Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold59
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: 3999109
ACGTcount: A:0.32, C:0.14, G:0.14, T:0.32
Warning! 268233 characters in sequence are not A, C, G, or T
File 2 of 25
Found at i:263055 original size:2 final size:2
Alignment explanation
Indices: 263048--263090 Score: 63
Period size: 2 Copynumber: 22.0 Consensus size: 2
263038 AGAAGAGAAG
263048 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT ACT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT AT
263089 AT
1 AT
263091 TACTGTATTA
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
1 2 0.05
2 34 0.89
3 2 0.05
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:265166 original size:21 final size:21
Alignment explanation
Indices: 265142--265182 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
265132 CTATAAATAA
265142 CATATTT-TTTGAAATAAAATT
1 CATATTTATTTGAAA-AAAATT
*
265163 CATATTTATTTGGAAAAAAT
1 CATATTTATTTGAAAAAAAT
265183 GAACAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.44
Consensus pattern (21 bp):
CATATTTATTTGAAAAAAATT
Found at i:266351 original size:3 final size:3
Alignment explanation
Indices: 266343--266368 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
266333 ATCCTTCAAA
266343 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
266369 AGAGGGATTA
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:266719 original size:29 final size:32
Alignment explanation
Indices: 266652--266723 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 32
266642 TGATGTTTTG
266652 ATTATTTAAATAAATAAAGCTTTTCACTCAAAA
1 ATTATTTAAATAAATAAAGCTTTTCAC-CAAAA
266685 A--A--TAAATAAATAAAG-TTTT-A-CAAAA
1 ATTATTTAAATAAATAAAGCTTTTCACCAAAA
266710 ATTATTTAAATAAA
1 ATTATTTAAATAAA
266724 ATATTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 12
0.74 0.00 0.26
Matches are distributed among these distances:
25 6 0.17
27 2 0.06
28 4 0.11
29 21 0.60
31 1 0.03
33 1 0.03
ACGTcount: A:0.56, C:0.07, G:0.03, T:0.35
Consensus pattern (32 bp):
ATTATTTAAATAAATAAAGCTTTTCACCAAAA
Found at i:267554 original size:21 final size:21
Alignment explanation
Indices: 267476--267556 Score: 58
Period size: 21 Copynumber: 3.8 Consensus size: 21
267466 TTTGATGCGG
*
267476 TTAAAATTAATAATAAAATAAA
1 TTAAAATTAATAAT-AATTAAA
* *
267498 AT-AAATTAGTATAATAATATTAA
1 TTAAAATTA--ATAATAAT-TAAA
** *
267521 TTATTATT-TTAATAATTAAA
1 TTAAAATTAATAATAATTAAA
267541 TTAAAATTAATAATAA
1 TTAAAATTAATAATAA
267557 AATATTTATT
Statistics
Matches: 43, Mismatches: 11, Indels: 11
0.66 0.17 0.17
Matches are distributed among these distances:
20 9 0.21
21 19 0.44
22 3 0.07
23 9 0.21
24 3 0.07
ACGTcount: A:0.58, C:0.00, G:0.01, T:0.41
Consensus pattern (21 bp):
TTAAAATTAATAATAATTAAA
Found at i:267730 original size:38 final size:38
Alignment explanation
Indices: 267665--267748 Score: 109
Period size: 36 Copynumber: 2.2 Consensus size: 38
267655 AATTTATTTG
*
267665 ATATTTATGAAATTAATAAATAATTAAAATTTATTAAAAAT
1 ATATTTATGAAA-TAATAAATAATTAAAA-TTAAT-AAAAT
*
267706 ATATTTATGTAA-AAT-AATAATTAAAATTAATAAAAT
1 ATATTTATGAAATAATAAATAATTAAAATTAATAAAAT
267742 ATATTTA
1 ATATTTA
267749 ATAATATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 5
0.85 0.04 0.10
Matches are distributed among these distances:
36 12 0.29
37 4 0.10
38 11 0.27
39 3 0.07
41 11 0.27
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (38 bp):
ATATTTATGAAATAATAAATAATTAAAATTAATAAAAT
Found at i:268496 original size:59 final size:62
Alignment explanation
Indices: 268428--268549 Score: 155
Period size: 60 Copynumber: 2.0 Consensus size: 62
268418 TTAAAAATGA
* *
268428 ATTATTATTAAA-ATATT-AAACATAATATTT-TAATCAAAAAATT-AATATTTAAA-TATTAT
1 ATTAATATTAAATAT-TTAAAACATAATATTTATAAT-AAAAAATTAAATATATAAATTATTAT
* *
268487 ATTAATATTAAATATTTAAAACATACTATTTATTATAAAAAATTAAATATATAAATTATTAT
1 ATTAATATTAAATATTTAAAACATAATATTTATAATAAAAAATTAAATATATAAATTATTAT
268549 A
1 A
268550 ATTGTTAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
59 13 0.24
60 22 0.41
61 12 0.22
62 7 0.13
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (62 bp):
ATTAATATTAAATATTTAAAACATAATATTTATAATAAAAAATTAAATATATAAATTATTAT
Found at i:268854 original size:16 final size:16
Alignment explanation
Indices: 268833--268863 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
268823 ATATTTCTAC
*
268833 TATTAAATTATAATTA
1 TATTAAAGTATAATTA
268849 TATTAAAGTATAATT
1 TATTAAAGTATAATT
268864 TAAATAATTT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (16 bp):
TATTAAAGTATAATTA
Found at i:269043 original size:24 final size:22
Alignment explanation
Indices: 268983--269046 Score: 69
Period size: 24 Copynumber: 2.8 Consensus size: 22
268973 AAGTAATATT
268983 TTTATTAAAA-AT-AATAAAAA
1 TTTATTAAAATATAAATAAAAA
*
269003 TTTATTAAAATAAATAAATAAATTA
1 TTTATTAAAAT--ATAAATAAA-AA
269028 TCTTATTAAAATATAAATA
1 T-TTATTAAAATATAAATA
269047 TATATTCTAA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
20 10 0.27
23 2 0.05
24 13 0.35
25 2 0.05
26 10 0.27
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (22 bp):
TTTATTAAAATATAAATAAAAA
Found at i:269510 original size:21 final size:20
Alignment explanation
Indices: 269467--269512 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
269457 TTGTAGGTTA
* * *
269467 ATTTAAAATTTTATTTTATT
1 ATTTAAAATATTATATTAAT
269487 ATTTAAAATAATTATATTAAT
1 ATTTAAAAT-ATTATATTAAT
269508 ATTTA
1 ATTTA
269513 TAGTTAAAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
20 9 0.41
21 13 0.59
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATTTAAAATATTATATTAAT
Found at i:269549 original size:21 final size:21
Alignment explanation
Indices: 269486--269564 Score: 61
Period size: 21 Copynumber: 3.7 Consensus size: 21
269476 TTTATTTTAT
* *
269486 TATTTAAAAT-AATTATATTAA
1 TATTTAAATTAAATTATA-AAA
* * *
269507 TATTTATAGTTAAAATAAAAAA
1 TATTTA-AATTAAATTATAAAA
269529 TATTTAAATTAAATTATAAAA
1 TATTTAAATTAAATTATAAAA
* * *
269550 TTTTTTATTTAAATT
1 TATTTAAATTAAATT
269565 TAATTTAATA
Statistics
Matches: 45, Mismatches: 11, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
21 30 0.67
22 10 0.22
23 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (21 bp):
TATTTAAATTAAATTATAAAA
Found at i:270129 original size:16 final size:14
Alignment explanation
Indices: 270097--270133 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 14
270087 TTAAATCACT
270097 TTAATTTAAAAAAA
1 TTAATTTAAAAAAA
270111 TTAATTTAAATATAAA
1 TTAATTTAAA-A-AAA
270127 TTAATTT
1 TTAATTT
270134 TTAAAATTTA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.48
15 1 0.05
16 10 0.48
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAATTTAAAAAAA
Found at i:270493 original size:16 final size:16
Alignment explanation
Indices: 270472--270504 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
270462 ATGTTCCTGA
270472 ATATAATATATATAAT
1 ATATAATATATATAAT
*
270488 ATATAATATATGTAAT
1 ATATAATATATATAAT
270504 A
1 A
270505 AAATTGGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
ATATAATATATATAAT
Found at i:274410 original size:14 final size:14
Alignment explanation
Indices: 274391--274426 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
274381 TTTACTGTAT
274391 GGCATCTGAAGTAG
1 GGCATCTGAAGTAG
*
274405 GGCATCTGCAGTAG
1 GGCATCTGAAGTAG
274419 GGCATCTG
1 GGCATCTG
274427 TACTCAAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.22, C:0.19, G:0.36, T:0.22
Consensus pattern (14 bp):
GGCATCTGAAGTAG
Found at i:278961 original size:48 final size:48
Alignment explanation
Indices: 278902--278995 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
278892 CCCCCACTTG
278902 AAAGAACCCTATGGTCCTTTTACCTTAAATTAACATGCCAAATAGTTA
1 AAAGAACCCTATGGTCCTTTTACCTTAAATTAACATGCCAAATAGTTA
* ** *
278950 AAAGAAGCCTATGGTTGTTTTACCTTAAGTTAACATGCCAAATAGT
