Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008798.1 Hibiscus syriacus cultivar Beakdansim tig00111947_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: 1825372
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 7 of 9
Found at i:1268840 original size:64 final size:64
Alignment explanation
Indices: 1268753--1268914 Score: 191
Period size: 64 Copynumber: 2.5 Consensus size: 64
1268743 TATTTAACAT
* * * * * *
1268753 GTGCATCGATGCACTACCCATGCATCAATACACAAATCACCTTTGATGTTTTCA-TTTTAAGGGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAA-GGG
* * * ** *
1268817 GTGCATCGATGCACTTCTTATGCATCGATGCACTAATTGCATTCGATGTTTCCATTTTTAATGG
1 GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
*
1268881 GTGCATCGATGCACTTCCTGTGCATCGATACACA
1 GTGCATCGATGCACTTCCTATGCATCGATACACA
1268915 CTGAACAATT
Statistics
Matches: 81, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
64 75 0.93
65 6 0.07
ACGTcount: A:0.25, C:0.23, G:0.19, T:0.33
Consensus pattern (64 bp):
GTGCATCGATGCACTTCCTATGCATCGATACACAAATCACATTCGATGTTTCCATTTTTAAGGG
Found at i:1273470 original size:24 final size:20
Alignment explanation
Indices: 1273417--1273473 Score: 69
Period size: 20 Copynumber: 2.6 Consensus size: 20
1273407 TTCCCCTTGA
*
1273417 AGTGCATCGATACATTCTAC
1 AGTGCATCGATGCATTCTAC
1273437 AGTGCATCGATGCATTCTTTAAC
1 AGTGCATCGATGCATTC--T-AC
1273460 ATGTGCATCGATGC
1 A-GTGCATCGATGC
1273474 GCTACCTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 16 0.50
22 1 0.03
23 3 0.09
24 12 0.38
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (20 bp):
AGTGCATCGATGCATTCTAC
Found at i:1276757 original size:37 final size:36
Alignment explanation
Indices: 1276690--1276932 Score: 189
Period size: 37 Copynumber: 6.8 Consensus size: 36
1276680 AAACAAGGGG
* * * *
1276690 TTGTCTCGCTTGAGACTAATTT-ACTCAAAACAAAGTT
1 TTGTCTCTCTTGAGAC-AGTTTCCCTTAAAACAAA-TT
*
1276727 TTGTCTCTCTTGAGATAGTTTCCCTTAAAACAAA--
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATT
* * *
1276761 ---T-TCT-TTGA-ATATGTTTTCCTTGAAACAAATT
1 TTGTCTCTCTTGAGACA-GTTTCCCTTAAAACAAATT
* * ** ** *
1276792 TCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAAC-AAATT
** *
1276829 TTGTCTCTCTTGAGACAGTTTTTCTTGAAACAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATT
*
1276865 TTGTCTCTCTTGAGACAGTTTCCCTTCAAACAAAGTT
1 TTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAA-TT
*
1276902 TTGTCTCTCTTGAGACAGTTTCTCTTGAAAA
1 TTGTCTCTCTTGAGACAGTTTCCCTT-AAAA
1276933 AAAAAACCTT
Statistics
Matches: 168, Mismatches: 25, Indels: 25
0.77 0.11 0.11
Matches are distributed among these distances:
28 3 0.02
29 19 0.11
30 3 0.02
31 1 0.01
34 1 0.01
35 2 0.01
36 53 0.32
37 83 0.49
38 3 0.02
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTAAAACAAATT
Found at i:1276776 original size:29 final size:29
Alignment explanation
Indices: 1276736--1276791 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
1276726 TTTGTCTCTC
1276736 TTGAGATAGTTTCCCTTAAAACAAATTCT
1 TTGAGATAGTTTCCCTTAAAACAAATTCT
* *
1276765 TTGA-ATATGTTTTCCTTGAAACAAATT
1 TTGAGATA-GTTTCCCTTAAAACAAATT
1276792 TCGTCTCCCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.34, C:0.14, G:0.11, T:0.41
Consensus pattern (29 bp):
TTGAGATAGTTTCCCTTAAAACAAATTCT
Found at i:1276874 original size:36 final size:36
Alignment explanation
Indices: 1276773--1276931 Score: 203
Period size: 37 Copynumber: 4.4 Consensus size: 36
1276763 CTTTGAATAT
* * *
1276773 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACA
1 GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
* *
1276809 GTTTCTT-TTGGAACTAAGTTTTGTCTCTCTTGAGACA
1 GTTT-TTCTTGAAAC-AAATTTTGTCTCTCTTGAGACA
1276846 GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
1 GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
** *
1276882 GTTTCCCTTCAAACAAAGTTTTGTCTCTCTTGAGACA
1 GTTTTTCTTGAAACAAA-TTTTGTCTCTCTTGAGACA
*
1276919 GTTTCTCTTGAAA
1 GTTTTTCTTGAAA
1276932 AAAAAAACCT
Statistics
Matches: 107, Mismatches: 12, Indels: 7
0.85 0.10 0.06
Matches are distributed among these distances:
36 47 0.44
37 60 0.56
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (36 bp):
GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACA
Found at i:1276901 original size:73 final size:73
Alignment explanation
Indices: 1276773--1276931 Score: 237
Period size: 73 Copynumber: 2.2 Consensus size: 73
1276763 CTTTGAATAT
* ** ** *
1276773 GTTTTCCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTC
1 GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTCAAACAAAGTTTTGTCTCTC
1276838 TTGAGACA
66 TTGAGACA
* *
1276846 GTTTTTCTTGAAACAAATTTTGTCTCTCTTGAGACAGTTTCCCTTCAAACAAAGTTTTGTCTCTC
1 GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTCAAACAAAGTTTTGTCTCTC
1276911 TTGAGACA
66 TTGAGACA
*
1276919 GTTTCTCTTGAAA
1 GTTTTTCTTGAAA
1276932 AAAAAAACCT
Statistics
Matches: 77, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
73 77 1.00
ACGTcount: A:0.23, C:0.20, G:0.15, T:0.42
Consensus pattern (73 bp):
GTTTTTCTTGAAACAAATTTCGTCTCCCTTGAGACAGTTTCCCTTCAAACAAAGTTTTGTCTCTC
TTGAGACA
Found at i:1277297 original size:2 final size:2
Alignment explanation
Indices: 1277290--1277319 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
1277280 TCGGGCTTAA
1277290 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
1277320 TACAATAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1277340 original size:3 final size:3
Alignment explanation
Indices: 1277327--1277378 Score: 52
Period size: 3 Copynumber: 17.0 Consensus size: 3
1277317 TATTACAATA
* * *
1277327 ATT ATTT ATT ATT AATT ATT ATT ATT A-T ATT ATT AAT ACT ATT AAT
1 ATT A-TT ATT ATT -ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1277373 ATT ATT
1 ATT ATT
1277379 TTTCAACAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 6
0.79 0.10 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.80
4 6 0.15
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (3 bp):
ATT
Found at i:1277353 original size:23 final size:24
Alignment explanation
Indices: 1277327--1277379 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
1277317 TATTACAATA
*
1277327 ATTATTTATTATTAAT-TATTATT
1 ATTATTTATTATTAATATATTAAT
1277350 ATTA--TATTATTAATACTATTAAT
1 ATTATTTATTATTAATA-TATTAAT
1277373 ATTATTT
1 ATTATTT
1277380 TTCAACAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
21 10 0.40
23 14 0.56
25 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (24 bp):
ATTATTTATTATTAATATATTAAT
Found at i:1277361 original size:14 final size:13
Alignment explanation
Indices: 1277325--1277361 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
1277315 TATATTACAA
1277325 TAATTATTTATTAT
1 TAATTA-TTATTAT
1277339 TAATTATTATTAT
1 TAATTATTATTAT
1277352 TATATTATTA
1 TA-ATTATTA
1277362 ATACTATTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 9 0.41
14 13 0.59
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (13 bp):
TAATTATTATTAT
Found at i:1278752 original size:12 final size:11
Alignment explanation
Indices: 1278716--1278771 Score: 55
Period size: 10 Copynumber: 5.3 Consensus size: 11
1278706 TCTAAGAAAC
1278716 ATTA-TATTAT
1 ATTATTATTAT
*
1278726 A-TAATATTAT
1 ATTATTATTAT
1278736 ATTATTATTACT
1 ATTATTATTA-T
1278748 ATTATTATTAT
1 ATTATTATTAT
* *
1278759 -TTTTTATTCT
1 ATTATTATTAT
1278769 ATT
1 ATT
1278772 TTCATATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
9 2 0.05
10 16 0.41
11 10 0.26
12 11 0.28
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (11 bp):
ATTATTATTAT
Found at i:1281262 original size:30 final size:30
Alignment explanation
Indices: 1281228--1281287 Score: 102
Period size: 30 Copynumber: 2.0 Consensus size: 30
1281218 ATCCCAAATT
*
1281228 GAAAAGGCTGTTTTGATATTTAAACTGCTA
1 GAAAAGGCTGTTTTGACATTTAAACTGCTA
*
1281258 GAAAAGGTTGTTTTGACATTTAAACTGCTA
1 GAAAAGGCTGTTTTGACATTTAAACTGCTA
1281288 ACATCCCAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (30 bp):
GAAAAGGCTGTTTTGACATTTAAACTGCTA
Found at i:1283140 original size:41 final size:39
Alignment explanation
Indices: 1283079--1283205 Score: 186
Period size: 39 Copynumber: 3.3 Consensus size: 39
1283069 AGCAGTAAAT
* *
1283079 TATTTGATTCAGTAGTTTAGATTAACTAGAACTCTATCC
1 TATTTGATTTAGTAGTTTAGATTAACTATAACTCTATCC
*
1283118 TATTTGATTTAGTATAGTTTAGATTAACTATAACTCTATCT
1 TATTTGATTTAG--TAGTTTAGATTAACTATAACTCTATCC
*
1283159 TATTTGATTTAGTAGTTTAGATTAACTATAACTTTATCC
1 TATTTGATTTAGTAGTTTAGATTAACTATAACTCTATCC
1283198 T-TTT-ATTT
1 TATTTGATTT
1283206 TCTAAATAGG
Statistics
Matches: 81, Mismatches: 5, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
37 4 0.05
38 3 0.04
39 37 0.46
41 37 0.46
ACGTcount: A:0.30, C:0.11, G:0.10, T:0.49
Consensus pattern (39 bp):
TATTTGATTTAGTAGTTTAGATTAACTATAACTCTATCC
Found at i:1283186 original size:39 final size:39
Alignment explanation
Indices: 1283078--1283196 Score: 184
Period size: 41 Copynumber: 3.0 Consensus size: 39
1283068 TAGCAGTAAA
* *
1283078 TTATTTGATTCAGTAGTTTAGATTAACTAGAACTCTATC
1 TTATTTGATTTAGTAGTTTAGATTAACTATAACTCTATC
*
1283117 CTATTTGATTTAGTATAGTTTAGATTAACTATAACTCTATC
1 TTATTTGATTTAG--TAGTTTAGATTAACTATAACTCTATC
*
1283158 TTATTTGATTTAGTAGTTTAGATTAACTATAACTTTATC
1 TTATTTGATTTAGTAGTTTAGATTAACTATAACTCTATC
1283197 CTTTTATTTT
Statistics
Matches: 73, Mismatches: 5, Indels: 4
0.89 0.06 0.05
Matches are distributed among these distances:
39 36 0.49
41 37 0.51
ACGTcount: A:0.31, C:0.11, G:0.11, T:0.47
Consensus pattern (39 bp):
TTATTTGATTTAGTAGTTTAGATTAACTATAACTCTATC
Found at i:1289752 original size:18 final size:18
Alignment explanation
Indices: 1289721--1289768 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1289711 ATTCCCAATC
1289721 TCTTC-TCTCCTCGCCGT
1 TCTTCTTCTCCTCGCCGT
*
1289738 TCTTCTTCTCTTCGCCGT
1 TCTTCTTCTCCTCGCCGT
1289756 TCTTCTTCTCCTC
1 TCTTCTTCTCCTC
1289769 CGACCATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.00, C:0.44, G:0.08, T:0.48
Consensus pattern (18 bp):
TCTTCTTCTCCTCGCCGT
Found at i:1294738 original size:14 final size:14
Alignment explanation
Indices: 1294719--1294752 Score: 68
Period size: 14 Copynumber: 2.4 Consensus size: 14
1294709 CAGCCTGCAT
1294719 TGGGCCATCTGATC
1 TGGGCCATCTGATC
1294733 TGGGCCATCTGATC
1 TGGGCCATCTGATC
1294747 TGGGCC
1 TGGGCC
1294753 GCTCCATTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.12, C:0.29, G:0.32, T:0.26
Consensus pattern (14 bp):
TGGGCCATCTGATC
Found at i:1294946 original size:18 final size:18
Alignment explanation
Indices: 1294915--1294962 Score: 80
Period size: 18 Copynumber: 2.7 Consensus size: 18
1294905 ATTCCCAATC
1294915 TCTTC-TCTCCTCGCCGT
1 TCTTCTTCTCCTCGCCGT
*
1294932 TCTTCTTCTCTTCGCCGT
1 TCTTCTTCTCCTCGCCGT
1294950 TCTTCTTCTCCTC
1 TCTTCTTCTCCTC
1294963 CGACCATAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
17 5 0.18
18 23 0.82
ACGTcount: A:0.00, C:0.44, G:0.08, T:0.48
Consensus pattern (18 bp):
TCTTCTTCTCCTCGCCGT
Found at i:1307273 original size:16 final size:16
Alignment explanation
Indices: 1307252--1307293 Score: 75
Period size: 16 Copynumber: 2.6 Consensus size: 16
1307242 AATGCGATGG
1307252 AGGTTGAAATGAAAAT
1 AGGTTGAAATGAAAAT
1307268 AGGTTGAAATGAAAAT
1 AGGTTGAAATGAAAAT
*
1307284 AGGTTAAAAT
1 AGGTTGAAAT
1307294 CAAATTTCTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 25 1.00
ACGTcount: A:0.50, C:0.00, G:0.24, T:0.26
Consensus pattern (16 bp):
AGGTTGAAATGAAAAT
Found at i:1316455 original size:3 final size:3
Alignment explanation
