Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167960.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_22, whole genome shotgun sequence
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: 19587844
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 68000 characters in sequence are not A, C, G, or T
File 29 of 105
Found at i:5817866 original size:19 final size:19
Alignment explanation
Indices: 5817838--5817876 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5817828 TTCCAGATTC
5817838 AGTTGAATTTTTCGACGAA
1 AGTTGAATTTTTCGACGAA
*
5817857 AGTTGTATTTTTCGACGAA
1 AGTTGAATTTTTCGACGAA
5817876 A
1 A
5817877 ATTTCGGCCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.31, C:0.10, G:0.21, T:0.38
Consensus pattern (19 bp):
AGTTGAATTTTTCGACGAA
Found at i:5818344 original size:8 final size:8
Alignment explanation
Indices: 5818331--5818375 Score: 54
Period size: 8 Copynumber: 5.4 Consensus size: 8
5818321 GCTTCAGGTT
5818331 TTTTTTTA
1 TTTTTTTA
5818339 TTTTTTTA
1 TTTTTTTA
*
5818347 TTTGTTTTT
1 TTT-TTTTA
5818356 TTTTATTTA
1 TTTT-TTTA
*
5818365 TTTCTTTA
1 TTTTTTTA
5818373 TTT
1 TTT
5818376 ATTAGATTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
8 19 0.59
9 13 0.41
ACGTcount: A:0.11, C:0.02, G:0.02, T:0.84
Consensus pattern (8 bp):
TTTTTTTA
Found at i:5818376 original size:12 final size:11
Alignment explanation
Indices: 5818332--5818378 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
5818322 CTTCAGGTTT
*
5818332 TTTTTTATTTT
1 TTTTTTATTTA
*
5818343 TTTATTTGTTT-
1 TTT-TTTATTTA
5818354 TTTTTTATTTA
1 TTTTTTATTTA
5818365 TTTCTTTATTTA
1 TTT-TTTATTTA
5818377 TT
1 TT
5818379 AGATTAGGTT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
10 6 0.19
11 9 0.29
12 16 0.52
ACGTcount: A:0.13, C:0.02, G:0.02, T:0.83
Consensus pattern (11 bp):
TTTTTTATTTA
Found at i:5818422 original size:6 final size:6
Alignment explanation
Indices: 5818401--5818477 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
5818391 TTTGATATTC
* * * * *
5818401 TTTTTA TCTTTA -TTTTA TTTTTA TTTTT- GTTTTA CTTTTC TTTATA
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA
* *
5818447 -TTTTA TTTTTA --TTTA TTTTCA CTTTTA TTTT
1 TTTTTA TTTTTA TTTTTA TTTTTA TTTTTA TTTT
5818478 GTTTCATTAT
Statistics
Matches: 53, Mismatches: 13, Indels: 10
0.70 0.17 0.13
Matches are distributed among these distances:
4 4 0.08
5 12 0.23
6 37 0.70
ACGTcount: A:0.16, C:0.06, G:0.01, T:0.77
Consensus pattern (6 bp):
TTTTTA
Found at i:5818423 original size:17 final size:16
Alignment explanation
Indices: 5818387--5818477 Score: 76
Period size: 17 Copynumber: 5.5 Consensus size: 16
5818377 TTAGATTAGG
* * *
5818387 TTTATTTGATATTCTT
1 TTTATTTTATTTTATT
5818403 TTTATCTTTATTTTATT
1 TTTAT-TTTATTTTATT
* *
5818420 TTTATTTTTGTTTTACT
1 TTTA-TTTTATTTTATT
*
5818437 TTTCTTTATATTTTATT
1 TTTATTT-TATTTTATT
*
5818454 TTTA-TTTATTTTCACT
1 TTTATTTTATTTT-ATT
5818470 TTTATTTT
1 TTTATTTT
5818478 GTTTCATTAT
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
15 6 0.10
16 16 0.27
17 37 0.62
18 1 0.02
ACGTcount: A:0.16, C:0.07, G:0.02, T:0.75
Consensus pattern (16 bp):
TTTATTTTATTTTATT
Found at i:5818433 original size:11 final size:11
Alignment explanation
Indices: 5818329--5818477 Score: 76
Period size: 11 Copynumber: 13.4 Consensus size: 11
5818319 CCGCTTCAGG
5818329 TTTTT-TTTTA
1 TTTTTATTTTA
* *
5818339 TTTTTTTATTTG
1 TTTTTAT-TTTA
5818351 TTTTT-TTTTA
1 TTTTTATTTTA
5818361 TTTATT-TCTTTA
1 TTT-TTAT-TTTA
**
5818373 TTTATTAGATTA
1 TTT-TTATTTTA
** *
5818385 GGTTTATTTGA
1 TTTTTATTTTA
*
5818396 TATTCT-TTTTA
1 T-TTTTATTTTA
*
5818407 TCTTTATTTTA
1 TTTTTATTTTA
5818418 TTTTTATTTT-
1 TTTTTATTTTA
*
5818428 TGTTTTACTTTTC
1 T-TTTTA-TTTTA
*
5818441 TTTATATTTTA
1 TTTTTATTTTA
5818452 TTTTTA-TTTA
1 TTTTTATTTTA
*
5818462 TTTTCACTTTTA
1 TTTTTA-TTTTA
5818474 TTTT
1 TTTT
5818478 GTTTCATTAT
Statistics
Matches: 107, Mismatches: 20, Indels: 22
0.72 0.13 0.15
Matches are distributed among these distances:
10 23 0.21
11 43 0.40
12 40 0.37
13 1 0.01
ACGTcount: A:0.16, C:0.05, G:0.04, T:0.75
Consensus pattern (11 bp):
TTTTTATTTTA
Found at i:5818599 original size:59 final size:57
Alignment explanation
Indices: 5818522--5819134 Score: 592
Period size: 59 Copynumber: 10.3 Consensus size: 57
5818512 AAAAATATAT
* *
5818522 ATTTTTAAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAGG
1 ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC-AAAAAA-G
*
5818581 ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTTCAAAAAAC
1 ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAA-TTTTCAAAAAAG
* * *
5818640 A-TTTTTAGGGAAAAGTTGAAAATATCAATTTTTCTTAAAAATAAATTTTCAAAAAAAAAAAAAG
1 ATTTTTTA-GGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC-------AAAAAA-
5818704 G
57 G
* * * *
5818705 GTTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTGAAAATCAAAGTTTTCAAAAAAT
1 ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAA-TTTTCAAAAAAG
* *
5818764 ATTTTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAGG
1 ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCAAAAAA-G
* * * * *
5818822 GTTTTTTAGGAAAAGTTAAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAGA-
1 ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTCAAAAAAG
* * *
5818879 ATATTTTTGGGAAAAAGTTGAAAGTATCAATTTTCCTTGAAAATCAAAGTTTCCAAAAA-
1 AT-TTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTTTCAAAAAAG
* * * * * *
5818938 ATATTTTTGGAGAAAAGTTGAAAGTATCAATTTTTCTCGAAATTAAAGTTTCAAGAAAAAA
1 AT-TTTTTAG-GAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTC-A-AAAAAG
* **
5818999 ATAAATTTTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAAATAAAATTTAAAAAAAAAG
1 AT---TTTTT-AGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAAT-AAATTT-TCAAAAAAG
* *
5819061 AGGTTTTT-GGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAA-TTTCAAAAAATG
1 A-TTTTTTAGG-AAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCAAAAAA-G
*
5819119 -TTTTTGAGGAAAAGTT
1 ATTTTTTAGGAAAAGTT
5819135 ATCAAAGTTT
Statistics
Matches: 478, Mismatches: 44, Indels: 67
0.81 0.07 0.11
Matches are distributed among these distances:
56 11 0.02
57 25 0.05
58 70 0.15
59 234 0.49
60 31 0.06
61 7 0.01
62 10 0.02
63 38 0.08
64 7 0.01
65 32 0.07
66 8 0.02
67 5 0.01
ACGTcount: A:0.45, C:0.07, G:0.13, T:0.35
Consensus pattern (57 bp):
ATTTTTTAGGAAAAGTTGAAAGTATCAATTTTCCTTGAAAATAAATTTTCAAAAAAG
Found at i:5818885 original size:32 final size:32
Alignment explanation
Indices: 5818849--5818944 Score: 80
Period size: 32 Copynumber: 3.2 Consensus size: 32
5818839 AAAAGTATCA
5818849 ATTTTCCTTGAAAATCAAAGTTTCCAAAGAAT
1 ATTTTCCTTGAAAATCAAAGTTTCCAAAGAAT
** * *
5818881 A-TTT--TTGGGAA--AAAG-TT-GAAAGTAT
1 ATTTTCCTTGAAAATCAAAGTTTCCAAAGAAT
*
5818906 CAATTTTCCTTGAAAATCAAAGTTTCCAAAAAAT
1 --ATTTTCCTTGAAAATCAAAGTTTCCAAAGAAT
5818940 ATTTT
1 ATTTT
5818945 TGGAGAAAAG
Statistics
Matches: 46, Mismatches: 9, Indels: 18
0.63 0.12 0.25
Matches are distributed among these distances:
25 6 0.13
26 2 0.04
27 5 0.11
28 3 0.07
29 5 0.11
30 5 0.11
31 3 0.07
32 10 0.22
33 2 0.04
34 5 0.11
ACGTcount: A:0.41, C:0.11, G:0.11, T:0.36
Consensus pattern (32 bp):
ATTTTCCTTGAAAATCAAAGTTTCCAAAGAAT
Found at i:5827991 original size:81 final size:81
Alignment explanation
Indices: 5827898--5828054 Score: 215
Period size: 81 Copynumber: 1.9 Consensus size: 81
5827888 TAACAAATTC
* * * * *
5827898 TTTAAGAACACTCTTTTGGGTTATTAGATTAAATAATATTTTTTAAAATATTAATTATAATCTAA
1 TTTAAGAACACTCTTTCGAGTTATTAGATTAAATAATATTTTTTAAAACATTAACTATAAACTAA
5827963 AAAAAAGGAAAATTTT
66 AAAAAAGGAAAATTTT
* * * **
5827979 TTTAAGAACACTCTTTCGAGTTGTTATATTAAATAATATTTTTTTATGCATTAACTATAAACTAA
1 TTTAAGAACACTCTTTCGAGTTATTAGATTAAATAATATTTTTTAAAACATTAACTATAAACTAA
*
5828044 TAAAAAGGAAA
66 AAAAAAGGAAA
5828055 CCTTTAGGAC
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
81 65 1.00
ACGTcount: A:0.43, C:0.07, G:0.09, T:0.41
Consensus pattern (81 bp):
TTTAAGAACACTCTTTCGAGTTATTAGATTAAATAATATTTTTTAAAACATTAACTATAAACTAA
AAAAAAGGAAAATTTT
Found at i:5828463 original size:34 final size:33
Alignment explanation
Indices: 5828422--5828529 Score: 94
Period size: 34 Copynumber: 3.2 Consensus size: 33
5828412 TATCTTTTAA
* * * *
5828422 ATAAATTATATAATTTATTAGATATATATTTTTG
1 ATAAATTATATAATTTATTA-AAATACATATTCG
*
5828456 ATGAA-T-TATAATTTATTTAAAATACATATTCG
1 ATAAATTATATAATTTA-TTAAAATACATATTCG
* * * *
5828488 ATAAATTATATAATTTATCAAATTTTCATATTTG
1 ATAAATTATATAATTTATTAAA-ATACATATTCG
5828522 ATAAATTA
1 ATAAATTA
5828530 AAAAAAAAAG
Statistics
Matches: 60, Mismatches: 10, Indels: 8
0.77 0.13 0.10
Matches are distributed among these distances:
32 22 0.37
33 9 0.15
34 29 0.48
ACGTcount: A:0.44, C:0.04, G:0.05, T:0.48
Consensus pattern (33 bp):
ATAAATTATATAATTTATTAAAATACATATTCG
Found at i:5828527 original size:17 final size:17
Alignment explanation
Indices: 5828480--5828529 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
5828470 ATTTAAAATA
*
5828480 CATATTCGATAAATTAT
1 CATATTTGATAAATTAT
*
5828497 -ATAATTT-ATCAAATTTT
1 CAT-ATTTGAT-AAATTAT
5828514 CATATTTGATAAATTA
1 CATATTTGATAAATTA
5828530 AAAAAAAAAG
Statistics
Matches: 26, Mismatches: 3, Indels: 8
0.70 0.08 0.22
Matches are distributed among these distances:
16 4 0.15
17 18 0.69
18 4 0.15
ACGTcount: A:0.42, C:0.08, G:0.04, T:0.46
Consensus pattern (17 bp):
CATATTTGATAAATTAT
Found at i:5828676 original size:17 final size:16
Alignment explanation
Indices: 5828654--5828686 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
5828644 CTATTAAGAG
5828654 TTTTCAAATTTTCAAAA
1 TTTTCAAATTTT-AAAA
5828671 TTTTCAAATTTTAAAA
1 TTTTCAAATTTTAAAA
5828687 CTCTAAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.48
Consensus pattern (16 bp):
TTTTCAAATTTTAAAA
Found at i:5830260 original size:3 final size:3
Alignment explanation
Indices: 5830239--5830281 Score: 52
Period size: 3 Copynumber: 14.7 Consensus size: 3
5830229 CATTTCAGTT
* **
5830239 TAA TAT TAA TAA TTT TAA TAA TAA TAA TAA TAA TAA TAA -AA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5830282 TATTTTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
2 2 0.06
3 31 0.94
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (3 bp):
TAA
Found at i:5831516 original size:21 final size:21
Alignment explanation
Indices: 5831433--5831516 Score: 71
Period size: 21 Copynumber: 3.9 Consensus size: 21
5831423 TTTATTTTTT
5831433 TAATAATAATAA-AAATAAAAA
1 TAATAATAATAATAAA-AAAAA
*
5831454 TAAGTAAGATAATAATTAAAAAAA
1 TAA-T-A-ATAATAATAAAAAAAA
* * ** *
5831478 TATTAAAAATGCTTAAAAAAA
1 TAATAATAATAATAAAAAAAA