1 AAAGAACCCTATGGTCCTTTTACCTTAAATTAACATGCCAAATAGT
278996 GCAAAAAAAT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (48 bp):
AAAGAACCCTATGGTCCTTTTACCTTAAATTAACATGCCAAATAGTTA
Found at i:279619 original size:30 final size:30
Alignment explanation
Indices: 279583--279643 Score: 88
Period size: 30 Copynumber: 2.0 Consensus size: 30
279573 TATTTTAATA
279583 TTTATATTATA-TAAATTTTAAAAATATATT
1 TTTATATTATATTAAATTTTAAAAAT-TATT
* *
279613 TTTATATTATATTATATTTTAAATATTATT
1 TTTATATTATATTAAATTTTAAAAATTATT
279643 T
1 T
279644 CGTGTGCGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 16 0.57
31 12 0.43
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (30 bp):
TTTATATTATATTAAATTTTAAAAATTATT
Found at i:282343 original size:18 final size:19
Alignment explanation
Indices: 282302--282343 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
282292 TTAAACCTTA
*
282302 ATAA-ATTTAAATACATAT
1 ATAATATTTAAATAAATAT
*
282320 AAAATATTTAAA-AAATAT
1 ATAATATTTAAATAAATAT
282338 ATAATA
1 ATAATA
282344 AATTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 13 0.65
19 7 0.35
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (19 bp):
ATAATATTTAAATAAATAT
Found at i:284302 original size:2 final size:2
Alignment explanation
Indices: 284263--284289 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
284253 TGCTAACTTT
284263 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
284290 GGTAGCATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:284956 original size:2 final size:2
Alignment explanation
Indices: 284949--284991 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
284939 CTTTCATCTT
284949 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
284991 T
1 T
284992 TTTGTCGACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:285169 original size:14 final size:16
Alignment explanation
Indices: 285145--285177 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
285135 ATAACATTTC
285145 AATTAGATA-TTATAA
1 AATTAGATATTTATAA
285160 AATT-GATATTTATAA
1 AATTAGATATTTATAA
285175 AAT
1 AAT
285178 ATATACTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (16 bp):
AATTAGATATTTATAA
Found at i:285421 original size:3 final size:3
Alignment explanation
Indices: 285403--285443 Score: 64
Period size: 3 Copynumber: 13.0 Consensus size: 3
285393 ATGTTTATGC
285403 TAT TAAT TAGT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TA-T TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
285444 CATCATTTAC
Statistics
Matches: 36, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
3 30 0.83
4 6 0.17
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:286596 original size:18 final size:19
Alignment explanation
Indices: 286559--286596 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 19
286549 AATCTTTTTC
**
286559 TACTATATTATTCATCATT
1 TACTATATTATTCAAAATT
286578 TACTA-ATTATTCAAAATT
1 TACTATATTATTCAAAATT
286596 T
1 T
286597 TTTATAAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 12 0.71
19 5 0.29
ACGTcount: A:0.37, C:0.13, G:0.00, T:0.50
Consensus pattern (19 bp):
TACTATATTATTCAAAATT
Found at i:289440 original size:49 final size:45
Alignment explanation
Indices: 289312--289449 Score: 125
Period size: 49 Copynumber: 2.8 Consensus size: 45
289302 TATTATATGG
* *
289312 ACTTTATTTTTTAAATATTTATTAATTTAAATTTAAATACATTAATA
1 ACTTTA-TTTTTAAATATTTATTAATTTAAATATAAATACATT-AGA
* *
289359 AATTTATATATTTAAAATTTTTATTAATTTTAAAGTAAATAAATACCATGT-GA
1 ACTTTAT-T-TTT-AAATATTTATTAA-TTTAAA-T--ATAAATA-CAT-TAGA
*
289412 ACTTTATTTTTAAATATTTATTAATTTAAATTTAAATA
1 ACTTTATTTTTAAATATTTATTAATTTAAATATAAATA
289450 TAAATAAATT
Statistics
Matches: 75, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
46 7 0.09
47 6 0.08
48 4 0.05
49 18 0.24
50 18 0.24
51 4 0.05
52 1 0.01
53 13 0.17
54 3 0.04
55 1 0.01
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (45 bp):
ACTTTATTTTTAAATATTTATTAATTTAAATATAAATACATTAGA
Found at i:289448 original size:50 final size:46
Alignment explanation
Indices: 289312--289449 Score: 136
Period size: 50 Copynumber: 2.8 Consensus size: 46
289302 TATTATATGG
*
289312 ACTTTATTTTTTAAATATTTATTAATTTAAATTTAAATACATTAATA
1 ACTTTA-TTTTTAAATATTTATTAATTTAAATTTAAATACAATAATA
* * *
289359 AATTTATATATTTAAAATTTTTATTAATTTTAAA-GTAAATA-AATACCATGTGA
1 ACTTTAT-T-TTT-AAATATTTATTAA-TTTAAATTTAAATACAATA--A--T-A
289412 ACTTTATTTTTAAATATTTATTAATTTAAATTTAAATA
1 ACTTTATTTTTAAATATTTATTAATTTAAATTTAAATA
289450 TAAATAAATT
Statistics
Matches: 74, Mismatches: 7, Indels: 17
0.76 0.07 0.17
Matches are distributed among these distances:
46 1 0.01
47 6 0.08
48 6 0.08
49 24 0.32
50 25 0.34
51 3 0.04
52 2 0.03
53 7 0.09
ACGTcount: A:0.43, C:0.04, G:0.02, T:0.51
Consensus pattern (46 bp):
ACTTTATTTTTAAATATTTATTAATTTAAATTTAAATACAATAATA
Found at i:290006 original size:13 final size:15
Alignment explanation
Indices: 289988--290027 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
289978 TATTAATATT
289988 ATATTT-TTAT-TAA
1 ATATTTATTATATAA
290001 ATATTTATTATATAA
1 ATATTTATTATATAA
*
290016 A-ATTTAATATAT
1 ATATTTATTATAT
290028 TAATTTATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
13 6 0.25
14 14 0.58
15 4 0.17
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (15 bp):
ATATTTATTATATAA
Found at i:298778 original size:3 final size:3
Alignment explanation
Indices: 298770--298821 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
298760 TACCATTACC
298770 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
298818 ATT A
1 ATT A
298822 CTGGTGAAAA
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:300095 original size:5 final size:5
Alignment explanation
Indices: 300085--300115 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
300075 CAATCTAACC
*
300085 AATAT AATAT AATAT AATAA AATAT AATAT A
1 AATAT AATAT AATAT AATAT AATAT AATAT A
300116 GCAGAATTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (5 bp):
AATAT
Found at i:301114 original size:3 final size:3
Alignment explanation
Indices: 301108--301139 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
301098 TATATATAAG
301108 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
301140 TAAAAGAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:304416 original size:19 final size:19
Alignment explanation
Indices: 304380--304418 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
304370 AGTATCAGCC
*
304380 ATATATATAGATCAATAAA
1 ATATATATAAATCAATAAA
304399 ATATA-ATAAATCATATAAA
1 ATATATATAAATCA-ATAAA
304418 A
1 A
304419 AGTTAATGCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.62, C:0.05, G:0.03, T:0.31
Consensus pattern (19 bp):
ATATATATAAATCAATAAA
Found at i:305170 original size:2 final size:2
Alignment explanation
Indices: 305163--305196 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
305153 GAAACAAGCA
305163 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
305197 CTCTTTATGT
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):
AT
Found at i:307356 original size:4 final size:4
Alignment explanation
Indices: 307341--307373 Score: 57
Period size: 4 Copynumber: 8.0 Consensus size: 4
307331 TCTAATGTCT
307341 ATCC ATTCC ATCC ATCC ATCC ATCC ATCC ATCC
1 ATCC A-TCC ATCC ATCC ATCC ATCC ATCC ATCC
307374 CTTGTTTCCA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.24, C:0.48, G:0.00, T:0.27
Consensus pattern (4 bp):
ATCC
Found at i:311197 original size:15 final size:15
Alignment explanation
Indices: 311177--311208 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
311167 ACATGACTTG
311177 ATCTTTGGATCTCGC
1 ATCTTTGGATCTCGC
311192 ATCTTTGGATCTCGC
1 ATCTTTGGATCTCGC
311207 AT
1 AT
311209 ATACTCACAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.41
Consensus pattern (15 bp):
ATCTTTGGATCTCGC
Found at i:313439 original size:2 final size:2
Alignment explanation
