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 152 of 168
Found at i:44923496 original size:68 final size:68
Alignment explanation
Indices: 44923375--44923584 Score: 388
Period size: 68 Copynumber: 3.1 Consensus size: 68
44923365 AAATTAATTG
*
44923375 TTAGTAAAATTATCAAATTATTAATTG--TTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
44923438 TGA
66 TGA
44923441 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
44923506 TGA
66 TGA
*
44923509 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAACAAAATCTAACATT
1 TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
44923574 TGA
66 TGA
44923577 TTAGTAAA
1 TTAGTAAA
44923585 ACAAATTTGA
Statistics
Matches: 140, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
66 26 0.19
68 114 0.81
ACGTcount: A:0.40, C:0.05, G:0.09, T:0.46
Consensus pattern (68 bp):
TTAGTAAATTTATCAAATTATTAATTGTATTAATTGTATTAATTGTTGTAATAAAATCTAACATT
TGA
Found at i:44923539 original size:9 final size:9
Alignment explanation
Indices: 44923527--44923554 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
44923517 TTTATCAAAT
44923527 TATTAATTG
1 TATTAATTG
44923536 TATTAATTG
1 TATTAATTG
44923545 TATTAATTG
1 TATTAATTG
44923554 T
1 T
44923555 TGTAACAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.32, C:0.00, G:0.11, T:0.57
Consensus pattern (9 bp):
TATTAATTG
Found at i:44939274 original size:6 final size:6
Alignment explanation
Indices: 44939260--44939290 Score: 53
Period size: 6 Copynumber: 5.0 Consensus size: 6
44939250 CTGACACTCA
44939260 CTGCAAT CTGCAT CTGCAT CTGCAT CTGCAT
1 CTGC-AT CTGCAT CTGCAT CTGCAT CTGCAT
44939291 GTAATTAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 20 0.83
7 4 0.17
ACGTcount: A:0.19, C:0.32, G:0.16, T:0.32
Consensus pattern (6 bp):
CTGCAT
Found at i:44941260 original size:18 final size:18
Alignment explanation
Indices: 44941237--44941274 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
44941227 ATTTATTATT
* *
44941237 TCTTATTTGGATCTGTTA
1 TCTTATTCGAATCTGTTA
44941255 TCTTATTCGAATCTGTTA
1 TCTTATTCGAATCTGTTA
44941273 TC
1 TC
44941275 AAATCCGTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.18, C:0.16, G:0.13, T:0.53
Consensus pattern (18 bp):
TCTTATTCGAATCTGTTA
Found at i:44953646 original size:21 final size:21
Alignment explanation
Indices: 44953604--44953648 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
44953594 TGTAACAAGA
* *
44953604 TTTTAATTTAATATGTTTAAT
1 TTTTAATTTAATATGATCAAT
44953625 TTTTAATTTAAT-TCGATCAAT
1 TTTTAATTTAATAT-GATCAAT
44953646 TTT
1 TTT
44953649 ACTTGATTAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (21 bp):
TTTTAATTTAATATGATCAAT
Found at i:44957756 original size:12 final size:12
Alignment explanation
Indices: 44957724--44957757 Score: 50
Period size: 13 Copynumber: 2.8 Consensus size: 12
44957714 CATTTATTAT
44957724 TTTTTTAAAAGA
1 TTTTTTAAAAGA
*
44957736 TTATTTTAAAATA
1 TT-TTTTAAAAGA
44957749 TTTTTTAAA
1 TTTTTTAAA
44957758 TTGAATTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (12 bp):
TTTTTTAAAAGA
Found at i:44961402 original size:20 final size:20
Alignment explanation
Indices: 44961376--44961424 Score: 73
Period size: 19 Copynumber: 2.5 Consensus size: 20
44961366 ATGTTTCGTC
*
44961376 AAAAAATAATTTAAAAATTC
1 AAAAAATAATTTAAAAATTA
*
44961396 TAAAAAT-ATTTAAAAATTA
1 AAAAAATAATTTAAAAATTA
44961415 AAAAAATAAT
1 AAAAAATAAT
44961425 GATGAAGTAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.68
20 8 0.32
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (20 bp):
AAAAAATAATTTAAAAATTA
Found at i:44962559 original size:2 final size:2
Alignment explanation
Indices: 44962552--44962609 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
44962542 TATGATAGGC
44962552 TA TA TA TA 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 TA TA TA TA
44962594 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
44962610 AATAATAAAT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:44968002 original size:33 final size:33
Alignment explanation
Indices: 44967965--44968042 Score: 97
Period size: 33 Copynumber: 2.4 Consensus size: 33
44967955 TGGCCCTGCC
*
44967965 ATGGTCTTACACTC-GTAATGCCATAACCCAGTT
1 ATGGTCTTACACTCAG-AATGCCATAACCCAGCT
* *
44967998 ATGGTCTTATCA-TCAGGATGCCATAGCCCAGCT
1 ATGGTCTTA-CACTCAGAATGCCATAACCCAGCT
44968031 ATGGTCTTACAC
1 ATGGTCTTACAC
44968043 ATATACATTT
Statistics
Matches: 39, Mismatches: 3, Indels: 6
0.81 0.06 0.12
Matches are distributed among these distances:
32 2 0.05
33 34 0.87
34 3 0.08
ACGTcount: A:0.26, C:0.27, G:0.18, T:0.29
Consensus pattern (33 bp):
ATGGTCTTACACTCAGAATGCCATAACCCAGCT
Found at i:44968135 original size:105 final size:101
Alignment explanation
Indices: 44967983--44968179 Score: 259
Period size: 105 Copynumber: 1.9 Consensus size: 101
44967973 ACACTCGTAA
* ** * *
44967983 TGCCATAACCCAGTTATGGTCTTATCATCAGGATGCCATAGCCCAGCTATGGTCTTACACATATA
1 TGCCATAACCCAGTTATGATCTTATCATCAAAATGCCATAACCCAGCTATGGTCTTACACATAAA
44968048 CATTTACTGCCATGGTCCAACCATGGTCTTACATTCAAGG
66 CATTT--T--CATGGTCCAACCATGGTCTTACATTCAAGG
* * * * *
44968088 TGCCATAACCCAGTTATGATCTTTTCATTAAAATGTCATAACTCAGCTATGGTCTTACATATAAA
1 TGCCATAACCCAGTTATGATCTTATCATCAAAATGCCATAACCCAGCTATGGTCTTACACATAAA
*
44968153 CATTTTCATGGTCCAACTATGGTCTTA
66 CATTTTCATGGTCCAACCATGGTCTTA
44968180 TTCATCAATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
101 20 0.25
103 1 0.01
105 60 0.74
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (101 bp):
TGCCATAACCCAGTTATGATCTTATCATCAAAATGCCATAACCCAGCTATGGTCTTACACATAAA
CATTTTCATGGTCCAACCATGGTCTTACATTCAAGG
Found at i:44984339 original size:38 final size:38
Alignment explanation
Indices: 44984292--44984375 Score: 159
Period size: 38 Copynumber: 2.2 Consensus size: 38
44984282 TATCGTCATT
*
44984292 ACCAGATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
1 ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
44984330 ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
1 ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
44984368 ACCAAATT
1 ACCAAATT
44984376 TTGAAACATA
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 45 1.00
ACGTcount: A:0.25, C:0.36, G:0.06, T:0.33
Consensus pattern (38 bp):
ACCAAATTGCCTCACCCTCTTAACAATGTTTCTCCTTC
Found at i:44984775 original size:18 final size:18
Alignment explanation
Indices: 44984752--44984788 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
44984742 AACAAATTAA
44984752 ACCTAACAATTTAAATAT
1 ACCTAACAATTTAAATAT
*
44984770 ACCTAACAATTTAACTAT
1 ACCTAACAATTTAAATAT
44984788 A
1 A
44984789 AGAATTCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (18 bp):
ACCTAACAATTTAAATAT
Found at i:44994262 original size:13 final size:13
Alignment explanation
Indices: 44994244--44994273 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
44994234 TCCAACAACT
44994244 ATGAATTTATTTC
1 ATGAATTTATTTC
*
44994257 ATGAATTTATTTG
1 ATGAATTTATTTC
44994270 ATGA
1 ATGA
44994274 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:44994438 original size:50 final size:50
Alignment explanation
Indices: 44994376--44994610 Score: 326
Period size: 50 Copynumber: 4.7 Consensus size: 50
44994366 AAAGATGTCA
* * *
44994376 CATGTAAGACCATGTCTGGGACACGGTATTGGCACCGAGATGAGAGGTCT
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
* *
44994426 CATGTAAGACCATGTCTGGGATATGGCATTGGCACCGAGATTAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
*
44994476 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
** * * * **
44994526 CCCGTAAGGCCATGTCTGGGACATGGCATGGGCACCGACATGAGAACATCC
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAG-AGGTCC
* *
44994577 CATGTAAGATCATGTCTGGGACATGGCTTTGGCA
1 CATGTAAGACCATGTCTGGGACATGGCATTGGCA
44994611 TGTTTTTATT
Statistics
Matches: 162, Mismatches: 22, Indels: 1
0.88 0.12 0.01
Matches are distributed among these distances:
50 130 0.80
51 32 0.20
ACGTcount: A:0.25, C:0.22, G:0.31, T:0.22
Consensus pattern (50 bp):
CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGGTCC
Found at i:44994850 original size:19 final size:19
Alignment explanation
Indices: 44994826--44994864 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
44994816 TAAACAAGCA
44994826 AGAAAACTAGAATGAGATT
1 AGAAAACTAGAATGAGATT
44994845 AGAAAACTAGAATGAGATT
1 AGAAAACTAGAATGAGATT
44994864 A
1 A
44994865 ACTAAAGAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.21
Consensus pattern (19 bp):
AGAAAACTAGAATGAGATT
Found at i:44996871 original size:19 final size:19
Alignment explanation
Indices: 44996844--44996881 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
44996834 ATGTAATTTA
*
44996844 TATTTTAAAAAATATTAAT
1 TATTGTAAAAAATATTAAT
*
44996863 TATTGTAAAAATTATTAAT
1 TATTGTAAAAAATATTAAT
44996882 AGGATAGAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
TATTGTAAAAAATATTAAT
Found at i:44997355 original size:18 final size:18
Alignment explanation
Indices: 44997334--44997376 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
