Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold409
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: 3905031
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 1 of 25
Found at i:264 original size:1 final size:1
Alignment explanation
Indices: 258--387 Score: 89
Period size: 1 Copynumber: 130.0 Consensus size: 1
248 GGCGTCCTTC
** ** ** ** **
258 AAAAAAAAAAAAAAAAAACGAAAAAAAATGAAAAACCAAAAAAAAAAAAACGAAAAAATGAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
** * * * * * * *
323 CCAAAAAAAAAAAAAAAAACAAAAGAAAAAAAACAAAAAACAATAAAAAAACAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
388 GAGGGGTCCG
Statistics
Matches: 99, Mismatches: 30, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 99 1.00
ACGTcount: A:0.85, C:0.08, G:0.04, T:0.02
Consensus pattern (1 bp):
A
Found at i:304 original size:32 final size:32
Alignment explanation
Indices: 263--352 Score: 136
Period size: 30 Copynumber: 2.9 Consensus size: 32
253 CCTTCAAAAA
263 AAAAAAAAAAAAACGAAAAAAAATGAAAAACC
1 AAAAAAAAAAAAACGAAAAAAAATGAAAAACC
295 AAAAAAAAAAAAACG--AAAAAATGAAAAACC
1 AAAAAAAAAAAAACGAAAAAAAATGAAAAACC
325 AAAAAAAAAAAAA--AAAACAAAA-GAAAAA
1 AAAAAAAAAAAAACGAAAA-AAAATGAAAAA
353 AAACAAAAAA
Statistics
Matches: 55, Mismatches: 0, Indels: 8
0.87 0.00 0.13
Matches are distributed among these distances:
30 36 0.65
31 4 0.07
32 15 0.27
ACGTcount: A:0.84, C:0.08, G:0.06, T:0.02
Consensus pattern (32 bp):
AAAAAAAAAAAAACGAAAAAAAATGAAAAACC
Found at i:351 original size:30 final size:30
Alignment explanation
Indices: 262--377 Score: 119
Period size: 30 Copynumber: 3.7 Consensus size: 30
252 TCCTTCAAAA
*
262 AAAAAAAAAAAAAACGAAAAAAAATGAAAAACC
1 AAAAAAAAAAAAAA--AAACAAAA-GAAAAACC
* *
295 AAAAAAAAAAAAACGAAA-AAATGAAAAACC
1 AAAAAAAAAAAAA-AAAACAAAAGAAAAACC
*
325 AAAAAAAAAAAAAAAAACAAAAGAAAAA-A
1 AAAAAAAAAAAAAAAAACAAAAGAAAAACC
354 AACAAAAAACAATAAAAAAACAAA
1 AA-AAAAAA-AA-AAAAAAACAAA
378 CAAAAAAAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 11
0.82 0.06 0.12
Matches are distributed among these distances:
29 5 0.07
30 36 0.49
31 5 0.07
32 14 0.19
33 13 0.18
ACGTcount: A:0.84, C:0.09, G:0.04, T:0.03
Consensus pattern (30 bp):
AAAAAAAAAAAAAAAAACAAAAGAAAAACC
Found at i:354 original size:32 final size:32
Alignment explanation
Indices: 259--387 Score: 129
Period size: 32 Copynumber: 3.9 Consensus size: 32
249 GCGTCCTTCA
259 AAAAAAAAAAAAAAAAACGAAAAAAAATGAAAAACC
1 AAAAAAAAAAAAAAAAAC--AAAAAAA--AAAAACC
** **
295 -AAAAAAAAAAAAACGA-AAAAATGAAAAACC
1 AAAAAAAAAAAAAAAAACAAAAAAAAAAAACC
325 AAAAAAAAAAAAAAAAACAAAAGAAAAAAAA-C
1 AAAAAAAAAAAAAAAAACAAAA-AAAAAAAACC
* *
357 AAAAAACAATAAAAAAACAAACAAAAAAAAA
1 AAAAAAAAAAAAAAAAACAAA-AAAAAAAAA
388 GAGGGGTCCG
Statistics
Matches: 79, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
30 7 0.09
31 14 0.18
32 37 0.47
33 7 0.09
35 14 0.18
ACGTcount: A:0.85, C:0.09, G:0.04, T:0.02
Consensus pattern (32 bp):
AAAAAAAAAAAAAAAAACAAAAAAAAAAAACC
Found at i:1870 original size:29 final size:30
Alignment explanation
Indices: 1831--2054 Score: 213
Period size: 33 Copynumber: 7.0 Consensus size: 30
1821 TTACCCTTCA
* *
1831 AAAGCCCACAAGTCAGTGGCA-TCTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC
1860 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCA-C-TC-T-TTTTC
*
1894 -AAGCCCATAACTCCGTGGCACTCTTTTT-
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC
1922 AAAGCCCACAACTCCGTGGCACT-TTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC
1951 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC
1 ----AAAGCCCACAACTCCGTGGCACTC----T---TTTTC
* *
1992 AAAGCCCACAACTCCGTGGCACTTTTTCCTTTT
1 AAAGCCCACAACTCCGTGGCAC-TCTT--TTTC
2025 AAAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC
2055 CCTTTTAAGT
Statistics
Matches: 165, Mismatches: 8, Indels: 43
0.76 0.04 0.20
Matches are distributed among these distances:
28 5 0.03
29 44 0.27
30 4 0.02
31 3 0.02
32 6 0.04
33 68 0.41
34 6 0.04
37 22 0.13
38 2 0.01
41 5 0.03
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (30 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTC
Found at i:1900 original size:33 final size:34
Alignment explanation
Indices: 1855--2085 Score: 282
Period size: 33 Copynumber: 6.9 Consensus size: 34
1845 AGTGGCATCT
*
1855 TTTTCAAAGCCCACAACTCCGTGGCACCTTCTT-C
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCC
* * *
1889 TTTTCAAGCCCATAACTCCGTGGCA-C----TCT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCC
*
1918 TTTTAAAGCCCACAACTCCGTGGCA-CTTTTTTC
1 TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCC
1951 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CC
1987 TTTTCAAAGCCCACAACTCCGTGGCA-CTTTTTCC
1 TTTT-AAAGCCCACAACTCCGTGGCACCTTTTTCC
2021 TTTTAAAGCCCACAACTCCGTGGCACTCTTTTTCCC
1 TTTTAAAGCCCACAACTCCGTGGCAC-CTTTTT-CC
* *
2057 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCACCTTT
2086 CTCCCTTCCT
Statistics
Matches: 175, Mismatches: 10, Indels: 24
0.84 0.05 0.11
Matches are distributed among these distances:
28 1 0.01
29 24 0.14
32 1 0.01
33 66 0.38
34 14 0.08
35 37 0.21
36 11 0.06
37 21 0.12
ACGTcount: A:0.20, C:0.34, G:0.12, T:0.33
Consensus pattern (34 bp):
TTTTAAAGCCCACAACTCCGTGGCACCTTTTTCC
Found at i:1929 original size:62 final size:63
Alignment explanation
Indices: 1831--2054 Score: 301
Period size: 62 Copynumber: 3.5 Consensus size: 63
1821 TTACCCTTCA
* * *
1831 AAAGCCCACAAGTCAGTGGCA-TCTTTTTCAAAGCCCACAACTCCGTGGCACCTTCTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
* * *
1893 CAAGCCCATAACTCCGTGGCACTCTTTTT-AAAGCCCACAACTCCGTGGCACTTTTTTCTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
1955 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCA-CTTTTT
1 AAAGCCCACAACTCCGTGGCACTC----T---TTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
2019 CCTTTT
59 -CTTTT
2025 AAAGCCCACAACTCCGTGGCACTCTTTTTC
1 AAAGCCCACAACTCCGTGGCACTCTTTTTC
2055 CCTTTTAAGT
Statistics
Matches: 143, Mismatches: 9, Indels: 19
0.84 0.05 0.11
Matches are distributed among these distances:
62 70 0.49
63 12 0.08
66 2 0.01
69 9 0.06
70 50 0.35
ACGTcount: A:0.22, C:0.34, G:0.13, T:0.31
Consensus pattern (63 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCAAAGCCCACAACTCCGTGGCACCTTTTTCTTTT
Found at i:2029 original size:70 final size:69
Alignment explanation
Indices: 1918--2085 Score: 293
Period size: 70 Copynumber: 2.4 Consensus size: 69
1908 GTGGCACTCT
*
1918 TTTTAAAGCCCACAACTCCGTGGCACTTTTTTCTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTTTAAAGCCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
1983 TCCC
66 TCCC
1987 TTTTCAAAGCCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
1 TTTT-AAAGCCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTT
2052 TTCCC
65 TTCCC
*
2057 TTTT-AAGTCCACAACTCCGTGGCATCTTT
1 TTTTAAAGCCCACAACTCCGTGGCA-CTTT
2086 CTCCCTTCCT
Statistics
Matches: 95, Mismatches: 2, Indels: 4
0.94 0.02 0.04
Matches are distributed among these distances:
68 19 0.20
69 8 0.08
70 68 0.72
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (69 bp):
TTTTAAAGCCCACAACTCCGTGGCACTTTTTCCTTTTAAAGCCCACAACTCCGTGGCACTCTTTT
TCCC
Found at i:2133 original size:33 final size:35
Alignment explanation
Indices: 2090--2159 Score: 117
Period size: 33 Copynumber: 2.1 Consensus size: 35
2080 ATCTTTCTCC
*
2090 CTTCCTAAAGCCGACACAAGTCGGTGGCAA-CCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
2124 CTTCC-AAAGCCCACACAAGTCGGTGGCAACCCTT
1 CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
2158 CT
1 CT
2160 AAGCCCAATA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
33 23 0.68
34 11 0.32
ACGTcount: A:0.26, C:0.36, G:0.19, T:0.20
Consensus pattern (35 bp):
CTTCCTAAAGCCCACACAAGTCGGTGGCAACCCTT
Found at i:2223 original size:49 final size:49
Alignment explanation
Indices: 2159--2358 Score: 304
Period size: 49 Copynumber: 4.2 Consensus size: 49
2149 GCAACCCTTC
* * *
2159 TAAGCCCAATATAGCTGGCCTTGAATCAGCATATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
* *
2208 TAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCTTCATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
2257 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C----T-TT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
*
2300 TAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
1 TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
2349 TAAGTCCAAT
1 TAAGTCCAAT
2359 ATCGCTAGCC
Statistics
Matches: 138, Mismatches: 7, Indels: 12
0.88 0.04 0.08
Matches are distributed among these distances:
43 40 0.29
44 2 0.01
48 2 0.01
49 94 0.68
ACGTcount: A:0.25, C:0.26, G:0.18, T:0.32
Consensus pattern (49 bp):
TAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTTTATCTT
Found at i:2317 original size:43 final size:43
