Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008378.1 Hibiscus syriacus cultivar Beakdansim tig00111138_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: 241419
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 2
Found at i:1761 original size:3 final size:3
Alignment explanation
Indices: 1744--1837 Score: 68
Period size: 3 Copynumber: 32.3 Consensus size: 3
1734 TTTCCCCATT
* * * *
1744 TTA TT- TTA ATA TTA TTA TTA ATA TTA TTA TT- TTA ATA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * * * * * *
1790 TTA TT- TTA ATA ATA ATA ATA ATA ATA TTA TTA TTA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1837 T
1 T
1838 AGGCACGAAT
Statistics
Matches: 78, Mismatches: 10, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
2 6 0.08
3 72 0.92
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (3 bp):
TTA
Found at i:1761 original size:14 final size:14
Alignment explanation
Indices: 1744--1788 Score: 67
Period size: 14 Copynumber: 3.4 Consensus size: 14
1734 TTTCCCCATT
1744 TTATTTTAATATTA
1 TTATTTTAATATTA
1758 TTA--TTAATATTA
1 TTATTTTAATATTA
*
1770 TTATTTTAATAATA
1 TTATTTTAATATTA
1784 TTATT
1 TTATT
1789 ATTATTTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
12 12 0.43
14 16 0.57
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTATTTTAATATTA
Found at i:1777 original size:26 final size:26
Alignment explanation
Indices: 1744--1837 Score: 104
Period size: 26 Copynumber: 3.7 Consensus size: 26
1734 TTTCCCCATT
*
1744 TTATTTTAATATTATTATTAATATTA
1 TTATTTTAATAATATTATTAATATTA
*
1770 TTATTTTAATAATATTATTATTATT-
1 TTATTTTAATAATATTATTAATATTA
* * *
1795 TTA--ATAATAATAATAATAATATTA
1 TTATTTTAATAATATTATTAATATTA
*
1819 TTATTATTAATATTATTAT
1 TTATT-TTAATAATATTAT
1838 AGGCACGAAT
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
23 16 0.30
24 3 0.06
25 3 0.06
26 23 0.43
27 9 0.17
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTATTTTAATAATATTATTAATATTA
Found at i:1790 original size:20 final size:20
Alignment explanation
Indices: 1765--1803 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
1755 TTATTATTAA
1765 TATTATTATTTTAATAATAT
1 TATTATTATTTTAATAATAT
1785 TATTATTATTTTAATAATA
1 TATTATTATTTTAATAATA
1804 ATAATAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (20 bp):
TATTATTATTTTAATAATAT
Found at i:4015 original size:3 final size:3
Alignment explanation
Indices: 4007--4054 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
3997 ACAAAATGAT
* *
4007 TAA TAA TAA TAA TAG TAA TAA TAA TAA TAA TAA -AT TAA TAA -AA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
4053 TA
1 TA
4055 TTTTTGGTAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 3 0.08
3 36 0.92
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:6201 original size:17 final size:17
Alignment explanation
Indices: 6171--6260 Score: 83
Period size: 17 Copynumber: 5.2 Consensus size: 17
6161 GTTGCATTAT
*
6171 AAAAGTGAGTTGCAATCTA
1 AAAAGTG-G-TGCAACCTA
** *
6190 AAGTGTGGTGCAA-CTT
1 AAAAGTGGTGCAACCTA
*
6206 AAAAGTGGTGCAACCCA
1 AAAAGTGGTGCAACCTA
6223 AAAAGTGGTGCAACCTA
1 AAAAGTGGTGCAACCTA
* *
6240 AAATGTGGTACAACCGTA
1 AAAAGTGGTGCAACC-TA
6258 AAA
1 AAA
6261 TAAGTTGCAA
Statistics
Matches: 59, Mismatches: 10, Indels: 5
0.80 0.14 0.07
Matches are distributed among these distances:
16 13 0.22
17 35 0.59
18 6 0.10
19 5 0.08
ACGTcount: A:0.40, C:0.16, G:0.23, T:0.21
Consensus pattern (17 bp):
AAAAGTGGTGCAACCTA
Found at i:6261 original size:18 final size:17
Alignment explanation
Indices: 6181--6276 Score: 95
Period size: 17 Copynumber: 5.6 Consensus size: 17
6171 AAAAGTGAGT
* *
6181 TGCAATCTAAAGTGTGG
1 TGCAACCTAAAATGTGG
*
6198 TGCAACTTAAAA-GTGG
1 TGCAACCTAAAATGTGG
* *
6214 TGCAACCCAAAAAGTGG
1 TGCAACCTAAAATGTGG
6231 TGCAACCTAAAATGTGG
1 TGCAACCTAAAATGTGG
* ** *
6248 TACAACCGTAAAATAAGT
1 TGCAACC-TAAAATGTGG
6266 TGCAACCTAAA
1 TGCAACCTAAA
6277 TGACAACGAT
Statistics
Matches: 65, Mismatches: 12, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
16 14 0.22
17 38 0.58
18 13 0.20
ACGTcount: A:0.40, C:0.18, G:0.21, T:0.22
Consensus pattern (17 bp):
TGCAACCTAAAATGTGG
Found at i:6877 original size:49 final size:49
Alignment explanation
Indices: 6802--6928 Score: 123
Period size: 49 Copynumber: 2.6 Consensus size: 49
6792 CACGATCACA
* * * * * *
6802 TGACGAATTT-ATTCAATATATCTTTTTATTTAAA-CTAGTCATGTCGAAG
1 TGACGAATTTCAAT-AAAATATATTTTTATTAAAATCTA-TCAAGTCGAAC
*
6851 TGACGAATTTCAATAAAATATATTTTTATTAAAATGTATCAAGTCGAAC
1 TGACGAATTTCAATAAAATATATTTTTATTAAAATCTATCAAGTCGAAC
* * *
6900 TAACAAATTTCAATAAAAAATATATTTTA
1 TGACGAATTTCAATAAAATATAT-TTTTA
6929 CTAGAGCTCG
Statistics
Matches: 65, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
49 56 0.86
50 9 0.14
ACGTcount: A:0.42, C:0.10, G:0.09, T:0.39
Consensus pattern (49 bp):
TGACGAATTTCAATAAAATATATTTTTATTAAAATCTATCAAGTCGAAC
Found at i:13682 original size:85 final size:85
Alignment explanation
Indices: 13539--13711 Score: 310
Period size: 85 Copynumber: 2.0 Consensus size: 85
13529 GATGAAAAAA
*
13539 GAAGGGAACAAAGTTGTTAACGATACGACGGGGATGTGTTCTTTTTTGGTACAAGGTTTAATTTT
1 GAAGGGAACAAAGTTGTTAACGATACGACGGGGATGTGTTCTTTTTTGGTAAAAGGTTTAATTTT
*
13604 AAAGGAGAAAGGAACTCTCT
66 AAAGGAGAAAGAAACTCTCT
* *
13624 GAAGGGAACAAAGTTTTTAACGATACGACGGGGCTGTGTTCTTTTTTGGTAAAAGGTTTAATTTT
1 GAAGGGAACAAAGTTGTTAACGATACGACGGGGATGTGTTCTTTTTTGGTAAAAGGTTTAATTTT
13689 AAAGGAGAAAGAAACTCTCT
66 AAAGGAGAAAGAAACTCTCT
13709 GAA
1 GAA
13712 TAAACATGAG
Statistics
Matches: 84, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
85 84 1.00
ACGTcount: A:0.33, C:0.10, G:0.26, T:0.31
Consensus pattern (85 bp):
GAAGGGAACAAAGTTGTTAACGATACGACGGGGATGTGTTCTTTTTTGGTAAAAGGTTTAATTTT
AAAGGAGAAAGAAACTCTCT
Found at i:14322 original size:50 final size:48
Alignment explanation
Indices: 14243--14339 Score: 158
Period size: 50 Copynumber: 2.0 Consensus size: 48
14233 ATCGTAACCG
14243 AGTAACTATTTGGACAGGTTTTGATGAAGGTAACGGCAAAGGTGCTCA
1 AGTAACTATTTGGACAGGTTTTGATGAAGGTAACGGCAAAGGTGCTCA
* *
14291 AGTAATTATTTGGTGCAGGTTTTTGATGAAGGTAACGGCAAAGGTGCTC
1 AGTAACTATTTGG-ACAGG-TTTTGATGAAGGTAACGGCAAAGGTGCTC
14340 GAGAACAACG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
48 12 0.27
49 4 0.09
50 29 0.64
ACGTcount: A:0.29, C:0.11, G:0.30, T:0.30
Consensus pattern (48 bp):
AGTAACTATTTGGACAGGTTTTGATGAAGGTAACGGCAAAGGTGCTCA
Found at i:16819 original size:22 final size:22
Alignment explanation
Indices: 16785--16861 Score: 59
Period size: 22 Copynumber: 3.5 Consensus size: 22
16775 TTCGTATAAA
* *
16785 TAATAACTAAAATATAATAATT
1 TAATAATTTAAATATAATAATT
* *
16807 TAATAATTTAAATAAAACTAAAT
1 TAATAATTTAAATATAA-TAATT
***
16830 T-ATAATTTTTTTATAAT-ATT
1 TAATAATTTAAATATAATAATT
*
16850 TAATTATTTAAA
1 TAATAATTTAAA
16862 ATACCAGAAT
Statistics
Matches: 40, Mismatches: 13, Indels: 5
0.69 0.22 0.09
Matches are distributed among these distances:
20 3 0.08
21 7 0.17
22 25 0.62
23 5 0.12
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATAATTTAAATATAATAATT
Found at i:16950 original size:2 final size:2
Alignment explanation
Indices: 16943--16981 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
16933 ATTTAAACAA
16943 AT AT AT AT AT AT -T 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
16982 GACTAAGATT
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:16955 original size:23 final size:23
Alignment explanation
Indices: 16929--16981 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
16919 AAATAAACAT
*
16929 TATTATTTAAACAAATATATATA
1 TATTATATAAACAAATATATATA
* * *
16952 TATTATATATATATATATATATA
1 TATTATATAAACAAATATATATA
16975 TA-TATAT
1 TATTATAT
16982 GACTAAGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
22 5 0.19
23 21 0.81
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
TATTATATAAACAAATATATATA
Found at i:18361 original size:3 final size:3
Alignment explanation
Indices: 18353--18397 Score: 56
Period size: 3 Copynumber: 14.7 Consensus size: 3
18343 ATTTATTTAT
*
18353 ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA A-A ATTA ATA AT
1 ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA AT
18398 TTTAATTTTA
Statistics
Matches: 37, Mismatches: 2, Indels: 6
0.82 0.04 0.13
Matches are distributed among these distances:
2 2 0.05
3 30 0.81
4 5 0.14
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:19497 original size:76 final size:76
Alignment explanation
Indices: 18529--19470 Score: 1654
Period size: 76 Copynumber: 12.4 Consensus size: 76
18519 GAAATGTTGA
* * * * *
18529 AAACATCATGCACTAAAGGGCTTACAGATGATCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
*
18594 AGGTTTTTTTGG
66 AGG-CTTTTTGG
* * *
18606 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGTTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
18671 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
18682 AAACATCATGCACTGCAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAAAATCCCG
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATC-AAAAAGATCCCG
18747 AAGGC--TTTGG
65 AAGGCTTTTTGG
*
18757 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
18822 AGGCTTTTTGG
66 AGGCTTTTTGG
18833 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
18898 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
18909 AAACATCATGCGCTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
18974 AGGCTTTTTGG
66 AGGCTTTTTGG
*
18985 AAACATCATGCACTGAAGGACGTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
19050 AGGCTTTTTGG
66 AGGCTTTTTGG
*
19061 AAACATCATGCACTGAATGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
19126 AGGCTTTTTGG
66 AGGCTTTTTGG
* * *
19137 AAACATCATGCACTGAAAGACTTACAGATGACTCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
19202 AGGCTTTTTGG
66 AGGCTTTTTGG
19213 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
19278 AGGCTTTTTGG
66 AGGCTTTTTGG
19289 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
19354 AGGCTTTTTGG
66 AGGCTTTTTGG
* *
19365 AAACATCATGCGCTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGCTCCCGA
1 AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
19430 AGGCTTTTTGG
66 AGGCTTTTTGG
*
19441 AAACATCATGCACTGAAGGATTTACAGATG
1 AAACATCATGCACTGAAGGACTTACAGATG
19471 TGGGAAATAG
Statistics
Matches: 833, Mismatches: 29, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