Indices: 1316437--1316498 Score: 81
Period size: 3 Copynumber: 20.3 Consensus size: 3
1316427 GCAAATGTAA
*
1316437 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
1316483 AAC AAT -AT AATT AAT A
1 AAT AAT AAT AA-T AAT A
1316499 TTTATAATAT
Statistics
Matches: 52, Mismatches: 4, Indels: 6
0.84 0.06 0.10
Matches are distributed among these distances:
2 2 0.04
3 44 0.85
4 6 0.12
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1317152 original size:55 final size:55
Alignment explanation
Indices: 1316699--1317159 Score: 416
Period size: 55 Copynumber: 8.6 Consensus size: 55
1316689 CTCTTTTTTG
* * * * ** * * *
1316699 CTTCAGGGAGTATAAAACTCAAACAATCTTCATA-AAACAAGTCTGTTCTCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCA-ACAATCGTGTCTGCTCCCTATTT
* * *
1316754 CTTCAGAGAGTATAGGACT---A-AATCTTCAACAAAT-GTGTCCGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTT
* *
1316805 CTTCAGAGAGTATAGGACT----CAATCTTCAATCAAACGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAA-CAATCGTGTCTGCTCCCTATTT
* * ** * *
1316857 CTTCAGATAGTATATGACTTAAACAACCTTCAACAAAT-GTGTCCT-CTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGT-CTGCTCCCTATTT
* * *
1316912 CTTCAGAAAGTATAGGACT----CAATCTTCAACAAAT-GTGTCTGCTCCCTATTC
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAAC-AATCGTGTCTGCTCCCTATTT
* * *
1316963 CTTCAGAGAGTATAAGACTCGAATAATTTTCAACATTCGTGTCTGCTCCCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT
* * * * * *
1317018 CTTCAGAGAGTATTAGACTCGAACAATTTTCAATATTCATGTCTGCTCCCTATTG
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT
* * * *
1317073 CTTAAGAGAGTATGAGACTTGAACAATCTTCAACAATCGTGTCTGCTCTCTATTT
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT
*
1317128 GTTCAGAGAGTATAAGACTCGAACAATCTTCA
1 CTTCAGAGAGTATAAGACTCGAACAATCTTCA
1317160 TTTGCTTCAC
Statistics
Matches: 345, Mismatches: 44, Indels: 34
0.82 0.10 0.08
Matches are distributed among these distances:
50 3 0.01
51 95 0.28
52 36 0.10
54 2 0.01
55 196 0.57
56 13 0.04
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (55 bp):
CTTCAGAGAGTATAAGACTCGAACAATCTTCAACAATCGTGTCTGCTCCCTATTT
Found at i:1329801 original size:4 final size:4
Alignment explanation
Indices: 1329794--1329819 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
1329784 AATGCAAAAA
1329794 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
1329820 CAAGTTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:1331362 original size:3 final size:3
Alignment explanation
Indices: 1331344--1331390 Score: 51
Period size: 3 Copynumber: 15.3 Consensus size: 3
1331334 GCAAATGTAA
* *
1331344 AAT AAT AAAT ATT AAT AAT AAT AAT AAT AAT AAC AAT -AT AATT AAT
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T AAT
1331390 A
1 A
1331391 TTTATAATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
2 2 0.05
3 29 0.78
4 6 0.16
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:1336068 original size:15 final size:16
Alignment explanation
Indices: 1336031--1336072 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
1336021 ATAATAAAAA
*
1336031 AATAAAAAAATTATTG
1 AATACAAAAATTATTG
1336047 AATACAAAAATTAATT-
1 AATACAAAAATT-ATTG
1336063 AA-ACAAAAAT
1 AATACAAAAAT
1336073 AATAAAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 8 0.33
16 13 0.54
17 3 0.12
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (16 bp):
AATACAAAAATTATTG
Found at i:1336088 original size:41 final size:39
Alignment explanation
Indices: 1336026--1336122 Score: 108
Period size: 39 Copynumber: 2.5 Consensus size: 39
1336016 ATTAAATAAT
* * *
1336026 AAAAAAAT-A-AAAAAATTATTGAATACAAAAATTAATTA
1 AAAAAAATAATAAAAAATGATTGAACAAAAAAATT-ATTA
*
1336064 AACAAAAATAATAAAAAATGATTGAACAAAAAAATTATTT
1 AA-AAAAATAATAAAAAATGATTGAACAAAAAAATTATTA
* *
1336104 AATAAGATAATAAAAAATG
1 AAAAAAATAATAAAAAATG
1336123 GGAAGGCGCC
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
38 2 0.04
39 21 0.42
40 6 0.12
41 21 0.42
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (39 bp):
AAAAAAATAATAAAAAATGATTGAACAAAAAAATTATTA
Found at i:1336114 original size:39 final size:41
Alignment explanation
Indices: 1336026--1336122 Score: 110
Period size: 41 Copynumber: 2.4 Consensus size: 41
1336016 ATTAAATAAT
* * *
1336026 AAAAA-AATAAAAAAATTATTGAATACAAAAATTAATTAAAC
1 AAAAATAAT-AAAAAATGATTGAACAAAAAAATTAATTAAAC
*
1336067 AAAAATAATAAAAAATGATTGAACAAAAAAATT-ATTTAA-
1 AAAAATAATAAAAAATGATTGAACAAAAAAATTAATTAAAC
* *
1336106 TAAGATAATAAAAAATG
1 AAAAATAATAAAAAATG
1336123 GGAAGGCGCC
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
39 15 0.31
40 5 0.10
41 26 0.53
42 3 0.06
ACGTcount: A:0.67, C:0.03, G:0.05, T:0.25
Consensus pattern (41 bp):
AAAAATAATAAAAAATGATTGAACAAAAAAATTAATTAAAC
Found at i:1341338 original size:18 final size:18
Alignment explanation
Indices: 1341315--1341349 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1341305 GCTGTTTGAG
*
1341315 GGCATGGGCGGTATGGGT
1 GGCATGGGCGGCATGGGT
1341333 GGCATGGGCGGCATGGG
1 GGCATGGGCGGCATGGG
1341350 CATGGGTGGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.11, C:0.14, G:0.57, T:0.17
Consensus pattern (18 bp):
GGCATGGGCGGCATGGGT
Found at i:1341339 original size:9 final size:9
Alignment explanation
Indices: 1341315--1341350 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
1341305 GCTGTTTGAG
1341315 GGCATGGGC
1 GGCATGGGC
* *
1341324 GGTATGGGT
1 GGCATGGGC
1341333 GGCATGGGC
1 GGCATGGGC
1341342 GGCATGGGC
1 GGCATGGGC
1341351 ATGGGTGGCC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.11, C:0.17, G:0.56, T:0.17
Consensus pattern (9 bp):
GGCATGGGC
Found at i:1344687 original size:3 final size:3
Alignment explanation
Indices: 1344679--1344733 Score: 56
Period size: 3 Copynumber: 18.3 Consensus size: 3
1344669 ATATTAATTA
* * * * * *
1344679 ATT ATT ATT ATT ATT ATA ATT ATA ATT ATA ATA ATA ATA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1344727 ATT ATT A
1 ATT ATT A
1344734 AATATATTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (3 bp):
ATT
Found at i:1345266 original size:11 final size:11
Alignment explanation
Indices: 1345250--1345286 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1345240 AACAACCATT
1345250 CAGAAAAGAAA
1 CAGAAAAGAAA
1345261 CAGAAAAG-AA
1 CAGAAAAGAAA
1345271 -AGAAAAGAAA
1 CAGAAAAGAAA
*
1345281 AAGAAA
1 CAGAAA
1345287 GAAGAGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.29
10 4 0.17
11 13 0.54
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (11 bp):
CAGAAAAGAAA
Found at i:1345274 original size:15 final size:15
Alignment explanation
Indices: 1345254--1345295 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1345244 ACCATTCAGA
1345254 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1345269 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1345284 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1345296 CTTATTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1345276 original size:20 final size:20
Alignment explanation
Indices: 1345251--1345295 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1345241 ACAACCATTC
*
1345251 AGAAAAGAAACAGAAAAGAA-
1 AGAAAAGAAAAAG-AAAGAAG
1345271 AGAAAAGAAAAAGAAAGAAG
1 AGAAAAGAAAAAGAAAGAAG
1345291 AGAAA
1 AGAAA
1345296 CTTATTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAAGAAAGAAG
Found at i:1346858 original size:6 final size:7
Alignment explanation
Indices: 1346837--1346861 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
1346827 TGTCTCCATT
1346837 AATTAAA
1 AATTAAA
1346844 AATTAAA
1 AATTAAA
1346851 AATTAAA
1 AATTAAA
1346858 AATT
1 AATT
1346862 TATATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (7 bp):
AATTAAA
Found at i:1351370 original size:14 final size:15
Alignment explanation
Indices: 1351351--1351379 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
1351341 CTCTTTTCTT
1351351 AATATTAA-AAAATA
1 AATATTAATAAAATA
1351365 AATATTAATAAAATA
1 AATATTAATAAAATA
1351380 TTTATCTAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
AATATTAATAAAATA
Found at i:1352736 original size:10 final size:10
Alignment explanation
Indices: 1352721--1352746 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
1352711 CTCCGACCGG
1352721 CCGCCATCGA
1 CCGCCATCGA
1352731 CCGCCATCGA
1 CCGCCATCGA
1352741 CCGCCA
1 CCGCCA
1352747 CTGCCGGCCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.54, G:0.19, T:0.08
Consensus pattern (10 bp):
CCGCCATCGA
Found at i:1361335 original size:83 final size:84
Alignment explanation
Indices: 1361227--1361507 Score: 415
Period size: 83 Copynumber: 3.3 Consensus size: 84
1361217 CAAACATTAA
1361227 TTGGAAGATGAATTTGC-CAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1 TTGGAAGATGAATTTGCTC-ATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTG
1361291 G-CAGAACCAATCATTGAAT
65 GACAGAACCAATCATTGAAT
* * *
1361310 TGGGAAGATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATATGG-TTGG
1 TTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1361374 ACAGAACCAATCATTGAAT
66 ACAGAACCAATCATTGAAT
* *
1361393 TTGGAAGATGAATTGGCTAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
1 TTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTT-G
1361458 TAAGAACTACAGAACCAATCATTGAAT
65 ---G----ACAGAACCAATCATTGAAT
1361485 TTGGAAGATGAATTTGCTCATAG
1 TTGGAAGATGAATTTGCTCATAG
1361508 TAGAAATAAG
Statistics
Matches: 177, Mismatches: 10, Indels: 13
0.88 0.05 0.06
Matches are distributed among these distances:
82 4 0.02
83 128 0.72
84 3 0.02
85 1 0.01
88 1 0.01
92 40 0.23
ACGTcount: A:0.28, C:0.13, G:0.24, T:0.35
Consensus pattern (84 bp):
TTGGAAGATGAATTTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG
ACAGAACCAATCATTGAAT
Found at i:1361724 original size:114 final size:115
Alignment explanation
Indices: 1361411--1361714 Score: 576
Period size: 114 Copynumber: 2.7 Consensus size: 115
1361401 TGAATTGGCT
*
1361411 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAAGAACTACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
1361476 TCATT-GAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
66 TCATTGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
1361525 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
*
1361590 TCA-TGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAGACTC
66 TCATTGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
1361639 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
1 AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
1361704 TCATTGGAATT
66 TCATTGGAATT
1361715 AAAAGATGAA
Statistics
Matches: 186, Mismatches: 2, Indels: 3
0.97 0.01 0.02
Matches are distributed among these distances:
113 1 0.01
114 178 0.96
115 7 0.04
ACGTcount: A:0.31, C:0.13, G:0.22, T:0.33
Consensus pattern (115 bp):
AATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGTAGGAACTACAGAACCAA
TCATTGGAATTTGGAAGATGAATTTGCTCATAGTAGAAATAAGGAAACTC
Found at i:1362741 original size:112 final size:111
Alignment explanation
Indices: 1362433--1363155 Score: 1157
Period size: 112 Copynumber: 6.5 Consensus size: 111
1362423 TGGATTGACA
1362433 TTTT-CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
* * * * *
1362497 AGAATTTGTTCAACCTTTTGTCTGAATTCATTACTTGATGGATTATT
66 AGAATTTGTTCAACCTTTT-ACTGAATCCATCACTTGATGGATCATC
1362544 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
1 TTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAG
*
1362609 AAGAATTTGTTCAACCTTTTACATGAATCCATCATTTGATGGATCATC