5831499 TAATAATAATAATAAAAA
1 TAATAATAATAATAAAAA
5831517 TAATTTTTAT
Statistics
Matches: 49, Mismatches: 10, Indels: 8
0.73 0.15 0.12
Matches are distributed among these distances:
21 29 0.59
22 2 0.04
23 2 0.04
24 14 0.29
25 2 0.04
ACGTcount: A:0.69, C:0.01, G:0.04, T:0.26
Consensus pattern (21 bp):
TAATAATAATAATAAAAAAAA
Found at i:5831767 original size:17 final size:16
Alignment explanation
Indices: 5831733--5831815 Score: 71
Period size: 16 Copynumber: 5.2 Consensus size: 16
5831723 TTGCATTTTC
5831733 TAAAATCCAAAACCCT
1 TAAAATCCAAAACCCT
*
5831749 TAAAATTCAAAATCCCT
1 TAAAATCCAAAA-CCCT
* * * *
5831766 TAAAA-CTAGACCCCC
1 TAAAATCCAAAACCCT
* *
5831781 TAAAATCTAAAACCCC
1 TAAAATCCAAAACCCT
*
5831797 TAAAATTC-AAACCCT
1 TAAAATCCAAAACCCT
5831812 TAAA
1 TAAA
5831816 TCGAAATCCC
Statistics
Matches: 54, Mismatches: 11, Indels: 5
0.77 0.16 0.07
Matches are distributed among these distances:
15 18 0.33
16 27 0.50
17 9 0.17
ACGTcount: A:0.48, C:0.29, G:0.01, T:0.22
Consensus pattern (16 bp):
TAAAATCCAAAACCCT
Found at i:5831899 original size:14 final size:14
Alignment explanation
Indices: 5831838--5831903 Score: 53
Period size: 14 Copynumber: 4.5 Consensus size: 14
5831828 ACCTCAATTT
*
5831838 TTAAAATCAAAATC
1 TTAAAATCAAACTC
*
5831852 CTAAAACCTCTAAACTC
1 TTAAAA--TC-AAACTC
* *
5831869 TT-AAATCCAACCCC
1 TTAAAAT-CAAACTC
5831883 TTAAAATCAAACTC
1 TTAAAATCAAACTC
5831897 TTAAAAT
1 TTAAAAT
5831904 TCGAACCCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 10
0.70 0.12 0.18
Matches are distributed among these distances:
14 24 0.60
15 5 0.12
16 5 0.12
17 6 0.15
ACGTcount: A:0.47, C:0.26, G:0.00, T:0.27
Consensus pattern (14 bp):
TTAAAATCAAACTC
Found at i:5831916 original size:28 final size:30
Alignment explanation
Indices: 5831863--5831932 Score: 76
Period size: 30 Copynumber: 2.4 Consensus size: 30
5831853 TAAAACCTCT
5831863 AAACTCTT-AAATCCAACCCCTTAAAAT-C-
1 AAACTCTTAAAATCCAACCCC-TAAAATCCA
*
5831891 AAACTCTTAAAATTCGAACCCC-AAAATCCA
1 AAACTCTTAAAA-TCCAACCCCTAAAATCCA
*
5831921 AAACCCTTAAAA
1 AAACTCTTAAAA
5831933 CCCTCCAAAC
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 13 0.36
29 4 0.11
30 19 0.53
ACGTcount: A:0.47, C:0.30, G:0.01, T:0.21
Consensus pattern (30 bp):
AAACTCTTAAAATCCAACCCCTAAAATCCA
Found at i:5831990 original size:24 final size:24
Alignment explanation
Indices: 5831950--5831997 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5831940 AACTCTAAAA
5831950 CCAAAACCCTAAACCTTCAAAACC
1 CCAAAACCCTAAACCTTCAAAACC
* *
5831974 CCAAAATCC-AAACCCTTTAAAACC
1 CCAAAACCCTAAA-CCTTCAAAACC
5831998 AAACCTTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
23 3 0.14
24 18 0.86
ACGTcount: A:0.46, C:0.40, G:0.00, T:0.15
Consensus pattern (24 bp):
CCAAAACCCTAAACCTTCAAAACC
Found at i:5832017 original size:22 final size:20
Alignment explanation
Indices: 5831991--5832043 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
5831981 CCAAACCCTT
5831991 TAAAAC-CAAACCTTAAAACCC
1 TAAAACTCAAACC--AAAACCC
5832012 TCAAAACTCAAACCAAAACCC
1 T-AAAACTCAAACCAAAACCC
*
5832033 TAAAATTCAAA
1 TAAAACTCAAA
5832044 GTTTCAAAAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
20 9 0.31
21 9 0.31
22 5 0.17
23 6 0.21
ACGTcount: A:0.55, C:0.30, G:0.00, T:0.15
Consensus pattern (20 bp):
TAAAACTCAAACCAAAACCC
Found at i:5832042 original size:20 final size:21
Alignment explanation
Indices: 5831983--5832043 Score: 63
Period size: 23 Copynumber: 2.9 Consensus size: 21
5831973 CCCAAAATCC
*
5831983 AAACCCTTTAAAAC-CAAACCTTA
1 AAACCC-TCAAAACTCAAACC--A
5832006 AAACCCTCAAAACTCAAACCA
1 AAACCCTCAAAACTCAAACCA
*
5832027 AAACCCT-AAAATTCAAA
1 AAACCCTCAAAACTCAAA
5832044 GTTTCAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 9 0.26
21 8 0.23
22 6 0.17
23 12 0.34
ACGTcount: A:0.52, C:0.31, G:0.00, T:0.16
Consensus pattern (21 bp):
AAACCCTCAAAACTCAAACCA
Found at i:5834739 original size:136 final size:136
Alignment explanation
Indices: 5834476--5834747 Score: 422
Period size: 137 Copynumber: 2.0 Consensus size: 136
5834466 TTTTATGTAT
* * * * *
5834476 TTATTGAAGGTATTTTTTACATAATACGCGTTCAATATCTCTCTCATTTTTATTTTACAATATCA
1 TTATTGAAGGTATTTTTTACATAATACGCCTTCAATAACTCCCTCATTTTTATCTTACAACATCA
* * *
5834541 ATGAAGACCGTTTTCTACAAAAAAAAATACCTTTAATAGTTTTTTTTTTAAAATTATTTGAGATT
66 ATGAAGACAGTTTTCTACAAAAAAAAATACCTTTAATAATTTTTTTTTAAAAATTATTTGAGATT
5834606 ATTAAA
131 ATTAAA
5834612 TTATTGAAGGCGT-TTTTTTACATAATACGCCTTCAATAACTCCCTCATTTTTATCTTACAACAT
1 TTATTGAA-G-GTATTTTTTACATAATACGCCTTCAATAACTCCCTCATTTTTATCTTACAACAT
* *
5834676 CAATGAAGATAGTTTTCTAC-AAAAAAAATACCTTTAATAATTTTTTTTTAAAAATTGTTTGAGA
64 CAATGAAGACAGTTTTCTACAAAAAAAAATACCTTTAATAATTTTTTTTTAAAAATTATTTGAGA
5834740 TTATTAAA
129 TTATTAAA
5834748 GGTGTCTTCT
Statistics
Matches: 124, Mismatches: 10, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
136 57 0.46
137 65 0.52
138 2 0.02
ACGTcount: A:0.36, C:0.13, G:0.08, T:0.43
Consensus pattern (136 bp):
TTATTGAAGGTATTTTTTACATAATACGCCTTCAATAACTCCCTCATTTTTATCTTACAACATCA
ATGAAGACAGTTTTCTACAAAAAAAAATACCTTTAATAATTTTTTTTTAAAAATTATTTGAGATT
ATTAAA
Found at i:5835632 original size:146 final size:147
Alignment explanation
Indices: 5835358--5835633 Score: 446
Period size: 146 Copynumber: 1.9 Consensus size: 147
5835348 CCTTTTATAA
* * *
5835358 AATTTTCCTCTAAAAAATTTTAGGATTATTAAAGGCTTCTTCTATTAACAAACACCTTCAATAAT
1 AATTTTCCTCTAAAAAATTTTAGGATTATTAAAAGCATCTTCTACTAACAAACACCTTCAATAAT
* **
5835423 TTTTTTTTAAATTTTTTACATAAATATTGAAGGCATTTATTGATAATAAATGCCTTAAATAATTT
66 TTTCTTTTAAATTTTTTACATAAATATTGAAGGCATTTATTGATAATAAACACCTTAAATAATTT
5835488 CAACAAACCCCTTCAAT
131 CAACAAACCCCTTCAAT
* * *
5835505 AATTTTCCTCTAAAAAATTTTAGGATTATTAAAAGCATCTTTTACTGACAAACGCCTTCAATAA-
1 AATTTTCCTCTAAAAAATTTTAGGATTATTAAAAGCATCTTCTACTAACAAACACCTTCAATAAT
* *
5835569 TTTCTTTTAAATTTTTTACATAAATATTGAAGGCGTTTATTGATAATAAACACCTTCAATAATTT
66 TTTCTTTTAAATTTTTTACATAAATATTGAAGGCATTTATTGATAATAAACACCTTAAATAATTT
5835634 TCTTCTAAAA
Statistics
Matches: 118, Mismatches: 11, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
146 60 0.51
147 58 0.49
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (147 bp):
AATTTTCCTCTAAAAAATTTTAGGATTATTAAAAGCATCTTCTACTAACAAACACCTTCAATAAT
TTTCTTTTAAATTTTTTACATAAATATTGAAGGCATTTATTGATAATAAACACCTTAAATAATTT
CAACAAACCCCTTCAAT
Found at i:5836716 original size:79 final size:80
Alignment explanation
Indices: 5836559--5836757 Score: 258
Period size: 79 Copynumber: 2.5 Consensus size: 80
5836549 ATATTGTAGA
* * *
5836559 TTGCTGAACCTTGTTGTCTGATATTATTTTGCTGAATGGTATTGTAAGATATTAGGGGATTGAAT
1 TTGCTGAACCTTGTTGTCTGATATTGTTTTGCTGAATGGTATTATAAGATATTAGGGGACTGAAT
*
5836624 CGTATGCTGAATGGT
66 CATATGCTGAATGGT
* * * *
5836639 TTGCTAAATCTTGTTGTCTGATATTGTTTTGCT-AATGGTATTATATGATATT-GGGAGGCTGAA
1 TTGCTGAACCTTGTTGTCTGATATTGTTTTGCTGAATGGTATTATAAGATATTAGGG-GACTGAA
*
5836702 TCATATGTTGAATGGT
65 TCATATGCTGAATGGT
* * **
5836718 TTGTTGAACCTTGTTGTTTGATATTGTTTTATTGAATGGT
1 TTGCTGAACCTTGTTGTCTGATATTGTTTTGCTGAATGGT
5836758 TTTCTATGAT
Statistics
Matches: 102, Mismatches: 15, Indels: 4
0.84 0.12 0.03
Matches are distributed among these distances:
78 3 0.03
79 63 0.62
80 36 0.35
ACGTcount: A:0.23, C:0.08, G:0.25, T:0.45
Consensus pattern (80 bp):
TTGCTGAACCTTGTTGTCTGATATTGTTTTGCTGAATGGTATTATAAGATATTAGGGGACTGAAT
CATATGCTGAATGGT
Found at i:5839964 original size:35 final size:34
Alignment explanation
Indices: 5839903--5839978 Score: 89
Period size: 35 Copynumber: 2.2 Consensus size: 34
5839893 TATATAAACG
* * *
5839903 AAATATTTTTTGGGCATAAATATACAATTGACATT
1 AAATATTTTTTAGGCATAAACATACAACTGAC-TT
* *
5839938 AAATGTTTTTTAGGCATAAACCTACAACTGACTT
1 AAATATTTTTTAGGCATAAACATACAACTGACTT
5839972 AACATAT
1 AA-ATAT
5839979 ACAATATTAA
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
34 4 0.12
35 30 0.88
ACGTcount: A:0.39, C:0.13, G:0.11, T:0.37
Consensus pattern (34 bp):
AAATATTTTTTAGGCATAAACATACAACTGACTT
Found at i:5841808 original size:209 final size:206
Alignment explanation
Indices: 5841255--5841808 Score: 534
Period size: 209 Copynumber: 2.6 Consensus size: 206
5841245 TTGTAATACT
* * * * * * *
5841255 CTAAGAAAAAGTAAATATAATTCTAAACGTAAT-GTAAAGTAAAAACAAGCATAAAAA-ACAATT
1 CTAAGAAATAGTAAA-GTAATTATAAACATAATAG-AATGTAAAAACAGGCATAAAAAGA-TATT
* * *
5841318 AATTTAACATAAATAGTTAAATTGGCAACGTAAAAATATTAATATTTTAAAATAACAAAATTCTA
63 -ATTTAACATAAATAATTAAATTGGCAACATAAAAATATTGATATTTTAAAATAA-AAAATTCTA
*
5841383 AATAAAAATTGTTAATGTAAAAAAAATAATTGTAAAATTTGTATCATTTTATATAAAATGGGTTA
126 AATAAAAATTGTTAAAGTAAAAAAAATAATTGTAAAATTTGTATCATTTTATATAAAATGGGTTA
* *
5841448 AAAGTGTAATAACACC
191 AAAGTATAACAACACC
* * * * **
5841464 TTAAGAAATAGTAAAGGTATTTATAAACTTAATAGAATGTAAAAACATGTGTAAAAAGATATTAT
1 CTAAGAAATAGTAAA-GTAATTATAAACATAATAGAATGTAAAAACAGGCATAAAAAGATATTAT
* *** *
5841529 TCTAACATAAATAATTAAGTTAATAACATAAAAGAT-TTGATATTTTAAAATATAAAAGTTCTAA
65 T-TAACATAAATAATTAAATTGGCAACATAAAA-ATATTGATATTTTAAAATA-AAAAATTCTAA
* * * *
5841593 ATAAAAATTTGTTAAAGTAAACATGTGAAAATAATT-TTAAATTTTTATCTTTTTATGTAAAATG
127 ATAAAAA-TTGTTAAAGTAAA-A----AAAATAATTGTAAAATTTGTATCATTTTATATAAAATG
* *
5841657 GGTTAAAAGTATTACAATACC
186 GGTTAAAAGTATAACAACACC
* * **
5841678 CT-AGGAA-AGTAAA-TAATTCTAAACATAAT-GTAA-GTTGGGAAA-AGGCATAAAAAGATATT
1 CTAAGAAATAGTAAAGTAATTATAAACATAATAG-AATG-T-AAAAACAGGCATAAAAAGATATT
* * *
5841737 ATTTAATATAAATAATTAAATTGGCAACATAAAAATATTGATATTTTAAAATTAAAAAAATCTAG
63 ATTTAACATAAATAATTAAATTGGCAACATAAAAATATTGATATTTTAAAA-TAAAAAATTCTAA
5841802 ATAAAAA
127 ATAAAAA
5841809 AATAAATTAT
Statistics
Matches: 282, Mismatches: 47, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
208 5 0.02
209 160 0.57
210 52 0.18
211 4 0.01
212 6 0.02
213 4 0.01
214 42 0.15
215 9 0.03
ACGTcount: A:0.51, C:0.06, G:0.10, T:0.33
Consensus pattern (206 bp):
CTAAGAAATAGTAAAGTAATTATAAACATAATAGAATGTAAAAACAGGCATAAAAAGATATTATT
TAACATAAATAATTAAATTGGCAACATAAAAATATTGATATTTTAAAATAAAAAATTCTAAATAA
AAATTGTTAAAGTAAAAAAAATAATTGTAAAATTTGTATCATTTTATATAAAATGGGTTAAAAGT
ATAACAACACC
Found at i:5842102 original size:32 final size:32
Alignment explanation
Indices: 5842060--5842128 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
5842050 AAGATAAATC
* *
5842060 ATAAATTAATCCCACTAAAATCAAATTTTGAA
1 ATAAACTAATCCCACTAAAATCAAATTTTAAA
* *
5842092 ATAAACTAATCCCATTAAAATGAAATTTTAAA
1 ATAAACTAATCCCACTAAAATCAAATTTTAAA
5842124 ATAAA
1 ATAAA
5842129 TATATAATAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.54, C:0.13, G:0.03, T:0.30
Consensus pattern (32 bp):
ATAAACTAATCCCACTAAAATCAAATTTTAAA
Found at i:5849564 original size:312 final size:313