74 15 0.02
75 56 0.07
76 683 0.82
77 79 0.09
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.23
Consensus pattern (76 bp):
AAACATCATGCACTGAAGGACTTACAGATGACCCTAAGGCTTTGAAAACATCAAAAAGATCCCGA
AGGCTTTTTGG
Found at i:20166 original size:22 final size:23
Alignment explanation
Indices: 20138--20194 Score: 82
Period size: 22 Copynumber: 2.6 Consensus size: 23
20128 CATAAAGCTT
20138 TCATCTTTGAA-AAGAGAATATA
1 TCATCTTTGAAGAAGAGAATATA
*
20160 TCATCTTT-AAGAAGAGAATCTA
1 TCATCTTTGAAGAAGAGAATATA
*
20182 TAATCTTTGAAGA
1 TCATCTTTGAAGA
20195 GTGTAGATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 2 0.06
22 25 0.81
23 4 0.13
ACGTcount: A:0.42, C:0.11, G:0.14, T:0.33
Consensus pattern (23 bp):
TCATCTTTGAAGAAGAGAATATA
Found at i:20641 original size:54 final size:54
Alignment explanation
Indices: 20559--20714 Score: 224
Period size: 54 Copynumber: 2.9 Consensus size: 54
20549 AGAATAGCAG
* * * *
20559 GTTCGTAAAACATTTGA-AAGCTCATTCATCCTCTCCTGTGGCTTCTGCTCAGAT
1 GTTCGTAAAACATTTGACAA-CACATTCATCCTTTCTTGTGGCTTCTGCTCAGAC
* * *
20613 GTTCGTAAAACATTTGACCACACATTCATCCTTTCTTGTGGTTTCTTCTCAGAC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAC
*
20667 GTTCGTAAGACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGC
1 GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGC
20715 CAAGATTTCT
Statistics
Matches: 90, Mismatches: 11, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
54 89 0.99
55 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.15, T:0.37
Consensus pattern (54 bp):
GTTCGTAAAACATTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCTCAGAC
Found at i:20814 original size:81 final size:81
Alignment explanation
Indices: 20679--20845 Score: 334
Period size: 81 Copynumber: 2.1 Consensus size: 81
20669 TCGTAAGACA
20679 TTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCAAGATTTCTCAATCATTGAAGCTCTTTG
1 TTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCAAGATTTCTCAATCATTGAAGCTCTTTG
20744 CCTAATGTTCAAAGCT
66 CCTAATGTTCAAAGCT
20760 TTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCAAGATTTCTCAATCATTGAAGCTCTTTG
1 TTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCAAGATTTCTCAATCATTGAAGCTCTTTG
20825 CCTAATGTTCAAAGCT
66 CCTAATGTTCAAAGCT
20841 TTTGA
1 TTTGA
20846 ATGAGGCCAC
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
81 86 1.00
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (81 bp):
TTTGACAACACATTCATCCTTTCTTGTGGCTTCTGCCAAGATTTCTCAATCATTGAAGCTCTTTG
CCTAATGTTCAAAGCT
Found at i:27126 original size:14 final size:14
Alignment explanation
Indices: 27109--27147 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
27099 TAAAAGTATG
27109 AATGCAAAATGAAA
1 AATGCAAAATGAAA
*
27123 AATGCAAAGATGTAA
1 AATGCAAA-ATGAAA
27138 AATG-AAAATG
1 AATGCAAAATG
27148 CATGTATGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
13 3 0.13
14 11 0.48
15 9 0.39
ACGTcount: A:0.59, C:0.05, G:0.18, T:0.18
Consensus pattern (14 bp):
AATGCAAAATGAAA
Found at i:31666 original size:3 final size:3
Alignment explanation
Indices: 31658--31705 Score: 62
Period size: 3 Copynumber: 15.7 Consensus size: 3
31648 ATTTATTTAT
*
31658 ATA ATA ATA ATA ATA ATA TATA TTA ATA ATA ATA ATA A-A ATTA ATA
1 ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A-TA ATA
31704 AT
1 AT
31706 TTTAATTTTA
Statistics
Matches: 40, Mismatches: 2, Indels: 6
0.83 0.04 0.12
Matches are distributed among these distances:
2 2 0.05
3 33 0.82
4 5 0.12
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
ATA
Found at i:31677 original size:19 final size:19
Alignment explanation
Indices: 31655--31694 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
31645 GTAATTTATT
31655 TATATAATAATAATAATAA
1 TATATAATAATAATAATAA
*
31674 TATATATTAATAATAATAA
1 TATATAATAATAATAATAA
31693 TA
1 TA
31695 AAATTAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TATATAATAATAATAATAA
Found at i:35308 original size:22 final size:22
Alignment explanation
Indices: 35277--35318 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
35267 AGGTTTGTTC
*
35277 TTTATTTAAAT-TTAACAATAAA
1 TTTATATAAATATT-ACAATAAA
35299 TTTATATAAATATTACAATA
1 TTTATATAAATATTACAATA
35319 TACTAGTATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 16 0.89
23 2 0.11
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (22 bp):
TTTATATAAATATTACAATAAA
Found at i:38207 original size:2 final size:2
Alignment explanation
Indices: 38200--38256 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
38190 CTATTTAATT
38200 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
38242 TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA
38257 AATACGAGTA
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:41342 original size:6 final size:6
Alignment explanation
Indices: 41332--41373 Score: 75
Period size: 6 Copynumber: 7.0 Consensus size: 6
41322 GACACCACTT
*
41332 CACTCT CACTCA CACTCA CACTCA CACTCA CACTCA CACTCA
1 CACTCA CACTCA CACTCA CACTCA CACTCA CACTCA CACTCA
41374 TCTCTCTTCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 35 1.00
ACGTcount: A:0.31, C:0.50, G:0.00, T:0.19
Consensus pattern (6 bp):
CACTCA
Found at i:42316 original size:17 final size:17
Alignment explanation
Indices: 42282--42316 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
42272 TTGAAACTCG
* *
42282 ACTCGAACTCGAAAAAA
1 ACTCAAACTCAAAAAAA
42299 ACTCAAACTCAAAAAAA
1 ACTCAAACTCAAAAAAA
42316 A
1 A
42317 TATTAAGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.60, C:0.23, G:0.06, T:0.11
Consensus pattern (17 bp):
ACTCAAACTCAAAAAAA
Found at i:42888 original size:16 final size:16
Alignment explanation
Indices: 42867--42900 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
42857 TTACTATTCA
*
42867 CGTGAATAGTGAATTT
1 CGTGAATAGTGAAATT
42883 CGTGAATAGTGAAATT
1 CGTGAATAGTGAAATT
42899 CG
1 CG
42901 GTCGGCGATA
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:0.09, G:0.26, T:0.32
Consensus pattern (16 bp):
CGTGAATAGTGAAATT
Found at i:47393 original size:23 final size:23
Alignment explanation
Indices: 47363--47414 Score: 95
Period size: 23 Copynumber: 2.3 Consensus size: 23
47353 TTTCCTAACA
47363 CTCGATTCAAGCTCAATATTGAG
1 CTCGATTCAAGCTCAATATTGAG
*
47386 CTCGATTCAAGCTCGATATTGAG
1 CTCGATTCAAGCTCAATATTGAG
47409 CTCGAT
1 CTCGAT
47415 ATTGAGCTCG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (23 bp):
CTCGATTCAAGCTCAATATTGAG
Found at i:47412 original size:12 final size:12
Alignment explanation
Indices: 47372--47426 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
47362 ACTCGATTCA
*
47372 AGCTCAATATTG
1 AGCTCGATATTG
**
47384 AGCTCGAT-TCA
1 AGCTCGATATTG
47395 AGCTCGATATTG
1 AGCTCGATATTG
47407 AGCTCGATATTG
1 AGCTCGATATTG
47419 AGCTCGAT
1 AGCTCGAT
47427 TCAAGCCACT
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
11 9 0.24
12 28 0.76
ACGTcount: A:0.27, C:0.20, G:0.22, T:0.31
Consensus pattern (12 bp):
AGCTCGATATTG
Found at i:49044 original size:7 final size:7
Alignment explanation
Indices: 49032--49249 Score: 159
Period size: 7 Copynumber: 31.3 Consensus size: 7
49022 TGGATTAAGT
49032 GTTTAGG
1 GTTTAGG
49039 GTTTAGG
1 GTTTAGG
49046 GTTTAGG
1 GTTTAGG
* **
49053 ATTTATA
1 GTTTAGG
49060 GTTTAGG
1 GTTTAGG
*
49067 GTTTATG
1 GTTTAGG
**
49074 ACTTAGG
1 GTTTAGG
49081 GTTTAGG
1 GTTTAGG
*
49088 GTTTAAG
1 GTTTAGG
*
49095 GTTTAGA
1 GTTTAGG
*
49102 GTTTAGA
1 GTTTAGG
*
49109 GTTTAGA
1 GTTTAGG
49116 GTTTAGG
1 GTTTAGG
* **
49123 GTGTAAT
1 GTTTAGG
**
49130 AATT-GG
1 GTTTAGG
* * *
49136 ATTAAGT
1 GTTTAGG
49143 GTTTAGG
1 GTTTAGG
49150 GTTTAGG
1 GTTTAGG
49157 GTTTAGG
1 GTTTAGG
* **
49164 ATTTATA
1 GTTTAGG
49171 GTTTAGG
1 GTTTAGG
*
49178 GTTTATG
1 GTTTAGG
**
49185 ACTTAGG
1 GTTTAGG
49192 GTTTAGG
1 GTTTAGG
*
49199 GTTTATG
1 GTTTAGG
*
49206 GTTTATG
1 GTTTAGG
**
49213 ACTTAGG
1 GTTTAGG
49220 GTTTAGG
1 GTTTAGG
*
49227 GTTTAGA
1 GTTTAGG
*
49234 GTTTAGA
1 GTTTAGG
49241 GTTTAGG
1 GTTTAGG
49248 GT
1 GT
49250 GTAATCTAAC
Statistics
Matches: 160, Mismatches: 50, Indels: 2
0.75 0.24 0.01
Matches are distributed among these distances:
6 2 0.01
7 158 0.99
ACGTcount: A:0.22, C:0.01, G:0.33, T:0.44
Consensus pattern (7 bp):
GTTTAGG
Found at i:49224 original size:111 final size:111
Alignment explanation
Indices: 49017--49232 Score: 380
Period size: 111 Copynumber: 1.9 Consensus size: 111
49007 CCCCTATCAT
49017 ATAATTGGATTAAGTGTTTAGGGTTTAGGGTTTAGGATTTATAGTTTAGGGTTTATGACTTAGGG
1 ATAATTGGATTAAGTGTTTAGGGTTTAGGGTTTAGGATTTATAGTTTAGGGTTTATGACTTAGGG
*
49082 TTTAGGGTTTAAGGTTTAGAGTTTAGAGTTTAGAGTTTAGGGTGTA
66 TTTAGGGTTTAAGGTTTAGAGCTTAGAGTTTAGAGTTTAGGGTGTA
49128 ATAATTGGATTAAGTGTTTAGGGTTTAGGGTTTAGGATTTATAGTTTAGGGTTTATGACTTAGGG
1 ATAATTGGATTAAGTGTTTAGGGTTTAGGGTTTAGGATTTATAGTTTAGGGTTTATGACTTAGGG
* * *
49193 TTTAGGGTTTATGGTTTATGA-CTTAGGGTTTAGGGTTTAG
66 TTTAGGGTTTAAGGTTTA-GAGCTTAGAGTTTAGAGTTTAG
49233 AGTTTAGAGT
Statistics
Matches: 100, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
111 98 0.98
112 2 0.02
ACGTcount: A:0.23, C:0.01, G:0.31, T:0.44
Consensus pattern (111 bp):
ATAATTGGATTAAGTGTTTAGGGTTTAGGGTTTAGGATTTATAGTTTAGGGTTTATGACTTAGGG
TTTAGGGTTTAAGGTTTAGAGCTTAGAGTTTAGAGTTTAGGGTGTA
Found at i:49335 original size:7 final size:7
Alignment explanation
Indices: 49320--49380 Score: 70
Period size: 7 Copynumber: 8.7 Consensus size: 7
49310 AATTGGATTA
49320 AGGGTTT
1 AGGGTTT
*
49327 AGAGTTT
1 AGGGTTT
49334 AGGGTTT
1 AGGGTTT
*
49341 ATGGTTT
1 AGGGTTT
49348 -GGGATTT
1 AGGG-TTT
*
49355 GGGGTTT
1 AGGGTTT
*
49362 AGAGTTT
1 AGGGTTT
49369 AGGGTTT
1 AGGGTTT
49376 AGGGT
1 AGGGT
49381 GTAATCTAAC
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
6 2 0.04
7 40 0.89
8 3 0.07
ACGTcount: A:0.16, C:0.00, G:0.41, T:0.43
Consensus pattern (7 bp):
AGGGTTT
Found at i:49370 original size:131 final size:131
Alignment explanation
Indices: 49189--49429 Score: 394
Period size: 131 Copynumber: 1.8 Consensus size: 131
49179 TTTATGACTT
* *
49189 AGGGTTTAGGGTTTATGGTTTATGACTTAGGGTTTAGGGTTTAGAGTTTAGAGTTTAGGGTGTAA
1 AGGGTTTAGAGTTTAGGGTTTATGACTTAGGGTTTAGGGTTTAGAGTTTAGAGTTTAGGGTGTAA
* *
49254 TCTAACTTGTGCTTAATTAAATGAGCTTTTATTTTTCTTTTAGTACCCTATCACATAATTGGATT
66 TCTAACATGTGCTTAATTAAATGAACTTTTATTTTTCTTTTAGTACCCTATCACATAATTGGATT
49319 A
131 A
* * * *
