Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-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: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 186 of 206
Found at i:56648396 original size:2 final size:2
Alignment explanation
Indices: 56648389--56648422 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
56648379 TTATGTATTT
56648389 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
56648423 AGTTTTATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:56652200 original size:23 final size:24
Alignment explanation
Indices: 56652159--56652203 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
56652149 ATTTTTTAGT
*
56652159 TTTTTTTAATTTTAGGGAAAATCA
1 TTTTTTTAACTTTAGGGAAAATCA
56652183 TTTTTTTAACTTTA-GGAAAAT
1 TTTTTTTAACTTTAGGGAAAAT
56652204 TTAGGTTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.33, C:0.04, G:0.11, T:0.51
Consensus pattern (24 bp):
TTTTTTTAACTTTAGGGAAAATCA
Found at i:56656110 original size:27 final size:28
Alignment explanation
Indices: 56656062--56656129 Score: 104
Period size: 27 Copynumber: 2.5 Consensus size: 28
56656052 AAATAAAAAA
*
56656062 TTACCAAAATGT-TATAACTTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
*
56656089 TTACCAAAGTATATATAA-TTTTTTTAT
1 TTACCAAAATATATATAACTTTTTTTAT
56656116 TTACCAAAATATAT
1 TTACCAAAATATAT
56656130 CAAAAAAACT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
27 32 0.86
28 5 0.14
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (28 bp):
TTACCAAAATATATATAACTTTTTTTAT
Found at i:56656154 original size:18 final size:19
Alignment explanation
Indices: 56656131--56656174 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
56656121 AAAATATATC
56656131 AAAAAAACT-AAAAAACAA
1 AAAAAAACTAAAAAAACAA
56656149 AAAAAAA-TAAAAAAACAA
1 AAAAAAACTAAAAAAACAA
56656167 AAAAAAAC
1 AAAAAAAC
56656175 CTGAACCGAT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 1 0.04
18 23 0.96
ACGTcount: A:0.86, C:0.09, G:0.00, T:0.05
Consensus pattern (19 bp):
AAAAAAACTAAAAAAACAA
Found at i:56656350 original size:18 final size:17
Alignment explanation
Indices: 56656327--56656502 Score: 78
Period size: 18 Copynumber: 10.0 Consensus size: 17
56656317 GAAGGAGAGG
56656327 GGAAG-AAGAAGAAAGAAA
1 GGAAGAAAGAA-AAAG-AA
56656345 GGAAGAAAGAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* *
56656362 GG-A-AAAGGAAAGGAGA
1 GGAAGAAAGAAAAAGA-A
56656378 GGAAAGAAAGAAAAAGAA
1 GG-AAGAAAGAAAAAGAA
** *
56656396 GGAAAGAAAAGGAAAGGGGA
1 GG-AAG-AAA-GAAAAAGAA
*
56656416 GGAAAGAAAGAAAAATAA
1 GG-AAGAAAGAAAAAGAA
*
56656434 GGAAAGAAAAGGAAAGGAGAA
1 GG-AAG-AAA-GAAA-AAGAA
*
56656455 -G-AGAAAAAAAAAGAA
1 GGAAGAAAGAAAAAGAA
* **
56656470 AGAAG-AAGAAGAGGGAA
1 GGAAGAAAGAA-AAAGAA
*
56656487 GGAAGGAA-AAAAAGAA
1 GGAAGAAAGAAAAAGAA
56656503 AATAAGGTAA
Statistics
Matches: 123, Mismatches: 21, Indels: 30
0.71 0.12 0.17
Matches are distributed among these distances:
15 13 0.11
16 16 0.13
17 19 0.15
18 32 0.26
19 23 0.19
20 17 0.14
21 3 0.02
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.01
Consensus pattern (17 bp):
GGAAGAAAGAAAAAGAA
Found at i:56656360 original size:22 final size:23
Alignment explanation
Indices: 56656329--56656430 Score: 73
Period size: 24 Copynumber: 4.3 Consensus size: 23
56656319 AGGAGAGGGG
*
56656329 AAGAAGAAGAAAG-AAAGGAAGA
1 AAGAAAAAGAAAGAAAAGGAAGA
*
56656351 AAGAAAAAGAAGGAAAAGGAA-A
1 AAGAAAAAGAAAGAAAAGGAAGA
* * *
56656373 GGAGAGGAAAGAAAGAAAAAGAAGGA
1 -AAGA-AAAAGAAAGAAAAGGAA-GA
* ***
56656399 AAGAAAAGGAAAGGGGAGGAAAGA
1 AAGAAAAAGAAAGAAAAGG-AAGA
56656423 AAGAAAAA
1 AAGAAAAA
56656431 TAAGGAAAGA
Statistics
Matches: 60, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
22 12 0.20
23 10 0.17
24 32 0.53
25 5 0.08
26 1 0.02
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (23 bp):
AAGAAAAAGAAAGAAAAGGAAGA
Found at i:56656387 original size:28 final size:28
Alignment explanation
Indices: 56656332--56656411 Score: 85
Period size: 34 Copynumber: 2.8 Consensus size: 28
56656322 AGAGGGGAAG
56656332 AAGAA-GAAAG-AAAGG-AAGAAAGAAA
1 AAGAAGGAAAGAAAAGGAAAGAAAGAAA
56656357 AAGAAGGAAAAGGAAAGGAGAGGAAAGAAAGAAA
1 AAGAAGG-AAA-G-AA--A-AGGAAAGAAAGAAA
56656391 AAGAAGGAAAGAAAAGGAAAG
1 AAGAAGGAAAGAAAAGGAAAG
56656412 GGGAGGAAAG
Statistics
Matches: 46, Mismatches: 0, Indels: 15
0.75 0.00 0.25
Matches are distributed among these distances:
25 5 0.11
26 1 0.02
27 3 0.07
28 8 0.17
29 1 0.02
30 1 0.02
31 2 0.04
32 2 0.04
33 6 0.13
34 17 0.37
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAGAAAAGGAAAGAAAGAAA
Found at i:56656405 original size:38 final size:36
Alignment explanation
Indices: 56656347--56656504 Score: 171
Period size: 38 Copynumber: 4.3 Consensus size: 36
56656337 GAAAGAAAGG
56656347 AAGAAAGAAAAAGAAG--GAAAAGGAAAGGAGAGGA
1 AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
*
56656381 AAGAAAGAAAAAGAAGGAAAGAAAAGGAAAGGGGAGGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAGAGGA
*
56656419 AAGAAAGAAAAATAAGGAAAGAAAAGGAAAGGAGAAGAGA
1 AAGAAAGAAAAAGAA-G-AAGAAAAGGAAAGGAG-AG-GA
* * *
56656459 AA-AAAAAAGAAAGAAGAAGAAGAGGGAAGGA-AGGA
1 AAGAAAGAA-AAAGAAGAAGAAAAGGAAAGGAGAGGA
*
56656494 AAAAAAGAAAA
1 AAGAAAGAAAA
56656505 TAAGGTAATT
Statistics
Matches: 108, Mismatches: 8, Indels: 15
0.82 0.06 0.11
Matches are distributed among these distances:
34 15 0.14
35 7 0.06
36 7 0.06
38 62 0.57
39 8 0.07
40 9 0.08
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (36 bp):
AAGAAAGAAAAAGAAGAAGAAAAGGAAAGGAGAGGA
Found at i:56656407 original size:10 final size:10
Alignment explanation
Indices: 56656349--56656473 Score: 82
Period size: 10 Copynumber: 12.7 Consensus size: 10
56656339 AAGAAAGGAA
*
56656349 GAAAGAAAAA
1 GAAAGAAAAG
*
56656359 GAAGGAAAAG
1 GAAAGAAAAG
* *
56656369 GAAAGGAGAG
1 GAAAGAAAAG
56656379 GAAAG-AAA-
1 GAAAGAAAAG
56656387 GAAA-AAGAAG
1 GAAAGAA-AAG
56656397 GAAAGAAAAG
1 GAAAGAAAAG
***
56656407 GAAAGGGGAG
1 GAAAGAAAAG
56656417 GAAAG-AAA-
1 GAAAGAAAAG
56656425 GAAA-AATAAG
1 GAAAGAA-AAG
56656435 GAAAGAAAAG
1 GAAAGAAAAG
*
56656445 GAAAGGAGAAG
1 GAAA-GAAAAG
* *
56656456 AGAAAAAAAAA
1 -GAAAGAAAAG
56656467 GAAAGAA
1 GAAAGAA
56656474 GAAGAAGAGG
Statistics
Matches: 89, Mismatches: 16, Indels: 20
0.71 0.13 0.16
Matches are distributed among these distances:
8 10 0.11
9 7 0.08
10 56 0.63
11 12 0.13
12 4 0.04
ACGTcount: A:0.67, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
GAAAGAAAAG
Found at i:56656471 original size:32 final size:33
Alignment explanation
Indices: 56656420--56656503 Score: 88
Period size: 32 Copynumber: 2.6 Consensus size: 33
56656410 AGGGGAGGAA
* *
56656420 AGAA-AGAAAAATAAGGAAAGAA-AAGGAA-AGG
1 AGAAGAGAAAAAAAAAGAAAGAAGAA-GAAGAGG
56656451 AGAAGAGAAAAAAAAAGAAAGAAGAAGAAGAGG
1 AGAAGAGAAAAAAAAAGAAAGAAGAAGAAGAGG
56656484 -GAAG-GAAGGAAAAAAAGAAA
1 AGAAGAGAA--AAAAAAAGAAA
56656504 ATAAGGTAAT
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
31 7 0.15
32 23 0.50
33 16 0.35
ACGTcount: A:0.69, C:0.00, G:0.30, T:0.01
Consensus pattern (33 bp):
AGAAGAGAAAAAAAAAGAAAGAAGAAGAAGAGG
Found at i:56656478 original size:10 final size:10
Alignment explanation
Indices: 56656329--56656479 Score: 59
Period size: 10 Copynumber: 15.1 Consensus size: 10
56656319 AGGAGAGGGG
56656329 AAGAAGAAGA
1 AAGAAGAAGA
56656339 AAGAAAGGAAGA
1 AAG-AA-GAAGA
*
56656351 AAGAAAAAGA
1 AAGAAGAAGA
*
56656361 AGGAA-AAGGA
1 AAGAAGAA-GA
* *
56656371 AAGGAGAGGA
1 AAGAAGAAGA
56656381 AAG-A-AAGA
1 AAGAAGAAGA
56656389 AA-AAGAAGGA
1 AAGAAGAA-GA
56656399 AAGAA-AAGGA
1 AAGAAGAA-GA
** *
56656409 AAGGGGAGGA
1 AAGAAGAAGA
56656419 AAG-A-AAGA
1 AAGAAGAAGA
*
56656427 AA-AATAAGGA
1 AAGAAGAA-GA
56656437 AAGAA-AAGGA
1 AAGAAGAA-GA
*
56656447 AAGGAGAAGAGA
1 AAGAAG-A-AGA
* *
56656459 AAAAAAAAGA
1 AAGAAGAAGA
56656469 AAGAAGAAGA
1 AAGAAGAAGA
56656479 A
1 A
56656480 GAGGGAAGGA
Statistics
Matches: 108, Mismatches: 17, Indels: 32
0.69 0.11 0.20
Matches are distributed among these distances:
8 12 0.11
9 7 0.06
10 63 0.58
11 11 0.10
12 14 0.13
13 1 0.01
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.01
Consensus pattern (10 bp):
AAGAAGAAGA
Found at i:56657308 original size:19 final size:18
Alignment explanation
Indices: 56657268--56657318 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
56657258 AAAAAATATA
**
56657268 TAATATTTTGGTATTTTT
1 TAATATTTTATTATTTTT
56657286 TAATATTTTATTATTTTT
1 TAATATTTTATTATTTTT
*
56657304 GTAATGTTTTATTAT
1 -TAATATTTTATTAT
56657319 GGGTTTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 16 0.55
19 13 0.45
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TAATATTTTATTATTTTT
Found at i:56657401 original size:29 final size:27
Alignment explanation
Indices: 56657357--56657422 Score: 107
Period size: 27 Copynumber: 2.4 Consensus size: 27
56657347 AAAAAATTAT
56657357 CAAAATAT-TATAATTTTTTTTTATTTAC
1 CAAAATATATATAA--TTTTTTTATTTAC
56657385 CAAAATATATATAATTTTTTTATTTAC
1 CAAAATATATATAATTTTTTTATTTAC
56657412 CAAAATATATA
1 CAAAATATATA
56657423 AAAAAACTAA
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
27 24 0.65
28 8 0.22
29 5 0.14
ACGTcount: A:0.42, C:0.08, G:0.00, T:0.50
Consensus pattern (27 bp):
CAAAATATATATAATTTTTTTATTTAC
Found at i:56657443 original size:18 final size:19
Alignment explanation
Indices: 56657422--56657465 Score: 74
Period size: 18 Copynumber: 2.4 Consensus size: 19
56657412 CAAAATATAT
56657422 AAAAAAACTAAAAAACA-A
1 AAAAAAACTAAAAAACAGA
56657440 AAAAAAA-TAAAAAACAGA
1 AAAAAAACTAAAAAACAGA
56657458 AAAAAAAC
1 AAAAAAAC
56657466 ACATTAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.84, C:0.09, G:0.02, T:0.05
Consensus pattern (19 bp):
AAAAAAACTAAAAAACAGA
Found at i:56657444 original size:17 final size:18
Alignment explanation
Indices: 56657422--56657464 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
56657412 CAAAATATAT
*
56657422 AAAAAAACTAAAAAACA-
1 AAAAAAAATAAAAAACAG
56657439 AAAAAAAATAAAAAACAG
1 AAAAAAAATAAAAAACAG
56657457 AAAAAAAA
1 AAAAAAAA
56657465 CACATTAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 16 0.67
18 8 0.33
ACGTcount: A:0.86, C:0.07, G:0.02, T:0.05
Consensus pattern (18 bp):
AAAAAAAATAAAAAACAG
Found at i:56658786 original size:17 final size:17
Alignment explanation
Indices: 56658764--56658800 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
56658754 ATGGGGTAAG
56658764 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
56658781 ATGCTATTCTAATATTC
1 ATGCTATTCTAATATTC
56658798 ATG
1 ATG
56658801 ACATCTTACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.30, C:0.16, G:0.08, T:0.46
Consensus pattern (17 bp):
ATGCTATTCTAATATTC
Found at i:56661944 original size:82 final size:82
Alignment explanation
Indices: 56661802--56661971 Score: 313
Period size: 82 Copynumber: 2.1 Consensus size: 82
56661792 ATATTCATGC
*
56661802 AAAAATATTAAAATAAATTTGTCTTTAAATCGGATTTGTGGTTACGAAACCACTATTCCGATAAC
1 AAAACTATTAAAATAAATTTGTCTTTAAATCGGATTTGTGGTTACGAAACCACTATTCCGATAAC
56661867 TTTGAATTTGGGCCATT
66 TTTGAATTTGGGCCATT
*
56661884 AAAACTATTAAAATAAATTTGTCTTTAAATCGGATTTGTGGTTACGAAACCACTATTCCGATATC
1 AAAACTATTAAAATAAATTTGTCTTTAAATCGGATTTGTGGTTACGAAACCACTATTCCGATAAC
56661949 TTTGAATTTGGGCCATT
66 TTTGAATTTGGGCCATT
*
56661966 ACAACT
1 AAAACT
56661972 CTCTCCCCTT
Statistics
Matches: 85, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (82 bp):
AAAACTATTAAAATAAATTTGTCTTTAAATCGGATTTGTGGTTACGAAACCACTATTCCGATAAC
TTTGAATTTGGGCCATT
Found at i:56666296 original size:17 final size:17
Alignment explanation
Indices: 56666270--56666303 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
56666260 GGAGGAGGAC
56666270 CCTTTAAAGGTCCCGCT
1 CCTTTAAAGGTCCCGCT
*
56666287 CCTTTGAAGGTCCCGCT
1 CCTTTAAAGGTCCCGCT
56666304 TATCTACTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.15, C:0.35, G:0.21, T:0.29
Consensus pattern (17 bp):
CCTTTAAAGGTCCCGCT
Found at i:56671565 original size:3 final size:3
Alignment explanation
