Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
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: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 9 of 171
Found at i:3983425 original size:15 final size:15
Alignment explanation
Indices: 3983405--3983458 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 15
3983395 ATACTACAAA
3983405 ATATTTATTATTAAT
1 ATATTTATTATTAAT
*
3983420 ATATTTATAATTGTAAT
1 ATATTTATTA-T-TAAT
*
3983437 AAATATTTATTATTAAA
1 --ATATTTATTATTAAT
3983454 ATATT
1 ATATT
3983459 AATATTGAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
15 14 0.44
16 1 0.03
17 7 0.22
18 1 0.03
19 9 0.28
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATATTTATTATTAAT
Found at i:3985968 original size:2 final size:2
Alignment explanation
Indices: 3985928--3985952 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3985918 TTGCCAAAAG
3985928 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
3985953 CACACACGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:3988544 original size:20 final size:19
Alignment explanation
Indices: 3988508--3988546 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
3988498 TTATAAATAC
3988508 ATATTTAAACAATTACAAA
1 ATATTTAAACAATTACAAA
3988527 ATATGTTAAATCAA-TACAAA
1 ATAT-TTAAA-CAATTACAAA
3988547 GAGCAAAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 11 0.61
21 3 0.17
ACGTcount: A:0.56, C:0.10, G:0.03, T:0.31
Consensus pattern (19 bp):
ATATTTAAACAATTACAAA
Found at i:4001180 original size:14 final size:14
Alignment explanation
Indices: 4001161--4001187 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
4001151 AATAACCCTA
4001161 AACCAAAATATGTT
1 AACCAAAATATGTT
4001175 AACCAAAATATGT
1 AACCAAAATATGT
4001188 GAATAACAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.15, G:0.07, T:0.26
Consensus pattern (14 bp):
AACCAAAATATGTT
Found at i:4001320 original size:40 final size:40
Alignment explanation
Indices: 4001243--4001322 Score: 99
Period size: 41 Copynumber: 2.0 Consensus size: 40
4001233 AGTAGCAATC
*
4001243 AAAATCCAATCAAAATCGAAATAACCCTAAATCAAAAATA
1 AAAATCCAATCAAAATCCAAATAACCCTAAATCAAAAATA
* * *
4001283 AAAATCCAAATCAAAA-CCACATAAACCTTAAATAAAAAAT
1 AAAATCC-AATCAAAATCCAAAT-AACCCTAAATCAAAAAT
4001323 CACAATCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
40 11 0.32
41 23 0.68
ACGTcount: A:0.61, C:0.20, G:0.01, T:0.17
Consensus pattern (40 bp):
AAAATCCAATCAAAATCCAAATAACCCTAAATCAAAAATA
Found at i:4033352 original size:96 final size:96
Alignment explanation
Indices: 4033182--4033374 Score: 325
Period size: 96 Copynumber: 2.0 Consensus size: 96
4033172 TCAAGTGTAG
* *
4033182 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTTATTGAAAAGGAAGGGTATCTTATGGTCCAAC
1 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
*
4033247 CTGGCCGACAGGGAAGTTACATTCCTGATAA
66 CAGGCCGACAGGGAAGTTACATTCCTGATAA
*
4033278 TGAAGGTGAAAACTTAGCTATGGAACCATCGGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
1 TGAAGGTGAAAACTTAGCTATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
*
4033343 CAAGG-CGACAGGGAAGTTATATTCCTGATAA
66 C-AGGCCGACAGGGAAGTTACATTCCTGATAA
4033374 T
1 T
4033375 CTTGGCCCAT
Statistics
Matches: 91, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
96 89 0.98
97 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.25, T:0.25
Consensus pattern (96 bp):
TGAAGGTGAAAACTTAGCTATGGAACCATCAGTCATTGAAAAGGAAGGGTATCTTATAGTCCAAC
CAGGCCGACAGGGAAGTTACATTCCTGATAA
Found at i:4039561 original size:20 final size:20
Alignment explanation
Indices: 4039536--4039576 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
4039526 AACCAATCTG
*
4039536 CATCATTGCTGCAAAATTTT
1 CATCATCGCTGCAAAATTTT
4039556 CATCATCGCTGCAAAATTTT
1 CATCATCGCTGCAAAATTTT
4039576 C
1 C
4039577 TTCTGATGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.29, C:0.24, G:0.10, T:0.37
Consensus pattern (20 bp):
CATCATCGCTGCAAAATTTT
Found at i:4042466 original size:59 final size:59
Alignment explanation
Indices: 4042397--4042837 Score: 284
Period size: 59 Copynumber: 7.7 Consensus size: 59
4042387 TTGTCAGATA
*
4042397 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTATCTGAT
1 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCTTTTTTATCTGAT
* * * *
4042456 AAAAAATCAAATTTTTTAGTGTTGGCCATTGCAT-GACAGACATCACTTTTTTTATCTGGA-
1 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTC-GACA-CCCCTTTTTTATCT-GAT
* * * * * **
4042516 AAAAAATC-AATTTTTTTATGTTGACCATTGCATGATCGACATCTCC-TTTTTGTCACAT
1 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACA-CCCCTTTTTTATCTGAT
* * * *
4042574 -AAAAA--AAA-----TTGTGTTAGCCATTACATGGTCAACATCACCTTTTTTATCT-A-
1 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACA-CCCCTTTTTTATCTGAT
* * ** * **
4042624 AAAAAATCAATTTTTTTTGTGTTGGACATTGCATGACCGACACCTCTTTTTTATCAAAT
1 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCTTTTTTATCTGAT
* ***
4042683 AAAAAA--AAA------T-TGTTGGTCATTATTTGGTCGACACCACCTTTTTTATCTGAT
1 AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACC-CCTTTTTTATCTGAT
* * ** * *
4042734 AAAAAAATCAAATTTTTTGGTGTTGGTCATTGCATGACCAACACCAAC-TTTTTATCTGAT
1 -AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACC-CCTTTTTTATCTGAT
* * * *
4042794 AAAAAAATTAATTTTTTTTGTGTTGGTCA-TGCATTGGCCGACAC
1 -AAAAAATCAAATTTTTTTGTGTTGGCCATTGCA-TGGTCGACAC
4042838 TAACTTTCCA
Statistics
Matches: 296, Mismatches: 57, Indels: 57
0.72 0.14 0.14
Matches are distributed among these distances:
50 19 0.06
51 43 0.15
52 13 0.04
53 2 0.01
54 3 0.01
56 2 0.01
57 19 0.06
58 30 0.10
59 76 0.26
60 66 0.22
61 23 0.08
ACGTcount: A:0.31, C:0.17, G:0.13, T:0.39
Consensus pattern (59 bp):
AAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCTTTTTTATCTGAT
Found at i:4042611 original size:110 final size:110
Alignment explanation
Indices: 4042396--4042800 Score: 379
Period size: 111 Copynumber: 3.6 Consensus size: 110
4042386 TTTGTCAGAT
* * * **
4042396 AAAAAAATCAAATTTTTTTGTGTTGGCCATTGCATGGTCGACACCCCCTTTTTATCTGATAAAAA
1 AAAAAAATCAAATTTTTTTGTGTTGACCATTGCATGATCGACACCTCCTTTTTATCAAAT-AAAA
* * *
4042461 ATCAAATTTTTTAGTGTTGGCCATTGCAT-GACAGACATCACTTTTTTTATCTGG
65 A--AAA----TT-GTGTTGGCCATTACATGGTCA-ACATCACCTTTTTTATCT-G
* * * *
4042515 AAAAAAATC-AATTTTTTTATGTTGACCATTGCATGATCGACATCTCCTTTTTGTCACATAAAAA
1 AAAAAAATCAAATTTTTTTGTGTTGACCATTGCATGATCGACACCTCCTTTTTATCAAATAAAAA
*
4042579 AAATTGTGTTAGCCATTACATGGTCAACATCACCTTTTTTATCT-
66 AAATTGTGTTGGCCATTACATGGTCAACATCACCTTTTTTATCTG
* * *
4042623 AAAAAAATCAATTTTTTTTGTGTTGGA-CATTGCATGACCGACACCTCTTTTTTATCAAATAAAA
1 AAAAAAATCAAATTTTTTTGTGTT-GACCATTGCATGATCGACACCTCCTTTTTATCAAATAAAA
* * ** * *
4042687 AAAAAT-TGTTGGTCATTATTTGGTCGACACCACCTTTTTTATCTG
65 AAAATTGTGTTGGCCATTACATGGTCAACATCACCTTTTTTATCTG
* ** * * ** **
4042732 ATAAAAAAATCAAATTTTTTGGTGTTGGTCATTGCATGACCAACACCAACTTTTTATCTGATAAA
1 --AAAAAAATCAAATTTTTTTGTGTTGACCATTGCATGATCGACACCTCCTTTTTATCAAATAAA
4042797 AAAA
64 AAAA
4042801 TTAATTTTTT
Statistics
Matches: 244, Mismatches: 35, Indels: 22
0.81 0.12 0.07
Matches are distributed among these distances:
108 41 0.17
109 49 0.20
110 34 0.14
111 61 0.25
115 3 0.01
117 5 0.02
118 42 0.17
119 9 0.04
ACGTcount: A:0.32, C:0.17, G:0.13, T:0.38
Consensus pattern (110 bp):
AAAAAAATCAAATTTTTTTGTGTTGACCATTGCATGATCGACACCTCCTTTTTATCAAATAAAAA
AAATTGTGTTGGCCATTACATGGTCAACATCACCTTTTTTATCTG
Found at i:4042844 original size:60 final size:60
Alignment explanation
Indices: 4042713--4042827 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
4042703 TATTTGGTCG
*
4042713 ACACCACCTTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGTCATTGCATGACCA
1 ACACCAAC-TTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGTCATTGCATGACCA
* * *
4042774 ACACCAACTTTTTATCTGATAAAAAAATTAATTTTTTTTGTGTTGGTCA-TGCAT
1 ACACCAACTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGTCATTGCAT
4042828 TGGCCGACAC
Statistics
Matches: 50, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
59 5 0.10
60 38 0.76
61 7 0.14
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (60 bp):
ACACCAACTTTTTATCTGATAAAAAAATCAAATTTTTTGGTGTTGGTCATTGCATGACCA
Found at i:4045098 original size:12 final size:12
Alignment explanation
Indices: 4045081--4045128 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
4045071 TATTTGTATA
4045081 AAAATTAATTTG
1 AAAATTAATTTG
*
4045093 AAAATTAAATTGAGTT
1 AAAATT-AATT---TG
4045109 AAAATTAATTTG
1 AAAATTAATTTG
4045121 AAAATTAA
1 AAAATTAA
4045129 GATACATGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
12 15 0.50
13 4 0.13
15 4 0.13
16 7 0.23