44997324 TATTCACCTA
**
44997334 AACCCAAGTATTCAACCC
1 AACCCAAGTACCCAACCC
*
44997352 AACCCAATTACCCAACCC
1 AACCCAAGTACCCAACCC
44997370 AACCCAA
1 AACCCAA
44997377 TCATAAAATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.42, C:0.44, G:0.02, T:0.12
Consensus pattern (18 bp):
AACCCAAGTACCCAACCC
Found at i:44997502 original size:9 final size:9
Alignment explanation
Indices: 44997490--44997532 Score: 59
Period size: 9 Copynumber: 4.8 Consensus size: 9
44997480 ATTCAATTTT
*
44997490 GTTAATTTG
1 GTTAATTCG
44997499 GTTAATTCG
1 GTTAATTCG
*
44997508 GGTAATTCG
1 GTTAATTCG
44997517 GTTAATTCG
1 GTTAATTCG
*
44997526 ATTAATT
1 GTTAATT
44997533 TTTAACCAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 30 1.00
ACGTcount: A:0.26, C:0.07, G:0.21, T:0.47
Consensus pattern (9 bp):
GTTAATTCG
Found at i:45012207 original size:2 final size:2
Alignment explanation
Indices: 45012200--45012227 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
45012190 AAATGTACGC
45012200 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
45012228 AAAGACAGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45013528 original size:31 final size:31
Alignment explanation
Indices: 45013493--45013570 Score: 92
Period size: 31 Copynumber: 2.5 Consensus size: 31
45013483 TATATTTCTA
45013493 ATTTATATTTTATACATT-ATTATATTAAATT
1 ATTTATATTTTATAC-TTCATTATATTAAATT
45013524 ATTTAAATATTTTAT--TTCATTATATTAAATT
1 ATTT--ATATTTTATACTTCATTATATTAAATT
*
45013555 ATTT-TATTTAATACTT
1 ATTTATATTTTATACTT
45013571 GAAAATATTT
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
28 7 0.17
30 4 0.10
31 21 0.51
33 9 0.22
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (31 bp):
ATTTATATTTTATACTTCATTATATTAAATT
Found at i:45013642 original size:21 final size:23
Alignment explanation
Indices: 45013604--45013656 Score: 67
Period size: 21 Copynumber: 2.4 Consensus size: 23
45013594 ATTTATAAAT
45013604 AATTTA-TTAATATAATTATATA
1 AATTTATTTAATATAATTATATA
*
45013626 AATTTATTTAA-AT-ATTATCTA
1 AATTTATTTAATATAATTATATA
*
45013647 AATTGATTTA
1 AATTTATTTA
45013657 TTTTTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 16 0.57
22 8 0.29
23 4 0.14
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
AATTTATTTAATATAATTATATA
Found at i:45015498 original size:31 final size:32
Alignment explanation
Indices: 45015433--45015498 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
45015423 ATATAAAAGT
*
45015433 TAAAAAAAATTATGAATATTTTTAGTTATTATA
1 TAAAAAAAATTATAAATATTTTTA-TTATTATA
*
45015466 TAAAAAATATTA-AAATATTTTT-TTATTAATA
1 TAAAAAAAATTATAAATATTTTTATTATT-ATA
45015497 TA
1 TA
45015499 GCGATAGTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
30 5 0.17
31 5 0.17
32 9 0.30
33 11 0.37
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (32 bp):
TAAAAAAAATTATAAATATTTTTATTATTATA
Found at i:45020912 original size:61 final size:61
Alignment explanation
Indices: 45020817--45020936 Score: 206
Period size: 61 Copynumber: 2.0 Consensus size: 61
45020807 GTAAATTGTA
*
45020817 AGGATCAAATAATTTAGTTCATTTGCTATCAAC-TTTGTGTTACTAAAAATTTTGTCACTCG
1 AGGATCAAATAATTTAGTTCATCTGCTATCAACTTTTG-GTTACTAAAAATTTTGTCACTCG
*
45020878 AGGATCAAATAATTTAGTTCCTCTGCTATCAACTTTTGGTTACTAAAAATTTTGTCACT
1 AGGATCAAATAATTTAGTTCATCTGCTATCAACTTTTGGTTACTAAAAATTTTGTCACT
45020937 TAACTGAGTG
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
61 52 0.93
62 4 0.07
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (61 bp):
AGGATCAAATAATTTAGTTCATCTGCTATCAACTTTTGGTTACTAAAAATTTTGTCACTCG
Found at i:45040385 original size:17 final size:17
Alignment explanation
Indices: 45040365--45040401 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
45040355 TATTTTAATA
*
45040365 AATTTAACATTTATTTT
1 AATTTAACATTTATCTT
*
45040382 AATTTAATATTTATCTT
1 AATTTAACATTTATCTT
45040399 AAT
1 AAT
45040402 AGTATTTTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
AATTTAACATTTATCTT
Found at i:45041755 original size:31 final size:32
Alignment explanation
Indices: 45041691--45041755 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 32
45041681 ATATAATGTA
* *
45041691 ACTTTCGCCCCTTGAACTTGGCAAATAGGTCC
1 ACTTTCGCCCCTTGAACTTAGCAAATAGATCC
* *
45041723 ACTTTGGCCCC-TGAACTTAGCAAGTAGATCC
1 ACTTTCGCCCCTTGAACTTAGCAAATAGATCC
45041754 AC
1 AC
45041756 ATTGTGATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.25, C:0.31, G:0.18, T:0.26
Consensus pattern (32 bp):
ACTTTCGCCCCTTGAACTTAGCAAATAGATCC
Found at i:45042136 original size:31 final size:31
Alignment explanation
Indices: 45042099--45042160 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
45042089 AGATAATTTT
45042099 AAAGAGTTTTATTA-TGATTCAATTACTCTTG
1 AAAGAGTTTTATTAGT-ATTCAATTACTCTTG
45042130 AAAGAGTTTTATTAGTATTCAATTACTCTTG
1 AAAGAGTTTTATTAGTATTCAATTACTCTTG
45042161 TAATTTGCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 29 0.97
32 1 0.03
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (31 bp):
AAAGAGTTTTATTAGTATTCAATTACTCTTG
Found at i:45043228 original size:76 final size:76
Alignment explanation
Indices: 45043102--45043273 Score: 328
Period size: 76 Copynumber: 2.3 Consensus size: 76
45043092 AGTGATTAAA
45043102 GTGGACCTGA-TTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAAT
1 GTGGACCT-ACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAAT
45043166 TTAGGGGCTAAT
65 TTAGGGGCTAAT
45043178 GTGGACCTACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAATT
1 GTGGACCTACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAATT
45043243 TAGGGGCTAAT
66 TAGGGGCTAAT
45043254 GTGGACCTACTTGTCAAGTT
1 GTGGACCTACTTGTCAAGTT
45043274 TAAGGGTTAA
Statistics
Matches: 95, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
75 1 0.01
76 94 0.99
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (76 bp):
GTGGACCTACTTGTCAAGTTCAAGTGAACCAAATACATGTACCAAAATGAACCTACTTGTCAATT
TAGGGGCTAAT
Found at i:45045654 original size:34 final size:34
Alignment explanation
Indices: 45045613--45045680 Score: 136
Period size: 34 Copynumber: 2.0 Consensus size: 34
45045603 TAAAGGGCAA
45045613 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
1 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
45045647 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
1 AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
45045681 TGTAATGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.35, C:0.03, G:0.18, T:0.44
Consensus pattern (34 bp):
AGCATTAGGGTTTAATGAATTTATTATAAAGTTT
Found at i:45052605 original size:17 final size:17
Alignment explanation
Indices: 45052585--45052618 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
45052575 ATAGAAGGTT
* *
45052585 AAATTTTAGTTTTAATC
1 AAATTTGAGATTTAATC
45052602 AAATTTGAGATTTAATC
1 AAATTTGAGATTTAATC
45052619 TTTATATTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.06, G:0.09, T:0.47
Consensus pattern (17 bp):
AAATTTGAGATTTAATC
Found at i:45064658 original size:2 final size:2
Alignment explanation
Indices: 45064651--45064677 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45064641 TGAGTGTAAT
45064651 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
45064678 GAGTAAACTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:45064968 original size:26 final size:26
Alignment explanation
Indices: 45064916--45064969 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 26
45064906 AGTAATTTCG
*
45064916 TTTTTTTCTTTATGTTCTTTTAACTCT
1 TTTTTTTCTTTATGTTCTATT-ACTCT
*
45064943 TTTTTTCTCTTTATTTTCTATT-CTCT
1 TTTTTT-TCTTTATGTTCTATTACTCT
45064969 T
1 T
45064970 CTGCTTCTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 5 0.21
27 6 0.25
28 13 0.54
ACGTcount: A:0.09, C:0.17, G:0.02, T:0.72
Consensus pattern (26 bp):
TTTTTTTCTTTATGTTCTATTACTCT
Found at i:45065436 original size:29 final size:31
Alignment explanation
Indices: 45065360--45065436 Score: 86
Period size: 29 Copynumber: 2.5 Consensus size: 31
45065350 TTAACGGCTC
* *
45065360 AGTGACTAAAATGTTACAGTGCGATAATGTA
1 AGTGACTAAAATGTAACAGTGCGATAATATA
** * *
45065391 AGTGACTAAAACATAACATTTC-A-AATATA
1 AGTGACTAAAATGTAACAGTGCGATAATATA
45065420 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
45065437 CTGAGGTAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
29 20 0.53
30 1 0.03
31 17 0.45
ACGTcount: A:0.45, C:0.12, G:0.16, T:0.27
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAGTGCGATAATATA
Found at i:45070039 original size:18 final size:18
Alignment explanation
Indices: 45070016--45070056 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
45070006 ATTCAAGGCA
45070016 TAATTAATTTAAAATT-TT
1 TAATTAA-TTAAAATTATT
*
45070034 TAATTAATTAAATTTATT
1 TAATTAATTAAAATTATT
45070052 TAATT
1 TAATT
45070057 GAAAACCTAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 7 0.33
18 14 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTAATTAAAATTATT
Found at i:45073881 original size:14 final size:14
Alignment explanation
Indices: 45073854--45073930 Score: 59
