Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01010573.1 Kokia drynarioides strain JFW-HI SEQ_125496, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 690509
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 15 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:213381 original size:166 final size:166
Alignment explanation
Indices: 213101--213466 Score: 660
Period size: 166 Copynumber: 2.2 Consensus size: 166
213091 CAATTATGGG
* *
213101 AGGACACTATCTCTTTGTCCAACCATGGGCTCCGGCTTAGTAAAATCCAGATCCTGTGGAAACCA
1 AGGACACTATCTCTTTGTCCAACCATGGACTCCGACTTAGTAAAATCCAGATCCTGTGGAAACCA
* * *
213166 AAGAACCAATTTTAGTTGATGGATTTAGAAAATAACTATTTTCGTTTTGTGGATAAAGGAGATCT
66 AAGAACCAATTTCAGTTGATGGATTTAGAAAATAACTATTATAGTTTTGTGGATAAAGGAGATCT
213231 GGAAAGGGCAATTATGGGAGGACCTTGGATGATGTT
131 GGAAAGGGCAATTATGGGAGGACCTTGGATGATGTT
*
213267 AGGACACTATCTCTTTGTCTAACCATGGACTCCGACTTAGTAAAATCCAGATCCTGTGGAAACCA
1 AGGACACTATCTCTTTGTCCAACCATGGACTCCGACTTAGTAAAATCCAGATCCTGTGGAAACCA
213332 AAGAACCAATTTCAGTTGATGGATTTAGAAAATAACTATTATAGTTTTGTGGATAAAGGAGATCT
66 AAGAACCAATTTCAGTTGATGGATTTAGAAAATAACTATTATAGTTTTGTGGATAAAGGAGATCT
213397 GGAAAGGGCAATTATGGGAGGACCTTGGATGATGTT
131 GGAAAGGGCAATTATGGGAGGACCTTGGATGATGTT
* *
213433 AGGACGCTATCTCTCTGTCCAACCATGGACTCCG
1 AGGACACTATCTCTTTGTCCAACCATGGACTCCG
213467 GCTTTCTCCA
Statistics
Matches: 191, Mismatches: 9, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
166 191 1.00
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (166 bp):
AGGACACTATCTCTTTGTCCAACCATGGACTCCGACTTAGTAAAATCCAGATCCTGTGGAAACCA
AAGAACCAATTTCAGTTGATGGATTTAGAAAATAACTATTATAGTTTTGTGGATAAAGGAGATCT
GGAAAGGGCAATTATGGGAGGACCTTGGATGATGTT
Found at i:223257 original size:20 final size:21
Alignment explanation
Indices: 223213--223259 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 21
223203 AATCCCAGTG
* *
223213 GTATCGATATTTTTTTACTAGA
1 GTATCGATATTTTTATAC-AAA
223235 GTATCGATATTTTTATA-AAA
1 GTATCGATATTTTTATACAAA
223255 GTATC
1 GTATC
223260 AATGCCAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 7 0.30
22 16 0.70
ACGTcount: A:0.32, C:0.09, G:0.13, T:0.47
Consensus pattern (21 bp):
GTATCGATATTTTTATACAAA
Found at i:228517 original size:21 final size:21
Alignment explanation
Indices: 228493--228543 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
228483 ATAAGCACAC
228493 TCAGATGCATCCATAACA-AA
1 TCAGATGCATCCATAACAGAA
* * *
228513 GTCAGATCCATTCATACCAGAA
1 -TCAGATGCATCCATAACAGAA
228535 TCAGATGCA
1 TCAGATGCA
228544 GCGACAACAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
21 23 0.92
22 2 0.08
ACGTcount: A:0.39, C:0.25, G:0.14, T:0.22
Consensus pattern (21 bp):
TCAGATGCATCCATAACAGAA
Found at i:247965 original size:24 final size:24
Alignment explanation
Indices: 247929--247979 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
247919 ATAGACAGCA
* *
247929 TTAGCTCTCACGAGCCCAGGATGG
1 TTAGATCTCACGAGCCCAGAATGG
*
247953 TTAGATCTTACGAGCCCAGAATGG
1 TTAGATCTCACGAGCCCAGAATGG
247977 TTA
1 TTA
247980 ACTAGTATAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.25
Consensus pattern (24 bp):
TTAGATCTCACGAGCCCAGAATGG
Found at i:250280 original size:5 final size:5
Alignment explanation
Indices: 250270--250294 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
250260 TTATTAAATA
250270 ATTTT ATTTT ATTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT ATTTT ATTTT
250295 TTACTTTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:252793 original size:32 final size:32
Alignment explanation
Indices: 252733--252795 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
252723 AGCCGAAATT
** ** *
252733 AATTAGCTGATTAATGTGTTTCAGGTACATGC
1 AATTAGCTGATTAAAATAATTCAAGTACATGC
252765 AATTAGCTGATTAAAATAATTCAAGTACATG
1 AATTAGCTGATTAAAATAATTCAAGTACATG
252796 TATGGATGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.37, C:0.11, G:0.17, T:0.35
Consensus pattern (32 bp):
AATTAGCTGATTAAAATAATTCAAGTACATGC
Found at i:254387 original size:18 final size:18
Alignment explanation
Indices: 254364--254407 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
254354 GTAGCCTGGA
254364 CAGATGC-GATCATAAAAC
1 CAGATGCAG-TCATAAAAC
* *
254382 CAGATGCAGTCATATAAT
1 CAGATGCAGTCATAAAAC
254400 CAGATGCA
1 CAGATGCA
254408 ACCACATGCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 22 0.96
19 1 0.04
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.20
Consensus pattern (18 bp):
CAGATGCAGTCATAAAAC
Found at i:259786 original size:32 final size:32
Alignment explanation
Indices: 259741--259803 Score: 81
Period size: 32 Copynumber: 2.0 Consensus size: 32
259731 AGCCGAAATT
* * *
259741 AATTAGCTGATTAATGTGTTTCAAGTACATGC
1 AATTAGCTAATTAATATATTTCAAGTACATGC
* *
259773 AATTAGTTAATTAATATATTTCAGGTACATG
1 AATTAGCTAATTAATATATTTCAAGTACATG
259804 TATGGATGGC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.35, C:0.10, G:0.16, T:0.40
Consensus pattern (32 bp):
AATTAGCTAATTAATATATTTCAAGTACATGC
Found at i:261490 original size:9 final size:9
Alignment explanation
Indices: 261476--261502 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
261466 AGGATAGCAT
261476 CAACAACAG
1 CAACAACAG
261485 CAACAACAG
1 CAACAACAG
261494 CAACAACAG
1 CAACAACAG
261503 TATTCTCAAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.56, C:0.33, G:0.11, T:0.00
Consensus pattern (9 bp):
CAACAACAG
Found at i:267715 original size:19 final size:17
Alignment explanation
Indices: 267688--267726 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
267678 TGAGGGTATT
267688 GAAGCAAAAGAGAAAAGAA
1 GAAGC-AAA-AGAAAAGAA
*
267707 GAAGGAAAAGAAAAGAA
1 GAAGCAAAAGAAAAGAA
267724 GAA
1 GAA
267727 AGAAGAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 12 0.63
18 3 0.16
19 4 0.21
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (17 bp):
GAAGCAAAAGAAAAGAA
Found at i:267720 original size:17 final size:18
Alignment explanation
Indices: 267698--267736 Score: 62
Period size: 17 Copynumber: 2.2 Consensus size: 18
267688 GAAGCAAAAG
*
267698 AGAAAAGAAGAAGGAA-A
1 AGAAAAGAAGAAAGAAGA
267715 AGAAAAGAAGAAAGAAGA
1 AGAAAAGAAGAAAGAAGA
267733 AGAA
1 AGAA
267737 GTTGCCTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AGAAAAGAAGAAAGAAGA
Found at i:285503 original size:13 final size:14
Alignment explanation
Indices: 285485--285514 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
285475 TTTGGTTGTA
285485 ATTAGAC-TTGGAC
1 ATTAGACATTGGAC
285498 ATTAGACATTGGAC
1 ATTAGACATTGGAC
285512 ATT
1 ATT
285515 TTTAATTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.44
14 9 0.56
ACGTcount: A:0.33, C:0.13, G:0.20, T:0.33
Consensus pattern (14 bp):
ATTAGACATTGGAC
Found at i:287297 original size:30 final size:29
Alignment explanation
Indices: 287212--287301 Score: 117
Period size: 30 Copynumber: 3.0 Consensus size: 29
287202 CATTAGCAAC
* * *
287212 ACACCCCCAAATTTTCAAGTGGTTGAAAG
1 ACACCCCCACATTTTCAAGTGGTTGTAGG
**
287241 ACACCCCTCACATTCCCAAGTGGTTGTAGG
1 ACACCCC-CACATTTTCAAGTGGTTGTAGG
287271 ACACCACCCACATTTTCAAGTGGTTGTAGG
1 ACACC-CCCACATTTTCAAGTGGTTGTAGG
287301 A
1 A
287302 TGGTTTTCTA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
29 7 0.13
30 43 0.83
31 2 0.04
ACGTcount: A:0.29, C:0.28, G:0.19, T:0.24
Consensus pattern (29 bp):
ACACCCCCACATTTTCAAGTGGTTGTAGG
Found at i:306236 original size:24 final size:24
Alignment explanation
Indices: 306209--306265 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
306199 AAGCCTAAAT
*
306209 CTAATAAATG-TAAAATATATTATG
1 CTAATAAATGCT-AAATATATTATA
306233 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATA
*
306257 CTACTAAAT
1 CTAATAAAT
306266 CTTCTAGAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 29 0.97
25 1 0.03
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATA
Found at i:306480 original size:32 final size:32
Alignment explanation
Indices: 306417--306480 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
306407 CATATTTTGT
* * *
306417 TAATTTCGTATAATTCTTAACAATATTTTAAA
1 TAATTTCCTATAATTATTAACAATATATTAAA
*
306449 TAATTTCCTATAATTAATTAATAAT-TATTAAA
1 TAATTTCCTATAATT-ATTAACAATATATTAAA
306481 GAAACACCTC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
32 20 0.74
33 7 0.26
ACGTcount: A:0.44, C:0.08, G:0.02, T:0.47
Consensus pattern (32 bp):
TAATTTCCTATAATTATTAACAATATATTAAA
Found at i:309610 original size:20 final size:21
Alignment explanation
Indices: 309587--309632 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
309577 GTTGTTCTGA
*
309587 TAGAAGC-ATACTTGTATCGG
1 TAGAAGCTATACTTGTATCAG
*
309607 TAGAA-CTATAGTTGTATCAG
1 TAGAAGCTATACTTGTATCAG
309627 TAGAAG
1 TAGAAG
309633 AGGAGTTCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 21 0.95
ACGTcount: A:0.35, C:0.11, G:0.24, T:0.30
Consensus pattern (21 bp):
TAGAAGCTATACTTGTATCAG
Found at i:309878 original size:20 final size:20
Alignment explanation
Indices: 309839--309878 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
309829 AGTCTTCAAG
* *
309839 GTATCGGTAGAACTGTAGTT
1 GTATCGATAGAACTGGAGTT
*
309859 GTATCGATAGAAGTGGAGTT
1 GTATCGATAGAACTGGAGTT
309879 ATACTGGTAG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.28, C:0.07, G:0.33, T:0.33
Consensus pattern (20 bp):
GTATCGATAGAACTGGAGTT
Found at i:313931 original size:19 final size:19
Alignment explanation
Indices: 313887--313922 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
313877 ACAAAATAAG
313887 TCAAAATAATTTTTAAAAA
1 TCAAAATAATTTTTAAAAA
313906 TCAAAAT-ATTTTTAAAA
1 TCAAAATAATTTTTAAAA
313923 TTCCAAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 10 0.59
19 7 0.41
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (19 bp):
TCAAAATAATTTTTAAAAA
Found at i:313933 original size:17 final size:17
Alignment explanation
Indices: 313894--313933 Score: 53
Period size: 18 Copynumber: 2.3 Consensus size: 17
313884 AAGTCAAAAT
313894 AATTTTTAAAAATCAAA
1 AATTTTTAAAAATCAAA
* *
313911 ATATTTTTAAAATTCCAA
1 A-ATTTTTAAAAATCAAA
313929 AATTT
1 AATTT
313934 ATATATTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 5 0.25
18 15 0.75
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.42
Consensus pattern (17 bp):
AATTTTTAAAAATCAAA
Found at i:327669 original size:17 final size:19
Alignment explanation
Indices: 327647--327685 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
327637 TTTACACAAC
327647 TTTTAC-TTAAT-TTTTGT
1 TTTTACTTTAATATTTTGT
*
327664 TTTTACTTTATTATTTTGT
1 TTTTACTTTAATATTTTGT
327683 TTT
1 TTT
327686 AGAAATGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
18 4 0.21
19 9 0.47
ACGTcount: A:0.15, C:0.05, G:0.05, T:0.74
Consensus pattern (19 bp):
TTTTACTTTAATATTTTGT
Found at i:331744 original size:21 final size:21
Alignment explanation
Indices: 331718--331758 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
331708 CTGTGACTTT
*
331718 TTTTGA-ATACTTTTTGTGACG
1 TTTTGAGAT-CTTTTCGTGACG
331739 TTTTGAGATCTTTTCGTGAC
1 TTTTGAGATCTTTTCGTGAC
331759 ACTTTTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 16 0.89
22 2 0.11
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51
Consensus pattern (21 bp):
TTTTGAGATCTTTTCGTGACG
Found at i:332577 original size:28 final size:27
Alignment explanation
Indices: 332524--332577 Score: 63
Period size: 27 Copynumber: 2.0 Consensus size: 27
332514 TTTTTAGTAT
* * * *
332524 TATTTTTATTTATACAAAATTTAAATA
1 TATTTTTATTGATAAAAAACTCAAATA
332551 TATTTTTATTGATTAAAAAACTCAAAT
1 TATTTTTATTGA-TAAAAAACTCAAAT
332578 TAGATTGAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 11 0.50
28 11 0.50
ACGTcount: A:0.44, C:0.06, G:0.02, T:0.48
Consensus pattern (27 bp):
TATTTTTATTGATAAAAAACTCAAATA
Found at i:333005 original size:18 final size:18
Alignment explanation
Indices: 332982--333021 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
332972 TCCTCCACTA
332982 CACCCACCGATCGACCAC
1 CACCCACCGATCGACCAC
