Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 195 of 198
Found at i:60785051 original size:28 final size:27
Alignment explanation
Indices: 60784981--60785076 Score: 183
Period size: 27 Copynumber: 3.5 Consensus size: 27
60784971 TTTAATAACT
60784981 CTATTTTAATTTAAAAAATTAAGTAAA
1 CTATTTTAATTTAAAAAATTAAGTAAA
60785008 CTATTTTAATTTAAAAAATTAAGTAAA
1 CTATTTTAATTTAAAAAATTAAGTAAA
60785035 CTATTTTAATTTAAAAAAATTAAGTAAA
1 CTATTTTAATTT-AAAAAATTAAGTAAA
60785063 CTATTTTAATTTAA
1 CTATTTTAATTTAA
60785077 TAGTTTATTA
Statistics
Matches: 68, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
27 41 0.60
28 27 0.40
ACGTcount: A:0.50, C:0.04, G:0.03, T:0.43
Consensus pattern (27 bp):
CTATTTTAATTTAAAAAATTAAGTAAA
Found at i:60785927 original size:19 final size:19
Alignment explanation
Indices: 60785905--60786007 Score: 95
Period size: 18 Copynumber: 5.6 Consensus size: 19
60785895 GTAAATTATT
* *
60785905 TTAATTTAAAATAGAGTTG
1 TTAAATTAAAATAGAGTTA
* * *
60785924 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
60785942 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * * **
60785961 TTAAATGAGACTA-TTTTA
1 TTAAATTAAAATAGAGTTA
60785979 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
60785998 TTAAA-TAAAA
1 TTAAATTAAAA
60786008 AAGTGAGTTG
Statistics
Matches: 64, Mismatches: 18, Indels: 5
0.74 0.21 0.06
Matches are distributed among these distances:
18 32 0.50
19 32 0.50
ACGTcount: A:0.49, C:0.01, G:0.12, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:60785952 original size:37 final size:37
Alignment explanation
Indices: 60785905--60786003 Score: 162
Period size: 37 Copynumber: 2.7 Consensus size: 37
60785895 GTAAATTATT
* *
60785905 TTAATTTAAAATAGAGTTGTTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
* *
60785942 TTAAATTAAAATAGAGTTATTAAATGAGACTATTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
60785979 TTAAATTAAAATAGAGTTATTAAAT
1 TTAAATTAAAATAGAGTTATTAAAT
60786004 AAAAAAGTGA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.46, C:0.01, G:0.12, T:0.40
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
Found at i:60786292 original size:26 final size:26
Alignment explanation
Indices: 60786240--60786304 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
60786230 TTTTTGATAC
* *
60786240 ATTTTGGTGAATAATTAAAAATGTAAT
1 ATTTTGGTAAATAA-TAAAAATATAAT
60786267 ATTTTGGTAAATAA-AAAAATTATAAT
1 ATTTTGGTAAATAATAAAAA-TATAAT
60786293 ATTTTGGTAAAT
1 ATTTTGGTAAAT
60786305 TTTTATTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
25 5 0.14
26 17 0.49
27 13 0.37
ACGTcount: A:0.46, C:0.00, G:0.12, T:0.42
Consensus pattern (26 bp):
ATTTTGGTAAATAATAAAAATATAAT
Found at i:60790813 original size:25 final size:25
Alignment explanation
Indices: 60790785--60790842 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 25
60790775 AAAAAAAATC
*
60790785 AAAATCAAAATG-AAAAACAAAAAAG
1 AAAATCAAAAAGCAAAAAC-AAAAAG
*
60790810 AAAAT-AAAAAGCAAAAGCAAAAAG
1 AAAATCAAAAAGCAAAAACAAAAAG
60790834 AGAAATCAA
1 A-AAATCAA
60790843 TCAAATTCAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
24 12 0.43
25 14 0.50
26 2 0.07
ACGTcount: A:0.74, C:0.09, G:0.10, T:0.07
Consensus pattern (25 bp):
AAAATCAAAAAGCAAAAACAAAAAG
Found at i:60791254 original size:14 final size:13
Alignment explanation
Indices: 60791236--60791270 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
60791226 AAAAGATGAT
60791236 GAAAAATGAAAAA
1 GAAAAATGAAAAA
*
60791249 GAAAAATGAAAGA
1 GAAAAATGAAAAA
60791262 GTAAAAATG
1 G-AAAAATG
60791271 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:60793440 original size:3 final size:3
Alignment explanation
Indices: 60793432--60793473 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
60793422 AAAACAGTAA
60793432 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
60793474 GGTGATAATT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:60803239 original size:20 final size:19
Alignment explanation
Indices: 60803214--60803257 Score: 61
Period size: 20 Copynumber: 2.3 Consensus size: 19
60803204 ATTTATAGAA
60803214 TTTTTTAAATTTTTGAAGAT
1 TTTTTTAAATTTTTGAA-AT
* *
60803234 TTTTTTGAATTTTTGTAAT
1 TTTTTTAAATTTTTGAAAT
60803253 TTTTT
1 TTTTT
60803258 CAAGGGAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 7 0.32
20 15 0.68
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.68
Consensus pattern (19 bp):
TTTTTTAAATTTTTGAAAT
Found at i:60813984 original size:44 final size:44
Alignment explanation
Indices: 60813916--60814004 Score: 160
Period size: 44 Copynumber: 2.0 Consensus size: 44
60813906 TTAAAATTAC
*
60813916 ATCATACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
1 ATCACACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
*
60813960 ATCACACTTTTACGGAGTCTAAAATCGGATACCAATATGGACCT
1 ATCACACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
60814004 A
1 A
60814005 ATTGCAAGAT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (44 bp):
ATCACACTTTTACGAAGTCTAAAATCGGATACCAATATGGACCT
Found at i:60815537 original size:20 final size:22
Alignment explanation
Indices: 60815508--60815553 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 22
60815498 AAAAAAAGTG
60815508 TTAAAGTTAGAT-TTT-GTTAA
1 TTAAAGTTAGATATTTAGTTAA
* *
60815528 TTAAATTTAGATATTTATTTAA
1 TTAAAGTTAGATATTTAGTTAA
60815550 TTAA
1 TTAA
60815554 CGAAATCGTC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
21 3 0.14
22 8 0.36
ACGTcount: A:0.39, C:0.00, G:0.09, T:0.52
Consensus pattern (22 bp):
TTAAAGTTAGATATTTAGTTAA
Found at i:60818381 original size:4 final size:5
Alignment explanation
Indices: 60818359--60818393 Score: 56
Period size: 5 Copynumber: 7.4 Consensus size: 5
60818349 CTAAATCAAA
60818359 TTAAT TTAAT TTAAT TTAA- TTAA- TTAAT TTAAT TT
1 TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TTAAT TT
60818394 TATCCGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
4 8 0.28
5 21 0.72
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (5 bp):
TTAAT
Found at i:60828637 original size:2 final size:2
Alignment explanation
Indices: 60828598--60828626 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
60828588 ATTACTTTTA
60828598 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
60828627 CACCTATATA
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:60836124 original size:30 final size:30
Alignment explanation
Indices: 60836090--60836147 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
60836080 GTAGTCGTTC
*
60836090 AACTATTAAAAAGTTTTTGTTTAAGTCACT
1 AACTATTAAAAAGTTTTTATTTAAGTCACT
*
60836120 AACTATTAGAAAGTTTTTATTTAAGTCA
1 AACTATTAAAAAGTTTTTATTTAAGTCA
60836148 TTGAATCGTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.38, C:0.09, G:0.10, T:0.43
Consensus pattern (30 bp):
AACTATTAAAAAGTTTTTATTTAAGTCACT
Found at i:60837395 original size:15 final size:15
Alignment explanation
Indices: 60837359--60837397 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
60837349 TTTTCCCTCA
*
60837359 TCTTTTATTCAAACT
1 TCTTTTATTTAAACT
*
60837374 T-TTTTATTTAAATT
1 TCTTTTATTTAAACT
60837388 TCTTTTATTT
1 TCTTTTATTT
60837398 TTTCCTCGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
14 12 0.57
15 9 0.43
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.67
Consensus pattern (15 bp):
TCTTTTATTTAAACT
Found at i:60838999 original size:36 final size:36
Alignment explanation
Indices: 60838952--60839024 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
60838942 AGGTACTTAA
60838952 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
1 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
60838988 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
1 AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
60839024 A
1 A
60839025 TACTTCATAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.37, C:0.03, G:0.16, T:0.44
Consensus pattern (36 bp):
AATTTAGATATGTATTTGATGATTTCATGAAAAGTT
Found at i:60843756 original size:32 final size:32
Alignment explanation
Indices: 60843720--60843783 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
60843710 TTTTTACCTG
60843720 AACTTATAGTTCATAGAGGGTCAATATCTTCA
1 AACTTATAGTTCATAGAGGGTCAATATCTTCA
60843752 AACTTATAGTTCATAGAGGGTCAATATCTTCA
1 AACTTATAGTTCATAGAGGGTCAATATCTTCA
60843784 TAACAATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (32 bp):
AACTTATAGTTCATAGAGGGTCAATATCTTCA
Found at i:60845509 original size:17 final size:18
Alignment explanation
Indices: 60845475--60845509 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
