Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gbar_A05
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: 102776486
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2328156 characters in sequence are not A, C, G, or T
File 87 of 325
Found at i:29355524 original size:21 final size:20
Alignment explanation
Indices: 29355486--29355524 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
29355476 TTTAAAATAT
**
29355486 TATAAAAACATATTAAATTC
1 TATAAAAACATAAAAAATTC
29355506 TATAAAAATCATAAAAAAT
1 TATAAAAA-CATAAAAAAT
29355525 AAAAAAAAGT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.62, C:0.08, G:0.00, T:0.31
Consensus pattern (20 bp):
TATAAAAACATAAAAAATTC
Found at i:29355558 original size:18 final size:18
Alignment explanation
Indices: 29355484--29355577 Score: 66
Period size: 18 Copynumber: 5.1 Consensus size: 18
29355474 TATTTAAAAT
*
29355484 ATTATAAAAACA-TATTAA
1 ATTATAAAAA-ATTATAAA
* *
29355502 ATTCTATAAAAATCATAAAA
1 ATTATA-AAAAATTAT-AAA
* * *
29355522 AATAAAAAAAAGTATTAAA
1 ATTATAAAAAATTA-TAAA
*
29355541 ATTGAT-ATAAATTATAAA
1 ATT-ATAAAAAATTATAAA
29355559 ATTATAAAAAATTATAAA
1 ATTATAAAAAATTATAAA
29355577 A
1 A
29355578 ACTTAAATTA
Statistics
Matches: 57, Mismatches: 13, Indels: 12
0.70 0.16 0.15
Matches are distributed among these distances:
17 2 0.04
18 25 0.44
19 23 0.40
20 7 0.12
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
ATTATAAAAAATTATAAA
Found at i:29356956 original size:17 final size:17
Alignment explanation
Indices: 29356934--29356970 Score: 74
Period size: 17 Copynumber: 2.2 Consensus size: 17
29356924 GGATTCTTTA
29356934 TTTTCGGGTTTTCGGGG
1 TTTTCGGGTTTTCGGGG
29356951 TTTTCGGGTTTTCGGGG
1 TTTTCGGGTTTTCGGGG
29356968 TTT
1 TTT
29356971 AGTCTTTATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.00, C:0.11, G:0.38, T:0.51
Consensus pattern (17 bp):
TTTTCGGGTTTTCGGGG
Found at i:29356970 original size:9 final size:8
Alignment explanation
Indices: 29356934--29356966 Score: 57
Period size: 8 Copynumber: 4.0 Consensus size: 8
29356924 GGATTCTTTA
29356934 TTTTCGGG
1 TTTTCGGG
29356942 TTTTCGGGG
1 TTTTC-GGG
29356951 TTTTCGGG
1 TTTTCGGG
29356959 TTTTCGGG
1 TTTTCGGG
29356967 GTTTAGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 16 0.67
9 8 0.33
ACGTcount: A:0.00, C:0.12, G:0.39, T:0.48
Consensus pattern (8 bp):
TTTTCGGG
Found at i:29360441 original size:34 final size:34
Alignment explanation
Indices: 29360387--29360466 Score: 99
Period size: 34 Copynumber: 2.4 Consensus size: 34
29360377 TTTAGTGTTC
* * *
29360387 TTTTTTAA-AAATTAATTAAATTAAGGTTTATGA
1 TTTTTAAATAAATTAAGTAAATTAAGGTTTAAGA
* *
29360420 TTTTTAAATAAATTAAGTAAATTAGGGTTTAAGG
1 TTTTTAAATAAATTAAGTAAATTAAGGTTTAAGA
*
29360454 GTTTTAAATAAAT
1 TTTTTAAATAAAT
29360467 AAATAAAATT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
33 7 0.17
34 33 0.82
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.45
Consensus pattern (34 bp):
TTTTTAAATAAATTAAGTAAATTAAGGTTTAAGA
Found at i:29360808 original size:125 final size:126
Alignment explanation
Indices: 29360579--29360943 Score: 502
Period size: 125 Copynumber: 2.9 Consensus size: 126
29360569 ATTTTTACCC
**
29360579 AAAAAAATAATTTTGAGAAGACCTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
1 AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
* * * *
29360644 CTATCAGCAAAATTACTAAAAAAAGCTACCACATGGACGCTCTTTTTCTA-TAGTAGTTTCT
66 CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACT-GTAGTTCCT
* *
29360705 -GAAAAATAATTTTGAGAAGATGTTTCTGAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
1 AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
* * * * * *
29360769 CTGTCAGCAAAAGTACTGAAAAATGCTCCCACGTAGACGCAATTTTTTTTTACTGTAGTTCCT
66 CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC--TCTTTTTCTACTGTAGTTCCT
* *
29360832 AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGT-AAAAATCACTTCAAGCAGGATGC
1 AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAA-CGCTTTAAGCAGGATGC
* * *
29360896 ACTATCAGTAAAATTACTGAAAAAAGCTCTCATGTGGACGCTCTTTTT
65 ACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTT
29360944 TTACAATAGT
Statistics
Matches: 208, Mismatches: 26, Indels: 10
0.85 0.11 0.04
Matches are distributed among these distances:
125 93 0.45
126 6 0.03
127 21 0.10
128 88 0.42
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (126 bp):
AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAACGCTTTAAGCAGGATGCA
CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTACTGTAGTTCCT
Found at i:29362817 original size:18 final size:18
Alignment explanation
Indices: 29362791--29362833 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
29362781 GACTGGGAAA
* * *
29362791 AGGAAACATATAAGGGTT
1 AGGATACATATAAAGGCT
29362809 AGGATACATATAAAGGCT
1 AGGATACATATAAAGGCT
29362827 AGGATAC
1 AGGATAC
29362834 GCACCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:29363426 original size:7 final size:7
Alignment explanation
Indices: 29363416--29363440 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
29363406 TTATATACAT
29363416 AATACTA
1 AATACTA
29363423 AATACTA
1 AATACTA
29363430 AATACTA
1 AATACTA
29363437 AATA
1 AATA
29363441 TGAAATGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:29368228 original size:30 final size:30
Alignment explanation
Indices: 29368194--29368257 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
29368184 AAATATCGAA
29368194 TCTTCCCAAGCTCCTAAATGCA-ATATTAAG
1 TCTTCCCAAGCTCCTAAATG-AGATATTAAG
* * *
29368224 TCTTCCCAAGCTTCTGAATGAGATATTAGG
1 TCTTCCCAAGCTCCTAAATGAGATATTAAG
29368254 TCTT
1 TCTT
29368258 ATCAATCCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 29 0.97
ACGTcount: A:0.28, C:0.23, G:0.14, T:0.34
Consensus pattern (30 bp):
TCTTCCCAAGCTCCTAAATGAGATATTAAG
Found at i:29370969 original size:33 final size:34
Alignment explanation
Indices: 29370921--29370984 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
29370911 AATAGATGTA
29370921 TTAACTATAAAAAATAA-TTACAAATAATTATCAT
1 TTAACTATAAAAAATAATTTA-AAATAATTATCAT
*
29370955 TTAA-TATAATAAATAATTTAAAATAATTAT
1 TTAACTATAAAAAATAATTTAAAATAATTAT
29370985 ATAATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAACTATAAAAAATAATTTAAAATAATTATCAT
Found at i:29370990 original size:18 final size:17
Alignment explanation
Indices: 29370927--29370981 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
29370917 TGTATTAACT
*
29370927 ATAAAAAATAA-TTACAA
1 ATAATAAATAATTTA-AA
* * *
29370944 ATAAT-TATCATTTAAT
1 ATAATAAATAATTTAAA
29370960 ATAATAAATAATTTAAA
1 ATAATAAATAATTTAAA
29370977 ATAAT
1 ATAAT
29370982 TATATAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATAAATAATTTAAA
Found at i:29370992 original size:17 final size:17
Alignment explanation
Indices: 29370934--29370992 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
29370924 ACTATAAAAA
29370934 ATAATTACAAATAATTAT
1 ATAATTA-AAATAATTAT
* *
29370952 CAT--TTAATATAA-TAA
1 -ATAATTAAAATAATTAT
29370967 ATAATTTAAAATAATTAT
1 ATAA-TTAAAATAATTAT
29370985 ATAATTAA
1 ATAATTAA
29370993 TTAGAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 2 0.06
15 2 0.06
16 5 0.16
17 15 0.47
18 6 0.19
19 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATAATTAT
Found at i:29371515 original size:22 final size:22
Alignment explanation
Indices: 29371490--29371531 Score: 75
Period size: 22 Copynumber: 1.9 Consensus size: 22
29371480 TATAAATTTA
*
29371490 TTTTAAATACAAAATTTAAAGG
1 TTTTAAATAAAAAATTTAAAGG
29371512 TTTTAAATAAAAAATTTAAA
1 TTTTAAATAAAAAATTTAAA
29371532 ATAAATTAAC
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:0.55, C:0.02, G:0.05, T:0.38
Consensus pattern (22 bp):
TTTTAAATAAAAAATTTAAAGG
Found at i:29375587 original size:26 final size:26
Alignment explanation
Indices: 29375551--29375658 Score: 171
Period size: 26 Copynumber: 4.2 Consensus size: 26
29375541 TGAAATTCCC
* *
29375551 ATCATGAAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
*
29375577 ATCATAGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
29375603 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
29375629 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
29375655 ATCA
1 ATCA
29375659 ATTTGTACCA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 74 1.00
ACGTcount: A:0.38, C:0.24, G:0.06, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:29376440 original size:23 final size:23
Alignment explanation
Indices: 29376409--29377053 Score: 526
Period size: 23 Copynumber: 28.1 Consensus size: 23
29376399 AAATAAGTAC
* *
29376409 TTAAACACTTCAATTTGCAACAT
1 TTAAACACTTCAATTTACAGCAT
* *
29376432 TTAAGCACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
*
29376455 TTAAACACTTCAATTTGCAGCAT
1 TTAAACACTTCAATTTACAGCAT
* **
29376478 TCAAACACTTCAATTTGTAGCACT
1 TTAAACACTTCAATTTACAGCA-T
* *
29376502 TT-AACACTTCAATTTGCAGTACT
1 TTAAACACTTCAATTTACAGCA-T
* *
29376525 TT-AACA-TATCAATTAACAACAT
1 TTAAACACT-TCAATTTACAGCAT
* *
29376547 TTATACACCTCAA-TTACAGCGA-
1 TTAAACACTTCAATTTACAGC-AT
* * * *
29376569 TAAAACA-TCTCAATGTCCAGCAA
1 TTAAACACT-TCAATTTACAGCAT
* * * *
29376592 CTAAACACTTCAATTTGCAGTAC
1 TTAAACACTTCAATTTACAGCAT
* * *
29376615 TTAAATACTTCAATTTGCAACAT
1 TTAAACACTTCAATTTACAGCAT
*
29376638 TTAAGCACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
* * *
29376661 TTAAATACTTCAATTTATAACAT
1 TTAAACACTTCAATTTACAGCAT
* **
29376684 TCAAACACTTCAATTTGTAGCACT
1 TTAAACACTTCAATTTACAGCA-T
29376708 TT-AACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
*
29376730 TTAAACACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
* *
29376753 TCAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
*
29376777 TT-AACACTTCAATTTACAACAT
1 TTAAACACTTCAATTTACAGCAT
* *
29376799 TAAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
* * *
29376823 TT-AACATTTCAATTAACAACAT
1 TTAAACACTTCAATTTACAGCAT
*
29376845 TTAAGCACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
* *
29376868 TCAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
29376892 TT-AACACTTCAATTTACAGCAT
1 TTAAACACTTCAATTTACAGCAT
* *
29376914 TAAAACACTTCAATTTGCAGCACT
1 TTAAACACTTCAATTTACAGCA-T
* * *
29376938 TT-AACATTTCAATTAACAACAT
1 TTAAACACTTCAATTTACAGCAT
* * *
29376960 TTATACACCTCAA-TTACAACGA-
1 TTAAACACTTCAATTTACAGC-AT
* * *
29376982 TAAAACA-TCTCAATTTCCAGCAA
1 TTAAACACT-TCAATTTACAGCAT
* * * * *
29377005 CTAAACACTTCAAATTGCAGTAC
1 TTAAACACTTCAATTTACAGCAT
* *
29377028 TTAAACACTTCAATTTGCAACAT
1 TTAAACACTTCAATTTACAGCAT
29377051 TTA
1 TTA
29377054 CTACTAAATA
