Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr06 ID=Chr06-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: 51074515
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 971674 characters in sequence are not A, C, G, or T
File 125 of 168
Found at i:36299441 original size:17 final size:17
Alignment explanation
Indices: 36299421--36299462 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
36299411 AATAATAAAC
36299421 AATAATATATAATATGT
1 AATAATATATAATATGT
*
36299438 AATAATATGTAATATGT
1 AATAATATATAATATGT
36299455 AAT-ATATA
1 AATAATATA
36299463 ATGTATAATG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 4 0.17
17 19 0.83
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.40
Consensus pattern (17 bp):
AATAATATATAATATGT
Found at i:36299601 original size:17 final size:17
Alignment explanation
Indices: 36299579--36299622 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
36299569 TAAACTACTA
*
36299579 ATATATTATATACCA-T
1 ATATATTATATAACATT
*
36299595 ATGATATGATATAACATT
1 AT-ATATTATATAACATT
36299613 ATATATTATA
1 ATATATTATA
36299623 GTAGGAGTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 2 0.09
17 18 0.78
18 3 0.13
ACGTcount: A:0.45, C:0.07, G:0.05, T:0.43
Consensus pattern (17 bp):
ATATATTATATAACATT
Found at i:36308955 original size:31 final size:29
Alignment explanation
Indices: 36308917--36308990 Score: 85
Period size: 29 Copynumber: 2.5 Consensus size: 29
36308907 CTAACGGCTC
*
36308917 AGTGACTAAAATGTTACAACGTGATAACATA
1 AGTGACTAAAATGTTAC-ACGTCA-AACATA
* **
36308948 AGTGACTAAAACGTTACATTTCAAACATA
1 AGTGACTAAAATGTTACACGTCAAACATA
*
36308977 AGTAACTAAAATGT
1 AGTGACTAAAATGT
36308991 AACCTGAGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
29 18 0.49
30 3 0.08
31 16 0.43
ACGTcount: A:0.46, C:0.14, G:0.14, T:0.27
Consensus pattern (29 bp):
AGTGACTAAAATGTTACACGTCAAACATA
Found at i:36313080 original size:21 final size:21
Alignment explanation
Indices: 36313054--36313107 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
36313044 CAGCGGTGGC
*
36313054 GGTGAGATTAGTTACTGTAGT
1 GGTGAGATTAGATACTGTAGT
*
36313075 GGTGAGATTGGATACTGTAGT
1 GGTGAGATTAGATACTGTAGT
*
36313096 AGTGAGATTAGA
1 GGTGAGATTAGA
36313108 AACAGCGGTG
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:0.28, C:0.04, G:0.35, T:0.33
Consensus pattern (21 bp):
GGTGAGATTAGATACTGTAGT
Found at i:36316070 original size:2 final size:2
Alignment explanation
Indices: 36316065--36316101 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
36316055 ACAGATGCAA
36316065 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
36316102 TAAACAGAGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:36317881 original size:6 final size:6
Alignment explanation
Indices: 36317870--36317907 Score: 58
Period size: 6 Copynumber: 6.2 Consensus size: 6
36317860 TTTGCAACCC
*
36317870 AAGGGG AAGGGG AAAGGG AAGGGG AAGGGG AAAGGGG A
1 AAGGGG AAGGGG AAGGGG AAGGGG AAGGGG -AAGGGG A
36317908 GAAGAAGGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (6 bp):
AAGGGG
Found at i:36317893 original size:18 final size:18
Alignment explanation
Indices: 36317870--36317905 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
36317860 TTTGCAACCC
36317870 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
36317888 AAGGGGAAGGGGAAAGGG
1 AAGGGGAAGGGGAAAGGG
36317906 GAGAAGAAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.00, G:0.61, T:0.00
Consensus pattern (18 bp):
AAGGGGAAGGGGAAAGGG
Found at i:36317914 original size:18 final size:18
Alignment explanation
Indices: 36317875--36317916 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36317865 AACCCAAGGG
**
36317875 GAAGGGGAAAGGGAAGGG
1 GAAGGGGAAAGGGAAGAA
*
36317893 GAAGGGGAAAGGGGAGAA
1 GAAGGGGAAAGGGAAGAA
36317911 GAAGGG
1 GAAGGG
36317917 TAACCAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.40, C:0.00, G:0.60, T:0.00
Consensus pattern (18 bp):
GAAGGGGAAAGGGAAGAA
Found at i:36326253 original size:24 final size:24
Alignment explanation
Indices: 36326225--36326279 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
36326215 GTGTCATGTT
* *
36326225 ATTATTCATTGATGATACATGAAAC
1 ATTATTCACT-ATGATACATCAAAC
*
36326250 -TTATGCACTATGATACATCAAAC
1 ATTATTCACTATGATACATCAAAC
36326273 ATTATTC
1 ATTATTC
36326280 CTTTTATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
23 13 0.52
24 12 0.48
ACGTcount: A:0.38, C:0.16, G:0.09, T:0.36
Consensus pattern (24 bp):
ATTATTCACTATGATACATCAAAC
Found at i:36334087 original size:153 final size:155
Alignment explanation
Indices: 36333878--36334188 Score: 509
Period size: 153 Copynumber: 2.0 Consensus size: 155
36333868 TAGAATACCC
*
36333878 TTAGCATTAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCATAAATTTGTTTTGGT-AA-GATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
* * * * *
36333943 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTTTTAAACCCATTTTAATTAAAA
64 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACACATTATAATTAAAA
*
36334008 TATATAATTTCATAAAATTCTTAATAA
129 TATATAATTTAATAAAATTCTTAATAA
36334035 TTAGCATAAATTTGTTTTGGT-A-ATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAAT
1 TTAGCATAAATTTGTTTTGGTAAGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAAT
* *
36334098 ATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAATA
66 ATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACACATTATAATTAAAATA
36334163 TATAATTTAATAAAATTCTTAATAA
131 TATAATTTAATAAAATTCTTAATAA
36334188 T
1 T
36334189 AATATTCTTA
Statistics
Matches: 145, Mismatches: 9, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
153 124 0.86
155 1 0.01
157 20 0.14
ACGTcount: A:0.43, C:0.05, G:0.05, T:0.48
Consensus pattern (155 bp):
TTAGCATAAATTTGTTTTGGTAAGATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTAAT
ATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAACACATTATAATTAAAATA
TATAATTTAATAAAATTCTTAATAA
Found at i:36334161 original size:16 final size:16
Alignment explanation
Indices: 36334124--36334165 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
36334114 TTAATCATAT
*
36334124 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
36334140 TT-AAATATATTATAA
1 TTAAAATATATTATAA
36334155 TTAAAATATAT
1 TTAAAATATAT
36334166 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:36334172 original size:14 final size:15
Alignment explanation
Indices: 36334133--36334174 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
36334123 TTTAAACATA
*
36334133 ATTATTATTAAATAT
1 ATTATAATTAAATAT
36334148 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
36334162 A-TATAATTTAATA
1 ATTATAATTAAATA
36334175 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:36334291 original size:14 final size:15
Alignment explanation
Indices: 36334242--36334293 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
36334232 GTAAAATATA
36334242 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
36334257 TATTAAATATATTAT
1 AATTAAATATATTAT
36334272 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
36334285 AATTTAATA
1 AATTAAATA
36334294 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:36334411 original size:14 final size:15
Alignment explanation
Indices: 36334362--36334413 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
36334352 ATAAAATATA
36334362 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
36334377 TATTAAATATATTAT
1 AATTAAATATATTAT
36334392 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
36334405 AATTTAATA
1 AATTAAATA
36334414 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:36334549 original size:120 final size:120
Alignment explanation
Indices: 36334127--36334538 Score: 706
Period size: 120 Copynumber: 3.4 Consensus size: 120
36334117 ATCATATTTA
36334127 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAA-TAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
36334191 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
36334246 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
36334311 TATTCTTATATGAATTTACTCAAATCATAATAAATGATACTATAAAATATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
36334366 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
*
36334431 TACTCTTATATGAATTTACTCAAATCATAATATATGATACTAT-AAATGA-AAATTT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAAT-ATAAA-TT
* * * *
36334486 GAA-ATAATTAATATTAAATATATTTTATTTAAAATATATGATTTAATAAAATT
1 -AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATT
36334539 TAAAATAATT
Statistics
Matches: 281, Mismatches: 8, Indels: 7
0.95 0.03 0.02
Matches are distributed among these distances:
119 68 0.24
120 211 0.75
121 2 0.01
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTATAAAATATAAATT
Found at i:36334625 original size:24 final size:25
Alignment explanation
Indices: 36334579--36334626 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
