Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
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: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 36 of 204
Found at i:12788395 original size:24 final size:24
Alignment explanation
Indices: 12788363--12788416 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
12788353 GCGGCGGTTG
12788363 TTCTTCCTCCGGTGGTGATTGTGA
1 TTCTTCCTCCGGTGGTGATTGTGA
* *
12788387 TTCTTCCTCCGGTGGTGGTTGTGG
1 TTCTTCCTCCGGTGGTGATTGTGA
12788411 TTCTTC
1 TTCTTC
12788417 TGGTTTGGCA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.04, C:0.22, G:0.30, T:0.44
Consensus pattern (24 bp):
TTCTTCCTCCGGTGGTGATTGTGA
Found at i:12788716 original size:18 final size:18
Alignment explanation
Indices: 12788672--12788717 Score: 56
Period size: 18 Copynumber: 2.6 Consensus size: 18
12788662 TATTCGGAAA
* *
12788672 AGGATACATGTAAGGGTT
1 AGGATACATATAAGGGCT
*
12788690 AGGGTACATATAAGGGCT
1 AGGATACATATAAGGGCT
*
12788708 AGGAAACATA
1 AGGATACATA
12788718 CCTGGCATCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.39, C:0.09, G:0.30, T:0.22
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:12789372 original size:7 final size:7
Alignment explanation
Indices: 12789362--12789386 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12789352 TTATATACAT
12789362 AATACTA
1 AATACTA
12789369 AATACTA
1 AATACTA
12789376 AATACTA
1 AATACTA
12789383 AATA
1 AATA
12789387 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:12790512 original size:30 final size:31
Alignment explanation
Indices: 12790468--12790531 Score: 112
Period size: 30 Copynumber: 2.1 Consensus size: 31
12790458 GCCATTGATG
12790468 AAAATATAAAAAAATTTAAAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
*
12790499 AAAATAT-AAAAAATTTATAATTATTTTAAA
1 AAAATATAAAAAAATTTAAAATTATTTTAAA
12790529 AAA
1 AAA
12790532 TGGATTTGAG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 25 0.78
31 7 0.22
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (31 bp):
AAAATATAAAAAAATTTAAAATTATTTTAAA
Found at i:12797685 original size:28 final size:28
Alignment explanation
Indices: 12797643--12797700 Score: 107
Period size: 28 Copynumber: 2.1 Consensus size: 28
12797633 CTAGACTATC
12797643 TGTTGCTTGGATAGTCATCTCAGGAGGA
1 TGTTGCTTGGATAGTCATCTCAGGAGGA
*
12797671 TGTTGCTTGGTTAGTCATCTCAGGAGGA
1 TGTTGCTTGGATAGTCATCTCAGGAGGA
12797699 TG
1 TG
12797701 AGTTCACAGG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.19, C:0.14, G:0.33, T:0.34
Consensus pattern (28 bp):
TGTTGCTTGGATAGTCATCTCAGGAGGA
Found at i:12799456 original size:125 final size:125
Alignment explanation
Indices: 12799220--12799465 Score: 368
Period size: 125 Copynumber: 2.0 Consensus size: 125
12799210 TTTTAAGTCC
* *
12799220 TGGAAGAAATAATTTTGAGTTGACGTTTCTAATCAAATAGTATAAAATCGCTTCTAGGAGGATGC
1 TGGAAGAAATAATTTTGAGTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGGAAGATGC
*
12799285 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTAGGCGCGCTTTTGCTACAGTAGGTCA
66 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTAGGCGCGCTTTTGCTAAAGTAGGTCA
*** * * * *
12799345 TGGAAGAAATAATTTTTTTTTTACGTTTCTGAGCAAATAGTATAAAATTGCTTCTAGTAAGATGC
1 TGGAAGAAATAATTTTGAGTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGGAAGATGC
* *
12799410 TATTTGAGAAGAATTTGTGAAATCGCGCCTTCGT-GGACGCGTTTTTGCTAAAGTAG
66 TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTAGG-CGCGCTTTTGCTAAAGTAG
12799466 CATGTTTGGG
Statistics
Matches: 108, Mismatches: 12, Indels: 2
0.89 0.10 0.02
Matches are distributed among these distances:
124 2 0.02
125 106 0.98
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.34
Consensus pattern (125 bp):
TGGAAGAAATAATTTTGAGTTGACGTTTCTAAGCAAATAGTATAAAATCGCTTCTAGGAAGATGC
TATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTAGGCGCGCTTTTGCTAAAGTAGGTCA
Found at i:12800364 original size:9 final size:9
Alignment explanation
Indices: 12800350--12800380 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
12800340 GTTAAACGAA
12800350 TCGAGTTAT
1 TCGAGTTAT
*
12800359 TCGAGTTAA
1 TCGAGTTAT
12800368 TCGAGTTAT
1 TCGAGTTAT
12800377 TCGA
1 TCGA
12800381 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:12800451 original size:9 final size:9
Alignment explanation
Indices: 12800434--12800470 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
12800424 TAAGTTTTCG
12800434 AATTCGAAT
1 AATTCGAAT
*
12800443 AACTCGAAT
1 AATTCGAAT
12800452 AATTCGAAT
1 AATTCGAAT
12800461 AATTCGAAT
1 AATTCGAAT
12800470 A
1 A
12800471 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:12800547 original size:21 final size:21
Alignment explanation
Indices: 12800506--12800548 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
12800496 ACCCTAAACT
* *
12800506 CTCAAACCTTTTTACTTTTCC
1 CTCAAAACTTTTTACTCTTCC
12800527 CTCAAAAC-TTTTACTCCTTCC
1 CTCAAAACTTTTTACT-CTTCC
12800548 C
1 C
12800549 ACTTTCCCCC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.21, C:0.37, G:0.00, T:0.42
Consensus pattern (21 bp):
CTCAAAACTTTTTACTCTTCC
Found at i:12801651 original size:24 final size:25
Alignment explanation
Indices: 12801617--12801669 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 25
12801607 CTGAAAGGAG
12801617 TTCAGATGAAGAAGAAAATCCACGA
1 TTCAGATGAAGAAGAAAATCCACGA
12801642 TTCAGA-GAAGAAGAAAATCCACGA
1 TTCAGATGAAGAAGAAAATCCACGA
12801666 TTCA
1 TTCA
12801670 AAGCATACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 22 0.79
25 6 0.21
ACGTcount: A:0.47, C:0.17, G:0.19, T:0.17
Consensus pattern (25 bp):
TTCAGATGAAGAAGAAAATCCACGA
Found at i:12804014 original size:116 final size:115
Alignment explanation
Indices: 12803754--12803971 Score: 359
Period size: 115 Copynumber: 1.9 Consensus size: 115
12803744 ATTATTAACT
12803754 GATAAATTGTATTAATGGTTAGTAAAAATT-TCAAATTATATAAAATTATTAATTGTTAGTATCA
1 GATAAATTGTATTAATGGTTAGT-AAAATTATCAAATTATATAAAATTATTAATTGTTAGTATCA
* **
12803818 GTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTATTATCC
65 GTAAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTAGGATCC
12803869 GATAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTA-CTA
1 GATAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTATC-A
*
12803933 GTAAAAAACATTTTTCTAAATCTAACATTATGTGAATGT
65 GT-AAAAACATTTTTCCAAATCTAACATTATGTGAATGT
12803972 TAAGGGTTAG
Statistics
Matches: 98, Mismatches: 2, Indels: 5
0.93 0.02 0.05
Matches are distributed among these distances:
114 7 0.07
115 57 0.58
116 34 0.35
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (115 bp):
GATAAATTGTATTAATGGTTAGTAAAATTATCAAATTATATAAAATTATTAATTGTTAGTATCAG
TAAAAACATTTTTCCAAATCTAACATTATGTGAATGTAAAATTAGGATCC
Found at i:12804070 original size:23 final size:23
Alignment explanation
Indices: 12804008--12804502 Score: 496
Period size: 23 Copynumber: 22.2 Consensus size: 23
12803998 GTTAAGGTAT
*
12804008 TTAATTAGGTTAGGATTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
12804031 TTAA--GGGTTAGGATTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
12804052 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
12804075 TTAA--AGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
* *
12804096 TTAATTAGTTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
*
12804119 TTAATTAGGTTAGAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
12804142 TTAA--GGGTTAGGGTTTCTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
12804163 TTAA--GGGTTTAGGGTTTTTAAG
1 TTAATTAGG-TTAGGGTTTTTAAG
*
12804185 TTAA--GGGTTAAGGGTTTTTAAG
1 TTAATTAGGTT-AGGGTTTTTAAG
*
12804207 TTAA--GGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
12804228 TTAATTAGGTTAGAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
12804251 TTAATTAGGTTAGAGTTTTAAAT
1 TTAATTAGGTTAGGGTTTTTAAG
*
12804274 TTAATTAGGTTAAGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* *
12804297 TTAA--GGGTTTAGGG-TTTTAAA
1 TTAATTAGG-TTAGGGTTTTTAAG
*
12804318 TTAAATTAGGTTAGGGTTTTTAAT
1 TT-AATTAGGTTAGGGTTTTTAAG
12804342 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
* * *
12804365 TTAA--GGGTTTAAGGTTTTTTA-
1 TTAATTAGG-TTAGGGTTTTTAAG
12804386 TTAAATTAGGTTAGGGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
* *
12804410 TTAA--GGGTTAGGGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAG
12804431 TTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAAG
*
12804454 TTAA--GGGTTTAGGGTTTTTAA-
1 TTAATTAGG-TTAGGGTTTTTAAG
*
12804475 TTAAATTAGGTTAGAGTTTTTAAG
1 TT-AATTAGGTTAGGGTTTTTAAG
12804499 TTAA
1 TTAA
12804503 GGTATTAATG
Statistics
Matches: 406, Mismatches: 41, Indels: 50
0.82 0.08 0.10
Matches are distributed among these distances:
21 115 0.28
22 76 0.19
23 197 0.49
24 18 0.04
ACGTcount: A:0.28, C:0.00, G:0.25, T:0.47
Consensus pattern (23 bp):
TTAATTAGGTTAGGGTTTTTAAG
Found at i:12804482 original size:45 final size:43
Alignment explanation
Indices: 12803970--12804504 Score: 454
Period size: 44 Copynumber: 12.2 Consensus size: 43
12803960 TTATGTGAAT
* * *
12803970 GTTAAGGGTTAGGGTTTTTAAGT--TTAGGGTTAAGGTATTTAA
1 GTTAAGGGTTAGGGTTTTTAATTAATTA-GGTTAGGGTTTTTAA
* * *
12804012 -TT-A-GGTTAGGATTTTTAAGTTAA--GGGTTAGGATTTTTAA
1 GTTAAGGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
* *
12804051 TTTAATTAGGTTAGGGTTTTTAAGTTAA--AGGTTAGGGTTTTTAA
1 GTTAA--GGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
* * * *
12804095 TTTAATTAGTTTAGGGTTTTTAATTTAATTAGGTTAGAGTTTTTAA
1 GTTAA--GGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
* *
12804141 GTTAAGGGTTAGGGTTTCTAAGTTAA--GGGTTTAGGGTTTTTAA
1 GTTAAGGGTTAGGGTTTTTAA-TTAATTAGG-TTAGGGTTTTTAA
*
12804184 GTTAAGGGTTAAGGGTTTTTAAGTTAA--GGGTTAGGGTTTTTAA
1 GTTAAGGGTT-AGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
* * * *
12804227 GTTAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGAGTTTTAAA
1 GTTAA--GGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
* * * *
12804273 TTTAATTAGGTTAAGGTTTTTAAGTTAA--GGGTTTAGGG-TTTTAA
1 GTTAA--GGGTTAGGGTTTTTAA-TTAATTAGG-TTAGGGTTTTTAA
* *
12804317 ATTAAATTAGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA
1 GTT-AA--GGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
* *
12804364 GTTAAGGGTTTAAGGTTTTTTATTAAATTAGGTTAGGGTTTTTAA
1 GTTAAGGG-TTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAA
12804409 GTTAAGGGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAA
1 GTTAAGGGTTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAA
*
12804453 GTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAA
1 GTTAAGGG-TTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAA
12804498 GTTAAGG
1 GTTAAGG
12804505 TATTAATGGT
Statistics
Matches: 423, Mismatches: 44, Indels: 49