60845465 AATTTATTTA
*
60845475 ATCAAACTGATCAAATTG
1 ATCAAACTGATAAAATTG
60845493 ATCAAACTGA-AAAATTG
1 ATCAAACTGATAAAATTG
60845510 TTGGTCTAAC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.49, C:0.14, G:0.11, T:0.26
Consensus pattern (18 bp):
ATCAAACTGATAAAATTG
Found at i:60852933 original size:23 final size:21
Alignment explanation
Indices: 60852907--60852960 Score: 54
Period size: 23 Copynumber: 2.5 Consensus size: 21
60852897 ATTTGGTTGG
* *
60852907 ACTTGAATATCATTTATTTAAGA
1 ACTTGAATATAACTTATTT--GA
* *
60852930 ACTTAAATCTAACTTATTTGA
1 ACTTGAATATAACTTATTTGA
60852951 ACTTGAATAT
1 ACTTGAATAT
60852961 GAATATATAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 10 0.40
23 15 0.60
ACGTcount: A:0.39, C:0.11, G:0.07, T:0.43
Consensus pattern (21 bp):
ACTTGAATATAACTTATTTGA
Found at i:60856363 original size:15 final size:16
Alignment explanation
Indices: 60856333--60856365 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
60856323 TTTAATACAC
60856333 ATGTCATAATTTTAAT
1 ATGTCATAATTTTAAT
*
60856349 ATGTCATTA-TTTAAT
1 ATGTCATAATTTTAAT
60856364 AT
1 AT
60856366 AATTTAATTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.52
Consensus pattern (16 bp):
ATGTCATAATTTTAAT
Found at i:60856386 original size:9 final size:9
Alignment explanation
Indices: 60856372--60856396 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
60856362 ATATAATTTA
60856372 ATTTTTAAT
1 ATTTTTAAT
60856381 ATTTTTAAT
1 ATTTTTAAT
60856390 ATTTTTA
1 ATTTTTA
60856397 TTTATAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (9 bp):
ATTTTTAAT
Found at i:60858378 original size:20 final size:20
Alignment explanation
Indices: 60858353--60858410 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
60858343 ATCCACATTT
60858353 AAAATATTTAATATTTAAAC
1 AAAATATTTAATATTTAAAC
* *
60858373 AAAATATTTCA-ATTT-CAC
1 AAAATATTTAATATTTAAAC
60858391 AAACAT-TTTAACTATTTAAA
1 AAA-ATATTTAA-TATTTAAA
60858411 ATTTAACGTC
Statistics
Matches: 30, Mismatches: 4, Indels: 7
0.73 0.10 0.17
Matches are distributed among these distances:
18 9 0.30
19 6 0.20
20 14 0.47
21 1 0.03
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (20 bp):
AAAATATTTAATATTTAAAC
Found at i:60864730 original size:12 final size:12
Alignment explanation
Indices: 60864713--60864748 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
60864703 TTTCAGGCAT
60864713 TGGTTCCGGTTC
1 TGGTTCCGGTTC
* *
60864725 TGGTTCTGATTC
1 TGGTTCCGGTTC
60864737 TGGTTCCGGTTC
1 TGGTTCCGGTTC
60864749 CTTCTTAACT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.03, C:0.22, G:0.31, T:0.44
Consensus pattern (12 bp):
TGGTTCCGGTTC
Found at i:60866309 original size:16 final size:16
Alignment explanation
Indices: 60866273--60866319 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
60866263 ACCTTATCAA
60866273 ATTAAATTTTATTATT
1 ATTAAATTTTATTATT
*
60866289 -GTAAATATTTATT-TT
1 ATTAAAT-TTTATTATT
*
60866304 ATTAAATTATATTATT
1 ATTAAATTTTATTATT
60866320 GCCTTTAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 6
0.74 0.09 0.18
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (16 bp):
ATTAAATTTTATTATT
Found at i:60875089 original size:111 final size:111
Alignment explanation
Indices: 60874895--60875118 Score: 421
Period size: 111 Copynumber: 2.0 Consensus size: 111
60874885 TCACGCGTAC
60874895 CTCATACTGATGTACAGGAACCAATTTTTAACAACAGAAATGGATGGAATTTTTAACAGAAAAAC
1 CTCATACTGATGTACAGGAACCAATTTTTAACAACAGAAATGGATGGAATTTTTAACAGAAAAAC
*
60874960 TAATTTGTTCTTTGCCTATTTTCTTAGTAGAGGTGCAAAATGTAAT
66 TAATTAGTTCTTTGCCTATTTTCTTAGTAGAGGTGCAAAATGTAAT
*
60875006 CTCATACTGATGTACAGGAACCAATTTTTAACAACAGAAATGGATGGAATTTTTAACAGAAAAAT
1 CTCATACTGATGTACAGGAACCAATTTTTAACAACAGAAATGGATGGAATTTTTAACAGAAAAAC
*
60875071 TAATTAGTTCTTTGCCTATTTTTTTAGTAGAGGTGCAAAATGTAAT
66 TAATTAGTTCTTTGCCTATTTTCTTAGTAGAGGTGCAAAATGTAAT
60875117 CT
1 CT
60875119 GACTCCTAAT
Statistics
Matches: 110, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 110 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (111 bp):
CTCATACTGATGTACAGGAACCAATTTTTAACAACAGAAATGGATGGAATTTTTAACAGAAAAAC
TAATTAGTTCTTTGCCTATTTTCTTAGTAGAGGTGCAAAATGTAAT
Found at i:60900864 original size:28 final size:28
Alignment explanation
Indices: 60900832--60900888 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
60900822 CATTTCAGCT
*
60900832 ATTTTTGAAAGGTTAA-TGTTCAAATTTA
1 ATTTTTGAAAGGTTAAGGGTT-AAATTTA
**
60900860 ATTTTTTTAAGGTTAAGGGTTAAATTTA
1 ATTTTTGAAAGGTTAAGGGTTAAATTTA
60900888 A
1 A
60900889 CTAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 22 0.88
29 3 0.12
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (28 bp):
ATTTTTGAAAGGTTAAGGGTTAAATTTA
Found at i:60902249 original size:31 final size:31
Alignment explanation
Indices: 60902192--60902250 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
60902182 ACAATTTATT
* *
60902192 TCTTTTTAGAAGGTTAATAGTCAAATTTGAC
1 TCTTTTTAAAAGGTTAATAGGCAAATTTGAC
*
60902223 TCTTTTTAAAAGGTTGA-AGGCTAAATTT
1 TCTTTTTAAAAGGTTAATAGGC-AAATTT
60902251 AGCTTAAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 21 0.88
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.42
Consensus pattern (31 bp):
TCTTTTTAAAAGGTTAATAGGCAAATTTGAC
Found at i:60904145 original size:26 final size:27
Alignment explanation
Indices: 60904085--60904144 Score: 102
Period size: 27 Copynumber: 2.2 Consensus size: 27
60904075 ATAAAAAATA
*
60904085 ACCAAAATATTATAACTTTTTTTATTT
1 ACCAAAACATTATAACTTTTTTTATTT
*
60904112 ACCAAAACATTATAATTTTTTTTATTT
1 ACCAAAACATTATAACTTTTTTTATTT
60904139 ACCAAA
1 ACCAAA
60904145 CTATACAAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.40, C:0.13, G:0.00, T:0.47
Consensus pattern (27 bp):
ACCAAAACATTATAACTTTTTTTATTT
Found at i:60904319 original size:18 final size:18
Alignment explanation
Indices: 60904296--60904359 Score: 83
Period size: 18 Copynumber: 3.5 Consensus size: 18
60904286 TAAAATAGAG
60904296 TTATTAAATGAGAATAGT
1 TTATTAAATGAGAATAGT
* * *
60904314 TTATTAAATTAAAATAGAG
1 TTATTAAATGAGAATAG-T
*
60904333 TTATTAAATGAGAATAAT
1 TTATTAAATGAGAATAGT
60904351 TTATTAAAT
1 TTATTAAAT
60904360 TAAAATAGAG
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
18 24 0.63
19 14 0.37
ACGTcount: A:0.48, C:0.00, G:0.11, T:0.41
Consensus pattern (18 bp):
TTATTAAATGAGAATAGT
Found at i:60904330 original size:37 final size:37
Alignment explanation
Indices: 60904280--60904375 Score: 183
Period size: 37 Copynumber: 2.6 Consensus size: 37
60904270 CTTAATTTTT
*
60904280 TTAAATTAAAATAGAGTTATTAAATGAGAATAGTTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
60904317 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
1 TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
60904354 TTAAATTAAAATAGAGTTATTA
1 TTAAATTAAAATAGAGTTATTA
60904376 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (37 bp):
TTAAATTAAAATAGAGTTATTAAATGAGAATAATTTA
Found at i:60904380 original size:18 final size:19
Alignment explanation
Indices: 60904280--60904375 Score: 124
Period size: 19 Copynumber: 5.2 Consensus size: 19
60904270 CTTAATTTTT
60904280 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
60904299 TTAAATGAGAATAG-TTTA
1 TTAAATTAAAATAGAGTTA
60904317 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
* * *
60904336 TTAAATGAGAATA-ATTTA
1 TTAAATTAAAATAGAGTTA
60904354 TTAAATTAAAATAGAGTTA
1 TTAAATTAAAATAGAGTTA
60904373 TTA
1 TTA
60904376 CTTAATTAGA
Statistics
Matches: 63, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
18 30 0.48
19 33 0.52
ACGTcount: A:0.50, C:0.00, G:0.11, T:0.39
Consensus pattern (19 bp):
TTAAATTAAAATAGAGTTA
Found at i:60904596 original size:25 final size:26
Alignment explanation
Indices: 60904551--60904602 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 26
60904541 GACTCGGCCC
* *
60904551 ATTTTTAAAATAAACATTAAAAAAAT
1 ATTTTAAAAATAAACAATAAAAAAAT
60904577 ATTTTAAAAATAAA-AATAAAAAAAT
1 ATTTTAAAAATAAACAATAAAAAAAT
60904602 A
1 A
60904603 AAAATAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 11 0.46
26 13 0.54
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (26 bp):
ATTTTAAAAATAAACAATAAAAAAAT
Found at i:60904615 original size:13 final size:14
Alignment explanation
Indices: 60904582--60904613 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
60904572 AAAATATTTT
60904582 AAAAATAAAAATAA
1 AAAAATAAAAATAA
60904596 AAAAATAAAAATAA
1 AAAAATAAAAATAA
60904610 AAAA
1 AAAA
60904614 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (14 bp):
AAAAATAAAAATAA
Found at i:60905026 original size:20 final size:20