Alignment explanation
Indices: 2254--2344 Score: 164
Period size: 43 Copynumber: 2.1 Consensus size: 43
2244 GCACCTTCAT
2254 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
* *
2297 TTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCAC
1 CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
2340 CTTTA
1 CTTTA
2345 TCTTTAAGTC
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.24, C:0.25, G:0.20, T:0.31
Consensus pattern (43 bp):
CTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAC
Found at i:2392 original size:92 final size:92
Alignment explanation
Indices: 2187--2392 Score: 233
Period size: 92 Copynumber: 2.2 Consensus size: 92
2177 CCTTGAATCA
*
2187 GCATATTGGCACCTTTAT-C-TTTAAGTCCAATGTAGCTGGCCTTGACTCAGCACATTGGCACCT
1 GCATATTGGC-CCTTTATCCTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
2250 TCATCTTTAAGTCCAATGTAGCTGGCCTT
65 TCATCTTTAAGTCCAATATAGCTAGCC-T
** * * ** *
2279 G-A-ATCAGCACATTGGCACTTTTAAGTCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACCT
1 GCATATTGGCCCTTTATC-CTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCT
* *
2342 TTATCTTTAAGTCCAATATCGCTAGCC-
65 TCATCTTTAAGTCCAATATAGCTAGCCT
2369 GCATATTGGCTCCTTTATCCTTTT
1 GCATATTGGC-CCTTTATCCTTTT
2393 TCTCATCTCT
Statistics
Matches: 90, Mismatches: 18, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
89 3 0.03
90 5 0.06
91 3 0.03
92 75 0.83
93 4 0.04
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.34
Consensus pattern (92 bp):
GCATATTGGCCCTTTATCCTTTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACCTT
CATCTTTAAGTCCAATATAGCTAGCCT
Found at i:3115 original size:33 final size:33
Alignment explanation
Indices: 3078--3144 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
3068 TTCAACGATT
3078 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
3111 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
3144 T
1 T
3145 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:3116 original size:13 final size:13
Alignment explanation
Indices: 3098--3122 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3088 CATAAAATGT
3098 TGTATCGATACAA
1 TGTATCGATACAA
3111 TGTATCGATACA
1 TGTATCGATACA
3123 TATTTTTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:3205 original size:13 final size:13
Alignment explanation
Indices: 3187--3211 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3177 ATTACTCACA
3187 TGTATCGATACAT
1 TGTATCGATACAT
3200 TGTATCGATACA
1 TGTATCGATACA
3212 CTGATCTTTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:3348 original size:52 final size:52
Alignment explanation
Indices: 3220--3340 Score: 224
Period size: 52 Copynumber: 2.3 Consensus size: 52
3210 CACTGATCTT
*
3220 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
3272 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
3324 TGTATCGATACATGCAG
1 TGTATCGATACATGCAG
3341 ATAAATTTTC
Statistics
Matches: 67, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 67 1.00
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:7318 original size:20 final size:20
Alignment explanation
Indices: 7293--7367 Score: 73
Period size: 20 Copynumber: 3.8 Consensus size: 20
7283 AAAAAACTGC
7293 ATGTATCGATACATTAAAGT
1 ATGTATCGATACATTAAAGT
* *
7313 ATGTATCGATACA-AAGCAAAT
1 ATGTATCGATACATTA--AAGT
** *
7334 -TGTATCGATACATCCAAGA
1 ATGTATCGATACATTAAAGT
7353 ATGTATCGATACATT
1 ATGTATCGATACATT
7368 TACTTATGTA
Statistics
Matches: 44, Mismatches: 7, Indels: 8
0.75 0.12 0.14
Matches are distributed among these distances:
19 3 0.07
20 38 0.86
21 3 0.07
ACGTcount: A:0.40, C:0.15, G:0.15, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACATTAAAGT
Found at i:7460 original size:20 final size:21
Alignment explanation
Indices: 7437--7487 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
7427 TTCAGACATG
7437 TATCAATACATTCACTTA-TA
1 TATCAATACATTCACTTATTA
* * *
7457 TATCGATACATTTACTTATTG
1 TATCAATACATTCACTTATTA
7478 TATCAATACA
1 TATCAATACA
7488 AATTGTTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.37, C:0.18, G:0.04, T:0.41
Consensus pattern (21 bp):
TATCAATACATTCACTTATTA
Found at i:8686 original size:26 final size:27
Alignment explanation
Indices: 8634--8691 Score: 82
Period size: 26 Copynumber: 2.2 Consensus size: 27
8624 GTAATGGCAT
* *
8634 TAACACAAACTAACAAAATATTTTCAA
1 TAACACAAAATAACAAAATATTCTCAA
*
8661 TAACACAAAATAA-AATATATTCTCAA
1 TAACACAAAATAACAAAATATTCTCAA
8687 TAACA
1 TAACA
8692 TAGTAACACA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
26 16 0.57
27 12 0.43
ACGTcount: A:0.57, C:0.17, G:0.00, T:0.26
Consensus pattern (27 bp):
TAACACAAAATAACAAAATATTCTCAA
Found at i:8733 original size:34 final size:34
Alignment explanation
Indices: 8658--8733 Score: 82
Period size: 34 Copynumber: 2.2 Consensus size: 34
8648 AAAATATTTT
* * *
8658 CAATAACACAAAATAAAATATATTCTCAATAACA
1 CAATAACACAAAATAAAAAACATTCTCAAAAACA
* * *
8692 TAGTAACACAAACTAATAAAACATTCT-AAAAACA
1 CAATAACACAAAATAA-AAAACATTCTCAAAAACA
8726 CAATAACA
1 CAATAACA
8734 TTTATATATA
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
34 25 0.76
35 8 0.24
ACGTcount: A:0.59, C:0.18, G:0.01, T:0.21
Consensus pattern (34 bp):
CAATAACACAAAATAAAAAACATTCTCAAAAACA
Found at i:10241 original size:19 final size:20
Alignment explanation
Indices: 10219--10263 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 20
10209 TAAACAAAAT
10219 AATATAAATTAAAAT-TTTA
1 AATATAAATTAAAATATTTA
*
10238 AATAT-TATTAAAATATTTA
1 AATATAAATTAAAATATTTA
*
10257 AAAATAA
1 AATATAA
10264 TTTATCAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
18 8 0.38
19 13 0.62
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
AATATAAATTAAAATATTTA
Found at i:12551 original size:20 final size:20
Alignment explanation
Indices: 12528--12566 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
12518 TTAGCATATA
12528 TTTTTCTAAATTTTAAATTT
1 TTTTTCTAAATTTTAAATTT
* **
12548 TTTTTGTATTTTTTAAATT
1 TTTTTCTAAATTTTAAATT
12567 ATAAAAGAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (20 bp):
TTTTTCTAAATTTTAAATTT
Found at i:13323 original size:37 final size:37
Alignment explanation
Indices: 13238--13433 Score: 162
Period size: 37 Copynumber: 5.3 Consensus size: 37
13228 AAACAGGTTT
* *
13238 CAAT-CGTGCCACCGGTTAAGAATAGTGATTTCTGTTC
1 CAATCCGTGCCACCGG-TAAGAATAGTGGTTTTTGTTC
* * * * *
13275 CGACCCATGCCACCGGTAAGAATAGTGGTTTTTATCC
1 CAATCCGTGCCACCGGTAAGAATAGTGGTTTTTGTTC
** * * *
13312 CAATCCGTGCCATTGATAAGAATAGTGATTTTTGTCC
1 CAATCCGTGCCACCGGTAAGAATAGTGGTTTTTGTTC
* * * * *
13349 CAATCTGTGCCACTGGTAAGAATAGTAGTTTTTATTTT
1 CAATCCGTGCCACCGGTAAGAATAGTGGTTTTT-GTTC
* * *
13387 AAAT-CGTGCCACCGATTAAGAATAGTAGTTTTTGTTC
1 CAATCCGTGCCACCG-GTAAGAATAGTGGTTTTTGTTC
*
13424 CAAACCGTGC
1 CAATCCGTGC
13434 TACTGAATTA
Statistics
Matches: 124, Mismatches: 31, Indels: 7
0.77 0.19 0.04
Matches are distributed among these distances:
37 88 0.71
38 36 0.29
ACGTcount: A:0.27, C:0.20, G:0.20, T:0.33
Consensus pattern (37 bp):
CAATCCGTGCCACCGGTAAGAATAGTGGTTTTTGTTC
Found at i:13395 original size:74 final size:76
Alignment explanation
Indices: 13242--13461 Score: 223
Period size: 74 Copynumber: 2.9 Consensus size: 76
13232 AGGTTTCAAT
* * * * * * *
13242 CGTGCCACCGGTTAAGAATAGTGATTTCTGTTCCGACCCATGCCACCGGTAAGAATAGTGGTTTT
1 CGTGCCACCGATTAAGAATAGTGATTTTTGTTCCAAACCGTGCCACTGGTAAGAATAGTAGTTTT
*
13307 TA-TCCCAATC
66 TATTCCAAATC
** * * *
13317 CGTGCCATTGA-TAAGAATAGTGATTTTTGTCCCAATCTGTGCCACTGGTAAGAATAGTAGTTTT
1 CGTGCCACCGATTAAGAATAGTGATTTTTGTTCCAAACCGTGCCACTGGTAAGAATAGTAGTTTT
**
13381 TATTTTAAAT-
66 TATTCCAAATC
* * * *
13391 CGTGCCACCGATTAAGAATAGT-AGTTTTTGTTCCAAACCGTGCTACTGAATTAGAATAGTAATT
1 CGTGCCACCGATTAAGAATAGTGA-TTTTTGTTCCAAACCGTGCCACTG-GTAAGAATAGTAGTT
13455 TTTATTC
64 TTTATTC
13462 TAACCTATGC
Statistics
Matches: 117, Mismatches: 24, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
74 57 0.49
75 42 0.36
76 18 0.15
ACGTcount: A:0.27, C:0.19, G:0.19, T:0.35
Consensus pattern (76 bp):
CGTGCCACCGATTAAGAATAGTGATTTTTGTTCCAAACCGTGCCACTGGTAAGAATAGTAGTTTT
TATTCCAAATC
Found at i:13414 original size:38 final size:39
Alignment explanation
Indices: 13291--13461 Score: 122
Period size: 37 Copynumber: 4.5 Consensus size: 39
13281 ATGCCACCGG
* * * **
13291 TAAGAATAGTGGTTTTTATCCCAATCCGTGCCATTG-A-
1 TAAGAATAGTAGTTTTTATTCCAAACCGTGCCACCGAAT
* * * * * *
13328 TAAGAATAGT-GATTTTTGTCCCAATCTGTGCCACTG--G
1 TAAGAATAGTAG-TTTTTATTCCAAACCGTGCCACCGAAT
** *
13365 TAAGAATAGTAGTTTTTATTTTAAATCGTGCCACCG-AT
1 TAAGAATAGTAGTTTTTATTCCAAACCGTGCCACCGAAT
* * *
13403 TAAGAATAGTAGTTTTTGTTCCAAACCGTGCTACTGAAT
1 TAAGAATAGTAGTTTTTATTCCAAACCGTGCCACCGAAT
*
13442 T-AGAATAGTAATTTTTATTC
1 TAAGAATAGTAGTTTTTATTC
13462 TAACCTATGC
Statistics
Matches: 109, Mismatches: 20, Indels: 9