0.82 0.09 0.09
Matches are distributed among these distances:
39 26 0.06
40 4 0.01
41 3 0.01
42 2 0.00
43 40 0.09
44 162 0.38
45 112 0.26
46 64 0.15
47 10 0.02
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (43 bp):
GTTAAGGGTTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAA
Found at i:12804591 original size:25 final size:25
Alignment explanation
Indices: 12804562--12804679 Score: 122
Period size: 25 Copynumber: 4.9 Consensus size: 25
12804552 ATTCAAAAAT
12804562 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
12804587 TTCTATTTTATTACATCAAAT-AA-
1 TTCTATTTTATTACATCAAATAAAC
** * * *
12804610 TATC-A--AAATAAC-TCAAAAAAAT
1 T-TCTATTTTATTACATCAAATAAAC
*
12804632 TTCTATTTTATTACATTAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
*
12804657 TTCTATTTTATTACGTCAAATAA
1 TTCTATTTTATTACATCAAATAA
12804680 TATCAAAATA
Statistics
Matches: 74, Mismatches: 12, Indels: 14
0.74 0.12 0.14
Matches are distributed among these distances:
20 5 0.07
21 8 0.11
22 2 0.03
23 2 0.03
24 8 0.11
25 49 0.66
ACGTcount: A:0.43, C:0.14, G:0.01, T:0.42
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:12804643 original size:70 final size:70
Alignment explanation
Indices: 12804556--12804689 Score: 250
Period size: 70 Copynumber: 1.9 Consensus size: 70
12804546 CAAAATATTC
12804556 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
12804621 CTCAA
66 CTCAA
* *
12804626 AAAAATTTCTATTTTATTACATTAAATAAACTTCTATTTTATTACGTCAAATAATATCAAAATA
1 AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATA
12804690 TTCAAAATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
70 62 1.00
ACGTcount: A:0.46, C:0.13, G:0.01, T:0.40
Consensus pattern (70 bp):
AAAAATTTCTATTTTATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAA
CTCAA
Found at i:12806961 original size:28 final size:27
Alignment explanation
Indices: 12806930--12807006 Score: 85
Period size: 27 Copynumber: 3.1 Consensus size: 27
12806920 ATATTTTTAA
12806930 AATTATTTAAAAAAAGGGAGTTAAGAG
1 AATTATTTAAAAAAAGGGAGTTAAGAG
* * *
12806957 AA--ATTT---AAGA-GGATTTGAGAG
1 AATTATTTAAAAAAAGGGAGTTAAGAG
12806978 AATTATTTAAAAAAAGGGAGTTAAGAG
1 AATTATTTAAAAAAAGGGAGTTAAGAG
12807005 AA
1 AA
12807007 ATTTAAGAAG
Statistics
Matches: 38, Mismatches: 6, Indels: 12
0.68 0.11 0.21
Matches are distributed among these distances:
21 11 0.29
22 3 0.08
23 4 0.11
25 4 0.11
26 3 0.08
27 13 0.34
ACGTcount: A:0.51, C:0.00, G:0.23, T:0.26
Consensus pattern (27 bp):
AATTATTTAAAAAAAGGGAGTTAAGAG
Found at i:12806985 original size:48 final size:49
Alignment explanation
Indices: 12806930--12807028 Score: 173
Period size: 48 Copynumber: 2.0 Consensus size: 49
12806920 ATATTTTTAA
* *
12806930 AATTATTTAAAAAAAGGGAGTTAAGAGAAATTTAAG-AGGATTTGAGAG
1 AATTATTTAAAAAAAGGGAGTTAAGAGAAATTTAAGAAGAACTTGAGAG
12806978 AATTATTTAAAAAAAGGGAGTTAAGAGAAATTTAAGAAGAACTTGAGAG
1 AATTATTTAAAAAAAGGGAGTTAAGAGAAATTTAAGAAGAACTTGAGAG
12807027 AA
1 AA
12807029 AATTGAAATA
Statistics
Matches: 48, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
48 36 0.75
49 12 0.25
ACGTcount: A:0.51, C:0.01, G:0.23, T:0.25
Consensus pattern (49 bp):
AATTATTTAAAAAAAGGGAGTTAAGAGAAATTTAAGAAGAACTTGAGAG
Found at i:12807081 original size:11 final size:11
Alignment explanation
Indices: 12807061--12807100 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
12807051 GAGAGAATTT
12807061 TTGA-AGGAAA
1 TTGAGAGGAAA
12807071 TTGAGAGGAAA
1 TTGAGAGGAAA
*
12807082 TTAAGAGGAAA
1 TTGAGAGGAAA
12807093 TTTGAGAG
1 -TTGAGAG
12807101 AGGATTAGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 4 0.15
11 16 0.62
12 6 0.23
ACGTcount: A:0.45, C:0.00, G:0.33, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:12809460 original size:8 final size:8
Alignment explanation
Indices: 12809447--12809471 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
12809437 CAGATTTGTC
12809447 ACCAATGG
1 ACCAATGG
12809455 ACCAATGG
1 ACCAATGG
12809463 ACCAATGG
1 ACCAATGG
12809471 A
1 A
12809472 AGTATTTCCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.24, G:0.24, T:0.12
Consensus pattern (8 bp):
ACCAATGG
Found at i:12815194 original size:10 final size:10
Alignment explanation
Indices: 12815179--12815212 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
12815169 TGATCTGTGT
12815179 GGGACCCTTG
1 GGGACCCTTG
12815189 GGGACCCTTG
1 GGGACCCTTG
*
12815199 GGGACCATTG
1 GGGACCCTTG
12815209 GGGA
1 GGGA
12815213 TAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.15, C:0.24, G:0.44, T:0.18
Consensus pattern (10 bp):
GGGACCCTTG
Found at i:12820251 original size:26 final size:26
Alignment explanation
Indices: 12820222--12820405 Score: 80
Period size: 25 Copynumber: 7.3 Consensus size: 26
12820212 ATCCTCTCTC
12820222 GAGCCATATAA-CAGGAAGCTCACAAA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* *
12820248 GAGCCATTAATCGGGAAGTTCACAAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* * *
12820274 TAGCC-TT--TCAGGAAGCTTATC-CA
1 GAGCCATTAATCAGGAAGCTCA-CAAA
* * *
12820297 G-GCTATATAA-CAGGAAGTTCACACA
1 GAGCCAT-TAATCAGGAAGCTCACAAA
* ** * *
12820322 GAACCA-TAATCATAAAGTTCACATA
1 GAGCCATTAATCAGGAAGCTCACAAA
* ** *
12820347 GAACTTTTAATCAGGAAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACAAA
* ** * *
12820373 GGGCTTTTAAAC-GGAAGCTCACGAA
1 GAGCCATTAATCAGGAAGCTCACAAA
12820398 GAGCCATT
1 GAGCCATT
12820406 TATTAGGAGC
Statistics
Matches: 119, Mismatches: 29, Indels: 21
0.70 0.17 0.12
Matches are distributed among these distances:
22 2 0.02
23 11 0.09
24 6 0.05
25 51 0.43
26 49 0.41
ACGTcount: A:0.38, C:0.21, G:0.20, T:0.21
Consensus pattern (26 bp):
GAGCCATTAATCAGGAAGCTCACAAA
Found at i:12820394 original size:25 final size:26
Alignment explanation
Indices: 12820350--12820398 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
12820340 TCACATAGAA
*
12820350 CTTTTAATCAGGAAGCTCACGAAGGG
1 CTTTTAAACAGGAAGCTCACGAAGGG
12820376 CTTTTAAAC-GGAAGCTCACGAAG
1 CTTTTAAACAGGAAGCTCACGAAG
12820399 AGCCATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 14 0.64
26 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.24, T:0.22
Consensus pattern (26 bp):
CTTTTAAACAGGAAGCTCACGAAGGG
Found at i:12820549 original size:65 final size:65
Alignment explanation
Indices: 12820462--12820644 Score: 185
Period size: 65 Copynumber: 2.8 Consensus size: 65
12820452 ATATCAAGAC
* * * *
12820462 GCTCATAAAAAGCTGCGTTTGTG-CCTGCAACATATGCAGGATCACAGCCGATCATAAAACAGGA
1 GCTCACAAAGAGCTGCGTTTGTGTCC-ACAACATATGCAGGATCACAACCGATCATAAAACAGGA
12820526 A
65 A
* * * * * *
12820527 TCTCACAAAGAGCTGTGTTTGTGTCCACAATATATGCATGATCACAACCGATCATATAACAGGAC
1 GCTCACAAAGAGCTGCGTTTGTGTCCACAACATATGCAGGATCACAACCGATCATAAAACAGGAA
* * * * *
12820592 GCTCACAAAGAGCTACAG--T-AGTCCACAACACATGCAGGATCACTACTGATCAT
1 GCTCACAAAGAGCTGC-GTTTGTGTCCACAACATATGCAGGATCACAACCGATCAT
12820645 GATGCTCGCA
Statistics
Matches: 97, Mismatches: 19, Indels: 6
0.80 0.16 0.05
Matches are distributed among these distances:
63 28 0.29
64 1 0.01
65 65 0.67
66 3 0.03
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.22
Consensus pattern (65 bp):
GCTCACAAAGAGCTGCGTTTGTGTCCACAACATATGCAGGATCACAACCGATCATAAAACAGGAA
Found at i:12826170 original size:2 final size:2
Alignment explanation
Indices: 12826163--12826190 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12826153 AATGGAGTTA
12826163 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
12826191 TGTGAAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12826269 original size:16 final size:16
Alignment explanation
Indices: 12826248--12826312 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
12826238 GAAGAAAATA
12826248 AAAATAAGTA-ATATAT
1 AAAATAA-TATATATAT
12826264 AAAATAATATATATAT
1 AAAATAATATATATAT
*
12826280 -ATAT-ATATATATAT
1 AAAATAATATATATAT
*
12826294 ATATATATATATATATAT
1 A-AAATA-ATATATATAT
12826312 A
1 A
12826313 CATGTTAATC
Statistics
Matches: 43, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
14 10 0.23
15 5 0.12
16 17 0.40
18 11 0.26
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.42
Consensus pattern (16 bp):
AAAATAATATATATAT
Found at i:12826275 original size:2 final size:2
Alignment explanation
Indices: 12826258--12826312 Score: 87
Period size: 2 Copynumber: 28.5 Consensus size: 2
12826248 AAAATAAGTA
*
12826258 AT AT AT A- AA AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12826298 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
12826313 CATGTTAATC
Statistics
Matches: 50, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
1 2 0.04
2 48 0.96
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:12826628 original size:24 final size:25
Alignment explanation
Indices: 12826586--12826632 Score: 78
Period size: 24 Copynumber: 1.9 Consensus size: 25
12826576 GAAAACTTAA
12826586 AATAAGTATATGATAAATTTAAAAT
1 AATAAGTATATGATAAATTTAAAAT
*
12826611 AATAA-TATGTGATAAATTTAAA
1 AATAAGTATATGATAAATTTAAA
12826633 CAACATTCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.55, C:0.00, G:0.09, T:0.36
Consensus pattern (25 bp):
AATAAGTATATGATAAATTTAAAAT
Found at i:12831433 original size:5 final size:5
Alignment explanation
Indices: 12831423--12831449 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
12831413 AATAAATTAT
12831423 ATAAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA AT
12831450 TTAAAACAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (5 bp):
ATAAA
Found at i:12841667 original size:24 final size:23
Alignment explanation
Indices: 12841631--12841676 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 23
12841621 CATTTAAATA
12841631 TATTTTAAATTTTAATG-TATAT
1 TATTTTAAATTTTAATGATATAT
12841653 TATTTCTAATATTTTAATGATATA
1 TATTT-TAA-ATTTTAATGATATA
12841677 AATGCTATGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 3 0.14
24 9 0.43
25 4 0.19
ACGTcount: A:0.37, C:0.02, G:0.04, T:0.57
Consensus pattern (23 bp):
TATTTTAAATTTTAATGATATAT
Found at i:12847540 original size:220 final size:213
Alignment explanation
Indices: 12847165--12847597 Score: 697
Period size: 220 Copynumber: 2.0 Consensus size: 213
12847155 CTTACAATGG
* * *
12847165 ATGAGTACAAATGAGGGGAGGCTCTCTATTTATAGTTGAGTTCCCCCAAAACTGACTACATTTAC
1 ATGAGTACAAATGAGCGGAGGCTCTCTATTTATAGTTGAGCTCCCCAAAAACTGACTACATTTAC
12847230 ATCGACGGACGAGATTAACCATATCCCTTGATTTTAGGGAATTACAAGATATGCCATATCAAATT
66 ATCGACGGACGAGATTAACCATATCCCTTGATTTTAGGGAATTACAAGATATGCCATATCAAATT
12847295 TAATCTAATCTTTACAAGATATGATTCCCTCAATCTTCTAAGAGTAGTTACCAAATTATCCTAAG
131 TAATCTAATCTTTACAAGATATGATTCCCTCAATCTTCTAAGAGTAGTTACCAAATTATCCTAAG
*
12847360 TTGCTATATCTTCATTAT
196 TTGCCATATCTTCATTAT
