Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold141
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: 2772588
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.32
Warning! 118404 characters in sequence are not A, C, G, or T
File 16 of 18
Found at i:2451646 original size:51 final size:51
Alignment explanation
Indices: 2451570--2451707 Score: 181
Period size: 51 Copynumber: 2.7 Consensus size: 51
2451560 TTATTTCTGA
* *
2451570 GGGGATACTCCAACCCCGA-TTTTATTTTCAAAATATCAACTTT-TCACCATC
1 GGGGATACTCCAA-CCCTATTTTTATTTCCAAAATATCAA-TTTCTCACCATC
** *
2451621 GGGGATACTCTGACCCTATTTTTATTTCCAAAATATCGATTTCTCACCATC
1 GGGGATACTCCAACCCTATTTTTATTTCCAAAATATCAATTTCTCACCATC
* *
2451672 GGGGATACTCCAACCCTGTTTTTATCTCCAAAATAT
1 GGGGATACTCCAACCCTATTTTTATTTCCAAAATAT
2451708 TAAATTTTTT
Statistics
Matches: 76, Mismatches: 9, Indels: 4
0.85 0.10 0.04
Matches are distributed among these distances:
50 7 0.09
51 69 0.91
ACGTcount: A:0.28, C:0.26, G:0.12, T:0.35
Consensus pattern (51 bp):
GGGGATACTCCAACCCTATTTTTATTTCCAAAATATCAATTTCTCACCATC
Found at i:2456413 original size:20 final size:20
Alignment explanation
Indices: 2456384--2456454 Score: 97
Period size: 20 Copynumber: 3.5 Consensus size: 20
2456374 AAAAAGACAT
2456384 AATGTATCGATACATTGAAA
1 AATGTATCGATACATTGAAA
* * *
2456404 AATATATCGATACATTCATA
1 AATGTATCGATACATTGAAA
* *
2456424 CATGTATCGATATATTGAAA
1 AATGTATCGATACATTGAAA
2456444 AATGTATCGAT
1 AATGTATCGAT
2456455 GCATCTAAGT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (20 bp):
AATGTATCGATACATTGAAA
Found at i:2457199 original size:29 final size:29
Alignment explanation
Indices: 2457017--2457756 Score: 951
Period size: 29 Copynumber: 25.3 Consensus size: 29
2457007 TTTTTAAAAA
* *
2457017 AAAAGGGTGCCACTAACTTATGTGGGCCTTG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
* *
2457048 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
* * *
2457080 AAAAGAGTTACCACTGGCTTGTGGGCTTT-
1 AAAAG-GGTGCCACTGACTTGTGGGCTTTG
2457109 AAAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
2457138 -GAAGGGTGCCACTGATTTGTGTGGGCTTTG
1 AAAAGGGTGCCACTGA-CT-TGTGGGCTTTG
* *
2457168 AAAAGAGTGCCACTGACTTGTGGGCATTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457197 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
2457226 AAAAGAGTGCCACTGACTTGTGGGTTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457255 AAAA-GGTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457283 AAAAGGGTGCCACTGACTTCTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
2457312 AAAGGGGTGCCACTGTCTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* * *
2457341 AAAAGAGTGCCACTAACTTATGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457369 AAAAGGCTGCCACTGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
2457400 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
2457429 -AAAGGCTGCCACTAACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
* *
2457457 AAAAGAGTTGCCACCGACTCGTGTGGGCTTTG
1 AAAAG-GGTGCCACTGACT--TGTGGGCTTTG
*
2457489 AAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457518 AAAAGAGTGCCACTGACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457546 AAAAGGGTGCCAATGACTTGCGTGGGCTTTG
1 AAAAGGGTGCCACTGACTT--GTGGGCTTTG
*
2457577 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
2457606 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457634 AAAAGAGTGCCACTGACTTGTGGGCTTT-
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
*
2457662 AAAAGGGTGCCAATGACTTGTGTGGGCTTTG
1 AAAAGGGTGCCACTGAC-T-TGTGGGCTTTG
*
2457693 AAAGGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
2457722 -AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAAGGGTGCCACTGACTTGTGGGCTTTG
2457750 -AAAGGGT
1 AAAAGGGT
2457757 TTGAACGTTC
Statistics
Matches: 630, Mismatches: 58, Indels: 45
0.86 0.08 0.06
Matches are distributed among these distances:
28 193 0.31
29 248 0.39
30 60 0.10
31 78 0.12
32 51 0.08
ACGTcount: A:0.22, C:0.18, G:0.33, T:0.28
Consensus pattern (29 bp):
AAAAGGGTGCCACTGACTTGTGGGCTTTG
Found at i:2458970 original size:10 final size:10
Alignment explanation
Indices: 2458956--2459012 Score: 71
Period size: 10 Copynumber: 5.7 Consensus size: 10
2458946 GACCCTTCTA
2458956 TTTTTTTGCT
1 TTTTTTTGCT
*
2458966 ATTTTTT-CT
1 TTTTTTTGCT
*
2458975 TTTTTTTTCT
1 TTTTTTTGCT
*
2458985 TTTTTTTGTTT
1 TTTTTTTG-CT
2458996 TTTTTTTGCT
1 TTTTTTTGCT
2459006 TTTTTTT
1 TTTTTTT
2459013 TGTGTAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
9 8 0.20
10 23 0.57
11 9 0.22
ACGTcount: A:0.02, C:0.07, G:0.05, T:0.86
Consensus pattern (10 bp):
TTTTTTTGCT
Found at i:2458979 original size:9 final size:9
Alignment explanation
Indices: 2458951--2459000 Score: 55
Period size: 9 Copynumber: 5.2 Consensus size: 9
2458941 ATCTAGACCC
2458951 TTCTATTTTT
1 TTCT-TTTTT
*
2458961 TTGCTATTTT
1 TT-CTTTTTT
2458971 TTCTTTTTTT
1 TTC-TTTTTT
2458981 TTCTTTTTT
1 TTCTTTTTT
*
2458990 TTGTTTTTT
1 TTCTTTTTT
2458999 TT
1 TT
2459001 TTGCTTTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
9 17 0.49
10 16 0.46
11 2 0.06
ACGTcount: A:0.04, C:0.08, G:0.04, T:0.84
Consensus pattern (9 bp):
TTCTTTTTT
Found at i:2458980 original size:19 final size:19
Alignment explanation
Indices: 2458951--2459000 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
2458941 ATCTAGACCC
2458951 TTCTATTTTTTTGCTATTTT
1 TTCT-TTTTTTTGCTATTTT
* *
2458971 TTCTTTTTTTTTCTTTTTT
1 TTCTTTTTTTTGCTATTTT
*
2458990 TTGTTTTTTTT
1 TTCTTTTTTTT
2459001 TTGCTTTTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 23 0.85
20 4 0.15
ACGTcount: A:0.04, C:0.08, G:0.04, T:0.84
Consensus pattern (19 bp):
TTCTTTTTTTTGCTATTTT
Found at i:2459013 original size:11 final size:11
Alignment explanation
Indices: 2458956--2459014 Score: 72
Period size: 11 Copynumber: 5.7 Consensus size: 11
2458946 GACCCTTCTA
2458956 TTTTTTTGC-T
1 TTTTTTTGCTT
*
2458966 ATTTTTT-CTT
1 TTTTTTTGCTT
2458976 TTTTTTT-C-T
1 TTTTTTTGCTT
*
2458985 TTTTTTTGTTT
1 TTTTTTTGCTT
2458996 TTTTTTTGCTT
1 TTTTTTTGCTT
2459007 TTTTTTTG
1 TTTTTTTG
2459015 TGTAAATGAT
Statistics
Matches: 42, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
9 9 0.21
10 14 0.33
11 19 0.45
ACGTcount: A:0.02, C:0.07, G:0.07, T:0.85
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:2471777 original size:20 final size:20
Alignment explanation
Indices: 2471713--2471779 Score: 71
Period size: 20 Copynumber: 3.4 Consensus size: 20
2471703 AAAAAGACAT
*
2471713 AATGTATCAATACATTGAAG
1 AATGTATCAATACATTGAAA
* * *
2471733 AATATATCAATACATTCATA
1 AATGTATCAATACATTGAAA
* * *
2471753 CATGTATCGATATATTGAAA
1 AATGTATCAATACATTGAAA
2471773 AATGTAT
1 AATGTAT
2471780 TGATACATCT
Statistics
Matches: 36, Mismatches: 11, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.34
Consensus pattern (20 bp):
AATGTATCAATACATTGAAA
Found at i:2472330 original size:3 final size:3
Alignment explanation
Indices: 2472322--2472356 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
2472312 ACATTAACTT
2472322 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
2472357 GTAGGAGAGA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:2474296 original size:54 final size:55
Alignment explanation
Indices: 2474209--2474326 Score: 186
Period size: 54 Copynumber: 2.2 Consensus size: 55
2474199 TTAGATATTA
* *
2474209 ATGTTAAATAATAGGTCAAGTTTGATGTGCTTTTGCCATATAACTTGACTATCTT
1 ATGTTAAATAATAGGTCAAGTTTGATGTACTTTTGCAATATAACTTGACTATCTT
*
2474264 ATGTT-AATAATAGGTCAAGTTTGGTGTACTTTTGCAATATAACTTGACTATCTT
1 ATGTTAAATAATAGGTCAAGTTTGATGTACTTTTGCAATATAACTTGACTATCTT
2474318 AATG-TAAAT
1 -ATGTTAAAT
2474327 GCTCTAGAAA
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
54 47 0.81
55 11 0.19
ACGTcount: A:0.31, C:0.11, G:0.16, T:0.42
Consensus pattern (55 bp):
ATGTTAAATAATAGGTCAAGTTTGATGTACTTTTGCAATATAACTTGACTATCTT
Found at i:2477351 original size:26 final size:26
Alignment explanation
Indices: 2477287--2477358 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 26
2477277 CTTATTATCA
2477287 TTATATTATATATATAATATATAATT
1 TTATATTATATATATAATATATAATT
* * **
2477313 TTAAATTAT-TATATTCATATATTGTTT
1 TTATATTATATATA-TAATATA-TAATT
*
2477340 TTATATTATATATAAAATA
1 TTATATTATATATATAATA
2477359 AAATTAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
25 4 0.11
26 14 0.39
27 14 0.39
28 4 0.11
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.54
Consensus pattern (26 bp):
TTATATTATATATATAATATATAATT
Found at i:2478774 original size:2 final size:2
Alignment explanation
Indices: 2478767--2478793 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2478757 TTCATGCTTT
2478767 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2478794 TGGATGATGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2479266 original size:17 final size:18
Alignment explanation
Indices: 2479226--2479276 Score: 56
Period size: 17 Copynumber: 2.9 Consensus size: 18
2479216 TTTTATTTAT
2479226 ATAAATTTAAATATATTA
1 ATAAATTTAAATATATTA
2479244 AT-AATTTAAAT-TA-TA
1 ATAAATTTAAATATATTA
2479259 CATAAATTTTAAA-ATATT
1 -ATAAA-TTTAAATATATT
2479277 TAAATTATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 9
0.76 0.00 0.24
Matches are distributed among these distances:
15 2 0.07
16 4 0.14
17 11 0.39
18 10 0.36
19 1 0.04
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (18 bp):
ATAAATTTAAATATATTA
Found at i:2480267 original size:19 final size:19
Alignment explanation
Indices: 2480193--2480335 Score: 88
Period size: 19 Copynumber: 7.4 Consensus size: 19
2480183 TGTCGTACTT
2480193 TATATTT-TATTATATTTTAA
1 TATATTTATATTATA--TTAA
2480213 TTATATTTAATATTATATATAA
1 -TATATTT-ATATTATAT-TAA
*
2480235 -AT-TTTA-A-AATATTAA
1 TATATTTATATTATATTAA
2480250 TATATTTATATTATATTAA
1 TATATTTATATTATATTAA
*
2480269 TATTTTATATATTATATTTTACA
1 TATATT-TATATTATA--TTA-A
2480292 TTATATTT-TAATTATTATT-A
1 -TATATTTAT-ATTA-TATTAA
*
2480312 TATATTCATATTATA-TAA
1 TATATTTATATTATATTAA
2480330 T-TATTT
1 TATATTT
2480336 TTTATCGTGT
Statistics
Matches: 100, Mismatches: 6, Indels: 36
0.70 0.04 0.25
Matches are distributed among these distances:
15 3 0.03
16 6 0.06
17 10 0.10
18 6 0.06
19 25 0.25
20 13 0.13
21 8 0.08
22 9 0.09
23 13 0.13
24 7 0.07
ACGTcount: A:0.40, C:0.01, G:0.00, T:0.59
Consensus pattern (19 bp):
TATATTTATATTATATTAA
Found at i:2480781 original size:27 final size:27
Alignment explanation
Indices: 2480743--2480817 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
2480733 TTTATATTTT
* *
2480743 ATATTATTTATTTTATAATTTTTTAAA
1 ATATTATATATTTTATAATATTTTAAA
*
2480770 ATATTATATATTTATATAA-ATTTTAAT
1 ATATTATATATTT-TATAATATTTTAAA
*
2480797 ATATTTATATTTTTTATAATA
1 ATA-TTATATATTTTATAATA