Period size: 14 Copynumber: 5.2 Consensus size: 14
45073844 TTAAAATTTA
*
45073854 AAAAATATAAAAATT
1 AAAAATA-ACAAATT
45073869 AAAAATAACAAATT
1 AAAAATAACAAATT
* *
45073883 -AAAGTACACAAACT
1 AAAAATA-ACAAATT
45073897 AAATCAGTATAA-AAATT
1 AAA--A--ATAACAAATT
45073914 AAAAATAACAAATT
1 AAAAATAACAAATT
45073928 AAA
1 AAA
45073931 GTATATAGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 15
0.71 0.07 0.21
Matches are distributed among these distances:
13 9 0.18
14 20 0.40
15 10 0.20
17 8 0.16
18 1 0.02
19 2 0.04
ACGTcount: A:0.68, C:0.08, G:0.03, T:0.22
Consensus pattern (14 bp):
AAAAATAACAAATT
Found at i:45081401 original size:17 final size:18
Alignment explanation
Indices: 45081367--45081402 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
45081357 TTAGAATTAT
45081367 TATTTAGATTTATTTTAG
1 TATTTAGATTTATTTTAG
*
45081385 TATTTATATTT-TTTTAG
1 TATTTAGATTTATTTTAG
45081402 T
1 T
45081403 TTATTTTTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TATTTAGATTTATTTTAG
Found at i:45081422 original size:27 final size:28
Alignment explanation
Indices: 45081360--45081422 Score: 67
Period size: 27 Copynumber: 2.2 Consensus size: 28
45081350 TCGACCCTTA
45081360 GAATTATTATTTAGATTTATTTTAGTATT
1 GAATT-TTATTTAGATTTATTTTAGTATT
* *
45081389 TATATTTT-TTTAG-TTTATTTTTGTACTT
1 GA-ATTTTATTTAGATTTATTTTAGTA-TT
45081417 GAATTT
1 GAATTT
45081423 GACAATTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
27 15 0.52
28 8 0.28
29 3 0.10
30 3 0.10
ACGTcount: A:0.25, C:0.02, G:0.10, T:0.63
Consensus pattern (28 bp):
GAATTTTATTTAGATTTATTTTAGTATT
Found at i:45082577 original size:19 final size:21
Alignment explanation
Indices: 45082540--45082579 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
45082530 ATAATAGTTC
45082540 AAAAATATATTACTAATATAA
1 AAAAATATATTACTAATATAA
45082561 AAAAATATATTA-T-ATATAA
1 AAAAATATATTACTAATATAA
45082580 TATATATTAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAATATATTACTAATATAA
Found at i:45083353 original size:51 final size:51
Alignment explanation
Indices: 45083277--45083376 Score: 173
Period size: 51 Copynumber: 2.0 Consensus size: 51
45083267 ATCTGAAAAG
45083277 CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
1 CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
* * *
45083328 CTCCGATTAGAACTAGGGGAGAGAGATTGGAGAAGTAAGAGATAAGGCA
1 CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCA
45083377 GTGGCTAGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.41, C:0.11, G:0.33, T:0.15
Consensus pattern (51 bp):
CTCCGATAAGAACTAGGAGAGAGAGACTGGAGAAGTAAGAGATAAGGCAAT
Found at i:45083819 original size:29 final size:29
Alignment explanation
Indices: 45083787--45083846 Score: 102
Period size: 29 Copynumber: 2.1 Consensus size: 29
45083777 ATTATGAAAA
*
45083787 ATTGTAGAATAGTAACTTAATCATTTAAG
1 ATTGTAGAATAGTAACTTAACCATTTAAG
*
45083816 ATTGTATAATAGTAACTTAACCATTTAAG
1 ATTGTAGAATAGTAACTTAACCATTTAAG
45083845 AT
1 AT
45083847 AATTGGATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (29 bp):
ATTGTAGAATAGTAACTTAACCATTTAAG
Found at i:45088512 original size:27 final size:27
Alignment explanation
Indices: 45088482--45088545 Score: 78
Period size: 27 Copynumber: 2.4 Consensus size: 27
45088472 TTGAAAGCTA
45088482 AATTTTATTTGT-TGAATTTTGTTGTTC
1 AATTTTATTTGTATGAA-TTTGTTGTTC
* *
45088509 AATTTT-TTTTTACTGCATTTGTTGTTC
1 AATTTTATTTGTA-TGAATTTGTTGTTC
45088536 AATTTTATTT
1 AATTTTATTT
45088546 TCAAATCATT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 4 0.12
27 22 0.69
28 6 0.19
ACGTcount: A:0.19, C:0.06, G:0.11, T:0.64
Consensus pattern (27 bp):
AATTTTATTTGTATGAATTTGTTGTTC
Found at i:45089046 original size:17 final size:18
Alignment explanation
Indices: 45089024--45089058 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
45089014 GATTGAATCG
*
45089024 AATTTTTAT-TTTTTTAA
1 AATTTTAATATTTTTTAA
45089041 AATTTTAATATTTTTTAA
1 AATTTTAATATTTTTTAA
45089059 TTGAATTGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTTAATATTTTTTAA
Found at i:45096711 original size:29 final size:29
Alignment explanation
Indices: 45096669--45096727 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
45096659 CCGTTACTTT
45096669 TTCTTAACTGGTTAGTAAAATAAGGTTAG
1 TTCTTAACTGGTTAGTAAAATAAGGTTAG
45096698 TTCTTAACTGGTTAGTAAAATAAGGTTAG
1 TTCTTAACTGGTTAGTAAAATAAGGTTAG
45096727 T
1 T
45096728 CAGAAAGGCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.34, C:0.07, G:0.20, T:0.39
Consensus pattern (29 bp):
TTCTTAACTGGTTAGTAAAATAAGGTTAG
Found at i:45098471 original size:21 final size:23
Alignment explanation
Indices: 45098447--45098496 Score: 77
Period size: 21 Copynumber: 2.3 Consensus size: 23
45098437 TTTAAAAATT
*
45098447 AAAAAAATCCCA-AAAATT-ATA
1 AAAAAAAGCCCATAAAATTCATA
45098468 AAAAAAAGCCCATAAAATTCATA
1 AAAAAAAGCCCATAAAATTCATA
45098491 AAAAAA
1 AAAAAA
45098497 TAGCAAGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
21 11 0.42
22 6 0.23
23 9 0.35
ACGTcount: A:0.68, C:0.14, G:0.02, T:0.16
Consensus pattern (23 bp):
AAAAAAAGCCCATAAAATTCATA
Found at i:45098976 original size:22 final size:22
Alignment explanation
Indices: 45098943--45098988 Score: 58
Period size: 23 Copynumber: 2.1 Consensus size: 22
45098933 AATTTAATCC
* *
45098943 TTTACTTTTCTTT-TTTTAAAA
1 TTTAATTTTCTTTCATTTAAAA
45098964 TTTAATTTATCTTTCATTTAAAA
1 TTTAATTT-TCTTTCATTTAAAA
45098987 TT
1 TT
45098989 CAAACCTAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 7 0.33
22 5 0.24
23 9 0.43
ACGTcount: A:0.28, C:0.09, G:0.00, T:0.63
Consensus pattern (22 bp):
TTTAATTTTCTTTCATTTAAAA
Found at i:45099969 original size:16 final size:17
Alignment explanation
Indices: 45099948--45099979 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45099938 TTTATTTTAA
45099948 TAAAAAT-TAATAAAAG
1 TAAAAATATAATAAAAG
45099964 TAAAAATATAATAAAA
1 TAAAAATATAATAAAA
45099980 TTTAAACTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (17 bp):
TAAAAATATAATAAAAG
Found at i:45102394 original size:2 final size:2
Alignment explanation
Indices: 45102387--45102422 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
45102377 NNNNNNNNTG
45102387 TA 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 TA
45102423 ATTTTCTCCT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45110031 original size:47 final size:47
Alignment explanation
Indices: 45109962--45110059 Score: 178
Period size: 47 Copynumber: 2.1 Consensus size: 47
45109952 AAAGACATGC
* *
45109962 CAATTCATGACAAAATATGATTAATTCTTTTGTTTAAAGGGGAACTG
1 CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
45110009 CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
1 CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
45110056 CAAT
1 CAAT
45110060 GCTTTAGTCT
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (47 bp):
CAATTCATGACAAAATATGATTAATTCTCTTGTTTAAAAGGGAACTG
Found at i:45112432 original size:323 final size:324
Alignment explanation
Indices: 45111844--45112490 Score: 1181
Period size: 323 Copynumber: 2.0 Consensus size: 324
45111834 TTTTGTATGG
45111844 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGATCTAATAAAGTAGT
1 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGATCTAATAAAGTAGT
* *
45111909 TCATTTGGTTTTCTTTTTCCGGTCTTTTAAGGGTTCATACTTACAGGTACAATTATTAAAAAATA
66 TCATTTGATTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAATA
*
45111974 ATAATTACAGATATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
131 ACAATTACAGATATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
*
45112039 ATATAAATCACAACAAGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTAAAAAAATTTA
196 ATATAAATCACAACAAGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTAAAAAAAATTA
*
45112104 ATTACGTTTTTATTC-TTTTTTTCATTTAATTTAGTACTTAAACTTTCAATATGCATCAAAAAA
261 ATTACGTTTTTATTCTTTTTTTTCATTCAATTTAGTACTTAAACTTTCAATATGCATCAAAAAA
*
45112167 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGGTCTAATAAAGTAGT
1 GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGATCTAATAAAGTAGT
45112232 TCATTTGATTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAA-A
66 TCATTTGATTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAATA
*
45112296 ACAATTACAGGTATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
131 ACAATTACAGATATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
* *
45112361 ATATAAATCACAACAGGTTAAAAATTAAAAGCCTGTAAAAATCATCAATTTTTTTAAAAAAAATT
196 ATATAAATCACAACAAGTTAAAAATTAAAAGCCTGTAAAAACCATCAA-TTTTTTAAAAAAAATT
*
45112426 AATTACGTTTTTATTCTTTTTTTTCATTCAATTTGGTACTTAAACTTTCAATATGCATCAAAAAA
260 AATTACGTTTTTATTCTTTTTTTTCATTCAATTTAGTACTTAAACTTTCAATATGCATCAAAAAA
45112491 ATCTTTAATT
Statistics
Matches: 312, Mismatches: 10, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
322 110 0.35
323 156 0.50
324 46 0.15
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.36
Consensus pattern (324 bp):
GCTTGTACAATACTGAAACTAACCCATTAAATTGATTGTCACAATAATCGATCTAATAAAGTAGT