Statistics
Matches: 498, Mismatches: 100, Indels: 48
0.77 0.15 0.07
Matches are distributed among these distances:
22 48 0.10
23 436 0.88
24 14 0.03
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.33
Consensus pattern (23 bp):
TTAAACACTTCAATTTACAGCAT
Found at i:29377444 original size:9 final size:9
Alignment explanation
Indices: 29377430--29377460 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
29377420 GTTAAACGAA
29377430 TCGAGTTAT
1 TCGAGTTAT
*
29377439 TCGAGTTAA
1 TCGAGTTAT
29377448 TCGAGTTAT
1 TCGAGTTAT
29377457 TCGA
1 TCGA
29377461 ATCAACTCGA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.26, C:0.13, G:0.23, T:0.39
Consensus pattern (9 bp):
TCGAGTTAT
Found at i:29377532 original size:9 final size:9
Alignment explanation
Indices: 29377515--29377551 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
29377505 TGAGTTTTCG
29377515 AATTCGAAT
1 AATTCGAAT
*
29377524 AACTCGAAT
1 AATTCGAAT
29377533 AATTCGAAT
1 AATTCGAAT
29377542 AATTCGAAT
1 AATTCGAAT
29377551 A
1 A
29377552 TCAAAGTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:29382763 original size:41 final size:40
Alignment explanation
Indices: 29382701--29382786 Score: 109
Period size: 41 Copynumber: 2.1 Consensus size: 40
29382691 AGTGAAAGTT
* * *
29382701 TTTTTGCGGCATTTTTACAAAAACACCACTATATCTCAAC
1 TTTTTGCAGCATTTTCACAAAAACACCACTATAGCTCAAC
* * *
29382741 TTTTTGCAGCGTTTTCACCAAAAACATCATTATAGCTCAAC
1 TTTTTGCAGCATTTTCA-CAAAAACACCACTATAGCTCAAC
29382782 TTTTT
1 TTTTT
29382787 TGCGGTATTT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
40 14 0.36
41 25 0.64
ACGTcount: A:0.30, C:0.23, G:0.08, T:0.38
Consensus pattern (40 bp):
TTTTTGCAGCATTTTCACAAAAACACCACTATAGCTCAAC
Found at i:29382983 original size:8 final size:8
Alignment explanation
Indices: 29382972--29383015 Score: 72
Period size: 8 Copynumber: 5.6 Consensus size: 8
29382962 AATATTAAAA
29382972 TTTTAAGT
1 TTTTAAGT
29382980 TTTTAAGT
1 TTTTAAGT
29382988 TTTTAAGT
1 TTTTAAGT
29382996 TTTTAA-T
1 TTTTAAGT
*
29383003 TTTTAATT
1 TTTTAAGT
29383011 TTTTA
1 TTTTA
29383016 TTTTAAAATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
7 7 0.20
8 28 0.80
ACGTcount: A:0.25, C:0.00, G:0.07, T:0.68
Consensus pattern (8 bp):
TTTTAAGT
Found at i:29382991 original size:16 final size:15
Alignment explanation
Indices: 29382972--29383035 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
29382962 AATATTAAAA
29382972 TTTTAAGTTTTTAAGT
1 TTTTAAGTTTTTAA-T
29382988 TTTTAAGTTTTTAAT
1 TTTTAAGTTTTTAAT
*
29383003 TTTTAA-TTTTTTAT
1 TTTTAAGTTTTTAAT
* * *
29383017 TTTAAAATTTTCAAT
1 TTTTAAGTTTTTAAT
29383032 TTTT
1 TTTT
29383036 TTGAAGTTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
14 12 0.29
15 16 0.38
16 14 0.33
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (15 bp):
TTTTAAGTTTTTAAT
Found at i:29383035 original size:8 final size:7
Alignment explanation
Indices: 29382972--29383035 Score: 65
Period size: 8 Copynumber: 8.6 Consensus size: 7
29382962 AATATTAAAA
29382972 TTTTAAGT
1 TTTTAA-T
29382980 TTTTAAGT
1 TTTTAA-T
29382988 TTTTAAGT
1 TTTTAA-T
29382996 TTTTAAT
1 TTTTAAT
29383003 TTTTAAT
1 TTTTAAT
*
29383010 TTTTTAT
1 TTTTAAT
*
29383017 TTTAAAAT
1 TTT-TAAT
*
29383025 TTTCAAT
1 TTTTAAT
29383032 TTTT
1 TTTT
29383036 TTGAAGTTTT
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
7 23 0.46
8 27 0.54
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.67
Consensus pattern (7 bp):
TTTTAAT
Found at i:29384355 original size:13 final size:13
Alignment explanation
Indices: 29384337--29384361 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
29384327 ATAAGTCCAA
29384337 AAACAAAAATAAT
1 AAACAAAAATAAT
29384350 AAACAAAAATAA
1 AAACAAAAATAA
29384362 AACGAAATCC
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:0.80, C:0.08, G:0.00, T:0.12
Consensus pattern (13 bp):
AAACAAAAATAAT
Found at i:29384550 original size:18 final size:18
Alignment explanation
Indices: 29384483--29384595 Score: 167
Period size: 17 Copynumber: 6.3 Consensus size: 18
29384473 ATAATCTTCA
29384483 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
29384502 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
29384521 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
29384538 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
29384556 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
29384573 ATGATTGCAATCTTAAAT
1 ATGATTGCAATCTTAGAT
29384591 ATGAT
1 ATGAT
29384596 ATACTATCTT
Statistics
Matches: 87, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
17 32 0.37
18 32 0.37
19 23 0.26
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.37
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:29384554 original size:35 final size:35
Alignment explanation
Indices: 29384491--29384596 Score: 194
Period size: 35 Copynumber: 3.0 Consensus size: 35
29384481 CAATGATATG
29384491 CAATCTTAGATATGATATGCAATCTTAGATATGATA
1 CAATCTTAGATATGAT-TGCAATCTTAGATATGATA
29384527 CAATCTTAGATATGATTGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
29384562 CAATCTTAGATATGATTGCAATCTTAAATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
29384597 TACTATCTTA
Statistics
Matches: 69, Mismatches: 1, Indels: 1
0.97 0.01 0.01
Matches are distributed among these distances:
35 53 0.77
36 16 0.23
ACGTcount: A:0.39, C:0.11, G:0.13, T:0.37
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:29385153 original size:17 final size:17
Alignment explanation
Indices: 29385088--29385153 Score: 64
Period size: 17 Copynumber: 3.9 Consensus size: 17
29385078 TCTAAACCAA
*
29385088 TATATTTTATATTTT-T
1 TATATATTATATTTTAT
* *
29385104 TATATAATTAT-TATTCT
1 TATAT-ATTATATTTTAT
* *
29385121 TATAAATTATTTTTTAT
1 TATATATTATATTTTAT
29385138 TATATATTATATTTTA
1 TATATATTATATTTTA
29385154 AATTTATTAT
Statistics
Matches: 40, Mismatches: 7, Indels: 5
0.77 0.13 0.10
Matches are distributed among these distances:
16 13 0.32
17 27 0.68
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TATATATTATATTTTAT
Found at i:29386648 original size:14 final size:14
Alignment explanation
Indices: 29386617--29386668 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
29386607 AATTAACTCC
* *
29386617 TAAACCTTAAACCC
1 TAAACCATAAACCT
* *
29386631 TAAACCATATATCT
1 TAAACCATAAACCT
29386645 TAAACCATAAACCT
1 TAAACCATAAACCT
*
29386659 TAAACTATAA
1 TAAACCATAA
29386669 TGATAATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.48, C:0.25, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:29386810 original size:17 final size:17
Alignment explanation
Indices: 29386785--29386836 Score: 52
Period size: 16 Copynumber: 3.0 Consensus size: 17
29386775 GGGTTATAGA
*
29386785 TTAGTGTTTATGATTTT
1 TTAGGGTTTATGATTTT
*
29386802 TTAGGGTTTA-GAGTTT
1 TTAGGGTTTATGATTTT
*
29386818 TAAGGGTTATATGACTTTT
1 TTAGGGTT-TATGA-TTTT
29386837 AGCGGCGTTT
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
16 12 0.43
17 11 0.39
18 2 0.07
19 3 0.11
ACGTcount: A:0.21, C:0.02, G:0.23, T:0.54
Consensus pattern (17 bp):
TTAGGGTTTATGATTTT
Found at i:29386878 original size:41 final size:41
Alignment explanation
Indices: 29386833--29387093 Score: 272
Period size: 41 Copynumber: 6.4 Consensus size: 41
29386823 GTTATATGAC
* * * *
29386833 TTTTAGCGGCGTTTTACCGAAAGTGCCGTTAATGTTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
*
29386874 TTTTAGCGTCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * * *
29386915 ATTAAGCGGCGTTTTATCGAAAGCGCCGCTAATGCTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
** ** *
29386956 TTTTAATGGCATTTTATAGAAAGTGCCGCTAATGCTCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
* * * *
29386997 TCTTAGCAGCATTTTACCAAAAGCGCCGCTAATGCCCTGGT
1 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
* ** * * *
29387038 TTTTAGCGGCGTTTTAGCATAAAACACCGCTATTGCTCT-GT
1 TTTTAGCGGCATTTTA-CCGAAAGCGCCGCTAATGCTCTGGT
* *
29387079 TTTTAACGGCGTTTT
1 TTTTAGCGGCATTTT
29387094 TGGTAAAACG
Statistics
Matches: 183, Mismatches: 36, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
41 167 0.91
42 16 0.09
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (41 bp):
TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGT
Found at i:29387052 original size:123 final size:123
Alignment explanation
Indices: 29386833--29387093 Score: 328
Period size: 123 Copynumber: 2.1 Consensus size: 123
29386823 GTTATATGAC
* * ** * * * *
29386833 TTTTAGCGGCGTTTTACCGAAAGTGCCGTTAATGTTCTGGTTTTTAGCGTCATTTTACCGAAAGC
1 TTTTAACGGCATTTTATAGAAAGTGCCGCTAATGCTCTGGTTCTTAGCGTCATTTTACCAAAAGC
* * * *
29386898 GCCGCTAATGCTCTGGTATTAAGCGGCGTTTTATC-GAAAGCGCCGCTAATGCTCTGGT
66 GCCGCTAATGCCCTGGTATTAAGCGGCGTTTTAGCAGAAAACACCGCTAATGCTCT-GT
*
29386956 TTTTAATGGCATTTTATAGAAAGTGCCGCTAATGCTCTGGTTCTTAGCAG-CATTTTACCAAAAG
1 TTTTAACGGCATTTTATAGAAAGTGCCGCTAATGCTCTGGTTCTTAGC-GTCATTTTACCAAAAG
* * * *
29387020 CGCCGCTAATGCCCTGGTTTTTAGCGGCGTTTTAGCATAAAACACCGCTATTGCTCTGT
65 CGCCGCTAATGCCCTGGTATTAAGCGGCGTTTTAGCAGAAAACACCGCTAATGCTCTGT
*
29387079 TTTTAACGGCGTTTT
1 TTTTAACGGCATTTT
29387094 TGGTAAAACG
Statistics
Matches: 117, Mismatches: 19, Indels: 4
0.84 0.14 0.03
Matches are distributed among these distances:
123 100 0.85
124 17 0.15
ACGTcount: A:0.21, C:0.21, G:0.23, T:0.35
Consensus pattern (123 bp):
TTTTAACGGCATTTTATAGAAAGTGCCGCTAATGCTCTGGTTCTTAGCGTCATTTTACCAAAAGC
GCCGCTAATGCCCTGGTATTAAGCGGCGTTTTAGCAGAAAACACCGCTAATGCTCTGT
Found at i:29387124 original size:41 final size:41
Alignment explanation
Indices: 29387036--29387124 Score: 117
Period size: 41 Copynumber: 2.2 Consensus size: 41
29387026 TAATGCCCTG
* *
29387036 GTTTTTAGCGGCGTTTTAGCATAAAACACCGCTATTGCTCT
1 GTTTTTAACGGCGTTTTAGCATAAAACACCACTATTGCTCT
* * *
29387077 GTTTTTAACGGCGTTTTTG-GTAAAACGCCACTATTGCTCT
1 GTTTTTAACGGCGTTTTAGCATAAAACACCACTATTGCTCT
29387117 GTGTTTTA
1 GT-TTTTA
29387125 CATTTTTTGC
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
40 20 0.48
41 22 0.52
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.40
Consensus pattern (41 bp):
GTTTTTAACGGCGTTTTAGCATAAAACACCACTATTGCTCT
Found at i:29388151 original size:21 final size:21
Alignment explanation
Indices: 29388125--29388168 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
29388115 GTCCAATCCA
*
29388125 AACAAACTCAAAACAAAACCC
1 AACAAACCCAAAACAAAACCC
29388146 AACAAACCCAAAACAAAACCC
1 AACAAACCCAAAACAAAACCC
29388167 AA
1 AA
29388169 ACACGAATGG
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:0.64, C:0.34, G:0.00, T:0.02
Consensus pattern (21 bp):
AACAAACCCAAAACAAAACCC