Alignment explanation
Indices: 60905003--60905040 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
60904993 TTATACTTTT
60905003 TAAAATAGT-TTTACTTTAGG
1 TAAAATA-TATTTACTTTAGG
60905023 TAAAATATATTTACTTTA
1 TAAAATATATTTACTTTA
60905041 ATAATAAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 1 0.06
20 16 0.94
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (20 bp):
TAAAATATATTTACTTTAGG
Found at i:60905395 original size:27 final size:27
Alignment explanation
Indices: 60905308--60905386 Score: 131
Period size: 27 Copynumber: 2.9 Consensus size: 27
60905298 TATTTTAGTC
*
60905308 CTTTGGCATCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
60905335 CTTTGGCACCATTGGTGCCGCCAATCT
1 CTTTGGCACCATTGGTGCCGCCAATCT
* *
60905362 CTTTGGCACCTTTGGTGCCTCCAAT
1 CTTTGGCACCATTGGTGCCGCCAAT
60905387 GTGATTGGCC
Statistics
Matches: 49, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
27 49 1.00
ACGTcount: A:0.14, C:0.32, G:0.22, T:0.33
Consensus pattern (27 bp):
CTTTGGCACCATTGGTGCCGCCAATCT
Found at i:60909730 original size:25 final size:27
Alignment explanation
Indices: 60909696--60909753 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
60909686 TCAGTACTTT
60909696 TTAACTCTAAGC-T-ATACTTGCTAAA
1 TTAACTCTAAGCATAATACTTGCTAAA
60909721 TTAACTCTAAGCAAGTAATACTTGCTAAA
1 TTAACTCTAAGC-A-TAATACTTGCTAAA
60909750 TTAA
1 TTAA
60909754 TGTCCATCTC
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
25 12 0.41
28 1 0.03
29 16 0.55
ACGTcount: A:0.40, C:0.17, G:0.09, T:0.34
Consensus pattern (27 bp):
TTAACTCTAAGCATAATACTTGCTAAA
Found at i:60915560 original size:18 final size:17
Alignment explanation
Indices: 60915521--60915554 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
60915511 TTAATGTAAG
60915521 TAATA-TTTAAAATAAA
1 TAATATTTTAAAATAAA
60915537 TAATATTTTATAAATAAA
1 TAATATTTTA-AAATAAA
60915555 ATATATGAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 5 0.31
17 4 0.25
18 7 0.44
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATATTTTAAAATAAA
Found at i:60924426 original size:31 final size:31
Alignment explanation
Indices: 60924341--60924428 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 31
60924331 ATGTCCCACT
* *
60924341 ATTAACTTAATTTAATTACATTATATAACTA
1 ATTAATTTAATTTAATCACATTATATAACTA
* *
60924372 TTTAGTTTAATTTAATCACATTATATAA-TA
1 ATTAATTTAATTTAATCACATTATATAACTA
* * *
60924402 ATTAATTTAGTTTTTATCATATTATAT
1 ATTAATTTA-ATTTAATCACATTATAT
60924429 TACTCACATC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
30 9 0.19
31 38 0.81
ACGTcount: A:0.40, C:0.07, G:0.02, T:0.51
Consensus pattern (31 bp):
ATTAATTTAATTTAATCACATTATATAACTA
Found at i:60933902 original size:25 final size:20
Alignment explanation
Indices: 60933856--60933895 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
60933846 AGAGTGTCAT
60933856 GTCATTATACTTTAACGGAA
1 GTCATTATACTTTAACGGAA
60933876 GTCATTATACTTTAACGGAA
1 GTCATTATACTTTAACGGAA
60933896 TTCAAGTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (20 bp):
GTCATTATACTTTAACGGAA
Found at i:60933971 original size:30 final size:28
Alignment explanation
Indices: 60933937--60934011 Score: 87
Period size: 32 Copynumber: 2.5 Consensus size: 28
60933927 TTTTATTTTT
60933937 ATTTTTTAATTTTAAAATACTTTTAAAATA
1 ATTTTTTAATTTTAAAAT--TTTTAAAATA
* *
60933967 ATTTTTTTTTATTTTTAAATTTTTAAAATA
1 A--TTTTTTAATTTTAAAATTTTTAAAATA
60933997 ATTTTTTAATGTTTA
1 ATTTTTTAAT-TTTA
60934012 TTTTAAAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
28 8 0.21
29 3 0.08
30 12 0.32
32 15 0.39
ACGTcount: A:0.36, C:0.01, G:0.01, T:0.61
Consensus pattern (28 bp):
ATTTTTTAATTTTAAAATTTTTAAAATA
Found at i:60935066 original size:14 final size:12
Alignment explanation
Indices: 60935050--60935074 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
60935040 ATTTTAAAGT
60935050 ATATAAAAATTA
1 ATATAAAAATTA
60935062 ATATAAAAATTA
1 ATATAAAAATTA
60935074 A
1 A
60935075 AATGGGCGGG
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:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (12 bp):
ATATAAAAATTA
Found at i:60937455 original size:15 final size:15
Alignment explanation
Indices: 60937410--60937510 Score: 80
Period size: 15 Copynumber: 6.7 Consensus size: 15
60937400 CCATGTAAAA
*
60937410 CCACCAGTTACAGTC
1 CCACCAGTGACAGTC
* * * *
60937425 CCTCCGGTCACTGTC
1 CCACCAGTGACAGTC
60937440 CCACCAGTGACAGTC
1 CCACCAGTGACAGTC
60937455 CCACCAGTGACAGTC
1 CCACCAGTGACAGTC
* * **
60937470 CCTCCAATAGTA-A-AA
1 CCACCAGT-G-ACAGTC
*
60937485 CCACCAGTTACAGTC
1 CCACCAGTGACAGTC
60937500 CCACCAGTGAC
1 CCACCAGTGAC
60937511 TGTTCCTCCT
Statistics
Matches: 64, Mismatches: 18, Indels: 8
0.71 0.20 0.09
Matches are distributed among these distances:
13 1 0.02
14 1 0.02
15 59 0.92
16 2 0.03
17 1 0.02
ACGTcount: A:0.27, C:0.40, G:0.16, T:0.18
Consensus pattern (15 bp):
CCACCAGTGACAGTC
Found at i:60937568 original size:72 final size:72
Alignment explanation
Indices: 60937406--60937668 Score: 271
Period size: 72 Copynumber: 3.6 Consensus size: 72
60937396 CAATCCATGT
* * * * *
60937406 AAAACCACCAGTTACAGTCCCTCCGGTCACTGTCCCACCAGTGACAGTCCCACCAG-TGACAGTC
1 AAAACCACCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGA-AG--CCACCAGTTGA-ACTC
* *
60937470 CCTCCAATAGT
62 CCTCCAATTGC
* *
60937481 AAAACCACCAGTTACAGTCCCACCAGTGACTGTTCCTCCTGTGAAGCCACCAGTTGAACTCCCTC
1 AAAACCACCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGAAGCCACCAGTTGAACTCCCTC
*
60937546 CGATTGC
66 CAATTGC
* * * * *
60937553 AAAACCACCCA-TTACAGTCCCACCAGTGACTGTTCCTCCTGTAAAGCCACCTGTTGATCTCCCT
1 AAAACCA-CCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGAAGCCACCAGTTGAACTCCCT
60937617 CCAATTGC
65 CCAATTGC
* * * * *
60937625 TAAGCCACCCA-TTACGGTTCCACCAGTGACAGTCCCTCCAGTGA
1 AAAACCA-CCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGA
60937669 CTCCTGTGAA
Statistics
Matches: 164, Mismatches: 22, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
72 118 0.72
73 6 0.04
74 2 0.01
75 38 0.23
ACGTcount: A:0.25, C:0.37, G:0.16, T:0.22
Consensus pattern (72 bp):
AAAACCACCAGTTACAGTCCCACCAGTGACTGTCCCTCCAGTGAAGCCACCAGTTGAACTCCCTC
CAATTGC
Found at i:60937807 original size:21 final size:21
Alignment explanation
Indices: 60937766--60937808 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60937756 CCACCCATCA
*
60937766 CAGTCCCTCCGGTGACAGTCC
1 CAGTCCCTCCAGTGACAGTCC
* *
60937787 CAGTCCCTCCAGTTACTGTCC
1 CAGTCCCTCCAGTGACAGTCC
60937808 C
1 C
60937809 TCCAGTGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.44, G:0.19, T:0.23
Consensus pattern (21 bp):
CAGTCCCTCCAGTGACAGTCC
Found at i:60937819 original size:15 final size:15
Alignment explanation
Indices: 60937789--60937826 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
60937779 GACAGTCCCA
*
60937789 GTCCCTCCAGTTACT
1 GTCCCTCCAGTGACT
60937804 GTCCCTCCAGTGACT
1 GTCCCTCCAGTGACT
*
60937819 GTTCCTCC
1 GTCCCTCC
60937827 CGTAAAGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.42, G:0.16, T:0.32
Consensus pattern (15 bp):
GTCCCTCCAGTGACT
Found at i:60938079 original size:21 final size:21
Alignment explanation
Indices: 60938038--60938080 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
60938028 CCACCCATCA
*
60938038 CAGTCCCTCCGGTGACAGTCC
1 CAGTCCCTCCAGTGACAGTCC
* *
60938059 CAGTCCCTCCAGTTACTGTCC
1 CAGTCCCTCCAGTGACAGTCC
60938080 C
1 C
60938081 TCCAGTGACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.14, C:0.44, G:0.19, T:0.23
Consensus pattern (21 bp):
CAGTCCCTCCAGTGACAGTCC
Found at i:60938091 original size:15 final size:15
Alignment explanation
Indices: 60938061--60938098 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
60938051 GACAGTCCCA
*
60938061 GTCCCTCCAGTTACT
1 GTCCCTCCAGTGACT
60938076 GTCCCTCCAGTGACT
1 GTCCCTCCAGTGACT
*
60938091 GTTCCTCC
1 GTCCCTCC
60938099 CGTAAAGCCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.11, C:0.42, G:0.16, T:0.32
Consensus pattern (15 bp):
GTCCCTCCAGTGACT
Found at i:60944268 original size:18 final size:18
Alignment explanation
Indices: 60944234--60944272 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
60944224 CCATGTGAAC
*
60944234 ATTATTATTATTTGTTTA
1 ATTATTATTATTGGTTTA
60944252 ATTATTATT-TTGGGTTTA
1 ATTATTATTATT-GGTTTA
60944270 ATT
1 ATT
60944273 TTTTTAAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 2 0.11
18 17 0.89
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (18 bp):
ATTATTATTATTGGTTTA
Found at i:60959267 original size:5 final size:5
Alignment explanation