TCATTTGATTTTCTTTTTCCGGTCTTTTAAGAGTTCATACTTACAGGTACAATTATTAAAAAATA
ACAATTACAGATATAATACATCATAAATGATAATTGTTCGATAAACTAAAATCGAAACTAACTCG
ATATAAATCACAACAAGTTAAAAATTAAAAGCCTGTAAAAACCATCAATTTTTTAAAAAAAATTA
ATTACGTTTTTATTCTTTTTTTTCATTCAATTTAGTACTTAAACTTTCAATATGCATCAAAAAA
Found at i:45112753 original size:20 final size:19
Alignment explanation
Indices: 45112720--45112773 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
45112710 TTATAAAAAT
* *
45112720 TAAAAATCAATAAAATTTAT
1 TAAAAAT-ATTAAAATTTAA
* *
45112740 TCAAAATTATTAAATTTTAA
1 T-AAAAATATTAAAATTTAA
45112760 TAAAAATATTAAAA
1 TAAAAATATTAAAA
45112774 ATTAGAAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 3
0.75 0.17 0.08
Matches are distributed among these distances:
19 11 0.41
20 11 0.41
21 5 0.19
ACGTcount: A:0.59, C:0.04, G:0.00, T:0.37
Consensus pattern (19 bp):
TAAAAATATTAAAATTTAA
Found at i:45116004 original size:9 final size:10
Alignment explanation
Indices: 45115971--45116026 Score: 53
Period size: 10 Copynumber: 5.6 Consensus size: 10
45115961 TTTAGACATT
*
45115971 ATTTCTAATA
1 ATTTTTAATA
45115981 AGTTTTT-ATCA
1 A-TTTTTAAT-A
45115992 ATTTTTAAT-
1 ATTTTTAATA
*
45116001 ATTTTTTATA
1 ATTTTTAATA
*
45116011 ATTTCTAATA
1 ATTTTTAATA
45116021 ATTTTT
1 ATTTTT
45116027 TAAATATTTT
Statistics
Matches: 37, Mismatches: 5, Indels: 8
0.74 0.10 0.16
Matches are distributed among these distances:
9 8 0.22
10 21 0.57
11 8 0.22
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:45116013 original size:19 final size:21
Alignment explanation
Indices: 45115971--45116028 Score: 84
Period size: 20 Copynumber: 2.9 Consensus size: 21
45115961 TTTAGACATT
*
45115971 ATTTCTAATAAGTTTTTATCA
1 ATTTCTAATAATTTTTTATCA
*
45115992 ATTTTTAAT-ATTTTTTAT-A
1 ATTTCTAATAATTTTTTATCA
45116011 ATTTCTAATAATTTTTTA
1 ATTTCTAATAATTTTTTA
45116029 AATATTTTTG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
19 9 0.27
20 16 0.48
21 8 0.24
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
ATTTCTAATAATTTTTTATCA
Found at i:45116089 original size:23 final size:23
Alignment explanation
Indices: 45116024--45116090 Score: 64
Period size: 23 Copynumber: 2.9 Consensus size: 23
45116014 TCTAATAATT
*
45116024 TTTTAAATATTTTTGTATAAATA
1 TTTTAAATATATTTGTATAAATA
** * * *
45116047 TATACAAAAACA-TTGAATAAATA
1 T-TTTAAATATATTTGTATAAATA
45116070 TTTTAAATATATTTGTATAAA
1 TTTTAAATATATTTGTATAAA
45116091 AAATTATAAA
Statistics
Matches: 31, Mismatches: 11, Indels: 4
0.67 0.24 0.09
Matches are distributed among these distances:
22 6 0.19
23 20 0.65
24 5 0.16
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.45
Consensus pattern (23 bp):
TTTTAAATATATTTGTATAAATA
Found at i:45118202 original size:12 final size:12
Alignment explanation
Indices: 45118185--45118209 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
45118175 AGTATATATA
45118185 TATTTTAAAATT
1 TATTTTAAAATT
45118197 TATTTTAAAATT
1 TATTTTAAAATT
45118209 T
1 T
45118210 TTAGTACTTT
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:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TATTTTAAAATT
Found at i:45126919 original size:2 final size:2
Alignment explanation
Indices: 45126912--45126947 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
45126902 AACAATTATG
45126912 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45126948 GTACTCATCC
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:45132363 original size:3 final size:3
Alignment explanation
Indices: 45132355--45132389 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
45132345 GTTCTCTGAG
45132355 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA GA
45132390 TTATTGTGTT
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:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:45134026 original size:2 final size:2
Alignment explanation
Indices: 45134019--45134044 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
45134009 CATGTCATCA
45134019 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
45134045 CATATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:45137828 original size:12 final size:13
Alignment explanation
Indices: 45137813--45137841 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
45137803 AAATTTTAGA
45137813 AATAATTT-TTTT
1 AATAATTTATTTT
45137825 AATAATTTATTTT
1 AATAATTTATTTT
45137838 AATA
1 AATA
45137842 CAAAATAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 8 0.50
13 8 0.50
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
AATAATTTATTTT
Found at i:45144812 original size:21 final size:20
Alignment explanation
Indices: 45144788--45144859 Score: 63
Period size: 21 Copynumber: 3.5 Consensus size: 20
45144778 TTTAGTTCTC
* *
45144788 ATGAGCTTCTGTTTAACTCAT
1 ATGAGCTTCCGTTCAACTC-T
* *
45144809 ATGAGTTTCCGTTCAACCCT
1 ATGAGCTTCCGTTCAACTCT
* *
45144829 AATGAGTTTCCGTTCAGCTCT
1 -ATGAGCTTCCGTTCAACTCT
45144850 ATTGAGCTTC
1 A-TGAGCTTC
45144860 TGTTTAACCC
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 2 0.05
21 40 0.95
ACGTcount: A:0.21, C:0.24, G:0.17, T:0.39
Consensus pattern (20 bp):
ATGAGCTTCCGTTCAACTCT
Found at i:45147691 original size:2 final size:2
Alignment explanation
Indices: 45147684--45147710 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
45147674 CCAGATTTGT
45147684 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
45147711 ACTTCCAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:45158138 original size:34 final size:33
Alignment explanation
Indices: 45158093--45158183 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 33
45158083 GATTCTTTTT
* *
45158093 AAAAATAATTAAATTAGGTTTTTGGGGTTTTAAA-
1 AAAATTAATTAAATTAGGTTTAT--GGTTTTAAAG
*
45158127 TAAATTAATTAAATTAGAGTTTATGGTTTTAAAG
1 AAAATTAATTAAATTAG-GTTTATGGTTTTAAAG
45158161 AAAATTAATTAAATTATGGTTTA
1 AAAATTAATTAAATTA-GGTTTA
45158184 GTTTTTTTAA
Statistics
Matches: 50, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
33 9 0.18
34 35 0.70
35 6 0.12
ACGTcount: A:0.43, C:0.00, G:0.14, T:0.43
Consensus pattern (33 bp):
AAAATTAATTAAATTAGGTTTATGGTTTTAAAG
Found at i:45158562 original size:126 final size:124
Alignment explanation
Indices: 45158252--45158642 Score: 465
Period size: 126 Copynumber: 3.2 Consensus size: 124
45158242 TTTTGTTTTT
* * * * *
45158252 TTTTTCTACAGTAGTTTCTGAAAAAATAATTTTTAGAATACGGTTCTGAAA-AGATAATGTAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCT-AAACAAATAGTGTAAAA
* * *
45158316 GACACTTTAAGTAGGATGCACTGTCAGAAAAATTACTGAAAAAAGCTCCCACGTGAACG--C
65 -ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTG-ACGCTC
* * *
45158376 ----TCTACAGTAGGTCCTGAAAAAATAA-TTTGAGAAGACAGTTCTGAACAAATAGTGTAAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGT-AAAA
* * * ** **
45158436 ACGCTTCAAGCAAGATGCACTGTGAGCAAAATTACTGAAAAAAGCTCTTATATAGACGCTC
65 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGT-GACGCTC
*
45158497 TTTTTCTACAGTAGTTCCTTAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTCAAAA
1 TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGT-AAAA
* *
45158562 ACTCTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAACTCCCACGTGGACGCTC
65 ACACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGT-GACGCTC
*
45158623 TTTTTCTACAATAGTTCCTG
1 TTTTTCTACAGTAGTTCCTG
45158643 TTTGGCCTTA
Statistics
Matches: 223, Mismatches: 34, Indels: 18
0.81 0.12 0.07
Matches are distributed among these distances:
118 2 0.01
119 67 0.30
120 28 0.13
121 1 0.00
125 23 0.10
126 102 0.46
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (124 bp):
TTTTTCTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTAAACAAATAGTGTAAAAA
CACTTCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCCCACGTGACGCTC
Found at i:45161785 original size:25 final size:25
Alignment explanation
Indices: 45161724--45161785 Score: 63
Period size: 25 Copynumber: 2.4 Consensus size: 25
45161714 AGAACTAGTA
*
45161724 TTTTATTAAAAATATAAAAATAAAT
1 TTTTATTAAATATATAAAAATAAAT
** *
45161749 TACTATTAAA-ATATTAAAAATAACTT
1 TTTTATTAAATATA-TAAAAATAA-AT
45161775 TTTTATTAAAT
1 TTTTATTAAAT
45161786 GAAACAATAT
Statistics
Matches: 29, Mismatches: 5, Indels: 4
0.76 0.13 0.11
Matches are distributed among these distances:
24 3 0.10
25 17 0.59
26 9 0.31
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (25 bp):
TTTTATTAAATATATAAAAATAAAT
Found at i:45161852 original size:90 final size:91
Alignment explanation
Indices: 45161727--45161917 Score: 287
Period size: 93 Copynumber: 2.1 Consensus size: 91
45161717 ACTAGTATTT
*
45161727 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAAC-TT-TTTTATTAAATGAAA
1 TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTATTTTATTAAATAAAA
*
45161790 CAATATAAAAACAATTTGTAAAAATA
66 CAATATAAAAACAATTTATAAAAATA
*
45161816 TATTAAAAATATAAAAAATAAATTACTATTAAAATATTAAAAATGACTTTTATTTTATTAAATAA
1 TATTAAAAATAT-AAAAATAAATTACTATTAAAATATTAAAAATAAC-TTTATTTTATTAAATAA
* * * *
45161881 AATAATATAAAATCAGTTTATACAAATA
64 AACAATATAAAAACAATTTATAAAAATA
45161909 TATTAAAAA