0.79 0.14 0.07
Matches are distributed among these distances:
36 1 0.01
37 57 0.52
38 48 0.44
39 3 0.03
ACGTcount: A:0.29, C:0.15, G:0.18, T:0.38
Consensus pattern (39 bp):
TAAGAATAGTAGTTTTTATTCCAAACCGTGCCACCGAAT
Found at i:15892 original size:39 final size:39
Alignment explanation
Indices: 15855--15987 Score: 69
Period size: 40 Copynumber: 3.4 Consensus size: 39
15845 ATTAATATTT
* * *
15855 TTTAAAATTAAATTATATATAATATTTAAATTTATATT-AT-
1 TTTAAATTTAAATTAT-TTTAA-ATTTAAA-TTATTTTAATA
*** * * *
15895 TTTAAATTTTGCTTATTTTAATTTTTAA-T-TTTAAATTA
1 TTTAAATTTAAATTATTTTAAATTTAAATTATTTTAA-TA
** *
15933 CTTTTAAATTTAAATTATTTTAAATTTAAATTAAATT-ATT
1 -TT-TAAATTTAAATTATTTTAAATTTAAATTATTTTAATA
15973 TTTAAATTTAAATTA
1 TTTAAATTTAAATTA
15988 AAAATTTTTA
Statistics
Matches: 68, Mismatches: 18, Indels: 16
0.67 0.18 0.16
Matches are distributed among these distances:
35 2 0.03
36 2 0.03
37 1 0.01
38 18 0.26
39 8 0.12
40 34 0.50
41 2 0.03
42 1 0.01
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.56
Consensus pattern (39 bp):
TTTAAATTTAAATTATTTTAAATTTAAATTATTTTAATA
Found at i:15900 original size:16 final size:16
Alignment explanation
Indices: 15862--15965 Score: 64
Period size: 16 Copynumber: 6.9 Consensus size: 16
15852 TTTTTTAAAA
*
15862 TTAAATTATATATAATAT
1 TTAAATT-TATATTAT-T
15880 TTAAATTTATATTATT
1 TTAAATTTATATTATT
*
15896 TTAAATTT-TGCTTATT
1 TTAAATTTAT-ATTATT
*
15912 TT-AATTT-T-TAATT
1 TTAAATTTATATTATT
*
15925 TTAAA--T-TA--CTT
1 TTAAATTTATATTATT
*
15936 TTAAATTTAAATTATT
1 TTAAATTTATATTATT
*
15952 TTAAATTTAAATTA
1 TTAAATTTATATTA
15966 AATTATTTTT
Statistics
Matches: 72, Mismatches: 6, Indels: 18
0.75 0.06 0.19
Matches are distributed among these distances:
11 7 0.10
12 2 0.03
13 7 0.10
14 3 0.04
15 7 0.10
16 32 0.44
17 7 0.10
18 7 0.10
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.58
Consensus pattern (16 bp):
TTAAATTTATATTATT
Found at i:15981 original size:56 final size:55
Alignment explanation
Indices: 15879--15987 Score: 139
Period size: 56 Copynumber: 2.0 Consensus size: 55
15869 ATATATAATA
* *** **
15879 TTTAAATTTATATTATTTTAAATTTTGCTTATTTTAATTTTTAATTTTAAATTACT
1 TTTAAATTTAAATTATTTTAAATTTAAATTAAATTAATTTTTAA-TTTAAATTACT
15935 TTTAAATTTAAATTATTTTAAATTTAAATTAAATT-ATTTTTAAATTTAAATTA
1 TTTAAATTTAAATTATTTTAAATTTAAATTAAATTAATTTTT-AATTTAAATTA
15988 AAAATTTTTA
Statistics
Matches: 46, Mismatches: 6, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 15 0.33
56 31 0.67
ACGTcount: A:0.39, C:0.02, G:0.01, T:0.59
Consensus pattern (55 bp):
TTTAAATTTAAATTATTTTAAATTTAAATTAAATTAATTTTTAATTTAAATTACT
Found at i:15987 original size:17 final size:16
Alignment explanation
Indices: 15917--15965 Score: 80
Period size: 16 Copynumber: 3.0 Consensus size: 16
15907 TTATTTTAAT
*
15917 TTTTAATTTTAAATTA
1 TTTTAAATTTAAATTA
15933 CTTTTAAATTTAAATTA
1 -TTTTAAATTTAAATTA
15950 TTTTAAATTTAAATTA
1 TTTTAAATTTAAATTA
15966 AATTATTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
16 16 0.52
17 15 0.48
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (16 bp):
TTTTAAATTTAAATTA
Found at i:15987 original size:22 final size:22
Alignment explanation
Indices: 15935--15997 Score: 94
Period size: 22 Copynumber: 2.9 Consensus size: 22
15925 TTAAATTACT
15935 TTTAAATTTAAATTA-TTTTAAA
1 TTTAAA-TTAAATTATTTTTAAA
15957 TTTAAATTAAATTATTTTTAAA
1 TTTAAATTAAATTATTTTTAAA
*
15979 TTTAAATTAAA-AATTTTTA
1 TTTAAATTAAATTATTTTTA
15998 TTATTAATTT
Statistics
Matches: 39, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
21 15 0.38
22 24 0.62
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
TTTAAATTAAATTATTTTTAAA
Found at i:16048 original size:20 final size:21
Alignment explanation
Indices: 16013--16057 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
16003 AATTTATTAT
16013 AATTAAATTAAATTAAATCAA
1 AATTAAATTAAATTAAATCAA
*
16034 AATTAAA-TGAATTAAATCAA
1 AATTAAATTAAATTAAATCAA
16054 AATT
1 AATT
16058 TTTGCGAAGG
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.60, C:0.04, G:0.02, T:0.33
Consensus pattern (21 bp):
AATTAAATTAAATTAAATCAA
Found at i:18277 original size:2 final size:2
Alignment explanation
Indices: 18270--18298 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
18260 ATATTTAATT
18270 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
18299 TCTTAGAGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:19395 original size:3 final size:3
Alignment explanation
Indices: 19387--19421 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
19377 GCTCTAAGTT
19387 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
19422 TCATAGAACT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:19905 original size:18 final size:18
Alignment explanation
Indices: 19882--19916 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
19872 TCAAGAGGGA
19882 ATATATGTATATATATTT
1 ATATATGTATATATATTT
*
19900 ATATATGTATGTATATT
1 ATATATGTATATATATT
19917 GCTTCTAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (18 bp):
ATATATGTATATATATTT
Found at i:22713 original size:24 final size:25
Alignment explanation
Indices: 22666--22714 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
22656 AAATTTTCTT
*
22666 TTTTAAAAAGTAAAATTTAGAAAAA
1 TTTTAAAAAGTAAAATTCAGAAAAA
*
22691 TTTTAAAAATTAAAATTCA-AAAAA
1 TTTTAAAAAGTAAAATTCAGAAAAA
22715 GTTCTTTTCA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (25 bp):
TTTTAAAAAGTAAAATTCAGAAAAA
Found at i:25589 original size:2 final size:2
Alignment explanation
Indices: 25582--25630 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
25572 ATTATAATAC
* *
25582 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AA AT A- AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
25623 TT AT AT AT
1 AT AT AT AT
25631 TTTTTAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:36071 original size:16 final size:16
Alignment explanation
Indices: 36052--36110 Score: 73
Period size: 16 Copynumber: 3.7 Consensus size: 16
36042 TCGAATTTAG
36052 AATAACTTAAATTCAA
1 AATAACTTAAATTCAA
* ** *
36068 AATAGCCCAAATTCGA
1 AATAACTTAAATTCAA
*
36084 AATAACTTAAACTCAA
1 AATAACTTAAATTCAA
36100 AATAACTTAAA
1 AATAACTTAAA
36111 CTTGAAATGA
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.54, C:0.17, G:0.03, T:0.25
Consensus pattern (16 bp):
AATAACTTAAATTCAA
Found at i:36118 original size:16 final size:16
Alignment explanation
Indices: 36052--36118 Score: 62
Period size: 16 Copynumber: 4.2 Consensus size: 16
36042 TCGAATTTAG
* *
36052 AATAACTTAAATTCAA
1 AATAACTTAAACTCGA
* ** *
36068 AATAGCCCAAATTCGA
1 AATAACTTAAACTCGA
*
36084 AATAACTTAAACTCAA
1 AATAACTTAAACTCGA
*
36100 AATAACTTAAACTTGA
1 AATAACTTAAACTCGA
36116 AAT
1 AAT
36119 GACCTGAATA
Statistics
Matches: 40, Mismatches: 11, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
16 40 1.00
ACGTcount: A:0.52, C:0.16, G:0.04, T:0.27
Consensus pattern (16 bp):
AATAACTTAAACTCGA
Found at i:36515 original size:16 final size:16
Alignment explanation
Indices: 36494--36524 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
36484 ATAACTCAAA
36494 CCTAAAATGGCCTGAC
1 CCTAAAATGGCCTGAC
36510 CCTAAAATGGCCTGA
1 CCTAAAATGGCCTGA
36525 ATTCGAAACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.29, G:0.19, T:0.19
Consensus pattern (16 bp):
CCTAAAATGGCCTGAC
Found at i:37173 original size:11 final size:12
Alignment explanation
Indices: 37155--37188 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
37145 AACGAATTCT
37155 ATTTTTTATTTA
1 ATTTTTTATTTA
*
37167 A-TTTTTAATTA
1 ATTTTTTATTTA
37178 ATTTTTTATTT
1 ATTTTTTATTT
37189 TTGATAATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (12 bp):
ATTTTTTATTTA
Found at i:39886 original size:16 final size:17
Alignment explanation
Indices: 39855--39891 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
39845 TTTTTGAATT
39855 ATTTTCGAGTTCGAGTC
1 ATTTTCGAGTTCGAGTC
*
39872 ATTTT-GAGTTTGAGTC
1 ATTTTCGAGTTCGAGTC
39888 ATTT
1 ATTT
39892 CGGATTCGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.19, C:0.11, G:0.22, T:0.49
Consensus pattern (17 bp):
ATTTTCGAGTTCGAGTC
Found at i:39907 original size:16 final size:15
Alignment explanation
Indices: 39885--39974 Score: 56
Period size: 16 Copynumber: 5.7 Consensus size: 15
39875 TTGAGTTTGA
39885 GTCATTTCGGATTCG
1 GTCATTTCGGATTCG
* ***
39900 GATTATTTTATATTCAG
1 G-TCATTTCGGATTC-G
*
39917 GTCATTTCGGGTTCGG
1 GTCATTTCGGATTC-G
*
39933 GTTACTTT-GGATTCAG
1 GTCA-TTTCGGATTC-G
*
39949 GTCATTTCGGGTTCG
1 GTCATTTCGGATTCG
39964 GATCATTTCGG
1 G-TCATTTCGG
39975 GTTCAGATTG
Statistics
Matches: 55, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
15 6 0.11
16 44 0.80
17 5 0.09
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.42
Consensus pattern (15 bp):
GTCATTTCGGATTCG