Found at i:29388170 original size:11 final size:11
Alignment explanation
Indices: 29388122--29388171 Score: 52
Period size: 11 Copynumber: 4.6 Consensus size: 11
29388112 ACAGTCCAAT
29388122 CCAAAC-AAAC
1 CCAAACAAAAC
*
29388132 TCAAAACAAAAC
1 -CCAAACAAAAC
29388144 CC-AAC-AAAC
1 CCAAACAAAAC
29388153 CCAAAACAAAAC
1 CC-AAACAAAAC
29388165 CCAAACA
1 CCAAACA
29388172 CGAATGGCCC
Statistics
Matches: 33, Mismatches: 2, Indels: 8
0.77 0.05 0.19
Matches are distributed among these distances:
9 6 0.18
10 3 0.09
11 14 0.42
12 10 0.30
ACGTcount: A:0.62, C:0.36, G:0.00, T:0.02
Consensus pattern (11 bp):
CCAAACAAAAC
Found at i:29389242 original size:3 final size:3
Alignment explanation
Indices: 29389234--29389308 Score: 96
Period size: 3 Copynumber: 25.0 Consensus size: 3
29389224 TTTAACATTG
* * * *
29389234 TAT TAT TAT TAT TAT TAT TAT CAT TAC TAT TAT CAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
29389282 TAC TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT
29389309 ATTTCTTTTT
Statistics
Matches: 60, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 60 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.59
Consensus pattern (3 bp):
TAT
Found at i:29391680 original size:6 final size:6
Alignment explanation
Indices: 29391646--29391676 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
29391636 TCTGTGTACC
*
29391646 GCTACT GCTACT GCTACT GCTACT GTTACT G
1 GCTACT GCTACT GCTACT GCTACT GCTACT G
29391677 TTACGATGTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.19, T:0.35
Consensus pattern (6 bp):
GCTACT
Found at i:29392199 original size:23 final size:24
Alignment explanation
Indices: 29392160--29392207 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
29392150 AGGTTAATCT
29392160 ATATAAGCAAAAATTATGTTTATA
1 ATATAAGCAAAAATTATGTTTATA
29392184 ATATAAGC-AAAATTATGTTTATA
1 ATATAAGCAAAAATTATGTTTATA
29392207 A
1 A
29392208 AATAGTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 16 0.67
24 8 0.33
ACGTcount: A:0.50, C:0.04, G:0.08, T:0.38
Consensus pattern (24 bp):
ATATAAGCAAAAATTATGTTTATA
Found at i:29392506 original size:40 final size:42
Alignment explanation
Indices: 29392449--29392526 Score: 108
Period size: 41 Copynumber: 1.9 Consensus size: 42
29392439 TTTTGAGTCT
*
29392449 ACACGGCATGTCACACGGGCGTG-TGATCAGA-CGTGTGAGAC
1 ACACGGCATGTCACACGGGCATGTTGAT-AGACCGTGTGAGAC
*
29392490 ACACGGCTTG-CACACGGGCATGTTGATAGACCGTGTG
1 ACACGGCATGTCACACGGGCATGTTGATAGACCGTGTG
29392527 TCCCTTGCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
40 14 0.42
41 19 0.58
ACGTcount: A:0.23, C:0.24, G:0.33, T:0.19
Consensus pattern (42 bp):
ACACGGCATGTCACACGGGCATGTTGATAGACCGTGTGAGAC
Found at i:29394221 original size:47 final size:44
Alignment explanation
Indices: 29394059--29394267 Score: 174
Period size: 47 Copynumber: 4.5 Consensus size: 44
29394049 TGCGCCAGTA
* * *
29394059 TAAGACCATGTCTGGGACATGGCATCGTCATTCAGA-TGAGGGCTAGTG
1 TAAGA-CATGTCTGGGACAT-GCATCGGC--TAAGAGT-AGTGCTAGTG
* * ** * *
29394107 TAAGACATGTCTGGGACATGCTTCAGCCATATTA-TGAGTGCCAGAG
1 TAAGACATGTCTGGGACATGCATC-GGC-TAAGAGT-AGTGCTAGTG
29394153 TAAGACATGTCTGGGACATGCATCGGCCTCGACAGAGATAGT-C-AGTG
1 TAAGACATGTCTGGGACATGCATCGG-CT--A-AGAG-TAGTGCTAGTG
* *
29394200 TAAGACATGTCTAGGACATGCATCGGCTAAGAGTTGTGCTAGTG
1 TAAGACATGTCTGGGACATGCATCGGCTAAGAGTAGTGCTAGTG
29394244 TAAGACATGTCTGGGACATGCATC
1 TAAGACATGTCTGGGACATGCATC
29394268 ATCACGCATA
Statistics
Matches: 135, Mismatches: 17, Indels: 22
0.78 0.10 0.13
Matches are distributed among these distances:
42 3 0.02
43 5 0.04
44 28 0.21
45 2 0.01
46 41 0.30
47 45 0.33
48 7 0.05
49 3 0.02
50 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (44 bp):
TAAGACATGTCTGGGACATGCATCGGCTAAGAGTAGTGCTAGTG
Found at i:29407754 original size:140 final size:139
Alignment explanation
Indices: 29407502--29407932 Score: 540
Period size: 140 Copynumber: 3.1 Consensus size: 139
29407492 ATGCTTACTA
** * * **
29407502 CGACACTTTTGAGG-CGACACTTTTTTAAATGTTGGGATAGACTTGTCGACATACGTTTTGGCCA
1 CGACACTTTTG-GGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCA
* * *
29407566 ACTATTTGTATAAGAGTTGGGATATACATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTC
65 AC-CTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTC
*
29407631 CAACATTATGC
129 CAACACTATGC
*
29407642 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCAATATACACTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
* * * * * *
29407707 TCCTTTATATAAGAGTTGGGATATGTATGCCTAAGGCAACGCTTAAATAGGAGCCGACTTTATCC
66 -CCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCC
29407772 AACACTATGC
130 AACACTATGC
* * * * * *
29407782 CGAAACTTTTGGGCCGAAACTTTTCCTAAGTGTTGGGATAAACTTGTTGATGTACACTTTGTCCA
1 CGACACTTTTGGGCCGACAC-TTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCA
* * * * * *
29407847 ACCCTTTGTATAAGAGTTGGGATATGCATGCCTAAGACAATGCTTATATAAGATTAGGCTTTGTT
65 A-CCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTC
29407912 CAACACTATGC
129 CAACACTATGC
*
29407923 CGGCACTTTT
1 CGACACTTTT
29407933 CTAAGTGCTG
Statistics
Matches: 249, Mismatches: 39, Indels: 5
0.85 0.13 0.02
Matches are distributed among these distances:
139 2 0.01
140 136 0.55
141 111 0.45
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (139 bp):
CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGATATACACTTTGGCCAA
CCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACGCTTAAATAAGAGTCGGCTTTGTCCA
ACACTATGC
Found at i:29408507 original size:52 final size:52
Alignment explanation
Indices: 29408445--29408544 Score: 200
Period size: 52 Copynumber: 1.9 Consensus size: 52
29408435 TTAATAATTT
29408445 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCACGAC
1 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCACGAC
29408497 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCA
1 CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCA
29408545 TGACAAGCAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 48 1.00
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (52 bp):
CGAGTGAGAATAAGGTTTAAGATTCATATATCCTCATTACATTTTTCACGAC
Found at i:29409250 original size:21 final size:21
Alignment explanation
Indices: 29409226--29409272 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
29409216 TATCTAATTA
*
29409226 ATTTAGAGTTTAAAGTTTATG
1 ATTTAGAGTTTAAAGTTTAGG
* *
29409247 ATTTAGTGTTTATAGTTTAGG
1 ATTTAGAGTTTAAAGTTTAGG
29409268 ATTTA
1 ATTTA
29409273 ATGATTCTGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (21 bp):
ATTTAGAGTTTAAAGTTTAGG
Found at i:29409551 original size:109 final size:109
Alignment explanation
Indices: 29409360--29409577 Score: 400
Period size: 109 Copynumber: 2.0 Consensus size: 109
29409350 GACAGATTAA
* *
29409360 ATGAAGACGAGAGTGAAGGAGAGACCAATGTTACTAAAGAACAGTTTAGTCTGTGAATCAATTAA
1 ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGTGAATCAATTAA
29409425 CCGATGTCAACCAGAACAGAGCTATTTTTAATCAAGTTTTTTTT
66 CCGATGTCAACCAGAACAGAGCTATTTTTAATCAAGTTTTTTTT
* *
29409469 ATGAAGACGGGAGTGAAGGAGAGACCAATGCTACTAAAGAACGGTTTAGTCAGTGAATCAATTAA
1 ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGTGAATCAATTAA
29409534 CCGATGTCAACCAGAACAGAGCTATTTTTAATCAAGTTTTTTTT
66 CCGATGTCAACCAGAACAGAGCTATTTTTAATCAAGTTTTTTTT
29409578 TCACCCTTAT
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
109 105 1.00
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.28
Consensus pattern (109 bp):
ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGTGAATCAATTAA
CCGATGTCAACCAGAACAGAGCTATTTTTAATCAAGTTTTTTTT
Found at i:29413363 original size:37 final size:36
Alignment explanation
Indices: 29413174--29413654 Score: 278
Period size: 35 Copynumber: 13.3 Consensus size: 36
29413164 CGTACTTATT
* * * * *
29413174 CCAACCTTTTTAAGATTGTCTTA-AATGGGTTTATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCTATC
* * * *
29413209 CCAACCTTTTAAAGGCTGCCTTAG-ACGGGTTTATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCTATC
* * *
29413244 CCAACCTTTTTAAAGGTTGTCTTAGGCAA-G-GTATGTC
1 CCAACCTTTTT-AAGGTTGCCTTA-G-AACGAGTCTATC
** * ** *
29413281 TTAACCTTTTTAAAGTTGTATTAG-ACG-GCTTTATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAG-TCTATC
*
29413316 TCAACCTTTTTAAAGGTTGCCTTAGACACG-GTCTATC
1 CCAACCTTTTT-AAGGTTGCCTTAGA-ACGAGTCTATC
** * *
29413353 CCAGTCTTTTTAGGGTTGCTTTAG-ACGAGTCTATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCTATC
* *
29413388 CTAACCTTTTTTAAGGGTTGCCTTAG-ACAATGTCTATC
1 CCAACC-TTTTTAA-GGTTGCCTTAGAACGA-GTCTATC
29413426 CCAACCTTTTTAAGGTTGCCTTA-AACGAGTCTATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCTATC
* * * * *
29413461 CCAACCTTTTGCAAGAATTACCTTAGATAAG-GTTTATC
1 CCAACCTTTT-TAAG-GTTGCCTTAGA-ACGAGTCTATC
*
29413499 CCAACCTTTTTGAGGTTGCCTTA-AACGAGT-TGATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCT-ATC
** * *
29413534 TTAACCTTTTTTAAGGGTTGCCTCAG-ACTGA-CCTATC
1 CCAACC-TTTTTAA-GGTTGCCTTAGAAC-GAGTCTATC
* * * *
29413571 CCAACCTTTTTAAGGTTGTCTTA-TATGGGTCTATC
1 CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCTATC
* * *
29413606 CTAACCTTTTTCAAAGATTGGCCTT-G-ACTAGGTCTATC
1 CCAACCTTTTT--AAGGTT-GCCTTAGAACGA-GTCTATC
29413644 CCAACCTTTTT
1 CCAACCTTTTT
29413655 TAAAGGTCGG
Statistics
Matches: 350, Mismatches: 63, Indels: 63
0.74 0.13 0.13
Matches are distributed among these distances:
33 1 0.00
34 9 0.03
35 115 0.33
36 83 0.24
37 81 0.23
38 58 0.17
39 3 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (36 bp):
CCAACCTTTTTAAGGTTGCCTTAGAACGAGTCTATC
Found at i:29413423 original size:73 final size:73
Alignment explanation
Indices: 29413205--29413654 Score: 383
Period size: 73 Copynumber: 6.2 Consensus size: 73
29413195 TAAATGGGTT
* * * * * * * *
29413205 TATCCCAACCTTTTAAAGGCTGCCTTAGACGGGTTTATCCCAACC-TTTTTAAAGGTTGTCTTAG
1 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACCTTTTTTAAGGGTTGCCTTAG
* *
29413269 GCAAGGTA
66 ACAAGGTC
* ** * ** * * *
29413277 TGTCTTAACCTTTTTAAAGTTGTATTAGACG-GCTTTAT-CTCAACC-TTTTTAAAGGTTGCCTT
1 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAG-TCTATCCT-AACCTTTTTTAAGGGTTGCCTT
*
29413339 AGACACGGTC
64 AGACAAGGTC
** * * *
29413349 TATCCCAGTCTTTTTAGGGTTGCTTTAGACGAGTCTATCCTAACCTTTTTTAAGGGTTGCCTTAG
1 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACCTTTTTTAAGGGTTGCCTTAG
*
29413414 ACAATGTC
66 ACAAGGTC
* ** ** *
29413422 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCCAACCTTTTGCAAGAATTACCTTAG
1 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACCTTTTTTAAGGGTTGCCTTAG
* *
29413487 ATAAGGTT
66 ACAAGGTC
