Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr02 ID=Chr02-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 62769430
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1067035 characters in sequence are not A, C, G, or T
File 119 of 206
Found at i:35449623 original size:30 final size:30
Alignment explanation
Indices: 35449553--35449640 Score: 104
Period size: 30 Copynumber: 2.9 Consensus size: 30
35449543 ACTGCATTTG
*
35449553 CACTATTACTGTATTGGGTTAAGGCGCACA
1 CACTATTACTGTATTGGGTTAAGGCCCACA
* * *
35449583 CTCTGTTACTGTATTGGGTTATGGCCCACA
1 CACTATTACTGTATTGGGTTAAGGCCCACA
* * * *
35449613 CACTACTACTGTATAGGGATCAGGCCCA
1 CACTATTACTGTATTGGGTTAAGGCCCA
35449641 GACTAATTCT
Statistics
Matches: 47, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.24, C:0.24, G:0.23, T:0.30
Consensus pattern (30 bp):
CACTATTACTGTATTGGGTTAAGGCCCACA
Found at i:35458637 original size:8 final size:8
Alignment explanation
Indices: 35458624--35458671 Score: 57
Period size: 8 Copynumber: 6.1 Consensus size: 8
35458614 AATTTCAATT
35458624 TTATTTAA
1 TTATTTAA
35458632 TTATTTAA
1 TTATTTAA
35458640 TT-TTTCACA
1 TTATTT-A-A
35458649 TTATTTAA
1 TTATTTAA
35458657 TTA-TTAA
1 TTATTTAA
35458664 -TATTTAA
1 TTATTTAA
35458671 T
1 T
35458672 GCAAATTAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 10
0.78 0.00 0.22
Matches are distributed among these distances:
6 2 0.06
7 11 0.31
8 15 0.43
9 4 0.11
10 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.60
Consensus pattern (8 bp):
TTATTTAA
Found at i:35466455 original size:16 final size:16
Alignment explanation
Indices: 35466411--35466457 Score: 60
Period size: 16 Copynumber: 2.9 Consensus size: 16
35466401 ATTTATTGTC
*
35466411 TTCACAATCTAGAGTT
1 TTCACAATCTATAGTT
35466427 TTCA-AAGTCTATAGTT
1 TTCACAA-TCTATAGTT
*
35466443 TTCACAATTTATAGT
1 TTCACAATCTATAGT
35466458 CTATAGTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 2 0.07
16 23 0.85
17 2 0.07
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.43
Consensus pattern (16 bp):
TTCACAATCTATAGTT
Found at i:35466458 original size:23 final size:23
Alignment explanation
Indices: 35466432--35466480 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
35466422 GAGTTTTCAA
*
35466432 AGTCTATAGTTTTCACAATTTAT
1 AGTCTATAGTTTTCACAATCTAT
*
35466455 AGTCTATAGTTTTCACAGTCTAT
1 AGTCTATAGTTTTCACAATCTAT
35466478 AGT
1 AGT
35466481 TTTGAATCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.14, G:0.12, T:0.45
Consensus pattern (23 bp):
AGTCTATAGTTTTCACAATCTAT
Found at i:35466677 original size:13 final size:13
Alignment explanation
Indices: 35466659--35466685 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35466649 ACTAAAAGTA
35466659 ACCCCTCAAATCG
1 ACCCCTCAAATCG
35466672 ACCCCTCAAATCG
1 ACCCCTCAAATCG
35466685 A
1 A
35466686 GCGTAGACAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.33, C:0.44, G:0.07, T:0.15
Consensus pattern (13 bp):
ACCCCTCAAATCG
Found at i:35467469 original size:51 final size:49
Alignment explanation
Indices: 35467390--35467531 Score: 194
Period size: 51 Copynumber: 2.9 Consensus size: 49
35467380 CGTAACACCA
* * * *
35467390 TTTGTGGGCAAGCCATCACTAATTTGCAGATAAACTGCCACTCATAACACT
1 TTTGTGGACAAGCCACCACTGATTTGCAGATATACTGCCACTCATAA-A-T
* *
35467441 TTTGTGGACAAGCCACCACTGATATGCAGATATACTGCCACTGATAAAT
1 TTTGTGGACAAGCCACCACTGATTTGCAGATATACTGCCACTCATAAAT
* *
35467490 TTTGTGTACAAGTCACCACTGATTTGCAGATATACTGCCACT
1 TTTGTGGACAAGCCACCACTGATTTGCAGATATACTGCCACT
35467532 ACTTCCACCT
Statistics
Matches: 82, Mismatches: 9, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
49 40 0.49
50 1 0.01
51 41 0.50
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (49 bp):
TTTGTGGACAAGCCACCACTGATTTGCAGATATACTGCCACTCATAAAT
Found at i:35481266 original size:10 final size:10
Alignment explanation
Indices: 35481253--35481294 Score: 50
Period size: 10 Copynumber: 4.1 Consensus size: 10
35481243 TTTAACTCTT
35481253 TTTTCCTTTC
1 TTTTCCTTTC
*
35481263 TTTT-CTTTT
1 TTTTCCTTTC
35481272 TGATTTCCTTTC
1 T--TTTCCTTTC
35481284 TTTTCCTTTC
1 TTTTCCTTTC
35481294 T
1 T
35481295 CACTTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
9 5 0.19
10 14 0.52
11 3 0.11
12 5 0.19
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTCCTTTC
Found at i:35481266 original size:21 final size:20
Alignment explanation
Indices: 35481248--35481292 Score: 58
Period size: 21 Copynumber: 2.3 Consensus size: 20
35481238 TCATTTTTAA
35481248 CTCTTT-TTTCCTTTCTTTT
1 CTCTTTATTTCCTTTCTTTT
*
35481267 CTTTTTGATTTCCTTTCTTTT
1 CTCTTT-ATTTCCTTTCTTTT
35481288 C-CTTT
1 CTCTTT
35481293 CTCACTTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 5 0.23
20 3 0.14
21 14 0.64
ACGTcount: A:0.02, C:0.24, G:0.02, T:0.71
Consensus pattern (20 bp):
CTCTTTATTTCCTTTCTTTT
Found at i:35483048 original size:65 final size:65
Alignment explanation
Indices: 35482946--35483083 Score: 240
Period size: 65 Copynumber: 2.1 Consensus size: 65
35482936 CCAAGTCAAA
* *
35482946 CACACCACCACCAGAGACGTTCCTCACGGGGCGCAAACCACCACCTTCGGCAACGTTTGATACAC
1 CACACCACCACCAGAGAAGTTCCTCACGGGGCACAAACCACCACCTTCGGCAACGTTTGATACAC
*
35483011 CACACCACCACCAGTGAAGTTCCTCACGGGGCACAAACCACCACCTTCGGCAACGTTTGATACAC
1 CACACCACCACCAGAGAAGTTCCTCACGGGGCACAAACCACCACCTTCGGCAACGTTTGATACAC
35483076 CACCACCA
1 CA-CACCA
35483084 GCGATATTTG
Statistics
Matches: 69, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
65 64 0.93
66 5 0.07
ACGTcount: A:0.29, C:0.41, G:0.17, T:0.14
Consensus pattern (65 bp):
CACACCACCACCAGAGAAGTTCCTCACGGGGCACAAACCACCACCTTCGGCAACGTTTGATACAC
Found at i:35497745 original size:32 final size:32
Alignment explanation
Indices: 35497704--35497781 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 32
35497694 TCTGAAATGT
* **
35497704 CCTT-GGTGTGAACAT-ATGTACTTGGATGGTC
1 CCTTGGGTGTGAACATCA-GGACTTGGACAGTC
*
35497735 CCTTGGGTGTGAACATCAGGAGTTGGACAGTC
1 CCTTGGGTGTGAACATCAGGACTTGGACAGTC
35497767 CCTTGGGTGTGAACA
1 CCTTGGGTGTGAACA
35497782 AAATAGTTAG
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
31 4 0.10
32 36 0.88
33 1 0.02
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (32 bp):
CCTTGGGTGTGAACATCAGGACTTGGACAGTC
Found at i:35499438 original size:20 final size:21
Alignment explanation
Indices: 35499410--35499451 Score: 52
Period size: 20 Copynumber: 2.0 Consensus size: 21
35499400 TGAATGTTTA
35499410 TATTGTATA-AGCTTAC-TATG
1 TATTGTATATA-CTTACTTATG
*
35499430 TATTTTATATACTTACTTATG
1 TATTGTATATACTTACTTATG
35499451 T
1 T
35499452 TAATACATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 13 0.68
21 6 0.32
ACGTcount: A:0.29, C:0.10, G:0.10, T:0.52
Consensus pattern (21 bp):
TATTGTATATACTTACTTATG
Found at i:35501320 original size:50 final size:49
Alignment explanation
Indices: 35501194--35501338 Score: 141
Period size: 50 Copynumber: 2.9 Consensus size: 49
35501184 GATAATAACA
* * *
35501194 TGCCAAAGCCATGTCCTAGATATTGTCTTACATGGGATGTT-TCCTGTAC
1 TGCCAAAGCCATGTCCTAGATATGGTCTTACATGGGA-GTTCTCATATAC
* * *
35501243 TGCCAATGCCGTATCCTAGATATGGTCTTACATGGGAGTTCTCATAT-C
1 TGCCAAAGCCATGTCCTAGATATGGTCTTACATGGGAGTTCTCATATAC
* * * * **
35501291 GGTGCCAACGCCATGTCCCAGACATGGTCTTACGTGGGACCTCTCATA
1 --TGCCAAAGCCATGTCCTAGATATGGTCTTACATGGGAGTTCTCATA
35501339 ACCCCAATCA
Statistics
Matches: 79, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
48 4 0.05
49 37 0.47
50 38 0.48
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (49 bp):
TGCCAAAGCCATGTCCTAGATATGGTCTTACATGGGAGTTCTCATATAC
Found at i:35506612 original size:19 final size:19
Alignment explanation
Indices: 35506587--35506632 Score: 67
Period size: 19 Copynumber: 2.4 Consensus size: 19
35506577 TTAAAGATTG
*
35506587 TTTAATTAAGATTTTATTAA
1 TTTAATTAAGA-TTAATTAA
35506607 -TTAATTAAGATTAATTAA
1 TTTAATTAAGATTAATTAA
35506625 TTTAATTA
1 TTTAATTA
35506633 TAAGTATAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTAATTAAGATTAATTAA
Found at i:35512605 original size:51 final size:51
Alignment explanation
Indices: 35512529--35512675 Score: 267
Period size: 51 Copynumber: 2.9 Consensus size: 51
35512519 AAAAAAGTAC
*
35512529 GAGTATAGGTATTTCATAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
1 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
*
35512580 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGAGTAGTGAGAGATAA
1 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
*
35512631 GAGTATAGGTATTTTGTAGAATTACTTAATAAGAAGGGTAGTGAG
1 GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAG
35512676 GGAGTTGTAG
Statistics
Matches: 92, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 92 1.00
ACGTcount: A:0.39, C:0.03, G:0.27, T:0.31
Consensus pattern (51 bp):
GAGTATAGGTATTTCGTAGAATTACTTAATAAGAAGGGTAGTGAGAGATAA
Found at i:35518275 original size:24 final size:25
Alignment explanation
Indices: 35518240--35518288 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
35518230 CTTTAAATTC
35518240 TAAATAATATTA-ATTTATTTTAAA
1 TAAATAATATTACATTTATTTTAAA
35518264 TAAA-AATGATTACATTTATTTTAAA
1 TAAATAAT-ATTACATTTATTTTAAA
35518289 ATTAATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 3 0.13
24 8 0.35
25 12 0.52
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (25 bp):
TAAATAATATTACATTTATTTTAAA
Found at i:35518984 original size:3 final size:3
Alignment explanation
Indices: 35518976--35519018 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
35518966 AAAAATCCCC
35518976 TTA TTA 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 TTA TTA T
35519019 ATAACCTTTT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:35519537 original size:29 final size:24
Alignment explanation
Indices: 35519481--35519528 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
35519471 TAGAGCTCAA
35519481 ATTGCAAAGCAAAACATTTTCCAC