Indices: 56671557--56671606 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
56671547 AGTAACATCT
56671557 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
56671605 TA
1 TA
56671607 CTACTACTAC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:56671611 original size:3 final size:3
Alignment explanation
Indices: 56671605--56671633 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
56671595 ATAATAATAA
56671605 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
1 TAC TAC TAC TAC TAC TAC TAC TAC TAC TA
56671634 TAAAATTTTT
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:0.34, C:0.31, G:0.00, T:0.34
Consensus pattern (3 bp):
TAC
Found at i:56671961 original size:27 final size:27
Alignment explanation
Indices: 56671919--56672019 Score: 94
Period size: 27 Copynumber: 3.7 Consensus size: 27
56671909 AACACGAGTA
* ** *
56671919 GTGCCGCCAATCTGGTTGGCAGGACTG
1 GTGCCGCCAACCTGGTTCCCACGACTG
* *
56671946 GTGTCGCCAACCTGGTTCCCTCGACTG
1 GTGCCGCCAACCTGGTTCCCACGACTG
* ** **
56671973 GTGCCGCCAACCTGCTTCCCTTGTTTG
1 GTGCCGCCAACCTGGTTCCCACGACTG
*
56672000 GTGCCGCCAACCTGCTTCCC
1 GTGCCGCCAACCTGGTTCCC
56672020 TCCACCCAAT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 63 1.00
ACGTcount: A:0.11, C:0.37, G:0.27, T:0.26
Consensus pattern (27 bp):
GTGCCGCCAACCTGGTTCCCACGACTG
Found at i:56672020 original size:27 final size:27
Alignment explanation
Indices: 56671941--56672021 Score: 117
Period size: 27 Copynumber: 3.0 Consensus size: 27
56671931 TGGTTGGCAG
* *
56671941 GACTGGTGTCGCCAACCTGGTTCCCTC
1 GACTGGTGCCGCCAACCTGCTTCCCTC
*
56671968 GACTGGTGCCGCCAACCTGCTTCCCTT
1 GACTGGTGCCGCCAACCTGCTTCCCTC
**
56671995 GTTTGGTGCCGCCAACCTGCTTCCCTC
1 GACTGGTGCCGCCAACCTGCTTCCCTC
56672022 CACCCAATGA
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 48 1.00
ACGTcount: A:0.10, C:0.40, G:0.23, T:0.27
Consensus pattern (27 bp):
GACTGGTGCCGCCAACCTGCTTCCCTC
Found at i:56672115 original size:27 final size:29
Alignment explanation
Indices: 56672085--56672153 Score: 108
Period size: 28 Copynumber: 2.5 Consensus size: 29
56672075 AGTTTTTTTG
56672085 ATATATTTTGGTAAAT-AAAAAAA-TTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
56672112 ATATATTTTGGTAAATAAAAAAAAGTTAT
1 ATATATTTTGGTAAATAAAAAAAAGTTAT
*
56672141 A-ACATTTTGGTAA
1 ATATATTTTGGTAA
56672154 TTTTTTTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
27 16 0.41
28 18 0.46
29 5 0.13
ACGTcount: A:0.49, C:0.01, G:0.10, T:0.39
Consensus pattern (29 bp):
ATATATTTTGGTAAATAAAAAAAAGTTAT
Found at i:56672658 original size:19 final size:20
Alignment explanation
Indices: 56672620--56672660 Score: 57
Period size: 19 Copynumber: 2.1 Consensus size: 20
56672610 TTTGGAGTTC
56672620 ACTAGTCGAATTAAAAAAAA
1 ACTAGTCGAATTAAAAAAAA
* *
56672640 ACTAGT-GACTTAAATAAAA
1 ACTAGTCGAATTAAAAAAAA
56672659 AC
1 AC
56672661 ATTCAAATAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.56, C:0.12, G:0.10, T:0.22
Consensus pattern (20 bp):
ACTAGTCGAATTAAAAAAAA
Found at i:56673592 original size:21 final size:21
Alignment explanation
Indices: 56673566--56673645 Score: 90
Period size: 21 Copynumber: 3.8 Consensus size: 21
56673556 GAATGTAGAA
* *
56673566 GCAGTGAAGCAAGGTGAAAAG
1 GCAGTGAACCAAAGTGAAAAG
56673587 GCAGTGAACCAAAGTGAAAAG
1 GCAGTGAACCAAAGTGAAAAG
* *
56673608 GCTGTGAACCAAAATG-AAAG
1 GCAGTGAACCAAAGTGAAAAG
**
56673628 AATAGTGAACCAAAGTGA
1 -GCAGTGAACCAAAGTGA
56673646 GGAAGCGTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
20 4 0.08
21 45 0.92
ACGTcount: A:0.46, C:0.12, G:0.29, T:0.12
Consensus pattern (21 bp):
GCAGTGAACCAAAGTGAAAAG
Found at i:56676631 original size:24 final size:24
Alignment explanation
Indices: 56676588--56676633 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56676578 CATAGCCCCA
* *
56676588 AAACACAAAAAGCAGGCATCTAAG
1 AAACACAAAAAGAACGCATCTAAG
*
56676612 AAACACAAAAAGAACTCATCTA
1 AAACACAAAAAGAACGCATCTA
56676634 CAGGTCCTGC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.22, G:0.11, T:0.11
Consensus pattern (24 bp):
AAACACAAAAAGAACGCATCTAAG
Found at i:56686061 original size:50 final size:50
Alignment explanation
Indices: 56686000--56686114 Score: 203
Period size: 50 Copynumber: 2.3 Consensus size: 50
56685990 TAAAAATTAA
56686000 AAAAGTATTTTAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAAGTATTTTAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
* *
56686050 AAAAGTATTTTAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
1 AAAAGTATTTTAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
*
56686100 AAAAATATTTTAAAA
1 AAAAGTATTTTAAAA
56686115 TTAAAAAATT
Statistics
Matches: 62, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
50 62 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (50 bp):
AAAAGTATTTTAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
Found at i:56686093 original size:39 final size:39
Alignment explanation
Indices: 56685985--56686131 Score: 158
Period size: 39 Copynumber: 3.7 Consensus size: 39
56685975 TACTAAAATT
*
56685985 TATTTTAAAAATTAAAAAAGTATTTTAAAAA--ATTTTAAAA
1 TATTTT-AAAATTAAAAAA--ATTTAAAAAAGTATTTTAAAA
*** **
56686025 T-TAAAAAAATTAAAAAAAGTATTTTAAAAGTATTTTAAAA
1 TATTTTAAAATTAAAAAAA-T-TTAAAAAAGTATTTTAAAA
56686065 TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT-AAAA
56686105 TATTTTAAAATT-AAAAAATTTAAAAAA
1 TATTTTAAAATTAAAAAAATTTAAAAAA
56686132 ATAAATATAT
Statistics
Matches: 92, Mismatches: 9, Indels: 13
0.81 0.08 0.11
Matches are distributed among these distances:
36 1 0.01
37 1 0.01
38 19 0.21
39 29 0.32
40 28 0.30
41 14 0.15
ACGTcount: A:0.60, C:0.00, G:0.03, T:0.37
Consensus pattern (39 bp):
TATTTTAAAATTAAAAAAATTTAAAAAAGTATTTTAAAA
Found at i:56686103 original size:11 final size:11
Alignment explanation
Indices: 56686038--56686114 Score: 67
Period size: 11 Copynumber: 7.4 Consensus size: 11
56686028 AAAAAATTAA
56686038 AAAAAGTATTTT
1 AAAAA-TATTTT
*
56686050 AAAAGTATTTT
1 AAAAATATTTT
56686061 -AAAATATTTT
1 AAAAATATTTT
56686071 --AAA-A--TT
1 AAAAATATTTT
* *
56686077 AAAAAAATTTA
1 AAAAATATTTT
56686088 AAAAAGTATTTT
1 AAAAA-TATTTT
56686100 AAAAATATTTT
1 AAAAATATTTT
56686111 AAAA
1 AAAA
56686115 TTAAAAAATT
Statistics
Matches: 54, Mismatches: 5, Indels: 13
0.75 0.07 0.18
Matches are distributed among these distances:
6 2 0.04
8 4 0.07
9 4 0.07
10 9 0.17
11 22 0.41
12 13 0.24
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:56686131 original size:17 final size:17
Alignment explanation
Indices: 56686061--56686144 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 17
56686051 AAAGTATTTT
*
56686061 AAAATATTTTAAAATTA
1 AAAATATTTAAAAATTA
*
56686078 AAAAAATTTAAAAAAGTATTTTA
1 AAAATATTT--AAAA--A--TTA
*
56686101 AAAATATTTTAAAATTA
1 AAAATATTTAAAAATTA
*
56686118 AAAA-ATTTAAAAAAATA
1 AAAATATTT-AAAAATTA
*
56686135 AATATATTTA
1 AAAATATTTA
56686145 TTATATCGGG
Statistics
Matches: 52, Mismatches: 7, Indels: 16
0.69 0.09 0.21
Matches are distributed among these distances:
16 4 0.08
17 25 0.48
18 4 0.08
19 4 0.08
21 4 0.08
23 11 0.21
ACGTcount: A:0.62, C:0.00, G:0.01, T:0.37
Consensus pattern (17 bp):
AAAATATTTAAAAATTA
Found at i:56686131 original size:50 final size:50
Alignment explanation
Indices: 56685999--56686133 Score: 175
Period size: 50 Copynumber: 2.7 Consensus size: 50
56685989 TTAAAAATTA
* **
56685999 AAAAAGTATTTTAAAAAATTTTAAAATTAAAAAAATTAAAAAAAGTATTTT
1 AAAAA-TATTTTAAAATATTAAAAAATTAAAAAAATTAAAAAAAGTATTTT
* ** *
56686050 AAAAGTATTTTAAAATATTTTAAAATTAAAAAAATTTAAAAAAGTATTTT
1 AAAAATATTTTAAAATATTAAAAAATTAAAAAAATTAAAAAAAGTATTTT
56686100 AAAAATATTTT-AAA-ATTAAAAAATTTAAAAAAAT
1 AAAAATATTTTAAAATATTAAAAAA-TTAAAAAAAT
56686134 AAATATATTT
Statistics
Matches: 77, Mismatches: 6, Indels: 4
0.89 0.07 0.05
Matches are distributed among these distances:
48 7 0.09
49 13 0.17
50 53 0.69
51 4 0.05
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (50 bp):
AAAAATATTTTAAAATATTAAAAAATTAAAAAAATTAAAAAAAGTATTTT
Found at i:56687857 original size:18 final size:17
Alignment explanation
Indices: 56687836--56687870 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
56687826 TTATTATTAA
*
56687836 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
56687854 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
56687871 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:56688355 original size:24 final size:25
Alignment explanation
Indices: 56688309--56688356 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
56688299 TATGAATTTG
56688309 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
56688335 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
56688357 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:56688484 original size:92 final size:92
Alignment explanation
Indices: 56688284--56688492 Score: 273
Period size: 92 Copynumber: 2.3 Consensus size: 92
56688274 NNNNNNNNNC
* * * * * *
56688284 TAATAAATTATATTTTATGAATTTGTATAATTTAAAATAATAATTATTACATATAATTTAATAAT
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAAT
* *
56688349 TAATATTAAATTTCATAAAATTCTTGA
66 GAATATTAAATTTCATAAAATTCTTAA
*
56688376 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAA-TATTAAATATAATTTAATAG
1 TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAA-TAATTATTAAATATAATTTAATAA
56688440 TG-ATA-TATAATTTCATAAAATTCTTAA
65 TGAATATTA-AATTTCATAAAATTCTTAA
56688467 TAATAAAATGTTT-TTATATGAATTTA
1 TAAT-AAAT-TTTCTTATATGAATTTA
56688493 CTAAAATCAA
Statistics
Matches: 104, Mismatches: 9, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
90 2 0.02
91 25 0.24
92 71 0.68
93 6 0.06
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (92 bp):
TAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATAATTATTAAATATAATTTAATAAT
GAATATTAAATTTCATAAAATTCTTAA
Found at i:56695956 original size:18 final size:17
Alignment explanation
Indices: 56695926--56695959 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
56695916 ATAATTGTAA
56695926 TTTAAAGTCTAATTATT
1 TTTAAAGTCTAATTATT
*
56695943 TTTAAGAGTGTAATTAT
1 TTTAA-AGTCTAATTAT
56695960 CACAATTTCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.35, C:0.03, G:0.12, T:0.50
Consensus pattern (17 bp):
TTTAAAGTCTAATTATT
Found at i:56696160 original size:6 final size:6
Alignment explanation
Indices: 56696146--56696177 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
56696136 TTATATATAT
*
56696146 TATATA TATAGA TATAGA TATAGA TATAGA TA
1 TATAGA TATAGA TATAGA TATAGA TATAGA TA
56696178 AAACATTAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (6 bp):
TATAGA
Found at i:56696714 original size:27 final size:27
Alignment explanation
Indices: 56696684--56696751 Score: 70
Period size: 26 Copynumber: 2.6 Consensus size: 27
56696674 ATTTGATATA
56696684 TTAATATAATAAATATAAT-TTATC-ATT
1 TTAATATAATAAAT-TAATATT-TCAATT
*
56696711 TTAATA-AATTAATTAATATTTCAATT
1 TTAATATAATAAATTAATATTTCAATT
* *
56696737 TTATTTTAATAAATT
1 TTAATATAATAAATT
56696752 TTAAAAATAA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 6 0.18
26 15 0.44
27 13 0.38
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
TTAATATAATAAATTAATATTTCAATT
Found at i:56696764 original size:16 final size:16
Alignment explanation
Indices: 56696743--56696776 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 16
56696733 AATTTTATTT
56696743 TAATAAATTTTAAA-AA
1 TAAT-AATTTTAAATAA
56696759 TAATAATTTTAAATAA
1 TAATAATTTTAAATAA
56696775 TA
1 TA
56696777 TTATTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TAATAATTTTAAATAA
Found at i:56701753 original size:17 final size:19
Alignment explanation
Indices: 56701726--56701764 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
56701716 CGTTAGAAAC
*
56701726 TTTTATTTATATAAT-TAA
1 TTTTATTTATACAATATAA
56701744 TTTT-TTTATACAATATAA
1 TTTTATTTATACAATATAA
56701762 TTT
1 TTT
56701765 CAAACCCACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTTATTTATACAATATAA
Found at i:56707330 original size:125 final size:125
Alignment explanation