333000 CACCCACCGATCGACCAC
1 CACCCACCGATCGACCAC
333018 CACC
1 CACC
333022 ATCATCATTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.28, C:0.57, G:0.10, T:0.05
Consensus pattern (18 bp):
CACCCACCGATCGACCAC
Found at i:343601 original size:15 final size:14
Alignment explanation
Indices: 343581--343612 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
343571 GAGGAGAAGG
343581 AAGAAGAAGAAAAGA
1 AAGAAGAAGAAAA-A
343596 AAGAAGAAGAAAAA
1 AAGAAGAAGAAAAA
343610 AAG
1 AAG
343613 GAATTTTTTT
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:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (14 bp):
AAGAAGAAGAAAAA
Found at i:343601 original size:18 final size:18
Alignment explanation
Indices: 343575--343612 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
343565 ATCACGGAGG
* *
343575 AGAAGGAAGAAGAAGAAA
1 AGAAAGAAGAAGAAAAAA
343593 AGAAAGAAGAAGAAAAAA
1 AGAAAGAAGAAGAAAAAA
343611 AG
1 AG
343613 GAATTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (18 bp):
AGAAAGAAGAAGAAAAAA
Found at i:354777 original size:17 final size:17
Alignment explanation
Indices: 354755--354797 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
354745 TGTATGCGTC
354755 TTTATTGTCATTGCATT
1 TTTATTGTCATTGCATT
*
354772 TTTATTTTGTCATTGTATT
1 TTTA--TTGTCATTGCATT
354791 TTT-TTGT
1 TTTATTGT
354798 TAATTTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
16 4 0.17
17 4 0.17
19 15 0.65
ACGTcount: A:0.14, C:0.07, G:0.12, T:0.67
Consensus pattern (17 bp):
TTTATTGTCATTGCATT
Found at i:361022 original size:18 final size:18
Alignment explanation
Indices: 361001--361035 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
360991 CCAAATACGA
361001 TCATAGAACCAGATGCAG
1 TCATAGAACCAGATGCAG
* *
361019 TCATATAATCAGATGCA
1 TCATAGAACCAGATGCA
361036 ACCATAAGCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.17, T:0.23
Consensus pattern (18 bp):
TCATAGAACCAGATGCAG
Found at i:367154 original size:18 final size:21
Alignment explanation
Indices: 367121--367175 Score: 62
Period size: 20 Copynumber: 2.7 Consensus size: 21
367111 GTATTGAACC
*
367121 AGAAGAAGAAGAA-AGAAAAGA
1 AGAAAAAGAAGAAGAG-AAAGA
*
367142 A-AAAAA-AAGAAGAGAATGA
1 AGAAAAAGAAGAAGAGAAAGA
367161 AGAAAAAGAAGAAGA
1 AGAAAAAGAAGAAGA
367176 CGTTGCCCCG
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
19 10 0.34
20 11 0.38
21 8 0.28
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (21 bp):
AGAAAAAGAAGAAGAGAAAGA
Found at i:367499 original size:17 final size:18
Alignment explanation
Indices: 367473--367514 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 18
367463 TCTCAGTCAC
367473 ATAAAAAAAG-GAAAG-TG
1 ATAAAAAAAGAG-AAGTTG
*
367490 ATAAAGAAAGAGAAGTTG
1 ATAAAAAAAGAGAAGTTG
367508 ATAAAAA
1 ATAAAAA
367515 GAATATATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.64, C:0.00, G:0.21, T:0.14
Consensus pattern (18 bp):
ATAAAAAAAGAGAAGTTG
Found at i:367524 original size:2 final size:2
Alignment explanation
Indices: 367517--367546 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
367507 GATAAAAAGA
*
367517 AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
367547 TATTATACAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:372677 original size:15 final size:15
Alignment explanation
Indices: 372658--372692 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
372648 CAAAATTAAT
*
372658 ATTTTTACAA-TTTC
1 ATTTTTACAACATTC
372672 ATTTTTACAACATTC
1 ATTTTTACAACATTC
372687 ATTTTT
1 ATTTTT
372693 CTTTAAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 10 0.53
15 9 0.47
ACGTcount: A:0.29, C:0.14, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTTACAACATTC
Found at i:373299 original size:8 final size:8
Alignment explanation
Indices: 373286--373310 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
373276 TAATTAAAAA
373286 TATTATTT
1 TATTATTT
373294 TATTATTT
1 TATTATTT
373302 TATTATTT
1 TATTATTT
373310 T
1 T
373311 TAAATAGTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
TATTATTT
Found at i:384031 original size:14 final size:14
Alignment explanation
Indices: 383998--384038 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
383988 AAGATTGATT
383998 AAGATGAA-AGTAA
1 AAGATGAATAGTAA
*
384011 AAGATGAATAGTGA
1 AAGATGAATAGTAA
*
384025 TAGATGAATAGTAA
1 AAGATGAATAGTAA
384039 GACATCGAGA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
13 8 0.33
14 16 0.67
ACGTcount: A:0.54, C:0.00, G:0.24, T:0.22
Consensus pattern (14 bp):
AAGATGAATAGTAA
Found at i:391788 original size:32 final size:32
Alignment explanation
Indices: 391747--391810 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
391737 ACTAGTGAAC
391747 TTGTTGTTTTGTAGATTTCATTTTGTGACTTG
1 TTGTTGTTTTGTAGATTTCATTTTGTGACTTG
*
391779 TTGTTGTTTTGTAGATTTCGTTTTGTGACTTG
1 TTGTTGTTTTGTAGATTTCATTTTGTGACTTG
391811 AAGATCGGAT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.11, C:0.06, G:0.23, T:0.59
Consensus pattern (32 bp):
TTGTTGTTTTGTAGATTTCATTTTGTGACTTG
Found at i:392983 original size:13 final size:14
Alignment explanation
Indices: 392964--392997 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
392954 TTCTTGTTCA
*
392964 TTCTTTTGACTTTT
1 TTCTTTTGAATTTT
392978 TT-TTTTGAATTTT
1 TTCTTTTGAATTTT
392991 TTCTTTT
1 TTCTTTT
392998 TTTTTTGGCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.09, C:0.09, G:0.06, T:0.76
Consensus pattern (14 bp):
TTCTTTTGAATTTT
Found at i:397581 original size:22 final size:22
Alignment explanation
Indices: 397527--397581 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
397517 AAAATTTATT
* *
397527 TTTTTATTTATTATTATATAAA
1 TTTTTATTTAATATAATATAAA
*
397549 TTCTTATTTTAATATAAT-TAAAA
1 TTTTTA-TTTAATATAATAT-AAA
397572 TTTTTATTTA
1 TTTTTATTTA
397582 TAAATGTGAT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
22 10 0.37
23 17 0.63
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
TTTTTATTTAATATAATATAAA
Found at i:398017 original size:30 final size:29
Alignment explanation
Indices: 397960--398034 Score: 79
Period size: 30 Copynumber: 2.7 Consensus size: 29
397950 TAAAAATATA
*
397960 ATTTTTAAAGA-ATTAAATTAAATTTTTAT
1 ATTTTTAAA-ATATTAAAATAAATTTTTAT
397989 CATTTTTAAAATATTAAAATATAA-TTTTAT
1 -ATTTTTAAAATATTAAAATA-AATTTTTAT
398019 -TTTTT-AAAT-TTAAAAT
1 ATTTTTAAAATATTAAAAT
398035 TTTTAAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 7 0.17
27 4 0.10
28 5 0.12
29 1 0.02
30 23 0.55
31 2 0.05
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (29 bp):
ATTTTTAAAATATTAAAATAAATTTTTAT
Found at i:398036 original size:16 final size:17
Alignment explanation
Indices: 398017--398050 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
398007 ATATAATTTT
*
398017 ATTTTTTAAA-TTTAAA
1 ATTTTTAAAATTTTAAA
398033 ATTTTTAAAATTTTAAA
1 ATTTTTAAAATTTTAAA
398050 A
1 A
398051 GATTTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTTTAAAATTTTAAA
Found at i:404493 original size:18 final size:18
Alignment explanation
Indices: 404467--404509 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
404457 CATAAAAATT
* *
404467 AAAACATATGCATGCAAC
1 AAAAAATATGCAAGCAAC
404485 AAAAAATATGCAAGCAAC
1 AAAAAATATGCAAGCAAC
404503 AAAAAAT
1 AAAAAAT
404510 CTAACACTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.60, C:0.16, G:0.09, T:0.14
Consensus pattern (18 bp):
AAAAAATATGCAAGCAAC
Found at i:406093 original size:18 final size:18
Alignment explanation
Indices: 406067--406102 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
406057 GTTTTGGAAG
406067 AAGAGTTTAAGAGTTTTA
1 AAGAGTTTAAGAGTTTTA
* *
406085 AAGATTTTAAGGGTTTTA
1 AAGAGTTTAAGAGTTTTA
406103 GGGTTTTAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.36, C:0.00, G:0.22, T:0.42
Consensus pattern (18 bp):
AAGAGTTTAAGAGTTTTA
Found at i:418511 original size:18 final size:18
Alignment explanation
Indices: 418476--418513 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
418466 TTGTCGAAAC
418476 ATTTTTTTTAAAGTATCGA
1 ATTTTTTTTAAAG-ATCGA
418495 ATTTTATTTTAAA-ATCGA
1 ATTTT-TTTTAAAGATCGA
418513 A
1 A
418514 AATGTAGTCG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.33
19 5 0.28
20 7 0.39
ACGTcount: A:0.37, C:0.05, G:0.08, T:0.50
Consensus pattern (18 bp):
ATTTTTTTTAAAGATCGA
Found at i:419008 original size:109 final size:107
Alignment explanation
Indices: 418884--419096 Score: 275
Period size: 109 Copynumber: 2.0 Consensus size: 107
418874 AATAAAGAAC
* * * ** *
418884 ATTTATCAATTTTAAATAGGATATTTAATTAT-TTAGGTTCAAGGAAAAATCATACTTAGTACGT
1 ATTTATCAATTTTAAATAGAATATTTAATTATGTAAGG-TCAACGAAAAATCATACCCAATACGT
*
418948 TAGGGCGCAATTTCTCGAATTCCCTAAAATAAAAGAACATTGAAT
65 TA-GGCACAATTTCTCGAA-TCCCTAAAATAAAAGAACATTGAAT
*
418993 ATTTATCGATTTTAAATAGAATATTTAATTATGTAAGGTCAACGAAAAATCATACCCAATACGTT
1 ATTTATCAATTTTAAATAGAATATTTAATTATGTAAGGTCAACGAAAAATCATACCCAATACGTT
* * * * *
419058 AGGCATAATTTTTTGAATCTCTTAAATAAAAGAACATTG
66 AGGCACAATTTCTCGAATCCCTAAAATAAAAGAACATTG
419097 TCTTTTTTCA
Statistics
Matches: 90, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
107 20 0.22
108 12 0.13
109 54 0.60
110 4 0.04
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.35
Consensus pattern (107 bp):
ATTTATCAATTTTAAATAGAATATTTAATTATGTAAGGTCAACGAAAAATCATACCCAATACGTT
AGGCACAATTTCTCGAATCCCTAAAATAAAAGAACATTGAAT
Found at i:420922 original size:17 final size:18
Alignment explanation
Indices: 420882--420926 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
420872 GATAGTGGGC
420882 TTGGGTGTTGGGCTTGTAAG
1 TTGGGT-TTGGGC-TGTAAG
*
420902 TTGGGTTTGGG-TGTAAT
1 TTGGGTTTGGGCTGTAAG
420919 TTGGGTTT
1 TTGGGTTT
420927 TGGTTGGTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
17 13 0.54
19 5 0.21
20 6 0.25
ACGTcount: A:0.09, C:0.02, G:0.42, T:0.47
Consensus pattern (18 bp):
TTGGGTTTGGGCTGTAAG
Found at i:421240 original size:49 final size:49
Alignment explanation
Indices: 421180--421422 Score: 201
Period size: 49 Copynumber: 4.9 Consensus size: 49
421170 AGACTTGCTT
**
421180 TTTGCAGCTTCAATCTACCTTTCTTCATCTTTAAGGTATAAGATTCACC
1 TTTGCAGCTTCAATCTACCCCTCTTCATCTTTAAGGTATAAGATTCACC
* * * **
421229 TTTGC-GACTTCAA-CCAGCCCCTCTTTATCTTT-AGAGTATAAGATCCATT
1 TTTGCAG-CTTCAATCTA-CCCCTCTTCATCTTTAAG-GTATAAGATTCACC
* * * * **
421278 TTTGCGGCTTCAATCTACCTCTCCTCATCTTTAGGGTATAAGATTTGCC
1 TTTGCAGCTTCAATCTACCCCTCTTCATCTTTAAGGTATAAGATTCACC
* * *
421327 TTTGCAGCTTCAATCGACCCCTCTAT-GTCTCTTAGGGTATAAGATTCA-C
1 TTTGCAGCTTCAATCTACCCCTCT-TCATCT-TTAAGGTATAAGATTCACC
** **
421376 TATTGCAGCTTCAATCTTTCCCTCCACATCTTT-AGAGTATAAGATTC
1 T-TTGCAGCTTCAATCTACCCCTCTTCATCTTTAAG-GTATAAGATTC
421423 GTCATTATGG
Statistics
Matches: 152, Mismatches: 31, Indels: 22
0.74 0.15 0.11
Matches are distributed among these distances:
48 6 0.04
49 104 0.68
50 42 0.28
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (49 bp):
TTTGCAGCTTCAATCTACCCCTCTTCATCTTTAAGGTATAAGATTCACC
Found at i:421348 original size:98 final size:99
Alignment explanation
Indices: 421178--421422 Score: 291
Period size: 98 Copynumber: 2.5 Consensus size: 99
421168 GAAGACTTGC
* * *
421178 TTTTTGCAGCTTCAATCTACCTTTCTTCATCTTTAAGGTATAAGATTCACCTTTGCGACTTCAAC
1 TTTTTGCAGCTTCAATCTACCTCTCCTCATCTTTAGGGTATAAGATTCACCTTTGCGACTTCAAC
*
421243 CAGCCCCTCTTTATCT-TTAGAGTATAAGATCCA
66 CAGCCCCTCTATATCTCTTAGAGTATAAGATCCA
* **
421276 TTTTTGCGGCTTCAATCTACCTCTCCTCATCTTTAGGGTATAAGATTTGCCTTTGC-AGCTTCAA
1 TTTTTGCAGCTTCAATCTACCTCTCCTCATCTTTAGGGTATAAGATTCACCTTTGCGA-CTTCAA
* * * *
421340 TC-GACCCCTCTATGTCTCTTAGGGTATAAGATTCA
65 CCAG-CCCCTCTATATCTCTTAGAGTATAAGATCCA
* * * * *
421375 CTATTGCAGCTTCAATCTTTCC-CTCCACATCTTTAGAGTATAAGATTC
1 TTTTTGCAGCTTCAATC-TACCTCTCCTCATCTTTAGGGTATAAGATTC
421423 GTCATTATGG
Statistics
Matches: 125, Mismatches: 18, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
97 2 0.02
98 68 0.54
99 52 0.42
100 3 0.02
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (99 bp):
