368565 TATTATTTATTTATTTTAT
1 TATTATTTATTTA-TTTAT
368584 TATTA-TTATTTCA-TTACT
1 TATTATTTATTT-ATTTA-T
368602 TATT-TTTATTTTATTT
1 TATTATTTA-TTTATTT
368618 TCTTTCGTTT
Statistics
Matches: 47, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.06
18 28 0.60
19 16 0.34
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (18 bp):
TATTATTTATTTATTTAT
Found at i:368574 original size:22 final size:22
Alignment explanation
Indices: 368549--368611 Score: 78
Period size: 22 Copynumber: 2.9 Consensus size: 22
368539 AAAATGTATA
368549 TTATTTATTTATTTATTATTAT
1 TTATTTATTTATTTATTATTAT
368571 TTATTTATTT-TATTATTATTAT
1 TTATTTATTTAT-TTATTATTAT
*
368593 TTCA-TTACTTATTT-TTATT
1 TT-ATTTATTTATTTATTATT
368612 TTATTTTCTT
Statistics
Matches: 37, Mismatches: 1, Indels: 7
0.82 0.02 0.16
Matches are distributed among these distances:
21 6 0.16
22 29 0.78
23 2 0.05
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.71
Consensus pattern (22 bp):
TTATTTATTTATTTATTATTAT
Found at i:368618 original size:11 final size:12
Alignment explanation
Indices: 368547--368618 Score: 55
Period size: 11 Copynumber: 6.0 Consensus size: 12
368537 TAAAAATGTA
*
368547 TATTATT-TATT
1 TATTATTATTTT
368558 TATTTATTATTATT
1 TA-TTATTATT-TT
368572 TA-T-TTA-TTT
1 TATTATTATTTT
368581 TATTATTATTATT
1 TATTATTATT-TT
368594 TCATTACTTATTTT
1 T-ATTA-TTATTTT
368608 TATT-TTATTTT
1 TATTATTATTTT
368619 CTTTCGTTTC
Statistics
Matches: 51, Mismatches: 1, Indels: 18
0.73 0.01 0.26
Matches are distributed among these distances:
9 4 0.08
10 2 0.04
11 15 0.29
12 7 0.14
13 7 0.14
14 11 0.22
15 5 0.10
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (12 bp):
TATTATTATTTT
Found at i:369733 original size:8 final size:8
Alignment explanation
Indices: 369720--369866 Score: 55
Period size: 8 Copynumber: 17.1 Consensus size: 8
369710 TTTAATTAAC
369720 TTTTTTAT
1 TTTTTTAT
*
369728 TTTTTTCT
1 TTTTTTAT
*
369736 TTATTCTAT
1 TT-TTTTAT
369745 TTTTATT-T
1 TTTT-TTAT
369753 ATTTTTTA-
1 -TTTTTTAT
**
369761 TTCCTTAT
1 TTTTTTAT
*
369769 TTATTTAT
1 TTTTTTAT
*
369777 TTATTTAT
1 TTTTTTAT
*
369785 TTATTTAT
1 TTTTTTAT
369793 TTTTACTTAT
1 TTTT--TTAT
*
369803 TTAATTTAAT
1 TT--TTTTAT
*
369813 TTTTTTCT
1 TTTTTTAT
*
369821 CTCTTTTTCGT
1 -T-TTTTT-AT
369832 TTTTTTAT
1 TTTTTTAT
*
369840 TTTGATTTGT
1 TTT--TTTAT
*
369850 TATTTTAT
1 TTTTTTAT
*
369858 TATTTTAT
1 TTTTTTAT
369866 T
1 T
369867 ATTATTATTA
Statistics
Matches: 108, Mismatches: 17, Indels: 28
0.71 0.11 0.18
Matches are distributed among these distances:
7 5 0.05
8 60 0.56
9 17 0.16
10 23 0.21
11 1 0.01
12 2 0.02
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.75
Consensus pattern (8 bp):
TTTTTTAT
Found at i:369747 original size:22 final size:21
Alignment explanation
Indices: 369722--369820 Score: 64
Period size: 23 Copynumber: 4.7 Consensus size: 21
369712 TAATTAACTT
369722 TTTTATTTTTTTCTTTATTCTA
1 TTTTATTTTTTTCTTTATT-TA
*
369744 TTTTTATTTATTT-TTTATTCCT-
1 -TTTTATTTTTTTCTTTATT--TA
* *
369766 TATTTATTTATTTATTTATTTA
1 T-TTTATTTTTTTCTTTATTTA
*
369788 -TTTA-TTTTTAC-TTATTTAA
1 TTTTATTTTTTTCTTTATTT-A
*
369807 TTTAATTTTTTTCT
1 TTTTATTTTTTTCT
369821 CTCTTTTTCG
Statistics
Matches: 62, Mismatches: 6, Indels: 17
0.73 0.07 0.20
Matches are distributed among these distances:
18 6 0.10
19 5 0.08
20 7 0.11
21 8 0.13
22 17 0.27
23 19 0.31
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (21 bp):
TTTTATTTTTTTCTTTATTTA
Found at i:369755 original size:4 final size:4
Alignment explanation
Indices: 369723--369794 Score: 71
Period size: 4 Copynumber: 18.8 Consensus size: 4
369713 AATTAACTTT
* * * *
369723 TTTA TTTT TTTC TTTA TTCTA -TT- TTTA TTTA TTT- TTTA -TTC CTTA
1 TTTA TTTA TTTA TTTA TT-TA TTTA TTTA TTTA TTTA TTTA TTTA TTTA
369768 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
369795 TTACTTATTT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
3 8 0.14
4 47 0.82
5 2 0.04
ACGTcount: A:0.18, C:0.06, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:369868 original size:3 final size:3
Alignment explanation
Indices: 369849--369881 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
369839 TTTTGATTTG
369849 TTA TT- TTA TTA TT- TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
369882 TTCCTCTAAC
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 4 0.14
3 24 0.86
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (3 bp):
TTA
Found at i:369881 original size:9 final size:8
Alignment explanation
Indices: 369849--369878 Score: 51
Period size: 8 Copynumber: 3.6 Consensus size: 8
369839 TTTTGATTTG
369849 TTATTTTA
1 TTATTTTA
369857 TTATTTTA
1 TTATTTTA
369865 TTATTATTA
1 TTATT-TTA
369874 TTATT
1 TTATT
369879 ATTTTCCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
8 13 0.62
9 8 0.38
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (8 bp):
TTATTTTA
Found at i:369979 original size:12 final size:13
Alignment explanation
Indices: 369957--369985 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
369947 ATAGGGTAAT
369957 TTTTAAATTTTAA
1 TTTTAAATTTTAA
369970 TTTT-AATTTTAA
1 TTTTAAATTTTAA
369982 TTTT
1 TTTT
369986 CGCAAATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 12 0.75
