Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008726.1 Hibiscus syriacus cultivar Beakdansim tig00111792_pilon, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 1298898
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 3 of 6
Found at i:508235 original size:21 final size:20
Alignment explanation
Indices: 508202--508242 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 20
508192 CCCAGAATGG
508202 GGGAACGGTACCCCTTCATA
1 GGGAACGGTACCCCTTCATA
*
508222 GGGAATGGATACCCCTTCATA
1 GGGAACGG-TACCCCTTCATA
508243 ATATTCAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.27, C:0.27, G:0.24, T:0.22
Consensus pattern (20 bp):
GGGAACGGTACCCCTTCATA
Found at i:508395 original size:34 final size:36
Alignment explanation
Indices: 508355--508439 Score: 138
Period size: 34 Copynumber: 2.4 Consensus size: 36
508345 AAACCATGCA
508355 GGGGAATCTGTACCCGGGGAATCGATA-CCCCT-GG
1 GGGGAATCTGTACCCGGGGAATCGATACCCCCTGGG
* *
508389 GGGGAATCTGTTCCCGGGTAATCGATACCCCCTGGG
1 GGGGAATCTGTACCCGGGGAATCGATACCCCCTGGG
508425 GGGGAATCTGTACCC
1 GGGGAATCTGTACCC
508440 CCTGGACAAT
Statistics
Matches: 46, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 25 0.54
35 5 0.11
36 16 0.35
ACGTcount: A:0.19, C:0.27, G:0.34, T:0.20
Consensus pattern (36 bp):
GGGGAATCTGTACCCGGGGAATCGATACCCCCTGGG
Found at i:508487 original size:50 final size:51
Alignment explanation
Indices: 508429--508531 Score: 199
Period size: 50 Copynumber: 2.0 Consensus size: 51
508419 CCTGGGGGGG
508429 AATCTGTACCCCCTGGACAATCTGATTTTTC-TGCAACCCTTTAAAAAGAA
1 AATCTGTACCCCCTGGACAATCTGATTTTTCTTGCAACCCTTTAAAAAGAA
508479 AATCTGTACCCCCTGGACAATCTGATTTTTCTTGCAACCCTTTAAAAAGAA
1 AATCTGTACCCCCTGGACAATCTGATTTTTCTTGCAACCCTTTAAAAAGAA
508530 AA
1 AA
508532 AATTTTTGGC
Statistics
Matches: 52, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 31 0.60
51 21 0.40
ACGTcount: A:0.33, C:0.25, G:0.12, T:0.30
Consensus pattern (51 bp):
AATCTGTACCCCCTGGACAATCTGATTTTTCTTGCAACCCTTTAAAAAGAA
Found at i:510502 original size:46 final size:45
Alignment explanation
Indices: 510398--510505 Score: 144
Period size: 45 Copynumber: 2.4 Consensus size: 45
510388 CGGTGCACTA
* *
510398 AGAGTGCATCGATGCATGAAATGCATTCGATGTTTCAGAATAGCC
1 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAGAAAAGCC
* **
510443 AGAGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAAATTC
1 AGAGTGCATCGATGCATCAAATGCATTCGATG-TTTCAGAAAAGCC
* *
510489 TGAGTTCATCGATGCAT
1 AGAGTGCATCGATGCAT
510506 AGTATATGCA
Statistics
Matches: 55, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
45 31 0.56
46 24 0.44
ACGTcount: A:0.31, C:0.18, G:0.21, T:0.31
Consensus pattern (45 bp):
AGAGTGCATCGATGCATCAAATGCATTCGATGTTTCAGAAAAGCC
Found at i:512748 original size:13 final size:13
Alignment explanation
Indices: 512730--512754 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
512720 AATCAAAAAC
512730 ATCAAATTTAGAA
1 ATCAAATTTAGAA
512743 ATCAAATTTAGA
1 ATCAAATTTAGA
512755 TTTTTGATTT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.08, G:0.08, T:0.32
Consensus pattern (13 bp):
ATCAAATTTAGAA
Found at i:513229 original size:21 final size:22
Alignment explanation
Indices: 513167--513248 Score: 71
Period size: 23 Copynumber: 3.6 Consensus size: 22
513157 GCATGGCCTT
513167 GTGCATCGATGCACATTCAAGGC
1 GTGCATCGATGCACATTC-AGGC
* *
513190 GTGCATC-AGTGCACCTTCATG-
1 GTGCATCGA-TGCACATTCAGGC
*
513211 GTGTATCGATGCACATTCAAAGG-
1 GTGCATCGATGCACATTC--AGGC
513234 GATGCATCGATGCAC
1 G-TGCATCGATGCAC
513249 TGTTAAGTGT
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
21 14 0.29
22 4 0.08
23 18 0.38
24 12 0.25
ACGTcount: A:0.26, C:0.24, G:0.26, T:0.24
Consensus pattern (22 bp):
GTGCATCGATGCACATTCAGGC
Found at i:515178 original size:20 final size:21
Alignment explanation
Indices: 515138--515214 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
515128 ATCAGATTGT
515138 CCAGGGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
515159 CCAGGGGGTATC-GATT---CC
1 CCAGGGGGTA-CAGATTCCCCC
*
515177 CC--GGGGAACAGATT-CCCC
1 CCAGGGGGTACAGATTCCCCC
515195 CCA-GGGGTACAGATTCCCCC
1 CCAGGGGGTACAGATTCCCCC
515215 TGCATGGTTT
Statistics
Matches: 48, Mismatches: 2, Indels: 13
0.76 0.03 0.21
Matches are distributed among these distances:
15 1 0.02
16 9 0.19
18 8 0.17
19 11 0.23
20 4 0.08
21 14 0.29
22 1 0.02
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.16
Consensus pattern (21 bp):
CCAGGGGGTACAGATTCCCCC
Found at i:515206 original size:19 final size:19
Alignment explanation
Indices: 515142--515214 Score: 82
Period size: 19 Copynumber: 3.9 Consensus size: 19
515132 GATTGTCCAG
515142 GGGGTACAGATTCCCCCCCA
1 GGGGTACAGATT-CCCCCCA
515162 GGGGGTATC-GATT--CCCC-
1 -GGGGTA-CAGATTCCCCCCA
*
515179 GGGGAACAGATTCCCCCCA
1 GGGGTACAGATTCCCCCCA
515198 GGGGTACAGATTCCCCC
1 GGGGTACAGATTCCCCC
515215 TGCATGGTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
15 1 0.02
16 9 0.20
18 8 0.18
19 16 0.36
21 10 0.22
22 1 0.02
ACGTcount: A:0.19, C:0.36, G:0.29, T:0.16
Consensus pattern (19 bp):
GGGGTACAGATTCCCCCCA
Found at i:518593 original size:19 final size:20
Alignment explanation
Indices: 518554--518594 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
518544 ATCAGATTGT
518554 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
518574 CCAGGGGGTACAGATTCCCC
1 CCAGGGGGTACAGATTCCCC
518594 C
1 C
518595 TGCATGGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.37, G:0.29, T:0.15
Consensus pattern (20 bp):
CCAGGGGGTACAGATTCCCC
Found at i:518733 original size:21 final size:21
Alignment explanation
Indices: 518707--518748 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
518697 ATTTGAATAT
* *
518707 TATGAAGGGGTATCGATTCCC
1 TATGAAGGGGTACCAATTCCC
518728 TATGAAGGGGTACCAATTCCC
1 TATGAAGGGGTACCAATTCCC
518749 CCCATTATGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (21 bp):
TATGAAGGGGTACCAATTCCC
Found at i:523532 original size:19 final size:19
Alignment explanation
Indices: 523508--523559 Score: 77
Period size: 19 Copynumber: 2.7 Consensus size: 19
523498 TTGTGCCCTT
523508 AGTGCATCGGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
*
523527 AGTGCATCAGTGCACTAAG
1 AGTGCATCGGTGCACTAAG
* *
523546 AGTACATCGATGCA
1 AGTGCATCGGTGCA
523560 TGAAATGCAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.31, C:0.21, G:0.27, T:0.21
Consensus pattern (19 bp):
AGTGCATCGGTGCACTAAG
Found at i:523630 original size:64 final size:65
Alignment explanation
Indices: 523550--523670 Score: 174
Period size: 65 Copynumber: 1.9 Consensus size: 65
523540 ACTAAGAGTA
* * *
523550 CATCGATGCATGAAATGCATTCGA-CGTTTCA-AAATAGTCAGAGTGCATCGATGCATGACTGGT
1 CATCGATGCATCAAATGCATTCGATAGTTTCATAAA-ACTCAGAGTGCATCGATGCATGACTGGT
523613 G
65 G
* *
523614 CATCGATGCATCAAATGCATTCGATATTTTCATAAAACTCTGAGTGCATCGATGCAT
1 CATCGATGCATCAAATGCATTCGATAGTTTCATAAAACTCAGAGTGCATCGATGCAT
523671 AGTATGTGCT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
64 23 0.46
65 24 0.48
66 3 0.06
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.29
Consensus pattern (65 bp):
CATCGATGCATCAAATGCATTCGATAGTTTCATAAAACTCAGAGTGCATCGATGCATGACTGGTG
Found at i:525361 original size:13 final size:12
Alignment explanation
Indices: 525327--525351 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
525317 ATTAAAGAAG
525327 TTTATTATTTTT
1 TTTATTATTTTT
525339 TTTATTATTTTT
1 TTTATTATTTTT
525351 T
1 T
525352 CTTTTCATTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (12 bp):
TTTATTATTTTT
Found at i:525367 original size:20 final size:20
Alignment explanation
Indices: 525339--525376 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
525329 TATTATTTTT
* *
525339 TTTATTATTTTTTCTTTTCA
1 TTTAATATTTTATCTTTTCA
525359 TTTAATATTTTATCTTTT
1 TTTAATATTTTATCTTTT
525377 AGTAAAATAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.08, G:0.00, T:0.74
Consensus pattern (20 bp):
TTTAATATTTTATCTTTTCA
Found at i:525518 original size:14 final size:14
Alignment explanation
Indices: 525499--525563 Score: 57
Period size: 14 Copynumber: 4.8 Consensus size: 14
525489 TCAAAATCCA
*
525499 TAAACCTTAAACTT
1 TAAACCATAAACTT
525513 TAAACC-TAAA-TT
1 TAAACCATAAACTT
*
525525 ATAAACTCA-AAA-TC
1 -TAAAC-CATAAACTT
*
525539 TAAACCATAAACCT
1 TAAACCATAAACTT
525553 TAAACCATAAA
1 TAAACCATAAA
525564 ATGAAAATGA
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
12 4 0.09
13 17 0.40
14 22 0.51
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACCATAAACTT
Found at i:525529 original size:20 final size:20
Alignment explanation
Indices: 525499--525563 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
525489 TCAAAATCCA
*
525499 TAAACCTTAAACTTTAAACC
1 TAAACCATAAACTTTAAACC
** ** *
525519 TAAATTATAAACTCAAAATC
1 TAAACCATAAACTTTAAACC
*
525539 TAAACCATAAACCTTAAACC
1 TAAACCATAAACTTTAAACC
525559 ATAAA
1 -TAAA
525564 ATGAAAATGA
Statistics
Matches: 32, Mismatches: 12, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
20 28 0.88
21 4 0.12
ACGTcount: A:0.52, C:0.22, G:0.00, T:0.26
Consensus pattern (20 bp):
TAAACCATAAACTTTAAACC
Found at i:526028 original size:23 final size:22
Alignment explanation
Indices: 526002--526055 Score: 65
Period size: 21 Copynumber: 2.5 Consensus size: 22
525992 ATATAACATT
*
526002 TAAATTATATTTATACTTATATA
1 TAAATTATATTCA-ACTTATATA
* *
526025 TAAATTTTA-TCAATTTATATA
1 TAAATTATATTCAACTTATATA
526046 TAAATTATAT
1 TAAATTATAT
526056 AACTTTTTGG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 16 0.62
22 2 0.08
23 8 0.31
ACGTcount: A:0.44, C:0.04, G:0.00, T:0.52
Consensus pattern (22 bp):
TAAATTATATTCAACTTATATA
Found at i:526288 original size:13 final size:14
Alignment explanation
Indices: 526263--526300 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
526253 TATTTATTTT
526263 TAAATTAATTAAAA
1 TAAATTAATTAAAA
526277 TAAATT-ATTAAAA
1 TAAATTAATTAAAA
* *
526290 TTAATAAATTA
1 TAAATTAATTA
526301 TTTTAAGGAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (14 bp):
TAAATTAATTAAAA
Found at i:526627 original size:2 final size:2
Alignment explanation
Indices: 526620--526668 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
526610 GTGGTGGGAC
526620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
526662 AT AT AT A
1 AT AT AT A
526669 AATTGTCGTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:527077 original size:5 final size:4
Alignment explanation
Indices: 527017--527054 Score: 58
Period size: 4 Copynumber: 9.0 Consensus size: 4