Alignment explanation
Indices: 5848972--5849595 Score: 1072
Period size: 312 Copynumber: 2.0 Consensus size: 313
5848962 AATTTCTCGT
* * * *
5848972 GACCTGGACCTCTAATGCACCTCAAGTACCTGGTCCTCTTAGTTGTCAGATTTTGTCCCTCTAAA
1 GACCTAGACCTCCAATGCACCTCAAGGACCTGGTCCTCTTAGTTGTCAGACTTTGTCCCTCTAAA
*
5849037 ACTTGAATTACTATTCAACTCGAAGAAAACTATTAGGCTTGGTCCTTTTCACAGACTATGACATT
66 ACTTGAATTACTATTCAACTCGAAGAAAACTATTAGGCTTAGTCCTTTTCACAGACTATGACATT
5849102 CTCATCCACTCATTCTAGCAACGCCCTCGTTGCTAGGGGGATGCTGCATTTGAACTGTACATCTC
131 CTCATCCACTCATTCTAGCAACGCCCTCGTTGCTAGGGGGATGCTGCATTTGAACTGTACATCTC
*
5849167 TGTACATGTCGGCTTTATCTTCTGCCCTTCGAACTAGATTTCCCCTATGTCAGTCCCATATCCAA
196 TGTACATGTCGGCTTTATCTTCTGCCCTTCGAACTAGATTTCCCCTATGTCAGTCCCATACCCAA
* *
5849232 ACAAGTACTCTGCTGGTTGTTCTTTCGAGTATCATTAGCCCCATGTTGCACTA
261 ACAAGTACTCTACTGGTTGTTCTTCCGAGTATCATTAGCCCCATGTTGCACTA
5849285 GACCTAGACCTCCAATGCACCTC-AGGACCTGGTCCTCTTAGTTGTCAGACTTTGTCCCTCTAAA
1 GACCTAGACCTCCAATGCACCTCAAGGACCTGGTCCTCTTAGTTGTCAGACTTTGTCCCTCTAAA
* * * *
5849349 ACTTGAATTGCTATTCAACTCGAAGAAAACTATTAGGCTTAGTCCTTCTT-GCAGACTTTGATAT
66 ACTTGAATTACTATTCAACTCGAAGAAAACTATTAGGCTTAGTCCTT-TTCACAGACTATGACAT
5849413 TCTCATCCACTCATTCTAGCAACGCCCTCGTTGCTAGGGGGATGCTGCATTTGAACTGTACATCT
130 TCTCATCCACTCATTCTAGCAACGCCCTCGTTGCTAGGGGGATGCTGCATTTGAACTGTACATCT
* * **
5849478 CTGTGCATGTTGGCTTTATCTTCTGCCCTTCGAACTAGATTTCCTTTATGTCAGTCCCATACCCA
195 CTGTACATGTCGGCTTTATCTTCTGCCCTTCGAACTAGATTTCCCCTATGTCAGTCCCATACCCA
*
5849543 AACAAGTACTCTACTGGTTGTTCTTCCGAGTATCATTAGCCCTATGTTGCACT
260 AACAAGTACTCTACTGGTTGTTCTTCCGAGTATCATTAGCCCCATGTTGCACT
5849596 GGTCCCTTTT
Statistics
Matches: 293, Mismatches: 17, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
312 270 0.92
313 23 0.08
ACGTcount: A:0.23, C:0.27, G:0.17, T:0.33
Consensus pattern (313 bp):
GACCTAGACCTCCAATGCACCTCAAGGACCTGGTCCTCTTAGTTGTCAGACTTTGTCCCTCTAAA
ACTTGAATTACTATTCAACTCGAAGAAAACTATTAGGCTTAGTCCTTTTCACAGACTATGACATT
CTCATCCACTCATTCTAGCAACGCCCTCGTTGCTAGGGGGATGCTGCATTTGAACTGTACATCTC
TGTACATGTCGGCTTTATCTTCTGCCCTTCGAACTAGATTTCCCCTATGTCAGTCCCATACCCAA
ACAAGTACTCTACTGGTTGTTCTTCCGAGTATCATTAGCCCCATGTTGCACTA
Found at i:5857748 original size:15 final size:14
Alignment explanation
Indices: 5857711--5857754 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 14
5857701 TATTAGAGTA
*
5857711 AATTTTTTAATTTT
1 AATTTTTTAATATT
5857725 ATATATTTTTAATCATT
1 A-AT-TTTTTAAT-ATT
5857742 AATTTTTTAATAT
1 AATTTTTTAATAT
5857755 ATTTAAAGGA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 3 0.12
15 10 0.38
16 10 0.38
17 3 0.12
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (14 bp):
AATTTTTTAATATT
Found at i:5864318 original size:19 final size:18
Alignment explanation
Indices: 5864282--5864338 Score: 53
Period size: 19 Copynumber: 2.9 Consensus size: 18
5864272 CTTTAAGTTT
5864282 AAATTATTTTAATTTTTTTCA
1 AAATTA-TTTAA--TTTTTCA
*
5864303 AAATT-TTTGGAATTTTTAA
1 AAATTATTT--AATTTTTCA
5864322 AAATTATTTAATTTTTC
1 AAATTATTTAATTTTTC
5864339 TTGAATTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 7 0.23
19 14 0.45
20 3 0.10
21 7 0.23
ACGTcount: A:0.35, C:0.04, G:0.04, T:0.58
Consensus pattern (18 bp):
AAATTATTTAATTTTTCA
Found at i:5864429 original size:18 final size:19
Alignment explanation
Indices: 5864389--5864430 Score: 52
Period size: 18 Copynumber: 2.3 Consensus size: 19
5864379 ATTTTAGGGT
* *
5864389 TTTTTTATTATTTTTTAGA
1 TTTTTTATTATTTTTAAAA
5864408 -TTTTTATT-TTTTTAAAA
1 TTTTTTATTATTTTTAAAA
5864425 TTTTTT
1 TTTTTT
5864431 TCAAACTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTTTATTATTTTTAAAA
Found at i:5864473 original size:17 final size:18
Alignment explanation
Indices: 5864453--5864487 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5864443 GGATTTTGAA
5864453 AATTTTTAATTTT-TTTT
1 AATTTTTAATTTTGTTTT
5864470 AATTTTTAATTTTGTTTT
1 AATTTTTAATTTTGTTTT
5864488 TTTCATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 13 0.76
18 4 0.24
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (18 bp):
AATTTTTAATTTTGTTTT
Found at i:5864630 original size:20 final size:20
Alignment explanation
Indices: 5864586--5864631 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
5864576 GAATTTAAGG
* * *
5864586 ATTTTTTTAATTTTTTAGAT
1 ATTTTTATAATCTTTTAAAT
*
5864606 TTTTTTATAATCTTTTAAAT
1 ATTTTTATAATCTTTTAAAT
5864626 ATTTTT
1 ATTTTT
5864632 CAAATTTGTT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTTTATAATCTTTTAAAT
Found at i:5865518 original size:20 final size:22
Alignment explanation
Indices: 5865493--5865533 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
5865483 ATCCCCTAAA
*
5865493 CCTAGG-TGATTGATC-CTTTG
1 CCTAGGATGATCGATCTCTTTG
5865513 CCTAGGATGATCGATCTCTTT
1 CCTAGGATGATCGATCTCTTT
5865534 TATGAAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 8 0.44
22 4 0.22
ACGTcount: A:0.17, C:0.22, G:0.22, T:0.39
Consensus pattern (22 bp):
CCTAGGATGATCGATCTCTTTG
Found at i:5874981 original size:30 final size:31
Alignment explanation
Indices: 5874936--5874999 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 31
5874926 CATTTTTTCC
*
5874936 TTGTTTTACTTTTTCTCTTTATTCTTT-TTTTT
1 TTGTTTTA-TTTTTCTCTTT-CTCTTTCTTTTT
5874968 TTGTTTT-TTTTTCTCTTTCTCTTTCTTTTT
1 TTGTTTTATTTTTCTCTTTCTCTTTCTTTTT
5874998 TT
1 TT
5875000 TCCCTTTTCC
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 5 0.17
30 18 0.60
32 7 0.23
ACGTcount: A:0.03, C:0.14, G:0.03, T:0.80
Consensus pattern (31 bp):
TTGTTTTATTTTTCTCTTTCTCTTTCTTTTT
Found at i:5875247 original size:14 final size:14
Alignment explanation
Indices: 5875230--5875289 Score: 50
Period size: 14 Copynumber: 3.9 Consensus size: 14
5875220 TTTTCTTCTT
5875230 ATTTTTCTTTTTTC
1 ATTTTTCTTTTTTC
5875244 ATTTCTCCTCTTTGTCTTC
1 ATTT-T--TCTTT-T-TTC
*
5875263 -TCTTTTCTTTTTCC
1 AT-TTTTCTTTTTTC
5875277 ATTTTTCTTTTTT
1 ATTTTTCTTTTTT
5875290 TTTAGAATAA
Statistics
Matches: 37, Mismatches: 2, Indels: 14
0.70 0.04 0.26
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 5 0.14
17 5 0.14
18 3 0.08
19 5 0.14
ACGTcount: A:0.05, C:0.22, G:0.02, T:0.72
Consensus pattern (14 bp):
ATTTTTCTTTTTTC
Found at i:5879226 original size:69 final size:71
Alignment explanation
Indices: 5879104--5879243 Score: 203
Period size: 69 Copynumber: 2.0 Consensus size: 71
5879094 TCCCAATTTA
* *
5879104 AAATCCCACACATATATTAAATTAAAAATTAAAAAAAAATCTCTTTTATCTTATGACTTATGATT
1 AAATCACACACATATATTAAATTAAAAATT-AAAAAAAATCTCTTTTATCTTATCACTTATGATT
5879169 TATTAAC
65 TATTAAC
* * * *
5879176 AAATCACACACATCTATT-AATTCAAAATT-AAATAAATCTCTTTTATCTTATCACTTATGGTTT
1 AAATCACACACATATATTAAATTAAAAATTAAAAAAAATCTCTTTTATCTTATCACTTATGATTT
5879239 ATTAA
66 ATTAA
5879244 TAATCTCCCA
Statistics
Matches: 62, Mismatches: 6, Indels: 3
0.87 0.08 0.04
Matches are distributed among these distances:
69 36 0.58
71 10 0.16
72 16 0.26
ACGTcount: A:0.43, C:0.15, G:0.03, T:0.39
Consensus pattern (71 bp):
AAATCACACACATATATTAAATTAAAAATTAAAAAAAATCTCTTTTATCTTATCACTTATGATTT
ATTAAC
Found at i:5884996 original size:20 final size:18
Alignment explanation
Indices: 5884971--5885019 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 18
5884961 TGAAATGTAC
5884971 TAATATTTTATTTTTAATTT
1 TAATATTTTATTTTTAA--T
5884991 TAATATTTGATATTTTTAAT
1 TAATATTT--TATTTTTAAT
5885011 TAATATTTT
1 TAATATTTT
5885020 CATCATTTCG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 1 0.04
20 17 0.63
22 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (18 bp):
TAATATTTTATTTTTAAT
Found at i:5885692 original size:22 final size:24
Alignment explanation
Indices: 5885659--5885708 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 24
5885649 ATATATTAAT
*
5885659 TTTAATTAATTTAA-AATAATA-A
1 TTTAATTAATTTAATAAAAATATA
5885681 TTTATATT-ATTTAATAAAAATATA
1 TTTA-ATTAATTTAATAAAAATATA
5885705 TTTA
1 TTTA
5885709 CTAAATATCT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
22 10 0.42
23 9 0.38
24 5 0.21
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (24 bp):
TTTAATTAATTTAATAAAAATATA
Found at i:5888168 original size:34 final size:37
Alignment explanation
Indices: 5888119--5888191 Score: 91
Period size: 34 Copynumber: 2.1 Consensus size: 37
5888109 ATGGGTATCA
* *
5888119 ATCTTTTTAATTGGTG-T-TTA-TTTAT-TGGATATTG
1 ATCTTTCTAACTGGTGCTCTTATTTTATGTGGAT-TTG
5888153 ATCTTTCTAACTGGTGCTCTTATTTTATGTGGATTTG
1 ATCTTTCTAACTGGTGCTCTTATTTTATGTGGATTTG
5888190 AT
1 AT
5888192 ATCGATCTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
34 14 0.42
35 1 0.03
36 3 0.09
37 10 0.30
38 5 0.15
ACGTcount: A:0.19, C:0.08, G:0.18, T:0.55
Consensus pattern (37 bp):
ATCTTTCTAACTGGTGCTCTTATTTTATGTGGATTTG
Found at i:5906338 original size:24 final size:24
Alignment explanation
Indices: 5906301--5906347 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
5906291 AAAGGGAGAG
* *
5906301 AAAAGATCCCAAAAGTATAAAATC
1 AAAAGATCCAAAAACTATAAAATC
* *
5906325 AAAAGATTCAAAAACTTTAAAAT
1 AAAAGATCCAAAAACTATAAAAT
5906348 TTTAGTGCTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.60, C:0.13, G:0.06, T:0.21
Consensus pattern (24 bp):
AAAAGATCCAAAAACTATAAAATC
Found at i:5906796 original size:12 final size:12
Alignment explanation
Indices: 5906769--5906813 Score: 51
Period size: 12 Copynumber: 3.8 Consensus size: 12
5906759 TTTGATATTA
5906769 ATTTTAATTCTA-
1 ATTTTAATT-TAG
5906781 ATTTTAATTTAG
1 ATTTTAATTTAG
5906793 A-TTTAGATTTAG
1 ATTTTA-ATTTAG
5906805 -TTTTAATTT
1 ATTTTAATTT
5906814 TGTGATATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
11 10 0.33
12 20 0.67
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (12 bp):
ATTTTAATTTAG
Found at i:5908446 original size:23 final size:23
Alignment explanation
Indices: 5908412--5908456 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
5908402 TAGTTTTTAT
5908412 AAAATCTCACCAACATATTGAAG
1 AAAATCTCACCAACATATTGAAG
*
5908435 AAAATCTTACCAACATATTGAA
1 AAAATCTCACCAACATATTGAA
5908457 AGATATTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.49, C:0.20, G:0.07, T:0.24
Consensus pattern (23 bp):
AAAATCTCACCAACATATTGAAG
Found at i:5910036 original size:37 final size:36
Alignment explanation
Indices: 5909973--5910044 Score: 101
Period size: 37 Copynumber: 2.0 Consensus size: 36
5909963 ATTTCCATTG
*
5909973 GAATATTTTTTAAAATTAATTTTTTATTTTTATTTTT
1 GAATATTTTTTAAAATTAATTCTTTA-TTTTATTTTT
*
5910010 GAATTTTTTTTAAAAGTTAA-TCTTTATTTTATTTT
1 GAATATTTTTTAAAA-TTAATTCTTTATTTTATTTT
5910045 CTTTATATTG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 9 0.28
37 19 0.59
38 4 0.12
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (36 bp):
GAATATTTTTTAAAATTAATTCTTTATTTTATTTTT
