Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000190.1 Hibiscus syriacus cultivar Beakdansim tig00000340_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: 14308945
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 5 of 62
Found at i:1086513 original size:12 final size:12
Alignment explanation
Indices: 1086498--1086528 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1086488 ATTATTTAAA
1086498 CGGGTATCGAGT
1 CGGGTATCGAGT
*
1086510 CGGGTATCGGGT
1 CGGGTATCGAGT
1086522 CGGGTAT
1 CGGGTAT
1086529 ATATATTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.13, C:0.16, G:0.45, T:0.26
Consensus pattern (12 bp):
CGGGTATCGAGT
Found at i:1086533 original size:2 final size:2
Alignment explanation
Indices: 1086526--1086615 Score: 130
Period size: 2 Copynumber: 46.0 Consensus size: 2
1086516 TCGGGTCGGG
* * * *
1086526 TA TA TA TA TT TA AA T- TA AA TA TA TA AA TA T- TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1086566 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1086608 TA TA TA TA
1 TA TA TA TA
1086616 ATTTAATTTA
Statistics
Matches: 78, Mismatches: 8, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
1 2 0.03
2 76 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:1086671 original size:40 final size:43
Alignment explanation
Indices: 1086597--1086676 Score: 105
Period size: 42 Copynumber: 1.9 Consensus size: 43
1086587 ATATATATAT
1086597 ATATATATATATATATATAATTTAATTTAATTTAA-ATTTTTTA
1 ATATATATATATATATATAA-TTAATTTAATTTAATATTTTTTA
*
1086640 ATAT-TATATATATATATAA-TAA-TTATTTTTAATATTT
1 ATATATATATATATATATAATTAATTTA-ATTTAATATTT
1086677 ATCGGGTCGG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
39 3 0.09
40 8 0.24
41 4 0.12
42 15 0.44
43 4 0.12
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (43 bp):
ATATATATATATATATATAATTAATTTAATTTAATATTTTTTA
Found at i:1086756 original size:36 final size:37
Alignment explanation
Indices: 1086716--1086796 Score: 105
Period size: 36 Copynumber: 2.2 Consensus size: 37
1086706 CTAAACCCGT
1086716 CCCCGTCCCT-GT-CCTCGTTTAACATAAACGATTTTC
1 CCCCGTCCCTCGTACC-CGTTTAACATAAACGATTTTC
* * *
1086752 CCCCGT-CCTCGTACCCGTTTAGCATAAACGGTTTTT
1 CCCCGTCCCTCGTACCCGTTTAACATAAACGATTTTC
1086788 CCCCGTCCC
1 CCCCGTCCC
1086797 CGTTTAATTC
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
35 3 0.08
36 32 0.82
37 4 0.10
ACGTcount: A:0.16, C:0.40, G:0.14, T:0.31
Consensus pattern (37 bp):
CCCCGTCCCTCGTACCCGTTTAACATAAACGATTTTC
Found at i:1087190 original size:75 final size:75
Alignment explanation
Indices: 1087080--1087220 Score: 264
Period size: 75 Copynumber: 1.9 Consensus size: 75
1087070 AATAAAAAAT
* *
1087080 AATAATTTAAATATTAAACTTATAATTTATCCAAAATTTTAACTATTCTTATATTAGTGTAGAAA
1 AATAATTTAAATACTAAACTTATAATTTATCCAAAATTTTAAATATTCTTATATTAGTGTAGAAA
1087145 TAAAAATAAA
66 TAAAAATAAA
1087155 AATAATTTAAATACTAAACTTATAATTTATCCAAAATTTTAAATATTCTTATATTAGTGTAGAAA
1 AATAATTTAAATACTAAACTTATAATTTATCCAAAATTTTAAATATTCTTATATTAGTGTAGAAA
1087220 T
66 T
1087221 TAAATTTACA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
75 64 1.00
ACGTcount: A:0.48, C:0.07, G:0.04, T:0.41
Consensus pattern (75 bp):
AATAATTTAAATACTAAACTTATAATTTATCCAAAATTTTAAATATTCTTATATTAGTGTAGAAA
TAAAAATAAA
Found at i:1087782 original size:31 final size:31
Alignment explanation
Indices: 1087739--1087811 Score: 94
Period size: 31 Copynumber: 2.4 Consensus size: 31
1087729 TTATATCTAA
*
1087739 AATTTAATAAACTTAAGAATTATTTTATGAC
1 AATTTAATAAACTTAAGAATAATTTTATGAC
* * *
1087770 AATTTGAA-AAACTTAATAATAATTTTATAAT
1 AATTT-AATAAACTTAAGAATAATTTTATGAC
1087801 AATTTAATAAA
1 AATTTAATAAA
1087812 AATTTAATCA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
30 2 0.06
31 32 0.89
32 2 0.06
ACGTcount: A:0.51, C:0.04, G:0.04, T:0.41
Consensus pattern (31 bp):
AATTTAATAAACTTAAGAATAATTTTATGAC
Found at i:1087801 original size:11 final size:11
Alignment explanation
Indices: 1087782--1087840 Score: 66
Period size: 11 Copynumber: 5.4 Consensus size: 11
1087772 TTTGAAAAAC
1087782 TTAATAATAAT
1 TTAATAATAAT
*
1087793 TTTATAATAAT
1 TTAATAATAAT
*
1087804 TTAATAAAAAT
1 TTAATAATAAT
*
1087815 TTAATCATCAAT
1 TTAATAAT-AAT
*
1087827 TT-ATAATTAT
1 TTAATAATAAT
1087837 TTAA
1 TTAA
1087841 AATTTAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
10 4 0.10
11 30 0.77
12 5 0.13
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.47
Consensus pattern (11 bp):
TTAATAATAAT
Found at i:1087819 original size:33 final size:33
Alignment explanation
Indices: 1087776--1087840 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1087766 TGACAATTTG
1087776 AAAAACTTAATAAT-AATTTTATAATAATTTAAT
1 AAAAACTTAATAATCAA-TTTATAATAATTTAAT
* * *
1087809 AAAAATTTAATCATCAATTTATAATTATTTAA
1 AAAAACTTAATAATCAATTTATAATAATTTAA
1087841 AATTTAAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.52, C:0.05, G:0.00, T:0.43
Consensus pattern (33 bp):
AAAAACTTAATAATCAATTTATAATAATTTAAT
Found at i:1087910 original size:5 final size:5
Alignment explanation
Indices: 1087902--1087926 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1087892 TATATATATT
1087902 TAATA TAATA TAATA TAATA TAATA
1 TAATA TAATA TAATA TAATA TAATA
1087927 ATTATTTATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
TAATA
Found at i:1088274 original size:122 final size:120
Alignment explanation
Indices: 1088030--1088273 Score: 325
Period size: 122 Copynumber: 2.0 Consensus size: 120
1088020 ATTTTTTTTT
* *
1088030 AAAATCATACCAAATGTTTAGTTTTCATTTTATTTTAGTACCCACCATTAAAAATTTAACTTGTT
1 AAAATCATACCAAATGTTTAGTTTTCATTTTATTTTAGTACCCACCATTAAAAACTTAACTCGTT
* * *
1088095 TAGTACCTAAGCTATTAGTTTTGGTCCTTTTTAGTACTTAAACTTTCATTTTTAAA
66 TAGTACCTAAACTATCAGTTTTGATCCTTTTTAGTACTTAAACTTT-ATTTTTAAA
* * **
1088151 AAAATCATACCTAATGTTTAGTTTTCATTTTATTTTAGTATCTCGTCATTAAAAACTTAA-TGCG
1 AAAATCATACCAAATGTTTAGTTTTCATTTTATTTTAGTA-CCCACCATTAAAAACTTAACT-CG
* *
1088215 TTTAGTACCTAAATTATCAGTTTTGAT-TTGTTTTAGTACTTAAA-TTT-TTTTTAAA
64 TTTAGTACCTAAACTATCAGTTTTGATCCT-TTTTAGTACTTAAACTTTATTTTTAAA
1088270 AAAA
1 AAAA
1088274 ACTTAACGTT
Statistics
Matches: 109, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
119 12 0.11
121 44 0.40
122 53 0.49
ACGTcount: A:0.32, C:0.13, G:0.09, T:0.46
Consensus pattern (120 bp):
AAAATCATACCAAATGTTTAGTTTTCATTTTATTTTAGTACCCACCATTAAAAACTTAACTCGTT
TAGTACCTAAACTATCAGTTTTGATCCTTTTTAGTACTTAAACTTTATTTTTAAA
Found at i:1089337 original size:19 final size:19
Alignment explanation
Indices: 1089313--1089355 Score: 77
Period size: 19 Copynumber: 2.3 Consensus size: 19
1089303 ATTTAAATCC
1089313 TTAATCTTGTTTAAAAGAT
1 TTAATCTTGTTTAAAAGAT
*
1089332 TTAATCTTGTTTAAAATAT
1 TTAATCTTGTTTAAAAGAT
1089351 TTAAT
1 TTAAT
1089356 GTATTATCTC
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.37, C:0.05, G:0.07, T:0.51
Consensus pattern (19 bp):
TTAATCTTGTTTAAAAGAT
Found at i:1095832 original size:18 final size:19
Alignment explanation
Indices: 1095809--1095845 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
1095799 TCAGTAATCC
1095809 TATTCC-CTGATAATCTTT
1 TATTCCACTGATAATCTTT
1095827 TATTCCAACTGATAATCTT
1 TATTCC-ACTGATAATCTT
1095846 ACATTCCGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
20 11 0.65
ACGTcount: A:0.27, C:0.22, G:0.05, T:0.46
Consensus pattern (19 bp):
TATTCCACTGATAATCTTT
Found at i:1095851 original size:20 final size:20
Alignment explanation
Indices: 1095815--1095852 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1095805 ATCCTATTCC
**
1095815 CTGATAATCTTTTATTCCAA
1 CTGATAATCTTACATTCCAA
1095835 CTGATAATCTTACATTCC
1 CTGATAATCTTACATTCC
1095853 GTAAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.29, C:0.24, G:0.05, T:0.42
Consensus pattern (20 bp):
CTGATAATCTTACATTCCAA
Found at i:1097240 original size:15 final size:15
Alignment explanation
Indices: 1097220--1097249 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1097210 TTTACCCTAA
1097220 TATATAATGTCCCTC
1 TATATAATGTCCCTC
*
1097235 TATATAATGTTCCTC
1 TATATAATGTCCCTC
1097250 GAGTCATATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.07, T:0.43
Consensus pattern (15 bp):
TATATAATGTCCCTC
Found at i:1097470 original size:11 final size:12
Alignment explanation
Indices: 1097452--1097481 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
1097442 CCCGAAATGA
1097452 ATCCCCATCCCG
1 ATCCCCATCCCG
1097464 A-CCCCATCCCG
1 ATCCCCATCCCG
1097475 ATCCCCA
1 ATCCCCA
1097482 ACAAGTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
11 11 0.65
12 6 0.35
ACGTcount: A:0.20, C:0.60, G:0.07, T:0.13
Consensus pattern (12 bp):
ATCCCCATCCCG
Found at i:1097605 original size:7 final size:7
Alignment explanation
Indices: 1097593--1097659 Score: 57
Period size: 7 Copynumber: 9.6 Consensus size: 7
1097583 TAATATAAAA
1097593 ATATTAT
1 ATATTAT
1097600 ATATTAT
1 ATATTAT
1097607 ATATTAT
1 ATATTAT
1097614 ATA-TAT
1 ATATTAT
1097620 A-ATTAAT
1 ATATT-AT
** *
1097627 ATAAAAA
1 ATATTAT
* *
1097634 ATATAAA
1 ATATTAT
1097641 ATATTAT
1 ATATTAT
1097648 ATATATAT
1 ATAT-TAT
1097656 ATAT
1 ATAT
1097660 AATCGGGGCA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
5 1 0.02
6 5 0.10
7 36 0.72
8 8 0.16
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (7 bp):
ATATTAT
Found at i:1097626 original size:40 final size:40
Alignment explanation
Indices: 1097573--1097662 Score: 146
Period size: 40 Copynumber: 2.2 Consensus size: 40
1097563 CGAAAAATTT
* *
1097573 TATATATAATTAATAT-AAAAATATTATATATTATATATTA
1 TATATATAATTAATATAAAAAATATAAAATATTATATA-TA
1097613 TATATATAATTAATATAAAAAATATAAAATATTATATATA
1 TATATATAATTAATATAAAAAATATAAAATATTATATATA
1097653 TATATATAAT
1 TATATATAAT
1097663 CGGGGCAGGG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
40 28 0.60
41 19 0.40
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (40 bp):
TATATATAATTAATATAAAAAATATAAAATATTATATATA
Found at i:1103247 original size:39 final size:39
Alignment explanation
Indices: 1103171--1103274 Score: 108
Period size: 39 Copynumber: 2.7 Consensus size: 39
1103161 TATACTTTGA
* *
1103171 GTTTAGGGTTTGGGATTTAAGGTTTAGGCATGATTTA-G
1 GTTTAGAGTTTAGGATTTAAGGTTTAGGCATGATTTAGG
*
1103209 GTGTTAGTGTTTAGGATTTAAGGTTTA-G-ATAGAGTTTAGG
1 GT-TTAGAGTTTAGGATTTAAGGTTTAGGCAT-GA-TTTAGG
*
