Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 10 of 31
Found at i:5167579 original size:33 final size:34
Alignment explanation
Indices: 5167542--5167632 Score: 112
Period size: 34 Copynumber: 2.7 Consensus size: 34
5167532 GTTTAATATC
*
5167542 ATATATTTTATTTTAATTT-TTTATTATAATCTT
1 ATATATTTTATTTTAATTTCTTTAATATAATCTT
* * *
5167575 ATATATTTTATTTTTATTTCTTTAATATATTTTT
1 ATATATTTTATTTTAATTTCTTTAATATAATCTT
* *
5167609 GTATATTTTATTATAATCTTCTTT
1 ATATATTTTATTTTAAT-TTCTTT
5167633 TCCCTTCTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
33 18 0.37
34 25 0.51
35 6 0.12
ACGTcount: A:0.27, C:0.04, G:0.01, T:0.67
Consensus pattern (34 bp):
ATATATTTTATTTTAATTTCTTTAATATAATCTT
Found at i:5180269 original size:17 final size:18
Alignment explanation
Indices: 5180244--5180281 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5180234 TTTTAATTAT
*
5180244 TTAAATAATC-AACTGAA
1 TTAAATAATCTAACTCAA
*
5180261 TTAATTAATCTAACTCAA
1 TTAAATAATCTAACTCAA
5180279 TTA
1 TTA
5180282 TTGGTTAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.47, C:0.13, G:0.03, T:0.37
Consensus pattern (18 bp):
TTAAATAATCTAACTCAA
Found at i:5185238 original size:29 final size:30
Alignment explanation
Indices: 5185173--5185249 Score: 90
Period size: 30 Copynumber: 2.6 Consensus size: 30
5185163 TAAAAATTTT
*
5185173 AATTTTTTATATTTTTATTATATTTAATCA
1 AATTTTTTATATTTTTATTATATGTAATCA
5185203 AA-TTTTTATATTTTTATT-T-TGT-ATCA
1 AATTTTTTATATTTTTATTATATGTAATCA
5185229 AATAACTTTTTATATTTTTAT
1 AAT---TTTTTATATTTTTAT
5185250 GTTGAGTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
26 6 0.14
27 2 0.05
28 1 0.02
29 16 0.38
30 17 0.40
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (30 bp):
AATTTTTTATATTTTTATTATATGTAATCA
Found at i:5185262 original size:30 final size:28
Alignment explanation
Indices: 5185176--5185263 Score: 88
Period size: 30 Copynumber: 3.0 Consensus size: 28
5185166 AAATTTTAAT
*
5185176 TTTTTATATTTTTATTAT-ATTTAATCAAA
1 TTTTTATATTTTTATT-TGATTAAAT-AAA
* *
5185205 TTTTTATATTTTTATTTTGTATCAAATAAC
1 TTTTTATATTTTTA-TTTG-ATTAAATAAA
5185235 TTTTTATATTTTTATGTTGAGTTAAATAA
1 TTTTTATATTTTTAT-TTGA-TTAAATAA
5185264 GTTCTTATTA
Statistics
Matches: 50, Mismatches: 4, Indels: 9
0.79 0.06 0.14
Matches are distributed among these distances:
29 17 0.34
30 28 0.56
31 5 0.10
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.60
Consensus pattern (28 bp):
TTTTTATATTTTTATTTGATTAAATAAA
Found at i:5202523 original size:29 final size:28
Alignment explanation
Indices: 5202459--5202523 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
5202449 TAAAAAAATT
* *
5202459 AAATAAATCTTTATTTTTATATTTGTTC
1 AAATAAATATTTATTTTTATATTTGATC
**
5202487 AACCAAATATTATATTTTTAT-TTTGAATC
1 AAATAAATATT-TATTTTTATATTTG-ATC
5202516 AAATAAAT
1 AAATAAAT
5202524 TCTTATGATT
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
28 12 0.41
29 17 0.59
ACGTcount: A:0.40, C:0.08, G:0.03, T:0.49
Consensus pattern (28 bp):
AAATAAATATTTATTTTTATATTTGATC
Found at i:5202763 original size:30 final size:30
Alignment explanation
Indices: 5202727--5202797 Score: 106
Period size: 30 Copynumber: 2.4 Consensus size: 30
5202717 AATCATTAAT
* * *
5202727 TATAAAGATTTATTTGGTTCGAAATAAAAG
1 TATAAAGATTTATTTGATTCAAAATAAAAA
5202757 TATAAAGATTTATTTGATTCAAAATAAAAA
1 TATAAAGATTTATTTGATTCAAAATAAAAA
*
5202787 TATAAAAATTT
1 TATAAAGATTT
5202798 GATTATATTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (30 bp):
TATAAAGATTTATTTGATTCAAAATAAAAA
Found at i:5207086 original size:40 final size:40
Alignment explanation
Indices: 5207018--5207093 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
5207008 AAAGGAAAAA
5207018 AAATAAAATAAATCATATAATATAAAAAAT-TATTTTAAG
1 AAATAAAATAAATCATATAATATAAAAAATATATTTTAAG
* *
5207057 AAATGAAAATAAAAT-ATATGATATTAAAAATATATTT
1 AAAT-AAAAT-AAATCATATAATATAAAAAATATATTT
5207094 AGAAGATAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
39 4 0.12
40 19 0.59
41 9 0.28
ACGTcount: A:0.61, C:0.01, G:0.04, T:0.34
Consensus pattern (40 bp):
AAATAAAATAAATCATATAATATAAAAAATATATTTTAAG
Found at i:5207132 original size:16 final size:17
Alignment explanation
Indices: 5207111--5207144 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
5207101 AATATTATAT
*
5207111 AAAAATTAATA-ATTAA
1 AAAAATAAATATATTAA
5207127 AAAAATAAATATATTAA
1 AAAAATAAATATATTAA
5207144 A
1 A
5207145 TTTACATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (17 bp):
AAAAATAAATATATTAA
Found at i:5207267 original size:23 final size:21
Alignment explanation
Indices: 5207225--5207267 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
5207215 AATACTGTAA
*
5207225 TATTATTTTTTATATTTTAAT
1 TATTATTTTTTATATATTAAT
5207246 TATTATTTTATTTATATATTAA
1 TATTA-TTT-TTTATATATTAA
5207268 ACATTCTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 3 0.16
23 11 0.58
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (21 bp):
TATTATTTTTTATATATTAAT
Found at i:5207462 original size:6 final size:6
Alignment explanation
Indices: 5207438--5207478 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
5207428 ACAAGCGCAA
* *
5207438 AAAAAT AAAACAG AGAAAG AAAAAG AAAAAG AAAAAG AAAA
1 AAAAAG AAAA-AG AAAAAG AAAAAG AAAAAG AAAAAG AAAA
5207479 TATTACTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
6 27 0.87
7 4 0.13
ACGTcount: A:0.80, C:0.02, G:0.15, T:0.02
Consensus pattern (6 bp):
AAAAAG
Found at i:5210610 original size:22 final size:22
Alignment explanation
Indices: 5210584--5210626 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
5210574 GATATAAATA
5210584 TGTCATCATTAATATTTATCTC
1 TGTCATCATTAATATTTATCTC
* * *
5210606 TGTCATCGTTTATGTTTATCT
1 TGTCATCATTAATATTTATCT
5210627 TTTATTCTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.53
Consensus pattern (22 bp):
TGTCATCATTAATATTTATCTC
Found at i:5228532 original size:24 final size:25
Alignment explanation
Indices: 5228499--5228550 Score: 97
Period size: 24 Copynumber: 2.1 Consensus size: 25
5228489 TGTGCAGTAT
5228499 TTAGACATGTTCACCTATCAATGAA
1 TTAGACATGTTCACCTATCAATGAA
5228524 TTAG-CATGTTCACCTATCAATGAA
1 TTAGACATGTTCACCTATCAATGAA
5228548 TTA
1 TTA
5228551 AATTTGCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
24 23 0.85
25 4 0.15
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (25 bp):
TTAGACATGTTCACCTATCAATGAA
Found at i:5232398 original size:2 final size:2
Alignment explanation
Indices: 5232391--5232424 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
5232381 TAACAATGTC
5232391 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
5232425 ATTTATTAAC
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:5245069 original size:24 final size:23
Alignment explanation
Indices: 5245023--5245078 Score: 58
Period size: 24 Copynumber: 2.4 Consensus size: 23
5245013 GGAGTTATTT
* ***
5245023 AAATAAATAATTATGTTTGTTGAA
1 AAATAGATAATTATGTACATTG-A
5245047 AAATAGATAATTATGTACATTGA
1 AAATAGATAATTATGTACATTGA
*
5245070 ACATAGATA
1 AAATAGATA
5245079 GTTGTGCTTA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
23 9 0.33
24 18 0.67
ACGTcount: A:0.48, C:0.04, G:0.12, T:0.36
Consensus pattern (23 bp):
AAATAGATAATTATGTACATTGA
Found at i:5246962 original size:22 final size:22
Alignment explanation
Indices: 5246928--5246971 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
5246918 GTCTTATTCG
* *
5246928 ATTCGATTAAAAAAAATCTTAA
1 ATTCAATTAAAAAAAACCTTAA
*
5246950 ATTCAATTTAAAAAAACCTTAA
1 ATTCAATTAAAAAAAACCTTAA
5246972 CTGATTTGAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.55, C:0.11, G:0.02, T:0.32
Consensus pattern (22 bp):
ATTCAATTAAAAAAAACCTTAA
Found at i:5247141 original size:21 final size:21
Alignment explanation
Indices: 5247117--5247196 Score: 72
Period size: 21 Copynumber: 3.9 Consensus size: 21
5247107 TCTTGTTCAT
* **
5247117 CAAATCTTAAAATTGATTTAA
1 CAAATCCTAAAATCAATTTAA
*
5247138 CAAACCCTAAAATCAATTTAA
1 CAAATCCTAAAATCAATTTAA
* *
5247159 CAAATCCT-AACTCAATTCAA
1 CAAATCCTAAAATCAATTTAA
* * *
5247179 AAAACCCTTAAATCAATT
1 CAAATCCTAAAATCAATT
5247197 CGATTGGATT
Statistics
Matches: 48, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
20 16 0.33
21 32 0.67
ACGTcount: A:0.49, C:0.21, G:0.01, T:0.29
Consensus pattern (21 bp):
CAAATCCTAAAATCAATTTAA
Found at i:5247175 original size:20 final size:21
Alignment explanation
Indices: 5247132--5247196 Score: 78
Period size: 21 Copynumber: 3.1 Consensus size: 21
5247122 CTTAAAATTG
5247132 ATTTAACAAACCCTAAAATCA
1 ATTTAACAAACCCTAAAATCA
* *
5247153 ATTTAACAAATCCT-AACTCA
1 ATTTAACAAACCCTAAAATCA
* * *
5247173 ATTCAAAAAACCCTTAAATCA
1 ATTTAACAAACCCTAAAATCA
5247194 ATT
1 ATT
5247197 CGATTGGATT
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 16 0.43
21 21 0.57
ACGTcount: A:0.49, C:0.23, G:0.00, T:0.28
Consensus pattern (21 bp):
ATTTAACAAACCCTAAAATCA