13 4 0.25
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TTTTAAATTTTAA
Found at i:370638 original size:17 final size:17
Alignment explanation
Indices: 370616--370652 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
370606 TAATGGGATT
370616 AGGACTAAGGGTCTGGA
1 AGGACTAAGGGTCTGGA
370633 AGGACTAAGGGTCTGGA
1 AGGACTAAGGGTCTGGA
370650 AGG
1 AGG
370653 CCCAAGGGGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.11, G:0.43, T:0.16
Consensus pattern (17 bp):
AGGACTAAGGGTCTGGA
Found at i:370659 original size:17 final size:17
Alignment explanation
Indices: 370616--370660 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
370606 TAATGGGATT
*
370616 AGGACTAAGGGTCTGGA
1 AGGACCAAGGGTCTGGA
*
370633 AGGACTAAGGGTCTGGA
1 AGGACCAAGGGTCTGGA
*
370650 AGGCCCAAGGG
1 AGGACCAAGGG
370661 GGCACCAACA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.29, C:0.16, G:0.42, T:0.13
Consensus pattern (17 bp):
AGGACCAAGGGTCTGGA
Found at i:371534 original size:19 final size:19
Alignment explanation
Indices: 371510--371555 Score: 92
Period size: 19 Copynumber: 2.4 Consensus size: 19
371500 CTAGACATAT
371510 TTTGCATTTCATTATTTTC
1 TTTGCATTTCATTATTTTC
371529 TTTGCATTTCATTATTTTC
1 TTTGCATTTCATTATTTTC
371548 TTTGCATT
1 TTTGCATT
371556 CTTATTAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.15, C:0.15, G:0.07, T:0.63
Consensus pattern (19 bp):
TTTGCATTTCATTATTTTC
Found at i:373783 original size:95 final size:94
Alignment explanation
Indices: 373615--373810 Score: 270
Period size: 95 Copynumber: 2.1 Consensus size: 94
373605 TATAAAATTA
* * *
373615 TATATATACAATAAAGCTTAAGTTGTTCCTCCAGAGCAATTGGTTAAACGACCTGACTTCATGGA
1 TATATATACAATAAAGCTTAAGTTGTCCCTCAAGAGCAATTGGTTAAACGACCTGACTTCATAGA
* *
373680 TAATATTCAGCTAGCCTGATAAAGGTGAT
66 TAAGATTCAGCTAACCTGATAAAGGTGAT
* *
373709 TATACTATACAATAAAGCTTGAGTTGTCCCTCTAAGA-CAATTGGTTAAACGCCCTGACATT-AT
1 TATA-TATACAATAAAGCTTAAGTTGTCCCTC-AAGAGCAATTGGTTAAACGACCTGAC-TTCAT
*
373772 AGATAAGATTCAGCTAACCTGATAAAGGTGTT
63 AGATAAGATTCAGCTAACCTGATAAAGGTGAT
*
373804 TACATAT
1 TATATAT
373811 TGAGCTGTCC
Statistics
Matches: 90, Mismatches: 9, Indels: 6
0.86 0.09 0.06
Matches are distributed among these distances:
94 7 0.08
95 78 0.87
96 5 0.06
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (94 bp):
TATATATACAATAAAGCTTAAGTTGTCCCTCAAGAGCAATTGGTTAAACGACCTGACTTCATAGA
TAAGATTCAGCTAACCTGATAAAGGTGAT
Found at i:375226 original size:36 final size:37
Alignment explanation
Indices: 375168--375247 Score: 135
Period size: 36 Copynumber: 2.2 Consensus size: 37
375158 AATTTACTCC
* *
375168 AAACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG
1 AAACAAAGTTGTGTCTCTCTTGAGACAGTTTATCTTG
375205 AAACAAA-TTGTGTCTCTCTTGAGACAGTTTATCTTG
1 AAACAAAGTTGTGTCTCTCTTGAGACAGTTTATCTTG
375241 AAACAAA
1 AAACAAA
375248 ATCTTTGAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
36 34 0.83
37 7 0.17
ACGTcount: A:0.31, C:0.17, G:0.15, T:0.36
Consensus pattern (37 bp):
AAACAAAGTTGTGTCTCTCTTGAGACAGTTTATCTTG
Found at i:375390 original size:37 final size:37
Alignment explanation
Indices: 375260--375404 Score: 154
Period size: 37 Copynumber: 4.0 Consensus size: 37
375250 CTTTGAATAT
* **
375260 GTTTTCCTTGAAACAAA-TTTCATCTC-CTTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTC-TTGAGACA
** * *
375296 GTTTCGTTTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
* * *
375333 GTTTCTCTTG-AA-ATATTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
*
375368 ATTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
375405 CCAATCTTTG
Statistics
Matches: 89, Mismatches: 16, Indels: 7
0.79 0.14 0.06
Matches are distributed among these distances:
35 28 0.31
36 16 0.18
37 44 0.49
38 1 0.01
ACGTcount: A:0.23, C:0.19, G:0.15, T:0.42
Consensus pattern (37 bp):
GTTTCCCTTGAAACAAAGTTTTGTCTCTCTTGAGACA
Found at i:375553 original size:36 final size:33
Alignment explanation
Indices: 375458--375573 Score: 171
Period size: 33 Copynumber: 3.4 Consensus size: 33
375448 CAGGAGACAA
* *
375458 TTTCTCTTGAAACACAAAATACCTTTGAAATCG
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATAG
375491 TTTCTCTTGAAACACAAAAAACCTTTGAAATAG
1 TTTCTCTTGAAACACAAAAAACCTTTGAAATAG
375524 TTTCTCTTGAAACACAAAAAAAAACCTTTGAAA-ATG
1 TTTCTCTTGAAACAC---AAAAAACCTTTGAAATA-G
375560 TTTCTCTTGAAACA
1 TTTCTCTTGAAACA
375574 TAAAGGCCTT
Statistics
Matches: 77, Mismatches: 2, Indels: 5
0.92 0.02 0.06
Matches are distributed among these distances:
33 46 0.60
35 1 0.01
36 30 0.39
ACGTcount: A:0.41, C:0.19, G:0.09, T:0.32
Consensus pattern (33 bp):
TTTCTCTTGAAACACAAAAAACCTTTGAAATAG
Found at i:375813 original size:81 final size:80
Alignment explanation
Indices: 375575--375973 Score: 399
Period size: 81 Copynumber: 5.0 Consensus size: 80
375565 CTTGAAACAT
* * * * *
375575 AAAGGCCTTCGAGCTCGACTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCT
1 AAAGACCTTCGAGTTCGATTACACTCAGC-TCAAAGGCACATCATTTGCAGCATAACTCAAGGCT
375640 AGAAGGGTTATCTGCC
65 AGAAGGGTTATCTGCC
* * * ** * * * *
375656 AAAGACCTTAGAGTTCGATTCCATTCAGCTCAAAGGTGCATCATTTGTAGCATAGCTTAAGGCAA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTA
* *
375721 GAAGGGCTATCTTCC