1103249 GTTTAGAATTTA-GAGTTTAAGGTTTA
1 GTTTAGAGTTTAGGA-TTTAAGGTTTA
1103275 TATTTAACTT
Statistics
Matches: 57, Mismatches: 4, Indels: 9
0.81 0.06 0.13
Matches are distributed among these distances:
37 2 0.04
38 7 0.12
39 45 0.79
40 3 0.05
ACGTcount: A:0.25, C:0.01, G:0.31, T:0.43
Consensus pattern (39 bp):
GTTTAGAGTTTAGGATTTAAGGTTTAGGCATGATTTAGG
Found at i:1104025 original size:36 final size:36
Alignment explanation
Indices: 1103937--1104039 Score: 116
Period size: 36 Copynumber: 2.8 Consensus size: 36
1103927 CTTTTCGTCA
* *
1103937 TACTAGGATTCAAACTCCTAAAAATATGATAGAATTT
1 TACTAGGATTCAAACTCCT-AAAATAGGATAGAATTC
** *
1103974 TGTTAGGATTCAAACTCCTAAAATAGGATAGAGTTC
1 TACTAGGATTCAAACTCCTAAAATAGGATAGAATTC
* * *
1104010 TACTATGATTTAAACTCTTAAAGATAGGAT
1 TACTAGGATTCAAACTCCTAAA-ATAGGAT
1104040 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
36 31 0.56
37 24 0.44
ACGTcount: A:0.40, C:0.13, G:0.15, T:0.33
Consensus pattern (36 bp):
TACTAGGATTCAAACTCCTAAAATAGGATAGAATTC
Found at i:1105885 original size:5 final size:5
Alignment explanation
Indices: 1105868--1105913 Score: 74
Period size: 5 Copynumber: 8.8 Consensus size: 5
1105858 CACTAACTCT
1105868 TTTTA TCTTTA TTTTA TTTTA TCTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA T-TTTA TTTTA TTTTA T-TTTA TTTTA TTTTA TTTTA TTTT
1105914 CATCACTTTC
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
5 29 0.74
6 10 0.26
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTTA
Found at i:1105889 original size:16 final size:16
Alignment explanation
Indices: 1105868--1105913 Score: 85
Period size: 16 Copynumber: 2.9 Consensus size: 16
1105858 CACTAACTCT
1105868 TTTTATCTTTATTTTA
1 TTTTATCTTTATTTTA
1105884 TTTTATCTTTATTTTA
1 TTTTATCTTTATTTTA
1105900 TTTTAT-TTTATTTT
1 TTTTATCTTTATTTT
1105914 CATCACTTTC
Statistics
Matches: 30, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 8 0.27
16 22 0.73
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.78
Consensus pattern (16 bp):
TTTTATCTTTATTTTA
Found at i:1105900 original size:21 final size:22
Alignment explanation
Indices: 1105869--1105910 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 22
1105859 ACTAACTCTT
1105869 TTTATCTTTATTTTATTTTATC
1 TTTATCTTTATTTTATTTTATC
1105891 TTTAT-TTTATTTTATTTTAT
1 TTTATCTTTATTTTATTTTAT
1105911 TTTCATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (22 bp):
TTTATCTTTATTTTATTTTATC
Found at i:1107826 original size:17 final size:18
Alignment explanation
Indices: 1107804--1107847 Score: 63
Period size: 18 Copynumber: 2.4 Consensus size: 18
1107794 ATCCAATCAA
1107804 AAAC-AAAGAAAAAAGAG
1 AAACAAAAGAAAAAAGAG
*
1107821 AAACAAAAGAAAAAAGAA
1 AAACAAAAGAAAAAAGAG
1107839 AGAACAAAA
1 A-AACAAAA
1107848 TCAAAAAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 4 0.17
18 13 0.54
19 7 0.29
ACGTcount: A:0.80, C:0.07, G:0.14, T:0.00
Consensus pattern (18 bp):
AAACAAAAGAAAAAAGAG
Found at i:1107844 original size:19 final size:18
Alignment explanation
Indices: 1107802--1107860 Score: 75
Period size: 19 Copynumber: 3.3 Consensus size: 18
1107792 AGATCCAATC
1107802 AAAAAC-AAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
*
1107819 AGAAACAAAAGAAAAAAG
1 AAAAACAAAAGAAAAAAG
**
1107837 AAAGAACAAAATCAAAAAG
1 AAA-AACAAAAGAAAAAAG
1107856 AAAAA
1 AAAAA
1107861 GGGACAAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
17 5 0.14
18 15 0.42
19 16 0.44
ACGTcount: A:0.80, C:0.07, G:0.12, T:0.02
Consensus pattern (18 bp):
AAAAACAAAAGAAAAAAG
Found at i:1108472 original size:22 final size:22
Alignment explanation
Indices: 1108444--1108520 Score: 111
Period size: 22 Copynumber: 3.5 Consensus size: 22
1108434 GCTACCCCAT
1108444 CAAACCTTTGAGCATCAAATGA
1 CAAACCTTTGAGCATCAAATGA
*
1108466 CAAACCTTTGAACATCAAAT-A
1 CAAACCTTTGAGCATCAAATGA
* *
1108487 CCAAACATTTGAGCATCAAATGC
1 -CAAACCTTTGAGCATCAAATGA
1108510 CAAACCTTTGA
1 CAAACCTTTGA
1108521 CCAAACACAA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
21 1 0.02
22 47 0.98
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (22 bp):
CAAACCTTTGAGCATCAAATGA
Found at i:1110666 original size:106 final size:106
Alignment explanation
Indices: 1109285--1110665 Score: 2219
Period size: 106 Copynumber: 13.0 Consensus size: 106
1109275 ATATCGTGCC
* * ** * *
1109285 ACTCGAGACAACACAAGTTCAACTTCACGACGAAGGGATGGCTGGTTGTCAACAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1109350 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
1109391 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1109456 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1109497 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACTGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1109562 AATTTCAGAGCCAATTTCAACTTCACGGCGAATGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1109603 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1109668 AATTTCAGAGCCAATTTCAACTTCACGGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1109709 ACTCCAGACAACGCAAGTTCAACTTCATGACGAAGGGACCGCTGGTTGTCAACAAATAACTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1109774 AATTTCAGAGCCAATTTCAACTTCACATCGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * * * * *
1109815 ACTCAAGACAACACAAGTTCAACTTCACAATGAAAGGACGGCTGGTTGTCAA-CAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1109879 AATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1109920 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCAGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1109985 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1110026 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCTC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1110091 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1110132 ACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
* *
1110197 AATTTCAGAGCTAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
1110238 ACTCTAGACAACGCAAGTTCAACTTCACGACGAAGAGACCACTGGTTGTCAATAAACAACTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1110303 AATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* *
1110344 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGATCGCTGGTTGTCAATAAATAACTTT-C
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA-TTTCC
*
1110408 CAATTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
1110450 ACTCCAGACAACGTAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
1110515 AATTTCAGAGCCAATTTCAACTTCACAGCAAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
1110556 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * *
1110621 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
1110662 ACTC
1 ACTC
1110666 GGAACAATGC
Statistics
Matches: 1184, Mismatches: 87, Indels: 8
0.93 0.07 0.01
Matches are distributed among these distances:
105 96 0.08
106 1086 0.92
107 2 0.00
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:1111453 original size:36 final size:36
Alignment explanation
Indices: 1111364--1111467 Score: 118
Period size: 36 Copynumber: 2.8 Consensus size: 36
1111354 CCTTTTTGTC
*
1111364 CTACTAGGATTCAAACTCCTAAAAATATGATAGAATT
1 CTACTAGGATTCAAACTCCT-AAAATAGGATAGAATT
* ** *
1111401 TTGTTAGGATTCAAACTCCTAAAATAGGATAGAGTT
1 CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
* * *
1111437 CTACTATGATTTAAACTCTTAAAGATAGGAT
1 CTACTAGGATTCAAACTCCTAAA-ATAGGAT
1111468 CCACAAGCAC
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 31 0.56
37 24 0.44
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.33
Consensus pattern (36 bp):
CTACTAGGATTCAAACTCCTAAAATAGGATAGAATT
Found at i:1113577 original size:26 final size:23
Alignment explanation
Indices: 1113545--1113600 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 23
1113535 AAAGTCCATT
*
1113545 AAAATATAATATTAAATTTAATATTA
1 AAAATATAATA-TAAA-AT-ATATTA
*
1113571 AAAATATACTATAAAATATATTA
1 AAAATATAATATAAAATATATTA
1113594 AAAATAT
1 AAAATAT
1113601 TTAGACATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 13 0.46
24 1 0.04
25 4 0.14
26 10 0.36
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (23 bp):
AAAATATAATATAAAATATATTA
Found at i:1117837 original size:32 final size:31
Alignment explanation
Indices: 1117796--1117863 Score: 100
Period size: 32 Copynumber: 2.2 Consensus size: 31
1117786 TGATCATTTT
*
1117796 ATAAATTTTAATAATTAAATAATTCGATAAA
1 ATAAATTTTAATAATCAAATAATTCGATAAA
* *
1117827 ATAAACTTTTAATAATCAAATGATTTGATAAA
1 ATAAA-TTTTAATAATCAAATAATTCGATAAA
1117859 ATAAA
1 ATAAA
1117864 GTCCTGAAGG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 5 0.15
32 28 0.85
ACGTcount: A:0.54, C:0.04, G:0.04, T:0.37
Consensus pattern (31 bp):
ATAAATTTTAATAATCAAATAATTCGATAAA
Found at i:1135871 original size:19 final size:20
Alignment explanation
Indices: 1135847--1135895 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
1135837 GACCCGACCT
1135847 AAAATAATATATTTATT-AA
1 AAAATAATATATTTATTCAA
* *
1135866 AAAATATTATTTTTATTCAA
1 AAAATAATATATTTATTCAA
*
1135886 TAAA-AATATA
1 AAAATAATATA
1135896 GATTTGATTG
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
19 19 0.79
20 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (20 bp):
AAAATAATATATTTATTCAA
Found at i:1137540 original size:19 final size:19
Alignment explanation
Indices: 1137516--1137582 Score: 71
Period size: 19 Copynumber: 3.3 Consensus size: 19
1137506 TCGTTGCGAT
1137516 TTTGGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
*
1137535 TTTGGAATAAATCGCAACGCGAA
1 TTTGGACT--ATCGCAA--CGAA
* *
1137558 CTTCGACTATCGCAACGAA
1 TTTGGACTATCGCAACGAA
1137577 TTTGGA
1 TTTGGA
1137583 AAATCGTAAC
Statistics
Matches: 38, Mismatches: 6, Indels: 8
0.73 0.12 0.15
Matches are distributed among these distances:
19 15 0.39
21 14 0.37
23 9 0.24
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.25
Consensus pattern (19 bp):
TTTGGACTATCGCAACGAA
Found at i:1137550 original size:21 final size:19
Alignment explanation
Indices: 1137516--1137593 Score: 66
Period size: 19 Copynumber: 3.9 Consensus size: 19
1137506 TCGTTGCGAT
*
1137516 TTTGGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
1137535 TTTGGAATAAATCGCAACGCGAA
1 TTTGGAAT--ATCGCAA--CGAA
* * *
1137558 CTTCGACTATCGCAACGAA
1 TTTGGAATATCGCAACGAA
* *
1137577 TTTGGAAAATCGTAACG
