Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr07 ID=Chr07-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 60982465
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 868082 characters in sequence are not A, C, G, or T
File 201 of 204
Found at i:59597006 original size:25 final size:25
Alignment explanation
Indices: 59596978--59597035 Score: 107
Period size: 25 Copynumber: 2.3 Consensus size: 25
59596968 GTTATGTAAG
59596978 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
59597003 TTATGTAAGTTATGTAAGTTGTGTA
1 TTATGTAAGTTATGTAAGTTGTGTA
*
59597028 TAATGTAA
1 TTATGTAA
59597036 TTAAGTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (25 bp):
TTATGTAAGTTATGTAAGTTGTGTA
Found at i:59597208 original size:29 final size:28
Alignment explanation
Indices: 59597162--59597216 Score: 65
Period size: 29 Copynumber: 1.9 Consensus size: 28
59597152 GTGTCAAAAA
* * * *
59597162 TTAACTTTAGTTTTTATCCAAATAAATAT
1 TTAACTTGAATTTGTAT-CAAAGAAATAT
59597191 TTAACTTGAATTTGTATCAAAGAAAT
1 TTAACTTGAATTTGTATCAAAGAAAT
59597217 TTGTTTATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
28 8 0.36
29 14 0.64
ACGTcount: A:0.40, C:0.09, G:0.07, T:0.44
Consensus pattern (28 bp):
TTAACTTGAATTTGTATCAAAGAAATAT
Found at i:59610194 original size:27 final size:27
Alignment explanation
Indices: 59610146--59610211 Score: 66
Period size: 25 Copynumber: 2.5 Consensus size: 27
59610136 AAAATGTATG
*
59610146 TATATGTAAAATA-AATAATT-AAGAA
1 TATATTTAAAATATAATAATTAAAGAA
* *
59610171 TATATTTAAAATATAATATTTTAAATAA
1 TATATTTAAAATATAATA-ATTAAAGAA
*
59610199 TA-ATTAAAAATAT
1 TATATTTAAAATAT
59610212 CAAAACTATG
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
25 12 0.35
26 4 0.12
27 12 0.35
28 6 0.18
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (27 bp):
TATATTTAAAATATAATAATTAAAGAA
Found at i:59613372 original size:3 final size:3
Alignment explanation
Indices: 59613366--59613427 Score: 70
Period size: 3 Copynumber: 20.7 Consensus size: 3
59613356 AAACTAATAA
* * * * *
59613366 ATT ATT ATT ATT AAT ATT ATT ATT AGT GTT ATT AAT ATT ATT ATT AAT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
*
59613414 ATT ATT GTT ATT AT
1 ATT ATT ATT ATT AT
59613428 CATCATATTT
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:59613427 original size:21 final size:21
Alignment explanation
Indices: 59613366--59613419 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
59613356 AAACTAATAA
*
59613366 ATTATTATTATTAATATTATT
1 ATTAATATTATTAATATTATT
* *
59613387 ATTAGTGTTATTAATATTATT
1 ATTAATATTATTAATATTATT
59613408 ATTAATATTATT
1 ATTAATATTATT
59613420 GTTATTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.37, C:0.00, G:0.04, T:0.59
Consensus pattern (21 bp):
ATTAATATTATTAATATTATT
Found at i:59624050 original size:72 final size:72
Alignment explanation
Indices: 59623929--59624081 Score: 272
Period size: 72 Copynumber: 2.1 Consensus size: 72
59623919 AGTGTCGGCA
*
59623929 TCTTCCGGAGTGGCTTCAACATCTAACAAATCTGCAACGGCTTTTTCTC-GTTAATTTGCCCAAT
1 TCTTCCGGAGTGGCTTCAACATCTAACAAATCTGCAACGGCTTTATCTCGGTT-ATTTGCCCAAT
59623993 TTAACATC
65 TTAACATC
*
59624001 TCTTCCGGAGTGGCTTCAACATCTAACAAATCTGCAAGGGCTTTATCTCGGTTATTTGCCCAATT
1 TCTTCCGGAGTGGCTTCAACATCTAACAAATCTGCAACGGCTTTATCTCGGTTATTTGCCCAATT
59624066 TAACATC
66 TAACATC
59624073 TCTTCCGGA
1 TCTTCCGGA
59624082 CGAGATGCGT
Statistics
Matches: 78, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
72 75 0.96
73 3 0.04
ACGTcount: A:0.24, C:0.26, G:0.16, T:0.34
Consensus pattern (72 bp):
TCTTCCGGAGTGGCTTCAACATCTAACAAATCTGCAACGGCTTTATCTCGGTTATTTGCCCAATT
TAACATC
Found at i:59635357 original size:12 final size:12
Alignment explanation
Indices: 59635331--59635364 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
59635321 CCACATATCA
*
59635331 ATTAA-TCCTTT
1 ATTAATTCCTTC
59635342 ATTAATTCCTTC
1 ATTAATTCCTTC
59635354 ATTAATTCCTT
1 ATTAATTCCTT
59635365 TGTTTAAGGG
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 5 0.24
12 16 0.76
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (12 bp):
ATTAATTCCTTC
Found at i:59637920 original size:36 final size:36
Alignment explanation
Indices: 59637873--59637944 Score: 144
Period size: 36 Copynumber: 2.0 Consensus size: 36
59637863 TGTACTATGA
59637873 AGTTCATAGTGGATTCATCTTTCGGCAAAGCCCCGC
1 AGTTCATAGTGGATTCATCTTTCGGCAAAGCCCCGC
59637909 AGTTCATAGTGGATTCATCTTTCGGCAAAGCCCCGC
1 AGTTCATAGTGGATTCATCTTTCGGCAAAGCCCCGC
59637945 GGACGTAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (36 bp):
AGTTCATAGTGGATTCATCTTTCGGCAAAGCCCCGC
Found at i:59644482 original size:17 final size:19
Alignment explanation
Indices: 59644438--59644483 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 19
59644428 ATATGTAAAA
59644438 TAAATAATTAAGAATATATT
1 TAAATAA-TAAGAATATATT
59644458 TAAA-AATAA-AATAT-TT
1 TAAATAATAAGAATATATT
59644474 TAAATAATAA
1 TAAATAATAA
59644484 TTAAAAAGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 6 0.24
17 10 0.40
18 3 0.12
19 2 0.08
20 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (19 bp):
TAAATAATAAGAATATATT
Found at i:59654392 original size:12 final size:12
Alignment explanation
Indices: 59654375--59654415 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
59654365 TGAAGCACTC
*
59654375 AATATAAACAAT
1 AATATATACAAT
*
59654387 AATATATA-TAT
1 AATATATACAAT
59654398 AA-ATATACAAT
1 AATATATACAAT
59654409 AATATAT
1 AATATAT
59654416 GTAAAAGTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
10 5 0.21
11 8 0.33
12 11 0.46
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (12 bp):
AATATATACAAT
Found at i:59655297 original size:44 final size:44
Alignment explanation
Indices: 59655248--59655354 Score: 135
Period size: 44 Copynumber: 2.4 Consensus size: 44
59655238 TTGCCTTCAT
*
59655248 TCTGCCATTTTGGCTTGCACCCATTC-GAGCTTGCATTTAGACCG
1 TCTGCCACTTTGGCTTGCACCCATTCAG-GCTTGCATTTAGACCG
* * *
59655292 TCTGCCACTTTGGTTTGCACCCATTCAGGTTTGCATTTAGACTG
1 TCTGCCACTTTGGCTTGCACCCATTCAGGCTTGCATTTAGACCG
* **
59655336 TCCGCCACTTCAGCTTGCA
1 TCTGCCACTTTGGCTTGCA
59655355 ATTCGACAGG
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
44 53 0.98
45 1 0.02
ACGTcount: A:0.16, C:0.30, G:0.20, T:0.35
Consensus pattern (44 bp):
TCTGCCACTTTGGCTTGCACCCATTCAGGCTTGCATTTAGACCG
Found at i:59659953 original size:16 final size:16
Alignment explanation
Indices: 59659928--59659975 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
59659918 TTAGCCAACA
*
59659928 AAATATATATAAATAT
1 AAATAAATATAAATAT
**
59659944 AAATAAATATTTATAT
1 AAATAAATATAAATAT
59659960 AAA-AAATA-AAATAT
1 AAATAAATATAAATAT
59659974 AA
1 AA
59659976 CTAGAATAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 6 0.22
15 5 0.19
16 16 0.59
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATAAATATAAATAT
Found at i:59659953 original size:20 final size:19
Alignment explanation
Indices: 59659928--59659974 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
59659918 TTAGCCAACA
59659928 AAATATATATA-AATATAAAT
1 AAATATATATATAA-A-AAAT
*
59659948 AAATATTTATATAAAAAAT
1 AAATATATATATAAAAAAT
59659967 AAA-ATATA
1 AAATATATA
59659975 ACTAGAATAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 4 0.17
19 7 0.29
20 11 0.46
21 2 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAATATATATATAAAAAAT
Found at i:59665993 original size:14 final size:14
Alignment explanation
Indices: 59665974--59666000 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
59665964 GTAAGCCACC
59665974 GGAGAGTAGTTTGG
1 GGAGAGTAGTTTGG
59665988 GGAGAGTAGTTTG
1 GGAGAGTAGTTTG
59666001 TTGAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.48, T:0.30
Consensus pattern (14 bp):
GGAGAGTAGTTTGG
Found at i:59683126 original size:31 final size:31
Alignment explanation
Indices: 59683089--59683148 Score: 86
Period size: 31 Copynumber: 1.9 Consensus size: 31
59683079 TATATAAATA
59683089 AAATTTTAATTATAATTTAAA-TGTATACAAG
1 AAATTTTAATTATAA-TTAAATTGTATACAAG
* *
59683120 AAATTTTTATTTTAATTAAATTGTATACA
1 AAATTTTAATTATAATTAAATTGTATACA
59683149 TTTATAGAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.45, C:0.03, G:0.05, T:0.47
Consensus pattern (31 bp):
AAATTTTAATTATAATTAAATTGTATACAAG
Found at i:59684179 original size:19 final size:18
Alignment explanation
Indices: 59684155--59684205 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 18
59684145 CACCTCATTT
59684155 GATCCAATCTCAATGAGTA
1 GATCCAATCTCAATGA-TA
*
59684174 GATCCAATCTC-AT--TT
1 GATCCAATCTCAATGATA
59684189 GATCCAATCTCAATGAT
1 GATCCAATCTCAATGAT
59684206 TAGAGAGCTT
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
15 12 0.43
16 2 0.07
18 3 0.11
19 11 0.39
ACGTcount: A:0.33, C:0.24, G:0.12, T:0.31
Consensus pattern (18 bp):
GATCCAATCTCAATGATA
Found at i:59684194 original size:15 final size:15
Alignment explanation
Indices: 59684148--59684200 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 15
59684138 AACAAAACAC
59684148 CTCATTTGATCCAAT