ACGTcount: A:0.54, C:0.00, G:0.08, T:0.38
Consensus pattern (12 bp):
AAAATTAATTTG
Found at i:4045578 original size:48 final size:48
Alignment explanation
Indices: 4045432--4045580 Score: 146
Period size: 48 Copynumber: 3.1 Consensus size: 48
4045422 AAATAAAAAC
*
4045432 TATTATTATATTATAATTTTTATCAAATAATGCGTTGATTTGACAATA
1 TATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATA
* ** * * ** * *
4045480 TATTATT-TATCA-AATTTTAATATTTAA-AAT-TATTTAAAT-AAAAAA
1 TATTATTATATTATAATTTT--TATCAAATAATGTGTTGATTTGACAATA
4045525 CTATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATA
1 -TATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATA
4045574 TATTATT
1 TATTATT
4045581 TATCAAATTT
Statistics
Matches: 74, Mismatches: 19, Indels: 16
0.68 0.17 0.15
Matches are distributed among these distances:
45 4 0.05
46 22 0.30
47 14 0.19
48 30 0.41
49 4 0.05
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (48 bp):
TATTATTATATTATAATTTTTATCAAATAATGTGTTGATTTGACAATA
Found at i:4045641 original size:94 final size:93
Alignment explanation
Indices: 4045222--4045611 Score: 683
Period size: 93 Copynumber: 4.2 Consensus size: 93
4045212 TTTAAATTAC
* *
4045222 ATTTAAAACTATTTAAATAAAAAACTGTTATTATATTATAATTTTTATCAAATAATGTGTTGATT
1 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
* *
4045287 TGATAATATATTATTTACCAAATTTAAT
66 TGACAATATATTATTTATCAAATTTAAT
* *
4045315 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTACAATTTTTATCAAATAATATGTTGATT
1 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
* *
4045380 TGACAATACATTTTTTATCAAATTTAAT
66 TGACAATATATTATTTATCAAATTTAAT
*
4045408 ATTTAAAATTATTTAAAT-AAAAACTATTATTATATTATAATTTTTATCAAATAATGCGTTGATT
1 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
4045472 TGACAATATATTATTTATCAAATTTTAAT
66 TGACAATATATTATTTATCAAA-TTTAAT
4045501 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
1 ATTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
4045566 TGACAATATATTATTTATCAAATTTAAT
66 TGACAATATATTATTTATCAAATTTAAT
4045594 ATTTAAAATTATTTAAAT
1 ATTTAAAATTATTTAAAT
4045612 CAATACAAAT
Statistics
Matches: 281, Mismatches: 14, Indels: 4
0.94 0.05 0.01
Matches are distributed among these distances:
92 63 0.22
93 151 0.54
94 67 0.24
ACGTcount: A:0.44, C:0.05, G:0.04, T:0.47
Consensus pattern (93 bp):
ATTTAAAATTATTTAAATAAAAAACTATTATTATATTATAATTTTTATCAAATAATGTGTTGATT
TGACAATATATTATTTATCAAATTTAAT
Found at i:4057431 original size:7 final size:7
Alignment explanation
Indices: 4057419--4057447 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
4057409 AGCAAAGAAA
4057419 GGAAATG
1 GGAAATG
4057426 GGAAATG
1 GGAAATG
4057433 GGAAATG
1 GGAAATG
4057440 GGAAATG
1 GGAAATG
4057447 G
1 G
4057448 AAAGAGAGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.41, C:0.00, G:0.45, T:0.14
Consensus pattern (7 bp):
GGAAATG
Found at i:4058524 original size:20 final size:20
Alignment explanation
Indices: 4058499--4058536 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4058489 GATATTTTTC
4058499 TATTATA-ATAATATTTTAGG
1 TATTATATATAAT-TTTTAGG
4058519 TATTATATATAATTTTTA
1 TATTATATATAATTTTTA
4058537 ATTGTTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (20 bp):
TATTATATATAATTTTTAGG
Found at i:4058863 original size:20 final size:21
Alignment explanation
Indices: 4058838--4058882 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
4058828 ATACTTTCAA
* *
4058838 TTATTTCAATTTTACTTTAT-
1 TTATTTCAATGTTACATTATC
*
4058858 TTATTTTAATGTTACATTATC
1 TTATTTCAATGTTACATTATC
4058879 TTAT
1 TTAT
4058883 AAAAATTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.27, C:0.09, G:0.02, T:0.62
Consensus pattern (21 bp):
TTATTTCAATGTTACATTATC
Found at i:4059086 original size:17 final size:17
Alignment explanation
Indices: 4059064--4059099 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4059054 TCCCTTGACT
* *
4059064 TTTAACCTTTCATTTTC
1 TTTAACCTATCATATTC
4059081 TTTAACCTATCATATTC
1 TTTAACCTATCATATTC
4059098 TT
1 TT
4059100 GTAATTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTAACCTATCATATTC
Found at i:4059607 original size:34 final size:35
Alignment explanation
Indices: 4059556--4059623 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 35
4059546 CTTTTCTGTT
* * *
4059556 ATGTTATGCTTGCAAGTTTTGTTAAGGGATTACTA
1 ATGTTATGCTTGAAAGTTTTGTTAAAGGACTACTA
4059591 ATGTT-TGCTTGAAAGTTTTGTTAAAGGACTACT
1 ATGTTATGCTTGAAAGTTTTGTTAAAGGACTACT
4059624 TATATTTATA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 25 0.83
35 5 0.17
ACGTcount: A:0.26, C:0.09, G:0.22, T:0.43
Consensus pattern (35 bp):
ATGTTATGCTTGAAAGTTTTGTTAAAGGACTACTA
Found at i:4064538 original size:24 final size:24
Alignment explanation
Indices: 4064503--4064548 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
4064493 TTGTATGTTC
*
4064503 AACCTTTCATCTCCCTTGACTTTT
1 AACCTTTCATCTCCCTTAACTTTT
*
4064527 AACC-TTCTATCTTCCTTAACTT
1 AACCTTTC-ATCTCCCTTAACTT
4064549 CTCTTAACTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 3 0.16
24 16 0.84
ACGTcount: A:0.20, C:0.33, G:0.02, T:0.46
Consensus pattern (24 bp):
AACCTTTCATCTCCCTTAACTTTT
Found at i:4064578 original size:17 final size:17
Alignment explanation
Indices: 4064558--4064593 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4064548 TCTCTTAACT
*
4064558 TTTAACCTTTCATCTTC
1 TTTAACCTTTCATATTC
*
4064575 TTTAACTTTTCATATTC
1 TTTAACCTTTCATATTC
4064592 TT
1 TT
4064594 ATAATTACTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.19, C:0.22, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTAACCTTTCATATTC
Found at i:4064892 original size:28 final size:28
Alignment explanation
Indices: 4064853--4064942 Score: 110
Period size: 28 Copynumber: 3.2 Consensus size: 28
4064843 ATTCTTTTAG
*
4064853 TATTTAA-TTTTTCAAATTATCAAATGA
1 TATTTAAGTTTTTCAAATTATCAAATAA
**
4064880 TATTTAAGTTTTTTTAATTGATCAAATAA
1 TATTTAAGTTTTTCAAATT-ATCAAATAA
* * *
4064909 TTTTTAAGTATTTCAATTTATCAAATAA
1 TATTTAAGTTTTTCAAATTATCAAATAA
4064937 TATTTA
1 TATTTA
4064943 GTACTTTCAT
Statistics
Matches: 52, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
27 7 0.13
28 23 0.44
29 22 0.42
ACGTcount: A:0.39, C:0.06, G:0.04, T:0.51
Consensus pattern (28 bp):
TATTTAAGTTTTTCAAATTATCAAATAA
Found at i:4065954 original size:12 final size:12
Alignment explanation
Indices: 4065939--4065963 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4065929 AAAAATAAAT
4065939 TTTTTAATATTA
1 TTTTTAATATTA
4065951 TTTTTAATATTA
1 TTTTTAATATTA
4065963 T
1 T
4065964 AAAAATATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTTTAATATTA
Found at i:4068064 original size:3 final size:3
Alignment explanation
Indices: 4068056--4068107 Score: 59
Period size: 3 Copynumber: 17.0 Consensus size: 3
4068046 GTTTTGGGAT
* * * *
4068056 GAG GAG GAG GAG GAG GAG GAG GAG GCG GCG GAG GCG GAG GCG GAG GAAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG GAG G-AG
4068105 GAG
1 GAG
4068108 AACCTTGATC
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
3 39 0.93
4 3 0.07
ACGTcount: A:0.27, C:0.08, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:4071641 original size:20 final size:21
Alignment explanation
Indices: 4071616--4071655 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4071606 CGTTGAGTTT
*
4071616 GTGGCA-GGGTCTCAAGGATA
1 GTGGCATGGATCTCAAGGATA
4071636 GTGGCATTGGATCTCAAGGA
1 GTGGCA-TGGATCTCAAGGA
4071656 ATCACCAACA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 6 0.35
22 11 0.65
ACGTcount: A:0.25, C:0.15, G:0.38, T:0.23
Consensus pattern (21 bp):
GTGGCATGGATCTCAAGGATA
Found at i:4078866 original size:27 final size:24
Alignment explanation
Indices: 4078816--4078866 Score: 57
Period size: 24 Copynumber: 2.0 Consensus size: 24
4078806 ATCTTTTCTT
* *
4078816 GCTTTCTTCTTATTTCTTGTATTG
1 GCTTTCTTCTAATTTCCTGTATTG
4078840 GCTTTCTTCTGAATATTCCTGTGATTG
1 GCTTTCTTCT-AAT-TTCCTGT-ATTG
4078867 TCTAGATTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
24 10 0.45
25 2 0.09
26 6 0.27
27 4 0.18
ACGTcount: A:0.12, C:0.18, G:0.16, T:0.55
Consensus pattern (24 bp):
GCTTTCTTCTAATTTCCTGTATTG
Found at i:4081597 original size:1 final size:1
Alignment explanation
Indices: 4081591--4081616 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
4081581 CGAATGCCAT
4081591 CCCCCCCCCCCCCCCCCCCCCCCCCC
1 CCCCCCCCCCCCCCCCCCCCCCCCCC
4081617 AAAATCTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:1.00, G:0.00, T:0.00
Consensus pattern (1 bp):
C
Found at i:4089138 original size:28 final size:27
Alignment explanation
Indices: 4089106--4089166 Score: 104