TTTTTGCAGCTTCAATCTACCTCTCCTCATCTTTAGGGTATAAGATTCACCTTTGCGACTTCAAC
CAGCCCCTCTATATCTCTTAGAGTATAAGATCCA
Found at i:421491 original size:98 final size:97
Alignment explanation
Indices: 421359--421744 Score: 407
Period size: 98 Copynumber: 3.9 Consensus size: 97
421349 CTATGTCTCT
* ** *
421359 TAGGGTATAAGATTCACTATTGCAGCTTCAATCTTTCCCTCCACATCTTTAGAGTATAAGATTCG
1 TAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTCCACATCTCTAG-GTATAAGATTCG
* ** * * * * * *
421424 TCATTATGGCTTTAGTTTTTCCCTTCATATCTC
65 TCGTTGCGACTTCAATCTTTCCCTCCATATTTC
* * * * * *
421457 TAAGGTATAAGATTCGTCGTTGCAGCTTCAATCTTTCCCTTCACATATTTAGGTTATATGATTCG
1 TAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTCCACATCTCTAGG-TATAAGATTCG
* *
421522 TTGTTGCGACTTCAATCTTTCCCTCCACATTTC
65 TCGTTGCGACTTCAATCTTTCCCTCCATATTTC
* * * * * * *
421555 TAGGGTAAAAGATTTGCCATTAC-GATTTCAATCTTTCCCTTCACATCTCCATGGTATAAGATTC
1 TAGGGTATAAGATTCGCCGTTGCAG-CTTCAATCTTTCCCTCCACATCTCTA-GGTATAAGATTC
421619 GTCGTTGCGACTTCAATCTTTCCCTCCATATTTC
64 GTCGTTGCGACTTCAATCTTTCCCTCCATATTTC
* * * *
421653 TAGGGTATAAGATTCACCGTTGCGGCATCAATCTTTCCCTCAACATCTCTAGGGTATAAGATTCG
1 TAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTCCACATCTCTA-GGTATAAGATTCG
*
421718 TCTTTGCTG-CTTCAATCTTTCCCTCCA
65 TCGTTGC-GACTTCAATCTTTCCCTCCA
421745 CATCTTTAGG
Statistics
Matches: 239, Mismatches: 44, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
97 2 0.01
98 233 0.97
99 4 0.02
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (97 bp):
TAGGGTATAAGATTCGCCGTTGCAGCTTCAATCTTTCCCTCCACATCTCTAGGTATAAGATTCGT
CGTTGCGACTTCAATCTTTCCCTCCATATTTC
Found at i:421494 original size:49 final size:48
Alignment explanation
Indices: 421354--421759 Score: 359
Period size: 49 Copynumber: 8.2 Consensus size: 48
421344 CCCCTCTATG
* * *
421354 TCTCTTAGGGTATAAGATTC-ACTATTGCAGCTTCAATCTTTCCCTCCACA
1 TCTC-TAGGGTATAAGATTCGTC-GTTGC-GCTTCAATCTTTCCCTTCACA
* * * * * * *
421404 TCTTTAGAGTATAAGATTCGTCATTATG-GCTTTAGTTTTTCCCTTCATA
1 TCTCTAGGGTATAAGATTCGTC-GT-TGCGCTTCAATCTTTCCCTTCACA
*
421453 TCTCTAAGGTATAAGATTCGTCGTTGCAGCTTCAATCTTTCCCTTCACA
1 TCTCTAGGGTATAAGATTCGTCGTTGC-GCTTCAATCTTTCCCTTCACA
* * * * * *
421502 TATTTAGGTTATATGATTCGTTGTTGCGACTTCAATCTTTCCCTCCACA
1 TCTCTAGGGTATAAGATTCGTCGTTGCG-CTTCAATCTTTCCCTTCACA
* * * * * * *
421551 TTTCTAGGGTAAAAGATTTGCCATTACGATTTCAATCTTTCCCTTCACA
1 TCTCTAGGGTATAAGATTCGTCGTTGCG-CTTCAATCTTTCCCTTCACA
* * * *
421600 TCTCCATGGTATAAGATTCGTCGTTGCGACTTCAATCTTTCCCTCCATA
1 TCTCTAGGGTATAAGATTCGTCGTTGCG-CTTCAATCTTTCCCTTCACA
* ** *
421649 TTTCTAGGGTATAAGATTCACCGTTGCGGCATCAATCTTTCCC-TCAACA
1 TCTCTAGGGTATAAGATTCGTCGTTGC-GCTTCAATCTTTCCCTTC-ACA
* *
421698 TCTCTAGGGTATAAGATTCGTCTTTGCTGCTTCAATCTTTCCCTCCACA
1 TCTCTAGGGTATAAGATTCGTCGTTGC-GCTTCAATCTTTCCCTTCACA
*
421747 TCTTTAGGTGTAT
1 TCTCTAGG-GTAT
421760 TATATTCGCC
Statistics
Matches: 283, Mismatches: 64, Indels: 18
0.78 0.18 0.05
Matches are distributed among these distances:
47 2 0.01
48 3 0.01
49 265 0.94
50 11 0.04
51 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.14, T:0.39
Consensus pattern (48 bp):
TCTCTAGGGTATAAGATTCGTCGTTGCGCTTCAATCTTTCCCTTCACA
Found at i:421568 original size:147 final size:147
Alignment explanation
Indices: 421359--421749 Score: 436
Period size: 147 Copynumber: 2.7 Consensus size: 147
421349 CTATGTCTCT
** *
421359 TAGGGTATAAGATTCACTATTGC-AGCTTCAATCTTTCCCTCCACATCTT-TAGAGTATAAGATT
1 TAGGGTATAAGATTCACCGTTGCGA-CTTCAATCTTTCCCTCCACAT-TTCTAGGGTATAAGATT
* * * * * *
421422 CGTCATTATGGCTTT-AGTTTTTCCCTTCATATCTCTAAGGTATAAGATTCGTCGTTGC-AGCTT
64 CGTCATTA-CGATTTCAATCTTTCCCTTCACATCTCCAAGGTATAAGATTCGTCGTTGCGA-CTT
421485 CAATCTTTCCCTTCACATA-TT-
127 CAATCTTTCCC-TC-CATATTTC
* * *** * *
421506 TAGGTTATATGATTCGTTGTTGCGACTTCAATCTTTCCCTCCACATTTCTAGGGTAAAAGATTTG
1 TAGGGTATAAGATTCACCGTTGCGACTTCAATCTTTCCCTCCACATTTCTAGGGTATAAGATTCG
* *
421571 CCATTACGATTTCAATCTTTCCCTTCACATCTCCATGGTATAAGATTCGTCGTTGCGACTTCAAT
66 TCATTACGATTTCAATCTTTCCCTTCACATCTCCAAGGTATAAGATTCGTCGTTGCGACTTCAAT
421636 CTTTCCCTCCATATTTC
131 CTTTCCCTCCATATTTC
* * * *
421653 TAGGGTATAAGATTCACCGTTGCGGCATCAATCTTTCCCTCAACATCTCTAGGGTATAAGATTCG
1 TAGGGTATAAGATTCACCGTTGCGACTTCAATCTTTCCCTCCACATTTCTAGGGTATAAGATTCG
* * * *
421718 TCTTTGCTG-CTTCAATCTTTCCCTCCACATCT
66 TCATTAC-GATTTCAATCTTTCCCTTCACATCT
421750 TTAGGTGTAT
Statistics
Matches: 205, Mismatches: 32, Indels: 14
0.82 0.13 0.06
Matches are distributed among these distances:
145 4 0.02
146 10 0.05
147 188 0.92
148 3 0.01
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.39
Consensus pattern (147 bp):
TAGGGTATAAGATTCACCGTTGCGACTTCAATCTTTCCCTCCACATTTCTAGGGTATAAGATTCG
TCATTACGATTTCAATCTTTCCCTTCACATCTCCAAGGTATAAGATTCGTCGTTGCGACTTCAAT
CTTTCCCTCCATATTTC
Found at i:421802 original size:50 final size:50
Alignment explanation
Indices: 421728--421859 Score: 119
Period size: 50 Copynumber: 2.6 Consensus size: 50
421718 TCTTTGCTGC
* * * * * *
421728 TTCAATCT-TTCCCTCCACATCTTTAGGTGTATTATATTCGCCCTTG-TGT
1 TTCAATCTGTT-CCTCTACAGCTTTAGGTGTATCAGATTCACCCTTGCAGT
*
421777 CTTTAATCTGTTCCTCTACAGCTTTAAGG-GTATCAGATTCACCCTTGCAGT
1 -TTCAATCTGTTCCTCTACAGCTTT-AGGTGTATCAGATTCACCCTTGCAGT
* *
421828 TTCAATCTG-CCCTTCTATAGCTTTAGGTGTAT
1 TTCAATCTGTTCC-TCTACAGCTTTAGGTGTAT
421860 GATTTGGTGT
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
49 5 0.07
50 55 0.82
51 7 0.10
ACGTcount: A:0.19, C:0.25, G:0.14, T:0.42
Consensus pattern (50 bp):
TTCAATCTGTTCCTCTACAGCTTTAGGTGTATCAGATTCACCCTTGCAGT
Found at i:422121 original size:99 final size:98
Alignment explanation
Indices: 421860--422518 Score: 519
Period size: 99 Copynumber: 6.7 Consensus size: 98
421850 TTAGGTGTAT
*
421860 GATTTGGTGTTGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTAGTTGT
1 GATTTGGTG-TGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
* * *
421925 TTTAATCC-TCTTCATTGTAGCTTCAGGAAG-ATAG
65 TTTAATCCGAC-TCACTGTAACTTCAGG-AGTATAG
* * *
421959 GA--T--T-T-CAAGCTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTACTT--TTG
1 GATTTGGTGTGTAA-CTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCT-GTTACTT-
* * * *
422016 GCTTTAATCCGACTCATTGTAACTTCAGGGGTATAA
63 GTTTTAATCCGACTCACTGTAACTTCAGGAGTATAG
* * * * *
422052 GATTTGGTGCTGTAACTTCACTCCATTGCACTGTAACCTCAAGTACACTGAGATCTGTTACTTGT
1 GATTTGGTG-TGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
** *
422117 TTTAATTTGA-TCCACTATAACATT-AGG-GATATAG
65 TTTAATCCGACT-CACTGTAAC-TTCAGGAG-TATAG
* * * * * *
422151 GATTTTGTGTAGTAGCTTCACTTCATTCTATTATAACCTTAGGGACATTGAGATCTGTTACTTGT
1 GATTTGGTGT-GTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
* * *
422216 TTTAATTC-ACTTCACTGCAACTTCAAGAAG-ATAG
65 TTTAATCCGAC-TCACTGTAACTTC-AGGAGTATAG
* * * * * *
422250 AATTTGTTGTTGAAACTTCACTCCATTCCACTATAACCCCAGGGACATTAAGATCTGCTT-CTGG
1 GATTTGGTG-TGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTG-TTACTTG
* * *
422314 CTTTAATCCGACCCACTGCAACTTCAGGAGTATAG
64 TTTTAATCCGACTCACTGTAACTTCAGGAGTATAG
* ** * * *
422349 GATTTGGTGTAGTAGCTTTGCTCCATTCCACTGTAACCTTAGGGACATTGAGATCTGCTACTTGT
1 GATTTGGTGT-GTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
* * * **
422414 TTTAATCAG-CTATACTGCAACTTCAAAAAG-ATAG
65 TTTAATCCGACT-CACTGTAACTTC-AGGAGTATAG
* * * * **
422448 GATTTGTTAT-TGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACTTTGAGATCTACTACTTG
1 GATTTGGTGTGT-AA-CTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTG
422512 TTTTAAT
64 TTTTAAT
422519 TCGCTTCACT
Statistics
Matches: 450, Mismatches: 77, Indels: 66
0.76 0.13 0.11
Matches are distributed among these distances:
92 5 0.01
93 70 0.16
94 3 0.01
95 2 0.00
97 3 0.01
98 16 0.04
99 333 0.74
100 17 0.04
101 1 0.00
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (98 bp):
GATTTGGTGTGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGTT
TTAATCCGACTCACTGTAACTTCAGGAGTATAG
Found at i:422270 original size:198 final size:198
Alignment explanation
Indices: 421873--422521 Score: 587
Period size: 198 Copynumber: 3.3 Consensus size: 198
421863 TTGGTGTTGT
* * ** *
421873 AACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTAGTTGTTTTAA-TCCTCTT
1 AACTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTACTTGTTTTAATTCGAC-C
* ** * * * *
421937 CATTGTAGCTTCAGGAAG-ATAGGA-TT--T-CA--AGCTTCACTCCATTCCACTGTAACCTCAG
65 CACTACAACTTCAGG-AGTATAGGATTTGGTGTAGTAGCTTCACTCCATTCCACTATAACCTTAG
* * * * * ***
421995 GGACATTGAGATCTACT-TTTGGCTTTAATCCGACTCAT--TGTAACTTC-AGGGGTATA-AGAT
129 GGACATTGAGATCTGCTACTT-GTTTTAATCAG-CT-ATACTGCAACTTCAAAAAG-ATAGA-AT
* ** *
422055 TTGGTGCTGT
189 TTGTTATTGA
* * * * * *
422065 AACTTCACTCCATTGCACTGTAACCTCAAGTACACTGAGATCTGTTACTTGTTTTAATTTGATCC
1 AACTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTACTTGTTTTAATTCGACCC
* * * * *
422130 ACTATAACATT-AGG-GATATAGGATTTTGTGTAGTAGCTTCACTTCATTCTATTATAACCTTAG
66 ACTACAAC-TTCAGGAG-TATAGGATTTGGTGTAGTAGCTTCACTCCATTCCACTATAACCTTAG
* *
422193 GGACATTGAGATCTGTTACTTGTTTTAATTCA-CT-TCACTGCAACTTCAAGAAGATAGAATTTG
129 GGACATTGAGATCTGCTACTTGTTTTAA-TCAGCTAT-ACTGCAACTTCAAAAAGATAGAATTTG
*
422256 TTGTTGA
192 TTATTGA
* * * * * *
422263 AACTTCACTCCATTCCACTATAACCCCAGGGACATTAAGATCTGCTT-CTGGCTTTAATCCGACC
1 AACTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTG-TTACTTGTTTTAATTCGACC
* ** *
422327 CACTGCAACTTCAGGAGTATAGGATTTGGTGTAGTAGCTTTGCTCCATTCCACTGTAACCTTAGG
65 CACTACAACTTCAGGAGTATAGGATTTGGTGTAGTAGCTTCACTCCATTCCACTATAACCTTAGG
*
422392 GACATTGAGATCTGCTACTTGTTTTAATCAGCTATACTGCAACTTCAAAAAGATAGGATTTGTTA
130 GACATTGAGATCTGCTACTTGTTTTAATCAGCTATACTGCAACTTCAAAAAGATAGAATTTGTTA
422457 TTGA
195 TTGA
* * **
422461 AGCTTCACTCCATTCCACTGTAACCTCAGGGACTTTGAGATCTACTACTTGTTTTAATTCG
1 AACTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTACTTGTTTTAATTCG
422522 CTTCACTACG
Statistics
Matches: 368, Mismatches: 66, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
190 1 0.00
192 66 0.18
193 5 0.01
195 2 0.01
196 1 0.00
197 8 0.02
198 273 0.74
199 12 0.03
ACGTcount: A:0.27, C:0.21, G:0.17, T:0.35
Consensus pattern (198 bp):
AACTTCACTCCATTCCACTGTAACCTCAGGGACATTGAGATCTGTTACTTGTTTTAATTCGACCC
ACTACAACTTCAGGAGTATAGGATTTGGTGTAGTAGCTTCACTCCATTCCACTATAACCTTAGGG
ACATTGAGATCTGCTACTTGTTTTAATCAGCTATACTGCAACTTCAAAAAGATAGAATTTGTTAT
TGA
Found at i:422403 original size:297 final size:291
Alignment explanation
Indices: 421860--422528 Score: 734
Period size: 297 Copynumber: 2.3 Consensus size: 291
421850 TTAGGTGTAT
* *
421860 GATTTGGTGTTGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTAGTTGT
1 GATTTGGTGTAGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
* * * * * * *
421925 TTTAATCCTCTTCATTGTAGCTTCAGGAAGATAGGATTTCAAGCTTCACTCCATTCCACTGTAAC
66 TTTAATCCACTTCACTGCAACTTCAAGAAGATAGGATTTCAAACTTCACTCCATTCCACTATAAC
* * * * * * *
421990 CTCAGGGACATTGAGATCTACTTTTGGCTTTAATCCGACTCATTGTAACTTCAGGGGTATAAGAT
131 CCCAGGGACATTAAGATCTACTTCTGGCTTTAATCCGACCCACTGCAACTTCAGGAGTATAAGAT
* * *
422055 TTGGTGCTGTAACTTCACTCCATTGCACTGTAACCTCAAGTACACTGAGATCTGTTACTTGTTTT
196 TTGGTGCTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACACTGAGATCTGCTACTTGTTTT
422120 AATTTGATCCACTATAACATTAGGGATATAG
261 AATTTGATCCACTATAACATTAGGGATATAG
* * * * * *
422151 GATTTTGTGTAGTAGCTTCACTTCATTCTATTATAACCTTAGGGACATTGAGATCTGTTACTTGT
1 GATTTGGTGTAGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
* * *
422216 TTTAATTCACTTCACTGCAACTTCAAGAAGATAGAATTTGTTGTTGAAACTTCACTCCATTCCAC
66 TTTAATCCACTTCACTGCAACTTCAAGAAGATAG-----GAT-TTCAAACTTCACTCCATTCCAC
*
422281 TATAACCCCAGGGACATTAAGATCTGCTTCTGGCTTTAATCCGACCCACTGCAACTTCAGGAGTA
125 TATAACCCCAGGGACATTAAGATCTACTTCTGGCTTTAATCCGACCCACTGCAACTTCAGGAGTA
* * ** * * *
422346 TAGGATTTGGTG-TAGTAGCTTTGCTCCATTCCACTGTAACCTTAGGGACATTGAGATCTGCTAC
190 TAAGATTTGGTGCT-GTAACTTCACTCCATTCCACTGTAACCTCAAGGACACTGAGATCTGCTAC
** * ** ** *** *
422410 TTGTTTTAATCAGCTATACTGCAAC-TTCAAAAAGATAG
254 TTGTTTTAATTTGATCCACTATAACATT-AGGGATATAG
