Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 9 of 202
Found at i:2996243 original size:18 final size:18
Alignment explanation
Indices: 2996209--2996434 Score: 92
Period size: 18 Copynumber: 11.8 Consensus size: 18
2996199 CCTTCCCTCT
*
2996209 TCTTCTTCTTT-TTTTTC
1 TCTTCTCCTTTCTTTTTC
2996226 TCTTCTCCTTTCTTTTTC
1 TCTTCTCCTTTCTTTTTC
*
2996244 TTTCTTTCTTTCTTTCTTTTT-
1 --TC-TTC-TCCTTTCTTTTTC
2996265 TCTTCTCCTTTCCTTTTCTTC
1 TCTTCTCCTTT-C-TTT-TTC
*
2996286 TTCTTTCTTTCTTTCTTTTTTTC
1 -TC-TTC-TCCTTTC--TTTTTC
* *
2996309 TGTTCTCCTTTCCTTTTC
1 TCTTCTCCTTTCTTTTTC
*
2996327 T-TTCCTTCTTT-TTCTTTC
1 TCTT-CTCCTTTCTT-TTTC
*
2996345 TTTCCTCTCCTTTCTTTTTTC
1 --TCTTCTCCTTTC-TTTTTC
* *
2996366 TGTTCTCCTTTCCTTTTC
1 TCTTCTCCTTTCTTTTTC
*
2996384 T-TTCCTTCTTT-TTCTTTC
1 TCTT-CTCCTTTCTT-TTTC
*
2996402 TTTCCTCTCCTTTCTTTCTT-
1 --TCTTCTCCTTTCTTT-TTC
2996422 TCTT-T-CTTTCTTT
1 TCTTCTCCTTTCTTT
2996435 CCCCCTCCTT
Statistics
Matches: 163, Mismatches: 19, Indels: 55
0.69 0.08 0.23
Matches are distributed among these distances:
16 8 0.05
17 22 0.13
18 45 0.28
19 15 0.09
20 25 0.15
21 16 0.10
22 16 0.10
23 7 0.04
24 9 0.06
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.70
Consensus pattern (18 bp):
TCTTCTCCTTTCTTTTTC
Found at i:2996309 original size:57 final size:55
Alignment explanation
Indices: 2996183--2996432 Score: 206
Period size: 57 Copynumber: 4.4 Consensus size: 55
2996173 AATACCTTTT
* * * * * * *
2996183 CTTTTTTTTTTTCCTTCCTTCCCTCTTC-TT-CTTCTTTTTTTTCTCTTCTCCTTTC
1 CTTTCTTTTTTTCTTTCTTTCTCTTTTCTTTCCTTCTTTTTCTT-TCTT-TCCTCTC
* * * * *
2996238 TTTTTCTTTCTTTCTTTCTTTCTTTTTTCTTCTCCTTTCCTTTTCTTCTTCTTT-CT-TT
1 -CTTTCTTTTTTTCTTTCTTTCTCTTTTCTT-TCC-TTCTTTTTC-T-TTCTTTCCTCTC
2996296 CTTTCTTTTTTTCTGTTCTCCTT-TCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
1 CTTTCTTTTTTTCT-TTCT--TTCT-CTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
*
2996354 CTTTCTTTTTTCTGTTCTCCTTTC-CTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
1 CTTTCTTTTTT-TCTT-T-CTTTCTCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
*
2996411 CTTTCTTTCTTTCTTTCTTTCT
1 CTTTCTTTTTTTCTTTCTTTCT
2996433 TTCCCCCTCC
Statistics
Matches: 158, Mismatches: 19, Indels: 35
0.75 0.09 0.17
Matches are distributed among these distances:
54 5 0.03
55 1 0.01
56 29 0.18
57 59 0.37
58 29 0.18
59 10 0.06
60 19 0.12
61 5 0.03
62 1 0.01
ACGTcount: A:0.00, C:0.30, G:0.01, T:0.69
Consensus pattern (55 bp):
CTTTCTTTTTTTCTTTCTTTCTCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTC
Found at i:2996446 original size:26 final size:28
Alignment explanation
Indices: 2996328--2996445 Score: 98
Period size: 30 Copynumber: 4.1 Consensus size: 28
2996318 TTCCTTTTCT
2996328 TTCCTTC-TTTTTCTTTCTTTCCTCTCC
1 TTCCTTCTTTTTTCTTTCTTTCCTCTCC
* * * * *
2996355 TTTCTTTTTTCTGTTC-TCCTTTCCTTTTCT
1 TTCCTTCTTT-T-TTCTTTCTTTCC-TCTCC
2996385 TTCCTTC-TTTTTCTTTCTTTCCTCTCC
1 TTCCTTCTTTTTTCTTTCTTTCCTCTCC
* *
2996412 TTTCTTTCTTTCTTTCTTTCTTTCCCCCTCC
1 -TTCCTTCTTT-TTTCTTTCTTT-CCTCTCC
2996443 TTC
1 TTC
2996446 TGGTCCCCCC
Statistics
Matches: 70, Mismatches: 12, Indels: 15
0.72 0.12 0.15
Matches are distributed among these distances:
27 11 0.16
28 16 0.23
29 12 0.17
30 25 0.36
31 6 0.09
ACGTcount: A:0.00, C:0.35, G:0.01, T:0.64
Consensus pattern (28 bp):
TTCCTTCTTTTTTCTTTCTTTCCTCTCC
Found at i:2996552 original size:27 final size:27
Alignment explanation
Indices: 2996475--2996553 Score: 95
Period size: 27 Copynumber: 2.9 Consensus size: 27
2996465 CCCCAATAAA
* *
2996475 CATTGGTGCCGCCAATGGTATTGGCGC
1 CATTGGTGCCGCCAATGGCATTGGCAC
* *
2996502 CAATGGTGCCGCCAATGGCTTTGGCAC
1 CATTGGTGCCGCCAATGGCATTGGCAC
* **
2996529 CTTTGGTGCCGCCAATCCCATTGGC
1 CATTGGTGCCGCCAATGGCATTGGC
2996554 GTGACCAAGG
Statistics
Matches: 43, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 43 1.00
ACGTcount: A:0.15, C:0.30, G:0.29, T:0.25
Consensus pattern (27 bp):
CATTGGTGCCGCCAATGGCATTGGCAC
Found at i:2996655 original size:23 final size:23
Alignment explanation
Indices: 2996625--2996668 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
2996615 TTTATTTTTT
2996625 TATATATTTTGGTAAATAAAATA
1 TATATATTTTGGTAAATAAAATA
2996648 TATATATTTTGGTAAATAAAA
1 TATATATTTTGGTAAATAAAA
2996669 AAAGTTATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
TATATATTTTGGTAAATAAAATA
Found at i:2998287 original size:16 final size:16
Alignment explanation
Indices: 2998237--2998288 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 16
2998227 GGGTGAGAAG
2998237 TAAAAGTTTAGAGGGAAAA
1 TAAAAGTTT-GAGGG--AA
2998256 TAAAAAGTTTTG-GGGAA
1 T-AAAAG-TTTGAGGGAA
2998273 TAAAAGTTTGAGGGAA
1 TAAAAGTTTGAGGGAA
2998289 AGTAAATAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
15 4 0.13
16 10 0.33
17 3 0.10
19 4 0.13
20 6 0.20
21 3 0.10
ACGTcount: A:0.46, C:0.00, G:0.29, T:0.25
Consensus pattern (16 bp):
TAAAAGTTTGAGGGAA
Found at i:2998408 original size:31 final size:30
Alignment explanation
Indices: 2998373--2998432 Score: 75
Period size: 30 Copynumber: 2.0 Consensus size: 30
2998363 GGAGGTGGGA
*
2998373 TGGGAAGAGAATAAAAGTTTTAGGGGAAAAG
1 TGGG-AGAGAATAAAAATTTTAGGGGAAAAG
* * *
2998404 TGGGAGGGAGTAAAAATTTTGGGGGAAAA
1 TGGGAGAGAATAAAAATTTTAGGGGAAAA
2998433 TAAAAGGCTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.42, C:0.00, G:0.38, T:0.20
Consensus pattern (30 bp):
TGGGAGAGAATAAAAATTTTAGGGGAAAAG
Found at i:2998644 original size:9 final size:9
Alignment explanation
Indices: 2998630--2998666 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
2998620 TATAGTTTGA
2998630 TATTCGAAT
1 TATTCGAAT
2998639 TATTCGAAT
1 TATTCGAAT
*
2998648 TATTCGAGT
1 TATTCGAAT
2998657 TATTCGAAT
1 TATTCGAAT
2998666 T
1 T
2998667 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:2998737 original size:9 final size:9
Alignment explanation
Indices: 2998720--2998750 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
2998710 TTGAGTTGAT
2998720 TCGAATAAC
1 TCGAATAAC
*
2998729 TCGATTAAC
1 TCGAATAAC
2998738 TCGAATAAC
1 TCGAATAAC
2998747 TCGA
1 TCGA
2998751 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3001938 original size:9 final size:9
Alignment explanation
Indices: 3001924--3001954 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3001914 GTTAAACAAA
3001924 TCGAGTTAT
1 TCGAGTTAT
*
3001933 TCGAGTTAA
1 TCGAGTTAT
3001942 TCGAGTTAT
1 TCGAGTTAT
3001951 TCGA
1 TCGA
3001955 ATCAACTCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:3002032 original size:9 final size:9
Alignment explanation
Indices: 3002008--3002044 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
3001998 TGAGATTTCG
*
3002008 AATTCTAAT
1 AATTCGAAT
*
3002017 AACTCGAAT
1 AATTCGAAT
3002026 AATTCGAAT
1 AATTCGAAT
3002035 AATTCGAAT
1 AATTCGAAT
3002044 A
1 A
3002045 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.14, G:0.08, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:3002778 original size:192 final size:193
Alignment explanation
Indices: 3002450--3002833 Score: 716
Period size: 192 Copynumber: 2.0 Consensus size: 193
3002440 CCCTCTAAAC
*
3002450 TTTTACTTCTCACCCTTTACTCTCAAATAAAAAATCAAAATTATCCAAAAAAAAAATCACTAAGT
1 TTTTACTTCTCACCCTTTACTCTCAAAGAAAAAATCAAAATTATCCAAAAAAAAAATCACTAAGT
3002515 TTAATTATGCCATAAAATATTCATGTTAAAATTTTATATTGGTATTAATTTCACATTTTATTTTT
66 TTAATTATGCCATAAAATATTCATGTTAAAATTTTATATTGGTATTAATTTCACATTTTATTTTT
*
3002580 AAAATAATTTTTATTAAAAAAATCATATTTTTACATTTAATATATTTTTTAATTCCAAAATAA
131 AAAATAACTTTTATTAAAAAAATCATATTTTTACATTTAATATATTTTTTAATTCCAAAATAA
* *
3002643 TTTTACTTCTCACCCTTTACTCTCAAAGAAAAATTTAAAATTAT-CAAAAAAAAAATCACTAAGT
1 TTTTACTTCTCACCCTTTACTCTCAAAGAAAAAATCAAAATTATCCAAAAAAAAAATCACTAAGT
3002707 TTAATTATGCCATAAAATATTCATGTTAAAATTTTATATTGGTATTAATTTCACATTTTATTTTT
66 TTAATTATGCCATAAAATATTCATGTTAAAATTTTATATTGGTATTAATTTCACATTTTATTTTT
*
3002772 AAAATAACTTTTATTAAAAAAGTCATATTTTTACATTTAATATATTTTTTAATTCCAAAATA
131 AAAATAACTTTTATTAAAAAAATCATATTTTTACATTTAATATATTTTTTAATTCCAAAATA
3002834 CATAGTGATA
Statistics
Matches: 186, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
192 145 0.78
193 41 0.22
ACGTcount: A:0.42, C:0.12, G:0.03, T:0.43
Consensus pattern (193 bp):
TTTTACTTCTCACCCTTTACTCTCAAAGAAAAAATCAAAATTATCCAAAAAAAAAATCACTAAGT
TTAATTATGCCATAAAATATTCATGTTAAAATTTTATATTGGTATTAATTTCACATTTTATTTTT
AAAATAACTTTTATTAAAAAAATCATATTTTTACATTTAATATATTTTTTAATTCCAAAATAA
Found at i:3003326 original size:15 final size:16
Alignment explanation
Indices: 3003302--3003334 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
3003292 CGCTTTTAAA
3003302 ATTATAATAC-TTTAT
1 ATTATAATACTTTTAT
*
3003317 ATTATGATACTTTTAT
1 ATTATAATACTTTTAT
3003333 AT
1 AT
3003335 ATTAAGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 9 0.56
16 7 0.44
ACGTcount: A:0.36, C:0.06, G:0.03, T:0.55
Consensus pattern (16 bp):
ATTATAATACTTTTAT
Found at i:3006126 original size:177 final size:173
Alignment explanation
Indices: 3005732--3006183 Score: 473
Period size: 173 Copynumber: 2.6 Consensus size: 173
3005722 TTTTAACCCC
* ** * * * *
3005732 TCTACCTTTTTATGATTATATAAGAATAGTTAAATTTCAGTTTTAATCCCTATATTTCACTCAAG
1 TCTACCTTTTTAAGACCATATAAAAATAGTTAAATTTCAATTTTGATCCCTATATTTCACTCAAA
* * * * * *
3005797 TTTGATATTTAATATCTGCACTTAAATTTTTACATAATTTAAACACCTATACATTTTTTATCTTC
66 TTTGAAATTTAATCTCTACACTTTAATTTTAACATAATCTAAACACCTATACATTTTTTATCTTC
* * * ** * *
3005862 CTTTTGACTTAAAAATTAATGGTTTAATTTCAATAGCAATCCC
131 CTTTTAACATAAAAAATAATGACTAAATTTCAATAGCAATCCA