Period size: 28 Copynumber: 2.2 Consensus size: 27
4089096 TAAAGTGTTG
4089106 TCTTTCAGACATGACATGTCTGCTAATT
1 TCTTTCAGACATGACATGTCTGCTAA-T
*
4089134 TCTTTCAGACATGGCATGTCTGCTAAT
1 TCTTTCAGACATGACATGTCTGCTAAT
4089161 TCTTTC
1 TCTTTC
4089167 TCCTCTTATG
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 7 0.22
28 25 0.78
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (27 bp):
TCTTTCAGACATGACATGTCTGCTAAT
Found at i:4091126 original size:28 final size:30
Alignment explanation
Indices: 4091094--4091161 Score: 77
Period size: 32 Copynumber: 2.3 Consensus size: 30
4091084 TTTAATATAA
4091094 TATTTTTGGA-T-ATAAAATAACTTAGTTT
1 TATTTTTGGATTCATAAAATAACTTAGTTT
* * *
4091122 TATTTTTGTATTGTCATAAATTTACTTAGTTT
1 TATTTTTGGA-T-TCATAAAATAACTTAGTTT
4091154 TATTTTTG
1 TATTTTTG
4091162 TATTGTCATA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 9 0.27
31 1 0.03
32 23 0.70
ACGTcount: A:0.28, C:0.04, G:0.10, T:0.57
Consensus pattern (30 bp):
TATTTTTGGATTCATAAAATAACTTAGTTT
Found at i:4091149 original size:32 final size:32
Alignment explanation
Indices: 4091113--4091180 Score: 136
Period size: 32 Copynumber: 2.1 Consensus size: 32
4091103 ATATAAAATA
4091113 ACTTAGTTTTATTTTTGTATTGTCATAAATTT
1 ACTTAGTTTTATTTTTGTATTGTCATAAATTT
4091145 ACTTAGTTTTATTTTTGTATTGTCATAAATTT
1 ACTTAGTTTTATTTTTGTATTGTCATAAATTT
4091177 ACTT
1 ACTT
4091181 TTTTGGCAGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.25, C:0.07, G:0.09, T:0.59
Consensus pattern (32 bp):
ACTTAGTTTTATTTTTGTATTGTCATAAATTT
Found at i:4102328 original size:24 final size:24
Alignment explanation
Indices: 4102296--4102342 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
4102286 ATTAATTAGC
4102296 CTATCAGCCTATGATTCTGTAACG
1 CTATCAGCCTATGATTCTGTAACG
4102320 CTATCAGCCTATGATTCTGTAAC
1 CTATCAGCCTATGATTCTGTAAC
4102343 AATAGTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.34
Consensus pattern (24 bp):
CTATCAGCCTATGATTCTGTAACG
Found at i:4120486 original size:3 final size:3
Alignment explanation
Indices: 4120478--4120503 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
4120468 GTGTACTATT
4120478 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
4120504 ACTGCAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:4140660 original size:2 final size:2
Alignment explanation
Indices: 4140653--4140678 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
4140643 GAAATTCTAA
4140653 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
4140679 TTGTTAGTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4154965 original size:17 final size:18
Alignment explanation
Indices: 4154929--4154966 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
4154919 TACCATTCTT
*
4154929 TTATTTTGATTTAGGGTA
1 TTATTTTGATTCAGGGTA
*
4154947 TTATTTTG-TTCATGGTA
1 TTATTTTGATTCAGGGTA
4154964 TTA
1 TTA
4154967 ACTTTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.21, C:0.03, G:0.18, T:0.58
Consensus pattern (18 bp):
TTATTTTGATTCAGGGTA
Found at i:4157238 original size:5 final size:6
Alignment explanation
Indices: 4157223--4157247 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
4157213 AAGTGGTGGT
4157223 GGGGGA GGGGGA GGGGGA GGGGGA G
1 GGGGGA GGGGGA GGGGGA GGGGGA G
4157248 CTGAAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.84, T:0.00
Consensus pattern (6 bp):
GGGGGA
Found at i:4157247 original size:87 final size:87
Alignment explanation
Indices: 4157151--4157322 Score: 299
Period size: 87 Copynumber: 2.0 Consensus size: 87
4157141 GAGTGGTGGA
* * *
4157151 GGAGGGGGAGCTGAAGATGAATTCTTTACAGTAGAAGATGGAGATATAGCTGAGGATGGAGGAAG
1 GGAGGGGGAGCTGAAAATGAATTCTTTACAGAAGAAAATGGAGATATAGCTGAGGATGGAGGAAG
4157216 TGGTGGTGGGGGAGGGGGAGGG
66 TGGTGGTGGGGGAGGGGGAGGG
* *
4157238 GGAGGGGGAGCTGAAAATGAATTCTTTACAGAAGAAAATGGAGATGTAGCTGAGGATGGAGGGAG
1 GGAGGGGGAGCTGAAAATGAATTCTTTACAGAAGAAAATGGAGATATAGCTGAGGATGGAGGAAG
4157303 TGGTGGTGGGGGAGGGGGAG
66 TGGTGGTGGGGGAGGGGGAG
4157323 ACTGGATCAA
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.28, C:0.05, G:0.49, T:0.18
Consensus pattern (87 bp):
GGAGGGGGAGCTGAAAATGAATTCTTTACAGAAGAAAATGGAGATATAGCTGAGGATGGAGGAAG
TGGTGGTGGGGGAGGGGGAGGG
Found at i:4177038 original size:2 final size:2
Alignment explanation
Indices: 4177031--4177063 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4177021 GTGTGGCGTA
4177031 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4177064 ACACTATGGA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4203160 original size:30 final size:30
Alignment explanation
Indices: 4203124--4203187 Score: 128
Period size: 30 Copynumber: 2.1 Consensus size: 30
4203114 GCAACTGCTT
4203124 TTTCTTGATCTCCCTCTGGCTTTGATTCAG
1 TTTCTTGATCTCCCTCTGGCTTTGATTCAG
4203154 TTTCTTGATCTCCCTCTGGCTTTGATTCAG
1 TTTCTTGATCTCCCTCTGGCTTTGATTCAG
4203184 TTTC
1 TTTC
4203188 AACTGGCCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 34 1.00
ACGTcount: A:0.09, C:0.27, G:0.16, T:0.48
Consensus pattern (30 bp):
TTTCTTGATCTCCCTCTGGCTTTGATTCAG
Found at i:4208859 original size:2 final size:2
Alignment explanation
Indices: 4208852--4208887 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
4208842 TAATACATGA
4208852 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4208888 TGTTTAAACT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4210217 original size:22 final size:22
Alignment explanation
Indices: 4210189--4210243 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4210179 AGTGAAATAG
* *
4210189 CAACAAAACATTGAGAAAGCAA
1 CAACAAAACAATGAAAAAGCAA
**
4210211 CAACAAAACAATGAAAAATTAA
1 CAACAAAACAATGAAAAAGCAA
4210233 CAACAAAACAA
1 CAACAAAACAA
4210244 CATTTTTTAT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.65, C:0.18, G:0.07, T:0.09
Consensus pattern (22 bp):
CAACAAAACAATGAAAAAGCAA
Found at i:4210864 original size:11 final size:11
Alignment explanation
Indices: 4210850--4210893 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
4210840 AAACAGAAGG
4210850 AAAACAACAAC
1 AAAACAACAAC
* *
4210861 AAAACAATGAAA
1 AAAACAA-CAAC
*
4210873 AAAATAACAAC
1 AAAACAACAAC
4210884 AAAACAACAA
1 AAAACAACAA
4210894 ATATTTTTTC
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
11 18 0.69
12 8 0.31
ACGTcount: A:0.75, C:0.18, G:0.02, T:0.05
Consensus pattern (11 bp):
AAAACAACAAC
Found at i:4210881 original size:20 final size:21
Alignment explanation
Indices: 4210835--4210882 Score: 53
Period size: 20 Copynumber: 2.3 Consensus size: 21
4210825 GGTGAAATAG
*
4210835 TAACAAAACAGAAGGAAAACAA
1 TAACAAAACA-AAGGAAAAAAA
* *
4210857 CAACAAAAC-AATGAAAAAAA
1 TAACAAAACAAAGGAAAAAAA
4210877 TAACAA
1 TAACAA
4210883 CAAAACAACA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 14 0.64
22 8 0.36
ACGTcount: A:0.71, C:0.15, G:0.08, T:0.06
Consensus pattern (21 bp):
TAACAAAACAAAGGAAAAAAA
Found at i:4211324 original size:62 final size:65
Alignment explanation
Indices: 4211181--4211336 Score: 209
Period size: 62 Copynumber: 2.5 Consensus size: 65
4211171 TCTATTTTTC
*
4211181 TTATTATTTTTATGAATATAAATAAAT--A-TAAAATAATATTTATTTTATTTTATTATTAATTT
1 TTATTA-TTTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTA-TTTATTATTAATTT
4211243 AT
64 AT
*
4211245 TTATTATTGTATGAATATAAATAAATAAATGTAAAATAATATTAATTTTA-TT-TT-TT-ATTTA
1 TTATTATTTTATGAATATAAATAAATAAAT-TAAAATAATATTAATTTTATTTATTATTAATTTA
4211306 T
65 T
*
4211307 TTATTATTTTATGAATATAGATAAATAAAT
1 TTATTATTTTATGAATATAAATAAATAAAT
4211337 AAATAAATAA
Statistics
Matches: 84, Mismatches: 4, Indels: 10
0.86 0.04 0.10
Matches are distributed among these distances:
62 34 0.40
63 21 0.25
64 8 0.10
65 3 0.04
67 18 0.21
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (65 bp):
TTATTATTTTATGAATATAAATAAATAAATTAAAATAATATTAATTTTATTTATTATTAATTTAT
Found at i:4231959 original size:20 final size:20
Alignment explanation
Indices: 4231934--4231981 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
4231924 TGTTTGTAGA
*
4231934 TTCATGAAGTTTAAAGTTGT
1 TTCATGAAGTTCAAAGTTGT
4231954 TTCATGAAGTTCAAAGTTGT
1 TTCATGAAGTTCAAAGTTGT
4231974 TTCATGAA
1 TTCATGAA
4231982 AAAAATAACC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.31, C:0.08, G:0.19, T:0.42
Consensus pattern (20 bp):
TTCATGAAGTTCAAAGTTGT
Found at i:4247467 original size:20 final size:20
Alignment explanation
Indices: 4247426--4247467 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
4247416 ATTGTATAAA
* *
4247426 AATTTCTATCTTTTTCTTTC
1 AATTTCTATCCTTATCTTTC
4247446 AATTTC-ATCCTTATCTTATC
1 AATTTCTATCCTTATCTT-TC
4247466 AA
1 AA
4247468 CTAATCACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