1 ATTGCAAAGCAAAACATTTTCCAC
35519505 ATTGCAAAGCAAAACATTTTCCAC
1 ATTGCAAAGCAAAACATTTTCCAC
35519529 CCCACATTGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.25, G:0.08, T:0.25
Consensus pattern (24 bp):
ATTGCAAAGCAAAACATTTTCCAC
Found at i:35519955 original size:5 final size:5
Alignment explanation
Indices: 35519945--35519973 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
35519935 TTGAGCTAGA
35519945 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
1 TTTTC TTTTC TTTTC TTTTC TTTTC TTTT
35519974 TAAAATACAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTC
Found at i:35522656 original size:246 final size:246
Alignment explanation
Indices: 35522222--35522709 Score: 922
Period size: 246 Copynumber: 2.0 Consensus size: 246
35522212 TGCATTCATT
35522222 TTCCTTTTTAATGTTTTCCCTTTATTTTTTACTTTTTTAGATAATTTAATTTAATTTAGATGCTT
1 TTCCTTTTTAATGTTTTCCCTTTATTTTTTACTTTTTTAGATAATTTAATTTAATTTAGATGCTT
* ** *
35522287 TTGAACTTGATATAGGTTCATGGAAGCTTAAGCCTCAGGTTTTGAGACCATCAGCGGATTAGACG
66 TTGAACTTGACATAGGTTCATGGAAGCTTAAGCCTCAGGTTTTGAGAAAATCAGCAGATTAGACG
*
35522352 AAGAATTGAGGCAAGGTATAGCAAAAAAGAAGAAGCTTGGAGCTTCGACATAGCATTTTGGCACC
131 AAGAATTGAGGCAAGGTATAGCAAAAAACAAGAAGCTTGGAGCTTCGACATAGCATTTTGGCACC
35522417 CTTGCACGCGAGCAGCGATGCCCTAGCATGGGAAGTGGTCAAGCTTCCCAC
196 CTTGCACGCGAGCAGCGATGCCCTAGCATGGGAAGTGGTCAAGCTTCCCAC
35522468 TTCCTTTTTAATGTTTTCCCTTTATTTTTTACTTTTTTAGATAATTTAATTTAATTTAGATGCTT
1 TTCCTTTTTAATGTTTTCCCTTTATTTTTTACTTTTTTAGATAATTTAATTTAATTTAGATGCTT
*
35522533 TTGAACTTGACATAGGTTCATGGAAGCTTAAGCCTCAGGTTTTGAGAAAATCGGCAGATTAGACG
66 TTGAACTTGACATAGGTTCATGGAAGCTTAAGCCTCAGGTTTTGAGAAAATCAGCAGATTAGACG
35522598 AAGAATTGAGGCAAGGTATAGCAAAAAACAAGAAGCTTGGAGCTTCGACATAGCATTTTGGCACC
131 AAGAATTGAGGCAAGGTATAGCAAAAAACAAGAAGCTTGGAGCTTCGACATAGCATTTTGGCACC
35522663 CTTGCACGCGAGCAGCGATGCCCTAGCATGGGAAGTGGTCAAGCTTC
196 CTTGCACGCGAGCAGCGATGCCCTAGCATGGGAAGTGGTCAAGCTTC
35522710 GTTGGCGCCC
Statistics
Matches: 236, Mismatches: 6, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
246 236 1.00
ACGTcount: A:0.28, C:0.17, G:0.22, T:0.33
Consensus pattern (246 bp):
TTCCTTTTTAATGTTTTCCCTTTATTTTTTACTTTTTTAGATAATTTAATTTAATTTAGATGCTT
TTGAACTTGACATAGGTTCATGGAAGCTTAAGCCTCAGGTTTTGAGAAAATCAGCAGATTAGACG
AAGAATTGAGGCAAGGTATAGCAAAAAACAAGAAGCTTGGAGCTTCGACATAGCATTTTGGCACC
CTTGCACGCGAGCAGCGATGCCCTAGCATGGGAAGTGGTCAAGCTTCCCAC
Found at i:35525190 original size:43 final size:43
Alignment explanation
Indices: 35525085--35525196 Score: 172
Period size: 44 Copynumber: 2.6 Consensus size: 43
35525075 TTTTATCTTA
* * * *
35525085 GAAAAAAAAATTTTAAAA-AGGAGAAGGTAATCTTGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTCGGGTTGTT
35525127 GAAAAAAGAATTTAAAAAAGAGGAGAAGATAATCTCGGGTTGTT
1 GAAAAAAGAATTT-AAAAAGAGGAGAAGATAATCTCGGGTTGTT
35525171 GAAAAAAGAATTTAAAAAGAGGAGAA
1 GAAAAAAGAATTTAAAAAGAGGAGAA
35525197 AGTAAACATG
Statistics
Matches: 64, Mismatches: 4, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
42 12 0.19
43 17 0.27
44 35 0.55
ACGTcount: A:0.51, C:0.03, G:0.24, T:0.22
Consensus pattern (43 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAGATAATCTCGGGTTGTT
Found at i:35525210 original size:43 final size:42
Alignment explanation
Indices: 35525085--35525214 Score: 165
Period size: 44 Copynumber: 3.0 Consensus size: 42
35525075 TTTTATCTTA
* * *
35525085 GAAAAAAAAATTTTAAAA-AGGAGAAGGTAATCTTGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAAGTAATC-TGGGTTGTT
35525127 GAAAAAAGAATTTAAAAAAGAGGAG-AAGATAATCTCGGGTTGTT
1 GAAAAAAGAATTT-AAAAAGAGGAGAAAG-TAATCT-GGGTTGTT
*
35525171 GAAAAAAGAATTTAAAAAGAGGAGAAAGTAAACATGGGTTGTT
1 GAAAAAAGAATTTAAAAAGAGGAGAAAGTAATC-TGGGTTGTT
35525214 G
1 G
35525215 GTTTTACCTT
Statistics
Matches: 78, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
42 12 0.15
43 31 0.40
44 35 0.45
ACGTcount: A:0.48, C:0.03, G:0.25, T:0.24
Consensus pattern (42 bp):
GAAAAAAGAATTTAAAAAGAGGAGAAAGTAATCTGGGTTGTT
Found at i:35529372 original size:19 final size:19
Alignment explanation
Indices: 35529337--35529375 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
35529327 CGAAATGTGT
*
35529337 TTCGTGCGCCAGGATGCAC
1 TTCGTGCGCCACGATGCAC
*
35529356 TTCGTGCGCCACTATGCAC
1 TTCGTGCGCCACGATGCAC
35529375 T
1 T
35529376 ATATGTGCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.15, C:0.33, G:0.26, T:0.26
Consensus pattern (19 bp):
TTCGTGCGCCACGATGCAC
Found at i:35536131 original size:21 final size:21
Alignment explanation
Indices: 35536105--35536156 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
35536095 AATTCAATTA
*
35536105 TTTTAATTTCTTTGTTTTTAG
1 TTTTAATTTCTTAGTTTTTAG
**
35536126 TTTTAAATTT-TTAGTTTTTCT
1 TTTT-AATTTCTTAGTTTTTAG
35536147 TTTTAATTTC
1 TTTTAATTTC
35536157 ATGCTTGTAT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 5 0.19
21 16 0.62
22 5 0.19
ACGTcount: A:0.17, C:0.06, G:0.06, T:0.71
Consensus pattern (21 bp):
TTTTAATTTCTTAGTTTTTAG
Found at i:35547651 original size:17 final size:17
Alignment explanation
Indices: 35547627--35547669 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
35547617 CTCCTCCTCC
*
35547627 TCTTCTTCTTTTTATCT
1 TCTTCTTCTTCTTATCT
* *
35547644 TTTTCTTCTTCTTCTCT
1 TCTTCTTCTTCTTATCT
35547661 TCTTCTTCT
1 TCTTCTTCT
35547670 ACTGCCTAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (17 bp):
TCTTCTTCTTCTTATCT
Found at i:35548397 original size:18 final size:18
Alignment explanation
Indices: 35548371--35548406 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
35548361 TTATTAATTT
35548371 TAAAATAGACTAGTATCA
1 TAAAATAGACTAGTATCA
*
35548389 TAAATTAGACTAGTATCA
1 TAAAATAGACTAGTATCA
35548407 CGTTAACTCT
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:0.47, C:0.11, G:0.11, T:0.31
Consensus pattern (18 bp):
TAAAATAGACTAGTATCA
Found at i:35563941 original size:20 final size:20
Alignment explanation
Indices: 35563916--35563954 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35563906 TACTTTCTTC
35563916 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
35563936 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
35563955 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:35564299 original size:50 final size:50
Alignment explanation
Indices: 35564157--35564398 Score: 189
Period size: 50 Copynumber: 4.7 Consensus size: 50
35564147 GATAATAACA
* * ** * * * *
35564157 TGCCAAAGCCATGTCCCAGATATGGTCTTACATGGGATGTTTCTTGT-AC
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* ** ** * ** *
35564206 TACCAATACCATACCCCAGATATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* * ** *
35564256 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCAG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
* *
35564306 TGCTAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---AG
* *
35564362 TGCCAATGCCATGTCCTAGACATGGTCTTACATGGGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGA
35564399 TCTCATTCCT
Statistics
Matches: 152, Mismatches: 34, Indels: 7
0.79 0.18 0.04
Matches are distributed among these distances:
49 37 0.24
50 78 0.51
53 2 0.01
56 35 0.23
ACGTcount: A:0.24, C:0.28, G:0.21, T:0.27
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCAG
Found at i:35566398 original size:13 final size:12
Alignment explanation
Indices: 35566371--35566405 Score: 54
Period size: 13 Copynumber: 2.9 Consensus size: 12
35566361 GTTGAAAAGT
35566371 AACTTGAAT-CA
1 AACTTGAATGCA
35566382 AACTTGAATGACA
1 AACTTGAATG-CA
35566395 AACTTGAATGC
1 AACTTGAATGC
35566406 CTTCTTTGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 9 0.41
12 1 0.05
13 12 0.55
ACGTcount: A:0.43, C:0.17, G:0.14, T:0.26
Consensus pattern (12 bp):
AACTTGAATGCA
Found at i:35566502 original size:22 final size:24
Alignment explanation
Indices: 35566477--35566526 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
35566467 TACAATTTCG
35566477 CATAGTTTC-TT-GATAAGGATGA
1 CATAGTTTCTTTGGATAAGGATGA
*
35566499 CATATTTTCTTTTGGATAAGGATGA
1 CATAGTTTC-TTTGGATAAGGATGA
35566524 CAT
1 CAT
35566527 CTTTGTCTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
22 8 0.33
24 2 0.08
25 14 0.58
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.40
Consensus pattern (24 bp):
CATAGTTTCTTTGGATAAGGATGA
Found at i:35568244 original size:19 final size:19
Alignment explanation
Indices: 35568205--35568244 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
35568195 ATCGTGAATT
*
35568205 AAAAAGTTATTCCTTTTAA
1 AAAAAGTTATTCCTTTCAA
35568224 AAAAAGTTATTACC-TTCAA
1 AAAAAGTTATT-CCTTTCAA
35568243 AA
1 AA
35568245 CCTTGGTGCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.35
Consensus pattern (19 bp):
AAAAAGTTATTCCTTTCAA
Found at i:35568867 original size:27 final size:27
Alignment explanation
Indices: 35568827--35568882 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
35568817 CAGTAACAAA
* *
35568827 ACAGAACAATGTGGGCTTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
35568854 ACAGAACAAGGTGGGCCTTAGCCCAAT
1 ACAGAACAAGGTGGGCCTTAGCCCAAT
35568881 AC
1 AC
35568883 CATATCAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.34, C:0.25, G:0.23, T:0.18
Consensus pattern (27 bp):
ACAGAACAAGGTGGGCCTTAGCCCAAT
Found at i:35570834 original size:27 final size:27
Alignment explanation
Indices: 35570814--35571022 Score: 122
Period size: 27 Copynumber: 7.8 Consensus size: 27
35570804 TTTTACCCTA
35570814 TAAGGGTATTTCGGTAATTTTCCAAAC
1 TAAGGGTATTTCGGTAATTTTCCAAAC
* * **
35570841 TAAGGGTATTTTGGTAATTTTGCAATT
1 TAAGGGTATTTCGGTAATTTTCCAAAC
*
35570868 TAGGGGTACTTT-GGTAA-TTTCTCAAAC
1 TAAGGGTA-TTTCGGTAATTTTC-CAAAC
* * *
35570895 TGAGGGTATTT-TGTAATTTTACAAA-
1 TAAGGGTATTTCGGTAATTTTCCAAAC
** * * * *
35570920 TCGGGGGTACTTCGATAATTTTAC-AAG
1 T-AAGGGTATTTCGGTAATTTTCCAAAC
* ** **
35570947 TCGAGGGTATTTTAGTAATTTTGTAAAC
