Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A10
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: 111961792
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4980000 characters in sequence are not A, C, G, or T
File 119 of 344
Found at i:40387738 original size:10 final size:10
Alignment explanation
Indices: 40387722--40387779 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
40387712 CAACTCCGAC
40387722 CAGCTCAATT
1 CAGCTCAATT
* *
40387732 GAGCTCATTT
1 CAGCTCAATT
40387742 CAGCTCAA-T
1 CAGCTCAATT
40387751 CGAGCTCAATT
1 C-AGCTCAATT
*
40387762 TAGCTACAATT
1 CAGCT-CAATT
40387773 CAGCTCA
1 CAGCTCA
40387780 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:40387745 original size:20 final size:20
Alignment explanation
Indices: 40387722--40387782 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40387712 CAACTCCGAC
40387722 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
40387742 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
40387763 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
40387783 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:40389166 original size:10 final size:11
Alignment explanation
Indices: 40389144--40389178 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
40389134 AAAAGATAAG
40389144 AAATTCAAAAA
1 AAATTCAAAAA
40389155 AAATTCAAAAA
1 AAATTCAAAAA
*
40389166 AAA-TCGAAAA
1 AAATTCAAAAA
40389176 AAA
1 AAA
40389179 GAAAAAAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.74, C:0.09, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:40390277 original size:18 final size:18
Alignment explanation
Indices: 40390251--40390300 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
40390241 AAATTGAAAG
*
40390251 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
40390269 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
40390287 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
40390301 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:40390279 original size:6 final size:6
Alignment explanation
Indices: 40390247--40390300 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
40390237 AAAGAAATTG
* * ** *
40390247 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
40390294 AAAGAA A
1 AAAGAA A
40390301 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:40390360 original size:18 final size:18
Alignment explanation
Indices: 40390339--40390373 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40390329 AGAAAATAAA
40390339 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
40390357 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
40390374 AAAAGAAAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:40392461 original size:10 final size:10
Alignment explanation
Indices: 40392445--40392502 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
40392435 CAACTCCGAC
40392445 CAGCTCAATT
1 CAGCTCAATT
* *
40392455 GAGCTCATTT
1 CAGCTCAATT
40392465 CAGCTCAA-T
1 CAGCTCAATT
40392474 CGAGCTCAATT
1 C-AGCTCAATT
*
40392485 TAGCTACAATT
1 CAGCT-CAATT
40392496 CAGCTCA
1 CAGCTCA
40392503 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:40392468 original size:20 final size:20
Alignment explanation
Indices: 40392445--40392505 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40392435 CAACTCCGAC
40392445 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
40392465 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
40392486 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
40392506 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:40394101 original size:49 final size:47
Alignment explanation
Indices: 40393781--40394282 Score: 752
Period size: 47 Copynumber: 10.6 Consensus size: 47
40393771 CCCTTCGGGA
* * * * * *
40393781 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40393828 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40393875 CTCATCACATATATACACTTTCACATTCATCACATCGGCTATTAGTC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40393922 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40393969 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGA
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40394016 CTTATCACATATATACACTTTCACATTCATCTCATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40394063 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40394112 CTTATCACATATATATACACTTTCATATTCATCACATCGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40394161 CTTATCACATATATATACACTTTCACATTCATCACATTGGCCATTCGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40394210 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40394257 CTTATCACATATATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
40394283 CACAATTATC
Statistics
Matches: 425, Mismatches: 28, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
47 285 0.67
49 140 0.33
ACGTcount: A:0.29, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40396978 original size:27 final size:27
Alignment explanation
Indices: 40396947--40396998 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
40396937 ACAAGTGAGG
40396947 AAAAAGAAAAAGAGAATGAAAAAGAGC
1 AAAAAGAAAAAGAGAATGAAAAAGAGC
* ** *
40396974 AAAAAGAGATTGAGAGTGAAAAAGA
1 AAAAAGAAAAAGAGAATGAAAAAGA
40396999 AATTGAAGAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.65, C:0.02, G:0.25, T:0.08
Consensus pattern (27 bp):
AAAAAGAAAAAGAGAATGAAAAAGAGC
Found at i:40401499 original size:10 final size:10
Alignment explanation
Indices: 40401483--40401540 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
40401473 CAACTCCGAC
40401483 CAGCTCAATT
1 CAGCTCAATT
* *
40401493 GAGCTCATTT
1 CAGCTCAATT
40401503 CAGCTCAA-T
1 CAGCTCAATT
40401512 CGAGCTCAATT
1 C-AGCTCAATT
*
40401523 TAGCTACAATT
1 CAGCT-CAATT
40401534 CAGCTCA
1 CAGCTCA
40401541 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:40401506 original size:20 final size:20
Alignment explanation
Indices: 40401483--40401543 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40401473 CAACTCCGAC
40401483 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
40401503 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
40401524 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
40401544 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:40402927 original size:10 final size:11
Alignment explanation
Indices: 40402905--40402941 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
40402895 AAAAGAGAAG
40402905 AAATTCAAAAA
1 AAATTCAAAAA
40402916 AAATTCAAAAA
1 AAATTCAAAAA
*
40402927 AAAATCGAAAAA
1 AAATTC-AAAAA
40402939 AAA
1 AAA
40402942 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 16 0.67
12 8 0.33
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (11 bp):
AAATTCAAAAA
Found at i:40402928 original size:12 final size:12
Alignment explanation
Indices: 40402905--40402941 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
40402895 AAAAGAGAAG
40402905 AAATTC-AAAAA
1 AAATTCAAAAAA
40402916 AAATTCAAAAAA
1 AAATTCAAAAAA
40402928 AAA-TCGAAAAAA
1 AAATTC-AAAAAA
40402940 AA
1 AA
40402942 GAAAAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.76, C:0.08, G:0.03, T:0.14
Consensus pattern (12 bp):
AAATTCAAAAAA
Found at i:40404538 original size:22 final size:22
Alignment explanation
Indices: 40404510--40404553 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40404500 TTTTGAACCA
40404510 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
40404532 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
40404554 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:40409328 original size:22 final size:22
Alignment explanation
Indices: 40409300--40409343 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40409290 TTTTGAACCA
40409300 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
40409322 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
40409344 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:40410390 original size:18 final size:18
Alignment explanation
Indices: 40410364--40410413 Score: 64
Period size: 18 Copynumber: 2.8 Consensus size: 18
40410354 AAATTGAAAG
*
40410364 AAAACAAAAAGAAAACGA
1 AAAAGAAAAAGAAAACGA
** *
40410382 AAAAGAAAAAGAAATTGC
1 AAAAGAAAAAGAAAACGA
40410400 AAAAGAAAAAGAAA
1 AAAAGAAAAAGAAA
40410414 TCAAAATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (18 bp):
AAAAGAAAAAGAAAACGA
Found at i:40410392 original size:6 final size:6
Alignment explanation
Indices: 40410360--40410413 Score: 56