12847378 ATGAGTACAAATGAGCGGAGGCTCTCTATTTATAGTTGAGCTCCCCAAAACCGACGGTCAAGA-T
1 ATGAGTACAAATGAGCGGAGGCTCTCTATTTATAGTTGAGCTCCCCAAAA---AC--T---GACT
* * * *
12847442 ACATTTGCATCGACGGATGAGATTAACCATATTCCTTGATTTTAGGGATTTACAAGATATGCCAT
58 ACATTTACATCGACGGACGAGATTAACCATATCCCTTGATTTTAGGGAATTACAAGATATGCCAT
* *
12847507 ATCAAATTTAATCTAATCTTTACAAGATATGATTCCCTCAATCTTCTAAGATTAGTTACCAAGTT
123 ATCAAATTTAATCTAATCTTTACAAGATATGATTCCCTCAATCTTCTAAGAGTAGTTACCAAATT
12847572 ATCCTAAGTTGCCATATCTTCATTAT
188 ATCCTAAGTTGCCATATCTTCATTAT
12847598 CGGGCCAACC
Statistics
Matches: 202, Mismatches: 10, Indels: 9
0.91 0.05 0.04
Matches are distributed among these distances:
213 47 0.23
216 2 0.01
218 1 0.00
220 150 0.74
221 2 0.01
ACGTcount: A:0.32, C:0.19, G:0.15, T:0.33
Consensus pattern (213 bp):
ATGAGTACAAATGAGCGGAGGCTCTCTATTTATAGTTGAGCTCCCCAAAAACTGACTACATTTAC
ATCGACGGACGAGATTAACCATATCCCTTGATTTTAGGGAATTACAAGATATGCCATATCAAATT
TAATCTAATCTTTACAAGATATGATTCCCTCAATCTTCTAAGAGTAGTTACCAAATTATCCTAAG
TTGCCATATCTTCATTAT
Found at i:12850206 original size:19 final size:19
Alignment explanation
Indices: 12850184--12850220 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
12850174 CTAGAGTATC
*
12850184 TGAAAAATTTCAAAATATT
1 TGAAAAATATCAAAATATT
*
12850203 TGAAATATATCAAAATAT
1 TGAAAAATATCAAAATAT
12850221 CATCTATATA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.35
Consensus pattern (19 bp):
TGAAAAATATCAAAATATT
Found at i:12855001 original size:16 final size:16
Alignment explanation
Indices: 12854972--12855041 Score: 113
Period size: 16 Copynumber: 4.4 Consensus size: 16
12854962 TTTGGTTCGC
* *
12854972 TGTATTGGATTAGAGG
1 TGTAATGGAATAGAGG
*
12854988 CGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12855004 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12855020 TGTAATGGAATAGAGG
1 TGTAATGGAATAGAGG
12855036 TGTAAT
1 TGTAAT
12855042 AGCAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.34, C:0.01, G:0.36, T:0.29
Consensus pattern (16 bp):
TGTAATGGAATAGAGG
Found at i:12855125 original size:39 final size:43
Alignment explanation
Indices: 12855020--12855129 Score: 129
Period size: 45 Copynumber: 2.6 Consensus size: 43
12855010 GGAATAGAGG
12855020 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTT--A
* * ***
12855065 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGG-T-
1 TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
12855105 TG-AATGGAATAGAGGTGTAATAGCA
1 TGTAATGGAATAGAGGTGTAATAGCA
12855130 TAAGGGAAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
39 20 0.35
40 2 0.04
43 1 0.02
44 11 0.19
45 23 0.40
ACGTcount: A:0.34, C:0.05, G:0.29, T:0.32
Consensus pattern (43 bp):
TGTAATGGAATAGAGGTGTAATAGCAAATCAACTGTTTGGTTA
Found at i:12860255 original size:50 final size:50
Alignment explanation
Indices: 12860180--12860419 Score: 264
Period size: 50 Copynumber: 4.7 Consensus size: 50
12860170 TTTCTTGTAC
* * **
12860180 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
* * ** * * *
12860230 TGCCCATGTCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTTGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
* *
12860280 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
* * *
12860330 TGCCAACGCCATGTCCCAGACATGGTCTTACACGAGACCTCTCATAATCTCAATGA
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCAT-A--T--A-GG
**
12860386 TGCCAATGCCATGTCTGAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
12860420 GGATCTCTTT
Statistics
Matches: 158, Mismatches: 26, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
50 126 0.80
53 1 0.01
56 31 0.20
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGG
Found at i:12860308 original size:100 final size:102
Alignment explanation
Indices: 12860180--12860419 Score: 295
Period size: 100 Copynumber: 2.3 Consensus size: 102
12860170 TTTCTTGTAC
* * ** * * *
12860180 TGCCAATGCCATATCCCAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCCATGTCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
** * *
12860245 CCAGACATGGTCTTACGGGGGACCTCTC-ATCT-TGG
66 CCAGACATGGTCTTACACGAGACCTCTCAATCTATGA
* *
12860280 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
12860345 CCAGACATGGTCTTACACGAGACCTCTCATAATCTCAATGA
66 CCAGACATGGTCTTACACGAGACCTCTC--AATCT--ATGA
**
12860386 TGCCAATGCCATGTCTGAGACATGGTCTTACATG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATG
12860420 GGATCTCTTT
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
100 81 0.68
103 4 0.03
106 34 0.29
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (102 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATATAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACACGAGACCTCTCAATCTATGA
Found at i:12870242 original size:6 final size:6
Alignment explanation
Indices: 12870231--12870262 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
12870221 TCTTGGGTTT
*
12870231 TTAGGG TTAGGG TTAGGA TTAGGG TTAGGG TT
1 TTAGGG TTAGGG TTAGGG TTAGGG TTAGGG TT
12870263 TAAGGTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.19, C:0.00, G:0.44, T:0.38
Consensus pattern (6 bp):
TTAGGG
Found at i:12872039 original size:49 final size:49
Alignment explanation
Indices: 12871848--12872015 Score: 327
Period size: 49 Copynumber: 3.4 Consensus size: 49
12871838 AGAATATTAT
12871848 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
12871897 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
*
12871946 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAATTAAA
1 CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
12871995 CTATTTTGTATTTTATTACAT
1 CTATTTTGTATTTTATTACAT
12872016 TAATATAAAC
Statistics
Matches: 118, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
49 118 1.00
ACGTcount: A:0.43, C:0.10, G:0.02, T:0.44
Consensus pattern (49 bp):
CTATTTTGTATTTTATTACATCAAATAATATCAAAATATTCAAAATAAA
Found at i:12872158 original size:21 final size:21
Alignment explanation
Indices: 12872134--12872173 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12872124 TTGTCCAGCT
* *
12872134 TCCGGCGGGGGTTGTGGTTGC
1 TCCGGCGGGGATTCTGGTTGC
12872155 TCCGGCGGGGATTCTGGTT
1 TCCGGCGGGGATTCTGGTT
12872174 CATCTGGTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.03, C:0.20, G:0.47, T:0.30
Consensus pattern (21 bp):
TCCGGCGGGGATTCTGGTTGC
Found at i:12872462 original size:18 final size:18
Alignment explanation
Indices: 12872436--12872478 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
12872426 GACTAGAAAA
* * *
12872436 AGGAAACATATAAGGGTT
1 AGGATACATAAAAGGGCT
12872454 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
12872472 AGGATAC
1 AGGATAC
12872479 GCACCTGGCA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:12874334 original size:11 final size:12
Alignment explanation
Indices: 12874320--12874367 Score: 50
Period size: 11 Copynumber: 4.2 Consensus size: 12
12874310 TTAAATATGG
12874320 ATTTGAGA-GAA
1 ATTTGAGAGGAA
12874331 ATTTG-GAAGGAA
1 ATTTGAG-AGGAA
*
12874343 A-TTGAGA-GCA
1 ATTTGAGAGGAA
12874353 ATTTGAGAGGAA
1 ATTTGAGAGGAA
12874365 ATT
1 ATT
12874368 GGGAAAATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
10 4 0.13
11 16 0.53
12 10 0.33
ACGTcount: A:0.42, C:0.02, G:0.29, T:0.27
Consensus pattern (12 bp):
ATTTGAGAGGAA
Found at i:12874347 original size:22 final size:22
Alignment explanation
Indices: 12874322--12874368 Score: 69
Period size: 22 Copynumber: 2.1 Consensus size: 22
12874312 AAATATGGAT
12874322 TTGAGAGAAATTTG-GAAGGAAA
1 TTGAGAGAAATTTGAG-AGGAAA
*
12874344 TTGAGAGCAATTTGAGAGGAAA
1 TTGAGAGAAATTTGAGAGGAAA
12874366 TTG
1 TTG
12874369 GGAAAATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 22 0.96
23 1 0.04
ACGTcount: A:0.40, C:0.02, G:0.32, T:0.26
Consensus pattern (22 bp):
TTGAGAGAAATTTGAGAGGAAA
Found at i:12874380 original size:34 final size:33
Alignment explanation
Indices: 12874320--12874383 Score: 85
Period size: 34 Copynumber: 1.9 Consensus size: 33
12874310 TTAAATATGG
* *
12874320 ATTTGAGAGAAATTTGGAAGGAAATTGAGAGCA
1 ATTTGAGAGAAATTGGGAAGAAAATTGAGAGCA
12874353 ATTTGAGAGGAAATTGGGAA-AATAATTGAGA
1 ATTTGAGA-GAAATTGGGAAGAA-AATTGAGA
12874384 AATTGATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
33 9 0.33
34 18 0.67
ACGTcount: A:0.44, C:0.02, G:0.30, T:0.25
Consensus pattern (33 bp):
ATTTGAGAGAAATTGGGAAGAAAATTGAGAGCA
Found at i:12878877 original size:29 final size:29
Alignment explanation
Indices: 12878840--12878895 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
12878830 TAACATCATT
* *
12878840 TTATGTTTAT-AAATTGCAATAATAAATAA
1 TTATATTTATCAAA-TGCAAAAATAAATAA
*
12878869 TTATATTTATCCAATGCAAAAATAAAT
1 TTATATTTATCAAATGCAAAAATAAAT
12878896 TAATGTATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 21 0.91
30 2 0.09
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (29 bp):
TTATATTTATCAAATGCAAAAATAAATAA
Found at i:12880304 original size:31 final size:29
Alignment explanation
Indices: 12880240--12880305 Score: 78
Period size: 29 Copynumber: 2.2 Consensus size: 29
12880230 ATGATAACTT
*** *
12880240 AAGTGACTAAAATGTAATATTTCAAACAT
1 AAGTGACTAAAATGTAATAAGGCAAACAA
12880269 AAGTGACTAAAATGTAATTAGAGGCAAACAA
1 AAGTGACTAAAATGTAA-TA-AGGCAAACAA
12880300 AAGTGA
1 AAGTGA
12880306 AATTGGGTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 17 0.55
30 2 0.06
31 12 0.39
ACGTcount: A:0.50, C:0.09, G:0.17, T:0.24
Consensus pattern (29 bp):
AAGTGACTAAAATGTAATAAGGCAAACAA
Found at i:12880438 original size:3 final size:3
Alignment explanation
Indices: 12880430--12880458 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12880420 AAACATCATT
12880430 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
12880459 TGATTTTGCC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:12886257 original size:33 final size:35
Alignment explanation
Indices: 12886194--12886261 Score: 122
Period size: 35 Copynumber: 2.0 Consensus size: 35
12886184 CAATTCAATC
12886194 CTTAGTCTGTTTAACTTCAATTTTTTTTATTTATT
1 CTTAGTCTGTTTAACTTCAATTTTTTTTATTTATT
12886229 CTTAGTCTGTTTAACTTC-A-TTTTTTTATTTATT
1 CTTAGTCTGTTTAACTTCAATTTTTTTTATTTATT
12886262 TAAAAAAAAC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 14 0.42
34 1 0.03
35 18 0.55
ACGTcount: A:0.19, C:0.12, G:0.06, T:0.63
Consensus pattern (35 bp):
CTTAGTCTGTTTAACTTCAATTTTTTTTATTTATT
Found at i:12886490 original size:12 final size:15
Alignment explanation
Indices: 12886443--12886508 Score: 73
Period size: 15 Copynumber: 4.4 Consensus size: 15
12886433 CAAAACTTAG
* *
12886443 ATTATTATTATTATT
1 ATTATTGTTATTATC
12886458 ATTATTGTTATTATC
1 ATTATTGTTATTATC
12886473 ATTATTGTTATTTAT-
1 ATTATTGTTA-TTATC
*
12886488 ATTATCGTT-TTCATC
