Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold11
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: 5230303
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 140504 characters in sequence are not A, C, G, or T
File 18 of 29
Found at i:2613031 original size:2 final size:2
Alignment explanation
Indices: 2613024--2613064 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
2613014 CATTAGTCTA
2613024 AT AT AT AT AT 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 AT AT AT AT AT A
2613065 AGCATGAATG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2620543 original size:2 final size:2
Alignment explanation
Indices: 2620536--2620560 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2620526 ACAACAGTAA
2620536 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
2620561 CACACCTGGC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2623188 original size:2 final size:2
Alignment explanation
Indices: 2623181--2623212 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2623171 ACACTTCGGT
*
2623181 TA TA TA TA TA TA TA CA 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
2623213 ACTAGGTTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2625181 original size:22 final size:21
Alignment explanation
Indices: 2625144--2625194 Score: 57
Period size: 22 Copynumber: 2.4 Consensus size: 21
2625134 ATAATTTTAC
*
2625144 AAAATTTAAAAGTTAATATTT
1 AAAATTTAAAAGTTAAAATTT
* **
2625165 GATAATTTAAATTTTAAAATTT
1 -AAAATTTAAAAGTTAAAATTT
2625187 AAAATTTA
1 AAAATTTA
2625195 TCATAATTCT
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (21 bp):
AAAATTTAAAAGTTAAAATTT
Found at i:2625182 original size:7 final size:7
Alignment explanation
Indices: 2625144--2625194 Score: 57
Period size: 7 Copynumber: 7.1 Consensus size: 7
2625134 ATAATTTTAC
2625144 AAAATTT
1 AAAATTT
*
2625151 AAAAGTT
1 AAAATTT
*
2625158 AATATTT
1 AAAATTT
*
2625165 GATAATTT
1 -AAAATTT
*
2625173 AAATTTT
1 AAAATTT
2625180 AAAATTT
1 AAAATTT
2625187 AAAATTT
1 AAAATTT
2625194 A
1 A
2625195 TCATAATTCT
Statistics
Matches: 35, Mismatches: 8, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
7 30 0.86
8 5 0.14
ACGTcount: A:0.51, C:0.00, G:0.04, T:0.45
Consensus pattern (7 bp):
AAAATTT
Found at i:2627128 original size:20 final size:20
Alignment explanation
Indices: 2627103--2627181 Score: 76
Period size: 20 Copynumber: 4.0 Consensus size: 20
2627093 TTTATAATAA
2627103 TATTAAAATATT-ATTTTTAT
1 TATT-AAATATTAATTTTTAT
2627123 TATT-AATATTAATATTTTA-
1 TATTAAATATTAAT-TTTTAT
*
2627142 TATTTAAT-TTAAATTTTTAT
1 TATTAAATATT-AATTTTTAT
*
2627162 TATTAAAATAATAATTTTTA
1 TATT-AAATATTAATTTTTA
2627182 CGAGCTATCT
Statistics
Matches: 50, Mismatches: 2, Indels: 13
0.77 0.03 0.20
Matches are distributed among these distances:
18 6 0.12
19 13 0.26
20 19 0.38
21 11 0.22
22 1 0.02
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTAAATATTAATTTTTAT
Found at i:2627142 original size:26 final size:25
Alignment explanation
Indices: 2627083--2627147 Score: 67
Period size: 26 Copynumber: 2.5 Consensus size: 25
2627073 TTCAAAAATT
*
2627083 TATTTTACTGTTTATAATAATATTAA
1 TATTTTA-TATTTATAATAATATTAA
* * * *
2627109 AATATTATTTTTATTATTAATATTAA
1 TATTTTATATTTA-TAATAATATTAA
2627135 TATTTTATATTTA
1 TATTTTATATTTA
2627148 ATTTAAATTT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
25 5 0.16
26 26 0.84
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (25 bp):
TATTTTATATTTATAATAATATTAA
Found at i:2627153 original size:19 final size:18
Alignment explanation
Indices: 2627115--2627162 Score: 53
Period size: 21 Copynumber: 2.5 Consensus size: 18
2627105 TTAAAATATT
2627115 ATTTTTATTATTAATATTAA
1 ATTTTTA-T-TTAATATTAA
2627135 TATTTTATATTTAAT-TTAA
1 -ATTTT-TATTTAATATTAA
2627154 ATTTTTATT
1 ATTTTTATT
2627163 ATTAAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
17 4 0.15
18 5 0.19
19 4 0.15
20 5 0.19
21 6 0.23
22 2 0.08
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
ATTTTTATTTAATATTAA
Found at i:2627407 original size:3 final size:3
Alignment explanation
Indices: 2627399--2627424 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2627389 AAGCCCCAAA
2627399 AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AA
2627425 ACTCCCAACA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:2635564 original size:2 final size:2
Alignment explanation
Indices: 2635496--2635556 Score: 104
Period size: 2 Copynumber: 30.5 Consensus size: 2
2635486 AAAGCTGAAA
2635496 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
* *
2635538 AA AG AG AG AG GG AG AG AG A
1 AG AG AG AG AG AG AG AG AG A
2635557 CTGAGAGACA
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2636968 original size:12 final size:12
Alignment explanation
Indices: 2636953--2636977 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2636943 AAAAAATAAT
2636953 TAAAATATGATA
1 TAAAATATGATA
2636965 TAAAATATGATA
1 TAAAATATGATA
2636977 T
1 T
2636978 GATTTGAAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (12 bp):
TAAAATATGATA
Found at i:2639861 original size:20 final size:21
Alignment explanation
Indices: 2639822--2639861 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
2639812 AATTAATCGT
**
2639822 ATCATATTCATATATCAAATA
1 ATCATATTCATATAAAAAATA
2639843 ATCATA-TCATATAAAAAAT
1 ATCATATTCATATAAAAAAT
2639862 GAGACATGAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (21 bp):
ATCATATTCATATAAAAAATA
Found at i:2642370 original size:2 final size:2
Alignment explanation
Indices: 2642363--2642388 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2642353 TGAGTAAACC
2642363 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
2642389 GCCCTCTGTG
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:2642608 original size:31 final size:32
Alignment explanation
Indices: 2642573--2642640 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
2642563 GTCGGATTTC
2642573 AGACTTCAA-AGGTACCTTTTTTTTTT-TTCTG
1 AGACTTCAATAGGTA-CTTTTTTTTTTATTCTG
* *
2642604 AGAC-TGAATTTGGTACTTTTTTTTTTATTCTG
1 AGACTTCAA-TAGGTACTTTTTTTTTTATTCTG
2642636 AGACT
1 AGACT
2642641 GAATTTTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
30 3 0.10
31 15 0.48
32 13 0.42
ACGTcount: A:0.21, C:0.13, G:0.15, T:0.51
Consensus pattern (32 bp):
AGACTTCAATAGGTACTTTTTTTTTTATTCTG
Found at i:2642619 original size:32 final size:32
Alignment explanation
Indices: 2642583--2642646 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
2642573 AGACTTCAAA
2642583 GGTACCTTTTTTTTTT-TTCTGAGACTGAATTT
1 GGTA-CTTTTTTTTTTATTCTGAGACTGAATTT
2642615 GGTACTTTTTTTTTTATTCTGAGACTGAATTT
1 GGTACTTTTTTTTTTATTCTGAGACTGAATTT
2642647 TAATGAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
31 11 0.35
32 20 0.65
ACGTcount: A:0.17, C:0.11, G:0.16, T:0.56
Consensus pattern (32 bp):
GGTACTTTTTTTTTTATTCTGAGACTGAATTT
Found at i:2642829 original size:23 final size:23
Alignment explanation
Indices: 2642802--2642845 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
2642792 ATATGATAAA
2642802 TATTAAA-ATTTTAATTTTAAATT
1 TATTAAATA-TTTAATTTTAAATT
*
2642825 TATTAAATATTTATTTTTAAA
1 TATTAAATATTTAATTTTAAA
2642846 AATAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 18 0.95
24 1 0.05
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (23 bp):
TATTAAATATTTAATTTTAAATT
Found at i:2647063 original size:18 final size:18
Alignment explanation
Indices: 2647031--2647069 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
2647021 TTTTTTTTTT
*
2647031 TTTTTAAATATATCTTCAA
1 TTTTGAAATATATCTT-AA
2647050 TTTTGAAATA-ATCTTAA
1 TTTTGAAATATATCTTAA
2647067 TTT
1 TTT
2647070 ATATTTTACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 5 0.26
18 5 0.26
19 9 0.47
ACGTcount: A:0.36, C:0.08, G:0.03, T:0.54
Consensus pattern (18 bp):
TTTTGAAATATATCTTAA
Found at i:2647971 original size:25 final size:22
Alignment explanation
Indices: 2647938--2647991 Score: 63
Period size: 25 Copynumber: 2.3 Consensus size: 22
2647928 TTATCAACTT
* *
2647938 TATTCATTTATAAAATATATAATTA