Indices: 60959257--60959286 Score: 60
Period size: 5 Copynumber: 6.0 Consensus size: 5
60959247 CAATGATTAT
60959257 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC
1 CTCTC CTCTC CTCTC CTCTC CTCTC CTCTC
60959287 AGGAAAGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.60, G:0.00, T:0.40
Consensus pattern (5 bp):
CTCTC
Found at i:60962865 original size:20 final size:20
Alignment explanation
Indices: 60962842--60962888 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
60962832 CCATTTTTAA
* **
60962842 TAAATATTAAAAATTTATTT
1 TAAAAATTAAAAAAATATTT
60962862 TAAAAATTAAAAAAATATTT
1 TAAAAATTAAAAAAATATTT
60962882 TAAAAAT
1 TAAAAAT
60962889 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAATTAAAAAAATATTT
Found at i:60962888 original size:11 final size:11
Alignment explanation
Indices: 60962872--60962935 Score: 68
Period size: 11 Copynumber: 6.4 Consensus size: 11
60962862 TAAAAATTAA
60962872 AAAAATATTTT
1 AAAAATATTTT
60962883 AAAAATATTTT
1 AAAAATATTTT
60962894 --AAA-A--TT
1 AAAAATATTTT
*
60962900 AAAAA-AATTT
1 AAAAATATTTT
*
60962910 AAAAGTATTTT
1 AAAAATATTTT
60962921 AAAAATATTTT
1 AAAAATATTTT
60962932 AAAA
1 AAAA
60962936 TTAAAAAAAT
Statistics
Matches: 45, Mismatches: 3, Indels: 10
0.78 0.05 0.17
Matches are distributed among these distances:
6 2 0.04
8 5 0.11
9 3 0.07
10 6 0.13
11 29 0.64
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:60962919 original size:38 final size:39
Alignment explanation
Indices: 60962863--60962945 Score: 141
Period size: 38 Copynumber: 2.2 Consensus size: 39
60962853 AATTTATTTT
60962863 AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAA
* *
60962902 AAAAATT-TAAAAGTATTTTAAAAATATTTTAAAATTAA
1 AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAA
60962940 AAAAAT
1 AAAAAT
60962946 AAATATATTT
Statistics
Matches: 42, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 35 0.83
39 7 0.17
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (39 bp):
AAAAATTAAAAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:60963793 original size:15 final size:15
Alignment explanation
Indices: 60963773--60963803 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
60963763 AAAATAAAAA
*
60963773 ATATATTTGTTATAT
1 ATATATTTATTATAT
60963788 ATATATTTATTATAT
1 ATATATTTATTATAT
60963803 A
1 A
60963804 AATACTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (15 bp):
ATATATTTATTATAT
Found at i:60964311 original size:21 final size:22
Alignment explanation
Indices: 60964258--60964313 Score: 60
Period size: 21 Copynumber: 2.5 Consensus size: 22
60964248 ATAAAATGAT
* *
60964258 ATTAAAACATTATATTTATCATAT
1 ATTAAAA-A-TATATTTATAATAA
*
60964282 ATTATAAATATATTTA-AATAA
1 ATTAAAAATATATTTATAATAA
60964303 ATTAAAAATAT
1 ATTAAAAATAT
60964314 TATAATATAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
21 13 0.46
22 8 0.29
23 1 0.04
24 6 0.21
ACGTcount: A:0.54, C:0.04, G:0.00, T:0.43
Consensus pattern (22 bp):
ATTAAAAATATATTTATAATAA
Found at i:60964313 original size:19 final size:21
Alignment explanation
Indices: 60964286--60964329 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 21
60964276 TCATATATTA
*
60964286 TAAATATATT-TAA-ATAAAT
1 TAAAAATATTATAATATAAAT
*
60964305 TAAAAATATTATAATATATAT
1 TAAAAATATTATAATATAAAT
60964326 TAAA
1 TAAA
60964330 TTGGTTGGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 9 0.43
20 3 0.14
21 9 0.43
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAAAATATTATAATATAAAT
Found at i:60964327 original size:21 final size:20
Alignment explanation
Indices: 60964268--60964329 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 20
60964258 ATTAAAACAT
*
60964268 TATATTTATCATATATTATAAA
1 TATATTTA-AATATATTA-AAA
*
60964290 TATATTTAAATAAATTAAAA
1 TATATTTAAATATATTAAAA
60964310 -ATATTATAATATATATTAAA
1 TATATT-TAA-ATATATTAAA
60964330 TTGGTTGGTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
19 5 0.14
20 6 0.17
21 16 0.46
22 8 0.23
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATTTAAATATATTAAAA
Found at i:60967796 original size:3 final size:3
Alignment explanation
Indices: 60967782--60967822 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
60967772 GGATGATAAA
*
60967782 ATG ATT ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
60967823 AAAAGCTTAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (3 bp):
ATG
Found at i:60969392 original size:6 final size:6
Alignment explanation
Indices: 60969358--60969389 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
60969348 TAACCCTTGC
60969358 TTTCTT TTTCTT TTTCTT TTTCTT TTT-TT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
60969390 TTTGAATAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (6 bp):
TTTCTT
Found at i:60971006 original size:13 final size:13
Alignment explanation
Indices: 60970964--60971006 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
60970954 TATACGACTC
*
60970964 AAAAGAAATTACT
1 AAAATAAATTACT
60970977 AAAATAACA-TA-T
1 AAAATAA-ATTACT
60970989 AAAATAAATTACT
1 AAAATAAATTACT
60971002 AAAAT
1 AAAAT
60971007 TTGATTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
11 1 0.04
12 10 0.38
13 14 0.54
14 1 0.04
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (13 bp):
AAAATAAATTACT
Found at i:60971417 original size:2 final size:2
Alignment explanation
Indices: 60971410--60971441 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
60971400 ATAAATTCAA
60971410 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
60971442 TGAGNNNNNN
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:60972518 original size:31 final size:32
Alignment explanation
Indices: 60972463--60972524 Score: 99
Period size: 31 Copynumber: 2.0 Consensus size: 32
60972453 GGATTTTATA
60972463 TTTGGTTTAAATGTTTCAATTTGGTACTTGAG
1 TTTGGTTTAAATGTTTCAATTTGGTACTTGAG
**
60972495 TTTGGTTTTGATGTTT-AATTTGGTACTTGA
1 TTTGGTTTAAATGTTTCAATTTGGTACTTGA
60972525 TTGTTCTTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
31 14 0.50
32 14 0.50
ACGTcount: A:0.19, C:0.05, G:0.23, T:0.53
Consensus pattern (32 bp):
TTTGGTTTAAATGTTTCAATTTGGTACTTGAG
Found at i:60983815 original size:12 final size:12
Alignment explanation
Indices: 60983798--60983823 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
60983788 TACATATATG
60983798 TACACACATACA
1 TACACACATACA
60983810 TACACACATACA
1 TACACACATACA
60983822 TA
1 TA
60983824 TAGCTAAATT
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:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (12 bp):
TACACACATACA
Found at i:60987568 original size:11 final size:11
Alignment explanation
Indices: 60987554--60987636 Score: 61
Period size: 11 Copynumber: 7.9 Consensus size: 11
60987544 TTTTTTTTAA
60987554 TTTTAAAATAT
1 TTTTAAAATAT
*
60987565 TTTTAAAATGCT
1 TTTTAAAAT-AT
** *
60987577 TTTTTTATTAT
1 TTTTAAAATAT
*
60987588 TTTT--TA-AT
1 TTTTAAAATAT
60987596 -TTTAAAATAT
1 TTTTAAAATAT
60987606 TTTTAAAATACT
1 TTTTAAAATA-T
60987618 TTTT-AAA-AT
1 TTTTAAAATAT
60987627 TTTTAAAATA
1 TTTTAAAATA
60987637 AATTTTTGAT
Statistics
Matches: 56, Mismatches: 8, Indels: 16
0.70 0.10 0.20
Matches are distributed among these distances:
7 3 0.05
8 2 0.04
9 6 0.11
10 6 0.11
11 27 0.48
12 12 0.21
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:60987581 original size:41 final size:41
Alignment explanation
Indices: 60987536--60987621 Score: 154
Period size: 41 Copynumber: 2.1 Consensus size: 41
60987526 AATATTTTTA
* *
60987536 TTTTTTATTTTTTTTTAATTTTAAAATATTTTTAAAATGCT
1 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
60987577 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
60987618 TTTT
1 TTTT
60987622 AAAATTTTTA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.66
Consensus pattern (41 bp):
TTTTTTATTATTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:60987630 original size:21 final size:22
Alignment explanation
Indices: 60987595--60987636 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 22
60987585 TATTTTTTAA
*
60987595 TTTTAAAATATTTTTAAAATACT
1 TTTTAAAATACTTTTAAAATA-T
60987618 TTTTAAAAT--TTTTAAAATA
1 TTTTAAAATACTTTTAAAATA
60987637 AATTTTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 10 0.53
23 9 0.47
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (22 bp):
TTTTAAAATACTTTTAAAATAT
Found at i:60987642 original size:21 final size:23
Alignment explanation
Indices: 60987593--60987642 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
60987583 ATTATTTTTT
60987593 AATTTTAAAATATTTTTAAAAT-
1 AATTTTAAAATATTTTTAAAATA
