Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007727.1 Hibiscus syriacus cultivar Beakdansim tig00109978_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: 640948
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 4 of 4
Found at i:464324 original size:13 final size:13
Alignment explanation
Indices: 464306--464332 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
464296 GGTTTTAATC
464306 ATCACTGCAAACT
1 ATCACTGCAAACT
464319 ATCACTGCAAACT
1 ATCACTGCAAACT
464332 A
1 A
464333 AAGAGCTAAA
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:0.41, C:0.30, G:0.07, T:0.22
Consensus pattern (13 bp):
ATCACTGCAAACT
Found at i:470493 original size:32 final size:32
Alignment explanation
Indices: 470452--470512 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
470442 CGGGTCGGGT
**
470452 TTTTTTAAGTGTGATATTTGGGTCGGGTTGAG
1 TTTTTTAAGTGTGATATTCAGGTCGGGTTGAG
*
470484 TTTTTTAAGTTTGATATTCAGGTCGGGTT
1 TTTTTTAAGTGTGATATTCAGGTCGGGTT
470513 CGGGTTTAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.16, C:0.05, G:0.30, T:0.49
Consensus pattern (32 bp):
TTTTTTAAGTGTGATATTCAGGTCGGGTTGAG
Found at i:470516 original size:38 final size:35
Alignment explanation
Indices: 470401--470518 Score: 93
Period size: 32 Copynumber: 3.3 Consensus size: 35
470391 TTTATTTTGT
* * *
470401 TCGGGTAGGGTCGGGTTTTTTAAG-TGATATTCGGG
1 TCGGGTCGGGTTGAGTTTTTTAAGTTGATATTC-GG
* * *
470436 TCGAGTCGGGTCGGGTTTTTTTAAGTGTGATATT---
1 TCGGGTCGGGTTGAG-TTTTTTAAGT-TGATATTCGG
470470 T-GGGTCGGGTTGAGTTTTTTAAGTTTGATATTCAGG
1 TCGGGTCGGGTTGAGTTTTTTAAG-TTGATATTC-GG
470506 TCGGGTTCGGGTT
1 TCGGG-TCGGGTT
470519 TAAGGTTAAA
Statistics
Matches: 68, Mismatches: 5, Indels: 17
0.76 0.06 0.19
Matches are distributed among these distances:
32 16 0.24
33 11 0.16
34 1 0.01
35 13 0.19
36 10 0.15
37 3 0.04
38 14 0.21
ACGTcount: A:0.14, C:0.08, G:0.36, T:0.42
Consensus pattern (35 bp):
TCGGGTCGGGTTGAGTTTTTTAAGTTGATATTCGG
Found at i:471870 original size:22 final size:22
Alignment explanation
Indices: 471842--471893 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
471832 GGTCGGATCG
*
471842 GGTCTCGGATGGAGGTTCCCTT
1 GGTCTCGGATAGAGGTTCCCTT
471864 GGTCTCGGATAGAGGTTCCCTT
1 GGTCTCGGATAGAGGTTCCCTT
*
471886 GTTCTCGG
1 GGTCTCGG
471894 GTCGGGTCGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.10, C:0.23, G:0.35, T:0.33
Consensus pattern (22 bp):
GGTCTCGGATAGAGGTTCCCTT
Found at i:472266 original size:18 final size:18
Alignment explanation
Indices: 472222--472275 Score: 65
Period size: 18 Copynumber: 3.1 Consensus size: 18
472212 ATATGGAATT
* *
472222 AGATTCCAATTCC-TGAC
1 AGATTCCAATTCCTTCAA
*
472239 AGATTTCAATTCCTTCAA
1 AGATTCCAATTCCTTCAA
*
472257 AGATTCCAATTACTTCAA
1 AGATTCCAATTCCTTCAA
472275 A
1 A
472276 AACATTCCAG
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
17 12 0.39
18 19 0.61
ACGTcount: A:0.35, C:0.24, G:0.07, T:0.33
Consensus pattern (18 bp):
AGATTCCAATTCCTTCAA
Found at i:485209 original size:26 final size:27
Alignment explanation
Indices: 485180--485231 Score: 72
Period size: 29 Copynumber: 1.9 Consensus size: 27
485170 TCAACTACAT
485180 CAAGAAG-A-AGAAGAAGAAACAAGAAA
1 CAAGAAGTAGAGAAGAAGAAA-AAGAAA
485206 CAAGAAGTAGTAGAAGAAGAAAAAGA
1 CAAGAAGTAG-AGAAGAAGAAAAAGA
485232 CACTGCAGGT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
26 7 0.30
27 1 0.04
28 4 0.17
29 11 0.48
ACGTcount: A:0.65, C:0.06, G:0.25, T:0.04
Consensus pattern (27 bp):
CAAGAAGTAGAGAAGAAGAAAAAGAAA
Found at i:486968 original size:29 final size:29
Alignment explanation
Indices: 486926--486985 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
486916 ATTCTACAGT
486926 GATCTCGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
*
486955 GATCTTGTAGGACGCCATGCAATCCAGGC
1 GATCTCGTAGGACGCCATGCAATCCAGGC
486984 GA
1 GA
486986 CATACGGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.18
Consensus pattern (29 bp):
GATCTCGTAGGACGCCATGCAATCCAGGC
Found at i:487117 original size:32 final size:32
Alignment explanation
Indices: 487076--487157 Score: 164
Period size: 32 Copynumber: 2.6 Consensus size: 32
487066 TATTATACGA
487076 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
487108 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
1 GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
487140 GGAGAGGTCGCCATGCAG
1 GGAGAGGTCGCCATGCAG
487158 TCTGGGCGAC
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 50 1.00
ACGTcount: A:0.27, C:0.27, G:0.37, T:0.10
Consensus pattern (32 bp):
GGAGAGGTCGCCATGCAGACGAGCCAGCCAAT
Found at i:487188 original size:29 final size:29
Alignment explanation
Indices: 487144--487238 Score: 163
Period size: 29 Copynumber: 3.3 Consensus size: 29
487134 GCCAATGGAG
* **
487144 AGGTCGCCATGCAGTCTGGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
487173 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
487202 AGGTCGCCATGTAGTCCCGGCGACCTTGT
1 AGGTCGCCATGTAGTCCCGGCGACCTTGT
487231 AGGTCGCC
1 AGGTCGCC
487239 CCGGCGTCAC
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.14, C:0.31, G:0.33, T:0.23
Consensus pattern (29 bp):
AGGTCGCCATGTAGTCCCGGCGACCTTGT
Found at i:487575 original size:16 final size:18
Alignment explanation
Indices: 487554--487592 Score: 55
Period size: 16 Copynumber: 2.3 Consensus size: 18
487544 GGAGATAAGG
*
487554 TAAATTTGTTTA-TATT-
1 TAAATTAGTTTATTATTA
487570 TAAATTAGTTTATTATTA
1 TAAATTAGTTTATTATTA
487588 TAAAT
1 TAAAT
487593 GTTAATTAGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 11 0.55
17 4 0.20
18 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TAAATTAGTTTATTATTA
Found at i:487957 original size:8 final size:8
Alignment explanation
Indices: 487944--487983 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
487934 TTTAAAAAGT
*
487944 TTAGTTTG
1 TTAGTTTA
487952 TTAGTTTA
1 TTAGTTTA
487960 TTAGTTTA
1 TTAGTTTA
487968 TTA-TTTA
1 TTAGTTTA
487975 -TAG-TTA
1 TTAGTTTA
487981 TTA
1 TTA
487984 TATTAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
6 5 0.17
7 6 0.21
8 18 0.62
ACGTcount: A:0.25, C:0.00, G:0.12, T:0.62
Consensus pattern (8 bp):
TTAGTTTA
Found at i:490161 original size:17 final size:17
Alignment explanation
Indices: 490139--490171 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
490129 CAATGATGTT
*
490139 TAGTATCAAATCATTAC
1 TAGTATCAAATAATTAC
490156 TAGTATCAAATAATTA
1 TAGTATCAAATAATTA
490172 AATATTTAGT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.06, T:0.36
Consensus pattern (17 bp):
TAGTATCAAATAATTAC
Found at i:490400 original size:14 final size:14
Alignment explanation
Indices: 490381--490407 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
490371 TAGTAATAAT
490381 TATTAAATCATTAG
1 TATTAAATCATTAG
490395 TATTAAATCATTA
1 TATTAAATCATTA
490408 TTATAATAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.44
Consensus pattern (14 bp):
TATTAAATCATTAG
Found at i:490442 original size:34 final size:37
Alignment explanation
Indices: 490363--490447 Score: 95
Period size: 37 Copynumber: 2.4 Consensus size: 37
490353 TTAGTATTCT
* * **
490363 ATAATTATTAGTAATAATTATTAAATCATTAGTATTAA
1 ATAATTATTA-TAATAATTACTAAATCAATAACATTAA
*
490401 ATCATTATTATAATAATTACTAAAT-AATAACA-T-A
1 ATAATTATTATAATAATTACTAAATCAATAACATTAA
490435 ATAATTATTATAA
1 ATAATTATTATAA
490448 AATCATTATT
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
34 13 0.32
35 1 0.02
36 4 0.10
37 14 0.34
38 9 0.22
ACGTcount: A:0.51, C:0.05, G:0.02, T:0.42
Consensus pattern (37 bp):
ATAATTATTATAATAATTACTAAATCAATAACATTAA
Found at i:490461 original size:26 final size:26
Alignment explanation
Indices: 490379--490729 Score: 254
Period size: 26 Copynumber: 14.2 Consensus size: 26
490369 ATTAGTAATA
* * *
490379 ATTATTA-AATCATTAGTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
490404 ATTATTATAAT-A--ATTA-CTAAAT-
1 ATTATTATAATGATTATTATC-AAATC
* ** * *
490426 AATAACATAATAATTATTATAAAATC
1 ATTATTATAATGATTATTATCAAATC
490452 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
490478 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
490501 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* *
490524 ATTTTTATAATTATTATTA-CTAAATC
1 ATTATTATAATGATTATTATC-AAATC
490550 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
490576 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
* * * * * *
490602 ATTACTA-AATCATCA-AATC-ATTA
1 ATTATTATAATGATTATTATCAAATC
* * *
490625 AATATT-TAA--ATCATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
* * *
490648 ATTTTTATAATTATTATTATTAAATC
1 ATTATTATAATGATTATTATCAAATC
490674 ATTATTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
*
490700 ATTACTATAATGATTATTATCAAATC
1 ATTATTATAATGATTATTATCAAATC
490726 ATTA
1 ATTA
490730 CTAAATCATC
Statistics
Matches: 257, Mismatches: 48, Indels: 41
0.74 0.14 0.12
Matches are distributed among these distances:
21 8 0.03
22 12 0.05
23 36 0.14
24 12 0.05
25 28 0.11
26 160 0.62
27 1 0.00
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (26 bp):
ATTATTATAATGATTATTATCAAATC
Found at i:490468 original size:98 final size:97
Alignment explanation
Indices: 490386--490715 Score: 298
Period size: 98 Copynumber: 3.3 Consensus size: 97
490376 ATAATTATTA
* * * * *
490386 AATCATTAGTATTAAATCATTATTATAATAATTACTAAAT-AATAACATAATAATTATTATAAAA
1 AATCATTATTATCAAATCATTACTA-AATCATTACTAAATCATTAA-ATAATAATTATTAT-AAA
490450 TCATTATTATAATGATTATTATCAAATCATTACTA-
63 TCATTATTATAATGATTATTAT-AAATCATTACTAT
* * * * ** *
490485 AATCATCAAATCATTAAAT-ATT--TAAATCATTATTAAATCATTTTTATAATTATTATTACTAA
1 AATCAT--TATTATCAAATCATTACTAAATCATTACTAAATCA-TTAAATAATAATTATTA-TAA
490547 ATCATTATTATAATGATTATTATCAAATCATTACTAT
62 ATCATTATTATAATGATTATTAT-AAATCATTACTAT
* * *
490584 AATGATTATTATCAAATCATTACTAAATCA-T-C-AAATCATTAAATATTTAAATCATTATTAAA
1 AATCATTATTATCAAATCATTACTAAATCATTACTAAATCATTAAATA-AT-AATTATTA-TAAA
* * *
490646 TCATTTTTATAATTATTATTATTAAATCATTATTAT
63 TCATTATTATAATGATTATTA-TAAATCATTACTAT
* *
490682 AATGATTATTATCAAATCATTACTATAATGATTA
1 AATCATTATTATCAAATCATTACTA-AATCATTA
490716 TTATCAAATC
Statistics
Matches: 192, Mismatches: 24, Indels: 28
0.79 0.10 0.11
Matches are distributed among these distances:
96 5 0.03
97 27 0.14
98 122 0.64
99 19 0.10
100 11 0.06
101 8 0.04
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (97 bp):
AATCATTATTATCAAATCATTACTAAATCATTACTAAATCATTAAATAATAATTATTATAAATCA
TTATTATAATGATTATTATAAATCATTACTAT
Found at i:490578 original size:124 final size:124
Alignment explanation
Indices: 490395--490787 Score: 668
Period size: 124 Copynumber: 3.2 Consensus size: 124
490385 AAATCATTAG
* * ** * *
490395 TATTAAATCATTATTATAA-TA--ATTACTAAAT-AATAACATAATAATTATTATAAAATCATTA
1 TATTAAATCATTTTTATAATTATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
*
490456 TTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
490515 TATTAAATCATTTTTATAATTATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATTATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
490580 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
*
490639 TATTAAATCATTTTTATAATTATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTA
1 TATTAAATCATTTTTATAATTATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
490704 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
66 CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
* *
490763 TATTAAATCTTTTTTATAATGATTA
1 TATTAAATCATTTTTATAATTATTA
490788 ATAAATATAT
Statistics
Matches: 259, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
120 18 0.07
121 2 0.01
123 10 0.04
124 229 0.88
ACGTcount: A:0.45, C:0.09, G:0.02, T:0.44
Consensus pattern (124 bp):
TATTAAATCATTTTTATAATTATTATTACTAAATCATTATTATAATGATTATTATCAAATCATTA
CTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTTAAATCAT
Found at i:490765 original size:98 final size:95
Alignment explanation
Indices: 490556--490787 Score: 227
Period size: 98 Copynumber: 2.4 Consensus size: 95
490546 AATCATTATT
* * * *
490556 ATAATGATTATTATCAAATCATTACTATAATGATTATTATCAAATCATTACTAAATCATCAAATC
1 ATAATTATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCAT-AAATC
* * **
490621 ATTAAATATTTAAATCATTATTAAATCATTTTT
65 ATCAAATATTTAAATC--TATCAAATCATTTAA
* * * *
490654 ATAATTATTATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTATAATGAT-TATT
1 ATAATTATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTA-AATCATAAATC
490718 ATCAAATCATTACTAAATC-ATCAAATCA-TTAA
65 ATCAAAT-ATT--TAAATCTATCAAATCATTTAA
* * *
490750 ATATTTAAATCATTATTAAATCTTTTTTATAATGATTA
1 ATAATT--ATCATTATTAAATCATTATTATAATGATTA
490788 ATAAATATAT
Statistics
Matches: 114, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
96 7 0.06
97 16 0.14
98 80 0.70
99 5 0.04
100 6 0.05
ACGTcount: A:0.44, C:0.10, G:0.02, T:0.44
Consensus pattern (95 bp):
ATAATTATCATTATTAAATCATTATTATAATGATTATTATCAAATCATTACTAAATCATAAATCA
TCAAATATTTAAATCTATCAAATCATTTAA
Found at i:493680 original size:26 final size:24
Alignment explanation
Indices: 493620--493680 Score: 59
Period size: 26 Copynumber: 2.4 Consensus size: 24
493610 TACTAATATT
*
493620 ATTAATAATGATTTAATAATTATT
1 ATTAATAATGATTTAATAATTATG
* *
493644 ATTAATCTAATGATTTGATATTTAATG
1 ATTAA--TAATGATTTAATAATT-ATG
493671 ATTTAATAAT
1 A-TTAATAAT
493681 AATATGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
24 5 0.17
26 18 0.60
27 3 0.10
28 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.07, T:0.49
Consensus pattern (24 bp):
ATTAATAATGATTTAATAATTATG
Found at i:494068 original size:14 final size:14
Alignment explanation
Indices: 494049--494075 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
494039 CACATACACA
494049 ACAACAAAAAATAG
1 ACAACAAAAAATAG
494063 ACAACAAAAAATA
1 ACAACAAAAAATA
494076 ATAATTACTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
ACAACAAAAAATAG
Found at i:494068 original size:17 final size:17
Alignment explanation
Indices: 494046--494078 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
494036 TTACACATAC
494046 ACAACAACAAAA-AATAG
1 ACAACAA-AAAATAATAG
494063 ACAACAAAAAATAATA
1 ACAACAAAAAATAATA
494079 ATTACTCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.73, C:0.15, G:0.03, T:0.09
Consensus pattern (17 bp):
ACAACAAAAAATAATAG
Found at i:494507 original size:21 final size:21
Alignment explanation
Indices: 494474--494522 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
494464 AATATAATAT
*
494474 ATAACTTAAACTAACCAACTA
1 ATAACTTAAACTAACAAACTA
* *
494495 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
494516 ATTAACT
1 A-TAACT
494523 AGATTTTAGT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.51, C:0.18, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:494997 original size:35 final size:35
Alignment explanation
Indices: 494957--495024 Score: 127
Period size: 35 Copynumber: 1.9 Consensus size: 35
494947 TGGATGCAAC
494957 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
*
494992 GCATGCATGAGTGCTACAGTTAAAGCTTGGTCG
1 GCATGCATGAGTGATACAGTTAAAGCTTGGTCG
495025 CGATGCAGGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.25, C:0.16, G:0.29, T:0.29
Consensus pattern (35 bp):
GCATGCATGAGTGATACAGTTAAAGCTTGGTCGTT
Found at i:495098 original size:36 final size:36
Alignment explanation
Indices: 495051--495135 Score: 112
Period size: 29 Copynumber: 2.6 Consensus size: 36
495041 CAGCTATGGA
495051 GACTCCATGGCGACCTACCACCTACCATGTCGTAGG
1 GACTCCATGGCGACCTACCACCTACCATGTCGTAGG
*
495087 GACTCCATGGCG-------ACCTACCATGTCGTCGG
1 GACTCCATGGCGACCTACCACCTACCATGTCGTAGG
495116 GACTCCATGGCGACCTACCA
1 GACTCCATGGCGACCTACCA
495136 TGTCGCGACC
Statistics
Matches: 41, Mismatches: 1, Indels: 14
0.73 0.02 0.25
Matches are distributed among these distances:
29 28 0.68
36 13 0.32
ACGTcount: A:0.21, C:0.36, G:0.24, T:0.19
Consensus pattern (36 bp):
GACTCCATGGCGACCTACCACCTACCATGTCGTAGG
Found at i:495112 original size:29 final size:29
Alignment explanation
Indices: 495070--495140 Score: 133
Period size: 29 Copynumber: 2.4 Consensus size: 29
495060 GCGACCTACC
495070 ACCTACCATGTCGTAGGGACTCCATGGCG
1 ACCTACCATGTCGTAGGGACTCCATGGCG
*
495099 ACCTACCATGTCGTCGGGACTCCATGGCG
1 ACCTACCATGTCGTAGGGACTCCATGGCG
495128 ACCTACCATGTCG
1 ACCTACCATGTCG
495141 CGACCTACCA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
29 41 1.00
ACGTcount: A:0.20, C:0.34, G:0.25, T:0.21
Consensus pattern (29 bp):
ACCTACCATGTCGTAGGGACTCCATGGCG
Found at i:495145 original size:15 final size:15
Alignment explanation
Indices: 495096--495152 Score: 59
Period size: 15 Copynumber: 3.9 Consensus size: 15
495086 GGACTCCATG
495096 GCGACCTACCATGTC
1 GCGACCTACCATGTC
495111 GTCGGGA-CT-CCATG--
1 G-C--GACCTACCATGTC
495125 GCGACCTACCATGTC
1 GCGACCTACCATGTC
495140 GCGACCTACCATG
1 GCGACCTACCATG
495153 CCGCCGGCAA
Statistics
Matches: 35, Mismatches: 0, Indels: 14
0.71 0.00 0.29
Matches are distributed among these distances:
11 2 0.06
12 2 0.06
13 6 0.17
14 1 0.03
15 14 0.40
16 6 0.17
17 2 0.06
18 2 0.06
ACGTcount: A:0.19, C:0.37, G:0.25, T:0.19
Consensus pattern (15 bp):
GCGACCTACCATGTC
Found at i:495452 original size:29 final size:30
Alignment explanation
Indices: 495369--495453 Score: 156
Period size: 29 Copynumber: 2.9 Consensus size: 30
495359 AAATAATGAT
495369 GGACGCCGGGCGTGCATGGCGACCT-TATA
1 GGACGCCGGGCGTGCATGGCGACCTATATA
495398 GGACGCCGGGCGTGCATGGCGACCTATA-A
1 GGACGCCGGGCGTGCATGGCGACCTATATA
495427 GGACGCCGGGCGTGCATGGCGACCTAT
1 GGACGCCGGGCGTGCATGGCGACCTAT
495454 GTTGCCACTG
Statistics
Matches: 55, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
29 53 0.96
30 2 0.04
ACGTcount: A:0.18, C:0.28, G:0.39, T:0.15
Consensus pattern (30 bp):
GGACGCCGGGCGTGCATGGCGACCTATATA
Found at i:505918 original size:22 final size:22
Alignment explanation
Indices: 505893--505934 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
505883 CTTTGGTATA
505893 TTTATATGATTCTTAAGGAATG
1 TTTATATGATTCTTAAGGAATG
* * *
505915 TTTATGTGGTTCTTATGGAA
1 TTTATATGATTCTTAAGGAA
505935 AAATCTTATA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.26, C:0.05, G:0.21, T:0.48
Consensus pattern (22 bp):
TTTATATGATTCTTAAGGAATG
Found at i:515893 original size:20 final size:20
Alignment explanation
Indices: 515868--515908 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
515858 CTCGTTGCTC
515868 GTTAAACTCGTTAAAATTTT
1 GTTAAACTCGTTAAAATTTT
* *
515888 GTTAAATTTGTTAAAATTTT
1 GTTAAACTCGTTAAAATTTT
515908 G
1 G
515909 CTTGACTCAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.34, C:0.05, G:0.12, T:0.49
Consensus pattern (20 bp):
GTTAAACTCGTTAAAATTTT
Found at i:515896 original size:10 final size:11
Alignment explanation
Indices: 515877--515908 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
515867 CGTTAAACTC
515877 GTTAAAATTTT
1 GTTAAAATTTT
515888 GTT-AAA-TTT
1 GTTAAAATTTT
515897 GTTAAAATTTT
1 GTTAAAATTTT
515908 G
1 G
515909 CTTGACTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 6 0.32
10 6 0.32
11 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.12, T:0.53
Consensus pattern (11 bp):
GTTAAAATTTT
Found at i:518041 original size:13 final size:14
Alignment explanation
Indices: 518023--518051 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
518013 AGATAAAAAT
518023 AAAAT-AAAATAAA
1 AAAATAAAAATAAA
518036 AAAATAAAAATAAA
1 AAAATAAAAATAAA
518050 AA
1 AA
518052 GAGGTGAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AAAATAAAAATAAA
Found at i:518160 original size:14 final size:14
Alignment explanation
Indices: 518141--518168 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
518131 TCTTCGAAAA
518141 GACATTTTCCCTTG
1 GACATTTTCCCTTG
518155 GACATTTTCCCTTG
1 GACATTTTCCCTTG
518169 TAGTTGTGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.29, G:0.14, T:0.43
Consensus pattern (14 bp):
GACATTTTCCCTTG
Found at i:519037 original size:194 final size:197
Alignment explanation
Indices: 518697--519057 Score: 507
Period size: 194 Copynumber: 1.8 Consensus size: 197
518687 TACATAAATT
* * * *
518697 TAAAAGTTAAGGGTTTTTTTTAACCATTTAACTCGGATCATAAATAATACGGATCGTCCCGCAGG
1 TAAAAGTTAAGGGTTGTTTTTAACCATTTAACTCAGACCATAAATAATACGGATCATCCCGCAGG
518762 GCAGGTCACCACAAGGTCGTTGAATATTCGAATGTTAGAAAATTAGCGGATTAGTTTGTGCAATA
66 GCAGGTCACCACAAGGTCGTTGAATATTCGAATGTTAGAAAATTAGCGGATTAGTTTGTGCAATA
* *
518827 AAATAAAATTTTAGTAAGTTCGTAAGAACAATAAAAAAATGTAGTATGTTAATATGAACAAATAA