49320 AGGGTTTAGAGTTTAGGGTTTATG-GTTTGGGATTTGGGGTTTAGAGTTTAGGGTTTAGGGTGTA
1 AGGGTTTAGAGTTTAGGGTTTATGACTTAGGG-TTTAGGGTTTAGAGTTTAGAGTTTAGGGTGTA
49384 ATCTAACATGTGCTTAATTAAATGAACTTTTATTTTTCTTTTAGTA
65 ATCTAACATGTGCTTAATTAAATGAACTTTTATTTTTCTTTTAGTA
49430 ATATACAATG
Statistics
Matches: 101, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
130 5 0.05
131 96 0.95
ACGTcount: A:0.24, C:0.07, G:0.25, T:0.45
Consensus pattern (131 bp):
AGGGTTTAGAGTTTAGGGTTTATGACTTAGGGTTTAGGGTTTAGAGTTTAGAGTTTAGGGTGTAA
TCTAACATGTGCTTAATTAAATGAACTTTTATTTTTCTTTTAGTACCCTATCACATAATTGGATT
A
Found at i:50730 original size:32 final size:32
Alignment explanation
Indices: 50689--50763 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 32
50679 AAATTAATCC
* ** *
50689 GAATCGAAAATTAATTAATTTGATATTGTCTT
1 GAATTGAAAATTAACCAATTTGATATTATCTT
* **
50721 GAATTGAAAATTGACCGGTTTGATATTATCTT
1 GAATTGAAAATTAACCAATTTGATATTATCTT
50753 GAATT-AAAATT
1 GAATTGAAAATT
50764 TGATTGATCT
Statistics
Matches: 36, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
31 6 0.17
32 30 0.83
ACGTcount: A:0.37, C:0.07, G:0.15, T:0.41
Consensus pattern (32 bp):
GAATTGAAAATTAACCAATTTGATATTATCTT
Found at i:50777 original size:32 final size:32
Alignment explanation
Indices: 50709--50780 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
50699 TTAATTAATT
* * *
50709 TGATATTGTCTTGAATTGAAAATTGACCGGTT
1 TGATATTATCTTGAATTGAAAATTGACCGATC
**
50741 TGATATTATCTTGAATT-AAAATTTGATTGATC
1 TGATATTATCTTGAATTGAAAA-TTGACCGATC
50773 TGATATTA
1 TGATATTA
50781 ATTCGAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
31 4 0.12
32 30 0.88
ACGTcount: A:0.32, C:0.07, G:0.17, T:0.44
Consensus pattern (32 bp):
TGATATTATCTTGAATTGAAAATTGACCGATC
Found at i:51301 original size:30 final size:30
Alignment explanation
Indices: 51234--51301 Score: 82
Period size: 30 Copynumber: 2.3 Consensus size: 30
51224 AATCATAAAC
** *
51234 TGGTCACTAATTTTATCATTTGTTACAAAT
1 TGGTCACTAACGTTATCATTTGTCACAAAT
** *
51264 TAATCACTAACGTTATCGTTTGTCACAAAT
1 TGGTCACTAACGTTATCATTTGTCACAAAT
51294 TGGTCACT
1 TGGTCACT
51302 CATCGTTAAC
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.29, C:0.18, G:0.12, T:0.41
Consensus pattern (30 bp):
TGGTCACTAACGTTATCATTTGTCACAAAT
Found at i:51856 original size:43 final size:43
Alignment explanation
Indices: 51792--51874 Score: 139
Period size: 43 Copynumber: 1.9 Consensus size: 43
51782 ATGTGAAAAT
*
51792 GAAAGGTTGAGAATAGAGAGATTTGGATTTGGAGAGAATTCAA
1 GAAAGGTTGAGAATAGAGAGATTTGGACTTGGAGAGAATTCAA
* *
51835 GAAAGGTTGAGAATGGGGAGATTTGGACTTGGAGAGAATT
1 GAAAGGTTGAGAATAGAGAGATTTGGACTTGGAGAGAATT
51875 AAACGATGGA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
43 37 1.00
ACGTcount: A:0.36, C:0.02, G:0.36, T:0.25
Consensus pattern (43 bp):
GAAAGGTTGAGAATAGAGAGATTTGGACTTGGAGAGAATTCAA
Found at i:52601 original size:35 final size:35
Alignment explanation
Indices: 52528--52613 Score: 91
Period size: 35 Copynumber: 2.5 Consensus size: 35
52518 AAAACAGTCA
* * * *
52528 TCAATTTCATTCTAAACCCCAATTTCCAAAGTAAT
1 TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
* * * *
52563 TCAATTTTATTCTAAACCATAAATTCTAAAATACT
1 TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
*
52598 TCAATTAAATTCTAAA
1 TCAATTTAATTCTAAA
52614 ATACTTCAAT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
35 42 1.00
ACGTcount: A:0.42, C:0.20, G:0.01, T:0.37
Consensus pattern (35 bp):
TCAATTTAATTCTAAACCACAAATTCCAAAATAAT
Found at i:52607 original size:21 final size:21
Alignment explanation
Indices: 52582--52624 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
52572 TTCTAAACCA
52582 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
52603 TAAATTCTAAAATACTTCAAT
1 TAAATTCTAAAATACTTCAAT
52624 T
1 T
52625 TAAGGTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.47, C:0.14, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTCTAAAATACTTCAAT
Found at i:52774 original size:14 final size:16
Alignment explanation
Indices: 52738--52774 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
52728 TATTAATGTA
52738 TGAATCATTTATATTTT
1 TGAAT-ATTTATATTTT
52755 TGAATATTT-TATTTT
1 TGAATATTTATATTTT
52770 T-AATA
1 TGAATA
52775 AGAAATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 4 0.20
15 7 0.35
16 4 0.20
17 5 0.25
ACGTcount: A:0.32, C:0.03, G:0.05, T:0.59
Consensus pattern (16 bp):
TGAATATTTATATTTT
Found at i:53438 original size:130 final size:130
Alignment explanation
Indices: 53235--53482 Score: 424
Period size: 130 Copynumber: 1.9 Consensus size: 130
53225 AATTTTCTTC
* * *
53235 TAATTAGGAGGTGACATGTGTCACCAATAACACATATCATGATCATGTGTTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
*
53300 CCTGATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
* * * *
53365 TAATTAGGTGGTAACACGTGTCACCAATGACACGTGTCATGATCATGTGCTAACACATGTCAGAT
1 TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
53430 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
66 CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGAT
53483 TATATAAATA
Statistics
Matches: 110, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
130 110 1.00
ACGTcount: A:0.37, C:0.13, G:0.15, T:0.35
Consensus pattern (130 bp):
TAATTAGGAGGTAACACGTGTCACCAATAACACATATCATGATCATGTGCTAACACATGTCAGAT
CCTAATTAAATGATTAATTTATTAAATTTTATTTAATTTAGGACCAAATTGATAGCATATATAAA
Found at i:55372 original size:30 final size:30
Alignment explanation
Indices: 55302--55360 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
55292 ATAATGAGTG
* *
55302 ACCAATTTATAACAAACGATAATGTTAGTA
1 ACCAATTTGTAACAAACGATAACGTTAGTA
*
55332 ACCAATTTGTAACAAATGATAACGTTAGT
1 ACCAATTTGTAACAAACGATAACGTTAGT
55361 GACCTCTTTG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.44, C:0.14, G:0.12, T:0.31
Consensus pattern (30 bp):
ACCAATTTGTAACAAACGATAACGTTAGTA
Found at i:59891 original size:21 final size:22
Alignment explanation
Indices: 59852--59899 Score: 71
Period size: 21 Copynumber: 2.2 Consensus size: 22
59842 CAAAAGTTTG
59852 TAGATTTTCAGGGGAAGGACAT
1 TAGATTTTCAGGGGAAGGACAT
*
59874 TAGATTTTCA-GTGAAGGACAT
1 TAGATTTTCAGGGGAAGGACAT
*
59895 AAGAT
1 TAGAT
59900 GCTGGAATTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.35, C:0.08, G:0.27, T:0.29
Consensus pattern (22 bp):
TAGATTTTCAGGGGAAGGACAT
Found at i:67491 original size:20 final size:18
Alignment explanation
Indices: 67427--67492 Score: 62
Period size: 20 Copynumber: 3.4 Consensus size: 18
67417 TAATTTTTTT
*
67427 TTTATTTTTCAATTTAGTTA
1 TTTATTTTTCAA-TTA-TCA
*
67447 TTTATTTTTCATAATATCA
1 TTTATTTTTCA-ATTATCA
67466 -TTATTTCTTCAATTCATCA
1 TTTATTT-TTCAATT-ATCA
67485 TTTATTTT
1 TTTATTTT
67493 AAGTATTTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
18 8 0.21
19 11 0.28
20 19 0.49
21 1 0.03
ACGTcount: A:0.26, C:0.11, G:0.02, T:0.62
Consensus pattern (18 bp):
TTTATTTTTCAATTATCA
Found at i:67586 original size:156 final size:158
Alignment explanation
Indices: 67304--67600 Score: 386
Period size: 156 Copynumber: 1.9 Consensus size: 158
67294 GTCTATGATT
* *
67304 TCATTATTTCTTCAATTCCTCCTTCATTTTAAGTTTATTTTTTTACCAAATTTGAACCACATGCT
1 TCATTATTTCTTCAATTCATCATTCATTTTAAG-TTATTTTTTTACCAAATTTGAACCACATGCT
* * * ** * **
67369 CCTAAACCATAATAGAATTCATGTGTACTTTCAATTCCTTTTTTATAGTAATTTTTTTTTTATTT
65 CCTAAACCATAACAAAATACACATGTACTTTCAATTCCTTTTTTATAATAAAATTTTTTTTATTT
* *
67434 TTCAATTTAGTTATTTATTTTTCATAATA
130 TTAAATGTAGTTATTTATTTTTCATAATA
* * *
67463 TCATTATTTCTTCAATTCATCATTTATTTTAAG-TA-TTTTTTATCAAATTTGAGCCACATGCTC
1 TCATTATTTCTTCAATTCATCATTCATTTTAAGTTATTTTTTTACCAAATTTGAACCACATGCTC
* *
67526 CTAAACCATAGCAAAATACACATGTATTTTCAATT-CTTCTTTT-TAATAACAATTTTTTTTATT
66 CTAAACCATAACAAAATACACATGTACTTTCAATTCCTT-TTTTATAATAA-AATTTTTTTTATT
67589 TTTAAATGTAGT
129 TTTAAATGTAGT
67601 CCTTCAATTT
Statistics
Matches: 119, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
155 8 0.07
156 79 0.66
157 2 0.02
159 30 0.25
ACGTcount: A:0.29, C:0.15, G:0.05, T:0.50
Consensus pattern (158 bp):
TCATTATTTCTTCAATTCATCATTCATTTTAAGTTATTTTTTTACCAAATTTGAACCACATGCTC
CTAAACCATAACAAAATACACATGTACTTTCAATTCCTTTTTTATAATAAAATTTTTTTTATTTT
TAAATGTAGTTATTTATTTTTCATAATA
Found at i:68282 original size:41 final size:41
Alignment explanation
Indices: 68237--68320 Score: 168
Period size: 41 Copynumber: 2.0 Consensus size: 41
68227 ACAAATCTGA
68237 TAACGGGTCACTGCTTCTAAGGTTAGGTCATTTTGCTAAAC
1 TAACGGGTCACTGCTTCTAAGGTTAGGTCATTTTGCTAAAC
68278 TAACGGGTCACTGCTTCTAAGGTTAGGTCATTTTGCTAAAC
1 TAACGGGTCACTGCTTCTAAGGTTAGGTCATTTTGCTAAAC
68319 TA
1 TA
68321 GCCAAAATTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 43 1.00
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (41 bp):
TAACGGGTCACTGCTTCTAAGGTTAGGTCATTTTGCTAAAC
Found at i:68314 original size:22 final size:22
Alignment explanation
Indices: 68248--68314 Score: 54
Period size: 22 Copynumber: 3.2 Consensus size: 22
68238 AACGGGTCAC
68248 TGCTTCTAAGGTTAGGTCATTT
1 TGCTTCTAAGGTTAGGTCATTT
* * *
68270 TGCTAAACTAACG---GGTCA--C
1 TGCT--TCTAAGGTTAGGTCATTT
68289 TGCTTCTAAGGTTAGGTCATTT
1 TGCTTCTAAGGTTAGGTCATTT
68311 TGCT
1 TGCT
68315 AAACTAGCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 14
0.62 0.12 0.27
Matches are distributed among these distances:
17 5 0.16
19 4 0.12
20 5 0.16
21 5 0.16
22 8 0.25
24 5 0.16
ACGTcount: A:0.21, C:0.18, G:0.22, T:0.39
Consensus pattern (22 bp):
TGCTTCTAAGGTTAGGTCATTT
Found at i:76672 original size:22 final size:22
Alignment explanation
Indices: 76618--76674 Score: 75
Period size: 19 Copynumber: 2.7 Consensus size: 22
76608 GCAACGCGAT
*
76618 TTTGAAAAATGTGTTGCGATAG
1 TTTGAAAAATGTGTTGCGAGAG
76640 -TT--AAAATGTGTTGCGAGAG
1 TTTGAAAAATGTGTTGCGAGAG
*
76659 TTTGAAAAACGTGTTG
1 TTTGAAAAATGTGTTG
76675 TTGCGATAGT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
19 16 0.53
20 2 0.07
21 2 0.07
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.28, T:0.35
Consensus pattern (22 bp):
TTTGAAAAATGTGTTGCGAGAG
Found at i:76689 original size:22 final size:19
Alignment explanation
Indices: 76623--76689 Score: 62
Period size: 19 Copynumber: 3.2 Consensus size: 19
76613 GCGATTTTGA
*
76623 AAAATGTGTTGCGATAGTT
1 AAAATGTGTTGCGATAGTG
*
76642 AAAATGTGTTGCGAGAGTTTG
1 AAAATGTGTTGCGATAG--TG
76663 AAAAACGTGTTGTTGCGATAGTG
1 -AAAA--TG-TGTTGCGATAGTG
76686 AAAA
1 AAAA