* *
60987615 ACTTTTTAAA-ATTTTTAAAATA
1 AATTTTAAAATATTTTTAAAATA
60987637 AATTTT
1 AATTTT
60987643 TGATATTTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 11 0.46
22 13 0.54
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
AATTTTAAAATATTTTTAAAATA
Found at i:60993858 original size:21 final size:21
Alignment explanation
Indices: 60993833--60993874 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
60993823 CGATATTATC
*
60993833 TATTTGTATCGTTTTATATTT
1 TATTTGTATCGTATTATATTT
* *
60993854 TATTTTTTTCGTATTATATTT
1 TATTTGTATCGTATTATATTT
60993875 ATATATATAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.19, C:0.05, G:0.07, T:0.69
Consensus pattern (21 bp):
TATTTGTATCGTATTATATTT
Found at i:61006265 original size:31 final size:31
Alignment explanation
Indices: 61006203--61006265 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
61006193 TACTCAAATT
* * **
61006203 TAAAAAAAAATTAATGATATAATGATTTAAA
1 TAAAAAAAAATTAATAATATAAGGACGTAAA
* *
61006234 TAAAAAAAATTTAATAATTTAAGGACGTAAA
1 TAAAAAAAAATTAATAATATAAGGACGTAAA
61006265 T
1 T
61006266 CAATACTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.59, C:0.02, G:0.08, T:0.32
Consensus pattern (31 bp):
TAAAAAAAAATTAATAATATAAGGACGTAAA
Found at i:61009300 original size:22 final size:24
Alignment explanation
Indices: 61009275--61009319 Score: 60
Period size: 22 Copynumber: 2.0 Consensus size: 24
61009265 TATTCAAAGC
61009275 TAACCC-TAAGCT-AAAA-CAAAAA
1 TAACCCGT-AGCTCAAAATCAAAAA
61009297 TAACCCGTAGCTCAAAATCAAAA
1 TAACCCGTAGCTCAAAATCAAAA
61009320 CCATGTCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
22 10 0.50
23 5 0.25
24 5 0.25
ACGTcount: A:0.53, C:0.24, G:0.07, T:0.16
Consensus pattern (24 bp):
TAACCCGTAGCTCAAAATCAAAAA
Found at i:61024301 original size:16 final size:16
Alignment explanation
Indices: 61024280--61024332 Score: 63
Period size: 16 Copynumber: 3.4 Consensus size: 16
61024270 ATATAATTAA
61024280 AATAAAATTCTATTTG
1 AATAAAATTCTATTTG
** **
61024296 AAT-AAATTAAATTAA
1 AATAAAATTCTATTTG
61024311 AATAAAATTCTATTTG
1 AATAAAATTCTATTTG
61024327 AATAAA
1 AATAAA
61024333 TTAAATTAAA
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 11 0.39
16 17 0.61
ACGTcount: A:0.55, C:0.04, G:0.04, T:0.38
Consensus pattern (16 bp):
AATAAAATTCTATTTG
Found at i:61024309 original size:31 final size:31
Alignment explanation
Indices: 61024274--61024347 Score: 148
Period size: 31 Copynumber: 2.4 Consensus size: 31
61024264 ATATTTATAT
61024274 AATTAAAATAAAATTCTATTTGAATAAATTA
1 AATTAAAATAAAATTCTATTTGAATAAATTA
61024305 AATTAAAATAAAATTCTATTTGAATAAATTA
1 AATTAAAATAAAATTCTATTTGAATAAATTA
61024336 AATTAAAATAAA
1 AATTAAAATAAA
61024348 TCAAAGTGAA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 43 1.00
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.36
Consensus pattern (31 bp):
AATTAAAATAAAATTCTATTTGAATAAATTA
Found at i:61024314 original size:15 final size:15
Alignment explanation
Indices: 61024296--61024348 Score: 61
Period size: 15 Copynumber: 3.5 Consensus size: 15
61024286 ATTCTATTTG
61024296 AATAAATTAAATTAA
1 AATAAATTAAATTAA
** **
61024311 AATAAAATTCTATTTG
1 AAT-AAATTAAATTAA
61024327 AATAAATTAAATTAA
1 AATAAATTAAATTAA
61024342 AATAAAT
1 AATAAAT
61024349 CAAAGTGAAT
Statistics
Matches: 29, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
15 18 0.62
16 11 0.38
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (15 bp):
AATAAATTAAATTAA
Found at i:61025390 original size:2 final size:2
Alignment explanation
Indices: 61025385--61025438 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
61025375 TTTTGTAAGA
61025385 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
61025427 AT AT AT AT AT AT
1 AT AT AT AT AT AT
61025439 CCTATGGTTA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:61041201 original size:13 final size:13
Alignment explanation
Indices: 61041183--61041223 Score: 57
Period size: 13 Copynumber: 3.2 Consensus size: 13
61041173 CTTCTACTTT
61041183 AATTTTTTTATAA
1 AATTTTTTTATAA
* *
61041196 AATTTTATTATAC
1 AATTTTTTTATAA
61041209 AATTTTTTT-TAA
1 AATTTTTTTATAA
61041221 AAT
1 AAT
61041224 ATTTAAATTC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
12 5 0.21
13 19 0.79
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (13 bp):
AATTTTTTTATAA
Found at i:61050351 original size:98 final size:97
Alignment explanation
Indices: 61050169--61050352 Score: 253
Period size: 98 Copynumber: 1.9 Consensus size: 97
61050159 GGTATTGTTG
** * *
61050169 ATTTTTGTTCATTTCATTTAAAAGGTATAATTTTAATTTTGGTCCCTATGCTATGCAGTTATTTG
1 ATTTTTGTTCATTTCATTTAAAAAATATAATTTTAATTTTGATCCCTATGCTAGGCAGTTATTTG
*
61050234 CATTTCGAGATCTCGTTGGTTGTTAATTGCCA
66 CATTTCGAGATCTCATTGGTTGTTAATTGCCA
* * * **
61050266 ATTTTTGTTCTTTTCATTTAAGAAAATATAATTTTTATTTTGATCCCTCTTTTAGGCAGTTATTT
1 ATTTTTGTTCATTTCATTTAA-AAAATATAATTTTAATTTTGATCCCTATGCTAGGCAGTTATTT
61050331 GCATTTCGAGATCGT-ATTGGTT
65 GCATTTCGAGATC-TCATTGGTT
61050353 AATAAATGAT
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
97 20 0.27
98 54 0.72
99 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.15, T:0.49
Consensus pattern (97 bp):
ATTTTTGTTCATTTCATTTAAAAAATATAATTTTAATTTTGATCCCTATGCTAGGCAGTTATTTG
CATTTCGAGATCTCATTGGTTGTTAATTGCCA
Found at i:61050491 original size:28 final size:29
Alignment explanation
Indices: 61050459--61050516 Score: 100
Period size: 28 Copynumber: 2.0 Consensus size: 29
61050449 TCATATTGGT
61050459 TGATAATTGCCTGA-CTTTTTTTTTTAGG
1 TGATAATTGCCTGATCTTTTTTTTTTAGG
*
61050487 TGATAATTGCCTGATTTTTTTTTTTTAGG
1 TGATAATTGCCTGATCTTTTTTTTTTAGG
61050516 T
1 T
61050517 TTAAGGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
28 14 0.50
29 14 0.50
ACGTcount: A:0.17, C:0.09, G:0.17, T:0.57
Consensus pattern (29 bp):
TGATAATTGCCTGATCTTTTTTTTTTAGG
Found at i:61050854 original size:8 final size:8
Alignment explanation
Indices: 61050838--61050879 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
61050828 TTATATTTTA
61050838 ATAAAAAT
1 ATAAAAAT
*
61050846 ATTAAAAT
1 ATAAAAAT
*
61050854 ATTAAAATT
1 A-TAAAAAT
61050863 ATAAAAAT
1 ATAAAAAT
61050871 ATAAAAAT
1 ATAAAAAT
61050879 A
1 A
61050880 GCAAAAAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 23 0.79
9 6 0.21
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (8 bp):
ATAAAAAT
Found at i:61050869 original size:17 final size:17
Alignment explanation
Indices: 61050839--61050878 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
61050829 TATATTTTAA
* *
61050839 TAAAAATATTAAAATAT
1 TAAAATTATAAAAATAT
61050856 TAAAATTATAAAAATAT
1 TAAAATTATAAAAATAT
*
61050873 AAAAAT
1 TAAAAT
61050879 AGCAAAAAAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
TAAAATTATAAAAATAT
Found at i:61050885 original size:25 final size:25
Alignment explanation
Indices: 61050838--61050885 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
61050828 TTATATTTTA
* **
61050838 ATAAAAATATTAAAATATTAAAATT
1 ATAAAAATATAAAAATAGCAAAATT
61050863 ATAAAAATATAAAAATAGCAAAA
1 ATAAAAATATAAAAATAGCAAAA
61050886 AATTTATAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (25 bp):
ATAAAAATATAAAAATAGCAAAATT
Found at i:61051173 original size:21 final size:20
Alignment explanation
Indices: 61051149--61051187 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
61051139 TTTTTTCTAA
61051149 TTTTAATAAAATTTTAATATT
1 TTTTAATAAAA-TTTAATATT
*
61051170 TTTTATTAAAATTTAATA
1 TTTTAATAAAATTTAATA
61051188 ACTTTTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTAATAAAATTTAATATT
Found at i:61051193 original size:20 final size:21
Alignment explanation
Indices: 61051149--61051195 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 21
61051139 TTTTTTCTAA
* **
61051149 TTTTAATAAAATTTTAATATT
1 TTTTATTAAAATTTTAATAAC
61051170 TTTTATTAAAA-TTTAATAAC
1 TTTTATTAAAATTTTAATAAC
61051190 TTTTAT
1 TTTTAT
61051196 AACTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
20 13 0.57
21 10 0.43
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TTTTATTAAAATTTTAATAAC
Found at i:61051193 original size:21 final size:21
Alignment explanation
Indices: 61051149--61051193 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
61051139 TTTTTTCTAA
*
61051149 TTTTAATAAAATTTTAATATT
1 TTTTAATAAAATTTTAATACT
*
61051170 TTTTATTAAAA-TTTAATAACT
1 TTTTAATAAAATTTTAAT-ACT
61051191 TTT
1 TTT
61051194 ATAACTTTTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (21 bp):
TTTTAATAAAATTTTAATACT
Found at i:61051309 original size:13 final size:14
Alignment explanation