2480818 AATTTTAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
27 26 0.63
28 15 0.37
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (27 bp):
ATATTATATATTTTATAATATTTTAAA
Found at i:2480789 original size:20 final size:20
Alignment explanation
Indices: 2480768--2480806 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2480758 TAATTTTTTA
2480768 AAATATT-ATATATTTATAT
1 AAATATTAATATATTTATAT
*
2480787 AAATTTTAATATATTTATAT
1 AAATATTAATATATTTATAT
2480807 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.33
20 12 0.67
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
AAATATTAATATATTTATAT
Found at i:2482482 original size:21 final size:20
Alignment explanation
Indices: 2482458--2482557 Score: 84
Period size: 20 Copynumber: 5.0 Consensus size: 20
2482448 TATTTTTACA
2482458 AAAAAGATTAGATCATTCTTT
1 AAAAAGATTA-ATCATTCTTT
* * * *
2482479 AAAAAAATTTATTATTCTTAA
1 AAAAAGATTAATCATTCTT-T
*
2482500 AAAAAGATTGATATC-TT-TTA
1 AAAAAGATT-A-ATCATTCTTT
2482520 AAAAAGATTAATCATTC-TT
1 AAAAAGATTAATCATTCTTT
2482539 AAAAA-ATTAATCATT-TTT
1 AAAAAGATTAATCATTCTTT
2482557 A
1 A
2482558 CAAACCAATA
Statistics
Matches: 65, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
18 16 0.25
19 9 0.14
20 18 0.28
21 18 0.28
22 2 0.03
23 2 0.03
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.40
Consensus pattern (20 bp):
AAAAAGATTAATCATTCTTT
Found at i:2482495 original size:20 final size:21
Alignment explanation
Indices: 2482457--2482544 Score: 85
Period size: 20 Copynumber: 4.3 Consensus size: 21
2482447 ATATTTTTAC
*
2482457 AAAAAAGATTAGATCATTCTTT
1 AAAAAAGATTA-ATTATTCTTT
* *
2482479 AAAAAA-ATTTATTATTCTTA
1 AAAAAAGATTAATTATTCTTT
*
2482499 AAAAAAGATTGA-TA-TCTTTT
1 AAAAAAGATTAATTATTC-TTT
*
2482519 AAAAAAGATTAATCATTC-TT
1 AAAAAAGATTAATTATTCTTT
2482539 AAAAAA
1 AAAAAA
2482545 TTAATCATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 10
0.76 0.10 0.14
Matches are distributed among these distances:
19 2 0.04
20 37 0.67
21 8 0.15
22 8 0.15
ACGTcount: A:0.51, C:0.07, G:0.06, T:0.36
Consensus pattern (21 bp):
AAAAAAGATTAATTATTCTTT
Found at i:2482524 original size:41 final size:42
Alignment explanation
Indices: 2482448--2482544 Score: 119
Period size: 41 Copynumber: 2.3 Consensus size: 42
2482438 AGCTCGTCCA
* *
2482448 TATTTTTACAAAAAAGATTAGATCATTCTTTAAAAAAATTTAT
1 TATTCTTA-AAAAAAGATTAGATCATTCTTTAAAAAAATTAAT
2482491 TATTCTTAAAAAAAGATT-GAT-A-TCTTTTAAAAAAGATTAAT
1 TATTCTTAAAAAAAGATTAGATCATTC-TTTAAAAAA-ATTAAT
*
2482532 CATTCTTAAAAAA
1 TATTCTTAAAAAA
2482545 TTAATCATTT
Statistics
Matches: 49, Mismatches: 3, Indels: 6
0.84 0.05 0.10
Matches are distributed among these distances:
39 2 0.04
40 10 0.20
41 20 0.41
42 10 0.20
43 7 0.14
ACGTcount: A:0.48, C:0.07, G:0.05, T:0.39
Consensus pattern (42 bp):
TATTCTTAAAAAAAGATTAGATCATTCTTTAAAAAAATTAAT
Found at i:2487630 original size:29 final size:29
Alignment explanation
Indices: 2487550--2487631 Score: 94
Period size: 29 Copynumber: 2.8 Consensus size: 29
2487540 TATAAAGGCT
2487550 AAGAAATTAAAAGTCAACTAAAACCAAAA
1 AAGAAATTAAAAGTCAACTAAAACCAAAA
* * **
2487579 AAAAGAATTAAAAGTCAATTAAAA-CACTGA
1 AAGA-AATTAAAAGTCAACTAAAACCA-AAA
*
2487609 ATGAAATTAAAAGTCAACTAAAA
1 AAGAAATTAAAAGTCAACTAAAA
2487632 TGTCAGAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
29 23 0.52
30 21 0.48
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.18
Consensus pattern (29 bp):
AAGAAATTAAAAGTCAACTAAAACCAAAA
Found at i:2493830 original size:93 final size:93
Alignment explanation
Indices: 2493671--2493848 Score: 293
Period size: 93 Copynumber: 1.9 Consensus size: 93
2493661 TTTTATTTTT
* * *
2493671 TTGTAGTTTCATAGCATATATGCGTGATAACTTGGTTACTCGCTTATATGCCCTAAGGATTTTGT
1 TTGTAGTTTCATAGCATATATGCATGATAACTTGGTTACTCACTTATATGACCTAAGGATTTTGT
2493736 TGCGTGGTAACTTGGTTACTCCAACACC
66 TGCGTGGTAACTTGGTTACTCCAACACC
** * *
2493764 TTGTAGTTTTGTAGCATTTATGCATGATAACTTGGTTATTCACTTATATGACCTAAGGATTTTGT
1 TTGTAGTTTCATAGCATATATGCATGATAACTTGGTTACTCACTTATATGACCTAAGGATTTTGT
2493829 TGCGTGGTAACTTGGTTACT
66 TGCGTGGTAACTTGGTTACT
2493849 TGCTTGTTCG
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
93 78 1.00
ACGTcount: A:0.22, C:0.16, G:0.21, T:0.41
Consensus pattern (93 bp):
TTGTAGTTTCATAGCATATATGCATGATAACTTGGTTACTCACTTATATGACCTAAGGATTTTGT
TGCGTGGTAACTTGGTTACTCCAACACC
Found at i:2500916 original size:33 final size:33
Alignment explanation
Indices: 2500854--2500918 Score: 80
Period size: 33 Copynumber: 2.0 Consensus size: 33
2500844 ACTATAATTT
* *
2500854 ATATAAATTTTAATTCGTTTGATATTTTATATG
1 ATATAAATTTTAATTCATTTGATAATTTATATG
2500887 ATATAAATTTTAATAT-ATTT-ATTAATTTATAT
1 ATATAAATTTTAAT-TCATTTGA-TAATTTATAT
2500919 TTTTTATCAT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
32 1 0.04
33 26 0.93
34 1 0.04
ACGTcount: A:0.38, C:0.02, G:0.05, T:0.55
Consensus pattern (33 bp):
ATATAAATTTTAATTCATTTGATAATTTATATG
Found at i:2505217 original size:20 final size:20
Alignment explanation
Indices: 2505136--2505220 Score: 66
Period size: 20 Copynumber: 4.2 Consensus size: 20
2505126 ATTTTTACAT
2505136 AAAAGAATAT-ATCATTCTTA
1 AAAAGAAT-TGATCATTCTTA
* * * *
2505156 AAAAGATTTTACCATTTTTA
1 AAAAGAATTGATCATTCTTA
* * *
2505176 AAAAAAGATTGGTC-TCTATTA
1 AAAAGA-ATTGATCAT-TCTTA
2505197 AAAAGAATTGATCATTCTTA
1 AAAAGAATTGATCATTCTTA
2505217 AAAA
1 AAAA
2505221 ATATCAATCA
Statistics
Matches: 49, Mismatches: 12, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
19 1 0.02
20 35 0.71
21 13 0.27
ACGTcount: A:0.47, C:0.09, G:0.08, T:0.35
Consensus pattern (20 bp):
AAAAGAATTGATCATTCTTA
Found at i:2508931 original size:19 final size:19
Alignment explanation
Indices: 2508907--2508947 Score: 55
Period size: 22 Copynumber: 2.0 Consensus size: 19
2508897 ACTAAGTAAT
2508907 ATATCAAATGATAATTCTCA
1 ATATCAAATGAT-ATTCTCA
2508927 TATCATCAAATGATATTCTCA
1 -AT-ATCAAATGATATTCTCA
2508948 TATTAGATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.41, C:0.17, G:0.05, T:0.37
Consensus pattern (19 bp):
ATATCAAATGATATTCTCA
Found at i:2508944 original size:21 final size:21
Alignment explanation
Indices: 2508905--2508950 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
2508895 ACACTAAGTA
2508905 ATATATCAAATGATAATTCTC
1 ATATATCAAATGATAATTCTC
2508926 ATATCATCAAATGAT-ATTCTC
1 ATAT-ATCAAATGATAATTCTC
2508947 ATAT
1 ATAT
2508951 TAGATCATCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.41, C:0.15, G:0.04, T:0.39
Consensus pattern (21 bp):
ATATATCAAATGATAATTCTC
Found at i:2510140 original size:18 final size:17
Alignment explanation
Indices: 2510093--2510160 Score: 58
Period size: 16 Copynumber: 4.2 Consensus size: 17
2510083 TATATCATAA
2510093 TTATATTTA-A-AATATT
1 TTATATTTATATAA-ATT
2510109 TTATATTTATATAAATT
1 TTATATTTATATAAATT
2510126 TTAATATATTA-AT-AA-T
1 TT-ATAT-TTATATAAATT
*
2510142 TCATATTT-TATAAATT
1 TTATATTTATATAAATT
2510158 TTA
1 TTA
2510161 AAATATATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 14
0.73 0.03 0.24
Matches are distributed among these distances:
14 4 0.09
15 6 0.14
16 14 0.33
17 8 0.19
18 8 0.19
19 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (17 bp):
TTATATTTATATAAATT
Found at i:2511088 original size:16 final size:17
Alignment explanation
Indices: 2511045--2511110 Score: 50
Period size: 16 Copynumber: 3.9 Consensus size: 17
2511035 GAATTAAAAT
2511045 TTAA-ATATTTTTTAAA
1 TTAATATATTTTTTAAA
* *
2511061 TTAATTAAATTTTTT-AC
1 TTAA-TATATTTTTTAAA
2511078 TTAATATA--TTTTAAA
1 TTAATATATTTTTTAAA
*
2511093 TTTAATATTTTTATTTAA
1 -TTAATATATTT-TTTAA
2511111 TATTTTTAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 11
0.70 0.09 0.20
Matches are distributed among these distances:
14 4 0.11
15 1 0.03
16 14 0.37
17 5 0.13
18 9 0.24
19 5 0.13
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (17 bp):
TTAATATATTTTTTAAA
Found at i:2511103 original size:28 final size:28
Alignment explanation
Indices: 2511063--2511126 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 28
2511053 TTTTTAAATT
*
2511063 AATTAAAT-TTTTTACTTAATATATTTTA
1 AATTTAATATTTTTACTTAATAT-TTTTA
*
2511091 AATTTAATATTTTTATTTAATATTTTTA
1 AATTTAATATTTTTACTTAATATTTTTA
2511119 AATATTAA
1 AAT-TTAA
2511127 ATCATCTTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 15 0.47
29 17 0.53
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.58
Consensus pattern (28 bp):
AATTTAATATTTTTACTTAATATTTTTA
Found at i:2511110 original size:13 final size:13
Alignment explanation
Indices: 2511071--2511118 Score: 60
Period size: 13 Copynumber: 3.5 Consensus size: 13
2511061 TTAATTAAAT
*
2511071 TTTTTACTTAATA
1 TTTTTATTTAATA
2511084 TATTTTAAATTTAATA
1 T-TTTT--ATTTAATA
2511100 TTTTTATTTAATA
1 TTTTTATTTAATA
2511113 TTTTTA
1 TTTTTA
2511119 AATATTAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
13 15 0.48
14 4 0.13
15 4 0.13
16 8 0.26
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (13 bp):
TTTTTATTTAATA
Found at i:2511371 original size:20 final size:19
Alignment explanation
Indices: 2511347--2511398 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
2511337 TTTATCGTGT
2511347 TTAATAAATATAAAAATAA
1 TTAATAAATATAAAAATAA
* * *
2511366 TATAATATATTTAAATATAA
1 T-TAATAAATATAAAAATAA
2511386 TTAATATAATATA
1 TTAATA-AATATA
2511399 TTTATCATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 3
0.76 0.15 0.09
Matches are distributed among these distances:
19 6 0.23
20 20 0.77
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TTAATAAATATAAAAATAA
Found at i:2511380 original size:26 final size:24
Alignment explanation
Indices: 2511351--2511402 Score: 77
Period size: 24 Copynumber: 2.1 Consensus size: 24
2511341 TCGTGTTTAA
2511351 TAAATATAAAAATAATATAATATATT
1 TAAATAT--AAATAATATAATATATT
*
2511377 TAAATATAATTAATATAATATATT
1 TAAATATAAATAATATAATATATT
2511401 TA
1 TA
2511403 TCATATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.72
26 7 0.28
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (24 bp):
TAAATATAAATAATATAATATATT
Found at i:2511409 original size:40 final size:37
Alignment explanation
Indices: 2511365--2511439 Score: 96
Period size: 40 Copynumber: 1.9 Consensus size: 37
2511355 TATAAAAATA
2511365 ATATAATATATTTAAATATAATTAATATAATATATTTATC
1 ATATAATATATTTAAATATAATT--T-TAATATATTTATC
* * *
2511405 ATATATTATATTTGATTATAATTTTAATATATTTA
1 ATATAATATATTTAAATATAATTTTAATATATTTA
2511440 ATAATTTTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
37 11 0.34
38 1 0.03
40 20 0.62
ACGTcount: A:0.45, C:0.01, G:0.01, T:0.52
Consensus pattern (37 bp):
ATATAATATATTTAAATATAATTTTAATATATTTATC
Found at i:2511445 original size:18 final size:17
Alignment explanation
