Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167926.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_19, 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: 20060819
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 113000 characters in sequence are not A, C, G, or T
File 21 of 117
Found at i:2465705 original size:333 final size:332
Alignment explanation
Indices: 2464835--2466399 Score: 2000
Period size: 333 Copynumber: 4.7 Consensus size: 332
2464825 AAAATATTCC
* * * * * * *
2464835 TTTAATAATCC-GAGAAAATTTTTTTA-AAAAAATATTAAAGGCGTTGTTATCTGAAACCACCTT
1 TTTAATAATCCTGA-AAACTTTTATTAGAAAAATTATTAAAGGCGTTGTTTTCTAAAATCGCCTT
* * * *
2464898 CAATAATTATATACAAACTGTGATAGGAATTATTAAAGGCATCTATCTTAAATATATGCCTTT-A
65 CAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACG-CTTTCA
* * * *
2464962 ATAACAATGTTACAATTTGTGTGGTGTTATATAAAAGGTATTTTACAGTAGAAGACGCCTTTACT
129 ATAACAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTACT
* * ** * *
2465027 AATTCCCAAAATATTTAGTGAAAAAATTTTGAAAGCTTCAGTTATTAACAAATGCCTTCAGTAAT
194 AATTCTCAAAATATTTAGTGAGAAAATTTTGATGGCATCTGTTATTAACAAAT-CCTTCAGTAAT
* * * ** *
2465092 TGAAGGAGCCATTTCTAATAAACGCCTTCGATTACCATCGTGGTATATTGAAGGTGTTTTATAAC
258 TAAAGGTGCCTTTTCTAATAAACGCCTTCGATTACCATCGTGGTATATTGAAGGCATTTTATAAT
* *
2465157 AAAAGATGCA
323 AAAAGACGCT
* * * *
2465167 ATTAATAATCCT-AGAAAC-TTTATTAGAAAAATTATTGAAGGCATTGTTTTCTACAATCGCCTT
1 TTTAATAATCCTGA-AAACTTTTATTAGAAAAATTATTAAAGGCGTTGTTTTCTAAAATCGCCTT
* * * * * *
2465230 CAATAATTATATAC-AACTGTGATAGGAATTATTAAAAGCGTTTATCTTAAATATACACCTTCAA
65 CAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACGCTTTCAA
* * *
2465294 TAATAGTGTTACAATTTGTGTGGTGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTATTA
130 TAACAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTACTA
* * *
2465359 ATTCTCAAAATATTTAGTGAGAAAATTTTGATGGCGTCTGTTATTAAC-AATCATATTTAGTAAT
195 ATTCTCAAAATATTTAGTGAGAAAATTTTGATGGCATCTGTTATTAACAAATC--CTTCAGTAAT
* * * * * * *
2465423 TGAAGGCGTCTTTTCTAATAAATGCTTTCAATTACCATCGTGGTATATTGAAGGTATTTTATAAT
258 TAAAGGTGCCTTTTCTAATAAACGCCTTCGATTACCATCGTGGTATATTGAAGGCATTTTATAAT
2465488 AAAAGACGCT
323 AAAAGACGCT
*
2465498 TTTAATAATCCTGAAAACTTTTATTAGAAAAATTATTAAAGGTGTTGTTTTCTAAAATCGCCTTC
1 TTTAATAATCCTGAAAACTTTTATTAGAAAAATTATTAAAGGCGTTGTTTTCTAAAATCGCCTTC
*
2465563 AGTAATTATATACAACCTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACGCTTTCAAT
66 AGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACGCTTTCAAT
* * *
2465628 AACAATGTTACAATTTGTGTTATGGTATATAGAAGGTATTTTACAGTAGAAGATGCCTTTACTAA
131 AACAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTACTAA
* * *
2465693 TTCTCAAAATATTTAGTGAGAAAATGTTGATGGCATTTGTTATTAACAAACACCTTCAGTAATTA
196 TTCTCAAAATATTTAGTGAGAAAATTTTGATGGCATCTGTTATTAACAAA-TCCTTCAGTAATTA
* *
2465758 AAGGTGCCTTTTCTAATAAACGTCTTCGATTACCATCGTGGTATATTAAAGGCATTTTATAATAA
260 AAGGTGCCTTTTCTAATAAACGCCTTCGATTACCATCGTGGTATATTGAAGGCATTTTATAATAA
2465823 AAGACGCT
325 AAGACGCT
* * *
2465831 TTTAATCATCCAGAAAACTTTTATTAGGAAAATTATTAAAGGCGTTGTTTTCTAAAA-CTGCCTT
1 TTTAATAATCCTGAAAACTTTTATTAGAAAAATTATTAAAGGCGTTGTTTTCTAAAATC-GCCTT
* * * *
2465895 CAGTAATTATATACAAACTGTGATAAAAATTATTAAAGGCGTCAATCTTAAATATACACCTTCAA
65 CAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACGCTTTCAA
* * * * *
2465960 TAATAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTATAGTAAAAGATGCATTTACTA
130 TAACAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTACTA
* * * *
2466025 ATTCCCAAAATATTTAGTAAGAAAATTTTGATGGCATATATTATTAACAAATGCCTTCAGTAATT
195 ATTCTCAAAATATTTAGTGAGAAAATTTTGATGGCATCTGTTATTAACAAAT-CCTTCAGTAATT
* * * * * *
2466090 AAAGGTACCTTTTCTAATAAATGCCTTCCATCACCATCGTAGTATATTGAAGGCATTTTATAATG
259 AAAGGTGCCTTTTCTAATAAACGCCTTCGATTACCATCGTGGTATATTGAAGGCATTTTATAATA
* *
2466155 AAAGATGCC
324 AAAGACGCT
* * * * *
2466164 TTTAATAAT-CTGAAAAAATTTTATTAGAAAAATTATTGAAGGTGTTATTTTCTGAAATCGCCTT
1 TTTAATAATCCTG-AAAACTTTTATTAGAAAAATTATTAAAGGCGTTGTTTTCTAAAATCGCCTT
* * * *
2466228 CAGTAATTATATACAAACTGTGAGAGAAATTATTAAAAGCATTTATCTTAAATATACGTCTTT-A
65 CAGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACG-CTTTCA
* * ** * * *
2466292 ATAACAGTGTTACAATATGTGTAACAGTATATAAAAGGTATTTTATAGTAGAAGACGCCTTTAAT
129 ATAACAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTACT
* * *
2466357 AATT-TCTAAAATATTTAGTGAAAAAATTTTGAAGGCGTCTGTT
194 AATTCTC-AAAATATTTAGTGAGAAAATTTTGATGGCATCTGTT
2466400 TCTAACAGAT
Statistics
Matches: 1080, Mismatches: 137, Indels: 31
0.87 0.11 0.02
Matches are distributed among these distances:
329 1 0.00
330 6 0.01
331 236 0.22
332 117 0.11
333 713 0.66
334 6 0.01
335 1 0.00
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.36
Consensus pattern (332 bp):
TTTAATAATCCTGAAAACTTTTATTAGAAAAATTATTAAAGGCGTTGTTTTCTAAAATCGCCTTC
AGTAATTATATACAAACTGTGATAGAAATTATTAAAGGCGTCTATCTTAAATATACGCTTTCAAT
AACAGTGTTACAATTTGTGTGATGGTATATAGAAGGTATTTTACAGTAGAAGACGCCTTTACTAA
TTCTCAAAATATTTAGTGAGAAAATTTTGATGGCATCTGTTATTAACAAATCCTTCAGTAATTAA
AGGTGCCTTTTCTAATAAACGCCTTCGATTACCATCGTGGTATATTGAAGGCATTTTATAATAAA
AGACGCT
Found at i:2470917 original size:28 final size:29
Alignment explanation
Indices: 2470851--2470917 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
2470841 ATCTCGAAAG
*
2470851 TTTTT-ATATTTCATATATATTTTATAAA
1 TTTTTAATATTTCAAATATATTTTATAAA
* *
2470879 ATATTAA-ATTT-AAATAGTATTTT-TAAA
1 TTTTTAATATTTCAAATA-TATTTTATAAA
2470906 TTTTTAATATTT
1 TTTTTAATATTT
2470918 TATTCATTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
27 13 0.42
28 17 0.55
29 1 0.03
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (29 bp):
TTTTTAATATTTCAAATATATTTTATAAA
Found at i:2471403 original size:11 final size:11
Alignment explanation
Indices: 2471368--2471407 Score: 57
Period size: 11 Copynumber: 3.8 Consensus size: 11
2471358 AAAAATCAAT
2471368 TTTTTCTTTAA
1 TTTTTCTTTAA
*
2471379 TTATT-TTT-A
1 TTTTTCTTTAA
2471388 TTTTTCTTTAA
1 TTTTTCTTTAA
2471399 TTTTTCTTT
1 TTTTTCTTT
2471408 TTTTTATAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
9 5 0.20
10 6 0.24
11 14 0.56
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (11 bp):
TTTTTCTTTAA
Found at i:2471411 original size:20 final size:20
Alignment explanation
Indices: 2471367--2471412 Score: 67
Period size: 20 Copynumber: 2.3 Consensus size: 20
2471357 AAAAAATCAA
2471367 TTTTTTCTTTAATTATTTTT
1 TTTTTTCTTTAATTATTTTT
*
2471387 ATTTTTCTTTAATT-TTTCTT
1 TTTTTTCTTTAATTATTT-TT
2471407 TTTTTT
1 TTTTTT
2471413 ATAAATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
19 3 0.13
20 20 0.87
ACGTcount: A:0.13, C:0.07, G:0.00, T:0.80
Consensus pattern (20 bp):
TTTTTTCTTTAATTATTTTT
Found at i:2475378 original size:17 final size:16
Alignment explanation
Indices: 2475349--2475380 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
2475339 TATGTGTTTA
2475349 ATATAAAATAAATATT
1 ATATAAAATAAATATT
2475365 ATATAAATATAAATAT
1 ATATAAA-ATAAATAT
2475381 AACAAATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
ATATAAAATAAATATT
Found at i:2481050 original size:12 final size:12
Alignment explanation
Indices: 2481033--2481057 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2481023 AAAAATTAAC
2481033 AAAAATAAAATA
1 AAAAATAAAATA
2481045 AAAAATAAAATA
1 AAAAATAAAATA
2481057 A
1 A
2481058 CTATGTATTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (12 bp):
AAAAATAAAATA
Found at i:2482832 original size:2 final size:2
Alignment explanation
Indices: 2482825--2482865 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2482815 ACATAATTTT
2482825 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2482866 TATATATATA
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:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2484648 original size:2 final size:2
Alignment explanation
Indices: 2484641--2484667 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2484631 AATCAAACTT
2484641 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2484668 TTTACATGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2490476 original size:18 final size:17
Alignment explanation
Indices: 2490453--2490511 Score: 63
Period size: 18 Copynumber: 3.6 Consensus size: 17
2490443 TTTACTTATA
2490453 AATAAATAATATTATATT
1 AATAAATAATA-TATATT
*
2490471 AATAAATATTATACTATT
1 AATAAATAATATA-TATT
2490489 AAT--AT-A-ATATATT
1 AATAAATAATATATATT
2490502 AATAAATAAT
1 AATAAATAAT
2490512 GTTATAACGA
Statistics
Matches: 34, Mismatches: 2, Indels: 11
0.72 0.04 0.23
Matches are distributed among these distances:
13 7 0.21
14 3 0.09
15 2 0.06
16 3 0.09
17 2 0.06
18 17 0.50
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAAATAATATATATT
Found at i:2490480 original size:15 final size:15
Alignment explanation
Indices: 2490460--2490509 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
2490450 ATAAATAAAT
2490460 AATATTATATTAATA
1 AATATTATATTAATA
* *
2490475 AATATTATACTATTA
1 AATATTATATTAATA
*
2490490 ATATAATATATTAATA
1 A-ATATTATATTAATA
2490506 AATA
1 AATA
2490510 ATGTTATAAC
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
15 17 0.59
16 12 0.41
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATATTATATTAATA
Found at i:2491254 original size:18 final size:18
Alignment explanation
Indices: 2491208--2491254 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 18
2491198 TTTAACTAAT
2491208 TTTTATTGTGATTATTTTTC
1 TTTTATT-T-ATTATTTTTC
*
2491228 TTTTTTTTATTA-TTTTC
1 TTTTATTTATTATTTTTC
2491245 TTATTATTTA
1 TT-TTATTTA
2491255 AATAAATATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
17 7 0.29
18 10 0.42
19 1 0.04
20 6 0.25
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (18 bp):
TTTTATTTATTATTTTTC
Found at i:2491735 original size:25 final size:24
Alignment explanation
Indices: 2491707--2491766 Score: 77
Period size: 24 Copynumber: 2.5 Consensus size: 24
2491697 AATTTTAAAC
2491707 AAATAACAAAAAT-AAAATAAAATGG
1 AAATAA-AAAAATAAAAATAAAAT-G
*
2491732 AAATCAAAAAATAAAAATAAAATG
1 AAATAAAAAAATAAAAATAAAATG
*
2491756 AAATAAGAAAA
1 AAATAAAAAAA
2491767 GTAACCAAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.75, C:0.03, G:0.07, T:0.15
Consensus pattern (24 bp):
AAATAAAAAAATAAAAATAAAATG
Found at i:2493113 original size:34 final size:34
Alignment explanation
Indices: 2493073--2493151 Score: 104
Period size: 34 Copynumber: 2.3 Consensus size: 34
2493063 AGAAGCTATA
* *
2493073 AAACTTTAAATGGCCTTTCTGACCAAAGGTAATG
1 AAACTTTAAATAGCCTTTCTGACCAAAGATAATG
* * * *
2493107 AGACTTTTAATAGCTTTTCTGACCAGAGATAATG
1 AAACTTTAAATAGCCTTTCTGACCAAAGATAATG
2493141 AAACTTTAAAT
1 AAACTTTAAAT
2493152 TTAAAAATTT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (34 bp):
AAACTTTAAATAGCCTTTCTGACCAAAGATAATG
Found at i:2505492 original size:3 final size:3
Alignment explanation
Indices: 2505486--2505512 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2505476 CTTAGTAATA
2505486 ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
2505513 TTGTTTATCC
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:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Found at i:2505870 original size:22 final size:22
Alignment explanation
Indices: 2505840--2505884 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