1 ATTATTGTTATT-ATC
12886503 ATTATT
1 ATTATT
12886509 ATTGTTTATG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
13 2 0.05
14 2 0.05
15 36 0.82
16 4 0.09
ACGTcount: A:0.27, C:0.06, G:0.05, T:0.62
Consensus pattern (15 bp):
ATTATTGTTATTATC
Found at i:12886511 original size:3 final size:3
Alignment explanation
Indices: 12886443--12886484 Score: 57
Period size: 3 Copynumber: 14.0 Consensus size: 3
12886433 CAAAACTTAG
* * *
12886443 ATT ATT ATT ATT ATT ATT ATT GTT ATT ATC ATT ATT GTT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
12886485 TATATTATCG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:12889792 original size:45 final size:43
Alignment explanation
Indices: 12889742--12889872 Score: 163
Period size: 45 Copynumber: 2.9 Consensus size: 43
12889732 CGTGCTTTCA
* *
12889742 CATGATGCCATAGCGTCTTTCAGCTACGATCTTACTCATTTCTTT
1 CATGATGCCATAGCGTCTTTCAGCTATG-TCTTACTCATTT-TAT
* *
12889787 CATGATGCCATAGCATCTTTCAGTTATGGTCTTACTCATCTTTAT
1 CATGATGCCATAGCGTCTTTCAGCTAT-GTCTTACTCAT-TTTAT
**
12889832 GGTGATGCCATAGCGTCTTTCAGCTATTGTCTTACTCATTT
1 CATGATGCCATAGCGTCTTTCAGCTA-TGTCTTACTCATTT
12889873 AAAGTACACA
Statistics
Matches: 75, Mismatches: 8, Indels: 7
0.83 0.09 0.08
Matches are distributed among these distances:
44 2 0.03
45 69 0.92
46 4 0.05
ACGTcount: A:0.20, C:0.24, G:0.15, T:0.41
Consensus pattern (43 bp):
CATGATGCCATAGCGTCTTTCAGCTATGTCTTACTCATTTTAT
Found at i:12890500 original size:20 final size:21
Alignment explanation
Indices: 12890472--12890512 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
12890462 AGAGAATTTC
* *
12890472 TTTTCTAAGCATA-AATTCTA
1 TTTTATAAGAATACAATTCTA
12890492 TTTTATAAGAATACAATTCTA
1 TTTTATAAGAATACAATTCTA
12890513 CCGGTTTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.39, C:0.12, G:0.05, T:0.44
Consensus pattern (21 bp):
TTTTATAAGAATACAATTCTA
Found at i:12894189 original size:3 final size:3
Alignment explanation
Indices: 12894181--12894222 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
12894171 ATTCCATAAA
12894181 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
12894223 CAAAGCTATA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:12901554 original size:6 final size:6
Alignment explanation
Indices: 12901543--12901575 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
12901533 TTTATTTTCA
*
12901543 TCATTT TCATTT TCATTT TCATTT TCACTT TCA
1 TCATTT TCATTT TCATTT TCATTT TCATTT TCA
12901576 AGTACCTGAA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.18, C:0.21, G:0.00, T:0.61
Consensus pattern (6 bp):
TCATTT
Found at i:12902488 original size:15 final size:15
Alignment explanation
Indices: 12902470--12902499 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
12902460 AATCTGAAAT
12902470 TAATCATTTAAACAA
1 TAATCATTTAAACAA
12902485 TAATCATTTAAACAA
1 TAATCATTTAAACAA
12902500 GCAATCTTGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.53, C:0.13, G:0.00, T:0.33
Consensus pattern (15 bp):
TAATCATTTAAACAA
Found at i:12902879 original size:30 final size:30
Alignment explanation
Indices: 12902843--12902899 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
12902833 AACTTTTATA
*
12902843 ATGAATTCTCAATTAATTTTTGCATCATAT
1 ATGAATTCTCAATTAATTTTCGCATCATAT
*
12902873 ATGAATTCTTAATTAATTTTCGCATCA
1 ATGAATTCTCAATTAATTTTCGCATCA
12902900 ATTAATTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.33, C:0.14, G:0.07, T:0.46
Consensus pattern (30 bp):
ATGAATTCTCAATTAATTTTCGCATCATAT
Found at i:12911102 original size:22 final size:22
Alignment explanation
Indices: 12911016--12911094 Score: 113
Period size: 22 Copynumber: 3.6 Consensus size: 22
12911006 AAAAATAGAC
** *
12911016 CTAAGCTCTCATGTTTAACGAA
1 CTAAGCTCTCATGGCTAACGTA
* *
12911038 CTAAACCCTCATGGCTAACGTA
1 CTAAGCTCTCATGGCTAACGTA
12911060 CTAAGCTCTCATGGCTAACGTA
1 CTAAGCTCTCATGGCTAACGTA
12911082 CTAAGCTCTCATG
1 CTAAGCTCTCATG
12911095 TTTCACGTGT
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 50 1.00
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.28
Consensus pattern (22 bp):
CTAAGCTCTCATGGCTAACGTA
Found at i:12916321 original size:41 final size:41
Alignment explanation
Indices: 12916276--12916432 Score: 161
Period size: 41 Copynumber: 3.8 Consensus size: 41
12916266 ACTTATTAAA
* **
12916276 ATACACCGGCATAAAGCCTTCTAGGCACAAAGCCAAATATG
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
** * *
12916317 ATACACCGGCACGAAGCCTGCTAGGCATAAAGCTTGATATG
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
* * * * * *
12916358 GTACACCGACATGAAGCCTGCTAGGCATAAAGCCTGCTATA
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
* * * *
12916399 ATTCACCAGTATAAAGCCTGCTAGGCACAGAGCC
1 ATACACCGGCATAAAGCCTGCTAGGCACAAAGCC
12916433 CGAATATCAC
Statistics
Matches: 95, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
41 95 1.00
ACGTcount: A:0.34, C:0.27, G:0.21, T:0.18
Consensus pattern (41 bp):
ATACACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATATG
Found at i:12917323 original size:28 final size:28
Alignment explanation
Indices: 12917292--12917345 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
12917282 CTTATAATGT
*
12917292 TTTATTATATCA-TAATAATATAATATAC
1 TTTATTATAACATTAATAA-ATAATATAC
*
12917320 TTTATTATAACATTTATAAATAATAT
1 TTTATTATAACATTAATAAATAATAT
12917346 TAATAATACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 18 0.78
29 5 0.22
ACGTcount: A:0.46, C:0.06, G:0.00, T:0.48
Consensus pattern (28 bp):
TTTATTATAACATTAATAAATAATATAC
Found at i:12919032 original size:3 final size:3
Alignment explanation
Indices: 12919024--12919083 Score: 70
Period size: 3 Copynumber: 20.3 Consensus size: 3
12919014 GCAAACAATG
* * *
12919024 TAA TAA TAA TGA T-A TAA TGA T-T TAA ATAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA -TAA TAA TAA TAA TAA TAA
12919068 TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA T
12919084 GGACTAAATT
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
2 3 0.06
3 44 0.88
4 3 0.06
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (3 bp):
TAA
Found at i:12921591 original size:42 final size:42
Alignment explanation
Indices: 12921537--12921636 Score: 137
Period size: 42 Copynumber: 2.4 Consensus size: 42
12921527 CTATACGAAT
* ** * *
12921537 GGCACTATGTGTGCGAAATTAAAATGATGATGTTGAATAATA
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAATA
* *
12921579 GGCACTAAGTGTGCGAAACAAAAATGGCGATGTCGAATAATG
1 GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAATA
12921621 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
12921637 TACCAAGATC
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.36, C:0.12, G:0.28, T:0.24
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAACAAAAATGACGATGTCGAATAATA
Found at i:12926951 original size:19 final size:20
Alignment explanation
Indices: 12926927--12926967 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
12926917 AAAACTCTAG
12926927 AAAAAATGC-AGA-AAAACTA
1 AAAAAAT-CTAGAGAAAACTA
12926946 AAAAAATCTAGAGAAAACTA
1 AAAAAATCTAGAGAAAACTA
12926966 AA
1 AA
12926968 TCTAAAATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 1 0.05
19 10 0.50
20 9 0.45
ACGTcount: A:0.68, C:0.10, G:0.10, T:0.12
Consensus pattern (20 bp):
AAAAAATCTAGAGAAAACTA
Found at i:12928494 original size:2 final size:2
Alignment explanation
Indices: 12928487--12928522 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
12928477 AGAAATTTAT
12928487 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12928523 AATTTTCCCA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12939916 original size:47 final size:47
Alignment explanation
Indices: 12939864--12940102 Score: 308
Period size: 47 Copynumber: 5.1 Consensus size: 47
12939854 ATTAATATGT
*
12939864 AAAAAACA-TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAG
1 AAAAAA-ATTAAATTTAAATGGAAA-AAAGATAATTTAAATGAAATGAG
* *
12939912 AAAAAAAATTAAATTTAAATGGAAAAAAGATCATTTAAATGAGATGAG
1 -AAAAAAATTAAATTTAAATGGAAAAAAGATAATTTAAATGAAATGAG
* * *
12939960 AAAAAAATTAAATTTAAATGGAAAAAAAATAATTTCAATGAAATGAC
1 AAAAAAATTAAATTTAAATGGAAAAAAGATAATTTAAATGAAATGAG
* *
12940007 AAAAAAATTAAATTAAAATGG---GAAGATAATTTAAATGAAATGAG
1 AAAAAAATTAAATTTAAATGGAAAAAAGATAATTTAAATGAAATGAG
*
12940051 AAAAAAATTAAATTTAAATGAAAAAAAAAAGATAATTTAAATGAAATG-G
1 AAAAAAATTAAATTTAAATG---GAAAAAAGATAATTTAAATGAAATGAG
12940100 AAA
1 AAA
12940103 TGGAAATGGA
Statistics
Matches: 167, Mismatches: 16, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
44 38 0.23
47 62 0.37
48 22 0.13
49 25 0.15
50 20 0.12
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.24
Consensus pattern (47 bp):
AAAAAAATTAAATTTAAATGGAAAAAAGATAATTTAAATGAAATGAG
Found at i:12939923 original size:22 final size:23
Alignment explanation
Indices: 12939898--12940080 Score: 130
Period size: 22 Copynumber: 8.0 Consensus size: 23
12939888 GAAAGATAAT
12939898 TTAAA-TGAAATGAGAAAAAAAA
1 TTAAATTGAAATGAGAAAAAAAA
*
12939920 TTAAATTTAAATG-GAAAAAAGATCA
1 TTAAATTGAAATGAGAAAAAA-A--A
*
12939945 TTTAAA-TGAGATGAG-AAAAAAA
1 -TTAAATTGAAATGAGAAAAAAAA
* *
12939967 TTAAATTTAAATGGAAAAAAAATAA
1 TTAAATTGAAAT-GAGAAAAAA-AA
* *
12939992 TTTCAA-TGAAATGA-CAAAAAAA
1 -TTAAATTGAAATGAGAAAAAAAA
* * * * *
12940014 TTAAATTAAAATGGGAAGATAAT
1 TTAAATTGAAATGAGAAAAAAAA
12940037 TTAAA-TGAAATGAG-AAAAAAA
1 TTAAATTGAAATGAGAAAAAAAA
* *
12940058 TTAAATTTAAATGAAAAAAAAAA
1 TTAAATTGAAATGAGAAAAAAAA
12940081 GATAATTTAA
Statistics
Matches: 123, Mismatches: 23, Indels: 29
0.70 0.13 0.17
Matches are distributed among these distances:
21 18 0.15
22 39 0.32
23 30 0.24
24 8 0.07
25 18 0.15
26 10 0.08
ACGTcount: A:0.62, C:0.02, G:0.12, T:0.25
Consensus pattern (23 bp):
TTAAATTGAAATGAGAAAAAAAA
Found at i:12940056 original size:91 final size:93
Alignment explanation
Indices: 12939864--12940102 Score: 306
Period size: 91 Copynumber: 2.5 Consensus size: 93
12939854 ATTAATATGT
* * *
12939864 AAAAAACA-TAAATTAAAATGGAAAGAAAGATAATTTAAATGAAATGAGAAAAAAAATTAAATTT
1 AAAAAA-ATTAAATTTAAATGGAAA-AAAAATAATTTAAATGAAATGAGAAAAAAAATTAAATTA
* *
12939928 AAATGGAAAAAAGATCATTTAAATGAGATGAG
64 AAATGG--AAAAGATAATTTAAATGAAATGAG
* *
12939960 AAAAAAATTAAATTTAAATGGAAAAAAAATAATTTCAATGAAATGA-CAAAAAAATTAAATTAAA
1 AAAAAAATTAAATTTAAATGGAAAAAAAATAATTTAAATGAAATGAGAAAAAAAATTAAATTAAA
*
12940024 ATGG-GAAGATAATTTAAATGAAATGAG
66 ATGGAAAAGATAATTTAAATGAAATGAG
*
12940051 AAAAAAATTAAATTTAAATGAAAAAAAAAAGATAATTTAAATGAAATG-GAAA
1 AAAAAAATTAAATTTAAATG--GAAAAAAA-ATAATTTAAATGAAATGAGAAA
12940103 TGGAAATGGA
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
91 40 0.31
93 7 0.06
94 38 0.30
95 21 0.17
96 21 0.17