* *
3005905 TCTACCTTTTTAAGATCATATAAAAAT-GATTAAAATTT-AATTTTGATCCCTATATTTTACTCA
1 TCTACCTTTTTAAGACCATATAAAAATAG-TT-AAATTTCAATTTTGATCCCTATATTTCACTCA
* * * * * * *
3005968 AATTTAAAATTTAATCCCTACACTTTAATTTTAATATAATCTAAACACTTGTCCATTCTTTTTTC
64 AATTTGAAATTTAATCTCTACACTTTAATTTTAACATAATCTAAACACCTATACA---TTTTTTA
* *
3006033 TCTATTCTTTTAACATAAGAAAATAATGACTAAATTTCAAT-TCTAATCCA
126 TCT-TCCTTTTAACATAA-AAAATAATGACTAAATTTCAATAGC-AATCCA
*
3006083 TCTA-CTTTTTAAGACCATATAAAAATAGTTAAATTTCAATTTTGACCCCTATATTTCACTCAAA
1 TCTACCTTTTTAAGACCATATAAAAATAGTTAAATTTCAATTTTGATCCCTATATTTCACTCAAA
* * * *
3006147 TTTGAGATTTGATCTCTATA-TTTAATTTTGACATAAT
66 TTTGAAATTTAATCTCTACACTTTAATTTTAACATAAT
3006184 TCAAATTAAA
Statistics
Matches: 230, Mismatches: 39, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
172 1 0.00
173 90 0.39
174 6 0.03
176 30 0.13
177 75 0.33
178 28 0.12
ACGTcount: A:0.35, C:0.16, G:0.05, T:0.44
Consensus pattern (173 bp):
TCTACCTTTTTAAGACCATATAAAAATAGTTAAATTTCAATTTTGATCCCTATATTTCACTCAAA
TTTGAAATTTAATCTCTACACTTTAATTTTAACATAATCTAAACACCTATACATTTTTTATCTTC
CTTTTAACATAAAAAATAATGACTAAATTTCAATAGCAATCCA
Found at i:3006329 original size:14 final size:13
Alignment explanation
Indices: 3006296--3006325 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3006286 ACACTAGCAA
3006296 ATTTAACATAAGG
1 ATTTAACATAAGG
3006309 ATTTAACATAAGG
1 ATTTAACATAAGG
3006322 ATTT
1 ATTT
3006326 TAACGATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.43, C:0.07, G:0.13, T:0.37
Consensus pattern (13 bp):
ATTTAACATAAGG
Found at i:3007316 original size:30 final size:28
Alignment explanation
Indices: 3007275--3007333 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 28
3007265 AAACTATAAT
* *
3007275 TGGTATTCAAATAAGCCCTTAATCTTTAAC
1 TGGTATCCAAATAAG-CCTTAA-CCTTAAC
3007305 TGGTATCCAAATAAGCCTTAACCTTAAC
1 TGGTATCCAAATAAGCCTTAACCTTAAC
3007333 T
1 T
3007334 TATACCTAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
28 7 0.26
29 6 0.22
30 14 0.52
ACGTcount: A:0.34, C:0.22, G:0.10, T:0.34
Consensus pattern (28 bp):
TGGTATCCAAATAAGCCTTAACCTTAAC
Found at i:3013792 original size:123 final size:123
Alignment explanation
Indices: 3013572--3013909 Score: 597
Period size: 123 Copynumber: 2.7 Consensus size: 123
3013562 TTAACATTTT
*
3013572 TGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGCGAAATCGCGCC
1 TGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCC
*
3013637 CTTGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTTGACGTTTC
66 CTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAA-TTTTTTTGACGTTTC
* *
3013696 TGAGCAAATAGTAT-AAATCGCTTCTACCAGGATGCTATTTGAGAAGAAACTGTGAAATCGTGCC
1 TGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCC
*
3013760 CTCGTGGACGCGATTTTGCTACAGTTGGTCATGTAAGAAATAATTTTTTTGACGTTTC
66 CTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACGTTTC
* *
3013818 TGAGCAAATAGTATAAAATCGTTTCTACCAGGATGCTATTTGAGAAGAAATTATGAAATCGCGCC
1 TGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCC
3013883 CTCGTGGACGCGATTTTGCTACAGTAG
66 CTCGTGGACGCGATTTTGCTACAGTAG
3013910 CAAGTTTGTG
Statistics
Matches: 203, Mismatches: 10, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
122 29 0.14
123 160 0.79
124 14 0.07
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (123 bp):
TGAGCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAATCGCGCC
CTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTTTTTTGACGTTTC
Found at i:3016812 original size:35 final size:29
Alignment explanation
Indices: 3016726--3016876 Score: 185
Period size: 29 Copynumber: 4.8 Consensus size: 29
3016716 ATTTTAAGCT
* *
3016726 GTTAAGGTTTTTAATTAAATTAGGTTAGG
1 GTTAGGGTTTTTAATTAAATTAGGTTAGA
3016755 GTTAGAGTAGAGTTTTTAATTAAATTAGGTTAAGGTTA
1 GTT--AG--G-GTTTTTAATTAAATTAGGTT-A-G--A
3016793 GGGTTAGGGTTTTTAATTAAATTAGGTTAGA
1 --GTTAGGGTTTTTAATTAAATTAGGTTAGA
3016824 GTTAGGGTTTTTAATTAAATTAGGTTAGA
1 GTTAGGGTTTTTAATTAAATTAGGTTAGA
3016853 GTTAGGGTTTTTAATTAAATTAGG
1 GTTAGGGTTTTTAATTAAATTAGG
3016877 GTTTTTATTA
Statistics
Matches: 109, Mismatches: 2, Indels: 22
0.82 0.02 0.17
Matches are distributed among these distances:
29 56 0.51
31 2 0.02
33 2 0.02
34 21 0.19
35 21 0.19
36 2 0.02
38 2 0.02
40 3 0.03
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (29 bp):
GTTAGGGTTTTTAATTAAATTAGGTTAGA
Found at i:3016962 original size:36 final size:36
Alignment explanation
Indices: 3016922--3017036 Score: 92
Period size: 36 Copynumber: 3.2 Consensus size: 36
3016912 ATATCAAATA
*
3016922 ATATCAAAATAACTCGAAAAAATTTCTATGCCTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
* **** * * *
3016958 ATATC-AAATAAACTTCTATTTTATTAC-AT-CAAATA
1 ATATCAAAAT-AAC-TCGAAAAAATTTCTATGCATATT
*
3016993 ATATCAAAATAACTCGAAAAAATTTCTATGCGTATT
1 ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
*
3017029 ACATCAAA
1 ATATCAAA
3017037 TAAACTTCTA
Statistics
Matches: 55, Mismatches: 19, Indels: 10
0.65 0.23 0.12
Matches are distributed among these distances:
34 7 0.13
35 17 0.31
36 24 0.44
37 7 0.13
ACGTcount: A:0.46, C:0.16, G:0.04, T:0.34
Consensus pattern (36 bp):
ATATCAAAATAACTCGAAAAAATTTCTATGCATATT
Found at i:3016988 original size:25 final size:25
Alignment explanation
Indices: 3016954--3017064 Score: 83
Period size: 25 Copynumber: 4.6 Consensus size: 25
3016944 TTTCTATGCC
*
3016954 TATTATATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
*
3016979 TATTACATCAAAT-AA-TATC-A--A
1 TATTACATCAAATAAACT-TCTATTT
* * * **
3017000 AATAAC-TCGAAA-AAATTTCTATGCG
1 TATTACATC-AAATAAACTTCTAT-TT
3017025 TATTACATCAAATAAACTTCTATTT
1 TATTACATCAAATAAACTTCTATTT
3017050 TATTACATCAAATAA
1 TATTACATCAAATAA
3017065 TAAATTTAAA
Statistics
Matches: 66, Mismatches: 10, Indels: 20
0.69 0.10 0.21
Matches are distributed among these distances:
20 2 0.03
21 11 0.17
22 2 0.03
23 2 0.03
24 4 0.06
25 34 0.52
26 11 0.17
ACGTcount: A:0.45, C:0.14, G:0.03, T:0.38
Consensus pattern (25 bp):
TATTACATCAAATAAACTTCTATTT
Found at i:3016989 original size:71 final size:71
Alignment explanation
Indices: 3016882--3017066 Score: 334
Period size: 71 Copynumber: 2.6 Consensus size: 71
3016872 TTAGGGTTTT
*
3016882 TATTACATCAAATAGAACTTCTATTTTATTATATCAAATAATATCAAAATAACTCGAAAAAATTT
1 TATTACATCAAATA-AACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTT
3016947 CTATGCC
65 CTATGCC
*
3016954 TATTATATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
*
3017019 TATGCG
66 TATGCC
3017025 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
1 TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATA
3017067 AATTTAAATA
Statistics
Matches: 109, Mismatches: 4, Indels: 1
0.96 0.04 0.01
Matches are distributed among these distances:
71 96 0.88
72 13 0.12
ACGTcount: A:0.45, C:0.15, G:0.03, T:0.37
Consensus pattern (71 bp):
TATTACATCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAACTCGAAAAAATTTC
TATGCC
Found at i:3018158 original size:7 final size:7
Alignment explanation
Indices: 3018148--3018172 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
3018138 TTATATACAT
3018148 AATACTA
1 AATACTA
3018155 AATACTA
1 AATACTA
3018162 AATACTA
1 AATACTA
3018169 AATA
1 AATA
3018173 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:3019272 original size:10 final size:10
Alignment explanation
Indices: 3019253--3019317 Score: 58
Period size: 10 Copynumber: 6.5 Consensus size: 10
3019243 GCCATTGATG
*
3019253 AAAATATAAA
1 AAAATTTAAA
3019263 AAAATTTAAA
1 AAAATTTAAA
** *
3019273 ATTATTTTAA
1 AAAATTTAAA
*
3019283 AAAATATAAA
1 AAAATTTAAA
3019293 AAAATTTAAA
1 AAAATTTAAA
** *
3019303 ATTATTTTAA
1 AAAATTTAAA
3019313 AAAAT
1 AAAAT
3019318 GAAATTGAGG
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
10 41 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (10 bp):
AAAATTTAAA
Found at i:3019287 original size:30 final size:30
Alignment explanation
Indices: 3019253--3019317 Score: 130
Period size: 30 Copynumber: 2.2 Consensus size: 30
3019243 GCCATTGATG
3019253 AAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
3019283 AAAATATAAAAAAATTTAAAATTATTTTAA
1 AAAATATAAAAAAATTTAAAATTATTTTAA
3019313 AAAAT
1 AAAAT
3019318 GAAATTGAGG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (30 bp):
AAAATATAAAAAAATTTAAAATTATTTTAA
Found at i:3019373 original size:51 final size:51
Alignment explanation
Indices: 3019318--3019439 Score: 192
Period size: 51 Copynumber: 2.4 Consensus size: 51
3019308 TTTAAAAAAT
* *
3019318 GAAATTGAGGGGAAATTGAAATTAAATATGGATTTTAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
*
3019369 GAAATTGAGAGGAAATTGAAATTAAATATGGGTTTGAGAGAATTTTGGAAG
1 GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
3019420 GAAATTTG-GAAGGAAATTGA
1 GAAA-TTGAG-AGGAAATTGA
3019440 GAGGATTAGA
Statistics
Matches: 66, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
51 53 0.80
52 13 0.20
ACGTcount: A:0.42, C:0.00, G:0.29, T:0.30
Consensus pattern (51 bp):
GAAATTGAGAGGAAATTGAAATTAAATATGGATTTGAGAGAATTTTGGAAG
Found at i:3019429 original size:12 final size:12
Alignment explanation
Indices: 3019412--3019437 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3019402 TTGAGAGAAT
3019412 TTTGGAAGGAAA
1 TTTGGAAGGAAA
3019424 TTTGGAAGGAAA
1 TTTGGAAGGAAA
3019436 TT
1 TT
3019438 GAGAGGATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (12 bp):
TTTGGAAGGAAA
Found at i:3020538 original size:17 final size:19
Alignment explanation
Indices: 3020511--3020547 Score: 60
