Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032247.1 Gossypioides kirkii chromosome KI_05
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 50980411
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 20 of 171
Found at i:9234837 original size:18 final size:17
Alignment explanation
Indices: 9234817--9234875 Score: 54
Period size: 18 Copynumber: 3.5 Consensus size: 17
9234807 AGTGACTATT
9234817 AAAATTAAACTTAAATA
1 AAAATTAAACTTAAATA
9234834 TAAAA-TAAGAC--AAA-A
1 -AAAATTAA-ACTTAAATA
*
9234849 AAAATTAAATTTAACATA
1 AAAATTAAACTTAA-ATA
9234867 AAAATTAAA
1 AAAATTAAA
9234876 TTCAGACACC
Statistics
Matches: 34, Mismatches: 1, Indels: 12
0.72 0.02 0.26
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 5 0.15
17 4 0.12
18 16 0.47
ACGTcount: A:0.68, C:0.05, G:0.02, T:0.25
Consensus pattern (17 bp):
AAAATTAAACTTAAATA
Found at i:9245645 original size:21 final size:21
Alignment explanation
Indices: 9245619--9245660 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9245609 AAACATATAA
9245619 AATTTAACCGAAATTTTAAGT
1 AATTTAACCGAAATTTTAAGT
9245640 AATTTAACCGAAATTTTAAGT
1 AATTTAACCGAAATTTTAAGT
9245661 CTTGAAACAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.10, G:0.10, T:0.38
Consensus pattern (21 bp):
AATTTAACCGAAATTTTAAGT
Found at i:9247909 original size:61 final size:60
Alignment explanation
Indices: 9247815--9247933 Score: 168
Period size: 61 Copynumber: 2.0 Consensus size: 60
9247805 TTACATTGAG
*
9247815 TGCTTTAGCTGTTTTTAGTTTATTATTATGGAGTTGCATT-AAATTTTGAACAAGGATGAA
1 TGCTTTAGCTGTTTTTAGTTTATTATTAAGGAGTTGC-TTCAAATTTTGAACAAGGATGAA
* * * *
9247875 TGCTTTAGTTTTTTTCTAGTTTATTTTTAAGGAGTTGCTTCAAATTTTGAACGAGGATG
1 TGCTTTAGCTGTTTT-TAGTTTATTATTAAGGAGTTGCTTCAAATTTTGAACAAGGATG
9247934 GACAAGGCCA
Statistics
Matches: 52, Mismatches: 5, Indels: 3
0.87 0.08 0.05
Matches are distributed among these distances:
60 15 0.29
61 37 0.71
ACGTcount: A:0.25, C:0.08, G:0.20, T:0.47
Consensus pattern (60 bp):
TGCTTTAGCTGTTTTTAGTTTATTATTAAGGAGTTGCTTCAAATTTTGAACAAGGATGAA
Found at i:9248718 original size:19 final size:21
Alignment explanation
Indices: 9248696--9248741 Score: 62
Period size: 19 Copynumber: 2.3 Consensus size: 21
9248686 TAAAATAAAT
9248696 AAATAATT-TATAAATT-TA-A
1 AAATAATTCT-TAAATTATATA
9248715 AAATAATTCTTAAATTATATA
1 AAATAATTCTTAAATTATATA
9248736 AAATAA
1 AAATAA
9248742 ATTAATTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 14 0.58
20 3 0.12
21 7 0.29
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
AAATAATTCTTAAATTATATA
Found at i:9248764 original size:18 final size:18
Alignment explanation
Indices: 9248727--9248761 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
9248717 ATAATTCTTA
9248727 AATTATATAAAATAAATT
1 AATTATATAAAATAAATT
*
9248745 AATTATCTAAAA-AAATT
1 AATTATATAAAATAAATT
9248762 TAAAATGAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.60, C:0.03, G:0.00, T:0.37
Consensus pattern (18 bp):
AATTATATAAAATAAATT
Found at i:9251427 original size:18 final size:17
Alignment explanation
Indices: 9251401--9251447 Score: 58
Period size: 18 Copynumber: 2.7 Consensus size: 17
9251391 ATTTTTTATA
*
9251401 TTTAGTTTTTATTTTCT
1 TTTAATTTTTATTTTCT
**
9251418 TTTATATTTTGGTTTTCT
1 TTTA-ATTTTTATTTTCT
9251436 TTTAATTTTTAT
1 TTTAATTTTTAT
9251448 CTGTCTTTGT
Statistics
Matches: 24, Mismatches: 5, Indels: 2
0.77 0.16 0.06
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.15, C:0.04, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTAATTTTTATTTTCT
Found at i:9251433 original size:23 final size:23
Alignment explanation
Indices: 9251394--9251438 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
9251384 TCCCTTAATT
*
9251394 TTTTATATTTAGTTTTTATTTTC
1 TTTTATATTTAGGTTTTATTTTC
* *
9251417 TTTTATATTTTGGTTTTCTTTT
1 TTTTATATTTAGGTTTTATTTT
9251439 AATTTTTATC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.13, C:0.04, G:0.07, T:0.76
Consensus pattern (23 bp):
TTTTATATTTAGGTTTTATTTTC
Found at i:9251480 original size:23 final size:23
Alignment explanation
Indices: 9251452--9251507 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
9251442 TTTTATCTGT
9251452 CTTTGTGGTACGCTTTTCATCTAC
1 CTTTGTGGTACG-TTTTCATCTAC
* **
9251476 C-TTGTGGCACGTTTTTGTCTAC
1 CTTTGTGGTACGTTTTCATCTAC
9251498 CTTTGTGGTA
1 CTTTGTGGTA
9251508 GATTTGCATT
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
22 10 0.37
23 16 0.59
24 1 0.04
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (23 bp):
CTTTGTGGTACGTTTTCATCTAC
Found at i:9251816 original size:18 final size:18
Alignment explanation
Indices: 9251790--9251837 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
9251780 TGATCTGATA
*
9251790 TTTATTTTTTCTAAATTT
1 TTTAATTTTTCTAAATTT
*
9251808 TTTAATTTTT-TTAATTT
1 TTTAATTTTTCTAAATTT
9251825 TATT-ATTTTTCTA
1 T-TTAATTTTTCTA
9251838 TTACATTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
17 13 0.52
18 12 0.48
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TTTAATTTTTCTAAATTT
Found at i:9251817 original size:9 final size:9
Alignment explanation
Indices: 9251793--9251834 Score: 50
Period size: 9 Copynumber: 4.7 Consensus size: 9
9251783 TCTGATATTT
9251793 ATTTTTTCTA
1 ATTTTTT-TA
*
9251803 AATTTTTTA
1 ATTTTTTTA
9251812 ATTTTTTTA
1 ATTTTTTTA
*
9251821 ATTTTATT-
1 ATTTTTTTA
9251829 ATTTTT
1 ATTTTT
9251835 CTATTACATT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
8 5 0.18
9 17 0.61
10 6 0.21
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.74
Consensus pattern (9 bp):
ATTTTTTTA
Found at i:9253519 original size:31 final size:31
Alignment explanation
Indices: 9253484--9253543 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
9253474 TCTTTCTTTA
* *
9253484 AATATATTTAATTGAATCAAAATTAAAATTT
1 AATATATATAATTAAATCAAAATTAAAATTT
* *
9253515 AATATATATATTTAAATTAAAATTAAAAT
1 AATATATATAATTAAATCAAAATTAAAAT
9253544 ATATAAATAC
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (31 bp):
AATATATATAATTAAATCAAAATTAAAATTT
Found at i:9266669 original size:7 final size:7
Alignment explanation
Indices: 9266657--9266687 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
9266647 GAGTTGCAAT
9266657 ACATATC
1 ACATATC
9266664 ACATATC
1 ACATATC
9266671 ACATATC
1 ACATATC
9266678 ACATATC
1 ACATATC
9266685 ACA
1 ACA
9266688 CAGAAGTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (7 bp):
ACATATC
Found at i:9269332 original size:32 final size:32
Alignment explanation
Indices: 9269295--9269364 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
9269285 GAATAGCAAT
9269295 TGCTATATAGCGGTAGCGATATCGTCCGAAAC
1 TGCTATATAGCGGTAGCGATATCGTCCGAAAC
*
9269327 TGCTATATAGCGGTAGCGGTATCGTCCGAAAC
1 TGCTATATAGCGGTAGCGATATCGTCCGAAAC
9269359 TGCTAT
1 TGCTAT
9269365 TGTTGAAAAT
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.27
Consensus pattern (32 bp):
TGCTATATAGCGGTAGCGATATCGTCCGAAAC
Found at i:9286768 original size:17 final size:16
Alignment explanation
Indices: 9286746--9286785 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
9286736 AATAATAAGT
*
9286746 TTATTATTATTATTTAA
1 TTATTATGATTATTT-A
9286763 TTATTATGATTATTTA
1 TTATTATGATTATTTA
9286779 TTATTAT
1 TTATTAT
9286786 ATTTCTCTGT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 8 0.36
17 14 0.64
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (16 bp):
TTATTATGATTATTTA
Found at i:9289904 original size:2 final size:2
Alignment explanation
Indices: 9289897--9289932 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
9289887 TCAATAACAA
*
9289897 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
9289933 TTAAATGATT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:9290978 original size:18 final size:18
Alignment explanation
Indices: 9290955--9290993 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
9290945 AAAATCGGGT
9290955 AATTAACCGAA-TTAATCA
1 AATTAACCGAACTTAAT-A
*
9290973 AATTAACTGAACTTAATA
1 AATTAACCGAACTTAATA
9290991 AAT
1 AAT
9290994 AATATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 14 0.74
19 5 0.26
ACGTcount: A:0.51, C:0.13, G:0.05, T:0.31
Consensus pattern (18 bp):
AATTAACCGAACTTAATA
Found at i:9291995 original size:15 final size:15
Alignment explanation
Indices: 9291977--9292023 Score: 67
Period size: 15 Copynumber: 3.0 Consensus size: 15
9291967 CTTTTAAAAA