1 CTCATTTGATCCAAT
*
59684163 CTCAATGAGTAGATCCAAT
1 CTC-AT---TTGATCCAAT
59684182 CTCATTTGATCCAAT
1 CTCATTTGATCCAAT
59684197 CTCA
1 CTCA
59684201 ATGATTAGAG
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
15 16 0.50
16 2 0.06
18 2 0.06
19 12 0.38
ACGTcount: A:0.30, C:0.26, G:0.09, T:0.34
Consensus pattern (15 bp):
CTCATTTGATCCAAT
Found at i:59688542 original size:24 final size:24
Alignment explanation
Indices: 59688515--59688566 Score: 77
Period size: 24 Copynumber: 2.2 Consensus size: 24
59688505 TTTTTAGAAA
* *
59688515 ATTTAGTATTTATTAATATAATAT
1 ATTTAGCATTTATTAACATAATAT
*
59688539 ATTTAGCATTTATTAGCATAATAT
1 ATTTAGCATTTATTAACATAATAT
59688563 ATTT
1 ATTT
59688567 GACATGGATT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.06, T:0.52
Consensus pattern (24 bp):
ATTTAGCATTTATTAACATAATAT
Found at i:59688577 original size:24 final size:24
Alignment explanation
Indices: 59688532--59688578 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
59688522 ATTTATTAAT
**
59688532 ATAATATATTTAGCATTTATTAGC
1 ATAATATATTTAGCATGGATTAGC
59688556 ATAATATATTT-GACATGGATTAG
1 ATAATATATTTAG-CATGGATTAG
59688579 AATTAGGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 1 0.05
24 19 0.95
ACGTcount: A:0.38, C:0.06, G:0.13, T:0.43
Consensus pattern (24 bp):
ATAATATATTTAGCATGGATTAGC
Found at i:59690216 original size:46 final size:45
Alignment explanation
Indices: 59690158--59690250 Score: 127
Period size: 45 Copynumber: 2.0 Consensus size: 45
59690148 AAATATCAAA
59690158 TTAAATAAATAACTTA-AAATTGA-ACTTTTTAAAACTTTTTGAATTT
1 TTAAATAAATAAC--ACAAATTGATA-TTTTTAAAACTTTTTGAATTT
* *
59690204 TTAAATAAATAACACACATTTATATTTTTAAAACTTTTTGAATTT
1 TTAAATAAATAACACAAATTGATATTTTTAAAACTTTTTGAATTT
59690249 TT
1 TT
59690251 GAGGATTTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 5
0.86 0.04 0.10
Matches are distributed among these distances:
44 1 0.02
45 28 0.65
46 14 0.33
ACGTcount: A:0.42, C:0.08, G:0.03, T:0.47
Consensus pattern (45 bp):
TTAAATAAATAACACAAATTGATATTTTTAAAACTTTTTGAATTT
Found at i:59696532 original size:15 final size:15
Alignment explanation
Indices: 59696514--59696548 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
59696504 TGGTTTAAAT
59696514 TTATATATTATCATC
1 TTATATATTATCATC
*
59696529 TTATATATTATTATC
1 TTATATATTATCATC
59696544 -TATAT
1 TTATAT
59696549 TAAAATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.34, C:0.09, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATATTATCATC
Found at i:59697397 original size:107 final size:106
Alignment explanation
Indices: 59697204--59697506 Score: 374
Period size: 106 Copynumber: 2.8 Consensus size: 106
59697194 TTATCTAAAT
* * * * * * *
59697204 AAGGAAATATTTTGTTTTTAGAAAATCGAGAAAATGTACCCTAACGTACTGGGTTTCGATTTCTT
1 AAGGAAATATTTTGTGTTTGGAAAATCGAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
59697269 GTTCGACCAAATAGCCAAATATCCTTTCAATAATTTCAAAAC
66 GTTCGACCAAATAGCCAAATATCCTTTCAA-AATTTCAAAAC
* * * *
59697311 AAGGTAATATTTTGTGTTTGGAAAATCGAAAAAACGTGCCCTAACTTGTTGGGTTTCGATTACTC
1 AAGGAAATATTTTGTGTTTGGAAAATCGAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
* * * *
59697376 GTTTGACCAAATAGTCGAATATCCTTTCGAAATTTCAAAAC
66 GTTCGACCAAATAGCCAAATATCCTTTCAAAATTTCAAAAC
* * * * * *
59697417 GAGGCAATGTTTTGCGTTTGGAAATTC-AAGAAAACGTGCCCTAACGTGCTGAGTTTCGATTTCT
1 AAGGAAATATTTTGTGTTTGGAAAATCGAA-AAAACGTGCCCTAACGTGCTGGGTTTCGATTTCT
* *
59697481 CATTCGACTAAATAGCCAAATATCCT
65 CGTTCGACCAAATAGCCAAATATCCT
59697507 CTTAAATCTC
Statistics
Matches: 166, Mismatches: 29, Indels: 3
0.84 0.15 0.02
Matches are distributed among these distances:
105 2 0.01
106 84 0.51
107 80 0.48
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (106 bp):
AAGGAAATATTTTGTGTTTGGAAAATCGAAAAAACGTGCCCTAACGTGCTGGGTTTCGATTTCTC
GTTCGACCAAATAGCCAAATATCCTTTCAAAATTTCAAAAC
Found at i:59701131 original size:21 final size:21
Alignment explanation
Indices: 59701105--59701144 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
59701095 TTTTCTTATA
*
59701105 ATTTTTTAATTTTTAAAATAT
1 ATTTTTGAATTTTTAAAATAT
*
59701126 ATTTTTGATTTTTTAAAAT
1 ATTTTTGAATTTTTAAAAT
59701145 TTTAAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (21 bp):
ATTTTTGAATTTTTAAAATAT
Found at i:59702186 original size:71 final size:71
Alignment explanation
Indices: 59702069--59702214 Score: 283
Period size: 71 Copynumber: 2.1 Consensus size: 71
59702059 AAAGATCATG
59702069 TCAATATACAAAATGATATTTTAATGATTTCTCAATTGATGATGTTTGATTAACTCATGACACCA
1 TCAATATACAAAATGATATTTTAATGATTTCTCAATTGATGATGTTTGATTAACTCATGACACCA
59702134 ACTTTT
66 ACTTTT
*
59702140 TCAATATACAAAATGATATTTTAATGATTTCTCAATTGATGGTGTTTGATTAACTCATGACACCA
1 TCAATATACAAAATGATATTTTAATGATTTCTCAATTGATGATGTTTGATTAACTCATGACACCA
59702205 ACTTTT
66 ACTTTT
59702211 TCAA
1 TCAA
59702215 GTGTTTGATA
Statistics
Matches: 74, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
71 74 1.00
ACGTcount: A:0.35, C:0.14, G:0.10, T:0.40
Consensus pattern (71 bp):
TCAATATACAAAATGATATTTTAATGATTTCTCAATTGATGATGTTTGATTAACTCATGACACCA
ACTTTT
Found at i:59702530 original size:20 final size:20
Alignment explanation
Indices: 59702505--59702543 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
59702495 CAATAAATAA
* *
59702505 TTTAAAAATTATAAAATATT
1 TTTAAAAAATAAAAAATATT
59702525 TTTAAAAAATAAAAAATAT
1 TTTAAAAAATAAAAAATAT
59702544 ATAAGTAGTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTTAAAAAATAAAAAATATT
Found at i:59702665 original size:18 final size:18
Alignment explanation
Indices: 59702631--59702665 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59702621 TTAGCATTTG
* *
59702631 AAATAATATTTTTATTAA
1 AAATAATAGTTTGATTAA
59702649 AAATAATAGTTTGATTA
1 AAATAATAGTTTGATTA
59702666 TTTTTAAAAG
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:0.49, C:0.00, G:0.06, T:0.46
Consensus pattern (18 bp):
AAATAATAGTTTGATTAA
Found at i:59707622 original size:3 final size:3
Alignment explanation
Indices: 59707614--59707638 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
59707604 TACCATTACA
59707614 GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT G
59707639 CCCAATGTTT
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:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Found at i:59709495 original size:47 final size:49
Alignment explanation
Indices: 59709395--59709495 Score: 118
Period size: 49 Copynumber: 2.1 Consensus size: 49
59709385 TAAAACATTT
* * * **
59709395 TAATATAAATATATTTGTAAAAATATTAAGATGATTAGATATAAAATTT
1 TAATAAAAATATATATGTAAAAATATTAAGATGATTAAATATAAAATAA
*
59709444 TAATAAAAATATATATGTAAAATTATTAA-AT-ATTAAAT-TAAAAATAA
1 TAATAAAAATATATATGTAAAAATATTAAGATGATTAAATAT-AAAATAA
59709491 TAATA
1 TAATA
59709496 TGGACGAGTT
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
46 1 0.02
47 16 0.36
48 2 0.04
49 26 0.58
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (49 bp):
TAATAAAAATATATATGTAAAAATATTAAGATGATTAAATATAAAATAA
Found at i:59709832 original size:3 final size:3
Alignment explanation
Indices: 59709820--59709858 Score: 64
Period size: 3 Copynumber: 13.7 Consensus size: 3
59709810 TGCTATTTTG
59709820 TTA TTA -TA TTA TTA TTA TTA TTA TT- TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
59709859 TAGATAGTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
2 4 0.12
3 30 0.88
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:59709839 original size:14 final size:13
Alignment explanation
Indices: 59709813--59709859 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 13
59709803 GTTTTACTGC
*
59709813 TATTTTGTTATTA
1 TATTTTATTATTA
59709826 TATTATTATTATTA
1 TATT-TTATTATTA
59709840 TTATTTTATTATTA
1 -TATTTTATTATTA
59709854 TTATTT
1 -TATTT
59709860 AGATAGTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
13 4 0.13
14 23 0.74
15 4 0.13
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TATTTTATTATTA
Found at i:59709842 original size:17 final size:17
Alignment explanation
Indices: 59709820--59709858 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
59709810 TGCTATTTTG
59709820 TTATTATATTATTATTA
1 TTATTATATTATTATTA
*
59709837 TTATTATTTTATTATTA
1 TTATTATATTATTATTA
59709854 TTATT
1 TTATT
59709859 TAGATAGTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (17 bp):
TTATTATATTATTATTA
Found at i:59710318 original size:2 final size:2
Alignment explanation
Indices: 59710311--59710360 Score: 91
Period size: 2 Copynumber: 25.0 Consensus size: 2
59710301 GTGTTCTACC
59710311 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
*
59710353 AT GT AT AT
1 AT AT AT AT
59710361 GTGGAATCAG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59710570 original size:44 final size:44
Alignment explanation
Indices: 59710506--59710703 Score: 183
Period size: 44 Copynumber: 4.6 Consensus size: 44
59710496 CCGTTACACG
59710506 GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
1 GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
* *
59710550 GTGGAATCAGCACTTGGCAACCTCCTCATGTTCAAAGGATCCCA