65 AAGAATTTGTTCAACCTTTTAC-TGAATCCATCACTTGATGGATCATC
1362657 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1362722 AGAATTTGTTCAACCTTTTACCTGAATCCATCACTTGATGGATCATC
66 AGAATTTGTTCAACCTTTTA-CTGAATCCATCACTTGATGGATCATC
*
1362769 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
*
1362834 AGAATTTGTTCAACCTTTTACCTGAATCCATCATTTGATGGATCATC
66 AGAATTTGTTCAACCTTTTA-CTGAATCCATCACTTGATGGATCATC
*
1362881 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCACAATGAGA
1 TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
** * *
1362946 AGAA-TTCATCAACCTTTTGTCTGAATTCATCACTTGATGGATCATC
66 AGAATTTGTTCAACCTTTT-ACTGAATCCATCACTTGATGGATCATC
1362992 TTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAG-AGAAAGTTCATAATGA
1 TTTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAG-AAGTTCATAATGA
** * * *
1363056 GAAGAGCTTGTTCAACCTTTTACATGAATTCATCAATTGATGGATCAAC
64 GAAGAATTTGTTCAACCTTTTAC-TGAATCCATCACTTGATGGATCATC
*
1363105 ATTTT-CAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGA
1 -TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGA
1363156 CAACTTTTTG
Statistics
Matches: 577, Mismatches: 24, Indels: 21
0.93 0.04 0.03
Matches are distributed among these distances:
111 52 0.09
112 374 0.65
113 147 0.25
114 4 0.01
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (111 bp):
TTTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
AGAATTTGTTCAACCTTTTACTGAATCCATCACTTGATGGATCATC
Found at i:1363499 original size:3 final size:3
Alignment explanation
Indices: 1363491--1363548 Score: 98
Period size: 3 Copynumber: 19.3 Consensus size: 3
1363481 ATATTAATTA
* *
1363491 ATT ATT ATT ATT ATT ATA ATT ATA ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1363539 ATT ATT ATT A
1 ATT ATT ATT A
1363549 AATATATTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:1364079 original size:11 final size:11
Alignment explanation
Indices: 1364063--1364099 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1364053 AACAACCATT
1364063 CAGAAAAGAAA
1 CAGAAAAGAAA
1364074 CAGAAAAG-AA
1 CAGAAAAGAAA
1364084 -AGAAAAGAAA
1 CAGAAAAGAAA
*
1364094 AAGAAA
1 CAGAAA
1364100 GAAGAGAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
9 7 0.29
10 4 0.17
11 13 0.54
ACGTcount: A:0.76, C:0.05, G:0.19, T:0.00
Consensus pattern (11 bp):
CAGAAAAGAAA
Found at i:1364087 original size:15 final size:15
Alignment explanation
Indices: 1364067--1364108 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
1364057 ACCATTCAGA
1364067 AAAGAAACAG-AAAAG
1 AAAGAAA-AGAAAAAG
1364082 AAAGAAAAGAAAAAG
1 AAAGAAAAGAAAAAG
*
1364097 AAAGAAGAGAAA
1 AAAGAAAAGAAA
1364109 CTTACTATCA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 2 0.08
15 23 0.92
ACGTcount: A:0.76, C:0.02, G:0.21, T:0.00
Consensus pattern (15 bp):
AAAGAAAAGAAAAAG
Found at i:1364089 original size:20 final size:20
Alignment explanation
Indices: 1364064--1364108 Score: 65
Period size: 20 Copynumber: 2.2 Consensus size: 20
1364054 ACAACCATTC
*
1364064 AGAAAAGAAACAGAAAAGAA-
1 AGAAAAGAAAAAG-AAAGAAG
1364084 AGAAAAGAAAAAGAAAGAAG
1 AGAAAAGAAAAAGAAAGAAG
1364104 AGAAA
1 AGAAA
1364109 CTTACTATCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.76, C:0.02, G:0.22, T:0.00
Consensus pattern (20 bp):
AGAAAAGAAAAAGAAAGAAG
Found at i:1367234 original size:4 final size:4
Alignment explanation
Indices: 1367225--1369855 Score: 4668
Period size: 4 Copynumber: 666.8 Consensus size: 4
1367215 CTCTTCTCTC
1367225 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367273 GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT- -ATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367319 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367367 GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367413 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367461 GATA GATA GATA GATA GATA GATA GATA GATA GAT- -ATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367507 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367555 GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367601 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367649 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367697 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367745 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GAT-
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367792 -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367839 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367887 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367935 GATA GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1367981 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368029 GATA GATA GATA GATA GATA GATA GATA GAT- -ATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368075 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368123 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368171 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368219 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368267 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368315 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368363 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368411 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368459 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368507 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368553 GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368599 GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368645 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* * * * * *
1368693 GATA GATA GATA GATA GATA G-TA GGTA GGTA GGTA GGTA GGTA GGTA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* * * * * * * * * * * *
1368740 GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* * * * * * * * * * * *
1368788 GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA GGTA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* * * * * *
1368836 GGTA GGTA GGTA GGTA GGTA GGTA G-TA GATA G-TA GATA GATA G-TA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
* *
1368881 GGTA GATA GATA GGTA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368929 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1368977 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369025 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369073 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369121 GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369167 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369215 GATA GATA GAT- -ATA GATA GATA GATA GATA GAT- -ATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369259 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369307 G--A GATA GATA GATA GATA GAT- -ATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369351 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369399 GATA GAT- -ATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369445 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369493 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369541 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369589 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369637 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369685 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369733 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369781 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1 GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA GATA
1369829 GATA GATA GATA GATA GATA GATA GAT
1 GATA GATA GATA GATA GATA GATA GAT
1369856 CCCTTGGGTC
Statistics
Matches: 2588, Mismatches: 3, Indels: 72
0.97 0.00 0.03
Matches are distributed among these distances:
2 32 0.01
3 12 0.00
4 2544 0.98
ACGTcount: A:0.48, C:0.00, G:0.26, T:0.25
Consensus pattern (4 bp):
GATA
Found at i:1373002 original size:2 final size:2
Alignment explanation
Indices: 1372995--1373074 Score: 160
Period size: 2 Copynumber: 40.0 Consensus size: 2
1372985 AAATGAATAA
1372995 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
1373037 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
1373075 GCATACTTTT
Statistics
Matches: 78, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 78 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1374671 original size:18 final size:17
Alignment explanation
Indices: 1374638--1374672 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
1374628 AAAAAAAAAC
*
1374638 TGCTTCTTGCTTTCAAT
1 TGCTTCTTGATTTCAAT
1374655 TGCTTCTTGGATTTCAAT
1 TGCTTCTT-GATTTCAAT
1374673 ACAATGGTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.14, C:0.20, G:0.14, T:0.51
Consensus pattern (17 bp):
TGCTTCTTGATTTCAAT
Found at i:1375404 original size:55 final size:55
Alignment explanation
Indices: 1375320--1375877 Score: 540
Period size: 55 Copynumber: 10.3 Consensus size: 55
1375310 ATACTTGAAA
* * * * * *
1375320 AATCTTCAA-ATAACGAGTCTGCTCTCTATTCATTCAGGGAGTATA-AGACTCAAAC
1 AATCTTCAATA-AACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * * *
1375375 AATCTTCAATAAACATGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAAT
1 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * * * * * *
1375430 AATCTTTAACAAATGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAAT
1 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* * *
1375485 AATCTTAAACAAACGGGTCCGCTCCCTATTCCTTCAGAGAGTATA-AGACTCG---
1 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGA-ACTCGAAC
* *
1375537 -ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAAC
1 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * *
1375591 AATCTTCAACAAATGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAAC
1 AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
1375646 AATCTTC-ATAAAACGTGTTCGCTCTCTATTCCTTCAGAGAGTATAGAACTCG---
1 AATCTTCAAT-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * * * *
1375698 -ATCTTC-ATAAAACGGGTTCGTTCTCTATTCCTTCAGAGAGTATAGAACTTGAAC
1 AATCTTCAAT-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* *
1375752 AATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 AATCTTCAAT-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
* * *
1375807 AATCTTC-ATAAAACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAAC
1 AATCTTCAAT-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
1375862 AATCTTC-ATCAAACGT
1 AATCTTCAAT-AAACGT
1375878 ATTTGCTTCA
Statistics
Matches: 449, Mismatches: 43, Indels: 22
0.87 0.08 0.04
Matches are distributed among these distances:
51 93 0.21
54 1 0.00
55 354 0.79
56 1 0.00
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (55 bp):
AATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGAACTCGAAC
Found at i:1375644 original size:161 final size:161
Alignment explanation
Indices: 1375376--1375859 Score: 627
Period size: 161 Copynumber: 3.0 Consensus size: 161
1375366 GACTCAAACA
* * * * * * *
1375376 ATCTTCAATAAACATGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCAAATAATCTTTAACA
1 ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACA
* * *
1375441 AATGTGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCGAATAATCTT-AAACAAACGGGTC
66 AATGTGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCATA-AAACGGGTC
*
1375504 CGCTCCCTATTCCTTCAGAGAGTATA-AGACTCG
129 CGCTCCCTATTCATTCAGAGAGTATAGA-ACTCG
1375537 ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACA
1 ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACA
* * *
1375602 AATGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGTGTTCG
66 AATGTGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCG
* *
1375667 CTCTCTATTCCTTCAGAGAGTATAGAACTCG
131 CTCCCTATTCATTCAGAGAGTATAGAACTCG
* * * * * **
1375698 ATCTTC-ATAAAACGGGTTCGTTCTCTATTCCTTCAGAGAGTATAGAACTTGAACAATCTTCATA
1 ATCTTCAAT-AAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCA-A
* * * * *
1375762 -AAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
64 CAAATGTGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTC
*
1375826 CGCTCCCTATTCATTCAGGGAGTATAGAACTCG
129 CGCTCCCTATTCATTCAGAGAGTATAGAACTCG
1375859 A
1 A
1375860 ACAATCTTCA
Statistics
Matches: 287, Mismatches: 31, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
160 2 0.01
161 280 0.98
162 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.29
Consensus pattern (161 bp):
ATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAATCTTCAACA
AATGTGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCG
CTCCCTATTCATTCAGAGAGTATAGAACTCG
Found at i:1375759 original size:216 final size:216
Alignment explanation
Indices: 1375312--1375877 Score: 663
Period size: 216 Copynumber: 2.6 Consensus size: 216
1375302 GAGAAGTGAT
* * * * *
1375312 ACTTGAAAAATCTTCAA-ATAACGAGTCTGCTCTCTATTCATTCAGGGAGTATAAGACTCAAACA
1 ACTTGAACAATCTTCAATA-AACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCAAACA
* * * * *
1375376 ATCTTCAATAAACATGTCTGCTCCCTATTCATTCAGGGAGTATA-AGACTCAAATAATCTTTA-A
65 ATCTTCAA-AAACGTGTCCGCTCCCTATTCATTCAGGGAGTATAGA-ACTCGAACAATCTTCATA
* *
1375439 CAAATGTGTCTGCTCCCTATTCATTCAGGGAGTATAAGACTCGAATAATCTTAAACAAACGGGTC
128 -AAACGTGTCTGCTCCCTATTCATTCAGAGAGTATAAGACTCG---AATCTTAAACAAACGGGTC
1375504 CGCTCCCTATTCCTTCAGAGAGTATAAG
189 CGCTCCCTATTCCTTCAGAGAGTATAAG
* * *
1375532 AC-T---CGATCTTCAATAAACGTGTCCGCTCCCTATTCCTTCAGAGAGTATAGGACTCAAACAA
1 ACTTGAACAATCTTCAATAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCAAACAA
* *
1375593 TCTTCAACAAATGTGTCCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
66 TCTTCAA-AAACGTGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAA
* * * * *
1375658 ACGTGT-TCGCTCTCTATTCCTTCAGAGAGTAT-AGAACTCG-ATCTTCATA-AAACGGGTTCGT
130 ACGTGTCT-GCTCCCTATTCATTCAGAGAGTATAAG-ACTCGAATCTT-AAACAAACGGGTCCGC
*
1375719 TCTCTATTCCTTCAGAGAGTAT-AG
192 TCCCTATTCCTTCAGAGAGTATAAG
* * *
1375743 AACTTGAACAATCTTC-ATAAAACGGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAAC
1 -ACTTGAACAATCTTCAAT-AAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCAAAC
* *
1375807 AATCTTCATAAAACGGGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATC
64 AATCTTCA-AAAACGTGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATA
1375872 AAACGT
128 AAACGT
1375878 ATTTGCTTCA
Statistics
Matches: 300, Mismatches: 33, Indels: 30
0.83 0.09 0.08
Matches are distributed among these distances:
211 2 0.01
212 38 0.13
213 3 0.01
215 5 0.02
216 245 0.82
217 4 0.01
219 1 0.00
220 2 0.01
ACGTcount: A:0.31, C:0.24, G:0.16, T:0.29
Consensus pattern (216 bp):
ACTTGAACAATCTTCAATAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGGACTCAAACAA
TCTTCAAAAACGTGTCCGCTCCCTATTCATTCAGGGAGTATAGAACTCGAACAATCTTCATAAAA
CGTGTCTGCTCCCTATTCATTCAGAGAGTATAAGACTCGAATCTTAAACAAACGGGTCCGCTCCC
TATTCCTTCAGAGAGTATAAG
Found at i:1375986 original size:37 final size:37
Alignment explanation
Indices: 1375880--1375989 Score: 132
Period size: 37 Copynumber: 3.0 Consensus size: 37
1375870 TCAAACGTAT
* * * * *
1375880 TTGCTTCACTATTCTTTCCTGAAGGCTTATA-TATGAT
1 TTGCTTCACAACTCTTTCATGAAGGCTTA-AGTTTGAA
* * *
1375917 TTGCTTCACCACTCTTCCGTGAAGGCTTAAGTTTGAA
1 TTGCTTCACAACTCTTTCATGAAGGCTTAAGTTTGAA
1375954 TTGCTTCACAACTCTTTCATGAAGGCTTAAGTTTGA
1 TTGCTTCACAACTCTTTCATGAAGGCTTAAGTTTGA
1375990 CTTGTTTCGA
Statistics
Matches: 63, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
36 1 0.02
37 62 0.98
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (37 bp):
TTGCTTCACAACTCTTTCATGAAGGCTTAAGTTTGAA
Found at i:1377208 original size:31 final size:32
Alignment explanation
Indices: 1377137--1377211 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 32
1377127 TTTCTTTTTT
* **
1377137 TTTTCATTTTTCTCTTTTTGTTTTTCTCTTTCA
1 TTTTCATTTTT-TCTTTTCGTTTTTCTCCATCA
1377170 --TTC-TTTTTTCTTTTCGTTTTT-TCCATCA
1 TTTTCATTTTTTCTTTTCGTTTTTCTCCATCA
1377198 TTTTCATTTTTTCT
1 TTTTCATTTTTTCT
1377212 CATTTTTTTC
Statistics
Matches: 36, Mismatches: 3, Indels: 8
0.77 0.06 0.17
Matches are distributed among these distances:
28 5 0.14
29 12 0.33
30 8 0.22
31 11 0.31
ACGTcount: A:0.07, C:0.19, G:0.03, T:0.72
Consensus pattern (32 bp):
TTTTCATTTTTTCTTTTCGTTTTTCTCCATCA
Found at i:1377214 original size:16 final size:15
Alignment explanation
Indices: 1377137--1377241 Score: 65
Period size: 16 Copynumber: 6.7 Consensus size: 15
1377127 TTTCTTTTTT
1377137 TTTTCA-TTTTTCTC
1 TTTTCATTTTTTCTC
1377151 TTTT--TGTTTTTCTC
1 TTTTCAT-TTTTTCTC
*
1377165 -TTTCATTCTTTTTTC
1 TTTTCATT-TTTTCTC
*
1377180 TTTTCGTTTTTTCCATC
1 TTTTCATTTTTT-C-TC
1377197 ATTTTCATTTTTTCTC
1 -TTTTCATTTTTTCTC
**
1377213 ATTTTTTTCTTTTTCTTC
1 -TTTTCAT-TTTTTC-TC
*
1377231 TTCTCATTTTT
1 TTTTCATTTTT
1377242 ATTATTATTT
Statistics
Matches: 71, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
13 3 0.04
14 13 0.18
15 11 0.15
16 18 0.25
17 13 0.18
18 13 0.18
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.72
Consensus pattern (15 bp):
TTTTCATTTTTTCTC
Found at i:1378158 original size:165 final size:166
Alignment explanation
Indices: 1377886--1378216 Score: 655
Period size: 165 Copynumber: 2.0 Consensus size: 166
1377876 AAATTCAACG
1377886 CATTATCGGAGATAATCCTCTCGGGCAAACCATATCTACAAATGATCTCCTTCTTCAAAAATTTG
1 CATTATCGGAGATAATCCTCTCGGGCAAACCATATCTACAAATGATCTCCTTCTTCAAAAATTTG
1377951 CATATTGTAGATTGGGTAACATTTGCGTAAAAAACTGCTTCTACCCACTTGGTGAAATAATCTAT
66 CATATTGTAGATTGGGTAACATTTGCGTAAAAAACTGCTTCTACCCACTTGGTGAAATAATCTAT
1378016 GG-TACCAGAATGAAGCGATGACCATTTGAAGCTTT
131 GGCTACCAGAATGAAGCGATGACCATTTGAAGCTTT
1378051 CATTATCGGAGATAATCCTCTCGGGCAAACCATATCTACAAATGATCTCCTTCTTCAAAAATTTG
1 CATTATCGGAGATAATCCTCTCGGGCAAACCATATCTACAAATGATCTCCTTCTTCAAAAATTTG
1378116 CATATTGTAGATTGGGTAACATTTGCGTAAAAAACTGCTTCTACCCACTTGGTGAAATAATCTAT
66 CATATTGTAGATTGGGTAACATTTGCGTAAAAAACTGCTTCTACCCACTTGGTGAAATAATCTAT
1378181 GGCTACCAGAATGAAGCGATGACCATTTGAAGCTTT
131 GGCTACCAGAATGAAGCGATGACCATTTGAAGCTTT
1378217 GGGCGAAATT
Statistics
Matches: 165, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
165 132 0.80
166 33 0.20
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Consensus pattern (166 bp):
CATTATCGGAGATAATCCTCTCGGGCAAACCATATCTACAAATGATCTCCTTCTTCAAAAATTTG
CATATTGTAGATTGGGTAACATTTGCGTAAAAAACTGCTTCTACCCACTTGGTGAAATAATCTAT
GGCTACCAGAATGAAGCGATGACCATTTGAAGCTTT
Found at i:1392855 original size:25 final size:25
Alignment explanation
Indices: 1392818--1392871 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
1392808 TTAGGCATGG
1392818 TCACCTGTCACCTGTTATATATTGT
1 TCACCTGTCACCTGTTATATATTGT
*
1392843 TCACCTGTTACCTGTTATATATTGT
1 TCACCTGTCACCTGTTATATATTGT
1392868 TCAC
1 TCAC
1392872 GTTTTGGTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.11, T:0.44
Consensus pattern (25 bp):
TCACCTGTCACCTGTTATATATTGT
Found at i:1406633 original size:28 final size:28
Alignment explanation
Indices: 1406602--1406658 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
1406592 CATGCAAAGC
* * **
1406602 ACATAGACGCACACACGCATGCATGCAT
1 ACATACACACACACACGCACACATGCAT
*
1406630 ACATACACACACAGACGCACACATGCAT
1 ACATACACACACACACGCACACATGCAT
1406658 A
1 A
1406659 AACAAAGAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.40, C:0.33, G:0.14, T:0.12
Consensus pattern (28 bp):
ACATACACACACACACGCACACATGCAT
Found at i:1411353 original size:230 final size:225
Alignment explanation
Indices: 1410910--1411358 Score: 643
Period size: 226 Copynumber: 2.0 Consensus size: 225
1410900 GGTCGGATCA
* *
1410910 GGTCGGGTGAAACTTTATTTTGGACGGGTCAGGTCGGTTTTTTAAGTGTGATATTCGGGTCGGGT
1 GGTCGGGTGAAACTTTATTTTGGACGGGTCAGATCGGTTTTTTAAGTGTGATATTCAGGTCGGGT
* * *
1410975 CGAGTTCGGGTTTAGGGTGAAAAAAACCCAACCCGAAAATATATATAATTTTACTTTAAATATTT
66 CGAGTTCGGGTTTAGGGTGAAAAAAACCCAACCCGAAAAAATATATAATTTTACCTTAAATACTT
* *
1411040 AGGAATAATTACAATAATACTCCTCTATATATAATTTTTTTCAATTAAGCCATTGTTTTTATTGA
131 AGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGCCAATGTTTTTATTGA
*
1411105 ATAAAAATAATTTTTTTATTATTTCGAGTCG
196 ATAAAAATAA-TTTTTTATAATTTCGAGTCG
*** *
1411136 GGTCGGGTGAAACTTTATTTTGTTTGGGTC-GATCGGGTTTTTTAAGTGTGATTTTCAGGTCGGG
1 GGTCGGGTGAAACTTTATTTTGGACGGGTCAGATC-GGTTTTTTAAGTGTGATATTCAGGTCGGG
** *
1411200 TCG-GATTCGGGTTTAGGGTGAAAAAACCGGACCGGACCCGAAAAAATATATAATTTTACCTTAT
65 TCGAG-TTCGGGTTTAGGGTGAAAAAA----ACCCAACCCGAAAAAATATATAATTTTACCTTAA
*
1411264 ATACTTAGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTTTCAATTAAGTCAATGTT
125 ATACTTAGGAATAATTACAATAATACCCCTCTATATATAA--TTTTTTTCAATTAAGCCAATGTT
*
1411329 TTTATTGAATAAAAATGA-TTTTTATAATTT
188 TTTATTGAATAAAAATAATTTTTTATAATTT
1411359 ATTGAAATGA
Statistics
Matches: 198, Mismatches: 17, Indels: 12
0.87 0.07 0.05
Matches are distributed among these distances:
225 4 0.02
226 78 0.39
230 78 0.39
232 38 0.19
ACGTcount: A:0.30, C:0.12, G:0.19, T:0.39
Consensus pattern (225 bp):
GGTCGGGTGAAACTTTATTTTGGACGGGTCAGATCGGTTTTTTAAGTGTGATATTCAGGTCGGGT
CGAGTTCGGGTTTAGGGTGAAAAAAACCCAACCCGAAAAAATATATAATTTTACCTTAAATACTT
AGGAATAATTACAATAATACCCCTCTATATATAATTTTTTTCAATTAAGCCAATGTTTTTATTGA
ATAAAAATAATTTTTTATAATTTCGAGTCG
Found at i:1411633 original size:18 final size:17
Alignment explanation
Indices: 1411592--1411638 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
1411582 TATGGAATTG
*
1411592 GATTCCAATTCCTGACA
1 GATTCCAATTCCTCACA
*
1411609 TATTCCAATTCCTTCACA
1 GATTCCAATTCC-TCACA
1411627 GATTCCAATTCC
1 GATTCCAATTCC
1411639 CTCAGAAACA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.28, C:0.32, G:0.06, T:0.34
Consensus pattern (17 bp):
GATTCCAATTCCTCACA
Found at i:1415418 original size:48 final size:48
Alignment explanation
Indices: 1415347--1415454 Score: 198
Period size: 48 Copynumber: 2.2 Consensus size: 48
1415337 ACACAACTAT
1415347 AGTAGCCAGAACTAAAGCTGAGTCAATGTTGTTCAATTTAACACCAAC
1 AGTAGCCAGAACTAAAGCTGAGTCAATGTTGTTCAATTTAACACCAAC
* *
1415395 AGTAGCCAGAACTAAAGGTGAGTCAATGTTGTTCAATTTAACACCAAT
1 AGTAGCCAGAACTAAAGCTGAGTCAATGTTGTTCAATTTAACACCAAC
1415443 AGTAGCCAGAAC
1 AGTAGCCAGAAC
1415455 ATTTACAATC
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
48 58 1.00
ACGTcount: A:0.38, C:0.19, G:0.19, T:0.24
Consensus pattern (48 bp):
AGTAGCCAGAACTAAAGCTGAGTCAATGTTGTTCAATTTAACACCAAC
Found at i:1416744 original size:11 final size:11
Alignment explanation
Indices: 1416728--1416759 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
1416718 CGTTAAGAAT
1416728 TCGAGTTCGAG
1 TCGAGTTCGAG
1416739 TCGAGTTC-AG
1 TCGAGTTCGAG
1416749 TCGA-TTCGAG
1 TCGAGTTCGAG
1416759 T
1 T
1416760 GTTTATCGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
9 3 0.15
10 9 0.45
11 8 0.40
ACGTcount: A:0.19, C:0.19, G:0.31, T:0.31
Consensus pattern (11 bp):
TCGAGTTCGAG
Found at i:1418036 original size:17 final size:16
Alignment explanation
Indices: 1418014--1418074 Score: 65
Period size: 15 Copynumber: 3.9 Consensus size: 16
1418004 CGGGCCGGCT
1418014 ATATATATTTAAATTAA
1 ATATATA-TTAAATTAA
*
1418031 ATATATA--AATATTAT
1 ATATATATTAA-ATTAA