Indices: 313432--313459 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
313422 CAAATGCCAT
313432 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
313460 GAGGGGCAAA
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:313911 original size:5 final size:5
Alignment explanation
Indices: 313898--313938 Score: 55
Period size: 5 Copynumber: 8.2 Consensus size: 5
313888 ATCCGCGTAA
* * *
313898 CATCT CATCG CATCG CATCG CATCG GATCG CATCG CCTCG C
1 CATCG CATCG CATCG CATCG CATCG CATCG CATCG CATCG C
313939 CTAGCCCATC
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.17, C:0.41, G:0.20, T:0.22
Consensus pattern (5 bp):
CATCG
Found at i:316696 original size:21 final size:21
Alignment explanation
Indices: 316670--316712 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
316660 TTTGTCATTG
316670 TGGTTCATCTCTTTTAAGCAC
1 TGGTTCATCTCTTTTAAGCAC
316691 TGGTTCATCTCTTTTAAGCAC
1 TGGTTCATCTCTTTTAAGCAC
316712 T
1 T
316713 TATATTCTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.19, C:0.23, G:0.14, T:0.44
Consensus pattern (21 bp):
TGGTTCATCTCTTTTAAGCAC
Found at i:317278 original size:16 final size:17
Alignment explanation
Indices: 317250--317283 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
317240 TTCTGGAGGT
317250 GAAGAATTTACTGTAAG
1 GAAGAATTTACTGTAAG
317267 GAAGAA-TTACTGTAAG
1 GAAGAATTTACTGTAAG
317283 G
1 G
317284 CAGCTGATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.06, G:0.26, T:0.26
Consensus pattern (17 bp):
GAAGAATTTACTGTAAG
Found at i:318971 original size:19 final size:19
Alignment explanation
Indices: 318947--318984 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
318937 TTGCTTCTCA
318947 CTTCTGCATATATATTGTG
1 CTTCTGCATATATATTGTG
318966 CTTCTGCATATATATTGTG
1 CTTCTGCATATATATTGTG
318985 TTGATTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.16, G:0.16, T:0.47
Consensus pattern (19 bp):
CTTCTGCATATATATTGTG
Found at i:320062 original size:3 final size:3
Alignment explanation
Indices: 320054--320082 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
320044 CATGTTTTTC
320054 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
320083 GCATATGTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:324042 original size:18 final size:19
Alignment explanation
Indices: 324002--324042 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
323992 AAAAAATTTG
*
324002 CAAT-TAGAATGAATAAAT
1 CAATCTAGAAAGAATAAAT
*
324020 GAATCTAGAAAGAA-AAAT
1 CAATCTAGAAAGAATAAAT
324038 CAATC
1 CAATC
324043 AAATAAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (19 bp):
CAATCTAGAAAGAATAAAT
Found at i:324300 original size:22 final size:22
Alignment explanation
Indices: 324270--324313 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
324260 TAAAATATAA
* *
324270 TAAAAAATAATTTTTTAAAAAT
1 TAAAAAATAATATTATAAAAAT
*
324292 TAAATAATAATATTATAAAAAT
1 TAAAAAATAATATTATAAAAAT
324314 ATTTATATTT
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TAAAAAATAATATTATAAAAAT
Found at i:325788 original size:2 final size:2
Alignment explanation
Indices: 325781--325805 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
325771 ATTCAACCCC
325781 CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT C
325806 CTTTCCTTTA
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:331494 original size:3 final size:3
Alignment explanation
Indices: 331481--331522 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
331471 ACTTACTTAC
331481 AAT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
331523 GTTGTAAGCA
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:335501 original size:4 final size:4
Alignment explanation
Indices: 335492--335517 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
335482 GCTGATTAAC
335492 AATA AATA AATA AATA AATA AATA AA
1 AATA AATA AATA AATA AATA AATA AA
335518 AAGTGCTGAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:340189 original size:6 final size:6
Alignment explanation
Indices: 340149--340188 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
340139 TAAAAATTAA
* *
340149 AAATTT AAATTT AAATTT AAATTC AAATTT AAATAT AAAT
1 AAATTT AAATTT AAATTT AAATTT AAATTT AAATTT AAAT
340189 AATTATTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (6 bp):
AAATTT
Found at i:340318 original size:35 final size:35
Alignment explanation
Indices: 340279--340347 Score: 86
Period size: 35 Copynumber: 2.0 Consensus size: 35
340269 ATCAATTAAA
*
340279 TTTAAATTTTA-AAAATAAAAAATATTTAATATATT
1 TTTAAAATTTATAAAATAAAAAATA-TTAATATATT
* * *
340314 TTTAAAATTTATATAATATAAATTATTAATATAT
1 TTTAAAATTTATAAAATAAAAAATATTAATATAT
340348 AAATTTTATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
35 19 0.66
36 10 0.34
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
TTTAAAATTTATAAAATAAAAAATATTAATATATT
Found at i:340336 original size:15 final size:15
Alignment explanation
Indices: 340318--340418 Score: 68
Period size: 15 Copynumber: 6.4 Consensus size: 15
340308 TATATTTTTA
340318 AAATTTATATAATAT
1 AAATTTATATAATAT
340333 AAA-TTAT-TAATATAT
1 AAATTTATAT-A-ATAT
340348 AAATTT-TATAATTAT
1 AAATTTATATAA-TAT
*
340363 AAAATATTTTAT-ATAT
1 -AAAT-TTATATAATAT
340379 -AATTATAATATAATAT
1 AAATT-T-ATATAATAT
340395 AATATATTAATATAATAT
1 AA-AT-TT-ATATAATAT
340413 AAATTT
1 AAATTT
340419 TAAATTATTA
Statistics
Matches: 71, Mismatches: 1, Indels: 27
0.72 0.01 0.27
Matches are distributed among these distances:
13 2 0.03
14 10 0.14
15 18 0.25
16 16 0.23
17 6 0.08
18 18 0.25
19 1 0.01
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
AAATTTATATAATAT
Found at i:340392 original size:5 final size:5
Alignment explanation
Indices: 340375--340414 Score: 57
Period size: 5 Copynumber: 8.2 Consensus size: 5
340365 AATATTTTAT
340375 ATATA ATTATA ATATA ATATA ATAT- AT-TA ATATA ATATA A
1 ATATA A-TATA ATATA ATATA ATATA ATATA ATATA ATATA A
340415 ATTTTAAATT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
3 1 0.03
4 4 0.12
5 22 0.69
6 5 0.16
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
ATATA
Found at i:340394 original size:18 final size:17
Alignment explanation
Indices: 340324--340414 Score: 72
Period size: 18 Copynumber: 5.6 Consensus size: 17
340314 TTTAAAATTT
340324 ATATAATATAAATTATTA
1 ATATAATAT-AATTATTA
340342 ATAT-ATA-AATT-TT-
1 ATATAATATAATTATTA
* *
340355 ATA-ATTATAAAATATT-
1 ATATAATAT-AATTATTA
*
340371 TTAT-ATATAATTA-TA
1 ATATAATATAATTATTA
340386 ATATAATATAATATATTA
1 ATATAATATAAT-TATTA
340404 ATATAATATAA
1 ATATAATATAA
340415 ATTTTAAATT
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
13 5 0.09
14 3 0.05
15 14 0.24
16 14 0.24
17 5 0.09
18 17 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATATAATTATTA
Found at i:340405 original size:13 final size:13
Alignment explanation
Indices: 340365--340413 Score: 53
Period size: 13 Copynumber: 3.5 Consensus size: 13
340355 ATAATTATAA
*
340365 AATATTTTATATAT
1 AATATATTA-ATAT
340379 AATTATAATATAATAT
1 AA-TAT-AT-TAATAT
340395 AATATATTAATAT
1 AATATATTAATAT
340408 AATATA
1 AATATA
340414 AATTTTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
13 12 0.39
14 4 0.13
15 6 0.19
16 7 0.23
17 2 0.06
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTAATAT
Found at i:348825 original size:216 final size:216
Alignment explanation
Indices: 348398--349471 Score: 2042
Period size: 216 Copynumber: 5.0 Consensus size: 216
348388 ATCTAAACCC
*
348398 ATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
348463 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCC--T-T--TATACACATACAATCAAAGGGG
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
348523 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
131 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
*
348588 ACAAAAGTATCAAGAAGCTCA
196 ACAAAAGTATTAAGAAGCTCA
*