19 9 0.47
20 10 0.53
ACGTcount: A:0.24, C:0.21, G:0.00, T:0.55
Consensus pattern (20 bp):
AATTTCTATCCTTATCTTTC
Found at i:4256538 original size:13 final size:13
Alignment explanation
Indices: 4256502--4256539 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
4256492 TTAAATTTTA
*
4256502 TTTA-TTAATAAT
1 TTTATTTAATATT
*
4256514 TTAATTTAATATT
1 TTTATTTAATATT
4256527 TTTATTTAATATT
1 TTTATTTAATATT
4256540 ATACACATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 3 0.14
13 19 0.86
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (13 bp):
TTTATTTAATATT
Found at i:4258369 original size:21 final size:22
Alignment explanation
Indices: 4258329--4258391 Score: 76
Period size: 22 Copynumber: 2.9 Consensus size: 22
4258319 TAGTGTTATT
4258329 TTTTTACTGTTTTGGTTGCTAC
1 TTTTTACTGTTTTGGTTGCTAC
*
4258351 TTTTTACTGTTTTGG-TGCT-T
1 TTTTTACTGTTTTGGTTGCTAC
* *
4258371 TTTTTCACTATTTTGATTGCT
1 TTTTT-ACTGTTTTGGTTGCT
4258392 GTTGTAATGT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
20 5 0.14
21 12 0.33
22 19 0.53
ACGTcount: A:0.10, C:0.13, G:0.16, T:0.62
Consensus pattern (22 bp):
TTTTTACTGTTTTGGTTGCTAC
Found at i:4258427 original size:22 final size:22
Alignment explanation
Indices: 4258402--4258450 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
4258392 GTTGTAATGT
4258402 TTTTTTTACTGTTTTAGTGTTA
1 TTTTTTTACTGTTTTAGTGTTA
* * * * *
4258424 TTTTGTTATTTTTTTATTGTTG
1 TTTTTTTACTGTTTTAGTGTTA
4258446 TTTTT
1 TTTTT
4258451 GTTGCTATTT
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.10, C:0.02, G:0.12, T:0.76
Consensus pattern (22 bp):
TTTTTTTACTGTTTTAGTGTTA
Found at i:4258467 original size:21 final size:23
Alignment explanation
Indices: 4258441--4258495 Score: 78
Period size: 21 Copynumber: 2.5 Consensus size: 23
4258431 ATTTTTTTAT
4258441 TGTTGTTTTTGTTGCTA-TTTG-
1 TGTTGTTTTTGTTGCTATTTTGC
*
4258462 TGTTGTTTTTGTTGTTATTTTGC
1 TGTTGTTTTTGTTGCTATTTTGC
*
4258485 TGTTATTTTTG
1 TGTTGTTTTTG
4258496 CTGTTGTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
21 16 0.53
22 4 0.13
23 10 0.33
ACGTcount: A:0.05, C:0.04, G:0.22, T:0.69
Consensus pattern (23 bp):
TGTTGTTTTTGTTGCTATTTTGC
Found at i:4258477 original size:12 final size:12
Alignment explanation
Indices: 4258424--4258518 Score: 65
Period size: 12 Copynumber: 8.3 Consensus size: 12
4258414 TTTAGTGTTA
*
4258424 TTTTGTTATT-T
1 TTTTGTTGTTGT
*
4258435 TTTTATTGTTGT
1 TTTTGTTGTTGT
*
4258447 TTTTGTTG--CT
1 TTTTGTTGTTGT
*
4258457 ATTTG-TGTTGT
1 TTTTGTTGTTGT
*
4258468 TTTTGTTGTT-A
1 TTTTGTTGTTGT
* *
4258479 TTTTGCTGTTAT
1 TTTTGTTGTTGT
*
4258491 TTTTGCTGTTGT
1 TTTTGTTGTTGT
* *
4258503 TTTGGTTGTTAT
1 TTTTGTTGTTGT
4258515 TTTT
1 TTTT
4258519 ATACCTTTTT
Statistics
Matches: 64, Mismatches: 15, Indels: 9
0.73 0.17 0.10
Matches are distributed among these distances:
9 2 0.03
10 5 0.08
11 22 0.34
12 35 0.55
ACGTcount: A:0.06, C:0.03, G:0.19, T:0.72
Consensus pattern (12 bp):
TTTTGTTGTTGT
Found at i:4260333 original size:11 final size:11
Alignment explanation
Indices: 4260314--4260381 Score: 50
Period size: 11 Copynumber: 6.2 Consensus size: 11
4260304 TTTGCTGTTG
4260314 TTTTATTATTA
1 TTTTATTATTA
4260325 TTATT-TTA-TA
1 TT-TTATTATTA
**
4260335 GTTTTGCTATTA
1 -TTTTATTATTA
4260347 TTTTATTATTA
1 TTTTATTATTA
* * *
4260358 TATTGTAATTA
1 TTTTATTATTA
*
4260369 TTTTATTGTTA
1 TTTTATTATTA
4260380 TT
1 TT
4260382 GTTTAGATAT
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
10 4 0.09
11 35 0.81
12 4 0.09
ACGTcount: A:0.25, C:0.01, G:0.06, T:0.68
Consensus pattern (11 bp):
TTTTATTATTA
Found at i:4272129 original size:23 final size:23
Alignment explanation
Indices: 4272102--4272171 Score: 72
Period size: 23 Copynumber: 3.0 Consensus size: 23
4272092 ACTCAATCAA
4272102 TTAAATATTAATTTTAAATATAT
1 TTAAATATTAATTTTAAATATAT
*
4272125 TTAAATAATTAA-TATAAAT-TAT
1 TTAAAT-ATTAATTTTAAATATAT
*
4272147 TTATCAATTTTAATTTTAATATATA
1 TTA--AATATTAATTTTAA-ATATA
4272172 AATTATATTT
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
22 6 0.16
23 16 0.42
24 12 0.32
25 2 0.05
26 2 0.05
ACGTcount: A:0.47, C:0.01, G:0.00, T:0.51
Consensus pattern (23 bp):
TTAAATATTAATTTTAAATATAT
Found at i:4273105 original size:10 final size:10
Alignment explanation
Indices: 4273090--4273125 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
4273080 TTATTTTAAA
4273090 TTTTTACAAT
1 TTTTTACAAT
*
4273100 TTTTTAAAAT
1 TTTTTACAAT
4273110 TTTTTACAAT
1 TTTTTACAAT
4273120 TTTTTA
1 TTTTTA
4273126 ATTTTAAATC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.31, C:0.06, G:0.00, T:0.64
Consensus pattern (10 bp):
TTTTTACAAT
Found at i:4276961 original size:29 final size:30
Alignment explanation
Indices: 4276929--4277010 Score: 87
Period size: 30 Copynumber: 2.8 Consensus size: 30
4276919 TTTTAAGTCT
* *
4276929 CTTAAAAGTTGGTAAAAAAAATTAG-GACC
1 CTTAAAAGTTGATAAAAAAAATTAGAAACC
* * *
4276958 CTTAAAAATT-AAAAACAAAAATTTGAAACC
1 CTTAAAAGTTGATAAA-AAAAATTAGAAACC
*
4276988 TTTAAAAGTTGATAAAAAAAATT
1 CTTAAAAGTTGATAAAAAAAATT
4277011 GACTTGTAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
28 3 0.07
29 17 0.40
30 18 0.43
31 4 0.10
ACGTcount: A:0.55, C:0.09, G:0.10, T:0.27
Consensus pattern (30 bp):
CTTAAAAGTTGATAAAAAAAATTAGAAACC
Found at i:4277012 original size:29 final size:29
Alignment explanation
Indices: 4276902--4277012 Score: 84
Period size: 30 Copynumber: 3.8 Consensus size: 29
4276892 AGTAAAATAA
* * **
4276902 TAAAAGTTGA-AAAAAAATTTTAAGTCTCT
1 TAAAAGTTGATAAAAAAAATTGAAACCT-T
* * *
4276931 TAAAAGTTGGTAAAAAAAATT-AGGACCCT
1 TAAAAGTTGATAAAAAAAATTGA-AACCTT
* *
4276960 TAAAAATT-AAAAACAAAAATTTGAAACCTT
1 TAAAAGTTGATAAA-AAAAA-TTGAAACCTT
4276990 TAAAAGTTGATAAAAAAAATTGA
1 TAAAAGTTGATAAAAAAAATTGA
4277013 CTTGTAAAAA
Statistics
Matches: 63, Mismatches: 13, Indels: 12
0.72 0.15 0.14
Matches are distributed among these distances:
28 3 0.05
29 27 0.43
30 28 0.44
31 5 0.08
ACGTcount: A:0.54, C:0.07, G:0.11, T:0.28
Consensus pattern (29 bp):
TAAAAGTTGATAAAAAAAATTGAAACCTT
Found at i:4304499 original size:3 final size:3
Alignment explanation
Indices: 4304491--4304521 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
4304481 TATCTAGTTT
4304491 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
4304522 ATGAATTAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:4305002 original size:4 final size:4
Alignment explanation
Indices: 4304993--4305019 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
4304983 TTGTATCTAA
4304993 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
4305020 ATATATAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:4311317 original size:65 final size:65
Alignment explanation
Indices: 4311236--4311361 Score: 234
Period size: 65 Copynumber: 1.9 Consensus size: 65
4311226 GCAGGACAAC
*
4311236 CCTTTTAGCCCTTTCTTGTTCCTTTTTTGTGGTGAGGATCTTTCTTCATTAATAAGATTGGGTTA
1 CCTTTTAGCCCTTTCTTGTTCCTTATTTGTGGTGAGGATCTTTCTTCATTAATAAGATTGGGTTA
*
4311301 CCTTTTAGCCCTTTCTTGTTTCTTATTTGTGGTGAGGATCTTTCTTCATTAATAAGATTGG
1 CCTTTTAGCCCTTTCTTGTTCCTTATTTGTGGTGAGGATCTTTCTTCATTAATAAGATTGG
4311362 CTGTTCAAGA
Statistics
Matches: 59, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 59 1.00
ACGTcount: A:0.16, C:0.17, G:0.18, T:0.49
Consensus pattern (65 bp):
CCTTTTAGCCCTTTCTTGTTCCTTATTTGTGGTGAGGATCTTTCTTCATTAATAAGATTGGGTTA
Found at i:4325422 original size:35 final size:35
Alignment explanation
Indices: 4325366--4325439 Score: 80
Period size: 35 Copynumber: 2.1 Consensus size: 35
4325356 TAAGTAAATT
*
4325366 AATATATTTAAAATGAAAAATA-AAAATAATTATCA
1 AATACATTTAAAATGAAAAATACAAAA-AATTATCA
* * *
4325401 AATACATTTAAAAT-ATTAAATACTAAAAATTTTCA
1 AATACATTTAAAATGA-AAAATACAAAAAATTATCA
4325436 AATA
1 AATA
4325440 AACATTTTTA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
34 1 0.03
35 29 0.88
36 3 0.09
ACGTcount: A:0.59, C:0.05, G:0.01, T:0.34
Consensus pattern (35 bp):
AATACATTTAAAATGAAAAATACAAAAAATTATCA
Found at i:4330136 original size:2 final size:2
Alignment explanation
Indices: 4330129--4330175 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
4330119 CTATTTTACA
4330129 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4330171 A- AT AT
1 AT AT AT
4330176 TTAAAATAAA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 43 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4336196 original size:30 final size:27
Alignment explanation
Indices: 4336154--4336266 Score: 82
Period size: 30 Copynumber: 3.8 Consensus size: 27
4336144 TAAATTTTAA
*
4336154 AATTATACATAAACTTTGATTTAATGTGT
1 AATTATACATAAACTTTAATTT-A-GTGT