Period size: 17 Copynumber: 2.1 Consensus size: 19
3020501 AATTGGTTTG
3020511 ATTTAAAAAATATT-AAAA
1 ATTTAAAAAATATTCAAAA
3020529 ATTT-AAAAATATTCAAAA
1 ATTTAAAAAATATTCAAAA
3020547 A
1 A
3020548 AAGAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (19 bp):
ATTTAAAAAATATTCAAAA
Found at i:3021572 original size:31 final size:30
Alignment explanation
Indices: 3021481--3021573 Score: 75
Period size: 31 Copynumber: 3.1 Consensus size: 30
3021471 AGCACCTAAA
* * * *
3021481 TTATACATGAACTTTT-ATCTAATGTACAATG
1 TTATACATGAA-TTTTAATTTGATAT-CAATT
*
3021512 TTATACATGAATTTTAATTTTATAT-AATT
1 TTATACATGAATTTTAATTTGATATCAATT
*
3021541 TTATACATGAAAATTTTGATTTGAT-TCAATT
1 TTATACATG--AATTTTAATTTGATATCAATT
3021572 TT
1 TT
3021574 CATAAATCAC
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
29 12 0.23
30 5 0.10
31 35 0.67
ACGTcount: A:0.35, C:0.08, G:0.08, T:0.49
Consensus pattern (30 bp):
TTATACATGAATTTTAATTTGATATCAATT
Found at i:3022142 original size:20 final size:17
Alignment explanation
Indices: 3022102--3022145 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
3022092 TCTCTTTCAG
*
3022102 TAAAAAGATATAAAAAA
1 TAAAAAAATATAAAAAA
3022119 TAAAAAAATCATAAAAGAA
1 TAAAAAAAT-ATAAAA-AA
3022138 TTAAAAAA
1 -TAAAAAA
3022146 GAACAATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 8 0.35
18 6 0.26
19 2 0.09
20 7 0.30
ACGTcount: A:0.75, C:0.02, G:0.05, T:0.18
Consensus pattern (17 bp):
TAAAAAAATATAAAAAA
Found at i:3022213 original size:26 final size:25
Alignment explanation
Indices: 3022184--3022232 Score: 64
Period size: 24 Copynumber: 1.9 Consensus size: 25
3022174 TATAAAACTC
3022184 TAAAAAATATATAAAAATGA-AAATTT
1 TAAAAAA-A-ATAAAAATGATAAATTT
*
3022210 TAAAAAAAATTAAAATGATAAAT
1 TAAAAAAAATAAAAATGATAAAT
3022233 AATTATCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 9 0.43
25 5 0.24
26 7 0.33
ACGTcount: A:0.67, C:0.00, G:0.04, T:0.29
Consensus pattern (25 bp):
TAAAAAAAATAAAAATGATAAATTT
Found at i:3026382 original size:17 final size:18
Alignment explanation
Indices: 3026360--3026394 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3026350 GGAGAAACAT
*
3026360 AATTTGC-ATAAATATAA
1 AATTTGCAATAAAGATAA
3026377 AATTTGCAATAAAGATAA
1 AATTTGCAATAAAGATAA
3026395 TTTACATTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.54, C:0.06, G:0.09, T:0.31
Consensus pattern (18 bp):
AATTTGCAATAAAGATAA
Found at i:3027589 original size:3 final size:3
Alignment explanation
Indices: 3027576--3027609 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
3027566 GTGTTAACCT
3027576 TAA TGAA TAA TAA TAA TAA TAA TAA TAA T-A TAA T
1 TAA T-AA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
3027610 TAAAATTAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:3028860 original size:14 final size:13
Alignment explanation
Indices: 3028839--3028887 Score: 50
Period size: 13 Copynumber: 3.9 Consensus size: 13
3028829 AAGGTAACCA
3028839 AATATTTAAATAT
1 AATATTTAAATAT
3028852 AATTATTT-AA-A-
1 AA-TATTTAAATAT
3028863 AATATTTAAATAT
1 AATATTTAAATAT
* *
3028876 AAAATATAAATA
1 AATATTTAAATA
3028888 ATCCTTCATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
10 5 0.17
11 4 0.13
12 2 0.07
13 14 0.47
14 5 0.17
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (13 bp):
AATATTTAAATAT
Found at i:3031429 original size:39 final size:39
Alignment explanation
Indices: 3031370--3031453 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
3031360 TTTTATATCC
*
3031370 AGTGCTCAATTCAATGGAGAAGAGCAAATCTCTGCACAT
1 AGTGATCAATTCAATGGAGAAGAGCAAATCTCTGCACAT
3031409 AGTGATCAATTCAATGGAGAAGAGCAAATCTCTGCACAT
1 AGTGATCAATTCAATGGAGAAGAGCAAATCTCTGCACAT
3031448 AGTGAT
1 AGTGAT
3031454 GTTCCCATGG
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.37, C:0.18, G:0.21, T:0.24
Consensus pattern (39 bp):
AGTGATCAATTCAATGGAGAAGAGCAAATCTCTGCACAT
Found at i:3051291 original size:24 final size:24
Alignment explanation
Indices: 3051264--3051310 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
3051254 TAGTCGTTAT
*
3051264 ATGTTAGATCCAAGGGTAAATTGG
1 ATGTTAGATCCAAGAGTAAATTGG
*
3051288 ATGTTAGATCTAAGAGTAAATTG
1 ATGTTAGATCCAAGAGTAAATTG
3051311 ATCTTTTCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.36, C:0.06, G:0.26, T:0.32
Consensus pattern (24 bp):
ATGTTAGATCCAAGAGTAAATTGG
Found at i:3055639 original size:153 final size:152
Alignment explanation
Indices: 3055458--3055808 Score: 569
Period size: 153 Copynumber: 2.3 Consensus size: 152
3055448 GACATGTTCG
* * * *
3055458 TATTTCAGCCATTTGTTCATATTTTTTTCTCGAATTTTATTACTTTAAAAAATATACTATTTTAT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAATATACTATTTTAT
* * *
3055523 AATTTTATTATTTTACATTATTTTAGTAGATTATGTTTGAAATGTATTCATTTAGTG-TGTTTTT
66 AATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTGTTTTT
**
3055587 TATTTAAATTTAAAAAAAAACCCT
131 TAAATAAA-TT-AAAAAAAACCCT
*
3055611 TATTTCGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTATTTTAAAAAATATACTATTTTAT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAATATACTATTTTAT
3055676 AATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTGTTTTT
66 AATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTGTTTTT
*
3055741 TAAATAAATTAAAAAAAACTCT
131 TAAATAAATTAAAAAAAACCCT
*
3055763 TATTTCGGCCCTTTGTTCGTATTTTTTTCCCGGATTTTATTACTTT
1 TATTTCGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTT
3055809 CAATAAAAAA
Statistics
Matches: 184, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
152 55 0.30
153 116 0.63
154 13 0.07
ACGTcount: A:0.29, C:0.09, G:0.09, T:0.53
Consensus pattern (152 bp):
TATTTCGGCCCTTTGTTCGTATTTTTTTCTCGGATTTTATTACTTTAAAAAATATACTATTTTAT
AATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTAATTTAGTGTTGTTTTT
TAAATAAATTAAAAAAAACCCT
Found at i:3056891 original size:150 final size:151
Alignment explanation
Indices: 3056574--3057055 Score: 670
Period size: 150 Copynumber: 3.2 Consensus size: 151
3056564 NNNNNNNNNN
* * *
3056574 ATAATGTAAAATTAGAAAATTAGAAAATAATATATTTTTATTGAAAGTAATAAAA-TCTGGGAAA
1 ATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTT-TT-AAAGTAATAAAATTC-GGGAAA
* * * *
3056638 AAAATATGAA-AAAGGACCGAAATAAGGATTTTTTTAAAATTTATTTAAAAAATACACTAAATGA
63 AAAATACGAACAAAGG-CCGAAATAAGGGTTTTTTT-TAATTTATTTAAAAAACACACTAAATGA
3056702 ATACATTTCAAACATAATGTACTAAA
126 ATACATTTCAAACATAATGTACTAAA
*
3056728 ATAATATAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGGAAAAAA
1 ATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGGAAAAAA
* * *
3056793 ATACGAACAAATAGCCGAAATAAGGGTTTTTTTTAATTTATTTAAAAAA-A-AGTAAATTAATAC
66 ATACGAACAAA-GGCCGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACACTAAATGAATAC
*
3056856 ATTTCAAGCATAATGTACTAAA
130 ATTTCAAACATAATGTACTAAA
* *
3056878 ATAATGTAAAATAATAAAATTAGAAAATAGTAT-TTTTTTTAAAGTAATAAAATCCCGGAAAAAA
1 ATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGGAAAAAA
* * *
3056942 ATACGAACAAAGGGCCGAAATAAGAG-TTTTTTTAATTTAAATAAAAAAACACACTAAATGAATA
66 ATACGAACAAA-GGCCGAAATAAGGGTTTTTTTTAATTT-ATTTAAAAAACACACTAAATGAATA
* * *
3057006 CATTTTAAACATAATCTATTAAA
129 CATTTCAAACATAATGTACTAAA
3057029 ATAATGTAAAATAATAAAATTAGAAAA
1 ATAATGTAAAATAATAAAATTAGAAAA
3057056 AAAGTGTACT
Statistics
Matches: 297, Mismatches: 25, Indels: 15
0.88 0.07 0.04
Matches are distributed among these distances:
148 12 0.04
149 60 0.20
150 65 0.22
151 57 0.19
152 42 0.14
153 25 0.08
154 36 0.12
ACGTcount: A:0.53, C:0.06, G:0.10, T:0.31
Consensus pattern (151 bp):
ATAATGTAAAATAATAAAATTAGAAAATAGTATATTTTTTTAAAGTAATAAAATTCGGGAAAAAA
ATACGAACAAAGGCCGAAATAAGGGTTTTTTTTAATTTATTTAAAAAACACACTAAATGAATACA
TTTCAAACATAATGTACTAAA
Found at i:3058385 original size:33 final size:33
Alignment explanation
Indices: 3058333--3058414 Score: 114
Period size: 33 Copynumber: 2.5 Consensus size: 33
3058323 TCTTCATCTT
3058333 AATTTCTCTTAG-ATATCTTCATGAATTCTT-AA
1 AATTTCTCTTAGAAT-TCTTCATGAATTCTTCAA
* *
3058365 AAGTTTCTCTAAGAATTCTTCATGAATTCTTCAT
1 AA-TTTCTCTTAGAATTCTTCATGAATTCTTCAA
3058399 AATTTCTCTTAGAATT
1 AATTTCTCTTAGAATT
3058415 TCTAATACAC
Statistics
Matches: 44, Mismatches: 3, Indels: 5
0.85 0.06 0.10
Matches are distributed among these distances:
32 2 0.05
33 37 0.84
34 5 0.11
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.46
Consensus pattern (33 bp):
AATTTCTCTTAGAATTCTTCATGAATTCTTCAA
Found at i:3059093 original size:63 final size:63
Alignment explanation
Indices: 3059020--3059147 Score: 220
Period size: 63 Copynumber: 2.0 Consensus size: 63
3059010 GAATATATTG
*
3059020 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCACGGTTTA
1 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCACGGTGTA
* * *
3059083 AGTTAGTTTCAAATTGAGAAGCATTTCAACTGAAAACACAACTAAGATTATAATCATGGTGTA
1 AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCACGGTGTA
3059146 AG
1 AG
3059148 GTGGTAATCA
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 61 1.00
ACGTcount: A:0.43, C:0.13, G:0.14, T:0.30
Consensus pattern (63 bp):
AGTTAGTTTCAAATTGAGAAACATTTCAACTAAAAACACAACTAAGATTATAATCACGGTGTA
Found at i:3071396 original size:24 final size:25
Alignment explanation
Indices: 3071354--3071405 Score: 70
Period size: 24 Copynumber: 2.1 Consensus size: 25
3071344 TGTATCGGGT
* *
3071354 AGCTCCGAAGAGCATTTAA-CAGGA
1 AGCTCCGAAGAGCACTTAATCAGAA
*
3071378 AGCTCCGAAGAGTACTTAATCAGAA
1 AGCTCCGAAGAGCACTTAATCAGAA
3071403 AGC
1 AGC
3071406 ACCGGATAAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
24 17 0.71
25 7 0.29