1 TATTAAAAA
45161918 AATCAATGTT
Statistics
Matches: 91, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
89 12 0.13
90 33 0.36
92 2 0.02
93 44 0.48
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (91 bp):
TATTAAAAATATAAAAATAAATTACTATTAAAATATTAAAAATAACTTTATTTTATTAAATAAAA
CAATATAAAAACAATTTATAAAAATA
Found at i:45164025 original size:11 final size:11
Alignment explanation
Indices: 45163999--45164038 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
45163989 ATAGAGCTTT
45163999 GAGAAATTTAGA
1 GAGAAATTT-GA
45164011 GAGAAATTTGA
1 GAGAAATTTGA
*
45164022 GAGAAAATTGA
1 GAGAAATTTGA
45164033 -AGAAAT
1 GAGAAAT
45164039 AATGTGTGGA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 5 0.19
11 12 0.46
12 9 0.35
ACGTcount: A:0.53, C:0.00, G:0.25, T:0.23
Consensus pattern (11 bp):
GAGAAATTTGA
Found at i:45169829 original size:49 final size:49
Alignment explanation
Indices: 45169775--45169931 Score: 296
Period size: 49 Copynumber: 3.2 Consensus size: 49
45169765 GTTTATATTA
45169775 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
45169824 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
* *
45169873 ATGTAATAAAATACTAAATAGTTTATTTTGAATAATTTGATATTATTTG
1 ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
45169922 ATGTAATAAA
1 ATGTAATAAA
45169932 GTATCTTACT
Statistics
Matches: 106, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 106 1.00
ACGTcount: A:0.42, C:0.02, G:0.10, T:0.46
Consensus pattern (49 bp):
ATGTAATAAAATACAAAATAGTTTATTTTGAATATTTTGATATTATTTG
Found at i:45171726 original size:20 final size:20
Alignment explanation
Indices: 45171682--45171726 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
45171672 TAATTAATTT
45171682 TTAAA-ATTTTAAAAAATAA
1 TTAAATATTTTAAAAAATAA
** *
45171701 AAAAATATTTTAAAAATTAA
1 TTAAATATTTTAAAAAATAA
45171721 TTAAAT
1 TTAAAT
45171727 GTTGACATGT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (20 bp):
TTAAATATTTTAAAAAATAA
Found at i:45178732 original size:9 final size:9
Alignment explanation
Indices: 45178675--45178739 Score: 60
Period size: 9 Copynumber: 6.9 Consensus size: 9
45178665 AGTTACTTAT
45178675 AAATTACTAA
1 AAATTA-TAA
*
45178685 AAATGATAA
1 AAATTATAA
45178694 GAAATTATAA
1 -AAATTATAA
* *
45178704 ACATT-TTA
1 AAATTATAA
45178712 AAATTAATTAA
1 AAATT-A-TAA
45178723 AAATTATAA
1 AAATTATAA
45178732 AAATTATA
1 AAATTATA
45178740 TTAAAGAATT
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
8 6 0.13
9 18 0.40
10 14 0.31
11 7 0.16
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
AAATTATAA
Found at i:45179974 original size:38 final size:38
Alignment explanation
Indices: 45179872--45179998 Score: 157
Period size: 38 Copynumber: 3.3 Consensus size: 38
45179862 ATATCATGTA
* **
45179872 AATAGTAGACATGTTTAACATGTATTCAGTTCAACAGT
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
** *
45179910 AGCATTAGACATGCTTAACATGTATTTGGTTCAACA-T
1 AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
*
45179947 CAATAGTAGACATGCTTAACATGTATTTGGTTTAACAGT
1 -AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
* *
45179986 ATTAGTAGGCATG
1 AATAGTAGACATG
45179999 TTGAATATGC
Statistics
Matches: 75, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
37 1 0.01
38 73 0.97
39 1 0.01
ACGTcount: A:0.34, C:0.13, G:0.18, T:0.35
Consensus pattern (38 bp):
AATAGTAGACATGCTTAACATGTATTTGGTTCAACAGT
Found at i:45182346 original size:4 final size:4
Alignment explanation
Indices: 45182337--45182401 Score: 64
Period size: 4 Copynumber: 17.0 Consensus size: 4
45182327 CTATAAAGTA
* *
45182337 ATAT ATAT ATAT ATAT ATAT ATAT ATAA ATAT ATA- ATGT AT-T A-AT
1 ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT ATAT
* * *
45182382 ATTT ATAT ATGT ATCT ATAT
1 ATAT ATAT ATAT ATAT ATAT
45182402 GAATATGTTC
Statistics
Matches: 50, Mismatches: 8, Indels: 6
0.78 0.12 0.09
Matches are distributed among these distances:
3 6 0.12
4 44 0.88
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (4 bp):
ATAT
Found at i:45182348 original size:6 final size:6
Alignment explanation
Indices: 45182337--45182401 Score: 64
Period size: 6 Copynumber: 11.3 Consensus size: 6
45182327 CTATAAAGTA
* *
45182337 ATATAT ATATAT ATATAT ATATAT ATAAAT ATATA- ATGTAT -TA-AT
1 ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT ATATAT
* * *
45182382 ATTTAT ATATGT ATCTAT AT
1 ATATAT ATATAT ATATAT AT
45182402 GAATATGTTC
Statistics
Matches: 47, Mismatches: 9, Indels: 6
0.76 0.15 0.10
Matches are distributed among these distances:
4 2 0.04
5 6 0.13
6 39 0.83
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.49
Consensus pattern (6 bp):
ATATAT
Found at i:45183314 original size:41 final size:41
Alignment explanation
Indices: 45183256--45183485 Score: 370
Period size: 41 Copynumber: 5.6 Consensus size: 41
45183246 NNNNNNNNNN
*
45183256 AGCAGGCTAAGTGCCGGTGAACTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
* *
45183297 GGCAGGCTAAGTGCCGGTGATTTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
*
45183338 AGCAAGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
45183379 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
* *
45183420 AGCAGGCTAAGTGCCGGTGATCTAAATCAGGCTTTAAGCCT
1 AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
* * *
45183461 AACAAGCTAAGTGCCAGTGAATCTG
1 AGCAGGCTAAGTGCCGGTG-ATCTG
45183486 TTTAAATTAA
Statistics
Matches: 175, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
41 171 0.98
42 4 0.02
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (41 bp):
AGCAGGCTAAGTGCCGGTGATCTGAATCAGGCTATAAGCCT
Found at i:45184917 original size:32 final size:32
Alignment explanation
Indices: 45184876--45184937 Score: 115
Period size: 32 Copynumber: 1.9 Consensus size: 32
45184866 CAAATGATGA
*
45184876 ACCTTGGTATTTCTGCAATTTAGCCAGGTAGT
1 ACCTTGGTATTTCTGCAATTTAACCAGGTAGT
45184908 ACCTTGGTATTTCTGCAATTTAACCAGGTA
1 ACCTTGGTATTTCTGCAATTTAACCAGGTA
45184938 AGTTCATATG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 29 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.37
Consensus pattern (32 bp):
ACCTTGGTATTTCTGCAATTTAACCAGGTAGT
Found at i:45190335 original size:13 final size:13
Alignment explanation
Indices: 45190283--45190335 Score: 63
Period size: 13 Copynumber: 4.1 Consensus size: 13
45190273 TCTAAACCAA
45190283 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
45190296 A-TTTCTTAAAAGC
1 ACTTT-TCAAAAGC
* *
45190309 ACTTTTCCACAGC
1 ACTTTTCAAAAGC
45190322 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
45190335 A
1 A
45190336 ATGAAGAACT
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
12 3 0.09
13 26 0.81
14 3 0.09
ACGTcount: A:0.36, C:0.25, G:0.08, T:0.32
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:45191883 original size:23 final size:23
Alignment explanation
Indices: 45191857--45191900 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
45191847 ATTTTAGCAC
45191857 ATCAAAGCATTAATGTCTTCCCA
1 ATCAAAGCATTAATGTCTTCCCA
45191880 ATCAAAGCATTAATGTCTTCC
1 ATCAAAGCATTAATGTCTTCC
45191901 TAATTTGTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.34, C:0.25, G:0.09, T:0.32
Consensus pattern (23 bp):
ATCAAAGCATTAATGTCTTCCCA
Found at i:45210990 original size:15 final size:16
Alignment explanation
Indices: 45210959--45210990 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45210949 GATATGCATA
45210959 AAAATTTTAAGAAATT
1 AAAATTTTAAGAAATT
45210975 AAAATTTTAA-AAATT
1 AAAATTTTAAGAAATT
45210990 A
1 A
45210991 TTTAATCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (16 bp):
AAAATTTTAAGAAATT
Found at i:45211257 original size:18 final size:18
Alignment explanation
Indices: 45211225--45211259 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
45211215 AACGAATAAA
45211225 ATAACAAATTAAAAATAT
1 ATAACAAATTAAAAATAT
45211243 ATAA-AAATTATAAAATA
1 ATAACAAATTA-AAAATA
45211260 ATTTAAACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.29
Consensus pattern (18 bp):
ATAACAAATTAAAAATAT
Found at i:45213482 original size:2 final size:2
Alignment explanation
Indices: 45213475--45213514 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
45213465 AAGCTACTCT
45213475 TA TA TA 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 TA TA TA
45213515 ACGAGAATTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:45217447 original size:15 final size:17
Alignment explanation
Indices: 45217420--45217454 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
45217410 AATTTCAGTA
45217420 ATTATTGTTATTTC-TC
1 ATTATTGTTATTTCTTC
45217436 ATTATT-TTATTTCTTC
1 ATTATTGTTATTTCTTC
45217452 ATT
1 ATT
45217455 TATCTTATGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.20, C:0.11, G:0.03, T:0.66
Consensus pattern (17 bp):
ATTATTGTTATTTCTTC
Found at i:45235578 original size:15 final size:15
Alignment explanation
Indices: 45235554--45235600 Score: 60
Period size: 15 Copynumber: 3.2 Consensus size: 15
45235544 ATCTACGTAT
45235554 AATA-AATTATTTAA