36334569 TATGAATTTG
36334579 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
36334605 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
36334627 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:36334630 original size:92 final size:92
Alignment explanation
Indices: 36334534--36334762 Score: 227
Period size: 92 Copynumber: 2.5 Consensus size: 92
36334524 TGATTTAATA
* * *
36334534 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
36334596 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
36334626 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* * *
36334691 ATTAAATATAATTTAA-CAGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
36334716 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
36334763 CTAAAATCAA
Statistics
Matches: 118, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 80 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:36335611 original size:17 final size:17
Alignment explanation
Indices: 36335589--36335627 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
36335579 AAGAGGTGAA
36335589 AATAAAAATACAATTTC
1 AATAAAAATACAATTTC
36335606 AATAAAAATACAATTTC
1 AATAAAAATACAATTTC
36335623 AATAA
1 AATAA
36335628 TAAAAAAAGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.62, C:0.10, G:0.00, T:0.28
Consensus pattern (17 bp):
AATAAAAATACAATTTC
Found at i:36341657 original size:138 final size:138
Alignment explanation
Indices: 36341503--36341772 Score: 459
Period size: 138 Copynumber: 2.0 Consensus size: 138
36341493 ACATAAATAT
* *
36341503 AATTAATATATTAATTTGATTCATACAAAATATTAATTGTATATATTTTACCGAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTATTAATA
* *
36341568 TAAACAGTTATATTAATTAATTTCGGCCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAAATTCGGCCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
36341633 AAAAATGC
131 AAAAATGC
* *
36341641 AATTAATATATGAATTTGATTCATACAAAATATTAATTTTATATATTTTACATAATTTATTAATA
1 AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTATTAATA
** *
36341706 TAAACAATTATATTAATTAAATTCGTTCAAAATATAAAAGACATGGAAATTAATATTCTTTTGGA
66 TAAACAATTATATTAATTAAATTCGGCCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
36341771 AA
131 AA
36341773 GAATATAATT
Statistics
Matches: 123, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
138 123 1.00
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (138 bp):
AATTAATATATGAATTTGATTCATACAAAATATTAATTGTATATATTTTACAGAATTTATTAATA
TAAACAATTATATTAATTAAATTCGGCCAAAATATAAAAGACATGAAAATTAATATTCTTTTGGA
AAAAATGC
Found at i:36349839 original size:25 final size:25
Alignment explanation
Indices: 36349703--36349839 Score: 70
Period size: 25 Copynumber: 5.5 Consensus size: 25
36349693 AGCTCATGTG
* * * *
36349703 AGCCATGTAACGGGAAGCTCAGAAG
1 AGCCATATATCGGGAAGCTCCGAAA
*
36349728 AGCCATA-ATCGGGAAG-TTC-AAGCA
1 AGCCATATATCGGGAAGCTCCGAA--A
* * *
36349752 AGCCA-ATATCGGGAAGCTTCGGAG
1 AGCCATATATCGGGAAGCTCCGAAA
* *
36349776 AGCCAT-TAATCGAGAAGCTCATGAAAA
1 AGCCATAT-ATCGGGAAGCTC-CG-AAA
* *
36349803 ATCC-TTTAATCGGGAAGCTCCGAAA
1 AGCCATAT-ATCGGGAAGCTCCGAAA
36349828 AGCCATATATCG
1 AGCCATATATCG
36349840 AAATGCTCAT
Statistics
Matches: 84, Mismatches: 17, Indels: 22
0.68 0.14 0.18
Matches are distributed among these distances:
22 2 0.02
23 2 0.02
24 28 0.33
25 29 0.35
26 6 0.07
27 17 0.20
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (25 bp):
AGCCATATATCGGGAAGCTCCGAAA
Found at i:36355358 original size:24 final size:24
Alignment explanation
Indices: 36355331--36355406 Score: 61
Period size: 24 Copynumber: 3.2 Consensus size: 24
36355321 GATATTTGAA
36355331 ATAATTAATTGAAACATTTTACAT
1 ATAATTAATTGAAACATTTTACAT
* * *
36355355 ATAA-AAATAAT-AATGATATTTGA-A-
1 ATAATTAAT--TGAA--ACATTTTACAT
36355379 ATAATTAATTGAAACATTTTACAT
1 ATAATTAATTGAAACATTTTACAT
36355403 ATAA
1 ATAA
36355407 AAATAATAAT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
22 6 0.16
23 5 0.13
24 16 0.42
25 5 0.13
26 6 0.16
ACGTcount: A:0.51, C:0.05, G:0.05, T:0.38
Consensus pattern (24 bp):
ATAATTAATTGAAACATTTTACAT
Found at i:36355365 original size:26 final size:26
Alignment explanation
Indices: 36355336--36355413 Score: 69
Period size: 26 Copynumber: 3.2 Consensus size: 26
36355326 TTGAAATAAT
36355336 TAATTGAAACATTTTACATATAAAAA
1 TAATTGAAACATTTTACATATAAAAA
* * *
36355362 TAA-T-AATGATATTTGA-A-AT--AAT
1 TAATTGAA--ACATTTTACATATAAAAA
36355384 TAATTGAAACATTTTACATATAAAAA
1 TAATTGAAACATTTTACATATAAAAA
36355410 TAAT
1 TAAT
36355414 AATGATATTT
Statistics
Matches: 38, Mismatches: 6, Indels: 16
0.63 0.10 0.27
Matches are distributed among these distances:
22 11 0.29
23 2 0.05
24 8 0.21
25 2 0.05
26 15 0.39
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.37
Consensus pattern (26 bp):
TAATTGAAACATTTTACATATAAAAA
Found at i:36355383 original size:48 final size:48
Alignment explanation
Indices: 36355278--36355433 Score: 237
Period size: 48 Copynumber: 3.3 Consensus size: 48
36355268 TTTGTATGTG
** ** * *
36355278 TATTTGAAATAATTGTTTGAAATGTTTCACATAT--AAA-CATAATGA
1 TATTTGAAATAATTAATTGAAACATTTTACATATAAAAATAATAATGA
36355323 TATTTGAAATAATTAATTGAAACATTTTACATATAAAAATAATAATGA
1 TATTTGAAATAATTAATTGAAACATTTTACATATAAAAATAATAATGA
36355371 TATTTGAAATAATTAATTGAAACATTTTACATATAAAAATAATAATGA
1 TATTTGAAATAATTAATTGAAACATTTTACATATAAAAATAATAATGA
36355419 TATTTGAAATAATTA
1 TATTTGAAATAATTA
36355434 CTTAATTTTA
Statistics
Matches: 102, Mismatches: 6, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
45 29 0.28
47 3 0.03
48 70 0.69
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (48 bp):
TATTTGAAATAATTAATTGAAACATTTTACATATAAAAATAATAATGA
Found at i:36355825 original size:19 final size:19
Alignment explanation
Indices: 36355801--36355837 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 19
36355791 GCTAATGTGT
36355801 TAAAAATAATAA-TTAAAAA
1 TAAAAATAA-AACTTAAAAA
36355820 TAAAAATAAAACTTAAAA
1 TAAAAATAAAACTTAAAA
36355838 CAATATGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAATAAAACTTAAAAA
Found at i:36366936 original size:19 final size:20
Alignment explanation
Indices: 36366899--36366937 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
36366889 TTTTTAGAAT
* *
36366899 TTTTTTGAAAATTTTTATAA
1 TTTTTTGAAAATATATATAA
36366919 TTTTTT-AAAATATATATAA
1 TTTTTTGAAAATATATATAA
36366938 AATTTGGAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (20 bp):
TTTTTTGAAAATATATATAA
Found at i:36366956 original size:18 final size:19
Alignment explanation
Indices: 36366933--36366969 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
36366923 TTAAAATATA
36366933 TATAAA-ATTTGGAATTTT
1 TATAAATATTTGGAATTTT
*
36366951 TATAAATCTTTGGAATTTT
1 TATAAATATTTGGAATTTT
36366970 AAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.35, C:0.03, G:0.11, T:0.51
Consensus pattern (19 bp):
TATAAATATTTGGAATTTT
Found at i:36366970 original size:18 final size:19
Alignment explanation
Indices: 36366940--36366975 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
36366930 ATATATAAAA
*
36366940 TTTGGAATTTTTATAAATC
1 TTTGGAATTTTTAAAAATC
36366959 TTTGGAA-TTTTAAAAAT
1 TTTGGAATTTTTAAAAAT
36366976 TATTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.36, C:0.03, G:0.11, T:0.50
Consensus pattern (19 bp):
TTTGGAATTTTTAAAAATC
Found at i:36366994 original size:20 final size:20
Alignment explanation
Indices: 36366966--36367006 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
36366956 ATCTTTGGAA
36366966 TTTTAAAAATTATTTTAAAT
1 TTTTAAAAATTATTTTAAAT
* *
36366986 TTTTGAAAATTATTTTGAAT
1 TTTTAAAAATTATTTTAAAT
36367006 T
1 T
36367007 ATTTTGTAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTTAAAAATTATTTTAAAT
Found at i:36367776 original size:22 final size:23
Alignment explanation
Indices: 36367723--36367781 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 23
36367713 ATGCAATCTT
* *
36367723 AGATATGA-TATGTAATCTTAGA
1 AGATATGATTCTGTAATATTAGA
36367745 AGATATGATTCTGTAATATTAG-
1 AGATATGATTCTGTAATATTAGA
* *
36367767 AGATTTGATTTTGTA
1 AGATATGATTCTGTA
36367782 GATAGCTTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.36, C:0.03, G:0.19, T:0.42
Consensus pattern (23 bp):
AGATATGATTCTGTAATATTAGA
Found at i:36371417 original size:22 final size:23
Alignment explanation
Indices: 36371358--36371418 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
36371348 TATGCAATCT
* *
36371358 AAGATATGA-TATGTAATTTTAG
1 AAGATATGATTCTGTAATCTTAG
*
36371380 AAGATATGGTTCTGTAATCTTAG
1 AAGATATGATTCTGTAATCTTAG
* *
36371403 -AGATTTGATTTTGTAA
1 AAGATATGATTCTGTAA
36371419 ATAGCTTTTA
Statistics
Matches: 32, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
22 21 0.66
23 11 0.34
ACGTcount: A:0.34, C:0.03, G:0.20, T:0.43
Consensus pattern (23 bp):
AAGATATGATTCTGTAATCTTAG
Found at i:36389050 original size:13 final size:11
Alignment explanation