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.17
Consensus pattern (25 bp):
AGCTCCGAAGAGCACTTAATCAGAA
Found at i:3076776 original size:2 final size:2
Alignment explanation
Indices: 3076769--3076794 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
3076759 AATGCACCAT
3076769 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
3076795 AATTGATATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3078385 original size:20 final size:20
Alignment explanation
Indices: 3078362--3078759 Score: 97
Period size: 20 Copynumber: 19.8 Consensus size: 20
3078352 TTTATATCCT
3078362 CTCATAATTTTTGGTACTTC
1 CTCATAATTTTTGGTACTTC
* **
3078382 CTCAT-TTTTTTTATA-TTC
1 CTCATAATTTTTGGTACTTC
**
3078400 CTCATAATTTTCCGTACATT-
1 CTCATAATTTTTGGTAC-TTC
* ** *
3078420 CTCGTGTTTTTTAGTA-TTC
1 CTCATAATTTTTGGTACTTC
* *
3078439 CATCATAAATTTTGATACTTC
1 C-TCATAATTTTTGGTACTTC
* *
3078460 CTCA-AGTTTTATAGTA-TTC
1 CTCATAATTTT-TGGTACTTC
* * *
3078479 TCTCGTCATTTTTTGTA-TTCC
1 -CTCATAATTTTTGGTACTT-C
*
3078500 CTCATAATTTTTCGTACTTC
1 CTCATAATTTTTGGTACTTC
* * * *
3078520 ATCATATGTTTTGTGGCACATC
1 CTCATA-ATTTT-TGGTACTTC
* * * * *
3078542 TTTAAAAATTTTGGTACATC
1 CTCATAATTTTTGGTACTTC
** *
3078562 CTCATTTTTTTTTTGTA-TTC
1 CTCA-TAATTTTTGGTACTTC
3078582 CTTCAT-ATTTTCTGGTACTTC
1 C-TCATAATTTT-TGGTACTTC
* *
3078603 CTCATATGTTTTATGGTACATC
1 CTCATA-ATTTT-TGGTACTTC
* * * *
3078625 TTTAAAATTTTTGGTACATC
1 CTCATAATTTTTGGTACTTC
**
3078645 CTCAT--TTTTTTATACTT-
1 CTCATAATTTTTGGTACTTC
* * *
3078662 C-CATAGGTATTATGATA-TTC
1 CTCATA-AT-TTTTGGTACTTC
* * *
3078682 TCTCATAATTTTTGATATTTT
1 -CTCATAATTTTTGGTACTTC
* * *
3078703 CTCGTATTTTTTAGTA-TTC
1 CTCATAATTTTTGGTACTTC
* *
3078722 TCTCATAATTTTTTGTGCTTC
1 -CTCATAATTTTTGGTACTTC
*
3078743 CTCATATTTTTTTGGTA
1 CTCATA-ATTTTTGGTA
3078760 ATTTCTAATT
Statistics
Matches: 268, Mismatches: 80, Indels: 59
0.66 0.20 0.14
Matches are distributed among these distances:
16 3 0.01
17 1 0.00
18 19 0.07
19 30 0.11
20 135 0.50
21 52 0.19
22 28 0.10
ACGTcount: A:0.21, C:0.17, G:0.09, T:0.53
Consensus pattern (20 bp):
CTCATAATTTTTGGTACTTC
Found at i:3078393 original size:39 final size:38
Alignment explanation
Indices: 3078350--3078469 Score: 116
Period size: 38 Copynumber: 3.1 Consensus size: 38
3078340 TCCTCGTAAA
*
3078350 TTTTTATATCCTCTCATAATTTTTGGTACTTCCTCATTT
1 TTTTTATATCC-CTCATAATTTTTGGTACTTCCTCATGT
* ** *
3078389 TTTTTATATTCCTCATAATTTTCCGTACATT-CTCGTGT
1 TTTTTATATCCCTCATAATTTTTGGTAC-TTCCTCATGT
* * * *
3078427 TTTTTAGTATTCCATCATAAATTTTGATACTTCCTCAAGT
1 TTTTTA-TA-TCCCTCATAATTTTTGGTACTTCCTCATGT
3078467 TTT
1 TTT
3078470 ATAGTATTCT
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
38 26 0.41
39 16 0.25
40 22 0.34
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (38 bp):
TTTTTATATCCCTCATAATTTTTGGTACTTCCTCATGT
Found at i:3078410 original size:18 final size:18
Alignment explanation
Indices: 3078348--3078410 Score: 63
Period size: 18 Copynumber: 3.3 Consensus size: 18
3078338 TATCCTCGTA
*
3078348 AATTTTTATATCCTCTCAT
1 AATTTTTATATTC-CTCAT
*
3078367 AATTTTTGGTACTTCCTCAT
1 AATTTTT-ATA-TTCCTCAT
**
3078387 TTTTTTTATATTCCTCAT
1 AATTTTTATATTCCTCAT
3078405 AATTTT
1 AATTTT
3078411 CCGTACATTC
Statistics
Matches: 35, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
18 12 0.34
19 9 0.26
20 12 0.34
21 2 0.06
ACGTcount: A:0.22, C:0.17, G:0.03, T:0.57
Consensus pattern (18 bp):
AATTTTTATATTCCTCAT
Found at i:3078469 original size:40 final size:38
Alignment explanation
Indices: 3078362--3078478 Score: 114
Period size: 40 Copynumber: 3.0 Consensus size: 38
3078352 TTTATATCCT
* *
3078362 CTCATAATTTTTGGTACTTCCTCATTTTTTTTA-TATTC
1 CTCATAAATTTT-GTACTTCCTCATGTTTTTTAGTATTC
*
3078400 CTCAT-AATTTTCCGTACATT-CTCGTGTTTTTTAGTATTC
1 CTCATAAATTTT--GTAC-TTCCTCATGTTTTTTAGTATTC
* *
3078439 CATCATAAATTTTGATACTTCCTCAAGTTTTATAGTATTC
1 C-TCATAAATTTTG-TACTTCCTCATGTTTTTTAGTATTC
3078479 TCTCGTCATT
Statistics
Matches: 65, Mismatches: 7, Indels: 12
0.77 0.08 0.14
Matches are distributed among these distances:
37 5 0.08
38 20 0.31
39 11 0.17
40 23 0.35
41 6 0.09
ACGTcount: A:0.22, C:0.19, G:0.08, T:0.51
Consensus pattern (38 bp):
CTCATAAATTTTGTACTTCCTCATGTTTTTTAGTATTC
Found at i:3078600 original size:83 final size:83
Alignment explanation
Indices: 3078487--3078655 Score: 268
Period size: 83 Copynumber: 2.0 Consensus size: 83
3078477 TCTCTCGTCA
*
3078487 TTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATATGTTTTGTGGCACATCTTTAAAAATT
1 TTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATATGTTTTATGGCACATCTTTAAAAATT
3078552 TTGGTACATCCTCATTTT
66 TTGGTACATCCTCATTTT
* * * * *
3078570 TTTTTTGTATTCCTTCAT-ATTTTCTGGTACTTCCTCATATGTTTTATGGTACATCTTTAAAATT
1 TTTTTTGTATTCCCTCATAATTTT-TCGTACTTCATCATATGTTTTATGGCACATCTTTAAAAAT
3078634 TTTGGTACATCCTCATTTT
65 TTTGGTACATCCTCATTTT
3078653 TTT
1 TTT
3078656 ATACTTCCAT
Statistics
Matches: 79, Mismatches: 6, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
82 5 0.06
83 74 0.94
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.53
Consensus pattern (83 bp):
TTTTTTGTATTCCCTCATAATTTTTCGTACTTCATCATATGTTTTATGGCACATCTTTAAAAATT
TTGGTACATCCTCATTTT
Found at i:3078647 original size:42 final size:41
Alignment explanation
Indices: 3078505--3078657 Score: 137
Period size: 42 Copynumber: 3.7 Consensus size: 41
3078495 ATTCCCTCAT
* * * * *
3078505 AATTTTTCGTACTTCATCATATGTTTTGTGGCACATCTTTAA
1 AATTTTTGGTACATCCTCAT-TGTTTTATGGTACATCTTTAA
* * * * * * *
3078547 AAATTTTGGTACATCCTCATTTTTTTTTTGTA-TTCCTTCA
1 AATTTTTGGTACATCCTCATTGTTTTATGGTACATCTTTAA
* *
3078587 TATTTTCTGGTACTTCCTCATATGTTTTATGGTACATCTTTAA
1 AATTTT-TGGTACATCCTCAT-TGTTTTATGGTACATCTTTAA
*
3078630 AATTTTTGGTACATCCTCATTTTTTTAT
1 AATTTTTGGTACATCCTCATTGTTTTAT
3078658 ACTTCCATAG
Statistics
Matches: 85, Mismatches: 23, Indels: 7
0.74 0.20 0.06
Matches are distributed among these distances:
40 9 0.11
41 28 0.33
42 38 0.45
43 10 0.12
ACGTcount: A:0.22, C:0.16, G:0.10, T:0.52
Consensus pattern (41 bp):
AATTTTTGGTACATCCTCATTGTTTTATGGTACATCTTTAA
Found at i:3079736 original size:19 final size:19
Alignment explanation
Indices: 3079712--3079760 Score: 80
Period size: 19 Copynumber: 2.6 Consensus size: 19
3079702 TAAAGCACGA
* *
3079712 TTTTATTTTTGTATATGCT
1 TTTTATTTTAGTATATACT
3079731 TTTTATTTTAGTATATACT
1 TTTTATTTTAGTATATACT
3079750 TTTTATTTTAG
1 TTTTATTTTAG
3079761 AATTTTAAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.20, C:0.04, G:0.08, T:0.67
Consensus pattern (19 bp):
TTTTATTTTAGTATATACT
Found at i:3092977 original size:18 final size:18
Alignment explanation
Indices: 3092951--3092988 Score: 67
Period size: 18 Copynumber: 2.1 Consensus size: 18
3092941 AGTTCTCCAT
*
3092951 AAAATCTTAATCAAAGAC
1 AAAACCTTAATCAAAGAC
3092969 AAAACCTTAATCAAAGAC
1 AAAACCTTAATCAAAGAC
3092987 AA
1 AA
3092989 TACTAATCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.58, C:0.18, G:0.05, T:0.18
Consensus pattern (18 bp):
AAAACCTTAATCAAAGAC
Found at i:3093302 original size:3 final size:3
Alignment explanation
Indices: 3093294--3093343 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
3093284 AATTCACCTT
3093294 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
3093342 TT
1 TT
3093344 CTATTTATTT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:3093950 original size:36 final size:37
Alignment explanation
Indices: 3093910--3093988 Score: 124
Period size: 37 Copynumber: 2.2 Consensus size: 37
3093900 TTTTTTCTTC
3093910 TTCTTTTTATCAG-AGCTTGAATCTGGGTTTTTGGGG
1 TTCTTTTTATCAGTAGCTTGAATCTGGGTTTTTGGGG
**
3093946 TTCTTTTTATTTGTAGCTTGAATCTGGGTTTTTGGGG
1 TTCTTTTTATCAGTAGCTTGAATCTGGGTTTTTGGGG
*
3093983 TACTTT
1 TTCTTT
3093989 CATTTGCAGG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
36 11 0.28
37 28 0.72
ACGTcount: A:0.13, C:0.10, G:0.25, T:0.52
Consensus pattern (37 bp):
TTCTTTTTATCAGTAGCTTGAATCTGGGTTTTTGGGG
Found at i:3096353 original size:184 final size:184
Alignment explanation
Indices: 3096033--3096400 Score: 673
Period size: 184 Copynumber: 2.0 Consensus size: 184
3096023 CCTATATGTT
*
3096033 TGTTTCTCTTTTTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
1 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
*
3096098 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGT
66 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
*
3096163 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACTCTCTTGTATAAGTTTC
131 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACACTCTTGTATAAGTTTC
*
3096217 TGTTTTTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
1 TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
*
3096282 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTTTCTTTTATTTTGACTGA
66 GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
* *
3096347 AAGTGAGTGTTTCAAAATTTTTTTTATTGGAAATGACACTCTTGTATAAGTTTC
131 AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACACTCTTGTATAAGTTTC
3096401 CAGTAACAAG
Statistics
Matches: 177, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
184 177 1.00
ACGTcount: A:0.22, C:0.10, G:0.19, T:0.49
Consensus pattern (184 bp):
TGTTTCTCTTATTCTCTTTTCTTTGGTCTGAAATTCTTCTGGAATGAAAAGCATTTTCTTTGTGG
GTGTATATATACTGTATGTATTTTTGAAGGTCTGGATTGGATAAGTTCTCTTTTATTTTGACTGA
AAGTGAGTGTTTCAAAAATTGTTTTATTGGAAATGACACTCTTGTATAAGTTTC
Found at i:3099622 original size:4 final size:4
Alignment explanation
Indices: 3099613--3099639 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3099603 ATTTTGCTTT
