Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold270
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: 409424
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.36
File 4 of 4
Found at i:300365 original size:2 final size:2
Alignment explanation
Indices: 300358--300424 Score: 134
Period size: 2 Copynumber: 33.5 Consensus size: 2
300348 ATTTCAAGTT
300358 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
300400 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
300425 TTGGATCAGA
Statistics
Matches: 65, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 65 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:306288 original size:18 final size:17
Alignment explanation
Indices: 306247--306301 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
306237 ACGAATATCT
306247 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
306263 T-AAA-TTAT-TAATATA
1 TAAAATTTATATAA-ATA
306278 TCAAAATTTATATAAATA
1 T-AAAATTTATATAAATA
306296 TAAAAT
1 TAAAAT
306302 ATTTTAAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 11
0.75 0.00 0.25
Matches are distributed among these distances:
13 1 0.03
14 5 0.15
15 7 0.21
16 1 0.03
17 8 0.24
18 8 0.24
19 3 0.09
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:306334 original size:20 final size:19
Alignment explanation
Indices: 306309--306358 Score: 55
Period size: 20 Copynumber: 2.5 Consensus size: 19
306299 AATATTTTAA
306309 ACATGATTACGATATAATAT
1 ACATGATTACGATATAA-AT
* * *
306329 ATATGAATAAGATATAAAT
1 ACATGATTACGATATAAAT
306348 ACATGAATTAC
1 ACATG-ATTAC
306359 TAAGTACTTG
Statistics
Matches: 23, Mismatches: 6, Indels: 2
0.74 0.19 0.06
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (19 bp):
ACATGATTACGATATAAAT
Found at i:307123 original size:3 final size:3
Alignment explanation
Indices: 307117--307147 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
307107 AACCAAACAA
307117 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG A
307148 TTGTGATGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:308194 original size:22 final size:23
Alignment explanation
Indices: 308169--308212 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
308159 AAAAATTAAT
* *
308169 TTTATATTTTTTA-ATAATTTTA
1 TTTAAATTTTTTATAAAATTTTA
308191 TTTAAATTTTTTATAAAATTTT
1 TTTAAATTTTTTATAAAATTTT
308213 TAATTGAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
TTTAAATTTTTTATAAAATTTTA
Found at i:308602 original size:26 final size:27
Alignment explanation
Indices: 308573--308633 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
308563 TTTTATTAAC
308573 TTTTAAAAAATAATATATTAATT-ATA
1 TTTTAAAAAATAATATATTAATTAATA
* * * *
308599 TTTTTATAAATATTATATTATTTAATA
1 TTTTAAAAAATAATATATTAATTAATA
308626 TTATTAAA
1 TT-TTAAA
308634 CACTAATTAT
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
26 19 0.70
27 5 0.19
28 3 0.11
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTAAAAAATAATATATTAATTAATA
Found at i:308627 original size:15 final size:17
Alignment explanation
Indices: 308593--308629 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
308583 TAATATATTA
*
308593 ATTATATTTTTATAAAT
1 ATTATATTATTATAAAT
308610 ATTATATTATT-T-AAT
1 ATTATATTATTATAAAT
308625 ATTAT
1 ATTAT
308630 TAAACACTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 8 0.42
16 1 0.05
17 10 0.53
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTATATTATTATAAAT
Found at i:309270 original size:21 final size:23
Alignment explanation
Indices: 309233--309279 Score: 71
Period size: 21 Copynumber: 2.1 Consensus size: 23
309223 CATATATGTT
*
309233 TAAAAATGATGTTTGAAAATTGA
1 TAAAAATGATGTTTGAAAATTAA
309256 TAAAAA-GAT-TTTGAAAATTAA
1 TAAAAATGATGTTTGAAAATTAA
309277 TAA
1 TAA
309280 TTTATACCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 14 0.61
22 3 0.13
23 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.13, T:0.34
Consensus pattern (23 bp):
TAAAAATGATGTTTGAAAATTAA
Found at i:310600 original size:16 final size:17
Alignment explanation
Indices: 310568--310632 Score: 59
Period size: 17 Copynumber: 4.1 Consensus size: 17
310558 ATTATCATAT
*
310568 TAAAATTTATATAAATA
1 TAAAATATATATAAATA
310585 TAAAATATAT-TAAATA
1 TAAAATATATATAAATA
*
310601 T--AAT-TATA-ACATGA
1 TAAAATATATATAAAT-A
*
310615 TAAAAAATATATAAATA
1 TAAAATATATATAAATA
310632 T
1 T
310633 GATATATAAG
Statistics
Matches: 38, Mismatches: 4, Indels: 12
0.70 0.07 0.22
Matches are distributed among these distances:
13 6 0.16
14 5 0.13
16 9 0.24
17 15 0.39
18 3 0.08
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.37
Consensus pattern (17 bp):
TAAAATATATATAAATA
Found at i:310641 original size:32 final size:29
Alignment explanation
Indices: 310575--310641 Score: 82
Period size: 30 Copynumber: 2.2 Consensus size: 29
310565 TATTAAAATT
*
310575 TATATAAATATAAAATATATTAAATATAA
1 TATATAAATATAAAAAATATTAAATATAA
*
310604 T-TATAACATGATAAAAAATATATAAATATGA
1 TATATAA-AT-ATAAAAAATAT-TAAATATAA
310635 TATATAA
1 TATATAA
310642 GTAAACTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
28 5 0.16
29 3 0.09
30 10 0.31
31 9 0.28
32 5 0.16
ACGTcount: A:0.60, C:0.01, G:0.03, T:0.36
Consensus pattern (29 bp):
TATATAAATATAAAAAATATTAAATATAA
Found at i:311198 original size:21 final size:21
Alignment explanation
Indices: 311160--311210 Score: 61
Period size: 21 Copynumber: 2.4 Consensus size: 21
311150 TATTAAAATT
311160 AATAATAATATATATATTTAAA
1 AATAATAATATATATA-TTAAA
*
311182 TATAA-AATATA-ATTATTAAA
1 AATAATAATATATA-TATTAAA
311202 AATAATAAT
1 AATAATAAT
311211 TTAAGCATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
20 10 0.40
21 11 0.44
22 4 0.16
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (21 bp):
AATAATAATATATATATTAAA
Found at i:311368 original size:21 final size:21
Alignment explanation
Indices: 311343--311385 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
311333 AAAAAAATAA
*
311343 TTTTAATTTAATTTGTTATAT
1 TTTTAATTTAATTTATTATAT
*
311364 TTTTAATTTACTTTATTATAT
1 TTTTAATTTAATTTATTATAT
311385 T
1 T
311386 CTGATTGTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (21 bp):
TTTTAATTTAATTTATTATAT
Found at i:312216 original size:2 final size:2
Alignment explanation
Indices: 312209--312234 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
312199 TGGCAATTGA
312209 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
312235 GAAAAAATAA
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:313014 original size:17 final size:17
Alignment explanation
Indices: 312994--313054 Score: 50
Period size: 17 Copynumber: 3.4 Consensus size: 17
312984 TGGTTCAAGG
312994 AATTAACCCTAAATAAA
1 AATTAACCCTAAATAAA
** *
313011 AATTAATAACATTATAGTAAA
1 AA-T--TAACCCTA-AATAAA
*
313032 TATTAACCCTAAATAAA
1 AATTAACCCTAAATAAA
313049 AATTAA
1 AATTAA
313055 TATCATTATA
Statistics
Matches: 32, Mismatches: 8, Indels: 8
0.67 0.17 0.17
Matches are distributed among these distances:
17 12 0.38
18 7 0.22
20 7 0.22
21 6 0.19
ACGTcount: A:0.57, C:0.11, G:0.02, T:0.30
Consensus pattern (17 bp):
AATTAACCCTAAATAAA
Found at i:317456 original size:2 final size:2
Alignment explanation
Indices: 317449--317484 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
317439 TTATTACATG
317449 TA TA TA TA TA TA TA TA T- 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
317485 CAAAATCTTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:317471 original size:17 final size:17
Alignment explanation
Indices: 317449--317482 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
317439 TTATTACATG
317449 TATATATATATATATAT
1 TATATATATATATATAT
317466 TATATATATATATATAT
1 TATATATATATATATAT
317483 ATCAAAATCT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATATATATATATAT
Found at i:318046 original size:2 final size:2
Alignment explanation
Indices: 318039--318065 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
318029 TAAGTAAATT
318039 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
318066 GTATGTATGT
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:318566 original size:27 final size:27
Alignment explanation
Indices: 318536--318613 Score: 90
Period size: 25 Copynumber: 3.0 Consensus size: 27
318526 ATAGTAACAT
* *
318536 TCATCATGGATAAAATGTGGCATATAA
1 TCATCATGGATAAAAAGTGGAATATAA
*
318563 TCATCA---ATAAAAGAGTGAAATATAA
1 TCATCATGGATAAAA-AGTGGAATATAA
*
318588 TCATCATGGATAAAACGTGGAATATA
1 TCATCATGGATAAAAAGTGGAATATA
318614 GTAATATAAG
Statistics
Matches: 42, Mismatches: 5, Indels: 8
0.76 0.09 0.15
Matches are distributed among these distances:
24 6 0.14
25 15 0.36
27 15 0.36
28 6 0.14
ACGTcount: A:0.46, C:0.10, G:0.17, T:0.27
Consensus pattern (27 bp):
TCATCATGGATAAAAAGTGGAATATAA
Found at i:318694 original size:21 final size:22
Alignment explanation
Indices: 318655--318695 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
318645 TTGGAAGATC
*
318655 GAAATCAAAATATAAATTTTAA
1 GAAACCAAAATATAAATTTTAA
318677 GAAACCAAAATA-AAATTTT
1 GAAACCAAAATATAAATTTT
318696 CGTTATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.59, C:0.07, G:0.05, T:0.29
Consensus pattern (22 bp):
GAAACCAAAATATAAATTTTAA
Found at i:319355 original size:2 final size:2
Alignment explanation
Indices: 319348--319376 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
319338 GCTTCGTCCC
319348 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 T
319377 GATGTTGACA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:319746 original size:51 final size:51
Alignment explanation
Indices: 319686--319822 Score: 202
Period size: 51 Copynumber: 2.7 Consensus size: 51
319676 TTTTAACTAG
* * * *
319686 ATGTATCGATACATTGAATAATGTATCCATACATTTGGGTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATACATTTAGGTAAAAAGACAAA
* *
319737 ATGTATCGATACATTGAAAAATATATCGATACATCTAGGTAAAAAGACAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATTTAGGTAAAAAGACAAA
* *
319788 ATATATCGATACATTGAAGAATGTATCGATACATT
1 ATGTATCGATACATTGAAAAATGTATCGATACATT
319823 CATACATGTA
Statistics
Matches: 76, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.44, C:0.12, G:0.15, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATTTAGGTAAAAAGACAAA
Found at i:319816 original size:20 final size:19
Alignment explanation
Indices: 319785--319858 Score: 85
Period size: 20 Copynumber: 3.7 Consensus size: 19
319775 GTAAAAAGAC
*
319785 AAAATATATCGATACATTG
1 AAAATGTATCGATACATTG
*
319804 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
*
319824 ATACATGTATCGATACATTG
1 A-AAATGTATCGATACATTG
*
319844 AAAAATATATCGATA
1 -AAAATGTATCGATA
319859 TATCTGGGTA
Statistics
Matches: 46, Mismatches: 6, Indels: 5
0.81 0.11 0.09
Matches are distributed among these distances:
19 2 0.04
20 42 0.91
21 2 0.04
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.31
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:321129 original size:12 final size:12
Alignment explanation
Indices: 321114--321155 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
321104 ATTTAAAATA
321114 TAATTTTTATAT
1 TAATTTTTATAT
*
321126 TAATATTTATA-
1 TAATTTTTATAT
321137 T-ATTTTTATAAT
1 TAATTTTTAT-AT
321149 TAATTTT
1 TAATTTT
321156 AATTAAAAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
10 7 0.28
11 2 0.08
12 11 0.44
13 5 0.20
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TAATTTTTATAT
Found at i:321137 original size:23 final size:22
Alignment explanation
Indices: 321111--321156 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 22
321101 ATTATTTAAA
321111 ATATAATTTTTAT-ATTAATATTT
1 ATAT-ATTTTTATAATTAAT-TTT
321134 ATATATTTTTATAATTAATTTT
1 ATATATTTTTATAATTAATTTT
321156 A
1 A
321157 ATTAAAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 12 0.55
23 10 0.45
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (22 bp):
ATATATTTTTATAATTAATTTT
Found at i:322808 original size:14 final size:14
Alignment explanation
Indices: 322789--322818 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
322779 CCTATATATA
322789 TATATATATGTATG
1 TATATATATGTATG
322803 TATATATATGTATG
1 TATATATATGTATG
322817 TA
1 TA
322819 AAAGGTGCTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (14 bp):
TATATATATGTATG
Found at i:323171 original size:170 final size:169
Alignment explanation
Indices: 322887--323229 Score: 560
Period size: 170 Copynumber: 2.0 Consensus size: 169
322877 TTCTTTTAAA
*
322887 GTAAAGTTTACATTTGATACATTGTCTATAAATAAATCATTGTTTGATATCTTTAGTTATATTCA
1 GTAAAGTTTACATTTGATACATTGTCTATAAATAAATCATTATTTGATATCTTTAGTTATATTCA
* * * *
322952 TTAATGGATGTCACTGTTTTGTTTCATTGACATTGTGTAGCTTTCATATATTATCTGTACTAAAT
66 TCAATGGATGTCACTGTTTTGTTTCACTAACATTGTGTAGCTCTCATATATTATCTGTACTAAAT
* *
323017 GTAAAATGTTTAAAATTTACGTTCAATTATTAAAAACTT
131 GTAAAATATTTAAAATTTACGTTCAATTATTAAAAAATT
* * *
323056 GTAAAGTTTACATTTGATGCATTGTCTATAAATAAATCATTATTTGATCTCTTTTAGTTTTATTC
1 GTAAAGTTTACATTTGATACATTGTCTATAAATAAATCATTATTTGATATC-TTTAGTTATATTC
* *
323121 GTCAATGGATGTCACTTTTTTGTTTCACTAACATTGTGTAGCTCTCATATATTATCTGTACTAAA
65 ATCAATGGATGTCACTGTTTTGTTTCACTAACATTGTGTAGCTCTCATATATTATCTGTACTAAA
*
323186 TGTAAAATATTTAAATTTTACGTTCAATTATTAAAAAATT
130 TGTAAAATATTTAAAATTTACGTTCAATTATTAAAAAATT
323226 GTAA
1 GTAA
323230 TTATATACAT
Statistics
Matches: 160, Mismatches: 13, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
169 48 0.30
170 112 0.70
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.45
Consensus pattern (169 bp):
GTAAAGTTTACATTTGATACATTGTCTATAAATAAATCATTATTTGATATCTTTAGTTATATTCA
TCAATGGATGTCACTGTTTTGTTTCACTAACATTGTGTAGCTCTCATATATTATCTGTACTAAAT
GTAAAATATTTAAAATTTACGTTCAATTATTAAAAAATT
Found at i:324197 original size:25 final size:25
Alignment explanation
Indices: 324147--324197 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
324137 ATATTATTAA
**
324147 ATTAAATATATATTTTTTATTTATT
1 ATTAAATATATATTTTTTATACATT
*
324172 ATTATATATATATTTATTTA-ACATT
