Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold173
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: 1189743
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 33358 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:40 original size:30 final size:29
Alignment explanation
Indices: 2--60 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 29
1 T
2 AAATTTAAAAAAACTT-AAATATTATATAA
1 AAATTTAAAAAAACTTGAAA-ATTATATAA
*
31 AAATATTAAAAAATCTTGAAAATTATATAA
1 AAAT-TTAAAAAAACTTGAAAATTATATAA
61 TAATGCTAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
29 4 0.15
30 20 0.74
31 3 0.11
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (29 bp):
AAATTTAAAAAAACTTGAAAATTATATAA
Found at i:10312 original size:30 final size:31
Alignment explanation
Indices: 10276--10339 Score: 121
Period size: 30 Copynumber: 2.1 Consensus size: 31
10266 ATCCCTATTA
10276 TGGAAAGTCAAAGATATGGGTATC-AAATAT
1 TGGAAAGTCAAAGATATGGGTATCGAAATAT
10306 TGGAAAGTCAAAGATATGGGTATCGAAATAT
1 TGGAAAGTCAAAGATATGGGTATCGAAATAT
10337 TGG
1 TGG
10340 CATAAGAAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 24 0.73
31 9 0.27
ACGTcount: A:0.41, C:0.06, G:0.27, T:0.27
Consensus pattern (31 bp):
TGGAAAGTCAAAGATATGGGTATCGAAATAT
Found at i:10316 original size:15 final size:16
Alignment explanation
Indices: 10274--10324 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
10264 TCATCCCTAT
10274 TATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
10290 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
10305 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
10320 TATGG
1 TATGG
10325 GTATCGAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.52
16 9 0.33
ACGTcount: A:0.43, C:0.06, G:0.25, T:0.25
Consensus pattern (16 bp):
TATGGAAAGTCAAAGA
Found at i:14939 original size:30 final size:31
Alignment explanation
Indices: 14905--14968 Score: 103
Period size: 30 Copynumber: 2.1 Consensus size: 31
14895 ATCCATATTA
*
14905 TGGAAAGTCAAAGATATGGGTA-TCAAATAT
1 TGGAAAGTCAAAGATATGAGTATTCAAATAT
*
14935 TGGAAAGTCAAAGATATGAGTATTGAAATAT
1 TGGAAAGTCAAAGATATGAGTATTCAAATAT
14966 TGG
1 TGG
14969 CATAAGAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 21 0.68
31 10 0.32
ACGTcount: A:0.42, C:0.05, G:0.25, T:0.28
Consensus pattern (31 bp):
TGGAAAGTCAAAGATATGAGTATTCAAATAT
Found at i:14945 original size:15 final size:16
Alignment explanation
Indices: 14903--14952 Score: 59
Period size: 15 Copynumber: 3.2 Consensus size: 16
14893 TTATCCATAT
14903 TATGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
** *
14919 TATGGGTA-TCAAATA
1 TATGGAAAGTCAAAGA
14934 T-TGGAAAGTCAAAGA
1 TATGGAAAGTCAAAGA
14949 TATG
1 TATG
14953 AGTATTGAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
14 4 0.15
15 14 0.54
16 8 0.31
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.26
Consensus pattern (16 bp):
TATGGAAAGTCAAAGA
Found at i:20399 original size:30 final size:30
Alignment explanation
Indices: 20342--20397 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
20332 TTTTATATAT
*
20342 ATATACATACTTACATTGTTTTATTTTACG
1 ATATACATACTTACATTCTTTTATTTTACG
*
20372 ATATACATACTTATA-TCTTTTATTTT
1 ATATACATACTTACATTCTTTTATTTT
20398 TATGTAATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.30, C:0.12, G:0.04, T:0.54
Consensus pattern (30 bp):
ATATACATACTTACATTCTTTTATTTTACG
Found at i:22940 original size:27 final size:27
Alignment explanation
Indices: 22910--22964 Score: 101
Period size: 27 Copynumber: 2.0 Consensus size: 27
22900 TCTTTGATTC
*
22910 TTTTATTCTTTTCGATTTTCTTCCAAA
1 TTTTATTCTTTTAGATTTTCTTCCAAA
22937 TTTTATTCTTTTAGATTTTCTTCCAAA
1 TTTTATTCTTTTAGATTTTCTTCCAAA
22964 T
1 T
22965 CAATCTTGCA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.20, C:0.16, G:0.04, T:0.60
Consensus pattern (27 bp):
TTTTATTCTTTTAGATTTTCTTCCAAA
Found at i:24208 original size:13 final size:13
Alignment explanation
Indices: 24192--24265 Score: 64
Period size: 13 Copynumber: 5.8 Consensus size: 13
24182 AAAAATTGTT
*
24192 AAAAAAATAAAGA
1 AAAAAAAGAAAGA
*
24205 AAAAAAAGAGAGA
1 AAAAAAAGAAAGA
24218 AAAAAAAGAAA-A
1 AAAAAAAGAAAGA
**
24230 AGAAGGAA-AAAGA
1 A-AAAAAAGAAAGA
*
24243 AAAAGAAGAAA-A
1 AAAAAAAGAAAGA
*
24255 AAGAAAAGAAA
1 AAAAAAAGAAA
24266 AAGGGAGAGG
Statistics
Matches: 50, Mismatches: 8, Indels: 7
0.77 0.12 0.11
Matches are distributed among these distances:
12 20 0.40
13 30 0.60
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (13 bp):
AAAAAAAGAAAGA
Found at i:24220 original size:22 final size:22
Alignment explanation
Indices: 24192--24268 Score: 86
Period size: 22 Copynumber: 3.5 Consensus size: 22
24182 AAAAATTGTT
24192 AAAAAAATAAAGAAAAAAAAGAG
1 AAAAAAA-AAAGAAAAAAAAGAG
* *
24215 AGAAAAAAAAGAAAAAGAAG-G
1 AAAAAAAAAAGAAAAAAAAGAG
*
24236 AAAAAGAAAAAGAAGAAAAA-AG
1 AAAAA-AAAAAGAAAAAAAAGAG
*
24258 AAAAGAAAAAG
1 AAAAAAAAAAG
24269 GGAGAGGCCA
Statistics
Matches: 46, Mismatches: 6, Indels: 6
0.79 0.10 0.10
Matches are distributed among these distances:
21 11 0.24
22 29 0.63
23 6 0.13
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (22 bp):
AAAAAAAAAAGAAAAAAAAGAG
Found at i:24223 original size:16 final size:16
Alignment explanation
Indices: 24204--24263 Score: 59
Period size: 15 Copynumber: 3.6 Consensus size: 16
24194 AAAAATAAAG
24204 AAAAAAAAGAGAGAAA
1 AAAAAAAAGAGAGAAA
*
24220 AAAAAGAAAAAGAAGGAAA
1 AAAAA-AAAGAG-A-GAAA
*
24239 AAGAAAAAGA-AGAAA
1 AAAAAAAAGAGAGAAA
*
24254 AAAGAAAAGA
1 AAAAAAAAGA
24264 AAAAGGGAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
15 12 0.33
16 6 0.17
17 5 0.14
18 5 0.14
19 8 0.22
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAGAGAAA
Found at i:24230 original size:32 final size:32
Alignment explanation
Indices: 24194--24265 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
24184 AAATTGTTAA
*
24194 AAAAATAAAGAAAAA-AAAGAGAGAA-AAAAAAG
1 AAAAAGAAAGAAAAAGAAA-A-AGAAGAAAAAAG
*
24226 AAAAAGAAGGAAAAAGAAAAAGAAGAAAAAAG
1 AAAAAGAAAGAAAAAGAAAAAGAAGAAAAAAG
24258 -AAAAGAAA
1 AAAAAGAAA
24266 AAGGGAGAGG
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 11 0.31
32 21 0.60
33 3 0.09
ACGTcount: A:0.81, C:0.00, G:0.18, T:0.01
Consensus pattern (32 bp):
AAAAAGAAAGAAAAAGAAAAAGAAGAAAAAAG
Found at i:25791 original size:100 final size:100
Alignment explanation
Indices: 25573--26894 Score: 1856
Period size: 100 Copynumber: 13.3 Consensus size: 100
25563 AAACCATAGT
* * *
25573 TTGCAATTCAAAAGATTGAAGCCACAACGACGACTCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
25638 TTGAAGCTACGAC-----ATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* *
25668 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTCCTTCCCAGGCGATGTAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
25733 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* *
25768 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAGGCGATGCAGCGGAACATA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
25833 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * *
25868 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATACAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * *
25933 TTGAAGCTATGATGGCGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * * *
25968 TTGCAACTTAAAAGATTGAAGCTACAACGGTGAATCTTACTTCCCAGGCAATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
26033 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* *
26068 TTGCAATTTAAAAGATTGAAGCCACAACGGTGAATCTTACTTCCCAAGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* ** * *
26133 TTGAAGCTACGATGACGAATCTCCCTCCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* ** *
26168 TTGCAATTAAAAAGATTGAAGCCACAACAACGAATCTTACTTCCCAGGCGATGCAGCAGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
** *
26233 TTGAAGCTACGATAGCGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* **
26268 TTGCAATTCAAAAGATTGAAGCCACAACAACGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* *
26333 TTGAAGCTACGACGGTGAATCTCACTTGCTCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * *
26368 TTGTAATTTAAAAGATTGAAGCCATAACAGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* **
26433 TTGAAGCTACGATGACGAATCTCACTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * * * *
26468 TTACAA-TTAAAATATTGAAGCCACAACGGCGAATCTTACTTTCCAGGTGGTGCAGCGGAACAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
* * ***
26532 TTGAAGCTACAACGGCGAATCTTGTTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * * ***
26567 TTGCAATTAAAAAGATTGAAGCTACAACGGTGAATCTTACTTTTGAGGC-AGTGCAGCGGAACAG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGA-TGCAGCGGAACAG
* **
26631 ATTGAAGCTATGACGGTGAATCTTGCTTCCCCGACA
65 ATTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * * * *
26667 TTGCAA-TTAAAAGATTGAGGCCAAAACGGTGAATCTTACTT-CCAGGCGGTGCAGCGGAACAAA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
**
26730 TTGAAGCTACGACGGTGAATCTTGCTTCCCCGACA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
* * * * *
26765 TTGCAA-TTAAAAGATTGAGGCCATAACGGCGAATCTTACTT-CCAGGCGGTGCAACGGAATAGA
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
** * * *
26828 TTGAAGCTACGACGGTGAATCTTGCTTTCTCGATA
66 TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
26863 TTGCAATTTAAAAGATTGAAGCCACAACGGCG
1 TTGCAATTTAAAAGATTGAAGCCACAACGGCG
26895 GATCATGCTT
Statistics
Matches: 1114, Mismatches: 104, Indels: 14
0.90 0.08 0.01
Matches are distributed among these distances:
95 73 0.07
98 147 0.13
99 140 0.13
100 754 0.68
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (100 bp):
TTGCAATTTAAAAGATTGAAGCCACAACGGCGAATCTTACTTCCCAGGCGATGCAGCGGAACAGA
TTGAAGCTACGACGGTGAATCTCACTTCCCCGACA
Found at i:26583 original size:50 final size:50
Alignment explanation
Indices: 25651--27019 Score: 848
Period size: 50 Copynumber: 27.5 Consensus size: 50
25641 AAGCTACGAC
* * * *
25651 ATCTCACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGCGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * * *** * *
25701 ATCTTCCTTCCCAGGCGA-TGTAGCGGAACAGATTGAAGCTACGACGGTGA
1 ATCTTACTTCCCCGAC-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *
25751 ATCTCACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *** * * *
25801 ATCTTACTTCCCAGGCGA-TGCAGCGGAACATATTGAAGCTACGACGGTGA
1 ATCTTACTTCCCCGAC-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *
25851 ATCTCACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *** * ** * *
25901 ATCTTACTT-CCCAAGCGA-TACAGCGGAACAGATTGAAGCTATGATGGCGA
1 ATCTTACTTCCCCGA-C-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
*
25951 ATCTCACTTCCCCGACATTGCAACTT-AAAAGATTGAAGCTACAACGGTGA
1 ATCTTACTTCCCCGACATTGCAA-TTGAAAAGATTGAAGCTACAACGGTGA
* * * *** * *
26001 ATCTTACTTCCCAGGCAATGCAGCGGAACAGATTGAAGCTACGACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *
26051 ATCTCACTTCCCCGACATTGCAATTTAAAAGATTGAAGCCACAACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* *** * * * **
26101 ATCTTACTT-CCCAAGCGA-TGCAGCGGAACAGATTGAAGCTACGATGACGA
1 ATCTTACTTCCCCGA-C-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
** * * * ***
26151 ATCTCCCTCCCCCGACATTGCAATTAAAAAGATTGAAGCCACAACAACGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *** * * ** *
26201 ATCTTACTTCCCAGGCGA-TGCAGCAGAACAGATTGAAGCTACGATAGCGA
1 ATCTTACTTCCCCGAC-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * ***
26251 ATCTCACTTCCCCGACATTGCAATTCAAAAGATTGAAGCCACAACAACGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *** * *
