Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold48
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: 4619657
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 18863 characters in sequence are not A, C, G, or T
File 20 of 27
Found at i:2942308 original size:3 final size:3
Alignment explanation
Indices: 2942300--2942325 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
2942290 GAATATTACG
2942300 ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT AT
2942326 ACGTGAGAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:2942406 original size:2 final size:2
Alignment explanation
Indices: 2942393--2942423 Score: 53
Period size: 2 Copynumber: 15.0 Consensus size: 2
2942383 TATTTAACAT
2942393 TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA
2942424 AAGATCATTT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 26 0.93
3 2 0.07
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
TA
Found at i:2942835 original size:16 final size:16
Alignment explanation
Indices: 2942816--2942858 Score: 70
Period size: 16 Copynumber: 2.8 Consensus size: 16
2942806 AATTTATATA
2942816 ATAATTTTTAAAATTT
1 ATAATTTTTAAAATTT
*
2942832 ATAATTTATAAAATTT
1 ATAATTTTTAAAATTT
2942848 -TAATTTTTAAA
1 ATAATTTTTAAA
2942859 TCTCAACCTA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 10 0.40
16 15 0.60
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
ATAATTTTTAAAATTT
Found at i:2943748 original size:18 final size:19
Alignment explanation
Indices: 2943689--2943749 Score: 63
Period size: 18 Copynumber: 3.2 Consensus size: 19
2943679 TCCAATATTT
*
2943689 TTTTATAGTAAAATTAATTAA
1 TTTTAT-GTATAATTAA-TAA
* *
2943710 TTTTATGTAT-TTTTATAA
1 TTTTATGTATAATTAATAA
2943728 TTTTATGTATAATTAAT-A
1 TTTTATGTATAATTAATAA
2943746 TTTT
1 TTTT
2943750 CATAATTTAA
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
18 18 0.53
19 7 0.21
20 3 0.09
21 6 0.18
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (19 bp):
TTTTATGTATAATTAATAA
Found at i:2945069 original size:7 final size:7
Alignment explanation
Indices: 2945058--2945092 Score: 61
Period size: 7 Copynumber: 5.0 Consensus size: 7
2945048 ACTTCCAACC
*
2945058 TCAAATC
1 TCAAATT
2945065 TCAAATT
1 TCAAATT
2945072 TCAAATT
1 TCAAATT
2945079 TCAAATT
1 TCAAATT
2945086 TCAAATT
1 TCAAATT
2945093 GAACTTCATC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 27 1.00
ACGTcount: A:0.43, C:0.17, G:0.00, T:0.40
Consensus pattern (7 bp):
TCAAATT
Found at i:2945182 original size:16 final size:16
Alignment explanation
Indices: 2945161--2945192 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
2945151 CTACCTAGAT
2945161 ATACTCTTATCTTTTC
1 ATACTCTTATCTTTTC
2945177 ATACTCTTATCTTTTC
1 ATACTCTTATCTTTTC
2945193 GTTATTTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.00, T:0.56
Consensus pattern (16 bp):
ATACTCTTATCTTTTC
Found at i:2959919 original size:2 final size:2
Alignment explanation
Indices: 2959914--2959942 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2959904 TATATATATA
2959914 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
2959943 CTATAATTGA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:2960405 original size:2 final size:2
Alignment explanation
Indices: 2960398--2960424 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2960388 ACATGCATAC
2960398 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 A
2960425 ATAGACCAAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2963346 original size:9 final size:9
Alignment explanation
Indices: 2963332--2963384 Score: 60
Period size: 9 Copynumber: 6.3 Consensus size: 9
2963322 ATATGAATCG
2963332 ATATATTTA
1 ATATATTTA
*
2963341 ATATATGTA
1 ATATATTTA
*
2963350 TTATATTT-
1 ATATATTTA
2963358 ATAT-TTTA
1 ATATATTTA
2963366 A-AT-TTTA
1 ATATATTTA
2963373 ATATATTTA
1 ATATATTTA
2963382 ATA
1 ATA
2963385 ATGTGTTGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
7 10 0.27
8 6 0.16
9 21 0.57
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.57
Consensus pattern (9 bp):
ATATATTTA
Found at i:2974294 original size:100 final size:100
Alignment explanation
Indices: 2974121--2974414 Score: 579
Period size: 100 Copynumber: 2.9 Consensus size: 100
2974111 AACAGATAGC
2974121 TTTGACGTTACCTATATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
1 TTTGACGTTACCTATATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
2974186 ATAATTGAATTGGTCTTCAGCCTCGAAATTTCTAG
66 ATAATTGAATTGGTCTTCAGCCTCGAAATTTCTAG
2974221 TTTGACGTTACCTATATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
1 TTTGACGTTACCTATATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
2974286 ATAATTGAATTGGTCTTCAGCCTCGAAATTTCTAG
66 ATAATTGAATTGGTCTTCAGCCTCGAAATTTCTAG
*
2974321 TTTGACGTTACCTCTATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
1 TTTGACGTTACCTATATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
2974386 ATAATTGAATTGGTCTTCAGCCTCGAAAT
66 ATAATTGAATTGGTCTTCAGCCTCGAAAT
2974415 GTCCTAACTA
Statistics
Matches: 193, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
100 193 1.00
ACGTcount: A:0.35, C:0.10, G:0.09, T:0.46
Consensus pattern (100 bp):
TTTGACGTTACCTATATAATTTTAATTTTGTAATATATATTATTTTTACATTAAAATAATATATA