2505830 TTCCTTTTAT
* *
2505840 CTCTTTCTCTAAAAGCCAGACC
1 CTCTCTCTCTAAAAGCCAAACC
2505862 CTCTCTCTCTAAAAGCCAAACC
1 CTCTCTCTCTAAAAGCCAAACC
2505884 C
1 C
2505885 CTCGTTGACC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.29, C:0.40, G:0.07, T:0.24
Consensus pattern (22 bp):
CTCTCTCTCTAAAAGCCAAACC
Found at i:2506510 original size:19 final size:19
Alignment explanation
Indices: 2506488--2506575 Score: 71
Period size: 19 Copynumber: 4.8 Consensus size: 19
2506478 AATTTCATTT
*
2506488 TTAATATTTTTATATTAAC
1 TTAATATTTTAATATTAAC
2506507 TTAATATTTTAATATTAA-
1 TTAATATTTTAATATTAAC
* * *
2506525 ATATTATTATTAAAATATAA-
1 TTAATATT-TTAATAT-TAAC
2506545 TT-ATATTTTAATA-TAA-
1 TTAATATTTTAATATTAAC
*
2506561 ATAAT-TTTTAATATT
1 TTAATATTTTAATATT
2506576 TTAATAGTTA
Statistics
Matches: 57, Mismatches: 8, Indels: 10
0.76 0.11 0.13
Matches are distributed among these distances:
16 12 0.21
17 3 0.05
18 11 0.19
19 27 0.47
20 4 0.07
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATATTTTAATATTAAC
Found at i:2506557 original size:16 final size:16
Alignment explanation
Indices: 2506510--2506574 Score: 60
Period size: 16 Copynumber: 3.8 Consensus size: 16
2506500 TATTAACTTA
2506510 ATATTTTAATATTAAAT
1 ATATTTTAATA-TAAAT
*
2506527 ATTATTATTAAAATATAATT
1 A-TATT-TT--AATATAAAT
2506547 ATATTTTAATATAAAT
1 ATATTTTAATATAAAT
2506563 A-ATTTTTAATAT
1 ATA-TTTTAATAT
2506575 TTTAATAGTT
Statistics
Matches: 41, Mismatches: 2, Indels: 11
0.76 0.04 0.20
Matches are distributed among these distances:
15 1 0.02
16 18 0.44
17 1 0.02
18 6 0.15
19 6 0.15
20 5 0.12
21 4 0.10
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (16 bp):
ATATTTTAATATAAAT
Found at i:2516636 original size:23 final size:22
Alignment explanation
Indices: 2516589--2516641 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
2516579 TATTTTAGAT
*
2516589 TTTTTTTATTTCATATTTATCA
1 TTTTTTTATTTCATATTGATCA
*
2516611 TTTTTTTATTT-ATTATCTGATTA
1 TTTTTTTATTTCA-TAT-TGATCA
2516634 TTTTTTTA
1 TTTTTTTA
2516642 AAAAAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 14 0.52
23 12 0.44
ACGTcount: A:0.21, C:0.06, G:0.02, T:0.72
Consensus pattern (22 bp):
TTTTTTTATTTCATATTGATCA
Found at i:2518684 original size:25 final size:26
Alignment explanation
Indices: 2518637--2518686 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 26
2518627 GCAAGATAAT
* *
2518637 CTTTTTTTTGGTATTTTATTTATTTA
1 CTTTTTTTTGGTATGTTAGTTATTTA
*
2518663 CTTTTTTTT-GTGTGTTAGTTATTT
1 CTTTTTTTTGGTATGTTAGTTATTT
2518687 TGAGGAGCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.12, C:0.04, G:0.12, T:0.72
Consensus pattern (26 bp):
CTTTTTTTTGGTATGTTAGTTATTTA
Found at i:2518814 original size:58 final size:58
Alignment explanation
Indices: 2518721--2519013 Score: 392
Period size: 58 Copynumber: 5.0 Consensus size: 58
2518711 TTTTTTGCAA
*
2518721 AAAAATAAAAATTTTCAAAGAGAAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAAT-AAAA-TTTCAAA-A-AAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
2518783 AAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* * * *
2518841 AAAAATCAAAATTTC-CAAAAATATTTTT-AGAAAAAAGTTGAAAGTATCAATTTTTCTT
1 AAAAAT-AAAATTTCAAAAAAAGATTTTTGAG-GAAAAGTTGAAAGTATCAATTTTCCTT
* * * *
2518899 AAAAATATAATTTCAAAAAAGGTTTTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTT
1 AAAAATAAAATTTCAAAAAAAG-ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
* ** *
2518958 AGAAATAAAATTTCAAAAATGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCC
2519014 CTACACAAAA
Statistics
Matches: 207, Mismatches: 19, Indels: 14
0.86 0.08 0.06
Matches are distributed among these distances:
57 9 0.04
58 122 0.59
59 58 0.28
60 8 0.04
61 4 0.02
62 6 0.03
ACGTcount: A:0.46, C:0.07, G:0.12, T:0.34
Consensus pattern (58 bp):
AAAAATAAAATTTCAAAAAAAGATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT
Found at i:2518984 original size:117 final size:116
Alignment explanation
Indices: 2518743--2519013 Score: 404
Period size: 117 Copynumber: 2.3 Consensus size: 116
2518733 TTTCAAAGAG
* *
2518743 AAATATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAGATT
1 AAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAGATT
2518808 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAA
66 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAA
* * * *
2518859 AAATATTTTT-AGAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATATAATTTCAAAAAAGGTT
1 AAATATTTTTAAG-AAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAG-A
* *
2518923 TTTTTGGGGAAAAGTTGAAAGTATCAATTTTCCTTAGAAAT-AAAATTT-CAA
64 TTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAA
*
2518974 AAATGGATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCC
1 AAAT--ATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCC
2519014 CTACACAAAA
Statistics
Matches: 141, Mismatches: 9, Indels: 9
0.89 0.06 0.06
Matches are distributed among these distances:
115 9 0.06
116 62 0.44
117 68 0.48
118 2 0.01
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (116 bp):
AAATATTTTTAAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAAATTTCAAAAAAAGATT
TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATCAAAATTTCCAA
Found at i:2520327 original size:159 final size:161
Alignment explanation
Indices: 2519861--2520435 Score: 639
Period size: 161 Copynumber: 3.6 Consensus size: 161
2519851 ATTTGGACAA
* * * *
2519861 ATTGTTCTATTTTAACAGTTTGAATAGCTCCAATACTTGATATTAAATTTGTTCGAATGATTGAA
1 ATTGTTCTATTTTAACAGTTTGAATAGCTTCAATACATGATATT-AACTTGTTCGAATAATTGAA
* * * * * *
2519926 CTTGATTTTCA-TAGTTGATATATGTGAAAAAGTTATCATTTACGTCTGTTTAAGACT-TTTTAT
65 CTTGGTTTCCACGA-TTGATATGTGTGAAAAAGTTATCGTTTACATCTGTTTAAGACTATTTTAT
* * *
2519989 GCTGTTAAGAGGCAAACATGCAAATTTGTTATT
129 GCTGTTAAAAGGCAAAAATGCAAATTTGATATT
* * *
2520022 ATTGTGCTATTTTAACAGTTTGCATAGCTTTAATACATGATATTAAACTTG-TCGTAATAATTGA
1 ATTGTTCTATTTTAACAGTTTGAATAGCTTCAATACATGATATT-AACTTGTTCG-AATAATTGA
* * * *
2520086 ACTTGGTTTCCAC-AGTTGATATGTGTAAAAAAGCTAACGTTTACATCTGTTTAGGAC-ATTTTA
64 ACTTGGTTTCCACGA-TTGATATGTGTGAAAAAGTTATCGTTTACATCTGTTTAAGACTATTTTA
* *
2520149 TGCTGTAAAAAAGGC-AAAATGCAAATTTGATGTT
128 TGCTGT-TAAAAGGCAAAAATGCAAATTTGATATT
* * *
2520183 ATTGTTCTATTATAACAATTT-AGATAGCTTCAATACATGATATT-ACTTGTTCGAATGATTGAA
1 ATTGTTCTATTTTAACAGTTTGA-ATAGCTTCAATACATGATATTAACTTGTTCGAATAATTGAA
* *
2520246 CTTGGTTTCTACGATTGATATGTGTGAAAAAGTTATCGTTTACATCTATTTAAGACTATTTT-TG
65 CTTGGTTTCCACGATTGATATGTGTGAAAAAGTTATCGTTTACATCTGTTTAAGACTATTTTATG
* * *
2520310 -TCGTTAATAGGCAAAAATACAAATTTGCTATT
130 CT-GTTAAAAGGCAAAAATGCAAATTTGATATT
** * * * * *
2520342 ATTAATCTATTTTAACAGTTTGGATGGCTTCAATACATGATATTTCATTTTTTCGAATAATTGAA
1 ATTGTTCTATTTTAACAGTTTGAATAGCTTCAATACATGATA-TTAACTTGTTCGAATAATTGAA
* * *
2520407 CTTAGTTTCCATGATTGATTTGTGTGAAA
65 CTTGGTTTCCACGATTGATATGTGTGAAA
2520436 GGCCTAAATG
Statistics
Matches: 350, Mismatches: 51, Indels: 26
0.82 0.12 0.06
Matches are distributed among these distances:
158 7 0.02
159 117 0.33
160 14 0.04
161 206 0.59
162 6 0.02
ACGTcount: A:0.32, C:0.11, G:0.15, T:0.41
Consensus pattern (161 bp):
ATTGTTCTATTTTAACAGTTTGAATAGCTTCAATACATGATATTAACTTGTTCGAATAATTGAAC
TTGGTTTCCACGATTGATATGTGTGAAAAAGTTATCGTTTACATCTGTTTAAGACTATTTTATGC
TGTTAAAAGGCAAAAATGCAAATTTGATATT
Found at i:2521650 original size:13 final size:13
Alignment explanation
Indices: 2521623--2521655 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
2521613 TAACGATAAT
*
2521623 AATAAA-TATAAA
1 AATAAATTAAAAA
2521635 AATAAATTAAAAA
1 AATAAATTAAAAA
2521648 AATAAATT
1 AATAAATT
2521656 TTTTAATTTC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 6 0.32
13 13 0.68
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (13 bp):
AATAAATTAAAAA
Found at i:2521777 original size:33 final size:34
Alignment explanation
Indices: 2521724--2521815 Score: 100
Period size: 33 Copynumber: 2.8 Consensus size: 34
2521714 TTGTGGCATA
*
2521724 AAACGCTA-CTAAATTTAGCAGTATTTTCCTATAC
1 AAACACTAGCTAAA-TTAGCAGTATTTTCCTATAC
* ** * *
2521758 AAACA-TCGCTAAATTAGCAGCGTTTTTCTATAT
1 AAACACTAGCTAAATTAGCAGTATTTTCCTATAC
2521791 AAACACTAG-TAAATTAGCAGTATTT
1 AAACACTAGCTAAATTAGCAGTATTT
2521816 GTATATACAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
33 36 0.77
34 11 0.23
ACGTcount: A:0.37, C:0.17, G:0.11, T:0.35
Consensus pattern (34 bp):
AAACACTAGCTAAATTAGCAGTATTTTCCTATAC
Found at i:2524646 original size:23 final size:23
Alignment explanation
Indices: 2524620--2524669 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
2524610 CATTAAGCAT
* *
2524620 AAATATATATTTTTATTTTT-TTA
1 AAATATATA-TATAATTTTTGTTA
*
2524643 AAATTTATATATAATTTTTGTTA
1 AAATATATATATAATTTTTGTTA
2524666 AAAT
1 AAAT
2524670 TTTAAGAGAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 8 0.35
23 15 0.65
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (23 bp):
AAATATATATATAATTTTTGTTA
Found at i:2529586 original size:17 final size:17
Alignment explanation
Indices: 2529566--2529603 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
2529556 TTATTGTATT
2529566 TAAATATTGTA-TTCAAA
1 TAAAT-TTGTATTTCAAA
*
2529583 TAAATTTTTATTTCAAA
1 TAAATTTGTATTTCAAA
2529600 TAAA
1 TAAA
2529604 AGATTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 4 0.21
17 15 0.79
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (17 bp):
TAAATTTGTATTTCAAA
Found at i:2531135 original size:2 final size:2
Alignment explanation
Indices: 2531128--2531160 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
2531118 TATGTGGGTG
*
2531128 TA TA TA TA TA TA TG 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 T
2531161 TAACATCATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2532635 original size:30 final size:29
Alignment explanation
Indices: 2532562--2532636 Score: 71
Period size: 30 Copynumber: 2.4 Consensus size: 29
2532552 AATTTTATTC
**
2532562 TAATAGATATAAACATTTAAATATACATGAA
1 TAATA-ATATAAA-ATTTAAATATACAAAAA
*
2532593 TATTAATAATAAAATTTAAA-ATAACAAAAA
1 TAATAAT-ATAAAATTTAAATAT-ACAAAAA
2532623 TAATATATATAAAA
1 TAATA-ATATAAAA
2532637 AAATTCCAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 7
0.77 0.08 0.15
Matches are distributed among these distances:
29 2 0.05
30 24 0.65
31 11 0.30
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (29 bp):
TAATAATATAAAATTTAAATATACAAAAA
Found at i:2533625 original size:3 final size:3
Alignment explanation
Indices: 2533608--2533641 Score: 50
Period size: 3 Copynumber: 11.3 Consensus size: 3
2533598 AAGAAAAAAA
* *
2533608 AAT AGT AAT AGT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
2533642 CAAAATGGTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2533881 original size:44 final size:44
Alignment explanation
Indices: 2533773--2534029 Score: 250
Period size: 44 Copynumber: 5.8 Consensus size: 44
2533763 AAAGGGCTCA
* * *
2533773 TCTAAACAGAGGTTCAACAACATTTTTGAAAATTTAAAAA-GTTTC
1 TCTAAACAGAGGCTCAACGAC--TTTTAAAAATTTAAAAAGGTTTC
* ** * * * * *
2533818 TCTGAGTAAAAGTTTAACGACTTTTAAAAATTAAAAAAGGTTTC
1 TCTAAACAGAGGCTCAACGACTTTTAAAAATTTAAAAAGGTTTC
*
2533862 TCTAAACAGAGGCTCAACGACTTTTAAAAATTTAAAGAGG-TTC
1 TCTAAACAGAGGCTCAACGACTTTTAAAAATTTAAAAAGGTTTC
* * *
2533905 TTCTAAGCAGAGGCTCAACGACTTTTGAAAATTTTAAAAA-GTTTT