* *
4336183 AATATATATATAAATTTTAATTTAGTGT
1 AAT-TATACATAAACTTTAATTTAGTGT
* *
4336211 AATTATACACGTGAAACTTTAATTGTGGTTT
1 AATTATACA--T-AAACTTTAATT-TAGTGT
*
4336242 AAATATATACTTGAAACTTTAATTT
1 -AAT-TATACAT-AAACTTTAATTT
4336267 TGATTTAATC
Statistics
Matches: 69, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
27 5 0.07
28 7 0.10
29 5 0.07
30 27 0.39
31 17 0.25
32 3 0.04
33 5 0.07
ACGTcount: A:0.39, C:0.06, G:0.10, T:0.45
Consensus pattern (27 bp):
AATTATACATAAACTTTAATTTAGTGT
Found at i:4336259 original size:31 final size:31
Alignment explanation
Indices: 4336222--4336282 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
4336212 ATTATACACG
*
4336222 TGAAACTTTAATTGTGGTTTAAAT-ATATACT
1 TGAAACTTTAATTGTGATTT-AATCATATACT
*
4336253 TGAAACTTTAATTTTGATTTAATCATATAC
1 TGAAACTTTAATTGTGATTTAATCATATAC
4336283 ATTTAAAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 24 0.89
ACGTcount: A:0.36, C:0.08, G:0.10, T:0.46
Consensus pattern (31 bp):
TGAAACTTTAATTGTGATTTAATCATATACT
Found at i:4336709 original size:18 final size:17
Alignment explanation
Indices: 4336667--4336709 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
4336657 TTATTATTTT
4336667 TAATA-TATATTTTAAA
1 TAATACTATATTTTAAA
*
4336683 TAATTCTATATTATTAAA
1 TAATACTATATT-TTAAA
*
4336701 TCATACTAT
1 TAATACTAT
4336710 TACTCTTAAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 4 0.18
17 6 0.27
18 12 0.55
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (17 bp):
TAATACTATATTTTAAA
Found at i:4362669 original size:39 final size:39
Alignment explanation
Indices: 4362596--4362671 Score: 93
Period size: 39 Copynumber: 1.9 Consensus size: 39
4362586 ATGACAAGTA
* *
4362596 AATATTTAATTAATTTTTAAAATTTTCAAAATTAAAAAAG
1 AATATATAATTAATTTTTAAAA-TTTAAAAATTAAAAAAG
4362636 AATATATAATT-ATTTTTAAAA-TTAAAATCATTAAAA
1 AATATATAATTAATTTTTAAAATTTAAAA--ATTAAAA
4362672 TCATTAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
37 5 0.16
39 17 0.53
40 10 0.31
ACGTcount: A:0.54, C:0.03, G:0.01, T:0.42
Consensus pattern (39 bp):
AATATATAATTAATTTTTAAAATTTAAAAATTAAAAAAG
Found at i:4373383 original size:13 final size:13
Alignment explanation
Indices: 4373365--4373392 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4373355 TAGAGAAGGA
4373365 ATTATATTAGGTT
1 ATTATATTAGGTT
4373378 ATTATATTAGGTT
1 ATTATATTAGGTT
4373391 AT
1 AT
4373393 GACCCTTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.32, C:0.00, G:0.14, T:0.54
Consensus pattern (13 bp):
ATTATATTAGGTT
Found at i:4373487 original size:31 final size:30
Alignment explanation
Indices: 4373429--4373505 Score: 84
Period size: 31 Copynumber: 2.6 Consensus size: 30
4373419 GTAAAAAATA
*
4373429 ATAT-AAAATTTAAAATATATAACACTTAT
1 ATATAAAAATATAAAATATATAACACTTAT
* * * *
4373458 ATATATATATATAAACTATCATAATACTTAT
1 ATATAAAAATATAAAATAT-ATAACACTTAT
*
4373489 TTATAAAAATATAAAAT
1 ATATAAAAATATAAAAT
4373506 TTTATCATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
29 4 0.11
30 10 0.27
31 23 0.62
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (30 bp):
ATATAAAAATATAAAATATATAACACTTAT
Found at i:4373845 original size:4 final size:4
Alignment explanation
Indices: 4373836--4373867 Score: 55
Period size: 4 Copynumber: 8.0 Consensus size: 4
4373826 AGTAAAGATA
*
4373836 AAAT AAAT AAGT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4373868 TTCATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:4386557 original size:14 final size:14
Alignment explanation
Indices: 4386538--4386566 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
4386528 TGATGTTGTG
4386538 ATGTAAAAATAAAA
1 ATGTAAAAATAAAA
4386552 ATGTAAAAATAAAA
1 ATGTAAAAATAAAA
4386566 A
1 A
4386567 AGAGTAATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (14 bp):
ATGTAAAAATAAAA
Found at i:4387315 original size:16 final size:16
Alignment explanation
Indices: 4387296--4387330 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
4387286 TATATTTATA
4387296 TAATAATAA-CCTAAAT
1 TAATAA-AACCCTAAAT
4387312 TAATAAAACCCTAAAT
1 TAATAAAACCCTAAAT
4387328 TAA
1 TAA
4387331 AAAGAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 2 0.11
16 16 0.89
ACGTcount: A:0.57, C:0.14, G:0.00, T:0.29
Consensus pattern (16 bp):
TAATAAAACCCTAAAT
Found at i:4392875 original size:5 final size:5
Alignment explanation
Indices: 4392865--4392904 Score: 71
Period size: 5 Copynumber: 8.0 Consensus size: 5
4392855 CATTTCTTCC
*
4392865 CCCTT CCCTT CTCTT CCCTT CCCTT CCCTT CCCTT CCCTT
1 CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT CCCTT
4392905 GCATTCAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
5 33 1.00
ACGTcount: A:0.00, C:0.57, G:0.00, T:0.42
Consensus pattern (5 bp):
CCCTT
Found at i:4406270 original size:411 final size:411
Alignment explanation
Indices: 4405498--4406327 Score: 1464
Period size: 411 Copynumber: 2.0 Consensus size: 411
4405488 TGACTCTAAT
*
4405498 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTTGCCGAAATGTTATGATGATTAGAAG
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAATGTTATGATGATTAGAAG
* * * *
4405563 TCATAGTCTCCAATTTTTCAGAAAGTTGATCCCTCTCAAGTGTAACTGATTGAAGGTCTGCCTCA
66 TCATAGTCTCCAATTTTTCAGAAAGCTGATCCCTCTCAAGCGTAACTGATTGAAGATCAGCCTCA
4405628 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
131 AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
* *
4405693 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCCTCTGTAAATGCCCTCCCTAACC
196 ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTCCCTAACC
4405758 ATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
261 ATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
* * * *
4405823 TCCTCCCATTTTTGCACCAAGTGGCTCCTTTCCATTAAGGATTGTTCCAACAGTTCATTTTGTTC
326 TCCTCCCATTTTTGCACCAAGTGGATCCTATCCATTAAGGACTGTTCCAACAGTTCATTTCGTTC
**
4405888 TGCCAACCTATAAATTTTGCC
391 TGCCAACCTATAAAACTTGCC
4405909 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAA-GATTATGATGATTAGAA
1 CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAATG-TTATGATGATTAGAA
4405973 GTCATAGTCTCCAATTTTTCAGAAAGCTGATCCCTCTCAAGCGTAACTGATTGAAGATCAGCCTC
65 GTCATAGTCTCCAATTTTTCAGAAAGCTGATCCCTCTCAAGCGTAACTGATTGAAGATCAGCCTC
4406038 AAGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAA
130 AAGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAA
*
4406103 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTTCCTAAC
195 GATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTCCCTAAC
* * * *
4406168 CATTCAATCTTTTCTTCAGGTTCCATGGGTTGCATTTGTGAGGGCATGTTGATTCCATCCAAAAG
260 CATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAG
* *
4406233 TTCCTCCCATTTTTGCACCAAGTGGATCCTATCCATTAAGGACTGTTCCAGCATTTCATTTCGTT
325 TTCCTCCCATTTTTGCACCAAGTGGATCCTATCCATTAAGGACTGTTCCAACAGTTCATTTCGTT
4406298 CTGCCAACCTATAAAACTTGCC
390 CTGCCAACCTATAAAACTTGCC
4406320 CTGAAGGT
1 CTGAAGGT
4406328 CCTCATATTT
Statistics
Matches: 398, Mismatches: 20, Indels: 2
0.95 0.05 0.00
Matches are distributed among these distances:
410 1 0.00
411 397 1.00
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.34
Consensus pattern (411 bp):
CTGAAGGTTTTCATTCTCAACTTCAAAATGAGCTGCCTTCGCCGAAATGTTATGATGATTAGAAG
TCATAGTCTCCAATTTTTCAGAAAGCTGATCCCTCTCAAGCGTAACTGATTGAAGATCAGCCTCA
AGATCAGCTACTCTCTTTTCTGACTCCTCCAAATCAGCAGCTAGTGACCCATAATAATTTTCAAG
ATTATCAATCTTCTTCTGCAAAGAATTTCTTTCATGATTAGCATCTGTAAACGCCCTCCCTAACC
ATTCAATCTTTTCTTCAGGTTCCACGGATTGCATTTGTGAAGGCATGTCGATTCCATCCAAAAGT
TCCTCCCATTTTTGCACCAAGTGGATCCTATCCATTAAGGACTGTTCCAACAGTTCATTTCGTTC
TGCCAACCTATAAAACTTGCC
Found at i:4411971 original size:6 final size:6
Alignment explanation
Indices: 4411960--4411985 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
4411950 GTTTTTGTCT
4411960 GGATTG GGATTG GGATTG GGATTG GG
1 GGATTG GGATTG GGATTG GGATTG GG
4411986 TTAGTGTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.54, T:0.31
Consensus pattern (6 bp):
GGATTG
Found at i:4417576 original size:29 final size:30
Alignment explanation
Indices: 4417530--4417586 Score: 98
Period size: 29 Copynumber: 1.9 Consensus size: 30
4417520 GAATTAGATC
4417530 AAATCAAAATTTAATATATAAAATTACACA
1 AAATCAAAATTTAATATATAAAATTACACA
*
4417560 AAATCAAAATTT-ATATATACAATTACA
1 AAATCAAAATTTAATATATAAAATTACA
4417587 TATTAAACCA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
29 14 0.54
30 12 0.46
ACGTcount: A:0.58, C:0.11, G:0.00, T:0.32
Consensus pattern (30 bp):
AAATCAAAATTTAATATATAAAATTACACA
Found at i:4418619 original size:28 final size:31
Alignment explanation
Indices: 4418560--4418619 Score: 72
Period size: 33 Copynumber: 2.0 Consensus size: 31