Indices: 2511422--2511456 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
2511412 ATATTTGATT
2511422 ATAATTTTAATATATTTA
1 ATAATTTTAAT-TATTTA
*
2511440 ATAATTTTTATTATTTA
1 ATAATTTTAATTATTTA
2511457 CCTTTTGAGA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTAATTATTTA
Found at i:2512537 original size:31 final size:32
Alignment explanation
Indices: 2512497--2512563 Score: 109
Period size: 31 Copynumber: 2.1 Consensus size: 32
2512487 GACTTTGAAT
* *
2512497 AAAATTCTTGGAAGATTAATTGTATGTGTTGG
1 AAAATTCTTGGAAAATTAATTGTATGTATTGG
2512529 AAAA-TCTTGGAAAATTAATTGTATGTATTGG
1 AAAATTCTTGGAAAATTAATTGTATGTATTGG
2512560 AAAA
1 AAAA
2512564 GAAAACAGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
31 29 0.88
32 4 0.12
ACGTcount: A:0.39, C:0.03, G:0.21, T:0.37
Consensus pattern (32 bp):
AAAATTCTTGGAAAATTAATTGTATGTATTGG
Found at i:2512941 original size:12 final size:12
Alignment explanation
Indices: 2512924--2512948 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2512914 GATTTGATTA
2512924 TAAATATAATTT
1 TAAATATAATTT
2512936 TAAATATAATTT
1 TAAATATAATTT
2512948 T
1 T
2512949 TTTAAAAAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAAATATAATTT
Found at i:2513816 original size:9 final size:9
Alignment explanation
Indices: 2513802--2513844 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
2513792 GCCAACAAAT
2513802 TAAAATAAA
1 TAAAATAAA
2513811 TAAAATAAA
1 TAAAATAAA
**
2513820 TAAAGGAAA
1 TAAAATAAA
*
2513829 TAAAAATAAC
1 T-AAAATAAA
2513839 TAAAAT
1 TAAAAT
2513845 GACGCACATG
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
9 22 0.79
10 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (9 bp):
TAAAATAAA
Found at i:2514083 original size:22 final size:22
Alignment explanation
Indices: 2514060--2514101 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
2514050 TAATTAATAT
*
2514060 TTTTAAT-TTATATTTATATTA
1 TTTTAATATTATAATTATATTA
2514081 TTTTAATATTATAATTATATT
1 TTTTAATATTATAATTATATT
2514102 TAAAATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTAATATTATAATTATATTA
Found at i:2514102 original size:28 final size:30
Alignment explanation
Indices: 2514053--2514123 Score: 92
Period size: 28 Copynumber: 2.4 Consensus size: 30
2514043 TATTAGGTAA
* * *
2514053 TTAATATTTTTAATTTATATTTATATTATT
1 TTAATATTTATAATTTATATTTAAAATATT
2514083 TTAATA-TTATAA-TTATATTTAAAATATT
1 TTAATATTTATAATTTATATTTAAAATATT
*
2514111 ATAATATTTATAA
1 TTAATATTTATAA
2514124 AAATTTTAAT
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
28 19 0.53
29 11 0.31
30 6 0.17
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (30 bp):
TTAATATTTATAATTTATATTTAAAATATT
Found at i:2514126 original size:20 final size:19
Alignment explanation
Indices: 2514085--2514138 Score: 67
Period size: 18 Copynumber: 2.8 Consensus size: 19
2514075 ATATTATTTT
2514085 AATATTATAATTATATTTAA
1 AATATTATAA-TATATTTAA
2514105 AATATTATAATAT-TTATAA
1 AATATTATAATATATT-TAA
*
2514124 AA-ATTTTAATATATT
1 AATATTATAATATATT
2514139 AATAATTAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
18 11 0.35
19 10 0.32
20 10 0.32
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
AATATTATAATATATTTAA
Found at i:2514482 original size:13 final size:13
Alignment explanation
Indices: 2514461--2514557 Score: 51
Period size: 13 Copynumber: 7.7 Consensus size: 13
2514451 ATAAAATATA
*
2514461 AAATAAAATAATT
1 AAATTAAATAATT
*
2514474 AAATTAAATAAATAA
1 AAATTAAAT-AAT-T
*
2514489 AAATTATATAA--
1 AAATTAAATAATT
* *
2514500 AAAATATA-AATT
1 AAATTAAATAATT
*
2514512 AAATT-AAT-TTT
1 AAATTAAATAATT
*
2514523 ATATTAAATAATT
1 AAATTAAATAATT
***
2514536 TTTTTAAATAATT
1 AAATTAAATAATT
2514549 AAATTAAAT
1 AAATTAAAT
2514558 TTTTTTATAT
Statistics
Matches: 63, Mismatches: 14, Indels: 14
0.69 0.15 0.15
Matches are distributed among these distances:
10 2 0.03
11 14 0.22
12 7 0.11
13 27 0.43
14 5 0.08
15 8 0.13
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (13 bp):
AAATTAAATAATT
Found at i:2514482 original size:18 final size:18
Alignment explanation
Indices: 2514461--2514515 Score: 64
Period size: 18 Copynumber: 3.2 Consensus size: 18
2514451 ATAAAATATA
2514461 AAATAAAATAATTAAATT
1 AAATAAAATAATTAAATT
2514479 AAAT-AAATAA--AAATT
1 AAATAAAATAATTAAATT
*
2514494 ATATAAAA-AATATAAATT
1 AAATAAAATAAT-TAAATT
2514512 AAAT
1 AAAT
2514516 TAATTTTATA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
15 10 0.32
16 3 0.10
17 6 0.19
18 12 0.39
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAATAAAATAATTAAATT
Found at i:2514575 original size:26 final size:23
Alignment explanation
Indices: 2514515--2514575 Score: 63
Period size: 23 Copynumber: 2.6 Consensus size: 23
2514505 ATAAATTAAA
2514515 TTAATTTTATATTAAATAATTTTT
1 TTAA-TTTATATTAAATAATTTTT
*
2514539 TTAA-ATA-ATTAAATTAAATTTTT
1 TTAATTTATATTAAA-T-AATTTTT
2514562 TTATATTTATATTA
1 TTA-ATTTATATTA
2514576 TTTTTAATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
21 6 0.20
22 3 0.10
23 10 0.33
24 5 0.17
25 2 0.07
26 4 0.13
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (23 bp):
TTAATTTATATTAAATAATTTTT
Found at i:2525240 original size:14 final size:14
Alignment explanation
Indices: 2525227--2525297 Score: 110
Period size: 14 Copynumber: 5.2 Consensus size: 14
2525217 TATATATATA
*
2525227 TATATGTATGTATA
1 TATATGTATGTATG
*
2525241 TGTATGTATGTATG
1 TATATGTATGTATG
2525255 TATATGTATGTATG
1 TATATGTATGTATG
2525269 --TATGTATGTATG
1 TATATGTATGTATG
2525281 TATATGTATGTATG
1 TATATGTATGTATG
2525295 TAT
1 TAT
2525298 TTATCAAATT
Statistics
Matches: 52, Mismatches: 3, Indels: 4
0.88 0.05 0.07
Matches are distributed among these distances:
12 12 0.23
14 40 0.77
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.51
Consensus pattern (14 bp):
TATATGTATGTATG
Found at i:2525246 original size:4 final size:4
Alignment explanation
Indices: 2525229--2525297 Score: 96
Period size: 4 Copynumber: 18.8 Consensus size: 4
2525219 TATATATATA
2525229 TATG TATG TA-- TATG TATG TATG TATG TA-- TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
2525273 TATG TATG TA-- TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TAT
2525298 TTATCAAATT
Statistics
Matches: 59, Mismatches: 0, Indels: 12
0.83 0.00 0.17
Matches are distributed among these distances:
2 6 0.10
4 53 0.90
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.51
Consensus pattern (4 bp):
TATG
Found at i:2525255 original size:22 final size:22
Alignment explanation
Indices: 2525229--2525297 Score: 120
Period size: 22 Copynumber: 3.1 Consensus size: 22
2525219 TATATATATA
2525229 TATGTATGTATATGTATGTATG
1 TATGTATGTATATGTATGTATG
* *
2525251 TATGTATATGTATGTATGTATG
1 TATGTATGTATATGTATGTATG
2525273 TATGTATGTATATGTATGTATG
1 TATGTATGTATATGTATGTATG
2525295 TAT
1 TAT
2525298 TTATCAAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.28, C:0.00, G:0.22, T:0.51
Consensus pattern (22 bp):
TATGTATGTATATGTATGTATG
Found at i:2525294 original size:18 final size:18
Alignment explanation
Indices: 2525219--2525297 Score: 104
Period size: 18 Copynumber: 4.2 Consensus size: 18
2525209 GATATCTTTA
* *
2525219 TATATATATATATGTATG
1 TATATGTATGTATGTATG
2525237 TATATGTATGTATGTATG
1 TATATGTATGTATGTATG
2525255 TATATGTATGTATGTATG
1 TATATGTATGTATGTATG
2525273 TATGTATGTATATGTATGTATG
1 TA--TATG--TATGTATGTATG
2525295 TAT
1 TAT
2525298 TTATCAAATT
Statistics
Matches: 55, Mismatches: 2, Indels: 6
0.87 0.03 0.10
Matches are distributed among these distances:
18 36 0.65
20 5 0.09
22 14 0.25
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (18 bp):
TATATGTATGTATGTATG
Found at i:2529823 original size:286 final size:286
Alignment explanation
Indices: 2529308--2529882 Score: 1071
Period size: 286 Copynumber: 2.0 Consensus size: 286
2529298 TTGTAAAATT
2529308 AAACCAACCATATGATGCATCTTGCATATGCATGCATTATCATAAACATGGTTACACATTTCATA
1 AAACCAACCATATGATGCATCTTGCATATGCATGCATTATCATAAACATGGTTACACATTTCATA
*
2529373 CTTGTAACTTAAAGGCTATTACTTATAGAGGTAAAATCATAAAGGGAATATGGATTCCTGAAAAA
66 CTTGTAACTTAAAGGCTATTACTTATAGAGGTAAAATCATAAAGGGAATATAGATTCCTGAAAAA
*
2529438 GTTAGCACATCTTAAGATGAGGCTACTAAATGGATTCCTAAAGGCACAAAATTATGACGACTAAT
131 GTTAGCACATCTCAAGATGAGGCTACTAAATGGATTCCTAAAGGCACAAAATTATGACGACTAAT
*
2529503 ACTTAAGGACCCAAGAAAATTTGGGTACCTAAAAACAAAATATAAATTTGTGTTTGTAGGAGGAA
196 ACTTAAGGACCCAAGAAAATTTGGGTAACTAAAAACAAAATATAAATTTGTGTTTGTAGGAGGAA
2529568 GAGCATTGCTTCAAGGCAAAAATAAC
261 GAGCATTGCTTCAAGGCAAAAATAAC
* * *
2529594 AAACCAACCATATGATGCATCTTGCATATGCATGCATTGTTATAAACATGGTTATACATTTCATA
1 AAACCAACCATATGATGCATCTTGCATATGCATGCATTATCATAAACATGGTTACACATTTCATA
2529659 CTTGTAACTTAAAGGCTATTACTTATAGAGGTAAAATCAT-AAGGAGAATATAGATTCCTGAAAA
66 CTTGTAACTTAAAGGCTATTACTTATAGAGGTAAAATCATAAAGG-GAATATAGATTCCTGAAAA
*
2529723 AGTTAGCACATCTCAAGATGAGGCTACTAAATGGATTCCTAAAGGCACAAAATTATTACGACTAA
130 AGTTAGCACATCTCAAGATGAGGCTACTAAATGGATTCCTAAAGGCACAAAATTATGACGACTAA
2529788 TACTTAAGGACCCAAGAAAATTTGGGTAACTAAAAACAAAATATAAATTTGTGTTTGTAGGAGGA
195 TACTTAAGGACCCAAGAAAATTTGGGTAACTAAAAACAAAATATAAATTTGTGTTTGTAGGAGGA
2529853 AGAGCATTGCTTCAAGGCAAAAATAAC
260 AGAGCATTGCTTCAAGGCAAAAATAAC
2529880 AAA
1 AAA
2529883 GAAGAACTAC
Statistics
Matches: 281, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
285 4 0.01
286 277 0.99
ACGTcount: A:0.41, C:0.15, G:0.17, T:0.27
Consensus pattern (286 bp):
AAACCAACCATATGATGCATCTTGCATATGCATGCATTATCATAAACATGGTTACACATTTCATA
CTTGTAACTTAAAGGCTATTACTTATAGAGGTAAAATCATAAAGGGAATATAGATTCCTGAAAAA
GTTAGCACATCTCAAGATGAGGCTACTAAATGGATTCCTAAAGGCACAAAATTATGACGACTAAT
ACTTAAGGACCCAAGAAAATTTGGGTAACTAAAAACAAAATATAAATTTGTGTTTGTAGGAGGAA
GAGCATTGCTTCAAGGCAAAAATAAC
Found at i:2533259 original size:15 final size:15
Alignment explanation
Indices: 2533239--2533269 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
2533229 GTTTTCTAGA
2533239 TTGTATCGATACAAT
1 TTGTATCGATACAAT
2533254 TTGTATCGATACAAT
1 TTGTATCGATACAAT
2533269 T
1 T
2533270 ACTAATGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.32, C:0.13, G:0.13, T:0.42
Consensus pattern (15 bp):
TTGTATCGATACAAT
Found at i:2540849 original size:34 final size:35
Alignment explanation
Indices: 2540811--2540876 Score: 125
Period size: 35 Copynumber: 1.9 Consensus size: 35
2540801 CTTCACAATA
2540811 CTATCTTTT-CAAAGGCTAAGATAGAACCTCTTCC
1 CTATCTTTTACAAAGGCTAAGATAGAACCTCTTCC
2540845 CTATCTTTTACAAAGGCTAAGATAGAACCTCT
1 CTATCTTTTACAAAGGCTAAGATAGAACCTCT
2540877 CAATCACTTA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
34 9 0.29
35 22 0.71
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (35 bp):
CTATCTTTTACAAAGGCTAAGATAGAACCTCTTCC
Found at i:2541564 original size:21 final size:21
Alignment explanation
Indices: 2541540--2541593 Score: 90