66 GAAGGGTTATCTGCC
* * * **
375736 AAAGACCCTCGAGTTCGATTATACTCAGTTTC-AAGAGCACATTGTTTGCAGCATAACTCAAGGC
1 AAAGACCTTCGAGTTCGATTACACTCAG-CTCAAAG-GCACATCATTTGCAGCATAACTCAAGGC
375800 TAGAAGGGTTATCTGCC
64 TAGAAGGGTTATCTGCC
* * * * * *
375817 AAAGACCTTAGAGTTCGATTCCACTTAGCTCAAAGGTACTATCATTTGTAGCACAACTCAAGGCT
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCAC-ATCATTTGCAGCATAACTCAAGGCT
* *
375882 AAAAGGGTTATTTGCC
65 AGAAGGGTTATCTGCC
* * * ** * *
375898 AAAGAACTTCGAGTTCGATTCCATTCAGCTC-AA-GCTACATCATTCACAGCATAGCTCAAGGCA
1 AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGC-ACATCATTTGCAGCATAACTCAAGGCT
*
375961 AGAAGGGCTATCT
65 AGAAGGGTTATCT
375974 ATCAACAAAA
Statistics
Matches: 254, Mismatches: 59, Indels: 12
0.78 0.18 0.04
Matches are distributed among these distances:
79 30 0.12
80 76 0.30
81 148 0.58
ACGTcount: A:0.30, C:0.23, G:0.21, T:0.26
Consensus pattern (80 bp):
AAAGACCTTCGAGTTCGATTACACTCAGCTCAAAGGCACATCATTTGCAGCATAACTCAAGGCTA
GAAGGGTTATCTGCC
Found at i:376011 original size:162 final size:161
Alignment explanation
Indices: 375583--375973 Score: 445
Period size: 161 Copynumber: 2.4 Consensus size: 161
375573 ATAAAGGCCT
* * * * ** *
375583 TCGAGCTCGACTACACTCAG-CTTCGAGGGCACATCATTTGCAGCATAACTCAAGGCTAGAAGGG
1 TCGAGTTCGATTACACTCAGTC-TCAAGAGCACATCATTCACAGCATAACTCAAGGCAAGAAGGG
* * * *
375647 TTATCTGCCAAAGACCTTAGAGTTCGATTCCATTCAGCTCAAAGGTGCATCATTTGTAGCATAGC
65 CTATCTGCCAAAGACCTTAGAGTTCGATTCCATTCAGCTCAAAGGTACATCATTTGTAGCACAAC
* *
375712 TTAAGGCAAGAAGGGCTATCTTCCAAAGACCC
130 TCAAGGCAAGAAGGGCTATCTTCCAAAGAACC
* * ** ** * *
375744 TCGAGTTCGATTATACTCAGTTTCAAGAGCACATTGTTTGCAGCATAACTCAAGGCTAGAAGGGT
1 TCGAGTTCGATTACACTCAGTCTCAAGAGCACATCATTCACAGCATAACTCAAGGCAAGAAGGGC
375809 TATCTGCCAAAGACCTTAGAGTTCGATTCCACTT-AGCTCAAAGGTACTATCATTTGTAGCACAA
66 TATCTGCCAAAGACCTTAGAGTTCGATTCCA-TTCAGCTCAAAGGTAC-ATCATTTGTAGCACAA
* *
375873 CTCAAGGCTAA-AAGGGTTAT-TTGCCAAAGAACT
129 CTCAAGGC-AAGAAGGGCTATCTT-CCAAAGAACC
* * *
375906 TCGAGTTCGATTCCATTCAG-CTC-A-AGCTACATCATTCACAGCATAGCTCAAGGCAAGAAGGG
1 TCGAGTTCGATTACACTCAGTCTCAAGAGC-ACATCATTCACAGCATAACTCAAGGCAAGAAGGG
375968 CTATCT
65 CTATCT
375974 ATCAACAAAA
Statistics
Matches: 198, Mismatches: 26, Indels: 13
0.84 0.11 0.05
Matches are distributed among these distances:
159 3 0.02
160 34 0.17
161 103 0.52
162 56 0.28
163 2 0.01
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (161 bp):
TCGAGTTCGATTACACTCAGTCTCAAGAGCACATCATTCACAGCATAACTCAAGGCAAGAAGGGC
TATCTGCCAAAGACCTTAGAGTTCGATTCCATTCAGCTCAAAGGTACATCATTTGTAGCACAACT
CAAGGCAAGAAGGGCTATCTTCCAAAGAACC
Found at i:376587 original size:36 final size:36
Alignment explanation
Indices: 376524--376757 Score: 197
Period size: 36 Copynumber: 6.2 Consensus size: 36
376514 TTATTATATA
376524 TATATATATATATAGTTTTTAAAAAAACATTTTGAAAA-T
1 TATATA-ATATATAGTTTTT---AAAACATTTTGAAAACT
376563 GTATATAATATATAGTTTTTAAAACATTTTAGAAAA-T
1 -TATATAATATATAGTTTTTAAAACATTTT-GAAAACT
* *
376600 ATATATAATATAT-GGTTTCAAAATCATTTTGAAAACT
1 -TATATAATATATAGTTTTTAAAA-CATTTTGAAAACT
* ****
376637 TATATAATATATAGTTTTTGATTTTTTTTGAAAACT
1 TATATAATATATAGTTTTTAAAACATTTTGAAAACT
* **
376673 TATATAATTTATAGTTTTTGAAAACATTTAAAAAAAAAACTT
1 TATATAATATATAGTTTTT-AAAACATTT----TGAAAAC-T
*
376715 ATATATAATATATAATTTTTAAAACATTTTTGAAAA-T
1 -TATATAATATATAGTTTTTAAAACA-TTTTGAAAACT
376752 TATATA
1 TATATA
376758 TTTTTTAAAA
Statistics
Matches: 160, Mismatches: 22, Indels: 28
0.76 0.10 0.13
Matches are distributed among these distances:
36 70 0.44
37 35 0.22
39 17 0.11
40 6 0.04
41 5 0.03
42 7 0.04
43 20 0.12
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (36 bp):
TATATAATATATAGTTTTTAAAACATTTTGAAAACT
Found at i:376701 original size:73 final size:74
Alignment explanation
Indices: 376521--376861 Score: 205
Period size: 73 Copynumber: 4.6 Consensus size: 74
376511 TTTTTATTAT
376521 ATATATATATATATATAGTTTTTAAAAAAACATTTTGAAAATGTATATAATATATAGTTTTTAAA
1 ATATATATA-ATATATAGTTTTT--AAAAACATTTTGAAAATGTATATAATATATAGTTTTTAAA
376586 ACATTTTAGAAA
63 ACATTTTAGAAA
* * * * **
376598 ATATATATAATATAT-GGTTTCAAAATCATTTTGAAAACT-TATATAATATATAGTTTTT-GATT
1 ATATATATAATATATAGTTTTTAAAAACATTTTGAAAA-TGTATATAATATATAGTTTTTAAAAC
* *
376660 TTTTTTGAAA
65 ATTTTAGAAA
* * ** * *
376670 ACT-TATATAATTTATAGTTTTTGAAAACATTTAAAAAAAAAACTTATATATAATATATAATTTT
1 A-TATATATAATATATAGTTTTTAAAAACATTT----TGAAAA--TGTATATAATATATAGTTTT
*
376734 TAAAACATTTTTG--A
59 TAAAACATTTTAGAAA
* * * *
376748 A-A-AT-T-ATATAT--TTTTTAAAAGCATTTTTGAAAA-CTATAT--TGT-T--TTTTAAAAAC
1 ATATATATAATATATAGTTTTTAAAAACA-TTTTGAAAATGTATATAATATATAGTTTTTAAAAC
*
376801 ATTTTTGAAA
65 ATTTTAGAAA
*
376811 ATTTATATATAATATATAGTTTTTAAAAGAAACAATTTTAAAAATGTATAT
1 A--TATATATAATATATAGTTTTT--AA-AAAC-ATTTTGAAAATGTATAT
376862 TATTTATTTA
Statistics
Matches: 205, Mismatches: 32, Indels: 56
0.70 0.11 0.19
Matches are distributed among these distances:
61 16 0.08
63 3 0.01
64 2 0.01
66 6 0.03
67 2 0.01
68 1 0.00
69 10 0.05
71 5 0.02
72 31 0.15
73 52 0.25
74 17 0.08
75 11 0.05
76 8 0.04
77 13 0.06
78 3 0.01
79 18 0.09
80 7 0.03
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (74 bp):
ATATATATAATATATAGTTTTTAAAAACATTTTGAAAATGTATATAATATATAGTTTTTAAAACA