131 AAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAAAAATGTAGTATGTTAATATGAACAAATAA
518892 AA
196 AA
* * * **
518894 TAAAAGTTAGGGGTTGTTTTTAATCGTTTAAC-CTAGACCATAAATAATGTGGATCATCCTC-CA
1 TAAAAGTTAAGGGTTGTTTTTAACCATTTAACTC-AGACCATAAATAATACGGATCATCC-CGCA
** ** * *
518957 GGGTGGGTCACCGTAAGGTCGTTG-A-A-TCGAATGTTTGAAAATTAGCGGGTTAGTTTGTGCAA
64 GGGCAGGTCACCACAAGGTCGTTGAATATTCGAATGTTAGAAAATTAGCGGATTAGTTTGTGCAA
*
519019 TAAAATAAAATGTTAGTAAGTTAGTAAGAACAGTAAAAA
129 TAAAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAAA
519058 TAAAGTTAGT
Statistics
Matches: 144, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
194 70 0.49
195 1 0.01
196 2 0.01
197 70 0.49
198 1 0.01
ACGTcount: A:0.38, C:0.11, G:0.20, T:0.30
Consensus pattern (197 bp):
TAAAAGTTAAGGGTTGTTTTTAACCATTTAACTCAGACCATAAATAATACGGATCATCCCGCAGG
GCAGGTCACCACAAGGTCGTTGAATATTCGAATGTTAGAAAATTAGCGGATTAGTTTGTGCAATA
AAATAAAATGTTAGTAAGTTAGTAAGAACAATAAAAAAATGTAGTATGTTAATATGAACAAATAA
AA
Found at i:519068 original size:24 final size:24
Alignment explanation
Indices: 519036--519085 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
519026 AAATGTTAGT
*
519036 AAGTTAGTAAGAACAGTAAAAATA
1 AAGTTAGTAAGAACAATAAAAATA
*
519060 AAGTTAGTATGAACAATAAAAATA
1 AAGTTAGTAAGAACAATAAAAATA
519084 AA
1 AA
519086 AAAGTTAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.60, C:0.04, G:0.14, T:0.22
Consensus pattern (24 bp):
AAGTTAGTAAGAACAATAAAAATA
Found at i:519126 original size:32 final size:34
Alignment explanation
Indices: 519064--519129 Score: 100
Period size: 32 Copynumber: 2.0 Consensus size: 34
519054 AAAATAAAGT
*
519064 TAGTATGAACAATAAAAATAAAAAAGTTAGAATGG
1 TAGTATAAACAATAAAAAT-AAAAAGTTAGAATGG
519099 TAGTATAAACAAT-AAAAT-AAAAGTTAGAATG
1 TAGTATAAACAATAAAAATAAAAAGTTAGAATG
519130 TTAATAAGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
32 13 0.43
34 5 0.17
35 12 0.40
ACGTcount: A:0.58, C:0.03, G:0.15, T:0.24
Consensus pattern (34 bp):
TAGTATAAACAATAAAAATAAAAAGTTAGAATGG
Found at i:520057 original size:122 final size:122
Alignment explanation
Indices: 519880--520161 Score: 325
Period size: 122 Copynumber: 2.3 Consensus size: 122
519870 TTCCTTCATG
* * * ** * *
519880 TTGAGAAAATTGGGTCAAT-TCAGAGATAATACGGTGTTGAAGATGACTCTTCTCATCCACATTG
1 TTGAGGAAATCGGGTCAATCT-GGAGATAATTTGGTGTTAAAGATGACTCTGCTCATCCACATTG
* ** * * *
519944 AAGAGATCTGGT-AGTTTTCAGATAAATTGTTTATTGAAGACGACGTTGTTCTTTCTCA
65 AAGAGATCTGGTCA-CTTTCAGATAAATCATTTACTGAAGACGACGTTATTCCTTCTCA
** *
520002 TTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTAAAGATGACTCTGCTCATCCATGTTTA
1 TTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTAAAGATGACTCTGCTCATCCACATTGA
* * * *
520067 AGAGATCTGGTCACTTTCAGATAAATCATTTGCTGAAGATGATGTTATTCCTTCTTA
66 AGAGATCTGGTCACTTTCAGATAAATCATTTACTGAAGACGACGTTATTCCTTCTCA
* * *
520124 TTAAGGAAGTCGGGTCAATCTGGAGGTAATTTGGTGTT
1 TTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTT
520162 GATGTTCTGG
Statistics
Matches: 135, Mismatches: 23, Indels: 4
0.83 0.14 0.02
Matches are distributed among these distances:
122 133 0.99
123 2 0.01
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.35
Consensus pattern (122 bp):
TTGAGGAAATCGGGTCAATCTGGAGATAATTTGGTGTTAAAGATGACTCTGCTCATCCACATTGA
AGAGATCTGGTCACTTTCAGATAAATCATTTACTGAAGACGACGTTATTCCTTCTCA
Found at i:520452 original size:138 final size:139
Alignment explanation
Indices: 520202--520604 Score: 542
Period size: 138 Copynumber: 2.9 Consensus size: 139
520192 GACAATACAA
* * * * * *
520202 TTCCTTCACGTTGAGCAAGTCTGATTGTCTAAGGATGACACTGCTCCTTCGCGTTGAGAAGAT-T
1 TTCCTTCGCGTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCACGTTGAGGAGATCT
* * * *
520266 TGATCGGTGGACGACATTGTTCCTTAGTGTTGAGGAAGTCTAGTCGTTTTAGAAGATAATTTGGA
66 AG-TCGGTGGAAGACATTGTTCCTTAGTGTTGAGGAAGTCTAGCCGTTTTAGGAGATAATTTGGA
520331 GACAACAAGG
130 GACAACAAGG
*
520341 TTCCTTCGCGTTGAGGAAGTCTGGTTGTCTGAGGATGACACTTC-CCTTCACGTTGAGGAGATCT
1 TTCCTTCGCGTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCACGTTGAGGAGATCT
* * * *
520405 AGTCAGTGGAAGACATTGTTCCTTCGTGTTGAGGAAGTATAACCGTTTTAGGAGATAATTTGGAG
66 AGTCGGTGGAAGACATTGTTCCTTAGTGTTGAGGAAGTCTAGCCGTTTTAGGAGATAATTTGGAG
* * *
520470 ACTATATGG
131 ACAACAAGG
* * * * *
520479 TTCTTTTGCGTTGAGGAAGTCTGGTTGTCTGAGGATGACAGTGCTCCTTCCCGTTGATGAGATCT
1 TTCCTTCGCGTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCACGTTGAGGAGATCT
* *
520544 GGTCGGT-GAACGACATTGTTCATTAGTGTTGAGGAAGTCTAGCCGTTTTAGGAGATAATTT
66 AGTCGGTGGAA-GACATTGTTCCTTAGTGTTGAGGAAGTCTAGCCGTTTTAGGAGATAATTT
520605 TTCTTTGGAA
Statistics
Matches: 231, Mismatches: 30, Indels: 6
0.87 0.11 0.02
Matches are distributed among these distances:
138 121 0.52
139 110 0.48
ACGTcount: A:0.23, C:0.16, G:0.28, T:0.33
Consensus pattern (139 bp):
TTCCTTCGCGTTGAGGAAGTCTGGTTGTCTGAGGATGACACTGCTCCTTCACGTTGAGGAGATCT
AGTCGGTGGAAGACATTGTTCCTTAGTGTTGAGGAAGTCTAGCCGTTTTAGGAGATAATTTGGAG
ACAACAAGG
Found at i:520968 original size:103 final size:103
Alignment explanation
Indices: 520759--520997 Score: 283
Period size: 103 Copynumber: 2.3 Consensus size: 103
520749 GGTGAGATAA
**
520759 AATTTTGTTTCAAGTGAAAC-ATTT-CAAAATTTGCGTTTCAAGGGAAAACTATCTCAATTGAGA
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGCGAGA
* * *
520822 AGAAAATTGTTTTTAAGAAAAATAATCTCAAATGTTATC
66 ACAAAATTGTTTTCAAGAAAAATAATCTCAAAAG-TATC
** * ** *
520861 AATTTTGTTTCAAGTGAAACAATTTCCAATTTTTGTGTTTTGAGGGAAAACTGTCTCAAGCGAG-
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGCGAGA
* *
520925 ACAAAATTAGTTTTCAGGAAAACT-ATCTCAAGCAAG-ATC
66 ACAAAATT-GTTTTCAAGAAAAATAATCTCAA--AAGTATC
520964 AATTTTGTTTCAAGTGAAACAATTT-CAAAATTTG
1 AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTG
520998 GGGAAAATTG
Statistics
Matches: 117, Mismatches: 15, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
102 27 0.23
103 46 0.39
104 42 0.36
105 2 0.02
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (103 bp):
AATTTTGTTTCAAGTGAAACAATTTCCAAAATTTGCGTTTCAAGGGAAAACTATCTCAAGCGAGA
ACAAAATTGTTTTCAAGAAAAATAATCTCAAAAGTATC
Found at i:523112 original size:24 final size:25
Alignment explanation
Indices: 523057--523124 Score: 84
Period size: 26 Copynumber: 2.7 Consensus size: 25
523047 TTTTATTTTC
* *
523057 AAAATTTTGGAAAAATATCAATTAA
1 AAAATTTTGAAAAAATATCAATCAA
* *
523082 AATAATTTTGAAAAAATTTCAA-CCA
1 AA-AATTTTGAAAAAATATCAATCAA
523107 AAAATTTTGAAAAAATAT
1 AAAATTTTGAAAAAATAT
523125 TGCCTATTTC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 15 0.41
25 5 0.14
26 17 0.46
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.32
Consensus pattern (25 bp):
AAAATTTTGAAAAAATATCAATCAA
Found at i:528487 original size:20 final size:21
Alignment explanation
Indices: 528462--528502 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
528452 TAATATGTTT
528462 AAATGC-AAATAAAAAAAATA
1 AAATGCGAAATAAAAAAAATA
528482 AAATGCTGGAAATAAAAAAAA
1 AAATGC--GAAATAAAAAAAA
528503 AGGACTGAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.33
23 12 0.67
ACGTcount: A:0.71, C:0.05, G:0.10, T:0.15
Consensus pattern (21 bp):
AAATGCGAAATAAAAAAAATA
Found at i:528498 original size:19 final size:19
Alignment explanation
Indices: 528476--528518 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
528466 GCAAATAAAA
*
528476 AAAATAAAATG-CTGGAAAT
1 AAAATAAAAGGACT-GAAAT
*
528495 AAAAAAAAAGGACTGAAAT
1 AAAATAAAAGGACTGAAAT
528514 AAAAT
1 AAAAT
528519 GCAGCAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
19 18 0.90
20 2 0.10
ACGTcount: A:0.65, C:0.05, G:0.14, T:0.16
Consensus pattern (19 bp):
AAAATAAAAGGACTGAAAT
Found at i:529058 original size:34 final size:32
Alignment explanation
Indices: 529005--529074 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
528995 ACCTTACAAC
*
529005 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
* *
529037 TCCCTAGCTTTTACACGGGCTAAGCTAGAATCTT
1 TCCCTAG-TTTTAC-CGGGCTAAACTAGAACCTT
529071 TCCC
1 TCCC
529075 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.21, C:0.30, G:0.16, T:0.33
Consensus pattern (32 bp):
TCCCTAGTTTTACCGGGCTAAACTAGAACCTT
Found at i:529314 original size:20 final size:22
Alignment explanation
Indices: 529289--529328 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
529279 TGTTGTATAT
529289 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
529309 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
529329 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:529459 original size:20 final size:21
Alignment explanation
Indices: 529430--529484 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
529420 GCAGCCTTCG
* *
529430 TGCATGGATGCATAG-CGGGA
1 TGCATCGATGCACAGCCGGGA
**
529450 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAGCCGGGA
529471 TGCATCGATGCACA
1 TGCATCGATGCACA
529485 TAAGGATGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.25, C:0.24, G:0.29, T:0.22
Consensus pattern (21 bp):
TGCATCGATGCACAGCCGGGA
Found at i:529571 original size:22 final size:23
Alignment explanation
Indices: 529538--529580 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
529528 ATGGATGCAC
529538 TGCATGGTGCATCGATGCACTAG
1 TGCATGGTGCATCGATGCACTAG
*
529561 TGCA-GGTGCATGGATGCACT
1 TGCATGGTGCATCGATGCACT
529581 GCAGGGGTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (23 bp):
TGCATGGTGCATCGATGCACTAG
Found at i:529728 original size:30 final size:30
Alignment explanation
Indices: 529681--529740 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
529671 AAACTTTGAA
529681 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
*
529710 TAAATTCATTTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
529741 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 10 0.36
30 11 0.39
31 7 0.25
ACGTcount: A:0.42, C:0.17, G:0.07, T:0.35
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:531056 original size:19 final size:20
Alignment explanation
Indices: 531013--531060 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
531003 TCTAAATCCT
*
531013 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
531033 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
531052 TTTTCAAAA
1 TTTTCAAAA
531061 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:531947 original size:34 final size:32