Period size: 21 Copynumber: 2.6 Consensus size: 21
2541530 GTCAACCTTT
*
2541540 ATGTATTGATACAAATAGTAC
1 ATGTATCGATACAAATAGTAC
2541561 ATGTATCGATACAAATAGTAC
1 ATGTATCGATACAAATAGTAC
*
2541582 ATATATCGATAC
1 ATGTATCGATAC
2541594 TTTGAATAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (21 bp):
ATGTATCGATACAAATAGTAC
Found at i:2543952 original size:11 final size:11
Alignment explanation
Indices: 2543931--2543962 Score: 50
Period size: 10 Copynumber: 3.1 Consensus size: 11
2543921 AAGGAAAACA
2543931 ATGAG-ATTTG
1 ATGAGAATTTG
2543941 ATGAGAATTTG
1 ATGAGAATTTG
2543952 ATGA-AATTTG
1 ATGAGAATTTG
2543962 A
1 A
2543963 AAAAGATTGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 12 0.57
11 9 0.43
ACGTcount: A:0.38, C:0.00, G:0.25, T:0.38
Consensus pattern (11 bp):
ATGAGAATTTG
Found at i:2544175 original size:29 final size:29
Alignment explanation
Indices: 2544125--2544181 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2544115 ACAATTTTTT
* *
2544125 TGTATCGATAGATCTAGGAAAAATCCAGC
1 TGTATCGATACATCTAGAAAAAATCCAGC
*
2544154 TGTATCGATACATTCT-GAAAAATTCCAG
1 TGTATCGATACA-TCTAGAAAAAATCCAG
2544182 AAGTACCTAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 21 0.88
30 3 0.12
ACGTcount: A:0.37, C:0.18, G:0.18, T:0.28
Consensus pattern (29 bp):
TGTATCGATACATCTAGAAAAAATCCAGC
Found at i:2544264 original size:10 final size:10
Alignment explanation
Indices: 2544249--2544285 Score: 56
Period size: 10 Copynumber: 3.7 Consensus size: 10
2544239 AATCAAAATT
2544249 CATTCAAAAA
1 CATTCAAAAA
*
2544259 CATTCAAGAA
1 CATTCAAAAA
*
2544269 CATTCATAAA
1 CATTCAAAAA
2544279 CATTCAA
1 CATTCAA
2544286 TTTGCACACA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.51, C:0.22, G:0.03, T:0.24
Consensus pattern (10 bp):
CATTCAAAAA
Found at i:2553392 original size:75 final size:76
Alignment explanation
Indices: 2553246--2553394 Score: 196
Period size: 75 Copynumber: 2.0 Consensus size: 76
2553236 TTTTACGTCA
* *
2553246 AAGGTATCCTTTAAGGGCATTTTTATATTTTTTTCAAAACCAACTCCTAGGTCGTCATCGGGTCT
1 AAGGTATCCCTTAAGGGCATTTTTATA-TTTTTTCAAAACCAACTCCTAGGTCGTCACCGGGTCT
*
2553311 GGTTTTATGCCG
65 GATTTTATGCCG
* * *
2553323 AAGGTATCCCTT-AGGAGCATTTTTGTA-TTTTTCAAAACTAACTCCTAGGTTGTCACCGGGT-T
1 AAGGTATCCCTTAAGG-GCATTTTTATATTTTTTCAAAACCAACTCCTAGGTCGTCACCGGGTCT
2553385 CGATTTTATG
65 -GATTTTATG
2553395 TAAAAAGTAG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
74 1 0.02
75 39 0.61
76 3 0.05
77 21 0.33
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (76 bp):
AAGGTATCCCTTAAGGGCATTTTTATATTTTTTCAAAACCAACTCCTAGGTCGTCACCGGGTCTG
ATTTTATGCCG
Found at i:2560769 original size:4 final size:4
Alignment explanation
Indices: 2560760--2560785 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
2560750 TAACAAAAGA
2560760 AAAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AA
2560786 TCATGGAACT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:2564907 original size:23 final size:22
Alignment explanation
Indices: 2564868--2564911 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
2564858 ATTAGTTATA
2564868 GTTTAAAAAACATATTTCAAAG
1 GTTTAAAAAACATATTTCAAAG
2564890 GTTT-AAAAACATGAATTTCAAA
1 GTTTAAAAAACAT--ATTTCAAA
2564912 TTTACAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 8 0.40
22 4 0.20
23 8 0.40
ACGTcount: A:0.50, C:0.09, G:0.09, T:0.32
Consensus pattern (22 bp):
GTTTAAAAAACATATTTCAAAG
Found at i:2564915 original size:21 final size:20
Alignment explanation
Indices: 2564867--2564915 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 20
2564857 AATTAGTTAT
2564867 AGTTTAAAAAACATATTTCAA
1 AGTTT-AAAAACATATTTCAA
2564888 AGGTTTAAAAACATGAATTTCAA
1 A-GTTTAAAAACAT--ATTTCAA
2564911 A-TTTA
1 AGTTTA
2564916 CAAATATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
21 13 0.52
22 4 0.16
23 8 0.32
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.35
Consensus pattern (20 bp):
AGTTTAAAAACATATTTCAA
Found at i:2565406 original size:9 final size:10
Alignment explanation
Indices: 2565380--2565439 Score: 58
Period size: 9 Copynumber: 6.3 Consensus size: 10
2565370 TATATATATA
2565380 TATATAATTAT
1 TATATAATT-T
2565391 TATATAATTT
1 TATATAATTT
2565401 TA-ATAATTT
1 TATATAATTT
*
2565410 TATAT--TTA
1 TATATAATTT
2565418 TATA-AATATT
1 TATATAAT-TT
2565428 TAT-TAATTT
1 TATATAATTT
2565437 TAT
1 TAT
2565440 CAATACGTAA
Statistics
Matches: 42, Mismatches: 2, Indels: 12
0.75 0.04 0.21
Matches are distributed among these distances:
8 6 0.14
9 15 0.36
10 12 0.29
11 9 0.21
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (10 bp):
TATATAATTT
Found at i:2565429 original size:27 final size:25
Alignment explanation
Indices: 2565390--2565439 Score: 73
Period size: 27 Copynumber: 1.9 Consensus size: 25
2565380 TATATAATTA
2565390 TTATATAATTTTAATAATTTTATAT
1 TTATATAATTTTAATAATTTTATAT
*
2565415 TTATATAAATATTTATTAATTTTAT
1 TTATAT-AAT-TTTAATAATTTTAT
2565440 CAATACGTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 6 0.27
26 3 0.14
27 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (25 bp):
TTATATAATTTTAATAATTTTATAT
Found at i:2567660 original size:13 final size:13
Alignment explanation
Indices: 2567642--2567675 Score: 50
Period size: 14 Copynumber: 2.5 Consensus size: 13
2567632 TTTATCATCA
2567642 AATAAATATATTT
1 AATAAATATATTT
*
2567655 AATAAAAGATATTT
1 AAT-AAATATATTT
2567669 AATAAAT
1 AATAAAT
2567676 TAAAATTCTT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (13 bp):
AATAAATATATTT
Found at i:2568110 original size:14 final size:14
Alignment explanation
Indices: 2568087--2568127 Score: 59
Period size: 14 Copynumber: 3.0 Consensus size: 14
2568077 GACTTATTTT
2568087 TTAT-TTATAT-AA
1 TTATATTATATAAA
2568099 TATATATTATATAAA
1 T-TATATTATATAAA
2568114 TTATATTATATAAA
1 TTATATTATATAAA
2568128 AAGTAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
12 1 0.04
13 3 0.12
14 19 0.73
15 3 0.12
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
TTATATTATATAAA
Found at i:2568991 original size:12 final size:12
Alignment explanation
Indices: 2568944--2569001 Score: 50
Period size: 12 Copynumber: 5.0 Consensus size: 12
2568934 AAAAACCATT
*
2568944 TTATTATTCATA
1 TTATTATTTATA
* *
2568956 ATATTATTAAATA
1 TTATTATT-TATA
*
2568969 TTAAT-TTTATA
1 TTATTATTTATA
2568980 TTATTATTTATA
1 TTATTATTTATA
2568992 -TATT-TTTATA
1 TTATTATTTATA
2569002 ATTAAATAGT
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
10 6 0.16
11 11 0.29
12 15 0.39
13 6 0.16
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (12 bp):
TTATTATTTATA
Found at i:2572917 original size:2 final size:2
Alignment explanation
Indices: 2572910--2572949 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
2572900 CTTTTTGTAA
2572910 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
2572950 GGCTGATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2573552 original size:2 final size:2
Alignment explanation
Indices: 2573545--2573585 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2573535 AAGCTATAGC
2573545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2573586 TATTTAGAAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2573719 original size:21 final size:21
Alignment explanation
Indices: 2573671--2573724 Score: 58
Period size: 21 Copynumber: 2.5 Consensus size: 21
2573661 TATGTGATTT
*
2573671 AATTAATTTTATAAATTAATTA
1 AATTAATATTATAAATT-ATTA
2573693 AATTAA-ATTATAAATT-TTA
1 AATTAATATTATAAATTATTA
2573712 AATTTTAATATTA
1 AA--TTAATATTA
2573725 CGAGCCACAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
19 5 0.18
21 13 0.46
22 10 0.36
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
AATTAATATTATAAATTATTA
Found at i:2573961 original size:21 final size:23
Alignment explanation
Indices: 2573935--2573988 Score: 67
Period size: 23 Copynumber: 2.4 Consensus size: 23
2573925 TAATTAAATG
* *
2573935 TAAATA-AATATTTTTATTGAT-
1 TAAATATAATAATTTAATTGATC
2573956 TAAATAATAATAATTTAATTGATC
1 TAAAT-ATAATAATTTAATTGATC
2573980 TAAATATAA
1 TAAATATAA
2573989 AAAAATTTGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
21 5 0.18
22 1 0.04
23 17 0.61
24 5 0.18
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (23 bp):
TAAATATAATAATTTAATTGATC
Found at i:2576570 original size:33 final size:33
Alignment explanation
Indices: 2576487--2576570 Score: 107
Period size: 32 Copynumber: 2.5 Consensus size: 33
2576477 ATAATTATGT
* *
2576487 TTAAAATATTATATATTTATATAATTTTTAATAAA
1 TTAATATATT-TATA-TTATATAAATTTTAATAAA
* *
2576522 TTAATA-ATTTATATTATTTAAATTTTAATATA
1 TTAATATATTTATATTATATAAATTTTAATAAA
2576554 TTAATATATTTATATTA
1 TTAATATATTTATATTA
2576571 AATATTTATT
Statistics
Matches: 44, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
32 22 0.50
33 14 0.32
34 3 0.07
35 5 0.11
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (33 bp):
TTAATATATTTATATTATATAAATTTTAATAAA
Found at i:2576571 original size:46 final size:46
Alignment explanation
Indices: 2576486--2576610 Score: 112
Period size: 46 Copynumber: 2.6 Consensus size: 46
2576476 TATAATTATG
* *
2576486 TTTAAAATATTATATATTTATATAATTTTTAATAAATT-AATAATTTATATTA
1 TTTAAATTATTATATA-TTATAT-ATATTT-AT--ATTAAAT-ATTTAT-TTA
*
2576538 TTTAAATT-TTAATATATTA-ATATATTTATATTAAATATTTATTTT
1 TTTAAATTATT-ATATATTATATATATTTATATTAAATATTTATTTA
* *
2576583 TTTATATTATTATATTTTATATATATTT
1 TTTAAATTATTATATATTATATATATTT
2576611 TAATTATTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 14
0.77 0.06 0.17
Matches are distributed among these distances:
45 16 0.25
46 19 0.30
47 3 0.05
48 2 0.03
49 5 0.08
50 2 0.03
51 5 0.08
52 12 0.19
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (46 bp):
TTTAAATTATTATATATTATATATATTTATATTAAATATTTATTTA
Found at i:2576589 original size:35 final size:36
Alignment explanation
Indices: 2576550--2576638 Score: 96
Period size: 35 Copynumber: 2.5 Consensus size: 36
2576540 TAAATTTTAA
* *
2576550 TATATTAATATATTTATATTAAATA-TTTATTTTTT
1 TATATTAATATATTTATATTAAATATTTTAATTATT
* *
2576585 TATATTATTATATTT-TA-TATATATTTTAATTATT
1 TATATTAATATATTTATATTAAATATTTTAATTATT
2576619 T-TATTATATAATATTTATAT
1 TATATTA-AT-ATATTTATAT
2576639 CATATAATTA
Statistics
Matches: 44, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
33 10 0.23
34 12 0.27
35 20 0.45
36 2 0.05
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (36 bp):
TATATTAATATATTTATATTAAATATTTTAATTATT
Found at i:2576609 original size:11 final size:11
Alignment explanation
Indices: 2576589--2576658 Score: 56
Period size: 13 Copynumber: 6.1 Consensus size: 11
2576579 TTTTTTTATA
2576589 TTAT-TATATT
1 TTATATATATT
2576599 TTATATATATT
1 TTATATATATT
2576610 TTA-AT-TATT
1 TTATATATATT
2576619 TTATTATATAATAT