TTTTAGAAA
Found at i:376775 original size:30 final size:29
Alignment explanation
Indices: 376723--376820 Score: 133
Period size: 31 Copynumber: 3.2 Consensus size: 29
376713 TTATATATAA
*
376723 TATATAATTTTTAAAACATTTTTGAAAAT
1 TATATATTTTTTAAAACATTTTTGAAAAT
*
376752 TATATATTTTTTAAAAGCATTTTTGAAAAC
1 TATATATTTTTTAAAA-CATTTTTGAAAAT
*
376782 TATATTGTTTTTTAAAAACATTTTTGAAAATT
1 TATA-TATTTTTT-AAAACATTTTTGAAAA-T
376814 TATATAT
1 TATATAT
376821 AATATATAGT
Statistics
Matches: 60, Mismatches: 5, Indels: 6
0.85 0.07 0.08
Matches are distributed among these distances:
29 15 0.25
30 16 0.27
31 21 0.35
32 8 0.13
ACGTcount: A:0.41, C:0.04, G:0.05, T:0.50
Consensus pattern (29 bp):
TATATATTTTTTAAAACATTTTTGAAAAT
Found at i:376870 original size:4 final size:4
Alignment explanation
Indices: 376861--376933 Score: 50
Period size: 4 Copynumber: 19.2 Consensus size: 4
376851 AAAATGTATA
* *
376861 TTAT TTAT TTA- TTA- TTA- TTGT TAAT ATTAT TTAT TTAT TTA- TTA-
1 TTAT TTAT TTAT TTAT TTAT TTAT TTAT -TTAT TTAT TTAT TTAT TTAT
* *
376905 TTA- TTCT TAAT ATTAT TTAT TTAT TTAT T
1 TTAT TTAT TTAT -TTAT TTAT TTAT TTAT T
376934 ATTATTATTA
Statistics
Matches: 57, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
3 16 0.28
4 35 0.61
5 6 0.11
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (4 bp):
TTAT
Found at i:376875 original size:3 final size:3
Alignment explanation
Indices: 376859--376951 Score: 78
Period size: 3 Copynumber: 28.3 Consensus size: 3
376849 TAAAAATGTA
* *
376859 TAT TATT TATT TAT TAT TAT TGT TAA TAT TATT TATT TATT TAT TAT
1 TAT TA-T TA-T TAT TAT TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT
* *
376906 TAT TCT TAA TAT TATT TATT TATT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TA-T TA-T TA-T TAT TAT TAT TAT TAT TAT TAT T
376952 TTCATTGCGT
Statistics
Matches: 79, Mismatches: 8, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
3 50 0.63
4 29 0.37
ACGTcount: A:0.30, C:0.01, G:0.01, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:376895 original size:30 final size:30
Alignment explanation
Indices: 376861--376952 Score: 157
Period size: 30 Copynumber: 3.1 Consensus size: 30
376851 AAAATGTATA
*
376861 TTATTTATTTATTATTATTGTTAATATTAT
1 TTATTTATTTATTATTATTATTAATATTAT
*
376891 TTATTTATTTATTATTATTCTTAATATTAT
1 TTATTTATTTATTATTATTATTAATATTAT
*
376921 TTATTTATTTATTATTATTATTATTATTAT
1 TTATTTATTTATTATTATTATTAATATTAT
376951 TT
1 TT
376953 TCATTGCGTA
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 59 1.00
ACGTcount: A:0.29, C:0.01, G:0.01, T:0.68
Consensus pattern (30 bp):
TTATTTATTTATTATTATTATTAATATTAT
Found at i:378088 original size:8 final size:8
Alignment explanation
Indices: 378075--378181 Score: 67
Period size: 8 Copynumber: 12.8 Consensus size: 8
378065 TAATTAACTT
378075 TTTTTTTA
1 TTTTTTTA
378083 TTTTTTTA
1 TTTTTTTA
*
378091 TTTAATTTA
1 TTT-TTTTA
378100 TTTTTTCT-
1 TTTTTT-TA
**
378108 TTAATTTA
1 TTTTTTTA
378116 -TTTTTTA
1 TTTTTTTA
378123 TTCCTTATTT-
1 TT--TT-TTTA
378133 TTTTATTTA
1 TTTT-TTTA
378142 TTTTTCCTTA
1 TTTTT--TTA
*
378152 TTTATTTA
1 TTTTTTTA
*
378160 TTTATTTA
1 TTTTTTTA
*
378168 TTTTTTCA
1 TTTTTTTA
378176 TTTTTT
1 TTTTTT
378182 CTCTTTTCAT
Statistics
Matches: 80, Mismatches: 9, Indels: 20
0.73 0.08 0.18
Matches are distributed among these distances:
7 6 0.08
8 48 0.60
9 12 0.15
10 11 0.14
11 3 0.04
ACGTcount: A:0.17, C:0.06, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTTTA
Found at i:378094 original size:4 final size:4
Alignment explanation
Indices: 378079--378170 Score: 73
Period size: 4 Copynumber: 22.8 Consensus size: 4
378069 TAACTTTTTT
* * *
378079 TTTA TTTT TTTA TTTAA TTTA TTT- TTTC TTTAA TTTA TTT- TTTA -TTC
1 TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTT-A TTTA TTTA TTTA TTTA
* * *
378126 CTTA TTTT TTTA TTTA TTTT TCCTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA T--TTA TTTA TTTA TTTA TTTA TTT
378171 TTTCATTTTT
Statistics
Matches: 71, Mismatches: 10, Indels: 14
0.75 0.11 0.15
Matches are distributed among these distances:
3 8 0.11
4 53 0.75
5 7 0.10
6 3 0.04
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:378103 original size:22 final size:21
Alignment explanation
Indices: 378078--378171 Score: 84
Period size: 22 Copynumber: 4.2 Consensus size: 21
378068 TTAACTTTTT
378078 TTTTATTTTTTTATTTAATTTA
1 TTTTATTTTTTTATTT-ATTTA
*
378100 TTTTTTCTTTAATTTATTT-TTTA
1 TTTTAT-TTT--TTTATTTATTTA
378123 TTCCTTATTTTTTTATTTATTT-
1 TT--TTATTTTTTTATTTATTTA
*
378145 TTCCTTATTTATTTATTTATTTA
1 TT--TTATTTTTTTATTTATTTA
378168 TTTT
1 TTTT
378172 TTCATTTTTT
Statistics
Matches: 62, Mismatches: 3, Indels: 15
0.77 0.04 0.19
Matches are distributed among these distances:
21 2 0.03
22 33 0.53
23 14 0.23
24 3 0.05
25 10 0.16
ACGTcount: A:0.18, C:0.05, G:0.00, T:0.77
Consensus pattern (21 bp):
TTTTATTTTTTTATTTATTTA
Found at i:378144 original size:26 final size:26
Alignment explanation
Indices: 378062--378173 Score: 84
Period size: 26 Copynumber: 4.2 Consensus size: 26
378052 TCCCTCGTTA
* *
378062 TTTTAATTAACTT-TTTTTTTATTTTT
1 TTTTTATTAA-TTATTTTTTTATTTAT
*
378088 TTATTTAATTTATT-TTTTCTTTAATTTAT