1418046 ATATATATTAAATTAA
1 ATATATATTAAATTAA
*
1418062 AT-TAAATTAAATT
1 ATATATATTAAATT
1418075 TATTAATATT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
14 2 0.05
15 21 0.55
16 6 0.16
17 9 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATATATATTAAATTAA
Found at i:1418085 original size:15 final size:15
Alignment explanation
Indices: 1418030--1418085 Score: 51
Period size: 15 Copynumber: 3.5 Consensus size: 15
1418020 ATTTAAATTA
1418030 AATATATAAATATTATAT
1 AATAT-TAAAT-TTAT-T
*
1418048 ATATATTAAATTAAATT
1 A-ATATTAAATT-TATT
1418065 AA-ATTAAATTTATT
1 AATATTAAATTTATT
1418079 AATATTA
1 AATATTA
1418086 TATATATATA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
14 5 0.15
15 12 0.36
16 1 0.03
17 3 0.09
18 8 0.24
19 4 0.12
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
AATATTAAATTTATT
Found at i:1420957 original size:16 final size:16
Alignment explanation
Indices: 1420932--1420981 Score: 82
Period size: 16 Copynumber: 3.1 Consensus size: 16
1420922 AATAATGATA
1420932 AAATATAATACATATAT
1 AAATA-AATACATATAT
1420949 AAATAAATACATATAT
1 AAATAAATACATATAT
*
1420965 AAATAAATAAATATAT
1 AAATAAATACATATAT
1420981 A
1 A
1420982 TATATTTGAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 27 0.84
17 5 0.16
ACGTcount: A:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATAAATACATATAT
Found at i:1420972 original size:20 final size:20
Alignment explanation
Indices: 1420947--1420985 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
1420937 TAATACATAT
1420947 ATAAATAAATACATATATAA
1 ATAAATAAATACATATATAA
*
1420967 ATAAATAAATATATATATA
1 ATAAATAAATACATATATA
1420986 TTTGAACAGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (20 bp):
ATAAATAAATACATATATAA
Found at i:1420986 original size:8 final size:8
Alignment explanation
Indices: 1420932--1420986 Score: 56
Period size: 8 Copynumber: 6.8 Consensus size: 8
1420922 AATAATGATA
1420932 AAATATAAT
1 AAATAT-AT
*
1420941 ACATATAT
1 AAATATAT
*
1420949 AAATAAAT
1 AAATATAT
*
1420957 ACATATAT
1 AAATATAT
*
1420965 AAATAAAT
1 AAATATAT
1420973 AAATATAT
1 AAATATAT
*
1420981 ATATAT
1 AAATAT
1420987 TTGAACAGCC
Statistics
Matches: 37, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
8 32 0.86
9 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.00, T:0.35
Consensus pattern (8 bp):
AAATATAT
Found at i:1423014 original size:12 final size:12
Alignment explanation
Indices: 1422999--1423023 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1422989 TTAATTGATG
1422999 TTTTACTAAGTT
1 TTTTACTAAGTT
1423011 TTTTACTAAGTT
1 TTTTACTAAGTT
1423023 T
1 T
1423024 GAGGATTTAT
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:0.24, C:0.08, G:0.08, T:0.60
Consensus pattern (12 bp):
TTTTACTAAGTT
Found at i:1423128 original size:23 final size:24
Alignment explanation
Indices: 1423088--1423146 Score: 70
Period size: 22 Copynumber: 2.5 Consensus size: 24
1423078 AAACATAAAT
*
1423088 AATTATTAAGATAT-TTAATAAATTA
1 AATTATTAA-AAATGTTAA-AAATTA
1423113 AA-TA-TAAAAATGTTAAAAATTA
1 AATTATTAAAAATGTTAAAAATTA
1423135 AATTATTAAAAA
1 AATTATTAAAAA
1423147 AATAGTTTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
22 11 0.37
23 9 0.30
24 8 0.27
25 2 0.07
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.37
Consensus pattern (24 bp):
AATTATTAAAAATGTTAAAAATTA
Found at i:1429665 original size:12 final size:12
Alignment explanation
Indices: 1429644--1429669 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
1429634 TTGAGGAATA
1429644 GGAGGAGGATTT
1 GGAGGAGGATTT
1429656 GGAGGAGGATTT
1 GGAGGAGGATTT
1429668 GG
1 GG
1429670 TTGACGACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.00, G:0.54, T:0.23
Consensus pattern (12 bp):
GGAGGAGGATTT
Found at i:1430436 original size:21 final size:21
Alignment explanation
Indices: 1430353--1430436 Score: 55
Period size: 21 Copynumber: 3.9 Consensus size: 21
1430343 CAGAACCCCA
*
1430353 GGGGGGTATCGATTCCC-C-T
1 GGGGGGGATCGATTCCCTCAT
* *
1430372 GTGGGGGGAATCGGTTCCTCTTCAA
1 G-GGGGGG-ATCGATTCC-C-TCAT
* * * *
1430397 AGGGGGAATCGGTTTCCTCAT
1 GGGGGGGATCGATTCCCTCAT
1430418 GGGGGGGATCGATTCCCTC
1 GGGGGGGATCGATTCCCTC
1430437 TGCACCAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 10
0.70 0.16 0.14
Matches are distributed among these distances:
19 1 0.02
20 5 0.10
21 26 0.54
22 2 0.04
23 8 0.17
24 6 0.12
ACGTcount: A:0.14, C:0.23, G:0.37, T:0.26
Consensus pattern (21 bp):
GGGGGGGATCGATTCCCTCAT
Found at i:1439500 original size:17 final size:17
Alignment explanation
Indices: 1439474--1439507 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
1439464 TAAAACTAAA
1439474 TGGTTCGCAGAATCTAT
1 TGGTTCGCAGAATCTAT
*
1439491 TGGTTTGCAGAATCTAT
1 TGGTTCGCAGAATCTAT
1439508 GGATAAAACG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.24, C:0.15, G:0.24, T:0.38
Consensus pattern (17 bp):
TGGTTCGCAGAATCTAT
Found at i:1441221 original size:2 final size:2
Alignment explanation
Indices: 1441214--1441256 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
1441204 TAATTTACTC
1441214 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
1441256 A
1 A
1441257 GGGTGGACAC
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:1442953 original size:17 final size:17
Alignment explanation
Indices: 1442931--1442968 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1442921 TTATTAGTTT
*
1442931 GTTAGTTTAAGGTTAGG
1 GTTAGTTCAAGGTTAGG
*
1442948 GTTAGTTCAGGGTTAGG
1 GTTAGTTCAAGGTTAGG
1442965 GTTA
1 GTTA
1442969 AAAATTTACT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.21, C:0.03, G:0.37, T:0.39
Consensus pattern (17 bp):
GTTAGTTCAAGGTTAGG
Found at i:1443202 original size:15 final size:16
Alignment explanation
Indices: 1443149--1443203 Score: 55
Period size: 15 Copynumber: 3.6 Consensus size: 16
1443139 TATTAGTTTA
1443149 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
**
1443165 AGTT-TATTAGTTG-A-
1 AGTTATATTA-AAGAAT
1443179 AGTTATATTAAAGAAT
1 AGTTATATTAAAGAAT
1443195 AGTT-TATTA
1 AGTTATATTA
1443204 GTTGTTTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 9
0.70 0.09 0.20
Matches are distributed among these distances:
14 5 0.16
15 17 0.55
16 9 0.29
ACGTcount: A:0.42, C:0.00, G:0.15, T:0.44
Consensus pattern (16 bp):
AGTTATATTAAAGAAT
Found at i:1443207 original size:30 final size:30
Alignment explanation
Indices: 1443102--1443207 Score: 140
Period size: 30 Copynumber: 3.5 Consensus size: 30
1443092 TTTAGTTAAT
* * * *
1443102 TAGTTTTTTAGTAGTAAATTATAATTAAAAAA
1 TAGTTTATTAGTTG-AAGTTAT-ATTAAAGAA
* *
1443134 TCGTTTATTAGTTTAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1443164 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1 TAGTTTATTAGTTGAAGTTATATTAAAGAA
1443194 TAGTTTATTAGTTG
1 TAGTTTATTAGTTG
1443208 TTTAAGGGAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
30 50 0.76
31 6 0.09
32 10 0.15
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (30 bp):
TAGTTTATTAGTTGAAGTTATATTAAAGAA
Found at i:1443289 original size:15 final size:16
Alignment explanation
Indices: 1443261--1443294 Score: 61
Period size: 15 Copynumber: 2.2 Consensus size: 16
1443251 GTTTGTTACT
1443261 TTATAAGTTTATTATA
1 TTATAAGTTTATTATA
1443277 TTATAAG-TTATTATA
1 TTATAAGTTTATTATA
1443292 TTA
1 TTA
1443295 ATTTTTTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
15 11 0.61
16 7 0.39
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TTATAAGTTTATTATA
Found at i:1443311 original size:16 final size:16
Alignment explanation
Indices: 1443290--1443322 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
1443280 TAAGTTATTA
1443290 TATTAATTTTTTTTGT
1 TATTAATTTTTTTTGT
1443306 TATTAATTTTTTTTGT
1 TATTAATTTTTTTTGT
1443322 T
1 T
1443323 GTGTTGTAAA
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:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (16 bp):
TATTAATTTTTTTTGT
Found at i:1444550 original size:23 final size:23
Alignment explanation
Indices: 1444522--1444566 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
1444512 TTTAATTATT
*
1444522 ATTTAAATTAACTATATTATTTG
1 ATTTAAATCAACTATATTATTTG
* *
1444545 ATTTAAATCAATTTTATTATTT
1 ATTTAAATCAACTATATTATTT
1444567 TTGTAATTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (23 bp):
ATTTAAATCAACTATATTATTTG
Found at i:1444566 original size:18 final size:21
Alignment explanation
Indices: 1444516--1444565 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
1444506 GTTATTTTTA
*
1444516 ATTATTATTTAAATTAACTAT
1 ATTATTATTTAAATCAACTAT
* *
1444537 ATTATTTGATTTAAATCAATTTT
1 ATTA-TT-ATTTAAATCAACTAT
1444560 ATTATT
1 ATTATT
1444566 TTTGTAATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.17
22 4 0.17
23 16 0.67
ACGTcount: A:0.38, C:0.04, G:0.02, T:0.56
Consensus pattern (21 bp):
ATTATTATTTAAATCAACTAT
Found at i:1445579 original size:59 final size:56
Alignment explanation
Indices: 1445515--1445635 Score: 188
Period size: 59 Copynumber: 2.1 Consensus size: 56
1445505 TATTATAATT
*
1445515 TCATTACTAGTAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTAATAATAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATT--TAA-AAA
* *
1445574 TCATTATTAATAATAATTAGTAAATCATTAGTATCAAATCATTAAATATTTAAAAA
1 TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
1445630 TCATTA
1 TCATTA
1445636 ATAAATTCGA
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
56 9 0.15
57 3 0.05
59 47 0.80
ACGTcount: A:0.50, C:0.07, G:0.04, T:0.39
Consensus pattern (56 bp):
TCATTACTAATAATAATTAGTAAATCATTAGTATCAAATAATTAAATATTTAAAAA
Found at i:1445741 original size:14 final size:14
Alignment explanation
Indices: 1445720--1445972 Score: 120
Period size: 14 Copynumber: 18.3 Consensus size: 14
1445710 ATTAGTAATA
1445720 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1445734 AGTATTAAATCATT
1 ATTATTAAATCATT
*
1445748 ATTA-TAAA--ATC
1 ATTATTAAATCATT
*
1445759 ATTACTAAATC---
1 ATTATTAAATCATT
*
1445770 ATTATTAAACCATT
1 ATTATTAAATCATT
*
1445784 ACTATTAAATCATT
1 ATTATTAAATCATT
*
1445798 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1445810 ATTATTAAATCAGT
1 ATTATTAAATCATT
* * * *
1445824 ATTATCATTATTACTAA
1 ATTATTA-AATCA-T-T
* *
1445841 ATCATCAAATCATT
1 ATTATTAAATCATT
*
1445855 AAATATTAAAATCATT
1 -ATTATT-AAATCATT
*
1445871 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1445883 ATTATCAAATCATT
1 ATTATTAAATCATT
*
1445897 ACTAAATCATCAAATCATT
1 A-T---T-ATTAAATCATT
* *
1445916 AAATATTAAA--ATC
1 -ATTATTAAATCATT
1445929 ATTATTAAATCATT
1 ATTATTAAATCATT
*
1445943 ATTA-T-AATGATT
1 ATTATTAAATCATT
*
1445955 ATTACTAAATCATT
1 ATTATTAAATCATT
1445969 ATTA
1 ATTA
1445973 AATTATTATT
Statistics
Matches: 180, Mismatches: 34, Indels: 50
0.68 0.13 0.19
Matches are distributed among these distances:
11 15 0.08
12 42 0.23
13 10 0.06
14 66 0.37
15 16 0.09
16 12 0.07
17 6 0.03
18 1 0.01
19 11 0.06
20 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.02, T:0.42
Consensus pattern (14 bp):
ATTATTAAATCATT
Found at i:1445812 original size:12 final size:12
Alignment explanation
Indices: 1445707--1446014 Score: 134
Period size: 11 Copynumber: 25.2 Consensus size: 12
1445697 TTATTCCATA
*
1445707 ATTATTAGTAATA
1 ATTATTA-TAATC
1445720 ATTATTA-AATC
1 ATTATTATAATC
*
1445731 ATTAGTATTAAATC
1 ATTATTA-T-AATC
1445745 ATTATTATAAAATC
1 ATTATTAT--AATC
*
1445759 ATTACTA-AATC
1 ATTATTATAATC
*
1445770 ATTATTA-AACC
1 ATTATTATAATC
*
1445781 ATTACTATTAAATC
1 ATTATTA-T-AATC
*
1445795 ATTATTATAATG
1 ATTATTATAATC