ATAATTGAATTGGTCTTCAGCCTCGAAATTTCTAG
Found at i:2978618 original size:19 final size:21
Alignment explanation
Indices: 2978594--2978641 Score: 57
Period size: 19 Copynumber: 2.4 Consensus size: 21
2978584 AAAGTTTGAA
*
2978594 TTTAATTTA-AAT-TTATTTT
1 TTTAATTTATAATCATATTTT
2978613 TTTAA-TTATAATCATATTTT
1 TTTAATTTATAATCATATTTT
2978633 TATTAATTT
1 T-TTAATTT
2978642 TAGATAGAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
18 3 0.12
19 8 0.33
20 7 0.29
21 4 0.17
22 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (21 bp):
TTTAATTTATAATCATATTTT
Found at i:2987980 original size:15 final size:15
Alignment explanation
Indices: 2987962--2987992 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2987952 AGTTATATTT
2987962 AAAAATAATATATAA
1 AAAAATAATATATAA
*
2987977 AAAATTAATATATAA
1 AAAAATAATATATAA
2987992 A
1 A
2987993 TTAATTAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAATATATAA
Found at i:2988014 original size:16 final size:17
Alignment explanation
Indices: 2987967--2988014 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 17
2987957 TATTTAAAAA
2987967 TAATATATAAA--AAAT
1 TAATATATAAATTAAAT
2987982 TAATATATAAATT-AAT
1 TAATATATAAATTAAAT
2987998 TAA-AT-TAAATTTAAAT
1 TAATATATAAA-TTAAAT
2988014 T
1 T
2988015 CGTATAATTT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
14 4 0.14
15 15 0.52
16 10 0.34
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATATATAAATTAAAT
Found at i:2988231 original size:26 final size:28
Alignment explanation
Indices: 2988162--2988232 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 28
2988152 TAAATGTATA
*
2988162 AAAATTATTATTTTATAAATAAAATTAAT
1 AAAATTATTATTTTATAAAT-AAATAAAT
* *
2988191 AAAATTA-CACATTTA-AAAT-AATAAAT
1 AAAATTATTA-TTTTATAAATAAATAAAT
2988217 AAAATTATTATTTTAT
1 AAAATTATTATTTTAT
2988233 TTTATAATAT
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
26 17 0.50
27 1 0.03
28 5 0.15
29 11 0.32
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (28 bp):
AAAATTATTATTTTATAAATAAATAAAT
Found at i:2988668 original size:21 final size:21
Alignment explanation
Indices: 2988644--2988769 Score: 68
Period size: 21 Copynumber: 6.0 Consensus size: 21
2988634 ATAAAACAGA
2988644 AAAATAAATATAATATAATAT
1 AAAATAAATATAATATAATAT
* *
2988665 AAAA-ATAATATAAAATATTAT
1 AAAATA-AATATAATATAATAT
* * *
2988686 ATAAATATAT-TAAAATTTATAT
1 A-AAATAAATATAATA-TAATAT
*
2988708 AATATAAAT-TAATAT-AT-T
1 AAAATAAATATAATATAATAT
* *
2988726 AAAATTATATAAACATATAATAT
1 AAAA-TAAATATA-ATATAATAT
*
2988749 --TATAAATATAATTATAATAT
1 AAAATAAATATAA-TATAATAT
2988769 A
1 A
2988770 CAAAATATAT
Statistics
Matches: 80, Mismatches: 14, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
18 4 0.05
19 7 0.09
20 17 0.21
21 38 0.47
22 12 0.15
23 2 0.03
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (21 bp):
AAAATAAATATAATATAATAT
Found at i:2988672 original size:16 final size:16
Alignment explanation
Indices: 2988647--2988677 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
2988637 AAACAGAAAA
*
2988647 ATAAATATAATATAAT
1 ATAAAAATAATATAAT
2988663 ATAAAAATAATATAA
1 ATAAAAATAATATAA
2988678 AATATTATAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATAAAAATAATATAAT
Found at i:2988732 original size:14 final size:14
Alignment explanation
Indices: 2988689--2988736 Score: 62
Period size: 14 Copynumber: 3.4 Consensus size: 14
2988679 ATATTATATA
2988689 AATATATTAAAATT
1 AATATATTAAAATT
* *
2988703 TATATAATATAAATT
1 AATATATTA-AAATT
2988718 AATATATTAAAATT
1 AATATATTAAAATT
2988732 -ATATA
1 AATATA
2988737 AACATATAAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
13 5 0.17
14 12 0.41
15 12 0.41
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (14 bp):
AATATATTAAAATT
Found at i:2988733 original size:48 final size:46
Alignment explanation
Indices: 2988647--2988783 Score: 133
Period size: 48 Copynumber: 3.0 Consensus size: 46
2988637 AAACAGAAAA
*
2988647 ATAAATATAATATAATATAAA--AATAATATAAAATATTATATAAATAT
1 ATAAA-ATTATATAATATAAATTAAT-ATATAAAA-ATTATATAAATAT
* *
2988694 ATTAAAATTTATATAATATAAATTAATATATTAAAATTATATAAACAT
1 A-TAAAA-TTATATAATATAAATTAATATATAAAAATTATATAAATAT
*
2988742 ATAATATTATA-AATAT-AATT-ATAATATACAAAA-TATATAAAT
1 ATAAAATTATATAATATAAATTAAT-ATATA-AAAATTATATAAAT
2988784 GAGAATCATT
Statistics
Matches: 78, Mismatches: 6, Indels: 15
0.79 0.06 0.15
Matches are distributed among these distances:
43 2 0.03
44 16 0.21
45 9 0.12
46 5 0.06
47 6 0.08
48 30 0.38
49 7 0.09
50 3 0.04
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (46 bp):
ATAAAATTATATAATATAAATTAATATATAAAAATTATATAAATAT
Found at i:2989925 original size:3 final size:3
Alignment explanation
Indices: 2989919--2989945 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
2989909 TATTATTCGT
2989919 TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA
2989946 ATTGATGGCT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:2996555 original size:18 final size:19
Alignment explanation
Indices: 2996526--2996563 Score: 60
Period size: 18 Copynumber: 2.1 Consensus size: 19
2996516 AAAATATATA
*
2996526 ATTTTTTAAATATTTAAAT
1 ATTTTTTAAATAATTAAAT
2996545 ATTTTTT-AATAATTAAAT
1 ATTTTTTAAATAATTAAAT
2996563 A
1 A
2996564 AATTTAAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.61