Found at i:5912826 original size:255 final size:254
Alignment explanation
Indices: 5912415--5912887 Score: 756
Period size: 255 Copynumber: 1.9 Consensus size: 254
5912405 TTCAATGCTA
*
5912415 GAAAAAGCTATTTTCAATAAGAATTTGAAAAAAAATTAAATAAATATGTACAACATAATGAATTC
1 GAAAAAGCTATTTTCAATAAGAATTTGAAAAAAAATTAAATAAATATATACAACATAATGAATTC
*
5912480 ATTTATTACATGCAATACATGTAAATAAATTTACTTAAAATAAAATATTTAAACTTGTAAAACTT
66 ATTTATTACATGCAATACATATAAATAAATTTACTTAAAATAAAATATTTAAACTTGTAAAACTT
* *
5912545 TCAAATTATTTTCTTTGGAGTAACATGAAACCTCTCCAAAATATTAATCCATTG-AA-ATATTTA
131 TCAAATTATTTCCTTTGAAGTAACATGAAACCTCTCCAAAATATTAATCCATTGAAATATATTTA
5912608 CCTGAATACATTAAACCAAAACAAAAAATTTTAAATAAATATTTAAAATTATTCTTATT
196 CCTGAATACATTAAACCAAAACAAAAAATTTTAAATAAATATTTAAAATTATTCTTATT
* *
5912667 GAAAAAGCTGTTTTCAATAAGAATTTGAAACAAAAAAATTAAATAAATATATCCAACATAATGAA
1 GAAAAAGCTATTTTCAATAAGAATTTG--A-AAAAAAATTAAATAAATATATACAACATAATGAA
* * * *
5912732 TTCATTTATTACATGCAATATATATAAATAAATTTACTTAAAGTAAAAATATTTAAACTTTTAAG
63 TTCATTTATTACATGCAATACATATAAATAAATTTACTTAAAAT-AAAATATTTAAACTTGTAAA
* *
5912797 AC-TTCAAATTATTTCCTCTT-AAGTAACATGCAACCTTTCCAAAATATTAATCCATTGAAATAT
127 ACTTTCAAATTATTTCCT-TTGAAGTAACATGAAACCTCTCCAAAATATTAATCCATTGAAATAT
*
5912860 ATTTACTTGAATACATTAAACCAAAACA
191 ATTTACCTGAATACATTAAACCAAAACA
5912888 TTTCCTAAAC
Statistics
Matches: 201, Mismatches: 13, Indels: 9
0.90 0.06 0.04
Matches are distributed among these distances:
252 26 0.13
254 1 0.00
255 121 0.60
256 24 0.12
257 29 0.14
ACGTcount: A:0.47, C:0.12, G:0.06, T:0.35
Consensus pattern (254 bp):
GAAAAAGCTATTTTCAATAAGAATTTGAAAAAAAATTAAATAAATATATACAACATAATGAATTC
ATTTATTACATGCAATACATATAAATAAATTTACTTAAAATAAAATATTTAAACTTGTAAAACTT
TCAAATTATTTCCTTTGAAGTAACATGAAACCTCTCCAAAATATTAATCCATTGAAATATATTTA
CCTGAATACATTAAACCAAAACAAAAAATTTTAAATAAATATTTAAAATTATTCTTATT
Found at i:5915590 original size:134 final size:139
Alignment explanation
Indices: 5915348--5915602 Score: 344
Period size: 140 Copynumber: 1.8 Consensus size: 139
5915338 TAGTCTTAAA
* * **
5915348 AAAATAAAAGTGATAAAAGAAAAGGTAAGTCAATGAATCTTACCAAATCTTTTTTCTTTTACTTT
1 AAAACAAAAGTGATAAAAGAAAAGGTAAATCAACAAATCTTACCAAATC-TTTTTCTTTTACTTT
* *
5915413 TCCAAGAATTTTTTTTTTCACAACAAAAGCTACAAAGACTACC-TTTTTTATGTAAAAGGCGTAG
65 TCCAAGAA--TTTTTTTTCACAAAAAAAACTACAAAGACTACCTTTTTTTATGTAAAAGGCGTAG
5915477 TCTTTGTACAAC
128 TCTTTGTACAAC
*
5915489 AAAACAAAAGTGAT-AAGGAAAAGGTAAATCAACAAAT-TTCACCAAATC-TTTTCTTTTACTTT
1 AAAACAAAAGTGATAAAAGAAAAGGTAAATCAACAAATCTT-ACCAAATCTTTTTCTTTTACTTT
*
5915551 TTCAA-AA-TTTTTTT-ACAATAAAAAACTACAAAGACTACCTTTTTTTATGTAA
65 TCCAAGAATTTTTTTTCACAA-AAAAAACTACAAAGACTACCTTTTTTTATGTAA
5915603 GAAAGGTAGT
Statistics
Matches: 103, Mismatches: 8, Indels: 12
0.84 0.07 0.10
Matches are distributed among these distances:
133 4 0.04
134 25 0.24
135 12 0.12
137 2 0.02
138 18 0.17
139 2 0.02
140 27 0.26
141 13 0.13
ACGTcount: A:0.41, C:0.15, G:0.09, T:0.35
Consensus pattern (139 bp):
AAAACAAAAGTGATAAAAGAAAAGGTAAATCAACAAATCTTACCAAATCTTTTTCTTTTACTTTT
CCAAGAATTTTTTTTCACAAAAAAAACTACAAAGACTACCTTTTTTTATGTAAAAGGCGTAGTCT
TTGTACAAC
Found at i:5915650 original size:104 final size:104
Alignment explanation
Indices: 5915541--5915759 Score: 278
Period size: 104 Copynumber: 2.1 Consensus size: 104
5915531 CAAATCTTTT
* * *
5915541 CTTTTACTTTTTCAA-AATTTTTTTACAATAAAAAACTACAAAGACTACCTTTTTTTATGTAAGA
1 CTTTTACTTTTTCAAGAATTTTTTTACAACAAAAAACTACAAAGACTACC-TTTCTTATGTAAAA
** * * * *
5915605 AAGGTAGTTTTTGTGCACTAAAATCTCATTAAATATTCTC
65 AACATAATCTTTGTGCACCAAAATCTCATCAAATATTCTC
* * * * *
5915645 TTTTTACTTTTTCAAGATTTTTTTTACAACAAAAAATTATAAAGATTACCTTTCTTATGTAAAAA
1 CTTTTACTTTTTCAAGAATTTTTTTACAACAAAAAACTACAAAGACTACCTTTCTTATGTAAAAA
* *
5915710 ACATAATCTTTGTGCACCAAAATCTCATCAAATTTTTTC
66 ACATAATCTTTGTGCACCAAAATCTCATCAAATATTCTC
5915749 CTTTTACTTTT
1 CTTTTACTTTT
5915760 CTTATATAAT
Statistics
Matches: 97, Mismatches: 17, Indels: 2
0.84 0.15 0.02
Matches are distributed among these distances:
104 68 0.70
105 29 0.30
ACGTcount: A:0.35, C:0.15, G:0.06, T:0.44
Consensus pattern (104 bp):
CTTTTACTTTTTCAAGAATTTTTTTACAACAAAAAACTACAAAGACTACCTTTCTTATGTAAAAA
ACATAATCTTTGTGCACCAAAATCTCATCAAATATTCTC
Found at i:5920404 original size:8 final size:8
Alignment explanation
Indices: 5920391--5920428 Score: 51
Period size: 8 Copynumber: 4.6 Consensus size: 8
5920381 TAAAAGACAT
5920391 AAAAATTA
1 AAAAATTA
5920399 AAAAATT-
1 AAAAATTA
5920406 AAAAATTAA
1 AAAAATT-A
5920415 AAGAAATTA
1 AA-AAATTA
5920424 AAAAA
1 AAAAA
5920429 AAGGAAAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
7 7 0.26
8 10 0.37
9 5 0.19
10 5 0.19
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.21
Consensus pattern (8 bp):
AAAAATTA
Found at i:5920421 original size:17 final size:17
Alignment explanation
Indices: 5920381--5920427 Score: 64
Period size: 15 Copynumber: 2.9 Consensus size: 17
5920371 TTATTTTAAA
*
5920381 TAAAAGACA-TAAAAAT
1 TAAAAGAAATTAAAAAT
5920397 T-AAA-AAATTAAAAAT
1 TAAAAGAAATTAAAAAT
5920412 TAAAAGAAATTAAAAA
1 TAAAAGAAATTAAAAA
5920428 AAAGGAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
14 2 0.07
15 11 0.41
16 4 0.15
17 10 0.37
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.21
Consensus pattern (17 bp):
TAAAAGAAATTAAAAAT
Found at i:5921409 original size:34 final size:34
Alignment explanation
Indices: 5921357--5921427 Score: 106
Period size: 34 Copynumber: 2.1 Consensus size: 34
5921347 GAATGAGTTT
* * *
5921357 CTATAATATCTCTCAAAATTACTTAAAAGGATAC
1 CTATAAAAACTCTCAAAATTACTTAAAAGAATAC
*
5921391 CTATAAAAACTCTTAAAATTACTTAAAAGAATAC
1 CTATAAAAACTCTCAAAATTACTTAAAAGAATAC
5921425 CTA
1 CTA
5921428 ATTCATTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.48, C:0.17, G:0.04, T:0.31
Consensus pattern (34 bp):
CTATAAAAACTCTCAAAATTACTTAAAAGAATAC
Found at i:5922818 original size:19 final size:19
Alignment explanation
Indices: 5922765--5922819 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
5922755 TTTTAATAAA
*
5922765 AAAAATAATTCAAATTTTTT
1 AAAAAT-ATTAAAATTTTTT
* * **
5922785 AGAAATTTTTTAATTTTTT
1 AAAAATATTAAAATTTTTT
5922804 AAAAATATTAAAATTT
1 AAAAATATTAAAATTT
5922820 AAAAATTACC
Statistics
Matches: 27, Mismatches: 8, Indels: 1
0.75 0.22 0.03
Matches are distributed among these distances:
19 22 0.81
20 5 0.19
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (19 bp):
AAAAATATTAAAATTTTTT
Found at i:5923732 original size:16 final size:14
Alignment explanation
Indices: 5923697--5923783 Score: 74
Period size: 14 Copynumber: 6.2 Consensus size: 14
5923687 AACTTTGATA
5923697 TATTAAT-TTAAAT
1 TATTAATATTAAAT
5923710 TATTAATATTATAAT
1 TATTAATATTA-AAT
5923725 TGATTAATA-TAAAT
1 T-ATTAATATTAAAT
* *
5923739 GA-TAATAGTAATAT
1 TATTAATATTAA-AT
* *
5923753 TATTAATATGATAT
1 TATTAATATTAAAT
5923767 TATTAATAATT-AAT
1 TATTAAT-ATTAAAT
5923781 TAT
1 TAT
5923784 ATATAATAAA
Statistics
Matches: 60, Mismatches: 7, Indels: 13
0.75 0.09 0.16
Matches are distributed among these distances:
12 5 0.08
13 11 0.18
14 23 0.38
15 14 0.23
16 7 0.12
ACGTcount: A:0.47, C:0.00, G:0.05, T:0.48
Consensus pattern (14 bp):
TATTAATATTAAAT
Found at i:5923782 original size:14 final size:14
Alignment explanation
Indices: 5923705--5923793 Score: 60
Period size: 14 Copynumber: 6.3 Consensus size: 14
5923695 TATATTAATT
*
5923705 TAAATTATTAATAT
1 TAAATTATTAATAA
5923719 TATAATTGATTAAT-A
1 TA-AATT-ATTAATAA
* *
5923734 TAAATGA-TAATAG
1 TAAATTATTAATAA
5923747 TAATATTATTAAT-A
1 TAA-ATTATTAATAA
*
5923761 TGATATTATTAATAA
1 T-AAATTATTAATAA
*
5923776 TTAATTA-TATATAA
1 TAAATTATTA-ATAA
5923790 TAAA
1 TAAA
5923794 AACTCAAATA
Statistics
Matches: 58, Mismatches: 9, Indels: 16
0.70 0.11 0.19
Matches are distributed among these distances:
12 4 0.07
13 6 0.10
14 29 0.50
15 13 0.22
16 6 0.10
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (14 bp):
TAAATTATTAATAA
Found at i:5925751 original size:17 final size:18
Alignment explanation
Indices: 5925711--5925751 Score: 50
Period size: 17 Copynumber: 2.4 Consensus size: 18
5925701 AGGATATGAT
*
5925711 AATTTATTTATTGGTCAA
1 AATTTATTTATTAGTCAA
*
5925729 AA-TTATTT-TTATTCAA
1 AATTTATTTATTAGTCAA
5925745 AATTTAT
1 AATTTAT
5925752 ATAATTAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
16 8 0.40
17 10 0.50
18 2 0.10
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
AATTTATTTATTAGTCAA
Found at i:5926399 original size:29 final size:31
Alignment explanation
Indices: 5926361--5926421 Score: 74
Period size: 29 Copynumber: 2.0 Consensus size: 31
5926351 ATAATATTTA
5926361 AAATTAATG-TAATGTT-TTTTA-TTTTTAAT
1 AAATTAATGTTAAT-TTATTTTATTTTTTAAT
* *
5926390 AAATTTATGTTTATTTATTTTATTTTTTAAT
1 AAATTAATGTTAATTTATTTTATTTTTTAAT
5926421 A
1 A
5926422 TTTAAATAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
29 10 0.37
30 8 0.30
31 9 0.33
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (31 bp):
AAATTAATGTTAATTTATTTTATTTTTTAAT
Found at i:5927460 original size:17 final size:18
Alignment explanation
Indices: 5927425--5927463 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
5927415 TACTTTTTTT
5927425 AAAATTACAATATTAAAA
1 AAAATTACAATATTAAAA
5927443 AAAATTA-AAT-TTACAAA
1 AAAATTACAATATTA-AAA
5927460 AAAA
1 AAAA
5927464 ATCAAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
16 3 0.15
17 10 0.50
18 7 0.35
ACGTcount: A:0.69, C:0.05, G:0.00, T:0.26
Consensus pattern (18 bp):
AAAATTACAATATTAAAA
Found at i:5927471 original size:19 final size:18
Alignment explanation
Indices: 5927439--5927474 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
5927429 TTACAATATT
*
5927439 AAAAAAAATTAAATTTAC
1 AAAAAAAATAAAATTTAC
5927457 AAAAAAAATCAAAATTTA
1 AAAAAAAAT-AAAATTTA
5927475 ATTGATTTTC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.69, C:0.06, G:0.00, T:0.25
Consensus pattern (18 bp):
AAAAAAAATAAAATTTAC
Found at i:5931603 original size:2 final size:2
Alignment explanation
Indices: 5931596--5931621 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5931586 TTTTTGTTTG
5931596 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
5931622 CAAATAGGTT
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:5946005 original size:282 final size:282
Alignment explanation
Indices: 5945501--5946068 Score: 1084
Period size: 282 Copynumber: 2.0 Consensus size: 282
5945491 AGAGGGTATT
5945501 GTAGATATGTGTGGGGCAACTTGGTCACTTGGAGGAGCAAGAAACAAGTAGCGGTAGCTCAAAGT
1 GTAGATATGTGTGGGGCAACTTGGTCACTTGGAGGAGCAAGAAACAAGTAGCGGTAGCTCAAAGT
5945566 AATTCTGAAGTTGAATTTAGGGCTATGTCTCACAGAATTTGTGAAGGAATTTGGCTAGAGAATAC
66 AATTCTGAAGTTGAATTTAGGGCTATGTCTCACAGAATTTGTGAAGGAATTTGGCTAGAGAATAC