3099613 TTTG TTTG TTTG TTTG TTTG TTTG TTT
1 TTTG TTTG TTTG TTTG TTTG TTTG TTT
3099640 TGCAATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.22, T:0.78
Consensus pattern (4 bp):
TTTG
Found at i:3102676 original size:24 final size:24
Alignment explanation
Indices: 3102649--3102697 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
3102639 CACTGAATTA
*
3102649 TTCAAAAGTTTTCATTTGAGTCAC
1 TTCAAAAGTCTTCATTTGAGTCAC
*
3102673 TTCAAAAGTCTTCATTTGTGTCAC
1 TTCAAAAGTCTTCATTTGAGTCAC
3102697 T
1 T
3102698 CGGATGTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.18, G:0.12, T:0.43
Consensus pattern (24 bp):
TTCAAAAGTCTTCATTTGAGTCAC
Found at i:3103036 original size:31 final size:31
Alignment explanation
Indices: 3102993--3103054 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
3102983 GTCTAGTGGC
* *
3102993 TTAAATAGAAATTTTTAAATAGTTTAATGAT
1 TTAAATAGAAATTTTTAAATAATTCAATGAT
*
3103024 TTAAAT-GAAAATTTTTGAATAATTCAATGAT
1 TTAAATAG-AAATTTTTAAATAATTCAATGAT
3103055 CAAATTATAG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
30 1 0.04
31 26 0.96
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.44
Consensus pattern (31 bp):
TTAAATAGAAATTTTTAAATAATTCAATGAT
Found at i:3103782 original size:16 final size:18
Alignment explanation
Indices: 3103761--3103806 Score: 51
Period size: 16 Copynumber: 2.6 Consensus size: 18
3103751 AAAATGAGGA
3103761 AAAAAAATAATTAA-A-T
1 AAAAAAATAATTAATATT
*
3103777 AAAAAATTATATTAATATT
1 AAAAAAATA-ATTAATATT
3103796 AAATAAAATAA
1 AAA-AAAATAA
3103807 AAAATTCCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
16 8 0.33
17 5 0.21
18 1 0.04
19 5 0.21
20 5 0.21
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAAAATAATTAATATT
Found at i:3104295 original size:2 final size:2
Alignment explanation
Indices: 3104288--3104312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3104278 GCAAAGAAGG
3104288 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
3104313 AAAAGCCTAA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3118611 original size:41 final size:42
Alignment explanation
Indices: 3118561--3118779 Score: 155
Period size: 41 Copynumber: 5.3 Consensus size: 42
3118551 TCGGATTTAT
* * * *
3118561 TGCCAGTGAAATTG-TTCAGACTATACGTCTAGCAGGCCAAG
1 TGCCGGTGAAATTGAATCAGACTATACGCCTAGCAGGCTAAG
* * * * *
3118602 TGCCGGTG-AATTTAACCGGACTGTACGTCC-AGTAGGCTAAG
1 TGCCGGTGAAATTGAATCAGACTATACG-CCTAGCAGGCTAAG
* * * *
3118643 TGCCGGTG-AACTGAATCAGGCTACAAGCCTAGCAGGCTAAG
1 TGCCGGTGAAATTGAATCAGACTATACGCCTAGCAGGCTAAG
* * * *
3118684 TGCCGGTG-GATTGAATCAGGCTATAGGCCTAGCAGGTTAAG
1 TGCCGGTGAAATTGAATCAGACTATACGCCTAGCAGGCTAAG
** * * **
3118725 TGCCGGTG-AACGGAATTAGACTATAAGCCTATTAGG-TGAAG
1 TGCCGGTGAAATTGAATCAGACTATACGCCTAGCAGGCT-AAG
*
3118766 TGCCAGTGAAATTG
1 TGCCGGTGAAATTG
3118780 TTTAAATTAA
Statistics
Matches: 139, Mismatches: 34, Indels: 9
0.76 0.19 0.05
Matches are distributed among these distances:
40 7 0.05
41 128 0.92
42 4 0.03
ACGTcount: A:0.28, C:0.20, G:0.29, T:0.23
Consensus pattern (42 bp):
TGCCGGTGAAATTGAATCAGACTATACGCCTAGCAGGCTAAG
Found at i:3119038 original size:33 final size:33
Alignment explanation
Indices: 3118967--3119044 Score: 95
Period size: 33 Copynumber: 2.4 Consensus size: 33
3118957 GTGTATATGA
* * *
3118967 ATGCGTTCGGCATAGGTGGATATATATGTATGT
1 ATGCATTCGGCATAGGTGGATATATATGAATAT
*
3119000 ATGCATTCGGCATAGGTGGGTATA-AGTGAATAT
1 ATGCATTCGGCATAGGTGGATATATA-TGAATAT
*
3119033 GTGCATTCGGCA
1 ATGCATTCGGCA
3119045 CTTATAGTTG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
32 1 0.03
33 38 0.97
ACGTcount: A:0.26, C:0.12, G:0.31, T:0.32
Consensus pattern (33 bp):
ATGCATTCGGCATAGGTGGATATATATGAATAT
Found at i:3121204 original size:102 final size:102
Alignment explanation
Indices: 3121021--3121212 Score: 260
Period size: 102 Copynumber: 1.9 Consensus size: 102
3121011 TGATTAATGT
* * * ** *
3121021 TATCCGGTACACATAGTAGCCTACACTTAGTACTACATATGTGACCAATACCATCTGATACACGT
1 TATCCAGTACACATAATAGCCTACACTTAGTACTACACATGTGACCAATAAAATCTGATACACAT
* * *
3121086 AGTAGCTTGCAGATAGTACTACACACGTGACTAAAGG
66 AGTAGCCTACACATAGTACTACACACGTGACTAAAGG
* * *
3121123 TATCCAGTACACATAATAGCCTACACTTAGTACTACACATGTTA-CAATAAAAATCTTATACTCA
1 TATCCAGTACACATAATAGCCTACACTTAGTACTACACATGTGACCAAT-AAAATCTGATACACA
3121187 TAGTAGCCTACACATAGTACTACACA
65 TAGTAGCCTACACATAGTACTACACA
3121213 TGAGTTCTCA
Statistics
Matches: 77, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
101 4 0.05
102 73 0.95
ACGTcount: A:0.36, C:0.24, G:0.13, T:0.27
Consensus pattern (102 bp):
TATCCAGTACACATAATAGCCTACACTTAGTACTACACATGTGACCAATAAAATCTGATACACAT
AGTAGCCTACACATAGTACTACACACGTGACTAAAGG
Found at i:3124318 original size:33 final size:33
Alignment explanation
Indices: 3124276--3124340 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
3124266 TCAATTTATA
* *
3124276 ACAAAATTTGTTGCAATGAATCT-AACTTAAATT
1 ACAAAATTTGTTCCAATAAATCTCAA-TTAAATT
3124309 ACAAAATTTGTTCCAATAAATCTCAATTAAAT
1 ACAAAATTTGTTCCAATAAATCTCAATTAAAT
3124341 AAATACAAAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 27 0.93
34 2 0.07
ACGTcount: A:0.45, C:0.14, G:0.06, T:0.35
Consensus pattern (33 bp):
ACAAAATTTGTTCCAATAAATCTCAATTAAATT
Found at i:3126790 original size:11 final size:11
Alignment explanation
Indices: 3126776--3126802 Score: 54
Period size: 11 Copynumber: 2.5 Consensus size: 11
3126766 AAATTACTAA
3126776 TAAAATAAATT
1 TAAAATAAATT
3126787 TAAAATAAATT
1 TAAAATAAATT
3126798 TAAAA
1 TAAAA
3126803 AACATAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 16 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
TAAAATAAATT
Found at i:3128024 original size:24 final size:25
Alignment explanation
Indices: 3127997--3128044 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3127987 AAAAGAAATT
*
3127997 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAACAACATAAAACGAAAAAAAA
* *
3128021 TTAAACTACTTAAAACGAAAAAAA
1 TTAAACAACATAAAACGAAAAAAA
3128045 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.08, G:0.06, T:0.17
Consensus pattern (25 bp):
TTAAACAACATAAAACGAAAAAAAA
Found at i:3130282 original size:31 final size:31
Alignment explanation
Indices: 3130218--3130286 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 31
3130208 CAGCTCAGTG
** * * *
3130218 ACTTAAATAAAATTTTTTAAATAGTTTATTA
1 ACTTAAATAAAAACTTTTAAATAATTCAATA
*
3130249 ACTTAAATAAAAACTTTTGAATAATTCAATA
1 ACTTAAATAAAAACTTTTAAATAATTCAATA
3130280 AC-TAAAT
1 ACTTAAAT
3130287 TGTAACTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
30 5 0.16
31 27 0.84
ACGTcount: A:0.49, C:0.07, G:0.03, T:0.41
Consensus pattern (31 bp):
ACTTAAATAAAAACTTTTAAATAATTCAATA
Found at i:3131386 original size:28 final size:28
Alignment explanation
Indices: 3131346--3131406 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 28
3131336 AGCCCCGTGA
*
3131346 CAAGTGGTATCCGAGCTAAGTTTTGAAC
1 CAAGTGGTATCCGAGCCAAGTTTTGAAC
*
3131374 CAAGTGGTATCCGAGCCAAGTTTTGAGC
1 CAAGTGGTATCCGAGCCAAGTTTTGAAC
3131402 CAAGT
1 CAAGT
3131407 CTTATTCGAG
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.26
Consensus pattern (28 bp):
CAAGTGGTATCCGAGCCAAGTTTTGAAC
Found at i:3131416 original size:28 final size:28
Alignment explanation
Indices: 3131346--3131416 Score: 88
Period size: 28 Copynumber: 2.5 Consensus size: 28
3131336 AGCCCCGTGA
* *
3131346 CAAGTGGTATCCGAGCTAAGTTTTGAAC
1 CAAGTCGTATCCGAGCCAAGTTTTGAAC
* *
3131374 CAAGTGGTATCCGAGCCAAGTTTTGAGC
1 CAAGTCGTATCCGAGCCAAGTTTTGAAC
* *
3131402 CAAGTCTTATTCGAG
1 CAAGTCGTATCCGAG
3131417 TTGGTTCGAA
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 38 1.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (28 bp):
CAAGTCGTATCCGAGCCAAGTTTTGAAC
Found at i:3135119 original size:87 final size:88
Alignment explanation
Indices: 3134973--3135149 Score: 320
Period size: 87 Copynumber: 2.0 Consensus size: 88
3134963 ATAGTTATGA
* *
3134973 GTCATCCAAGGAATTATAAAAGATGAAAAACGATAAGATGGTAATTAGTCAAGTAGATATTTTTG
1 GTCATCCAAGGAATTATAAAAGATGAAAAACGATAAGATGATAATTAGTCAAGTAGATATTTTTA
3135038 GACATAATGATT-AGACTAAAGT
66 GACATAATGATTAAGACTAAAGT
*
3135060 GTCATCCAAGGAATTATAAAAGATGAAAAATGATAAGATGATAATTAGTCAAGTAGATATTTTTA
1 GTCATCCAAGGAATTATAAAAGATGAAAAACGATAAGATGATAATTAGTCAAGTAGATATTTTTA
3135125 GACATAATGATTAAGACTAAAGT
66 GACATAATGATTAAGACTAAAGT
3135148 GT
1 GT
3135150 AAAGATGGAT
Statistics
Matches: 86, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
87 74 0.86
88 12 0.14
ACGTcount: A:0.45, C:0.07, G:0.19, T:0.29
Consensus pattern (88 bp):
GTCATCCAAGGAATTATAAAAGATGAAAAACGATAAGATGATAATTAGTCAAGTAGATATTTTTA
GACATAATGATTAAGACTAAAGT
Found at i:3137034 original size:27 final size:27
Alignment explanation
Indices: 3136996--3137047 Score: 104
Period size: 27 Copynumber: 1.9 Consensus size: 27
3136986 TAAATGTGAA
3136996 AGGGGTTGCTAAGTGTTGATTCCCCCG
1 AGGGGTTGCTAAGTGTTGATTCCCCCG
3137023 AGGGGTTGCTAAGTGTTGATTCCCC
1 AGGGGTTGCTAAGTGTTGATTCCCC
3137048 AAATCATTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.15, C:0.21, G:0.33, T:0.31
Consensus pattern (27 bp):
AGGGGTTGCTAAGTGTTGATTCCCCCG
Found at i:3137097 original size:102 final size:102
Alignment explanation
Indices: 3136921--3137122 Score: 350
Period size: 102 Copynumber: 2.0 Consensus size: 102
3136911 TAAATGTGAA
* * *
3136921 AGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTTGCTAAGTGCTGATTCCACCATATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCT
*
3136986 TAAATGTGAAAGGGGTTGCTAAGTGTTGATTCCCCCG
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
* *
3137023 AGGGGTTGCTAAGTGTTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATCCCACCGTATCT
1 AGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCT
3137088 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
66 TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCC
3137123 GACTCATTGG
Statistics
Matches: 94, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
102 94 1.00
ACGTcount: A:0.21, C:0.20, G:0.27, T:0.32
Consensus pattern (102 bp):
AGGGGTTGCTAAGTGCTGATTCCCCAAATCATTGGTGGTTGCTAAGTGCTGATCCCACCATATCT
TAAATGTGAAAGGGGTTGCTAAGTGCTGATTCCCCCG
Found at i:3138492 original size:2 final size:2
Alignment explanation
Indices: 3138485--3138514 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3138475 TAGAAATGTA
3138485 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3138515 TAAACAAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3138857 original size:22 final size:22
Alignment explanation
Indices: 3138832--3138874 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
3138822 CTCAGATTAT
3138832 TAGCACATTCA-TGCTCTTTGTA
1 TAGCACATT-AGTGCTCTTTGTA
*
3138854 TAGCACCTTAGTGCTCTTTGT
1 TAGCACATTAGTGCTCTTTGT
3138875 TCATTAGTGC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 1 0.05
22 18 0.95
ACGTcount: A:0.19, C:0.23, G:0.16, T:0.42
Consensus pattern (22 bp):
TAGCACATTAGTGCTCTTTGTA
Found at i:3141206 original size:23 final size:23
Alignment explanation
Indices: 3141109--3141199 Score: 146
Period size: 23 Copynumber: 4.0 Consensus size: 23
3141099 ATAAGTGCCA
*
3141109 CACTGATATGTAGCCGAAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
* *
3141132 CACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
*
3141155 CACTGAAATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTAC
3141178 CACTGAAATGTAGCCGAAGCTA
1 CACTGAAATGTAGCCGAAGCTA
3141200 TCGCTGATCA
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 65 1.00
ACGTcount: A:0.31, C:0.25, G:0.22, T:0.22
Consensus pattern (23 bp):
CACTGAAATGTAGCCGAAGCTAC
Found at i:3141307 original size:8 final size:8
Alignment explanation
Indices: 3141294--3141322 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3141284 AGCCGGGACT
3141294 CACTGTAA
1 CACTGTAA
3141302 CACTGTAA
1 CACTGTAA
3141310 CACTGTAA
1 CACTGTAA
3141318 CACTG
1 CACTG
3141323 GCCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:3143176 original size:18 final size:21
Alignment explanation
Indices: 3143153--3143200 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 21
3143143 AGGTAAATTT
3143153 TATTATTTA-TTA-TTT-TTA
1 TATTATTTATTTATTTTATTA
3143171 TATTA-TTATTTATTTTATTA
1 TATTATTTATTTATTTTATTA
3143191 TATATATTTA
1 TAT-TATTTA
3143201 AACTCAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 3 0.12
18 8 0.32
19 3 0.12
20 6 0.24
21 2 0.08
22 3 0.12
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (21 bp):
TATTATTTATTTATTTTATTA
Found at i:3143178 original size:21 final size:20
Alignment explanation
Indices: 3143152--3143198 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 20
3143142 AAGGTAAATT
*
3143152 TTATTATTTATTATTTTTATA
1 TTATTATTTATT-TTATTATA
3143173 TTATTATTTATTTTATTATA
1 TTATTATTTATTTTATTATA
3143193 TATATT
1 T-TATT
3143199 TAAACTCAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
20 8 0.33
21 16 0.67
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
TTATTATTTATTTTATTATA
Found at i:3143199 original size:14 final size:12
Alignment explanation
Indices: 3143149--3143191 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
3143139 CACAAGGTAA
3143149 ATTTTATTATTT
1 ATTTTATTATTT
3143161 A--TTATT-TTT
1 ATTTTATTATTT
*
3143170 ATATTATTATTT
1 ATTTTATTATTT
3143182 ATTTTATTAT
1 ATTTTATTAT
3143192 ATATATTTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
9 4 0.15
10 5 0.19
11 5 0.19
12 13 0.48
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTTATTATTT
Found at i:3154670 original size:53 final size:54
Alignment explanation
Indices: 3154612--3154732 Score: 145
Period size: 53 Copynumber: 2.2 Consensus size: 54
3154602 TAAAATTTGA
* * *
3154612 TGCCTCCATTAAAGGAGGCGGCACCAAAAAACATTAAAAAAATTCTTA-ACCGG
1 TGCCTCCATTAAAGGAAGCGGCACCAAAAAACAATAAAAAAATTCCTACACCGG
* * ** *
3154665 TGCCTCCATTGAAGGAAGCGGCACCATAAATTAATAAAAAAATTCCTACACTGG
1 TGCCTCCATTAAAGGAAGCGGCACCAAAAAACAATAAAAAAATTCCTACACCGG
*
3154719 TGCCGCCACTTAAA
1 TGCCTCCA-TTAAA
3154733 AACCTGTCAC
Statistics
Matches: 56, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
53 41 0.73
54 11 0.20
55 4 0.07
ACGTcount: A:0.39, C:0.24, G:0.17, T:0.21
Consensus pattern (54 bp):
TGCCTCCATTAAAGGAAGCGGCACCAAAAAACAATAAAAAAATTCCTACACCGG
Found at i:3158435 original size:60 final size:57
Alignment explanation
Indices: 3158325--3158445 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 57
3158315 CAATATAATG
* * * * * *
3158325 GTTTTGCCTTTTAACTTAATAGGTGAACATTTATTAAAATGACGTAGTTTTACCTTT
1 GTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAGTTTTACCTTT
* *
3158382 GTTTTGACTTTTAACTTTAGAAAAGGTAAACATTTATCAAAACGATATAGTTTTGCCTTT
1 GTTTTGACTTTTAAC-TT--AAAAGGTAAACATTTATCAAAACGACATAGTTTTACCTTT
3158442 -TTTT
1 GTTTT
3158446 ATTCAGATTT
Statistics
Matches: 53, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
57 14 0.26
58 2 0.04
59 4 0.08
60 33 0.62
ACGTcount: A:0.30, C:0.12, G:0.13, T:0.45
Consensus pattern (57 bp):
GTTTTGACTTTTAACTTAAAAGGTAAACATTTATCAAAACGACATAGTTTTACCTTT
Found at i:3162750 original size:21 final size:21
Alignment explanation
Indices: 3162726--3162766 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3162716 TTATCATTGC
3162726 CTTTATTATTTTTT-CAAATTA
1 CTTT-TTATTTTTTACAAATTA
*
3162747 CTTTTTTTTTTTTACAAATT
1 CTTTTTATTTTTTACAAATT
3162767 TGATGAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.24, C:0.10, G:0.00, T:0.66
Consensus pattern (21 bp):
CTTTTTATTTTTTACAAATTA
Found at i:3166369 original size:13 final size:14
Alignment explanation
Indices: 3166351--3166379 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
3166341 GATATTCTGC
3166351 AAAGGAAAAAA-AA
1 AAAGGAAAAAAGAA
3166364 AAAGGAAAAAAGAA
1 AAAGGAAAAAAGAA
3166378 AA
1 AA
3166380 CGATGATGGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (14 bp):
AAAGGAAAAAAGAA
Found at i:3174150 original size:13 final size:13
Alignment explanation
Indices: 3174132--3174169 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
3174122 AGTTCTTCAT
3174132 TGCTTTTGAGAAG
1 TGCTTTTGAGAAG
*
3174145 TGCTTTTCAGAAG
1 TGCTTTTGAGAAG
*
3174158 TACTTTTGAGAA
1 TGCTTTTGAGAA
3174170 ATTTGAGTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.26, C:0.11, G:0.24, T:0.39
Consensus pattern (13 bp):
TGCTTTTGAGAAG
Found at i:3179571 original size:22 final size:22
Alignment explanation
Indices: 3179546--3179592 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
3179536 GGTATCAATG
*
3179546 AGGGTACATTGGTTAGACACCT
1 AGGGTACATTGCTTAGACACCT
**
3179568 AGGGTACATTGCTTAGGTACCT
1 AGGGTACATTGCTTAGACACCT
3179590 AGG
1 AGG
3179593 ATGTATGTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.26, C:0.17, G:0.30, T:0.28
Consensus pattern (22 bp):
AGGGTACATTGCTTAGACACCT
Found at i:3181873 original size:50 final size:50
Alignment explanation
Indices: 3181798--3181897 Score: 173
Period size: 50 Copynumber: 2.0 Consensus size: 50
3181788 ATAGAACATA
* *
3181798 CAAAATGAAATCTAACGTCTAATATAATGATCTTCATGGTACTTTTACCG
1 CAAAATGAAATCTAACGTCAAATATAATGATCTCCATGGTACTTTTACCG
*
3181848 CAAAATGAAATCTATCGTCAAATATAATGATCTCCATGGTACTTTTACCG
1 CAAAATGAAATCTAACGTCAAATATAATGATCTCCATGGTACTTTTACCG
3181898 TGATAAATCT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 47 1.00
ACGTcount: A:0.36, C:0.19, G:0.12, T:0.33
Consensus pattern (50 bp):
CAAAATGAAATCTAACGTCAAATATAATGATCTCCATGGTACTTTTACCG
Found at i:3186230 original size:6 final size:6
Alignment explanation
Indices: 3186219--3186243 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3186209 CCTTTGAGGT
3186219 TTCATC TTCATC TTCATC TTCATC T
1 TTCATC TTCATC TTCATC TTCATC T
3186244 ATGCAATCAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.52
Consensus pattern (6 bp):
TTCATC
Found at i:3191425 original size:34 final size:35
Alignment explanation
Indices: 3191381--3191447 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3191371 CAGTAAAATA
3191381 TTTTCCGTAAAATGATTT-CGGGAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
3191415 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
3191448 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:3199969 original size:17 final size:16
Alignment explanation
Indices: 3199949--3200009 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 16
3199939 TAGGAAAGTG
3199949 TAAAAAATAAAAAGAGA
1 TAAAAAATAAAAAGA-A
*
3199966 TAAAATAATGTAAAAGAA
1 TAAAA-AAT-AAAAAGAA
* *
3199984 AAAAGAAATTAAAAGAA
1 TAAA-AAATAAAAAGAA
*
3200001 TTAAAAATA
1 TAAAAAATA
3200010 TTTTTCAAAG
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 4 0.11
17 15 0.42
18 10 0.28
19 7 0.19
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.18
Consensus pattern (16 bp):
TAAAAAATAAAAAGAA
Found at i:3199987 original size:26 final size:28
Alignment explanation
Indices: 3199947--3200007 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
3199937 AATAGGAAAG
* *
3199947 TGTAAAAAATAAAAAGAGA-TAAAATAA
1 TGTAAAAAATAAAAAGAAATTAAAAGAA
*
