Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008007.1 Hibiscus syriacus cultivar Beakdansim tig00110469_pilon, 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: 1953294
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 6 of 11
Found at i:875060 original size:2 final size:2
Alignment explanation
Indices: 875055--875082 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
875045 AAAAAACTTA
875055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
875083 TTAATTTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:910981 original size:31 final size:31
Alignment explanation
Indices: 910943--911013 Score: 99
Period size: 31 Copynumber: 2.3 Consensus size: 31
910933 CTTTTAAAAC
*
910943 TTGCAATATAATCTCC-CAACATTTAGTCCGT
1 TTGCAATATAAGC-CCTCAACATTTAGTCCGT
**
910974 TTGCAATATGGGCCCTCAACATTTAGTCCGT
1 TTGCAATATAAGCCCTCAACATTTAGTCCGT
911005 TTGCAATAT
1 TTGCAATAT
911014 GGTCCCTGAC
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
30 2 0.06
31 34 0.94
ACGTcount: A:0.27, C:0.24, G:0.14, T:0.35
Consensus pattern (31 bp):
TTGCAATATAAGCCCTCAACATTTAGTCCGT
Found at i:911014 original size:31 final size:31
Alignment explanation
Indices: 910959--911020 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
910949 TATAATCTCC
910959 CAACATTTAGTCCGTTTGCAATATGGGCCCT
1 CAACATTTAGTCCGTTTGCAATATGGGCCCT
*
910990 CAACATTTAGTCCGTTTGCAATATGGTCCCT
1 CAACATTTAGTCCGTTTGCAATATGGGCCCT
911021 GACGTAACTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.26, G:0.18, T:0.34
Consensus pattern (31 bp):
CAACATTTAGTCCGTTTGCAATATGGGCCCT
Found at i:911427 original size:3 final size:3
Alignment explanation
Indices: 911419--911476 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
911409 GACCTGGTTG
*
911419 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTAA TAA TT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA
*
911463 TTT TTA -TA TTA TTA
1 TTA TTA TTA TTA TTA
911477 AAATATATTT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
2 6 0.13
3 40 0.85
4 1 0.02
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:911487 original size:20 final size:20
Alignment explanation
Indices: 911464--911504 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
911454 ATAATTTTAT
911464 TTTTAT-ATTATTAAAATATA
1 TTTTATAATTATTAAAA-ATA
*
911484 TTTTTTAATTATTAAAAATA
1 TTTTATAATTATTAAAAATA
911504 T
1 T
911505 AAAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
TTTTATAATTATTAAAAATA
Found at i:911488 original size:22 final size:22
Alignment explanation
Indices: 911463--911505 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
911453 AATAATTTTA
911463 TTTTTATATTATT-AAAATATAT
1 TTTTTA-ATTATTAAAAATATAT
911485 TTTTTAATTATTAAAAATATA
1 TTTTTAATTATTAAAAATATA
911506 AAAATATTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTTTTAATTATTAAAAATATAT
Found at i:911570 original size:12 final size:13
Alignment explanation
Indices: 911547--911590 Score: 56
Period size: 15 Copynumber: 3.4 Consensus size: 13
911537 TTAAATATAA
911547 TAAATA-ATTA-T
1 TAAATATATTATT
911558 TAAATATATTATT
1 TAAATATATTATT
911571 ATAAAATATATTATT
1 -T-AAATATATTATT
911586 TAAAT
1 TAAAT
911591 TAGTTTAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 6 0.21
12 4 0.14
13 5 0.17
14 2 0.07
15 12 0.41
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
TAAATATATTATT
Found at i:911571 original size:15 final size:15
Alignment explanation
Indices: 911553--911589 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
911543 ATAATAAATA
*
911553 ATTATTAAATATATT
1 ATTATAAAATATATT
911568 ATTATAAAATATATT
1 ATTATAAAATATATT
911583 ATT-TAAA
1 ATTATAAA
911590 TTAGTTTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 4 0.19
15 17 0.81
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
ATTATAAAATATATT
Found at i:912832 original size:34 final size:34
Alignment explanation
Indices: 912794--912870 Score: 154
Period size: 34 Copynumber: 2.3 Consensus size: 34
912784 GCGATCATTT
912794 TCAAATGATTGAGAGTGTTTAGAATAGATATTAG
1 TCAAATGATTGAGAGTGTTTAGAATAGATATTAG
912828 TCAAATGATTGAGAGTGTTTAGAATAGATATTAG
1 TCAAATGATTGAGAGTGTTTAGAATAGATATTAG
912862 TCAAATGAT
1 TCAAATGAT
912871 CCTATTAGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.39, C:0.04, G:0.22, T:0.35
Consensus pattern (34 bp):
TCAAATGATTGAGAGTGTTTAGAATAGATATTAG
Found at i:913511 original size:31 final size:31
Alignment explanation
Indices: 913467--913525 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
913457 TACAATATAA
*
913467 TCCCCCAACATTTAGTCTATTTGCAATATGG
1 TCCCCCAACATTTAGTCCATTTGCAATATGG
* * *
913498 TCCCTCAATATTTAGTCCGTTTGCAATA
1 TCCCCCAACATTTAGTCCATTTGCAATA
913526 AGGTTCCTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.25, C:0.25, G:0.12, T:0.37
Consensus pattern (31 bp):
TCCCCCAACATTTAGTCCATTTGCAATATGG
Found at i:919455 original size:2 final size:2
Alignment explanation
Indices: 919448--919515 Score: 136
Period size: 2 Copynumber: 34.0 Consensus size: 2
919438 TGATAATACA
919448 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
919490 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
919516 TTAAAATTCT
Statistics
Matches: 66, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 66 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:921462 original size:5 final size:5
Alignment explanation
Indices: 921452--921535 Score: 56
Period size: 5 Copynumber: 17.6 Consensus size: 5
921442 TAGATATAAA
* * **
921452 AAAAT AAAAT -AAAT -AAAT -AAAT AAATT CAACC AAAAT AAAA- AGAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT A-AAAT
921499 AAAAT AAAAT AAAAT AATAA- ATAAAT -AAAT -AAAT AAA
1 AAAAT AAAAT AAAAT AA-AAT A-AAAT AAAAT AAAAT AAA
921536 GCATAGAAAA
Statistics
Matches: 65, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
4 21 0.32
5 40 0.62
6 4 0.06
ACGTcount: A:0.75, C:0.04, G:0.01, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:921467 original size:4 final size:4
Alignment explanation
Indices: 921447--921535 Score: 60
Period size: 4 Copynumber: 21.2 Consensus size: 4
921437 CATGTTAGAT
*
921447 ATAA AAAA ATAAA ATAA ATAA ATAA ATAA ATTCAA CCA-AA AT-A A-AA
1 ATAA ATAA AT-AA ATAA ATAA ATAA ATAA A-T-AA --ATAA ATAA ATAA
*
921493 AGAA ATAAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA ATAA A
1 ATAA AT-AA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA ATAA A
921536 GCATAGAAAA
Statistics
Matches: 71, Mismatches: 3, Indels: 22
0.74 0.03 0.23
Matches are distributed among these distances:
3 6 0.08
4 45 0.63
5 17 0.24
6 2 0.03
8 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.01, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:922340 original size:34 final size:35
Alignment explanation
Indices: 922262--922362 Score: 143
Period size: 34 Copynumber: 2.9 Consensus size: 35
922252 ATAGTAGAAC
922262 TCTATCCTATTTTTAGGAGTTTGAATCCTAACAAAAT
1 TCTATCCTATTTTTAGGAGTTTGAATCCT-A-AAAAT
*
922299 T-TCATCCTATTTTTAGGAGTTTGAATCCT-GAAAT
1 TCT-ATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
*
922333 TCTATCCTATTTTTAGGAGTTCGAATCCTA
1 TCTATCCTATTTTTAGGAGTTTGAATCCTA
922363 GTAGGACGAA
Statistics
Matches: 59, Mismatches: 2, Indels: 8
0.86 0.03 0.12
Matches are distributed among these distances:
34 30 0.51
35 1 0.02
36 1 0.02
37 27 0.46
ACGTcount: A:0.28, C:0.17, G:0.13, T:0.43
Consensus pattern (35 bp):
TCTATCCTATTTTTAGGAGTTTGAATCCTAAAAAT
Found at i:923227 original size:105 final size:105
Alignment explanation
Indices: 922911--923570 Score: 929
Period size: 105 Copynumber: 6.3 Consensus size: 105
922901 CATTGTTCCA
* * ** *
922911 AGTCCAATATCCTCCGTCGTGAAGTTGAAATTGGCTCTG-GAACCGGGAAATTGTTTGTTGACAA
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAG-ATTGGGAAGTTG-TTGTTGACAA
* * * * * *
922975 CCAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTTTCTCG
64 GCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
** *
923017 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGAATCTGA-A-T--GAAATT-TTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
923077 AGCGGT-CCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
923116 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAATTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
923181 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCATTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
*
923221 AGTCCAATATCCTTCGTTGTGAAGTTGAAAATGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
*
923286 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGA
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
923326 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTAAAATTGAGAAGTTGTTGTTGACAAGC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
923391 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
66 AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* ** *
923431 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTAAGAAGTTGTTTGTTGACAAC
1 AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTG-TTGTTGACAAG
* * * *
923496 CAGCCGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTCG
65 CAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
* * *
923537 AGTGCCACGATATCCTCCGTCGTGGAGTTGAAAT
1 AGT-CCA--ATATCCTTCGTTGTGAAGTTGAAAT
923571 CGCGGATGGC
Statistics
Matches: 509, Mismatches: 34, Indels: 19
0.91 0.06 0.03
Matches are distributed among these distances:
99 67 0.13
100 17 0.03
101 1 0.00
102 6 0.01
103 5 0.01
104 18 0.04
105 285 0.56
106 85 0.17
107 3 0.01
109 22 0.04
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
AGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAGATTGGGAAGTTGTTGTTGACAAGC
AGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGG
Found at i:924022 original size:29 final size:27
Alignment explanation
Indices: 923966--924023 Score: 64
Period size: 29 Copynumber: 2.0 Consensus size: 27
923956 GAATCTTGAT
*
923966 TCTTGAATCTTCAAATTTTGATCCCTGA
1 TCTTGAATCTTCAAATTTAGAT-CCTGA
923994 TCTTGAATTCTTCAAATGTTCAGAT-CTGA
1 TCTTGAA-TCTTCAAAT-TT-AGATCCTGA
924023 T
1 T
924024 GTGCACATTC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 7 0.27
29 14 0.54
30 2 0.08
31 3 0.12
ACGTcount: A:0.26, C:0.19, G:0.12, T:0.43
Consensus pattern (27 bp):
TCTTGAATCTTCAAATTTAGATCCTGA
Found at i:924304 original size:66 final size:68
Alignment explanation
Indices: 924161--924330 Score: 213
Period size: 68 Copynumber: 2.5 Consensus size: 68
924151 GGAAACGATC
* * *
924161 TCAAAGATATCTGTTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTGTGTTTTAAGGGAAA
1 TCAAAGAT-TTTG-TGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTGTGTTTTAAGGGAAA
924226 TAAAT
64 TAAAT
** * * *
924231 TTGAAGATTTTGTGTTTCAAGAGTAACTGTCTCAAGGGAGAC-AAATT-TGTTTTAGGGGAAATA
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTGTGTTTTAAGGGAAATA
924294 AAT
66 AAT
*
924297 TCAAAGA-TTT-TGTTTCAAGGGAAACTGTCTCAAG
1 TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAG
924331 ATAGACGAAA
Statistics
Matches: 88, Mismatches: 12, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
64 22 0.25
65 3 0.03
66 23 0.26
67 5 0.06
68 26 0.30
69 3 0.03
70 6 0.07
ACGTcount: A:0.35, C:0.10, G:0.22, T:0.32
Consensus pattern (68 bp):
TCAAAGATTTTGTGTTTCAAGAGAAACTGTCTCAAGGGAAACAAAATTGTGTTTTAAGGGAAATA
AAT
Found at i:924343 original size:66 final size:66
Alignment explanation
Indices: 924174--924566 Score: 235
Period size: 65 Copynumber: 5.8 Consensus size: 66
924164 AAGATATCTG
* * * **
924174 TTGTTTCATGAGAAACGGTCTCAAGGGAAACAAAATTGTGTTTTAAGGGAAATAAATTTGAAGAT
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATT-TGTTTTAAGGGAAATAAATTCAAAGAT
924239 TT
65 TT
* *
924241 TGTGTTTCAAGAGTAACTGTCTCAAGGGAGAC-AAATTTGTTTTAGGGGAAATAAATTCAAAGA-
1 T-TGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGAT
924304 TT
65 TT
* ** * * *
924306 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACT--GTCTCAAGA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGAC-AAAATTTGTTTTAAGGGAAA-TAAAT-TC-A-A
**
924368 GAGACAAAACT
61 -AG----ATTT
* * * ** * * * * * *
924379 TAGTTCCAAAAGAAACTGTCTCAAGGGAGAGGAAATTTGTTTCAAAGAAAACATATTCAAATA-T
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
924443 T
66 T
* * * *
924444 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGA-T-
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA-----T-AA-ATTC
* **
924507 AGACGAAAT
59 A-AAGATTT
* *
924516 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTGTTTCAAGGGAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAA
924567 CTGTCTCAAG
Statistics
Matches: 253, Mismatches: 48, Indels: 45
0.73 0.14 0.13
Matches are distributed among these distances:
64 27 0.11
65 59 0.23
66 29 0.11
67 7 0.03
68 28 0.11
70 2 0.01
71 5 0.02
72 56 0.22
73 39 0.15
74 1 0.00
ACGTcount: A:0.39, C:0.12, G:0.21, T:0.28
Consensus pattern (66 bp):
TTGTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTTAAGGGAAATAAATTCAAAGATT
T
Found at i:924357 original size:36 final size:35
Alignment explanation
Indices: 924306--924586 Score: 272
Period size: 36 Copynumber: 8.0 Consensus size: 35
924296 TTCAAAGATT
* *
924306 TTGTTTCAAGGGAAACTGTCTCAAGATAGACGAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
924342 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * * *
924377 CTTAGTTCCAAAAGAAACTGTCTCAAGGGAGAGGAAAT
1 -TT-GTTTCAAGAGAAACTGTCTCAAGAGAGA-CAAAA
* * **
924415 TTGTTTCAA-AGAAAACATAT-TC---A-A-A-TATT
1 TTGTTTCAAGAG-AAAC-TGTCTCAAGAGAGACAAAA
*
924444 TTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
* * * *
924479 TTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAAT
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGAC-AAAA
924516 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
1 TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
*
924551 TTTGTTTCAAGGGAAACTGTCTCAAGAGAGACAAAA
1 -TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
924587 CTCTTCTAGT
Statistics
Matches: 204, Mismatches: 25, Indels: 32
0.78 0.10 0.12
Matches are distributed among these distances:
28 2 0.01
29 17 0.08
30 1 0.00
31 1 0.00
32 2 0.01
33 1 0.00
34 1 0.00
35 10 0.05
36 134 0.66
37 32 0.16
38 3 0.01
ACGTcount: A:0.41, C:0.14, G:0.20, T:0.26
Consensus pattern (35 bp):
TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAA
Found at i:924445 original size:138 final size:136
Alignment explanation
Indices: 924255--924560 Score: 407
Period size: 138 Copynumber: 2.2 Consensus size: 136
924245 TTTCAAGAGT
* * ** * *
924255 AACTGTCTCAAGGGAGACAAATTTGTTTTAGGGGAAATAAATTCAAAGATTTTGTTTCAAGGGAA
1 AACTGTCTCAAGGGAGAAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAA
* *
924320 ACTGTCTCAAGATAGACGAAAA-TTGTTTCAAGAGAAACTGTCTCAAGAGAGACAAAACTTAGTT
66 ACTGTCTCAAGAGAGAC-AAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTAGTT
924384 CCAAAAGA
129 CCAAAAGA
* * *
924392 AACTGTCTCAAGGGAGAGGAAATTTGTTTCAAAGAAAACATATTCAAATATTTTGTTTCAAGGGA
1 AACTGTCTCAAGGGAGA-AAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGA
* * * * *
924457 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGTTT
65 AACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTC
*
924522 CAAGAGA
130 CAAAAGA
*
924529 AACTGTCTCAAGAGAGACAAAATTTGTTTCAA
1 AACTGTCTCAAGGGAGA-AAAATTTGTTTCAA
924561 GGGAAACTGT
Statistics
Matches: 148, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
137 61 0.41
138 87 0.59
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (136 bp):
AACTGTCTCAAGGGAGAAAAATTTGTTTCAAAGAAAACAAATTCAAAGATTTTGTTTCAAGGGAA
ACTGTCTCAAGAGAGACAAAATTTATTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTAGTTCC
AAAAGA
Found at i:924608 original size:35 final size:36
Alignment explanation
Indices: 924448--924620 Score: 172
Period size: 36 Copynumber: 4.8 Consensus size: 36
924438 AATATTTTGT
* * **
924448 TTCAAGGGAAACTGTCTCAAGAGAGACAAAATTTAT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * * * *
924484 TTCAAGGGAAACTGTCTCAAGATAGACGAAATTTGT
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* *
924520 TTCAA-GAGAAACTGTCTCAAGAGAGACAAAATTTGT
1 TTCAAGGA-AAACTGTCTCAAGAGAGACAAAATCTGC
*
924556 TTCAAGGGAAACTGTCTCAAGAGAGACAAAA-CT-C
1 TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
* * *
924590 TTCTAGTGAAAACGGTCTCAAGCGAGACAAA
1 TTCAAG-GAAAACTGTCTCAAGAGAGACAAA
924621 TCTTGTTTTA
Statistics
Matches: 121, Mismatches: 13, Indels: 7
0.86 0.09 0.05
Matches are distributed among these distances:
34 5 0.04
35 23 0.19
36 92 0.76
37 1 0.01
ACGTcount: A:0.40, C:0.16, G:0.21, T:0.23
Consensus pattern (36 bp):
TTCAAGGAAAACTGTCTCAAGAGAGACAAAATCTGC
Found at i:925092 original size:18 final size:18
Alignment explanation
Indices: 925065--925100 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
925055 TGTTGAATCC
* *
925065 CCAAAGATGCCTCAATAT
1 CCAAAAATGCCCCAATAT
925083 CCAAAAATGCCCCAATAT
1 CCAAAAATGCCCCAATAT
925101 TTGATGTTGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.42, C:0.31, G:0.08, T:0.19
Consensus pattern (18 bp):
CCAAAAATGCCCCAATAT
Found at i:925542 original size:22 final size:22
Alignment explanation
Indices: 925516--925571 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
925506 TTGTGTTTGG
*
925516 TCAAAGGTTTGGCATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
925538 TCAAAGGTTTGACATTTGATGC
1 TCAAAGGTTTGACATTTGATGC
925560 TCAAAGGTTTGA
1 TCAAAGGTTTGA
925572 TGGGATAGCC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.12, G:0.25, T:0.36
Consensus pattern (22 bp):
TCAAAGGTTTGACATTTGATGC
Found at i:926238 original size:19 final size:20
Alignment explanation
Indices: 926203--926241 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
926193 TTTGTCCCTC
*
926203 TTTCTTTTTGATTCTTGTTT
1 TTTCCTTTTGATTCTTGTTT
926223 TTTCCTTTTG-TTCTTGTTT
1 TTTCCTTTTGATTCTTGTTT
926242 CTCTTTTTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.03, C:0.13, G:0.10, T:0.74
Consensus pattern (20 bp):
TTTCCTTTTGATTCTTGTTT
Found at i:926266 original size:18 final size:19
Alignment explanation
Indices: 926239--926289 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 19
926229 TTTGTTCTTG
* *
926239 TTTCTCTTTTTCTTTGTTTT
1 TTTCT-TTTTTCTTTATTCT
*
926259 TTTGTTTTTT-TTTATTCT
1 TTTCTTTTTTCTTTATTCT
926277 TTTCTTTTTTCTT
1 TTTCTTTTTTCTT
926290 CTTGATTGGA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
18 15 0.58
19 7 0.27
20 4 0.15
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (19 bp):
TTTCTTTTTTCTTTATTCT
Found at i:926288 original size:12 final size:12
Alignment explanation
Indices: 926239--926289 Score: 50
Period size: 12 Copynumber: 4.1 Consensus size: 12
926229 TTTGTTCTTG
926239 TTTCTCTTTTTCT
1 TTTCT-TTTTTCT
*
926252 TTGT-TTTTTTGT
1 TT-TCTTTTTTCT
*
926264 TTTTTTTTATTCT
1 TTTCTTTT-TTCT
926277 TTTCTTTTTTCT
1 TTTCTTTTTTCT
926289 T
1 T
926290 CTTGATTGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
11 1 0.03
12 17 0.53
13 13 0.41
14 1 0.03
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.82
Consensus pattern (12 bp):
TTTCTTTTTTCT
Found at i:929308 original size:5 final size:5
Alignment explanation
Indices: 929298--929371 Score: 75
Period size: 5 Copynumber: 15.4 Consensus size: 5
929288 TAGATATAAA
* * **
929298 AAAAT AAAAT AAAAT -AAAT AAAAT -AAAT -AAAT AAATT CAACC AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
929345 AAAA- AGAAAT AAAAT AAAAT AAAAT AA