4418550 TAAGTCATGT
*
4418560 AATATTTTTAATTCAAATAAAAATATATAGTTC
1 AATATTTTTAATT--AATAAAAATATACAGTTC
4418593 AATATTTTTAATT-A-AAAAATA-ACAGTT
1 AATATTTTTAATTAATAAAAATATACAGTT
4418620 TTTTAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
28 5 0.19
29 7 0.27
30 1 0.04
33 13 0.50
ACGTcount: A:0.50, C:0.05, G:0.03, T:0.42
Consensus pattern (31 bp):
AATATTTTTAATTAATAAAAATATACAGTTC
Found at i:4420059 original size:18 final size:19
Alignment explanation
Indices: 4420036--4420071 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
4420026 TTTAATTTTC
*
4420036 ATTTTT-AATGTTATATTA
1 ATTTTTAAATATTATATTA
4420054 ATTTTTAAATATTATATT
1 ATTTTTAAATATTATATT
4420072 TATTAAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 6 0.38
19 10 0.62
ACGTcount: A:0.36, C:0.00, G:0.03, T:0.61
Consensus pattern (19 bp):
ATTTTTAAATATTATATTA
Found at i:4420087 original size:16 final size:15
Alignment explanation
Indices: 4420048--4420089 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
4420038 TTTTAATGTT
4420048 ATATTA-ATTTTTAA
1 ATATTATATTTTTAA
4420062 ATATTATATTTATTAA
1 ATATTATATTT-TTAA
4420078 ATAATT-TATTTT
1 AT-ATTATATTTT
4420090 ATTTCGTACT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
14 6 0.24
15 5 0.20
16 11 0.44
17 3 0.12
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
ATATTATATTTTTAA
Found at i:4423415 original size:12 final size:12
Alignment explanation
Indices: 4423398--4423428 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
4423388 GAAGAAACCC
4423398 CATCATCATCGT
1 CATCATCATCGT
4423410 CATCATCATCGT
1 CATCATCATCGT
*
4423422 CTTCATC
1 CATCATC
4423429 TTCATTTTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.23, C:0.35, G:0.06, T:0.35
Consensus pattern (12 bp):
CATCATCATCGT
Found at i:4425431 original size:22 final size:20
Alignment explanation
Indices: 4425385--4425433 Score: 53
Period size: 22 Copynumber: 2.4 Consensus size: 20
4425375 AAATATTTGA
*
4425385 ATTAATAAAAATTTTGAAAT
1 ATTATTAAAAATTTTGAAAT
* *
4425405 TTTATTAATAAATTATTTAAAT
1 ATTATTAA-AAATT-TTGAAAT
4425427 ATTATTA
1 ATTATTA
4425434 TTCAAATTTA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
20 6 0.26
21 5 0.22
22 12 0.52
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (20 bp):
ATTATTAAAAATTTTGAAAT
Found at i:4426641 original size:9 final size:9
Alignment explanation
Indices: 4426627--4426654 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
4426617 ACCAAGATGA
4426627 TTTTCTTTC
1 TTTTCTTTC
4426636 TTTTCTTTC
1 TTTTCTTTC
4426645 TTTTCTTTC
1 TTTTCTTTC
4426654 T
1 T
4426655 CAAGTATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (9 bp):
TTTTCTTTC
Found at i:4434402 original size:29 final size:27
Alignment explanation
Indices: 4434357--4434412 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 27
4434347 TAATAAATTA
*
4434357 TAAAATAATGAGTAA-TTAAGTTTTTAT
1 TAAAATAATGAGCAATTTAA-TTTTTAT
4434384 TAAAATAAATGATGCAATTTAATTTTTAT
1 TAAAAT-AATGA-GCAATTTAATTTTTAT
4434413 AGTAGTGGAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
27 6 0.24
28 5 0.20
29 10 0.40
30 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (27 bp):
TAAAATAATGAGCAATTTAATTTTTAT
Found at i:4437752 original size:41 final size:41
Alignment explanation
Indices: 4437695--4437789 Score: 163
Period size: 41 Copynumber: 2.3 Consensus size: 41
4437685 AATTGAGGGT
4437695 TGTCTTTGGATCAGTTATTTTAGGTGGAAGAGATAGTTGGA
1 TGTCTTTGGATCAGTTATTTTAGGTGGAAGAGATAGTTGGA
* *
4437736 TGTCTTTGGATCAGTTATTTTAGGTGGAAGAGATGGTTGGG
1 TGTCTTTGGATCAGTTATTTTAGGTGGAAGAGATAGTTGGA
*
4437777 TGTCTTCGGATCA
1 TGTCTTTGGATCA
4437790 TGGGATGTTT
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.21, C:0.07, G:0.33, T:0.39
Consensus pattern (41 bp):
TGTCTTTGGATCAGTTATTTTAGGTGGAAGAGATAGTTGGA
Found at i:4443557 original size:2 final size:2
Alignment explanation
Indices: 4443552--4443584 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
4443542 ACAAGCACAC
4443552 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
4443585 AATAAATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:4444606 original size:16 final size:15
Alignment explanation
Indices: 4444585--4444614 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
4444575 AAAAATATTG
4444585 TTTTCTTTTTCTTTTC
1 TTTTCTTTTT-TTTTC
4444601 TTTTCTTTTTTTTT
1 TTTTCTTTTTTTTT
4444615 AACTTTAAGC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTTTTTTC
Found at i:4448849 original size:11 final size:11
Alignment explanation
Indices: 4448833--4448871 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
4448823 ATCCAGAGTG
4448833 AATGCAACTCC
1 AATGCAACTCC
* *
4448844 AATGCAAAT-T
1 AATGCAACTCC
4448854 AATGCAACTCC
1 AATGCAACTCC
4448865 AATGCAA
1 AATGCAA
4448872 ATTTAAATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
10 8 0.35
11 15 0.65
ACGTcount: A:0.44, C:0.26, G:0.10, T:0.21
Consensus pattern (11 bp):
AATGCAACTCC
Found at i:4448858 original size:21 final size:21
Alignment explanation
Indices: 4448833--4448874 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
4448823 ATCCAGAGTG
4448833 AATGCAACTCCAATGCAAATT
1 AATGCAACTCCAATGCAAATT
4448854 AATGCAACTCCAATGCAAATT
1 AATGCAACTCCAATGCAAATT
4448875 TAAATTTCTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.24, G:0.10, T:0.24
Consensus pattern (21 bp):
AATGCAACTCCAATGCAAATT
Found at i:4451724 original size:24 final size:24
Alignment explanation
Indices: 4451697--4451776 Score: 99
Period size: 24 Copynumber: 3.3 Consensus size: 24
4451687 CTCTGTCCCC
*
4451697 GCCTTTTGCTCTGCTTCTGCT-TCT
1 GCCTTTTGCTCTGCCTCTG-TATCT
* *
4451721 GCCTTTGGCTCTGCCTCTGTCTCT
1 GCCTTTTGCTCTGCCTCTGTATCT
*
4451745 GTCTTTTGCTCTGCCTCTGTATCT
1 GCCTTTTGCTCTGCCTCTGTATCT
*
4451769 GTCTTTTG
1 GCCTTTTG
4451777 TTCCACCTCT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
23 1 0.02
24 49 0.98
ACGTcount: A:0.01, C:0.31, G:0.19, T:0.49
Consensus pattern (24 bp):
GCCTTTTGCTCTGCCTCTGTATCT
Found at i:4451733 original size:12 final size:12
Alignment explanation
Indices: 4451697--4451760 Score: 51
Period size: 12 Copynumber: 5.3 Consensus size: 12
4451687 CTCTGTCCCC
*
4451697 GCCTTTTGCTCT
1 GCCTTTGGCTCT
4451709 G-CTTCT-GCTTCT
1 GCCTT-TGGC-TCT
4451721 GCCTTTGGCTCT
1 GCCTTTGGCTCT
* *
4451733 GCCTCTGTCTCT
1 GCCTTTGGCTCT
* *
4451745 GTCTTTTGCTCT
1 GCCTTTGGCTCT
4451757 GCCT
1 GCCT
4451761 CTGTATCTGT
Statistics
Matches: 41, Mismatches: 7, Indels: 8
0.73 0.12 0.14
Matches are distributed among these distances:
11 5 0.12
12 31 0.76
13 5 0.12
ACGTcount: A:0.00, C:0.34, G:0.19, T:0.47
Consensus pattern (12 bp):
GCCTTTGGCTCT
Found at i:4451757 original size:48 final size:48
Alignment explanation
Indices: 4451685--4451798 Score: 131
Period size: 48 Copynumber: 2.4 Consensus size: 48
4451675 AACATTTGCT
* * * * *
4451685 ACCTCTGTCCCCGCCTTTTGCTCTGCTTCTGCT-TCTGCCTTTGGCTCT
1 ACCTCTGTCTCTGTCTTTTGCTCTGCCTCTG-TATCTGCCTTTGGCTCC
* * * *
4451733 GCCTCTGTCTCTGTCTTTTGCTCTGCCTCTGTATCTGTCTTTTGTTCC
1 ACCTCTGTCTCTGTCTTTTGCTCTGCCTCTGTATCTGCCTTTGGCTCC
4451781 ACCTCTGTCTCTGTCTTT
1 ACCTCTGTCTCTGTCTTT
4451799 GGCCCTGGCT
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.02
48 54 0.98
ACGTcount: A:0.03, C:0.35, G:0.16, T:0.46
Consensus pattern (48 bp):
ACCTCTGTCTCTGTCTTTTGCTCTGCCTCTGTATCTGCCTTTGGCTCC
Found at i:4451785 original size:24 final size:24
Alignment explanation
Indices: 4451734--4451798 Score: 94
Period size: 24 Copynumber: 2.7 Consensus size: 24
4451724 TTTGGCTCTG
**
4451734 CCTCTGTCTCTGTCTTTTGCTCTG
1 CCTCTGTCTCTGTCTTTTGCTCCA
* *
4451758 CCTCTGTATCTGTCTTTTGTTCCA
1 CCTCTGTCTCTGTCTTTTGCTCCA
4451782 CCTCTGTCTCTGTCTTT
1 CCTCTGTCTCTGTCTTT
4451799 GGCCCTGGCT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.03, C:0.32, G:0.14, T:0.51
Consensus pattern (24 bp):
CCTCTGTCTCTGTCTTTTGCTCCA
Found at i:4451860 original size:24 final size:25
Alignment explanation
Indices: 4451809--4451872 Score: 69
Period size: 24 Copynumber: 2.6 Consensus size: 25
4451799 GGCCCTGGCT
* *
4451809 TTTGCTGTGCCTCT-GTCTCTACCT
1 TTTGCTCTGCCTCTGGTCTCTACCC
* *
4451833 TTTGGTCTGCCTCTGGT-TCTGCCC
1 TTTGCTCTGCCTCTGGTCTCTACCC
*
4451857 TTTGCTCTGTCTCTGG
1 TTTGCTCTGCCTCTGG
4451873 CTTTGCGTCT
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
24 31 0.94
25 2 0.06
ACGTcount: A:0.02, C:0.31, G:0.22, T:0.45
Consensus pattern (25 bp):
TTTGCTCTGCCTCTGGTCTCTACCC
Found at i:4452248 original size:18 final size:18
Alignment explanation
Indices: 4452227--4452263 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
4452217 ACTGACTCTG