348609 ATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
348674 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
348739 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
131 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
348804 ACAAAAGTATTAAGAAGCTCA
196 ACAAAAGTATTAAGAAGCTCA
*
348825 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAGTCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
348890 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCC--T-T--TATACACATACAATCAAAGGGG
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
348950 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
131 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
349015 ACAAAAGTATTAAGAAGCTCA
196 ACAAAAGTATTAAGAAGCTCA
349036 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
349101 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
349166 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
131 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
349231 ACAAAAGTATTAAGAAGCTCA
196 ACAAAAGTATTAAGAAGCTCA
349252 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
349317 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
349382 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
131 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
349447 ACAAAAGTATTAAGAAGCTCA
196 ACAAAAGTATTAAGAAGCTCA
349468 ATAA
1 ATAA
349472 TTGAAAACGT
Statistics
Matches: 849, Mismatches: 4, Indels: 15
0.98 0.00 0.02
Matches are distributed among these distances:
211 309 0.36
213 3 0.00
214 3 0.00
216 534 0.63
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (216 bp):
ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
ACAAAAGTATTAAGAAGCTCA
Found at i:349193 original size:427 final size:427
Alignment explanation
Indices: 348398--349471 Score: 2067
Period size: 427 Copynumber: 2.5 Consensus size: 427
348388 ATCTAAACCC
*
348398 ATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
348463 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACACATACAATCAAAGGGGGGTAA
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACACATACAATCAAAGGGGGGTAA
348528 AACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAAACAAA
131 AACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAAACAAA
*
348593 AGTATCAAGAAGCTCAATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAA
196 AGTATTAAGAAGCTCAATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAA
348658 TTTTATCATCCAATCAGACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACA
261 TTTTATCATCCAATCAGACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACA
348723 CATACAATCAAAGGGGGGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTA
326 CATACAATCAAAGGGGGGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTA
348788 TATCACTTTAAGGAAAACAAAAGTATTAAGAAGCTCA
391 TATCACTTTAAGGAAAACAAAAGTATTAAGAAGCTCA
*
348825 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAGTCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
348890 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACACATACAATCAAAGGGGGGTAA
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACACATACAATCAAAGGGGGGTAA
348955 AACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAAACAAA
131 AACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAAACAAA
*
349020 AGTATTAAGAAGCTCAATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAA
196 AGTATTAAGAAGCTCAATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAA
349085 TTTTATCATCCAATCAGACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACA
261 TTTTATCATCCAATCAGACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACA
349150 CATACAATCAAAGGGGGGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTA
326 CATACAATCAAAGGGGGGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTA
349215 TATCACTTTAAGGAAAACAAAAGTATTAAGAAGCTCA
391 TATCACTTTAAGGAAAACAAAAGTATTAAGAAGCTCA
349252 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
1 ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
349317 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACACATACAATCAAAGGGG
66 GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCC--T-T--TATACACATACAATCAAAGGGG
349382 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
126 GGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAA
349447 ACAAAAGTATTAAGAAGCTCAATAA
191 ACAAAAGTATTAAGAAGCTCAATAA
349472 TTGAAAACGT
Statistics
Matches: 637, Mismatches: 5, Indels: 5
0.98 0.01 0.01
Matches are distributed among these distances:
427 523 0.82
429 1 0.00
430 1 0.00
432 112 0.18
ACGTcount: A:0.39, C:0.16, G:0.15, T:0.31
Consensus pattern (427 bp):
ATAAAATTTTCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAATTTTATCATCCAATCA
GACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACACATACAATCAAAGGGGGGTAA
AACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTATATCACTTTAAGGAAAACAAA
AGTATTAAGAAGCTCAATAAAATTTGCACCCTCAATATTCGTTTTCTTTTAGCAGTCTTTTAAAA
TTTTATCATCCAATCAGACGTGTAAAAGCAGATGTTGAGTATGTTGCTTTCCTTTATACTATACA
CATACAATCAAAGGGGGGTAAAACTTTATAACATGATCAGCTGAAAAGAAAAAGAAGGAACACTA
TATCACTTTAAGGAAAACAAAAGTATTAAGAAGCTCA
Found at i:352285 original size:35 final size:34
Alignment explanation
Indices: 352246--352351 Score: 94
Period size: 31 Copynumber: 3.1 Consensus size: 34
352236 TTTAATATTT
* * *
352246 TTTAAAATTTTATATTTTTTTATATTATAATTATA
1 TTTAAAATTTTATATTTATATAAATTATAA-TATA
*
352281 TTTAAAATATTATATATTTATATAAATTTTAATATA
1 TTTAAAAT-TT-TATATTTATATAAATTATAATATA
* *
352317 -TTAATAA-TTT-TA-TTATAAAAATTTTAATATA
1 TTTAA-AATTTTATATTTATATAAATTATAATATA
352348 TTTA
1 TTTA
352352 TATTATATTT
Statistics
Matches: 62, Mismatches: 5, Indels: 11
0.79 0.06 0.14
Matches are distributed among these distances:
31 18 0.29
32 5 0.08
33 1 0.02
34 2 0.03
35 12 0.19
36 8 0.13
37 16 0.26
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (34 bp):
TTTAAAATTTTATATTTATATAAATTATAATATA
Found at i:352306 original size:20 final size:20
Alignment explanation
Indices: 352267--352306 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
352257 ATATTTTTTT
*
352267 ATATTATAATTATATTTAAA
1 ATATTATAATTATATATAAA
352287 ATATTATATATT-TATATAAA
1 ATATTATA-ATTATATATAAA
352307 TTTTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATTATAATTATATATAAA
Found at i:352315 original size:20 final size:20
Alignment explanation
Indices: 352292--352388 Score: 70
Period size: 21 Copynumber: 5.2 Consensus size: 20
352282 TTAAAATATT
352292 ATATATTTATATAAATTTTA
1 ATATATTTATATAAATTTTA
352312 ATATA-TTA-AT-AATTTT-
1 ATATATTTATATAAATTTTA
352328 AT-TA--TA-A-AAATTTTA
1 ATATATTTATATAAATTTTA
*
352343 ATATATTTATATTATATTTT-
1 ATATATTTATA-TAAATTTTA
* *
352363 TTATATTTTATATAATATTTAA
1 ATATA-TTTATATAA-ATTTTA
352385 ATAT
1 ATAT
352389 TAATAAATCT
Statistics
Matches: 61, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
14 9 0.15
15 4 0.07
16 4 0.07
17 6 0.10
18 4 0.07
19 4 0.07
20 11 0.18
21 16 0.26
22 3 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
ATATATTTATATAAATTTTA
Found at i:352389 original size:20 final size:20
Alignment explanation
Indices: 352310--352389 Score: 70
Period size: 22 Copynumber: 3.8 Consensus size: 20
352300 ATATAAATTT
*
352310 TAATATATTAATAATTTTATTA
1 TAATATTTTAAT-ATTTTA-TA
*
352332 TAAAAATTTTAATATATTTATA
1 T-AATATTTTAATAT-TTTATA
* *
352354 TTATATTTTTTATATTTTATA
1 TAATA-TTTTAATATTTTATA
*
352375 TAATATTTAAATATT
1 TAATATTTTAATATT
352390 AATAAATCTA
Statistics
Matches: 47, Mismatches: 8, Indels: 8
0.75 0.13 0.13
Matches are distributed among these distances:
20 8 0.17
21 12 0.26
22 14 0.30
23 13 0.28
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TAATATTTTAATATTTTATA
Found at i:356560 original size:19 final size:20
Alignment explanation
Indices: 356519--356564 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
356509 TTCACATAAA
*
356519 TTTTAAATAAATATTATATT