1 AAAAT A-AAAT AAAAT AAAAT AAAAT AA
929372 TAAATAAATA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
4 13 0.22
5 44 0.76
6 1 0.02
ACGTcount: A:0.76, C:0.04, G:0.01, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:929318 original size:4 final size:4
Alignment explanation
Indices: 929293--929387 Score: 54
Period size: 4 Copynumber: 22.2 Consensus size: 4
929283 CATGTTAGAT
*
929293 ATAA AAAA ATAAA ATAAA ATAA ATAAA ATAA ATAA ATAA ATTCAA CCA-AA
1 ATAA ATAA AT-AA AT-AA ATAA AT-AA ATAA ATAA ATAA A-T-AA --ATAA
*
929343 AT-A A-AA AGAA ATAAA ATAAA ATAA A-ATA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA AT-AA AT-AA ATAA ATA-A ATAA ATAA ATAA ATAA A
929388 GCATAGAAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 24
0.74 0.03 0.23
Matches are distributed among these distances:
3 6 0.08
4 41 0.54
5 26 0.34
6 2 0.03
8 1 0.01
ACGTcount: A:0.76, C:0.03, G:0.01, T:0.20
Consensus pattern (4 bp):
ATAA
Found at i:930155 original size:37 final size:35
Alignment explanation
Indices: 930113--930211 Score: 139
Period size: 34 Copynumber: 2.8 Consensus size: 35
930103 AGTAGAACTC
930113 TATCCTATTTTTAGGAGTTTGAATCCTAACAAAATT-
1 TATCCTATTTTTAGGAGTTTGAATCCT-A-AAAATTA
*
930149 TCATCCTATTTTTAGGAGTTTGAATCCT-GAAATTA
1 T-ATCCTATTTTTAGGAGTTTGAATCCTAAAAATTA
*
930184 TATCCTATTTTTAGGAGTTCGAATCCTA
1 TATCCTATTTTTAGGAGTTTGAATCCTA
930212 GTAAGACGAA
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
34 30 0.52
35 1 0.02
36 1 0.02
37 26 0.45
ACGTcount: A:0.29, C:0.15, G:0.13, T:0.42
Consensus pattern (35 bp):
TATCCTATTTTTAGGAGTTTGAATCCTAAAAATTA
Found at i:930939 original size:3 final size:3
Alignment explanation
Indices: 930931--930976 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
930921 GATAAGGGAA
930931 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
930977 TGATATGAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:933479 original size:19 final size:17
Alignment explanation
Indices: 933438--933480 Score: 50
Period size: 19 Copynumber: 2.4 Consensus size: 17
933428 CTTAACGCTA
*
933438 AATAAAATATAAATATT
1 AATAATATATAAATATT
933455 ATATAATATATTAAATATTT
1 A-ATAATATA-TAAATA-TT
933475 AATAAT
1 AATAAT
933481 TTTGACTAAT
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 1 0.05
18 7 0.32
19 11 0.50
20 3 0.14
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
AATAATATATAAATATT
Found at i:938222 original size:2 final size:2
Alignment explanation
Indices: 938215--938243 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
938205 TTCTTCTTCT
938215 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
938244 TTGTGAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:942540 original size:6 final size:6
Alignment explanation
Indices: 942522--942607 Score: 52
Period size: 6 Copynumber: 14.0 Consensus size: 6
942512 TGAAAGATAG
* *
942522 AAAT-A AAAGAA AAATAA AAA-AGA AAGTAA AAATAA ATAGATAA AATATAA
1 AAATAA AAATAA AAATAA AAATA-A AAATAA AAATAA A-A-ATAA AA-ATAA
* * * *
942572 AAGT-A AAATAGA AAATAA TAATAA TAATAA TAATAA
1 AAATAA AAATA-A AAATAA AAATAA AAATAA AAATAA
942608 TAGAAATAAT
Statistics
Matches: 66, Mismatches: 8, Indels: 13
0.76 0.09 0.15
Matches are distributed among these distances:
5 8 0.12
6 38 0.58
7 15 0.23
8 5 0.08
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:942587 original size:33 final size:30
Alignment explanation
Indices: 942513--942589 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 30
942503 AAAGGGAGAT
942513 GAAAGATAG-AAATAAAAGAAAAATAAAAAA
1 GAAA-ATAGAAAATAAAAGAAAAATAAAAAA
* *
942543 GAAAGTA-AAAATAAATAGATAAAATATAAAA
1 GAAAATAGAAAATAAA-AGA-AAAATAAAAAA
942574 GTAAAATAGAAAATAA
1 G-AAAATAGAAAATAA
942590 TAATAATAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
29 9 0.23
30 7 0.18
31 11 0.28
32 5 0.13
33 7 0.18
ACGTcount: A:0.73, C:0.00, G:0.12, T:0.16
Consensus pattern (30 bp):
GAAAATAGAAAATAAAAGAAAAATAAAAAA
Found at i:942593 original size:3 final size:3
Alignment explanation
Indices: 942585--942619 Score: 54
Period size: 3 Copynumber: 11.7 Consensus size: 3
942575 TAAAATAGAA
942585 AAT AAT AAT AAT AAT AAT AAT AAT AGA- AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AA
942620 AAGAGTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 1 0.03
3 28 0.93
4 1 0.03
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (3 bp):
AAT
Found at i:942705 original size:18 final size:17
Alignment explanation
Indices: 942675--942709 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
942665 ATATATGAAT
942675 AAAAAATAATAATAATA
1 AAAAAATAATAATAATA
*
942692 AAAAGAATACTAATAATA
1 AAAA-AATAATAATAATA
942710 GTTATAATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.23
Consensus pattern (17 bp):
AAAAAATAATAATAATA
Found at i:945442 original size:23 final size:23
Alignment explanation
Indices: 945416--945461 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
945406 CAAAATATTA
*
945416 TGTACTTTAACTATGTATTTTTT
1 TGTACTATAACTATGTATTTTTT
*
945439 TGTACTATAACTATGTCTTTTTT
1 TGTACTATAACTATGTATTTTTT
945462 AACTAAGTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.22, C:0.11, G:0.09, T:0.59
Consensus pattern (23 bp):
TGTACTATAACTATGTATTTTTT
Found at i:945466 original size:21 final size:23
Alignment explanation
Indices: 945423--945466 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
945413 TTATGTACTT
* *
945423 TAACTATGTATTTTTTTGTACTA
1 TAACTATGTACTTTTTTGAACTA
945446 TAACTATGT-CTTTTTT-AACTA
1 TAACTATGTACTTTTTTGAACTA
945467 AGTTTTTTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 6 0.32
23 9 0.47
ACGTcount: A:0.27, C:0.11, G:0.07, T:0.55
Consensus pattern (23 bp):
TAACTATGTACTTTTTTGAACTA
Found at i:948629 original size:41 final size:41
Alignment explanation
Indices: 948602--948693 Score: 130
Period size: 41 Copynumber: 2.2 Consensus size: 41
948592 GCGAATTGGG
* * * *
948602 AAAATCGCAATGCGATACTTACTATCGCAATGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
948643 AAAATCGCAACGAGATACTGACTTTCGCAACGCGATAATAC
1 AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
*
948684 ATAATCGCAA
1 AAAATCGCAA
948694 TGCGATTTTC
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 45 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.22
Consensus pattern (41 bp):
AAAATCGCAACGAGATACTGACTATCGCAACGCGATAATAC
Found at i:948651 original size:21 final size:20
Alignment explanation
Indices: 948603--948699 Score: 72
Period size: 20 Copynumber: 4.8 Consensus size: 20
948593 CGAATTGGGA
*
948603 AAATCGCAATGCGATACTTAC
1 AAATCGCAATGCGATA-ATAC
*
948624 -TATCGCAATGCGATAATAC
1 AAATCGCAATGCGATAATAC
* * *
948643 AAAATCGCAACGAGATACTGAC
1 -AAATCGCAATGCGATAAT-AC
** *
948665 -TTTCGCAACGCGATAATAC
1 AAATCGCAATGCGATAATAC
948684 ATAATCGCAATGCGAT
1 A-AATCGCAATGCGAT
948700 TTTCAAAGCG
Statistics
Matches: 58, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
19 5 0.09
20 27 0.47
21 24 0.41
22 2 0.03
ACGTcount: A:0.38, C:0.23, G:0.16, T:0.23
Consensus pattern (20 bp):
AAATCGCAATGCGATAATAC
Found at i:948876 original size:22 final size:22
Alignment explanation
Indices: 948848--948891 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
948838 CACTCTCTCA
948848 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
948870 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
948892 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:949208 original size:20 final size:20
Alignment explanation
Indices: 949154--949212 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
949144 GCGATTCTCT
**
949154 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
949174 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
949194 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
949213 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:949403 original size:25 final size:24
Alignment explanation
Indices: 949349--949403 Score: 58
Period size: 25 Copynumber: 2.2 Consensus size: 24
949339 TGTTTATTAT
* *
949349 TGTTTTTGGTATATCTTCACAGTG
1 TGTTTTTGGTATATCTTAACAGTA
949373 TAGTTTTTGGTATATC-TAACTTAGTA
1 T-GTTTTTGGTATATCTTAAC--AGTA
949399 TGTTT
1 TGTTT
949404 ATTGTTTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
24 4 0.15
25 18 0.69
26 4 0.15
ACGTcount: A:0.20, C:0.09, G:0.18, T:0.53
Consensus pattern (24 bp):
TGTTTTTGGTATATCTTAACAGTA
Found at i:950555 original size:18 final size:18
Alignment explanation
Indices: 950534--950578 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
950524 TCCACTTCGG
*
950534 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
950552 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
950570 GAGCCATCA
1 GAGCCATCA
950579 TCTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:951087 original size:20 final size:20
Alignment explanation
Indices: 951056--951106 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
951046 GTTTACTTGA
*
951056 GCAACACGAAAATGACTATC
1 GCAACGCGAAAATGACTATC
* *
951076 GTAACGCGAAAATGGCTATC
1 GCAACGCGAAAATGACTATC
*
951096 GCAATGCGAAA
1 GCAACGCGAAA
951107 TGAAAATCAC
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.41, C:0.22, G:0.22, T:0.16
Consensus pattern (20 bp):
GCAACGCGAAAATGACTATC
Found at i:951152 original size:32 final size:33
Alignment explanation
Indices: 951093--951217 Score: 153
Period size: 32 Copynumber: 3.7 Consensus size: 33
951083 GAAAATGGCT
*
951093 ATCGCAATGCGAAATGAAAATCACAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
951126 ATCGCAATGCGAAATG-AAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGACAAA
* * *
951158 ATTGCAACGCGAAATGAAAATCGCAATACGAAATGAA
1 ATCGCAATGCGAAATGAAAATCGC-A-ACGACA--AA
* *
951195 ATCGTAACGCGAAATGAAAATCG