Alignment explanation
Indices: 531887--531956 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 32
531877 ACCTTACGAC
* *
531887 TCCCTAGTTTTTCCGGGCTAAACTAGAACCTT
1 TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
*
531919 TCCCTAGCTTTTACACGAGCTAAGCTAGAACCTT
1 TCCCTAG-TTTTAC-CGAGCTAAACTAGAACCTT
531953 TCCC
1 TCCC
531957 CTTTACAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 21 0.64
ACGTcount: A:0.23, C:0.31, G:0.14, T:0.31
Consensus pattern (32 bp):
TCCCTAGTTTTACCGAGCTAAACTAGAACCTT
Found at i:532196 original size:20 final size:22
Alignment explanation
Indices: 532171--532210 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
532161 TGTTGTATAT
532171 AGCCG-TTGGGGATG-TTTTGG
1 AGCCGTTTGGGGATGATTTTGG
532191 AGCCGTTTGGGGATGATTTT
1 AGCCGTTTGGGGATGATTTT
532211 TCTACTCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
21 9 0.50
22 4 0.22
ACGTcount: A:0.12, C:0.10, G:0.40, T:0.38
Consensus pattern (22 bp):
AGCCGTTTGGGGATGATTTTGG
Found at i:532352 original size:20 final size:20
Alignment explanation
Indices: 532323--532376 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 20
532313 GCAGCCTTCG
*
532323 TGCATGGATGCACAG-TAGGA
1 TGCATCGATGCACAGCT-GGA
*
532343 TGCATCGATGCACAGCCTTGA
1 TGCATCGATGCACAG-CTGGA
532364 TGCATCGATGCAC
1 TGCATCGATGCAC
532377 TAATTGCATT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
20 14 0.47
21 15 0.50
22 1 0.03
ACGTcount: A:0.26, C:0.24, G:0.28, T:0.22
Consensus pattern (20 bp):
TGCATCGATGCACAGCTGGA
Found at i:532560 original size:28 final size:31
Alignment explanation
Indices: 532529--532587 Score: 88
Period size: 28 Copynumber: 2.0 Consensus size: 31
532519 AAACTTTGAA
*
532529 TAAATTCAATT-AAG-TCCAAAA-CATTTTG
1 TAAATTCAATTCAAGTTCAAAAACCATTTTG
532557 TAAATTCAATTCAAGTTCAAAAACCATTTTG
1 TAAATTCAATTCAAGTTCAAAAACCATTTTG
532588 CCTTAAATTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 11 0.41
29 3 0.11
30 6 0.22
31 7 0.26
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAGTTCAAAAACCATTTTG
Found at i:532851 original size:34 final size:33
Alignment explanation
Indices: 532799--532890 Score: 127
Period size: 34 Copynumber: 2.8 Consensus size: 33
532789 TTAGTTTGTG
*
532799 CAATAAAATAAAATGTTAGTAA-GTTAGTA-AGAA
1 CAATAAAATAAAAAGTTAG-AATGTTAGTATA-AA
532832 CAATAAAAATAAAAAGTTAGAATGTTAGTATAAA
1 CAAT-AAAATAAAAAGTTAGAATGTTAGTATAAA
532866 CAATAAAAT-AAAAGTTAGAATGTTA
1 CAATAAAATAAAAAGTTAGAATGTTA
532891 ATAAGTTAGA
Statistics
Matches: 55, Mismatches: 1, Indels: 7
0.87 0.02 0.11
Matches are distributed among these distances:
32 16 0.29
33 11 0.20
34 27 0.49
35 1 0.02
ACGTcount: A:0.57, C:0.03, G:0.13, T:0.27
Consensus pattern (33 bp):
CAATAAAATAAAAAGTTAGAATGTTAGTATAAA
Found at i:537105 original size:21 final size:21
Alignment explanation
Indices: 537079--537118 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
537069 TTGTACATTT
537079 TGGTAGGAGTAAAATGGTTAA
1 TGGTAGGAGTAAAATGGTTAA
537100 TGGTAGGAGTAAAATGGTT
1 TGGTAGGAGTAAAATGGTT
537119 CATCTATTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.35, C:0.00, G:0.35, T:0.30
Consensus pattern (21 bp):
TGGTAGGAGTAAAATGGTTAA
Found at i:551042 original size:19 final size:19
Alignment explanation
Indices: 551018--551070 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
551008 CCTTAGCCAG
551018 AGTGCATCGATGCATGACT
1 AGTGCATCGATGCATGACT
*
551037 AGTGCATCGATGCATGGCT
1 AGTGCATCGATGCATGACT
*
551056 GGTGCATCGATGCAT
1 AGTGCATCGATGCAT
551071 CAAATGCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 32 1.00
ACGTcount: A:0.23, C:0.21, G:0.30, T:0.26
Consensus pattern (19 bp):
AGTGCATCGATGCATGACT
Found at i:552987 original size:41 final size:37
Alignment explanation
Indices: 552904--552986 Score: 125
Period size: 36 Copynumber: 2.3 Consensus size: 37
552894 AACGATTATG
552904 TTACTCGACTCATTGTTCATTAAAC-CAGTTAAAATT
1 TTACTCGACTCATTGTTCATTAAACTCAGTTAAAATT
* *
552940 TTACTCGACTCGTTGTTCGTTAAACTC-GTTAAAATT
1 TTACTCGACTCATTGTTCATTAAACTCAGTTAAAATT
*
552976 TTACTTGACTC
1 TTACTCGACTC
552987 GGCTCATTGC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 42 0.98
37 1 0.02
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (37 bp):
TTACTCGACTCATTGTTCATTAAACTCAGTTAAAATT
Found at i:553004 original size:41 final size:42
Alignment explanation
Indices: 552906--553008 Score: 121
Period size: 36 Copynumber: 2.6 Consensus size: 42
552896 CGATTATGTT
*
552906 ACTCGACTCATTGTTCATTAAAC-CAGTTAAAATTTTACTCG
1 ACTCGGCTCATTGTTCATTAAACTCAGTTAAAATTTTACTCG
* *
552947 ACTC-G----TTGTTCGTTAAACTC-GTTAAAATTTTACTTG
1 ACTCGGCTCATTGTTCATTAAACTCAGTTAAAATTTTACTCG
*
552983 ACTCGGCTCATTGCTCATTAAACTCA
1 ACTCGGCTCATTGTTCATTAAACTCA
553009 CCAGAATATT
Statistics
Matches: 50, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
36 31 0.62
37 2 0.04
41 17 0.34
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (42 bp):
ACTCGGCTCATTGTTCATTAAACTCAGTTAAAATTTTACTCG
Found at i:555786 original size:38 final size:37
Alignment explanation
Indices: 555742--556183 Score: 518
Period size: 36 Copynumber: 11.9 Consensus size: 37
555732 AAAAATTGTT
* * *
555742 TTTTGAAAATATATATATAATAAATAGTCTTTAAAGCA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACA
555780 TTTTGAAAGAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAA-AATATATATAATATATAGTTTTTAAAACA
555818 TTTTGAATATATATATATATATATATAATATATAGTTTTTAAAACA
1 TTTTG-----A-A-A-A-ATATATATAATATATAGTTTTTAAAACA
* *
555864 TTTTGAAAACT-TATATAGTATATAGTTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAG-TTTTTAAAACA
555901 TTTTGAAAATATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAA-ATATATATAATATATAGTTTTTAAAACA
* *
555939 TTTTGAAAACT-TATATAATATATAATTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
555975 TTTTG-AAAATATATATAATATATAGTTTTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
556011 TTTTGAAAAAATATATATAATATATAGTTTTTAAAACA
1 TTTTG-AAAAATATATATAATATATAGTTTTTAAAACA
*
556049 TTTTG-AAAATATATATAATATATAGTTTTTAAAATA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
*
556085 TTTTG--AAA-A-CT-T-ATATA-A---TTTAAAACA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
* *
556112 TTTTGAAACTATATATATAATATATAGTTTTTAAAAAA
1 TTTTGAAA-AATATATATAATATATAGTTTTTAAAACA
* * *
556150 ATTTGAAAACT-TATATAATATATAGTTTTGAAAA
1 TTTTGAAAAATATATATAATATATAGTTTTTAAAA
556184 AAATATTTTT
Statistics
Matches: 356, Mismatches: 22, Indels: 54
0.82 0.05 0.12
Matches are distributed among these distances:
27 13 0.04
29 1 0.00
30 2 0.01
31 6 0.02
32 2 0.01
33 2 0.01
34 6 0.02
35 8 0.02
36 128 0.36
37 23 0.06
38 111 0.31
39 15 0.04
40 1 0.00
41 1 0.00
43 1 0.00
44 1 0.00
45 2 0.01
46 33 0.09
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.44
Consensus pattern (37 bp):
TTTTGAAAAATATATATAATATATAGTTTTTAAAACA
Found at i:556028 original size:74 final size:73
Alignment explanation
Indices: 555834--556183 Score: 497
Period size: 74 Copynumber: 4.9 Consensus size: 73
555824 ATATATATAT
* *
555834 ATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAGTATATAGTTTTTTAAAA
1 ATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATA-ATTTTTAAAA
555899 CATTTTGAAA
65 CATTTTG-AA
555909 ATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAATTTTTAAAAC
1 ATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAATTTTTAAAAC
555974 ATTTTGAA
66 ATTTTGAA
* *
555982 A-ATATATATAATATATAGTTTTTAAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAA
1 ATATATATATAATATATAGTTTTTAAAACATTTTG-AAAACT-TATATAATATATAATTTTTAAA
556046 ACATTTTGAA
64 ACATTTTGAA
*
556056 A-ATATATATAATATATAGTTTTTAAAATATTTTGAAAAC-----T--TATATAA--TTTAAAAC
1 ATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAATTTTTAAAAC
556111 ATTTTGAA
66 ATTTTGAA
* * * *
556119 ACTATATATATAATATATAGTTTTTAAAAAAATTTGAAAACTTATATAATATATAGTTTTGAAAA
1 A-TATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAATTTTTAAAA
556184 AAATATTTTT
Statistics
Matches: 251, Mismatches: 11, Indels: 27
0.87 0.04 0.09
Matches are distributed among these distances:
63 17 0.07
65 42 0.17
67 1 0.00
70 1 0.00
72 39 0.16
73 12 0.05
74 86 0.34
75 53 0.21
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.44
Consensus pattern (73 bp):
ATATATATATAATATATAGTTTTTAAAACATTTTGAAAACTTATATAATATATAATTTTTAAAAC
ATTTTGAA
Found at i:556100 original size:65 final size:64
Alignment explanation
Indices: 556040--556168 Score: 224
Period size: 65 Copynumber: 2.0 Consensus size: 64
556030 ATATATAGTT
* *
556040 TTTAAAACATTTTGAAA-ATATATATAATATATAGTTTTTAAAATATTTTGAAAACTTATATAA
1 TTTAAAACATTTTGAAACATATATATAATATATAGTTTTTAAAAAAATTTGAAAACTTATATAA
556103 TTTAAAACATTTTGAAACTATATATATAATATATAGTTTTTAAAAAAATTTGAAAACTTATATAA
1 TTTAAAACATTTTGAAAC-ATATATATAATATATAGTTTTTAAAAAAATTTGAAAACTTATATAA
556168 T
1 T
556169 ATATAGTTTT
Statistics
Matches: 62, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
63 17 0.27
65 45 0.73
ACGTcount: A:0.48, C:0.04, G:0.05, T:0.43
Consensus pattern (64 bp):
TTTAAAACATTTTGAAACATATATATAATATATAGTTTTTAAAAAAATTTGAAAACTTATATAA
Found at i:556129 original size:29 final size:27
Alignment explanation
Indices: 556076--556128 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
556066 ATATATAGTT
*
556076 TTTAAAATATTTTGAAAACTTATATAA
1 TTTAAAACATTTTGAAAACTTATATAA
556103 TTTAAAACATTTTG-AAACTATATATA
1 TTTAAAACATTTTGAAAACT-TATATA
556129 TAATATATAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 19 0.79
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (27 bp):
TTTAAAACATTTTGAAAACTTATATAA
Found at i:556169 original size:101 final size:101
Alignment explanation
Indices: 556002--556183 Score: 303
Period size: 101 Copynumber: 1.8 Consensus size: 101
555992 ATATATAGTT
* *
556002 TTTAAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAAACATTTTGAAAATATATATAA
1 TTTAAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAAAAAATTTGAAAATATATATAA
*
556067 TATATAGTTTTTAAAATATTTTGAAAACTTATATAA
66 TATATAGTTTTGAAAATATTTTGAAAACTTATATAA
**
556103 TTTAAAACATTTTGAAACTATATATATAATATATAGTTTTTAAAAAAATTTGAAAACT-TATATA
1 TTTAAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAAAAAATTTGAAAA-TATATATA
556167 ATATATAGTTTTGAAAA
65 ATATATAGTTTTGAAAA
556184 AAATATTTTT
Statistics
Matches: 75, Mismatches: 5, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
101 74 0.99
102 1 0.01
ACGTcount: A:0.48, C:0.03, G:0.05, T:0.43
Consensus pattern (101 bp):
TTTAAAACATTTTGAAAAAATATATATAATATATAGTTTTTAAAAAAATTTGAAAATATATATAA
TATATAGTTTTGAAAATATTTTGAAAACTTATATAA
Found at i:558041 original size:12 final size:12
Alignment explanation
Indices: 558024--558049 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
558014 TTATACAAAC
558024 AGGGGTTAATCA
1 AGGGGTTAATCA
558036 AGGGGTTAATCA
1 AGGGGTTAATCA
558048 AG
1 AG
558050 TGGTAAGCTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.35, T:0.23
Consensus pattern (12 bp):
AGGGGTTAATCA
Found at i:560228 original size:26 final size:26
Alignment explanation
Indices: 560189--560238 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
560179 TTTTATAATA
**
560189 ATAAATTTTTTATAATTTT-AAAAATT
1 ATAAATTTCATAT-ATTTTGAAAAATT
560215 ATAAATTTCATATATTTTGAAAAA
1 ATAAATTTCATATATTTTGAAAAA
560239 AATATTAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 16 0.76
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (26 bp):
ATAAATTTCATATATTTTGAAAAATT
Found at i:560858 original size:329 final size:330
Alignment explanation
Indices: 560246--561048 Score: 1168
Period size: 329 Copynumber: 2.4 Consensus size: 330
560236 AAAAATATTA
* * *
560246 AATAATAATTCATTTGATCCCTCAATTGTAATTAAAAGGTTATTTTAATA-TTTAATATTTTTAA
1 AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAA
* *
560310 ATAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTTAAATTAT
66 ACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTAT
*
560375 -AAA-TA-T-TTATCATCATCATCATTTTGTAAAAGAAATATTAGTTATAAAACTTTTAAAAAAT
131 AAAATTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAGTTAT--AA---TT-AAAAAT
* * *
560436 TATTCATATTTTAAAATACTTATCCTCAAAGTTTTTATATACTAGATTATATGTATTGTGTAATT
190 TATTCATATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATACGTATTGTGAAATT
* ** *
560501 TTAATGTAAAAATTTAAATAATTTTATTAAAAATGAATAAACATTATTAACTGTTCTTAAAAATT
255 TTAATGCAAAAATCAAAATAAATTTATTAAAAATGAATAAACATTATTAACTGTTCTTAAAAATT
560566 AATAA-TTAATG
320 AA-AATTTAATG
560577 AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTCTTTTATATTTTT
1 AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATA-T-TTTTATATTTTT
*
560642 AAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATTAAATTTATAA-TTTTAAAATT
64 AAACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATT
*
560706 ATAAAATTTATTATTATCATCATCATCATCATTTGTAAAATAAATACTAG-T-T-A-T-AAAATT
129 ATAAAA-TTATTATTATCATCATCATCAT--TTTGTAAAAGAAATACTAGTTATAATTAAAAATT
* *
560766 ATTCATATTTTAAAATAGTTACCCTCAAAGTTTTCT-TATATTAGATTATACGTATTGTGAAATT
191 ATTCATATTTTAAAATACTTACCCTCAAAGTTTT-TATATACTAGATTATACGTATTGTGAAATT
*
560830 TTAATGCAAAAATCAAAATAAATTTATTAAAAATGAATAAACATTATTAACTGTTGTTAAAAATT
255 TTAATGCAAAAATCAAAATAAATTTATTAAAAATGAATAAACATTATTAACTGTTCTTAAAAATT
560895 AAAATTTAATG
320 AAAATTTAATG
*
560906 AATAATAATTCATTTGATCTCTTAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAA
1 AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAA
** *
560971 ACAATTAATTTTAAAAGAAAATATTTTTTTTC-AAAATATATGAAATTTATAATTTTTAAAATTA
66 ACAATTAATTTTAAAAGGTAATA-ATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTA
*
561035 TAAAA-AATTATTAT
130 TAAAATTATTATTAT
561049 AAAAAATAAA
Statistics
Matches: 434, Mismatches: 24, Indels: 33
0.88 0.05 0.07
Matches are distributed among these distances:
326 8 0.02
327 54 0.12
328 26 0.06
329 180 0.41
330 1 0.00
331 49 0.11
333 11 0.03
334 66 0.15
335 1 0.00
336 2 0.00
337 1 0.00
338 17 0.04
339 1 0.00
340 17 0.04
ACGTcount: A:0.44, C:0.06, G:0.05, T:0.45
Consensus pattern (330 bp):
AATAATAATTCATTTGATCTCTCAATTGTAATTAAAAGTTTATTTTAATATTTTTATATTTTTAA
ACAATTAATTTTAAAAGGTAATAATTTTTTCAAAAATATATGAAATTTATAATTTTTAAAATTAT
AAAATTATTATTATCATCATCATCATTTTGTAAAAGAAATACTAGTTATAATTAAAAATTATTCA
TATTTTAAAATACTTACCCTCAAAGTTTTTATATACTAGATTATACGTATTGTGAAATTTTAATG
CAAAAATCAAAATAAATTTATTAAAAATGAATAAACATTATTAACTGTTCTTAAAAATTAAAATT
TAATG
Found at i:561049 original size:13 final size:13
Alignment explanation
Indices: 561031--561055 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
561021 AATTTTTAAA
561031 ATTATAAAAAATT
1 ATTATAAAAAATT
561044 ATTATAAAAAAT
1 ATTATAAAAAAT
561056 AAACTTGTGA
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:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATTATAAAAAATT
Found at i:561876 original size:10 final size:10
Alignment explanation
Indices: 561861--561895 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 10
561851 TTTATCACAC
561861 CAAATTCTCT
1 CAAATTCTCT
561871 CAAATTCTCT
1 CAAATTCTCT
561881 -AAATTTCTCT
1 CAAA-TTCTCT
561891 CAAAT
1 CAAAT
561896 AATCTATCTT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.13
10 17 0.74
11 3 0.13
ACGTcount: A:0.34, C:0.26, G:0.00, T:0.40
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:562165 original size:111 final size:112
Alignment explanation
Indices: 562027--562249 Score: 385
Period size: 111 Copynumber: 2.0 Consensus size: 112
562017 TGGAAATCAT
* *
562027 ATATCTCTACACTTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTTAATTATTAGTA
1 ATATCTCGACACTTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
*
562092 ATATTTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
562139 ATATCTCGACAC-TTTGCTGATACGGTATCATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
1 ATATCTCGACACTTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
* *
562203 GTAATTAGTTGATTTATTTGATGCATGATTATTAGATTAAGAATTAA
66 ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
562250 TTTTTGTAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
111 94 0.90
112 11 0.10
ACGTcount: A:0.34, C:0.08, G:0.12, T:0.46
Consensus pattern (112 bp):
ATATCTCGACACTTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTA
ATAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Found at i:564591 original size:12 final size:12
Alignment explanation
Indices: 564574--564610 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
564564 ATTTATAAGA
564574 GAGGAGAGATGC
1 GAGGAGAGATGC
*
564586 GA-G-GAGATGT
1 GAGGAGAGATGC
564596 GAGGAGAGATGC
1 GAGGAGAGATGC
564608 GAG
1 GAG
564611 AACCGTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.32, C:0.05, G:0.51, T:0.11
Consensus pattern (12 bp):
GAGGAGAGATGC
Found at i:565025 original size:19 final size:19
Alignment explanation
Indices: 565001--565045 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
564991 AGACGAGATT
*
565001 GTGAAGTCCAATCTGCGCA
1 GTGAAGTCCAATCTACGCA
565020 GTGAAGTCCAATCTACGCA
1 GTGAAGTCCAATCTACGCA
565039 GTGAAGT
1 GTGAAGT
565046 GAAACATGTC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.22, G:0.27, T:0.22
Consensus pattern (19 bp):
GTGAAGTCCAATCTACGCA
Found at i:568935 original size:14 final size:14
Alignment explanation
Indices: 568916--568943 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
568906 TTAATTAATC
568916 CTAATTTAATCACT
1 CTAATTTAATCACT
568930 CTAATTTAATCACT
1 CTAATTTAATCACT
568944 AAAGTTTAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.21, G:0.00, T:0.43
Consensus pattern (14 bp):
CTAATTTAATCACT
Found at i:569292 original size:28 final size:28
Alignment explanation
Indices: 569257--569322 Score: 132
Period size: 28 Copynumber: 2.4 Consensus size: 28
569247 TTTAGTTTAG
569257 AACAATTTTTATATTCTTTTATCTAAAT
1 AACAATTTTTATATTCTTTTATCTAAAT
569285 AACAATTTTTATATTCTTTTATCTAAAT
1 AACAATTTTTATATTCTTTTATCTAAAT
569313 AACAATTTTT
1 AACAATTTTT
569323 TCCCAGAAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.53
Consensus pattern (28 bp):
AACAATTTTTATATTCTTTTATCTAAAT
Found at i:570060 original size:27 final size:27
Alignment explanation
Indices: 570000--570060 Score: 63
Period size: 27 Copynumber: 2.3 Consensus size: 27
569990 TTTTCATCAC
* *
570000 CTTAAAATTTTATAAATTTATATCTTT
1 CTTAAAATTTTATAAATCTATACCTTT
*
570027 -TTCAAAATTTTATAAATCTA-CCCTTAT
1 CTT-AAAATTTTATAAATCTATACCTT-T
570054 CTTAAAA
1 CTTAAAA
570061 AGTTCGAGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
26 5 0.18
27 21 0.75
28 2 0.07
ACGTcount: A:0.39, C:0.13, G:0.00, T:0.48
Consensus pattern (27 bp):
CTTAAAATTTTATAAATCTATACCTTT
Found at i:575671 original size:34 final size:34
Alignment explanation
Indices: 575624--575733 Score: 99
Period size: 34 Copynumber: 3.2 Consensus size: 34
575614 AGTGTTATAT
575624 TATATTTTAAAAATATTAATTAGTA-TAAT-TTAAA
1 TATATTTTAAAAATATT-ATTA-TATTAATATTAAA
575658 TATATTATT-AAAATATTATTATATTAATATTAAA
1 TATATT-TTAAAAATATTATTATATTAATATTAAA
575692 TATA---TAAATAATATTATTCATTATTAAATATATAAA
1 TATATTTTAAA-AATATTATT-A-TATT-AATAT-TAAA
575728 TA-ATTT
1 TATATTT
575734 ATTATATATT
Statistics
Matches: 64, Mismatches: 0, Indels: 20
0.76 0.00 0.24
Matches are distributed among these distances:
30 1 0.02
31 2 0.03
32 11 0.17
33 9 0.14
34 27 0.42
35 8 0.12
36 6 0.09
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.48
Consensus pattern (34 bp):
TATATTTTAAAAATATTATTATATTAATATTAAA
Found at i:575723 original size:28 final size:29
Alignment explanation
Indices: 575668--575847 Score: 121
Period size: 29 Copynumber: 6.2 Consensus size: 29
575658 TATATTATTA
*
575668 AAAT-ATTATTATATTAATATTAAATATAT
1 AAATAATTATTATA-TATTATTAAATATAT
575697 AAATAA-TATTAT-TCATTATTAAATATAT
1 AAATAATTATTATAT-ATTATTAAATATAT
*
575725 AAATAATTTATTATATATTATTAAA-ATAA
1 AAATAA-TTATTATATATTATTAAATATAT
* *
575754 AAATATAATATCT-TATATTA-T-ATTATTAT
1 AAATA-ATTAT-TATATATTATTAAATA-TAT
575783 AATATAATTGATTAT-T-TTATTATAATAT-T
1 AA-ATAATT-ATTATATATTATTA-AATATAT
* *
575812 AAA-AATATAATATCATATTATTAGATATAT
1 AAATAAT-TATTAT-ATATTATTAAATATAT
*
575842 TAATAA
1 AAATAA
575848 ATATATTTTA
Statistics
Matches: 120, Mismatches: 10, Indels: 40
0.71 0.06 0.24
Matches are distributed among these distances:
27 9 0.08
28 26 0.22
29 45 0.38
30 34 0.28
31 6 0.05
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (29 bp):
AAATAATTATTATATATTATTAAATATAT
Found at i:575842 original size:31 final size:31
Alignment explanation
Indices: 575711--575852 Score: 106