Indices: 56707006--56707382 Score: 589
Period size: 123 Copynumber: 3.0 Consensus size: 125
56706996 TTAGGGTTTT
* **** * *
56707006 TAGGTCTTGGAAGAAATAATTTCGAGTTGACGTTTCTGATCAAATAGTATAAAATCGCTTCTAGC
1 TAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGC
* * *
56707071 AAGATTCTATTTGAGAAGAATTTGTGAAATCACGCCCTCGTGGACGCGCTTTTGCTA-AG
66 AAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
56707130 TAGGTCATGGAAGAAAT-ACTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGC
1 TAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGC
*
56707194 AGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
66 AAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
56707254 TCA-GTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAG
1 T-AGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAG
* *
56707318 CATGATGCTATTTGAGAAGAATTTGTGAAAATCGCACCCTCGTGGACGCGCTTTTGCTACAG
65 CAAGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
56707380 TAG
1 TAG
56707383 CATGTTTGGG
Statistics
Matches: 233, Mismatches: 15, Indels: 8
0.91 0.06 0.03
Matches are distributed among these distances:
123 93 0.40
124 33 0.14
125 72 0.31
126 35 0.15
ACGTcount: A:0.29, C:0.16, G:0.22, T:0.33
Consensus pattern (125 bp):
TAGGTCATGGAAGAAATAATTTTTTTTTGACGTTTCTGAGCAAATAGTATAAAATCGCTTTTAGC
AAGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
Found at i:56710573 original size:17 final size:17
Alignment explanation
Indices: 56710506--56710573 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
56710496 TATGTGAATG
*
56710506 TAAAATTATTAATT-GA
1 TAAAATTATTAATTATA
* *
56710522 TAAATTGTATTAATGATTA
1 TAAAAT-TATTAATTA-TA
*
56710541 GTAAAATTATCAAATTATA
1 -TAAAATTAT-TAATTATA
56710560 TAAAATTATTAATT
1 TAAAATTATTAATT
56710574 GTTAGGACTA
Statistics
Matches: 40, Mismatches: 7, Indels: 9
0.71 0.12 0.16
Matches are distributed among these distances:
16 5 0.12
17 11 0.28
18 9 0.22
19 6 0.15
20 9 0.22
ACGTcount: A:0.49, C:0.01, G:0.06, T:0.44
Consensus pattern (17 bp):
TAAAATTATTAATTATA
Found at i:56710595 original size:115 final size:116
Alignment explanation
Indices: 56710392--56710634 Score: 434
Period size: 115 Copynumber: 2.1 Consensus size: 116
56710382 TAAGTTTGTG
*
56710392 AAATTATTAATTGATAAATTGTATTAATGGTTAGTTAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTTAAAATTATCAAATTATATAAAATTATTAA
* *
56710457 TTGTTAGTACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAATGTA
66 TTGTTAGGACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
56710508 AAATTATTAATTGATAAATTGTATTAATGATTAG-TAAAATTATCAAATTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTTAAAATTATCAAATTATATAAAATTATTAA
*
56710572 TTGTTAGGACTAGTCAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGGACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
*
56710623 AAGTTATTAATT
1 AAATTATTAATT
56710635 TAGTTTATGG
Statistics
Matches: 122, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
115 89 0.73
116 33 0.27
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.40
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTTAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGGACCAGTCAAAACATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:56710665 original size:28 final size:23
Alignment explanation
Indices: 56710628--56711372 Score: 312
Period size: 23 Copynumber: 33.1 Consensus size: 23
56710618 AAGTAAAGTT
* * *
56710628 ATTAATTTAGTTTATGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
56710651 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
56710674 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* * **
56710697 AGTGAA-GGGTGTTAGGGTTTTTA
1 ATTAAATTAG-GTTAGGGTTTTTA
* * *
56710720 AGT---TTA-G---GGTTTTTAA
1 ATTAAATTAGGTTAGGGTTTTTA
* * ** * * * *
56710736 TTTAATTAGGTTTGGGTTTTTAA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
56710759 GTTAAT-TAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* **
56710781 AGT---TTAGGGTTTAAAGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
* *
56710803 ATTTAATTACGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
56710826 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*** **
56710849 AGTTAAGGGA-GTTA-ATTTATTTA
1 A-TTAAATTAGGTTAGGGTT-TTTA
56710872 AGTTAATTAGGTTAGGGTTTAGGGTTTTTA
1 A-TTAA--A--TTA-GG-TTAGGGTTTTTA
*
56710902 ATTAAATTAGGTTAGAGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
56710925 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
56710948 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
* *
56710971 AGTT-AA-GAGGTT-GAGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
56710992 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*
56711015 AGTTAAGA--GGGTTAGGGTTTTTA
1 A-TTAA-ATTAGGTTAGGGTTTTTA
* * *
56711038 AGT---TTA-G---GGTTTTTAA
1 ATTAAATTAGGTTAGGGTTTTTA
* * * *
56711054 TTAAATTAA-GTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
56711076 AGTT-AATTAGGTTAGAGTTTTAA
1 A-TTAAATTAGGTTAGGGTTTTTA
** *
56711099 AGTTAAA-GGGGTTAGAGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
* *
56711122 AGT---TTAGAGTTTAAGGTTTTTA
1 ATTAAATTAG-G-TTAGGGTTTTTA
56711144 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*
56711167 AGT---TTAGGATTTAGGG-TTTTA
1 ATTAAATTAGG--TTAGGGTTTTTA
56711188 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
56711211 AGT---TTAGGGTTTAGGGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
* *
56711233 ATTAAATTAGATTAGGGTTTGTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
56711256 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
56711279 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
***
56711302 AGTT-AAGGGGGTTAGGGTTTTT-
1 A-TTAAATTAGGTTAGGGTTTTTA
*
56711324 ATGT---TTAGGGTTTAAAGG-TTTTA
1 AT-TAAATTA-GG-TT-AGGGTTTTTA
56711347 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
56711370 ATT
1 ATT
56711373 TAAGGGTAAT
Statistics
Matches: 559, Mismatches: 94, Indels: 138
0.71 0.12 0.17
Matches are distributed among these distances:
16 15 0.03
19 6 0.01
20 11 0.02
21 29 0.05
22 98 0.18
23 343 0.61
24 23 0.04
25 17 0.03
27 2 0.00
29 5 0.01
30 8 0.01
31 2 0.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (23 bp):
ATTAAATTAGGTTAGGGTTTTTA
Found at i:56710696 original size:46 final size:46
Alignment explanation
Indices: 56710629--56711372 Score: 480
Period size: 46 Copynumber: 16.5 Consensus size: 46
56710619 AGTAAAGTTA
* *
56710629 TTAATTTAGTTTATGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
1 TTAA-TTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
* * **
56710676 TTAATTAGGTTAGGGTTTTTAAGTGAA-GGGTGTTAGGG---TT--T
1 TTAATTAGGTTAGGGTTTTTAATTAAATTAG-GTTAGGGTTTTTAAT
* * * *
56710717 TT-A--AGTTTAGGGTTTTTAATTTAATTAGGTTTGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
* **
56710760 TTAATTAGGTTAGGGTTTTTAAGT---TTAGGGTTTAAAGTTTTTAAT
1 TTAATTAGGTTAGGGTTTTTAATTAAATTA-GG-TTAGGGTTTTTAAT
* *
56710805 TTAATTACGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAT
** **
56710851 TTAA-GGGAGTTA-ATTTATTTAAGTTAATTAGGTTAGGGTTTAGGGTTTTTAAT
1 TTAATTAG-GTTAGGGTT-TTTAA-TTAA--A--TTA-GG-TTAGGGTTTTTAAT
* * * *
56710904 TAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
* * *
56710950 TTAATTAGGTTAGGGTTTTTAAGTT-AA-GAGGTT-GAGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAT
*
56710994 TTAATTAGGTTAGGGTTTTTAAGTTAAGA--GGGTTAGGG---TT--T
1 TTAATTAGGTTAGGGTTTTTAA-TTAA-ATTAGGTTAGGGTTTTTAAT
* * *
56711035 TT-A--AGTTTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
* * ** *
56711078 TTAATTAGGTTAGAGTTTTAAAGTTAAA-GGGGTTAGAGTTTTTAAGT
1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAA-T
* * *
56711125 TT-A-GAGTTTAAGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAA-
1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAT
*
56711168 GT--TTAGGATTTAGGG-TTTTAATTAAATTAGGTTAGGGTTTTTAAGT
1 TTAATTAGG--TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAA-T
* * *
56711214 TT-A--GGGTTTAGGGTTTTTAATTAAATTAGATTAGGGTTTGTAAT
1 TTAATTAGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
*
56711258 TTAATTAGGTTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG
1 TTAATTAGGTTAGGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAT
*** *
56711304 TTAAGGGGGTTAGGGTTTTT-ATGT---TTAGGGTTTAAAGG-TTTTAAT
1 TTAATTAGGTTAGGGTTTTTAAT-TAAATTA-GG-TT-AGGGTTTTTAAT
*
56711349 TAAATTAGGTTAGGGTTTTTAATT
1 TTAATTAGGTTAGGGTTTTTAATT
56711373 TAAGGGTAAT
Statistics
Matches: 553, Mismatches: 84, Indels: 122
0.73 0.11 0.16
Matches are distributed among these distances:
36 1 0.00
37 4 0.01
38 46 0.08
39 1 0.00
40 2 0.00
41 9 0.02
43 19 0.03
44 80 0.14
45 135 0.24
46 189 0.34
47 22 0.04
48 6 0.01
49 1 0.00
50 1 0.00
51 3 0.01
52 5 0.01
53 25 0.05
54 4 0.01
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.48
Consensus pattern (46 bp):
TTAATTAGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAT
Found at i:56710739 original size:14 final size:15
Alignment explanation
Indices: 56710708--56710739 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
56710698 GTGAAGGGTG
56710708 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
56710723 TTAGGGTTTTTAA-T
1 TTAGGGTTTTTAAGT
56710737 TTA
1 TTA
56710740 ATTAGGTTTG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
TTAGGGTTTTTAAGT
Found at i:56710757 original size:61 final size:61
Alignment explanation
Indices: 56710662--56710857 Score: 241
Period size: 61 Copynumber: 3.1 Consensus size: 61
56710652 TTAAATTAGG
*
56710662 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTGAA-GGGTGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTGAATGAG-GTTAGGGTTTTTAAGT
* * *
56710723 TTAGGGTTTTTAATTTAATTAGGTTTGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTGAATGAGGTTAGGGTTTTTAAGT
* * *
56710784 TTAGGGTTTAAAGTTTTTAATTTAATTACGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTA
1 TTA-GG------GTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTGAATGAGGTTAGGGTTTTTA
56710849 AGT
59 AGT
*
56710852 TAAGGG
1 TTAGGG
56710858 AGTTAATTTA
Statistics
Matches: 120, Mismatches: 7, Indels: 16
0.84 0.05 0.11
Matches are distributed among these distances:
61 59 0.49
62 3 0.03
67 2 0.02
68 56 0.47
ACGTcount: A:0.24, C:0.01, G:0.26, T:0.49
Consensus pattern (61 bp):
TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTGAATGAGGTTAGGGTTTTTAAGT
Found at i:56710801 original size:68 final size:67
Alignment explanation
Indices: 56710660--56711375 Score: 503
Period size: 68 Copynumber: 10.6 Consensus size: 67
56710650 AATTAAATTA
* * **
56710660 GGTTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTGAA-GGGTGTTAGGGTTTTTAAG--
1 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAG-GTTAGGGTTTTTAAGTT
56710722 T--
65 TAG
* *
56710723 --TTAGGGTTTTTAATTTAATTAGGTTTGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTT
1 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTT
56710786 AG
66 AG
** * *
56710788 GGTTTAAAGTTTTTAATTTAATTACGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTT
1 GG-TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTT
*
56710853 AAGG
65 TA-G
** *
56710857 GAGTTA-ATTTATTTAAGTTAATTAGGTTAGGGTTTAGGGTTTTTAA-TTAAATTAGGTTAGAGT
1 G-GTTAGGGTT-TTTAAGTT-A--A--TTA-GG-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGT
*
56710920 TTTTAA-TTTAATTA
56 TTTTAAGTTT-A--G
* *
56710934 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA-GAGGTT-GAGTTTTTAAGTTA
1 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAG-T-
56710997 ATTA-
64 -TTAG
*
56711001 GGTTAGGGTTTTTAAGTTAA-GAGGGTTAGGGTTTTTAAG-T--TTAGGGTT----TTTAATTAA
1 GGTTAGGGTTTTTAAGTTAATTA-GGTTAGGGTTTTTAAGTTAATTA-GGTTAGGGTTT--TTAA
*
56711058 -ATTA-
62 GTTTAG
* * * *** *
56711062 AGTTAGGGTTTTTAAGTTAATTAGGTTAGAGTTTTAAAGTTAAAGGGGTTAGAGTTTTTAAGTTT
1 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTT
56711127 AG
66 AG
* *
56711129 AGTTTAAGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAG-T--TTAGGATTTAGGGTTTTAATT