1 TATTTATTTAAAAAATAT-TAA--A
2647963 TATTTATTTAAAAAATATTAAA
1 TATTTATTTAAAAAATATTAAA
2647985 TATTTAT
1 TATTTAT
2647992 ACGTAACAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
22 8 0.30
24 3 0.11
25 16 0.59
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (22 bp):
TATTTATTTAAAAAATATTAAA
Found at i:2648007 original size:2 final size:2
Alignment explanation
Indices: 2648000--2648036 Score: 58
Period size: 2 Copynumber: 18.5 Consensus size: 2
2647990 ATACGTAACA
2648000 AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AGT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT A
2648037 GATAATTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.03
2 30 0.91
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2648375 original size:16 final size:15
Alignment explanation
Indices: 2648354--2648392 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
2648344 TAATTAGTTT
2648354 AATTTAATTAAATAAA
1 AATTTAATTAAAT-AA
* *
2648370 AATTTAATTTAATCA
1 AATTTAATTAAATAA
2648385 AATTTAAT
1 AATTTAAT
2648393 GTTAGAATAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTTAATTAAATAA
Found at i:2648502 original size:22 final size:21
Alignment explanation
Indices: 2648472--2648525 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
2648462 CGATTTTTTC
* *
2648472 GGTTGAGATGGACTTGAGTTTA
1 GGTTTAGATGG-CTTGAATTTA
2648494 GGTTTAGATTGGCTTGAATTTA
1 GGTTTAGA-TGGCTTGAATTTA
2648516 GGTTTAGATG
1 GGTTTAGATG
2648526 TATTTTTAGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 24 0.83
23 3 0.10
ACGTcount: A:0.22, C:0.04, G:0.33, T:0.41
Consensus pattern (21 bp):
GGTTTAGATGGCTTGAATTTA
Found at i:2648665 original size:9 final size:9
Alignment explanation
Indices: 2648649--2648757 Score: 64
Period size: 9 Copynumber: 11.9 Consensus size: 9
2648639 AAATTAATCG
2648649 AATTAATT-
1 AATTAATTA
2648657 AATTAAATTA
1 AATT-AATTA
2648667 ATATT-A-TA
1 A-ATTAATTA
*
2648675 AATCAATTAA
1 AATTAATT-A
*
2648685 AATTTAAATCA
1 AA-TT-AATTA
2648696 AATTAATTA
1 AATTAATTA
* *
2648705 TATCAATTA
1 AATTAATTA
*
2648714 AATTAAATTT
1 AATT-AATTA
2648724 AATTAATT-
1 AATTAATTA
**
2648732 TTTTAATTA
1 AATTAATTA
*
2648741 AATTAATTT
1 AATTAATTA
2648750 AATTAATT
1 AATTAATT
2648758 TTTACTTTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 19
0.70 0.13 0.17
Matches are distributed among these distances:
7 2 0.03
8 14 0.18
9 37 0.48
10 14 0.18
11 7 0.09
12 3 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (9 bp):
AATTAATTA
Found at i:2648684 original size:17 final size:17
Alignment explanation
Indices: 2648661--2648725 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 17
2648651 TTAATTAATT
2648661 AAATTAATATTATAAATC
1 AAATTAATATT-TAAATC
*
2648679 -AATTAAAATTTAAATC
1 AAATTAATATTTAAATC
* * *
2648695 AAATTAATTATATCAATT
1 AAATTAA-TATTTAAATC
2648713 AAATTAA-ATTTAA
1 AAATTAATATTTAA
2648726 TTAATTTTTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
16 10 0.26
17 15 0.39
18 13 0.34
ACGTcount: A:0.55, C:0.05, G:0.00, T:0.40
Consensus pattern (17 bp):
AAATTAATATTTAAATC
Found at i:2648760 original size:27 final size:27
Alignment explanation
Indices: 2648709--2648760 Score: 97
Period size: 26 Copynumber: 2.0 Consensus size: 27
2648699 TAATTATATC
2648709 AATTAAATTAAATTTAATTAATTTTTT
1 AATTAAATTAAATTTAATTAATTTTTT
2648736 AATTAAATT-AATTTAATTAATTTTT
1 AATTAAATTAAATTTAATTAATTTTT
2648761 ACTTTTTTAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
26 16 0.64
27 9 0.36
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (27 bp):
AATTAAATTAAATTTAATTAATTTTTT
Found at i:2648854 original size:9 final size:11
Alignment explanation
Indices: 2648835--2648941 Score: 59
Period size: 10 Copynumber: 9.9 Consensus size: 11
2648825 TTAATAATTT
2648835 TAAATATAATA
1 TAAATATAATA
2648846 TAAA-A-AATA
1 TAAATATAATA
2648855 TTAAATATAATA
1 -TAAATATAATA
*
2648867 TAAAT-TATTA
1 TAAATATAATA
* *
2648877 AAAAT-TTATA
1 TAAATATAATA
2648887 T-AATATTAATTA
1 TAAATA-TAA-TA
*
2648899 TTAATATAAATA
1 TAAATAT-AATA
2648911 TTAAATA-AATA
1 -TAAATATAATA
*
2648922 TATAATAT--TT
1 TA-AATATAATA
2648932 TAAATATAAT
1 TAAATATAAT
2648942 TATATAATTT
Statistics
Matches: 75, Mismatches: 8, Indels: 26
0.69 0.07 0.24
Matches are distributed among these distances:
9 12 0.16
10 21 0.28
11 21 0.28
12 10 0.13
13 11 0.15
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATATAATA
Found at i:2648913 original size:37 final size:37
Alignment explanation
Indices: 2648851--2648976 Score: 116
Period size: 37 Copynumber: 3.4 Consensus size: 37
2648841 TAATATAAAA
*
2648851 AATATTAAATATAATATAAATTATTAAA-AATTTATAT
1 AATATTAAATATAATATAAATTATTAAATAA-ATATAT
*
2648888 AATATTAATTATTAATATAAA-TATTAAATAAATATAT
1 AATATTAAATA-TAATATAAATTATTAAATAAATATAT
* * *
2648925 AATATTTTAAATATAAT-TATATAATTTAA-AAATATAT
1 AATA--TTAAATATAATATAAATTATTAAATAAATATAT
*
2648962 GAAGTATCAAATATA
1 -AA-TATTAAATATA
2648977 TCACAATCAC
Statistics
Matches: 75, Mismatches: 7, Indels: 14
0.78 0.07 0.15
Matches are distributed among these distances:
37 45 0.60
38 22 0.29
39 8 0.11
ACGTcount: A:0.56, C:0.01, G:0.02, T:0.42
Consensus pattern (37 bp):
AATATTAAATATAATATAAATTATTAAATAAATATAT
Found at i:2648954 original size:19 final size:20
Alignment explanation
Indices: 2648828--2648954 Score: 101
Period size: 19 Copynumber: 6.5 Consensus size: 20
2648818 TATAAATTTA
* *
2648828 ATAATTTTAAATATAATATAA
1 ATAATATTAAATATAAT-TAT
*
2648849 AAAATATTAAATATAA-TAT
1 ATAATATTAAATATAATTAT
*
2648868 A-AATTATTAAA-A-ATTTAT
1 ATAA-TATTAAATATAATTAT
*
2648886 ATAATATTAATTATTAA-TAT
1 ATAATATTAAATA-TAATTAT
2648906 A-AATATTAAATA-AA-TAT
1 ATAATATTAAATATAATTAT
2648923 ATAATATTTTAAATATAATTAT
1 ATAATA--TTAAATATAATTAT
2648945 ATAAT-TTAAA
1 ATAATATTAAA
2648955 AATATATGAA
Statistics
Matches: 88, Mismatches: 7, Indels: 24
0.74 0.06 0.20
Matches are distributed among these distances:
17 7 0.08
18 17 0.19
19 28 0.32
20 11 0.12
21 17 0.19
22 8 0.09
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (20 bp):
ATAATATTAAATATAATTAT
Found at i:2653863 original size:22 final size:19
Alignment explanation
Indices: 2653838--2653888 Score: 68
Period size: 22 Copynumber: 2.6 Consensus size: 19
2653828 AATGTTTAGG
2653838 TTATTAAATATTAATTTTAAAA
1 TTATTAAATATT-A-TTT-AAA
2653860 TTATTAAATATTATTTAAA
1 TTATTAAATATTATTTAAA
2653879 TT-TTAAATAT
1 TTATTAAATAT
2653889 AAAATGCTTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.28
19 5 0.17
20 3 0.10
21 1 0.03
22 12 0.41
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTAAATATTATTTAAA
Found at i:2654698 original size:14 final size:14
Alignment explanation
Indices: 2654679--2654739 Score: 68
Period size: 14 Copynumber: 4.1 Consensus size: 14
2654669 TTTTTTTATC
2654679 AAATTATATTATTA
1 AAATTATATTATTA
2654693 AAATTATATTATTAA
1 AAATTATATTATT-A
* *
2654708 TAAATTAAATTATTT
1 -AAATTATATTATTA
*
2654723 AAATTATTTTTATTA
1 AAATTA-TATTATTA
2654738 AA
1 AA
2654740 TAATTTTAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
14 19 0.49
15 8 0.21
16 12 0.31
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (14 bp):
AAATTATATTATTA
Found at i:2654713 original size:30 final size:31
Alignment explanation
Indices: 2654679--2654738 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
2654669 TTTTTTTATC
*
2654679 AAATTATATTATTAAAATTA-TATTATTAAT
1 AAATTAAATTATTAAAATTATTATTATTAAT
* *
2654709 AAATTAAATTATTTAAATTATTTTTATTAA
1 AAATTAAATTATTAAAATTATTATTATTAA
2654739 ATAATTTTAA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 18 0.69
31 8 0.31
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (31 bp):
AAATTAAATTATTAAAATTATTATTATTAAT
Found at i:2655189 original size:26 final size:25
Alignment explanation
Indices: 2655155--2655210 Score: 80
Period size: 25 Copynumber: 2.3 Consensus size: 25
2655145 GATTTTTAAA
*
2655155 TATTT-AAATTTAAATTTATTTAATT
1 TATTTAAAATTTAAA-TTAATTAATT
2655180 TATTTAAAATTTAAATTAATTAATT
1 TATTTAAAATTTAAATTAATTAATT
2655205 T-TTTAA
1 TATTTAA
2655211 TTCATATTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