Period size: 30 Copynumber: 4.8 Consensus size: 31
575701 AATATTATTC
* * *
575711 ATTATTAAATATA-TAAATAATTTATTAT-AT
1 ATTATTATATATATTAAA-AATATAATATCAT
*
575741 ATTATTA-A-A-A-TAAAAATATAATATCTT
1 ATTATTATATATATTAAAAATATAATATCAT
* *
575768 A-TATTATAT-TATT-ATAATATAATTGATTAT
1 ATTATTATATATATTAAAAATATAA-T-ATCAT
*
575798 TTTATTATA-ATATTAAAAATATAATATCAT
1 ATTATTATATATATTAAAAATATAATATCAT
*
575828 ATTATTAGATATATTAATAAATATA
1 ATTATTATATATATTAA-AAATATA
575853 TTTTAAATAT
Statistics
Matches: 89, Mismatches: 11, Indels: 22
0.73 0.09 0.18
Matches are distributed among these distances:
26 13 0.15
27 8 0.09
28 10 0.11
29 3 0.03
30 21 0.24
31 19 0.21
32 15 0.17
ACGTcount: A:0.50, C:0.01, G:0.01, T:0.47
Consensus pattern (31 bp):
ATTATTATATATATTAAAAATATAATATCAT
Found at i:575862 original size:23 final size:24
Alignment explanation
Indices: 575826--575894 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
575816 ATATAATATC
*
575826 ATATTATTAGATATATTAATAAAT
1 ATATTATTAAATATATTAATAAAT
* *
575850 ATATT-TTAAATATTTTAATAATT
1 ATATTATTAAATATATTAATAAAT
*
575873 AATATGATTAAAATGATATTAA
1 -ATATTATT-AAAT-ATATTAA
575895 AATGTTTTAT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 15 0.42
24 9 0.25
25 2 0.06
26 4 0.11
27 6 0.17
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.46
Consensus pattern (24 bp):
ATATTATTAAATATATTAATAAAT
Found at i:576122 original size:42 final size:42
Alignment explanation
Indices: 576075--576164 Score: 119
Period size: 42 Copynumber: 2.1 Consensus size: 42
576065 TTCCTCCAAC
* * *
576075 CAAACAC-TGAAAAACATTTTTCGAAAAACAAATTACGTGAAA
1 CAAACACATG-AAAACATTTTCCAAAAAACAAATTACATGAAA
* *
576117 CAAACACATGAAAATATTTTCCAAAAAACAAATTATATGAAA
1 CAAACACATGAAAACATTTTCCAAAAAACAAATTACATGAAA
576159 CAAACA
1 CAAACA
576165 TAGAATTTTG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
42 40 0.95
43 2 0.05
ACGTcount: A:0.56, C:0.17, G:0.07, T:0.21
Consensus pattern (42 bp):
CAAACACATGAAAACATTTTCCAAAAAACAAATTACATGAAA
Found at i:580145 original size:2 final size:2
Alignment explanation
Indices: 580138--580176 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
580128 AACAATGAAT
580138 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
580177 CTTAACCGTG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:581139 original size:73 final size:75
Alignment explanation
Indices: 581008--581167 Score: 236
Period size: 73 Copynumber: 2.2 Consensus size: 75
580998 CTTAACCGGT
* * * * *
581008 TAAAATAAAATAGGAGCTACCTATTATGTTAAATTATCTACCGGTTTGTTTTAAGGTTACTAATA
1 TAAAATAAAATAGGAGCTACCTATTAGGTTAAAATACCTACAGGTTTGATTTAAGGTTACTAATA
*
581073 ATGTAAACGG
66 ATGTAAAAGG
581083 TAAAATAAAATA-G-GCTACCTATTAGGTTAAAATACCTACAGGTTT-ATTTAATGGTTACTAAT
1 TAAAATAAAATAGGAGCTACCTATTAGGTTAAAATACCTACAGGTTTGATTTAA-GGTTACTAAT
581145 AATGTAAAAGG
65 AATGTAAAAGG
581156 TAAAATAAAATA
1 TAAAATAAAATA
581168 AGTGTTATAT
Statistics
Matches: 78, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
72 5 0.06
73 60 0.77
74 1 0.01
75 12 0.15
ACGTcount: A:0.42, C:0.09, G:0.14, T:0.34
Consensus pattern (75 bp):
TAAAATAAAATAGGAGCTACCTATTAGGTTAAAATACCTACAGGTTTGATTTAAGGTTACTAATA
ATGTAAAAGG
Found at i:581203 original size:23 final size:23
Alignment explanation
Indices: 581177--581233 Score: 96
Period size: 23 Copynumber: 2.5 Consensus size: 23
581167 AAGTGTTATA
581177 TATTATGTTAAACAGGCGCTACC
1 TATTATGTTAAACAGGCGCTACC
* *
581200 TATTACGTTAAATAGGCGCTACC
1 TATTATGTTAAACAGGCGCTACC
581223 TATTATGTTAA
1 TATTATGTTAA
581234 TTTATCTATC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (23 bp):
TATTATGTTAAACAGGCGCTACC
Found at i:581394 original size:75 final size:75
Alignment explanation
Indices: 581209--581679 Score: 345
Period size: 75 Copynumber: 6.3 Consensus size: 75
581199 CTATTACGTT
* * ** * * **
581209 AAATAGGCGCTACCTATTATGTTAATTTATCTATCGGTTTGTTTAAAGGTTACTAATAATGTAAA
1 AAATAGACGCTACTTATTATGTTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATGTAAA
581274 CGATAAAAATA
66 CGAT-AAAATA
** * * * *
581285 AAATAGAATCTACATATTATATTAAAATATCTACCAATTTGTTTAAAGGTTACTAATAATATAAA
1 AAATAGACGCTACTTATTATGTTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATGTAAA
*
581350 TGATAAAATA
66 CGATAAAATA
* **
581360 AAATAGACGCTACTTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAA
1 AAATAGACGCTACTTATTATGTTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATGTAAA
*
581425 CGGTAAAATA
66 CGATAAAATA
* * ** * ** *
581435 AAATAGGCGATACTTATTATGTT-AAATAGGCGCTACTTATTATGTTAAATAGG-CGCTACCT-A
1 AAATAGACGCTACTTATTATGTTAAAATA--C-CTACCAATT-TGTTTAA-AGGTTACTA-ATAA
*
581497 T-T--ACG-TTAAATA
60 TGTAAACGATAAAATA
** ** * * ** *
581509 AGTTCTAC-CTA-TTA-T-G-TTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATAATGTAAA
1 AAATAGACGCTACTTATTATGTTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATGTAAA
*
581569 CGGTAAAATA
66 CGATAAAATA
* * * * *** *
581579 AAATAGGCGCTACCTATTACGTTAAAATACATACTGGTTTGTTTAAAGGTTACTAATAATGTATA
1 AAATAGACGCTACTTATTATGTTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATGTAAA
*
581644 CGGTAAAATA
66 CGATAAAATA
* * *
581654 AAATAGGCACTACCTATTATGTTAAA
1 AAATAGACGCTACTTATTATGTTAAA
581680 TAGGCGCTAC
Statistics
Matches: 312, Mismatches: 65, Indels: 37
0.75 0.16 0.09
Matches are distributed among these distances:
65 4 0.01
66 10 0.03
67 7 0.02
68 1 0.00
69 5 0.02
70 13 0.04
71 4 0.01
72 5 0.02
73 3 0.01
74 14 0.04
75 166 0.53
76 58 0.19
77 7 0.02
78 11 0.04
79 4 0.01
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (75 bp):
AAATAGACGCTACTTATTATGTTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATGTAAA
CGATAAAATA
Found at i:581464 original size:23 final size:23
Alignment explanation
Indices: 581435--581529 Score: 127
Period size: 23 Copynumber: 4.1 Consensus size: 23
581425 CGGTAAAATA
*
581435 AAATAGGCGATACTTATTATGTT
1 AAATAGGCGCTACTTATTATGTT
581458 AAATAGGCGCTACTTATTATGTT
1 AAATAGGCGCTACTTATTATGTT
* *
581481 AAATAGGCGCTACCTATTACGTT
1 AAATAGGCGCTACTTATTATGTT
* ** *
581504 AAATAAGTTCTACCTATTATGTT
1 AAATAGGCGCTACTTATTATGTT
581527 AAA
1 AAA
581530 CTACCTACCG
Statistics
Matches: 65, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.37
Consensus pattern (23 bp):
AAATAGGCGCTACTTATTATGTT
Found at i:581493 original size:272 final size:270
Alignment explanation
Indices: 581009--581505 Score: 744
Period size: 272 Copynumber: 1.8 Consensus size: 270
580999 TTAACCGGTT
* * * * ** *
581009 AAAATAAAATAGGAGCTACCTATTATGTTAAATTATCTACCGGTTTGTTTTAAGGTTACTAATAA
1 AAAATAAAATAGAAGCTACATATTATATTAAAATATCTACCAATTTGTTTAAAGGTTACTAATAA
* * * *
581074 TGTAAACGGTAAAATAAAATAGGCTACCTATTAGGTTAAAATACCTACAGGTTTATTTAATGGTT
66 TATAAACGATAAAATAAAATAGGCTACCTATTACGTTAAAATACCTACAGGTTTATTTAAAGGTT
* *
581139 ACTAATAATGTAAAAGGTAAAATAAAATAAGTGTTATATATTATGTTAAACAGGCGCTACCTATT
131 ACTAATAATGTAAAAGGTAAAATAAAATAAGCGATATATATTATGTTAAACAGGCGCTACCTATT
*
581204 ACGTTAAATAGGCGCTACCTATTATGTTAATTTATCTATCGGTTTGTTTAAAGGTTACTAATAAT
196 ACGTTAAATAGGCGCTACCTATTACGTTAATTTATCTATCGGTTTGTTTAAAGGTTACTAATAAT
581269 GTAAACGATA
261 GTAAACGATA
*
581279 AAAATAAAATAGAATCTACATATTATATTAAAATATCTACCAATTTGTTTAAAGGTTACTAATAA
1 AAAATAAAATAGAAGCTACATATTATATTAAAATATCTACCAATTTGTTTAAAGGTTACTAATAA
* * * *
581344 TATAAATGATAAAATAAAATAGACGCTACTTATTACGTTAAAATACCTACCGGTTTGTTTAAAGG
66 TATAAACGATAAAATAAAATAG--GCTACCTATTACGTTAAAATACCTACAGGTTTATTTAAAGG
* * * *
581409 TTACTAATAATGTAAACGGTAAAATAAAATAGGCGATACT-TATTATGTTAAATAGGCGCTACTT
129 TTACTAATAATGTAAAAGGTAAAATAAAATAAGCGATA-TATATTATGTTAAACAGGCGCTACCT
*
581473 ATTATGTTAAATAGGCGCTACCTATTACGTTAA
193 ATTACGTTAAATAGGCGCTACCTATTACGTTAA
581506 ATAAGTTCTA
Statistics
Matches: 200, Mismatches: 24, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
270 76 0.38
272 123 0.62
273 1 0.00
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (270 bp):
AAAATAAAATAGAAGCTACATATTATATTAAAATATCTACCAATTTGTTTAAAGGTTACTAATAA
TATAAACGATAAAATAAAATAGGCTACCTATTACGTTAAAATACCTACAGGTTTATTTAAAGGTT
ACTAATAATGTAAAAGGTAAAATAAAATAAGCGATATATATTATGTTAAACAGGCGCTACCTATT
ACGTTAAATAGGCGCTACCTATTACGTTAATTTATCTATCGGTTTGTTTAAAGGTTACTAATAAT
GTAAACGATA
Found at i:581580 original size:219 final size:219
Alignment explanation
Indices: 581293--581689 Score: 634
Period size: 219 Copynumber: 1.8 Consensus size: 219
581283 TAAAATAGAA
* *
581293 TCTACATATTATATTAAAATATCTACCAATTTGTTTAAAGGTTACTAATAATATAAATGATAAAA
1 TCTACATATTATATTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATATAAACGATAAAA
* *
581358 TAAAATAGACGCTACTTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTA
66 TAAAATAGACGCTACCTATTACGTTAAAATACATACCGGTTTGTTTAAAGGTTACTAATAATGTA
*
581423 AACGGTAAAATAAAATAGGCGA-TACTTATTATGTTAAATAGGCGCTACTTATTATGTTAAATAG
131 AACGGTAAAATAAAATAGGC-ACTACCTATTATGTTAAATAGGCGCTACTTATTATGTTAAATAG
581487 GCGCTACCTATTACGTTAAATAAGT
195 GCGCTACCTATTACGTTAAATAAGT
* * * ** * * *
581512 TCTACCTATTATGTTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATAATGTAAACGGTAAAA
1 TCTACATATTATATTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATATAAACGATAAAA
* *
581577 TAAAATAGGCGCTACCTATTACGTTAAAATACATACTGGTTTGTTTAAAGGTTACTAATAATGTA
66 TAAAATAGACGCTACCTATTACGTTAAAATACATACCGGTTTGTTTAAAGGTTACTAATAATGTA
*
581642 TACGGTAAAATAAAATAGGCACTACCTATTATGTTAAATAGGCGCTAC
131 AACGGTAAAATAAAATAGGCACTACCTATTATGTTAAATAGGCGCTAC
581690 CTTTTACATT
Statistics
Matches: 161, Mismatches: 16, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
218 1 0.01
219 160 0.99
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (219 bp):
TCTACATATTATATTAAAATACCTACCAATTTGTTTAAAGGTTACTAATAATATAAACGATAAAA
TAAAATAGACGCTACCTATTACGTTAAAATACATACCGGTTTGTTTAAAGGTTACTAATAATGTA
AACGGTAAAATAAAATAGGCACTACCTATTATGTTAAATAGGCGCTACTTATTATGTTAAATAGG
CGCTACCTATTACGTTAAATAAGT
Found at i:581701 original size:23 final size:23
Alignment explanation
Indices: 581654--581704 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
581644 CGGTAAAATA
**
581654 AAATAGGCACTACCTATTATGTT
1 AAATAGGCACTACCTATTACATT
* *
581677 AAATAGGCGCTACCTTTTACATT
1 AAATAGGCACTACCTATTACATT
581700 AAATA
1 AAATA
581705 AACGCTATAT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.37, C:0.18, G:0.12, T:0.33