1 T-AAGGGTATTTCGGTAATTTTCCAAAC
** **
35570975 TAAGGGTATTTTAGTAATTTTGTAAAC
1 TAAGGGTATTTCGGTAATTTTCCAAAC
* *
35571002 TAAGAGTATTTCAGTAATTTT
1 TAAGGGTATTTCGGTAATTTT
35571023 GTAAACCAAA
Statistics
Matches: 148, Mismatches: 27, Indels: 14
0.78 0.14 0.07
Matches are distributed among these distances:
25 1 0.01
26 24 0.16
27 117 0.79
28 6 0.04
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (27 bp):
TAAGGGTATTTCGGTAATTTTCCAAAC
Found at i:35570885 original size:54 final size:54
Alignment explanation
Indices: 35570817--35571023 Score: 179
Period size: 54 Copynumber: 3.9 Consensus size: 54
35570807 TACCCTATAA
* *
35570817 GGGTA-TTTCGGTAATTTTCCAAACTAAGGGTATTTTGGTAATTTTGCAATTTAG
1 GGGTACTTT-GGTAATTTTCCAAACTAAGGGTATTTTAGTAATTTTGCAAATTAG
* * **
35570871 GGGTACTTTGGTAA-TTTCTCAAACTGAGGGTATTTT-GTAATTTTACAAATCGG
1 GGGTACTTTGGTAATTTTC-CAAACTAAGGGTATTTTAGTAATTTTGCAAATTAG
* * * * * * * *
35570924 GGGTACTTCGATAATTTTAC-AAGTCGAGGGTATTTTAGTAATTTTGTAAACTAA
1 GGGTACTTTGGTAATTTTCCAAACT-AAGGGTATTTTAGTAATTTTGCAAATTAG
* * ** * *
35570978 GGGTATTTTAGTAATTTTGTAAACTAAGAGTATTTCAGTAATTTTG
1 GGGTACTTTGGTAATTTTCCAAACTAAGGGTATTTTAGTAATTTTG
35571024 TAAACCAAAG
Statistics
Matches: 122, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
52 3 0.02
53 41 0.34
54 72 0.59
55 6 0.05
ACGTcount: A:0.29, C:0.09, G:0.21, T:0.42
Consensus pattern (54 bp):
GGGTACTTTGGTAATTTTCCAAACTAAGGGTATTTTAGTAATTTTGCAAATTAG
Found at i:35570939 original size:53 final size:53
Alignment explanation
Indices: 35570817--35570968 Score: 164
Period size: 53 Copynumber: 2.8 Consensus size: 53
35570807 TACCCTATAA
* * * * * *
35570817 GGGTATTTCGGTAATTTTCCAAACTAAGGGTATTTTGGTAATTTTGCAATTTAG
1 GGGTACTTCGGTAATTTT-CAAACTGAGGGTATTTTAGTAATTTTACAAATCAG
* *
35570871 GGGTACTTTGGTAATTTCTCAAACTGAGGGTATTTT-GTAATTTTACAAATCGG
1 GGGTACTTCGGTAATTT-TCAAACTGAGGGTATTTTAGTAATTTTACAAATCAG
* *
35570924 GGGTACTTCGATAATTTT-ACAAGTCGAGGGTATTTTAGTAATTTT
1 GGGTACTTCGGTAATTTTCA-AACT-GAGGGTATTTTAGTAATTTT
35570969 GTAAACTAAG
Statistics
Matches: 84, Mismatches: 10, Indels: 8
0.82 0.10 0.08
Matches are distributed among these distances:
51 1 0.01
52 4 0.05
53 39 0.46
54 39 0.46
55 1 0.01
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.41
Consensus pattern (53 bp):
GGGTACTTCGGTAATTTTCAAACTGAGGGTATTTTAGTAATTTTACAAATCAG
Found at i:35571023 original size:27 final size:27
Alignment explanation
Indices: 35570953--35571037 Score: 136
Period size: 27 Copynumber: 3.2 Consensus size: 27
35570943 CAAGTCGAGG
*
35570953 GTATTTTAGTAATTTTGTAAACTAAGG
1 GTATTTTAGTAATTTTGTAAACTAAGA
35570980 GTATTTTAGTAATTTTGTAAACTAAGA
1 GTATTTTAGTAATTTTGTAAACTAAGA
* *
35571007 GTATTTCAGTAATTTTGTAAACCAA-A
1 GTATTTTAGTAATTTTGTAAACTAAGA
35571033 GTATT
1 GTATT
35571038 CTAAATAGAG
Statistics
Matches: 55, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
26 6 0.11
27 49 0.89
ACGTcount: A:0.35, C:0.06, G:0.15, T:0.44
Consensus pattern (27 bp):
GTATTTTAGTAATTTTGTAAACTAAGA
Found at i:35574095 original size:22 final size:22
Alignment explanation
Indices: 35574069--35574114 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
35574059 GCATCTCACC
35574069 AATCTCCTTAACTCTAGTCTCA
1 AATCTCCTTAACTCTAGTCTCA
35574091 AATCTCCTTAACTCTAGTCTCA
1 AATCTCCTTAACTCTAGTCTCA
35574113 AA
1 AA
35574115 CACTTCCTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.30, C:0.30, G:0.04, T:0.35
Consensus pattern (22 bp):
AATCTCCTTAACTCTAGTCTCA
Found at i:35575330 original size:27 final size:27
Alignment explanation
Indices: 35575290--35575345 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
35575280 CAGTAACAGA
*
35575290 ACAGAACAATGTGGG-CTTTAGCCCAAT
1 ACAGAACAAGGTGGGTC-TTAGCCCAAT
35575317 ACAGAACAAGGTGGGTCTTAGCCCAAT
1 ACAGAACAAGGTGGGTCTTAGCCCAAT
35575344 AC
1 AC
35575346 CATACCAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
27 26 0.96
28 1 0.04
ACGTcount: A:0.34, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
ACAGAACAAGGTGGGTCTTAGCCCAAT
Found at i:35575934 original size:81 final size:81
Alignment explanation
Indices: 35575832--35576019 Score: 218
Period size: 81 Copynumber: 2.3 Consensus size: 81
35575822 GTAATTCTCC
* * * **
35575832 AAACTAAGGGTATTTTAGTAATTTTGCAATTC-AGAGGTCATTT-GGTAATTTTGCAAACTGAGG
1 AAACTAAGGGTATTTCAGTAATTTTGCAAGTCGAG-GGT-ATTTCAGTAATTTTGCAAACCAAGG
* * *
35575895 ATATTTCAGTAGTTTTGT
64 ATATTTAAATAATTTTGT
* * * * *
35575913 AAACTAAGGGTACTTCAGTAATTTTACAGGTCGAGGGTATTTCAGTAATTTTGTAAACCAAGGGT
1 AAACTAAGGGTATTTCAGTAATTTTGCAAGTCGAGGGTATTTCAGTAATTTTGCAAACCAAGGAT
35575978 ATTTAAATAATTTTGT
66 ATTTAAATAATTTTGT
*
35575994 AAACCAAGGGTATTTCAGTAATTTTG
1 AAACTAAGGGTATTTCAGTAATTTTG
35576020 TAAACCAAAG
Statistics
Matches: 89, Mismatches: 16, Indels: 4
0.82 0.15 0.04
Matches are distributed among these distances:
80 4 0.04
81 83 0.93
82 2 0.02
ACGTcount: A:0.32, C:0.10, G:0.20, T:0.38
Consensus pattern (81 bp):
AAACTAAGGGTATTTCAGTAATTTTGCAAGTCGAGGGTATTTCAGTAATTTTGCAAACCAAGGAT
ATTTAAATAATTTTGT
Found at i:35576025 original size:27 final size:27
Alignment explanation
Indices: 35575810--35576027 Score: 179
Period size: 27 Copynumber: 8.1 Consensus size: 27
35575800 TTTACCCTAT
* * * *
35575810 AAGGGTATTTCGGTAATTCTCCAAACT
1 AAGGGTATTTCAGTAATTTTGCAAACC
* **
35575837 AAGGGTATTTTAGTAATTTTGCAATTC
1 AAGGGTATTTCAGTAATTTTGCAAACC
* *
35575864 -AGAGGTCATTT-GGTAATTTTGCAAACT
1 AAG-GGT-ATTTCAGTAATTTTGCAAACC
* * * * *
35575891 GAGGATATTTCAGTAGTTTTGTAAACT
1 AAGGGTATTTCAGTAATTTTGCAAACC
* * ***
35575918 AAGGGTACTTCAGTAATTTTACAGGTC
1 AAGGGTATTTCAGTAATTTTGCAAACC
* *
35575945 GAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTCAGTAATTTTGCAAACC
* * *
35575972 AAGGGTATTTAAATAATTTTGTAAACC
1 AAGGGTATTTCAGTAATTTTGCAAACC
*
35575999 AAGGGTATTTCAGTAATTTTGTAAACC
1 AAGGGTATTTCAGTAATTTTGCAAACC
35576026 AA
1 AA
35576028 AGTATTCTAA
Statistics
Matches: 150, Mismatches: 37, Indels: 8
0.77 0.19 0.04
Matches are distributed among these distances:
26 6 0.04
27 138 0.92
28 6 0.04
ACGTcount: A:0.32, C:0.11, G:0.20, T:0.37
Consensus pattern (27 bp):
AAGGGTATTTCAGTAATTTTGCAAACC
Found at i:35587439 original size:22 final size:22
Alignment explanation
Indices: 35587408--35587461 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
35587398 TGCCTAGCAG
*
35587408 GCTTTATGCCGGTGTTATTCAA
1 GCTTTGTGCCGGTGTTATTCAA
*
35587430 GCTTTGTGCCGGTGTTATTCAG
1 GCTTTGTGCCGGTGTTATTCAA
35587452 GCTTTGTGCC
1 GCTTTGTGCC
35587462 TAGCAGGCTA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.11, C:0.20, G:0.28, T:0.41
Consensus pattern (22 bp):
GCTTTGTGCCGGTGTTATTCAA
Found at i:35589546 original size:41 final size:41
Alignment explanation
Indices: 35589487--35589890 Score: 438
Period size: 41 Copynumber: 9.9 Consensus size: 41
35589477 TTTTGCGACT
** * *
35589487 TTTAGCGGCGTTCCTGAAAAAGCGCCACTAATGCTTGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* *
35589528 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTTGGGCC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* * * * *
35589569 TTTAACAGCGTTTTT-AGTAAAGCGCCGATAATGCTCGGGGT
1 TTTAGCGGCGTTTTTGA-AAAAGCGCCGCTAATGCTCGGGGC
* * *
35589610 TTTAGCGGCATTTTCGAAAAGGCGCCGCTAATGCTCGGGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* * * *
35589651 TTTAGCGGCGTTTTCGAAAAGGCGCCGCTAATGCTCGAGCC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* * * * *
35589692 TTTAGCGGC-ATTTTCAAAAAGACGTCGCTAATGCTCGAGCC
1 TTTAGCGGCGTTTTTGAAAAAG-CGCCGCTAATGCTCGGGGC
* *
35589733 TTTAGCGGCATTTTTGAAAAAGCGCCGCTAATGCTCGGGAC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* * * *
35589774 TTTAGCGGCGTGTTTTGGAAAAGCACTGCTAATGCTCAGGGC
1 TTTAGCGGCGT-TTTTGAAAAAGCGCCGCTAATGCTCGGGGC
** * *
35589816 TTTAGCGATGTTTGTG-AAAAGCGCTGCTAATGCTC-GGGC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
* *
35589855 TTTAGCGGCGTTTTTGAAGAAGCGCTGCTAATGCTC
1 TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
35589891 TATTTTTAGC
Statistics
Matches: 311, Mismatches: 46, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
39 17 0.05
40 45 0.14
41 204 0.66
42 45 0.14
ACGTcount: A:0.22, C:0.22, G:0.28, T:0.28
Consensus pattern (41 bp):
TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGGGC
Found at i:35589983 original size:21 final size:21
Alignment explanation
Indices: 35589959--35590161 Score: 64
Period size: 21 Copynumber: 9.6 Consensus size: 21
35589949 TATCATTATA
35589959 GTTTAGGATTTATGGTTTAGG
1 GTTTAGGATTTATGGTTTAGG
* *
35589980 GTTTAAGATTTAAGAGTTACTA--
1 GTTTAGGATTTATG-GTT--TAGG
* * ** *
35590002 TTTTAAGG-TTTAGGGAGTATGT
1 GTTT-AGGATTTATGGTTTA-GG
* *
35590024 GTTTAGGGA-TTATGGATTATG
1 GTTTA-GGATTTATGGTTTAGG
35590045 GTTTATGG-TTTATGGTTTAAGG
1 GTTTA-GGATTTATGGTTT-AGG
* * * *
35590067 G-TTGGGGTTTAAGGGTTAGG
1 GTTTAGGATTTATGGTTTAGG
* *
35590087 GGTTAGGAGTTATGGGTTTA-G
1 GTTTAGGATTTAT-GGTTTAGG
* * *
35590108 GTTTATGTTTTATGATTTAGG
1 GTTTAGGATTTATGGTTTAGG
*
35590129 GTTTAGGAATTGA-GG-TTAGGG
1 GTTTAGG-ATTTATGGTTTA-GG
*
35590150 GTTTAGGGTTTA
1 GTTTAGGATTTA
35590162 GATTAATTGA
Statistics
Matches: 131, Mismatches: 34, Indels: 35
0.65 0.17 0.17
Matches are distributed among these distances:
19 2 0.02
20 17 0.13
21 73 0.56
22 35 0.27
23 2 0.02
24 2 0.02
ACGTcount: A:0.22, C:0.00, G:0.34, T:0.44
Consensus pattern (21 bp):
GTTTAGGATTTATGGTTTAGG
Found at i:35590028 original size:22 final size:21
Alignment explanation
Indices: 35590003--35590056 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 21
35589993 GAGTTACTAT
35590003 TTTAAGGTTTAGGGAGTATGTG
1 TTTAAGGTTTAGGGAGTATG-G
* * * *
35590025 TTTAGGGATTATGGATTATGG
1 TTTAAGGTTTAGGGAGTATGG
*
35590046 TTTATGGTTTA
1 TTTAAGGTTTA
35590057 TGGTTTAAGG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 10 0.38
22 16 0.62
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.46