Indices: 61051291--61051323 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
61051281 AATTAAAGAC
61051291 GGTTAACT-TTAAA
1 GGTTAACTATTAAA
61051304 GGTTAACTATTAAA
1 GGTTAACTATTAAA
61051318 -GTTAAC
1 GGTTAAC
61051324 GGTCAAAGAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 14 0.74
14 5 0.26
ACGTcount: A:0.39, C:0.09, G:0.15, T:0.36
Consensus pattern (14 bp):
GGTTAACTATTAAA
Found at i:61051438 original size:94 final size:92
Alignment explanation
Indices: 61051330--61051579 Score: 225
Period size: 86 Copynumber: 2.8 Consensus size: 92
61051320 TAACGGTCAA
* * * * *
61051330 AGAGTTTTTTTGATGTATTTTGGCAA-TTTAAGTA-CTCAATCGAGTGCAAAGAAAACAAAGGCT
1 AGAGCTTTTTTGATGCATTTT-GAAAGTTCAAGTACCT-AATCGAGTGCAAAAAAAACAAAGGCT
61051393 TAATTGTTTTTATTTTTATTTTTTATGTTTG
64 TAA-T-TTTTTATTTTTATTTTTTATGTTTG
* * *
61051424 AGAGCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTGGAAAAAAAACAAGGGCTTA
1 AGAGCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATCGAGTGCAAAAAAAACAAAGGCTTA
*
61051489 A-----T-TTTTTATTTTTTAAGTTTG
66 ATTTTTTATTTTTATTTTTTATGTTTG
* * * * * * * *
61051510 AGGGTCTTTTTT-ATGTATTTTAAAAGTTTAAGTACCCAATTGAGTG--AAAAAAATAAAGACTT
1 AGAG-CTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATCGAGTGCAAAAAAAACAAAGGCTT
61051572 AATTTTTT
65 AATTTTTT
61051580 TTGAAATTTT
Statistics
Matches: 131, Mismatches: 17, Indels: 21
0.78 0.10 0.12
Matches are distributed among these distances:
84 15 0.11
86 51 0.39
87 8 0.06
89 1 0.01
93 3 0.02
94 51 0.39
95 2 0.02
ACGTcount: A:0.32, C:0.08, G:0.17, T:0.43
Consensus pattern (92 bp):
AGAGCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATCGAGTGCAAAAAAAACAAAGGCTTA
ATTTTTTATTTTTATTTTTTATGTTTG
Found at i:61051581 original size:86 final size:86
Alignment explanation
Indices: 61051405--61051579 Score: 241
Period size: 86 Copynumber: 2.1 Consensus size: 86
61051395 ATTGTTTTTA
* * *
61051405 TTTTTATTTTTTATGTTTGAGAGCTTTTTTGATGCATTTTGAAAGTTCAAGTACCTAATTGAGTG
1 TTTTTATTTTTTAAGTTTGAGAGCTTTTTTGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTG
*
61051470 GAAAAAAAACAAGGGCTTAAT
66 GAAAAAAAACAAGGACTTAAT
* * *
61051491 TTTTTATTTTTTAAGTTTGAGGGTCTTTTTT-ATGTATTTTAAAAGTTTAAGTACCCAATTGAGT
1 TTTTTATTTTTTAAGTTTGAGAG-CTTTTTTGATGCATTTTAAAAGTTCAAGTACCCAATTGAGT
61051555 -GAAAAAAATA-AA-GACTTAAT
65 GGAAAAAAA-ACAAGGACTTAAT
61051575 TTTTT
1 TTTTT
61051580 TTGAAATTTT
Statistics
Matches: 80, Mismatches: 7, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
84 12 0.15
85 10 0.12
86 51 0.64
87 7 0.09
ACGTcount: A:0.32, C:0.07, G:0.16, T:0.45
Consensus pattern (86 bp):
TTTTTATTTTTTAAGTTTGAGAGCTTTTTTGATGCATTTTAAAAGTTCAAGTACCCAATTGAGTG
GAAAAAAAACAAGGACTTAAT
Found at i:61054739 original size:9 final size:9
Alignment explanation
Indices: 61054725--61054749 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
61054715 TTCATTACGC
61054725 TTTTAAAAA
1 TTTTAAAAA
61054734 TTTTAAAAA
1 TTTTAAAAA
61054743 TTTTAAA
1 TTTTAAA
61054750 TTAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTTAAAAA
Found at i:61055620 original size:83 final size:81
Alignment explanation
Indices: 61055487--61055638 Score: 216
Period size: 83 Copynumber: 1.9 Consensus size: 81
61055477 ATTTCGAGAT
* * * * *
61055487 CTTAGTTAGGCTTATCGTAGGATTTGATTTTCATTTCTTTATAGGCCGGATCTTCAATTATTTAT
1 CTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCCTTACAGGCCGGATCTTCAA--ATTTAT
61055552 TTATTTTTGAAATTTTCA
64 TTATTTTTGAAATTTTCA
*
61055570 CTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCCTTACATGG-CGGATCTTCAAATTTTTT
1 CTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCCTTACA-GGCCGGATCTTCAAATTTATT
61055634 TATTT
65 TATTT
61055639 CTTTGCTTTT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
81 11 0.18
83 49 0.79
84 2 0.03
ACGTcount: A:0.22, C:0.14, G:0.14, T:0.49
Consensus pattern (81 bp):
CTTAGTTAAGCTTATCGTAGCATTTGACTTTCATTTCCTTACAGGCCGGATCTTCAAATTTATTT
ATTTTTGAAATTTTCA
Found at i:61055805 original size:183 final size:182
Alignment explanation
Indices: 61055461--61055822 Score: 479
Period size: 184 Copynumber: 2.0 Consensus size: 182
61055451 TCCTCTGTTT
* * *
61055461 TTTTTTTTTAATTTTCATTTCGAGATCTTAGTTAGGCTTATCGTAGGATTTGATTTTCATTTCTT
1 TTTTTTTTTAATTTTCATTTCGAGATCTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTA
* *
61055526 TATAGGCCGGATCTTCAATTATTTATTTATTTTTGAAATTTTCACTTAGTTAAGCTTATCGTAGC
66 TATAGGCCGGATCATCAATTATTTATTTAATTTT-AAATTTTCACTTAGTTAAGCTTATCGTAGC
61055591 ATTTGACTTTCATTTCCTTACATGGCGGATCTTCAAATTTTTTTATTTCTTTGC
130 ATTTGACTTTCATTTCCTTACATGGCGGATCTTC-AATTTTTTTATTTCTTTGC
*
61055645 TTTTTTTTTAATTTTCATTTCGA-ACTCTTAGTTAAGCTTATCGTAGCATTTTATTTTCA-TT-T
1 TTTTTTTTTAATTTTCATTTCGAGA-TCTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCT
* *
61055707 ATAT-GG-CGGATCATCAATTTTTTATTTCTAATTTT-CA-TTTCGAACTCTTAGTTAAGCTTAT
65 ATATAGGCCGGATCATCAATTATTTA-TT-TAATTTTAAATTTTC--A--CTTAGTTAAGCTTAT
* * *
61055768 CGTAGCATTTGATTTTCATTT-CTTAATATGTCGGATCTTCAATTTTTTTATTTCT
124 CGTAGCATTTGACTTTCATTTCCTT-ACATGGCGGATCTTCAATTTTTTTATTTCT
61055823 CTCTCTCTCT
Statistics
Matches: 159, Mismatches: 11, Indels: 18
0.85 0.06 0.10
Matches are distributed among these distances:
179 4 0.03
180 17 0.11
181 5 0.03
182 28 0.18
183 51 0.32
184 54 0.34
ACGTcount: A:0.22, C:0.14, G:0.12, T:0.52
Consensus pattern (182 bp):
TTTTTTTTTAATTTTCATTTCGAGATCTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTA
TATAGGCCGGATCATCAATTATTTATTTAATTTTAAATTTTCACTTAGTTAAGCTTATCGTAGCA
TTTGACTTTCATTTCCTTACATGGCGGATCTTCAATTTTTTTATTTCTTTGC
Found at i:61055837 original size:82 final size:80
Alignment explanation
Indices: 61055667--61055831 Score: 199
Period size: 82 Copynumber: 2.0 Consensus size: 80
61055657 TTTCATTTCG
*
61055667 AACTCTTAGTTAAGCTTATCGTAGCATTTTATTTTCATTTATATGGCGGATCATCAATTTTTTAT
1 AACTCTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTATATGGCGGATCATCAATTTTTTAT
* * *
61055732 TTCTAATTTTCATTTC
66 TTCT-ACTCTCATCTC
* *
61055748 GAACTCTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTCTTAATATGTCGGATCTTCAATTT
1 -AACTCTTAGTTAAGCTTATCGTAGCATTTGATTTTCA--T-TT-ATATGGCGGATCATCAA-TT
61055813 TTTTATTTCT-CTCTC-TCTC
60 TTTTATTTCTACTCTCATCTC
61055832 TCTCTTTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
82 36 0.50
84 4 0.06
85 5 0.07
86 15 0.21
87 12 0.17
ACGTcount: A:0.22, C:0.17, G:0.10, T:0.50
Consensus pattern (80 bp):
AACTCTTAGTTAAGCTTATCGTAGCATTTGATTTTCATTTATATGGCGGATCATCAATTTTTTAT
TTCTACTCTCATCTC
Found at i:61064627 original size:22 final size:23
Alignment explanation
Indices: 61064584--61064627 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
61064574 TAGTAAAATT
61064584 TTTAAAATCATTAATTATAAAAA
1 TTTAAAATCATTAATTATAAAAA
61064607 TTTAACAAT-ATTAA-TATAAAA
1 TTTAA-AATCATTAATTATAAAA
61064628 TATATTTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
22 7 0.35
23 10 0.50
24 3 0.15
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (23 bp):
TTTAAAATCATTAATTATAAAAA
Found at i:61069699 original size:29 final size:30
Alignment explanation
Indices: 61069640--61069697 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 30
61069630 TCCGAGCCTT
*
61069640 GGGGCAAAAATGTAATTATGTAAAAGTTTA
1 GGGGCAAAAATGTAATTATGAAAAAGTTTA
* *
61069670 GGGGCAAAATTGTAATTTTGAAAAAGTT
1 GGGGCAAAAATGTAATTATGAAAAAGTT
61069698 AGAGTCGAGG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.31
Consensus pattern (30 bp):
GGGGCAAAAATGTAATTATGAAAAAGTTTA
Found at i:61069927 original size:13 final size:13
Alignment explanation
Indices: 61069909--61069940 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
61069899 TTTCCAGCAA
61069909 TTATGAATTTATT
1 TTATGAATTTATT
61069922 TTATGAATTTATT
1 TTATGAATTTATT
*
61069935 TGATGA
1 TTATGA
61069941 TGATCCAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (13 bp):
TTATGAATTTATT
Found at i:61070110 original size:50 final size:50
Alignment explanation
Indices: 61070035--61070227 Score: 305
Period size: 50 Copynumber: 3.8 Consensus size: 50
61070025 ATTTGGGTAA
61070035 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
*
61070085 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** * *
61070135 AGAGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
** *
61070185 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
61070228 TGTTATTATC
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
50 96 0.74
51 34 0.26
ACGTcount: A:0.25, C:0.23, G:0.31, T:0.20
Consensus pattern (50 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATG
Found at i:61075164 original size:44 final size:44