Found at i:5247197 original size:21 final size:21
Alignment explanation
Indices: 5247139--5247197 Score: 66
Period size: 20 Copynumber: 2.9 Consensus size: 21
5247129 TTGATTTAAC
* * *
5247139 AAACCCTAAAATCAATTTAAC
1 AAACCCTTAAATCAATTCAAA
* *
5247160 AAATCC-TAACTCAATTCAAA
1 AAACCCTTAAATCAATTCAAA
5247180 AAACCCTTAAATCAATTC
1 AAACCCTTAAATCAATTC
5247198 GATTGGATTT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 15 0.50
21 15 0.50
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
AAACCCTTAAATCAATTCAAA
Found at i:5261771 original size:33 final size:33
Alignment explanation
Indices: 5261711--5261783 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
5261701 CGTTAATGAT
* * *
5261711 ATACTAACATATTATAATAAATGATAATGTAAC
1 ATACTAACATATTATAATAAATAATAATATAAA
* *
5261744 ATACTGACATATTATAAGT-GATAATAATATAAA
1 ATACTAACATATTATAA-TAAATAATAATATAAA
5261777 ATACTAA
1 ATACTAA
5261784 TTTGATATGA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.52, C:0.08, G:0.07, T:0.33
Consensus pattern (33 bp):
ATACTAACATATTATAATAAATAATAATATAAA
Found at i:5262752 original size:20 final size:18
Alignment explanation
Indices: 5262719--5262775 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 18
5262709 TGTTGAATGA
5262719 AAAATATTTTTTAAAAAT
1 AAAATATTTTTTAAAAAT
5262737 AAAATATTTATTTTAAAAATT
1 AAAATA-TT-TTTTAAAAA-T
5262758 AATAAATATTTTTGTAAA
1 -A-AAATATTTTT-TAAA
5262776 TTAATCAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
18 6 0.18
19 2 0.06
20 9 0.27
21 4 0.12
22 7 0.21
23 5 0.15
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (18 bp):
AAAATATTTTTTAAAAAT
Found at i:5278960 original size:120 final size:120
Alignment explanation
Indices: 5278747--5278987 Score: 455
Period size: 120 Copynumber: 2.0 Consensus size: 120
5278737 GCGATAAAGG
*
5278747 GATATAGAAGTTTCCTGGTAGGATTTCAAGGAGATTGCCACTATATTTGATCACTATATATTAAT
1 GATATAGAAGTTTCCTGGTAGGATTGCAAGGAGATTGCCACTATATTTGATCACTATATATTAAT
*
5278812 AGTAACGTTCAAAATGAGATTGTTTACTTTTGAAGAAGTGATAGTTGTGATTGGA
66 AGCAACGTTCAAAATGAGATTGTTTACTTTTGAAGAAGTGATAGTTGTGATTGGA
5278867 GATATAGAAGTTTCCTGGTAGGATTGCAAGGAGATTGCCACTATATTTGATCACTATATATTAAT
1 GATATAGAAGTTTCCTGGTAGGATTGCAAGGAGATTGCCACTATATTTGATCACTATATATTAAT
*
5278932 AGCAATGTTCAAAATGAGATTGTTTACTTTTGAAGAAGTGATAGTTGTGATTGGA
66 AGCAACGTTCAAAATGAGATTGTTTACTTTTGAAGAAGTGATAGTTGTGATTGGA
5278987 G
1 G
5278988 GTTGGCTTCT
Statistics
Matches: 118, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
120 118 1.00
ACGTcount: A:0.32, C:0.09, G:0.22, T:0.36
Consensus pattern (120 bp):
GATATAGAAGTTTCCTGGTAGGATTGCAAGGAGATTGCCACTATATTTGATCACTATATATTAAT
AGCAACGTTCAAAATGAGATTGTTTACTTTTGAAGAAGTGATAGTTGTGATTGGA
Found at i:5292771 original size:3 final size:3
Alignment explanation
Indices: 5292763--5292806 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
5292753 ATATTTTGTG
5292763 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
5292807 AATATATTTC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:5296283 original size:14 final size:14
Alignment explanation
Indices: 5296264--5296297 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 14
5296254 GTAGATAAAT
5296264 AATGAAAAGACA-AA
1 AATGAAAAGA-ATAA
5296278 AATGAAAAGAATAA
1 AATGAAAAGAATAA
5296292 AATGAA
1 AATGAA
5296298 TATAGAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 1 0.05
14 18 0.95
ACGTcount: A:0.71, C:0.03, G:0.15, T:0.12
Consensus pattern (14 bp):
AATGAAAAGAATAA
Found at i:5301836 original size:36 final size:36
Alignment explanation
Indices: 5301790--5301860 Score: 97
Period size: 36 Copynumber: 2.0 Consensus size: 36
5301780 ACACGTTTAA
*
5301790 TTAATCGTGTTATCGTATTTAAACGTATAAATGTGT
1 TTAATCGTGTTATCATATTTAAACGTATAAATGTGT
* * * *
5301826 TTAATTGTGTTATCATGTTTAAACGTGTATATGTG
1 TTAATCGTGTTATCATATTTAAACGTATAAATGTG
5301861 ACACATTTAT
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.28, C:0.07, G:0.18, T:0.46
Consensus pattern (36 bp):
TTAATCGTGTTATCATATTTAAACGTATAAATGTGT
Found at i:5302071 original size:34 final size:35
Alignment explanation
Indices: 5302005--5302084 Score: 101
Period size: 34 Copynumber: 2.3 Consensus size: 35
5301995 TAAGTTTAAA
* *
5302005 ATTTTATTTTGTTATATTTGATGTTATTATTATT-
1 ATTTTATTTTGTTATAATTGATGTTATAATTATTG
*
5302039 ATTTTATTTTGTTATAATT-ATTTTTATAATTATTG
1 ATTTTATTTTGTTATAATTGA-TGTTATAATTATTG
5302074 ATTTTAATTTT
1 ATTTT-ATTTT
5302085 TTTTTCAGAG
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
33 1 0.03
34 29 0.73
35 5 0.12
36 5 0.12
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (35 bp):
ATTTTATTTTGTTATAATTGATGTTATAATTATTG
Found at i:5302849 original size:243 final size:239
Alignment explanation
Indices: 5302398--5302860 Score: 631
Period size: 239 Copynumber: 1.9 Consensus size: 239
5302388 TATATACATA
* * * * * * ** *
5302398 TTTTAGATTTAACATACGAATATTATTCATATCATGTTCATGTTTAATCTGAATGCTTTTTGTGT
1 TTTTAAATTTAACATACAAATATTATTCATATCATATTCATATTTAATCTAAACGCTTTTCATAT
* * * * * *
5302463 CGAATCATGTTTGACATATTTAAGATATGAAAATACGAATGGTTAGGTCTAATTTTAATAATCGT
66 CGAATCATGTTTGACATATTTAAGACATGAAAACACGAATGATCAAGTCTAATTCTAATAATCGT
* *
5302528 ATAGTTATATATATATATATAAGGTGATTATTATGCTTTCTAAGAGGGTTTGATATGAAGAAAAG
131 ATAGTTATATATATATATATAAGGGGATTATTATGCTTTCTAAGAGGATTTGATATGAAGAAAAG
**
5302593 TGACACAAAATCCAGTAACACAAAAGGGTACATATATATATGTG
196 CAACACAAAATCCAGTAACACAAAAGGGTACATATATATATGTG
* * *
5302637 TTTTAAATTTAACATACAAATATTATTCATGTCGTATTTATATTTAATCTAAACG-TGTTTCATA
1 TTTTAAATTTAACATACAAATATTATTCATATCATATTCATATTTAATCTAAACGCT-TTTCATA
* * *
5302701 TCTAATCGTGTTTGACATATTTAAGACATGAAAACACGAATGATCAAGTCTAATTCTAATAATTG
65 TCGAATCATGTTTGACATATTTAAGACATGAAAACACGAATGATCAAGTCTAATTCTAATAATCG
5302766 TATAGTTTTATATATATATATATATAAGGGGATTATTATGCTTTCTAAGAGGATTTGATATGAAG
130 TATAG---T-TATATATATATATATAAGGGGATTATTATGCTTTCTAAGAGGATTTGATATGAAG
* *
5302831 AAAAGCAACACTAAATCCAGTTACACAAAA
191 AAAAGCAACACAAAATCCAGTAACACAAAA
5302861 AAGTACATGC
Statistics
Matches: 192, Mismatches: 27, Indels: 6
0.85 0.12 0.03
Matches are distributed among these distances:
238 1 0.01
239 111 0.58
242 1 0.01
243 79 0.41
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (239 bp):
TTTTAAATTTAACATACAAATATTATTCATATCATATTCATATTTAATCTAAACGCTTTTCATAT
CGAATCATGTTTGACATATTTAAGACATGAAAACACGAATGATCAAGTCTAATTCTAATAATCGT
ATAGTTATATATATATATATAAGGGGATTATTATGCTTTCTAAGAGGATTTGATATGAAGAAAAG
CAACACAAAATCCAGTAACACAAAAGGGTACATATATATATGTG
Found at i:5303939 original size:22 final size:23
Alignment explanation
Indices: 5303904--5303947 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
5303894 GATGATATTA
5303904 TTTTTTAATGAAAAAATTAAATAT
1 TTTTTTAA-GAAAAAATTAAATAT
*
5303928 TTTTTTAA-AAAAGATTAAAT
1 TTTTTTAAGAAAAAATTAAAT
5303948 TGATATAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 11 0.58
24 8 0.42
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (23 bp):
TTTTTTAAGAAAAAATTAAATAT
Found at i:5303970 original size:29 final size:29
Alignment explanation
Indices: 5303929--5304010 Score: 73
Period size: 31 Copynumber: 2.8 Consensus size: 29
5303919 ATTAAATATT
5303929 TTTTTAAAA-AAGATTAAATTGA-TATAA
1 TTTTTAAAATAAGATTAAATTGATTATAA
*
5303956 TTTTTAAAATTAAGATATTAAATT-ATTTTAA
1 TTTTTAAAA-TAAG--ATTAAATTGATTATAA
*
5303987 -TTTTAAATATAAAAATTAAATTGA
1 TTTTTAAA-AT-AAGATTAAATTGA
5304011 ACAAAATTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
27 9 0.20
29 11 0.24
30 10 0.22
31 15 0.33
ACGTcount: A:0.50, C:0.00, G:0.05, T:0.45
Consensus pattern (29 bp):
TTTTTAAAATAAGATTAAATTGATTATAA
Found at i:5305746 original size:108 final size:108
Alignment explanation
Indices: 5305605--5305814 Score: 321
Period size: 108 Copynumber: 1.9 Consensus size: 108
5305595 TAAAATGACT
* * * *
5305605 AAATATATTAATTTGGCTACAACTTTCACAATTTATAAAGACACATTTTTTTGAAATTATTCAAC
1 AAATATATTAATTTAGCTACAACTTTCACAATTTACAAAGACACATTCTTTTAAAATTATTCAAC
* *
5305670 TCTTATCCAATTTACCTTTTATTTAAATTTTCTCAAATTAGTA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGTA
* * * * *
5305713 AAATATATTGATTTAGTTATAACTTTCATAATTTACAAATACACATTCTTTTAAAATTATTCAAC
1 AAATATATTAATTTAGCTACAACTTTCACAATTTACAAAGACACATTCTTTTAAAATTATTCAAC
5305778 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
66 TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAA
5305815 ATTTATTATA
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
108 91 1.00
ACGTcount: A:0.37, C:0.15, G:0.03, T:0.44
Consensus pattern (108 bp):
AAATATATTAATTTAGCTACAACTTTCACAATTTACAAAGACACATTCTTTTAAAATTATTCAAC
TCTTACCCAATTTACCTTTTATTTAAATTTACTCAAATTAGTA
Found at i:5306049 original size:19 final size:19
Alignment explanation
Indices: 5305997--5306050 Score: 56
Period size: 18 Copynumber: 2.8 Consensus size: 19
5305987 AATTTCAACT
*
5305997 TAAAAAATATAACTTAAAATA
1 TAAAAAATA-AA-TAAAAATA
* *
5306018 TTAAATA-AAATAAAAATA
1 TAAAAAATAAATAAAAATA