Consensus pattern (21 bp):
TTTAAGGTTTAGGGAGTATGG
Found at i:35590060 original size:7 final size:7
Alignment explanation
Indices: 35590019--35590063 Score: 54
Period size: 7 Copynumber: 6.3 Consensus size: 7
35590009 GTTTAGGGAG
35590019 TATGTGTT
1 TATG-GTT
* *
35590027 TAGGGAT
1 TATGGTT
*
35590034 TATGGAT
1 TATGGTT
35590041 TATGGTT
1 TATGGTT
35590048 TATGGTT
1 TATGGTT
35590055 TATGGTT
1 TATGGTT
35590062 TA
1 TA
35590064 AGGGTTGGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 1
0.87 0.11 0.03
Matches are distributed among these distances:
7 30 0.91
8 3 0.09
ACGTcount: A:0.20, C:0.00, G:0.29, T:0.51
Consensus pattern (7 bp):
TATGGTT
Found at i:35590133 original size:7 final size:7
Alignment explanation
Indices: 35590024--35590162 Score: 56
Period size: 7 Copynumber: 19.9 Consensus size: 7
35590014 GGGAGTATGT
35590024 GTTTAGG
1 GTTTAGG
* *
35590031 GATTATG
1 GTTTAGG
* *
35590038 GATTATG
1 GTTTAGG
*
35590045 GTTTATG
1 GTTTAGG
*
35590052 GTTTATG
1 GTTTAGG
35590059 GTTTAAGG
1 GTTT-AGG
*
35590067 G-TTGGG
1 GTTTAGG
35590073 GTTTAAGG
1 GTTT-AGG
35590081 G-TTAGG
1 GTTTAGG
*
35590087 GGTTAGG
1 GTTTAGG
35590094 AG-TTATGG
1 -GTTTA-GG
35590102 GTTTA-G
1 GTTTAGG
*
35590108 GTTTATG
1 GTTTAGG
* *
35590115 TTTTATG
1 GTTTAGG
*
35590122 ATTTAGG
1 GTTTAGG
35590129 GTTTAGG
1 GTTTAGG
**
35590136 AATT-GAG
1 GTTTAG-G
35590143 G-TTAGGG
1 GTTTA-GG
35590150 GTTTAGG
1 GTTTAGG
35590157 GTTTAG
1 GTTTAG
35590163 ATTAATTGAT
Statistics
Matches: 107, Mismatches: 13, Indels: 24
0.74 0.09 0.17
Matches are distributed among these distances:
6 16 0.15
7 75 0.70
8 16 0.15
ACGTcount: A:0.19, C:0.00, G:0.37, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:35591760 original size:29 final size:29
Alignment explanation
Indices: 35591664--35591766 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
35591654 GATCCTTGAT
*
35591664 TTTATTTTATTTTTCCAGTATTTTTCCTC
1 TTTATTTTGTTTTTCCAGTATTTTTCCTC
* * * **
35591693 TTTATTTTCTTCGCTT-CA-TTTTCTTTGAGAT-
1 TTTATTTTGTT--TTTCCAGTATT-TTT--CCTC
35591724 TTTATTTTGTTTTTCCAGTATTTTTCCTC
1 TTTATTTTGTTTTTCCAGTATTTTTCCTC
*
35591753 TTTATTTTGATTTT
1 TTTATTTTGTTTTT
35591767 AATTTTTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 16
0.67 0.13 0.20
Matches are distributed among these distances:
28 1 0.02
29 28 0.51
30 10 0.18
31 15 0.27
32 1 0.02
ACGTcount: A:0.13, C:0.15, G:0.07, T:0.66
Consensus pattern (29 bp):
TTTATTTTGTTTTTCCAGTATTTTTCCTC
Found at i:35594186 original size:43 final size:43
Alignment explanation
Indices: 35594120--35594205 Score: 127
Period size: 43 Copynumber: 2.0 Consensus size: 43
35594110 AGTTCATTAT
* * *
35594120 AAGATTTTCTTGATTAAGTAAATGTATTATATCTTTTATTACC
1 AAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
* *
35594163 AAGATTTACTTGATTAAGAAAATGCATTGTATTTTTTATTACC
1 AAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
35594206 TTGCAATGTG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
43 38 1.00
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.47
Consensus pattern (43 bp):
AAGATTTACTTGATTAAGAAAATGCATTATATCTTTTATTACC
Found at i:35594512 original size:24 final size:22
Alignment explanation
Indices: 35594483--35594526 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 22
35594473 AAATTTAAAA
35594483 AATAAAACATAATATAATATTTAC
1 AATAAAA-ATAA-ATAATATTTAC
*
35594507 AATAAAAATAAATATTATTT
1 AATAAAAATAAATAATATTT
35594527 GATTAAAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 8 0.42
23 4 0.21
24 7 0.37
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (22 bp):
AATAAAAATAAATAATATTTAC
Found at i:35594654 original size:43 final size:43
Alignment explanation
Indices: 35594545--35594741 Score: 236
Period size: 43 Copynumber: 4.6 Consensus size: 43
35594535 TAATTTTTTT
* * * *
35594545 TAAAGGTTATGTT-TTTAGCGGCGTTTTTGCTAGAAGCACCGC
1 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
*
35594587 TAAATGTT-TGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
1 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* *
35594629 TAAAGGTTATGTTCTTTAGTGGCGTTTGTGACAAAAGCGCCGC
1 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* * * * * *
35594672 TAAAGGTCATGATCTTTAGCGGTGTTTGTGATCAAAGTGCCAC
1 TAAAGGTTATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
* * *
35594715 TAAAAGTCATGATCTTTAGCGGCGTTT
1 TAAAGGTTATGTTCTTTAGCGGCGTTT
35594742 TTTCACATAA
Statistics
Matches: 135, Mismatches: 18, Indels: 3
0.87 0.12 0.02
Matches are distributed among these distances:
41 4 0.03
42 39 0.29
43 92 0.68
ACGTcount: A:0.23, C:0.16, G:0.26, T:0.35
Consensus pattern (43 bp):
TAAAGGTTATGTTCTTTAGCGGCGTTTGTGATAAAAGCGCCGC
Found at i:35596973 original size:2 final size:2
Alignment explanation
Indices: 35596968--35597004 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
35596958 ACATTATATA
35596968 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
35597005 TTAAATACAT
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:0.00, C:0.00, G:0.49, T:0.51
Consensus pattern (2 bp):
TG
Found at i:35598287 original size:3 final size:3
Alignment explanation
Indices: 35598279--35598313 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
35598269 GGCTCCATCT
35598279 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
35598314 CAAATAGAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:35603374 original size:13 final size:13
Alignment explanation
Indices: 35603358--35603422 Score: 80
Period size: 13 Copynumber: 5.1 Consensus size: 13
35603348 TTTAAACCAA
35603358 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
35603371 ACTTCTC-AAAGC
1 ACTTTTCAAAAGC
*
35603383 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
*
35603396 ACTTCTCAAAAGC
1 ACTTTTCAAAAGC
35603409 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
35603422 A
1 A
35603423 TTGCTAAACT
Statistics
Matches: 43, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
12 14 0.33
13 27 0.63
14 2 0.05
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:35603386 original size:25 final size:26
Alignment explanation
Indices: 35603358--35603422 Score: 98
Period size: 25 Copynumber: 2.5 Consensus size: 26
35603348 TTTAAACCAA
35603358 ACTTTTCAAAAGCACTTCTC-AAAGC
1 ACTTTTCAAAAGCACTTCTCAAAAGC
*
35603383 ACTTTTCCACAA-CACTTCTCAAAAGC
1 ACTTTT-CAAAAGCACTTCTCAAAAGC
35603409 ACTTTTCAAAAGCA
1 ACTTTTCAAAAGCA
35603423 TTGCTAAACT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 18 0.51
26 17 0.49
ACGTcount: A:0.37, C:0.29, G:0.06, T:0.28
Consensus pattern (26 bp):
ACTTTTCAAAAGCACTTCTCAAAAGC
Found at i:35607836 original size:10 final size:10
Alignment explanation
Indices: 35607819--35607891 Score: 67
Period size: 10 Copynumber: 7.2 Consensus size: 10
35607809 ACCAATTTTT
35607819 TTAAAAAATA
1 TTAAAAAATA
*
35607829 TAAAAAAATA
1 TTAAAAAATA
*
35607839 TTTTAAAAATA
1 -TTAAAAAATA
*
35607850 TTTTAAAAATA
1 -TTAAAAAATA
**
35607861 TTTTAAAAT-
1 TTAAAAAATA
35607870 TTAAAAAATA
1 TTAAAAAATA
*
35607880 TAAAAAAATA
1 TTAAAAAATA
35607890 TT
1 TT
35607892 TTTATATATT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.13
10 27 0.51
11 19 0.36
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TTAAAAAATA
Found at i:35607845 original size:22 final size:23
Alignment explanation
Indices: 35607817--35607868 Score: 72
Period size: 22 Copynumber: 2.3 Consensus size: 23
35607807 ACACCAATTT
35607817 TTTTAAAAAATA-TAAAAAAATA
1 TTTTAAAAAATATTAAAAAAATA
**
35607839 TTTT-AAAAATATTTTAAAAATA
1 TTTTAAAAAATATTAAAAAAATA
35607861 TTTTAAAA
1 TTTTAAAA
35607869 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 7 0.27
22 16 0.62
23 3 0.12
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
TTTTAAAAAATATTAAAAAAATA
Found at i:35607846 original size:11 final size:11
Alignment explanation
Indices: 35607832--35607868 Score: 74
Period size: 11 Copynumber: 3.4 Consensus size: 11
35607822 AAAAATATAA
35607832 AAAAATATTTT
1 AAAAATATTTT
35607843 AAAAATATTTT
1 AAAAATATTTT
35607854 AAAAATATTTT
1 AAAAATATTTT
35607865 AAAA
1 AAAA
35607869 TTTAAAAAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 26 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:35609086 original size:15 final size:15
Alignment explanation
Indices: 35609066--35609104 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
35609056 TTTACACTAA
* *
35609066 TATTATTTTTTTAAT
1 TATTATTATTATAAT
35609081 TATTATTATTATAAT
1 TATTATTATTATAAT
35609096 TATTATTAT
1 TATTATTAT
35609105 CACATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTATTATTATAAT
Found at i:35609212 original size:21 final size:21
Alignment explanation
Indices: 35609188--35609228 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35609178 TTATAAATAC
35609188 ATGTATATATTATTTACATAT
1 ATGTATATATTATTTACATAT
* * *
35609209 ATGTTTATTTTATTTTCATA
1 ATGTATATATTATTTACATA
35609229 ACTTTTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
ATGTATATATTATTTACATAT
Found at i:35609415 original size:16 final size:16
Alignment explanation
Indices: 35609385--35609432 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
35609375 TCATTCATGT
**
35609385 TTTATATATGTGTATA
1 TTTATATATACGTATA
*
35609401 TTTATATATACGTATC
1 TTTATATATACGTATA
* *
35609417 TTAATATATACATATA
1 TTTATATATACGTATA
35609433 CATATTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTATATATACGTATA
Found at i:35609470 original size:2 final size:2
Alignment explanation
Indices: 35609465--35609505 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
35609455 ATATTGTTCT
35609465 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
35609506 TGTAAACACA
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:35621888 original size:50 final size:49
Alignment explanation
Indices: 35621831--35621975 Score: 139