* * *
29413495 TATCCCAACCTTTTTGAGGTTGCCTTAAACGAGT-TGATCTTAACCTTTTTTAAGGGTTGCCTCA
1 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCT-ATCCTAACCTTTTTTAAGGGTTGCCTTA
* **
29413559 GAC-TGACC
65 GACAAGGTC
* * * * * * *
29413567 TATCCCAACCTTTTTAAGGTTGTCTTATATGGGTCTATCCTAACCTTTTTCAAAGATTGGCCTT-
1 TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACCTTTTTTAAGGGTT-GCCTTA
*
29413631 GACTAGGTC
65 GACAAGGTC
29413640 TATCCCAACCTTTTT
1 TATCCCAACCTTTTT
29413655 TAAAGGTCGG
Statistics
Matches: 302, Mismatches: 67, Indels: 17
0.78 0.17 0.04
Matches are distributed among these distances:
71 2 0.01
72 137 0.45
73 163 0.54
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (73 bp):
TATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACCTTTTTTAAGGGTTGCCTTAG
ACAAGGTC
Found at i:29413438 original size:145 final size:141
Alignment explanation
Indices: 29413173--29413654 Score: 427
Period size: 145 Copynumber: 3.3 Consensus size: 141
29413163 ACGTACTTAT
* * ** * ** * *
29413173 TCCAACCTTTTT-AAGATTGTCTTAAATGGGTTTATCCCAACCTTTTAAAGGCTGCCTTAGACGG
1 TCCAACCTTTTTAAAGATTGCCTTAGACAGGTCTATCCCAACCTTTTTGAGGTTGCCTTAGACGA
* * * * * * * ** * *
29413237 GTTTATCCCAACC-TTTTTAAAGGTTGTCTTAGGCAAGGTATGTCTTAACCTTTTTAAAGTTGTA
66 G-TTATCCTAACCTTTTTTAAGGGTTGCCTTAGACAATGTCTATCCCAACCTTTTTAAGGTTGTC
* *
29413301 TTAGACGGCTTTA
130 TTAAACGG-TCTA
* ** *
29413314 TCTCAACCTTTTTAAAGGTTGCCTTAGACACGGTCTATCCCAGTCTTTTT-AGGGTTGCTTTAGA
1 TC-CAACCTTTTTAAAGATTGCCTTAGACA-GGTCTATCCCAACCTTTTTGA-GGTTGCCTTAGA
29413378 CGAGTCTATCCTAACCTTTTTTAAGGGTTGCCTTAGACAATGTCTATCCCAACCTTTTTAAGGTT
63 CGAGT-TATCCTAACCTTTTTTAAGGGTTGCCTTAGACAATGTCTATCCCAACCTTTTTAAGGTT
*
29413443 GCCTTAAACGAGTCTA
127 GTCTTAAACG-GTCTA
** * * * *
29413459 TCCCAACCTTTTGCAAGAATTACCTTAGATAAGGTTTATCCCAACCTTTTTGAGGTTGCCTTAAA
1 T-CCAACCTTTTTAAAG-ATTGCCTTAGA-CAGGTCTATCCCAACCTTTTTGAGGTTGCCTTAGA
* * *
29413524 CGAGTTGATCTTAACCTTTTTTAAGGGTTGCCTCAGAC--TGACCTATCCCAACCTTTTTAAGGT
63 CGAGTT-ATCCTAACCTTTTTTAAGGGTTGCCTTAGACAATG-TCTATCCCAACCTTTTTAAGGT
**
29413587 TGTCTTATATGGGTCTA
126 TGTCTTA-AACGGTCTA
29413604 TCCTAACCTTTTTCAAAGATTGGCCTT-GACTAGGTCTATCCCAACCTTTTT
1 TCC-AACCTTTTT-AAAGATT-GCCTTAGAC-AGGTCTATCCCAACCTTTTT
29413655 TAAAGGTCGG
Statistics
Matches: 276, Mismatches: 47, Indels: 32
0.78 0.13 0.09
Matches are distributed among these distances:
141 2 0.01
142 10 0.04
143 13 0.05
144 41 0.15
145 128 0.46
146 80 0.29
147 2 0.01
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.38
Consensus pattern (141 bp):
TCCAACCTTTTTAAAGATTGCCTTAGACAGGTCTATCCCAACCTTTTTGAGGTTGCCTTAGACGA
GTTATCCTAACCTTTTTTAAGGGTTGCCTTAGACAATGTCTATCCCAACCTTTTTAAGGTTGTCT
TAAACGGTCTA
Found at i:29413671 original size:38 final size:38
Alignment explanation
Indices: 29413598--29413673 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
29413588 GTCTTATATG
* * *
29413598 GGTCTATCCTAACCTTTTTCAAAGATTGGCCTTGACTA
1 GGTCTATCCCAACCTTTTTCAAAGATCGGCATTGACTA
* *
29413636 GGTCTATCCCAACCTTTTTTAAAGGTCGGCATTGACTA
1 GGTCTATCCCAACCTTTTTCAAAGATCGGCATTGACTA
29413674 AGCCTTTCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (38 bp):
GGTCTATCCCAACCTTTTTCAAAGATCGGCATTGACTA
Found at i:29413687 original size:38 final size:38
Alignment explanation
Indices: 29413608--29413687 Score: 88
Period size: 38 Copynumber: 2.1 Consensus size: 38
29413598 GGTCTATCCT
* * * * *
29413608 AACCTTTTTCAAAGATTGGCCTTGACTAGGTCTATCCC
1 AACCTTTTTCAAAGATCGGCATTGACTAAGCCTATCAC
* * *
29413646 AACCTTTTTTAAAGGTCGGCATTGACTAAGCCTTTCAC
1 AACCTTTTTCAAAGATCGGCATTGACTAAGCCTATCAC
29413684 AACC
1 AACC
29413688 CTTTAATAAG
Statistics
Matches: 34, Mismatches: 8, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.33
Consensus pattern (38 bp):
AACCTTTTTCAAAGATCGGCATTGACTAAGCCTATCAC
Found at i:29414379 original size:44 final size:44
Alignment explanation
Indices: 29414308--29414515 Score: 163
Period size: 44 Copynumber: 4.7 Consensus size: 44
29414298 AAGATAGTGA
* *
29414308 ATCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGTCATAG
1 ATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGTCATAG
* *
29414352 A-CATTATCTCCTTGAAGTTGCAATGGAGCAGATTAAAGTTATAG
1 ATC-TTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGTCATAG
* ** * **
29414396 ATCTTATCTCCCTGATGTTGTGATGGAGTAGATCGAAG--ATAG
1 ATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGTCATAG
* * * * * * *
29414438 CAAATATTATCTCTCTAAAGTTTCAATAGAACAGATTAAAGCCATA-
1 ---ATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGTCATAG
* **
29414484 AGCCTTATCTCCCTGAAGTTGCAGCGGAGCAG
1 A-TCTTATCTCCCTGAAGTTGCAATGGAGCAG
29414516 GTTGAAGATA
Statistics
Matches: 124, Mismatches: 32, Indels: 16
0.72 0.19 0.09
Matches are distributed among these distances:
42 4 0.03
43 2 0.02
44 88 0.71
45 27 0.22
47 3 0.02
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (44 bp):
ATCTTATCTCCCTGAAGTTGCAATGGAGCAGATTAAAGTCATAG
Found at i:29415422 original size:13 final size:13
Alignment explanation
Indices: 29415404--29415434 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
29415394 GGAGGGAAGG
*
29415404 AAAGAAAGAAAGA
1 AAAGAAAGAAAAA
29415417 AAAGAAAGAAAAA
1 AAAGAAAGAAAAA
29415430 AAAGA
1 AAAGA
29415435 GAAAATTTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (13 bp):
AAAGAAAGAAAAA
Found at i:29416851 original size:18 final size:18
Alignment explanation
Indices: 29416818--29416920 Score: 98
Period size: 18 Copynumber: 5.7 Consensus size: 18
29416808 GTACTGGATG
* *
29416818 ACTGACTGTTATTGAATA
1 ACTGATTGTTACTGAATA
* *
29416836 ATTGATCGTTACTGAATA
1 ACTGATTGTTACTGAATA
* **
29416854 ACTGATTGCTACTGAGCA
1 ACTGATTGTTACTGAATA
*
29416872 AATGATTGTTACTGAATA
1 ACTGATTGTTACTGAATA
* *
29416890 ACTAATTGCTACTGAATA
1 ACTGATTGTTACTGAATA
* *
29416908 ATTGAATGTTACT
1 ACTGATTGTTACT
29416921 AAATGAAGCT
Statistics
Matches: 65, Mismatches: 20, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 65 1.00
ACGTcount: A:0.34, C:0.13, G:0.17, T:0.37
Consensus pattern (18 bp):
ACTGATTGTTACTGAATA
Found at i:29416918 original size:36 final size:36
Alignment explanation
Indices: 29416830--29416920 Score: 121
Period size: 36 Copynumber: 2.5 Consensus size: 36
29416820 TGACTGTTAT
*
29416830 TGAATAATTG-ATCGTTACTGAATAACTGATTGCTAC
1 TGAATAATTGAAT-GTTACTGAATAACTAATTGCTAC
** * *
29416866 TGAGCAAATGATTGTTACTGAATAACTAATTGCTAC
1 TGAATAATTGAATGTTACTGAATAACTAATTGCTAC
29416902 TGAATAATTGAATGTTACT
1 TGAATAATTGAATGTTACT
29416921 AAATGAAGCT
Statistics
Matches: 45, Mismatches: 9, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
36 44 0.98
37 1 0.02
ACGTcount: A:0.35, C:0.12, G:0.16, T:0.36
Consensus pattern (36 bp):
TGAATAATTGAATGTTACTGAATAACTAATTGCTAC
Found at i:29418745 original size:50 final size:50
Alignment explanation
Indices: 29418691--29418790 Score: 200
Period size: 50 Copynumber: 2.0 Consensus size: 50
29418681 ACAAACAACC
29418691 AAGAAACAACAAAGCAATCGAGAAAAAAACAAAACATGCTAAAGTCCTTT
1 AAGAAACAACAAAGCAATCGAGAAAAAAACAAAACATGCTAAAGTCCTTT
29418741 AAGAAACAACAAAGCAATCGAGAAAAAAACAAAACATGCTAAAGTCCTTT
1 AAGAAACAACAAAGCAATCGAGAAAAAAACAAAACATGCTAAAGTCCTTT
29418791 TTTTCCTTTT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.56, C:0.18, G:0.12, T:0.14
Consensus pattern (50 bp):
AAGAAACAACAAAGCAATCGAGAAAAAAACAAAACATGCTAAAGTCCTTT
Found at i:29419539 original size:3 final size:3
Alignment explanation
Indices: 29419525--29419584 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
29419515 TTTAACATTG
* * * * * *
29419525 TAT TAT TCT TAT TAT TAT TAT CAT TAC TAC TAC TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
29419573 TAG TAT TAT TAT
1 TAT TAT TAT TAT
29419585 ATTTCTTTTT
Statistics
Matches: 48, Mismatches: 9, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:29419561 original size:21 final size:21
Alignment explanation
Indices: 29419537--29419584 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
29419527 TTATTCTTAT
29419537 TATTATTATCATTACTACTAC
1 TATTATTATCATTACTACTAC
* * *
29419558 TATTATTATTATTACTAGTAT
1 TATTATTATCATTACTACTAC
29419579 TATTAT
1 TATTAT
29419585 ATTTCTTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.33, C:0.10, G:0.02, T:0.54
Consensus pattern (21 bp):
TATTATTATCATTACTACTAC
Found at i:29419942 original size:16 final size:16
Alignment explanation
Indices: 29419916--29419949 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
29419906 CTTTTAATTA
29419916 ATTTTTTACGCAT-TT
1 ATTTTTTACGCATGTT
29419931 ATTTTATTACGCATGTT
1 ATTTT-TTACGCATGTT
29419948 AT
1 AT
29419950 CATTGTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (16 bp):
ATTTTTTACGCATGTT
Found at i:29422925 original size:21 final size:21
Alignment explanation
Indices: 29422901--29422967 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29422891 TGTTTACTTC
29422901 TTATCAAGTTTGTTTTAAACA
1 TTATCAAGTTTGTTTTAAACA
* * * **
29422922 TTATCTACTATG-TTTACTTC-
1 TTATCAAGTTTGTTTTA-AACA
*
29422942 TTATCAAGTTTGTTGTAAACA
1 TTATCAAGTTTGTTTTAAACA
29422963 TTATC
1 TTATC
29422968 TACTATGTTG
Statistics
Matches: 32, Mismatches: 11, Indels: 6
0.65 0.22 0.12
Matches are distributed among these distances:
20 14 0.44
21 18 0.56
ACGTcount: A:0.28, C:0.13, G:0.09, T:0.49
Consensus pattern (21 bp):
TTATCAAGTTTGTTTTAAACA
Found at i:29422948 original size:41 final size:41
Alignment explanation
Indices: 29422891--29422976 Score: 163
Period size: 41 Copynumber: 2.1 Consensus size: 41
29422881 TATGAGAATG
*
29422891 TGTTTACTTCTTATCAAGTTTGTTTTAAACATTATCTACTA
1 TGTTTACTTCTTATCAAGTTTGTTGTAAACATTATCTACTA
29422932 TGTTTACTTCTTATCAAGTTTGTTGTAAACATTATCTACTA
1 TGTTTACTTCTTATCAAGTTTGTTGTAAACATTATCTACTA
29422973 TGTT
1 TGTT
29422977 GATTTGGTGT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 44 1.00
ACGTcount: A:0.26, C:0.14, G:0.09, T:0.51
Consensus pattern (41 bp):
TGTTTACTTCTTATCAAGTTTGTTGTAAACATTATCTACTA
Found at i:29422955 original size:20 final size:20
Alignment explanation
Indices: 29422891--29422955 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
29422881 TATGAGAATG
29422891 TGTTTACTTCTTATCAAGTT
1 TGTTTACTTCTTATCAAGTT
** * * *
29422911 TGTTTTA-AACATTATCTACTA
1 TG-TTTACTTC-TTATCAAGTT
29422932 TGTTTACTTCTTATCAAGTT
1 TGTTTACTTCTTATCAAGTT
29422952 TGTT
1 TGTT
29422956 GTAAACATTA
Statistics
Matches: 32, Mismatches: 10, Indels: 6
0.67 0.21 0.12
Matches are distributed among these distances:
20 18 0.56
21 14 0.44
ACGTcount: A:0.23, C:0.14, G:0.09, T:0.54
Consensus pattern (20 bp):
TGTTTACTTCTTATCAAGTT
Found at i:29422976 original size:21 final size:21