1 ATTAAATATATATTT-TTTATACATT
324197 A
1 A
324198 AATCTAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTAAATATATATTTTTTATACATT
Found at i:325350 original size:17 final size:19
Alignment explanation
Indices: 325330--325366 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 19
325320 AATTTAGTAA
325330 ATATTT-AATAAAA-ATAT
1 ATATTTGAATAAAAGATAT
*
325347 ATATTTGATTAAAAGATAT
1 ATATTTGAATAAAAGATAT
325366 A
1 A
325367 ACCTTTAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
17 6 0.35
18 6 0.35
19 5 0.29
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (19 bp):
ATATTTGAATAAAAGATAT
Found at i:327271 original size:33 final size:33
Alignment explanation
Indices: 327221--327313 Score: 98
Period size: 33 Copynumber: 2.8 Consensus size: 33
327211 AAACTTAACG
*
327221 TATAGTAATATTTATCATGAATAAAATGTAAAA
1 TATAATAATATTTATCATGAATAAAATGTAAAA
* * * * *
327254 TATTATAATATTCATCAT-AGATAAAACGTTACA
1 TATAATAATATTTATCATGA-ATAAAATGTAAAA
* *
327287 TATAATCATATTTATTATGAATAAAAT
1 TATAATAATATTTATCATGAATAAAAT
327314 ATGACATATA
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
32 1 0.02
33 45 0.96
34 1 0.02
ACGTcount: A:0.48, C:0.06, G:0.06, T:0.39
Consensus pattern (33 bp):
TATAATAATATTTATCATGAATAAAATGTAAAA
Found at i:327980 original size:21 final size:21
Alignment explanation
Indices: 327954--327996 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
327944 AATTCTGGTA
327954 TTTTGTGTATTTAGATTATAT
1 TTTTGTGTATTTAGATTATAT
327975 TTTTGTGTATTTAGATTATAT
1 TTTTGTGTATTTAGATTATAT
327996 T
1 T
327997 CGTAGTATAA
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:0.23, C:0.00, G:0.14, T:0.63
Consensus pattern (21 bp):
TTTTGTGTATTTAGATTATAT
Found at i:329718 original size:22 final size:21
Alignment explanation
Indices: 329683--329733 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 21
329673 TTTAAAATAT
329683 TTAAA-TTATAATTTTTAT-A
1 TTAAATTTATAATTTTTATAA
329702 TTAATATTTATATATTTTTATAA
1 TTAA-ATTTATA-ATTTTTATAA
329725 TTAAATTTA
1 TTAAATTTA
329734 AATAAAAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.14
20 1 0.04
21 5 0.18
22 13 0.46
23 5 0.18
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TTAAATTTATAATTTTTATAA
Found at i:331835 original size:2 final size:2
Alignment explanation
Indices: 331828--331864 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
331818 TTGATTAATC
331828 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
331865 TATGAGTTAA
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:332710 original size:11 final size:12
Alignment explanation
Indices: 332694--332724 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
332684 TTACATATAA
332694 TTAATATT-AAT
1 TTAATATTAAAT
332705 TTAATATTAAAT
1 TTAATATTAAAT
332717 TTAATATT
1 TTAATATT
332725 TGAATATATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TTAATATTAAAT
Found at i:335685 original size:16 final size:16
Alignment explanation
Indices: 335664--335751 Score: 54
Period size: 16 Copynumber: 5.5 Consensus size: 16
335654 GACCTGAACT
335664 CAAAATGATTCGAATC
1 CAAAATGATTCGAATC
**
335680 CAAAATGGCTCGAATC
1 CAAAATGATTCGAATC
* * *
335696 TAGAATGACTT-GAACC
1 CAAAATGA-TTCGAATC
* *
335712 CGAAATGATCCGAATC
1 CAAAATGATTCGAATC
* * *
335728 CCAAATAATCCGAA-C
1 CAAAATGATTCGAATC
335743 TCAAAATGA
1 -CAAAATGA
335752 CCTAAATAAT
Statistics
Matches: 53, Mismatches: 16, Indels: 6
0.71 0.21 0.08
Matches are distributed among these distances:
15 2 0.04
16 50 0.94
17 1 0.02
ACGTcount: A:0.42, C:0.23, G:0.15, T:0.20
Consensus pattern (16 bp):
CAAAATGATTCGAATC
Found at i:335696 original size:48 final size:48
Alignment explanation
Indices: 335641--335733 Score: 125
Period size: 48 Copynumber: 1.9 Consensus size: 48
335631 AGTTAACAAT
* *
335641 TCGAATCTA-AATTGACCTGAACTCAAAATGATTCGAATCCAAAATGGC
1 TCGAATCTAGAA-TGACCTGAACCCAAAATGATCCGAATCCAAAATGGC
* * *
335689 TCGAATCTAGAATGACTTGAACCCGAAATGATCCGAATCCCAAAT
1 TCGAATCTAGAATGACCTGAACCCAAAATGATCCGAATCCAAAAT
335734 AATCCGAACT
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
48 37 0.95
49 2 0.05
ACGTcount: A:0.39, C:0.23, G:0.15, T:0.24
Consensus pattern (48 bp):
TCGAATCTAGAATGACCTGAACCCAAAATGATCCGAATCCAAAATGGC
Found at i:336852 original size:53 final size:53
Alignment explanation
Indices: 336742--336852 Score: 116
Period size: 53 Copynumber: 2.1 Consensus size: 53
336732 AATTCGAATG
* * * ** *
336742 TTAAACCCGATTAACCCGAATCCAAAATGACCCGAATCCGATTAACCCGAGTA
1 TTAAACCCGATTAACCCGAACCCAAAATGACCCGAATCCAAGTAACCAAAATA
* * * *
336795 TTAAACCCGATTGACTCGAACCCGAAATGACCCGAATCCAAAGTGACCAAAAT-
1 TTAAACCCGATTAACCCGAACCCAAAATGACCCGAATCC-AAGTAACCAAAATA
336848 TTAAA
1 TTAAA
336853 ATGACCCAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
53 40 0.85
54 7 0.15
ACGTcount: A:0.40, C:0.28, G:0.14, T:0.19
Consensus pattern (53 bp):
TTAAACCCGATTAACCCGAACCCAAAATGACCCGAATCCAAGTAACCAAAATA
Found at i:337219 original size:24 final size:24
Alignment explanation
Indices: 337161--337231 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
337151 GCTTGGTATG
* * *
337161 AATTTAAAATATTTAAA-AAAATT
1 AATTTTAAATAATTAAATAAAATA
*
337184 AA-CTTAATATAATTAAATAAAATA
1 AATTTTAA-ATAATTAAATAAAATA
337208 AATTTTAAATAAATT-AATAAAATA
1 AATTTTAAAT-AATTAAATAAAATA
337232 TATACGTGTA
Statistics
Matches: 39, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
22 3 0.08
23 10 0.26
24 18 0.46
25 8 0.21
ACGTcount: A:0.62, C:0.01, G:0.00, T:0.37
Consensus pattern (24 bp):
AATTTTAAATAATTAAATAAAATA
Found at i:337825 original size:3 final size:3
Alignment explanation
Indices: 337817--337842 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
337807 GAAATTTAAG
337817 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
337843 GGACTTTAAT
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:338425 original size:17 final size:18
Alignment explanation
Indices: 338402--338454 Score: 54
Period size: 19 Copynumber: 2.9 Consensus size: 18
338392 AAATCTAGTA
338402 AATATTTAATAAAAATAT
1 AATATTTAATAAAAATAT
*
338420 -ATATTTAGCTAAATAATAT
1 AATATTTA-ATAAA-AATAT
* *
338439 AATCTTTAATATAAAT
1 AATATTTAATAAAAAT
338455 CTAACAAGTT
Statistics
Matches: 28, Mismatches: 4, Indels: 6
0.74 0.11 0.16
Matches are distributed among these distances:
17 7 0.25
18 7 0.25
19 8 0.29
20 6 0.21
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (18 bp):
AATATTTAATAAAAATAT
Found at i:339181 original size:50 final size:50
Alignment explanation
Indices: 339106--339315 Score: 375
Period size: 50 Copynumber: 4.2 Consensus size: 50
339096 AGTTGCTTAG
*
339106 AGTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
339156 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
*
339206 CGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* **
339256 AGTAAACAATTACGGTTACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
339306 AGTCAACAAT
1 AGTCAACAAT
339316 GGCAATACCT
Statistics
