Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167838.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_11, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 23775123
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 69000 characters in sequence are not A, C, G, or T
File 115 of 129
Found at i:20657376 original size:38 final size:38
Alignment explanation
Indices: 20657289--20657376 Score: 108
Period size: 38 Copynumber: 2.3 Consensus size: 38
20657279 CCTAAACTTT
* *
20657289 AAACCCTAAACCAAACTCTAAACCATAAACTTTGAACC
1 AAACCCAAAACCAAACTCTAAACCATAAACTTTAAACC
* *
20657327 AAACCCTAAACCAAACTCTAAACCCTAAAC-TTAAACCCC
1 AAACCCAAAACCAAACTCTAAACCATAAACTTTAAA--CC
20657366 AAA-CCAAAACC
1 AAACCCAAAACC
20657377 TTACACCTAA
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
37 4 0.09
38 36 0.80
39 5 0.11
ACGTcount: A:0.49, C:0.35, G:0.01, T:0.15
Consensus pattern (38 bp):
AAACCCAAAACCAAACTCTAAACCATAAACTTTAAACC
Found at i:20658230 original size:19 final size:20
Alignment explanation
Indices: 20658190--20658235 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
20658180 GTTATATTAT
20658190 TTTTAATAAATTTTTACTTA
1 TTTTAATAAATTTTTACTTA
*
20658210 TTTTAATATATTTTTAC-TA
1 TTTTAATAAATTTTTACTTA
20658229 TTTTAAT
1 TTTTAAT
20658236 TTTATGTTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 9 0.36
20 16 0.64
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (20 bp):
TTTTAATAAATTTTTACTTA
Found at i:20658398 original size:13 final size:13
Alignment explanation
Indices: 20658366--20658421 Score: 51
Period size: 14 Copynumber: 4.0 Consensus size: 13
20658356 ATTAAAATAG
20658366 TATTAACTTTGAAA-
1 TATTAA-TTT-AAAT
20658380 TATTAATTTAAAT
1 TATTAATTTAAAT
20658393 TATTAATATTATAAT
1 TATTAAT-TTA-AAT
*
20658408 TGATTAATATAAAT
1 T-ATTAATTTAAAT
20658422 GATAACAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
12 3 0.08
13 10 0.27
14 12 0.32
15 6 0.16
16 6 0.16
ACGTcount: A:0.46, C:0.02, G:0.04, T:0.48
Consensus pattern (13 bp):
TATTAATTTAAAT
Found at i:20658415 original size:16 final size:14
Alignment explanation
Indices: 20658380--20658466 Score: 65
Period size: 14 Copynumber: 6.2 Consensus size: 14
20658370 AACTTTGAAA
20658380 TATTAAT-TTAAAT
1 TATTAATATTAAAT
20658393 TATTAATATTATAAT
1 TATTAATATTA-AAT
20658408 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
* * *
20658422 GA-TAACAATAATAT
1 TATTAATATTAA-AT
* *
20658436 TATTAATATGATAT
1 TATTAATATTAAAT
20658450 TATTAATAATT-AAT
1 TATTAAT-ATTAAAT
20658464 TAT
1 TAT
20658467 ATATAATAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.07
13 11 0.19
14 23 0.40
15 13 0.22
16 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:20658465 original size:14 final size:14
Alignment explanation
Indices: 20658388--20658476 Score: 60
Period size: 14 Copynumber: 6.3 Consensus size: 14
20658378 AATATTAATT
*
20658388 TAAATTATTAATAT
1 TAAATTATTAATAA
20658402 TATAATTGATTAAT-A
1 TA-AATT-ATTAATAA
* *
20658417 TAAATGA-TAACAA
1 TAAATTATTAATAA
20658430 TAATATTATTAAT-A
1 TAA-ATTATTAATAA
*
20658444 TGATATTATTAATAA
1 T-AAATTATTAATAA
*
20658459 TTAATTA-TATATAA
1 TAAATTATTA-ATAA
20658473 TAAA
1 TAAA
20658477 AACAAACATA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 30 0.52
15 12 0.21
16 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (14 bp):
TAAATTATTAATAA
Found at i:20661066 original size:34 final size:33
Alignment explanation
Indices: 20661017--20661087 Score: 115
Period size: 34 Copynumber: 2.1 Consensus size: 33
20661007 AACAGATGAG
20661017 TAAATGATAAATTTGCTTAGTCATGTGAAAGAC
1 TAAATGATAAATTTGCTTAGTCATGTGAAAGAC
* *
20661050 TAAAGTGATAAGTTTGCTTAGTTATGTGAAAGAC
1 TAAA-TGATAAATTTGCTTAGTCATGTGAAAGAC
20661084 TAAA
1 TAAA
20661088 AAATTAAATT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
33 4 0.11
34 31 0.89
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (33 bp):
TAAATGATAAATTTGCTTAGTCATGTGAAAGAC
Found at i:20663379 original size:23 final size:23
Alignment explanation
Indices: 20663353--20663396 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
20663343 AACTTCAACC
20663353 AAATTAAGCCCAAACAGAGTAAA
1 AAATTAAGCCCAAACAGAGTAAA
*
20663376 AAATTAAGCCCAAATAGAGTA
1 AAATTAAGCCCAAACAGAGTA
20663397 TCATAAAGCC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.55, C:0.16, G:0.14, T:0.16
Consensus pattern (23 bp):
AAATTAAGCCCAAACAGAGTAAA
Found at i:20667249 original size:20 final size:20
Alignment explanation
Indices: 20667224--20667263 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
20667214 AAAACTAAGT
20667224 GGTGGAATCGAATGGAGGTA
1 GGTGGAATCGAATGGAGGTA
20667244 GGTGGAATCGAATGGAGGTA
1 GGTGGAATCGAATGGAGGTA
20667264 TGTAGAATCT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.30, C:0.05, G:0.45, T:0.20
Consensus pattern (20 bp):
GGTGGAATCGAATGGAGGTA
Found at i:20667271 original size:20 final size:20
Alignment explanation
Indices: 20667228--20667272 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
20667218 CTAAGTGGTG
*
20667228 GAATCGAATGGAGGTAGGTG
1 GAATCGAATGGAGGTAGGTA
*
20667248 GAATCGAATGGAGGTATGTA
1 GAATCGAATGGAGGTAGGTA
20667268 GAATC
1 GAATC
20667273 TCACACACTT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.33, C:0.07, G:0.38, T:0.22
Consensus pattern (20 bp):
GAATCGAATGGAGGTAGGTA
Found at i:20669653 original size:28 final size:28
Alignment explanation
Indices: 20669613--20669693 Score: 92
Period size: 27 Copynumber: 2.9 Consensus size: 28
20669603 TTTGGTTAAG
*
20669613 AATGATTATTTGAAATCTTACAAGTGCA
1 AATGATTGTTTGAAATCTTACAAGTGCA
* * *
20669641 AATGATTGTTTG-AATTTTACAAGGGTA
1 AATGATTGTTTGAAATCTTACAAGTGCA
* * *
20669668 AAAGATTGGTTGAAATCTTATAAGTG
1 AATGATTGTTTGAAATCTTACAAGTG
20669694 ATGATTTTGT
Statistics
Matches: 43, Mismatches: 9, Indels: 2
0.80 0.17 0.04
Matches are distributed among these distances:
27 22 0.51
28 21 0.49
ACGTcount: A:0.37, C:0.06, G:0.20, T:0.37
Consensus pattern (28 bp):
AATGATTGTTTGAAATCTTACAAGTGCA
Found at i:20675137 original size:60 final size:60
Alignment explanation
Indices: 20675067--20675184 Score: 202
Period size: 60 Copynumber: 2.0 Consensus size: 60
20675057 TTTGAATAAC
20675067 TGATCGAAAAAAGCAAGTTTTGAGGCATAGAACTATTC-CCTTTGTAAAAGTTTAATGGAG
1 TGATCGAAAAAAGCAAGTTTTGAGGCATAGAACTA-TCACCTTTGTAAAAGTTTAATGGAG
* *
20675127 TGATCGAAAAAAGTAAGTTTTGAGGCATAGAACTATCATCTTTGTAAAAGTTTAATGG
1 TGATCGAAAAAAGCAAGTTTTGAGGCATAGAACTATCACCTTTGTAAAAGTTTAATGG
20675185 GGCAATCTTA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
59 2 0.04
60 53 0.96
ACGTcount: A:0.37, C:0.10, G:0.21, T:0.31
Consensus pattern (60 bp):
TGATCGAAAAAAGCAAGTTTTGAGGCATAGAACTATCACCTTTGTAAAAGTTTAATGGAG
Found at i:20683722 original size:26 final size:26
Alignment explanation
Indices: 20683691--20683744 Score: 99
Period size: 26 Copynumber: 2.1 Consensus size: 26
20683681 GCAAATTTTT
*
20683691 TTTAGTATTGTTTGCTGCAGAAAATC
1 TTTAGTATTGTTTGCTACAGAAAATC
20683717 TTTAGTATTGTTTGCTACAGAAAATC
1 TTTAGTATTGTTTGCTACAGAAAATC
20683743 TT
1 TT
20683745 GTTAAAGATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.17, T:0.44
Consensus pattern (26 bp):
TTTAGTATTGTTTGCTACAGAAAATC
Found at i:20687519 original size:31 final size:31
Alignment explanation
Indices: 20687484--20687564 Score: 135
Period size: 31 Copynumber: 2.6 Consensus size: 31
20687474 TTATACTCAT
* *
20687484 ATAAAATTTGAAATTTAGTCTCTATATTTAC
1 ATAAAATTTGAAATTTAATCTCAATATTTAC
20687515 ATAAAATTTGAAATTTAATCTCAATATTTAC
1 ATAAAATTTGAAATTTAATCTCAATATTTAC
*
20687546 ATGAAATTTGAAATTTAAT
1 ATAAAATTTGAAATTTAAT
20687565 TCCTTTAATA
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.43, C:0.07, G:0.06, T:0.43
Consensus pattern (31 bp):
ATAAAATTTGAAATTTAATCTCAATATTTAC
Found at i:20688264 original size:13 final size:13
Alignment explanation
Indices: 20688245--20688375 Score: 74
Period size: 12 Copynumber: 9.7 Consensus size: 13
20688235 AAAACTCCAG
20688245 CTCTAAACCTAAA
1 CTCTAAACCTAAA
*
20688258 CTTTAAACCTAAA
1 CTCTAAACCTAAA
*
20688271 ATCTAAACGCTAAACCAA
1 CTCTAAAC-CT--A--AA
* *
20688289 CCCTTAAACCCTAAG
1 CTC-TAAA-CCTAAA
20688304 C-CTAAACCTTAAA
1 CTCTAAACC-TAAA
*
20688317 CCCTAAA-CTAAA
1 CTCTAAACCTAAA
20688329 CTCTAAACCATAAA
1 CTCTAAACC-TAAA
*
20688343 C-CTTGAACC-AAA
1 CTC-TAAACCTAAA
*
20688355 CCCTAAACC-AAA
1 CTCTAAACCTAAA
20688367 CTCTAAACC
1 CTCTAAACC
20688376 CCAAACTTAA
Statistics
Matches: 94, Mismatches: 11, Indels: 27
0.71 0.08 0.20
Matches are distributed among these distances:
12 32 0.34
13 30 0.32
14 18 0.19
15 2 0.02
16 1 0.01
17 1 0.01
18 3 0.03
19 6 0.06
20 1 0.01
ACGTcount: A:0.45, C:0.33, G:0.02, T:0.20
Consensus pattern (13 bp):
CTCTAAACCTAAA
Found at i:20688283 original size:7 final size:6
Alignment explanation
Indices: 20688247--20688375 Score: 77
Period size: 7 Copynumber: 20.2 Consensus size: 6
20688237 AACTCCAGCT
* * *
20688247 CTAAAC CTAAAC TTTAAAC CTAAAAT CTAAAC GCTAAAC C-AACC CTTAAACC
1 CTAAAC CTAAAC -CTAAAC CT-AAAC CTAAAC -CTAAAC CTAAAC C-TAAA-C
* *
20688299 CTAAGC CTAAAC CTTAAACC CTAAA- CTAAAC TCTAAAC CATAAAC CTTGAAC
1 CTAAAC CTAAAC C-TAAA-C CTAAAC CTAAAC -CTAAAC C-TAAAC C-TAAAC
20688351 C-AAACC CTAAAC C-AAAC TCTAAAC C
1 CTAAA-C CTAAAC CTAAAC -CTAAAC C
20688376 CCAAACTTAA
Statistics
Matches: 97, Mismatches: 11, Indels: 30
0.70 0.08 0.22
Matches are distributed among these distances:
5 15 0.15
6 25 0.26
7 53 0.55
8 4 0.04
ACGTcount: A:0.46, C:0.33, G:0.02, T:0.19
Consensus pattern (6 bp):
CTAAAC
Found at i:20688364 original size:26 final size:26
Alignment explanation
Indices: 20688304--20688364 Score: 77
Period size: 26 Copynumber: 2.3 Consensus size: 26
20688294 AAACCCTAAG
* *