Period size: 50 Copynumber: 2.9 Consensus size: 49
35621821 TTTGGCATTA
*
35621831 CAGTGGAATAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTG
1 CAGTGGAATAGATTGAAGCCACAACG-CGAATCTTACTTCCCTGGCAGTG
* * * * * * * *
35621881 TAGTGGAACAGATTGAAGTCACGATA-GTGAATCTTATTTCCCCGACATTG
1 CAGTGGAATAGATTGAAGCCAC-A-ACGCGAATCTTACTTCCCTGGCAGTG
** *
35621931 CAGTTAAATAAATTGAAGCCACAACGGCGAATCTTACTTCCCTGG
1 CAGTGGAATAGATTGAAGCCACAAC-GCGAATCTTACTTCCCTGG
35621976 TGTTACAATG
Statistics
Matches: 72, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
48 1 0.01
49 1 0.01
50 67 0.93
51 2 0.03
52 1 0.01
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (49 bp):
CAGTGGAATAGATTGAAGCCACAACGCGAATCTTACTTCCCTGGCAGTG
Found at i:35622015 original size:100 final size:100
Alignment explanation
Indices: 35621837--35622022 Score: 228
Period size: 100 Copynumber: 1.9 Consensus size: 100
35621827 ATTACAGTGG
* ** * * *
35621837 AATAGATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGTCA
1 AATAAATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTACAATGGAACAGATTAAAGCCA
* * *
35621902 CGATAGTGAATCTTATTTCCCCGACATTGCAGTTA
66 CGACAGCGAATCTTATCTCCCCGACATTGCAGTTA
* * * *
35621937 AATAAATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGTTACAATGGAGCAGATTAAAGCCA
1 AATAAATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTACAATGGAACAGATTAAAGCCA
* * *
35622002 TGACGGCGGATCTTATCTCCC
66 CGACAGCGAATCTTATCTCCC
35622023 TGGCGTTAAG
Statistics
Matches: 70, Mismatches: 16, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
100 70 1.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.26
Consensus pattern (100 bp):
AATAAATTGAAGCCACAACGACGAATCTTACTTCCCTGGCGGTACAATGGAACAGATTAAAGCCA
CGACAGCGAATCTTATCTCCCCGACATTGCAGTTA
Found at i:35622134 original size:267 final size:267
Alignment explanation
Indices: 35621670--35622239 Score: 827
Period size: 267 Copynumber: 2.1 Consensus size: 267
35621660 ATTGCAATGG
* ** * * * *
35621670 AATAGATTGAAGCCACAACGGCGAATCTTACTTCTTTTGCGTTGCAGCGGAGCAGATTGAAGCCA
1 AATAAATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGTTACAACGGAGCAGATTAAAGCCA
* * * *
35621735 CGACGGCGGGTCTTATCTCCCTGGTGTTAAGGCTTGGATTAGCTGAAGTGGAGCGGGTTGAAGCT
66 CGACGGCGGATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGATTGAAGCT
* *
35621800 GTGGGTAGCGAATCCTATCTCTTTGGCATTACAGTGGAATAGATTGAAGCCACAACGACGAATCT
131 GTGGGTAGCAAATCCTATCTCTTTGGCATTACAGTGGAATAGATAGAAGCCACAACGACGAATCT
* * * *
35621865 TACTTCCCTGGCGGTGTAGTGGAACAGATTGAAGTCACGATAGTGAATCTTATTTCCCCGACATT
196 TACTTCCCTGGCGGTGTAGTAGAACAGATTGAAGTCACGACAGCGAATCTCATTTCCCCGACATT
*
35621930 GCAGTTA
261 ACAGTTA
* *
35621937 AATAAATTGAAGCCACAACGGCGAATCTTACTTCCCTGGTGTTACAATGGAGCAGATTAAAGCCA
1 AATAAATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGTTACAACGGAGCAGATTAAAGCCA
* *
35622002 TGACGGCGGATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGTTGAAGTGGAGCGGATTGAAGCT
66 CGACGGCGGATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGATTGAAGCT
* * **
35622067 GTGGGTAGCAAATCTTATCTCTTTGGCATTATAGTGGAATAGATAGAAGCCACAACGGTGAATCT
131 GTGGGTAGCAAATCCTATCTCTTTGGCATTACAGTGGAATAGATAGAAGCCACAACGACGAATCT
* *
35622132 TACTTCCCTGGCGGTGTAGTAGAACAGATTGAAGTCACGACGGCGAATCTCGTTTCCCCGACATT
196 TACTTCCCTGGCGGTGTAGTAGAACAGATTGAAGTCACGACAGCGAATCTCATTTCCCCGACATT
35622197 ACAGTTA
261 ACAGTTA
* * * * *
35622204 AACATATTGAAGCTACGAA-GACGAATCTTATTTCCC
1 AATAAATTGAAGCCAC-AACGGCGAATCTTACTTCCC
35622240 CGACATTGCA
Statistics
Matches: 269, Mismatches: 33, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
267 267 0.99
268 2 0.01
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.27
Consensus pattern (267 bp):
AATAAATTGAAGCCACAACGGCGAATCTTACTTCCCTGGCGTTACAACGGAGCAGATTAAAGCCA
CGACGGCGGATCTTATCTCCCTGGCGTTAAGGCTTAGATTAGCTGAAGTGGAGCGGATTGAAGCT
GTGGGTAGCAAATCCTATCTCTTTGGCATTACAGTGGAATAGATAGAAGCCACAACGACGAATCT
TACTTCCCTGGCGGTGTAGTAGAACAGATTGAAGTCACGACAGCGAATCTCATTTCCCCGACATT
ACAGTTA
Found at i:35622455 original size:126 final size:127
Alignment explanation
Indices: 35622262--35622591 Score: 477
Period size: 126 Copynumber: 2.6 Consensus size: 127
35622252 CAAACAAATT
*
35622262 GAAGAAAATAATCCTATCTCCTTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
1 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
*
35622327 GAAGTTGCAGAAGAATAGATCACATCCAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGATTA
66 GAAGTTGCAGAAGAATAGATCACATCCAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGA-CA
* *
35622390 -AAGAAAATAATCCTATCTCCCTG-AGTTGCAGTGGAGCGGATTAACATCCGATCTTATCTCTCT
1 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
* * * * *
35622453 GAAGTTGCAGTAGAGTAGATCGCGTCCAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACA
66 GAAGTTGCAGAAGAATAGATCACATCCAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACA
* * * * *
35622515 GAAGAAACTAATCCTATCGCCCTGAAGTTGCAGTGGAGCGAATTAAAATGATGAATCATATAC-C
1 GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCA-G-ATCTTAT-CTC
35622579 TCTGAAGTTGCAG
63 TCTGAAGTTGCAG
35622592 TAGGTCGGAT
Statistics
Matches: 181, Mismatches: 16, Indels: 9
0.88 0.08 0.04
Matches are distributed among these distances:
125 1 0.01
126 114 0.63
127 44 0.24
128 1 0.01
129 20 0.11
130 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (127 bp):
GAAGAAAATAATCCTATCTCCCTGAAGTTGCAGTGGAGCGGATTAAAATCAGATCTTATCTCTCT
GAAGTTGCAGAAGAATAGATCACATCCAGTCTTATCTCCCTGAAGTTACAGTGGAGCAGACA
Found at i:35623896 original size:15 final size:15
Alignment explanation
Indices: 35623876--35623916 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
35623866 TTACACTAAT
* *
35623876 ATTATTTTTTTTAAA
1 ATTATTATTATTAAA
*
35623891 ATTATTATTATTATA
1 ATTATTATTATTAAA
35623906 ATTATTATTAT
1 ATTATTATTAT
35623917 CACATTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 23 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTATTAAA
Found at i:35624024 original size:21 final size:21
Alignment explanation
Indices: 35624000--35624040 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
35623990 TTATAAATAC
35624000 ATGTATATATTATTTACATAT
1 ATGTATATATTATTTACATAT
* * *
35624021 ATGTTTATTTTATTTTCATA
1 ATGTATATATTATTTACATA
35624041 ACTTTTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.32, C:0.05, G:0.05, T:0.59
Consensus pattern (21 bp):
ATGTATATATTATTTACATAT
Found at i:35624227 original size:16 final size:16
Alignment explanation
Indices: 35624197--35624244 Score: 51
Period size: 16 Copynumber: 3.0 Consensus size: 16
35624187 TCATTCATGT
**
35624197 TTTATATATGTGTATA
1 TTTATATATACGTATA
*
35624213 TTTATATATACGTATC
1 TTTATATATACGTATA
* *
35624229 TTAATATATACATATA
1 TTTATATATACGTATA
35624245 CATATTTTCA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.50
Consensus pattern (16 bp):
TTTATATATACGTATA
Found at i:35631856 original size:45 final size:43
Alignment explanation
Indices: 35631795--35631881 Score: 102
Period size: 45 Copynumber: 2.0 Consensus size: 43
35631785 TAAGGATGAT
**
35631795 ATTAATGGTTACTTCCACGTAGCTTTCTTTTTGTCTTGTCATATC
1 ATTAATGGTTACTTCCACGTAGCAATCTTTTTGT-TTGT-ATATC
** * *
35631840 ATTAATGGTTTGTTCCATGTTGCAATCTTTTTGTTTGTATAT
1 ATTAATGGTTACTTCCACGTAGCAATCTTTTTGTTTGTATAT
35631882 AGATGTCTTA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
43 4 0.11
44 4 0.11
45 28 0.78
ACGTcount: A:0.18, C:0.15, G:0.15, T:0.52
Consensus pattern (43 bp):
ATTAATGGTTACTTCCACGTAGCAATCTTTTTGTTTGTATATC
Found at i:35636017 original size:40 final size:40
Alignment explanation
Indices: 35635962--35636062 Score: 175
Period size: 40 Copynumber: 2.5 Consensus size: 40
35635952 AATTTCAGAA
*
35635962 CACCGGCATTAAGCCTGCTAGACATTAAGTTTGAATAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
*
35636002 CACCGGCATTAAGCCTGCTAAACATTAAGTCTGAATAATT
1 CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
*
35636042 CACCGACATTAAGCCTGCTAG
1 CACCGGCATTAAGCCTGCTAG
35636063 GTACAGAACC
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 57 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.27
Consensus pattern (40 bp):
CACCGGCATTAAGCCTGCTAGACATTAAGTCTGAATAATT
Found at i:35637072 original size:89 final size:90
Alignment explanation
Indices: 35636963--35637137 Score: 325
Period size: 89 Copynumber: 2.0 Consensus size: 90
35636953 CTCGATCTAA
*
35636963 ATATATTCAAAATGAGCTAGTTTAATTATTAACACATTCAATTTAGTCC-AAAAAATACATAAAT
1 ATATATTCAAAATGAGCTAGTCTAATTATTAACACATTCAATTTAGTCCAAAAAAATACATAAAT
*
35637027 GGGCAAATTACCATTTTGCCCATTT
66 GGGAAAATTACCATTTTGCCCATTT
35637052 ATATATTCAAAATGAGCTAGTCTAATTATTAACACATTCAATTTAGTCCAAAAAAATACATAAAT
1 ATATATTCAAAATGAGCTAGTCTAATTATTAACACATTCAATTTAGTCCAAAAAAATACATAAAT
35637117 GGGAAAATTACCATTTTGCCC
66 GGGAAAATTACCATTTTGCCC
35637138 CTAACATTTA
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
89 48 0.58
90 35 0.42
ACGTcount: A:0.42, C:0.16, G:0.09, T:0.33
Consensus pattern (90 bp):
ATATATTCAAAATGAGCTAGTCTAATTATTAACACATTCAATTTAGTCCAAAAAAATACATAAAT
GGGAAAATTACCATTTTGCCCATTT
Found at i:35643040 original size:40 final size:40
Alignment explanation
Indices: 35642929--35643024 Score: 192
Period size: 40 Copynumber: 2.4 Consensus size: 40
35642919 CAGAACACAA
35642929 GCATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCG
1 GCATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCG
35642969 GCATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCG
1 GCATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCG
35643009 GCATTAAGCCTGCTAG
1 GCATTAAGCCTGCTAG
35643025 GTACAGAACT
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 56 1.00
ACGTcount: A:0.31, C:0.23, G:0.19, T:0.27
Consensus pattern (40 bp):
GCATTAAGCCTGCTAGACATTAAGTCTGAATAATTCACCG
Found at i:35643637 original size:2 final size:2
Alignment explanation
Indices: 35643630--35643672 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