Found at i:39908 original size:32 final size:33
Alignment explanation
Indices: 39872--39971 Score: 109
Period size: 32 Copynumber: 3.1 Consensus size: 33
39862 AGTTCGAGTC
* *
39872 ATTTTGAGTTTGA-GTCATTTCGGATTCGGATT
1 ATTTTGAGTTTCAGGTCATTTCGGGTTCGGATT
*
39904 ATTTT-A-TATTCAGGTCATTTCGGGTTCGGGTT
1 ATTTTGAGT-TTCAGGTCATTTCGGGTTCGGATT
* * *
39936 ACTTTG-GATTCAGGTCATTTCGGGTTCGGATC
1 ATTTTGAGTTTCAGGTCATTTCGGGTTCGGATT
39968 ATTT
1 ATTT
39972 CGGGTTCAGA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
30 1 0.02
31 4 0.07
32 51 0.91
ACGTcount: A:0.17, C:0.13, G:0.25, T:0.45
Consensus pattern (33 bp):
ATTTTGAGTTTCAGGTCATTTCGGGTTCGGATT
Found at i:39975 original size:16 final size:15
Alignment explanation
Indices: 39916--39978 Score: 65
Period size: 16 Copynumber: 4.0 Consensus size: 15
39906 TTTATATTCA
39916 GGTCATTTCGGGTTC
1 GGTCATTTCGGGTTC
* *
39931 GGGTTACTTT-GGATTC
1 -GGTCA-TTTCGGGTTC
39947 AGGTCATTTCGGGTTC
1 -GGTCATTTCGGGTTC
39963 GGATCATTTCGGGTTC
1 GG-TCATTTCGGGTTC
39979 AGATTGTTTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
15 5 0.13
16 31 0.79
17 3 0.08
ACGTcount: A:0.11, C:0.17, G:0.32, T:0.40
Consensus pattern (15 bp):
GGTCATTTCGGGTTC
Found at i:39980 original size:32 final size:31
Alignment explanation
Indices: 39885--39980 Score: 111
Period size: 32 Copynumber: 3.0 Consensus size: 31
39875 TTGAGTTTGA
* **
39885 GTCATTTCGGATTCGGATTATTTTATATTCAG
1 GTCATTTCGGGTTCGGATTA-TTTGGATTCAG
*
39917 GTCATTTCGGGTTCGGGTTACTTTGGATTCAG
1 GTCATTTCGGGTTCGGATTA-TTTGGATTCAG
* *
39949 GTCATTTCGGGTTCGGATCATTTCGGGTTCAG
1 GTCATTTCGGGTTCGGATTATTT-GGATTCAG
39981 ATTGTTTTAG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
31 3 0.05
32 52 0.95
ACGTcount: A:0.16, C:0.16, G:0.27, T:0.42
Consensus pattern (31 bp):
GTCATTTCGGGTTCGGATTATTTGGATTCAG
Found at i:40635 original size:17 final size:18
Alignment explanation
Indices: 40599--40639 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
40589 AATACATATA
* *
40599 TAATTATTACATTATTTT
1 TAATAATTAAATTATTTT
40617 TAATAATTAAATT-TTTT
1 TAATAATTAAATTATTTT
40634 TAATAA
1 TAATAA
40640 AAAGTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATAATTAAATTATTTT
Found at i:41085 original size:32 final size:32
Alignment explanation
Indices: 41034--41149 Score: 106
Period size: 32 Copynumber: 3.6 Consensus size: 32
41024 GAGGTTAATT
*
41034 ATTCGGATCATTTCAGGTTCAAATCATTTCGG
1 ATTCGGATCATTTCGGGTTCAAATCATTTCGG
* ** *
41066 ATTCTGATCATTTCGGGTTCAGGTCATTTTGG
1 ATTCGGATCATTTCGGGTTCAAATCATTTCGG
* * *** **
41098 ATTCGGGTCATTTCGAGTTTGGATCATTTTAG
1 ATTCGGATCATTTCGGGTTCAAATCATTTCGG
* *
41130 ATTAGGATCATTTCGAGTTC
1 ATTCGGATCATTTCGGGTTC
41150 GAGTCATTCC
Statistics
Matches: 69, Mismatches: 15, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.21, C:0.16, G:0.22, T:0.41
Consensus pattern (32 bp):
ATTCGGATCATTTCGGGTTCAAATCATTTCGG
Found at i:41092 original size:16 final size:16
Alignment explanation
Indices: 41034--41112 Score: 70
Period size: 16 Copynumber: 4.9 Consensus size: 16
41024 GAGGTTAATT
*
41034 ATTCGGATCATTTCAGG
1 ATTCAGATCATTTC-GG
*
41051 -TTCAAATCATTTCGG
1 ATTCAGATCATTTCGG
*
41066 ATTCTGATCATTTCGG
1 ATTCAGATCATTTCGG
* * *
41082 GTTCAGGTCATTTTGG
1 ATTCAGATCATTTCGG
* *
41098 ATTCGGGTCATTTCG
1 ATTCAGATCATTTCG
41113 AGTTTGGATC
Statistics
Matches: 50, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
15 2 0.04
16 48 0.96
ACGTcount: A:0.19, C:0.18, G:0.23, T:0.41
Consensus pattern (16 bp):
ATTCAGATCATTTCGG
Found at i:41124 original size:16 final size:16
Alignment explanation
Indices: 41105--41148 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
41095 TGGATTCGGG
*
41105 TCATTTCGAGTTTGGA
1 TCATTTCGAGTTAGGA
*
41121 TCATTT-TAGATTAGGA
1 TCATTTCGAG-TTAGGA
41137 TCATTTCGAGTT
1 TCATTTCGAGTT
41149 CGAGTCATTC
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.09
16 19 0.83
17 2 0.09
ACGTcount: A:0.23, C:0.11, G:0.20, T:0.45
Consensus pattern (16 bp):
TCATTTCGAGTTAGGA
Found at i:41156 original size:16 final size:16
Alignment explanation
Indices: 41137--41185 Score: 64
Period size: 16 Copynumber: 3.1 Consensus size: 16
41127 TAGATTAGGA
41137 TCATTTCGAGTTCGAG
1 TCATTTCGAGTTCGAG
*
41153 TCATTCCGAGTTCGAG
1 TCATTTCGAGTTCGAG
*
41169 TCAATTCG-GATTCGAG
1 TCATTTCGAG-TTCGAG
41185 T
1 T
41186 TGTTGATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
15 1 0.03
16 28 0.97
ACGTcount: A:0.20, C:0.20, G:0.24, T:0.35
Consensus pattern (16 bp):
TCATTTCGAGTTCGAG
Found at i:43366 original size:38 final size:39
Alignment explanation
Indices: 43307--43385 Score: 108
Period size: 38 Copynumber: 2.1 Consensus size: 39
43297 AACGGTCCCT
* *
43307 AAATCATAGTAAATTATTAAAACGA-TCTTAAAATGCATG
1 AAATCATAGAAAATTAATAAAA-GAGTCTTAAAATGCATG
*
43346 AAATCAT-GAAAATTAATAAAATAGTCTTAAAATGCATG
1 AAATCATAGAAAATTAATAAAAGAGTCTTAAAATGCATG
43384 AA
1 AA
43386 TTTATATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
37 1 0.03
38 28 0.78
39 7 0.19
ACGTcount: A:0.52, C:0.09, G:0.10, T:0.29
Consensus pattern (39 bp):
AAATCATAGAAAATTAATAAAAGAGTCTTAAAATGCATG
Found at i:43643 original size:57 final size:57
Alignment explanation
Indices: 43518--43675 Score: 174
Period size: 57 Copynumber: 2.7 Consensus size: 57
43508 TATTTCATGG
* * * *
43518 AAAATTACTATAATGACATACAAATGCATGAAATGATATAAAAATTCCTAAATCATAC
1 AAAATTACTAAAATGACATAAAAATGCATGAAA-GACATAAAAATTCCTAAATCATAA
* * * * * *
43576 GAAATGACTAAAATGACGTAAAAATGCATAGAAA-ACATGAAATTTCCTAAGTCATAA
1 AAAATTACTAAAATGACATAAAAATGCAT-GAAAGACATAAAAATTCCTAAATCATAA
* *
43633 AAAATTACTAAAATGACATAAAAATGTATGAAATGACACAAAA
1 AAAATTACTAAAATGACATAAAAATGCATGAAA-GACATAAAA
43676 GTCCTTAATA
Statistics
Matches: 81, Mismatches: 16, Indels: 6
0.79 0.16 0.06
Matches are distributed among these distances:
56 4 0.05
57 43 0.53
58 30 0.37
59 4 0.05
ACGTcount: A:0.54, C:0.12, G:0.10, T:0.24
Consensus pattern (57 bp):
AAAATTACTAAAATGACATAAAAATGCATGAAAGACATAAAAATTCCTAAATCATAA
Found at i:43657 original size:20 final size:20
Alignment explanation
Indices: 43632--43675 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
43622 CTAAGTCATA
*
43632 AAAAAT-TACTAAAATGACAT
1 AAAAATGTA-TAAAATGACAC
*
43652 AAAAATGTATGAAATGACAC
1 AAAAATGTATAAAATGACAC
43672 AAAA
1 AAAA
43676 GTCCTTAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 19 0.90
21 2 0.10
ACGTcount: A:0.61, C:0.09, G:0.09, T:0.20
Consensus pattern (20 bp):
AAAAATGTATAAAATGACAC
Found at i:45589 original size:17 final size:17
Alignment explanation
Indices: 45569--45601 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
45559 AATGTCATTT
45569 CAAAGAAAATATCTTTG
1 CAAAGAAAATATCTTTG
*
45586 CAAAGAAAGTATCTTT
1 CAAAGAAAATATCTTT
45602 ACAGGTGCTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.45, C:0.12, G:0.12, T:0.30
Consensus pattern (17 bp):
CAAAGAAAATATCTTTG
Found at i:47283 original size:29 final size:29
Alignment explanation
Indices: 47248--47353 Score: 140
Period size: 29 Copynumber: 3.7 Consensus size: 29
47238 TAAAGCTAAG
* *
47248 GAATTAAAAGTCAACTAAAATGCAAAAAA
1 GAATTAAAAGTCAACTAAAACGCTAAAAA
*
47277 GAATTAAAAGTCAACTAAAACACTAAAAA
1 GAATTAAAAGTCAACTAAAACGCTAAAAA
* * * *
47306 GAATTAAAAGTCGATTAAAACGTTAAAAG
1 GAATTAAAAGTCAACTAAAACGCTAAAAA
*
47335 GAATTAAAAGTCGACTAAA
1 GAATTAAAAGTCAACTAAA
47354 GCACCAAAAC
Statistics
Matches: 68, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
29 68 1.00
ACGTcount: A:0.58, C:0.10, G:0.12, T:0.20
Consensus pattern (29 bp):
GAATTAAAAGTCAACTAAAACGCTAAAAA
Found at i:49184 original size:23 final size:23
Alignment explanation
Indices: 49141--49184 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
49131 AATGAAATAA
* *
49141 AAAATAATGGATAAATTTACACC
1 AAAATAATGCATAAATATACACC
49164 AAAATACATGCATAAA-ATACA
1 AAAATA-ATGCATAAATATACA
49185 AAAATTTACA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.57, C:0.14, G:0.07, T:0.23
Consensus pattern (23 bp):
AAAATAATGCATAAATATACACC
Found at i:49342 original size:80 final size:79
Alignment explanation
Indices: 49247--49416 Score: 223
Period size: 79 Copynumber: 2.1 Consensus size: 79
49237 ATCTCAATGA
* * *
49247 TGAAAAATTTAATATTTTAGAAGTAAAAACGAGACTGGAGTATCCCATCAAAAATAATGGGGTTG
1 TGAAAAATTTGATATTTTAGAAGTAAAAACGAGACTGGAGTAT-CCAACAAAAATAATGAGGTTG
49312 AAGTATCCCCGATAG
65 AAGTATCCCCGATAG
* * ** * * *
49327 TGAAAAATTTGATATTTTGGAAGTAAAAATGAGGTTGGAGTATCTAACAAAAATGATGAGGTTGG
1 TGAAAAATTTGATATTTTAGAAGTAAAAACGAGACTGGAGTATCCAACAAAAATAATGAGGTTGA
*
49392 AGTATCTCCGATAG
66 AGTATCCCCGATAG
*
49406 TAAAAAATTTG
1 TGAAAAATTTG
49417 GAAGTAAAAA
Statistics
Matches: 78, Mismatches: 12, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
79 40 0.51
80 38 0.49
ACGTcount: A:0.41, C:0.09, G:0.22, T:0.29
Consensus pattern (79 bp):