527007 AAAAGGTAAG
527017 AAAT AAAT AAAT AAAT AAAT AAAT AAATT AAATT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA-T AAA-T AAAT
527055 TAAAATGAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 24 0.73
5 9 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (4 bp):
AAAT
Found at i:527201 original size:12 final size:12
Alignment explanation
Indices: 527154--527203 Score: 50
Period size: 12 Copynumber: 4.2 Consensus size: 12
527144 AGAAGAAAAA
527154 AAAAT-ATAAAT
1 AAAATAATAAAT
* *
527165 AAAACAAATTAAT
1 AAAA-TAATAAAT
527178 AAAATAATAAAT
1 AAAATAATAAAT
527190 AAAAGTAA-AAAT
1 AAAA-TAATAAAT
527202 AA
1 AA
527204 TATATATATA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
11 4 0.12
12 16 0.50
13 12 0.38
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (12 bp):
AAAATAATAAAT
Found at i:527231 original size:26 final size:26
Alignment explanation
Indices: 527188--527254 Score: 89
Period size: 26 Copynumber: 2.5 Consensus size: 26
527178 AAAATAATAA
*
527188 ATAAAAGTAAAAATAATATATATATAT
1 ATAAAA-TAAAAAAAATATATATATAT
* *
527215 ATTAAATAAAAAAAATATTTATATAT
1 ATAAAATAAAAAAAATATATATATAT
*
527241 ATAAAATAATAAAA
1 ATAAAATAAAAAAA
527255 CTGATAATAA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
26 30 0.86
27 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (26 bp):
ATAAAATAAAAAAAATATATATATAT
Found at i:528563 original size:36 final size:36
Alignment explanation
Indices: 528514--528747 Score: 213
Period size: 36 Copynumber: 6.6 Consensus size: 36
528504 GTTTGTTTTG
* *
528514 TGTTTCAAGAGAAACTGTCTCAAGAGGGACAAAATT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
528550 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAA-TT
* *
528587 AG-TTCTAAAAGAAACTGTCTCAAGGGAGACAAAATT
1 TGTTTC-AAAAGAAACTGTCTCAAGAGAGACAAAATT
* *
528623 TGTTTCAAGGAA-AAGA-TAT-TC-A-A-AG----ATTT
1 TGTTTCAA--AAGAA-ACTGTCTCAAGAGAGACAAAATT
*
528652 TGTTTC-AAGGAAAACTGTCTCAAGAGAGACAAAATT
1 TGTTTCAAAAG-AAACTGTCTCAAGAGAGACAAAATT
** *
528688 TGTTTCAAGGGAAACTGTCTCAAGAGAGACAAGATTT
1 TGTTTCAAAAGAAACTGTCTCAAGAGAGACAA-AATT
**
528725 TGTTTCAAGGGAAACTGTCTCAA
1 TGTTTCAAAAGAAACTGTCTCAA
528748 AACTCGTTTT
Statistics
Matches: 166, Mismatches: 13, Indels: 37
0.77 0.06 0.17
Matches are distributed among these distances:
26 1 0.01
27 1 0.01
28 5 0.03
29 11 0.07
30 1 0.01
31 1 0.01
32 2 0.01
33 2 0.01
35 1 0.01
36 72 0.43
37 66 0.40
38 3 0.02
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (36 bp):
TGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAATT
Found at i:528748 original size:102 final size:102
Alignment explanation
Indices: 528548--528734 Score: 272
Period size: 102 Copynumber: 1.8 Consensus size: 102
528538 AGGGACAAAA
*
528548 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGGG
1 TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
528613 AGACAAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
66 AGACAAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
* * **
528650 TTTGTTTC-AAGGAAAACTGTCTCAAGAGAGACAAAA-TTTGTT-TCAAGGGAAACTGTCTCAAG
1 TTTGTTTCAAAAG-AAACTGTCTCAAGAGAGACAAAACTTAGTTCT-AAAAGAAACTGTCTCAAG
*
528712 AGAGACAAGATTTTGTTTCAAGG
64 AGAGACAA-AATTTGTTTCAAGG
528735 GAAACTGTCT
Statistics
Matches: 76, Mismatches: 6, Indels: 6
0.86 0.07 0.07
Matches are distributed among these distances:
100 1 0.01
101 31 0.41
102 44 0.58
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.28
Consensus pattern (102 bp):
TTTGTTTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTAGTTCTAAAAGAAACTGTCTCAAGAG
AGACAAAATTTGTTTCAAGGAAAAGATATTCAAAGAT
Found at i:528864 original size:37 final size:37
Alignment explanation
Indices: 528812--528884 Score: 121
Period size: 37 Copynumber: 2.0 Consensus size: 37
528802 TCAAGGTTTA
*
528812 TGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTT
1 TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
528849 TGTTTCAAG-GAAAACTATCTCAAGAGAGACAAAATT
1 TGTTTCAAGAG-AAACTATCTCAAGAGAGACAAAATT
528885 AATTTCAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
36 1 0.03
37 33 0.97
ACGTcount: A:0.42, C:0.14, G:0.18, T:0.26
Consensus pattern (37 bp):
TGTTTCAAGAGAAACTATCTCAAGAGAGACAAAATTT
Found at i:528896 original size:37 final size:37
Alignment explanation
Indices: 528814--528898 Score: 111
Period size: 37 Copynumber: 2.3 Consensus size: 37
528804 AAGGTTTATG
* **
528814 TTTCAA-GAGAAACTATCTCAAGGGAGACAAAATTTTG
1 TTTCAAGGA-AAACTATCTCAAGAGAGACAAAATTTAA
528851 TTTCAAGGAAAACTATCTCAAGAGAGACAAAA-TTAA
1 TTTCAAGGAAAACTATCTCAAGAGAGACAAAATTTAA
528887 TTTCAAAGGAAA
1 TTTC-AAGGAAA
528899 TGTTTTCAAT
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
36 6 0.14
37 35 0.81
38 2 0.05
ACGTcount: A:0.46, C:0.13, G:0.16, T:0.25
Consensus pattern (37 bp):
TTTCAAGGAAAACTATCTCAAGAGAGACAAAATTTAA
Found at i:528913 original size:102 final size:102
Alignment explanation
Indices: 528785--529024 Score: 363
Period size: 102 Copynumber: 2.4 Consensus size: 102
528775 ATATTTTTTG
* *
528785 TTTCAAGGGAAACATTTTCAAGGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATATTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* *
528850 GTTTCAAGGAAAACTATCTCAAGAGAGACAAAATTAA
66 GTTTCAAGGAAAACTACCCCAAGAGAGACAAAATTAA
* * *
528887 TTTCAAAGGAAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTT
1 TTTCAAGGGAAATATTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
* * * *
528952 GTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTA
66 GTTTCAAGGAAAACTACCCCAAGAGAGACAAAATTAA
* *
528989 TTTCAGGGGAAATTTTTTCAATGTTTATGTTTCAAG
1 TTTCAAGGGAAATATTTTCAATGTTTATGTTTCAAG
529025 GGAGACAAAA
Statistics
Matches: 124, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
102 124 1.00
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (102 bp):
TTTCAAGGGAAATATTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTT
GTTTCAAGGAAAACTACCCCAAGAGAGACAAAATTAA
Found at i:528985 original size:37 final size:36
Alignment explanation
Indices: 528914--529000 Score: 93
Period size: 37 Copynumber: 2.4 Consensus size: 36
528904 TCAATGTTTA
* ** * *
528914 TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAA-TT
*
528951 TGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATT
1 TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
* *
528987 TATTTCAGGGGAAA
1 TGTTTCAAGGGAAA
529001 TTTTTTCAAT
Statistics
Matches: 42, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
36 14 0.33
37 28 0.67
ACGTcount: A:0.38, C:0.15, G:0.22, T:0.25
Consensus pattern (36 bp):
TGTTTCAAGGGAAACTACCCCAAGCGAGACAAAATT
Found at i:529035 original size:87 final size:87
Alignment explanation
Indices: 528933--529111 Score: 288
Period size: 87 Copynumber: 2.1 Consensus size: 87
528923 AGAAACTGTC
*
528933 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTTATTTC-AGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
*
528997 GAAATTTTTTCAATGTTTATGTT
66 G-AATGTTTTCAATGTTTATGTT
* ** *
529020 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTTAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
529085 GAATGTTTTCAATGTTTATGTT
66 GAATGTTTTCAATGTTTATGTT
529107 TCAAG
1 TCAAG
529112 AGAAACTATC
Statistics
Matches: 85, Mismatches: 6, Indels: 2
0.91 0.06 0.02
Matches are distributed among these distances:
87 80 0.94
88 5 0.06
ACGTcount: A:0.35, C:0.12, G:0.20, T:0.34
Consensus pattern (87 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTACCCCAAGCGAGATAAAATTCATTTCAAGGG
GAATGTTTTCAATGTTTATGTT
Found at i:529211 original size:189 final size:189
Alignment explanation
Indices: 528831--529212 Score: 473
Period size: 189 Copynumber: 2.0 Consensus size: 189
528821 AGAAACTATC
528831 TCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
* * **
528896 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTGTTTCAAGG
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTTCAAAA
* * * * **** *
528961 GAAACTACCCCAAGCGAGATAAAATTTATTTCAGGGGAAATTTTTTCAATGTTTATGTT
131 GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAACAGATTCAATATTTATGTT
* * ** * * *
529020 TCAAGGGAGACAAAATTTTGTTTCAAGGGAAACTATCTTAATCGAGATAAAATTCATTTCAAGGG
1 TCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
*
529085 GAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAG-TTCGAAA
66 AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTTC-AAA
** * * * *
529149 AGAAAATGTCTCAAGGGAGACGAAA-TTAGTTTCAATGAAAACAGATTCAAATATTT-TGTT
130 AGAAAATACCCCAAGCGAGACAAAATTTA-TTTCAAGGAAAACAGATTC-AATATTTATGTT
529209 TCAA
1 TCAA
529213 TCGTCGTGAA
Statistics
Matches: 163, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
188 6 0.04
189 151 0.93
190 6 0.04
ACGTcount: A:0.38, C:0.12, G:0.19, T:0.31
Consensus pattern (189 bp):
TCAAGGGAGACAAAATTTTGTTTCAAGGAAAACTATCTCAAGAGAGACAAAATTAATTTCAAAGG
AAATGTTTTCAATGTTTATGTTTCAAGAGAAACTATCTCAAGGGAGACAAAATTTAGTTTCAAAA
GAAAATACCCCAAGCGAGACAAAATTTATTTCAAGGAAAACAGATTCAATATTTATGTT
Found at i:529796 original size:32 final size:32
Alignment explanation
Indices: 529743--529854 Score: 129
Period size: 32 Copynumber: 3.5 Consensus size: 32
529733 TTGCATCAAT
* * * *
529743 ATGTTGAAT-TCCCAAACATGCCCCAATATTCG
1 ATGTTGAATCT-CAAAAAATGCCCCAACATTTG
529775 ATGTTGAATCTCAAAAAATGCCCCAACATTTG
1 ATGTTGAATCTCAAAAAATGCCCCAACATTTG
* *
529807 ATGTTAAATCT-AAAAGAATGCTCCAACATTTG
1 ATGTTGAATCTCAAAA-AATGCCCCAACATTTG
529839 ATGTTGAATCTTCAAA
1 ATGTTGAATC-TCAAA
529855 GATGCCCTCA
Statistics
Matches: 69, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
31 4 0.06
32 60 0.87
33 2 0.03
34 3 0.04
ACGTcount: A:0.37, C:0.21, G:0.12, T:0.30
Consensus pattern (32 bp):
ATGTTGAATCTCAAAAAATGCCCCAACATTTG
Found at i:531036 original size:47 final size:47
Alignment explanation
Indices: 530976--531132 Score: 250
Period size: 47 Copynumber: 3.4 Consensus size: 47
530966 CATTTATCTG
530976 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTCC
*
531023 ATAAGCTCATAAGCTTATTTTACCAAAATACTTACCATTTAAATTCC
1 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTCC
* * *
531070 ATAAGCTCGTAAGCTTATTTTATCAATATACTTGCCA-TT--ATT-C
1 ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTCC
531113 ATAAGCTCGTAAGCTTATTT
1 ATAAGCTCGTAAGCTTATTT
531133 GCATACTTAC
Statistics
Matches: 105, Mismatches: 5, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
43 21 0.20
44 3 0.03
46 2 0.02
47 79 0.75
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (47 bp):
ATAAGCTCGTAAGCTTATTTTACCAAAATACTTACCATTTAAATTCC