35643620 GAACCACTTG
35643630 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
35643671 TA
1 TA
35643673 ATACTAATTC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35646105 original size:51 final size:50
Alignment explanation
Indices: 35645983--35646225 Score: 240
Period size: 51 Copynumber: 4.8 Consensus size: 50
35645973 TATCATTCGA
* * * * *
35645983 TACATGTAGTAGCCTTCACATAGTACTACACACGTGATCA-AAATTTTCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TTCCGG
* * * *
35646033 TTCACGTAGTAGCCTGCACATAGTACTACACGCGTGACCATTAATATCTGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAAT-TCCGG
* *
35646084 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATTA-AT-TCCGG
* * * * * * *
35646135 TACGCATAGTAGCCTGCACATAGTACTATACATGCGACCTTTCATTCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATTCCGG
**
35646185 TACACGTAGTAGCCAACACATAGTACTACACACGTGACCAT
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
35646226 CACTTTCACT
Statistics
Matches: 155, Mismatches: 32, Indels: 12
0.78 0.16 0.06
Matches are distributed among these distances:
50 76 0.49
51 77 0.50
52 2 0.01
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATTCCGG
Found at i:35646189 original size:101 final size:100
Alignment explanation
Indices: 35645975--35646221 Score: 298
Period size: 101 Copynumber: 2.5 Consensus size: 100
35645965 TTAACTATTA
* * * * * *
35645975 TCATT-CGATACATGTAGTAGCCTTCACATAGTACTACACACGTGATCAAAATTTTCGGTTCACG
1 TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAAATATCCGGTACACA
* *
35646039 TAGTAGCCTGCACATAGTACTACACGCGTGACCAT
66 TAGTAGCCTGCACATAGTACTACACACGCGACCAT
* * * ** *
35646074 TAATATCTGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTACG
1 TCAT-TCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATC-AAAATATCCGGTACA
* * *
35646139 CATAGTAGCCTGCACATAGTACTATACATGCGACCTT
64 CATAGTAGCCTGCACATAGTACTACACACGCGACCAT
* *
35646176 TCATTCCGGTACACGTAGTAGCCAACACATAGTACTACACACGTGA
1 TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGA
35646222 CCATCACTTT
Statistics
Matches: 124, Mismatches: 21, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
99 3 0.02
100 1 0.01
101 77 0.62
102 43 0.35
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (100 bp):
TCATTCCGATACACGTAGTAGCCTACACATAGTACTACACACGTGATCAAAATATCCGGTACACA
TAGTAGCCTGCACATAGTACTACACACGCGACCAT
Found at i:35650880 original size:11 final size:11
Alignment explanation
Indices: 35650851--35650880 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
35650841 GATGCTCTAG
*
35650851 TAATTAAGTTC
1 TAATTAATTTC
35650862 TAATTAATTTC
1 TAATTAATTTC
35650873 TAATTAAT
1 TAATTAAT
35650881 GATGAGCTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.40, C:0.07, G:0.03, T:0.50
Consensus pattern (11 bp):
TAATTAATTTC
Found at i:35651430 original size:4 final size:4
Alignment explanation
Indices: 35651421--35651445 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
35651411 AAGATGAAGG
35651421 TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA T
35651446 AATCAATTGA
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:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:35652116 original size:52 final size:52
Alignment explanation
Indices: 35652053--35652156 Score: 208
Period size: 52 Copynumber: 2.0 Consensus size: 52
35652043 TTTAGTAATG
35652053 ATGTATATATATGTAATATGCGCATTTTTGTTTAAAAAAATAAAAAGGGAAT
1 ATGTATATATATGTAATATGCGCATTTTTGTTTAAAAAAATAAAAAGGGAAT
35652105 ATGTATATATATGTAATATGCGCATTTTTGTTTAAAAAAATAAAAAGGGAAT
1 ATGTATATATATGTAATATGCGCATTTTTGTTTAAAAAAATAAAAAGGGAAT
35652157 CACATTAGTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 52 1.00
ACGTcount: A:0.44, C:0.04, G:0.15, T:0.37
Consensus pattern (52 bp):
ATGTATATATATGTAATATGCGCATTTTTGTTTAAAAAAATAAAAAGGGAAT
Found at i:35652493 original size:44 final size:44
Alignment explanation
Indices: 35652429--35652569 Score: 185
Period size: 44 Copynumber: 3.2 Consensus size: 44
35652419 ACCATTGAAA
* * * *
35652429 TTCTTACCTAAACAATCAACCAAGACAATTATATTACATGTCCAT
1 TTCTTACCAAAACAATCAACCAA-ACAATTATAATGCATGTTCAT
*
35652474 TTCTTACC-AAACAATCAACCAAACATTTATAATGCATGTTCAT
1 TTCTTACCAAAACAATCAACCAAACAATTATAATGCATGTTCAT
* * * *
35652517 TTATTACCAAAACAATCAATCAAACGATTATAATGCCTGTTCAT
1 TTCTTACCAAAACAATCAACCAAACAATTATAATGCATGTTCAT
35652561 TTCTTACCA
1 TTCTTACCA
35652570 TTTAACAACT
Statistics
Matches: 85, Mismatches: 10, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
43 24 0.28
44 53 0.62
45 8 0.09
ACGTcount: A:0.39, C:0.23, G:0.05, T:0.33
Consensus pattern (44 bp):
TTCTTACCAAAACAATCAACCAAACAATTATAATGCATGTTCAT
Found at i:35653354 original size:42 final size:44
Alignment explanation
Indices: 35653308--35653404 Score: 108
Period size: 44 Copynumber: 2.2 Consensus size: 44
35653298 TCCTAGATAG
* * * *
35653308 GGTCTTACACGT-AATCATATA-CGATGCCAAAGTCCCAGTCTT
1 GGTCTTACACGTAAACCATAAATCGATGCCAAAGTCCCAGACCT
* * * *
35653350 GGTCTTACATGTAAACCTTAAATTGATGCCAACGTCCCAGACCT
1 GGTCTTACACGTAAACCATAAATCGATGCCAAAGTCCCAGACCT
35653394 GGTCTTACACG
1 GGTCTTACACG
35653405 AATTCACATT
Statistics
Matches: 44, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 11 0.25
43 6 0.14
44 27 0.61
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.28
Consensus pattern (44 bp):
GGTCTTACACGTAAACCATAAATCGATGCCAAAGTCCCAGACCT
Found at i:35662260 original size:16 final size:16
Alignment explanation
Indices: 35662239--35662269 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
35662229 GGTGGTGTGA
35662239 GTGTAGGTGTGTGGGT
1 GTGTAGGTGTGTGGGT
35662255 GTGTAGGTGTGTGGG
1 GTGTAGGTGTGTGGG
35662270 CCACACGAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.00, G:0.58, T:0.35
Consensus pattern (16 bp):
GTGTAGGTGTGTGGGT
Found at i:35662788 original size:53 final size:53
Alignment explanation
Indices: 35662719--35662825 Score: 214
Period size: 53 Copynumber: 2.0 Consensus size: 53
35662709 ATATGGTGTG
35662719 TAAGGATGGGTGGGTGTTTTTAAGCCTACATGGTGTGATGAGATGGTCGGAGA
1 TAAGGATGGGTGGGTGTTTTTAAGCCTACATGGTGTGATGAGATGGTCGGAGA
35662772 TAAGGATGGGTGGGTGTTTTTAAGCCTACATGGTGTGATGAGATGGTCGGAGA
1 TAAGGATGGGTGGGTGTTTTTAAGCCTACATGGTGTGATGAGATGGTCGGAGA
35662825 T
1 T
35662826 GGTGCTTAGA
Statistics
Matches: 54, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 54 1.00
ACGTcount: A:0.22, C:0.07, G:0.39, T:0.31
Consensus pattern (53 bp):
TAAGGATGGGTGGGTGTTTTTAAGCCTACATGGTGTGATGAGATGGTCGGAGA
Found at i:35672618 original size:2 final size:2
Alignment explanation
Indices: 35672611--35672640 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
35672601 TTAGTTTTGC
35672611 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
35672641 TTCTTTTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:35683581 original size:24 final size:24
Alignment explanation
Indices: 35683554--35683613 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
35683544 ATATATAACC
35683554 AAATAATATTAAATTA-AAGAATAA
1 AAATAATATTAAATTATAA-AATAA
*
35683578 AAATAATATAAAATTATAAAATAA
1 AAATAATATTAAATTATAAAATAA
35683602 AAA-ATATATTAA
1 AAATA-ATATTAA
35683614 GATATTCAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 1 0.03
24 29 0.91
25 2 0.06
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (24 bp):
AAATAATATTAAATTATAAAATAA
Found at i:35689247 original size:19 final size:19
Alignment explanation
Indices: 35689223--35689270 Score: 87
Period size: 19 Copynumber: 2.5 Consensus size: 19
35689213 AATACGTGTT
35689223 TGAATAGAAATGAACAAAA
1 TGAATAGAAATGAACAAAA
*
35689242 TGAATAGAAATGAACGAAA
1 TGAATAGAAATGAACAAAA
35689261 TGAATAGAAA
1 TGAATAGAAA
35689271 AATATAAATG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.60, C:0.04, G:0.19, T:0.17
Consensus pattern (19 bp):
TGAATAGAAATGAACAAAA
Found at i:35689372 original size:6 final size:6
Alignment explanation
Indices: 35689364--35689429 Score: 87
Period size: 6 Copynumber: 11.0 Consensus size: 6
35689354 CTAAAAATAG
* * * * *
35689364 AAATGG AAATGG AAATGG AAATGA AAATGA AAATGA AAATGG AAACGA
1 AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA AAATGA
35689412 AAATGA AAATGA AAATGA
1 AAATGA AAATGA AAATGA
35689430 TCCATTTGCA
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.61, C:0.02, G:0.23, T:0.15
Consensus pattern (6 bp):
AAATGA
Found at i:35689391 original size:24 final size:24
Alignment explanation
Indices: 35689364--35689428 Score: 103
Period size: 24 Copynumber: 2.7 Consensus size: 24
35689354 CTAAAAATAG
* * *
35689364 AAATGGAAATGGAAATGGAAATGA
1 AAATGAAAATGAAAATGGAAACGA
35689388 AAATGAAAATGAAAATGGAAACGA
1 AAATGAAAATGAAAATGGAAACGA
35689412 AAATGAAAATGAAAATG
1 AAATGAAAATGAAAATG
35689429 ATCCATTTGC
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 38 1.00
ACGTcount: A:0.60, C:0.02, G:0.23, T:0.15
Consensus pattern (24 bp):
AAATGAAAATGAAAATGGAAACGA
Found at i:35689610 original size:26 final size:26
Alignment explanation
Indices: 35689574--35689635 Score: 88
Period size: 26 Copynumber: 2.4 Consensus size: 26
35689564 ACATATTTTC
*
35689574 TTAAAATTTTACCAGGGGCAAAATCG
1 TTAAAATTTTACCAGGAGCAAAATCG
* *
35689600 TTAAAATTTTACCAGGAGTAAAATTG
1 TTAAAATTTTACCAGGAGCAAAATCG
*
35689626 TCAAAATTTT
1 TTAAAATTTT
35689636 CCTAGAGTAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.40, C:0.11, G:0.15, T:0.34
Consensus pattern (26 bp):
TTAAAATTTTACCAGGAGCAAAATCG
Found at i:35702496 original size:15 final size:16
Alignment explanation
Indices: 35702467--35702496 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35702457 CAAACGTGCT
35702467 TTAACACATTATCAAA
1 TTAACACATTATCAAA
35702483 TTAACACA-TATCAA
1 TTAACACATTATCAA
35702497 CAAGATACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:35710584 original size:19 final size:17
Alignment explanation