76690 ATCCAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
19 16 0.41
21 1 0.03
22 8 0.21
23 2 0.05
24 2 0.05
25 10 0.26
ACGTcount: A:0.34, C:0.06, G:0.28, T:0.31
Consensus pattern (19 bp):
AAAATGTGTTGCGATAGTG
Found at i:77212 original size:53 final size:53
Alignment explanation
Indices: 77132--77349 Score: 328
Period size: 53 Copynumber: 4.0 Consensus size: 53
77122 CGACTATCGC
*
77132 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCACAACGCGAACTTCG
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
*
77185 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAATGCGAACTTCGACTATCG
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCG-A-----ACT-TCG
*
77245 CAACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCCAACTTCG
1 -AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
*
77299 AACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGCAACGCGAACTT
1 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTT
77350 GGACTATCGC
Statistics
Matches: 151, Mismatches: 6, Indels: 16
0.87 0.03 0.09
Matches are distributed among these distances:
53 93 0.62
54 4 0.03
55 3 0.02
59 3 0.02
60 4 0.03
61 44 0.29
ACGTcount: A:0.35, C:0.23, G:0.21, T:0.22
Consensus pattern (53 bp):
AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGCAACGCGAACTTCG
Found at i:77244 original size:21 final size:20
Alignment explanation
Indices: 77106--77417 Score: 130
Period size: 21 Copynumber: 16.4 Consensus size: 20
77096 ATTTTAAAAA
*
77106 ATCGCAACGCGAACTTCGACT
1 ATCGCAA-GCGAACTTGGACT
*
77127 ATCGCAACGTGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
* **
77148 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTGGACT
* *
77167 ATCACAA-CG--C--GAACT
1 ATCGCAAGCGAACTTGGACT
*
77182 -TCG-AACGTGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
* **
77201 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTGGACT
*
77220 ATCGCAATGCGAACTTCGACT
1 ATCGCAA-GCGAACTTGGACT
*
77241 ATCGCAACGTGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
* **
77262 ATCGCAA-CGAATTTGGAAA
1 ATCGCAAGCGAACTTGGACT
**
77281 ATCGCAA-CG--C--CAACT
1 ATCGCAAGCGAACTTGGACT
*
77296 -TCG-AACGTGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
* * **
77315 ATCGCAA-CGAATTTGAAAA
1 ATCGCAAGCGAACTTGGACT
77334 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
*
77355 ATCGCAA-CGAATTTGGACT
1 ATCGCAAGCGAACTTGGACT
* * * **
77374 AACG-TA---AATTTGGAAA
1 ATCGCAAGCGAACTTGGACT
77390 ATCGCAACGCGAACTTGGACT
1 ATCGCAA-GCGAACTTGGACT
77411 ATCGCAA
1 ATCGCAA
77418 AATCGCGTTG
Statistics
Matches: 210, Mismatches: 56, Indels: 50
0.66 0.18 0.16
Matches are distributed among these distances:
13 4 0.02
14 5 0.02
15 5 0.02
16 11 0.05
17 3 0.01
18 1 0.00
19 83 0.40
20 6 0.03
21 92 0.44
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (20 bp):
ATCGCAAGCGAACTTGGACT
Found at i:77303 original size:114 final size:114
Alignment explanation
Indices: 77102--77405 Score: 501
Period size: 114 Copynumber: 2.7 Consensus size: 114
77092 TGCGATTTTA
77102 AAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 AAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
*
77167 ATCACAACGCGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
66 ATCGCAACGCGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
* *
77216 GAAAATCGCAATGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
1 AAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
*
77281 ATCGCAACGCCAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
66 ATCGCAACGCGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
* * * *
77330 AAAAATCGCAACGCGAACTTGGACTATCGCAAC--GAATTTGGACTAACG-TA--AATTTGGAAA
1 AAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
77390 ATCGCAACGCGAACTT
66 ATCGCAACGCGAACTT
77406 GGACTATCGC
Statistics
Matches: 179, Mismatches: 11, Indels: 5
0.92 0.06 0.03
Matches are distributed among these distances:
109 25 0.14
111 1 0.01
112 13 0.07
114 140 0.78
ACGTcount: A:0.35, C:0.23, G:0.20, T:0.21
Consensus pattern (114 bp):
AAAAATCGCAACGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGCAACGAATTTGGAAA
ATCGCAACGCGAACTTCGAACGTGAACTTGGACTATCGCAACGAATTTG
Found at i:77359 original size:40 final size:40
Alignment explanation
Indices: 77185--77371 Score: 165
Period size: 40 Copynumber: 4.8 Consensus size: 40
77175 GCGAACTTCG
*
77185 AACGTGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
1 AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
* * * **
77225 AATGCGAACTTCGACTATCGCAACGTGAACTTGGACTATCGC
1 AACGCGAACTTGGACTATCGCAAC--GAATTTGGAAAATCGC
* ** ** **
77267 AA--CGAATTTGGAAAATCGCAACG-----CCAACTTCG-
1 AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
* *
77299 AACGTGAACTTGGACTATCGCAACGAATTTGAAAAATCGC
1 AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
77339 AACGCGAACTTGGACTATCGCAACGAATTTGGA
1 AACGCGAACTTGGACTATCGCAACGAATTTGGA
77372 CTAACGTAAA
Statistics
Matches: 112, Mismatches: 25, Indels: 20
0.71 0.16 0.13
Matches are distributed among these distances:
32 2 0.02
33 4 0.04
34 17 0.15
38 1 0.01
39 5 0.04
40 68 0.61
42 15 0.13
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.22
Consensus pattern (40 bp):
AACGCGAACTTGGACTATCGCAACGAATTTGGAAAATCGC
Found at i:82694 original size:33 final size:32
Alignment explanation
Indices: 82634--82695 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
82624 GATGAATTTT
* ** *
82634 TCGCAGAGGCAAGCTTGGGGGAGAAGAAGATA
1 TCGCAGAGGCAAACTACGGGGAAAAGAAGATA
82666 TCGCAGAGGCAAACTCACGGGGAAAAGAAG
1 TCGCAGAGGCAAACT-ACGGGGAAAAGAAG
82696 GGTATTTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 14 0.56
33 11 0.44
ACGTcount: A:0.37, C:0.16, G:0.37, T:0.10
Consensus pattern (32 bp):
TCGCAGAGGCAAACTACGGGGAAAAGAAGATA
Found at i:83518 original size:20 final size:20
Alignment explanation
Indices: 83493--83532 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
83483 ATCTCATATC
*
83493 GGATCTAGACGTTGCAATCA
1 GGATCTAGACGTTACAATCA
83513 GGATCTAGACGTTACAATCA
1 GGATCTAGACGTTACAATCA
83533 AGTATTACGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (20 bp):
GGATCTAGACGTTACAATCA
Found at i:88462 original size:22 final size:22
Alignment explanation
Indices: 88437--88507 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 22
88427 ATAATCATTC
88437 AAACAAACCAAATATTCAAAAT
1 AAACAAACCAAATATTCAAAAT
* * *
88459 AAACAATCCAAACTAAATATCCAAAC
1 AAACAAACCAAA-T--AT-TCAAAAT
88485 AAACAAAGCCAAATATTCAAAAT
1 AAACAAA-CCAAATATTCAAAAT
88508 GTTTAAACAC
Statistics
Matches: 38, Mismatches: 6, Indels: 9
0.72 0.11 0.17
Matches are distributed among these distances:
22 11 0.29
23 6 0.16
24 2 0.05
25 2 0.05
26 12 0.32
27 5 0.13
ACGTcount: A:0.61, C:0.21, G:0.01, T:0.17
Consensus pattern (22 bp):
AAACAAACCAAATATTCAAAAT
Found at i:90289 original size:38 final size:38
Alignment explanation
Indices: 90235--90311 Score: 145
Period size: 38 Copynumber: 2.0 Consensus size: 38
90225 CCTTGAAAAG
90235 TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
1 TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
*
90273 TTTCGGATTGAGTGGAATGTAGTGATGATTGCAGGATT
1 TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
90311 T
1 T
90312 GTTGATGCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.23, C:0.06, G:0.32, T:0.38
Consensus pattern (38 bp):
TTTCGGATTGACTGGAATGTAGTGATGATTGCAGGATT
Found at i:90590 original size:44 final size:44
Alignment explanation
Indices: 90494--90604 Score: 129
Period size: 44 Copynumber: 2.5 Consensus size: 44
90484 TGTATCGATG
* * * ** *
90494 CACTGT-ATAGTGTATCGATGCACATTCAAGGAATGTATTGGTG
1 CACTGTCATAGTGTATCGATGCATATTCAAAGAATGCATCAGTA
90537 CATCT-TCATAGTGTATCGATGCATATTCAAA-AGATGCATCAGTA
1 CA-CTGTCATAGTGTATCGATGCATATTCAAAGA-ATGCATCAGTA
90581 CACTGTCATAGTGTATCGATGCAT
1 CACTGTCATAGTGTATCGATGCAT
90605 TGCGCATAAA
Statistics
Matches: 58, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
43 6 0.10
44 52 0.90
ACGTcount: A:0.30, C:0.17, G:0.21, T:0.32
Consensus pattern (44 bp):
CACTGTCATAGTGTATCGATGCATATTCAAAGAATGCATCAGTA
Found at i:96286 original size:65 final size:64
Alignment explanation
Indices: 96217--96352 Score: 204
Period size: 65 Copynumber: 2.1 Consensus size: 64
96207 ACACTAATTA
*
96217 CATTCGATGTTTCAA-AAGAGCCAGGAGTGCATCGATGCATGGTCTGTGCATCGGTACAT-AAAA
1 CATTCGATGTTTCAATAA-AACCAGGAGTGCATCGATGCATGG-CTGTGCATCGGTAC-TCAAAA
96280 TG
63 TG
**
96282 CATTCGATGTTTCAATAAAATTAGGAGTGCATCGATGCATGGCTGTGCATCGGTACTCAAAATG
1 CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACTCAAAATG
96346 CATTCGA
1 CATTCGA
96353 ATTAGGGTGT
Statistics
Matches: 66, Mismatches: 3, Indels: 5
0.89 0.04 0.07
Matches are distributed among these distances:
63 1 0.02
64 27 0.41
65 36 0.55
66 2 0.03
ACGTcount: A:0.29, C:0.18, G:0.24, T:0.28
Consensus pattern (64 bp):
CATTCGATGTTTCAATAAAACCAGGAGTGCATCGATGCATGGCTGTGCATCGGTACTCAAAATG
Found at i:102209 original size:23 final size:23
Alignment explanation
Indices: 102179--102245 Score: 109
Period size: 23 Copynumber: 3.0 Consensus size: 23
102169 GGACATATAT
102179 GTGGTCCTTCGGGACAATTCTAC
1 GTGGTCCTTCGGGACAATTCTAC
* *
102202 GTGGTCCTTTGGGATAATTCTAC
1 GTGGTCCTTCGGGACAATTCTAC
102225 GTGGTCCTTCGGGAC-ATTCTA
1 GTGGTCCTTCGGGACAATTCTA
102246 TATGGCACTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
22 6 0.15
23 34 0.85
ACGTcount: A:0.16, C:0.22, G:0.27, T:0.34
Consensus pattern (23 bp):
GTGGTCCTTCGGGACAATTCTAC
Found at i:104383 original size:21 final size:23
Alignment explanation
Indices: 104327--104391 Score: 66
Period size: 21 Copynumber: 3.0 Consensus size: 23
104317 AACATATATT
*
104327 TGGTCTTTCGGTATAATTCTATG
1 TGGTCTTTCGGGATAATTCTATG
*
104350 TGGTCCATT-GGGAT-A-TCTATG
1 TGGT-CTTTCGGGATAATTCTATG
*
104371 TGGTCTTTCGGGA-CATTCTAT
1 TGGTCTTTCGGGATAATTCTAT
104392 ATGGCACTCG
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
20 3 0.09
21 15 0.43
22 6 0.17
23 8 0.23
24 3 0.09
ACGTcount: A:0.17, C:0.15, G:0.25, T:0.43
Consensus pattern (23 bp):
TGGTCTTTCGGGATAATTCTATG
Found at i:109510 original size:23 final size:23
Alignment explanation
Indices: 109480--109541 Score: 124
Period size: 23 Copynumber: 2.7 Consensus size: 23
109470 GGCAAGGACC
109480 TTTCAACAAATAAGCCCTTATAA
1 TTTCAACAAATAAGCCCTTATAA
109503 TTTCAACAAATAAGCCCTTATAA
1 TTTCAACAAATAAGCCCTTATAA