1 TTTTAATTAAATATTATATT
356539 TTTTAATTAAATA-TAT-TGT
1 TTTTAATTAAATATTATAT-T
356558 TTTTAAT
1 TTTTAAT
356565 ATATATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 1 0.04
19 11 0.46
20 12 0.50
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (20 bp):
TTTTAATTAAATATTATATT
Found at i:356603 original size:23 final size:24
Alignment explanation
Indices: 356573--356618 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
356563 ATATATATTT
356573 AATAATT-AAT-TTTTTAAATTAAA
1 AATAATTAAATATTTTT-AATTAAA
356596 AATAATTAAATATTTTTAATTAA
1 AATAATTAAATATTTTTAATTAA
356619 TTAAATCATG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 7 0.33
24 9 0.43
25 5 0.24
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (24 bp):
AATAATTAAATATTTTTAATTAAA
Found at i:356624 original size:26 final size:24
Alignment explanation
Indices: 356541--356624 Score: 68
Period size: 24 Copynumber: 3.4 Consensus size: 24
356531 ATTATATTTT
*
356541 TTAATTAAATATATT--GTTTTTAA
1 TTAATTAAATA-ATTAATTTTTTAA
*
356564 TATATATTTAATAATTAATTTTTTAAA
1 T-TA-ATTAAATAATTAATTTTTT-AA
356591 TTAA--AAATAATTAAATATTTTTAA
1 TTAATTAAATAATT-AAT-TTTTTAA
356615 TTAATTAAAT
1 TTAATTAAAT
356625 CATGATTTAT
Statistics
Matches: 49, Mismatches: 3, Indels: 15
0.73 0.04 0.22
Matches are distributed among these distances:
23 8 0.16
24 14 0.29
25 13 0.27
26 11 0.22
27 3 0.06
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.52
Consensus pattern (24 bp):
TTAATTAAATAATTAATTTTTTAA
Found at i:356695 original size:17 final size:18
Alignment explanation
Indices: 356670--356703 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
356660 TTAAATTAAA
*
356670 TAAATTTAA-AAAAATTT
1 TAAAATTAATAAAAATTT
356687 TAAAATTAATAAAAATT
1 TAAAATTAATAAAAATT
356704 AAATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (18 bp):
TAAAATTAATAAAAATTT
Found at i:373046 original size:2 final size:2
Alignment explanation
Indices: 373039--373064 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
373029 AGGTACAAGC
373039 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
373065 TTGAAACAAA
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:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:374033 original size:2 final size:2
Alignment explanation
Indices: 374026--374050 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
374016 ATATCAATAC
374026 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
374051 AGACAATCCA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:375277 original size:2 final size:2
Alignment explanation
Indices: 375272--375308 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
375262 ATATATATAA
375272 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
375309 TCTTATCTAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:376378 original size:6 final size:6
Alignment explanation
Indices: 376369--376403 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
376359 CCACTGCAGC
*
376369 CACAGG CACAAG CACAGG CACAGG CACAGG CACAG
1 CACAGG CACAGG CACAGG CACAGG CACAGG CACAG
376404 CCTGCCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.37, C:0.34, G:0.29, T:0.00
Consensus pattern (6 bp):
CACAGG
Found at i:378103 original size:2 final size:2
Alignment explanation
Indices: 378096--378126 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
378086 ATTTACTATG
378096 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
378127 GAATATCTTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:379433 original size:2 final size:2
Alignment explanation
Indices: 379428--379465 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
379418 GAAGTATTCA
379428 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
379466 GACAAAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:380319 original size:19 final size:19
Alignment explanation
Indices: 380276--380319 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
380266 TTTTAATATT
**
380276 TTAATTTTTATTTAAAAAA
1 TTAATTTTTAAATAAAAAA
*
380295 TT-ATTTTTAAATGAAAAA
1 TTAATTTTTAAATAAAAAA
380313 TTAATTT
1 TTAATTT
380320 ATATTACAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (19 bp):
TTAATTTTTAAATAAAAAA
Found at i:380344 original size:15 final size:17
Alignment explanation
Indices: 380310--380348 Score: 55
Period size: 15 Copynumber: 2.4 Consensus size: 17
380300 TTTAAATGAA
*
380310 AAATTAATTTATATTAC
1 AAATTAATTTATAGTAC
380327 AAATTAA-TTA-AGTAC
1 AAATTAATTTATAGTAC
380342 AAATTAA
1 AAATTAA
380349 ACCCTAAAAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.52
16 3 0.14
17 7 0.33
ACGTcount: A:0.54, C:0.05, G:0.03, T:0.38
Consensus pattern (17 bp):
AAATTAATTTATAGTAC
Found at i:384338 original size:18 final size:18
Alignment explanation
Indices: 384311--384346 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
384301 ATATAGACTA
*
384311 AGTTTTAAAGGTTAAAAC
1 AGTTTCAAAGGTTAAAAC
384329 AGTTTCAAAGGTTAAAAC
1 AGTTTCAAAGGTTAAAAC
384347 TTTAAAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.44, C:0.08, G:0.17, T:0.31
Consensus pattern (18 bp):
AGTTTCAAAGGTTAAAAC
Found at i:387661 original size:2 final size:2
Alignment explanation
Indices: 387654--387687 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
387644 AACAAGCAAT
387654 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
387688 CACACACAGT
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:395365 original size:56 final size:56
Alignment explanation
Indices: 395271--395381 Score: 161
Period size: 56 Copynumber: 2.0 Consensus size: 56
395261 GTCTGATAAC
* * *
395271 ATTATAAGGTGTTGAATATTAACAGTTCCCATGGTTTGATCTTTTAATCATTGTTT
1 ATTATAAAGTGCTGAATATTAACAGTTCCCATGATTTGATCTTTTAATCATTGTTT
* *
395327 ATTATAAAGTGCTGAATATTAACAGTT-TCAGTGATTTGATTTTTTAATCATTGTT
1 ATTATAAAGTGCTGAATATTAACAGTTCCCA-TGATTTGATCTTTTAATCATTGTT
395382 GGTTGTGCAA
Statistics
Matches: 49, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
55 2 0.04
56 47 0.96
ACGTcount: A:0.29, C:0.09, G:0.15, T:0.47
Consensus pattern (56 bp):
ATTATAAAGTGCTGAATATTAACAGTTCCCATGATTTGATCTTTTAATCATTGTTT
Found at i:397307 original size:2 final size:2
Alignment explanation
Indices: 397300--397335 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
397290 TTTAACATTA
397300 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
397336 GTGTGTGTAT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:397460 original size:72 final size:72
Alignment explanation
Indices: 397379--397524 Score: 249
Period size: 72 Copynumber: 2.0 Consensus size: 72
397369 CATTGCTCCT
*
397379 GATCTGGCGTTGCTGATGCATTAGAAACATCA-GAATATAAATTGGTTGGATAAAGAAGAAGATT
1 GATCTGGCGTTGCTGATGCATTAGAAACATCAGGAA-ATAAATTGGTTGGATAAAGAAGAAAATT
397443 CAAGCTTC
65 CAAGCTTC
* *
397451 GATCTGGCGTTGCTGATGCATTAGAAACATCAGGGAATAAGTTGGTTGGATAAAGAAGAAAATTC
1 GATCTGGCGTTGCTGATGCATTAGAAACATCAGGAAATAAATTGGTTGGATAAAGAAGAAAATTC
397516 AAGCTTC
66 AAGCTTC
397523 GA
1 GA
397525 CTGAAATGAA
Statistics
Matches: 70, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
72 68 0.97
73 2 0.03
ACGTcount: A:0.36, C:0.12, G:0.25, T:0.27
Consensus pattern (72 bp):
GATCTGGCGTTGCTGATGCATTAGAAACATCAGGAAATAAATTGGTTGGATAAAGAAGAAAATTC
AAGCTTC
Found at i:409546 original size:20 final size:20
Alignment explanation
Indices: 409481--409548 Score: 63
Period size: 20 Copynumber: 3.5 Consensus size: 20
409471 TAATTTTACA
*
409481 TATTT-TTATAATTTTTATAT
1 TATTTATTAT-ATTTTTATTT
*
409501 CATTTA-TAT-TTATTTAATTT
1 TATTTATTATATT-TTT-ATTT
409521 TA-TTATTATATTTTTATTT
1 TATTTATTATATTTTTATTT
409540 TATTTATTA
1 TATTTATTA
409549 AAATTATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
18 2 0.05
19 12 0.31
20 23 0.59
21 2 0.05
ACGTcount: A:0.29, C:0.01, G:0.00, T:0.69
Consensus pattern (20 bp):
TATTTATTATATTTTTATTT
Found at i:409628 original size:2 final size:2
Alignment explanation