Matches: 153, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 153 1.00
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (50 bp):
AGTCAACAATTACGGCCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:343786 original size:50 final size:50
Alignment explanation
Indices: 343718--343901 Score: 188
Period size: 50 Copynumber: 3.7 Consensus size: 50
343708 TTGCTTAGAA
* *
343718 TCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAG
1 TCAACAATTACGGTCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAG
* * * * *
343768 TCAATAATTACGGTCACCTCTCTCGTTTGTCAAAGGTTGGTAAAGAATCG
1 TCAACAATTACGGTCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAG
* * ** ** * *
343818 TTAACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAA
1 TCAACAATTACGGTCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAG
* ****
343868 TCAATAATTATAACCACCTCTCTCGATTATCAAA
1 TCAACAATTACGGTCACCTCTCTCGATTATCAAA
343902 AATTAATAAA
Statistics
Matches: 110, Mismatches: 24, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
50 110 1.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (50 bp):
TCAACAATTACGGTCACCTCTCTCGATTATCAAAGGTTGGTGAAGAATAG
Found at i:343901 original size:100 final size:100
Alignment explanation
Indices: 343720--343901 Score: 229
Period size: 100 Copynumber: 1.8 Consensus size: 100
343710 GCTTAGAATC
** * ** ** * * ***
343720 AACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAATAATTACGGTCAC
1 AACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTACAACCAC
* *
343785 CTCTCTCGTTTGTCAAAGGTTGGTAAAGAATCGTT
66 CTCTCTCGATTATCAAAGGTTGGTAAAGAATCGTT
*
343820 AACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTATAACCAC
1 AACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTACAACCAC
343885 CTCTCTCGATTATCAAA
66 CTCTCTCGATTATCAAA
343902 AATTAATAAA
Statistics
Matches: 67, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
100 67 1.00
ACGTcount: A:0.35, C:0.20, G:0.14, T:0.31
Consensus pattern (100 bp):
AACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTACAACCAC
CTCTCTCGATTATCAAAGGTTGGTAAAGAATCGTT
Found at i:343902 original size:50 final size:50
Alignment explanation
Indices: 343832--343930 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
343822 CAATTACCGT
* * *
343832 CACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTATAAC
1 CACCTCTCTCGATTATCAAAAATTAATAAAAAATAATCAACAATAATAAC
343882 CACCTCTCTCGATTATCAAAAATTAATAAAAAATAATCAACAATAATAA
1 CACCTCTCTCGATTATCAAAAATTAATAAAAAATAATCAACAATAATAA
343931 TATTCTTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.51, C:0.18, G:0.03, T:0.28
Consensus pattern (50 bp):
CACCTCTCTCGATTATCAAAAATTAATAAAAAATAATCAACAATAATAAC
Found at i:343924 original size:100 final size:100
Alignment explanation
Indices: 343716--343925 Score: 213
Period size: 100 Copynumber: 2.1 Consensus size: 100
343706 AGTTGCTTAG
** * ** ** * * **
343716 AATCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAATAGTCAATAATTACGG
1 AATCAACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTACAA
* * * ** ** *
343781 TCACCTCTCTCGTTTGTCAAAGGTTGGTAAAGAAT
66 CCACCTCTCTCGATTATCAAAAATTAATAAAAAAT
** * *
343816 CGTTAACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTATAA
1 AATCAACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTACAA
343881 CCACCTCTCTCGATTATCAAAAATTAATAAAAAAT
66 CCACCTCTCTCGATTATCAAAAATTAATAAAAAAT
343916 AATCAACAAT
1 AATCAACAAT
343926 AATAATATTC
Statistics
Matches: 84, Mismatches: 26, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
100 84 1.00
ACGTcount: A:0.39, C:0.19, G:0.12, T:0.30
Consensus pattern (100 bp):
AATCAACAATTACCGTCACCTCTCTCGATTATCAAAAATTAATGAAAAATAATCAATAATTACAA
CCACCTCTCTCGATTATCAAAAATTAATAAAAAAT
Found at i:344470 original size:2 final size:2
Alignment explanation
Indices: 344463--344493 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
344453 TTCGTCCTTA
344463 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
344494 AAAGATGTTT
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:345048 original size:20 final size:20
Alignment explanation
Indices: 345027--345064 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
345017 ATAATATTTA
345027 AAATATTT-TATATTTATAT
1 AAATATTTATATATTTATAT
*
345046 AAATTTTTATATATTTATA
1 AAATATTTATATATTTATA
345065 AATTAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
AAATATTTATATATTTATAT
Found at i:345055 original size:18 final size:18
Alignment explanation
Indices: 345020--345068 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 18
345010 TATTATAATA
345020 ATATTTA-AAATATTTTAT
1 ATATTTATAAAT-TTTTAT
345038 AT-TTATATAAATTTTTAT
1 ATATT-TATAAATTTTTAT
345056 ATATTTATAAATT
1 ATATTTATAAATT
345069 AAATTATATA
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.07
18 20 0.71
19 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
ATATTTATAAATTTTTAT
Found at i:345134 original size:15 final size:15
Alignment explanation
Indices: 345106--345142 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
345096 TTATATTTTA
345106 TTATATTAATCAAAT
1 TTATATTAATCAAAT
345121 TTAATATT-ATCAAAT
1 TT-ATATTAATCAAAT
345136 TTATATT
1 TTATATT
345143 TTTGGTAGGG
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 5 0.24
15 11 0.52
16 5 0.24
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.51
Consensus pattern (15 bp):
TTATATTAATCAAAT
Found at i:345630 original size:2 final size:2
Alignment explanation
Indices: 345618--345658 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
345608 TTAAAGCTAA
* * *
345618 TC TC TC CC TC TC TC TC TC TG TC TC TC TC TC TC TG TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
345659 TTAATTATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.46, G:0.05, T:0.49
Consensus pattern (2 bp):
TC
Found at i:345642 original size:14 final size:14
Alignment explanation
Indices: 345625--345658 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
345615 TAATCTCTCC
345625 CTCTCTCTCTCTGT
1 CTCTCTCTCTCTGT
345639 CTCTCTCTCTCTGT
1 CTCTCTCTCTCTGT
345653 CTCTCT
1 CTCTCT
345659 TTAATTATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.00, C:0.44, G:0.06, T:0.50
Consensus pattern (14 bp):
CTCTCTCTCTCTGT
Found at i:348469 original size:33 final size:33
Alignment explanation
Indices: 348399--348558 Score: 122
Period size: 33 Copynumber: 4.7 Consensus size: 33
348389 AATATGGTGT
* *
348399 TGTATTCTCCTAAGATGTAAAATACCTATTGCT
1 TGTATTCTCCTAAGATGTAAAATACCTAGTGCA
* * *
348432 TGTATTCTCCTAAGATGTAAAATACTTGGTGGA
1 TGTATTCTCCTAAGATGTAAAATACCTAGTGCA
** * *
348465 TGTATTCTCCTGGGATGTAAAACACTACTAGCGCA
1 TGTATTCTCCTAAGATGTAAAATAC--CTAGTGCA
* * ** * *
348500 TGAATCCTCCTGGGATGTGAAATACTACTAGTGCT
1 TGTATTCTCCTAAGATGTAAAATAC--CTAGTGCA
*
348535 TGTATTCTTCTAAGTATGTGAAAA
1 TGTATTCTCCTAAG-ATGT-AAAA
348559 ATTGCTAGTG
Statistics
Matches: 99, Mismatches: 24, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
33 50 0.51
35 42 0.42