3199974 TGTAAAAGA-AAAAAGAAATTAAAAGAA
1 TGTAAAAAATAAAAAGAAATTAAAAGAA
3200001 T-TAAAAA
1 TGTAAAAA
3200008 TATTTTTCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
26 13 0.45
27 16 0.55
ACGTcount: A:0.70, C:0.00, G:0.11, T:0.18
Consensus pattern (28 bp):
TGTAAAAAATAAAAAGAAATTAAAAGAA
Found at i:3215087 original size:19 final size:20
Alignment explanation
Indices: 3215041--3215084 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
3215031 TAATAAACAC
3215041 AAAAAAT-ATTTTAAAAATA
1 AAAAAATAATTTTAAAAATA
*
3215060 AAAAAATAATTTTAAAATTA
1 AAAAAATAATTTTAAAAATA
3215080 AAAAA
1 AAAAA
3215085 TAAAATAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 7 0.30
20 16 0.70
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
AAAAAATAATTTTAAAAATA
Found at i:3215095 original size:19 final size:19
Alignment explanation
Indices: 3215052--3215098 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
3215042 AAAAATATTT
* **
3215052 TAAAAATAAAAAAATAATT
1 TAAAAATTAAAAAATAAAA
*
3215071 TTAAAATTAAAAAATAAAA
1 TAAAAATTAAAAAATAAAA
3215090 TAAAAATTA
1 TAAAAATTA
3215099 TATATTTATT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
TAAAAATTAAAAAATAAAA
Found at i:3216955 original size:74 final size:74
Alignment explanation
Indices: 3216829--3216975 Score: 231
Period size: 74 Copynumber: 2.0 Consensus size: 74
3216819 TAACAAAAAT
* * *
3216829 CCAACCAAACTCAATCCCTAAAACCCCTAGTAATCAACTTCGCTACCACCAAGTCTACCAAGATG
1 CCAACCAAACCCAATCCCTAAAACCCCTAGTAATCAACTTCGCTACCACCAAGTCAACCAAGAAG
3216894 AGGGAGAAC
66 AGGGAGAAC
* * * *
3216903 CCAATCAAACCCAATCCTTAAAACCCCTAGTAATCAACTTTGCTACCACCAAGTCAACGAAGAAG
1 CCAACCAAACCCAATCCCTAAAACCCCTAGTAATCAACTTCGCTACCACCAAGTCAACCAAGAAG
3216968 AGGGAGAA
66 AGGGAGAA
3216976 AATAGGGGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
74 66 1.00
ACGTcount: A:0.39, C:0.31, G:0.13, T:0.16
Consensus pattern (74 bp):
CCAACCAAACCCAATCCCTAAAACCCCTAGTAATCAACTTCGCTACCACCAAGTCAACCAAGAAG
AGGGAGAAC
Found at i:3220249 original size:22 final size:21
Alignment explanation
Indices: 3220200--3220274 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
3220190 AAAACTGTTG
* *
3220200 TTTTGCTGCTATTTTCCA-TA
1 TTTTGTTGTTATTTTCCACTA
3220220 GTTTTGTTGTTATTTTCCCACTA
1 -TTTTGTTGTTATTTT-CCACTA
*
3220243 TTTTGTTGTCA-TTT-CACTA
1 TTTTGTTGTTATTTTCCACTA
*
3220262 TTTTATTGTTATT
1 TTTTGTTGTTATT
3220275 GTTTAGATAT
Statistics
Matches: 46, Mismatches: 5, Indels: 7
0.79 0.09 0.12
Matches are distributed among these distances:
19 14 0.30
20 1 0.02
21 16 0.35
22 13 0.28
23 2 0.04
ACGTcount: A:0.15, C:0.15, G:0.11, T:0.60
Consensus pattern (21 bp):
TTTTGTTGTTATTTTCCACTA
Found at i:3224673 original size:16 final size:16
Alignment explanation
Indices: 3224631--3224676 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
3224621 TTTTATAGCT
*
3224631 TGTAATGTTTTATATTA
1 TGTAAT-TTATATATTA
3224648 TGTTATATTTATATATTA
1 TG-TA-ATTTATATATTA
3224666 TGTAATTTATA
1 TGTAATTTATA
3224677 ACACATAAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 7 0.27
17 4 0.15
18 13 0.50
19 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.09, T:0.59
Consensus pattern (16 bp):
TGTAATTTATATATTA
Found at i:3225095 original size:16 final size:17
Alignment explanation
Indices: 3225069--3225109 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
3225059 GATGTAATAC
*
3225069 ATTATTATTAATATATG
1 ATTATTATTAAAATATG
3225086 ATTA-TATTAAAATAT-
1 ATTATTATTAAAATATG
*
3225101 AATATTATT
1 ATTATTATT
3225110 TGTAATTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (17 bp):
ATTATTATTAAAATATG
Found at i:3229014 original size:24 final size:25
Alignment explanation
Indices: 3228987--3229034 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
3228977 AGAGGAAAGT
3228987 TTAAAGAACATAAAA-GAAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAAA
** *
3229011 TTAAATTACTTAAAACGAAAAAAA
1 TTAAAGAACATAAAACGAAAAAAA
3229035 TATGGGGATC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 12 0.60
25 8 0.40
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (25 bp):
TTAAAGAACATAAAACGAAAAAAAA
Found at i:3229326 original size:38 final size:40
Alignment explanation
Indices: 3229275--3229363 Score: 105
Period size: 38 Copynumber: 2.2 Consensus size: 40
3229265 TAAAATTATA
* *
3229275 TTTAATACAATAAAAT-ATTTA-TCATATTTAT-TTGTGT-T
1 TTTAATATAAT-AAATCATTTACT-ATATTTATGTAGTGTCT
3229313 TTTAATATAATAAATCATTTACTATATTTATGGTAGTGTCT
1 TTTAATATAATAAATCATTTACTATATTTAT-GTAGTGTCT
3229354 TTTAATATAA
1 TTTAATATAA
3229364 ATATTTTTAA
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
37 4 0.09
38 23 0.52
39 1 0.02
40 5 0.11
41 11 0.25
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.51
Consensus pattern (40 bp):
TTTAATATAATAAATCATTTACTATATTTATGTAGTGTCT
Found at i:3239668 original size:34 final size:35
Alignment explanation
Indices: 3239624--3239690 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3239614 CAGTAAAATA
3239624 TTTTCCGTAAAATGATTT-CTGAAAAATATTTTAC
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
* *
3239658 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAAATATTTT
3239691 CTGGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.34, C:0.09, G:0.10, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGAAAAATATTTTAC
Found at i:3242569 original size:24 final size:21
Alignment explanation
Indices: 3242542--3242584 Score: 59
Period size: 21 Copynumber: 1.9 Consensus size: 21
3242532 TATAGGGTAC
3242542 AATATAGGTATTTCACAATATTAA
1 AATATA-GTATTT-A-AATATTAA
3242566 AATATAGTATTTAAATATT
1 AATATAGTATTTAAATATT
3242585 TACAACAGAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
21 6 0.32
22 1 0.05
23 6 0.32
24 6 0.32
ACGTcount: A:0.47, C:0.05, G:0.07, T:0.42
Consensus pattern (21 bp):
AATATAGTATTTAAATATTAA
Found at i:3243896 original size:115 final size:116
Alignment explanation
Indices: 3243693--3243927 Score: 436
Period size: 115 Copynumber: 2.0 Consensus size: 116
3243683 TTAAGTTTGC
*
3243693 TTAATGAAATGTTCTTTTTTTCGACAAATCATAAGTGTTTTCATCCGTTTTACGACCTGAAATTA
1 TTAATGAAATGTTCTTTTTTTCGACAAATCATAAGTATTTTCATCCGTTTTACGACCTGAAATTA
*
3243758 ATCCTATTCAAACCAGAAGAATATTCAAGTGATGCACTCCCGATATCAGAA
66 ATCCTATTCAAACCAGAAGAATATTCAAGTGATACACTCCCGATATCAGAA
3243809 TTAATGAAATGTTC-TTTTTTCGACAAATCATAAGTATTTTCATCCGTTTTACGACCTGAAATTA
1 TTAATGAAATGTTCTTTTTTTCGACAAATCATAAGTATTTTCATCCGTTTTACGACCTGAAATTA
*
3243873 ATCCTATTCGAACCAGAAGAATATTCAAGTGATACACTCCCGATATCAGAA
66 ATCCTATTCAAACCAGAAGAATATTCAAGTGATACACTCCCGATATCAGAA
3243924 TTAA
1 TTAA
3243928 AACAACTTTG
Statistics
Matches: 116, Mismatches: 3, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
115 102 0.88
116 14 0.12
ACGTcount: A:0.34, C:0.19, G:0.12, T:0.34
Consensus pattern (116 bp):
TTAATGAAATGTTCTTTTTTTCGACAAATCATAAGTATTTTCATCCGTTTTACGACCTGAAATTA
ATCCTATTCAAACCAGAAGAATATTCAAGTGATACACTCCCGATATCAGAA
Found at i:3253216 original size:20 final size:19
Alignment explanation
Indices: 3253180--3253229 Score: 64
Period size: 20 Copynumber: 2.6 Consensus size: 19
3253170 TTGATCTCAA
*
3253180 GAAATTAAAAACAAAAATT
1 GAAAATAAAAACAAAAATT
*
3253199 GAAAATAAAATCATAAAATT
1 GAAAATAAAAACA-AAAATT
*
3253219 AAAAATAAAAA
1 GAAAATAAAAA
3253230 AGCAAACTGA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 11 0.42
20 15 0.58
ACGTcount: A:0.72, C:0.04, G:0.04, T:0.20
Consensus pattern (19 bp):
GAAAATAAAAACAAAAATT
Found at i:3256021 original size:14 final size:14
Alignment explanation
Indices: 3256002--3256041 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
3255992 TTGATTGCCA
3256002 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
3256016 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
3256030 GGAAAATGTTTT
1 GTAAAATGTTTT
3256042 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:3256050 original size:20 final size:20
Alignment explanation
Indices: 3256025--3256064 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3256015 CGTAAAATGA
*
3256025 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
3256045 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
3256065 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:3256054 original size:34 final size:35
Alignment explanation
Indices: 3256010--3256076 Score: 109
Period size: 34 Copynumber: 1.9 Consensus size: 35
3256000 CAGTAAAATG
*
3256010 TTTTCCGTAAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
3256044 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
3256077 CTAGTGTTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 17 0.57
35 13 0.43
ACGTcount: A:0.31, C:0.09, G:0.13, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:3257139 original size:11 final size:11
Alignment explanation
Indices: 3257123--3257147 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3257113 TTGAGTTAGC
3257123 TAAAAATAGTT
1 TAAAAATAGTT
3257134 TAAAAATAGTT
1 TAAAAATAGTT
3257145 TAA
1 TAA
3257148 CGAATCTAGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (11 bp):
TAAAAATAGTT
Found at i:3260933 original size:173 final size:173
Alignment explanation
Indices: 3260624--3260965 Score: 512
Period size: 173 Copynumber: 2.0 Consensus size: 173
3260614 TTCGAAATTG
* *
3260624 CTATTATGTTGATGATGCCATAAAGCAGTGTTAATGTTGCTTGAAGGAAAAGCGAGTCTCTCCCC
1 CTATTATGTTGATGATGCCATAAAGCAGTGTTAATGTGGCTTGAAGGAAAAGAGAGTCTCTCCCC
* * *
3260689 TGAGATGTATCTATTCTGCTGGAAGGAGCAGTCATATACTAAAATATGAGGTCATAGTGGAATCA