Indices: 409621--409645 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
409611 TAATCATTAA
409621 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
409646 AGAAAATAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:413357 original size:32 final size:32
Alignment explanation
Indices: 413316--413376 Score: 104
Period size: 32 Copynumber: 1.9 Consensus size: 32
413306 TAACAATTTA
413316 GTCATTGTTACTTTCCATTGTTAGCACATCGT
1 GTCATTGTTACTTTCCATTGTTAGCACATCGT
* *
413348 GTCATTGTTATTTTTCATTGTTAGCACAT
1 GTCATTGTTACTTTCCATTGTTAGCACAT
413377 TAACAATTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.20, C:0.18, G:0.15, T:0.48
Consensus pattern (32 bp):
GTCATTGTTACTTTCCATTGTTAGCACATCGT
Found at i:415182 original size:2 final size:2
Alignment explanation
Indices: 415175--415223 Score: 53
Period size: 2 Copynumber: 24.5 Consensus size: 2
415165 AAAACAATAA
* * * * *
415175 AT AT AT AT AT AT AT AT AC AT AT AC AC AT AC AT AT CT 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
415217 AT AT AT A
1 AT AT AT A
415224 CCTCTAATTT
Statistics
Matches: 39, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:417169 original size:2 final size:2
Alignment explanation
Indices: 417164--417204 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
417154 AAGAAAAAAG
417164 TA 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 TA T
417205 TGTGGAAAGG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:418965 original size:17 final size:16
Alignment explanation
Indices: 418936--418986 Score: 57
Period size: 17 Copynumber: 3.1 Consensus size: 16
418926 CATTTATTTT
*
418936 TAAATAATATAAATAAA
1 TAAATTATATAAA-AAA
*
418953 TAAATTATTTAAAAATA
1 TAAATTATATAAAAA-A
*
418970 TAATTTATATAAAAAA
1 TAAATTATATAAAAAA
418986 T
1 T
418987 TATCTTATCA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
16 4 0.14
17 25 0.86
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (16 bp):
TAAATTATATAAAAAA
Found at i:420195 original size:19 final size:19
Alignment explanation
Indices: 420171--420212 Score: 59
Period size: 19 Copynumber: 2.2 Consensus size: 19
420161 ATAGCTAAAC
*
420171 GTTT-AAAATTACTTATGAA
1 GTTTAAAAATTACGT-TGAA
420190 GTTTAAAAATTACGTTGAA
1 GTTTAAAAATTACGTTGAA
420209 GTTT
1 GTTT
420213 TGACCTAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (19 bp):
GTTTAAAAATTACGTTGAA
Found at i:420251 original size:3 final size:3
Alignment explanation
Indices: 420245--420274 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
420235 CAACAACAAC
420245 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
420275 GATGATAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:427599 original size:2 final size:2
Alignment explanation
Indices: 427592--427626 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
427582 GATTAAAGCT
427592 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 T
427627 TGGGTGTCAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:435553 original size:11 final size:11
Alignment explanation
Indices: 435537--435578 Score: 57
Period size: 11 Copynumber: 3.7 Consensus size: 11
435527 ATATCAAACT
*
435537 TTAAATTTTAA
1 TTAAATTTAAA
435548 TTAAATTTAAA
1 TTAAATTTAAA
435559 TTAAATTTCAAA
1 TTAAATTT-AAA
*
435571 TCAAATTT
1 TTAAATTT
435579 CAACTTTCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
11 18 0.64
12 10 0.36
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (11 bp):
TTAAATTTAAA
Found at i:435810 original size:30 final size:30
Alignment explanation
Indices: 435765--435826 Score: 90
Period size: 30 Copynumber: 2.1 Consensus size: 30
435755 TTTACAATTT
435765 TTTTATTAATATAATTTTGTAAATATTGTAA
1 TTTTATTAATATAATTTTGTAAATATT-TAA
* *
435796 TTTT-TTATTATAATTTTGTAATTATTTAA
1 TTTTATTAATATAATTTTGTAAATATTTAA
435825 TT
1 TT
435827 ACAATAATTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 5 0.17
30 20 0.69
31 4 0.14
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (30 bp):
TTTTATTAATATAATTTTGTAAATATTTAA
Found at i:438925 original size:13 final size:13
Alignment explanation
Indices: 438909--438945 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
438899 ATAAATTTTA
438909 AATATATTAAATT
1 AATATATTAAATT
* *
438922 AATATAATATATT
1 AATATATTAAATT
438935 AATATATTAAA
1 AATATATTAAA
438946 ATTTATATAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AATATATTAAATT
Found at i:438938 original size:26 final size:25
Alignment explanation
Indices: 438890--438969 Score: 90
Period size: 26 Copynumber: 3.1 Consensus size: 25
438880 AAGTAATTAA
*
438890 AAATATAATATAAATTTTAAATATATT
1 AAAT-TAATATAAATATT-AATATATT
438917 AAATTAATATAATATATTAATATATT
1 AAATTAATATAA-ATATTAATATATT
* *
438943 AAAATTTATATAAATA-TAAAATATT
1 -AAATTAATATAAATATTAATATATT
438968 AA
1 AA
438970 TTCGTACCGA
Statistics
Matches: 48, Mismatches: 3, Indels: 7
0.83 0.05 0.12
Matches are distributed among these distances:
24 2 0.04
25 8 0.17
26 19 0.40
27 19 0.40
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (25 bp):
AAATTAATATAAATATTAATATATT
Found at i:439432 original size:18 final size:19
Alignment explanation
Indices: 439397--439437 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
439387 TTTCATATTT
*
439397 TTTATTTTTAATAATTAAA
1 TTTATTTATAATAATTAAA
439416 TTTATTTATAA-AATTAAA
1 TTTATTTATAATAATTAAA
439434 TTTA
1 TTTA
439438 AAAAATGGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 11 0.52
19 10 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TTTATTTATAATAATTAAA
Found at i:440466 original size:13 final size:14
Alignment explanation
Indices: 440437--440469 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
440427 TAAAAGAATG
*
440437 ATTATTAATTTTAA
1 ATTATTAATTATAA
440451 ATTATTAA-TATAA
1 ATTATTAATTATAA
440464 ATTATT
1 ATTATT
440470 TTCTTACATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.56
14 8 0.44
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATTATTAATTATAA
Found at i:441980 original size:15 final size:15
Alignment explanation
Indices: 441960--441993 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
441950 ATAAATAAAT
441960 ATTTTTAAT-TAATTA
1 ATTTTTAATATAA-TA
441975 ATTTTTAATATAATA
1 ATTTTTAATATAATA
441990 ATTT
1 ATTT
441994 AAAATTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 15 0.83
16 3 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATTTTTAATATAATA
Found at i:442334 original size:8 final size:8
Alignment explanation
Indices: 442321--442349 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
442311 GTTTACATTC
442321 AGAAAAAA
1 AGAAAAAA
442329 AGAAAAAA
1 AGAAAAAA
442337 A-AAAAAA
1 AGAAAAAA
442344 AGAAAA
1 AGAAAA
442350 GACATGTTCA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (8 bp):
AGAAAAAA
Found at i:443941 original size:22 final size:23
Alignment explanation
Indices: 443882--443944 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
443872 AATGATATTC
* * *
443882 AATATATAAAAATTTAAATTTTA
1 AATATATAAAATTTTTATTTTTA
443905 AATATATAAAATTTTTATTTTTA
1 AATATATAAAATTTTTATTTTTA
**
443928 AAT-TATAATTTTTTTAT
1 AATATATAAAATTTTTAT
443945 AAAAATAATA
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
22 12 0.34
23 23 0.66
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (23 bp):
AATATATAAAATTTTTATTTTTA
Found at i:444413 original size:20 final size:22
Alignment explanation
Indices: 444388--444427 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
444378 ATATAATTAT
444388 TTTTAA-AAT-ATAATATTTAA
1 TTTTAATAATCATAATATTTAA
*
444408 TTTTAATATTCATAATATTT
1 TTTTAATAATCATAATATTT
444428 TTATTTTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
21 2 0.12
22 9 0.53
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (22 bp):
TTTTAATAATCATAATATTTAA
Found at i:446228 original size:24 final size:23
Alignment explanation
Indices: 446201--446245 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