20688304 CCTAAACCTTAAACCCTAAACTAAAC
1 CCTAAACCATAAACCCTAAACCAAAC
* * *
20688330 TCTAAACCATAAACCTTGAACCAAAC
1 CCTAAACCATAAACCCTAAACCAAAC
20688356 CCTAAACCA
1 CCTAAACCA
20688365 AACTCTAAAC
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.46, C:0.34, G:0.02, T:0.18
Consensus pattern (26 bp):
CCTAAACCATAAACCCTAAACCAAAC
Found at i:20688374 original size:19 final size:20
Alignment explanation
Indices: 20688247--20688386 Score: 107
Period size: 19 Copynumber: 7.2 Consensus size: 20
20688237 AACTCCAGCT
**
20688247 CTAAAC-CTAAACTTTAAAC
1 CTAAACTCTAAACCCTAAAC
* *
20688266 CTAAAATCTAAACGCTAAAC
1 CTAAACTCTAAACCCTAAAC
* *
20688286 C--AACCCTTAAACCCTAAGC
1 CTAAACTC-TAAACCCTAAAC
20688305 CTAAAC-CTTAAACCCTAAA-
1 CTAAACTC-TAAACCCTAAAC
*
20688324 CTAAACTCTAAACCATAAAC
1 CTAAACTCTAAACCCTAAAC
*
20688344 CTTGAAC-C-AAACCCTAAAC
1 C-TAAACTCTAAACCCTAAAC
*
20688363 C-AAACTCTAAACCCCAAAC
1 CTAAACTCTAAACCCTAAAC
*
20688382 TTAAA
1 CTAAA
20688387 GCCCAAACCA
Statistics
Matches: 97, Mismatches: 14, Indels: 19
0.75 0.11 0.15
Matches are distributed among these distances:
17 3 0.03
18 4 0.04
19 53 0.55
20 30 0.31
21 7 0.07
ACGTcount: A:0.46, C:0.32, G:0.02, T:0.19
Consensus pattern (20 bp):
CTAAACTCTAAACCCTAAAC
Found at i:20688391 original size:13 final size:14
Alignment explanation
Indices: 20688350--20688394 Score: 51
Period size: 12 Copynumber: 3.4 Consensus size: 14
20688340 AAACCTTGAA
*
20688350 CCAAACCCTAAA--
1 CCAAACTCTAAACC
20688362 CCAAACTCTAAACC
1 CCAAACTCTAAACC
*
20688376 CCAAACT-TAAAGC
1 CCAAACTCTAAACC
20688389 CCAAAC
1 CCAAAC
20688395 CAAAACCTTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 11 0.38
14 7 0.24
ACGTcount: A:0.47, C:0.40, G:0.02, T:0.11
Consensus pattern (14 bp):
CCAAACTCTAAACC
Found at i:20688662 original size:3 final size:3
Alignment explanation
Indices: 20688654--20688704 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
20688644 CATGCCTTCA
20688654 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
20688702 TAT
1 TAT
20688705 GTCATGCATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:20689290 original size:19 final size:20
Alignment explanation
Indices: 20689250--20689295 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
20689240 GTTATATTAT
*
20689250 TTTTAATAAATTTTTACTTA
1 TTTTAATAAATTTTTACGTA
*
20689270 TTTTAATATATTTTTA-GTA
1 TTTTAATAAATTTTTACGTA
20689289 TTTTAAT
1 TTTTAAT
20689296 TTTATGTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
19 9 0.38
20 15 0.62
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (20 bp):
TTTTAATAAATTTTTACGTA
Found at i:20689472 original size:16 final size:14
Alignment explanation
Indices: 20689437--20689523 Score: 65
Period size: 14 Copynumber: 6.2 Consensus size: 14
20689427 AACTTTGATA
20689437 TATTAAT-TTAAAT
1 TATTAATATTAAAT
20689450 TATTAATATTATAAT
1 TATTAATATTA-AAT
20689465 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
* * *
20689479 GA-CAATAATAATAT
1 TATTAATATTAA-AT
* *
20689493 TATTAATATGATAT
1 TATTAATATTAAAT
20689507 TATTAATAATT-AAT
1 TATTAAT-ATTAAAT
20689521 TAT
1 TAT
20689524 ATATAATAAA
Statistics
Matches: 58, Mismatches: 9, Indels: 13
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.07
13 11 0.19
14 23 0.40
15 13 0.22
16 7 0.12
ACGTcount: A:0.48, C:0.01, G:0.03, T:0.47
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:20689522 original size:14 final size:14
Alignment explanation
Indices: 20689445--20689533 Score: 60
Period size: 14 Copynumber: 6.3 Consensus size: 14
20689435 TATATTAATT
*
20689445 TAAATTATTAATAT
1 TAAATTATTAATAA
20689459 TATAATTGATTAAT-A
1 TA-AATT-ATTAATAA
* *
20689474 TAAATGA-CAATAA
1 TAAATTATTAATAA
20689487 TAATATTATTAAT-A
1 TAA-ATTATTAATAA
*
20689501 TGATATTATTAATAA
1 T-AAATTATTAATAA
*
20689516 TTAATTA-TATATAA
1 TAAATTATTA-ATAA
20689530 TAAA
1 TAAA
20689534 AACAAATATA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
12 3 0.05
13 7 0.12
14 30 0.52
15 12 0.21
16 6 0.10
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (14 bp):
TAAATTATTAATAA
Found at i:20689658 original size:31 final size:33
Alignment explanation
Indices: 20689620--20689690 Score: 101
Period size: 31 Copynumber: 2.2 Consensus size: 33
20689610 TATATTAGAG
* *
20689620 GGATTAAATTTTAAATTTCGTGC-AAT-TATAA
1 GGATTAAATTTCAAATTTCATGCAAATATATAA
20689651 GGATTAAATTTCAAATTTCATGCAAATAGTATAA
1 GGATTAAATTTCAAATTTCATGCAAATA-TATAA
20689685 GGATTA
1 GGATTA
20689691 TTTGTATAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
31 21 0.60
32 3 0.09
34 11 0.31
ACGTcount: A:0.41, C:0.07, G:0.14, T:0.38
Consensus pattern (33 bp):
GGATTAAATTTCAAATTTCATGCAAATATATAA
Found at i:20689776 original size:21 final size:21
Alignment explanation
Indices: 20689750--20689809 Score: 75
Period size: 21 Copynumber: 2.9 Consensus size: 21
20689740 AAGTCAATGT
*
20689750 CATGTCAACATGATCAACGAC
1 CATGTCAACATGATCAACAAC
*
20689771 CATGTCAACATAATCAACAAC
1 CATGTCAACATGATCAACAAC
* * *
20689792 CATGCCAGCATGGTCAAC
1 CATGTCAACATGATCAAC
20689810 TATCATATAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.38, C:0.30, G:0.13, T:0.18
Consensus pattern (21 bp):
CATGTCAACATGATCAACAAC
Found at i:20692116 original size:34 final size:34
Alignment explanation
Indices: 20692064--20692133 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
20692054 ATATATGAGT
*
20692064 AAGTGATAAATTTACTTAGTCATGTGAAAGACTA
1 AAGTAATAAATTTACTTAGTCATGTGAAAGACTA
* *
20692098 AAGTAATAAGTTTGCTTAGTCATGTGAAAGACTA
1 AAGTAATAAATTTACTTAGTCATGTGAAAGACTA
20692132 AA
1 AA
20692134 AAATTAAATT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.09, G:0.19, T:0.31
Consensus pattern (34 bp):
AAGTAATAAATTTACTTAGTCATGTGAAAGACTA
Found at i:20703119 original size:21 final size:21
Alignment explanation
Indices: 20703095--20703145 Score: 95
Period size: 21 Copynumber: 2.5 Consensus size: 21
20703085 TCCGAAATTA
20703095 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
20703116 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
20703137 AT-AAATATT
1 ATAAAATATT
20703146 TAAAAATATC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
20 7 0.23
21 23 0.77
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:20703180 original size:30 final size:30
Alignment explanation
Indices: 20703111--20703181 Score: 79
Period size: 30 Copynumber: 2.3 Consensus size: 30
20703101 TATTATTTTT
* * *
20703111 TAAATATAAAATATTATTTTTTAAATATAAA
1 TAAATA-AAAATATCATTATATAAATATAAA
** *
20703142 TATTTAAAAATATCATTATATAAATATATA
1 TAAATAAAAATATCATTATATAAATATAAA
20703172 TAAATAAAAA
1 TAAATAAAAA
20703182 ATTAAATAAT
Statistics
Matches: 32, Mismatches: 8, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
30 28 0.88
31 4 0.12
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (30 bp):
TAAATAAAAATATCATTATATAAATATAAA
Found at i:20713396 original size:19 final size:20
Alignment explanation
Indices: 20713358--20713396 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
20713348 AGAATTATTT
*
20713358 AACATAAATAATTAAGTTAAC
1 AACATAAAT-ATTAAATTAAC
20713379 AACATAAAT-TTAAATTAA
1 AACATAAATATTAAATTAA
20713397 TAATTTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
21 9 0.53
ACGTcount: A:0.59, C:0.08, G:0.03, T:0.31
Consensus pattern (20 bp):
AACATAAATATTAAATTAAC
Found at i:20713967 original size:95 final size:95
Alignment explanation
Indices: 20713855--20714067 Score: 383
Period size: 95 Copynumber: 2.2 Consensus size: 95
20713845 TAATAACGTA
* *
20713855 AAAATATATTATT-GTAACGTAAATAATTATGATGATAATGTAAAATTTTGATTAATTATTATTT
1 AAAATATA-AATTGGTAACATAAATAATTATGATGATAATGTAAAATTTTGATTAATTATTATTT
20713919 TGTATATATATAAAAAAAATAGTTATAAATT
65 TGTATATATATAAAAAAAATAGTTATAAATT
20713950 AAAATATAAATTGGTAACATAAATAATTATGATGATAATGTAAAATTTTGATTAATTATTATTTT
1 AAAATATAAATTGGTAACATAAATAATTATGATGATAATGTAAAATTTTGATTAATTATTATTTT
*
20714015 GTATATATATAAAGAAAATAGTTATAAATT
66 GTATATATATAAAAAAAATAGTTATAAATT
20714045 AAAATATAAATTGGTAACATAAA
1 AAAATATAAATTGGTAACATAAA
20714068 CAAGTGAGAA
Statistics
Matches: 114, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
94 3 0.03
95 111 0.97
ACGTcount: A:0.49, C:0.01, G:0.09, T:0.40
Consensus pattern (95 bp):
AAAATATAAATTGGTAACATAAATAATTATGATGATAATGTAAAATTTTGATTAATTATTATTTT
GTATATATATAAAAAAAATAGTTATAAATT
Found at i:20717944 original size:14 final size:14
Alignment explanation
Indices: 20717925--20717959 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
20717915 TAATGTTATT
20717925 AATAAAAATAAAAA
1 AATAAAAATAAAAA
*
20717939 AATAAAAATGAAAA
1 AATAAAAATAAAAA
20717953 AATAAAA
1 AATAAAA
20717960 TCCGGTAGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.83, C:0.00, G:0.03, T:0.14
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:20720800 original size:16 final size:16
Alignment explanation
Indices: 20720739--20720883 Score: 111
Period size: 16 Copynumber: 9.2 Consensus size: 16
20720729 CTAGGTTTCT
*
20720739 AAAACCCCTAAAATCC
1 AAAACCCTTAAAATCC
* *
20720755 -AAA-TCTTAAAGTCC
1 AAAACCCTTAAAATCC
* *
20720769 AAAATCC-TAAAGTCC
1 AAAACCCTTAAAATCC
20720784 AAAACCCTTAAAATCC
1 AAAACCCTTAAAATCC
* *
20720800 AAAA-TCTTAAAATTC
1 AAAACCCTTAAAATCC
* *
20720815 GAAACTCCTAAAAATCC
1 AAAAC-CCTTAAAATCC
*
20720832 AAAATCTCTT-AAATCC
1 AAAA-CCCTTAAAATCC
* *
20720848 AAACCCCTTAAAATTC
1 AAAACCCTTAAAATCC
* *
20720864 GAAACCCTTAATATCC
1 AAAACCCTTAAAATCC
20720880 AAAA
1 AAAA
20720884 TCCCCCAAAA
Statistics
Matches: 99, Mismatches: 23, Indels: 14
0.73 0.17 0.10
Matches are distributed among these distances:
14 8 0.08
15 36 0.36
16 41 0.41
17 13 0.13
18 1 0.01
ACGTcount: A:0.48, C:0.27, G:0.03, T:0.23
Consensus pattern (16 bp):