1 -GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGG--TTAGGG-TTT--TT
*
56711191 AA-ATTA-
60 AAGTTTAG
* *
56711197 GGTTAGGGTTTTTAAG-T--TTAGGGTTTAGGGTTTTTAA-TTAAATTAGATTAGGGTTTGTAA-
1 GGTTAGGGTTTTTAAGTTAATTA-GG-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAG
*
56711257 TTTAATTA
63 TTT-A--G
*** *
56711265 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGGTTAGGGTTTTTATGTTT
1 GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTT
56711330 AG
66 AG
* *
56711332 GGTTTAAAGG-TTTTAA-TTAAATTAGGTTAGGGTTTTTAATTTAA
1 GG-TT-AGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAA
56711376 GGGTAATGGT
Statistics
Matches: 533, Mismatches: 54, Indels: 127
0.75 0.08 0.18
Matches are distributed among these distances:
61 90 0.17
62 3 0.01
63 8 0.02
64 8 0.02
65 14 0.03
66 27 0.05
67 79 0.15
68 152 0.29
69 67 0.13
70 18 0.03
71 8 0.02
72 1 0.00
73 1 0.00
74 3 0.01
75 6 0.01
76 45 0.08
77 3 0.01
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (67 bp):
GGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTT
AG
Found at i:56710894 original size:53 final size:53
Alignment explanation
Indices: 56710837--56710944 Score: 139
Period size: 53 Copynumber: 2.0 Consensus size: 53
56710827 GTTAATTAGG
* *
56710837 TTAGGGTTTTTAAGTTAAGGGA-GTTA-ATTTATTTAAGTTAATTAGGTTAGGGT
1 TTAGGGTTTTTAA-TTAAAGGAGGTTAGAGTT-TTTAAGTTAATTAGGTTAGGGT
** *
56710890 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGT
1 TTAGGGTTTTTAATTAAAGGAGGTTAGAGTTTTTAAGTTAATTAGGTTAGGGT
56710943 TT
1 TT
56710945 TTAAGTTAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
52 5 0.10
53 40 0.83
54 3 0.06
ACGTcount: A:0.28, C:0.00, G:0.24, T:0.48
Consensus pattern (53 bp):
TTAGGGTTTTTAATTAAAGGAGGTTAGAGTTTTTAAGTTAATTAGGTTAGGGT
Found at i:56710899 original size:76 final size:76
Alignment explanation
Indices: 56710814--56711321 Score: 263
Period size: 67 Copynumber: 7.0 Consensus size: 76
56710804 TTTAATTACG
* *
56710814 TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAAGG-GAGTTA-ATTTATTTAAGTT
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGAGTTTTTAAGTTAAGGAG-GTTAGAGTT-TTTAAGTT
56710876 AATTAGGTTAGGGT
63 AATTAGGTTAGGGT
* ** *
56710890 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTT-A-
1 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTTAAT
56710953 -A--TTA-GG-
66 TAGGTTAGGGT
* ** *
56710959 TTAGGGTTTTTAAGTT-AA-GAGGTT-GAGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA
1 TTAGGGTTTTTAA-TTAAATTAGGTTAGAGTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTT-A
*
56711021 GAGGGTTAGGGTTTTTA-AGT
64 -A---TTA-GG---TTAGGGT
* * ** *
56711041 TTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGTTAATTAGGTTAGAGTTTTAAAGTTAA-
1 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTTAAT
56711105 -A-G---GGG-
66 TAGGTTAGGGT
* * ** *
56711110 TTAGAGTTTTTAAGT---TTAGAGTTTA-AGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAG-T
1 TTAGGGTTTTTAATTAAATTAG-G-TTAGA-GTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTT
56711170 --TTAGG--A---T
63 AATTAGGTTAGGGT
* * * *
56711177 TTAGGGTTTT-AATTAAATTAGGTTAGGGTTTTTAAGTTTAGG-GTTTAGGGTTTTTAA-TTAA-
1 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTTAAT
*
56711238 -A--TTA--GA
66 TAGGTTAGGGT
* * * ** * *
56711244 TTAGGGTTTGTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTTAAT
**
56711309 GGGGTTAGGGT
66 TAGGTTAGGGT
56711320 TT
1 TT
56711322 TTATGTTTAG
Statistics
Matches: 345, Mismatches: 37, Indels: 100
0.72 0.08 0.21
Matches are distributed among these distances:
66 23 0.07
67 71 0.21
68 68 0.20
69 46 0.13
70 10 0.03
71 3 0.01
73 1 0.00
74 3 0.01
75 5 0.01
76 51 0.15
77 4 0.01
81 6 0.02
82 16 0.05
83 5 0.01
84 33 0.10
ACGTcount: A:0.27, C:0.00, G:0.26, T:0.47
Consensus pattern (76 bp):
TTAGGGTTTTTAATTAAATTAGGTTAGAGTTTTTAAGTTAAGGAGGTTAGAGTTTTTAAGTTAAT
TAGGTTAGGGT
Found at i:56711045 original size:38 final size:37
Alignment explanation
Indices: 56711003--56711079 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 37
56710993 GTTAATTAGG
**
56711003 TTAGGGTTTTTAAGTTAAGA-GGGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAA-TTAA-ATAAGTTAGGGTTTTTAAGT
56711041 TTAGGGTTTTTAATTAAATTAAGTTAGGGTTTTTAAGT
1 TTAGGGTTTTTAATTAAA-TAAGTTAGGGTTTTTAAGT
56711079 T
1 T
56711080 AATTAGGTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
36 1 0.03
37 4 0.11
38 30 0.86
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (37 bp):
TTAGGGTTTTTAATTAAATAAGTTAGGGTTTTTAAGT
Found at i:56711430 original size:23 final size:23
Alignment explanation
Indices: 56711404--56711459 Score: 67
Period size: 25 Copynumber: 2.3 Consensus size: 23
56711394 TTCTCAAATA
**
56711404 ATATCAAAATTTTCTATTTTATT
1 ATATCAAAAACTTCTATTTTATT
56711427 ATATCAAATAAACTTCTATTTTATT
1 ATATC-AA-AAACTTCTATTTTATT
*
56711452 ACATCAAA
1 ATATCAAA
56711460 TAATATCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
23 6 0.21
24 4 0.14
25 18 0.64
ACGTcount: A:0.41, C:0.12, G:0.00, T:0.46
Consensus pattern (23 bp):
ATATCAAAAACTTCTATTTTATT
Found at i:56711447 original size:25 final size:25
Alignment explanation
Indices: 56711415--56711462 Score: 87
Period size: 25 Copynumber: 1.9 Consensus size: 25
56711405 TATCAAAATT
*
56711415 TTCTATTTTATTATATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
56711440 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
56711463 TATCAAAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.40, C:0.12, G:0.00, T:0.48
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:56711914 original size:18 final size:18
Alignment explanation
Indices: 56711891--56711930 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
56711881 GACTCGGAAA
*
56711891 AGGATACATATAAGGGTT
1 AGGATACATATAAGGGCT
56711909 AGGATACATATAAGGGCT
1 AGGATACATATAAGGGCT
56711927 AGGA
1 AGGA
56711931 AACGCACCTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.07, G:0.30, T:0.23
Consensus pattern (18 bp):
AGGATACATATAAGGGCT
Found at i:56712813 original size:20 final size:20
Alignment explanation
Indices: 56712776--56712813 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
56712766 TTTATTTTTA
*
56712776 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
56712796 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
56712814 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:56713833 original size:14 final size:11
Alignment explanation
Indices: 56713790--56713829 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
56713780 AAGAGAATTT
56713790 TTGA-AGGAAA
1 TTGAGAGGAAA
56713800 TTGAGAGGAAA
1 TTGAGAGGAAA
56713811 TTGAGAGGAAA
1 TTGAGAGGAAA
56713822 TTTGAGAG
1 -TTGAGAG
56713830 AGGATTAGTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 4 0.14
11 17 0.61
12 7 0.25
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (11 bp):
TTGAGAGGAAA
Found at i:56714158 original size:12 final size:12
Alignment explanation
Indices: 56714141--56714166 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
56714131 ATGCCCATCA
56714141 ATCTTTAATGGT
1 ATCTTTAATGGT
56714153 ATCTTTAATGGT
1 ATCTTTAATGGT
56714165 AT
1 AT
56714167 AATAACAAAT
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:0.27, C:0.08, G:0.15, T:0.50
Consensus pattern (12 bp):
ATCTTTAATGGT
Found at i:56715130 original size:18 final size:19
Alignment explanation
Indices: 56715099--56715142 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
56715089 AATTAACAAG
56715099 AAAATAATAAC-AAAACAGT
1 AAAA-AATAACAAAAACAGT
* *
56715118 AAAAAATAGCAAAAATAGT
1 AAAAAATAACAAAAACAGT
56715137 AAAAAA
1 AAAAAA
56715143 AAAACAACCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 5 0.23
19 17 0.77
ACGTcount: A:0.73, C:0.07, G:0.07, T:0.14
Consensus pattern (19 bp):
AAAAAATAACAAAAACAGT
Found at i:56715785 original size:3 final size:3
Alignment explanation
Indices: 56715777--56715812 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
56715767 TTAGGGTTAG
* *
56715777 AGA AGA AGA AGA AGA AGA AGA AGG AGA AGG AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
56715813 GGAAAAATAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.61, C:0.00, G:0.39, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:56716192 original size:36 final size:37
Alignment explanation
Indices: 56716175--56716245 Score: 110
Period size: 36 Copynumber: 2.0 Consensus size: 37
56716165 AATATTGTTG
*
56716175 CTGGTATATTGTTGCTTATG-TTGGTATACATGGCTT
1 CTGGGATATTGTTGCTTATGTTTGGTATACATGGCTT
*
56716211 CTGGGATATTGTTGCTTATG-TTGTTATACATGGCT
1 CTGGGATATTGTTGCTTATGTTTGGTATACATGGCT
56716246 ACTAGTATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 33 1.00
ACGTcount: A:0.17, C:0.11, G:0.25, T:0.46
Consensus pattern (37 bp):
CTGGGATATTGTTGCTTATGTTTGGTATACATGGCTT
Found at i:56716942 original size:18 final size:18
Alignment explanation
Indices: 56716921--56716980 Score: 66
Period size: 18 Copynumber: 3.2 Consensus size: 18
56716911 CAGTAGGTAA
56716921 TTGAGTTGGGGTAGCCTG
1 TTGAGTTGGGGTAGCCTG
*
56716939 TTGAGTTGGGGTACTCTCTTG
1 TTGAGTTGGGGTA-GC-C-TG
* *
56716960 CTGATTTGGGGTAGCCTG
1 TTGAGTTGGGGTAGCCTG
56716978 TTG
1 TTG
56716981 CTGAGTTGGG
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
18 17 0.50
19 2 0.06
20 2 0.06
21 13 0.38
ACGTcount: A:0.10, C:0.13, G:0.38, T:0.38
Consensus pattern (18 bp):
TTGAGTTGGGGTAGCCTG
Found at i:56716970 original size:21 final size:21
Alignment explanation
Indices: 56716922--56716990 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
56716912 AGTAGGTAAT
*
56716922 TGAGTTGGGGTAG-C-C-TGT
1 TGAGTTGGGGTAGCCTCTTGC
56716940 TGAGTTGGGGTA-CTCTCTTGC
1 TGAGTTGGGGTAGC-CTCTTGC
* *
56716961 TGATTTGGGGTAGCCTGTTGC
1 TGAGTTGGGGTAGCCTCTTGC
56716982 TGAGTTGGG
1 TGAGTTGGG
56716991 ACACCAACTT
Statistics
Matches: 42, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
18 12 0.29
19 1 0.02
20 1 0.02
21 27 0.64
22 1 0.02
ACGTcount: A:0.10, C:0.13, G:0.41, T:0.36
Consensus pattern (21 bp):
TGAGTTGGGGTAGCCTCTTGC
Found at i:56717647 original size:9 final size:9
Alignment explanation
Indices: 56717633--56717672 Score: 53
Period size: 9 Copynumber: 4.2 Consensus size: 9
56717623 TTTGGTTAAA
56717633 AATTACCCG
1 AATTACCCG
56717642 AATTACCCG
1 AATTACCCG
56717651 AAAATTACCCG
1 --AATTACCCG
*
56717662 AATTAACCG
1 AATTACCCG
56717671 AA
1 AA
56717673 AAGTATGTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
9 19 0.68
11 9 0.32
ACGTcount: A:0.42, C:0.28, G:0.10, T:0.20
Consensus pattern (9 bp):
AATTACCCG
Found at i:56717656 original size:20 final size:20
Alignment explanation
Indices: 56717631--56717674 Score: 79
Period size: 20 Copynumber: 2.2 Consensus size: 20
56717621 TGTTTGGTTA
*
56717631 AAAATTACCCGAATTACCCG
1 AAAATTACCCGAATTAACCG
56717651 AAAATTACCCGAATTAACCG
1 AAAATTACCCGAATTAACCG
56717671 AAAA
1 AAAA
56717675 GTATGTTTTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.48, C:0.25, G:0.09, T:0.18
Consensus pattern (20 bp):
AAAATTACCCGAATTAACCG
Found at i:56717658 original size:11 final size:11
Alignment explanation
Indices: 56717631--56717663 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
56717621 TGTTTGGTTA
56717631 AAAATTACCCG
1 AAAATTACCCG
56717642 --AATTACCCG
1 AAAATTACCCG
56717651 AAAATTACCCG
1 AAAATTACCCG
56717662 AA
1 AA
56717664 TTAACCGAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.45
11 11 0.55
ACGTcount: A:0.45, C:0.27, G:0.09, T:0.18
Consensus pattern (11 bp):
AAAATTACCCG
Found at i:56717668 original size:68 final size:66
Alignment explanation
Indices: 56717592--56717733 Score: 257
Period size: 68 Copynumber: 2.1 Consensus size: 66
56717582 GGTTAGTTAA
56717592 CGAATTAACCGAAAAGTATGCTTTGTGCATGTTTGGTTAAAAATTACCCGAATTACCCGAAAATT
1 CGAATTAACCGAAAAGTATGCTTTGTGCATGTTTGGTTAAAAATTACCCGAATTACCCG--AATT
56717657 ACC
64 ACC
*
56717660 CGAATTAACCGAAAAGTATGTTTTGTGCATGTTTGGTTAAAAATTACCCGAATTACCCGAATTAC
1 CGAATTAACCGAAAAGTATGCTTTGTGCATGTTTGGTTAAAAATTACCCGAATTACCCGAATTAC
56717725 C
66 C
56717726 CGAATTAA
