Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr5
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: 39371879
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2227820 characters in sequence are not A, C, G, or T
File 14 of 103
Found at i:5385099 original size:29 final size:29
Alignment explanation
Indices: 5385067--5385137 Score: 90
Period size: 32 Copynumber: 2.3 Consensus size: 29
5385057 CATCATGATG
*
5385067 TTCAACTCA-TGTCGTGTTTTGCCACGTCA
1 TTCAACT-ATTGTCGTGTTTTGCCACATCA
5385096 TTCAACTATTTTTGTCGTGTTTTGCCACATCA
1 TTCAACTA---TTGTCGTGTTTTGCCACATCA
5385128 TTCAACTATT
1 TTCAACTATT
5385138 TATGTCTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
28 1 0.03
29 9 0.24
32 27 0.73
ACGTcount: A:0.20, C:0.24, G:0.13, T:0.44
Consensus pattern (29 bp):
TTCAACTATTGTCGTGTTTTGCCACATCA
Found at i:5385114 original size:32 final size:32
Alignment explanation
Indices: 5385075--5385143 Score: 120
Period size: 32 Copynumber: 2.2 Consensus size: 32
5385065 TGTTCAACTC
*
5385075 ATGTCGTGTTTTGCCACGTCATTCAACTATTT
1 ATGTCGTGTTTTGCCACATCATTCAACTATTT
*
5385107 TTGTCGTGTTTTGCCACATCATTCAACTATTT
1 ATGTCGTGTTTTGCCACATCATTCAACTATTT
5385139 ATGTC
1 ATGTC
5385144 TTATTTCACC
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 34 1.00
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.45
Consensus pattern (32 bp):
ATGTCGTGTTTTGCCACATCATTCAACTATTT
Found at i:5387040 original size:2 final size:2
Alignment explanation
Indices: 5387033--5387069 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
5387023 AGTTTGATTT
*
5387033 TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5387070 CTAATTTTTC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5390320 original size:20 final size:20
Alignment explanation
Indices: 5390287--5390326 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
5390277 GTTGGTAACT
*
5390287 GATGAATATCGTCGTTAATA
1 GATGAATATCGTCGGTAATA
* *
5390307 GATGAATTTTGTCGGTAATA
1 GATGAATATCGTCGGTAATA
5390327 CTATCAGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.38
Consensus pattern (20 bp):
GATGAATATCGTCGGTAATA
Found at i:5390543 original size:13 final size:13
Alignment explanation
Indices: 5390525--5390549 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5390515 TTAACCTATA
5390525 ATCCAATGTAAAG
1 ATCCAATGTAAAG
5390538 ATCCAATGTAAA
1 ATCCAATGTAAA
5390550 TACAAATCTC
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:0.48, C:0.16, G:0.12, T:0.24
Consensus pattern (13 bp):
ATCCAATGTAAAG
Found at i:5392736 original size:24 final size:24
Alignment explanation
Indices: 5392703--5392751 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
5392693 TTTAAATAAG
5392703 TTTAAATAATTCATTAATTACTAA
1 TTTAAATAATTCATTAATTACTAA
* * *
5392727 TTTAAGTAATTGATTGATTACTAA
1 TTTAAATAATTCATTAATTACTAA
5392751 T
1 T
5392752 ATATGATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.41, C:0.06, G:0.06, T:0.47
Consensus pattern (24 bp):
TTTAAATAATTCATTAATTACTAA
Found at i:5393078 original size:17 final size:17
Alignment explanation
Indices: 5393049--5393096 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
5393039 ACTCTTAATT
5393049 AATTTAACTAATTTT-A
1 AATTTAACTAATTTTCA
*
5393065 AATTTTACTAAATTTTCA
1 AATTTAACT-AATTTTCA
*
5393083 AATTTAATTAATTT
1 AATTTAACTAATTT
5393097 CTTCATTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 8 0.30
17 11 0.41
18 8 0.30
ACGTcount: A:0.42, C:0.06, G:0.00, T:0.52
Consensus pattern (17 bp):
AATTTAACTAATTTTCA
Found at i:5400853 original size:19 final size:20
Alignment explanation
Indices: 5400812--5400855 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
5400802 ATGTGTGAAA
* *
5400812 GCATACATTCAATCATCATAT
1 GCATACATT-AATAATCACAT
5400833 GCATACATT-ATAATCACAT
1 GCATACATTAATAATCACAT
5400852 GCAT
1 GCAT
5400856 GCAACCATAG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 12 0.57
21 9 0.43
ACGTcount: A:0.39, C:0.23, G:0.07, T:0.32
Consensus pattern (20 bp):
GCATACATTAATAATCACAT
Found at i:5406268 original size:18 final size:18
Alignment explanation
Indices: 5406245--5406280 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
5406235 AGCTTTTCAA
5406245 AAATAAA-AATAAATAAAT
1 AAATAAATAAT-AATAAAT
5406263 AAATAAATAATAATAAAT
1 AAATAAATAATAATAAAT
5406281 GATGCTTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (18 bp):
AAATAAATAATAATAAAT
Found at i:5406989 original size:11 final size:12
Alignment explanation
Indices: 5406965--5407019 Score: 53
Period size: 11 Copynumber: 4.8 Consensus size: 12
5406955 AAAATTTTAT
*
5406965 TAAA-AAAATCA
1 TAAAGAAAATAA
*
5406976 TAAACAAAA-AA
1 TAAAGAAAATAA
5406987 TAAATGAAAATAA
1 TAAA-GAAAATAA
*
5407000 CAAA-AAAATAA
1 TAAAGAAAATAA
5407011 TAAAGAAAA
1 TAAAGAAAA
5407020 AAATGAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 7
0.77 0.09 0.15
Matches are distributed among these distances:
11 19 0.53
12 12 0.33
13 5 0.14
ACGTcount: A:0.76, C:0.05, G:0.04, T:0.15
Consensus pattern (12 bp):
TAAAGAAAATAA
Found at i:5407656 original size:62 final size:61
Alignment explanation
Indices: 5407540--5407765 Score: 204
Period size: 62 Copynumber: 3.6 Consensus size: 61
5407530 GAGAGAAAGA
* * *
5407540 AAGGGAGACCGATCGGCTGCCAGAGAGAGAGAGAGAGAGTGAAAAAGGGAGGACCGATCGGACC
1 AAGGGAGACCGGTCGGCTACCAGAGA-A-AGAGAGAGAGTGAAAGAGGGAGGACCGATCGG-CC
** * * *
5407604 AAGGGAGACCGGTCAACTACCAGAGAAAGAGAGAGAGTGAGAGAGGGAGGACCAATTAGGCC
1 AAGGGAGACCGGTCGGCTACCAGAGAAAGAGAGAGAGTGAAAGAGGGAGGACCGA-TCGGCC
* * * * * *
5407666 AAGGGAAACCAGTCGGC-AGCCAAAGAGAGAGAGAGAGTAAAAGAGGGAGGACCGATCGGGTC
1 AAGGGAGACCGGTCGGCTA-CCAGAGAAAGAGAGAGAGTGAAAGAGGGAGGACCGATC-GGCC
* * * **
5407728 AAAGGAGATCGATCGGCGGCCAGAGAAAGA-AGGAGAGT
1 AAGGGAGACCGGTCGGCTACCAGAGAAAGAGA-GAGAGT
5407766 TAGATCTGGC
Statistics
Matches: 130, Mismatches: 27, Indels: 12
0.77 0.16 0.07
Matches are distributed among these distances:
61 3 0.02
62 101 0.78
63 4 0.03
64 22 0.17
ACGTcount: A:0.38, C:0.16, G:0.39, T:0.07
Consensus pattern (61 bp):
AAGGGAGACCGGTCGGCTACCAGAGAAAGAGAGAGAGTGAAAGAGGGAGGACCGATCGGCC
Found at i:5409305 original size:29 final size:28
Alignment explanation
Indices: 5409242--5409307 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 28
5409232 GTAAAGTATG
5409242 AAAAAATAATAATTAGAAATAAAATAAAA
1 AAAAAATAATAATTA-AAATAAAATAAAA
**
5409271 TGAAAATAATAATT-AAATAATAATAAATA
1 AAAAAATAATAATTAAAATAA-AATAAA-A
5409300 AAAAAATA
1 AAAAAATA
5409308 GACAACTGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
27 6 0.19
28 6 0.19
29 19 0.61
ACGTcount: A:0.73, C:0.00, G:0.03, T:0.24
Consensus pattern (28 bp):
AAAAAATAATAATTAAAATAAAATAAAA
Found at i:5411704 original size:16 final size:16
Alignment explanation
Indices: 5411679--5411717 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
5411669 CATGAATATT
5411679 TATTAATTAATCGATA
1 TATTAATTAATCGATA
* *
5411695 TATTATTTAATTGATA
1 TATTAATTAATCGATA
*
5411711 AATTAAT
1 TATTAAT
5411718 AATTTATTAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (16 bp):
TATTAATTAATCGATA
Found at i:5412165 original size:17 final size:17
Alignment explanation
Indices: 5412138--5412185 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
5412128 AAAAAATTTT
5412138 ATTTAATCGAGATTATTA
1 ATTT-ATCGAGATTATTA
5412156 ATTTATCGAG--TATTA
1 ATTTATCGAGATTATTA
*
5412171 ATTTATAGAGATTAT
1 ATTTATCGAGATTAT
5412186 ACTTTATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
15 14 0.52
17 9 0.33
18 4 0.15
ACGTcount: A:0.38, C:0.04, G:0.12, T:0.46
Consensus pattern (17 bp):
ATTTATCGAGATTATTA
Found at i:5423168 original size:26 final size:26
Alignment explanation
Indices: 5423139--5423203 Score: 85
Period size: 26 Copynumber: 2.5 Consensus size: 26
5423129 TCTTTTCTAA
* * *
5423139 AAATTACCATTTTGTCCCTAGGTGGC
1 AAATGACCATTTTGTCCCCAAGTGGC
*
5423165 AAATGATCATTTTGTCCCCAAGTGGC
1 AAATGACCATTTTGTCCCCAAGTGGC
*
5423191 AAATGACTATTTT
1 AAATGACCATTTT
5423204 ACCCTTGGAT
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.28, C:0.20, G:0.17, T:0.35
Consensus pattern (26 bp):
AAATGACCATTTTGTCCCCAAGTGGC
Found at i:5423432 original size:108 final size:106
Alignment explanation
Indices: 5423298--5423506 Score: 366
Period size: 108 Copynumber: 2.0 Consensus size: 106
5423288 GACGATCTTA
*
5423298 ATCTCACCTTAAAATTCCTATTTGATCTAGTTCGAGGATTAATTCAACTTTGTTGTACCTCTAGG
1 ATCTCACCTTAAAATTCCTATTTGATCTAGTTCGAGGATTAAATCAACTTTGTTGTACCTCTAGG
5423363 TACAATACCGACTTTTGTAAATTTTTCGGGACTCTCNAATCT
66 TACAATACCGACTTTTGTAAATTTTTCGGGACTCTC-AATCT
*
5423405 ATCTCACCTTAAAAATTCCCTA-TTGATCTAGTTCGAGGATTAAATCCACTTTGTTGTACCTCTA
1 ATCTCACCTT-AAAATT-CCTATTTGATCTAGTTCGAGGATTAAATCAACTTTGTTGTACCTCTA
5423469 GGTACAATACCGACTTTTGTAAATTTTTCGGGACTCTC
64 GGTACAATACCGACTTTTGTAAATTTTTCGGGACTCTC
5423507 CTAGCATGCA
Statistics
Matches: 98, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
107 10 0.10
108 84 0.86
109 4 0.04
ACGTcount: A:0.26, C:0.22, G:0.13, T:0.38
Consensus pattern (106 bp):
ATCTCACCTTAAAATTCCTATTTGATCTAGTTCGAGGATTAAATCAACTTTGTTGTACCTCTAGG
TACAATACCGACTTTTGTAAATTTTTCGGGACTCTCAATCT
Found at i:5431644 original size:14 final size:14
Alignment explanation
Indices: 5431620--5431653 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
5431610 TTTTAGATTA
*
5431620 AATTTTGGTTAATT
1 AATTTTAGTTAATT
*
5431634 AGTTTTAGTTAATT
1 AATTTTAGTTAATT
5431648 AATTTT
1 AATTTT
5431654 GATTATTTGG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.29, C:0.00, G:0.12, T:0.59
Consensus pattern (14 bp):
AATTTTAGTTAATT
Found at i:5432281 original size:19 final size:19
Alignment explanation
Indices: 5432254--5432291 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
5432244 CCATATGACT
5432254 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
*
5432273 TATTTGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
5432292 GTTTAGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.45
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:5438532 original size:40 final size:40
Alignment explanation
Indices: 5438385--5438587 Score: 212
Period size: 40 Copynumber: 5.0 Consensus size: 40
5438375 TGTTTAACTA
*
5438385 GTTGTTTGGATAATTAT-TTTAGTTATTTAAGTTTATTTTGTT
1 GTTGTTTGGATATTTATGTTTAGTTATTTAAGTTTA---TGTT
* * *
5438427 GTTGTTTGGATATATGTGTTTGGTTATTTAAGTTTATGTT
1 GTTGTTTGGATATTTATGTTTAGTTATTTAAGTTTATGTT
* * *
5438467 ATTTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTATGTT
1 -GTTGTTTGGATATTTATGTTTAGTTATTTAAGTTTATGTT
* * * *
5438508 GTTATTTGGATATTTATGTATAGTTATTTAAGTTTATATC
1 GTTGTTTGGATATTTATGTTTAGTTATTTAAGTTTATGTT
* * * *
5438548 ATTGTATGGATATTTGT-TGTTAGTTATTTAACTTTATGTT
1 GTTGTTTGGATATTTATGT-TTAGTTATTTAAGTTTATGTT
5438588 TAAAATCTTT
Statistics
Matches: 135, Mismatches: 23, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
39 1 0.01
40 67 0.50
41 36 0.27
42 14 0.10
43 17 0.13
ACGTcount: A:0.21, C:0.01, G:0.19, T:0.59
Consensus pattern (40 bp):
GTTGTTTGGATATTTATGTTTAGTTATTTAAGTTTATGTT
Found at i:5438536 original size:22 final size:21
Alignment explanation
Indices: 5438383--5438536 Score: 65
Period size: 21 Copynumber: 7.4 Consensus size: 21
5438373 GTTGTTTAAC
* * *
5438383 TAGTTGTTTGGATAATTATTT
1 TAGTTATTTGGATATTTATGT
**
5438404 TAGTTATTTAAGTTTATTT-TGT
1 TAGTTATTT--GGATATTTATGT
* * *
5438426 T-GTTGTTTGGATATATGTGTT
1 TAGTTATTTGGATATTTATG-T
*
5438447 TGGTTATTT--A-AGTTTATGT
1 TAGTTATTTGGATA-TTTATGT
* * * *
5438466 TATTTGTTTGGATCTTTGTGTT
1 TAGTTATTTGGATATTTATG-T
5438488 TAGTTATTT--A-AGTTTATGT
1 TAGTTATTTGGATA-TTTATGT
5438507 T-GTTATTTGGATATTTATGT
1 TAGTTATTTGGATATTTATGT
5438527 ATAGTTATTT
1 -TAGTTATTT
5438537 AAGTTTATAT
Statistics
Matches: 96, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
18 7 0.07
19 15 0.16
20 21 0.22
21 24 0.25
22 24 0.25
23 5 0.05
ACGTcount: A:0.20, C:0.01, G:0.19, T:0.60
Consensus pattern (21 bp):
TAGTTATTTGGATATTTATGT
Found at i:5438537 original size:81 final size:79
Alignment explanation
Indices: 5438386--5438587 Score: 233
Period size: 81 Copynumber: 2.5 Consensus size: 79
5438376 GTTTAACTAG
* * * * * * *
5438386 TTGTTTGGATAATTATTTTAGTTATTTAAGTTTATTTTGTTGTTGTTTGGATATATGTGTTTGGT
1 TTGTATGGATATTTGTTTTAGTTATTTAAGTTTA---TGTTGTTATTTGGATATATATGTATAGT
* *
5438451 TATTTAAGTTTATGTTA
63 TATTTAAGTTTATATCA
* * *
5438468 TTTGTTTGGATCTTTGTGTTTAGTTATTTAAGTTTATGTTGTTATTTGGATATTTATGTATAGTT
1 -TTGTATGGATATTTGT-TTTAGTTATTTAAGTTTATGTTGTTATTTGGATATATATGTATAGTT
5438533 ATTTAAGTTTATATCA
64 ATTTAAGTTTATATCA
*
5438549 TTGTATGGATATTTGTTGTTAGTTATTTAACTTTATGTT
1 TTGTATGGATATTTGTT-TTAGTTATTTAAGTTTATGTT
5438588 TAAAATCTTT
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
79 1 0.01
80 34 0.33
81 38 0.37
83 13 0.12
84 18 0.17
ACGTcount: A:0.21, C:0.01, G:0.18, T:0.59
Consensus pattern (79 bp):
TTGTATGGATATTTGTTTTAGTTATTTAAGTTTATGTTGTTATTTGGATATATATGTATAGTTAT
TTAAGTTTATATCA
Found at i:5443374 original size:19 final size:16
Alignment explanation
Indices: 5443339--5443415 Score: 63
Period size: 16 Copynumber: 4.9 Consensus size: 16
5443329 ATTATAAAAA
5443339 TTATTTTAAAATATTT
1 TTATTTTAAAATATTT
* *
5443355 TTATCTTT-AAAGATTA
1 TTAT-TTTAAAATATTT
*
5443371 TT-TTTAAAAATATTTT
1 TTATTTTAAAATA-TTT
*
5443387 TTATCTTTAAAA-ATTA
1 TTAT-TTTAAAATATTT
5443403 TT-TTTTAAAATAT
1 TTATTTTAAAATAT
5443416 CCCATAATAA
Statistics
Matches: 48, Mismatches: 7, Indels: 13
0.71 0.10 0.19
Matches are distributed among these distances:
14 9 0.19
15 8 0.17
16 20 0.42
17 5 0.10
18 6 0.12
ACGTcount: A:0.39, C:0.03, G:0.01, T:0.57
Consensus pattern (16 bp):
TTATTTTAAAATATTT
Found at i:5443393 original size:32 final size:31
Alignment explanation
Indices: 5443333--5443415 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 31
5443323 ATTAAAATTA
5443333 TAAAAATTA-TTTTAAAATA-TTTTTATCTT
1 TAAAAATTATTTTTAAAATATTTTTTATCTT
*
5443362 TAAAGATTATTTTTAAAAATATTTTTTATCTT
1 TAAAAATTATTTTT-AAAATATTTTTTATCTT
5443394 TAAAAATTATTTTTTAAAATAT
1 TAAAAATTA-TTTTTAAAATAT
5443416 CCCATAATAA
Statistics
Matches: 48, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
29 8 0.17
30 4 0.08
31 6 0.12
32 25 0.52
33 5 0.10
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (31 bp):
TAAAAATTATTTTTAAAATATTTTTTATCTT
Found at i:5443404 original size:20 final size:19
Alignment explanation
Indices: 5443368--5443409 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
5443358 TCTTTAAAGA
*
5443368 TTATTTTTAAAAATATTTT
1 TTATCTTTAAAAATATTTT
5443387 TTATCTTTAAAAATTATTTT
1 TTATCTTTAAAAA-TATTTT
5443407 TTA
1 TTA
5443410 AAATATCCCA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTATCTTTAAAAATATTTT
Found at i:5450600 original size:35 final size:35
Alignment explanation
Indices: 5450561--5450627 Score: 116
Period size: 35 Copynumber: 1.9 Consensus size: 35
5450551 TATTTTTTTT
*
5450561 TTTTTGTTTTGAAATGTGAAAGGATTTTATTGTGA
1 TTTTTGTTTTGAAAAGTGAAAGGATTTTATTGTGA
*
5450596 TTTTTTTTTTGAAAAGTGAAAGGATTTTATTG
1 TTTTTGTTTTGAAAAGTGAAAGGATTTTATTG
5450628 ATCACAAGGA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 30 1.00
ACGTcount: A:0.27, C:0.00, G:0.21, T:0.52
Consensus pattern (35 bp):
TTTTTGTTTTGAAAAGTGAAAGGATTTTATTGTGA
Found at i:5459406 original size:22 final size:20
Alignment explanation
Indices: 5459359--5459406 Score: 60
Period size: 20 Copynumber: 2.3 Consensus size: 20
5459349 AGGGAATTTA
*
5459359 TAAAACTATGCAATTTCCTT
1 TAAAACAATGCAATTTCCTT
*
5459379 TGAAACAATGCAATTTTCACTT
1 TAAAACAATGCAA-TTTC-CTT
5459401 TAAAAC
1 TAAAAC
5459407 CAAATCCATG
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 11 0.48
21 4 0.17
22 8 0.35
ACGTcount: A:0.40, C:0.19, G:0.06, T:0.35
Consensus pattern (20 bp):
TAAAACAATGCAATTTCCTT
Found at i:5460040 original size:22 final size:22
Alignment explanation
Indices: 5460015--5460065 Score: 59
Period size: 22 Copynumber: 2.3 Consensus size: 22
5460005 TATTTTCAAA
*
5460015 ATGAAAAACTATGTCTCTTC-AT
1 ATGAAAAACTATGTCT-TGCTAT
**
5460037 ATGAAAAGTTATGTCTTGCTAT
1 ATGAAAAACTATGTCTTGCTAT
5460059 ATGAAAA
1 ATGAAAA
5460066 GTTATGACTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 2 0.08
22 23 0.92
ACGTcount: A:0.39, C:0.12, G:0.14, T:0.35
Consensus pattern (22 bp):
ATGAAAAACTATGTCTTGCTAT
Found at i:5463698 original size:2 final size:2
Alignment explanation
Indices: 5463691--5463729 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5463681 AACATTATTN
5463691 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5463730 GGAAAAGAAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5474038 original size:89 final size:91
Alignment explanation
Indices: 5473827--5474074 Score: 265
Period size: 96 Copynumber: 2.7 Consensus size: 91
5473817 ATACAATTCG
* * *
5473827 TATTCTCATAAT-AGTGATATAAATTAATATTTTAAATATATAATATATAAAATATTTTTAAAAA
1 TATTCTCATAATGATTGGTAT-GATTAATATTTTAAATATATAATATATAAAATA-TTTTAAAAA
*
5473891 TTTTAAAATAAATATTTTNGAATTAATGT
64 TTTTAAAATAAATATTTT-GAATTAATGC
* *
5473920 TATTTTTCA-AAAGAATTTGGTATGAATTAATATTTTAAATATATAATATATAAAATATTTTAAA
1 TA-TTCTCATAATG-A-TTGGTATG-ATTAATATTTTAAATATATAATATATAAAATATTTTAAA
* **
5473984 AATTTTGAAATTAAATATTTT-CCTT-AT-C
62 AATTTT-AAAATAAATATTTTGAATTAATGC
* * *
5474012 TATTCTCATAATGA-TGGTATCGATTAATGTTTTAAATATATAATACATAAAATATTTGAAAAA
1 TATTCTCATAATGATTGGTAT-GATTAATATTTTAAATATATAATATATAAAATATTTTAAAAA
5474075 AAAATTAAGC
Statistics
Matches: 133, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
89 44 0.33
90 1 0.01
91 6 0.05
92 5 0.04
93 6 0.05
94 7 0.05
95 14 0.11
96 50 0.38
ACGTcount: A:0.45, C:0.04, G:0.06, T:0.44
Consensus pattern (91 bp):
TATTCTCATAATGATTGGTATGATTAATATTTTAAATATATAATATATAAAATATTTTAAAAATT
TTAAAATAAATATTTTGAATTAATGC
Found at i:5480619 original size:23 final size:23
Alignment explanation
Indices: 5480589--5480640 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
5480579 GTTTAACTTA
5480589 GCGTGACTGATTTCTAGGTTATT
1 GCGTGACTGATTTCTAGGTTATT
*
5480612 GCGTGACTGGTTTCTAGGTTATT
1 GCGTGACTGATTTCTAGGTTATT
5480635 GCGTGA
1 GCGTGA
5480641 ATATTGTTCA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.15, C:0.13, G:0.31, T:0.40
Consensus pattern (23 bp):
GCGTGACTGATTTCTAGGTTATT
Found at i:5484305 original size:26 final size:26
Alignment explanation
Indices: 5484275--5484326 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
5484265 AGCATTATTC
*
5484275 TGTATCATTTTCATATTAGTCTTTGT
1 TGTATCATTTACATATTAGTCTTTGT
*
5484301 TGTATCATTTACATATTATTCTTTGT
1 TGTATCATTTACATATTAGTCTTTGT
5484327 ATTCATTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.21, C:0.12, G:0.10, T:0.58
Consensus pattern (26 bp):
TGTATCATTTACATATTAGTCTTTGT
Found at i:5484653 original size:23 final size:23
Alignment explanation
Indices: 5484600--5484656 Score: 60
Period size: 23 Copynumber: 2.5 Consensus size: 23
5484590 GAGTATTTGT
*
5484600 TATGGAGTCACGTGAGTACTAAA
1 TATGGAATCACGTGAGTACTAAA
* * * * *
5484623 TTTTGAATCACGTTAGTAGTTAA
1 TATGGAATCACGTGAGTACTAAA
5484646 TATGGAATCAC
1 TATGGAATCAC
5484657 TTCACTAATC
Statistics
Matches: 26, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
23 26 1.00
ACGTcount: A:0.33, C:0.12, G:0.21, T:0.33
Consensus pattern (23 bp):
TATGGAATCACGTGAGTACTAAA
Found at i:5484953 original size:23 final size:22
Alignment explanation
Indices: 5484926--5485001 Score: 55
Period size: 23 Copynumber: 3.3 Consensus size: 22
5484916 GAGTAGAAAA
5484926 ATGGAGTCACGTGACTAGCTATT
1 ATGGAGTCACGTGACTAG-TATT
* ** * *
5484949 ATGGAATTGCGTTACTA-TTTGAT
1 ATGGAGTCACGTGACTAGTAT--T
*
5484972 ATGGAGTCACGTGAATAGTATAT
1 ATGGAGTCACGTGACTAGTAT-T
5484995 ATGGAGT
1 ATGGAGT
5485002 GATGTTACGA
Statistics
Matches: 39, Mismatches: 11, Indels: 6
0.70 0.20 0.11
Matches are distributed among these distances:
21 2 0.05
23 35 0.90
24 2 0.05
ACGTcount: A:0.29, C:0.11, G:0.26, T:0.34
Consensus pattern (22 bp):
ATGGAGTCACGTGACTAGTATT
Found at i:5486623 original size:216 final size:216
Alignment explanation
Indices: 5486249--5486652 Score: 718
Period size: 216 Copynumber: 1.9 Consensus size: 216
5486239 GATTGATGTT
*
5486249 GTTTTTCACTTTGAGTGCTACCCAAACCATTTGGTGTATCCTAGCCAATTGAACTTGCTGGTTGA
1 GTTTTTCACTTTGAGTGCTACCCAAACCATTTGGTGTATCCTAGCCAATTGAACTTGCTAGTTGA
5486314 TTTGACTCATCAAGAGAGCCCCAACCTTCATAACATTCTGGTGACTTTTGTTGTTCCCAACCAGT
66 TTTGACTCATCAAGAGAGCCCCAACCTTCATAACATTCTGGTGACTTTTGTTGTTCCCAACCAGT
* * *
5486379 ATATTTGGAAGAATTGTCCAAGGTTTTCGTAGGAATGACATCTTCTGTTCCCTAACCAGACCGTG
131 AGATTTGGAAGAATCGTCCAAGGTTTTCGTAGGAATGACATCTTCTGTTCCCCAACCAGACCGTG
5486444 GCAGTGCATCACTAGCATAAG
196 GCAGTGCATCACTAGCATAAG
*
5486465 GTTTTTCACTTTGAGTGCTACCCAAACCATTTGGTGTATCCTAGCCATTTGAACTTGCTAGTTGA
1 GTTTTTCACTTTGAGTGCTACCCAAACCATTTGGTGTATCCTAGCCAATTGAACTTGCTAGTTGA
* * * *
5486530 TTTGACTCATTAAGAGAGCCTCAACCTTCATAACATTCTGGTGACTTTTGTTGTTTCCAGCCAGT
66 TTTGACTCATCAAGAGAGCCCCAACCTTCATAACATTCTGGTGACTTTTGTTGTTCCCAACCAGT
*