ACGTcount: A:0.62, C:0.02, G:0.13, T:0.24
Consensus pattern (93 bp):
AAAAAAATTAAATTTAAATGGAAAAAAAATAATTTAAATGAAATGAGAAAAAAAATTAAATTAAA
ATGGAAAAGATAATTTAAATGAAATGAG
Found at i:12940104 original size:6 final size:5
Alignment explanation
Indices: 12940089--12940194 Score: 113
Period size: 5 Copynumber: 19.6 Consensus size: 5
12940079 AAGATAATTT
* *
12940089 AAATG AAATGG AAATGG AAATGG AAATG AAATA AAATGG AAATAC AAATG
1 AAATG AAAT-G AAAT-G AAAT-G AAATG AAATG AAAT-G AAAT-G AAATG
*
12940139 GAATG AAATG AAATG AAATG AAATGG AAATAG AAATAG AAATG AAATG
1 AAATG AAATG AAATG AAATG AAAT-G AAAT-G AAAT-G AAATG AAATG
12940187 AAATG AAA
1 AAATG AAA
12940195 AAAAAAAGAT
Statistics
Matches: 90, Mismatches: 8, Indels: 6
0.87 0.08 0.06
Matches are distributed among these distances:
5 49 0.54
6 41 0.46
ACGTcount: A:0.59, C:0.01, G:0.22, T:0.18
Consensus pattern (5 bp):
AAATG
Found at i:12940422 original size:22 final size:21
Alignment explanation
Indices: 12940389--12940430 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 21
12940379 AATGATATTT
12940389 AAATTGAGAAAAATTTTAAATA
1 AAATTGAGAAAAA-TTTAAATA
12940411 AAATATGA-AAAAATTTAAAT
1 AAAT-TGAGAAAAATTTAAAT
12940431 GACCCTGATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.37
22 9 0.47
23 3 0.16
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.31
Consensus pattern (21 bp):
AAATTGAGAAAAATTTAAATA
Found at i:12940572 original size:16 final size:16
Alignment explanation
Indices: 12940553--12940602 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
12940543 TATTAGGAAA
12940553 AAAATAAATTTAAATG
1 AAAATAAATTTAAATG
* *
12940569 AAAAAAAAATT-AATG
1 AAAATAAATTTAAATG
12940584 -AAATGAAATGTTAAATG
1 AAAAT-AAAT-TTAAATG
12940601 AA
1 AA
12940603 TATGAAATGA
Statistics
Matches: 26, Mismatches: 4, Indels: 6
0.72 0.11 0.17
Matches are distributed among these distances:
14 3 0.12
15 7 0.27
16 11 0.42
17 4 0.15
18 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AAAATAAATTTAAATG
Found at i:12940587 original size:20 final size:21
Alignment explanation
Indices: 12940550--12940591 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
12940540 GTATATTAGG
*
12940550 AAAAAAATAAATTTAAATGAA
1 AAAAAAATAAATTGAAATGAA
*
12940571 AAAAAAATTAA-TGAAATGAA
1 AAAAAAATAAATTGAAATGAA
12940591 A
1 A
12940592 TGTTAAATGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.71, C:0.00, G:0.07, T:0.21
Consensus pattern (21 bp):
AAAAAAATAAATTGAAATGAA
Found at i:12940611 original size:23 final size:23
Alignment explanation
Indices: 12940581--12940667 Score: 120
Period size: 23 Copynumber: 3.6 Consensus size: 23
12940571 AAAAAAATTA
12940581 ATGAAATGAAATGTTAAATGAAT
1 ATGAAATGAAATGTTAAATGAAT
*
12940604 ATGAAATGAAATGTAATTTGTAATGAAT
1 ATGAAATGAAATG----TT-AAATGAAT
12940632 ATGAAATGAAATGTTAAATGAAT
1 ATGAAATGAAATGTTAAATGAAT
12940655 ATGAAATGAAATG
1 ATGAAATGAAATG
12940668 ATGATTATGA
Statistics
Matches: 57, Mismatches: 2, Indels: 10
0.83 0.03 0.14
Matches are distributed among these distances:
23 33 0.58
24 2 0.04
27 2 0.04
28 20 0.35
ACGTcount: A:0.51, C:0.00, G:0.18, T:0.31
Consensus pattern (23 bp):
ATGAAATGAAATGTTAAATGAAT
Found at i:12940612 original size:28 final size:28
Alignment explanation
Indices: 12940580--12940668 Score: 109
Period size: 28 Copynumber: 3.4 Consensus size: 28
12940570 AAAAAAAATT
12940580 AATGAAATGAAATGTTAAATGAATATGA
1 AATGAAATGAAATGTTAAATGAATATGA
* *
12940608 AATGAAATGTAA--TT---TGTA-ATGA
1 AATGAAATGAAATGTTAAATGAATATGA
12940630 ATATGAAATGAAATGTTAAATGAATATGA
1 A-ATGAAATGAAATGTTAAATGAATATGA
12940659 AATGAAATGA
1 AATGAAATGA
12940669 TGATTATGAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
22 5 0.10
23 13 0.26
25 2 0.04
26 2 0.04
28 23 0.46
29 5 0.10
ACGTcount: A:0.52, C:0.00, G:0.18, T:0.30
Consensus pattern (28 bp):
AATGAAATGAAATGTTAAATGAATATGA
Found at i:12940676 original size:19 final size:19
Alignment explanation
Indices: 12940598--12940687 Score: 77
Period size: 17 Copynumber: 5.1 Consensus size: 19
12940588 GAAATGTTAA
12940598 ATGAATATGAAATGAAATG
1 ATGAATATGAAATGAAATG
* *
12940617 -T-AATTTGTAATG-AAT-
1 ATGAATATGAAATGAAATG
*
12940632 ATGAA-ATGAAATGTTAA--
1 ATGAATATGAAATG-AAATG
12940649 ATGAATATGAAATGAAATG
1 ATGAATATGAAATGAAATG
* *
12940668 ATGATTATGAAATGGAATG
1 ATGAATATGAAATGAAATG
12940687 A
1 A
12940688 AAGTGTAAAT
Statistics
Matches: 57, Mismatches: 7, Indels: 14
0.73 0.09 0.18
Matches are distributed among these distances:
16 10 0.18
17 18 0.32
18 11 0.19
19 18 0.32
ACGTcount: A:0.49, C:0.00, G:0.20, T:0.31
Consensus pattern (19 bp):
ATGAATATGAAATGAAATG
Found at i:12940720 original size:6 final size:5
Alignment explanation
Indices: 12940580--12940701 Score: 86
Period size: 5 Copynumber: 22.4 Consensus size: 5
12940570 AAAAAAAATT
* *
12940580 AATGA AATGA AATGTTA AATGA ATATGA AATGA AATGTA ATTTGT AATGA
1 AATGA AATGA AATG--A AATGA A-ATGA AATGA AATG-A A-ATGA AATGA
*
12940630 ATATGA AATGA AATGTTA AATGA ATATGA AATGA AATG- -ATGA TTATGA
1 A-ATGA AATGA AATG--A AATGA A-ATGA AATGA AATGA AATGA -AATGA
*
12940678 AATGG AATGA AAGTGTA AATGA AA
1 AATGA AATGA AA-TG-A AATGA AA
12940702 ATAAATTATA
Statistics
Matches: 96, Mismatches: 7, Indels: 28
0.73 0.05 0.21
Matches are distributed among these distances:
3 3 0.03
5 52 0.54
6 26 0.27
7 15 0.16
ACGTcount: A:0.51, C:0.00, G:0.20, T:0.30
Consensus pattern (5 bp):
AATGA
Found at i:12940805 original size:8 final size:8
Alignment explanation
Indices: 12940792--12940822 Score: 53
Period size: 8 Copynumber: 3.8 Consensus size: 8
12940782 GCTTTTTTAA
12940792 AAAAAAAT
1 AAAAAAAT
12940800 AAAAAAAT
1 AAAAAAAT
12940808 ACAAAAAAT
1 A-AAAAAAT
12940817 AAAAAA
1 AAAAAA
12940823 TTATATTTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 14 0.64
9 8 0.36
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:12940861 original size:30 final size:29
Alignment explanation
Indices: 12940820--12940934 Score: 115
Period size: 30 Copynumber: 3.9 Consensus size: 29
12940810 AAAAAATAAA
*
12940820 AAATTATATTTTGACCCCCTAAACTTTTTG
1 AAATTACATTTTGA-CCCCTAAACTTTTTG
* * * *
12940850 AAATTGCATTTTCACCCCTAAACTTTCCTA
1 AAATTACATTTTGACCCCTAAACTTT-TTG
* * * *
12940880 AAATTACATTTTGGCCCATCAACTTCTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
*
12940909 AAATTATATTTTGACCCCTAAA-TTTT
1 AAATTACATTTTGACCCCTAAACTTTT
12940935 CTCAAAATTA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
28 3 0.05
29 31 0.47
30 32 0.48
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTTTG
Found at i:12941507 original size:11 final size:10
Alignment explanation
Indices: 12941471--12941543 Score: 62
Period size: 10 Copynumber: 7.3 Consensus size: 10
12941461 GTTCAGCCCG
12941471 AAGAAG-AAA
1 AAGAAGAAAA
*
12941480 AAGAAAAAAGGA
1 AAGAAGAAA--A
12941492 AAGAATGAAAA
1 AAGAA-GAAAA
12941503 AAGAAGAAAA
1 AAGAAGAAAA
*
12941513 AAAAAGAAAA
1 AAGAAGAAAA
*
12941523 AA-AAG-AGA
1 AAGAAGAAAA
*
12941531 AAGAAAAAAA
1 AAGAAGAAAA
12941541 AAG
1 AAG
12941544 GGAAAAAATA
Statistics
Matches: 52, Mismatches: 6, Indels: 11
0.75 0.09 0.16
Matches are distributed among these distances:
8 4 0.08
9 10 0.19
10 23 0.44
11 6 0.12
12 6 0.12
13 3 0.06
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (10 bp):
AAGAAGAAAA
Found at i:12941512 original size:24 final size:22
Alignment explanation
Indices: 12941471--12941539 Score: 70
Period size: 22 Copynumber: 3.1 Consensus size: 22
12941461 GTTCAGCCCG
* **
12941471 AAGAAGAAAAAGAA-AAAAGGA
1 AAGAAAAAAAAGAAGAAAAAAA
12941492 AAGAATGAAAAAAGAAGAAAAAAA
1 AAGAA--AAAAAAGAAGAAAAAAA
12941516 AAGAAAAAAAAG-AGAAAGAAAA
1 AAGAAAAAAAAGAAGAAA-AAAA
12941538 AA
1 AA
12941540 AAAGGGAAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
21 10 0.24
22 13 0.32
23 8 0.20
24 10 0.24
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.01
Consensus pattern (22 bp):
AAGAAAAAAAAGAAGAAAAAAA
Found at i:12941548 original size:16 final size:15
Alignment explanation
Indices: 12941502--12941541 Score: 57
Period size: 15 Copynumber: 2.8 Consensus size: 15
12941492 AAGAATGAAA
*
12941502 AAAGAAGAAAAA-A-
1 AAAGAAAAAAAAGAG
12941515 AAAGAAAAAAAAGAG
1 AAAGAAAAAAAAGAG
12941530 AAAGAAAAAAAA
1 AAAGAAAAAAAA
12941542 AGGGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 11 0.46
14 1 0.04
15 12 0.50
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAAAGAG
Found at i:12941551 original size:25 final size:23
Alignment explanation
Indices: 12941480--12941543 Score: 74
Period size: 25 Copynumber: 2.6 Consensus size: 23
12941470 GAAGAAGAAA
*
12941480 AAGAAAAAAGGAAAGAATGAAAAAAG
1 AAGAAAAAA--AAAGAA-AAAAAAAG
12941506 AAGAAAAAAAAAGAAAAAAAAGAG
1 AAGAAAAAAAAAGAAAAAAAA-AG
12941530 AAAGAAAAAAAAAG
1 -AAGAAAAAAAAAG
12941544 GGAAAAAATA
Statistics
Matches: 35, Mismatches: 1, Indels: 5
0.85 0.02 0.12
Matches are distributed among these distances:
23 5 0.14
24 8 0.23
25 13 0.37
26 9 0.26
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (23 bp):
AAGAAAAAAAAAGAAAAAAAAAG
Found at i:12941799 original size:33 final size:33
Alignment explanation
Indices: 12941762--12941856 Score: 145
Period size: 33 Copynumber: 2.8 Consensus size: 33
12941752 GCAGCAGGTG
*
12941762 CAGCAGCACGCCGAGCGCCCAGGCCCAGCGCAC
1 CAGCAGCAGGCCGAGCGCCCAGGCCCAGCGCAC
12941795 CAGCAGCAGGCCGAGCGCCCAGGCCCAGCGCAC
1 CAGCAGCAGGCCGAGCGCCCAGGCCCAGCGCAC
* *
12941828 CAGCATCAGGCCCAGCAGTCCCAGGCCCA
1 CAGCAGCAGGCCGAGC-G-CCCAGGCCCA
12941857 ATCTGTAGCA
Statistics
Matches: 57, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
33 46 0.81
34 1 0.02
35 10 0.18
ACGTcount: A:0.22, C:0.46, G:0.29, T:0.02
Consensus pattern (33 bp):
CAGCAGCAGGCCGAGCGCCCAGGCCCAGCGCAC
Found at i:12941806 original size:20 final size:19
Alignment explanation
Indices: 12941781--12941843 Score: 57
Period size: 20 Copynumber: 3.5 Consensus size: 19
12941771 GCCGAGCGCC
12941781 CAGGCCCAGCGCACCAGCA
1 CAGGCCCAGCGCACCAGCA
*
12941800 GCAGGCCGAGCG---C--C-
1 -CAGGCCCAGCGCACCAGCA
12941814 CAGGCCCAGCGCACCAGCA
1 CAGGCCCAGCGCACCAGCA
12941833 TCAGGCCCAGC
1 -CAGGCCCAGC
12941844 AGTCCCAGGC
Statistics
Matches: 34, Mismatches: 2, Indels: 14
0.68 0.04 0.28
Matches are distributed among these distances:
13 10 0.29
15 1 0.03
16 1 0.03
17 1 0.03
18 1 0.03
20 20 0.59
ACGTcount: A:0.22, C:0.46, G:0.30, T:0.02
Consensus pattern (19 bp):
CAGGCCCAGCGCACCAGCA
Found at i:12941907 original size:18 final size:18
Alignment explanation
Indices: 12941886--12941941 Score: 78
Period size: 18 Copynumber: 3.1 Consensus size: 18
12941876 AAAAAGAAGT
12941886 AAAAAAAGAAAAGAGAAA
1 AAAAAAAGAAAAGAGAAA
*
12941904 AAAAAAAGGAAAGAGAAA
1 AAAAAAAGAAAAGAGAAA
*
12941922 AAGAAAAAAAAAAG-GAAA