*
5945631 TACAAGAACTGAAGAAGTCAGCTGGAAATTCAATGGAACTGTTTTGTGATAATAAAGCAGCCATT
131 TACAAGAACTGAAGAAGTCAGCTGGAAATTCAATGAAACTGTTTTGTGATAATAAAGCAGCCATT
*
5945696 AACATTGCCAAGAATTCTGTTCATCATGATCGAACGAAACATATAGAGATTGATTGCCACTTCAT
196 AACATTGCCAAGAATCCTGTTCATCATGATCGAACGAAACATATAGAGATTGATTGCCACTTCAT
*
5945761 CAAAGAGAAGATTGAAGAGGGC
261 CAAAGAGAAGATTGAAGAAGGC
*
5945783 GTAGATATGTGTGGGGCAACTTGGTCACTTGGAGGAGCAAGAAACAAGTAGTGGTAGCTCAAAGT
1 GTAGATATGTGTGGGGCAACTTGGTCACTTGGAGGAGCAAGAAACAAGTAGCGGTAGCTCAAAGT
5945848 AATTCTGAAGTTGAATTTAGGGCTATGTCTCACAGAATTTGTGAAGGAATTTGGCTAGAGAATAC
66 AATTCTGAAGTTGAATTTAGGGCTATGTCTCACAGAATTTGTGAAGGAATTTGGCTAGAGAATAC
5945913 TACAAGAACTGAAGAAGTCAGCTGGAAATTCAATGAAACTGTTTTGTGATAATAAAG-ATGCCAT
131 TACAAGAACTGAAGAAGTCAGCTGGAAATTCAATGAAACTGTTTTGTGATAATAAAGCA-GCCAT
5945977 TAACATTGCCAAGAATCCTGTTCATCATGATCGAACGAAACATATAGAGATTGATTGCCACTTCA
195 TAACATTGCCAAGAATCCTGTTCATCATGATCGAACGAAACATATAGAGATTGATTGCCACTTCA
5946042 TCAAAGAGAAGATTGAAGAAGGC
260 TCAAAGAGAAGATTGAAGAAGGC
5946065 GTAG
1 GTAG
5946069 TCAAACTGGT
Statistics
Matches: 281, Mismatches: 4, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
281 1 0.00
282 280 1.00
ACGTcount: A:0.35, C:0.14, G:0.25, T:0.26
Consensus pattern (282 bp):
GTAGATATGTGTGGGGCAACTTGGTCACTTGGAGGAGCAAGAAACAAGTAGCGGTAGCTCAAAGT
AATTCTGAAGTTGAATTTAGGGCTATGTCTCACAGAATTTGTGAAGGAATTTGGCTAGAGAATAC
TACAAGAACTGAAGAAGTCAGCTGGAAATTCAATGAAACTGTTTTGTGATAATAAAGCAGCCATT
AACATTGCCAAGAATCCTGTTCATCATGATCGAACGAAACATATAGAGATTGATTGCCACTTCAT
CAAAGAGAAGATTGAAGAAGGC
Found at i:5953305 original size:68 final size:68
Alignment explanation
Indices: 5953191--5953330 Score: 221
Period size: 68 Copynumber: 2.1 Consensus size: 68
5953181 TAAATAAAGG
*
5953191 GGCCTAACCTGAATATAAGACTATGAGATATTAGAAATTTATTAGATGTAGGATAACCCACTTTA
1 GGCCCAACCTGAATATAAGACTATGAGATATTAGAAATTTATTAGATGTAGGATAACCCACTTTA
5953256 ACA
66 ACA
*
5953259 GGCCCAACCTGAATATAAGACTAT-AGGATATT-GAAAATTTATTAGATGTGGGATAACCCACTT
1 GGCCCAACCTGAATATAAGACTATGA-GATATTAG-AAATTTATTAGATGTAGGATAACCCACTT
*
5953322 TAATA
64 TAACA
5953327 GGCC
1 GGCC
5953331 TTAGGCGAAG
Statistics
Matches: 67, Mismatches: 3, Indels: 4
0.91 0.04 0.05
Matches are distributed among these distances:
67 2 0.03
68 65 0.97
ACGTcount: A:0.38, C:0.16, G:0.18, T:0.29
Consensus pattern (68 bp):
GGCCCAACCTGAATATAAGACTATGAGATATTAGAAATTTATTAGATGTAGGATAACCCACTTTA
ACA
Found at i:5958603 original size:26 final size:27
Alignment explanation
Indices: 5958547--5958603 Score: 62
Period size: 26 Copynumber: 2.1 Consensus size: 27
5958537 TTTTTTGTTG
* * *
5958547 TTTTGATATTTATATTATTTCTAATTC
1 TTTTGATATTTAGATTAATTCTAATTA
**
5958574 TTTTGATA-TTAGATTAATTCTTTTTA
1 TTTTGATATTTAGATTAATTCTAATTA
5958600 TTTT
1 TTTT
5958604 TGTGTAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.25, C:0.05, G:0.05, T:0.65
Consensus pattern (27 bp):
TTTTGATATTTAGATTAATTCTAATTA
Found at i:5958790 original size:26 final size:26
Alignment explanation
Indices: 5958762--5958810 Score: 82
Period size: 25 Copynumber: 1.9 Consensus size: 26
5958752 AAAAAAATAA
*
5958762 AAAATATAGGTTTGAAAA-TTTTATT
1 AAAATATAAGTTTGAAAACTTTTATT
5958787 AAAATATAAGTTTGAAAACTTTTA
1 AAAATATAAGTTTGAAAACTTTTA
5958811 ATTTTTGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
25 17 0.77
26 5 0.23
ACGTcount: A:0.47, C:0.02, G:0.10, T:0.41
Consensus pattern (26 bp):
AAAATATAAGTTTGAAAACTTTTATT
Found at i:5959706 original size:30 final size:30
Alignment explanation
Indices: 5959670--5959730 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
5959660 ATTCACCAAA
5959670 TAGCAAGATTGCTATTATGATTGTTTATGT
1 TAGCAAGATTGCTATTATGATTGTTTATGT
5959700 TAGCAAGATTGCTATTATGATTGTTTATGT
1 TAGCAAGATTGCTATTATGATTGTTTATGT
5959730 T
1 T
5959731 GACGGTATTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.26, C:0.07, G:0.20, T:0.48
Consensus pattern (30 bp):
TAGCAAGATTGCTATTATGATTGTTTATGT
Found at i:5965523 original size:17 final size:17
Alignment explanation
Indices: 5965492--5965524 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
5965482 AGTCAGTGAC
5965492 GGATCTGAAACAGGTCG
1 GGATCTGAAACAGGTCG
5965509 GGATCATGAAA-AGGTC
1 GGATC-TGAAACAGGTC
5965525 CCTTGCGTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.33, C:0.15, G:0.33, T:0.18
Consensus pattern (17 bp):
GGATCTGAAACAGGTCG
Found at i:5970204 original size:11 final size:11
Alignment explanation
Indices: 5970156--5970214 Score: 59
Period size: 11 Copynumber: 5.3 Consensus size: 11
5970146 TTCAAAAATT
5970156 TATTCTATATA
1 TATTCTATATA
*
5970167 TA-ACTATATA
1 TATTCTATATA
*
5970177 TAAATT-TATCCTA
1 T--ATTCTAT-ATA
5970190 TATTCTATATA
1 TATTCTATATA
5970201 TATTCTATATA
1 TATTCTATATA
5970212 TAT
1 TAT
5970215 AATAGATAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 10
0.74 0.08 0.19
Matches are distributed among these distances:
10 8 0.21
11 21 0.54
12 7 0.18
13 3 0.08
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (11 bp):
TATTCTATATA
Found at i:5970234 original size:13 final size:13
Alignment explanation
Indices: 5970218--5970258 Score: 57
Period size: 13 Copynumber: 3.1 Consensus size: 13
5970208 TATATATAAT
5970218 AGATAATAGAATA
1 AGATAATAGAATA
5970231 AGATAATAGAATA
1 AGATAATAGAATA
5970244 A-ATAGAATAGAATA
1 AGAT--AATAGAATA
5970258 A
1 A
5970259 AAAAATGAAT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
12 2 0.08
13 14 0.54
14 10 0.38
ACGTcount: A:0.63, C:0.00, G:0.15, T:0.22
Consensus pattern (13 bp):
AGATAATAGAATA
Found at i:5973643 original size:14 final size:15
Alignment explanation
Indices: 5973619--5973668 Score: 59
Period size: 14 Copynumber: 3.3 Consensus size: 15
5973609 TTATTTTTAG
5973619 TATAA-AAATATAAA
1 TATAATAAATATAAA
5973633 TA-AATAAATATAAA
1 TATAATAAATATAAA
*
5973647 TATTATAAATTATAAA
1 TATAATAAA-TATAAA
5973663 TTATAA
1 -TATAA
5973669 AACATTAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
13 2 0.07
14 13 0.43
15 5 0.17
16 6 0.20
17 4 0.13
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (15 bp):
TATAATAAATATAAA
Found at i:5973687 original size:17 final size:19
Alignment explanation
Indices: 5973667--5973705 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
5973657 TATAAATTAT
*
5973667 AAAACATTAAA-CAAAT-A
1 AAAAAATTAAATCAAATCA
5973684 AAAAAATTAAATCAAATCA
1 AAAAAATTAAATCAAATCA
5973703 AAA
1 AAA
5973706 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 10 0.53
18 5 0.26
19 4 0.21
ACGTcount: A:0.72, C:0.10, G:0.00, T:0.18
Consensus pattern (19 bp):
AAAAAATTAAATCAAATCA
Found at i:5974615 original size:16 final size:16
Alignment explanation
Indices: 5974590--5974624 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
5974580 TTTTTTTAAC
5974590 TTTTTTATTA-ATTTT
1 TTTTTTATTATATTTT
5974605 TTTTATTATTATATTTT
1 TTTT-TTATTATATTTT
5974622 TTT
1 TTT
5974625 GATGGACAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 4 0.22
16 6 0.33
17 8 0.44
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (16 bp):
TTTTTTATTATATTTT
Found at i:5974914 original size:40 final size:40
Alignment explanation
Indices: 5974870--5975047 Score: 186
Period size: 40 Copynumber: 4.5 Consensus size: 40
5974860 AGAGGCTATA
5974870 AAACTTTAAATTTAAAAAGCTCCTT-TGACCAGAGGTAATG
1 AAACTTTAAATTTAAAAAGCT-CTTCTGACCAGAGGTAATG
* * *
5974910 AAACTTTAAATTTAAAAGGCTTTTCTGTCCAGAGGCT-ATG
1 AAACTTTAAATTTAAAAAGCTCTTCTGACCAGAGG-TAATG
* *
5974950 AAACTTTAAATTT-AAAA-CTCTTCTAACCAGAGGTTATG
1 AAACTTTAAATTTAAAAAGCTCTTCTGACCAGAGGTAATG
* * * *
5974988 AAACTTTTGAAAATTTAAAAAGCTCTTTTGCCCAAAGGCAATG
1 AAAC-TTT--AAATTTAAAAAGCTCTTCTGACCAGAGGTAATG
*
5975031 AAACTTT-AATTAAAAAA
1 AAACTTTAAATTTAAAAA
5975048 AATCTAAGAG
Statistics
Matches: 116, Mismatches: 14, Indels: 17
0.79 0.10 0.12
Matches are distributed among these distances:
37 1 0.01
38 20 0.17
39 17 0.15
40 45 0.39
41 7 0.06
42 7 0.06
43 19 0.16
ACGTcount: A:0.40, C:0.15, G:0.13, T:0.32
Consensus pattern (40 bp):
AAACTTTAAATTTAAAAAGCTCTTCTGACCAGAGGTAATG
Found at i:5974954 original size:80 final size:81
Alignment explanation
Indices: 5974860--5975047 Score: 226
Period size: 81 Copynumber: 2.3 Consensus size: 81
5974850 TCATCTGATT
* *
5974860 AGAGGCTATAAAACTTTAAATTTAAAAAGCTCCTT-TGACCAGAGGTAATGAAAC-TTT-AAATT
1 AGAGGCTATGAAACTTTAAATTTAAAAA-CT-CTTCTAACCAGAGGTAATGAAACTTTTAAAATT
* *
5974922 TAAAAGGCT-TTTCTGTCC
64 TAAAAAGCTCTTT-TGCCC
*
5974940 AGAGGCTATGAAACTTTAAATTT-AAAACTCTTCTAACCAGAGGTTATGAAACTTTTGAAAATTT
1 AGAGGCTATGAAACTTTAAATTTAAAAACTCTTCTAACCAGAGGTAATGAAACTTTT-AAAATTT
5975004 AAAAAGCTCTTTTGCCC
65 AAAAAGCTCTTTTGCCC
* * *
5975021 AAAGGCAATGAAACTTT-AATTAAAAAA
1 AGAGGCTATGAAACTTTAAATTTAAAAA
5975048 AATCTAAGAG
Statistics
Matches: 94, Mismatches: 8, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
77 3 0.03
78 19 0.20
79 7 0.07
80 26 0.28
81 36 0.38
82 3 0.03
ACGTcount: A:0.40, C:0.14, G:0.14, T:0.31
Consensus pattern (81 bp):
AGAGGCTATGAAACTTTAAATTTAAAAACTCTTCTAACCAGAGGTAATGAAACTTTTAAAATTTA
AAAAGCTCTTTTGCCC
Found at i:5975172 original size:33 final size:33
Alignment explanation
Indices: 5975135--5975279 Score: 85
Period size: 33 Copynumber: 4.2 Consensus size: 33
5975125 GCTTTTAAAA
*
5975135 TTAAAAAGCTCCTCTGACTAGAGGCTATGAAAC
1 TTAAAAAGCTCCTCTGACTAGAGGCAATGAAAC
** * * * * *
5975168 TTAAATGGCTCATTTGACCAGAGGCAATGACAT
1 TTAAAAAGCTCCTCTGACTAGAGGCAATGAAAC
* * *
5975201 TTAAAAGAAAGCTCCTCTAAGC-AGAGGCTATGACACAT
1 TT--AA-AAAGCTCCTCTGA-CTAGAGGCAATGA-A-AC
* * *
5975239 TTAAAGAAAACTCCTATGACTAGAAGCAATGAAAC
1 TT-AA-AAAGCTCCTCTGACTAGAGGCAATGAAAC
5975274 TTAAAA
1 TTAAAA
5975280 TTTAAAAGTC
Statistics
Matches: 84, Mismatches: 21, Indels: 14
0.71 0.18 0.12
Matches are distributed among these distances:
33 29 0.35
34 2 0.02
35 5 0.06
36 20 0.24
37 24 0.29
38 4 0.05
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (33 bp):
TTAAAAAGCTCCTCTGACTAGAGGCAATGAAAC
Found at i:5975497 original size:18 final size:19
Alignment explanation
Indices: 5975459--5975498 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
5975449 GAAGAGACCA
*
5975459 TTTTTTTTCTTTTTTTGCT
1 TTTTTTTTCTTATTTTGCT
*
5975478 TTTTTTTTGTTATTTT-CT
1 TTTTTTTTCTTATTTTGCT
5975496 TTT
1 TTT
5975499 AATCTTTGAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 5 0.26
19 14 0.74
ACGTcount: A:0.03, C:0.07, G:0.05, T:0.85
Consensus pattern (19 bp):
TTTTTTTTCTTATTTTGCT
Found at i:5983640 original size:3 final size:3
Alignment explanation
Indices: 5983632--5983680 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
5983622 ATAATATTGC
* * *