1 GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
* * * * ** * *
59710594 ATGGAATCAACACTTAGAAACCACCTTATAATC-AATGAT-AC-
1 GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
* * *** * *
59710635 GGGGAATCAGCACATAGCAACC-CCTTTCACAATC-AAGGAT-ACG
1 GTGGAATCAGCACTTAGCAACCACC--TCATGTTCAAAGGATCCCA
59710678 GTGGAATCAGCACTTAGCAACCACCT
1 GTGGAATCAGCACTTAGCAACCACCT
59710704 TATAATCAAT
Statistics
Matches: 128, Mismatches: 22, Indels: 10
0.80 0.14 0.06
Matches are distributed among these distances:
40 2 0.02
41 17 0.13
42 15 0.12
43 25 0.20
44 69 0.54
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (44 bp):
GTGGAATCAGCACTTAGCAACCACCTCATGTTCAAAGGATCCCA
Found at i:59710703 original size:84 final size:83
Alignment explanation
Indices: 59710595--59710786 Score: 280
Period size: 84 Copynumber: 2.3 Consensus size: 83
59710585 AGGATCCCAA
* *
59710595 TGGAATCAACACTTAGAAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
59710660 TTCACAATCAAGGATACGG
66 TT-ACAATCAAGGATACGG
*
59710679 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGTAACCCCT
1 TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
*** * *
59710744 TTTTGATCAATGATTCGG
66 TTACAATCAAGGATACGG
*
59710762 -GGAATCTGCACTTAGCAACC-CCTTA
1 TGGAATCAGCACTTAGCAACCACCTTA
59710787 CATTCAAAGA
Statistics
Matches: 99, Mismatches: 9, Indels: 3
0.89 0.08 0.03
Matches are distributed among these distances:
81 5 0.05
82 19 0.19
83 11 0.11
84 64 0.65
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (83 bp):
TGGAATCAGCACTTAGCAACCACCTTATAATCAATGATACGGGGAATCAGCACATAGCAACCCCT
TTACAATCAAGGATACGG
Found at i:59710753 original size:41 final size:41
Alignment explanation
Indices: 59710596--59710785 Score: 222
Period size: 41 Copynumber: 4.6 Consensus size: 41
59710586 GGATCCCAAT
* * *
59710596 GGAATCAACACTTAGAAACCACC-TTATAATCAATGATACGG
1 GGAATCAGCACATAGCAACC-CCTTTATAATCAATGATACGG
* *
59710637 GGAATCAGCACATAGCAACCCCTTTCACAATCAAGGATACGG
1 GGAATCAGCACATAGCAACCCCTTT-ATAATCAATGATACGG
*
59710679 TGGAATCAGCACTTAGCAACCACC-TTATAATCAATGATACGG
1 -GGAATCAGCACATAGCAACC-CCTTTATAATCAATGATACGG
* * * *
59710721 GGAATCAGCACATAGTAACCCCTTTTTGATCAATGATTCGG
1 GGAATCAGCACATAGCAACCCCTTTATAATCAATGATACGG
* *
59710762 GGAATCTGCACTTAGCAACCCCTT
1 GGAATCAGCACATAGCAACCCCTT
59710786 ACATTCAAAG
Statistics
Matches: 128, Mismatches: 16, Indels: 10
0.83 0.10 0.06
Matches are distributed among these distances:
40 4 0.03
41 73 0.57
42 28 0.22
43 21 0.16
44 2 0.02
ACGTcount: A:0.34, C:0.25, G:0.17, T:0.23
Consensus pattern (41 bp):
GGAATCAGCACATAGCAACCCCTTTATAATCAATGATACGG
Found at i:59713116 original size:2 final size:2
Alignment explanation
Indices: 59713109--59713141 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
59713099 GTTTGACAAC
59713109 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
59713142 TTGTAAATCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59722554 original size:3 final size:3
Alignment explanation
Indices: 59722546--59722609 Score: 128
Period size: 3 Copynumber: 21.3 Consensus size: 3
59722536 TTAGTATGGA
59722546 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG
59722594 ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG A
59722610 CGACGACAAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.34, C:0.00, G:0.33, T:0.33
Consensus pattern (3 bp):
ATG
Found at i:59723522 original size:144 final size:144
Alignment explanation
Indices: 59723279--59723561 Score: 460
Period size: 144 Copynumber: 2.0 Consensus size: 144
59723269 GCCTCAAAAA
*
59723279 ATTAACAATAGGAGATTGCAAGGAGGTTGATTTCGAGGGCATGAAATGGGAACTCCTTAAGAATC
1 ATTAACAATAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGAAATGGGAACTCCTTAAGAATC
* ** * *
59723344 TCTCTCATTTGGAGATTAATAATAATCCGCAGCTGGTGTCTCTCCCCTTTTGGCTTCAACATCTT
66 TCTCTCATTTGGAGATTAAGAATAATCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCTT
59723409 GTTCAATTGAAAGG
131 GTTCAATTGAAAGG
* *
59723423 ATTAACAGTAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGCAATGGGAAGC-CCTTAAGAAT
1 ATTAACAATAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGAAATGGGAA-CTCCTTAAGAAT
* *
59723487 CTCTCTCGTTTGGAGATTAAGAATATTCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCT
65 CTCTCTCATTTGGAGATTAAGAATAATCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCT
59723552 TGTTCAATTG
130 TGTTCAATTG
59723562 GAAACATTAG
Statistics
Matches: 128, Mismatches: 10, Indels: 2
0.91 0.07 0.01
Matches are distributed among these distances:
144 127 0.99
145 1 0.01
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (144 bp):
ATTAACAATAGGAGATTGCAAGGAGGTTGATTTAGAGGGCATGAAATGGGAACTCCTTAAGAATC
TCTCTCATTTGGAGATTAAGAATAATCCAAAGCTGGTGTCTCTCCCCATTGGGCTTCAACATCTT
GTTCAATTGAAAGG
Found at i:59728383 original size:30 final size:30
Alignment explanation
Indices: 59728347--59728407 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
59728337 TAATATCAAG
59728347 TTTACTCCAGGGATTCAACTATTTCATTAA
1 TTTACTCCAGGGATTCAACTATTTCATTAA
*
59728377 TTTACTCCAGGGATTCAACTATTTCGTTAA
1 TTTACTCCAGGGATTCAACTATTTCATTAA
59728407 T
1 T
59728408 CCATTAATAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.28, C:0.20, G:0.11, T:0.41
Consensus pattern (30 bp):
TTTACTCCAGGGATTCAACTATTTCATTAA
Found at i:59729662 original size:17 final size:18
Alignment explanation
Indices: 59729640--59729673 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
59729630 TTAAGGGTTC
59729640 AATTTAAAT-TAGTTTTT
1 AATTTAAATCTAGTTTTT
*
59729657 AATTTAATTCTAGTTTT
1 AATTTAAATCTAGTTTT
59729674 CGATTTCATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.32, C:0.03, G:0.06, T:0.59
Consensus pattern (18 bp):
AATTTAAATCTAGTTTTT
Found at i:59740195 original size:11 final size:11
Alignment explanation
Indices: 59740179--59740208 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59740169 TATATATATT
59740179 TAAAAATTATA
1 TAAAAATTATA
*
59740190 TAAAAATAATA
1 TAAAAATTATA
59740201 TAAAAATT
1 TAAAAATT
59740209 TTAATATGGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAAATTATA
Found at i:59744562 original size:20 final size:20
Alignment explanation
Indices: 59744539--59744576 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
59744529 CACGTGTATT
59744539 AAATAAAAATTTAATAATTA
1 AAATAAAAATTTAATAATTA
*
59744559 AAATATAAATTTAATAAT
1 AAATAAAAATTTAATAAT
59744577 AATTTAGTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (20 bp):
AAATAAAAATTTAATAATTA
Found at i:59753328 original size:28 final size:27
Alignment explanation
Indices: 59753269--59753328 Score: 70
Period size: 28 Copynumber: 2.2 Consensus size: 27
59753259 TTTAAATTAA
*
59753269 TAAA-AATAAAATTATATTTTAATCTT
1 TAAATAATAAAATTATAATTTAATCTT
59753295 TAAAATAATAAAAATT-TAATTTAATCCTT
1 T-AAATAAT-AAAATTATAATTTAAT-CTT
59753324 TAAAT
1 TAAAT
59753329 CTATCATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 6
0.81 0.03 0.17
Matches are distributed among these distances:
26 1 0.03
27 3 0.10
28 15 0.52
29 10 0.34
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (27 bp):
TAAATAATAAAATTATAATTTAATCTT
Found at i:59761127 original size:3 final size:3
Alignment explanation
Indices: 59761119--59761167 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
59761109 TACCATTACA
59761119 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT GAT
59761167 G
1 G
59761168 CTCAATGTCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.35, T:0.33
Consensus pattern (3 bp):
GAT
Found at i:59763803 original size:18 final size:20
Alignment explanation
Indices: 59763762--59763810 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
59763752 TTTTTTAGGC
*
59763762 TAAAATATTTATCGTTTTAG
1 TAAAATATTAATCGTTTTAG
*
59763782 TAAAATA-TAATC-TTTTAT
1 TAAAATATTAATCGTTTTAG
59763800 TAAAATGATTA
1 TAAAAT-ATTA
59763811 GTTTTTTAGG
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 11 0.44
19 5 0.20
20 9 0.36
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (20 bp):
TAAAATATTAATCGTTTTAG
Found at i:59770158 original size:30 final size:26
Alignment explanation
Indices: 59770090--59770160 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 26
59770080 CATCTTGTAT
*
59770090 ATTTAAAATTTAATCTCTTGCTTCTAT
1 ATTTAAAATTTAATCTCTTGCTTC-AA
*
59770117 TTTTAATAATTTAATCTCTCTGCTTTTCAA
1 ATTTAA-AATTTAATCTCT-TGC--TTCAA
59770147 ATTTGAAAATTTAA
1 ATTT-AAAATTTAA
59770161 GTCCATAGTC
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
27 5 0.14
28 12 0.33
29 3 0.08
30 11 0.31
31 5 0.14
ACGTcount: A:0.32, C:0.13, G:0.04, T:0.51
Consensus pattern (26 bp):
ATTTAAAATTTAATCTCTTGCTTCAA
Found at i:59772585 original size:13 final size:13
Alignment explanation
Indices: 59772567--59772596 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
59772557 GTTGCATCAC
59772567 TAAATTTACTGTT
1 TAAATTTACTGTT
59772580 TAAATTTACTGTT
1 TAAATTTACTGTT
59772593 TAAA
1 TAAA
59772597 GATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (13 bp):
TAAATTTACTGTT