1 -TCTAAACAGAGGCTCAACGACTTTT-AAAAATTTAAAAAGGTTTC
* * * * *
2533950 TCTAAGCAGAGACTCAATGACTTTTAAAAATTTAAAAAGGCTCC
1 TCTAAACAGAGGCTCAACGACTTTTAAAAATTTAAAAAGGTTTC
* * *
2533994 TCTAAATAGAGGCTCAACAACTTTTGAAAATTTAAA
1 TCTAAACAGAGGCTCAACGACTTTTAAAAATTTAAA
2534030 GAGGCTCATC
Statistics
Matches: 173, Mismatches: 34, Indels: 11
0.79 0.16 0.05
Matches are distributed among these distances:
43 30 0.17
44 116 0.67
45 27 0.16
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.32
Consensus pattern (44 bp):
TCTAAACAGAGGCTCAACGACTTTTAAAAATTTAAAAAGGTTTC
Found at i:2533946 original size:132 final size:131
Alignment explanation
Indices: 2533760--2534061 Score: 374
Period size: 132 Copynumber: 2.3 Consensus size: 131
2533750 AATCTTTTTT
* * *
2533760 TTTAAAG-GGCTCATCTAAACAGAGGTTCAACAACATTTTTGAAAATTTAAAAAGTTTCTCTGAG
1 TTTAAAGAGGCTCATCTAAGCAGAGGCTCAACAAC--TTTTGAAAATTTAAAAAGTTTCTCTAAG
* * * * *
2533824 TAAAAG-TTTAACGACTTTTAAAAATTAAAAAAGGTTTCTCTAAACAGAGGCTCAACGACTTTTA
64 -AAAAGACTCAACGACTTTTAAAAATTAAAAAAGGCTCCTCTAAACAGAGGCTCAACAACTTTTA
2533888 AAAA
128 AAAA
* * * * *
2533892 TTTAAAGAGGTTCTTCTAAGCAGAGGCTCAACGACTTTTGAAAATTTTAAAAAGTTTTTCTAAGC
1 TTTAAAGAGGCTCATCTAAGCAGAGGCTCAACAACTTTTGAAAA-TTTAAAAAGTTTCTCTAAGA
* * * * *
2533957 AGAGACTCAATGACTTTTAAAAATTTAAAAAGGCTCCTCTAAATAGAGGCTCAACAACTTTTGAA
65 AAAGACTCAACGACTTTTAAAAATTAAAAAAGGCTCCTCTAAACAGAGGCTCAACAACTTTTAAA
2534022 AA
130 AA
* *
2534024 TTTAAAGAGGCTCATCTAAGTAAAGGCTCAACAACTTT
1 TTTAAAGAGGCTCATCTAAGCAGAGGCTCAACAACTTT
2534062 AAAAATCCAT
Statistics
Matches: 144, Mismatches: 23, Indels: 6
0.83 0.13 0.03
Matches are distributed among these distances:
131 12 0.08
132 110 0.76
133 22 0.15
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (131 bp):
TTTAAAGAGGCTCATCTAAGCAGAGGCTCAACAACTTTTGAAAATTTAAAAAGTTTCTCTAAGAA
AAGACTCAACGACTTTTAAAAATTAAAAAAGGCTCCTCTAAACAGAGGCTCAACAACTTTTAAAA
A
Found at i:2534035 original size:44 final size:44
Alignment explanation
Indices: 2533833--2534067 Score: 249
Period size: 44 Copynumber: 5.4 Consensus size: 44
2533823 GTAAAAGTTT
* * * *
2533833 AACGACTTTTAAAAATTAAAAAAGGTTTCTCTAAACAGAGGCTC
1 AACGACTTTTAAAAATTTAAAGAGGTTCCTCTAAGCAGAGGCTC
*
2533877 AACGACTTTTAAAAATTTAAAGAGGTTCTTCTAAGCAGAGGCTC
1 AACGACTTTTAAAAATTTAAAGAGGTTCCTCTAAGCAGAGGCTC
* * ** *
2533921 AACGACTTTTGAAAATTTTAAA-AAGTTTTTCTAAGCAGAGACTC
1 AACGACTTTT-AAAAATTTAAAGAGGTTCCTCTAAGCAGAGGCTC
* * * **
2533965 AATGACTTTTAAAAATTTAAAAAGGCTCCTCTAAATAGAGGCTC
1 AACGACTTTTAAAAATTTAAAGAGGTTCCTCTAAGCAGAGGCTC
* * * * * *
2534009 AACAACTTTTGAAAATTTAAAGAGGCTCATCTAAGTAAAGGCTC
1 AACGACTTTTAAAAATTTAAAGAGGTTCCTCTAAGCAGAGGCTC
*
2534053 AACAAC-TTTAAAAAT
1 AACGACTTTTAAAAAT
2534068 CCATCCTGAA
Statistics
Matches: 163, Mismatches: 26, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
43 18 0.11
44 135 0.83
45 10 0.06
ACGTcount: A:0.41, C:0.15, G:0.14, T:0.29
Consensus pattern (44 bp):
AACGACTTTTAAAAATTTAAAGAGGTTCCTCTAAGCAGAGGCTC
Found at i:2534146 original size:47 final size:47
Alignment explanation
Indices: 2534033--2534160 Score: 166
Period size: 47 Copynumber: 2.7 Consensus size: 47
2534023 ATTTAAAGAG
*
2534033 GCTCATCTAAGTAAAGGCTCAACAACTTTAAAAATCCATCCTGAAAAA
1 GCTCATCTAAGTAAAGGCTCAACAA-TTTTAAAATCCATCCTGAAAAA
* * * *
2534081 GCTCATCAAAGTAAAGGCTCAACAATTTTAAACTTCATCTTGAAAAA
1 GCTCATCTAAGTAAAGGCTCAACAATTTTAAAATCCATCCTGAAAAA
* * * *
2534128 GCTCTTCTAAGCAGAGGCTCAATAATTTTAAAA
1 GCTCATCTAAGTAAAGGCTCAACAATTTTAAAA
2534161 ATACATAAAC
Statistics
Matches: 69, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
47 45 0.65
48 24 0.35
ACGTcount: A:0.41, C:0.20, G:0.12, T:0.27
Consensus pattern (47 bp):
GCTCATCTAAGTAAAGGCTCAACAATTTTAAAATCCATCCTGAAAAA
Found at i:2534178 original size:78 final size:78
Alignment explanation
Indices: 2534095--2534240 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 78
2534085 ATCAAAGTAA
* * *
2534095 AGGCTCAACAATTTTAAACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATAATTTTAAA
1 AGGCTCAACAACTCTAAACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAATTTTAAA
2534160 AATACATAAACAG
66 AATACATAAACAG
*
2534173 AGGCTCAACAACTCTAAACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACGATTTTAAA
1 AGGCTCAACAACTCTAAACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAATTTTAAA
2534238 AAT
66 AAT
2534241 TTTATCTTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
78 64 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.27
Consensus pattern (78 bp):
AGGCTCAACAACTCTAAACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACAATTTTAAA
AATACATAAACAG
Found at i:2534255 original size:49 final size:49
Alignment explanation
Indices: 2534170--2534289 Score: 136
Period size: 49 Copynumber: 2.5 Consensus size: 49
2534160 AATACATAAA
* * * * * *
2534170 CAGAGGCTCAACAACTCT--AAACTTCATCTTGAAAAAGCTCTTCTAAG
1 CAGAGGCTCAACAATTTTAAAAATTTTATCTTGAAAAAGCACCTCTAAG
*
2534217 CAGAGGCTCAACGATTTTAAAAATTTTATCTTGAAAAAGCACCTCTAAG
1 CAGAGGCTCAACAATTTTAAAAATTTTATCTTGAAAAAGCACCTCTAAG
* * *
2534266 TAGAGGTTCAATAATTTTAAAAAT
1 CAGAGGCTCAACAATTTTAAAAAT
2534290 CTCATATGTT
Statistics
Matches: 60, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 15 0.25
49 45 0.75
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (49 bp):
CAGAGGCTCAACAATTTTAAAAATTTTATCTTGAAAAAGCACCTCTAAG
Found at i:2534277 original size:127 final size:126
Alignment explanation
Indices: 2534047--2534289 Score: 326
Period size: 127 Copynumber: 1.9 Consensus size: 126
2534037 ATCTAAGTAA
* *
2534047 AGGCTCAACAACTTTAAAAATCCATCCTGAAAAAGCTCATCAAAGTAAAGGCTCAACAATTTTAA
1 AGGCTCAACAACTCTAAAAATCCATCCTGAAAAAGCTCATCAAAGCAAAGGCTCAACAATTTTAA
* *
2534112 ACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAATAATTTTAAAAATACATAAACAG
66 ACTTCATCTTGAAAAAGCACCTCTAAGCAGAGGCTCAATAATTTTAAAAATACATAAACAG
* * * * * * *
2534173 AGGCTCAACAACTCT-AAACTTCATCTTGAAAAAGCTCTTCTAAGCAGAGGCTCAACGATTTTAA
1 AGGCTCAACAACTCTAAAAATCCATCCTGAAAAAGCTCATCAAAGCAAAGGCTCAACAATTTT--
* * * *
2534237 AAATTTTATCTTGAAAAAGCACCTCTAAGTAGAGGTTCAATAATTTTAAAAAT
64 AAACTTCATCTTGAAAAAGCACCTCTAAGCAGAGGCTCAATAATTTTAAAAAT
2534290 CTCATATGTT
Statistics
Matches: 100, Mismatches: 15, Indels: 3
0.85 0.13 0.03
Matches are distributed among these distances:
125 39 0.39
126 14 0.14
127 47 0.47
ACGTcount: A:0.42, C:0.19, G:0.12, T:0.28
Consensus pattern (126 bp):
AGGCTCAACAACTCTAAAAATCCATCCTGAAAAAGCTCATCAAAGCAAAGGCTCAACAATTTTAA
ACTTCATCTTGAAAAAGCACCTCTAAGCAGAGGCTCAATAATTTTAAAAATACATAAACAG
Found at i:2534749 original size:75 final size:74
Alignment explanation
Indices: 2534618--2534770 Score: 245
Period size: 75 Copynumber: 2.1 Consensus size: 74
2534608 TTAACAAAAG
* *
2534618 TTTTCTTCTTTAAAAGTCTGTAACATTAATGTCTTGTCATGCTTTTTTCATATTTTTTCATCTGT
1 TTTTCTTCTTTAAAAGTCTGCAACATTAATGTCTTGTCATGCTTTTTTCATATTTTTT-ATCTGC
2534683 CTTTGTCAAA
65 CTTTGTCAAA
*
2534693 TTTTCTTCTTTAAAAGTCTGCAACATTAATGTCTTGTC-TGCTTTTTTCATATTTTTTTATTTGC
1 TTTTCTTCTTTAAAAGTCTGCAACATTAATGTCTTGTCATGCTTTTTTCATA-TTTTTTATCTGC
*
2534757 CTTTGTCAAC
65 CTTTGTCAAA
2534767 TTTT
1 TTTT
2534771 AAAAAGTAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
74 30 0.41
75 43 0.59
ACGTcount: A:0.20, C:0.16, G:0.09, T:0.55
Consensus pattern (74 bp):
TTTTCTTCTTTAAAAGTCTGCAACATTAATGTCTTGTCATGCTTTTTTCATATTTTTTATCTGCC
TTTGTCAAA
Found at i:2545511 original size:18 final size:17
Alignment explanation
Indices: 2545484--2545528 Score: 63
Period size: 18 Copynumber: 2.5 Consensus size: 17
2545474 GCATGTAAAA
2545484 ATTTTCTTTTCATTTTTG
1 ATTTT-TTTTCATTTTTG
*
2545502 ATTTGTTTTTTATTTTTG
1 ATTT-TTTTTCATTTTTG
2545520 ATTTTTTTT
1 ATTTTTTTT
2545529 AAAAGGAATC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 19 0.76
19 1 0.04
ACGTcount: A:0.11, C:0.04, G:0.07, T:0.78
Consensus pattern (17 bp):
ATTTTTTTTCATTTTTG
Found at i:2548198 original size:3 final size:3
Alignment explanation
Indices: 2548192--2548230 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
2548182 AGAAAAAAAT
2548192 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2548231 TACAAAATGG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2553112 original size:11 final size:11
Alignment explanation
Indices: 2553096--2553147 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
2553086 TGATCGTAAA
2553096 ATATTATATTT
1 ATATTATATTT
2553107 ATATTATATTTT
1 ATATTATA-TTT
* * *
2553119 ATATAAAAATT
1 ATATTATATTT
*
2553130 ATATCATAATTT
1 ATATTAT-ATTT
2553142 ATATTA
1 ATATTA
2553148 ATATAAAAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
11 15 0.47
12 17 0.53
ACGTcount: A:0.44, C:0.02, G:0.00, T:0.54
Consensus pattern (11 bp):
ATATTATATTT
Found at i:2553169 original size:30 final size:30
Alignment explanation
Indices: 2553110--2553171 Score: 74
Period size: 30 Copynumber: 2.1 Consensus size: 30
2553100 TATATTTATA
* *
2553110 TTATATTTTATATAAAAATTATATCATAAT
1 TTATATTTAATATAAAAATTAAATCATAAT
2553140 TTATA-TTAATATAAAAATATAAAAT-ATAAT
1 TTATATTTAATATAAAAAT-T-AAATCATAAT
2553170 TT
1 TT
2553172 TTTAATTTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 12 0.43
30 13 0.46
31 3 0.11
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (30 bp):
TTATATTTAATATAAAAATTAAATCATAAT
Found at i:2553176 original size:28 final size:27
Alignment explanation
Indices: 2553115--2553177 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
2553105 TTATATTATA
*
2553115 TTTT-ATATAAAAATTATATCATAATT
1 TTTTAATATAAAAATTAAATCATAATT
2553141 TATATTAATATAAAAATATAAAAT-ATAATT
1 T-T-TTAATATAAAAAT-T-AAATCATAATT
2553171 TTTTAAT
1 TTTTAAT
2553178 TTTATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
26 1 0.03
27 1 0.03
28 7 0.23
29 11 0.35
30 8 0.26
31 3 0.10
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (27 bp):
TTTTAATATAAAAATTAAATCATAATT
Found at i:2553205 original size:20 final size:18
Alignment explanation
Indices: 2553167--2553206 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 18
2553157 TATAAAATAT
2553167 AATTTTTTAATTTTATTA
1 AATTTTTTAATTTTATTA
*
2553185 AATTTATTTATATTTTTTTA
1 AATTT-TTTA-ATTTTATTA
2553205 AA
1 AA
2553207 AATTTTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 5 0.26
19 4 0.21
20 10 0.53
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
AATTTTTTAATTTTATTA
Found at i:2553227 original size:24 final size:25
Alignment explanation
Indices: 2553192--2553252 Score: 72
Period size: 24 Copynumber: 2.5 Consensus size: 25
2553182 TTAAATTTAT
*
2553192 TTATATTTTTTTAAAAATTTTA-AA
1 TTATATTATTTTAAAAATTTTATAA
* * *
2553216 TTATATTATTTT-TACATTTTATAT
1 TTATATTATTTTAAAAATTTTATAA
2553240 TTATATTATTTTA
1 TTATATTATTTTA
2553253 TTATATCATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
23 7 0.23
24 24 0.77
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (25 bp):
TTATATTATTTTAAAAATTTTATAA
Found at i:2554018 original size:29 final size:29
Alignment explanation
Indices: 2553985--2554051 Score: 80
Period size: 29 Copynumber: 2.3 Consensus size: 29
2553975 AAGCAATCAC
* *
2553985 ACTTCTTTTCTAAAATTTAATAATTATAT
1 ACTTCTTTTCTAAAATCTAATAATTATAA
* * *
2554014 ACTTCCTTTGTAAAGTCTAATAATTATAA
1 ACTTCTTTTCTAAAATCTAATAATTATAA
*
2554043 ACTTTTTTT
1 ACTTCTTTT
2554052 TTCATCTTTT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.34, C:0.12, G:0.03, T:0.51