1445807 ATTATTATTAAATC
1 ATTATTA-T-AATC
* * *
1445821 AGTATTATCATT
1 ATTATTATAATC
*
1445833 ATTACTA-AATC
1 ATTATTATAATC
* * * *
1445844 ATCA-AATCATTA
1 ATTATTAT-AATC
* *
1445856 AATATTAAAATC
1 ATTATTATAATC
*
1445868 ATTATTATAATG
1 ATTATTATAATC
1445880 ATTATTATCAAATC
1 ATTATTAT--AATC
*
1445894 ATTACTA-AATC
1 ATTATTATAATC
* * * *
1445905 ATCA-AATCATTA
1 ATTATTAT-AATC
* *
1445917 AATATTAAAATC
1 ATTATTATAATC
1445929 ATTATTA-AATC
1 ATTATTATAATC
*
1445940 ATTATTATAATG
1 ATTATTATAATC
1445952 ATTATTACTAAATC
1 ATTATTA-T-AATC
*
1445966 ATTATTA-AATT
1 ATTATTATAATC
1445977 ATTATTA-AATC
1 ATTATTATAATC
*
1445988 ATAATATTAAAATC
1 AT--TATTATAATC
*
1446002 ATTACTA-AATC
1 ATTATTATAATC
1446013 AT
1 AT
1446015 CAAATCATTA
Statistics
Matches: 223, Mismatches: 49, Indels: 48
0.70 0.15 0.15
Matches are distributed among these distances:
10 2 0.01
11 72 0.32
12 66 0.30
13 19 0.09
14 64 0.29
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (12 bp):
ATTATTATAATC
Found at i:1445836 original size:26 final size:26
Alignment explanation
Indices: 1445722--1445839 Score: 89
Period size: 25 Copynumber: 4.7 Consensus size: 26
1445712 TAGTAATAAT
* * *
1445722 TATTA-AATCATTAGTATTAAATCAT
1 TATTATAATGATTACTATTAAATCAG
* * * * *
1445747 TATTATAA-AATCATTACTAAATCAT
1 TATTATAATGATTACTATTAAATCAG
** *
1445772 TATTA-AACCATTACTATTAAATCAT
1 TATTATAATGATTACTATTAAATCAG
*
1445797 TATTATAATGATTATTATTAAATCAG
1 TATTATAATGATTACTATTAAATCAG
* *
1445823 TATTATCATTATTACTA
1 TATTATAATGATTACTA
1445840 AATCATCAAA
Statistics
Matches: 75, Mismatches: 15, Indels: 5
0.79 0.16 0.05
Matches are distributed among these distances:
24 2 0.03
25 41 0.55
26 32 0.43
ACGTcount: A:0.43, C:0.10, G:0.03, T:0.44
Consensus pattern (26 bp):
TATTATAATGATTACTATTAAATCAG
Found at i:1445874 original size:19 final size:19
Alignment explanation
Indices: 1445852--1446072 Score: 60
Period size: 19 Copynumber: 11.7 Consensus size: 19
1445842 TCATCAAATC
1445852 ATTAAATATTAAAATCATT
1 ATTAAATATTAAAATCATT
1445871 ATTATAATGATTATTATCAAATCATT
1 A-T-TAA--A-TATTA--AAATCATT
* *
1445897 ACTAAATCA-TCAAATC---
1 ATTAAAT-ATTAAAATCATT
1445913 ATTAAATATTAAAATCATT
1 ATTAAATATTAAAATCATT
** * *
1445932 ATTAAATCATTATTATAATG
1 ATTAAAT-ATTAAAATCATT
* *
1445952 ATT-ATTACT-AAATCATT
1 ATTAAATATTAAAATCATT
1445969 ATTAAATTATTATTAAATC---
1 ATTAAA-TATTA--AAATCATT
1445988 A-T-AATATTAAAATCATT
1 ATTAAATATTAAAATCATT
* *
1446005 ACTAAATCA-TCAAATCATT
1 ATTAAAT-ATTAAAATCATT
* * *
1446024 ACTAAATCA-T-CAA-C-TC
1 ATTAAAT-ATTAAAATCATT
*
1446040 ATTAAATATTAAAATCATG
1 ATTAAATATTAAAATCATT
*
1446059 ACTAAATCATTAAA
1 ATTAAAT-ATTAAA
1446073 TATTTAAATC
Statistics
Matches: 150, Mismatches: 23, Indels: 57
0.65 0.10 0.25
Matches are distributed among these distances:
14 5 0.03
15 2 0.01
16 25 0.17
17 13 0.09
18 8 0.05
19 48 0.32
20 19 0.13
21 5 0.03
22 7 0.05
23 1 0.01
24 8 0.05
26 9 0.06
ACGTcount: A:0.48, C:0.11, G:0.01, T:0.39
Consensus pattern (19 bp):
ATTAAATATTAAAATCATT
Found at i:1445898 original size:61 final size:60
Alignment explanation
Indices: 1445810--1446095 Score: 282
Period size: 61 Copynumber: 4.6 Consensus size: 60
1445800 TATAATGATT
* *
1445810 ATTATTAAATCAGTATTATC--ATTATTACTAAATCATCAAATCATTAAATATTAAAATC
1 ATTATTAAATCATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
*
1445868 ATTATTATAATGATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
1 ATTATTA-AATCATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
*
1445929 ATTATTAAATCATTATTAT-AATGATTATTACTAAATCAT----T-ATTAAATTATTATTAAATC
1 ATTATTAAATCATTATTATCAA--ATCATTACTAAATCATCAAATCATTAAA-TATTA--AAATC
*
1445988 ATAATATTAAAATCATTACTAAATCATCAAATCATTACTAAATCATCAACTCATTAAATATTAAA
1 AT--TATT-AAATCATTA-T---T-ATCAAATCATTACTAAATCATCAAATCATTAAATATTAAA
1446053 ATC
58 ATC
* * * * *
1446056 ATGACTAAATCATTAAATATTTAAATCATTATTAAATCAT
1 ATTATTAAATCATT-ATTA-TCAAATCATTACTAAATCAT
1446096 TTTTATGGTT
Statistics
Matches: 193, Mismatches: 11, Indels: 44
0.78 0.04 0.18
Matches are distributed among these distances:
56 6 0.03
57 6 0.03
58 7 0.04
59 20 0.10
60 11 0.06
61 64 0.33
62 28 0.15
63 1 0.01
65 8 0.04
66 19 0.10
67 2 0.01
68 9 0.05
70 6 0.03
71 6 0.03
ACGTcount: A:0.47, C:0.12, G:0.01, T:0.40
Consensus pattern (60 bp):
ATTATTAAATCATTATTATCAAATCATTACTAAATCATCAAATCATTAAATATTAAAATC
Found at i:1446030 original size:11 final size:11
Alignment explanation
Indices: 1445889--1446033 Score: 80
Period size: 11 Copynumber: 13.6 Consensus size: 11
1445879 GATTATTATC
1445889 AAATCATTACT
1 AAATCATTACT
1445900 AAATCA-T-C-
1 AAATCATTACT
1445908 AAATCA-T--T
1 AAATCATTACT
1445916 AAAT-ATTA--
1 AAATCATTACT
*
1445924 AAATCATTATT
1 AAATCATTACT
*
1445935 AAATCATTATTAT
1 AAATCATTA--CT
*
1445948 AATGATTATTACT
1 AA--ATCATTACT
*
1445961 AAATCATTATT
1 AAATCATTACT
* *
1445972 AAATTATTATT
1 AAATCATTACT
*
1445983 AAATCATAATATT
1 AAATCAT--TACT
1445996 AAAATCATTACT
1 -AAATCATTACT
1446008 AAATCA-T-C-
1 AAATCATTACT
1446016 AAATCATTACT
1 AAATCATTACT
1446027 AAATCAT
1 AAATCAT
1446034 CAACTCATTA
Statistics
Matches: 110, Mismatches: 8, Indels: 32
0.73 0.05 0.21
Matches are distributed among these distances:
7 1 0.01
8 22 0.20
9 7 0.06
10 3 0.03
11 51 0.46
12 3 0.03
13 10 0.09
14 7 0.06
15 6 0.05
ACGTcount: A:0.48, C:0.12, G:0.01, T:0.39
Consensus pattern (11 bp):
AAATCATTACT
Found at i:1446073 original size:19 final size:19
Alignment explanation
Indices: 1445997--1446043 Score: 85
Period size: 19 Copynumber: 2.5 Consensus size: 19
1445987 CATAATATTA
1445997 AAATCATTACTAAATCATC
1 AAATCATTACTAAATCATC
1446016 AAATCATTACTAAATCATC
1 AAATCATTACTAAATCATC
*
1446035 AACTCATTA
1 AAATCATTA
1446044 AATATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.47, C:0.21, G:0.00, T:0.32
Consensus pattern (19 bp):
AAATCATTACTAAATCATC
Found at i:1446364 original size:49 final size:49
Alignment explanation
Indices: 1446303--1446624 Score: 445
Period size: 49 Copynumber: 6.6 Consensus size: 49
1446293 ATTACTAATA
* * *
1446303 ATTACTAAATCATTACCATCAAATCATTAAATATTAATAATAGTTTCATT
1 ATTACT-AATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
* *
1446353 ATTACAAATCATTACTACCAAATCATTAAATATTAATGATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1446402 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1446451 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
* * *
1446500 TTTATTAATCATTACTATCAAATCATTAAATATTAATAATAATTTCATT
1 ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
* * * *
1446549 ATTACTAATCATTACTA-AATAATTATTATAATTTTAA-ATATAAATTCATT
1 ATTACTAATCATTACTACCA-AATCATTA-AATATTAATA-ATAATTTCATT
* * *
1446599 ATTA--AATCATGATTAGCAAATCATTA
1 ATTACTAATCATTACTACCAAATCATTA
1446625 CTAAATCAAA
Statistics
Matches: 248, Mismatches: 20, Indels: 10
0.89 0.07 0.04
Matches are distributed among these distances:
48 17 0.07
49 205 0.83
50 26 0.10
ACGTcount: A:0.45, C:0.12, G:0.01, T:0.42
Consensus pattern (49 bp):
ATTACTAATCATTACTACCAAATCATTAAATATTAATAATAATTTCATT
Found at i:1446366 original size:13 final size:14
Alignment explanation
Indices: 1446348--1446380 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1446338 AATAATAGTT
*
1446348 TCATTATTA-CAAA
1 TCATTACTACCAAA
1446361 TCATTACTACCAAA
1 TCATTACTACCAAA
1446375 TCATTA
1 TCATTA
1446381 AATATTAATG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 8 0.44
14 10 0.56
ACGTcount: A:0.42, C:0.21, G:0.00, T:0.36
Consensus pattern (14 bp):
TCATTACTACCAAA
Found at i:1449782 original size:83 final size:82
Alignment explanation
Indices: 1449634--1449795 Score: 279
Period size: 83 Copynumber: 2.0 Consensus size: 82
1449624 TTTTTAAAAC
* *
1449634 AACACTTAATATTTTTAAACACAATATTTTTTTAAATGGAATAAATTAAACAAATTAATTTTATA
1 AACACTAAATATTTTTAAACACAATATTTTTTTAAACGGAATAAATTAAACAAATTAATTTTATA
1449699 TAATCTAATATAAAATA
66 TAATCTAATATAAAATA
*
1449716 AACACTAAATATTTTTAAATACAATATTTTTTTAAACGAGAATAAATTAAACAAATTAATTTTAT
1 AACACTAAATATTTTTAAACACAATATTTTTTTAAACG-GAATAAATTAAACAAATTAATTTTAT
*
1449781 ATACTCTAATATAAA
65 ATAATCTAATATAAA
1449796 CTAACTAACT
Statistics
Matches: 75, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
82 35 0.47
83 40 0.53
ACGTcount: A:0.50, C:0.08, G:0.02, T:0.40
Consensus pattern (82 bp):
AACACTAAATATTTTTAAACACAATATTTTTTTAAACGGAATAAATTAAACAAATTAATTTTATA
TAATCTAATATAAAATA
Found at i:1449844 original size:14 final size:14
Alignment explanation
Indices: 1449825--1449851 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1449815 ACACATACAC
1449825 AACAACAAAAAATG
1 AACAACAAAAAATG
1449839 AACAACAAAAAAT
1 AACAACAAAAAAT
1449852 AATAAATTAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.74, C:0.15, G:0.04, T:0.07
Consensus pattern (14 bp):
AACAACAAAAAATG
Found at i:1450289 original size:28 final size:28
Alignment explanation
Indices: 1450258--1450311 Score: 99
Period size: 28 Copynumber: 1.9 Consensus size: 28
1450248 AGAATCTAAT
*
1450258 ATATAACTTAAACTAACAAATTAATATA
1 ATATAACTTAAACTAACAAACTAATATA
1450286 ATATAACTTAAACTAACAAACTAATA
1 ATATAACTTAAACTAACAAACTAATA
1450312 ATTTATACTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (28 bp):
ATATAACTTAAACTAACAAACTAATATA
Found at i:1450318 original size:28 final size:28
Alignment explanation
Indices: 1450254--1450318 Score: 96
Period size: 28 Copynumber: 2.3 Consensus size: 28
1450244 TTATAGAATC
*
1450254 TAATATATAACTTAAACTAACAAATTAA
1 TAATATATAACTTAAACTAACAAACTAA
1450282 T-ATAATATAACTTAAACTAACAAACTAA
1 TAAT-ATATAACTTAAACTAACAAACTAA
*
1450310 TAATTTATA
1 TAATATATA
1450319 CTAACAAACT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 2 0.06
28 29 0.88
29 2 0.06
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (28 bp):
TAATATATAACTTAAACTAACAAACTAA
Found at i:1450321 original size:21 final size:21
Alignment explanation
Indices: 1450288--1450336 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
1450278 TTAATATAAT
1450288 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
1450309 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
1450330 ATTAACT
1 A-TAACT
1450337 AAATTTTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:1463970 original size:23 final size:22
Alignment explanation
Indices: 1463935--1463977 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
1463925 ATAATTATTT
1463935 AAAAAATTAAATAAAAAATACC
1 AAAAAATTAAATAAAAAATACC
*
1463957 AAAAATATTTAATAAAAAATA
1 AAAAA-ATTAAATAAAAAATA
1463978 ATTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.72, C:0.05, G:0.00, T:0.23
Consensus pattern (22 bp):
AAAAAATTAAATAAAAAATACC
Found at i:1465562 original size:30 final size:31
Alignment explanation
Indices: 1465499--1465571 Score: 96
Period size: 31 Copynumber: 2.4 Consensus size: 31
1465489 GGACTGAGTA
*
1465499 AAATATATCATATGTAATAAGTATCAAAAGC
1 AAATATATCATCTGTAATAAGTATCAAAAGC
* *
1465530 AAATATATCATCTGTAATCAGCT-TC-GAAGC
1 AAATATATCATCTGTAATAAG-TATCAAAAGC
1465560 AAATATATCATC
1 AAATATATCATC
1465572 AATATCAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
30 16 0.42
31 21 0.55
32 1 0.03
ACGTcount: A:0.45, C:0.15, G:0.10, T:0.30
Consensus pattern (31 bp):
AAATATATCATCTGTAATAAGTATCAAAAGC
Found at i:1466969 original size:19 final size:18
Alignment explanation
Indices: 1466916--1466971 Score: 60
Period size: 19 Copynumber: 3.0 Consensus size: 18
1466906 AATGTCAACA
1466916 GTCAAAGTCAACGGG-CAG
1 GTCAAAGTCAA-GGGTCAG
* *
1466934 GTCAACGATCAACGGTCAG
1 GTCAAAG-TCAAGGGTCAG
1466953 GTCAAAGTCAAGTGGTCAG
1 GTCAAAGTCAAG-GGTCAG