24 5 0.17
25 15 0.52
26 9 0.31
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
TATTTAAAATTTAAATTAATTAATT
Found at i:2655210 original size:33 final size:34
Alignment explanation
Indices: 2655149--2655221 Score: 89
Period size: 33 Copynumber: 2.1 Consensus size: 34
2655139 ATTTGTGATT
2655149 TTTAAATATTTAAATTTAAATTTATTTAATT-TA
1 TTTAAATATTTAAATTTAAATTTATTTAATTATA
*
2655182 TTTAAA-ATTTAAATTAATTAATTT-TTTAATTCATA
1 TTTAAATATTTAAATT--TAAATTTATTTAATT-ATA
2655217 TTTAA
1 TTTAA
2655222 TTTAAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 6
0.83 0.02 0.14
Matches are distributed among these distances:
32 9 0.26
33 13 0.37
34 6 0.17
35 7 0.20
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (34 bp):
TTTAAATATTTAAATTTAAATTTATTTAATTATA
Found at i:2655225 original size:16 final size:15
Alignment explanation
Indices: 2655154--2655226 Score: 55
Period size: 16 Copynumber: 4.9 Consensus size: 15
2655144 TGATTTTTAA
2655154 ATATTTAAATTTAAATT
1 ATATTT-AATTT-AATT
*
2655171 -TATTTAATTTATTT
1 ATATTTAATTTAATT
* *
2655185 AAAATTTAAATTAATT
1 -ATATTTAATTTAATT
2655201 A-ATTT--TTTAATT
1 ATATTTAATTTAATT
2655213 CATATTTAATTTAA
1 -ATATTTAATTTAA
2655227 AAAATAATAT
Statistics
Matches: 45, Mismatches: 5, Indels: 13
0.71 0.08 0.21
Matches are distributed among these distances:
12 6 0.13
13 1 0.02
14 11 0.24
15 6 0.13
16 21 0.47
ACGTcount: A:0.42, C:0.01, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTAATTTAATT
Found at i:2655274 original size:11 final size:11
Alignment explanation
Indices: 2655258--2655311 Score: 56
Period size: 12 Copynumber: 4.7 Consensus size: 11
2655248 TTAAATTTAT
2655258 TAAAATAAATA
1 TAAAATAAATA
2655269 TAAAATTAAATA
1 TAAAA-TAAATA
*
2655281 -ATAATTAAATA
1 TA-AAATAAATA
2655292 TATAAATAAATA
1 TA-AAATAAATA
*
2655304 TCAAATAA
1 TAAAATAA
2655312 CGAATTTAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAAATAAATA
Found at i:2655280 original size:12 final size:12
Alignment explanation
Indices: 2655258--2655309 Score: 56
Period size: 11 Copynumber: 4.5 Consensus size: 12
2655248 TTAAATTTAT
2655258 TAAAA-TAAATA
1 TAAAATTAAATA
2655269 TAAAATTAAATA
1 TAAAATTAAATA
*
2655281 -ATAATTAAATA
1 TAAAATTAAATA
2655292 TATAAA-TAAATA
1 TA-AAATTAAATA
*
2655304 TCAAAT
1 TAAAAT
2655310 AACGAATTTA
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
11 18 0.53
12 14 0.41
13 2 0.06
ACGTcount: A:0.65, C:0.02, G:0.00, T:0.33
Consensus pattern (12 bp):
TAAAATTAAATA
Found at i:2665024 original size:21 final size:22
Alignment explanation
Indices: 2664984--2665032 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
2664974 AATTATATAA
* * *
2664984 TATATATTAATTTTATCTTTTT
1 TATATATTAATATAATCTTTAT
2665006 TATATATTAA-ATAATCTTTAT
1 TATATATTAATATAATCTTTAT
2665027 TATATA
1 TATATA
2665033 AAGAATACAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.59
Consensus pattern (22 bp):
TATATATTAATATAATCTTTAT
Found at i:2668093 original size:4 final size:4
Alignment explanation
Indices: 2668086--2668114 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
2668076 CCCCTGTCTG
2668086 TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT T
2668115 CCTCACTTCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:2668567 original size:11 final size:11
Alignment explanation
Indices: 2668551--2668586 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
2668541 TCATAAAAAA
*
2668551 TTAAAATTAAT
1 TTAAAATAAAT
2668562 TTAAAATAAAT
1 TTAAAATAAAT
2668573 TT-AAATAAAT
1 TTAAAATAAAT
2668583 TTAA
1 TTAA
2668587 TTTTTCATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 10 0.43
11 13 0.57
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TTAAAATAAAT
Found at i:2668578 original size:10 final size:10
Alignment explanation
Indices: 2668544--2668586 Score: 52
Period size: 10 Copynumber: 4.3 Consensus size: 10
2668534 TTTTATATCA
2668544 TAAA-AAATT
1 TAAATAAATT
* *
2668553 AAAATTAATT
1 TAAATAAATT
2668563 TAAAATAAATT
1 T-AAATAAATT
2668574 TAAATAAATT
1 TAAATAAATT
2668584 TAA
1 TAA
2668587 TTTTTCATTT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
9 3 0.11
10 16 0.57
11 9 0.32
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (10 bp):
TAAATAAATT
Found at i:2668918 original size:4 final size:4
Alignment explanation
Indices: 2668909--2668944 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
2668899 CAAAGAATTG
2668909 CATA CATA CATA CATA CATA CATA CATA CATA CATA
1 CATA CATA CATA CATA CATA CATA CATA CATA CATA
2668945 GACATGATCG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
CATA
Found at i:2669596 original size:32 final size:32
Alignment explanation
Indices: 2669560--2669633 Score: 139
Period size: 32 Copynumber: 2.3 Consensus size: 32
2669550 TTTGATCTAT
2669560 TTCAAAACTTCGTTTGTCCTTACACTCCTTAC
1 TTCAAAACTTCGTTTGTCCTTACACTCCTTAC
*
2669592 TTCAAAACTTCGTTTGTCCTTACATTCCTTAC
1 TTCAAAACTTCGTTTGTCCTTACACTCCTTAC
2669624 TTCAAAACTT
1 TTCAAAACTT
2669634 TGTCAATCAG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.24, C:0.28, G:0.05, T:0.42
Consensus pattern (32 bp):
TTCAAAACTTCGTTTGTCCTTACACTCCTTAC
Found at i:2672412 original size:30 final size:33
Alignment explanation
Indices: 2672372--2672431 Score: 81
Period size: 30 Copynumber: 1.9 Consensus size: 33
2672362 TTTTTAACAG
*
2672372 AAAATTAAAAAATTAA-A-T-TTTATTATTTAA
1 AAAATAAAAAAATTAATATTATTTATTATTTAA
*
2672402 AAAATAAAAAATTTAATATTATTTATTATT
1 AAAATAAAAAAATTAATATTATTTATTATT
2672432 AAATTTTTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 14 0.56
31 1 0.04
32 1 0.04
33 9 0.36
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (33 bp):
AAAATAAAAAAATTAATATTATTTATTATTTAA
Found at i:2672416 original size:23 final size:22
Alignment explanation
Indices: 2672376--2672421 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
2672366 TAACAGAAAA
* * *
2672376 TTAAAAAATTAAATTTTATTAT
1 TTAAAAAATAAAAATTTAATAT
2672398 TTAAAAAATAAAAAATTTAATAT
1 TTAAAAAAT-AAAAATTTAATAT
2672421 T
1 T
2672422 ATTTATTATT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TTAAAAAATAAAAATTTAATAT
Found at i:2676322 original size:2 final size:2
Alignment explanation
Indices: 2676317--2676349 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2676307 TAAAAAAGAA
2676317 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
2676350 AATATATACA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:2677919 original size:13 final size:13
Alignment explanation
Indices: 2677901--2677925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2677891 ATTTTTTTTA
2677901 ATATTTATATTTG
1 ATATTTATATTTG
2677914 ATATTTATATTT
1 ATATTTATATTT
2677926 ACGTATTTAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.00, G:0.04, T:0.64
Consensus pattern (13 bp):
ATATTTATATTTG
Found at i:2677999 original size:13 final size:14
Alignment explanation
Indices: 2677983--2678011 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
2677973 AAATTAAAAA
2677983 ATTAAAT-ATTTAT
1 ATTAAATCATTTAT
2677996 ATTAAATCATTTAT
1 ATTAAATCATTTAT
2678010 AT
1 AT
2678012 GCATTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATTAAATCATTTAT
Found at i:2686012 original size:2 final size:2
Alignment explanation
Indices: 2686005--2686040 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
2685995 GATTTAAGTA
2686005 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2686041 CATAGCGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2698608 original size:6 final size:6
Alignment explanation
Indices: 2698599--2698650 Score: 70
Period size: 6 Copynumber: 8.7 Consensus size: 6
2698589 ATTCCCATAT
* *
2698599 CCATGC CCATGC CCATGC CCATGC CCATGC CCAT-C CCAATTC CCATTC
1 CCATGC CCATGC CCATGC CCATGC CCATGC CCATGC CC-ATGC CCATGC
2698647 CCAT
1 CCAT
2698651 TGTTGGCATG
Statistics
Matches: 44, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
5 3 0.07
6 38 0.86
7 3 0.07
ACGTcount: A:0.19, C:0.50, G:0.10, T:0.21
Consensus pattern (6 bp):
CCATGC
Found at i:2704240 original size:1 final size:1