1 ATCGCAATGCGAAATGAAAATCG
951218 TAATGCGATT
Statistics
Matches: 81, Mismatches: 6, Indels: 6
0.87 0.06 0.06
Matches are distributed among these distances:
32 29 0.36
33 23 0.28
34 1 0.01
35 5 0.06
37 23 0.28
ACGTcount: A:0.48, C:0.19, G:0.18, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGACAAA
Found at i:951177 original size:19 final size:19
Alignment explanation
Indices: 951123--951217 Score: 87
Period size: 18 Copynumber: 5.4 Consensus size: 19
951113 TCACAACGAC
*
951123 AAAATCGCAATGCGAAATG
1 AAAATCGCAACGCGAAATG
*
951142 -AAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAATG
*
951155 AAAATTGCAACGCGAAATG
1 AAAATCGCAACGCGAAATG
**
951174 AAAATCGCAATACGAAATG
1 AAAATCGCAACGCGAAATG
*
951193 -AAATCGTAACGCGAAATG
1 AAAATCGCAACGCGAAATG
951211 AAAATCG
1 AAAATCG
951218 TAATGCGATT
Statistics
Matches: 60, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 9 0.15
16 4 0.07
18 25 0.42
19 22 0.37
ACGTcount: A:0.48, C:0.18, G:0.19, T:0.15
Consensus pattern (19 bp):
AAAATCGCAACGCGAAATG
Found at i:951218 original size:19 final size:19
Alignment explanation
Indices: 951163--951225 Score: 83
Period size: 19 Copynumber: 3.4 Consensus size: 19
951153 ACAAAATTGC
*
951163 AACGCGAAATGAAAATCGC
1 AACGCGAAATGAAAATCGT
**
951182 AATACGAAATG-AAATCGT
1 AACGCGAAATGAAAATCGT
951200 AACGCGAAATGAAAATCGT
1 AACGCGAAATGAAAATCGT
*
951219 AATGCGA
1 AACGCGA
951226 TTTGTGTTTC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
18 15 0.41
19 22 0.59
ACGTcount: A:0.48, C:0.16, G:0.21, T:0.16
Consensus pattern (19 bp):
AACGCGAAATGAAAATCGT
Found at i:951256 original size:14 final size:14
Alignment explanation
Indices: 951237--951327 Score: 74
Period size: 14 Copynumber: 5.9 Consensus size: 14
951227 TTGTGTTTCG
951237 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
951251 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
951267 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
951283 CGTTGCGATTTTCATTT
1 CGTTGCGA-TTT--TGT
951300 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
*
951316 TGTTGCGATTTT
1 CGTTGCGATTTT
951328 TATTTCGCAT
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
14 27 0.43
15 3 0.05
16 11 0.17
17 4 0.06
18 12 0.19
19 6 0.10
ACGTcount: A:0.11, C:0.16, G:0.23, T:0.49
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:951301 original size:33 final size:33
Alignment explanation
Indices: 951232--951343 Score: 190
Period size: 33 Copynumber: 3.4 Consensus size: 33
951222 GCGATTTGTG
*
951232 TTTCGCGTTGCGATTTTGTCGTTGCGA-TTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
951264 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
* *
951297 TTTCGCATTGCGATTTTGTTGTTGCGATTTTTA
1 TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
951330 TTTCGCATTGCGAT
1 TTTCGCATTGCGAT
951344 AGCCATTTCC
Statistics
Matches: 76, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
32 26 0.34
33 50 0.66
ACGTcount: A:0.12, C:0.17, G:0.22, T:0.49
Consensus pattern (33 bp):
TTTCGCATTGCGATTTTGTCGTTGCGATTTTCA
Found at i:951358 original size:20 final size:19
Alignment explanation
Indices: 951329--951383 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
951319 TGCGATTTTT
951329 ATTTCGCATTGCGATAGCC
1 ATTTCGCATTGCGATAGCC
* *
951348 ATTTCCGCATTGTGATAGTC
1 ATTT-CGCATTGCGATAGCC
*
951368 ATTTTCGCGTTGCGAT
1 A-TTTCGCATTGCGAT
951384 TTTAAGTTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 4 0.13
20 23 0.77
21 3 0.10
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (19 bp):
ATTTCGCATTGCGATAGCC
Found at i:953275 original size:14 final size:14
Alignment explanation
Indices: 953256--953291 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
953246 ATTGTTTAAT
953256 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
953270 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
953284 TGATTTGT
1 TGATTTGT
953292 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:953432 original size:19 final size:19
Alignment explanation
Indices: 953408--953475 Score: 101
Period size: 19 Copynumber: 3.8 Consensus size: 19
953398 ATCGCAACGA
953408 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
953427 GAAAATCGCAATGCGAAAT
1 GAAAATCGCAATGCGAAAT
953446 GAAAATCGCAA--CG--A-
1 GAAAATCGCAATGCGAAAT
953460 GAAAATCGCAATGCGA
1 GAAAATCGCAATGCGA
953476 TTTTCATTTC
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 11 0.24
15 1 0.02
16 2 0.04
17 2 0.04
19 30 0.65
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.13
Consensus pattern (19 bp):
GAAAATCGCAATGCGAAAT
Found at i:953519 original size:20 final size:20
Alignment explanation
Indices: 953502--953589 Score: 106
Period size: 20 Copynumber: 4.4 Consensus size: 20
953492 CGATTTTCTA
953502 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
*** *
953522 GTTGCGATTTTTCA-TTTCGA
1 GTTGCGA-TAGCCATTTTCGC
* *
953542 ATTACGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
953562 GTTGCGATAGCCATTTTCGC
1 GTTGCGATAGCCATTTTCGC
953582 GTTGCGAT
1 GTTGCGAT
953590 TTCCCCGTTG
Statistics
Matches: 54, Mismatches: 12, Indels: 4
0.77 0.17 0.06
Matches are distributed among these distances:
19 3 0.06
20 48 0.89
21 3 0.06
ACGTcount: A:0.17, C:0.22, G:0.23, T:0.39
Consensus pattern (20 bp):
GTTGCGATAGCCATTTTCGC
Found at i:953923 original size:20 final size:21
Alignment explanation
Indices: 953879--953927 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
953869 ATAGTCAGTA
*
953879 TCGCATTGCGATTTTCCAAAT
1 TCGCATTGCGATTTTACAAAT
**
953900 TCGCATTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACAAAT
953920 TCGCATTG
1 TCGCATTG
953928 TGAATTATTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 14 0.56
21 11 0.44
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTACAAAT
Found at i:953937 original size:16 final size:16
Alignment explanation
Indices: 953916--953950 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
953906 TGCGATTTAC
953916 TTATTCGCATTGTGAA
1 TTATTCGCATTGTGAA
953932 TTATTCGCATTGTGAA
1 TTATTCGCATTGTGAA
953948 TTA
1 TTA
953951 GGAAAATCGC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.26, C:0.11, G:0.17, T:0.46
Consensus pattern (16 bp):
TTATTCGCATTGTGAA
Found at i:954162 original size:12 final size:12
Alignment explanation
Indices: 954143--954176 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
954133 CTCTCCGACG
954143 ACATCCGTTCCT
1 ACATCCGTTCCT
*
954155 ATATCCGTTCCT
1 ACATCCGTTCCT
954167 ACATCC-TTCC
1 ACATCCGTTCC
954177 CCATCCGACA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 4 0.20
12 16 0.80
ACGTcount: A:0.18, C:0.41, G:0.06, T:0.35
Consensus pattern (12 bp):
ACATCCGTTCCT
Found at i:954758 original size:24 final size:24
Alignment explanation
Indices: 954731--954784 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
954721 GTATTCGAAA
*
954731 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATATTGGTCAATACCCGGAC
* *
954755 TTTGATATTGGTCAATACTCGGAT
1 TTTGATATTGGTCAATACCCGGAC
954779 TTTGAT
1 TTTGAT
954785 GATGTTTCAG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.22, C:0.17, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATATTGGTCAATACCCGGAC
Found at i:954976 original size:12 final size:12
Alignment explanation
Indices: 954959--954995 Score: 74
Period size: 12 Copynumber: 3.1 Consensus size: 12
954949 ATATAATCCT
954959 GAAGAAGAAAAA
1 GAAGAAGAAAAA
954971 GAAGAAGAAAAA
1 GAAGAAGAAAAA
954983 GAAGAAGAAAAA
1 GAAGAAGAAAAA
954995 G
1 G
954996 TCCCCGAAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.73, C:0.00, G:0.27, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:957324 original size:33 final size:33
Alignment explanation
Indices: 957287--957380 Score: 161
Period size: 33 Copynumber: 2.8 Consensus size: 33
957277 GGAAATTACT
* *
957287 ATCGCAATGTGAAATGAAAATCGCACCGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
957320 ATCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
957353 ATCGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
957381 CGAATTTAAT
Statistics
Matches: 58, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 58 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:957343 original size:19 final size:19
Alignment explanation
Indices: 957287--957384 Score: 72
Period size: 19 Copynumber: 5.7 Consensus size: 19
957277 GGAAATTACT
*
957287 ATCGCAATGTGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
957306 ATCGC-A-CCG--A-GAGA
1 ATCGCAATGCGAAATGAAA
957320 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
957339 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
957353 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
957372 ATCGCAACGCGAA
1 ATCGCAATGCGAA
957385 TTTAATTTCG
Statistics
Matches: 59, Mismatches: 10, Indels: 20
0.66 0.11 0.22
Matches are distributed among these distances:
14 17 0.29
15 3 0.05
16 4 0.07
17 3 0.05
18 3 0.05
19 29 0.49
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.13
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:957412 original size:14 final size:14
Alignment explanation
Indices: 957395--957451 Score: 51
Period size: 14 Copynumber: 3.7 Consensus size: 14
957385 TTTAATTTCG
957395 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
* *
957409 CGTTGTGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
957428 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
957442 CGTTGCGATT
1 CGTTGCGATT
957452 TTCATTTCGC
Statistics
Matches: 34, Mismatches: 4, Indels: 10
0.71 0.08 0.21
Matches are distributed among these distances:
14 19 0.56
16 3 0.09
17 3 0.09
19 9 0.26
ACGTcount: A:0.09, C:0.23, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:957431 original size:33 final size:33