Consensus pattern (23 bp):
AAATAGGCACTACCTATTACATT
Found at i:581795 original size:196 final size:195
Alignment explanation
Indices: 581458--582064 Score: 874
Period size: 196 Copynumber: 3.1 Consensus size: 195
581448 TTATTATGTT
* * *
581458 AAATAGGCGCTACTTATTATGTTAAATAGGCGCTACCTATTACGTTAAATAAGTTCTACCTATTA
1 AAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTATTACATTAAATAAGTGCTACCTATTA
*
581523 TGTTAAACTACCTACCGGTTTGTTTGAAGGTTACTAATAATGTAAACGGTAAAATAAAATAGGCG
66 TGTTAAACTACCTACCGGTTTGTTTGAAGGTTATTAATAATGTAAACGGTAAAATAAAATAGGCG
* * *
581588 CTACCTATTACGTTAAAATACATACTGGTTTGTTTAAAGGTTACTAATAATGTATACGGTAAAAT
131 CTACCTATTACGTTAAAATAC-TACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAAT
581653 A
195 A
* * ** **
581654 AAATAGGCACTACCTATTATGTTAAATAGGCGCTACCTTTTACATTAAATAAACGCTATATATTA
1 AAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTATTACATTAAATAAGTGCTACCTATTA
* * * ***
581719 TGTTAAACTACCTACCGGTTTGTTTGAATGTTATTAATAATGTAAACGGTAAAATAAAGTTGATA
66 TGTTAAACTACCTACCGGTTTGTTTGAAGGTTATTAATAATGTAAACGGTAAAATAAAATAGGCG
* *
581784 ATACTTATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAAT
131 CTACCTATTACGTTAAAATA-CTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAAT
581849 A
195 A
* *
581850 AAATAGGCGCTACCTATTTTGTTAAATAGGCGCTACATATTACGA-TAAATAAGTGCTACCTATT
1 AAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTATTAC-ATTAAATAAGTGCTACCTATT
* * * * *
581914 ATGTTAAATTGCCTACCGATTTTTTTTAAGGTTATTAATAATGTAAACGGTAAAATAAAATAGGC
65 ATGTTAAACTACCTACCGGTTTGTTTGAAGGTTATTAATAATGTAAACGGTAAAATAAAATAGGC
* *
581979 GCTACCTATTACGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAATAATGAAAACGACAAAA
130 GCTACCTATTACGTTAAAATA-CTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAA
582044 TA
194 TA
* * *
582046 AAATTGACGTTACCTATTA
1 AAATAGGCGCTACCTATTA
582065 ACCGTTTGAA
Statistics
Matches: 360, Mismatches: 49, Indels: 4
0.87 0.12 0.01
Matches are distributed among these distances:
196 358 0.99
197 2 0.01
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.34
Consensus pattern (195 bp):
AAATAGGCGCTACCTATTATGTTAAATAGGCGCTACCTATTACATTAAATAAGTGCTACCTATTA
TGTTAAACTACCTACCGGTTTGTTTGAAGGTTATTAATAATGTAAACGGTAAAATAAAATAGGCG
CTACCTATTACGTTAAAATACTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATA
Found at i:581874 original size:75 final size:75
Alignment explanation
Indices: 581714--581875 Score: 198
Period size: 75 Copynumber: 2.2 Consensus size: 75
581704 AAACGCTATA
* * * * * *
581714 TATTATGTTAAACTACCTACCGGTTTGTTTGAATGTTATTAATAATGTAAACGGTAAAATAAAGT
1 TATTATGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAAT
* * *
581779 TGATAATACT
66 AGACAATACC
*
581789 TATTACGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAAT
1 TATTATGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAAT
* **
581854 AGGCGCTACC
66 AGACAATACC
*
581864 TATTTTGTTAAA
1 TATTATGTTAAA
581876 TAGGCGCTAC
Statistics
Matches: 72, Mismatches: 15, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (75 bp):
TATTATGTTAAAATACCTACCGGTTTGTTTAAAGGTTACTAATAATGTAAACGATAAAATAAAAT
AGACAATACC
Found at i:581879 original size:23 final size:23
Alignment explanation
Indices: 581850--581922 Score: 92
Period size: 23 Copynumber: 3.2 Consensus size: 23
581840 CGATAAAATA
*
581850 AAATAGGCGCTACCTATTTTGTT
1 AAATAGGCGCTACCTATTATGTT
* * *
581873 AAATAGGCGCTACATATTACGAT
1 AAATAGGCGCTACCTATTATGTT
* *
581896 AAATAAGTGCTACCTATTATGTT
1 AAATAGGCGCTACCTATTATGTT
581919 AAAT
1 AAAT
581923 TGCCTACCGA
Statistics
Matches: 41, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (23 bp):
AAATAGGCGCTACCTATTATGTT
Found at i:582020 original size:75 final size:75
Alignment explanation
Indices: 581904--582064 Score: 196
Period size: 75 Copynumber: 2.1 Consensus size: 75
581894 ATAAATAAGT
* * * * * * * **
581904 GCTACCTATTATGTTAAATTGCCTACCGATTTTTTTTAAGGTTATTAATAATGTAAACGGTAAAA
1 GCTACCTATTACGTTAAAATACCTACCGATTTGTTTAAAGGTTACTAATAATGAAAACGACAAAA
*
581969 TAAAATAGGC
66 TAAAATAGAC
* *
581979 GCTACCTATTACGTTAAAATATCTACCGGTTTGTTTAAAGGTTACTAATAATGAAAACGACAAAA
1 GCTACCTATTACGTTAAAATACCTACCGATTTGTTTAAAGGTTACTAATAATGAAAACGACAAAA
*
582044 TAAAATTGAC
66 TAAAATAGAC
*
582054 GTTACCTATTA
1 GCTACCTATTA
582065 ACCGTTTGAA
Statistics
Matches: 72, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
75 72 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.35
Consensus pattern (75 bp):
GCTACCTATTACGTTAAAATACCTACCGATTTGTTTAAAGGTTACTAATAATGAAAACGACAAAA
TAAAATAGAC
Found at i:582665 original size:107 final size:106
Alignment explanation
Indices: 582527--583030 Score: 390
Period size: 107 Copynumber: 4.6 Consensus size: 106
582517 TGTTATTATT
* * * *
582527 TATTTATAGCAAAATAAAAAATTAACCTATTTTGTTGTCGT-GAGATTTCGAAGGCTTCATCAGC
1 TATTAATAACAAAAT-AAAAATTAACCTATTTTGTTATCGTCG-GATTTCTAAGGC-TCATCAGC
* * *
582591 TTAAATTTTGGTAATATTTTAAGTGCTACCTAATATGTTGATAA
63 TTAAACTTTGATAATATTTTAAGCGCTACCTAATATGTTGATAA
* * * * * *
582635 TATTAATAACAAAATAAAAATTAACATATTTTGTTTTCATCGGATTTTTAAGTCCCATCAGCTTA
1 TATTAATAACAAAATAAAAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCATCAGCTTA
* * *
582700 AACTTTGATAATATTTTAGGCGTTACCTAATTTGTTGATAA
66 AACTTTGATAATATTTTAAGCGCTACCTAATATGTTGATAA
* * *
582741 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGC-CTATCAGCT
1 TATTAATAACAAAATAA-AAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTC-ATCAGC-
* * * * ** *
582805 TTAAAAAGGCGCTACTT-ATTACATTAAATAAGCGCTACTTGTTATGTT-ATTA
63 TT--AAA----CT--TTGATAATATT--TTAAGCGCTACCTAATATGTTGATAA
* * **** * * *
582857 TGGTTGATAA-TGTTTACAGTAATTAACCTATTTTGTTATCGTTGAATTTCTAAGGCTCCATCAG
1 T-ATTAATAACAAAATA-A-AAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCT-CATCAG
* *
582921 CTTAAACTTTGATAACATTTTAGGCGCTACCTAATATGTTGATAA
62 CTTAAACTTTGATAATATTTTAAGCGCTACCTAATATGTTGATAA
* * * **
582966 TATTGATAACAAATTAAGTAATTAACCTATTTTGTTATCGTTAGATTTCTAAGG-TCCATCAGCT
1 TATTAATAACAAAATAA-AAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCT-CATCAGCT
583030 T
64 T
583031 TAAAATGTGC
Statistics
Matches: 323, Mismatches: 52, Indels: 43
0.77 0.12 0.10
Matches are distributed among these distances:
106 61 0.19
107 79 0.24
108 75 0.23
109 9 0.03
110 10 0.03
111 2 0.01
114 2 0.01
115 9 0.03
116 9 0.03
117 60 0.19
118 6 0.02
119 1 0.00
ACGTcount: A:0.33, C:0.13, G:0.13, T:0.40
Consensus pattern (106 bp):
TATTAATAACAAAATAAAAATTAACCTATTTTGTTATCGTCGGATTTCTAAGGCTCATCAGCTTA
AACTTTGATAATATTTTAAGCGCTACCTAATATGTTGATAA
Found at i:585399 original size:27 final size:26
Alignment explanation
Indices: 585369--585423 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
585359 TTGCATATAT
*
585369 TAAATTTTAAAA-TAAGTCTTGGAAATA
1 TAAA-TTTAAAACTAA-TCTTAGAAATA
*
585396 TAAATTTAAAACTTATCTTAGAAATA
1 TAAATTTAAAACTAATCTTAGAAATA
585422 TA
1 TA
585424 TTATAAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 19 0.76
27 6 0.24
ACGTcount: A:0.49, C:0.05, G:0.07, T:0.38
Consensus pattern (26 bp):
TAAATTTAAAACTAATCTTAGAAATA
Found at i:586248 original size:10 final size:9
Alignment explanation
Indices: 586225--586268 Score: 52
Period size: 10 Copynumber: 4.7 Consensus size: 9
586215 CTTCTGGAAA
*
586225 ACCGGTTTG
1 ACCGGTTCG
586234 ACCGGTTCCG
1 ACCGGTT-CG
586244 ACCGGTTCG
1 ACCGGTTCG
*
586253 AACCGGTTTG
1 -ACCGGTTCG
586263 ACCGGT
1 ACCGGT
586269 CTGAACCAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
9 15 0.48
10 16 0.52
ACGTcount: A:0.14, C:0.30, G:0.32, T:0.25
Consensus pattern (9 bp):
ACCGGTTCG
Found at i:586274 original size:19 final size:19
Alignment explanation
Indices: 586225--586275 Score: 52
Period size: 19 Copynumber: 2.6 Consensus size: 19
586215 CTTCTGGAAA
586225 ACCGGTTTG-ACCGGTTCCG
1 ACCGG-TTGAACCGGTTCCG
*
586244 ACCGGTTCGAACCGGTT-TG
1 ACCGGTT-GAACCGGTTCCG
586263 ACCGGTCTGAACC
1 ACCGGT-TGAACC
586276 AACTCGACCC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 2 0.07
19 18 0.64
20 8 0.29
ACGTcount: A:0.16, C:0.31, G:0.29, T:0.24
Consensus pattern (19 bp):
ACCGGTTGAACCGGTTCCG
Found at i:586282 original size:29 final size:29
Alignment explanation
Indices: 586224--586282 Score: 66
Period size: 29 Copynumber: 2.0 Consensus size: 29
586214 GCTTCTGGAA
***
586224 AACCGGTTTGACCGGTTCCGACCGGTTCG
1 AACCGGTTTGACCGGTTCCGACCAACTCG
*
586253 AACCGGTTTGACCGG-TCTGAACCAACTCG
1 AACCGGTTTGACCGGTTCCG-ACCAACTCG
586282 A
1 A
586283 CCCTACTGAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
28 3 0.12
29 22 0.88
ACGTcount: A:0.20, C:0.31, G:0.27, T:0.22
Consensus pattern (29 bp):
AACCGGTTTGACCGGTTCCGACCAACTCG
Found at i:586339 original size:7 final size:7
Alignment explanation
Indices: 586327--586370 Score: 61
Period size: 7 Copynumber: 6.3 Consensus size: 7
586317 GACCCGACCC
586327 GACCGTT
1 GACCGTT
586334 GACCGTT
1 GACCGTT
*
586341 AACCGTT
1 GACCGTT
*
586348 GACCGTG
1 GACCGTT
*
586355 GACCGTG
1 GACCGTT
586362 GACCGTT
1 GACCGTT
586369 GA
1 GA
586371 TTTCCTTTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
7 33 1.00
ACGTcount: A:0.18, C:0.27, G:0.32, T:0.23
Consensus pattern (7 bp):
GACCGTT
Found at i:589117 original size:18 final size:18
Alignment explanation
Indices: 589078--589132 Score: 65
Period size: 18 Copynumber: 3.0 Consensus size: 18
589068 GTTTAATCTC
* * *
589078 AAGAAGAAGAAAATGAAG
1 AAGAAGAAGAAGATTAAA
589096 AAGAAGAAGAAGATTAAA
1 AAGAAGAAGAAGATTAAA
*
589114 AAGAAAAAGAAGAGTTAAA
1 AAGAAGAAGAAGA-TTAAA
589133 GGAGTTAACG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
18 27 0.84
19 5 0.16
ACGTcount: A:0.67, C:0.00, G:0.24, T:0.09
Consensus pattern (18 bp):
AAGAAGAAGAAGATTAAA
Found at i:592265 original size:15 final size:15
Alignment explanation
Indices: 592245--592280 Score: 63
Period size: 15 Copynumber: 2.4 Consensus size: 15
592235 TCCTATGGTA
592245 GAAGAAGAGTCAGAT
1 GAAGAAGAGTCAGAT
*
592260 GAAGAAGAGTCATAT
1 GAAGAAGAGTCAGAT
592275 GAAGAA
1 GAAGAA
592281 TAAGTTCAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.50, C:0.06, G:0.31, T:0.14
Consensus pattern (15 bp):
GAAGAAGAGTCAGAT
Found at i:593680 original size:24 final size:24
Alignment explanation
Indices: 593652--593697 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