Found at i:59791413 original size:20 final size:20
Alignment explanation
Indices: 59791385--59791422 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
59791375 TCACTAAATT
59791385 ATTAATAAATTTATATTTTA
1 ATTAATAAATTTATATTTTA
* *
59791405 ATTATTAAATTTTTATTT
1 ATTAATAAATTTATATTT
59791423 AATGCACGTG
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:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
ATTAATAAATTTATATTTTA
Found at i:59799997 original size:19 final size:21
Alignment explanation
Indices: 59799973--59800013 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
59799963 ACACTTCACT
59799973 TTCTTTGC-TTTC-TTTTCTC
1 TTCTTTGCTTTTCATTTTCTC
*
59799992 TTCTTTTCTTTTCATTTTCTC
1 TTCTTTGCTTTTCATTTTCTC
59800013 T
1 T
59800014 CGATTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 7 0.37
20 4 0.21
21 8 0.42
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCTTTGCTTTTCATTTTCTC
Found at i:59803419 original size:120 final size:120
Alignment explanation
Indices: 59803206--59803451 Score: 465
Period size: 120 Copynumber: 2.0 Consensus size: 120
59803196 CGTTGGAATC
* *
59803206 ATCATCGATTGGTTTTGTCGTCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGTT
1 ATCATCGATTGGTTTTGTCATCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
59803271 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGACTATT
66 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGACTATT
59803326 ATCATCGATTGGTTTTGTCATCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
1 ATCATCGATTGGTTTTGTCATCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
*
59803391 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGGCTATT
66 GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGACTATT
59803446 ATCATC
1 ATCATC
59803452 CATGTACTCC
Statistics
Matches: 123, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 123 1.00
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.35
Consensus pattern (120 bp):
ATCATCGATTGGTTTTGTCATCCTCCACCAACTCTTCATATTCGGACAGTCCCAGAGCCAAAGAT
GCTTAAGTGATGGGAAGAATGATTGTGGTTCTCCTTGACTTCCTTTTGGACTATT
Found at i:59813272 original size:21 final size:21
Alignment explanation
Indices: 59813247--59813287 Score: 66
Period size: 20 Copynumber: 2.0 Consensus size: 21
59813237 TTATTTTTTA
*
59813247 ATTTTTTTAATG-TTTAAAAT
1 ATTTTTTAAATGTTTTAAAAT
59813267 ATTTTTTAAATGTTTTAAAAT
1 ATTTTTTAAATGTTTTAAAAT
59813288 TTTAAAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.37, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
ATTTTTTAAATGTTTTAAAAT
Found at i:59814902 original size:15 final size:15
Alignment explanation
Indices: 59814882--59814914 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
59814872 AATTCTAATG
59814882 TAATAAA-AGTAAAAA
1 TAATAAAGA-TAAAAA
59814897 TAATAAAGATAAAAA
1 TAATAAAGATAAAAA
59814912 TAA
1 TAA
59814915 GCAAAAAGGA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 16 0.94
16 1 0.06
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.21
Consensus pattern (15 bp):
TAATAAAGATAAAAA
Found at i:59819624 original size:42 final size:42
Alignment explanation
Indices: 59819560--59819646 Score: 165
Period size: 42 Copynumber: 2.1 Consensus size: 42
59819550 AATCAGAGAG
*
59819560 ATAAAGAAATTGCAACCTCAAGATGAATACACTATGAACTTC
1 ATAAAGAAATTGCAACCACAAGATGAATACACTATGAACTTC
59819602 ATAAAGAAATTGCAACCACAAGATGAATACACTATGAACTTC
1 ATAAAGAAATTGCAACCACAAGATGAATACACTATGAACTTC
59819644 ATA
1 ATA
59819647 GTACAAAGAA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.47, C:0.18, G:0.11, T:0.23
Consensus pattern (42 bp):
ATAAAGAAATTGCAACCACAAGATGAATACACTATGAACTTC
Found at i:59826857 original size:10 final size:10
Alignment explanation
Indices: 59826844--59826869 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
59826834 TTCAAAGGTG
59826844 AATAAAGTAA
1 AATAAAGTAA
59826854 AATAAAGTAA
1 AATAAAGTAA
59826864 AATAAA
1 AATAAA
59826870 AACTAAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.73, C:0.00, G:0.08, T:0.19
Consensus pattern (10 bp):
AATAAAGTAA
Found at i:59829617 original size:216 final size:216
Alignment explanation
Indices: 59828922--59829578 Score: 1251
Period size: 216 Copynumber: 3.0 Consensus size: 216
59828912 ATAACTCCAG
* * *
59828922 CTCCTTGCAGTCCTCTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGTG
1 CTCCTTGCAGTCCTTTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
* *
59828987 ACCTCAATCCATTGCAGTTATGAATTTTTAATCTTTTCAATTGAACAAGATGTTGAAGCCCAATG
66 ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
*
59829052 GGGAGAGACACCAGCTTTGGAATATTATCAATCTTCAAATGAGAGAGATTCTTAAGGGGTTCCCA
131 GGGAGAGACACCAGCTTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
59829117 TTGCATGCCCTCTAAATCAAC
196 TTGCATGCCCTCTAAATCAAC
59829138 CTCCTTGCAGTCCTTTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
1 CTCCTTGCAGTCCTTTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
59829203 ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
66 ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
*
59829268 GGGAGAGACACCAGCGTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
131 GGGAGAGACACCAGCTTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
59829333 TTGCATGCCCTCTAAATCAAC
196 TTGCATGCCCTCTAAATCAAC
59829354 CTCCTTGCAGTCCTTTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
1 CTCCTTGCAGTCCTTTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
59829419 ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
66 ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
59829484 GGGAGAGACACCAGCTTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
131 GGGAGAGACACCAGCTTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
59829549 TTGCATGCCCTCTAAATCAAC
196 TTGCATGCCCTCTAAATCAAC
59829570 CTCCTTGCA
1 CTCCTTGCA
59829579 ATCTCTTATT
Statistics
Matches: 433, Mismatches: 8, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
216 433 1.00
ACGTcount: A:0.31, C:0.21, G:0.20, T:0.28
Consensus pattern (216 bp):
CTCCTTGCAGTCCTTTACTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGCG
ACCTCAATCCATTGCAGTTATGAATTTTTAATGTTTTCAATTGAAGAAGATGTTGAAGCCCAATG
GGGAGAGACACCAGCTTTGGAATATTATCAATCTCCAAATGAGAGAGATTCTTAAGGGGTTCCCA
TTGCATGCCCTCTAAATCAAC
Found at i:59833031 original size:15 final size:16
Alignment explanation
Indices: 59832998--59833035 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
59832988 GTCATTCACC
*
59832998 ATTAAAATCAAATATT
1 ATTAAATTCAAATATT
*
59833014 ATTAAATTCGAATA-T
1 ATTAAATTCAAATATT
59833029 ATTAAAT
1 ATTAAAT
59833036 CAATAATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (16 bp):
ATTAAATTCAAATATT
Found at i:59836955 original size:30 final size:32
Alignment explanation
Indices: 59836894--59836970 Score: 97
Period size: 30 Copynumber: 2.4 Consensus size: 32
59836884 ACGTTAGCAA
59836894 TTAATTATTTAAAAATATTTTCTTATAATTTTT
1 TTAATT-TTTAAAAATATTTTCTTATAATTTTT
59836927 TTAATTTTT-AAAATATATTT-TT-TAATTTTT
1 TTAATTTTTAAAAATAT-TTTCTTATAATTTTT
* *
59836957 TAAAATTTTAAAAA
1 TTAATTTTTAAAAA
59836971 ATAATTACTG
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
30 15 0.38
31 13 0.32
32 6 0.15
33 6 0.15
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.58
Consensus pattern (32 bp):
TTAATTTTTAAAAATATTTTCTTATAATTTTT
Found at i:59840962 original size:31 final size:31
Alignment explanation
Indices: 59840924--59840988 Score: 130
Period size: 31 Copynumber: 2.1 Consensus size: 31
59840914 ACGTCTCAAG
59840924 TGAAGTCAGCTTCCCTATTCCACGTGGCATA
1 TGAAGTCAGCTTCCCTATTCCACGTGGCATA
59840955 TGAAGTCAGCTTCCCTATTCCACGTGGCATA
1 TGAAGTCAGCTTCCCTATTCCACGTGGCATA
59840986 TGA
1 TGA
59840989 GTTAAACTAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (31 bp):
TGAAGTCAGCTTCCCTATTCCACGTGGCATA
Found at i:59841125 original size:50 final size:50
Alignment explanation
Indices: 59841070--59841174 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
59841060 AGTAGTAGCA
*
59841070 TTTTATTTTTCTTTTAAATATACATATATTTATTAAGAAAGGATCGAAGC
1 TTTTATTTTTCTTTTAAATATACATATATTTATTAAAAAAGGATCGAAGC
*
59841120 TTTTATTTTTCTTTTAAATATACATATATTTATTAAAAAAGGGTCGAAGC
1 TTTTATTTTTCTTTTAAATATACATATATTTATTAAAAAAGGATCGAAGC
59841170 TTTTA
1 TTTTA
59841175 ACTTGTTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.35, C:0.08, G:0.10, T:0.48
Consensus pattern (50 bp):
TTTTATTTTTCTTTTAAATATACATATATTTATTAAAAAAGGATCGAAGC
Found at i:59841299 original size:2 final size:2
Alignment explanation
Indices: 59841292--59841320 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
59841282 ATTGTGGGTC
59841292 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59841321 CATGAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:59841660 original size:30 final size:32
Alignment explanation
Indices: 59841602--59841668 Score: 95
Period size: 30 Copynumber: 2.2 Consensus size: 32
59841592 TAATAATGAT
59841602 AAAATTATAATTTAATCCTCTAAAAAATTATA
1 AAAATTATAATTTAATCCTCTAAAAAATTATA
*
59841634 AAAATT-TAATTTAA--CTCTTTAAAAATTATA