Alignment explanation
Indices: 957380--957469 Score: 144
Period size: 33 Copynumber: 2.7 Consensus size: 33
957370 AAATCGCAAC
* *
957380 GCGAATTTAATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
957413 GTGATTTTCATTTCGCGTTGCGATTCTCTCGTT
1 GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
*
957446 GCGATTTTCATTTCGCATTGCGAT
1 GCGATTTTCATTTCGCGTTGCGAT
957470 AGTACTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 52 1.00
ACGTcount: A:0.13, C:0.21, G:0.21, T:0.44
Consensus pattern (33 bp):
GCGATTTTCATTTCGCGTTGCGATTCTCTCGTT
Found at i:957437 original size:19 final size:19
Alignment explanation
Indices: 957409--957469 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
957399 GCGATTCTCT
*
957409 CGTTGTGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
957428 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
957442 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
957461 CATTGCGAT
1 CGTTGCGAT
957470 AGTACTTTTT
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 10 0.30
16 3 0.09
17 3 0.09
19 17 0.52
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:959017 original size:42 final size:41
Alignment explanation
Indices: 958958--959108 Score: 160
Period size: 42 Copynumber: 3.6 Consensus size: 41
958948 GTGAATCGGG
* *
958958 CTCTTGAATGGTGGGAGGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGA-CTCTTCAAGGATGACAGTGGC
* * *
959000 CTCTTGAACGGTGGGAGGGGACTC-TCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGA-GGGACTCTTCAAGG-ATGACAGTGGC
* * * * *
959042 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGTGGC
1 CTCTTGAACGGTGGGAG-GGACTCTTCAAGGATGACAGTGGC
959084 CTCTTGAACGGTGGGAGGGGACTCT
1 CTCTTGAACGGTGGGA-GGGACTCT
959109 CGAGGAATGA
Statistics
Matches: 88, Mismatches: 16, Indels: 10
0.77 0.14 0.09
Matches are distributed among these distances:
41 5 0.06
42 75 0.85
43 8 0.09
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGACTCTTCAAGGATGACAGTGGC
Found at i:959099 original size:84 final size:78
Alignment explanation
Indices: 958988--959157 Score: 286
Period size: 84 Copynumber: 2.1 Consensus size: 78
958978 CCTCTTCAAC
958988 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGCCTCTTCAACGA
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATA--GG----TTCAACGA
959053 TAGGAGTGGACTCTTGAGG
60 TAGGAGTGGACTCTTGAGG
959072 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGTTCAACGATAGGAG
1 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGTTCAACGATAGGAG
959137 TGGACTCTTGAGG
66 TGGACTCTTGAGG
959150 GATGACAG
1 GATGACAG
959158 GCGAGTCGGG
Statistics
Matches: 86, Mismatches: 0, Indels: 6
0.93 0.00 0.07
Matches are distributed among these distances:
78 35 0.41
82 2 0.02
84 49 0.57
ACGTcount: A:0.24, C:0.16, G:0.38, T:0.21
Consensus pattern (78 bp):
GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGTTCAACGATAGGAG
TGGACTCTTGAGG
Found at i:959108 original size:21 final size:21
Alignment explanation
Indices: 958958--959108 Score: 58
Period size: 21 Copynumber: 7.2 Consensus size: 21
958948 GTGAATCGGG
*
958958 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
958978 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
959000 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** *
959021 CTCTCG-A-GGAATGATAGGGGC
1 CTCTTGAACGG--TGGGAGGGGA
* * * *
959042 CTCTTCAACGATAGGAGTGGA
1 CTCTTGAACGGTGGGAGGGGA
* ** * *
959063 CTCTTG-AGGGATGACAGTGGC
1 CTCTTGAACGG-TGGGAGGGGA
959084 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
959105 CTCT
1 CTCT
959109 CGAGGAATGA
Statistics
Matches: 86, Mismatches: 37, Indels: 14
0.63 0.27 0.10
Matches are distributed among these distances:
19 2 0.02
20 3 0.03
21 74 0.86
22 6 0.07
23 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.37, T:0.23
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:959551 original size:91 final size:90
Alignment explanation
Indices: 959376--959560 Score: 282
Period size: 91 Copynumber: 2.0 Consensus size: 90
959366 ATTTCAAACT
*
959376 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAAGAATACACAGTTTAGC
1 TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTT--A-AATAAACAGTTTAGC
959441 AGAATTGGCAGCAACCGAATAAATTTAC
63 AGAATTGGCAGCAACCGAATAAATTTAC
*
959469 TTCAACCAAAAGACAAAACAAAAAGACAAATACTAACTTTACAGTGTT-AATAAACAGTTTAGCA
1 TTCAACCAAAAGACAAAAC--AAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCA
* *
959533 GTATTGGCGGCAACCGAATAAATTTAC
64 GAATTGGCAGCAACCGAATAAATTTAC
959560 T
1 T
959561 AAGCAATCTA
Statistics
Matches: 86, Mismatches: 4, Indels: 6
0.90 0.04 0.06
Matches are distributed among these distances:
91 41 0.48
93 19 0.22
95 26 0.30
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (90 bp):
TTCAACCAAAAGACAAAACAAAGACAAATACTAACTTCACAGTGTTAAATAAACAGTTTAGCAGA
ATTGGCAGCAACCGAATAAATTTAC
Found at i:959737 original size:21 final size:21
Alignment explanation
Indices: 959692--959731 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
959682 ACTACCATCT
*
959692 CACGTAGAGTGACAACCTCAC
1 CACGTAAAGTGACAACCTCAC
959713 CACGTAAAGTAGAC-ACCTC
1 CACGTAAAGT-GACAACCTC
959732 CACACGCCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.35, C:0.33, G:0.17, T:0.15
Consensus pattern (21 bp):
CACGTAAAGTGACAACCTCAC
Found at i:961272 original size:20 final size:20
Alignment explanation
Indices: 961247--961284 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
961237 TCTTTTGGTT
961247 GAAATGAAAATCGCAACGCG
1 GAAATGAAAATCGCAACGCG
**
961267 GAAATGACTATCGCAACG
1 GAAATGAAAATCGCAACG
961285 AGAGAATCAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.42, C:0.21, G:0.24, T:0.13
Consensus pattern (20 bp):
GAAATGAAAATCGCAACGCG
Found at i:961328 original size:14 final size:14
Alignment explanation
Indices: 961276--961362 Score: 57
Period size: 14 Copynumber: 5.5 Consensus size: 14
961266 GGAAATGACT
961276 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
* *
961290 ATCACAACGTGAAATGA
1 ATCGCAAC--GAGA-GA
961307 CTATCGCAACGAGAGA
1 --ATCGCAACGAGAGA
*
961323 ATCGCAACGCGAAATGAAA
1 ATCGCAA--CG--A-GAGA
961342 ATCGCAACGAGAGA
1 ATCGCAACGAGAGA
961356 ATCGCAA
1 ATCGCAA
961363 GAAATGAAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 24 0.42
15 1 0.02
16 7 0.12
17 7 0.12
18 1 0.02
19 17 0.30
ACGTcount: A:0.44, C:0.22, G:0.23, T:0.11
Consensus pattern (14 bp):
ATCGCAACGAGAGA
Found at i:961359 original size:33 final size:33
Alignment explanation
Indices: 961255--961378 Score: 155
Period size: 33 Copynumber: 3.8 Consensus size: 33
961245 TTGAAATGAA
**
961255 AATCGCAACGCGGAAATGACTATCGCAACGAGAG
1 AATCGCAACGC-GAAATGAAAATCGCAACGAGAG
* * **
961289 AATCACAACGTGAAATGACTATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
961322 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAGAG
*
961355 AATCGCAA---GAAATGAAAATTGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
961379 TGCGATTTTG
Statistics
Matches: 83, Mismatches: 7, Indels: 4
0.88 0.07 0.04
Matches are distributed among these distances:
30 15 0.18
33 59 0.71
34 9 0.11
ACGTcount: A:0.44, C:0.20, G:0.23, T:0.13
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAGAG
Found at i:961976 original size:20 final size:20
Alignment explanation
Indices: 961947--961999 Score: 72
Period size: 20 Copynumber: 2.6 Consensus size: 20
961937 GCGCTATGTA
*
961947 AATCGCGTTGCGAAAGTCAG
1 AATCGTGTTGCGAAAGTCAG
961967 AATCGTGTTGCGAAAGTCAG
1 AATCGTGTTGCGAAAGTCAG
*
961987 TATC-TCGTTGCGA
1 AATCGT-GTTGCGA
962000 TTTTGTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 1 0.03
20 29 0.97
ACGTcount: A:0.26, C:0.19, G:0.28, T:0.26
Consensus pattern (20 bp):
AATCGTGTTGCGAAAGTCAG
Found at i:962033 original size:20 final size:20
Alignment explanation
Indices: 962008--962061 Score: 99
Period size: 20 Copynumber: 2.7 Consensus size: 20
961998 GATTTTGTAT
962008 TATCGCATTGCGATAGTAAG
1 TATCGCATTGCGATAGTAAG
*
962028 TATCGCATTGCGATAGTCAG
1 TATCGCATTGCGATAGTAAG
962048 TATCGCATTGCGAT
1 TATCGCATTGCGAT
962062 TTTCCCAATT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.26, C:0.19, G:0.24, T:0.31
Consensus pattern (20 bp):
TATCGCATTGCGATAGTAAG
Found at i:962080 original size:61 final size:61
Alignment explanation
Indices: 961948--962082 Score: 146
Period size: 61 Copynumber: 2.2 Consensus size: 61
961938 CGCTATGTAA
* * ** * * ** *
961948 ATCGCGTTGCGAAAGTCAGAATCGTGTTGCGAAAGTCAGTATCTCGTTGCGATTTTGTATT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
* * *
962009 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-CCAAT
962071 -TCGCGTTGCGAT
1 ATCGCGTTGCGAT
962083 TTACTTATTC
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
61 58 0.97
62 2 0.03
ACGTcount: A:0.23, C:0.19, G:0.24, T:0.33
Consensus pattern (61 bp):
ATCGCGTTGCGATAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTCCAAT
Found at i:963636 original size:2 final size:2
Alignment explanation
Indices: 963629--963665 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
963619 ATATTAACAT
963629 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
963666 TTGAAACATG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:964308 original size:16 final size:17
Alignment explanation
Indices: 964273--964310 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
964263 TTATGATCCT
* *
964273 ATTTGTAATTTAATTAA
1 ATTTATAATTCAATTAA
964290 ATTTATAATTCAA-TAA
1 ATTTATAATTCAATTAA
964306 ATTTA
1 ATTTA
964311 ATTCTCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 8 0.42
17 11 0.58
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (17 bp):
ATTTATAATTCAATTAA
Found at i:973686 original size:102 final size:102
Alignment explanation