1 TT-TTT-ATTAATTATTTT-TTT-ATTTAT
**
378117 TTTTTATTCCTTATTTTTTTATTTAT
1 TTTTTATTAATTATTTTTTTATTTAT
** * *
378143 TTTTCCTTATTTATTTATTTATTTAT
1 TTTTTATTAATTATTTTTTTATTTAT
378169 TTTTT
1 TTTTT
378174 CATTTTTTCT
Statistics
Matches: 70, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
26 33 0.47
27 16 0.23
28 14 0.20
29 7 0.10
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (26 bp):
TTTTTATTAATTATTTTTTTATTTAT
Found at i:378200 original size:14 final size:15
Alignment explanation
Indices: 378170--378201 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
378160 TTTATTTATT
378170 TTTTCATTTTTTCTC
1 TTTTCATTTTTTCTC
378185 TTTTCATTTTTT-TC
1 TTTTCATTTTTTCTC
378199 TTT
1 TTT
378202 ATTTTGATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.06, C:0.16, G:0.00, T:0.78
Consensus pattern (15 bp):
TTTTCATTTTTTCTC
Found at i:378235 original size:10 final size:10
Alignment explanation
Indices: 378216--378258 Score: 50
Period size: 10 Copynumber: 4.0 Consensus size: 10
378206 TGATTTGCTG
378216 TTTTATTATT
1 TTTTATTATT
*
378226 TTTTAATATT
1 TTTTATTATT
378236 TGTTTATTATT
1 T-TTTATTATT
378247 ATTATTATTATT
1 -TT-TTATTATT
378259 ATCCTCTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
10 10 0.36
11 9 0.32
12 9 0.32
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (10 bp):
TTTTATTATT
Found at i:379115 original size:21 final size:21
Alignment explanation
Indices: 379091--379137 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
379081 AATTTCACAA
*
379091 GAAAAGCTGGTTACATCTCAG
1 GAAAAGCTGGTTACATCCCAG
*
379112 GAAAAGCTGGTTATATCCCAG
1 GAAAAGCTGGTTACATCCCAG
379133 GAAAA
1 GAAAA
379138 ATTTGAAAGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.21
Consensus pattern (21 bp):
GAAAAGCTGGTTACATCCCAG
Found at i:386608 original size:15 final size:15
Alignment explanation
Indices: 386588--386654 Score: 57
Period size: 15 Copynumber: 4.6 Consensus size: 15
386578 GTTTTGATTA
386588 ATATGTGAACATGTT
1 ATATGTGAACATGTT
**
386603 ATATGTGAATGTGTT
1 ATATGTGAACATGTT
* * * *
386618 CTACGTGAAAATG-C
1 ATATGTGAACATGTT
*
386632 A-ATGTGAACGTGTT
1 ATATGTGAACATGTT
386646 ATATGTGAA
1 ATATGTGAA
386655 TAAAAGATAC
Statistics
Matches: 38, Mismatches: 12, Indels: 4
0.70 0.22 0.07
Matches are distributed among these distances:
13 8 0.21
14 1 0.03
15 29 0.76
ACGTcount: A:0.33, C:0.07, G:0.24, T:0.36
Consensus pattern (15 bp):
ATATGTGAACATGTT
Found at i:391168 original size:24 final size:24
Alignment explanation
Indices: 391130--391176 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
391120 AACCAATATA
*
391130 TATTCCTCAATAGAAATGAGAAAC
1 TATTCCTCAAAAGAAATGAGAAAC
*
391154 TATTCCTTAAAAGAAATGAGAAA
1 TATTCCTCAAAAGAAATGAGAAA
391177 GAGTTGCAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.49, C:0.13, G:0.13, T:0.26
Consensus pattern (24 bp):
TATTCCTCAAAAGAAATGAGAAAC
Found at i:393859 original size:24 final size:24
Alignment explanation
Indices: 393827--393873 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
393817 ACAAAACTAT
*
393827 GTGGAACTTAAGTGCATATTCTAC
1 GTGGAACTTAAGTGCAAATTCTAC
* **
393851 GTGGCACTTCGGTGCAAATTCTA
1 GTGGAACTTAAGTGCAAATTCTA
393874 TGCTACAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (24 bp):
GTGGAACTTAAGTGCAAATTCTAC
Found at i:406084 original size:19 final size:18
Alignment explanation
Indices: 406060--406099 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
406050 TTGTTATAGC
*
406060 ATTATATTGTTTCTTTATT
1 ATTATATTGTTTATTT-TT
*
406079 ATTATATTTTTTATTTTT
1 ATTATATTGTTTATTTTT
406097 ATT
1 ATT
406100 GATTTATTCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.23, C:0.03, G:0.03, T:0.72
Consensus pattern (18 bp):
ATTATATTGTTTATTTTT
Found at i:406097 original size:21 final size:21
Alignment explanation
Indices: 406073--406117 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
406063 ATATTGTTTC
* *
406073 TTTATT-ATTATATTTTTTATT
1 TTTATTGATT-TATTCTCTATT
406094 TTTATTGATTTATTCTCTATT
1 TTTATTGATTTATTCTCTATT
406115 TTT
1 TTT
406118 GTTTACCCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 18 0.86
22 3 0.14
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (21 bp):
TTTATTGATTTATTCTCTATT
Found at i:407750 original size:17 final size:17
Alignment explanation
Indices: 407728--407760 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
407718 ACTTCATGTG
407728 GAGAGCACATTAAAGGA
1 GAGAGCACATTAAAGGA
407745 GAGAGCACATTAAAGG
1 GAGAGCACATTAAAGG
407761 TCCTACAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.45, C:0.12, G:0.30, T:0.12
Consensus pattern (17 bp):
GAGAGCACATTAAAGGA
Found at i:419055 original size:23 final size:23
Alignment explanation
Indices: 419029--419094 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
419019 CACATATATA
419029 TCCCGAAGTACCGCGTAGAAATG
1 TCCCGAAGTACCGCGTAGAAATG
* * * *
419052 TCCCGAAGGACCACATAGAATTG
1 TCCCGAAGTACCGCGTAGAAATG
*
419075 -CTTCGAAGTACCGCGTAGAA
1 TC-CCGAAGTACCGCGTAGAA
419095 CCCTCGACTC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 1 0.03
23 33 0.97
ACGTcount: A:0.32, C:0.26, G:0.24, T:0.18
Consensus pattern (23 bp):
TCCCGAAGTACCGCGTAGAAATG
Found at i:419217 original size:14 final size:14