5486595 AGATTTGGATGAATCGTCCAAGGTTTTCGTAGGAATGACATCTTCTGTTCCCCAACCA
131 AGATTTGGAAGAATCGTCCAAGGTTTTCGTAGGAATGACATCTTCTGTTCCCCAACCA
5486653 AACTGTGAAA
Statistics
Matches: 178, Mismatches: 10, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
216 178 1.00
ACGTcount: A:0.24, C:0.23, G:0.19, T:0.34
Consensus pattern (216 bp):
GTTTTTCACTTTGAGTGCTACCCAAACCATTTGGTGTATCCTAGCCAATTGAACTTGCTAGTTGA
TTTGACTCATCAAGAGAGCCCCAACCTTCATAACATTCTGGTGACTTTTGTTGTTCCCAACCAGT
AGATTTGGAAGAATCGTCCAAGGTTTTCGTAGGAATGACATCTTCTGTTCCCCAACCAGACCGTG
GCAGTGCATCACTAGCATAAG
Found at i:5487507 original size:15 final size:15
Alignment explanation
Indices: 5487487--5487517 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5487477 ATGCTCAACA
*
5487487 AATATTTAGTCACGT
1 AATATTCAGTCACGT
5487502 AATATTCAGTCACGT
1 AATATTCAGTCACGT
5487517 A
1 A
5487518 TTGCCTGTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (15 bp):
AATATTCAGTCACGT
Found at i:5487608 original size:15 final size:15
Alignment explanation
Indices: 5487590--5487622 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
5487580 ATGCTCAACA
5487590 AATATTCAGTCAAGT
1 AATATTCAGTCAAGT
*
5487605 AATATTCAGTCACGT
1 AATATTCAGTCAAGT
5487620 AAT
1 AAT
5487623 GCCTGTCACG
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:0.39, C:0.15, G:0.12, T:0.33
Consensus pattern (15 bp):
AATATTCAGTCAAGT
Found at i:5487633 original size:103 final size:103
Alignment explanation
Indices: 5487474--5487728 Score: 447
Period size: 103 Copynumber: 2.5 Consensus size: 103
5487464 AACAGGTCAT
*
5487474 GCAATGCTCAACAAATATTTAGTCACGTAATATTCAGTCACGTATTGCCTGTCACGCAACGCTCA
1 GCAATGCTCAACAAATATTTAGTCACGTAATATTCAGTCACGTAATGCCTGTCACGCAACGCTCA
5487539 ACAAATATTCAATCACGTAATGCCTATAAAGAACTCAC
66 ACAAATATTCAATCACGTAATGCCTATAAAGAACTCAC
* * *
5487577 GTAATGCTCAACAAATATTCAGTCAAGTAATATTCAGTCACGTAATGCCTGTCACGCAACGCTCA
1 GCAATGCTCAACAAATATTTAGTCACGTAATATTCAGTCACGTAATGCCTGTCACGCAACGCTCA
*
5487642 ACAAATATTCATTCACGTAATGCCTATAAAGAACTCAC
66 ACAAATATTCAATCACGTAATGCCTATAAAGAACTCAC
* *
5487680 GCAATGCTCAACAAATATTTAGTCACGTAATATTCAGGCACCTAATGCC
1 GCAATGCTCAACAAATATTTAGTCACGTAATATTCAGTCACGTAATGCC
5487729 AAATAAACAG
Statistics
Matches: 142, Mismatches: 10, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
103 142 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.26
Consensus pattern (103 bp):
GCAATGCTCAACAAATATTTAGTCACGTAATATTCAGTCACGTAATGCCTGTCACGCAACGCTCA
ACAAATATTCAATCACGTAATGCCTATAAAGAACTCAC
Found at i:5500636 original size:6 final size:6
Alignment explanation
Indices: 5500627--5500658 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
5500617 GGGGATGGGA
5500627 GTCGGG GTCGGG GTCGGG GTCGGG GTCGGG GT
1 GTCGGG GTCGGG GTCGGG GTCGGG GTCGGG GT
5500659 GGCGGAAGGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.00, C:0.16, G:0.66, T:0.19
Consensus pattern (6 bp):
GTCGGG
Found at i:5501927 original size:146 final size:146
Alignment explanation
Indices: 5501650--5501960 Score: 552
Period size: 146 Copynumber: 2.1 Consensus size: 146
5501640 CTAGTATGGC
* *
5501650 TATGCTT-TAACCCTGCCAATGGGGGTTAAATGTTGGCCATGTCGACATGTATTCCGTGATTAGA
1 TATGCTTCTGACCCTGCCAATGGGGGTTAAATGTTGGCCATGTCGACATGTATTCCATGATTAGA
* ** *
5501714 GATCGATCTCCCAACCGCACTACTGGTTACAGAATAGTAGTATTTGTGATATCTGTTCAGTGCAG
66 GATCGATCTCCCAACCGCACCACCAGTTACAGAATAGTAGTATTTGTGATATCTGTTCAGTGAAG
5501779 CCAATGGTTGCTTTGA
131 CCAATGGTTGCTTTGA
5501795 TATGCTTCTGACCCTGCCAATGGGGGTTAAATGTTGGCCATGTCGACATGTATTCCATGATTAGA
1 TATGCTTCTGACCCTGCCAATGGGGGTTAAATGTTGGCCATGTCGACATGTATTCCATGATTAGA
5501860 GATCGATCTCCCAACCGCACCACCAGTTACAGAATAGTAGTATTTGTGATATCTGTTCAGTGAAG
66 GATCGATCTCCCAACCGCACCACCAGTTACAGAATAGTAGTATTTGTGATATCTGTTCAGTGAAG
5501925 CCAATGGTTGCTTTGA
131 CCAATGGTTGCTTTGA
5501941 TATGCTTCTGACCCGTGCCA
1 TATGCTTCTGACCC-TGCCA
5501961 CCTGGGTTAA
Statistics
Matches: 158, Mismatches: 6, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
145 7 0.04
146 146 0.92
147 5 0.03
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.32
Consensus pattern (146 bp):
TATGCTTCTGACCCTGCCAATGGGGGTTAAATGTTGGCCATGTCGACATGTATTCCATGATTAGA
GATCGATCTCCCAACCGCACCACCAGTTACAGAATAGTAGTATTTGTGATATCTGTTCAGTGAAG
CCAATGGTTGCTTTGA
Found at i:5503474 original size:168 final size:169
Alignment explanation
Indices: 5503282--5503592 Score: 400
Period size: 170 Copynumber: 1.8 Consensus size: 169
5503272 ACCTTAAGTA
* *
5503282 GTTTTATAACTTTATAAATAATTTTAAATT-ACATTTTTTT-TTT-T-AGGTAAAAACATATCAT
1 GTTTTATAACCTTATAAATAATTTTAAATTGA-ATTTTTTTATTTCTCA--TAAAAACATACCAT
* * * *
5503343 AATTTATTGTTTGCAATCTGAAACGTGAAG-TCAAAGGCATCCATTGACAAGAAAAGTCTACTTA
63 AATTTATTGTTTGCAATCGGAAACATGAAGCT-AAAGCCATCCATTGACAAGAAAAGTCCACTTA
*
5503407 -TAGTCATTCATGCCTTCAAGAGACTCGCTCCCCACTTCAATTG
127 CT-GTCACTCATGCCTTCAAGAGACTCGCTCCCCACTTCAATTG
* *
5503450 GTTTTATAACCTTATAAGTAATTTTAAATTGAATTTTTTTCATTTCTCATTAAAACATACCATAA
1 GTTTTATAACCTTATAAATAATTTTAAATTGAATTTTTTT-ATTTCTCATAAAAACATACCATAA
* * * * *
5503515 TTTGTTGTTTGTACTGGGAAACATGAAGCTAAAGCCATCCATTGACAAGAAAAGTCCATTTACTG
65 TTTATTGTTTGCAATCGGAAACATGAAGCTAAAGCCATCCATTGACAAGAAAAGTCCACTTACTG
5503580 TCACTCATGCCTT
130 TCACTCATGCCTT
5503593 TGAACGTCTA
Statistics
Matches: 122, Mismatches: 14, Indels: 12
0.82 0.09 0.08
Matches are distributed among these distances:
168 36 0.30
169 1 0.01
170 81 0.66
171 3 0.02
172 1 0.01
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (169 bp):
GTTTTATAACCTTATAAATAATTTTAAATTGAATTTTTTTATTTCTCATAAAAACATACCATAAT
TTATTGTTTGCAATCGGAAACATGAAGCTAAAGCCATCCATTGACAAGAAAAGTCCACTTACTGT
CACTCATGCCTTCAAGAGACTCGCTCCCCACTTCAATTG
Found at i:5503624 original size:170 final size:167
Alignment explanation
Indices: 5503448--5503764 Score: 388
Period size: 169 Copynumber: 1.9 Consensus size: 167
5503438 CCACTTCAAT
*
5503448 TGGTTTTATAACCTTATAAGTA-ATTTTAAATTGAATTTTTTTCATTTCTCA-TTAAAACATACC
1 TGGTTTTATAACCTTAT-AG-ACATTTT-AATTGAATTTTTTTCATTT-T-AGTTAAAACAGACC
* ** * *
5503511 ATAATTTGTTGTTTGTACTGGGAAACATGAAGCTAAAGCCATCCATTGACAAGAAAAGTCCATTT
61 ATAATTTGATGTTTACACTGGGAAACATGAAACGAAAGCCATCCATTGACAAGAAAAGTCCATTT
*
5503576 ACT-GTCACTCATGCCTTTGAACGTCTAGTTATTTACTTTAAA
126 -CTAGTAACTCATGCCTTTGAACGTCTAGTTATTTACTTTAAA
* * * * * *
5503618 TGGTTTTATAATCTTATAGACGATTTTAATTTATTTTTTTTTATTTTAGGTTAAAGCAGATCATA
1 TGGTTTTATAACCTTATAGAC-ATTTTAATTGAATTTTTTTCATTTTA-GTTAAAACAGACCATA
* * * *
5503683 ATTTGATGTTTACATTGGGAAACGTGAAACGAAAGTCATCCATTGACAAGAAAAGTCCATTTGTA
64 ATTTGATGTTTACACTGGGAAACATGAAACGAAAGCCATCCATTGACAAGAAAAGTCCATTTCTA
5503748 GTAACTCATGCCTTTGA
129 GTAACTCATGCCTTTGA
5503765 GAGCCTTAAT
Statistics
Matches: 125, Mismatches: 17, Indels: 11
0.82 0.11 0.07
Matches are distributed among these distances:
167 1 0.01
168 3 0.02
169 100 0.80
170 21 0.17
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.40
Consensus pattern (167 bp):
TGGTTTTATAACCTTATAGACATTTTAATTGAATTTTTTTCATTTTAGTTAAAACAGACCATAAT
TTGATGTTTACACTGGGAAACATGAAACGAAAGCCATCCATTGACAAGAAAAGTCCATTTCTAGT
AACTCATGCCTTTGAACGTCTAGTTATTTACTTTAAA
Found at i:5504732 original size:43 final size:43
Alignment explanation
Indices: 5504670--5504780 Score: 152
Period size: 43 Copynumber: 2.6 Consensus size: 43
5504660 ACTGACTTGA
* * *
5504670 CTATGTGTGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGG
1 CTATGTGCGAGTAGGGAGTGCGCATAA-CCCAGTGATGACCCAG
* *
5504713 TTATGTGCGAGTAGAGAGTGCGCATAACCCAGTGATGACCCAG
1 CTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCAG
*
5504756 CCATGTGCGAGTAGGGAGTGCGCAT
1 CTATGTGCGAGTAGGGAGTGCGCAT
5504781 GAGCTGGTGA
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
42 4 0.07
43 55 0.93
ACGTcount: A:0.24, C:0.20, G:0.36, T:0.20
Consensus pattern (43 bp):
CTATGTGCGAGTAGGGAGTGCGCATAACCCAGTGATGACCCAG
Found at i:5504791 original size:43 final size:43
Alignment explanation
Indices: 5504672--5504793 Score: 147
Period size: 43 Copynumber: 2.8 Consensus size: 43
5504662 TGACTTGACT
* * **
5504672 ATGTGTGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
* * *
5504715 ATGTGCGAGTAGAGAGTGCGCATAACCCAGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
5504758 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
5504794 TGATGATAGG
Statistics
Matches: 66, Mismatches: 12, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
42 1 0.02
43 65 0.98
ACGTcount: A:0.25, C:0.18, G:0.38, T:0.20
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:5507406 original size:69 final size:70
Alignment explanation
Indices: 5507273--5507414 Score: 207
Period size: 70 Copynumber: 2.0 Consensus size: 70
5507263 ATTATATTTC
*
5507273 TTTCAATACAAATTTATTTATTGTATATATTTTTTAAAGCTTTCAAAATAGTATTTTATTTAATA
1 TTTCAATACAAATTTATTTATTATATATATTTTTTAAAGCTTTCAAAATAGTATTTTATTTAATA
5507338 ATTAG
66 ATTAG
* * * * *
5507343 TTTCAATGCAATTTTATTTATTATTTATA-TTTTTAATGGCTTTCAAAATA-TTTTTTATTTAAT
1 TTTCAATACAAATTTATTTATTATATATATTTTTTAA-AGCTTTCAAAATAGTATTTTATTTAAT
5507406 AATTAG
65 AATTAG
5507412 TTT
1 TTT
5507415 TATTTTTCAA
Statistics
Matches: 65, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
69 28 0.43
70 37 0.57
ACGTcount: A:0.34, C:0.06, G:0.06, T:0.55
Consensus pattern (70 bp):
TTTCAATACAAATTTATTTATTATATATATTTTTTAAAGCTTTCAAAATAGTATTTTATTTAATA
ATTAG
Found at i:5507653 original size:41 final size:41
Alignment explanation
Indices: 5507575--5507657 Score: 105
Period size: 41 Copynumber: 2.0 Consensus size: 41
5507565 AAATCTAAAT
* *
5507575 CTATCATAACATATTATATCTTAACAGTCTAACCTAATAAC
1 CTATCATAACATATTATATCTCAAAAGTCTAACCTAATAAC
* * *
5507616 CTATCATAATATATTATATCTCAATAATTC-AATCTAATAAC
1 CTATCATAACATATTATATCTCAA-AAGTCTAACCTAATAAC
5507657 C
1 C
5507658 CAATATATTA
Statistics
Matches: 36, Mismatches: 5, Indels: 2
0.84 0.12 0.05
Matches are distributed among these distances:
41 33 0.92
42 3 0.08
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.36
Consensus pattern (41 bp):
CTATCATAACATATTATATCTCAAAAGTCTAACCTAATAAC
Found at i:5509875 original size:27 final size:27
Alignment explanation
Indices: 5509844--5509908 Score: 71
Period size: 27 Copynumber: 2.4 Consensus size: 27
5509834 AATAGGAACG
*
5509844 AGAAAAAGAATGAAAAGTGAAAA-AGAA
1 AGAAAAAGAATGAAAAATGAAAAGA-AA
*
5509871 AGAAAGAAGGA-GAAAAATGAAAAGAAA
1 AGAAA-AAGAATGAAAAATGAAAAGAAA
*
5509898 AAAAAAAGAAT
1 AGAAAAAGAAT
5509909 AATGATAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
26 4 0.13
27 22 0.71
28 5 0.16
ACGTcount: A:0.72, C:0.00, G:0.22, T:0.06