Indices: 973505--973708 Score: 381
Period size: 102 Copynumber: 2.0 Consensus size: 102
973495 TCGGGATTTA
973505 CACTACAAAGAACATTGTAATCATACAAATCCATCACAAAGAACAAAAGCAACCAAATTTTACTC
1 CACTACAAAGAACATTGTAATCATACAAATCCATCACAAAGAACAAAAGCAACCAAATTTTACTC
973570 CTAGGTTCAAACTTCGAACCACGTATGGTTAATGGAC
66 CTAGGTTCAAACTTCGAACCACGTATGGTTAATGGAC
*
973607 CACTACAAAGAACATTGTAATCATACAAATCCATCACAAAGAACGAAAGCAACCAAATTTTACTC
1 CACTACAAAGAACATTGTAATCATACAAATCCATCACAAAGAACAAAAGCAACCAAATTTTACTC
* *
973672 CTAGGTTCATACTTCGAACCATGTATGGTTAATGGAC
66 CTAGGTTCAAACTTCGAACCACGTATGGTTAATGGAC
973709 TTTTATCAAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
102 99 1.00
ACGTcount: A:0.41, C:0.23, G:0.12, T:0.24
Consensus pattern (102 bp):
CACTACAAAGAACATTGTAATCATACAAATCCATCACAAAGAACAAAAGCAACCAAATTTTACTC
CTAGGTTCAAACTTCGAACCACGTATGGTTAATGGAC
Found at i:978175 original size:59 final size:60
Alignment explanation
Indices: 978098--978214 Score: 146
Period size: 60 Copynumber: 2.0 Consensus size: 60
978088 TACAATGGTC
* * * ** * *
978098 CCAACTATAGGGTGTTGCTGTATTGAG-TCTTTGACTATTAAAAGTTATAAAACGATCTT
1 CCAACAATAAGGTGTTGCTGTATTGAGTTCCTCAACTATTAAAAATTACAAAACGATCTT
* *
978157 CCAACAATAAGGTGTTGCTTTGTTGAGTTCCTCAACTATTAAAAATTACAAAACGATC
1 CCAACAATAAGGTGTTGCTGTATTGAGTTCCTCAACTATTAAAAATTACAAAACGATC
978215 ATTTGACTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 1
0.83 0.16 0.02
Matches are distributed among these distances:
59 23 0.48
60 25 0.52
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Consensus pattern (60 bp):
CCAACAATAAGGTGTTGCTGTATTGAGTTCCTCAACTATTAAAAATTACAAAACGATCTT
Found at i:978281 original size:24 final size:24
Alignment explanation
Indices: 978253--978300 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
978243 GGTTGATTAG
*
978253 GATATGTTAATATATATAATCTCA
1 GATATGCTAATATATATAATCTCA
978277 GATATGCTAATATATATAATCTCA
1 GATATGCTAATATATATAATCTCA
978301 TAATCTCAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (24 bp):
GATATGCTAATATATATAATCTCA
Found at i:979186 original size:3 final size:3
Alignment explanation
Indices: 979180--979226 Score: 67
Period size: 3 Copynumber: 15.3 Consensus size: 3
979170 TAAAATTAAA
* *
979180 ATT ATT ATT ATT ATC ATT ATT ATT AAT ATAT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT ATT ATT
979226 A
1 A
979227 AAAAAATACA
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
3 36 0.92
4 3 0.08
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:980775 original size:16 final size:15
Alignment explanation
Indices: 980754--980786 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
980744 AAAGATCCTA
980754 TTTATA-AAATTAAT
1 TTTATATAAATTAAT
*
980768 TTTATATAAATTACT
1 TTTATATAAATTAAT
980783 TTTA
1 TTTA
980787 GGAAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAAATTAAT
Found at i:989735 original size:75 final size:74
Alignment explanation
Indices: 989654--989892 Score: 313
Period size: 75 Copynumber: 3.2 Consensus size: 74
989644 AAGCAAATGT
*
989654 TGGGGCATGCTGAAAGCCCATTTCAATCAGAAAT-TGGAATATTAATGCATTTTGAACGTTTGTA
1 TGGGGCATGCTGAAAGCCCATTTCAATCAG-AATCAGGAATATTAAT-CATTTTGAACGTTTGTA
989718 TCAGTAAATAC
64 TCAGTAAATAC
* * *
989729 TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAAGAATATTGACTCATTTTGAACATTTGTAT
1 TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATT-AATCATTTTGAACGTTTGTAT
*
989794 CAGCAAATAC
65 CAGTAAATAC
* * *
989804 TGGGGCATGCTGAAAGCTCATTTCAATCAGAATCAGGAATGTTGACA-CATTTTGAACGTTCGTA
1 TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATT-A-ATCATTTTGAACGTTTGTA
*
989868 TCAGTAAACT-T
64 TCAGTAAA-TAC
*
989879 TGGGGCATGTTGAA
1 TGGGGCATGCTGAA
989893 GATCCATATA
Statistics
Matches: 146, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
74 3 0.02
75 140 0.96
76 3 0.02
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (74 bp):
TGGGGCATGCTGAAAGCCCATTTCAATCAGAATCAGGAATATTAATCATTTTGAACGTTTGTATC
AGTAAATAC
Found at i:990824 original size:54 final size:54
Alignment explanation
Indices: 990729--990890 Score: 245
Period size: 54 Copynumber: 3.0 Consensus size: 54
990719 CTGACCAGAA
* * * * *
990729 ATCTGTGCAGAAGCCACAGGAAATGATAAATGTGTTGTCAAATGTTTTACGAAT
1 ATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
*
990783 ATCT-ATGCCGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
1 ATCTGA-GCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
*
990837 ATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTATCAAATGTTTTACGAAC
1 ATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
990891 CAGTTATTCT
Statistics
Matches: 98, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
54 97 0.99
55 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.27
Consensus pattern (54 bp):
ATCTGAGCAGAAACCACAGGAAAAGATGAATGTGTTGTCAAATGTTTTACGAAC
Found at i:993790 original size:16 final size:15
Alignment explanation
Indices: 993769--993801 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
993759 AAGGATCCTA
993769 TTTATA-AAATTAAT
1 TTTATATAAATTAAT
*
993783 TTTATATAAATTACT
1 TTTATATAAATTAAT
993798 TTTA
1 TTTA
993802 GGAAAGATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 6 0.35
15 11 0.65
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (15 bp):
TTTATATAAATTAAT
Found at i:993918 original size:17 final size:17
Alignment explanation
Indices: 993896--993928 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
993886 TATTAAATAA
993896 ATAAA-TATCATATTTTT
1 ATAAATTAT-ATATTTTT
993913 ATAAATTATATATTTT
1 ATAAATTATATATTTT
993929 AAATATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 12 0.80
18 3 0.20
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (17 bp):
ATAAATTATATATTTTT
Found at i:1009114 original size:25 final size:26
Alignment explanation
Indices: 1009080--1009130 Score: 95
Period size: 25 Copynumber: 2.0 Consensus size: 26
1009070 ATGTAATTTT
1009080 TGGACTATGTGCATC-ATGCACATTC
1 TGGACTATGTGCATCAATGCACATTC
1009105 TGGACTATGTGCATCAATGCACATTC
1 TGGACTATGTGCATCAATGCACATTC
1009131 AATGTGTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
25 15 0.60
26 10 0.40
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.31
Consensus pattern (26 bp):
TGGACTATGTGCATCAATGCACATTC
Found at i:1009201 original size:19 final size:19
Alignment explanation
Indices: 1009177--1009228 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
1009167 GAATGCCCTT
1009177 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1009196 AGTGCATCGATGCATAAGG
1 AGTGCATCGATGCATAAGG
1009215 AGTGCATCGATGCA
1 AGTGCATCGATGCA
1009229 CCCCCTTAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.31, C:0.17, G:0.31, T:0.21
Consensus pattern (19 bp):
AGTGCATCGATGCATAAGG
Found at i:1009590 original size:20 final size:20
Alignment explanation
Indices: 1009567--1009609 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1009557 CATCACCGTT
*
1009567 CGCCGACCACCGTCTGCCGC
1 CGCCGACCACCGTCCGCCGC
*
1009587 CGCCGACCGCCGTCCGCCGC
1 CGCCGACCACCGTCCGCCGC
1009607 CGC
1 CGC
1009610 ACTCTGATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.07, C:0.58, G:0.28, T:0.07
Consensus pattern (20 bp):
CGCCGACCACCGTCCGCCGC
Found at i:1011297 original size:27 final size:27
Alignment explanation
Indices: 1011259--1011315 Score: 87
Period size: 27 Copynumber: 2.1 Consensus size: 27
1011249 TGCAAATCGA
*
1011259 GGAAGCGGTGGAACATGAGGAAGTGCT
1 GGAAGCGGTGGAACACGAGGAAGTGCT
* *
1011286 GGAAGCGGTGGAACACGAGGTAGTGTT
1 GGAAGCGGTGGAACACGAGGAAGTGCT
1011313 GGA
1 GGA
1011316 TCACGTGCTG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.28, C:0.11, G:0.46, T:0.16
Consensus pattern (27 bp):
GGAAGCGGTGGAACACGAGGAAGTGCT
Found at i:1016782 original size:3 final size:3
Alignment explanation
Indices: 1016774--1016801 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1016764 GAATAGGGTT
1016774 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG T
1016802 ATGTATGTGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:1017163 original size:18 final size:18
Alignment explanation
Indices: 1017123--1017192 Score: 61
Period size: 18 Copynumber: 3.9 Consensus size: 18
1017113 GAGGGTCTAC
*
1017123 GTGGTCTTTCGGGACATA
1 GTGGTCTTTCGGGACACA
*
1017141 ATGGTCATTT-GGGACACA
1 GTGGTC-TTTCGGGACACA
* * *
1017159 GTGGTCCTTCGGGATATA
1 GTGGTCTTTCGGGACACA
* *
1017177 GTGGTCCTACGGGACA
1 GTGGTCTTTCGGGACA
1017193 AATTCTATGC
Statistics
Matches: 42, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
17 2 0.05
18 37 0.88
19 3 0.07
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (18 bp):
GTGGTCTTTCGGGACACA
Found at i:1017191 original size:36 final size:36
Alignment explanation
Indices: 1017123--1017192 Score: 86
Period size: 36 Copynumber: 1.9 Consensus size: 36
1017113 GAGGGTCTAC
* **
1017123 GTGGTCTTTCGGGACATAATGGTCATTTGGGACACA
1 GTGGTCCTTCGGGACATAATGGTCATACGGGACACA
* * *
1017159 GTGGTCCTTCGGGATATAGTGGTCCTACGGGACA
1 GTGGTCCTTCGGGACATAATGGTCATACGGGACA
1017193 AATTCTATGC
Statistics
Matches: 28, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
36 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.33, T:0.29
Consensus pattern (36 bp):
GTGGTCCTTCGGGACATAATGGTCATACGGGACACA
Found at i:1023929 original size:90 final size:88
Alignment explanation
Indices: 1023773--1023945 Score: 310
Period size: 90 Copynumber: 1.9 Consensus size: 88
1023763 CTAACACACT
1023773 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
*
1023838 TTAATTAATTAGAATTTAATAATC
66 TTAATTAATT-GAAATTAATAATC
*
1023862 CTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTATA
1 CTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTATA
1023927 TTTAATTAATTGAAATTAA
65 TTTAATTAATTGAAATTAA