66 TGAGATGTATCTAATCTGCTGGAAGGAGCAGTAAAATACTAAAATATGAGGTCATAGTGGAATCA
3260754 AATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTAATCA
131 AATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTAATCA
*
3260797 CTATTATGTTGATGATGCCATAAATTG-A-TGTTTATGTGGCTTGAACGGAAAA-AGAGTCTCTC
1 CTATTATGTTGATGATGCCATAAA--GCAGTGTTAATGTGGCTTGAA-GGAAAAGAGAGTCTCTC
* * *
3260859 TCCTGAGATGTCTCTAATCTGCTGTAAGGAGCAGTAAAATACTAAAATATGAGGGTCATAGT-GA
63 CCCTGAGATGTATCTAATCTGCTGGAAGGAGCAGTAAAATACTAAAATATGA-GGTCATAGTGGA
* * *
3260923 ATCGAATGTCATCCTATAGTGTTCATGAGGTGTTTCTATTGTA
127 ATCAAATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTA
3260966 TATATTTAAA
Statistics
Matches: 153, Mismatches: 12, Indels: 8
0.88 0.07 0.05
Matches are distributed among these distances:
173 136 0.89
174 16 0.10
175 1 0.01
ACGTcount: A:0.30, C:0.15, G:0.22, T:0.33
Consensus pattern (173 bp):
CTATTATGTTGATGATGCCATAAAGCAGTGTTAATGTGGCTTGAAGGAAAAGAGAGTCTCTCCCC
TGAGATGTATCTAATCTGCTGGAAGGAGCAGTAAAATACTAAAATATGAGGTCATAGTGGAATCA
AATGTCATCCTATAGCGTTCATGAGATGTTTCTATTGTAATCA
Found at i:3263642 original size:68 final size:68
Alignment explanation
Indices: 3263533--3263671 Score: 278
Period size: 68 Copynumber: 2.0 Consensus size: 68
3263523 TTTACGATAG
3263533 TTTTTACTCATATTTTTAATTGTAGGTTTGAAATTGTACTAATCTTTTTTTATTTTATATCTAAC
1 TTTTTACTCATATTTTTAATTGTAGGTTTGAAATTGTACTAATCTTTTTTTATTTTATATCTAAC
3263598 TAT
66 TAT
3263601 TTTTTACTCATATTTTTAATTGTAGGTTTGAAATTGTACTAATCTTTTTTTATTTTATATCTAAC
1 TTTTTACTCATATTTTTAATTGTAGGTTTGAAATTGTACTAATCTTTTTTTATTTTATATCTAAC
3263666 TAT
66 TAT
3263669 TTT
1 TTT
3263672 AAAGCGTGTT
Statistics
Matches: 71, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 71 1.00
ACGTcount: A:0.26, C:0.09, G:0.07, T:0.58
Consensus pattern (68 bp):
TTTTTACTCATATTTTTAATTGTAGGTTTGAAATTGTACTAATCTTTTTTTATTTTATATCTAAC
TAT
Found at i:3263752 original size:3 final size:3
Alignment explanation
Indices: 3263744--3263786 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
3263734 GTTATATTTG
3263744 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3263787 GTATAAGTTA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:3272705 original size:33 final size:34
Alignment explanation
Indices: 3272635--3272713 Score: 87
Period size: 33 Copynumber: 2.4 Consensus size: 34
3272625 TACGTTTGCC
*
3272635 TATATTATATT-TTTTAATTTAAAAATACATATT
1 TATATTATATTATTTTAATTTAAAAATACATATA
*
3272668 TATATTATATTATTTTAACATTT-AATA-AC-TATA
1 TATATTATATTATTTT-A-ATTTAAAAATACATATA
3272701 TATATTAT-TTATT
1 TATATTATATTATT
3272714 AAAATTTTAT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
32 5 0.12
33 22 0.54
34 6 0.15
35 4 0.10
36 4 0.10
ACGTcount: A:0.41, C:0.04, G:0.00, T:0.56
Consensus pattern (34 bp):
TATATTATATTATTTTAATTTAAAAATACATATA
Found at i:3272728 original size:28 final size:26
Alignment explanation
Indices: 3272668--3272728 Score: 61
Period size: 28 Copynumber: 2.2 Consensus size: 26
3272658 AATACATATT
*
3272668 TATAT-TATATTATTTTAACATTTAA
1 TATATATATATTATTTTAAAATTTAA
*
3272693 TAACTATATATATTATTTATTAAAATTTTA
1 T-A-TATATATATTA-TT-TTAAAATTTAA
3272723 TATATA
1 TATATA
3272729 ATCATCTCAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
25 1 0.03
26 1 0.03
27 3 0.10
28 11 0.38
29 3 0.10
30 10 0.34
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (26 bp):
TATATATATATTATTTTAAAATTTAA
Found at i:3273884 original size:31 final size:31
Alignment explanation
Indices: 3273823--3273888 Score: 80
Period size: 31 Copynumber: 2.1 Consensus size: 31
3273813 TTATAGTTTG
*
3273823 GTCACTGAACTATCCAAAAAATTTCTTTTAA
1 GTCACTGAACCATCCAAAAAATTTCTTTTAA
* * *
3273854 GTCACTGAACCAT-TAAAATATTTTTATTTAA
1 GTCACTGAACCATCCAAAAAATTTCT-TTTAA
3273885 GTCA
1 GTCA
3273889 TTAGACTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
30 9 0.30
31 21 0.70
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.38
Consensus pattern (31 bp):
GTCACTGAACCATCCAAAAAATTTCTTTTAA
Found at i:3274347 original size:31 final size:31
Alignment explanation
Indices: 3274312--3274373 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
3274302 TACCCTTATT
3274312 TTTTGGGTGGATTGTAGAGGTATCTATAGGC
1 TTTTGGGTGGATTGTAGAGGTATCTATAGGC
*
3274343 TTTTGGGTGGATTGTAGAGGTATTTATAGGC
1 TTTTGGGTGGATTGTAGAGGTATCTATAGGC
3274374 CAAATTGGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.19, C:0.05, G:0.35, T:0.40
Consensus pattern (31 bp):
TTTTGGGTGGATTGTAGAGGTATCTATAGGC
Found at i:3285633 original size:18 final size:17
Alignment explanation
Indices: 3285602--3285635 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
3285592 GGCGAGACTC
*
3285602 TAAATTAAATATTAAAT
1 TAAATTAAAAATTAAAT
3285619 TAAATTTAAAAATTAAA
1 TAAA-TTAAAAATTAAA
3285636 AAACAGTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 4 0.27
18 11 0.73
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (17 bp):
TAAATTAAAAATTAAAT
Found at i:3292346 original size:31 final size:31
Alignment explanation
Indices: 3292286--3292346 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
3292276 CATACTAGTA
* **
3292286 ATTTAAATAAAAACTTTCGAATAGTTCAATG
1 ATTTAAATAAAAACTTCCGAATAACTCAATG
3292317 ATTTAAATAAAAACTTCCGAATAACTCAAT
1 ATTTAAATAAAAACTTCCGAATAACTCAAT
3292347 AATTATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.48, C:0.13, G:0.07, T:0.33
Consensus pattern (31 bp):
ATTTAAATAAAAACTTCCGAATAACTCAATG
Found at i:3292969 original size:13 final size:14
Alignment explanation
Indices: 3292945--3292981 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3292935 ATGTTAATGA
3292945 TTAAATTAAAATTT
1 TTAAATTAAAATTT
3292959 TTAAA-TAAAA-TT
1 TTAAATTAAAATTT
*
3292971 TTAATTTAAAA
1 TTAAATTAAAA
3292982 AATATAATGT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
12 6 0.29
13 10 0.48
14 5 0.24
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (14 bp):
TTAAATTAAAATTT
Found at i:3296002 original size:19 final size:19
Alignment explanation
Indices: 3295928--3296002 Score: 70
Period size: 20 Copynumber: 4.1 Consensus size: 19
3295918 TATTTGTAAA
3295928 AAAAAATATTAATAGTTTT
1 AAAAAATATTAATAGTTTT
3295947 AATAAAATA--AA-A-TTTT
1 AA-AAAATATTAATAGTTTT
* **
3295963 -AAAAATATGTATTAGAATT
1 AAAAAATAT-TAATAGTTTT
3295982 AAAAAATATTAATAGTTTT
1 AAAAAATATTAATAGTTTT
3296001 AA
1 AA
3296003 TAGACACATG
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
14 6 0.14
15 1 0.02
16 4 0.09
17 2 0.05
18 3 0.07
19 13 0.30
20 14 0.33
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.39
Consensus pattern (19 bp):
AAAAAATATTAATAGTTTT
Found at i:3298280 original size:31 final size:31
Alignment explanation
Indices: 3298241--3298317 Score: 93
Period size: 31 Copynumber: 2.5 Consensus size: 31
3298231 TTAATATAAC
*
3298241 ATTTGGTACCTAAACTTGACA-TTTGTTTCTA
1 ATTTGGTACCTAAACTTGACACTTT-TTCCTA
* * *
3298272 TTTTGGTACTTGAACTTGACACTTTTTCCTA
1 ATTTGGTACCTAAACTTGACACTTTTTCCTA
*
3298303 ATTTGGAACCTAAAC
1 ATTTGGTACCTAAAC
3298318 CTTTTTGGCA
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
31 34 0.92
32 3 0.08
ACGTcount: A:0.26, C:0.18, G:0.13, T:0.43
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTGACACTTTTTCCTA
Found at i:3301934 original size:3 final size:3
Alignment explanation
Indices: 3301926--3301955 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
3301916 TCACAGTTGA
3301926 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
3301956 TCAATTATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3306710 original size:3 final size:3
Alignment explanation
Indices: 3306702--3306727 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3306692 TTCATTTTGT
3306702 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3306728 TAGGATATTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3310426 original size:22 final size:22
Alignment explanation
Indices: 3310401--3310444 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
3310391 ACAAGTATGG
3310401 TATTGAAATTTAAAAT-AAAATA
1 TATTGAAATTT-AAATCAAAATA
* *
3310423 TATTTAGATTTAAATCAAAATA
1 TATTGAAATTTAAATCAAAATA
3310445 AATTCATATA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.55, C:0.02, G:0.05, T:0.39
Consensus pattern (22 bp):
TATTGAAATTTAAATCAAAATA
Found at i:3312930 original size:27 final size:27
Alignment explanation
Indices: 3312900--3312997 Score: 87
Period size: 27 Copynumber: 3.7 Consensus size: 27
3312890 TTTTAACTTG
*
3312900 ATTTTATTATATTTTTAGCTTTTAAAA
1 ATTTTATTATATTTTTAGATTTTAAAA
* * **
3312927 ATTTTATTTTATTTTTA-TTTTTAAGT
1 ATTTTATTATATTTTTAGATTTTAAAA
* *
3312953 A-TTTA-TAGATTTTATAGATTTTTAAA
1 ATTTTATTATATTTT-TAGATTTTAAAA
3312979 ATTTCTATT-TATTTTTAGA
1 ATTT-TATTATATTTTTAGA
3312998 ATCTTCTAAA
Statistics
Matches: 55, Mismatches: 11, Indels: 10
0.72 0.14 0.13
Matches are distributed among these distances:
24 6 0.11
25 6 0.11
26 13 0.24
27 22 0.40
28 7 0.13
29 1 0.02
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.62
Consensus pattern (27 bp):
ATTTTATTATATTTTTAGATTTTAAAA
Found at i:3313692 original size:29 final size:29
Alignment explanation
Indices: 3313629--3313693 Score: 112
Period size: 29 Copynumber: 2.2 Consensus size: 29
3313619 GTATTTTTAT
*
3313629 AAAATATCCAATACGGTACTTGTACTTTG
1 AAAATGTCCAATACGGTACTTGTACTTTG
*
3313658 AAAATGTCCAATGCGGTACTTGTACTTTG
1 AAAATGTCCAATACGGTACTTGTACTTTG
3313687 AAAATGT
1 AAAATGT
3313694 TTAACGTAGT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Consensus pattern (29 bp):
AAAATGTCCAATACGGTACTTGTACTTTG
Done.