1466972 ACCGGTTTGG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
18 12 0.39
19 19 0.61
ACGTcount: A:0.32, C:0.21, G:0.30, T:0.16
Consensus pattern (18 bp):
GTCAAAGTCAAGGGTCAG
Found at i:1475234 original size:14 final size:12
Alignment explanation
Indices: 1475203--1475243 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 12
1475193 TAAATCATTA
1475203 AAATT-TTAATC
1 AAATTATTAATC
1475214 AAATTATTAATC
1 AAATTATTAATC
1475226 ATTAATTATTAAT-
1 A--AATTATTAATC
1475239 AAATT
1 AAATT
1475244 TTTTAAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
11 9 0.33
12 7 0.26
13 1 0.04
14 10 0.37
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (12 bp):
AAATTATTAATC
Found at i:1476350 original size:57 final size:58
Alignment explanation
Indices: 1476256--1476366 Score: 197
Period size: 57 Copynumber: 1.9 Consensus size: 58
1476246 TTTACATTTT
* *
1476256 CTCTATCTTTTATACAAGGATAAAAAGATGTAAACCAGAAACCTCTCAAAGTAAACCA
1 CTCTATCTTTTACACAAGGATAAAAAGATGTAAACCAGAAACCTCTAAAAGTAAACCA
1476314 CTCTA-CTTTTACACAAGGATAAAAAGATGTAAACCAGAAACCTCTAAAAGTAA
1 CTCTATCTTTTACACAAGGATAAAAAGATGTAAACCAGAAACCTCTAAAAGTAA
1476367 GGTGTTTTCG
Statistics
Matches: 51, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
57 46 0.90
58 5 0.10
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.23
Consensus pattern (58 bp):
CTCTATCTTTTACACAAGGATAAAAAGATGTAAACCAGAAACCTCTAAAAGTAAACCA
Found at i:1479355 original size:55 final size:54
Alignment explanation
Indices: 1479296--1479795 Score: 280
Period size: 55 Copynumber: 9.1 Consensus size: 54
1479286 GTCAGGATAA
* * *
1479296 ATAAGACTTGAAAAATCTTCAAATGACGAGCCTGCTCCCTATTCCTTCAG-GAAGT
1 ATAAGACTTGAACAATCTTCAAA-AACGAGCCTGCTCCCTATTCATTCAGAG-AGT
* * * * * *
1479351 ATAAGACTCGAACAATCTTCATAAAATGTGTCTTCTCTCTATTCATTCAGAGAGT
1 ATAAGACTTGAACAATCTTCA-AAAACGAGCCTGCTCCCTATTCATTCAGAGAGT
** * *
1479406 ATAAGACTTGAACAATCTTCAATAAAACG-GGTTCGCTCTCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTTC-A-AAAACGAGCCT-GCTCCCTATTCATTCAGAGAGT
* *
1479462 AT-AGAACTCCGAA-AATCTTCAATAAAC-ATGTCC-GCTCCCTATTCTTTCAGAGAGT
1 ATAAG-ACT-TGAACAATCTTCAA-AAACGA-G-CCTGCTCCCTATTCATTCAGAGAGT
* * * *
1479517 ATAGGAC-T---CAATCTTTAACAAACGTGTCC-GCTCCCTATTCCTTCAGAGAGT
1 ATAAGACTTGAACAATCTTCAA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * * * *
1479568 AT-AGAACTCGAGCAATCTTCATAAAACGGGTCCT-TTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCA-AAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * *
1479623 AT-AGAACTCGAACAATCTTCAACAAACGTGTCC-GCTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCAA-AAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * * * * *
1479678 AT-AGAACTCGAACAATCTTCATGAAACGGGTCC-ACTCTCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCA-AAAACGAG-CCTGCTCCCTATTCATTCAGAGAGT
* * ** * *
1479733 AT-AGAACTCGAACAATCTTTAACAAACTTGTCTGCTCCCTATTCCTTCAGAGAGT
1 ATAAG-ACTTGAACAATCTTCAA-AAACGAGCCTGCTCCCTATTCATTCAGAGAGT
*
1479788 ATATGACT
1 ATAAGACT
1479796 CAATCTTCAA
Statistics
Matches: 373, Mismatches: 46, Indels: 52
0.79 0.10 0.11
Matches are distributed among these distances:
50 1 0.00
51 41 0.11
54 3 0.01
55 279 0.75
56 46 0.12
57 3 0.01
ACGTcount: A:0.31, C:0.24, G:0.15, T:0.30
Consensus pattern (54 bp):
ATAAGACTTGAACAATCTTCAAAAACGAGCCTGCTCCCTATTCATTCAGAGAGT
Found at i:1479682 original size:110 final size:110
Alignment explanation
Indices: 1479329--1479790 Score: 591
Period size: 110 Copynumber: 4.2 Consensus size: 110
1479319 TGACGAGCCT
* * *
1479329 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTTCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGGGTCCTCTCTCTA
* * * * *
1479392 TTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGTTC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAA-CAAACGTGTCC
* ** * *
1479440 GCTCTCTATTCCTTCAGAGAGTATAGAACTCCGAA-AATCTTCA-ATAAACATGTCCGCTCCCTA
1 GCTCCCTATTCCTTCAGAGAGTATAGAACT-CGAACAATCTTCATA-AAACGGGTCCTCTCTCTA
* * *
1479503 TTCTTTCAGAGAGTATAGGACT----CAATCTTTAACAAACGTGTCC
64 TTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* *
1479546 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCTTTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCTCTCTCTATT
1479611 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
* * *
1479656 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCACTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCTCTCTCTATT
* * *
1479721 CCTTCAGAGAGTATAGAACTCGAACAATCTTTAACAAACTTGTCT
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
1479766 GCTCCCTATTCCTTCAGAGAGTATA
1 GCTCCCTATTCCTTCAGAGAGTATA
1479791 TGACTCAATC
Statistics
Matches: 309, Mismatches: 31, Indels: 23
0.85 0.09 0.06
Matches are distributed among these distances:
105 3 0.01
106 78 0.25
107 10 0.03
110 147 0.48
111 65 0.21
112 6 0.02
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (110 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGGGTCCTCTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGTGTCC
Found at i:1479789 original size:165 final size:164
Alignment explanation
Indices: 1479329--1479790 Score: 559
Period size: 161 Copynumber: 2.8 Consensus size: 164
1479319 TGACGAGCCT
* **
1479329 GCTCCCTATTCCTTCAG-GAAGTATA-AGACTCGAACAATCTTCATAAAATGTGTCTTCTCTCTA
1 GCTCCCTATTCCTTCAGAG-AGTATAGA-ACTCGAACAATCTTCATAAAACGTGTCCACTCTCTA
* *
1479392 TTCATTCAGAGAGTATA-AGACTTGAACAATCTTCAATAAAACGGGT-TCGCTCTCTATTCCTTC
64 TTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTC-A-AAAACGGGTCT-GCTCTCTATTCCTTC
*
1479455 AGAGAGTATAGAACTCCGAAAATCTTCAATAAACATGTCC
125 AGAGAGTATAGAACTCCGAAAATCTTCAACAAACATGTCC
* * * * *
1479495 GCTCCCTATTCTTTCAGAGAGTATAGGACT----CAATCTTTA-ACAAACGTGTCCGCTCCCTAT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGTGTCCACTCTCTAT
* *
1479555 TCCTTCAGAGAGTATAGAACTCGAGCAATCTTCATAAAACGGGTCCT-TTCTCTATTCCTTCAGA
65 TCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-AAAACGGGT-CTGCTCTCTATTCCTTCAGA
*
1479619 GAGTATAGAACT-CGAACAATCTTCAACAAACGTGTCC
128 GAGTATAGAACTCCGAA-AATCTTCAACAAACATGTCC
* * *
1479656 GCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATGAAACGGGTCCACTCTCTATT
1 GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCCACTCTCTATT
* ** *
1479721 CCTTCAGAGAGTATAGAACTCGAACAATCTTTAACAAACTTGTCTGCTCCCTATTCCTTCAGAGA
66 CCTTCAGAGAGTATAGAACTCGAACAATCTTCAA-AAACGGGTCTGCTCTCTATTCCTTCAGAGA
1479786 GTATA
130 GTATA
1479791 TGACTCAATC
Statistics
Matches: 255, Mismatches: 27, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
160 4 0.02
161 85 0.33
162 51 0.20
163 2 0.01
164 3 0.01
165 84 0.33
166 25 0.10
167 1 0.00
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.30
Consensus pattern (164 bp):
GCTCCCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATAAAACGTGTCCACTCTCTATT
CCTTCAGAGAGTATAGAACTCGAACAATCTTCAAAAACGGGTCTGCTCTCTATTCCTTCAGAGAG
TATAGAACTCCGAAAATCTTCAACAAACATGTCC
Found at i:1481149 original size:20 final size:22
Alignment explanation
Indices: 1481126--1481171 Score: 53
Period size: 20 Copynumber: 2.2 Consensus size: 22
1481116 GAACCCTCTT
1481126 TTTTCT-TCTTCTT-TTTTTCA
1 TTTTCTCTCTTCTTGTTTTTCA
*
1481146 TTTT-TCTCTTTTTGTTTTTCA
1 TTTTCTCTCTTCTTGTTTTTCA
*
1481167 CTTTC
1 TTTTC
1481172 ATTTTATCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
19 1 0.05
20 10 0.48
21 10 0.48
ACGTcount: A:0.04, C:0.20, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTCTCTCTTCTTGTTTTTCA
Found at i:1481151 original size:21 final size:21
Alignment explanation
Indices: 1481125--1481166 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
1481115 TGAACCCTCT
1481125 TTTTTCTTCTTCTT-TTTTTCA
1 TTTTTC-TCTTCTTGTTTTTCA
*
1481146 TTTTTCTCTTTTTGTTTTTCA
1 TTTTTCTCTTCTTGTTTTTCA
1481167 CTTTCATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.05, C:0.17, G:0.02, T:0.76
Consensus pattern (21 bp):
TTTTTCTCTTCTTGTTTTTCA
Found at i:1481241 original size:31 final size:30
Alignment explanation
Indices: 1481185--1481243 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 30
1481175 TTATCTTCCA
* *
1481185 TTTTTCATTATTTCTCTTTTTTTCTTTTCG
1 TTTTTCATCATTTCTCTTTTCTTCTTTTCG
*
1481215 TTTTTCCATCATTTTTCTTTTCTTCTTTT
1 TTTTT-CATCATTTCTCTTTTCTTCTTTT
1481244 TCTTCTTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 5 0.20
31 20 0.80
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.73
Consensus pattern (30 bp):
TTTTTCATCATTTCTCTTTTCTTCTTTTCG
Found at i:1481282 original size:10 final size:9
Alignment explanation
Indices: 1481267--1481313 Score: 51
Period size: 9 Copynumber: 5.2 Consensus size: 9
1481257 TTTATTATTA
1481267 TTTTTTTTC
1 TTTTTTTTC
*
1481276 GTTTTTTTC
1 TTTTTTTTC
1481285 ATTTTTTTTC
1 -TTTTTTTTC
*
1481295 -TTTTTCTC
1 TTTTTTTTC
*
1481303 TTTTATTTC
1 TTTTTTTTC
1481312 TT
1 TT
1481314 CTTCAAGCGA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
8 7 0.23
9 16 0.52
10 8 0.26
ACGTcount: A:0.04, C:0.13, G:0.02, T:0.81
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:1481288 original size:31 final size:30
Alignment explanation
Indices: 1481204--1481290 Score: 77
Period size: 31 Copynumber: 2.8 Consensus size: 30
1481194 ATTTCTCTTT
* *
1481204 TTTTCTTTTCGTTTTTCCATCATTTTTCTTTTC
1 TTTT-TTTTCGTTTTT--ATCATTTTTATTTTA
* * *
1481237 TTCTTTTTC-TTCTTCTCATTTTTATTATTA
1 TTTTTTTTCGTTTTTATCATTTTTATT-TTA
*
1481267 TTTTTTTTCGTTTTTTTCATTTTT
1 TTTTTTTTCGTTTTTATCATTTTT
1481291 TTTCTTTTTC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
29 10 0.23
30 10 0.23
31 16 0.36
32 5 0.11
33 3 0.07
ACGTcount: A:0.08, C:0.16, G:0.02, T:0.74
Consensus pattern (30 bp):
TTTTTTTTCGTTTTTATCATTTTTATTTTA
Found at i:1481298 original size:17 final size:18
Alignment explanation
Indices: 1481266--1481313 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
1481256 TTTTATTATT
*
1481266 ATTTTTTTTCGTTTTTTTC
1 ATTTTTTTTC-TTTTTCTC
1481285 ATTTTTTTTCTTTTTCTC
1 ATTTTTTTTCTTTTTCTC
*
1481303 -TTTTATTTCTT
1 ATTTTTTTTCTT
1481314 CTTCAAGCGA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
17 10 0.37
18 7 0.26
19 10 0.37
ACGTcount: A:0.06, C:0.12, G:0.02, T:0.79
Consensus pattern (18 bp):
ATTTTTTTTCTTTTTCTC
Found at i:1489908 original size:149 final size:149
Alignment explanation
Indices: 1489537--1490140 Score: 1154
Period size: 149 Copynumber: 4.0 Consensus size: 149
1489527 CCGAAGTGCA
*
1489537 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAAGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1489602 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
1489667 TATATATATCCCGAAGGACCG
129 TATATATATCCCGAAGGACCG
*
1489688 CGTAGAAATGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1489753 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACATAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1489818 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1489837 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1489902 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1489967 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
1489986 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1490051 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
1490116 TATATATCCTGAAGGACCG
131 TATATATCCCGAAGGACCG
1490135 CGTAGA
1 CGTAGA
1490141 CCCTCGACTC
Statistics
Matches: 447, Mismatches: 6, Indels: 2
0.98 0.01 0.00
Matches are distributed among these distances:
149 325 0.73
150 1 0.00
151 121 0.27
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1490297 original size:8 final size:8