9291977 ATTTAAAAATATTTT
1 ATTTAAAAATATTTT
*
9291992 ATTTAATAATATTTTT
1 ATTTAAAAATA-TTTT
9292008 ATCTTAAAAATATTTT
1 AT-TTAAAAATATTTT
9292024 TAAAAAATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
15 10 0.36
16 10 0.36
17 8 0.29
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (15 bp):
ATTTAAAAATATTTT
Found at i:9292019 original size:17 final size:16
Alignment explanation
Indices: 9291977--9292025 Score: 73
Period size: 17 Copynumber: 3.1 Consensus size: 16
9291967 CTTTTAAAAA
9291977 ATTTAAAAATA-TTTT
1 ATTTAAAAATATTTTT
*
9291992 ATTTAATAATATTTTT
1 ATTTAAAAATATTTTT
9292008 ATCTTAAAAATATTTTT
1 AT-TTAAAAATATTTTT
9292025 A
1 A
9292026 AAAAATAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 10 0.33
16 6 0.20
17 14 0.47
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (16 bp):
ATTTAAAAATATTTTT
Found at i:9304953 original size:2 final size:2
Alignment explanation
Indices: 9304948--9304974 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
9304938 AGTTAAAGCA
9304948 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
9304975 ACACACACAC
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:9304979 original size:2 final size:2
Alignment explanation
Indices: 9304974--9304998 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9304964 CTCTCTCTCT
9304974 CA CA CA CA CA CA CA CA CA CA CA CA C
1 CA CA CA CA CA CA CA CA CA CA CA CA C
9304999 TTATTCATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:9320064 original size:71 final size:70
Alignment explanation
Indices: 9319948--9320083 Score: 200
Period size: 71 Copynumber: 1.9 Consensus size: 70
9319938 CTTCCTCCAA
* *
9319948 CTTTTCGTCAAGCGAAGTGTTCGATAAAATGCTTCACTGATGAAAAAGAAAGGCCTTTCAAATTC
1 CTTTTCGTCAACCGAAGTGTTCGATAAAATGCTTCACCGATGAAAAAGAAA-GCCTTTCAAATTC
9320013 TTTCAT
65 TTTCAT
* * * * *
9320019 CTTTTCGTCGACCTAAGTGTTTGATAAAATGCTTCACCGTTGAAAAAGAAAGCCTTTCACATTCT
1 CTTTTCGTCAACCGAAGTGTTCGATAAAATGCTTCACCGATGAAAAAGAAAGCCTTTCAAATTCT
9320084 AACGTTTGTG
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
70 13 0.22
71 45 0.78
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (70 bp):
CTTTTCGTCAACCGAAGTGTTCGATAAAATGCTTCACCGATGAAAAAGAAAGCCTTTCAAATTCT
TTCAT
Found at i:9322034 original size:15 final size:16
Alignment explanation
Indices: 9321998--9322037 Score: 55
Period size: 15 Copynumber: 2.5 Consensus size: 16
9321988 ATAATAAAAA
9321998 TATAATTTTATCATTTT
1 TATAA-TTTATCATTTT
*
9322015 AATAATTTAT-ATTTT
1 TATAATTTATCATTTT
9322030 TATAATTT
1 TATAATTT
9322038 TTTAAAAAAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 12 0.57
16 5 0.24
17 4 0.19
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (16 bp):
TATAATTTATCATTTT
Found at i:9324812 original size:32 final size:32
Alignment explanation
Indices: 9324776--9324837 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
9324766 AGCTTTTGGT
9324776 TTTTTCATCTTGTCAAAGAGTTGAACAATGGA
1 TTTTTCATCTTGTCAAAGAGTTGAACAATGGA
** *
9324808 TTTTTTGTGTTGTCAAAGAGTTGAACAATG
1 TTTTTCATCTTGTCAAAGAGTTGAACAATG
9324838 AAAATAGATG
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.29, C:0.10, G:0.21, T:0.40
Consensus pattern (32 bp):
TTTTTCATCTTGTCAAAGAGTTGAACAATGGA
Found at i:9328424 original size:44 final size:44
Alignment explanation
Indices: 9328311--9328466 Score: 137
Period size: 44 Copynumber: 3.6 Consensus size: 44
9328301 AAACATTAGT
*
9328311 AAAAAT-GC-ATAAAAATAACATCC-AAATAACTAAAATAACAAC
1 AAAAATAGCAATAAAAATAACA-CCAAAACAACTAAAATAACAAC
* * * *
9328353 CAAAACAGCAGTAAAAATAACAGCAAAACAACTACAAA-AACAAC
1 AAAAATAGCAATAAAAATAACACCAAAACAACTA-AAATAACAAC
* * * *
9328397 AAAAATAGCAATAAAAACAACACCAAAAC-AGTAAAAAAAGCATC
1 AAAAATAGCAATAAAAATAACACCAAAACAACTAAAATAA-CAAC
* *
9328441 -AAAATAGTAA-AAAAATAACATCAAAA
1 AAAAATAGCAATAAAAATAACACCAAAA
9328467 TAGCAAAAAA
Statistics
Matches: 93, Mismatches: 15, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
42 21 0.23
43 17 0.18
44 52 0.56
45 3 0.03
ACGTcount: A:0.66, C:0.17, G:0.05, T:0.12
Consensus pattern (44 bp):
AAAAATAGCAATAAAAATAACACCAAAACAACTAAAATAACAAC
Found at i:9328433 original size:32 final size:33
Alignment explanation
Indices: 9328377--9328438 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 33
9328367 AAATAACAGC
*
9328377 AAAACAACTACAAAAACAACAAAAATAGCAATA
1 AAAACAACTACAAAAACAACAAAAAAAGCAATA
* **
9328410 AAAACAAC-ACCAAAACAGTAAAAAAAGCA
1 AAAACAACTACAAAAACAACAAAAAAAGCA
9328439 TCAAAATAGT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
32 17 0.68
33 8 0.32
ACGTcount: A:0.69, C:0.19, G:0.05, T:0.06
Consensus pattern (33 bp):
AAAACAACTACAAAAACAACAAAAAAAGCAATA
Found at i:9328434 original size:22 final size:22
Alignment explanation
Indices: 9328342--9328512 Score: 100
Period size: 21 Copynumber: 7.8 Consensus size: 22
9328332 CCAAATAACT
* * *
9328342 AAAATAACAACCAAAACAGCAGTA
1 AAAACAAC-ACCAAAACAGTA-AA
* * * *
9328366 AAAATAACAGCAAAACAACTACA
1 AAAACAACACCAAAAC-AGTAAA
* *
9328389 AAAACAACA--AAAATAGCAATA
1 AAAACAACACCAAAACAGTAA-A
9328410 AAAACAACACCAAAACAGT-AA
1 AAAACAACACCAAAACAGTAAA
* * *
9328431 AAAA-AGCATCAAAATAGTAAA
1 AAAACAACACCAAAACAGTAAA
* * * *
9328452 AAAATAACATCAAAATAG-CAA
1 AAAACAACACCAAAACAGTAAA
*
9328473 AAAACAATAACCAAAACAGTAAA
1 AAAACAA-CACCAAAACAGTAAA
*
9328496 AAAACAGCACCAAAACA
1 AAAACAACACCAAAACA
9328513 ACAATATAAT
Statistics
Matches: 116, Mismatches: 23, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
20 13 0.11
21 33 0.28
22 30 0.26
23 30 0.26
24 10 0.09
ACGTcount: A:0.67, C:0.19, G:0.06, T:0.09
Consensus pattern (22 bp):
AAAACAACACCAAAACAGTAAA
Found at i:9328481 original size:24 final size:22
Alignment explanation
Indices: 9328398--9328499 Score: 68
Period size: 22 Copynumber: 4.7 Consensus size: 22
9328388 AAAAACAACA
* * *
9328398 AAAATAGCAATAAAAACAACACC
1 AAAATAG-AAAAAAAATAACATC
* * *
9328421 AAAACAG-TAAAAAA-AGCATC
1 AAAATAGAAAAAAAATAACATC
*
9328441 AAAATAGTAAAAAAATAACATC
1 AAAATAGAAAAAAAATAACATC
9328463 AAAATAGCAAAAAACAATAAC--C
1 AAAATAG-AAAAAA-AATAACATC
* *
9328485 AAAACAGTAAAAAAA
1 AAAATAGAAAAAAAA
9328500 CAGCACCAAA
Statistics
Matches: 64, Mismatches: 11, Indels: 11
0.74 0.13 0.13
Matches are distributed among these distances:
20 12 0.19
21 16 0.25
22 19 0.30
23 11 0.17
24 6 0.09
ACGTcount: A:0.69, C:0.15, G:0.06, T:0.11
Consensus pattern (22 bp):
AAAATAGAAAAAAAATAACATC
Found at i:9336762 original size:2 final size:2
Alignment explanation
Indices: 9336755--9336791 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9336745 CGAATAAGTG
9336755 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA G
9336792 GTGTAGTGTC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.51, T:0.00
Consensus pattern (2 bp):
GA
Found at i:9341846 original size:11 final size:11
Alignment explanation
Indices: 9341823--9341856 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
9341813 TTTTGTATCC
9341823 ATTTTTAACTTT
1 ATTTTTAA-TTT
*
9341835 ATTTTTTATTT
1 ATTTTTAATTT
9341846 ATTTTTAATTT
1 ATTTTTAATTT
9341857 GAAGGGAATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 13 0.65
12 7 0.35
ACGTcount: A:0.24, C:0.03, G:0.00, T:0.74
Consensus pattern (11 bp):
ATTTTTAATTT
Found at i:9341917 original size:24 final size:24
Alignment explanation
Indices: 9341869--9341920 Score: 63
Period size: 22 Copynumber: 2.2 Consensus size: 24
9341859 AGGGAATTAA
*
9341869 TTTAAAAAATTGTTTTAAAACTAT
1 TTTAAAAAATTGTATTAAAACTAT
*
9341893 TTTAAAAAA-T-TATTAAAACAAT
1 TTTAAAAAATTGTATTAAAACTAT
9341915 ATTTAA
1 -TTTAA
9341921 TGTATTGTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 6 0.24
24 9 0.36
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.42
Consensus pattern (24 bp):
TTTAAAAAATTGTATTAAAACTAT
Found at i:9349243 original size:20 final size:20
Alignment explanation
Indices: 9349220--9349256 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
9349210 TCTTTAAAGA
9349220 AAAAAG-ATCATAAATATGG
1 AAAAAGAATCATAAATATGG
*
9349239 AAAAAGAATGATAAATAT
1 AAAAAGAATCATAAATAT
9349257 AAAGGGGGTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.62, C:0.03, G:0.14, T:0.22
Consensus pattern (20 bp):
AAAAAGAATCATAAATATGG
Found at i:9349483 original size:3 final size:3
Alignment explanation
Indices: 9349475--9349501 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
9349465 CTGAGTATTC