1 TTTGGAATATCGCAACG
1137594 CGAACTTCGA
Statistics
Matches: 46, Mismatches: 9, Indels: 8
0.73 0.14 0.13
Matches are distributed among these distances:
19 23 0.50
21 14 0.30
23 9 0.20
ACGTcount: A:0.35, C:0.21, G:0.21, T:0.24
Consensus pattern (19 bp):
TTTGGAATATCGCAACGAA
Found at i:1137609 original size:21 final size:21
Alignment explanation
Indices: 1137545--1137618 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
1137535 TTTGGAATAA
1137545 ATCGCAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
* * **
1137566 ATCGCAA--CGAATTTGGAAA
1 ATCGCAACGCGAACTTCGACT
*
1137585 ATCGTAACGCGAACTTCGACT
1 ATCGCAACGCGAACTTCGACT
*
1137606 ATCGCAATGCGAA
1 ATCGCAACGCGAA
1137619 TATGTAAATC
Statistics
Matches: 40, Mismatches: 11, Indels: 4
0.73 0.20 0.07
Matches are distributed among these distances:
19 14 0.35
21 26 0.65
ACGTcount: A:0.34, C:0.26, G:0.20, T:0.20
Consensus pattern (21 bp):
ATCGCAACGCGAACTTCGACT
Found at i:1137619 original size:42 final size:42
Alignment explanation
Indices: 1137520--1137612 Score: 163
Period size: 40 Copynumber: 2.3 Consensus size: 42
1137510 TGCGATTTTG
1137520 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
*
1137562 GACTATCGCAACGAATTTGG-A-AAATCGTAACGCGAACTTC
1 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1137602 GACTATCGCAA
1 GACTATCGCAA
1137613 TGCGAATATG
Statistics
Matches: 50, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
40 29 0.58
41 1 0.02
42 20 0.40
ACGTcount: A:0.35, C:0.24, G:0.19, T:0.22
Consensus pattern (42 bp):
GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
Found at i:1137652 original size:21 final size:21
Alignment explanation
Indices: 1137627--1137866 Score: 253
Period size: 21 Copynumber: 11.6 Consensus size: 21
1137617 AATATGTAAA
1137627 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1137648 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* *
1137668 ATCGCATTGCGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
1137689 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1137710 TCGCATTGCGATAGTCGAAGT
1 TCGCATTGCGATAGTCCAAGT
*
1137731 TCGCGTTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1137752 TCGCATTGCGATAGT-CGACT
1 TCGCATTGCGATAGTCCAAGT
* * *
1137772 ATCGCATTACGAT-TTACATA-T
1 -TCGCATTGCGATAGTCCA-AGT
*
1137793 TCGCATTGCGATA-TACATA-T
1 TCGCATTGCGATAGTCCA-AGT
1137813 TCGCATTGCGATAGTCCAAGT
1 TCGCATTGCGATAGTCCAAGT
* *
1137834 TCGCATTGCGATAGTCGAATT
1 TCGCATTGCGATAGTCCAAGT
1137855 TCGCATTGCGAT
1 TCGCATTGCGAT
1137867 TTAGTTGGTC
Statistics
Matches: 189, Mismatches: 19, Indels: 22
0.82 0.08 0.10
Matches are distributed among these distances:
20 53 0.28
21 134 0.71
22 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (21 bp):
TCGCATTGCGATAGTCCAAGT
Found at i:1137673 original size:62 final size:63
Alignment explanation
Indices: 1137600--1137866 Score: 261
Period size: 62 Copynumber: 4.3 Consensus size: 63
1137590 AACGCGAACT
*
1137600 TCGACTATCGCAATGCGAATATGTA-A-ATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCG-ATATGTACAGATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
*
1137662 TCGACTATCGCATTGCGAT-T-TACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
1 TCGACTATCGCATTGCGATATGTACAGA-TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
* * * * * * *
1137724 TCGAAGT-TCGCGTTGCGATA-GTCCAAGTTCGCATTGCGATAGT-CGACTATCGCATTACGAT-
1 TCG-ACTATCGCATTGCGATATGTAC-AGATCGCATTGCGATAGTCCAAGT-TCGCATTGCGATA
1137785 -
63 G
* *
1137785 T-TACATATTCGCATTGCGATA--TACATATTCGCATTGCGATAGTCCAAGTTCGCATTGCGATA
1 TCGAC-TA-TCGCATTGCGATATGTACAGA-TCGCATTGCGATAGTCCAAGTTCGCATTGCGATA
1137847 G
63 G
* *
1137848 TCGAATTTCGCATTGCGAT
1 TCGACTATCGCATTGCGAT
1137867 TTAGTTGGTC
Statistics
Matches: 168, Mismatches: 21, Indels: 32
0.76 0.10 0.14
Matches are distributed among these distances:
59 3 0.02
60 4 0.02
61 32 0.19
62 95 0.57
63 32 0.19
64 2 0.01
ACGTcount: A:0.25, C:0.22, G:0.22, T:0.31
Consensus pattern (63 bp):
TCGACTATCGCATTGCGATATGTACAGATCGCATTGCGATAGTCCAAGTTCGCATTGCGATAG
Found at i:1137752 original size:104 final size:103
Alignment explanation
Indices: 1137627--1137866 Score: 401
Period size: 104 Copynumber: 2.3 Consensus size: 103
1137617 AATATGTAAA
*
1137627 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTGCGATTTACATATTCG
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCG
* *
1137692 CATTGCGATAGTCCA-AGTTCGCATTGCGATAGTCGAAGT
66 CATTGCGATA-TACATA-TTCGCATTGCGATAGTCCAAGT
*
1137731 TCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCG
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCG
1137796 CATTGCGATATACATATTCGCATTGCGATAGTCCAAGT
66 CATTGCGATATACATATTCGCATTGCGATAGTCCAAGT
* *
1137834 TCGCATTGCGATAGTCGAATTTCGCATTGCGAT
1 TCGCATTGCGATAGTCCAAGTTCGCATTGCGAT
1137867 TTAGTTGGTC
Statistics
Matches: 128, Mismatches: 7, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
103 54 0.42
104 74 0.58
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (103 bp):
TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATCGCATTACGATTTACATATTCG
CATTGCGATATACATATTCGCATTGCGATAGTCCAAGT
Found at i:1137838 original size:82 final size:83
Alignment explanation
Indices: 1137627--1137869 Score: 268
Period size: 83 Copynumber: 2.9 Consensus size: 83
1137617 AATATGTAAA
* * * *
1137627 TCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGT-CGACTATCGCATTGCGAT--T-TACATA
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGT-TCGCATTGCGATAGTCGA-ATA
* * *
1137688 TTCGCATTGCGATAGTCCA-AGT
64 -TCGCATTACGAT-TTACATA-T
* *
1137710 TCGCATTGCGATAGTCGAAGTTCGCGTTGCGATAGTCCAAGTTCGCATTGCGATAGTCGACTATC
1 TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAATATC
1137775 GCATTACGATTTACATAT
66 GCATTACGATTTACATAT
*
1137793 TCGCATTGCGATA-TAC-ATA-TTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAATT
1 TCGCATTGCGATAGT-CGA-AGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAATA
*
1137855 TCGCATTGCGATTTA
64 TCGCATTACGATTTA
1137870 GTTGGTCATT
Statistics
Matches: 140, Mismatches: 13, Indels: 15
0.83 0.08 0.09
Matches are distributed among these distances:
82 56 0.40
83 65 0.46
84 15 0.11
85 3 0.02
86 1 0.01
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.32
Consensus pattern (83 bp):
TCGCATTGCGATAGTCGAAGTTCGCATTGCGATAGTCCAAGTTCGCATTGCGATAGTCGAATATC
GCATTACGATTTACATAT
Found at i:1138158 original size:60 final size:60
Alignment explanation
Indices: 1138064--1138253 Score: 157
Period size: 60 Copynumber: 3.1 Consensus size: 60
1138054 ATCATATCTC
* * * ** * *
1138064 CAAATTATAACTCTCATTTTAAATTGGTTGTTAAACGTTTAAATATTTTAATTTCATCCT
1 CAAATTATAACTCTTATTCTAAATTAGTCCTTAAACGTTTGAATATTCTAATTTCATCCT
* * *
1138124 CAAATTATAACTCTTATTCTAAGTTAGTCCTTAAACTTTGTTCCGAACATTCTAATTTCATCC-
1 CAAATTATAACTCTTATTCTAAATTAGTCCTTAAAC---GTT-TGAATATTCTAATTTCATCCT
** * * * ** * *
1138187 CTAAACAATGACTCTTTTTCTAATTTAGTCCCCAAACTTTTGAATATTCAAATTTCATCCT
1 C-AAATTATAACTCTTATTCTAAATTAGTCCTTAAACGTTTGAATATTCTAATTTCATCCT
1138248 CAAATT
1 CAAATT
1138254 CATCCAAATA
Statistics
Matches: 101, Mismatches: 23, Indels: 12
0.74 0.17 0.09
Matches are distributed among these distances:
60 50 0.50
61 3 0.03
63 4 0.04
64 44 0.44
ACGTcount: A:0.32, C:0.19, G:0.06, T:0.43
Consensus pattern (60 bp):
CAAATTATAACTCTTATTCTAAATTAGTCCTTAAACGTTTGAATATTCTAATTTCATCCT
Found at i:1138994 original size:37 final size:37
Alignment explanation
Indices: 1138953--1139028 Score: 152
Period size: 37 Copynumber: 2.1 Consensus size: 37
1138943 ATGAAAATAT
1138953 CCAACTCAACCCGACTCGAAAAAATAATATAAATTTA
1 CCAACTCAACCCGACTCGAAAAAATAATATAAATTTA
1138990 CCAACTCAACCCGACTCGAAAAAATAATATAAATTTA
1 CCAACTCAACCCGACTCGAAAAAATAATATAAATTTA
1139027 CC
1 CC
1139029 TTATATTTAG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.47, C:0.26, G:0.05, T:0.21
Consensus pattern (37 bp):
CCAACTCAACCCGACTCGAAAAAATAATATAAATTTA
Found at i:1139998 original size:2 final size:2
Alignment explanation
Indices: 1139985--1140017 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
1139975 ACTTCATCCT
*
1139985 TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1140018 TATTTTTATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
TA
Found at i:1148762 original size:16 final size:16
Alignment explanation
Indices: 1148738--1148771 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
1148728 TATCGCCGAC
*
1148738 CGAATTTCACTATTCA
1 CGAAATTCACTATTCA
1148754 CGAAATTCACTATTCA
1 CGAAATTCACTATTCA
1148770 CG
1 CG
1148772 TGAATAGTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.26, G:0.09, T:0.32
Consensus pattern (16 bp):
CGAAATTCACTATTCA
Found at i:1151955 original size:2 final size:2
Alignment explanation
Indices: 1151948--1151972 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1151938 TATAAATGAT
1151948 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1151973 TAACTTCTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1157460 original size:24 final size:24
Alignment explanation
Indices: 1157433--1157490 Score: 57
Period size: 24 Copynumber: 2.4 Consensus size: 24
1157423 CATTTAGTTC
1157433 TTAAATTATT-AGTTTTAATCTATT
1 TTAAATTATTAAGTTTTAAT-TATT
* *
1157457 TTAATATT-TTAATTTTTAATTTTT
1 TTAA-ATTATTAAGTTTTAATTATT
1157481 TTAAAATTAT
1 TT-AAATTAT
1157491 ACTTAACGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 7
0.76 0.05 0.19
Matches are distributed among these distances:
24 14 0.50
25 14 0.50
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.62
Consensus pattern (24 bp):
TTAAATTATTAAGTTTTAATTATT
Found at i:1184866 original size:111 final size:111
Alignment explanation
Indices: 1184648--1184870 Score: 286
Period size: 111 Copynumber: 2.0 Consensus size: 111
1184638 TAGCCTATTG
* * **
1184648 TAGTATTTAAACTATTAAAATTTTCAAAATCATATCCTACATTTAATTTTTGTTTCATTTTAGTA
1 TAGTACTTAAACTATCAAAATTTTCAAAATCATATAATACATTTAATTTTTGTTTCATTTTAGTA
* * **
1184713 ACTCACCATGAAAAAATTAACTCGTTTAGTACATGAGGTATCATTT
66 ACCCACCATGAAAAAATTAACTCGTTTAGTACATAAACTATCATTT
* * *
1184759 TAGTACTTAAACTATCAAAATTTTTAAAATCATATAATACTTTTAGTTTTTGTTTCATTTTAGTA
1 TAGTACTTAAACTATCAAAATTTTCAAAATCATATAATACATTTAATTTTTGTTTCATTTTAGTA
* * * * *
1184824 ACCCACTATTAAAAATTTAACGT-TTTTAGTGCATAAACTATCATTT
66 ACCCACCATGAAAAAATTAAC-TCGTTTAGTACATAAACTATCATTT