* * * **
422448 GATTT-GT-TATTGAAGCTTCACTCCATTCCACTGTAACCTCAGGGACTTTGAGATCTACTACTT
1 GATTTGGTGTAGT-AA-CTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTT
* *
422511 GTTTTAATTCGCTTCACT
64 GTTTTAATCCACTTCACT
422529 ACGACATTGA
Statistics
Matches: 310, Mismatches: 58, Indels: 14
0.81 0.15 0.04
Matches are distributed among these distances:
291 85 0.27
295 3 0.01
296 8 0.03
297 214 0.69
ACGTcount: A:0.26, C:0.21, G:0.17, T:0.36
Consensus pattern (291 bp):
GATTTGGTGTAGTAACTTCACTCCATTCCACTATAACCTCAGGGACATTGAGATCTGTTACTTGT
TTTAATCCACTTCACTGCAACTTCAAGAAGATAGGATTTCAAACTTCACTCCATTCCACTATAAC
CCCAGGGACATTAAGATCTACTTCTGGCTTTAATCCGACCCACTGCAACTTCAGGAGTATAAGAT
TTGGTGCTGTAACTTCACTCCATTCCACTGTAACCTCAAGGACACTGAGATCTGCTACTTGTTTT
AATTTGATCCACTATAACATTAGGGATATAG
Found at i:422558 original size:40 final size:40
Alignment explanation
Indices: 422495--422606 Score: 161
Period size: 40 Copynumber: 2.8 Consensus size: 40
422485 CTCAGGGACT
*
422495 TTGAGATCTACTACTTGTTTTAATTCGCTTCACTACGACA
1 TTGAGATCTACTACTTGTTTTAATCCGCTTCACTACGACA
* *
422535 TTGAGATCTACTAGTTGTCTTAATCCGCTTCACTACGACA
1 TTGAGATCTACTACTTGTTTTAATCCGCTTCACTACGACA
* * * *
422575 TTAAGATATACTACTTGTTTTAACCCACTTCA
1 TTGAGATCTACTACTTGTTTTAATCCGCTTCA
422607 TTACAACTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
40 63 1.00
ACGTcount: A:0.27, C:0.23, G:0.12, T:0.38
Consensus pattern (40 bp):
TTGAGATCTACTACTTGTTTTAATCCGCTTCACTACGACA
Found at i:426787 original size:108 final size:108
Alignment explanation
Indices: 426586--426798 Score: 254
Period size: 108 Copynumber: 2.0 Consensus size: 108
426576 AAGAAAGAAC
* ** * * *
426586 ATTTATCGATTTTAATTAGGATATTCAATTATTTTGGTTCAAGGAAAAATATACCCAGTACGTTA
1 ATTTATCGATTTTAAATAGGATATTCAATTATTAAGGTTAAACGAAAAATATACCCACTACGTTA
*
426651 GGGCACAATTTCTCGAGTTCCTTAAAATAAAAGAACATTGAAT
66 GGGCACAATTTCTCGAATTCCTTAAAATAAAAGAACATTGAAT
* * *
426694 ATTTATCGATTTTAAATATGATATTTAATTATGTAAGG-TAAACGAAAAATCGTACCCACTACGT
1 ATTTATCGATTTTAAATAGGATATTCAATTAT-TAAGGTTAAACGAAAAAT-ATACCCACTACGT
* *
426758 TAGGGCATAATTT-TCTGAA-TCTCTT-AAATAGAAGAACATTG
64 TAGGGCACAATTTCTC-GAATTC-CTTAAAATAAAAGAACATTG
426799 CCTTTTTTTG
Statistics
Matches: 89, Mismatches: 12, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
108 58 0.65
109 31 0.35
ACGTcount: A:0.38, C:0.13, G:0.15, T:0.35
Consensus pattern (108 bp):
ATTTATCGATTTTAAATAGGATATTCAATTATTAAGGTTAAACGAAAAATATACCCACTACGTTA
GGGCACAATTTCTCGAATTCCTTAAAATAAAAGAACATTGAAT
Found at i:429672 original size:20 final size:20
Alignment explanation
Indices: 429648--429714 Score: 73
Period size: 20 Copynumber: 3.4 Consensus size: 20
429638 TTTGGTGCCA
429648 CTATTTGAGCTTCGATGTCC
1 CTATTTGAGCTTCGATGTCC
* * *
429668 TTATTTGCA-CTTCAATGCCC
1 CTATTTG-AGCTTCGATGTCC
*
429688 CTATTTGTGCTTCGATGTCC
1 CTATTTGAGCTTCGATGTCC
*
429708 CTGTTTG
1 CTATTTG
429715 CACTTTGGTG
Statistics
Matches: 37, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
20 36 0.97
21 1 0.03
ACGTcount: A:0.13, C:0.25, G:0.18, T:0.43
Consensus pattern (20 bp):
CTATTTGAGCTTCGATGTCC
Found at i:429727 original size:40 final size:40
Alignment explanation
Indices: 429629--429727 Score: 135
Period size: 40 Copynumber: 2.5 Consensus size: 40
429619 TGAAATGTCG
* *
429629 TGTTTGCACTTTGGTGCCACTATTTGAGCTTCGATGTCCT
1 TGTTTGCACTTTGGTGCCCCTATTTGAGCTTCGATGTCCC
* *** *
429669 TATTTGCACTTCAATGCCCCTATTTGTGCTTCGATGTCCC
1 TGTTTGCACTTTGGTGCCCCTATTTGAGCTTCGATGTCCC
429709 TGTTTGCACTTTGGTGCCC
1 TGTTTGCACTTTGGTGCCC
429728 TTGTTTGCAC
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.12, C:0.26, G:0.20, T:0.41
Consensus pattern (40 bp):
TGTTTGCACTTTGGTGCCCCTATTTGAGCTTCGATGTCCC
Found at i:429768 original size:19 final size:20
Alignment explanation
Indices: 429706--429772 Score: 93
Period size: 20 Copynumber: 3.5 Consensus size: 20
429696 GCTTCGATGT
429706 CCCTGTTTGCACTTTGGTGC
1 CCCTGTTTGCACTTTGGTGC
*
429726 CCTTGTTTGCACTTTGGTG-
1 CCCTGTTTGCACTTTGGTGC
* *
429745 GCCTG-TTGCACTTCGGTGC
1 CCCTGTTTGCACTTTGGTGC
429764 CCCTGTTTG
1 CCCTGTTTG
429773 TACAATTGTA
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
18 12 0.30
19 7 0.17
20 21 0.52
ACGTcount: A:0.04, C:0.28, G:0.27, T:0.40
Consensus pattern (20 bp):
CCCTGTTTGCACTTTGGTGC
Found at i:432289 original size:26 final size:26
Alignment explanation
Indices: 432260--432332 Score: 119
Period size: 26 Copynumber: 2.8 Consensus size: 26
432250 GCGCAATTTC
432260 GGACATGCTCATGCAGCGACAATTCT
1 GGACATGCTCATGCAGCGACAATTCT
* *
432286 GGACATGTTCATGCAGTGACAATTCT
1 GGACATGCTCATGCAGCGACAATTCT
*
432312 AGACATGCTCATGCAGCGACA
1 GGACATGCTCATGCAGCGACA
432333 TTAGTAGTAA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 42 1.00
ACGTcount: A:0.29, C:0.25, G:0.23, T:0.23
Consensus pattern (26 bp):
GGACATGCTCATGCAGCGACAATTCT
Found at i:432792 original size:16 final size:16
Alignment explanation
Indices: 432771--432806 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
432761 GATACATAAA
432771 TTTTTTCTTTTCCTTT
1 TTTTTTCTTTTCCTTT
432787 TTTTTTCTTTTCCTTT
1 TTTTTTCTTTTCCTTT
432803 TTTT
1 TTTT
432807 ATGTGACTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (16 bp):
TTTTTTCTTTTCCTTT
Found at i:442187 original size:26 final size:26
Alignment explanation
Indices: 442131--442210 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 26
442121 TATTAGGGCG
* * * * *
442131 CAATTTTGGACATGCTCATGCTGCAA
1 CAATTCTGAACATGCTTATGCAGCGA
* *
442157 TAATTCT-AGACATG-TTCATGCAGTGA
1 CAATTCTGA-ACATGCTT-ATGCAGCGA
442183 CAATTCTGAACATGCTTATGCAGCGA
1 CAATTCTGAACATGCTTATGCAGCGA
442209 CA
1 CA
442211 TTAATAGTAA
Statistics
Matches: 41, Mismatches: 9, Indels: 8
0.71 0.16 0.14
Matches are distributed among these distances:
25 1 0.02
26 37 0.90
27 3 0.07
ACGTcount: A:0.30, C:0.21, G:0.19, T:0.30
Consensus pattern (26 bp):
CAATTCTGAACATGCTTATGCAGCGA
Found at i:450325 original size:14 final size:14
Alignment explanation
Indices: 450308--450344 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
450298 AACATTTACA
450308 TTTACTTTTATCTT-
1 TTTACTTTTA-CTTG
450322 TTTACTTTTACTTG
1 TTTACTTTTACTTG
450336 TTTA-TTTTA
1 TTTACTTTTA
450345 AATCTTATGC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 8 0.36
14 14 0.64
ACGTcount: A:0.16, C:0.11, G:0.03, T:0.70
Consensus pattern (14 bp):
TTTACTTTTACTTG
Found at i:450343 original size:20 final size:20
Alignment explanation
Indices: 450302--450343 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
450292 CATTTTAACA
*
450302 TTTACATTTACTTTTATCTT
1 TTTACATTTACTTTTATATT
*
450322 TTTACTTTTACTTGTT-TATT
1 TTTACATTTACTT-TTATATT
450342 TT
1 TT
450344 AAATCTTATG
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 17 0.89
21 2 0.11
ACGTcount: A:0.17, C:0.12, G:0.02, T:0.69
Consensus pattern (20 bp):
TTTACATTTACTTTTATATT
Found at i:453290 original size:10 final size:10
Alignment explanation
Indices: 453277--453322 Score: 53
Period size: 10 Copynumber: 4.9 Consensus size: 10
453267 AAAAAATCAC
453277 AAAAAGAAAG
1 AAAAAGAAAG
453287 AAAAAGAAAG
1 AAAAAGAAAG
*
453297 AAGAAGAAA-
1 AAAAAGAAAG
*
453306 AAAGA-AAAG
1 AAAAAGAAAG
453315 -AAAAGAAA
1 AAAAAGAAA
453323 AACATTGCCA
Statistics
Matches: 30, Mismatches: 4, Indels: 5
0.77 0.10 0.13
Matches are distributed among these distances:
8 6 0.20
9 6 0.20
10 18 0.60
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (10 bp):
AAAAAGAAAG
Found at i:453307 original size:17 final size:17
Alignment explanation
Indices: 453278--453324 Score: 64
Period size: 17 Copynumber: 2.9 Consensus size: 17
453268 AAAAATCACA
453278 AAAAG-AAAG-AAAAAG
1 AAAAGAAAAGAAAAAAG
453293 -AAAGAAGAAGAAAAAAG
1 AAAAGAA-AAGAAAAAAG
453310 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
453325 CATTGCCATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
14 4 0.14
15 1 0.04
16 3 0.11
17 14 0.50
18 6 0.21
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (17 bp):
AAAAGAAAAGAAAAAAG
Found at i:457879 original size:96 final size:97
Alignment explanation
Indices: 457705--457895 Score: 246
Period size: 96 Copynumber: 2.0 Consensus size: 97
457695 AACCTTGGAA
* * * *
457705 AAGGGTATTCGATTATCCTGATTTGAAGAAAAGTCACGACTAGTAAGTTAAGGCACGAATTTTCA
1 AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGACTAATAAGTTAAGGCACAAATTTTCA
*
457770 AAACCAGAGATAAA-AAACATTGCCTCGTTCT
66 AAACCAGAAATAAAGAAACATTGCCTCGTTCT
* *
457801 AAGGGTATTCGATTATCCCGGTTT-AATGAAAAATCACGCCTAATAAGTTAAGGCACAAAATTTT
1 AAGGGTATTCGATTATCCCGATTTGAA-GAAAAATCACGACTAATAAGTTAAGGCAC-AAATTTT
* *
457865 -AAAACCCA-AAATAAAGGAATATTGCCTCGTT
64 CAAAA-CCAGAAATAAAGAAACATTGCCTCGTT
457896 TTTAAATATT
Statistics
Matches: 82, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
95 2 0.02
96 58 0.71
97 22 0.27
ACGTcount: A:0.39, C:0.17, G:0.17, T:0.27
Consensus pattern (97 bp):
AAGGGTATTCGATTATCCCGATTTGAAGAAAAATCACGACTAATAAGTTAAGGCACAAATTTTCA
AAACCAGAAATAAAGAAACATTGCCTCGTTCT
Found at i:458343 original size:145 final size:144
Alignment explanation
Indices: 458179--458580 Score: 381
Period size: 145 Copynumber: 2.8 Consensus size: 144
458169 GGAAGATTCG
* *
458179 GGGTAAAAATGTG-ATTTTTGGAAGTTCGGGGGCAAAAATGTGATTTTTCCAAGTTCGGG-GATA
1 GGGTAAAAATG-GAATTTTTGGAAGTTCGGGGGTAAAAATGTGATTTTTCCAAGTTCGGGTG-CA
* * * ** *
458242 AAAATGGATTTTTTGGAAGTTTGAGGGGTAAAAATGTTATTTTTGGGAA-TTCGGAGGTAAAACA
64 AAAATGAAATTTTTGGAAGTTT-AGGGGTAAAAATGTAATTTTTGAAAAGTTAGGAGGTAAAA-A
*
458306 GTGA-TTTTGAAAGTTCAA
127 GTAATTTTTGAAAGTT-AA
* * **
458324 GGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTAAAAATATGATTTTTGGAAGTTCGGGTGCAAA
1 GGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTGATTTTTCCAAGTTCGGGTGCAAA
* * * * *
458389 AATGAAATTTTTGGAAGTTTAGGGGTACAATTGTAATTTTTTAAAAGTTTAGGAGTTAAAATGTA
66 AATGAAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAG-TTAGGAGGTAAAAAGTA
*
458454 ATTTTTGAAAGTTTA
130 ATTTTTGAAAGTTAA
* * ** * * *
458469 GGGTAAAAAAGGAATTTTTGGAAATTTAGGGGTAAAAATGT-AATTTT-AAATGTTCGAGTGTC-
1 GGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTGATTTTTCCAA-GTTCGGGTG-CA
* * * * *
458531 AAAATGTAATTATTGAAAAGTTTA--GGTTAAAATGTGATTTTTGAAAAGTT
64 AAAATGAAATTTTTG-GAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTT
458581 CGGGATCAAA
Statistics
Matches: 213, Mismatches: 36, Indels: 19
0.79 0.13 0.07
Matches are distributed among these distances:
142 2 0.01
143 21 0.10
144 47 0.22
145 120 0.56
146 23 0.11
ACGTcount: A:0.35, C:0.03, G:0.26, T:0.36
Consensus pattern (144 bp):
GGGTAAAAATGGAATTTTTGGAAGTTCGGGGGTAAAAATGTGATTTTTCCAAGTTCGGGTGCAAA
AATGAAATTTTTGGAAGTTTAGGGGTAAAAATGTAATTTTTGAAAAGTTAGGAGGTAAAAAGTAA
TTTTTGAAAGTTAA
Found at i:458398 original size:29 final size:28
Alignment explanation
Indices: 458144--458515 Score: 257
Period size: 29 Copynumber: 12.9 Consensus size: 28
458134 AATTTTAGAG
* * *
458144 AGTTTGGGGTTAAAATGTCAA-TTTGGGA
1 AGTTCGGGGTAAAAATGT-AATTTTTGGA
*
458172 AGATTCGGGGTAAAAATGTGATTTTTGGA
1 AG-TTCGGGGTAAAAATGTAATTTTTGGA
* * **
458201 AGTTCGGGGGCAAAAATGTGATTTTTCCA
1 AGTTC-GGGGTAAAAATGTAATTTTTGGA
* *
458230 AGTTCGGGGATAAAAATGGATTTTTTGGA
1 AGTTCGGGG-TAAAAATGTAATTTTTGGA
* *
458259 AGTTTGAGGGGTAAAAATGTTATTTTTGGGA
1 AG-TT-CGGGGTAAAAATGTAATTTTT-GGA
* *
458290 A-TTCGGAGGTAAAACA-GTGA-TTTTGAA
1 AGTTCGG-GGTAAAA-ATGTAATTTTTGGA
* *
458317 AGTTCAAGGGTAAAAATGGAATTTTTGGA
1 AGTTC-GGGGTAAAAATGTAATTTTTGGA
* *
458346 AGTTCGAGGGTAAAAATATGATTTTTGGA
1 AGTTCG-GGGTAAAAATGTAATTTTTGGA
* *
458375 AGTTCGGGTGCAAAAATGAAATTTTTGGA
1 AGTTCGGG-GTAAAAATGTAATTTTTGGA
* * * **
458404 AGTTTAGGGGTACAATTGTAATTTTTTAAA
1 AG-TTCGGGGTAAAAATGTAA-TTTTTGGA
* * * *
458434 AGTTTAGGAGTTAAAATGTAATTTTTGAA
1 AG-TTCGGGGTAAAAATGTAATTTTTGGA
** * *
458463 AGTTTAGGGTAAAAAAGGAATTTTTGGAA
1 AGTTCGGGGTAAAAATGTAATTTTTGG-A
* *
458492 ATTTAGGGGTAAAAATGTAATTTT
1 AGTTCGGGGTAAAAATGTAATTTT
458516 AAATGTTCGA
Statistics
Matches: 270, Mismatches: 56, Indels: 35
0.75 0.16 0.10