9349475 TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
9349502 AACATGGAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9366914 original size:3 final size:3
Alignment explanation
Indices: 9366901--9366952 Score: 97
Period size: 3 Copynumber: 17.7 Consensus size: 3
9366891 AAGATAACTG
9366901 TTC TT- TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
9366948 TTC TT
1 TTC TT
9366953 TATTTTATCT
Statistics
Matches: 48, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
2 2 0.04
3 46 0.96
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9371496 original size:19 final size:20
Alignment explanation
Indices: 9371474--9371515 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
9371464 TACTTTTTTT
*
9371474 AATAATTTT-AATTTTTAAA
1 AATAATTTTAAAATTTTAAA
9371493 AATAATTTTAAAATTTTAAA
1 AATAATTTTAAAATTTTAAA
9371513 AAT
1 AAT
9371516 TTAATTAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (20 bp):
AATAATTTTAAAATTTTAAA
Found at i:9371729 original size:23 final size:25
Alignment explanation
Indices: 9371693--9371738 Score: 69
Period size: 23 Copynumber: 1.9 Consensus size: 25
9371683 TAAATAAATT
*
9371693 AATAATATATAAGTTTAGATTAAAA
1 AATAATATATAAGTTTAAATTAAAA
9371718 AATAA-AT-TAAGTTTAAATTAA
1 AATAATATATAAGTTTAAATTAA
9371739 TATTAGATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 13 0.65
24 2 0.10
25 5 0.25
ACGTcount: A:0.57, C:0.00, G:0.07, T:0.37
Consensus pattern (25 bp):
AATAATATATAAGTTTAAATTAAAA
Found at i:9383349 original size:16 final size:16
Alignment explanation
Indices: 9383318--9383358 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
9383308 ATATCAACAA
*
9383318 AAAAATAATTATTTTTT
1 AAAAAT-ATAATTTTTT
*
9383335 TAAAATATAATTTTTT
1 AAAAATATAATTTTTT
9383351 AAAAATAT
1 AAAAATAT
9383359 TTTAAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
16 16 0.76
17 5 0.24
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (16 bp):
AAAAATATAATTTTTT
Found at i:9384102 original size:24 final size:24
Alignment explanation
Indices: 9384074--9384129 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
9384064 TTTAGGCTTT
*
9384074 TTCTCCTTTGGAACCTTT-GGTTCC
1 TTCTCCTTAGG-ACCTTTGGGTTCC
* *
9384098 TTCTCCTTAGGAGCTTTGGGTTTC
1 TTCTCCTTAGGACCTTTGGGTTCC
9384122 TTCTCCTT
1 TTCTCCTT
9384130 CACACTCAGC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
23 5 0.18
24 23 0.82
ACGTcount: A:0.07, C:0.27, G:0.18, T:0.48
Consensus pattern (24 bp):
TTCTCCTTAGGACCTTTGGGTTCC
Found at i:9384344 original size:11 final size:11
Alignment explanation
Indices: 9384308--9384343 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
9384298 TTATATTTAA
9384308 AAAATAATTTT
1 AAAATAATTTT
*
9384319 AAATTAATTTT
1 AAAATAATTTT
9384330 AAAAT-ATTTT
1 AAAATAATTTT
9384340 AAAA
1 AAAA
9384344 AATATATATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
10 9 0.39
11 14 0.61
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (11 bp):
AAAATAATTTT
Found at i:9384372 original size:17 final size:16
Alignment explanation
Indices: 9384333--9384363 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
9384323 TAATTTTAAA
9384333 ATATTTTAAAAAATAT
1 ATATTTTAAAAAATAT
9384349 ATATTTTAAAAAATA
1 ATATTTTAAAAAATA
9384364 ATTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
ATATTTTAAAAAATAT
Found at i:9385089 original size:16 final size:16
Alignment explanation
Indices: 9385068--9385117 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
9385058 TGATGGGGAT
9385068 ATTATTTTTATAATTA
1 ATTATTTTTATAATTA
9385084 ATTATTTTT-T-A-T-
1 ATTATTTTTATAATTA
9385096 ATTATATTTTAGTAATTA
1 ATTAT-TTTTA-TAATTA
9385114 ATTA
1 ATTA
9385118 GTTAGGTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 10
0.74 0.00 0.26
Matches are distributed among these distances:
12 5 0.18
13 5 0.18
14 1 0.04
15 2 0.07
16 10 0.36
17 1 0.04
18 4 0.14
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (16 bp):
ATTATTTTTATAATTA
Found at i:9401599 original size:3 final size:3
Alignment explanation
Indices: 9401591--9401618 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
9401581 TGATTAAGAA
9401591 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT A
9401619 CTTTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:9418588 original size:2 final size:2
Alignment explanation
Indices: 9418583--9418610 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
9418573 GAGAACATTC
9418583 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
9418611 TGGTGCATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9420578 original size:29 final size:29
Alignment explanation
Indices: 9420546--9420604 Score: 109
Period size: 29 Copynumber: 2.0 Consensus size: 29
9420536 AACTTCAAAT
9420546 ACTCAAATGACACTAATTACCAGAGTAAA
1 ACTCAAATGACACTAATTACCAGAGTAAA
*
9420575 ACTCAAATGACACTAATTACCAGGGTAAA
1 ACTCAAATGACACTAATTACCAGAGTAAA
9420604 A
1 A
9420605 AAGAATTGTA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.47, C:0.20, G:0.12, T:0.20
Consensus pattern (29 bp):
ACTCAAATGACACTAATTACCAGAGTAAA
Found at i:9424422 original size:22 final size:22
Alignment explanation
Indices: 9424364--9424422 Score: 55
Period size: 23 Copynumber: 2.6 Consensus size: 22
9424354 TTAACTTTCT
*
9424364 AAATATTTATAAAAAAAATCCAA
1 AAATATATAT-AAAAAAATCCAA
* * * *
9424387 AATTTAAATTTAAAAAAATCTAA
1 AA-ATATATATAAAAAAATCCAA
9424410 AAATATATATAAA
1 AAATATATATAAA
9424423 GAAAGTTAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 3
0.71 0.21 0.08
Matches are distributed among these distances:
22 8 0.30
23 15 0.56
24 4 0.15
ACGTcount: A:0.64, C:0.05, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATATATAAAAAAATCCAA
Found at i:9427011 original size:15 final size:17
Alignment explanation
Indices: 9426980--9427012 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
9426970 TTTAGAGCAC
9426980 ATATTATGTATTCTAAA
1 ATATTATGTATTCTAAA
9426997 ATATTAT-TA-TCTAAA
1 ATATTATGTATTCTAAA
9427012 A
1 A
9427013 AATAACATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 2 0.12
17 7 0.44
ACGTcount: A:0.45, C:0.06, G:0.03, T:0.45
Consensus pattern (17 bp):
ATATTATGTATTCTAAA
Found at i:9430650 original size:22 final size:23
Alignment explanation
Indices: 9430625--9430667 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
9430615 AATAAAATAG
9430625 AATAAATACT-AAAAGATTTATA
1 AATAAATACTGAAAAGATTTATA
* *
9430647 AATACATACTGAAAATATTTA
1 AATAAATACTGAAAAGATTTA
9430668 AATATGATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 9 0.50
23 9 0.50
ACGTcount: A:0.56, C:0.07, G:0.05, T:0.33
Consensus pattern (23 bp):
AATAAATACTGAAAAGATTTATA
Found at i:9431793 original size:2 final size:2
Alignment explanation
Indices: 9431786--9431825 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
9431776 CAAAGCACTG
9431786 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
9431826 GCCCATTCTT
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:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:9444326 original size:24 final size:23
Alignment explanation
Indices: 9444278--9444332 Score: 60
Period size: 25 Copynumber: 2.3 Consensus size: 23
9444268 CACATCGCAA
*
9444278 ATAT-AAATCTATAAAACATGTT
1 ATATAAAATCTATAAAAAATGTT
9444300 ATATAAAATCATATAAACAAATG-T
1 ATATAAAATC-TATAAA-AAATGTT
9444324 ATAATAAAA
1 AT-ATAAAA
9444333 CTTTCAAATC
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
22 4 0.14
23 5 0.18
24 9 0.32
25 10 0.36
ACGTcount: A:0.58, C:0.07, G:0.04, T:0.31
Consensus pattern (23 bp):
ATATAAAATCTATAAAAAATGTT
Found at i:9444376 original size:34 final size:33
Alignment explanation
Indices: 9444338--9444415 Score: 99
Period size: 31 Copynumber: 2.4 Consensus size: 33
9444328 TAAAACTTTC
9444338 AAATCTATATATATAAGACTCATAGAGAAATAAT
1 AAATCTATATATATAA-ACTCATAGAGAAATAAT
* * *
9444372 AAATCTAT-T-TGTCAACTCATAGAGTAATAAT
1 AAATCTATATATATAAACTCATAGAGAAATAAT
9444403 AAATCTATA-ATAT
1 AAATCTATATATAT
9444416 TAGGAAGAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
31 24 0.63
32 5 0.13
33 1 0.03
34 8 0.21
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (33 bp):
AAATCTATATATATAAACTCATAGAGAAATAAT
Found at i:9445001 original size:29 final size:30
Alignment explanation
Indices: 9444969--9445076 Score: 94
Period size: 30 Copynumber: 3.6 Consensus size: 30
9444959 TAAAGATTTG
*