36 4 0.04
37 3 0.03
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Consensus pattern (33 bp):
TGTATTCTCCTAAGATGTAAAATACCTAGTGCA
Found at i:350755 original size:19 final size:20
Alignment explanation
Indices: 350715--350758 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
350705 TATTTTACAC
350715 AATTTATTATAAAACATAAA
1 AATTTATTATAAAACATAAA
*
350735 AATTATATTAT-AATCATAAA
1 AATT-TATTATAAAACATAAA
350755 AATT
1 AATT
350759 CTTCTTTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.73
21 6 0.27
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.39
Consensus pattern (20 bp):
AATTTATTATAAAACATAAA
Found at i:350850 original size:2 final size:2
Alignment explanation
Indices: 350843--350877 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
350833 AAATGAAATT
350843 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
350878 GTATGTGTGT
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:356800 original size:28 final size:28
Alignment explanation
Indices: 356768--356825 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
356758 TATACCATTT
356768 TTGACTTGTTAGGACCTTGTTTTCGCAC
1 TTGACTTGTTAGGACCTTGTTTTCGCAC
356796 TTGACTTGTTAGGACCTTGTTTTCGCAC
1 TTGACTTGTTAGGACCTTGTTTTCGCAC
356824 TT
1 TT
356826 ACATGCTCCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.14, C:0.21, G:0.21, T:0.45
Consensus pattern (28 bp):
TTGACTTGTTAGGACCTTGTTTTCGCAC
Found at i:360141 original size:21 final size:21
Alignment explanation
Indices: 360117--360157 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
360107 GCAAATTTTT
360117 ATTTTT-ATTAGCCAATTCATC
1 ATTTTTCATTAG-CAATTCATC
*
360138 ATTTTTCATTTGCAATTCAT
1 ATTTTTCATTAGCAATTCAT
360158 TTCTTTTCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.27, C:0.17, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTTTTCATTAGCAATTCATC
Found at i:360175 original size:21 final size:21
Alignment explanation
Indices: 360151--360208 Score: 71
Period size: 21 Copynumber: 2.8 Consensus size: 21
360141 TTTCATTTGC
*
360151 AATTCATTTCTTTTCTCCTCT
1 AATTCATTTATTTTCTCCTCT
**
360172 AATTCATTTATTTTCTTTTCT
1 AATTCATTTATTTTCTCCTCT
* *
360193 AATTCACTTAATTTCT
1 AATTCATTTATTTTCT
360209 TTTCAAGAAT
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 32 1.00
ACGTcount: A:0.21, C:0.21, G:0.00, T:0.59
Consensus pattern (21 bp):
AATTCATTTATTTTCTCCTCT
Found at i:366968 original size:24 final size:23
Alignment explanation
Indices: 366930--366985 Score: 60
Period size: 24 Copynumber: 2.3 Consensus size: 23
366920 AAGTCTTGAT
*
366930 AATTTTAATTAT-AAATAAATAAA
1 AATTATAATTATAAAATAAA-AAA
*
366953 AGATTATAATTTTAAAAATAAAAAA
1 A-ATTATAATTAT-AAAATAAAAAA
366978 AATTATAA
1 AATTATAA
366986 ATGTTGATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 1 0.04
24 16 0.57
25 4 0.14
26 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (23 bp):
AATTATAATTATAAAATAAAAAA
Found at i:367207 original size:16 final size:16
Alignment explanation
Indices: 367157--367207 Score: 50
Period size: 16 Copynumber: 3.2 Consensus size: 16
367147 ATTTTTAAAT
*
367157 TTTTAAATTTGAGTCA
1 TTTTAATTTTGAGTCA
* *
367173 CTTTAGTTTGTGA-TCA
1 TTTTAATTT-TGAGTCA
*
367189 TTTTAATTTTGAGTTA
1 TTTTAATTTTGAGTCA
367205 TTT
1 TTT
367208 AGGATTCAGG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
15 3 0.11
16 21 0.78
17 3 0.11
ACGTcount: A:0.24, C:0.06, G:0.14, T:0.57
Consensus pattern (16 bp):
TTTTAATTTTGAGTCA
Found at i:369737 original size:18 final size:18
Alignment explanation
Indices: 369703--369737 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
369693 CAGTGGTTTG
**
369703 GCTGTTGTCATTTGAGTA
1 GCTGTTGTCATCGGAGTA
369721 GCTGTTGTCATCGGAGT
1 GCTGTTGTCATCGGAGT
369738 TGCAGAAGTC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.14, C:0.14, G:0.31, T:0.40
Consensus pattern (18 bp):
GCTGTTGTCATCGGAGTA
Found at i:374089 original size:30 final size:30
Alignment explanation
Indices: 374032--374089 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 30
374022 ATTGTATTTA
* * **
374032 TTTATTAAATTTTACATTTAATATATTATT
1 TTTATTAAATTTAAAAAATAATATATTATT
*
374062 TTTATTAAATTTAAAAAATAATTTATTA
1 TTTATTAAATTTAAAAAATAATATATTA
374090 ATTAATTTTT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (30 bp):
TTTATTAAATTTAAAAAATAATATATTATT
Found at i:374558 original size:13 final size:13
Alignment explanation
Indices: 374534--374567 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
374524 TTCTTCTTAG
374534 TATAGTATTAGATT
1 TATAG-ATTAGATT
374548 TATAGATTAGATT
1 TATAGATTAGATT
374561 TATAGAT
1 TATAGAT
374568 GAGGAGAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.38, C:0.00, G:0.15, T:0.47
Consensus pattern (13 bp):
TATAGATTAGATT
Found at i:375390 original size:15 final size:16
Alignment explanation
Indices: 375370--375399 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
375360 TCTTTGATCG
375370 TATTATA-AAAATTAA
1 TATTATATAAAATTAA
375385 TATTATATAAAATTA
1 TATTATATAAAATTA
375400 TTAATTACTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (16 bp):
TATTATATAAAATTAA
Found at i:375701 original size:8 final size:8
Alignment explanation
Indices: 375678--375712 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
375668 ATATTGCTTG
*
375678 TATGTATG
1 TATGTATA
375686 TATGTATA
1 TATGTATA
375694 TATGTATA
1 TATGTATA
*
375702 TATATATA
1 TATGTATA
375710 TAT
1 TAT
375713 ACATACATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.11, T:0.51
Consensus pattern (8 bp):
TATGTATA
Found at i:375705 original size:4 final size:4
Alignment explanation
Indices: 375690--375735 Score: 56
Period size: 4 Copynumber: 11.5 Consensus size: 4
375680 TGTATGTATG
* * * *
375690 TATA TATG TATA TATA TATA TATA CATA CATA TATA CATA TATA TA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TA
375736 GATGTGTAAG
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 36 1.00
ACGTcount: A:0.48, C:0.07, G:0.02, T:0.43
Consensus pattern (4 bp):
TATA
Found at i:375713 original size:12 final size:12
Alignment explanation
Indices: 375691--375735 Score: 63
Period size: 12 Copynumber: 3.8 Consensus size: 12
375681 GTATGTATGT
* *
375691 ATATATGTATAT
1 ATATATATATAC
375703 ATATATATATAC
1 ATATATATATAC
*
375715 ATACATATATAC
1 ATATATATATAC
375727 ATATATATA
1 ATATATATA
375736 GATGTGTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.49, C:0.07, G:0.02, T:0.42
Consensus pattern (12 bp):
ATATATATATAC
Found at i:375772 original size:12 final size:12
Alignment explanation
Indices: 375751--375783 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
375741 GTAAGAGGAG
375751 TGTATATATGTA
1 TGTATATATGTA
*
375763 TGTATGTATGTA
1 TGTATATATGTA
375775 TGTATATAT
1 TGTATATAT
375784 AGTCCAGCTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.30, C:0.00, G:0.18, T:0.52
Consensus pattern (12 bp):
TGTATATATGTA
Found at i:376210 original size:2 final size:2
Alignment explanation