Alignment explanation
Indices: 419198--419261 Score: 51
Period size: 14 Copynumber: 4.4 Consensus size: 14
419188 TATAGTTCTG
419198 TATCACATAGATTA
1 TATCACATAGATTA
419212 TATCACAT-G-TTCACA
1 TATCACATAGATT---A
**
419227 TAGTCACATAGACCA
1 TA-TCACATAGATTA
*
419242 TATCACATAGCTTA
1 TATCACATAGATTA
419256 TATCAC
1 TATCAC
419262 CTTTTCATGT
Statistics
Matches: 39, Mismatches: 5, Indels: 12
0.70 0.09 0.21
Matches are distributed among these distances:
12 2 0.05
13 1 0.03
14 23 0.59
15 6 0.15
16 6 0.15
17 1 0.03
ACGTcount: A:0.38, C:0.23, G:0.08, T:0.31
Consensus pattern (14 bp):
TATCACATAGATTA
Found at i:424885 original size:7 final size:7
Alignment explanation
Indices: 424873--424900 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
424863 ACTAAAGAAG
424873 AAGATTC
1 AAGATTC
424880 AAGATTC
1 AAGATTC
424887 AAGATTC
1 AAGATTC
424894 AAGATTC
1 AAGATTC
424901 TCAATGGTGG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (7 bp):
AAGATTC
Found at i:425532 original size:43 final size:41
Alignment explanation
Indices: 425465--425771 Score: 334
Period size: 41 Copynumber: 7.4 Consensus size: 41
425455 TGACAATTGT
* *
425465 GGCGTTTCGTATTAATACGCCACTAAAGTACGAGTCTATAGC
1 GGCGTTT-GTATAAAAACGCCACTAAAGTACGAGTCTATAGC
* *
425507 GGCGTTTGTGA-ACACAAACGCCACTAAAGTATGAATCTATAGC
1 GGCGTTTGT-ATA-A-AAACGCCACTAAAGTACGAGTCTATAGC
* *
425550 GGCGTTTGT-TAACACAAACGCTACTAAGGTACGAGTCTATAGC
1 GGCGTTTGTAT-A-A-AAACGCCACTAAAGTACGAGTCTATAGC
* *
425593 GGCGTTTGTATAAAAACGCCACTAAAGTACAAGTCTATAGA
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGC
* * * *
425634 GACGTTTGTATTAAAACGCCACGAAAGTACGAGTCTTTAGC
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGC
* * *
425675 GGCATTTGTATAAAAACGCCACTAAAGTACTAGTTTATAGC
1 GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGC
* * * * *
425716 GACGTTTGTATAAAAACGCCACGAAAGT-CTAAGTCTTTTGC
1 GGCGTTTGTATAAAAACGCCACTAAAGTAC-GAGTCTATAGC
425757 GGCGTTTGT-TAAAAA
1 GGCGTTTGTATAAAAA
425772 AATGCCGCTA
Statistics
Matches: 225, Mismatches: 33, Indels: 16
0.82 0.12 0.06
Matches are distributed among these distances:
40 7 0.03
41 135 0.60
42 10 0.04
43 72 0.32
44 1 0.00
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.27
Consensus pattern (41 bp):
GGCGTTTGTATAAAAACGCCACTAAAGTACGAGTCTATAGC
Found at i:438905 original size:40 final size:40
Alignment explanation
Indices: 438845--438920 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
438835 CATTTACCTC
438845 AGTACGCGAATATTGATACCTTGAAGGCTACTTATGTATA
1 AGTACGCGAATATTGATACCTTGAAGGCTACTTATGTATA
*
438885 AGTACGCGAATATTGTTACCTTGAAGGCTACTTATG
1 AGTACGCGAATATTGATACCTTGAAGGCTACTTATG
438921 AGGATGACAA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (40 bp):
AGTACGCGAATATTGATACCTTGAAGGCTACTTATGTATA
Found at i:439937 original size:22 final size:21
Alignment explanation
Indices: 439887--439938 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 21
439877 CCGGAAATGA
439887 AAAATATAAAAAATTAATAAGAT
1 AAAATA-AAAAAA-TAATAAGAT
439910 AAAATAAAACAAATAATAA-AT
1 AAAATAAAA-AAATAATAAGAT
439931 AATAATAA
1 AA-AATAA
439939 TATATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 4 0.15
22 14 0.52
23 9 0.33
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (21 bp):
AAAATAAAAAAATAATAAGAT
Found at i:440011 original size:37 final size:38
Alignment explanation
Indices: 439970--440252 Score: 188
Period size: 36 Copynumber: 7.8 Consensus size: 38
439960 TTCCAAAAAT
439970 TATATAATATATATTTTTCAAAAAT-ATTTAAAAACTA
1 TATATAATATATATTTTTCAAAAATGATTTAAAAACTA
* * **
440007 TATAT--TATATATTTTTAAAAAATGTTTTCGAAACTA
1 TATATAATATATATTTTTCAAAAATGATTTAAAAACTA
* * *
440043 TATAT--TATATAGTTTACAAAAATG-TTTTAAAA-T-
1 TATATAATATATATTTTTCAAAAATGATTTAAAAACTA
* * *
440076 TATATATTATATATGTTTTCAAAAA-AAATT-AAAACTA
1 TATATAATATATAT-TTTTCAAAAATGATTTAAAAACTA
* * *
440113 TATATTATATA-AGTTTTC-AAAATGATTTCAAAACTA
1 TATATAATATATATTTTTCAAAAATGATTTAAAAACTA
* *** * *
440149 TATATTATATACGCTTTTC-AAAATAATTTCAAAACTA
1 TATATAATATATATTTTTCAAAAATGATTTAAAAACTA
* *
440186 TATATTATATA-AGTTTTT--AAAATGTTTTCAAAAA--A
1 TATATAATATATA-TTTTTCAAAAATGATTT-AAAAACTA
* *
440221 CTATATAATATATACATTTTCAAAAATCATTT
1 -TATATAATATATA-TTTTTCAAAAATGATTT
440253 TCTAAAAAAT
Statistics
Matches: 199, Mismatches: 31, Indels: 30
0.77 0.12 0.12
Matches are distributed among these distances:
33 5 0.03
34 5 0.03
35 42 0.21
36 79 0.40
37 60 0.30
39 8 0.04
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (38 bp):
TATATAATATATATTTTTCAAAAATGATTTAAAAACTA
Found at i:440048 original size:36 final size:35
Alignment explanation
Indices: 439952--440252 Score: 236
Period size: 35 Copynumber: 8.3 Consensus size: 35
439942 ATTATATCTA
* *
439952 AAAAAT-ATTTCCAAAAATTATATAATATATATTTTT
1 AAAAATGATTT-C-AAAACTATATATTATATATTTTT
*
439988 CAAAAAT-ATTTAAAAACTATATATTATATATTTTT
1 -AAAAATGATTTCAAAACTATATATTATATATTTTT
* * **
440023 AAAAAATGTTTTCGAAACTATATATTATATAGTTTAC
1 -AAAAATGATTTCAAAACTATATATTATATA-TTTTT
* *
440060 AAAAATG-TTTTAAAATTATATATTATATATGTTTT
1 AAAAATGATTTCAAAACTATATATTATATAT-TTTT
* * *
440095 CAAAAA-AAATT-AAAACTATATATTATATAAGTTTT
1 -AAAAATGATTTCAAAACTATATATTATAT-ATTTTT
* *