Alignment explanation
Indices: 1490284--1490308 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
1490274 TTTCATATTA
1490284 TCACATAG
1 TCACATAG
1490292 TCACATAG
1 TCACATAG
1490300 TCACATAG
1 TCACATAG
1490308 T
1 T
1490309 TCACTTACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.12, T:0.28
Consensus pattern (8 bp):
TCACATAG
Found at i:1494961 original size:149 final size:149
Alignment explanation
Indices: 1494599--1495198 Score: 1132
Period size: 149 Copynumber: 4.0 Consensus size: 149
1494589 CCGAAGTGCA
1494599 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1494664 CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAG-A-ATA
66 CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1494727 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
1494746 CGTAGAATTGCACTGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1494811 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
1494876 TATATATCCCGAAGGACCG
131 TATATATCCCGAAGGACCG
*
1494895 CGTAGAATTGCACCGTAGTGCCATGTAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1494960 CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
1495025 TATATATCCCGAAGGACCA
131 TATATATCCCGAAGGACCG
1495044 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
1 CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
*
1495109 CATATACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
66 CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
*
1495174 TATATATCCTGAAGGACCG
131 TATATATCCCGAAGGACCG
1495193 CGTAGA
1 CGTAGA
1495199 CCCTCGACTC
Statistics
Matches: 441, Mismatches: 10, Indels: 2
0.97 0.02 0.00
Matches are distributed among these distances:
147 122 0.28
148 1 0.00
149 318 0.72
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (149 bp):
CGTAGAATTGCACCGTAGTGCCATATAATAATGTCCATAAGGACCACATATTATTCCTTAAGAAT
CATAAACATATACTAGGGATCAAGTATGTGTCTTACAAGACTTCACACATGTTCCACAGAATATA
TATATATCCCGAAGGACCG
Found at i:1499449 original size:45 final size:46
Alignment explanation
Indices: 1499376--1499479 Score: 165
Period size: 45 Copynumber: 2.3 Consensus size: 46
1499366 CCATGCTTTG
1499376 TTATTCACAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1 TTATTCA-AAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
* * *
1499423 TTATTCAAAAAATAAA-CCTGATCGCATGATATCTAGTTCGCATGC
1 TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
1499468 TTATTCAAAAAA
1 TTATTCAAAAAA
1499480 CGAAAATAAA
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
45 38 0.70
46 9 0.17
47 7 0.13
ACGTcount: A:0.39, C:0.20, G:0.10, T:0.31
Consensus pattern (46 bp):
TTATTCAAAAAATAAATCCTAACCGCATGATATCTAATTCGCATGC
Found at i:1503257 original size:34 final size:34
Alignment explanation
Indices: 1503129--1503396 Score: 127
Period size: 34 Copynumber: 7.5 Consensus size: 34
1503119 TATATATATG
* *
1503129 TATATAGTAATATAGTTTGTGAAAATGTTTTTGACAAA
1 TATATA-T-ATATAGTTTTTGAAAATATTTTT-A-AAA
* * *
1503167 -ATATAATATATAATTTTCAGAAAATGATTTTTGAAAGTT
1 TATAT-ATATATAGTTTT-TGAAAAT-ATTTTT-AAA--A
* *
1503206 TGTATATTATATGGTTTTTGAAAATATTTTTAAAA
1 TATATA-TATATAGTTTTTGAAAATATTTTTAAAA
* *
1503241 TATATATATATAG-TTTTGAAAACATTTTGAAAA
1 TATATATATATAGTTTTTGAAAATATTTTTAAAA
* * * * *
1503274 CATTTATATTATA-TTTTTTAAAACATTTTGAAAA
1 TATATATA-TATAGTTTTTGAAAATATTTTTAAAA
* * *
1503308 CTTATATATATATAGTTTTT-AACACATTTTGAAAA
1 --TATATATATATAGTTTTTGAAAATATTTTTAAAA
* *
1503343 CT-TATAGTATAAAGTTTTT-TAAAT-TTTTTGGAAAA
1 -TATATA-TATATAGTTTTTGAAAATATTTTT--AAAA
*
1503378 TTATATAATATATAATTTT
1 -TATAT-ATATATAGTTTT
1503397 AAAAAACGTT
Statistics
Matches: 184, Mismatches: 29, Indels: 36
0.74 0.12 0.14
Matches are distributed among these distances:
33 32 0.17
34 43 0.23
35 28 0.15
36 31 0.17
37 17 0.09
38 14 0.08
39 7 0.04
40 12 0.07
ACGTcount: A:0.41, C:0.03, G:0.09, T:0.47
Consensus pattern (34 bp):
TATATATATATAGTTTTTGAAAATATTTTTAAAA
Found at i:1503270 original size:11 final size:11
Alignment explanation
Indices: 1503254--1503278 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1503244 ATATATATAG
1503254 TTTTGAAAACA
1 TTTTGAAAACA
1503265 TTTTGAAAACA
1 TTTTGAAAACA
1503276 TTT
1 TTT
1503279 ATATTATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (11 bp):
TTTTGAAAACA
Found at i:1503335 original size:35 final size:35
Alignment explanation
Indices: 1503208--1503540 Score: 210
Period size: 34 Copynumber: 9.5 Consensus size: 35
1503198 TGAAAGTTTG
* * *
1503208 TATAT-TATATGGTTTTTGAAAATATTTTTAAAA--
1 TATATATATATAGTTTTT-AAAACATTTTGAAAACT
*
1503241 TATATATATATAGTTTTGAAAACATTTTGAAAACAT
1 TATATATATATAGTTTTTAAAACATTTTGAAAAC-T
*
1503277 T-TATAT-TATATTTTTTAAAACATTTTGAAAACT
1 TATATATATATAGTTTTTAAAACATTTTGAAAACT
*
1503310 TATATATATATAGTTTTTAACACATTTTGAAAACT
1 TATATATATATAGTTTTTAAAACATTTTGAAAACT
* **
1503345 TATAGTATA-A-AGTTTTTTAAATTTTTTGGAAAA-T
1 TATA-TATATATAGTTTTTAAAACATTTT-GAAAACT
* * * *
1503379 TATATAATATATAATTTTAAAAAACGTTTTTTTTTGAAAAAT
1 TATAT-ATATATAGTTTT-TAAAAC-----ATTTTGAAAACT
* * *
1503421 TATATAACATATAGTTTTAAAAACATTTTTGAAAAAT
1 TATAT-ATATATAGTTTTTAAAACA-TTTTGAAAACT
* ** **
1503458 TATATAATATATAATTTAAAAAAACATTTT-TTAAC-
1 TATAT-ATATATAGTTT-TTAAAACATTTTGAAAACT
* *
1503493 T-TATATA-ATA-TTTTAAAATAAATTTTGAAAAC-
1 TATATATATATAGTTTTTAAA-ACATTTTGAAAACT
1503525 TATATA-ATATAGTTTT
1 TATATATATATAGTTTT
1503541 GGAAATTTTT
Statistics
Matches: 246, Mismatches: 29, Indels: 49
0.76 0.09 0.15
Matches are distributed among these distances:
30 4 0.02
31 9 0.04
32 8 0.03
33 31 0.13
34 67 0.27
35 42 0.17
36 12 0.05
37 33 0.13
38 7 0.03
41 11 0.04
42 22 0.09
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.47
Consensus pattern (35 bp):
TATATATATATAGTTTTTAAAACATTTTGAAAACT
Found at i:1503361 original size:69 final size:68
Alignment explanation
Indices: 1503219--1503401 Score: 201
Period size: 69 Copynumber: 2.6 Consensus size: 68
1503209 ATATTATATG
*
1503219 GTTTTTGAAAATATTTTTAAAA-TATATATATATAGTTTTGAAAACATTTTGAAAACATTTATAT
1 GTTTTT-AAAATATTTTGAAAATTATATATATATAGTTTTGAAAACATTTTGAAAACATTTATAT
*
1503283 TATA
65 TAAA
* * * *
1503287 TTTTTTAAAACATTTTGAAAACTTATATATATATAGTTTTTAACACATTTTGAAAAC--TTATAG
1 GTTTTTAAAATATTTTGAAAA-TTATATATATATAGTTTTGAAAACATTTTGAAAACATTTATA-
1503350 TATAAA
64 T-TAAA
* * * *
1503356 GTTTTTTAAATTTTTTGGAAAATTATATAATATATAATTTTAAAAA
1 GTTTTTAAAATATTTT-GAAAATTATAT-ATATATAGTTTTGAAAA
1503402 ACGTTTTTTT
Statistics
Matches: 96, Mismatches: 13, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
67 18 0.19
68 6 0.06
69 53 0.55
70 19 0.20
ACGTcount: A:0.43, C:0.04, G:0.07, T:0.47
Consensus pattern (68 bp):
GTTTTTAAAATATTTTGAAAATTATATATATATAGTTTTGAAAACATTTTGAAAACATTTATATT
AAA
Found at i:1503420 original size:42 final size:41
Alignment explanation
Indices: 1503366--1503489 Score: 157
Period size: 42 Copynumber: 3.1 Consensus size: 41
1503356 GTTTTTTAAA
*
1503366 TTTTTTGGAAAATTATATAATATATAATTTTAAAAAACGTTT
1 TTTTTTGAAAAATTATATAATATATAATTTTAAAAAAC-TTT
* *
1503408 TTTTTTGAAAAATTATATAACATATAGTTTT-AAAAAC---
1 TTTTTTGAAAAATTATATAATATATAATTTTAAAAAACTTT
* * *
1503445 ATTTTTGAAAAATTATATAATATATAATTTAAAAAAACATT
1 TTTTTTGAAAAATTATATAATATATAATTTTAAAAAACTTT
1503486 TTTT
1 TTTT
1503490 AACTTATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
37 27 0.39
38 6 0.09
41 9 0.13
42 28 0.40
ACGTcount: A:0.46, C:0.03, G:0.05, T:0.46
Consensus pattern (41 bp):
TTTTTTGAAAAATTATATAATATATAATTTTAAAAAACTTT
Found at i:1503575 original size:29 final size:29
Alignment explanation
Indices: 1503459--1503594 Score: 71
Period size: 30 Copynumber: 4.4 Consensus size: 29
1503449 TTGAAAAATT
*
1503459 ATATAATATATAATTTAAAAAAACATTTTTTA
1 ATATAATATATAGTTT--AAAAA-ATTTTTTA
* * *
1503491 ACT-T-ATATAATATTTTAAAATAAATTTTGA
1 A-TATAATAT-ATAGTTTAAAA-AATTTTTTA
* ***
1503521 AAACTATATAATATAGTTTTGGAAATTTTTTA
1 ATA-TA-AT-ATATAGTTTAAAAAATTTTTTA
1503553 ATATAATATATAGTTTAAAAAATGTTTTTGA
1 ATATAATATATAGTTTAAAAAAT-TTTTT-A
1503584 A-ATATATATAT
1 ATATA-ATATAT
1503595 TATATTTTAG
Statistics
Matches: 79, Mismatches: 14, Indels: 23
0.68 0.12 0.20
Matches are distributed among these distances:
29 13 0.16
30 21 0.27
31 16 0.20
32 17 0.22
33 10 0.13
34 2 0.03
ACGTcount: A:0.47, C:0.02, G:0.05, T:0.46
Consensus pattern (29 bp):
ATATAATATATAGTTTAAAAAATTTTTTA
Found at i:1504702 original size:14 final size:15
Alignment explanation
Indices: 1504683--1504714 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1504673 TAATTTATCA
1504683 TCATTATTATT-ATT
1 TCATTATTATTAATT
1504697 TCATTATTATTAATT
1 TCATTATTATTAATT
1504712 TCA
1 TCA
1504715 AACTTTAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.31, C:0.09, G:0.00, T:0.59
Consensus pattern (15 bp):
TCATTATTATTAATT
Found at i:1513094 original size:17 final size:16
Alignment explanation
Indices: 1513063--1513093 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
1513053 AATATTGAAA
*
1513063 CTTGAACTCAAAAAAG
1 CTTGAACTAAAAAAAG
1513079 CTTGAACTAAAAAAA
1 CTTGAACTAAAAAAA
1513094 ATTTAGAATC
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:0.55, C:0.16, G:0.10, T:0.19
Consensus pattern (16 bp):
CTTGAACTAAAAAAAG
Found at i:1514582 original size:22 final size:21
Alignment explanation
Indices: 1514547--1514588 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
1514537 ATTAATTATT
1514547 TAAAAAATTAAATAAAAATAC
1 TAAAAAATTAAATAAAAATAC
*
1514568 TAAAAACATTTAATAAAAATA
1 TAAAAA-ATTAAATAAAAATA
1514589 GTTTTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (21 bp):
TAAAAAATTAAATAAAAATAC
Found at i:1516461 original size:21 final size:21
Alignment explanation
Indices: 1516437--1516526 Score: 144
Period size: 21 Copynumber: 4.3 Consensus size: 21
1516427 TGAAGGTACT
**
1516437 GGTTCAACCGGGTTCAACAGC
1 GGTTCAACCGTATTCAACAGC
*
1516458 GGTTCAACCGTGTTCAACAGC
1 GGTTCAACCGTATTCAACAGC
*
1516479 GGTTCAGCCGTATTCAACAGC
1 GGTTCAACCGTATTCAACAGC
1516500 GGTTCAACCGTATTCAACAGC
1 GGTTCAACCGTATTCAACAGC
1516521 GGTTCA
1 GGTTCA
1516527 GCCGGATTTT
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 65 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.23
Consensus pattern (21 bp):
GGTTCAACCGTATTCAACAGC
Found at i:1516483 original size:42 final size:42
Alignment explanation
Indices: 1516437--1516534 Score: 160
Period size: 42 Copynumber: 2.3 Consensus size: 42
1516427 TGAAGGTACT
* * *
1516437 GGTTCAACCGGGTTCAACAGCGGTTCAACCGTGTTCAACAGC
1 GGTTCAGCCGGATTCAACAGCGGTTCAACCGTATTCAACAGC
*
1516479 GGTTCAGCCGTATTCAACAGCGGTTCAACCGTATTCAACAGC
1 GGTTCAGCCGGATTCAACAGCGGTTCAACCGTATTCAACAGC
1516521 GGTTCAGCCGGATT
1 GGTTCAGCCGGATT
1516535 TTATATAAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.23, C:0.28, G:0.26, T:0.23
Consensus pattern (42 bp):
GGTTCAGCCGGATTCAACAGCGGTTCAACCGTATTCAACAGC
Found at i:1518690 original size:57 final size:58
Alignment explanation
Indices: 1518601--1518716 Score: 207
Period size: 57 Copynumber: 2.0 Consensus size: 58
1518591 ACCTATCCAG
*
1518601 AGGTCACAAAGATCCTCGGTAACTGTCCAGAGGTCACAAAGATCCTC-GTAACTGTCC
1 AGGTCACAAAGATCCTCGGTAACTGTCAAGAGGTCACAAAGATCCTCGGTAACTGTCC
*
1518658 AGGTCATAAAGATCCTCGGTAACTGTCAAGAGGTCACAAAGATCCTCGGTAACTGTCC
1 AGGTCACAAAGATCCTCGGTAACTGTCAAGAGGTCACAAAGATCCTCGGTAACTGTCC
1518716 A
1 A
1518717 TAGGTCCCGA
Statistics
Matches: 56, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
57 45 0.80
58 11 0.20
ACGTcount: A:0.31, C:0.26, G:0.22, T:0.22
Consensus pattern (58 bp):
AGGTCACAAAGATCCTCGGTAACTGTCAAGAGGTCACAAAGATCCTCGGTAACTGTCC
Done.