Period size: 6 Copynumber: 9.2 Consensus size: 6
40410350 AAAGAAATTG
* * ** *
40410360 AAAG-A AAACAA AAAGAA AACGAA AAAGAA AAAGAA ATTGCA AAAGAA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA
40410407 AAAGAA A
1 AAAGAA A
40410414 TCAAAATAGT
Statistics
Matches: 38, Mismatches: 10, Indels: 1
0.78 0.20 0.02
Matches are distributed among these distances:
5 3 0.08
6 35 0.92
ACGTcount: A:0.76, C:0.06, G:0.15, T:0.04
Consensus pattern (6 bp):
AAAGAA
Found at i:40410473 original size:18 final size:18
Alignment explanation
Indices: 40410452--40410486 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
40410442 AGAAAAGAAA
40410452 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
40410470 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
40410487 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:40412571 original size:10 final size:10
Alignment explanation
Indices: 40412555--40412612 Score: 64
Period size: 10 Copynumber: 5.7 Consensus size: 10
40412545 CAACTCCGAC
40412555 CAGCTCAATT
1 CAGCTCAATT
* *
40412565 GAGCTCATTT
1 CAGCTCAATT
40412575 CAGCTCAA-T
1 CAGCTCAATT
40412584 CGAGCTCAATT
1 C-AGCTCAATT
*
40412595 TAGCTACAATT
1 CAGCT-CAATT
40412606 CAGCTCA
1 CAGCTCA
40412613 TTTATTTTAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
9 2 0.05
10 27 0.69
11 10 0.26
ACGTcount: A:0.29, C:0.28, G:0.14, T:0.29
Consensus pattern (10 bp):
CAGCTCAATT
Found at i:40412578 original size:20 final size:20
Alignment explanation
Indices: 40412555--40412615 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
40412545 CAACTCCGAC
40412555 CAGCTCAATTGAGCTCATTT
1 CAGCTCAATTGAGCTCATTT
*
40412575 CAGCTCAATCGAGCTCAATTT
1 CAGCTCAATTGAGCTC-ATTT
*
40412596 -AGCTACAATTCAGCTCATTT
1 CAGCT-CAATTGAGCTCATTT
40412616 ATTTTATTGG
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 23 0.64
21 13 0.36
ACGTcount: A:0.28, C:0.26, G:0.13, T:0.33
Consensus pattern (20 bp):
CAGCTCAATTGAGCTCATTT
Found at i:40416050 original size:47 final size:47
Alignment explanation
Indices: 40415972--40416428 Score: 671
Period size: 47 Copynumber: 9.6 Consensus size: 47
40415962 CCCTTCGGGA
* * * * * *
40415972 CTTATCACATTTATACACTTTCACATCCATCACGTTGGCCACTCGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* *
40416019 CCTGTCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40416066 CTCATCACATATATATACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40416113 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
*
40416160 CTTATCACATATATACACTTTCACATTCATCACATCGGCTATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40416207 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40416254 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40416303 CTTATCACATATATATATACACTTTCACACTCATCACATTGGCCATTCGGC
1 CTTATCAC----ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
40416354 CTTATCACATATATATACACTTTCACATTCATCACATCGGCCATTAGGC
1 CTTATCAC--ATATATACACTTTCACATTCATCACATCGGCCATTAGGC
* * *
40416403 CTTATCACATAAATATACATTCACAT
1 CTTATCACATATATACACTTTCACAT
40416429 CACAATTATC
Statistics
Matches: 381, Mismatches: 25, Indels: 8
0.92 0.06 0.02
Matches are distributed among these distances:
47 242 0.64
49 93 0.24
51 46 0.12
ACGTcount: A:0.30, C:0.29, G:0.08, T:0.33
Consensus pattern (47 bp):
CTTATCACATATATACACTTTCACATTCATCACATCGGCCATTAGGC
Found at i:40419896 original size:27 final size:27
Alignment explanation
Indices: 40419866--40420043 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
40419856 ATATTGAGCC
* * * *
40419866 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
40419893 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40419920 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
40419948 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
40419975 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
40420002 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
40420029 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40420044 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:40420005 original size:82 final size:81
Alignment explanation
Indices: 40419887--40420042 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
40419877 TGCTATATAA
* *
40419887 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40419952 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
40419969 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40420033 CACTTAGTGC
65 CACTTAGTGC
40420043 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40420615 original size:13 final size:13
Alignment explanation
Indices: 40420597--40420621 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40420587 TACTAAATTT
40420597 TCATGGATTCAAG
1 TCATGGATTCAAG
40420610 TCATGGATTCAA
1 TCATGGATTCAA
40420622 TATACCATTA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.32
Consensus pattern (13 bp):
TCATGGATTCAAG
Found at i:40425557 original size:15 final size:14
Alignment explanation
Indices: 40425537--40425584 Score: 60
Period size: 15 Copynumber: 3.3 Consensus size: 14
40425527 CTCATTTTCA
40425537 TCTTTTTCTTTTATT
1 TCTTTTTCTTTT-TT
*
40425552 TCTTTTTCTTTTTC
1 TCTTTTTCTTTTTT
*
40425566 TCTCATTTCTTTTTT
1 TCT-TTTTCTTTTTT
40425581 TCTT
1 TCTT
40425585 CTCTCAATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
14 4 0.14
15 24 0.86
ACGTcount: A:0.04, C:0.19, G:0.00, T:0.77
Consensus pattern (14 bp):
TCTTTTTCTTTTTT
Found at i:40425589 original size:22 final size:21
Alignment explanation
Indices: 40425537--40425595 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
40425527 CTCATTTTCA
* *
40425537 TCTTTTTCTTTTATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
40425558 TCTTTTTCTCTCATTTCTTTT
1 TCTTTTTCTCTCATTTCTTTT
*
40425579 T-TTCTTCTCTCAATTTC
1 TCTTTTTCTCTC-ATTTC
40425596 ATTCAAGATT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
20 9 0.26
21 25 0.74
ACGTcount: A:0.07, C:0.22, G:0.00, T:0.71
Consensus pattern (21 bp):
TCTTTTTCTCTCATTTCTTTT
Found at i:40426527 original size:29 final size:31
Alignment explanation
Indices: 40426482--40426545 Score: 89
Period size: 30 Copynumber: 2.2 Consensus size: 31
40426472 TTTCAATCAC
**
40426482 TCTT-TTTTTTTTCAATTTTG-ATTTTTTTT
1 TCTTCTTTTTTTTCAATTCCGAATTTTTTTT
40426511 TCTTCTTTTTTTT-AATTCCGAATTTTTTTT
1 TCTTCTTTTTTTTCAATTCCGAATTTTTTTT
40426541 TCTTC
1 TCTTC
40426546 AATACTAAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
29 9 0.29
30 22 0.71
ACGTcount: A:0.11, C:0.12, G:0.03, T:0.73
Consensus pattern (31 bp):
TCTTCTTTTTTTTCAATTCCGAATTTTTTTT
Found at i:40426603 original size:12 final size:12
Alignment explanation
Indices: 40426586--40426630 Score: 63
Period size: 13 Copynumber: 3.6 Consensus size: 12
40426576 GAATACAAAC
40426586 TTTTTTTTTTAA
1 TTTTTTTTTTAA
40426598 TTTTTTTTTTCAA
1 TTTTTTTTTT-AA
*
40426611 ATTTTTTTTTATA
1 TTTTTTTTTTA-A
40426624 TTTTTTT
1 TTTTTTT
40426631 ACAATACCGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
12 11 0.38
13 18 0.62
ACGTcount: A:0.16, C:0.02, G:0.00, T:0.82
Consensus pattern (12 bp):
TTTTTTTTTTAA
Found at i:40426605 original size:14 final size:14
Alignment explanation
Indices: 40426581--40426620 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
40426571 AAATTGAATA
40426581 CAAACTTTTTTTTTT
1 CAAA-TTTTTTTTTT
40426596 --AATTTTTTTTTT
1 CAAATTTTTTTTTT
40426608 CAAATTTTTTTTT
1 CAAATTTTTTTTT
40426621 ATATTTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 10 0.43
13 2 0.09
14 11 0.48
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.72
Consensus pattern (14 bp):
CAAATTTTTTTTTT
Found at i:40429865 original size:46 final size:46
Alignment explanation
Indices: 40429798--40430020 Score: 254
Period size: 46 Copynumber: 4.8 Consensus size: 46
40429788 ATATTTGGGA
**
40429798 ATCCGAACTCGTTGAGTTGAGTCTAAGTTCACTTATGGATGCGAAC
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
40429844 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
** * * * * * * *
40429890 GCCCGAGCTCATTGAGTTGAGTCCGAGTTCA-TGAAATGTA-ACTAGGC
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACT--TATGGATGCGA-AC
*
40429937 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGC
1 ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
* * *
40429983 A-CCCAAGCTCTTTGAGTTGAGTCCGAGTTCGCTTATGG
1 ATCCGAA-CTCGTTGAGTTGAGTCCGAGTTCACTTATGG
40430021 GCGGGTTACA
Statistics
Matches: 149, Mismatches: 22, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
45 5 0.03
46 109 0.73
47 34 0.23