Indices: 35710542--35710585 Score: 52
Period size: 19 Copynumber: 2.5 Consensus size: 17
35710532 TGAATTCGGT
*
35710542 CGTGTGGGCCACATGGG
1 CGTGTGGGCCACACGGG
*
35710559 TGTGTGGGCTCTACACGGG
1 CGTGTGGGC-C-ACACGGG
35710578 CGTGTGGG
1 CGTGTGGG
35710586 AATATTGAGC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
17 8 0.36
18 1 0.05
19 13 0.59
ACGTcount: A:0.09, C:0.20, G:0.48, T:0.23
Consensus pattern (17 bp):
CGTGTGGGCCACACGGG
Found at i:35718485 original size:17 final size:17
Alignment explanation
Indices: 35718446--35718478 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
35718436 AATTATGTTT
35718446 TGTTTTTAGGACTTTTA
1 TGTTTTTAGGACTTTTA
*
35718463 TGTTTTTATGACTTTT
1 TGTTTTTAGGACTTTT
35718479 TATTTTTCTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.15, C:0.06, G:0.15, T:0.64
Consensus pattern (17 bp):
TGTTTTTAGGACTTTTA
Found at i:35722481 original size:11 final size:11
Alignment explanation
Indices: 35722465--35722491 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
35722455 ATTCCTTCAC
35722465 TTTATGACATT
1 TTTATGACATT
35722476 TTTATGACATT
1 TTTATGACATT
35722487 TTTAT
1 TTTAT
35722492 ATATTAAGTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.26, C:0.07, G:0.07, T:0.59
Consensus pattern (11 bp):
TTTATGACATT
Found at i:35746527 original size:25 final size:25
Alignment explanation
Indices: 35746473--35746527 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
35746463 AATTATTAAA
*
35746473 TTTAATTTAATATTAAGATAATCAC
1 TTTAATTTAATATTAAGAAAATCAC
*
35746498 TTTAATATTAA-ATTAATAAAAT-AC
1 TTTAAT-TTAATATTAAGAAAATCAC
35746522 TATTAA
1 T-TTAA
35746528 GATAAGTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
24 3 0.12
25 19 0.73
26 4 0.15
ACGTcount: A:0.49, C:0.05, G:0.02, T:0.44
Consensus pattern (25 bp):
TTTAATTTAATATTAAGAAAATCAC
Found at i:35751379 original size:14 final size:12
Alignment explanation
Indices: 35751349--35751374 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35751339 ATCATTATTT
35751349 TAACATAAAAAA
1 TAACATAAAAAA
35751361 TAACATAAAAAA
1 TAACATAAAAAA
35751373 TA
1 TA
35751375 TAACAAAATG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.73, C:0.08, G:0.00, T:0.19
Consensus pattern (12 bp):
TAACATAAAAAA
Found at i:35755262 original size:21 final size:24
Alignment explanation
Indices: 35755238--35755295 Score: 61
Period size: 21 Copynumber: 2.6 Consensus size: 24
35755228 GCCCTTTTTC
*
35755238 TTTTTATTATTTTTA-T-TCA-TA
1 TTTTTATTATTATTAGTATCATTA
*
35755259 TTTTTTTTATTATTAGTATCATTA
1 TTTTTATTATTATTAGTATCATTA
*
35755283 TTTTT-TTGTTATT
1 TTTTTATTATTATT
35755296 TTTTATTACT
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
21 13 0.42
22 1 0.03
23 10 0.32
24 7 0.23
ACGTcount: A:0.21, C:0.03, G:0.03, T:0.72
Consensus pattern (24 bp):
TTTTTATTATTATTAGTATCATTA
Found at i:35755270 original size:24 final size:24
Alignment explanation
Indices: 35755238--35755325 Score: 76
Period size: 23 Copynumber: 3.7 Consensus size: 24
35755228 GCCCTTTTTC
35755238 TTTTTATTATTTTTATTCATATTT
1 TTTTTATTATTTTTATTCATATTT
**
35755262 TTTTTATTATTAGTA-TCAT-TATT
1 TTTTTATTATTTTTATTCATAT-TT
*
35755285 TTTTTGTTATTTTTTATT-ACTATTT
1 TTTTTATTA-TTTTTATTCA-TATTT
* *
35755310 ATTTTATT-TTCTTATT
1 TTTTTATTATTTTTATT
35755326 ATTTTTCTTA
Statistics
Matches: 51, Mismatches: 8, Indels: 11
0.73 0.11 0.16
Matches are distributed among these distances:
22 1 0.02
23 21 0.41
24 18 0.35
25 10 0.20
26 1 0.02
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (24 bp):
TTTTTATTATTTTTATTCATATTT
Found at i:35755333 original size:12 final size:12
Alignment explanation
Indices: 35755241--35755350 Score: 68
Period size: 12 Copynumber: 9.2 Consensus size: 12
35755231 CTTTTTCTTT
35755241 TTATTATTTTTA
1 TTATTATTTTTA
*
35755253 TTCA-TATTTTTT
1 TT-ATTATTTTTA
**
35755265 TTATTATTAGTA
1 TTATTATTTTTA
*
35755277 TCATTATTTTT-
1 TTATTATTTTTA
*
35755288 TTGTTATTTTTTA
1 TTATTA-TTTTTA
*
35755301 TTACTATTTATT-
1 TTATTATTT-TTA
*
35755313 TTATT-TTCTTA
1 TTATTATTTTTA
35755324 TTATT-TTTCTTA
1 TTATTATTT-TTA
* *
35755336 GTATTAATTTTA
1 TTATTATTTTTA
35755348 TTA
1 TTA
35755351 AGTTCTTGTT
Statistics
Matches: 73, Mismatches: 17, Indels: 16
0.69 0.16 0.15
Matches are distributed among these distances:
10 2 0.03
11 14 0.19
12 48 0.66
13 9 0.12
ACGTcount: A:0.23, C:0.05, G:0.03, T:0.70
Consensus pattern (12 bp):
TTATTATTTTTA
Found at i:35755346 original size:32 final size:33
Alignment explanation
Indices: 35755280--35755349 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 33
35755270 ATTAGTATCA
* * *
35755280 TTATTTTTTTGTTATTTTTTATTACTATTTATT
1 TTATTTTCTTATTATTTTTTATTACTATTAATT
* *
35755313 TTATTTTCTTATTA-TTTTTCTTAGTATTAATT
1 TTATTTTCTTATTATTTTTTATTACTATTAATT
35755345 TTATT
1 TTATT
35755350 AAGTTCTTGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 20 0.62
33 12 0.38
ACGTcount: A:0.20, C:0.04, G:0.03, T:0.73
Consensus pattern (33 bp):
TTATTTTCTTATTATTTTTTATTACTATTAATT
Found at i:35755376 original size:15 final size:16
Alignment explanation
Indices: 35755349--35755378 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
35755339 TTAATTTTAT
35755349 TAAGTTCTTGTTTTTG
1 TAAGTTCTTGTTTTTG
35755365 TAAGTT-TTGTTTTT
1 TAAGTTCTTGTTTTT
35755379 AGTTTTATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.13, C:0.03, G:0.17, T:0.67
Consensus pattern (16 bp):
TAAGTTCTTGTTTTTG
Found at i:35756871 original size:6 final size:6
Alignment explanation
Indices: 35756856--35756893 Score: 51
Period size: 6 Copynumber: 6.2 Consensus size: 6
35756846 TTATTTCATG
35756856 TTTA-T TTTATT TTTATT TTTATT GCTTTATT TTTATT T
1 TTTATT TTTATT TTTATT TTTATT --TTTATT TTTATT T
35756894 CTTAGACTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.13
6 20 0.67
8 6 0.20
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:35756886 original size:14 final size:12
Alignment explanation
Indices: 35756856--35756893 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 12
35756846 TTATTTCATG
35756856 TTTA-TTTTATT
1 TTTATTTTTATT
35756867 TTTATTTTTATT
1 TTTATTTTTATT
35756879 GCTTTATTTTTATT
1 --TTTATTTTTATT
35756893 T
1 T
35756894 CTTAGACTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
11 4 0.17
12 8 0.33
14 12 0.50
ACGTcount: A:0.16, C:0.03, G:0.03, T:0.79
Consensus pattern (12 bp):
TTTATTTTTATT
Found at i:35758634 original size:19 final size:19
Alignment explanation
Indices: 35758610--35758651 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
35758600 CCCGCTGAAT
35758610 ATTTTTTAATTTTTATTGG
1 ATTTTTTAATTTTTATTGG
35758629 ATTTTTTAATTTTTATTGG
1 ATTTTTTAATTTTTATTGG
35758648 ATTT
1 ATTT
35758652 CGTATTTTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.10, T:0.69
Consensus pattern (19 bp):
ATTTTTTAATTTTTATTGG
Found at i:35758660 original size:19 final size:19
Alignment explanation
Indices: 35758616--35758660 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
35758606 GAATATTTTT
**
35758616 TAATTTTTATTGGATTTTT
1 TAATTTTTATTGGATTTCG
35758635 TAATTTTTATTGGATTTCG
1 TAATTTTTATTGGATTTCG
35758654 T-ATTTTT
1 TAATTTTT
35758661 CAATTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 6 0.25
19 18 0.75
ACGTcount: A:0.20, C:0.02, G:0.11, T:0.67
Consensus pattern (19 bp):
TAATTTTTATTGGATTTCG
Found at i:35761229 original size:47 final size:46
Alignment explanation
Indices: 35761157--35761277 Score: 158
Period size: 47 Copynumber: 2.6 Consensus size: 46
35761147 AAGTGTGGGG
*
35761157 ATATTTGATAAGTGATAAAAGTAACATATTTTAAT-CTCA-T-TCTTA
1 ATATTTGATAAGTGATAAAAGTAACATATTTT-ATGCTAAGTAT-TTA
*
35761202 ATGAGTTTGATAAGTGATAAAAGTAACATATTTTATGCTAAGGTATTTG
1 AT-A-TTTGATAAGTGATAAAAGTAACATATTTTATGCTAA-GTATTTA
35761251 ATATTTGATAAGTGATAAAAGTAACAT
1 ATATTTGATAAGTGATAAAAGTAACAT
35761278 GAATCCTAGG
Statistics
Matches: 68, Mismatches: 2, Indels: 10
0.85 0.03 0.12
Matches are distributed among these distances:
45 2 0.03
46 3 0.04
47 56 0.82
48 1 0.01
49 5 0.07
50 1 0.01
ACGTcount: A:0.40, C:0.06, G:0.15, T:0.39
Consensus pattern (46 bp):
ATATTTGATAAGTGATAAAAGTAACATATTTTATGCTAAGTATTTA
Found at i:35767702 original size:30 final size:31
Alignment explanation
Indices: 35767661--35767722 Score: 99
Period size: 30 Copynumber: 2.0 Consensus size: 31
35767651 AAACCTTTTT
*
35767661 ACTTTCCCCCCAAAACTTTTAC-TCCCTCCC
1 ACTTTCCCCCCAAAACTTTTACACCCCTCCC
*
35767691 ACTTTCTCCCCAAAACTTTTACACCCCTCCC
1 ACTTTCCCCCCAAAACTTTTACACCCCTCCC
35767722 A
1 A
35767723 TCTCACCTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 21 0.72
31 8 0.28
ACGTcount: A:0.23, C:0.48, G:0.00, T:0.29
Consensus pattern (31 bp):
ACTTTCCCCCCAAAACTTTTACACCCCTCCC
Found at i:35773560 original size:29 final size:31
Alignment explanation
Indices: 35773500--35773559 Score: 86
Period size: 31 Copynumber: 2.0 Consensus size: 31
35773490 CCCTAGTTTC
* *
35773500 ACATATATATTTGTATCATAATAAAAATTTT
1 ACATATATAATTGTACCATAATAAAAATTTT
*
35773531 ACATATATAATTGTACCA-AATCAAAATTT
1 ACATATATAATTGTACCATAATAAAAATTT
35773560 ATGTATTAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 10 0.38
31 16 0.62
ACGTcount: A:0.47, C:0.10, G:0.03, T:0.40
Consensus pattern (31 bp):
ACATATATAATTGTACCATAATAAAAATTTT
Found at i:35784649 original size:12 final size:12
Alignment explanation
Indices: 35784634--35784659 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
35784624 TGGAGGAACA
35784634 GATGGAAATGAT
1 GATGGAAATGAT
35784646 GATGGAAATGAT
1 GATGGAAATGAT
35784658 GA
1 GA
35784660 CTACAATGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.35, T:0.23
Consensus pattern (12 bp):
GATGGAAATGAT
Found at i:35793147 original size:42 final size:42
Alignment explanation
Indices: 35793100--35793266 Score: 196
Period size: 42 Copynumber: 4.0 Consensus size: 42
35793090 AAGGAAAAAA
*