19 7 0.39
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTTTTTAAATAATTAAAT
Found at i:2997964 original size:32 final size:32
Alignment explanation
Indices: 2997898--2997979 Score: 89
Period size: 32 Copynumber: 2.5 Consensus size: 32
2997888 AGGTGATATA
* *
2997898 TTTATAT-AAGTTTAATTTATTAATTATTTAT
1 TTTATATAAATTTTAATATATTAATTATTTAT
2997929 TTTATATAAATTTTAATATATTTATATTA-TT-T
1 TTTATATAAATTTTAATATA-TTA-ATTATTTAT
2997961 TTTATATTATAATTTTAAT
1 TTTATA-TA-AATTTTAAT
2997980 TCTTTTTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 7 0.16
32 17 0.39
33 7 0.16
34 13 0.30
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (32 bp):
TTTATATAAATTTTAATATATTAATTATTTAT
Found at i:2997975 original size:34 final size:31
Alignment explanation
Indices: 2997898--2997979 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 31
2997888 AGGTGATATA
* *
2997898 TTTATATAAGTTTAATTTATTAATTATTTAT
1 TTTATATAATTTTAATATATTAATTATTTAT
2997929 TTTATATAAATTTTAATATATTTATATTATTT-T
1 TTTATAT-AATTTTAATATA-TTA-ATTATTTAT
2997962 TTATATTATAATTTTAAT
1 TT-TA-TATAATTTTAAT
2997980 TCTTTTTATC
Statistics
Matches: 44, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
31 7 0.16
32 10 0.23
33 6 0.14
34 18 0.41
35 3 0.07
ACGTcount: A:0.37, C:0.00, G:0.01, T:0.62
Consensus pattern (31 bp):
TTTATATAATTTTAATATATTAATTATTTAT
Found at i:2999426 original size:2 final size:2
Alignment explanation
Indices: 2999419--2999468 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
2999409 TACCTGTAAG
2999419 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
2999461 TA TA TA TA
1 TA TA TA TA
2999469 CACACACACA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:2999473 original size:2 final size:2
Alignment explanation
Indices: 2999468--2999494 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2999458 ATATATATAT
2999468 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 A
2999495 AACATACATA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:3004783 original size:8 final size:8
Alignment explanation
Indices: 3004770--3004799 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
3004760 CGAAAGTGGA
3004770 AAAAAAAT
1 AAAAAAAT
*
3004778 AAAAAAGT
1 AAAAAAAT
3004786 AAAAAAAT
1 AAAAAAAT
3004794 AAAAAA
1 AAAAAA
3004800 GGGAAGGGAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.87, C:0.00, G:0.03, T:0.10
Consensus pattern (8 bp):
AAAAAAAT
Found at i:3004791 original size:16 final size:16
Alignment explanation
Indices: 3004770--3004800 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
3004760 CGAAAGTGGA
3004770 AAAAAAATAAAAAAGT
1 AAAAAAATAAAAAAGT
3004786 AAAAAAATAAAAAAG
1 AAAAAAATAAAAAAG
3004801 GGAAGGGAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.06, T:0.10
Consensus pattern (16 bp):
AAAAAAATAAAAAAGT
Found at i:3014388 original size:6 final size:6
Alignment explanation
Indices: 3014373--3014405 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
3014363 CTTCTTGAAT
*
3014373 AAAATG AAAATA AAAATA AAAATA AAAATA AAA
1 AAAATA AAAATA AAAATA AAAATA AAAATA AAA
3014406 TGAATAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (6 bp):
AAAATA
Found at i:3015304 original size:17 final size:17
Alignment explanation
Indices: 3015284--3015317 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3015274 ATCATGTTAT
3015284 TTTTATAGTATATTTTA
1 TTTTATAGTATATTTTA
* *
3015301 TTTTATATTTTATTTTA
1 TTTTATAGTATATTTTA
3015318 ATTATTATGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (17 bp):
TTTTATAGTATATTTTA
Found at i:3015325 original size:12 final size:12
Alignment explanation
Indices: 3015292--3015317 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3015282 ATTTTTATAG
3015292 TATATTTTATTT
1 TATATTTTATTT
3015304 TATATTTTATTT
1 TATATTTTATTT
3015316 TA
1 TA
3015318 ATTATTATGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (12 bp):
TATATTTTATTT
Found at i:3015386 original size:2 final size:2
Alignment explanation
Indices: 3015379--3015411 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3015369 TGTTTCCTTA
3015379 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
3015412 TTTTAATAGA
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:3015986 original size:20 final size:20
Alignment explanation
Indices: 3015949--3015987 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3015939 TATATATATA
3015949 TATATATATAATAATTTGTG
1 TATATATATAATAATTTGTG
* * *
3015969 TATATGTATTATATTTTGT
1 TATATATATAATAATTTGT
3015988 AATTTTTATA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.56
Consensus pattern (20 bp):
TATATATATAATAATTTGTG
Found at i:3016074 original size:15 final size:16
Alignment explanation
Indices: 3016040--3016088 Score: 57
Period size: 15 Copynumber: 3.2 Consensus size: 16
3016030 AAATTTTTAA
*
3016040 ATAAAAATA-TATATT
1 ATAAATATATTATATT
*
3016055 ATAAATCTATTATATT
1 ATAAATATATTATATT
*
3016071 -TAAATATATCATATT
1 ATAAATATATTATATT
3016086 ATA
1 ATA
3016089 TTTATTAAAT
Statistics
Matches: 28, Mismatches: 4, Indels: 3
0.80 0.11 0.09
Matches are distributed among these distances:
15 20 0.71
16 8 0.29
ACGTcount: A:0.51, C:0.04, G:0.00, T:0.45
Consensus pattern (16 bp):
ATAAATATATTATATT