Alignment explanation
Indices: 2704229--2704258 Score: 51
Period size: 1 Copynumber: 30.0 Consensus size: 1
2704219 AGAAGACTTC
*
2704229 TTTTCTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2704259 CTTTCTCAGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.03, G:0.00, T:0.97
Consensus pattern (1 bp):
T
Found at i:2704768 original size:12 final size:12
Alignment explanation
Indices: 2704745--2704785 Score: 50
Period size: 12 Copynumber: 3.5 Consensus size: 12
2704735 ATTATTCATA
2704745 AAATTA-AA-TT
1 AAATTATAATTT
2704755 AAATTATAATTT
1 AAATTATAATTT
*
2704767 AAATTATTATTT
1 AAATTATAATTT
2704779 ATAATTA
1 A-AATTA
2704786 ATAACAATTT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 6 0.22
11 2 0.07
12 14 0.52
13 5 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AAATTATAATTT
Found at i:2704822 original size:28 final size:29
Alignment explanation
Indices: 2704751--2704826 Score: 77
Period size: 29 Copynumber: 2.7 Consensus size: 29
2704741 CATAAAATTA
*
2704751 AATTAAATTATAATTTAAATTATTATTTAT
1 AATT-AATTATAATTTAAATAATTATTTAT
* *
2704781 AATTAATAACAATTTAAA-AATTATTTAT
1 AATTAATTATAATTTAAATAATTATTTAT
*
2704809 ATATT-TTTATAA-TTAAAT
1 A-ATTAATTATAATTTAAAT
2704827 TTAAATAAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
27 5 0.13
28 14 0.37
29 15 0.39
30 4 0.11
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (29 bp):
AATTAATTATAATTTAAATAATTATTTAT
Found at i:2704858 original size:18 final size:19
Alignment explanation
Indices: 2704827--2704863 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
2704817 ATAATTAAAT
2704827 TTAAATAAAAAATTTATTA
1 TTAAATAAAAAATTTATTA
*
2704846 TTAAAT-AATAATTTATTA
1 TTAAATAAAAAATTTATTA
2704864 ATTCAAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
TTAAATAAAAAATTTATTA
Found at i:2704936 original size:11 final size:11
Alignment explanation
Indices: 2704920--2704993 Score: 64
Period size: 11 Copynumber: 6.7 Consensus size: 11
2704910 TTAATTTTTA
2704920 ATTTATATTAT
1 ATTTATATTAT
2704931 ATTTATATTAT
1 ATTTATATTAT
2704942 -TTT-TATTAT
1 ATTTATATTAT
*
2704951 AATTATATTTGAT
1 ATTTATA-TT-AT
2704964 ATGTTATATTA-
1 AT-TTATATTAT
* *
2704975 ACTTATATAAT
1 ATTTATATTAT
*
2704986 AATTATAT
1 ATTTATAT
2704994 CATACTTAAA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
9 6 0.12
10 12 0.23
11 21 0.40
12 3 0.06
13 5 0.10
14 5 0.10
ACGTcount: A:0.38, C:0.01, G:0.03, T:0.58
Consensus pattern (11 bp):
ATTTATATTAT
Found at i:2704948 original size:20 final size:20
Alignment explanation
Indices: 2704920--2704959 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2704910 TTAATTTTTA
*
2704920 ATTTATATTATATTTATATT
1 ATTTATATTATAATTATATT
*
2704940 ATTTTTATTATAATTATATT
1 ATTTATATTATAATTATATT
2704960 TGATATGTTA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (20 bp):
ATTTATATTATAATTATATT
Found at i:2705052 original size:23 final size:23
Alignment explanation
Indices: 2705010--2705055 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
2705000 TAAAATTATT
2705010 TAATTTAATTTAATAAAATAAAA
1 TAATTTAATTTAATAAAATAAAA
*
2705033 TAATTTAA-TTATTAATAATAAAA
1 TAATTTAATTTAATAA-AATAAAA
2705056 AAAGATAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 6 0.29
23 15 0.71
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TAATTTAATTTAATAAAATAAAA
Found at i:2705420 original size:23 final size:22
Alignment explanation
Indices: 2705394--2705444 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
2705384 TTTTTATTTT
*
2705394 TAATATAATAA-TATTATTATAAA
1 TAATATAATAATTA-AATT-TAAA
*
2705417 TAATATATTAATTAAATTTAAA
1 TAATATAATAATTAAATTTAAA
2705439 TAATAT
1 TAATAT
2705445 TTGTTAATTA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
22 10 0.40
23 13 0.52
24 2 0.08
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
TAATATAATAATTAAATTTAAA
Found at i:2705441 original size:22 final size:23
Alignment explanation
Indices: 2705413--2705460 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
2705403 AATATTATTA
2705413 TAAATAATA-TATTAATTAAATT
1 TAAATAATATTATTAATTAAATT
*
2705435 TAAATAATATTTGTTAATTAAATT
1 TAAATAATA-TTATTAATTAAATT
2705459 TA
1 TA
2705461 TATTTATATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.39
24 14 0.61
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (23 bp):
TAAATAATATTATTAATTAAATT
Found at i:2706763 original size:3 final size:3
Alignment explanation
Indices: 2706757--2706800 Score: 79
Period size: 3 Copynumber: 14.7 Consensus size: 3
2706747 AATAATAATC
*
2706757 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATC ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
2706801 AAGGTTTGCT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 39 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
ATT
Found at i:2707083 original size:3 final size:3
Alignment explanation
Indices: 2707075--2707119 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
2707065 TTAAATGAAC
2707075 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
2707120 CATGTTTTCC
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2707241 original size:2 final size:2
Alignment explanation
Indices: 2707198--2707222 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2707188 TTTTTCTGTG
2707198 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
2707223 TAATACTTTT
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:2707579 original size:17 final size:17
Alignment explanation
Indices: 2707544--2707578 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
2707534 AGTACTCTGG
2707544 TATTATTTTATAATATA
1 TATTATTTTATAATATA
2707561 TATTATTTTA-AAT-TA
1 TATTATTTTATAATATA
2707576 TAT
1 TAT
2707579 AATAAAATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 5 0.28
16 3 0.17
17 10 0.56
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (17 bp):
TATTATTTTATAATATA
Found at i:2708624 original size:2 final size:2
Alignment explanation
Indices: 2708619--2708647 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2708609 TTTTTAATTG
2708619 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 A
2708648 ATTTCTCTTA
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:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2708818 original size:15 final size:14
Alignment explanation
Indices: 2708781--2708822 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
2708771 ATTAAATTCT
*
2708781 TAATTTTAATT-TT
1 TAATTTTAATTATA
*
2708794 TAAATTTAATTATGA
1 TAATTTTAATTAT-A
2708809 TAATTTTAATTATA
1 TAATTTTAATTATA
2708823 AAAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
13 10 0.42
14 2 0.08
15 12 0.50
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (14 bp):
TAATTTTAATTATA
Found at i:2709117 original size:16 final size:15
Alignment explanation
Indices: 2709098--2709144 Score: 60
Period size: 16 Copynumber: 3.1 Consensus size: 15
2709088 ATTTATATTC
*
2709098 ATAT-TTAAAATATT
1 ATATATTAAAATTTT
*
2709112 ATATATAAAAATTTT
1 ATATATTAAAATTTT
2709127 GATATATTAAAATTTT
1 -ATATATTAAAATTTT
2709143 AT
1 AT
2709145 TTTATATATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
14 4 0.14
15 10 0.36
16 14 0.50
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (15 bp):
ATATATTAAAATTTT
Found at i:2709134 original size:32 final size:33
Alignment explanation
Indices: 2709098--2709169 Score: 85
Period size: 32 Copynumber: 2.2 Consensus size: 33
2709088 ATTTATATTC
*
2709098 ATATTTAAAATATTA-TATATAAAAATTTTGAT
1 ATATTTAAAATATTATTATATAAAAATTTTAAT
* * * *
2709130 ATA-TTAAAATTTTATTTTATATATATTTTAAT
1 ATATTTAAAATATTATTATATAAAAATTTTAAT
2709162 ATATTTAA
1 ATATTTAA
2709170 CCATTCATGT
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
31 10 0.30
32 19 0.58
33 4 0.12
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (33 bp):
ATATTTAAAATATTATTATATAAAAATTTTAAT
Found at i:2709860 original size:16 final size:16
Alignment explanation
Indices: 2709839--2709899 Score: 51
Period size: 16 Copynumber: 3.9 Consensus size: 16
2709829 TTTATTTTAA
2709839 ATTAATATTAATATTT