Indices: 376203--376229 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
376193 GTAGAAATTA
376203 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
376230 CACACATTAG
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:376855 original size:3 final size:3
Alignment explanation
Indices: 376847--376883 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
376837 ACCAAAACAT
376847 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
376884 CTTTTTGACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:377110 original size:39 final size:38
Alignment explanation
Indices: 377067--377147 Score: 94
Period size: 39 Copynumber: 2.1 Consensus size: 38
377057 TTTTTAAAAT
377067 TAATATATTGAGTTTAAT--AATAATTAAAAGATAAATATA
1 TAATATATTGA-TTTAATAGAAT-ATTAAAAGATAAATA-A
* * *
377106 TAATATATTTATTTGATAGAATATTAAAATATAAATAA
1 TAATATATTGATTTAATAGAATATTAAAAGATAAATAA
377144 TAAT
1 TAAT
377148 GCATTAAAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
38 10 0.27
39 24 0.65
40 3 0.08
ACGTcount: A:0.53, C:0.00, G:0.06, T:0.41
Consensus pattern (38 bp):
TAATATATTGATTTAATAGAATATTAAAAGATAAATAA
Found at i:378384 original size:16 final size:17
Alignment explanation
Indices: 378357--378389 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
378347 ATATGTCTAT
*
378357 ATGTATTTATATTTTTA
1 ATGTATTTATATATTTA
378374 ATGTA-TTATATATTTA
1 ATGTATTTATATATTTA
378390 TCTTTTACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (17 bp):
ATGTATTTATATATTTA
Found at i:379540 original size:21 final size:23
Alignment explanation
Indices: 379498--379541 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
379488 ATTTTAATAT
*
379498 TTATAATATTTTTTATTTTTAAA
1 TTATAATATTTTTTATTATTAAA
379521 TTATAAT-TTTTTTA-TATTAAA
1 TTATAATATTTTTTATTATTAAA
379542 AAAAATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 6 0.30
22 7 0.35
23 7 0.35
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (23 bp):
TTATAATATTTTTTATTATTAAA
Found at i:380815 original size:10 final size:10
Alignment explanation
Indices: 380800--380830 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
380790 AAAATATAAA
380800 ATATATTTTT
1 ATATATTTTT
380810 ATATATTTTTT
1 ATATA-TTTTT
380821 ATATATTTTT
1 ATATATTTTT
380831 TTTAACAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (10 bp):
ATATATTTTT
Found at i:380834 original size:13 final size:11
Alignment explanation
Indices: 380800--380831 Score: 57
Period size: 11 Copynumber: 3.0 Consensus size: 11
380790 AAAATATAAA
380800 ATATA-TTTTT
1 ATATATTTTTT
380810 ATATATTTTTT
1 ATATATTTTTT
380821 ATATATTTTTT
1 ATATATTTTTT
380832 TTAACAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.24
11 16 0.76
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (11 bp):
ATATATTTTTT
Found at i:381271 original size:28 final size:28
Alignment explanation
Indices: 381208--381271 Score: 76
Period size: 28 Copynumber: 2.3 Consensus size: 28
381198 TTAAATATTA
381208 AAAAAATAAATATATTTTCACAGAAAAT
1 AAAAAATAAATATATTTTCACAGAAAAT
* * **
381236 TAAAAATAAATATCTTTT-ACCTAAAAT
1 AAAAAATAAATATATTTTCACAGAAAAT
381263 AAAATAATA
1 AAAA-AATA
381272 TACGAGCTTA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
27 10 0.33
28 20 0.67
ACGTcount: A:0.59, C:0.08, G:0.02, T:0.31
Consensus pattern (28 bp):
AAAAAATAAATATATTTTCACAGAAAAT
Found at i:381633 original size:22 final size:25
Alignment explanation
Indices: 381589--381635 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 25
381579 TTAAATATTA
*
381589 AATAAATTATTTTAATATTAAATAT
1 AATAAATTATTTTAATATAAAATAT
381614 AATAAA-TA-TTTAATA-AAAATAT
1 AATAAATTATTTTAATATAAAATAT
381636 GTTTTAATAT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 6 0.29
23 7 0.33
24 2 0.10
25 6 0.29
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (25 bp):
AATAAATTATTTTAATATAAAATAT
Found at i:382082 original size:3 final size:3
Alignment explanation
Indices: 382074--382122 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
382064 CATGTTTCAC
382074 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
382122 T
1 T
382123 GAACAAAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:382772 original size:21 final size:21
Alignment explanation
Indices: 382719--382781 Score: 78
Period size: 19 Copynumber: 3.1 Consensus size: 21
382709 AATTTATATT
*
382719 ATTATATAA-ATTATTAAAAAA
1 ATTATA-AATATTAATAAAAAA
382740 ATT-TAAAT-TTAATAAAAAA
1 ATTATAAATATTAATAAAAAA
*
382759 ATTATAAATATTAATATAAAA
1 ATTATAAATATTAATAAAAAA
382780 AT
1 AT
382782 AATTTTAAAA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
19 15 0.41
20 7 0.19
21 15 0.41
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (21 bp):
ATTATAAATATTAATAAAAAA
Found at i:382803 original size:25 final size:23
Alignment explanation
Indices: 382733--382796 Score: 73
Period size: 19 Copynumber: 2.9 Consensus size: 23
382723 TATAAATTAT
382733 TAAAAAAATT-TAAAT-TT-A-A
1 TAAAAAAATTATAAATATTAATA
382752 TAAAAAAATTATAAATATTAATA
1 TAAAAAAATTATAAATATTAATA
*
382775 TAAAAATAATTTTAAAATATTA
1 TAAAAA-AATTAT-AAATATTA
382797 TTTTAAACTA
Statistics
Matches: 38, Mismatches: 1, Indels: 6
0.84 0.02 0.13
Matches are distributed among these distances:
19 10 0.26
20 5 0.13
21 2 0.05
22 1 0.03
23 7 0.18
24 5 0.13
25 8 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (23 bp):
TAAAAAAATTATAAATATTAATA
Found at i:382846 original size:16 final size:16
Alignment explanation
Indices: 382820--382859 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
382810 AATAAATTAC
*
382820 TAAATTAATTTAAATT
1 TAAAATAATTTAAATT
*
382836 TAATATAATTTAAATT
1 TAAAATAATTTAAATT
382852 TAAAATAA
1 TAAAATAA
382860 AAAATTATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (16 bp):
TAAAATAATTTAAATT
Found at i:383769 original size:23 final size:23
Alignment explanation
Indices: 383717--383766 Score: 68
Period size: 23 Copynumber: 2.3 Consensus size: 23
383707 AACTCGATTG
*
383717 ATTTTTAGAATTTATTTATTTTT
1 ATTTTTAAAATTTATTTATTTTT
*
383740 ATCTTTAAAATTTA-TT-TTTTT
1 ATTTTTAAAATTTATTTATTTTT
383761 ATTTTT
1 ATTTTT
383767 TTATCTCAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 10 0.42
22 2 0.08
23 12 0.50
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (23 bp):
ATTTTTAAAATTTATTTATTTTT
Found at i:384032 original size:22 final size:22
Alignment explanation
Indices: 384007--384050 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
383997 ACTTGAAATT
* *
384007 CTATATAGTTAATAATAATTAA
1 CTATATAATTAACAATAATTAA
384029 CTATATAATTAACAATAATTAA
1 CTATATAATTAACAATAATTAA
384051 GATTATATTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.02, T:0.39
Consensus pattern (22 bp):
CTATATAATTAACAATAATTAA
Found at i:386297 original size:5 final size:5
Alignment explanation
Indices: 386287--386314 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
386277 CCAACCACAA
386287 TAAAT TAAAT TAAAT TAAAT TAAAT TAA
1 TAAAT TAAAT TAAAT TAAAT TAAAT TAA