9444969 AAATTAAATTATAATTTTTATGA-TAATAA
1 AAATTAAATTATAATTTTTATAATTAATAA
* * **
9444998 AAATATAATTTATTATTTTTATAATTTTTAA
1 AAAT-TAAATTATAATTTTTATAATTAATAA
* * **
9445029 AAGTTAAATTA-AATTTTTATATTTTTTAA
1 AAATTAAATTATAATTTTTATAATTAATAA
*
9445058 AAGATTAAAGTATAATTTT
1 AA-ATTAAATTATAATTTT
9445077 AAAATTTTAT
Statistics
Matches: 64, Mismatches: 11, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
29 22 0.34
30 29 0.45
31 13 0.20
ACGTcount: A:0.45, C:0.00, G:0.04, T:0.51
Consensus pattern (30 bp):
AAATTAAATTATAATTTTTATAATTAATAA
Found at i:9445077 original size:30 final size:29
Alignment explanation
Indices: 9445012--9445084 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
9445002 ATAATTTATT
*
9445012 ATTTTTATAATTTTTAAAAGTTAAATTAA
1 ATTTTTATAATTTTTAAAAGTTAAAGTAA
*
9445041 ATTTTTATATTTTTTAAAAGATTAAAGTATA
1 ATTTTTATAATTTTTAAAAG-TTAAAGTA-A
*
9445072 A-TTTTAAAATTTT
1 ATTTTTATAATTTT
9445085 ATGGAATGGA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
29 19 0.50
30 17 0.45
31 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.53
Consensus pattern (29 bp):
ATTTTTATAATTTTTAAAAGTTAAAGTAA
Found at i:9451898 original size:25 final size:24
Alignment explanation
Indices: 9451868--9451918 Score: 75
Period size: 25 Copynumber: 2.1 Consensus size: 24
9451858 TGAAAAATAT
*
9451868 ATTAAAATAAAATAATGTCTTTAAA
1 ATTAAAACAAAATAATGT-TTTAAA
*
9451893 ATTAAAACAAAATAATGTTTTCAA
1 ATTAAAACAAAATAATGTTTTAAA
9451917 AT
1 AT
9451919 CAAGTGGAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
24 7 0.29
25 17 0.71
ACGTcount: A:0.55, C:0.06, G:0.04, T:0.35
Consensus pattern (24 bp):
ATTAAAACAAAATAATGTTTTAAA
Found at i:9453039 original size:20 final size:18
Alignment explanation
Indices: 9453000--9453035 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
9452990 CCACCAAAAA
9453000 TAAAATATATATTTAAAT
1 TAAAATATATATTTAAAT
*
9453018 TAAACTATATATTTAAAT
1 TAAAATATATATTTAAAT
9453036 ATTATATAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATATATATTTAAAT
Found at i:9453252 original size:21 final size:20
Alignment explanation
Indices: 9453218--9453263 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 20
9453208 GAAACCACTC
* **
9453218 AAAAAAATTTAATTTTTTAA
1 AAAAAAATTAAATTGCTTAA
9453238 AAAATAAATTAAATTGCTTAA
1 AAAA-AAATTAAATTGCTTAA
9453259 AAAAA
1 AAAAA
9453264 TTGAAATATG
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.35
Consensus pattern (20 bp):
AAAAAAATTAAATTGCTTAA
Found at i:9453407 original size:105 final size:100
Alignment explanation
Indices: 9453183--9453466 Score: 251
Period size: 105 Copynumber: 2.9 Consensus size: 100
9453173 AAAATTCTTA
* * * * * *
9453183 GGGAAGTGGTGACGCCATTTCATATGAAACCACTC-AAAAAAATTTAATTTTTTAAAAAAT--AA
1 GGGAAGTCGTGGCGCCATTTAATATGACACCAC-CAAAAAAAAATTAATTTTTAAAAAAATAAAA
* *** * ***
9453245 ATTAAAT--TGCTTAAAAAAA-T-TGAAATATGCAG
65 AATAAATCATGGAAAAAAAAAGTCTGATATATTTTG
* *
9453277 GGGAAGTCGTGGCGCCATTTGATATGACACTACCAAAAAAAGAAATTTAAATTTTTAAAAATAA-
1 GGGAAGTCGTGGCGCCATTTAATATGACACCACC-AAAAAA-AAA-TT-AATTTTTAAAAA-AAT
9453341 AAAATAATAAATCATGGAAAAAAAAAGTCTGATATATTTTG
61 AAAA-AATAAATCATGGAAAAAAAAAGTCTGATATATTTTG
* * *
9453382 GGGAAGTGGTGGCGTCATTTAATATGACACCACCCAAAAAAAATTAATTTTTAAAAAAATAAAAA
1 GGGAAGTCGTGGCGCCATTTAATATGACACCACCAAAAAAAAATTAATTTTTAAAAAAATAAAAA
* **
9453447 ATAAATTATTTAAAAAAAAA
66 ATAAATCATGGAAAAAAAAA
9453467 CTAAAATATG
Statistics
Matches: 153, Mismatches: 23, Indels: 22
0.77 0.12 0.11
Matches are distributed among these distances:
93 1 0.01
94 28 0.18
95 5 0.03
96 2 0.01
97 2 0.01
98 11 0.07
99 2 0.01
100 22 0.14
101 22 0.14
102 2 0.01
103 12 0.08
104 6 0.04
105 38 0.25
ACGTcount: A:0.49, C:0.10, G:0.14, T:0.28
Consensus pattern (100 bp):
GGGAAGTCGTGGCGCCATTTAATATGACACCACCAAAAAAAAATTAATTTTTAAAAAAATAAAAA
ATAAATCATGGAAAAAAAAAGTCTGATATATTTTG
Found at i:9453453 original size:23 final size:24
Alignment explanation
Indices: 9453419--9453464 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 24
9453409 CACCACCCAA
*
9453419 AAAAAATTAATT-TTTAAAAAAAT
1 AAAAAATAAATTATTTAAAAAAAT
9453442 AAAAAATAAATTATTTAAAAAAA
1 AAAAAATAAATTATTTAAAAAAA
9453465 AACTAAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 11 0.52
24 10 0.48
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (24 bp):
AAAAAATAAATTATTTAAAAAAAT
Found at i:9453457 original size:26 final size:27
Alignment explanation
Indices: 9453417--9453472 Score: 71
Period size: 26 Copynumber: 2.1 Consensus size: 27
9453407 GACACCACCC
**
9453417 AAAAAAAATTAATTTTTAAAAAAA-TA
1 AAAAAAAATTAATTTAAAAAAAAACTA
9453443 AAAAATAAATT-ATTTAAAAAAAAACTA
1 AAAAA-AAATTAATTTAAAAAAAAACTA
9453470 AAA
1 AAA
9453473 TATGTAGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 16 0.62
27 10 0.38
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (27 bp):
AAAAAAAATTAATTTAAAAAAAAACTA
Found at i:9454092 original size:21 final size:21
Alignment explanation
Indices: 9454068--9454110 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
9454058 TGCTTCCTTA
*
9454068 GCTTCTCTCGCTGCTGCCTCC
1 GCTTCCCTCGCTGCTGCCTCC
*
9454089 GCTTCCCTCGTTGCTGCCTCC
1 GCTTCCCTCGCTGCTGCCTCC
9454110 G
1 G
9454111 TTTTAAGTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.00, C:0.47, G:0.21, T:0.33
Consensus pattern (21 bp):
GCTTCCCTCGCTGCTGCCTCC
Found at i:9455718 original size:23 final size:23
Alignment explanation
Indices: 9455685--9455742 Score: 89
Period size: 23 Copynumber: 2.5 Consensus size: 23
9455675 TATTATTTGT
* *
9455685 TATTAATATTAAGTAATTACTAA
1 TATTTATATTAAGTAATTAATAA
*
9455708 TCTTTATATTAAGTAATTAATAA
1 TATTTATATTAAGTAATTAATAA
9455731 TATTTATATTAA
1 TATTTATATTAA
9455743 TATTACATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.48
Consensus pattern (23 bp):
TATTTATATTAAGTAATTAATAA
Found at i:9455760 original size:29 final size:29
Alignment explanation
Indices: 9455728--9455791 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
9455718 AAGTAATTAA
9455728 TAATATTT-ATATTAATATTACATTTATAT
1 TAATATTTAATA-TAATATTACATTTATAT
* * * *
9455757 TAATAATTAATATACTTTTATATTTATAT
1 TAATATTTAATATAATATTACATTTATAT
9455786 TAATAT
1 TAATAT
9455792 ATTTCGATTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 26 0.90
30 3 0.10
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (29 bp):
TAATATTTAATATAATATTACATTTATAT
Found at i:9455777 original size:40 final size:40
Alignment explanation
Indices: 9455710--9455787 Score: 115
Period size: 40 Copynumber: 1.9 Consensus size: 40
9455700 ATTACTAATC
9455710 TTTATATTAAGTAATTAATAATATTTATATTAATATTACA
1 TTTATATTAAGTAATTAATAATATTTATATTAATATTACA
*
9455750 TTTATATTAA-TAATTAAT-ATACTTTTATATTTATATTA
1 TTTATATTAAGTAATTAATAATA--TTTATATTAATATTA
9455788 ATATATTTCG
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
38 3 0.09
39 8 0.23
40 24 0.69
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (40 bp):
TTTATATTAAGTAATTAATAATATTTATATTAATATTACA
Found at i:9455832 original size:22 final size:22
Alignment explanation
Indices: 9455814--9455885 Score: 85
Period size: 22 Copynumber: 3.3 Consensus size: 22
9455804 AAATTTATAT
9455814 TTCTATATTATTTATTTTATTA
1 TTCTATATTATTTATTTTATTA
** *
9455836 TTCTATATT-TAGAAATTTATCT-
1 TTCTATATTAT-TTATTTTAT-TA
9455858 TTCTATATTATTTATTTTATTA
1 TTCTATATTATTTATTTTATTA
9455880 TTCTAT
1 TTCTAT
9455886 CTATTATCAT
Statistics
Matches: 40, Mismatches: 6, Indels: 8
0.74 0.11 0.15
Matches are distributed among these distances:
21 2 0.05
22 36 0.90
23 2 0.05
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.64
Consensus pattern (22 bp):
TTCTATATTATTTATTTTATTA
Found at i:9455848 original size:44 final size:44
Alignment explanation
Indices: 9455798--9455885 Score: 167
Period size: 44 Copynumber: 2.0 Consensus size: 44
9455788 ATATATTTCG
9455798 ATTTAGAAATTTATATTTCTATATTATTTATTTTATTATTCTAT
1 ATTTAGAAATTTATATTTCTATATTATTTATTTTATTATTCTAT
*
9455842 ATTTAGAAATTTATCTTTCTATATTATTTATTTTATTATTCTAT
1 ATTTAGAAATTTATATTTCTATATTATTTATTTTATTATTCTAT
9455886 CTATTATCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
44 43 1.00
ACGTcount: A:0.31, C:0.06, G:0.02, T:0.61
Consensus pattern (44 bp):
ATTTAGAAATTTATATTTCTATATTATTTATTTTATTATTCTAT
Found at i:9455914 original size:44 final size:44
Alignment explanation
Indices: 9455815--9455915 Score: 116
Period size: 44 Copynumber: 2.3 Consensus size: 44