Consensus pattern (27 bp):
AGAAAAAGAATGAAAAATGAAAAGAAA
Found at i:5518338 original size:10 final size:10
Alignment explanation
Indices: 5518323--5518366 Score: 79
Period size: 10 Copynumber: 4.4 Consensus size: 10
5518313 TTGAGTAATT
5518323 ATGATGAATA
1 ATGATGAATA
5518333 ATGATGAATA
1 ATGATGAATA
5518343 ATGATGAATA
1 ATGATGAATA
*
5518353 ATGATGAATT
1 ATGATGAATA
5518363 ATGA
1 ATGA
5518367 GCCTAGAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
10 33 1.00
ACGTcount: A:0.48, C:0.00, G:0.20, T:0.32
Consensus pattern (10 bp):
ATGATGAATA
Found at i:5527373 original size:14 final size:15
Alignment explanation
Indices: 5527354--5527383 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
5527344 TTTGGAAATT
5527354 TTTAATTT-TATTTG
1 TTTAATTTCTATTTG
5527368 TTTAATTTCTATTTG
1 TTTAATTTCTATTTG
5527383 T
1 T
5527384 AATTCTAGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (15 bp):
TTTAATTTCTATTTG
Found at i:5533195 original size:180 final size:184
Alignment explanation
Indices: 5532902--5533264 Score: 484
Period size: 180 Copynumber: 2.0 Consensus size: 184
5532892 TTTTAAGCCA
* *
5532902 ATTTTTTTCTCTCCCAAATTTTGTCAAATTTTTCCCTTTTTTTTTTCCTAATCACAATTTGGAGG
1 ATTTTTTTCTCT-CCAAATTTTGTCAAATTTTTCCC--TTTTTCTTCCTAATCACAATTTAGAGG
* * * **
5532967 ATAACGATTTTTTCCTCTCTCAAATTATGGAATTTTCCCTTTACTAAACCCCCTTTCTCATATTC
63 ATAACCAATTTTTCCTCTCCCAAATTATAAAATTTTCCCTTTACTAAACCCCCTTTCTCATATTC
* *
5533032 TTTTCTTTTTTCATTTTGAACATTGCATTATTGTATATAATATGTTATGGTATAACCT
128 TTTT-TTTTTTCATTTTGAACATTGCATTATTATATATAATATGTCATGGTATAACCT
* * * * *
5533090 ATTTTTTTCTCT-GAAATTTTGTCTAA-TTTTCCC-TTTTCTTCTTGATCAGAATTTAGAGGAT-
1 ATTTTTTTCTCTCCAAATTTTGTCAAATTTTTCCCTTTTTCTTCCTAATCACAATTTAGAGGATA
* *
5533151 ACCAATTTTT-CTCTCCCAAATTTTAAAATTTTCCCTTTACTAAACCCCCTTTCTCCTATTCTTT
66 ACCAATTTTTCCTCTCCCAAATTATAAAATTTTCCCTTTACTAAACCCCCTTTCTCATATTCTTT
* **
5533215 TTTTTTTCGTTTTGTTCATTGCATTATTATATATAATATGTCATGGTATA
131 TTTTTTTCATTTTGAACATTGCATTATTATATATAATATGTCATGGTATA
5533265 TTCTTTATTT
Statistics
Matches: 156, Mismatches: 19, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
179 44 0.28
180 50 0.32
181 8 0.05
182 23 0.15
185 7 0.04
186 12 0.08
188 12 0.08
ACGTcount: A:0.23, C:0.19, G:0.07, T:0.50
Consensus pattern (184 bp):
ATTTTTTTCTCTCCAAATTTTGTCAAATTTTTCCCTTTTTCTTCCTAATCACAATTTAGAGGATA
ACCAATTTTTCCTCTCCCAAATTATAAAATTTTCCCTTTACTAAACCCCCTTTCTCATATTCTTT
TTTTTTTCATTTTGAACATTGCATTATTATATATAATATGTCATGGTATAACCT
Found at i:5533454 original size:159 final size:156
Alignment explanation
Indices: 5533192--5533504 Score: 447
Period size: 159 Copynumber: 2.0 Consensus size: 156
5533182 TCCCTTTACT
*
5533192 AAACCCCCTTTCTCCTATTCTTTTTTTTTTCGTTTTGTTCATTGCATTATTATATATAATATGTC
1 AAACCCCCTTTCTCCTATTCTTTTTTTTTTCATTTTGTTCATTGCATTATTATATATAATATGTC
*
5533257 ATGGTATATTCTTTATTTTGTTAATCAAATTTTAATCATTGCTAGAGTGAGTTTCTTTAACTATT
66 ATGGTATATTCTTTATTTTGTTAATCAAATTTTAATCATTGCTAGAGTGAGTTTCTTCAACTATT
*
5533322 AATATGCATTTTTCATTATTGATCCA
131 AATATGCATTGTTCATTATTGATCCA
*
5533348 AAACCCCCTTTCTCCTATTCTTTTTTTTCATTAATCAAATTTTGATT-ATTGCATTATTGTATA-
1 AAACCCCCTTTCTCCTATTC-TTTTTTT--TT--TC--ATTTTG-TTCATTGCATTATTATATAT
* * *
5533411 AATATGTTAT-G-ATATT-TTTTTTTTGTTAATCAAATTTTGATCATTGCTAGAGTGAGTTTCTT
58 AATATGTCATGGTATATTCTTTATTTTGTTAATCAAATTTTAATCATTGCTAGAGTGAGTTTCTT
*
5533473 CAACTATTAATATGCATTGTTCATTGTTGATC
123 CAACTATTAATATGCATTGTTCATTATTGATC
5533505 ATAATTTGGA
Statistics
Matches: 141, Mismatches: 8, Indels: 13
0.87 0.05 0.08
Matches are distributed among these distances:
156 20 0.14
157 7 0.05
159 75 0.53
160 5 0.04
161 3 0.02
162 9 0.06
163 20 0.14
164 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.51
Consensus pattern (156 bp):
AAACCCCCTTTCTCCTATTCTTTTTTTTTTCATTTTGTTCATTGCATTATTATATATAATATGTC
ATGGTATATTCTTTATTTTGTTAATCAAATTTTAATCATTGCTAGAGTGAGTTTCTTCAACTATT
AATATGCATTGTTCATTATTGATCCA
Found at i:5551147 original size:16 final size:17
Alignment explanation
Indices: 5551123--5551158 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5551113 TTTTGAATAT
*
5551123 AAAATGATTAAATTT-A
1 AAAAAGATTAAATTTGA
5551139 AAAAAGATTAAATTTGA
1 AAAAAGATTAAATTTGA
5551156 AAA
1 AAA
5551159 GACTTGAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.08, T:0.31
Consensus pattern (17 bp):
AAAAAGATTAAATTTGA
Found at i:5551728 original size:22 final size:21
Alignment explanation
Indices: 5551689--5551735 Score: 60
Period size: 23 Copynumber: 2.2 Consensus size: 21
5551679 TATAGATAAT
5551689 TTTTAAATTAATTTA-TTTTA
1 TTTTAAATTAATTTATTTTTA
*
5551709 TTTTAAATATTATTTAATTTTTA
1 TTTTAAAT-TAATTT-ATTTTTA
5551732 TTTT
1 TTTT
5551736 TATTCTTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
20 8 0.35
21 5 0.22
22 1 0.04
23 9 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TTTTAAATTAATTTATTTTTA
Found at i:5553184 original size:3 final size:3
Alignment explanation
Indices: 5553176--5553201 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
5553166 TCCTTAGTAT
5553176 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
5553202 TATTTCTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:5563230 original size:19 final size:18
Alignment explanation
Indices: 5563195--5563230 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5563185 ATGTCAAGAC
*
5563195 TATGCTAAAAGTCTTAAA
1 TATGCTAAAACTCTTAAA
5563213 TATGCTAAAACCTCTTAA
1 TATGCTAAAA-CTCTTAA
5563231 TTTCCTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.42, C:0.17, G:0.08, T:0.33
Consensus pattern (18 bp):
TATGCTAAAACTCTTAAA
Found at i:5565363 original size:20 final size:20
Alignment explanation
Indices: 5565318--5565355 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
5565308 TTTTGGTCCC
5565318 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
5565338 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
5565356 AGATTTGAGG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:5565746 original size:30 final size:31
Alignment explanation
Indices: 5565712--5565770 Score: 77
Period size: 30 Copynumber: 1.9 Consensus size: 31
5565702 CCCTAGAGAG
5565712 AGAAAATCAA-AGAAAAAGTGTGA-ATTTTCA
1 AGAAAATCAAGAGAAAAAG-GTGAGATTTTCA
* *
5565742 AGAAAATTAAGTGAAAAAGGTGAGATTTT
1 AGAAAATCAAGAGAAAAAGGTGAGATTTT
5565771 TTCTATTAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 13 0.52
31 12 0.48
ACGTcount: A:0.51, C:0.03, G:0.20, T:0.25
Consensus pattern (31 bp):
AGAAAATCAAGAGAAAAAGGTGAGATTTTCA
Found at i:5566632 original size:13 final size:13
Alignment explanation
Indices: 5566614--5566638 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5566604 AGAGAAATTG
5566614 TGATTTTATAAAA
1 TGATTTTATAAAA
5566627 TGATTTTATAAA
1 TGATTTTATAAA
5566639 TTTTCTGGAA
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:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:5569046 original size:21 final size:20
Alignment explanation
Indices: 5569022--5569069 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
5569012 ATTTTACCTT
*
5569022 TTTTTCACTTGTTTCCTTGAA
1 TTTTTCACTT-TTCCCTTGAA
*
5569043 TTTTCACACTTTTCCCTTGAA
1 TTTT-TCACTTTTCCCTTGAA
5569064 TTTTTC
1 TTTTTC
5569070 CACCTAGGGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.15, C:0.23, G:0.06, T:0.56
Consensus pattern (20 bp):
TTTTTCACTTTTCCCTTGAA
Found at i:5569069 original size:22 final size:22
Alignment explanation
Indices: 5569027--5569067 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
5569017 ACCTTTTTTT
*
5569027 CACTTGTTTCCTTGAATTTTCA
1 CACTTGTTCCCTTGAATTTTCA
5569049 CACTT-TTCCCTTGAATTTT
1 CACTTGTTCCCTTGAATTTT
5569068 TCCACCTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.17, C:0.24, G:0.07, T:0.51
Consensus pattern (22 bp):
CACTTGTTCCCTTGAATTTTCA
Found at i:5569368 original size:28 final size:28
Alignment explanation
Indices: 5569332--5569396 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
5569322 GTCGGGTGGT
5569332 GTAAAATTACAATTTTGCCACTGAGGTG
1 GTAAAATTACAATTTTGCCACTGAGGTG
5569360 GTAAAATTACAATTTTGCCACTGAGGTG
1 GTAAAATTACAATTTTGCCACTGAGGTG
*
5569388 GCAAAATTA
1 GTAAAATTA
5569397 TCATTTTACC
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.35, C:0.14, G:0.20, T:0.31
Consensus pattern (28 bp):
GTAAAATTACAATTTTGCCACTGAGGTG
Found at i:5571672 original size:22 final size:23
Alignment explanation
Indices: 5571628--5571669 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
5571618 CGATACCTTC
5571628 CAAAACCTTAAAACTCAAGTTAA
1 CAAAACCTTAAAACTCAAGTTAA
*
5571651 CAAAA-CTTAGAA-TCAAGTT
1 CAAAACCTTAAAACTCAAGTT
5571670 TAATGACTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 7 0.39
22 6 0.33
23 5 0.28
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (23 bp):
CAAAACCTTAAAACTCAAGTTAA
Found at i:5575998 original size:21 final size:20
Alignment explanation
Indices: 5575974--5576021 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 20
5575964 ATTTTACCTT
5575974 TTTTTCACTTCTTTCCTTGAA
1 TTTTTCACTT-TTTCCTTGAA
*
5575995 TTTTCACACTTTTTCCTTGAA
1 TTTT-TCACTTTTTCCTTGAA
5576016 TTTTTC
1 TTTTTC
5576022 CACCTAGGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
20 1 0.04
21 18 0.75
22 5 0.21
ACGTcount: A:0.15, C:0.23, G:0.04, T:0.58
Consensus pattern (20 bp):
TTTTTCACTTTTTCCTTGAA
Found at i:5576021 original size:22 final size:22
Alignment explanation
Indices: 5575979--5576019 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
5575969 ACCTTTTTTT
5575979 CACTTCTTTCCTTGAATTTTCA
1 CACTTCTTTCCTTGAATTTTCA
5576001 CACTT-TTTCCTTGAATTTT
1 CACTTCTTTCCTTGAATTTT
5576020 TCCACCTAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 14 0.74
22 5 0.26
ACGTcount: A:0.17, C:0.24, G:0.05, T:0.54
Consensus pattern (22 bp):
CACTTCTTTCCTTGAATTTTCA
Found at i:5576852 original size:17 final size:18
Alignment explanation
Indices: 5576830--5576867 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
5576820 AGTTGTGAAG
5576830 AAAAGAA-AAA-AACAAAA
1 AAAAGAAGAAATAA-AAAA
5576847 AAAAGAAGAAATAAAAAA
1 AAAAGAAGAAATAAAAAA
5576865 AAA
1 AAA
5576868 TGAGAGAATG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.37
18 10 0.53
19 2 0.11
ACGTcount: A:0.87, C:0.03, G:0.08, T:0.03
Consensus pattern (18 bp):
AAAAGAAGAAATAAAAAA
Found at i:5577310 original size:20 final size:19
Alignment explanation
Indices: 5577283--5577325 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 19
5577273 TATGAAAATT
*