109526 TTTCAACAAATAAGCC
1 TTTCAACAAATAAGCC
109542 TTAAATCTGC
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.44, C:0.23, G:0.05, T:0.29
Consensus pattern (23 bp):
TTTCAACAAATAAGCCCTTATAA
Found at i:109575 original size:4 final size:4
Alignment explanation
Indices: 109568--110773 Score: 1984
Period size: 4 Copynumber: 308.5 Consensus size: 4
109558 ATATGCATGC
109568 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109616 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109664 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109712 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109760 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109806 ATGT ATGT A-GT ATGT ATGGT ATGT ATGT ATGT A--T ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT AT-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109852 ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT A-GT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109897 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
109945 ATGT ATGT ATGT ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
109992 ATGT ATGT GTAT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
110040 ATGT ATGT ATGT ATGT ATGT ATGC ATGC ATGC ATGT AT-T ATGT ATG-
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
110086 ATGT ATGT ATGC ATGT ATGT ATGT A--T ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
110132 ATGT ATGT ATGT ATGT ATGT ATGT ATGT -TGT ATGT ATGT ATGT A--T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
110177 ATGT ATGT ATGT ATGT ATGT ATGT ATGT A--T ATGT ATGT ATTT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
110223 ATGT ATGT ATGT ATGT ATGT ATGT AGGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
110271 ATGT A-GT ATGT ATGT ATGT ATGT ATGT ATAT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
110318 ATGT ATGT -TGT -TGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
110364 ATGT ATGT ATGT ATGT ATGT ATG- -TGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
110410 A-GT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
*
110457 ATGT AGGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT-T
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
110504 ATGT A--T ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
110550 ATG- ATGT ATGT ATGT A-GT ATGT ATGC ATGT ATGT ATGT ATGT ATGC
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
110596 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * * * * * *
110644 ATGT ATGC ATGC ATGC ATGT ATGT ATGT ATGC ATGC ATGC ATGC ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* * *
110692 ATGC ATGC ATGC ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT
* *
110740 ATGT ATGT ATGT ATGT ATGT ATAT ATGC ATGT AT
1 ATGT ATGT ATGT ATGT ATGT ATGT ATGT ATGT AT
110774 AATAGGTACT
Statistics
Matches: 1143, Mismatches: 30, Indels: 58
0.93 0.02 0.05
Matches are distributed among these distances:
2 16 0.01
3 39 0.03
4 1084 0.95
5 4 0.00
ACGTcount: A:0.25, C:0.01, G:0.25, T:0.48
Consensus pattern (4 bp):
ATGT
Found at i:111092 original size:39 final size:39
Alignment explanation
Indices: 111035--111112 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
111025 ATAATCACTC
*
111035 TTATCAACCTATTTGATCTCA-ACTTGAACATAACATATT
1 TTATCAACCTATTCGATCT-ATACTTGAACATAACATATT
* *
111074 TTATCAACCTCTTCGATCTATTCTTGAACATAACATATT
1 TTATCAACCTATTCGATCTATACTTGAACATAACATATT
111113 ATTAACTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 34 0.97
ACGTcount: A:0.33, C:0.22, G:0.05, T:0.40
Consensus pattern (39 bp):
TTATCAACCTATTCGATCTATACTTGAACATAACATATT
Found at i:115597 original size:21 final size:21
Alignment explanation
Indices: 115565--115604 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
115555 AAACTACCAG
115565 TATAGAGGGTATCGATACTCC
1 TATAGAGGGTATCGATACTCC
*
115586 TATAG-GGAGTATCGGTACT
1 TATAGAGG-GTATCGATACT
115605 ATCTTTGCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (21 bp):
TATAGAGGGTATCGATACTCC
Found at i:122261 original size:2 final size:2
Alignment explanation
Indices: 122254--122278 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
122244 TATCGATGAT
122254 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
122279 GATAATGTGT
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:123464 original size:26 final size:26
Alignment explanation
Indices: 123433--123490 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 26
123423 GTCATAACCC
*
123433 GACCCGACCCA-TTTACCCGACCCGTT
1 GACCCGA-CCAGTTAACCCGACCCGTT
*
123459 TACCCGACCAGTTAACCCGACCCGTT
1 GACCCGACCAGTTAACCCGACCCGTT
123485 GACCCG
1 GACCCG
123491 TTGACCTGTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 3 0.11
26 25 0.89
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (26 bp):
GACCCGACCAGTTAACCCGACCCGTT
Found at i:123489 original size:13 final size:13
Alignment explanation
Indices: 123433--123490 Score: 71
Period size: 13 Copynumber: 4.5 Consensus size: 13
123423 GTCATAACCC
*
123433 GACCCGACCCATT
1 GACCCGACCCGTT
*
123446 TACCCGACCCGTT
1 GACCCGACCCGTT
* *
123459 TACCCGACCAGTT
1 GACCCGACCCGTT
*
123472 AACCCGACCCGTT
1 GACCCGACCCGTT
123485 GACCCG
1 GACCCG
123491 TTGACCTGTT
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 39 1.00
ACGTcount: A:0.21, C:0.45, G:0.17, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:123490 original size:8 final size:8
Alignment explanation
Indices: 123477--123531 Score: 58
Period size: 8 Copynumber: 6.5 Consensus size: 8
123467 CAGTTAACCC
123477 GACCCGTT
1 GACCCGTT
123485 GACCCGTT
1 GACCCGTT
*
123493 GACCTGTT
1 GACCCGTT
123501 GA-CCGTT
1 GACCCGTT
123508 GACCGACGTT
1 GACC--CGTT
123518 GACCACTGTT
1 GACC-C-GTT
123528 GACC
1 GACC
123532 AAAACTTTGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
7 6 0.15
8 18 0.44
9 2 0.05
10 15 0.37
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.25
Consensus pattern (8 bp):
GACCCGTT
Found at i:123508 original size:15 final size:16
Alignment explanation
Indices: 123477--123531 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 16
123467 CAGTTAACCC
123477 GACCCGTTGACCCGTT
1 GACCCGTTGACCCGTT
*
123493 GACCTGTTGA-CCGTT
1 GACCCGTTGACCCGTT
123508 GACCGACGTTGACCACTGTT
1 GACC--CGTTGACC-C-GTT
123528 GACC
1 GACC
123532 AAAACTTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
15 9 0.28
16 9 0.28
17 5 0.16
18 1 0.03
19 1 0.03
20 7 0.22
ACGTcount: A:0.16, C:0.33, G:0.25, T:0.25
Consensus pattern (16 bp):
GACCCGTTGACCCGTT
Found at i:125276 original size:31 final size:31
Alignment explanation
Indices: 125238--125305 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
125228 CAACGGTCAA
* *
125238 CGGGTCGGGTCAACGGGT-TGGATCAACGGGT
1 CGGGTCGGGTCAACGGGTCAGG-TAAACGGGT
*
125269 CGGGTCGGGTCAACTGGTCAGGTAAACGGGT
1 CGGGTCGGGTCAACGGGTCAGGTAAACGGGT
125300 CGGGTC
1 CGGGTC
125306 ATGTTATGAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
31 31 0.94
32 2 0.06
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (31 bp):
CGGGTCGGGTCAACGGGTCAGGTAAACGGGT
Found at i:125287 original size:13 final size:13
Alignment explanation
Indices: 125232--125274 Score: 68
Period size: 13 Copynumber: 3.3 Consensus size: 13
125222 AACGGTCAAC
125232 GGTCAACGGGTCG
1 GGTCAACGGGTCG
*
125245 GGTCAACGGGTTG
1 GGTCAACGGGTCG
*
125258 GATCAACGGGTCG
1 GGTCAACGGGTCG
125271 GGTC
1 GGTC
125275 GGGTCAACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.16, C:0.21, G:0.44, T:0.19
Consensus pattern (13 bp):
GGTCAACGGGTCG
Found at i:127226 original size:334 final size:335
Alignment explanation
Indices: 126616--127287 Score: 1260
Period size: 334 Copynumber: 2.0 Consensus size: 335
126606 GGAAGTCACA
*
126616 TTAGGGCCACCGGAGTGACCCACTGTAAAAATAGCGGAAAATTTAAAACTTTTTTTCAGAACATG
1 TTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTTTTTTTCAGAACATG
*
126681 TAAACTTATAAAATCAGTTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
66 TAAACTTATAAAATCAATTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
126746 AAAATACAATTACATGCCCCCTTATCACATGTACCATACTCCGCAACAACGCCGGACGAATTCCT
131 AAAATACAATTACATGCCCCCTTATCACATGTACCATACTCCGCAACAACGCCGGACGAATTCCT
126811 TTACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTAAAAAGGTGAGTAATAGAGTGAG
196 TTACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTAAAAAGGTGAGTAATAGAGTGAG
*
126876 CTTTGGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGCAGATACAGATAAAC
261 CTTTGGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGAAGATACAGATAAAC
126941 ATACATATCC
326 ATACATATCC
126951 TTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAAC-TTTTTTCAGAACATG
1 TTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTTTTTTTCAGAACATG
127015 TAAACTTATAAAATCAATTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
66 TAAACTTATAAAATCAATTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
*
127080 AAAATACAATTACATG-CCCCTTAATCACATGTACCATACTCTGCAACAACGCCGGACGAATTCC
131 AAAATACAATTACATGCCCCCTT-ATCACATGTACCATACTCCGCAACAACGCCGGACGAATTCC
*
127144 TTTATTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTGAAAAA-GTGAGTAATAGAGTG
195 TTTACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCT-AAAAAGGTGAGTAATAGAGTG
127208 AGCTTTGGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGAAGATACAGATAA
259 AGCTTTGGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGAAGATACAGATAA
127273 ACATACATATCC
324 ACATACATATCC
127285 TTA
1 TTA
127288 TTATTTCTGA
Statistics
Matches: 330, Mismatches: 5, Indels: 5
0.97 0.01 0.01
Matches are distributed among these distances:
333 6 0.02
334 271 0.82
335 53 0.16
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (335 bp):
TTAGGGCCACCGGAGCGACCCACTGTAAAAATAGCGGAAAATTTAAAACTTTTTTTCAGAACATG
TAAACTTATAAAATCAATTTTCACTATTTAAAAATAAAACAGATTTCCAAACTCGTATATAAATC
AAAATACAATTACATGCCCCCTTATCACATGTACCATACTCCGCAACAACGCCGGACGAATTCCT
TTACTGATGTCGATAACTGCACTGGTATAATTCTTTTAACCTAAAAAGGTGAGTAATAGAGTGAG
CTTTGGAAAGCTCAGTAATACAGAACTACCAGATGATGCTGATGAACGTGAAGATACAGATAAAC
ATACATATCC
Found at i:127620 original size:35 final size:35
Alignment explanation
Indices: 127547--127620 Score: 121
Period size: 35 Copynumber: 2.1 Consensus size: 35
127537 CGTCACGTCC
**
127547 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGGTA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