48 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.26, T:0.29
Consensus pattern (46 bp):
ATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAAC
Found at i:40429967 original size:93 final size:93
Alignment explanation
Indices: 40429843--40430012 Score: 304
Period size: 93 Copynumber: 1.8 Consensus size: 93
40429833 TGGATGCGAA
* *
40429843 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACGCCCGAGCTCATTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCAAGCTCATTGAGTT
40429908 GAGTCCGAGTTCATGAAATGTAACTAGG
66 GAGTCCGAGTTCATGAAATGTAACTAGG
* *
40429936 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAGCACCCAAGCTCTTTGAGTT
1 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCAAGCTCATTGAGTT
40430001 GAGTCCGAGTTC
66 GAGTCCGAGTTC
40430013 GCTTATGGGC
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.23, C:0.23, G:0.26, T:0.28
Consensus pattern (93 bp):
CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAACACCCAAGCTCATTGAGTT
GAGTCCGAGTTCATGAAATGTAACTAGG
Found at i:40432746 original size:30 final size:31
Alignment explanation
Indices: 40432687--40432747 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
40432677 TCTTTGGAAA
**
40432687 CACTCGTTTCTTTTACCTCAATTTCTTTTTC
1 CACTCGTTTCTTTTACCTCAAACTCTTTTTC
* *
40432718 CACTCTTTTCTTTTA-TTCAAACTCTTTTTC
1 CACTCGTTTCTTTTACCTCAAACTCTTTTTC
40432748 TTTTTGATTC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 12 0.46
31 14 0.54
ACGTcount: A:0.15, C:0.28, G:0.02, T:0.56
Consensus pattern (31 bp):
CACTCGTTTCTTTTACCTCAAACTCTTTTTC
Found at i:40432763 original size:12 final size:12
Alignment explanation
Indices: 40432746--40432787 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
40432736 AAACTCTTTT
* *
40432746 TCTTTTTGATTC
1 TCTTTTTCAATC
40432758 TCTTTTTCAATC
1 TCTTTTTCAATC
40432770 TCTTTTT-AATC
1 TCTTTTTCAATC
*
40432781 TCATTTT
1 TCTTTTT
40432788 GTTTCCTCTC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.14, C:0.19, G:0.02, T:0.64
Consensus pattern (12 bp):
TCTTTTTCAATC
Found at i:40432907 original size:14 final size:15
Alignment explanation
Indices: 40432881--40432934 Score: 62
Period size: 13 Copynumber: 3.9 Consensus size: 15
40432871 TTTTCTTGCC
*
40432881 TCTCTTTTCTTTTGA
1 TCTCTTTTCTTTTCA
40432896 TCTCTTTT-TTTTCA
1 TCTCTTTTCTTTTCA
40432910 TCT-TTTTCTTTTC-
1 TCTCTTTTCTTTTCA
*
40432923 TC-ATTTTCTTTT
1 TCTCTTTTCTTTT
40432935 TACAAGAGGT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
13 15 0.42
14 13 0.36
15 8 0.22
ACGTcount: A:0.06, C:0.20, G:0.02, T:0.72
Consensus pattern (15 bp):
TCTCTTTTCTTTTCA
Found at i:40436612 original size:18 final size:18
Alignment explanation
Indices: 40436589--40436642 Score: 72
Period size: 18 Copynumber: 3.0 Consensus size: 18
40436579 AGCGAATTTG
*
40436589 AAAAGAAATTGAGAAAGA
1 AAAAGAAATTGAAAAAGA
40436607 AAAAGAAATTGAAAAAGA
1 AAAAGAAATTGAAAAAGA
* **
40436625 AAACGAAAAAGAAAAAGA
1 AAAAGAAATTGAAAAAGA
40436643 GAATGAAATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.72, C:0.02, G:0.19, T:0.07
Consensus pattern (18 bp):
AAAAGAAATTGAAAAAGA
Found at i:40436613 original size:6 final size:6
Alignment explanation
Indices: 40436602--40436642 Score: 55
Period size: 6 Copynumber: 6.8 Consensus size: 6
40436592 AGAAATTGAG
** *
40436602 AAAGAA AAAGAA ATTGAA AAAGAA AACGAA AAAGAA AAAGA
1 AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGAA AAAGA
40436643 GAATGAAATA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.76, C:0.02, G:0.17, T:0.05
Consensus pattern (6 bp):
AAAGAA
Found at i:40436650 original size:12 final size:11
Alignment explanation
Indices: 40436588--40436639 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 11
40436578 GAGCGAATTT
**
40436588 GAAAAGAAATT
1 GAAAAGAAAAA
40436599 GAGAAAGAAAAA
1 GA-AAAGAAAAA
*
40436611 GAAATTGAAAAA
1 GAAA-AGAAAAA
40436623 GAAAACGAAAAA
1 GAAAA-GAAAAA
40436635 GAAAA
1 GAAAA
40436640 AGAGAATGAA
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
11 4 0.12
12 30 0.88
ACGTcount: A:0.71, C:0.02, G:0.19, T:0.08
Consensus pattern (11 bp):
GAAAAGAAAAA
Found at i:40436650 original size:18 final size:20
Alignment explanation
Indices: 40436617--40436665 Score: 57
Period size: 18 Copynumber: 2.5 Consensus size: 20
40436607 AAAAGAAATT
*
40436617 GAAAAAGAAAACGAAA-A-A
1 GAAAAAGAGAACGAAATAGA
*
40436635 GAAAAAGAGAATGAAATAGA
1 GAAAAAGAGAACGAAATAGA
40436655 GCAAAAAGAGA
1 G-AAAAAGAGA
40436666 TTGAGAGTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
18 14 0.54
19 1 0.04
20 2 0.08
21 9 0.35
ACGTcount: A:0.69, C:0.04, G:0.22, T:0.04
Consensus pattern (20 bp):
GAAAAAGAGAACGAAATAGA
Found at i:40441238 original size:23 final size:22
Alignment explanation
Indices: 40441186--40441238 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40441176 TCCACGTCTT
*
40441186 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40441208 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40441231 TTTCTTTT
1 TTTCTTTT
40441239 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40448287 original size:13 final size:12
Alignment explanation
Indices: 40448269--40448325 Score: 78
Period size: 12 Copynumber: 4.7 Consensus size: 12
40448259 GACCGTATGC
40448269 ATTTTTTTTTCAA
1 ATTTTTTTTTC-A
40448282 ATTTTTTTTTCA
1 ATTTTTTTTTCA
*
40448294 ATTTTTTTTTGA
1 ATTTTTTTTTCA
* *
40448306 TTTTTTTTTTCG
1 ATTTTTTTTTCA
40448318 ATTTTTTT
1 ATTTTTTT
40448326 AATCTACAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
12 28 0.72
13 11 0.28
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (12 bp):
ATTTTTTTTTCA
Found at i:40456541 original size:22 final size:22
Alignment explanation
Indices: 40456513--40456556 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40456503 TTTTGAACCA
40456513 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
40456535 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
40456557 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:40459036 original size:18 final size:19
Alignment explanation
Indices: 40458998--40459063 Score: 62
Period size: 19 Copynumber: 3.4 Consensus size: 19
40458988 TCAAATGAGA
*
40458998 GAAAAAGAAAAGAGCAAAAAT
1 GAAAAA-AAAAAAG-AAAAAT
* *
40459019 -ACAAAAGAAAAGAAAAAT
1 GAAAAAAAAAAAGAAAAAT
*
40459037 GAAAAAAAAAAAGAAAATT
1 GAAAAAAAAAAAGAAAAAT
*
40459056 CAAAAAAA
1 GAAAAAAA
40459064 GAGAATGAAA
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
18 6 0.16
19 27 0.73
20 4 0.11
ACGTcount: A:0.77, C:0.05, G:0.12, T:0.06
Consensus pattern (19 bp):
GAAAAAAAAAAAGAAAAAT
Found at i:40459040 original size:7 final size:6
Alignment explanation
Indices: 40458997--40459053 Score: 53
Period size: 6 Copynumber: 9.0 Consensus size: 6
40458987 ATCAAATGAG
* *
40458997 AGAAAA AGAAAA GAGCAAAA ATACAAA AG-AAA AGAAAA ATGAAAA AAAAAA
1 AGAAAA AGAAAA -AG-AAAA AGA-AAA AGAAAA AGAAAA A-GAAAA AGAAAA
40459048 AGAAAA
1 AGAAAA
40459054 TTCAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
5 5 0.12
6 20 0.48
7 13 0.31
8 4 0.10
ACGTcount: A:0.79, C:0.04, G:0.14, T:0.04
Consensus pattern (6 bp):
AGAAAA
Found at i:40463158 original size:22 final size:22
Alignment explanation
Indices: 40463130--40463173 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
40463120 TTTTGAACCA
40463130 TTACCATTTCGTACCAAATCCC
1 TTACCATTTCGTACCAAATCCC
*
40463152 TTACCATTTCGTACCAATTCCC
1 TTACCATTTCGTACCAAATCCC
40463174 AAATACCAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.25, C:0.36, G:0.05, T:0.34
Consensus pattern (22 bp):
TTACCATTTCGTACCAAATCCC
Found at i:40464103 original size:30 final size:30
Alignment explanation
Indices: 40464018--40464114 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40464008 TAAACTAAAA
* *
40464018 TGAGCTAAGCTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
* * * * *
40464048 TGAGCTGAGATTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
*
40464078 TGAGCTAAGGTTTAGCTCGTGAGCTGAA-T
1 TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
40464107 ATGAGCTA
1 -TGAGCTA
40464115 GGAGTGAGCT
Statistics
Matches: 53, Mismatches: 13, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
29 1 0.02
30 52 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGATTTAGCTCGTGAGCTGAAGT
Found at i:40465774 original size:20 final size:20
Alignment explanation
Indices: 40465751--40465807 Score: 69
Period size: 20 Copynumber: 2.8 Consensus size: 20
40465741 GGGTTAAGAT
*
40465751 TGAGCTGAATTGAGCTTGAG
1 TGAGCTGAATTGAGCTCGAG
* *
40465771 TGAGTTGACTTGAGCTCGAG
1 TGAGCTGAATTGAGCTCGAG
*