Found at i:531140 original size:38 final size:41
Alignment explanation
Indices: 530961--531146 Score: 153
Period size: 47 Copynumber: 4.2 Consensus size: 41
530951 TTTAAATTCT
* *
530961 CTTACCATTTATCTGATAAGCTCGTAAGCTTATTTTACCAAAATA
1 CTTACCA-TTAT-TCATAAGCTCGTAAGCTTATTTTAGC--AATA
* *
531006 CTTACCATTTAAATTCCATAAGCTCATAAGCTTATTTTACCAAAATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC--AATA
*
531053 CTTACCATTTAAATTCCATAAGCTCGTAAGCTTATTTTATCAATATA
1 CTTACCA-TT--ATT-CATAAGCTCGTAAGCTTATTTTAGC-A-ATA
*
531100 CTTGCCATTATTCATAAGCTCGTAAGCTTA-TTT-GC-ATA
1 CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
531138 CTTACCATT
1 CTTACCATT
531147 TATTAACCAT
Statistics
Matches: 130, Mismatches: 7, Indels: 15
0.86 0.05 0.10
Matches are distributed among these distances:
38 11 0.08
41 1 0.01
42 3 0.02
43 18 0.14
44 3 0.02
45 10 0.08
46 5 0.04
47 79 0.61
ACGTcount: A:0.33, C:0.21, G:0.08, T:0.39
Consensus pattern (41 bp):
CTTACCATTATTCATAAGCTCGTAAGCTTATTTTAGCAATA
Found at i:533516 original size:25 final size:25
Alignment explanation
Indices: 533476--533538 Score: 92
Period size: 25 Copynumber: 2.6 Consensus size: 25
533466 AGCTCGGATT
*
533476 GTGCGA-TGCCTTATCAAGGAATTC
1 GTGCGATTGCCTCATCAAGGAATTC
*
533500 GTGCGATTGCCTCATCAAGGAATTT
1 GTGCGATTGCCTCATCAAGGAATTC
*
533525 GTGCGATCGCCTCA
1 GTGCGATTGCCTCA
533539 GCTACCCAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
24 6 0.17
25 29 0.83
ACGTcount: A:0.22, C:0.24, G:0.25, T:0.29
Consensus pattern (25 bp):
GTGCGATTGCCTCATCAAGGAATTC
Found at i:535358 original size:8 final size:7
Alignment explanation
Indices: 535327--535360 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
535317 TGAAATGTAG
*
535327 ATGCAAG
1 ATGCAAA
535334 ATGCAAA
1 ATGCAAA
535341 ATGCAAA
1 ATGCAAA
535348 ATGCAAAA
1 ATGC-AAA
535356 ATGCA
1 ATGCA
535361 TGAAATGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
7 18 0.72
8 7 0.28
ACGTcount: A:0.53, C:0.15, G:0.18, T:0.15
Consensus pattern (7 bp):
ATGCAAA
Found at i:537282 original size:9 final size:9
Alignment explanation
Indices: 537268--537336 Score: 52
Period size: 9 Copynumber: 7.6 Consensus size: 9
537258 AAGAAAATAT
537268 ATAAATAAA
1 ATAAATAAA
537277 ATAAATAAA
1 ATAAATAAA
*
537286 ATAATTAAA
1 ATAAATAAA
*
537295 A-AAGTAAAA
1 ATAAAT-AAA
*
537304 ATAATATATAT
1 ATAA-ATA-AA
* *
537315 ATATATATA
1 ATAAATAAA
537324 ATAAAT-AA
1 ATAAATAAA
537332 ATAAA
1 ATAAA
537337 ATAGTAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 9
0.72 0.14 0.14
Matches are distributed among these distances:
8 9 0.19
9 27 0.57
10 6 0.13
11 5 0.11
ACGTcount: A:0.70, C:0.00, G:0.01, T:0.29
Consensus pattern (9 bp):
ATAAATAAA
Found at i:537296 original size:43 final size:47
Alignment explanation
Indices: 537227--537336 Score: 115
Period size: 47 Copynumber: 2.4 Consensus size: 47
537217 ATAGTAAGTA
*
537227 AAATAAATATAAA-AAAATAAAG-AAAAAG-AAGAAGAA-A-ATATAT
1 AAATAAA-ATAAATAAAATAAAGAAAAAAGTAAAAAGAATATATATAT
** *
537270 AAATAAAATAAATAAAATAATTAAAAAAGTAAAAATAATATATATAT
1 AAATAAAATAAATAAAATAAAGAAAAAAGTAAAAAGAATATATATAT
* *
537317 ATATATAATAAAT-AAATAAA
1 AAATAAAATAAATAAAATAAA
537337 ATAGTAAATA
Statistics
Matches: 55, Mismatches: 7, Indels: 7
0.80 0.10 0.10
Matches are distributed among these distances:
42 5 0.09
43 14 0.25
44 6 0.11
45 6 0.11
46 7 0.13
47 17 0.31
ACGTcount: A:0.72, C:0.00, G:0.05, T:0.24
Consensus pattern (47 bp):
AAATAAAATAAATAAAATAAAGAAAAAAGTAAAAAGAATATATATAT
Found at i:537339 original size:33 final size:32
Alignment explanation
Indices: 537301--537369 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 32
537291 TAAAAAAGTA
*
537301 AAAATAATATATATATATATATAATAAATAAAT
1 AAAATAATAAATATATATATAT-ATAAATAAAT
* *
537334 AAAATAGTAAATATATATATATATAAATTAAT
1 AAAATAATAAATATATATATATATAAATAAAT
537366 AAAA
1 AAAA
537370 CTGATAATAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 13 0.39
33 20 0.61
ACGTcount: A:0.64, C:0.00, G:0.01, T:0.35
Consensus pattern (32 bp):
AAAATAATAAATATATATATATATAAATAAAT
Found at i:539395 original size:21 final size:18
Alignment explanation
Indices: 539346--539397 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 18
539336 AAACATTAAT
539346 TATAAAAGTTAGTATAAA
1 TATAAAAGTTAGTATAAA
*
539364 TA-AAAAATTAGTATAAGAAA
1 TATAAAAGTTAGTAT---AAA
539384 TATAAAAGTTAGTA
1 TATAAAAGTTAGTA
539398 ATTTACCACA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
17 11 0.39
18 2 0.07
20 5 0.18
21 10 0.36
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (18 bp):
TATAAAAGTTAGTATAAA
Found at i:541277 original size:54 final size:54
Alignment explanation
Indices: 541187--541289 Score: 125
Period size: 54 Copynumber: 1.9 Consensus size: 54
541177 TGAAATGTAA
* * *
541187 ATTCAAAAACTCATTATGAATTCCATAGATCGCACATATAGTACCGAAATGGTC
1 ATTCAAAAACACATTATGAATACCATAGATCACACATATAGTACCGAAATGGTC
* * * * * *
541241 ATTCATAAACACATTATGAATACCATGGGTTACACATTTAGTGCCGAAA
1 ATTCAAAAACACATTATGAATACCATAGATCACACATATAGTACCGAAA
541290 ATGCACCGTT
Statistics
Matches: 40, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 40 1.00
ACGTcount: A:0.39, C:0.19, G:0.14, T:0.28
Consensus pattern (54 bp):
ATTCAAAAACACATTATGAATACCATAGATCACACATATAGTACCGAAATGGTC
Found at i:545824 original size:5 final size:5
Alignment explanation
Indices: 545816--546306 Score: 815
Period size: 5 Copynumber: 98.4 Consensus size: 5
545806 ATATAGATAC
545816 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
545866 ATATT ATA-T ATTATAT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT A-TAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT
545917 ATA-T -TATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
545965 ATATT ATATT ATA-T -TATT ATATT ATATT ATATT ATATT ATATAT ATTATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATAT-T A-TATT
546015 ATATT ATATT ATATT AT-TT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
546064 ATATT -TATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
546113 ATATT ATATT ATATTAT ATATT ATATT ATATT ATATT ATATT ATA-T -TATT
1 ATATT ATATT ATA-T-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT
546163 ATATT ATA-T ATATT ATATT ATATT ATATAT ATATTT ATATT ATATT ATATT
1 ATATT ATATT ATATT ATATT ATATT ATAT-T ATA-TT ATATT ATATT ATATT
546214 ATTATAT ATATT ATATT ATATT ATATT ATA-T ATATT ATATT ATATT ATATT
1 A-TAT-T ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT
546265 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT ATATT AT
546307 TGTTCATTGT
Statistics
Matches: 465, Mismatches: 0, Indels: 42
0.92 0.00 0.08
Matches are distributed among these distances:
3 6 0.01
4 24 0.05
5 400 0.86
6 23 0.05
7 12 0.03
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
ATATT
Found at i:547933 original size:15 final size:15
Alignment explanation
Indices: 547906--548140 Score: 325
Period size: 15 Copynumber: 15.5 Consensus size: 15
547896 ATTTAAGGTT
547906 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
547920 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
547935 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
547950 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
*
547964 ATTTATTAT-AAATA
1 ATTTATTTTAAAATA
547978 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
547993 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
548008 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
548023 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
548038 ATTTATTTTAAAATA
1 ATTTATTTTAAAATA
*
548053 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
*
548068 ATTTATTATAAAATA
1 ATTTATTTTAAAATA
548083 ATTTATTTTAAAATATGGA
1 ATTTATTTT-AAA-AT--A
548102 TTGATTTATTTTAAAATA
1 ---ATTTATTTTAAAATA
548120 ATTTATTTT-AAATA
1 ATTTATTTTAAAATA
548134 ATTTATT
1 ATTTATT
548141 AGTATGGATT
Statistics
Matches: 202, Mismatches: 10, Indels: 18
0.88 0.04 0.08
Matches are distributed among these distances:
14 47 0.23
15 134 0.66
16 3 0.01
17 2 0.01
18 1 0.00
19 1 0.00
20 2 0.01
21 3 0.01
22 9 0.04
ACGTcount: A:0.47, C:0.00, G:0.01, T:0.52
Consensus pattern (15 bp):
ATTTATTTTAAAATA
Found at i:548108 original size:22 final size:22
Alignment explanation
Indices: 548083--548185 Score: 98
Period size: 22 Copynumber: 4.5 Consensus size: 22
548073 TTATAAAATA
548083 ATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAAATATGGATTG
** *
548105 ATTTATTTTAAAATAATTTATTTT
1 ATTTATTTTAAAAT-ATGGA-TTG
** * * *
548129 AAATAATTTATTAGTATGGATTG
1 ATTTATTTTA-AAATATGGATTG
*
548152 ATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAAATATGGATTG
548174 ATTTATTTTAAA
1 ATTTATTTTAAA
548186 TAATTTATTA
Statistics
Matches: 61, Mismatches: 17, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
22 35 0.57
23 12 0.20
24 12 0.20
25 2 0.03
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.53
Consensus pattern (22 bp):
ATTTATTTTAAAATATGGATTG
Found at i:548178 original size:69 final size:67
Alignment explanation
Indices: 548038--548195 Score: 230
Period size: 69 Copynumber: 2.3 Consensus size: 67
548028 TTATAAAATA
548038 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGAT
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGAT
548103 TG
66 TG
* * * *
548105 ATTTATTTTAAAATAATTTATT-TTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATG
1 ATTTATTTTAAAATAATTTATTATAAAATAATTTATTA-TA--AAATAATTTATTTTAAAATATG
*
548169 GATTT
63 GATTG
548174 ATTTATTTT-AAATAATTTATTA
1 ATTTATTTTAAAATAATTTATTA
548196 GTATGGATTG
Statistics
Matches: 82, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
66 14 0.17
67 24 0.29
68 12 0.15
69 32 0.39
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.53
Consensus pattern (67 bp):
ATTTATTTTAAAATAATTTATTATAAAATAATTTATTATAAAATAATTTATTTTAAAATATGGAT
TG
Found at i:548185 original size:54 final size:54
Alignment explanation
Indices: 548120--549088 Score: 868
Period size: 54 Copynumber: 18.1 Consensus size: 54
548110 TTTTAAAATA
*
548120 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
548174 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
** *
548228 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATAAATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
548282 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
548336 ATTTA--GT--AT--TGTAGTT-GTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * ***
548380 ATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
548442 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
548496 ATTTATTTTAAATATTTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
548550 ATTTA--TT--AT--TGTAGTT-GTATGGATTGATATATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTA-TTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * *
548598 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTAAATAATTTATTTGTATGG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAA-AA--TA--TGGATTG
* * * ***
548657 ATTGA-TTT--AT--TTTA-AAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
*
548709 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * **
548763 ATTTA--TT--AT--TGTA-GATGTATGGATTGATTTATTTT-AAATAATTTATTAG
1 ATTTATTTTAAATAATTTATTA-GTATGGATTGATTTATTTTAAAAT-ATGGATT-G
* ** ** * * *
548812 TATGTA-TCGATTTATTTTA-AAATATGGATTGATTTATTTTAAAATATGGATTG
1 -ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
548865 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
*
548919 ATTTATTTTAAATAA--T-TTAGTATGGATTGATTTATTTT-AAATA---ATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* * ** * * * ***
548966 ATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTG
1 ATTTATTTTAAATAATTTA--TT--AGTATGGATTGATTTA-T-TT-TA-AAATATGGATTG
* *
549028 ATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
549082 ATTTATT
1 ATTTATT
549089 ATTGTAGTTG
Statistics
Matches: 744, Mismatches: 102, Indels: 138
0.76 0.10 0.14
Matches are distributed among these distances:
44 7 0.01
47 22 0.03
48 89 0.12
49 5 0.01
50 20 0.03
51 24 0.03
52 23 0.03
53 30 0.04
54 382 0.51
55 22 0.03
56 13 0.02
57 11 0.01
58 47 0.06
59 13 0.02
60 4 0.01
62 32 0.04
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (54 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
Found at i:548222 original size:22 final size:22
Alignment explanation
Indices: 548197--548239 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
548187 AATTTATTAG
548197 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548219 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548240 TAATTTATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548299 original size:14 final size:15
Alignment explanation
Indices: 548275--548303 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
548265 TTTTAAAATA
548275 TAAATTAATTTATTT
1 TAAATTAATTTATTT
548290 TAAA-TAATTTATTT
1 TAAATTAATTTATTT
548304 GTATGGATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TAAATTAATTTATTT
Found at i:548330 original size:22 final size:22
Alignment explanation
Indices: 548305--548373 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
548295 AATTTATTTG
548305 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
548327 TATGGATTGATTTAGTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
548353 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548374 TAATTTATTT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 14 0.37
23 3 0.08
24 4 0.11
25 3 0.08
26 14 0.37
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548382 original size:80 final size:80
Alignment explanation
Indices: 548120--548637 Score: 437
Period size: 80 Copynumber: 6.5 Consensus size: 80
548110 TTTTAAAATA
*
548120 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTTATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--
*
548185 ATAATTTA-TTAGTATGGATTG
62 AT--TGTAGTT-GTATGGATTG
** ** * ** * * *
548206 ATTTATTTTAAA-ATATGGATT-G-ATTTATTTTAAATAATTTATTAGTATGGATTGATTTA-T-
1 ATTTATTTTAAATA-ATTTATTAGTATGGA-TTGATTTATTTTA-AAATATGGATTGATTTATTA
*** ** *
548266 TT-TA-AAATATAAATTA
63 TTGTAGTTGTATGGATTG
* *
548282 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTAGTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
548347 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
*
548362 ATTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
548427 TAGTTGTATGGATTG
66 TAGTTGTATGGATTG
548442 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAA
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTA---T--
*
548507 ATATTTTA-TTAGTATGGATTG
61 -TATTGTAGTT-GTATGGATTG
* * * * ***
548528 ATTTATTTT-AA-AA--TA-T-GGATTGATTTA-TTATTGTAGTTGTATGGATTGA--TA-TATT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTA-AAATATGGATTGATTTATTATT
* ***
548583 TTA-AAATATGGATTG
65 GTAGTTGTATGGATTG
548598 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
1 ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTT
548638 AAATAATTTA
Statistics
Matches: 357, Mismatches: 50, Indels: 59
0.77 0.11 0.13
Matches are distributed among these distances:
70 18 0.05
71 9 0.03
72 2 0.01
74 2 0.01
75 1 0.00
76 46 0.13
77 19 0.05
78 8 0.02
79 9 0.03
80 162 0.45
81 1 0.00
82 2 0.01
83 2 0.01
84 5 0.01
85 15 0.04
86 56 0.16
ACGTcount: A:0.33, C:0.00, G:0.14, T:0.53
Consensus pattern (80 bp):
ATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTG
TAGTTGTATGGATTG
Found at i:548397 original size:18 final size:18
Alignment explanation
Indices: 548350--548401 Score: 58
Period size: 18 Copynumber: 3.1 Consensus size: 18
548340 AGTATTGTAG
548350 TTGTATGGATTGATTTAT
1 TTGTATGGATTGATTTAT
* *
548368 TT-TA---AATAATTTAT
1 TTGTATGGATTGATTTAT
548382 TTGTATGGATTGATTTAT
1 TTGTATGGATTGATTTAT
548400 TT
1 TT
548402 TAAAATATGG
Statistics
Matches: 26, Mismatches: 4, Indels: 8
0.68 0.11 0.21
Matches are distributed among these distances:
14 10 0.38
15 2 0.08
17 2 0.08
18 12 0.46
ACGTcount: A:0.27, C:0.00, G:0.15, T:0.58
Consensus pattern (18 bp):
TTGTATGGATTGATTTAT
Found at i:548410 original size:22 final size:22
Alignment explanation
Indices: 548385--548609 Score: 81
Period size: 26 Copynumber: 9.0 Consensus size: 22
548375 AATTTATTTG
548385 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
***
548407 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
548433 TATGGATTGATTTATTTTAAATAA
1 TATGGATTGATTTATTTT-AA-AA
* * *
548457 TTTATTAGTATGGATTGATTTATTTTAAAA
1 --TA-T-GGATTGATTTA-TT---TTAAAA
548487 TATGGATTGATTTATTTTAAATA
1 TATGGATTGATTTATTTTAAA-A
* * *
548510 TTTTATTAGTATGGATTGATTTATTTTAAAA
1 ---TA-T-GGATTGATTTA-TT---TTAAAA
***
548541 TATGGATTGATTTATTATTGTAGTTG
1 TATGGATTGATTTA-T-TT-TA-AAA
*
548567 TATGGATTGATATATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548589 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548610 TAATTTATTA
Statistics
Matches: 150, Mismatches: 26, Indels: 54
0.65 0.11 0.23
Matches are distributed among these distances:
22 39 0.26
23 5 0.03
24 8 0.05
25 8 0.05
26 49 0.33
27 5 0.03
28 20 0.13
29 4 0.03
30 2 0.01
31 3 0.02
32 7 0.05
ACGTcount: A:0.32, C:0.00, G:0.16, T:0.52
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548659 original size:27 final size:29
Alignment explanation
Indices: 548596--548668 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 29
548586 AAATATGGAT
548596 TGATTTATTTTAAATAATTTATTAGTATGG
1 TGATTTA-TTTAAATAATTTATTAGTATGG
*
548626 ATTGATTTATTTAAATAATTTATTTGTATGG
1 --TGATTTATTTAAATAATTTATTAGTATGG
548657 ATTGATTTATTT
1 --TGATTTATTT
548669 TAAAATATGG
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
31 33 0.82
32 7 0.17
ACGTcount: A:0.32, C:0.00, G:0.12, T:0.56
Consensus pattern (29 bp):
TGATTTATTTAAATAATTTATTAGTATGG
Found at i:548678 original size:347 final size:327
Alignment explanation
Indices: 548566--549184 Score: 1049
Period size: 319 Copynumber: 1.9 Consensus size: 327
548556 TATTGTAGTT
548566 GTATGGATTGATATATTTTAAAATATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGA
1 GTATGGATTGATATATTTTAAAATATGGATTGATTTATTTTAAATAA--T-TTAGTATGGATTGA
548631 TTTA-TTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
63 TTTATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGT
548695 AGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGA
128 AGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGA
* * * *
548760 TTAATTTATTATTGTAGATGTATGGATTGATTTATTTTAAATAATTTATTAGTATGTATCGATTT
193 TTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTT
548825 ATTTTAAAATATGGATTGATTTATTTT--A-A---A--ATATGGATTGATTTATTTTAAATAATT
258 ATTTTAAAATATGGATTGATTTATTTTAAATATTTATTATATGGATTGATTTATTTTAAATAATT
548882 TATTA
323 TATTA
*
548887 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTATGGATTGATTT
1 GTATGGATTGATATATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTATGGATTGATTT
548952 ATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGT
66 ATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGT
* *
549017 TGTATGGATTGATTTATTTTAAATAATTTATTAGTATGTATTGATTTATTTTAAAATATAGATTG
131 TGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
* *
549082 ATTTATTATTGTAGTTGTATGAATTGATTTATTTTAAATAATTTATTAGAATGGATTGATTTATT
196 ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
*
549147 TTAAAATATAGATTGATTTATTTTAAATAATTTATTAT
261 TTAAAATATGGATTGATTTATTTTAAAT-ATTTATTAT
549185 TGTAGTTGTA
Statistics
Matches: 278, Mismatches: 10, Indels: 13
0.92 0.03 0.04
Matches are distributed among these distances:
318 18 0.06
319 209 0.75
321 47 0.17
323 1 0.00
326 1 0.00
328 2 0.01
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (327 bp):
GTATGGATTGATATATTTTAAAATATGGATTGATTTATTTTAAATAATTTAGTATGGATTGATTT
ATTTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGT
TGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTG
ATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATT
TTAAAATATGGATTGATTTATTTTAAATATTTATTATATGGATTGATTTATTTTAAATAATTTAT
TA
Found at i:548747 original size:80 final size:80
Alignment explanation
Indices: 548566--549168 Score: 896
Period size: 80 Copynumber: 7.5 Consensus size: 80
548556 TATTGTAGTT
* *
548566 GTATGGATTGATATATTTTAAAATATGGATTGATTTATTTTAAATAATTTA-TTAGTATGGATTG
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTA--TT--AT--TGTAGTT-GTATGGATTG
*
548630 ATTTA-TTTAAATAATTTATTT
59 ATTTATTTTAAATAATTTATTA
548651 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
548716 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* *
548731 GTATGGATTGATTTATTTTAAAATATGGATTAATTTATTATTGTAGATGTATGGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
548796 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* * ***
548811 GTATGTATCGATTTATTTTAAAATATGGATTGATTTA-T-TT-TA-AAATATGGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
548872 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* *
548887 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATT-TTAAATAATTTAGTATGGATTGATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATT--GT-AGTT-GTATGGATTGATT
*
548951 TATTTTAAATAATTTATTT