26301 ATCTTACTTCCCAGGCGA-TGCAGCGGAACAGATTGAAGCTACGACGGTGA
1 ATCTTACTTCCCCGAC-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * * * * * * *
26351 ATCTCACTTGCTCGACATTGTAATTTAAAAGATTGAAGCCATAACAGCGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * *** * * * **
26401 ATCTTACTTCCCAGGCGA-TGCAGCGGAACAGATTGAAGCTACGATGACGA
1 ATCTTACTTCCCCGAC-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * * *
26451 ATCTCACTTCCCCGACATTACAATT-AAAATATTGAAGCCACAACGGCGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * **** *** * *
26500 ATCTTACTTTCCAGGTGGTGCAGCGGAACAGATTGAAGCTACAACGGCGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
** *
26550 ATCTTGTTTCCCCGACATTGCAATTAAAAAGATTGAAGCTACAACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
**** * * *** * **
26600 ATCTTACTTTTGAGGCAGTGCAGCGGAACAGATTGAAGCTATGACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * *
26650 ATCTTGCTTCCCCGACATTGCAATT-AAAAGATTGAGGCCAAAACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * ** *** *
26699 ATCTTACTT-CCAGGCGGTGCAGCGGAACAA-ATTGAAGCTACGACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAA-AAGATTGAAGCTACAACGGTGA
* * * * *
26748 ATCTTGCTTCCCCGACATTGCAATT-AAAAGATTGAGGCCATAACGGCGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * ** ** * *
26797 ATCTTACTT-CCAGGCGGTGCAACGGAATAGATTGAAGCTACGACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * * * * * *
26846 ATCTTGCTTTCTCGATATTGCAATTTAAAAGATTGAAGCCACAACGGCGG
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * *
26896 ATCATGCTTCCCCGACATTGCAATT-AAAAGATTGAGGCCACAACGGTGA
1 ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
* * * * **
26945 ATCTTACCTTCCCAGACGA-TGCAGTGGAATAGATTGAAGCTACAACGGCAA
1 ATCTTA-CTTCCCCGAC-ATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
*
26996 ATCTTCCTTCCCCGACATTGCAAT
1 ATCTTACTTCCCCGACATTGCAAT
27020 CTCATTTCCC
Statistics
Matches: 956, Mismatches: 332, Indels: 62
0.71 0.25 0.05
Matches are distributed among these distances:
48 19 0.02
49 175 0.18
50 722 0.76
51 40 0.04
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.23
Consensus pattern (50 bp):
ATCTTACTTCCCCGACATTGCAATTGAAAAGATTGAAGCTACAACGGTGA
Found at i:32089 original size:37 final size:36
Alignment explanation
Indices: 32039--32122 Score: 116
Period size: 36 Copynumber: 2.3 Consensus size: 36
32029 GAGGATATGG
32039 CTTTT-AAGCTACACATAGAACAAATGAAGAGACATGC
1 CTTTTCAA-CTACACAT-GAACAAATGAAGAGACATGC
** *
32076 CTTTTCAACTACACATGGTCAAGTGAAGAGACATGC
1 CTTTTCAACTACACATGAACAAATGAAGAGACATGC
32112 CTTTTCAACTA
1 CTTTTCAACTA
32123 TACACCATAA
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
36 28 0.65
37 13 0.30
38 2 0.05
ACGTcount: A:0.37, C:0.21, G:0.15, T:0.26
Consensus pattern (36 bp):
CTTTTCAACTACACATGAACAAATGAAGAGACATGC
Found at i:33975 original size:99 final size:98
Alignment explanation
Indices: 33853--34051 Score: 344
Period size: 99 Copynumber: 2.0 Consensus size: 98
33843 TAAAACCCTA
* *
33853 AGGTAAGAGAGTGTTACCAACATTAACAACGAAAAGGAAAAGAAAACTAGGTTTAGGAGCCGCAT
1 AGGTAAGAGAGTGTTACCAACATTAACAACAAAAAGGAAAAGAAAACTAGGTTTAGCAGCCGCAT
33918 TTTTTTCAAAAAAAAAACTCTTTGAAACATTCAG
66 TTTTTT-AAAAAAAAAACTCTTTGAAACATTCAG
*
33952 AGGTAAGAGAGTGTTACCGACATTAACAACAAAAAGGAAAAGAAAACTAGGTTTAGCAGCCGCAT
1 AGGTAAGAGAGTGTTACCAACATTAACAACAAAAAGGAAAAGAAAACTAGGTTTAGCAGCCGCAT
**
34017 TTTTTTTGAAAAAAAACTCTTTGAAACATTCAG
66 TTTTTTAAAAAAAAAACTCTTTGAAACATTCAG
34050 AG
1 AG
34052 AGAGTTTTTG
Statistics
Matches: 95, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
98 27 0.28
99 68 0.72
ACGTcount: A:0.44, C:0.14, G:0.19, T:0.24
Consensus pattern (98 bp):
AGGTAAGAGAGTGTTACCAACATTAACAACAAAAAGGAAAAGAAAACTAGGTTTAGCAGCCGCAT
TTTTTTAAAAAAAAAACTCTTTGAAACATTCAG
Found at i:37571 original size:108 final size:108
Alignment explanation
Indices: 37365--37597 Score: 249
Period size: 108 Copynumber: 2.1 Consensus size: 108
37355 ACTGATCATC
* *
37365 ATATGAAGATATGCGTAAGTCTATGTGGTAGAGACCCATGGCATTATACGAAAACTAAAACACTC
1 ATATGAAGATAT--GTAAGTCCATGTGGTAGAGACCCATGGCATAATACGAAAACTAAAACACTC
* * *
37430 ATGGTGTTGCCTCTAGTGAGATGAAGATTGGACTGAA-AGATCACG
64 ATGGTGATGCCTCTAGTAAGATGAAGATCGGACT-AATAGATCACG
* * * * ** *
37475 ATATGAGGATGTGTAAGTCCATGTGGTTGAGACCCATGGCATAATATGGTAA-TAAGAATACTCA
1 ATATGAAGATATGTAAGTCCATGTGGTAGAGACCCATGGCATAATACGAAAACTAA-AACACTCA
* * *
37539 TGGTGATGCCT-TCGGTAATATGTAA-ATCGGACTAATAGATCATG
65 TGGTGATGCCTCT-AGTAAGATG-AAGATCGGACTAATAGATCACG
37583 ATATGAAGATATGTA
1 ATATGAAGATATGTA
37598 TAAGTCTGCT
Statistics
Matches: 102, Mismatches: 17, Indels: 10
0.79 0.13 0.08
Matches are distributed among these distances:
107 6 0.06
108 84 0.82
109 2 0.02
110 10 0.10
ACGTcount: A:0.34, C:0.13, G:0.24, T:0.28
Consensus pattern (108 bp):
ATATGAAGATATGTAAGTCCATGTGGTAGAGACCCATGGCATAATACGAAAACTAAAACACTCAT
GGTGATGCCTCTAGTAAGATGAAGATCGGACTAATAGATCACG
Found at i:42949 original size:27 final size:27
Alignment explanation
Indices: 42880--42953 Score: 89
Period size: 27 Copynumber: 2.8 Consensus size: 27
42870 TTCTCATCCT
* *
42880 ATTTTACCTCTAGT-TAATTTTTGATG
1 ATTTTACCCCTAGTAAAATTTTTGATG
* *
42906 ATTTTACCCC-CGATAAAATTTTTTATG
1 ATTTTACCCCTAG-TAAAATTTTTGATG
42933 ATTTTACCCCTAGTAAAATTT
1 ATTTTACCCCTAGTAAAATTT
42954 CGAGATAATA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
25 1 0.03
26 10 0.25
27 28 0.70
28 1 0.03
ACGTcount: A:0.28, C:0.16, G:0.08, T:0.47
Consensus pattern (27 bp):
ATTTTACCCCTAGTAAAATTTTTGATG
Found at i:43112 original size:6 final size:6
Alignment explanation
Indices: 43101--43129 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
43091 ACAAATGAAT
43101 CATTTC CATTTC CATTTC CATTTC CATTT
1 CATTTC CATTTC CATTTC CATTTC CATTT
43130 TTGGAAACCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.31, G:0.00, T:0.52
Consensus pattern (6 bp):
CATTTC
Found at i:45169 original size:27 final size:27
Alignment explanation
Indices: 45139--45195 Score: 105
Period size: 27 Copynumber: 2.1 Consensus size: 27
45129 TGTCATTGAG
45139 TTAGTATTAAAGTTTCATTAGAAAATT
1 TTAGTATTAAAGTTTCATTAGAAAATT
*
45166 TTAGTATTAAAGTTTCGTTAGAAAATT
1 TTAGTATTAAAGTTTCATTAGAAAATT
45193 TTA
1 TTA
45196 ATGTTTTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.39, C:0.04, G:0.12, T:0.46
Consensus pattern (27 bp):
TTAGTATTAAAGTTTCATTAGAAAATT
Found at i:46430 original size:21 final size:21
Alignment explanation
Indices: 46355--46507 Score: 85
Period size: 21 Copynumber: 7.3 Consensus size: 21
46345 TCCATTTAGA
* *
46355 TCTTACGAGCTTCAGTT-AAC
1 TCTTATGAGCTTCAGTTCAGC
* * * *
46375 TCATATGAGTTTCAGTTTAAC
1 TCTTATGAGCTTCAGTTCAGC
* * * *
46396 CCTAATGGGTTTCAGTTCAGC
1 TCTTATGAGCTTCAGTTCAGC
* * * *
46417 TCTTTTGAGCTTCATTTTAAC
1 TCTTATGAGCTTCAGTTCAGC
* * *
46438 CCTTATGAGTTTTC-GTTCAGT
1 TCTTATGAG-CTTCAGTTCAGC
* *
46459 TCTTATGAGCTTCCGTTCAGT
1 TCTTATGAGCTTCAGTTCAGC
* *
46480 TCTTATGAGCTTCCGTTCAAC
1 TCTTATGAGCTTCAGTTCAGC
*
46501 CCTTATG
1 TCTTATG
46508 GGTTTTCGTT
Statistics
Matches: 101, Mismatches: 29, Indels: 5
0.75 0.21 0.04
Matches are distributed among these distances:
20 17 0.17
21 81 0.80
22 3 0.03
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (21 bp):
TCTTATGAGCTTCAGTTCAGC
Found at i:46438 original size:42 final size:42
Alignment explanation
Indices: 46378--46471 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
46368 AGTTAACTCA
*
46378 TATGAGTTTCAGTTTAACCCTAATG-GGTTTCAGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTAATGAGGTTTC-GTTCAGCTCT
* * * * *
46420 TTTGAGCTTCATTTTAACCCTTATGAGTTTTCGTTCAGTTCT
1 TATGAGCTTCAGTTTAACCCTAATGAGGTTTCGTTCAGCTCT
46462 TATGAGCTTC
1 TATGAGCTTC
46472 CGTTCAGTTC
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
42 39 0.89
43 5 0.11
ACGTcount: A:0.19, C:0.19, G:0.17, T:0.45
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCCTAATGAGGTTTCGTTCAGCTCT
Found at i:46534 original size:63 final size:63
Alignment explanation
Indices: 46355--46534 Score: 157
Period size: 63 Copynumber: 2.9 Consensus size: 63
46345 TCCATTTAGA
* * * * * * * * *
46355 TCTTACGAGCTTCAGTT-AACTCATATGAG-TTTCAGTTTAACCCTAATGGGTTTCAGTTCAGC
1 TCTTATGAGCTTCAGTTCAACCCTTATGAGTTTTC-GTTCAGCCCTTATGAGCTTCCGTTCAGC
* * * ** *
46417 TCTTTTGAGCTTCATTTTAACCCTTATGAGTTTTCGTTCAGTTCTTATGAGCTTCCGTTCAGT
1 TCTTATGAGCTTCAGTTCAACCCTTATGAGTTTTCGTTCAGCCCTTATGAGCTTCCGTTCAGC
* * * * *
46480 TCTTATGAGCTTCCGTTCAACCCTTATGGGTTTTCGTTTAGCCCTTGTGTGCTTC
1 TCTTATGAGCTTCAGTTCAACCCTTATGAGTTTTCGTTCAGCCCTTATGAGCTTC
46535 TGTACAGCCT
Statistics
Matches: 92, Mismatches: 24, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
62 14 0.15
63 74 0.80
64 4 0.04
ACGTcount: A:0.17, C:0.22, G:0.18, T:0.43
Consensus pattern (63 bp):
TCTTATGAGCTTCAGTTCAACCCTTATGAGTTTTCGTTCAGCCCTTATGAGCTTCCGTTCAGC
Found at i:56167 original size:22 final size:23
Alignment explanation
Indices: 56141--56190 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
56131 TCGAGAGGAA
* *
56141 TGGCAATTTATC-GTATTTTTAC
1 TGGCAACTTATCTGCATTTTTAC
* *
56163 TGGCAGCTTGTCTGCATTTTTAC
1 TGGCAACTTATCTGCATTTTTAC
56186 TGGCA
1 TGGCA
56191 GAATTTTTTG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
22 9 0.39
23 14 0.61
ACGTcount: A:0.18, C:0.18, G:0.20, T:0.44
Consensus pattern (23 bp):
TGGCAACTTATCTGCATTTTTAC
Found at i:61840 original size:50 final size:50
Alignment explanation
Indices: 61785--61885 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
61775 ATAGAATATC
61785 AATTTGGTATCAATTTTAGAATGGGTTTTGATATATTGAAAACTATTCTT
1 AATTTGGTATCAATTTTAGAATGGGTTTTGATATATTGAAAACTATTCTT
61835 AATTTGGTATCAATTTTAGAATGGGTTTTGATATATTGAAAACTATTCTT
1 AATTTGGTATCAATTTTAGAATGGGTTTTGATATATTGAAAACTATTCTT
61885 A
1 A
61886 CTCTTTGGCC
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.33, C:0.06, G:0.16, T:0.46
Consensus pattern (50 bp):
AATTTGGTATCAATTTTAGAATGGGTTTTGATATATTGAAAACTATTCTT
Found at i:62045 original size:23 final size:22
Alignment explanation
Indices: 62003--62046 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
61993 TTTTTTCAAC
62003 TTTAACTTTTATTCAGAAACAT
1 TTTAACTTTTATTCAGAAACAT
*
62025 TTTAATTTATTATATCA-AAACA
1 TTTAACTT-TTAT-TCAGAAACA
62047 CAAATAAAGC
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
22 7 0.37
23 9 0.47
24 3 0.16
ACGTcount: A:0.41, C:0.11, G:0.02, T:0.45
Consensus pattern (22 bp):
TTTAACTTTTATTCAGAAACAT
Found at i:71709 original size:65 final size:65
Alignment explanation
Indices: 71399--71698 Score: 293
Period size: 65 Copynumber: 4.6 Consensus size: 65
71389 TGATATCTAA
** * * * * *
71399 GTTCACTTTAAAGAAGCATATTACTTTAAAGAGGTAAAGCCACTTTAAATAATTGTGCAACATAG
1 GTTCACTTTAAAGAAGTGTGTTACCTTAAAGAGGTAAAGCCACTTTAAAGAAGTGTGCAACAAAG
* * * * * *
71464 GTTCTCTTTAAAGAAGCGTGATACCTAAAAAAAGGTAAAGCCATTTTAAAGAAGTGTGGCAACAC
1 GTTCACTTTAAAGAAGTGTGTTACCT-TAAAGAGGTAAAGCCACTTTAAAGAAGTGT-GCAACA-
71529 AA-
63 AAG
* * * * * *
71531 GTTTAATTTAAA-AATGTGTATTACCTTATAA-AGGTAAAGCCACTTTAAAGAAATGTGTAATAA
1 GTTCACTTTAAAGAA-GTGTGTTACCTTA-AAGAGGTAAAGCCACTTTAAAGAAGTGTGCAACAA
71594 AG
64 AG
* * * ** *
71596 GTTCACTTTAAAGAACTATGTTACCTTAAAGAGGTAAATCCACTTTAAAGAAGTGTATAACATAG
1 GTTCACTTTAAAGAAGTGTGTTACCTTAAAGAGGTAAAGCCACTTTAAAGAAGTGTGCAACAAAG
*
71661 GTT-ACTTTAAAGAAGTGTGTTACCTTAAAGAAGTAAAG
1 GTTCACTTTAAAGAAGTGTGTTACCTTAAAGAGGTAAAG
71699 TCATTTTTAA
Statistics
Matches: 191, Mismatches: 36, Indels: 17
0.78 0.15 0.07
Matches are distributed among these distances:
64 35 0.18
65 77 0.40
66 53 0.28
67 25 0.13
68 1 0.01
ACGTcount: A:0.41, C:0.12, G:0.17, T:0.30
Consensus pattern (65 bp):
GTTCACTTTAAAGAAGTGTGTTACCTTAAAGAGGTAAAGCCACTTTAAAGAAGTGTGCAACAAAG
Found at i:78079 original size:23 final size:23
Alignment explanation
Indices: 78052--78760 Score: 536
Period size: 23 Copynumber: 30.3 Consensus size: 23
78042 ACCCTGTTTA
*
78052 GACAGCATGTATATACAAAATTA
1 GACAGCATGTATATACAAAATTG
*
78075 GACAGCATTTAT-TCACCAAAATTTG
1 GACAGCATGTATAT-A-CAAAA-TTG
* *
78100 G-CAGCATATATATACAAATTTG
1 GACAGCATGTATATACAAAATTG
* * *
78122 GACAGCATTTATACACAAAATTT
1 GACAGCATGTATATACAAAATTG
*
78145 GACAGCATGTATATACAAAATTA
1 GACAGCATGTATATACAAAATTG
*
78168 GACAGCATTTAT-TCACCAAAATTTG
1 GACAGCATGTATAT-A-CAAAA-TTG
* *
78193 G-CAGCATATATATACAAATTTG
1 GACAGCATGTATATACAAAATTG
* * *
78215 GACAGCATTTATACACAAAATTT
1 GACAGCATGTATATACAAAATTG
78238 GACAGCATGTATATACAAAATTG
1 GACAGCATGTATATACAAAATTG
*
78261 GACAGCATTTAT-TCACCAAAATTG
1 GACAGCATGTATAT-A-CAAAATTG
* * * * * *
78285 GGCAACATATATATGCCAATTTG
1 GACAGCATGTATATACAAAATTG
*
78308 GACAGCACT-TATACACAAAAATT-
1 GACAGCA-TGTATATAC-AAAATTG
78331 GACAGCATGTATATACAAAATTG
1 GACAGCATGTATATACAAAATTG
* *
78354 GACATCATTTAT-TCACCAAAATTG
1 GACAGCATGTATAT-A-CAAAATTG
* * * *
78378 GGCAGCATATATATATACCAATTTG
1 GACAGC--ATGTATATACAAAATTG
* * *
78403 GACAGGAAT-TATACACAAAATTT
1 GACA-GCATGTATATACAAAATTG
78426 GACAGCATGTATATACAAAATTG
1 GACAGCATGTATATACAAAATTG
*
78449 GACAGCATTTAT-TCACCAAAATTG
1 GACAGCATGTATAT-A-CAAAATTG
* * * *
78473 GGCAGCATATATATACCAATTTG
1 GACAGCATGTATATACAAAATTG
*
78496 GACAGCACT-TATACACAAAAATT-
1 GACAGCA-TGTATATAC-AAAATTG
78519 GACAGCATGTATATACAAAAATTG
1 GACAGCATGTATATAC-AAAATTG
78543 GACAGCACT-TAT-TCACCAAAATTG
1 GACAGCA-TGTATAT-A-CAAAATTG
* * * *
78567 GGCAGCATATATATACCAATTTG
1 GACAGCATGTATATACAAAATTG
* *
78590 GACAGCACT-TATACACAAAATTT
1 GACAGCA-TGTATATACAAAATTG
*
78613 GACAGCATGTATATACGAAATTG
1 GACAGCATGTATATACAAAATTG
*
78636 GACAGCATTTAT-TCACCAAAATTG
1 GACAGCATGTATAT-A-CAAAATTG
** * * *
78660 GGTAGCATATATATACCAATTTG
1 GACAGCATGTATATACAAAATTG
* *
78683 GACAGCACT-TATACACAAAATTT
1 GACAGCA-TGTATATACAAAATTG
*
78706 GACAGCATGTATATACGAAATTG
1 GACAGCATGTATATACAAAATTG
*
78729 GACAGCATTTAT-TCACCAAAATTG
1 GACAGCATGTATAT-A-CAAAATTG
*
78753 GGCAGCAT
1 GACAGCAT
78761 AAATACAACA
Statistics
Matches: 549, Mismatches: 92, Indels: 89
0.75 0.13 0.12
Matches are distributed among these distances:
22 28 0.05
23 339 0.62
24 151 0.28
25 23 0.04
26 7 0.01
27 1 0.00
ACGTcount: A:0.40, C:0.17, G:0.14, T:0.28
Consensus pattern (23 bp):
GACAGCATGTATATACAAAATTG
Found at i:78112 original size:47 final size:47
Alignment explanation
Indices: 78054--78786 Score: 827
Period size: 47 Copynumber: 15.7 Consensus size: 47
78044 CCTGTTTAGA
* *
78054 CAGCATGTATATACAAAATTAGACAGCATTTATTCACCAAAATTTGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * *
78101 CAGCATATATATACAAATTTGGACAGCATTTATACA-CAAAATTTGA
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* *
78147 CAGCATGTATATACAAAATTAGACAGCATTTATTCACCAAAATTTGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * *
78194 CAGCATATATATACAAATTTGGACAGCATTTATACA-CAAAATTTGA
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* *
78240 CAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * * * * * * *
78287 CAACATATATATGCCAATTTGGACAGCACTTATACA-CAAAAATTGA
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * *
78333 CAGCATGTATATACAAAATTGGACATCATTTATTCACCAAAATTGGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * * * * *
78380 CAGCATATATATATACCAATTTGGACAGGAATTATACA-CAAAATTTGA
1 CAGC--ATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* *
78428 CAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * * * * *
78475 CAGCATATATATACCAATTTGGACAGCACTTATACA-CAAAAATTGA
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * *
78521 CAGCATGTATATACAAAAATTGGACAGCACTTATTCACCAAAATTGGG
1 CAGCATATATATAC-AAAATTGGACAGCATTTATTCACCAAAATTTGG
* * * * *
78569 CAGCATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGA
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * *
78615 CAGCATGTATATACGAAATTGGACAGCATTTATTCACCAAAATTGGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * * * * *
78662 TAGCATATATATACCAATTTGGACAGCACTTATACA-CAAAATTTGA
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
* * *
78708 CAGCATGTATATACGAAATTGGACAGCATTTATTCACCAAAATTGGG
1 CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
**
78755 CAGCATA-A-ATACAACAAATTGGGTAGCATTTA
1 CAGCATATATATAC-A-AAATTGGACAGCATTTA
78787 AGCATAAAAA
Statistics
Matches: 568, Mismatches: 106, Indels: 24
0.81 0.15 0.03
Matches are distributed among these distances:
45 4 0.01
46 242 0.43
47 265 0.47
48 32 0.06
49 25 0.04
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (47 bp):
CAGCATATATATACAAAATTGGACAGCATTTATTCACCAAAATTTGG
Found at i:78158 original size:93 final size:93
Alignment explanation
Indices: 78052--78761 Score: 1222
Period size: 93 Copynumber: 7.6 Consensus size: 93
78042 ACCCTGTTTA
* * *
78052 GACAGCATGTATATACAAAATTAGACAGCATTTATTCACCAAAATTTGGCAGCATATATATACAA
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
*
78117 ATTTGGACAGCATTTATACACAAAATTT
66 ATTTGGACAGCACTTATACACAAAATTT
* * *
78145 GACAGCATGTATATACAAAATTAGACAGCATTTATTCACCAAAATTTGGCAGCATATATATACAA
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
*
78210 ATTTGGACAGCATTTATACACAAAATTT
66 ATTTGGACAGCACTTATACACAAAATTT
* *
78238 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAACATATATATGCCA
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
*
78303 ATTTGGACAGCACTTATACACAAAAATT
66 ATTTGGACAGCACTTATACACAAAATTT
*
78331 GACAGCATGTATATACAAAATTGGACATCATTTATTCACCAAAATTGGGCAGCATATATATATAC
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGC--ATATATATAC
* *
78396 CAATTTGGACAGGAATTATACACAAAATTT
64 CAATTTGGACAGCACTTATACACAAAATTT
78426 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
*
78491 ATTTGGACAGCACTTATACACAAAAATT
66 ATTTGGACAGCACTTATACACAAAATTT
*
78519 GACAGCATGTATATACAAAAATTGGACAGCACTTATTCACCAAAATTGGGCAGCATATATATACC
1 GACAGCATGTATATAC-AAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACC
78584 AATTTGGACAGCACTTATACACAAAATTT
65 AATTTGGACAGCACTTATACACAAAATTT
* *
78613 GACAGCATGTATATACGAAATTGGACAGCATTTATTCACCAAAATTGGGTAGCATATATATACCA
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
78678 ATTTGGACAGCACTTATACACAAAATTT
66 ATTTGGACAGCACTTATACACAAAATTT
*
78706 GACAGCATGTATATACGAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATA
1 GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATA
78762 AATACAACAA
Statistics
Matches: 591, Mismatches: 23, Indels: 6
0.95 0.04 0.01
Matches are distributed among these distances:
93 412 0.70
94 91 0.15
95 88 0.15
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (93 bp):
GACAGCATGTATATACAAAATTGGACAGCATTTATTCACCAAAATTGGGCAGCATATATATACCA
ATTTGGACAGCACTTATACACAAAATTT
Found at i:79540 original size:28 final size:28
Alignment explanation
Indices: 79508--79633 Score: 162
Period size: 28 Copynumber: 4.5 Consensus size: 28
79498 TTTAATAAGT
** * *
79508 TCGCACACTTAGTGCTCAATAATCAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
79536 TCGCACACTTAGTGTTTTACCATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
* *
79564 TCGCAGACTTAGCGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
79592 TCGCACACTTGGTGCTTTACAATTAAAC
1 TCGCACACTTAGTGCTTTACAATTAAAC
*
79620 TCTCACACTTAGTG
1 TCGCACACTTAGTG
79634 ACGAAAGTCA
Statistics
Matches: 83, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 83 1.00
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (28 bp):
TCGCACACTTAGTGCTTTACAATTAAAC
Found at i:84608 original size:50 final size:50
Alignment explanation
Indices: 84528--84665 Score: 186
Period size: 50 Copynumber: 2.8 Consensus size: 50
84518 GGGTTGTTAC
* * *
84528 AAGATGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGAT
1 AAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAT
* *
84578 AAGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATAT
1 AAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAT
* * * * *
84628 GAGAACTCCCATGTAAGACCATATTTGGGATATGGCAT
1 AAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCAT
84666 TTGCAGTACA
Statistics
Matches: 78, Mismatches: 10, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
50 78 1.00
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (50 bp):
AAGAAGTCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGAGAT
Found at i:92724 original size:23 final size:23
Alignment explanation
Indices: 92698--92742 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
92688 AGTTTTAAAA
92698 TATTGTTAAAAACATTCTAAATT
1 TATTGTTAAAAACATTCTAAATT
*
92721 TATTGTTAAAACCATTCTAAAT
1 TATTGTTAAAAACATTCTAAAT
92743 CGATTGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.42, C:0.11, G:0.04, T:0.42
Consensus pattern (23 bp):
TATTGTTAAAAACATTCTAAATT
Found at i:92748 original size:23 final size:23
Alignment explanation
Indices: 92699--92748 Score: 73
Period size: 23 Copynumber: 2.2 Consensus size: 23
92689 GTTTTAAAAT
**
92699 ATTGTTAAAAACATTCTAAATTT
1 ATTGTTAAAAACATTCTAAATCG
*
92722 ATTGTTAAAACCATTCTAAATCG
1 ATTGTTAAAAACATTCTAAATCG
92745 ATTG
1 ATTG
92749 AAATGTGTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (23 bp):
ATTGTTAAAAACATTCTAAATCG
Found at i:93618 original size:19 final size:19
Alignment explanation
Indices: 93594--93631 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
93584 ATCATGCCTT
93594 TACTTTAACATTTCATCCA
1 TACTTTAACATTTCATCCA
93613 TACTTTAACATTTCATCCA
1 TACTTTAACATTTCATCCA
93632 CATAGTTTCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (19 bp):
TACTTTAACATTTCATCCA
Found at i:114886 original size:12 final size:12
Alignment explanation
Indices: 114851--114897 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
114841 ATTATATTTG
114851 ATTATATTT-CT
1 ATTATATTTACT
114862 ATATATATATTACT
1 AT-TATAT-TTACT
114876 -TTATTATTTACT
1 ATTA-TATTTACT
114888 ATTATATTTA
1 ATTATATTTA
114898 AACTGTTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
11 2 0.06
12 18 0.58
13 9 0.29
14 2 0.06
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (12 bp):
ATTATATTTACT
Found at i:122363 original size:26 final size:26
Alignment explanation
Indices: 122327--122388 Score: 97
Period size: 26 Copynumber: 2.4 Consensus size: 26
122317 TCCTGAAGTG
*
122327 TTCTGAAACTGATACAGGCTATGGTA
1 TTCTGAAACTGATACAGGCTATGATA
* *
122353 TTCTGAAACTGATACATGTTATGATA
1 TTCTGAAACTGATACAGGCTATGATA
122379 TTCTGAAACT
1 TTCTGAAACT
122389 ATTATAGGTA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 33 1.00
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (26 bp):
TTCTGAAACTGATACAGGCTATGATA
Found at i:132532 original size:34 final size:35
Alignment explanation
Indices: 132493--132568 Score: 136
Period size: 34 Copynumber: 2.2 Consensus size: 35
132483 AAATAGAATT
*
132493 AAATTAATTAGTTCTTATGAATTCGTTGAATAAGG
1 AAATTAATTAGTTATTATGAATTCGTTGAATAAGG
132528 -AATTAATTAGTTATTATGAATTCGTTGAATAAGG
1 AAATTAATTAGTTATTATGAATTCGTTGAATAAGG
132562 AAATTAA
1 AAATTAA
132569 ATATATTTTC
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
34 33 0.85
35 6 0.15
ACGTcount: A:0.41, C:0.04, G:0.16, T:0.39
Consensus pattern (35 bp):
AAATTAATTAGTTATTATGAATTCGTTGAATAAGG
Found at i:134050 original size:20 final size:20