AAAACCCTTAAAATCC
Found at i:20720981 original size:30 final size:30
Alignment explanation
Indices: 20720926--20720998 Score: 78
Period size: 30 Copynumber: 2.4 Consensus size: 30
20720916 TTTAAAACCG
*
20720926 AAACCCTAAAATCTTCAAACTCTAAAATCA
1 AAACCCTAAAACCTTCAAACTCTAAAATCA
*
20720956 AAACCCT-AAACCTTCAATA-TCCTAAAATCC
1 AAACCCTAAAACCTTCAA-ACT-CTAAAATCA
* *
20720986 AAGCCTTAAAACC
1 AAACCCTAAAACC
20720999 CTCTAAGCCT
Statistics
Matches: 36, Mismatches: 4, Indels: 5
0.80 0.09 0.11
Matches are distributed among these distances:
29 10 0.28
30 21 0.58
31 5 0.14
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.22
Consensus pattern (30 bp):
AAACCCTAAAACCTTCAAACTCTAAAATCA
Found at i:20727482 original size:18 final size:18
Alignment explanation
Indices: 20727458--20727493 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
20727448 ATGGGGGCAT
20727458 AAAAAAAACAAACAAAAAC
1 AAAAAAAA-AAACAAAAAC
*
20727477 AAAAAAAAAAAGAAAAA
1 AAAAAAAAAAACAAAAA
20727494 ATTGGTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAACAAAAAC
Found at i:20727938 original size:13 final size:12
Alignment explanation
Indices: 20727909--20727949 Score: 50
Period size: 13 Copynumber: 3.4 Consensus size: 12
20727899 AAGGATACAG
20727909 AAAAAA-AAGAA
1 AAAAAAGAAGAA
20727920 AGAAAAAGAAGAA
1 A-AAAAAGAAGAA
20727933 TAAAAAAGAA-AA
1 -AAAAAAGAAGAA
20727945 AAAAA
1 AAAAA
20727950 TGAATGGGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 6 0.22
12 7 0.26
13 13 0.48
14 1 0.04
ACGTcount: A:0.85, C:0.00, G:0.12, T:0.02
Consensus pattern (12 bp):
AAAAAAGAAGAA
Found at i:20727941 original size:23 final size:22
Alignment explanation
Indices: 20727907--20727949 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
20727897 GAAAGGATAC
*
20727907 AGAAAAAAAAGAAAGAAAAAGA
1 AGAAAAAAAAGAAAAAAAAAGA
20727929 AGAATAAAAAAGAAAAAAAAA
1 AGAA-AAAAAAGAAAAAAAAA
20727950 TGAATGGGCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 4 0.21
23 15 0.79
ACGTcount: A:0.84, C:0.00, G:0.14, T:0.02
Consensus pattern (22 bp):
AGAAAAAAAAGAAAAAAAAAGA
Found at i:20728902 original size:33 final size:32
Alignment explanation
Indices: 20728757--20728940 Score: 165
Period size: 32 Copynumber: 5.7 Consensus size: 32
20728747 TAAAAGAAAA
* * * * **
20728757 AATGACATTTAAGCCCAATTTGTCTAGCTATC
1 AATGAAATTTAAGCCCAGTTTATCTGGCCGTC
*
20728789 AATGACATTTAAGCCCAGTTTATCTGGCCGTC
1 AATGAAATTTAAGCCCAGTTTATCTGGCCGTC
* *
20728821 AATGACATTTAAGCTCAGTTTATCTGGCCGTC
1 AATGAAATTTAAGCCCAGTTTATCTGGCCGTC
*
20728853 AATAAAATTTAAGCCCAGTTTATCTGGCC-TC
1 AATGAAATTTAAGCCCAGTTTATCTGGCCGTC
** * **
20728884 AAATGAGGTTTTAAGCCCAATTTAGT-TGGCATTC
1 -AATGA-AATTTAAGCCCAGTTTA-TCTGGCCGTC
* * *
20728918 AATAAAATTTAAACCCAATTTAT
1 AATGAAATTTAAGCCCAGTTTAT
20728941 TTGACCCAAA
Statistics
Matches: 130, Mismatches: 18, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
31 3 0.02
32 102 0.78
33 22 0.17
34 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (32 bp):
AATGAAATTTAAGCCCAGTTTATCTGGCCGTC
Found at i:20728940 original size:65 final size:64
Alignment explanation
Indices: 20728757--20728940 Score: 205
Period size: 64 Copynumber: 2.9 Consensus size: 64
20728747 TAAAAGAAAA
* * *
20728757 AATGACATTTAAGCCCAATTT-GTCTAGCTATCAATGACATTTAAGCCCAGTTTATCTGGCCGTC
1 AATGACATTTAAGCCCAATTTAGTCTGGCT-TCAATAAAATTTAAGCCCAGTTTATCTGGCCGTC
* * *
20728821 AATGACATTTAAGCTCAGTTTA-TCTGGCCGTCAATAAAATTTAAGCCCAGTTTATCTGGCC-TC
1 AATGACATTTAAGCCCAATTTAGTCTGG-CTTCAATAAAATTTAAGCCCAGTTTATCTGGCCGTC
** * *
20728884 AAATGAGGTTTTAAGCCCAATTTAGT-TGGCATTCAATAAAATTTAAACCCAATTTAT
1 -AATGA-CATTTAAGCCCAATTTAGTCTGGC-TTCAATAAAATTTAAGCCCAGTTTAT
20728941 TTGACCCAAA
Statistics
Matches: 101, Mismatches: 13, Indels: 11
0.81 0.10 0.09
Matches are distributed among these distances:
63 2 0.02
64 58 0.57
65 40 0.40
66 1 0.01
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Consensus pattern (64 bp):
AATGACATTTAAGCCCAATTTAGTCTGGCTTCAATAAAATTTAAGCCCAGTTTATCTGGCCGTC
Found at i:20729736 original size:37 final size:38
Alignment explanation
Indices: 20729691--20729777 Score: 142
Period size: 37 Copynumber: 2.3 Consensus size: 38
20729681 GTTCCAATTG
20729691 ATTCTTTATTTCTT-GATTCACGGTGTTATCCTGATCA
1 ATTCTTTATTTCTTCGATTCACGGTGTTATCCTGATCA
*
20729728 ATTTTTTATTT-TTCGATTCACGGTGTTATCCTGATCA
1 ATTCTTTATTTCTTCGATTCACGGTGTTATCCTGATCA
*
20729765 ATTCTTTACTTCT
1 ATTCTTTATTTCT
20729778 AGACTCGCTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 2 0.04
37 42 0.93
38 1 0.02
ACGTcount: A:0.18, C:0.18, G:0.11, T:0.52
Consensus pattern (38 bp):
ATTCTTTATTTCTTCGATTCACGGTGTTATCCTGATCA
Found at i:20731170 original size:18 final size:19
Alignment explanation
Indices: 20731149--20731198 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
20731139 TTGATTTTGA
*
20731149 ATTTTTTTATATATT-ATT
1 ATTTTTTTATATATTCAGT
20731167 ATTTTTGTTAT-T-TTCAGT
1 ATTTTT-TTATATATTCAGT
20731185 A-TTTTTTATATATT
1 ATTTTTTTATATATT
20731199 TATGCATGAT
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
16 4 0.15
17 7 0.26
18 12 0.44
19 4 0.15
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.70
Consensus pattern (19 bp):
ATTTTTTTATATATTCAGT
Found at i:20731592 original size:16 final size:16
Alignment explanation
Indices: 20731573--20731750 Score: 141
Period size: 15 Copynumber: 11.2 Consensus size: 16
20731563 CTAGGTTTCT
20731573 AAAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
* * *
20731589 AAAA-TCTTAAAGTCC
1 AAAACCCCTAAAATCC
* *
20731604 AAAA-TCCTAAAGTCC
1 AAAACCCCTAAAATCC
20731619 -AAACCCCTAAAATCC
1 AAAACCCCTAAAATCC
**
20731634 AAAACCCCTAAAATTT
1 AAAACCCCTAAAATCC
* *
20731650 AAAATCTCTTAAAATCC
1 AAAA-CCCCTAAAATCC
*
20731667 AAAA-TCCTAAAATCC
1 AAAACCCCTAAAATCC
*
20731682 GAAACCCCTAAAAATCC
1 AAAACCCCT-AAAATCC
* *
20731699 AAAATCCCTTAAATCC
1 AAAACCCCTAAAATCC
**
20731715 -AAACCCCTTAAAATTT
1 AAAACCCC-TAAAATCC
* *
20731731 GAAACCCTTAAAATCC
1 AAAACCCCTAAAATCC
20731747 AAAA
1 AAAA
20731751 TCTCCCAAAA
Statistics
Matches: 129, Mismatches: 26, Indels: 14
0.76 0.15 0.08
Matches are distributed among these distances:
14 3 0.02
15 50 0.39
16 44 0.34
17 32 0.25
ACGTcount: A:0.48, C:0.29, G:0.02, T:0.21
Consensus pattern (16 bp):
AAAACCCCTAAAATCC
Found at i:20731594 original size:7 final size:7
Alignment explanation
Indices: 20731582--20731705 Score: 50
Period size: 7 Copynumber: 16.0 Consensus size: 7
20731572 TAAAACCCCT
20731582 AAAATCC
1 AAAATCC
*
20731589 AAAATCTT
1 AAAATC-C
*
20731597 AAAGTCC
1 AAAATCC
20731604 AAAATCC
1 AAAATCC
*
20731611 TAAAGTCC
1 -AAAATCC
**
20731619 AAACCCC
1 AAAATCC
20731626 TAAAATCC
1 -AAAATCC
*
20731634 AAAACCCC
1 AAAA-TCC
**
20731642 TAAAATTT
1 -AAAATCC
20731650 AAAATCTC
1 AAAATC-C
20731658 TTAAAATCC
1 --AAAATCC
20731667 AAAATCC
1 AAAATCC
20731674 TAAAATCC
1 -AAAATCC
**
20731682 GAAACCCC
1 -AAAATCC
20731690 TAAAAATCC
1 --AAAATCC
20731699 AAAATCC
1 AAAATCC
20731706 CTTAAATCCA
Statistics
Matches: 86, Mismatches: 21, Indels: 20
0.68 0.17 0.16
Matches are distributed among these distances:
7 40 0.47
8 30 0.35
9 10 0.12
10 6 0.07
ACGTcount: A:0.49, C:0.28, G:0.02, T:0.20
Consensus pattern (7 bp):
AAAATCC
Found at i:20731687 original size:48 final size:47
Alignment explanation
Indices: 20731573--20731754 Score: 172
Period size: 48 Copynumber: 3.8 Consensus size: 47
20731563 CTAGGTTTCT
** * *
20731573 AAAACCCCTAAAATCC-AAAATCTTAAAGTCCAAAATC-C-TAAAGTCC
1 AAAA-CCCTAAAATCCGAAACCCCTAAAATCCAAAATCTCTTAAA-TCC
* * **
20731619 AAACCCCTAAAATCCAAAACCCCTAAAATTTAAAATCTCTTAAAATCC
1 AAAACCCTAAAATCCGAAACCCCTAAAATCCAAAATCTCTT-AAATCC
* *
20731667 AAAATCCTAAAATCCGAAACCCCTAAAAATCCAAAATCCCTTAAATCC
1 AAAACCCTAAAATCCGAAACCCCT-AAAATCCAAAATCTCTTAAATCC
* ** *
20731715 AAACCCCTTAAAATTTGAAACCCTTAAAATCCAAAATCTC
1 AAAACCC-TAAAATCCGAAACCCCTAAAATCCAAAATCTC
20731755 CCAAAATTCG
Statistics
Matches: 111, Mismatches: 19, Indels: 10
0.79 0.14 0.07
Matches are distributed among these distances:
45 11 0.10
46 18 0.16
47 1 0.01
48 50 0.45
49 31 0.28
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.21
Consensus pattern (47 bp):
AAAACCCTAAAATCCGAAACCCCTAAAATCCAAAATCTCTTAAATCC
Found at i:20731696 original size:32 final size:31
Alignment explanation
Indices: 20731579--20731728 Score: 151
Period size: 32 Copynumber: 4.8 Consensus size: 31
20731569 TTCTAAAACC
** *
20731579 CCTAAAATCCAAA-ATCTTAAAGTCCAAAAT
1 CCTAAAATCCAAACCCCTTAAAATCCAAAAT
* *
20731609 CCTAAAGTCCAAACCCC-TAAAATCCAAAACC
1 CCTAAAATCCAAACCCCTTAAAATCCAAAA-T
** * *
20731640 CCTAAAATTTAAAATCTCTTAAAATCCAAAAT
1 CCTAAAA-TCCAAACCCCTTAAAATCCAAAAT
*
20731672 CCTAAAATCCGAAACCCCTAAAAATCCAAAAT
1 CCTAAAATCC-AAACCCCTTAAAATCCAAAAT
*
20731704 CCCTTAAATCCAAACCCCTTAAAAT
1 -CCTAAAATCCAAACCCCTTAAAAT
20731729 TTGAAACCCT
Statistics
Matches: 96, Mismatches: 18, Indels: 10
0.77 0.15 0.08
Matches are distributed among these distances:
30 23 0.24
31 8 0.08
32 44 0.46
33 21 0.22
ACGTcount: A:0.47, C:0.29, G:0.02, T:0.21
Consensus pattern (31 bp):
CCTAAAATCCAAACCCCTTAAAATCCAAAAT
Found at i:20733170 original size:16 final size:17
Alignment explanation
Indices: 20733142--20733180 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
20733132 TTTCAATAAA
**
20733142 AAATATGAAAAATTTTT
1 AAATATGAAAAATAATT
20733159 AAATAT-AAAAATAATT
1 AAATATGAAAAATAATT
20733175 AAATAT
1 AAATAT
20733181 TTTCGATGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 14 0.70
17 6 0.30
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (17 bp):
AAATATGAAAAATAATT
Found at i:20733182 original size:26 final size:25
Alignment explanation
Indices: 20733120--20733183 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 25