1184870 T
1 T
1184871 TGTCTATTTT
Statistics
Matches: 95, Mismatches: 16, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
111 94 0.99
112 1 0.01
ACGTcount: A:0.36, C:0.13, G:0.07, T:0.44
Consensus pattern (111 bp):
TAGTACTTAAACTATCAAAATTTTCAAAATCATATAATACATTTAATTTTTGTTTCATTTTAGTA
ACCCACCATGAAAAAATTAACTCGTTTAGTACATAAACTATCATTT
Found at i:1184919 original size:22 final size:22
Alignment explanation
Indices: 1184894--1184946 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
1184884 ATTTAAATTT
*
1184894 TTAATTTTTTTAAAATTTAACG
1 TTAATTTTTTTAAAATTTAACA
**
1184916 TTAATTTTTTTTTAATTTAACA
1 TTAATTTTTTTAAAATTTAACA
*
1184938 TTAAATTTT
1 TTAATTTTT
1184947 GAACTGTGCT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (22 bp):
TTAATTTTTTTAAAATTTAACA
Found at i:1192491 original size:37 final size:36
Alignment explanation
Indices: 1192396--1192492 Score: 98
Period size: 37 Copynumber: 2.8 Consensus size: 36
1192386 TATATATTTG
*
1192396 TTTTTTTAAC-AAGTTGAAAA-AT---ATTTATATA
1 TTTTTTTAACAAAATTGAAAATATAAAATTTATATA
* *
1192427 TTTTCTTTAA-AAAATTTAAATTCATAAAATTTATATAA
1 TTTT-TTTAACAAAATTGAAAAT-ATAAAATTTATAT-A
1192465 TTTTTTTAACAAAATTGAAAATATAAAA
1 TTTTTTTAACAAAATTGAAAATATAAAA
1192493 AAGTTTAATT
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
31 4 0.08
32 12 0.23
34 2 0.04
37 19 0.37
38 15 0.29
ACGTcount: A:0.47, C:0.04, G:0.03, T:0.45
Consensus pattern (36 bp):
TTTTTTTAACAAAATTGAAAATATAAAATTTATATA
Found at i:1192972 original size:24 final size:23
Alignment explanation
Indices: 1192935--1192992 Score: 62
Period size: 24 Copynumber: 2.4 Consensus size: 23
1192925 TTTCCAGACC
* *
1192935 AATTTAAAAAATTAAGACCTAATA
1 AATTTTAAAAATTAAAACC-AATA
* *
1192959 AATTTTAAACATTAAAACCATTA
1 AATTTTAAAAATTAAAACCAATA
1192982 ATATTTTAAAA
1 A-ATTTTAAAA
1192993 CTCAATAAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
23 4 0.14
24 24 0.86
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (23 bp):
AATTTTAAAAATTAAAACCAATA
Found at i:1192992 original size:17 final size:17
Alignment explanation
Indices: 1192970--1193008 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
1192960 ATTTTAAACA
*
1192970 TTAAAAC-CATTAATATT
1 TTAAAACTCAATAA-ATT
1192987 TTAAAACTCAATAAATT
1 TTAAAACTCAATAAATT
1193004 TTAAA
1 TTAAA
1193009 CCCAAATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 15 0.75
18 5 0.25
ACGTcount: A:0.51, C:0.10, G:0.00, T:0.38
Consensus pattern (17 bp):
TTAAAACTCAATAAATT
Found at i:1193864 original size:32 final size:28
Alignment explanation
Indices: 1193791--1193881 Score: 164
Period size: 28 Copynumber: 3.2 Consensus size: 28
1193781 AACCGGGTTG
1193791 TTGAAGATTCAAGCAAGCAATATAAGGA
1 TTGAAGATTCAAGCAAGCAATATAAGGA
1193819 TTGAAGATTCAAGCAAGCAATATAAGGA
1 TTGAAGATTCAAGCAAGCAATATAAGGA
* *
1193847 TTGAAGATTCAAGCAAGCAATTTAAGGG
1 TTGAAGATTCAAGCAAGCAATATAAGGA
1193875 TTGAAGA
1 TTGAAGA
1193882 AAGTGGAATG
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 61 1.00
ACGTcount: A:0.44, C:0.10, G:0.23, T:0.23
Consensus pattern (28 bp):
TTGAAGATTCAAGCAAGCAATATAAGGA
Found at i:1196019 original size:20 final size:20
Alignment explanation
Indices: 1195925--1196293 Score: 449
Period size: 20 Copynumber: 18.4 Consensus size: 20
1195915 GATTTTCCAT
* ** *
1195925 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
1195945 AATCGCAACGCG-AACACATA
1 AATCGCAACGCGTATC-CGTA
1195965 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1195985 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
1196005 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
1196025 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1196045 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1196065 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* *
1196085 AACCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
1196105 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1196125 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1196145 AATCGCAGCGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1196165 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
1196185 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
1196205 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1196225 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1196245 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
1196265 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
1196285 AATCACAAC
1 AATCGCAAC
1196294 ACTGAAATTT
Statistics
Matches: 303, Mismatches: 38, Indels: 16
0.85 0.11 0.04
Matches are distributed among these distances:
19 3 0.01
20 297 0.98
21 3 0.01
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.20
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:1197006 original size:24 final size:24
Alignment explanation
Indices: 1196967--1197013 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1196957 AAATTTGGTC
1196967 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
1196991 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
1197014 GATGTTTCAG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:1197205 original size:12 final size:12
Alignment explanation
Indices: 1197188--1197212 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
1197178 ATATAATCCT
1197188 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1197200 GAAGAAGAAAAA
1 GAAGAAGAAAAA
1197212 G
1 G
1197213 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:1199538 original size:19 final size:19
Alignment explanation
Indices: 1199516--1199822 Score: 358
Period size: 19 Copynumber: 17.4 Consensus size: 19
1199506 CGGAAAATAC
*
1199516 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1199535 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
1199549 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
1199569 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1199583 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1199602 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
1199621 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
1199635 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1199654 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
* *
1199673 AATCG-AA-CCGACAT---
1 AATCGCAATGCGAAATGAA
*
1199687 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
1199706 AATCGCAATACGAAATGAA
1 AATCGCAATGCGAAATGAA
1199725 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1199744 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1199763 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
1199777 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1199796 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
1199815 AATCGCAA
1 AATCGCAA
1199823 CGAGATAATC
Statistics
Matches: 249, Mismatches: 13, Indels: 52
0.79 0.04 0.17
Matches are distributed among these distances:
14 45 0.18
15 4 0.02
16 16 0.06
17 15 0.06
18 5 0.02
19 151 0.61
20 13 0.05
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:1199631 original size:52 final size:53
Alignment explanation
Indices: 1199544--1199822 Score: 358
Period size: 52 Copynumber: 5.2 Consensus size: 53
1199534 AAATCCCAAC
*
1199544 ATGAAAATCGCAATGCGGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
*
1199597 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-CGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* * *
1199649 ATGAAAATCGCAATGCGAAATGAAAATCG-AACCGACATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
* *
1199701 ATTAAAATCGCAATACGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
1199758 ATGAAAATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA-GCG--A-GAAAATCGCAATGCGAA
1199810 ATGAAAATCGCAA
1 ATGAAAATCGCAA
1199823 CGAGATAATC
Statistics
Matches: 212, Mismatches: 8, Indels: 13
0.91 0.03 0.06
Matches are distributed among these distances:
51 2 0.01
52 156 0.74
53 18 0.08
54 3 0.01
55 5 0.02
56 1 0.00
57 27 0.13
ACGTcount: A:0.47, C:0.17, G:0.21, T:0.15
Consensus pattern (53 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAAGCGAGAAAATCGCAATGCGAA
Found at i:1199667 original size:71 final size:71
Alignment explanation
Indices: 1199583--1199822 Score: 355
Period size: 71 Copynumber: 3.4 Consensus size: 71
1199573 GCAACGAGAG
*
1199583 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1199648 AATGAA
66 AATGAA
* * *
1199654 AATCGCAATGCGAAATGAAAATCG-AA-CCGACAT---AATCGCAATGCGAAATTAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG-AA--AGAATCGCAA
*
1199714 TACGAAATGAA
61 TGCGAAATGAA
1199725 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
1199790 AATGAA
66 AATGAA
1199796 AATCGCAATGCGAAATGAAAATCGCAA
1 AATCGCAATGCGAAATGAAAATCGCAA
1199823 CGAGATAATC
Statistics
Matches: 150, Mismatches: 9, Indels: 20
0.84 0.05 0.11
Matches are distributed among these distances:
66 8 0.05
68 2 0.01
69 6 0.04
70 2 0.01
71 113 0.75
72 2 0.01
73 7 0.05
74 2 0.01
76 8 0.05
ACGTcount: A:0.47, C:0.17, G:0.20, T:0.15
Consensus pattern (71 bp):
AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGA
AATGAA
Found at i:1199768 original size:142 final size:137
Alignment explanation
Indices: 1199516--1199854 Score: 497
Period size: 142 Copynumber: 2.4 Consensus size: 137
1199506 CGGAAAATAC
* * * *
1199516 AATCGCAACGCGAAATGAAAATCCCAACATGAA-AATCGCAATGCGGAAATGAAAATCGC-AACG
1 AATCGCAATGCGAAATGAAAAT-CGAAC-CGAATAATCGCAATGC-GAAATTAAAATCGCAAACG
* *
1199579 AGAGAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAAT
63 AGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAAT
1199644 GCGAAATGAA
128 GCGAAATGAA
1199654 AATCGCAATGCGAAATGAAAATCGAACCGACATAATCGCAATGCGAAATTAAAATCGCAATACGA
1 AATCGCAATGCGAAATGAAAATCGAACCGA-ATAATCGCAATGCGAAATTAAAATCGCAA-ACG-
1199719 AATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
63 -A-GAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCA
1199784 ATGCGAAATGAA
126 ATGCGAAATGAA
1199796 AATCGCAATGCGAAATGAAAATCGCAA-CGAGATAATCGCAATGCGAAATTATAAA-CGCA
1 AATCGCAATGCGAAATGAAAATCG-AACCGA-ATAATCGCAATGCGAAATTA-AAATCGCA
1199855 TTGCGATTTT
Statistics
Matches: 185, Mismatches: 7, Indels: 14
0.90 0.03 0.07
Matches are distributed among these distances:
136 2 0.01
137 18 0.10
138 33 0.18
139 3 0.02
141 1 0.01
142 123 0.66