Indices: 36389014--36389044 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
36389004 CCGTCCGTAT
36389014 TAATTTTTATA
1 TAATTTTTATA
*
36389025 TTATTTTTATA
1 TAATTTTTATA
36389036 TAATTTTTA
1 TAATTTTTA
36389045 AATATATATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (11 bp):
TAATTTTTATA
Found at i:36389187 original size:30 final size:30
Alignment explanation
Indices: 36389160--36389228 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
36389150 GATATAACTT
36389160 ATCAAGCAAATGCCTCTAAAATAATAACAGA
1 ATCAA-CAAATGCCTCTAAAATAATAACAGA
* *
36389191 ATTAACAAATGCCTCTAAAATAATAACAAA
1 ATCAACAAATGCCTCTAAAATAATAACAGA
*
36389221 ATTAACAA
1 ATCAACAA
36389229 TAAAACAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
30 32 0.89
31 4 0.11
ACGTcount: A:0.55, C:0.17, G:0.06, T:0.22
Consensus pattern (30 bp):
ATCAACAAATGCCTCTAAAATAATAACAGA
Found at i:36390935 original size:66 final size:62
Alignment explanation
Indices: 36390827--36390950 Score: 176
Period size: 66 Copynumber: 1.9 Consensus size: 62
36390817 ATAATGTGGT
36390827 AAGCAAAAATTTTATTGTTTCATAAATGCTTTTACTATTAAATTATAAATGTTATTATGAGG
1 AAGCAAAAATTTTATTGTTTCATAAATGCTTTTACTATTAAATTATAAATGTTATTATGAGG
* * * *
36390889 AAGCGAAAATTTTGATTGTTTTATAAATGGTTTTTTTACTATTAAATTATAATTGTTATTAT
1 AAGCAAAAATTTT-ATTGTTTCATAAAT-G--CTTTTACTATTAAATTATAAATGTTATTAT
36390951 TAAAGTAAAG
Statistics
Matches: 54, Mismatches: 4, Indels: 4
0.87 0.06 0.06
Matches are distributed among these distances:
62 12 0.22
63 13 0.24
64 1 0.02
66 28 0.52
ACGTcount: A:0.36, C:0.05, G:0.11, T:0.48
Consensus pattern (62 bp):
AAGCAAAAATTTTATTGTTTCATAAATGCTTTTACTATTAAATTATAAATGTTATTATGAGG
Found at i:36392508 original size:13 final size:14
Alignment explanation
Indices: 36392492--36392525 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
36392482 ATTTTTTCGG
36392492 AAATTTTTTAT-TA
1 AAATTTTTTATCTA
36392505 AAATTTTTTATCGTA
1 AAATTTTTTATC-TA
36392520 AAATTT
1 AAATTT
36392526 AACTACATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 11 0.58
15 8 0.42
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.56
Consensus pattern (14 bp):
AAATTTTTTATCTA
Found at i:36394510 original size:6 final size:6
Alignment explanation
Indices: 36394501--36394531 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
36394491 CAAAATAGTC
36394501 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA A
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA A
36394532 GTACTTGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:36395623 original size:30 final size:31
Alignment explanation
Indices: 36395579--36395658 Score: 112
Period size: 30 Copynumber: 2.6 Consensus size: 31
36395569 CATTTACCTA
36395579 AATGTGGAAA-CCTTTGTGGCCGTTATTTGAT
1 AATGT-GAAAGCCTTTGTGGCCGTTATTTGAT
36395610 -ATGTGAAAGCCTTTGTGGCCGTTATTTGAT
1 AATGTGAAAGCCTTTGTGGCCGTTATTTGAT
* *
36395640 AAAGT-AAAGCCTTAGTGGC
1 AATGTGAAAGCCTTTGTGGC
36395659 TAATTCTGTT
Statistics
Matches: 45, Mismatches: 2, Indels: 5
0.87 0.04 0.10
Matches are distributed among these distances:
29 4 0.09
30 38 0.84
31 3 0.07
ACGTcount: A:0.25, C:0.14, G:0.26, T:0.35
Consensus pattern (31 bp):
AATGTGAAAGCCTTTGTGGCCGTTATTTGAT
Found at i:36397690 original size:56 final size:56
Alignment explanation
Indices: 36397604--36397713 Score: 202
Period size: 56 Copynumber: 2.0 Consensus size: 56
36397594 CTTTTGAAGC
*
36397604 ATTGCTATGAGTAGTATTGGTTGTATCATTGCGATAAAAAAAAGATAAACACAACA
1 ATTGCTATGAGCAGTATTGGTTGTATCATTGCGATAAAAAAAAGATAAACACAACA
*
36397660 ATTGCTATGAGCAGTATTGGTTGTATCATTGCGATAAAACAAAGATAAACACAA
1 ATTGCTATGAGCAGTATTGGTTGTATCATTGCGATAAAAAAAAGATAAACACAA
36397714 TAAATTATTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
56 52 1.00
ACGTcount: A:0.42, C:0.12, G:0.18, T:0.28
Consensus pattern (56 bp):
ATTGCTATGAGCAGTATTGGTTGTATCATTGCGATAAAAAAAAGATAAACACAACA
Found at i:36403483 original size:2 final size:2
Alignment explanation
Indices: 36403478--36403511 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
36403468 AAATCGAAAG
36403478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
36403512 GTTCACAATA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36409834 original size:3 final size:3
Alignment explanation
Indices: 36409826--36409855 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
36409816 ATGTTTTTAC
36409826 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
36409856 AGGAATTACT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:36410483 original size:26 final size:24
Alignment explanation
Indices: 36410435--36410484 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 24
36410425 ATGCGAACGC
**
36410435 ATAATTGTAAATTTATTTGTATAT
1 ATAATTGTAAATTTATTCATATAT
36410459 ATAATTGTAAATATTTATTCATATAT
1 ATAATTGT-AA-ATTTATTCATATAT
36410485 GTTTGTAATT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 2 0.09
26 12 0.55
ACGTcount: A:0.40, C:0.02, G:0.06, T:0.52
Consensus pattern (24 bp):
ATAATTGTAAATTTATTCATATAT
Found at i:36413989 original size:14 final size:14
Alignment explanation
Indices: 36413958--36413994 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
36413948 CCTTAATTTT
36413958 AATCCTAAAACTCTA
1 AATCCTAAAAC-CTA
*
36413973 AATCTTAAAACCTA
1 AATCCTAAAACCTA
36413987 AATCCTAA
1 AATCCTAA
36413995 TAAGCCTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
14 10 0.50
15 10 0.50
ACGTcount: A:0.49, C:0.24, G:0.00, T:0.27
Consensus pattern (14 bp):
AATCCTAAAACCTA
Found at i:36414968 original size:24 final size:23
Alignment explanation
Indices: 36414913--36414970 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 23
36414903 CGTTCTGATT
*
36414913 TTTTTTCTTTATCGATTTATTTG
1 TTTTTTATTTATCGATTTATTTG
*
36414936 TTTATTTATTTATCTATTTACTTT-
1 TTT-TTTATTTATCGATTTA-TTTG
36414960 TATTTTTATTT
1 T-TTTTTATTT
36414971 TCTTTTTGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 3 0.10
24 22 0.73
25 5 0.17
ACGTcount: A:0.17, C:0.07, G:0.03, T:0.72
Consensus pattern (23 bp):
TTTTTTATTTATCGATTTATTTG
Found at i:36418872 original size:25 final size:24
Alignment explanation
Indices: 36418844--36418907 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
36418834 CTTTGTGAGG
* *
36418844 TTCCTGATTAATGGCTTTCTAGAGC
1 TTCCTGA-TAATGGCTTGCTAGAAC
* *
36418869 TTCCCGAT-ATGGCTTGCTTGAAC
1 TTCCTGATAATGGCTTGCTAGAAC
36418892 TTCCTGATATATGGCT
1 TTCCTGATA-ATGGCT
36418908 ATCCGGAGTT
Statistics
Matches: 32, Mismatches: 5, Indels: 4
0.78 0.12 0.10
Matches are distributed among these distances:
23 19 0.59
24 1 0.03
25 12 0.38
ACGTcount: A:0.19, C:0.22, G:0.20, T:0.39
Consensus pattern (24 bp):
TTCCTGATAATGGCTTGCTAGAAC
Found at i:36426039 original size:30 final size:30
Alignment explanation
Indices: 36425995--36426056 Score: 97
Period size: 30 Copynumber: 2.1 Consensus size: 30
36425985 ACTTAACAAG
36425995 CAAATGCCTATAAAAAAATAACAAAATTAA
1 CAAATGCCTATAAAAAAATAACAAAATTAA
* * *
36426025 CAAATGTCTTTAAAATAATAACAAAATTAA
1 CAAATGCCTATAAAAAAATAACAAAATTAA
36426055 CA
1 CA
36426057 GTAAAATAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.60, C:0.13, G:0.03, T:0.24
Consensus pattern (30 bp):
CAAATGCCTATAAAAAAATAACAAAATTAA
Found at i:36427811 original size:17 final size:17
Alignment explanation
Indices: 36427783--36427823 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
36427773 AAAAAAAATC
36427783 ATTTTATCATTTTATTT-A
1 ATTTT-TCATTTT-TTTAA
36427801 ATTTTTCATTTTTTTAA
1 ATTTTTCATTTTTTTAA
36427818 ATTTTT
1 ATTTTT
36427824 AAACTTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 3 0.14
17 14 0.64
18 5 0.23
ACGTcount: A:0.24, C:0.05, G:0.00, T:0.71
Consensus pattern (17 bp):
ATTTTTCATTTTTTTAA
Found at i:36428528 original size:31 final size:31
Alignment explanation
Indices: 36428461--36428538 Score: 93
Period size: 32 Copynumber: 2.5 Consensus size: 31
36428451 AAAGTATAAT
*
36428461 TTTTTGACAAGTTCAGATACCAACTAGGCAC
1 TTTTTGACAAGTTCAGATACCAAATAGGCAC
** * *
36428492 TTTTTGAACAAGTTTTGATACTAAATAGGTAC
1 TTTTTG-ACAAGTTCAGATACCAAATAGGCAC
*
36428524 TTTTGGACAAGTTCA
1 TTTTTGACAAGTTCA
36428539 AAGGGTAAAC
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 13 0.34
32 25 0.66
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (31 bp):
TTTTTGACAAGTTCAGATACCAAATAGGCAC
Found at i:36431996 original size:17 final size:17
Alignment explanation
Indices: 36431953--36432015 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
36431943 ATTGAAATTT
*
36431953 TTAAAAATTATTTAATATA
1 TTAAATATT-TTTAA-ATA
*
36431972 TTTCAATATTTTTAAATA
1 -TTAAATATTTTTAAATA
*
36431990 TTAAATAATTTTAAATA
1 TTAAATATTTTTAAATA
*
36432007 TAAAATATT
1 TTAAATATT
36432016 CACAAAATAT
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
17 22 0.59
18 3 0.08
19 5 0.14
20 7 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
TTAAATATTTTTAAATA
Found at i:36432050 original size:20 final size:20
Alignment explanation