20733110 ATTATGGATA
* *
20733120 AATTAGATATATTTTCAATAAAAAAT
1 AATTAAATAT-TTTTAAATAAAAAAT
* *
20733146 -ATGAAAAATTTTTAAATATAAAAAT
1 AATTAAATATTTTTAAATA-AAAAAT
20733171 AATTAAATATTTT
1 AATTAAATATTTT
20733184 CGATGACGGA
Statistics
Matches: 30, Mismatches: 6, Indels: 4
0.75 0.15 0.10
Matches are distributed among these distances:
24 8 0.27
25 12 0.40
26 10 0.33
ACGTcount: A:0.55, C:0.02, G:0.03, T:0.41
Consensus pattern (25 bp):
AATTAAATATTTTTAAATAAAAAAT
Found at i:20734091 original size:20 final size:20
Alignment explanation
Indices: 20734068--20734138 Score: 72
Period size: 20 Copynumber: 3.5 Consensus size: 20
20734058 AGAAATAAGT
20734068 ATAAAAAATATTATTATAAC
1 ATAAAAAATATTATTATAAC
* * *
20734088 ATAAATAATATTTTTGGTAAC
1 ATAAAAAATATTATT-ATAAC
*
20734109 ATAAAAGATTATTATTATAA-
1 ATAAAA-AATATTATTATAAC
*
20734129 ATAAATAATA
1 ATAAAAAATA
20734139 ATTCTAAACA
Statistics
Matches: 40, Mismatches: 9, Indels: 5
0.74 0.17 0.09
Matches are distributed among these distances:
19 3 0.08
20 18 0.45
21 12 0.30
22 7 0.17
ACGTcount: A:0.55, C:0.03, G:0.04, T:0.38
Consensus pattern (20 bp):
ATAAAAAATATTATTATAAC
Found at i:20734922 original size:67 final size:67
Alignment explanation
Indices: 20734807--20734934 Score: 159
Period size: 67 Copynumber: 1.9 Consensus size: 67
20734797 AAGTAAGTAT
* *
20734807 TAACGTAAAAATGTGAGAATAATCGTAAAATAAGTATAATTTAATGTAAAAT-GTGTTAAAAATA
1 TAACATAAAAATGTAAGAATAATCGTAAAATAAGTATAATTTAATGTAAAATAG-GTTAAAAATA
20734871 TTG
65 TTG
* * * * * **
20734874 TAACATAAAAATGTAAGAATAGTTGTAAAATTAGTCTCATTTGGTGTAAAATAGGTTAAAA
1 TAACATAAAAATGTAAGAATAATCGTAAAATAAGTATAATTTAATGTAAAATAGGTTAAAA
20734935 CTATCATAAC
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
67 50 0.98
68 1 0.02
ACGTcount: A:0.48, C:0.04, G:0.16, T:0.33
Consensus pattern (67 bp):
TAACATAAAAATGTAAGAATAATCGTAAAATAAGTATAATTTAATGTAAAATAGGTTAAAAATAT
TG
Found at i:20735237 original size:21 final size:20
Alignment explanation
Indices: 20735213--20735280 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 20
20735203 AGAACAAGTG
20735213 TAAAAACATATTATTATAATA
1 TAAAAA-ATATTATTATAATA
* * *
20735234 TAAATAAT-TAAATTGATAATG
1 TAAAAAATAT-TATT-ATAATA
20735255 TAAAAAATTATTATTATAA-A
1 TAAAAAA-TATTATTATAATA
20735275 TAAAAA
1 TAAAAA
20735281 GTAATTTCAA
Statistics
Matches: 37, Mismatches: 6, Indels: 9
0.71 0.12 0.17
Matches are distributed among these distances:
19 1 0.03
20 11 0.30
21 20 0.54
22 4 0.11
23 1 0.03
ACGTcount: A:0.59, C:0.01, G:0.03, T:0.37
Consensus pattern (20 bp):
TAAAAAATATTATTATAATA
Found at i:20735509 original size:15 final size:16
Alignment explanation
Indices: 20735473--20735509 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
20735463 AAATTAATAT
20735473 TTTTAAATTAAAAGAA
1 TTTTAAATTAAAAGAA
20735489 TTTTAAA-TAAAA-AA
1 TTTTAAATTAAAAGAA
20735503 TTGTTAA
1 TT-TTAA
20735510 TGTAAAAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 9 0.45
16 7 0.35
ACGTcount: A:0.54, C:0.00, G:0.05, T:0.41
Consensus pattern (16 bp):
TTTTAAATTAAAAGAA
Found at i:20736976 original size:2 final size:2
Alignment explanation
Indices: 20736971--20737005 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
20736961 TGTATGTGTG
* *
20736971 TA TA TA TA TA CA TA TA TA TA TA TA TA TG TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20737006 CATGTCTTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:20737357 original size:2 final size:2
Alignment explanation
Indices: 20737346--20737374 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
20737336 AACTCTCCAA
20737346 AT AT -T 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
20737375 GTCAGGGCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:20738447 original size:2 final size:2
Alignment explanation
Indices: 20738440--20738464 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20738430 ACCTATTTAA
20738440 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
20738465 AATACAAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:20740362 original size:29 final size:28
Alignment explanation
Indices: 20740314--20740406 Score: 109
Period size: 29 Copynumber: 3.2 Consensus size: 28
20740304 TATAGTTTTT
*
20740314 TATT-TTTTAAAAATTTAATTTTTATGAA
1 TATTATTTAAAAAATTTAATTTTTAT-AA
20740342 TATTATTTAAAAAATTTAATTTTTATAA
1 TATTATTTAAAAAATTTAATTTTTATAA
* *
20740370 TATTATTTTTTAAAAAACTTAATCTTTAT-A
1 TATTA---TTTAAAAAATTTAATTTTTATAA
20740400 TATTATT
1 TATTATT
20740407 AATGATTGAA
Statistics
Matches: 58, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
27 2 0.03
28 11 0.19
29 20 0.34
30 6 0.10
31 19 0.33
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (28 bp):
TATTATTTAAAAAATTTAATTTTTATAA
Found at i:20740385 original size:31 final size:31
Alignment explanation
Indices: 20740313--20740406 Score: 126
Period size: 31 Copynumber: 3.2 Consensus size: 31
20740303 TTATAGTTTT
20740313 TTATTTTTT-AAAAATTTAATTTTTATGAATA
1 TTATTTTTTAAAAAATTTAATTTTTAT-AATA
20740344 TTA---TTTAAAAAATTTAATTTTTATAATA
1 TTATTTTTTAAAAAATTTAATTTTTATAATA
* *
20740372 TTATTTTTTAAAAAACTTAATCTTTAT-ATA
1 TTATTTTTTAAAAAATTTAATTTTTATAATA
20740402 TTATT
1 TTATT
20740407 AATGATTGAA
Statistics
Matches: 57, Mismatches: 2, Indels: 9
0.84 0.03 0.13
Matches are distributed among these distances:
28 10 0.18
29 17 0.30
30 8 0.14
31 22 0.39
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.56
Consensus pattern (31 bp):
TTATTTTTTAAAAAATTTAATTTTTATAATA
Found at i:20740397 original size:16 final size:15
Alignment explanation
Indices: 20740317--20740397 Score: 51
Period size: 15 Copynumber: 5.4 Consensus size: 15
20740307 AGTTTTTTAT
*
20740317 TTTTTAAAAATTTAA
1 TTTTTAAAAAATTAA
**
20740332 TTTTT-ATGAA-T-A
1 TTTTTAAAAAATTAA
20740344 TTATTTAAAAAATTTAA
1 TT-TTTAAAAAA-TTAA
* * *
20740361 TTTTTATAATATTAT
1 TTTTTAAAAAATTAA
20740376 TTTTTAAAAAACTTAA
1 TTTTTAAAAAA-TTAA
*
20740392 TCTTTA
1 TTTTTA
20740398 TATATTATTA
Statistics
Matches: 48, Mismatches: 12, Indels: 11
0.68 0.17 0.15
Matches are distributed among these distances:
12 3 0.06
13 4 0.08
14 5 0.10
15 17 0.35
16 16 0.33
17 3 0.06
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.54
Consensus pattern (15 bp):
TTTTTAAAAAATTAA
Found at i:20748367 original size:18 final size:19
Alignment explanation
Indices: 20748334--20748370 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
20748324 GCACCGTAGA
*
20748334 TTTTAATTTTTATATTATT
1 TTTTAATTTATATATTATT
20748353 TTTTAATTTAT-TATTATT
1 TTTTAATTTATATATTATT
20748371 GTTATAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (19 bp):
TTTTAATTTATATATTATT
Found at i:20749618 original size:3 final size:3
Alignment explanation
Indices: 20749610--20749636 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
20749600 TTTTGTCCAA
20749610 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
20749637 GAAATTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:20751022 original size:204 final size:206
Alignment explanation
Indices: 20750654--20751029 Score: 464
Period size: 204 Copynumber: 1.8 Consensus size: 206
20750644 GCATTGAAGT
* * * ** *
20750654 TTTTCTATAAATATGTCAATACACTGGTAATATTTAAAAAAATCATCTCACCTAGGGATTTCTTA
1 TTTTCTATAAATATCTCAATACACTGATAACATTTAAAAAAATCATCTCACCTAAAGATTTCGTA
* * * *
20750719 AAGCATCTCTACTCGGAATACTTTTATAATCCCATCATTGGATAAAATTTATTTTCTTCTCATTT
66 AAGCATCACTACTCGAAATACCTTTAGAATCCCATCATTGGATAAAATTTATTTTCTTCTCATTT
*
20750784 TTATTACTTATTTTTGTTATATTAATCAATTTTTAT-TTATTACTTTAAAAAAAAATTTTTACTA
131 TTATTACTTATTTTTATTATATTAATCAATTTTTATATTATTACTTTAAAAAAAAATTTTTACTA
20750848 TACTGAAAAAA
196 TACTGAAAAAA
*
20750859 TTTT-TATAAATA-CTCTAATACACTGATAACATTTTAAAAAAATCTTCTCACCTAAAGATTTCG
1 TTTTCTATAAATATCTC-AATACACTGATAACA-TTTAAAAAAATCATCTCACCTAAAGATTTCG
* * * *
20750922 T-AGGCATCACTACTCGAAATACCTTT-GAATCTCATCATTGGATAAAATTTTCCTTTTCTT-AC
64 TAAAGCATCACTACTCGAAATACCTTTAGAATCCCATCATTGGATAAAA-TTT-ATTTTCTTCTC
**
20750984 ATTTTT-TTA-TTACTTTTTTATTA-ATTAAATTTATTTTTATATTATT
127 ATTTTTATTACTTA--TTTTTATTATATT-AATCAATTTTTATATTATT
20751030 GTTTTTAAAG
Statistics
Matches: 145, Mismatches: 18, Indels: 16
0.81 0.10 0.09
Matches are distributed among these distances:
202 3 0.02
203 27 0.19
204 71 0.49
205 44 0.30
ACGTcount: A:0.34, C:0.14, G:0.06, T:0.45
Consensus pattern (206 bp):
TTTTCTATAAATATCTCAATACACTGATAACATTTAAAAAAATCATCTCACCTAAAGATTTCGTA
AAGCATCACTACTCGAAATACCTTTAGAATCCCATCATTGGATAAAATTTATTTTCTTCTCATTT
TTATTACTTATTTTTATTATATTAATCAATTTTTATATTATTACTTTAAAAAAAAATTTTTACTA
TACTGAAAAAA
Found at i:20752181 original size:29 final size:28
Alignment explanation
Indices: 20752125--20752181 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 28
20752115 AATAAGGATG
*
20752125 AAGAAGAAGGAAAAAGGAAGAAGGAAATA
1 AAGAAGAA-GAAAAAGGAAGAAGCAAATA
20752154 AAGAAGAA-AAAAAGAGAAGAAGACAAAT
1 AAGAAGAAGAAAAAG-GAAGAAG-CAAAT
20752182 GTAGAAAACG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 7 0.28
29 12 0.48
ACGTcount: A:0.68, C:0.02, G:0.26, T:0.04
Consensus pattern (28 bp):
AAGAAGAAGAAAAAGGAAGAAGCAAATA
Found at i:20752599 original size:49 final size:48
Alignment explanation
Indices: 20752420--20752989 Score: 562
Period size: 46 Copynumber: 11.9 Consensus size: 48
20752410 TTGAAAGTTT
* * * *
20752420 AAAAGGCTCCTCTTAGCAGAGGCTCAACAACTTTTAAA-TCTCATATCATG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTC-T-T-TTG
* * * * *
20752470 AAAAGGGCTCCTTTCAGCAGAGGTTCAACAACTTTAAAATTTTTATTTTG
1 AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TTCTCTTTTG
* * *
20752520 AAAAGGGCTCCTATCAGCAGAGGCTTAACAACTTTAAAATTCTCTTCTTGG
1 AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTT-TT-G