1 AATATAATTATTTAA
* *
45235568 AATATATTTATTTCA
1 AATATAATTATTTAA
*
45235583 AATATAATAATTTAA
1 AATATAATTATTTAA
45235598 AAT
1 AAT
45235601 TATGAAGAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
14 4 0.15
15 23 0.85
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (15 bp):
AATATAATTATTTAA
Found at i:45250898 original size:40 final size:40
Alignment explanation
Indices: 45250757--45250891 Score: 132
Period size: 40 Copynumber: 3.4 Consensus size: 40
45250747 GACTTCGAGT
* * *
45250757 CGATGAGACATTGGGTGTCAAATTATTACTTCGAATATATT
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAAT-TATC
* * ** *
45250798 CGATGAGGCACTAGGTG-CCAA-T-TTACTTCGGTTTAGC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
** *
45250835 TAATGAGACACTGGGTGTCAAATTATTACTTCGAATTATC
1 CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
*
45250875 CGATAAGGCACTGGGTG
1 CGATGAGGCACTGGGTG
45250892 CTAAATTGGT
Statistics
Matches: 71, Mismatches: 20, Indels: 7
0.72 0.20 0.07
Matches are distributed among these distances:
37 15 0.21
38 12 0.17
39 2 0.03
40 28 0.39
41 14 0.20
ACGTcount: A:0.28, C:0.16, G:0.24, T:0.32
Consensus pattern (40 bp):
CGATGAGGCACTGGGTGTCAAATTATTACTTCGAATTATC
Found at i:45251544 original size:13 final size:13
Alignment explanation
Indices: 45251526--45251550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45251516 TTAAATGATA
45251526 TTTTGATGATATG
1 TTTTGATGATATG
45251539 TTTTGATGATAT
1 TTTTGATGATAT
45251551 AATTGTTGTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.24, C:0.00, G:0.20, T:0.56
Consensus pattern (13 bp):
TTTTGATGATATG
Found at i:45255955 original size:153 final size:152
Alignment explanation
Indices: 45255671--45256583 Score: 1193
Period size: 153 Copynumber: 6.0 Consensus size: 152
45255661 TTTTGGCCTC
* * * * *
45255671 TGTTGGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATATAATATTTTCTAATTTTTTTATT
1 TGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTATT
* * * *
45255736 TTATATTATTTTAGTACATTATATTTTAAATTTATTAATTTAGTGTGTTTTTTAAATAAA-TTAA
66 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTAA
*
45255800 AAAAATCT-TTATTTCGGCCATT
130 AAAAAACTCTTATTTCGGCCATT
* * * * *
45255822 TATTTGTATTTTTTTCTCGGCTTTTATTACTTTCAATAAAAATATACTATTTTCTAATTTTCTAA
1 TGTTCGTATTTTTTTCTCGGATTTTATTACTTT-AA-AAAAATATACTATTTTCTAATTTTATTA
* *
45255887 TTTTACATTATTTTAGTACATCAAGTTTGAAATGTATTAATTTA-GTGTTTTTTAAATAAATTTA
64 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTA
*
45255951 AAAAAAACTCTTATTTCAGCCATT
129 AAAAAAACTCTTATTTCGGCCATT
* * *
45255975 TGTTCGTATTTTTTTCCCCAGAGTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
1 TGTTCGTATTTTTTT-CTCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
* *
45256040 TTTACATTATTTTAGTACATGATGTTTGAAATGTATTAATTTACTGCGTTTTTTAAATAAATTT-
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTA
* *
45256104 -AAAAAA-TCATTATTTCGTCCCTT
129 AAAAAAACTC-TTATTTCGGCCATT
* * * *
45256127 TGTTCGTATTTTTTTCCCCGAATTTTATTACTTT-AAAAAATATAATATTTCCTAATTTTATTAT
1 TGTTCGTATTTTTTT-CTCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
*
45256191 TTTACATTATCTTAGTACATTATGTTTGAAATGTATTAATTTACTGTG-TTTTTAAATAAATTTA
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTA
*
45256255 AAAAAAACTATTATTTCGGTCC-TT
129 AAAAAAACTCTTATTTCGG-CCATT
* * * *
45256279 TGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAAC-ATTTTATTATTTTAATAT
1 TGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAAATAT-ACTATTTTCTAATTTTATTAT
* * *
45256343 TTTACATTATTTTAGTTCATTATGTTTGAAATGTATTAATTTACTGTATTTTTTAAATAAATTTT
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAATTTA
* * *
45256408 AAAAAAACCCTTATTTCGGTCTTT
129 AAAAAAACTCTTATTTCGGCCATT
* * *
45256432 TGTTCGTATTTTTTTC-CTTGATTTTATTACTTTTAAAAAAA-ATATTATTTTATAATTTTATTA
1 TGTTCGTATTTTTTTCTC-GGATTTTATTAC-TTTAAAAAAATATACTATTTTCTAATTTTATTA
*
45256495 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTTTTAAATAAATTT
64 TTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTA-TGTGTTTTTTAAATAAA--T
45256560 TTAAAAAAAACTCTTATTTCGGCC
126 TTAAAAAAAACTCTTATTTCGGCC
45256584 CTTNNNNNNN
Statistics
Matches: 675, Mismatches: 66, Indels: 38
0.87 0.08 0.05
Matches are distributed among these distances:
150 15 0.02
151 136 0.20
152 230 0.34
153 231 0.34
154 41 0.06
155 22 0.03
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (152 bp):
TGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTATT
TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTATGTGTTTTTTAAATAAATTTAAA
AAAAACTCTTATTTCGGCCATT
Found at i:45256261 original size:305 final size:302
Alignment explanation
Indices: 45255671--45256579 Score: 1243
Period size: 305 Copynumber: 3.0 Consensus size: 302
45255661 TTTTGGCCTC
* * *
45255671 TGTTGGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATATAATATTTTCTAATTTTTTTATT
1 TGTTCGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTATT
* * * * * *
45255736 TTATATTATTTTAGTACATTATATTTTAAATTTATTAATTTAGTGTGTTTTTTAAATAAATTAAA
66 TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTAA
* * * * *
45255801 AAAATCTTTATTTCGGCCATTTATTTGTATTTTTTT-CTCGGCTTTTATTACTTTCAATAAAAAT
131 AAAATCATTATTTCGTCCATTTGTTCGTATTTTTTTCCTC-GATTTTATTACTTT--A-AAAAAT
* * * * *
45255865 ATACTATTTTCTAATTTTCTAATTTTACATTATTTTAGTACATCAAGTTTGAAATGTATTAATTT
192 ATAATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTT
45255930 AGTGT-TTTTTAAATAAATTTAAAAAAAACTCTTATTTCAG-CCATT
257 AGTGTGTTTTTAAATAAATTTAAAAAAAACTCTTATTTCAGTCC-TT
* * *
45255975 TGTTCGTATTTTTTTCCCCAGAGTTTATTACTTTAAAAAAATATACTATTTTCTAATTTTATTAT
1 TGTTCGTATTTTTTT-CTCAGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTAT
* *
45256040 TTTACATTATTTTAGTACATGATGTTTGAAATGTATTAATTTACTGCGTTTTTTAAATAAATTTA
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTA
* *
45256105 AAAAATCATTATTTCGTCCCTTTGTTCGTATTTTTTTCCCCGAATTTTATTACTTTAAAAAATAT
130 AAAAATCATTATTTCGTCCATTTGTTCGTATTTTTTTCCTCG-ATTTTATTACTTTAAAAAATAT
* * *
45256170 AATATTTCCTAATTTTATTATTTTACATTATCTTAGTACATTATGTTTGAAATGTATTAATTTAC
194 AATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAG
* *
45256235 TGTGTTTTTAAATAAATTTAAAAAAAACTATTATTTCGGTCCTT
259 TGTGTTTTTAAATAAATTTAAAAAAAACTCTTATTTCAGTCCTT
* * * *
45256279 TGTTCGTATTTTTTTCTCGGATTTTATTACTTTTAAAAAATATAAC-ATTTTATTATTTTAATAT
1 TGTTCGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATAT-ACTATTTTCTAATTTTATTAT
* *
45256343 TTTACATTATTTTAGTTCATTATGTTTGAAATGTATTAATTTACTGTATTTTTTAAATAAATTTT
65 TTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAA-TTT
* * * *
45256408 AAAAAAACCCTTATTTCGGT-CTTTTGTTCGTATTTTTTTCCTTGATTTTATTACTTTTAAAAAA
129 -AAAAAATCATTATTTC-GTCCATTTGTTCGTATTTTTTTCCTCGATTTTATTAC-TTTAAAAAA
* * * *
45256472 AATATTATTTTATAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATT
191 TATAATATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATT
45256537 TAGTGTGTTTTTTAAATAAATTTTTAAAAAAAACTCTTATTTC
256 TAGTGTG-TTTTTAAATAAA--TTTAAAAAAAACTCTTATTTC
45256580 GGCCCTTNNN
Statistics
Matches: 537, Mismatches: 55, Indels: 22
0.87 0.09 0.04
Matches are distributed among these distances:
303 164 0.31
304 80 0.15
305 245 0.46
306 28 0.05
308 20 0.04
ACGTcount: A:0.32, C:0.09, G:0.07, T:0.52
Consensus pattern (302 bp):
TGTTCGTATTTTTTTCTCAGATTTTATTACTTTTAAAAAATATACTATTTTCTAATTTTATTATT
TTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTACTGTGTTTTTTAAATAAATTTAA
AAAATCATTATTTCGTCCATTTGTTCGTATTTTTTTCCTCGATTTTATTACTTTAAAAAATATAA
TATTTTCTAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTG
TGTTTTTAAATAAATTTAAAAAAAACTCTTATTTCAGTCCTT
Found at i:45269525 original size:11 final size:11
Alignment explanation
Indices: 45269511--45269546 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
45269501 AGCCCGGCCC
45269511 ATATTAAATAT
1 ATATTAAATAT
45269522 ATATTAAATAT
1 ATATTAAATAT
45269533 ATA-T-AATAT
1 ATATTAAATAT
45269542 ATATT
1 ATATT
45269547 TGATTAAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
9 8 0.33
10 2 0.08
11 14 0.58
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (11 bp):
ATATTAAATAT
Found at i:45271674 original size:15 final size:16
Alignment explanation
Indices: 45271644--45271675 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
45271634 TTATATTATA
45271644 AAAATATTATTAAATT
1 AAAATATTATTAAATT
45271660 AAAATATTA-TAAATT
1 AAAATATTATTAAATT
45271675 A
1 A
45271676 TATTAATTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.44
16 9 0.56
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
AAAATATTATTAAATT
Found at i:45271679 original size:25 final size:26
Alignment explanation
Indices: 45271636--45271688 Score: 74
Period size: 24 Copynumber: 2.1 Consensus size: 26
45271626 TTCTTGATTT
45271636 ATATTATAAAAATATTATTAAATTAAA
1 ATATTATAAAAATATTATT-AATTAAA
*
45271663 ATATTAT-AAATTA-TATTAATTAAA
1 ATATTATAAAAATATTATTAATTAAA
45271687 AT
1 AT
45271689 TAAGATAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 9 0.36
25 4 0.16
26 5 0.20