Indices: 36432001--36432051 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 20
36431991 TAAATAATTT
*
36432001 TAAATATAAAATATTCACAA
1 TAAATATAAAATACTCACAA
36432021 -AATATATAAAATACTCATCAA
1 TAA-ATATAAAATACTCA-CAA
36432042 TAAAT-TAAAA
1 TAAATATAAAA
36432052 AAAAAACTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 2 0.07
20 18 0.67
21 5 0.19
22 2 0.07
ACGTcount: A:0.61, C:0.10, G:0.00, T:0.29
Consensus pattern (20 bp):
TAAATATAAAATACTCACAA
Found at i:36432281 original size:13 final size:13
Alignment explanation
Indices: 36432273--36432302 Score: 51
Period size: 13 Copynumber: 2.2 Consensus size: 13
36432263 TATTTTTTTA
36432273 TTATATTTTAATT
1 TTATATTTTAATT
36432286 TTATATTTTAAATT
1 TTATATTTT-AATT
36432300 TTA
1 TTA
36432303 AAGTTGCCCC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 9 0.56
14 7 0.44
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (13 bp):
TTATATTTTAATT
Found at i:36432873 original size:91 final size:91
Alignment explanation
Indices: 36432713--36432989 Score: 319
Period size: 91 Copynumber: 3.0 Consensus size: 91
36432703 TGTCACATTC
* * * * * * *
36432713 GGTACATATATTTTTATAAAATGTCCAATGTGGTATTTGTACTTT-AAAAAAGTCTAATGTGATA
1 GGTACCTATACTTTCATAAAATGTCCAATGTGGTACTTGTACTTTGAAAATA-TCCAATGTGGTA
*
36432777 TTTGAACTATCAAATTGTGTATTATTT
65 CTTGAACTATCAAATTGTGTATTATTT
* *
36432804 GGTACCTATACTTTCATAAAATGTCTAATGTGGTACTTGTAGTTTGAAAATATCCAATGTGGTAC
1 GGTACCTATACTTTCATAAAATGTCCAATGTGGTACTTGTACTTTGAAAATATCCAATGTGGTAC
* *
36432869 TTGAACTATCAATTTGTGTATTGTTT
66 TTGAACTATCAAATTGTGTATTATTT
* * * * *
36432895 GGTACCTATACTTTCATAAGATGTCCAATGTGATACTTATACTTTGAAAATGTTCAATGT-GTCA
1 GGTACCTATACTTTCATAAAATGTCCAATGTGGTACTTGTACTTTGAAAATATCCAATGTGGT-A
* *
36432959 CCTG-ACTATCAAGA-TGTATATTATTAT
65 CTTGAACTATCAA-ATTGTGTATTATT-T
36432986 GGTA
1 GGTA
36432990 TCTGAAGTTA
Statistics
Matches: 159, Mismatches: 23, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
90 19 0.12
91 135 0.85
92 5 0.03
ACGTcount: A:0.31, C:0.12, G:0.16, T:0.41
Consensus pattern (91 bp):
GGTACCTATACTTTCATAAAATGTCCAATGTGGTACTTGTACTTTGAAAATATCCAATGTGGTAC
TTGAACTATCAAATTGTGTATTATTT
Found at i:36439249 original size:12 final size:13
Alignment explanation
Indices: 36439224--36439252 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
36439214 TGTGACATGC
36439224 ATATATGTATTGA
1 ATATATGTATTGA
36439237 ATATATG-ATTGA
1 ATATATGTATTGA
36439249 ATAT
1 ATAT
36439253 TCCTTATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.56
13 7 0.44
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (13 bp):
ATATATGTATTGA
Found at i:36440330 original size:20 final size:20
Alignment explanation
Indices: 36440267--36440333 Score: 70
Period size: 20 Copynumber: 3.5 Consensus size: 20
36440257 CTCACACTCG
*
36440267 TATAGGCTCGCTTGCATGTA
1 TATAGGCTCGCATGCATGTA
*
36440287 TATAAGG-TTGCATAG-ATG--
1 TAT-AGGCTCGCAT-GCATGTA
36440305 TATAGGCTCGCATGCATGTA
1 TATAGGCTCGCATGCATGTA
36440325 TATAGGCTC
1 TATAGGCTC
36440334 CCATACATAT
Statistics
Matches: 38, Mismatches: 3, Indels: 12
0.72 0.06 0.23
Matches are distributed among these distances:
17 4 0.11
18 11 0.29
20 19 0.50
21 4 0.11
ACGTcount: A:0.25, C:0.16, G:0.25, T:0.33
Consensus pattern (20 bp):
TATAGGCTCGCATGCATGTA
Found at i:36442046 original size:21 final size:22
Alignment explanation
Indices: 36442022--36442062 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
36442012 AGGAATTACC
*
36442022 TGGGT-TTTATAAGAAAAAACT
1 TGGGTATTTACAAGAAAAAACT
*
36442043 TGGGTATTTACAGGAAAAAA
1 TGGGTATTTACAAGAAAAAA
36442063 ACATATTATC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.44, C:0.05, G:0.22, T:0.29
Consensus pattern (22 bp):
TGGGTATTTACAAGAAAAAACT
Found at i:36443342 original size:29 final size:28
Alignment explanation
Indices: 36443284--36443344 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
36443274 GATTTCGCGG
*
36443284 AAAATGGCCCATTCCGGTAAATAATCAA
1 AAAATGGCCCATTCCGGTAAATAATAAA
* * **
36443312 AAAATCGGCCCATTTCGTTAAATTTTAAA
1 AAAAT-GGCCCATTCCGGTAAATAATAAA
36443341 AAAA
1 AAAA
36443345 AACGGCTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 5 0.19
29 22 0.81
ACGTcount: A:0.44, C:0.18, G:0.11, T:0.26
Consensus pattern (28 bp):
AAAATGGCCCATTCCGGTAAATAATAAA
Found at i:36450354 original size:10 final size:9
Alignment explanation
Indices: 36450323--36450354 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
36450313 GATGGATGCT
36450323 TTTTTTTTG
1 TTTTTTTTG
36450332 TTTTTTTTG
1 TTTTTTTTG
36450341 TTTTTTTTG
1 TTTTTTTTG
*
36450350 CTTTT
1 TTTTT
36450355 GTTTACTTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.88
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:36459374 original size:15 final size:15
Alignment explanation
Indices: 36459354--36459387 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
36459344 ACCTTTAACA
36459354 AATCAAATTGAATCG
1 AATCAAATTGAATCG
36459369 AATCAAATTGAATCG
1 AATCAAATTGAATCG
36459384 AATC
1 AATC
36459388 TGAATATTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.26
Consensus pattern (15 bp):
AATCAAATTGAATCG
Found at i:36466299 original size:14 final size:14
Alignment explanation
Indices: 36466282--36466314 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
36466272 CCAAAAAAAG
36466282 AAGAAGAAAAAGAA
1 AAGAAGAAAAAGAA
*
36466296 AAGAAGAAGAAGAA
1 AAGAAGAAAAAGAA
36466310 AAGAA
1 AAGAA
36466315 ATGGAAAAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AAGAAGAAAAAGAA
Found at i:36466302 original size:20 final size:19
Alignment explanation
Indices: 36466274--36466315 Score: 66
Period size: 20 Copynumber: 2.2 Consensus size: 19
36466264 TCCTTTAACC
36466274 AAAAAAAGAAGAAGAAAAAG
1 AAAAAAAGAAGAAG-AAAAG
*
36466294 AAAAGAAGAAGAAGAAAAG
1 AAAAAAAGAAGAAGAAAAG
36466313 AAA
1 AAA
36466316 TGGAAAAGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAAAAGAAGAAGAAAAG
Found at i:36470971 original size:3 final size:3
Alignment explanation
Indices: 36470963--36470997 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
36470953 GTGCACATGC
36470963 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TC
36470998 AAGGATATGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.00, C:0.34, G:0.00, T:0.66
Consensus pattern (3 bp):
TCT
Found at i:36471720 original size:39 final size:39
Alignment explanation
Indices: 36471677--36471780 Score: 111
Period size: 42 Copynumber: 2.6 Consensus size: 39
36471667 GGCGAGGAAA
* * *
36471677 AGATCAATTTCAATTTTTTTCATCAACATGGCGAA-GTGG
1 AGATCAATTTCATTTTTTTTCACCAACATGAC-AAGGTGG
*
36471716 AGATCAATTCCATTTTTTTTTACCACCAACATGACAAGGTGG
1 AGATCAATTTCA-TTTTTTTT--CACCAACATGACAAGGTGG
*
36471758 AGATCAATATTGATTTTTTTTCA
1 AGATCAAT-TTCATTTTTTTTCA
36471781 ACATCAACAC
Statistics
Matches: 54, Mismatches: 6, Indels: 9
0.78 0.09 0.13
Matches are distributed among these distances:
39 11 0.20
40 9 0.17
41 2 0.04
42 30 0.56
43 2 0.04
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.38
Consensus pattern (39 bp):
AGATCAATTTCATTTTTTTTCACCAACATGACAAGGTGG
Found at i:36471789 original size:43 final size:42
Alignment explanation
Indices: 36471677--36471902 Score: 131
Period size: 43 Copynumber: 5.4 Consensus size: 42
36471667 GGCGAGGAAA
* * *
36471677 AGATCAATTTCAATTTTTTT---CATCAACATGGCGAA-GTGG
1 AGATCAATTCCATTTTTTTTCAACATCAACATGAC-AAGGTGG
* * *
36471716 AGATCAATTCCATTTTTTTTTACCACCAACATGACAAGGTGG
1 AGATCAATTCCATTTTTTTTCAACATCAACATGACAAGGTGG
** ** *
36471758 AGATCAATATTGATTTTTTTTCAACATCAACACAACAAGGCGG
1 AGATCAAT-TCCATTTTTTTTCAACATCAACATGACAAGGTGG
* * *** * ***
36471801 AGATTAGTTCTGGGTTTTTTTCAACA-CTAACATGGCAAGGCAA
1 AGATCAATTC-CATTTTTTTTCAACATC-AACATGACAAGGTGG
* * * * * *
36471844 AGATCAGTTCCAATTTTTTT-AACACCAATATGGCAAGATGG
1 AGATCAATTCCATTTTTTTTCAACATCAACATGACAAGGTGG
*
36471885 AGATCAATTCCAATTTTT
1 AGATCAATTCCATTTTTT
36471903 GCCTCTCTTT
Statistics
Matches: 147, Mismatches: 32, Indels: 14
0.76 0.17 0.07
Matches are distributed among these distances:
39 18 0.12
41 33 0.22
42 32 0.22
43 64 0.44
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.34
Consensus pattern (42 bp):
AGATCAATTCCATTTTTTTTCAACATCAACATGACAAGGTGG
Found at i:36474709 original size:5 final size:6
Alignment explanation
Indices: 36474695--36474724 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
36474685 AGTTTATTTG
*
36474695 TTTTAT TTTTAT TTTTAT TTTTAT GTTTAT
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT
36474725 ACTTATTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.80
Consensus pattern (6 bp):
TTTTAT
Found at i:36474730 original size:18 final size:18
Alignment explanation
Indices: 36474695--36474733 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
36474685 AGTTTATTTG
* **
36474695 TTTTATTTTTATTTTTAT
1 TTTTATGTTTATACTTAT
36474713 TTTTATGTTTATACTTAT
1 TTTTATGTTTATACTTAT
36474731 TTT
1 TTT
36474734 CTTAGACTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.03, G:0.03, T:0.77