Alignment explanation
Indices: 29422911--29422977 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
29422901 TTATCAAGTT
*
29422911 TGTTTTAAACATTATCTACTA
1 TGTTGTAAACATTATCTACTA
** * * *
29422932 TGTT-TACTTC-TTATCAAGTT
1 TGTTGTA-AACATTATCTACTA
29422952 TGTTGTAAACATTATCTACTA
1 TGTTGTAAACATTATCTACTA
29422973 TGTTG
1 TGTTG
29422978 ATTTGGTGTT
Statistics
Matches: 33, Mismatches: 10, Indels: 6
0.67 0.20 0.12
Matches are distributed among these distances:
20 14 0.42
21 19 0.58
ACGTcount: A:0.27, C:0.13, G:0.10, T:0.49
Consensus pattern (21 bp):
TGTTGTAAACATTATCTACTA
Found at i:29424234 original size:6 final size:7
Alignment explanation
Indices: 29424212--29424237 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
29424202 AGAAAGAGTA
29424212 TTTAATT
1 TTTAATT
29424219 TTTAATT
1 TTTAATT
29424226 TTTAATT
1 TTTAATT
29424233 TTTAA
1 TTTAA
29424238 ATATAAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTAATT
Found at i:29431349 original size:16 final size:16
Alignment explanation
Indices: 29431305--29431356 Score: 86
Period size: 16 Copynumber: 3.2 Consensus size: 16
29431295 TTTGGTTCGC
*
29431305 TGTATTGGATTAAAGG
1 TGTATTGGATTAGAGG
*
29431321 CGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29431337 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
29431353 TGTA
1 TGTA
29431357 ATAGCTAATC
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 33 1.00
ACGTcount: A:0.27, C:0.02, G:0.35, T:0.37
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:29431421 original size:44 final size:45
Alignment explanation
Indices: 29431337--29431427 Score: 121
Period size: 45 Copynumber: 2.0 Consensus size: 45
29431327 GGATTAGAGG
* * *
29431337 TGTATTGGATTAGAGGTGTAATAGCTAATCCACTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
***
29431382 TGTAATGGAATAGAGGCGTAATAG-TAATCTTGTGTTTGGTTGAA
1 TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
29431426 TG
1 TG
29431428 GAATAGAGGT
Statistics
Matches: 40, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.27, C:0.07, G:0.29, T:0.37
Consensus pattern (45 bp):
TGTAATGGAATAGAGGCGTAATAGCTAATCCACTGTTTGGTTGAA
Found at i:29431663 original size:38 final size:38
Alignment explanation
Indices: 29431602--29432025 Score: 150
Period size: 39 Copynumber: 10.6 Consensus size: 38
29431592 ATATATTTTA
*
29431602 ATTAAAATATATAATTTAATGAAATTCTTAATAATTAAT
1 ATTAAAATAT-TAATTTACTGAAATTCTTAATAATTAAT
*** * *
29431641 ATTCTTATATTAATTTACTGAAA-TCATAAT-ATATGAT
1 ATTAAAATATTAATTTACTGAAATTCTTAATAAT-TAAT
* * * **
29431678 ACTGTAAAATATAAATTAACAT-AATTATTATTAAATATATTTTT
1 A-T-TAAAATATTAATTTAC-TGAA--ATTCTT-AATA-ATTAAT
*
29431722 AATTAAAATATATAATTTAATGAAATTCTTAATAATTAAT
1 -ATTAAAATAT-TAATTTACTGAAATTCTTAATAATTAAT
*** * *
29431762 ATTCTTATATTAATTTACTGAAA-TCATAAT-ATATGAT
1 ATTAAAATATTAATTTACTGAAATTCTTAATAAT-TAAT
* * * *
29431799 ACTGTAAAATATAAATTAACAT-AATTATTATTAAATATATT-TT
1 A-T-TAAAATATTAATTTAC-TGAA--ATTCTT-AATA-ATTAAT
* * *
29431842 AATTAAACTATATAATTTAATAAAATTCTTAATAATTAAT
1 -ATTAAAATAT-TAATTTACTGAAATTCTTAATAATTAAT
*** * * *
29431882 ATTCTTATATTAATTTACTCAAA-TCATAAT-ATATGAT
1 ATTAAAATATTAATTTACTGAAATTCTTAATAAT-TAAT
* * * *
29431919 ACTGTAAAATATAAATTAACAT-AATTATTATTAAATATATT-TT
1 A-T-TAAAATATTAATTTAC-TGAA--ATTCTT-AATA-ATTAAT
*
29431962 AATTAAAATATATAATTTAATGAAATTCTTAATAATTAAT
1 -ATTAAAATAT-TAATTTACTGAAATTCTTAATAATTAAT
***
29432002 ATTCTTATATTAATTTACTGAAAT
1 ATTAAAATATTAATTTACTGAAAT
29432026 CATAATATAT
Statistics
Matches: 278, Mismatches: 66, Indels: 83
0.65 0.15 0.19
Matches are distributed among these distances:
36 6 0.02
37 30 0.11
38 51 0.18
39 72 0.26
40 17 0.06
41 17 0.06
42 28 0.10
43 36 0.13
44 14 0.05
45 7 0.03
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (38 bp):
ATTAAAATATTAATTTACTGAAATTCTTAATAATTAAT
Found at i:29431713 original size:120 final size:120
Alignment explanation
Indices: 29431575--29432100 Score: 998
Period size: 120 Copynumber: 4.4 Consensus size: 120
29431565 ATCATATTTA
29431575 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
29431640 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
29431695 AACATAATTATTATTAAATATATTTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTA
1 AACATAATTATTATTAAATATA-TTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTA
29431760 ATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
65 ATATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
* *
29431816 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
*
29431881 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
29431936 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
29432001 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
66 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
*
29432056 AACATAATTATTATTAAACTATATTTTAATTAAACTATATAATTT
1 AACATAATTATTATTAAA-TATATTTTAATTAAAATATATAATTT
29432101 GAACATCAAA
Statistics
Matches: 397, Mismatches: 7, Indels: 3
0.98 0.02 0.01
Matches are distributed among these distances:
120 252 0.63
121 145 0.37
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:29432081 original size:241 final size:241
Alignment explanation
Indices: 29431575--29432100 Score: 1009
Period size: 241 Copynumber: 2.2 Consensus size: 241
29431565 ATCATATTTA
* *
29431575 AACATAATTATTATTAAATATATTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
*
29431640 TATTCTTATATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
29431705 TTATTAAATATATTTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAATATTCTTAT
131 TTATTAAATATATTTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAATATTCTTAT
29431770 ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
29431816 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
29431881 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
66 TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
29431946 TTATTAAATATA-TTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAATATTCTTAT
131 TTATTAAATATATTTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAATATTCTTAT
29432010 ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
196 ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
29432056 AACATAATTATTATTAAACTATATTTTAATTAAACTATATAATTT
1 AACATAATTATTATTAAA-TATATTTTAATTAAACTATATAATTT
29432101 GAACATCAAA
Statistics
Matches: 281, Mismatches: 3, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
240 116 0.41
241 165 0.59
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.44
Consensus pattern (241 bp):
AACATAATTATTATTAAATATATTTTAATTAAACTATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATTAATTTACTCAAATCATAATATATGATACTGTAAAATATAAATTAACATAATTA
TTATTAAATATATTTTTAATTAAAATATATAATTTAATGAAATTCTTAATAATTAATATTCTTAT
ATTAATTTACTGAAATCATAATATATGATACTGTAAAATATAAATT
Found at i:29437880 original size:13 final size:13
Alignment explanation
Indices: 29437862--29437900 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
29437852 CAGCTAAACT
29437862 GAAACAGAAGGAA
1 GAAACAGAAGGAA
*
29437875 GAAACAGAAAGAA
1 GAAACAGAAGGAA
*
29437888 GAAATAGAAGGAA
1 GAAACAGAAGGAA
29437901 CGGCTAAGTT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.64, C:0.05, G:0.28, T:0.03
Consensus pattern (13 bp):
GAAACAGAAGGAA
Found at i:29445049 original size:25 final size:25
Alignment explanation
Indices: 29445007--29445055 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
29444997 AAATTATTTA
*
29445007 AAAATTAAAAAACAAAAATATCATT
1 AAAATTAAAAAACAAAAAAATCATT
* **
29445032 AAAATTAGAAAATTAAAAAATCAT
1 AAAATTAAAAAACAAAAAAATCAT
29445056 AAGTTATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.67, C:0.06, G:0.02, T:0.24
Consensus pattern (25 bp):
AAAATTAAAAAACAAAAAAATCATT
Found at i:29445526 original size:28 final size:29
Alignment explanation
Indices: 29445491--29445553 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
29445481 TTACAGAACT
* *
29445491 AAAATACAGG-GCTAAACTTAT-AATAAA
1 AAAATACAGGAGCCAAACTGATAAATAAA
29445518 AAAAGTACAGGAGCCAAACTGATAAATAAA
1 AAAA-TACAGGAGCCAAACTGATAAATAAA
*
29445548 ATAATA
1 AAAATA
29445554 TAAGTATTAA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 4 0.13
28 6 0.20
29 11 0.37
30 9 0.30
ACGTcount: A:0.57, C:0.11, G:0.13, T:0.19
Consensus pattern (29 bp):
AAAATACAGGAGCCAAACTGATAAATAAA
Found at i:29449169 original size:47 final size:45
Alignment explanation
Indices: 29449101--29449188 Score: 124
Period size: 47 Copynumber: 1.9 Consensus size: 45
29449091 CTAATTAAAA
* *
29449101 AAAAGTGAAATTTAGATAATAATTTGTGGATTAAACTTTTTTTTAAT
1 AAAAGTGAAATTTAAATAATAATTTGAGGATT-AA-TTTTTTTTAAT
29449148 AAAAGT-ATAATTTAAATAATAATTTGAGGATTAATTTTTTT
1 AAAAGTGA-AATTTAAATAATAATTTGAGGATTAATTTTTTT
29449189 AAAATAAATT
Statistics
Matches: 38, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
45 7 0.18
46 3 0.08
47 28 0.74
ACGTcount: A:0.42, C:0.01, G:0.11, T:0.45
Consensus pattern (45 bp):
AAAAGTGAAATTTAAATAATAATTTGAGGATTAATTTTTTTTAAT
Found at i:29453974 original size:22 final size:22
Alignment explanation
Indices: 29453948--29453990 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
29453938 TCGAAGTTAA
*
29453948 TAGATGATCCATACATAAATAG
1 TAGATGATCCATAAATAAATAG
*
29453970 TAGATGATCTATAAATAAATA
1 TAGATGATCCATAAATAAATA
29453991 CTCTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.09, G:0.12, T:0.30
Consensus pattern (22 bp):
TAGATGATCCATAAATAAATAG
Found at i:29454574 original size:108 final size:108
Alignment explanation
Indices: 29454371--29454579 Score: 244
Period size: 108 Copynumber: 1.9 Consensus size: 108
29454361 TTTGGGTTAA
* ** * **
29454371 TATTTGGTACGTTGGTAGTGAACTTTTTTTATTTCACAAATAGTCTTACAAAATTATCATGTGTC
1 TATTTGGTACATTGACAGTGAACTTTTTTTATTTCACAAACAACCTTACAAAATTATCATGTGTC
* ** * * *
29454436 CCCTTTTTTTAAAAATATTTTGTTATATTTTACTATGGATGAG
66 CCATTTTTAAAAAAAAATTTTGTAACATTTTACTATGGATGAG
*
29454479 TATTTGGTACATTGACAGTGTAACTTTTTTTATTTCACAAACAACCTTA-AAATTTGA-CATGTG
1 TATTTGGTACATTGACAGTG-AACTTTTTTTATTTCACAAACAACCTTACAAAATT-ATCATGTG
*
29454542 TCTCATTTTTAAAAAAAAATTTCT-TAACATTTTACTAT
64 TCCCATTTTTAAAAAAAAATTT-TGTAACATTTTACTAT
29454580 TATAGGACAC
Statistics
Matches: 84, Mismatches: 14, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
108 57 0.68
109 27 0.32
ACGTcount: A:0.31, C:0.12, G:0.11, T:0.45
Consensus pattern (108 bp):
TATTTGGTACATTGACAGTGAACTTTTTTTATTTCACAAACAACCTTACAAAATTATCATGTGTC
CCATTTTTAAAAAAAAATTTTGTAACATTTTACTATGGATGAG
Found at i:29458295 original size:19 final size:19
Alignment explanation