9455805 AATTTATATT
* * *
9455815 TCTATATTATTTATTTTATTATTCTATATTTAGAAATTTATCTT
1 TCTATATTATTTATTTTATTATTCTATATTTACAAATATATCTA
* *
9455859 TCTATATTATTTATTTTATTATTCTATCTATTATCATATATAT-TA
1 TCTATATTATTTATTTTATTATTCTATAT-TTA-CAAATATATCTA
*
9455904 T-TATTTTATTTA
1 TCTATATTATTTA
9455916 AATATTATTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
44 38 0.78
45 5 0.10
46 6 0.12
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.62
Consensus pattern (44 bp):
TCTATATTATTTATTTTATTATTCTATATTTACAAATATATCTA
Found at i:9455951 original size:29 final size:28
Alignment explanation
Indices: 9455900--9455955 Score: 85
Period size: 29 Copynumber: 2.0 Consensus size: 28
9455890 TATCATATAT
9455900 ATTATTATTTTATTTAAATATTATTTAA
1 ATTATTATTTTATTTAAATATTATTTAA
**
9455928 ATTATTATTATTATTTAGTTATTATTTA
1 ATTATTATT-TTATTTAAATATTATTTA
9455956 TATTTAGTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (28 bp):
ATTATTATTTTATTTAAATATTATTTAA
Found at i:9455956 original size:18 final size:17
Alignment explanation
Indices: 9455918--9455968 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
9455908 TTTATTTAAA
*
9455918 TATTATTTAAATTATTAT
1 TATTATTT-AGTTATTAT
9455936 TATTATTTAGTTATTAT
1 TATTATTTAGTTATTAT
9455953 T-TATATTTAGTGTATT
1 TAT-TATTTAGT-TATT
9455969 TAGAATTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
16 1 0.03
17 17 0.57
18 12 0.40
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (17 bp):
TATTATTTAGTTATTAT
Found at i:9456308 original size:170 final size:170
Alignment explanation
Indices: 9456021--9456693 Score: 1118
Period size: 170 Copynumber: 4.0 Consensus size: 170
9456011 CGACAAATAC
* * * *
9456021 ACATCCACGGGAATTAGCTTATCCACCCCCCGAACAATACTATAAGAATCAGTACTGAATATCCC
1 ACATCCACGGGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
**
9456086 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTTAGGCATTTGTTCATATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
*
9456151 TCTCACTAAAGAGGGCGCCATTTTCATTGTTGCTGTATAG
131 TCTCACTAAAGAGGGCGCCATTTTCATTGTTACTGTATAG
* *
9456191 ACATCCACGGGAATTAGCTTATCGACCCTCCGAATAGTACTATAAGAATCAGTATTGAACATCCC
1 ACATCCACGGGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
*
9456256 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTTGGGCATTTGTTCATATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
*
9456321 TCTCACTAAAGAGGGCACCATTTTCATTGTTACTGTATAG
131 TCTCACTAAAGAGGGCGCCATTTTCATTGTTACTGTATAG
* *
9456361 ACATTCACGGGAATTAGCTTATCGACCCCCCGAATAGTACTATAAGAATCAGTATTGAACATCCC
1 ACATCCACGGGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
* *
9456426 TCTTGTAATTATACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
* *
9456491 TCTCACTAAAGAGGGCGCCATTTTCATTATTACTGTATAA
131 TCTCACTAAAGAGGGCGCCATTTTCATTGTTACTGTATAG
* * * *
9456531 ACATCCACGGGAATTAGCTTATTGA-CCCCCGAACAGTACTATAAGAATCATTGTTGAACATCCT
1 ACATCCACGGGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
*
9456595 TCCTGTAATTGTACACGTGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTC--ATATAA
66 TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
*
9456658 TCTCACTAAAGAGGGCGCTATTTTCATTGTTACTGT
131 TCTCACTAAAGAGGGCGCCATTTTCATTGTTACTGT
9456694 TCCAACTGTT
Statistics
Matches: 475, Mismatches: 28, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
167 40 0.08
169 89 0.19
170 346 0.73
ACGTcount: A:0.30, C:0.22, G:0.16, T:0.31
Consensus pattern (170 bp):
ACATCCACGGGAATTAGCTTATCGACCCCCCGAACAGTACTATAAGAATCAGTATTGAACATCCC
TCCTGTAATTGTACACGCGCCCATAGCAATAACATATTTAGGTTCGGGCATTTGTTCATATATAA
TCTCACTAAAGAGGGCGCCATTTTCATTGTTACTGTATAG
Found at i:9457355 original size:41 final size:40
Alignment explanation
Indices: 9457293--9457481 Score: 209
Period size: 41 Copynumber: 4.7 Consensus size: 40
9457283 GCGCTAGCAA
* *
9457293 CGTTTATGATAAAGCGTCGCTAATAACCTGACCTTTAGCGG
1 CGTTTATGAGAAAGCGCCGCTAAT-ACCTGACCTTTAGCGG
* *
9457334 TGTTTATGAGAAAGCGCCGCTAATGACTTGACCTTTAGCGG
1 CGTTTATGAGAAAGCGCCGCTAAT-ACCTGACCTTTAGCGG
* * *
9457375 CGTTTATGGGAAAGCGCCACTAATGCCTGACCTTTAGCGG
1 CGTTTATGAGAAAGCGCCGCTAATACCTGACCTTTAGCGG
* * *
9457415 CGCTTATGGGAAAGAGCCGCTAATACCTTGACCTTTAGCGG
1 CGTTTATGAGAAAGCGCCGCTAATACC-TGACCTTTAGCGG
* * * *
9457456 TGCTTAT-AGGAAAGCACCGCAAATAC
1 CGTTTATGA-GAAAGCGCCGCTAATAC
9457482 TGTAACCTTT
Statistics
Matches: 127, Mismatches: 19, Indels: 4
0.85 0.13 0.03
Matches are distributed among these distances:
40 37 0.29
41 90 0.71
ACGTcount: A:0.26, C:0.23, G:0.25, T:0.26
Consensus pattern (40 bp):
CGTTTATGAGAAAGCGCCGCTAATACCTGACCTTTAGCGG
Found at i:9457434 original size:81 final size:81
Alignment explanation
Indices: 9457319--9457470 Score: 225
Period size: 81 Copynumber: 1.9 Consensus size: 81
9457309 TCGCTAATAA
* * * * *
9457319 CCTGACCTTTAGCGGTGTTTATGAGAAAGCGCCGCTAATGA-CTTGACCTTTAGCGGCGTTTATG
1 CCTGACCTTTAGCGGCGCTTATGAGAAAGAGCCGCTAAT-ACCTTGACCTTTAGCGGCGCTTATA
9457383 GGAAAGCGCCACTAATG
65 GGAAAGCGCCACTAATG
* *
9457400 CCTGACCTTTAGCGGCGCTTATGGGAAAGAGCCGCTAATACCTTGACCTTTAGCGGTGCTTATAG
1 CCTGACCTTTAGCGGCGCTTATGAGAAAGAGCCGCTAATACCTTGACCTTTAGCGGCGCTTATAG
9457465 GAAAGC
66 GAAAGC
9457471 ACCGCAAATA
Statistics
Matches: 63, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
80 1 0.02
81 62 0.98
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.26
Consensus pattern (81 bp):
CCTGACCTTTAGCGGCGCTTATGAGAAAGAGCCGCTAATACCTTGACCTTTAGCGGCGCTTATAG
GAAAGCGCCACTAATG
Found at i:9457490 original size:41 final size:41
Alignment explanation
Indices: 9457310--9457501 Score: 194
Period size: 41 Copynumber: 4.7 Consensus size: 41
9457300 GATAAAGCGT
* * * * *
9457310 CGCTAATAACCTGACCTTTAGCGGTGTTTATGAGAAAGCGC
1 CGCTAATGACTTGACCTTTAGCGGTGCTTATGGGAAAGCAC
* * *
9457351 CGCTAATGACTTGACCTTTAGCGGCGTTTATGGGAAAGCGC
1 CGCTAATGACTTGACCTTTAGCGGTGCTTATGGGAAAGCAC
* * *
9457392 CACTAATG-CCTGACCTTTAGCGGCGCTTATGGGAAAG-AGC
1 CGCTAATGACTTGACCTTTAGCGGTGCTTATGGGAAAGCA-C
*
9457432 CGCTAAT-ACCTTGACCTTTAGCGGTGCTTATAGGAAAGCAC
1 CGCTAATGA-CTTGACCTTTAGCGGTGCTTATGGGAAAGCAC
* * *
9457473 CGCAAAT-ACTGTAACCTTTATCGGTGCTT
1 CGCTAATGACT-TGACCTTTAGCGGTGCTT
9457502 TGACATAAAC
Statistics
Matches: 131, Mismatches: 15, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
40 36 0.27
41 94 0.72
42 1 0.01
ACGTcount: A:0.25, C:0.23, G:0.24, T:0.27
Consensus pattern (41 bp):
CGCTAATGACTTGACCTTTAGCGGTGCTTATGGGAAAGCAC
Found at i:9472268 original size:2 final size:2
Alignment explanation
Indices: 9472261--9472285 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
9472251 TTACAACACT
9472261 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 T
9472286 CATAGAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9476367 original size:2 final size:2
Alignment explanation
Indices: 9476360--9476385 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
9476350 TTAACTTTTG
9476360 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
9476386 TATTTTCAAT
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:9476856 original size:82 final size:81
Alignment explanation
Indices: 9476720--9476871 Score: 200
Period size: 82 Copynumber: 1.9 Consensus size: 81
9476710 GTTTTCCAAC
* ** * *
9476720 TTTGCCTAAAACAAAATTTAGTCTGCTATAGTTGTTGGTTGTGTTGAATCATACTACAG-GTGGG
1 TTTGCCTAAAACAAAATTTAGTCTGCTATAGATGTTGGTTGTGTAAAACCATACTA-AGAGTGGA
9476784 TTTGAATAGACAGTGTG
65 TTTGAATAGACAGTGTG
* *
9476801 TTTGCCTTAAACAAAAATTTAGTCT-ATCATAGATGTTGGTTGTGTAAAACCATACTAAGAGTGG
1 TTTGCCTAAAAC-AAAATTTAGTCTGCT-ATAGATGTTGGTTGTGTAAAACCATACTAAGAGTGG
9476865 ATTTGAA
64 ATTTGAA
9476872 AGGACGGAAC
Statistics
Matches: 61, Mismatches: 7, Indels: 5
0.84 0.10 0.07
Matches are distributed among these distances:
81 14 0.23
82 47 0.77
ACGTcount: A:0.31, C:0.11, G:0.22, T:0.36
Consensus pattern (81 bp):
TTTGCCTAAAACAAAATTTAGTCTGCTATAGATGTTGGTTGTGTAAAACCATACTAAGAGTGGAT
TTGAATAGACAGTGTG
Found at i:9489422 original size:2 final size:2
Alignment explanation
Indices: 9489417--9489450 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
9489407 AAACATAATT
9489417 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
9489451 ACCAAATTTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:9491384 original size:3 final size:3
Alignment explanation
Indices: 9491376--9491404 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
9491366 CGATCACCTT