1 ATTAATATTAATATTT
2709855 ATTAAT-TT-A-A-TT
1 ATTAATATTAATATTT
2709867 ATTAATATATAAATATTT
1 ATTAATAT-T-AATATTT
*
2709885 -TTATTATTTAATATT
1 ATTAATA-TTAATATT
2709900 ATTGTAAATA
Statistics
Matches: 37, Mismatches: 1, Indels: 14
0.71 0.02 0.27
Matches are distributed among these distances:
12 8 0.22
13 2 0.05
14 2 0.05
15 2 0.05
16 13 0.35
17 7 0.19
18 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (16 bp):
ATTAATATTAATATTT
Found at i:2709860 original size:31 final size:32
Alignment explanation
Indices: 2709816--2709942 Score: 91
Period size: 36 Copynumber: 3.8 Consensus size: 32
2709806 AAATATTTTA
2709816 TAAT-TTTAATTAATTTATTTTAAATTAATAT
1 TAATATTTAATTAATTTATTTTAAATTAATAT
2709847 TAATATTT-ATTAATTTAATTATTAATATATAAATAT
1 TAATATTTAATTAATTT-ATT-TTAA-AT-T-AATAT
** * *
2709883 TTTTA-TTATTTAATATTATTGTAAA-TAATAAT
1 TAATATTTAATTAAT-TTATTTTAAATTAAT-AT
* *
2709915 ATAATTTTTGAATTAATTTAATTTAAAT
1 -TAATATTT-AATTAATTTATTTTAAAT
2709943 ATAAATAAAT
Statistics
Matches: 73, Mismatches: 10, Indels: 22
0.70 0.10 0.21
Matches are distributed among these distances:
31 15 0.21
32 9 0.12
33 6 0.08
34 13 0.18
35 12 0.16
36 16 0.22
37 2 0.03
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (32 bp):
TAATATTTAATTAATTTATTTTAAATTAATAT
Found at i:2709884 original size:30 final size:27
Alignment explanation
Indices: 2709829--2709900 Score: 78
Period size: 30 Copynumber: 2.6 Consensus size: 27
2709819 TTTTAATTAA
2709829 TTTAT-TTTAA-ATTAATATTAATATT
1 TTTATATTTAATATTAATATTAATATT
2709854 TATTA-ATTTAATTATTAATATATAAATATT
1 T-TTATATTTAA-TATTAATAT-T-AATATT
2709884 TTTATTATTTAATATTA
1 TTTA-TATTTAATATTA
2709901 TTGTAAATAA
Statistics
Matches: 39, Mismatches: 0, Indels: 11
0.78 0.00 0.22
Matches are distributed among these distances:
25 1 0.03
26 8 0.21
28 8 0.21
29 4 0.10
30 12 0.31
31 6 0.15
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (27 bp):
TTTATATTTAATATTAATATTAATATT
Found at i:2709896 original size:36 final size:38
Alignment explanation
Indices: 2709856--2709955 Score: 100
Period size: 36 Copynumber: 2.6 Consensus size: 38
2709846 TTAATATTTA
*
2709856 TTAATTTAATTATTAATATATAAAT-ATTTTT-ATT-AT
1 TTAATTTAATTATAAATA-ATAAATAATTTTTAATTAAT
*
2709892 TTAATATT-ATTGTAAATAATAATATAATTTTTGAATTAAT
1 TTAAT-TTAATTATAAATAATAA-ATAATTTTT-AATTAAT
*
2709932 TTAATTTAAATATAAATAAATAAA
1 TTAATTTAATTATAAAT-AATAAA
2709956 ATAAATTCAA
Statistics
Matches: 52, Mismatches: 4, Indels: 12
0.76 0.06 0.18
Matches are distributed among these distances:
35 4 0.08
36 15 0.29
37 8 0.15
39 5 0.10
40 15 0.29
41 5 0.10
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (38 bp):
TTAATTTAATTATAAATAATAAATAATTTTTAATTAAT
Found at i:2711026 original size:32 final size:31
Alignment explanation
Indices: 2710990--2711059 Score: 79
Period size: 32 Copynumber: 2.2 Consensus size: 31
2710980 TTATCATATG
2710990 AATATAAATATATAA-AAAATTAATTATATTAA
1 AATATAAATATA-AATAAAA-TAATTATATTAA
* *
2711022 AATATTAAATATAAATATAATATTTATATTAA
1 AATA-TAAATATAAATAAAATAATTATATTAA
2711054 ACATAT
1 A-ATAT
2711060 TATATTAATT
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
32 19 0.58
33 14 0.42
ACGTcount: A:0.59, C:0.01, G:0.00, T:0.40
Consensus pattern (31 bp):
AATATAAATATAAATAAAATAATTATATTAA
Found at i:2711083 original size:24 final size:23
Alignment explanation
Indices: 2711012--2711090 Score: 88
Period size: 24 Copynumber: 3.4 Consensus size: 23
2711002 TAAAAAATTA
*
2711012 ATTATATTAA-AATATTAAATAT
1 ATTATATTAATTATATTAAATAT
* * * *
2711034 AAATATAATATTTATATTAAACAT
1 -ATTATATTAATTATATTAAATAT
2711058 ATTATATTAATTATATTTAAATAT
1 ATTATATTAATTATA-TTAAATAT
2711082 ATTATATTA
1 ATTATATTA
2711091 TTTTCATATT
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
23 19 0.42
24 26 0.58
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.48
Consensus pattern (23 bp):
ATTATATTAATTATATTAAATAT
Found at i:2713784 original size:17 final size:18
Alignment explanation
Indices: 2713754--2713787 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
2713744 TGGATAAATA
2713754 AAAAATTTACTTATCAAC
1 AAAAATTTACTTATCAAC
*
2713772 AAAAA-TTATTTATCAA
1 AAAAATTTACTTATCAA
2713788 ATAATAATTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.53, C:0.12, G:0.00, T:0.35
Consensus pattern (18 bp):
AAAAATTTACTTATCAAC
Found at i:2714200 original size:2 final size:2
Alignment explanation
Indices: 2714189--2714221 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
2714179 TTGATGGTTG
*
2714189 AT AT -T AT AT AT AT AT AT AT AT TT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2714222 CAAAAGAAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:2717305 original size:31 final size:31
Alignment explanation
Indices: 2717267--2717328 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
2717257 GCAATGGAAA
2717267 CTCTTTCACATTATAAGCATACTACCATTTT
1 CTCTTTCACATTATAAGCATACTACCATTTT
*
2717298 CTCTTTCACATTATAAGCTTACTACCATTTT
1 CTCTTTCACATTATAAGCATACTACCATTTT
2717329 ACTTCTATGC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.27, C:0.26, G:0.03, T:0.44
Consensus pattern (31 bp):
CTCTTTCACATTATAAGCATACTACCATTTT
Found at i:2732431 original size:22 final size:21
Alignment explanation
Indices: 2732393--2732434 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
2732383 AATTTTTATT
2732393 TAAATTTAATTATAAAATATA
1 TAAATTTAATTATAAAATATA
2732414 TAAATATTAA-TATAAAA-ATA
1 TAAAT-TTAATTATAAAATATA
2732434 T
1 T
2732435 TTTTTAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 4 0.20
21 12 0.60
22 4 0.20
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (21 bp):
TAAATTTAATTATAAAATATA
Found at i:2732467 original size:13 final size:13
Alignment explanation
Indices: 2732449--2732476 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
2732439 TAATTTTTAT
2732449 TAATTATAAATAA
1 TAATTATAAATAA
2732462 TAATTATAAATAA
1 TAATTATAAATAA
2732475 TA
1 TA
2732477 TGAATAAATC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
TAATTATAAATAA
Found at i:2734671 original size:17 final size:17
Alignment explanation
Indices: 2734635--2734667 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
2734625 AATATTTATA
*
2734635 ATTTTTATATAATTAAT
1 ATTTTAATATAATTAAT
2734652 ATTTTAATA-AATTAAT
1 ATTTTAATATAATTAAT
2734668 TATTAAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (17 bp):
ATTTTAATATAATTAAT
Found at i:2734796 original size:27 final size:27
Alignment explanation
Indices: 2734755--2734821 Score: 82
Period size: 27 Copynumber: 2.4 Consensus size: 27
2734745 ATACATATAA
*
2734755 AATTATAAATTTAATATTTTTAT-TATATC
1 AATTA-AAA-TTAATATTTTAATCT-TATC
*
2734784 AATTAAAATTAATATTTTAATCTTATT
1 AATTAAAATTAATATTTTAATCTTATC
2734811 AATTAAAATTA
1 AATTAAAATTA
2734822 TTAATTATAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
27 26 0.74
28 4 0.11
29 5 0.14
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (27 bp):
AATTAAAATTAATATTTTAATCTTATC
Found at i:2735098 original size:22 final size:23
Alignment explanation
Indices: 2735069--2735118 Score: 61
Period size: 21 Copynumber: 2.3 Consensus size: 23
2735059 TTTATTAAAG
*
2735069 TTAA-ATTTTAAATAAAATT-TT
1 TTAATATTTTAAATAAAATTAAT
*
2735090 TTAATA-TTTAAATTAAATTAAT
1 TTAATATTTTAAATAAAATTAAT
2735112 TTAATAT
1 TTAATAT
2735119 GAATTATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
21 16 0.67
22 8 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAATATTTTAAATAAAATTAAT
Found at i:2735526 original size:49 final size:50
Alignment explanation
Indices: 2735469--2735592 Score: 151
Period size: 50 Copynumber: 2.5 Consensus size: 50
2735459 AATAGGTGTA
* * * * **
2735469 AAAGAGGTGATCGTAATTGTTGATTATTCTTTATTAA-CTTTGACAATCG
1 AAAGAGGTGGTCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCG
* *
2735518 AAAGAGGTGGCCGTAATTGTTTACTATTCCTCACCAACCTTTGACAATCG
1 AAAGAGGTGGTCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCG
* *
2735568 AGAGAGGTGGTCATAATTGTTGACT
1 AAAGAGGTGGTCGTAATTGTTGACT
2735593 CTAAGCATCT
Statistics