1 AA-AAAAAGAAAAGAGAAA
12941940 AA
1 AA
12941942 GGAAAAAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
18 25 0.74
19 9 0.26
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (18 bp):
AAAAAAAGAAAAGAGAAA
Found at i:12941923 original size:19 final size:19
Alignment explanation
Indices: 12941871--12941930 Score: 68
Period size: 18 Copynumber: 3.2 Consensus size: 19
12941861 GTAGCAGGCC
* **
12941871 AAAGGAAAAAGAAGTAAAA
1 AAAGGAAAGAGAAAAAAAA
*
12941890 AAAGAAAAGAG-AAAAAAA
1 AAAGGAAAGAGAAAAAAAA
12941908 AAAGGAAAGAGAAAAAGAAA
1 AAAGGAAAGAGAAAAA-AAA
12941928 AAA
1 AAA
12941931 AAAAGGAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
18 15 0.44
19 13 0.38
20 6 0.18
ACGTcount: A:0.78, C:0.00, G:0.20, T:0.02
Consensus pattern (19 bp):
AAAGGAAAGAGAAAAAAAA
Found at i:12941924 original size:31 final size:30
Alignment explanation
Indices: 12941888--12941946 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 30
12941878 AAAGAAGTAA
12941888 AAAAAGAAAAGAGAAAAA-AAAAAGGAAAGAG
1 AAAAAGAAAA-A-AAAAAGAAAAAGGAAAGAG
12941919 AAAAAGAAAAAAAAAAGGAAAAAGGAAA
1 AAAAAGAAAAAAAAAA-GAAAAAGGAAA
12941947 AAAAGGAAGG
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
29 5 0.19
30 1 0.04
31 20 0.77
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (30 bp):
AAAAAGAAAAAAAAAAGAAAAAGGAAAGAG
Found at i:12941926 original size:24 final size:24
Alignment explanation
Indices: 12941888--12941948 Score: 95
Period size: 24 Copynumber: 2.5 Consensus size: 24
12941878 AAAGAAGTAA
12941888 AAAAAGAAAAGAGAAAAAAAAAAGG
1 AAAAAGAAAA-AGAAAAAAAAAAGG
*
12941913 AAAGAGAAAAAGAAAAAAAAAAGG
1 AAAAAGAAAAAGAAAAAAAAAAGG
12941937 AAAAAGGAAAAA
1 AAAAA-GAAAAA
12941949 AAGGAAGGCT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
24 18 0.55
25 15 0.45
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (24 bp):
AAAAAGAAAAAGAAAAAAAAAAGG
Found at i:12941934 original size:12 final size:12
Alignment explanation
Indices: 12941876--12941941 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
12941866 AGGCCAAAGG
*
12941876 AAAAAGAAGTAAA
1 AAAAAAAAG-AAA
12941889 AAAAGAAAAGAGAA
1 AAAA-AAAAGA-AA
12941903 AAAAAAAAGGAAA
1 AAAAAAAA-GAAA
* *
12941916 GAGAAAAAGAAA
1 AAAAAAAAGAAA
*
12941928 AAAAAAAGGAAA
1 AAAAAAAAGAAA
12941940 AA
1 AA
12941942 GGAAAAAAAG
Statistics
Matches: 44, Mismatches: 6, Indels: 7
0.77 0.11 0.12
Matches are distributed among these distances:
12 15 0.34
13 17 0.39
14 12 0.27
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.02
Consensus pattern (12 bp):
AAAAAAAAGAAA
Found at i:12941940 original size:43 final size:41
Alignment explanation
Indices: 12941871--12941950 Score: 108
Period size: 42 Copynumber: 1.9 Consensus size: 41
12941861 GTAGCAGGCC
*
12941871 AAAGGAAAAAGAAGTAAAAAAAGAAAAGAGAAAAAAAAAAGG
1 AAAGGAAAAAGAAGAAAAAAAAGAAAA-AGAAAAAAAAAAGG
*
12941913 AAAGAGAAAAAGAA-AAAAAAAAGGAAAAAGGAAAAAAA
1 AAAG-GAAAAAGAAGAAAAAAAA-GAAAAAGAAAAAAAA
12941951 GGAAGGCTCG
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
42 20 0.59
43 14 0.41
ACGTcount: A:0.79, C:0.00, G:0.20, T:0.01
Consensus pattern (41 bp):
AAAGGAAAAAGAAGAAAAAAAAGAAAAAGAAAAAAAAAAGG
Found at i:12941942 original size:18 final size:17
Alignment explanation
Indices: 12941875--12941941 Score: 64
Period size: 18 Copynumber: 3.7 Consensus size: 17
12941865 CAGGCCAAAG
*
12941875 GAAAAAGAAGTAAAAAAA
1 GAAAAAGAA-AAAAAAAA
12941893 GAAAAGAGAAAAAAAAAA
1 GAAAA-AGAAAAAAAAAA
*
12941911 GGAAAGAGAAAAAGAAAAA
1 -GAAAAAGAAAAA-AAAAA
12941930 -AAAAAGGAAAAA
1 GAAAAA-GAAAAA
12941942 GGAAAAAAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
17 4 0.10
18 25 0.60
19 13 0.31
ACGTcount: A:0.79, C:0.00, G:0.19, T:0.01
Consensus pattern (17 bp):
GAAAAAGAAAAAAAAAA
Found at i:12941947 original size:18 final size:19
Alignment explanation
Indices: 12941887--12941950 Score: 78
Period size: 19 Copynumber: 3.4 Consensus size: 19
12941877 AAAAGAAGTA
12941887 AAAAAAGAAAAGAGAAAAA-
1 AAAAAA-AAAAGAGAAAAAG
**
12941906 AAAAAGGAAAGAGAAAAAG
1 AAAAAAAAAAGAGAAAAAG
12941925 AAAAAAAAAAG-GAAAAAGG
1 AAAAAAAAAAGAGAAAAA-G
12941944 AAAAAAA
1 AAAAAAA
12941951 GGAAGGCTCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
18 17 0.44
19 22 0.56
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (19 bp):
AAAAAAAAAAGAGAAAAAG
Found at i:12942480 original size:17 final size:17
Alignment explanation
Indices: 12942460--12942921 Score: 259
Period size: 17 Copynumber: 25.9 Consensus size: 17
12942450 TTAAAAAAAA
12942460 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
12942477 TCGTGTTTTCAAAAAAATTT
1 TCGTG-TTTC--AAAAATTT
*
12942497 CTCGTCTTTCAAAAATTT
1 -TCGTGTTTCAAAAATTT
* ***
12942515 CCGTGTTTTTTTTTAAA--T
1 TCGTG---TTTCAAAAATTT
* *
12942533 TCCTGTTTTCAAAAATTC
1 TCGTG-TTTCAAAAATTT
* *
12942551 TCATGTTTCAAAAATCT
1 TCGTGTTTCAAAAATTT
12942568 TCGTGTTTTCAAAATATAATT
1 TCGTG-TTTCAAAA-AT--TT
** *
12942589 TTATGTTTTAAAAATTT
1 TCGTGTTTCAAAAATTT
12942606 TCGTGTTTTCAAAAAAATTT
1 TCGTG-TTTC--AAAAATTT
* *
12942626 CCCGTGTTTTCAAAAATTC
1 -TCGTG-TTTCAAAAATTT
* *
12942645 CCGTGTTTTCAAAAAATT
1 TCGTG-TTTCAAAAATTT
* * * *
12942663 CCATTTTTCAAAATTTT
1 TCGTGTTTCAAAAATTT
12942680 TCGTGTCTTCTAAAAATTT
1 TCGTGT-TTC-AAAAATTT
* * *
12942699 CCATGTTTCTAAAATTT
1 TCGTGTTTCAAAAATTT
12942716 TCGTGTTTCAAAAATTT
1 TCGTGTTTCAAAAATTT
12942733 TCGTGTTTTCAAAAATTT
1 TCGTG-TTTCAAAAATTT
* * *
12942751 GCGTGTTTTCAACAATTC
1 TCGTG-TTTCAAAAATTT
* *
12942769 TCGTGTTTTACAAATTT
1 TCGTGTTTCAAAAATTT
* * **
12942786 TCGCGCTTCAAAAA-AA
1 TCGTGTTTCAAAAATTT
* * *
12942802 TCGGGTTTTCAAAAAAAATC
1 TCGTG-TTTC--AAAAATTT
* *
12942822 GCGTGTTTC-AAAATTG
1 TCGTGTTTCAAAAATTT
12942838 TCGTGTTTTCAAAAATTT
1 TCGTG-TTTCAAAAATTT
* *
12942856 TCGTGTTTTAATAATTT
1 TCGTGTTTCAAAAATTT
* * *
12942873 TCGTGTCTCTAAAATTC
1 TCGTGTTTCAAAAATTT
*
12942890 TCGTGTTTTAAAAATTTT
1 TCGTGTTTCAAAAA-TTT
12942908 TCGTGTTT-AAAAAT
1 TCGTGTTTCAAAAAT
12942922 AAAAATAAAA
Statistics
Matches: 342, Mismatches: 76, Indels: 55
0.72 0.16 0.12
Matches are distributed among these distances:
16 21 0.06
17 129 0.38
18 108 0.32
19 31 0.09
20 36 0.11
21 17 0.05
ACGTcount: A:0.30, C:0.14, G:0.11, T:0.45
Consensus pattern (17 bp):
TCGTGTTTCAAAAATTT
Found at i:12942486 original size:18 final size:18
Alignment explanation
Indices: 12942460--12942915 Score: 314
Period size: 18 Copynumber: 25.4 Consensus size: 18
12942450 TTAAAAAAAA
12942460 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
12942477 TCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTC--AAAAATTT
*
12942497 CTCGT-CTTTCAAAAATTT
1 -TCGTGTTTTCAAAAATTT
* ***
12942515 CCGTGTTTTTTTTTAAA--T
1 TCGTG--TTTTCAAAAATTT
* *
12942533 TCCTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
12942551 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
12942568 TCGTGTTTTCAAAATATAATT
1 TCGTGTTTTCAAAA-AT--TT
**
12942589 TTATGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
12942606 TCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTC--AAAAATTT
* *
12942626 CCCGTGTTTTCAAAAATTC
1 -TCGTGTTTTCAAAAATTT
* *
12942645 CCGTGTTTTCAAAAAATT
1 TCGTGTTTTCAAAAATTT
* * *
12942663 CCAT-TTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTT
*
12942680 TCGTGTCTTCTAAAAATTT
1 TCGTGTTTTC-AAAAATTT
* * *
12942699 CCATG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTT
12942716 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
12942733 TCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* * *
12942751 GCGTGTTTTCAACAATTC
1 TCGTGTTTTCAAAAATTT
*
12942769 TCGTGTTTT-ACAAATTT
1 TCGTGTTTTCAAAAATTT
* * **
12942786 TCGCG-CTTCAAAAA-AA
1 TCGTGTTTTCAAAAATTT
* ***
12942802 TCGGGTTTTCAAAAAAAA
1 TCGTGTTTTCAAAAATTT
* *
12942820 TCGCGTGTTTC-AAAATTG
1 TCGTGT-TTTCAAAAATTT
12942838 TCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
*
12942856 TCGTGTTTT-AATAATTT
1 TCGTGTTTTCAAAAATTT
* * *
12942873 TCGTG-TCTCTAAAATTC
1 TCGTGTTTTCAAAAATTT
12942890 TCGTGTTTT-AAAAATTTT
1 TCGTGTTTTCAAAAA-TTT
12942908 TCGTGTTT
1 TCGTGTTT
12942916 AAAAATAAAA
Statistics
Matches: 344, Mismatches: 67, Indels: 55
0.74 0.14 0.12
Matches are distributed among these distances:
16 15 0.04
17 121 0.35
18 132 0.38
19 25 0.07
20 30 0.09
21 21 0.06
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:12942725 original size:53 final size:53
Alignment explanation
Indices: 12942532--12942906 Score: 180
Period size: 53 Copynumber: 7.0 Consensus size: 53
12942522 TTTTTTTAAA
* * * * *
12942532 TTCC-TGTTTTCAAAAATTCTCATGTTTCAAAAATCTTCGTGTTTTCAAAATAT
1 TTCCATGTTTTCAACAATTCTCGTGTTTCAAAATTTTTCGTGTCTTCAAAA-AT
** * * ** *
12942585 AATTTTATGTTTT-AAAAATTTTCGTGTTTTCAAAAAAATTTCCCGTGTTTTCAAAAAT
1 --TTCCATGTTTTCAACAATTCTCGTG-TTTC---AAAATTTTTCGTGTCTTCAAAAAT
* * * * *
12942643 TCCCGTGTTTTCAAAAAATTC-CATTTTTCAAAATTTTTCGTGTCTTCTAAAAAT
1 TTCCATGTTTTC-AACAATTCTCGTGTTTCAAAATTTTTCGTGTCTTC-AAAAAT
* * *
12942697 TTCCATG-TTTCTAA-AATTTTCGTGTTTCAAAAATTTTCGTGTTTTCAAAAAT
1 TTCCATGTTTTC-AACAATTCTCGTGTTTCAAAATTTTTCGTGTCTTCAAAAAT
* * * * *
12942749 TTGCGTGTTTTCAACAATTCTCGTGTTTTACAAA-TTTTCGCG-CTTCAAAAAA
1 TTCCATGTTTTCAACAATTCTCGTGTTTCA-AAATTTTTCGTGTCTTCAAAAAT
* ** * * * * *
12942801 AT-CGGGTTTTCAAAAAAAATCGCGTGTTTCAAAA-TTGTCGTGTTTTCAAAAAT
1 TTCCATGTTTTC--AACAATTCTCGTGTTTCAAAATTTTTCGTGTCTTCAAAAAT
* * * * * * *
12942854 TTTCGTGTTTT-AATAATTTTCGTGTCTCTAAAA-TTCTCGTGT-TTTAAAAAT
1 TTCCATGTTTTCAACAATTCTCGTGTTTC-AAAATTTTTCGTGTCTTCAAAAAT
12942905 TT
1 TT
12942907 TTCGTGTTTA
Statistics
Matches: 251, Mismatches: 52, Indels: 38
0.74 0.15 0.11
Matches are distributed among these distances:
51 30 0.12
52 47 0.19
53 90 0.36
54 21 0.08
55 13 0.05
56 21 0.08
57 2 0.01
58 9 0.04
59 18 0.07
ACGTcount: A:0.30, C:0.15, G:0.11, T:0.45
Consensus pattern (53 bp):
TTCCATGTTTTCAACAATTCTCGTGTTTCAAAATTTTTCGTGTCTTCAAAAAT
Found at i:12942773 original size:36 final size:36
Alignment explanation
Indices: 12942460--12942915 Score: 275
Period size: 35 Copynumber: 12.7 Consensus size: 36
12942450 TTAAAAAAAA
*
12942460 TCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTCAAAAATTCTCGTGTTTTC--AAAAATTT
* ***
12942497 CTCGT-CTTTCAAAAATT-TCCGTGTTTTTTTTTAAA--T
1 -TCGTGTTTTCAAAAATTCT-CGTG--TTTTCAAAAATTT
* * *
12942533 TCCTGTTTTCAAAAATTCTCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTT
* **
12942568 TCGTGTTTTCAAAATATAATTTTATGTTTT-AAAAATTT
1 TCGTGTTTTCAAAA-AT--TCTCGTGTTTTCAAAAATTT
* *
12942606 TCGTGTTTTCAAAAAAATTTCCCGTGTTTTCAAAAATTC
1 TCGTGTTTTC--AAAAA-TTCTCGTGTTTTCAAAAATTT
* * *
12942645 CCGTGTTTTCAAAAAATTC-CAT-TTTTCAAAATTTT
1 TCGTGTTTTC-AAAAATTCTCGTGTTTTCAAAAATTT
* * *
12942680 TCGTGTCTTCTAAAAATT-TCCATG-TTTCTAAAATTT