Found at i:3016085 original size:20 final size:18
Alignment explanation
Indices: 3016039--3016109 Score: 67
Period size: 18 Copynumber: 4.0 Consensus size: 18
3016029 AAAATTTTTA
*
3016039 AATAAAAATA-TATA-TT
1 AATAAATATATTATATTT
*
3016055 -ATAAATCTATTATATTT
1 AATAAATATATTATATTT
*
3016072 AAATATATCATATTATATTT
1 -AATAAAT-ATATTATATTT
*
3016092 ATTAAATATATTATATTT
1 AATAAATATATTATATTT
3016110 TTATATTATT
Statistics
Matches: 44, Mismatches: 6, Indels: 8
0.76 0.10 0.14
Matches are distributed among these distances:
15 7 0.16
16 4 0.09
17 2 0.05
18 11 0.25
19 10 0.23
20 10 0.23
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.49
Consensus pattern (18 bp):
AATAAATATATTATATTT
Found at i:3016359 original size:9 final size:9
Alignment explanation
Indices: 3016337--3016369 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
3016327 TGACCTATCA
3016337 TTTATTTA-
1 TTTATTTAT
3016345 TTTATTTAT
1 TTTATTTAT
3016354 TTTATTTAT
1 TTTATTTAT
3016363 TATTATT
1 T-TTATT
3016370 GTAAATTCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.35
9 10 0.43
10 5 0.22
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:3016491 original size:25 final size:25
Alignment explanation
Indices: 3016457--3016541 Score: 73
Period size: 25 Copynumber: 3.2 Consensus size: 25
3016447 TGTACGAAAG
*
3016457 AATTTTTTAAAAAAATTAAATTTAT
1 AATTTATTAAAAAAATTAAATTTAT
* *
3016482 AATTTATTAATAAAA-TAATTTTATT
1 AATTTATTAAAAAAATTAAATTTA-T
*
3016507 AAATTTAATTAAAAATATATAAATATTAAT
1 -AATTT-ATTAAAAAAAT-TAAAT-TT-AT
3016537 AATTT
1 AATTT
3016542 TAAATTTTAA
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
24 7 0.15
25 14 0.30
26 5 0.11
27 8 0.17
29 9 0.19
30 3 0.06
31 1 0.02
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTATTAAAAAAATTAAATTTAT
Found at i:3017429 original size:58 final size:59
Alignment explanation
Indices: 3017334--3017446 Score: 201
Period size: 58 Copynumber: 1.9 Consensus size: 59
3017324 ATCAATTCCA
* *
3017334 CCCCTAAAATTCTGATTAAAAATTATTAATTGACCCCTTGATATATCGATTTGTAATCC
1 CCCCTAAAATTCCGATTAAAAATTATTAATTGACCCCTCGATATATCGATTTGTAATCC
3017393 CCCCTAAAATTCCGATT-AAAATTATTAATTGACCCCTCGATATATCGATTTGTA
1 CCCCTAAAATTCCGATTAAAAATTATTAATTGACCCCTCGATATATCGATTTGTA
3017447 TCAATTTTAA
Statistics
Matches: 52, Mismatches: 2, Indels: 1
0.95 0.04 0.02
Matches are distributed among these distances:
58 36 0.69
59 16 0.31
ACGTcount: A:0.34, C:0.21, G:0.09, T:0.36
Consensus pattern (59 bp):
CCCCTAAAATTCCGATTAAAAATTATTAATTGACCCCTCGATATATCGATTTGTAATCC
Found at i:3017992 original size:18 final size:16
Alignment explanation
Indices: 3017971--3018004 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 16
3017961 CAAAAACTCC
3017971 TCAAATAAATAAAAAAAT
1 TCAAA-AAA-AAAAAAAT
3017989 TCAAAAAAAAAAAAAT
1 TCAAAAAAAAAAAAAT
3018005 CTATATGGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 8 0.50
17 3 0.19
18 5 0.31
ACGTcount: A:0.76, C:0.06, G:0.00, T:0.18
Consensus pattern (16 bp):
TCAAAAAAAAAAAAAT
Found at i:3018746 original size:64 final size:64
Alignment explanation
Indices: 3018640--3018766 Score: 188
Period size: 64 Copynumber: 2.0 Consensus size: 64
3018630 ACTAAAAAAA
* *
3018640 AAATTGAACATACTCATATCGGACACATATTGATATCCACAAT-TGCACCCGA-TTATGAGTAAC
1 AAATTGAACATACCCATATCGAACACATATTGATATCCACAATCT-CACCCGAGTT-TGAGTAAC
3018703 G
64 G
3018704 AAATTGAACATACCCATATCGAACACAT-TTGATATCCGACAATCTCACCCGAGTTTGAGTAAC
1 AAATTGAACATACCCATATCGAACACATATTGATATCC-ACAATCTCACCCGAGTTTGAGTAAC
3018767 ATAAGAACAA
Statistics
Matches: 58, Mismatches: 2, Indels: 6
0.88 0.03 0.09
Matches are distributed among these distances:
63 9 0.16
64 46 0.79
65 3 0.05
ACGTcount: A:0.37, C:0.24, G:0.13, T:0.26
Consensus pattern (64 bp):
AAATTGAACATACCCATATCGAACACATATTGATATCCACAATCTCACCCGAGTTTGAGTAACG
Found at i:3022576 original size:2 final size:2
Alignment explanation
Indices: 3022569--3022599 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3022559 AGTTGACATT
3022569 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3022600 TCATGTTTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3023627 original size:2 final size:2
Alignment explanation
Indices: 3023615--3023657 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
3023605 TAAAAGTTGG
3023615 AT AT A- AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3023656 AT
1 AT
3023658 CAGACATAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3028854 original size:20 final size:21
Alignment explanation
Indices: 3028819--3028877 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
3028809 AATATTTTAA
3028819 TTTTAAATTAATAAAAAAA-AC
1 TTTTAAATT-ATAAAAAAATAC
* *
3028840 TTTTAAAATATAAAAAAATAT
1 TTTTAAATTATAAAAAAATAC
*
3028861 TTTTAAATTTTAAAAAA
1 TTTTAAATTATAAAAAA
3028878 TATTAACTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
20 9 0.27
21 24 0.73
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (21 bp):
TTTTAAATTATAAAAAAATAC
Found at i:3028878 original size:20 final size:20
Alignment explanation
Indices: 3028819--3028881 Score: 63
Period size: 20 Copynumber: 3.0 Consensus size: 20
3028809 AATATTTTAA
* *
3028819 TTTTAAATTAATAAAAAAAACT
1 TTTTAAATT-TTAAAAAATA-T
* * *
3028841 TTTAAAATATAAAAAAATAT
1 TTTTAAATTTTAAAAAATAT
3028861 TTTTAAATTTTAAAAAATAT