Consensus pattern (29 bp):
ACTTCTTTTCTAAAATCTAATAATTATAA
Found at i:2554198 original size:21 final size:21
Alignment explanation
Indices: 2554153--2554198 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
2554143 AATAAATGAT
*
2554153 TATTTTTTATACTTTTAAATT
1 TATTTTTTATACTTTTAAATA
2554174 TATTTATTTA-ACTTTTTAAA-A
1 TATTT-TTTATAC-TTTTAAATA
2554195 TATT
1 TATT
2554199 ACATATTTAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (21 bp):
TATTTTTTATACTTTTAAATA
Found at i:2554229 original size:32 final size:32
Alignment explanation
Indices: 2554171--2554231 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
2554161 ATACTTTTAA
* * *
2554171 ATTTATTTATTTAACTTTTTAAAATATTACAT
1 ATTTATTTATATAAATTATTAAAATATTACAT
2554203 ATTTATTT-TATAAATTATTAATAATATTA
1 ATTTATTTATATAAATTATTAA-AATATTA
2554232 TTACGTATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 10 0.40
32 15 0.60
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (32 bp):
ATTTATTTATATAAATTATTAAAATATTACAT
Found at i:2558033 original size:14 final size:15
Alignment explanation
Indices: 2558005--2558035 Score: 55
Period size: 14 Copynumber: 2.1 Consensus size: 15
2557995 TTGATCTGAA
2558005 TAAAATATATATAAT
1 TAAAATATATATAAT
2558020 TAAAATAT-TATAAT
1 TAAAATATATATAAT
2558034 TA
1 TA
2558036 TATAAATATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.50
15 8 0.50
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (15 bp):
TAAAATATATATAAT
Found at i:2560878 original size:3 final size:3
Alignment explanation
Indices: 2560872--2560896 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
2560862 GATAGAATTC
2560872 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
2560897 CAAATCCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2561704 original size:15 final size:15
Alignment explanation
Indices: 2561686--2561733 Score: 69
Period size: 15 Copynumber: 3.2 Consensus size: 15
2561676 TTTTTTTCTA
* *
2561686 TGATTTGGTTTTTTG
1 TGATTTGATTTCTTG
2561701 TGATTTGATTTCTTG
1 TGATTTGATTTCTTG
*
2561716 TGGTTTGATTTCTTG
1 TGATTTGATTTCTTG
2561731 TGA
1 TGA
2561734 CTTTCCTTTT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.10, C:0.04, G:0.25, T:0.60
Consensus pattern (15 bp):
TGATTTGATTTCTTG
Found at i:2561929 original size:6 final size:6
Alignment explanation
Indices: 2561897--2562013 Score: 69
Period size: 6 Copynumber: 19.2 Consensus size: 6
2561887 ATTGTTGACC
* * * * *
2561897 AAAATT AAAAAT AAAATC ACAATTT AAAATT AAAATCC AAAATT AAACTT
1 AAAATT AAAATT AAAATT A-AAATT AAAATT AAAAT-T AAAATT AAAATT
* * * * *
2561947 GAAAA-T AGAATT AAATTT TAAA-T AAAAGTT CAAAA-T AAAATT AACATC
1 -AAAATT AAAATT AAAATT AAAATT AAAA-TT -AAAATT AAAATT AAAATT
*
2561995 AACATT AAAATT AAAATT A
1 AAAATT AAAATT AAAATT A
2562014 TGGGCTTTTA
Statistics
Matches: 83, Mismatches: 20, Indels: 16
0.70 0.17 0.13
Matches are distributed among these distances:
5 11 0.13
6 55 0.66
7 13 0.16
8 4 0.05
ACGTcount: A:0.61, C:0.08, G:0.03, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:2561942 original size:19 final size:19
Alignment explanation
Indices: 2561895--2561943 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2561885 GGATTGTTGA
2561895 CCAAAATTAAAAATAAAAT
1 CCAAAATTAAAAATAAAAT
* *
2561914 -CACAATTTAAAATTAAAAT
1 CCA-AAATTAAAAATAAAAT
2561933 CCAAAATTAAA
1 CCAAAATTAAA
2561944 CTTGAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
18 2 0.08
19 21 0.84
20 2 0.08
ACGTcount: A:0.63, C:0.12, G:0.00, T:0.24
Consensus pattern (19 bp):
CCAAAATTAAAAATAAAAT
Found at i:2565469 original size:113 final size:122
Alignment explanation
Indices: 2565316--2565592 Score: 315
Period size: 123 Copynumber: 2.3 Consensus size: 122
2565306 TTTTTTTTGG
*
2565316 AATA-TTTTAATAAAATCACCACTTGTGATTTTATTGTTTT-G-AAT-AT-TTCTTGTT-TG-AA
1 AATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTTTGGTAATAATATT-TTGTTATGTAA
*
2565374 AAAAA-AT-CTAAAATATTGCTAACAATTTTAGAACAGTTTAGAAAATTTCTTTG-TA
65 AAAAATATCCTAAAATATTGCTAACAATTTTAGAACAGTTTAGAAAATTCCTTTGATA
* * *
2565429 AA-ATTTTTATTTAAATCACCACTTGTGATTTTATTTTTTTGGTTAATAATATTTTTTTATGTTT
1 AATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTTTGG-TAATAATATTTTGTTATG--T
* * * * * *
2565493 AAAAAAATTTCCTAAAATATTTCTAACACTTTTAGAATATTTTAGGAAATTCCTTTGTATA
63 AAAAAAATATCCTAAAATATTGCTAACAATTTTAGAACAGTTTAGAAAATTCCTTTG-ATA
* *
2565554 AATATTTTTAATAAAAACACCATTTGTGATTTTATTTTT
1 AATATTTTTAATAAAATCACCACTTGTGATTTTATTTTT
2565593 ATCAAATTTT
Statistics
Matches: 134, Mismatches: 15, Indels: 17
0.81 0.09 0.10
Matches are distributed among these distances:
112 1 0.01
113 35 0.26
114 1 0.01
116 3 0.02
117 6 0.04
118 4 0.03
121 7 0.05
122 1 0.01
123 40 0.30
125 4 0.03
126 32 0.24
ACGTcount: A:0.36, C:0.09, G:0.08, T:0.48
Consensus pattern (122 bp):
AATATTTTTAATAAAATCACCACTTGTGATTTTATTTTTTTGGTAATAATATTTTGTTATGTAAA
AAAATATCCTAAAATATTGCTAACAATTTTAGAACAGTTTAGAAAATTCCTTTGATA
Found at i:2565746 original size:11 final size:11
Alignment explanation
Indices: 2565728--2565813 Score: 61
Period size: 11 Copynumber: 7.8 Consensus size: 11
2565718 TGAAAATTTT
2565728 ATAAAAAAATA
1 ATAAAAAAATA
2565739 A-AATAAAAATA
1 ATAA-AAAAATA
*
2565750 ATAAAAAAATC
1 ATAAAAAAATA
*
2565761 ATAAATTAAATA
1 ATAAA-AAAATA
* *
2565773 ATAGAAATAT-
1 ATAAAAAAATA
*
2565783 ATAAAAAATTGA
1 ATAAAAAAAT-A
**
2565795 GCAAAAAAATA
1 ATAAAAAAATA
2565806 A-AAAAAAA
1 ATAAAAAAA
2565814 GTTATGATGA
Statistics
Matches: 57, Mismatches: 13, Indels: 11
0.70 0.16 0.14
Matches are distributed among these distances:
10 16 0.28
11 24 0.42
12 17 0.30
ACGTcount: A:0.74, C:0.02, G:0.03, T:0.20
Consensus pattern (11 bp):
ATAAAAAAATA
Found at i:2566701 original size:8 final size:8
Alignment explanation
Indices: 2566685--2566722 Score: 51
Period size: 8 Copynumber: 4.9 Consensus size: 8
2566675 TCAAATAGAT
2566685 AAAAAAAG
1 AAAAAAAG
*
2566693 AAAAGAAG
1 AAAAAAAG
*
2566701 -AAAAGAG
1 AAAAAAAG
2566708 AAAAAAAG
1 AAAAAAAG
2566716 AAAAAAA
1 AAAAAAA
2566723 ATATAATAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
7 5 0.20
8 20 0.80
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (8 bp):
AAAAAAAG
Found at i:2566709 original size:15 final size:15
Alignment explanation
Indices: 2566686--2566721 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
2566676 CAAATAGATA
*
2566686 AAAAAAGAAAAGAAG
1 AAAAAAGAAAAAAAG
*
2566701 AAAAGAGAAAAAAAG
1 AAAAAAGAAAAAAAG
2566716 AAAAAA
1 AAAAAA
2566722 AATATAATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (15 bp):
AAAAAAGAAAAAAAG
Found at i:2566753 original size:3 final size:3
Alignment explanation
Indices: 2566747--2566784 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2566737 GTAGTCGTAG
2566747 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
2566785 CAAAATGAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:2572752 original size:21 final size:19
Alignment explanation
Indices: 2572712--2572764 Score: 63
Period size: 21 Copynumber: 2.7 Consensus size: 19
2572702 ATAGGATTAC
2572712 TCTAACTTTTCTTTTCTTT
1 TCTAACTTTTCTTTTCTTT
* *
2572731 TCTCACTTTTACTTTTTTTTT
1 TCTAACTTTT-C-TTTTCTTT
2572752 TCTAAC-TTTCTTT
1 TCTAACTTTTCTTT
2572765 AAAGCATCTA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
18 3 0.10
19 10 0.34
20 4 0.14
21 12 0.41
ACGTcount: A:0.11, C:0.21, G:0.00, T:0.68
Consensus pattern (19 bp):
TCTAACTTTTCTTTTCTTT
Found at i:2584092 original size:356 final size:356
Alignment explanation
Indices: 2583132--2585003 Score: 2443
Period size: 357 Copynumber: 5.2 Consensus size: 356
2583122 ATATAGGTGT
* * **
2583132 TTACTGAAGGC-GATTGCAGATAACAATGTCTTCAATAATTTCCCTAAAAAGCTTTTTTTAGATT
1 TTACTGAAGGCAG-TTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAA-AATTTTTTAGATT
* * * *
2583196 ATTAAAGGCATCTTTTATTATGACACACCTTCCATATACGACGATGGTAATGGAAGGTGTTTATT
64 ATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCGTTTATT
* * * *
2583261 AGAAAA-AGCACCTTCAATATATCTTTAAACTTAGTAATCCATTA-TAGAAGGCATTAGTTAATA
129 AGAAAAGA-CGCCTTCAATATACCTTTAAACTTAGTAATCCATTACT-GAAGGCGTTTGTTAATA
* * * * ** *
2583324 ACAAACACTTTCAAAATTTTCCCACTAAAAATTTGGAGAATTATTAAAGGCATCTTCTATTGTAA
192 ACAGACGCCTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAA
*
2583389 AATACCTTCTATATACCGCCACATAAATTCTAACACTGTTATT-AAAGGCATATATCCAAGAAAG
257 AATACCTTCTATATACCGTCACATAAATTCTAACACTGTTATTGAAA-GCATATATCCAAGAAAG
2583453 ATGCCTTTAATAATTTCTATCACAGTTTGTATATAA
321 ATGCCTTTAATAATTTCTATCACAGTTTGTATATAA
* * **
2583489 TTACTGAAGGCAATTGCAGATAACAATGCCTTCAATAATTTTCATAAAAAAAATTTCCTAGATTA
1 TTACTGAAGGCAGTTGCAGATAACAATGCCTTCAATAATTTTCCT-AAAAAAATTTTTTAGATTA
* ** *
2583554 TTAAAGGCGTCTTTTATTATGACACGCCTTCAATATACGATAATAGTAATAGAAGGCGTTTATTA
65 TTAAAGGCATCTTTTATTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCGTTTATTA
* * *
2583619 GAAAAGATGCCTTCAATATACATTTAAACTTAGTAATCCATTACTGAAGGCGTTTGCTAATAACA
130 GAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACA
* * *
2583684 GACACCTTCAAAATTTT-TCCACTAAAAATTTTAAAAATTATTAAAAGCATCTTCTACTGTAAAA
195 GACGCCTTCAAAATTTTCT-CACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAA
* * *
2583748 TACATTTTATATACCGTCACATAAATTCTAACACTGTTATTAAAAGCATATATCCAAGAAAGATG
259 TACCTTCTATATACCGTCACATAAATTCTAACACTGTTATTGAAAGCATATATCCAAGAAAGATG
*
2583813 CCTTTAATAATTTCTATCACAGTTTATATATAA
324 CCTTTAATAATTTCTATCACAGTTTGTATATAA
* * * * *
2583846 TTACTGAAGGCTGTTGCATATAACAACGCCTTCAATAATTTTCCT-AAAAGATTTTTTCGGATTA
1 TTACTGAAGGCAGTTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAAATTTTTT-AGATTA
* * * * * * **
2583910 TTAAATGCGTCTTTTATTATGACATGCCTTCAATATACAACGATGGTAATGGAAAGCGTTTAGCA
65 TTAAAGGCATCTTTTATTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCGTTTATTA
* *
2583975 GAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACCGAAGGCGTTTGTTAATAACG
130 GAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACA
* *
2584040 GACGTCTTCAAAATTTTTTCACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAAT
195 GACGCCTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAAT
* * * *
2584105 ACCTTCTATATACTGTCACATAAATTCTAACACTATTATTGAATGCATATACCCAAGAAAGATGC
260 ACCTTCTATATACCGTCACATAAATTCTAACACTGTTATTGAAAGCATATATCCAAGAAAGATGC
* *
2584170 CTTTAATAATTTCTATCACAATTTGAATATAA
325 CTTTAATAATTTCTATCACAGTTTGTATATAA
* * * *
2584202 TTACTGAAGG-TGATTACAGATAACAATGCCTTTAATAATTTCCCTAAAAAAATTTTCTTAGATT
1 TTACTGAAGGCAG-TTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAAATTTT-TTAGATT
* * * *
2584266 ATTAAAGGCGTCTTTTAGTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCATTTTTT
64 ATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCGTTTATT
* ** *
2584331 AAAAAAGGTGCCTTCAATATACTTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAAC
129 AGAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAAC
* * * *
2584396 AGACGCCTTCAAAATTTTCTCACTAAAAATTTTAAAAATTATTAAAGGCGTTTTTTACTGTAAAA
194 AGACGCCTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAA
* * * * *
2584461 TACCTTCTATATACCATCACACAAATTCTAACACTATTATTGAAAGCGTATATCCAAGGAAGATG
259 TACCTTCTATATACCGTCACATAAATTCTAACACTGTTATTGAAAGCATATATCCAAGAAAGATG
*
2584526 CCTTTAATAATTTCTATCACAGTTTGTAGATAA
324 CCTTTAATAATTTCTATCACAGTTTGTATATAA
* * * *