5306036 TAAAAAATAAATAAA
1 TAAAAAATAAATAAA
5306051 TAATTGAAAT
Statistics
Matches: 27, Mismatches: 5, Indels: 4
0.75 0.14 0.11
Matches are distributed among these distances:
18 12 0.44
19 9 0.33
20 1 0.04
21 5 0.19
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAATAAATAAAAATA
Found at i:5306889 original size:31 final size:29
Alignment explanation
Indices: 5306851--5306919 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
5306841 AAGAGGAGGA
* *
5306851 ATTAAATTGA-TATAATTTTCTAATTCAAATG
1 ATTAAATT-ATTATAATTTT-GAATACAAA-G
*
5306882 ATTAAATTATTTTAATTTTGAATACAAAG
1 ATTAAATTATTATAATTTTGAATACAAAG
5306911 ATTAAATTA
1 ATTAAATTA
5306920 AATAAAATTA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
29 10 0.29
30 8 0.24
31 16 0.47
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.45
Consensus pattern (29 bp):
ATTAAATTATTATAATTTTGAATACAAAG
Found at i:5317526 original size:22 final size:22
Alignment explanation
Indices: 5317500--5317548 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 22
5317490 AATGAACCAA
5317500 TAAATA-AAT-TAACAAGTAAATT
1 TAAATATAATATAA-AAGTAAA-T
*
5317522 TAAATATAATATAAAATTAAAT
1 TAAATATAATATAAAAGTAAAT
5317544 TAAAT
1 TAAAT
5317549 TCACATACGA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 12 0.50
23 9 0.38
24 3 0.12
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (22 bp):
TAAATATAATATAAAAGTAAAT
Found at i:5325759 original size:11 final size:11
Alignment explanation
Indices: 5325725--5325775 Score: 50
Period size: 11 Copynumber: 4.6 Consensus size: 11
5325715 ATTATGATTA
* *
5325725 TTTATTTTTAC
1 TTTATTTCTAT
5325736 TTTATTT-TAT
1 TTTATTTCTAT
*
5325746 TTTATTTCTTT
1 TTTATTTCTAT
*
5325757 TTTATTTCAAT
1 TTTATTTCTAT
5325768 ATTTATTT
1 -TTTATTT
5325776 TTAAAATATA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
10 9 0.26
11 18 0.53
12 7 0.21
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.75
Consensus pattern (11 bp):
TTTATTTCTAT
Found at i:5325822 original size:21 final size:20
Alignment explanation
Indices: 5325784--5325822 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5325774 TTTTAAAATA
* *
5325784 TAAAAAATTTATAGTTTACT
1 TAAAAAATTAATAATTTACT
5325804 TAAAAATATTAATAATTTA
1 TAAAAA-ATTAATAATTTA
5325823 TAAATAAAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.44
Consensus pattern (20 bp):
TAAAAAATTAATAATTTACT
Found at i:5325876 original size:13 final size:13
Alignment explanation
Indices: 5325844--5325876 Score: 50
Period size: 13 Copynumber: 2.5 Consensus size: 13
5325834 TTAATATGGT
5325844 TATTTTATTTTTA
1 TATTTTATTTTTA
5325857 T-TCTTTATTTTTA
1 TAT-TTTATTTTTA
5325870 TATTTTA
1 TATTTTA
5325877 AATATTAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.06
13 16 0.89
14 1 0.06
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (13 bp):
TATTTTATTTTTA
Found at i:5329727 original size:2 final size:2
Alignment explanation
Indices: 5329720--5329744 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5329710 GAGAGTATTT
5329720 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5329745 TCATAGTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5335744 original size:34 final size:34
Alignment explanation
Indices: 5335692--5335779 Score: 95
Period size: 34 Copynumber: 2.6 Consensus size: 34
5335682 AGCATCTTCT
* * * *
5335692 ACTTTGGCTTTGACGTGTAATATTTGGTGATGAA
1 ACTTTGACCTTGACGTGTAATATCTGGTGATAAA
* * *
5335726 GCTTTGACCTTGATGTGTAATATCTGGTGCTAAA
1 ACTTTGACCTTGACGTGTAATATCTGGTGATAAA
* *
5335760 ACTTTGACCTGGGCGTGTAA
1 ACTTTGACCTTGACGTGTAA
5335780 CATTTACTAC
Statistics
Matches: 43, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.23, C:0.14, G:0.26, T:0.38
Consensus pattern (34 bp):
ACTTTGACCTTGACGTGTAATATCTGGTGATAAA
Found at i:5335970 original size:19 final size:19
Alignment explanation
Indices: 5335938--5335974 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5335928 AATTAAAACA
*
5335938 TGTAACAATTTTTTTTAAT
1 TGTAACAATATTTTTTAAT
*
5335957 TGTAATAATATTTTTTAA
1 TGTAACAATATTTTTTAA
5335975 AATGTAACAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.35, C:0.03, G:0.05, T:0.57
Consensus pattern (19 bp):
TGTAACAATATTTTTTAAT
Found at i:5335980 original size:20 final size:19
Alignment explanation
Indices: 5335937--5335983 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
5335927 GAATTAAAAC
*
5335937 ATGTAACAATTTTTTTTAA
1 ATGTAACAATTTTTTTAAA
* *
5335956 TTGTAATAATATTTTTTAAA
1 ATGTAACAAT-TTTTTTAAA
5335976 ATGTAACA
1 ATGTAACA
5335984 TGTAATAACA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 8 0.36
20 14 0.64
ACGTcount: A:0.40, C:0.04, G:0.06, T:0.49
Consensus pattern (19 bp):
ATGTAACAATTTTTTTAAA
Found at i:5336720 original size:16 final size:17
Alignment explanation
Indices: 5336701--5336734 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
5336691 TAAAATTAAA
5336701 AAAAATAA-TTATTTTT
1 AAAAATAATTTATTTTT
5336717 AAAAATAATTTATTTTT
1 AAAAATAATTTATTTTT
5336734 A
1 A
5336735 GGGGTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.47
17 9 0.53
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAAAATAATTTATTTTT
Found at i:5336720 original size:17 final size:18
Alignment explanation
Indices: 5336700--5336734 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
5336690 TTAAAATTAA
5336700 AAAAAATAA-TTATTTTT
1 AAAAAATAATTTATTTTT
5336717 -AAAAATAATTTATTTTT
1 AAAAAATAATTTATTTTT
5336734 A
1 A
5336735 GGGGTAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
AAAAAATAATTTATTTTT
Found at i:5337450 original size:5 final size:5
Alignment explanation
Indices: 5337440--5337513 Score: 78
Period size: 5 Copynumber: 14.2 Consensus size: 5
5337430 ATATTATAAT
* *
5337440 TAAAA TAAAA TATAT TAAAA TAAAA TATATAA TATAAA TAAAA TAAAA
1 TAAAA TAAAA TAAAA TAAAA TAAAA TA-A-AA TA-AAA TAAAA TAAAA
*
5337488 TAAAA TAAAA TATAAA -AAAT TAAAA T
1 TAAAA TAAAA TA-AAA TAAAA TAAAA T
5337514 TTATATAATA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
4 2 0.03
5 43 0.73
6 8 0.14
7 6 0.10
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (5 bp):
TAAAA
Found at i:5337479 original size:33 final size:33
Alignment explanation
Indices: 5337429--5337501 Score: 103
Period size: 33 Copynumber: 2.2 Consensus size: 33
5337419 AATATTTTAT
* *
5337429 AATATTATAATTAAAATAAAATATATTAAAATAA
1 AATA-TATAATTAAAATAAAATAAAATAAAATAA
5337463 AATATATAA-TATAAATAAAATAAAATAAAATAA
1 AATATATAATTA-AAATAAAATAAAATAAAATAA
5337496 AATATA
1 AATATA
5337502 AAAAATTAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
32 2 0.06
33 30 0.83
34 4 0.11
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (33 bp):
AATATATAATTAAAATAAAATAAAATAAAATAA
Found at i:5337480 original size:9 final size:9
Alignment explanation
Indices: 5337457--5337496 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
5337447 AAATATATTA
5337457 AAATAAAAT
1 AAATAAAAT
* *
5337466 ATATAATAT
1 AAATAAAAT
5337475 AAATAAAAT
1 AAATAAAAT
5337484 AAAATAAAAT
1 -AAATAAAAT
5337494 AAA
1 AAA
5337497 ATATAAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
9 17 0.65
10 9 0.35
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (9 bp):
AAATAAAAT
Found at i:5337521 original size:26 final size:27
Alignment explanation
Indices: 5337436--5337566 Score: 85
Period size: 26 Copynumber: 4.9 Consensus size: 27
5337426 TATAATATTA
* *
5337436 TAAT-TAAAATA-AAATATATTAAAAT
1 TAATATAAAATATAAAGAAATTAAAAT
* * * *
5337461 AAAATATATAATATAAATAAAATAAAA-
1 -TAATATAAAATATAAAGAAATTAAAAT
*
5337488 TAAAATAAAATATAAA-AAATTAAAAT
1 TAATATAAAATATAAAGAAATTAAAAT
* *
5337514 TTATATAATATAGGTAAAAGAAATTAAAAT
1 TAATATAAAATA--T-AAAGAAATTAAAAT
5337544 ATAATATATAAA-ATAAA-AAATTA
1 -TAATATA-AAATATAAAGAAATTA
5337567 TATTAAAGAA
Statistics
Matches: 83, Mismatches: 13, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
25 8 0.10
26 25 0.30
27 12 0.14
28 15 0.18
29 4 0.05
30 10 0.12
31 7 0.08
32 2 0.02
ACGTcount: A:0.67, C:0.00, G:0.02, T:0.31
Consensus pattern (27 bp):
TAATATAAAATATAAAGAAATTAAAAT
Found at i:5337542 original size:50 final size:49
Alignment explanation
Indices: 5337437--5337621 Score: 167
Period size: 50 Copynumber: 4.0 Consensus size: 49
5337427 ATAATATTAT
*
5337437 AATTAAAATAAAATATATTAAAA-TAAAA-TATATAATATAAATAAAATA
1 AATTAAAATAAAATATA-TAAAATTAAAATTATATAATATAAATAAAAGA
* * **
5337485 AAATAAAATAAAATATAAAAAATTAAAATTTATATAATATAGGTAAAAGA
1 AATTAAAATAAAATATATAAAATTAAAA-TTATATAATATAAATAAAAGA
* *
5337535 AATTAAAATATAATATATAAAA-TAAAA--A-AT--TAT--ATTAAAGA
1 AATTAAAATAAAATATATAAAATTAAAATTATATAATATAAATAAAAGA
* * * * *
5337576 AATAAAAATAAAATATATAAGATTATAATAATA-AATAAAAATAAAA
1 AATTAAAATAAAATATATAAAATTAAAATTATATAATATAAATAAAA
5337622 TGTATGACAT
Statistics
Matches: 110, Mismatches: 16, Indels: 22
0.74 0.11 0.15
Matches are distributed among these distances:
41 25 0.23
42 4 0.04
43 3 0.03
44 1 0.01