1 TTTTAAATTTTAAAAAATAT
3028881 T
1 T
3028882 AACTAAACCT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
20 19 0.58
21 7 0.21
22 7 0.21
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTAAATTTTAAAAAATAT
Found at i:3028936 original size:2 final size:2
Alignment explanation
Indices: 3028929--3028963 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
3028919 TCAAACGAAT
*
3028929 TA TA TA TA TA TA TA TA TA TA TA TA TA AA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3028964 CAATTTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3033405 original size:10 final size:10
Alignment explanation
Indices: 3033390--3033424 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
3033380 TTTAAATTTT
*
3033390 AAAATAAATA
1 AAAATAATTA
3033400 AAAATAATTA
1 AAAATAATTA
3033410 TAAAATAATTA
1 -AAAATAATTA
3033421 AAAA
1 AAAA
3033425 ATTTTACATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.57
11 10 0.43
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (10 bp):
AAAATAATTA
Found at i:3033413 original size:21 final size:21
Alignment explanation
Indices: 3033384--3033424 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3033374 ATTAATTTTA
*
3033384 AATTTTAAAATAAATAAAAAT
1 AATTATAAAATAAATAAAAAT
*
3033405 AATTATAAAATAATTAAAAA
1 AATTATAAAATAAATAAAAA
3033425 ATTTTACATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (21 bp):
AATTATAAAATAAATAAAAAT
Found at i:3033416 original size:11 final size:11
Alignment explanation
Indices: 3033384--3033426 Score: 52
Period size: 11 Copynumber: 4.0 Consensus size: 11
3033374 ATTAATTTTA
*
3033384 AATTTTAAAAT
1 AATTATAAAAT
*
3033395 AAATA-AAAAT
1 AATTATAAAAT
3033405 AATTATAAAAT
1 AATTATAAAAT
*
3033416 AATTAAAAAAT
1 AATTATAAAAT
3033427 TTTACATTTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
10 9 0.33
11 18 0.67
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (11 bp):
AATTATAAAAT
Found at i:3037693 original size:11 final size:11
Alignment explanation
Indices: 3037662--3037729 Score: 66
Period size: 11 Copynumber: 6.0 Consensus size: 11
3037652 CTGGATGATA
3037662 TTAAATATAAT
1 TTAAATATAAT
*
3037673 TAAATTATATAAT
1 TTAA--ATATAAT
3037686 TTAAATATAAT
1 TTAAATATAAT
* *
3037697 ATAAAAATAA-
1 TTAAATATAAT
3037707 TTAATATATAAT
1 TTAA-ATATAAT
*
3037719 ATAAATATAAT
1 TTAAATATAAT
3037730 ATGAATATTT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
10 3 0.07
11 30 0.65
12 3 0.07
13 10 0.22
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (11 bp):
TTAAATATAAT
Found at i:3037730 original size:11 final size:11
Alignment explanation
Indices: 3037679--3037737 Score: 75
Period size: 11 Copynumber: 5.4 Consensus size: 11
3037669 TAATTAAATT
*
3037679 ATATAATTTAA
1 ATATAATATAA
3037690 ATATAATATAA
1 ATATAATATAA
*
3037701 AAATAAT-TAA
1 ATATAATATAA
3037711 TATATAATATAA
1 -ATATAATATAA
*
3037723 ATATAATATGA
1 ATATAATATAA
3037734 ATAT
1 ATAT
3037738 TTTAAATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
10 3 0.07
11 36 0.86
12 3 0.07
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (11 bp):
ATATAATATAA
Found at i:3037737 original size:22 final size:21
Alignment explanation
Indices: 3037661--3037729 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 21
3037651 TCTGGATGAT
3037661 ATTAAATATAAT-TAAATTATATA
1 ATTAAATATAATAT-AA--ATATA
*
3037684 ATTTAAATATAATATAAAAATA
1 A-TTAAATATAATATAAATATA
3037706 ATTAATATATAATATAAATATA
1 ATTAA-ATATAATATAAATATA
3037728 AT
1 AT
3037730 ATGAATATTT
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
21 4 0.10
22 22 0.54
23 1 0.02
24 13 0.32
25 1 0.02
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
ATTAAATATAATATAAATATA
Found at i:3039096 original size:10 final size:10
Alignment explanation
Indices: 3039081--3039105 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
3039071 TAACACCGGC
3039081 ATTTTTGGCA
1 ATTTTTGGCA
3039091 ATTTTTGGCA
1 ATTTTTGGCA
3039101 ATTTT
1 ATTTT
3039106 ACAAATCTAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.20, C:0.08, G:0.16, T:0.56
Consensus pattern (10 bp):
ATTTTTGGCA
Found at i:3039718 original size:20 final size:19
Alignment explanation
Indices: 3039674--3039719 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 19
3039664 ATCTTTTCCT
3039674 AAAAC-TACAAGAGGTAAA
1 AAAACATACAAGAGGTAAA
3039692 AAAACATACAAGAGGTAAA
1 AAAACATACAAGAGGTAAA
3039711 AGAAACATA
1 A-AAACATA
3039720 GCTCTGTTCT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
18 5 0.19
19 14 0.54
20 7 0.27
ACGTcount: A:0.63, C:0.11, G:0.15, T:0.11
Consensus pattern (19 bp):
AAAACATACAAGAGGTAAA
Found at i:3043829 original size:28 final size:26
Alignment explanation
Indices: 3043798--3043854 Score: 87
Period size: 28 Copynumber: 2.1 Consensus size: 26
3043788 TATTTTTTTA
3043798 AAACAATTATAATAATAAAAAAATTATC
1 AAACAATTATAATAAT-AAAAAA-TATC
*
3043826 AAACATTTATAATAATAAAAAATATC
1 AAACAATTATAATAATAAAAAATATC
3043852 AAA
1 AAA
3043855 AAAAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
26 7 0.25
27 6 0.21
28 15 0.54
ACGTcount: A:0.65, C:0.07, G:0.00, T:0.28
Consensus pattern (26 bp):
AAACAATTATAATAATAAAAAATATC
Found at i:3043862 original size:29 final size:28
Alignment explanation