62 TATTTTAAATAATTTATTA
548970 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
549035 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* * *
549050 GTATGTATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTGTATGAATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
549115 TTAAATAATTTATTA
66 TTAAATAATTTATTA
* *
549130 GAATGGATTGATTTATTTTAAAATATAGATTGATTTATT
1 GTATGGATTGATTTATTTTAAAATATGGATTGATTTATT
549169 TTAAATAATT
Statistics
Matches: 484, Mismatches: 24, Indels: 25
0.91 0.05 0.05
Matches are distributed among these distances:
76 67 0.14
77 5 0.01
78 2 0.00
79 19 0.04
80 275 0.57
81 6 0.01
82 1 0.00
83 71 0.15
84 2 0.00
85 36 0.07
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (80 bp):
GTATGGATTGATTTATTTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATT
TTAAATAATTTATTA
Found at i:548757 original size:22 final size:22
Alignment explanation
Indices: 548732--548800 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
548722 AATTTATTAG
548732 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
* **
548754 TATGGATTAATTTATTATTGTAGATG
1 TATGGATTGATTTA-T-TT-TA-AAA
548780 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548801 TAATTTATTA
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 14 0.37
23 3 0.08
24 4 0.11
25 3 0.08
26 14 0.37
ACGTcount: A:0.33, C:0.00, G:0.16, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548837 original size:22 final size:22
Alignment explanation
Indices: 548820--548876 Score: 114
Period size: 22 Copynumber: 2.6 Consensus size: 22
548810 AGTATGTATC
548820 GATTTATTTTAAAATATGGATT
1 GATTTATTTTAAAATATGGATT
548842 GATTTATTTTAAAATATGGATT
1 GATTTATTTTAAAATATGGATT
548864 GATTTATTTTAAA
1 GATTTATTTTAAA
548877 TAATTTATTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (22 bp):
GATTTATTTTAAAATATGGATT
Found at i:548894 original size:32 final size:30
Alignment explanation
Indices: 548856--548991 Score: 164
Period size: 32 Copynumber: 4.7 Consensus size: 30
548846 TATTTTAAAA
548856 TATGGATTGATTTATTTTAAATAATTTATTAG
1 TATGGATTGATTTATTTTAAATAA--TATTAG
548888 TATGGATTGATTTA-TTT---TAA-A--A-
1 TATGGATTGATTTATTTTAAATAATATTAG
548910 TATGGATTGATTTATTTTAAATAAT-TTAG
1 TATGGATTGATTTATTTTAAATAATATTAG
*
548939 TATGGATTGATTTATTTTAAATAATTTATTTG
1 TATGGATTGATTTATTTTAAATAA--TATTAG
548971 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548992 ATATGGATTG
Statistics
Matches: 92, Mismatches: 1, Indels: 22
0.80 0.01 0.19
Matches are distributed among these distances:
22 14 0.15
23 4 0.04
25 1 0.01
26 3 0.03
28 4 0.04
29 24 0.26
31 4 0.04
32 38 0.41
ACGTcount: A:0.34, C:0.00, G:0.13, T:0.53
Consensus pattern (30 bp):
TATGGATTGATTTATTTTAAATAATATTAG
Found at i:548913 original size:22 final size:22
Alignment explanation
Indices: 548888--548930 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
548878 AATTTATTAG
548888 TATGGATTGATTTATTTTAAAA
1 TATGGATTGATTTATTTTAAAA
548910 TATGGATTGATTTATTTTAAA
1 TATGGATTGATTTATTTTAAA
548931 TAATTTAGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.35, C:0.00, G:0.14, T:0.51
Consensus pattern (22 bp):
TATGGATTGATTTATTTTAAAA
Found at i:548983 original size:18 final size:18
Alignment explanation
Indices: 548933--548987 Score: 55
Period size: 14 Copynumber: 3.2 Consensus size: 18
548923 ATTTTAAATA
548933 ATTTAGTATGGATTGATTT
1 ATTT-GTATGGATTGATTT
* *
548952 ATTT-TA---AATAATTT
1 ATTTGTATGGATTGATTT
548966 ATTTGTATGGATTGATTT
1 ATTTGTATGGATTGATTT
548984 ATTT
1 ATTT
548988 TAAAATATGG
Statistics
Matches: 28, Mismatches: 4, Indels: 9
0.68 0.10 0.22
Matches are distributed among these distances:
14 10 0.36
15 2 0.07
17 2 0.07
18 10 0.36
19 4 0.14
ACGTcount: A:0.29, C:0.00, G:0.15, T:0.56
Consensus pattern (18 bp):
ATTTGTATGGATTGATTT
Found at i:548983 original size:239 final size:243
Alignment explanation
Indices: 548621--549180 Score: 922
Period size: 239 Copynumber: 2.3 Consensus size: 243
548611 AATTTATTAG
*
548621 TATGGATTGATTTA-TTTAAATAATTTATTTGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
* *
548685 TTATTATT--GT-AGTT-GTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA
66 TTATT-TTAAATAATTTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTA
548746 TTTTAAAATATGGATTAATTTATTATTGTAGATGTATGGATTGATTTATTTTAAATAATTTATTA
130 TTTTAAAATATGGATTAATTTATTATTGTAGATGTATGGATTGATTTATTTTAAATAATTTATTA
*
548811 GTATGTATCGATTTATTTTAAAATATGGATTGATTTA-T-TT-TA-AAA
195 GTATGTATCGATTTATTTTAAAATATAGATTGATTTATTATTGTAGAAA
548856 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
*
548921 TTATTTTAAATAATTTAGTATGGATTGATTTATTTTAAATAATTTATTTGTATGGATTGATTTAT
66 TTATTTTAAATAATTTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
* *
548986 TTTAAAATATGGATTGATTTATTATTGTAGTTGTATGGATTGATTTATTTTAAATAATTTATTAG
131 TTTAAAATATGGATTAATTTATTATTGTAGATGTATGGATTGATTTATTTTAAATAATTTATTAG
* ***
549051 TATGTATTGATTTATTTTAAAATATAGATTGATTTATTATTGTAGTTG
196 TATGTATCGATTTATTTTAAAATATAGATTGATTTATTATTGTAGAAA
* * *
549099 TATGAATTGATTTATTTTAAATAATTTATTAGAATGGATTGATTTATTTTAAAATATAGATTGAT
1 TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
549164 TTATTTTAAATAATTTA
66 TTATTTTAAATAATTTA
549181 TTATTGTAGT
Statistics
Matches: 302, Mismatches: 14, Indels: 10
0.93 0.04 0.03
Matches are distributed among these distances:
235 16 0.05
236 54 0.18
237 1 0.00
238 3 0.01
239 144 0.48
240 1 0.00
241 2 0.01
242 2 0.01
243 79 0.26
ACGTcount: A:0.34, C:0.00, G:0.14, T:0.52
Consensus pattern (243 bp):
TATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTATTTTAAAATATGGATTGAT
TTATTTTAAATAATTTAGTATGGATTGATTTATTTTAAATAATTTATTAGTATGGATTGATTTAT
TTTAAAATATGGATTAATTTATTATTGTAGATGTATGGATTGATTTATTTTAAATAATTTATTAG
TATGTATCGATTTATTTTAAAATATAGATTGATTTATTATTGTAGAAA
Found at i:549233 original size:30 final size:30
Alignment explanation
Indices: 549197--549253 Score: 96
Period size: 30 Copynumber: 1.9 Consensus size: 30
549187 TAGTTGTATG
* *
549197 AATTATTTAAATTTCAGTATTGTAAAATAA
1 AATTATTTAAATCTCAGTATTGCAAAATAA
549227 AATTATTTAAATCTCAGTATTGCAAAA
1 AATTATTTAAATCTCAGTATTGCAAAA
549254 CTCTTTTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (30 bp):
AATTATTTAAATCTCAGTATTGCAAAATAA
Found at i:558127 original size:262 final size:260
Alignment explanation
Indices: 557620--558231 Score: 800
Period size: 262 Copynumber: 2.3 Consensus size: 260
557610 ATGAATATAT
*** * * *
557620 ATAATAGATACGGTTGTTTCCAATAATATCATGGTTATACAAGAAATAAGTTGTGATTTGTAATG
1 ATAATAGATACGGTTGCACCCAATAATATCATGGTT-TAAAAGAAATAAGTAG-CATTTGTAATG
* *
557685 TTAATATTTTTATTAATAAAATAGATTGCGCCCAAAATGTCATGGCTCCCTAAGAAAGCATGTTG
64 TTAATATTTTTATTAATAAAATAGATTGCGCCCAAAATGTCATGACTCCCTAAGAAAGCATATTG
* * ** * *
557750 CAATCTAGAATGTTACTATTTTTAATAATAAAGTTGGTTGCGCCTAAATATTATGAAAGTTTCAT
129 CAATCTAGAATCTTACTATTTTTAATAATAAAATTAATTGCGCCTAAATATTATCAAAGTTTAAT
* *
557815 CCGATGGAGTCTTGAAGTTTCCCACGATAATAAAATAAGTTAAAAGCTTAAAATTTTATGAACAT
194 CCGATGGAGCCTTGAAGTTTCCCACGATAATAAAATAAGTTAAAAGCTTAAAATTTTATGAACAC
*
557880 GT
259 GC
* * * *
557882 ATAATATATATGGTTGCACCCAATAATAACATGGTTCTAAAAGAAATATGTAGCATTTGTAATGT
1 ATAATAGATACGGTTGCACCCAATAATATCATGGTT-TAAAAGAAATAAGTAGCATTTGTAATGT
* *
557947 TAATATTTTTATTAATAAAATAGATTGCGCCCAGAATTTCATGACTCCCTAAGAAAGCATATTGC
65 TAATATTTTTATTAATAAAATAGATTGCGCCCAAAATGTCATGACTCCCTAAGAAAGCATATTGC
*
558012 AATCT-GAAATCTTACTATTTTTTAATAATAAAATTAATTGTGCCTAAAATATTATCAAAGTTTA
130 AATCTAG-AATCTTACTA-TTTTTAATAATAAAATTAATTGCGCCT-AAATATTATCAAAGTTTA
* * * *
558076 AGT-CGAT-GAGCCTTGGAGTTTGCTACGATAATAAAATAAGTTAAAAGCTTAAACTTTTATGAA
192 A-TCCGATGGAGCCTTGAAGTTTCCCACGATAATAAAATAAGTTAAAAGCTTAAAATTTTATGAA
*
558139 TACGC
256 CACGC
** * *
558144 ATAATAGATACGGTTGCATTCAATTATATCATGGTTTAATAAAAAATAAGTTA-CGATTTGTAAT
1 ATAATAGATACGGTTGCACCCAATAATATCATGGTTTAA-AAGAAATAAG-TAGC-ATTTGTAAT
*
558208 GTCAATATTTTTATTAATAAAATA
63 GTTAATATTTTTATTAATAAAATA
558232 AACTGTGCCT
Statistics
Matches: 304, Mismatches: 39, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
260 1 0.00
261 89 0.29
262 158 0.52
263 55 0.18
264 1 0.00
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (260 bp):
ATAATAGATACGGTTGCACCCAATAATATCATGGTTTAAAAGAAATAAGTAGCATTTGTAATGTT
AATATTTTTATTAATAAAATAGATTGCGCCCAAAATGTCATGACTCCCTAAGAAAGCATATTGCA
ATCTAGAATCTTACTATTTTTAATAATAAAATTAATTGCGCCTAAATATTATCAAAGTTTAATCC
GATGGAGCCTTGAAGTTTCCCACGATAATAAAATAAGTTAAAAGCTTAAAATTTTATGAACACGC
Found at i:563159 original size:15 final size:14
Alignment explanation
Indices: 563135--563171 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
563125 GAGGTAAGGG
563135 AAAGAAAAGAGAGAA
1 AAAGAAAAGAGA-AA
*
563150 AAATAAAAGAGAAA
1 AAAGAAAAGAGAAA
563164 AAAGAAAA
1 AAAGAAAA
563172 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 9 0.45
15 11 0.55
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (14 bp):
AAAGAAAAGAGAAA
Found at i:563169 original size:20 final size:19
Alignment explanation
Indices: 563135--563192 Score: 80
Period size: 20 Copynumber: 2.9 Consensus size: 19
563125 GAGGTAAGGG
*
563135 AAAGAAAAGAGAGAAAAATA
1 AAAGAAAA-AAAGAAAAATA
563155 AAAGAGAAAAAAGAAAAATA
1 AAAGA-AAAAAAGAAAAATA
*
563175 AAAGAAAGAAAGAAAAAT
1 AAAGAAAAAAAGAAAAAT
563193 GAATGAAGAA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
19 12 0.34
20 20 0.57
21 3 0.09
ACGTcount: A:0.78, C:0.00, G:0.17, T:0.05
Consensus pattern (19 bp):
AAAGAAAAAAAGAAAAATA
Found at i:564176 original size:47 final size:47
Alignment explanation
Indices: 564119--564214 Score: 117
Period size: 47 Copynumber: 2.0 Consensus size: 47
564109 AGCATTCATT
* *
564119 ATTTTCCTCTCATGAGGAT-ATTCTCAAAATTTTTGT-TT-CTTAAGACC
1 ATTTTCCTCTCATGAGAATAATT-TC-AAA-TTGTGTCTTCCTTAAGACC
*
564166 ATTTTTCTCTCATGAGAATAATTTCAAATTGTGTCTTCCTTAAGACC
1 ATTTTCCTCTCATGAGAATAATTTCAAATTGTGTCTTCCTTAAGACC
564213 AT
1 AT
564215 AAGACTATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
45 5 0.12
46 5 0.12
47 30 0.70
48 3 0.07
ACGTcount: A:0.27, C:0.19, G:0.10, T:0.44
Consensus pattern (47 bp):
ATTTTCCTCTCATGAGAATAATTTCAAATTGTGTCTTCCTTAAGACC
Found at i:564441 original size:18 final size:19
Alignment explanation
Indices: 564403--564446 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
564393 CTTAAGATTG
*
564403 TTTC-TCTTTAAACATAAA
1 TTTCATCTTGAAACATAAA
*
564421 TTTTATCTTGAAACA-AAA
1 TTTCATCTTGAAACATAAA
564439 TTTCATCT
1 TTTCATCT
564447 CACTTTAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 13 0.59
19 9 0.41
ACGTcount: A:0.36, C:0.16, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTCATCTTGAAACATAAA
Found at i:564559 original size:62 final size:64
Alignment explanation
Indices: 564485--564613 Score: 156
Period size: 62 Copynumber: 2.0 Consensus size: 64
564475 TTCCATCTCA
* *
564485 TTCAAGACAGTTTCTCTCGAAAC-AAAATTCCT-TCTCCCTTTAGATA-TTTCCCTTGAAAATTT
1 TTCAAGACAGTTTCTCTCGAAACGAAAATT-CTATCTCCCATGAGATATTTTCCCTTGAAAATTT
* * * * * *
564547 TTCAAGATAGTTTTTCTTGAAACGAATATTTTATCTCCCATGAGATATTTTCCTTTGAAAATTT
1 TTCAAGACAGTTTCTCTCGAAACGAAAATTCTATCTCCCATGAGATATTTTCCCTTGAAAATTT
564611 TTC
1 TTC
564614 GTCTCGCTCG
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
62 21 0.38
63 17 0.30
64 18 0.32
ACGTcount: A:0.29, C:0.19, G:0.09, T:0.43
Consensus pattern (64 bp):
TTCAAGACAGTTTCTCTCGAAACGAAAATTCTATCTCCCATGAGATATTTTCCCTTGAAAATTT
Found at i:564725 original size:72 final size:72
Alignment explanation
Indices: 564555--564759 Score: 277
Period size: 72 Copynumber: 2.8 Consensus size: 72
564545 TTTTCAAGAT
* * * * * *
564555 AGTTTTTCTTGAAACGAATATTTTATCTCCCATGAGATATTTTCCTTTGAAAATTTTTCGTCTCG
1 AGTTTTTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCTTTGAAAATTTTT-GTCCCA
564620 CTCGAGAC
65 CTCGAGAC
** * *
564628 AGTTCCTCTTGAAACAAAAAATTCATCTCCCTTGATATATTTTCCTTTGAAAATTTTTGTCCCAC
1 AGTTTTTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCTTTGAAAATTTTTGTCCCAC
564693 TCGAGAC
66 TCGAGAC
* * *
564700 AGTTTTTCTTGAAATAAAAATTTCATCTCACTTGAGATATTTTCCCTTG-AAATTTTTGTC
1 AGTTTTTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCTTTGAAAATTTTTGTC
564760 TTACTCGAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
71 11 0.10
72 54 0.47
73 50 0.43
ACGTcount: A:0.27, C:0.20, G:0.11, T:0.42
Consensus pattern (72 bp):
AGTTTTTCTTGAAACAAAAATTTCATCTCCCTTGAGATATTTTCCTTTGAAAATTTTTGTCCCAC
TCGAGAC
Found at i:565065 original size:37 final size:34
Alignment explanation
Indices: 564992--565082 Score: 103
Period size: 37 Copynumber: 2.6 Consensus size: 34
564982 CAAACTTTGT
*
564992 GATTGTTTTTCTTAAA-AAAATCATCTCACTCAA
1 GATTGTTTTTCTTAAACAAAATCATCTCAATCAA
**
565025 GATTGTTTTTCTTCAAACAAAATTTCATCTCAATTGA
1 GATTGTTTTTCTT-AAACAAAA--TCATCTCAATCAA
*
565062 GATTGTTGTTCTTAAAACAAA
1 GATTGTTTTTCTT-AAACAAA
565083 TTTTGTCTCG
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
33 13 0.27
34 3 0.06
35 4 0.08
37 29 0.59
ACGTcount: A:0.35, C:0.15, G:0.09, T:0.41
Consensus pattern (34 bp):
GATTGTTTTTCTTAAACAAAATCATCTCAATCAA
Found at i:565264 original size:101 final size:102
Alignment explanation
Indices: 565024--565334 Score: 417
Period size: 102 Copynumber: 3.1 Consensus size: 102
565014 ATCTCACTCA
* *
565024 AGATTGTTTTTCTTCAAACAAAATTTCATCTCAATTGAGATTGTTGTTCTTAAAACAAATTTTGT
1 AGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
*
565089 CTCGGTTGAGATAGTTTCTCATGAAACTCAAACTTTG
66 CTCGCTTGAGATAGTTTCTCATGAAACTCAAACTTTG
* * * * *
565126 AGATTGTTTTGCGTAAAACAAAATTTCATCTCACTTGAGATTATTGTTCTTGAAACAAATTTTCT
1 AGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
* * * *
565191 CTCCCTTGAGACAGTTT-TCATGAAATTCAAACTTTT
66 CTCGCTTGAGATAGTTTCTCATGAAACTCAAACTTTG
* * * * *
565227 AGATCGTTTTTCTTAAAACAAAATTCCATCTCGCTTGAGAATGTTTTTCTTAAAACAAATTTTGT
1 AGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
* * ** *
565292 CTCGCTTGAGATAGTTTCCCTTGAAAAACGAACTTTG
66 CTCGCTTGAGATAGTTTCTCATGAAACTCAAACTTTG
565329 AGATTG
1 AGATTG
565335 CTTAATTCAA
Statistics
Matches: 177, Mismatches: 31, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
101 87 0.49
102 90 0.51
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.40
Consensus pattern (102 bp):
AGATTGTTTTTCTTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
CTCGCTTGAGATAGTTTCTCATGAAACTCAAACTTTG
Found at i:565295 original size:36 final size:37
Alignment explanation
Indices: 565232--565302 Score: 108
Period size: 36 Copynumber: 1.9 Consensus size: 37
565222 CTTTTAGATC
565232 GTTTTTCTTAAAACAAAATTCCATCTCGCTTGAGAAT
1 GTTTTTCTTAAAACAAAATTCCATCTCGCTTGAGAAT
***
565269 GTTTTTCTTAAAAC-AAATTTTGTCTCGCTTGAGA
1 GTTTTTCTTAAAACAAAATTCCATCTCGCTTGAGA
565303 TAGTTTCCCT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
36 17 0.55
37 14 0.45
ACGTcount: A:0.30, C:0.17, G:0.13, T:0.41
Consensus pattern (37 bp):
GTTTTTCTTAAAACAAAATTCCATCTCGCTTGAGAAT
Found at i:565352 original size:101 final size:100
Alignment explanation
Indices: 565024--565369 Score: 383
Period size: 102 Copynumber: 3.4 Consensus size: 100
565014 ATCTCACTCA
* *
565024 AGATTGTTTTTCTTCAAACAAAATTTCATCTCAATTGAGATTGTTGTTCTTAAAACAAATTTTGT
1 AGATTG-TTTTC-TAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
* *
565089 CTCGGTTGAGATAGTTTCTCATGAAACTCAAACTTTG
64 CTCGCTTGAGATAGTTTCTCATGAAAATCAAACTTTG
* * *
565126 AGATTGTTTTGCGTAAAACAAAATTTCATCTCACTTGAGATTATTGTTCTTGAAACAAATTTTCT
1 AGATTGTTTT-C-TAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
* * * *
565191 CTCCCTTGAGACAGTTT-TCATGAAATTCAAACTTTT
64 CTCGCTTGAGATAGTTTCTCATGAAAATCAAACTTTG
* * * * *
565227 AGATCGTTTTTCTTAAAACAAAATTCCATCTCGCTTGAGAATGTTTTTCTTAAAACAAATTTTGT
1 AGATTG-TTTTC-TAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGT
* * * *
565292 CTCGCTTGAGATAGTTTCCCTTGAAAAACGAACTTTG
64 CTCGCTTGAGATAGTTTCTCATGAAAATCAAACTTTG
* *
565329 AGATTGCTTAATTC-AAAAC-AAATTTATATCTCCCTTGAGAT
1 AGATTG-TT--TTCTAAAACAAAATTT-CATCTCACTTGAGAT
565370 AAAGATCATT
Statistics
Matches: 204, Mismatches: 34, Indels: 12
0.82 0.14 0.05
Matches are distributed among these distances:
101 92 0.45
102 109 0.53
104 3 0.01
ACGTcount: A:0.31, C:0.16, G:0.13, T:0.40
Consensus pattern (100 bp):
AGATTGTTTTCTAAAACAAAATTTCATCTCACTTGAGATTGTTGTTCTTAAAACAAATTTTGTCT
CGCTTGAGATAGTTTCTCATGAAAATCAAACTTTG
Found at i:565527 original size:3 final size:3
Alignment explanation
Indices: 565519--565548 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
565509 TTTTAATTCT
565519 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
565549 ATTTTATTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:566850 original size:15 final size:14
Alignment explanation
Indices: 566817--566848 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
566807 CATTTTAATC
566817 ATTTAATTTTCAGT
1 ATTTAATTTTCAGT
*
566831 ATTTAATTTTTAGT
1 ATTTAATTTTCAGT
566845 ATTT
1 ATTT
566849 TATGCACCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.28, C:0.03, G:0.06, T:0.62
Consensus pattern (14 bp):
ATTTAATTTTCAGT
Found at i:574223 original size:3 final size:3
Alignment explanation
Indices: 574204--574291 Score: 158
Period size: 3 Copynumber: 29.3 Consensus size: 3
574194 ATTAGGATAA
* *
574204 TAT TGT TAT TGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
574252 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
574292 TTAAAGCAGT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 81 1.00
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:574692 original size:5 final size:5
Alignment explanation
Indices: 574676--574709 Score: 59
Period size: 5 Copynumber: 6.6 Consensus size: 5
574666 TTTGGCTTAT
574676 TATCC ATATCC TATCC TATCC TATCC TATCC TAT
1 TATCC -TATCC TATCC TATCC TATCC TATCC TAT
574710 TTGTTTCTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 23 0.82
6 5 0.18
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (5 bp):
TATCC
Found at i:580304 original size:185 final size:184
Alignment explanation
Indices: 579983--580339 Score: 642
Period size: 185 Copynumber: 1.9 Consensus size: 184
579973 GTATGAACGT
*
579983 TGTCTTTAATTACTCAATAAATGAATGAATACATACTACACATATTTTTTCTTTTTAAACAAAGT
1 TGTCTTTAATTACTCAATAAATGAATGAATACATACTACACATATTTTTTCTTATTAAACAAAGT
* *
580048 TTGTATAATTTAAACTCGTAAAATACATTTGATCAATTACGTTTCTATATCATCTAATAAAATTT
66 TTGTATAATTTAAACTCGTAAAATACATTTGATCAATTACGTTTCCATATCATCAAATAAAATTT
*
580113 ATATCATACATAACGATAAAAAATATTATTTTAATAACTAATAGACATTATATA
131 ATATCATACATAACAATAAAAAATATTATTTTAATAACTAATAGACATTATATA
* *
580167 TGTCTTTAATTACTCAATAAATGAATGAATATATACTATACATATTTTTTCTTATTAAACAAAGT
1 TGTCTTTAATTACTCAATAAATGAATGAATACATACTACACATATTTTTTCTTATTAAACAAAGT
580232 TTGTATAAATTTAAACTCGTAAAATACATTTGATCAATTACGTTTCCATATCATCAAATAAAATT
66 TTGTAT-AATTTAAACTCGTAAAATACATTTGATCAATTACGTTTCCATATCATCAAATAAAATT
*
580297 TATATCATACATAACAATAAAAAATATTATTTTAATAATTAAT
130 TATATCATACATAACAATAAAAAATATTATTTTAATAACTAAT
580340 TGAGAATATA
Statistics
Matches: 165, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
184 68 0.41
185 97 0.59
ACGTcount: A:0.43, C:0.11, G:0.05, T:0.40
Consensus pattern (184 bp):
TGTCTTTAATTACTCAATAAATGAATGAATACATACTACACATATTTTTTCTTATTAAACAAAGT
TTGTATAATTTAAACTCGTAAAATACATTTGATCAATTACGTTTCCATATCATCAAATAAAATTT
ATATCATACATAACAATAAAAAATATTATTTTAATAACTAATAGACATTATATA
Found at i:580352 original size:2 final size:2
Alignment explanation
Indices: 580345--580376 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
580335 TTAATTGAGA
580345 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
580377 TTAACTTTTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:585825 original size:4 final size:4
Alignment explanation
Indices: 585818--585854 Score: 74
Period size: 4 Copynumber: 9.2 Consensus size: 4
585808 ATCTCTCTCT
585818 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC C
1 CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC CTCC C
585855 CTCACTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 33 1.00
ACGTcount: A:0.00, C:0.76, G:0.00, T:0.24
Consensus pattern (4 bp):
CTCC
Found at i:587960 original size:14 final size:14
Alignment explanation
Indices: 587943--587975 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
587933 AATAATTCAT
587943 TATATTA-TATTATA
1 TATATTATTA-TATA
587957 TATATTATTATATA
1 TATATTATTATATA
587971 TATAT
1 TATAT
587976 AATAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 16 0.89
15 2 0.11
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
TATATTATTATATA
Found at i:587965 original size:12 final size:12
Alignment explanation
Indices: 587941--587973 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
587931 TAAATAATTC
587941 ATTATAT-TA-T
1 ATTATATATATT
587951 ATTATATATATT
1 ATTATATATATT
587963 ATTATATATAT
1 ATTATATATAT
587974 ATAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 7 0.33
11 2 0.10
12 12 0.57
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (12 bp):
ATTATATATATT
Found at i:595777 original size:2 final size:2
Alignment explanation
Indices: 595772--595815 Score: 88
Period size: 2 Copynumber: 22.0 Consensus size: 2
595762 ACACACACAC