1 CGAATTAA
56717734 ATCACTACAT
Statistics
Matches: 73, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
66 15 0.21
68 58 0.79
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.30
Consensus pattern (66 bp):
CGAATTAACCGAAAAGTATGCTTTGTGCATGTTTGGTTAAAAATTACCCGAATTACCCGAATTAC
C
Found at i:56717715 original size:9 final size:9
Alignment explanation
Indices: 56717701--56717732 Score: 64
Period size: 9 Copynumber: 3.6 Consensus size: 9
56717691 TTTGGTTAAA
56717701 AATTACCCG
1 AATTACCCG
56717710 AATTACCCG
1 AATTACCCG
56717719 AATTACCCG
1 AATTACCCG
56717728 AATTA
1 AATTA
56717733 AATCACTACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.38, C:0.28, G:0.09, T:0.25
Consensus pattern (9 bp):
AATTACCCG
Found at i:56717946 original size:14 final size:14
Alignment explanation
Indices: 56717927--56717955 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
56717917 AAAATAAGAT
56717927 TGCATACATATACA
1 TGCATACATATACA
56717941 TGCATACATATACA
1 TGCATACATATACA
56717955 T
1 T
56717956 ATATAACCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.21, G:0.07, T:0.31
Consensus pattern (14 bp):
TGCATACATATACA
Found at i:56722011 original size:6 final size:6
Alignment explanation
Indices: 56722002--56722275 Score: 314
Period size: 6 Copynumber: 44.7 Consensus size: 6
56721992 AAATAACCCT
* * *
56722002 AAATCG AAATCA AAATAA AAATAA AAATCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
56722050 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* **
56722098 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AGATCA AAATTG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* * * * **
56722146 AAATCA AAATCA AAATCT AAATCG AGATCG AAATTG AAATCA AAATCA
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* ** ** *
56722194 GAATCA GTGAGTGTTTCA AAATTG AAATCA AAATCA AAATCA AAATCG
1 AAATCA ---A---AATCA AAATCA AAATCA AAATCA AAATCA AAATCA
**
56722242 AAATTG AAATCA AAATCA AAATCA AAATCA AAAT
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAAT
56722276 TGCAATCGAA
Statistics
Matches: 232, Mismatches: 30, Indels: 12
0.85 0.11 0.04
Matches are distributed among these distances:
6 228 0.98
9 1 0.00
12 3 0.01
ACGTcount: A:0.61, C:0.14, G:0.05, T:0.20
Consensus pattern (6 bp):
AAATCA
Found at i:56722761 original size:21 final size:21
Alignment explanation
Indices: 56722735--56722775 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
56722725 CAACGTGGCA
56722735 AGTTAACTTGCCACATCAGCT
1 AGTTAACTTGCCACATCAGCT
* *
56722756 AGTTAACTTGTCACGTCAGC
1 AGTTAACTTGCCACATCAGC
56722776 GGTCCCATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.27, G:0.17, T:0.29
Consensus pattern (21 bp):
AGTTAACTTGCCACATCAGCT
Found at i:56727009 original size:21 final size:21
Alignment explanation
Indices: 56726985--56727029 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
56726975 CTAAGATTCA
*
56726985 ACTCATTCTAAGTAAAGAGTT
1 ACTCATTCTAAGTAAAGAGGT
56727006 ACTCATTCTAAGTAAAGAGGT
1 ACTCATTCTAAGTAAAGAGGT
56727027 ACT
1 ACT
56727030 TGAGGCTCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.38, C:0.16, G:0.16, T:0.31
Consensus pattern (21 bp):
ACTCATTCTAAGTAAAGAGGT
Found at i:56733207 original size:21 final size:21
Alignment explanation
Indices: 56733149--56733235 Score: 104
Period size: 21 Copynumber: 4.1 Consensus size: 21
56733139 CCTGATCAGT
56733149 ATACGACACAT-AAGTGCCTG
1 ATACGACACATAAAGTGCCTG
* ** *
56733169 AAACGACACACGAGGTGCCTG
1 ATACGACACATAAAGTGCCTG
56733190 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
*
56733211 ATGTACAACACATAAAGTGCCTG
1 A--TACGACACATAAAGTGCCTG
56733234 AT
1 AT
56733236 CGGCAAAGCC
Statistics
Matches: 56, Mismatches: 8, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
20 9 0.16
21 27 0.48
23 20 0.36
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (21 bp):
ATACGACACATAAAGTGCCTG
Found at i:56733225 original size:23 final size:22
Alignment explanation
Indices: 56733183--56733235 Score: 81
Period size: 23 Copynumber: 2.4 Consensus size: 22
56733173 GACACACGAG
*
56733183 GTGCCTGA-TACGACACATAAA
1 GTGCCTGATTACAACACATAAA
56733204 GTGCCTGATGTACAACACATAAA
1 GTGCCTGAT-TACAACACATAAA
56733227 GTGCCTGAT
1 GTGCCTGAT
56733236 CGGCAAAGCC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 8 0.28
23 21 0.72
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.23
Consensus pattern (22 bp):
GTGCCTGATTACAACACATAAA
Found at i:56733234 original size:44 final size:41
Alignment explanation
Indices: 56733149--56733235 Score: 102
Period size: 44 Copynumber: 2.0 Consensus size: 41
56733139 CCTGATCAGT
* * *
56733149 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACAACACACAAAGTGCCTG
* *
56733190 ATACGACACATAAAGTGCCTGATGTACAACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA--AACAACACACAAAGTGCCTG
56733234 AT
1 AT
56733236 CGGCAAAGCC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
44 17 0.45
ACGTcount: A:0.37, C:0.24, G:0.21, T:0.18
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACAACACACAAAGTGCCTG
Found at i:56733530 original size:16 final size:17
Alignment explanation
Indices: 56733509--56733540 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
56733499 TAATAATAGT
56733509 ACTTACCTTA-TATTTC
1 ACTTACCTTATTATTTC
56733525 ACTTACCTTATTATTT
1 ACTTACCTTATTATTT
56733541 GCTTATCATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.25, C:0.22, G:0.00, T:0.53
Consensus pattern (17 bp):
ACTTACCTTATTATTTC
Found at i:56734171 original size:12 final size:11
Alignment explanation
Indices: 56734148--56734191 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
56734138 TAAACCCTAT
56734148 TTTTTTCCTTTC
1 TTTTTT-CTTTC
*
56734160 TTTTTCTTTTTC
1 TTTTT-TCTTTC
56734172 TTTTTTCTTTC
1 TTTTTTCTTTC
56734183 TTTCTTTCT
1 TTT-TTTCT
56734192 CCCCTGTTTC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 8 0.29
12 19 0.68
13 1 0.04
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (11 bp):
TTTTTTCTTTC
Found at i:56734579 original size:7 final size:7
Alignment explanation
Indices: 56734563--56734591 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
56734553 TATTTTAATT
56734563 TAAT-AA
1 TAATAAA
56734569 TAATAAA
1 TAATAAA
56734576 TAATAAA
1 TAATAAA
56734583 TAATAAA
1 TAATAAA
56734590 TA
1 TA
56734592 TCTTATGCTT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 4 0.18
7 18 0.82
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
TAATAAA
Found at i:56734762 original size:18 final size:20
Alignment explanation
Indices: 56734718--56734771 Score: 51
Period size: 18 Copynumber: 2.8 Consensus size: 20
56734708 TATAAAAATC
56734718 TTATAATATAGTTTATAACTA
1 TTATAATATA-TTTATAACTA
**
56734739 AAATAATATATTTATAA-T-
1 TTATAATATATTTATAACTA
56734757 TTATAACT-TATTTAT
1 TTATAA-TATATTTAT
56734772 CATATAAAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
18 11 0.39
19 2 0.07
20 7 0.25
21 8 0.29
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
TTATAATATATTTATAACTA
Found at i:56736368 original size:41 final size:40
Alignment explanation
Indices: 56736316--56736395 Score: 106
Period size: 41 Copynumber: 2.0 Consensus size: 40
56736306 CATGTTAACG
* * *
56736316 CATATCGATGCCACTATTCCAGACAGGGTCTTATACGAAT
1 CATATCGATGCCAATATCCCAGACAGGGTCTTACACGAAT
* *
56736356 CATATACGATGCCAATGTCCCAGACATGGTCTTACACGAA
1 CATAT-CGATGCCAATATCCCAGACAGGGTCTTACACGAA
56736396 ATCACACCTT
Statistics
Matches: 34, Mismatches: 5, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
40 5 0.15
41 29 0.85
ACGTcount: A:0.31, C:0.26, G:0.17, T:0.25
Consensus pattern (40 bp):
CATATCGATGCCAATATCCCAGACAGGGTCTTACACGAAT
Found at i:56736859 original size:185 final size:185
Alignment explanation
Indices: 56736540--56736916 Score: 567
Period size: 185 Copynumber: 2.0 Consensus size: 185
56736530 AATATATATC
* *
56736540 CATATACGAATCAAATTCGGCAATGTATATCTATATACAAATCAATTCGGCAATGAATATCCATA
1 CATATACGAATCAAATTCAGCAATGTATATCTATATACAAATCAATTCAGCAATGAATATCCATA
* * *
56736605 TACAAATCAAATTCGACAATGTATAACCATATATAAATCAAATTCGACAATGTATATCTATATAC
66 AACAAATCAAATTCGACAATGTATAACCATAAATAAATCAAATTCGACAATGTATATCTATAAAC
*
56736670 AAATCAAATTCGGCAATGTATAACCATATACAAATAAAATTCAGCAATGTATA-AT
131 AAATCAAATTCGGCAATGTATAACCATATACAAAT-AAATTCAGCAATGTATACAA
* * *
56736725 CATATACGAATCAAATTCAGCAATGTATATCTATATACAAATCGATTCAGCAATGTATATCTATA
1 CATATACGAATCAAATTCAGCAATGTATATCTATATACAAATCAATTCAGCAATGAATATCCATA
* * * * *
56736790 AACAAATCAAATTCGACAATGTATATCTATAAATAAATTAATTTCGGCAATGTATATCTATAAAC
66 AACAAATCAAATTCGACAATGTATAACCATAAATAAATCAAATTCGACAATGTATATCTATAAAC
* ** * *
56736855 AAATCAAATTCGGCAATGTATATCTTTATACAAATCAATTCGGCAATGTATACAA
131 AAATCAAATTCGGCAATGTATAACCATATACAAATAAATTCAGCAATGTATACAA
56736910 CATATAC
1 CATATAC
56736917 ATTTAAATTT
Statistics
Matches: 172, Mismatches: 19, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
184 15 0.09
185 157 0.91
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (185 bp):
CATATACGAATCAAATTCAGCAATGTATATCTATATACAAATCAATTCAGCAATGAATATCCATA
AACAAATCAAATTCGACAATGTATAACCATAAATAAATCAAATTCGACAATGTATATCTATAAAC
AAATCAAATTCGGCAATGTATAACCATATACAAATAAATTCAGCAATGTATACAA
Found at i:56736917 original size:31 final size:31
Alignment explanation
Indices: 56736516--56736906 Score: 495
Period size: 31 Copynumber: 12.7 Consensus size: 31
56736506 ATCCAATACT
* * *
56736516 CAAATC-AATTCGGTAATATATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
56736546 CGAATCAAATTCGGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
56736577 CAAATC-AATTCGGCAATGAATATCCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
56736607 CAAATCAAATTCGACAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
56736638 TAAATCAAATTCGACAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
56736669 CAAATCAAATTCGGCAATGTATAACCATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
56736700 CAAATAAAATTCAGCAATGTATAATC-ATATA
1 CAAATCAAATTCGGCAATGTAT-ATCTATATA
* *
56736731 CGAATCAAATTCAGCAATGTATATCTATATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * *
56736762 CAAATC-GATTCAGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* *
56736792 CAAATCAAATTCGACAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
* * * *
56736823 TAAATTAATTTCGGCAATGTATATCTATAAA
1 CAAATCAAATTCGGCAATGTATATCTATATA
*
56736854 CAAATCAAATTCGGCAATGTATATCTTTATA
1 CAAATCAAATTCGGCAATGTATATCTATATA
56736885 CAAATC-AATTCGGCAATGTATA
1 CAAATCAAATTCGGCAATGTATA
56736907 CAACATATAC
Statistics
Matches: 319, Mismatches: 37, Indels: 10
0.87 0.10 0.03
Matches are distributed among these distances:
30 80 0.25
31 237 0.74
32 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (31 bp):
CAAATCAAATTCGGCAATGTATATCTATATA
Found at i:56736925 original size:123 final size:121
Alignment explanation
Indices: 56736516--56736906 Score: 494
Period size: 123 Copynumber: 3.2 Consensus size: 121
56736506 ATCCAATACT
* * *
56736516 CAAATCAATTCGGTAATATATATCCATATACGAATCAAATTCGGCAATGTATATCTATATACAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
* * * * *
56736581 TCAATTCGGCAATGAATATCCATATACAAATCAAATTCGACAATGTATAACCATATA
66 TAAATTCGGCAATGTATAT-CATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * * *
56736638 TAAATCAAATTCGACAATGTATATCTATATACAAATCAAATTCGGCAATGTATAACCATATACAA
1 CAAATC-AATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAA
* * *
56736703 ATAAAATTCAGCAATGTATAATCATATACGAATCAAATTCAGCAATGTATATCTATATA
65 AT-AAATTCGGCAATGTAT-ATCATATACAAATCAAATTCGGCAATGTATATCTATATA
* * * * * * *
56736762 CAAATCGATTCAGCAATGTATATCTATAAACAAATCAAATTCGACAATGTATATCTATAAATAAA
1 CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
* * *
56736827 TTAATTTCGGCAATGTATATCTATAAACAAATCAAATTCGGCAATGTATATCTTTATA
66 -TAAATTCGGCAATGTATATC-ATATACAAATCAAATTCGGCAATGTATATCTATATA
56736885 CAAATCAATTCGGCAATGTATA
1 CAAATCAATTCGGCAATGTATA
56736907 CAACATATAC
Statistics
Matches: 230, Mismatches: 34, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
122 8 0.03