Consensus pattern (18 bp):
TTTTATGTTTATACTTAT
Found at i:36491159 original size:11 final size:10
Alignment explanation
Indices: 36491048--36491170 Score: 51
Period size: 10 Copynumber: 12.3 Consensus size: 10
36491038 AATATGATTT
36491048 TTAAATAATTA
1 TTAAA-AATTA
36491059 TTTAAAAATT-
1 -TTAAAAATTA
*
36491069 TATATAAATTTA
1 T-TA-AAAATTA
* **
36491081 TTTAAAATGG
1 TTAAAAATTA
*
36491091 TTAAGAATTA
1 TTAAAAATTA
*
36491101 TAAAAAATTA
1 TTAAAAATTA
* *
36491111 TAAAAAATCA
1 TTAAAAATTA
36491121 TT--AAATTGA
1 TTAAAAATT-A
*
36491130 TTAAGAA--A
1 TTAAAAATTA
*
36491138 TGAAAAA-TA
1 TTAAAAATTA
36491147 TTTAAAAATTA
1 -TTAAAAATTA
*
36491158 TTAAAAATAA
1 TTAAAAATTA
36491168 TTA
1 TTA
36491171 TTGGAATGAA
Statistics
Matches: 83, Mismatches: 19, Indels: 20
0.68 0.16 0.16
Matches are distributed among these distances:
8 10 0.12
9 5 0.06
10 48 0.58
11 14 0.17
12 6 0.07
ACGTcount: A:0.56, C:0.01, G:0.05, T:0.38
Consensus pattern (10 bp):
TTAAAAATTA
Found at i:36492464 original size:13 final size:13
Alignment explanation
Indices: 36492446--36492492 Score: 94
Period size: 13 Copynumber: 3.6 Consensus size: 13
36492436 AGTATCAGGG
36492446 GACACACGGCTGT
1 GACACACGGCTGT
36492459 GACACACGGCTGT
1 GACACACGGCTGT
36492472 GACACACGGCTGT
1 GACACACGGCTGT
36492485 GACACACG
1 GACACACG
36492493 TCCGTGTGAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 34 1.00
ACGTcount: A:0.26, C:0.32, G:0.30, T:0.13
Consensus pattern (13 bp):
GACACACGGCTGT
Found at i:36493505 original size:50 final size:49
Alignment explanation
Indices: 36493435--36493531 Score: 117
Period size: 50 Copynumber: 1.9 Consensus size: 49
36493425 TACGAGCCAT
* *
36493435 AATCGGTAAGCTCTTCCGAGCT-AAAATACGGTAAGCTCATACGAGCTGAG
1 AATCGATAAGCTCTTCCGAGCTCAAAAT--GGTAAGCTCATACAAGCTGAG
*
36493485 AATCGATAAGCTC-TCACGAGCTGCAAAGTGGTAAGCTCATACAAGCT
1 AATCGATAAGCTCTTC-CGAGCT-CAAAATGGTAAGCTCATACAAGCT
36493532 ATGGTGAGTC
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
49 2 0.05
50 35 0.85
52 4 0.10
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (49 bp):
AATCGATAAGCTCTTCCGAGCTCAAAATGGTAAGCTCATACAAGCTGAG
Found at i:36493531 original size:25 final size:25
Alignment explanation
Indices: 36493435--36493531 Score: 85
Period size: 25 Copynumber: 3.9 Consensus size: 25
36493425 TACGAGCCAT
* * *
36493435 AATCGGTAAGCTCTTCCGAGCT-AA
1 AATCGGTAAGCTCATACGAGCTGAG
36493459 AATACGGTAAGCTCATACGAGCTGAG
1 AAT-CGGTAAGCTCATACGAGCTGAG
*
36493485 AATCGATAAGCTC-TCACGAGCTGCA-
1 AATCGGTAAGCTCAT-ACGAGCTG-AG
*
36493510 AAGT-GGTAAGCTCATACAAGCT
1 AA-TCGGTAAGCTCATACGAGCT
36493532 ATGGTGAGTC
Statistics
Matches: 61, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
24 4 0.07
25 50 0.82
26 7 0.11
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.22
Consensus pattern (25 bp):
AATCGGTAAGCTCATACGAGCTGAG
Found at i:36494720 original size:15 final size:14
Alignment explanation
Indices: 36494699--36494734 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
36494689 ATAATCATTA
36494699 ATAATTATCCTAAT
1 ATAATTATCCTAAT
36494713 ATTAATTATCCTAAT
1 A-TAATTATCCTAAT
36494728 ATAATTA
1 ATAATTA
36494735 AAATAGAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.44
Consensus pattern (14 bp):
ATAATTATCCTAAT
Found at i:36494964 original size:11 final size:11
Alignment explanation
Indices: 36494948--36494980 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
36494938 TGATCATACT
36494948 CATAATAAATA
1 CATAATAAATA
*
36494959 CATAATTAATA
1 CATAATAAATA
36494970 CATAA-AAATA
1 CATAATAAATA
36494980 C
1 C
36494981 GTTATTCTAG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
10 5 0.25
11 15 0.75
ACGTcount: A:0.61, C:0.12, G:0.00, T:0.27
Consensus pattern (11 bp):
CATAATAAATA
Found at i:36499166 original size:42 final size:42
Alignment explanation
Indices: 36499114--36499202 Score: 126
Period size: 42 Copynumber: 2.1 Consensus size: 42
36499104 GTCCCCTCCC
* * *
36499114 AAGG-CTAGGTAGTCTTGTTGTGAGTCTTGGGCTTGGGAGGG
1 AAGGACTAGGTAGTCTTGTGGTGAGTCTTGGGCATGGGAAGG
*
36499155 AAGGACTAGGTAGTCTTGTGGTGAGTTTTGGGCATGGGAAGG
1 AAGGACTAGGTAGTCTTGTGGTGAGTCTTGGGCATGGGAAGG
*
36499197 ATGGAC
1 AAGGAC
36499203 CAAGGCTAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.10
42 38 0.90
ACGTcount: A:0.19, C:0.09, G:0.43, T:0.29
Consensus pattern (42 bp):
AAGGACTAGGTAGTCTTGTGGTGAGTCTTGGGCATGGGAAGG
Found at i:36503380 original size:14 final size:14
Alignment explanation
Indices: 36503361--36503387 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
36503351 CTAAATATTT
36503361 TTTGAATAATTATG
1 TTTGAATAATTATG
36503375 TTTGAATAATTAT
1 TTTGAATAATTAT
36503388 TTGATTTTAA
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:0.37, C:0.00, G:0.11, T:0.52
Consensus pattern (14 bp):
TTTGAATAATTATG
Found at i:36515769 original size:19 final size:20
Alignment explanation
Indices: 36515742--36515786 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
36515732 TGTTAAAATT
* *
36515742 AAATTAATTAA-CTATATGC
1 AAATGAATTAACCTAAATGC
36515761 AAATGAATTAACCTAAATGC
1 AAATGAATTAACCTAAATGC
36515781 -AATGAA
1 AAATGAA
36515787 ATGGTTTAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 16 0.70
20 7 0.30
ACGTcount: A:0.51, C:0.11, G:0.09, T:0.29
Consensus pattern (20 bp):
AAATGAATTAACCTAAATGC
Found at i:36517442 original size:14 final size:14
Alignment explanation
Indices: 36517425--36517454 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
36517415 TTAGATTGTA
*
36517425 AAGATTAGTACTGT
1 AAGATTAGAACTGT
36517439 AAGATTAGAACTGT
1 AAGATTAGAACTGT
36517453 AA
1 AA
36517455 TGTTTAATAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.07, G:0.20, T:0.30
Consensus pattern (14 bp):
AAGATTAGAACTGT
Found at i:36518934 original size:12 final size:12
Alignment explanation
Indices: 36518917--36518945 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
36518907 GGTTTCGTGA
36518917 CCACACGGGTGG
1 CCACACGGGTGG
36518929 CCACACGGGTGG
1 CCACACGGGTGG
36518941 CCACA
1 CCACA
36518946 TGGGCGTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.38, G:0.34, T:0.07
Consensus pattern (12 bp):
CCACACGGGTGG
Found at i:36522961 original size:50 final size:50
Alignment explanation
Indices: 36522846--36523288 Score: 670
Period size: 50 Copynumber: 8.8 Consensus size: 50
36522836 GATCATAACA
* ** *
36522846 TGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGA-CCTCTCATCTCGG
* **
36522897 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * *
36522947 TGCCAACGCCATGTCCCAGACATGGTCTTATATGGGACCTCTCATCCCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
36522997 TGCCCATGCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
36523047 TGCCAATGCCATGTCCCAGACATGGTCTTACATGAGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
36523097 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* * * *
36523147 TGCCCATGCCAATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGG
1 TGCCAATGCC-ATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
36523198 TGCCAATGTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
*
36523248 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTC
36523289 CCGGTATCAA
Statistics
Matches: 354, Mismatches: 37, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
50 276 0.78
51 78 0.22
ACGTcount: A:0.21, C:0.31, G:0.23, T:0.25
Consensus pattern (50 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:36523237 original size:151 final size:150
Alignment explanation
Indices: 36522853--36523288 Score: 737
Period size: 151 Copynumber: 2.9 Consensus size: 150
36522843 ACATGCCAAA
* * ** * * *
36522853 GCCATGTCCCAGACATGGTCTTACATGGGATGTTCTCATATCGGTGCCCATGCCATGTCCCAGAC
1 GCCATGTCCCAGACATGGTCTTATAGGGGA-CCTATCATCTCGGTGCCAATGCCATGTCCCAGAC
** *
36522918 ATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTATATGGG
65 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGG
36522983 ACCTCTCATCCCGGTGCCCAT
130 ACCTCTCATCCCGGTGCCCAT
36523004 GCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGGTGCCAATGCCATGTCCCAGACA
1 GCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGGTGCCAATGCCATGTCCCAGACA
*
36523069 TGGTCTTACATGAGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
66 TGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
*
36523134 CCTCTCATCTCGGTGCCCAT
131 CCTCTCATCCCGGTGCCCAT
*
36523154 GCCAATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGGTGCCAATGTCATGTCCCAGAC
1 GCC-ATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGGTGCCAATGCCATGTCCCAGAC
36523219 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGG
65 ATGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGG
36523284 ACCTC
130 ACCTC
36523289 CCGGTATCAA
Statistics
Matches: 270, Mismatches: 14, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
150 113 0.42
151 157 0.58
ACGTcount: A:0.20, C:0.31, G:0.23, T:0.25