595772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
595814 AT
1 AT
595816 TCACACTGAA
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 42 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:598938 original size:18 final size:18
Alignment explanation
Indices: 598901--598938 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
598891 TTTTAAGATT
*
598901 TTATATTCGATTTAAATA
1 TTATATTCGATTCAAATA
*
598919 TTATATTCGATTCAATTA
1 TTATATTCGATTCAAATA
598937 TT
1 TT
598939 CTAATATCAC
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:0.34, C:0.08, G:0.05, T:0.53
Consensus pattern (18 bp):
TTATATTCGATTCAAATA
Found at i:599374 original size:21 final size:21
Alignment explanation
Indices: 599350--599389 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
599340 TTTTCAAAGG
599350 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
599371 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
599390 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:599439 original size:19 final size:19
Alignment explanation
Indices: 599415--599453 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
599405 TCGAATGCAT
599415 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
599434 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
599453 T
1 T
599454 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:599486 original size:64 final size:65
Alignment explanation
Indices: 599350--599514 Score: 192
Period size: 64 Copynumber: 2.5 Consensus size: 65
599340 TTTTCAAAGG
*
599350 CATGCACCGATGCA-TCAATACCATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGC
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCACTC-ATGAATAAATTAAAACATCGAATGC
599413 ATTC
62 ATTC
* * * *
599417 CATGCACCGATGCACTCTCCATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGTATTT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
* * **
599481 GATGCATCGATGCACAATCCATGCATCGATGCAC
1 CATGCACCGATGCACTCTCCATGCATCGATGCAC
599515 CAGGCTATTT
Statistics
Matches: 87, Mismatches: 9, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
64 53 0.61
65 15 0.17
66 3 0.03
67 14 0.16
68 2 0.02
ACGTcount: A:0.33, C:0.25, G:0.16, T:0.26
Consensus pattern (65 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTCATGAATAAATTAAAACATCGAATGCATTC
Found at i:599532 original size:64 final size:63
Alignment explanation
Indices: 599350--599559 Score: 190
Period size: 64 Copynumber: 3.2 Consensus size: 63
599340 TTTTCAAAGG
* ** ** *
599350 CATGCACCGATGCATCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCAT
1 CATGCATCGATGCA-CAAT-CCATGCATCGATGCA-CGCTG-ATTTATTAAAACATCGAATGCAT
*
599415 TC
62 TT
* ** * *
599417 CATGCACCGATGCACTCTCCATGCATCGATGCACTCTGATTTAATTAAAACATCGAATGTATTT
1 CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTT-ATTAAAACATCGAATGCATTT
* * *
599481 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCT-ATTT-TTCAAACATCGAATGCACT
1 CATGCATCGATGCACAATCCATGCATCGATGCA-C--GCTGATTTATTAAAACATCGAATGCATT
599544 T
63 T
*
599545 CATGCATCGTTGCAC
1 CATGCATCGATGCAC
599560 TCTTAGTGCA
Statistics
Matches: 120, Mismatches: 19, Indels: 11
0.80 0.13 0.07
Matches are distributed among these distances:
63 2 0.02
64 80 0.67
65 16 0.13
66 6 0.05
67 16 0.13
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (63 bp):
CATGCATCGATGCACAATCCATGCATCGATGCACGCTGATTTATTAAAACATCGAATGCATTT
Found at i:605381 original size:24 final size:22
Alignment explanation
Indices: 605353--605432 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 22
605343 CACTTAACAA
605353 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
605377 TGCATCGATGCATCC--GCATG
1 TGCATCGATGCATCCTTGAATG
* *
605397 ATACACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
605421 TGCATCGATGCA
1 TGCATCGATGCA
605433 CAAGATCATG
Statistics
Matches: 46, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
20 4 0.09
21 11 0.24
22 2 0.04
23 12 0.26
24 17 0.37
ACGTcount: A:0.24, C:0.26, G:0.23, T:0.28
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:607967 original size:21 final size:21
Alignment explanation
Indices: 607943--607982 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
607933 TTTTCAAAGG
607943 CATGCACCGATGCATCAATAC
1 CATGCACCGATGCATCAATAC
*
607964 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
607983 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.30, G:0.15, T:0.23
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAC
Found at i:608032 original size:19 final size:19
Alignment explanation
Indices: 608008--608044 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
607998 TCGAATGCAT
608008 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
608027 TCCATGCATCGATGCACT
1 TCCATGCACCGATGCACT
608045 ATGATTTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.38, G:0.16, T:0.24
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:608071 original size:64 final size:63
Alignment explanation
Indices: 607943--608173 Score: 218
Period size: 64 Copynumber: 3.6 Consensus size: 63
607933 TTTTCAAAGG
* * * *
607943 CATGCACCGATGCA-TCAATACCATGCATCGATGCATCAATGAATAAATTGAAACATCGAATGCA
1 CATGCACCGATGCACTC--T-CCATGCATCGATGCA-CTATGATTTAATTAAAACATCGAATGCA
608007 TT
62 TT
608009 CCATGCACCGATGCACTCTCCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCATTT
1 -CATGCACCGATGCACTCTCCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCA-TT
* * ** * * *
608074 GATGCATCGATGCACAATCCATGCATCGATGCACCAGGCTATTT--TTCAAACATCGAATGCACT
1 CATGCACCGATGCACTCTCCATGCATCGATGCACTATG--ATTTAATTAAAACATCGAATGCA-T
608137 T
63 T
* * *
608138 CATGCATCGATGCACTCT-TAGTGCACCGATGCACTA
1 CATGCACCGATGCACTCTCCA-TGCATCGATGCACTA
608174 GTAGTCCAAC
Statistics
Matches: 141, Mismatches: 18, Indels: 13
0.82 0.10 0.08
Matches are distributed among these distances:
63 1 0.01
64 102 0.72
65 17 0.12
66 5 0.04
67 14 0.10
68 2 0.01
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.26
Consensus pattern (63 bp):
CATGCACCGATGCACTCTCCATGCATCGATGCACTATGATTTAATTAAAACATCGAATGCATT
Found at i:608152 original size:17 final size:19
Alignment explanation
Indices: 608124--608172 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
608114 ATTTTTCAAA
608124 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
608142 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
608161 CACCGATGCACT
1 CATCGATGCACT
608173 AGTAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:608178 original size:19 final size:19
Alignment explanation
Indices: 608140--608178 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
608130 ATGCACTTCA
* **
608140 TGCATCGATGCACTCTTAG
1 TGCACCGATGCACTAGTAG
608159 TGCACCGATGCACTAGTAG
1 TGCACCGATGCACTAGTAG
608178 T
1 T
608179 CCAACGGTTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.23, C:0.26, G:0.23, T:0.28
Consensus pattern (19 bp):
TGCACCGATGCACTAGTAG
Found at i:612429 original size:22 final size:22
Alignment explanation
Indices: 612399--612459 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
612389 GGGTTTACGC
*
612399 GGTCCTTCGGGACAAATACATA
1 GGTCTTTCGGGACAAATACATA
612421 GGTCTTTCGGGACAAATACATA
1 GGTCTTTCGGGACAAATACATA
*
612443 GGT-TCTTCGAGACAAAT
1 GGTCT-TTCGGGACAAAT
612460 TTCATATGTC
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 35 0.97
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (22 bp):
GGTCTTTCGGGACAAATACATA
Found at i:624823 original size:3 final size:3
Alignment explanation
Indices: 624817--624841 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
624807 CTGTCCTCTG
624817 CAC CAC CAC CAC CAC CAC CAC CAC C
1 CAC CAC CAC CAC CAC CAC CAC CAC C
624842 TTCTTCACCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.68, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:626385 original size:20 final size:20
Alignment explanation
Indices: 626362--626421 Score: 120
Period size: 20 Copynumber: 3.0 Consensus size: 20
626352 GAAGTGTTAG
626362 AAAGGATTAAGAACAAGTTT
1 AAAGGATTAAGAACAAGTTT
626382 AAAGGATTAAGAACAAGTTT
1 AAAGGATTAAGAACAAGTTT
626402 AAAGGATTAAGAACAAGTTT
1 AAAGGATTAAGAACAAGTTT
626422 GAAGAATTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 40 1.00
ACGTcount: A:0.50, C:0.05, G:0.20, T:0.25
Consensus pattern (20 bp):
AAAGGATTAAGAACAAGTTT
Found at i:626727 original size:20 final size:20
Alignment explanation
Indices: 626702--626753 Score: 61
Period size: 20 Copynumber: 2.6 Consensus size: 20
626692 GGTTGAAGAA
*
626702 GTATCGATACTGATG-TGAAG
1 GTATCGATACTGAGGAT-AAG
**
626722 GTATCGATACCAAGGATAAG
1 GTATCGATACTGAGGATAAG
626742 GTATCGATACTG
1 GTATCGATACTG
626754 TAAGTAAAGA
Statistics
Matches: 26, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
20 25 0.96
21 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.27, T:0.27
Consensus pattern (20 bp):
GTATCGATACTGAGGATAAG
Found at i:627588 original size:23 final size:23
Alignment explanation
Indices: 627551--627633 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
627541 GTCGAGGGTT
627551 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGACAAAA
* * *
627574 CTATGTCGTCCTTCGGGACAAAC
1 CTATGTGGTCATTCGGGACAAAA
*
627597 CTATGTGGTCATTCGAGAC-AAA
1 CTATGTGGTCATTCGGGACAAAA
627619 -TATGTGG-CACTTCGG
1 CTATGTGGTCA-TTCGG
627634 TGCAAATTAT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
20 2 0.04
21 11 0.22
22 2 0.04
23 36 0.71
ACGTcount: A:0.25, C:0.22, G:0.25, T:0.28
Consensus pattern (23 bp):
CTATGTGGTCATTCGGGACAAAA
Found at i:627624 original size:21 final size:22
Alignment explanation
Indices: 627551--627646 Score: 99
Period size: 23 Copynumber: 4.3 Consensus size: 22
627541 GTCGAGGGTT
627551 CTATGTGGTCATTCGGGACAAAA
1 CTATGTGGTCATTCGGGAC-AAA
* *
627574 CTATGTCGTCCTTCGGGACAAA
1 CTATGTGGTCATTCGGGACAAA
*
627596 CCTATGTGGTCATTCGAGACAAA
1 -CTATGTGGTCATTCGGGACAAA
627619 -TATGTGG-CACTTCGGTG-CAAA
1 CTATGTGGTCA-TTCGG-GACAAA
*
627640 TTATGTG
1 CTATGTG
627647 AGCTGTGGTG
Statistics
Matches: 63, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
20 2 0.03
21 15 0.24
22 10 0.16
23 36 0.57
ACGTcount: A:0.26, C:0.20, G:0.25, T:0.29
Consensus pattern (22 bp):
CTATGTGGTCATTCGGGACAAA
Found at i:631256 original size:30 final size:29
Alignment explanation
Indices: 631222--631286 Score: 78
Period size: 30 Copynumber: 2.2 Consensus size: 29
631212 TAAGATTTTG
*
631222 AAAGTTT-GGTGACCAAAGTATAAACTTTAA
1 AAAGTTTAGG-GACCAAAATAT-AACTTTAA
* *
631252 AAAGTTTAGGGACCAAAATGTAATTTTAA
1 AAAGTTTAGGGACCAAAATATAACTTTAA