9491376 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
9491405 TGCTGCTGCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:9499001 original size:17 final size:17
Alignment explanation
Indices: 9498981--9499059 Score: 56
Period size: 17 Copynumber: 4.6 Consensus size: 17
9498971 ATAGAACTCA
9498981 ATTTTAAATTTTAAATT
1 ATTTTAAATTTTAAATT
* *
9498998 A-TTT-AAGTTTAAGTTT
1 ATTTTAAATTTTAA-ATT
9499014 ATTTTAAA-TTTAAACTT
1 ATTTTAAATTTTAAA-TT
* * * *
9499031 ATTTTTGAGTTTGAATTT
1 A-TTTTAAATTTTAAATT
9499049 ATTTTAAATTT
1 ATTTTAAATTT
9499060 ATTAAATTTA
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
15 7 0.15
16 6 0.13
17 20 0.43
18 10 0.21
19 4 0.09
ACGTcount: A:0.34, C:0.01, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTTTAAATTTTAAATT
Found at i:9499050 original size:35 final size:32
Alignment explanation
Indices: 9498981--9499060 Score: 99
Period size: 35 Copynumber: 2.4 Consensus size: 32
9498971 ATAGAACTCA
9498981 ATTTTAAATTTTAAATTATTTAAGTTTAAGTTT
1 ATTTTAAA-TTTAAATTATTTAAGTTTAAGTTT
*
9499014 ATTTTAAATTTAAACTTATTTTTGAGTTTGAA-TTT
1 ATTTTAAATTTAAA-TTA--TTTAAGTTT-AAGTTT
9499049 ATTTTAAATTTA
1 ATTTTAAATTTA
9499061 TTAAATTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
32 6 0.14
33 11 0.26
35 23 0.55
36 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.06, T:0.57
Consensus pattern (32 bp):
ATTTTAAATTTAAATTATTTAAGTTTAAGTTT
Found at i:9499077 original size:12 final size:12
Alignment explanation
Indices: 9499060--9499085 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
9499050 TTTTAAATTT
9499060 ATTAAATTTAAA
1 ATTAAATTTAAA
9499072 ATTAAATTTAAA
1 ATTAAATTTAAA
9499084 AT
1 AT
9499086 GTCCAAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTAAATTTAAA
Found at i:9499140 original size:14 final size:15
Alignment explanation
Indices: 9499120--9499157 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
9499110 AATTACAATT
9499120 CAAACCCAATTTATA
1 CAAACCCAATTTATA
*
9499135 -AAACCC-ATTTTTA
1 CAAACCCAATTTATA
9499148 CAAACCCAAT
1 CAAACCCAAT
9499158 ACCCAAGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 4
0.80 0.04 0.16
Matches are distributed among these distances:
13 6 0.30
14 12 0.60
15 2 0.10
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.26
Consensus pattern (15 bp):
CAAACCCAATTTATA
Found at i:9501317 original size:6 final size:6
Alignment explanation
Indices: 9501283--9501356 Score: 71
Period size: 6 Copynumber: 12.5 Consensus size: 6
9501273 TAATAGGGAT
* * *
9501283 TTTCAA TTTACAA -TTC-A TATCAC TTTCAA TTTCAA TTTCAA TTTCAC
1 TTTCAA TTT-CAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA TTTCAA
* * *
9501330 TTTCAC TTTCAC TTTCAC TTTCAA TTT
1 TTTCAA TTTCAA TTTCAA TTTCAA TTT
9501357 TGATCACAAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
4 1 0.02
5 3 0.05
6 52 0.88
7 3 0.05
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (6 bp):
TTTCAA
Found at i:9503391 original size:57 final size:57
Alignment explanation
Indices: 9503307--9503577 Score: 380
Period size: 57 Copynumber: 4.7 Consensus size: 57
9503297 TAAAAATCAT
* * *
9503307 ATTTTGACCCTGAACATCCAAAAATTACCATTTTGCCCCCGAACATCTAAAAATTACC
1 ATTTTGACCCCGAACATCC-AAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
* *
9503365 ATTTTGACCCCGAACATCTAAAATTACCATTTTGCTCTCGAACATCCAAAAATTACC
1 ATTTTGACCCCGAACATCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
** * **
9503422 ATTTTGACCAAGAACATCCAAAATTACCATTTTACCCTCGAACATTTAAAAATTACC
1 ATTTTGACCCCGAACATCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
*
9503479 ATTTTGACCCCGAACTTTTCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
1 ATTTTGACCCCGAAC--ATCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
* * *
9503538 ATTTTGCCCCCGAGCATCTAAAAATTACCATTTTGCCCTC
1 ATTTTGACCCCGAACATC-CAAAATTACCATTTTGCCCTC
9503578 AAATTTCCAA
Statistics
Matches: 188, Mismatches: 22, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
57 100 0.53
58 37 0.20
59 51 0.27
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (57 bp):
ATTTTGACCCCGAACATCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
Found at i:9503589 original size:29 final size:29
Alignment explanation
Indices: 9503307--9503577 Score: 329
Period size: 29 Copynumber: 9.4 Consensus size: 29
9503297 TAAAAATCAT
9503307 ATTTTGACCCT-GAACATCCAAAAATTACC
1 ATTTTG-CCCTCGAACATCCAAAAATTACC
* *
9503336 ATTTTGCCCCCGAACATCTAAAAATTACC
1 ATTTTGCCCTCGAACATCCAAAAATTACC
*
9503365 ATTTTGACCC-CGAACAT-CTAAAATTACC
1 ATTTTG-CCCTCGAACATCCAAAAATTACC
*
9503393 ATTTTGCTCTCGAACATCCAAAAATTACC
1 ATTTTGCCCTCGAACATCCAAAAATTACC
* **
9503422 ATTTTGACCAAGAACATCC-AAAATTACC
1 ATTTTGCCCTCGAACATCCAAAAATTACC
* **
9503450 ATTTTACCCTCGAACATTTAAAAATTACC
1 ATTTTGCCCTCGAACATCCAAAAATTACC
*
9503479 ATTTTGACCC-CGAACTTTTCC-AAAATTACC
1 ATTTTG-CCCTCGAAC--ATCCAAAAATTACC
9503509 ATTTTGCCCTCGAACATCCAAAAATTACC
1 ATTTTGCCCTCGAACATCCAAAAATTACC
* * *
9503538 ATTTTGCCCCCGAGCATCTAAAAATTACC
1 ATTTTGCCCTCGAACATCCAAAAATTACC
9503567 ATTTTGCCCTC
1 ATTTTGCCCTC
9503578 AAATTTCCAA
Statistics
Matches: 207, Mismatches: 25, Indels: 20
0.82 0.10 0.08
Matches are distributed among these distances:
27 2 0.01
28 50 0.24
29 128 0.62
30 26 0.13
31 1 0.00
ACGTcount: A:0.34, C:0.29, G:0.07, T:0.30
Consensus pattern (29 bp):
ATTTTGCCCTCGAACATCCAAAAATTACC
Found at i:9503614 original size:116 final size:116
Alignment explanation
Indices: 9503307--9503619 Score: 352
Period size: 116 Copynumber: 2.7 Consensus size: 116
9503297 TAAAAATCAT
** * * * *
9503307 ATTTTGACCCTGAACATCCAAAAATTACCATTTTGCCCCCGAACATCTAAAAATTACCATTTTGA
1 ATTTTGACCAAGAACAT-CAAAAATTACCATTTTACCCTCGAACATTTAAAAATCACCATTTTGA
* *
9503372 CCCCGAACA---TCTAAAATTACCATTTTGCTCTCGAACATCCAAAAATTACC
65 CCCCGAA-ATTTTCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
* *
9503422 ATTTTGACCAAGAACATCCAAAATTACCATTTTACCCTCGAACATTTAAAAATTACCATTTTGAC
1 ATTTTGACCAAGAACATCAAAAATTACCATTTTACCCTCGAACATTTAAAAATCACCATTTTGAC
*
9503487 CCCGAACTTTTCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
66 CCCGAAATTTTCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
* ** * * * *
9503538 ATTTTGCCCCCGAGCATCTAAAAATTACCATTTTGCCCTC-AA-ATTTCCAAAAGTCA-CTTTTT
1 ATTTTGACCAAGAACATC-AAAAATTACCATTTTACCCTCGAACATTT--AAAAATCACCATTTT
*
9503600 CGACCTC-AAATTTTCCAAAA
63 -GACCCCGAAATTTTCCAAAA
9503620 GTTCAATTTT
Statistics
Matches: 171, Mismatches: 20, Indels: 13
0.84 0.10 0.06
Matches are distributed among these distances:
114 50 0.29
115 19 0.11
116 72 0.42
117 30 0.18
ACGTcount: A:0.35, C:0.28, G:0.07, T:0.30
Consensus pattern (116 bp):
ATTTTGACCAAGAACATCAAAAATTACCATTTTACCCTCGAACATTTAAAAATCACCATTTTGAC
CCCGAAATTTTCCAAAATTACCATTTTGCCCTCGAACATCCAAAAATTACC
Found at i:9503665 original size:30 final size:30
Alignment explanation
Indices: 9503606--9503671 Score: 80
Period size: 29 Copynumber: 2.2 Consensus size: 30
9503596 TTTTCGACCT
9503606 CAAATTTTCCAAAAGTTCAATTTTAAT-CC
1 CAAATTTTCCAAAAGTTCAATTTTAATCCC
* ** *
9503635 CAAATTTTCCAAAATTTTTTATTTTGATCCC
1 CAAATTTTCCAAAA-GTTCAATTTTAATCCC
9503666 CAAATT
1 CAAATT
9503672 CCTCGAAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
29 14 0.45
30 9 0.29
31 8 0.26
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (30 bp):
CAAATTTTCCAAAAGTTCAATTTTAATCCC
Found at i:9505168 original size:29 final size:30
Alignment explanation
Indices: 9505126--9505184 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 30
9505116 GAATCAGATC
*
9505126 AAATCGAAATTTCATGTATAAAATTGCACA
1 AAATCGAAAGTTCATGTATAAAATTGCACA
*
9505156 AAATC-AAAGTTCATGTATATAATTGCACA
1 AAATCGAAAGTTCATGTATAAAATTGCACA
9505185 TTAAACCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.46, C:0.14, G:0.10, T:0.31
Consensus pattern (30 bp):
AAATCGAAAGTTCATGTATAAAATTGCACA
Found at i:9505202 original size:31 final size:29
Alignment explanation
Indices: 9505138--9505206 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
9505128 ATCGAAATTT
* *
9505138 CATGTATAAAATTGCACAAAATCAAAGTT
1 CATGTATAAAATTGCACAAAACCAAAGTG
* *
9505167 CATGTATATAATTGCACATTAAACCATAGTG
1 CATGTATAAAATTGCACA--AAACCAAAGTG
9505198 CATGTATAA
1 CATGTATAA
9505207 TTTTGATATT
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
29 17 0.52
31 16 0.48
ACGTcount: A:0.43, C:0.14, G:0.12, T:0.30
Consensus pattern (29 bp):
CATGTATAAAATTGCACAAAACCAAAGTG