1 TTA-TATAT-AT-T
*
2576633 TTATATCATATAA
1 TTATAT-ATAT-T
2576646 TTATATTATATT
1 TTATA-TATATT
2576658 T
1 T
2576659 AAAATAATAT
Statistics
Matches: 50, Mismatches: 2, Indels: 14
0.76 0.03 0.21
Matches are distributed among these distances:
9 7 0.14
10 6 0.12
11 11 0.22
12 2 0.04
13 17 0.34
14 7 0.14
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (11 bp):
TTATATATATT
Found at i:2576609 original size:19 final size:19
Alignment explanation
Indices: 2576531--2576652 Score: 77
Period size: 18 Copynumber: 6.7 Consensus size: 19
2576521 ATTAATAATT
*
2576531 TATATTATTTAAATTTTA-A
1 TATATTA-TTATATTTTATA
*
2576550 TATATTAATATA-TTTATA
1 TATATTATTATATTTTATA
* *
2576568 T-TAAATATT-TATTTT-TT
1 TAT-ATTATTATATTTTATA
2576585 TATATTATTATATTTTATA
1 TATATTATTATATTTTATA
2576604 TATATT-TTAATTATTTTAT-
1 TATATTATT-A-TATTTTATA
2576623 TATA-TA--ATA-TTTATA
1 TATATTATTATATTTTATA
*
2576638 TCATATAATTATATT
1 T-ATATTATTATATT
2576653 ATATTTAAAA
Statistics
Matches: 80, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 5 0.06
15 3 0.04
16 4 0.05
17 15 0.19
18 22 0.28
19 22 0.28
20 9 0.11
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.61
Consensus pattern (19 bp):
TATATTATTATATTTTATA
Found at i:2576623 original size:25 final size:25
Alignment explanation
Indices: 2576550--2576656 Score: 80
Period size: 25 Copynumber: 4.2 Consensus size: 25
2576540 TAAATTTTAA
*
2576550 TATATTAATATATTTATATTA-AATAT
1 TATA-TAATAT-TTTATATTATTATAT
*
2576576 T-TAT--TTTTTTATATTATTATAT
1 TATATAATATTTTATATTATTATAT
* *
2576598 TTTATATATATTTTA-ATTATTTTAT
1 TATATA-ATATTTTATATTATTATAT
2576623 TATATAATATTTATATCATATAATTATAT
1 TATATAATATTT-TAT-AT-T-ATTATAT
2576652 TATAT
1 TATAT
2576657 TTAAAATAAT
Statistics
Matches: 65, Mismatches: 6, Indels: 17
0.74 0.07 0.19
Matches are distributed among these distances:
21 9 0.14
22 7 0.11
23 3 0.05
24 7 0.11
25 18 0.28
26 7 0.11
27 2 0.03
28 1 0.02
29 11 0.17
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (25 bp):
TATATAATATTTTATATTATTATAT
Found at i:2577240 original size:13 final size:13
Alignment explanation
Indices: 2577222--2577246 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2577212 ATAAATTATA
2577222 TTTATATCATATT
1 TTTATATCATATT
2577235 TTTATATCATAT
1 TTTATATCATAT
2577247 CTAAAATTAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTATATCATATT
Found at i:2578998 original size:41 final size:41
Alignment explanation
Indices: 2578952--2579034 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
2578942 AATATTTATA
*
2578952 AATTATAATCGGTATTTAAAATCCTTTCATAGATAAACATG
1 AATTATAATCGGTATTTAAAATCCCTTCATAGATAAACATG
2578993 AATTATAATCGGTATTTAAAATCCCTTCATAGATAAACATG
1 AATTATAATCGGTATTTAAAATCCCTTCATAGATAAACATG
2579034 A
1 A
2579035 TTTGAACGAA
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.42, C:0.13, G:0.10, T:0.35
Consensus pattern (41 bp):
AATTATAATCGGTATTTAAAATCCCTTCATAGATAAACATG
Found at i:2579957 original size:23 final size:23
Alignment explanation
Indices: 2579931--2579998 Score: 68
Period size: 23 Copynumber: 3.0 Consensus size: 23
2579921 TTTATTATAT
2579931 TATTAAAATATTATTTATATTAA
1 TATTAAAATATTATTTATATTAA
* *
2579954 TATTAATATATT-TTTAAAATTAA
1 TATTAAAATATTATTT-ATATTAA
* *
2579977 -ATTTAAAATAATATTTTTATTA
1 TA-TTAAAATATTATTTATATTA
2579999 TTAAATATTA
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
22 4 0.11
23 29 0.81
24 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (23 bp):
TATTAAAATATTATTTATATTAA
Found at i:2579981 original size:34 final size:34
Alignment explanation
Indices: 2579926--2580013 Score: 85
Period size: 34 Copynumber: 2.6 Consensus size: 34
2579916 CAATTTTTAT
* * *
2579926 TATATTATTAAAATATTATTTATATTAATATTAA
1 TATATTATTAAAATATAATTTAAAATAATATTAA
*
2579960 TATATTTTTAAAAT-TAAATTTAAAATAATATT--
1 TATATTATTAAAATAT-AATTTAAAATAATATTAA
*
2579992 TTTATTATT-AAATATTAATTTA
1 TATATTATTAAAATA-TAATTTA
2580014 GTTGAATCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
31 4 0.09
32 13 0.29
33 2 0.04
34 26 0.58
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (34 bp):
TATATTATTAAAATATAATTTAAAATAATATTAA
Found at i:2580200 original size:18 final size:18
Alignment explanation
Indices: 2580173--2580215 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
2580163 TTAATTGAAA
*
2580173 TTTATATTATGTATAAAG
1 TTTATATTATATATAAAG
*
2580191 TTTATTTTATATATAAA-
1 TTTATATTATATATAAAG
2580208 -TTATATTA
1 TTTATATTA
2580216 CATTGTTATA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.56
Consensus pattern (18 bp):
TTTATATTATATATAAAG
Found at i:2583091 original size:16 final size:16
Alignment explanation
Indices: 2583044--2583115 Score: 72
Period size: 16 Copynumber: 4.4 Consensus size: 16
2583034 CAACAATTTG
*
2583044 AAAATGATCCGAACCC
1 AAAATGACCCGAACCC
* *
2583060 GAAAATAACCCAAACCC
1 -AAAATGACCCGAACCC
* *
2583077 AAAATGACTCGAACCT
1 AAAATGACCCGAACCC
* *
2583093 GAAATGACCCGAAACC
1 AAAATGACCCGAACCC
2583109 AAAATGA
1 AAAATGA
2583116 TATGAACTCG
Statistics
Matches: 43, Mismatches: 12, Indels: 1
0.77 0.21 0.02
Matches are distributed among these distances:
16 30 0.70
17 13 0.30
ACGTcount: A:0.49, C:0.28, G:0.12, T:0.11
Consensus pattern (16 bp):
AAAATGACCCGAACCC
Found at i:2583129 original size:16 final size:16
Alignment explanation
Indices: 2583110--2583163 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
2583100 CCCGAAACCA
2583110 AAATGATATGAACTCG
1 AAATGATATGAACTCG
***** *
2583126 AAATGGCCCAAACTCA
1 AAATGATATGAACTCG
2583142 AAATGATATGAACTCG
1 AAATGATATGAACTCG
2583158 AAATGA
1 AAATGA
2583164 CCTAAATAAT
Statistics
Matches: 26, Mismatches: 12, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.46, C:0.17, G:0.17, T:0.20
Consensus pattern (16 bp):
AAATGATATGAACTCG
Found at i:2583129 original size:32 final size:32
Alignment explanation
Indices: 2583044--2583165 Score: 124
Period size: 32 Copynumber: 3.8 Consensus size: 32
2583034 CAACAATTTG
** * * *
2583044 AAAATGATCCGAACCCGAAAATAACCCAAACCC
1 AAAATGATATGAACTCG-AAATGACCCAAACTC
*
2583077 AAAATGACT-CGAAC-CTGAAATGACCCGAAAC-C
1 AAAATGA-TATGAACTC-GAAATGACCC-AAACTC
*
2583109 AAAATGATATGAACTCGAAATGGCCCAAACTC
1 AAAATGATATGAACTCGAAATGACCCAAACTC
2583141 AAAATGATATGAACTCGAAATGACC
1 AAAATGATATGAACTCGAAATGACC
2583166 TAAATAATTA
Statistics
Matches: 79, Mismatches: 4, Indels: 13
0.82 0.04 0.14
Matches are distributed among these distances:
31 5 0.06
32 55 0.70
33 18 0.23
34 1 0.01
ACGTcount: A:0.46, C:0.25, G:0.14, T:0.15
Consensus pattern (32 bp):
AAAATGATATGAACTCGAAATGACCCAAACTC
Found at i:2583184 original size:23 final size:23
Alignment explanation
Indices: 2583158--2583216 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
2583148 TATGAACTCG
* *
2583158 AAATGACCTAAATAATTAACCCA
1 AAATGACCCAAACAATTAACCCA
* *
2583181 AAATGACCCGAACAATTAACCTA
1 AAATGACCCAAACAATTAACCCA
2583204 AAATGACCCAAAC
1 AAATGACCCAAAC
2583217 TTAAATTAAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.51, C:0.25, G:0.07, T:0.17
Consensus pattern (23 bp):
AAATGACCCAAACAATTAACCCA
Found at i:2583748 original size:53 final size:55
Alignment explanation
Indices: 2583643--2583764 Score: 133
Period size: 53 Copynumber: 2.3 Consensus size: 55
2583633 CCTAAGCTTA
* *
2583643 AAATGACTTAAACCCGATTTAACCCAAATATTAAAACCCAATTAACCCGAATCTAG
1 AAATGACCTGAACCCGATTTAACCCAAATATTAAAACCCAATTAACCCGAATC-AG
* * * * ** *
2583699 -AATGACCTGAACCCGA-TTAACCCGAGTGTT-AAACCCGATTAACTTGAATCCG
1 AAATGACCTGAACCCGATTTAACCCAAATATTAAAACCCAATTAACCCGAATCAG
2583751 AAATGACCTGAACC
1 AAATGACCTGAACC
2583765 TAAAATGACC
Statistics
Matches: 56, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
52 1 0.02
53 30 0.54
54 11 0.20
55 14 0.25
ACGTcount: A:0.39, C:0.26, G:0.12, T:0.22
Consensus pattern (55 bp):
AAATGACCTGAACCCGATTTAACCCAAATATTAAAACCCAATTAACCCGAATCAG
Found at i:2583770 original size:16 final size:16
Alignment explanation
Indices: 2583751--2583821 Score: 54
Period size: 16 Copynumber: 4.4 Consensus size: 16
2583741 CTTGAATCCG
* *
2583751 AAATGACCTGAACCTA
1 AAATGACCTAAACCCA
*
2583767 AAATGACCTAAACCCG
1 AAATGACCTAAACCCA
* **
2583783 AAATGATCC-GAACCTG
1 AAATGA-CCTAAACCCA
* *
2583799 AAGTGACCCAAACCCA
1 AAATGACCTAAACCCA
2583815 AAATGAC
1 AAATGAC
2583822 TCGAACTCGA
Statistics
Matches: 43, Mismatches: 10, Indels: 4
0.75 0.18 0.07
Matches are distributed among these distances:
15 2 0.05
16 39 0.91
17 2 0.05
ACGTcount: A:0.44, C:0.28, G:0.14, T:0.14
Consensus pattern (16 bp):
AAATGACCTAAACCCA
Found at i:2583796 original size:32 final size:32
Alignment explanation
Indices: 2583748--2583821 Score: 96
Period size: 32 Copynumber: 2.3 Consensus size: 32
2583738 TAACTTGAAT
*
2583748 CCGAAATGACCTGAACCTAAAATGACCTAAAC
1 CCGAAATGACCTGAACCTAAAATGACCCAAAC
* *
2583780 CCGAAATGATCC-GAACCTGAAGTGACCCAAAC
1 CCGAAATGA-CCTGAACCTAAAATGACCCAAAC
*
2583812 CCAAAATGAC
1 CCGAAATGAC
2583822 TCGAACTCGA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 1 0.03
32 34 0.92
33 2 0.05
ACGTcount: A:0.42, C:0.30, G:0.15, T:0.14
Consensus pattern (32 bp):
CCGAAATGACCTGAACCTAAAATGACCCAAAC
Found at i:2591043 original size:28 final size:28
Alignment explanation
Indices: 2590909--2592152 Score: 1002
Period size: 28 Copynumber: 43.1 Consensus size: 28
2590899 TATAAAAAAA
*
2590909 GGTGCCACTAACTTGCGTGGGCTTTGAAAAG
1 GGTGCCACTGACTT--GTGGGCTTTG-AAAG
* * *
2590940 AGTTGCCACCGGCTCGTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACT--TGTGGGCTTTG-AAAG
* * *
2590972 AGTTACCACT-AGTTTGTGGGCTTTGAAAAG
1 -GGTGCCACTGA-CTTGTGGGCTTTG-AAAG
* * *
2591002 AGTGCTACTAACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591030 GGTGCCATTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2591058 GGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591086 GGTGCCACTGACTTGTGGACTTTG-AAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591113 GGATGCCACTAACTTGTGGGCTTTGAAAG
1 GG-TGCCACTGACTTGTGGGCTTTGAAAG
2591142 GGTGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* **
2591171 AGTGCCGTTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
2591199 GATGCCACTGACTTGCGTGGACTTTAAAAG
1 GGTGCCACTGACTT--GTGGGCTTTGAAAG
*
2591229 GCTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591257 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
2591286 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
2591314 AGCGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2591342 GGTGCCACTGACTTGTGTGAGCTTTGAAAG
1 GGTGCCACTGACTTGTG-G-GCTTTGAAAG
* *
2591372 GGTGCCATTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* *
2591400 GATGCCACTAACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
*
2591429 AGTGCCACTGACTTGTGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591457 GGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591485 GGTGCCACTGACTTATGGGCTTTGAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
*
2591513 GGTGCCACTAACTTGTGGGCTTTTG-AAG
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
* * *
2591541 AGATGCCATTAACTTGTGGGCTTTGAAAAG
1 -GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
2591571 AGTTGCCA-TCGACTTGTGTGGGCTTTGAAAT
1 -GGTGCCACT-GAC-T-TGTGGGCTTTGAAAG
* * *
2591602 GGTGCCACGGACTTGTGGTCTTTTGAAAA
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
*
2591631 GATGCCACTGACTTGTGGGCTTTGAAAAG
1 GGTGCCACTGACTTGTGGGCTTTG-AAAG
* *
2591660 AGTTGCCACCGACTTGTGTGGGCTTTGAAAG
1 -GGTGCCACTGAC-T-TGTGGGCTTTGAAAG
* *
2591691 GATGCCACTGACTTGTGGGCTTTTGAAAA
1 GGTGCCACTGACTTGTGGGC-TTTGAAAG
* *
2591720 GATGCCACTGACTTATGGGCTTTGAAATAG
1 GGTGCCACTGACTTGTGGGCTTTG-AA-AG
* * *
2591750 GTTGCCACCGACTTGTGTGGATTTTGAAATG
1 GGTGCCACTGACTTGTG-GG-CTTTGAAA-G
* *
2591781 GGTTGCCACCGACTTGTGTGGGCTTTCAAATG
1 GG-TGCCACTGAC-T-TGTGGGCTTTGAAA-G
* *
2591813 AGTTGCCACTCACTTGTGTGGGCTTTGAAATG
1 -GGTGCCACTGAC-T-TGTGGGCTTTGAAA-G
** * * ** *
2591845 AATTGCTACCGACTTGTGTACTTTAAAAGG
1 -GGTGCCACTGACTTGTGGGCTTTGAAA-G
* * * * *
2591875 GTGCTGCCACAGAGTTGTGGAC-TTAAAAA
1 G-G-TGCCACTGACTTGTGGGCTTTGAAAG
* * * *
2591904 GATGCCAC-GAAGTTGTGGAC-TTAAAAG
1 GGTGCCACTG-ACTTGTGGGCTTTGAAAG
* * * *
2591931 GATGCCACGGACTTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
2591958 GGTGCCACGGAGTTGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
2591986 AGTGCCACGGAGTTGTGGACTTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * *
2592013 GGTGCCACAGAGTTGTGGACTTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * ** * *
2592040 GATGTCACAAAGTTGTGGACTTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * *
2592067 GGTGCCACGGAGTTGTGGAC-TTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * * * *
2592094 GATGCCACGGAGTGGTGGACTTTAAAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
* * * **
2592122 GGTGTCACGGAGTTGTGGAATTT-AAAG
1 GGTGCCACTGACTTGTGGGCTTTGAAAG
2592149 GGTG
1 GGTG
2592153 TCATGGAGTT
Statistics
Matches: 1049, Mismatches: 120, Indels: 91
0.83 0.10 0.07
Matches are distributed among these distances:
26 3 0.00
27 168 0.16
28 404 0.39
29 181 0.17
30 142 0.14
31 30 0.03
32 112 0.11
33 4 0.00
34 5 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (28 bp):
GGTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:2591212 original size:57 final size:57
Alignment explanation
Indices: 2590906--2592035 Score: 971
Period size: 57 Copynumber: 19.5 Consensus size: 57
2590896 TTTTATAAAA
* * *
2590906 AAAGG-TGCCACTAACTTGCGTGGGCTTTGAAAAGAGTTGCCACCGGCTCGTGTGGGCTTTG
1 AAAGGATGCCACTGACTT--GTGGGCTTTGAAAAGAG-TGCCACTGACT--TGTGGGCTTTG
* * * * *
2590967 AAAAGAGTTACCACT-AGTTTGTGGGCTTTGAAAAGAGTGCTACTAACTTGTGGGCTTTG
1 -AAAG-GATGCCACTGA-CTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
2591026 AAAGGGTGCCATTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * ** *
2591082 AAAGGGTGCCACTGACTTGTGGACTTTGAAGGGA-TGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* **
2591138 AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCGTTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
*
2591195 AAAGGATGCCACTGACTTGCGTGGACTTT-AAAAG-GCTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTT--GTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG
2591253 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* *
2591310 AAA-GAGCGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGTGAGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTG-G-GCTTTG
* * * * *
2591368 AAAGGGTGCCATTGACTTATGGGCTTTGAAAGGA-TGCCACTAACTTGTGGGCTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
2591424 AAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTATGGGCTTTG
1 AAAGGA-TGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
2591481 AAAGGGTGCCACTGACTTATGGGCTTTG-AAAGGGTGCCACTAACTTGTGGGCTTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC-TTTG
* *
2591538 -AAGAGATGCCATTAACTTGTGGGCTTTGAAAAGAGTTGCCA-TCGACTTGTGTGGGCTTTG
1 AAAG-GATGCCACTGACTTGTGGGCTTTGAAAAGAG-TGCCACT-GAC-T-TGTGGGCTTTG
* *
2591598 AAATGG-TGCCACGGACTTGTGGTCTTTTGAAAAGA-TGCCACTGACTTGTGGGCTTTG
1 AAA-GGATGCCACTGACTTGTGGGC-TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * *
2591655 AAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTTG
1 -AAAG-GATGCCACTGAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGC-TTTG
* * * *
2591716 AAAAGATGCCACTGACTTATGGGCTTTGAAATAG-GTTGCCACCGACTTGTGTGGATTTTG
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAA-AGAG-TGCCACTGACTTGTG-GG-CTTTG
* * * * *
2591776 AAATGGGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCACTCACTTGTGTGGGCTTTG
1 AAA--GGATGCCACTGAC-T-TGTGGGCTTTGAAAAGAG-TGCCACTGAC-T-TGTGGGCTTTG
* * * ** * * * * *
2591840 AAATGAATTGCTACCGACTTGTGTACTTT-AAAAGGGTGCTGCCACAGAGTTGTGGAC-TTA
1 AAA-GGA-TGCCACTGACTTGTGGGCTTTGAAAA--GAG-TGCCACTGACTTGTGGGCTTTG
* * * * * *
2591900 AAAAGATGCCAC-GAAGTTGTGGAC-TT-AAAAG-GATGCCACGGACTTGTGGAC-TTA
1 AAAGGATGCCACTG-ACTTGTGGGCTTTGAAAAGAG-TGCCACTGACTTGTGGGCTTTG
* * * * * * *
2591954 AAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGAGTGCCACGGAGTTGTGGACTTT-
1 AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
* * * *
2592009 AAAGGGTGCCACAGAGTTGTGGACTTT
1 AAAGGATGCCACTGACTTGTGGGCTTT
2592036 AAAGGATGTC
Statistics
Matches: 906, Mismatches: 107, Indels: 117
0.80 0.09 0.10
Matches are distributed among these distances:
54 40 0.04
55 52 0.06
56 195 0.22
57 210 0.23
58 117 0.13
59 72 0.08
60 65 0.07
61 46 0.05
62 41 0.05
63 15 0.02
64 46 0.05
65 3 0.00
66 4 0.00
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (57 bp):
AAAGGATGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG
Found at i:2591314 original size:143 final size:141
Alignment explanation
Indices: 2590909--2592101 Score: 1079
Period size: 143 Copynumber: 8.3 Consensus size: 141
2590899 TATAAAAAAA
* * * *
2590909 GGTGCCACTAACTTGCGTGGGCTTTGAAAAGAGTTGCCACCGGCTCGTGTGGGCTTTGAAAAGAG
1 GGTGCCACTGACTT--GTGGGCTTT-AAAAG-GGTGCCACTGACT--TGTGGGCTTTG-AAAG-G
* * ** * * * *
2590974 TTACCACTAGTTTGTGGGCTTTGAAAAGAGTGCTACTAACTTGTGGGCTTTGAAAGGGTGCCATT
58 ATGCCACTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACT
2591039 GACTTGTGGGCTTTGAAAG
123 GACTTGTGGGCTTTGAAAG
* * *
2591058 GGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGACTTTGAAGGGATGCCACT
1 GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT
* **
2591123 AACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGAAAAGAGTGCCGTTGACTTGT
66 AACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTG-AAAGAGTGCCACTGACTTGT
2591187 GGGCTTTGAAAG
130 GGGCTTTGAAAG
* * *
2591199 GATGCCACTGACTTGCGTGGACTTTAAAAGGCTGCCACTGACTTGTGGGCTTTGAAAGGATGCCA
1 GGTGCCACTGACTT--GTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCA
* *
2591264 CTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGCGCCACTGACTTG
64 CTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG
2591329 TGGGCTTTGAAAG
129 TGGGCTTTGAAAG
* * *
2591342 GGTGCCACTGACTTGTGTGAGCTTTGAAAGGGTGCCATTGACTTATGGGCTTTGAAAGGATGCCA
1 GGTGCCACTGACTTGTG-G-GCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCA
* *
2591407 CTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTA
64 CTAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTG
2591472 TGGGCTTTGAAAG
129 TGGGCTTTGAAAG
* * *
2591485 GGTGCCACTGACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCTTTTG-AAGAGATGCCA
1 GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGC-TTTGAAAG-GATGCCA
* *
2591549 TTAACTTGTGGGCTTTGAAAAGAGTTGCCA-TCGACTTGTGTGGGCTTTGAAATG-GTGCCACGG
64 CTAACTTGTGGGCTTTGAAAAGAG-TGCCACT-GAC-T-TGTGGGCTTTGAAA-GAGTGCCACTG
* *
2591612 ACTTGTGGTCTTTTGAAAA
124 ACTTGTGGGC-TTTGAAAG
* * *
2591631 GATGCCACTGACTTGTGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGATGC
1 GGTGCCACTGACTTGTGGGCTTT-AAAAG-GGTGCCACTGAC-T-TGTGGGCTTTGAAAGGATGC
* * * *
2591696 CACTGACTTGTGGGCTTTTGAAAAGA-TGCCACTGACTTATGGGCTTTGAAATAGGTTGCCACCG
62 CACTAACTTGTGGGC-TTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGA-G-TGCCACTG
*
2591760 ACTTGTGTGGATTTTGAAATG
124 ACTTGTG-GG-CTTTGAAA-G
* * * * *
2591781 GGTTGCCACCGACTTGTGTGGGCTTTCAAATGAGTTGCCACTCACTTGTGTGGGCTTTGAAATGA
1 GG-TGCCACTGAC-T-TGTGGGCTTT-AAAAG-GGTGCCACTGAC-T-TGTGGGCTTTGAAA-GG
* ** ** * * * * **
2591846 ATTGCTACCGACTTGTGTACTTT-AAAAGGGTGCTGCCACAGAGTTGTGGACTTAAAAAGA-TGC
58 A-TGCCACTAACTTGTGGGCTTTGAAAA--GAG-TGCCACTGACTTGTGGGCTTTGAAAGAGTGC
* * *
2591909 CAC-GAAGTTGTGGAC-TTAAAAG
119 CACTG-ACTTGTGGGCTTTGAAAG
* * * * * * *
2591931 GATGCCACGGACTTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGAGTGCCAC
1 GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGA-TGCCAC
** * * * * * * * ** *
2591994 GGAGTTGTGGACTTT--AAAGGGTGCCACAGAGTTGTGGACTTT-AAAG-GATGTCACAAAGTTG
65 TAACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAG-TGCCACTGACTTG
*
2592055 TGGACTTT-AAAG
129 TGGGCTTTGAAAG
* * * *
2592067 GGTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCAC
1 GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCAC
2592102 GGAGTGGTGG
Statistics
Matches: 897, Mismatches: 106, Indels: 95
0.82 0.10 0.09
Matches are distributed among these distances:
135 4 0.00
136 71 0.08
137 4 0.00
139 3 0.00
140 43 0.05
141 99 0.11
142 49 0.05
143 251 0.28
144 36 0.04
145 44 0.05
146 48 0.05
147 21 0.02
148 32 0.04
149 54 0.06
150 23 0.03
151 14 0.02
152 1 0.00
153 48 0.05
154 17 0.02
155 15 0.02
157 20 0.02
ACGTcount: A:0.23, C:0.17, G:0.31, T:0.29
Consensus pattern (141 bp):
GGTGCCACTGACTTGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACT
AACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGAGTGCCACTGACTTGTG
GGCTTTGAAAG
Found at i:2591911 original size:27 final size:27
Alignment explanation
Indices: 2591879--2592308 Score: 452
Period size: 27 Copynumber: 15.7 Consensus size: 27
2591869 AAAAGGGTGC
* *
2591879 TGCCACAGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
2591906 TGCCACGAAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2591933 TGCCACGGACTTGTGGACTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
2591960 TGCCACGGAGTTGTGGACTTTAAAA-GA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
2591987 GTGCCACGGAGTTGTGGACTTTAAAGGG
1 -TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2592015 TGCCACAGAGTTGTGGACTTTAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* ** * *
2592042 TGTCACAAAGTTGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
2592069 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2592096 TGCCACGGAGTGGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* * * *