Matches: 62, Mismatches: 12, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
49 29 0.47
50 33 0.53
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.35
Consensus pattern (50 bp):
AAAGAGGTGGTCGTAATTGTTGACTATTCCTCACCAACCTTTGACAATCG
Found at i:2740021 original size:50 final size:50
Alignment explanation
Indices: 2739946--2740215 Score: 289
Period size: 50 Copynumber: 5.4 Consensus size: 50
2739936 GGTGCAAAAG
* *
2739946 AGGTGGTCGTAATTATTGACTATTCTTCACCAACCTTTGATAATCGAGAA
1 AGGTGGTCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
* * *
2739996 AGGTGGTCGTAATTGTTGACTATTCTTTACCAACCTTTGACAATTGAGAG
1 AGGTGGTCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
** * * * * * *
2740046 ATATGGTTGTAATTATTGACTATTCCTCACTAACCTTTGACAATCAAGAG
1 AGGTGGTCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
* * *
2740096 AGGTGGCCATAATTGTTGAC-ATT-TCTCACTAACCTTTGACAATC-A-AA
1 AGGTGGTCGTAATTGTTGACTATTCT-TCACCAACCTTTGACAATCGAGAA
*
2740143 AGAAGTGGTCGTAATTGTTGACTATT-TATCACCAACCTTTGACAATAGAGAA
1 AG--GTGGTCGTAATTGTTGACTATTCT-TCACCAACCTTTGACAATCGAGAA
* * *
2740195 AAGTGATCATAATTGTTGACT
1 AGGTGGTCGTAATTGTTGACT
2740216 CTAAGCATCT
Statistics
Matches: 184, Mismatches: 30, Indels: 12
0.81 0.13 0.05
Matches are distributed among these distances:
47 3 0.02
48 1 0.01
49 38 0.21
50 138 0.75
51 1 0.01
52 3 0.02
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Consensus pattern (50 bp):
AGGTGGTCGTAATTGTTGACTATTCTTCACCAACCTTTGACAATCGAGAA
Found at i:2740180 original size:99 final size:99
Alignment explanation
Indices: 2739940--2740215 Score: 317
Period size: 99 Copynumber: 2.8 Consensus size: 99
2739930 TAAATGGGTG
* * * *
2739940 CAAAAGAGGTGGTCGTAATTATTGACTATTCTTCACCAACCTTTGATAATCGAGAAAGGTGGTCG
1 CAAAAGAAGTGGTCGTAATTATTGACTATT-TTCACCAACCTTTGACAATCAAGAAAGGTGGTCA
*
2740005 TAATTGTTGACTATTCTTTACCAACCTTTGACAAT
65 TAATTGTTGACTATTCTTCACCAACCTTTGACAAT
** * * * * * *
2740040 TGAGAGATA-TGGTTGTAATTATTGACTATTCCTCACTAACCTTTGACAATCAAGAGAGGTGGCC
1 CAAAAGA-AGTGGTCGTAATTATTGACTATT-TTCACCAACCTTTGACAATCAAGAAAGGTGGTC
*
2740104 ATAATTGTTGAC-ATT-TCTCACTAACCTTTGACAAT
64 ATAATTGTTGACTATTCT-TCACCAACCTTTGACAAT
* * *
2740139 CAAAAGAAGTGGTCGTAATTGTTGACTATTTATCACCAACCTTTGACAAT-AGAGAAAAGTGATC
1 CAAAAGAAGTGGTCGTAATTATTGACTATTT-TCACCAACCTTTGACAATCA-AGAAAGGTGGTC
2740203 ATAATTGTTGACT
64 ATAATTGTTGACT
2740216 CTAAGCATCT
Statistics
Matches: 145, Mismatches: 25, Indels: 12
0.80 0.14 0.07
Matches are distributed among these distances:
98 3 0.02
99 79 0.54
100 63 0.43
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Consensus pattern (99 bp):
CAAAAGAAGTGGTCGTAATTATTGACTATTTTCACCAACCTTTGACAATCAAGAAAGGTGGTCAT
AATTGTTGACTATTCTTCACCAACCTTTGACAAT
Found at i:2743293 original size:16 final size:16
Alignment explanation
Indices: 2743247--2743294 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
2743237 ATGTAGCACA
*
2743247 TATTTAAA-ATATAAA
1 TATTTAAATATATAAT
* *
2743262 TATATATATATATAAT
1 TATTTAAATATATAAT
2743278 TATTTAAATATATAAT
1 TATTTAAATATATAAT
2743294 T
1 T
2743295 TTTTTTAAAA
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
15 6 0.22
16 21 0.78
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (16 bp):
TATTTAAATATATAAT
Found at i:2744084 original size:29 final size:30
Alignment explanation
Indices: 2744040--2744105 Score: 93
Period size: 29 Copynumber: 2.3 Consensus size: 30
2744030 TCAACTACTG
*
2744040 TTAATTTTTAAATAAATTA-CTAAAATATTA
1 TTAATTTTAAAATAAATTATC-AAAATATTA
2744070 TTAA-TTTAAAATAAATTATCAAAATATTA
1 TTAATTTTAAAATAAATTATCAAAATATTA
2744099 TT-ATTTT
1 TTAATTTT
2744106 GACTAGTAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
28 1 0.03
29 27 0.82
30 5 0.15
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (30 bp):
TTAATTTTAAAATAAATTATCAAAATATTA
Found at i:2744334 original size:13 final size:13
Alignment explanation
Indices: 2744318--2744360 Score: 50
Period size: 13 Copynumber: 3.1 Consensus size: 13
2744308 AAAATAATAA
*
2744318 TATTTTAGTAATT
1 TATTTTAATAATT
2744331 TATTTTAAATTAATAT
1 TATTTT-AA-TAAT-T
2744347 TATTTTAATAATT
1 TATTTTAATAATT
2744360 T
1 T
2744361 GTTTAAAAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
13 8 0.31
14 5 0.19
15 6 0.23
16 7 0.27
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (13 bp):
TATTTTAATAATT
Found at i:2744339 original size:29 final size:29
Alignment explanation
Indices: 2744306--2744370 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 29
2744296 TTTTTATAAG
*
2744306 TTAAAATAATAATATTTTAGTAATTTATT
1 TTAAAATAATAATATTTTAATAATTTATT
* * *
2744335 TTAAATTAATATTATTTTAATAATTTGTT
1 TTAAAATAATAATATTTTAATAATTTATT
*
2744364 TAAAAAT
1 TTAAAAT
2744371 TAACAGTTGT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (29 bp):
TTAAAATAATAATATTTTAATAATTTATT
Found at i:2746076 original size:2 final size:2
Alignment explanation
Indices: 2746069--2746094 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
2746059 TATTGAAGTT
2746069 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
2746095 CACACTAGCG
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):
TA
Found at i:2746788 original size:2 final size:2
Alignment explanation
Indices: 2746783--2746812 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
2746773 ATATATATAT
2746783 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2746813 TTGAAGCTGA
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:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2749626 original size:24 final size:24
Alignment explanation
Indices: 2749599--2749647 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
2749589 CGATATTATA
2749599 TTAAGCATTTAACTTAAAATCAAC
1 TTAAGCATTTAACTTAAAATCAAC
2749623 TTAAGCATTTAACTTAAAATCAAC
1 TTAAGCATTTAACTTAAAATCAAC
2749647 T
1 T
2749648 GATAATAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.45, C:0.16, G:0.04, T:0.35
Consensus pattern (24 bp):
TTAAGCATTTAACTTAAAATCAAC
Found at i:2749638 original size:13 final size:13
Alignment explanation
Indices: 2749599--2749639 Score: 50
Period size: 13 Copynumber: 3.3 Consensus size: 13
2749589 CGATATTATA
2749599 TTAAGCATTTAAC
1 TTAAGCATTTAAC
* *
2749612 TTAA--AATCAAC
1 TTAAGCATTTAAC
2749623 TTAAGCATTTAAC
1 TTAAGCATTTAAC
2749636 TTAA
1 TTAA
2749640 AATCAACTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 4
0.73 0.13 0.13
Matches are distributed among these distances:
11 9 0.41
13 13 0.59
ACGTcount: A:0.44, C:0.15, G:0.05, T:0.37
Consensus pattern (13 bp):
TTAAGCATTTAAC
Found at i:2750623 original size:17 final size:17
Alignment explanation
Indices: 2750603--2750638 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
2750593 TATATAGTAA
2750603 AATTTTAATAAATTAAT
1 AATTTTAATAAATTAAT
* *
2750620 AATTTTAATTAATTCAT
1 AATTTTAATAAATTAAT
2750637 AA
1 AA
2750639 AATCTCACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (17 bp):
AATTTTAATAAATTAAT
Found at i:2752538 original size:2 final size:2
Alignment explanation
Indices: 2752531--2752557 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2752521 TCCATAAAAT
2752531 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
2752558 CAATCTGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2752857 original size:19 final size:20
Alignment explanation
Indices: 2752821--2752858 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
2752811 GGATGTGTGT
*
2752821 ATTAAATATATGAATATTAC
1 ATTAAATATATAAATATTAC
2752841 ATTAAAT-TATAAATATTA
1 ATTAAATATATAAATATTA
2752859 AATATATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.42
Consensus pattern (20 bp):
ATTAAATATATAAATATTAC
Found at i:2758078 original size:3 final size:3
Alignment explanation
Indices: 2758072--2758097 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2758062 ATTATTAGTA
2758072 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
2758098 ATTATTGCTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:2758439 original size:2 final size:2
Alignment explanation
Indices: 2758432--2758460 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2758422 GACTAAATTC