143 5 0.03
ACGTcount: A:0.47, C:0.18, G:0.20, T:0.15
Consensus pattern (137 bp):
AATCGCAATGCGAAATGAAAATCGAACCGAATAATCGCAATGCGAAATTAAAATCGCAAACGAGA
AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCG
AAATGAA
Found at i:1199960 original size:19 final size:19
Alignment explanation
Indices: 1199851--1199952 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
1199841 AAATTATAAA
1199851 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1199870 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
1199890 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
1199906 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1199923 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
1199942 CGCATTGCGAT
1 CGCATTGCGAT
1199953 AGTCATTTTT
Statistics
Matches: 75, Mismatches: 2, Indels: 11
0.85 0.02 0.12
Matches are distributed among these distances:
14 6 0.08
16 7 0.09
17 7 0.09
19 36 0.48
20 19 0.25
ACGTcount: A:0.15, C:0.24, G:0.18, T:0.44
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:1200075 original size:13 final size:14
Alignment explanation
Indices: 1200059--1200093 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
1200049 CATCAATTAC
1200059 ACAAATCA-CTTTT
1 ACAAATCATCTTTT
1200072 ACAAATCATCTTTT
1 ACAAATCATCTTTT
1200086 ACAAATCA
1 ACAAATCA
1200094 ATTAAACAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 8 0.38
14 13 0.62
ACGTcount: A:0.43, C:0.23, G:0.00, T:0.34
Consensus pattern (14 bp):
ACAAATCATCTTTT
Found at i:1202072 original size:14 final size:14
Alignment explanation
Indices: 1202053--1202109 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
1202043 GCGAAATGAA
*
1202053 AATCGCAACGACAG
1 AATCGCAACGAAAG
1202067 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
1202084 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
1202100 AATCGCAACG
1 AATCGCAACG
1202110 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:1202080 original size:33 final size:33
Alignment explanation
Indices: 1202034--1202126 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
1202024 GCGAAACCAA
*
1202034 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
1202067 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
1202100 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
1202127 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:1202091 original size:19 final size:19
Alignment explanation
Indices: 1201997--1202131 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
1201987 TAGTTTACTT
* *
1201997 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
1202017 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
1202036 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1202055 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
1202069 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
1202088 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
1202102 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
1202121 TCGCAATGCGA
1 TCGCAACGCGA
1202132 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:1202149 original size:19 final size:19
Alignment explanation
Indices: 1202127--1202255 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
1202117 AAAATCGCAA
1202127 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1202146 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
1202160 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
1202179 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
1202193 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
1202212 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
1202231 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
1202251 TGCGA
1 TGCGA
1202256 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:1202169 original size:33 final size:33
Alignment explanation
Indices: 1202127--1202218 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
1202117 AAAATCGCAA
1202127 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
1202160 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
1202193 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
1202219 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:1202458 original size:93 final size:93
Alignment explanation
Indices: 1202299--1202771 Score: 930
Period size: 93 Copynumber: 5.1 Consensus size: 93
1202289 TTGAATGGAT
1202299 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202364 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1202392 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202457 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1202485 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202550 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1202578 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202642 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
*
1202670 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTAACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202735 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
1202763 AAATTTACT
1 AAATTTACT
1202772 AAGCAATCTA
Statistics
Matches: 378, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 92 0.24
93 286 0.76
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1202744 original size:185 final size:186
Alignment explanation
Indices: 1202299--1202771 Score: 930
Period size: 185 Copynumber: 2.5 Consensus size: 186
1202289 TTGAATGGAT
1202299 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202364 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1202429 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
1202485 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202550 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
1202615 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
*
1202670 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTAACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1202735 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACT
1202772 AAGCAATCTA
Statistics
Matches: 286, Mismatches: 1, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
185 154 0.54
186 132 0.46
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.22
Consensus pattern (186 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:1204494 original size:14 final size:14
Alignment explanation
Indices: 1204475--1204564 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
1204465 TTGAAATGAA
1204475 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1204489 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
1204506 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
1204522 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
1204541 AATCGCAACGAGAG
1 AATCGCAACGAGAG
1204555 AATCGCAACG
1 AATCGCAACG
1204565 CGAAATGAAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.42, C:0.23, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:1204512 original size:33 final size:33
Alignment explanation
Indices: 1204467--1204581 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
1204457 TCTTTTGGTT
1204467 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
1204500 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1204533 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1204566 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
1204582 TGCGATTTTG
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.45, C:0.21, G:0.24, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:1204513 original size:19 final size:18
Alignment explanation
Indices: 1204474--1204586 Score: 88
Period size: 19 Copynumber: 6.8 Consensus size: 18
1204464 GTTGAAATGA
1204474 AAATCGCAA--CGAGA-G
1 AAATCGCAACGCGAGATG
1204489 -AATCGCAACGCGAGATG
1 AAATCGCAACGCGAGATG
1204506 ACAATCGCAA--CGAGA-G
1 A-AATCGCAACGCGAGATG
*
1204522 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
1204539 AAAATCGCAA--CGAGA-G
1 -AAATCGCAACGCGAGATG
*
1204555 -AATCGCAACGCGAAATG
1 AAATCGCAACGCGAGATG
*
1204572 AAAATCGCAATGCGA
1 -AAATCGCAACGCGA
1204587 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 4, Indels: 26
0.72 0.04 0.24
Matches are distributed among these distances:
14 24 0.30
16 15 0.19
17 12 0.15
19 28 0.35
ACGTcount: A:0.43, C:0.22, G:0.25, T:0.10
Consensus pattern (18 bp):
AAATCGCAACGCGAGATG
Found at i:1204617 original size:14 final size:14
Alignment explanation
Indices: 1204598--1204652 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
1204588 TTTGGTTTCG
1204598 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
1204612 CGTTGCGATTTCCATTTCG
1 CGTTGCGA-TT-C---TCT
1204631 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
1204645 CGTTGCGA
1 CGTTGCGA
1204653 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 2 0.06
16 1 0.03
17 1 0.03
18 2 0.06
19 10 0.29
ACGTcount: A:0.09, C:0.27, G:0.24, T:0.40
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:1204814 original size:33 final size:33
Alignment explanation
Indices: 1204772--1204842 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
1204762 AATACTAACT
*
1204772 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
* *
1204805 TGAAAATCGCAACGACAGAATCGTAACGCGAAA
1 TGAAAATCGCAACGACAGAATAGCAACGCGAAA
1204838 TGAAA
1 TGAAA
1204843 TCTAAGTGAA
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.48, C:0.18, G:0.23, T:0.11
Consensus pattern (33 bp):
TGAAAATCGCAACGACAGAATAGCAACGCGAAA
Found at i:1205076 original size:22 final size:22
Alignment explanation
Indices: 1205024--1205078 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
1205014 TGGTTGTGAG
**
1205024 GGATTTCGCCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
1205046 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
1205068 GGATTTCTTCG
1 GGATTTCTTCG
1205079 CCGTAGAGAG
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.40, T:0.24
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:1205250 original size:20 final size:20
Alignment explanation
Indices: 1205225--1205418 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
1205215 CTTTAAATAT
1205225 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1205245 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