Matches are distributed among these distances:
27 4 0.01
28 48 0.18
29 166 0.61
30 44 0.16
31 8 0.03
ACGTcount: A:0.34, C:0.04, G:0.27, T:0.35
Consensus pattern (28 bp):
AGTTCGGGGTAAAAATGTAATTTTTGGA
Found at i:458415 original size:87 final size:87
Alignment explanation
Indices: 458121--458515 Score: 287
Period size: 87 Copynumber: 4.6 Consensus size: 87
458111 AAAAAAATTG
* * * * *
458121 GGGT-CAAAAAT-AAAATTTTAGAGAGTTT-GGGGTTAAAATGTCAA-TTTGGGAAGATTCG-GG
1 GGGTGCAAAAATGAAATTTTTGGA-AGTTTAGGGGTAAAAATG-GAATTTTTGGAAG-TTCGAGG
458181 GTAAAAATGTGATTTTTGGAAGTTC
63 GTAAAAATGTGATTTTTGGAAGTTC
* ** ** * * *
458206 GGGGGCAAAAATGTGATTTTTCCAAG-TTCGGGGATAAAAATGGATTTTTTGGAAGTTTGAGGGG
1 GGGTGCAAAAATGAAATTTTTGGAAGTTTAGGGG-TAAAAATGGAATTTTTGGAAGTTCGA-GGG
*
458270 TAAAAATGTTATTTTTGGGAA-TTC
64 TAAAAATGTGATTTTT-GGAAGTTC
* * * *
458294 GGAG-GTAAAACAGTG--A-TTTTGAAAGTTCAAGGGTAAAAATGGAATTTTTGGAAGTTCGAGG
1 GG-GTGCAAAA-A-TGAAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTCGAGG
*
458355 GTAAAAATATGATTTTTGGAAGTTC
63 GTAAAAATGTGATTTTTGGAAGTTC
* * * ** *
458380 GGGTGCAAAAATGAAATTTTTGGAAGTTTAGGGGTACAATTGTAATTTTTTAAAAGTT-TAGGAG
1 GGGTGCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATGGAA-TTTTTGGAAGTTCGAGG-G
* * * *
458444 TTAAAATGTAATTTTTGAAAGTTTA
64 TAAAAATGTGATTTTTGGAAG-TTC
* * * *
458469 GGGT--AAAAAAGGAATTTTTGGAAATTTAGGGGTAAAAATGTAATTTT
1 GGGTGCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTT
458516 AAATGTTCGA
Statistics
Matches: 248, Mismatches: 42, Indels: 39
0.75 0.13 0.12
Matches are distributed among these distances:
84 2 0.01
85 11 0.04
86 49 0.20
87 111 0.45
88 61 0.25
89 12 0.05
90 2 0.01
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.35
Consensus pattern (87 bp):
GGGTGCAAAAATGAAATTTTTGGAAGTTTAGGGGTAAAAATGGAATTTTTGGAAGTTCGAGGGTA
AAAATGTGATTTTTGGAAGTTC
Found at i:458562 original size:28 final size:29
Alignment explanation
Indices: 458310--458580 Score: 184
Period size: 29 Copynumber: 9.4 Consensus size: 29
458300 AAAACAGTGA
* *
458310 TTTTG-AAAGTTCAAGGGTAAAAATGGAAT
1 TTTTGAAAAGTT-TAGGGTAAAAATGTAAT
* * * *
458339 TTTTG-GAAGTTCGAGGGTAAAAATATGAT
1 TTTTGAAAAGTT-TAGGGTAAAAATGTAAT
* * *
458368 TTTTG-GAAG-TTCGGGTGCAAAAATGAAAT
1 TTTTGAAAAGTTTAGGGT--AAAAATGTAAT
* * *
458397 TTTTG-GAAGTTTAGGGGTACAATTGTAAT
1 TTTTGAAAAGTTTA-GGGTAAAAATGTAAT
* *
458426 TTTTTAAAAGTTTAGGAGTTAAAATGTAAT
1 TTTTGAAAAGTTTAGG-GTAAAAATGTAAT
* *
458456 TTTTG-AAAGTTTAGGGTAAAAAAGGAAT
1 TTTTGAAAAGTTTAGGGTAAAAATGTAAT
*
458484 TTTTGGAAA-TTTAGGGGTAAAAATGTAA-
1 TTTTGAAAAGTTTA-GGGTAAAAATGTAAT
* * * *
458512 TTTT-AAATGTTCGAGTGTCAAAATGTAAT
1 TTTTGAAAAGTT-TAGGGTAAAAATGTAAT
* * *
458541 TATTGAAAAGTTTA-GGTTAAAATGTGAT
1 TTTTGAAAAGTTTAGGGTAAAAATGTAAT
458569 TTTTGAAAAGTT
1 TTTTGAAAAGTT
458581 CGGGATCAAA
Statistics
Matches: 193, Mismatches: 37, Indels: 25
0.76 0.15 0.10
Matches are distributed among these distances:
27 6 0.03
28 60 0.31
29 94 0.49
30 29 0.15
31 4 0.02
ACGTcount: A:0.37, C:0.03, G:0.23, T:0.37
Consensus pattern (29 bp):
TTTTGAAAAGTTTAGGGTAAAAATGTAAT
Found at i:458592 original size:57 final size:56
Alignment explanation
Indices: 458420--458592 Score: 156
Period size: 57 Copynumber: 3.0 Consensus size: 56
458410 GGGGTACAAT
* * *
458420 TGTAATTTTTTAAAAGTTTAGGAGTTAAAATGTAATTTTTG-AAAGTTTAGGGTAAAAA
1 TGTAATTTTTGAAAAGTTTAGG-GTTAAAATGT-ATTTTTGAAAAG-TTCGGGTCAAAA
* * * * * *
458478 AGGAATTTTTGGAAA-TTTAGGGGTAAAAATGTAATTTT-AAATGTTCGAGTGTCAAAA
1 TGTAATTTTTGAAAAGTTTA-GGGTTAAAATGTATTTTTGAAAAGTTCG-G-GTCAAAA
*
458535 TGTAATTATTGAAAAGTTTA-GGTTAAAATGTGATTTTTGAAAAGTTCGGGATCAAAA
1 TGTAATTTTTGAAAAGTTTAGGGTTAAAATGT-ATTTTTGAAAAGTTCGGG-TCAAAA
458592 T
1 T
458593 ATGAGTTCTG
Statistics
Matches: 91, Mismatches: 16, Indels: 17
0.73 0.13 0.14
Matches are distributed among these distances:
55 3 0.03
56 20 0.22
57 43 0.47
58 25 0.27
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.38
Consensus pattern (56 bp):
TGTAATTTTTGAAAAGTTTAGGGTTAAAATGTATTTTTGAAAAGTTCGGGTCAAAA
Found at i:458963 original size:41 final size:36
Alignment explanation
Indices: 458865--458954 Score: 153
Period size: 36 Copynumber: 2.5 Consensus size: 36
458855 AGGCCAGAGG
* *
458865 CTCAAAACGACGTCGTTTTGGGGCTGAAACTCAGCT
1 CTCAAAACGACATCGTTTTGGGGCTGAAACTCAACT
458901 CTCAAAACGACATCGTTTTGGGGCTGAAACTCAACT
1 CTCAAAACGACATCGTTTTGGGGCTGAAACTCAACT
*
458937 CTCAAAACGGCATCGTTT
1 CTCAAAACGACATCGTTT
458955 CCCATTGGGT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.26
Consensus pattern (36 bp):
CTCAAAACGACATCGTTTTGGGGCTGAAACTCAACT
Found at i:460117 original size:17 final size:17
Alignment explanation
Indices: 460091--460158 Score: 73
Period size: 17 Copynumber: 3.9 Consensus size: 17
460081 TTCCTTGATT
*
460091 AATTTTAATTTAAAATA
1 AATTTAAATTTAAAATA
*
460108 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAAATA
* *
460125 AATTCAAACTTAAAATAA
1 AATTTAAATTTAAAAT-A
**
460143 AATGAAAATTTAAAAT
1 AATTTAAATTTAAAAT
460159 TTGGGCTTAA
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
17 28 0.67
18 14 0.33
ACGTcount: A:0.57, C:0.03, G:0.03, T:0.37
Consensus pattern (17 bp):
AATTTAAATTTAAAATA
Found at i:460903 original size:162 final size:161
Alignment explanation
Indices: 460637--461142 Score: 654
Period size: 162 Copynumber: 3.1 Consensus size: 161
460627 TCTCAATACA
*
460637 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTTGTTTCATTGATTTGGTATACT
1 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACT
* *
460702 TCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAATCCGCTTCTCTGTATCTCATCA
66 TCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCA
460767 GGAAGACAAATTTGGTTCACTTCTAAGTATC
131 GGAAGACAAATTTGGTTCACTTCTAAGTATC
*
460798 TCATCAGGAAGAC-GGGGTTCGAAGTTTCGCTCACATTGAGCTTTGGTTTCATTGATTTGGTCTA
1 TCATCAGGAAG-CTGGGGTTCGAAGTTTCGCTCACATTGAGCTTT-GTTTCATTGATTTGGTATA
* * *
460862 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCTGCTTCTCTGTATCTCAT
64 CTTCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCAT
** * *
460927 CAGGAAGACGACCGCTTTATTGCTTCTACCTGCTTCACAGTATC
129 CAGGAAGAC-A----AAT-TTGGTTC-A-CTTC-T-A-AGTATC
* * *
460971 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCCTTATTTCATTGATTTGGTATACT
1 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACT
* * * * *
461036 TCTCTGTATATCATCAGGAAGATGACCGCATCACTTGTTTTAATTCACTTCTCTATATCTCATTA
66 TCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCA
** * ** *
461101 GGAAGACGGATTTGGTCCACTTCTCTGTACC
131 GGAAGACAAATTTGGTTCACTTCTAAGTATC
*
461132 TCATCAAGAAG
1 TCATCAGGAAG
461143 ACGATCATTT
Statistics
Matches: 298, Mismatches: 33, Indels: 28
0.83 0.09 0.08
Matches are distributed among these distances:
161 55 0.18
162 88 0.30
163 2 0.01
164 3 0.01
165 1 0.00
166 5 0.02
167 2 0.01
168 6 0.02
169 1 0.00
170 3 0.01
171 1 0.00
172 85 0.29
173 46 0.15
ACGTcount: A:0.23, C:0.22, G:0.19, T:0.36
Consensus pattern (161 bp):
TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACT
TCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAATCCGCTTCTCTGTATCTCATCA
GGAAGACAAATTTGGTTCACTTCTAAGTATC
Found at i:460979 original size:48 final size:49
Alignment explanation
Indices: 460862--460981 Score: 154
Period size: 49 Copynumber: 2.5 Consensus size: 49
460852 ATTTGGTCTA
* * *
460862 CTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGATCTG
1 CTTCTCAGTATCTCATCAGGAAGACGACCGCATCACTTGTTCTGACCTG
* * *
460911 CTTCTCTGTATCTCATCAGGAAGACGACCGCTTTA-TTGCTTCT-ACCTG
1 CTTCTCAGTATCTCATCAGGAAGACGACCGCATCACTTG-TTCTGACCTG
*
460959 CTTCACAGTATCTCATCAGGAAG
1 CTTCTCAGTATCTCATCAGGAAG
460982 CTGGGGTTCG
Statistics
Matches: 62, Mismatches: 8, Indels: 3
0.85 0.11 0.04
Matches are distributed among these distances:
48 28 0.45
49 34 0.55
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (49 bp):
CTTCTCAGTATCTCATCAGGAAGACGACCGCATCACTTGTTCTGACCTG
Found at i:461089 original size:172 final size:170
Alignment explanation
Indices: 460573--461108 Score: 682
Period size: 172 Copynumber: 3.2 Consensus size: 170
460563 ATGGATTTGG
* * * ** * *
460573 TTCACTTGTCTGCATCTCGTCAGGAAGGTGACCACTTTATTGCTTCGACCTGCTTCTCAATA-CA
1 TTCACTTCTCTGTATCTCATCAGGAAGACGACC-CTTTATTGCTTC-ACCTGCTTCACAGTATC-
*
460637 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTAAGCTTTGTTTCATTGATTTGGTATACT
63 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACT
* *
460702 TCTCTGTATCTCATCAGGAAGATGACCGCCTCACTTGTTTCAA
128 TCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAA
* * ** * *
460745 TCCGCTTCTCTGTATCTCATCAGGAAGAC-A---AAT-TTGGTTCA-CTTC-T-A-AGTATCTCA
1 TTCACTTCTCTGTATCTCATCAGGAAGACGACCCTTTATTGCTTCACCTGCTTCACAGTATCTCA
*
460801 TCAGGAAGAC-GGGGTTCGAAGTTTCGCTCACATTGAGCTTTGGTTTCATTGATTTGGTCTACTT
66 TCAGGAAG-CTGGGGTTCGAAGTTTCGCTCACATTGAGCTTT-GTTTCATTGATTTGGTATACTT
* *
460865 CTCAGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTGA
129 CTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAA
*
460907 -TCTGCTTCTCTGTATCTCATCAGGAAGACGACCGCTTTATTGCTTCTACCTGCTTCACAGTATC
1 TTC-ACTTCTCTGTATCTCATCAGGAAGACGACC-CTTTATTGCTTC-ACCTGCTTCACAGTATC
* * *
460971 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCATATTGAGCCTTATTTCATTGATTTGGTATACT
63 TCATCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACT
*
461036 TCTCTGTATATCATCAGGAAGATGACCGCATCACTTGTTTTAA
128 TCTCTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAA
* *
461079 TTCACTTCTCTATATCTCATTAGGAAGACG
1 TTCACTTCTCTGTATCTCATCAGGAAGACG
461109 GATTTGGTCC
Statistics
Matches: 313, Mismatches: 34, Indels: 34
0.82 0.09 0.09
Matches are distributed among these distances:
161 45 0.14
162 87 0.28
163 2 0.01
164 3 0.01
165 1 0.00
166 6 0.02
167 2 0.01
168 6 0.02
169 1 0.00
170 3 0.01
171 2 0.01
172 107 0.34
173 48 0.15
ACGTcount: A:0.22, C:0.23, G:0.19, T:0.36
Consensus pattern (170 bp):
TTCACTTCTCTGTATCTCATCAGGAAGACGACCCTTTATTGCTTCACCTGCTTCACAGTATCTCA
TCAGGAAGCTGGGGTTCGAAGTTTCGCTCACATTGAGCTTTGTTTCATTGATTTGGTATACTTCT
CTGTATCTCATCAGGAAGATGACCGCATCACTTGTTTTAA
Found at i:466488 original size:20 final size:20
Alignment explanation
Indices: 466459--466498 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
466449 TGACAGCCTC
*
466459 TTCATCTGTTACGACATAAG
1 TTCATCTGTTACAACATAAG
* *
466479 TTCATTTGTTCCAACATAAG
1 TTCATCTGTTACAACATAAG
466499 GTGAATCACT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (20 bp):
TTCATCTGTTACAACATAAG
Found at i:472885 original size:95 final size:97
Alignment explanation
Indices: 472714--472906 Score: 275
Period size: 95 Copynumber: 2.0 Consensus size: 97
472704 CCTTGGAAAT
* *
472714 GGGTATTCGATTATCTCGATTTGAAGAAAAGTCGCACCTAGTAAGTTAAGGCACAAATTTTCAAA
1 GGGTATTCGATTATCACGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAA
*
472779 ACCAGAGATAAA-AAAATTGCCTC-ATTTTAA
66 ACCAGAAATAAAGAAAATTGCCTCAATTTTAA
** *
472809 GGGTATTCGATTATCAC-AGTTTGAAGAAAAATCGTGCCTAGTAAGTTAAGGCATAAATTTTCAA
1 GGGTATTCGATTATCACGA-TTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAA
* *
472873 AACCCGAAATAAAGGAATATTGCCTCAATTTTAA
65 AACCAGAAATAAA-GAAAATTGCCTCAATTTTAA
472907 ATATTTTGGA
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
94 1 0.01
95 68 0.79
97 10 0.12
98 7 0.08
ACGTcount: A:0.39, C:0.15, G:0.17, T:0.29
Consensus pattern (97 bp):
GGGTATTCGATTATCACGATTTGAAGAAAAATCGCACCTAGTAAGTTAAGGCACAAATTTTCAAA
ACCAGAAATAAAGAAAATTGCCTCAATTTTAA
Found at i:473278 original size:29 final size:28
Alignment explanation
Indices: 473228--473411 Score: 137
Period size: 29 Copynumber: 6.4 Consensus size: 28
473218 AAAAACATAA
* *
473228 TTTTGGAAGTTTAGGGCCAAAAACGTGAT
1 TTTTGGAAG-TTAGGGACAAAAATGTGAT
*
473257 TTTTGGAAGTTAGAGGATAAAAATG-GAAT
1 TTTTGGAAGTTAG-GGACAAAAATGTG-AT
*
473286 TTTTGAAAGTTCGAGGGGA-AAAAATGTGAT
1 TTTTGGAAGTT--A-GGGACAAAAATGTGAT
*
473316 CTTTGGGAA-TTCAGGGACAAAAATGTGA-
1 -TTTTGGAAGTT-AGGGACAAAAATGTGAT
* * *
473344 TTTTGGAATTTATGGGGCAAAAATATGAT