4452227 AGGCTCGGGCTCAGTCTC
1 AGGCTCGGGCTCAGTCTC
* *
4452245 AGGCTCTGTCTCAGTCTC
1 AGGCTCGGGCTCAGTCTC
4452263 A
1 A
4452264 CTATGTTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.14, C:0.32, G:0.27, T:0.27
Consensus pattern (18 bp):
AGGCTCGGGCTCAGTCTC
Found at i:4464337 original size:18 final size:19
Alignment explanation
Indices: 4464311--4464349 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
4464301 ACTATTTTAG
4464311 TTTCCCTTTTA-TTTATTT
1 TTTCCCTTTTATTTTATTT
*
4464329 TTTCTCTTTTATTTTATTT
1 TTTCCCTTTTATTTTATTT
4464348 TT
1 TT
4464350 ATACCTCTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.10, C:0.13, G:0.00, T:0.77
Consensus pattern (19 bp):
TTTCCCTTTTATTTTATTT
Found at i:4464736 original size:22 final size:20
Alignment explanation
Indices: 4464710--4464752 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 20
4464700 ATAAATTTTG
4464710 AAATAAAATATAAAATTCTTAA
1 AAATAAAA-ATAAAATT-TTAA
*
4464732 AAATAAAAATTAAATTTTAA
1 AAATAAAAATAAAATTTTAA
4464752 A
1 A
4464753 TTTTAAATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 5 0.25
21 7 0.35
22 8 0.40
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (20 bp):
AAATAAAAATAAAATTTTAA
Found at i:4477200 original size:20 final size:19
Alignment explanation
Indices: 4477167--4477205 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 19
4477157 CGAATAATTT
4477167 TTTCTCATATTCAAATATAA
1 TTTCTCATATTCAAA-ATAA
4477187 TTTCATCATA-TCAAAATAA
1 TTTC-TCATATTCAAAATAA
4477206 AATTTGGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.22
20 9 0.50
21 5 0.28
ACGTcount: A:0.44, C:0.15, G:0.00, T:0.41
Consensus pattern (19 bp):
TTTCTCATATTCAAAATAA
Found at i:4477209 original size:21 final size:20
Alignment explanation
Indices: 4477167--4477210 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 20
4477157 CGAATAATTT
*
4477167 TTTCTCATATTCAAATATAA
1 TTTCTCATATTCAAATAAAA
4477187 TTTCATCATA-TCAAAATAAAA
1 TTTC-TCATATTC-AAATAAAA
4477208 TTT
1 TTT
4477211 GGATAGGAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 6 0.29
21 15 0.71
ACGTcount: A:0.43, C:0.14, G:0.00, T:0.43
Consensus pattern (20 bp):
TTTCTCATATTCAAATAAAA
Found at i:4486025 original size:2 final size:2
Alignment explanation
Indices: 4486018--4486042 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4486008 AAAGATTCTA
4486018 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4486043 ATGTGGAATG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4499011 original size:12 final size:12
Alignment explanation
Indices: 4498994--4499029 Score: 63
Period size: 12 Copynumber: 3.0 Consensus size: 12
4498984 ATAGTCGTAG
*
4498994 TCATCATAGTCA
1 TCATCATAATCA
4499006 TCATCATAATCA
1 TCATCATAATCA
4499018 TCATCATAATCA
1 TCATCATAATCA
4499030 ATTCCATAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.39, C:0.25, G:0.03, T:0.33
Consensus pattern (12 bp):
TCATCATAATCA
Found at i:4500130 original size:28 final size:28
Alignment explanation
Indices: 4500086--4500147 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 28
4500076 TTCAATTAAA
4500086 ATAA-ATTATTAATATAATTAT-TTATAT
1 ATAATATTATTAATATAATTATATT-TAT
4500113 ATAATATTATGTAA-ATAATTATATTTAT
1 ATAATATTAT-TAATATAATTATATTTAT
*
4500141 TTAATAT
1 ATAATAT
4500148 AAAAATTATA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 4 0.13
28 22 0.71
29 5 0.16
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.52
Consensus pattern (28 bp):
ATAATATTATTAATATAATTATATTTAT
Found at i:4507099 original size:14 final size:14
Alignment explanation
Indices: 4507080--4507111 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
4507070 AAATTAATAA
4507080 AATAATATATTTAT
1 AATAATATATTTAT
4507094 AATAATATATTTAT
1 AATAATATATTTAT
4507108 AATA
1 AATA
4507112 CGTGAGAGAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
AATAATATATTTAT
Found at i:4518230 original size:56 final size:56
Alignment explanation
Indices: 4518136--4518244 Score: 182
Period size: 56 Copynumber: 1.9 Consensus size: 56
4518126 CTTTTAAGCA
*
4518136 TGTCAAATGGCACAATGTCGAAAATGACACTGACCCTTCCATCACCAATCCATAGT
1 TGTCAAATGGCACAATGTCGAAAATGACACAGACCCTTCCATCACCAATCCATAGT
* * *
4518192 TGTCAAATGGCACAATGTCGTAAATGACACAGATCCTTCCATCACCGATCCAT
1 TGTCAAATGGCACAATGTCGAAAATGACACAGACCCTTCCATCACCAATCCAT
4518245 GATTTGGTTA
Statistics
Matches: 49, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
56 49 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.24
Consensus pattern (56 bp):
TGTCAAATGGCACAATGTCGAAAATGACACAGACCCTTCCATCACCAATCCATAGT
Found at i:4518534 original size:2 final size:2
Alignment explanation
Indices: 4518519--4518552 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
4518509 AATATCCAAC
4518519 TA TA TA -A TA T- TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4518553 AAGCAAGATT
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4527449 original size:11 final size:11
Alignment explanation
Indices: 4527435--4527465 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
4527425 TTAATTTATT
*
4527435 AATAAAATTAA
1 AATATAATTAA
4527446 AATATAATTAA
1 AATATAATTAA
4527457 AATATAATT
1 AATATAATT
4527466 TTGTTTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATAATTAA
Found at i:4533030 original size:23 final size:23
Alignment explanation
Indices: 4532999--4533062 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 23
4532989 AGTTTTTATC
4532999 TGCCTTTGTGGCACGCTTTTTCTT
1 TGCC-TTGTGGCACGCTTTTTCTT
*
4533023 TGCCTTGTGGCACGCGTTTTCTT
1 TGCCTTGTGGCACGCTTTTTCTT
*
4533046 TGCCTTGTGACACGCTT
1 TGCCTTGTGGCACGCTT
4533063 CTGCCTTATG
Statistics
Matches: 37, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
23 33 0.89
24 4 0.11
ACGTcount: A:0.06, C:0.27, G:0.23, T:0.44
Consensus pattern (23 bp):
TGCCTTGTGGCACGCTTTTTCTT
Found at i:4534401 original size:153 final size:153
Alignment explanation
Indices: 4534123--4534430 Score: 598
Period size: 153 Copynumber: 2.0 Consensus size: 153
4534113 AAGATGTAAA
*
4534123 ACTGTCACGTGCTTCTTTCCAATTTCTTTACAAAATTGTTTATGGACTGCCCTTAAAACTAGGAA
1 ACTGTCACGTGCTTCTTTCCAATTTCTTTACAAAATTGTTTACGGACTGCCCTTAAAACTAGGAA
4534188 AATTGAACGTTTTACATATATGTATACATATAATAACTACTTTACAACTATGAGTAATTTTAGAC
66 AATTGAACGTTTTACATATATGTATACATATAATAACTACTTTACAACTATGAGTAATTTTAGAC
4534253 TAACAGATACAAATGAAATATCG
131 TAACAGATACAAATGAAATATCG
4534276 ACTGTCACGTGCTTCTTTCCAATTTCTTTACAAAATTGTTTACGGACTGCCCTTAAAACTAGGAA
1 ACTGTCACGTGCTTCTTTCCAATTTCTTTACAAAATTGTTTACGGACTGCCCTTAAAACTAGGAA
*
4534341 AATTGAACGTTTTACATATATGTATACATATAATAACTCCTTTACAACTATGAGTAATTTTAGAC
66 AATTGAACGTTTTACATATATGTATACATATAATAACTACTTTACAACTATGAGTAATTTTAGAC
4534406 TAACAGATACAAATGAAATATCG
131 TAACAGATACAAATGAAATATCG
4534429 AC
1 AC
4534431 CATCCATTTA
Statistics
Matches: 153, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
153 153 1.00
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (153 bp):
ACTGTCACGTGCTTCTTTCCAATTTCTTTACAAAATTGTTTACGGACTGCCCTTAAAACTAGGAA
AATTGAACGTTTTACATATATGTATACATATAATAACTACTTTACAACTATGAGTAATTTTAGAC
TAACAGATACAAATGAAATATCG
Found at i:4553163 original size:30 final size:30
Alignment explanation
Indices: 4553095--4553198 Score: 93
Period size: 30 Copynumber: 3.5 Consensus size: 30
4553085 CAAAACATAG
* * *
4553095 TTCGTGCAAATGCAGCTCGTGTGACCTGC-C
1 TTCGTGTAAATGCAGCTCGTGCGA-CTGCAA
* * *
4553125 TTCTTGTAAATGCAGTTCGTGCGATTGCAA
1 TTCGTGTAAATGCAGCTCGTGCGACTGCAA
** * *
4553155 TTCGTGTAAATATAGCTCGTGCGACTGTAG
1 TTCGTGTAAATGCAGCTCGTGCGACTGCAA
*
4553185 TTTGTGTAAATGCA
1 TTCGTGTAAATGCA
4553199 ACAGTTTATG
Statistics
Matches: 57, Mismatches: 16, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
29 3 0.05
30 54 0.95
ACGTcount: A:0.22, C:0.19, G:0.25, T:0.34
Consensus pattern (30 bp):
TTCGTGTAAATGCAGCTCGTGCGACTGCAA
Found at i:4553953 original size:33 final size:33
Alignment explanation
Indices: 4553911--4553978 Score: 127
Period size: 33 Copynumber: 2.1 Consensus size: 33
4553901 TAAAATATTT
4553911 TTTTACACAGTTTCATCCAAACACCAAAAAATA
1 TTTTACACAGTTTCATCCAAACACCAAAAAATA
*
4553944 TTTTACACAGTTTCATCCAAACACCAAAAATTA
1 TTTTACACAGTTTCATCCAAACACCAAAAAATA
4553977 TT
1 TT
4553979 AACTTTTCCA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.43, C:0.24, G:0.03, T:0.31
Consensus pattern (33 bp):
TTTTACACAGTTTCATCCAAACACCAAAAAATA
Found at i:4554015 original size:14 final size:14
Alignment explanation
Indices: 4553996--4554034 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
4553986 CCAGAAAAAT
4553996 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
4554010 AAATCATTTTCCGG