5983632 ATT ATT ATT ATT ATT ATT GTT ATT ATT -GT ATT ATT ATT GTT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
5983679 AT
1 AT
5983681 CATCATTTCT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
2 1 0.03
3 38 0.97
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5983642 original size:29 final size:29
Alignment explanation
Indices: 5983607--5983678 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 29
5983597 ATTATTTTTG
5983607 TTATTATCA-TATTGTATAATATTGCATTA
1 TTATTATCATTATTGT-TAATATTGCATTA
* * *
5983636 TTATTATTATTATTGTTATTATTGTATTA
1 TTATTATCATTATTGTTAATATTGCATTA
* *
5983665 TTATTGTTATTATT
1 TTATTATCATTATT
5983679 ATCATCATTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
29 32 0.84
30 6 0.16
ACGTcount: A:0.29, C:0.03, G:0.07, T:0.61
Consensus pattern (29 bp):
TTATTATCATTATTGTTAATATTGCATTA
Found at i:5983663 original size:20 final size:20
Alignment explanation
Indices: 5983640--5983678 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
5983630 GCATTATTAT
5983640 TATTATTATTGTTATTATTG
1 TATTATTATTGTTATTATTG
5983660 TATTATTATTGTTATTATT
1 TATTATTATTGTTATTATT
5983679 ATCATCATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.67
Consensus pattern (20 bp):
TATTATTATTGTTATTATTG
Found at i:5983674 original size:17 final size:17
Alignment explanation
Indices: 5983634--5983680 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 17
5983624 AATATTGCAT
5983634 TATTATTATTATTATTG
1 TATTATTATTATTATTG
5983651 TTATTATTGTATTATTATTG
1 -TATTA-T-TATTATTATTG
5983671 TTATTATTAT
1 -TATTATTAT
5983681 CATCATTTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
18 8 0.30
19 2 0.07
20 17 0.63
ACGTcount: A:0.28, C:0.00, G:0.06, T:0.66
Consensus pattern (17 bp):
TATTATTATTATTATTG
Found at i:5983708 original size:25 final size:24
Alignment explanation
Indices: 5983671--5983729 Score: 64
Period size: 25 Copynumber: 2.4 Consensus size: 24
5983661 ATTATTATTG
* * *
5983671 TTATTATTATCATCATTTCTATTTT
1 TTATTTTTTTCATCATTTCT-TTCT
**
5983696 TTATTTTTTTCATTTTTTCTTTCT
1 TTATTTTTTTCATCATTTCTTTCT
5983720 TTATTTTTTT
1 TTATTTTTTT
5983730 GATTTTTGGC
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
24 13 0.45
25 16 0.55
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.75
Consensus pattern (24 bp):
TTATTTTTTTCATCATTTCTTTCT
Found at i:5983712 original size:16 final size:16
Alignment explanation
Indices: 5983686--5983728 Score: 52
Period size: 16 Copynumber: 2.7 Consensus size: 16
5983676 ATTATCATCA
*
5983686 TTTCTATTTTTTATTTT
1 TTTC-ATTTTTTATTTC
*
5983703 TTTCATTTTTTCTTTC
1 TTTCATTTTTTATTTC
5983719 TTT-ATTTTTT
1 TTTCATTTTTT
5983729 TGATTTTTGG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 7 0.29
16 13 0.54
17 4 0.17
ACGTcount: A:0.09, C:0.09, G:0.00, T:0.81
Consensus pattern (16 bp):
TTTCATTTTTTATTTC
Found at i:5983727 original size:24 final size:25
Alignment explanation
Indices: 5983686--5983736 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 25
5983676 ATTATCATCA
*
5983686 TTTCTATTTTTTATTTTTTTCATTT
1 TTTCTATTCTTTATTTTTTTCATTT
*
5983711 TTTCT-TTCTTTATTTTTTTGATTT
1 TTTCTATTCTTTATTTTTTTCATTT
5983735 TT
1 TT
5983737 GGCAAGAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 19 0.79
25 5 0.21
ACGTcount: A:0.10, C:0.08, G:0.02, T:0.80
Consensus pattern (25 bp):
TTTCTATTCTTTATTTTTTTCATTT
Found at i:5984253 original size:31 final size:31
Alignment explanation
Indices: 5984181--5984268 Score: 104
Period size: 31 Copynumber: 2.8 Consensus size: 31
5984171 TAGATTTTGG
5984181 ATGAATTTTTCGATGAATTTTCTAGCGAAGT
1 ATGAATTTTTCGATGAATTTTCTAGCGAAGT
** * *
5984212 ACAAATTTTTCGATGAATTTTCTGGTGAAGT
1 ATGAATTTTTCGATGAATTTTCTAGCGAAGT
* * *
5984243 ATGAACTTTTCGGTGGGATTTTCTAG
1 ATGAATTTTTCGAT-GAATTTTCTAG
5984269 AAATCGGTAA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
31 37 0.80
32 9 0.20
ACGTcount: A:0.26, C:0.10, G:0.22, T:0.42
Consensus pattern (31 bp):
ATGAATTTTTCGATGAATTTTCTAGCGAAGT
Found at i:5984524 original size:19 final size:19
Alignment explanation
Indices: 5984497--5984536 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5984487 GATCGTAAGG
* *
5984497 TTTTCTTTTTTCATTTTAT
1 TTTTATTTTTTCATTTGAT
*
5984516 TTTTATTTTTTGATTTGAT
1 TTTTATTTTTTCATTTGAT
5984535 TT
1 TT
5984537 GATTTTATTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.05, T:0.78
Consensus pattern (19 bp):
TTTTATTTTTTCATTTGAT
Found at i:5984805 original size:16 final size:18
Alignment explanation
Indices: 5984774--5984810 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
5984764 TAAAATAACA
*
5984774 AAAAATCCTTTTC-AAAT
1 AAAAATCCTTTACAAAAT
5984791 AAAAATCC-TTACAAAAT
1 AAAAATCCTTTACAAAAT
5984808 AAA
1 AAA
5984811 TTTATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 3 0.17
17 15 0.83
ACGTcount: A:0.57, C:0.16, G:0.00, T:0.27
Consensus pattern (18 bp):
AAAAATCCTTTACAAAAT
Found at i:5988414 original size:55 final size:55
Alignment explanation
Indices: 5988325--5988458 Score: 146
Period size: 55 Copynumber: 2.4 Consensus size: 55
5988315 TGTTTTTTTT
* *
5988325 AAGAAAAAAAAAGA-AGAAGAAAAATTGATAGGGCAAAATTCTAATATGCTCCACCAA
1 AAGAAAAAAAAA-ACA-AAGAAAAATTGATAGGGCAAAATGCCAATATGCTCCA-CAA
* * * * * * *
5988382 AA-AAAAAGAAAATAAAGAGAAATTGTTGGGGCAAAATGCCCATATGCTTCACAA
1 AAGAAAAAAAAAACAAAGAAAAATTGATAGGGCAAAATGCCAATATGCTCCACAA
5988436 AAGAAAAAAAAAACAAAGAAAAA
1 AAGAAAAAAAAAACAAAGAAAAA
5988459 GGAAAAAGAA
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
54 5 0.08
55 48 0.75
56 9 0.14
57 2 0.03
ACGTcount: A:0.59, C:0.11, G:0.16, T:0.14
Consensus pattern (55 bp):
AAGAAAAAAAAAACAAAGAAAAATTGATAGGGCAAAATGCCAATATGCTCCACAA
Found at i:5988765 original size:12 final size:12
Alignment explanation
Indices: 5988750--5988833 Score: 54
Period size: 11 Copynumber: 7.3 Consensus size: 12
5988740 AAAAAAAATG
5988750 AAAAGCAAAAAAA
1 AAAAGC-AAAAAA
5988763 AAAAG-AAAAAA
1 AAAAGCAAAAAA
*
5988774 AAAA-C-GAAAA
1 AAAAGCAAAAAA
*
5988784 AAAA-CACAACAA
1 AAAAGCA-AAAAA
*
5988796 CAAA-CAAAAAA
1 AAAAGCAAAAAA
*
5988807 AAAAG-AGAAAA
1 AAAAGCAAAAAA
* *
5988818 ATAAGGAAAAAA
1 AAAAGCAAAAAA
5988830 AAAA
1 AAAA
5988834 CTTAAACTGA
Statistics
Matches: 56, Mismatches: 10, Indels: 11
0.73 0.13 0.14
Matches are distributed among these distances:
10 9 0.16
11 26 0.46
12 16 0.29
13 5 0.09
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.01
Consensus pattern (12 bp):
AAAAGCAAAAAA
Found at i:5988766 original size:13 final size:12
Alignment explanation
Indices: 5988750--5988833 Score: 60
Period size: 12 Copynumber: 6.2 Consensus size: 12
5988740 AAAAAAAATG
5988750 AAAAGCAAAAAAA
1 AAAAG-AAAAAAA
5988763 AAAAGAAAAAAA
1 AAAAGAAAAAAA
*
5988775 AAACGAAAAAAA
1 AAAAGAAAAAAA
*
5988787 ACACAACAACAAACAA
1 A-A-AAGAA-AAA-AA
*
5988803 AAAAAAAAGAGAAA
1 AAAAGAAA-A-AAA
5988817 AATAAGGAAAAAAA
1 AA-AA-GAAAAAAA
5988831 AAA
1 AAA
5988834 CTTAAACTGA
Statistics
Matches: 58, Mismatches: 5, Indels: 16
0.73 0.06 0.20
Matches are distributed among these distances:
12 19 0.33
13 8 0.14
14 17 0.29
15 8 0.14
16 6 0.10
ACGTcount: A:0.82, C:0.08, G:0.08, T:0.01
Consensus pattern (12 bp):
AAAAGAAAAAAA
Found at i:5989738 original size:119 final size:117
Alignment explanation
Indices: 5989527--5990151 Score: 536
Period size: 119 Copynumber: 5.3 Consensus size: 117
5989517 TATCACTCAT
* * * * *
5989527 CTTGATCTTGGCTTAGTCCAGATCATTTCTTATGA-TTCATGGTTTCATCTCAATCATCCATTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTT-GTGGTTTCATCCCGATCAT-TATTTT
* * *
5989591 TTACCTCAACTCGATCTTGGTCACTTCATTTTGACCCATGGTTTCATCCCAATCA
64 TTACCTCAACTCGATCTTGGTAACTTCATTTTGACCCGTGGTTTCATCCC-GTCA
* * * * *
5989646 CTTGATCTTGGCTCAATCAAGATCATTTTTTATGACTTGTAGTTTCATCCCGATCATTAATTTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTTGTGGTTTCATCCCGATCATT-ATTTTT
* * *** **
5989711 TACCTCAAATTGATCTTGGTTGTTTCATTTTGACTTGTGGTTTCATCCTCGTCA
65 TACCTCAACTCGATCTTGGTAACTTCATTTTGACCCGTGGTTTCATCC-CGTCA
* * *
5989765 CTTGATCTTGGGTTAGTCTAGATCATTTCTTATGACTCGTGATTTCATCCCGATCATCTATTTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTTGTGGTTTCATCCCGATCAT-TATTTTT
* * * * *
5989830 GACCTTAACTCGATCTTGGAAACTTCATTCTT-ACCCGTGGTTTCATCACGGTTA
65 TACCTCAACTCGATCTTGGTAACTTCATT-TTGACCCGTGGTTTCATC-CCGTCA
* * ** *
5989884 CTTAATCTTGGCTTAGTCTAGATAATTTCTTATGACTTGTGGTTTCATCTGGGTCATCTATTTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTTGTGGTTTCATCCCGATCAT-TATTTTT
* ** * * ** * *
5989949 GACCTTGACTCAATCTTGGTCACTTCATTTCAACTCGTGGTTTCGTCCCGATCA
65 TACCTCAACTCGATCTTGGTAACTTCATTTTGACCCGTGGTTTCATCCCG-TCA
** * * * * * ** * * *
5990003 CTTGATCTTGGCCCAATATAGACCATTTCTTATGACCTGTGATTTTGT-TCGGTAATTTATTTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTTGTGGTTTCATCCCGATCA-TTATTTTT
* * * * * ***
5990067 GACTTCAACTCGGTATTGGTAACTTCATTTTAACTTATGGTTTCATCCCGATCA
65 TACCTCAACTCGATCTTGGTAACTTCATTTTGACCCGTGGTTTCATCCCG-TCA
* * *
5990121 CTTAATCTTGGCTCAGTCCAGATCATTTCTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTT
5990152 CTAACTCATG
Statistics
Matches: 412, Mismatches: 85, Indels: 19
0.80 0.16 0.04
Matches are distributed among these distances:
118 83 0.20
119 322 0.78
120 7 0.02
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.43
Consensus pattern (117 bp):
CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTTGTGGTTTCATCCCGATCATTATTTTTT
ACCTCAACTCGATCTTGGTAACTTCATTTTGACCCGTGGTTTCATCCCGTCA
Found at i:5989967 original size:238 final size:237
Alignment explanation
Indices: 5989527--5990229 Score: 696
Period size: 238 Copynumber: 3.0 Consensus size: 237
5989517 TATCACTCAT
* * * * * *
5989527 CTTGATCTTGGCTTAGTCCAGATCATTTCTTATGATTCATGGTTTCATCTCAATCATCCATTTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTCGTGATTTCATCTCGATCATCTATTTTT
* * * * * *
5989592 TACCTCAACTCGATCTTGGTCACTTCATTTTGACCCATGGTTTCATCCCAATCACTTGATCTTGG
66 GACCTTAACTCGATCTTGGTAACTTCATTTTAACCCATGGTTTCATCCCGATCACTTAATCTTGG
* * * * * * * * *
5989657 CTCAATCAAGATCATTTTTTATGACTTGTAGTTTCATCCCGATCATTAATTTTTTACCTCAAATT
131 CTCAGTCAAGATCATTTCTTATGACTTGTGGTTTCATCTCGGTCATT-ATTTTTCACCTCGACTC
* *
5989722 GATCTTGGTTGTTTCATTTTGACTTGTGGTTTCATCCTCG-TCA
195 GATCTTGGTTATTTCATTTTGACTCGTGGTTTCATCC-CGATCA
* *
5989765 CTTGATCTTGGGTTAGTCTAGATCATTTCTTATGACTCGTGATTTCATCCCGATCATCTATTTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTCGTGATTTCATCTCGATCATCTATTTTT
* * * * *
5989830 GACCTTAACTCGATCTTGGAAACTTCATTCTT-ACCCGTGGTTTCATCACGGTTACTTAATCTTG
66 GACCTTAACTCGATCTTGGTAACTTCATT-TTAACCCATGGTTTCATCCCGATCACTTAATCTTG
* * * * * *
5989894 GCTTAGTCTAGATAATTTCTTATGACTTGTGGTTTCATCTGGGTCATCTATTTTTGACCTTGACT
130 GCTCAGTCAAGATCATTTCTTATGACTTGTGGTTTCATCTCGGTCAT-TATTTTTCACCTCGACT