Alignment explanation
Indices: 134025--134066 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
134015 ATCAATTCCT
134025 ATCATTAATCCAATTCAAAC
1 ATCATTAATCCAATTCAAAC
* *
134045 ATCATTTATCCAATTCATAC
1 ATCATTAATCCAATTCAAAC
134065 AT
1 AT
134067 TATCTTCCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.40, C:0.24, G:0.00, T:0.36
Consensus pattern (20 bp):
ATCATTAATCCAATTCAAAC
Found at i:136013 original size:25 final size:25
Alignment explanation
Indices: 135971--136027 Score: 87
Period size: 25 Copynumber: 2.3 Consensus size: 25
135961 GTGGCAAACC
*
135971 AAGCCTTTGCGGCAAAATGTTTGGG
1 AAGCCTTTACGGCAAAATGTTTGGG
* *
135996 AAGCCTTTATGGCGAAATGTTTGGG
1 AAGCCTTTACGGCAAAATGTTTGGG
136021 AAGCCTT
1 AAGCCTT
136028 GTGGCAGGTT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.25, C:0.16, G:0.30, T:0.30
Consensus pattern (25 bp):
AAGCCTTTACGGCAAAATGTTTGGG
Found at i:139546 original size:26 final size:26
Alignment explanation
Indices: 139512--139581 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
139502 AACACACCAA
* * *
139512 TATCATAGCAAAGCTGTCAGTAATAG
1 TATCGTAGCAAAGCTGCCAGTAACAG
139538 TATCGTAGCAAAGCTGCCAGTAACAG
1 TATCGTAGCAAAGCTGCCAGTAACAG
*
139564 TATCGCAGCAAAGCTGCC
1 TATCGTAGCAAAGCTGCC
139582 TGTAGTATAC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 40 1.00
ACGTcount: A:0.34, C:0.23, G:0.21, T:0.21
Consensus pattern (26 bp):
TATCGTAGCAAAGCTGCCAGTAACAG
Found at i:141986 original size:38 final size:38
Alignment explanation
Indices: 141935--142012 Score: 138
Period size: 38 Copynumber: 2.1 Consensus size: 38
141925 TATCGAAACG
141935 AGATAAAATAAGATTGCTTTCATAAAGAGAATACAATA
1 AGATAAAATAAGATTGCTTTCATAAAGAGAATACAATA
* *
141973 AGATAAAATAAGATTGCTTTCGTAAAGAGTATACAATA
1 AGATAAAATAAGATTGCTTTCATAAAGAGAATACAATA
142011 AG
1 AG
142013 GTGTTTTCAA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.50, C:0.08, G:0.15, T:0.27
Consensus pattern (38 bp):
AGATAAAATAAGATTGCTTTCATAAAGAGAATACAATA
Found at i:143938 original size:28 final size:27
Alignment explanation
Indices: 143892--143946 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
143882 TATATTTGTT
* *
143892 TTATAATTGTTTATAATATTATGTAATG
1 TTATAATTGTATATAATA-TATGAAATG
143920 TTATAATTGTGATAT-ATATATGAAATG
1 TTATAATTGT-ATATAATATATGAAATG
143947 ATCCACAGTT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 8 0.33
28 13 0.54
29 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.13, T:0.49
Consensus pattern (27 bp):
TTATAATTGTATATAATATATGAAATG
Found at i:183478 original size:25 final size:26
Alignment explanation
Indices: 183432--183497 Score: 89
Period size: 25 Copynumber: 2.5 Consensus size: 26
183422 CCATGTAGGG
* *
183432 TAAAATGACCAAAAAACCCTCATAGAC
1 TAAAATGACCAAAAAA-CCTCACAAAC
183459 TAAAATGACCAAAAAA-CTCACAAAC
1 TAAAATGACCAAAAAACCTCACAAAC
*
183484 TAAAATTACCAAAA
1 TAAAATGACCAAAA
183498 TACCCCCATA
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 20 0.56
27 16 0.44
ACGTcount: A:0.58, C:0.23, G:0.05, T:0.15
Consensus pattern (26 bp):
TAAAATGACCAAAAAACCTCACAAAC
Found at i:183580 original size:27 final size:27
Alignment explanation
Indices: 183404--183661 Score: 173
Period size: 27 Copynumber: 9.6 Consensus size: 27
183394 CTTACTATTT
* * *
183404 GTAAAATGACTGTAATACCCAT-GTAGG
1 GTAAAATGACCGAAATACCC-TCATAGG
* * *
183431 GTAAAATGACCAAAAAACCCTCATAGA
1 GTAAAATGACCGAAATACCCTCATAGG
* ** * **
183458 CTAAAATGACC-AAA-AAACTCACAAA
1 GTAAAATGACCGAAATACCCTCATAGG
* * * *
183483 CTAAAATTACCAAAATACCCCCATAGG
1 GTAAAATGACCGAAATACCCTCATAGG
* * * *
183510 GTAAAATAATCGAAATACCCCCCATAGA
1 GTAAAATGACCGAAATA-CCCTCATAGG
* * *
183538 TTAAAATAACCAAAATACCCTCATAGG
1 GTAAAATGACCGAAATACCCTCATAGG
*
183565 GTAAAATGACCGAAATA-CCTCCATAAG
1 GTAAAATGACCGAAATACCCT-CATAGG
* * *
183592 GTAAAATGATCGAAATACCCCCATTGG
1 GTAAAATGACCGAAATACCCTCATAGG
* * *
183619 GTAGAATGACCGTAATACCCCCATAGG
1 GTAAAATGACCGAAATACCCTCATAGG
* *
183646 GTTAAATGACTGAAAT
1 GTAAAATGACCGAAAT
183662 TGATACGAGT
Statistics
Matches: 181, Mismatches: 44, Indels: 12
0.76 0.19 0.05
Matches are distributed among these distances:
25 17 0.09
26 10 0.06
27 129 0.71
28 25 0.14
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.20
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCTCATAGG
Found at i:183621 original size:54 final size:54
Alignment explanation
Indices: 183430--183655 Score: 206
Period size: 54 Copynumber: 4.2 Consensus size: 54
183420 ACCCATGTAG
* * ** * * * *
183430 GGTAAAATGACCAAAAAACCCTCATAGACTAAAATGACCAAAAAACTCACA-AA
1 GGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAA
* * * *
183483 -CTAAAATTACCAAAATACCCCCATAGGGTAAAATAATCGAAATACCCCCCAT-A
1 GGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATA-CCCCCATAA
* * * *
183536 GATTAAAATAACCAAAATACCCTCATAGGGTAAAATGACCGAAATACCTCCATAA
1 G-GTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAA
* * * * * *
183591 GGTAAAATGATCGAAATACCCCCATTGGGTAGAATGACCGTAATACCCCCATAG
1 GGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAA
*
183645 GGTTAAATGAC
1 GGTAAAATGAC
183656 TGAAATTGAT
Statistics
Matches: 138, Mismatches: 30, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
52 34 0.25
53 5 0.04
54 58 0.42
55 41 0.30
ACGTcount: A:0.45, C:0.23, G:0.13, T:0.19
Consensus pattern (54 bp):
GGTAAAATGACCAAAATACCCCCATAGGGTAAAATGACCGAAATACCCCCATAA
Found at i:185296 original size:32 final size:32
Alignment explanation
Indices: 185238--185394 Score: 120
Period size: 32 Copynumber: 4.9 Consensus size: 32
185228 CCTACGATGG
* ***
185238 TACTGATGGCTTTGTGATGATCATATTACCGT
1 TACTGACGGCTTTGTGCCAATCATATTACCGT
** * *
185270 TTTTGACGGCTTTGTGTCAATTATATTACCGT
1 TACTGACGGCTTTGTGCCAATCATATTACCGT
* *
185302 TACTGATGGCTTTGTGCCAATCATATTACCAT
1 TACTGACGGCTTTGTGCCAATCATATTACCGT
* * * * * * *
185334 TACTGATGGCTATGAGTCGATTATATCAATCC--
1 TACTGACGGCTTTGTGCCAATCATAT-TA-CCGT
*
185366 TACTGATGGCTTTGTGCCAATCATATTAC
1 TACTGACGGCTTTGTGCCAATCATATTAC
185395 TGTACTTATG
Statistics
Matches: 98, Mismatches: 25, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
30 1 0.01
31 1 0.01
32 93 0.95
33 1 0.01
34 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (32 bp):
TACTGACGGCTTTGTGCCAATCATATTACCGT
Found at i:185357 original size:64 final size:64
Alignment explanation
Indices: 185238--185394 Score: 183
Period size: 64 Copynumber: 2.5 Consensus size: 64
185228 CCTACGATGG
*** * ** * * *
185238 TACTGATGGCTTTGTGATGATCATATTACCGTTTTTGACGGCTTTGTGTCAATTATAT-TA-CC
1 TACTGATGGCTTTGTGCCAATCATATTACCATTACTGACGGCTATGAGTCAATTATATCAATCC
* *
185300 GTTACTGATGGCTTTGTGCCAATCATATTACCATTACTGATGGCTATGAGTCGATTATATCAATC
1 --TACTGATGGCTTTGTGCCAATCATATTACCATTACTGACGGCTATGAGTCAATTATATCAATC
185365 C
64 C
185366 TACTGATGGCTTTGTGCCAATCATATTAC
1 TACTGATGGCTTTGTGCCAATCATATTAC
185395 TGTACTTATG
Statistics
Matches: 80, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
64 77 0.96
65 1 0.01
66 2 0.03
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (64 bp):
TACTGATGGCTTTGTGCCAATCATATTACCATTACTGACGGCTATGAGTCAATTATATCAATCC
Found at i:195278 original size:14 final size:13
Alignment explanation
Indices: 195250--195285 Score: 54
Period size: 14 Copynumber: 2.7 Consensus size: 13
195240 GCTGTATAGT
195250 AGAAGAAAAAAAA
1 AGAAGAAAAAAAA
*
195263 AGAAGAAGAGAAAA
1 AGAAGAA-AAAAAA
195277 AGAAGAAAA
1 AGAAGAAAA
195286 TGAGAAAATG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
13 8 0.40
14 12 0.60
ACGTcount: A:0.78, C:0.00, G:0.22, T:0.00
Consensus pattern (13 bp):
AGAAGAAAAAAAA
Found at i:195282 original size:17 final size:17
Alignment explanation
Indices: 195250--195299 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
195240 GCTGTATAGT
*
195250 AGAAGA-AAAAAAAAGA
1 AGAAGAGAAAAAGAAGA
195266 AGAAGAGAAAAAGAAGA
1 AGAAGAGAAAAAGAAGA
*
195283 A-AATGAGAAAATGAAGA
1 AGAA-GAGAAAAAGAAGA
195300 TGCCGACCGT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
16 8 0.27
17 22 0.73
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (17 bp):
AGAAGAGAAAAAGAAGA
Found at i:197210 original size:10 final size:9
Alignment explanation
Indices: 197197--197260 Score: 51
Period size: 9 Copynumber: 7.0 Consensus size: 9
197187 AAATTACAAC
197197 AAATATTTAA
1 AAATA-TTAA
197207 AAATATTAA
1 AAATATTAA
197216 AAAT-TGTAA
1 AAATAT-TAA
* *
197225 AATTACTAA
1 AAATATTAA
197234 AAAT-TGTAA
1 AAATAT-TAA
*
197243 AATTATTAA
1 AAATATTAA
*
197252 AAACATTAA
1 AAATATTAA
197261 CAATTTGTAA
Statistics
Matches: 43, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
8 1 0.02
9 36 0.84
10 6 0.14
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.34
Consensus pattern (9 bp):
AAATATTAA
Found at i:197234 original size:18 final size:18
Alignment explanation
Indices: 197186--197254 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
197176 TTTAAAATTA
*
197186 AAAATTAC-AACAAATATTT
1 AAAATTACTAA-AAAT-TGT
* *
197205 AAAAATATTAAAAATTGT
1 AAAATTACTAAAAATTGT
197223 AAAATTACTAAAAATTGT
1 AAAATTACTAAAAATTGT
*
197241 AAAATTATTAAAAA
1 AAAATTACTAAAAA
197255 CATTAACAAT
Statistics
Matches: 43, Mismatches: 6, Indels: 3
0.83 0.12 0.06
Matches are distributed among these distances:
18 31 0.72
19 10 0.23
20 2 0.05
ACGTcount: A:0.61, C:0.04, G:0.03, T:0.32
Consensus pattern (18 bp):
AAAATTACTAAAAATTGT
Found at i:197287 original size:22 final size:23
Alignment explanation
Indices: 197249--197293 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
197239 GTAAAATTAT
* *
197249 TAAAAACATTAACAATTTGTAAA
1 TAAAAAAATTAACAATTAGTAAA
197272 TAAAAAAATTAA-AATTAGTAAA
1 TAAAAAAATTAACAATTAGTAAA
197294 GAATTTGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (23 bp):
TAAAAAAATTAACAATTAGTAAA
Found at i:199932 original size:12 final size:11
Alignment explanation
Indices: 199917--200023 Score: 72
Period size: 12 Copynumber: 9.0 Consensus size: 11
199907 TTTTTTTATT
199917 AAGTTTTGCATC
1 AAGTTTT-CATC
*
199929 AAGTTCTT-TTC
1 AAGTT-TTCATC
199940 AAGCTTTTCATC
1 AAG-TTTTCATC
199952 AAGTCTTTCATC
1 AAGT-TTTCATC
199964 AAGTGTTTTTCATC
1 AA--G-TTTTCATC
* *
199978 AAGTTTTTAAGC
1 AAG-TTTTCATC
*
199990 AAGTTTCCATC
1 AAGTTTTCATC
*
200001 AAGTTTTTAATC
1 AAG-TTTTCATC
*
200013 AAGCTTTCATC
1 AAGTTTTCATC
200024 TTCTGAAATA
Statistics
Matches: 76, Mismatches: 11, Indels: 17
0.73 0.11 0.16
Matches are distributed among these distances:
11 22 0.29
12 41 0.54
13 2 0.03
14 10 0.13
15 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.11, T:0.44
Consensus pattern (11 bp):
AAGTTTTCATC
Found at i:199951 original size:23 final size:23
Alignment explanation
Indices: 199909--200023 Score: 94
Period size: 23 Copynumber: 4.9 Consensus size: 23
199899 TACCAAATTT
*
199909 TTTTTATTAAG-TTTTGCATCAAG
1 TTTTTATCAAGCTTTT-CATCAAG
199932 TTCTTT-TCAAGCTTTTCATCAAG
1 TT-TTTATCAAGCTTTTCATCAAG
* *
199955 TCTTTCATCAAGTGTTTTTCATCAAG
1 T-TTTTATCAA--GCTTTTCATCAAG
* *
199981 TTTTTAAGCAAG-TTTCCATCAAG
1 TTTTT-ATCAAGCTTTTCATCAAG
200004 TTTTTAATCAAGC-TTTCATC
1 TTTTT-ATCAAGCTTTTCATC
200024 TTCTGAAATA
Statistics
Matches: 76, Mismatches: 8, Indels: 16
0.76 0.08 0.16
Matches are distributed among these distances:
23 43 0.57
24 13 0.17
25 3 0.04
26 17 0.22
ACGTcount: A:0.25, C:0.17, G:0.10, T:0.47
Consensus pattern (23 bp):
TTTTTATCAAGCTTTTCATCAAG
Found at i:199976 original size:14 final size:14
Alignment explanation
Indices: 199944--199985 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