Found at i:9511497 original size:2 final size:2
Alignment explanation
Indices: 9511490--9511518 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
9511480 CGCCCCAAGT
9511490 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
9511519 AATGCAGAAG
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:9518468 original size:2 final size:2
Alignment explanation
Indices: 9518461--9518497 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
9518451 TTTTATTACA
9518461 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
9518498 GTTTCTGTCT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:9522574 original size:14 final size:15
Alignment explanation
Indices: 9522544--9522577 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
9522534 AAATTAAAAT
*
9522544 TATTTAATAATTTTA
1 TATTTAATAAATTTA
9522559 TATTTAA-AAATTTA
1 TATTTAATAAATTTA
9522573 TATTT
1 TATTT
9522578 TTAAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
TATTTAATAAATTTA
Found at i:9522582 original size:16 final size:15
Alignment explanation
Indices: 9522544--9522584 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
9522534 AAATTAAAAT
*
9522544 TATTTAATAATTTTA
1 TATTTAAAAATTTTA
9522559 TATTTAAAAATTTATA
1 TATTTAAAAATTT-TA
*
9522575 TTTTTAAAAA
1 TATTTAAAAA
9522585 ATAATTTTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 12 0.52
16 11 0.48
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (15 bp):
TATTTAAAAATTTTA
Found at i:9528663 original size:20 final size:19
Alignment explanation
Indices: 9528634--9528681 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
9528624 TTTTTCAAAT
* *
9528634 TAAAAAATATGTTTGATAAA
1 TAAAATATATGTTTAAT-AA
*
9528654 TAAAATATATTTTTAATAA
1 TAAAATATATGTTTAATAA
*
9528673 TGAAATATA
1 TAAAATATA
9528682 AACTACATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.54, C:0.00, G:0.06, T:0.40
Consensus pattern (19 bp):
TAAAATATATGTTTAATAA
Found at i:9529392 original size:21 final size:20
Alignment explanation
Indices: 9529367--9529479 Score: 85
Period size: 21 Copynumber: 5.7 Consensus size: 20
9529357 TGGTGCTGTT
9529367 TTTTTTTACTGTTTTGATTG
1 TTTTTTTACTGTTTTGATTG
* *
9529387 CTTTTTTGCTGTTTTGGAATT-
1 TTTTTTTACTGTTTT-G-ATTG
* *
9529408 ATTTTTTACTATTTTG---G
1 TTTTTTTACTGTTTTGATTG
9529425 TATTTTTTACTGTTTTGA-TG
1 T-TTTTTTACTGTTTTGATTG
9529445 CTGTTTTTTACTGTTTTGA-TG
1 -T-TTTTTTACTGTTTTGATTG
*
9529466 TTATTTTTGCTGTT
1 TT-TTTTTACTGTT
9529480 ATTTTTGTTG
Statistics
Matches: 76, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
18 14 0.18
19 1 0.01
20 26 0.34
21 32 0.42
22 3 0.04
ACGTcount: A:0.12, C:0.07, G:0.16, T:0.65
Consensus pattern (20 bp):
TTTTTTTACTGTTTTGATTG
Found at i:9529430 original size:18 final size:18
Alignment explanation
Indices: 9529407--9529441 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9529397 GTTTTGGAAT
9529407 TATTTTTTACTATTTTGG
1 TATTTTTTACTATTTTGG
*
9529425 TATTTTTTACTGTTTTG
1 TATTTTTTACTATTTTG
9529442 ATGCTGTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.14, C:0.06, G:0.11, T:0.69
Consensus pattern (18 bp):
TATTTTTTACTATTTTGG
Found at i:9529530 original size:12 final size:11
Alignment explanation
Indices: 9529458--9529537 Score: 61
Period size: 12 Copynumber: 6.9 Consensus size: 11
9529448 TTTTTTACTG
*
9529458 TTTTGATGTTA
1 TTTTGTTGTTA
*
9529469 TTTTTGCTGTTA
1 -TTTTGTTGTTA
*
9529481 TTTTTGTTGCTA
1 -TTTTGTTGTTA
* *
9529493 TTTTTTTGTTG
1 TTTTGTTGTTA
* *
9529504 TTTTGCTGTTG
1 TTTTGTTGTTA
9529515 TTTTGATTGTTA
1 TTTTG-TTGTTA
9529527 TTTTGGTTGTT
1 TTTT-GTTGTT
9529538 TGGATATTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
11 22 0.39
12 33 0.59
13 1 0.02
ACGTcount: A:0.07, C:0.04, G:0.20, T:0.69
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:9530135 original size:6 final size:6
Alignment explanation
Indices: 9530120--9530152 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
9530110 ACAAACAAGT
*
9530120 GCAACC GCAACA GCAACA GCAACA GCAACA GCA
1 GCAACA GCAACA GCAACA GCAACA GCAACA GCA
9530153 TCATTGCACC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.45, C:0.36, G:0.18, T:0.00
Consensus pattern (6 bp):
GCAACA
Found at i:9530204 original size:6 final size:6
Alignment explanation
Indices: 9530193--9530217 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
9530183 AGATCCTTTG
9530193 CCATCT CCATCT CCATCT CCATCT C
1 CCATCT CCATCT CCATCT CCATCT C
9530218 TTGTATGTTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.52, G:0.00, T:0.32
Consensus pattern (6 bp):
CCATCT
Found at i:9537394 original size:25 final size:25
Alignment explanation
Indices: 9537320--9537395 Score: 111
Period size: 24 Copynumber: 3.1 Consensus size: 25
9537310 AGTTTGACTC
9537320 AAACAAATAAACAG-AGTTTAATTG
1 AAACAAATAAACAGAAGTTTAATTG
9537344 AAACAAATAAACA-AAGTTTAATTG
1 AAACAAATAAACAGAAGTTTAATTG
* * *
9537368 AAACAATTAAACAGAATTTTAACTG
1 AAACAAATAAACAGAAGTTTAATTG
9537393 AAA
1 AAA
9537396 GATTATTTCT
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
24 35 0.74
25 12 0.26
ACGTcount: A:0.57, C:0.09, G:0.09, T:0.25
Consensus pattern (25 bp):
AAACAAATAAACAGAAGTTTAATTG
Found at i:9537400 original size:24 final size:24
Alignment explanation
Indices: 9537310--9537395 Score: 91
Period size: 24 Copynumber: 3.5 Consensus size: 24
9537300 GACTAGTAAG
* * * *
9537310 AGTTTGACTCAAACAAATAAACAG
1 AGTTTAACTGAAACAATTAAACAA
* *
9537334 AGTTTAATTGAAACAAATAAACAA
1 AGTTTAACTGAAACAATTAAACAA
*
9537358 AGTTTAATTGAAACAATTAAACAGA
1 AGTTTAACTGAAACAATTAAACA-A
*
9537383 ATTTTAACTGAAA
1 AGTTTAACTGAAA
9537396 GATTATTTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
24 42 0.78
25 12 0.22
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.27
Consensus pattern (24 bp):
AGTTTAACTGAAACAATTAAACAA
Found at i:9549121 original size:3 final size:3
Alignment explanation
Indices: 9549113--9549147 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
9549103 GAGACTCAGT
9549113 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TT
9549148 GTATCAGTGT
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:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:9554941 original size:17 final size:17
Alignment explanation
Indices: 9554910--9554955 Score: 60
Period size: 16 Copynumber: 2.8 Consensus size: 17
9554900 AAATTTAAAC
*
9554910 ATTTT-ATTGAAATAAT
1 ATTTTAATTAAAATAAT
9554926 ATTTTAATTAAAATAAT
1 ATTTTAATTAAAATAAT
*
9554943 -TTTTATTTAAAAT
1 ATTTTAATTAAAAT
9554956 TGTAAACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
16 17 0.63
17 10 0.37
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTTAATTAAAATAAT
Found at i:9557845 original size:2 final size:2
Alignment explanation
Indices: 9557838--9557867 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
9557828 CATAACACAA
9557838 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
9557868 CGCATATTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:9558176 original size:26 final size:26
Alignment explanation
Indices: 9558124--9558176 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
9558114 TGCATGCATC
* *
9558124 ATTTGAATTCCTTAAAAGAAGATAAT
1 ATTTGAATTCATTAAAAGAAGAGAAT
*
9558150 ATTT-AATTCATTCAAAGAACGAGAAT
1 ATTTGAATTCATTAAAAGAA-GAGAAT
9558176 A
1 A
9558177 ACGTCTTTCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 13 0.57
26 10 0.43
ACGTcount: A:0.47, C:0.09, G:0.11, T:0.32
Consensus pattern (26 bp):
ATTTGAATTCATTAAAAGAAGAGAAT
Found at i:9560305 original size:20 final size:18
Alignment explanation
Indices: 9560275--9560314 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 18
9560265 CATGCCTTAC
9560275 ATTTAAAAAATAAATAAAT
1 ATTTAAAAAATAAA-AAAT
9560294 ATTTATAAAAATAAAAAAT
1 ATTTA-AAAAATAAAAAAT
9560313 AT
1 AT
9560315 ACTAATTTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (18 bp):
ATTTAAAAAATAAAAAAT
Found at i:9574985 original size:2 final size:2
Alignment explanation
Indices: 9574978--9575008 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9574968 CGTAGTTGTA
9574978 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
9575009 CCTACCTGTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:9580651 original size:23 final size:23
Alignment explanation
Indices: 9580620--9580664 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
9580610 AATGTAGAGA
9580620 ATTAGAATTAATTTATTAAATCGT