TGAAAAATTTGATATTTTAGAAGTAAAAACGAGACTGGAGTATCCAACAAAAATAATGAGGTTGA
AGTATCCCCGATAG
Found at i:49416 original size:79 final size:77
Alignment explanation
Indices: 49249--49521 Score: 247
Period size: 80 Copynumber: 3.5 Consensus size: 77
49239 CTCAATGATG
* * ** * * *
49249 AAAAATTTAATATTTTAGAAGTAAAAACGAGACTGGAGTATCCCATCAAAAATAATGGGGTTGAA
1 AAAAATTTGATATTTTGGAAGTAAAAACGAGGTTGGAGTAT-CTATCAAAAATGATGGGGTTGGA
49314 GTATCCCCGATAGT
65 GTAT-CCCGATAGT
* * *
49328 GAAAAATTTGATATTTTGGAAGTAAAAATGAGGTTGGAGTATCTAACAAAAATGATGAGGTTGGA
1 -AAAAATTTGATATTTTGGAAGTAAAAACGAGGTTGGAGTATCTATCAAAAATGATGGGGTTGGA
49393 GTATCTCCGATAGT
65 GTATC-CCGATAGT
* * * * *
49407 -AAAA----A-A-TTTGGAAGTAAAAA-TAGGATTAGAGTATCTCCTCGAAAATGATGGGGTTAG
1 AAAAATTTGATATTTTGGAAGTAAAAACGAGG-TTGGAGTATCT-ATCAAAAATGATGGGGTTGG
* * *
49464 AGTATCCCAAATGGC
64 AGTATCCC-GATAGT
*
49479 AAAAATTTTGATATTTTGGAAGTAAAAACGGGGTTGGAGTATC
1 AAAAA-TTTGATATTTTGGAAGTAAAAACGAGGTTGGAGTATC
49522 CCAATGGTGA
Statistics
Matches: 157, Mismatches: 23, Indels: 26
0.76 0.11 0.13
Matches are distributed among these distances:
70 3 0.02
71 26 0.17
72 25 0.16
73 5 0.03
77 4 0.03
78 2 0.01
79 31 0.20
80 59 0.38
81 2 0.01
ACGTcount: A:0.40, C:0.09, G:0.23, T:0.28
Consensus pattern (77 bp):
AAAAATTTGATATTTTGGAAGTAAAAACGAGGTTGGAGTATCTATCAAAAATGATGGGGTTGGAG
TATCCCGATAGT
Found at i:49483 original size:71 final size:71
Alignment explanation
Indices: 49342--49486 Score: 161
Period size: 71 Copynumber: 2.0 Consensus size: 71
49332 AATTTGATAT
* * * *
49342 TTTGGAAGTAAAAATGAGGTTGGAGTATCTAACAAAAATGATGAGGTTGGAGTATCTCCGATAGT
1 TTTGGAAGTAAAAATGAGGTTAGAGTATCTAACAAAAATGATGAGGTTAGAGTATCTCCAATAGG
49407 AAAAAA
66 AAAAAA
** * *
49413 TTTGGAAGTAAAAAT-AGGATTAGAGTATCTCCTCGAAAATGATGGGGTTAGAGTATC-CCAA-A
1 TTTGGAAGTAAAAATGAGG-TTAGAGTATCT-AACAAAAATGATGAGGTTAGAGTATCTCCAATA
*
49475 TGGCAAAAA
64 -GGAAAAAA
49484 TTT
1 TTT
49487 TGATATTTTG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
70 4 0.06
71 37 0.60
72 21 0.34
ACGTcount: A:0.39, C:0.09, G:0.24, T:0.28
Consensus pattern (71 bp):
TTTGGAAGTAAAAATGAGGTTAGAGTATCTAACAAAAATGATGAGGTTAGAGTATCTCCAATAGG
AAAAAA
Found at i:49542 original size:51 final size:52
Alignment explanation
Indices: 49456--49573 Score: 184
Period size: 51 Copynumber: 2.3 Consensus size: 52
49446 CGAAAATGAT
49456 GGGGTTAGAGTATCCCAAATGGCAAAAATTTTGATATTTTGGAAGTAAAAAC
1 GGGGTTAGAGTATCCCAAATGGCAAAAATTTTGATATTTTGGAAGTAAAAAC
* ** *
49508 GGGGTTGGAGTATCCC-AATGGTGAAAATTTTGATATTTTTGAAGTAAAAAC
1 GGGGTTAGAGTATCCCAAATGGCAAAAATTTTGATATTTTGGAAGTAAAAAC
*
49559 AGGGTTAGAGTATCC
1 GGGGTTAGAGTATCC
49574 TCTCAAAAAT
Statistics
Matches: 60, Mismatches: 6, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
51 45 0.75
52 15 0.25
ACGTcount: A:0.35, C:0.09, G:0.25, T:0.31
Consensus pattern (52 bp):
GGGGTTAGAGTATCCCAAATGGCAAAAATTTTGATATTTTGGAAGTAAAAAC
Found at i:51834 original size:23 final size:23
Alignment explanation
Indices: 51808--51871 Score: 119
Period size: 23 Copynumber: 2.8 Consensus size: 23
51798 TCAAAATTAC
51808 CTTGTTTAAATTTGATTTTGAAA
1 CTTGTTTAAATTTGATTTTGAAA
51831 CTTGTTTAAATTTGATTTTGAAA
1 CTTGTTTAAATTTGATTTTGAAA
*
51854 CGTGTTTAAATTTGATTT
1 CTTGTTTAAATTTGATTT
51872 CGACCCCAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.28, C:0.05, G:0.14, T:0.53
Consensus pattern (23 bp):
CTTGTTTAAATTTGATTTTGAAA
Found at i:52076 original size:52 final size:50
Alignment explanation
Indices: 51997--52131 Score: 155
Period size: 52 Copynumber: 2.6 Consensus size: 50
51987 AATTGCCTAC
51997 ATGTATCGATACATTAAAAAATGTATCGATACATTTGGCTCAAAAA-CTCAAA
1 ATGTATCGATACATTAAAAAATGTATCGATAC--TTGGCTCAAAAATC-CAAA
* * * * * *
52049 ATGTATCGATACTTTGAAGAATTTATCGATACTTGGGTCAAAAATCCAGA
1 ATGTATCGATACATTAAAAAATGTATCGATACTTGGCTCAAAAATCCAAA
* *
52099 ATGTATCGATATATTATAAACATGTATCGATAC
1 ATGTATCGATACATTA-AAAAATGTATCGATAC
52132 ATTGCAAGCA
Statistics
Matches: 69, Mismatches: 12, Indels: 5
0.80 0.14 0.06
Matches are distributed among these distances:
50 27 0.39
51 14 0.20
52 28 0.41
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.32
Consensus pattern (50 bp):
ATGTATCGATACATTAAAAAATGTATCGATACTTGGCTCAAAAATCCAAA
Found at i:52166 original size:20 final size:21
Alignment explanation
Indices: 52099--52173 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
52089 AAAATCCAGA
* ** *
52099 ATGTATCGATATATTATAAAC
1 ATGTATCGATACATTGCAAGC
52120 ATGTATCGATACATTGCAAGC
1 ATGTATCGATACATTGCAAGC
***
52141 ATGTATCGATACATT-CACTT
1 ATGTATCGATACATTGCAAGC
52161 ATGTATCGATACA
1 ATGTATCGATACA
52174 ATTTCTTTCC
Statistics
Matches: 47, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
20 15 0.32
21 32 0.68
ACGTcount: A:0.36, C:0.16, G:0.13, T:0.35
Consensus pattern (21 bp):
ATGTATCGATACATTGCAAGC
Found at i:52262 original size:20 final size:20
Alignment explanation
Indices: 52215--52264 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
52205 CATGGTCCAA
*
52215 TATCGATACATTTACTTATG
1 TATCGATACATTCACTTATG
* * *
52235 CATAGATACATTCACTTTTG
1 TATCGATACATTCACTTATG
52255 TATCGATACA
1 TATCGATACA
52265 AATTGTAGAA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.32, C:0.18, G:0.10, T:0.40
Consensus pattern (20 bp):
TATCGATACATTCACTTATG
Found at i:52492 original size:15 final size:15
Alignment explanation
Indices: 52474--52503 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
52464 ATCCCTATCT
52474 ACTAAGCATGCCTCG
1 ACTAAGCATGCCTCG
52489 ACTAAGCATGCCTCG
1 ACTAAGCATGCCTCG
52504 GGTTGCCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.27, C:0.33, G:0.20, T:0.20
Consensus pattern (15 bp):
ACTAAGCATGCCTCG
Found at i:56425 original size:29 final size:29
Alignment explanation
Indices: 56375--56519 Score: 114
Period size: 29 Copynumber: 4.9 Consensus size: 29
56365 AATTAAACAC
* *
56375 AAAAGCGAATTAAAAGTCAACTAAAATATT
1 AAAAG-GAATTAAAAGTAAACTAAAATATA
* *
56405 AAAAGGAATTAAATGTAAACTAAAATGTA
1 AAAAGGAATTAAAAGTAAACTAAAATATA
* * *
56434 AAAAGAAATTAAAAGTAAACCAAAAACACTA
1 AAAAGGAATTAAAAGTAAA-CTAAAATA-TA
* * * *
56465 AAAAGAAATGAAAA-TCAACTAAAACACT-
1 AAAAGGAATTAAAAGTAAACTAAAATA-TA
* * *
56493 AAACGAAATTATAAGTAAACTAAAATA
1 AAAAGGAATTAAAAGTAAACTAAAATA
56520 CCAAAACTTT
Statistics
Matches: 95, Mismatches: 17, Indels: 7
0.80 0.14 0.06
Matches are distributed among these distances:
28 11 0.12
29 56 0.59
30 13 0.14
31 15 0.16
ACGTcount: A:0.62, C:0.10, G:0.09, T:0.19
Consensus pattern (29 bp):
AAAAGGAATTAAAAGTAAACTAAAATATA
Found at i:56470 original size:31 final size:31
Alignment explanation
Indices: 56432--56517 Score: 97
Period size: 31 Copynumber: 2.9 Consensus size: 31
56422 AACTAAAATG
56432 TAAAAAGAAATTAAAAGTAAACCAAAAACAC
1 TAAAAAGAAATTAAAAGTAAACCAAAAACAC
* * *
56463 TAAAAAGAAATGAAAA-TCAA-CTAAAACAC
1 TAAAAAGAAATTAAAAGTAAACCAAAAACAC
* * *
56492 T-AAACGAAATTATAAGTAAACTAAAA
1 TAAAAAGAAATTAAAAGTAAACCAAAA
56518 TACCAAAACT
Statistics
Matches: 44, Mismatches: 9, Indels: 5
0.76 0.16 0.09
Matches are distributed among these distances:
28 11 0.25
29 12 0.27
30 6 0.14
31 15 0.34
ACGTcount: A:0.65, C:0.12, G:0.07, T:0.16
Consensus pattern (31 bp):
TAAAAAGAAATTAAAAGTAAACCAAAAACAC
Found at i:59367 original size:15 final size:16
Alignment explanation
Indices: 59337--59367 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
59327 AAAAATTAAA
59337 AATTTGAAGATAAAAT
1 AATTTGAAGATAAAAT
59353 AATTTGAAG-TAAAAT
1 AATTTGAAGATAAAAT
59368 TTAACTTTAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.55, C:0.00, G:0.13, T:0.32
Consensus pattern (16 bp):
AATTTGAAGATAAAAT
Found at i:60502 original size:7 final size:7
Alignment explanation
Indices: 60492--60524 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
60482 TTTCAAAATT
60492 TTAAAAA
1 TTAAAAA
60499 TTAAAAA
1 TTAAAAA
60506 TTAAAAA
1 TTAAAAA
60513 TTAAAAA
1 TTAAAAA
60520 TTAAA
1 TTAAA
60525 TTTATCGTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (7 bp):
TTAAAAA
Found at i:61566 original size:2 final size:2
Alignment explanation
Indices: 61559--61595 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
61549 CCACCTGAAT
61559 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
61596 TTAAAATCCA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:61841 original size:18 final size:18
Alignment explanation
Indices: 61818--61853 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
61808 ATAAATTAAT
61818 TAATTA-TACTTATTACTA
1 TAATTATTAC-TATTACTA
61836 TAATTATTACTATTACTA
1 TAATTATTACTATTACTA
61854 GCACAAAGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.82
19 3 0.18
ACGTcount: A:0.39, C:0.11, G:0.00, T:0.50
Consensus pattern (18 bp):
TAATTATTACTATTACTA
Found at i:63107 original size:42 final size:42
Alignment explanation
Indices: 63056--63150 Score: 145