45 3 0.03
46 3 0.03
47 4 0.04
48 26 0.24
49 5 0.05
50 36 0.33
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (49 bp):
AATTAAAATAAAATATATAAAATTAAAATTATATAATATAAATAAAAGA
Found at i:5337555 original size:24 final size:23
Alignment explanation
Indices: 5337437--5337595 Score: 79
Period size: 26 Copynumber: 6.9 Consensus size: 23
5337427 ATAATATTAT
*
5337437 AATTAAAATAAAATATATTAAAATAA
1 AATTAAAATATAATATA-T-AAA-AA
*
5337463 AATATATAATATAA-ATA-AAATAA
1 AAT-TAAAATATAATATATAAA-AA
5337486 AA-TAAAATA-AA-ATAT-AAAA
1 AATTAAAATATAATATATAAAAA
5337505 AATTAAAATTTATATAATATAGGTAAAAGA
1 AATT-AAA---ATATAATATA--TAAAA-A
*
5337535 AATTAAAATATAATATATAAAAT
1 AATTAAAATATAATATATAAAAA
*
5337558 AA--AAAAT-T-ATAT-TAAAGA
1 AATTAAAATATAATATATAAAAA
* *
5337576 AATAAAAATAAAATATATAA
1 AATTAAAATATAATATATAA
5337596 GATTATAATA
Statistics
Matches: 108, Mismatches: 7, Indels: 39
0.70 0.05 0.25
Matches are distributed among these distances:
18 6 0.06
19 8 0.07
20 14 0.13
21 14 0.13
22 4 0.04
23 13 0.12
24 8 0.07
25 2 0.02
26 19 0.18
27 8 0.07
28 1 0.01
29 6 0.06
30 5 0.05
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (23 bp):
AATTAAAATATAATATATAAAAA
Found at i:5337865 original size:15 final size:15
Alignment explanation
Indices: 5337845--5337898 Score: 81
Period size: 15 Copynumber: 3.6 Consensus size: 15
5337835 TTTTCCTTGC
5337845 AATCACATTACCTGT
1 AATCACATTACCTGT
*
5337860 AATCACATTGCCTGT
1 AATCACATTACCTGT
* *
5337875 AATTACATTACATGT
1 AATCACATTACCTGT
5337890 AATCACATT
1 AATCACATT
5337899 GCATTATAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 34 1.00
ACGTcount: A:0.35, C:0.22, G:0.07, T:0.35
Consensus pattern (15 bp):
AATCACATTACCTGT
Found at i:5340763 original size:28 final size:29
Alignment explanation
Indices: 5340703--5340763 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
5340693 CTGTATAATG
* **
5340703 TTAATTGAAAAAAAAATACCTATAAGATG
1 TTAATTGAAAAAAAAATACATATAAGAAC
5340732 TTAATTGAAAAAAAAAT-CATATGAA-AAC
1 TTAATTGAAAAAAAAATACATAT-AAGAAC
5340760 TTAA
1 TTAA
5340764 AGATTAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.57, C:0.07, G:0.08, T:0.28
Consensus pattern (29 bp):
TTAATTGAAAAAAAAATACATATAAGAAC
Found at i:5371099 original size:24 final size:24
Alignment explanation
Indices: 5371071--5371162 Score: 75
Period size: 24 Copynumber: 3.9 Consensus size: 24
5371061 CTAATTGTTT
5371071 TTTTTATTATT-TTTTCCTTTTTTA
1 TTTTTATT-TTATTTTCCTTTTTTA
* *
5371095 TTTTTCTTTTATTTTCC-TTTTTC
1 TTTTTATTTTATTTTCCTTTTTTA
** * *
5371118 CCTTCATTTTA-TTTCTTTACTTTTA
1 TTTTTATTTTATTTTCCTT--TTTTA
5371143 -TTTTATTTTATTTTCCTTTT
1 TTTTTATTTTATTTTCCTTTT
5371163 CTTTAAAAAA
Statistics
Matches: 52, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
22 4 0.08
23 17 0.33
24 21 0.40
25 10 0.19
ACGTcount: A:0.11, C:0.14, G:0.00, T:0.75
Consensus pattern (24 bp):
TTTTTATTTTATTTTCCTTTTTTA
Found at i:5371118 original size:31 final size:36
Alignment explanation
Indices: 5371080--5371146 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
5371070 TTTTTTATTA
*
5371080 TTTTTTCCTT-TTTTA-TT-TTT-CTTTTATTTTCC
1 TTTTTCCCTTATTTTATTTCTTTACTTTTATTTTCC
5371112 TTTTTCCCTTCATTTTATTTCTTTACTTTTATTTT
1 TTTTTCCCTT-ATTTTATTTCTTTACTTTTATTTT
5371147 ATTTTATTTT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
32 9 0.31
34 5 0.17
35 2 0.07
36 3 0.10
37 10 0.34
ACGTcount: A:0.09, C:0.16, G:0.00, T:0.75
Consensus pattern (36 bp):
TTTTTCCCTTATTTTATTTCTTTACTTTTATTTTCC
Found at i:5371423 original size:19 final size:22
Alignment explanation
Indices: 5371400--5371442 Score: 54
Period size: 20 Copynumber: 2.0 Consensus size: 22
5371390 TTTACATTAT
*
5371400 TTTTTTCCCTTT-TTTTT-TTC
1 TTTTCTCCCTTTCTTTTTCTTC
*
5371420 TTTTCTTCCTTTCTTTTTCTTC
1 TTTTCTCCCTTTCTTTTTCTTC
5371442 T
1 T
5371443 CTCATTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 10 0.53
21 5 0.26
22 4 0.21
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (22 bp):
TTTTCTCCCTTTCTTTTTCTTC
Found at i:5387555 original size:25 final size:27
Alignment explanation
Indices: 5387509--5387559 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
5387499 AAATATTTTT
5387509 AAATTCTAATAATATTGAATAATTGATA
1 AAATTCTAATAATATT-AATAATTGATA
*
5387537 AAATTTTAATAATA-T-ATAATTGA
1 AAATTCTAATAATATTAATAATTGA
5387560 AACATTAATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
25 8 0.36
27 1 0.05
28 13 0.59
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (27 bp):
AAATTCTAATAATATTAATAATTGATA
Found at i:5390704 original size:2 final size:2
Alignment explanation
Indices: 5390699--5390748 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
5390689 NNNNNNNNNA
5390699 TC TC TC TC TC TC TC TC 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 TC TC TC TC TC TC TC TC
5390741 TC TC TC TC
1 TC TC TC TC
5390749 GCTAAATTCT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:5392550 original size:60 final size:61
Alignment explanation
Indices: 5392445--5392566 Score: 167
Period size: 60 Copynumber: 2.0 Consensus size: 61
5392435 AGTCATCTTG
* * * *
5392445 AACCTGCAATTTGTTGAAACCCTTAGGAATGAACGTTGAA-CTGTGTGTATGGTTTTGTGT
1 AACCAGCAATTTGTTGAAACCCTGACGAATGAACGTCGAAGCTGTGTGTATGGTTTTGTGT
*
5392505 AACCAGCAATTTGTTGAAACCCTGACGAATGAAC-TCCGAAGTGTGTGTGTATGGTTTTGTGT
1 AACCAGCAATTTGTTGAAACCCTGACGAATGAACGT-CGAAG-CTGTGTGTATGGTTTTGTGT
5392567 TTAAGTTGGC
Statistics
Matches: 54, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
59 1 0.02
60 34 0.63
62 19 0.35
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (61 bp):
AACCAGCAATTTGTTGAAACCCTGACGAATGAACGTCGAAGCTGTGTGTATGGTTTTGTGT
Found at i:5401431 original size:30 final size:30
Alignment explanation
Indices: 5401382--5401451 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
5401372 GGAAACCCCG
* *
5401382 ACATATATATATATATACATATATATGTAT
1 ACATATGTATACATATACATATATATGTAT
*
5401412 ACATATGTATACATGTACATATATATGTAT
1 ACATATGTATACATATACATATATATGTAT
*
5401442 ACAGATGTAT
1 ACATATGTAT
5401452 GTATGTGTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.43, C:0.09, G:0.09, T:0.40
Consensus pattern (30 bp):
ACATATGTATACATATACATATATATGTAT
Found at i:5401451 original size:10 final size:10
Alignment explanation
Indices: 5401404--5401451 Score: 51
Period size: 10 Copynumber: 4.8 Consensus size: 10
5401394 ATATACATAT
5401404 ATATGTATAC
1 ATATGTATAC
5401414 ATATGTATAC
1 ATATGTATAC
* ** *
5401424 ATGTACATAT
1 ATATGTATAC
5401434 ATATGTATAC
1 ATATGTATAC
*
5401444 AGATGTAT
1 ATATGTAT
5401452 GTATGTGTGT
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
10 29 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (10 bp):
ATATGTATAC
Found at i:5415892 original size:15 final size:16
Alignment explanation
Indices: 5415868--5415907 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
5415858 TTGATGGCTT
*
5415868 ACATCACAACC-ACCA
1 ACATCCCAACCAACCA
*
5415883 ACATCCCAACCAACTA
1 ACATCCCAACCAACCA
5415899 ACATCCCAA
1 ACATCCCAA
5415908 GTCCTAAATG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.45, C:0.45, G:0.00, T:0.10
Consensus pattern (16 bp):
ACATCCCAACCAACCA
Found at i:5421216 original size:20 final size:20
Alignment explanation
Indices: 5421184--5421223 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5421174 AGTTTTTAAA
5421184 TTTTTTATTTTTTAT-ATAT
1 TTTTTTATTTTTTATCATAT
5421203 TTTTTTATTTTTTTATCATAT
1 TTTTTTA-TTTTTTATCATAT
5421224 CTAAATAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 7 0.37
20 8 0.42
21 4 0.21
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.78
Consensus pattern (20 bp):
TTTTTTATTTTTTATCATAT
Found at i:5422959 original size:43 final size:43
Alignment explanation
Indices: 5422865--5422965 Score: 107
Period size: 43 Copynumber: 2.3 Consensus size: 43
5422855 AAATATCACA
* *
5422865 ACAAATCAAGGATATCAAATATTATAATTGAAATTGTAGCACCT
1 ACAAATCAA-GATATCAAATATTATAATTGAAAATGTAACACCT
* * **
5422909 -CATATCAAGACTATCAAGTATTATGCTTGAAAATGTAACA-CT
1 ACAAATCAAGA-TATCAAATATTATAATTGAAAATGTAACACCT
5422951 ACAAATCAAGGATAT
1 ACAAATCAA-GATAT
5422966 AATTAAGCAG
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
42 4 0.09
43 41 0.87
44 2 0.04
ACGTcount: A:0.45, C:0.15, G:0.12, T:0.29
Consensus pattern (43 bp):
ACAAATCAAGATATCAAATATTATAATTGAAAATGTAACACCT
Found at i:5429482 original size:33 final size:33
Alignment explanation
Indices: 5429422--5429484 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
5429412 TCACACTCAG
** *
5429422 CAGAACATCAACATCGGAAGCAGCACACAGCAA
1 CAGAACATCAACATCACAAGCAACACACAGCAA
*
5429455 CAGAACATCAACATCACAGGCAACACACAG
1 CAGAACATCAACATCACAAGCAACACACAG
5429485 GATAGAGCTC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.46, C:0.32, G:0.16, T:0.06
Consensus pattern (33 bp):
CAGAACATCAACATCACAAGCAACACACAGCAA
Found at i:5429511 original size:6 final size:6
Alignment explanation