1 TTTTGGAAGTTA-GGGACAAAAATGTGAT
**
473373 TTTTGGAAGTTCGAGGG--AAAAATGAAAT
1 TTTTGGAAGTT--AGGGACAAAAATGTGAT
473401 TTTTGGAAGTT
1 TTTTGGAAGTT
473412 CAAGGGGTAA
Statistics
Matches: 128, Mismatches: 14, Indels: 27
0.76 0.08 0.16
Matches are distributed among these distances:
27 8 0.06
28 43 0.34
29 50 0.39
30 14 0.11
31 12 0.09
32 1 0.01
ACGTcount: A:0.35, C:0.05, G:0.28, T:0.32
Consensus pattern (28 bp):
TTTTGGAAGTTAGGGACAAAAATGTGAT
Found at i:473424 original size:29 final size:29
Alignment explanation
Indices: 473371--473462 Score: 91
Period size: 29 Copynumber: 3.2 Consensus size: 29
473361 CAAAAATATG
* *
473371 ATTTTTGGAAGTTCGA-GGGAAAAATGAA
1 ATTTTTGGAAGTTCAAGGGGTAAAATGAA
473399 ATTTTTGGAAGTTCAAGGGGTAAAAT-ATA
1 ATTTTTGGAAGTTCAAGGGGTAAAATGA-A
** * *
473428 ATTTTTTTAAGTT-TAGGGGTCAAAATGTA
1 ATTTTTGGAAGTTCAAGGGGT-AAAATGAA
473457 ATTTTT
1 ATTTTT
473463 AAAAGTTTAG
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
28 22 0.41
29 32 0.59
ACGTcount: A:0.35, C:0.03, G:0.23, T:0.39
Consensus pattern (29 bp):
ATTTTTGGAAGTTCAAGGGGTAAAATGAA
Found at i:473424 original size:57 final size:58
Alignment explanation
Indices: 473253--473433 Score: 165
Period size: 57 Copynumber: 3.1 Consensus size: 58
473243 GCCAAAAACG
* * * * * *
473253 TGATTTTTGGAAGTTAGAGGATAAAAATGGAATTTTTGAAAGTTCGAGGGGAAAAAATG
1 TGATTTTTGGAAGTTCGAGG-GAAAAATGAAATTTTTGGAAGTTCAAGGGGAAAAAATA
* ** * * *
473312 TGATCTTTGGGAA-TTC-AGGGACAAAAATGTGA-TTTTGGAA-TTTATGGGGCAAAAATA
1 TGAT-TTTTGGAAGTTCGAGGG--AAAAATGAAATTTTTGGAAGTTCAAGGGGAAAAAATA
*
473369 TGATTTTTGGAAGTTCGAGGGAAAAATGAAATTTTTGGAAGTTCAAGGGG-TAAAATA
1 TGATTTTTGGAAGTTCGAGGGAAAAATGAAATTTTTGGAAGTTCAAGGGGAAAAAATA
*
473426 TAATTTTT
1 TGATTTTT
473434 TTAAGTTTAG
Statistics
Matches: 97, Mismatches: 18, Indels: 16
0.74 0.14 0.12
Matches are distributed among these distances:
56 15 0.15
57 40 0.41
58 21 0.22
59 14 0.14
60 7 0.07
ACGTcount: A:0.36, C:0.04, G:0.27, T:0.33
Consensus pattern (58 bp):
TGATTTTTGGAAGTTCGAGGGAAAAATGAAATTTTTGGAAGTTCAAGGGGAAAAAATA
Found at i:473432 original size:28 final size:27
Alignment explanation
Indices: 473362--473432 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 27
473352 TTTATGGGGC
* *
473362 AAAAATATGATTTTTGGAAGTTCGAGGG
1 AAAAATAT-AATTTTGGAAGTTCAAGGG
473390 AAAAATGA-AATTTTTGGAAGTTCAAGGGG
1 AAAAAT-ATAA-TTTTGGAAGTTCAA-GGG
*
473419 TAAAATATAATTTT
1 AAAAATATAATTTT
473433 TTTAAGTTTA
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
27 1 0.03
28 24 0.67
29 11 0.31
ACGTcount: A:0.41, C:0.03, G:0.23, T:0.34
Consensus pattern (27 bp):
AAAAATATAATTTTGGAAGTTCAAGGG
Found at i:473468 original size:29 final size:29
Alignment explanation
Indices: 473391--473605 Score: 138
Period size: 29 Copynumber: 7.5 Consensus size: 29
473381 GTTCGAGGGA
* ** *
473391 AAAATGAAATTTTTGGAAGTTCAAGGGGT-
1 AAAATGTAATTTTTAAAAGTT-TAGGGGTC
* **
473420 AAAATATAATTTTTTTAAGTTTAGGGGTC
1 AAAATGTAATTTTTAAAAGTTTAGGGGTC
* *
473449 AAAATGTAATTTTTAAAAGTTTA-GAGTA
1 AAAATGTAATTTTTAAAAGTTTAGGGGTC
* *
473477 AAAATGGAATTTTTAGAAGTTTAGGGG-C
1 AAAATGTAATTTTTAAAAGTTTAGGGGTC
* * *
473505 AAAAATATGATTTTTAAAAG-TTGGAGGGTC
1 -AAAATGTAATTTTTAAAAGTTTAG-GGGTC
* * * *
473535 AAACTGTAATTTTTGAAAAGCTTA--AGTT
1 AAAATGTAATTTTT-AAAAGTTTAGGGGTC
* *
473563 AAAATGTGATTTTTGAAAAATTTA-GGGTC
1 AAAATGTAATTTTT-AAAAGTTTAGGGGTC
* *
473592 AAAATATGATTTTT
1 AAAATGTAATTTTT
473606 GGAAAGTTCA
Statistics
Matches: 146, Mismatches: 32, Indels: 16
0.75 0.16 0.08
Matches are distributed among these distances:
28 55 0.38
29 83 0.57
30 6 0.04
31 2 0.01
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (29 bp):
AAAATGTAATTTTTAAAAGTTTAGGGGTC
Found at i:473469 original size:86 final size:87
Alignment explanation
Indices: 473371--473554 Score: 198
Period size: 86 Copynumber: 2.1 Consensus size: 87
473361 CAAAAATATG
* * *
473371 ATTTTTG-GAAGTTCGAG-GGAAAAATGAAATTTTTGGAAGTTCAAGGGG-TAAAATATAATTTT
1 ATTTTTGAAAAGTT-GAGAGGAAAAATGAAATTTTTAGAAGTT-AAGGGGCAAAAATATAATTTT
**
473433 TTTAAGTTTAG-GGGTCAAAATGTA
64 TAAAAG-TTAGAGGGTCAAAATGTA
* * * * *
473457 ATTTTT-AAAAGTTTAGAGTAAAAATGGAATTTTTAGAAGTTTAGGGGCAAAAATATGATTTTTA
1 ATTTTTGAAAAGTTGAGAGGAAAAATGAAATTTTTAGAAGTTAAGGGGCAAAAATATAATTTTTA
* *
473521 AAAGTTGGAGGGTCAAACTGTA
66 AAAGTTAGAGGGTCAAAATGTA
473543 ATTTTTGAAAAG
1 ATTTTTGAAAAG
473555 CTTAAGTTAA
Statistics
Matches: 81, Mismatches: 12, Indels: 9
0.79 0.12 0.09
Matches are distributed among these distances:
85 10 0.12
86 66 0.81
87 5 0.06
ACGTcount: A:0.38, C:0.03, G:0.23, T:0.36
Consensus pattern (87 bp):
ATTTTTGAAAAGTTGAGAGGAAAAATGAAATTTTTAGAAGTTAAGGGGCAAAAATATAATTTTTA
AAAGTTAGAGGGTCAAAATGTA
Found at i:473567 original size:86 final size:85
Alignment explanation
Indices: 473390--473605 Score: 231
Period size: 86 Copynumber: 2.5 Consensus size: 85
473380 AGTTCGAGGG
* * * * * ** *
473390 AAAAATGAAATTTTTGGAAGTTCAAGGGGTAAAATATAATTTTTTTAAGTTTAGGGGTCAAAATG
1 AAAAATGGAATTTTTAGAAGTT-TAGGGGCAAAATATGATTTTTAAAAGTTGAGGGGTCAAAATG
*
473455 TAATTTTTAAAAGTTTAGAGT
65 TAATTTTTAAAAGCTTAGAGT
*
473476 AAAAATGGAATTTTTAGAAGTTTAGGGGCAAAAATATGATTTTTAAAAGTTG-GAGGGTCAAACT
1 AAAAATGGAATTTTTAGAAGTTTAGGGGC-AAAATATGATTTTTAAAAGTTGAG-GGGTCAAAAT
473540 GTAATTTTTGAAAAGCTTA-AGT
64 GTAATTTTT-AAAAGCTTAGAGT
* * * *
473562 TAAAATGTG-ATTTTTGAAAAATTTAGGGTCAAAATATGATTTTT
1 AAAAATG-GAATTTTT-AGAAGTTTAGGGGCAAAATATGATTTTT
473606 GGAAAGTTCA
Statistics
Matches: 111, Mismatches: 14, Indels: 10
0.82 0.10 0.07
Matches are distributed among these distances:
85 6 0.05
86 85 0.77
87 20 0.18
ACGTcount: A:0.39, C:0.03, G:0.20, T:0.38
Consensus pattern (85 bp):
AAAAATGGAATTTTTAGAAGTTTAGGGGCAAAATATGATTTTTAAAAGTTGAGGGGTCAAAATGT
AATTTTTAAAAGCTTAGAGT
Found at i:475084 original size:17 final size:17
Alignment explanation
Indices: 475064--475157 Score: 107
Period size: 17 Copynumber: 5.5 Consensus size: 17
475054 TTAATTTTAT
*
475064 TTTAGAATAAATTTAAA
1 TTTAAAATAAATTTAAA
* *
475081 TTTAAAGTAAATTCAAA
1 TTTAAAATAAATTTAAA
* *
475098 CTTAAAATAAGTTTAAA
1 TTTAAAATAAATTTAAA
* *
475115 TTTAAAATAAACTCAAA
1 TTTAAAATAAATTTAAA
*
475132 CTTAAAATAAATTTAAA
1 TTTAAAATAAATTTAAA
475149 TTTTAAAAT
1 -TTTAAAAT
475158 TTAAAATTTG
Statistics
Matches: 61, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
17 54 0.89
18 7 0.11
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.37
Consensus pattern (17 bp):
TTTAAAATAAATTTAAA
Found at i:475113 original size:34 final size:34
Alignment explanation
Indices: 475069--475157 Score: 142
Period size: 34 Copynumber: 2.6 Consensus size: 34
475059 TTTATTTTAG
* *
475069 AATAAATTTAAATTTAAAGTAAATTCAAACTTAA
1 AATAAATTTAAATTTAAAATAAACTCAAACTTAA
*
475103 AATAAGTTTAAATTTAAAATAAACTCAAACTTAA
1 AATAAATTTAAATTTAAAATAAACTCAAACTTAA
475137 AATAAATTTAAATTTTAAAAT
1 AATAAATTTAAA-TTTAAAAT
475158 TTAAAATTTG
Statistics
Matches: 50, Mismatches: 4, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
34 42 0.84
35 8 0.16
ACGTcount: A:0.56, C:0.06, G:0.02, T:0.36
Consensus pattern (34 bp):
AATAAATTTAAATTTAAAATAAACTCAAACTTAA
Found at i:477637 original size:20 final size:20
Alignment explanation
Indices: 477609--477697 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
477599 AGATGAAATG
*
477609 CCCTGTTTGCACTTCGATAC
1 CCCTATTTGCACTTCGATAC
* * * *
477629 CCCTATTTGCGCTTTGGTGC
1 CCCTATTTGCACTTCGATAC
* * *
477649 CCCTGTTTGCACTTCAATGC
1 CCCTATTTGCACTTCGATAC
*
477669 CGCTATTTGCACTTCGATGA-
1 CCCTATTTGCACTTCGAT-AC
477689 CCCTATTTG
1 CCCTATTTG
477698 TACAACTGTA
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.13, C:0.31, G:0.18, T:0.37
Consensus pattern (20 bp):
CCCTATTTGCACTTCGATAC
Found at i:482025 original size:19 final size:19
Alignment explanation
Indices: 482001--482042 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
481991 TGGAATGCAT
*
482001 ACCTAAGATCCTCACCTTC
1 ACCTAAGATACTCACCTTC
*
482020 ACCTAATATACTCACCTTC
1 ACCTAAGATACTCACCTTC
482039 ACCT
1 ACCT
482043 TCATCTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.29, C:0.40, G:0.02, T:0.29
Consensus pattern (19 bp):
ACCTAAGATACTCACCTTC
Found at i:503802 original size:51 final size:51
Alignment explanation
Indices: 503725--503912 Score: 209
Period size: 51 Copynumber: 3.6 Consensus size: 51
503715 GCTATAAACG
503725 AAAGGATCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
1 AAAGG-TCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
* * *
503777 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATAATGGATT
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
* * * * * **
503828 AAAGGTCCAATTACTCAGTGTCATCGTAAGTATATGAATTCCTATC-CGGAAC
1 AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAA-TCCT-TCACGGATT
* *
503880 AAGAGGTCTGATGATTATA-TGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-AGTGTCATCGTGAGTA
503913 TTAAATGAAA
Statistics
Matches: 113, Mismatches: 19, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
51 76 0.67
52 13 0.12
53 23 0.20
54 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (51 bp):
AAAGGTCCGATGACTAAGTGTCATCGTGAGTAAATGAATCCTTCACGGATT
Found at i:503965 original size:61 final size:60
Alignment explanation
Indices: 503876--504032 Score: 201
Period size: 61 Copynumber: 2.6 Consensus size: 60
503866 TTCCTATCCG
* * *
503876 GAACAAGAGGTCTGATGATTATATGTCATCGTGAGTATTAAATGAAATGAGTTCCTAA-AC
1 GAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTT-CTAATAA
* * * *
503936 GAAACAAGAGGTCCGATAACTATACGTCATCATCAGTATTAAATGAAATGAGTTCTAATAA
1 G-AACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTTCTAATAA
* *
503997 GAACAAG-GGTCCGATGACTTTGTGTCATCGTGAGTA
1 GAACAAGAGGTCCGATGACTATATGTCATCGTGAGTA
504033 AAGAATGCGA
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
59 23 0.28
60 11 0.13
61 48 0.59
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (60 bp):
GAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAGTTCTAATAA
Found at i:509254 original size:41 final size:38
Alignment explanation
Indices: 509154--509257 Score: 93
Period size: 37 Copynumber: 2.7 Consensus size: 38
509144 TTCGAATCAA
* *
509154 TAAAGTGACACCCAGTGTCTCATCG-GTCTAGCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAATCTAGCCGAAG
* ** ** * *
509191 TAAAGTGGTACCCAGTACCTCATCGAATTTATCCGAAG
1 TAAAATGACACCCAGTGTCTCATCGAATCTAGCCGAAG
509229 TAAAATAATGACACCCAGTGTCTCATCGA
1 T--AA-AATGACACCCAGTGTCTCATCGA
509258 CTCAAAGTCG
Statistics
Matches: 51, Mismatches: 12, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
37 21 0.41
38 10 0.20
40 2 0.04
41 18 0.35
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (38 bp):
TAAAATGACACCCAGTGTCTCATCGAATCTAGCCGAAG
Found at i:509383 original size:18 final size:18
Alignment explanation
Indices: 509360--509396 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
509350 ACAATTCATA
509360 TCACTTTCAATTCCAATT
1 TCACTTTCAATTCCAATT
* *
509378 TCACTTTCACTTTCAATT
1 TCACTTTCAATTCCAATT
509396 T
1 T
509397 TGATCACAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.24, C:0.27, G:0.00, T:0.49
Consensus pattern (18 bp):
TCACTTTCAATTCCAATT
Found at i:514040 original size:51 final size:50
Alignment explanation
Indices: 513963--514150 Score: 178
Period size: 51 Copynumber: 3.6 Consensus size: 50
513953 GCTATAGACG
* * *
513963 AAAGGATCCGATAACTAAGTGCCATCGTGAGTAAATGAATCCTTTACAGATT
1 AAAGG-TCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATT
* * * *
514015 AAAGGTTCGATGACTAAGTGTCATCGTGAGTAAATGAATCCATGATGGATT
1 AAAGGTCCGATGACTAA-TGTCATCGTGAGTAAATGAATCCTTTACGGATT
** * ** * **
514066 AAAGGTCCGATGACTCAAACTCATCATGAGTATGTGAATTCCTATACGGAAC
1 AAAGGTCCGATGACT-AATGTCATCGTGAGTAAATGAA-TCCTTTACGGATT
514118 AAGAGGTCCGATGACTATATGTCATCGTGAGTA
1 AA-AGGTCCGATGACTA-ATGTCATCGTGAGTA
514151 TTAACTGAGA
Statistics
Matches: 110, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
51 68 0.62
52 17 0.15
53 25 0.23
ACGTcount: A:0.34, C:0.16, G:0.22, T:0.27