1205267 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1205286 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
1205306 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
1205326 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
1205346 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
1205366 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
1205386 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
1205406 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1205419 TGGAAAATCG
Statistics
Matches: 147, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 128 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:1205412 original size:60 final size:60
Alignment explanation
Indices: 1205225--1205418 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
1205215 CTTTAAATAT
**
1205225 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
1205286 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
1205346 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
1205406 CGCGTTGCGATTT
1 CGCGTTGCGATTT
1205419 TGGAAAATCG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 84 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.36
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:1205435 original size:21 final size:20
Alignment explanation
Indices: 1205411--1205487 Score: 57
Period size: 21 Copynumber: 3.7 Consensus size: 20
1205401 ATATTCGCGT
1205411 TGCGATTTTGGAAAATCGCAA
1 TGCGATTTTGGAAAATCGC-A
* * **
1205432 TGCGAATTTGTACTATCGCA
1 TGCGATTTTGGAAAATCGCA
* *
1205452 TCGCGATTTT-CAAGAATCGCGT
1 T-GCGATTTTGGAA-AATCGC-A
1205474 TGCGATTTTGGAAA
1 TGCGATTTTGGAAA
1205488 CTGATTTGCG
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
20 3 0.07
21 36 0.86
22 3 0.07
ACGTcount: A:0.27, C:0.17, G:0.23, T:0.32
Consensus pattern (20 bp):
TGCGATTTTGGAAAATCGCA
Found at i:1205498 original size:20 final size:20
Alignment explanation
Indices: 1205473--1205524 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
1205463 AAGAATCGCG
*
1205473 TTGCGATTTTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1205493 TTGCGATTCTGGAAACTGAT
1 TTGCGATTCTGGAAACTGAT
1205513 TTGCGATTCTGG
1 TTGCGATTCTGG
1205525 GGATCGCGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.21, C:0.13, G:0.27, T:0.38
Consensus pattern (20 bp):
TTGCGATTCTGGAAACTGAT
Found at i:1206040 original size:3 final size:3
Alignment explanation
Indices: 1206032--1206128 Score: 112
Period size: 3 Copynumber: 33.0 Consensus size: 3
1206022 TATCCATTTG
*
1206032 TTA TTA TTA TTA TTA TTA TTA -TA TTA TTA TT- TTA TTTA TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA
* * *
1206076 TTA TTA TT- TTA TAA TTA -TA TTA TTA TAA TTTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1206120 TTA TTA TTA
1 TTA TTA TTA
1206129 GTTACAGACC
Statistics
Matches: 80, Mismatches: 8, Indels: 12
0.80 0.08 0.12
Matches are distributed among these distances:
2 8 0.10
3 67 0.84
4 5 0.06
ACGTcount: A:0.35, C:0.01, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:1206078 original size:32 final size:31
Alignment explanation
Indices: 1206035--1206127 Score: 98
Period size: 32 Copynumber: 2.9 Consensus size: 31
1206025 CCATTTGTTA
1206035 TTATTATTATTATTATTATATTATTATTTTAT
1 TTATTA-TATTATTATTATATTATTATTTTAT
* * *
1206067 TTATTACTATTATTATTTTATAATTATATTAT
1 TTATTA-TATTATTATTATATTATTATTTTAT
*
1206099 TATAATT-TATTAATATTATTATTATTATT
1 T-T-ATTATATTATTATTA-TATTATTATT
1206128 AGTTACAGAC
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
32 38 0.76
33 9 0.18
34 3 0.06
ACGTcount: A:0.34, C:0.01, G:0.00, T:0.65
Consensus pattern (31 bp):
TTATTATATTATTATTATATTATTATTTTAT
Found at i:1207518 original size:14 final size:13
Alignment explanation
Indices: 1207495--1207524 Score: 51
Period size: 14 Copynumber: 2.2 Consensus size: 13
1207485 TTATTGCTTT
1207495 TATATTTTAAATA
1 TATATTTTAAATA
1207508 TATAGTTTTAAATA
1 TATA-TTTTAAATA
1207522 TAT
1 TAT
1207525 TTATTTTAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (13 bp):
TATATTTTAAATA
Found at i:1208653 original size:15 final size:15
Alignment explanation
Indices: 1208635--1208665 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1208625 AAATTCTAAA
1208635 TATTTAAATAAAAAT
1 TATTTAAATAAAAAT
*
1208650 TATTTATATAAAAAT
1 TATTTAAATAAAAAT
1208665 T
1 T
1208666 CTATTTGTTG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (15 bp):
TATTTAAATAAAAAT
Found at i:1212250 original size:2 final size:2
Alignment explanation
Indices: 1212243--1212267 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1212233 TTTACATTCT
1212243 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
1212268 TAATGACCTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:1215707 original size:3 final size:3
Alignment explanation
Indices: 1215699--1215736 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
1215689 TTCAATCAGA
1215699 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1 AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AAC AA
1215737 ACAGAGATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
AAC
Found at i:1216215 original size:3 final size:3
Alignment explanation
Indices: 1216207--1216238 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
1216197 TATATTTGAA
1216207 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1216239 ATATTTATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:1217582 original size:4 final size:4
Alignment explanation
Indices: 1217573--1217603 Score: 53
Period size: 4 Copynumber: 7.8 Consensus size: 4
1217563 ATAACCGAAT
*
1217573 ATAC ATAC ATAC ATAC ATGC ATAC ATAC ATA
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATA
1217604 TATTCAAACC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.48, C:0.23, G:0.03, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:1220132 original size:17 final size:17
Alignment explanation
Indices: 1220110--1220151 Score: 57
Period size: 17 Copynumber: 2.5 Consensus size: 17
1220100 TTGGATATTA
**
1220110 TAAATAAATTTAAGTAT
1 TAAATAAATAAAAGTAT
*
1220127 TAAATAAATAAAAGTCT
1 TAAATAAATAAAAGTAT
1220144 TAAATAAA
1 TAAATAAA
1220152 ATATAATAAC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.60, C:0.02, G:0.05, T:0.33
Consensus pattern (17 bp):
TAAATAAATAAAAGTAT
Found at i:1220974 original size:22 final size:22
Alignment explanation
Indices: 1220940--1220982 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
1220930 TTAATCGATT
*
1220940 AATTTAGATTAAATA-TAATTAA
1 AATTTAGAATAAA-AGTAATTAA
*
1220962 AATTTATAATAAAAGTAATTA
1 AATTTAGAATAAAAGTAATTA
1220983 TTTAAACATG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.06
22 17 0.94
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (22 bp):
AATTTAGAATAAAAGTAATTAA
Found at i:1223703 original size:16 final size:16
Alignment explanation
Indices: 1223684--1223714 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
1223674 ATTTTAATTT
1223684 TTTTATTTCCTTTTTG
1 TTTTATTTCCTTTTTG
1223700 TTTTATTTCCTTTTT
1 TTTTATTTCCTTTTT
1223715 TAAACTAACC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.06, C:0.13, G:0.03, T:0.77
Consensus pattern (16 bp):
TTTTATTTCCTTTTTG
Found at i:1224522 original size:14 final size:14
Alignment explanation
Indices: 1224503--1224530 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
1224493 AATATTATAT
1224503 ATCTTTAGTAATAA
1 ATCTTTAGTAATAA
1224517 ATCTTTAGTAATAA
1 ATCTTTAGTAATAA
1224531 TAATAAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.07, T:0.43
Consensus pattern (14 bp):
ATCTTTAGTAATAA
Found at i:1228796 original size:31 final size:31
Alignment explanation
Indices: 1228758--1228858 Score: 150
Period size: 31 Copynumber: 3.3 Consensus size: 31
1228748 TGAAAGATTA
*
1228758 GTACTAAAACGGACCGAAACTAATAGTTTAG
1 GTACTAAAACGAACCGAAACTAATAGTTTAG
* *
1228789 GTACTAAAACGAATCGAAACTGATAGTTTAG
1 GTACTAAAACGAACCGAAACTAATAGTTTAG
*
1228820 GTACTAAAAC-ATACCGAAACTAATAGTTAAG
1 GTACTAAAACGA-ACCGAAACTAATAGTTTAG
1228851 GTACTAAA
1 GTACTAAA
1228859 CACGTTAAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
30 1 0.02
31 62 0.98
ACGTcount: A:0.45, C:0.15, G:0.17, T:0.24
Consensus pattern (31 bp):
GTACTAAAACGAACCGAAACTAATAGTTTAG
Found at i:1231567 original size:3 final size:3
Alignment explanation
Indices: 1231559--1231596 Score: 67
Period size: 3 Copynumber: 12.3 Consensus size: 3
1231549 AATTTTAATT
1231559 TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA T
1231597 GTTTATTAAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
3 31 0.91
4 3 0.09
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1231608 original size:22 final size:22
Alignment explanation
Indices: 1231561--1231608 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
1231551 TTTTAATTTT
*
1231561 ATTATTATTATTATTATTATTT
1 ATTATTATTATTATTATTATTA
1231583 ATTATTATTATTATGT-TTATTA
1 ATTATTATTATTAT-TATTATTA
1231605 ATTA
1 ATTA
1231609 CATATTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
22 23 0.96
23 1 0.04
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTATTATTATTATTATTATTA
Found at i:1231741 original size:25 final size:25
Alignment explanation
Indices: 1231711--1231782 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
1231701 ACCAACCCAT
1231711 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
*
1231736 TAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
* *
1231761 CAAATTAGGGTTT-TAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
1231783 TCCCCTAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 8 0.19
25 35 0.81
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:1235438 original size:31 final size:32
Alignment explanation
Indices: 1235402--1235463 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
1235392 ATTTTACATG
*
1235402 TACTAACTTATTT-TTCTCTTTTGTTTGTGTA
1 TACTAACTTATTTCTTATCTTTTGTTTGTGTA
1235433 TACTAACTTATTTCTTATCTTTTGTTTGTGT
1 TACTAACTTATTTCTTATCTTTTGTTTGTGT
1235464 CATTTTGTCA
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.16, C:0.13, G:0.10, T:0.61
Consensus pattern (32 bp):
TACTAACTTATTTCTTATCTTTTGTTTGTGTA
Found at i:1237924 original size:26 final size:25
Alignment explanation
Indices: 1237895--1237972 Score: 76
Period size: 26 Copynumber: 3.2 Consensus size: 25