2584559 TTACTTTAAGGCAGTAGTAGATAACAATGCCCTT-AATAA-TTTCCTTAAAAAAATATTTTTGGA
1 TTAC-TGAAGGCAGTTGCAGATAACAATG-CCTTCAATAATTTTCC-TAAAAAAAT-TTTTTAGA
* * * * * *
2584622 TTATTAAACGCATATTTTATTATGACACACCTTCAATATATGACGATGGTAATAGAAAGTGTTTA
62 TTATTAAAGGCATCTTTTATTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCGTTTA
* * *
2584687 TTAGAAAAAAGGTACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCATTTGTTAA
127 TTAGAAAAGACG--CCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAA
* * * ***
2584752 TAACAGACGCCTTCAGAATTTTCTCACTAAAAATTTT-GGCAACTATTAAAGTTGTCTTCTACTG
190 TAACAGACGCCTTCAAAATTTTCTCACTAAAAATTTTAAG-AATTATTAAAGGCATCTTCTACTG
* *** * * *
2584816 TAAATTACCTTCTATATACTACCACATAAATTCTAACACTGTTATTGAAGGCGTATATCCAAGGA
254 TAAAATACCTTCTATATACCGTCACATAAATTCTAACACTGTTATTGAAAGCATATATCCAAGAA
** * * *
2584881 AGACACCTTTAATAA-TTCTTACCATAGTTTGTAGATAA
319 AGATGCCTTTAATAATTTC-TATCACAGTTTGTATATAA
* * *
2584919 TTATTGAAGGCGGTTGCAGATAACAACGCCTTCAATAATTTTCCTAAAAAAATTTTTTTAGATTA
1 TTACTGAAGGCAGTTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAAA-TTTTTTAGATTA
2584984 TTAAAGGCATCTTTTATTAT
65 TTAAAGGCATCTTTTATTAT
2585004 AAAACACTTT
Statistics
Matches: 1330, Mismatches: 162, Indels: 44
0.87 0.11 0.03
Matches are distributed among these distances:
355 11 0.01
356 303 0.23
357 629 0.47
358 114 0.09
359 71 0.05
360 202 0.15
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (356 bp):
TTACTGAAGGCAGTTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAAATTTTTTAGATTAT
TAAAGGCATCTTTTATTATGACACGCCTTCAATATACGACGATGGTAATAGAAGGCGTTTATTAG
AAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCGTTTGTTAATAACAG
ACGCCTTCAAAATTTTCTCACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAATA
CCTTCTATATACCGTCACATAAATTCTAACACTGTTATTGAAAGCATATATCCAAGAAAGATGCC
TTTAATAATTTCTATCACAGTTTGTATATAA
Found at i:2584114 original size:713 final size:710
Alignment explanation
Indices: 2583132--2585003 Score: 2613
Period size: 713 Copynumber: 2.6 Consensus size: 710
2583122 ATATAGGTGT
* * * *
2583132 TTACTGAAGGCGATTGCAGATAACAATGTCTTCAATAATTTCCCTAAAAAGCTTTTTTTAGATTA
1 TTACTGAAGGCG-TTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAG-ATTTTTTGGATTA
* * *
2583197 TTAAAGGCATCTTTTATTATGACACACCTTCCATATACGACGATGGTAATGGAAGGTGTTTATTA
64 TTAAACGCATCTTTTATTATGACACACCTTCAATATACGACGATGGTAATGGAAAGTGTTTATTA
* * * *
2583262 GAAAAAGCACCTTCAATATATCTTTAAACTTAGTAATCCATTATAGAAGGCATTAGTTAATAACA
129 GAAAAA-CGCCTTCAATATACCTTTAAACTTAGTAATCCATTACAGAAGGCATTTGTTAATAACA
* * * *
2583327 AAC-ACTTTCAAAATTTTCCCACTAAAAATTTGGAGAATTATTAAAGGCATCTTCTATTGTAAAA
193 GACGAC-TTCAAAATTTTCTCACTAAAAATTT-TAGAATTATTAAAGGCATCTTCTACTGTAAAA
* *
2583391 TACCTTCTATATACCGCCACATAAATTCTAACACTGTTATTAAAGGCATATATCCAAGAAAGATG
256 TACCTTCTATATACTGCCACATAAATTCTAACACTGTTATTGAAGGCATATATCCAAGAAAGATG
*
2583456 CCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCAATTGCAGATAACAATGCCTT
321 CCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTGCAGATAACAATGCCTT
* * *
2583521 CAATAATTTTCATAAAAAAAATTTCCTAGATTATTAAAGGCGTCTTTTATTATGACACGCCTTCA
386 CAATAATTTTCCTAAAAAAATTTTCTTAGATTATTAAAGGCGTCTTTTATTATGACACGCCTTCA
* * *
2583586 ATATACGATAATAGTAATAGAAGGCGTTTATTAGAAAAGATGCCTTCAATATACATTTAAACTTA
451 ATATACGACAATAGTAATAGAAGGCATTTATTAAAAAAGATGCCTTCAATATACATTTAAACTTA
2583651 GTAATCCATTACTGAAGGCGTTTGCTAATAACAGACACCTTCAAAATTTT-TCCACTAAAAATTT
516 GTAATCCATTACTGAAGGCGTTTGCTAATAACAGACACCTTCAAAATTTTCT-CACTAAAAATTT
* * *
2583715 TAAAAATTATTAAAAGCATCTTCTACTGTAAAATACATTTTATATACCGTCACATAAATTCTAAC
580 TAAAAATTATTAAAAGCATCTTCTACTGTAAAATACATTCTATATACCATCACACAAATTCTAAC
* *
2583780 ACTGTTATTAAAAGCATATATCCAAGAAAGATGCCTTTAATAATTTCTATCACAGTTTATATATA
645 ACTATTATTAAAAGCATATATCCAAGAAAGATGCCTTTAATAATTTCTATCACAGTTTATAGATA
2583845 A
710 A
* *
2583846 TTACTGAAGGCTGTTGCATATAACAACGCCTTCAATAATTTTCCT-AAAAGATTTTTTCGGATTA
1 TTACTGAAGGC-GTTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAGATTTTTT-GGATTA
* * ** * * **
2583910 TTAAATGCGTCTTTTATTATGACATGCCTTCAATATACAACGATGGTAATGGAAAGCGTTTAGCA
64 TTAAACGCATCTTTTATTATGACACACCTTCAATATACGACGATGGTAATGGAAAGTGTTTATTA
* * *
2583975 GAAAAGACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACCGAAGGCGTTTGTTAATAACG
129 GAAAA-ACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACAGAAGGCATTTGTTAATAACA
* *
2584040 GACGTCTTCAAAATTTTTTCACTAAAAATTTTAAGAATTATTAAAGGCATCTTCTACTGTAAAAT
193 GACGACTTCAAAATTTTCTCACTAAAAATTTT-AGAATTATTAAAGGCATCTTCTACTGTAAAAT
* * * *
2584105 ACCTTCTATATACTGTCACATAAATTCTAACACTATTATTGAATGCATATACCCAAGAAAGATGC
257 ACCTTCTATATACTGCCACATAAATTCTAACACTGTTATTGAAGGCATATATCCAAGAAAGATGC
* * * * *
2584170 CTTTAATAATTTCTATCACAATTTGAATATAATTACTGAAGGTGATTACAGATAACAATGCCTTT
322 CTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTGCAGATAACAATGCCTTC
* *
2584235 AATAATTTCCCTAAAAAAATTTTCTTAGATTATTAAAGGCGTCTTTTAGTATGACACGCCTTCAA
387 AATAATTTTCCTAAAAAAATTTTCTTAGATTATTAAAGGCGTCTTTTATTATGACACGCCTTCAA
* * * * *
2584300 TATACGACGATGGTAATAGAAGGCATTTTTTAAAAAAGGTGCCTTCAATATACTTTTAAACTTAG
452 TATACGACAATAGTAATAGAAGGCATTTATTAAAAAAGATGCCTTCAATATACATTTAAACTTAG
* *
2584365 TAATCCATTACTGAAGGCGTTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAAAATTTTA
517 TAATCCATTACTGAAGGCGTTTGCTAATAACAGACACCTTCAAAATTTTCTCACTAAAAATTTTA
* * * * *
2584430 AAAATTATTAAAGGCGTTTTTTACTGTAAAATACCTTCTATATACCATCACACAAATTCTAACAC
582 AAAATTATTAAAAGCATCTTCTACTGTAAAATACATTCTATATACCATCACACAAATTCTAACAC
* * * *
2584495 TATTATTGAAAGCGTATATCCAAGGAAGATGCCTTTAATAATTTCTATCACAGTTTGTAGATAA
647 TATTATTAAAAGCATATATCCAAGAAAGATGCCTTTAATAATTTCTATCACAGTTTATAGATAA
* * * *
2584559 TTACTTTAAGGCAGTAGTAGATAACAATGCCCTT-AATAA-TTTCCTTAAAAAAATATTTTTGGA
1 TTAC-TGAAGGC-GTTGCAGATAACAATG-CCTTCAATAATTTTCC-TAAAAAGAT-TTTTTGGA
* * *
2584622 TTATTAAACGCATATTTTATTATGACACACCTTCAATATATGACGATGGTAATAGAAAGTGTTTA
61 TTATTAAACGCATCTTTTATTATGACACACCTTCAATATACGACGATGGTAATGGAAAGTGTTTA
* *
2584687 TTAGAAAAAAGGTACCTTCAATATACCTTTAAACTTAGTAATCCATTACTGAAGGCATTTGTTAA
126 TTAG-AAAAACG--CCTTCAATATACCTTTAAACTTAGTAATCCATTACAGAAGGCATTTGTTAA
* * * * ***
2584752 TAACAGACGCCTTCAGAATTTTCTCACTAAAAATTTTGGCAACTATTAAAGTTGTCTTCTACTGT
188 TAACAGACGACTTCAAAATTTTCTCACTAAAAATTTTAG-AATTATTAAAGGCATCTTCTACTGT
* * * *
2584817 AAATTACCTTCTATATACTACCACATAAATTCTAACACTGTTATTGAAGGCGTATATCCAAGGAA
252 AAAATACCTTCTATATACTGCCACATAAATTCTAACACTGTTATTGAAGGCATATATCCAAGAAA
** * * * * * *
2584882 GACACCTTTAATAA-TTCTTACCATAGTTTGTAGATAATTATTGAAGGCGGTTGCAGATAACAAC
317 GATGCCTTTAATAATTTC-TATCACAGTTTGTATATAATTACTGAAGGCGATTGCAGATAACAAT
* *
2584946 GCCTTCAATAATTTTCCTAAAAAAATTTTTTTAGATTATTAAAGGCATCTTTTATTAT
381 GCCTTCAATAATTTTCCTAAAAAAATTTTCTTAGATTATTAAAGGCGTCTTTTATTAT
2585004 AAAACACTTT
Statistics
Matches: 1017, Mismatches: 125, Indels: 29
0.87 0.11 0.02
Matches are distributed among these distances:
712 6 0.01
713 597 0.59
714 66 0.06
715 74 0.07
716 13 0.01
717 261 0.26
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (710 bp):
TTACTGAAGGCGTTGCAGATAACAATGCCTTCAATAATTTTCCTAAAAAGATTTTTTGGATTATT
AAACGCATCTTTTATTATGACACACCTTCAATATACGACGATGGTAATGGAAAGTGTTTATTAGA
AAAACGCCTTCAATATACCTTTAAACTTAGTAATCCATTACAGAAGGCATTTGTTAATAACAGAC
GACTTCAAAATTTTCTCACTAAAAATTTTAGAATTATTAAAGGCATCTTCTACTGTAAAATACCT
TCTATATACTGCCACATAAATTCTAACACTGTTATTGAAGGCATATATCCAAGAAAGATGCCTTT
AATAATTTCTATCACAGTTTGTATATAATTACTGAAGGCGATTGCAGATAACAATGCCTTCAATA
ATTTTCCTAAAAAAATTTTCTTAGATTATTAAAGGCGTCTTTTATTATGACACGCCTTCAATATA
CGACAATAGTAATAGAAGGCATTTATTAAAAAAGATGCCTTCAATATACATTTAAACTTAGTAAT
CCATTACTGAAGGCGTTTGCTAATAACAGACACCTTCAAAATTTTCTCACTAAAAATTTTAAAAA
TTATTAAAAGCATCTTCTACTGTAAAATACATTCTATATACCATCACACAAATTCTAACACTATT
ATTAAAAGCATATATCCAAGAAAGATGCCTTTAATAATTTCTATCACAGTTTATAGATAA
Found at i:2585795 original size:18 final size:18
Alignment explanation
Indices: 2585772--2585818 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2585762 TTTGCTGAAT
2585772 GGGTTTGAATGAAATTAG
1 GGGTTTGAATGAAATTAG
2585790 GGGTTTGAATGAAATTAG
1 GGGTTTGAATGAAATTAG
*
2585808 GGGGTTGAATG
1 GGGTTTGAATG
2585819 GTGTTTCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.38, T:0.32
Consensus pattern (18 bp):
GGGTTTGAATGAAATTAG
Found at i:2594884 original size:23 final size:23
Alignment explanation
Indices: 2594852--2594901 Score: 64
Period size: 23 Copynumber: 2.2 Consensus size: 23
2594842 TTTATAAAGC
*
2594852 TTTCTGGGATCCAAATCTTAGAT
1 TTTCTAGGATCCAAATCTTAGAT
** *
2594875 TTTCTAGGATTTAAATTTTAGAT
1 TTTCTAGGATCCAAATCTTAGAT
2594898 TTTC
1 TTTC
2594902 AATCAGCCTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.12, G:0.14, T:0.48
Consensus pattern (23 bp):
TTTCTAGGATCCAAATCTTAGAT
Found at i:2595035 original size:3 final size:3
Alignment explanation
Indices: 2595027--2595080 Score: 99
Period size: 3 Copynumber: 18.0 Consensus size: 3
2595017 TTTAATGCAC
*
2595027 TAA TAA TAA CAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
2595075 TAA TAA
1 TAA TAA
2595081 ATATCTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:2603250 original size:191 final size:191
Alignment explanation
Indices: 2602924--2603302 Score: 731
Period size: 191 Copynumber: 2.0 Consensus size: 191
2602914 TCATTCTTTG
* *
2602924 TTATCATTTAGATGTTTGGCAATGAAATCTCGAAAAAACTCTTAAGGAATACTTTTATGCCCTTT
1 TTATCATTTAAATGTTTGGCAATGAAATCTCGAAAAAACGCTTAAGGAATACTTTTATGCCCTTT
2602989 TTTTCTTGAACATGTGAATCTATGGGCTCCTCGTCTACTCTTAAAATATGGGCTAACTTTTTACG
66 TTTTCTTGAACATGTGAATCTATGGGCTCCTCGTCTACTCTTAAAATATGGGCTAACTTTTTACG
2603054 ATATCTTGGCTTTTGCTACTTCACATAAACTCTGTCTGAATATTGGAGATGCATACTTTTA
131 ATATCTTGGCTTTTGCTACTTCACATAAACTCTGTCTGAATATTGGAGATGCATACTTTTA
2603115 TTATCATTTAAATGTTTGGCAATGAAATCTCGAAAAAACGCTTAAGGAATACTTTTATGCCCTTT
1 TTATCATTTAAATGTTTGGCAATGAAATCTCGAAAAAACGCTTAAGGAATACTTTTATGCCCTTT
*
2603180 TTTTCTTGAACATGTGAATCTATGGGCTCCTCGTCTACTCTTAAAATATGGGCTAACTTTTTATG
66 TTTTCTTGAACATGTGAATCTATGGGCTCCTCGTCTACTCTTAAAATATGGGCTAACTTTTTACG
2603245 ATATCTTGGCTTTTGCTACTTCACATAAACTCTGTCTGAATATTGGAGATGCATACTT
131 ATATCTTGGCTTTTGCTACTTCACATAAACTCTGTCTGAATATTGGAGATGCATACTT
2603303 ACTAGAATCG
Statistics
Matches: 185, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
191 185 1.00
ACGTcount: A:0.27, C:0.18, G:0.15, T:0.40
Consensus pattern (191 bp):
TTATCATTTAAATGTTTGGCAATGAAATCTCGAAAAAACGCTTAAGGAATACTTTTATGCCCTTT
TTTTCTTGAACATGTGAATCTATGGGCTCCTCGTCTACTCTTAAAATATGGGCTAACTTTTTACG
ATATCTTGGCTTTTGCTACTTCACATAAACTCTGTCTGAATATTGGAGATGCATACTTTTA
Found at i:2604794 original size:22 final size:22
Alignment explanation
Indices: 2604765--2604813 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
2604755 GAAACAATTA
2604765 GTAA-AATCTTTCAATAGTTTG
1 GTAAGAATCTTTCAATAGTTTG
*
2604786 GTAAGAATCTTTGAATAGTTTG
1 GTAAGAATCTTTCAATAGTTTG
2604808 GTAAGA
1 GTAAGA
2604814 TTTTACTTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
21 4 0.15
22 22 0.85
ACGTcount: A:0.35, C:0.06, G:0.20, T:0.39
Consensus pattern (22 bp):
GTAAGAATCTTTCAATAGTTTG
Found at i:2605333 original size:6 final size:6
Alignment explanation
Indices: 2605304--2605367 Score: 53
Period size: 6 Copynumber: 10.8 Consensus size: 6
2605294 TGGGAAACAT
* * * *
2605304 AATTAA AATTTA AATCT-A AA-TAA AGTTAA AATTAA AATTAA CATCAA
1 AATTAA AATTAA AAT-TAA AATTAA AATTAA AATTAA AATTAA AATTAA