199934 CTTTTCAAGC
199944 TTTTCATCAA--GT
1 TTTTCATCAAGTGT
*
199956 CTTTCATCAAGTGT
1 TTTTCATCAAGTGT
199970 TTTTCATCAAGT-T
1 TTTTCATCAAGTGT
199983 TTT
1 TTT
199986 AAGCAAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
12 9 0.35
13 4 0.15
14 13 0.50
ACGTcount: A:0.21, C:0.17, G:0.10, T:0.52
Consensus pattern (14 bp):
TTTTCATCAAGTGT
Found at i:208735 original size:6 final size:6
Alignment explanation
Indices: 208724--208769 Score: 58
Period size: 6 Copynumber: 7.8 Consensus size: 6
208714 AGAAATACAC
* * *
208724 ATTTTA ATTTTA ATTTTA A-TTTA TTTTTA TTTTTA ACTTTA ATTTT
1 ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTTA ATTTT
208770 TATATAAATT
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
5 4 0.11
6 31 0.89
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (6 bp):
ATTTTA
Found at i:208757 original size:23 final size:23
Alignment explanation
Indices: 208725--208768 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
208715 GAAATACACA
*
208725 TTTTAATTTTAATTTTAATTTAT
1 TTTTAATTTTAACTTTAATTTAT
*
208748 TTTTATTTTTAACTTTAATTT
1 TTTTAATTTTAACTTTAATTT
208769 TTATATAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.70
Consensus pattern (23 bp):
TTTTAATTTTAACTTTAATTTAT
Found at i:208781 original size:29 final size:29
Alignment explanation
Indices: 208725--208784 Score: 75
Period size: 29 Copynumber: 2.1 Consensus size: 29
208715 GAAATACACA
* * **
208725 TTTTAATTTTAATTTTAATTTATTTTTAT
1 TTTTAACTTTAATTTTAATATAAATTTAT
*
208754 TTTTAACTTTAATTTTTATATAAATTTAT
1 TTTTAACTTTAATTTTAATATAAATTTAT
208783 TT
1 TT
208785 ATATTTATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (29 bp):
TTTTAACTTTAATTTTAATATAAATTTAT
Found at i:208791 original size:6 final size:6
Alignment explanation
Indices: 208780--208814 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
208770 TATATAAATT
*
208780 TATTTA TATTTA TATTTA CATTTA TATTTA TATTT
1 TATTTA TATTTA TATTTA TATTTA TATTTA TATTT
208815 TGTAGGTAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (6 bp):
TATTTA
Found at i:209100 original size:21 final size:21
Alignment explanation
Indices: 209051--209103 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
209041 ATACCTTAAC
*
209051 CTTTCACCCATCAAATCCTAAT
1 CTTTCACCTATCAAATCC-AAT
*
209073 CTTTCACCTATCACATCC-AT
1 CTTTCACCTATCAAATCCAAT
209093 CTTTTCACCTA
1 C-TTTCACCTA
209104 GAAAACTACA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
20 3 0.11
21 9 0.32
22 16 0.57
ACGTcount: A:0.26, C:0.38, G:0.00, T:0.36
Consensus pattern (21 bp):
CTTTCACCTATCAAATCCAAT
Found at i:212232 original size:23 final size:22
Alignment explanation
Indices: 212196--212240 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
212186 AATTTTTTTA
212196 TTAAGTTTTGCATCAAGTTCTTT
1 TTAAGTTTTGCATCAAG-TCTTT
212219 TTAAGCTTTT-CATCAAGTCTTT
1 TTAAG-TTTTGCATCAAGTCTTT
212241 CATCAAGTGT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
22 5 0.24
23 12 0.57
24 4 0.19
ACGTcount: A:0.22, C:0.16, G:0.11, T:0.51
Consensus pattern (22 bp):
TTAAGTTTTGCATCAAGTCTTT
Found at i:212243 original size:12 final size:12
Alignment explanation
Indices: 212198--212296 Score: 69
Period size: 12 Copynumber: 8.2 Consensus size: 12
212188 TTTTTTTATT
*
212198 AAGTTTTGCATC
1 AAGTTTTTCATC
*
212210 AAGTTCTTT--TT
1 AAGTT-TTTCATC
*
212221 AAGCTTTTCATC
1 AAGTTTTTCATC
*
212233 AAGTCTTTCATC
1 AAGTTTTTCATC
*
212245 AAGTGTTTTTTATC
1 AA--GTTTTTCATC
* *
212259 AAGTTTTTAAGC
1 AAGTTTTTCATC
*
212271 AAG-TTTCCATC
1 AAGTTTTTCATC
*
212282 AAGTTTTTGATC
1 AAGTTTTTCATC
212294 AAG
1 AAG
212297 CTTTCCATCT
Statistics
Matches: 66, Mismatches: 15, Indels: 12
0.71 0.16 0.13
Matches are distributed among these distances:
10 3 0.05
11 13 0.20
12 38 0.58
13 2 0.03
14 10 0.15
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.45
Consensus pattern (12 bp):
AAGTTTTTCATC
Found at i:212273 original size:26 final size:26
Alignment explanation
Indices: 212225--212274 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
212215 CTTTTTAAGC
* *
212225 TTTTCATCAAGTCTTTCATCAAGTGT
1 TTTTCATCAAGTCTTTAAGCAAGTGT
* *
212251 TTTTTATCAAGTTTTTAAGCAAGT
1 TTTTCATCAAGTCTTTAAGCAAGT
212275 TTCCATCAAG
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
26 20 1.00
ACGTcount: A:0.26, C:0.14, G:0.12, T:0.48
Consensus pattern (26 bp):
TTTTCATCAAGTCTTTAAGCAAGTGT
Found at i:212286 original size:23 final size:24
Alignment explanation
Indices: 212256--212305 Score: 75
Period size: 23 Copynumber: 2.1 Consensus size: 24
212246 AGTGTTTTTT
212256 ATCAAGTTTTTAAGCAAG-TTTCC
1 ATCAAGTTTTTAAGCAAGCTTTCC
* *
212279 ATCAAGTTTTTGATCAAGCTTTCC
1 ATCAAGTTTTTAAGCAAGCTTTCC
212303 ATC
1 ATC
212306 TTCTAAAACA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.28, C:0.20, G:0.12, T:0.40
Consensus pattern (24 bp):
ATCAAGTTTTTAAGCAAGCTTTCC
Found at i:215361 original size:19 final size:19
Alignment explanation
Indices: 215337--215375 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
215327 TAAGACTAAG
215337 TTGCTATTTGAACGCTCAA
1 TTGCTATTTGAACGCTCAA
215356 TTGCTATTTGAACGCTCAA
1 TTGCTATTTGAACGCTCAA
215375 T
1 T
215376 AATATCTGAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (19 bp):
TTGCTATTTGAACGCTCAA
Found at i:221662 original size:63 final size:63
Alignment explanation
Indices: 221570--221778 Score: 188
Period size: 63 Copynumber: 3.3 Consensus size: 63
221560 CACGGGTTGA
* * * * * *
221570 CACACGGGCGTGTGTCCAAGCTATGTAACTTAATGAATTTGGATTTGGGTCATACGGGCAAGC
1 CACACGGGTGTGTGTCCAGGCTATATAACTCAATGAATTTGGATTTAGGTCACACGGGCAAGC
* * * * *
221633 CACACGGGTATGTGTCCAGGCTGTATAACTCACTGACTTTGGATTTAGGTCACACGGGTAAGC
1 CACACGGGTGTGTGTCCAGGCTATATAACTCAATGAATTTGGATTTAGGTCACACGGGCAAGC
* * * * * ** * * *
221696 CACACAGGTGTGTGTCTAGGCCATGTAACTCACT-AACTTCAGATTTCGGTCACACAGGCAAGT
1 CACACGGGTGTGTGTCCAGGCTATATAACTCAATGAA-TTTGGATTTAGGTCACACGGGCAAGC
**
221759 CACACGATTGTGTG-CCAGGC
1 CACACGGGTGTGTGTCCAGGC
221779 CGTGTAGAGG
Statistics
Matches: 117, Mismatches: 28, Indels: 3
0.79 0.19 0.02
Matches are distributed among these distances:
62 6 0.05
63 111 0.95
ACGTcount: A:0.25, C:0.23, G:0.26, T:0.26
Consensus pattern (63 bp):
CACACGGGTGTGTGTCCAGGCTATATAACTCAATGAATTTGGATTTAGGTCACACGGGCAAGC
Found at i:223460 original size:89 final size:89
Alignment explanation
Indices: 223356--223531 Score: 300
Period size: 89 Copynumber: 2.0 Consensus size: 89
223346 TAGATACCAC
223356 TACACCAATAATAATTCTTATATTAATTTAAAAAAAATTAAATTTTAACATAAA-TATTTTTCTT
1 TACACCAATAATAATTCTTATATTAATTT-AAAAAAATTAAATTTTAACATAAAGTATTTTTCTT
* *
223420 AGCCAATTTACCACTTAACCAAAGT
65 AGCAAATTTACCACCTAACCAAAGT
* *
223445 TACACCAATAATAATTCTTATATTAATTTTAAAAAATTAATTTTTAACATAAAGTATTTTTCTTA
1 TACACCAATAATAATTCTTATATTAATTTAAAAAAATTAAATTTTAACATAAAGTATTTTTCTTA
223510 GCAAATTTACCACCTAACCAAA
66 GCAAATTTACCACCTAACCAAA
223532 ATTTCATTTT
Statistics
Matches: 82, Mismatches: 4, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
88 22 0.27
89 60 0.73
ACGTcount: A:0.44, C:0.15, G:0.02, T:0.39
Consensus pattern (89 bp):
TACACCAATAATAATTCTTATATTAATTTAAAAAAATTAAATTTTAACATAAAGTATTTTTCTTA
GCAAATTTACCACCTAACCAAAGT
Found at i:224170 original size:33 final size:33
Alignment explanation
Indices: 224128--224191 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
224118 CGCTAATGAT
**
224128 CTGGGCTTTAGCGGTGTTTTTGAAGAAGCGCTG
1 CTGGGCTTTAGCGGCATTTTTGAAGAAGCGCTG
*
224161 CTGGGCTTTAGCGGCATTTTTTAAGAAGCGC
1 CTGGGCTTTAGCGGCATTTTTGAAGAAGCGC
224192 CGCTATTGAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.17, C:0.17, G:0.33, T:0.33
Consensus pattern (33 bp):
CTGGGCTTTAGCGGCATTTTTGAAGAAGCGCTG
Found at i:224264 original size:41 final size:42
Alignment explanation
Indices: 224208--224393 Score: 197
Period size: 41 Copynumber: 4.6 Consensus size: 42
224198 TGATCTGGGC
*
224208 TTTAGAAA-CGCCGCTAATT-CTCTAGGCTTTAGCGGCATTT
1 TTTAGAAAGCGCCGCTAATTGCTCTGGGCTTTAGCGGCATTT
* *
224248 TTTAGAAAGCGCCGCT-ATTGCTTTGGGCTTTAGTGGCATTT
1 TTTAGAAAGCGCCGCTAATTGCTCTGGGCTTTAGCGGCATTT
* * * *
224289 TTTAGGAAGCACCGCTAA-TACTCTGGGCATTA-CGGCATTT
1 TTTAGAAAGCGCCGCTAATTGCTCTGGGCTTTAGCGGCATTT
* * ** *
224329 TTGAAGAAAGCACCAAT-ATTGCTCTGGGCTTTAGCGGCGTTT
1 TT-TAGAAAGCGCCGCTAATTGCTCTGGGCTTTAGCGGCATTT
*
224371 TTTAGAAAGCGCAGCTAA-TGCTC
1 TTTAGAAAGCGCCGCTAATTGCTC
224394 AGGGGATTTT
Statistics
Matches: 118, Mismatches: 21, Indels: 13
0.78 0.14 0.09
Matches are distributed among these distances:
40 21 0.18
41 86 0.73
42 11 0.09
ACGTcount: A:0.23, C:0.20, G:0.24, T:0.33
Consensus pattern (42 bp):
TTTAGAAAGCGCCGCTAATTGCTCTGGGCTTTAGCGGCATTT
Found at i:224626 original size:7 final size:7
Alignment explanation
Indices: 224616--224675 Score: 59
Period size: 7 Copynumber: 8.7 Consensus size: 7
224606 AGAGTTTTGA
224616 GTTTAGG
1 GTTTAGG
*
224623 GTTTACG
1 GTTTAGG
*
224630 GTGTA-G
1 GTTTAGG
*
224636 GTTTAAG
1 GTTTAGG
*
224643 GTTTGGG
1 GTTTAGG
*
224650 GTTTGGG
1 GTTTAGG
*
224657 GTTTAAG
1 GTTTAGG
224664 GTTTAGG
1 GTTTAGG
224671 GTTTA
1 GTTTA
224676 TGTTTTAATG
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
6 5 0.11
7 39 0.89
ACGTcount: A:0.15, C:0.02, G:0.40, T:0.43
Consensus pattern (7 bp):
GTTTAGG
Found at i:224660 original size:21 final size:21
Alignment explanation
Indices: 224635--224674 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
224625 TTACGGTGTA
*
224635 GGTTTAAGGTTTGGGGTTTGG
1 GGTTTAAGGTTTAGGGTTTGG
224656 GGTTTAAGGTTTAGGGTTT
1 GGTTTAAGGTTTAGGGTTT
224675 ATGTTTTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.42, T:0.45
Consensus pattern (21 bp):
GGTTTAAGGTTTAGGGTTTGG
Found at i:224770 original size:21 final size:21
Alignment explanation
Indices: 224746--224787 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
224736 TTAGGGCTTG
* * *
224746 GTGTTTATGGTTTACGGTTTA
1 GTGTTAATGATTTAAGGTTTA
224767 GTGTTAATGATTTAAGGTTTA
1 GTGTTAATGATTTAAGGTTTA
224788 CAATGTATGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.21, C:0.02, G:0.26, T:0.50
Consensus pattern (21 bp):
GTGTTAATGATTTAAGGTTTA
Found at i:224819 original size:14 final size:14
Alignment explanation
Indices: 224796--224851 Score: 51
Period size: 14 Copynumber: 3.9 Consensus size: 14
224786 TACAATGTAT
* *
224796 GATTTTGGGTTTTG
1 GATTTAGGGTTTAG
224810 GATTTAGGGTTTAG
1 GATTTAGGGTTTAG
* *
224824 GGTTTAGTG-TTACG
1 GATTTAGGGTTTA-G
224838 GATTTTAGGGTTTA
1 GA-TTTAGGGTTTA
224852 ATTACTTTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
13 3 0.09
14 21 0.64
15 6 0.18
16 3 0.09
ACGTcount: A:0.16, C:0.02, G:0.34, T:0.48
Consensus pattern (14 bp):
GATTTAGGGTTTAG
Found at i:226248 original size:31 final size:31
Alignment explanation
Indices: 226210--226289 Score: 142
Period size: 31 Copynumber: 2.6 Consensus size: 31
226200 TTGGATTTTA
*
226210 ATTGGTTTTTGCAGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
226241 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
1 ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
*
226272 ATTGATTTTTGCTGCTAA
1 ATTGGTTTTTGCTGCTAA
226290 ATCAACCATG
Statistics
Matches: 47, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
31 47 1.00
ACGTcount: A:0.19, C:0.15, G:0.21, T:0.45
Consensus pattern (31 bp):
ATTGGTTTTTGCTGCTAAGATGGTACCTTCT
Found at i:228527 original size:43 final size:43
Alignment explanation
Indices: 228466--228563 Score: 153
Period size: 43 Copynumber: 2.3 Consensus size: 43