Period size: 42 Copynumber: 2.3 Consensus size: 42
63046 CTATTGACAA
* * *
63056 AGATGTACCACCAAAAACACTAGTGCCTGTGCTTGTAGTAGC
1 AGATGTACCACCAAAAACACTACTGCCTGTGCCTATAGTAGC
* *
63098 AGATGTACCACCAAAAACACTACTGCTTGTGCCTATAGTTGC
1 AGATGTACCACCAAAAACACTACTGCCTGTGCCTATAGTAGC
63140 AGATGTACCAC
1 AGATGTACCAC
63151 TAAAGATACC
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.32, C:0.25, G:0.19, T:0.24
Consensus pattern (42 bp):
AGATGTACCACCAAAAACACTACTGCCTGTGCCTATAGTAGC
Found at i:71464 original size:1 final size:1
Alignment explanation
Indices: 71458--71486 Score: 58
Period size: 1 Copynumber: 29.0 Consensus size: 1
71448 TCGGTTTCTC
71458 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTT
71487 AAGGTTGAGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 28 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:72039 original size:17 final size:18
Alignment explanation
Indices: 72015--72061 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
72005 TTTTTTTAAA
*
72015 TATATATTTATATTATCT
1 TATATATTTATATCATCT
*
72033 T-TATATTTATA-CATGT
1 TATATATTTATATCATCT
72049 TATATATTTATAT
1 TATATATTTATAT
72062 ATAAAGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
16 4 0.16
17 20 0.80
18 1 0.04
ACGTcount: A:0.34, C:0.04, G:0.02, T:0.60
Consensus pattern (18 bp):
TATATATTTATATCATCT
Found at i:74224 original size:24 final size:24
Alignment explanation
Indices: 74197--74242 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
74187 ATTAGTTAAA
74197 AAATTTAGTATTATTTAATTTTGC
1 AAATTTAGTATTATTTAATTTTGC
* * *
74221 AAATTTCGTTTTATTTTATTTT
1 AAATTTAGTATTATTTAATTTT
74243 TCTTTCAACC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.04, G:0.07, T:0.61
Consensus pattern (24 bp):
AAATTTAGTATTATTTAATTTTGC
Found at i:74671 original size:19 final size:20
Alignment explanation
Indices: 74647--74693 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
74637 TTTTAATATA
74647 AATATAAATTTTAATT-TTT
1 AATATAAATTTTAATTATTT
* *
74666 AATAT-ATTTTTTATTATTT
1 AATATAAATTTTAATTATTT
74685 AATATAAAT
1 AATATAAAT
74694 ATATTTATAA
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 8 0.35
19 13 0.57
20 2 0.09
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATAAATTTTAATTATTT
Found at i:74862 original size:21 final size:21
Alignment explanation
Indices: 74825--74874 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
74815 AACCATTGAT
*
74825 TTTAATTTTACTATTACAGTA
1 TTTAATTTTACTATTACAATA
*
74846 TTTAATTTTA-TCGTTACAATA
1 TTTAATTTTACT-ATTACAATA
*
74867 ATTAATTT
1 TTTAATTT
74875 CATTATTAAC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 1 0.04
21 24 0.96
ACGTcount: A:0.34, C:0.08, G:0.04, T:0.54
Consensus pattern (21 bp):
TTTAATTTTACTATTACAATA
Found at i:75064 original size:2 final size:2
Alignment explanation
Indices: 75057--75090 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
75047 ATCAAAAGAG
75057 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
75091 TGGTTATATT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:76222 original size:7 final size:6
Alignment explanation
Indices: 76214--76245 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
76204 AACAAAATTA
*
76214 AAAAAT AAAAAT AAAAAT AAAACT AAAAAT AA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AA
76246 GAGCTTTCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.81, C:0.03, G:0.00, T:0.16
Consensus pattern (6 bp):
AAAAAT
Found at i:76337 original size:13 final size:14
Alignment explanation
Indices: 76319--76347 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
76309 TCGTAAATTT
76319 AATATTTATA-AAA
1 AATATTTATAGAAA
76332 AATATTTATAGAAA
1 AATATTTATAGAAA
76346 AA
1 AA
76348 AAATTACCGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.67
14 5 0.33
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (14 bp):
AATATTTATAGAAA
Found at i:77951 original size:61 final size:58
Alignment explanation
Indices: 77853--78064 Score: 189
Period size: 61 Copynumber: 3.6 Consensus size: 58
77843 TTATCCATGC
* * *
77853 CTAATTCTATCACAGAGTG-TCAGATGACCATTTTCGACTTATCAAGGTTGATGCAGCGA
1 CTAATTCTATCACATAGAGAT-AG-TGACCATTTTCGACTTATCTAGGTTGATGCAGCGA
* * ** *
77912 CTAATTCTATCACATAGAGCATTAGGTGACCATTTTCGACTTACCTGGGCAGATACAGCGA
1 CTAATTCTATCACATAGAG-A-TA-GTGACCATTTTCGACTTATCTAGGTTGATGCAGCGA
* * * * **
77973 CTAATTCTATCAC--ACAGA-AGTGTCCGTTTTCTACTTATCTAGGTTGATGCTTCGA
1 CTAATTCTATCACATAGAGATAGTGACCATTTTCGACTTATCTAGGTTGATGCAGCGA
*
78028 ATAATTCTATCACATAGAGGATGAAGTGACCATTTTC
1 CTAATTCTATCACATAGA-GAT--AGTGACCATTTTC
78065 AATGCAGGAA
Statistics
Matches: 120, Mismatches: 23, Indels: 18
0.75 0.14 0.11
Matches are distributed among these distances:
55 38 0.32
56 1 0.01
57 2 0.02
58 3 0.03
59 20 0.17
61 54 0.45
62 2 0.02
ACGTcount: A:0.29, C:0.21, G:0.18, T:0.32
Consensus pattern (58 bp):
CTAATTCTATCACATAGAGATAGTGACCATTTTCGACTTATCTAGGTTGATGCAGCGA
Found at i:78242 original size:61 final size:62
Alignment explanation
Indices: 78074--78250 Score: 214
Period size: 61 Copynumber: 2.9 Consensus size: 62
78064 CAATGCAGGA
* * *
78074 ACTAATTCTATCTCATAGAGCATGAAGTGACCATTTTCGACTTATCAAGATTGA-TGACGCG
1 ACTAATTCTATCTCATAGAGCATGAAGTGACCATTTTCGACTTATCTAGGTTGATTCACGCG
** * * **
78135 ACTAATTCTATGACATAGAGCGTGATGTGACCATTTTCGACTTATCTAGGTTGATTCA-TTG
1 ACTAATTCTATCTCATAGAGCATGAAGTGACCATTTTCGACTTATCTAGGTTGATTCACGCG
* ** * *
78196 ACTAATTCTATCTCATAGAGCAAGAAGCAACCATTTTTGACTTATCTAGGCTGAT
1 ACTAATTCTATCTCATAGAGCATGAAGTGACCATTTTCGACTTATCTAGGTTGAT
78251 GTAGTGACCA
Statistics
Matches: 97, Mismatches: 18, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
61 95 0.98
62 2 0.02
ACGTcount: A:0.30, C:0.19, G:0.18, T:0.34
Consensus pattern (62 bp):
ACTAATTCTATCTCATAGAGCATGAAGTGACCATTTTCGACTTATCTAGGTTGATTCACGCG
Found at i:78673 original size:21 final size:22
Alignment explanation
Indices: 78647--78691 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
78637 TAAACGATCA
*
78647 TTGCAAAG-ACATGCCTGCTCC
1 TTGCAAAGAACATGCCTACTCC
* *
78668 TTGCAATGAACATGCTTACTCC
1 TTGCAAAGAACATGCCTACTCC
78690 TT
1 TT
78692 ACTATACAAA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.24, C:0.29, G:0.16, T:0.31
Consensus pattern (22 bp):
TTGCAAAGAACATGCCTACTCC
Found at i:85487 original size:2 final size:2
Alignment explanation
Indices: 85480--85517 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
85470 TTCAACTTGA
85480 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
85518 CAAACAATGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:85978 original size:18 final size:18
Alignment explanation
Indices: 85955--85990 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
85945 AATAAAATTT
85955 TAATTTAATTT-AATTTAA
1 TAATTT-ATTTAAATTTAA
85973 TAATTTATTTAAATTTAA
1 TAATTTATTTAAATTTAA
85991 ATTATAATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATTTATTTAAATTTAA
Found at i:85997 original size:22 final size:22
Alignment explanation
Indices: 85957--86026 Score: 70
Period size: 22 Copynumber: 3.2 Consensus size: 22
85947 TAAAATTTTA
* *
85957 ATTTAATTTAATTTAATAATTT
1 ATTTAATTTAAATTAATAATAT
85979 ATTTAAATTTAAATT-ATAATAT
1 ATTT-AATTTAAATTAATAATAT
* * * *
86001 ATTTTATTAAAAATAATAATAA
1 ATTTAATTTAAATTAATAATAT
86023 ATTT
1 ATTT
86027 TTATTAATAT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
21 7 0.17
22 24 0.60
23 9 0.22
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATTTAATTTAAATTAATAATAT
Found at i:86027 original size:22 final size:23
Alignment explanation
Indices: 85989--86033 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
85979 ATTTAAATTT
* *
85989 AAATTATAATATA-TTTTATTAA
1 AAATAATAATAAATTTTTATTAA
86011 AAATAATAATAAATTTTTATTAA
1 AAATAATAATAAATTTTTATTAA
86034 TATTTATATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (23 bp):
AAATAATAATAAATTTTTATTAA
Found at i:86052 original size:32 final size:32
Alignment explanation
Indices: 86016--86080 Score: 80
Period size: 32 Copynumber: 2.0 Consensus size: 32
86006 ATTAAAAATA
* *
86016 ATAA-TAAATTTTTATT-AATATTTATATATTTT
1 ATAATTAAA-TTTAATTAAATATATAT-TATTTT
86048 ATAATTAAATTTAATTAAATATATATTATTTT
1 ATAATTAAATTTAATTAAATATATATTATTTT
86080 A
1 A
86081 ATTAAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
32 17 0.59
33 12 0.41
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (32 bp):
ATAATTAAATTTAATTAAATATATATTATTTT
Found at i:86090 original size:27 final size:27
Alignment explanation
Indices: 86038--86091 Score: 65
Period size: 30 Copynumber: 1.9 Consensus size: 27
86028 TATTAATATT
86038 TATATATTTTATAATTAAATTTAATTAAA
1 TATATATTTTATAATTAAA--TAATTAAA
*
86067 TATATATTATTTTAATTAAA-AATTA
1 TATATATT-TTATAATTAAATAATTA
86092 TTGTTTTTAG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
27 5 0.22
29 8 0.35