* * * ** *
5989959 CAATCTTGGTCACTTCATTTCAACTCGTGGTTTCGTCCCGATCA
194 CGATCTTGGTTATTTCATTTTGACTCGTGGTTTCATCCCGATCA
** * * * ** * * *
5990003 CTTGATCTTGGCCCAATATAGACCATTTCTTATGAC-CTGTGATTTTGT-TCGGTAATTTATTTT
1 CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTC-GTGATTTCATCTCGATCATCTATTTT
* * **
5990066 TGA-CTTCAACTCGGTATTGGTAACTTCATTTTAACTTATGGTTTCATCCCGATCACTTAATCTT
65 TGACCTT-AACTCGATCTTGGTAACTTCATTTTAACCCATGGTTTCATCCCGATCACTTAATCTT
* * * ** * ** *
5990130 GGCTCAGTCCAGATCATTTCTTCTAACTCATGGTTTCGTCTTAGTCATTTATTTTTCATCTCGAC
129 GGCTCAGTCAAGATCATTTCTTATGACTTGTGGTTTCATCTCGGTCA-TTATTTTTCACCTCGAC
* *
5990195 TCGATTTTGGTTATTTCATTCTTGACTCATGGTTT
193 TCGATCTTGGTTATTTCATT-TTGACTCGTGGTTT
5990230 TGTCCAGGTC
Statistics
Matches: 376, Mismatches: 81, Indels: 16
0.79 0.17 0.03
Matches are distributed among these distances:
236 5 0.01
237 128 0.34
238 240 0.64
239 3 0.01
ACGTcount: A:0.20, C:0.22, G:0.15, T:0.44
Consensus pattern (237 bp):
CTTGATCTTGGCTTAGTCTAGATCATTTCTTATGACTCGTGATTTCATCTCGATCATCTATTTTT
GACCTTAACTCGATCTTGGTAACTTCATTTTAACCCATGGTTTCATCCCGATCACTTAATCTTGG
CTCAGTCAAGATCATTTCTTATGACTTGTGGTTTCATCTCGGTCATTATTTTTCACCTCGACTCG
ATCTTGGTTATTTCATTTTGACTCGTGGTTTCATCCCGATCA
Found at i:5990446 original size:38 final size:38
Alignment explanation
Indices: 5990386--5990458 Score: 110
Period size: 38 Copynumber: 1.9 Consensus size: 38
5990376 TTTGGGGTCA
* *
5990386 ATTGAATAGTATTTCATCATTATTTTTATTATTATCAT
1 ATTGAATAGTATTACATCATTATTATTATTATTATCAT
* *
5990424 ATTGTATAGTATTACATTATTATTATTATTATTAT
1 ATTGAATAGTATTACATCATTATTATTATTATTAT
5990459 TGTTGTTGTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 31 1.00
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.56
Consensus pattern (38 bp):
ATTGAATAGTATTACATCATTATTATTATTATTATCAT
Found at i:5994048 original size:31 final size:32
Alignment explanation
Indices: 5993989--5994048 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
5993979 CTTTATGTTA
*
5993989 TAATTTATATAAATTTAGTTTTTGCATTATTT
1 TAATTTATATAAATTTAGTTTCTGCATTATTT
*
5994021 TAATTTA-ATAATTTTAGTTTACT-CATTA
1 TAATTTATATAAATTTAGTTT-CTGCATTA
5994049 ATTCTATTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
31 17 0.68
32 8 0.32
ACGTcount: A:0.33, C:0.05, G:0.05, T:0.57
Consensus pattern (32 bp):
TAATTTATATAAATTTAGTTTCTGCATTATTT
Found at i:5994333 original size:19 final size:19
Alignment explanation
Indices: 5994307--5994359 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
5994297 TTTTTATTTA
5994307 AAAAAAATCATATTTTTTT
1 AAAAAAATCATATTTTTTT
** *
5994326 TTAAAAATCATATATTTTT
1 AAAAAAATCATATTTTTTT
*
5994345 AAAAAAATCAAATTT
1 AAAAAAATCATATTT
5994360 CAAAATTTTT
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
19 27 1.00
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAAAATCATATTTTTTT
Found at i:5994932 original size:23 final size:23
Alignment explanation
Indices: 5994892--5994940 Score: 64
Period size: 24 Copynumber: 2.1 Consensus size: 23
5994882 TTCTTTTTTT
* *
5994892 AAAATTTAT-AAACTTTTTTAAA
1 AAAATTTATAAAAATTTTCTAAA
5994914 AAAATATTATAAAAATTTTCTAAA
1 AAAAT-TTATAAAAATTTTCTAAA
5994938 AAA
1 AAA
5994941 CATAAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 5 0.22
23 4 0.17
24 14 0.61
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (23 bp):
AAAATTTATAAAAATTTTCTAAA
Found at i:5994971 original size:8 final size:8
Alignment explanation
Indices: 5994960--5994987 Score: 56
Period size: 8 Copynumber: 3.5 Consensus size: 8
5994950 AAAAAATATG
5994960 AAAATTTT
1 AAAATTTT
5994968 AAAATTTT
1 AAAATTTT
5994976 AAAATTTT
1 AAAATTTT
5994984 AAAA
1 AAAA
5994988 AAATTAAAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AAAATTTT
Found at i:5994971 original size:16 final size:16
Alignment explanation
Indices: 5994952--5994987 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
5994942 ATAAAAATAA
5994952 AAAATATGAAAATTTT
1 AAAATATGAAAATTTT
* *
5994968 AAAATTTTAAAATTTT
1 AAAATATGAAAATTTT
5994984 AAAA
1 AAAA
5994988 AAATTAAAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (16 bp):
AAAATATGAAAATTTT
Found at i:5997821 original size:29 final size:29
Alignment explanation
Indices: 5997767--5997822 Score: 69
Period size: 29 Copynumber: 1.9 Consensus size: 29
5997757 AATTGAAATC
*
5997767 CAATTAGTTGTAAATTAGTTTGTAATATT
1 CAATTAGTTGTAAATTAATTTGTAATATT
* *
5997796 CAATTAGTTTTCAAA-TAATTTTTAATA
1 CAATTAGTTGT-AAATTAATTTGTAATA
5997823 AAAGTTTTTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
29 20 0.87
30 3 0.13
ACGTcount: A:0.38, C:0.05, G:0.09, T:0.48
Consensus pattern (29 bp):
CAATTAGTTGTAAATTAATTTGTAATATT
Found at i:5998272 original size:86 final size:84
Alignment explanation
Indices: 5998131--5998297 Score: 282
Period size: 86 Copynumber: 2.0 Consensus size: 84
5998121 TATTTATTAC
5998131 TTAACCTTTTCTTGATTGATGTTCATCAAAATAATTTAATAATTCATATTAAAATTAATATATAT
1 TTAACCTTTTCTTGATTGATGTTCATCAAAATAATTTAATAATTCATATTAAAATT-A-ATATAT
5998196 CTGAATTTAAAGATAAATATA
64 CTGAATTTAAAGATAAATATA
* *
5998217 TTAACCTTTTCTTGATTGATGTTTATCAAAATAATTTAATACATTCATCTT-AAATTAATATATC
1 TTAACCTTTTCTTGATTGATGTTCATCAAAATAATTTAATA-ATTCATATTAAAATTAATATATC
5998281 TGAATTTAAAGATAAAT
65 TGAATTTAAAGATAAAT
5998298 TTAGTATATT
Statistics
Matches: 78, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
84 24 0.31
85 1 0.01
86 45 0.58
87 8 0.10
ACGTcount: A:0.41, C:0.09, G:0.06, T:0.44
Consensus pattern (84 bp):
TTAACCTTTTCTTGATTGATGTTCATCAAAATAATTTAATAATTCATATTAAAATTAATATATCT
GAATTTAAAGATAAATATA
Found at i:6003860 original size:2 final size:2
Alignment explanation
Indices: 6003847--6003882 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
6003837 CGAATTGCAA
* *
6003847 AG AG AA AG AG AG AG AG AG AG AG AG AG AG GG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
6003883 GGAGGGAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:6003883 original size:8 final size:8
Alignment explanation
Indices: 6003853--6003899 Score: 58
Period size: 8 Copynumber: 5.9 Consensus size: 8
6003843 GCAAAGAGAA
*
6003853 AGAGAGAG
1 AGAGAGGG
*
6003861 AGAGAGAG
1 AGAGAGGG
6003869 AGAGAGGG
1 AGAGAGGG
6003877 AGAGAGGG
1 AGAGAGGG
*
6003885 AGGGAGGG
1 AGAGAGGG
*
6003893 AGGGAGG
1 AGAGAGG
6003900 AAGGAACTAG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 37 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (8 bp):
AGAGAGGG
Found at i:6003895 original size:12 final size:12
Alignment explanation
Indices: 6003853--6003899 Score: 58
Period size: 12 Copynumber: 3.9 Consensus size: 12
6003843 GCAAAGAGAA
* *
6003853 AGAGAGAGAGAG
1 AGAGAGGGAGGG
*
6003865 AGAGAGAGAGGG
1 AGAGAGGGAGGG
6003877 AGAGAGGGAGGG
1 AGAGAGGGAGGG
*
6003889 AGGGAGGGAGG
1 AGAGAGGGAGG
6003900 AAGGAACTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.38, C:0.00, G:0.62, T:0.00
Consensus pattern (12 bp):
AGAGAGGGAGGG
Found at i:6013660 original size:12 final size:12
Alignment explanation
Indices: 6013645--6013698 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
6013635 GGAGTTAGTA
*
6013645 TTTTGTTTAGGG
1 TTTTATTTAGGG
6013657 TTTTAATTCTAGGG
1 TTTT-ATT-TAGGG
*
6013671 TTTCATTTAGGG
1 TTTTATTTAGGG
*
6013683 TTATATTTA-GG
1 TTTTATTTAGGG
6013694 TTTTA
1 TTTTA
6013699 AAATTGGGGT
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
11 6 0.17
12 16 0.46
13 5 0.14
14 8 0.23
ACGTcount: A:0.19, C:0.04, G:0.22, T:0.56
Consensus pattern (12 bp):
TTTTATTTAGGG
Found at i:6015947 original size:5 final size:5
Alignment explanation
Indices: 6015937--6015970 Score: 68
Period size: 5 Copynumber: 6.8 Consensus size: 5
6015927 ATGATGACAA
6015937 ATATT ATATT ATATT ATATT ATATT ATATT ATAT
1 ATATT ATATT ATATT ATATT ATATT ATATT ATAT
6015971 AAATATTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 29 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (5 bp):
ATATT
Found at i:6017397 original size:22 final size:23
Alignment explanation
Indices: 6017355--6017405 Score: 86
Period size: 22 Copynumber: 2.3 Consensus size: 23
6017345 AAATTTATTG
6017355 GTATTTCTTTGGTATTTTTGCTA
1 GTATTTCTTTGGTATTTTTGCTA
6017378 GTATTTCTTTGGT-TTTTTGCTA
1 GTATTTCTTTGGTATTTTTGCTA
*
6017400 CTATTT
1 GTATTT
6017406 GTTTTCTAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
22 14 0.52
23 13 0.48
ACGTcount: A:0.12, C:0.10, G:0.16, T:0.63
Consensus pattern (23 bp):
GTATTTCTTTGGTATTTTTGCTA
Found at i:6018069 original size:17 final size:16
Alignment explanation
Indices: 6018047--6018083 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 16
6018037 TAATATGAGA
6018047 CAATCTAATAATAAATG
1 CAATCTAATAATAAA-G
*
6018064 CAATCTTATAATAAAG
1 CAATCTAATAATAAAG
6018080 CAAT
1 CAAT
6018084 ATGATGAATA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.51, C:0.14, G:0.05, T:0.30
Consensus pattern (16 bp):
CAATCTAATAATAAAG
Found at i:6018850 original size:12 final size:12
Alignment explanation
Indices: 6018835--6018884 Score: 55
Period size: 12 Copynumber: 3.9 Consensus size: 12
6018825 ACTAGAATGA
6018835 AAACTAGATTTG
1 AAACTAGATTTG
6018847 AAACTAGATTTGTTG
1 AAACTAGA--T-TTG
*
6018862 AAGCTAGATTTG
1 AAACTAGATTTG
*
6018874 AAACTGGATTT
1 AAACTAGATTT
6018885 AAGGTTTGTG
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
12 20 0.62
13 1 0.03
14 1 0.03
15 10 0.31
ACGTcount: A:0.36, C:0.08, G:0.20, T:0.36
Consensus pattern (12 bp):
AAACTAGATTTG
Found at i:6018868 original size:15 final size:15
Alignment explanation
Indices: 6018844--6018873 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
6018834 AAAACTAGAT
6018844 TTGAAACTAGATTTG
1 TTGAAACTAGATTTG
*
6018859 TTGAAGCTAGATTTG
1 TTGAAACTAGATTTG
6018874 AAACTGGATT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.23, T:0.40
Consensus pattern (15 bp):
TTGAAACTAGATTTG
Found at i:6018979 original size:18 final size:18
Alignment explanation
Indices: 6018939--6018980 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
6018929 TATATTAGCT
*
6018939 AAAGCAGATGCAAATGTA
1 AAAGCAGATGCAAATGCA
*
6018957 TAAGCAGAT-CTAAATGCA
1 AAAGCAGATGC-AAATGCA
6018975 AAAGCA
1 AAAGCA
6018981 AAGCTGATAT
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 1 0.05
18 19 0.95
ACGTcount: A:0.50, C:0.14, G:0.19, T:0.17
Consensus pattern (18 bp):
AAAGCAGATGCAAATGCA
Found at i:6021615 original size:42 final size:42
Alignment explanation
Indices: 6021568--6021665 Score: 135
Period size: 42 Copynumber: 2.3 Consensus size: 42
6021558 GTTTCTATCT
6021568 TTTCATTCCCTACTGTC-TCACCAATATGTTAATTTTTTACCC
1 TTTCATTCCCTACTG-CATCACCAATATGTTAATTTTTTACCC
* * * *
6021610 TTTCATTCCCTACTGCATCAGCTATGTGTTGATTTTTTACCC