386315 TAAATATTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (5 bp):
TAAAT
Found at i:386731 original size:26 final size:24
Alignment explanation
Indices: 386672--386738 Score: 73
Period size: 24 Copynumber: 2.7 Consensus size: 24
386662 TTTTAATACA
*
386672 TTAATAATTTATTTTTTATAAATT
1 TTAATTATTTATTTTTTATAAATT
**
386696 TTAATATATTTATATTTTTATCGTATT
1 TTAAT-TATTTAT-TTTTTAT-AAATT
386723 TTAATTA-TTATTTTTT
1 TTAATTATTTATTTTTT
386739 TGATAATTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
24 10 0.27
25 10 0.27
26 9 0.24
27 8 0.22
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.66
Consensus pattern (24 bp):
TTAATTATTTATTTTTTATAAATT
Found at i:387544 original size:50 final size:50
Alignment explanation
Indices: 387474--387729 Score: 368
Period size: 50 Copynumber: 5.1 Consensus size: 50
387464 AGTTGCTTAG
* * *
387474 AGTCAACAATTATAGTCACCTCTCTCTATTGTCAAAGGTTGGTGAAAAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
387524 AGTTAACAATTATGGCCACCTCTTTCGATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * * *
387574 AGTCAACAATAACGGCCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
387624 AGTCAACAATTATGATCACTTCTCTCAATTGTCAAAGGTTGGTGAAGAAT
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
* * *
387674 ATTCAACAATTACGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAC
1 AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
387724 AGTCAA
1 AGTCAA
387730 ATCACTTTGC
Statistics
Matches: 181, Mismatches: 25, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 181 1.00
ACGTcount: A:0.33, C:0.19, G:0.19, T:0.29
Consensus pattern (50 bp):
AGTCAACAATTATGGTCACCTCTCTCGATTGTCAAAGGTTGGTGAAGAAT
Found at i:392164 original size:50 final size:50
Alignment explanation
Indices: 392105--392336 Score: 272
Period size: 50 Copynumber: 4.7 Consensus size: 50
392095 ACTTAGAGTT
* * *
392105 AACAATTACGATAACCTCTCTCTATTGTCAAAGGTTTGTGAAGAATAGAC
1 AACAATTACGATCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGAC
*
392155 AACAATTACGA-CTACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGTC
1 AACAATTACGATC-ACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGAC
* * *
392205 AACAATAACGGTCACCTCTCTCGATTGTCAAAGGTTAGTAAAGAATA-ATC
1 AACAATTACGATCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGA-C
* ** * * *
392255 AACAATTATGGGCACCTC-CTCGATTGTGAAAGGTTGGTGAAGAATAGTC
1 AACAATTACGATCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGAC
* * * *
392304 AACAATTATGACCACCTCTCTCGGTTGTTAAAG
1 AACAATTACGATCACCTCTCTCGATTGTCAAAG
392337 ATCGATAAAG
Statistics
Matches: 158, Mismatches: 19, Indels: 10
0.84 0.10 0.05
Matches are distributed among these distances:
49 42 0.27
50 115 0.73
51 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (50 bp):
AACAATTACGATCACCTCTCTCGATTGTCAAAGGTTAGTGAAGAATAGAC
Found at i:392323 original size:99 final size:100
Alignment explanation
Indices: 392118--392355 Score: 286
Period size: 99 Copynumber: 2.4 Consensus size: 100
392108 AATTACGATA
* * *
392118 ACCTCTCTCTATTGTCAAAGGTTTGTGAAGAATAGA-CAACAATTACGACTACCTCTCTCGATTG
1 ACCTCTCTCGATTGTCAAAGGTTAGTAAAGAATA-ATCAACAATTACGACTACCTCTCTCGATTG
**
392182 TCAAAGGTTAGTGAAGAATAGTCAACAATAACGGTC
65 TCAAAGGTTAGTGAAGAATAGTCAACAATAACGACC
* *
392218 ACCTCTCTCGATTGTCAAAGGTTAGTAAAGAATAATCAACAATTATGGGC-ACCTC-CTCGATTG
1 ACCTCTCTCGATTGTCAAAGGTTAGTAAAGAATAATCAACAATTA-CGACTACCTCTCTCGATTG
* * * *
392281 TGAAAGGTTGGTGAAGAATAGTCAACAATTATGACC
65 TCAAAGGTTAGTGAAGAATAGTCAACAATAACGACC
* * * *
392317 ACCTCTCTCGGTTGTTAAA-GATCGATAAAGAATAATCAA
1 ACCTCTCTCGATTGTCAAAGGTTAG-TAAAGAATAATCAA
392356 ATCACTTCGC
Statistics
Matches: 120, Mismatches: 15, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
98 3 0.03
99 70 0.58
100 45 0.38
101 2 0.02
ACGTcount: A:0.35, C:0.19, G:0.18, T:0.28
Consensus pattern (100 bp):
ACCTCTCTCGATTGTCAAAGGTTAGTAAAGAATAATCAACAATTACGACTACCTCTCTCGATTGT
CAAAGGTTAGTGAAGAATAGTCAACAATAACGACC
Found at i:392509 original size:2 final size:2
Alignment explanation
Indices: 392504--392539 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
392494 CTCCATCTTT
392504 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
392540 AACCAAAAAC
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:393517 original size:18 final size:19
Alignment explanation
Indices: 393488--393540 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 19
393478 TTTCACTTTC
393488 ACATATTTATATTATTTTTA
1 ACATA-TTATATTATTTTTA
*
393508 A-ATATTATATTATATTTA
1 ACATATTATATTATTTTTA
*
393526 ACATGTTATA-TATTT
1 ACATATTATATTATTT
393541 ATATAAATTT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 18 0.62
19 10 0.34
20 1 0.03
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.57
Consensus pattern (19 bp):
ACATATTATATTATTTTTA
Found at i:393627 original size:28 final size:27
Alignment explanation
Indices: 393595--393647 Score: 70
Period size: 28 Copynumber: 1.9 Consensus size: 27
393585 GATATGTTCA
*
393595 TATATTTGTATTGTATTTATATTATTTT
1 TATATTTGTATTATATTTA-ATTATTTT
* *
393623 TATATTTTTATTATGTTTAATTATT
1 TATATTTGTATTATATTTAATTATT
393648 GTTTTTTTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
27 6 0.27
28 16 0.73
ACGTcount: A:0.26, C:0.00, G:0.06, T:0.68
Consensus pattern (27 bp):
TATATTTGTATTATATTTAATTATTTT
Found at i:393628 original size:17 final size:17
Alignment explanation
Indices: 393608--393662 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
393598 ATTTGTATTG
393608 TATTTATATTATTTTTA
1 TATTTATATTATTTTTA
* *
393625 TATTTTTATTATGTTTA
1 TATTTATATTATTTTTA
* *
393642 -A-TTATTGTTTTTTTTA
1 TATTTA-TATTATTTTTA
393658 TATTT
1 TATTT
393663 GAATAAATTG
Statistics
Matches: 29, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
15 2 0.07
16 9 0.31
17 16 0.55
18 2 0.07
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.73
Consensus pattern (17 bp):
TATTTATATTATTTTTA
Found at i:396372 original size:21 final size:23
Alignment explanation
Indices: 396342--396383 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
396332 AATTACTCTA
*
396342 AAAAATATTTTTGAA-AAAATTT
1 AAAAATATTTATGAATAAAATTT
396364 AAAAA-ATTTATGAATAAAAT
1 AAAAATATTTATGAATAAAAT
396384 CAATATGAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.36
Consensus pattern (23 bp):
AAAAATATTTATGAATAAAATTT
Found at i:397567 original size:13 final size:13
Alignment explanation
Indices: 397535--397585 Score: 50
Period size: 13 Copynumber: 4.0 Consensus size: 13
397525 AAATTTATCG
* *
397535 TAAAAATTATATT
1 TAAAAATAATAAT
* *
397548 TATAAATGATAAT
1 TAAAAATAATAAT
*
397561 TAAAAATAATAAA
1 TAAAAATAATAAT
397574 TAAAAA-AATAAT
1 TAAAAATAATAAT
397586 GAGGAGGAAC
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
12 5 0.16
13 26 0.84
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (13 bp):
TAAAAATAATAAT
Found at i:398212 original size:22 final size:22
Alignment explanation
Indices: 398187--398231 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