123 169 0.73
124 51 0.22
125 2 0.01
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (121 bp):
CAAATCAATTCGGCAATGTATATCCATATACAAATCAAATTCGGCAATGTATATCTATATACAAA
TAAATTCGGCAATGTATATCATATACAAATCAAATTCGGCAATGTATATCTATATA
Found at i:56739159 original size:6 final size:6
Alignment explanation
Indices: 56739148--56739176 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
56739138 CCAAGACCCA
56739148 CACACC CACACC CACACC CACACC CACAC
1 CACACC CACACC CACACC CACACC CACAC
56739177 ACCCAAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (6 bp):
CACACC
Found at i:56747448 original size:31 final size:31
Alignment explanation
Indices: 56747413--56747473 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
56747403 AATAACACAA
**
56747413 TGACTTAAAT-AAAATCTTTTGAATAATTTAG
1 TGACTTAAATGAAAA-CTTTCAAATAATTTAG
56747444 TGACTTAAATGAAAACTTTCAAATAATTTA
1 TGACTTAAATGAAAACTTTCAAATAATTTA
56747474 CCAAATTGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (31 bp):
TGACTTAAATGAAAACTTTCAAATAATTTAG
Found at i:56750961 original size:28 final size:28
Alignment explanation
Indices: 56750930--56750983 Score: 81
Period size: 28 Copynumber: 1.9 Consensus size: 28
56750920 TTGTGTTACT
*
56750930 AAAATTTGCCAACACAAAATATGACACC
1 AAAATTTACCAACACAAAATATGACACC
* *
56750958 AAAATTTACCGACACAAGATATGACA
1 AAAATTTACCAACACAAAATATGACA
56750984 AGTTTTTGAG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.50, C:0.22, G:0.09, T:0.19
Consensus pattern (28 bp):
AAAATTTACCAACACAAAATATGACACC
Found at i:56751720 original size:16 final size:16
Alignment explanation
Indices: 56751699--56751751 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
56751689 TTAGTTCGCC
*
56751699 GTAATGAAATAGAGGT
1 GTAATGGAATAGAGGT
*
56751715 GTAATGGAATAGATGT
1 GTAATGGAATAGAGGT
*
56751731 GTAATGGAATAGAGGC
1 GTAATGGAATAGAGGT
56751747 GTAAT
1 GTAAT
56751752 AGGTAAATCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.40, C:0.02, G:0.32, T:0.26
Consensus pattern (16 bp):
GTAATGGAATAGAGGT
Found at i:56751785 original size:46 final size:44
Alignment explanation
Indices: 56751733--56751821 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
56751723 ATAGATGTGT
*
56751733 AATGGAATAGAGGCGTAATAGGTAAATCTTTTGTTTGGTTGAATGG
1 AATGGAATAGAGGCGTAAT-GGT-AATCTTGTGTTTGGTTGAATGG
*
56751779 AATGGAATAGAGGCGTAATGGTATTCTTGTGTTTGGTTGAATG
1 AATGGAATAGAGGCGTAATGGTAATCTTGTGTTTGGTTGAATG
56751822 TAATAGAGAT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 19 0.46
45 3 0.07
46 19 0.46
ACGTcount: A:0.28, C:0.04, G:0.31, T:0.36
Consensus pattern (44 bp):
AATGGAATAGAGGCGTAATGGTAATCTTGTGTTTGGTTGAATGG
Found at i:56760624 original size:114 final size:114
Alignment explanation
Indices: 56760424--56760733 Score: 410
Period size: 114 Copynumber: 2.7 Consensus size: 114
56760414 GCGTTTTCCA
* * * * *
56760424 GAAAGCGCCGC-AAAATACCTAAGCCCAACGACGCCATTTTCCGAGCTGTCGGGGGATTTAGCGG
1 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTC-GGGGATTTAGCGG
* *
56760488 CGTTTTTAAGGAAGCACCGCTAATG-CTCAGGGCTTTAGTGGC-ATTTTTGC
65 CGTTTTTGAGGAAGCACCGCTAATGCCT-AGGGCTTTAGCGGCGA-TTTTGC
56760538 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
1 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
* * *
56760603 TTTTTTGGGGAAGCGCCGCTAATGCCTAGGGCTTTAGCGGCGATTTTGC
66 GTTTTTGAGGAAGCACCGCTAATGCCTAGGGCTTTAGCGGCGATTTTGC
* * * * * *
56760652 GAAAGTGCCACAAAAAAACCTAAGTCCAATGATGACGTTTTCTGTGCTTTCGGGGATTTAGCGGC
1 GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
**
56760717 GTTTTTGATAAAGCACC
66 GTTTTTGAGGAAGCACC
56760734 ACAAAAAAAC
Statistics
Matches: 172, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
114 134 0.78
115 38 0.22
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.25
Consensus pattern (114 bp):
GAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGC
GTTTTTGAGGAAGCACCGCTAATGCCTAGGGCTTTAGCGGCGATTTTGC
Found at i:56760754 original size:73 final size:73
Alignment explanation
Indices: 56760635--56760795 Score: 189
Period size: 73 Copynumber: 2.2 Consensus size: 73
56760625 TGCCTAGGGC
* * ** * * **
56760635 TTTAGCGGCGATTTTGCGAAAGTGCCACAAAAAAACCTAAGTCCAATGATGACGTTTTCTGTGCT
1 TTTAGCGGCGTTTTTGAGAAAGCACCACAAAAAAACCCAAGTCCAATGACGACGTTTTCTAAGCT
56760700 TTCGGGGA
66 TTCGGGGA
* *
56760708 TTTAGCGGCGTTTTTGATAAAGCACCACAAAAAAACCCAA-TCCCAATGACGTCGTTTTCTAAGC
1 TTTAGCGGCGTTTTTGAGAAAGCACCACAAAAAAACCCAAGT-CCAATGACGACGTTTTCTAAGC
*
56760772 TTTTGGGGA
65 TTTCGGGGA
* *
56760781 TTTTGCGACGTTTTT
1 TTTAGCGGCGTTTTT
56760796 CGGGAAGCGA
Statistics
Matches: 74, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
72 1 0.01
73 73 0.99
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.32
Consensus pattern (73 bp):
TTTAGCGGCGTTTTTGAGAAAGCACCACAAAAAAACCCAAGTCCAATGACGACGTTTTCTAAGCT
TTCGGGGA
Found at i:56760860 original size:187 final size:187
Alignment explanation
Indices: 56760521--56760917 Score: 515
Period size: 187 Copynumber: 2.1 Consensus size: 187
56760511 TGCTCAGGGC
* * ** * * *
56760521 TTTAGTGGCATTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCT
1 TTTAGCGGCGTTTTTGATAAAGCACCACAAAAAAACCCAAGCCCAACGACGCCGTTTTCTAAGCT
* * * * * * * * *
56760586 TTCGGGGATTTAGCGGCTTTTTTGGGGAAGCGCCGCTAATGCCTAGGGCTTTAGCGGCGATTTTG
66 TTCGGGGATTTAGCGACGTTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAACGGCGATTTTC
* * * * *
56760651 CGAAAGTGCCACAAAAAAACCTAAGTCCAATGATGACGTTTTCTGTGCTTTCGGGGA
131 CGAAAGCGCCACAAAAAAACCTAAGCCCAATGACGACATTTTCTGAGCTTTCGGGGA
* * *
56760708 TTTAGCGGCGTTTTTGATAAAGCACCACAAAAAAACCCAATCCCAATGACGTCGTTTTCTAAGCT
1 TTTAGCGGCGTTTTTGATAAAGCACCACAAAAAAACCCAAGCCCAACGACGCCGTTTTCTAAGCT
* * *
56760773 TTTGGGGATTTTGCGACGTTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAACGGCGTTTTTC
66 TTCGGGGATTTAGCGACGTTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAACGGCGATTTTC
* *
56760838 CTAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCATTTTCTGAGCTTTCGGGGA
131 CGAAAGCGCCACAAAAAAACCTAAGCCCAATGACGACATTTTCTGAGCTTTCGGGGA
* *
56760895 TTTAGCGACGTTTTTAATAAAGC
1 TTTAGCGGCGTTTTTGATAAAGC
56760918 GCCGCTAATG
Statistics
Matches: 179, Mismatches: 31, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
187 179 1.00
ACGTcount: A:0.26, C:0.22, G:0.23, T:0.28
Consensus pattern (187 bp):
TTTAGCGGCGTTTTTGATAAAGCACCACAAAAAAACCCAAGCCCAACGACGCCGTTTTCTAAGCT
TTCGGGGATTTAGCGACGTTTTTCGGGAAGCGACGCTAATACCCAAGGCTTTAACGGCGATTTTC
CGAAAGCGCCACAAAAAAACCTAAGCCCAATGACGACATTTTCTGAGCTTTCGGGGA
Found at i:56760971 original size:301 final size:299
Alignment explanation
Indices: 56760435--56761101 Score: 899
Period size: 301 Copynumber: 2.2 Consensus size: 299
56760425 AAAGCGCCGC
* * ** * *
56760435 AAAATACCTAAGCCCAACGACGCCATTTTCCGAGCTGTCGGGGGATTTAGCGGCGTTTTTAAGGA
1 AAAAAACCCAAGCCCAACGACGCC-TTTTCTAAGCTTTC-GGGGATTTAGCGGCGTTTTT-GGGA
* * * ** *
56760500 AGCACCGCTAATGCTCAGGGCTTTAGTGGCATTTTTGCGAAAGCGCCACAAAAAAACCTAAGCCC
63 AGCACCGCTAATACCCAAGGCTTTAACGGCATTTTTCCGAAAGCGCCACAAAAAAACCTAAGCCC
* * * ** *
56760565 AACGACGCCGTTTTCTGAGCTTTCGGGGATTTAGCGGCTTTTTTGGGGAAGCGCCGCTAATGCCT
128 AACGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCCT
* * *
56760630 AGGGCTTTAGCGGCGATTTTGCGAAAGTGCCACAAAAAAACCTAAGTCCAATGATGACGTTTTCT
193 AGGGCTTTAGCGGCGATTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGATGACGTTTTCT
*
56760695 GTGCTTTCGGGGATTTAGCGGCGTTTTTGATAAAGCACCACA
258 GAGCTTTCGGGGATTTAGCGGCGTTTTTGATAAAGCACCACA
* * * * * *
56760737 AAAAAACCCAATCCCAATGACGTCGTTTTCTAAGCTTTTGGGGATTTTGCGACGTTTTTCGGGAA
1 AAAAAACCCAAGCCCAACGACG-CCTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTT-GGGAA
* *
56760802 GCGA-CGCTAATACCCAAGGCTTTAACGGCGTTTTTCCTAAAGCGCCACAAAAAAACCTAAGCCC
64 GC-ACCGCTAATACCCAAGGCTTTAACGGCATTTTTCCGAAAGCGCCACAAAAAAACCTAAGCCC
* *
56760866 AATGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGACGTTTTTAATAAAGCGCCGCTAATG-CT
128 AACGACGCCATTTTCTGAGCTTTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCCT
* * *
56760930 CAGGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCAC-AAAAAACCTAAGCCCAACGATGCCGTTTT
193 -A-GGGCTTTAGCGGCGATTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGATGACGTTTT
*
56760994 CTGAGCTTTCGGGGATTTAGCGGCGTTTTTGATAAAGCGCCACA
256 CTGAGCTTTCGGGGATTTAGCGGCGTTTTTGATAAAGCACCACA
* *
56761038 AAAAAACCTAAGCCCAACGACGCCTTTTCTGAGCTTTCGGGGATTTAGCGGCGTTTTTGGGAAG
1 AAAAAACCCAAGCCCAACGACGCCTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTGGGAAG
56761102 GTGCCGCAAA
Statistics
Matches: 316, Mismatches: 45, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
299 6 0.02
300 33 0.10
301 218 0.69
302 58 0.18
303 1 0.00
ACGTcount: A:0.26, C:0.23, G:0.24, T:0.27
Consensus pattern (299 bp):
AAAAAACCCAAGCCCAACGACGCCTTTTCTAAGCTTTCGGGGATTTAGCGGCGTTTTTGGGAAGC
ACCGCTAATACCCAAGGCTTTAACGGCATTTTTCCGAAAGCGCCACAAAAAAACCTAAGCCCAAC
GACGCCATTTTCTGAGCTTTCGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCCTAGG
GCTTTAGCGGCGATTTTGCGAAAGCGCCACAAAAAAACCTAAGCCCAACGATGACGTTTTCTGAG
CTTTCGGGGATTTAGCGGCGTTTTTGATAAAGCACCACA
Found at i:56761033 original size:114 final size:115
Alignment explanation
Indices: 56760703--56761034 Score: 436
Period size: 114 Copynumber: 2.9 Consensus size: 115
56760693 CTGTGCTTTC
* * * * * *
56760703 GGGGATTTAGCGGCGTTTTTGATAAAGCACCACAAAAAAACCCAATCCCAATGACGTCGTTTTCT
1 GGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCGTTTTCT
* * * ** *
56760768 AAGCTTTTGGGGATTTTGCGACGTTTTTCG-GGAAGCGACGCTAATACCCA
66 GAGCTTTCGGGGATTTAGCGACGTTTTT-GATAAAGCGCCGCTAATACCCA
* * * *
56760818 -AGGCTTTAACGGCGTTTTTCCTAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCATTTTCT
1 GGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCGTTTTCT
* * *
56760882 GAGCTTTCGGGGATTTAGCGACGTTTTTAATAAAGCGCCGCTAATGCTCA
66 GAGCTTTCGGGGATTTAGCGACGTTTTTGATAAAGCGCCGCTAATACCCA
* *
56760932 GGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCAC-AAAAAACCTAAGCCCAACGATGCCGTTTTCT
1 GGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCGTTTTCT
*
56760996 GAGCTTTCGGGGATTTAGCGGCGTTTTTGATAAAGCGCC
66 GAGCTTTCGGGGATTTAGCGACGTTTTTGATAAAGCGCC
56761035 ACAAAAAAAC
Statistics
Matches: 188, Mismatches: 27, Indels: 5
0.85 0.12 0.02
Matches are distributed among these distances:
114 159 0.85
115 29 0.15
ACGTcount: A:0.26, C:0.23, G:0.23, T:0.27
Consensus pattern (115 bp):
GGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAAACCTAAGCCCAATGACGCCGTTTTCT
GAGCTTTCGGGGATTTAGCGACGTTTTTGATAAAGCGCCGCTAATACCCA
Found at i:56761180 original size:72 final size:72
Alignment explanation
Indices: 56760932--56761178 Score: 354
Period size: 72 Copynumber: 3.4 Consensus size: 72
56760922 CTAATGCTCA
* * *
56760932 GGGGCTTTAGCGGCGTTTTTGCTAAAGCGCCACAAAAAACCTAAGCCCAACGATGCCGTTTTCTG
1 GGGGATTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
56760997 AGCTTTC
66 AGCTTTC
56761004 GGGGATTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAAACCTAAGCCCAACGACGCC-TTTTCT
1 GGGGATTTAGCGGCGTTTTTGATAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGCCGTTTTCT
56761068 GAGCTTTC
65 GAGCTTTC
** * * *
56761076 GGGGATTTAGCGGCGTTTTTGGGAAGGTGCCGCAAAGAAACCTAAGCCCAACGA-GCCGTTTTCT
1 GGGGATTTAGCGGCGTTTTTGATAAAGCGCCACAAA-AAACCTAAGCCCAACGACGCCGTTTTCT
*
56761140 TAGCTTTC
65 GAGCTTTC
* * *
56761148 GTGGATTTAGTGGCGTTTTTAATAAAGCGCC
1 GGGGATTTAGCGGCGTTTTTGATAAAGCGCC
56761179 GCTAATGCTT
Statistics
Matches: 156, Mismatches: 16, Indels: 6
0.88 0.09 0.03
Matches are distributed among these distances:
71 6 0.04
72 127 0.81
73 23 0.15
ACGTcount: A:0.24, C:0.23, G:0.26, T:0.27
Consensus pattern (72 bp):
GGGGATTTAGCGGCGTTTTTGATAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTG
AGCTTTC
Found at i:56761731 original size:15 final size:14
Alignment explanation
Indices: 56761711--56761785 Score: 60
Period size: 14 Copynumber: 5.1 Consensus size: 14
56761701 AAGTTTTATA
56761711 GATTATGGAATTAAG
1 GATTATGG-ATTAAG
*
56761726 GATTATGGATTAGG
1 GATTATGGATTAAG
* *
56761740 GATTCTGGTTTAAG
1 GATTATGGATTAAG
*