1 AAAATTATAATTTAATCCTC-TAAAAAATTATA
59841664 AAAAT
1 AAAAT
59841669 ATACTACTAT
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
29 3 0.09
30 16 0.48
31 8 0.24
32 6 0.18
ACGTcount: A:0.54, C:0.07, G:0.00, T:0.39
Consensus pattern (32 bp):
AAAATTATAATTTAATCCTCTAAAAAATTATA
Found at i:59843070 original size:29 final size:30
Alignment explanation
Indices: 59843038--59843120 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
59843028 ATTTTAATTT
* *
59843038 ATAAATAAATTTATTTTTATAATA-TAAAA
1 ATAAATAAATTTATTTTAAAAATAGTAAAA
* *
59843067 ATAAAT-ATTTTATATTTAAAAATAGTGAAA
1 ATAAATAAATTTAT-TTTAAAAATAGTAAAA
*
59843097 ATAAATAAATATATTTTAAAAATA
1 ATAAATAAATTTATTTTAAAAATA
59843121 TTATATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.13
29 14 0.31
30 20 0.44
31 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAATAAATTTATTTTAAAAATAGTAAAA
Found at i:59843086 original size:21 final size:22
Alignment explanation
Indices: 59843026--59843090 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 22
59843016 ATTTTATTCT
*
59843026 TTATTTTA-ATTTATAAATAAA
1 TTATTTTATATTTAAAAATAAA
*
59843047 TTTATTTTTATAATATAAAAATAAA
1 -TTA-TTTTAT-ATTTAAAAATAAA
59843072 -TATTTTATATTTAAAAATA
1 TTATTTTATATTTAAAAATA
59843091 GTGAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 10 0.27
22 9 0.24
23 7 0.19
25 11 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTTATATTTAAAAATAAA
Found at i:59846229 original size:48 final size:48
Alignment explanation
Indices: 59846146--59846240 Score: 140
Period size: 48 Copynumber: 2.0 Consensus size: 48
59846136 TTCTTGGCTT
* *
59846146 AAAAACGCCTAAGTCAGCCTAACTTCCACCGATAAAGGATTCAACAGC
1 AAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACAGC
59846194 AAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAACAG
1 AAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAACAG
59846241 AATTCCCTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
47 4 0.09
48 39 0.91
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.16
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAACAGC
Found at i:59847532 original size:48 final size:48
Alignment explanation
Indices: 59847449--59847540 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
59847439 TTCTTGGCTT
* *
59847449 AAAAACGCCTAAGTCAACCTAACTTCCACCGATAAAGGATTCAATAGC
1 AAAAACGCCTAAGTCAACCTAACTTCCAACAATAAAGGATTCAATAGC
*
59847497 AAAAACGCCTAAGTC-AGCTCAAC-TCGCAACAATAAAGGATTCAA
1 AAAAACGCCTAAGTCAACCT-AACTTC-CAACAATAAAGGATTCAA
59847541 CAGAATTCCC
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
47 5 0.13
48 34 0.87
ACGTcount: A:0.43, C:0.26, G:0.13, T:0.17
Consensus pattern (48 bp):
AAAAACGCCTAAGTCAACCTAACTTCCAACAATAAAGGATTCAATAGC
Found at i:59856152 original size:26 final size:26
Alignment explanation
Indices: 59856123--59856174 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
59856113 GACGAAAAAG
59856123 TTTGTCAATCTGATGAAGCATGCTGA
1 TTTGTCAATCTGATGAAGCATGCTGA
59856149 TTTGTCAATCTGATGAAGCATGCTGA
1 TTTGTCAATCTGATGAAGCATGCTGA
59856175 AGATGGTATC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.35
Consensus pattern (26 bp):
TTTGTCAATCTGATGAAGCATGCTGA
Found at i:59862430 original size:31 final size:30
Alignment explanation
Indices: 59862394--59862458 Score: 78
Period size: 29 Copynumber: 2.1 Consensus size: 30
59862384 AAAATATTAA
*
59862394 AAAATATTTCCTTATAAATTTTTT-AATTTTT
1 AAAATATTT--TTATAAATTTTTTAAAATTTT
* *
59862425 AAAATATTTTTTTGAATTTTTTAAAATTTT
1 AAAATATTTTTATAAATTTTTTAAAATTTT
59862455 AAAA
1 AAAA
59862459 ATGAGTAATT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
29 11 0.37
30 10 0.33
31 9 0.30
ACGTcount: A:0.40, C:0.03, G:0.02, T:0.55
Consensus pattern (30 bp):
AAAATATTTTTATAAATTTTTTAAAATTTT
Found at i:59862442 original size:21 final size:21
Alignment explanation
Indices: 59862412--59862451 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
59862402 TCCTTATAAA
59862412 TTTTTTAA-TTTTTAAAATAT
1 TTTTTTAATTTTTTAAAATAT
59862432 TTTTTTGAATTTTTTAAAAT
1 TTTTTT-AATTTTTTAAAAT
59862452 TTTAAAAATG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 6 0.33
21 2 0.11
22 10 0.56
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (21 bp):
TTTTTTAATTTTTTAAAATAT
Found at i:59864510 original size:3 final size:3
Alignment explanation
Indices: 59864502--59864556 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
59864492 TTTGATAAGA
59864502 TAT TAT TAT TAT 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
59864550 TAT TAT T
1 TAT TAT T
59864557 TGCTCTGGGC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:59864839 original size:21 final size:21
Alignment explanation
Indices: 59864815--59864855 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
59864805 ATTATATCAA
59864815 ATTGTAACAGAATTAACATTT
1 ATTGTAACAGAATTAACATTT
59864836 ATTGTAACAGAATTAACATT
1 ATTGTAACAGAATTAACATT
59864856 AACAGAGTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.44, C:0.10, G:0.10, T:0.37
Consensus pattern (21 bp):
ATTGTAACAGAATTAACATTT
Found at i:59870018 original size:16 final size:16
Alignment explanation
Indices: 59869997--59870029 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
59869987 TATTAAGAGA
59869997 AAACATAAATATATAT
1 AAACATAAATATATAT
59870013 AAACATAAATATATAT
1 AAACATAAATATATAT
59870029 A
1 A
59870030 TATATATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (16 bp):
AAACATAAATATATAT
Found at i:59891058 original size:10 final size:10
Alignment explanation
Indices: 59891023--59891069 Score: 51
Period size: 10 Copynumber: 4.5 Consensus size: 10
59891013 TTAAAAAAAT
59891023 ATTTTCTTATAA
1 ATTTT-TTA-AA
*
59891035 A-TTTTAAAA
1 ATTTTTTAAA
59891044 TATTTTTTAAA
1 -ATTTTTTAAA
59891055 ATTTTTTAAA
1 ATTTTTTAAA
59891065 ATTTT
1 ATTTT
59891070 AAAAAATATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 18 0.58
11 10 0.32
12 1 0.03
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (10 bp):
ATTTTTTAAA
Found at i:59891066 original size:22 final size:22
Alignment explanation
Indices: 59891018--59891059 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
59891008 AAATATTAAA
59891018 AAAATATTTTCTTATAAATTTT
1 AAAATATTTTCTTATAAATTTT
59891040 AAAATATTTT-TTA-AAATTTT
1 AAAATATTTTCTTATAAATTTT
59891060 TTAAAATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
20 7 0.35
21 3 0.15
22 10 0.50
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (22 bp):
AAAATATTTTCTTATAAATTTT
Found at i:59891383 original size:2 final size:2
Alignment explanation
Indices: 59891376--59891400 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
59891366 TTATTATTGT
59891376 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
59891401 TTTTTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59891660 original size:24 final size:24
Alignment explanation
Indices: 59891633--59891697 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 24
59891623 ATCAAATTCT
* *
59891633 ATTTTTTATTTAATTTATAAATAA
1 ATTTTTTATTTAATATAAAAATAA
*
59891657 ATTTATTTTTTATAATATAAAAATAA
1 ATTT-TTTATT-TAATATAAAAATAA
59891683 ATCTTTTATATTTAA
1 AT-TTTT-TATTTAA
59891698 AAATAGTGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
24 4 0.12
25 5 0.15
26 19 0.58
27 5 0.15
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTTTATTTAATATAAAAATAA
Found at i:59891672 original size:26 final size:28
Alignment explanation
Indices: 59891620--59891684 Score: 80
Period size: 26 Copynumber: 2.3 Consensus size: 28
59891610 TATCCGAAAC
*
59891620 TAAATCAAATTCTATTTTTTATTTAATTTA
1 TAAAT-AAATTCTATTTTTTA-TTAATATA
59891650 TAAATAAATT-TATTTTTTA-TAATATA
1 TAAATAAATTCTATTTTTTATTAATATA
*
59891676 AAAATAAAT
1 TAAATAAAT
59891685 CTTTTATATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
26 14 0.42
28 9 0.27
29 5 0.15
30 5 0.15
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (28 bp):
TAAATAAATTCTATTTTTTATTAATATA
Found at i:59893475 original size:27 final size:28
Alignment explanation
Indices: 59893419--59893478 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
59893409 TAATTTATAA
*
59893419 TTTAATATAAAATATAATTTTAATTATT
1 TTTAATATAAAACATAATTTTAATTATT
* *
59893447 TTTAATAT-AAACATAGTTTTGA-TATT
1 TTTAATATAAAACATAATTTTAATTATT
59893473 TTTAAT
1 TTTAAT
59893479 TATTATTTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
26 10 0.34
27 11 0.38
28 8 0.28
ACGTcount: A:0.42, C:0.02, G:0.03, T:0.53
Consensus pattern (28 bp):
TTTAATATAAAACATAATTTTAATTATT
Found at i:59895141 original size:102 final size:102
Alignment explanation
Indices: 59894960--59895243 Score: 378
Period size: 102 Copynumber: 2.8 Consensus size: 102
59894950 TATCGATGAA
* * * * * * *
59894960 CACGCGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGAT-AAGTAATGTTCACATGGGTAGTA
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGGTAAACT-ATGATCACATGTGTAGTA
59895024 CTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* * * *
59895062 CACGTGTGTAGTACTGTGTGAATGCTACCACGTGTCTCGGTAAACTACGGTCACATGTGTAGTAC