1023946 ATATTCAGGA
Statistics
Matches: 81, Mismatches: 2, Indels: 2
0.95 0.02 0.02
Matches are distributed among these distances:
89 40 0.49
90 41 0.51
ACGTcount: A:0.38, C:0.11, G:0.06, T:0.45
Consensus pattern (88 bp):
CTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATAT
TTAATTAATTGAAATTAATAATC
Found at i:1033648 original size:90 final size:89
Alignment explanation
Indices: 1033491--1033667 Score: 309
Period size: 90 Copynumber: 2.0 Consensus size: 89
1033481 CCTAACACAC
*
1033491 CCTTTTATAGCCAAGTTACTCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
* *
1033556 TTTAATTAATTGGAATTTAATAAT
66 TTTAATTAATTGAAATTAAATAAT
*
1033580 CCTTTTATATCCAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATCTAT
1 CCTTTTATAGCCAAGTTACCCTAATCATATTAGGG-TTTTATTATTTCAAATTAATTAAATCTAT
1033645 ATTTAATTAATTGAAATTAAATA
65 ATTTAATTAATTGAAATTAAATA
1033668 TTCAGGATTA
Statistics
Matches: 83, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
89 33 0.40
90 50 0.60
ACGTcount: A:0.37, C:0.11, G:0.07, T:0.45
Consensus pattern (89 bp):
CCTTTTATAGCCAAGTTACCCTAATCATATTAGGGTTTTATTATTTCAAATTAATTAAATCTATA
TTTAATTAATTGAAATTAAATAAT
Found at i:1034570 original size:2 final size:2
Alignment explanation
Indices: 1034563--1034590 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
1034553 TGTTAAAAAC
1034563 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1034591 GAAAATAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1048497 original size:28 final size:28
Alignment explanation
Indices: 1048453--1048511 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
1048443 TCATAACTAA
*
1048453 TTATGTGATAAGGTTTAAGGTTTAGAGT
1 TTATGTGATAAGGTTTAAGGTTTAAAGT
1048481 TTATGTGAT-AGGATTTAAGGTTTAAAGT
1 TTATGTGATAAGG-TTTAAGGTTTAAAGT
1048509 TTA
1 TTA
1048512 GAGTTTAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
27 3 0.10
28 26 0.90
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (28 bp):
TTATGTGATAAGGTTTAAGGTTTAAAGT
Found at i:1048503 original size:21 final size:21
Alignment explanation
Indices: 1048479--1048562 Score: 75
Period size: 21 Copynumber: 4.0 Consensus size: 21
1048469 AAGGTTTAGA
*
1048479 GTTTATGTGATAGGATTTAAG
1 GTTTATGTGTTAGGATTTAAG
* *
1048500 GTTTAAAGT-TTA-GAGTTTAGG
1 GTTT-ATGTGTTAGGA-TTTAAG
*
1048521 GTTTATGTGTTAAGG-TTTAGG
1 GTTTATGTGTT-AGGATTTAAG
*
1048542 GTTTATGTGTTAGGGTTTAAG
1 GTTTATGTGTTAGGATTTAAG
1048563 TTATGCCATG
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
20 8 0.15
21 39 0.75
22 4 0.08
23 1 0.02
ACGTcount: A:0.24, C:0.00, G:0.31, T:0.45
Consensus pattern (21 bp):
GTTTATGTGTTAGGATTTAAG
Found at i:1048525 original size:28 final size:28
Alignment explanation
Indices: 1048457--1048525 Score: 77
Period size: 28 Copynumber: 2.5 Consensus size: 28
1048447 AACTAATTAT
* * *
1048457 GTGATAAGGTTTAAGGTTTAGAGTTTAT
1 GTGATAGGGTTTAAGGTTTAAAGTTTAA
*
1048485 GTGATAGGATTTAAGGTTTAAAGTTTAGA
1 GTGATAGGGTTTAAGGTTTAAAGTTTA-A
*
1048514 GT-TTAGGGTTTA
1 GTGATAGGGTTTA
1048526 TGTGTTAAGG
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
28 32 0.94
29 2 0.06
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.42
Consensus pattern (28 bp):
GTGATAGGGTTTAAGGTTTAAAGTTTAA
Found at i:1048546 original size:35 final size:35
Alignment explanation
Indices: 1048453--1048560 Score: 105
Period size: 35 Copynumber: 3.1 Consensus size: 35
1048443 TCATAACTAA
* *
1048453 TTATGTGATAAGGTTTAAGGTTTAGAGTTTA-TGT
1 TTATGTGTTAAGGTTTAAGGTTTAGAGTTTAGGGT
* * *
1048487 GATAGGAT-TTAAGGTTTAAAGTTTAGAGTTTAGGGT
1 -TTATG-TGTTAAGGTTTAAGGTTTAGAGTTTAGGGT
* *
1048523 TTATGTGTTAAGGTTTAGGGTTTA-TGTGTTAGGGT
1 TTATGTGTTAAGGTTTAAGGTTTAGAGT-TTAGGGT
1048558 TTA
1 TTA
1048561 AGTTATGCCA
Statistics
Matches: 59, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
34 3 0.05
35 53 0.90
36 3 0.05
ACGTcount: A:0.25, C:0.00, G:0.30, T:0.45
Consensus pattern (35 bp):
TTATGTGTTAAGGTTTAAGGTTTAGAGTTTAGGGT
Found at i:1048858 original size:17 final size:17
Alignment explanation
Indices: 1048832--1048868 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
1048822 ATTCGAGTTT
* *
1048832 GAGTTTGAGCTTTAATC
1 GAGTTCGAGCTTGAATC
1048849 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCTTGAATC
1048866 GAG
1 GAG
1048869 CTTGAATCGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.24, C:0.14, G:0.30, T:0.32
Consensus pattern (17 bp):
GAGTTCGAGCTTGAATC
Found at i:1048869 original size:11 final size:11
Alignment explanation
Indices: 1048853--1048904 Score: 59
Period size: 11 Copynumber: 4.6 Consensus size: 11
1048843 TTAATCGAGT
1048853 TCGAGCTTGAA
1 TCGAGCTTGAA
1048864 TCGAGCTTGAA
1 TCGAGCTTGAA
**
1048875 TCGAGCTCAAAA
1 TCGAGCT-TGAA
* *
1048887 TCGAGTTTCAA
1 TCGAGCTTGAA
1048898 TCGAGCT
1 TCGAGCT
1048905 CTTAAATTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
11 26 0.76
12 8 0.24
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (11 bp):
TCGAGCTTGAA
Found at i:1048891 original size:23 final size:23
Alignment explanation
Indices: 1048862--1048905 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
1048852 TTCGAGCTTG
*
1048862 AATCGAGCTTGAATCGAGCTCAA
1 AATCGAGCTTCAATCGAGCTCAA
*
1048885 AATCGAGTTTCAATCGAGCTC
1 AATCGAGCTTCAATCGAGCTC
1048906 TTAAATTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (23 bp):
AATCGAGCTTCAATCGAGCTCAA
Found at i:1049219 original size:29 final size:30
Alignment explanation
Indices: 1049184--1049259 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
1049174 CAAAAATAAC
* *
1049184 AAATAGTATTAATAATACTT-AAAGGACTA
1 AAATAGTATTAATAAAAATTAAAAGGACTA
*
1049213 ATATAGTATTAATAAAAATTAAAAGGACTA
1 AAATAGTATTAATAAAAATTAAAAGGACTA
* *
1049243 AAATGGTATTAACAAAA
1 AAATAGTATTAATAAAA
1049260 TAAACTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.55, C:0.05, G:0.11, T:0.29
Consensus pattern (30 bp):
AAATAGTATTAATAAAAATTAAAAGGACTA
Found at i:1051096 original size:128 final size:127
Alignment explanation
Indices: 1050765--1051107 Score: 348
Period size: 128 Copynumber: 2.6 Consensus size: 127
1050755 AGGGTGATAA
* * *
1050765 AACTCCTACATAATGAGGATATCTAGTCAGGGGATGAGACTGCTCATACGTGATGAAGAGTTCTT
1 AACTCCTACATAATGAGGAAATCTAGTCAGGTGATGACAC-GCTCATACGTGATGAAGAGTTC-T
** * * *
1050830 TTCCATCTTTAGGAAAGGTGATAACTCAGTTCCTACGTGATGAGGACAGCTGGTTATCTAGGTTG
64 AGCCATC--T---AAAGGTGATAACACAGTTCCTACGTGATGAGGACAGCTGGCTATATAGGTTG
*
1050895 ACAT
124 ACAC
* * * * * *
1050899 AGCTCCTACATAATGAGGAAATCTAGTCGGGTGATGACACGGTTCCTACGTGATGAGGACG-AC-
1 AACTCCTACATAATGAGGAAATCTAGTCAGGTGATGACAC-GCTCATACGTGATGAAGA-GTTCT
* * *
1050962 AGGCCATCTAAGGGTGATAACACGGTTCCTACGTGATGAGGACGGCTGGCTATATAGGTTGACAC
64 A-GCCATCTAAAGGTGATAACACAGTTCCTACGTGATGAGGACAGCTGGCTATATAGGTTGACAC
* * * * * *
1051027 AATTTCTACATAATGAGGAGATATGGTCAGTTGATGACACGACTCATACGTGATGAAGAGTTCTA
1 AACTCCTACATAATGAGGAAATCTAGTCAGGTGATGACACG-CTCATACGTGATGAAGAGTTCTA
*
1051092 GCCATCTAAAGATGAT
65 GCCATCTAAAGGTGAT
1051108 TTGGTTTCAA
Statistics
Matches: 171, Mismatches: 33, Indels: 16
0.78 0.15 0.07
Matches are distributed among these distances:
127 2 0.01
128 110 0.64
129 1 0.01
131 1 0.01
133 5 0.03
134 51 0.30
135 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (127 bp):
AACTCCTACATAATGAGGAAATCTAGTCAGGTGATGACACGCTCATACGTGATGAAGAGTTCTAG
CCATCTAAAGGTGATAACACAGTTCCTACGTGATGAGGACAGCTGGCTATATAGGTTGACAC
Found at i:1052238 original size:41 final size:41
Alignment explanation
Indices: 1052193--1052278 Score: 120
Period size: 41 Copynumber: 2.1 Consensus size: 41
1052183 TCTTTACATG
*
1052193 TGTTTATTGTTCCTTTTTCTTTGTT-TATTCTTTTTGTTCTT
1 TGTTT-TTGTTCCTTTTTCTTTGTTCTATTCTTTTTGCTCTT
* * *
1052234 TGTTTTTGTTTCTTTTTCTTTTTTCTTTTCTTTTTGCTCTT
1 TGTTTTTGTTCCTTTTTCTTTGTTCTATTCTTTTTGCTCTT
1052275 TGTT
1 TGTT
1052279 GCTCTAGTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
40 17 0.43
41 23 0.57
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.76
Consensus pattern (41 bp):
TGTTTTTGTTCCTTTTTCTTTGTTCTATTCTTTTTGCTCTT
Found at i:1052264 original size:12 final size:13
Alignment explanation
Indices: 1052205--1052268 Score: 53
Period size: 12 Copynumber: 4.9 Consensus size: 13
1052195 TTTATTGTTC
1052205 CTTTTTCTTTGTTT
1 CTTTTTCTTT-TTT
* * *
1052219 ATTCTT-TTTGTT
1 CTTTTTCTTTTTT
1052231 CTTTGTT-TTTGTTT
1 CTTT-TTCTTT-TTT
1052245 CTTTTTCTTTTTT
1 CTTTTTCTTTTTT
1052258 C-TTTTCTTTTT
1 CTTTTTCTTTTT
1052269 GCTCTTTGTT
Statistics
Matches: 41, Mismatches: 6, Indels: 8
0.75 0.11 0.15
Matches are distributed among these distances:
12 14 0.34
13 14 0.34
14 13 0.32
ACGTcount: A:0.02, C:0.12, G:0.06, T:0.80
Consensus pattern (13 bp):
CTTTTTCTTTTTT
Found at i:1054637 original size:57 final size:60
Alignment explanation
Indices: 1054535--1054828 Score: 306
Period size: 63 Copynumber: 4.8 Consensus size: 60
1054525 TGTGAATATG
* *
1054535 CAAATGCAGATGCAAAATTGATGATCCTCTTAAATACAATGCATCATGCAGAATG-AG-A
1 CAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATGCAGAATGAAGAA
* * * * * *
1054593 -AGATGCAGATGCAAAATTGATTATCCTCTGAAATGCAATACATCATACAGAATGCGAAGATG
1 CAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATGCAGAAT--GAAGA-A
* * * * *
1054655 CAAATGCAAATGCTAAATTGATGATCATCTAAAATGTAATGCATCATACAGAATGTGAAGATA
1 CAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATGCAGAA--TGAAGA-A
* * * *
1054718 CAAATACATATGCTAAATTGATGATCGTCTAAAATGCAATGCATCATGCAGAATGCAAAGATA
1 CAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATGCAGAATG--AAGA-A
* * *
1054781 CAAATGCAAATGCAAAATTGATAATCCTCTGAAATGCAATGCATCATG
1 CAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATG
1054829 AAAAAATACG
Statistics
Matches: 199, Mismatches: 27, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