Consensus pattern (150 bp):
GCCATGTCCCAGACATGGTCTTATAGGGGACCTATCATCTCGGTGCCAATGCCATGTCCCAGACA
TGGTCTTACATGGGACCTCTCATCTCGGTGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
CCTCTCATCCCGGTGCCCAT
Found at i:36525120 original size:15 final size:16
Alignment explanation
Indices: 36525096--36525134 Score: 53
Period size: 15 Copynumber: 2.5 Consensus size: 16
36525086 GGTTTAGATA
*
36525096 CTTTTTTTTATATTT-
1 CTTTTCTTTATATTTC
*
36525111 CTTTTCTTTATTTTTC
1 CTTTTCTTTATATTTC
36525127 CTTTTCTT
1 CTTTTCTT
36525135 GTAAACAGTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.08, C:0.15, G:0.00, T:0.77
Consensus pattern (16 bp):
CTTTTCTTTATATTTC
Found at i:36531702 original size:13 final size:14
Alignment explanation
Indices: 36531684--36531712 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
36531674 AGTAGTGATA
36531684 GCTTACAT-AGTTC
1 GCTTACATGAGTTC
36531697 GCTTACATGAGTTC
1 GCTTACATGAGTTC
36531711 GC
1 GC
36531713 GTCATCATGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.21, C:0.24, G:0.21, T:0.34
Consensus pattern (14 bp):
GCTTACATGAGTTC
Found at i:36534514 original size:6 final size:7
Alignment explanation
Indices: 36534498--36534525 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
36534488 TGTGTATTGA
36534498 TTTTAGT
1 TTTTAGT
36534505 TTTTAGT
1 TTTTAGT
36534512 TTTTAGT
1 TTTTAGT
36534519 TTTTAGT
1 TTTTAGT
36534526 ATTGGAATGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.71
Consensus pattern (7 bp):
TTTTAGT
Found at i:36541803 original size:18 final size:17
Alignment explanation
Indices: 36541777--36541812 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
36541767 TTTGGTTATA
36541777 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
36541795 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
36541812 T
1 T
36541813 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:36542409 original size:27 final size:27
Alignment explanation
Indices: 36542377--36542435 Score: 118
Period size: 27 Copynumber: 2.2 Consensus size: 27
36542367 TCATATAATA
36542377 TATGTATATTTCTGTAGAACTAGAAAC
1 TATGTATATTTCTGTAGAACTAGAAAC
36542404 TATGTATATTTCTGTAGAACTAGAAAC
1 TATGTATATTTCTGTAGAACTAGAAAC
36542431 TATGT
1 TATGT
36542436 TTTTTGAATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 32 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.39
Consensus pattern (27 bp):
TATGTATATTTCTGTAGAACTAGAAAC
Found at i:36545998 original size:58 final size:58
Alignment explanation
Indices: 36545936--36546074 Score: 154
Period size: 58 Copynumber: 2.4 Consensus size: 58
36545926 TTAATTCATA
*
36545936 TAATAATAATTTTATTAAGAATTTTATTAAATTATATATCA-TTTTATTAAATTATATT
1 TAATAATAATTTTATTAA-AATTTGATTAAATTATATATCATTTTTATTAAATTATATT
* * * * * * * * *
36545994 TAATAATTATTATGTTAAAATATGGTTAAATTATTTATTATTTTTATTAAATTGTTTT
1 TAATAATAATTTTATTAAAATTTGATTAAATTATATATCATTTTTATTAAATTATATT
* *
36546052 TAACAATAATCTTATTAAAATTT
1 TAATAATAATTTTATTAAAATTT
36546075 AATAACAATA
Statistics
Matches: 64, Mismatches: 16, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
57 17 0.27
58 47 0.73
ACGTcount: A:0.41, C:0.02, G:0.04, T:0.53
Consensus pattern (58 bp):
TAATAATAATTTTATTAAAATTTGATTAAATTATATATCATTTTTATTAAATTATATT
Found at i:36546224 original size:43 final size:46
Alignment explanation
Indices: 36546169--36546256 Score: 114
Period size: 45 Copynumber: 2.0 Consensus size: 46
36546159 AACATCGTTC
36546169 CATTCAACCAAACACA-AGAA-TACT-ATTACAG-TTCTATTTCATTT
1 CATTCAACCAAACA-ATAGAATTACTGATTACAGCTT-TATTTCATTT
*
36546213 CATT-AACCAAACAATTGAATTACTGATTACAGCTTTATTTCATT
1 CATTCAACCAAACAATAGAATTACTGATTACAGCTTTATTTCATT
36546257 ACAGCTCTAT
Statistics
Matches: 39, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
42 1 0.03
43 12 0.31
44 8 0.21
45 16 0.41
46 2 0.05
ACGTcount: A:0.38, C:0.20, G:0.06, T:0.36
Consensus pattern (46 bp):
CATTCAACCAAACAATAGAATTACTGATTACAGCTTTATTTCATTT
Found at i:36546259 original size:16 final size:16
Alignment explanation
Indices: 36546238--36546291 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
36546228 TGAATTACTG
*
36546238 ATTACAGCTTTATTTC
1 ATTACAGCTCTATTTC
36546254 ATTACAGCTCTA-TTC
1 ATTACAGCTCTATTTC
*
36546269 AATTACAGCTCTATTCC
1 -ATTACAGCTCTATTTC
36546286 ATTACA
1 ATTACA
36546292 ATAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
15 3 0.09
16 29 0.85
17 2 0.06
ACGTcount: A:0.30, C:0.24, G:0.06, T:0.41
Consensus pattern (16 bp):
ATTACAGCTCTATTTC
Found at i:36555051 original size:11 final size:12
Alignment explanation
Indices: 36555027--36555056 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
36555017 TTAAACTGTC
36555027 AAAATGTATAAA
1 AAAATGTATAAA
36555039 AAAATGTATAAA
1 AAAATGTATAAA
36555051 AAAATG
1 AAAATG
36555057 CCATTTGATC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (12 bp):
AAAATGTATAAA
Found at i:36555247 original size:10 final size:10
Alignment explanation
Indices: 36555234--36555306 Score: 85
Period size: 10 Copynumber: 7.4 Consensus size: 10
36555224 TAAAAATAGA
36555234 AAAAAATTAT
1 AAAAAATTAT
* *
36555244 AAAAAATCAA
1 AAAAAATTAT
36555254 AAAAAATTAT
1 AAAAAATTAT
*
36555264 AAAAAATTGT
1 AAAAAATTAT
**
36555274 AAAATTTTAT
1 AAAAAATTAT
*
36555284 -AAAAATCAT
1 AAAAAATTAT
36555293 AAAAAATTAT
1 AAAAAATTAT
36555303 AAAA
1 AAAA
36555307 TGTATCAAAA
Statistics
Matches: 50, Mismatches: 12, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
9 6 0.12
10 44 0.88
ACGTcount: A:0.68, C:0.03, G:0.01, T:0.27
Consensus pattern (10 bp):
AAAAAATTAT
Found at i:36555248 original size:19 final size:19
Alignment explanation
Indices: 36555224--36555306 Score: 78
Period size: 20 Copynumber: 4.3 Consensus size: 19
36555214 AAATATATAT
36555224 TAAAAAT-AGAAAAAAATTA
1 TAAAAATCA-AAAAAAATTA
36555243 TAAAAAATCAAAAAAAATTA
1 T-AAAAATCAAAAAAAATTA
*** **
36555263 TAAAAAATTGTAAAATTTTA
1 T-AAAAATCAAAAAAAATTA
*
36555283 TAAAAATCATAAAAAATTA
1 TAAAAATCAAAAAAAATTA
36555302 TAAAA
1 TAAAA
36555307 TGTATCAAAA
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
19 20 0.38
20 32 0.60
21 1 0.02
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.27
Consensus pattern (19 bp):
TAAAAATCAAAAAAAATTA
Found at i:36555316 original size:29 final size:29
Alignment explanation
Indices: 36555255--36555317 Score: 83
Period size: 29 Copynumber: 2.2 Consensus size: 29
36555245 AAAAATCAAA
* * *
36555255 AAAAATTATAAAAAATTGTAAAATTTTAT
1 AAAAATCATAAAAAATTATAAAATTGTAT
36555284 AAAAATCATAAAAAATTATAAAA-TGTAT
1 AAAAATCATAAAAAATTATAAAATTGTAT
36555312 CAAAAA
1 -AAAAA
36555318 GGCCCTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 4 0.13
29 26 0.87
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.30
Consensus pattern (29 bp):
AAAAATCATAAAAAATTATAAAATTGTAT
Found at i:36556193 original size:15 final size:16
Alignment explanation
Indices: 36556173--36556209 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
36556163 ACGTGACAAT
36556173 AATATTATCATT-CTA
1 AATATTATCATTACTA
*
36556188 AATATTATGATTACTA
1 AATATTATCATTACTA
36556204 AA-ATTA
1 AATATTA
36556210 ACTTTACACA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.46, C:0.08, G:0.03, T:0.43
Consensus pattern (16 bp):
AATATTATCATTACTA
Found at i:36558766 original size:20 final size:20
Alignment explanation
Indices: 36558737--36558774 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
36558727 TGTTATACTT
* *
36558737 TGATTGATTAAGTAAAAATA
1 TGATTAATTAAGGAAAAATA
36558757 TGATTAATTAAGGAAAAA
1 TGATTAATTAAGGAAAAA
36558775 AAACATGATT
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:0.53, C:0.00, G:0.16, T:0.32
Consensus pattern (20 bp):
TGATTAATTAAGGAAAAATA
Found at i:36559455 original size:17 final size:18
Alignment explanation
Indices: 36559433--36559466 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
36559423 ATTTGAACCA
*
36559433 TTATAAT-TGTTGCATAT
1 TTATAATATATTGCATAT
36559450 TTATAATATATTGCATA
1 TTATAATATATTGCATA
36559467 GTATGATGTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.35, C:0.06, G:0.09, T:0.50
Consensus pattern (18 bp):
TTATAATATATTGCATAT
Found at i:36563540 original size:15 final size:15
Alignment explanation
Indices: 36563522--36563569 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
36563512 AATTAAGTAA
36563522 ATGTTAATTAATATG
1 ATGTTAATTAATATG
*
36563537 ATGTTATATTAATGTG
1 ATGTTA-ATTAATATG
** *
36563553 AAATTAATTAATTTG
1 ATGTTAATTAATATG
36563568 AT
1 AT
36563570 CATATCTTTT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
15 15 0.56
16 12 0.44
ACGTcount: A:0.40, C:0.00, G:0.12, T:0.48
Consensus pattern (15 bp):
ATGTTAATTAATATG
Found at i:36565093 original size:2 final size:2
Alignment explanation
Indices: 36565088--36565125 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
36565078 AAAAAAAAAA
36565088 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