228456 TTTGTGGTTA
* * *
228466 TTAGCGGCGATTGTGGGTAAAGCGCCGCTAAAGATCAT-ATTCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCAAAAGAACATGA-TCT
228509 TTAGCGGCGTTTGTGGGTAAAGCGCCGCAAAAGAACATGATCT
1 TTAGCGGCGTTTGTGGGTAAAGCGCCGCAAAAGAACATGATCT
228552 TTAGCGGCGTTT
1 TTAGCGGCGTTT
228564 TTTCTCATAA
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
43 50 0.98
44 1 0.02
ACGTcount: A:0.24, C:0.18, G:0.30, T:0.28
Consensus pattern (43 bp):
TTAGCGGCGTTTGTGGGTAAAGCGCCGCAAAAGAACATGATCT
Found at i:235278 original size:7 final size:7
Alignment explanation
Indices: 235266--235301 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
235256 TCAATAAAAA
235266 TTATTTT
1 TTATTTT
235273 TTATTTT
1 TTATTTT
235280 TTA--TT
1 TTATTTT
235285 TTATTTT
1 TTATTTT
235292 TTATTTT
1 TTATTTT
235299 TTA
1 TTA
235302 AATTTATATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
5 5 0.19
7 22 0.81
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:235286 original size:12 final size:12
Alignment explanation
Indices: 235271--235298 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
235261 AAAAATTATT
235271 TTTTATTTTTTA
1 TTTTATTTTTTA
235283 TTTTATTTTTTA
1 TTTTATTTTTTA
235295 TTTT
1 TTTT
235299 TTAAATTTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTATTTTTTA
Found at i:235290 original size:19 final size:20
Alignment explanation
Indices: 235266--235316 Score: 77
Period size: 19 Copynumber: 2.5 Consensus size: 20
235256 TCAATAAAAA
*
235266 TTATTTTTTATTTTTT-ATT
1 TTATTTTTTATTTTTTAAAT
235285 TTATTTTTTATTTTTTAAAT
1 TTATTTTTTATTTTTTAAAT
235305 TTATATTTTTAT
1 TTAT-TTTTTAT
235317 CAAATTATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 16 0.55
20 6 0.21
21 7 0.24
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (20 bp):
TTATTTTTTATTTTTTAAAT
Found at i:238039 original size:15 final size:15
Alignment explanation
Indices: 238016--238046 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
238006 ATTCAACCTT
*
238016 TACCTTAACCATTTC
1 TACCCTAACCATTTC
238031 TACCCTAACCATTTC
1 TACCCTAACCATTTC
238046 T
1 T
238047 TGATCAAATC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.35, G:0.00, T:0.39
Consensus pattern (15 bp):
TACCCTAACCATTTC
Found at i:240308 original size:12 final size:12
Alignment explanation
Indices: 240291--240357 Score: 53
Period size: 12 Copynumber: 5.6 Consensus size: 12
240281 CTTTATACCT
*
240291 TATATATGTACA
1 TATATATATACA
240303 TATATATATACA
1 TATATATATACA
* *
240315 CATATACATACA
1 TATATATATACA
* * **
240327 TATTTTTATTTA
1 TATATATATACA
*
240339 TACATATATACA
1 TATATATATACA
*
240351 TACATAT
1 TATATAT
240358 TTATCTCTTT
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
12 41 1.00
ACGTcount: A:0.43, C:0.12, G:0.01, T:0.43
Consensus pattern (12 bp):
TATATATATACA
Found at i:240371 original size:28 final size:28
Alignment explanation
Indices: 240303--240361 Score: 91
Period size: 28 Copynumber: 2.1 Consensus size: 28
240293 TATATGTACA
* *
240303 TATATATATACACATATACATACATATT
1 TATATTTATACATATATACATACATATT
*
240331 TTTATTTATACATATATACATACATATT
1 TATATTTATACATATATACATACATATT
240359 TAT
1 TAT
240362 CTCTTTACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.42, C:0.12, G:0.00, T:0.46
Consensus pattern (28 bp):
TATATTTATACATATATACATACATATT
Found at i:245363 original size:42 final size:42
Alignment explanation
Indices: 245293--245373 Score: 99
Period size: 42 Copynumber: 1.9 Consensus size: 42
245283 CTTAAAAAGG
*
245293 GCAGCTCAAAAATTGATCAAAATGGGGCATAAGGTGATCAGA
1 GCAGCTCAAAAATTGATCAAAATAGGGCATAAGGTGATCAGA
** * * **
245335 GCAGCTCAAATTTTGATCAGATTAGGGCATGTGGTGATC
1 GCAGCTCAAAAATTGATCAAAATAGGGCATAAGGTGATC
245374 TTGCTATACC
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.33, C:0.15, G:0.27, T:0.25
Consensus pattern (42 bp):
GCAGCTCAAAAATTGATCAAAATAGGGCATAAGGTGATCAGA
Found at i:246630 original size:44 final size:44
Alignment explanation
Indices: 246571--246784 Score: 182
Period size: 44 Copynumber: 4.9 Consensus size: 44
246561 AAACCACCAC
* * * * *
246571 TCCTATCTTCTTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGTAAA
* * * *
246615 TCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCAAAGACGGTGAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGTAAA
* * * ** ** * *
246659 TCTTATCTTCCC-AAGGTAGTAG-GGAAACAGATTTAA-ACCATCAG
1 TCCTATC-TCCCTAA-GCAGTAGTGG-AGCAGATCGAAGACTGTAAA
* * *
246703 TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAA
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGTAAA
*
246747 TCCTATCTCCCTAAGCAGTACTGGAGCAGATCGAAGAC
1 TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAC
246785 AGCGAATCTT
Statistics
Matches: 129, Mismatches: 35, Indels: 12
0.73 0.20 0.07
Matches are distributed among these distances:
43 16 0.12
44 95 0.74
45 18 0.14
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (44 bp):
TCCTATCTCCCTAAGCAGTAGTGGAGCAGATCGAAGACTGTAAA
Found at i:246823 original size:132 final size:132
Alignment explanation
Indices: 246429--246801 Score: 586
Period size: 132 Copynumber: 2.8 Consensus size: 132
246419 CAGATCGGTG
* * * *
246429 AAACCACCAGTCCTATCTCCCTGAGCAGCAGTGGAGTAGGTCAAAGATTGTAGATCCTGTCTCCC
1 AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTCCC
* * * *
246494 TAAGCAGTAGTAGAGCAAATCGAAGACAATGAATCTTATCTTCCCAAGGTAGTAGGGAAATAGAT
66 TAAGCAGTAGTGGAGCAGATCGAAGACAGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGAT
246559 TT
131 TT
* * *
246561 AAACCACCACTCCTATCTTCTTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTCCC
1 AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTCCC
* *
246626 TAAGCAGTAGTGGAGCAGATCAAAGACGGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGAT
66 TAAGCAGTAGTGGAGCAGATCGAAGACAGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGAT
246691 TT
131 TT
* *
246693 AAACCATCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTATCTCCC
1 AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTCCC
* *
246758 TAAGCAGTACTGGAGCAGATCGAAGACAGCGAATCTTA-CTTCCC
66 TAAGCAGTAGTGGAGCAGATCGAAGACAGTGAATCTTATCTTCCC
246802 TGGCGGTCCA
Statistics
Matches: 219, Mismatches: 22, Indels: 1
0.90 0.09 0.00
Matches are distributed among these distances:
131 6 0.03
132 213 0.97
ACGTcount: A:0.31, C:0.22, G:0.22, T:0.25
Consensus pattern (132 bp):
AAACCACCAGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTCCC
TAAGCAGTAGTGGAGCAGATCGAAGACAGTGAATCTTATCTTCCCAAGGTAGTAGGGAAACAGAT
TT
Found at i:246847 original size:50 final size:50
Alignment explanation
Indices: 246786--247349 Score: 434
Period size: 50 Copynumber: 11.3 Consensus size: 50
246776 ATCGAAGACA
* * * *
246786 GCGAATCTTACTTCCCTGGCGGTCCAGTGGAACAGATTGAAACTACAACG
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * * * ** * *
246836 GTGAATCTTACTTCCCTGACATTGCAATTAAAAAGATTGAAGCCACAACA
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* ** * *
246886 ACGAATCTTACTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCTACAACG
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * ** * * * *
246936 ACGAATCTTGCTT-CCTCAACATTGCAGTTGAAAAAATTGAAGCTACAACA
1 GCGAATCTTACTTCCCT-GGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* ** * * *
246986 GTGAATCTTACTTTTTCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACG
1 GCGAATCTTAC-TTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * * * * * * * *
247037 ACGAATCTTGCTTCCCCGACATTGCAAT-TAAAAGATTGAGGCCACAACG
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * * * *
247086 GCGAATCTTACTTCCCTAGCGGTGCATTGGAACATATTGAAGCTACAACG
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * * ** * * * *
247136 GCGAATCTTGCTTCCAC-GACATTATAAT-TAAAAGATTGAAGCCACAACA
1 GCGAATCTTACTTCC-CTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * * *
247185 GTGAATCTTACTTCCCTGGCAGTGTAGTGGAATAGATTGAAGCTACAACA
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * * * * * * * *
247235 ACGAATCTTGCTTCCCCGACATTACAGTTGAAAAGATTGAAACCACAACG
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
* * *
247285 GCGAATCTTACTTCCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAACA
1 GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
*
247335 GTGAATCTTACTTCC
1 GCGAATCTTACTTCC
247350 TCGACATTGC
Statistics
Matches: 383, Mismatches: 124, Indels: 14
0.74 0.24 0.03
Matches are distributed among these distances:
48 1 0.00
49 76 0.20
50 269 0.70
51 36 0.09
52 1 0.00
ACGTcount: A:0.32, C:0.23, G:0.20, T:0.25
Consensus pattern (50 bp):
GCGAATCTTACTTCCCTGGCAGTGCAGTGGAAAAGATTGAAGCTACAACG
Found at i:246960 original size:100 final size:100
Alignment explanation
Indices: 246783--247365 Score: 742
Period size: 100 Copynumber: 5.8 Consensus size: 100
246773 CAGATCGAAG
* * ** *
246783 ACAGCGAATCTTACTTCCCTGGCGGTCCAGTGGAACAGATTGAAACTACAACGGTGAATCTTACT
1 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCT
*
246848 TCCCTGACATTGCAATTAAAAAGATTGAAGCCACA
66 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACA
* * *
246883 ACAACGAATCTTACTTCCCTGGTGGTGTAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCT
1 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCT
* * * *
246948 TCCTCAACATTGCAGTTGAAAAA-ATTGAAGCTACA
66 TCCCCGACATTGCAATT-AAAAAGATTGAAGCCACA
* ** *
246983 ACAGTGAATCTTACTTTTTCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGC
1 ACAGCGAATCTTAC-TTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGC
*
247048 TTCCCCGACATTGCAATT-AAAAGATTGAGGCCACA
65 TTCCCCGACATTGCAATTAAAAAGATTGAAGCCACA
* * * * *
247083 ACGGCGAATCTTACTTCCCTAGCGGTGCATTGGAACATATTGAAGCTACAACGGCGAATCTTGCT
1 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCT
* **
247148 TCCACGACATTATAATT-AAAAGATTGAAGCCACA
66 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACA
* * * * *
247182 ACAGTGAATCTTACTTCCCTGGCAGTGTAGTGGAATAGATTGAAGCTACAACAACGAATCTTGCT
1 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCT
* * * *
247247 TCCCCGACATTACAGTTGAAAAGATTGAAACCACA
66 TCCCCGACATTGCAATTAAAAAGATTGAAGCCACA
* * * *
247282 ACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAATAGATTGAAGCTACAAC-AGTGAATCTTAC
1 ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGA-CGAATCTTGC
* *
247346 TTCCTCGACATTGCAGTTAA
65 TTCCCCGACATTGCAATTAA
247366 TTAAAACTGA
Statistics
Matches: 417, Mismatches: 61, Indels: 10
0.85 0.12 0.02
Matches are distributed among these distances:
99 148 0.35
100 204 0.49
101 65 0.16
ACGTcount: A:0.32, C:0.22, G:0.20, T:0.25
Consensus pattern (100 bp):
ACAGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCT
TCCCCGACATTGCAATTAAAAAGATTGAAGCCACA
Found at i:247616 original size:44 final size:46
Alignment explanation
Indices: 247566--247855 Score: 142
Period size: 45 Copynumber: 6.4 Consensus size: 46
247556 TCAGACTTTA
* * * *
247566 TGCAGTAAAGCAAG-TTAAAGCTACAAG-TCTTATCTCACTGAGGT
1 TGCAGTAGAGCAAGACTAAAGATACAAGATCTTATCTCACTGAAGT
* * *
247610 TGCAGTAGA-CTAGACTAAAGATACCAGATCTTATCTCTCTGAAGT
1 TGCAGTAGAGCAAGACTAAAGATACAAGATCTTATCTCACTGAAGT
** * *
247655 TGCAGTAGAGC-AGA-TCACACCATAACAAG-TCTTATCTCCCTAAAGT
1 TGCAGTAGAGCAAGACT-A-AAGAT-ACAAGATCTTATCTCACTGAAGT
* *
247701 TGCAGT-GAAGC-AGACTGAAGATAGCAA-ACCTTATCTC-CTTGAAGT
1 TGCAGTAG-AGCAAGACTAAAGATA-CAAGATCTTATCTCAC-TGAAGT
* * ** * * * *
247746 TACAGTGGAGC-AGGTTGAAGATACCTCAA-ACCTTATCACCCTGAAGT
1 TGCAGTAGAGCAAGACTAAAGATA---CAAGATCTTATCTCACTGAAGT
* * * * *
247793 TGCAGTGGAGCAAG-TTGAAGATACAAG-TCTTATCTCCCTGACGT