593642 GGCTTTGTCT
593652 ACTACAGAGGCAGAGTATATGGAA
1 ACTACAGAGGCAGAGTATATGGAA
*
593676 ACTACAGATGCAGAGTATATGG
1 ACTACAGAGGCAGAGTATATGG
593698 TAGTTATAGA
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:0.39, C:0.13, G:0.28, T:0.20
Consensus pattern (24 bp):
ACTACAGAGGCAGAGTATATGGAA
Found at i:596248 original size:20 final size:22
Alignment explanation
Indices: 596212--596259 Score: 64
Period size: 20 Copynumber: 2.3 Consensus size: 22
596202 ATTAAATTTA
* *
596212 ATATTTTGTGACTTTATACAAT
1 ATATTTTGTGACTTTATAAAAC
596234 ATATTTTGT-AC-TTATAAAAC
1 ATATTTTGTGACTTTATAAAAC
596254 ATATTT
1 ATATTT
596260 AAACAATTTC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 13 0.54
21 2 0.08
22 9 0.38
ACGTcount: A:0.35, C:0.08, G:0.06, T:0.50
Consensus pattern (22 bp):
ATATTTTGTGACTTTATAAAAC
Found at i:596509 original size:14 final size:12
Alignment explanation
Indices: 596484--596542 Score: 57
Period size: 12 Copynumber: 4.8 Consensus size: 12
596474 AAAACTTATC
596484 TTAAAAATATAT
1 TTAAAAATATAT
596496 TATAAAATATATAT
1 T-TAAAA-ATATAT
*
596510 TTAAAACT-TAT
1 TTAAAAATATAT
*
596521 CTTAGAAATATAT
1 -TTAAAAATATAT
*
596534 TAAAAAATA
1 TTAAAAATA
596543 CATGTTATGT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
11 3 0.08
12 15 0.39
13 13 0.34
14 7 0.18
ACGTcount: A:0.56, C:0.03, G:0.02, T:0.39
Consensus pattern (12 bp):
TTAAAAATATAT
Found at i:611718 original size:22 final size:21
Alignment explanation
Indices: 611690--611744 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 21
611680 AATATACGGT
*
611690 ATGAACAGTGATGAACAATACC
1 ATGAACAGT-ATAAACAATACC
*
611712 ATGAACAGCTATAAACAGTACC
1 ATGAACAG-TATAAACAATACC
*
611734 GTGAACAGTAT
1 ATGAACAGTAT
611745 CGAATGCTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 3 0.10
22 25 0.86
23 1 0.03
ACGTcount: A:0.44, C:0.18, G:0.18, T:0.20
Consensus pattern (21 bp):
ATGAACAGTATAAACAATACC
Found at i:612228 original size:3 final size:3
Alignment explanation
Indices: 612222--612262 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
612212 ATGATAACAT
612222 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
612263 GCAATTACCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:613815 original size:17 final size:17
Alignment explanation
Indices: 613793--613826 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
613783 TCCATAAATC
*
613793 CAAAATCCAACAATCCA
1 CAAAATCAAACAATCCA
*
613810 CAAAATCAAACATTCCA
1 CAAAATCAAACAATCCA
613827 AAATATTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.32, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAATCAAACAATCCA
Found at i:613916 original size:51 final size:51
Alignment explanation
Indices: 613861--613967 Score: 196
Period size: 51 Copynumber: 2.1 Consensus size: 51
613851 AAGTACCGGC
*
613861 TGAAATGTATTCCGCTTCAGTGGTAGATAATGCCACACAATTTTATTTCTT
1 TGAAATGTATTCCGCTTCAGTGATAGATAATGCCACACAATTTTATTTCTT
*
613912 TGAAATGTATTCCGCTTCAGTGATAGATAATGCCACACAGTTTTATTTCTT
1 TGAAATGTATTCCGCTTCAGTGATAGATAATGCCACACAATTTTATTTCTT
613963 TGAAA
1 TGAAA
613968 ACCAAGAAAT
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 54 1.00
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (51 bp):
TGAAATGTATTCCGCTTCAGTGATAGATAATGCCACACAATTTTATTTCTT
Found at i:617188 original size:22 final size:21
Alignment explanation
Indices: 617146--617185 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
617136 GAGTTTGTTT
*
617146 TCATTTTTCAATTTTGAAACA
1 TCATTTTTCAATTTTAAAACA
617167 TCATTTTT-ATATTTTAAAA
1 TCATTTTTCA-ATTTTAAAA
617186 ACAATTTCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.35, C:0.10, G:0.03, T:0.53
Consensus pattern (21 bp):
TCATTTTTCAATTTTAAAACA
Found at i:619504 original size:22 final size:22
Alignment explanation
Indices: 619478--619522 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
619468 GGCATATGAA
* *
619478 ATTTGTCCCGAAGGACCTCTGT
1 ATTTGTCCCAAAGGACCTATGT
619500 ATTTGTCCCAAAGGACCTATGT
1 ATTTGTCCCAAAGGACCTATGT
619522 A
1 A
619523 CTATATTTGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.31
Consensus pattern (22 bp):
ATTTGTCCCAAAGGACCTATGT
Found at i:621045 original size:16 final size:16
Alignment explanation
Indices: 621026--621075 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
621016 ATATATATAT
621026 ATATATTCAAAACCGA
1 ATATATTCAAAACCGA
* * *
621042 ATAT-TTGAAAATC-T
1 ATATATTCAAAACCGA
621056 ATATATTCAAAACCGA
1 ATATATTCAAAACCGA
621072 ATAT
1 ATAT
621076 TTAAATATCT
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.48, C:0.14, G:0.06, T:0.32
Consensus pattern (16 bp):
ATATATTCAAAACCGA
Found at i:621076 original size:30 final size:30
Alignment explanation
Indices: 621010--621088 Score: 115
Period size: 30 Copynumber: 2.6 Consensus size: 30
621000 CCGAGTATTT
* * *
621010 GAATATATATATATATATATATTCAAAACC
1 GAATATTTAAATATCTATATATTCAAAACC
621040 GAATATTTGAAA-ATCTATATATTCAAAACC
1 GAATATTT-AAATATCTATATATTCAAAACC
621070 GAATATTTAAATATCTATA
1 GAATATTTAAATATCTATA
621089 CGACTGTCTA
Statistics
Matches: 44, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
29 3 0.07
30 39 0.89
31 2 0.05
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (30 bp):
GAATATTTAAATATCTATATATTCAAAACC
Found at i:634569 original size:3 final size:3
Alignment explanation
Indices: 634561--634590 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
634551 TTACTATGTA
634561 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
634591 CTTTCTTCAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:634619 original size:25 final size:26
Alignment explanation
Indices: 634581--634652 Score: 69
Period size: 25 Copynumber: 2.9 Consensus size: 26
634571 ATTATTATTA
*
634581 TTATTATTATCTTT-CTTCATTTTAT
1 TTATTATTACCTTTACTTCATTTTAT
* **
634606 TTATTTTTACCTTTACTTTTTTTTAT
1 TTATTATTACCTTTACTTCATTTTAT
* *
634632 TTTTTATTA-TTTTA-TTCATTT
1 TTATTATTACCTTTACTTCATTT
634653 GTTTTCTTTA
Statistics
Matches: 37, Mismatches: 9, Indels: 3
0.76 0.18 0.06
Matches are distributed among these distances:
24 5 0.14
25 16 0.43
26 16 0.43
ACGTcount: A:0.18, C:0.10, G:0.00, T:0.72
Consensus pattern (26 bp):
TTATTATTACCTTTACTTCATTTTAT
Found at i:634644 original size:41 final size:40
Alignment explanation
Indices: 634575--634694 Score: 125
Period size: 41 Copynumber: 2.9 Consensus size: 40
634565 ATTATTATTA
* *
634575 TTATTATTATTATTATCTTTCTTCATTTTATTTATTTTTACCT
1 TTATT-TTA-TATTAT-TTTCTTTATTTTATTCATTTTTACCT
* * **
634618 TTACTTTT-TTTTATTTTTTATTATTTTATTCATTTGTTTTCT
1 TTA-TTTTATATTATTTTCT-TTATTTTATTCATTT-TTACCT
634660 TTATTTTATATTATTTTCTTTATTTTATTCATTTT
1 TTATTTTATATTATTTTCTTTATTTTATTCATTTT
634695 GCATTTTCTT
Statistics
Matches: 65, Mismatches: 8, Indels: 11
0.77 0.10 0.13
Matches are distributed among these distances:
40 5 0.08
41 37 0.57
42 16 0.25
43 5 0.08
44 2 0.03
ACGTcount: A:0.18, C:0.08, G:0.01, T:0.72
Consensus pattern (40 bp):
TTATTTTATATTATTTTCTTTATTTTATTCATTTTTACCT
Found at i:634652 original size:19 final size:18
Alignment explanation
Indices: 634630--634694 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 18
634620 ACTTTTTTTT
634630 ATTTTTTATTATTTTATTC
1 ATTTTTT-TTATTTTATTC
*
634649 ATTTGTTTTCTTTATTTTATATT
1 A--T-TTTT-TTTATTTTAT-TC
*
634672 ATTTTCTTTATTTTATTC
1 ATTTTTTTTATTTTATTC
634690 ATTTT
1 ATTTT
634695 GCATTTTCTT
Statistics
Matches: 38, Mismatches: 3, Indels: 11
0.73 0.06 0.21
Matches are distributed among these distances:
18 6 0.16
19 11 0.29
20 3 0.08
21 2 0.05
22 13 0.34
23 3 0.08
ACGTcount: A:0.18, C:0.06, G:0.02, T:0.74
Consensus pattern (18 bp):
ATTTTTTTTATTTTATTC
Found at i:634667 original size:37 final size:41
Alignment explanation
Indices: 634621--634717 Score: 121
Period size: 44 Copynumber: 2.4 Consensus size: 41
634611 TTTACCTTTA
634621 CTTT-TTTTTATTTTTT-ATTATTTTATTCA-TTTG-TTTT
1 CTTTATTTTTATTTTTTCATTATTTTATTCATTTTGATTTT
*
634658 CTTTATTTTATATTATTTTCTTTATTTTATTCATTTTGCATTTT
1 CTTTATTTT-TATT-TTTTCATTATTTTATTCATTTTG-ATTTT
634702 CTTTATTATTTATTTT
1 CTTTATT-TTTATTTT
634718 CATTTTCTTT
Statistics
Matches: 51, Mismatches: 1, Indels: 10
0.82 0.02 0.16
Matches are distributed among these distances:
37 4 0.08
38 4 0.08
39 4 0.08
40 4 0.08
41 12 0.24
42 4 0.08
43 2 0.04
44 15 0.29
45 2 0.04
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.74
Consensus pattern (41 bp):
CTTTATTTTTATTTTTTCATTATTTTATTCATTTTGATTTT
Found at i:634693 original size:9 final size:8
Alignment explanation
Indices: 634561--634694 Score: 55
Period size: 9 Copynumber: 15.8 Consensus size: 8
634551 TTACTATGTA
634561 TATTATTAT
1 TATT-TTAT
634570 TATTATTAT
1 TATT-TTAT
634579 TATTATTAT
1 TATT-TTAT
*
634588 TATCTTTCT
1 TAT-TTTAT
634597 TCATTTTAT
1 T-ATTTTAT
634606 T-TATTT-T
1 TAT-TTTAT
*
634613 TACCTTTACTT
1 TA-TTTTA--T
*
634624 TTTTTTAT
1 TATTTTAT
634632 T-TTTTAT
1 TATTTTAT
634639 TATTTTAT
1 TATTTTAT
634647 TCATTTGT-T
1 T-ATTT-TAT
634656 T-TCTTTAT
1 TAT-TTTAT
*
634664 T-TTATAT
1 TATTTTAT
*
634671 TATTTTCTT
1 TATTTT-AT
634680 TATTTTAT
1 TATTTTAT
634688 TCATTTT
1 T-ATTTT
634695 GCATTTTCTT
Statistics
Matches: 100, Mismatches: 9, Indels: 32
0.71 0.06 0.23
Matches are distributed among these distances:
7 17 0.17
8 25 0.25
9 48 0.48
10 8 0.08
11 2 0.02
ACGTcount: A:0.20, C:0.07, G:0.01, T:0.72
Consensus pattern (8 bp):
TATTTTAT
Found at i:634715 original size:41 final size:40
Alignment explanation
Indices: 634581--634718 Score: 124
Period size: 41 Copynumber: 3.4 Consensus size: 40
634571 ATTATTATTA
* * * *
634581 TTATTA-TTATCTTTCTTCATTTTATTTATTTTTACCTTTACT
1 TTATTATTTAT-TTTCTTTATTTTATTCA-TTTT-GCTTTTCT
*
634623 TT-TT-TTTATTTTTTATTATTTTATTCA-TTTG-TTTTCT
1 TTATTATTTATTTTCT-TTATTTTATTCATTTTGCTTTTCT
634660 TTATTTTATATTATTTTCTTTATTTTATTCATTTTGCATTTTCT
1 TTA--TTAT-TTATTTTCTTTATTTTATTCATTTTGC-TTTTCT
634704 TTATTATTTATTTTC
1 TTATTATTTATTTTC
634719 ATTTTCTTTT
Statistics
Matches: 80, Mismatches: 6, Indels: 21
0.75 0.06 0.20
Matches are distributed among these distances:
37 7 0.09
39 3 0.04
40 6 0.08
41 37 0.46
42 18 0.22
44 9 0.11
ACGTcount: A:0.17, C:0.09, G:0.01, T:0.72
Consensus pattern (40 bp):
TTATTATTTATTTTCTTTATTTTATTCATTTTGCTTTTCT
Done.