36565126 CCGTTGTCCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:36565740 original size:25 final size:27
Alignment explanation
Indices: 36565687--36565750 Score: 89
Period size: 25 Copynumber: 2.4 Consensus size: 27
36565677 TAAAAAAATA
36565687 ACCAAAATAT-TATAACTTTTTTTAATT
1 ACCAAAATATATATAAC-TTTTTTAATT
*
36565714 ACCAAAATATATAT-A-TTTTTTATTT
1 ACCAAAATATATATAACTTTTTTAATT
36565739 ACCAAAATATAT
1 ACCAAAATATAT
36565751 CAAAAAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
25 21 0.60
27 11 0.31
28 3 0.09
ACGTcount: A:0.44, C:0.11, G:0.00, T:0.45
Consensus pattern (27 bp):
ACCAAAATATATATAACTTTTTTAATT
Found at i:36565856 original size:27 final size:27
Alignment explanation
Indices: 36565801--36565900 Score: 110
Period size: 27 Copynumber: 3.7 Consensus size: 27
36565791 CCTTGGTCAC
* **
36565801 GCCAAAACGATTGGCGGCACCAAAAGT
1 GCCAAAACCATTGGCGGCACCAATGGT
* *
36565828 GCCAAAACCATTTGCGGCACTAATGGT
1 GCCAAAACCATTGGCGGCACCAATGGT
** *
36565855 GCCAATGCCATTGGTGGCACCAATGGT
1 GCCAAAACCATTGGCGGCACCAATGGT
**
36565882 GCCAATGCCATTGGCGGCA
1 GCCAAAACCATTGGCGGCA
36565901 TTACTCGTGT
Statistics
Matches: 62, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 62 1.00
ACGTcount: A:0.28, C:0.27, G:0.27, T:0.18
Consensus pattern (27 bp):
GCCAAAACCATTGGCGGCACCAATGGT
Found at i:36566001 original size:11 final size:11
Alignment explanation
Indices: 36565985--36566023 Score: 62
Period size: 11 Copynumber: 3.6 Consensus size: 11
36565975 GGTGCTGCGG
36565985 AAAAGAAGAGA
1 AAAAGAAGAGA
36565996 AAAAG-AGAGA
1 AAAAGAAGAGA
*
36566006 AAGAGAAGAGA
1 AAAAGAAGAGA
36566017 AAAAGAA
1 AAAAGAA
36566024 TGTATTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.36
11 16 0.64
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:36566014 original size:21 final size:20
Alignment explanation
Indices: 36565984--36566022 Score: 69
Period size: 21 Copynumber: 1.9 Consensus size: 20
36565974 AGGTGCTGCG
36565984 GAAAAGAAGAGAAAAAGAGA
1 GAAAAGAAGAGAAAAAGAGA
36566004 GAAAGAGAAGAGAAAAAGA
1 GAAA-AGAAGAGAAAAAGA
36566023 ATGTATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 4 0.22
21 14 0.78
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (20 bp):
GAAAAGAAGAGAAAAAGAGA
Found at i:36566058 original size:26 final size:26
Alignment explanation
Indices: 36566022--36566073 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
36566012 AGAGAAAAAG
36566022 AATGTATTTTTTTAAAAATAATTGAT
1 AATGTATTTTTTTAAAAATAATTGAT
36566048 AATGTATTTTTTTAAAAATAATTGAT
1 AATGTATTTTTTTAAAAATAATTGAT
36566074 TATATTGTTG
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:0.42, C:0.00, G:0.08, T:0.50
Consensus pattern (26 bp):
AATGTATTTTTTTAAAAATAATTGAT
Found at i:36567088 original size:18 final size:18
Alignment explanation
Indices: 36567065--36567102 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
36567055 GGTTGGTGGT
36567065 GAAGAAGAAGGTGCTGGC
1 GAAGAAGAAGGTGCTGGC
*
36567083 GAAGAAGAAGGTGGTGGC
1 GAAGAAGAAGGTGCTGGC
36567101 GA
1 GA
36567103 TCATTGGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.34, C:0.08, G:0.47, T:0.11
Consensus pattern (18 bp):
GAAGAAGAAGGTGCTGGC
Found at i:36571805 original size:160 final size:155
Alignment explanation
Indices: 36571591--36572064 Score: 421
Period size: 160 Copynumber: 3.0 Consensus size: 155
36571581 CTGCAAGTTG
* * * ** * **
36571591 AAAAAAAAGTTAGTAAAAAAATCTTACTTCGGCCATTTATTCGTATTTTTTTCTCCGCATTTTAT
1 AAAAAAAAGTTAGTAATACACTCTTACCCCTGCCATTTGCTCGTATTTTTTTCTCCGCATTTTAT
36571656 T-CATTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATAATGTTTG
66 TAC-TTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATAATGTTTG
36571720 AAATTTATTAATTTAGTGTGTTATTT
130 AAATTTATTAATTTAGTGTGTTATTT
* * * *
36571746 -AAATAAATTTGATGTAAAAAAATA-ACTCTTACCCCTGCCCTTTGCTCGTATTATTTTCT-CG-
1 AAAAAAAAGTT-A-GT-----AATACACTCTTACCCCTGCCATTTGCTCGTATTTTTTTCTCCGC
* * *
36571807 ATTTTTATTACTTTAAATAAAAATAT-ATTATTCTCGT-ATTTTATTATTTTATATTATTTCAGT
59 A-TTTTATTACTTT--A-AAAAATATCATAATT-TC-TAATTTTATAATTTTACATTATTTCAGT
** * *
36571870 ACATTTTCTTTGAAATATTTTGTATTAA-TTA-T-TTTTGAATTT
118 ACATAATGTTTG-AA-A--TT-TATTAATTTAGTGTGTT--ATTT
** *
36571912 AAAAAAAAGTTAGTAATACACTCTTACTTCTGCCATTTGTTCGTATTTTTTTCTCCGCATTTTAT
1 AAAAAAAAGTTAGTAATACACTCTTACCCCTGCCATTTGCTCGTATTTTTTTCTCCGCATTTTAT
* ** * *
36571977 TATTTTAAAAAATATCATAAGCT-TAGTCTTTTATAATTTTACATTATTTCAGTGCATAATGTTT
66 TACTTTAAAAAATATCATAATTTCTA--ATTTTATAATTTTACATTATTTCAGTACATAATGTTT
36572041 GAAATTTATTAATTTAGTGTGTTA
129 GAAATTTATTAATTTAGTGTGTTA
36572065 AAGGGGAATA
Statistics
Matches: 250, Mismatches: 37, Indels: 63
0.71 0.11 0.18
Matches are distributed among these distances:
154 8 0.03
155 7 0.03
156 8 0.03
157 2 0.01
158 5 0.02
159 23 0.09
160 67 0.27
161 39 0.16
162 56 0.22
163 4 0.02
164 4 0.02
165 3 0.01
166 10 0.04
167 14 0.06
ACGTcount: A:0.32, C:0.11, G:0.08, T:0.48
Consensus pattern (155 bp):
AAAAAAAAGTTAGTAATACACTCTTACCCCTGCCATTTGCTCGTATTTTTTTCTCCGCATTTTAT
TACTTTAAAAAATATCATAATTTCTAATTTTATAATTTTACATTATTTCAGTACATAATGTTTGA
AATTTATTAATTTAGTGTGTTATTT
Found at i:36572342 original size:15 final size:16
Alignment explanation
Indices: 36572316--36572345 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
36572306 AATAAAAATA
36572316 TATTATTTTTATATTT
1 TATTATTTTTATATTT
36572332 TATTA-TTTTATATT
1 TATTATTTTTATATT
36572346 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTTTTATATTT
Found at i:36572930 original size:4 final size:4
Alignment explanation
Indices: 36572914--36573052 Score: 65
Period size: 4 Copynumber: 34.0 Consensus size: 4
36572904 TTCCTTTCCT
*
36572914 TTTC TTTC CTTC TTTC TTTC TTT- TTTC TTCTCC TTTCC TTT- TCTTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-T-C TTT-C TTTC T-TTC
* * * * * *
36572960 -TTC TGTC ATTC TTTT TTTC TCTTC -TCC TTTCC TTTTC CTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
* * *
36573007 TTTC TTTC TTTCC TCTCC TTCC TGTC TTTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TTT-C T-TTC TTTC TTTC TTTC TTTC TTTC TTTC TTTC
36573053 CCTCTCCTTC
Statistics
Matches: 106, Mismatches: 15, Indels: 28
0.71 0.10 0.19
Matches are distributed among these distances:
3 13 0.12
4 70 0.66
5 16 0.15
6 7 0.07
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:36572931 original size:45 final size:43
Alignment explanation
Indices: 36572877--36573017 Score: 152
Period size: 44 Copynumber: 3.3 Consensus size: 43
36572867 CTTCCTTCCC
36572877 TCTTC-TTCTTTTTTTTACTCTTCTCCTTTCCTTTCCTTTTCTT
1 TCTTCTTTCTTTTTTTT-CTCTTCTCCTTTCCTTTCCTTTTCTT
*
36572920 TCCTTCTTTCTTTCTTTTT-TCTTCTCCTTTCCTTT--TCTTC-T
1 T-CTTCTTTCTTT-TTTTTCTCTTCTCCTTTCCTTTCCTTTTCTT
*
36572961 TCTGTCATTC-TTTTTTTCTCTTCTCCTTTCCTTTTCCTTCCTTCTT
1 TCT-TCTTTCTTTTTTTTCTCTTCTCCTTTCC-TTTCCTT--TTCTT
36573007 T-TTCTTTCTTT
1 TCTTCTTTCTTT
36573018 CCTCTCCTTC
Statistics
Matches: 82, Mismatches: 4, Indels: 22
0.76 0.04 0.20
Matches are distributed among these distances:
39 5 0.06
40 17 0.21
41 10 0.12
42 4 0.05
43 2 0.02
44 25 0.30
45 12 0.15
46 7 0.09
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.67
Consensus pattern (43 bp):
TCTTCTTTCTTTTTTTTCTCTTCTCCTTTCCTTTCCTTTTCTT
Found at i:36572944 original size:44 final size:42
Alignment explanation
Indices: 36572878--36573052 Score: 133
Period size: 40 Copynumber: 4.3 Consensus size: 42
36572868 TTCCTTCCCT
36572878 CTTC-TTCTTT-TTTTTACTCTTCTCCTTTCCTTTCCTTTTCTTTC
1 CTTCTTTCTTTCTTTTT--TCTTCT-C-TTCCTTTCCTTTTCTTTC
36572922 CTTCTTTCTTTCTTTTTTC-T-TC-TCCTTTCCTTTTC-TT-
1 CTTCTTTCTTTCTTTTTTCTTCTCTTCCTTTCCTTTTCTTTC
* * *
36572959 CTTCTGTCATTC-TTTTT-TTCTCTTCTCCTTTCCTTTTCCTTC
1 CTTCTTTCTTTCTTTTTTCTTCTC-T-TCCTTTCCTTTTCTTTC
* *
36573001 CTTC-TT-TTTCTTTCTTTCCTCTCCTTCCTGT-C-TTTCTTTC
1 CTTCTTTCTTTCTTT-TTTCTTCT-CTTCCTTTCCTTTTCTTTC
*
36573041 TTTCTTTCTTTC
1 CTTCTTTCTTTC
36573053 CCTCTCCTTC
Statistics
Matches: 108, Mismatches: 8, Indels: 32
0.73 0.05 0.22
Matches are distributed among these distances:
36 6 0.06
37 12 0.11
38 2 0.02
39 13 0.12
40 26 0.24
41 9 0.08
42 17 0.16
43 5 0.05
44 7 0.06
45 6 0.06
46 5 0.05
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.66
Consensus pattern (42 bp):
CTTCTTTCTTTCTTTTTTCTTCTCTTCCTTTCCTTTTCTTTC
Found at i:36572951 original size:84 final size:83
Alignment explanation
Indices: 36572854--36573018 Score: 204
Period size: 84 Copynumber: 2.0 Consensus size: 83
36572844 TACCTTTTTT
*
36572854 TTTC-TTTTT-TTTCC-TTCC-TTCCCTCTTCT-TC-TT-TTTTTTACTCTTCTCCTTTCC-TTT
1 TTTCTTTTTTCTTTCCTTTCCTTTTCCTCTTCTGTCATTCTTTTTTACTCTTCTCCTTTCCTTTT
36572911 CCTT-TTCTTTCCTTCTTTC
66 CCTTCTTCTTT--TTCTTTC
* *
36572930 TTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTGTCATTCTTTTTTTCTCTTCTCCTTTCCTTT
1 TTTCTTTTTTCTT-TCCTTTCCTTTTCCTCTTCTGTCATTCTTTTTTACTCTTCTCCTTTCCTTT
36572995 TCCTTCCTTCTTTTTCTTTC
65 TCCTT-CTTCTTTTTCTTTC
36573015 TTTC
1 TTTC
36573019 CTCTCCTTCC