40465791 TGAGCTGGAAATGAGCT
1 TGAGCT-GAATTGAGCT
40465808 AAACGGAGCT
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 22 0.73
21 8 0.27
ACGTcount: A:0.25, C:0.12, G:0.35, T:0.28
Consensus pattern (20 bp):
TGAGCTGAATTGAGCTCGAG
Found at i:40470849 original size:33 final size:33
Alignment explanation
Indices: 40470811--40470873 Score: 85
Period size: 33 Copynumber: 1.9 Consensus size: 33
40470801 GATTACTCAC
40470811 TTCACTCG-TTTCTTTT-ATAGACTCTCTTTCTTT
1 TTCACTCGATTTCTTTTCA-AG-CTCTCTTTCTTT
*
40470844 TTCACTTGATTTCTTTTCAAGCTCTCTTTC
1 TTCACTCGATTTCTTTTCAAGCTCTCTTTC
40470874 AATTTCTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
33 16 0.59
34 10 0.37
35 1 0.04
ACGTcount: A:0.13, C:0.25, G:0.06, T:0.56
Consensus pattern (33 bp):
TTCACTCGATTTCTTTTCAAGCTCTCTTTCTTT
Found at i:40470900 original size:21 final size:21
Alignment explanation
Indices: 40470871--40470926 Score: 51
Period size: 21 Copynumber: 2.7 Consensus size: 21
40470861 CAAGCTCTCT
*
40470871 TTCAATTTCTTTTTTCGCTTT-
1 TTCATTTTCTTTTTTC-CTTTC
* ** *
40470892 TTCTTTTTCAATTTTCTTTTC
1 TTCATTTTCTTTTTTCCTTTC
40470913 TTCATTTTCTTTTT
1 TTCATTTTCTTTTT
40470927 CTCTCACTTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
20 3 0.12
21 23 0.88
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.71
Consensus pattern (21 bp):
TTCATTTTCTTTTTTCCTTTC
Found at i:40470919 original size:14 final size:14
Alignment explanation
Indices: 40470870--40470926 Score: 57
Period size: 14 Copynumber: 4.1 Consensus size: 14
40470860 TCAAGCTCTC
40470870 TTTCAA-TTTCTTT
1 TTTCAATTTTCTTT
**
40470883 TTTCGCTTTT-TCTT
1 TTTCAATTTTCT-TT
40470897 TTTCAATTTTCTTT
1 TTTCAATTTTCTTT
40470911 TCTTC-ATTTTCTTT
1 T-TTCAATTTTCTTT
40470925 TT
1 TT
40470927 CTCTCACTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
13 6 0.17
14 26 0.72
15 4 0.11
ACGTcount: A:0.09, C:0.18, G:0.02, T:0.72
Consensus pattern (14 bp):
TTTCAATTTTCTTT
Found at i:40470986 original size:18 final size:18
Alignment explanation
Indices: 40470888--40470991 Score: 84
Period size: 18 Copynumber: 5.6 Consensus size: 18
40470878 TCTTTTTTCG
40470888 CTTTTTCTTTTTCAATTTT
1 CTTTTTCTTTTTC-ATTTT
* *
40470907 CTTTTCTTCATTTTCTTTTT
1 C-TTT-TTCTTTTTCATTTT
* **
40470927 CTCTCACTTTTTCGA-TTT
1 CTTTTTCTTTTTC-ATTTT
* *
40470945 CTTTTTCTTTTGCAATTT
1 CTTTTTCTTTTTCATTTT
*
40470963 CTTTTTCTTTTTCGTTTT
1 CTTTTTCTTTTTCATTTT
*
40470981 CTTTTTGTTTT
1 CTTTTTCTTTT
40470992 CTTTCAATTT
Statistics
Matches: 66, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
17 1 0.02
18 46 0.70
19 3 0.05
20 8 0.12
21 8 0.12
ACGTcount: A:0.07, C:0.18, G:0.04, T:0.71
Consensus pattern (18 bp):
CTTTTTCTTTTTCATTTT
Found at i:40471008 original size:6 final size:6
Alignment explanation
Indices: 40470888--40470995 Score: 74
Period size: 6 Copynumber: 17.7 Consensus size: 6
40470878 TCTTTTTTCG
* * * **
40470888 CTTTTT CTTTTT CAATTTT CTTTTCTT CATTTT CTTTTT CTCTCA CTTTTT
1 CTTTTT CTTTTT C-TTTTT C-TTT-TT CTTTTT CTTTTT CTTTTT CTTTTT
** * ** *
40470939 CGATTT CTTTTT CTTTTG CAATTT CTTTTT CTTTTT CGTTTT CTTTTT
1 CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT CTTTTT
*
40470987 -GTTTT CTTT
1 CTTTTT CTTT
40470996 CAATTTCTTT
Statistics
Matches: 74, Mismatches: 25, Indels: 6
0.70 0.24 0.06
Matches are distributed among these distances:
5 4 0.05
6 58 0.78
7 9 0.12
8 3 0.04
ACGTcount: A:0.06, C:0.19, G:0.04, T:0.71
Consensus pattern (6 bp):
CTTTTT
Found at i:40478016 original size:20 final size:21
Alignment explanation
Indices: 40477981--40478022 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
40477971 CTGCTTGTTG
40477981 AGCTCAATTCAGCTCGTTTCT
1 AGCTCAATTCAGCTCGTTTCT
*
40478002 AGCTTAATT-AGCTCGTTTCT
1 AGCTCAATTCAGCTCGTTTCT
40478022 A
1 A
40478023 ATTCCATGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.21, C:0.24, G:0.14, T:0.40
Consensus pattern (21 bp):
AGCTCAATTCAGCTCGTTTCT
Found at i:40478190 original size:19 final size:19
Alignment explanation
Indices: 40478166--40478202 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
40478156 TACTACAACA
40478166 ATTTAAGTTGTCTTAGTTC
1 ATTTAAGTTGTCTTAGTTC
*
40478185 ATTTAATTTGTCTTAGTT
1 ATTTAAGTTGTCTTAGTT
40478203 TAATGCATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.22, C:0.08, G:0.14, T:0.57
Consensus pattern (19 bp):
ATTTAAGTTGTCTTAGTTC
Found at i:40488316 original size:9 final size:10
Alignment explanation
Indices: 40488302--40488337 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
40488292 AAGTAAGTTT
40488302 AAAAAAACAA
1 AAAAAAACAA
40488312 AAAAAAAC-A
1 AAAAAAACAA
*
40488321 AAAAAAACGA
1 AAAAAAACAA
40488331 AAAAAAA
1 AAAAAAA
40488338 TTCAAACAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.89, C:0.08, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAACAA
Found at i:40488373 original size:17 final size:19
Alignment explanation
Indices: 40488341--40488375 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
40488331 AAAAAAATTC
40488341 AAACAAAAATTCTGAAAAA
1 AAACAAAAATTCTGAAAAA
40488360 AAAC-AAAA-TCTGAAAA
1 AAACAAAAATTCTGAAAA
40488376 TTTGAACATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 4 0.25
19 4 0.25
ACGTcount: A:0.69, C:0.11, G:0.06, T:0.14
Consensus pattern (19 bp):
AAACAAAAATTCTGAAAAA
Found at i:40489440 original size:30 final size:28
Alignment explanation
Indices: 40489404--40489459 Score: 76
Period size: 30 Copynumber: 1.9 Consensus size: 28
40489394 AAGCGAAAAA
* *
40489404 GAAAAAGAGTGTGTGCAAGAAAGTAAAGTT
1 GAAAAAGAGAGTGAGCAA-AAAG-AAAGTT
40489434 GAAAAAGAGAGTGAGCAAAAAGAAAG
1 GAAAAAGAGAGTGAGCAAAAAGAAAG
40489460 CGTGGAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 4 0.17
29 4 0.17
30 16 0.67
ACGTcount: A:0.54, C:0.04, G:0.30, T:0.12
Consensus pattern (28 bp):
GAAAAAGAGAGTGAGCAAAAAGAAAGTT
Found at i:40491622 original size:15 final size:15
Alignment explanation
Indices: 40491602--40491649 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40491592 TCAAAGATGG
40491602 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
40491617 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
40491632 -TTTATGGATATAAA
1 GTTTATGGATATGAA
40491646 GTTT
1 GTTT
40491650 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:40491629 original size:29 final size:29
Alignment explanation
Indices: 40491596--40491655 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
40491586 AAGGATTCAA
* *
40491596 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
40491625 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
40491654 AG
1 AG
40491656 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:40493009 original size:10 final size:10
Alignment explanation
Indices: 40492994--40493020 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
40492984 TACTCCTTCA
40492994 AGCTCAAATC
1 AGCTCAAATC
40493004 AGCTCAAATC
1 AGCTCAAATC
40493014 AGCTCAA
1 AGCTCAA
40493021 CTTCAACTCA
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:0.41, C:0.30, G:0.11, T:0.19
Consensus pattern (10 bp):
AGCTCAAATC
Found at i:40493042 original size:10 final size:10
Alignment explanation
Indices: 40492994--40493042 Score: 53
Period size: 10 Copynumber: 4.8 Consensus size: 10
40492984 TACTCCTTCA
*
40492994 AGCTCAAATC
1 AGCTCAACTC
*
40493004 AGCTCAAATC
1 AGCTCAACTC
40493014 AGCTCAACTTC
1 AGCTCAAC-TC
* *
40493025 AACTCAACTT
1 AGCTCAACTC
40493035 AGCTCAAC
1 AGCTCAAC
40493043 AAGCTCGTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
10 25 0.74
11 9 0.26
ACGTcount: A:0.37, C:0.33, G:0.08, T:0.22
Consensus pattern (10 bp):
AGCTCAACTC
Found at i:40496159 original size:80 final size:79
Alignment explanation
Indices: 40496075--40496246 Score: 211
Period size: 79 Copynumber: 2.2 Consensus size: 79
40496065 GGACTAAGAT
*
40496075 CCGAAGGCATTTGTGCGAGAT-ACAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATGACAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
40496139 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * ** * * * *
40496155 CCGAAGGCATTCGTGCGAGTTGTTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
40496220 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
40496234 CCGAAGGCATTTG
1 CCGAAGGCATTTG
40496247 AACGAGGAGC
Statistics
Matches: 78, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
79 38 0.49
80 37 0.47
81 3 0.04
ACGTcount: A:0.24, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATGACAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:40496226 original size:39 final size:39