*
127582 AGTAAGGCCCTGAGCACACAGCCGAGGAACCTCCA
1 AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
127617 AGTA
1 AGTA
127621 TTCTTCCTCC
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 36 1.00
ACGTcount: A:0.32, C:0.30, G:0.28, T:0.09
Consensus pattern (35 bp):
AGTAAGGCCCTGAGCACACAGCCGAGGAACCGCCA
Found at i:127726 original size:24 final size:24
Alignment explanation
Indices: 127699--127789 Score: 112
Period size: 24 Copynumber: 3.8 Consensus size: 24
127689 CATAATTCAA
*
127699 GTCAAGTATCATATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* *
127723 GTCATGTATCAGATCAGAATCCAT
1 GTCAAGTATCAGATCAGAATCCAG
*
127747 GTCAA-TATTAGATCAGAATCCAG
1 GTCAAGTATCAGATCAGAATCCAG
* * *
127770 GTCAGGTATCATAACAGAAT
1 GTCAAGTATCAGATCAGAAT
127790 TCAAATTTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 20 0.36
24 36 0.64
ACGTcount: A:0.37, C:0.19, G:0.18, T:0.26
Consensus pattern (24 bp):
GTCAAGTATCAGATCAGAATCCAG
Found at i:127763 original size:23 final size:24
Alignment explanation
Indices: 127705--127773 Score: 95
Period size: 23 Copynumber: 2.9 Consensus size: 24
127695 TCAAGTCAAG
* *
127705 TATCATATCAGAATCCAGGTCATG
1 TATCAGATCAGAATCCAGGTCATA
*
127729 TATCAGATCAGAATCCATGTCA-A
1 TATCAGATCAGAATCCAGGTCATA
*
127752 TATTAGATCAGAATCCAGGTCA
1 TATCAGATCAGAATCCAGGTCA
127774 GGTATCATAA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 20 0.50
24 20 0.50
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (24 bp):
TATCAGATCAGAATCCAGGTCATA
Found at i:133787 original size:19 final size:20
Alignment explanation
Indices: 133750--133787 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
133740 CACTCACTAT
**
133750 TGTATTACTTGCATTGATTG
1 TGTATTACTTGCACAGATTG
133770 TGTA-TACTTGCACAGATT
1 TGTATTACTTGCACAGATT
133788 TACGTGTCAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 12 0.75
20 4 0.25
ACGTcount: A:0.24, C:0.13, G:0.18, T:0.45
Consensus pattern (20 bp):
TGTATTACTTGCACAGATTG
Found at i:138309 original size:28 final size:28
Alignment explanation
Indices: 138267--138325 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
138257 TAATCTAGGG
*
138267 TAAGTACAAGACAATATTTGTTCAAAGA
1 TAAGTACAAGACAATATATGTTCAAAGA
* *
138295 TAAGTACAAGGCAATATATGTTTAAAGA
1 TAAGTACAAGACAATATATGTTCAAAGA
138323 TAA
1 TAA
138326 CTCTCAATCA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.47, C:0.08, G:0.15, T:0.29
Consensus pattern (28 bp):
TAAGTACAAGACAATATATGTTCAAAGA
Found at i:160653 original size:30 final size:29
Alignment explanation
Indices: 160596--160655 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 29
160586 GATTTTATTA
160596 TTTTATTAGGAATTTAGTTTGCATAGAAT
1 TTTTATTAGGAATTTAGTTTGCATAGAAT
* *
160625 TTTTATTTAGGATTTTTAGTTTG-TTAGAAT
1 TTTTA-TTAGGA-ATTTAGTTTGCATAGAAT
160655 T
1 T
160656 AAGAGTTTGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
29 5 0.19
30 13 0.48
31 9 0.33
ACGTcount: A:0.27, C:0.02, G:0.17, T:0.55
Consensus pattern (29 bp):
TTTTATTAGGAATTTAGTTTGCATAGAAT
Found at i:164505 original size:123 final size:123
Alignment explanation
Indices: 164282--164527 Score: 465
Period size: 123 Copynumber: 2.0 Consensus size: 123
164272 TTCTACACTT
*
164282 TTTATCTCGGTTTCTTCCATCTCTAGTAACTCAATGTTCTCTGCAAATTCCTCAGAAGCTTCTTC
1 TTTATCTCAGTTTCTTCCATCTCTAGTAACTCAATGTTCTCTGCAAATTCCTCAGAAGCTTCTTC
*
164347 AACCATCTCTTCAGATTCGACAACTGTATTCTCTATCTCCAAGCTAACTACGTGTCCC
66 AACCATCTCTTCAGATTCGACAACTGTATTATCTATCTCCAAGCTAACTACGTGTCCC
*
164405 TTTATCTCAGTTTCTTCCATCTCTAGTAACTCAATGTTCTCTTCAAATTCCTCAGAAGCTTCTTC
1 TTTATCTCAGTTTCTTCCATCTCTAGTAACTCAATGTTCTCTGCAAATTCCTCAGAAGCTTCTTC
164470 AACCATCTCTTCAGATTCGACAACTGTATTATCTATCTCCAAGCTAACTACGTGTCCC
66 AACCATCTCTTCAGATTCGACAACTGTATTATCTATCTCCAAGCTAACTACGTGTCCC
164528 AAGTTAGCCT
Statistics
Matches: 120, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 120 1.00
ACGTcount: A:0.24, C:0.30, G:0.10, T:0.37
Consensus pattern (123 bp):
TTTATCTCAGTTTCTTCCATCTCTAGTAACTCAATGTTCTCTGCAAATTCCTCAGAAGCTTCTTC
AACCATCTCTTCAGATTCGACAACTGTATTATCTATCTCCAAGCTAACTACGTGTCCC
Found at i:169346 original size:20 final size:21
Alignment explanation
Indices: 169308--169360 Score: 58
Period size: 20 Copynumber: 2.6 Consensus size: 21
169298 CAATCTTCCG
*
169308 TATGGATACTAG-TCATTCGGC
1 TATGGAGACTAGTTCATTC-GC
*
169329 T-TGGAGACTAGTTC-TTCGT
1 TATGGAGACTAGTTCATTCGC
169348 TATGGAGACTAGT
1 TATGGAGACTAGT
169361 CCTACAGTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
19 2 0.07
20 23 0.82
21 3 0.11
ACGTcount: A:0.23, C:0.15, G:0.26, T:0.36
Consensus pattern (21 bp):
TATGGAGACTAGTTCATTCGC
Found at i:169371 original size:20 final size:20
Alignment explanation
Indices: 169330--169376 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
169320 TCATTCGGCT
* *
169330 TGGAGACTAGTTCTTCGTTA
1 TGGAGACTAGTCCTACGTTA
169350 TGGAGACTAGTCCTACAG-TA
1 TGGAGACTAGTCCTAC-GTTA
169370 TGGAGAC
1 TGGAGAC
169377 CAGCCAATCT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
20 23 0.96
21 1 0.04
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.30
Consensus pattern (20 bp):
TGGAGACTAGTCCTACGTTA
Found at i:170050 original size:27 final size:25
Alignment explanation
Indices: 170013--170062 Score: 64
Period size: 25 Copynumber: 1.9 Consensus size: 25
170003 TGGCTACTTA
* *
170013 AAGAAGATGAATGAAGAAGATATGACG
1 AAGAAAATGAA-G-AGAAGACATGACG
170040 AAGAAAATGAAGAGAAGACATGA
1 AAGAAAATGAAGAGAAGACATGA
170063 GAAATGAGAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 10 0.48
26 1 0.05
27 10 0.48
ACGTcount: A:0.56, C:0.04, G:0.28, T:0.12
Consensus pattern (25 bp):
AAGAAAATGAAGAGAAGACATGACG
Found at i:173696 original size:32 final size:32
Alignment explanation
Indices: 173655--173740 Score: 118
Period size: 32 Copynumber: 2.7 Consensus size: 32
173645 CATTCATGTG
173655 CATTGTCTGAATGCAAACCTGAACATACTATA
1 CATTGTCTGAATGCAAACCTGAACATACTATA
* * * * *
173687 CATTGTCTGAATGTAGACCTGAACATATTGTG
1 CATTGTCTGAATGCAAACCTGAACATACTATA
*
173719 CATTATCTGAATGCAAACCTGA
1 CATTGTCTGAATGCAAACCTGA
173741 CTAGTATCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.34, C:0.20, G:0.16, T:0.30
Consensus pattern (32 bp):
CATTGTCTGAATGCAAACCTGAACATACTATA
Found at i:174788 original size:20 final size:20
Alignment explanation
Indices: 174759--174809 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
174749 GACCACTTTG
* * *
174759 GGTATTGATATTGAGCCTTC
1 GGTATGGATATTCAACCTTC
* *
174779 GGTATGGATACTCAATCTTC
1 GGTATGGATATTCAACCTTC
174799 GGTATGGATAT
1 GGTATGGATAT
174810 CAGTCCTGCG
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.24, C:0.14, G:0.25, T:0.37
Consensus pattern (20 bp):
GGTATGGATATTCAACCTTC
Found at i:174821 original size:20 final size:19
Alignment explanation
Indices: 174778--174832 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
174768 ATTGAGCCTT
* *
174778 CGGTATGGATACTCAATCTT
1 CGGTATGGATA-TCAGTCTG
174798 CGGTATGGATATCAGTCCTG
1 CGGTATGGATATCAGT-CTG
*
174818 CGGTATGGAGATCAG
1 CGGTATGGATATCAG
174833 CCTTAGTCGA
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
19 4 0.13
20 27 0.87
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (19 bp):
CGGTATGGATATCAGTCTG
Found at i:175508 original size:14 final size:14
Alignment explanation
Indices: 175489--175529 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
175479 AGACGAAGGT
175489 AGAAGATATGAAGA
1 AGAAGATATGAAGA
*
175503 AGAAGAAATGAAG-
1 AGAAGATATGAAGA
175516 AGAAGATAT-AAGA
1 AGAAGATATGAAGA
175529 A
1 A
175530 ATGAAACACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
12 3 0.12
13 9 0.38
14 12 0.50
ACGTcount: A:0.61, C:0.00, G:0.27, T:0.12
Consensus pattern (14 bp):
AGAAGATATGAAGA
Found at i:178366 original size:37 final size:35
Alignment explanation
Indices: 178316--178387 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 35
178306 ATTTGTCAAC
178316 AAACATCTACCAAACTTTGAAAACCCATTTTTCAAAG
1 AAACATCTACCAAACTTTGAAAA-CCA-TTTTCAAAG
*
178353 AAACATTTACCAAACTTTGAAAACCATTTTCAAAG
1 AAACATCTACCAAACTTTGAAAACCATTTTCAAAG
178388 TTGGTTGCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 9 0.26
36 3 0.09
37 22 0.65
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (35 bp):
AAACATCTACCAAACTTTGAAAACCATTTTCAAAG
Found at i:181550 original size:8 final size:8
Alignment explanation
Indices: 181537--181564 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
181527 GATTAAAGTA
181537 TAATAGTT
1 TAATAGTT
181545 TAATAGTT
1 TAATAGTT
181553 TAATAGTT
1 TAATAGTT
181561 TAAT
1 TAAT
181565 GATTTGTTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.39, C:0.00, G:0.11, T:0.50
Consensus pattern (8 bp):
TAATAGTT
Found at i:182917 original size:31 final size:31
Alignment explanation
Indices: 182879--183063 Score: 327
Period size: 31 Copynumber: 6.0 Consensus size: 31
182869 GGGTCGAGGG
182879 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
182910 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
182941 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
182972 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
183003 TTACCTATGTTCTTCGGGACATATGGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
183034 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
183064 GTCCTTCGGG
Statistics
Matches: 150, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
31 149 0.99
32 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.23, T:0.38
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:187321 original size:31 final size:31
Alignment explanation
Indices: 187283--187467 Score: 300
Period size: 31 Copynumber: 6.0 Consensus size: 31
187273 GGGTCGAGGG
*
187283 TTACCTATGTTCTTCGGGATATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
187314 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
*
187345 TTACCTATGTTCTTCGGGACATATGTACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
187376 TTACCTATGTTCTTCGGGACATATGGACTGT
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
187407 TTACCTATGTTCTTCGGGACATATAGACTGA
1 TTACCTATGTTCTTCGGGACATATGGACTGT
* *
187438 TTACCTAGGTTCTTCGGAATC-TATGGACTG
1 TTACCTATGTTCTTCGGGA-CATATGGACTG
187468 GTCCTTCGGG
Statistics
Matches: 145, Mismatches: 8, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
31 144 0.99