5577283 GAAAAAAATACA-AGAAAAA
1 GAAAAAAAAACATAG-AAAA
5577302 GAAAGAAAAAACATAGAAAA
1 GAAA-AAAAAACATAGAAAA
5577322 GAAA
1 GAAA
5577326 TGATGGAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 4 0.19
20 15 0.71
21 2 0.10
ACGTcount: A:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (19 bp):
GAAAAAAAAACATAGAAAA
Found at i:5578431 original size:31 final size:31
Alignment explanation
Indices: 5578393--5578454 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
5578383 TAAATGTAAA
5578393 GACCTTCTTGCTAGAGAGAATTTTTTTCATT
1 GACCTTCTTGCTAGAGAGAATTTTTTTCATT
5578424 GACCTTCTTGCTAGAGAGAATTTTTTTCATT
1 GACCTTCTTGCTAGAGAGAATTTTTTTCATT
5578455 CTTTCCTTCG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.23, C:0.16, G:0.16, T:0.45
Consensus pattern (31 bp):
GACCTTCTTGCTAGAGAGAATTTTTTTCATT
Found at i:5579686 original size:58 final size:58
Alignment explanation
Indices: 5579590--5579709 Score: 152
Period size: 58 Copynumber: 2.1 Consensus size: 58
5579580 GACATATTTA
* * ** * * * *
5579590 GAATGTGTGACACAGCTGTGACATGGCAGGGTTTAGAGTTTA-TGATACGTCATGGTGG
1 GAATGTGTGACACAGCTGTGACACGCCAGCATTCAGAG-TTAGTGACACGCCATGGAGG
5579648 GAATGTGTGACACAGCTGTGACACGCCAGCATTCAGAGTTAGTGACACGCCATGGAGG
1 GAATGTGTGACACAGCTGTGACACGCCAGCATTCAGAGTTAGTGACACGCCATGGAGG
5579706 GAAT
1 GAAT
5579710 CTATGACATG
Statistics
Matches: 53, Mismatches: 8, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
57 3 0.06
58 50 0.94
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.24
Consensus pattern (58 bp):
GAATGTGTGACACAGCTGTGACACGCCAGCATTCAGAGTTAGTGACACGCCATGGAGG
Found at i:5579740 original size:47 final size:47
Alignment explanation
Indices: 5579666--5579968 Score: 349
Period size: 47 Copynumber: 6.5 Consensus size: 47
5579656 GACACAGCTG
* *
5579666 TGACACGCCAGCATTCAGAGTTAGTGACACGCCATGGAGGGAATCTA
1 TGACACGCCAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
* ** * *
5579713 TGACATGCCAAAGTTCAGAGTTGGTGACACACCATGGAAGGAATCTA
1 TGACACGCCAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
* * *
5579760 TGACACGTCAGCGTTCAGAGTTGGTGACACACCATGGAGGGAATCTG
1 TGACACGCCAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
* * * * *
5579807 TGACACGCCAGTGTTAAGAGTTGGTGACATGCCCTCGAGGGAATCTA
1 TGACACGCCAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
* * *
5579854 TGACAC-CTCAGCGTTCAGAGTTGGTGACATGCCATGAAGGGAATCTG
1 TGACACGC-CAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
* * * * * * *
5579901 TGAGATGTCACCATTCAAAGTT-GTGACACGCCATGGAGGGAATCTG
1 TGACACGCCAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
*
5579947 TGACACGCCAACGTTCAGAGTT
1 TGACACGCCAGCGTTCAGAGTT
5579969 TGTCAGATTC
Statistics
Matches: 213, Mismatches: 41, Indels: 5
0.82 0.16 0.02
Matches are distributed among these distances:
46 39 0.18
47 174 0.82
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (47 bp):
TGACACGCCAGCGTTCAGAGTTGGTGACACGCCATGGAGGGAATCTA
Found at i:5580683 original size:31 final size:31
Alignment explanation
Indices: 5580645--5580835 Score: 250
Period size: 31 Copynumber: 6.3 Consensus size: 31
5580635 TCAGTGTTGA
*
5580645 CGTGTTACTACAGTTTACGTTATATGCATGG
1 CGTGTTACCACAGTTTACGTTATATGCATGG
* *
5580676 CGTGTTACCACATTTTACGTTACATGCATGG
1 CGTGTTACCACAGTTTACGTTATATGCATGG
5580707 CGTGTTACCACAGTTTACG-T-TAT--AT-G
1 CGTGTTACCACAGTTTACGTTATATGCATGG
* ** *
5580733 CGTGTTACCACATTTTACGTTATGCGTATGG
1 CGTGTTACCACAGTTTACGTTATATGCATGG
5580764 CGTGTTACCACAGTTTACGTTATATGCATGG
1 CGTGTTACCACAGTTTACGTTATATGCATGG
* *
5580795 TGTGTTACCAC-TTTCTACGTTATATGCATGG
1 CGTGTTACCACAGTT-TACGTTATATGCATGG
5580826 CGTGTTACCA
1 CGTGTTACCA
5580836 TAATATGGGT
Statistics
Matches: 139, Mismatches: 15, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
26 19 0.14
27 3 0.02
28 1 0.01
29 2 0.01
30 5 0.04
31 109 0.78
ACGTcount: A:0.21, C:0.20, G:0.21, T:0.38
Consensus pattern (31 bp):
CGTGTTACCACAGTTTACGTTATATGCATGG
Found at i:5580794 original size:88 final size:88
Alignment explanation
Indices: 5580645--5580821 Score: 257
Period size: 88 Copynumber: 2.0 Consensus size: 88
5580635 TCAGTGTTGA
* * *
5580645 CGTGTTACTACAGTTTACGTTATATGCATGGCGTGTTACCACATTTTACGTTACATGCATGGCGT
1 CGTGTTACCACAGTTTACGTTATACGCATGGCGTGTTACCACAGTTTACGTTACATGCATGGCGT
5580710 GTTACCACAGTT-TACGTTATATG
66 GTTACCAC-GTTCTACGTTATATG
* * * * *
5580733 CGTGTTACCACATTTTACGTTATGCGTATGGCGTGTTACCACAGTTTACGTTATATGCATGGTGT
1 CGTGTTACCACAGTTTACGTTATACGCATGGCGTGTTACCACAGTTTACGTTACATGCATGGCGT
*
5580798 GTTACCACTTTCTACGTTATATG
66 GTTACCACGTTCTACGTTATATG
5580821 C
1 C
5580822 ATGGCGTGTT
Statistics
Matches: 79, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
87 2 0.03
88 77 0.97
ACGTcount: A:0.21, C:0.20, G:0.20, T:0.38
Consensus pattern (88 bp):
CGTGTTACCACAGTTTACGTTATACGCATGGCGTGTTACCACAGTTTACGTTACATGCATGGCGT
GTTACCACGTTCTACGTTATATG
Found at i:5585661 original size:21 final size:21
Alignment explanation
Indices: 5585637--5585680 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
5585627 CATCTGACGG
*
5585637 TGCTGGTGAAGACCACGATGA
1 TGCTGATGAAGACCACGATGA
* **
5585658 TGCTGATGATGGGCACGATGA
1 TGCTGATGAAGACCACGATGA
5585679 TG
1 TG
5585681 AACCTGGTGT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.25, C:0.16, G:0.36, T:0.23
Consensus pattern (21 bp):
TGCTGATGAAGACCACGATGA
Found at i:5587401 original size:118 final size:118
Alignment explanation
Indices: 5587188--5587664 Score: 618
Period size: 118 Copynumber: 4.1 Consensus size: 118
5587178 ACAAGTAAAA
* * * *
5587188 GTGTCACGCCAAGTATCTGGTTCCATTCAACATGTCACCACAA-TTGGGGCGTGCCGTGTCACCT
1 GTGTCACGCCAAGTATCTGGTTCCACTCAACGTGTCACCACAAGATGGGGCGTGCCGTGTCACCC
* *
5587252 CACAATACATCAAGAAGTCAGCAG-GTCACCACAGAAATCTACATGCACTCAAC
66 CACAATACAGCAAGAAGTCAGC-GTGTCACCACAGAAATCTGCATGCACTCAAC
*
5587305 GTGTCACGCCAAGTATCTGGTTCCACTCAGCGTGTCACCACAAGATGGGGCGTGCCGTGTCACCC
1 GTGTCACGCCAAGTATCTGGTTCCACTCAACGTGTCACCACAAGATGGGGCGTGCCGTGTCACCC
* * * *
5587370 CACAATACAGCAATAAGTCAGCGTATTACCACAGAAATCTGCATGCACT-AAGT
66 CACAATACAGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAA-C
* * *
5587423 GTGTCACGCCAAGTATCTGGTGCCACTCAACGTGTCAACACAAGATGGGGCGTGTCGTGTCACCC
1 GTGTCACGCCAAGTATCTGGTTCCACTCAACGTGTCACCACAAGATGGGGCGTGCCGTGTCACCC
* * * * *
5587488 CACAATACTGCAATAAGTCAACGTGTCACCATAGAAATCTGCATGCCCTCAAC
66 CACAATACAGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAAC
* ** * * ** * * *
5587541 GTGTCACACCAACAATCCGGTTCCACTCAGCGTGTCATTATAAGATGGGGTGTGTCGTGTCACCC
1 GTGTCACGCCAAGTATCTGGTTCCACTCAACGTGTCACCACAAGATGGGGCGTGCCGTGTCACCC
* * * *
5587606 AACAATACTGCAAGAAGTCAGCATGTCACCACAGAAATCTGCATGCACTCAGC
66 CACAATACAGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAAC
5587659 GTGTCA
1 GTGTCA
5587665 ACTTAGCATA
Statistics
Matches: 317, Mismatches: 39, Indels: 7
0.87 0.11 0.02
Matches are distributed among these distances:
117 43 0.14
118 272 0.86
119 2 0.01
ACGTcount: A:0.29, C:0.29, G:0.21, T:0.22
Consensus pattern (118 bp):
GTGTCACGCCAAGTATCTGGTTCCACTCAACGTGTCACCACAAGATGGGGCGTGCCGTGTCACCC
CACAATACAGCAAGAAGTCAGCGTGTCACCACAGAAATCTGCATGCACTCAAC
Found at i:5591315 original size:31 final size:31
Alignment explanation
Indices: 5591280--5591385 Score: 169
Period size: 31 Copynumber: 3.4 Consensus size: 31
5591270 TATAATGTAG
*
5591280 AATGTGGTAACACGCCATGCATATAACTTAC
1 AATGTGGTAACACGCCATGCATATAACTTAA
5591311 AATGTGGTAACACGCCATGCATATAA-TGTAA
1 AATGTGGTAACACGCCATGCATATAACT-TAA
*
5591342 AATGTGGTAACACGCCATGCATATAACGTAA
1 AATGTGGTAACACGCCATGCATATAACTTAA
*
5591373 AATGTTGTAACAC
1 AATGTGGTAACAC
5591386 ACCAATGTTG
Statistics
Matches: 70, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
30 1 0.01
31 69 0.99
ACGTcount: A:0.38, C:0.19, G:0.18, T:0.25
Consensus pattern (31 bp):
AATGTGGTAACACGCCATGCATATAACTTAA
Found at i:5591366 original size:62 final size:62
Alignment explanation
Indices: 5591250--5591385 Score: 209
Period size: 62 Copynumber: 2.2 Consensus size: 62
5591240 TTTGTCAGTC
* * * * * *
5591250 ATGTTGTACCACGGCATGTATATAATGTAGAATGTGGTAACACGCCATGCATATAACTTACA
1 ATGTTGTAACACGCCATGCATATAATGTAAAATGTGGTAACACGCCATGCATATAACGTAAA
*
5591312 ATGTGGTAACACGCCATGCATATAATGTAAAATGTGGTAACACGCCATGCATATAACGTAAA
1 ATGTTGTAACACGCCATGCATATAATGTAAAATGTGGTAACACGCCATGCATATAACGTAAA
5591374 ATGTTGTAACAC
1 ATGTTGTAACAC
5591386 ACCAATGTTG
Statistics
Matches: 66, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 66 1.00
ACGTcount: A:0.36, C:0.18, G:0.19, T:0.27
Consensus pattern (62 bp):
ATGTTGTAACACGCCATGCATATAATGTAAAATGTGGTAACACGCCATGCATATAACGTAAA
Found at i:5591850 original size:63 final size:63
Alignment explanation
Indices: 5591742--5591864 Score: 165
Period size: 63 Copynumber: 2.0 Consensus size: 63
5591732 CCATAGCCCA
* *
5591742 ATGAAGATGGTGCTCAACAGAGAGTTGATAGAGCTCATACAGTTCAGAGAGCTGAGAGAGCTG
1 ATGAAGATGGTGCTCAACAGAGAGTTGACAGAGCTCAGACAGTTCAGAGAGCTGAGAGAGCTG
* * * * * * *
5591805 ATGACGATGGTGCTCAACAGAGAGTTGGCAGAGTTGAGACTGTTCAGATAGTTGAGAGAG
1 ATGAAGATGGTGCTCAACAGAGAGTTGACAGAGCTCAGACAGTTCAGAGAGCTGAGAGAG
5591865 AAAGATGATC
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
63 51 1.00
ACGTcount: A:0.32, C:0.13, G:0.33, T:0.22
Consensus pattern (63 bp):
ATGAAGATGGTGCTCAACAGAGAGTTGACAGAGCTCAGACAGTTCAGAGAGCTGAGAGAGCTG
Found at i:5592649 original size:16 final size:16
Alignment explanation
Indices: 5592618--5592658 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5592608 TATTATTCCC
5592618 TTTGTTAATT--TTTT
1 TTTGTTAATTAATTTT
5592632 TTCT-TTAATTAATTTT
1 TT-TGTTAATTAATTTT
5592648 TTTGTTAATTA
1 TTTGTTAATTA
5592659 TTTCCTTTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
14 8 0.35
15 2 0.09
16 13 0.57
ACGTcount: A:0.22, C:0.02, G:0.05, T:0.71
Consensus pattern (16 bp):
TTTGTTAATTAATTTT
Found at i:5597502 original size:29 final size:28
Alignment explanation
Indices: 5597449--5597504 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 28
5597439 TTTGATTCAA
*
5597449 AATAAAAGTATAAGAATTTGATTAAATGT
1 AATAAAAGAATAAGAATTT-ATTAAATGT
5597478 AATAAAAGAATAAGTAA-TTATTTAAAT
1 AATAAAAGAATAAG-AATTTA-TTAAAT
5597505 TTTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 1 0.04
29 21 0.88
30 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (28 bp):
AATAAAAGAATAAGAATTTATTAAATGT
Found at i:5602445 original size:38 final size:38
Alignment explanation
Indices: 5602402--5602494 Score: 91
Period size: 38 Copynumber: 2.4 Consensus size: 38
5602392 TAATATCATA