1 TTTCATTCCCTACTGCATCACCAATATGTTAATTTTTTACCC
*
6021652 TTTCATTCTCTACT
1 TTTCATTCCCTACT
6021666 ACCTTAGCTA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
41 1 0.02
42 49 0.98
ACGTcount: A:0.18, C:0.28, G:0.07, T:0.47
Consensus pattern (42 bp):
TTTCATTCCCTACTGCATCACCAATATGTTAATTTTTTACCC
Found at i:6022128 original size:38 final size:39
Alignment explanation
Indices: 6022081--6022155 Score: 91
Period size: 40 Copynumber: 1.9 Consensus size: 39
6022071 TAAACCCTAA
*
6022081 ATTTTAGCAACAA-CAAT-TGATAAGTGTTATAAGAATC
1 ATTTTAGCAAAAATCAATGTGATAAGTGTTATAAGAATC
** *
6022118 ATTTCTAGCAAAAATTTATGTTATAAGTGTTATAAGAA
1 ATTT-TAGCAAAAATCAATGTGATAAGTGTTATAAGAA
6022156 ACCCTAAATC
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
37 4 0.13
38 8 0.26
39 2 0.06
40 17 0.55
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (39 bp):
ATTTTAGCAAAAATCAATGTGATAAGTGTTATAAGAATC
Found at i:6022284 original size:32 final size:32
Alignment explanation
Indices: 6022222--6022285 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
6022212 GTTGTTATCT
* * **
6022222 AATTTTTGTTATAATCTTTTACTTTATTATAA
1 AATTTATGTTATAAGCTTTTACCATATTATAA
*
6022254 AATTTATGTTATAAGCTTTTACCATCTTATAA
1 AATTTATGTTATAAGCTTTTACCATATTATAA
6022286 CCAAGGGTCT
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.33, C:0.09, G:0.05, T:0.53
Consensus pattern (32 bp):
AATTTATGTTATAAGCTTTTACCATATTATAA
Found at i:6022611 original size:42 final size:42
Alignment explanation
Indices: 6022564--6022657 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 42
6022554 TTAATTCGAC
* *
6022564 TAATTAAGAACAATAGCATA-AAACCTCAAATGTAAATTTGAA
1 TAATTAAAAACAATAGCA-AGAAACCTCAAATATAAATTTGAA
* * *
6022606 TAATTAAAAACAATAGCAAGAAACCTTAATTATAAATTTGAG
1 TAATTAAAAACAATAGCAAGAAACCTCAAATATAAATTTGAA
*
6022648 CAATTAAAAA
1 TAATTAAAAA
6022658 TGATAACACA
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
41 1 0.02
42 44 0.98
ACGTcount: A:0.54, C:0.11, G:0.09, T:0.27
Consensus pattern (42 bp):
TAATTAAAAACAATAGCAAGAAACCTCAAATATAAATTTGAA
Found at i:6023283 original size:62 final size:63
Alignment explanation
Indices: 6023154--6023283 Score: 174
Period size: 63 Copynumber: 2.1 Consensus size: 63
6023144 TGGGATTATG
* * * * *
6023154 AAAACGCCTTGAATAATCTTTTTAAAAAAATTAAACGGGATTATTTAAGGCATTTTCTGATAA
1 AAAATGCCTTGAATAATCTTTTTAAAAAAATTAAACGGGATTATTCAAGACAGTTTCTGACAA
**
6023217 AAAATGCCTTGAATAATCTTTTTAAAAAAATTGAATTGGG-TTATTCAAGAC-GTTTCTGACAA
1 AAAATGCCTTGAATAATCTTTTTAAAAAAATT-AAACGGGATTATTCAAGACAGTTTCTGACAA
6023279 AAAAT
1 AAAAT
6023284 ATATTGAACA
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
62 14 0.24
63 40 0.68
64 5 0.08
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.35
Consensus pattern (63 bp):
AAAATGCCTTGAATAATCTTTTTAAAAAAATTAAACGGGATTATTCAAGACAGTTTCTGACAA
Found at i:6023291 original size:62 final size:63
Alignment explanation
Indices: 6023162--6023297 Score: 159
Period size: 63 Copynumber: 2.2 Consensus size: 63
6023152 TGAAAACGCC
* * * * * *
6023162 TTGAATAATCTTTTTAAAAAAATTAAACGGGATTATTTAAGGCATTTTCTGATAAAAAATGCC
1 TTGAATAATCTTTTTAAAAAAATTAAACGGGATTATTCAAGACAGTTTCTGACAAAAAATACA
** *
6023225 TTGAATAATCTTTTTAAAAAAATTGAATTGGG-TTATTCAAGAC-GTTTCTGACAAAAAATATA
1 TTGAATAATCTTTTTAAAAAAATT-AAACGGGATTATTCAAGACAGTTTCTGACAAAAAATACA
*
6023287 TTGAACAATCT
1 TTGAATAATCT
6023298 CCTTCAATTT
Statistics
Matches: 62, Mismatches: 10, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
62 24 0.39
63 33 0.53
64 5 0.08
ACGTcount: A:0.41, C:0.10, G:0.12, T:0.37
Consensus pattern (63 bp):
TTGAATAATCTTTTTAAAAAAATTAAACGGGATTATTCAAGACAGTTTCTGACAAAAAATACA
Found at i:6023418 original size:65 final size:62
Alignment explanation
Indices: 6023287--6023486 Score: 187
Period size: 65 Copynumber: 3.2 Consensus size: 62
6023277 AAAAAATATA
* * * * * **
6023287 TTGAACAATCTCCTTCAATTTTTA-TAAAAAGATTATTCAAGGTGTTTTTGACCAAAACAGTT
1 TTGAATAATCTCCTTCAATTTTTATTGAAGAGATTATTCAAGGTATTTTTGACCAAAATA-CC
*
6023349 TTGAATAATCTCCTTCAATTTTTAATTGAAGTAGATTATTCAAGGCATTTTTGACCAGAAATACC
1 TTGAATAATCTCCTTCAATTTTT-ATTGAAG-AGATTATTCAAGGTATTTTTGACCA-AAATACC
* * *
6023414 TTGAATAATC-CCCTCTTATTTTT-TTG--G-GATTATTCAAGGTATTTTTGGCCAAAAAAATAC
1 TTGAATAATCTCCTTC-AATTTTTATTGAAGAGATTATTCAAGGTATTTTTGACC---AAAATAC
6023474 C
62 C
6023475 TTGAATAATCTC
1 TTGAATAATCTC
6023487 TTATAAAAAA
Statistics
Matches: 117, Mismatches: 12, Indels: 18
0.80 0.08 0.12
Matches are distributed among these distances:
59 21 0.18
61 18 0.15
62 24 0.21
63 4 0.03
64 7 0.06
65 39 0.33
66 4 0.03
ACGTcount: A:0.33, C:0.15, G:0.12, T:0.40
Consensus pattern (62 bp):
TTGAATAATCTCCTTCAATTTTTATTGAAGAGATTATTCAAGGTATTTTTGACCAAAATACC
Found at i:6025477 original size:11 final size:11
Alignment explanation
Indices: 6025461--6025520 Score: 61
Period size: 12 Copynumber: 5.4 Consensus size: 11
6025451 GCTGTTTCTA
6025461 TTTTTTTATA-
1 TTTTTTTATAT
6025471 TTTTTTTA-AT
1 TTTTTTTATAT
*
6025481 TTTATTTAGTAT
1 TTTTTTTA-TAT
*
6025493 TTTATTTATAT
1 TTTTTTTATAT
6025504 GTTTTTTTAGTAT
1 -TTTTTTTA-TAT
6025517 TTTT
1 TTTT
6025521 GCATGATTAA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
9 1 0.02
10 15 0.35
11 3 0.07
12 21 0.49
13 3 0.07
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (11 bp):
TTTTTTTATAT
Found at i:6025494 original size:12 final size:10
Alignment explanation
Indices: 6025459--6025520 Score: 63
Period size: 10 Copynumber: 5.7 Consensus size: 10
6025449 GAGCTGTTTC
6025459 TATTTTTTTA
1 TATTTTTTTA
6025469 TATTTTTTTA
1 TATTTTTTTA
6025479 -ATTTTATTTA
1 TATTTT-TTTA
6025489 GTATTTTATTTA
1 -TATTTT-TTTA
6025501 TATGTTTTTTTA
1 TA--TTTTTTTA
6025513 GTATTTTT
1 -TATTTTT
6025521 GCATGATTAA
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
9 5 0.11
10 14 0.30
11 7 0.15
12 14 0.30
13 6 0.13
ACGTcount: A:0.21, C:0.00, G:0.05, T:0.74
Consensus pattern (10 bp):
TATTTTTTTA
Found at i:6025517 original size:24 final size:21
Alignment explanation
Indices: 6025461--6025520 Score: 77
Period size: 24 Copynumber: 2.8 Consensus size: 21
6025451 GCTGTTTCTA
6025461 TTTTTTTA-TATTTTTTTAAT
1 TTTTTTTAGTATTTTTTTAAT
*
6025481 TTTATTTAGTATTTTATTTATAT
1 TTTTTTTAGTATTTT-TTTA-AT
6025504 GTTTTTTTAGTATTTTT
1 -TTTTTTTAGTATTTTT
6025521 GCATGATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 7 0.21
21 6 0.18
22 4 0.12
23 3 0.09
24 14 0.41
ACGTcount: A:0.20, C:0.00, G:0.05, T:0.75
Consensus pattern (21 bp):
TTTTTTTAGTATTTTTTTAAT
Found at i:6027479 original size:18 final size:18
Alignment explanation
Indices: 6027443--6027480 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
6027433 AGAAAATGAG
*
6027443 AAAATGAAAGAATGGAAA
1 AAAATGAAAGAATGAAAA
6027461 AAAATGAAAAGAA-GAAAA
1 AAAATG-AAAGAATGAAAA
6027479 AA
1 AA
6027481 GAAAGACTCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 12 0.67
19 6 0.33
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (18 bp):
AAAATGAAAGAATGAAAA
Found at i:6028287 original size:23 final size:22
Alignment explanation
Indices: 6028261--6028304 Score: 52
Period size: 23 Copynumber: 2.0 Consensus size: 22
6028251 AAAGCCTATG
*
6028261 AATGGCGATCAAGTGATGAAAAT
1 AATGACGATCAAGTGAT-AAAAT
* *
6028284 AATGATGATCAATTGATAAAA
1 AATGACGATCAAGTGATAAAA
6028305 CTTATTCTAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
22 4 0.22
23 14 0.78
ACGTcount: A:0.48, C:0.07, G:0.20, T:0.25
Consensus pattern (22 bp):
AATGACGATCAAGTGATAAAAT
Found at i:6028673 original size:21 final size:21
Alignment explanation
Indices: 6028649--6028963 Score: 346
Period size: 21 Copynumber: 14.8 Consensus size: 21
6028639 GTGAATCCTC
6028649 AAATGAGAATCTTTGAGTTTT
1 AAATGAGAATCTTTGAGTTTT
* *
6028670 AAATGAGAATCTTTAAGTCTT
1 AAATGAGAATCTTTGAGTTTT
* *
6028691 AAATGAG--TTTTTGAGTTTC
1 AAATGAGAATCTTTGAGTTTT
* *
6028710 AAATGGGAATGTTTGAGTTTT
1 AAATGAGAATCTTTGAGTTTT
* *
6028731 AAACGAAAATCTTTGAGTTTT
1 AAATGAGAATCTTTGAGTTTT
*
6028752 CCAATGAGAATCTTTGAGTTTTT
1 -AAATGAGAATCTTTGAG-TTTT
* *
6028775 AAATGAGTATCTTTGAGTTTC
1 AAATGAGAATCTTTGAGTTTT
* * * *
6028796 AAATGAAAATCTTTTAGTCTC
1 AAATGAGAATCTTTGAGTTTT
*
6028817 AAATGAGAATCTTTGAGTGTTC
1 AAATGAGAATCTTTGAGT-TTT
* *
6028839 AAATAAGAATCTTTGAGTGTTC
1 AAATGAGAATCTTTGAGT-TTT
*
6028861 AAATGAGAATCTTTAAGTTTT
1 AAATGAGAATCTTTGAGTTTT
*
6028882 CAAATGAGAATCTTTAAGTTTT
1 -AAATGAGAATCTTTGAGTTTT
*
6028904 CAAATGAGAATCTTTGAGTTTC
1 -AAATGAGAATCTTTGAGTTTT
*
6028926 AAATGAGAATCTCTGAGTTTT
1 AAATGAGAATCTTTGAGTTTT
* *
6028947 TAATGAAAATCTTTGAG
1 AAATGAGAATCTTTGAG
6028964 ATGTGAAACC
Statistics
Matches: 251, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
19 14 0.06
21 124 0.49
22 109 0.43
23 4 0.02
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (21 bp):
AAATGAGAATCTTTGAGTTTT
Found at i:6028766 original size:22 final size:22
Alignment explanation
Indices: 6028647--6028963 Score: 375
Period size: 22 Copynumber: 14.9 Consensus size: 22
6028637 TTGTGAATCC
6028647 TCAAATGAGAATCTTTGAGTTT
1 TCAAATGAGAATCTTTGAGTTT
* *
6028669 T-AAATGAGAATCTTTAAGTCT
1 TCAAATGAGAATCTTTGAGTTT
*
6028690 T-AAATGAG--TTTTTGAG-TT
1 TCAAATGAGAATCTTTGAGTTT
* *
6028708 TCAAATGGGAATGTTTGAGTTT
1 TCAAATGAGAATCTTTGAGTTT
* *
6028730 T-AAACGAAAATCTTTGAGTTT
1 TCAAATGAGAATCTTTGAGTTT
*
6028751 TCCAATGAGAATCTTTGAGTTT
1 TCAAATGAGAATCTTTGAGTTT
* *
6028773 TTAAATGAGTATCTTTGAG-TT
1 TCAAATGAGAATCTTTGAGTTT
* * *
6028794 TCAAATGAAAATCTTTTAG-TC
1 TCAAATGAGAATCTTTGAGTTT
*
6028815 TCAAATGAGAATCTTTGAGTGT
1 TCAAATGAGAATCTTTGAGTTT
* *
6028837 TCAAATAAGAATCTTTGAGTGT
1 TCAAATGAGAATCTTTGAGTTT
*
6028859 TCAAATGAGAATCTTTAAGTTT
1 TCAAATGAGAATCTTTGAGTTT
*
6028881 TCAAATGAGAATCTTTAAGTTT
1 TCAAATGAGAATCTTTGAGTTT
6028903 TCAAATGAGAATCTTTGAG-TT
1 TCAAATGAGAATCTTTGAGTTT
*
6028924 TCAAATGAGAATCTCTGAGTTT
1 TCAAATGAGAATCTTTGAGTTT
* *
6028946 T-TAATGAAAATCTTTGAG
1 TCAAATGAGAATCTTTGAG
6028964 ATGTGAAACC
Statistics
Matches: 253, Mismatches: 35, Indels: 15
0.83 0.12 0.05
Matches are distributed among these distances:
18 2 0.01
19 12 0.05
21 119 0.47
22 120 0.47
ACGTcount: A:0.33, C:0.09, G:0.18, T:0.40
Consensus pattern (22 bp):
TCAAATGAGAATCTTTGAGTTT
Found at i:6029476 original size:16 final size:16
Alignment explanation
Indices: 6029455--6029501 Score: 62
Period size: 16 Copynumber: 3.0 Consensus size: 16
6029445 AAAAACATTA
6029455 TGAATCTGAAATTTTG
1 TGAATCTGAAATTTTG
6029471 TGAATC--AAATTATTG
1 TGAATCTGAAATT-TTG
*
6029486 TGAAACTGAAATTTTG
1 TGAATCTGAAATTTTG
6029502 AAAATCAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
14 5 0.19
15 8 0.30
16 9 0.33
17 5 0.19
ACGTcount: A:0.36, C:0.06, G:0.17, T:0.40
Consensus pattern (16 bp):
TGAATCTGAAATTTTG
Done.