446191 ATCTTTGTTT
*
446201 TAAATCGAAATAGAATCTTAAATG
1 TAAAACGAAATAGAAT-TTAAATG
**
446225 TAAAACTCAATAGAATTTAAA
1 TAAAACGAAATAGAATTTAAA
446246 CTTTTAATTC
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 5 0.28
24 13 0.72
ACGTcount: A:0.53, C:0.09, G:0.09, T:0.29
Consensus pattern (23 bp):
TAAAACGAAATAGAATTTAAATG
Found at i:450856 original size:25 final size:25
Alignment explanation
Indices: 450799--450857 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
450789 GTCTATTTTT
450799 CATATA-TTATAGTATTAATAAATA
1 CATATATTTATAGTATTAATAAATA
* *
450823 -ATATAATTTATATTTATTAA-ATATA
1 CATAT-ATTTATA-GTATTAATAAATA
450848 CATATATTTA
1 CATATATTTA
450858 CACACAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
23 4 0.14
24 1 0.03
25 14 0.48
26 10 0.34
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.47
Consensus pattern (25 bp):
CATATATTTATAGTATTAATAAATA
Found at i:451768 original size:2 final size:2
Alignment explanation
Indices: 451761--451787 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
451751 TTATACATAC
451761 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
451788 AGTTGCTGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:452728 original size:2 final size:2
Alignment explanation
Indices: 452721--452745 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
452711 AAACATAACC
452721 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
452746 TGTTAATTTA
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:459243 original size:21 final size:21
Alignment explanation
Indices: 459210--459253 Score: 63
Period size: 20 Copynumber: 2.1 Consensus size: 21
459200 GCCATTTTAT
459210 ATAAAAAGAATTAATTAATCAA
1 ATAAAAAGAATTAA-TAATCAA
*
459232 ATAAAAAG-ATTAATGATCAA
1 ATAAAAAGAATTAATAATCAA
459252 AT
1 AT
459254 CTACATTTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 8 0.38
21 5 0.24
22 8 0.38
ACGTcount: A:0.61, C:0.05, G:0.07, T:0.27
Consensus pattern (21 bp):
ATAAAAAGAATTAATAATCAA
Found at i:461334 original size:14 final size:15
Alignment explanation
Indices: 461310--461339 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
461300 GCAACTTTGG
461310 TTCCTTTTTATTTTT
1 TTCCTTTTTATTTTT
461325 TTCC-TTTTATTTTT
1 TTCCTTTTTATTTTT
461339 T
1 T
461340 AATTTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.73
15 4 0.27
ACGTcount: A:0.07, C:0.13, G:0.00, T:0.80
Consensus pattern (15 bp):
TTCCTTTTTATTTTT
Found at i:462249 original size:14 final size:15
Alignment explanation
Indices: 462230--462258 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
462220 TACAAATGTT
462230 ATTTTTAT-TAATTA
1 ATTTTTATGTAATTA
462244 ATTTTTATGTAATTA
1 ATTTTTATGTAATTA
462259 TATAAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.62
Consensus pattern (15 bp):
ATTTTTATGTAATTA
Found at i:463284 original size:17 final size:17
Alignment explanation
Indices: 463259--463293 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
463249 ATTATTAAAA
*
463259 TTTTGGCTGAATTTTGT
1 TTTTAGCTGAATTTTGT
*
463276 TTTTAGCTGACTTTTGT
1 TTTTAGCTGAATTTTGT
463293 T
1 T
463294 AGGCTATAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.11, C:0.09, G:0.20, T:0.60
Consensus pattern (17 bp):
TTTTAGCTGAATTTTGT
Found at i:467315 original size:3 final size:3
Alignment explanation
Indices: 467307--467339 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
467297 TATATATTTA
467307 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
467340 ATAAAATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:468474 original size:2 final size:2
Alignment explanation
Indices: 468467--468493 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
468457 CAATAACGTA
468467 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
468494 AGACTTGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:468833 original size:22 final size:21
Alignment explanation
Indices: 468807--468848 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
468797 TATAAATTAT
468807 TAAATTTATTTGTT-TTAAAAAA
1 TAAATTT-TTT-TTATTAAAAAA
468829 TAAATTTTTTTTATTAAAAA
1 TAAATTTTTTTTATTAAAAA
468849 TGATTTTTGC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 2 0.11
21 10 0.53
22 7 0.37
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (21 bp):
TAAATTTTTTTTATTAAAAAA
Found at i:474655 original size:3 final size:3
Alignment explanation
Indices: 474647--474684 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
474637 TTAATCAACA
474647 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 AT
474685 AACAGTGGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:475435 original size:2 final size:2
Alignment explanation
Indices: 475423--475452 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
475413 GATCCAATAC
475423 AG AG A- AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
475453 TCAATGGTGG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (2 bp):
AG
Found at i:480816 original size:34 final size:34
Alignment explanation
Indices: 480749--480964 Score: 265
Period size: 34 Copynumber: 6.4 Consensus size: 34
480739 ATGAAGTTAA
* * * *
480749 TGTTGATTAAAT-AGTGATTTAGTAGTTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * * * * *
480782 TATTGATTAAATGGGTGATTTGATGGTTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
480816 TGTTGACTAAAT-GGAGATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
*
480849 TGTTGATTAAATGGGAAATTTGGTAGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* *
480883 TGTTGATTAAATGGGTGATTTGGTGGCTTACCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
* * *
480917 TGTTGACTAAATGGGAGATTTGGTAGGTTGCCAT
1 TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
480951 TGTTGATTAAATGG
1 TGTTGATTAAATGG
480965 TGGTTTTTAC
Statistics
Matches: 157, Mismatches: 24, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
33 38 0.24
34 119 0.76
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (34 bp):
TGTTGATTAAATGGGAGATTTGGTAGCTTACCAT
Found at i:480930 original size:68 final size:67
Alignment explanation
Indices: 480749--480966 Score: 292
Period size: 67 Copynumber: 3.2 Consensus size: 67
480739 ATGAAGTTAA
* * * * * * * *
480749 TGTTGATTAAATAGTGATTTAGTAGTTTACCATTATTGATTAAATGGGTGATTTGATGGTTTGCC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
480814 AT
66 AT
* * * *
480816 TGTTGACTAAATGGAGATTTGGTAGCTTACCATTGTTGATTAAATGGGAAATTTGGTAGCTTACC
1 TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
480881 AT
66 AT
* * *
480883 TGTTGATTAAATGGGTGATTTGGTGGCTTACCATTGTTGACTAAATGGGAGATTTGGTAGGTTGC
1 TGTTGATTAAAT-GGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGC
480948 CAT
65 CAT
480951 TGTTGATTAAATGGTG
1 TGTTGATTAAATGGTG
480967 GTTTTTACCA
Statistics
Matches: 131, Mismatches: 19, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
67 70 0.53
68 61 0.47
ACGTcount: A:0.26, C:0.08, G:0.26, T:0.40
Consensus pattern (67 bp):
TGTTGATTAAATGGTGATTTGGTAGCTTACCATTGTTGATTAAATGGGAGATTTGGTAGCTTGCC
AT
Found at i:481958 original size:13 final size:12
Alignment explanation
Indices: 481923--481982 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
481913 TAATAATTTA
* *
481923 TTTTATATAAAT
1 TTTTATATTATT
*
481935 TTTAATA-TATT
1 TTTTATATTATT
481946 TATTTATATTATT
1 T-TTTATATTATT
481959 TTTTATATTATAT
1 TTTTATATTAT-T
*
481972 TTTTATTTTAT
1 TTTTATATTAT
481983 ATTTATATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 3 0.08
12 21 0.52
13 16 0.40
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTATATTATT
Found at i:481961 original size:24 final size:24
Alignment explanation
Indices: 481912--481978 Score: 68
Period size: 23 Copynumber: 2.8 Consensus size: 24
481902 ATTTTATATA
*
481912 TTAATA-ATTTATTTTATATAAATT
1 TTAATATATTTA-TTTATATTAATT
481936 TTAATATATTTATTTATATT-ATT
1 TTAATATATTTATTTATATTAATT
* *