35793100 TTCATTACATTTAGAGGCCCAGGTGTGGAGGTCCATTTACTT
1 TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * *
35793142 TTCATTGCATTTAGAGACCTAGGTGTGGAGGTCCATTCACTT
1 TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * **
35793184 TTCATTGCATCTAGAGACCTAGGTGTGGAGGTCTGTTTACTT
1 TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
* * * *
35793226 TTC--TA-GTTTAGAGGCTCAGGTGTGGAGGTCCGTTTACTT
1 TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
35793265 TT
1 TT
35793267 TTTAGTTTAC
Statistics
Matches: 110, Mismatches: 15, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
39 30 0.27
40 1 0.01
42 79 0.72
ACGTcount: A:0.19, C:0.17, G:0.26, T:0.38
Consensus pattern (42 bp):
TTCATTACATTTAGAGACCCAGGTGTGGAGGTCCATTTACTT
Found at i:35793853 original size:20 final size:20
Alignment explanation
Indices: 35793821--35793859 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35793811 ACTACATGCA
35793821 TTCTATTTCTTTTTTTTTTC
1 TTCTATTTCTTTTTTTTTTC
35793841 TTCTACTTT-TTTTTTTTTT
1 TTCTA-TTTCTTTTTTTTTT
35793860 GCCATAAGCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 15 0.83
21 3 0.17
ACGTcount: A:0.05, C:0.13, G:0.00, T:0.82
Consensus pattern (20 bp):
TTCTATTTCTTTTTTTTTTC
Found at i:35794331 original size:23 final size:21
Alignment explanation
Indices: 35794291--35794354 Score: 56
Period size: 23 Copynumber: 2.9 Consensus size: 21
35794281 TTTAATCTTT
*
35794291 AAGAAAATAGTTTTTTTTTTAAA
1 AAGAAAA-A-TTTGTTTTTTAAA
* *
35794314 AAGAGAAATTTTAGTTTTTGAAA
1 AAGA-AAAATTT-GTTTTTTAAA
*
35794337 AATAAAAATTTGTTTTTT
1 AAGAAAAATTTGTTTTTT
35794355 TAAGTTGAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
21 6 0.18
22 9 0.27
23 15 0.45
24 3 0.09
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (21 bp):
AAGAAAAATTTGTTTTTTAAA
Found at i:35794335 original size:145 final size:150
Alignment explanation
Indices: 35794024--35794355 Score: 435
Period size: 145 Copynumber: 2.2 Consensus size: 150
35794014 TTGGGAAAAG
* * * *
35794024 TTTAGATTTT-AACAAATAAAAATTTG-TTTTTTTAGTTATTTTTAAGGAAAGTTTAAATTTTTA
1 TTTAGTTTTTGAA-AAATAAAAATTTGTTTTTTTTAGTCATTTCT-----AAGTTTAAAATTTTA
* * * *
35794087 AAACAAAGTTTTGATTTTTTTTTTCAACTATTTCAAAGTAAAAGCTTTAATATTTTAAAAAAAAT
60 AAACAAAGTTTTGATTTTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATACTTTAAAAAAAAT
35794152 AGTGTTTTTCTTTAAAAAAAAGAAAT
125 AGTGTTTTTCTTTAAAAAAAAGAAAT
* *
35794178 TTTAGTTTTTGAAAATTAAAAATTTGTTTTTTTTAGTCATTTCTAAGTTTAAAATTTTAAAACAG
1 TTTAGTTTTTGAAAAATAAAAATTTGTTTTTTTTAGTCATTTCTAAGTTTAAAATTTTAAAACAA
* *
35794243 AGTTTTGA-TTTTTTTTTCAACTACTCCAAAATAACAGCTTTAAT-CTTT-AAGAAAATAGT-TT
66 AGTTTTGATTTTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATACTTTAAAAAAAATAGTGTT
* *
35794304 TTT-TTTTAAAAAGAGAAAT
131 TTTCTTTAAAAAAAAGAAAT
35794323 TTTAGTTTTTGAAAAATAAAAATTTGTTTTTTT
1 TTTAGTTTTTGAAAAATAAAAATTTGTTTTTTT
35794356 AAGTTGAAAA
Statistics
Matches: 161, Mismatches: 15, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
145 46 0.29
146 5 0.03
147 10 0.06
148 3 0.02
149 32 0.20
150 27 0.17
154 21 0.13
155 17 0.11
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (150 bp):
TTTAGTTTTTGAAAAATAAAAATTTGTTTTTTTTAGTCATTTCTAAGTTTAAAATTTTAAAACAA
AGTTTTGATTTTTTTTTTCAACTACTCCAAAATAAAAGCTTTAATACTTTAAAAAAAATAGTGTT
TTTCTTTAAAAAAAAGAAAT
Found at i:35794365 original size:27 final size:27
Alignment explanation
Indices: 35794331--35794386 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
35794321 ATTTTAGTTT
* *
35794331 TTGAAAAATAAAAATTTGTTTTTTTAAG
1 TTGAAAAACAAAAA-TTGATTTTTTAAG
35794359 TTGAAAAACAAAAATTGATTTTTTAAG
1 TTGAAAAACAAAAATTGATTTTTTAAG
35794386 T
1 T
35794387 CATTTTAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.45, C:0.02, G:0.11, T:0.43
Consensus pattern (27 bp):
TTGAAAAACAAAAATTGATTTTTTAAG
Found at i:35795049 original size:10 final size:9
Alignment explanation
Indices: 35795031--35795099 Score: 61
Period size: 10 Copynumber: 7.1 Consensus size: 9
35795021 CACTTGTATA
35795031 ATTTTATTT
1 ATTTTATTT
35795040 ATTCTTATTT
1 ATT-TTATTT
35795050 CATTTTATTT
1 -ATTTTATTT
35795060 ATTTTCATGTTT
1 ATTTT-A--TTT
35795072 ATTTATATTT
1 ATTT-TATTT
35795082 ATATTT-TTT
1 AT-TTTATTT
35795091 ATTTT-TTT
1 ATTTTATTT
35795099 A
1 A
35795100 AACATTCCCC
Statistics
Matches: 53, Mismatches: 0, Indels: 15
0.78 0.00 0.22
Matches are distributed among these distances:
8 7 0.13
9 13 0.25
10 19 0.36
11 5 0.09
12 8 0.15
13 1 0.02
ACGTcount: A:0.22, C:0.04, G:0.01, T:0.72
Consensus pattern (9 bp):
ATTTTATTT
Found at i:35795072 original size:16 final size:15
Alignment explanation
Indices: 35795047--35795095 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
35795037 TTTATTCTTA
35795047 TTTCATTTTATTTAT
1 TTTCATTTTATTTAT
35795062 TTTCATGTTTATTTAT
1 TTTCAT-TTTATTTAT
35795078 ATTT-ATATTT-TTTAT
1 -TTTCAT-TTTATTTAT
35795093 TTT
1 TTT
35795096 TTTAAACATT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 3 0.10
15 11 0.35
16 14 0.45
17 3 0.10
ACGTcount: A:0.20, C:0.04, G:0.02, T:0.73
Consensus pattern (15 bp):
TTTCATTTTATTTAT
Found at i:35799683 original size:22 final size:22
Alignment explanation
Indices: 35799655--35799795 Score: 201
Period size: 22 Copynumber: 6.4 Consensus size: 22
35799645 TCCTGTAAAA
*
35799655 CTCATGTTTCACGTACTAAGCT
1 CTCATGTTTAACGTACTAAGCT
35799677 CTCATGTTTAACGTACTAAGCT
1 CTCATGTTTAACGTACTAAGCT
* * *
35799699 CTCATGTTTAACGAACTAAACC
1 CTCATGTTTAACGTACTAAGCT
**
35799721 CTCATGGCTAACGTACTAAGCT
1 CTCATGTTTAACGTACTAAGCT
**
35799743 CTCATGGCTAACGTACTAAGCT
1 CTCATGTTTAACGTACTAAGCT
*
35799765 CTCATGTTTCACGTACTAAGCT
1 CTCATGTTTAACGTACTAAGCT
35799787 CTCATGTTT
1 CTCATGTTT
35799796 GAACAATAAA
Statistics
Matches: 107, Mismatches: 12, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 107 1.00
ACGTcount: A:0.26, C:0.26, G:0.14, T:0.33
Consensus pattern (22 bp):
CTCATGTTTAACGTACTAAGCT
Found at i:35810165 original size:6 final size:6
Alignment explanation
Indices: 35810156--35810186 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
35810146 AAAATTTAAA
35810156 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
1 ATTTTT ATTTTT ATTTTT ATTTTT ATTTTT A
35810187 GTACTTTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (6 bp):
ATTTTT
Found at i:35810480 original size:5 final size:5
Alignment explanation
Indices: 35810470--35810494 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
35810460 ACTATTTATA
35810470 TAAAT TAAAT TAAAT TAAAT TAAAT
1 TAAAT TAAAT TAAAT TAAAT TAAAT
35810495 AATTTGTATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAAAT
Found at i:35815376 original size:86 final size:86
Alignment explanation
Indices: 35815091--35815500 Score: 435
Period size: 86 Copynumber: 4.8 Consensus size: 86
35815081 TTAAGTCTTT
* ** * * ** * *
35815091 GTTTGGAAACAAAATC-AAGATCAAATAAAATCAGTTAAACATCGGGAATAAATCCTGAAACAGA
1 GTTTGGAAACAAAATCAAAAATGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAAA
* *
35815155 --TTATTCAA--TT--TTCTA
66 TTTTATTTAACTTTAATTCTC
* * * * ** * * *
35815170 ATTTGGAAACAAAATC-AAAATCGAATAAAATTTGTTAAACGATGGGAATAAATCCAGAAATAGA
1 GTTTGGAAACAAAATCAAAAATGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAAA
*
35815234 TTTTATTTAATTTTAATTTCTC
66 TTTTATTTAACTTTAA-TTCTC
*
35815256 GTTTTGGAAACAAAATCAAAATTGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAA
1 G-TTTGGAAACAAAATCAAAAATGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAA
*
35815321 ATTTTATTTAACTTTAATTCTT
65 ATTTTATTTAACTTTAATTCTC
* * *
35815343 GTTTGG-AACTAAAATCAAAAATGGAATAAAATCTGTTGAACGGCGAGAATAAATCTCGAAACAG
1 GTTTGGAAAC-AAAATCAAAAATGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAA
35815407 ATTTTATTTAACTTTAATTCTC
65 ATTTTATTTAACTTTAATTCTC
* * * *
35815429 ATTTGGAAATAAAATCAAAAAAT-GAATAAAATCCGTTGAACGGCGGGAATAAATCCCAAAACAA
1 GTTTGGAAACAAAATC-AAAAATGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAA
*
35815493 ATCTTATT
65 ATTTTATT
35815501 CAATTTTTAT
Statistics
Matches: 282, Mismatches: 37, Indels: 17
0.84 0.11 0.05
Matches are distributed among these distances:
79 54 0.19
81 7 0.02
83 2 0.01
85 3 0.01
86 134 0.48
87 28 0.10
88 54 0.19
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (86 bp):
GTTTGGAAACAAAATCAAAAATGGAATAAAATCTGTTGAACGGCGGGAATAAATCCCGAAACAAA
TTTTATTTAACTTTAATTCTC
Found at i:35816000 original size:20 final size:20
Alignment explanation
Indices: 35815962--35816014 Score: 54
Period size: 20 Copynumber: 2.7 Consensus size: 20
35815952 ATTAAAGGAG
* * *
35815962 AAATTAAATCAATTTGATTA
1 AAATCAAATCAAATAGATTA
*
35815982 AAATCAAATCAAATAGATTG
1 AAATCAAATCAAATAGATTA
*
35816002 GAATCAAAT-AAAT
1 AAATCAAATCAAAT
35816015 CAGGATATAT
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.55, C:0.08, G:0.08, T:0.30
Consensus pattern (20 bp):
AAATCAAATCAAATAGATTA
Found at i:35816748 original size:22 final size:20
Alignment explanation
Indices: 35816720--35816760 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
35816710 TCCCTGCATA
*
35816720 AAAGTTTCATTTGTTTAATTTC
1 AAAGTTT-ATTT-TATAATTTC
35816742 AAAGTTTATTTTATAATTT
1 AAAGTTTATTTTATAATTT
35816761 AAGATAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 7 0.39
21 4 0.22
22 7 0.39
ACGTcount: A:0.32, C:0.05, G:0.07, T:0.56
Consensus pattern (20 bp):
AAAGTTTATTTTATAATTTC
Found at i:35822162 original size:26 final size:27
Alignment explanation
Indices: 35822133--35822184 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
35822123 GGTCCTTATG
35822133 AACTTTCC-ATTAACATATTCATGGAA
1 AACTTTCCAATTAACATATTCATGGAA
*
35822159 AACTTTCCATATTAAGATATTCATGG
1 AACTTTCCA-ATTAACATATTCATGG
35822185 CGGAGTTTCC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 8 0.35
28 15 0.65
ACGTcount: A:0.37, C:0.17, G:0.10, T:0.37
Consensus pattern (27 bp):
AACTTTCCAATTAACATATTCATGGAA
Done.