32 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.22, T:0.39
Consensus pattern (31 bp):
TTACCTATGTTCTTCGGGACATATGGACTGT
Found at i:189820 original size:36 final size:37
Alignment explanation
Indices: 189745--189826 Score: 107
Period size: 37 Copynumber: 2.3 Consensus size: 37
189735 CCCCATTACA
*
189745 ATTTTTC-AACAAACATCTACCAAACTTTGAAAAACC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACC
* * *
189781 ATTTTTCAAAGAAATATTTACCAAACTTTG-AAAATC
1 ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACC
189817 A-TTTTCAAAG
1 ATTTTTCAAAG
189827 TTGGTTGCCA
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
35 9 0.22
36 13 0.32
37 19 0.46
ACGTcount: A:0.44, C:0.18, G:0.05, T:0.33
Consensus pattern (37 bp):
ATTTTTCAAAGAAACATCTACCAAACTTTGAAAAACC
Found at i:191476 original size:102 final size:101
Alignment explanation
Indices: 191175--191476 Score: 433
Period size: 102 Copynumber: 3.0 Consensus size: 101
191165 CCCTAGTCGC
191175 TACCTATATTATTATAAATGTAAACTTGATTTATCTTATAATTTTAAAATAAAAAAAGGTTTACA
1 TACCTATATTATTATAAATGTAAACTTGATTTATCTTATAATTTTAAAAT-AAAAAAGGTTTACA
*
191240 TAATGTAATTTATACGATTTACCATTTCAAGAAGGAGC
65 TAATGTAATTTATACG-TTTACCATTTCAAGAAGGAGA
* * *
191278 TACCTATATTATTATAAATGTAAACTTGAATTATGTTATAATTTTAAAATAAAAAAGGTTTACAC
1 TACCTATATTATTATAAATGTAAACTTGATTTATCTTATAATTTTAAAATAAAAAAGGTTTACAT
* ** *
191343 AATGTAATTTATATGGTTTACCATACCAAGAAGGCGA
66 AATGTAATTTATA-CGTTTACCATTTCAAGAAGGAGA
* * * *
191380 TATCTATATTATTATAAATGTAAACTTGATTTATCTTATAATTGTAAAATTAAAAAGGTTGACAT
1 TACCTATATTATTATAAATGTAAACTTGATTTATCTTATAATTTTAAAATAAAAAAGGTTTACAT
* * *
191445 AATGTAACTTATACAGTTTACAATTTTAAGAA
66 AATGTAATTTATAC-GTTTACCATTTCAAGAA
191477 TGCACAACTT
Statistics
Matches: 176, Mismatches: 21, Indels: 5
0.87 0.10 0.02
Matches are distributed among these distances:
102 127 0.72
103 49 0.28
ACGTcount: A:0.42, C:0.09, G:0.10, T:0.39
Consensus pattern (101 bp):
TACCTATATTATTATAAATGTAAACTTGATTTATCTTATAATTTTAAAATAAAAAAGGTTTACAT
AATGTAATTTATACGTTTACCATTTCAAGAAGGAGA
Found at i:194960 original size:17 final size:19
Alignment explanation
Indices: 194923--194960 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
194913 CCTTTTTTTC
*
194923 TTTCGAACAGTCTCTCTTT
1 TTTCGAACAGTCTCGCTTT
194942 TTTCGAACAG-CT-GCTTT
1 TTTCGAACAGTCTCGCTTT
194959 TT
1 TT
194961 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
17 6 0.33
18 2 0.11
19 10 0.56
ACGTcount: A:0.16, C:0.24, G:0.13, T:0.47
Consensus pattern (19 bp):
TTTCGAACAGTCTCGCTTT
Found at i:195842 original size:13 final size:12
Alignment explanation
Indices: 195822--195856 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
195812 GCTTAATCGG
195822 AAAAAAAAATAA
1 AAAAAAAAATAA
*
195834 AAGAAAAAATAA
1 AAAAAAAAATAA
*
195846 AAATAAAAATA
1 AAAAAAAAATA
195857 TAACGGAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.86, C:0.00, G:0.03, T:0.11
Consensus pattern (12 bp):
AAAAAAAAATAA
Found at i:210072 original size:2 final size:2
Alignment explanation
Indices: 210065--210097 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
210055 ATGAAACTTA
210065 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
210098 CACACACGCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:216772 original size:51 final size:51
Alignment explanation
Indices: 216718--216912 Score: 245
Period size: 50 Copynumber: 3.8 Consensus size: 51
216708 AGACGTACAT
* * * *
216718 ACTTACACCAGTGTAAGTATATATTAAGTATTATATTTTTTTATTTTATTT
1 ACTTACACCAGTGTAAGTATGTGTTAAGTATTACATTTTTTTATTTTATTC
*
216769 ACTTACATCAGTCAGTGTAAGTATGTGTTAAGTACTACA-TTTTTTATTTTATTC
1 ACTTACA-C---CAGTGTAAGTATGTGTTAAGTATTACATTTTTTTATTTTATTC
* *
216823 ACTTACACCAGTGT-AGTATGTGTTAAGTGA-TACACTTGTTTATTTTATTC
1 ACTTACACCAGTGTAAGTATGTGTTAAGT-ATTACATTTTTTTATTTTATTC
*
216873 ACTTACACCAGTGTAAGTATGTGTTAAGTGTTA-ATTTTTT
1 ACTTACACCAGTGTAAGTATGTGTTAAGTATTACATTTTTT
216913 GTAGTATGAA
Statistics
Matches: 127, Mismatches: 9, Indels: 17
0.83 0.06 0.11
Matches are distributed among these distances:
49 18 0.14
50 40 0.31
51 23 0.18
52 1 0.01
53 1 0.01
54 21 0.17
55 23 0.18
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.47
Consensus pattern (51 bp):
ACTTACACCAGTGTAAGTATGTGTTAAGTATTACATTTTTTTATTTTATTC
Found at i:218317 original size:25 final size:24
Alignment explanation
Indices: 218254--218318 Score: 85
Period size: 24 Copynumber: 2.6 Consensus size: 24
218244 ACATAATCTA
218254 AAAAATATTATATTATTAAAATGAC
1 AAAAATATTA-ATTATTAAAATGAC
* *
218279 AAAAATACTAATTATTAAAATGAT
1 AAAAATATTAATTATTAAAATGAC
*
218303 AAAAATGTTACATTAT
1 AAAAATATTA-ATTAT
218319 ATATTTTTTG
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 21 0.60
25 14 0.40
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (24 bp):
AAAAATATTAATTATTAAAATGAC
Found at i:219620 original size:13 final size:13
Alignment explanation
Indices: 219602--219632 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
219592 AGTGAGGATG
*
219602 AATATATAATTAA
1 AATATATAAATAA
219615 AATATATAAATAA
1 AATATATAAATAA
219628 AATAT
1 AATAT
219633 GCTTTTAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (13 bp):
AATATATAAATAA
Found at i:221474 original size:20 final size:21
Alignment explanation
Indices: 221434--221474 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
221424 TTTTGGTTAC
* *
221434 ATTAGTAGAGTTAATGATCAA
1 ATTAGTAGAGATAACGATCAA
221455 ATTAGTAGA-ATAACGATCAA
1 ATTAGTAGAGATAACGATCAA
221475 TGACCAAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.46, C:0.07, G:0.17, T:0.29
Consensus pattern (21 bp):
ATTAGTAGAGATAACGATCAA
Found at i:222773 original size:2 final size:2
Alignment explanation
Indices: 222768--222799 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
222758 TCAAAAAACA
*
222768 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
222800 CTAAGTTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:228163 original size:2 final size:2
Alignment explanation
Indices: 228156--228205 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
228146 TTTTCGGGGT
228156 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
228198 TA TA TA TA
1 TA TA TA TA
228206 ATGAGGTAAA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:229216 original size:15 final size:15
Alignment explanation
Indices: 229196--229226 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
229186 GTAAATGTCC
229196 TTCCTACTCCTGATG
1 TTCCTACTCCTGATG
*
229211 TTCCTACTCTTGATG
1 TTCCTACTCCTGATG
229226 T
1 T
229227 CGCAAAATCT
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:0.13, C:0.29, G:0.13, T:0.45
Consensus pattern (15 bp):
TTCCTACTCCTGATG
Found at i:231384 original size:127 final size:127
Alignment explanation
Indices: 231157--231412 Score: 388
Period size: 127 Copynumber: 2.0 Consensus size: 127
231147 ACGAAAGCTA
*
231157 ATTCATATTCGATTTCGATATACACTAGTTCATTAAAAACATACCATTCGATCTAACATCATCAG
1 ATTCATATTCGATTTCGATATACACTAGTTCATT-AAAACATACCATTCGACCTAACATCATCAG
* * *
231222 AATTCTAATAATATCTAAGAACAAATACAACCACTAATCAAGAAATGGAAGACCAGAATTGAT
65 AATTCTAATAATATCTAAAAACAAATACAACCACTAAACAACAAATGGAAGACCAGAATTGAT
* * **
231285 ATTCATATTCGGTTTCGATATTAGACTAGTTCATT-AAACATACCATTCGACCTAGTATCATCAG
1 ATTCATATTCGATTTCGATA-TACACTAGTTCATTAAAACATACCATTCGACCTAACATCATCAG
* * *
231349 AATTCTAATAATCTCTAAAAACAGATAGAACCACTAAACAACAAATGGAAGACCAGAATTGAT
65 AATTCTAATAATATCTAAAAACAAATACAACCACTAAACAACAAATGGAAGACCAGAATTGAT
231412 A
1 A
231413 AATTATTGTT
Statistics
Matches: 116, Mismatches: 11, Indels: 3
0.89 0.08 0.02
Matches are distributed among these distances:
127 84 0.72
128 19 0.16
129 13 0.11
ACGTcount: A:0.43, C:0.19, G:0.11, T:0.28
Consensus pattern (127 bp):
ATTCATATTCGATTTCGATATACACTAGTTCATTAAAACATACCATTCGACCTAACATCATCAGA
ATTCTAATAATATCTAAAAACAAATACAACCACTAAACAACAAATGGAAGACCAGAATTGAT
Found at i:232645 original size:15 final size:16
Alignment explanation
Indices: 232619--232648 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
232609 AATCAGTTAA
232619 AAAATATTTTGAGTTT
1 AAAATATTTTGAGTTT
232635 AAAAT-TTTTGAGTT
1 AAAATATTTTGAGTT
232649 GACTCAAACT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (16 bp):
AAAATATTTTGAGTTT
Found at i:233207 original size:5 final size:5
Alignment explanation
Indices: 233199--233481 Score: 78
Period size: 5 Copynumber: 55.8 Consensus size: 5
233189 GAAAGAAAGG
* * *
233199 AAAAT AAAAT AATAAAG AAAAT AAAA- GAAAT AAAAA ACAAAT AATAAT
1 AAAAT AAAAT -A-AAAT AAAAT AAAAT AAAAT AAAAT A-AAAT AA-AAT
* * *
233247 AATAAT AATAAT -ATAT AGAAT -AAAT AAAAAC AAGAAT AAAAT AAAA-
1 AA-AAT AA-AAT AAAAT AAAAT AAAAT -AAAAT AA-AAT AAAAT AAAAT
* * *
233293 AATAG AGAAAT AAAAT -AAAT ATAAAG AAAAT -AAA- AAAAT AAAGA-
1 AAAAT A-AAAT AAAAT AAAAT A-AAAT AAAAT AAAAT AAAAT AAA-AT
* *
233337 AAAAG AGAGAA- GAAAT -AAAT AAAA- AGAAAT AAAAT --AAT AGAAAT
1 AAAAT A-A-AAT AAAAT AAAAT AAAAT A-AAAT AAAAT AAAAT A-AAAT
** * * * * *
233381 ATGCAT ATAAT AAAATGT ATAAT AAAAC ATAAT -AAAT -AAAT AACAT
1 A-AAAT AAAAT AAAA--T AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT
* *
233427 AAAAT -AAAT AAAAT AAAAT -AAAT AAAGT AAAAAA AAAGAT AAAAT AAATAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT AAAAT -AAAAT AAA-AT AAAAT AAA-AT
233478 AAAA
1 AAAA
233482 GGTAAAAAGG
Statistics
Matches: 208, Mismatches: 36, Indels: 68
0.67 0.12 0.22
Matches are distributed among these distances:
3 3 0.01
4 44 0.21
5 95 0.46
6 57 0.27
7 9 0.04
ACGTcount: A:0.73, C:0.02, G:0.06, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:233208 original size:23 final size:22
Alignment explanation
Indices: 233176--233218 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
233166 AACGAAATAA
*
233176 AAAATGAAATAGAGAAAGAAAGG
1 AAAATAAAATA-AGAAAGAAAGG
*
233199 AAAATAAAATAATAAAGAAA
1 AAAATAAAATAAGAAAGAAA
233219 ATAAAAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.16, T:0.12
Consensus pattern (22 bp):
AAAATAAAATAAGAAAGAAAGG
Found at i:233218 original size:17 final size:17
Alignment explanation
Indices: 233198--233339 Score: 71
Period size: 17 Copynumber: 8.3 Consensus size: 17
233188 AGAAAGAAAG
233198 GAAAATAAAATAATAAA
1 GAAAATAAAATAATAAA
*
233215 GAAAATAAAAGAAATAAAA
1 GAAAATAAAA-TAAT-AAA
*
233234 AACAAATAATAATAATAATA
1 GA-AAATAA-AATAATAA-A
* * *
233254 -ATAATATATAGAATAAA
1 GAAAATA-AAATAATAAA
* * *