481959 TT-TTATATTATATTTTTATT
1 TTAATATATT-TATTTATATT
481979 TTATATTTAT
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
22 6 0.16
23 14 0.37
24 13 0.34
25 5 0.13
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (24 bp):
TTAATATATTTATTTATATTAATT
Found at i:481983 original size:13 final size:13
Alignment explanation
Indices: 481933--481986 Score: 54
Period size: 13 Copynumber: 3.8 Consensus size: 13
481923 TTTTATATAA
*
481933 ATTTTAATATATTT
1 ATTTT-ATATTTTT
481947 ATTTATATTATTTTTT
1 ATTT-TA-TA-TTTTT
*
481963 ATATTATATTTTT
1 ATTTTATATTTTT
481976 ATTTTATATTT
1 ATTTTATATTT
481987 ATATAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
13 15 0.44
14 7 0.21
15 5 0.15
16 7 0.21
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (13 bp):
ATTTTATATTTTT
Found at i:485796 original size:16 final size:16
Alignment explanation
Indices: 485777--485826 Score: 68
Period size: 16 Copynumber: 3.1 Consensus size: 16
485767 AAATATAATA
485777 TAAATATATTAAAATT
1 TAAATATATTAAAATT
485793 TAAATA-ATATAAAATAT
1 TAAATATAT-TAAAAT-T
485810 T-AATATATTAAAATT
1 TAAATATATTAAAATT
485825 TA
1 TA
485827 TATAATATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
15 4 0.13
16 22 0.73
17 4 0.13
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TAAATATATTAAAATT
Found at i:485804 original size:30 final size:30
Alignment explanation
Indices: 485763--485839 Score: 109
Period size: 32 Copynumber: 2.5 Consensus size: 30
485753 TAAAATTATA
*
485763 TAAAAAATATAATATAAATATATTAAAATT
1 TAAATAATATAATATAAATATATTAAAATT
*
485793 TAAATAATATAAAATATTAATATATTAAAATT
1 TAAATAATAT--AATATAAATATATTAAAATT
*
485825 TATATAATATAATAT
1 TAAATAATATAATAT
485840 TTTAAATTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
30 14 0.33
32 28 0.67
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (30 bp):
TAAATAATATAATATAAATATATTAAAATT
Found at i:485805 original size:25 final size:25
Alignment explanation
Indices: 485771--485821 Score: 77
Period size: 25 Copynumber: 2.0 Consensus size: 25
485761 TATAAAAAAT
485771 ATAATATAAATATATTAAAAT-TTAA
1 ATAATATAAA-ATATTAAAATATTAA
*
485796 ATAATATAAAATATTAATATATTAA
1 ATAATATAAAATATTAAAATATTAA
485821 A
1 A
485822 ATTTATATAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 9 0.38
25 15 0.62
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATATAAAATATTAAAATATTAA
Found at i:485815 original size:32 final size:32
Alignment explanation
Indices: 485773--485836 Score: 110
Period size: 32 Copynumber: 2.0 Consensus size: 32
485763 TAAAAAATAT
485773 AATATAAATATATTAAAATTTAAATAATATAA
1 AATATAAATATATTAAAATTTAAATAATATAA
* *
485805 AATATTAATATATTAAAATTTATATAATATAA
1 AATATAAATATATTAAAATTTAAATAATATAA
485837 TATTTTAAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (32 bp):
AATATAAATATATTAAAATTTAAATAATATAA
Found at i:485841 original size:16 final size:16
Alignment explanation
Indices: 485786--485841 Score: 62
Period size: 16 Copynumber: 3.5 Consensus size: 16
485776 ATAAATATAT
*
485786 TAAAATTTAAATAATA
1 TAAAATTTATATAATA
485802 TAAAATATTA-AT-ATA
1 TAAAAT-TTATATAATA
485817 TTAAAATTTATATAATA
1 -TAAAATTTATATAATA
*
485834 TAATATTT
1 TAAAATTT
485842 TAAATTTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 8
0.80 0.02 0.18
Matches are distributed among these distances:
15 6 0.17
16 23 0.66
17 6 0.17
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATTTATATAATA
Found at i:489447 original size:176 final size:175
Alignment explanation
Indices: 488972--489483 Score: 760
Period size: 176 Copynumber: 2.9 Consensus size: 175
488962 GGTTCTTTAA
* * * *
488972 TAAGGTAATGTTTTGCTAGGCTATGGTTTCAACCATAGGAGTCATTTTTATGGCATAGGATTGTG
1 TAAGGTAATGTTTTGGTAGGCTATGGTTTCAACTATAGGAGTCA-TTTTATGGCATAGAATTGTC
* * *
489037 CTTGCGATGGCTTGTTATATTCTTGAGGTTCATGATGTTGGTGGAATTATTTTAATTATATTTCA
65 CTTGCGATGGCTTGTTACATTCTTAAGGTTCATGATGTTGGTGGAATTATTTTAAGTATATTTCA
* * *
489102 ATTTGATAGTAATTT-CTATATATTTTGTATCCCCTGAAGTTTGTAC
130 ATTTGATAATAATTTCCT-GATATTTTGTATCCCCTGAAGTTTGCAC
*
489148 TAAGGTAATATTTTGGTAGGCTATGGTTTTTCAACTATAGGAGTCATTTTAATGGCATAGAATTG
1 TAAGGTAATGTTTTGGTAGGCTATGG--TTTCAACTATAGGAGTCATTTT-ATGGCATAGAATTG
*
489213 TGCC-TGCGGTGGCTTGTTACATTCTTAAGGTTCATGATGTTGGTGGAATTATTTTAAGTATATT
63 T-CCTTGCGATGGCTTGTTACATTCTTAAGGTTCATGATGTTGGTGGAATTATTTTAAGTATATT
*
489277 TGAATTTGATAATAATTTCCTGATATTTTGTATCTCCCTGAAGTTTGCAC
127 TCAATTTGATAATAATTTCCTGATATTTTGTATC-CCCTGAAGTTTGCAC
* * *
489327 TAAGGTAATGCTTTGGTAGGCTATGGTTTCAACTAT-GTGAATCATTTTATGGCTTAGAATTGTC
1 TAAGGTAATGTTTTGGTAGGCTATGGTTTCAACTATAG-GAGTCATTTTATGGCATAGAATTGTC
* *
489391 CTTGTGATGGCTTGTTACATTCTTAAGGTTCATGATGTTGATGGAATTATTTTAAGTATATTTCA
65 CTTGCGATGGCTTGTTACATTCTTAAGGTTCATGATGTTGGTGGAATTATTTTAAGTATATTTCA
*
489456 ATTTGATAATAATTTCCTGATGTTTTGT
130 ATTTGATAATAATTTCCTGATATTTTGT
489484 TTTTGTATCT
Statistics
Matches: 306, Mismatches: 22, Indels: 16
0.89 0.06 0.05
Matches are distributed among these distances:
175 2 0.01
176 125 0.41
177 23 0.08
178 115 0.38
179 41 0.13
ACGTcount: A:0.25, C:0.11, G:0.21, T:0.44
Consensus pattern (175 bp):
TAAGGTAATGTTTTGGTAGGCTATGGTTTCAACTATAGGAGTCATTTTATGGCATAGAATTGTCC
TTGCGATGGCTTGTTACATTCTTAAGGTTCATGATGTTGGTGGAATTATTTTAAGTATATTTCAA
TTTGATAATAATTTCCTGATATTTTGTATCCCCTGAAGTTTGCAC
Found at i:500144 original size:19 final size:19
Alignment explanation
Indices: 500120--500159 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
500110 AAACTTCGTA
500120 TCAGATGTAGATACTTCTT
1 TCAGATGTAGATACTTCTT
500139 TCAGATGTAGATACTTCTT
1 TCAGATGTAGATACTTCTT
500158 TC
1 TC
500160 GATAGTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.25, C:0.17, G:0.15, T:0.42
Consensus pattern (19 bp):
TCAGATGTAGATACTTCTT
Found at i:501588 original size:55 final size:55
Alignment explanation
Indices: 501504--501608 Score: 174
Period size: 55 Copynumber: 1.9 Consensus size: 55
501494 CTCATCAAGC
* *
501504 CATGTCTATATTGCGAATTTTACAATTTTATTCGGTAATTTCGGATATGACATAA
1 CATGTCTATACTGCGAATTTTACAATTTTATTCGATAATTTCGGATATGACATAA
* *
501559 CATGTCTATACTGCGAATTTTATAATTTTATTCGATAATTTGGGATATGA
1 CATGTCTATACTGCGAATTTTACAATTTTATTCGATAATTTCGGATATGA
501609 TATGAGATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
55 46 1.00
ACGTcount: A:0.30, C:0.11, G:0.15, T:0.43
Consensus pattern (55 bp):
CATGTCTATACTGCGAATTTTACAATTTTATTCGATAATTTCGGATATGACATAA
Found at i:502027 original size:11 final size:11
Alignment explanation
Indices: 502011--502071 Score: 50
Period size: 12 Copynumber: 5.1 Consensus size: 11
502001 GACGTACATA
502011 AAAATAAAAAT
1 AAAATAAAAAT
502022 AAAATATAAACAT
1 AAAATA-AAA-AT
* *
502035 AACATATTAAAT
1 AAAATA-AAAAT
502047 AAATATAAAAAT
1 AAA-ATAAAAAT
*
502059 AATATAATAAAT
1 AAAATAA-AAAT
502071 A
1 A
502072 TGATATAATA
Statistics
Matches: 41, Mismatches: 5, Indels: 7
0.77 0.09 0.13
Matches are distributed among these distances:
11 10 0.24
12 18 0.44
13 13 0.32
ACGTcount: A:0.70, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
AAAATAAAAAT
Found at i:502055 original size:24 final size:24
Alignment explanation
Indices: 502014--502071 Score: 73
Period size: 24 Copynumber: 2.4 Consensus size: 24
502004 GTACATAAAA
*
502014 ATAA-AAATAAAATATAAACATAAC
1 ATAATAAAT-AAATATAAAAATAAC
* *
502038 ATATTAAATAAATATAAAAATAAT
1 ATAATAAATAAATATAAAAATAAC
502062 ATAATAAATA
1 ATAATAAATA
502072 TGATATAATA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 25 0.86
25 4 0.14
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (24 bp):
ATAATAAATAAATATAAAAATAAC
Found at i:502785 original size:4 final size:4
Alignment explanation
Indices: 502776--502800 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
502766 TGACCAAAAT
502776 TGGA TGGA TGGA TGGA TGGA TGGA T
1 TGGA TGGA TGGA TGGA TGGA TGGA T
502801 ATCGATGTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.48, T:0.28
Consensus pattern (4 bp):
TGGA
Done.