398177 AAAAATACAT
*
398187 AATTATTAAATAAT-TATTTTAA
1 AATT-TTAAATAATAAATTTTAA
*
398209 AATTTTTAATAATAAATTTTAA
1 AATTTTAAATAATAAATTTTAA
398231 A
1 A
398232 TGAAAATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 8 0.40
22 12 0.60
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (22 bp):
AATTTTAAATAATAAATTTTAA
Found at i:402663 original size:2 final size:2
Alignment explanation
Indices: 402656--402693 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
402646 CGCTTGTTGG
402656 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
402694 TAATAAATTT
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:402750 original size:2 final size:2
Alignment explanation
Indices: 402743--402770 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
402733 TTTAATTAAT
402743 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
402771 GCTTACTTCA
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:402865 original size:19 final size:19
Alignment explanation
Indices: 402843--402960 Score: 109
Period size: 18 Copynumber: 6.2 Consensus size: 19
402833 TATTTAATTT
402843 AATTATAGTTTTTTAAAAA
1 AATTATAGTTTTTTAAAAA
*
402862 AATTATA-ATTTTT-AAAA
1 AATTATAGTTTTTTAAAAA
402879 AATTAATAGTTTTTTAAAAAATA
1 AATT-ATAGTTTTTT--AAAA-A
*
402902 AATAATAGTTTTTT-AAAA
1 AATTATAGTTTTTTAAAAA
* *
402920 AATTATA-ATTTTTAAATA
1 AATTATAGTTTTTTAAAAA
* *
402938 AATTAATAATTTTTTTAAAA
1 AATT-ATAGTTTTTTAAAAA
402958 AAT
1 AAT
402961 AAATATTAGT
Statistics
Matches: 81, Mismatches: 9, Indels: 17
0.76 0.08 0.16
Matches are distributed among these distances:
17 13 0.16
18 22 0.27
19 18 0.22
20 11 0.14
22 13 0.16
23 4 0.05
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
AATTATAGTTTTTTAAAAA
Found at i:402888 original size:37 final size:36
Alignment explanation
Indices: 402843--402960 Score: 121
Period size: 37 Copynumber: 3.1 Consensus size: 36
402833 TATTTAATTT
402843 AATTATAGTTTTTTAAAAAAATTATAATTTTTAAAA
1 AATTATAGTTTTTTAAAAAAATTATAATTTTTAAAA
* *
402879 AATTAATAGTTTTTTAAAAAATAAATAATAGTTTTTTAAAA
1 AATT-ATAGTTTTTT--AAAA-AAATTATA-ATTTTTAAAA
* *
402920 AATTATA-ATTTTTAAATAAATTAATAATTTTTTTAAAA
1 AATTATAGTTTTTTAAAAAAATT-ATAA--TTTTTAAAA
402958 AAT
1 AAT
402961 AAATATTAGT
Statistics
Matches: 68, Mismatches: 6, Indels: 14
0.77 0.07 0.16
Matches are distributed among these distances:
36 8 0.12
37 16 0.24
38 12 0.18
39 9 0.13
40 10 0.15
41 13 0.19
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.47
Consensus pattern (36 bp):
AATTATAGTTTTTTAAAAAAATTATAATTTTTAAAA
Found at i:402910 original size:59 final size:60
Alignment explanation
Indices: 402847--402970 Score: 207
Period size: 60 Copynumber: 2.1 Consensus size: 60
402837 TAATTTAATT
402847 ATAGTTTTTTAAAAAAATTATAATTTTTAAA-AAATTAAT-AGTTTTTTAAAAAATAAATA
1 ATAGTTTTTT-AAAAAATTATAATTTTTAAATAAATTAATAAGTTTTTTAAAAAATAAATA
*
402906 ATAGTTTTTTAAAAAATTATAATTTTTAAATAAATTAATAATTTTTTTAAAAAATAAATA
1 ATAGTTTTTTAAAAAATTATAATTTTTAAATAAATTAATAAGTTTTTTAAAAAATAAATA
*
402966 TTAGT
1 ATAGT
402971 AGGTAAAAGA
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
58 20 0.33
59 18 0.30
60 23 0.38
ACGTcount: A:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (60 bp):
ATAGTTTTTTAAAAAATTATAATTTTTAAATAAATTAATAAGTTTTTTAAAAAATAAATA
Found at i:403206 original size:18 final size:18
Alignment explanation
Indices: 403171--403229 Score: 52
Period size: 18 Copynumber: 3.4 Consensus size: 18
403161 CAATGAATGA
*
403171 AATAATAAATAATTAAAT
1 AATAATAAATAATAAAAT
403189 AATATATAAA-AATAAAAT
1 AATA-ATAAATAATAAAAT
* *
403207 -AT-TTAAATAAAAAAAT
1 AATAATAAATAATAAAAT
*
403223 AAAAATA
1 AATAATA
403230 CTAAAAACTT
Statistics
Matches: 32, Mismatches: 5, Indels: 8
0.71 0.11 0.18
Matches are distributed among these distances:
15 4 0.12
16 7 0.22
17 3 0.09
18 13 0.41
19 5 0.16
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (18 bp):
AATAATAAATAATAAAAT
Found at i:404640 original size:43 final size:41
Alignment explanation
Indices: 404486--404640 Score: 111
Period size: 41 Copynumber: 3.7 Consensus size: 41
404476 TTTCAATATG
* *
404486 ATATAAATAT-AATATTATAAAAATTATTAAAATATATTATAAA
1 ATATAAATATAAATA-TAT-AAAATTATAAAAATATATT-TTAA
* * *** * *
404529 ATATAAA-ATAATTATCA-AAAAATATTTTTAATTTAATTTAA
1 ATATAAATATAAATAT-ATAAAATTA-TAAAAATATATTTTAA
* *
404570 ATATATATATATATAT-TAAAATTTATAAAAATATATTTTAA
1 ATATAAATATAAATATATAAAA-TTATAAAAATATATTTTAA
404611 ATATAAATATAAATATGATATAAATTATAA
1 ATATAAATATAAATAT-ATA-AAATTATAA
404641 TTTTAGAGAA
Statistics
Matches: 85, Mismatches: 18, Indels: 18
0.70 0.15 0.15
Matches are distributed among these distances:
41 44 0.52
42 19 0.22
43 19 0.22
44 3 0.04
ACGTcount: A:0.57, C:0.01, G:0.01, T:0.42
Consensus pattern (41 bp):
ATATAAATATAAATATATAAAATTATAAAAATATATTTTAA
Found at i:404820 original size:29 final size:29
Alignment explanation
Indices: 404778--404833 Score: 112
Period size: 29 Copynumber: 1.9 Consensus size: 29
404768 AGATGGATAT
404778 ATATAATTAATTAAATAATTGTAAAATAC
1 ATATAATTAATTAAATAATTGTAAAATAC
404807 ATATAATTAATTAAATAATTGTAAAAT
1 ATATAATTAATTAAATAATTGTAAAAT
404834 TTAAAATCTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.55, C:0.02, G:0.04, T:0.39
Consensus pattern (29 bp):
ATATAATTAATTAAATAATTGTAAAATAC
Found at i:405670 original size:3 final size:3
Alignment explanation
Indices: 405664--405702 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
405654 TCATCATCAT
405664 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CA- CAG CAG C
1 CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG CAG C
405703 TTGGTTTGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.33, C:0.36, G:0.31, T:0.00
Consensus pattern (3 bp):
CAG
Found at i:406623 original size:2 final size:2
Alignment explanation
Indices: 406616--406647 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
406606 AAGGTCTAAG
406616 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
406648 CTTTAAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:406673 original size:4 final size:4
Alignment explanation
Indices: 406664--406690 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
406654 AAATCTAAGT
406664 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
406691 CGATATAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:408827 original size:53 final size:53
Alignment explanation
Indices: 408746--408851 Score: 194
Period size: 53 Copynumber: 2.0 Consensus size: 53
408736 CTTTTCTCTG
*
408746 GATCTCAGATTTGCTTCCGATTCAAATTTGTTCAAACTATTATAGATTGAGAA
1 GATCTCAGATCTGCTTCCGATTCAAATTTGTTCAAACTATTATAGATTGAGAA
*
408799 GATCTCAGATCTGCTTCCGATTCTAATTTGTTCAAACTATTATAGATTGAGAA
1 GATCTCAGATCTGCTTCCGATTCAAATTTGTTCAAACTATTATAGATTGAGAA
408852 TTGAAAGAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 51 1.00
ACGTcount: A:0.31, C:0.16, G:0.15, T:0.38
Consensus pattern (53 bp):
GATCTCAGATCTGCTTCCGATTCAAATTTGTTCAAACTATTATAGATTGAGAA
Done.