440130 CAAAATGATTTCAAAACTATATATTATATACGCTTTT
1 AAAAATGATTTCAAAACTATATATTATATA--TTTTT
* *
440167 CAAAATAATTTCAAAACTATATATTATATAAGTTTTT
1 AAAAATGATTTCAAAACTATATATTATAT-A-TTTTT
* * *
440204 -AAAATGTTTTCAAAAAACTATATAATATATACATTTTC
1 AAAAATGATTTC--AAAACTATAT-AT-TATATATTTTT
*
440242 AAAAATCATTT
1 AAAAATGATTT
440253 TCTAAAAAAT
Statistics
Matches: 218, Mismatches: 30, Indels: 30
0.78 0.11 0.11
Matches are distributed among these distances:
34 5 0.02
35 72 0.33
36 61 0.28
37 50 0.23
38 15 0.07
39 11 0.05
40 4 0.02
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.43
Consensus pattern (35 bp):
AAAAATGATTTCAAAACTATATATTATATATTTTT
Found at i:440114 original size:106 final size:109
Alignment explanation
Indices: 439965--440207 Score: 309
Period size: 106 Copynumber: 2.3 Consensus size: 109
439955 AATATTTCCA
* * * *
439965 AAAATTATATAATATATAT-TTTTCAAAAATATTTAAAAACTATATATTATAT-ATTTTTAAAAA
1 AAAATTATATATTATATATGTTTTCAAAAAAAATTAAAAACTATATATTATATAAGTTTT-AAAA
* * * *
440028 ATGTTTTCGAAACTATATATTATATA-G-TTTACAAAA-ATGTTTT
65 ATGATTTCAAAACTATATATTATATACGCTTTACAAAATA-ATTTC
*
440071 AAAATTATATATTATATATGTTTTCAAAAAAAATT-AAAACTATATATTATATAAGTTTTCAAAA
1 AAAATTATATATTATATATGTTTTCAAAAAAAATTAAAAACTATATATTATATAAGTTTTAAAAA
*
440135 TGATTTCAAAACTATATATTATATACGCTTTTCAAAATAATTTC
66 TGATTTCAAAACTATATATTATATACGCTTTACAAAATAATTTC
* * *
440179 AAAACTATATATTATATAAGTTTTTAAAA
1 AAAATTATATATTATATATGTTTTCAAAA
440208 TGTTTTCAAA
Statistics
Matches: 119, Mismatches: 13, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
106 62 0.52
107 19 0.16
108 37 0.31
109 1 0.01
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (109 bp):
AAAATTATATATTATATATGTTTTCAAAAAAAATTAAAAACTATATATTATATAAGTTTTAAAAA
TGATTTCAAAACTATATATTATATACGCTTTACAAAATAATTTC
Found at i:440198 original size:73 final size:71
Alignment explanation
Indices: 439965--440245 Score: 284
Period size: 71 Copynumber: 3.9 Consensus size: 71
439955 AATATTTCCA
* * * * * *
439965 AAAATTATATAATATATATTTTTCAAAAAT-ATTTAAAAACTATATATTATATATTTTTAAAAAA
1 AAAACTATATATTATATAGTTTTCAAAAATGATTTCAAAACTATATATTATATACTTTT-CAAAA
**
440029 TGTTTTC
65 TAATTTC
* * * * *
440036 GAAACTATATATTATATAGTTTACAAAAATG-TTTTAAAATTATATATTATATATGTTTTCAAAA
1 AAAACTATATATTATATAGTTTTCAAAAATGATTTCAAAACTATATATTATATA-CTTTTCAAAA
* *
440100 AAAATT-
65 TAATTTC
440106 AAAACTATATATTATATAAGTTTTC-AAAATGATTTCAAAACTATATATTATATACGCTTTTCAA
1 AAAACTATATATTATAT-AGTTTTCAAAAATGATTTCAAAACTATATATTATATA--CTTTTCAA
440170 AATAATTTC
63 AATAATTTC
* * *
440179 AAAACTATATATTATATAAGTTTT-TAAAATGTTTTCAAAAAACTATATAATATATACATTTTCA
1 AAAACTATATATTATAT-AGTTTTCAAAAATGATTTC--AAAACTATATATTATATAC-TTTTCA
440243 AAA
62 AAA
440246 ATCATTTTCT
Statistics
Matches: 177, Mismatches: 23, Indels: 17
0.82 0.11 0.08
Matches are distributed among these distances:
70 22 0.12
71 77 0.44
72 17 0.10
73 35 0.20
74 9 0.05
75 17 0.10
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.43
Consensus pattern (71 bp):
AAAACTATATATTATATAGTTTTCAAAAATGATTTCAAAACTATATATTATATACTTTTCAAAAT
AATTTC
Found at i:440266 original size:14 final size:14
Alignment explanation
Indices: 440235--440272 Score: 53
Period size: 13 Copynumber: 2.8 Consensus size: 14
440225 ATAATATATA
440235 CATTTTC-AAAAAT
1 CATTTTCAAAAAAT
440248 CATTTTCTAAAAAAT
1 CATTTTC-AAAAAAT
440263 -ATTTTCAAAA
1 CATTTTCAAAA
440273 TTTATACTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
13 11 0.48
14 6 0.26
15 6 0.26
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.39
Consensus pattern (14 bp):
CATTTTCAAAAAAT
Found at i:441218 original size:85 final size:84
Alignment explanation
Indices: 441109--441699 Score: 758
Period size: 85 Copynumber: 7.0 Consensus size: 84
441099 ACTTGACAGT
* * * * * * * *
441109 TTTTTTTGACATACAACTCTTCTCGACTTAAGTTATGTTGTAAATTTGACATGCCCTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTGA
*
441174 ATGGAATCGAACTCGAAGG
66 ATGTAATCGAACTCGAAGG
* ** * * *
441193 TATTTGTTGACAAATAACCCTTCTCGCCTTTCGTTATGTTGTAAATTTGATATGTCCTTGAGTTG
1 T-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTG
*
441258 AATGTAATCGAACTCAAAGG
65 AATGTAATCGAACTCGAAGG
* * * * *
441278 TATTTGTTGGCAGATAACCCTTCTAGCCTTTAGTTATGTTGTAAATTTGATATGCCTTTGAGCTG
1 T-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTG
*
441343 AATGTAATCAAACTCGAAGG
65 AATGTAATCGAACTCGAAGG
* *
441363 TCTTTGTTGACAGATAACCCTTCTTGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTAAGCTG
1 T-TTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTG
* *
441428 AATGTAATCAAACTCAAAGG
65 AATGTAATCGAACTCGAAGG
* ** * * * * *
441448 -TTTGTTGGCAGATAGTCCTTCTCTCCTTGAGCTATGCTATAACTTTGATATGCCATTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTGA
*
441512 ATATAATCGAACTCGAAGG
66 ATGTAATCGAACTCGAAGG
*
441531 -TTTGTTGGA-AGATAACCCTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCCCTTGAGCTG
1 TTTTGTT-GACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTG
*
441594 AATGTAATCGAACTTGAAGG
65 AATGTAATCGAACTCGAAGG
* * *
441614 -TTTGTTGGCAGATAACTCTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGA
1 TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTGA
441678 ATGTAATCGAACTCGAAGG
66 ATGTAATCGAACTCGAAGG
441697 TTT