1 TGCAGTAGAGCAAGACTAAAGATACAAGATCTTATCTCACTGAAGT
* *
247837 TGCATTGGAGC-AGACTAAA
1 TGCAGTAGAGCAAGACTAAA
247856 ACTACGAATC
Statistics
Matches: 199, Mismatches: 29, Indels: 36
0.75 0.11 0.14
Matches are distributed among these distances:
43 5 0.03
44 51 0.26
45 66 0.33
46 32 0.16
47 42 0.21
48 3 0.02
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (46 bp):
TGCAGTAGAGCAAGACTAAAGATACAAGATCTTATCTCACTGAAGT
Found at i:247744 original size:91 final size:91
Alignment explanation
Indices: 247588--247758 Score: 213
Period size: 91 Copynumber: 1.9 Consensus size: 91
247578 AGTTAAAGCT
* * * *
247588 ACAAGTCTTATCTCACTGAGGTTGCAGTAGACTAGACTAAAGATACCAGATCTTATCTCTCTGAA
1 ACAAGTCTTATCTCACTAAAGTTGCAGTAGACTAGACTAAAGATACCAAACCTTATCTCTCTGAA
*
247653 GTTGCAGTAGAGCAGATCACACCATA
66 GTTACAGTAGAGCAGATCACACCATA
* * *
247679 ACAAGTCTTATCTCCCTAAAGTTGCAGT-GAAGC-AGACTGAAGATAGCAAACCTTATCTC-CTT
1 ACAAGTCTTATCTCACTAAAGTTGCAGTAG-A-CTAGACTAAAGATACCAAACCTTATCTCTC-T
*
247741 GAAGTTACAGTGGAGCAG
63 GAAGTTACAGTAGAGCAG
247759 GTTGAAGATA
Statistics
Matches: 68, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
90 2 0.03
91 65 0.96
92 1 0.01
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (91 bp):
ACAAGTCTTATCTCACTAAAGTTGCAGTAGACTAGACTAAAGATACCAAACCTTATCTCTCTGAA
GTTACAGTAGAGCAGATCACACCATA
Found at i:247752 original size:45 final size:44
Alignment explanation
Indices: 247594--247852 Score: 191
Period size: 45 Copynumber: 5.7 Consensus size: 44
247584 AGCTACAAGT
* * * * * *
247594 CTTATCTCACTGAGGTTGCAGTAGA-CTAGACTAAAGATACCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGC-AGACTGAAGATA-CAAAC
* * * * **
247639 CTTATCTCTCTGAAGTTGCAGTAGAGCAGA-TCACACCATAACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-A-GAT-ACAAAC
* *
247685 CTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATAGCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA-CAAAC
* * **
247730 CTTATCTCCTTGAAGTTACAGTGGAGCAGGTTGAAGATACCTCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATA---CAAAC
* * **
247777 CTTATCACCCTGAAGTTGCAGTGGAGCA-AGTTGAAGATACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-CTGAAGATACAAAC
* *
247821 CTTATCTCCCTGACGTTGCATTGGAGCAGACT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGACT
247853 AAAACTACGA
Statistics
Matches: 173, Mismatches: 31, Indels: 21
0.77 0.14 0.09
Matches are distributed among these distances:
44 32 0.18
45 66 0.38
46 33 0.19
47 42 0.24
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (44 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATACAAAC
Found at i:247793 original size:47 final size:46
Alignment explanation
Indices: 247685--247849 Score: 183
Period size: 47 Copynumber: 3.6 Consensus size: 46
247675 CATAACAAGT
* * **
247685 CTTATCTCCCTAAAGTTGCAGTGAAGCAGACTGAAGATA-GCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACGCAAAC
* * *
247730 CTTATCTCCTTGAAGTTACAGTGGAGCAGGTTGAAGATACCTCAAAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATA-CGCAAAC
* * **
247777 CTTATCACCCTGAAGTTGCAGTGGAGCAAGTTGAAGATA--CAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACGCAAAC
* *
247821 CTTATCTCCCTGACGTTGCATTGGAGCAG
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAG
247850 ACTAAAACTA
Statistics
Matches: 101, Mismatches: 17, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
44 28 0.28
45 33 0.33
47 40 0.40
ACGTcount: A:0.30, C:0.22, G:0.22, T:0.26
Consensus pattern (46 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACGCAAAC
Found at i:249685 original size:26 final size:26
Alignment explanation
Indices: 249656--249722 Score: 71
Period size: 26 Copynumber: 2.5 Consensus size: 26
249646 CTTTATACCT
*
249656 TATATGTACATATATATATTTACACA
1 TATATATACATATATATATTTACACA
* * * *
249682 TATACATACATATTTTTATTTATACA
1 TATATATACATATATATATTTACACA
249708 TATATACATACATAT
1 TATAT--ATACATAT
249723 TTATCTCTTT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
26 25 0.76
28 8 0.24
ACGTcount: A:0.42, C:0.12, G:0.01, T:0.45
Consensus pattern (26 bp):
TATATATACATATATATATTTACACA
Found at i:249735 original size:28 final size:27
Alignment explanation
Indices: 249662--249736 Score: 89
Period size: 28 Copynumber: 2.7 Consensus size: 27
249652 ACCTTATATG
* *
249662 TACATATATATA-TTTACACATATACA
1 TACATATTTATATTTTACATATATACA
*
249688 TACATATTTTTATTTATACATATATACA
1 TACATATTTATATTT-TACATATATACA
*
249716 TACATATTTATCTCTTTACAT
1 TACATATTTATAT-TTTACAT
249737 TTTTAACCTT
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
26 10 0.24
27 2 0.05
28 27 0.66
29 2 0.05
ACGTcount: A:0.39, C:0.15, G:0.00, T:0.47
Consensus pattern (27 bp):
TACATATTTATATTTTACATATATACA
Found at i:252979 original size:23 final size:22
Alignment explanation
Indices: 252947--253008 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
252937 CCCGACCCGT
*
252947 TTTTTAATTAAAATTAAAATTATA
1 TTTTT-ATTAAAATTAAAACTA-A
*
252971 TTTTTATTAAAATTAAAACTAC
1 TTTTTATTAAAATTAAAACTAA
*
252993 TTGTTATTAAAATTAA
1 TTTTTATTAAAATTAA
253009 TTGTTATCAA
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
22 15 0.43
23 15 0.43
24 5 0.14
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (22 bp):
TTTTTATTAAAATTAAAACTAA
Found at i:253003 original size:16 final size:16
Alignment explanation
Indices: 252982--253038 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
252972 TTTTATTAAA
* *
252982 ATTAAAACTACTTGTT
1 ATTAAAATTAATTGTT
252998 ATTAAAATTAATTGTT
1 ATTAAAATTAATTGTT
*
253014 ATCAAAATTAATTGTT
1 ATTAAAATTAATTGTT
253030 ATTAAAATT
1 ATTAAAATT
253039 GTATCAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 37 1.00
ACGTcount: A:0.44, C:0.05, G:0.05, T:0.46
Consensus pattern (16 bp):
ATTAAAATTAATTGTT
Found at i:253121 original size:19 final size:18
Alignment explanation
Indices: 253099--253153 Score: 58
Period size: 19 Copynumber: 3.0 Consensus size: 18
253089 ATTTTGTTCT
253099 TAAAATTATTAATTGTTA
1 TAAAATTATTAATTGTTA
* *
253117 CTAAAATTATCAAATT-ATA
1 -TAAAATTAT-TAATTGTTA
*
253136 TCAAATTATTAATTGTTA
1 TAAAATTATTAATTGTTA
253154 ATTGTATTAA
Statistics
Matches: 29, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
17 4 0.14
18 10 0.34
19 11 0.38
20 4 0.14
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.45
Consensus pattern (18 bp):
TAAAATTATTAATTGTTA
Found at i:253248 original size:21 final size:22
Alignment explanation
Indices: 253207--253249 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
253197 AAACTTAAAA
* *
253207 TAAAACTAAAACTAGTATATTT
1 TAAAAATAAAAATAGTATATTT
253229 TAAAAATAAAAATA-TATATTT
1 TAAAAATAAAAATAGTATATTT
253250 AATATATTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.56, C:0.05, G:0.02, T:0.37
Consensus pattern (22 bp):
TAAAAATAAAAATAGTATATTT
Found at i:253413 original size:68 final size:68
Alignment explanation
Indices: 253304--253583 Score: 542
Period size: 68 Copynumber: 4.1 Consensus size: 68
253294 CCTGAAGCCC
*
253304 TTAATTGTATTAATTGTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
1 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
253369 GTA
66 GTA
253372 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
1 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
253437 GTA
66 GTA
253440 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
1 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
253505 GTA
66 GTA
*
253508 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAATT
1 TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
253573 GTA
66 GTA
253576 TTAATTGT
1 TTAATTGT
253584 TGTAACAAAA
Statistics
Matches: 210, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
68 210 1.00
ACGTcount: A:0.39, C:0.05, G:0.08, T:0.47
Consensus pattern (68 bp):
TTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAGTAAATTTATCAAATTATTAACT
GTA
Found at i:253420 original size:59 final size:61
Alignment explanation
Indices: 253354--253609 Score: 320
Period size: 68 Copynumber: 4.0 Consensus size: 61
253344 TAGTAAATTT
253354 ATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAG
1 ATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAG
253415 TAAATTTATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGAT
1 -------ATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGAT
253480 TAG
59 TAG
253483 TAAATTTATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGAT
1 -------ATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGAT
253548 TAG
59 TAG
* * * *
253551 -T-AAATTTATCAAAT-TATTAATTGTATTAATTGTTGTAACAAAATCTAACATTTGATTAG
1 ATCAAA-TTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAG
253610 TAAAACAAAC
Statistics
Matches: 183, Mismatches: 4, Indels: 11
0.92 0.02 0.06
Matches are distributed among these distances:
59 46 0.25
60 8 0.04
68 129 0.70
ACGTcount: A:0.40, C:0.06, G:0.08, T:0.46
Consensus pattern (61 bp):
ATCAAATTATTAACTGTATTAATTGTATTAATTTTTGTAATAAAATCTAACATTTGATTAG
Found at i:253720 original size:22 final size:24
Alignment explanation
Indices: 253678--253727 Score: 61
Period size: 23 Copynumber: 2.2 Consensus size: 24
253668 GTAAATAAAC
*
253678 TTAAAAACTAAAACTAGTATAT-T
1 TTAAAAACTAAAACTAATATATAT
253701 TTAAAAA-TAAAA-TATATATATAT
1 TTAAAAACTAAAACTA-ATATATAT
253724 TTAA
1 TTAA
253728 TATATTTTCG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
21 2 0.08
22 10 0.42
23 12 0.50
ACGTcount: A:0.56, C:0.04, G:0.02, T:0.38
Consensus pattern (24 bp):
TTAAAAACTAAAACTAATATATAT
Found at i:254009 original size:26 final size:26
Alignment explanation
Indices: 253944--254010 Score: 75
Period size: 26 Copynumber: 2.5 Consensus size: 26
253934 AAACATTGAA
253944 TTTTTTATTTTTTATATTTTTAAAATG
1 TTTTTT-TTTTTTATATTTTTAAAATG
*
253971 TCTTTATTTTTTT-TATTTTTAAAGA-G
1 T-TTTTTTTTTTTATATTTTTAAA-ATG
253997 TTTTTTTTATTTTA
1 TTTTTTTT-TTTTA
254011 AAAATTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
25 6 0.18
26 16 0.47
27 8 0.24
28 4 0.12
ACGTcount: A:0.22, C:0.01, G:0.04, T:0.72
Consensus pattern (26 bp):
TTTTTTTTTTTTATATTTTTAAAATG
Found at i:254174 original size:9 final size:8
Alignment explanation
Indices: 254144--254171 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
254134 TGAAGGTTAA
254144 AAAATTTT
1 AAAATTTT
254152 AAAATTTT
1 AAAATTTT
254160 AAAATTTT
1 AAAATTTT
254168 AAAA
1 AAAA
254172 ATTAACATAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATTTT
Found at i:257333 original size:34 final size:29
Alignment explanation
Indices: 257271--257368 Score: 160
Period size: 29 Copynumber: 3.4 Consensus size: 29
257261 ATAAAAATCG
257271 TAATTAAAAACCCTAACCCTACCCTAATT
1 TAATTAAAAACCCTAACCCTACCCTAATT
*
257300 TAATTAAAAACCCTACCCCTACCCTAATT
1 TAATTAAAAACCCTAACCCTACCCTAATT
* * *
257329 TAATTTAAAACCCTAACCTTAACCTAATT
1 TAATTAAAAACCCTAACCCTACCCTAATT
257358 TAATTAAAAAC
1 TAATTAAAAAC
257369 NNNNNNNNNN
Statistics
Matches: 63, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 63 1.00
ACGTcount: A:0.43, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
TAATTAAAAACCCTAACCCTACCCTAATT
Found at i:257501 original size:29 final size:29
Alignment explanation
Indices: 257459--257835 Score: 592
Period size: 29 Copynumber: 13.0 Consensus size: 29
257449 NNNNNNNNNN
*
257459 ACCCTACCCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
257488 ACCCTATCCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
257517 ACCCTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