* *
20752571 AAAAA-CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTC--TTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTTTG
* * * * *
20752616 AAAAAGCTCTTCTCAACAGAGGCTCAATTGATATTTTTAAAA-----GTTT-
1 AAAAAGCTCCTCTCAGCAGAGGCTCAA--CA-A-CTTTAAAATTCTCTTTTG
* * * * *
20752662 AAAAGGTTCCTCTCAGCAGAGCCTCAACAACTTTAAAAATTTTATTTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTCTCTTTTG
* * *
20752711 GAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTC--TTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTTTG
*
20752757 AAAAAGTTCCTCTCAGCAGAGGCTCAACAACTTTAAAATT-T-TTTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTTTG
20752803 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA-TCT-TATCTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCT-T-TTG
* * *
20752851 AAAAAGCTCTTCTCAGTAGAGGCTCAATAACTTTAAAATTCTCATTTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTC-TTTTG
* * *
20752900 AAAAAGCTCCTCTCAGTAGAGGTTGAACAACTTTAAAATTCTC-TTTG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTTTG
*
20752947 AAAAAGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAATTCTC
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTC
20752990 ATCTATTTTC
Statistics
Matches: 439, Mismatches: 54, Indels: 57
0.80 0.10 0.10
Matches are distributed among these distances:
42 3 0.01
43 5 0.01
44 1 0.00
45 8 0.02
46 123 0.28
47 46 0.10
48 48 0.11
49 113 0.26
50 52 0.12
51 37 0.08
52 1 0.00
53 2 0.00
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (48 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTCTCTTTTG
Found at i:20752689 original size:92 final size:92
Alignment explanation
Indices: 20752420--20752984 Score: 494
Period size: 95 Copynumber: 5.9 Consensus size: 92
20752410 TTGAAAGTTT
* * * * * *
20752420 AAAAGGCTCCTCTTAGCAGAGGCTCAACAACTTT-TAAATCTCATATCATGAAAAGGGCTCCTTT
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTC---T--TGAAAA-AGTTCCTCT
* *
20752484 CAGCAGAGGTTCAACAACTTTAAAATTTTTATTTTG
60 CAGCAGAGGCTCAACAACTTTAAAA---ATATTTTG
* * * * *
20752520 AAAAGGGCTCCTATCAGCAGAGGCTTAACAACTTTAAAATTCTCTTCTTGGAAAAA-CTCCTCTC
1 AAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAA--ATC-TCTT-GAAAAAGTTCCTCTC
* * *
20752584 AGTAGAGGCTCAACAACTTTAAAAATCTCTTG
61 AGCAGAGGCTCAACAACTTTAAAAATATTTTG
* * * * * * *
20752616 AAAAAGCTCTTCTCAACAGAGGCTCAATTGATATTTTTAAAA-GT-TT-AAAAGGTTCCTCTCAG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAA--CA-ACTTTAAAAATCTCTTGAAAAAGTTCCTCTCAG
*
20752678 CAGAGCCTCAACAACTTTAAAAATTTTATTTTG
63 CAGAGGCTCAACAACTTTAAAAA---TATTTTG
* *
20752711 GAAAAGCTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGTTCCTCTCAGCAG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGTTCCTCTCAGCAG
* *
20752776 AGGCTCAACAACTTTAAAATTTTTTTG
66 AGGCTCAACAACTTTAAAAATATTTTG
* *
20752803 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATCTTATCTTGAAAAAGCTCTTCTCAG
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATC---TCTTGAAAAAGTTCCTCTCAG
* * *
20752867 TAGAGGCTCAATAACTTTAAAATTCTCATTTTG
63 CAGAGGCTCAACAACTTTAAAA--AT-ATTTTG
* * * * *
20752900 AAAAAGCTCCTCTCAGTAGAGGTTGAACAACTTTAAAATTCTCTTTGAAAAAGCTCCTCTCAGCA
1 AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTC-TTGAAAAAGTTCCTCTCAGCA
*
20752965 GAGGCTCAATAACTTTAAAA
65 GAGGCTCAACAACTTTAAAA
20752985 TTCTCATCTA
Statistics
Matches: 387, Mismatches: 54, Indels: 52
0.78 0.11 0.11
Matches are distributed among these distances:
91 10 0.03
92 76 0.20
93 4 0.01
94 42 0.11
95 84 0.22
96 49 0.13
97 37 0.10
98 12 0.03
99 29 0.07
100 5 0.01
101 32 0.08
102 3 0.01
104 2 0.01
105 2 0.01
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.30
Consensus pattern (92 bp):
AAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGTTCCTCTCAGCAG
AGGCTCAACAACTTTAAAAATATTTTG
Found at i:20752714 original size:141 final size:138
Alignment explanation
Indices: 20752426--20752986 Score: 545
Period size: 141 Copynumber: 3.9 Consensus size: 138
20752416 GTTTAAAAGG
* * * * * *
20752426 CTCCTCTTAGCAGAGGCTCAACAACTTT-TAAATCTCATATCATGAAAAGGGCTCCTTTCAGCAG
1 CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTC---T--TGAAAA-AGCTCCTCTCAACAG
* * * * *
20752490 AGGTTCAACAACTTTAAAATTTTTATTTTGAAAAGGGCTCCTATCAGCAGAGGCTTAACAACTTT
60 AGGCTCAACAACTTTAAAA----T-GTTTGAAAA-AGCTCCTCTCAGCAGAGGCTCAACAACTTT
* *
20752555 AAAATTCTCTTCTTGGAAAAA
119 AAAATTTTATT-TTGGAAAAA
*
20752576 CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCTTCTCAACAGAGGCTC
1 CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAACAGAGGCTC
* * * * *
20752641 AATTGATATTTTTAAAA-GTTT-AAAAGGTTCCTCTCAGCAGAGCCTCAACAACTTTAAAAATTT
66 AA--CA-A-CTTTAAAATGTTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTT-AAAATTT
*
20752704 TATTTTGGAAAAG
126 TATTTTGGAAAAA
* *
20752717 CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGTTCCTCTCAGCAGAGGCTC
1 CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAACAGAGGCTC
* *
20752782 AACAACTTTAAAATTTTTTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATCTTAT
66 AACAACTTTAAAA--TGTTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTTAT
*
20752847 CTT-GAAAAA
129 TTTGGAAAAA
* * * **
20752856 GCTCTTCTCAGTAGAGGCTCAATAACTTTAAAATTCTCATTTTGAAAAAGCTCCTCTCAGTAGAG
1 -CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTC---TTGAAAAAGCTCCTCTCAACAGAG
* * * *
20752921 GTTGAACAACTTTAAAATTCTCTTTGAAAAAGCTCCTCTCAGCAGAGGCTCAATAACTTTAAAAT
62 GCTCAACAACTTTAAAA---TGTTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAAT
20752986 T
124 T
20752987 CTCATCTATT
Statistics
Matches: 355, Mismatches: 41, Indels: 36
0.82 0.09 0.08
Matches are distributed among these distances:
137 7 0.02
138 1 0.00
139 6 0.02
140 48 0.14
141 129 0.36
142 13 0.04
143 40 0.11
144 44 0.12
145 18 0.05
146 6 0.02
147 1 0.00
148 2 0.01
149 7 0.02
150 26 0.07
151 7 0.02
ACGTcount: A:0.35, C:0.21, G:0.14, T:0.31
Consensus pattern (138 bp):
CTCCTCTCAGTAGAGGCTCAACAACTTTAAAAATCTCTTGAAAAAGCTCCTCTCAACAGAGGCTC
AACAACTTTAAAATGTTTGAAAAAGCTCCTCTCAGCAGAGGCTCAACAACTTTAAAATTTTATTT
TGGAAAAA
Found at i:20757274 original size:14 final size:14
Alignment explanation
Indices: 20757252--20757295 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
20757242 CAAAAATGGA
*
20757252 ATGGCAAGAAAATG
1 ATGGAAAGAAAATG
20757266 ATGGAAAGAAAA-G
1 ATGGAAAGAAAATG
20757279 AATGGAAAGTAAAATG
1 -ATGGAAAG-AAAATG
20757295 A
1 A
20757296 AAATAATAGA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
13 1 0.04
14 19 0.73
15 5 0.19
16 1 0.04
ACGTcount: A:0.57, C:0.02, G:0.27, T:0.14
Consensus pattern (14 bp):
ATGGAAAGAAAATG
Found at i:20764031 original size:5 final size:5
Alignment explanation
Indices: 20764022--20764055 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
20764012 TGCTTTTTAT
*
20764022 TTTTG ATTTG TTTTG TTTTG TTTTG TTTTG TTTT
1 TTTTG TTTTG TTTTG TTTTG TTTTG TTTTG TTTT
20764056 TACTAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.03, C:0.00, G:0.18, T:0.79
Consensus pattern (5 bp):
TTTTG
Found at i:20764989 original size:13 final size:13
Alignment explanation
Indices: 20764971--20764996 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
20764961 TTATTTTCTT
20764971 CTTATTTTTATTA
1 CTTATTTTTATTA
20764984 CTTATTTTTATTA
1 CTTATTTTTATTA
20764997 TATTAATCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.69
Consensus pattern (13 bp):
CTTATTTTTATTA
Found at i:20765129 original size:202 final size:201
Alignment explanation
Indices: 20764821--20765202 Score: 488
Period size: 202 Copynumber: 1.9 Consensus size: 201
20764811 TTTGAAGAAA
* * *
20764821 AAAAAAGAATTTTATTTGTATTGAAGTTTTTCTATAAATATTCTAATACACTGGTAATATTTAAA
1 AAAAAAGAATTTTATTTGTATTGAAATTTTTCTATAAATACTCTAATACACTAGTAATATTTAAA
* * * * *
20764886 AAAATATTATCACCTAGGGATTTCTTAAAGCATCTCTACTCGAAATACTTTTAGAATCCCATCAT
66 AAAATATTATCACCTAGAGATTTCGTAAAGCATCACTACTCGAAATACCTAT-GAATCCCATCAT
*
20764951 TGGAT-AAAATTT-ATTTTCTT-CTTATTTTTATTACTTATTTTTATTATATTAATCAATTTCTA
130 TGGATAAAAATTTCATTTTCTTACAT-TTTTTATTAC-T-TTTTTATTA-ATTAATCAATTTCTA
20765013 TTTATTACTTT
191 TTTATTACTTT
* * * *
20765024 AAAAAA-ATTTTTA-TTGTATTGAAAATTTTTTTATAAATACTCTAATATACTAGTAGTATTTTA
1 AAAAAAGAATTTTATTTGTATTG-AAATTTTTCTATAAATACTCTAATACACTAGTAATA-TTTA
* * * * *
20765087 AAAAAATCTTCTCACCTAGAGATTTCGT-AGGCATCACTACTCGAAATACCTATGAATCTCATCG
64 AAAAAATATTATCACCTAGAGATTTCGTAAAGCATCACTACTCGAAATACCTATGAATCCCATCA
*
20765151 TTGGATAAAAATTTCTTTTTCTTACATTTTTTATTACTTTTTTATTAATTAA
129 TTGGATAAAAATTTCATTTTCTTACATTTTTTATTACTTTTTTATTAATTAA
20765203 ATTTATTTTT
Statistics
Matches: 155, Mismatches: 19, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
200 5 0.03
201 32 0.21
202 65 0.42
203 51 0.33
204 2 0.01
ACGTcount: A:0.35, C:0.12, G:0.07, T:0.46
Consensus pattern (201 bp):
AAAAAAGAATTTTATTTGTATTGAAATTTTTCTATAAATACTCTAATACACTAGTAATATTTAAA
AAAATATTATCACCTAGAGATTTCGTAAAGCATCACTACTCGAAATACCTATGAATCCCATCATT
GGATAAAAATTTCATTTTCTTACATTTTTTATTACTTTTTTATTAATTAATCAATTTCTATTTAT
TACTTT
Found at i:20766397 original size:18 final size:18
Alignment explanation
Indices: 20766366--20766407 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
20766356 GGATAAGGAT
*
20766366 GAAG-AAGAAGGAAA-AA
1 GAAGAAAGAAAGAAAGAA
20766382 GGAAGAAAGAAAGAAAGAA
1 -GAAGAAAGAAAGAAAGAA
20766401 GAAGAAA
1 GAAGAAA
20766408 AGAGAAGAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
17 4 0.18
18 16 0.73
19 2 0.09
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (18 bp):
GAAGAAAGAAAGAAAGAA
Found at i:20766447 original size:16 final size:15
Alignment explanation
Indices: 20766426--20766455 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