27 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (26 bp):
ATATTATAAAAATATTATTAATTAAA
Found at i:45271696 original size:25 final size:22
Alignment explanation
Indices: 45271646--45271703 Score: 53
Period size: 24 Copynumber: 2.4 Consensus size: 22
45271636 ATATTATAAA
**
45271646 AATATTATTAAATTAAAATATTAT
1 AATA-TATT-AATTAAAATAAGAT
45271670 AAATTATATTAATTAAAATTAAGAT
1 -AA-TATATTAATTAAAA-TAAGAT
45271695 AATATATTA
1 AATATATTA
45271704 TAGGAAGCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
23 7 0.24
24 10 0.34
25 10 0.34
26 2 0.07
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.43
Consensus pattern (22 bp):
AATATATTAATTAAAATAAGAT
Found at i:45271703 original size:28 final size:27
Alignment explanation
Indices: 45271647--45271705 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 27
45271637 TATTATAAAA
45271647 ATATTATTAAATTAAAATATTATAAATT
1 ATATTATTAAATTAAAATA-TATAAATT
* *
45271675 ATATTAATTAAAATTAAGATA-ATATATT
1 ATATT-ATT-AAATTAAAATATATAAATT
45271703 ATA
1 ATA
45271706 GGAAGCAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
28 14 0.52
29 3 0.11
30 10 0.37
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATATTATTAAATTAAAATATATAAATT
Found at i:45271869 original size:19 final size:22
Alignment explanation
Indices: 45271831--45271870 Score: 59
Period size: 19 Copynumber: 2.0 Consensus size: 22
45271821 TTGTGAATAA
45271831 AATATTATTATATGATTATTAT
1 AATATTATTATATGATTATTAT
45271853 AATA-TATTAT-T-ATTATTA
1 AATATTATTATATGATTATTA
45271871 ACTAATGCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
20 1 0.06
21 6 0.33
22 4 0.22
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (22 bp):
AATATTATTATATGATTATTAT
Found at i:45271954 original size:22 final size:22
Alignment explanation
Indices: 45271915--45271962 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
45271905 AACAAAAAGA
45271915 AAAAGAAACAAAAGAAGA-ACAG
1 AAAAGAAACAAAAGAAGAGAC-G
*
45271937 AAAAGAAAC-AGAGAAAGAGACG
1 AAAAGAAACAAAAG-AAGAGACG
45271959 AAAA
1 AAAA
45271963 CAGGAGAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
21 3 0.13
22 18 0.78
23 2 0.09
ACGTcount: A:0.71, C:0.08, G:0.21, T:0.00
Consensus pattern (22 bp):
AAAAGAAACAAAAGAAGAGACG
Found at i:45271990 original size:29 final size:29
Alignment explanation
Indices: 45271903--45271990 Score: 78
Period size: 29 Copynumber: 3.1 Consensus size: 29
45271893 GTAAGTAAGT
*
45271903 AAAACA-AAAAGAAA-A-AGAAACAAAAG
1 AAAACAGAAAAGAAACAGAGAAAGAAAAG
* *
45271929 AAGAACAGAAAAGAAACAGAGAAAGAGACG
1 AA-AACAGAAAAGAAACAGAGAAAGAAAAG
*
45271959 AAAACAGGAGAAA-AAA-AGGGAAAGAAAAG
1 AAAACA-GA-AAAGAAACAGAGAAAGAAAAG
45271988 AAA
1 AAA
45271991 GAGGGAAAAT
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
26 2 0.04
27 4 0.08
28 8 0.16
29 18 0.36
30 15 0.30
31 3 0.06
ACGTcount: A:0.72, C:0.07, G:0.22, T:0.00
Consensus pattern (29 bp):
AAAACAGAAAAGAAACAGAGAAAGAAAAG
Found at i:45272923 original size:21 final size:21
Alignment explanation
Indices: 45272875--45272958 Score: 80
Period size: 21 Copynumber: 4.0 Consensus size: 21
45272865 TTTGCCGATA
*
45272875 AGGCACTTTATGTGTCGTTTCTC
1 AGGCACTTTATGTGTCG--TATC
*
45272898 AGGCACTTTATGTGTCGTAGC
1 AGGCACTTTATGTGTCGTATC
* ** *
45272919 AGGCACCTCGTGTGTCGTTTC
1 AGGCACTTTATGTGTCGTATC
*
45272940 AGGAAC-TTATGTGTCGTAT
1 AGGCACTTTATGTGTCGTAT
45272959 ACTGATCAGG
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
20 10 0.20
21 23 0.46
23 17 0.34
ACGTcount: A:0.17, C:0.20, G:0.26, T:0.37
Consensus pattern (21 bp):
AGGCACTTTATGTGTCGTATC
Found at i:45280878 original size:18 final size:18
Alignment explanation
Indices: 45280855--45280899 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
45280845 TTTCTTCATA
45280855 TATAAATTCTGGAATTTT
1 TATAAATTCTGGAATTTT
* *
45280873 TATAAATATTTTGAATTTT
1 TATAAAT-TCTGGAATTTT
*
45280892 TAAAAATT
1 TATAAATT
45280900 ATTTTGAATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
18 8 0.35
19 15 0.65
ACGTcount: A:0.40, C:0.02, G:0.07, T:0.51
Consensus pattern (18 bp):
TATAAATTCTGGAATTTT
Found at i:45280892 original size:20 final size:20
Alignment explanation
Indices: 45280866--45280912 Score: 78
Period size: 20 Copynumber: 2.4 Consensus size: 20
45280856 ATAAATTCTG
45280866 GAATTTTTATAAA-TATTTT
1 GAATTTTTATAAATTATTTT
*
45280885 GAATTTTTAAAAATTATTTT
1 GAATTTTTATAAATTATTTT
45280905 GAATTTTT
1 GAATTTTT
45280913 TTTAAACTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 12 0.46
20 14 0.54
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.57
Consensus pattern (20 bp):
GAATTTTTATAAATTATTTT
Found at i:45281413 original size:2 final size:2
Alignment explanation
Indices: 45281406--45281478 Score: 146
Period size: 2 Copynumber: 36.5 Consensus size: 2
45281396 GTTAAATCTG
45281406 TA TA TA TA 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 TA TA TA TA
45281448 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
45281479 GAAAAGGCTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 71 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45284532 original size:14 final size:14
Alignment explanation
Indices: 45284513--45284543 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
45284503 CAGACTAATT
45284513 TAAAATAAATATTA
1 TAAAATAAATATTA
45284527 TAAAATAAATATTA
1 TAAAATAAATATTA
45284541 TAA
1 TAA
45284544 GTTAGAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (14 bp):
TAAAATAAATATTA
Found at i:45287506 original size:22 final size:23
Alignment explanation
Indices: 45287463--45287506 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
45287453 TTAACTTAAA
*
45287463 TTTAATACTTAATTACTTAATTT
1 TTTAATACTTAATTACTAAATTT
*
45287486 TTTAATAC-TACTTACTAAATT
1 TTTAATACTTAATTACTAAATT
45287507 ATTGTGTTAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.36, C:0.11, G:0.00, T:0.52
Consensus pattern (23 bp):
TTTAATACTTAATTACTAAATTT
Found at i:45294202 original size:5 final size:5
Alignment explanation
Indices: 45294192--45294216 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
45294182 GAGACGAACA
45294192 GTTTT GTTTT GTTTT GTTTT GTTTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT
45294217 AAATATTGCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.00, C:0.00, G:0.20, T:0.80
Consensus pattern (5 bp):
GTTTT
Found at i:45295886 original size:39 final size:38
Alignment explanation
Indices: 45295827--45295903 Score: 118
Period size: 39 Copynumber: 2.0 Consensus size: 38
45295817 CAATTACTTA
* *
45295827 AATTTTGATTTCAAATTATTTATTTTTGAATGTTATAT
1 AATTTTGATTTCAAAATATTTATTTTTGAATATTATAT
*
45295865 AATTTATGATTTTAAAATATTTATTTTTGAATATTATAT
1 AATTT-TGATTTCAAAATATTTATTTTTGAATATTATAT
45295904 GTTTTAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
38 5 0.14
39 30 0.86
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (38 bp):
AATTTTGATTTCAAAATATTTATTTTTGAATATTATAT
Found at i:45303636 original size:112 final size:112
Alignment explanation
Indices: 45303439--45303665 Score: 454
Period size: 112 Copynumber: 2.0 Consensus size: 112
45303429 TTGTATAAAT
45303439 TTCATTAGCCAAACCAATAAACAAAATTAAAAAAAGAAAAGAAAAAAAGAGTAATCAAAGAAATG
1 TTCATTAGCCAAACCAATAAACAAAATTAAAAAAAGAAAAGAAAAAAAGAGTAATCAAAGAAATG
45303504 TGAAGTCGTATGCTATACTCTTATCCGAGAGAAATCACAAAATGCCA
66 TGAAGTCGTATGCTATACTCTTATCCGAGAGAAATCACAAAATGCCA
45303551 TTCATTAGCCAAACCAATAAACAAAATTAAAAAAAGAAAAGAAAAAAAGAGTAATCAAAGAAATG
1 TTCATTAGCCAAACCAATAAACAAAATTAAAAAAAGAAAAGAAAAAAAGAGTAATCAAAGAAATG
45303616 TGAAGTCGTATGCTATACTCTTATCCGAGAGAAATCACAAAATGCCA
66 TGAAGTCGTATGCTATACTCTTATCCGAGAGAAATCACAAAATGCCA
45303663 TTC
1 TTC
45303666 TTAAAGTTGG
Statistics
Matches: 115, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 115 1.00
ACGTcount: A:0.51, C:0.15, G:0.13, T:0.20
Consensus pattern (112 bp):
TTCATTAGCCAAACCAATAAACAAAATTAAAAAAAGAAAAGAAAAAAAGAGTAATCAAAGAAATG
TGAAGTCGTATGCTATACTCTTATCCGAGAGAAATCACAAAATGCCA
Found at i:45339999 original size:20 final size:20
Alignment explanation
Indices: 45339963--45340000 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
45339953 TATATATAGG
*
45339963 TATGTAAACAAATTATAAAC
1 TATGTAAACAAAATATAAAC
45339983 TATGTATAA-AAAATATAA
1 TATGTA-AACAAAATATAA
45340001 GGGTGCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (20 bp):
TATGTAAACAAAATATAAAC
Found at i:45340078 original size:37 final size:37
Alignment explanation
Indices: 45340032--45340102 Score: 115
Period size: 37 Copynumber: 1.9 Consensus size: 37
45340022 AAATATGTAC
*
45340032 GTATCTATGTATATATATATGTATAAATTACAAAAAT
1 GTATCTATGTATATATATATATATAAATTACAAAAAT
* *
45340069 GTATGTATGTATATATGTATATATAAATTACAAA
1 GTATCTATGTATATATATATATATAAATTACAAA
45340103 GTATAAAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 31 1.00
ACGTcount: A:0.45, C:0.04, G:0.10, T:0.41
Consensus pattern (37 bp):
GTATCTATGTATATATATATATATAAATTACAAAAAT
Found at i:45340211 original size:3 final size:3
Alignment explanation
Indices: 45340192--45340261 Score: 122
Period size: 3 Copynumber: 23.3 Consensus size: 3