1 TTT
441700 GTGGGGTAGA
Statistics
Matches: 447, Mismatches: 56, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
82 1 0.00
83 218 0.49
84 4 0.01
85 224 0.50
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (84 bp):
TTTTGTTGACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTGAGCTGA
ATGTAATCGAACTCGAAGG
Found at i:441510 original size:83 final size:83
Alignment explanation
Indices: 441127--441742 Score: 773
Period size: 83 Copynumber: 7.3 Consensus size: 83
441117 ACATACAACT
* * * * * *
441127 CTTCTCGACTTAAGTTATGTTGTAAATTTGACATGCCCTTGAGCTGAATGGAATCGAACTCGAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
* *
441192 GTATTTGTTGACAAATAACC
66 G--TTTGTTGGCAGATAACC
** * * * * *
441212 CTTCTCGCCTTTCGTTATGTTGTAAATTTGATATGTCCTTGAGTTGAATGTAATCGAACTCAAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
441277 GTATTTGTTGGCAGATAACC
66 G--TTTGTTGGCAGATAACC
* * * * * *
441297 CTTCTAGCCTTTAGTTATGTTGTAAATTTGATATGCCTTTGAGCTGAATGTAATCAAACTCGAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
*
441362 GTCTTTGTTGACAGATAACC
66 G--TTTGTTGGCAGATAACC
* * * * *
441382 CTTCTTGCCTTGAGCTATGTTGTAAATTTGATATGCCCTTAAGCTGAATGTAATCAAACTCAAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
**
441447 GTTTGTTGGCAGATAGTC
66 GTTTGTTGGCAGATAACC
* * * * *
441465 CTTCTCTCCTTGAGCTATGCTATAACTTTGATATGCCATTGAGCTGAATATAATCGAACTCGAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
*
441530 GTTTGTTGGAAGATAACC
66 GTTTGTTGGCAGATAACC
* *
441548 CTTCTCGCCTTGAGCTATGATGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTTGAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
*
441613 GTTTGTTGGCAGATAACT
66 GTTTGTTGGCAGATAACC
441631 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
1 CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
* * *
441696 GTTTGTGGGGTAGATAGCC
66 GTTTGT-TGGCAGATAACC
* * *
441715 CTTCTCTCCTTGAGTTATGCTATAAATT
1 CTTCTCGCCTTGAGCTATGCTGTAAATT
441743 GTTCCTTTAA
Statistics
Matches: 471, Mismatches: 59, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
83 227 0.48
84 33 0.07
85 211 0.45
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.36
Consensus pattern (83 bp):
CTTCTCGCCTTGAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAATCGAACTCGAAG
GTTTGTTGGCAGATAACC
Found at i:443210 original size:99 final size:100
Alignment explanation
Indices: 443035--443232 Score: 301
Period size: 99 Copynumber: 2.0 Consensus size: 100
443025 GGATAGCTCA
* * * *
443035 ATATTATAATCACCTTTTATCAGGCTAGTTGAATCTTATCAATAAAGCCGAGGTGTTTAACCAAT
1 ATATTATAATCACCTTTTAGCAAGCTAGTTAAATCTTATCAATAAAGCCGAGGCGTTTAACCAAT
* *
443100 TGCTTTAGAGGGACAACTCAAGCTTTGTTGTATAG
66 TGCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
*
443135 ATATTATAATCACC-TTTAGCAAGCTAGTTAAATCTTAT-ACATAAAGCCGGGGCGTTTAACCAA
1 ATATTATAATCACCTTTTAGCAAGCTAGTTAAATCTTATCA-ATAAAGCCGAGGCGTTTAACCAA
*
443198 TTGCTCTGGAGGGACAACTCAAGCTTTATTGTATA
65 TTGCTCTAGAGGGACAACTCAAGCTTTATTGTATA
443233 CATAATATTA
Statistics
Matches: 89, Mismatches: 8, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
98 1 0.01
99 74 0.83
100 14 0.16
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (100 bp):
ATATTATAATCACCTTTTAGCAAGCTAGTTAAATCTTATCAATAAAGCCGAGGCGTTTAACCAAT
TGCTCTAGAGGGACAACTCAAGCTTTATTGTATAG
Found at i:448348 original size:33 final size:34
Alignment explanation
Indices: 448281--448356 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 34
448271 AGTAAAATTA
*
448281 AAAAAAATATTCAATAACTCAAAGGAAAATAAAT
1 AAAAAAATATTAAATAACTCAAAGGAAAATAAAT
448315 AAAAAAATATTAAAT-ACATCAAAAGG-AAA-AAAT
1 AAAAAAATATTAAATAAC-TC-AAAGGAAAATAAAT
*
448348 AAAATAATA
1 AAAAAAATA
448357 AAACATAAAT
Statistics
Matches: 38, Mismatches: 2, Indels: 5
0.84 0.04 0.11
Matches are distributed among these distances:
33 14 0.37
34 19 0.50
35 5 0.13
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (34 bp):
AAAAAAATATTAAATAACTCAAAGGAAAATAAAT
Found at i:448369 original size:33 final size:35
Alignment explanation
Indices: 448281--448371 Score: 91
Period size: 33 Copynumber: 2.7 Consensus size: 35
448271 AGTAAAATTA
** *
448281 AAAAAAATATTCAATAACTC-AAAGGAAAATAAAT
1 AAAAAAATATAAAATAAATCAAAAGGAAAATAAAT
* *
448315 AAAAAAATATTAAATACATCAAAAGG-AAA-AAAT
1 AAAAAAATATAAAATAAATCAAAAGGAAAATAAAT
*
448348 AAAATAATA-AAACATAAATCAAAA
1 AAAAAAATATAAA-ATAAATCAAAA
448372 AATATTAAAT
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
32 2 0.04
33 22 0.45
34 20 0.41
35 5 0.10
ACGTcount: A:0.69, C:0.08, G:0.04, T:0.19
Consensus pattern (35 bp):
AAAAAAATATAAAATAAATCAAAAGGAAAATAAAT
Found at i:448382 original size:26 final size:26
Alignment explanation
Indices: 448309--448389 Score: 83
Period size: 26 Copynumber: 3.1 Consensus size: 26
448299 TCAAAGGAAA
*
448309 ATAAATAAAAAAATATTAAATACATC
1 ATAAATAAAAAAATATTAAATAAATC
** ** *
448335 A-AAAGGAAAAAATAAAATAATAAAAC
1 ATAAATAAAAAAATATTA-AATAAATC
*
448361 ATAAATCAAAAAATATTAAATAAATC
1 ATAAATAAAAAAATATTAAATAAATC
448387 ATA
1 ATA
448390 GGGGAAAATG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
25 12 0.29
26 18 0.43
27 12 0.29
ACGTcount: A:0.69, C:0.06, G:0.02, T:0.22
Consensus pattern (26 bp):
ATAAATAAAAAAATATTAAATAAATC
Done.