2592124 TGTCACGGAGTTGTGGAATTTAAAGGG
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* * *
2592151 TGTCATGGAGTTATGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
* *
2592178 TGCCATGGAGTTGTGTACTTTAAAAAGG-
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGA
* * *
2592206 TGCCACGGAATTATGAACTTTAAAAAGG-
1 TGCCACGGAGTTGTGGAC-TT-AAAAGGA
* ** *
2592234 TACCATAGAGTGGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGAC-TTAAAAGGA
* *
2592262 TACCACGGAGTTGTGGACTTAAAAAGA
1 TGCCACGGAGTTGTGGACTTAAAAGGA
*
2592289 TGCCACGGAGTTATGGACTT
1 TGCCACGGAGTTGTGGACTT
2592309 TGAAAAGAAA
Statistics
Matches: 345, Mismatches: 51, Indels: 14
0.84 0.12 0.03
Matches are distributed among these distances:
27 236 0.68
28 103 0.30
29 6 0.02
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTAAAAGGA
Found at i:2592007 original size:82 final size:83
Alignment explanation
Indices: 2591858--2592316 Score: 509
Period size: 82 Copynumber: 5.5 Consensus size: 83
2591848 TGCTACCGAC
* * * *
2591858 TTGTGTACTTTAAAAGGGTGCTGCCACAGAGTTGTGGACTTAAAAAGA-TGCCACGAAGTTGTGG
1 TTGTGGACTTTAAAA-GG-G-TGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGG
*
2591922 ACTTAAAAGGATGCCACGGAC
63 ACTTAAAAGGATGCCACGGAG
2591943 TTGTGGAC-TTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACT
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACT
* * *
2592007 TTAAAGGGTGCCACAGAG
66 TAAAAGGATGCCACGGAG
* * ** *
2592025 TTGTGGACTTT-AAAGGATGTCACAAAGTTGTGGACTTT-AAAGGGTGCCACGGAGTTGTGGACT
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACT
2592088 TAAAAGGATGCCACGGAG
66 TAAAAGGATGCCACGGAG
* * * * * * *
2592106 TGGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGAATTT-AAAGGGTGTCATGGAGTTATGGACT
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACT
*
2592170 TAAAAGGATGCCATGGAG
66 TAAAAGGATGCCACGGAG
* * * * * * ** *
2592188 TTGTGTACTTTAAAAAGGTGCCACGGAATTATGAACTTTAAAA-AGGTACCATAGAGTGGTGGAC
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGA-GTGCCACGGAGTTGTGGAC
*
2592252 TTTAAAAGGATACCACGGAG
65 -TTAAAAGGATGCCACGGAG
* * *
2592272 TTGTGGAC-TTAAAAAGATGCCACGGAGTTATGGACTTTGAAAAGA
1 TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT-AAAAGA
2592317 AATGCCACTG
Statistics
Matches: 321, Mismatches: 45, Indels: 16
0.84 0.12 0.04
Matches are distributed among these distances:
81 74 0.23
82 157 0.49
83 48 0.15
84 34 0.11
85 8 0.02
ACGTcount: A:0.31, C:0.13, G:0.31, T:0.26
Consensus pattern (83 bp):
TTGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACT
TAAAAGGATGCCACGGAG
Found at i:2592131 original size:136 final size:135
Alignment explanation
Indices: 2591879--2592308 Score: 527
Period size: 136 Copynumber: 3.1 Consensus size: 135
2591869 AAAAGGGTGC
* * * * *
2591879 TGCCACAGAGTTGTGGACTTAAAAAGATGCCACGAAGTTGTGGACTTAAAAGGATGCCACGGACT
1 TGCCACAGAGTTATGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAGGGTGCCACGGAAT
* *
2591944 TGTGGACTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGAGTGCCACGGAGTTGTGGACTTT
66 TGTGGACTTAAAA-GGTGCCACGGAGTGGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT
2592009 AAAGGG
130 AAAGGG
* * * * *
2592015 TGCCACAGAGTTGTGGACTTTAAAGGATGTCACAAAGTTGTGGACTTTAAAGGGTGCCACGGAGT
1 TGCCACAGAGTTATGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAGGGTGCCACGGAAT
* *
2592080 TGTGGACTTAAAAGGATGCCACGGAGTGGTGGACTTTAAAAGGGTGTCACGGAGTTGTGGAATTT
66 TGTGGACTTAAAAGG-TGCCACGGAGTGGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTT
2592145 AAAGGG
130 AAAGGG
* ** * * * *
2592151 TGTCATGGAGTTATGGACTTAAAAGGATGCCATGGAGTTGTGTACTTTAAAAAGGTGCCACGGAA
1 TGCCACAGAGTTATGGACTTAAAAGGATGCCACGAAGTTGTGGACTTT-AAAGGGTGCCACGGAA
* * * ** * *
2592216 TTATGAACTTTAAAAAGGTACCATAGAGTGGTGGACTTTAAAAGGATACCACGGAGTTGTGGACT
65 TTGTGGAC-TT-AAAAGGTGCCACGGAGTGGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACT
* * *
2592281 TAAAAAGA
128 TTAAAGGG
*
2592289 TGCCACGGAGTTATGGACTT
1 TGCCACAGAGTTATGGACTT
2592309 TGAAAAGAAA
Statistics
Matches: 253, Mismatches: 37, Indels: 6
0.85 0.12 0.02
Matches are distributed among these distances:
135 2 0.01
136 160 0.63
137 20 0.08
138 65 0.26
139 6 0.02
ACGTcount: A:0.30, C:0.13, G:0.31, T:0.26
Consensus pattern (135 bp):
TGCCACAGAGTTATGGACTTAAAAGGATGCCACGAAGTTGTGGACTTTAAAGGGTGCCACGGAAT
TGTGGACTTAAAAGGTGCCACGGAGTGGTGGACTTTAAAAGGGTGCCACGGAGTTGTGGACTTTA
AAGGG
Found at i:2593650 original size:24 final size:25
Alignment explanation
Indices: 2593602--2593650 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
2593592 TGTTGTTCCC
*
2593602 TTTTTATTTTGCTTTTGCATCTTTT
1 TTTTTATTTTGCTTTTGCATATTTT
* *
2593627 TTTTTGTTTTTCTTTT-CATATTTT
1 TTTTTATTTTGCTTTTGCATATTTT
2593651 GTACTTTTGC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.08, C:0.10, G:0.06, T:0.76
Consensus pattern (25 bp):
TTTTTATTTTGCTTTTGCATATTTT
Found at i:2601063 original size:104 final size:104
Alignment explanation
Indices: 2600883--2601078 Score: 392
Period size: 104 Copynumber: 1.9 Consensus size: 104
2600873 CGGTGCCCGA
2600883 CGAAGTTCGTCCCCACATATATCCGATCCTCTACCTACTACGAATGCCTCGGGGTGTTAAAGTTT
1 CGAAGTTCGTCCCCACATATATCCGATCCTCTACCTACTACGAATGCCTCGGGGTGTTAAAGTTT
2600948 GATCTGAACAAAATGAGGAAGAATGGCGTTGGCACTCAG
66 GATCTGAACAAAATGAGGAAGAATGGCGTTGGCACTCAG
2600987 CGAAGTTCGTCCCCACATATATCCGATCCTCTACCTACTACGAATGCCTCGGGGTGTTAAAGTTT
1 CGAAGTTCGTCCCCACATATATCCGATCCTCTACCTACTACGAATGCCTCGGGGTGTTAAAGTTT
2601052 GATCTGAACAAAATGAGGAAGAATGGC
66 GATCTGAACAAAATGAGGAAGAATGGC
2601079 ATTTGTAGTT
Statistics
Matches: 92, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 92 1.00
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.25
Consensus pattern (104 bp):
CGAAGTTCGTCCCCACATATATCCGATCCTCTACCTACTACGAATGCCTCGGGGTGTTAAAGTTT
GATCTGAACAAAATGAGGAAGAATGGCGTTGGCACTCAG
Found at i:2603847 original size:10 final size:10
Alignment explanation
Indices: 2603830--2603879 Score: 56
Period size: 9 Copynumber: 5.5 Consensus size: 10
2603820 TAATTAAAAA
2603830 ATAT-TAATT
1 ATATATAATT
*
2603839 TTATATAATT
1 ATATATAATT
2603849 AT-TA-AATT
1 ATATATAATT
2603857 ATATATAATT
1 ATATATAATT
2603867 A-ATATAA-T
1 ATATATAATT
2603875 ATATA
1 ATATA
2603880 ATTATAAAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
8 8 0.23
9 16 0.46
10 11 0.31
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (10 bp):
ATATATAATT
Found at i:2603860 original size:16 final size:16
Alignment explanation
Indices: 2603839--2603891 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
2603829 AATATTAATT
2603839 TTATATAATTATTAAA
1 TTATATAATTATTAAA
*
2603855 TTATAT-ATAATTAATA
1 TTATATAATTATTAA-A
*
2603871 TAATATATAATTATAAAA
1 T--TATATAATTATTAAA
2603889 TTA
1 TTA
2603892 AAAAAAATTC
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 7 0.23
16 10 0.33
18 7 0.23
19 6 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
TTATATAATTATTAAA
Found at i:2603860 original size:27 final size:29
Alignment explanation
Indices: 2603804--2603877 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 29
2603794 TTCCTCTATT
2603804 TTAATTTTATA-AATTATAATTAAAAAATA
1 TTAATTTTATATAA-TATAATTAAAAAATA
**
2603833 TTAATTTTATATAAT-T-ATTAAATTATA
1 TTAATTTTATATAATATAATTAAAAAATA
*
2603860 TATAA-TTAATATAATATA
1 T-TAATTTTATATAATATA
2603878 TAATTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
27 19 0.50
28 5 0.13
29 12 0.32
30 2 0.05
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
TTAATTTTATATAATATAATTAAAAAATA
Found at i:2603861 original size:18 final size:18
Alignment explanation
Indices: 2603831--2603891 Score: 65
Period size: 18 Copynumber: 3.6 Consensus size: 18
2603821 AATTAAAAAA
*
2603831 TATT-AATTTTATATAAT
1 TATTAAATTATATATAAT
2603848 TATTAAATTATATATAAT
1 TATTAAATTATATATAAT
* *
2603866 TA--ATATAATATATAAT
1 TATTAAATTATATATAAT
*
2603882 TATAAAATTA
1 TATTAAATTA
2603892 AAAAAAATTC
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
16 14 0.39
17 4 0.11
18 18 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
TATTAAATTATATATAAT
Found at i:2604252 original size:13 final size:14
Alignment explanation
Indices: 2604228--2604268 Score: 59
Period size: 13 Copynumber: 3.1 Consensus size: 14
2604218 CTCCTCATTC
*
2604228 TCCTTCTTTCTTTT
1 TCCTTTTTTCTTTT
2604242 T-CTTTTTTCTTTT
1 TCCTTTTTTCTTTT
2604255 TCCTTTTTT-TTTT
1 TCCTTTTTTCTTTT
2604268 T
1 T
2604269 TTGCCGCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
13 17 0.68
14 8 0.32
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (14 bp):
TCCTTTTTTCTTTT
Found at i:2610720 original size:3 final size:3
Alignment explanation
Indices: 2610712--2610757 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
2610702 TCAAAAGAAT
2610712 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC T
2610758 ACATTAATTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:2611863 original size:22 final size:22
Alignment explanation
Indices: 2611835--2611877 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
2611825 TATTAAAAAA
2611835 ATATTTTTAT-ATTAATATTTAT
1 ATATTTTTATAATTAA-ATTTAT
2611857 ATATTTTTATAATTAAATTTA
1 ATATTTTTATAATTAAATTTA
2611878 AATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 15 0.75
23 5 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
ATATTTTTATAATTAAATTTAT
Found at i:2611948 original size:20 final size:21
Alignment explanation
Indices: 2611925--2611974 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
2611915 TGAATCGAAA
*
2611925 TTAAATTAAA-AAATTCACAC
1 TTAAATTAAACAAATTCAAAC
*
2611945 TTAAATTCAAACGAATTCAAAC
1 TTAAATT-AAACAAATTCAAAC
2611967 -TAAATTAA
1 TTAAATTAA
2611975 CTGCTCAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
20 9 0.35
21 9 0.35
22 8 0.31
ACGTcount: A:0.54, C:0.14, G:0.02, T:0.30
Consensus pattern (21 bp):
TTAAATTAAACAAATTCAAAC
Found at i:2612609 original size:20 final size:19
Alignment explanation
Indices: 2612572--2612611 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2612562 TTTTTATTTA
*
2612572 AAAAAAATTATAATTTAAG
1 AAAAAAATTATAAGTTAAG
2612591 AAAAAAATTATAACGTTAAG
1 AAAAAAATTATAA-GTTAAG
2612611 A
1 A
2612612 TTTATATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 13 0.68
20 6 0.32
ACGTcount: A:0.62, C:0.03, G:0.07, T:0.28
Consensus pattern (19 bp):
AAAAAAATTATAAGTTAAG
Found at i:2614297 original size:20 final size:20
Alignment explanation
Indices: 2614261--2614299 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
2614251 TAATACCAAT
*
2614261 TTAATTATGAAATTAAAAAA
1 TTAATTATGAAAATAAAAAA
2614281 TTAAGTTAT-AAAATAAAAA
1 TTAA-TTATGAAAATAAAAA
2614300 TTATATATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
TTAATTATGAAAATAAAAAA