2758432 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 G
2758461 GACCTGGTGA
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:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2760301 original size:2 final size:2
Alignment explanation
Indices: 2760288--2760317 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
2760278 TTATTGATGG
*
2760288 AT AT AC 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
2760318 GATTTCTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:2760671 original size:208 final size:210
Alignment explanation
Indices: 2760288--2760702 Score: 554
Period size: 208 Copynumber: 2.0 Consensus size: 210
2760278 TTATTGATGG
*
2760288 ATATACATATATATATATATATATATATATGATTTCTAAGGCAAAAAAAATGCTCCCTAAATTAT
1 ATATACATATATATATATATATATATATATGATTTATAAGGCAAAAAAAATGCTCCCTAAATTAT
** * *
2760353 AGAATAACAAATAAGGGAATTTTTTCTCAAAAATTTTCTGTCGAAAAAATATTAATCATTGAAAT
66 AGAATAACAAATAAAAGAATTTTTTCTCAAAAATTTGCTATCGAAAAAATATTAATCATTGAAAT
* * * **
2760418 CAAAATTTTAATATTTGTTGATATAAAATAAATTATAATTTAAAT-A-AAAAATTA-TAAATTTT
131 CAAAATTTTAATATTTATTGATATAAAAAAAATTATAACTTAAATAAGAAAAAAAATTAAATTTT
2760480 AAAATTTTAAATATT
196 AAAATTTTAAATATT
*
2760495 ATAT-CATATATATATATATGAATATATGATATGATTTATAAGGCAAAAAAAATGTTCCCTAAAT
1 ATATACATATATATATATAT--ATATAT-ATATGATTTATAAGGCAAAAAAAATGCTCCCTAAAT
* * ** * * * *
2760559 TATAGAATGACAAATAAAAGAATTTTTTTTTTGAACA-TTGCTATCG-AAGAATTTTAATTATTG
63 TATAGAATAACAAATAAAAGAA-TTTTTTCTCAAAAATTTGCTATCGAAAAAATATTAATCATTG
* * *
2760622 AAATTAAAATTTTAATATTTATTGATATAAAAAAAATTGTTACTTAAATAAGAAAAAAAATTAAA
127 AAATCAAAATTTTAATATTTATTGATATAAAAAAAATTATAACTTAAATAAGAAAAAAAATTAAA
2760687 TTTTAAAATTTTAAAT
192 TTTTAAAATTTTAAAT
2760703 TTCAAATATA
Statistics
Matches: 179, Mismatches: 22, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
206 15 0.08
207 4 0.02
208 63 0.35
209 61 0.34
210 16 0.09
211 20 0.11
ACGTcount: A:0.48, C:0.06, G:0.07, T:0.39
Consensus pattern (210 bp):
ATATACATATATATATATATATATATATATGATTTATAAGGCAAAAAAAATGCTCCCTAAATTAT
AGAATAACAAATAAAAGAATTTTTTCTCAAAAATTTGCTATCGAAAAAATATTAATCATTGAAAT
CAAAATTTTAATATTTATTGATATAAAAAAAATTATAACTTAAATAAGAAAAAAAATTAAATTTT
AAAATTTTAAATATT
Found at i:2761128 original size:16 final size:16
Alignment explanation
Indices: 2761107--2761152 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
2761097 TTAAATAGAT
2761107 ATTAAATATATTAAAA
1 ATTAAATATATTAAAA
**
2761123 ATTAAATATATATTTAA
1 ATTAAATATAT-TAAAA
*
2761140 TTTAAATATATTA
1 ATTAAATATATTA
2761153 TTTTTAATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
16 12 0.48
17 13 0.52
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (16 bp):
ATTAAATATATTAAAA
Found at i:2761957 original size:19 final size:19
Alignment explanation
Indices: 2761935--2761972 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
2761925 TATTTTTATT
2761935 TAAT-TTAATTATAAAAATA
1 TAATATTAA-TATAAAAATA
2761954 TAATATTAATATAAAAATA
1 TAATATTAATATAAAAATA
2761973 ATTTTAATAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
TAATATTAATATAAAAATA
Found at i:2761979 original size:17 final size:19
Alignment explanation
Indices: 2761938--2761982 Score: 58
Period size: 17 Copynumber: 2.4 Consensus size: 19
2761928 TTTTATTTAA
2761938 TTTAATTATAAAAATATAAT
1 TTTAA-TATAAAAATATAAT
*
2761958 ATTAATAT-AAAA-ATAAT
1 TTTAATATAAAAATATAAT
2761975 TTTAATAT
1 TTTAATAT
2761983 TTTTAAAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 3 0.13
20 4 0.17
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (19 bp):
TTTAATATAAAAATATAAT
Found at i:2764210 original size:201 final size:201
Alignment explanation
Indices: 2763865--2764262 Score: 654
Period size: 201 Copynumber: 2.0 Consensus size: 201
2763855 TTCACACCGG
* *
2763865 TTATTTAGACTTTGCTGACGATCCCATGAACTTTGTACTGCAGGAATTATGGCCCAATTTGTATT
1 TTATTTAGACTTTGCTGACGATCCCATGAACTTCGTAATGCAGGAATTATGGCCCAATTTGTATT
*
2763930 CGGACAAGTAGCTGATAAGCTCCTTTCATTTATGTTTACAGAATCCCATTCAAGCAGTGGCAAAT
66 CGGACAAGTAGCTGATAAGCTCCTTTCATTCATGTTTACAGAATCCCATTCAAGCAGTGGCAAAT
* * *
2763995 GTGGCTCTCTTCCAGGCAAAAATCCATTTGGATCATGCGAATCATCTAGCTCTTTGAAAGAACTA
131 GTGGCTCTCTTCCAGGCAAAAATCCAATTGGATCATGCAAATCATCGAGCTCTTTGAAAGAACTA
2764060 AACGGC
196 AACGGC
* *
2764066 TTATTTAGACTTTGCTGATGATCCCATGAACTTCGTAATGCAGGAATTATGGTCCAATTTGTATT
1 TTATTTAGACTTTGCTGACGATCCCATGAACTTCGTAATGCAGGAATTATGGCCCAATTTGTATT
* *
2764131 CTGG-CGAGTAGCTGATAAGCTCCTTTCATTCATGTTTACAGAATCCCATTCAAGCAGTGGCAGA
66 C-GGACAAGTAGCTGATAAGCTCCTTTCATTCATGTTTACAGAATCCCATTCAAGCAGTGGCAAA
* * * *
2764195 TTTGGCTCTCTTCCAGGCAAAGATCCAATTGGATCATGCAAATCATCGGGCTCTTTGAAAGAATT
130 TGTGGCTCTCTTCCAGGCAAAAATCCAATTGGATCATGCAAATCATCGAGCTCTTTGAAAGAACT
2764260 AAA
195 AAA
2764263 TGGTAGAAAG
Statistics
Matches: 182, Mismatches: 14, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
201 180 0.99
202 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (201 bp):
TTATTTAGACTTTGCTGACGATCCCATGAACTTCGTAATGCAGGAATTATGGCCCAATTTGTATT
CGGACAAGTAGCTGATAAGCTCCTTTCATTCATGTTTACAGAATCCCATTCAAGCAGTGGCAAAT
GTGGCTCTCTTCCAGGCAAAAATCCAATTGGATCATGCAAATCATCGAGCTCTTTGAAAGAACTA
AACGGC
Found at i:2764733 original size:300 final size:300
Alignment explanation
Indices: 2764165--2764747 Score: 792
Period size: 300 Copynumber: 1.9 Consensus size: 300
2764155 TTCATTCATG
* ** *
2764165 TTTACAGAATCCCATTCAAGCAGTGGCAGATTTGGCTCTCTTCCAGGCAAAGATCCAATTGGATC
1 TTTACAGAATCCCATTCAAGCAGCGGCAGAAGTGGCTCTCTTCCAGGCAAAGATCCAACTGGATC
* * * *
2764230 ATGCAAATCATCGGGCTCTTTGAAAGAATTAAATGGTAGAAAGGATCCATGTTTCACAAATGGAA
66 ATGCAAATCATCGGGCTCTTTGAAAGAACTAAATGGCAGAAAAGATCCATGTCTCACAAATGGAA
* * *
2764295 AGCCAAAAGTGGAGTCACCTTCAATGCAGCAGATCAGATTTTTCTCTCCTGGTTCATAGCTAGGT
131 AGCCAAAAGTGGAGTCACCTTCAATGCAGCAGATCAGATTTTTCTCTCCTAGTTCACAGCAAGGT
* * * * * * *
2764360 GACTCTAAATTCTTTTGAAGTGTGCGGTGGTTGTTATACAGTGGAGAGTAGATATAATAGAGCGT
196 AACTCTAAATTCTTTCGAAGGGTGCGGTGATTGTTATACAGTGGAGAGTAGACATAAGAGAGCAT
* * *
2764425 GTTCTCCCTCGATCTGTCTGACCTGGAACATGATGTAACA
261 GGTCTCCCTCCATATGTCTGACCTGGAACATGATGTAACA
* * * * *
2764465 TTTACAGCATCCCATTCAAGCAGCGG-TGAAAGTGGCTCTCTTCCAGGGAAAGATCCAGCTGGGT
1 TTTACAGAATCCCATTCAAGCAGCGGCAG-AAGTGGCTCTCTTCCAGGCAAAGATCCAACTGGAT
*
2764529 CATGCAAATCATCTGGCTCTTTGAAAGAACTAAATGGCAGAAAAGATCCATGTCTCACAAATGGA
65 CATGCAAATCATCGGGCTCTTTGAAAGAACTAAATGGCAGAAAAGATCCATGTCTCACAAATGGA
* * * ** *
2764594 AAGCCAAAAGTGGAGTCACCTTCAATGCAGGAGGTCAGATTTTTCTCTCTTAGTTTGCCGCAAGG
130 AAGCCAAAAGTGGAGTCACCTTCAATGCAGCAGATCAGATTTTTCTCTCCTAGTTCACAGCAAGG
* * * * *
2764659 TAACTCTAAATTCTTTCGAAGGGTGCTGTGATTGTTATA-GGTTGTAGAGTCGACATTAGAGAGC
195 TAACTCTAAATTCTTTCGAAGGGTGCGGTGATTGTTATACAG-TGGAGAGTAGACATAAGAGAGC
2764723 ATGGTCTCCCTCCATATGTCTGACC
259 ATGGTCTCCCTCCATATGTCTGACC
2764748 AATAAGATGA
Statistics
Matches: 243, Mismatches: 38, Indels: 4
0.85 0.13 0.01
Matches are distributed among these distances:
299 2 0.01
300 241 0.99
ACGTcount: A:0.28, C:0.20, G:0.23, T:0.28
Consensus pattern (300 bp):
TTTACAGAATCCCATTCAAGCAGCGGCAGAAGTGGCTCTCTTCCAGGCAAAGATCCAACTGGATC
ATGCAAATCATCGGGCTCTTTGAAAGAACTAAATGGCAGAAAAGATCCATGTCTCACAAATGGAA
AGCCAAAAGTGGAGTCACCTTCAATGCAGCAGATCAGATTTTTCTCTCCTAGTTCACAGCAAGGT
AACTCTAAATTCTTTCGAAGGGTGCGGTGATTGTTATACAGTGGAGAGTAGACATAAGAGAGCAT
GGTCTCCCTCCATATGTCTGACCTGGAACATGATGTAACA
Found at i:2768095 original size:16 final size:16
Alignment explanation
Indices: 2768074--2768115 Score: 54
Period size: 16 Copynumber: 2.8 Consensus size: 16
2768064 AAAATTAATT
2768074 TAATTTA-ATTTTTATA
1 TAATTTATATTTTT-TA
2768090 TAATTTATATTTTTTA
1 TAATTTATATTTTTTA
2768106 T-A-TTATATTT
1 TAATTTATATTT
2768116 ATATGATAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
14 8 0.32
15 1 0.04
16 10 0.40
17 6 0.24
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (16 bp):
TAATTTATATTTTTTA
Found at i:2768117 original size:20 final size:18
Alignment explanation
Indices: 2768074--2768119 Score: 60
Period size: 18 Copynumber: 2.6 Consensus size: 18
2768064 AAAATTAATT
2768074 TAATTTA-A-TTTTTATA