57 47 0.24
59 1 0.01
60 2 0.01
61 2 0.01
63 146 0.73
65 1 0.01
ACGTcount: A:0.42, C:0.16, G:0.17, T:0.25
Consensus pattern (60 bp):
CAAATGCAGATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATGCAGAATGAAGAA
Found at i:1054779 original size:126 final size:120
Alignment explanation
Indices: 1054514--1054827 Score: 367
Period size: 126 Copynumber: 2.6 Consensus size: 120
1054504 ATTTATGATG
* * * * * *
1054514 ATCATGGAGAATGTGAATATGCAAATGCAGATGCAAAATTGATGATCCTCTTAAATACAATGCAT
1 ATCATGCAGAATGCGAAGATGCAAATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCAT
* * * * *
1054579 CATGCAGAATGAGAAGATGCAGATGCAAAATTGATTATCCTCTGAAATGCAATAC
66 CATACAGAATGAGAAAATACAGATGCAAAATTGATGATCCTCTAAAATGCAATAC
* * * *
1054634 ATCATACAGAATGCGAAGATGCAAATGCAAATGCTAAATTGATGATCATCTAAAATGTAATGCAT
1 ATCATGCAGAATGCGAAGATGCAAATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCAT
* * * *
1054699 CATACAGAATGTGAAGATACAAATACATATGCTAAATTGATGATCGTCTAAAATGCAATGC
66 CATACAGAA--TG-AG--A-AAATACAGATGCAAAATTGATGATCCTCTAAAATGCAATAC
* * * *
1054760 ATCATGCAGAATGCAAAGATACAAATGCAAATGCAAAATTGATAATCCTCTGAAATGCAATGCAT
1 ATCATGCAGAATGCGAAGATGCAAATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCAT
1054825 CAT
66 CAT
1054828 GAAAAAATAC
Statistics
Matches: 161, Mismatches: 27, Indels: 6
0.83 0.14 0.03
Matches are distributed among these distances:
120 63 0.39
122 2 0.01
123 2 0.01
125 1 0.01
126 93 0.58
ACGTcount: A:0.42, C:0.15, G:0.17, T:0.25
Consensus pattern (120 bp):
ATCATGCAGAATGCGAAGATGCAAATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCAT
CATACAGAATGAGAAAATACAGATGCAAAATTGATGATCCTCTAAAATGCAATAC
Found at i:1054828 original size:63 final size:63
Alignment explanation
Indices: 1054595--1054827 Score: 313
Period size: 63 Copynumber: 3.7 Consensus size: 63
1054585 GAATGAGAAG
* * * * *
1054595 ATGCAGATGCAAAATTGATTATCCTCTGAAATGCAATACATCATACAGAATGCGAAGATGCAA
1 ATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATACAGAATGCGAAGATACAA
* * * *
1054658 ATGCAAATGCTAAATTGATGATCATCTAAAATGTAATGCATCATACAGAATGTGAAGATACAA
1 ATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATACAGAATGCGAAGATACAA
* * * * * *
1054721 ATACATATGCTAAATTGATGATCGTCTAAAATGCAATGCATCATGCAGAATGCAAAGATACAA
1 ATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATACAGAATGCGAAGATACAA
* *
1054784 ATGCAAATGCAAAATTGATAATCCTCTGAAATGCAATGCATCAT
1 ATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCATCAT
1054828 GAAAAAATAC
Statistics
Matches: 148, Mismatches: 22, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
63 148 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.26
Consensus pattern (63 bp):
ATGCAAATGCAAAATTGATGATCCTCTAAAATGCAATGCATCATACAGAATGCGAAGATACAA
Found at i:1058638 original size:32 final size:32
Alignment explanation
Indices: 1058602--1058663 Score: 99
Period size: 32 Copynumber: 1.9 Consensus size: 32
1058592 ACGAAAAATG
*
1058602 ACACAATCAAAAGAAAAGAAA-TAAGTTAGTGT
1 ACACAAACAAAAGAAAAGAAATTAA-TTAGTGT
1058634 ACACAAACAAAAGAAAAGAAATTAATTAGT
1 ACACAAACAAAAGAAAAGAAATTAATTAGT
1058664 ACATGTAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.60, C:0.10, G:0.13, T:0.18
Consensus pattern (32 bp):
ACACAAACAAAAGAAAAGAAATTAATTAGTGT
Found at i:1059717 original size:15 final size:16
Alignment explanation
Indices: 1059693--1059735 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
1059683 TAAAAACGTC
1059693 TTTTAA-AAAAA-CAA
1 TTTTAAGAAAAATCAA
*
1059707 TTTTAAGAAAAATCAT
1 TTTTAAGAAAAATCAA
1059723 TTTTAAGACAAAA
1 TTTTAAGA-AAAA
1059736 AACTGGTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 10 0.40
17 4 0.16
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (16 bp):
TTTTAAGAAAAATCAA
Found at i:1060075 original size:20 final size:19
Alignment explanation
Indices: 1060050--1060087 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1060040 CCCAAGGACA
*
1060050 AAATAAAATTAAATAAAACG
1 AAATAAAAATAAA-AAAACG
1060070 AAATAAAAATAAAAAAAC
1 AAATAAAAATAAAAAAAC
1060088 TGTGGAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.76, C:0.05, G:0.03, T:0.16
Consensus pattern (19 bp):
AAATAAAAATAAAAAAACG
Found at i:1060851 original size:29 final size:30
Alignment explanation
Indices: 1060808--1060883 Score: 100
Period size: 30 Copynumber: 2.6 Consensus size: 30
1060798 CAAAAATAAC
* *
1060808 AAATAGTATTGATAAAACTT-AAAGGACTA
1 AAATAGTATTAATAAAAATTAAAAGGACTA
*
1060837 ATATAGTATTAATAAAAATTAAAAGGACTA
1 AAATAGTATTAATAAAAATTAAAAGGACTA
* *
1060867 AAATGGTATTAACAAAA
1 AAATAGTATTAATAAAA
1060884 TAAACTAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
29 17 0.43
30 23 0.57
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (30 bp):
AAATAGTATTAATAAAAATTAAAAGGACTA
Found at i:1063935 original size:30 final size:29
Alignment explanation
Indices: 1063874--1063938 Score: 96
Period size: 29 Copynumber: 2.2 Consensus size: 29
1063864 TATTTTAGTA
*
1063874 CTATTATGGTAATTAATTCAAAATGAGTG
1 CTATTTTGGTAATTAATTCAAAATGAGTG
1063903 CTATTTTGGTAATTAATTCGAAAA-GAAGTG
1 CTATTTTGGTAATTAATTC-AAAATG-AGTG
1063933 CTATTT
1 CTATTT
1063939 CTGTAAAATG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
29 19 0.58
30 14 0.42
ACGTcount: A:0.35, C:0.08, G:0.17, T:0.40
Consensus pattern (29 bp):
CTATTTTGGTAATTAATTCAAAATGAGTG
Found at i:1071068 original size:17 final size:17
Alignment explanation
Indices: 1071046--1071088 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
1071036 ACGACCCGAC
1071046 CCGTTGACCCAACCCAA
1 CCGTTGACCCAACCCAA
* *
1071063 CCGTTGACCCGACCCGA
1 CCGTTGACCCAACCCAA
1071080 CCGTTGACC
1 CCGTTGACC
1071089 GGTGCTATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.21, C:0.47, G:0.19, T:0.14
Consensus pattern (17 bp):
CCGTTGACCCAACCCAA
Found at i:1071195 original size:29 final size:29
Alignment explanation
Indices: 1071149--1071245 Score: 92
Period size: 29 Copynumber: 3.3 Consensus size: 29
1071139 CTCTCGAAAA
* * *
1071149 AGTGATATTATAGGAATTAATTC-AATTTT
1 AGTGCTATTAT-GGAATTAATTCAAAATGT
1071178 AGTGCTATTATGGAAATTAATTCAAAATGT
1 AGTGCTATTATGG-AATTAATTCAAAATGT
*
1071208 -GTGCTATTTTGGTAATTAATTCGAAAATG-
1 AGTGCTATTATGG-AATTAATTC-AAAATGT
*
1071237 GGTGCTATT
1 AGTGCTATT
1071246 TCTGTAAAAT
Statistics
Matches: 59, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
28 2 0.03
29 39 0.66
30 18 0.31
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (29 bp):
AGTGCTATTATGGAATTAATTCAAAATGT
Found at i:1071242 original size:30 final size:29
Alignment explanation
Indices: 1071179--1071246 Score: 100
Period size: 29 Copynumber: 2.3 Consensus size: 29
1071169 TTCAATTTTA
* *
1071179 GTGCTATTATGGAAATTAATTCAAAATGT
1 GTGCTATTTTGGAAATTAATTCAAAATGG
*
1071208 GTGCTATTTTGGTAATTAATTCGAAAATGG
1 GTGCTATTTTGGAAATTAATTC-AAAATGG
1071238 GTGCTATTT
1 GTGCTATTT
1071247 CTGTAAAATG
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.31, C:0.07, G:0.21, T:0.41
Consensus pattern (29 bp):
GTGCTATTTTGGAAATTAATTCAAAATGG
Found at i:1073796 original size:258 final size:258
Alignment explanation
Indices: 1073337--1073809 Score: 640
Period size: 258 Copynumber: 1.8 Consensus size: 258
1073327 CTAACCCATG
* ** * * * *
1073337 TCTTCTTCTTGAGTTAAAGACCTTGGTTTAAAATTCAACCGGAAAGTAGTTCATCGCTGCTACCA
1 TCTTCTTCTTGACTTAAAGACCCCGATTTAAAATTCAACCGAAAAATAGTTCATCACTGCTACCA
* * *
1073402 TGCGGTTGATATGTCATCGAGCTGAATGGAATCAAAATCGGCGGTCTTCATTGACAGATAACCCT
66 TGCGGTTGATATGCCATCGAGCTGAATGGAATCAAAATCGACAGTCTTCATTGACAGATAACCCT
* * *
1073467 TATCGCCTTGAGCTATGCTGTAAAATTGTTATGCCCTTGAGCTGAATGAAATCGAACTCAAAGAA
131 TATCGACTTAAGCTATGCTGTAAAATTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGAA
1073532 TTTTATTGATAGATAACCCTCATTGCCTTGTATTATGTTATACTAGATTAAGATTGCCCCAGA
196 TTTTATTGATAGATAACCCTCATTGCCTTGTATTATGTTATACTAGATTAAGATTGCCCCAGA
* * *
1073595 TCTTCTTCTTGACTTGAAGACCCCGATTTAAACTTCAACCGAAAAATAGTTCCTCACTGCTACCA
1 TCTTCTTCTTGACTTAAAGACCCCGATTTAAAATTCAACCGAAAAATAGTTCATCACTGCTACCA
* ** * * ** ***
1073660 TGTGGTTGATATGCCATCGAGCTGAATGGAATTGAACTCGACAGTGTTTTTTGACAGATAATTTT
66 TGCGGTTGATATGCCATCGAGCTGAATGGAATCAAAATCGACAGTCTTCATTGACAGATAACCCT
* * * * * * **
1073725 TCTCGACTTAAGCTATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAGTCGAACTCGATGGT
131 TATCGACTTAAGCTATGCTGTAAAATTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGAA
1073790 TTTTATTGATAGATAACCCT
196 TTTTATTGATAGATAACCCT
1073810 TATCGTCTTG
Statistics
Matches: 181, Mismatches: 34, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
258 181 1.00
ACGTcount: A:0.28, C:0.19, G:0.19, T:0.34
Consensus pattern (258 bp):
TCTTCTTCTTGACTTAAAGACCCCGATTTAAAATTCAACCGAAAAATAGTTCATCACTGCTACCA
TGCGGTTGATATGCCATCGAGCTGAATGGAATCAAAATCGACAGTCTTCATTGACAGATAACCCT
TATCGACTTAAGCTATGCTGTAAAATTGATATGCCCTTGAGCTGAATGAAATCGAACTCAAAGAA
TTTTATTGATAGATAACCCTCATTGCCTTGTATTATGTTATACTAGATTAAGATTGCCCCAGA
Found at i:1073889 original size:85 final size:85
Alignment explanation
Indices: 1073738--1073895 Score: 235
Period size: 85 Copynumber: 1.9 Consensus size: 85
1073728 CGACTTAAGC
* * * * * *
1073738 TATGCTGTAAATTTGATATGCCCTTGAGCTGAATGTAGTCGAACTCGATGGTTTTTATTGATAGA
1 TATGCTGTAAATTTGATATGCCCTTGAGCTAAATGTAATCGAACTCGAAGATTTTGATTGACAGA
1073803 TAACCCTTATCGTCTTGAAT
66 TAACCCTTATCGTCTTGAAT
* *
1073823 TATGCTGTAAATTTGATATGTCCTTGAGCTAAATGTAATCGAACTCGAAGATTTTGGTTGACAGA
1 TATGCTGTAAATTTGATATGCCCTTGAGCTAAATGTAATCGAACTCGAAGATTTTGATTGACAGA
*
1073888 TAGCCCTT
66 TAACCCTT
1073896 TTCGCTTTGA
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
85 64 1.00
ACGTcount: A:0.27, C:0.15, G:0.20, T:0.37
Consensus pattern (85 bp):
TATGCTGTAAATTTGATATGCCCTTGAGCTAAATGTAATCGAACTCGAAGATTTTGATTGACAGA
TAACCCTTATCGTCTTGAAT
Done.