Indices: 3043804--3043866 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
3043794 TTTAAAACAA
* ** *
3043804 TTATAATAATAAAAAAATTATCAAACAT
1 TTATAATAATAAAAAAATCAAAAAAAAT
3043832 TTATAATAATAAAAAATATCAAAAAAAAT
1 TTATAATAATAAAAAA-ATCAAAAAAAAT
3043861 TTATAA
1 TTATAA
3043867 ATCCTTAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.63, C:0.05, G:0.00, T:0.32
Consensus pattern (28 bp):
TTATAATAATAAAAAAATCAAAAAAAAT
Found at i:3043934 original size:59 final size:56
Alignment explanation
Indices: 3043871--3043992 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 56
3043861 TTATAAATCC
3043871 TTAAAATTAAACTTGATAAATATGTGATTATAATTGTATTTTTTTTATTATAATCATAT
1 TTAAAATTAAACTTGATAAATATGTGATTATAATTGTA---TTTTTATTATAATCATAT
* *
3043930 TTAAAATTAAATTTGATAAATATGTGATTATAATTGTATTTTTATTATAATTATAT
1 TTAAAATTAAACTTGATAAATATGTGATTATAATTGTATTTTTATTATAATCATAT
3043986 TTAAAAT
1 TTAAAAT
3043993 ATTTTTATTT
Statistics
Matches: 61, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
56 24 0.39
59 37 0.61
ACGTcount: A:0.41, C:0.02, G:0.07, T:0.51
Consensus pattern (56 bp):
TTAAAATTAAACTTGATAAATATGTGATTATAATTGTATTTTTATTATAATCATAT
Found at i:3044066 original size:20 final size:20
Alignment explanation
Indices: 3044022--3044101 Score: 57
Period size: 19 Copynumber: 4.2 Consensus size: 20
3044012 TTGATAAATT
3044022 TATTTTTTTAATTATCTTTA
1 TATTTTTTTAATTATCTTTA
3044042 T-TTTTTTTACATT-T-TATTA
1 TATTTTTTTA-ATTATCT-TTA
* *
3044061 TATTTTATTTTATT-T-TTAAA
1 TATTTT-TTTAATTATCTT-TA
3044081 TATTTTTTTAA-TAT-TTTA
1 TATTTTTTTAATTATCTTTA
3044099 TAT
1 TAT
3044102 GATATTTAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 14
0.74 0.06 0.21
Matches are distributed among these distances:
18 6 0.12
19 21 0.42
20 20 0.40
21 3 0.06
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (20 bp):
TATTTTTTTAATTATCTTTA
Found at i:3044110 original size:31 final size:30
Alignment explanation
Indices: 3044052--3044111 Score: 75
Period size: 31 Copynumber: 2.0 Consensus size: 30
3044042 TTTTTTTTAC
* * *
3044052 ATTTTATTATATTTTATTTTATTTTTAAAT
1 ATTTTATTATATTTTATATGATATTTAAAT
*
3044082 ATTTTTTTAATATTTTATATGATATTTAAA
1 ATTTTATT-ATATTTTATATGATATTTAAA
3044112 ATGATTAAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 7 0.28
31 18 0.72
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (30 bp):
ATTTTATTATATTTTATATGATATTTAAAT
Found at i:3046103 original size:18 final size:18
Alignment explanation
Indices: 3046080--3046118 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
3046070 ACAAAGTGAC
*
3046080 TTCCTCGGTTAATATTCT
1 TTCCTCAGTTAATATTCT
3046098 TTCCTCAGTTAATATTCT
1 TTCCTCAGTTAATATTCT
3046116 TTC
1 TTC
3046119 TTTTCATATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.23, G:0.08, T:0.51
Consensus pattern (18 bp):
TTCCTCAGTTAATATTCT
Found at i:3056357 original size:17 final size:18
Alignment explanation
Indices: 3056335--3056390 Score: 64
Period size: 17 Copynumber: 3.2 Consensus size: 18
3056325 TTAAAGATGC
3056335 AATTATATT-TTTATTTT
1 AATTATATTATTTATTTT
3056352 AATTATATTATTTA-TTT
1 AATTATATTATTTATTTT
* *
3056369 ATTTAT-TTATTAATATTT
1 AATTATATTATTTAT-TTT
3056387 AATT
1 AATT
3056391 CGAAATATTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
16 6 0.18
17 17 0.52
18 10 0.30
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTATATTATTTATTTT
Found at i:3058588 original size:11 final size:11
Alignment explanation
Indices: 3058572--3058651 Score: 55
Period size: 11 Copynumber: 7.4 Consensus size: 11
3058562 TTAATAATTT
3058572 TAAATATAAAA
1 TAAATATAAAA
*
3058583 TAAATATAATA
1 TAAATATAAAA
3058594 T-AATA-AATAA
1 TAAATATAA-AA
3058604 TTAAA-ATAAAA
1 -TAAATATAAAA
*
3058615 -ATTATATAAAA
1 TA-AATATAAAA
3058626 -ATAAT-TAAAA
1 TA-AATATAAAA
3058636 TATAATATAAAA
1 TA-AATATAAAA
3058648 TAAA
1 TAAA
3058652 AATTAATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
9 3 0.05
10 11 0.19
11 32 0.56
12 11 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (11 bp):
TAAATATAAAA
Found at i:3058613 original size:27 final size:26
Alignment explanation
Indices: 3058578--3058654 Score: 109
Period size: 27 Copynumber: 2.9 Consensus size: 26
3058568 ATTTTAAATA
3058578 TAAAATAAATATAATATAATAAATAAT
1 TAAAATAAATATAATATAA-AAATAAT
* *
3058605 TAAAATAAAAATTATATAAAAATAAT
1 TAAAATAAATATAATATAAAAATAAT
*
3058631 TAAAATATAATATAAAATAAAAAT
1 TAAAATA-AATATAATATAAAAAT
3058655 TAATATTAAA
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 14 0.32
27 30 0.68
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (26 bp):
TAAAATAAATATAATATAAAAATAAT
Found at i:3058628 original size:17 final size:17
Alignment explanation
Indices: 3058606--3058667 Score: 61
Period size: 19 Copynumber: 3.4 Consensus size: 17
3058596 ATAAATAATT
3058606 AAAATAAAAATTATATA
1 AAAATAAAAATTATATA
*
3058623 AAAATAATTAAAATATAATA
1 AAAATAA--AAATTAT-ATA
*
3058643 TAAAATAAAAATTAATATT
1 -AAAATAAAAATT-ATATA
3058662 AAAATA
1 AAAATA
3058668 TTAAAATTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
17 7 0.19
18 6 0.16
19 12 0.32
20 5 0.14
21 7 0.19
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATAAAAATTATATA
Found at i:3058634 original size:26 final size:27
Alignment explanation
Indices: 3058578--3058667 Score: 98