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGGTAAACTATGATCACATGTGTAGTAC
59895127 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
66 TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
* * *
59895164 CACGTGTGTAGTACTGAGTGAAGGCTACTACGTGAGC-C-GTAAAACT-TGATCACGTGTGTAGT
1 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTG-TCTCGGT-AAACTATGATCACATGTGTAGT
*
59895226 ACTATGTGAAGGCTACTA
64 ACTAAGTGAAGGCTACTA
59895244 CGTGAATTGT
Statistics
Matches: 161, Mismatches: 18, Indels: 7
0.87 0.10 0.04
Matches are distributed among these distances:
101 32 0.20
102 125 0.78
103 4 0.02
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (102 bp):
CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTCTCGGTAAACTATGATCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACCAAGAAGCTTTGAG
Found at i:59895282 original size:49 final size:50
Alignment explanation
Indices: 59894960--59895296 Score: 244
Period size: 51 Copynumber: 6.7 Consensus size: 50
59894950 TATCGATGAA
* * * * * *
59894960 CACGCGTGTAGTATTGTGTGAAGGCTACTACGTGTATCGATAAGTAA--TGTT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAA--AACTTGAT
* * * * * *
59895011 CACATGGGTAGTACTAAGTGAAGGCTACTATGTGTACC--AAGAAGCTTTGAG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAA-AA-C-TTGAT
* * * * * *
59895062 CACGTGTGTAGTACTGTGTGAATGCTACCACGTG-TCTCGGT-AAACTACGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAAC-C-GTAAAACT-TGAT
* * * * *
59895113 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACC--AAGAAGCTTTGAG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAA-AA-C-TTGAT
*
59895164 CACGTGTGTAGTACTGA-GTGAAGGCTACTACGTGAGCCGTAAAACTTGAT
1 CACGTGTGTAGTACT-ATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
**
59895214 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAATTGTAAAAC-TGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
*
59895263 CACGTGTGTAGTACTATGTGAAGACTACTACGTG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG
59895297 TATCGAATGA
Statistics
Matches: 227, Mismatches: 41, Indels: 38
0.74 0.13 0.12
Matches are distributed among these distances:
47 2 0.01
48 2 0.01
49 39 0.17
50 48 0.21
51 126 0.56
52 7 0.03
53 3 0.01
ACGTcount: A:0.28, C:0.17, G:0.27, T:0.29
Consensus pattern (50 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGTAAAACTTGAT
Found at i:59896331 original size:2 final size:2
Alignment explanation
Indices: 59896324--59896367 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
59896314 AGTTTAAACT
*
59896324 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59896366 TA
1 TA
59896368 AAATATCGTT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:59901786 original size:216 final size:216
Alignment explanation
Indices: 59901535--59901976 Score: 762
Period size: 216 Copynumber: 2.0 Consensus size: 216
59901525 TTCAAGGAAA
**
59901535 GTGAGATGTTGGAACACAGGAAAGAGTGACCTCAATCCATGGCA-TTCACGAATTTCTAATGTTT
1 GTGAGATGTTCAAACACAGGAAAGAGTGACCTCAATCCATGGCAGTTC-CGAATTTCTAATGTTT
*
59901599 TCAATTGAACAAGATGTTGAAGAGAAATGAGGAGAGACACCAGCTTTGGAATATTATCAATCTTC
65 CCAATTGAACAAGATGTTGAAGAGAAATGAGGAGAGACACCAGCTTTGGAATATTATCAATCTTC
*
59901664 AATTGAGAGAGATTCTTAAGGGGTTCCCATTGCATGCCCTCTAAATCAACCTCCTTGCAATCTCT
130 AAATGAGAGAGATTCTTAAGGGGTTCCCATTGCATGCCCTCTAAATCAACCTCCTTGCAATCTCT
59901729 TATTGTTAATCTTTTGAGGCTG
195 TATTGTTAATCTTTTGAGGCTG
* * * *
59901751 GTGAGATGTTCAAACACAGG-AAGCAGTGACCTCAATCGATTGCAGTTCTGAATTTTTAATGTTT
1 GTGAGATGTTCAAACACAGGAAAG-AGTGACCTCAATCCATGGCAGTTCCGAATTTCTAATGTTT
*
59901815 CCAATTGAACAAGATGTTGAAGAGAAATGGGGAGAGACACCAGCTTTGGAATATTATCAATCTTC
65 CCAATTGAACAAGATGTTGAAGAGAAATGAGGAGAGACACCAGCTTTGGAATATTATCAATCTTC
*
59901880 AAATGAGAGAGATTCTTAAGTGGTTCCCATTGCATGCCCTCTAAATCAACCTCCTTGCAATCTCT
130 AAATGAGAGAGATTCTTAAGGGGTTCCCATTGCATGCCCTCTAAATCAACCTCCTTGCAATCTCT
59901945 TATTGTTAATCTTTTGAGGCTG
195 TATTGTTAATCTTTTGAGGCTG
59901967 GTGAGATGTT
1 GTGAGATGTT
59901977 GCAGGCACTC
Statistics
Matches: 214, Mismatches: 10, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
215 3 0.01
216 208 0.97
217 3 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (216 bp):
GTGAGATGTTCAAACACAGGAAAGAGTGACCTCAATCCATGGCAGTTCCGAATTTCTAATGTTTC
CAATTGAACAAGATGTTGAAGAGAAATGAGGAGAGACACCAGCTTTGGAATATTATCAATCTTCA
AATGAGAGAGATTCTTAAGGGGTTCCCATTGCATGCCCTCTAAATCAACCTCCTTGCAATCTCTT
ATTGTTAATCTTTTGAGGCTG
Found at i:59905777 original size:2 final size:2
Alignment explanation
Indices: 59905772--59905806 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
59905762 AAAAAAAAAA
59905772 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
59905807 GGACTTGGGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:59911399 original size:225 final size:225
Alignment explanation
Indices: 59911008--59911471 Score: 874
Period size: 225 Copynumber: 2.1 Consensus size: 225
59910998 CAGATTTGTT
* *
59911008 AGATGTTGAAGCCACTCCGGCAGATGCCGACACTTTGGAATATTTTGCAGCGATAGAGAGCGTAG
1 AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTGCAGCCATAGAGAGCGTAG
59911073 GCTTGTATGATCTTGGAATATTTGGATGCCAGCTCCAGATAACTCCAGCTCCTTGCAGTCCTCTA
66 GCTTGTATGATCTTGGAATATTTGGATGCCAGCTCCAGATAACTCCAGCTCCTTGCAGTCCTCTA
59911138 CTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGTGACCTCAATCCATTGCAG
131 CTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGTGACCTCAATCCATTGCAG
59911203 TTACGAATTTTTAATGTTTTCAATTGAACA
196 TTACGAATTTTTAATGTTTTCAATTGAACA
59911233 AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTGCAGCCATAGAGAGCGTAG
1 AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTGCAGCCATAGAGAGCGTAG
* *
59911298 GTTTGTATGATCTTGGAATATTTGGATGCCAGCTCCAGATAACTCCAGCTCCTTGCAGTCCTTTA
66 GCTTGTATGATCTTGGAATATTTGGATGCCAGCTCCAGATAACTCCAGCTCCTTGCAGTCCTCTA
*
59911363 CTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAGCAGTGACCTCAATCCATTGCAG
131 CTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGTGACCTCAATCCATTGCAG
*
59911428 TTATGAATTTTTAATGTTTTCAATTGAACA
196 TTACGAATTTTTAATGTTTTCAATTGAACA
59911458 AGATGTTGAAGCCA
1 AGATGTTGAAGCCA
59911472 AATGGGGAGA
Statistics
Matches: 233, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
225 233 1.00
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (225 bp):
AGATGTTGAAGCCACTCCGGAAGATGCCGACACTTTGGAATATTTTGCAGCCATAGAGAGCGTAG
GCTTGTATGATCTTGGAATATTTGGATGCCAGCTCCAGATAACTCCAGCTCCTTGCAGTCCTCTA
CTTCAAACTCTTCAAGGAAAGTGAGATGTTGGAACACAGGAAACAGTGACCTCAATCCATTGCAG
TTACGAATTTTTAATGTTTTCAATTGAACA
Found at i:59912876 original size:12 final size:12
Alignment explanation
Indices: 59912858--59912892 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
59912848 TCCCTTAAAC
59912858 AAAGGAATTAAT
1 AAAGGAATTAAT
*
59912870 GAAGGAATTAAT
1 AAAGGAATTAAT
59912882 AAAGG-ATTAAT
1 AAAGGAATTAAT
59912893 TGATATGTGG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 6 0.29
12 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.20, T:0.26
Consensus pattern (12 bp):
AAAGGAATTAAT
Found at i:59915284 original size:16 final size:14
Alignment explanation
Indices: 59915263--59915308 Score: 60
Period size: 12 Copynumber: 3.3 Consensus size: 14
59915253 TTTTGGTTTT
59915263 TTTTTAAGATATTTTA
1 TTTTTAA-ATA-TTTA
59915279 TTTTTAAATA--TA
1 TTTTTAAATATTTA
59915291 TTTTTAAATATTTA
1 TTTTTAAATATTTA
59915305 TTTT
1 TTTT
59915309 ACACATACAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 12 0.43
14 6 0.21
15 3 0.11
16 7 0.25
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (14 bp):
TTTTTAAATATTTA
Found at i:59916526 original size:29 final size:30
Alignment explanation
Indices: 59916494--59916576 Score: 98
Period size: 30 Copynumber: 2.8 Consensus size: 30
59916484 ATTTTAATTT
* *
59916494 ATAAATAAATTTATTTTTATAATA-TAAAA
1 ATAAATAAATTTATTTTAAAAATAGTAAAA
* *
59916523 ATAAAT-ATTTTATATTTAAAAATAGTGAAA
1 ATAAATAAATTTAT-TTTAAAAATAGTAAAA
*
59916553 ATAAATAAATATATTTTAAAAATA
1 ATAAATAAATTTATTTTAAAAATA
59916577 TTATATAAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
28 6 0.13
29 14 0.31
30 20 0.44
31 5 0.11
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
ATAAATAAATTTATTTTAAAAATAGTAAAA
Found at i:59916542 original size:21 final size:22
Alignment explanation
Indices: 59916482--59916546 Score: 71
Period size: 25 Copynumber: 2.9 Consensus size: 22
59916472 ATTATATTCT
*
59916482 TTATTTTA-ATTTATAAATAAA
1 TTATTTTATATTTAAAAATAAA
*
59916503 TTTATTTTTATAATATAAAAATAAA
1 -TTA-TTTTAT-ATTTAAAAATAAA
59916528 -TATTTTATATTTAAAAATA
1 TTATTTTATATTTAAAAATA
59916547 GTGAAAATAA
Statistics
Matches: 37, Mismatches: 3, Indels: 7
0.79 0.06 0.15
Matches are distributed among these distances:
21 10 0.27
22 9 0.24
23 7 0.19
25 11 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
TTATTTTATATTTAAAAATAAA
Found at i:59922458 original size:3 final size:3
Alignment explanation
Indices: 59922450--59922479 Score: 51
Period size: 3 Copynumber: 10.0 Consensus size: 3
59922440 AAGTGACTTC
*