**
257546 ACATTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
* **
257575 ACCGTGCCCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
257604 ACCCTACCCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
257633 ACCTTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
257662 ACCTTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
257691 ACCTTAACCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
*
257720 ACCCTACCCTAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
* *
257749 ACCTTAACATAATTTAATTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
* *
257778 ACCCTACCCTAATTTATTTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
* *
257807 ACCTTAACCTAATTTATTTAAAAACCCTA
1 ACCCTAACCTAATTTAATTAAAAACCCTA
257836 NNNNNNNNNN
Statistics
Matches: 325, Mismatches: 23, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 325 1.00
ACGTcount: A:0.43, C:0.27, G:0.01, T:0.30
Consensus pattern (29 bp):
ACCCTAACCTAATTTAATTAAAAACCCTA
Found at i:264888 original size:123 final size:124
Alignment explanation
Indices: 264667--264942 Score: 500
Period size: 123 Copynumber: 2.2 Consensus size: 124
264657 NNNNNNNNNN
*
264667 ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTGTTTGAGAAGAAATTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
* *
264732 TCGCGCTCTCGTGGACGCGTTTTTGCTACAGTAGGTCATGTAAGAAATAATT-TTTTTG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTGTTTTTG
264790 ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
1 ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
* *
264855 TCGCGCCCTCGTGGACGCGATTTTGCTATAGTAGGTCATGTAAGAAATATTTGTTTTTG
66 TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTGTTTTTG
264914 ACGTTTCTGAGCAAATAGTATAAAATCGC
1 ACGTTTCTGAGCAAATAGTATAAAATCGC
264943 TTTTACNNNN
Statistics
Matches: 147, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
123 112 0.76
124 35 0.24
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (124 bp):
ACGTTTCTGAGCAAATAGTATAAAATCGCCTCTACCAGGATGCTATTTGAGAAGAAATTGTGAAA
TCGCGCCCTCGTGGACGCGATTTTGCTACAGTAGGTCATGTAAGAAATAATTGTTTTTG
Found at i:266658 original size:156 final size:156
Alignment explanation
Indices: 266374--266687 Score: 576
Period size: 156 Copynumber: 2.0 Consensus size: 156
266364 AGCTATGTTA
* *
266374 GCTAGCTTGATACTACCCACGATAAAAGTAAATCCTAGGACTTCAGTGCCGGTGATAATTGGCAA
1 GCTAGCTTGATACTACCCACGATAAAAGCAAATCCTAGGACTTCAGTGCCGGTGATAATTGCCAA
*
266439 TATCCGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAAGGCGT
66 TATCAGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAAGGCGT
266504 TGGAGAAGATGCATAGTGGGTGGGAC
131 TGGAGAAGATGCATAGTGGGTGGGAC
*
266530 GCTAGCTTGATACTGCCCACGATAAAAGCAAATCCT-GAGACTTCAGTGCCGGTGATAATTGCCA
1 GCTAGCTTGATACTACCCACGATAAAAGCAAATCCTAG-GACTTCAGTGCCGGTGATAATTGCCA
266594 ATATCAGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAAGGCG
65 ATATCAGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAAGGCG
266659 TTGGAGAAGATGCATAGTGGGTGGGAC
130 TTGGAGAAGATGCATAGTGGGTGGGAC
266686 GC
1 GC
266688 CTCAAATAAT
Statistics
Matches: 153, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
155 1 0.01
156 152 0.99
ACGTcount: A:0.29, C:0.22, G:0.28, T:0.21
Consensus pattern (156 bp):
GCTAGCTTGATACTACCCACGATAAAAGCAAATCCTAGGACTTCAGTGCCGGTGATAATTGCCAA
TATCAGTAGCCAAATGGGGTACACGCCCTCTTACCGCAAGGCTTGGATAGCTAAGCAGAAGGCGT
TGGAGAAGATGCATAGTGGGTGGGAC
Found at i:268211 original size:10 final size:10
Alignment explanation
Indices: 268196--268222 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
268186 TAAAATTATC
268196 AAATTATGTA
1 AAATTATGTA
268206 AAATTATGTA
1 AAATTATGTA
268216 AAATTAT
1 AAATTAT
268223 TAAGCCAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (10 bp):
AAATTATGTA
Found at i:268388 original size:55 final size:55
Alignment explanation
Indices: 268304--268423 Score: 204
Period size: 55 Copynumber: 2.2 Consensus size: 55
268294 NNNNNNNNNN
*
268304 TGTAAAATTATTAAGTCCAAAAATTGTGTTAATGGTTAGTAAAATTATCAAATTA
1 TGTAAAATTATTAAGTCCAAAAATTGTGTTAACGGTTAGTAAAATTATCAAATTA
* * *
268359 TGTAAAATTATTAATTCTAACAATTGTGTTAACGGTTAGTAAAATTATCAAATTA
1 TGTAAAATTATTAAGTCCAAAAATTGTGTTAACGGTTAGTAAAATTATCAAATTA
268414 TGTAAAATTA
1 TGTAAAATTA
268424 GGTTAGGGTT
Statistics
Matches: 61, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
55 61 1.00
ACGTcount: A:0.43, C:0.06, G:0.12, T:0.39
Consensus pattern (55 bp):
TGTAAAATTATTAAGTCCAAAAATTGTGTTAACGGTTAGTAAAATTATCAAATTA
Found at i:268498 original size:75 final size:77
Alignment explanation
Indices: 268418--268564 Score: 226
Period size: 75 Copynumber: 1.9 Consensus size: 77
268408 AAATTATGTA
* ** *
268418 AAATTAGGTTAGGGTTAGGGTTTTTAATTAAGTTA-GG-TTAGGGTTAGGGTTTTTAATTAAGTT
1 AAATTAGATTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTAGAATTAAGGTTTTTAATTAAGTT
268481 AGGGTTTTAATT
66 AGGGTTTTAATT
**
268493 AAATTAGATTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTTTAATTAAGGTTTTTAATTAAGTT
1 AAATTAGATTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTAGAATTAAGGTTTTTAATTAAGTT
268558 AGGGTTT
66 AGGGTTT
268565 AGGGTTAGGG
Statistics
Matches: 64, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
75 34 0.53
76 2 0.03
77 28 0.44
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (77 bp):
AAATTAGATTAGGGTTAGGGTTTTTAATTAAGTTAGGGTTTAGAATTAAGGTTTTTAATTAAGTT
AGGGTTTTAATT
Found at i:268547 original size:13 final size:13
Alignment explanation
Indices: 268529--268555 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
268519 ATTAAGTTAG
268529 GGTTTTTAATTAA
1 GGTTTTTAATTAA
268542 GGTTTTTAATTAA
1 GGTTTTTAATTAA
268555 G
1 G
268556 TTAGGGTTTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.52
Consensus pattern (13 bp):
GGTTTTTAATTAA
Found at i:268549 original size:31 final size:31
Alignment explanation
Indices: 268478--268657 Score: 276
Period size: 31 Copynumber: 5.9 Consensus size: 31
268468 TTTTAATTAA
* *
268478 GTTAGGG-TTTTAATTAAATTA--GATTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
***
268506 GTTAGGGTTTTTAATTAAGTTAGGGTTTTTA
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
* *
268537 ATTAAGGTTTTTAATTAAGTTAGGGTTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
268568 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
268599 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
1 GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
268630 GTTAGGGTTTTTAATTAAGTTAGGGTTT
1 GTTAGGGTTTTTAATTAAGTTAGGGTTT
268658 NNNNNNNNNN
Statistics
Matches: 137, Mismatches: 12, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
28 7 0.05
29 13 0.09
31 117 0.85
ACGTcount: A:0.25, C:0.00, G:0.28, T:0.47
Consensus pattern (31 bp):
GTTAGGGTTTTTAATTAAGTTAGGGTTTAGG
Found at i:273583 original size:30 final size:29
Alignment explanation
Indices: 273548--273611 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
273538 AAAAAGCTAT
273548 TTTTTTTCAAAATTTACCGAAATGGGTCGA
1 TTTTTTTCAAAATTTACCGAAATGGGTC-A
* ** *
273578 -TTTTTTGATTATTTACCGGAATGGGTCA
1 TTTTTTTCAAAATTTACCGAAATGGGTCA
273606 TTTTTT
1 TTTTTT
273612 GGGAAATCGC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
28 1 0.03
29 28 0.97
ACGTcount: A:0.23, C:0.11, G:0.17, T:0.48
Consensus pattern (29 bp):
TTTTTTTCAAAATTTACCGAAATGGGTCA
Found at i:278947 original size:19 final size:20
Alignment explanation
Indices: 278909--278947 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
278899 ACATGTGGAA
*
278909 TAATAATAAACATATGTATT
1 TAATAACAAACATATGTATT
*
278929 TAATAACAAA-ATATTTATT
1 TAATAACAAACATATGTATT
278948 GCTTATTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.51, C:0.05, G:0.03, T:0.41
Consensus pattern (20 bp):
TAATAACAAACATATGTATT
Found at i:278993 original size:26 final size:29
Alignment explanation
Indices: 278928--278993 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 29
278918 ACATATGTAT
* * *
278928 TTAATAACAAAATATTTATTGCTTATTAA
1 TTAAGAACAAAATATATATTGATTATTAA
*
278957 TTAAGTA-AAAATATATATT-ATTA-TAA
1 TTAAGAACAAAATATATATTGATTATTAA
278983 TTAA-AACAAAA
1 TTAAGAACAAAA
278994 CAAATAAAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
25 1 0.03
26 11 0.35
27 3 0.10
28 11 0.35
29 5 0.16
ACGTcount: A:0.53, C:0.05, G:0.03, T:0.39
Consensus pattern (29 bp):
TTAAGAACAAAATATATATTGATTATTAA
Found at i:293698 original size:24 final size:25
Alignment explanation
Indices: 293657--293705 Score: 73
Period size: 24 Copynumber: 2.0 Consensus size: 25
293647 TAAAAATCTA
293657 AAAAAAATGTAATATTTAAAAAAAT
1 AAAAAAATGTAATATTTAAAAAAAT
* *
293682 AAAAAATTGTACT-TTTAAAAAAAT
1 AAAAAAATGTAATATTTAAAAAAAT
293706 TATGAAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 11 0.50
25 11 0.50
ACGTcount: A:0.63, C:0.02, G:0.04, T:0.31
Consensus pattern (25 bp):
AAAAAAATGTAATATTTAAAAAAAT
Found at i:294229 original size:24 final size:26
Alignment explanation
Indices: 294201--294249 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
294191 TATATTTTTT
*
294201 AAAATTTT-ATTTT-TTAAATATAAA
1 AAAATTTTAATTTTGTTAAAAATAAA
294225 AAAATTTTAATTTTGTTAAAAATAA
1 AAAATTTTAATTTTGTTAAAAATAA
294250 TACATATTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 8 0.36
25 5 0.23
26 9 0.41
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (26 bp):
AAAATTTTAATTTTGTTAAAAATAAA
Found at i:299432 original size:16 final size:16
Alignment explanation
Indices: 299377--299435 Score: 50
Period size: 16 Copynumber: 3.7 Consensus size: 16
299367 CCAAATTATA
299377 TATTAAATATATATTTT
1 TATTAAATATA-ATTTT
* * *
299394 T-TT-ATTTTTATTTT
1 TATTAAATATAATTTT
*
299408 TAATCAAATATAATTTT
1 T-ATTAAATATAATTTT
299425 TATTAAATATA
1 TATTAAATATA
299436 TATATTTTGG
Statistics
Matches: 31, Mismatches: 8, Indels: 7
0.67 0.17 0.15
Matches are distributed among these distances:
14 6 0.19
15 3 0.10
16 12 0.39
17 10 0.32
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTAAATATAATTTT
Found at i:299506 original size:6 final size:7
Alignment explanation
Indices: 299474--299505 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
299464 ATATTAAATA
299474 TTTTTAT
1 TTTTTAT
299481 TTTTTAT
1 TTTTTAT
*
299488 TTTTTAG
1 TTTTTAT
299495 TTTTTAT
1 TTTTTAT
299502 TTTT
1 TTTT
299506 AATCAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
7 23 1.00
ACGTcount: A:0.12, C:0.00, G:0.03, T:0.84
Consensus pattern (7 bp):
TTTTTAT
Found at i:300557 original size:13 final size:13
Alignment explanation
Indices: 300539--300564 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
300529 AAACCTATTT
300539 GAACAACTTATAC
1 GAACAACTTATAC
300552 GAACAACTTATAC
1 GAACAACTTATAC
300565 TGAGATAATT
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:0.46, C:0.23, G:0.08, T:0.23
Consensus pattern (13 bp):
GAACAACTTATAC
Found at i:302791 original size:3 final size:3
Alignment explanation
Indices: 302783--302826 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
302773 CATTTAAATA
302783 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
302827 AAAACTAGAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:307033 original size:20 final size:20
Alignment explanation
Indices: 306999--307040 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
306989 AACTATTTAA
** *
306999 ATAATATTATTTGAATAGTT
1 ATAATATTAAATGAATAATT
307019 ATAATATTAAATGAATAATT
1 ATAATATTAAATGAATAATT
307039 AT
1 AT
307041 GTGTTTATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (20 bp):
ATAATATTAAATGAATAATT
Done.