20766416 AGATAAACGC
20766426 AAAAAATAAGAAAAAG
1 AAAAAATAA-AAAAAG
20766442 AAAAAATAAAAAAA
1 AAAAAATAAAAAAA
20766456 TTAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.87, C:0.00, G:0.07, T:0.07
Consensus pattern (15 bp):
AAAAAATAAAAAAAG
Found at i:20767011 original size:13 final size:13
Alignment explanation
Indices: 20767001--20767080 Score: 72
Period size: 13 Copynumber: 6.0 Consensus size: 13
20766991 TTCTTTTTTC
20767001 TTTTTCATTTTAT
1 TTTTTCATTTTAT
*
20767014 TTTTTTATTTTATT
1 TTTTTCATTTTA-T
*
20767028 TTATTTTATTTT-T
1 TT-TTTCATTTTAT
*
20767041 GTTTTCATTTTAT
1 TTTTTCATTTTAT
* *
20767054 TATTTCATTTTGT
1 TTTTTCATTTTAT
*
20767067 TTTGTTTATTTTAT
1 TTT-TTCATTTTAT
20767081 GATATTATTA
Statistics
Matches: 54, Mismatches: 9, Indels: 7
0.77 0.13 0.10
Matches are distributed among these distances:
12 8 0.15
13 26 0.48
14 11 0.20
15 9 0.17
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.78
Consensus pattern (13 bp):
TTTTTCATTTTAT
Found at i:20767015 original size:5 final size:5
Alignment explanation
Indices: 20767002--20767108 Score: 73
Period size: 5 Copynumber: 21.2 Consensus size: 5
20766992 TCTTTTTTCT
*
20767002 TTTTCA TTTTA -TTT- TTTTA TTTTA TTTTA TTTTA TTTTTG TTTTCA
1 TTTT-A TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA -TTTTA TTTT-A
* * *
20767048 TTTTA --TTA TTTCA TTTTG TTTT- GTTTA TTTTA TGATATTA TTATTA
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA T--T-TTA TT-TTA
20767094 -TTTA TTTTA TTTTA T
1 TTTTA TTTTA TTTTA T
20767109 AGAGAAATAA
Statistics
Matches: 83, Mismatches: 7, Indels: 23
0.73 0.06 0.20
Matches are distributed among these distances:
3 3 0.04
4 12 0.14
5 46 0.55
6 17 0.20
7 1 0.01
8 4 0.05
ACGTcount: A:0.19, C:0.03, G:0.04, T:0.75
Consensus pattern (5 bp):
TTTTA
Found at i:20767051 original size:35 final size:34
Alignment explanation
Indices: 20767008--20767108 Score: 89
Period size: 35 Copynumber: 2.9 Consensus size: 34
20766998 TTCTTTTTCA
20767008 TTTTATTTTTTTATTTTATTTTATTTTATTT-TT
1 TTTTATTTTTTTATTTTATTTTATTTTATTTATT
* * * *
20767041 GTTTTCATTTTATTATTTCATTTTGTTTTGTTTATT
1 -TTTT-ATTTTTTTATTTTATTTTATTTTATTTATT
*
20767077 TTATGATATTATTATTA-TTTATTTTATTTTAT
1 TT-T--TATT-TTTTTATTTTATTTTATTTTAT
20767109 AGAGAAATAA
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
34 4 0.07
35 25 0.46
36 3 0.06
37 15 0.28
38 7 0.13
ACGTcount: A:0.19, C:0.02, G:0.04, T:0.75
Consensus pattern (34 bp):
TTTTATTTTTTTATTTTATTTTATTTTATTTATT
Found at i:20767326 original size:9 final size:9
Alignment explanation
Indices: 20767302--20767333 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
20767292 TATTTGTTAC
20767302 ATAATAAAA
1 ATAATAAAA
20767311 AT-A-AAAA
1 ATAATAAAA
20767318 ATAATAAAA
1 ATAATAAAA
20767327 ATAATAA
1 ATAATAA
20767334 TTGATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
7 6 0.29
8 2 0.10
9 13 0.62
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (9 bp):
ATAATAAAA
Found at i:20767626 original size:3 final size:3
Alignment explanation
Indices: 20767618--20767682 Score: 130
Period size: 3 Copynumber: 21.7 Consensus size: 3
20767608 TTATTTAAAC
20767618 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20767666 AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AA
20767683 ACAATAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 62 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20767690 original size:7 final size:6
Alignment explanation
Indices: 20767613--20767699 Score: 57
Period size: 6 Copynumber: 14.0 Consensus size: 6
20767603 AATATTTATT
* * * * * * *
20767613 TAAACAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA TAATAA
1 TAAA-AA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
* * *
20767662 TAATAA TAATAA TAATAA TAAACAA TAAAAA TATAAAA
1 TAAAAA TAAAAA TAAAAA TAAA-AA TAAAAA TA-AAAA
20767700 ATATAAAAAT
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
6 63 0.83
7 13 0.17
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (6 bp):
TAAAAA
Found at i:20775307 original size:232 final size:231
Alignment explanation
Indices: 20774751--20775636 Score: 866
Period size: 232 Copynumber: 3.9 Consensus size: 231
20774741 CTTTTGATGC
* * * ** **
20774751 TTTTTTACTTTAGGTGACGTTATAATTTTATCACCAATTTAAAATTTTATAAATG-ATGAATTTT
1 TTTTTTATTTTAGATGACGTTATAATTTTGTCACCAATTTAAAATTTTAT-TCTGTAACAATTTT
* ** * *
20774815 TCTAATAGATTTTAGGTGATGTTATTAATTTTTATCACAAATTGAATACTTTAGTTAATTATTAA
65 TCTTATAGATTTTAGGTGACATTATTAATTTTTATCACAAATTGAATACTTTAATTAACTATTAA
* * * * * * *
20774880 CGACATTGCAATTTCGTCACATCAATATATGGTGTTATATAACGATAATATAAGTGTCACAAACT
130 TGACATTGCAATTTCATCACGTCAATATATAGTGTTATATGACGATAACATAAATGTCACAAACT
* *
20774945 TTTAC-CACTAAAATTATTTAGTGAAAAAATTTTTTGTAACA
195 TTTACGC-C-AAATTTATTT-G-G-AAAAATTTTTTGTGACA
* * * **
20774986 TTTTTTATTTTAGATGATGTTATAAGTTTGTCACCAATTT-AAATGTTA-TCTGTGATGAATTTT
1 TTTTTTATTTTAGATGACGTTATAATTTTGTCACCAATTTAAAATTTTATTCTGT-AACAATTTT
* * * * *
20775049 TCTGATAAATTTTAGGTGACATTATTAATTTTTGTCACAAATTAAATACTTTAGTTAACTATTAA
65 TCTTATAGATTTTAGGTGACATTATTAATTTTTATCACAAATTGAATACTTTAATTAACTATTAA
* * * *
20775114 TGACATTGTAATTTCACCACGTCAATATATGGTGTTATATGATGATAACATAAA-GTCACAAACT
130 TGACATTGCAATTTCATCACGTCAATATATAGTGTTATATGACGATAACATAAATGTCACAAACT
*
20775178 TTTATCGCCAAATTTATTTGGCAAGAAATTTTTTATGACA
195 TTTA-CGCCAAATTTATTTGG-AA-AAATTTTTTGTGACA
20775218 TTTTTTATTTTAGATGACGTTATAATTTTGTCACCAATTTAAAATTTT-TTCTGTAACAATTTTT
1 TTTTTTATTTTAGATGACGTTATAATTTTGTCACCAATTTAAAATTTTATTCTGTAACAATTTTT
* * *
20775282 TTTATAGATTTTAGGTGATATTATTAATTTTTATCACAAATTGAATACTTTAATTAATTATTAAT
66 CTTATAGATTTTAGGTGACATTATTAATTTTTATCACAAATTGAATACTTTAATTAACTATTAAT
* * * * * * * *
20775347 GACGTTGCAATTT-AGTCATGTCAATGTATACTAG-TATATGATGATAACATAAATATCATAAAA
131 GACATTGCAATTTCA-TCACGTCAATATATAGT-GTTATATGACGATAACATAAATGTCACAAAC
* * *
20775410 TTTTACTGTCAAATTTATTTGGTGAAAATTTGTTGTG--A
194 TTTTAC-GCCAAATTTATTTGG-AAAAATTTTTTGTGACA
* * * *
20775448 -----TA----AG-TGACATTATGATTTTGTAACCAATTTAAAATTTTATT-TGTGACGAATGTT
1 TTTTTTATTTTAGATGACGTTATAATTTTGTCACCAATTTAAAATTTTATTCTGTAAC-AAT-TT
* * *
20775502 TT-TTATAGATTTTAAGTAACATTA-TAAATTTTAGTCACAAATTGAATACTTTAATTAACTATT
64 TTCTTATAGATTTTAGGTGACATTATTAATTTTTA-TCACAAATTGAATACTTTAATTAACTATT
** * * * *
20775565 AATGGTTATTGCAA-TTCTGTCACGTCAATGTATAGTGTTATATTACCATAACATAAATGTCACA
128 AAT-GACATTGCAATTTC-ATCACGTCAATATATAGTGTTATATGACGATAACATAAATGTCACA
20775629 AACTTTTA
191 AACTTTTA
20775637 AATGATATTA
Statistics
Matches: 555, Mismatches: 77, Indels: 51
0.81 0.11 0.07
Matches are distributed among these distances:
220 44 0.08
221 60 0.11
222 54 0.10
225 2 0.00
230 1 0.00
231 4 0.01
232 172 0.31
233 61 0.11
234 121 0.22
235 36 0.06
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.44
Consensus pattern (231 bp):
TTTTTTATTTTAGATGACGTTATAATTTTGTCACCAATTTAAAATTTTATTCTGTAACAATTTTT
CTTATAGATTTTAGGTGACATTATTAATTTTTATCACAAATTGAATACTTTAATTAACTATTAAT
GACATTGCAATTTCATCACGTCAATATATAGTGTTATATGACGATAACATAAATGTCACAAACTT
TTACGCCAAATTTATTTGGAAAAATTTTTTGTGACA
Found at i:20775900 original size:15 final size:15
Alignment explanation
Indices: 20775882--20775919 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
20775872 AAATATTAAT
*
20775882 AAAAGAAATGAAAGG
1 AAAAGAAAAGAAAGG
*
20775897 AAAAGAAAAGAATGG
1 AAAAGAAAAGAAAGG
20775912 AAAAGAAA
1 AAAAGAAA
20775920 GTTTTTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.24, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAGAAAGG
Found at i:20776958 original size:20 final size:20
Alignment explanation
Indices: 20776930--20776970 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
20776920 GAAAATTTTA
* *
20776930 TAAATTTAATTTTTTATAAT
1 TAAAATTAATTTTTAATAAT
20776950 TAAAATTAATTTTTAATAAT
1 TAAAATTAATTTTTAATAAT
20776970 T
1 T
20776971 TATTAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TAAAATTAATTTTTAATAAT
Found at i:20782242 original size:6 final size:6
Alignment explanation
Indices: 20782231--20782258 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
20782221 AATGTTGTTG
20782231 AAAATA AAAATA AAAATA AAAATA AAAA
1 AAAATA AAAATA AAAATA AAAATA AAAA
20782259 AGTAATTTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (6 bp):
AAAATA
Found at i:20783366 original size:41 final size:39
Alignment explanation
Indices: 20783248--20783380 Score: 126
Period size: 41 Copynumber: 3.3 Consensus size: 39
20783238 TAGTTATAGA
*
20783248 AGCCTTTTAAATTTAAAGTTTCATAGTT-TTTGGTCAGATG
1 AGCCTTTTAAATTTAAAGTTT--TAGTTCTCTGGTCAGATG
* * * * *
20783288 AGTCTTTTAAATTCTAAACTTTCA-TTACCTCTAGTCAGAAG
1 AGCCTTTTAAATT-TAAAGTTTTAGTT--CTCTGGTCAGATG
20783329 AGCCTTTTAAACTTTAAAGTTTTAGTGTCTCTGGTCAGATG
1 AGCCTTTTAAA-TTTAAAGTTTTAGT-TCTCTGGTCAGATG
*
20783370 AGCCATTTAAA
1 AGCCTTTTAAA
20783381 GTTTTATAGC
Statistics
Matches: 74, Mismatches: 12, Indels: 13
0.75 0.12 0.13
Matches are distributed among these distances:
38 2 0.03
39 1 0.01
40 12 0.16
41 55 0.74
42 3 0.04
43 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.15, T:0.41
Consensus pattern (39 bp):
AGCCTTTTAAATTTAAAGTTTTAGTTCTCTGGTCAGATG
Found at i:20783420 original size:41 final size:42
Alignment explanation
Indices: 20783375--20783480 Score: 117
Period size: 41 Copynumber: 2.5 Consensus size: 42
20783365 AGATGAGCCA
* * ** *
20783375 TTTAAAGTTTTATAGCTTCTGACCAGGGGAGCC-TTTTAAAT
1 TTTAAAGTTTCATAGCCTCTGACCAAAGGAACCTTTTTAAAT
*
20783416 TTTAAAGTTTCATAGCCTCTGATCAAAGGAACCTTTTTAAAT
1 TTTAAAGTTTCATAGCCTCTGACCAAAGGAACCTTTTTAAAT
20783458 TTTCAAAAGTTATCA-AGCCTCTG
1 TTT--AAAGTT-TCATAGCCTCTG
20783481 CTTAGAAGAG
Statistics
Matches: 55, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