Alignment explanation
Indices: 40496022--40496244 Score: 200
Period size: 40 Copynumber: 5.6 Consensus size: 39
40496012 TTGAATGCTG
* * * * *
40496022 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
40496062 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
40496101 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* **
40496142 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
40496182 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
40496221 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
40496245 TGAACGAGGA
Statistics
Matches: 155, Mismatches: 20, Indels: 17
0.81 0.10 0.09
Matches are distributed among these distances:
39 39 0.25
40 102 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:40496264 original size:79 final size:80
Alignment explanation
Indices: 40496102--40496279 Score: 198
Period size: 79 Copynumber: 2.2 Consensus size: 80
40496092 AGATACAAAT
* * * *
40496102 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** ** *
40496167 GTGCGAGTTGTTAAA
66 GAACGAGGAGCTAAA
* * * * *
40496182 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
40496246 GAACGAGGAGCTATA
66 GAACGAGGAGCTAAA
*
40496261 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
40496280 TACGTGATTT
Statistics
Matches: 81, Mismatches: 17, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
78 14 0.17
79 49 0.60
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.29, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGGAGCTAAA
Found at i:40502253 original size:22 final size:22
Alignment explanation
Indices: 40502228--40502269 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
40502218 CACTCTTTTT
40502228 TTTTATACTTCGATTTTTTTAA
1 TTTTATACTTCGATTTTTTTAA
* **
40502250 TTTTTTTTTTCGATTTTTTT
1 TTTTATACTTCGATTTTTTT
40502270 TTCAATTTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.14, C:0.07, G:0.05, T:0.74
Consensus pattern (22 bp):
TTTTATACTTCGATTTTTTTAA
Found at i:40502257 original size:13 final size:13
Alignment explanation
Indices: 40502241--40502291 Score: 70
Period size: 12 Copynumber: 4.0 Consensus size: 13
40502231 TATACTTCGA
40502241 TTTTTTT-AATTT
1 TTTTTTTCAATTT
*
40502253 TTTTTTTCGA-TT
1 TTTTTTTCAATTT
40502265 TTTTTTTCAATTT
1 TTTTTTTCAATTT
40502278 TTTTTTTCGAATTT
1 TTTTTTTC-AATTT
40502292 CCTCTTCTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
12 18 0.53
13 11 0.32
14 5 0.15
ACGTcount: A:0.14, C:0.06, G:0.04, T:0.76
Consensus pattern (13 bp):
TTTTTTTCAATTT
Found at i:40512668 original size:27 final size:27
Alignment explanation
Indices: 40512638--40512815 Score: 180
Period size: 27 Copynumber: 6.6 Consensus size: 27
40512628 ATATTGAGTC
* *
40512638 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAATCAACT
* *
40512665 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAATCAACT
*
40512692 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAATC-AACT
** ** *
40512720 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAATCAACT
* **
40512747 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAATCAACT
* *
40512774 CGCACACTTAGTGCAACATAGTCGAA-T
1 CGCACACTTAGTGCTACATAATC-AACT
40512801 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
40512816 GTACAATTTA
Statistics
Matches: 129, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
27 104 0.81
28 25 0.19
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAATCAACT
Found at i:40512777 original size:82 final size:81
Alignment explanation
Indices: 40512659--40512814 Score: 224
Period size: 82 Copynumber: 1.9 Consensus size: 81
40512649 TGCTATATAA
* *
40512659 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
40512724 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * ** *
40512741 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCGAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
40512805 CACTTAGTGC
65 CACTTAGTGC
40512815 TGTACAATTT
Statistics
Matches: 66, Mismatches: 7, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
81 16 0.24
82 50 0.76
ACGTcount: A:0.29, C:0.28, G:0.16, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:40516703 original size:13 final size:13
Alignment explanation
Indices: 40516685--40516713 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
40516675 AATAGTTGTG
40516685 TGTTATTTAATTA
1 TGTTATTTAATTA
40516698 TGTTATTTAATTA
1 TGTTATTTAATTA
40516711 TGT
1 TGT
40516714 AGGTTAGCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.10, T:0.62
Consensus pattern (13 bp):
TGTTATTTAATTA
Found at i:40518912 original size:8 final size:8
Alignment explanation
Indices: 40518899--40518924 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
40518889 TGGCGTTCAC
40518899 CTATCCAT
1 CTATCCAT
40518907 CTATCCAT
1 CTATCCAT
40518915 CTATCCAT
1 CTATCCAT
40518923 CT
1 CT
40518925 TTTCACCTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.38
Consensus pattern (8 bp):
CTATCCAT
Found at i:40519738 original size:14 final size:14
Alignment explanation
Indices: 40519719--40519763 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40519709 AACTCATCTT
*
40519719 AGTTTAATTAAATG
1 AGTTTAATTTAATG
*
40519733 AGTTT-ATTTGATG
1 AGTTTAATTTAATG
*
40519746 AATTTAATTTAATG
1 AGTTTAATTTAATG
40519760 AGTT
1 AGTT
40519764 GCTTCTTTAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.49
Consensus pattern (14 bp):
AGTTTAATTTAATG
Found at i:40520773 original size:29 final size:29
Alignment explanation
Indices: 40520740--40520799 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
40520730 ATAACCAAAC
* *
40520740 CTACAAAAACTTTATATCCATAAATCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
*
40520769 CTACATAAACTTCATATCCATAAACCCAT
1 CTACAAAAACTTCATATCCATAAACCCAT
40520798 CT
1 CT
40520800 TTGAATCCTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (29 bp):
CTACAAAAACTTCATATCCATAAACCCAT
Found at i:40520792 original size:15 final size:15
Alignment explanation
Indices: 40520746--40520793 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40520736 AAACCTACAA
*
40520746 AAACTTTATATCCAT
1 AAACTTCATATCCAT
* * *
40520761 AAA-TCCATCTACAT
1 AAACTTCATATCCAT
40520775 AAACTTCATATCCAT
1 AAACTTCATATCCAT
40520790 AAAC
1 AAAC
40520794 CCATCTTTGA
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.44, C:0.25, G:0.00, T:0.31
Consensus pattern (15 bp):
AAACTTCATATCCAT
Found at i:40523456 original size:35 final size:33
Alignment explanation
Indices: 40523411--40523493 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 33
40523401 AATCTTACAA
* * *
40523411 TCTTTCTCTTTTTC-ATTTTCTTTTTCTTTCATGT
1 TCTTTTTCTTTTTCTA-TTTCATTTTCTATCAT-T
40523445 GTCTTTTTCTTTTTCTATTTCATTTTCTATCATT
1 -TCTTTTTCTTTTTCTATTTCATTTTCTATCATT
40523479 TCTTTTT-TTTCTTCT
1 TCTTTTTCTTT-TTCT
40523494 CTCAATTTAT
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
32 3 0.07
33 11 0.26
34 1 0.02
35 27 0.63
36 1 0.02
ACGTcount: A:0.07, C:0.19, G:0.02, T:0.71
Consensus pattern (33 bp):
TCTTTTTCTTTTTCTATTTCATTTTCTATCATT
Found at i:40527089 original size:56 final size:55
Alignment explanation
Indices: 40526973--40527090 Score: 159
Period size: 55 Copynumber: 2.1 Consensus size: 55
40526963 TGCATGCTTT
* * * *
40526973 CATT-AATGCCGTCCATGCATGGTGAATATCTCATTTAATTCATGTTTTGCTTCC
1 CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
*
40527027 CTTTAAATGCCGTTCCATACATGG-GAACATCTCATTTAATTCATGTCTTTGCTGCA
1 CATTAAATGCCG-TCCATACATGGTGAACATCTCATTTAATTCATGT-TTTGCTGCA
40527083 CATTAAAT
1 CATTAAAT
40527091 CAGCAAGCAG
Statistics
Matches: 55, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
54 3 0.05
55 28 0.51
56 24 0.44
ACGTcount: A:0.25, C:0.22, G:0.14, T:0.39
Consensus pattern (55 bp):
CATTAAATGCCGTCCATACATGGTGAACATCTCATTTAATTCATGTTTTGCTGCA
Found at i:40530576 original size:15 final size:16
Alignment explanation
Indices: 40530537--40530577 Score: 50
Period size: 15 Copynumber: 2.7 Consensus size: 16
40530527 AACAACACTC
40530537 CTTTCTTTTTCACTTT
1 CTTTCTTTTTCACTTT
* *
40530553 C-ATCCTTTTCA-TTT
1 CTTTCTTTTTCACTTT
40530567 CTTTCTTTTTC
1 CTTTCTTTTTC
40530578 CAACTCATTT
Statistics
Matches: 20, Mismatches: 4, Indels: 3
0.74 0.15 0.11
Matches are distributed among these distances:
14 4 0.20
15 15 0.75
16 1 0.05
ACGTcount: A:0.07, C:0.27, G:0.00, T:0.66
Consensus pattern (16 bp):
CTTTCTTTTTCACTTT
Found at i:40530772 original size:17 final size:15
Alignment explanation
Indices: 40530735--40530773 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 15