59922450 TCA TCA TCA TCA TCA TCA TCT TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
59922480 GAATCAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:59930006 original size:22 final size:22
Alignment explanation
Indices: 59929981--59930055 Score: 132
Period size: 22 Copynumber: 3.4 Consensus size: 22
59929971 AAGTATAAGT
*
59929981 TTAGTTCGTTAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
59930003 TTAGTACGTTAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
*
59930025 TTAGTACGTGAAACATGAGAGC
1 TTAGTACGTTAAACATGAGAGC
59930047 TTAGTACGT
1 TTAGTACGT
59930056 ACTATCAACA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 51 1.00
ACGTcount: A:0.33, C:0.13, G:0.24, T:0.29
Consensus pattern (22 bp):
TTAGTACGTTAAACATGAGAGC
Found at i:59930338 original size:26 final size:24
Alignment explanation
Indices: 59930295--59930356 Score: 63
Period size: 25 Copynumber: 2.5 Consensus size: 24
59930285 AAACTTAGGA
* * *
59930295 TAATATATATAA-ACCAAAACTGTT
1 TAATATAAATAATACCAAAAAT-CT
59930319 TAATATAAATAATACACAAAAATCT
1 TAATATAAATAATAC-CAAAAATCT
*
59930344 TAAAATAAATAAT
1 TAATATAAATAAT
59930357 GATTGAACTG
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
24 11 0.34
25 15 0.47
26 6 0.19
ACGTcount: A:0.58, C:0.10, G:0.02, T:0.31
Consensus pattern (24 bp):
TAATATAAATAATACCAAAAATCT
Found at i:59934986 original size:18 final size:18
Alignment explanation
Indices: 59934937--59934986 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
59934927 AAGGAAATAA
59934937 AGAAAGAAAAAG-AACAG
1 AGAAAGAAAAAGAAACAG
* *
59934954 AG-AAGTAGAACGAAACAG
1 AGAAAG-AAAAAGAAACAG
59934972 AGAAAGAAAAAGAAA
1 AGAAAGAAAAAGAAA
59934987 AAAGGAAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
16 3 0.12
17 6 0.23
18 14 0.54
19 3 0.12
ACGTcount: A:0.68, C:0.06, G:0.24, T:0.02
Consensus pattern (18 bp):
AGAAAGAAAAAGAAACAG
Found at i:59939118 original size:30 final size:30
Alignment explanation
Indices: 59939084--59939147 Score: 76
Period size: 30 Copynumber: 2.1 Consensus size: 30
59939074 CAAATTTGGG
* *
59939084 AAATTCGAATTAAGC-CTTCAATTTTTTTGA
1 AAATTCGAATTAAACTCCTCAATTTTTTT-A
**
59939114 AAATTTTAATTAAACTCCTCAATTTTTTTA
1 AAATTCGAATTAAACTCCTCAATTTTTTTA
59939144 AAAT
1 AAAT
59939148 CTTCACTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 17 0.59
31 12 0.41
ACGTcount: A:0.38, C:0.12, G:0.05, T:0.45
Consensus pattern (30 bp):
AAATTCGAATTAAACTCCTCAATTTTTTTA
Found at i:59939297 original size:15 final size:15
Alignment explanation
Indices: 59939258--59939301 Score: 53
Period size: 11 Copynumber: 3.3 Consensus size: 15
59939248 TTTCGCTACC
59939258 TTGTTGAAAATTACA
1 TTGTTGAAAATTACA
59939273 TT-TT---AATTACA
1 TTGTTGAAAATTACA
59939284 TTGTTGAAAATTAC-
1 TTGTTGAAAATTACA
59939298 TTGT
1 TTGT
59939302 ATTTTGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 9
0.74 0.00 0.26
Matches are distributed among these distances:
11 9 0.36
12 2 0.08
14 6 0.24
15 8 0.32
ACGTcount: A:0.34, C:0.07, G:0.11, T:0.48
Consensus pattern (15 bp):
TTGTTGAAAATTACA
Found at i:59941760 original size:3 final size:3
Alignment explanation
Indices: 59941752--59941790 Score: 60
Period size: 3 Copynumber: 13.0 Consensus size: 3
59941742 AAGTGACTTC
* *
59941752 TCA TCA TCA TCA TAA TCA TCA TCA TCA TAA TCA TCA TCA
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA
59941791 GAATCAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (3 bp):
TCA
Found at i:59941772 original size:15 final size:15
Alignment explanation
Indices: 59941752--59941790 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
59941742 AAGTGACTTC
59941752 TCATCATCATCATAA
1 TCATCATCATCATAA
59941767 TCATCATCATCATAA
1 TCATCATCATCATAA
59941782 TCATCATCA
1 TCATCATCA
59941791 GAATCAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.38, C:0.28, G:0.00, T:0.33
Consensus pattern (15 bp):
TCATCATCATCATAA
Found at i:59946083 original size:21 final size:20
Alignment explanation
Indices: 59946059--59946114 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
59946049 TTTAAAAAAT
* *
59946059 ATTTTCTTATAATTTTTTTTA
1 ATTTT-TTAAAATTTTTTTGA
59946080 A-TTTTTAAAATATTTTTTGA
1 ATTTTTTAAAAT-TTTTTTGA
59946100 ATTTTTTAAAATTTT
1 ATTTTTTAAAATTTT
59946115 AAAAAATAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 6 0.19
20 14 0.45
21 11 0.35
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (20 bp):
ATTTTTTAAAATTTTTTTGA
Found at i:59946113 original size:30 final size:32
Alignment explanation
Indices: 59946048--59946119 Score: 85
Period size: 30 Copynumber: 2.3 Consensus size: 32
59946038 AAAAATATAC
* * **
59946048 ATTTAAAAAATATTTTCTTATAATTTTTTTTA
1 ATTTTAAAAATATTTTCTTAGAATTTTTTAAA
*
59946080 ATTTTTAAAATATTTT-TT-GAATTTTTTAAA
1 ATTTTAAAAATATTTTCTTAGAATTTTTTAAA
59946110 ATTTTAAAAA
1 ATTTTAAAAA
59946120 ATAATTAATT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
30 18 0.53
31 2 0.06
32 14 0.41
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.57
Consensus pattern (32 bp):
ATTTTAAAAATATTTTCTTAGAATTTTTTAAA
Found at i:59948548 original size:19 final size:21
Alignment explanation
Indices: 59948505--59948546 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
59948495 TTTGCCTGCC
59948505 ATTGGCACTACTTTGAAATAT
1 ATTGGCACTACTTTGAAATAT
59948526 ATTGGCACTACTTTGAAATAT
1 ATTGGCACTACTTTGAAATAT
59948547 TGCTGATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.14, G:0.14, T:0.38
Consensus pattern (21 bp):
ATTGGCACTACTTTGAAATAT
Found at i:59967569 original size:41 final size:41
Alignment explanation
Indices: 59967493--59967576 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
59967483 GATAAGAGAT
59967493 AAAACCGATCGAGCTTTCAATTCTCAAATTCAAATTTATAG
1 AAAACCGATCGAGCTTTCAATTCTCAAATTCAAATTTATAG
59967534 AAAACCGATCGAGCTTTCAATTCTCAAATTCAAATTTATAG
1 AAAACCGATCGAGCTTTCAATTCTCAAATTCAAATTTATAG
59967575 AA
1 AA
59967577 GACTATTTCC
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.31
Consensus pattern (41 bp):
AAAACCGATCGAGCTTTCAATTCTCAAATTCAAATTTATAG
Found at i:59970698 original size:2 final size:2
Alignment explanation
Indices: 59970691--59970720 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
59970681 TTCTATCTTA
59970691 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
59970721 TATTTTTATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:59971103 original size:30 final size:32
Alignment explanation
Indices: 59971042--59971103 Score: 76
Period size: 30 Copynumber: 2.0 Consensus size: 32
59971032 TTGTTTTTAA
* *
59971042 AAAAATATTTATATTATTTTAATTTAATATTT
1 AAAAATATTTAGATTATTTTAATATAATATTT
59971074 AAAAAT-TTTAGATT-TTTT-ATATAATTATTT
1 AAAAATATTTAGATTATTTTAATATAA-TATTT
59971104 TAACATTATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.19
30 9 0.33
31 7 0.26
32 6 0.22
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (32 bp):
AAAAATATTTAGATTATTTTAATATAATATTT
Found at i:59973445 original size:2 final size:2
Alignment explanation
Indices: 59973440--59973466 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59973430 GTTAAAAAAG
59973440 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
59973467 GGATTATATG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:59974152 original size:20 final size:20
Alignment explanation
Indices: 59974114--59974153 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
59974104 TATAACCACA
* *
59974114 TAAACACAACCTAATAACCC
1 TAAACACAACCCAAAAACCC
*
59974134 TAAACCCAACCCAAAAACCC
1 TAAACACAACCCAAAAACCC
59974154 AAGGTTGGTT
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:0.50, C:0.40, G:0.00, T:0.10
Consensus pattern (20 bp):
TAAACACAACCCAAAAACCC
Found at i:59977931 original size:2 final size:2
Alignment explanation
Indices: 59977924--59977957 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
59977914 AATCACGATT
* *
59977924 TA TA TA TA CA TA CA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59977958 GAGAGAGAGA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.06, G:0.00, T:0.44
Consensus pattern (2 bp):
TA
Found at i:59981791 original size:20 final size:20
Alignment explanation
Indices: 59981738--59981779 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
59981728 TTTGTTATTG
59981738 TATTGCATTTTAATAAATTA
1 TATTGCATTTTAATAAATTA
59981758 TATTGCATTTTAATAAATTA
1 TATTGCATTTTAATAAATTA
59981778 TA
1 TA
59981780 CTTTTATTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.40, C:0.05, G:0.05, T:0.50
Consensus pattern (20 bp):
TATTGCATTTTAATAAATTA
Found at i:59986505 original size:11 final size:11
Alignment explanation
Indices: 59986489--59986513 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
59986479 GCTCATGGGC
59986489 CGGGCCGGGTT
1 CGGGCCGGGTT
59986500 CGGGCCGGGTT
1 CGGGCCGGGTT
59986511 CGG
1 CGG
59986514 CCCGAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.00, C:0.28, G:0.56, T:0.16
Consensus pattern (11 bp):
CGGGCCGGGTT
Found at i:59986640 original size:10 final size:10
Alignment explanation