233271 TAAAA-ACAAGAATAAA
1 GAAAATAAAATAATAAA
* *
233287 -ATAA-AAAATAGAGAAA
1 GAAAATAAAATA-ATAAA
*
233303 TAAAAT-AAAT-ATAAA
1 GAAAATAAAATAATAAA
*
233318 GAAAATAAAAAAATAAA
1 GAAAATAAAATAATAAA
233335 GAAAA
1 GAAAA
233340 AGAGAGAAGA
Statistics
Matches: 96, Mismatches: 17, Indels: 24
0.70 0.12 0.18
Matches are distributed among these distances:
15 16 0.17
16 15 0.16
17 29 0.30
18 16 0.17
19 8 0.08
20 10 0.10
21 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (17 bp):
GAAAATAAAATAATAAA
Found at i:233223 original size:9 final size:8
Alignment explanation
Indices: 233199--233339 Score: 63
Period size: 9 Copynumber: 16.5 Consensus size: 8
233189 GAAAGAAAGG
233199 AAAATAAA
1 AAAATAAA
*
233207 ATAATAAA
1 AAAATAAA
233215 GAAAATAAA
1 -AAAATAAA
233224 AGAAATAAA
1 A-AAATAAA
233233 AAACA-AATA
1 AAA-ATAA-A
*
233242 ATAATAATA
1 AAAATAA-A
*
233251 ATAAT-AA
1 AAAATAAA
* *
233258 TATATAGAA
1 AAAATA-AA
*
233267 TAAATAAA
1 AAAATAAA
* *
233275 AACAAGAAT
1 AA-AATAAA
233284 AAAAT-AA
1 AAAATAAA
*
233291 AAAATAGA
1 AAAATAAA
*
233299 GAAATAAAA
1 AAAAT-AAA
233308 TAAATATAAA
1 -AAA-ATAAA
233318 GAAAATAAA
1 -AAAATAAA
233327 AAAATAAA
1 AAAATAAA
233335 GAAAA
1 -AAAA
233340 AGAGAGAAGA
Statistics
Matches: 103, Mismatches: 17, Indels: 25
0.71 0.12 0.17
Matches are distributed among these distances:
7 9 0.09
8 32 0.31
9 52 0.50
10 8 0.08
11 2 0.02
ACGTcount: A:0.75, C:0.01, G:0.06, T:0.18
Consensus pattern (8 bp):
AAAATAAA
Found at i:233356 original size:44 final size:42
Alignment explanation
Indices: 233265--233375 Score: 118
Period size: 43 Copynumber: 2.6 Consensus size: 42
233255 TAATATATAG
* * * *
233265 AATAAATAAAAA-CAAGAATAAAATAAAAAATAGAGAAATAA
1 AATAAATAAAAAGAAATAAAAAAATAAAAAAAAGAGAAATAA
* *
233306 AATAAATATAAAGAAAATAAAAAAATAAAGAAAAAGAGAGAA-GA
1 AATAAATAAAAAG-AAATAAAAAAATAAA-AAAAAGAGA-AATAA
*
233350 AATAAATAAAAAGAAATAAAATAATA
1 AATAAATAAAAAGAAATAAAAAAATA
233376 GAAATATGCA
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
41 11 0.19
43 24 0.41
44 21 0.36
45 2 0.03
ACGTcount: A:0.76, C:0.01, G:0.09, T:0.14
Consensus pattern (42 bp):
AATAAATAAAAAGAAATAAAAAAATAAAAAAAAGAGAAATAA
Found at i:233420 original size:4 final size:4
Alignment explanation
Indices: 233411--233476 Score: 53
Period size: 4 Copynumber: 15.0 Consensus size: 4
233401 AATAAAACAT
233411 AATA AATA AATA ACATAA AATA AATAA AATAA AATA AATA AAGTA AA-A
1 AATA AATA AATA A-AT-A AATA AAT-A AAT-A AATA AATA AA-TA AATA
*
233459 AAAA AGATAA AATA AATA
1 AATA A-AT-A AATA AATA
233477 TAAAAGGTAA
Statistics
Matches: 54, Mismatches: 1, Indels: 14
0.78 0.01 0.20
Matches are distributed among these distances:
3 3 0.06
4 27 0.50
5 20 0.37
6 4 0.07
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:233420 original size:14 final size:14
Alignment explanation
Indices: 233401--233452 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
233391 TAAAATGTAT
233401 AATAAAACATAATA
1 AATAAAACATAATA
233415 AATAAATAACATAAAATA
1 AAT-AA-AACAT--AATA
* *
233433 AATAAAATAAAATA
1 AATAAAACATAATA
233447 AATAAA
1 AATAAA
233453 GTAAAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
14 13 0.41
15 2 0.06
16 8 0.25
17 2 0.06
18 7 0.22
ACGTcount: A:0.75, C:0.04, G:0.00, T:0.21
Consensus pattern (14 bp):
AATAAAACATAATA
Found at i:233431 original size:10 final size:9
Alignment explanation
Indices: 233414--233476 Score: 60
Period size: 9 Copynumber: 7.0 Consensus size: 9
233404 AAAACATAAT
233414 AAATAAATA
1 AAATAAATA
*
233423 ACATAAA-A
1 AAATAAATA
233431 TAAATAAAATA
1 -AAAT-AAATA
233442 AAATAAATA
1 AAATAAATA
*
233451 AAGTAAA-A
1 AAATAAATA
233459 AAA-AAGATA
1 AAATAA-ATA
233468 AAATAAATA
1 AAATAAATA
233477 TAAAAGGTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
7 2 0.05
8 5 0.11
9 27 0.61
10 9 0.20
11 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (9 bp):
AAATAAATA
Found at i:233457 original size:14 final size:14
Alignment explanation
Indices: 233414--233476 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
233404 AAAACATAAT
233414 AAATAAATAACA-TA
1 AAATAAATAA-AGTA
*
233428 AAATAAATAAAATA
1 AAATAAATAAAGTA
233442 AAATAAATAAAGT-
1 AAATAAATAAAGTA
233455 AAA-AAA-AAAGATA
1 AAATAAATAAAG-TA
233468 AAATAAATA
1 AAATAAATA
233477 TAAAAGGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
11 4 0.09
12 4 0.09
13 7 0.16
14 27 0.63
15 1 0.02
ACGTcount: A:0.76, C:0.02, G:0.03, T:0.19
Consensus pattern (14 bp):
AAATAAATAAAGTA
Found at i:233523 original size:2 final size:2
Alignment explanation
Indices: 233516--233550 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
233506 AATAAAAATA
*
233516 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
233551 ATAAAAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:234693 original size:35 final size:35
Alignment explanation
Indices: 234641--235129 Score: 214
Period size: 36 Copynumber: 13.5 Consensus size: 35
234631 ATATTTTCAA
* *
234641 AAAATCTATATAATATATATTTTTTAAAAATATTTT
1 AAAA-CTATATATTATATATTTTTTAAAAATGTTTT
*
234677 AAAATTATATATTATATATATTTTTAAAAATGTTTT
1 AAAACTATATATTATATAT-TTTTTAAAAATGTTTT
* * * *
234713 ----C-A-AAATTATATAGTTTTCAAAAATATTTTT
1 AAAACTATATATTATATATTTTTTAAAAAT-GTTTT
* * *
234743 AAAACTATATATTATA-A-GTTTTCAAAATAATTTT
1 AAAACTATATATTATATATTTTTTAAAAAT-GTTTT
* * * * *
234777 AAAATTATATATGAT-TGA-TTTTCAAAAGTTTTTTT
1 AAAACTATATATTATAT-ATTTTTTAAAA-ATGTTTT
* * *
234812 AAAAACTATAATATATATATATGTTTTCAAAATGCTTT
1 -AAAACTAT-ATAT-TATATATTTTTTAAAAATGTTTT
* * * * * * *
234850 ATATATTATATATTTTCAAAATCTTTTAAAAA--CTAT
1 A-AAACTATATATTAT--ATATTTTTTAAAAATGTTTT
* * * *
234886 AATA-TATATATATATATATATATTGAAAAATGTTTA
1 AAAACTATATAT-TATATAT-TTTTTAAAAATGTTTT
*
234922 AAAACTATATATTATATTTATTTTTAAAAATGTTTT
1 AAAACTATATATTATATAT-TTTTTAAAAATGTTTT
* * * *
234958 AAAAACTGTATAATATATAAATGTTTTCAAAATGTTTT
1 -AAAACTATAT-AT-TATATATTTTTTAAAAATGTTTT
* *
234996 CGAAACTATATATTATATATATTTTAAAAATGTTTT
1 -AAAACTATATATTATATATTTTTTAAAAATGTTTT
* ** **
235032 CAAAAACTATATAATATATAAATTTTCGAAAACCGTTTTCT
1 --AAAACTATAT-AT-TATATATTTTTTAAAAATG-TTT-T
* * *
235073 GAAAATTATATATTATAT-TTTGTTAAAAACGTTTT
1 -AAAACTATATATTATATATTTTTTAAAAATGTTTT
*
235108 CAAAAACTATATTACTATATAT
1 --AAAACTATA-TATTATATAT
235130 ACATATATAA
Statistics
Matches: 341, Mismatches: 77, Indels: 68
0.70 0.16 0.14
Matches are distributed among these distances:
29 10 0.03
30 13 0.04
31 1 0.00
33 3 0.01
34 41 0.12
35 32 0.09
36 95 0.28
37 52 0.15
38 54 0.16
39 27 0.08
40 12 0.04
41 1 0.00
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
AAAACTATATATTATATATTTTTTAAAAATGTTTT
Found at i:234697 original size:37 final size:37
Alignment explanation
Indices: 234626--234724 Score: 128
Period size: 37 Copynumber: 2.6 Consensus size: 37
234616 AAATAAACTA
* *
234626 AAAATATATTTTCAAAAAATCTATATAATATATATTTTTT
1 AAAA-ATATTTTC-AAAATTATATATAATATATA-TTTTT
*
234666 AAAAATATTTT-AAAATTATATATTATATATATTTTT
1 AAAAATATTTTCAAAATTATATATAATATATATTTTT
*
234702 AAAAATGTTTTCAAAATTATATA
1 AAAAATATTTTCAAAATTATATA
234725 GTTTTCAAAA
Statistics
Matches: 54, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
36 15 0.28
37 28 0.52
39 7 0.13
40 4 0.07
ACGTcount: A:0.48, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
AAAAATATTTTCAAAATTATATATAATATATATTTTT
Found at i:234721 original size:30 final size:30
Alignment explanation
Indices: 234687--234788 Score: 93
Period size: 29 Copynumber: 3.3 Consensus size: 30
234677 AAAATTATAT
* *
234687 ATTATATATATTTTTAAAAATGTTTTCAAA
1 ATTATATATATTTTCAAAAATATTTTCAAA
* *
234717 ATTATATA-GTTTTCAAAAATATTTTTAAA
1 ATTATATATATTTTCAAAAATATTTTCAAA
234746 ACTATATATTATAAGTTTTC-AAAATAATTTT-AAA
1 A-T-TATA-TAT-A-TTTTCAAAAAT-ATTTTCAAA
234780 ATTATATAT
1 ATTATATAT
234789 GATTGATTTT
Statistics
Matches: 60, Mismatches: 5, Indels: 13
0.77 0.06 0.17
Matches are distributed among these distances:
29 18 0.30
30 9 0.15
31 7 0.12
32 6 0.10
33 1 0.02
34 9 0.15
35 10 0.17
ACGTcount: A:0.45, C:0.04, G:0.03, T:0.48
Consensus pattern (30 bp):
ATTATATATATTTTCAAAAATATTTTCAAA
Found at i:234785 original size:63 final size:67
Alignment explanation
Indices: 234654--234898 Score: 224
Period size: 65 Copynumber: 3.7 Consensus size: 67
234644 ATCTATATAA
* * * *
234654 TATATATTTTTTAAAAATA-TTTTAAAATTAT-ATATTATATATAT-TTTTAAAAAT-GTTTTCA
1 TATATAGTTTTCAAAAATATTTTTAAAACTATAATA-TATATATATGTTTTCAAAATAGTTTT-A
234715 AAAT
64 AAAT
*
234719 TATATAGTTTTCAAAAATATTTTTAAAACTAT-ATAT-TATA-A-GTTTTCAAAATAATTTTAAA
1 TATATAGTTTTCAAAAATATTTTTAAAACTATAATATATATATATGTTTTCAAAATAGTTTTAAA
234780 ATT
66 A-T
* * *
234783 ATATATGATTGATTTTCAAAAGTTTTTTTAAAAACTATAATATATATATATGTTTTCAAAAT-GC
1 -TATAT-A--G-TTTTCAAAAATATTTTT-AAAACTATAATATATATATATGTTTTCAAAATAGT
*
234847 TTTATATAT
60 TTTA-AAAT
* *
234856 TATATA-TTTTC-AAAATCTTTTAAAAACTATAATATATATATAT
1 TATATAGTTTTCAAAAATATTTTTAAAACTATAATATATATATAT
234899 ATATATATAT
Statistics
Matches: 152, Mismatches: 13, Indels: 30
0.78 0.07 0.15
Matches are distributed among these distances:
63 14 0.09
64 9 0.06
65 44 0.29
66 23 0.15
67 5 0.03
68 1 0.01
69 15 0.10
70 8 0.05
71 5 0.03
72 9 0.06
73 6 0.04
74 13 0.09
ACGTcount: A:0.44, C:0.04, G:0.03, T:0.49
Consensus pattern (67 bp):
TATATAGTTTTCAAAAATATTTTTAAAACTATAATATATATATATGTTTTCAAAATAGTTTTAAA
AT
Found at i:234877 original size:27 final size:28
Alignment explanation
Indices: 234822--234875 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
234812 AAAAACTATA
*
234822 ATATATATATATGTTTTCAAAATGCTTT
1 ATATATATATATATTTTCAAAATGCTTT
234850 ATATAT-TATATATTTTCAAAAT-CTTT
1 ATATATATATATATTTTCAAAATGCTTT
234876 TAAAAACTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 4 0.16
27 15 0.60
28 6 0.24
ACGTcount: A:0.37, C:0.07, G:0.04, T:0.52
Consensus pattern (28 bp):
ATATATATATATATTTTCAAAATGCTTT
Found at i:234886 original size:27 final size:27
Alignment explanation
Indices: 234829--234886 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
234819 ATAATATATA
* * * *
234829 TATATGTTTTCAAAATGCTTTATATAT
1 TATATATTTTCAAAATGCTTTAAAAAC
234856 TATATATTTTCAAAAT-CTTTTAAAAAC
1 TATATATTTTCAAAATGC-TTTAAAAAC
234883 TATA
1 TATA
234887 ATATATATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
26 1 0.04
27 25 0.96
ACGTcount: A:0.40, C:0.09, G:0.03, T:0.48
Consensus pattern (27 bp):
TATATATTTTCAAAATGCTTTAAAAAC
Done.