40530725 TATCTCCCAC
40530735 TCATCTTCTTTTTCTT
1 TCAT-TTCTTTTTCTT
40530751 TCATTTCTTTTTCATGT
1 TCATTTCTTTTTC-T-T
40530768 TCATTT
1 TCATTT
40530774 TCTCGCTCGC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
15 9 0.43
16 5 0.24
17 7 0.33
ACGTcount: A:0.10, C:0.21, G:0.03, T:0.67
Consensus pattern (15 bp):
TCATTTCTTTTTCTT
Found at i:40534891 original size:18 final size:18
Alignment explanation
Indices: 40534851--40534891 Score: 50
Period size: 16 Copynumber: 2.4 Consensus size: 18
40534841 GCCCATTCCG
* *
40534851 AAGTATATATATACATAT
1 AAGTATGTATATACACAT
40534869 -A-TATGTATATACACAT
1 AAGTATGTATATACACAT
40534885 AAGTATG
1 AAGTATG
40534892 CCCATTCGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 4
0.76 0.08 0.16
Matches are distributed among these distances:
16 13 0.68
17 2 0.11
18 4 0.21
ACGTcount: A:0.46, C:0.07, G:0.10, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATACACAT
Found at i:40538682 original size:18 final size:18
Alignment explanation
Indices: 40538640--40538682 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
40538630 GCCCATTCCG
* *
40538640 AAGTATATATATATACAT
1 AAGTATGTATATACACAT
40538658 ATA-TATGTATATACACAT
1 A-AGTATGTATATACACAT
40538676 AAGTATG
1 AAGTATG
40538683 CCCATTCGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
17 1 0.05
18 19 0.90
19 1 0.05
ACGTcount: A:0.47, C:0.07, G:0.09, T:0.37
Consensus pattern (18 bp):
AAGTATGTATATACACAT
Found at i:40539194 original size:28 final size:28
Alignment explanation
Indices: 40539156--40539304 Score: 255
Period size: 28 Copynumber: 5.4 Consensus size: 28
40539146 TGTACACCAG
40539156 TAAGTGTGCGAGTTTGATTATGTAGCAC
1 TAAGTGTGCGAGTTTGATTATGTAGCAC
40539184 TAAGTGTGCGAGTTTGATTATGTAGCAC
1 TAAGTGTGCGAGTTTGATTATGTAGCAC
*
40539212 TAAGTGTGCGAGCTTGATTATGTAGCAC
1 TAAGTGTGCGAGTTTGATTATGTAGCAC
*
40539240 TAAGTGTGCGAGTTTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATGTAGCAC
*
40539268 TAAGTGTGCGAG-TTGATTATATAGCAC
1 TAAGTGTGCGAGTTTGATTATGTAGCAC
*
40539295 TGAGTGTGCG
1 TAAGTGTGCG
40539305 GACTTAATAT
Statistics
Matches: 117, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 24 0.21
28 93 0.79
ACGTcount: A:0.26, C:0.11, G:0.29, T:0.34
Consensus pattern (28 bp):
TAAGTGTGCGAGTTTGATTATGTAGCAC
Found at i:40541669 original size:17 final size:17
Alignment explanation
Indices: 40541647--40541681 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
40541637 GTTCGGGGCA
*
40541647 TAAAAAAAATTTACTTT
1 TAAAAAAAATTTAATTT
*
40541664 TAAAAAAATTTTAATTT
1 TAAAAAAAATTTAATTT
40541681 T
1 T
40541682 CTCACATTCA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (17 bp):
TAAAAAAAATTTAATTT
Found at i:40542517 original size:15 final size:15
Alignment explanation
Indices: 40542497--40542544 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
40542487 TCAAAGATGG
40542497 GTTTATGGATATGAA
1 GTTTATGGATATGAA
* * *
40542512 GTTTATGTAGATGGA
1 GTTTATGGATATGAA
*
40542527 -TTTATGGATATAAA
1 GTTTATGGATATGAA
40542541 GTTT
1 GTTT
40542545 TTGTAGGTTT
Statistics
Matches: 25, Mismatches: 7, Indels: 2
0.74 0.21 0.06
Matches are distributed among these distances:
14 10 0.40
15 15 0.60
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (15 bp):
GTTTATGGATATGAA
Found at i:40542524 original size:29 final size:29
Alignment explanation
Indices: 40542491--40542550 Score: 93
Period size: 29 Copynumber: 2.1 Consensus size: 29
40542481 AAGGATTCAA
* *
40542491 AGATGGGTTTATGGATATGAAGTTTATGT
1 AGATGGATTTATGGATATAAAGTTTATGT
*
40542520 AGATGGATTTATGGATATAAAGTTTTTGT
1 AGATGGATTTATGGATATAAAGTTTATGT
40542549 AG
1 AG
40542551 GTTTGGTTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.28, T:0.42
Consensus pattern (29 bp):
AGATGGATTTATGGATATAAAGTTTATGT
Found at i:40543175 original size:14 final size:14
Alignment explanation
Indices: 40543133--40543177 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
40543123 TTAAAGAAGC
40543133 AACTCATTAAATTA
1 AACTCATTAAATTA
* *
40543147 AATTCATCAAA-TA
1 AACTCATTAAATTA
*
40543160 AACTCATTTAATTA
1 AACTCATTAAATTA
40543174 AACT
1 AACT
40543178 AAGATGAGTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
13 10 0.40
14 15 0.60
ACGTcount: A:0.49, C:0.16, G:0.00, T:0.36
Consensus pattern (14 bp):
AACTCATTAAATTA
Found at i:40544168 original size:54 final size:53
Alignment explanation
Indices: 40544031--40544184 Score: 200
Period size: 53 Copynumber: 2.9 Consensus size: 53
40544021 CTTTCCTTTT
* * * * *
40544031 TAAACTTACCATTGCCATGTCTTGACATGGTCTTACGTGGTATACTTGCCTTA
1 TAAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTA
* * * *
40544084 TGAACTCACCATTGCCATGCCTTGGCATGGTCTTACATGATTTCCTTGCCTTG
1 TAAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTA
* *
40544137 TAAAACTTACCAATGCCATGCCTTGGCATGGTCTTACTTGATATCCTT
1 T-AAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTT
40544185 AAACCCTAAT
Statistics
Matches: 86, Mismatches: 14, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
53 45 0.52
54 41 0.48
ACGTcount: A:0.21, C:0.25, G:0.17, T:0.36
Consensus pattern (53 bp):
TAAACTTACCATTGCCATGCCTTGGCATGGTCTTACATGATATCCTTGCCTTA
Found at i:40547361 original size:19 final size:19
Alignment explanation
Indices: 40547337--40547424 Score: 76
Period size: 19 Copynumber: 4.8 Consensus size: 19
40547327 AATAAATTAC
*
40547337 TCATCTTAGTTAATTGAGT
1 TCATCTTAGTTAATTAAGT
40547356 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
** * *
40547375 TGC-T-GGAATAAATT-A-T
1 T-CATCTTAGTTAATTAAGT
* *
40547391 TCATGTTAGTAAATTAAGT
1 TCATCTTAGTTAATTAAGT
40547410 TCATCTTAGTTAATT
1 TCATCTTAGTTAATT
40547425 TAGTGCTGGA
Statistics
Matches: 54, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
15 1 0.02
16 3 0.06
17 8 0.15
18 7 0.13
19 34 0.63
20 1 0.02
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:40547388 original size:54 final size:54
Alignment explanation
Indices: 40547311--40547438 Score: 204
Period size: 54 Copynumber: 2.4 Consensus size: 54
40547301 CTTAGTTTAA
* *
40547311 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTTAATTGAGTTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTAAATTAAGTTCATCTTAG
* *
40547365 TTAATTAAGTTGCTGGAATAAATTATTCATGTTAGTAAATTAAGTTCATCTTAG
1 TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTAAATTAAGTTCATCTTAG
*
40547419 TTAATTTAG-TGCTGGAATAA
1 TTAATTAAGTTGCTGGAATAA
40547439 TCTAATGATG
Statistics
Matches: 69, Mismatches: 5, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
53 11 0.16
54 58 0.84
ACGTcount: A:0.34, C:0.09, G:0.16, T:0.42
Consensus pattern (54 bp):
TTAATTAAGTTGCTGGAATAAATTACTCATCTTAGTAAATTAAGTTCATCTTAG
Found at i:40547507 original size:9 final size:9
Alignment explanation
Indices: 40547493--40547532 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
40547483 TTAAGTTAAG
40547493 TGTTTAATA
1 TGTTTAATA
40547502 TGTTTAATA
1 TGTTTAATA
*
40547511 TGTTTAAATG
1 TGTTT-AATA
40547521 TGTTTAATA
1 TGTTTAATA
40547530 TGT
1 TGT
40547533 CTGCTTTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
9 20 0.71
10 8 0.29
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (9 bp):
TGTTTAATA
Found at i:40547526 original size:19 final size:18
Alignment explanation
Indices: 40547493--40547532 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 18
40547483 TTAAGTTAAG
40547493 TGTTTAATATGTTTAATA
1 TGTTTAATATGTTTAATA
*
40547511 TGTTTAAATGTGTTTAATA
1 TGTTT-AATATGTTTAATA
40547530 TGT
1 TGT
40547533 CTGCTTTAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 5 0.25
19 15 0.75
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.55
Consensus pattern (18 bp):
TGTTTAATATGTTTAATA
Found at i:40549156 original size:22 final size:22
Alignment explanation
Indices: 40549126--40549169 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
40549116 TTTGGTATTT
*
40549126 GGGAATTGGTACGAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
*
40549148 GGGATTTGGTACAAAATGGTAA
1 GGGAATTGGTACAAAATGGTAA
40549170 TGGTTCAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.36, C:0.05, G:0.34, T:0.25
Consensus pattern (22 bp):
GGGAATTGGTACAAAATGGTAA
Found at i:40561433 original size:23 final size:22
Alignment explanation
Indices: 40561381--40561433 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
40561371 TCCACGTCTT
*
40561381 TTTCTTTTGTTTCTTTTTCTAA
1 TTTCTTTTCTTTCTTTTTCTAA
40561403 -TTCATTTTCTCTTCTTTCTTC-AA
1 TTTC-TTTTCT-TTCTTT-TTCTAA
40561426 TTTCTTTT
1 TTTCTTTT
40561434 TCACTCTCAA
Statistics
Matches: 26, Mismatches: 1, Indels: 7