Indices: 59986596--59986656 Score: 72
Period size: 11 Copynumber: 6.1 Consensus size: 10
59986586 CCGGCCATTT
59986596 TATTTTAAAA
1 TATTTTAAAA
59986606 T-TTTTAAAA
1 TATTTTAAAA
* *
59986615 -AATTAAAAA
1 TATTTTAAAA
59986624 GTATTTTAAAA
1 -TATTTTAAAA
59986635 TATTTTTAAAA
1 TA-TTTTAAAA
59986646 TATTTTAAAA
1 TATTTTAAAA
59986656 T
1 T
59986657 TAAAAAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
9 14 0.33
10 12 0.28
11 17 0.40
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.48
Consensus pattern (10 bp):
TATTTTAAAA
Found at i:59986663 original size:40 final size:38
Alignment explanation
Indices: 59986598--59986751 Score: 166
Period size: 41 Copynumber: 3.8 Consensus size: 38
59986588 GGCCATTTTA
* **
59986598 TTTTAAAAT-TTTTAAAAAATTAAAAAGTATTTTAAAATAT
1 TTTTAAAATATTTT--AAAATTAAAAA-AATTAAAAAATAT
59986638 TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAATAT
1 TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAATAT
*
59986676 ATTTTAAAAATATTTTAAAATTTAAAAAAATTAAAAAAAGTAG
1 -TTTT-AAAATATTTTAAAA-TTAAAAAAATT-AAAAAA-TAT
**
59986719 TTAAAAAATATTTTAAAATTAAAAAAAATTAAA
1 TTTTAAAATATTTTAAAATT-AAAAAAATTAAA
59986752 TATTTTTATT
Statistics
Matches: 101, Mismatches: 6, Indels: 14
0.83 0.05 0.12
Matches are distributed among these distances:
38 10 0.10
39 15 0.15
40 28 0.28
41 38 0.38
42 8 0.08
43 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (38 bp):
TTTTAAAATATTTTAAAATTAAAAAAATTAAAAAATAT
Found at i:59986664 original size:41 final size:40
Alignment explanation
Indices: 59986598--59986751 Score: 149
Period size: 40 Copynumber: 3.9 Consensus size: 40
59986588 GGCCATTTTA
* **
59986598 TTTTAAAAT-TTTTAAAAAATT-AAAAAGTATTTTAAAATAT
1 TTTTAAAATATTTT--AAAATTAAAAAAATATTAAAAAATAT
59986638 TTTTAAAATATTTTAAAATT-AAAAAA-ATTAAAAAATAT
1 TTTTAAAATATTTTAAAATTAAAAAAATATTAAAAAATAT
* *
59986676 ATTTTAAAAATATTTTAAAATTTAAAAAAAT-TAAAAAAAGTAG
1 -TTTT-AAAATATTTTAAAA-TTAAAAAAATATTAAAAAA-TAT
**
59986719 TTAAAAAATATTTTAAAATTAAAAAAA-ATTAAA
1 TTTTAAAATATTTTAAAATTAAAAAAATATTAAA
59986752 TATTTTTATT
Statistics
Matches: 98, Mismatches: 8, Indels: 16
0.80 0.07 0.13
Matches are distributed among these distances:
38 10 0.10
39 15 0.15
40 36 0.37
41 20 0.20
42 15 0.15
43 2 0.02
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (40 bp):
TTTTAAAATATTTTAAAATTAAAAAAATATTAAAAAATAT
Found at i:59986679 original size:50 final size:49
Alignment explanation
Indices: 59986596--59986737 Score: 146
Period size: 50 Copynumber: 2.8 Consensus size: 49
59986586 CCGGCCATTT
* *
59986596 TATTTTAAAATTTTTAAAAAATTAAAAAGTATTTTAAAATAT-TTTTAAAA
1 TATTTTAAAA--TTAAAAAAATTAAAAAATATTTTAAAATATATTTTAAAA
59986646 TATTTTAAAATTAAAAAAATTAAAAAATATATTTTAAAA-ATATTTTAAAA
1 TATTTTAAAATTAAAAAAATT-AAAAA-ATATTTTAAAATATATTTTAAAA
**
59986696 T-TTAAAAAAATTAAAAAAAGTAGTTAAAAAATATTTTAAAAT
1 TATT-TTAAAATT-AAAAAA--A-TTAAAAAATATTTTAAAAT
59986738 TAAAAAAAAT
Statistics
Matches: 79, Mismatches: 4, Indels: 15
0.81 0.04 0.15
Matches are distributed among these distances:
48 10 0.13
49 9 0.11
50 35 0.44
51 6 0.08
52 11 0.14
53 6 0.08
54 2 0.03
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (49 bp):
TATTTTAAAATTAAAAAAATTAAAAAATATTTTAAAATATATTTTAAAA
Found at i:59986736 original size:11 final size:11
Alignment explanation
Indices: 59986596--59986695 Score: 69
Period size: 11 Copynumber: 9.9 Consensus size: 11
59986586 CCGGCCATTT
59986596 TATTTT-AAAA
1 TATTTTAAAAA
59986606 T-TTTTAAAAA
1 TATTTTAAAAA
59986616 -A--TTAAAAA
1 TATTTTAAAAA
59986624 GTATTTT-AAAA
1 -TATTTTAAAAA
*
59986635 TATTTTTAAAA
1 TATTTTAAAAA
59986646 TATTTT--AAA
1 TATTTTAAAAA
59986655 -A--TTAAAAA
1 TATTTTAAAAA
* **
59986663 AATTAAAAAATA
1 TATTTTAAAA-A
59986675 TATTTTAAAAA
1 TATTTTAAAAA
59986686 TATTTTAAAA
1 TATTTTAAAA
59986696 TTTAAAAAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 25
0.71 0.05 0.25
Matches are distributed among these distances:
6 2 0.03
8 11 0.15
9 8 0.11
10 12 0.17
11 29 0.40
12 10 0.14
ACGTcount: A:0.56, C:0.00, G:0.01, T:0.43
Consensus pattern (11 bp):
TATTTTAAAAA
Found at i:59986764 original size:41 final size:39
Alignment explanation
Indices: 59986642--59986764 Score: 133
Period size: 41 Copynumber: 3.0 Consensus size: 39
59986632 AAATATTTTT
59986642 AAAATATTTTAAAATTAAAAAAATTAAAAAATATATT-TT-A
1 AAAATATTTTAAAATTAAAAAAATT--AAAAT-TATTATTAA
** *
59986682 AAAATATTTTAAAATTTAAAAAAATTAAAAAAAGTAGTTAA
1 AAAATATTTTAAAA-TTAAAAAAATTAAAATTATTA-TTAA
*
59986723 AAAATATTTTAAAATTAAAAAAAATTAAATATTTTTATTAA
1 AAAATATTTTAAAATT-AAAAAAATTAAA-ATTATTATTAA
59986764 A
1 A
59986765 TCGGGCCGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
38 2 0.03
39 4 0.06
40 18 0.26
41 43 0.61
42 3 0.04
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.37
Consensus pattern (39 bp):
AAAATATTTTAAAATTAAAAAAATTAAAATTATTATTAA
Found at i:59990338 original size:28 final size:28
Alignment explanation
Indices: 59990298--59990351 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
59990288 AATTTCAAGC
*
59990298 CTTAGATATTTTGATTTTTTAGTAAATT
1 CTTAAATATTTTGATTTTTTAGTAAATT
59990326 CTTAAATATTTTGATTTTTTAGTAAA
1 CTTAAATATTTTGATTTTTTAGTAAA
59990352 GTATTAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.31, C:0.04, G:0.09, T:0.56
Consensus pattern (28 bp):
CTTAAATATTTTGATTTTTTAGTAAATT
Found at i:59990358 original size:28 final size:28
Alignment explanation
Indices: 59990303--59990359 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
59990293 CAAGCCTTAG
* *
59990303 ATATTTTGATTTTTTAGTAAATTCTTAA
1 ATATTTTGATTTTTTAGTAAAGTATTAA
59990331 ATATTTTGATTTTTTAGTAAAGTATTAA
1 ATATTTTGATTTTTTAGTAAAGTATTAA
59990359 A
1 A
59990360 AAATTTAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.35, C:0.02, G:0.09, T:0.54
Consensus pattern (28 bp):
ATATTTTGATTTTTTAGTAAAGTATTAA
Found at i:59990422 original size:20 final size:20
Alignment explanation
Indices: 59990342--59990433 Score: 55
Period size: 20 Copynumber: 4.6 Consensus size: 20
59990332 TATTTTGATT
* * *
59990342 TTTTAGTAAAGTATTAAAAA
1 TTTTAGTAAATTCTTAGAAA
* * *
59990362 ATTTAATAAA-TCTTAAGATA
1 TTTTAGTAAATTCTT-AGAAA
*
59990382 TTTT-GATAAAATT-TTATAAA
1 TTTTAG-T-AAATTCTTAGAAA
59990402 TTTTAGTAAATTCTTAGAAA
1 TTTTAGTAAATTCTTAGAAA
* *
59990422 TATTAATAAATT
1 TTTTAGTAAATT
59990434 AACCTTTCAT
Statistics
Matches: 54, Mismatches: 12, Indels: 12
0.69 0.15 0.15
Matches are distributed among these distances:
19 8 0.15
20 39 0.72
21 6 0.11
22 1 0.02
ACGTcount: A:0.47, C:0.02, G:0.07, T:0.45
Consensus pattern (20 bp):
TTTTAGTAAATTCTTAGAAA
Found at i:59997038 original size:24 final size:26
Alignment explanation
Indices: 59997003--59997065 Score: 76
Period size: 25 Copynumber: 2.4 Consensus size: 26
59996993 GGTCCCCATA
59997003 TTTTTTCGTTTTAAG-TAATTTAA-TT
1 TTTTTTC-TTTTAAGTTAATTTAACTT
* *
59997028 TTTTTTCTTTTATGTTATTTTAACTTT
1 TTTTTTCTTTTAAGTTAATTTAAC-TT
59997055 TTTTTTCTTTT
1 TTTTTTCTTTT
59997066 TTTTCACTCT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 6 0.18
25 14 0.42
27 13 0.39
ACGTcount: A:0.16, C:0.06, G:0.05, T:0.73
Consensus pattern (26 bp):
TTTTTTCTTTTAAGTTAATTTAACTT
Found at i:60001479 original size:2 final size:2
Alignment explanation
Indices: 60001472--60001519 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
60001462 TCTTATAGTG
60001472 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
60001514 AT AT AT
1 AT AT AT
60001520 TCGAGTATCA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:60003584 original size:17 final size:16
Alignment explanation
Indices: 60003564--60003595 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
60003554 TTATTTAAAA
60003564 TTTAAATTTAACTCGAT
1 TTTAAATTTAA-TCGAT
60003581 TTTAAATTTAATCGA
1 TTTAAATTTAATCGA
60003596 GATATGAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.38, C:0.09, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAATCGAT
Found at i:60009093 original size:15 final size:15
Alignment explanation
Indices: 60009073--60009122 Score: 66
Period size: 15 Copynumber: 3.3 Consensus size: 15
60009063 AATAAATAAA
60009073 TGAATCGAACCGAAC
1 TGAATCGAACCGAAC
*
60009088 TGAATCGAATCGAA-
1 TGAATCGAACCGAAC
60009102 TCGAATCGAACCGAAC
1 T-GAATCGAACCGAAC
*
60009118 CGAAT
1 TGAAT
60009123 TGAATATAAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
14 1 0.03
15 29 0.97
ACGTcount: A:0.40, C:0.24, G:0.20, T:0.16
Consensus pattern (15 bp):
TGAATCGAACCGAAC
Found at i:60009097 original size:5 final size:5
Alignment explanation
Indices: 60009074--60009127 Score: 56
Period size: 5 Copynumber: 10.8 Consensus size: 5
60009064 ATAAATAAAT
* * * *
60009074 GAATC GAACC GAA-C TGAATC GAATC GAATC GAATC GAACC GAACC GAATT
1 GAATC GAATC GAATC -GAATC GAATC GAATC GAATC GAATC GAATC GAATC
60009124 GAAT
1 GAAT
60009128 ATAAATTAAA
Statistics
Matches: 43, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
4 1 0.02
5 41 0.95
6 1 0.02
ACGTcount: A:0.41, C:0.22, G:0.20, T:0.17
Consensus pattern (5 bp):
GAATC
Done.