30 10 0.43
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TATATATTTTATAATTAAATAATTAAA
Found at i:86100 original size:20 final size:20
Alignment explanation
Indices: 86057--86098 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
86047 TATAATTAAA
*
86057 TTTAATTAAATATATATTAT
1 TTTAATTAAAAATATATTAT
*
86077 TTTAATTAAAAAT-TATTGT
1 TTTAATTAAAAATATATTAT
86096 TTT
1 TTT
86099 TAGTAGGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 8 0.40
20 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (20 bp):
TTTAATTAAAAATATATTAT
Found at i:86332 original size:13 final size:16
Alignment explanation
Indices: 86300--86339 Score: 59
Period size: 13 Copynumber: 2.7 Consensus size: 16
86290 TTAATAATAA
86300 AAAATTATATATTATT
1 AAAATTATATATTATT
86316 AAAATT-TA-ATT-TT
1 AAAATTATATATTATT
86329 AAAATTATATA
1 AAAATTATATA
86340 AATATTAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 8 0.36
14 5 0.23
15 3 0.14
16 6 0.27
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAAATTATATATTATT
Found at i:86592 original size:20 final size:19
Alignment explanation
Indices: 86558--86662 Score: 72
Period size: 22 Copynumber: 5.2 Consensus size: 19
86548 AATTAATAGA
*
86558 AAAATATTT-ATATATAAT
1 AAAATTTTTAATATATAAT
86576 AAAATTATTTAATATATTATCAAT
1 AAAATT-TTT-A-ATA-TAT-AAT
86600 AAAATTTTTAAATATTATATAT
1 AAAATTTTT-AATA-TATA-AT
* *
86622 AAAA-TTTGAATA-GTAAT
1 AAAATTTTTAATATATAAT
*
86639 ATAAATTTTTAAGATATAAT
1 A-AAATTTTTAATATATAAT
86659 AAAA
1 AAAA
86663 AATAAAAAAA
Statistics
Matches: 71, Mismatches: 6, Indels: 19
0.74 0.06 0.20
Matches are distributed among these distances:
17 3 0.04
18 10 0.14
19 12 0.17
20 9 0.13
21 4 0.06
22 16 0.23
23 8 0.11
24 9 0.13
ACGTcount: A:0.53, C:0.01, G:0.03, T:0.43
Consensus pattern (19 bp):
AAAATTTTTAATATATAAT
Found at i:86617 original size:22 final size:22
Alignment explanation
Indices: 86566--86628 Score: 85
Period size: 22 Copynumber: 2.8 Consensus size: 22
86556 GAAAAATATT
86566 TATA-TATAATAAAATTATTTAA
1 TATATTATAATAAAATT-TTTAA
86588 TATATTATCAATAAAATTTTTAA
1 TATATTAT-AATAAAATTTTTAA
86611 -ATATTATATATAAAATTT
1 TATATTATA-ATAAAATTT
86629 GAATAGTAAT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
21 1 0.03
22 20 0.53
23 8 0.21
24 9 0.24
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.48
Consensus pattern (22 bp):
TATATTATAATAAAATTTTTAA
Found at i:86904 original size:34 final size:36
Alignment explanation
Indices: 86839--86920 Score: 91
Period size: 35 Copynumber: 2.3 Consensus size: 36
86829 GTTCAACAAT
86839 TATATAAATTTATTTATTATATTGAATAAAT-AATAA
1 TATATAAATTTA-TTATTATATTGAATAAATAAATAA
86875 TATATAAATTTA-TATCT-TATT-AATAAAATAAATAA
1 TATATAAATTTATTAT-TATATTGAAT-AAATAAATAA
* *
86910 TTTAAAAATTT
1 TATATAAATTT
86921 TTAAGTAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 3 0.07
34 11 0.27
35 15 0.37
36 12 0.29
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (36 bp):
TATATAAATTTATTATTATATTGAATAAATAAATAA
Found at i:87301 original size:21 final size:21
Alignment explanation
Indices: 87277--87317 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
87267 AATGTTATCA
*
87277 TAATCAATTATATTAA-AATAT
1 TAATC-ATAATATTAATAATAT
87298 TAATCATAATATTAATAATA
1 TAATCATAATATTAATAATA
87318 AAAAATATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (21 bp):
TAATCATAATATTAATAATAT
Found at i:88178 original size:3 final size:3
Alignment explanation
Indices: 88172--88212 Score: 73
Period size: 3 Copynumber: 13.7 Consensus size: 3
88162 TGTTGTTATT
*
88172 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATT ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
88213 TATTATTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:89633 original size:15 final size:15
Alignment explanation
Indices: 89613--89659 Score: 51
Period size: 17 Copynumber: 3.1 Consensus size: 15
89603 TGATAAAAAT
89613 AATATAATATATAAA
1 AATATAATATATAAA
*
89628 AATATAATTAATATAAT
1 AATATAA-T-ATATAAA
*
89645 TATATAAT-TATAAA
1 AATATAATATATAAA
89659 A
1 A
89660 TGAGATAAAT
Statistics
Matches: 26, Mismatches: 4, Indels: 5
0.74 0.11 0.14
Matches are distributed among these distances:
14 5 0.19
15 7 0.27
16 2 0.08
17 12 0.46
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (15 bp):
AATATAATATATAAA
Found at i:89641 original size:17 final size:17
Alignment explanation
Indices: 89613--89654 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 17
89603 TGATAAAAAT
89613 AATATAA-T-ATATAAA
1 AATATAATTAATATAAA
*
89628 AATATAATTAATATAAT
1 AATATAATTAATATAAA
*
89645 TATATAATTA
1 AATATAATTA
89655 TAAAATGAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
15 7 0.30
16 1 0.04
17 15 0.65
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
AATATAATTAATATAAA
Found at i:89649 original size:8 final size:8
Alignment explanation
Indices: 89614--89656 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
89604 GATAAAAATA
89614 ATATAA-T
1 ATATAATT
**
89621 ATATAAAA
1 ATATAATT
89629 ATATAATT
1 ATATAATT
89637 AATATAATT
1 -ATATAATT
89646 ATATAATT
1 ATATAATT
89654 ATA
1 ATA
89657 AAATGAGATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
7 6 0.19
8 17 0.55
9 8 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (8 bp):
ATATAATT
Found at i:91966 original size:29 final size:29
Alignment explanation
Indices: 91925--92009 Score: 68
Period size: 29 Copynumber: 2.9 Consensus size: 29
91915 AAAAAATGAA
*
91925 AAAAATGATCCTAAAATACATGAAATTA-T
1 AAAAA-GACCCTAAAATACATGAAATTACT
*
91954 AAAAAAGTCCCTATAACATA-AT-AAATTACT
1 -AAAAAGACCCTA-AA-ATACATGAAATTACT
* * *
91984 AAAATGACCTTAAAATGCATGAAATT
1 AAAAAGACCCTAAAATACATGAAATT
92010 GCATAAATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
27 2 0.05
28 4 0.09
29 25 0.57
30 10 0.23
31 3 0.07
ACGTcount: A:0.53, C:0.13, G:0.07, T:0.27
Consensus pattern (29 bp):
AAAAAGACCCTAAAATACATGAAATTACT
Found at i:92310 original size:31 final size:31
Alignment explanation
Indices: 92225--92327 Score: 76
Period size: 29 Copynumber: 3.5 Consensus size: 31
92215 AAATGATTCG
* * * * *
92225 AAAATGTATAAAATTACACAATAGT-CCTTG
1 AAAATGCATAAAATTACATAACAGTAACTTT
*
92255 AAACATG-A-AAAATGAC-TAAC-GTAACTTT
1 AAA-ATGCATAAAATTACATAACAGTAACTTT
92283 AAAATGCATAAAATTACATAACAGTAAC--T
1 AAAATGCATAAAATTACATAACAGTAACTTT
* *
92312 AAGATGCATGAAATTA
1 AAAATGCATAAAATTA
92328 GATAGTGATC
Statistics
Matches: 59, Mismatches: 8, Indels: 13
0.74 0.10 0.16
Matches are distributed among these distances:
27 5 0.08
28 9 0.15
29 29 0.49
30 8 0.14
31 8 0.14
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.26
Consensus pattern (31 bp):
AAAATGCATAAAATTACATAACAGTAACTTT
Found at i:92382 original size:29 final size:29
Alignment explanation
Indices: 92342--92400 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
92332 GTGATCTCTA
* *
92342 AAAATGTATGAAATGACATAAAAGTCTTT
1 AAAATGTATGAAATGAAAAAAAAGTCTTT
*
92371 AAAATGTATGAAATGAAAAAAAAGTTTTT
1 AAAATGTATGAAATGAAAAAAAAGTCTTT
92400 A
1 A
92401 GATTATGGGA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.53, C:0.03, G:0.14, T:0.31
Consensus pattern (29 bp):
AAAATGTATGAAATGAAAAAAAAGTCTTT
Found at i:92711 original size:56 final size:57
Alignment explanation
Indices: 92623--92730 Score: 164
Period size: 56 Copynumber: 1.9 Consensus size: 57
92613 TAAAAATATA
* * *
92623 TAAAAATCTCTAAGTTATGGGAAATGAATAAAATGACATACAAATGCATCAAGTGAC
1 TAAAAATCTCTAAGTCATGGGAAATGAATAAAATGACAAAAAAATGCATCAAGTGAC
* *
92680 TAAAAATCT-TAAGTCATGGGAAATGATTAAAATGATAAAAAAATGCATCAA
1 TAAAAATCTCTAAGTCATGGGAAATGAATAAAATGACAAAAAAATGCATCAA
92731 ATAACAAAAG
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
56 37 0.80
57 9 0.20
ACGTcount: A:0.50, C:0.10, G:0.15, T:0.25
Consensus pattern (57 bp):
TAAAAATCTCTAAGTCATGGGAAATGAATAAAATGACAAAAAAATGCATCAAGTGAC
Found at i:93699 original size:18 final size:18
Alignment explanation
Indices: 93678--93713 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
93668 ATCGATTTCA
93678 TTGTATCGATATATTTTG
1 TTGTATCGATATATTTTG
93696 TTGTATCGATATATTTTG
1 TTGTATCGATATATTTTG
93714 GGTTTTTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.22, C:0.06, G:0.17, T:0.56
Consensus pattern (18 bp):
TTGTATCGATATATTTTG
Found at i:95865 original size:13 final size:13
Alignment explanation
Indices: 95847--95872 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
95837 CAATTTTTGG
95847 TGTATCGATACAT
1 TGTATCGATACAT
95860 TGTATCGATACAT
1 TGTATCGATACAT
95873 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:95884 original size:32 final size:33
Alignment explanation
Indices: 95827--95890 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
95817 TACAAGCCAA
**
95827 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
95860 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