1 TAATTTATATTTTTTATA
2768090 TAATTTATATTTTTTATA
1 TAATTTATATTTTTTATA
2768108 TTATATTTATAT
1 -TA-ATTTATAT
2768120 GATAAAATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 7 0.27
17 1 0.04
18 8 0.31
19 2 0.08
20 8 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (18 bp):
TAATTTATATTTTTTATA
Found at i:2768177 original size:18 final size:20
Alignment explanation
Indices: 2768134--2768177 Score: 56
Period size: 18 Copynumber: 2.3 Consensus size: 20
2768124 AAATTTTAAA
*
2768134 TAAATAAAATATTTATTTAT
1 TAAATAAAATATTTAATTAT
*
2768154 TTAATAAAA-A-TTAATTAT
1 TAAATAAAATATTTAATTAT
2768172 TAAATA
1 TAAATA
2768178 TATAAAAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
18 12 0.57
19 1 0.05
20 8 0.38
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TAAATAAAATATTTAATTAT
Found at i:2771518 original size:2 final size:2
Alignment explanation
Indices: 2771513--2771553 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2771503 TCTCTCTCTC
*
2771513 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2771554 CCCTATCCCT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2776242 original size:27 final size:27
Alignment explanation
Indices: 2776211--2776263 Score: 79
Period size: 27 Copynumber: 2.0 Consensus size: 27
2776201 AAATATCACT
*
2776211 TCTTAAAGACAGCTAAATAAACTAATC
1 TCTTAAAGACAACTAAATAAACTAATC
* *
2776238 TCTTAAAGATAACTAGATAAACTAAT
1 TCTTAAAGACAACTAAATAAACTAAT
2776264 TAAGCTAAGC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.49, C:0.15, G:0.08, T:0.28
Consensus pattern (27 bp):
TCTTAAAGACAACTAAATAAACTAATC
Found at i:2779732 original size:3 final size:3
Alignment explanation
Indices: 2779719--2779754 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
2779709 GATGTGAGAG
*
2779719 AGA ACA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
2779755 CGAGAAGGAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.67, C:0.03, G:0.31, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:2780373 original size:30 final size:31
Alignment explanation
Indices: 2780300--2780375 Score: 102
Period size: 30 Copynumber: 2.5 Consensus size: 31
2780290 GTTAATTTAT
**
2780300 GTTAAGAGTTTATTTAGTTATAAATTAAAAA
1 GTTAAGAGTTTATTTAAATATAAATTAAAAA
**
2780331 GTT-AGAAATTATTTAAATATAAATTAAAAA
1 GTTAAGAGTTTATTTAAATATAAATTAAAAA
2780361 -TTAAGAGTTTATTTA
1 GTTAAGAGTTTATTTA
2780376 GATGTAATAA
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
29 2 0.05
30 33 0.87
31 3 0.08
ACGTcount: A:0.47, C:0.00, G:0.11, T:0.42
Consensus pattern (31 bp):
GTTAAGAGTTTATTTAAATATAAATTAAAAA
Found at i:2780413 original size:29 final size:28
Alignment explanation
Indices: 2780349--2780414 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 28
2780339 TTATTTAAAT
* * *
2780349 ATAAATTAAAAATTAAGAGTTTATTTAG
1 ATAAAATAAAAATTAAAAGTTTATTCAG
** *
2780377 ATGTAATAAACATATAAAAGTTTATTCAG
1 ATAAAATAAAAAT-TAAAAGTTTATTCAG
2780406 ATAAAATAA
1 ATAAAATAA
2780415 TAAAGTTTAA
Statistics
Matches: 29, Mismatches: 8, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
28 9 0.31
29 20 0.69
ACGTcount: A:0.53, C:0.03, G:0.09, T:0.35
Consensus pattern (28 bp):
ATAAAATAAAAATTAAAAGTTTATTCAG
Found at i:2782019 original size:11 final size:11
Alignment explanation
Indices: 2782003--2782037 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
2781993 CTGTGCTGCC
*
2782003 TGTTTTGTTTT
1 TGTTTTTTTTT
2782014 TGTTTTTTTTT
1 TGTTTTTTTTT
*
2782025 TTTTTTTTTTT
1 TGTTTTTTTTT
2782036 TG
1 TG
2782038 AGTATTTTAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.00, C:0.00, G:0.11, T:0.89
Consensus pattern (11 bp):
TGTTTTTTTTT
Found at i:2786671 original size:20 final size:18
Alignment explanation
Indices: 2786642--2786682 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
2786632 GAAAGAGAAA
2786642 TTAAATAATTATATAAATT
1 TTAAATAATTATAT-AATT
*
2786661 TTAATATAATTTTATAATT
1 TTAA-ATAATTATATAATT
2786680 TTA
1 TTA
2786683 TATTATATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 11 0.55
20 9 0.45
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAATAATTATATAATT
Found at i:2786685 original size:18 final size:19
Alignment explanation
Indices: 2786642--2786697 Score: 62
Period size: 18 Copynumber: 3.0 Consensus size: 19
2786632 GAAAGAGAAA
*
2786642 TTAA-ATAATTATATAAATT
1 TTAATATAATTTTAT-AATT
2786661 TTAATATAATTTTATAATT
1 TTAATATAATTTTATAATT
* *
2786680 TT-ATATTATATTATAATT
1 TTAATATAATTTTATAATT
2786698 ATTTTTATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
18 14 0.42
19 10 0.30
20 9 0.27
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATATAATTTTATAATT
Found at i:2786707 original size:17 final size:19
Alignment explanation
Indices: 2786672--2786715 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
2786662 TAATATAATT
2786672 TTATAATT-TTATATTATA
1 TTATAATTATTATATTATA
2786690 TTATAATTATT-T-TTATA
1 TTATAATTATTATATTATA
2786707 TTATAATTA
1 TTATAATTA
2786716 ACTTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
17 14 0.56
18 9 0.36
19 2 0.08
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TTATAATTATTATATTATA
Found at i:2787183 original size:27 final size:27
Alignment explanation
Indices: 2787153--2787235 Score: 68
Period size: 28 Copynumber: 3.1 Consensus size: 27
2787143 AAATATAATA
2787153 ATTTATTTATTTATATTATATTTATAT
1 ATTTATTTATTTATATTATATTTATAT
* * *
2787180 ATTTTATTAAATAATAATTAT-TTTA-A-
1 A-TTTATTTATTTAT-ATTATATTTATAT
2787206 ATTT-TTTATTTATATTA-ATTTTAATAT
1 ATTTATTTATTTATATTATA-TTT-ATAT
2787233 ATT
1 ATT
2787236 AATAATTCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 14
0.68 0.10 0.22
Matches are distributed among these distances:
23 4 0.09
24 9 0.21
25 4 0.09
26 2 0.05
27 5 0.12
28 14 0.33
29 5 0.12
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (27 bp):
ATTTATTTATTTATATTATATTTATAT
Found at i:2787187 original size:28 final size:28
Alignment explanation
Indices: 2787149--2787218 Score: 70
Period size: 28 Copynumber: 2.5 Consensus size: 28
2787139 GGTTAAATAT
* *
2787149 AATAATTTATTTATTTAT-ATTATATTTA
1 AATATTTTATTTATTAATAATTAT-TTTA
* * *
2787177 TATATTTTATTAAATAATAATTATTTTA
1 AATATTTTATTTATTAATAATTATTTTA
*
2787205 AATTTTTTATTTAT
1 AATATTTTATTTAT
2787219 ATTAATTTTA
Statistics
Matches: 32, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
28 27 0.84
29 5 0.16
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (28 bp):
AATATTTTATTTATTAATAATTATTTTA
Found at i:2787222 original size:23 final size:23
Alignment explanation
Indices: 2787152--2787229 Score: 66
Period size: 24 Copynumber: 3.0 Consensus size: 23
2787142 TAAATATAAT
2787152 AATTTATTTATTTATATTATATTTA
1 AATTT-TTTATTTATATTAT-TTTA
* *
2787177 TATATTTTATTAAATAATAATTATTTTA
1 -A-ATTTT-TT-ATTTAT-ATTATTTTA
2787205 AATTTTTTATTTATATTAATTTTA
1 AATTTTTTATTTATATT-ATTTTA
2787229 A
1 A
2787230 TATATTAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
23 3 0.07
24 11 0.26
25 2 0.05
26 7 0.16
27 7 0.16
28 8 0.19
29 5 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (23 bp):
AATTTTTTATTTATATTATTTTA
Found at i:2789109 original size:2 final size:2
Alignment explanation
Indices: 2789102--2789135 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2789092 CCATACGTAC
2789102 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2789136 GTAATTTTTA
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):
AT
Found at i:2789405 original size:2 final size:2
Alignment explanation
Indices: 2789398--2789430 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2789388 AAATCAAAAT
2789398 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 G
2789431 CCATTAATCT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2789718 original size:2 final size:2
Alignment explanation
Indices: 2789711--2789757 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
2789701 AAAATCTTCT
2789711 TA TA TA TA 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 TA TA TA TA
2789753 TA TA T
1 TA TA T
2789758 TAAAAAGCCA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.