Period size: 27 Copynumber: 3.5 Consensus size: 27
3058568 ATTTTAAATA
*
3058578 TAAAATAAATATAATATAATAAATAAT
1 TAAAATAAAAATAATATAATAAATAAT
*
3058605 TAAAATAAAAATTATATAA-AAATAAT
1 TAAAATAAAAATAATATAATAAATAAT
* *
3058631 TAAAAT-ATAAT-ATAAAATAAA-AAT
1 TAAAATAAAAATAATATAATAAATAAT
* *
3058655 TAATATTAAAATA
1 TAAAATAAAAATA
3058668 TTAAAATTTA
Statistics
Matches: 54, Mismatches: 6, Indels: 7
0.81 0.09 0.10
Matches are distributed among these distances:
24 13 0.24
25 11 0.20
26 13 0.24
27 17 0.31
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (27 bp):
TAAAATAAAAATAATATAATAAATAAT
Found at i:3058635 original size:20 final size:19
Alignment explanation
Indices: 3058612--3058675 Score: 62
Period size: 20 Copynumber: 3.3 Consensus size: 19
3058602 AATTAAAATA
3058612 AAAATTATATAAAAATAATT
1 AAAATTATATAAAAAT-ATT
3058632 AAAA-TATAATATAAAATA--
1 AAAATTAT-ATA-AAAATATT
*
3058650 AAAATTAATATTAAAATATT
1 AAAATT-ATATAAAAATATT
3058670 AAAATT
1 AAAATT
3058676 TAAATAATAT
Statistics
Matches: 37, Mismatches: 1, Indels: 12
0.74 0.02 0.24
Matches are distributed among these distances:
18 10 0.27
19 6 0.16
20 16 0.43
21 5 0.14
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAATTATATAAAAATATT
Found at i:3058644 original size:22 final size:22
Alignment explanation
Indices: 3058584--3058647 Score: 74
Period size: 26 Copynumber: 2.7 Consensus size: 22
3058574 AATATAAAAT
3058584 AAATATAATATAATAAATAATTA
1 AAATATAATATAA-AAATAATTA
*
3058607 AAATAAAAATTATATAAAAATAATTA
1 AAAT----ATAATATAAAAATAATTA
3058633 AAATATAATATAAAA
1 AAATATAATATAAAA
3058648 TAAAAATTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 9
0.76 0.04 0.20
Matches are distributed among these distances:
22 10 0.29
23 4 0.11
26 13 0.37
27 8 0.23
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (22 bp):
AAATATAATATAAAAATAATTA
Found at i:3058647 original size:38 final size:39
Alignment explanation
Indices: 3058573--3058711 Score: 133
Period size: 38 Copynumber: 3.5 Consensus size: 39
3058563 TAATAATTTT
* * * *
3058573 AAATATAAAATAAATATAATATAATAAATAAT-TAAAATAA
1 AAAT-TAATATAAAAATAAT-TAAAATATAATATAAAATAA
3058613 AAATT-ATATAAAAATAATTAAAATATAATATAAAATAA
1 AAATTAATATAAAAATAATTAAAATATAATATAAAATAA
* * *
3058651 AAATTAATATTAAAAT-ATTAAAATTTAA-ATAATATAA
1 AAATTAATATAAAAATAATTAAAATATAATATAAAATAA
*
3058688 ATTATTAATATAATAAATATATTA
1 A-AATTAATATAA-AAATA-ATTA
3058712 TTTTTAAATA
Statistics
Matches: 84, Mismatches: 9, Indels: 11
0.81 0.09 0.11
Matches are distributed among these distances:
37 18 0.21
38 44 0.52
39 14 0.17
40 4 0.05
41 4 0.05
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (39 bp):
AAATTAATATAAAAATAATTAAAATATAATATAAAATAA
Found at i:3059073 original size:27 final size:26
Alignment explanation
Indices: 3059029--3059105 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 26
3059019 ATTTAATATA
**
3059029 AATATATTTAAATTTTTTAAAATTATT
1 AATATATTTAAAAATTTTAAAATTA-T
* **
3059056 AATATATTTAAAAATTTTTATCTTAT
1 AATATATTTAAAAATTTTAAAATTAT
* *
3059082 ATTATATTTAAAAATATGTAAAAT
1 AATATATTTAAAAAT-TTTAAAAT
3059106 AAAAATAATA
Statistics
Matches: 39, Mismatches: 10, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
26 15 0.38
27 24 0.62
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.51
Consensus pattern (26 bp):
AATATATTTAAAAATTTTAAAATTAT
Found at i:3063979 original size:15 final size:15
Alignment explanation
Indices: 3063961--3063994 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
3063951 CAGCAATGGT
*
3063961 GAAAGTAGCAGAAGC
1 GAAAGCAGCAGAAGC
*
3063976 GAAAGCAGCAGCAGC
1 GAAAGCAGCAGAAGC
3063991 GAAA
1 GAAA
3063995 ACAGTCCGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.18, G:0.32, T:0.03
Consensus pattern (15 bp):
GAAAGCAGCAGAAGC
Found at i:3064125 original size:44 final size:44
Alignment explanation
Indices: 3064070--3064155 Score: 145
Period size: 44 Copynumber: 2.0 Consensus size: 44
3064060 CATCAAAACG
*
3064070 TTATTTCCAGATCTACTCAGAATATTAAAGATTTTCAAATCTCA
1 TTATTTCCAGATCTACTCAAAATATTAAAGATTTTCAAATCTCA
* *
3064114 TTATTTTCAGATCTACTCAAAATATTAAAGATTTTCGAATCT
1 TTATTTCCAGATCTACTCAAAATATTAAAGATTTTCAAATCT
3064156 TGTTAGGTAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 39 1.00
ACGTcount: A:0.36, C:0.16, G:0.07, T:0.41
Consensus pattern (44 bp):
TTATTTCCAGATCTACTCAAAATATTAAAGATTTTCAAATCTCA
Found at i:3072234 original size:138 final size:138
Alignment explanation
Indices: 3071987--3072676 Score: 1154
Period size: 138 Copynumber: 5.0 Consensus size: 138
3071977 TCCTAATTGA
* * * *
3071987 AGTCAAAGCGATTAGCGGTCATTGAAAGAAGCCAAACCAAACACCAGATA-GAATTTTCCCCCAT
1 AGTCAAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATG-ATTTTCTCCCAT
* * *
3072051 TAATCCCGACTAGAATTTAAAGTGACCAATAAATTTCCCAGAATAATGAAACAATAAATAAACAT
65 TAATCCCAACTAGAATTTAAAGTGACCAGTAAATTTCCCATAATAATGAAACAATAAATAAACAT
3072116 CTTAATTAT
130 CTTAATTAT
* *
3072125 AGTCTAAGGGATTAGCAGTCACTGAAAGAAACCAAACCAAACACCAGATATGATTTTCTCCCATT
1 AGTCAAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATGATTTTCTCCCATT
*
3072190 AATCCCAACTAGAATTTAAAGTGACCAGTAAATTTCCAATAATAATGAAACAATAAATAAACATC
66 AATCCCAACTAGAATTTAAAGTGACCAGTAAATTTCCCATAATAATGAAACAATAAATAAACATC
3072255 TTAATTGA-
131 TTAATT-AT
* *