Indices: 29458256--29458315 Score: 59
Period size: 20 Copynumber: 3.1 Consensus size: 19
29458246 TTTAAAAAAA
*
29458256 TTGT-ATAATTTTTATTCTT
1 TTGTAATAATTTTTAAT-TT
29458275 TTGTAATAATTTTTAATTT
1 TTGTAATAATTTTTAATTT
** *
29458294 TTAAAATATTTTTTGAATTT
1 TTGTAATAATTTTT-AATTT
29458314 TT
1 TT
29458316 TAAATTTTAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.49
20 18 0.51
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (19 bp):
TTGTAATAATTTTTAATTT
Found at i:29461753 original size:22 final size:22
Alignment explanation
Indices: 29461728--29461800 Score: 78
Period size: 22 Copynumber: 3.3 Consensus size: 22
29461718 AAAAAATTCC
29461728 ACAAGTAAGATTAAAATGATAG
1 ACAAGTAAGATTAAAATGATAG
* **
29461750 ACAAGTGAA-ATTTAAAA-AATTCC
1 ACAAGT-AAGA-TTAAAATGA-TAG
29461773 ACAAGTAAGATTAAAATGATAG
1 ACAAGTAAGATTAAAATGATAG
29461795 ACAAGT
1 ACAAGT
29461801 GTATATAAAG
Statistics
Matches: 40, Mismatches: 6, Indels: 10
0.71 0.11 0.18
Matches are distributed among these distances:
22 23 0.57
23 17 0.43
ACGTcount: A:0.53, C:0.08, G:0.15, T:0.23
Consensus pattern (22 bp):
ACAAGTAAGATTAAAATGATAG
Found at i:29461772 original size:45 final size:45
Alignment explanation
Indices: 29461708--29461801 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
29461698 GTATACTATT
29461708 AGTGAAATTTAAAAAATTCCACAAGTAAGATTAAAATGATAGACA
1 AGTGAAATTTAAAAAATTCCACAAGTAAGATTAAAATGATAGACA
29461753 AGTGAAATTTAAAAAATTCCACAAGTAAGATTAAAATGATAGACA
1 AGTGAAATTTAAAAAATTCCACAAGTAAGATTAAAATGATAGACA
29461798 AGTG
1 AGTG
29461802 TATATAAAGT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.52, C:0.09, G:0.15, T:0.24
Consensus pattern (45 bp):
AGTGAAATTTAAAAAATTCCACAAGTAAGATTAAAATGATAGACA
Found at i:29466035 original size:20 final size:20
Alignment explanation
Indices: 29466012--29466077 Score: 57
Period size: 20 Copynumber: 3.3 Consensus size: 20
29466002 GCTGAAAGGT
29466012 AAAGCAAATTATAAATCGCA
1 AAAGCAAATTATAAATCGCA
* **
29466032 AAAGCAGCAA-CATCAAA--GGT
1 AAAGCA--AATTAT-AAATCGCA
29466052 AAAGCAAATTATAAATCGCA
1 AAAGCAAATTATAAATCGCA
29466072 AAAGCA
1 AAAGCA
29466078 GCAACATCAT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 5 0.15
19 2 0.06
20 20 0.59
21 2 0.06
22 5 0.15
ACGTcount: A:0.55, C:0.17, G:0.14, T:0.15
Consensus pattern (20 bp):
AAAGCAAATTATAAATCGCA
Found at i:29466050 original size:40 final size:40
Alignment explanation
Indices: 29466006--29466086 Score: 162
Period size: 40 Copynumber: 2.0 Consensus size: 40
29465996 AAAATTGCTG
29466006 AAAGGTAAAGCAAATTATAAATCGCAAAAGCAGCAACATC
1 AAAGGTAAAGCAAATTATAAATCGCAAAAGCAGCAACATC
29466046 AAAGGTAAAGCAAATTATAAATCGCAAAAGCAGCAACATC
1 AAAGGTAAAGCAAATTATAAATCGCAAAAGCAGCAACATC
29466086 A
1 A
29466087 TATTTATTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.53, C:0.17, G:0.15, T:0.15
Consensus pattern (40 bp):
AAAGGTAAAGCAAATTATAAATCGCAAAAGCAGCAACATC
Found at i:29469062 original size:31 final size:31
Alignment explanation
Indices: 29469000--29469059 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
29468990 CAATGTTCAA
* *
29469000 TTAATTTTTTATATTTATCTTTATTTAAATT
1 TTAATTATTTATATTTATATTTATTTAAATT
29469031 TTAATTATTTAT-TTTATAATTATATTTAA
1 TTAATTATTTATATTTAT-ATT-TATTTAA
29469060 TTTCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 13 0.52
32 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (31 bp):
TTAATTATTTATATTTATATTTATTTAAATT
Found at i:29471435 original size:16 final size:16
Alignment explanation
Indices: 29471390--29471437 Score: 69
Period size: 16 Copynumber: 3.0 Consensus size: 16
29471380 CCGGCCGGAA
*
29471390 CCCCTCTCTCCTTTCT
1 CCCCTCTCTCTTTTCT
29471406 CCCCTCTCTCTTTTCT
1 CCCCTCTCTCTTTTCT
* *
29471422 CCCTTCTCTTTTTTCT
1 CCCCTCTCTCTTTTCT
29471438 TTTTTTCTTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (16 bp):
CCCCTCTCTCTTTTCT
Found at i:29472084 original size:24 final size:25
Alignment explanation
Indices: 29472056--29472123 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 25
29472046 TATATGTATC
* *
29472056 ATATTTTTTTAATGTTGTATTAT-T
1 ATATTTTTTTAATATTATATTATAT
29472080 ATA---TTTTAATATTATATTATAT
1 ATATTTTTTTAATATTATATTATAT
29472102 ATATTTTTTCT--TATTATATTAT
1 ATATTTTTT-TAATATTATATTAT
29472124 GTACATATAT
Statistics
Matches: 37, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
21 15 0.41
22 4 0.11
24 14 0.38
25 3 0.08
26 1 0.03
ACGTcount: A:0.31, C:0.01, G:0.03, T:0.65
Consensus pattern (25 bp):
ATATTTTTTTAATATTATATTATAT
Found at i:29472115 original size:21 final size:21
Alignment explanation
Indices: 29472036--29472108 Score: 73
Period size: 21 Copynumber: 3.5 Consensus size: 21
29472026 ATACTTTAAA
29472036 TATTATATTTT-ATATGTATCA-
1 TATTATATTTTAATAT-TAT-AT
* *
29472057 TATT-T-TTTTAATGTTGTAT
1 TATTATATTTTAATATTATAT
29472076 TATTATATTTTAATATTATAT
1 TATTATATTTTAATATTATAT
29472097 TATATATATTTT
1 TAT-TATATTTT
29472109 TTCTTATTAT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
18 1 0.02
19 10 0.23
20 5 0.12
21 19 0.44
22 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.04, T:0.63
Consensus pattern (21 bp):
TATTATATTTTAATATTATAT
Found at i:29472138 original size:26 final size:24
Alignment explanation
Indices: 29472079--29472138 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 24
29472069 GTTGTATTAT
** *
29472079 TATATTTTAATATTATATTATATA
1 TATATTTTCTTATTATATTATACA
*
29472103 TATTTTTTCTTATTATATTATGTACA
1 TATATTTTCTTATTATATTA--TACA
29472129 TATATTTTCT
1 TATATTTTCT
29472139 AATATTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 17 0.59
26 12 0.41
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.62
Consensus pattern (24 bp):
TATATTTTCTTATTATATTATACA
Found at i:29472225 original size:21 final size:24
Alignment explanation
Indices: 29472188--29472244 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
29472178 TTACTAGTTA
29472188 TATATTATTTATATATT-TCC-ATG
1 TATA-TATTTATATATTGTCCTATG
29472211 TATATATTT-TATATTGTCCTATG
1 TATATATTTATATATTGTCCTATG
*
29472234 TACATATTTAT
1 TATATATTTAT
29472245 GTGGTGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.20
22 8 0.27
23 15 0.50
24 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (24 bp):
TATATATTTATATATTGTCCTATG
Found at i:29472442 original size:28 final size:28
Alignment explanation
Indices: 29472399--29472460 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
29472389 TTATCTTATG
*
29472399 TATATATTCTTAAATACTAT-TATATGTA
1 TATATATTCTTAAATACCATAT-TATGTA
* *
29472427 TATATATTTTTTAATACCATATTATGTA
1 TATATATTCTTAAATACCATATTATGTA
29472455 TATATA
1 TATATA
29472461 GTAGTGTCCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
28 29 0.97
29 1 0.03
ACGTcount: A:0.39, C:0.06, G:0.03, T:0.52
Consensus pattern (28 bp):
TATATATTCTTAAATACCATATTATGTA
Found at i:29484833 original size:74 final size:72
Alignment explanation
Indices: 29484750--29485046 Score: 252
Period size: 74 Copynumber: 4.1 Consensus size: 72
29484740 TCATTTTTGT
*
29484750 TTTCAAAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCGAGGCACGCCGAGGTATTTT
1 TTTC-AAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTATTTT
*
29484815 CAAATTCTAC
63 CAAATTCTGC
** * * *
29484825 TTTCAAAAAAATCAACTCATATCACGAGAGGTGAGTTGAGCCT-TGGCTTACG-TGTTGAGTCAC
1 TTTC-AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGC--ACGCTG-AG-GT-AT
*
29484888 TTTCAATTTCTG-
60 TTTCAAATTCTGC
** * *
29484900 TTT----TTATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTC-
1 TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-AGGCACGCTGAGGTATTTTCA
*
29484960 AATTGCTGT
65 AATT-CTGC
* * *
29484969 TTGTC-AAAAATCAACTCATAATTGTGAGAGGTGAGTTGAGCCTCAGGGCACACTGAGGTAGTTT
1 TT-TCAAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCA-GGCACGCTGAGGTATTTT
*
29485033 CAATTTCTGC
63 CAAATTCTGC
29485043 TTTC
1 TTTC
29485047 CGATTTCTGC
Statistics
Matches: 179, Mismatches: 26, Indels: 36
0.74 0.11 0.15
Matches are distributed among these distances:
67 3 0.02
68 8 0.04
69 4 0.02
70 35 0.20
71 2 0.01
72 6 0.03
73 13 0.07
74 69 0.39
75 28 0.16
76 11 0.06
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.32
Consensus pattern (72 bp):
TTTCAAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGCACGCTGAGGTATTTTCAA
ATTCTGC
Found at i:29485197 original size:87 final size:87
Alignment explanation
Indices: 29484955--29485213 Score: 356
Period size: 89 Copynumber: 2.9 Consensus size: 87
29484945 CGCTGAGGTA
* * *
29484955 TTTTCAATTGCTGTTTGTCAAAAATCAACTCATAATTGTGAGAGGTGAGTTGAGCCTCAGGGCAC
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGGCAC
* * *
29485020 ACTGAGGTAGTTTCAATTTCTGC
65 GCTGAGGTATTTTCAATTTCCGC
* * * * *
29485043 TTTCCGATTTCTGCTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACA
1 TTTTCAATTTCTGTTTTTC--AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
* *
29485108 CGCTGAGGTATTTTCGATTTCCGT
64 CGCTGAGGTATTTTCAATTTCCGC
* *
29485132 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
1 TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
29485197 CTGAGGTATTTTCAATT
66 CTGAGGTATTTTCAATT
29485214 ACTGTTTGTC
Statistics
Matches: 148, Mismatches: 21, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
87 59 0.40
88 14 0.09
89 61 0.41
90 14 0.09
ACGTcount: A:0.26, C:0.18, G:0.22, T:0.35
Consensus pattern (87 bp):
TTTTCAATTTCTGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
CTGAGGTATTTTCAATTTCCGC
Found at i:29485264 original size:161 final size:160
Alignment explanation
Indices: 29485064--29485386 Score: 574
Period size: 161 Copynumber: 2.0 Consensus size: 160
29485054 TGCTTTTCAA
29485064 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCGATTTC
1 AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCGATTTC
*
29485129 CGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGC
66 CGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
* *
29485194 ACGCTGAGGTATTTTCAATTACTGTTTGTC
131 ACGCTGAGGTATTCTCAATTAATGTTTGTC
* *
29485224 AAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCGATTT
1 AAAAATCAACTCAT-ATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCGATTT
29485289 CCGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
65 CCGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGA
* *
29485354 CACGCTGAGTTATTCTCAATTAATGTTTTTC
130 CACGCTGAGGTATTCTCAATTAATGTTTGTC
29485385 AA
1 AA
29485387 TTTATGCTTT
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
160 14 0.09
161 141 0.91
ACGTcount: A:0.27, C:0.17, G:0.22, T:0.34
Consensus pattern (160 bp):
AAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGACACGCTGAGGTATTTTCGATTTC
CGTTTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGAC
ACGCTGAGGTATTCTCAATTAATGTTTGTC
Found at i:29485270 original size:74 final size:73
Alignment explanation
Indices: 29485132--29485288 Score: 262
Period size: 74 Copynumber: 2.1 Consensus size: 73
29485122 CGATTTCCGT
* *
29485132 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACG
1 TTTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
29485197 CTGAGGTA
66 CTGAGGTA
29485205 TTTTCAA-TTACTGTTTGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTA-TGTTTGTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
29485269 CGCTGAGGTA
64 CGCTGAGGTA
*
29485279 TTTTCGATTT
1 TTTTCAATTT
29485289 CCGTTTTTCA
Statistics
Matches: 78, Mismatches: 3, Indels: 4
0.92 0.04 0.05
Matches are distributed among these distances:
72 3 0.04
73 28 0.36
74 45 0.58
75 2 0.03
ACGTcount: A:0.26, C:0.17, G:0.24, T:0.34
Consensus pattern (73 bp):
TTTTCAATTTATGTTTGTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
CTGAGGTA
Found at i:29485360 original size:87 final size:87
Alignment explanation
Indices: 29485205--29485432 Score: 334
Period size: 87 Copynumber: 2.6 Consensus size: 87
29485195 CGCTGAGGTA
*
29485205 TTTTCAA-TTACTGTTTGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
1 TTTTCAATTTA-TGTTTTTCAAAAATCAACTCAT-ATTGCGAGAGGTGAGTTGAGCCTCAGGGCA
* * **
29485269 CGCTGAGGTATTTTCGATTTCCGT
64 CGCTGAGGTATTCTCAATTAACGT
29485293 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTC-GGGACAC
1 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGG-CAC
* *
29485357 GCTGAGTTATTCTCAATTAATGT
65 GCTGAGGTATTCTCAATTAACGT
* *
29485380 TTTTCAATTTATGCTTTTCAAAAATCAACTCATATTGCGAGAAGTGAGTTGAG
1 TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAG
29485433 TCTTTGCTCA
Statistics
Matches: 129, Mismatches: 9, Indels: 5
0.90 0.06 0.03
Matches are distributed among these distances:
86 3 0.02
87 95 0.74
88 28 0.22
89 3 0.02
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.36
Consensus pattern (87 bp):
TTTTCAATTTATGTTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGGCACG
CTGAGGTATTCTCAATTAACGT
Found at i:29485463 original size:250 final size:249
Alignment explanation
Indices: 29484905--29485432 Score: 842
Period size: 250 Copynumber: 2.1 Consensus size: 249
29484895 TTCTGTTTTT
* *
29484905 ATCAACTCATATTGCGGGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTGCTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTGTT
*
29484970 TGTCAAAAATCAACTCATAATTGTGAGAGGTGAGTTGAGCCTCAGGGCACACTGAGGTAGTTTCA
66 TGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCACACTGAGGTAGTTTCA
* * *
29485035 ATTTCTGCTTTCCGATTTCTGCTTTTCAAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCC
131 ATTTCCGCTTTCCAATTTATGCTTTTC-AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCC
* * ** *
29485100 TCAGGACACGCTGAGGTATTTTCGATTTCCGTTTTTCAATTTATGTTTTTCAAAA
195 TCAGGACACGCTGAGGTATTCTCAATTAACGTTTTTCAATTTATGCTTTTCAAAA
29485155 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTGTT
1 ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTGTT
* * *
29485220 TGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCACGCTGAGGTATTTTCG
66 TGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCACACTGAGGTAGTTTCA
* * * *
29485285 ATTTCCGTTTTTCAATTTATGTTTTTC-AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
131 ATTTCCGCTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
* * *
29485349 CGGGACACGCTGAGTTATTCTCAATTAATGTTTTTCAATTTATGCTTTTCAAAA
196 CAGGACACGCTGAGGTATTCTCAATTAACGTTTTTCAATTTATGCTTTTCAAAA
*
29485403 ATCAACTCATATTGCGAGAAGTGAGTTGAG
1 ATCAACTCATATTGCGAGAGGTGAGTTGAG
29485433 TCTTTGCTCA
Statistics
Matches: 256, Mismatches: 22, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
248 111 0.43
250 145 0.57
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (249 bp):
ATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGGCACGCTGAGGTATTTTCAATTACTGTT
TGTCAAAAATCAACTCATAATTGCGAGAGGTGAGTTGAGCCTCAGGGCACACTGAGGTAGTTTCA
ATTTCCGCTTTCCAATTTATGCTTTTCAAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCT
CAGGACACGCTGAGGTATTCTCAATTAACGTTTTTCAATTTATGCTTTTCAAAA
Found at i:29487414 original size:25 final size:25
Alignment explanation
Indices: 29487386--29487434 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
29487376 AATGTTGTAT
29487386 TATTATATTTTAATATTATATTATA
1 TATTATATTTTAATATTATATTATA
* * *
29487411 TATTTTTTTTTCATATTATATTAT
1 TATTATATTTTAATATTATATTAT
29487435 GTACATATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (25 bp):
TATTATATTTTAATATTATATTATA
Found at i:29487537 original size:21 final size:24
Alignment explanation
Indices: 29487500--29487556 Score: 75
Period size: 23 Copynumber: 2.5 Consensus size: 24
29487490 TTACTAGTTA
29487500 TATATTATTTATATATT-TCC-ATG
1 TATA-TATTTATATATTGTCCTATG
29487523 TATATATTT-TATATTGTCCTATG
1 TATATATTTATATATTGTCCTATG
*
29487546 TACATATTTAT
1 TATATATTTAT
29487557 GTGGTGTTAT
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 6 0.20
22 8 0.27
23 15 0.50
24 1 0.03
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (24 bp):
TATATATTTATATATTGTCCTATG
Found at i:29487755 original size:28 final size:30
Alignment explanation
Indices: 29487712--29487773 Score: 85
Period size: 28 Copynumber: 2.1 Consensus size: 30
29487702 TTATCTTATG
*
29487712 TATATATTCTTAAATACTAT-TATATGTATA
1 TATATATTCTTAAATACCATAT-TATGTATA
29487742 TATATATT-TT-AATACCATATTATGTATA
1 TATATATTCTTAAATACCATATTATGTATA
29487770 TATA
1 TATA
29487774 GTAGTGTCCA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
28 19 0.63
29 3 0.10
30 8 0.27
ACGTcount: A:0.40, C:0.06, G:0.03, T:0.50
Consensus pattern (30 bp):
TATATATTCTTAAATACCATATTATGTATA
Found at i:29495514 original size:20 final size:21
Alignment explanation
Indices: 29495476--29495514 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 21
29495466 ATCAAAATTA
*
29495476 ATTTTCTCAAAAATCATTTAG
1 ATTTTCTCAAAAATAATTTAG
*
29495497 ATTTT-TCAAAATTAATTT
1 ATTTTCTCAAAAATAATTT
29495515 TTCAAGAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (21 bp):
ATTTTCTCAAAAATAATTTAG
Found at i:29499763 original size:24 final size:24
Alignment explanation
Indices: 29499710--29499765 Score: 94
Period size: 24 Copynumber: 2.3 Consensus size: 24
29499700 TTTGTTCGTA
*
29499710 AACATATTCAATTATATGTTCATG
1 AACATGTTCAATTATATGTTCATG
*
29499734 AACATGTTCAATTATATGTTCATT
1 AACATGTTCAATTATATGTTCATG
29499758 AACATGTT
1 AACATGTT
29499766 TGAAACACAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (24 bp):
AACATGTTCAATTATATGTTCATG
Found at i:29499787 original size:34 final size:34
Alignment explanation
Indices: 29499749--29499831 Score: 96
Period size: 34 Copynumber: 2.4 Consensus size: 34
29499739 GTTCAATTAT
*
29499749 ATGTTCATTAACATGTTTGAA-ACACATTCCTTTA
1 ATGTTCATGAACATGTTT-AAGACACATTCCTTTA
* * *
29499783 ATGTTCGTGAACATGTTTAAGACACGTTCGTTTA
1 ATGTTCATGAACATGTTTAAGACACATTCCTTTA
**
29499817 ATGTTTGTGAACATG
1 ATGTTCATGAACATG
29499832 GTCAATTAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
33 2 0.05
34 41 0.95
ACGTcount: A:0.29, C:0.14, G:0.17, T:0.40
Consensus pattern (34 bp):
ATGTTCATGAACATGTTTAAGACACATTCCTTTA
Found at i:29500247 original size:31 final size:31
Alignment explanation
Indices: 29500212--29500274 Score: 108
Period size: 31 Copynumber: 2.0 Consensus size: 31
29500202 AGTATTTTTC
*
29500212 TTCTAATTTTCTTTTTTTCAAATTTTAACAT
1 TTCTAATTTTCTTTTTTTCAAATTTCAACAT
*
29500243 TTCTAATTTTGTTTTTTTCAAATTTCAACAT
1 TTCTAATTTTCTTTTTTTCAAATTTCAACAT
29500274 T
1 T
29500275 GTACTAAGAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.25, C:0.13, G:0.02, T:0.60
Consensus pattern (31 bp):
TTCTAATTTTCTTTTTTTCAAATTTCAACAT
Found at i:29508079 original size:21 final size:20
Alignment explanation
Indices: 29508054--29508092 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
29508044 TTTTTAAAAT
*
29508054 TTTAAAGAAACTGATTATATA
1 TTTAAAGAAAATG-TTATATA
29508075 TTTAAAGAAAATGTTATA
1 TTTAAAGAAAATGTTATA
29508093 AATAATTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.49, C:0.03, G:0.10, T:0.38
Consensus pattern (20 bp):
TTTAAAGAAAATGTTATATA
Found at i:29511205 original size:6 final size:6
Alignment explanation
Indices: 29511194--29511222 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
29511184 CTTCTCTTTT
29511194 CCCTTC CCCTTC CCCTTC CCCTTC CCCTT
1 CCCTTC CCCTTC CCCTTC CCCTTC CCCTT
29511223 TCACTGAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.00, C:0.66, G:0.00, T:0.34
Consensus pattern (6 bp):
CCCTTC
Found at i:29513802 original size:31 final size:31
Alignment explanation
Indices: 29513766--29513826 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
29513756 TCTTTAGGTT
29513766 GATGGATGAATTTTATTCACTCATTTACTTG
1 GATGGATGAATTTTATTCACTCATTTACTTG
29513797 GATGGATGAATTTTATTCACTCATTTACTT
1 GATGGATGAATTTTATTCACTCATTTACTT
29513827 AGGAATGTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.46
Consensus pattern (31 bp):
GATGGATGAATTTTATTCACTCATTTACTTG
Found at i:29514629 original size:17 final size:17
Alignment explanation
Indices: 29514609--29514641 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
29514599 AACATATTGT
29514609 ATTTATTTT-ATAATTTG
1 ATTT-TTTTCATAATTTG
29514626 ATTTTTTTCATAATTT
1 ATTTTTTTCATAATTT
29514642 TCTCATTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.27, C:0.03, G:0.03, T:0.67
Consensus pattern (17 bp):
ATTTTTTTCATAATTTG
Found at i:29515424 original size:20 final size:19
Alignment explanation
Indices: 29515399--29515452 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
29515389 ATTTGTGTGC
29515399 TTATTATATTTATAATATAA
1 TTATTATATTT-TAATATAA
* *
29515419 TTATTAATATTTTTATTTAA
1 TTATT-ATATTTTAATATAA
*
29515439 TTATTATATATTAA
1 TTATTATATTTTAA
29515453 AAATAATATA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 7 0.24
20 16 0.55
21 6 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TTATTATATTTTAATATAA
Found at i:29517206 original size:9 final size:8
Alignment explanation
Indices: 29517191--29517215 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
29517181 TATCCCACAA
29517191 ATTTTTTT
1 ATTTTTTT
29517199 ATTTTTTT
1 ATTTTTTT
29517207 ATTTTTTT
1 ATTTTTTT
29517215 A
1 A
29517216 ATAAATGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (8 bp):
ATTTTTTT
Found at i:29528792 original size:26 final size:26
Alignment explanation
Indices: 29528743--29528812 Score: 115
Period size: 26 Copynumber: 2.7 Consensus size: 26