** *
5602402 TATTTTATTTTCATTTCCTA-TTATAATCTTATATATTT
1 TATTTTATTTTC-TTTAATATTTATAATATTATATATTT
* *
5602440 TATTTT-TATTTCTTTAATATTTTTTATATTATATATTT
1 TATTTTAT-TTTCTTTAATATTTATAATATTATATATTT
*
5602478 TATTTTAATTTTTTTTA
1 TATTTT-ATTTTCTTTA
5602495 CCTATATTAT
Statistics
Matches: 45, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
37 6 0.13
38 31 0.69
39 7 0.16
40 1 0.02
ACGTcount: A:0.26, C:0.05, G:0.00, T:0.69
Consensus pattern (38 bp):
TATTTTATTTTCTTTAATATTTATAATATTATATATTT
Found at i:5602484 original size:29 final size:28
Alignment explanation
Indices: 5602452--5602583 Score: 101
Period size: 30 Copynumber: 4.5 Consensus size: 28
5602442 TTTTTATTTC
5602452 TTTAATATTTTTTATATTATATATTTTAT
1 TTTAAT-TTTTTTATATTATATATTTTAT
* **
5602481 TTTAATTTTTTT-TACCTATATTATATAAAT
1 TTTAATTTTTTTATA-TTATA-TAT-TTTAT
*
5602511 TTTAATTCTTTT-TATT-T-TATTTTAT
1 TTTAATTTTTTTATATTATATATTTTAT
*
5602536 TTTAATTTCTAATTCTTATATTATACATTTTAT
1 TTTAA-TT-T--TT-TTATATTATATATTTTAT
5602569 TTTAATATTTTTTAT
1 TTTAAT-TTTTTTAT
5602584 TTTGATTATA
Statistics
Matches: 82, Mismatches: 9, Indels: 24
0.71 0.08 0.21
Matches are distributed among these distances:
25 8 0.10
26 5 0.06
27 2 0.02
28 11 0.13
29 16 0.20
30 20 0.24
31 4 0.05
32 3 0.04
33 13 0.16
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (28 bp):
TTTAATTTTTTTATATTATATATTTTAT
Found at i:5602505 original size:38 final size:38
Alignment explanation
Indices: 5602430--5602506 Score: 91
Period size: 38 Copynumber: 2.0 Consensus size: 38
5602420 TATTATAATC
* * * *
5602430 TTATATATTTTATTTTTATTTCTTTAATATTTTTTATA
1 TTATATATTTTATTTTAATTTCTTTAACATATATTATA
* * *
5602468 TTATATATTTTATTTTAATTTTTTTTACCTATATTATA
1 TTATATATTTTATTTTAATTTCTTTAACATATATTATA
5602506 T
1 T
5602507 AAATTTTAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.27, C:0.04, G:0.00, T:0.69
Consensus pattern (38 bp):
TTATATATTTTATTTTAATTTCTTTAACATATATTATA
Found at i:5611077 original size:27 final size:26
Alignment explanation
Indices: 5611018--5611080 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 26
5611008 TCTTTACTAT
*
5611018 TCATCCATTTTTGATAGATAAAGATA
1 TCATCCATTTCTGATAGATAAAGATA
*
5611044 TCTATCCATTTCTGATAGGTAAA-AGTA
1 TC-ATCCATTTCTGATAGATAAAGA-TA
5611071 TACATCCATT
1 T-CATCCATT
5611081 GGGTAAAGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 3 0.09
27 28 0.88
28 1 0.03
ACGTcount: A:0.35, C:0.16, G:0.11, T:0.38
Consensus pattern (26 bp):
TCATCCATTTCTGATAGATAAAGATA
Found at i:5611152 original size:27 final size:27
Alignment explanation
Indices: 5611080--5611153 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
5611070 ATACATCCAT
*
5611080 TGGGTAAAGATATCTATCCACGTCTGA
1 TGGGTAAAGGTATCTATCCACGTCTGA
* * *
5611107 TGGATAAAGGTATCCATCCACTTCTGA
1 TGGGTAAAGGTATCTATCCACGTCTGA
*
5611134 -GAGGTAAAGGTATTTATCCA
1 TG-GGTAAAGGTATCTATCCA
5611154 TTTTTCGTTA
Statistics
Matches: 39, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
26 1 0.03
27 38 0.97
ACGTcount: A:0.31, C:0.18, G:0.22, T:0.30
Consensus pattern (27 bp):
TGGGTAAAGGTATCTATCCACGTCTGA
Found at i:5611221 original size:27 final size:27
Alignment explanation
Indices: 5611179--5611297 Score: 94
Period size: 27 Copynumber: 4.4 Consensus size: 27
5611169 GATATATGTT
* * * *
5611179 CACTTCTAATGAGTAAAGGTATACATT
1 CACTTCTAGTGCGTAAAGGTATCCATC
* * * * *
5611206 TACTTCTGGTGGGTAAAGTTATCCATT
1 CACTTCTAGTGCGTAAAGGTATCCATC
* * *
5611233 CATTTCTAGTACGTAAAAGTATCCATC
1 CACTTCTAGTGCGTAAAGGTATCCATC
* * *
5611260 CACTTTTGGTGCGTAAAGGTATCTATC
1 CACTTCTAGTGCGTAAAGGTATCCATC
*
5611287 TACTTCTAGTG
1 CACTTCTAGTG
5611298 GTTAAATGTC
Statistics
Matches: 69, Mismatches: 23, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
27 69 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.37
Consensus pattern (27 bp):
CACTTCTAGTGCGTAAAGGTATCCATC
Found at i:5611715 original size:2 final size:2
Alignment explanation
Indices: 5611705--5611754 Score: 86
Period size: 2 Copynumber: 26.0 Consensus size: 2
5611695 TAGAAAAAAG
5611705 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5611746 AT AT A- AT AT
1 AT AT AT AT AT
5611755 TCATGCTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
1 2 0.04
2 44 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5612554 original size:20 final size:22
Alignment explanation
Indices: 5612514--5612556 Score: 63
Period size: 20 Copynumber: 2.0 Consensus size: 22
5612504 GTGCAGAATG
5612514 AAGAAAATATATTCCAAAAATA
1 AAGAAAATATATTCCAAAAATA
*
5612536 AAGAAAAT-T-TTCCATAAATA
1 AAGAAAATATATTCCAAAAATA
5612556 A
1 A
5612557 TTAAACTCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 11 0.55
21 1 0.05
22 8 0.40
ACGTcount: A:0.60, C:0.09, G:0.05, T:0.26
Consensus pattern (22 bp):
AAGAAAATATATTCCAAAAATA
Found at i:5618515 original size:17 final size:17
Alignment explanation
Indices: 5618493--5618528 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
5618483 AAATATGAAT
5618493 TTATAAAATAAATGGAA
1 TTATAAAATAAATGGAA
*
5618510 TTATAAAATAAATTGAA
1 TTATAAAATAAATGGAA
5618527 TT
1 TT
5618529 TTTTATAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (17 bp):
TTATAAAATAAATGGAA
Found at i:5628082 original size:11 final size:11
Alignment explanation
Indices: 5628065--5628098 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
5628055 TTAATTGAAT
5628065 TCCGTTGGAAA
1 TCCGTTGGAAA
* *
5628076 TCTGTTGCAAA
1 TCCGTTGGAAA
5628087 TCCGTTGGAAA
1 TCCGTTGGAAA
5628098 T
1 T
5628099 TTCCAATGAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (11 bp):
TCCGTTGGAAA
Found at i:5629387 original size:43 final size:43
Alignment explanation
Indices: 5629319--5629406 Score: 140
Period size: 43 Copynumber: 2.0 Consensus size: 43
5629309 AAATTCGGAC
* *
5629319 AAAGAAATTTCTTTGAACCTTTAGAAAGTTTCTTACTGCAGCG
1 AAAGAAATTTCTTTAAACCTCTAGAAAGTTTCTTACTGCAGCG
* *
5629362 AAAGAAATTTTTTTAAATCTCTAGAAAGTTTCTTACTGCAGCG
1 AAAGAAATTTCTTTAAACCTCTAGAAAGTTTCTTACTGCAGCG
5629405 AA
1 AA
5629407 TTTCTGAGCA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
43 41 1.00
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (43 bp):
AAAGAAATTTCTTTAAACCTCTAGAAAGTTTCTTACTGCAGCG
Found at i:5638812 original size:2 final size:2
Alignment explanation
Indices: 5638805--5638832 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5638795 CCGTATATCT
5638805 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
5638833 ATAAAGTACA
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:5646565 original size:16 final size:16
Alignment explanation
Indices: 5646544--5646575 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5646534 CCAAAAAGAA
5646544 AACAGTAAATAGCCCT
1 AACAGTAAATAGCCCT
5646560 AACAGTAAATAGCCCT
1 AACAGTAAATAGCCCT
5646576 GCATGTTTTC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.25, G:0.12, T:0.19
Consensus pattern (16 bp):
AACAGTAAATAGCCCT
Found at i:5648937 original size:18 final size:20
Alignment explanation
Indices: 5648889--5648938 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
5648879 ATATGTTTTA
* *
5648889 ATTTGATCATTTTAATTGTG
1 ATTTAATCATGTTAATTGTG
*
5648909 TTTTAATCATGTTAATTGT-
1 ATTTAATCATGTTAATTGTG
5648928 ATTT-ATCATGT
1 ATTTAATCATGT
5648939 GTTAATCGTG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
18 7 0.27
19 3 0.12
20 16 0.62
ACGTcount: A:0.26, C:0.06, G:0.12, T:0.56
Consensus pattern (20 bp):
ATTTAATCATGTTAATTGTG
Found at i:5652695 original size:2 final size:2
Alignment explanation
Indices: 5652690--5652726 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
5652680 TGTGTGTGTG
5652690 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5652727 TAGTTGNNNN
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5656369 original size:2 final size:2
Alignment explanation
Indices: 5656362--5656397 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5656352 NNNNNNTAAT
5656362 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
5656398 AATACAGAGG
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:5673574 original size:23 final size:22
Alignment explanation
Indices: 5673531--5673574 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
5673521 ACATACAAAT
* **
5673531 ATATTTTTATTATAATTTAATA
1 ATATTTTTATTAGAAGATAATA
5673553 ATATTTTGTATTAGAAGATAAT
1 ATATTTT-TATTAGAAGATAAT
5673575 TAAACCTTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (22 bp):
ATATTTTTATTAGAAGATAATA
Found at i:5673594 original size:192 final size:190
Alignment explanation
Indices: 5673249--5673630 Score: 649
Period size: 192 Copynumber: 2.0 Consensus size: 190
5673239 AAATTAAAGA
*
5673249 ATTTATTTTGTCAAAAAAAAAATATTCTAAGTAATAAAATCAAAATAACTTTTACTATAATTAAA
1 ATTTATTTTGTCAAAAAAAAAATATTCAAAGTAATAAAATCAAAATAACTTTTACTATAATTAAA
*
5673314 TAATATTTTTCATCAAAATAAAAATATATTTTTGTTATAATTTAATAATAGTTTGTATTAGAAGA
66 TAATATTTTTCATCAAAATAAAAATATATTTTTATTATAATTTAATAATAGTTTGTATTAGAAGA
* *
5673379 TAATTAAATCGTTTATTATAATTAAATAATATTTAATATTAAAAGACAAAATTTATTCTT
131 TAATTAAACCGTTTATTATAATTAAATAATATTTAATATTAAAAGACAAAATATATTCTT
*
5673439 NATTTATTTTGTTAAAAGATAAAAATATTCAAAGTAATAAAATCAAAATAACTTTTACTATAATT
1 -ATTTATTTTGTCAAAA-A-AAAAATATTCAAAGTAATAAAATCAAAATAACTTTTACTATAATT
* * *
5673504 AAATAATA-TTTTCATCAACATACAAATATATTTTTATTATAATTTAATAATATTTTGTATTAGA
63 AAATAATATTTTTCATCAAAATAAAAATATATTTTTATTATAATTTAATAATAGTTTGTATTAGA
*
5673568 AGATAATTAAACCTTTTATTATAATTAAATAATATTTAATATTAAAAGACAAAATATATTCTT
128 AGATAATTAAACCGTTTATTATAATTAAATAATATTTAATATTAAAAGACAAAATATATTCTT
5673631 CATTAAATTT
Statistics
Matches: 180, Mismatches: 9, Indels: 3
0.94 0.05 0.02
Matches are distributed among these distances:
191 15 0.08
192 113 0.63
193 52 0.29
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.42
Consensus pattern (190 bp):
ATTTATTTTGTCAAAAAAAAAATATTCAAAGTAATAAAATCAAAATAACTTTTACTATAATTAAA
TAATATTTTTCATCAAAATAAAAATATATTTTTATTATAATTTAATAATAGTTTGTATTAGAAGA
TAATTAAACCGTTTATTATAATTAAATAATATTTAATATTAAAAGACAAAATATATTCTT
Found at i:5673703 original size:45 final size:45
Alignment explanation
Indices: 5673642--5673735 Score: 136
Period size: 45 Copynumber: 2.1 Consensus size: 45
5673632 ATTAAATTTA
*
5673642 AATAATACTAAATAATATTCTTTATTACATTTATTATA-TTCAAAT
1 AATAATACTAAATAATATTCTTTATAACATTTATTATAGTT-AAAT
* * *
5673687 AATAATATTAAGTAATATTCTTTATAATATTTATTATAGTTAAAT
1 AATAATACTAAATAATATTCTTTATAACATTTATTATAGTTAAAT
5673732 AATA
1 AATA