1 ATTAGAATTAATTT-TTAAATCGT
* *
9580644 ATTA-AATTCATTTTTACATCG
1 ATTAGAATTAATTTTTAAATCG
9580665 AGCATAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 8 0.42
24 4 0.21
ACGTcount: A:0.38, C:0.09, G:0.07, T:0.47
Consensus pattern (23 bp):
ATTAGAATTAATTTTTAAATCGT
Found at i:9581241 original size:19 final size:16
Alignment explanation
Indices: 9581207--9581249 Score: 59
Period size: 16 Copynumber: 2.6 Consensus size: 16
9581197 ATTTAAATTT
9581207 TTAAATTATAAAAATA
1 TTAAATTATAAAAATA
*
9581223 TTAAATTATTAAAATA
1 TTAAATTATAAAAATA
*
9581239 ATATAATTATA
1 TTA-AATTATA
9581250 TTTTATTATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
16 17 0.74
17 6 0.26
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (16 bp):
TTAAATTATAAAAATA
Found at i:9581255 original size:24 final size:22
Alignment explanation
Indices: 9581214--9581276 Score: 65
Period size: 22 Copynumber: 2.8 Consensus size: 22
9581204 TTTTTAAATT
*
9581214 ATAAAAA-TATTAAATTATTAAA
1 ATAAAAATTA-TAATTTATTAAA
* *
9581236 ATAATATAATTATATTTTATTATA
1 ATAA-A-AATTATAATTTATTAAA
9581260 ATAAAAATTATAATTTA
1 ATAAAAATTATAATTTA
9581277 ATTCCGTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
22 15 0.44
23 2 0.06
24 15 0.44
25 2 0.06
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAAAAATTATAATTTATTAAA
Found at i:9582392 original size:26 final size:24
Alignment explanation
Indices: 9582334--9582399 Score: 75
Period size: 26 Copynumber: 2.7 Consensus size: 24
9582324 TCTAATAATT
9582334 TTTATAAA--TTATTTTTTTAAAA
1 TTTATAAATTTTATTTTTTTAAAA
9582356 TTTATAGAATTTTATTATTTTTAATTAA
1 TTTATA-AATTTTATT-TTTTTAA--AA
9582384 -TTATAAATTTTATTTT
1 TTTATAAATTTTATTTT
9582400 ATCTAATAAA
Statistics
Matches: 38, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
22 6 0.16
23 2 0.05
25 7 0.18
26 16 0.42
27 5 0.13
28 2 0.05
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (24 bp):
TTTATAAATTTTATTTTTTTAAAA
Found at i:9587898 original size:38 final size:38
Alignment explanation
Indices: 9587847--9587929 Score: 157
Period size: 38 Copynumber: 2.2 Consensus size: 38
9587837 TGTTGACAAA
*
9587847 AATGTGATTGAATGATTTTTAGGTGTAAACATATTAAT
1 AATGTTATTGAATGATTTTTAGGTGTAAACATATTAAT
9587885 AATGTTATTGAATGATTTTTAGGTGTAAACATATTAAT
1 AATGTTATTGAATGATTTTTAGGTGTAAACATATTAAT
9587923 AATGTTA
1 AATGTTA
9587930 ACATTGAAAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 44 1.00
ACGTcount: A:0.37, C:0.02, G:0.17, T:0.43
Consensus pattern (38 bp):
AATGTTATTGAATGATTTTTAGGTGTAAACATATTAAT
Found at i:9592905 original size:20 final size:21
Alignment explanation
Indices: 9592868--9592906 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
9592858 TCATGAAGTT
* *
9592868 AAAAAAATAACTCTTAATTTA
1 AAAAAAATAACACATAATTTA
9592889 AAAAAAATAA-ACATAATT
1 AAAAAAATAACACATAATT
9592907 ATCTAAAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 6 0.38
21 10 0.62
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (21 bp):
AAAAAAATAACACATAATTTA
Found at i:9593118 original size:29 final size:29
Alignment explanation
Indices: 9593057--9593119 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
9593047 ATATTAAAAG
* *
9593057 TTATTTTTTTAATTTCATGTATGATTTAT
1 TTATTTTATTAATTTCATGTATGAATTAT
* *
9593086 TTATTTTATTATTTTCATGTGT-AATTAT
1 TTATTTTATTAATTTCATGTATGAATTAT
9593114 CTTATT
1 -TTATT
9593120 GAATTACCCA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
28 5 0.17
29 24 0.83
ACGTcount: A:0.24, C:0.05, G:0.06, T:0.65
Consensus pattern (29 bp):
TTATTTTATTAATTTCATGTATGAATTAT
Found at i:9594445 original size:14 final size:14
Alignment explanation
Indices: 9594398--9594446 Score: 52
Period size: 13 Copynumber: 3.7 Consensus size: 14
9594388 TTAGTATTGT
*
9594398 TTTTGAGAAA-TG-
1 TTTTGAAAAAGTGA
9594410 TTTTGAAAAAGTGA
1 TTTTGAAAAAGTGA
9594424 TTTT-AAAAAGT-A
1 TTTTGAAAAAGTGA
9594436 TTTTTGAAAAA
1 -TTTTGAAAAA
9594447 ATAGGTTTAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 10 0.31
13 13 0.41
14 9 0.28
ACGTcount: A:0.43, C:0.00, G:0.16, T:0.41
Consensus pattern (14 bp):
TTTTGAAAAAGTGA
Found at i:9594672 original size:39 final size:41
Alignment explanation
Indices: 9594593--9594672 Score: 103
Period size: 41 Copynumber: 2.0 Consensus size: 41
9594583 TTTAATAAGA
* *
9594593 ATATAAAAAATAATTTATTATGATTTTTTAAATATTTTAAT
1 ATATAAAAAATAATTTATAATGATTTTTTAAATATATTAAT
*
9594634 ATATAAAAAATAAATTTA-AAT-ATTTTTTAAGTA-ATTAAT
1 ATATAAAAAAT-AATTTATAATGATTTTTTAAATATATTAAT
9594673 CAAAAAAGGG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
39 5 0.14
40 11 0.31
41 13 0.37
42 6 0.17
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (41 bp):
ATATAAAAAATAATTTATAATGATTTTTTAAATATATTAAT
Found at i:9613155 original size:58 final size:58
Alignment explanation
Indices: 9613041--9613155 Score: 153
Period size: 58 Copynumber: 2.0 Consensus size: 58
9613031 ATCAACAAAC
* * *
9613041 TAAACCCAAATATTTTTAAACCTAAATATAATTTCATTCTTCAAAAACATTTATAAAT
1 TAAACCCAAATATTTTTAAACCTAAATATAATTTCATTCCTCAAAAACACTCATAAAT
* *
9613099 TAAACTCAAATATTTTTAAA-CTCAAATATAATTTTATTCCT-AAATAACACTCATAAA
1 TAAACCCAAATATTTTTAAACCT-AAATATAATTTCATTCCTCAAA-AACACTCATAAA
9613156 CAACTCATTT
Statistics
Matches: 50, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
57 5 0.10
58 45 0.90
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (58 bp):
TAAACCCAAATATTTTTAAACCTAAATATAATTTCATTCCTCAAAAACACTCATAAAT
Found at i:9635837 original size:18 final size:17
Alignment explanation
Indices: 9635814--9635848 Score: 61
Period size: 18 Copynumber: 2.0 Consensus size: 17
9635804 AAATAAATAT
9635814 TTAATTAAATAAATTTAA
1 TTAATTAAA-AAATTTAA
9635832 TTAATTAAAAAATTTAA
1 TTAATTAAAAAATTTAA
9635849 ACCCTAAACC
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATTAAAAAATTTAA
Found at i:9635912 original size:12 final size:12
Alignment explanation
Indices: 9635895--9635926 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
9635885 CACACACTTC
9635895 TCTTCTTCATCT
1 TCTTCTTCATCT
9635907 TCTTCTTCATCT
1 TCTTCTTCATCT
*
9635919 TCATCTTC
1 TCTTCTTC
9635927 TTCCCTTTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.09, C:0.34, G:0.00, T:0.56
Consensus pattern (12 bp):
TCTTCTTCATCT
Found at i:9646119 original size:6 final size:6
Alignment explanation
Indices: 9646099--9646147 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
9646089 CTGTCGCTTC
* *
9646099 CACTGT CACTG- --CTGT CACTGT CACTGT CACTAT CACTGC CACTGT
1 CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT CACTGT
9646144 CACT
1 CACT
9646148 AGCACTATTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
3 3 0.08
6 33 0.92
ACGTcount: A:0.18, C:0.37, G:0.14, T:0.31
Consensus pattern (6 bp):
CACTGT
Found at i:9646136 original size:18 final size:18
Alignment explanation
Indices: 9646113--9646153 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
9646103 GTCACTGCTG
*
9646113 TCACTGTCACTGTCACTA
1 TCACTGCCACTGTCACTA
9646131 TCACTGCCACTGTCACTA
1 TCACTGCCACTGTCACTA
*
9646149 GCACT
1 TCACT
9646154 ATTTGCTTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.22, C:0.37, G:0.12, T:0.29
Consensus pattern (18 bp):
TCACTGCCACTGTCACTA
Found at i:9646153 original size:12 final size:12
Alignment explanation
Indices: 9646086--9646147 Score: 61
Period size: 12 Copynumber: 4.9 Consensus size: 12
9646076 GCTGTGGCTT
* *
9646086 CCACTGTCGCTT
1 CCACTGTCACTG
9646098 CCACTGTCACTG
1 CCACTGTCACTG
9646110 CTGTCACTGTCACTG
1 C---CACTGTCACTG
* *
9646125 TCACTATCACTG
1 CCACTGTCACTG
9646137 CCACTGTCACT
1 CCACTGTCACT
9646148 AGCACTATTT
Statistics
Matches: 41, Mismatches: 6, Indels: 6
0.77 0.11 0.11
Matches are distributed among these distances:
12 30 0.73
15 11 0.27
ACGTcount: A:0.16, C:0.39, G:0.15, T:0.31
Consensus pattern (12 bp):
CCACTGTCACTG
Found at i:9653236 original size:21 final size:20
Alignment explanation
Indices: 9653203--9653256 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 20
9653193 ATAAATTTGT
9653203 TTTTTA-AACTTTTGTTA-AA
1 TTTTTACAA-TTTTGTTATAA
*
9653222 TAGTTTTGCAATTTTGTTATAA
1 T--TTTTACAATTTTGTTATAA
9653244 TTTTTACAATTTT
1 TTTTTACAATTTT
9653257 TTTACATTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
19 1 0.03
20 11 0.38
21 12 0.41
22 5 0.17
ACGTcount: A:0.28, C:0.06, G:0.07, T:0.59
Consensus pattern (20 bp):
TTTTTACAATTTTGTTATAA
Done.