0.76 0.03 0.21
Matches are distributed among these distances:
21 3 0.12
22 5 0.19
23 12 0.46
24 6 0.23
ACGTcount: A:0.09, C:0.19, G:0.02, T:0.70
Consensus pattern (22 bp):
TTTCTTTTCTTTCTTTTTCTAA
Found at i:40573226 original size:21 final size:21
Alignment explanation
Indices: 40573196--40573261 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
40573186 TTGGTATTTG
*
40573196 GGAATCGGTACGAAATGGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40573217 GGAATTGGTATG-AATAGTAT
1 GGAATTGGTACGAAATGGTAT
* *
40573237 GGTATTTGGTACGAATTGGTTAT
1 GG-AATTGGTACGAAATGG-TAT
40573260 GG
1 GG
40573262 TTCAAAGAGG
Statistics
Matches: 35, Mismatches: 7, Indels: 4
0.76 0.15 0.09
Matches are distributed among these distances:
20 9 0.26
21 18 0.51
22 3 0.09
23 5 0.14
ACGTcount: A:0.29, C:0.05, G:0.33, T:0.33
Consensus pattern (21 bp):
GGAATTGGTACGAAATGGTAT
Found at i:40574599 original size:29 final size:30
Alignment explanation
Indices: 40574545--40574610 Score: 73
Period size: 29 Copynumber: 2.2 Consensus size: 30
40574535 CCCCTTAATC
* *
40574545 TTTTTTAATTTTTTTGATTGTCTTTTTG-A
1 TTTTTTAACTTTTTTGACTGTCTTTTTGAA
*
40574574 TTTTTT-ACTTTTTTGACTGATTTTTTTGTAA
1 TTTTTTAACTTTTTTGACTG-TCTTTTTG-AA
40574605 TTTTTT
1 TTTTTT
40574611 TTATTCATCA
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
28 11 0.35
29 13 0.42
31 7 0.23
ACGTcount: A:0.14, C:0.05, G:0.09, T:0.73
Consensus pattern (30 bp):
TTTTTTAACTTTTTTGACTGTCTTTTTGAA
Found at i:40579257 original size:20 final size:20
Alignment explanation
Indices: 40579210--40579257 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 20
40579200 AGTAAGCTCG
40579210 GTTGAGCTCAAACGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
**** *
40579230 AACAAGCTCAAATGAGCTGA
1 GTTGAGCTCAAACGAGCTGA
40579250 GTTGAGCT
1 GTTGAGCT
40579258 GGACGGTGCT
Statistics
Matches: 19, Mismatches: 9, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.33, C:0.19, G:0.27, T:0.21
Consensus pattern (20 bp):
GTTGAGCTCAAACGAGCTGA
Found at i:40580656 original size:17 final size:18
Alignment explanation
Indices: 40580634--40580667 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
40580624 ACAACACTCC
*
40580634 TTTCTT-CTTCACTCTCG
1 TTTCTTCCTTCAATCTCG
40580651 TTTCTTCCTTCAATCTC
1 TTTCTTCCTTCAATCTC
40580668 ACTCTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.09, C:0.35, G:0.03, T:0.53
Consensus pattern (18 bp):
TTTCTTCCTTCAATCTCG
Found at i:40581753 original size:13 final size:13
Alignment explanation
Indices: 40581683--40581813 Score: 66
Period size: 13 Copynumber: 9.2 Consensus size: 13
40581673 CTCGCAAGAC
40581683 TTTTCACTTTTTT
1 TTTTCACTTTTTT
*
40581696 TTTTAACTTGATTTT
1 TTTTCACTT--TTTT
40581711 TTTGGTCACCCTTTTTT
1 TTT--TCA--CTTTTTT
* * *
40581728 TTTGCTCGATTTTT
1 TTTTCAC-TTTTTT
40581742 TTTTCACTTTTTT
1 TTTTCACTTTTTT
* *
40581755 TTTTGAATTTTTT
1 TTTTCACTTTTTT
40581768 TTTTCAATCAATTTTTT
1 TTTTC-A-C--TTTTTT
* *
40581785 TTTTGAAATTTTTT
1 TTTT-CACTTTTTT
*
40581799 TTTTGA-TTTTTT
1 TTTTCACTTTTTT
40581811 TTT
1 TTT
40581814 GTTACTCCAA
Statistics
Matches: 91, Mismatches: 15, Indels: 25
0.69 0.11 0.19
Matches are distributed among these distances:
12 9 0.10
13 30 0.33
14 21 0.23
15 8 0.09
17 20 0.22
19 3 0.03
ACGTcount: A:0.13, C:0.10, G:0.06, T:0.71
Consensus pattern (13 bp):
TTTTCACTTTTTT
Found at i:40581756 original size:30 final size:29
Alignment explanation
Indices: 40581683--40581758 Score: 91
Period size: 30 Copynumber: 2.6 Consensus size: 29
40581673 CTCGCAAGAC
*
40581683 TTTTCACTTTTTTTTTTAACTTGATTTTT
1 TTTTCACTTTTTTTTTTAACTCGATTTTT
* * *
40581712 TTGGTCACCCTTTTTTTTT-GCTCGATTTTT
1 TT-TTCA-CTTTTTTTTTTAACTCGATTTTT
40581742 TTTTCACTTTTTTTTTT
1 TTTTCACTTTTTTTTTT
40581759 GAATTTTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.26
29 5 0.13
30 14 0.36
31 10 0.26
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (29 bp):
TTTTCACTTTTTTTTTTAACTCGATTTTT
Found at i:40581771 original size:30 final size:30
Alignment explanation
Indices: 40581737--40581802 Score: 93
Period size: 30 Copynumber: 2.3 Consensus size: 30
40581727 TTTTGCTCGA
*
40581737 TTTTTTTT--TCACTTTTTTTTTTG-AATT
1 TTTTTTTTAATCAATTTTTTTTTTGAAATT
40581764 TTTTTTTTCAATCAATTTTTTTTTTGAAATT
1 TTTTTTTT-AATCAATTTTTTTTTTGAAATT
40581795 TTTTTTTT
1 TTTTTTTT
40581803 GATTTTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 4
0.87 0.03 0.10
Matches are distributed among these distances:
27 8 0.24
30 14 0.41
31 12 0.35
ACGTcount: A:0.15, C:0.06, G:0.03, T:0.76
Consensus pattern (30 bp):
TTTTTTTTAATCAATTTTTTTTTTGAAATT
Found at i:40581794 original size:14 final size:13
Alignment explanation
Indices: 40581737--40581813 Score: 75
Period size: 14 Copynumber: 5.6 Consensus size: 13
40581727 TTTTGCTCGA
* *
40581737 TTTTTTTTTCACT
1 TTTTTTTTTGAAT
40581750 TTTTTTTTTGAATT
1 TTTTTTTTTGAA-T
*
40581764 TTTTTTTTCAATCAAT
1 TTTTTTTT---TGAAT
40581780 TTTTTTTTTGAAAT
1 TTTTTTTTTG-AAT
40581794 TTTTTTTTTG-AT
1 TTTTTTTTTGAAT
40581806 TTTTTTTT
1 TTTTTTTT
40581814 GTTACTCCAA
Statistics
Matches: 55, Mismatches: 4, Indels: 11
0.79 0.06 0.16
Matches are distributed among these distances:
12 10 0.18
13 11 0.20
14 22 0.40
16 9 0.16
17 3 0.05
ACGTcount: A:0.14, C:0.05, G:0.04, T:0.77
Consensus pattern (13 bp):
TTTTTTTTTGAAT
Found at i:40584766 original size:10 final size:10
Alignment explanation
Indices: 40584753--40584790 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40584743 TTGTAGCTAA
40584753 ATTGAGCTCG
1 ATTGAGCTCG
40584763 ATTGAGCT-G
1 ATTGAGCTCG
40584772 ACTTGAGCTCG
1 A-TTGAGCTCG
*
40584783 AGTGAGCT
1 ATTGAGCT
40584791 GGAAACGAGC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.21, C:0.18, G:0.32, T:0.29
Consensus pattern (10 bp):
ATTGAGCTCG
Found at i:40584770 original size:20 final size:20
Alignment explanation
Indices: 40584730--40584790 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
40584720 ACCAATAAAA
40584730 TAAA-TGAGCT-GAATTGTAGC
1 TAAATTGAGCTCG-ATTG-AGC
40584750 TAAATTGAGCTCGATTGAGC
1 TAAATTGAGCTCGATTGAGC
* * *
40584770 TGACTTGAGCTCGAGTGAGC
1 TAAATTGAGCTCGATTGAGC
40584790 T
1 T
40584791 GGAAACGAGC
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 25 0.69
21 10 0.28
22 1 0.03
ACGTcount: A:0.28, C:0.15, G:0.28, T:0.30
Consensus pattern (20 bp):
TAAATTGAGCTCGATTGAGC
Found at i:40584791 original size:20 final size:20
Alignment explanation
Indices: 40584754--40584791 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40584744 TGTAGCTAAA
*
40584754 TTGAGCTCGATTGAGCTGAC
1 TTGAGCTCGAGTGAGCTGAC
40584774 TTGAGCTCGAGTGAGCTG
1 TTGAGCTCGAGTGAGCTG
40584792 GAAACGAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.18, C:0.18, G:0.34, T:0.29
Consensus pattern (20 bp):
TTGAGCTCGAGTGAGCTGAC
Found at i:40587791 original size:30 final size:30
Alignment explanation
Indices: 40587757--40587853 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
40587747 TAAACTAAAA
*
40587757 TGAGCTAAGTTTTAGCTCGTGAGCTAAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
* * * * * * *
40587787 TGAGCTGAGGCTAAACTCCTAAGCTGAAGT
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
40587817 TGAGCTAAGGTTTAGCTCGTGAGCTAAA-T
1 TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
40587846 ATGAGCTA
1 -TGAGCTA
40587854 GGAGTGAGCT
Statistics
Matches: 51, Mismatches: 15, Indels: 2
0.75 0.22 0.03
Matches are distributed among these distances:
29 1 0.02
30 50 0.98
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (30 bp):
TGAGCTAAGGTTTAGCTCGTGAGCTAAAGT
Found at i:40588820 original size:21 final size:22
Alignment explanation
Indices: 40588796--40588841 Score: 76
Period size: 21 Copynumber: 2.1 Consensus size: 22
40588786 TTTTATATAC
40588796 TTCGATTTTTTTT-AATTTTTT
1 TTCGATTTTTTTTAAATTTTTT
40588817 TTCGATTTTTTTTAAAATTTTTT
1 TTCGATTTTTTTT-AAATTTTTT
40588840 TT
1 TT
40588842 TTCGAATTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 13 0.57
23 10 0.43
ACGTcount: A:0.17, C:0.04, G:0.04, T:0.74
Consensus pattern (22 bp):
TTCGATTTTTTTTAAATTTTTT
Found at i:40592134 original size:10 final size:10
Alignment explanation
Indices: 40592119--40592156 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
40592109 GCTCGTTTCC
*
40592119 AGCTCACTCG
1 AGCTCAATCG
40592129 AGCTCAAGTC-
1 AGCTCAA-TCG
40592139 AGCTCAATCG
1 AGCTCAATCG
40592149 AGCTCAAT
1 AGCTCAAT
40592157 TTAGCTACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 2 0.08
10 21 0.84
11 2 0.08