2605351 CAA-TAA AATTAA AATTA
1 -AATTAA AATTAA AATTA
2605368 TGGGTTTTTA
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
4 1 0.02
5 4 0.09
6 39 0.85
7 2 0.04
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (6 bp):
AATTAA
Found at i:2616754 original size:18 final size:18
Alignment explanation
Indices: 2616731--2616766 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
2616721 GTCTCAGCAC
2616731 AGTATTCAATTTCACCAT
1 AGTATTCAATTTCACCAT
2616749 AGTATTCAATTTCACCAT
1 AGTATTCAATTTCACCAT
2616767 TACATGTCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.22, G:0.06, T:0.39
Consensus pattern (18 bp):
AGTATTCAATTTCACCAT
Found at i:2627472 original size:15 final size:16
Alignment explanation
Indices: 2627446--2627476 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
2627436 TTAAAATTAT
2627446 TTTAATAAAATTTTAA
1 TTTAATAAAATTTTAA
2627462 TTTAA-AAAATTTTAA
1 TTTAATAAAATTTTAA
2627477 AAGTGATTTG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTAATAAAATTTTAA
Found at i:2637078 original size:13 final size:13
Alignment explanation
Indices: 2637060--2637091 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
2637050 TCCCGTGGTT
*
2637060 TTTTCCTCCGGGG
1 TTTTCCTCCGAGG
2637073 TTTTCCTCCGAGG
1 TTTTCCTCCGAGG
2637086 TTTTCC
1 TTTTCC
2637092 ACGTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.03, C:0.31, G:0.22, T:0.44
Consensus pattern (13 bp):
TTTTCCTCCGAGG
Found at i:2640479 original size:10 final size:10
Alignment explanation
Indices: 2640459--2640506 Score: 62
Period size: 10 Copynumber: 4.8 Consensus size: 10
2640449 AATCAATCTT
2640459 TAAAGTCATCA
1 TAAA-TCATCA
2640470 TAAATCATCA
1 TAAATCATCA
*
2640480 T-CATCATCA
1 TAAATCATCA
2640489 TAAATCATCA
1 TAAATCATCA
*
2640499 TTAATCAT
1 TAAATCAT
2640507 TAGTTTATCG
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
9 8 0.24
10 21 0.64
11 4 0.12
ACGTcount: A:0.44, C:0.21, G:0.02, T:0.33
Consensus pattern (10 bp):
TAAATCATCA
Found at i:2643752 original size:6 final size:6
Alignment explanation
Indices: 2643729--2643780 Score: 54
Period size: 6 Copynumber: 8.7 Consensus size: 6
2643719 ATTTATGGGC
* *
2643729 TTTATTT TTTATT CTTATT TTTATT TTGATT TTT-TT ATTTA-T TTTATT
1 TTTA-TT TTTATT TTTATT TTTATT TTTATT TTTATT -TTTATT TTTATT
2643777 TTTA
1 TTTA
2643781 GTTGATAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
5 6 0.16
6 28 0.74
7 4 0.11
ACGTcount: A:0.17, C:0.02, G:0.02, T:0.79
Consensus pattern (6 bp):
TTTATT
Found at i:2648881 original size:34 final size:34
Alignment explanation
Indices: 2648804--2648884 Score: 126
Period size: 34 Copynumber: 2.4 Consensus size: 34
2648794 AAAACATCGT
* *
2648804 TAAATTTAGAAGCATTTTTAAACACAAATGCCAC
1 TAAATTTAGTAGCATTTTTAAACACAAAAGCCAC
* *
2648838 TAAATTTAGTGGCATTTTTAAGCACAAAAGCCAC
1 TAAATTTAGTAGCATTTTTAAACACAAAAGCCAC
2648872 TAAATTTAGTAGC
1 TAAATTTAGTAGC
2648885 GTTTGTATCA
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.41, C:0.16, G:0.12, T:0.31
Consensus pattern (34 bp):
TAAATTTAGTAGCATTTTTAAACACAAAAGCCAC
Found at i:2653662 original size:33 final size:33
Alignment explanation
Indices: 2653622--2653688 Score: 125
Period size: 33 Copynumber: 2.0 Consensus size: 33
2653612 TGAAGTTTGT
*
2653622 TTTATTTAGCTGTTGTAAAAACAATTGTATATG
1 TTTATTTAGCTATTGTAAAAACAATTGTATATG
2653655 TTTATTTAGCTATTGTAAAAACAATTGTATATG
1 TTTATTTAGCTATTGTAAAAACAATTGTATATG
2653688 T
1 T
2653689 AATTTATGTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.34, C:0.06, G:0.13, T:0.46
Consensus pattern (33 bp):
TTTATTTAGCTATTGTAAAAACAATTGTATATG
Found at i:2657067 original size:19 final size:19
Alignment explanation
Indices: 2657043--2657079 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2657033 GGTGTTGGAA
2657043 CCAATCCAAGGCCTCGGAG
1 CCAATCCAAGGCCTCGGAG
2657062 CCAATCCAAGGCCTCGGA
1 CCAATCCAAGGCCTCGGA
2657080 CCCATCCATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.27, C:0.38, G:0.24, T:0.11
Consensus pattern (19 bp):
CCAATCCAAGGCCTCGGAG
Found at i:2662524 original size:333 final size:333
Alignment explanation
Indices: 2661804--2663404 Score: 2131
Period size: 333 Copynumber: 4.8 Consensus size: 333
2661794 TCTATTACAG
* * *
2661804 AAGGCGTTTGTTAGA-AACAGACGGCTTCAAAATTTTTTCACTAAATATTTTAAGAATTATTAAA
1 AAGGCGTTTGTTA-ATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAA
* * * * *
2661868 GGTATTTTCTACTGTAAAATGCCGTCTATATACCGCTACACATATTGTAACACTCTTATTGAAAG
65 GGCATCTTCTACTGTAAAATGCCTTCTATATACCGCTACACATATTGTAACATTGTTATTGAAAG
* *
2661933 CGTATATTTAAGATAGATGCCTTTAATAATTCCTATCATAGTTTGTAGT-TAATTACTGAAGGGG
130 CGTATATTTAAGATAGATGCCTTTAATAATTCCTATCACAGTTTGTA-TATAATTACTGAAGGCG
* *
2661997 GTTTCAGATAACAACACCTTCAATAATTTCTCTAATAAAAG-TTTC-----CATTAAAAGCGTCT
194 GTTTCAGATAACAACACCTTCAATAATTTCTCTAATAAAAGTTTTCAGGATTATTAAAAGCATCT
* * *
2662056 TTTATTATAAGCCGCCTTCGATATACCACGTTGGTAATCGAAGGTGAGTATTAGAAAAGGCGCCT
259 TTTATTATAAGCCGCCTTCGATATACCACGATGGTAATCGAAGGCGAGTATTAGAAAAGGTGCCT
*
2662121 TCAATTACTG
324 TCAATTACTA
* * *
2662131 AAGGCATTTGTTAATAATAGACGCCTTCAAAATTTTTTCACTAAATATTTT-AGAAATTATTAAA
1 AAGGCGTTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTGAG-AATTATTAAA
* * * * *
2662195 GGCATCTTCTACTATAAAATACCTTCTATATACCGTTACACGTATTGTAACACTGTTATTGAAAG
65 GGCATCTTCTACTGTAAAATGCCTTCTATATACCGCTACACATATTGTAACATTGTTATTGAAAG
* * ** * *
2662260 CGTATATTTAAGATAAATACCTTTAATAATTTTTATCACAGTTTGTATATAATTATTAAAGGCGG
130 CGTATATTTAAGATAGATGCCTTTAATAATTCCTATCACAGTTTGTATATAATTACTGAAGGCGG
* *
2662325 TTTCAGATAACAACACCTTCAATAATTTTTCTAATAAAAGTTTTCATGATTATTAAAAGCATCTT
195 TTTCAGATAACAACACCTTCAATAATTTCTCTAATAAAAGTTTTCAGGATTATTAAAAGCATCTT
* * * **
2662390 TTATTATAAGTCACCTTCGATATACCATGATGGTAATCGAAGGCGTTTATTAGAAAAGGTGCCTT
260 TTATTATAAGCCGCCTTCGATATACCACGATGGTAATCGAAGGCGAGTATTAGAAAAGGTGCCTT
2662455 CAATTACTA
325 CAATTACTA
* * *
2662464 AAAGCGTTTGTTAATAACATACGCCTTCAAAATTTTCTCACTAAATATTTTGGGAATTATTAAAG
1 AAGGCGTTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAG
* * * * * *
2662529 GCGTCTTCTACTATAAAATACCTTCTATATACCACTACACATATTGTAACATTGCTATTGAAGGC
66 GCATCTTCTACTGTAAAATGCCTTCTATATACCGCTACACATATTGTAACATTGTTATTGAAAGC
* * * * *
2662594 ATATATTTAAGATAGACGCCTTTAATAATTTCTATCACAGTTTGTATATAATTACTGAAGGTGAT
131 GTATATTTAAGATAGATGCCTTTAATAATTCCTATCACAGTTTGTATATAATTACTGAAGGCGGT
** *
2662659 TTCAGATAACAATGCCTTCAATAATTTTTCTAATAAAAGTTTTCAGGATTATT-AAAGACATCTT
196 TTCAGATAACAACACCTTCAATAATTTCTCTAATAAAAGTTTTCAGGATTATTAAAAG-CATCTT
* *
2662723 TTATTATAAGCCGCCTTTGATATACCACGATGGTAATCGAAGGCGAGTATTAGAAAATGTGCCTT
260 TTATTATAAGCCGCCTTCGATATACCACGATGGTAATCGAAGGCGAGTATTAGAAAAGGTGCCTT
*
2662788 CAATTACTG
325 CAATTACTA
* * *
2662797 AAGGCGTTTGTTAATAACAGATGCCTTCAAAAGTTTCTCACTAAATATTTTGAAAATTATTAAAG
1 AAGGCGTTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAG
** * *
2662862 GTGTCTTCTACTGTAAAATGCCTTTTATATATCGCTACACATATTGTAACATTGTTATT-AAATG
66 GCATCTTCTACTGTAAAATGCCTTCTATATACCGCTACACATATTGTAACATTGTTATTGAAA-G
* * *
2662926 TGTATATTTAAGATAGATGCCTTTAATAATTCTTATCACAGTTTGTATATAATTACTGAAGGTGG
130 CGTATATTTAAGATAGATGCCTTTAATAATTCCTATCACAGTTTGTATATAATTACTGAAGGCGG
* * * * *
2662991 -TTCAGATAATAACGCCTTCAATAATTTCTCTAATAAAAATTTTCAGGATTATTAAAGGCATATT
195 TTTCAGATAACAACACCTTCAATAATTTCTCTAATAAAAGTTTTCAGGATTATTAAAAGCATCTT
* * **
2663055 TTATTATAAGCTGCCTTCGATATACCACGATGGTAATCGAAGGC-ATTTATTAGAAAAAGGAACC
260 TTATTATAAGCCGCCTTCGATATACCACGATGGTAATCGAAGGCGA-GTATTAG-AAAAGGTGCC
2663119 TTCAATTACTA
323 TTCAATTACTA
* *
2663130 AAGGCGTTTGTTAATAACAGACACATTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAG
1 AAGGCGTTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAG
* * *
2663195 GCATCTTCAATTGTAAAATGCCTTCTATATACCGTTACACATATTGTAACATTGTTATTG-AAGA
66 GCATCTTCTACTGTAAAATGCCTTCTATATACCGCTACACATATTGTAACATTGTTATTGAAAG-
* * ** *
2663259 TGTATATTTAAGATCGACACCTTTAATAATTCCTATCACAGTTTGTATATAATTACTAAAGGCGG
130 CGTATATTTAAGATAGATGCCTTTAATAATTCCTATCACAGTTTGTATATAATTACTGAAGGCGG
* ** * * * * * *
2663324 TTTCAAATAACAATGCCTTTAATATTTTCTC-AAAAACAAATTTT--GGATTATTAAATGCGT-T
195 TTTCAGATAACAACACCTTCAATAATTTCTCTAATAA-AAGTTTTCAGGATTATTAAAAGCATCT
2663385 GTTTATTATAAGCCGCCTTC
259 -TTTATTATAAGCCGCCTTC
2663405 AATAATTTGT
Statistics
Matches: 1130, Mismatches: 124, Indels: 35
0.88 0.10 0.03
Matches are distributed among these distances:
326 4 0.00
327 207 0.18
328 4 0.00
331 2 0.00
332 141 0.12
333 739 0.65
334 33 0.03
ACGTcount: A:0.35, C:0.15, G:0.13, T:0.37
Consensus pattern (333 bp):
AAGGCGTTTGTTAATAACAGACGCCTTCAAAATTTTCTCACTAAATATTTTGAGAATTATTAAAG
GCATCTTCTACTGTAAAATGCCTTCTATATACCGCTACACATATTGTAACATTGTTATTGAAAGC
GTATATTTAAGATAGATGCCTTTAATAATTCCTATCACAGTTTGTATATAATTACTGAAGGCGGT
TTCAGATAACAACACCTTCAATAATTTCTCTAATAAAAGTTTTCAGGATTATTAAAAGCATCTTT
TATTATAAGCCGCCTTCGATATACCACGATGGTAATCGAAGGCGAGTATTAGAAAAGGTGCCTTC
AATTACTA
Found at i:2667462 original size:36 final size:36
Alignment explanation
Indices: 2667398--2667467 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
2667388 ATATATAAAC
* *
2667398 CAAATGTTTTTCTGGGCATAAATATACAACTGACAG
1 CAAACGTTTTTCTGGGCATAAACATACAACTGACAG
* *
2667434 CAAACGTTTTTCTGGGCATAAACGTACAATTGAC
1 CAAACGTTTTTCTGGGCATAAACATACAACTGAC
2667468 TTCACATATC
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.34, C:0.19, G:0.17, T:0.30
Consensus pattern (36 bp):
CAAACGTTTTTCTGGGCATAAACATACAACTGACAG
Found at i:2670034 original size:16 final size:16
Alignment explanation
Indices: 2670013--2670043 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
2670003 TGTTTAAAAT
2670013 CATCATAAATCATCAA
1 CATCATAAATCATCAA
2670029 CATCATAAATCATCA
1 CATCATAAATCATCA
2670044 TTATAATTCA
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:0.48, C:0.26, G:0.00, T:0.26
Consensus pattern (16 bp):
CATCATAAATCATCAA
Found at i:2672540 original size:28 final size:27
Alignment explanation
Indices: 2672492--2672549 Score: 64
Period size: 28 Copynumber: 2.1 Consensus size: 27
2672482 TTAAAAAAAA
*
2672492 AAATTTTTTTAATTCCAAAAACACTTTT
1 AAATTTTTTTAAATCCAAAAACA-TTTT
* *
2672520 AAATTTTTTTAAAAT-CTAAAATATTTT
1 AAATTTTTTT-AAATCCAAAAACATTTT
2672547 AAA
1 AAA
2672550 AATTATAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
27 7 0.27
28 16 0.62
29 3 0.12
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.47
Consensus pattern (27 bp):
AAATTTTTTTAAATCCAAAAACATTTT
Found at i:2693653 original size:52 final size:51
Alignment explanation
Indices: 2693565--2693710 Score: 159
Period size: 52 Copynumber: 2.8 Consensus size: 51
2693555 ATAATCATAT
* * * **
2693565 AAACTTACCCATTAAGAATCACTCTCCTCTTAGAATTCTTTTACTGTAAGTC
1 AAACTTACCTATTAAGAATCTCTTTCCTCTTAGAATTCTTTT-CTAAAAGTC
* * * * * *
2693617 AAATTTATCTATTAAGAATCTGTTTCCTTTTAGAATTCTTCTTTTAAAAGTT
1 AAACTTACCTATTAAGAATCTCTTTCCTCTTAGAATTCTT-TTCTAAAAGTC
2693669 AAACTTACCTATTAAGAATCCTCTTT-CTCTTAGAATTCTTTT
1 AAACTTACCTATTAAGAAT-CTCTTTCCTCTTAGAATTCTTTT
2693711 TTTGCAAGTC
Statistics
Matches: 77, Mismatches: 15, Indels: 5
0.79 0.15 0.05
Matches are distributed among these distances:
51 2 0.03
52 68 0.88
53 7 0.09
ACGTcount: A:0.30, C:0.19, G:0.07, T:0.44
Consensus pattern (51 bp):
AAACTTACCTATTAAGAATCTCTTTCCTCTTAGAATTCTTTTCTAAAAGTC
Found at i:2693759 original size:11 final size:11
Alignment explanation