Alignment explanation
Indices: 61075114--61075245 Score: 201
Period size: 44 Copynumber: 3.0 Consensus size: 44
61075104 TACAAAAAAC
*
61075114 TAAATCCACAAGGATTAATAGCAGAATTTGACTATTTTTAGCAT
1 TAAATCCACAAGGATTAATAGCAGAATTTGACCATTTTTAGCAT
*
61075158 TAAATCCACAAGGATTAGTAGCAGAATTTGACCATTTTTAGCAT
1 TAAATCCACAAGGATTAATAGCAGAATTTGACCATTTTTAGCAT
* * * * *
61075202 TAAATTCACAAGGACTAATATCAGAACTTGACCATTTTAAGCAT
1 TAAATCCACAAGGATTAATAGCAGAATTTGACCATTTTTAGCAT
61075246 AGAAAGAGGA
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
44 80 1.00
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.32
Consensus pattern (44 bp):
TAAATCCACAAGGATTAATAGCAGAATTTGACCATTTTTAGCAT
Found at i:61075408 original size:247 final size:248
Alignment explanation
Indices: 61074954--61075447 Score: 780
Period size: 247 Copynumber: 2.0 Consensus size: 248
61074944 AATAAAAAAC
* * * *
61074954 TAAATCCACAAGGACTAATAGCAAAATTTGACCATTTTTAGCATATAATCAGGATTTGCCTTACT
1 TAAATCCACAAGGACTAATAGCAAAACTTGACCATTTTAAGCATAGAAACAGGATTTGCCTTACT
* *
61075019 GGATCAAGACGAAGGTAAACAATCCTTTTGCATGGTTCATTGAAGCTTCAAAAACTATAAGAACT
66 GGATCAAGACGAAGGTAAACAATCCTCTTGCATGGTTCATTGAAGCTTCAAAAACAATAAGAACT
*
61075084 AAAACTGACCAAATTTAGAGTACAAAAAACTAAATCCACAAGGATTAATAGCAGAATTTGACTAT
131 AAAACTGACCAAATTTAGAATACAAAAAACTAAATCCACAAGGATTAATAGCAGAATTTGACTAT
* *
61075149 TTTTAGCATTAAATCCACAAGGATTAGTAGCAGAATTTGACCATTTTTAGCAT
196 TTTTAGCATTAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCAT
* * * *
61075202 TAAATTCACAAGGACTAATATCAGAACTTGACCATTTTAAGCATAGAAAGAGGATTTGCCTTACT
1 TAAATCCACAAGGACTAATAGCAAAACTTGACCATTTTAAGCATAGAAACAGGATTTGCCTTACT
* *
61075267 GGATCAAGAC-AAGGGT-AACAATCCTCTTGCATGGTTCATTGGAGCTTTCAAAAAGAATAAGAA
66 GGATCAAGACGAA-GGTAAACAATCCTCTTGCATGGTTCATTGAAGC-TTCAAAAACAATAAGAA
* *
61075330 CTAAAACTGAGCAAA-TTAGAATACAGAAAACTAAATCCACAAGGATTAATAGCAGAATTTGAGC
129 CTAAAACTGACCAAATTTAGAATACAAAAAACTAAATCCACAAGGATTAATAGCAGAATTTGA-C
61075394 -ATTTTTAGCATTAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCA
193 TATTTTTAGCATTAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCA
61075448 ATATAAGAGG
Statistics
Matches: 226, Mismatches: 17, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
247 126 0.56
248 100 0.44
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.28
Consensus pattern (248 bp):
TAAATCCACAAGGACTAATAGCAAAACTTGACCATTTTAAGCATAGAAACAGGATTTGCCTTACT
GGATCAAGACGAAGGTAAACAATCCTCTTGCATGGTTCATTGAAGCTTCAAAAACAATAAGAACT
AAAACTGACCAAATTTAGAATACAAAAAACTAAATCCACAAGGATTAATAGCAGAATTTGACTAT
TTTTAGCATTAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCAT
Found at i:61075424 original size:44 final size:44
Alignment explanation
Indices: 61075361--61075447 Score: 156
Period size: 44 Copynumber: 2.0 Consensus size: 44
61075351 TACAGAAAAC
* *
61075361 TAAATCCACAAGGATTAATAGCAGAATTTGAGCATTTTTAGCAT
1 TAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCAT
61075405 TAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCA
1 TAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCA
61075448 ATATAAGAGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
44 41 1.00
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (44 bp):
TAAATCCACAAGGATTAATAACAGAATTTGACCATTTTTAGCAT
Found at i:61076457 original size:20 final size:21
Alignment explanation
Indices: 61076422--61076463 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 21
61076412 TTAAAAAATT
61076422 AAATTTAAATGAAAATT-TTG
1 AAATTTAAATGAAAATTGTTG
61076442 AAATTTAGAATG-AAATTGTTG
1 AAATTTA-AATGAAAATTGTTG
61076463 A
1 A
61076464 TGTCATATTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.48, C:0.00, G:0.14, T:0.38
Consensus pattern (21 bp):
AAATTTAAATGAAAATTGTTG
Found at i:61076561 original size:31 final size:32
Alignment explanation
Indices: 61076526--61076597 Score: 87
Period size: 31 Copynumber: 2.3 Consensus size: 32
61076516 CTTCTGATCG
* * *
61076526 ATTTTAGTCTTTGTATTTTTTG-AATTGATTA
1 ATTTTAATCTTTGTACTTTTCGAAATTGATTA
61076557 ATTTTAATCTTTGTACTTTTCGAAATTGA--A
1 ATTTTAATCTTTGTACTTTTCGAAATTGATTA
*
61076587 AGTTTAATCTT
1 ATTTTAATCTT
61076598 GACCCAAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
30 11 0.31
31 19 0.53
32 6 0.17
ACGTcount: A:0.26, C:0.07, G:0.11, T:0.56
Consensus pattern (32 bp):
ATTTTAATCTTTGTACTTTTCGAAATTGATTA
Found at i:61076910 original size:8 final size:8
Alignment explanation
Indices: 61076881--61076909 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
61076871 TTAACGAGGA
61076881 TTAAAATT
1 TTAAAATT
61076889 TTAAAATT
1 TTAAAATT
61076897 TTAAAA-T
1 TTAAAATT
61076904 TTAAAA
1 TTAAAA
61076910 AAATATAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.33
8 14 0.67
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (8 bp):
TTAAAATT
Found at i:61076934 original size:14 final size:15
Alignment explanation
Indices: 61076908--61076938 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
61076898 TAAAATTTAA
61076908 AAAAATATAGAAATT
1 AAAAATATAGAAATT
61076923 AAAAATAT-GAAATT
1 AAAAATATAGAAATT
61076937 AA
1 AA
61076939 TTTAGACTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.68, C:0.00, G:0.06, T:0.26
Consensus pattern (15 bp):
AAAAATATAGAAATT
Found at i:61080630 original size:17 final size:17
Alignment explanation
Indices: 61080610--61080646 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
61080600 CTTGAAGGTC
61080610 ATTGTATTAAATGTCAG
1 ATTGTATTAAATGTCAG
*
61080627 ATTGTATTAAATGTTAG
1 ATTGTATTAAATGTCAG
61080644 ATT
1 ATT
61080647 TATGTATGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.35, C:0.03, G:0.16, T:0.46
Consensus pattern (17 bp):
ATTGTATTAAATGTCAG
Found at i:61080795 original size:24 final size:23
Alignment explanation
Indices: 61080768--61080812 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
61080758 ATATATATTA
61080768 TTTTTAATTTAACATTTTAAATAG
1 TTTTTAATTTAA-ATTTTAAATAG
*
61080792 TTTTTTATTTAAATTTTAAAT
1 TTTTTAATTTAAATTTTAAAT
61080813 TTAGACAATT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 9 0.45
24 11 0.55
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (23 bp):
TTTTTAATTTAAATTTTAAATAG
Found at i:61081127 original size:2 final size:2
Alignment explanation
Indices: 61081117--61081148 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
61081107 AAAAAAAAAA
61081117 AT AT A- 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 A
61081149 AATTTACGCT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:61089838 original size:16 final size:18
Alignment explanation
Indices: 61089806--61089839 Score: 54
Period size: 16 Copynumber: 2.0 Consensus size: 18
61089796 AATTCTTTGA
61089806 AAGTAATTTATTATCAAT
1 AAGTAATTTATTATCAAT
61089824 AAGTAA-TTA-TATCAAT
1 AAGTAATTTATTATCAAT
61089840 TGTAATAAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.44
17 3 0.19
18 6 0.38
ACGTcount: A:0.47, C:0.06, G:0.06, T:0.41
Consensus pattern (18 bp):
AAGTAATTTATTATCAAT
Found at i:61098767 original size:7 final size:7
Alignment explanation
Indices: 61098755--61098779 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
61098745 TCCAATAAAA
61098755 ACATGAC
1 ACATGAC
61098762 ACATGAC
1 ACATGAC
61098769 ACATGAC
1 ACATGAC
61098776 ACAT
1 ACAT
61098780 TCTTATTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.44, C:0.28, G:0.12, T:0.16
Consensus pattern (7 bp):
ACATGAC
Found at i:61102042 original size:21 final size:21
Alignment explanation
Indices: 61102018--61102057 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
61102008 TATTTCTTGC
**
61102018 TATTTTCTTTTTATTTTTTAT
1 TATTTTCTTACTATTTTTTAT
61102039 TATTTTCTTACTATTTTTT
1 TATTTTCTTACTATTTTTT
61102058 TGTTGTTTTT
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:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TATTTTCTTACTATTTTTTAT
Found at i:61102067 original size:32 final size:32
Alignment explanation
Indices: 61102010--61102076 Score: 82
Period size: 32 Copynumber: 2.1 Consensus size: 32
61102000 GCCTCAGATA
* * *
61102010 TTTCTTGCTATTTTCTTTTTATTTTTTATTAT
1 TTTCTTACTATTTTCTTTTTATTTTTCACTAT
*
61102042 TTTCTTACTATTTT-TTTGTTGTTTTTCACTAT
1 TTTCTTACTATTTTCTTT-TTATTTTTCACTAT
61102074 TTT
1 TTT
61102077 GCTACCATTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.10
32 27 0.90
ACGTcount: A:0.12, C:0.10, G:0.04, T:0.73
Consensus pattern (32 bp):
TTTCTTACTATTTTCTTTTTATTTTTCACTAT
Found at i:61114106 original size:20 final size:19
Alignment explanation
Indices: 61114065--61114106 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
61114055 TTATTTAAAT