1237885 AATTTTTGAC
1237895 ATTCTATCTCTTTGAGACCTTGAAAT
1 ATTCT-TCTCTTTGAGACCTTGAAAT
* *
1237921 A---TTCT-TTT-CGACCTTGAAAC
1 ATTCTTCTCTTTGAGACCTTGAAAT
*
1237941 ATTCCCTCTCTTTGAGACCTTGAAAT
1 ATT-CTTCTCTTTGAGACCTTGAAAT
1237967 ATTCTT
1 ATTCTT
1237973 TCCACCTTGA
Statistics
Matches: 40, Mismatches: 6, Indels: 13
0.68 0.10 0.22
Matches are distributed among these distances:
20 11 0.28
21 3 0.08
22 3 0.08
23 1 0.03
24 3 0.08
25 5 0.12
26 14 0.35
ACGTcount: A:0.24, C:0.23, G:0.10, T:0.42
Consensus pattern (25 bp):
ATTCTTCTCTTTGAGACCTTGAAAT
Found at i:1237933 original size:20 final size:20
Alignment explanation
Indices: 1237910--1237984 Score: 62
Period size: 20 Copynumber: 3.5 Consensus size: 20
1237900 ATCTCTTTGA
1237910 GACCTTGAAATATTCTTTTC
1 GACCTTGAAATATTCTTTTC
* *
1237930 GACCTTGAAACATTCCCTCTCTTTGA
1 GACCTTGAAATA-T---TCT-TTT-C
1237956 GACCTTGAAATATTC-TTTC
1 GACCTTGAAATATTCTTTTC
*
1237975 CACCTTGAAA
1 GACCTTGAAA
1237985 CACTGTATTT
Statistics
Matches: 44, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
19 9 0.20
20 14 0.32
21 1 0.02
22 2 0.05
24 3 0.07
25 4 0.09
26 11 0.25
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (20 bp):
GACCTTGAAATATTCTTTTC
Found at i:1238605 original size:18 final size:17
Alignment explanation
Indices: 1238561--1238607 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 17
1238551 GAGTGCAAAG
*
1238561 ATCAAACCAAAGAAAAA
1 ATCAAAGCAAAGAAAAA
1238578 A-CAAAGAGCAAAGAGAAAA
1 ATC-AA-AGCAAAGA-AAAA
1238597 ATCAAAGCAAA
1 ATCAAAGCAAA
1238608 AATCAAAGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
16 1 0.04
17 3 0.12
18 13 0.52
19 7 0.28
20 1 0.04
ACGTcount: A:0.68, C:0.15, G:0.13, T:0.04
Consensus pattern (17 bp):
ATCAAAGCAAAGAAAAA
Found at i:1238610 original size:12 final size:11
Alignment explanation
Indices: 1238591--1238628 Score: 58
Period size: 11 Copynumber: 3.4 Consensus size: 11
1238581 AAGAGCAAAG
1238591 AGAAAAATCAA
1 AGAAAAATCAA
1238602 AGCAAAAATCAA
1 AG-AAAAATCAA
*
1238614 AGAAAAAGCAA
1 AGAAAAATCAA
1238625 AGAA
1 AGAA
1238629 CAAAAAGAGG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
11 14 0.56
12 11 0.44
ACGTcount: A:0.71, C:0.11, G:0.13, T:0.05
Consensus pattern (11 bp):
AGAAAAATCAA
Found at i:1239815 original size:4 final size:4
Alignment explanation
Indices: 1239806--1239859 Score: 85
Period size: 4 Copynumber: 14.0 Consensus size: 4
1239796 AAAAGTATAC
*
1239806 ACAT ACAT ACAT ACAT ACAT ACGT ACAT ACAT ACAT ACAT ACAT --AT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1239852 ACAT ACAT
1 ACAT ACAT
1239860 GATACATAAA
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
4 44 0.96
ACGTcount: A:0.48, C:0.24, G:0.02, T:0.26
Consensus pattern (4 bp):
ACAT
Found at i:1240537 original size:35 final size:36
Alignment explanation
Indices: 1240498--1240593 Score: 108
Period size: 36 Copynumber: 2.7 Consensus size: 36
1240488 GTTTCACATT
*
1240498 AAACAAA-GTTGATCTCACTTGAGATC-GTTTCTC-AA
1 AAACAAACGTTG-TCTCACTTGAGA-CAATTTCTCTAA
*
1240533 AAACAAACGTTGTCTCTCTTGAGACAATTTCTCTAA
1 AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
** *
1240569 AAACAAATTTTGTCTCATTTGAGAC
1 AAACAAACGTTGTCTCACTTGAGAC
1240594 TATATCTTAA
Statistics
Matches: 52, Mismatches: 6, Indels: 5
0.83 0.10 0.08
Matches are distributed among these distances:
34 1 0.02
35 24 0.46
36 27 0.52
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.33
Consensus pattern (36 bp):
AAACAAACGTTGTCTCACTTGAGACAATTTCTCTAA
Found at i:1240582 original size:36 final size:36
Alignment explanation
Indices: 1240525--1240628 Score: 108
Period size: 36 Copynumber: 3.0 Consensus size: 36
1240515 CTTGAGATCG
**
1240525 TTTCTC-AAAAACAAACGTTGTCTCTCTTGAGACAA
1 TTTCTCTAAAAACAAATTTTGTCTCTCTTGAGACAA
*
1240560 TTTCTCTAAAAACAAATTTTGTCTCAT-TTGAGACTA
1 TTTCTCTAAAAACAAATTTTGTCTC-TCTTGAGACAA
* * * *
1240596 TATCT-T-AAAGCAAATTTCGTCTCGCTTGAGACA
1 TTTCTCTAAAAACAAATTTTGTCTCTCTTGAGACA
1240629 TCATTTTCTC
Statistics
Matches: 58, Mismatches: 8, Indels: 7
0.79 0.11 0.10
Matches are distributed among these distances:
34 22 0.38
35 7 0.12
36 28 0.48
37 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.12, T:0.36
Consensus pattern (36 bp):
TTTCTCTAAAAACAAATTTTGTCTCTCTTGAGACAA
Found at i:1240919 original size:29 final size:28
Alignment explanation
Indices: 1240881--1241125 Score: 171
Period size: 29 Copynumber: 8.5 Consensus size: 28
1240871 GTTTCTCTTG
1240881 AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
1240909 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
1240938 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* * * **
1240965 -AAAAATATTTGAGTCTATTTATTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
* *** * *
1240992 AACAAAGTTTTGTCTCTCTTGAGACAGTTTCTCTTG-
1 AA-AAA-------ATCT-TTGAGTTTGTTCCTTTTGA
1241028 AAAAAATCTTTGAGTTTGTTCCTTTTGA
1 AAAAAATCTTTGAGTTTGTTCCTTTTGA
*
1241056 ATAAAAATCTTGGAGTTTGTTCCTTTTGA
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
* *
1241085 ATAAATATCTTTGAG-TTGTTTCTTTTG-
1 A-AAAAATCTTTGAGTTTGTTCCTTTTGA
1241112 -AAAAATCTTTGAGT
1 AAAAAATCTTTGAGT
1241126 CTATTTATTT
Statistics
Matches: 174, Mismatches: 27, Indels: 34
0.74 0.11 0.14
Matches are distributed among these distances:
25 23 0.13
26 9 0.05
27 13 0.07
28 28 0.16
29 81 0.47
35 3 0.02
36 4 0.02
37 13 0.07
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.47
Consensus pattern (28 bp):
AAAAAATCTTTGAGTTTGTTCCTTTTGA
Found at i:1240992 original size:54 final size:56
Alignment explanation
Indices: 1240878--1240993 Score: 132
Period size: 57 Copynumber: 2.1 Consensus size: 56
1240868 ACAGTTTCTC
* * *
1240878 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTCTATTCATT
* * *
1240934 TTGAATAAATATCTTTGAG-TTGTTTCTTTTGAA-AAATAT-TT-GAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTCTATTCATT
1240988 TTGAAA
1 TTGAAA
1240994 CAAAGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
53 1 0.02
54 14 0.27
55 2 0.04
56 10 0.19
57 16 0.31
58 9 0.17
ACGTcount: A:0.29, C:0.08, G:0.15, T:0.48
Consensus pattern (56 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTCTATTCATT
Found at i:1240993 original size:26 final size:26
Alignment explanation
Indices: 1240932--1240993 Score: 72
Period size: 26 Copynumber: 2.3 Consensus size: 26
1240922 AGTTTGTTCC
* *
1240932 TTTTGAATAAATATCTTTGAGTTGTTTC
1 TTTTGAA-AAATA-CTTTGAGTTATTTA
1240960 TTTTGAAAAATA-TTTGAGTCTATTTA
1 TTTTGAAAAATACTTTGAGT-TATTTA
1240986 TTTTGAAA
1 TTTTGAAA
1240994 CAAAGTTTTG
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 7 0.23
26 12 0.39
27 5 0.16
28 7 0.23
ACGTcount: A:0.31, C:0.05, G:0.13, T:0.52
Consensus pattern (26 bp):
TTTTGAAAAATACTTTGAGTTATTTA
Found at i:1241024 original size:147 final size:147
Alignment explanation
Indices: 1240852--1241186 Score: 613
Period size: 147 Copynumber: 2.3 Consensus size: 147
1240842 AACGGTTTTT
*
1240852 TTTTGTCTCTCCTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1240917 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATATTTGAGTCTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATATTTGAGTCTA
1240982 TTTATTTTGAAACAAAG
131 TTTATTTTGAAACAAAG
1240999 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
*
1241064 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATCTTTGAGTCTA
66 CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATATTTGAGTCTA
1241129 TTTATTTTGAAACAAAG
131 TTTATTTTGAAACAAAG
* *
1241146 TTTTGTCTCTCTTGAGACA-ATT-TCGTG-AAAAATCTTTGAGT
1 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGT
1241187 CTGAAACAAA
Statistics
Matches: 184, Mismatches: 4, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
144 14 0.08
145 4 0.02
146 2 0.01
147 164 0.89
ACGTcount: A:0.27, C:0.12, G:0.15, T:0.46
Consensus pattern (147 bp):
TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAAT
CTTGGAGTTTGTTCCTTTTGAATAAATATCTTTGAGTTGTTTCTTTTGAAAAATATTTGAGTCTA
TTTATTTTGAAACAAAG
Found at i:1241137 original size:54 final size:54
Alignment explanation
Indices: 1241025--1241140 Score: 128
Period size: 54 Copynumber: 2.1 Consensus size: 54
1241015 ACAGTTTCTC
* * *
1241025 TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAATAAAAATCTTGGAGTTTGTTCCTT
1 TTGAAAAAATCTTTGAGTTTGTTCCTTTTG-A-AAAAATCTTGGAGTCTATTCATT
* * *
1241081 TTGAATAAATATCTTTGAG-TTGTTTCTTTTG-AAAAATCTTTGAGTCTATTTATT
1 TTGAA-AAA-ATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
1241135 TTGAAA
1 TTGAAA
1241141 CAAAGTTTTG
Statistics
Matches: 52, Mismatches: 6, Indels: 7
0.80 0.09 0.11
Matches are distributed among these distances:
53 1 0.02
54 23 0.44
56 5 0.10
57 14 0.27
58 9 0.17
ACGTcount: A:0.28, C:0.09, G:0.15, T:0.48
Consensus pattern (54 bp):
TTGAAAAAATCTTTGAGTTTGTTCCTTTTGAAAAAATCTTGGAGTCTATTCATT
Found at i:1241214 original size:52 final size:53
Alignment explanation
Indices: 1241136--1241239 Score: 183
Period size: 52 Copynumber: 2.0 Consensus size: 53
1241126 CTATTTATTT
1241136 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAATCTTTGAGTC
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
*
1241188 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTTGTGAAAAAAATCTTTGAG
1 TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTG-AAAAAATCTTTGAG
1241240 ATTGTTTCTT
Statistics
Matches: 49, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
52 36 0.73
54 13 0.27
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (53 bp):
TGAAACAAAGTTTTGTCTCTCTTGAGACAATTTCGTGAAAAAATCTTTGAGTC
Found at i:1241317 original size:67 final size:66
Alignment explanation
Indices: 1241238--1241410 Score: 249
Period size: 67 Copynumber: 2.6 Consensus size: 66
1241228 AAAATCTTTG
*
1241238 AGATTGTTTCTTTTAAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1 AGATAGTTTCTTTT-AAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1241303 TA
65 TA
* *
1241305 AGATAGTTTCTTTTGAAACAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTTTCTCTCT
1 AGATAGTTTCTTTT-AAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCT
1241370 TA
65 TA
* * * * *
1241372 AAATAATTTCTTTT-GAAAAAAATCTTTGAATCTGTTTCT
1 AGATAGTTTCTTTTAAAAAAAAATCTTTGAGTTTGTTTCT
1241411 CTTAAAATGA
Statistics
Matches: 96, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
65 21 0.22