Found at i:2617517 original size:17 final size:18
Alignment explanation
Indices: 2617492--2617537 Score: 60
Period size: 17 Copynumber: 2.6 Consensus size: 18
2617482 TTCCAAAGTG
*
2617492 ATAACTAAAATA-TTTAA
1 ATAATTAAAATATTTTAA
2617509 ATAATTAAAA-ATTTTAA
1 ATAATTAAAATATTTTAA
2617526 ATAAATTAAAAT
1 AT-AATTAAAAT
2617538 CATATATATG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 16 0.64
18 8 0.32
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (18 bp):
ATAATTAAAATATTTTAA
Found at i:2617532 original size:18 final size:18
Alignment explanation
Indices: 2617498--2617536 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
2617488 AGTGATAACT
2617498 AAAATATTTAAATAATTA
1 AAAATATTTAAATAATTA
2617516 AAAAT-TTTAAATAAATTA
1 AAAATATTTAAAT-AATTA
2617534 AAA
1 AAA
2617537 TCATATATAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
AAAATATTTAAATAATTA
Found at i:2618168 original size:21 final size:21
Alignment explanation
Indices: 2618139--2618182 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
2618129 AAATGATATC
2618139 AATTCAATTATTATATTTATA
1 AATTCAATTATTATATTTATA
*
2618160 AATTTAATTATTATATTTATA
1 AATTCAATTATTATATTTATA
2618181 AA
1 AA
2618183 AACAATCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (21 bp):
AATTCAATTATTATATTTATA
Found at i:2619311 original size:16 final size:17
Alignment explanation
Indices: 2619269--2619311 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
2619259 GTTAATATTT
* *
2619269 ATAAAATTTTTATTTAA
1 ATAAAATTTATAATTAA
2619286 ATAAAA-TTATAATT-A
1 ATAAAATTTATAATTAA
2619301 ATAAAATTTAT
1 ATAAAATTTAT
2619312 TTAAAAATAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 7 0.30
16 10 0.43
17 6 0.26
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATAAAATTTATAATTAA
Found at i:2619323 original size:14 final size:14
Alignment explanation
Indices: 2619264--2619324 Score: 52
Period size: 14 Copynumber: 4.1 Consensus size: 14
2619254 GAAGTGTTAA
*
2619264 TATTTATAAAATTTT
1 TATTTA-AAAATATT
*
2619279 TATTTAAATAAAATT
1 TATTTAAA-AATATT
*
2619294 ATAATTAATAAA-ATT
1 -TATTTAA-AAATATT
2619309 TATTTAAAAATATT
1 TATTTAAAAATATT
2619323 TA
1 TA
2619325 ATAAATAAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
13 3 0.08
14 13 0.34
15 13 0.34
16 8 0.21
17 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (14 bp):
TATTTAAAAATATT
Found at i:2619372 original size:27 final size:26
Alignment explanation
Indices: 2619280--2619374 Score: 79
Period size: 29 Copynumber: 3.5 Consensus size: 26
2619270 TAAAATTTTT
2619280 ATTTAAATAAAATTATAATTAATAAAA
1 ATTTAAATAAAATT-TAATTAATAAAA
* *
2619307 TTTATTTAAA-AATATTTAA-TAA-ATAA
1 ---ATTTAAATAAAATTTAATTAATAAAA
2619333 ATTTAAAGTTAAAATTTAATTATATAAAA
1 ATTTAAA--TAAAATTTAATTA-ATAAAA
*
2619362 ATTTATATAAAAT
1 ATTTAAATAAAAT
2619375 ATAAGATAAA
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
23 7 0.13
26 11 0.20
27 11 0.20
28 4 0.07
29 14 0.26
30 7 0.13
ACGTcount: A:0.57, C:0.00, G:0.01, T:0.42
Consensus pattern (26 bp):
ATTTAAATAAAATTTAATTAATAAAA
Found at i:2619384 original size:55 final size:53
Alignment explanation
Indices: 2619280--2619385 Score: 128
Period size: 55 Copynumber: 2.0 Consensus size: 53
2619270 TAAAATTTTT
* *
2619280 ATTTAAATAAAATTATAATTAATAAAATTTATTTAAAAATATTTAATAAATAA
1 ATTTAAATAAAATTATAATTAATAAAATTTATATAAAAATATTAAATAAATAA
2619333 ATTTAAAGTTAAAATT-TAATTATATAAAAATTTATAT-AAAATA-TAAGATAAAT
1 ATTTAAA--TAAAATTATAATTA-AT-AAAATTTATATAAAAATATTAA-ATAAAT
2619386 TTTAATATAA
Statistics
Matches: 46, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
53 7 0.15
54 8 0.17
55 21 0.46
56 10 0.22
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.41
Consensus pattern (53 bp):
ATTTAAATAAAATTATAATTAATAAAATTTATATAAAAATATTAAATAAATAA
Found at i:2619720 original size:22 final size:22
Alignment explanation
Indices: 2619694--2619735 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
2619684 AACACGACAT
2619694 AAACACAATATAAAAATAATTA
1 AAACACAATATAAAAATAATTA
*
2619716 AAACACAGTATAAAAATAAT
1 AAACACAATATAAAAATAAT
2619736 ATGAATATGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.10, G:0.02, T:0.21
Consensus pattern (22 bp):
AAACACAATATAAAAATAATTA
Found at i:2619780 original size:19 final size:21
Alignment explanation
Indices: 2619727--2619780 Score: 53
Period size: 19 Copynumber: 2.7 Consensus size: 21
2619717 AACACAGTAT
2619727 AAAAATAATATGAATATGATACA
1 AAAAAT-ATAT-AATATGATACA
*
2619750 AATAA-ATA-AATAT-AT-CA
1 AAAAATATATAATATGATACA
2619767 AAAAATATATAATA
1 AAAAATATATAATA
2619781 CTAATTATTG
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
17 6 0.22
18 5 0.19
19 9 0.33
21 3 0.11
23 4 0.15
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.28
Consensus pattern (21 bp):
AAAAATATATAATATGATACA
Found at i:2620627 original size:16 final size:16
Alignment explanation
Indices: 2620600--2620718 Score: 102
Period size: 16 Copynumber: 7.4 Consensus size: 16
2620590 AAAAATGAAA
2620600 AAATTAATTTTAGATTT
1 AAATT-ATTTTAGATTT
*
2620617 AAATTATTTTAAATTT
1 AAATTATTTTAGATTT
2620633 AAATTATTTT-GATTTT
1 AAATTATTTTAGA-TTT
*
2620649 AATTTATTTTA-ATTTT
1 AAATTATTTTAGA-TTT
* * *
2620665 AATTTATTTTAAATTA
1 AAATTATTTTAGATTT
2620681 AAATTATTTTA-ATTTT
1 AAATTATTTTAGA-TTT
* *
2620697 TAATTA-ATTAGATTT
1 AAATTATTTTAGATTT
2620712 AATATTA
1 AA-ATTA
2620719 CGGTGAATTG
Statistics
Matches: 87, Mismatches: 9, Indels: 13
0.80 0.08 0.12
Matches are distributed among these distances:
15 9 0.10
16 72 0.83
17 6 0.07
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (16 bp):
AAATTATTTTAGATTT
Found at i:2620650 original size:32 final size:32
Alignment explanation
Indices: 2620600--2620711 Score: 118
Period size: 32 Copynumber: 3.5 Consensus size: 32
2620590 AAAAATGAAA
*
2620600 AAATTAATTTTAGA-TTTAAATTATTTTAAATTT
1 AAATT-ATTTT-GATTTTAAATTATTTTAATTTT
*
2620633 AAATTATTTTGATTTTAATTTATTTTAATTTT
1 AAATTATTTTGATTTTAAATTATTTTAATTTT
* * * *
2620665 AATTTATTTTAAATTAAAATTATTTTAATTTT
1 AAATTATTTTGATTTTAAATTATTTTAATTTT
* * *
2620697 TAATTAATTAGATTT
1 AAATTATTTTGATTT
2620712 AATATTACGG
Statistics
Matches: 65, Mismatches: 13, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
31 2 0.03
32 58 0.89
33 5 0.08
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.59
Consensus pattern (32 bp):
AAATTATTTTGATTTTAAATTATTTTAATTTT
Found at i:2620672 original size:48 final size:49
Alignment explanation
Indices: 2620601--2620718 Score: 154
Period size: 48 Copynumber: 2.4 Consensus size: 49
2620591 AAAATGAAAA
* *
2620601 AATTAATTTTAGATTTAAATTATTTTAAATTTAAATTATTTTGA-TTTT
1 AATTAATTTTAGATTTAAATTATTTTAAATTAAAATTATTTTAATTTTT
* *
2620649 AATTTATTTTA-ATTTTAATTTATTTTAAATTAAAATTATTTTAATTTTT
1 AATTAATTTTAGA-TTTAAATTATTTTAAATTAAAATTATTTTAATTTTT
2620698 AATTAA--TTAGATTTAATATTA
1 AATTAATTTTAGATTTAA-ATTA
2620719 CGGTGAATTG
Statistics
Matches: 60, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
47 9 0.15
48 42 0.70
49 9 0.15
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (49 bp):
AATTAATTTTAGATTTAAATTATTTTAAATTAAAATTATTTTAATTTTT
Found at i:2620758 original size:15 final size:14
Alignment explanation
Indices: 2620733--2620785 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 14
2620723 GAATTGAGGT
2620733 TTAATATTTAAATAAA
1 TTAA-ATTTAAAT-AA
2620749 TTAAATTTAAATCAA
1 TTAAATTTAAAT-AA
* *
2620764 TCAAATTT-AATAT
1 TTAAATTTAAATAA
2620777 TTAAATTTA
1 TTAAATTTA
2620786 CAGAGTTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
13 8 0.25
14 3 0.09
15 17 0.53
16 4 0.12
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (14 bp):
TTAAATTTAAATAA
Found at i:2620863 original size:16 final size:16
Alignment explanation
Indices: 2620844--2620910 Score: 100
Period size: 16 Copynumber: 4.2 Consensus size: 16
2620834 TTATTTTAAA
2620844 TTTAAATTTAAATT-T
1 TTTAAATTTAAATTAT
* *
2620859 TTTTATTTTAAATTAT
1 TTTAAATTTAAATTAT
2620875 TTTAAATTTAAATTAT
1 TTTAAATTTAAATTAT
*
2620891 TTTAAATTTATATTAT
1 TTTAAATTTAAATTAT
2620907 TTTA
1 TTTA
2620911 CGTTATTTTT
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
15 12 0.26
16 34 0.74
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
TTTAAATTTAAATTAT
Found at i:2620875 original size:60 final size:64
Alignment explanation
Indices: 2620776--2620892 Score: 161
Period size: 60 Copynumber: 1.9 Consensus size: 64
2620766 AAATTTAATA
*
2620776 TTTAAATTTACAGAGTTAAATCTTTTTAAATTAACTTATTTTAAA-TT-AATTATTTAGTTTAT
1 TTTAAATTTACAGAGTTAAATCTTTTTAAATTAAATTATTTTAAATTTAAATTATTTAGTTTAT
* * **
2620838 TTTAAATTTA-A-ATTTAAATTTTTTTATTTTAAATTATTTTAAATTTAAATTATTT
1 TTTAAATTTACAGAGTTAAATCTTTTTAAATTAAATTATTTTAAATTTAAATTATTT
2620893 TAAATTTATA
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
60 27 0.56
61 3 0.06
62 18 0.38
ACGTcount: A:0.38, C:0.03, G:0.03, T:0.57
Consensus pattern (64 bp):
TTTAAATTTACAGAGTTAAATCTTTTTAAATTAAATTATTTTAAATTTAAATTATTTAGTTTAT
Found at i:2620882 original size:31 final size:32
Alignment explanation
Indices: 2620791--2620910 Score: 101
Period size: 31 Copynumber: 3.9 Consensus size: 32
2620781 ATTTACAGAG
*
2620791 TTAAATCT-TTTTAAA-TTAACTTATTTTAAA-
1 TTAAAT-TATTTTAAATTTAAATTATTTTAAAT
* ** *
2620821 TT-AATTA-TTT-AGTTTATTTTAAATTTAAAT
1 TTAAATTATTTTAAATTTAAATT-ATTTTAAAT
* *
2620851 TTAAATTTTTTTAT-TTTAAATTATTTTAAAT
1 TTAAATTATTTTAAATTTAAATTATTTTAAAT
*
2620882 TTAAATTATTTTAAATTTATATTATTTTA
1 TTAAATTATTTTAAATTTAAATTATTTTA
2620911 CGTTATTTTT
Statistics
Matches: 70, Mismatches: 12, Indels: 14
0.73 0.12 0.15
Matches are distributed among these distances:
27 1 0.01
28 9 0.13
29 10 0.14
30 4 0.06
31 24 0.34
32 22 0.31
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (32 bp):
TTAAATTATTTTAAATTTAAATTATTTTAAAT
Found at i:2620978 original size:28 final size:28
Alignment explanation
Indices: 2620925--2620982 Score: 73
Period size: 28 Copynumber: 2.1 Consensus size: 28
2620915 ATTTTTTATT
*
2620925 AAATTAAGTTAGATAAAATTTGAATTTA
1 AAATTAAGTTAGATAAAATTTAAATTTA
* *
2620953 AAATTAA-TTAGTTAAATTTTTAAATTTA
1 AAATTAAGTTAGATAAA-ATTTAAATTTA
2620981 AA
1 AA
2620983 TAAAAAAAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 8 0.31
28 18 0.69
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (28 bp):
AAATTAAGTTAGATAAAATTTAAATTTA
Found at i:2621948 original size:24 final size:24
Alignment explanation
Indices: 2621921--2621980 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
2621911 ATAATTTAAA
**
2621921 TTATTATTTAATTAATAAAAATAT
1 TTATTATTTAAAAAATAAAAATAT
* *
2621945 TTATTATTTAAAAAATATAGATAT
1 TTATTATTTAAAAAATAAAAATAT
2621969 TTATTATTTAAA
1 TTATTATTTAAA
2621981 TTTAATTATA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (24 bp):
TTATTATTTAAAAAATAAAAATAT
Done.