Consensus pattern (50 bp):
AAAGGTCCGATGACTAATGTCATCGTGAGTAAATGAATCCTTTACGGATT
Found at i:514143 original size:53 final size:55
Alignment explanation
Indices: 513985--514212 Score: 167
Period size: 51 Copynumber: 4.2 Consensus size: 55
513975 AACTAAGTGC
* * ** *
513985 CATCGTGAGTA-A-ATGAA-TCCTTTACAGATTAA-AGGTTCGATGACTA-AGTGT
1 CATCGTGAGTATAGATGAATTCCTATACGGAACAAGAGGTCCGATGACTATA-TGT
* ** **
514036 CATCGTGAGTA-A-ATGAA-TCC-ATGATGGATTAA-AGGTCCGATGACTCA-AACT
1 CATCGTGAGTATAGATGAATTCCTAT-ACGGAACAAGAGGTCCGATGACT-ATATGT
*
514087 CATCATGAGTAT-G-TGAATTCCTATACGGAACAAGAGGTCCGATGACTATATGT
1 CATCGTGAGTATAGATGAATTCCTATACGGAACAAGAGGTCCGATGACTATATGT
* *
514140 CATCGTGAGTATTAACTGAGATGAGTTCCTATACGGAACAAGAGGTCCGATAACTATATGT
1 CATCGTGAG---T-A-T-AGATGAATTCCTATACGGAACAAGAGGTCCGATGACTATATGT
514201 CATCGTGAGTAT
1 CATCGTGAGTAT
514213 TAAATGAAAT
Statistics
Matches: 146, Mismatches: 15, Indels: 27
0.78 0.08 0.14
Matches are distributed among these distances:
50 1 0.01
51 54 0.37
52 12 0.08
53 25 0.17
56 2 0.01
57 2 0.01
58 2 0.01
60 1 0.01
61 47 0.32
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.29
Consensus pattern (55 bp):
CATCGTGAGTATAGATGAATTCCTATACGGAACAAGAGGTCCGATGACTATATGT
Found at i:514276 original size:59 final size:61
Alignment explanation
Indices: 514104--514277 Score: 246
Period size: 61 Copynumber: 2.9 Consensus size: 61
514094 AGTATGTGAA
* *
514104 TTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAACTGAGATGAG
1 TTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAG
*
514165 TTCCTATACGGAACAAGAGGTCCGATAACTATATGTCATCGTGAGTATTAAATGAAATGAG
1 TTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAG
* * * * *
514226 TTCC-A-ATGTGAACAAG-GGTCCGATGACTTTGTGTCATCATGAGTAATAAATG
1 TTCCTATACG-GAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATG
514278 CGAGTGAAAC
Statistics
Matches: 103, Mismatches: 9, Indels: 4
0.89 0.08 0.03
Matches are distributed among these distances:
59 33 0.32
60 8 0.08
61 62 0.60
ACGTcount: A:0.33, C:0.16, G:0.23, T:0.29
Consensus pattern (61 bp):
TTCCTATACGGAACAAGAGGTCCGATGACTATATGTCATCGTGAGTATTAAATGAAATGAG
Found at i:517084 original size:25 final size:26
Alignment explanation
Indices: 517046--517098 Score: 81
Period size: 25 Copynumber: 2.1 Consensus size: 26
517036 ATACTAAATC
* *
517046 TATATTTATTTTAATATTAAATA-AA
1 TATAATTATATTAATATTAAATATAA
517071 TATAATTATATTAATATTAAATATAA
1 TATAATTATATTAATATTAAATATAA
517097 TA
1 TA
517099 AAAAATCTCC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 21 0.84
26 4 0.16
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (26 bp):
TATAATTATATTAATATTAAATATAA
Found at i:517093 original size:21 final size:19
Alignment explanation
Indices: 517059--517097 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 19
517049 ATTTATTTTA
517059 ATATTAAATAAATATAATT
1 ATATTAAATAAATATAATT
517078 ATATTAATATTAAATATAAT
1 ATATTAA-A-TAAATATAAT
517098 AAAAAATCTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 10 0.56
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
ATATTAAATAAATATAATT
Found at i:519412 original size:96 final size:96
Alignment explanation
Indices: 519228--519419 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
519218 TTTTTACGAA
** * * *
519228 AAGGGTATTCGATTATCTCGATTTGAAGAAAGGTTGCACGTTGTAAGTTAAGGCGCAATATTTCA
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* *
519293 GGACTGAAGATAAGGAAACATTGCCTCGATT
66 GAACTGAAGATAAAGAAACATTGCCTCGATT
* *
519324 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTTAGTTAAGGCACAACT-TTTC
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-TATTTC
*
519388 -GAAACTCGAA-ATAAA-AGAATATTGCCTCGATT
65 AG-AACT-GAAGATAAAGA-AACATTGCCTCGATT
519420 TTAAAGCTGT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 76 0.93
97 4 0.05
ACGTcount: A:0.34, C:0.14, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAACTGAAGATAAAGAAACATTGCCTCGATT
Found at i:519712 original size:28 final size:26
Alignment explanation
Indices: 519681--519757 Score: 73
Period size: 28 Copynumber: 2.7 Consensus size: 26
519671 GGATTATCGG
519681 GGGTAAAATGGTAATTTTGAGGAAATTC
1 GGGTAAAATGG-AATTTTGA-GAAATTC
* *
519709 GGGTTTAAAAATGGAATTTTTAGACATTC
1 GGG--T-AAAATGGAATTTTGAGAAATTC
519738 GAGGTAGAAATGGAATTTTG
1 G-GGTA-AAATGGAATTTTG
519758 GAAGTTTTGG
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
27 1 0.02
28 16 0.39
29 7 0.17
30 10 0.24
31 7 0.17
ACGTcount: A:0.35, C:0.04, G:0.27, T:0.34
Consensus pattern (26 bp):
GGGTAAAATGGAATTTTGAGAAATTC
Found at i:519814 original size:28 final size:29
Alignment explanation
Indices: 519714--519814 Score: 77
Period size: 28 Copynumber: 3.5 Consensus size: 29
519704 AATTCGGGTT
519714 TAAAAATGGAATTTT--TAGACATTCGA-GG
1 TAAAAATGGAATTTTGGTAG--ATTCGAGGG
* * * *
519742 TAGAAATGGAATTTTGGAAGTTTTG-GGG
1 TAAAAATGGAATTTTGGTAGATTCGAGGG
**
519770 TCAAAAATGGGTTTTTTGGTAG-TTCGAGGG
1 T-AAAAAT-GGAATTTTGGTAGATTCGAGGG
519800 TAAAAATGGAATTTT
1 TAAAAATGGAATTTT
519815 TGAGGTTAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 12
0.71 0.14 0.15
Matches are distributed among these distances:
28 26 0.46
29 14 0.25
30 16 0.29
ACGTcount: A:0.33, C:0.04, G:0.28, T:0.36
Consensus pattern (29 bp):
TAAAAATGGAATTTTGGTAGATTCGAGGG
Found at i:519814 original size:29 final size:28
Alignment explanation
Indices: 519714--519816 Score: 86
Period size: 29 Copynumber: 3.6 Consensus size: 28
519704 AATTCGGGTT
* *
519714 TAAAAATGGAATTTTTAGACATTCGA-GG
1 TAAAAATGGAATTTTTGGA-GTTCGAGGG
* *
519742 TAGAAATGGAA-TTTTGGAAGTTTTG-GGG
1 TAAAAATGGAATTTTTGG-AG-TTCGAGGG
**
519770 TCAAAAATGGGTTTTTTGGTAGTTCGAGGG
1 T-AAAAATGGAATTTTTGG-AGTTCGAGGG
519800 TAAAAATGGAATTTTTG
1 TAAAAATGGAATTTTTG
519817 AGGTTAAATG
Statistics
Matches: 58, Mismatches: 11, Indels: 11
0.73 0.14 0.14
Matches are distributed among these distances:
27 5 0.09
28 17 0.29
29 24 0.41
30 12 0.21
ACGTcount: A:0.32, C:0.04, G:0.28, T:0.36
Consensus pattern (28 bp):
TAAAAATGGAATTTTTGGAGTTCGAGGG
Found at i:519861 original size:29 final size:29
Alignment explanation
Indices: 519822--519972 Score: 133
Period size: 29 Copynumber: 5.1 Consensus size: 29
519812 TTTTGAGGTT
519822 AAATGGGATTTTAGGAAGTTTGGGGGTAA
1 AAATGGGATTTTAGGAAGTTTGGGGGTAA
* * *** *
519851 AAATGGAATTTTTGGAAGTTTCATGGTCA
1 AAATGGGATTTTAGGAAGTTTGGGGGTAA
* * *
519880 AAATGGGATTTTGGGAAGTTTTAGGGTTAA
1 AAATGGGATTTTAGGAAG-TTTGGGGGTAA
* *
519910 AAATGGGATTTT-GAGAAGTTTCGTGGTTAA
1 AAATGGGATTTTAG-GAAGTTT-GGGGGTAA
* * * *
519940 AAATTGGATTTTAGAAAGTTCGGGGGTGA
1 AAATGGGATTTTAGGAAGTTTGGGGGTAA
519969 AAAT
1 AAAT
519973 AGAATTTTTA
Statistics
Matches: 97, Mismatches: 21, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
29 52 0.54
30 44 0.45
31 1 0.01
ACGTcount: A:0.32, C:0.03, G:0.31, T:0.34
Consensus pattern (29 bp):
AAATGGGATTTTAGGAAGTTTGGGGGTAA
Found at i:519915 original size:30 final size:29
Alignment explanation
Indices: 519822--519951 Score: 136
Period size: 29 Copynumber: 4.4 Consensus size: 29
519812 TTTTGAGGTT
* * *
519822 AAATGGGATTTTAGGAAGTTTGGGGGTAA
1 AAATGGGATTTTGGGAAGTTTAGGGTTAA
* * * *
519851 AAATGGAATTTTTGGAAGTTTCATGG-TCA
1 AAATGGGATTTTGGGAAGTTT-AGGGTTAA
519880 AAATGGGATTTTGGGAAGTTTTAGGGTTAA
1 AAATGGGATTTTGGGAAG-TTTAGGGTTAA
* *
519910 AAATGGGATTTTGAGAAGTTTCGTGGTTAA
1 AAATGGGATTTTGGGAAGTTTAG-GGTTAA
*
519940 AAATTGGATTTT
1 AAATGGGATTTT
519952 AGAAAGTTCG
Statistics
Matches: 85, Mismatches: 12, Indels: 7
0.82 0.12 0.07
Matches are distributed among these distances:
29 44 0.52
30 41 0.48
ACGTcount: A:0.31, C:0.02, G:0.30, T:0.37
Consensus pattern (29 bp):
AAATGGGATTTTGGGAAGTTTAGGGTTAA
Found at i:519959 original size:30 final size:30
Alignment explanation
Indices: 519822--519959 Score: 140
Period size: 30 Copynumber: 4.7 Consensus size: 30
519812 TTTTGAGGTT
* *
519822 AAATGGGATTTTAGGAAGTTT-GGGGGTAA
1 AAATGGGATTTTAGGAAGTTTCGTGGTTAA
* * * *
519851 AAATGGAATTTTTGGAAGTTTCATGG-TCA
1 AAATGGGATTTTAGGAAGTTTCGTGGTTAA
* *
519880 AAATGGGATTTTGGGAAGTTTTAG-GGTTAA
1 AAATGGGATTTTAGGAAG-TTTCGTGGTTAA
519910 AAATGGGATTTT-GAGAAGTTTCGTGGTTAA
1 AAATGGGATTTTAG-GAAGTTTCGTGGTTAA
* *
519940 AAATTGGATTTTAGAAAGTT
1 AAATGGGATTTTAGGAAGTT
519960 CGGGGGTGAA
Statistics
Matches: 90, Mismatches: 13, Indels: 11
0.79 0.11 0.10
Matches are distributed among these distances:
29 44 0.49
30 45 0.50
31 1 0.01
ACGTcount: A:0.32, C:0.02, G:0.30, T:0.36
Consensus pattern (30 bp):
AAATGGGATTTTAGGAAGTTTCGTGGTTAA
Found at i:519972 original size:59 final size:58
Alignment explanation
Indices: 519822--519981 Score: 187
Period size: 59 Copynumber: 2.7 Consensus size: 58
519812 TTTTGAGGTT
*
519822 AAATGGGATTTTAGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCATGGTCA
1 AAATGGGATTTTAGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCATGGTAA
* * * * *
519880 AAATGGGATTTTGGGAAGTTTTAGGGTTAAAAATGGGA-TTTTGAGAAGTTTCGTGGTTAA
1 AAATGGGATTTTAGGAAG-TTTGGGGGTAAAAATGGAATTTTTG-GAAGTTTCATGG-TAA
* * * * *
519940 AAATTGGATTTTAGAAAGTTCGGGGGTGAAAATAGAATTTTT
1 AAATGGGATTTTAGGAAGTTTGGGGGTAAAAATGGAATTTTT
519982 AGACAATTTA
Statistics
Matches: 83, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
58 22 0.27
59 40 0.48
60 21 0.25
ACGTcount: A:0.32, C:0.03, G:0.30, T:0.36
Consensus pattern (58 bp):
AAATGGGATTTTAGGAAGTTTGGGGGTAAAAATGGAATTTTTGGAAGTTTCATGGTAA
Found at i:521704 original size:18 final size:18
Alignment explanation
Indices: 521681--521766 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
521671 TTTTTTAATT
521681 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
521699 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
521716 ATTTAAA-TTTAAACTTAA
1 AATTAAATTTTAAACTT-A
** *
521734 AAGAAAAGTTTAAACTTTA
1 AATTAAATTTTAAAC-TTA
*
521753 AACTAAA-TTTAAAC
1 AATTAAATTTTAAAC
521767 CCAAAATGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 22 0.39
18 20 0.35
19 13 0.23
20 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:522545 original size:205 final size:205
Alignment explanation
Indices: 522131--522781 Score: 860
Period size: 205 Copynumber: 3.2 Consensus size: 205
522121 TTGACTTGCC
* ** * * ** * * *
522131 CTTCTTCTCAGTATCTCATCGGGAAGATGACCGTATCACTTGTTTTGATCCACTTCTCTGTGTTT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCACTGGCTTCAATCCGCTTCTCTGTATCT
* * * * * * *
522196 CATCAGGAAGATGATTTTGGTTTACTTCCCCGTAT-TTCATCAGGAAGCTAACCATTTTATTACT
66 CATCAAGAAGACGAATTTGGTCTACTTCTCAGTATCTT-ATCAGGAAGCTAACC-TTTTATTGCT
* * * *
522260 TCGACCTGCTTCTCAGTATCTCATCAGGAAGCTGGGGTTCAAAGATTTG-T-TCATCAAGCGTGG
129 TCGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGG
522323 GTTTGATTTGAGT
194 GTTTGATTTG-GT
* * ** ** *
522336 CTTCTTCTCAATATCTCATTATAAAGATGACCGCGTCGTTTGCTTCAATCCGCTTCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCACTGGCTTCAATCCGCTTCTCTGTATCT
*
522401 CATCAAGAAGACGAATTTGGTCCACTTCTCAGTATCTTATCAGGAAGCTAACCTTTTATTGCTTC
66 CATCAAGAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGCTAACCTTTTATTGCTTC
* * *
522466 GACCTGCTTCTCGGTGTCTCATCAGGAAGTTGGGGTTCGAAGGTTTGCTCACATCGAGCGTGGGT
131 GACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGGGT
522531 TTGATTTGGT
196 TTGATTTGGT
* * *
522541 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCATCACTGGTTTCAATCCGCATCTCTGTATCT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCACTGGCTTCAATCCGCTTCTCTGTATCT
* * * *
522606 CAT-AAGGAAGACGAATTTGGTCTACTTATCAGTATCTCATCAGGAAGCTAACGTTTTATTGTTT
66 CATCAA-GAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGCTAACCTTTTATTGCTT
* *
522670 CGACTTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCTAGCGTGGG
130 CGACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGGG
*
522735 TTTAATTTGGT
195 TTTGATTTGGT
522746 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGT
1 CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGT
522782 TATTGTTTGT
Statistics