*
61114065 AAATTATTAAAAATACATA
1 AAATTATTAAAAATACAAA
*
61114084 AAATTATTTAAAAATAGAAA
1 AAATTA-TTAAAAATACAAA
61114104 AAA
1 AAA
61114107 AAACCAATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 6 0.30
20 14 0.70
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.29
Consensus pattern (19 bp):
AAATTATTAAAAATACAAA
Found at i:61115437 original size:15 final size:15
Alignment explanation
Indices: 61115382--61115438 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
61115372 TTTATACTAC
61115382 AAAATATTTATTATT
1 AAAATATTTATTATT
** *
61115397 ACTATATTTATAACTGT
1 AAAATATTTATTA-T-T
61115414 AATAAATATTTATTATT
1 -A-AAATATTTATTATT
61115431 AAAATATT
1 AAAATATT
61115439 AATATTGATA
Statistics
Matches: 32, Mismatches: 6, Indels: 8
0.70 0.13 0.17
Matches are distributed among these distances:
15 17 0.53
16 2 0.06
17 2 0.06
18 2 0.06
19 9 0.28
ACGTcount: A:0.46, C:0.04, G:0.02, T:0.49
Consensus pattern (15 bp):
AAAATATTTATTATT
Found at i:61115479 original size:16 final size:17
Alignment explanation
Indices: 61115460--61115496 Score: 60
Period size: 16 Copynumber: 2.3 Consensus size: 17
61115450 TTTTGAATAA
61115460 TATTATTTAAAA-TTAT
1 TATTATTTAAAATTTAT
61115476 TATT-TTTAAAATTTAT
1 TATTATTTAAAATTTAT
61115492 TATTA
1 TATTA
61115497 AAATAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
15 7 0.37
16 12 0.63
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TATTATTTAAAATTTAT
Found at i:61115556 original size:16 final size:16
Alignment explanation
Indices: 61115510--61115559 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
61115500 TAAAATTAAA
61115510 ATATTAAATAATTTATT
1 ATATT-AATAATTTATT
**
61115527 A-A--AATAATAAATT
1 ATATTAATAATTTATT
61115540 ATATTAATAATTTATT
1 ATATTAATAATTTATT
61115556 ATAT
1 ATAT
61115560 GACTAAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 7
0.70 0.11 0.19
Matches are distributed among these distances:
13 10 0.38
14 1 0.04
16 14 0.54
17 1 0.04
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
ATATTAATAATTTATT
Found at i:61121725 original size:71 final size:71
Alignment explanation
Indices: 61121593--61121725 Score: 169
Period size: 71 Copynumber: 1.9 Consensus size: 71
61121583 ACTAACATGT
** *
61121593 ATGTTAAGGCTTGAACTCAAGGCCTCTAGTACATAAAAGATCTCGAGTGTACTATGGTACTACTT
1 ATGTTAAGGCTTGAACTCAAAACCTCTAG-ACATAAAAGATCTCGAGTGAACTATGGTACTACTT
61121658 GACCTAG
65 GACCTAG
* * * * *
61121665 ATGTTAAGGTTTGAACTCAAAACCTTTAG-CATTAAAGGTTCTCGAGTGAATTATGGTACTA
1 ATGTTAAGGCTTGAACTCAAAACCTCTAGACA-TAAAAGATCTCGAGTGAACTATGGTACTA
61121726 TTTAAGCTAG
Statistics
Matches: 52, Mismatches: 8, Indels: 3
0.83 0.13 0.05
Matches are distributed among these distances:
70 2 0.04
71 25 0.48
72 25 0.48
ACGTcount: A:0.32, C:0.17, G:0.20, T:0.32
Consensus pattern (71 bp):
ATGTTAAGGCTTGAACTCAAAACCTCTAGACATAAAAGATCTCGAGTGAACTATGGTACTACTTG
ACCTAG
Found at i:61124840 original size:179 final size:177
Alignment explanation
Indices: 61124495--61124870 Score: 551
Period size: 179 Copynumber: 2.1 Consensus size: 177
61124485 AGGATATGAT
61124495 CCTCCAAGA-GCATGCATGTATATATGTGTTTATGTATGCCATTTGGATTTTGTATGATTCCCTT
1 CCTCCAA-ATGCATGCATGTATATATGTGTTTATGTATGCCATTTGGATTTTGTATGATTCCCTT
* * *
61124559 GTTAATGTCATTCCCTTGTGTTAATGTGTTTATCTTTTGTCAATGCATGCATGCCTGCATGTCAT
65 GTTAATGTCATTACCTTGTGTTAATGTGTTCATCTTTTGTCAATGCATGCATGCATGCATGTCAT
* *
61124624 TTGGTTTTTATGGATTTTCTATGGTTCCCGGGATATGATTCTCCAAGAAC
130 TTGGTTTTTATGGACTTTCTATGGTT-CC-GGATATGATCCTCCAAGAAC
* *
61124674 CCTCCAAATGCATGCATGTATATATGTGTTTATGTATGTCATTTGGATTTTGTATGGTTCCCTTG
1 CCTCCAAATGCATGCATGTATATATGTGTTTATGTATGCCATTTGGATTTTGTATGATTCCCTTG
* * * *
61124739 TTAATGTTATTACCTTGTGTTATTGTGTTCATCTTTTGTCAATGTATGTATGTATGCATGCATGT
66 TTAATGTCATTACCTTGTGTTAATGTGTTCATCTTTTGTC-A---ATGCATGCATGCATGCATGT
* *
61124804 CATTTGTTTTTTATGGACTTTGTATGGTT-C-GATATGATCCTCCAAGAAC
127 CATTTGGTTTTTATGGACTTTCTATGGTTCCGGATATGATCCTCCAAGAAC
61124853 CCTCCAAATGCATGCATG
1 CCTCCAAATGCATGCATG
61124871 CATGCATGTA
Statistics
Matches: 179, Mismatches: 13, Indels: 10
0.89 0.06 0.05
Matches are distributed among these distances:
178 1 0.01
179 133 0.74
180 1 0.01
181 1 0.01
183 43 0.24
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (177 bp):
CCTCCAAATGCATGCATGTATATATGTGTTTATGTATGCCATTTGGATTTTGTATGATTCCCTTG
TTAATGTCATTACCTTGTGTTAATGTGTTCATCTTTTGTCAATGCATGCATGCATGCATGTCATT
TGGTTTTTATGGACTTTCTATGGTTCCGGATATGATCCTCCAAGAAC
Found at i:61136597 original size:18 final size:20
Alignment explanation
Indices: 61136574--61136615 Score: 61
Period size: 18 Copynumber: 2.2 Consensus size: 20
61136564 AATTATTTTC
61136574 ATTATTTTA-AATATAA-AA
1 ATTATTTTATAATATAATAA
*
61136592 ATTATTTTATATTATAATAA
1 ATTATTTTATAATATAATAA
61136612 ATTA
1 ATTA
61136616 AAATTAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTATTTTATAATATAATAA
Found at i:61136617 original size:27 final size:27
Alignment explanation
Indices: 61136564--61136618 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
61136554 ATCAATTTTG
**
61136564 AATTATTTTCATTATTTTAAATATAAA
1 AATTATTTTCATTATAATAAATATAAA
*
61136591 AATTATTTTATATTATAATAAAT-TAAA
1 AATTATTTT-CATTATAATAAATATAAA
61136618 A
1 A
61136619 TTAATTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 14 0.58
28 10 0.42
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
AATTATTTTCATTATAATAAATATAAA
Found at i:61137029 original size:29 final size:30
Alignment explanation
Indices: 61136973--61137064 Score: 89
Period size: 29 Copynumber: 3.1 Consensus size: 30
61136963 ATATATTTTA
* *
61136973 AGTCTTTATACTTTTTGTAAATTT-AAAATTT
1 AGTCATTATAC-TTTT-TACATTTAAAAATTT
*
61137004 AGTCATTATA-TTTTTACTTTTAAAAATTT
1 AGTCATTATACTTTTTACATTTAAAAATTT
* * * *
61137033 AGTCCTTTTACTTTTTAGATTTCAAAATTT
1 AGTCATTATACTTTTTACATTTAAAAATTT
61137063 AG
1 AG
61137065 GTTCAATTGT
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
28 5 0.10
29 19 0.37
30 18 0.35
31 9 0.18
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.53
Consensus pattern (30 bp):
AGTCATTATACTTTTTACATTTAAAAATTT
Found at i:61137060 original size:30 final size:28
Alignment explanation
Indices: 61136993--61137064 Score: 81
Period size: 30 Copynumber: 2.5 Consensus size: 28
61136983 CTTTTTGTAA
61136993 ATTTAAAATTTAGTCATTATATTTTTAC
1 ATTTAAAATTTAGTCATTATATTTTTAC
* * * *
61137021 TTTTAAAAATTTAGTCCTTTTACTTTTTAG
1 ATTT-AAAATTTAGTCATTATA-TTTTTAC
61137051 ATTTCAAAATTTAG
1 ATTT-AAAATTTAG
61137065 GTTCAATTGT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
28 3 0.08
29 15 0.42
30 18 0.50
ACGTcount: A:0.33, C:0.08, G:0.06, T:0.53
Consensus pattern (28 bp):
ATTTAAAATTTAGTCATTATATTTTTAC
Found at i:61145610 original size:25 final size:26
Alignment explanation
Indices: 61145582--61145639 Score: 68
Period size: 27 Copynumber: 2.3 Consensus size: 26
61145572 ATTTTTGAAA
*
61145582 TTTTTT-GGAATTT-AA-ATAATAATT
1 TTTTTTAGG-ATTTAAATATAAGAATT
61145606 TTTTTTAGGATTTAGAATATAAGAATT
1 TTTTTTAGGATTTA-AATATAAGAATT
61145633 TTTTTTA
1 TTTTTTA
61145640 CCATAACCAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 10 0.34
25 2 0.07
26 2 0.07
27 15 0.52
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.55
Consensus pattern (26 bp):
TTTTTTAGGATTTAAATATAAGAATT
Found at i:61146582 original size:6 final size:6
Alignment explanation
Indices: 61146571--61146606 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
61146561 GCGGGTTTCT
61146571 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC
1 TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC TTTTGC
61146607 ATGCTCTGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.00, C:0.17, G:0.17, T:0.67
Consensus pattern (6 bp):
TTTTGC
Found at i:61147193 original size:2 final size:2
Alignment explanation
Indices: 61147188--61147221 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
61147178 TATGTTTATG
61147188 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
61147222 ATTTATTTGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:61149234 original size:31 final size:29
Alignment explanation
Indices: 61149181--61149244 Score: 74
Period size: 31 Copynumber: 2.1 Consensus size: 29
61149171 AATTTTTACT
*
61149181 TAAACCCCAAAATTTTTAAAATTTCTAAA
1 TAAACCCCAAAAGTTTTAAAATTTCTAAA
* * *
61149210 TAAACCCTACAAAAGTTTTGAAATTTTTAAT
1 TAAACCC--CAAAAGTTTTAAAATTTCTAAA
61149241 TAAA
1 TAAA
61149245 TCCTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 7 0.24
31 22 0.76
ACGTcount: A:0.47, C:0.14, G:0.03, T:0.36
Consensus pattern (29 bp):
TAAACCCCAAAAGTTTTAAAATTTCTAAA
Done.