1 TCGTGTTTTC-AAAAATTCT-CGTGTTTTCAAAAATTT
*
12942716 TCGTG-TTTCAAAAATTTTCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTT
* * *
12942751 GCGTGTTTTCAACAATTCTCGTGTTTT-ACAAATTT
1 TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTT
* * ** * ***
12942786 TCGCG-CTTCAAAAA-AATCGGGTTTTCAAAAAAAA
1 TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTT
* *
12942820 TCGCGTGTTTC-AAAATTGTCGTGTTTTCAAAAATTT
1 TCGTGT-TTTCAAAAATTCTCGTGTTTTCAAAAATTT
* * * * *
12942856 TCGTGTTTT-AATAATTTTCGTG-TCTCTAAAATTC
1 TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTT
*
12942890 TCGTGTTTT-AAAAATTTTTCGTGTTT
1 TCGTGTTTTCAAAAA-TTCTCGTGTTT
12942916 AAAAATAAAA
Statistics
Matches: 329, Mismatches: 60, Indels: 60
0.73 0.13 0.13
Matches are distributed among these distances:
33 14 0.04
34 48 0.15
35 97 0.29
36 79 0.24
37 5 0.02
38 57 0.17
39 20 0.06
40 9 0.03
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (36 bp):
TCGTGTTTTCAAAAATTCTCGTGTTTTCAAAAATTT
Found at i:12944423 original size:16 final size:16
Alignment explanation
Indices: 12944386--12944425 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
12944376 TAAATAAAAT
* *
12944386 TAAAACTAATTGTTAT
1 TAAAATTAATTGTTAG
12944402 TAAAATTAATTGTTAG
1 TAAAATTAATTGTTAG
12944418 TAAAATTA
1 TAAAATTA
12944426 TCAAATTATT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.47, C:0.03, G:0.07, T:0.42
Consensus pattern (16 bp):
TAAAATTAATTGTTAG
Found at i:12945362 original size:9 final size:9
Alignment explanation
Indices: 12945348--12945397 Score: 91
Period size: 9 Copynumber: 5.6 Consensus size: 9
12945338 TGAAGAAACC
12945348 TCGTCGTCA
1 TCGTCGTCA
12945357 TCGTCGTCA
1 TCGTCGTCA
12945366 TCGTCGTCA
1 TCGTCGTCA
*
12945375 TCTTCGTCA
1 TCGTCGTCA
12945384 TCGTCGTCA
1 TCGTCGTCA
12945393 TCGTC
1 TCGTC
12945398 CTTTTTGCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 39 1.00
ACGTcount: A:0.10, C:0.34, G:0.20, T:0.36
Consensus pattern (9 bp):
TCGTCGTCA
Found at i:12947703 original size:92 final size:92
Alignment explanation
Indices: 12947546--12948122 Score: 983
Period size: 92 Copynumber: 6.3 Consensus size: 92
12947536 ATATATACAA
* * * *
12947546 ATATTTTATTAAATATACAAATAGGTTAAAACAAAATGCATACTTGCTGTCTAAATTGTAACTTA
1 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
12947611 TATGCATACTTTGATACAAATAGGTTT
66 TATGCATACTTTGATACAAATAGGTTT
12947638 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
1 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
*
12947703 TATGCATACTTTAATACAAATAGGTTT
66 TATGCATACTTTGATACAAATAGGTTT
* *
12947730 ATATTTTATTAAATAGAAGAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
1 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
12947795 TATGCATACTTTGATACAAATAGGTTT
66 TATGCATACTTTGATACAAATAGGTTT
* *
12947822 ATATTTTATTAAATATAAAAACAAGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
1 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
*
12947887 TATGCATACTTTAATACAAATAGGTTT
66 TATGCATACTTTGATACAAATAGGTTT
* * *
12947914 ATATTTTATTAAATATAAGAATAGGTTCAAACAAAATGTATACTTGCTATTTAAATTGTAGCTTA
1 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
12947979 TATGCATACTTTGATACAAATAGGTTT
66 TATGCATACTTTGATACAAATAGGTTT
* * *
12948006 ATATTTTATTAAATATAAAAACAAGTTCAAACAAAATGCATACTTGCTGTCTAAATTGTAGCTTA
1 ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
* *
12948071 TACGCATACTTTGATACAAATAGGTTC
66 TATGCATACTTTGATACAAATAGGTTT
*
12948098 ATATTTTATTAAATATACAAATAGG
1 ATATTTTATTAAATATAAAAATAGG
12948123 CTAAAAATTG
Statistics
Matches: 455, Mismatches: 30, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
92 455 1.00
ACGTcount: A:0.40, C:0.10, G:0.11, T:0.38
Consensus pattern (92 bp):
ATATTTTATTAAATATAAAAATAGGTTCAAACAAAATGCATACTTGCTGTTTAAATTGTAGCTTA
TATGCATACTTTGATACAAATAGGTTT
Found at i:12948678 original size:18 final size:17
Alignment explanation
Indices: 12948637--12948699 Score: 90
Period size: 17 Copynumber: 3.5 Consensus size: 17
12948627 AAAATTAATG
12948637 AAATCTATTACAGTGAATAA
1 AAATCTATTACAGT--A-AA
12948657 AAATCTATTAGCAGTAAA
1 AAATCTATTA-CAGTAAA
12948675 AAATCTATTACAGTAAA
1 AAATCTATTACAGTAAA
12948692 AAATCTAT
1 AAATCTAT
12948700 GAGGAGCGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 5
0.89 0.00 0.11
Matches are distributed among these distances:
17 15 0.36
18 12 0.29
19 1 0.02
20 10 0.24
21 4 0.10
ACGTcount: A:0.51, C:0.11, G:0.08, T:0.30
Consensus pattern (17 bp):
AAATCTATTACAGTAAA
Found at i:12950494 original size:20 final size:20
Alignment explanation
Indices: 12950464--12950510 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
12950454 GTGGATTGGG
*
12950464 AAATGAAAACTAAAAC-TAA
1 AAATAAAAACTAAAACATAA
*
12950483 AAAGTAAAAACTTAAACATAA
1 AAA-TAAAAACTAAAACATAA
12950504 AAATAAA
1 AAATAAA
12950511 TATATATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 3 0.12
20 15 0.62
21 6 0.25
ACGTcount: A:0.70, C:0.09, G:0.04, T:0.17
Consensus pattern (20 bp):
AAATAAAAACTAAAACATAA
Found at i:12950555 original size:30 final size:30
Alignment explanation
Indices: 12950494--12950576 Score: 95
Period size: 30 Copynumber: 2.8 Consensus size: 30
12950484 AAGTAAAAAC
*
12950494 TTAAACAT-AAAAA--TAAATATATATTTT
1 TTAAACATAAAAAATTTAAATATATATATT
12950521 TTAAACATAAAAAATTTAAACTAT-TATATT
1 TTAAACATAAAAAATTTAAA-TATATATATT
12950551 TTAAACATAAAATATATTT-AATATAT
1 TTAAACATAAAA-A-ATTTAAATATAT
12950577 TTAATATATT
Statistics
Matches: 48, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
27 8 0.17
28 5 0.10
30 24 0.50
31 7 0.15
32 4 0.08
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (30 bp):
TTAAACATAAAAAATTTAAATATATATATT
Found at i:12950575 original size:9 final size:9
Alignment explanation
Indices: 12950561--12950587 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
12950551 TTAAACATAA
12950561 AATATATTT
1 AATATATTT
12950570 AATATATTT
1 AATATATTT
12950579 AATATATTT
1 AATATATTT
12950588 TCAGGCCGGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
AATATATTT
Found at i:12955551 original size:82 final size:82
Alignment explanation
Indices: 12955166--12955528 Score: 549
Period size: 83 Copynumber: 4.5 Consensus size: 82
12955156 ACTCCCGTTC
*
12955166 AAAAATCAACTCATATTGCGAGAGGTGAGTTAAGCCTCGGGTCGCACGCTGAGGTA----TTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
*
12955227 AATTTTTGTTTTTTC-A
66 AATTTCTGTTTTTTCAA
12955243 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
12955308 AATTTCTGTTTTTTCAAA
66 AATTTCTGTTTTTTC-AA
* *
12955326 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCGTTTA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
***
12955391 AATTTCTGTTTTTTTTTT
66 AATTTCTG-TTTTTTCAA
* * * *
12955409 AAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACATGCCGAGGTATTTTCTTTT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTA-TTTCTTTT
12955474 AAATTTCTG-TTTTTCAA
65 AAATTTCTGTTTTTTCAA
*
12955491 AAAAATCAACTCATATTGCGAGAAGTGAGTTGAGCCTC
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC
12955529 AGGCCACACG
Statistics
Matches: 260, Mismatches: 18, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
77 55 0.21
81 19 0.07
82 41 0.16
83 123 0.47
84 22 0.08
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (82 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCGCACGCTGAGGTATTTCTTTTA
AATTTCTGTTTTTTCAA
Found at i:12955776 original size:30 final size:29
Alignment explanation
Indices: 12955735--12955849 Score: 115
Period size: 30 Copynumber: 3.9 Consensus size: 29
12955725 CAAAAATAAA
*
12955735 AAATTATATTTTGACCCCCTAAACTTTTTG
1 AAATTACATTTTGA-CCCCTAAACTTTTTG
* * * *
12955765 AAATTGCATTTTCACCCCTAAACTTTCCTA
1 AAATTACATTTTGACCCCTAAACTTT-TTG
* * * *
12955795 AAATTACATTTTGGCCCATCAACTTCTTG
1 AAATTACATTTTGACCCCTAAACTTTTTG
*
12955824 AAATTATATTTTGACCCCTAAA-TTTT
1 AAATTACATTTTGACCCCTAAACTTTT
12955850 CTCAAAATTA
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
28 3 0.05
29 31 0.47
30 32 0.48
ACGTcount: A:0.30, C:0.23, G:0.06, T:0.41
Consensus pattern (29 bp):
AAATTACATTTTGACCCCTAAACTTTTTG
Found at i:12956301 original size:21 final size:20
Alignment explanation
Indices: 12956276--12956334 Score: 73
Period size: 21 Copynumber: 2.8 Consensus size: 20
12956266 AACAGCAGCC
12956276 AAAAAGAAGGAAGAGAAGAAA
1 AAAAAGAA-GAAGAGAAGAAA
12956297 AAAAATGAAGAAGAGAAGAAA
1 AAAAA-GAAGAAGAGAAGAAA
*
12956318 GAAAAGAGAGAGAGAGA
1 AAAAAGA-AGA-AGAGA
12956335 GGAAGAGAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
20 2 0.06
21 24 0.71
22 8 0.24
ACGTcount: A:0.68, C:0.00, G:0.31, T:0.02
Consensus pattern (20 bp):
AAAAAGAAGAAGAGAAGAAA
Found at i:12956459 original size:35 final size:35
Alignment explanation
Indices: 12956427--12956500 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
12956417 CCCGAAGAAG
*
12956427 AAAAAGAA-AAAAGGAAATAAGGAAAAAAGAAGAAAA
1 AAAAAGAAGAAAAAGAAA-AA-GAAAAAAGAAGAAAA
* *
12956463 AAAAAGAAGAAAAAGAGAAAGAAAAAAGAA-ATAA
1 AAAAAGAAGAAAAAGAAAAAGAAAAAAGAAGAAAA
12956497 AAAA
1 AAAA
12956501 GGGAAAAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
34 7 0.21
35 10 0.29
36 10 0.29
37 7 0.21
ACGTcount: A:0.80, C:0.00, G:0.18, T:0.03
Consensus pattern (35 bp):
AAAAAGAAGAAAAAGAAAAAGAAAAAAGAAGAAAA
Found at i:12956462 original size:32 final size:32
Alignment explanation
Indices: 12956421--12956508 Score: 101
Period size: 32 Copynumber: 2.8 Consensus size: 32
12956411 GTTCAGCCCG
12956421 AAGAAGAAAAAGAAAAAAGGAAATAAG-GAAA-A
1 AAGAAGAAAAA-AAAAAAGGAAA-AAGAGAAAGA
12956453 AAGAAGAAAAAAAAAGAA-GAAAAAGAGAAAGA
1 AAGAAGAAAAAAAAA-AAGGAAAAAGAGAAAGA
* * *
12956485 AAAAAGAAATAAAAAAGGGAAAAA
1 AAGAAGAAAAAAAAAAAGGAAAAA
12956509 AATATCACAG
Statistics
Matches: 49, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
30 3 0.06
31 13 0.27
32 33 0.67
ACGTcount: A:0.77, C:0.00, G:0.20, T:0.02
Consensus pattern (32 bp):
AAGAAGAAAAAAAAAAAGGAAAAAGAGAAAGA
Found at i:12956467 original size:13 final size:13
Alignment explanation
Indices: 12956449--12956489 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
12956439 GGAAATAAGG
12956449 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
12956462 AAAAAAGAAGAAA
1 AAAAAAGAAGAAA
12956475 AAGAGAAAGAA-AAA
1 AA-A-AAAGAAGAAA
12956489 A
1 A
12956490 GAAATAAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.58
14 5 0.19
15 6 0.23
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (13 bp):
AAAAAAGAAGAAA
Found at i:12956498 original size:22 final size:22
Alignment explanation
Indices: 12956421--12956492 Score: 78
Period size: 22 Copynumber: 3.2 Consensus size: 22
12956411 GTTCAGCCCG
12956421 AAGAAGAAAAAGAA-AAAAGGAAA
1 AAGAAGAAAAAGAAGAAAA--AAA
*