95891 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:95897 original size:19 final size:18
Alignment explanation
Indices: 95827--95897 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
95817 TACAAGCCAA
95827 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
95847 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
95860 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
95879 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
95898 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:95967 original size:20 final size:20
Alignment explanation
Indices: 95921--95997 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
95911 TTCCCAATGA
***
95921 CATGTATCGATACATATTTTT
1 CATGTATCGATACAT-TGAAT
95942 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
95962 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
95982 TGTGTATCGATACATT
1 CATGTATCGATACATT
95998 TAAGGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:96592 original size:39 final size:40
Alignment explanation
Indices: 96514--96599 Score: 113
Period size: 39 Copynumber: 2.2 Consensus size: 40
96504 TTCTTTTATT
**
96514 TCTCCCTTAATCAAAATAATTTTAACAAATTCGTACATTC
1 TCTCCCTTAATCAAAATAATTTTAACAAATTCACACATTC
* * *
96554 TCTCCCTTAAT-AAAGTAATTTTAGCAAATTCACGCATTC
1 TCTCCCTTAATCAAAATAATTTTAACAAATTCACACATTC
96593 TC-CCCTT
1 TCTCCCTT
96600 TCTAAAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
38 5 0.12
39 25 0.61
40 11 0.27
ACGTcount: A:0.33, C:0.26, G:0.05, T:0.37
Consensus pattern (40 bp):
TCTCCCTTAATCAAAATAATTTTAACAAATTCACACATTC
Found at i:98459 original size:13 final size:13
Alignment explanation
Indices: 98441--98479 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
98431 ATAATCACCC
*
98441 TGTATCGATACAG
1 TGTATCGATACAA
98454 TGTATCGATACAA
1 TGTATCGATACAA
*
98467 TGTATCTATACAA
1 TGTATCGATACAA
98480 AGAAAAATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:103030 original size:12 final size:12
Alignment explanation
Indices: 103015--103048 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
103005 TCCGAGTCAC
103015 CATCTTCATCAA
1 CATCTTCATCAA
*
103027 CATCTTCATCAT
1 CATCTTCATCAA
*
103039 CTTCTTCATC
1 CATCTTCATC
103049 CTTGGTGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.24, C:0.35, G:0.00, T:0.41
Consensus pattern (12 bp):
CATCTTCATCAA
Found at i:104673 original size:13 final size:13
Alignment explanation
Indices: 104655--104680 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
104645 CAATTTTTGG
104655 TGTATCGATACAT
1 TGTATCGATACAT
104668 TGTATCGATACAT
1 TGTATCGATACAT
104681 ACTTGGTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:104775 original size:20 final size:20
Alignment explanation
Indices: 104729--104805 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
104719 TTCCCAATGA
***
104729 CATGTATCGATACATATTTTT
1 CATGTATCGATACAT-TGAAT
104750 CATGTATCGATACATTGCAA-
1 CATGTATCGATACATTG-AAT
*
104770 CATGTATCGATACTTTGAAT
1 CATGTATCGATACATTGAAT
**
104790 TGTGTATCGATACATT
1 CATGTATCGATACATT
104806 TAAGGGTTTT
Statistics
Matches: 47, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
19 2 0.04
20 30 0.64
21 15 0.32
ACGTcount: A:0.30, C:0.16, G:0.14, T:0.40
Consensus pattern (20 bp):
CATGTATCGATACATTGAAT
Found at i:107309 original size:31 final size:33
Alignment explanation
Indices: 107264--107325 Score: 92
Period size: 31 Copynumber: 1.9 Consensus size: 33
107254 TTTAAATCAC
* *
107264 TATATGTTTAATGTTACTCTATTATTATATAAT
1 TATATGTTTAATGTTACTATATTACTATATAAT
107297 TATAT-TTT-ATGTTACTATATTACTATATA
1 TATATGTTTAATGTTACTATATTACTATATA
107326 CTCTATGCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 19 0.70
32 3 0.11
33 5 0.19
ACGTcount: A:0.34, C:0.06, G:0.05, T:0.55
Consensus pattern (33 bp):
TATATGTTTAATGTTACTATATTACTATATAAT
Found at i:112316 original size:14 final size:14
Alignment explanation
Indices: 112299--112327 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
112289 GTTATTATTG
112299 TTTTATGTTGTTAT
1 TTTTATGTTGTTAT
112313 TTTTATGTTGTTAT
1 TTTTATGTTGTTAT
112327 T
1 T
112328 ATATTTGGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.14, C:0.00, G:0.14, T:0.72
Consensus pattern (14 bp):
TTTTATGTTGTTAT
Found at i:112420 original size:27 final size:26
Alignment explanation
Indices: 112383--112435 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 26
112373 GGTGTTTTTT
112383 TAAATTAATAAAAGATTATATTATTA
1 TAAATTAATAAAAGATTATATTATTA
* * *
112409 TAAATATAATAATAGTTTTTATTATTA
1 TAAAT-TAATAAAAGATTATATTATTA
112436 ATTTTTTATT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 5 0.22
27 18 0.78
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (26 bp):
TAAATTAATAAAAGATTATATTATTA
Found at i:114500 original size:20 final size:20
Alignment explanation
Indices: 114427--114501 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 20
114417 AATCTGAAAA
* *
114427 AATTGTATCGATACATAAGT
1 AATTGTATCGATACATCACT
*
114447 GAA-TGTATTGATACATGC-CT
1 -AATTGTATCGATACAT-CACT
* *
114467 ATAATGTATTGATACATCACT
1 A-ATTGTATCGATACATCACT
114488 AATTGTATCGATAC
1 AATTGTATCGATAC
114502 GTTCTGGGTT
Statistics
Matches: 45, Mismatches: 5, Indels: 9
0.76 0.08 0.15
Matches are distributed among these distances:
19 1 0.02
20 26 0.58
21 18 0.40
ACGTcount: A:0.36, C:0.13, G:0.15, T:0.36
Consensus pattern (20 bp):
AATTGTATCGATACATCACT
Found at i:125173 original size:13 final size:14
Alignment explanation
Indices: 125155--125183 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
125145 CGCCAGTACG
125155 TCGCC-AACACGGA
1 TCGCCAAACACGGA
125168 TCGCCAAACACGGA
1 TCGCCAAACACGGA
125182 TC
1 TC
125184 ACCAGGGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.31, C:0.38, G:0.21, T:0.10
Consensus pattern (14 bp):
TCGCCAAACACGGA
Found at i:140216 original size:129 final size:130
Alignment explanation
Indices: 139983--140215 Score: 355
Period size: 130 Copynumber: 1.8 Consensus size: 130
139973 AATTATTTCT
* * *
139983 AAAAAATTATTTCGTACCTTAATAGGTACCTAAAAAGATACGAAAAGTTTTTTGAAATCTTTTAG
1 AAAAAATCATTTCGTACCTTAATAGGTACCCAAAAAGATACAAAAAGTTTTTTGAAATCTTTTAG
*
140048 ACCCCTACGGATACCCATAGGAATATAAAAGACTTAAAAATAATTGATATTTATTTATGTTTGAA
66 ACCCCTACGGATACCCATAAGAATATAAAAGACTTAAAAATAATTGATATTTATTTATGTTTGAA
* * *
140113 AAAAAATCATTTCGTGCCTTGAT-GGATACCCGAAAAGATACAAAAAGTTTTTT-AAATCTTTTA
1 AAAAAATCATTTCGTACCTTAATAGG-TACCCAAAAAGATACAAAAAGTTTTTTGAAATCTTTTA
* *
140176 TACCCCTACGGATACCCGTAAGAATATAAAAGA-TTAAAAA
65 GACCCCTACGGATACCCATAAGAATATAAAAGACTTAAAAA
140216 AATATTTGCT
Statistics
Matches: 93, Mismatches: 9, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
128 7 0.08
129 42 0.45
130 44 0.47
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.31
Consensus pattern (130 bp):
AAAAAATCATTTCGTACCTTAATAGGTACCCAAAAAGATACAAAAAGTTTTTTGAAATCTTTTAG
ACCCCTACGGATACCCATAAGAATATAAAAGACTTAAAAATAATTGATATTTATTTATGTTTGAA
Found at i:141181 original size:166 final size:162
Alignment explanation
Indices: 140868--141357 Score: 551
Period size: 166 Copynumber: 3.0 Consensus size: 162
140858 TTTTGAAAAC
* * * * *
140868 TGAAATAAATAATAATATTTGATAAATTTTAAAAATCAAAAACCAATAAAAATCTCCTCGAAAAA
1 TGAAATAAATAAAAATATTTGATGAATTTT-AAAATTAAAAA-CAAGAAAAATCCCCTCG-AAAA
* * * * * *
140933 AATTCACGGAGTAAAAAATTTCGTATTTTG--AAAAAA-AATATTAAGAAAAAAATTCAAAAACT
63 AATTCACGGAATAAAAAACTCCGTATTTTGAAAAAAAAGAATTTTAAGGAAAAAATTTAAAAACT
*
140995 AATGAAAATAAAATAATTTTTAAAAACTGAATTAATA
128 AATGAAAATAAAACAATTTTTAAAAACT-AATT-ATA
141032 TGAAATAAATAAAAATATTTGATGAATTTTAAAATTAAAAATCAAGAAAAATCCCCTCGAAAAAA
1 TGAAATAAATAAAAATATTTGATGAATTTTAAAATTAAAAA-CAAGAAAAATCCCCTCGAAAAAA
* * *
141097 TTCATGGACTAGAAAACTCCGTATTTTGAAAAAAAGAGAATTTTAAGGAAAAAATTTAAAAACTA
65 TTCACGGAATAAAAAACTCCGTATTTTGAAAAAAA-AGAATTTTAAGGAAAAAATTTAAAAACTA
* * *
141162 ATGAAAATAAAAGAATTTTTGAAAACTAATTTTA
129 ATGAAAATAAAACAATTTTTAAAAACTAATTATA
* * *
141196 TGTAAATTAAATAAAAATATTTTATGAATTTTTAAAATTAAAAACTAAGAAAAAT-CTCTCCAAA
1 TG-AAA-TAAATAAAAATATTTGATGAA-TTTTAAAATTAAAAAC-AAGAAAAATCCCCT-CGAA
* * * ** * *
141260 AAAATTTACGGAAGAAAAAACTCCATATTTAAAAAAAAAAGAACTTCAAGGAAAAAA-TTAAAAA
61 AAAATTCACGGAATAAAAAACTCCGTATTTTGAAAAAAAAGAATTTTAAGGAAAAAATTTAAAAA
* *
141324 TTCAA-GAAAATAAAACAATTTTTCAAAACTAATT
126 CT-AATGAAAATAAAACAATTTTTAAAAACTAATT
141358 TGATGGAAAT
Statistics
Matches: 283, Mismatches: 33, Indels: 19
0.84 0.10 0.06
Matches are distributed among these distances:
162 29 0.10
163 25 0.09
164 37 0.13
165 43 0.15
166 91 0.32
167 58 0.20
ACGTcount: A:0.56, C:0.08, G:0.08, T:0.28
Consensus pattern (162 bp):
TGAAATAAATAAAAATATTTGATGAATTTTAAAATTAAAAACAAGAAAAATCCCCTCGAAAAAAT
TCACGGAATAAAAAACTCCGTATTTTGAAAAAAAAGAATTTTAAGGAAAAAATTTAAAAACTAAT
GAAAATAAAACAATTTTTAAAAACTAATTATA
Done.