56761754 GGTTAATGTGATTTAAG
1 GATT-ATG-GA-TTAAG
* *
56761771 GTTTATGGGTTAAG
1 GATTATGGATTAAG
56761785 G
1 G
56761786 GTTAGGGGTT
Statistics
Matches: 48, Mismatches: 9, Indels: 7
0.75 0.14 0.11
Matches are distributed among these distances:
14 25 0.52
15 11 0.23
16 4 0.08
17 8 0.17
ACGTcount: A:0.28, C:0.01, G:0.32, T:0.39
Consensus pattern (14 bp):
GATTATGGATTAAG
Found at i:56761785 original size:14 final size:14
Alignment explanation
Indices: 56761766--56761805 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
56761756 TTAATGTGAT
* *
56761766 TTAAGGTTTATGGG
1 TTAAGGGTTAGGGG
56761780 TTAAGGGTTAGGGG
1 TTAAGGGTTAGGGG
*
56761794 TTAGGGGTTAGG
1 TTAAGGGTTAGG
56761806 TTAGGGGTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.20, C:0.00, G:0.45, T:0.35
Consensus pattern (14 bp):
TTAAGGGTTAGGGG
Found at i:56761809 original size:12 final size:13
Alignment explanation
Indices: 56761777--56761815 Score: 53
Period size: 12 Copynumber: 3.0 Consensus size: 13
56761767 TAAGGTTTAT
*
56761777 GGGTTAAGGGTTA
1 GGGTTAGGGGTTA
56761790 GGGGTTAGGGGTTA
1 -GGGTTAGGGGTTA
56761804 -GGTTAGGGGTTA
1 GGGTTAGGGGTTA
56761816 AATGTTAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 12 0.50
14 12 0.50
ACGTcount: A:0.18, C:0.00, G:0.51, T:0.31
Consensus pattern (13 bp):
GGGTTAGGGGTTA
Found at i:56761822 original size:19 final size:20
Alignment explanation
Indices: 56761778--56761832 Score: 58
Period size: 19 Copynumber: 2.7 Consensus size: 20
56761768 AAGGTTTATG
**
56761778 GGTTAAGGGTTAGGGGTTAGG
1 GGTTAA-GGTTAGGGGTTAAA
56761799 GGTT-AGGTTAGGGGTTAAA
1 GGTTAAGGTTAGGGGTTAAA
*
56761818 TGTTAAGAGTTAGGG
1 GGTTAAG-GTTAGGG
56761833 ATTTAGGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 15 0.52
20 3 0.10
21 11 0.38
ACGTcount: A:0.24, C:0.00, G:0.45, T:0.31
Consensus pattern (20 bp):
GGTTAAGGTTAGGGGTTAAA
Found at i:56761947 original size:14 final size:14
Alignment explanation
Indices: 56761910--56761948 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
56761900 ATATATTAAA
*
56761910 TAAGGTTTAGGGGT
1 TAAGGATTAGGGGT
*
56761924 TATGGATTAGGGGT
1 TAAGGATTAGGGGT
*
56761938 TAAGGGTTAGG
1 TAAGGATTAGG
56761949 AATTCAGGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.23, C:0.00, G:0.44, T:0.33
Consensus pattern (14 bp):
TAAGGATTAGGGGT
Found at i:56762410 original size:24 final size:24
Alignment explanation
Indices: 56762382--56762462 Score: 99
Period size: 24 Copynumber: 3.2 Consensus size: 24
56762372 AACAAACAAA
56762382 TAAATAAATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
* *
56762406 TAAATTAATTTTTAGGTAATTAATTGTT
1 TAAA-TAA---ATAGGTAATTAATTATT
*
56762434 TAAATAGATAGGTAATTAATTATT
1 TAAATAAATAGGTAATTAATTATT
56762458 TAAAT
1 TAAAT
56762463 GAATGATACA
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
24 24 0.50
25 3 0.06
27 2 0.04
28 19 0.40
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (24 bp):
TAAATAAATAGGTAATTAATTATT
Found at i:56764524 original size:13 final size:13
Alignment explanation
Indices: 56764508--56764672 Score: 127
Period size: 13 Copynumber: 12.5 Consensus size: 13
56764498 TTACTAAAAT
*
56764508 TTACTTTAATATA
1 TTACTTAAATATA
*
56764521 TTACTTGAATATA
1 TTACTTAAATATA
*
56764534 TTACTTAAATAAA
1 TTACTTAAATATA
*
56764547 TTACTTAAATACA
1 TTACTTAAATATA
*
56764560 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** * *
56764574 TTGGTTAAATTTG
1 TTACTTAAATATA
*
56764587 TTACTTAAATATG
1 TTACTTAAATATA
*
56764600 TTACTTAAATACA
1 TTACTTAAATATA
*
56764613 TTACTTACTAAAAT-
1 TTACTTA--AATATA
** *
56764627 TTGTTTAAATTTA
1 TTACTTAAATATA
*
56764640 TTACTTAAATATG
1 TTACTTAAATATA
*
56764653 TTACTTAAATACA
1 TTACTTAAATATA
56764666 TTACTTA
1 TTACTTA
56764673 CTAAAATTTA
Statistics
Matches: 119, Mismatches: 27, Indels: 12
0.75 0.17 0.08
Matches are distributed among these distances:
12 6 0.05
13 97 0.82
14 10 0.08
15 6 0.05
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (13 bp):
TTACTTAAATATA
Found at i:56764594 original size:53 final size:53
Alignment explanation
Indices: 56764532--56764681 Score: 264
Period size: 53 Copynumber: 2.8 Consensus size: 53
56764522 TACTTGAATA
**
56764532 TATTACTTAAATAAATTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
* *
56764585 TGTTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGTTTAAATT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
56764638 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
1 TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTT
56764682 AAGTATATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
53 92 1.00
ACGTcount: A:0.41, C:0.10, G:0.04, T:0.45
Consensus pattern (53 bp):
TATTACTTAAATATGTTACTTAAATACATTACTTACTAAAATTTGGTTAAATT
Found at i:56764904 original size:23 final size:23
Alignment explanation
Indices: 56764876--56764919 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
56764866 CTTATATGTA
*
56764876 AACTTACATAATACATTACTTTT
1 AACTTACATAATACATAACTTTT
56764899 AACTTACATAATACATAACTT
1 AACTTACATAATACATAACTT
56764920 ATAAATTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.43, C:0.18, G:0.00, T:0.39
Consensus pattern (23 bp):
AACTTACATAATACATAACTTTT
Found at i:56766613 original size:21 final size:21
Alignment explanation
Indices: 56766556--56766645 Score: 99
Period size: 21 Copynumber: 4.3 Consensus size: 21
56766546 CTACAACTTA
* * * *
56766556 AAGCAGAGGCGGCAACAAGGG
1 AAGCAGAGGCTGCAGCGAGAG
* *
56766577 AAGCAGAGACTGCAGCGAGGG
1 AAGCAGAGGCTGCAGCGAGAG
*
56766598 AAGCAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTGCAGCGAGAG
* *
56766619 AAGCAGGGGCTGCAGCGCGAG
1 AAGCAGAGGCTGCAGCGAGAG
56766640 AAGCAG
1 AAGCAG
56766646 CGAGAGAAGC
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 59 1.00
ACGTcount: A:0.34, C:0.20, G:0.42, T:0.03
Consensus pattern (21 bp):
AAGCAGAGGCTGCAGCGAGAG
Found at i:56767271 original size:43 final size:43
Alignment explanation
Indices: 56767029--56767300 Score: 279
Period size: 42 Copynumber: 6.4 Consensus size: 43
56767019 AATCCCAAAA
* * *
56767029 TTAGTGGCG-TTTTTTACAAAAGCGCCGCTAAAGAACATTA-CTT
1 TTAGCGGCGTTTTTTTTC-AAAGCGCCGCTAAAGAACATGATC-T
* * ** * *
56767072 TTCGCGGCGTTTGTGATGAAAGCGTCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTTTTTCAAAGCGCCGCTAAAGAACATGATCT
* * * * * *
56767115 ATAGCGAC-ATTTTTTACCAAGCGCCGCTAAAGAATATGATCT
1 TTAGCGGCGTTTTTTTTCAAAGCGCCGCTAAAGAACATGATCT
* *
56767157 TTAGCAGCGTTTTTCTGT--AAGCGCCGCTAAAGAACATGATCT
1 TTAGCGGCGTTTTT-TTTCAAAGCGCCGCTAAAGAACATGATCT
*
56767199 TTAGCGGCGTCTTTTTTT--AAGTGCCGCTAAAGAACATGATCT
1 TTAGCGGCGT-TTTTTTTCAAAGCGCCGCTAAAGAACATGATCT
*
56767241 TTAGCGGCGTTTTTTTTCAAAGCGCCGCTAAAGAACATGACCT
1 TTAGCGGCGTTTTTTTTCAAAGCGCCGCTAAAGAACATGATCT
*
56767284 TTAGAGGCGTTTTTTTT
1 TTAGCGGCGTTTTTTTT
56767301 TCTATAAACG
Statistics
Matches: 188, Mismatches: 34, Indels: 14
0.80 0.14 0.06
Matches are distributed among these distances:
41 7 0.04
42 97 0.52
43 79 0.42
44 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.33
Consensus pattern (43 bp):
TTAGCGGCGTTTTTTTTCAAAGCGCCGCTAAAGAACATGATCT
Found at i:56767301 original size:85 final size:84
Alignment explanation
Indices: 56767048--56767301 Score: 287
Period size: 85 Copynumber: 3.0 Consensus size: 84
56767038 TTTTTTACAA
* * * * *
56767048 AAGCGCCGCTAAAGAACATTA-CTTTTCGCGGCGTTTGTGATGAAAGCGTCGCTAAAGAACATGA
1 AAGCGCCGCTAAAGAACATGATC-TTTAGCGGCGTTTTTTAT-AAAGCGCCGCTAAAGAACATGA
* * * ***
56767112 TCTATAGCGACATTTTTTACC
64 TCTTTAGCGGCGTTTTTTTTT
* * *
56767133 AAGCGCCGCTAAAGAATATGATCTTTAGCAGCGTTTTTCTGT-AAGCGCCGCTAAAGAACATGAT
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTT-TATAAAGCGCCGCTAAAGAACATGAT
*
56767197 CTTTAGCGGCGTCTTTTTTT
65 CTTTAGCGGCGTTTTTTTTT
* * *
56767217 AAGTGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTTTCAAAGCGCCGCTAAAGAACATGAC
1 AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTAT-AAAGCGCCGCTAAAGAACATGAT
*
56767282 CTTTAGAGGCGTTTTTTTTT
65 CTTTAGCGGCGTTTTTTTTT
56767302 CTATAAACGC
Statistics
Matches: 143, Mismatches: 22, Indels: 8
0.83 0.13 0.05
Matches are distributed among these distances:
83 2 0.01
84 69 0.48
85 70 0.49
86 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (84 bp):
AAGCGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTTTATAAAGCGCCGCTAAAGAACATGATC
TTTAGCGGCGTTTTTTTTT
Found at i:56767401 original size:21 final size:22
Alignment explanation
Indices: 56767359--56767401 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
56767349 TAGCGGCGCT
**
56767359 AAAAAGCGTCGCTAAAGGCCTA
1 AAAAAGCGTCGCTAAAAACCTA
56767381 AAAAAG-GTCGCTAAAAACCTA
1 AAAAAGCGTCGCTAAAAACCTA
56767402 TTTTGGTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.47, C:0.21, G:0.19, T:0.14
Consensus pattern (22 bp):
AAAAAGCGTCGCTAAAAACCTA
Found at i:56768930 original size:19 final size:19
Alignment explanation
Indices: 56768906--56768959 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
56768896 AGTCTTCAAG
*
56768906 GATATGCAATCTTAGGTAT
1 GATATGCAATCTTAGATAT
56768925 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
56768944 GATATGCAATCTTAGA
1 GATATGCAATCTTAGA
56768960 AGATATAATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.35
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:56769731 original size:25 final size:25
Alignment explanation
Indices: 56769674--56769731 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
56769664 TTTTAAACTC
*
56769674 ATTTATATATTATTACTTTATATATT
1 ATTTAT-TATTATTACTATATATATT
** * *
56769700 ACCTATTTTTATTTCTATATATATT
1 ATTTATTATTATTACTATATATATT
56769725 ATTTATT
1 ATTTATT
56769732 CCAAACTTAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.31, C:0.07, G:0.00, T:0.62
Consensus pattern (25 bp):
ATTTATTATTATTACTATATATATT
Found at i:56771644 original size:19 final size:19
Alignment explanation
Indices: 56771620--56771664 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
56771610 TCTTTCTTTT
*
56771620 TGCATT-CATTCCATGCATC
1 TGCATTACATTCCAT-CATA
*
56771639 TGCATTACATTGCATCATA
1 TGCATTACATTCCATCATA
56771658 TGCATTA
1 TGCATTA
56771665 GATTTTCACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (19 bp):
TGCATTACATTCCATCATA
Found at i:56775930 original size:24 final size:24
Alignment explanation
Indices: 56775898--56775953 Score: 112
Period size: 24 Copynumber: 2.3 Consensus size: 24
56775888 GTCCCAAAAG
56775898 TACAGTGGATTGAACCTTGAAGAT
1 TACAGTGGATTGAACCTTGAAGAT
56775922 TACAGTGGATTGAACCTTGAAGAT
1 TACAGTGGATTGAACCTTGAAGAT
56775946 TACAGTGG
1 TACAGTGG
56775954 GGGCATTTGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.32, C:0.12, G:0.27, T:0.29
Consensus pattern (24 bp):
TACAGTGGATTGAACCTTGAAGAT
Found at i:56776287 original size:44 final size:44
Alignment explanation
Indices: 56776237--56776683 Score: 382
Period size: 44 Copynumber: 10.1 Consensus size: 44
56776227 CCACAAATCC
* *
56776237 TATCTCCCTGAGGTTGTAGTGGAGCAGATTAAAGTTACAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCT
* * * **
56776281 TATCTCCCTGAAGTTGCAGTGAAACAGATTGAAGAAAGCAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA-CAAGTCT
* * * * * * *
56776326 TAT-TCCCCTAAAGTTGCAGTGGGGTAGACTGAAAATGGA-AAATCT
1 TATCT-CCCTGAAGTTGCAGTGGAGCAGA-TTAAAGT-TACAAGTCT
* ** * *
56776371 TATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACA-AGTCT
* *
56776415 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCT
* * * ** *
56776459 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAAGTAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTA-CAAGTCT
* * * * * **
56776504 TATCCCCCTAAAGTTGCAGTGGGGCAGACTGAAGATGGCGAA-TCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-TTAC-AAGTCT
* ** * *
56776549 TATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCA-ATAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACA-AGTCT
* * *
56776593 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCC
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCT
* *