Matches: 391, Mismatches: 51, Indels: 8
0.87 0.11 0.02
Matches are distributed among these distances:
204 55 0.14
205 313 0.80
206 23 0.06
ACGTcount: A:0.22, C:0.22, G:0.21, T:0.36
Consensus pattern (205 bp):
CTTCTTCTCAGTATCTCATCAGGAAGATGACCGCGTCACTGGCTTCAATCCGCTTCTCTGTATCT
CATCAAGAAGACGAATTTGGTCTACTTCTCAGTATCTTATCAGGAAGCTAACCTTTTATTGCTTC
GACCTGCTTCTCGGTGTCTCATCAGGAAGCTGGGGTTCGAAGATTTGCTCACATCAAGCGTGGGT
TTGATTTGGT
Found at i:533945 original size:96 final size:96
Alignment explanation
Indices: 533757--533948 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
533747 TTTTTACGAA
** **
533757 AAGGGTATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* * *
533822 GGACTGAAGATAAGGAAACATTGCCTCGATT
66 GAACTGAAGATAAAGAAACATTACCTCGATT
* *
533853 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAAGT-TTTC
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-TATTTC
*
533917 -GAAACTTGAA-ATAAA-AGAATATTACCTCGATT
65 AG-AAC-TGAAGATAAAGA-AACATTACCTCGATT
533949 TTAAAGCTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 75 0.91
97 5 0.06
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAACTGAAGATAAAGAAACATTACCTCGATT
Found at i:534269 original size:59 final size:58
Alignment explanation
Indices: 534206--534374 Score: 162
Period size: 59 Copynumber: 2.9 Consensus size: 58
534196 TTTTGGATTC
*
534206 TCGAGGAT-GAAATGGTAATTTTGAGAAAATTTGGGGTTAAAAATGGAATTTTTAGACAT
1 TCGAGGATAGAAATGG-AATTTTG-GAAAATTTAGGGTTAAAAATGGAATTTTTAGACAT
* ** * *
534265 TCGAGGGTAGAAATGGAATTTTGGAAGTTTTAGGGTTAAAAATGGGATTTTTGGA-AGT
1 TCGAGGATAGAAATGGAATTTTGGAAAATTTAGGGTTAAAAATGGAATTTTTAGACA-T
* * ** ** * *
534323 TCGAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTT
1 TCGAGGATAGAAATGGAA-TTTTGGAAAATTTAGGGTTAAAAATGGAATTTT
534375 AAGGGTAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.01
58 43 0.44
59 46 0.47
60 7 0.07
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
TCGAGGATAGAAATGGAATTTTGGAAAATTTAGGGTTAAAAATGGAATTTTTAGACAT
Found at i:534319 original size:30 final size:30
Alignment explanation
Indices: 534239--534550 Score: 244
Period size: 29 Copynumber: 10.9 Consensus size: 30
534229 AGAAAATTTG
* * **
534239 GGGTTAAAAATGGAATTTTTAGACA-TTCGA
1 GGGTTAAAAATGGGATTTTTGGA-AGTTTTA
* *
534269 GGG-TAGAAAT-GGAATTTTGGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
**
534297 GGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
***
534327 GGG-TAAAAATAAAATTTTTGGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
*
534356 GGGTCAAAAATGGGA-TTTT---A-----A
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* *
534377 GGG-TAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* * *
534406 GGGTCAAAAATGGGATTTTGGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* * *
534436 GGGTT-AAAATGAGATTTTGGGAAGTTTAA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
*** *
534465 GGG-TAAAAATAAAATTTTTAGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* *
534494 GGGTTAAAAATGGGATTTTGGGAAG-TTTC
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
*
534523 GAGGTTAAAAATAGGATTTTTGGAAGTT
1 G-GGTTAAAAATGGGATTTTTGGAAGTT
534551 CGGGGGTAAA
Statistics
Matches: 222, Mismatches: 42, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
20 9 0.04
21 8 0.04
24 1 0.00
26 1 0.00
27 1 0.00
28 15 0.07
29 93 0.42
30 93 0.42
31 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (30 bp):
GGGTTAAAAATGGGATTTTTGGAAGTTTTA
Found at i:534395 original size:21 final size:20
Alignment explanation
Indices: 534345--534394 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
534335 ATAAAATTTT
534345 TGGAAGTTTTAGGGTCAAAAA
1 TGGAA-TTTTAGGGTCAAAAA
*
534366 TGGGATTTTAAGGGT-AAAAA
1 TGGAATTTT-AGGGTCAAAAA
534386 TGGAATTTT
1 TGGAATTTT
534395 TGGAAGTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 17 0.65
21 9 0.35
ACGTcount: A:0.36, C:0.02, G:0.28, T:0.34
Consensus pattern (20 bp):
TGGAATTTTAGGGTCAAAAA
Found at i:534401 original size:50 final size:50
Alignment explanation
Indices: 534326--534424 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
534316 TGGAAGTTCG
534326 AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTA
1 AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTA
** *
534376 AGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTT
1 AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTT
534425 GGGAAGTTTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.36, C:0.02, G:0.27, T:0.34
Consensus pattern (50 bp):
AGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTA
Found at i:534481 original size:88 final size:89
Alignment explanation
Indices: 534372--534580 Score: 278
Period size: 88 Copynumber: 2.3 Consensus size: 89
534362 AAAATGGGAT
** * * *
534372 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTGGGAAGTTTTGG
1 TTTAAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTGGGAAGTTTCGA
534437 GGTT-AAAAT-GAGATTTTGGGAAG
66 GGTTAAAAATAG-GATTTTGGGAAG
* *
534460 TTTAAGGGTAAAAATAAAATTTTTAGAAGTTTTAGGGTTAAAAATGGGATTTTGGGAAGTTTCGA
1 TTTAAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTGGGAAGTTTCGA
*
534525 GGTTAAAAATAGGATTTTTGGAAG
66 GGTTAAAAATAGGATTTTGGGAAG
*** *
534549 TTCGGGGGTAAAAACAAAATTTTTGGACAGTT
1 TTTAAGGGTAAAAATAAAATTTTTGGA-AGTT
534581 CAGGGACCTT
Statistics
Matches: 105, Mismatches: 13, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
88 62 0.59
89 38 0.36
90 5 0.05
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (89 bp):
TTTAAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTTGGGAAGTTTCGA
GGTTAAAAATAGGATTTTGGGAAG
Found at i:534560 original size:29 final size:29
Alignment explanation
Indices: 534372--534585 Score: 162
Period size: 30 Copynumber: 7.2 Consensus size: 29
534362 AAAATGGGAT
*
534372 TTTAAGGGTAAAAAT-GGAATTTTTGGAAG
1 TTTAGGGGTAAAAATAGG-ATTTTTGGAAG
* * *
534401 TTTTGGGGTCAAAAATGGGATTTTGGGAAG
1 TTTAGGGGT-AAAAATAGGATTTTTGGAAG
* * *
534431 TTTTGGGGTTAAAAT-GAGATTTTGGGAAG
1 TTTAGGGGTAAAAATAG-GATTTTTGGAAG
* ** *
534460 TTTAAGGGTAAAAATAAAATTTTTAGAAG
1 TTTAGGGGTAAAAATAGGATTTTTGGAAG
* * *
534489 TTTTAGGGTTAAAAATGGGATTTTGGGAAG
1 -TTTAGGGGTAAAAATAGGATTTTTGGAAG
* *
534519 TTTCGAGGTTAAAAATAGGATTTTTGGAAG
1 TTTAG-GGGTAAAAATAGGATTTTTGGAAG
** * **
534549 TTCGGGGGTAAAAACAAAATTTTTGGACAG
1 TTTAGGGGTAAAAATAGGATTTTTGGA-AG
*
534579 TTCAGGG
1 TTTAGGG
534586 ACCTTCATGG
Statistics
Matches: 150, Mismatches: 28, Indels: 13
0.79 0.15 0.07
Matches are distributed among these distances:
28 1 0.01
29 67 0.45
30 80 0.53
31 2 0.01
ACGTcount: A:0.34, C:0.03, G:0.29, T:0.34
Consensus pattern (29 bp):
TTTAGGGGTAAAAATAGGATTTTTGGAAG
Found at i:534561 original size:59 final size:58
Alignment explanation
Indices: 534372--534562 Score: 193
Period size: 59 Copynumber: 3.2 Consensus size: 58
534362 AAAATGGGAT
* * * * * * *
534372 TTTAAGGGTAAAAATGGAATTTTTGGAAGTTTTGGGGTCAAAAATGGGATTTTGGGAAG
1 TTTAGGGGTAAAAATGGGATTTTGGGAAG-TTTGAGGTTAAAAATAGGATTTTTGGAAG
* * * * * ** *
534431 TTTTGGGGTTAAAATGAGATTTTGGGAAGTTTAAGGGTAAAAATAAAATTTTTAGAAG
1 TTTAGGGGTAAAAATGGGATTTTGGGAAGTTTGAGGTTAAAAATAGGATTTTTGGAAG
*
534489 TTTTAGGGTTAAAAATGGGATTTTGGGAAGTTTCGAGGTTAAAAATAGGATTTTTGGAAG
1 -TTTAGGGGTAAAAATGGGATTTTGGGAAGTTT-GAGGTTAAAAATAGGATTTTTGGAAG
**
534549 TTCGGGGGTAAAAA
1 TTTAGGGGTAAAAA
534563 CAAAATTTTT
Statistics
Matches: 103, Mismatches: 27, Indels: 4
0.77 0.20 0.03
Matches are distributed among these distances:
58 20 0.19
59 62 0.60
60 21 0.20
ACGTcount: A:0.34, C:0.02, G:0.30, T:0.35
Consensus pattern (58 bp):
TTTAGGGGTAAAAATGGGATTTTGGGAAGTTTGAGGTTAAAAATAGGATTTTTGGAAG
Found at i:536246 original size:18 final size:18
Alignment explanation
Indices: 536223--536308 Score: 72
Period size: 17 Copynumber: 4.8 Consensus size: 18
536213 TTTTTTAATT
536223 AATTAAATTTTAAA-TTCA
1 AATTAAATTTTAAACTT-A
536241 AATT-AATTTTAAACTTA
1 AATTAAATTTTAAACTTA
*
536258 ATTTAAA-TTTAAACTTAA
1 AATTAAATTTTAAACTT-A
** *
536276 AAGAAAAGTTTAAACTTTA
1 AATTAAATTTTAAAC-TTA
*
536295 AACTAAA-TTTAAAC
1 AATTAAATTTTAAAC
536309 CCAAAATGAA
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
17 22 0.39
18 20 0.35
19 13 0.23
20 2 0.04
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (18 bp):
AATTAAATTTTAAACTTA
Found at i:537333 original size:2 final size:2
Alignment explanation
Indices: 537326--537353 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
537316 TTATGGAAGA
537326 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
537354 TTATGGTTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:545032 original size:96 final size:96
Alignment explanation
Indices: 544844--545035 Score: 230
Period size: 96 Copynumber: 2.0 Consensus size: 96
544834 TTTTTACGAA
** **
544844 AAGGGTATTCGATTATCTCGATTTGAAGAAAGGTTGCACCTAGTAAGTTAAGGCGTAATATTTCA
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
* * *
544909 GGACTGAAGATAAGGAAACATTGCCTCGATT
66 GAACTGAAGATAAAGAAACATTACCTCGATT
* *
544940 AAGGGTATTCGATTATTTCGATTTGAAGAAAAATTGCACCTAGTGAGTTAAGGCACAAGT-TTTC
1 AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAA-TATTTC
*
545004 -GAAACTTGAA-ATAAA-AGAATATTACCTCGATT
65 AG-AAC-TGAAGATAAAGA-AACATTACCTCGATT
545036 TTAAAGCTTT
Statistics
Matches: 82, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
95 2 0.02
96 75 0.91
97 5 0.06
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.30
Consensus pattern (96 bp):
AAGGGTATTCGATTATCTCGATTTGAAGAAAAATTGCACCTAGTAAGTTAAGGCACAATATTTCA
GAACTGAAGATAAAGAAACATTACCTCGATT
Found at i:545356 original size:59 final size:58
Alignment explanation
Indices: 545293--545461 Score: 162
Period size: 59 Copynumber: 2.9 Consensus size: 58
545283 TTTTGGATTC
*
545293 TCGAGGAT-GAAATGGTAATTTTGAGAAAATTTGGGGTTAAAAATGGAATTTTTAGACAT
1 TCGAGGATAGAAATGG-AATTTTG-GAAAATTTAGGGTTAAAAATGGAATTTTTAGACAT
* ** * *
545352 TCGAGGGTAGAAATGGAATTTTGGAAGTTTTAGGGTTAAAAATGGGATTTTTGGA-AGT
1 TCGAGGATAGAAATGGAATTTTGGAAAATTTAGGGTTAAAAATGGAATTTTTAGACA-T
* * ** ** * *
545410 TCGAGGGTAAAAATAAAATTTTTGGAAGTTTTAGGGTCAAAAATGGGATTTT
1 TCGAGGATAGAAATGGAA-TTTTGGAAAATTTAGGGTTAAAAATGGAATTTT
545462 AAGGGTAAAA
Statistics
Matches: 97, Mismatches: 10, Indels: 6
0.86 0.09 0.05
Matches are distributed among these distances:
57 1 0.01
58 43 0.44
59 46 0.47
60 7 0.07
ACGTcount: A:0.35, C:0.03, G:0.28, T:0.34
Consensus pattern (58 bp):
TCGAGGATAGAAATGGAATTTTGGAAAATTTAGGGTTAAAAATGGAATTTTTAGACAT
Found at i:545406 original size:30 final size:30
Alignment explanation
Indices: 545326--545637 Score: 244
Period size: 29 Copynumber: 10.9 Consensus size: 30
545316 AGAAAATTTG
* * **
545326 GGGTTAAAAATGGAATTTTTAGACA-TTCGA
1 GGGTTAAAAATGGGATTTTTGGA-AGTTTTA
* *
545356 GGG-TAGAAAT-GGAATTTTGGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
**
545384 GGGTTAAAAATGGGATTTTTGGAAGTTCGA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
***
545414 GGG-TAAAAATAAAATTTTTGGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
*
545443 GGGTCAAAAATGGGA-TTTT---A-----A
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* *
545464 GGG-TAAAAATGGAATTTTTGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* * *
545493 GGGTCAAAAATGGGATTTTGGGAAGTTTTG
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* * *
545523 GGGTT-AAAATGAGATTTTGGGAAGTTTAA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
*** *
545552 GGG-TAAAAATAAAATTTTTAGAAGTTTTA
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
* *
545581 GGGTTAAAAATGGGATTTTGGGAAG-TTTC
1 GGGTTAAAAATGGGATTTTTGGAAGTTTTA
*
545610 GAGGTTAAAAATAGGATTTTTGGAAGTT
1 G-GGTTAAAAATGGGATTTTTGGAAGTT
545638 CGGGGGTAAA
Statistics
Matches: 222, Mismatches: 42, Indels: 35
0.74 0.14 0.12
Matches are distributed among these distances:
20 9 0.04
21 8 0.04
24 1 0.00
26 1 0.00
27 1 0.00
28 15 0.07
29 93 0.42
30 93 0.42
31 1 0.00
ACGTcount: A:0.34, C:0.02, G:0.29, T:0.35
Consensus pattern (30 bp):
GGGTTAAAAATGGGATTTTTGGAAGTTTTA
Done.