29528733 TCAGCATTTT
29528743 CCACGACCCTCAA-GTATTGGACTGC
1 CCACGACCCTCAAGGTATTGGACTGC
*
29528768 CCACGACCTTCAAGGTATTGGACTGC
1 CCACGACCCTCAAGGTATTGGACTGC
*
29528794 CCACGACCCTCTAGGTATT
1 CCACGACCCTCAAGGTATT
29528813 AGGGCTAACA
Statistics
Matches: 41, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
25 12 0.29
26 29 0.71
ACGTcount: A:0.23, C:0.34, G:0.20, T:0.23
Consensus pattern (26 bp):
CCACGACCCTCAAGGTATTGGACTGC
Found at i:29533106 original size:31 final size:32
Alignment explanation
Indices: 29533071--29533131 Score: 79
Period size: 32 Copynumber: 1.9 Consensus size: 32
29533061 TTCATACTTT
29533071 ATATTTCA-TAACACTGGGCCGAAGCCTTTTC
1 ATATTTCATTAACACTGGGCCGAAGCCTTTTC
* ** *
29533102 ATATTTTATTATTACTGGGCCGATGCCTTT
1 ATATTTCATTAACACTGGGCCGAAGCCTTT
29533132 ACCGGTATGG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
31 7 0.28
32 18 0.72
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.39
Consensus pattern (32 bp):
ATATTTCATTAACACTGGGCCGAAGCCTTTTC
Found at i:29533415 original size:24 final size:24
Alignment explanation
Indices: 29533319--29533414 Score: 140
Period size: 24 Copynumber: 4.0 Consensus size: 24
29533309 GCTTTATCAT
*
29533319 ATAACTGGAGGCCT-AGCCTCTTTTA
1 ATAACTGG-GGCATAAGCC-CTTTTA
*
29533344 ATAACTGGGGCAAAAGCCCTTTTA
1 ATAACTGGGGCATAAGCCCTTTTA
*
29533368 ATAACTGGGGCATAAGCCCTTTTG
1 ATAACTGGGGCATAAGCCCTTTTA
29533392 ATAACTGGGGCATAAGCCCTTTT
1 ATAACTGGGGCATAAGCCCTTTT
29533415 GTACTTCCTC
Statistics
Matches: 66, Mismatches: 4, Indels: 3
0.90 0.05 0.04
Matches are distributed among these distances:
24 54 0.82
25 12 0.18
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (24 bp):
ATAACTGGGGCATAAGCCCTTTTA
Found at i:29533486 original size:9 final size:9
Alignment explanation
Indices: 29533472--29533524 Score: 52
Period size: 9 Copynumber: 5.4 Consensus size: 9
29533462 ACATCATGTG
29533472 CATATCATA
1 CATATCATA
29533481 CATATCATGTA
1 CATATCA--TA
29533492 CATATCATA
1 CATATCATA
* *
29533501 CATGTCATGTG
1 CATATCA--TA
29533512 CATATCATA
1 CATATCATA
29533521 CATA
1 CATA
29533525 CCATGTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 8
0.75 0.08 0.17
Matches are distributed among these distances:
9 20 0.56
11 16 0.44
ACGTcount: A:0.38, C:0.21, G:0.08, T:0.34
Consensus pattern (9 bp):
CATATCATA
Found at i:29533489 original size:20 final size:20
Alignment explanation
Indices: 29533464--29533530 Score: 107
Period size: 20 Copynumber: 3.4 Consensus size: 20
29533454 TTATAAATAC
29533464 ATCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29533484 ATCATGTACATATCATACAT
1 ATCATGTGCATATCATACAT
*
29533504 GTCATGTGCATATCATACAT
1 ATCATGTGCATATCATACAT
*
29533524 ACCATGT
1 ATCATGT
29533531 TTATCAAAAT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.21, G:0.10, T:0.34
Consensus pattern (20 bp):
ATCATGTGCATATCATACAT
Found at i:29533493 original size:11 final size:11
Alignment explanation
Indices: 29533464--29533519 Score: 57
Period size: 11 Copynumber: 5.5 Consensus size: 11
29533454 TTATAAATAC
*
29533464 ATCATGTGCAT
1 ATCATGTACAT
29533475 ATCA--TACAT
1 ATCATGTACAT
29533484 ATCATGTACAT
1 ATCATGTACAT
29533495 ATCA--TACAT
1 ATCATGTACAT
* *
29533504 GTCATGTGCAT
1 ATCATGTACAT
29533515 ATCAT
1 ATCAT
29533520 ACATACCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
9 16 0.43
11 21 0.57
ACGTcount: A:0.34, C:0.20, G:0.11, T:0.36
Consensus pattern (11 bp):
ATCATGTACAT
Found at i:29533613 original size:25 final size:25
Alignment explanation
Indices: 29533567--29533614 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
29533557 ATACCTAAAC
* * * *
29533567 CCTAGGGGTATAATGGTTATTTTTA
1 CCTAGGGGCAAAACGGTCATTTTTA
29533592 CCTAGGGGCAAAACGGTCATTTT
1 CCTAGGGGCAAAACGGTCATTTT
29533615 CATGTTATAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.35
Consensus pattern (25 bp):
CCTAGGGGCAAAACGGTCATTTTTA
Found at i:29537522 original size:20 final size:20
Alignment explanation
Indices: 29537475--29537513 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
29537465 ATACCTTCTA
29537475 AATTTTTATAATATTTTTTC
1 AATTTTTATAATATTTTTTC
29537495 AATTTTTAT-ATATTATTTT
1 AATTTTTATAATATT-TTTT
29537514 GATTTTTTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (20 bp):
AATTTTTATAATATTTTTTC
Found at i:29537931 original size:23 final size:25
Alignment explanation
Indices: 29537872--29537932 Score: 65
Period size: 23 Copynumber: 2.6 Consensus size: 25
29537862 ATATATATAA
* **
29537872 AAAAGTTTAAAAATATTATTTTCAT
1 AAAATTTTAAAAATATTATAATCAT
*
29537897 AAAATTCT-AAAATA-TATAATCAT
1 AAAATTTTAAAAATATTATAATCAT
29537920 -AAATTTTAAAAAT
1 AAAATTTTAAAAAT
29537933 TCAAAATAAT
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
22 6 0.20
23 12 0.40
24 6 0.20
25 6 0.20
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (25 bp):
AAAATTTTAAAAATATTATAATCAT
Found at i:29537959 original size:21 final size:19
Alignment explanation
Indices: 29537935--29537976 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
29537925 TTAAAAATTC
29537935 AAAATAATA-TATAAAAACT
1 AAAA-AATATTATAAAAACT
* *
29537954 AAAAAATGTTATAAAAATT
1 AAAAAATATTATAAAAACT
29537973 AAAA
1 AAAA
29537977 GGTATCTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
18 3 0.15
19 17 0.85
ACGTcount: A:0.69, C:0.02, G:0.02, T:0.26
Consensus pattern (19 bp):
AAAAAATATTATAAAAACT
Found at i:29542766 original size:46 final size:46
Alignment explanation
Indices: 29542713--29542837 Score: 225
Period size: 46 Copynumber: 2.7 Consensus size: 46
29542703 GAGTAAGCAC
*
29542713 CATTGAGATAGCTTC-GACTATGTATTGGCACTTTGTGTGCGAGATT
1 CATTGAGATAGCTTCAG-CTATGTATTGGCACTTCGTGTGCGAGATT
29542759 CATTGAGATAGCTTCAGCTATGTATTGGCACTTCGTGTGCGAGATT
1 CATTGAGATAGCTTCAGCTATGTATTGGCACTTCGTGTGCGAGATT
29542805 CATTGAGATAGCTTCAGCTATGTATTGGCACTT
1 CATTGAGATAGCTTCAGCTATGTATTGGCACTT
29542838 AGGGTGCAAG
Statistics
Matches: 77, Mismatches: 1, Indels: 2
0.96 0.01 0.03
Matches are distributed among these distances:
46 76 0.99
47 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.25, T:0.36
Consensus pattern (46 bp):
CATTGAGATAGCTTCAGCTATGTATTGGCACTTCGTGTGCGAGATT
Found at i:29545233 original size:25 final size:25
Alignment explanation
Indices: 29545205--29545278 Score: 76
Period size: 25 Copynumber: 3.0 Consensus size: 25
29545195 CAAGCTTCTC
*
29545205 TGAGCTGAATAATAGGAAGCTCATG
1 TGAGCTAAATAATAGGAAGCTCATG
* ** *
29545230 TGAGCTAAATTACGGGAAGCTTATG
1 TGAGCTAAATAATAGGAAGCTCATG
* * *
29545255 AGTGCTAAATATTAGGAAGCTCAT
1 TGAGCTAAATAATAGGAAGCTCAT
29545279 AAGAGCTGTG
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.35, C:0.12, G:0.26, T:0.27
Consensus pattern (25 bp):
TGAGCTAAATAATAGGAAGCTCATG
Found at i:29546882 original size:44 final size:44
Alignment explanation
Indices: 29546805--29546889 Score: 107
Period size: 44 Copynumber: 1.9 Consensus size: 44
29546795 ATGCAGGGGT
* * * * *
29546805 CACACGGTCGTGTGGTCGGGCTGTGTGGACATTCGAAATAGAGG
1 CACACGGTCATGTGGTCAGGCCGTATGGACATTCAAAATAGAGG
* *
29546849 CACACGGTCATTTGGTCAGGCCGTATGGGCATTCAAAATAG
1 CACACGGTCATGTGGTCAGGCCGTATGGACATTCAAAATAG
29546890 GGGTACATGG
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
44 34 1.00
ACGTcount: A:0.24, C:0.20, G:0.33, T:0.24
Consensus pattern (44 bp):
CACACGGTCATGTGGTCAGGCCGTATGGACATTCAAAATAGAGG
Found at i:29559738 original size:15 final size:15
Alignment explanation
Indices: 29559718--29559774 Score: 89
Period size: 15 Copynumber: 3.9 Consensus size: 15
29559708 CGATGAATTT
*
29559718 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
29559733 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
29559748 ATTGAAATTATATTG
1 ATTGAAATTATATTG
29559763 ATTG-AATTATAT
1 ATTGAAATTATAT
29559775 AATATATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
14 8 0.21
15 31 0.79
ACGTcount: A:0.37, C:0.00, G:0.12, T:0.51
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:29560173 original size:23 final size:23
Alignment explanation
Indices: 29560143--29560229 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
29560133 GCTTTACTGA
* *
29560143 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
29560166 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
29560187 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
29560209 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
29560230 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:29565200 original size:20 final size:20
Alignment explanation
Indices: 29565163--29565202 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
29565153 TAGGGATTAA
*
29565163 ATGAAAATAAATTCGAAATT
1 ATGAAAATAAACTCGAAATT
*
29565183 ATGAAAATAAACTGGAAATT
1 ATGAAAATAAACTCGAAATT
29565203 TAATAGTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.05, G:0.12, T:0.28
Consensus pattern (20 bp):
ATGAAAATAAACTCGAAATT
Found at i:29565742 original size:15 final size:15
Alignment explanation
Indices: 29565722--29565779 Score: 98
Period size: 15 Copynumber: 3.9 Consensus size: 15
29565712 CGATGAATTT
*
29565722 ATTGAATTTATATTG
1 ATTGAAATTATATTG
*
29565737 ATTGAAATTATTTTG
1 ATTGAAATTATATTG
29565752 ATTGAAATTATATTG
1 ATTGAAATTATATTG
29565767 ATTGAAATTATAT
1 ATTGAAATTATAT
29565780 AATATATATG
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 40 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (15 bp):
ATTGAAATTATATTG
Found at i:29566182 original size:23 final size:23
Alignment explanation
Indices: 29566152--29566238 Score: 92
Period size: 21 Copynumber: 4.0 Consensus size: 23
29566142 GCTTTACTGA
* *
29566152 TCAGGCACTTTATGTGTCGTATT
1 TCAGGCACCTCATGTGTCGTATT
*
29566175 TCAGGCACCTCGTGTGTCGTA--
1 TCAGGCACCTCATGTGTCGTATT
*
29566196 TCAGGCACCTCGTGTGTCGT-TT
1 TCAGGCACCTCATGTGTCGTATT
* *
29566218 T-AGGCACTTTATGTGTCGTAT
1 TCAGGCACCTCATGTGTCGTAT
29566239 ACTGATCAGG
Statistics
Matches: 55, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
21 35 0.64
22 2 0.04
23 18 0.33
ACGTcount: A:0.15, C:0.22, G:0.25, T:0.38
Consensus pattern (23 bp):
TCAGGCACCTCATGTGTCGTATT
Found at i:29574530 original size:14 final size:15
Alignment explanation
Indices: 29574507--29574540 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
29574497 ATATAATGCG
29574507 CACT-ACACACAAA-
1 CACTCACACACAAAT
29574520 CACTCACACACAAAT
1 CACTCACACACAAAT
29574535 CACTCA
1 CACTCA
29574541 GAATCATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 4 0.21
14 9 0.47
15 6 0.32
ACGTcount: A:0.47, C:0.41, G:0.00, T:0.12
Consensus pattern (15 bp):
CACTCACACACAAAT
Done.