Indices: 5429500--5429527 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5429490 AGCTCTGCTG
5429500 AGCACC AGCACC AGCACC AGCACC AGCA
1 AGCACC AGCACC AGCACC AGCACC AGCA
5429528 GCTCAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.36, C:0.46, G:0.18, T:0.00
Consensus pattern (6 bp):
AGCACC
Found at i:5431608 original size:16 final size:16
Alignment explanation
Indices: 5431587--5431630 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
5431577 CTCAAAATAC
*
5431587 TATTTTTTTCCTGTTT
1 TATTTTTTTCCTCTTT
*
5431603 TATTTTTATCCTCTTT
1 TATTTTTTTCCTCTTT
*
5431619 T-TCTTTTTCCTC
1 TATTTTTTTCCTC
5431631 CTAATTTCCC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
15 9 0.38
16 15 0.62
ACGTcount: A:0.07, C:0.20, G:0.02, T:0.70
Consensus pattern (16 bp):
TATTTTTTTCCTCTTT
Found at i:5431726 original size:23 final size:25
Alignment explanation
Indices: 5431690--5431736 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 25
5431680 AACCGATGAG
**
5431690 AGAAGAAATTGAAAA-A-AAAATAA
1 AGAAGAAAAGGAAAACATAAAATAA
5431713 AGAAGAAAAGGAAAACATAAAATA
1 AGAAGAAAAGGAAAACATAAAATA
5431737 TAAAGAGAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 1 0.05
25 6 0.30
ACGTcount: A:0.72, C:0.02, G:0.15, T:0.11
Consensus pattern (25 bp):
AGAAGAAAAGGAAAACATAAAATAA
Found at i:5437521 original size:29 final size:30
Alignment explanation
Indices: 5437444--5437515 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
5437434 TATATTTAAT
* * *
5437444 TAAATTTTTATATTTTTATTTCGAATCAAG
1 TAAATTTTTATATTTTAATTTCAAATCAAA
* *
5437474 TAAGTTTTTATATTTTAATTTTAAATCAAA
1 TAAATTTTTATATTTTAATTTCAAATCAAA
5437504 TAAATTTTTATA
1 TAAATTTTTATA
5437516 ATTAATAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.54
Consensus pattern (30 bp):
TAAATTTTTATATTTTAATTTCAAATCAAA
Found at i:5438181 original size:2 final size:2
Alignment explanation
Indices: 5438174--5438205 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5438164 AACTTTCAAA
5438174 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
5438206 CTATCTAGAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5442615 original size:2 final size:2
Alignment explanation
Indices: 5442604--5442646 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
5442594 GTTCTGTCTT
*
5442604 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TT TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5442645 TC
1 TC
5442647 ACTGTAATTA
Statistics
Matches: 38, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:5454357 original size:16 final size:16
Alignment explanation
Indices: 5454338--5454373 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
5454328 TAAAAATTAC
5454338 ATATTATAAACTATAA
1 ATATTATAAACTATAA
5454354 ATATTATAAACTATAA
1 ATATTATAAACTATAA
5454370 ATAT
1 ATAT
5454374 CAAGTAACGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.56, C:0.06, G:0.00, T:0.39
Consensus pattern (16 bp):
ATATTATAAACTATAA
Found at i:5455802 original size:33 final size:33
Alignment explanation
Indices: 5455736--5455802 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
5455726 CATCATTATC
* * *
5455736 AATTATGATATATCAACATGTTAAATCATCATT
1 AATTATGATATATAAACATGTCAAATCAGCATT
* * *
5455769 AATTATGATATATAAATATGTCATATTAGCATT
1 AATTATGATATATAAACATGTCAAATCAGCATT
5455802 A
1 A
5455803 TGCGATATAA
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.43, C:0.09, G:0.07, T:0.40
Consensus pattern (33 bp):
AATTATGATATATAAACATGTCAAATCAGCATT
Found at i:5458791 original size:2 final size:2
Alignment explanation
Indices: 5458784--5458819 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5458774 ACACAGAAAC
5458784 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
5458820 GTATGTATAA
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):
AT
Found at i:5468551 original size:2 final size:2
Alignment explanation
Indices: 5468544--5468573 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5468534 TTAAAATGGT
*
5468544 TC TC TC TC TC TC TC TC TC TT TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
5468574 ATATATAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.47, G:0.00, T:0.53
Consensus pattern (2 bp):
TC
Found at i:5468579 original size:2 final size:2
Alignment explanation
Indices: 5468574--5468615 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
5468564 TCTCTCTCTC
*
5468574 AT AT AT AA AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5468616 CTCTCTTTTC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5471820 original size:100 final size:100
Alignment explanation
Indices: 5471690--5471889 Score: 355
Period size: 100 Copynumber: 2.0 Consensus size: 100
5471680 TTTTCATATG
* *
5471690 TAAGATTTTTTTGGTATCAAGAGTGCTGAGCTACACAATGGGAGGTAGCCCTCTCTCATCCCAAA
1 TAAGAGTTTTTCGGTATCAAGAGTGCTGAGCTACACAATGGGAGGTAGCCCTCTCTCATCCCAAA
5471755 AATCTCACCCCACATAGGATTTGAACCAAGGATCT
66 AATCTCACCCCACATAGGATTTGAACCAAGGATCT
** *
5471790 TAAGAGTTTTTCGGTATCAAGAGTTTTGAGCTACACAATGGGAGGTAGCCCTCTCTCATCCCACA
1 TAAGAGTTTTTCGGTATCAAGAGTGCTGAGCTACACAATGGGAGGTAGCCCTCTCTCATCCCAAA
5471855 AATCTCACCCCACATAGGATTTGAACCAAGGATCT
66 AATCTCACCCCACATAGGATTTGAACCAAGGATCT
5471890 CCTAGATGGA
Statistics
Matches: 95, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
100 95 1.00
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.27
Consensus pattern (100 bp):
TAAGAGTTTTTCGGTATCAAGAGTGCTGAGCTACACAATGGGAGGTAGCCCTCTCTCATCCCAAA
AATCTCACCCCACATAGGATTTGAACCAAGGATCT
Found at i:5474730 original size:3 final size:3
Alignment explanation
Indices: 5474722--5474753 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
5474712 CTGAGAAAAT
*
5474722 AAG AAG AAG AAA AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
5474754 AGCAGGGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:5478309 original size:10 final size:9
Alignment explanation
Indices: 5478284--5478317 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
5478274 TAAAGTTATC
5478284 AAAATTTTT
1 AAAATTTTT
5478293 AAAATTTTT
1 AAAATTTTT
*
5478302 AAATATTTAT
1 AAA-ATTTTT
5478312 AAAATT
1 AAAATT
5478318 AAACTTTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (9 bp):
AAAATTTTT
Found at i:5482237 original size:200 final size:199
Alignment explanation
Indices: 5481894--5482289 Score: 679
Period size: 200 Copynumber: 2.0 Consensus size: 199
5481884 GTGAGTTGGT
5481894 AGGTTTAGACTTGTTATACATCTCAGACAGGTATCAGTATCCGTTCTCCAAAGGTGTTAAAATTG
1 AGGTTTAGACTTGTTATACATCTCAGACAGGTATCAGTATCCGTTCTCCAAAGGTGTTAAAATTG
* *
5481959 ATAGTATTATGGTCTTGTTTTTGTTTTCTTTGTAATTCTGAGATCTATATTGGGAAAAAGTTGAG
66 ATAGTAATATGGTCTTGTTTTTGTTTTCTTTGTAATTCTGAGATCTATATTAGGAAAAAGTTGAG
* *
5482024 AATATGAGGTAGACACATGGCCACATAGTGTGTTTGTACGTGCTTGCTGTTCGAATGTATAATTT
131 AATATGAGGTAGACACATGGCCACATAGTGTG-TTGTACATGCCTGCTGTTCGAATGTATAATTT
5482089 GCGTC
195 GCGTC
* *
5482094 AGGTTTAGCCTTGTTATACATCTCAGACAGGTTTCAGTATCC-TCTCTCCAAAGGTGTTAAAATT
1 AGGTTTAGACTTGTTATACATCTCAGACAGGTATCAGTATCCGT-TCTCCAAAGGTGTTAAAATT
*
5482158 GATGGTAATATGGTCTTG-TTTTGTTTTTCTTTGTAATTCTGAGATCTATATTAGGAAAAAGTTG
65 GATAGTAATATGGTCTTGTTTTTG-TTTTCTTTGTAATTCTGAGATCTATATTAGGAAAAAGTTG
*
5482222 AGAATATGAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTTGAATGTATAATT
129 AGAATATGAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTCGAATGTATAATT
5482287 TGC
194 TGC
5482290 ATCTGACTGC
Statistics
Matches: 186, Mismatches: 8, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
199 37 0.20
200 149 0.80
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.38
Consensus pattern (199 bp):
AGGTTTAGACTTGTTATACATCTCAGACAGGTATCAGTATCCGTTCTCCAAAGGTGTTAAAATTG
ATAGTAATATGGTCTTGTTTTTGTTTTCTTTGTAATTCTGAGATCTATATTAGGAAAAAGTTGAG
AATATGAGGTAGACACATGGCCACATAGTGTGTTGTACATGCCTGCTGTTCGAATGTATAATTTG
CGTC
Found at i:5486786 original size:13 final size:13
Alignment explanation
Indices: 5486770--5486808 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
5486760 CTAAACCCCG
*
5486770 TTTATAAATATTT
1 TTTATAAATATAT
5486783 TTTATAAATTATAT
1 TTTATAAA-TATAT
*
5486797 TTAATAAATATA
1 TTTATAAATATA
5486809 ATCAGTTTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
TTTATAAATATAT
Found at i:5487113 original size:2 final size:2
Alignment explanation
Indices: 5487106--5487131 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5487096 GGAAATTTTT
5487106 CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA
5487132 TTGTGCGCTA
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:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:5492790 original size:33 final size:34
Alignment explanation
Indices: 5492722--5492790 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
5492712 TCGCAGTCCA
5492722 ATGACATTGAAAATGGAGTAGAAAATTTGAAGTT
1 ATGACATTGAAAATGGAGTAGAAAATTTGAAGTT
*
5492756 ATGACATTGAAAATGGAGTAGAGAA-TTGAAGTT