631281 AAAGTT
1 AAAGTT
631287 ACAAATTGGT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 13 0.42
30 16 0.52
31 2 0.06
ACGTcount: A:0.45, C:0.08, G:0.17, T:0.31
Consensus pattern (29 bp):
AAAGTTTAGGGACCAAAATATAACTTTAA
Found at i:634478 original size:20 final size:20
Alignment explanation
Indices: 634449--634488 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
634439 GTAAGGAGTT
634449 GAGTTCGGCATAAATCACCA
1 GAGTTCGGCATAAATCACCA
*
634469 GAGTTTGGCATAAATCACCA
1 GAGTTCGGCATAAATCACCA
634489 AGGAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.23
Consensus pattern (20 bp):
GAGTTCGGCATAAATCACCA
Found at i:637991 original size:30 final size:31
Alignment explanation
Indices: 637957--638016 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
637947 AAAAAAATTT
637957 GGGGACC-ATTATG-TAATTTT-TGAAAAGTTA
1 GGGGACCAATT-TGATAATTTTGT-AAAAGTTA
637987 GGGGACCAATTTGATAATTTTGTAAAAGTT
1 GGGGACCAATTTGATAATTTTGTAAAAGTT
638017 GTGAATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 9 0.33
31 17 0.63
32 1 0.04
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (31 bp):
GGGGACCAATTTGATAATTTTGTAAAAGTTA
Found at i:638014 original size:31 final size:30
Alignment explanation
Indices: 637957--638016 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
637947 AAAAAAATTT
637957 GGGGACCATTATGTAATTTTTGAAAAGTTA
1 GGGGACCATTATGTAATTTTTGAAAAGTTA
637987 GGGGACCAATT-TGATAA-TTTTGTAAAAGTT
1 GGGGACC-ATTATG-TAATTTTTG-AAAAGTT
638017 GTGAATGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
30 14 0.52
31 13 0.48
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (30 bp):
GGGGACCATTATGTAATTTTTGAAAAGTTA
Found at i:640180 original size:20 final size:20
Alignment explanation
Indices: 640155--640194 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
640145 GTAAGGAGTT
640155 GAGTTTGGCATAAATCACCA
1 GAGTTTGGCATAAATCACCA
*
640175 GAGTTTGGCATCAATCACCA
1 GAGTTTGGCATAAATCACCA
640195 AGGAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.25
Consensus pattern (20 bp):
GAGTTTGGCATAAATCACCA
Found at i:651469 original size:21 final size:21
Alignment explanation
Indices: 651419--651470 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 21
651409 TGAAGGAAAT
651419 AGTA-TGA-ACTGGATGAACA
1 AGTATTGATACTGGATGAACA
* * *
651438 A-TATCGATACTGGTTGAAGA
1 AGTATTGATACTGGATGAACA
651458 AGTATTGATACTG
1 AGTATTGATACTG
651471 ATGTGAAGGT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 11 0.42
21 10 0.38
ACGTcount: A:0.37, C:0.10, G:0.25, T:0.29
Consensus pattern (21 bp):
AGTATTGATACTGGATGAACA
Found at i:652347 original size:23 final size:23
Alignment explanation
Indices: 652310--652385 Score: 102
Period size: 23 Copynumber: 3.4 Consensus size: 23
652300 GTCGAGGGTT
652310 CTATGTGGTCCTTCGGGACAAAA
1 CTATGTGGTCCTTCGGGACAAAA
* * *
652333 CTATGTCGTCATTCGGGACAAAC
1 CTATGTGGTCCTTCGGGACAAAA
*
652356 CTCTGTGGTCCTTCGGGAC-AAA
1 CTATGTGGTCCTTCGGGACAAAA
652378 -TATGTGGT
1 CTATGTGGT
652386 ACTTTGGTGT
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
21 7 0.16
22 2 0.04
23 36 0.80
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.29
Consensus pattern (23 bp):
CTATGTGGTCCTTCGGGACAAAA
Found at i:653349 original size:16 final size:17
Alignment explanation
Indices: 653319--653353 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
653309 TTAGTGAGGC
*
653319 AACATAATAAGATAAAT
1 AACATAATAAAATAAAT
653336 AACAT-ATAAAATAAAT
1 AACATAATAAAATAAAT
653352 AA
1 AA
653354 ATTTTGTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.69, C:0.06, G:0.03, T:0.23
Consensus pattern (17 bp):
AACATAATAAAATAAAT
Found at i:656573 original size:30 final size:31
Alignment explanation
Indices: 656505--656600 Score: 81
Period size: 30 Copynumber: 3.2 Consensus size: 31
656495 GAAGGACCTA
* ** *
656505 TCCAGAGGTCACAAAG-ACCCCGGT-AACTA
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
* * * * *
656534 TCCAGAGGTCATAAAGAACTTCGG-CAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
*
656564 TCCATAGGTCCCAAAGAACCTAGGTAAACTG
1 TCCATAGGTCACAAAGAACCTAGGTAAACTG
656595 TCCATA
1 TCCATA
656601 TATTCCTTAG
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
29 15 0.28
30 28 0.52
31 11 0.20
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (31 bp):
TCCATAGGTCACAAAGAACCTAGGTAAACTG
Found at i:658862 original size:29 final size:30
Alignment explanation
Indices: 658829--658898 Score: 106
Period size: 29 Copynumber: 2.4 Consensus size: 30
658819 TTAACGTCTT
* * *
658829 AGTGATCAAATTGTTATTAATCGT-ATGGA
1 AGTGACCAAATTGTTATTAATCATAATGCA
658858 AGTGACCAAATTGTTATTAATCATAATGCA
1 AGTGACCAAATTGTTATTAATCATAATGCA
658888 AGTGACCAAAT
1 AGTGACCAAAT
658899 CAAAATAATT
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 22 0.59
30 15 0.41
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (30 bp):
AGTGACCAAATTGTTATTAATCATAATGCA
Found at i:659067 original size:12 final size:12
Alignment explanation
Indices: 659050--659075 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
659040 ATTAATTTGC
659050 ACAGACGATTTT
1 ACAGACGATTTT
659062 ACAGACGATTTT
1 ACAGACGATTTT
659074 AC
1 AC
659076 CTAAAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (12 bp):
ACAGACGATTTT
Found at i:661362 original size:17 final size:17
Alignment explanation
Indices: 661340--661373 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
661330 GGATGCGCTT
661340 TTCGAAAGCTCTTTTGG
1 TTCGAAAGCTCTTTTGG
661357 TTCGAAAGCTCTTTTGG
1 TTCGAAAGCTCTTTTGG
661374 GGGAACACGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.24, T:0.41
Consensus pattern (17 bp):
TTCGAAAGCTCTTTTGG
Found at i:665127 original size:20 final size:21
Alignment explanation
Indices: 665078--665128 Score: 86
Period size: 21 Copynumber: 2.5 Consensus size: 21
665068 TATGAATCAA
665078 TCATTCAAATATATTAATTAT
1 TCATTCAAATATATTAATTAT
*
665099 TCTTTCAAATATATTAATTAT
1 TCATTCAAATATATTAATTAT
665120 T-ATTCAAAT
1 TCATTCAAAT
665129 TTAAAAAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 7 0.25
21 21 0.75
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (21 bp):
TCATTCAAATATATTAATTAT
Found at i:665318 original size:18 final size:18
Alignment explanation
Indices: 665295--665332 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
665285 TTACATTTTA
*
665295 TAAACATTTAACAAACAT
1 TAAACATTTAAAAAACAT
665313 TAAACATTTAAAAAACAT
1 TAAACATTTAAAAAACAT
665331 TA
1 TA
665333 TATAATCTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (18 bp):
TAAACATTTAAAAAACAT
Found at i:665740 original size:21 final size:21
Alignment explanation
Indices: 665716--665777 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 21
665706 ACCCTACAGG
*
665716 CTAGGAATGTAACCTTGCGGA
1 CTAGGAATGTAACCCTGCGGA
* * * *
665737 CTAGGTATGTACCCCTGTGGG
1 CTAGGAATGTAACCCTGCGGA
665758 CTAGGAATGTAACCCTGCGG
1 CTAGGAATGTAACCCTGCGG
665778 TGGTGGCATA
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.23, C:0.23, G:0.31, T:0.24
Consensus pattern (21 bp):
CTAGGAATGTAACCCTGCGGA
Found at i:665817 original size:42 final size:42
Alignment explanation
Indices: 665770--665855 Score: 118
Period size: 42 Copynumber: 2.0 Consensus size: 42
665760 AGGAATGTAA
* * *
665770 CCCTGCGGTGGTGGCATATGAATTGTTGGACTGGGCATATAC
1 CCCTGCGGAGGTGGCATATGAACTGGTGGACTGGGCATATAC
* * *
665812 CCCTGCGGAGGTGGCATTTGAACTGGTGGGCTGGGCATGTAC
1 CCCTGCGGAGGTGGCATATGAACTGGTGGACTGGGCATATAC
665854 CC
1 CC
665856 ATGTGGGTTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.16, C:0.22, G:0.36, T:0.26
Consensus pattern (42 bp):
CCCTGCGGAGGTGGCATATGAACTGGTGGACTGGGCATATAC
Found at i:673663 original size:74 final size:71
Alignment explanation
Indices: 673571--673705 Score: 207
Period size: 74 Copynumber: 1.9 Consensus size: 71
673561 AATTCCTACA
673571 AGTTCCATATAATTTTTAACCTCGAAATTTTAAAATTTTTAATAATTTTTTCAAATTTAATAATA
1 AGTTCCATATAATTTTTAACCTCGAAATTTTAAAATTTTTAAT-A-TTTTTC-AATTTAATAATA
673636 ATTTGTATT
63 ATTTGTATT
* * * *
673645 AGTTTCATATTATTTTTAACTTCGAAATTTTAAAATTTTTAATATTTTTCAATTTATTAAT
1 AGTTCCATATAATTTTTAACCTCGAAATTTTAAAATTTTTAATATTTTTCAATTTAATAAT
673706 TACTGTAAAT
Statistics
Matches: 57, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
71 10 0.18
72 6 0.11
73 1 0.02
74 40 0.70
ACGTcount: A:0.36, C:0.07, G:0.04, T:0.53
Consensus pattern (71 bp):
AGTTCCATATAATTTTTAACCTCGAAATTTTAAAATTTTTAATATTTTTCAATTTAATAATAATT
TGTATT
Found at i:676686 original size:16 final size:15
Alignment explanation
Indices: 676663--676720 Score: 57
Period size: 16 Copynumber: 3.8 Consensus size: 15
676653 TTGATTAAAG
676663 TTTAAAATAAATTAT
1 TTTAAAATAAATTAT
676678 TTGTAAAATAAA-TA-
1 TT-TAAAATAAATTAT
* *
676692 TTTAAATTATATTATT
1 TTTAAAATAAATTA-T
676708 TTTATAAATAAAT
1 TTTA-AAATAAAT
676721 ATCCAAGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 7 0.21
14 4 0.12
15 4 0.12
16 13 0.38
17 6 0.18
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (15 bp):
TTTAAAATAAATTAT
Found at i:676705 original size:29 final size:30
Alignment explanation
Indices: 676663--676722 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 30
676653 TTGATTAAAG
676663 TTTAAAATAAATTATTTGTA-AAATAAATA
1 TTTAAAATAAATTATTTGTATAAATAAATA
* * *
676692 TTTAAATTATATTATTTTTATAAATAAATA
1 TTTAAAATAAATTATTTGTATAAATAAATA
676722 T
1 T
676723 CCAAGTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
29 17 0.63
30 10 0.37
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (30 bp):
TTTAAAATAAATTATTTGTATAAATAAATA
Found at i:679954 original size:21 final size:19
Alignment explanation
Indices: 679916--679961 Score: 58
Period size: 20 Copynumber: 2.3 Consensus size: 19
679906 AATTAATCCT
679916 ACTAAGTATTAAAGCTAAGA
1 ACTAA-TATTAAAGCTAAGA
679936 ACTAATATTAAGGAGCTAAGA
1 ACTAATATTAA--AGCTAAGA
679957 A-TAAT
1 ACTAAT
679962 GATTCAATGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 6 0.25
20 9 0.38
21 9 0.38
ACGTcount: A:0.50, C:0.09, G:0.15, T:0.26
Consensus pattern (19 bp):
ACTAATATTAAAGCTAAGA
Found at i:692593 original size:17 final size:17
Alignment explanation
Indices: 692566--692612 Score: 76
Period size: 17 Copynumber: 2.7 Consensus size: 17
692556 GCTATACAAG
692566 TGTGACTATTCTAAGACT
1 TGTG-CTATTCTAAGACT
*
692584 TGTGCTATTCCAAGACT
1 TGTGCTATTCTAAGACT
692601 TGTGCTATTCTA
1 TGTGCTATTCTA
692613 TATATAAAGG
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 23 0.85
18 4 0.15
ACGTcount: A:0.23, C:0.19, G:0.17, T:0.40
Consensus pattern (17 bp):
TGTGCTATTCTAAGACT
Done.