1 AAATCATTTTCCAG
*
4554024 AAACCATTTTC
1 AAATCATTTTC
4554035 AATCAAACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.33, C:0.23, G:0.08, T:0.36
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:4580220 original size:6 final size:6
Alignment explanation
Indices: 4580176--4580218 Score: 68
Period size: 6 Copynumber: 7.2 Consensus size: 6
4580166 GCTATATGTT
* *
4580176 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTTCC CATCCC C
1 CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC CTTCCC C
4580219 ATTCATTGCA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.02, C:0.65, G:0.00, T:0.33
Consensus pattern (6 bp):
CTTCCC
Found at i:4581710 original size:14 final size:14
Alignment explanation
Indices: 4581688--4581733 Score: 58
Period size: 14 Copynumber: 3.2 Consensus size: 14
4581678 ATGAGAAGAC
*
4581688 AATAAAAATTCTTA
1 AATATAAATTCTTA
4581702 AATATAAATT-TAATA
1 AATATAAATTCT--TA
4581717 AATATAAATTCTTA
1 AATATAAATTCTTA
4581731 AAT
1 AAT
4581734 GTATGTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 1 0.04
14 14 0.50
15 12 0.43
16 1 0.04
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (14 bp):
AATATAAATTCTTA
Found at i:4586317 original size:14 final size:15
Alignment explanation
Indices: 4586285--4586316 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
4586275 ATATTAAAAA
*
4586285 TTTAATATGTATTTT
1 TTTAATATTTATTTT
4586300 TTTAATATTTATTTT
1 TTTAATATTTATTTT
4586315 TT
1 TT
4586317 ACTATTTTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.25, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TTTAATATTTATTTT
Found at i:4586327 original size:15 final size:14
Alignment explanation
Indices: 4586285--4586323 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
4586275 ATATTAAAAA
*
4586285 TTTAATATGTATTTT
1 TTTAATATTTA-TTT
4586300 TTTAATATTTATTT
1 TTTAATATTTATTT
*
4586314 TTTACTATTT
1 TTTAATATTT
4586324 TATTATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
14 12 0.55
15 10 0.45
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.69
Consensus pattern (14 bp):
TTTAATATTTATTT
Found at i:4586775 original size:31 final size:30
Alignment explanation
Indices: 4586751--4586808 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
4586741 ATTTGTTCTT
* *
4586751 TTTCCATTAGATAAGTTGTCAATTTTAATCA
1 TTTCCATTAGATAAATTATCAATTTT-ATCA
4586782 TTTCCATTAGATAAATTATCAATTTTA
1 TTTCCATTAGATAAATTATCAATTTTA
4586809 GTTAATCTAC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 1 0.04
31 24 0.96
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (30 bp):
TTTCCATTAGATAAATTATCAATTTTATCA
Found at i:4586966 original size:15 final size:16
Alignment explanation
Indices: 4586929--4586968 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
4586919 TTAAACCCCT
*
4586929 TTAAAATTTATAAAAA
1 TTAAAATTAATAAAAA
*
4586945 TTTAAATTAATAAAAA
1 TTAAAATTAATAAAAA
4586961 -TAAAATTA
1 TTAAAATTA
4586969 TACTTTATCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 7 0.33
16 14 0.67
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (16 bp):
TTAAAATTAATAAAAA
Found at i:4589636 original size:2 final size:2
Alignment explanation
Indices: 4589629--4589656 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
4589619 TAGTATTCAA
4589629 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4589657 GTGAAGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4590343 original size:126 final size:126
Alignment explanation
Indices: 4590196--4590588 Score: 714
Period size: 126 Copynumber: 3.1 Consensus size: 126
4590186 AACATTTGTT
*
4590196 TTTTTTTTTTGAATTACAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGAAT
1 TTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGAAT
*
4590261 CCAAAATATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
66 CCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
4590322 TTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGAAT
1 TTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGAAT
4590387 CCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
66 CCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
4590448 TTTTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
1 --TTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
* * *
4590513 ATCTAAATTATATTTGAAACAGTAAACACTTAATTATCAAGTCAACACAAGAAATTCAGAACA
64 ATCCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
4590576 TTTGTTTTTTTGA
1 TTT-TTTTTTTGA
4590589 GTTAAAAAGT
Statistics
Matches: 259, Mismatches: 5, Indels: 5
0.96 0.02 0.02
Matches are distributed among these distances:
126 127 0.49
127 9 0.03
128 123 0.47
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (126 bp):
TTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGAAT
CCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
Found at i:4590521 original size:128 final size:128
Alignment explanation
Indices: 4590194--4590586 Score: 718
Period size: 128 Copynumber: 3.1 Consensus size: 128
4590184 ACAACATTTG
*
4590194 TTTTTTTTTTTTGAATTACAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
1 TTTTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
*
4590259 ATCCAAAATATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
66 ATCCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
4590322 --TTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
1 TTTTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
4590385 ATCCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
66 ATCCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
4590448 TTTTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
1 TTTTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
* * *
4590513 ATCTAAATTATATTTGAAACAGTAAACACTTAATTATCAAGTCAACACAAGAAATTCAGAACA
66 ATCCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
*
4590576 TTTGTTTTTTT
1 TTTTTTTTTTT
4590587 GAGTTAAAAA
Statistics
Matches: 257, Mismatches: 6, Indels: 4
0.96 0.02 0.01
Matches are distributed among these distances:
126 124 0.48
128 133 0.52
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.33
Consensus pattern (128 bp):
TTTTTTTTTTTTGAATTATAATATGAGGGTAAAATTCTAATAGCAACGTGACTAGTGCGACTCGA
ATCCAAATTATATTTGAGACAGTAAACACTTAATCATCAAGTCAACACAAGAAATTCAGAACA
Found at i:4592689 original size:29 final size:29
Alignment explanation
Indices: 4592635--4592700 Score: 71
Period size: 28 Copynumber: 2.3 Consensus size: 29
4592625 TATATATCAG
* **
4592635 TTTTGATTTAATGAATTATATGCAT-AAA
1 TTTTAATTTAATGAATTATACACATAAAA
*
4592663 TTTTAATTTGATGTAATTATACACATAAAA
1 TTTTAATTTAATG-AATTATACACATAAAA
*
4592693 CTTTAATT
1 TTTTAATT
4592701 GCGATTTAAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
28 11 0.35
29 10 0.32
30 10 0.32
ACGTcount: A:0.39, C:0.06, G:0.08, T:0.47
Consensus pattern (29 bp):
TTTTAATTTAATGAATTATACACATAAAA
Found at i:4615441 original size:2 final size:2
Alignment explanation
Indices: 4615434--4615486 Score: 106
Period size: 2 Copynumber: 26.5 Consensus size: 2
4615424 ATTATAGCTA
4615434 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
4615476 TC TC TC TC TC T
1 TC TC TC TC TC T
4615487 TTTCTTTTCT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:4616431 original size:8 final size:7
Alignment explanation
Indices: 4616414--4616445 Score: 55
Period size: 7 Copynumber: 4.4 Consensus size: 7
4616404 GTGTGCCTTG
4616414 AAAAAGA
1 AAAAAGA
4616421 AAAAAGA
1 AAAAAGA
4616428 AAAAAGGA
1 AAAAA-GA
4616436 AAAAAGA
1 AAAAAGA
4616443 AAA
1 AAA
4616446 GTTGGAGTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 17 0.71
8 7 0.29
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:4616437 original size:15 final size:14
Alignment explanation
Indices: 4616414--4616445 Score: 55
Period size: 15 Copynumber: 2.2 Consensus size: 14
4616404 GTGTGCCTTG
4616414 AAAAAGAAAAAAGA
1 AAAAAGAAAAAAGA
4616428 AAAAAGGAAAAAAGA
1 AAAAA-GAAAAAAGA
4616443 AAA
1 AAA
4616446 GTTGGAGTGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAGA
Found at i:4623066 original size:33 final size:32
Alignment explanation
Indices: 4622995--4623072 Score: 86
Period size: 33 Copynumber: 2.4 Consensus size: 32
4622985 AGTTAAACTG
* * * *
4622995 TATTTTATTTTTTAATTCAAAAATAGATAAAT
1 TATTTTATATATTAAATCAAAAATAAATAAAT
*
4623027 TAATTTTATATATTAAATCAAATAATAAATTAAT
1 T-ATTTTATATATTAAATCAAA-AATAAATAAAT
4623061 TATTTTA-ATATT
1 TATTTTATATATT
4623073 TTTTATCAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
32 6 0.15
33 23 0.59
34 10 0.26
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (32 bp):
TATTTTATATATTAAATCAAAAATAAATAAAT
Done.