1 ATGACATTGAAAATGGAGTAGAAAATTTGAAGTT
5492789 AT
1 AT
5492791 CTCCGAAAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
33 10 0.29
34 24 0.71
ACGTcount: A:0.43, C:0.03, G:0.25, T:0.29
Consensus pattern (34 bp):
ATGACATTGAAAATGGAGTAGAAAATTTGAAGTT
Found at i:5498704 original size:2 final size:2
Alignment explanation
Indices: 5498697--5498724 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5498687 CAACCCCTTG
5498697 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
5498725 GTTACAATAA
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):
AT
Found at i:5504761 original size:157 final size:156
Alignment explanation
Indices: 5504476--5504784 Score: 451
Period size: 157 Copynumber: 2.0 Consensus size: 156
5504466 AACAACAGTA
*
5504476 AATCACTTCATTATCAATTATAAGCAGCAAAAGATAAACAAAAACGTTGAAAAATATATGGAAGT
1 AATCACTTCATTATCAATTATAAGCAGCAAAAGATAAACAAAAACGCTGAAAAATATATGGAAGT
* * * *
5504541 ACTGCATCCCTGTGATTACTGGTATAAATTGACAAAACTATTTGATTATATAACATAAATAATGG
66 ACTACATCCCTATGATTACTCGTATAAATTGACAAAACTATTTGATTATATAACATAAATAATGA
*
5504606 AATGGAAGCTCATAAGGATAACCATG
131 AATGGAAGCTCACAAGGATAACCATG
* ** * * *
5504632 AATCACTTCTTTATGGATTATAAGCAGCAAAAGATAACACAAAAATGCTGAAACATATATGGAGG
1 AATCACTTCATTATCAATTATAAGCAGCAAAAGATAA-ACAAAAACGCTGAAAAATATATGGAAG
* *
5504697 TACTACATCCCTATGACTGT-C-CGTATAAATTGACAAAACTATTTGATTATATGATATAAATAA
65 TACTACATCCCTATGA-T-TACTCGTATAAATTGACAAAACTATTTGATTATATAACATAAATAA
5504760 TGAAATGGAAGCTCACAAGGATAAC
128 TGAAATGGAAGCTCACAAGGATAAC
5504785 TGCATATACA
Statistics
Matches: 136, Mismatches: 14, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
156 34 0.25
157 99 0.73
158 2 0.01
159 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.15, T:0.28
Consensus pattern (156 bp):
AATCACTTCATTATCAATTATAAGCAGCAAAAGATAAACAAAAACGCTGAAAAATATATGGAAGT
ACTACATCCCTATGATTACTCGTATAAATTGACAAAACTATTTGATTATATAACATAAATAATGA
AATGGAAGCTCACAAGGATAACCATG
Found at i:5507367 original size:45 final size:45
Alignment explanation
Indices: 5507316--5507408 Score: 168
Period size: 45 Copynumber: 2.1 Consensus size: 45
5507306 AAACTACTAG
5507316 CCTCTTTCTTTAGCTTCTTCTCTTCCAACATACGAATTCGTTCCT
1 CCTCTTTCTTTAGCTTCTTCTCTTCCAACATACGAATTCGTTCCT
* *
5507361 CCTCTTTCTTTAGCTTTTTCTCTTCCAACATATGAATTCGTTCCT
1 CCTCTTTCTTTAGCTTCTTCTCTTCCAACATACGAATTCGTTCCT
5507406 CCT
1 CCT
5507409 TTGTCATCTT
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.15, C:0.32, G:0.06, T:0.46
Consensus pattern (45 bp):
CCTCTTTCTTTAGCTTCTTCTCTTCCAACATACGAATTCGTTCCT
Found at i:5511923 original size:2 final size:2
Alignment explanation
Indices: 5511916--5511955 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
5511906 AGCATGTAAG
5511916 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5511956 GATGTGGGCG
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):
AT
Found at i:5512110 original size:28 final size:28
Alignment explanation
Indices: 5512079--5512143 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
5512069 TTATATCGCA
* * * *
5512079 TAACAGCTAAATTTTTTAATATAGCATG
1 TAACAACTAAAATCTTTAATATAACATG
*
5512107 TAACAATTAAAATCTTTAATATAACATG
1 TAACAACTAAAATCTTTAATATAACATG
*
5512135 TAATAACTA
1 TAACAACTA
5512144 TATTTTTCAA
Statistics
Matches: 30, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (28 bp):
TAACAACTAAAATCTTTAATATAACATG
Found at i:5512238 original size:27 final size:27
Alignment explanation
Indices: 5512086--5512242 Score: 113
Period size: 27 Copynumber: 5.7 Consensus size: 27
5512076 GCATAACAGC
* *
5512086 TAAATTTTTTAATAT-AGCATGTAACAAT
1 TAAA-TTTTTAACATGA-CATGTAATAAT
* * * *
5512114 TAAAATCTTTAATATAACATGTAATAAC
1 T-AAATTTTTAACATGACATGTAATAAT
* * *
5512142 TATATTTTTCAACATTATATGTAATAAT
1 TAAATTTTT-AACATGACATGTAATAAT
* * *
5512170 TAATTTTTTAACAT-A-GTGTATAATAAC
1 TAAATTTTTAACATGACATG--TAATAAT
* *
5512197 TAATTTTTTAACATGACGTGTAATAAT
1 TAAATTTTTAACATGACATGTAATAAT
5512224 TAAATTTTTAACATGACAT
1 TAAATTTTTAACATGACAT
5512243 ACAACAATTA
Statistics
Matches: 106, Mismatches: 16, Indels: 15
0.77 0.12 0.11
Matches are distributed among these distances:
25 2 0.02
26 1 0.01
27 54 0.51
28 42 0.40
29 7 0.07
ACGTcount: A:0.42, C:0.08, G:0.06, T:0.43
Consensus pattern (27 bp):
TAAATTTTTAACATGACATGTAATAAT
Found at i:5512251 original size:27 final size:27
Alignment explanation
Indices: 5512201--5512258 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
5512191 AATAACTAAT
* ** *
5512201 TTTTTAACATGACGTGTAATAATTAAA
1 TTTTTAACATGACATACAACAATTAAA
*
5512228 TTTTTAACATGACATACAACAATTAGA
1 TTTTTAACATGACATACAACAATTAAA
5512255 TTTT
1 TTTT
5512259 CAATGTGATT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.40, C:0.10, G:0.09, T:0.41
Consensus pattern (27 bp):
TTTTTAACATGACATACAACAATTAAA
Found at i:5533524 original size:33 final size:33
Alignment explanation
Indices: 5533447--5533528 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
5533437 TGTGTAATGC
* *
5533447 TAACATAATATGCTAATATATTATAATTGATAA
1 TAACATAATATGTTAATATATTATAATTAATAA
**
5533480 TAATGTAATATGTTAATATATTATAATTAATAA
1 TAACATAATATGTTAATATATTATAATTAATAA
*
5533513 TAACATGATATGTTAA
1 TAACATAATATGTTAA
5533529 CATAATAATA
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.48, C:0.04, G:0.07, T:0.41
Consensus pattern (33 bp):
TAACATAATATGTTAATATATTATAATTAATAA
Found at i:5538269 original size:3 final size:3
Alignment explanation
Indices: 5538250--5538286 Score: 56
Period size: 3 Copynumber: 12.3 Consensus size: 3
5538240 CCTTTTTCTT
* *
5538250 TTA TTA ATA TCA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
5538287 AAGCTCTAAC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5546032 original size:238 final size:235
Alignment explanation
Indices: 5545733--5546388 Score: 715
Period size: 242 Copynumber: 2.7 Consensus size: 235
5545723 AGTTTTGTGG
* * * * * *
5545733 AAAACAAACA-TTACATTTATGTTCTTAGATTAAAAATATTTAATAATTTATAAATTTTAATTTA
1 AAAACAAACATTTAAATTTATATTCTCA-ATTAAAAGTATTTAATGATTTACAAATTTTAATTTA
**
5545797 AAAATAAATAATAATAATAATAAAAATAATTATTGATAAAAGTCGTCATTGAAAAGATTTGATAT
65 AAAATAAATAATAATAATAATAAAAATAATTATTGATAAAAGTTATCATTGAAAAGATTTGATAT
* * *
5545862 AAAATTCTAAGAATTAGA-ATAAAAACTCATAAAGGTAAAACAAATATATTTAAAATGC-T-A-A
130 AAAATTGTAAGAATTA-ACATAAAAACTCATAAA-GTAAAATAAATATAATTAAAAT-CTTAACA
**
5545923 TAT-A-AATCTAACA-AGTCAATTAAGTTACAAAAAATTTAATTTTAAAGA
192 TATGATAAT-TAACATAG-C-A-T-A-TTA-AAAAAATCCAATTTTAAAGA
*
5545971 AAAACAAACATTTAAATTTATATTCTCGAATTAAAAGTATTTAA-GATTTACACATTTTAATTTA
1 AAAACAAACATTTAAATTTATATTCTC-AATTAAAAGTATTTAATGATTTACAAATTTTAATTTA
* * * **
5546035 AAAATAAATAATAGTAA-AGATAAAAATAATTA-TAATTAAAAGTTATCATTGAAAGGCCTTGAT
65 AAAATAAATAATAATAATA-ATAAAAATAATTATTGA-TAAAAGTTATCATTGAAAAGATTTGAT
* *
5546098 ATAAAGTTGTAAGAATTAACGTAAAAACTCATAAAAGTAAAATATATAAGTATAATTAAAATCTT
128 ATAAAATTGTAAGAATTAACATAAAAACTCAT-AAAGT-AAA-ATA-AA-TATAATTAAAATCTT
* * *
5546163 AAACATGTGATAGTTAACATAGCATATTAAAAAAATCCAATTTTAATGA
188 -AACATATGATAATTAACATAGCATATTAAAAAAATCCAATTTTAAAGA
* * * *
5546212 AAATCAAACATTTAATTTTATATTATCAAGATAAAAGTATTTAATGATTTACAAATTTTAATTTA
1 AAAACAAACATTTAAATTTATATTCTCAA-TTAAAAGTATTTAATGATTTACAAATTTTAATTTA
* * * * *
5546277 AAAATAAATAATAATAATGATAAAAATAATTATTGTTAAAAGTTATCATTGAAGAGTTTTGACAT
65 AAAATAAATAATAATAATAATAAAAATAATTATTGATAAAAGTTATCATTGAAAAGATTTGATAT
*
5546342 AAAGA-TGTAAGAATTAACATAAAAACTCATTAAAATAAAATAAATAT
130 AAA-ATTGTAAGAATTAACATAAAAACTCA-TAAAGTAAAATAAATAT
5546389 TGTCAAAATA
Statistics
Matches: 354, Mismatches: 41, Indels: 46
0.80 0.09 0.10
Matches are distributed among these distances:
237 4 0.01
238 110 0.31
239 35 0.10
240 8 0.02
241 60 0.17
242 117 0.33
243 3 0.01
244 2 0.01
245 4 0.01
246 7 0.02
247 4 0.01
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.34
Consensus pattern (235 bp):
AAAACAAACATTTAAATTTATATTCTCAATTAAAAGTATTTAATGATTTACAAATTTTAATTTAA
AAATAAATAATAATAATAATAAAAATAATTATTGATAAAAGTTATCATTGAAAAGATTTGATATA
AAATTGTAAGAATTAACATAAAAACTCATAAAGTAAAATAAATATAATTAAAATCTTAACATATG
ATAATTAACATAGCATATTAAAAAAATCCAATTTTAAAGA
Found at i:5546561 original size:20 final size:22
Alignment explanation
Indices: 5546525--5546565 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
5546515 AAAAAAATTA
5546525 AAAATAAAATAACATTTAAAAT
1 AAAATAAAATAACATTTAAAAT
5546547 AAAAT-AAAT-ACATTTAAAA
1 AAAATAAAATAACATTTAAAA
5546566 ATTACCTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 10 0.53
21 4 0.21
22 5 0.26
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (22 bp):
AAAATAAAATAACATTTAAAAT
Found at i:5551825 original size:3 final size:3
Alignment explanation
Indices: 5551817--5551858 Score: 84
Period size: 3 Copynumber: 14.0 Consensus size: 3
5551807 GTTTCGAGAT
5551817 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
5551859 AGACATACGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5558608 original size:15 final size:16