Indices: 2693741--2693776 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2693731 TCAAGCAATA
2693741 TCTAACAAATC
1 TCTAACAAATC
*
2693752 TTTAACAAATC
1 TCTAACAAATC
*
2693763 TCAAACAAATC
1 TCTAACAAATC
2693774 TCT
1 TCT
2693777 TATGGGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:2694066 original size:24 final size:25
Alignment explanation
Indices: 2694024--2694088 Score: 82
Period size: 24 Copynumber: 2.7 Consensus size: 25
2694014 GCACTTTCCA
2694024 AACC-TTTAGCTCTTCTCACATCTCG
1 AACCTTTTAGCTCTT-TCACATCTCG
*
2694049 AA-CTTTTAGCTCTTTCACGTCTCG
1 AACCTTTTAGCTCTTTCACATCTCG
*
2694073 AACCTTCT-GCTCTTTC
1 AACCTTTTAGCTCTTTC
2694089 TACGTCTTGA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
24 20 0.56
25 16 0.44
ACGTcount: A:0.17, C:0.34, G:0.09, T:0.40
Consensus pattern (25 bp):
AACCTTTTAGCTCTTTCACATCTCG
Found at i:2694104 original size:25 final size:24
Alignment explanation
Indices: 2694024--2694104 Score: 76
Period size: 25 Copynumber: 3.3 Consensus size: 24
2694014 GCACTTTCCA
*
2694024 AACCTT-TAGCTCTTCTCACATCTCG
1 AACCTTCT-GCTCTT-TCACGTCTCG
*
2694049 AA-CTTTTAGCTCTTTCACGTCTCG
1 AACCTTCT-GCTCTTTCACGTCTCG
*
2694073 AACCTTCTGCTCTTTCTACGTCTTG
1 AACCTTCTGCTCTTTC-ACGTCTCG
*
2694098 AATCTTC
1 AACCTTC
2694105 AAGTCTTCTC
Statistics
Matches: 49, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
24 22 0.45
25 27 0.55
ACGTcount: A:0.17, C:0.32, G:0.10, T:0.41
Consensus pattern (24 bp):
AACCTTCTGCTCTTTCACGTCTCG
Found at i:2694759 original size:52 final size:52
Alignment explanation
Indices: 2694674--2694817 Score: 191
Period size: 52 Copynumber: 2.8 Consensus size: 52
2694664 ATAATCATAT
* * *
2694674 AAACTTGCCCATTAAGAATCTCTCTCCTCTTAGAATTCTTCTACTGTAAGTC
1 AAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTACTATAAGTC
* * **
2694726 AAATTTGCCTATTAAGAATCTCTTTCCTTTTAGAATTCTTCTTTTATAAGTC
1 AAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTACTATAAGTC
* *
2694778 AAACTTACCTATTAAGAATCCACTTT-CTCTTAGAATTCTT
1 AAACTTGCCTATTAAGAAT-CTCTTTCCTCTTAGAATTCTT
2694818 TTTTTGCAAG
Statistics
Matches: 80, Mismatches: 11, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
52 75 0.94
53 5 0.06
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (52 bp):
AAACTTGCCTATTAAGAATCTCTTTCCTCTTAGAATTCTTCTACTATAAGTC
Found at i:2694866 original size:11 final size:11
Alignment explanation
Indices: 2694850--2694885 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
2694840 TCAAGCAATA
2694850 TCTAACAAATC
1 TCTAACAAATC
2694861 TCTAACAAATC
1 TCTAACAAATC
* *
2694872 CCAAACAAATC
1 TCTAACAAATC
2694883 TCT
1 TCT
2694886 TATTGGATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.44, C:0.31, G:0.00, T:0.25
Consensus pattern (11 bp):
TCTAACAAATC
Found at i:2699294 original size:15 final size:14
Alignment explanation
Indices: 2699274--2699303 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
2699264 TATTTTAGAA
2699274 CTTCTTCCTGTCTCT
1 CTTCTTCCT-TCTCT
2699289 CTTCTTCCTTCTCT
1 CTTCTTCCTTCTCT
2699303 C
1 C
2699304 CTTACCTCTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 6 0.40
15 9 0.60
ACGTcount: A:0.00, C:0.43, G:0.03, T:0.53
Consensus pattern (14 bp):
CTTCTTCCTTCTCT
Found at i:2714486 original size:27 final size:28
Alignment explanation
Indices: 2714441--2714495 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
2714431 AAAAAAGCGT
**
2714441 TAAAAGTTATTAATTAAAATTATTTTAA
1 TAAAAGTTATTAATTAAAAAAATTTTAA
2714469 TAAAA-TT-TTAATTTAAAAAAATTTTAA
1 TAAAAGTTATTAA-TTAAAAAAATTTTAA
2714496 AAGTGAGTAG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 4 0.17
27 15 0.62
28 5 0.21
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.45
Consensus pattern (28 bp):
TAAAAGTTATTAATTAAAAAAATTTTAA
Found at i:2714489 original size:16 final size:16
Alignment explanation
Indices: 2714464--2714495 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2714454 TTAAAATTAT
*
2714464 TTTAATAAAATTTTAA
1 TTTAAAAAAATTTTAA
2714480 TTTAAAAAAATTTTAA
1 TTTAAAAAAATTTTAA
2714496 AAGTGAGTAG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTTAAAAAAATTTTAA
Found at i:2714555 original size:15 final size:17
Alignment explanation
Indices: 2714537--2714578 Score: 54
Period size: 15 Copynumber: 2.6 Consensus size: 17
2714527 CTTTTATAAA
2714537 TTTTAATT-TTA-ATTT
1 TTTTAATTATTAGATTT
2714552 TTTT-ATTATTAGATTT
1 TTTTAATTATTAGATTT
2714568 TTTATAATTAT
1 TTT-TAATTAT
2714579 ATTGAAAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
14 3 0.13
15 7 0.30
16 7 0.30
17 1 0.04
18 5 0.22
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (17 bp):
TTTTAATTATTAGATTT
Found at i:2714709 original size:151 final size:151
Alignment explanation
Indices: 2714441--2714727 Score: 370
Period size: 151 Copynumber: 1.9 Consensus size: 151
2714431 AAAAAAGCGT
* ** * *
2714441 TAAAAGTTATTAATTAAAATTATTTTAATAAAATTTTAATTTAAAAAAATTTTAAAAGTGAGTAG
1 TAAAAGTGATTAATTAAAATTACCTTAATAAAATTTTAATTT-AAAAAATATTAAAAGTCAGTAG
* * *
2714506 TTAAAATATTTTTAGTAAATTCTTTTATAAATTTTAATTTTAATTTTTTTATTATTAGA-TTTTT
65 TTAAAATATTATTAGTAAATTCTTTTATAAATTTTAATTTAAATTTTCTTATTATTAGACTTTTT
2714570 TATAATTATATTGAAAATTTTC
130 TATAATTATATTGAAAATTTTC
* *
2714592 TAAAAGTGATTAATTAAAA-TACCCTTAATAAAATTTTAATTT-CAAAATATTAAAAGTCA-TTG
1 TAAAAGTGATTAATTAAAATTA-CCTTAATAAAATTTTAATTTAAAAAATATTAAAAGTCAGTAG
2714654 ATTAAAATATTATTAGT-AATT-TTTTATAAATTTTAATTTAAATAGCTTCTCTTATTATTAGAC
65 -TTAAAATATTATTAGTAAATTCTTTTATAAATTTTAATTTAAAT---TT-TCTTATTATTAGAC
2714717 TTTTTTTATAA
125 -TTTTTTATAA
2714728 ATAGAATGAT
Statistics
Matches: 118, Mismatches: 10, Indels: 14
0.83 0.07 0.10
Matches are distributed among these distances:
147 21 0.18
148 6 0.05
149 29 0.25
150 4 0.03
151 48 0.41
153 10 0.08
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (151 bp):
TAAAAGTGATTAATTAAAATTACCTTAATAAAATTTTAATTTAAAAAATATTAAAAGTCAGTAGT
TAAAATATTATTAGTAAATTCTTTTATAAATTTTAATTTAAATTTTCTTATTATTAGACTTTTTT
ATAATTATATTGAAAATTTTC
Found at i:2717449 original size:14 final size:14
Alignment explanation
Indices: 2717430--2717457 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
2717420 TTAAAAGATG
2717430 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
2717444 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
2717458 TCGAATTTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATTTAAAATTTAAT
Found at i:2717626 original size:9 final size:9
Alignment explanation
Indices: 2717614--2717643 Score: 51
Period size: 9 Copynumber: 3.2 Consensus size: 9
2717604 TAAATTTTAT
2717614 TAATTAAAA
1 TAATTAAAA
2717623 TAATTAAAA
1 TAATTAAAA
2717632 TATATTAAAA
1 TA-ATTAAAA
2717642 TA
1 TA
2717644 TAAAATTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 11 0.55
10 9 0.45
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (9 bp):
TAATTAAAA
Found at i:2717640 original size:10 final size:10
Alignment explanation
Indices: 2717616--2717645 Score: 53
Period size: 10 Copynumber: 3.1 Consensus size: 10
2717606 AATTTTATTA
2717616 ATTAAAATA-
1 ATTAAAATAT
2717625 ATTAAAATAT
1 ATTAAAATAT
2717635 ATTAAAATAT
1 ATTAAAATAT
2717645 A
1 A
2717646 AAATTTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
ATTAAAATAT
Found at i:2717657 original size:19 final size:20
Alignment explanation
Indices: 2717613--2717658 Score: 53
Period size: 19 Copynumber: 2.4 Consensus size: 20
2717603 ATAAATTTTA
2717613 TTAATTAAAATAATTAAAAT
1 TTAATTAAAATAATTAAAAT
*
2717633 AT-ATTAAAAT-A-TAAAATT
1 TTAATTAAAATAATTAAAA-T
2717651 TTAATTAA
1 TTAATTAA
2717659 TCTCATAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
17 5 0.23
18 3 0.14
19 13 0.59
20 1 0.05
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (20 bp):
TTAATTAAAATAATTAAAAT
Found at i:2717707 original size:11 final size:11
Alignment explanation
Indices: 2717691--2717784 Score: 58
Period size: 11 Copynumber: 8.7 Consensus size: 11
2717681 ATATAAAAAT
2717691 ATTTAAATTTA
1 ATTTAAATTTA
2717702 ATTT-AA-TTA
1 ATTTAAATTTA
2717711 ATCAATTAAA-TT-
1 AT---TTAAATTTA
*
2717723 ATTTAAATTCA
1 ATTTAAATTTA
*
2717734 A-TTAAATAATA
1 ATTTAAAT-TTA
2717745 A-TT-AATTTAA
1 ATTTAAATTT-A
*
2717755 ATTTAAATTTT
1 ATTTAAATTTA
*
2717766 ATTTAAATTAA
1 ATTTAAATTTA
2717777 ATTTAAAT
1 ATTTAAAT
2717785 AATTTATAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 20
0.71 0.08 0.22
Matches are distributed among these distances:
9 11 0.17
10 14 0.21
11 28 0.42
12 9 0.14
13 4 0.06
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (11 bp):
ATTTAAATTTA
Found at i:2717724 original size:53 final size:53
Alignment explanation
Indices: 2717650--2717760 Score: 129
Period size: 53 Copynumber: 2.1 Consensus size: 53
2717640 AATATAAAAT
* * *
2717650 TTTAATTAATCTCATAAATTATTCGAATTAAATATAAA-AATATTTAAATTT-AA
1 TTTAATTAATCTAATAAATTATTCAAATTAAAT-TAAATAATAATT-AATTTAAA
* *
2717703 TTTAATTAATC-AATTAAATTATTTAAATTCAATTAAATAATAATTAATTTAAA
1 TTTAATTAATCTAA-TAAATTATTCAAATTAAATTAAATAATAATTAATTTAAA
2717756 TTTAA
1 TTTAA
2717761 ATTTTATTTA
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
52 10 0.20
53 40 0.80
ACGTcount: A:0.50, C:0.05, G:0.01, T:0.45
Consensus pattern (53 bp):
TTTAATTAATCTAATAAATTATTCAAATTAAATTAAATAATAATTAATTTAAA
Found at i:2717727 original size:32 final size:31
Alignment explanation
Indices: 2717690--2717790 Score: 98
Period size: 32 Copynumber: 3.2 Consensus size: 31
2717680 AATATAAAAA
2717690 TATTTAAATTTAATTTAATTAATCAATTAAAT
1 TATTTAAATTTAATTTAATTAAT-AATTAAAT
* * *
2717722 TATTTAAATTCAA-TTAAATAATAATTAATT
1 TATTTAAATTTAATTTAATTAATAATTAAAT
* *
2717752 TAAATTTAAATTTTATTTAAATTAA-ATTTAAAT
1 T--ATTTAAATTTAATTT-AATTAATAATTAAAT
*
2717785 AATTTA
1 TATTTA
2717791 TAAATATTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
30 8 0.14
31 13 0.23
32 22 0.39
33 8 0.14
34 5 0.09
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.50
Consensus pattern (31 bp):
TATTTAAATTTAATTTAATTAATAATTAAAT
Found at i:2717731 original size:27 final size:26
Alignment explanation
Indices: 2717696--2717760 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
2717686 AAAATATTTA
2717696 AATTT-AATTTAATT-AATCAATTAAATT
1 AATTTAAATTTAATTAAAT-AA-T-AATT
*
2717723 -ATTTAAATTCAATTAAATAATAATT
1 AATTTAAATTTAATTAAATAATAATT
2717748 AATTTAAATTTAA
1 AATTTAAATTTAA
2717761 ATTTTATTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
25 4 0.12
26 16 0.48
27 10 0.30
28 3 0.09
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (26 bp):
AATTTAAATTTAATTAAATAATAATT
Found at i:2717763 original size:16 final size:15
Alignment explanation
Indices: 2717691--2717779 Score: 53
Period size: 17 Copynumber: 5.9 Consensus size: 15
2717681 ATATAAAAAT
*
2717691 ATTTAAATTTAATTTA
1 ATTTAAA-TTAAATTA
*
2717707 ATTAATCAATTAAATT-
1 ATT--TAAATTAAATTA
*
2717723 ATTTAAATTCAATTA
1 ATTTAAATTAAATTA
*
2717738 A-AT-AA-T-AATTA
1 ATTTAAATTAAATTA
*
2717749 ATTTAAATTTAAATTTT
1 ATTTAAA-TTAAA-TTA
2717766 ATTTAAATTAAATT
1 ATTTAAATTAAATT
2717780 TAAATAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 19
0.69 0.08 0.23
Matches are distributed among these distances:
11 6 0.11
12 2 0.04
13 4 0.07
14 10 0.18
15 4 0.07
16 13 0.23
17 15 0.26
18 3 0.05
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTTAAATTAAATTA
Found at i:2717763 original size:27 final size:27
Alignment explanation
Indices: 2717677--2717763 Score: 69
Period size: 26 Copynumber: 3.3 Consensus size: 27
2717667 ATTATTCGAA
*
2717677 TTAAATATAAA-AATATTTAAATTT-AAT
1 TTAAAT-TAAATAATAATT-AATTTAAAT
2717704 TT-AATT-AATCAATTAAATT-ATTTAAA-
1 TTAAATTAAAT-AA-T-AATTAATTTAAAT
*
2717730 TTCAATTAAATAATAATTAATTTAAAT
1 TTAAATTAAATAATAATTAATTTAAAT
2717757 TTAAATT
1 TTAAATT
2717764 TTATTTAAAT
Statistics
Matches: 49, Mismatches: 2, Indels: 18
0.71 0.03 0.26
Matches are distributed among these distances:
24 2 0.04
25 5 0.10
26 19 0.39
27 17 0.35
28 6 0.12
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (27 bp):
TTAAATTAAATAATAATTAATTTAAAT
Found at i:2717766 original size:7 final size:6
Alignment explanation
Indices: 2717748--2717784 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
2717738 AATAATAATT
*
2717748 AATTTA AATTTA AATTT- TATTTA AA-TTA AATTTA AAT
1 AATTTA AATTTA AATTTA AATTTA AATTTA AATTTA AAT
2717785 AATTTATAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 9 0.33
6 18 0.67
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (6 bp):
AATTTA
Found at i:2717771 original size:17 final size:16
Alignment explanation
Indices: 2717749--2717780 Score: 55
Period size: 16 Copynumber: 1.9 Consensus size: 16
2717739 ATAATAATTA
2717749 ATTTAAATTTAAATTTT
1 ATTTAAA-TTAAATTTT
2717766 ATTTAAATTAAATTT
1 ATTTAAATTAAATTT
2717781 AAATAATTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATTTAAATTAAATTTT
Found at i:2717771 original size:22 final size:22
Alignment explanation
Indices: 2717691--2717784 Score: 79
Period size: 22 Copynumber: 4.4 Consensus size: 22
2717681 ATATAAAAAT
*
2717691 ATTTAAATTTAATTT-AATTAA
1 ATTTAAATTTTATTTAAATTAA
* *
2717712 TCAATTAAA--TTATTTAAATTCA
1 --ATTTAAATTTTATTTAAATTAA
** * *
2717734 A-TTAAATAATAATTAATTTAA
1 ATTTAAATTTTATTTAAATTAA
2717755 ATTTAAATTTTATTTAAATTAA
1 ATTTAAATTTTATTTAAATTAA
2717777 ATTTAAAT
1 ATTTAAAT
2717785 AATTTATAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 9
0.74 0.14 0.12
Matches are distributed among these distances:
19 5 0.09
20 1 0.02
21 15 0.27
22 29 0.52
23 6 0.11
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (22 bp):
ATTTAAATTTTATTTAAATTAA
Found at i:2717794 original size:22 final size:23
Alignment explanation
Indices: 2717725--2717795 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 23
2717715 ATTAAATTAT
* *
2717725 TTAAATTCAA-TTAAATAA-TAA
1 TTAAATTAAATTTAAATAATTTA
*
2717746 TTAATTTAAATTTAAAT--TTTA
1 TTAAATTAAATTTAAATAATTTA
2717767 TTTAAATTAAATTTAAATAATTTA
1 -TTAAATTAAATTTAAATAATTTA
2717791 -TAAAT
1 TTAAAT
2717796 ATTAATATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 9
0.76 0.07 0.17
Matches are distributed among these distances:
21 10 0.24
22 27 0.66
24 4 0.10
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
TTAAATTAAATTTAAATAATTTA
Found at i:2721855 original size:16 final size:16
Alignment explanation
Indices: 2721836--2721868 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
2721826 TCAAATTGTC
2721836 CACATATCATATCCTT
1 CACATATCATATCCTT
2721852 CACATATCATATCCTT
1 CACATATCATATCCTT
2721868 C
1 C
2721869 CCAGAAGAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.36
Consensus pattern (16 bp):
CACATATCATATCCTT
Found at i:2734612 original size:13 final size:14
Alignment explanation
Indices: 2734585--2734614 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
2734575 TTATTCGAAT
2734585 TTTATTAATAATTA
1 TTTATTAATAATTA
2734599 TTTATTAA-AATTA
1 TTTATTAATAATTA
2734612 TTT
1 TTT
2734615 CAAATGTATG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (14 bp):
TTTATTAATAATTA
Found at i:2737862 original size:24 final size:24
Alignment explanation
Indices: 2737806--2737879 Score: 82
Period size: 24 Copynumber: 3.1 Consensus size: 24
2737796 TAATTTCGAT
*
2737806 AAAATTA--ATAATAATAA-TAATA
1 AAAATTATTATAATTATAATTAA-A
2737828 ATAAATTATTATAATTATAATTAAA
1 A-AAATTATTATAATTATAATTAAA
* *
2737853 AAAATTATTATAATTGTGATTAAA
1 AAAATTATTATAATTATAATTAAA
2737877 AAA
1 AAA
2737880 TTAATAAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
22 1 0.02
23 6 0.13
24 24 0.53
25 11 0.24
26 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (24 bp):
AAAATTATTATAATTATAATTAAA
Found at i:2738958 original size:18 final size:18
Alignment explanation
Indices: 2738935--2738991 Score: 55
Period size: 18 Copynumber: 3.1 Consensus size: 18
2738925 AAATTGATAA
2738935 ATATTTATTATTTTTTAT
1 ATATTTATTATTTTTTAT
2738953 ATATTT-TTAATTTTTT-T
1 ATATTTATT-ATTTTTTAT
* *
2738970 AAAATATATTATATTTTTAT
1 -ATATTTATTAT-TTTTTAT
2738990 AT
1 AT
2738992 GCATCACCTT
Statistics
Matches: 31, Mismatches: 3, Indels: 9
0.72 0.07 0.21
Matches are distributed among these distances:
17 3 0.10
18 19 0.61
19 8 0.26
20 1 0.03
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (18 bp):
ATATTTATTATTTTTTAT
Found at i:2745305 original size:2 final size:2
Alignment explanation
Indices: 2745298--2745338 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2745288 TCCTTTCACA
2745298 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2745339 AACGTACAGT
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2745893 original size:20 final size:19
Alignment explanation
Indices: 2745839--2745901 Score: 56
Period size: 20 Copynumber: 3.2 Consensus size: 19
2745829 TTTATATATA
*
2745839 TTTTTAAAATATTTATAATTT
1 TTTTTAAAA-ATATA-AATTT
* * *
2745860 CTTTTCAAATTATAAACTTT
1 TTTTTAAAAATATAAA-TTT
2745880 TTTTTAAAAATAT-AATTT
1 TTTTTAAAAATATAAATTT
2745898 TTTT
1 TTTT
2745902 GTTCAATGAT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 7 0.21
19 4 0.12
20 16 0.47
21 7 0.21
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.59
Consensus pattern (19 bp):
TTTTTAAAAATATAAATTT
Found at i:2747669 original size:16 final size:16
Alignment explanation
Indices: 2747648--2747678 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2747638 AATTTAGATT
*
2747648 TTTTTTTAATTTATTA
1 TTTTTTAAATTTATTA
2747664 TTTTTTAAATTTATT
1 TTTTTTAAATTTATT
2747679 TTAACCCATC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTTAAATTTATTA
Found at i:2748772 original size:3 final size:3
Alignment explanation
Indices: 2748760--2748790 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
2748750 AATCTCATTT
2748760 ATA A-A ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
2748791 TAATTAATTA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.07
3 25 0.93
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:2749286 original size:20 final size:19
Alignment explanation
Indices: 2749236--2749277 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
2749226 ATAGAATTTG
*
2749236 TTTATCATAAATTCTAAAA
1 TTTATGATAAATTCTAAAA
2749255 TTTATGATAAATTCTAAAA
1 TTTATGATAAATTCTAAAA
2749274 TTTA
1 TTTA
2749278 AATATAAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.45, C:0.07, G:0.02, T:0.45
Consensus pattern (19 bp):
TTTATGATAAATTCTAAAA
Found at i:2756925 original size:20 final size:21
Alignment explanation
Indices: 2756884--2756929 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
2756874 TTCGAAATTA
2756884 ATAAAATATTATTTTTTAAAT
1 ATAAAATATTATTTTTTAAAT
2756905 ATAAAATATTATTTTTT-AAT
1 ATAAAATATTATTTTTTAAAT
2756925 ATAAA
1 ATAAA
2756930 TATAAAATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 8 0.32
21 17 0.68
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
ATAAAATATTATTTTTTAAAT
Found at i:2756930 original size:19 final size:19
Alignment explanation
Indices: 2756881--2756932 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 19
2756871 TAATTCGAAA
2756881 TTAATA-AAATATTATTTT
1 TTAATATAAATATTATTTT
2756899 TTAAATATAAAATATTATTTT
1 TT-AATAT-AAATATTATTTT
2756920 TTAATATAAATAT
1 TTAATATAAATAT
2756933 AAAATTAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 2 0.06
19 10 0.32
20 5 0.16
21 14 0.45
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (19 bp):
TTAATATAAATATTATTTT
Found at i:2761201 original size:15 final size:16
Alignment explanation
Indices: 2761176--2761216 Score: 50
Period size: 15 Copynumber: 2.6 Consensus size: 16
2761166 ATCCAAACCC
*
2761176 AAAGGAAAAGTAAAT-A
1 AAAGAAAAAGT-AATGA
2761192 AAA-AAAAAGTAATGA
1 AAAGAAAAAGTAATGA
2761207 AAAGAAAAAG
1 AAAGAAAAAG
2761217 AAAGTTCTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 10 0.45
16 9 0.41
ACGTcount: A:0.73, C:0.00, G:0.17, T:0.10
Consensus pattern (16 bp):
AAAGAAAAAGTAATGA
Found at i:2770784 original size:31 final size:32
Alignment explanation
Indices: 2770731--2770794 Score: 94
Period size: 31 Copynumber: 2.0 Consensus size: 32
2770721 GTGGTATTAG
** *
2770731 GCTGTGGTGATTTTCTAACAAGTTGTATCAGA
1 GCTGTGGTGATCCTCTAACAAGTAGTATCAGA
2770763 GCTGTGGTGATCCT-TAACAAGTAGTATCAGA
1 GCTGTGGTGATCCTCTAACAAGTAGTATCAGA
2770794 G
1 G
2770795 TCGAAGGCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 17 0.59
32 12 0.41
ACGTcount: A:0.27, C:0.14, G:0.27, T:0.33
Consensus pattern (32 bp):
GCTGTGGTGATCCTCTAACAAGTAGTATCAGA
Found at i:2770825 original size:25 final size:25
Alignment explanation
Indices: 2770797--2770859 Score: 74
Period size: 25 Copynumber: 2.5 Consensus size: 25
2770787 TATCAGAGTC
*
2770797 GAAGGCTCAAGATATAGCAAA-AGCT
1 GAAGGTTCAAGATATAG-AAAGAGCT
** *
2770822 GAAGGTTCAAGACGTTGAAAGAGCT
1 GAAGGTTCAAGATATAGAAAGAGCT
2770847 GAAGGTTCAAGAT
1 GAAGGTTCAAGAT
2770860 GTGGGAAGAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
24 3 0.09
25 29 0.91
ACGTcount: A:0.40, C:0.13, G:0.29, T:0.19
Consensus pattern (25 bp):
GAAGGTTCAAGATATAGAAAGAGCT
Found at i:2770868 original size:25 final size:25
Alignment explanation
Indices: 2770818--2770868 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
2770808 ATATAGCAAA
*
2770818 AGCTGAAGGTTCAAGACGTTGAAAG
1 AGCTGAAGGTTCAAGACGTGGAAAG
* *
2770843 AGCTGAAGGTTCAAGATGTGGGAAG
1 AGCTGAAGGTTCAAGACGTGGAAAG
2770868 A
1 A
2770869 ATATGATTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.35, C:0.10, G:0.35, T:0.20
Consensus pattern (25 bp):
AGCTGAAGGTTCAAGACGTGGAAAG
Found at i:2776224 original size:19 final size:19
Alignment explanation
Indices: 2776196--2776251 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
2776186 CATAACTTTT
2776196 AATATCAAAAAATAAAAATA
1 AATAT-AAAAAATAAAAATA
* ***
2776216 ATTATAAAAAATAATTTTA
1 AATATAAAAAATAAAAATA
2776235 AATAT-AAAAATAAAAAT
1 AATATAAAAAATAAAAAT
2776252 TTTAGATGTT
Statistics
Matches: 28, Mismatches: 8, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
18 9 0.32
19 15 0.54
20 4 0.14
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.29
Consensus pattern (19 bp):
AATATAAAAAATAAAAATA
Found at i:2776595 original size:26 final size:25
Alignment explanation
Indices: 2776551--2776609 Score: 66
Period size: 26 Copynumber: 2.2 Consensus size: 25
2776541 AGATTAAGAA
2776551 ACATATTTTTTAATTTTTTAAATTTAT
1 ACATATTTTTTAA-TTTTTAAA-TTAT
*
2776578 ACATATTTTATTAA-TTTTATATTAT
1 ACATATTTT-TTAATTTTTAAATTAT
2776603 ATCATAT
1 A-CATAT
2776610 CATTATATTG
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
25 5 0.17
26 11 0.38
27 9 0.31
28 4 0.14
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (25 bp):
ACATATTTTTTAATTTTTAAATTAT
Done.