41 27 0.49
42 11 0.20
44 14 0.25
45 3 0.05
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (42 bp):
TTTAAAGTTTCATAGCCTCTGACCAAAGGAACCTTTTTAAAT
Found at i:20784818 original size:9 final size:9
Alignment explanation
Indices: 20784801--20784833 Score: 59
Period size: 9 Copynumber: 3.8 Consensus size: 9
20784791 TTTTTGTTAC
20784801 ATAATAAAA
1 ATAATAAAA
20784810 ATAA-AAAA
1 ATAATAAAA
20784818 ATAATAAAA
1 ATAATAAAA
20784827 ATAATAA
1 ATAATAA
20784834 TTAGTTATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 15 0.65
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (9 bp):
ATAATAAAA
Found at i:20785542 original size:51 final size:50
Alignment explanation
Indices: 20785428--20785542 Score: 126
Period size: 50 Copynumber: 2.3 Consensus size: 50
20785418 TAGAAAATTT
* * *
20785428 AGATGATCCTAAAATTAGTTTAAAAATTTTTAAGATGTCGTCAATGAGTT
1 AGATAATCCTAAAATTAGTTTAAAAATTTTTAAGATGTCGTCAAAGAGTA
* * * *
20785478 GGATAATCTTAAAATCT-GTTTAATAAA-TTTTAAGATTTTGTCAAAGAGTCA
1 AGATAATCCTAAAAT-TAGTTTAA-AAATTTTTAAGATGTCGTCAAAGAGT-A
20785529 AGATAATCCTAAAA
1 AGATAATCCTAAAA
20785543 CCAATTTTAA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
50 37 0.70
51 16 0.30
ACGTcount: A:0.41, C:0.09, G:0.14, T:0.37
Consensus pattern (50 bp):
AGATAATCCTAAAATTAGTTTAAAAATTTTTAAGATGTCGTCAAAGAGTA
Found at i:20788415 original size:13 final size:13
Alignment explanation
Indices: 20788399--20788423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20788389 TTTTTATGTT
20788399 ATTTTAATATAAA
1 ATTTTAATATAAA
20788412 ATTTTAATATAA
1 ATTTTAATATAA
20788424 TTAAATATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTAATATAAA
Found at i:20788490 original size:16 final size:16
Alignment explanation
Indices: 20788469--20788500 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
20788459 TTATAAAAAT
20788469 TTAAAATATATATATA
1 TTAAAATATATATATA
20788485 TTAAAATATATATATA
1 TTAAAATATATATATA
20788501 ATTGATTCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (16 bp):
TTAAAATATATATATA
Found at i:20792091 original size:22 final size:23
Alignment explanation
Indices: 20792066--20792119 Score: 92
Period size: 22 Copynumber: 2.3 Consensus size: 23
20792056 CTCGAAATTA
20792066 ATAAAATATTATTTTTTAAA-AT
1 ATAAAATATTATTTTTTAAATAT
20792088 ATAAAATATTATTTTTTAAATAT
1 ATAAAATATTATTTTTTAAATAT
20792111 ATATAAATA
1 ATA-AAATA
20792120 AAAAATTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
22 20 0.67
23 5 0.17
24 5 0.17
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (23 bp):
ATAAAATATTATTTTTTAAATAT
Found at i:20792840 original size:3 final size:3
Alignment explanation
Indices: 20792832--20792860 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20792822 ATAAACTCAA
20792832 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20792861 CATCAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:20795861 original size:18 final size:18
Alignment explanation
Indices: 20795830--20795871 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
20795820 GAAGAATTTT
**
20795830 TTTTTTATCTTAAATGTA
1 TTTTTTATCTTAAAAATA
20795848 TTTTTTAT-TGTAAAAATA
1 TTTTTTATCT-TAAAAATA
20795866 TTTTTT
1 TTTTTT
20795872 GAAGAGTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.29, C:0.02, G:0.05, T:0.64
Consensus pattern (18 bp):
TTTTTTATCTTAAAAATA
Found at i:20797196 original size:2 final size:2
Alignment explanation
Indices: 20797185--20797222 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
20797175 GAAATGATTT
20797185 TA TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20797223 GGAAGAGCAT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:20801759 original size:12 final size:12
Alignment explanation
Indices: 20801742--20801772 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20801732 TTTTCAAAAA
20801742 TTTTATTAATTG
1 TTTTATTAATTG
*
20801754 TTTTATTAATTT
1 TTTTATTAATTG
20801766 TTTTATT
1 TTTTATT
20801773 TTTAATTTTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (12 bp):
TTTTATTAATTG
Found at i:20801958 original size:18 final size:19
Alignment explanation
Indices: 20801935--20801970 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
20801925 TTTTCTTATT
*
20801935 TATATT-ATTATTTTTTAA
1 TATATTAATTAATTTTTAA
20801953 TATATTAATTAATTTTTA
1 TATATTAATTAATTTTTA
20801971 TTTATTGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (19 bp):
TATATTAATTAATTTTTAA
Found at i:20802187 original size:17 final size:17
Alignment explanation
Indices: 20802156--20802197 Score: 52
Period size: 15 Copynumber: 2.6 Consensus size: 17
20802146 TTTTATTATA
*
20802156 AAATTTCATTAT-TTTT
1 AAATTTTATTATATTTT
*
20802172 -CATTTTATTATATTTT
1 AAATTTTATTATATTTT
20802188 AAATTTTATT
1 AAATTTTATT
20802198 TTAAAATTAA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
15 9 0.43
16 4 0.19
17 8 0.38
ACGTcount: A:0.31, C:0.05, G:0.00, T:0.64
Consensus pattern (17 bp):
AAATTTTATTATATTTT
Found at i:20803041 original size:22 final size:23
Alignment explanation
Indices: 20803016--20803065 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 23
20803006 AGAAAGCTCT
* *
20803016 ATTTTTTTGTTATTTTTTCTCA-
1 ATTTTTTTCTTATTTTTTCACAG
*
20803038 ATTTTTTTCTTTTTTTTTCACAG
1 ATTTTTTTCTTATTTTTTCACAG
20803061 ATTTT
1 ATTTT
20803066 ATAGAGCTTA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
22 19 0.79
23 5 0.21
ACGTcount: A:0.14, C:0.10, G:0.04, T:0.72
Consensus pattern (23 bp):
ATTTTTTTCTTATTTTTTCACAG
Found at i:20803264 original size:10 final size:10
Alignment explanation
Indices: 20803241--20803291 Score: 52
Period size: 10 Copynumber: 5.1 Consensus size: 10
20803231 TGAATCGGAT
*
20803241 AAGAAAGAAG
1 AAGAAAGAAA
*
20803251 AAGAAGGAAA
1 AAGAAAGAAA
20803261 AAGAAAGAAGA
1 AAGAAAGAA-A
20803272 AAGAAA-AAA
1 AAGAAAGAAA
20803281 TAAGAAA-AAA
1 -AAGAAAGAAA
20803291 A
1 A
20803292 TTAAATAATA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
9 2 0.06
10 27 0.75
11 7 0.19
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (10 bp):
AAGAAAGAAA
Found at i:20803271 original size:7 final size:7
Alignment explanation
Indices: 20803241--20803287 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
20803231 TGAATCGGAT
20803241 AAGAAAG
1 AAGAAAG
20803248 AAG-AAG
1 AAGAAAG
20803254 AAGGAAA-
1 AA-GAAAG
20803261 AAGAAAG
1 AAGAAAG
20803268 AAGAAAG
1 AAGAAAG
* *
20803275 AAAAAAT
1 AAGAAAG
20803282 AAGAAA
1 AAGAAA
20803288 AAAATTAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
6 9 0.26
7 23 0.68
8 2 0.06
ACGTcount: A:0.74, C:0.00, G:0.23, T:0.02
Consensus pattern (7 bp):
AAGAAAG
Found at i:20803286 original size:17 final size:17
Alignment explanation
Indices: 20803244--20803279 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
20803234 ATCGGATAAG
*
20803244 AAAG-AAGAAGAAGGAA
1 AAAGAAAGAAGAAAGAA
20803260 AAAGAAAGAAGAAAGAA
1 AAAGAAAGAAGAAAGAA
20803277 AAA
1 AAA
20803280 ATAAGAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (17 bp):
AAAGAAAGAAGAAAGAA
Found at i:20805177 original size:22 final size:22
Alignment explanation
Indices: 20805152--20805197 Score: 83
Period size: 22 Copynumber: 2.1 Consensus size: 22
20805142 TAATAAAATT
*
20805152 TATTATAATTATTATTAAAAAA
1 TATTATAATTATAATTAAAAAA
20805174 TATTATAATTATAATTAAAAAA
1 TATTATAATTATAATTAAAAAA
20805196 TA
1 TA
20805198 ATAAAAAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TATTATAATTATAATTAAAAAA
Found at i:20806729 original size:16 final size:17
Alignment explanation
Indices: 20806708--20806739 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
20806698 TATTTTTAAA
20806708 ATATAAATATA-AAATT
1 ATATAAATATATAAATT
20806724 ATATAAATATATAAAT
1 ATATAAATATATAAAT
20806740 AAAAATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
ATATAAATATATAAATT
Found at i:20806734 original size:8 final size:8
Alignment explanation
Indices: 20806704--20806740 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
20806694 ATATTATTTT
20806704 TAAA-ATA
1 TAAATATA
20806711 TAAATATA
1 TAAATATA
20806719 -AAATTATA
1 TAAA-TATA
20806727 TAAATATA
1 TAAATATA
20806735 TAAATA
1 TAAATA
20806741 AAAATTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
7 7 0.26
8 17 0.63
9 3 0.11
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (8 bp):
TAAATATA
Found at i:20806761 original size:23 final size:23
Alignment explanation
Indices: 20806704--20806752 Score: 73
Period size: 23 Copynumber: 2.1 Consensus size: 23
20806694 ATATTATTTT
*
20806704 TAAA-ATATAAATATAAAATTATA
1 TAAATATATAAATA-AAAATTAAA
20806727 TAAATATATAAATAAAAATTAAA
1 TAAATATATAAATAAAAATTAAA
20806750 TAA
1 TAA
20806753 TTAATTAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 15 0.62
24 9 0.38
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (23 bp):
TAAATATATAAATAAAAATTAAA
Found at i:20807740 original size:30 final size:30
Alignment explanation
Indices: 20807699--20807762 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 30
20807689 AAATGAGCAC
20807699 CCATTGGTTTTGGAACTAATAGCCACAAAA
1 CCATTGGTTTTGGAACTAATAGCCACAAAA
* *
20807729 GCCATT-GTTTTGGAGCTAATTGCCACAAAA
1 -CCATTGGTTTTGGAACTAATAGCCACAAAA
20807759 CCAT
1 CCAT
20807763 GGAAAAGAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
29 4 0.13
30 22 0.71
31 5 0.16
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (30 bp):
CCATTGGTTTTGGAACTAATAGCCACAAAA
Found at i:20808441 original size:24 final size:22
Alignment explanation
Indices: 20808409--20808464 Score: 69
Period size: 24 Copynumber: 2.5 Consensus size: 22
20808399 ATAATATAAA
*
20808409 AATAATAATAATATTTAAAATTTT
1 AATAATAATAATATAT-AAA-TTT
*