67 75 0.78
ACGTcount: A:0.32, C:0.11, G:0.11, T:0.46
Consensus pattern (66 bp):
AGATAGTTTCTTTTAAAAAAAAATCTTTGAGTTTGTTTCTTTGGAAACAAAATTTTGTCTCTCTT
A
Found at i:1241323 original size:37 final size:37
Alignment explanation
Indices: 1241273--1241399 Score: 108
Period size: 37 Copynumber: 3.6 Consensus size: 37
1241263 CTTTGAGTTT
1241273 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* * * * *
1241310 GTTTCTTTTGAAACAAAA------ATCT-TTGAGTTT
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
1241340 GTTTCTTTGGAAACAAAATTTTTTCTCTCTTAAAATA
1 GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
* *
1241377 ATTTCTTTTGAAA-AAAATCTTTG
1 GTTTCTTTGGAAACAAAAT-TTTG
1241400 AATCTGTTTC
Statistics
Matches: 68, Mismatches: 14, Indels: 16
0.69 0.14 0.16
Matches are distributed among these distances:
30 22 0.32
31 3 0.04
36 8 0.12
37 35 0.51
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.46
Consensus pattern (37 bp):
GTTTCTTTGGAAACAAAATTTTGTCTCTCTTAAGATA
Found at i:1241660 original size:120 final size:119
Alignment explanation
Indices: 1241510--1241734 Score: 269
Period size: 120 Copynumber: 1.9 Consensus size: 119
1241500 CTTAACAAAA
* * * *
1241510 TCATCTTTGAGTCTATTTCTTTAAAAAC-AAATGTTGTCTCTCTT-GAGACAGTTTCTAATGAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAAT-TT-TATCTCTTAAAGACAATTTCTAATGAAA
1241573 AACTAA-CTTTTGAGATTGTTTCATTTGAAAC-AAATTTGGTCTCACTTAAGATATGAT
64 AA--AATC-TTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATATGAT
* ** **
1241630 TCATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAA
1 TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
* * *
1241695 AATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTC
66 AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTC
1241735 TCGAGACAAC
Statistics
Matches: 89, Mismatches: 12, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
118 23 0.26
119 19 0.21
120 43 0.48
121 4 0.04
ACGTcount: A:0.31, C:0.14, G:0.12, T:0.43
Consensus pattern (119 bp):
TCATCTTTGAGTATATTTCTTTAAAAACAAAATTTTATCTCTTAAAGACAATTTCTAATGAAAAA
AATCTTTGAGATTGTTTCATTTGAAACAAAATTTGGTCTCACTTAAGATATGAT
Found at i:1241711 original size:64 final size:63
Alignment explanation
Indices: 1241632--1241756 Score: 187
Period size: 64 Copynumber: 2.0 Consensus size: 63
1241622 GATATGATTC
* *
1241632 ATCTTTGAGTATGTTTCTTTTGAAACAAAATTTTATCTCTTAAAGACAATTTCTTTTGAAAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTC-TAAAGACAACTTCTTTTGAAAAAA
* * **
1241696 ATCTTTGAGTTTGTTTCCTTTGAAACAAAATTTTGTCTCTCGAGACAACTTCTTTTGAAAA
1 ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAA
1241757 CACCAACCTT
Statistics
Matches: 55, Mismatches: 6, Indels: 1
0.89 0.10 0.02
Matches are distributed among these distances:
63 19 0.35
64 36 0.65
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (63 bp):
ATCTTTGAGTATGTTTCCTTTGAAACAAAATTTTATCTCTAAAGACAACTTCTTTTGAAAAAA
Found at i:1241943 original size:15 final size:15
Alignment explanation
Indices: 1241923--1241957 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
1241913 GTTTCACTTG
1241923 AAACATTGTCTCTTA
1 AAACATTGTCTCTTA
*
1241938 AAACATTTTCTCTTA
1 AAACATTGTCTCTTA
1241953 AAACA
1 AAACA
1241958 AGATCATCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.40, C:0.20, G:0.03, T:0.37
Consensus pattern (15 bp):
AAACATTGTCTCTTA
Found at i:1242343 original size:66 final size:64
Alignment explanation
Indices: 1242261--1242439 Score: 191
Period size: 66 Copynumber: 2.8 Consensus size: 64
1242251 AACAAACAAA
*
1242261 CATCTTTGAGATCGTTTCCCTTGAAATGAATTTTGTCTCATTTGAGACAATTTCCCATGAAACAC
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAA-TTCCCATGAAACAC
* * * * * * * **
1242326 CGATCTTTGAGAACGTTTCCCTTAAAAACAAATTTTGTCTCACTTAAGACAATTCCCTTTAAATG
1 C-ATCTTTGAGATCGTTTCCCTT-GAAACGAATTTTGTCTCATTTGAGACAATTCCCATGAAACA
1242391 C
64 C
* * *
1242392 CATCTTTG-GGTTGTTTCCTTTGAAACGAATTTTGTCTC-TTTCGAGACA
1 CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCATTT-GAGACA
1242440 GTTGCTTCTG
Statistics
Matches: 93, Mismatches: 18, Indels: 8
0.78 0.15 0.07
Matches are distributed among these distances:
62 2 0.02
63 20 0.22
64 9 0.10
65 8 0.09
66 31 0.33
67 23 0.25
ACGTcount: A:0.27, C:0.21, G:0.14, T:0.38
Consensus pattern (64 bp):
CATCTTTGAGATCGTTTCCCTTGAAACGAATTTTGTCTCATTTGAGACAATTCCCATGAAACAC
Found at i:1242693 original size:40 final size:39
Alignment explanation
Indices: 1242638--1242877 Score: 149
Period size: 40 Copynumber: 5.6 Consensus size: 39
1242628 TGGCCAGTAG
* *
1242638 TCCTCATCTCATAGGAACCGTGTCATCCCCAGACCAGACC
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG-CC
* * ** *
1242678 TCCTCATCACGTAGGAGCCGTGTCAACCATAGATAACCAGCAG
1 TCCTCATCACGTAGGAACCGTGTCATCCCCAG---ACCAGC-C
* *
1242721 TCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGGCCAGCC
1 TCCTCATCACGTAGGAACC--G-TGTCATC-C-CC---AGA---CCAGCC
*
1242771 GTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACC
1 -TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAG-CC
* *
1242812 TCCTCATCACGTAGGAGCCGTGTCA-CCCTTAGATAACCAGCC
1 TCCTCATCACGTAGGAACCGTGTCATCCC-CAG---ACCAGCC
*
1242854 GTCCTCATCATGTAGGAACCGTGT
1 -TCCTCATCACGTAGGAACCGTGT
1242878 TATCACCTTT
Statistics
Matches: 157, Mismatches: 21, Indels: 41
0.72 0.10 0.19
Matches are distributed among these distances:
39 3 0.02
40 55 0.35
41 2 0.01
42 3 0.02
43 51 0.32
45 1 0.01
46 7 0.04
47 2 0.01
48 6 0.04
49 1 0.01
51 26 0.17
ACGTcount: A:0.26, C:0.35, G:0.19, T:0.21
Consensus pattern (39 bp):
TCCTCATCACGTAGGAACCGTGTCATCCCCAGACCAGCC
Found at i:1242728 original size:43 final size:44
Alignment explanation
Indices: 1242678--1242877 Score: 155
Period size: 43 Copynumber: 4.5 Consensus size: 44
1242668 AGACCAGACC
*
1242678 TCCTCATCACGTAGGAGCCGTGTCA-ACCATAGATAACCAGCAG
1 TCCTCATCACGTAGGAACCGTGTCACACCATAGATAACCAGCAG
* * ** *
1242721 TCCTCATCACGTAGGAACCAAGTTATCACCACTCCTAAAGATGGCCAGCCG
1 TCCTCATCACGTAGGAACC--G-TGTCA-CA--CC-ATAGATAACCAGCAG
* *
1242772 TCCTCATCACGTAGGAACCGTGTCATC-CCCT-G---ACCAG-ACC
1 TCCTCATCACGTAGGAACCGTGTCA-CACCATAGATAACCAGCA-G
* * *
1242812 TCCTCATCACGTAGGAGCCGTGTCAC-CCTTAGATAACCAGCCG
1 TCCTCATCACGTAGGAACCGTGTCACACCATAGATAACCAGCAG
*
1242855 TCCTCATCATGTAGGAACCGTGT
1 TCCTCATCACGTAGGAACCGTGT
1242878 TATCACCTTT
Statistics
Matches: 124, Mismatches: 19, Indels: 28
0.73 0.11 0.16
Matches are distributed among these distances:
39 4 0.03
40 29 0.23
43 45 0.36
45 3 0.02
46 4 0.03
48 6 0.05
49 1 0.01
50 2 0.02
51 30 0.24
ACGTcount: A:0.26, C:0.34, G:0.20, T:0.21
Consensus pattern (44 bp):
TCCTCATCACGTAGGAACCGTGTCACACCATAGATAACCAGCAG
Found at i:1242869 original size:134 final size:134
Alignment explanation
Indices: 1242625--1242884 Score: 421
Period size: 134 Copynumber: 1.9 Consensus size: 134
1242615 TTATCCTTAG
* *
1242625 AGATGGCCAGTAGTCCTCATCTCATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGT
1 AGATGGCCAGCAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGT
1242690 AGGAGCCGTGTCAACCATAGATAACCAGCAGTCCTCATCACGTAGGAACCAAGTTATCACCACTC
66 AGGAGCCGTGTCAACCATAGATAACCAGCAGTCCTCATCACGTAGGAACCAAGTTATCACCACTC
1242755 CTAA
131 CTAA
* * *
1242759 AGATGGCCAGCCGTCCTCATCACGTAGGAACCGTGTCATCCCCTGACCAGACCTCCTCATCACGT
1 AGATGGCCAGCAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGT
* * * * **
1242824 AGGAGCCGTGTCACCCTTAGATAACCAGCCGTCCTCATCATGTAGGAACCGTGTTATCACC
66 AGGAGCCGTGTCAACCATAGATAACCAGCAGTCCTCATCACGTAGGAACCAAGTTATCACC
1242885 TTTAGATGGC
Statistics
Matches: 115, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
134 115 1.00
ACGTcount: A:0.26, C:0.34, G:0.19, T:0.21
Consensus pattern (134 bp):
AGATGGCCAGCAGTCCTCATCACATAGGAACCGTGTCATCCCCAGACCAGACCTCCTCATCACGT
AGGAGCCGTGTCAACCATAGATAACCAGCAGTCCTCATCACGTAGGAACCAAGTTATCACCACTC
CTAA
Found at i:1243107 original size:3 final size:3
Alignment explanation
Indices: 1243099--1243145 Score: 85
Period size: 3 Copynumber: 15.3 Consensus size: 3
1243089 AATTTTAATT
1243099 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA
1243145 T
1 T
1243146 GTTTATTAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 40 0.93
4 3 0.07
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1243152 original size:22 final size:22
Alignment explanation
Indices: 1243099--1243145 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
1243089 AATTTTAATT
1243099 TTATTATTA-TTATTATTATTA
1 TTATTATTATTTATTATTATTA
1243120 TTATTATTATTTATTATTATTA
1 TTATTATTATTTATTATTATTA
1243142 TTAT
1 TTAT
1243146 GTTTATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 9 0.36
22 16 0.64
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (22 bp):
TTATTATTATTTATTATTATTA
Found at i:1243289 original size:25 final size:25
Alignment explanation
Indices: 1243260--1243331 Score: 110
Period size: 25 Copynumber: 2.9 Consensus size: 25
1243250 ACCAAACCAT
1243260 CAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
*
1243285 TAGATTAGGGTTTCAAACCCTAAAA
1 CAGATTAGGGTTTCAAACCCTAAAA
* *
1243310 CAAATTAGGGTTT-TAACCCTAA
1 CAGATTAGGGTTTCAAACCCTAA
1243332 TCCCCTAATG
Statistics
Matches: 43, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
24 8 0.19
25 35 0.81
ACGTcount: A:0.39, C:0.18, G:0.15, T:0.28
Consensus pattern (25 bp):
CAGATTAGGGTTTCAAACCCTAAAA
Found at i:1247808 original size:30 final size:31
Alignment explanation
Indices: 1247739--1247809 Score: 83
Period size: 30 Copynumber: 2.3 Consensus size: 31
1247729 ACATCATTTC
*
1247739 TCACAGAACTATATTTTCTGGTCTATTTTAA
1 TCACTGAACTATATTTTCTGGTCTATTTTAA
* *
1247770 TCATTGAACTATATTTT-T-GTCATATTTTAC
1 TCACTGAACTATATTTTCTGGTC-TATTTTAA
*
1247800 TTACTGAACT
1 TCACTGAACT
1247810 TTTGAATTGT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
29 3 0.09
30 16 0.47
31 15 0.44
ACGTcount: A:0.28, C:0.15, G:0.08, T:0.48
Consensus pattern (31 bp):
TCACTGAACTATATTTTCTGGTCTATTTTAA
Found at i:1249016 original size:3 final size:3
Alignment explanation
Indices: 1249008--1249035 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
1248998 TGCTAAAGGA
1249008 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1 GAT GAT GAT GAT GAT GAT GAT GAT GAT G
1249036 CTGTTGAAGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.36, T:0.32
Consensus pattern (3 bp):
GAT
Done.