5673736 TTTAAATATT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
45 42 0.95
46 2 0.05
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (45 bp):
AATAATACTAAATAATATTCTTTATAACATTTATTATAGTTAAAT
Found at i:5687742 original size:23 final size:24
Alignment explanation
Indices: 5687700--5687746 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
5687690 TTAGTAATTT
5687700 ATTTGATTTAAAATAAAATATAAAA
1 ATTTGATTTAAAATAAAATA-AAAA
*
5687725 ATTT-ATTT-AAATATAATAAAAA
1 ATTTGATTTAAAATAAAATAAAAA
5687747 TTAAAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 4 0.19
23 9 0.43
24 4 0.19
25 4 0.19
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (24 bp):
ATTTGATTTAAAATAAAATAAAAA
Found at i:5689010 original size:5 final size:5
Alignment explanation
Indices: 5689000--5689024 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
5688990 TGAAGTCCAG
5689000 TTTCT TTTCT TTTCT TTTCT TTTCT
1 TTTCT TTTCT TTTCT TTTCT TTTCT
5689025 CTTTAGAGTT
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:0.20, G:0.00, T:0.80
Consensus pattern (5 bp):
TTTCT
Found at i:5690842 original size:21 final size:21
Alignment explanation
Indices: 5690813--5690892 Score: 133
Period size: 21 Copynumber: 3.8 Consensus size: 21
5690803 TCATAACCGA
*
5690813 CTTTCATTAAAAAGCAACTAC
1 CTTTTATTAAAAAGCAACTAC
5690834 CTTTTATTAAAAAGCAACTAC
1 CTTTTATTAAAAAGCAACTAC
*
5690855 CTTTTATTAAAAAGTAACTAC
1 CTTTTATTAAAAAGCAACTAC
*
5690876 TTTTTATTAAAAAGCAA
1 CTTTTATTAAAAAGCAA
5690893 TTGACTTAAG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 55 1.00
ACGTcount: A:0.44, C:0.16, G:0.05, T:0.35
Consensus pattern (21 bp):
CTTTTATTAAAAAGCAACTAC
Found at i:5700258 original size:21 final size:21
Alignment explanation
Indices: 5700232--5700271 Score: 64
Period size: 21 Copynumber: 1.9 Consensus size: 21
5700222 TGACTGATCA
5700232 TAACTAGCTT-TTATTAAAAAG
1 TAACTA-CTTCTTATTAAAAAG
5700253 TAACTACTTCTTATTAAAA
1 TAACTACTTCTTATTAAAA
5700272 GCAACTCACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.42, C:0.12, G:0.05, T:0.40
Consensus pattern (21 bp):
TAACTACTTCTTATTAAAAAG
Found at i:5700282 original size:21 final size:21
Alignment explanation
Indices: 5700233--5700283 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
5700223 GACTGATCAT
*
5700233 AACTAGCTT-TTATTAAAAAGT
1 AACTA-CTTCTTATTAAAAAGC
5700254 AACTACTTCTTATT-AAAAGC
1 AACTACTTCTTATTAAAAAGC
5700274 AACTCACTTC
1 AACT-ACTTC
5700284 AACTACTTAG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.39, C:0.20, G:0.06, T:0.35
Consensus pattern (21 bp):
AACTACTTCTTATTAAAAAGC
Found at i:5700371 original size:45 final size:44
Alignment explanation
Indices: 5700302--5700386 Score: 134
Period size: 45 Copynumber: 1.9 Consensus size: 44
5700292 AGGAACATGT
*
5700302 AAATTCAAAACTGACTCCACAATAATTTAAAATTAGAATGATAGA
1 AAATGCAAAACTGACTCCACAATAATTT-AAATTAGAATGATAGA
* *
5700347 AAATGCAAAATTGACTCCATAATAATTTAAATTAGAATGA
1 AAATGCAAAACTGACTCCACAATAATTTAAATTAGAATGA
5700387 CAATTAATAC
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
44 12 0.32
45 25 0.68
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (44 bp):
AAATGCAAAACTGACTCCACAATAATTTAAATTAGAATGATAGA
Found at i:5702211 original size:14 final size:14
Alignment explanation
Indices: 5702186--5702223 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
5702176 TCATTATTAC
5702186 TATTTTTG-TTCAT
1 TATTTTTGTTTCAT
5702199 TATTTTTGTTTCAT
1 TATTTTTGTTTCAT
5702213 T-TTTGTTGTTT
1 TATTT-TTGTTT
5702224 GCTTTGTTAC
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 11 0.48
14 12 0.52
ACGTcount: A:0.11, C:0.05, G:0.11, T:0.74
Consensus pattern (14 bp):
TATTTTTGTTTCAT
Found at i:5703085 original size:22 final size:22
Alignment explanation
Indices: 5703060--5703111 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
5703050 TATTCTTTCC
* *
5703060 CTCTTTTTCCCGGCTTCTCTCT
1 CTCTTTTTCCCGACTTATCTCT
* *
5703082 CTCTCTTTCTCGACTTATCTCT
1 CTCTTTTTCCCGACTTATCTCT
*
5703104 CTTTTTTT
1 CTCTTTTT
5703112 TCCTCTATTT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.04, C:0.35, G:0.06, T:0.56
Consensus pattern (22 bp):
CTCTTTTTCCCGACTTATCTCT
Found at i:5703173 original size:33 final size:34
Alignment explanation
Indices: 5703131--5703282 Score: 103
Period size: 33 Copynumber: 4.3 Consensus size: 34
5703121 TCTCGACATC
* * *
5703131 TCTCTCTCTCCTTCTCGGCTTCTTTCTCT-TTCT
1 TCTCTCTCTCCTTCTCGGCATCTCTCTCTCTCCT
*
5703164 TCTCTCTCTCTTTCTCGGCATCTCTCTCTCTCCT
1 TCTCTCTCTCCTTCTCGGCATCTCTCTCTCTCCT
* * ** * *
5703198 TCTCGGCTTCTCTCTTTTTCTTCTTCTTCTCTTTCTCGACGT
1 TCT---C-TCTCTCCTTCTCGGCATC-TCTCTCTCTC--C-T
*
5703240 CTCTCTCTCTCCTTCTCGGCTTCTCTC-CT-TCCT
1 -TCTCTCTCTCCTTCTCGGCATCTCTCTCTCTCCT
5703273 TCTCTCTCTC
1 TCTCTCTCTC
5703283 TCTTTCCCCA
Statistics
Matches: 95, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
32 10 0.11
33 27 0.28
34 7 0.07
36 2 0.02
37 2 0.02
38 18 0.19
39 23 0.24
40 1 0.01
41 1 0.01
42 1 0.01
43 3 0.03
ACGTcount: A:0.01, C:0.41, G:0.07, T:0.51
Consensus pattern (34 bp):
TCTCTCTCTCCTTCTCGGCATCTCTCTCTCTCCT
Found at i:5703192 original size:22 final size:22
Alignment explanation
Indices: 5703164--5703212 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
5703154 TTCTCTTTCT
*
5703164 TCTCTCTCTCTTTCTCGGCATC
1 TCTCTCTCTCCTTCTCGGCATC
*
5703186 TCTCTCTCTCCTTCTCGGCTTC
1 TCTCTCTCTCCTTCTCGGCATC
5703208 TCTCT
1 TCTCT
5703213 TTTTCTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.02, C:0.43, G:0.08, T:0.47
Consensus pattern (22 bp):
TCTCTCTCTCCTTCTCGGCATC
Found at i:5703194 original size:55 final size:55
Alignment explanation
Indices: 5703075--5703283 Score: 289
Period size: 55 Copynumber: 3.8 Consensus size: 55
5703065 TTTCCCGGCT
* * * * * *
5703075 TCTCTCTCTCTCTTTCTCGACTTATCTCTCTTTTTTTTC-CTCTATTTCTCGACA
1 TCTCTCTCTCTCCTTCTCGGCTTCTCTCTCTTTCTTCTCTCTCTCTTTCTCGACA
* *
5703129 TCTCTCTCTCTCCTTCTCGGCTTCTTTCTCTTTCTTCTCTCTCTCTTTCTCGGCA
1 TCTCTCTCTCTCCTTCTCGGCTTCTCTCTCTTTCTTCTCTCTCTCTTTCTCGACA
* *
5703184 TCTCTCTCTCTCCTTCTCGGCTTCTCTCTTTTTCTTCT-TCTTCTCTTTCTCGACG
1 TCTCTCTCTCTCCTTCTCGGCTTCTCTCTCTTTCTTCTCTC-TCTCTTTCTCGACA
*
5703239 TCTCTCTCTCTCCTTCTCGGCTTCTCTC-CTTCCTTCTCTCTCTCT
1 TCTCTCTCTCTCCTTCTCGGCTTCTCTCTCTTTCTTCTCTCTCTCT
5703284 CTTTCCCCAC
Statistics
Matches: 138, Mismatches: 14, Indels: 6
0.87 0.09 0.04
Matches are distributed among these distances:
54 47 0.34
55 91 0.66
ACGTcount: A:0.03, C:0.39, G:0.06, T:0.52
Consensus pattern (55 bp):
TCTCTCTCTCTCCTTCTCGGCTTCTCTCTCTTTCTTCTCTCTCTCTTTCTCGACA
Found at i:5703280 original size:16 final size:17
Alignment explanation
Indices: 5703131--5703282 Score: 55
Period size: 16 Copynumber: 8.6 Consensus size: 17
5703121 TCTCGACATC
5703131 TCTCTCTCTCCTTCTCG
1 TCTCTCTCTCCTTCTCG
* * *
5703148 GCT-TCTTTCTCTT-TCT
1 TCTCTCTCTC-CTTCTCG
*
5703164 TCTCTCTCTCTTTCTCGG
1 TCTCTCTCTCCTTCTC-G
5703182 CATCTCTCTCTCTCCTTCTCG
1 ----TCTCTCTCTCCTTCTCG
* * * *
5703203 GCT-TCTCTCTTTTTCT
1 TCTCTCTCTCCTTCTCG
*
5703219 TCT-TCTTCTCTTTCTCGACG
1 TCTCTC-TCTCCTTCT---CG
5703239 TCTCTCTCTCTCCTTCTCG
1 --TCTCTCTCTCCTTCTCG
* *
5703258 GCT-TCTCTCCTTC-CT
1 TCTCTCTCTCCTTCTCG
5703273 TCTCTCTCTC
1 TCTCTCTCTC
5703283 TCTTTCCCCA
Statistics
Matches: 100, Mismatches: 19, Indels: 33
0.66 0.12 0.22
Matches are distributed among these distances:
15 3 0.03
16 41 0.41
17 24 0.24
19 2 0.02
20 1 0.01
21 1 0.01
22 26 0.26
23 2 0.02
ACGTcount: A:0.01, C:0.41, G:0.07, T:0.51
Consensus pattern (17 bp):
TCTCTCTCTCCTTCTCG
Found at i:5703284 original size:8 final size:7
Alignment explanation
Indices: 5703129--5703286 Score: 61
Period size: 6 Copynumber: 23.1 Consensus size: 7
5703119 TTTCTCGACA
5703129 TCTCTC-
1 TCTCTCT
5703135 TCTCTCCT
1 TCTCT-CT
*
5703143 TCTCGGCT
1 TCTC-TCT
*
5703151 TCTTTC-
1 TCTCTCT
*
5703157 TCTTTCT
1 TCTCTCT
5703164 TCTCTC-
1 TCTCTCT
5703170 TCTCT-T
1 TCTCTCT
* *
5703176 TCTCGGCA
1 TCTC-TCT
5703184 TCTCTC-
1 TCTCTCT
5703190 TCTCTCCT
1 TCTCT-CT
*
5703198 TCTCGGCT
1 TCTC-TCT
5703206 TCTCTCT
1 TCTCTCT
*
5703213 T-TTTCT
1 TCTCTCT
5703219 TCT-TCT
1 TCTCTCT
5703225 TCTCT-T
1 TCTCTCT
* *
5703231 TCTCGACG
1 TCTC-TCT
5703239 TCTCTC-
1 TCTCTCT
5703245 TCTCTCCT
1 TCTCT-CT
*
5703253 TCTCGGCT
1 TCTC-TCT
*
5703261 TCTCTCC
1 TCTCTCT
5703268 T-TC-CT
1 TCTCTCT
5703273 TCTCTC-
1 TCTCTCT
5703279 TCTCTCT
1 TCTCTCT
5703286 T
1 T
5703287 TCCCCACCGA
Statistics
Matches: 115, Mismatches: 17, Indels: 39
0.67 0.10 0.23
Matches are distributed among these distances:
5 2 0.02
6 56 0.49
7 20 0.17
8 37 0.32
ACGTcount: A:0.01, C:0.41, G:0.06, T:0.51
Consensus pattern (7 bp):
TCTCTCT
Found at i:5703803 original size:8 final size:8
Alignment explanation
Indices: 5703748--5703808 Score: 50
Period size: 8 Copynumber: 6.8 Consensus size: 8
5703738 TTCTTTTTCT
5703748 TTTTTTTA
1 TTTTTTTA
*
5703756 TTGTTTTA
1 TTTTTTTA
5703764 TTTTTTTA
1 TTTTTTTA
5703772 TTATATTTCATTA
1 -T-T-TTT--TTA
5703785 TTATTTATTA
1 TT-TTT-TTA
5703795 TTTTTTTA
1 TTTTTTTA
5703803 TTTTTT
1 TTTTTT
5703809 GAAATAGGTG
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
8 23 0.50
9 4 0.09
10 7 0.15
11 8 0.17
12 1 0.02
13 3 0.07
ACGTcount: A:0.18, C:0.02, G:0.02, T:0.79
Consensus pattern (8 bp):
TTTTTTTA
Found at i:5710750 original size:64 final size:64
Alignment explanation
Indices: 5710677--5710796 Score: 188
Period size: 64 Copynumber: 1.9 Consensus size: 64
5710667 TTAACAATTA
* * *
5710677 GTCATCCAATTTATCTTTAAATAAATC-AAGATAATTTAGAAATAATATTTAAATTTACTTATTC
1 GTCACCCAATTTATCTCTAAATAAATCAAAG-TAATTTAGAAATAAAATTTAAATTTACTTATTC
*
5710741 GTCACCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAGATAAAATTTAAATTT
1 GTCACCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAAATAAAATTTAAATTT
5710797 GGTCATCCAA
Statistics
Matches: 51, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
64 48 0.94
65 3 0.06
ACGTcount: A:0.43, C:0.12, G:0.06, T:0.39
Consensus pattern (64 bp):
GTCACCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAAATAAAATTTAAATTTACTTATTC
Found at i:5710809 original size:57 final size:58
Alignment explanation
Indices: 5710662--5710842 Score: 170
Period size: 64 Copynumber: 3.0 Consensus size: 58
5710652 TGGACCAATA
* * * *
5710662 AAAATTTAACAATTAGTCATCCAATTTATCTTTAAATAAATC-AAGATAATTTAGAAAT
1 AAAATTTAATATTTAGTCATCCAATTTATCTCTAAATAAATCAAAG-TAATTTAGAGAT
* * *
5710720 AATATTTAAATTTACTTATTCGTCACCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAGAT
1 AAAATTT-AA--TA--T-TTAGTCATCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAGAT
* * * *
5710784 AAAATTTAA-ATTTGGTCATCCAATTTGTCTCTAAATAGACCAATA-TAATTTAGAGAT
1 AAAATTTAATATTTAGTCATCCAATTTATCTCTAAATAAATCAA-AGTAATTTAGAGAT
5710841 AA
1 AA
5710843 TACTTAAATT
Statistics
Matches: 102, Mismatches: 13, Indels: 17
0.77 0.10 0.13
Matches are distributed among these distances:
57 41 0.40
58 8 0.08
59 2 0.02
60 1 0.01
61 1 0.01
63 2 0.02
64 44 0.43
65 3 0.03
ACGTcount: A:0.44, C:0.12, G:0.07, T:0.37
Consensus pattern (58 bp):
AAAATTTAATATTTAGTCATCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAGAT
Found at i:5710850 original size:57 final size:57
Alignment explanation
Indices: 5710741--5710852 Score: 154
Period size: 57 Copynumber: 2.0 Consensus size: 57
5710731 TTACTTATTC
* *
5710741 GTCACCCAATTTATCTCTAAATAAATCAAAGTAATTTAGAGATAAAATTTAAATTTG
1 GTCACCCAATTTATCTCTAAATAAACCAAAGTAATTTAGAGATAAAACTTAAATTTG
* * * *
5710798 GTCATCCAATTTGTCTCTAAATAGACCAATA-TAATTTAGAGATAATACTTAAATT
1 GTCACCCAATTTATCTCTAAATAAACCAA-AGTAATTTAGAGATAAAACTTAAATT
5710853 CGACCAATCA
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
57 47 0.98
58 1 0.02
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.36
Consensus pattern (57 bp):
GTCACCCAATTTATCTCTAAATAAACCAAAGTAATTTAGAGATAAAACTTAAATTTG
Found at i:5711467 original size:50 final size:50
Alignment explanation
Indices: 5711312--5711854 Score: 503
Period size: 50 Copynumber: 11.0 Consensus size: 50
5711302 CTACAAGTCG
* * * *
5711312 AAGTCTCCAAATCATTCGTTTAAGGTCAAGTTG-CAAGACCCTTGAAGCA
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
* * *
5711361 AAGTCTCCTAATCATTCTTTCAAGATCAAGTCGT-AAGACTCTTGAAGCA
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
* * * * *
5711410 AAGTTTCCAAATCACTT-GTTCAAAATCAAGTCGTCAAGACCATTGAAGCG
1 AAGTCTCCAAATCA-TTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
* * * * **
5711460 AAGTTTCCAAATCATTCATTCAAAATCAAGTTG-CGAGACCCTTGAAGTG
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
* ** * * *
5711509 AAGTCTCCAAATCGTTCAACCAAGATCAAGTTGTCAAGACTCTTGAACCA
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
** * * * * *
5711559 AAGTCTCCAAATTGTTCGTTAAAGATCAAGTTGTCAAGTCCTTTGAAG-A
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
** ** * * *
5711608 TAAGTCTTTAAATTGTTCATTCGAGATCAAGTCGTCAAGACCTTTGAAGCG
1 -AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
**
5711659 AAGTCTCCAAATTTTTC-TTCAAGATCAAGTCGTCAAGACCCTTGAAGCCA
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAG-CA
** *
5711709 AA-TCTCCAAATCATTTTTTCAAGATCAAGTCGTCAAGACCCTTGAAACA
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
** * **
5711758 AAGTCTTTAAATCATTCATTCAAGATCAAGTCGTTAAGACCC-TGAAATA
1 AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
* ** * *
5711807 AAGTCTCTAAATTGTTGC-TTCAAGATCAAGTCAT-AAGACCCTTAAAGC
1 AAGTCTCCAAATCATT-CATTCAAGATCAAGTCGTCAAGACCCTTGAAGC
5711855 GAATTCAAGA
Statistics
Matches: 414, Mismatches: 68, Indels: 24
0.82 0.13 0.05
Matches are distributed among these distances:
48 7 0.02
49 193 0.47
50 214 0.52
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (50 bp):
AAGTCTCCAAATCATTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCA
Found at i:5711488 original size:99 final size:100
Alignment explanation
Indices: 5711312--5711854 Score: 482
Period size: 99 Copynumber: 5.5 Consensus size: 100
5711302 CTACAAGTCG
* * * * *
5711312 AAGTCTCCAAATCA-TTCGTTTAAGGTCAAGTTG-CAAGACCCTTGAAGCAAAGTCTCCTAATCA
1 AAGTCTCCAAATCAGTTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCAAAGTCTCCAAATCA
* *
5711375 TTCTTTCAAGATCAAGTCGTAAGACTCTTGAAGCA
66 TTCATTCAAGATCAAGTCGTAAGACCCTTGAAGCA
* * * * * * *
5711410 AAGTTTCCAAATCACTT-GTTCAAAATCAAGTCGTCAAGACCATTGAAGCGAAGTTTCCAAATCA
1 AAGTCTCCAAATCAGTTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCAAAGTCTCCAAATCA
* * ** **
5711474 TTCATTCAAAATCAAGTTGCGAGACCCTTGAAGTG
66 TTCATTCAAGATCAAGTCGTAAGACCCTTGAAGCA
** * * * **
5711509 AAGTCTCCAAATC-GTTCAACCAAGATCAAGTTGTCAAGACTCTTGAACCAAAGTCTCCAAATTG
1 AAGTCTCCAAATCAGTTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCAAAGTCTCCAAATCA
* * * * *
5711573 TTCGTTAAAGATCAAGTTGTCAAGTCCTTTGAAG-A
66 TTCATTCAAGATCAAGTCGT-AAGACCCTTGAAGCA
** * * * * *
5711608 TAAGTCTTTAAAT-TGTTCATTCGAGATCAAGTCGTCAAGACCTTTGAAGCGAAGTCTCCAAATT
1 -AAGTCTCCAAATCAGTTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCAAAGTCTCCAAATC
*
5711672 TTTC-TTCAAGATCAAGTCGTCAAGACCCTTGAAGCCA
65 ATTCATTCAAGATCAAGTCGT-AAGACCCTTGAAG-CA
** * **
5711709 AA-TCTCCAAATCA-TTTTTTCAAGATCAAGTCGTCAAGACCCTTGAAACAAAGTCTTTAAATCA
1 AAGTCTCCAAATCAGTTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCAAAGTCTCCAAATCA
**
5711772 TTCATTCAAGATCAAGTCGTTAAGACCC-TGAAATA
66 TTCATTCAAGATCAAGTCG-TAAGACCCTTGAAGCA
* * * *
5711807 AAGTCTCTAAAT-TGTTGC-TTCAAGATCAAGTCAT-AAGACCCTTAAAGC
1 AAGTCTCCAAATCAGTT-CATTCAAGATCAAGTCGTCAAGACCCTTGAAGC
5711855 GAATTCAAGA
Statistics
Matches: 356, Mismatches: 75, Indels: 28
0.78 0.16 0.06
Matches are distributed among these distances:
98 42 0.12
99 223 0.63
100 89 0.25
101 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.29
Consensus pattern (100 bp):
AAGTCTCCAAATCAGTTCATTCAAGATCAAGTCGTCAAGACCCTTGAAGCAAAGTCTCCAAATCA
TTCATTCAAGATCAAGTCGTAAGACCCTTGAAGCA
Found at i:5711627 original size:149 final size:147
Alignment explanation
Indices: 5711320--5711838 Score: 492
Period size: 149 Copynumber: 3.5 Consensus size: 147
5711310 CGAAGTCTCC
* * * * *
5711320 AAATCATTCGTTTAAGGTCAAGTTGCAAGACCCTTGAAGCAAAGTCTCCTAATCATTCTTTCAAG
1 AAATCATTCATTCAAGATCAAGTTGCAAGACCCTTGAAGCGAAGTCTCCAAATCATTC-TTCAAG
* * *
5711385 ATCAAGTCGT-AAGACTCTTGAAGCAAAGTTTCCAAATCACTTGTTCAAA-ATCAAGTCGTCAAG
65 ATCAAGTCGTCAAGACTCTTGAACCAAAGTCTCCAAAT-AATTGTT-AAAGATCAAGTCGTCAAG
** *
5711448 ACCATTGAAGCGAAGT-TTCC
128 ACCATTGAAGAAAAGTCTT-T
* * * * **
5711468 AAATCATTCATTCAAAATCAAGTTGCGAGACCCTTGAAGTGAAGTCTCCAAATCGTTCAACCAAG
1 AAATCATTCATTCAAGATCAAGTTGCAAGACCCTTGAAGCGAAGTCTCCAAATCATTC-TTCAAG
* ** * *
5711533 ATCAAGTTGTCAAGACTCTTGAACCAAAGTCTCCAAATTGTTCGTTAAAGATCAAGTTGTCAAGT
65 ATCAAGTCGTCAAGACTCTTGAACCAAAGTCTCCAAATAATT-GTTAAAGATCAAGTCGTCAAGA
* *
5711598 CCTTTGAAGATAAGTCTTT
129 CCATTGAAGAAAAGTCTTT
** * * * **
5711617 AAATTGTTCATTCGAGATCAAGTCGTCAAGACCTTTGAAGCGAAGTCTCCAAATTTTTCTTCAAG
1 AAATCATTCATTCAAGATCAAGTTG-CAAGACCCTTGAAGCGAAGTCTCCAAATCATTCTTCAAG
* * * *
5711682 ATCAAGTCGTCAAGACCCTTGAAGCCAAA-TCTCCAAATCATTTTTTCAAGATCAAGTCGTCAAG
65 ATCAAGTCGTCAAGACTCTTGAA-CCAAAGTCTCCAAAT-AATTGTTAAAGATCAAGTCGTCAAG
*
5711746 ACCCTTGAA-ACAAAGTCTTT
128 ACCATTGAAGA-AAAGTCTTT
* * *** * **
5711766 AAATCATTCATTCAAGATCAAGTCGTTAAGACCC-TGAAATAAAGTCTCTAAATTGTTGCTTCAA
1 AAATCATTCATTCAAGATCAAGTTG-CAAGACCCTTGAAGCGAAGTCTCCAAATCATT-CTTCAA
5711830 GATCAAGTC
64 GATCAAGTC
5711839 ATAAGACCCT
Statistics
Matches: 307, Mismatches: 55, Indels: 17
0.81 0.15 0.04
Matches are distributed among these distances:
148 86 0.28
149 184 0.60
150 37 0.12
ACGTcount: A:0.34, C:0.21, G:0.15, T:0.29
Consensus pattern (147 bp):
AAATCATTCATTCAAGATCAAGTTGCAAGACCCTTGAAGCGAAGTCTCCAAATCATTCTTCAAGA
TCAAGTCGTCAAGACTCTTGAACCAAAGTCTCCAAATAATTGTTAAAGATCAAGTCGTCAAGACC
ATTGAAGAAAAGTCTTT
Found at i:5711867 original size:33 final size:31
Alignment explanation
Indices: 5711825--5711885 Score: 95
Period size: 33 Copynumber: 1.9 Consensus size: 31
5711815 AAATTGTTGC
5711825 TTCAAGATCAAGTCATAAGACCCTTAAAGCGAA
1 TTCAAGATCAAGTCA-AAG-CCCTTAAAGCGAA
*
5711858 TTCAAGATCAAGTCAAAGCCCTTGAAGC
1 TTCAAGATCAAGTCAAAGCCCTTAAAGC
5711886 AAAGTAATAA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
31 9 0.33
32 3 0.11
33 15 0.56
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.21
Consensus pattern (31 bp):
TTCAAGATCAAGTCAAAGCCCTTAAAGCGAA
Found at i:5714283 original size:36 final size:36
Alignment explanation
Indices: 5714112--5714282 Score: 236
Period size: 36 Copynumber: 4.7 Consensus size: 36
5714102 GTGATGGTGG
5714112 TGTGCGGTGTGGGAGTGCACACGTTGATGATATATGCCA
1 TGTGCGGTGTGGGAGTGCACA---TGATGATATATGCCA
* *
5714151 TGTGTGGTGTGGGAGTGCACATGATGTTATATGCCA
1 TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
*
5714187 TGTGCGGTGTGGGAGTGCACATGATGATATTTGCCA
1 TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
* * *
5714223 TGTGCGGTGTAGGAGTGCACATGAGGATAT-TAGCTA
1 TGTGCGGTGTGGGAGTGCACATGATGATATAT-GCCA
*
5714259 TGTGCGATGTGGGAGTGCACATGA
1 TGTGCGGTGTGGGAGTGCACATGA
5714283 GCTAAGTTGA
Statistics
Matches: 121, Mismatches: 10, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
35 1 0.01
36 100 0.83
39 20 0.17
ACGTcount: A:0.21, C:0.13, G:0.37, T:0.29
Consensus pattern (36 bp):
TGTGCGGTGTGGGAGTGCACATGATGATATATGCCA
Found at i:5715447 original size:92 final size:92
Alignment explanation
Indices: 5715290--5715474 Score: 352
Period size: 92 Copynumber: 2.0 Consensus size: 92
5715280 GGAAAGTGTC
5715290 ACTCAGCCTTCCTACACTTATGCAAAACCATACTCCCAAAGGATTGATCACATGAGAACGCTAGA
1 ACTCAGCCTTCCTACACTTATGCAAAACCATACTCCCAAAGGATTGATCACATGAGAACGCTAGA
5715355 GAATTATCAACCACCAAAGTTTCAACA
66 GAATTATCAACCACCAAAGTTTCAACA
*
5715382 ACTCAGCCTTCCTACACTTATGCAAAACCATACTCCCAAAGGATTGATCACATGAGAATGCTAGA
1 ACTCAGCCTTCCTACACTTATGCAAAACCATACTCCCAAAGGATTGATCACATGAGAACGCTAGA
*
5715447 GAATTATCAACCACTAAAGTTTCAACA
66 GAATTATCAACCACCAAAGTTTCAACA
5715474 A
1 A
5715475 TTCGATGGTA
Statistics
Matches: 91, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
92 91 1.00
ACGTcount: A:0.38, C:0.27, G:0.12, T:0.23
Consensus pattern (92 bp):
ACTCAGCCTTCCTACACTTATGCAAAACCATACTCCCAAAGGATTGATCACATGAGAACGCTAGA
GAATTATCAACCACCAAAGTTTCAACA
Found at i:5718583 original size:51 final size:50
Alignment explanation
Indices: 5718472--5718585 Score: 117
Period size: 51 Copynumber: 2.3 Consensus size: 50
5718462 AGATCAAAGC
* * * *
5718472 CTCCAAAGTTCC-A-TAAATCCAAGAAGGAAGATTGAAGCACCAAAGCTT
1 CTCCAAGGTTCCAACTAAATCCAACAAGGAAGATTGAAGAACAAAAGCTT
* * * *
5718520 -TTCTAGATTTCCAACTAAGTCCAACAAGGAAGATTTGAAGAACAAAAGCTT
1 CTCCAAG-GTTCCAACTAAATCCAACAAGGAAGA-TTGAAGAACAAAAGCTT
5718571 CTCCAAGGTTCCAAC
1 CTCCAAGGTTCCAAC
5718586 CTACAAGTCT
Statistics
Matches: 50, Mismatches: 11, Indels: 7
0.74 0.16 0.10
Matches are distributed among these distances:
47 3 0.06
48 4 0.08
49 1 0.02
50 16 0.32
51 22 0.44
52 4 0.08
ACGTcount: A:0.39, C:0.23, G:0.16, T:0.22
Consensus pattern (50 bp):
CTCCAAGGTTCCAACTAAATCCAACAAGGAAGATTGAAGAACAAAAGCTT
Done.