ACGTcount: A:0.29, C:0.32, G:0.18, T:0.21
Consensus pattern (10 bp):
AGCTCAATCG
Found at i:40592143 original size:20 final size:20
Alignment explanation
Indices: 40592118--40592155 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
40592108 AGCTCGTTTC
*
40592118 CAGCTCACTCGAGCTCAAGT
1 CAGCTCAATCGAGCTCAAGT
40592138 CAGCTCAATCGAGCTCAA
1 CAGCTCAATCGAGCTCAA
40592156 TTTAGCTACA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.29, C:0.34, G:0.18, T:0.18
Consensus pattern (20 bp):
CAGCTCAATCGAGCTCAAGT
Found at i:40592162 original size:20 final size:20
Alignment explanation
Indices: 40592119--40592179 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
40592109 GCTCGTTTCC
* * *
40592119 AGCTCACTCGAGCTCAAGTC
1 AGCTCAATCGAGCTCAATTT
40592139 AGCTCAATCGAGCTCAATTT
1 AGCTCAATCGAGCTCAATTT
40592159 AGCTACAATTC-AGCTC-ATTT
1 AGCT-CAA-TCGAGCTCAATTT
40592179 A
1 A
40592180 TTTTATTGGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 26 0.72
21 8 0.22
22 2 0.06
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.28
Consensus pattern (20 bp):
AGCTCAATCGAGCTCAATTT
Found at i:40592173 original size:11 final size:10
Alignment explanation
Indices: 40592129--40592175 Score: 51
Period size: 10 Copynumber: 4.6 Consensus size: 10
40592119 AGCTCACTCG
*
40592129 AGCTCAAGTC
1 AGCTCAATTC
40592139 AGCTCAA-TC
1 AGCTCAATTC
*
40592148 GAGCTCAATTT
1 -AGCTCAATTC
40592159 AGCTACAATTC
1 AGCT-CAATTC
40592170 AGCTCA
1 AGCTCA
40592176 TTTATTTTAT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
9 2 0.06
10 20 0.62
11 10 0.31
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.26
Consensus pattern (10 bp):
AGCTCAATTC
Found at i:40592679 original size:13 final size:13
Alignment explanation
Indices: 40592661--40592685 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40592651 GTATTGATCA
40592661 TGTGTTCACACCT
1 TGTGTTCACACCT
40592674 TGTGTTCACACC
1 TGTGTTCACACC
40592686 ATGATGACCA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTGTTCACACCT
Found at i:40601344 original size:13 final size:12
Alignment explanation
Indices: 40601308--40601343 Score: 72
Period size: 12 Copynumber: 3.0 Consensus size: 12
40601298 AGACCGTATG
40601308 CAATTTTTTTTT
1 CAATTTTTTTTT
40601320 CAATTTTTTTTT
1 CAATTTTTTTTT
40601332 CAATTTTTTTTT
1 CAATTTTTTTTT
40601344 TTTTTTGATT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.17, C:0.08, G:0.00, T:0.75
Consensus pattern (12 bp):
CAATTTTTTTTT
Found at i:40601346 original size:18 final size:17
Alignment explanation
Indices: 40601323--40601359 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
40601313 TTTTTTTCAA
*
40601323 TTTTTTTTTCAATTTTT
1 TTTTTTTTTTAATTTTT
*
40601340 TTTTTTTTTTGATTTTT
1 TTTTTTTTTTAATTTTT
40601357 TTT
1 TTT
40601360 GAATCTACAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.08, C:0.03, G:0.03, T:0.86
Consensus pattern (17 bp):
TTTTTTTTTTAATTTTT
Found at i:40613838 original size:40 final size:40
Alignment explanation
Indices: 40613783--40613863 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
40613773 TAAAAAATGG
40613783 ACAAAAATCATGCCTTACTGAGCTAGGAAAGCTTGGCCGA
1 ACAAAAATCATGCCTTACTGAGCTAGGAAAGCTTGGCCGA
40613823 ACAAAAATCATGCCTTACTGAGCTAGGAAAGCTTGGCCGA
1 ACAAAAATCATGCCTTACTGAGCTAGGAAAGCTTGGCCGA
40613863 A
1 A
40613864 TGAAAACCCA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.20
Consensus pattern (40 bp):
ACAAAAATCATGCCTTACTGAGCTAGGAAAGCTTGGCCGA
Found at i:40618912 original size:26 final size:26
Alignment explanation
Indices: 40618874--40618923 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
40618864 TGGCTACCCG
*
40618874 ATACAGGTCTAGATATAGAAGGCGCT
1 ATACAGGTCTAGATACAGAAGGCGCT
*
40618900 ATACAGGTTTAGATACAGAAGGCG
1 ATACAGGTCTAGATACAGAAGGCG
40618924 TTATCCCTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.28, T:0.22
Consensus pattern (26 bp):
ATACAGGTCTAGATACAGAAGGCGCT
Found at i:40625418 original size:29 final size:29
Alignment explanation
Indices: 40625344--40625475 Score: 180
Period size: 29 Copynumber: 4.7 Consensus size: 29
40625334 CCCTTACAAA
* *
40625344 GCCC-AAT-ACATGCATATGGCCCACTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
*
40625371 GCCC-AATCTCATTCATATGGCCCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
** *
40625399 GCTTAAATCACATTCGTATGGCCCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
*
40625428 GCCCAAATCACATTCATATGGACCATTAG
1 GCCCAAATCACATTCATATGGCCCATTAG
40625457 GCCCAAATCACATTCATAT
1 GCCCAAATCACATTCATAT
40625476 TCATGCTTTC
Statistics
Matches: 92, Mismatches: 11, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
27 7 0.08
28 19 0.21
29 66 0.72
ACGTcount: A:0.30, C:0.30, G:0.14, T:0.26
Consensus pattern (29 bp):
GCCCAAATCACATTCATATGGCCCATTAG
Found at i:40625713 original size:16 final size:16
Alignment explanation
Indices: 40625687--40625739 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
40625677 GTAGCCAAAC
*
40625687 TTTCGGCTTTTCTGCA
1 TTTCAGCTTTTCTGCA
* *
40625703 TTTTAGCTTTTTTGGCA
1 TTTCAGCTTTTCT-GCA
* *
40625720 TTTCAGCATTTCGGCA
1 TTTCAGCTTTTCTGCA
40625736 TTTC
1 TTTC
40625740 GGTAATAAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
16 17 0.59
17 12 0.41
ACGTcount: A:0.11, C:0.21, G:0.17, T:0.51
Consensus pattern (16 bp):
TTTCAGCTTTTCTGCA
Found at i:40630294 original size:27 final size:27
Alignment explanation
Indices: 40630242--40630331 Score: 119
Period size: 27 Copynumber: 3.2 Consensus size: 27
40630232 GTGACAGAGT
40630242 CACCAGATACAGATATTTTGTGGCAGTGC
1 CACCAGA-ACAGATA-TTTGTGGCAGTGC
* *
40630271 CACCAGAACAGATATATGTGGCAGGGC
1 CACCAGAACAGATATTTGTGGCAGTGC
40630298 CACCAGAACAGATAATTTGTGGCA-TAGC
1 CACCAGAACAGAT-ATTTGTGGCAGT-GC
40630326 CACCAG
1 CACCAG
40630332 GACTCTTCCT
Statistics
Matches: 55, Mismatches: 4, Indels: 5
0.86 0.06 0.08
Matches are distributed among these distances:
27 24 0.44
28 24 0.44
29 7 0.13
ACGTcount: A:0.32, C:0.23, G:0.24, T:0.20
Consensus pattern (27 bp):
CACCAGAACAGATATTTGTGGCAGTGC
Found at i:40636987 original size:28 final size:27
Alignment explanation
Indices: 40636930--40637081 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
40636920 TAAATTGTGC
*
40636930 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
40636957 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
40636985 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40637012 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
40637040 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
40637067 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
40637082 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:40636994 original size:55 final size:55
Alignment explanation
Indices: 40636930--40637081 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
40636920 TAAATTGTGC
*
40636930 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
40636985 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
40637040 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
40637082 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:40641455 original size:55 final size:56
Alignment explanation
Indices: 40641390--40641504 Score: 144
Period size: 55 Copynumber: 2.1 Consensus size: 56
40641380 AGCATGGCTG
* * * *
40641390 CCAGATACAGA-AAATGTGACAGAGTCACCAGATACAGATATTTTGTGGTAGTGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGA-ACAGATAATTTGTGGCAGGGCCA
* * *
40641446 CCAGA-ACAGATATATGTGGCAGGGCCACCAGAACAGATAATTTGTGGCAGGGCCA
1 CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCAGGGCCA
40641501 CCAG
1 CCAG
40641505 GACGCTTCCT
Statistics
Matches: 51, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
55 29 0.57
56 22 0.43
ACGTcount: A:0.34, C:0.21, G:0.26, T:0.19
Consensus pattern (56 bp):
CCAGATACAGATAAATGTGACAGAGCCACCAGAACAGATAATTTGTGGCAGGGCCA
Found at i:40641500 original size:28 final size:28
Alignment explanation
Indices: 40641415--40641504 Score: 128
Period size: 28 Copynumber: 3.2 Consensus size: 28
40641405 GTGACAGAGT
* * *
40641415 CACCAGATACAGATATTTTGTGGTAGTGC
1 CACCAGA-ACAGATAATTTGTGGCAGGGC
*
40641444 CACCAGAACAGAT-ATATGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
40641471 CACCAGAACAGATAATTTGTGGCAGGGC
1 CACCAGAACAGATAATTTGTGGCAGGGC
40641499 CACCAG
1 CACCAG
40641505 GACGCTTCCT
Statistics
Matches: 55, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
27 23 0.42
28 25 0.45
29 7 0.13
ACGTcount: A:0.31, C:0.22, G:0.27, T:0.20
Consensus pattern (28 bp):
CACCAGAACAGATAATTTGTGGCAGGGC
Done.