Alignment explanation
Indices: 5558584--5558618 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
5558574 CACTAAAATC
*
5558584 TTTATGAATTAAT-AT
1 TTTATAAATTAATAAT
5558599 TTTATAAATTAATAAT
1 TTTATAAATTAATAAT
5558615 TTTA
1 TTTA
5558619 ATTAAACAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 12 0.67
16 6 0.33
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (16 bp):
TTTATAAATTAATAAT
Found at i:5562357 original size:74 final size:77
Alignment explanation
Indices: 5562261--5562422 Score: 240
Period size: 74 Copynumber: 2.1 Consensus size: 77
5562251 GAATGCATGT
* *
5562261 ACTGTTATAGTTGGTACTTTCACTCATCCGCGTAAGTACTCTGC-TTA-T-TTGAAAGCAGGCCA
1 ACTGTTATAGTTGGTACTTTCACACATCCGCATAAGTACTCTGCTTTATTGTTGAAAGCAGGCCA
5562323 CTGTGTTAATAC
66 CTGTGTTAATAC
* *
5562335 ACTGTTATAGTTTGTATTTTCACACATCCGCATAAGTACTCTGCTTTATTGGCTTGAAAGCAGGC
1 ACTGTTATAGTTGGTACTTTCACACATCCGCATAAGTACTCTGCTTTATT-G-TTGAAAGCAGGC
*
5562400 CACTGTGTTAATAT
64 CACTGTGTTAATAC
5562414 ACTGTTATA
1 ACTGTTATA
5562423 TTTTTGTTAG
Statistics
Matches: 78, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
74 40 0.51
75 3 0.04
76 1 0.01
79 34 0.44
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.37
Consensus pattern (77 bp):
ACTGTTATAGTTGGTACTTTCACACATCCGCATAAGTACTCTGCTTTATTGTTGAAAGCAGGCCA
CTGTGTTAATAC
Found at i:5566629 original size:39 final size:35
Alignment explanation
Indices: 5566589--5566716 Score: 120
Period size: 39 Copynumber: 3.5 Consensus size: 35
5566579 AAAGGAAAGG
*
5566589 GAGAGGGAGAGGAGAGATAGGGATAAGGAGAAAGAGAGG
1 GAGAGGGAGAGGAGAGA-AGGGA-AA-G-GAAAGAGAGA
* *
5566628 GATAGGGAGAGAAGAGAGAGGGAAAAGGAAAGAGAGA
1 GAGAGGGAGAGGAGAGA-AGGG-AAAGGAAAGAGAGA
*
5566665 G-GAGGGAAAGG-GAGAA-GGAGAAGGAAAGAGAGA
1 GAGAGGGAGAGGAGAGAAGGGA-AAGGAAAGAGAGA
5566698 GAGAGAGGAGA-GAGAGAAG
1 GAGAG-GGAGAGGAGAGAAG
5566717 CAGTAGTCGG
Statistics
Matches: 75, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
32 1 0.01
33 16 0.21
34 5 0.07
35 13 0.17
36 7 0.09
37 10 0.13
38 1 0.01
39 21 0.28
40 1 0.01
ACGTcount: A:0.48, C:0.00, G:0.50, T:0.02
Consensus pattern (35 bp):
GAGAGGGAGAGGAGAGAAGGGAAAGGAAAGAGAGA
Found at i:5566630 original size:18 final size:19
Alignment explanation
Indices: 5566607--5566705 Score: 73
Period size: 18 Copynumber: 5.2 Consensus size: 19
5566597 GAGGAGAGAT
5566607 AGGGATAAGGAGA-AAGAG
1 AGGGATAAGGAGAGAAGAG
*
5566625 AGGGATAGGGAGAGAAGAGAG
1 AGGGATAAGGAGAG-A-AGAG
* *
5566646 AGGGAAAAGGAAAGAGAGAGG
1 AGGGATAAGGAGAGA-AGA-G
5566667 AGGGA-AAGG-GAGAAGGAG
1 AGGGATAAGGAGAGAA-GAG
*
5566685 AAGGA-AA-GAGAGAGAGAG
1 AGGGATAAGGAGAGA-AGAG
5566703 AGG
1 AGG
5566706 AGAGAGAGAA
Statistics
Matches: 67, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
17 1 0.01
18 29 0.43
19 6 0.09
20 10 0.15
21 21 0.31
ACGTcount: A:0.48, C:0.00, G:0.49, T:0.02
Consensus pattern (19 bp):
AGGGATAAGGAGAGAAGAG
Found at i:5573254 original size:61 final size:61
Alignment explanation
Indices: 5573179--5573301 Score: 246
Period size: 61 Copynumber: 2.0 Consensus size: 61
5573169 TTTACATTTA
5573179 TGATTCTGAACTAAGAACTAAAATTAATATTAAACAAGTCAAGATATATGTAGTTAGATTG
1 TGATTCTGAACTAAGAACTAAAATTAATATTAAACAAGTCAAGATATATGTAGTTAGATTG
5573240 TGATTCTGAACTAAGAACTAAAATTAATATTAAACAAGTCAAGATATATGTAGTTAGATTG
1 TGATTCTGAACTAAGAACTAAAATTAATATTAAACAAGTCAAGATATATGTAGTTAGATTG
5573301 T
1 T
5573302 ACCGTTAACA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
61 62 1.00
ACGTcount: A:0.44, C:0.08, G:0.15, T:0.33
Consensus pattern (61 bp):
TGATTCTGAACTAAGAACTAAAATTAATATTAAACAAGTCAAGATATATGTAGTTAGATTG
Found at i:5579453 original size:30 final size:30
Alignment explanation
Indices: 5579417--5579476 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
5579407 GGAATTGTTT
*
5579417 TGTTTTAATGTTTTTCTTTTAATCTAGTAC
1 TGTTTTAACGTTTTTCTTTTAATCTAGTAC
5579447 TGTTTTAACGTTTTTCTTTTAATCTAGTAC
1 TGTTTTAACGTTTTTCTTTTAATCTAGTAC
5579477 CTTACTACTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.20, C:0.12, G:0.10, T:0.58
Consensus pattern (30 bp):
TGTTTTAACGTTTTTCTTTTAATCTAGTAC
Found at i:5580593 original size:2 final size:2
Alignment explanation
Indices: 5580586--5580610 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5580576 TTCATAAGAT
5580586 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
5580611 GTCTCTTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5582044 original size:15 final size:15
Alignment explanation
Indices: 5582024--5582056 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5582014 GTTGTCACCA
*
5582024 TTGCTGCTGCTGTTG
1 TTGCTGCTGCTGCTG
5582039 TTGCTGCTGCTGCTG
1 TTGCTGCTGCTGCTG
5582054 TTG
1 TTG
5582057 TTATCTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.21, G:0.33, T:0.45
Consensus pattern (15 bp):
TTGCTGCTGCTGCTG
Found at i:5611922 original size:3 final size:3
Alignment explanation
Indices: 5611916--5611942 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5611906 AGGGGGCGGT
5611916 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
5611943 AGTTGTTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:5616121 original size:16 final size:16
Alignment explanation
Indices: 5616096--5616162 Score: 57
Period size: 17 Copynumber: 4.1 Consensus size: 16
5616086 TTTTTCTCAT
*
5616096 TTCTCCCTTTACTCTC
1 TTCTCTCTTTACTCTC
5616112 TTCTCTCTTT--TCTC
1 TTCTCTCTTTACTCTC
*
5616126 TTCTCTCCATTTTGCTCTC
1 TTCTCT-C--TTTACTCTC
*
5616145 TCTCTCTCTTCACTCTC
1 T-TCTCTCTTTACTCTC
5616162 T
1 T
5616163 AGTTTCTCTT
Statistics
Matches: 42, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
14 10 0.24
15 1 0.02
16 9 0.21
17 11 0.26
19 6 0.14
20 5 0.12
ACGTcount: A:0.04, C:0.40, G:0.01, T:0.54
Consensus pattern (16 bp):
TTCTCTCTTTACTCTC
Found at i:5616127 original size:14 final size:14
Alignment explanation
Indices: 5616108--5616174 Score: 55
Period size: 14 Copynumber: 4.6 Consensus size: 14
5616098 CTCCCTTTAC
5616108 TCTCTTCTCTCTTT
1 TCTCTTCTCTCTTT
5616122 TCTCTTCTCTCCATTT
1 TCTCTTCTCT-C-TTT
*
5616138 TGCTCTCTCTCTCTCT
1 T-CTCT-TCTCTCTTT
* **
5616154 TCAC-TCTCTAGTT
1 TCTCTTCTCTCTTT
5616167 TCTCTTCT
1 TCTCTTCT
5616175 TTCCCTTCTA
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
13 9 0.21
14 13 0.31
15 3 0.07
16 7 0.17
17 5 0.12
18 5 0.12
ACGTcount: A:0.04, C:0.37, G:0.03, T:0.55
Consensus pattern (14 bp):
TCTCTTCTCTCTTT
Found at i:5616133 original size:32 final size:34
Alignment explanation
Indices: 5616087--5616154 Score: 88
Period size: 32 Copynumber: 2.1 Consensus size: 34
5616077 TCGGGATTCT
5616087 TTTTCTCATTTCTCC-CTTTACTCTCT-TCTCTC
1 TTTTCTCATTTCTCCACTTTACTCTCTCTCTCTC
* *
5616119 TTTTCTC-TTCTCTCCATTTTGCTCTCTCTCTCTC
1 TTTTCTCATT-TCTCCACTTTACTCTCTCTCTCTC
5616153 TT
1 TT
5616155 CACTCTCTAG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 2 0.06
32 12 0.39
33 9 0.29
34 8 0.26
ACGTcount: A:0.04, C:0.37, G:0.01, T:0.57
Consensus pattern (34 bp):
TTTTCTCATTTCTCCACTTTACTCTCTCTCTCTC
Found at i:5616424 original size:24 final size:24
Alignment explanation
Indices: 5616397--5616442 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
5616387 TGATAAATTG
5616397 AATATTTGAGGATTTT-GTTGTTTA
1 AATATTTGA-GATTTTGGTTGTTTA
5616421 AATATTTGAGATTTTGGTTGTT
1 AATATTTGAGATTTTGGTTGTT
5616443 GTGGATTTAG
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (24 bp):
AATATTTGAGATTTTGGTTGTTTA
Found at i:5625333 original size:77 final size:77
Alignment explanation
Indices: 5625232--5625376 Score: 211
Period size: 77 Copynumber: 1.9 Consensus size: 77
5625222 AAATTTGGGT
* * ** *
5625232 TTTATTTCTAAATTATTTTGATTTATTTAGAGTTAAATTGAATGACTCATAGGT-CAGTTTTGAT
1 TTTATCTCTAAATTATCTAAATTTATTTAGAGATAAATTGAATGACTCATAGGTGCA-TTTTGAT
5625296 TAGCCAAGTTGAA
65 TAGCCAAGTTGAA
* *
5625309 TTTATCTCTAAATTATCTAAATTTATTTAGAGATATATTGAATGACTCATAGGTGTATTTTGATT
1 TTTATCTCTAAATTATCTAAATTTATTTAGAGATAAATTGAATGACTCATAGGTGCATTTTGATT
5625374 AGC
66 AGC
5625377 AAAATTATAT
Statistics
Matches: 60, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
77 59 0.98
78 1 0.02
ACGTcount: A:0.32, C:0.08, G:0.14, T:0.46
Consensus pattern (77 bp):
TTTATCTCTAAATTATCTAAATTTATTTAGAGATAAATTGAATGACTCATAGGTGCATTTTGATT
AGCCAAGTTGAA
Found at i:5632884 original size:15 final size:16
Alignment explanation
Indices: 5632866--5632899 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
5632856 TGTTATATGG
*
5632866 ATTTT-ATTTTTAATA
1 ATTTTAATTTTTAAAA
5632881 ATTTTAATTTTTAAAA
1 ATTTTAATTTTTAAAA
5632897 ATT
1 ATT
5632900 AAAAAAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTTTAATTTTTAAAA
Found at i:5634803 original size:82 final size:80
Alignment explanation
Indices: 5634712--5634902 Score: 283
Period size: 82 Copynumber: 2.4 Consensus size: 80
5634702 AAAATAAACG
*
5634712 TTATATTTAACAATTGATTCATATTTATCATACACAAAGTTTTAATTCAATTTAATATTTTATTA