45340182 TAAATGAGTA
* *
45340192 AAT AAT AAA AAT GAT 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 AAT AAT
45340240 AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
45340262 CAAGATTAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 63 1.00
ACGTcount: A:0.67, C:0.00, G:0.01, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:45340321 original size:23 final size:22
Alignment explanation
Indices: 45340295--45340348 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 22
45340285 TAGATAAATG
*
45340295 AATAAAATAACAATAATAACGAT
1 AATAAAATAAAAATAATAAC-AT
* * *
45340318 AATAATACAAAAATAATAGCAT
1 AATAAAATAAAAATAATAACAT
*
45340340 AATATAATA
1 AATAAAATA
45340349 TGAGGAATAA
Statistics
Matches: 24, Mismatches: 7, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
22 8 0.33
23 16 0.67
ACGTcount: A:0.65, C:0.07, G:0.04, T:0.24
Consensus pattern (22 bp):
AATAAAATAAAAATAATAACAT
Found at i:45341241 original size:2 final size:2
Alignment explanation
Indices: 45341234--45341267 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
45341224 NNNNNNNNNC
45341234 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
45341268 AAGAAAAACA
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:45342187 original size:17 final size:17
Alignment explanation
Indices: 45342165--45342200 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
45342155 ATGAGATTTC
45342165 TCAATTACAAAAGGACT
1 TCAATTACAAAAGGACT
45342182 TCAATTACAAAAGGACT
1 TCAATTACAAAAGGACT
45342199 TC
1 TC
45342201 GAAGGTTTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (17 bp):
TCAATTACAAAAGGACT
Found at i:45343634 original size:25 final size:25
Alignment explanation
Indices: 45343585--45343634 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
45343575 CACAAATTGC
**
45343585 AAGTCTGCTTCTAATAGCATGTTTT
1 AAGTCTGCTTCTAATAGCACATTTT
*
45343610 AAGTCTGCTTCTGATAGCACATTTT
1 AAGTCTGCTTCTAATAGCACATTTT
45343635 TGAATCAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.24, C:0.18, G:0.16, T:0.42
Consensus pattern (25 bp):
AAGTCTGCTTCTAATAGCACATTTT
Found at i:45346090 original size:25 final size:26
Alignment explanation
Indices: 45346062--45346110 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
45346052 ATTTAATATA
45346062 AAAATTATAATA-TATAAAG-AAAAGG
1 AAAA-TATAATATTATAAAGTAAAAGG
*
45346087 AAAATATCATATTATAAAGTAAAA
1 AAAATATAATATTATAAAGTAAAA
45346111 AATAAGTTGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 6 0.29
25 11 0.52
26 4 0.19
ACGTcount: A:0.63, C:0.02, G:0.08, T:0.27
Consensus pattern (26 bp):
AAAATATAATATTATAAAGTAAAAGG
Found at i:45346461 original size:30 final size:30
Alignment explanation
Indices: 45346425--45346484 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
45346415 TTGTTGCCTA
*
45346425 AGTTTCTTCCATATTCATCTATGGAACATG
1 AGTTTCTTCCATATTCATCTATGAAACATG
*
45346455 AGTTTCTTCCATATTCATGTATGAAACATG
1 AGTTTCTTCCATATTCATCTATGAAACATG
45346485 TTCCTTGTCG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.28, C:0.18, G:0.13, T:0.40
Consensus pattern (30 bp):
AGTTTCTTCCATATTCATCTATGAAACATG
Found at i:45351840 original size:11 final size:11
Alignment explanation
Indices: 45351820--45351885 Score: 72
Period size: 11 Copynumber: 6.4 Consensus size: 11
45351810 TAAAAACTAA
45351820 AAAAAGTATTTT
1 AAAAA-TATTTT
45351832 AAAAATATTTT
1 AAAAATATTTT
45351843 --AAA-A--TT
1 AAAAATATTTT
45351849 AAAAAT-TTTT
1 AAAAATATTTT
45351859 AAAAAGTATTTT
1 AAAAA-TATTTT
45351871 AAAAATATTTT
1 AAAAATATTTT
45351882 AAAA
1 AAAA
45351886 TTAAAAAATT
Statistics
Matches: 47, Mismatches: 0, Indels: 15
0.76 0.00 0.24
Matches are distributed among these distances:
6 2 0.04
8 4 0.09
9 3 0.06
10 7 0.15
11 17 0.36
12 14 0.30
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:45351858 original size:16 final size:17
Alignment explanation
Indices: 45351830--45351912 Score: 73
Period size: 17 Copynumber: 4.7 Consensus size: 17
45351820 AAAAAGTATT
45351830 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
45351847 TTAAAAAT-TTTTAAAAAGTA
1 TTAAAAATATTTT--AAA--A
45351867 TTTTAAAAATATTTTAAAA
1 --TTAAAAATATTTTAAAA
45351886 TTAAAAA-A-TTTAAAA
1 TTAAAAATATTTTAAAA
* *
45351901 ATAAATATATTT
1 TTAAAAATATTT
45351913 ATTATATCGG
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
15 12 0.22
16 6 0.11
17 17 0.31
18 3 0.05
19 1 0.02
20 1 0.02
21 3 0.05
22 8 0.15
23 4 0.07
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:45351865 original size:39 final size:38
Alignment explanation
Indices: 45351820--45351901 Score: 146
Period size: 39 Copynumber: 2.1 Consensus size: 38
45351810 TAAAAACTAA
*
45351820 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAATTTTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAA-ATTT
45351859 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTT
1 AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTT
45351897 AAAAA
1 AAAAA
45351902 TAAATATATT
Statistics
Matches: 42, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
38 8 0.19
39 34 0.81
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (38 bp):
AAAAAGTATTTTAAAAATATTTTAAAATTAAAAAATTT
Found at i:45351913 original size:16 final size:16
Alignment explanation
Indices: 45351873--45351913 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
45351863 AGTATTTTAA
*
45351873 AAATAT-TTTAAAATT
1 AAATATATTTAAAAAT
*
45351888 AAA-AAATTTAAAAAT
1 AAATATATTTAAAAAT
45351903 AAATATATTTA
1 AAATATATTTA
45351914 TTATATCGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
14 1 0.05
15 14 0.67
16 6 0.29
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (16 bp):
AAATATATTTAAAAAT
Found at i:45358474 original size:13 final size:13
Alignment explanation
Indices: 45358456--45358480 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
45358446 GCAGATACAA
45358456 ATATACAGAACAG
1 ATATACAGAACAG
45358469 ATATACAGAACA
1 ATATACAGAACA
45358481 TACCCCCATC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (13 bp):
ATATACAGAACAG
Found at i:45362212 original size:23 final size:23
Alignment explanation
Indices: 45362186--45362261 Score: 68
Period size: 23 Copynumber: 3.3 Consensus size: 23
45362176 GACATTAGAA
45362186 TAAAATTTTATTTATATTATAAT
1 TAAAATTTTATTTATATTATAAT
* *
45362209 TAAAATTTGAATATTAAATTAT-AT
1 TAAAATTT-TAT-TTATATTATAAT
*
45362233 T-AAATTATAGTTT-TATTATAAT
1 TAAAATTTTA-TTTATATTATAAT
*
45362255 TTAAATT
1 TAAAATT
45362262 ATTGAATTTT
Statistics
Matches: 43, Mismatches: 5, Indels: 10
0.74 0.09 0.17
Matches are distributed among these distances:
21 5 0.12
22 6 0.14
23 19 0.44
24 5 0.12
25 8 0.19
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (23 bp):
TAAAATTTTATTTATATTATAAT
Found at i:45364951 original size:2 final size:2
Alignment explanation
Indices: 45364944--45364996 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
45364934 NNNNNNNNNT
45364944 TA TA TA TA 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 TA TA TA TA
45364986 TA TA TA TA TA T
1 TA TA TA TA TA T
45364997 TAATGTGTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:45373815 original size:23 final size:22
Alignment explanation
Indices: 45373789--45373833 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
45373779 GCCCACTACC
*
45373789 CAAACTTAACCCTAAACCCAAAA
1 CAAACATAACCCT-AACCCAAAA
*
45373812 CAAACATAACCCTAGCCCAAAA
1 CAAACATAACCCTAACCCAAAA
45373834 TTAACCCCAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 8 0.40
23 12 0.60
ACGTcount: A:0.51, C:0.36, G:0.02, T:0.11
Consensus pattern (22 bp):
CAAACATAACCCTAACCCAAAA
Found at i:45378403 original size:18 final size:17
Alignment explanation
Indices: 45378360--45378394 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
45378350 ATGTGATTTA
45378360 TAAAATTTTAAATATAT
1 TAAAATTTTAAATATAT
45378377 TAAAATTTTAAATATAT
1 TAAAATTTTAAATATAT
45378394 T
1 T
45378395 TTTAATTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (17 bp):
TAAAATTTTAAATATAT
Found at i:45379069 original size:17 final size:19
Alignment explanation
Indices: 45379043--45379083 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
45379033 TTTTAGAATT
* *
45379043 TTTTTGAAAATTTTAT-AA
1 TTTTTGAAAAATATATAAA
45379061 TTTTT-AAAAATATATAAA
1 TTTTTGAAAAATATATAAA
45379079 TTTTT
1 TTTTT
45379084 TTGAATTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTTTGAAAAATATATAAA
Found at i:45379118 original size:19 final size:21
Alignment explanation
Indices: 45379073--45379132 Score: 65
Period size: 19 Copynumber: 3.0 Consensus size: 21
45379063 TTTAAAAATA
**
45379073 TATAAATTTTTTTGAA-TTTT
1 TATAAATCATTTTGAATTTTT
45379093 TATAAAT-ATTTTGAATTTTT
1 TATAAATCATTTTGAATTTTT
*
45379113 TA-AAATCAATTT-AATTTTT
1 TATAAATCATTTTGAATTTTT
45379132 T
1 T
45379133 TTTGTAATTT
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
19 19 0.53
20 17 0.47
ACGTcount: A:0.35, C:0.02, G:0.03, T:0.60
Consensus pattern (21 bp):
TATAAATCATTTTGAATTTTT
Done.