56776637 TATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCT
56776681 TAT
1 TAT
56776684 TGAAGAAAGC
Statistics
Matches: 325, Mismatches: 65, Indels: 26
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.00
43 3 0.01
44 188 0.58
45 126 0.39
46 6 0.02
47 1 0.00
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCT
Found at i:56776535 original size:178 final size:178
Alignment explanation
Indices: 56776232--56776661 Score: 680
Period size: 178 Copynumber: 2.4 Consensus size: 178
56776222 TGAAACCACA
* *
56776232 AATCCTATCTCCCTGAGGTTGTAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTG
* * * * *
56776297 CAGTGAAACAGATTGAAGAAAGCAAGTCTTATTCCCCTAAAGTTGCAGTGGGGTAGACTGAAAAT
66 CAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGGCAGACTGAAAAT
56776362 GGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
131 GGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* *
56776410 AATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTG
* * *
56776475 TAGTGGAGCAGACTGAAGAAAGTAAGTCTTATCCCCCTAAAGTTGCAGTGGGGCAGACTGAAGAT
66 CAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGGCAGACTGAAAAT
** * *
56776540 GGCGAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTAAAGCCAAT
131 GGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
* * * *
56776588 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCCTATCTCCTTGAAGTTG
1 AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTG
56776653 CAGTGGAGC
66 CAGTGGAGC
56776662 GGATTAAAGT
Statistics
Matches: 229, Mismatches: 23, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
178 229 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.27
Consensus pattern (178 bp):
AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTG
CAGTGGAGCAGACTGAAGAAAGCAAGTCTTATCCCCCTAAAGTTGCAGTGGGGCAGACTGAAAAT
GGAAAATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCAAT
Found at i:56776607 original size:134 final size:132
Alignment explanation
Indices: 56776249--56776620 Score: 338
Period size: 134 Copynumber: 2.8 Consensus size: 132
56776239 TCTCCCTGAG
* * ** * * * * *
56776249 GTTGTAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTGAAACAGATTGAA
1 GTTGCAGTGGAGCAGATGAAAGCCAGAA-TCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
** * * * * * * * * *
56776314 GAAAGCAAGTCTTAT-TCCCCTAAAGTTGCAGTGGGGTAGACTGAA-AATGGAAAATCTTATCTC
65 GCCA-CAAATCCTATCT-CCCTGAAGTTGCAGTGGAGCAGACTGAAGAA-AGTAAGTCTTATCCC
56776377 CCTAAA
127 CCTAAA
* * * *
56776383 GTTGCAGTGGAGCAGATTAAAGCCAATAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAA
1 GTTGCAGTGGAGCAGATGAAAGCC-AGAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
** * * *
56776448 GTTACAAGTCTTATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAAGTAAGTCTTATCCCCCT
65 GCCACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGTAAGTCTTATCCCCCT
56776513 AAA
130 AAA
* * * *
56776516 GTTGCAGTGGGGCAGACTGAAGATGGC-GAATCTTATCTCCCTGAAGTTGCAGTGGAGTAGATTA
1 GTTGCAGTGGAGCAGA-TGAA-A-GCCAGAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTA
56776580 AAGCCA-ATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
63 AAGCCACA-AATCCTATCTCCCTGAAGTTGCAGTGGAGCAGA
56776621 TTAAAGCTAC
Statistics
Matches: 198, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
133 67 0.34
134 125 0.63
135 4 0.02
136 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.27
Consensus pattern (132 bp):
GTTGCAGTGGAGCAGATGAAAGCCAGAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG
CCACAAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGAAAGTAAGTCTTATCCCCCTA
AA
Found at i:56776623 original size:222 final size:222
Alignment explanation
Indices: 56776237--56776683 Score: 609
Period size: 222 Copynumber: 2.0 Consensus size: 222
56776227 CCACAAATCC
* * ** * *
56776237 TATCTCCCTGAGGTTGTAGTGGAGCAGATTAAAGTTACAAGTCTTATCTCCCTGAAGTTGCAGTG
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAACAAGTCTTATCCCCCTAAAGTTGCAGTG
* * *
56776302 AAACAGATTGAAGAAAGCAAGTCTTATTCCCCTAAAGTTGCAGTGGGGTAGACTGAAAATGGAAA
66 AAACAGACTGAAGAAAGCAAGTCTTATTCCCCTAAAGTTGCAGTGGAGTAGACTGAAAATGCAAA
*
56776367 ATCTTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCA-ATAATCCTATCTCCTTGAAGTTG
131 ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACA-AATCCTATCTCCTTGAAGTTG
56776431 CAGTGGAGCGGATTAAAGTTACAAGTCT
195 CAGTGGAGCGGATTAAAGTTACAAGTCT
* *
56776459 TATCTCCCTGAAGTTGTAGTGGAGCAGACTGAAGAAAGTAAGTCTTATCCCCCTAAAGTTGCAGT
1 TATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAA-CAAGTCTTATCCCCCTAAAGTTGCAGT
*** ** * *
56776524 GGGGCAGACTGAAGATGGCGAA-TCTTA-TCTCCCTGAAGTTGCAGTGGAGTAGA-T-TAAA-GC
65 GAAACAGACTGAAGAAAGC-AAGTCTTATTC-CCCTAAAGTTGCAGTGGAGTAGACTGAAAATG-
* *
56776584 CAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTACAAATCCTATCTCCTTGAA
127 CAA-AATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCCTATCTCCTTGAA
56776649 GTTGCAGTGGAGCGGATTAAAGTTACAAGTCT
191 GTTGCAGTGGAGCGGATTAAAGTTACAAGTCT
56776681 TAT
1 TAT
56776684 TGAAGAAAGC
Statistics
Matches: 198, Mismatches: 21, Indels: 12
0.86 0.09 0.05
Matches are distributed among these distances:
220 1 0.01
221 5 0.03
222 126 0.64
223 64 0.32
224 2 0.01
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.28
Consensus pattern (222 bp):
TATCTCCCTGAAGTTGTAGTGGAGCAGACTAAAGAAACAAGTCTTATCCCCCTAAAGTTGCAGTG
AAACAGACTGAAGAAAGCAAGTCTTATTCCCCTAAAGTTGCAGTGGAGTAGACTGAAAATGCAAA
ATCCTATCTCCCTAAAGTTGCAGTGGAGCAGATTAAAGCCACAAATCCTATCTCCTTGAAGTTGC
AGTGGAGCGGATTAAAGTTACAAGTCT
Found at i:56777077 original size:41 final size:41
Alignment explanation
Indices: 56777020--56777182 Score: 137
Period size: 41 Copynumber: 3.7 Consensus size: 41
56777010 ATCATAAGAT
*
56777020 CTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATCAAAC
1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATCACATCAAAC
* * * * * *
56777061 CTTATCTCCCTAAAGTTGCAGTGGAATAGATCAAAGATATAAATCATAAGAT
1 CTTATCTCCCTGAAGTTACA---G--TAGAGC--AGAT-CACATC--AA-AC
*
56777113 CTTATCTCTCTGAAGTTACAGTAGAGCAGATCACATCAAAC
1 CTTATCTCCCTGAAGTTACAGTAGAGCAGATCACATCAAAC
* *
56777154 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
1 CTTATCTCCCTGAAGTTACAGTAGAGCAG
56777183 GTTGAAAATA
Statistics
Matches: 94, Mismatches: 17, Indels: 22
0.71 0.13 0.17
Matches are distributed among these distances:
41 44 0.47
42 2 0.02
44 5 0.05
45 4 0.04
46 5 0.05
47 5 0.05
48 4 0.04
49 5 0.05
51 2 0.02
52 18 0.19
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (41 bp):
CTTATCTCCCTGAAGTTACAGTAGAGCAGATCACATCAAAC
Found at i:56777099 original size:93 final size:93
Alignment explanation
Indices: 56776973--56777178 Score: 394
Period size: 93 Copynumber: 2.2 Consensus size: 93
56776963 AAATCTCATT
56776973 TCCCTAAAGATTGCAGTGGAATAGATCAAAGATATAAATCATAAGATCTTATCTCTCTGAAGTTA
1 TCCCTAAAG-TTGCAGTGGAATAGATCAAAGATATAAATCATAAGATCTTATCTCTCTGAAGTTA
56777038 CAGTAGAGCAGATCACATCAAACCTTATC
65 CAGTAGAGCAGATCACATCAAACCTTATC
56777067 TCCCTAAAGTTGCAGTGGAATAGATCAAAGATATAAATCATAAGATCTTATCTCTCTGAAGTTAC
1 TCCCTAAAGTTGCAGTGGAATAGATCAAAGATATAAATCATAAGATCTTATCTCTCTGAAGTTAC
56777132 AGTAGAGCAGATCACATCAAACCTTATC
66 AGTAGAGCAGATCACATCAAACCTTATC
*
56777160 TCCCTGAAGTTGCAGTGGA
1 TCCCTAAAGTTGCAGTGGA
56777179 GCAGGTTGAA
Statistics
Matches: 111, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
93 102 0.92
94 9 0.08
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (93 bp):
TCCCTAAAGTTGCAGTGGAATAGATCAAAGATATAAATCATAAGATCTTATCTCTCTGAAGTTAC
AGTAGAGCAGATCACATCAAACCTTATC
Found at i:56777211 original size:44 final size:44
Alignment explanation
Indices: 56777154--56777278 Score: 191
Period size: 44 Copynumber: 2.9 Consensus size: 44
56777144 CACATCAAAC
56777154 CTTATCTCCCTGAAGTTGCAGTGGAGCAGG-TTGAAAATACCAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-GGATTGAAAATACCAAT
** *
56777198 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAGCTACTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAATACCAAT
*
56777242 CCTATCTCCCTGAAGTTGCAGTGGAGCGGATT-AAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAAT
56777279 GATGAATCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
43 5 0.07
44 69 0.93
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCGGATTGAAAATACCAAT
Found at i:56777446 original size:89 final size:89
Alignment explanation
Indices: 56777350--56777627 Score: 362
Period size: 89 Copynumber: 3.1 Consensus size: 89
56777340 CTCCTTAAAG
*
56777350 TTGCAGCGGAGCAGACTGACGATAGCAGATCTTGTCTTCCTATATTGGCAGCAAAGCAGATCGAA
1 TTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCAAAGCAGATCGAA
56777415 GACACCAGCCTTACCTCCTTGAGT
66 GACACCAGCCTTACCTCCTTGAGT
* *
56777439 TTGCAGCGGAGCAGACTGAAGATAGTAGATCTTGTCTTTCTATATTGGCAGCGAAA-CAGATCGA
1 TTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGC-AAAGCAGATCGA
* * *
56777503 AGACACTAGTCTTACCTCCCTGAGT
65 AGACACCAGCCTTACCTCCTTGAGT
* * * * * * * **
56777528 TTGCAACGGAGCAGACTGAAAACAACAGATCTTGTCTTCTTGTACTGGCAGTGAAGCAGATCGAA
1 TTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCAAAGCAGATCGAA
* *
56777593 AACACCAGCCTTGCCT-CTCTGAGT
66 GACACCAGCCTTACCTCCT-TGAGT
*
56777617 TTGCAGTGGAG
1 TTGCAGCGGAG
56777628 TATGTAATAC
Statistics
Matches: 162, Mismatches: 24, Indels: 6
0.84 0.12 0.03
Matches are distributed among these distances:
88 3 0.02
89 156 0.96
90 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.25
Consensus pattern (89 bp):
TTGCAGCGGAGCAGACTGAAGATAGCAGATCTTGTCTTCCTATATTGGCAGCAAAGCAGATCGAA
GACACCAGCCTTACCTCCTTGAGT
Found at i:56780260 original size:131 final size:132
Alignment explanation
Indices: 56779951--56780318 Score: 569
Period size: 131 Copynumber: 2.8 Consensus size: 132
56779941 GGGTGTTACA
56779951 GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAA
1 GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAA
* * *
56780016 TATTATCTTCCCA-AGGTAGTAGGGAAGCAAATTTAAGTCATCAGTCCTATCTCCCTGAGCAGCA
66 TATTATCTT-CCAGAGGTAGTAGGGAAGCAGATTTAAGCCAGCAGTCCTATCTCCCTGAGCAGCA
56780080 ATG
130 ATG
* * *
56780083 GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAATGGAGCAGATCGAAGACGGCAAA
1 GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAA
* * * * *
56780148 TCTTATCTTCCTGAGATAGTA-GGAAGCAGATTTAAGCCAGCAGTCCTATCTCCCTGAGCAGTAG
66 TATTATCTTCCAGAGGTAGTAGGGAAGCAGATTTAAGCCAGCAGTCCTATCTCCCTGAGCAGCAA
56780212 TG
131 TG
* * * *
56780214 GAGTAGGTTGAAGATTATATATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATAAAAGACGGCGAG
1 GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAA
*
56780279 TTTTATCTTCCAGAGGTAGTAGGGAAGCAGATTTAAGCCA
66 TATTATCTTCCAGAGGTAGTAGGGAAGCAGATTTAAGCCA
56780319 CCAGCCTTAT
Statistics
Matches: 213, Mismatches: 21, Indels: 4
0.89 0.09 0.02
Matches are distributed among these distances:
131 118 0.55
132 95 0.45
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.25
Consensus pattern (132 bp):
GAGTAGGTTGAAGATTGTAGATCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGCGAA
TATTATCTTCCAGAGGTAGTAGGGAAGCAGATTTAAGCCAGCAGTCCTATCTCCCTGAGCAGCAA
TG
Found at i:56780668 original size:15 final size:14
Alignment explanation
Indices: 56780641--56780671 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
56780631 GGGCTCACAA
56780641 AAAAATAATAAACC
1 AAAAATAATAAACC
*
56780655 AAAAATAATAAAAC
1 AAAAATAATAAACC
56780669 AAA
1 AAA
56780672 GTCCAAGTCC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.77, C:0.10, G:0.00, T:0.13
Consensus pattern (14 bp):
AAAAATAATAAACC
Found at i:56780806 original size:19 final size:19
Alignment explanation
Indices: 56780782--56780837 Score: 85
Period size: 19 Copynumber: 2.9 Consensus size: 19
56780772 ATAATCTTCA
*
56780782 ATGATATGCAATCATAGGT
1 ATGATATGCAATCATAGAT
*
56780801 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCATAGAT
*
56780820 ATGATATGCAATCTTAGA
1 ATGATATGCAATCATAGA
56780838 AGATGTGATT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 35 1.00
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (19 bp):
ATGATATGCAATCATAGAT
Done.