1 TTATATTTAACAATTGATTCATATTTATCATACACAAAGTTTTAATTCAACTTAATATTTTATTA
**
5634777 AATATTATTTAATTTTT
66 AATATTA-TTAA-AATT
* * * *
5634794 TTATATTTAACAATCGATTCATACTTATCATATACAAAGTTTTAATTTAACTTAATATTTTATTA
1 TTATATTTAACAATTGATTCATATTTATCATACACAAAGTTTTAATTCAACTTAATATTTTATTA
5634859 AATATTATTAAAATT
66 AATATTATTAAAATT
* *
5634874 TTATATTTAACAACTGATCCATATTTATC
1 TTATATTTAACAATTGATTCATATTTATC
5634903 GTATAATAGG
Statistics
Matches: 98, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
80 27 0.28
81 4 0.04
82 67 0.68
ACGTcount: A:0.39, C:0.09, G:0.03, T:0.49
Consensus pattern (80 bp):
TTATATTTAACAATTGATTCATATTTATCATACACAAAGTTTTAATTCAACTTAATATTTTATTA
AATATTATTAAAATT
Found at i:5645987 original size:30 final size:30
Alignment explanation
Indices: 5645926--5646078 Score: 82
Period size: 30 Copynumber: 5.2 Consensus size: 30
5645916 TTACACATCG
* ** * *
5645926 TGCTTAAAATTCTTAAAATGCTACCCACCA
1 TGCTTAAAAATCTTAAGTTGCTACACGCCA
*
5645956 TGCTTAAAAATCTTAAGTTGCTACATGCCA
1 TGCTTAAAAATCTTAAGTTGCTACACGCCA
** * *
5645986 TGC---ATCATCCTAAGTTGTTACACGCCA
1 TGCTTAAAAATCTTAAGTTGCTACACGCCA
* * * *
5646013 TACTTAACAATC-TAAGTTGCTATACACCA
1 TGCTTAAAAATCTTAAGTTGCTACACGCCA
* * * * *
5646042 TG-TTGAAATTCATAAATAATGCTACAGGCCA
1 TGCTTAAAAATCTTAAGT--TGCTACACGCCA
5646073 TGCTTA
1 TGCTTA
5646079 TATTCATGCA
Statistics
Matches: 90, Mismatches: 26, Indels: 12
0.70 0.20 0.09
Matches are distributed among these distances:
27 21 0.23
28 6 0.07
29 19 0.21
30 31 0.34
31 11 0.12
32 2 0.02
ACGTcount: A:0.34, C:0.23, G:0.12, T:0.31
Consensus pattern (30 bp):
TGCTTAAAAATCTTAAGTTGCTACACGCCA
Found at i:5649801 original size:29 final size:29
Alignment explanation
Indices: 5649769--5649824 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
5649759 TTTGATCCAA
* *
5649769 AATAAAAGTATAAAAGTTTAATTAAATAG
1 AATAAAAGAATAAAAATTTAATTAAATAG
*
5649798 AATAAAAGAATAAAAATTTATTTAAAT
1 AATAAAAGAATAAAAATTTAATTAAAT
5649825 TTTTTTGAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (29 bp):
AATAAAAGAATAAAAATTTAATTAAATAG
Found at i:5664012 original size:13 final size:12
Alignment explanation
Indices: 5663973--5664015 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
5663963 AAACAGTACA
5663973 TTTTTAAAATATG
1 TTTTTAAAAT-TG
* *
5663986 TTATTAAAAATG
1 TTTTTAAAATTG
5663998 TTTTTAATAATTG
1 TTTTTAA-AATTG
5664011 TTTTT
1 TTTTT
5664016 TATACTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
12 8 0.32
13 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (12 bp):
TTTTTAAAATTG
Found at i:5675766 original size:30 final size:30
Alignment explanation
Indices: 5675697--5675821 Score: 173
Period size: 30 Copynumber: 4.2 Consensus size: 30
5675687 AAAACAATTC
* * *
5675697 AAATAAATCTTTATATTTTTA--TTATGTT
1 AAATAAGTTTTTATATTTTTATTTTAAGTT
*
5675725 CAATCAAGTTTTTATATTTTTATTTTAAGTT
1 AAAT-AAGTTTTTATATTTTTATTTTAAGTT
5675756 AAATAAGTTTTTATATTTTTATTTTAAGTT
1 AAATAAGTTTTTATATTTTTATTTTAAGTT
* *
5675786 AAATAAGTTTTTATATTTTTATTTTAAATC
1 AAATAAGTTTTTATATTTTTATTTTAAGTT
5675816 AAATAA
1 AAATAA
5675822 ACCTTTTCAA
Statistics
Matches: 87, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
28 3 0.03
29 15 0.17
30 60 0.69
31 9 0.10
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (30 bp):
AAATAAGTTTTTATATTTTTATTTTAAGTT
Found at i:5676227 original size:44 final size:43
Alignment explanation
Indices: 5676158--5676244 Score: 138
Period size: 44 Copynumber: 2.0 Consensus size: 43
5676148 TAAAGACTTA
* *
5676158 TTTAAATTTTTTTTCATAATTTAAAGATTTATTTGAGTTTTAT
1 TTTAAATTTTTTTTCATAATTTAAAGACTTATTTGAGTATTAT
*
5676201 TTTAAATTTTTTTTACATAGTTTAAAGACTTATTTGAGTATTAT
1 TTTAAATTTTTTTT-CATAATTTAAAGACTTATTTGAGTATTAT
5676245 GTCAAGAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
43 14 0.35
44 26 0.65
ACGTcount: A:0.31, C:0.03, G:0.08, T:0.57
Consensus pattern (43 bp):
TTTAAATTTTTTTTCATAATTTAAAGACTTATTTGAGTATTAT
Found at i:5680081 original size:2 final size:2
Alignment explanation
Indices: 5680065--5680099 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
5680055 TTGTCTTTCT
* *
5680065 TC TC TC CC TC CC 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 TC TC TC TC T
5680100 ATATATATAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (2 bp):
TC
Found at i:5681848 original size:51 final size:51
Alignment explanation
Indices: 5681773--5681870 Score: 178
Period size: 51 Copynumber: 1.9 Consensus size: 51
5681763 GCATATATAC
**
5681773 ATATATATATATATATTATTATGTGTTCATGATTATTTGATTTGTTTTAGT
1 ATATATATATATATATTACCATGTGTTCATGATTATTTGATTTGTTTTAGT
5681824 ATATATATATATATATTACCATGTGTTCATGATTATTTGATTTGTTT
1 ATATATATATATATATTACCATGTGTTCATGATTATTTGATTTGTTT
5681871 AGAAAAGTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.30, C:0.04, G:0.11, T:0.55
Consensus pattern (51 bp):
ATATATATATATATATTACCATGTGTTCATGATTATTTGATTTGTTTTAGT
Found at i:5685466 original size:6 final size:6
Alignment explanation
Indices: 5685455--5685481 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5685445 TATGGGTGGA
5685455 GAAGAG GAAGAG GAAGAG GAAGAG GAA
1 GAAGAG GAAGAG GAAGAG GAAGAG GAA
5685482 AAGAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
GAAGAG
Found at i:5689419 original size:33 final size:33
Alignment explanation
Indices: 5689376--5689438 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
5689366 ATGTAAAGAG
* *
5689376 TTGTTTCCTTTTATAATATAACTATTCAAACAA
1 TTGTTACCTTTCATAATATAACTATTCAAACAA
* *
5689409 TTGTTACCTTTCATAGTATAGCTATTCAAA
1 TTGTTACCTTTCATAATATAACTATTCAAA
5689439 GAGGTATATT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.16, G:0.06, T:0.44
Consensus pattern (33 bp):
TTGTTACCTTTCATAATATAACTATTCAAACAA
Found at i:5696323 original size:8 final size:8
Alignment explanation
Indices: 5696278--5696337 Score: 52
Period size: 8 Copynumber: 7.4 Consensus size: 8
5696268 ACTATTGGTA
5696278 ATTAAATT
1 ATTAAATT
5696286 ATT-AATT
1 ATTAAATT
* *
5696293 -TTACATA
1 ATTAAATT
5696300 ATTAAATAT
1 ATTAAAT-T
*
5696309 ATAAAATT
1 ATTAAATT
5696317 ATTAAATT
1 ATTAAATT
5696325 AATTAAAATT
1 -ATT-AAATT
5696335 ATT
1 ATT
5696338 TTTTTGACCC
Statistics
Matches: 41, Mismatches: 6, Indels: 9
0.73 0.11 0.16
Matches are distributed among these distances:
6 2 0.05
7 6 0.15
8 16 0.39
9 12 0.29
10 5 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (8 bp):
ATTAAATT
Found at i:5702817 original size:2 final size:2
Alignment explanation
Indices: 5702812--5702853 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
5702802 TACATGCAAC
5702812 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
5702854 ATGTAAGCTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5703020 original size:49 final size:49
Alignment explanation
Indices: 5702949--5703078 Score: 233
Period size: 49 Copynumber: 2.7 Consensus size: 49
5702939 AACTCTACAT
*
5702949 ATTTAATTTTGAAAAGATTTATAACTGTCTTGAATGTGTTTGTCATCAA
1 ATTTAATTTTGAAAAGACTTATAACTGTCTTGAATGTGTTTGTCATCAA
*
5702998 ATTTAATTTTGAAAAGACTTATAACTGTCTTGAATGTGTTTGTCCTCAA
1 ATTTAATTTTGAAAAGACTTATAACTGTCTTGAATGTGTTTGTCATCAA
*
5703047 ATTTAATTTTGAAAAGACTTACAACTGTCTTG
1 ATTTAATTTTGAAAAGACTTATAACTGTCTTG
5703079 TGTCACGGGA
Statistics
Matches: 78, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 78 1.00
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (49 bp):
ATTTAATTTTGAAAAGACTTATAACTGTCTTGAATGTGTTTGTCATCAA
Found at i:5703114 original size:113 final size:113
Alignment explanation
Indices: 5702976--5703304 Score: 523
Period size: 113 Copynumber: 2.9 Consensus size: 113
5702966 TTTATAACTG
* * *
5702976 TCTTGAATGTGTTTGTCATCAAATTTAATTTTGAAAAGACTTATAACTGTCTTGAATGTGTTTGT
1 TCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTAAAACTGTCTTGAATGTGTTTGT
5703041 CCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTTGTGTCACGGGA
66 CCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTTGTGTCACGGGA
* * * * * *
5703089 TCTTGAATGTGTTTATCCTGAAATTTAATTTTGAAAAGACTTACAATTTTCTTAAATGTGGTTGT
1 TCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTAAAACTGTCTTGAATGTGTTTGT
* *
5703154 TCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTTGTGTCACGGGG
66 CCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTTGTGTCACGGGA
5703202 TCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTACAAACTGTCTTGAATGTGTTTG
1 TCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTA-AAACTGTCTTGAATGTGTTTG
* * *
5703267 TCTTGAAATTTAATTTTGAAAAGACTTACAATTGTCTT
65 TCCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTT
5703305 AAATGTGGTT
Statistics
Matches: 195, Mismatches: 20, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
113 145 0.74
114 50 0.26
ACGTcount: A:0.29, C:0.12, G:0.16, T:0.42
Consensus pattern (113 bp):
TCTTGAATGTGTTTGTCCTGAAATTTAATTTTGAAAAGACTTAAAACTGTCTTGAATGTGTTTGT
CCTCAAATTTAATTTTGAAAAGACTTACAACTGTCTTGTGTCACGGGA
Done.