20808433 AATAATAATTATATATAAATTT
1 AATAATAATAATATATAAATTT
20808455 AATAA-AATAA
1 AATAATAATAA
20808465 AAAATTTTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.14
22 8 0.28
23 3 0.10
24 14 0.48
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AATAATAATAATATATAAATTT
Found at i:20808508 original size:31 final size:31
Alignment explanation
Indices: 20808473--20808544 Score: 92
Period size: 31 Copynumber: 2.3 Consensus size: 31
20808463 AAAAAATTTT
* * *
20808473 ATTTTTATATAGATATAA-ATTATTATATATA
1 ATTTTTATATAAATATAATATAAATATATA-A
20808504 ATTTTTATATAAATATAATATAAATATATAA
1 ATTTTTATATAAATATAATATAAATATATAA
*
20808535 ATTTTAATAT
1 ATTTTTATAT
20808545 TTGATATGAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
31 27 0.75
32 9 0.25
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
ATTTTTATATAAATATAATATAAATATATAA
Found at i:20808511 original size:13 final size:12
Alignment explanation
Indices: 20808485--20808528 Score: 54
Period size: 13 Copynumber: 3.7 Consensus size: 12
20808475 TTTTATATAG
20808485 ATATAAATTATT
1 ATATAAATTATT
*
20808497 ATATATAATTTTT
1 ATATA-AATTATT
*
20808510 ATATAAA-TATA
1 ATATAAATTATT
20808521 ATATAAAT
1 ATATAAAT
20808529 ATATAAATTT
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
11 9 0.33
12 7 0.26
13 11 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (12 bp):
ATATAAATTATT
Found at i:20808533 original size:30 final size:31
Alignment explanation
Indices: 20808473--20808540 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 31
20808463 AAAAAATTTT
* *
20808473 ATTTTTATATAGATATAAATTATTATATATA
1 ATTTTTATATAAATATAAATTATAATATATA
20808504 ATTTTTATATAAATAT-AA-TATAAATATATA
1 ATTTTTATATAAATATAAATTAT-AATATATA
*
20808534 AATTTTA
1 ATTTTTA
20808541 ATATTTGATA
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 3 0.09
30 15 0.45
31 15 0.45
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (31 bp):
ATTTTTATATAAATATAAATTATAATATATA
Found at i:20808769 original size:14 final size:15
Alignment explanation
Indices: 20808752--20808780 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20808742 AAGGAAAGAT
20808752 ATTTTTT-GAAAAAA
1 ATTTTTTAGAAAAAA
20808766 ATTTTTTAGAAAAAA
1 ATTTTTTAGAAAAAA
20808781 TTCATCAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (15 bp):
ATTTTTTAGAAAAAA
Found at i:20808864 original size:22 final size:22
Alignment explanation
Indices: 20808836--20808888 Score: 97
Period size: 22 Copynumber: 2.4 Consensus size: 22
20808826 TAATTTACTT
20808836 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATATTAATAA
20808858 ATAAATAATATTATATTAATAA
1 ATAAATAATATTATATTAATAA
20808880 ATAATATAA
1 ATAA-ATAA
20808889 AAATCATAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
ATAAATAATATTATATTAATAA
Found at i:20809002 original size:36 final size:36
Alignment explanation
Indices: 20808935--20809003 Score: 88
Period size: 36 Copynumber: 1.9 Consensus size: 36
20808925 TAACATAAAA
* *
20808935 TTTTAATATTAAATATTATTATTAATTATAATTATT
1 TTTTAATATTAAATATTATTAGTAATAATAATTATT
20808971 TTTTAATATT-AATAATT-TTAGTAATAAATAATT
1 TTTTAATATTAAAT-ATTATTAGTAAT-AATAATT
20809004 TCAATATGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
35 10 0.34
36 19 0.66
ACGTcount: A:0.43, C:0.00, G:0.01, T:0.55
Consensus pattern (36 bp):
TTTTAATATTAAATATTATTAGTAATAATAATTATT
Found at i:20811134 original size:15 final size:14
Alignment explanation
Indices: 20811107--20811133 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20811097 AAAAACTTAC
20811107 AAAAAAAATTTTTA
1 AAAAAAAATTTTTA
20811121 AAAAAAAATTTTT
1 AAAAAAAATTTTT
20811134 TTTAATAAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (14 bp):
AAAAAAAATTTTTA
Found at i:20814103 original size:20 final size:20
Alignment explanation
Indices: 20814080--20814121 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
20814070 TGGTGTGGTG
* *
20814080 TTGACTTCAATGATGTGGCA
1 TTGACTTCAATAATGTAGCA
20814100 TTGACTTCAATAATGTAGCA
1 TTGACTTCAATAATGTAGCA
20814120 TT
1 TT
20814122 TATTTGCTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.14, G:0.19, T:0.38
Consensus pattern (20 bp):
TTGACTTCAATAATGTAGCA
Found at i:20814313 original size:18 final size:20
Alignment explanation
Indices: 20814285--20814326 Score: 61
Period size: 19 Copynumber: 2.2 Consensus size: 20
20814275 CTCTAATATA
20814285 AAAAATATTTTGAA-TTTTT
1 AAAAATATTTTGAATTTTTT
*
20814304 AAAAAT-TTTTTAATTTTTT
1 AAAAATATTTTGAATTTTTT
20814323 AAAA
1 AAAA
20814327 CATTAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (20 bp):
AAAAATATTTTGAATTTTTT
Found at i:20816195 original size:20 final size:20
Alignment explanation
Indices: 20816167--20816233 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
20816157 CCATGTCAGC
* *
20816167 AAGTTAATGCCACATTATTG
1 AAGTCAATGCCACATCATTG
20816187 AAGTCAATGCCACATCATTG
1 AAGTCAATGCCACATCATTG
* * **
20816207 AAGTCAACGTCATGTCATTG
1 AAGTCAATGCCACATCATTG
20816227 AAGTCAA
1 AAGTCAA
20816234 CACCATGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.36, C:0.19, G:0.16, T:0.28
Consensus pattern (20 bp):
AAGTCAATGCCACATCATTG
Found at i:20816240 original size:20 final size:20
Alignment explanation
Indices: 20816201--20816243 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
20816191 CAATGCCACA
**
20816201 TCATTGAAGTCAACGTCATG
1 TCATTGAAGTCAACACCATG
20816221 TCATTGAAGTCAACACCATG
1 TCATTGAAGTCAACACCATG
20816241 TCA
1 TCA
20816244 GCATGATCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.28
Consensus pattern (20 bp):
TCATTGAAGTCAACACCATG
Found at i:20816524 original size:12 final size:12
Alignment explanation
Indices: 20816507--20816547 Score: 50
Period size: 11 Copynumber: 3.6 Consensus size: 12
20816497 GTAATACAAT
20816507 TAAAAATTTTAA
1 TAAAAATTTTAA
*
20816519 TAAAAATTAT-A
1 TAAAAATTTTAA
*
20816530 TATAAA-TTTAA
1 TAAAAATTTTAA
20816541 TAAAAAT
1 TAAAAAT
20816548 ATATTTCTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 4
0.74 0.13 0.13
Matches are distributed among these distances:
10 2 0.09
11 12 0.52
12 9 0.39
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (12 bp):
TAAAAATTTTAA
Found at i:20816947 original size:21 final size:21
Alignment explanation
Indices: 20816892--20816948 Score: 61
Period size: 21 Copynumber: 2.9 Consensus size: 21
20816882 AAAATAAATA
*
20816892 AATAATTAAA-AATTA-TTTT
1 AATAAATAAATAATTATTTTT
20816911 -A-AAATCAAATAA-TATTTTT
1 AATAAAT-AAATAATTATTTTT
20816930 AATAAATAAATAATTATTT
1 AATAAATAAATAATTATTT
20816949 ATTAGTTTAT
Statistics
Matches: 31, Mismatches: 1, Indels: 10
0.74 0.02 0.24
Matches are distributed among these distances:
17 3 0.10
18 6 0.19
19 6 0.19
20 7 0.23
21 9 0.29
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (21 bp):
AATAAATAAATAATTATTTTT
Found at i:20816965 original size:34 final size:35
Alignment explanation
Indices: 20816923--20817004 Score: 98
Period size: 34 Copynumber: 2.4 Consensus size: 35
20816913 AATCAAATAA
* * *
20816923 TATT-TTTAATAAATAAA-TAATTATTTATTAGTT
1 TATTATTTAATAAATAAATTAATTATTAACTAATT
*
20816956 TATTATTTAATAAA-AAATTATTTATTAACTAATT
1 TATTATTTAATAAATAAATTAATTATTAACTAATT
*
20816990 TATTATATAATAAAT
1 TATTATTTAATAAAT
20817005 TTTATTTTTA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
33 7 0.17
34 34 0.83
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (35 bp):
TATTATTTAATAAATAAATTAATTATTAACTAATT
Found at i:20816989 original size:15 final size:15
Alignment explanation
Indices: 20816936--20816989 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
20816926 TTTTAATAAA
20816936 TAAATAATTATTTAT
1 TAAATAATTATTTAT
** * *
20816951 TAGTTTATTATTTAA
1 TAAATAATTATTTAT
*
20816966 TAAAAAATTATTTAT
1 TAAATAATTATTTAT
*
20816981 TAACTAATT
1 TAAATAATT
20816990 TATTATATAA
Statistics
Matches: 28, Mismatches: 11, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
15 28 1.00
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (15 bp):
TAAATAATTATTTAT
Found at i:20823104 original size:13 final size:14
Alignment explanation
Indices: 20823086--20823115 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
20823076 TTTTCCCTCT
20823086 TTTATTCTTT-TTC
1 TTTATTCTTTATTC
20823099 TTTATTCTTTATTC
1 TTTATTCTTTATTC
20823113 TTT
1 TTT
20823116 TTGAGCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTCTTTATTC
Found at i:20823108 original size:7 final size:7
Alignment explanation
Indices: 20823086--20823115 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
20823076 TTTTCCCTCT
20823086 TTTATTC
1 TTTATTC
20823093 TTT-TTC
1 TTTATTC
20823099 TTTATTC
1 TTTATTC
20823106 TTTATTC
1 TTTATTC
20823113 TTT
1 TTT
20823116 TTGAGCCAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTATTC
Found at i:20825625 original size:30 final size:29
Alignment explanation
Indices: 20825571--20825627 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 29
20825561 TAATAAGATC
* *
20825571 TTATATTTTTATTGTATTTAAATAAATTT
1 TTATATTTTAATTGTATCTAAATAAATTT
*
20825600 TTATATTTTAATTTGTGTCTAAATAAAT
1 TTATATTTTAA-TTGTATCTAAATAAAT
20825628 CCTCATTTCA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.35, C:0.02, G:0.05, T:0.58
Consensus pattern (29 bp):
TTATATTTTAATTGTATCTAAATAAATTT
Found at i:20825691 original size:23 final size:23
Alignment explanation
Indices: 20825665--20825709 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
20825655 TATTAAGAGT
20825665 TTATTTAGATAAAAATTAAAAAA
1 TTATTTAGATAAAAATTAAAAAA
* **
20825688 TTATTTGGATCCAAATTAAAAA
1 TTATTTAGATAAAAATTAAAAA
20825710 TTAAATGCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.53, C:0.04, G:0.07, T:0.36
Consensus pattern (23 bp):
TTATTTAGATAAAAATTAAAAAA
Done.