Statistics
Matches: 75, Mismatches: 3, Indels: 13
0.82 0.03 0.14
Matches are distributed among these distances:
76 4 0.05
77 5 0.07
78 2 0.03
79 3 0.04
80 4 0.05
81 9 0.12
82 2 0.03
83 2 0.03
84 20 0.27
85 18 0.24
87 6 0.08
ACGTcount: A:0.01, C:0.32, G:0.01, T:0.67
Consensus pattern (83 bp):
TTTCTTTTTTCTTTCCTTTCCTTTTCCTCTTCTGTCATTCTTTTTTACTCTTCTCCTTTCCTTTT
CCTTCTTCTTTTTCTTTC
Found at i:36573063 original size:26 final size:26
Alignment explanation
Indices: 36573008--36573063 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 26
36572998 TTCCTTCTTT
* *
36573008 TTCTTTCTTTCCTCTCCTTCCTGTCT
1 TTCTTTCTTTCCTCTCCTTCCTCTCC
* *
36573034 TTCTTTCTTT-CTTTCTTTCCCTCTCC
1 TTCTTTCTTTCCTCTCCTT-CCTCTCC
36573060 TTCT
1 TTCT
36573064 GCCCCCCACC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
25 6 0.24
26 19 0.76
ACGTcount: A:0.00, C:0.38, G:0.02, T:0.61
Consensus pattern (26 bp):
TTCTTTCTTTCCTCTCCTTCCTCTCC
Found at i:36573130 original size:27 final size:27
Alignment explanation
Indices: 36573092--36573143 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
36573082 CCCTATTATA
*
36573092 CATTGGTGCCGCCAATGGCATTGGCAC
1 CATTGGTGCCGCCAATGCCATTGGCAC
36573119 CATTGGTGCCGCCAATGCCATTGGC
1 CATTGGTGCCGCCAATGCCATTGGC
36573144 GTGACCAGTG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.17, C:0.31, G:0.29, T:0.23
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGCCATTGGCAC
Found at i:36573226 original size:25 final size:25
Alignment explanation
Indices: 36573192--36573240 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
36573182 GGTTTTTTTT
36573192 TATATATTTTGGTAAATAAAAAAAA
1 TATATATTTTGGTAAATAAAAAAAA
*
36573217 TATATTTTTTGGTAAATAAAAAAA
1 TATATATTTTGGTAAATAAAAAAA
36573241 GTTATAACAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.53, C:0.00, G:0.08, T:0.39
Consensus pattern (25 bp):
TATATATTTTGGTAAATAAAAAAAA
Found at i:36583866 original size:24 final size:24
Alignment explanation
Indices: 36583818--36583864 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
36583808 ACTGGTCATA
*
36583818 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
36583842 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
36583865 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:36584892 original size:27 final size:27
Alignment explanation
Indices: 36584851--36585016 Score: 199
Period size: 27 Copynumber: 6.2 Consensus size: 27
36584841 AGGTCGATAT
36584851 ATGACCGAAATACCCCCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
36584878 ATAACCGAAATA-CCCCATAGAGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* * *
36584904 ATGACCGAAGTATCCCAATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* ** * * *
36584931 ATAACCGAAATAATCTCACAGGATAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
*
36584958 ATGACCGAAATACCCCCATATGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
* *
36584985 ATGATCGAAATACCCTCATAGGGTAAA
1 ATGACCGAAATACCCCCATAGGGTAAA
36585012 ATGAC
1 ATGAC
36585017 TGTTATACCC
Statistics
Matches: 113, Mismatches: 25, Indels: 2
0.81 0.18 0.01
Matches are distributed among these distances:
26 23 0.20
27 90 0.80
ACGTcount: A:0.44, C:0.22, G:0.16, T:0.18
Consensus pattern (27 bp):
ATGACCGAAATACCCCCATAGGGTAAA
Found at i:36585024 original size:27 final size:26
Alignment explanation
Indices: 36584864--36585050 Score: 83
Period size: 27 Copynumber: 7.0 Consensus size: 26
36584854 ACCGAAATAC
* * **
36584864 CCCCATAGGGTAAAATAACCGAAATA
1 CCCCATAGGGTAAAATGACTGTTATA
* * *
36584890 CCCCATAGAGTAAAATGACCG-AAGTA
1 CCCCATAGGGTAAAATGACTGTTA-TA
* * * **
36584916 TCCCAATAGGGTAAAATAACCGAAATAA
1 -CCCCATAGGGTAAAATGACTGTTAT-A
* * * * * **
36584944 TCTCACAGGATAAAATGACCGAAATA
1 CCCCATAGGGTAAAATGACTGTTATA
* **
36584970 CCCCCATATGGTAAAATGA-TCGAAATA
1 -CCCCATAGGGTAAAATGACT-GTTATA
36584997 CCCTCATAGGGTAAAATGACTGTTATA
1 CCC-CATAGGGTAAAATGACTGTTATA
36585024 CCCC-TAGGAGATAAAATGACTGTTATA
1 CCCCATAGG-G-TAAAATGACTGTTATA
36585051 GCCTTGTCTT
Statistics
Matches: 131, Mismatches: 20, Indels: 19
0.77 0.12 0.11
Matches are distributed among these distances:
25 6 0.05
26 27 0.21
27 94 0.72
28 4 0.03
ACGTcount: A:0.42, C:0.20, G:0.17, T:0.21
Consensus pattern (26 bp):
CCCCATAGGGTAAAATGACTGTTATA
Found at i:36585304 original size:26 final size:26
Alignment explanation
Indices: 36585250--36585304 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
36585240 TTTGCAACAT
* *
36585250 ATACTGTTACTGGCAGCTTTGCTGCG
1 ATACTATTACTGGCAGCTTTGCTACG
*
36585276 ATACTATTACTGGCAGCTTTGCTATG
1 ATACTATTACTGGCAGCTTTGCTACG
36585302 ATA
1 ATA
36585305 TTGGTGTGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (26 bp):
ATACTATTACTGGCAGCTTTGCTACG
Found at i:36585455 original size:28 final size:28
Alignment explanation
Indices: 36585415--36585516 Score: 125
Period size: 28 Copynumber: 3.6 Consensus size: 28
36585405 GCATTGTTAC
* *
36585415 TGTATTGGGCTAAGGCCTACACTGATTA
1 TGTATTAGGCTAAGGCCCACACTGATTA
*
36585443 TGTATTAGGCTAAGGCCCACACTGATTC
1 TGTATTAGGCTAAGGCCCACACTGATTA
* * * *
36585471 TATATTGGGATAAGACCCACACT-ATTA
1 TGTATTAGGCTAAGGCCCACACTGATTA
36585498 CTGTATTAGGCTAAGGCCC
1 -TGTATTAGGCTAAGGCCC
36585517 TATAATGGCC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
27 3 0.05
28 58 0.95
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (28 bp):
TGTATTAGGCTAAGGCCCACACTGATTA
Found at i:36591019 original size:78 final size:78
Alignment explanation
Indices: 36590930--36591087 Score: 264
Period size: 78 Copynumber: 2.0 Consensus size: 78
36590920 ATTCATGGCT
* *
36590930 AATCACATCTTTATAAGAGTGAATTATTGTAATTTAGGCA-AATGATTACAACTCTCAATAGAAT
1 AATCACATCTTTATAAGAGTGAATCATTGTAATTTAGG-AGAATGATTACAACTCTCAATAGAAG
36590994 GAGCTAATCAAAGG
65 GAGCTAATCAAAGG
* *
36591008 AATCACATCTTTATAAGTGTGAATCATTGTAGTTTAGGAGAATGATTACAACTCTCAATAGAAGG
1 AATCACATCTTTATAAGAGTGAATCATTGTAATTTAGGAGAATGATTACAACTCTCAATAGAAGG
36591073 AGCTAATCAAAGG
66 AGCTAATCAAAGG
36591086 AA
1 AA
36591088 AGGATTCATA
Statistics
Matches: 75, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
77 1 0.01
78 74 0.99
ACGTcount: A:0.41, C:0.13, G:0.17, T:0.30
Consensus pattern (78 bp):
AATCACATCTTTATAAGAGTGAATCATTGTAATTTAGGAGAATGATTACAACTCTCAATAGAAGG
AGCTAATCAAAGG
Found at i:36595123 original size:3 final size:3
Alignment explanation
Indices: 36595115--36595176 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
36595105 TTTTTTGCCC
36595115 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
36595163 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
36595177 TCATTATTCA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:36601283 original size:3 final size:3
Alignment explanation
Indices: 36601275--36601310 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
36601265 AAATAGGCAT
*
36601275 TGA TGA TGA TGA TGA TGG TGA TGA TGA TGA TGA TGA
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA
36601311 AGGAGAGGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.31, C:0.00, G:0.36, T:0.33
Consensus pattern (3 bp):
TGA
Found at i:36617612 original size:31 final size:31
Alignment explanation
Indices: 36617577--36617635 Score: 75
Period size: 31 Copynumber: 1.9 Consensus size: 31
36617567 ATTTTTAAGG
*
36617577 ATAAA-TATCAAAATTATACATTAACTTTGAT
1 ATAAATTA-CAAAATTATACATCAACTTTGAT
**
36617608 ATAAATTACAATGTTATACATCAACTTT
1 ATAAATTACAAAATTATACATCAACTTT
36617636 AGTTTGGTGC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 22 0.92
32 2 0.08
ACGTcount: A:0.46, C:0.12, G:0.03, T:0.39
Consensus pattern (31 bp):
ATAAATTACAAAATTATACATCAACTTTGAT
Found at i:36628936 original size:37 final size:37
Alignment explanation
Indices: 36628895--36628968 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
36628885 ATCTATCAAT
* * *
36628895 CGATCTCACTTAAATAGTGAATTATCAAAAATAAATC
1 CGATCTCACTCAAATACTGAATTATCAAAAAAAAATC
*
36628932 CGATCTCACTCAATTACTGAATTATCAAAAAAAAATC
1 CGATCTCACTCAAATACTGAATTATCAAAAAAAAATC
36628969 ATTTTATTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.46, C:0.19, G:0.07, T:0.28
Consensus pattern (37 bp):
CGATCTCACTCAAATACTGAATTATCAAAAAAAAATC
Found at i:36629303 original size:16 final size:16
Alignment explanation
Indices: 36629278--36629308 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
36629268 TTCCAAATTA
*
36629278 TATATTTTATTTTTAT
1 TATATGTTATTTTTAT
36629294 TATATGTTATTTTTA
1 TATATGTTATTTTTA
36629309 AATACACATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (16 bp):
TATATGTTATTTTTAT
Found at i:36630546 original size:18 final size:18
Alignment explanation
Indices: 36630523--36630559 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
36630513 ATTAAGTTAA
36630523 ACCAATCCTGATTTAATT
1 ACCAATCCTGATTTAATT
36630541 ACCAATCCTGATTTAATT
1 ACCAATCCTGATTTAATT
36630559 A
1 A
36630560 AGTAAGTAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
ACCAATCCTGATTTAATT
Done.