12956444 TAAGGA-AAAAAGAAGAAAAAAA
1 -AAGAAGAAAAAGAAGAAAAAAA
12956466 AAGAAGAAAAAG-AGAAAGAAAA
1 AAGAAGAAAAAGAAGAAA-AAAA
12956488 AAGAA
1 AAGAA
12956493 ATAAAAAAGG
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 9 0.21
22 18 0.42
23 8 0.19
24 8 0.19
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
AAGAAGAAAAAGAAGAAAAAAA
Found at i:12956499 original size:11 final size:10
Alignment explanation
Indices: 12956448--12956501 Score: 63
Period size: 11 Copynumber: 5.1 Consensus size: 10
12956438 AGGAAATAAG
*
12956448 GAAAAAAGAA
1 GAAAAAAAAA
12956458 GAAAAAAAAA
1 GAAAAAAAAA
*
12956468 GAAGAAAAAGA
1 GAA-AAAAAAA
12956479 GAAAGAAAAAA
1 GAAA-AAAAAA
12956490 GAAATAAAAAA
1 GAAA-AAAAAA
12956501 G
1 G
12956502 GGAAAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
10 13 0.34
11 25 0.66
ACGTcount: A:0.80, C:0.00, G:0.19, T:0.02
Consensus pattern (10 bp):
GAAAAAAAAA
Found at i:12956509 original size:11 final size:11
Alignment explanation
Indices: 12956449--12956510 Score: 56
Period size: 12 Copynumber: 5.5 Consensus size: 11
12956439 GGAAATAAGG
12956449 AAAAAAGAAGAA
1 AAAAAAG-AGAA
12956461 AAAAAA-AGAA
1 AAAAAAGAGAA
*
12956471 GAAAAAGAGAA
1 AAAAAAGAGAA
12956482 AGAAAAA-AGAAA
1 A-AAAAAGAG-AA
*
12956494 TAAAAAAGGGAA
1 -AAAAAAGAGAA
12956506 AAAAA
1 AAAAA
12956511 TATCACAGTC
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
10 9 0.21
11 11 0.26
12 20 0.48
13 2 0.05
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.02
Consensus pattern (11 bp):
AAAAAAGAGAA
Found at i:12956786 original size:16 final size:16
Alignment explanation
Indices: 12956765--12956816 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
12956755 AAAAAGAAGT
12956765 AAAAAAAGAAAAGAGA
1 AAAAAAAGAAAAGAGA
*
12956781 AAAAAAAGGAAAGAGA
1 AAAAAAAGAAAAGAGA
*
12956797 AAAAGAAAAAAAAG-GA
1 AAAA-AAAGAAAAGAGA
12956813 AAAA
1 AAAA
12956817 GGAAAAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
16 25 0.78
17 7 0.22
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAAAAGAGA
Found at i:12956806 original size:22 final size:22
Alignment explanation
Indices: 12956767--12956823 Score: 87
Period size: 22 Copynumber: 2.5 Consensus size: 22
12956757 AAAGAAGTAA
12956767 AAAAAGAAAAGAGAAAAAAAAGG
1 AAAAAGAAAA-AGAAAAAAAAGG
*
12956790 AAAGAGAAAAAGAAAAAAAAGG
1 AAAAAGAAAAAGAAAAAAAAGG
12956812 AAAAAGGAAAAA
1 AAAAA-GAAAAA
12956824 AAGGAAGGCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAGAAAAAAAAGG
Found at i:12956817 original size:16 final size:17
Alignment explanation
Indices: 12956755--12956826 Score: 69
Period size: 16 Copynumber: 4.4 Consensus size: 17
12956745 AGGCCAAAGG
*
12956755 AAAAAGAAGTAAAA-AAA
1 AAAAAG-AGAAAAAGAAA
*
12956772 GAAAAGAGAAAAA-AAA
1 AAAAAGAGAAAAAGAAA
**
12956788 GGAAAGAGAAAAAGAAA
1 AAAAAGAGAAAAAGAAA
*
12956805 AAAAAG-GAAAAAGGAA
1 AAAAAGAGAAAAAGAAA
12956821 AAAAAG
1 AAAAAG
12956827 GAAGGCTCGA
Statistics
Matches: 48, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
16 36 0.75
17 12 0.25
ACGTcount: A:0.78, C:0.00, G:0.21, T:0.01
Consensus pattern (17 bp):
AAAAAGAGAAAAAGAAA
Found at i:12956823 original size:38 final size:39
Alignment explanation
Indices: 12956750--12956829 Score: 110
Period size: 38 Copynumber: 2.1 Consensus size: 39
12956740 GTAGCAGGCC
12956750 AAAGGAAAAAGAAGTAAAAAAAGAAAAGAGAAAAAAAAGG
1 AAAGGAAAAAGAAG-AAAAAAAGAAAAGAGAAAAAAAAGG
* *
12956790 AAAGAGAAAAAGAA-AAAAAAGGAAAA-AGGAAAAAAAGG
1 AAAG-GAAAAAGAAGAAAAAAAGAAAAGAGAAAAAAAAGG
12956828 AA
1 AA
12956830 GGCTCGAGTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
38 13 0.35
39 11 0.30
40 4 0.11
41 9 0.24
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (39 bp):
AAAGGAAAAAGAAGAAAAAAAGAAAAGAGAAAAAAAAGG
Found at i:12957347 original size:17 final size:18
Alignment explanation
Indices: 12957327--12957368 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
12957317 GTACTTATTT
12957327 AAAAAAAATCGTG-TTTC
1 AAAAAAAATCGTGTTTTC
***
12957344 AAAAATTTTCGTGTTTTC
1 AAAAAAAATCGTGTTTTC
12957362 AAAAAAA
1 AAAAAAA
12957369 TTTCTCGTCT
Statistics
Matches: 19, Mismatches: 5, Indels: 1
0.76 0.20 0.04
Matches are distributed among these distances:
17 10 0.53
18 9 0.47
ACGTcount: A:0.48, C:0.10, G:0.10, T:0.33
Consensus pattern (18 bp):
AAAAAAAATCGTGTTTTC
Found at i:12957361 original size:18 final size:18
Alignment explanation
Indices: 12957335--12957664 Score: 221
Period size: 18 Copynumber: 18.2 Consensus size: 18
12957325 TTAAAAAAAA
12957335 TCGTG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
12957352 TCGTGTTTTCAAAAAAATTT
1 TCGTGTTTTC--AAAAATTT
*
12957372 CTCGT-CTTTCAAAAATTT
1 -TCGTGTTTTCAAAAATTT
* ***
12957390 CCGTGTTTTTTTTTTAAA--T
1 TCGTG---TTTTCAAAAATTT
* *
12957409 TCCTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
12957427 TCATG-TTTCAAAAATCT
1 TCGTGTTTTCAAAAATTT
12957444 TCGTGTTTTCAAAATATAATT
1 TCGTGTTTTCAAAA-AT--TT
**
12957465 TTATGTTTT-AAAAATTT
1 TCGTGTTTTCAAAAATTT
*
12957482 TCGTGTTTTCAAAAAAAATTC
1 TCGTGTTTTC---AAAAATTT
* *
12957503 CCGTGTTTTCAAAAATTC
1 TCGTGTTTTCAAAAATTT
* *
12957521 CCGTGTTTTCAAAAAATT
1 TCGTGTTTTCAAAAATTT
* * *
12957539 CCAT-TTTTCAAAATTTT
1 TCGTGTTTTCAAAAATTT
*
12957556 TCGTGTCTTCTAAAAATTT
1 TCGTGTTTTC-AAAAATTT
* * *
12957575 CCATG-TTTCTAAAATTT
1 TCGTGTTTTCAAAAATTT
*
12957592 TCATG-TTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
12957609 TCGTGTTTTCAAAAATTT
1 TCGTGTTTTCAAAAATTT
* * *
12957627 GCGTGTTTTCAACAATTC
1 TCGTGTTTTCAAAAATTT
*
12957645 TCGTGTTTT-ACAAATTT
1 TCGTGTTTTCAAAAATTT
12957662 TCG
1 TCG
12957665 CGCTTCAAAA
Statistics
Matches: 246, Mismatches: 46, Indels: 42
0.74 0.14 0.13
Matches are distributed among these distances:
16 7 0.03
17 78 0.32
18 93 0.38
19 18 0.07
20 16 0.07
21 34 0.14
ACGTcount: A:0.29, C:0.15, G:0.09, T:0.47
Consensus pattern (18 bp):
TCGTGTTTTCAAAAATTT
Found at i:12957435 original size:17 final size:17
Alignment explanation
Indices: 12957415--12957675 Score: 125
Period size: 17 Copynumber: 14.5 Consensus size: 17
12957405 AAATTCCTGT
*
12957415 TTTCAAAAATTCTCATG
1 TTTCAAAAATTCTCGTG
12957432 TTTCAAAAA-TCTTCGTG
1 TTTCAAAAATTC-TCGTG
* **
12957449 TTTTCAAAATATAATTTTATG
1 -TTTCAAAA-AT--TCTCGTG
* *
12957470 TTTTAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
*
12957487 TTTTCAAAAAAAATTCCCGTG
1 -TTTC---AAAAATTCTCGTG
*
12957508 TTTTCAAAAATTCCCGTG
1 -TTTCAAAAATTCTCGTG
* *
12957526 TTTTCAAAAAATTC-CATT
1 -TTTC-AAAAATTCTCGTG
* *
12957544 TTTCAAAATTTTTCGTG
1 TTTCAAAAATTCTCGTG
*
12957561 TCTTCTAAAAATT-TCCATG
1 T-TTC-AAAAATTCT-CGTG
* * *
12957580 TTTCTAAAATTTTCATG
1 TTTCAAAAATTCTCGTG
*
12957597 TTTCAAAAATTTTCGTG
1 TTTCAAAAATTCTCGTG
12957614 TTTTCAAAAATT-TGCGTG
1 -TTTCAAAAATTCT-CGTG
*
12957632 TTTTCAACAATTCTCGTG
1 -TTTCAAAAATTCTCGTG
* * * *
12957650 TTTTACAAATTTTCGCG
1 TTTCAAAAATTCTCGTG
*
12957667 CTTCAAAAA
1 TTTCAAAAA
12957676 AATCGGGTTT
Statistics
Matches: 195, Mismatches: 30, Indels: 38
0.74 0.11 0.14
Matches are distributed among these distances:
16 8 0.04
17 69 0.35
18 69 0.35
19 22 0.11
20 7 0.04
21 19 0.10
22 1 0.01
ACGTcount: A:0.31, C:0.15, G:0.09, T:0.44
Consensus pattern (17 bp):
TTTCAAAAATTCTCGTG
Found at i:12957649 original size:36 final size:36
Alignment explanation
Indices: 12957412--12957664 Score: 216
Period size: 35 Copynumber: 7.0 Consensus size: 36
12957402 TTTAAATTCC
*
12957412 TGTTTTCAAAAATTCTCATG-TTTCAAAAATCTTCG
1 TGTTTTCAAAAATTCTCATGTTTTCAAAAATTTTCG
* *
12957447 TGTTTTCAAAATATAATTTTATGTTTT-AAAAATTTTCG
1 TGTTTTCAAAA-AT--TCTCATGTTTTCAAAAATTTTCG
* * **
12957485 TGTTTTCAAAAAAAATTCCCGTGTTTTCAAAAATTCCCG
1 TGTTTTC---AAAAATTCTCATGTTTTCAAAAATTTTCG
*
12957524 TGTTTTCAAAAAATTC-CAT-TTTTCAAAATTTTTCG
1 TGTTTTC-AAAAATTCTCATGTTTTCAAAAATTTTCG
* * *
12957559 TGTCTTCTAAAAATT-TCCATG-TTTCTAAAATTTTCA
1 TGTTTTC-AAAAATTCT-CATGTTTTCAAAAATTTTCG
* * *
12957595 TG-TTTCAAAAATTTTCGTGTTTTCAAAAATTTGCG
1 TGTTTTCAAAAATTCTCATGTTTTCAAAAATTTTCG
* * *
12957630 TGTTTTCAACAATTCTCGTGTTTT-ACAAATTTTCG
1 TGTTTTCAAAAATTCTCATGTTTTCAAAAATTTTCG
12957665 CGCTTCAAAA
Statistics
Matches: 177, Mismatches: 27, Indels: 28
0.76 0.12 0.12
Matches are distributed among these distances:
34 10 0.06
35 64 0.36
36 40 0.23
37 9 0.05
38 29 0.16
39 19 0.11
40 2 0.01
41 4 0.02
ACGTcount: A:0.30, C:0.15, G:0.09, T:0.46
Consensus pattern (36 bp):
TGTTTTCAAAAATTCTCATGTTTTCAAAAATTTTCG
Found at i:12957823 original size:17 final size:16
Alignment explanation
Indices: 12957799--12957871 Score: 83
Period size: 17 Copynumber: 4.3 Consensus size: 16
12957789 NNNNNNTTCA
12957799 AAAATTTTCGTGTTTT
1 AAAATTTTCGTGTTTT
*
12957815 AAGAATTTTCGTGTCTCT
1 AA-AATTTTCGTGT-TTT
*
12957833 AAAATTCTCGTGTTTT
1 AAAATTTTCGTGTTTT
*
12957849 AAAAATTTTTCGTGTTTA
1 -AAAA-TTTTCGTGTTTT
12957867 AAAAT
1 AAAAT
12957872 AAAAATAAAA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
16 5 0.10
17 29 0.60
18 14 0.29
ACGTcount: A:0.30, C:0.10, G:0.12, T:0.48
Consensus pattern (16 bp):
AAAATTTTCGTGTTTT
Found at i:12957871 original size:34 final size:35
Alignment explanation
Indices: 12957798--12957871 Score: 100
Period size: 34 Copynumber: 2.2 Consensus size: 35
12957788 NNNNNNNTTC
* *
12957798 AAAAATTTTCGTGTTTTAAGAATTTTCGTGTCTCT
1 AAAAATTCTCGTGTTTTAAAAATTTTCGTGTCTCT
12957833 -AAAATTCTCGTGTTTTAAAAATTTTTCGTGT-T-T
1 AAAAATTCTCGTGTTTTAAAAA-TTTTCGTGTCTCT
12957866 AAAAAT
1 AAAAAT
12957872 AAAAATAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
33 1 0.03
34 25 0.71
35 9 0.26
ACGTcount: A:0.31, C:0.09, G:0.12, T:0.47
Consensus pattern (35 bp):
AAAAATTCTCGTGTTTTAAAAATTTTCGTGTCTCT
Found at i:12958313 original size:22 final size:20
Alignment explanation
Indices: 12958287--12958338 Score: 61
Period size: 22 Copynumber: 2.5 Consensus size: 20
12958277 CGCTACAACT
12958287 GAAATAAAAAAATTTTAAATG
1 GAAATAAAAAAA-TTTAAATG
**
12958308 AGAAATAATTAAATTTAAATG
1 -GAAATAAAAAAATTTAAATG
12958329 GAAA-AAAAAA
1 GAAATAAAAAA
12958339 TTAAATGAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 4 0.15
20 4 0.15
21 8 0.31
22 10 0.38
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.25
Consensus pattern (20 bp):
GAAATAAAAAAATTTAAATG
Found at i:12958363 original size:12 final size:11
Alignment explanation
Indices: 12958341--12958381 Score: 50
Period size: 10 Copynumber: 3.8 Consensus size: 11
12958331 AAAAAAAATT
12958341 AAATG-AATGG
1 AAATGAAATGG
12958351 AAATGGAAATGG
1 AAAT-GAAATGG
12958363 AAATGAAAT-G
1 AAATGAAATGG
*
12958373 AAATAAAAT
1 AAATGAAAT
12958382 AAGAAAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 13 0.46
11 6 0.21
12 9 0.32
ACGTcount: A:0.59, C:0.00, G:0.22, T:0.20
Consensus pattern (11 bp):
AAATGAAATGG
Done.