3072263 AGTCAAAGCGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATA-GAATTTTCCCCCAT
1 AGTCAAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATG-ATTTTCTCCCAT
*
3072327 TAATCCCGACTAGAATTTAAAGTGACCAGTAAATTTCCCATAATAATGAAACAATAAATAAACAT
65 TAATCCCAACTAGAATTTAAAGTGACCAGTAAATTTCCCATAATAATGAAACAATAAATAAACAT
3072392 CTTAATTAT
130 CTTAATTAT
*
3072401 AGTCTAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATGATTTTCTCCCATT
1 AGTCAAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATGATTTTCTCCCATT
*
3072466 AATCCCAACTAGAATTTAAAGTGACCAGAAAATTTCCCATAATAATGAAACAATAAATAAACATC
66 AATCCCAACTAGAATTTAAAGTGACCAGTAAATTTCCCATAATAATGAAACAATAAATAAACATC
3072531 TTAATTAT
131 TTAATTAT
*
3072539 AGTCAAAGGGATTAGCAGTCATTGAAAGAAACAAAACCAAACACCAGATATGATTTTCTCCCATT
1 AGTCAAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATGATTTTCTCCCATT
3072604 AATCCCAACTAGAATTTAAAGTGACCCA-TAAATTTCCCATAATAATGAAACAATAAATAAACAT
66 AATCCCAACTAGAATTTAAAGTGA-CCAGTAAATTTCCCATAATAATGAAACAATAAATAAACAT
*
3072668 GCATAATTA
130 -CTTAATTA
3072677 ACATAACAAA
Statistics
Matches: 520, Mismatches: 25, Indels: 13
0.93 0.04 0.02
Matches are distributed among these distances:
137 2 0.00
138 505 0.97
139 13 0.03
ACGTcount: A:0.44, C:0.19, G:0.11, T:0.25
Consensus pattern (138 bp):
AGTCAAAGGGATTAGCAGTCATTGAAAGAAACCAAACCAAACACCAGATATGATTTTCTCCCATT
AATCCCAACTAGAATTTAAAGTGACCAGTAAATTTCCCATAATAATGAAACAATAAATAAACATC
TTAATTAT
Found at i:3076838 original size:18 final size:20
Alignment explanation
Indices: 3076798--3076838 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
3076788 TTATATTACT
*
3076798 AAATAATAATTACTTAATGTA
1 AAATAATAATTA-TTAATATA
3076819 AAATAATAATT-TTAA-ATA
1 AAATAATAATTATTAATATA
3076837 AA
1 AA
3076839 TTTAAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
18 4 0.21
19 4 0.21
21 11 0.58
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.37
Consensus pattern (20 bp):
AAATAATAATTATTAATATA
Found at i:3076993 original size:20 final size:19
Alignment explanation
Indices: 3076965--3077028 Score: 51
Period size: 20 Copynumber: 3.3 Consensus size: 19
3076955 ATTACAAAAT
*
3076965 TAATTTTAATTTTATTATTA
1 TAATATTAATTTTA-TATTA
* *
3076985 TAATATTAA-ATCATA-TA
1 TAATATTAATTTTATATTA
*
3077002 TAATAATTAATTTTACTATAA
1 TAAT-ATTAATTTTA-TATTA
3077023 TAATAT
1 TAATAT
3077029 ATTTTAATAT
Statistics
Matches: 34, Mismatches: 6, Indels: 8
0.71 0.12 0.17
Matches are distributed among these distances:
17 6 0.18
18 7 0.21
19 4 0.12
20 12 0.35
21 5 0.15
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (19 bp):
TAATATTAATTTTATATTA
Found at i:3077021 original size:18 final size:18
Alignment explanation
Indices: 3076999--3077040 Score: 59
Period size: 18 Copynumber: 2.3 Consensus size: 18
3076989 ATTAAATCAT
3076999 ATATAATAAT-TAATTTTA
1 ATATAATAATAT-ATTTTA
*
3077017 CTATAATAATATATTTTA
1 ATATAATAATATATTTTA
3077035 ATATAA
1 ATATAA
3077041 CTAAATACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 20 0.95
19 1 0.05
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (18 bp):
ATATAATAATATATTTTA
Found at i:3077884 original size:2 final size:2
Alignment explanation
Indices: 3077877--3077903 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
3077867 ATTGAAAGAA
3077877 AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG A
3077904 ATAAAGGTAC
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:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:3078304 original size:24 final size:23
Alignment explanation
Indices: 3078273--3078345 Score: 71
Period size: 22 Copynumber: 3.1 Consensus size: 23
3078263 ATATTAATTA
3078273 ATTAAATATAAATATAATATTTAT
1 ATTAAATAT-AATATAATATTTAT
3078297 ATTAAATAT-ATCATAATA-TTAT
1 ATTAAATATAAT-ATAATATTTAT
* *
3078319 ATTAATTAT-ATTTAAATATATTAT
1 ATTAAATATAATAT-AATAT-TTAT
3078343 ATT
1 ATT
3078346 TATTTTATTA
Statistics
Matches: 43, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
21 1 0.02
22 20 0.47
23 6 0.14
24 16 0.37
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.49
Consensus pattern (23 bp):
ATTAAATATAATATAATATTTAT
Found at i:3078346 original size:15 final size:15
Alignment explanation
Indices: 3078288--3078347 Score: 54
Period size: 15 Copynumber: 4.0 Consensus size: 15
3078278 ATATAAATAT
3078288 AATAT-TTATA-TTA
1 AATATATTATATTTA
*
3078301 AATATATCATAATATTA
1 AATATATTAT-AT-TTA
*
3078318 TAT-TAATTATATTTA
1 AATAT-ATTATATTTA
3078333 AATATATTATATTTA
1 AATATATTATATTTA
3078348 TTTTATTAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
13 5 0.14
14 3 0.08
15 16 0.43
16 4 0.11
17 9 0.24
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.52
Consensus pattern (15 bp):
AATATATTATATTTA
Found at i:3099376 original size:25 final size:24
Alignment explanation
Indices: 3099338--3099384 Score: 58
Period size: 25 Copynumber: 1.9 Consensus size: 24
3099328 AACACAGGTC
* *
3099338 TACTTATGAATATTATTATAAATTT
1 TACTAATGAATATT-TTAAAAATTT
*
3099363 TACTAATGAGTATTTTAAAAAT
1 TACTAATGAATATTTTAAAAAT
3099385 ATTGTTTAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 7 0.37
25 12 0.63
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.47
Consensus pattern (24 bp):
TACTAATGAATATTTTAAAAATTT
Found at i:3099889 original size:2 final size:2
Alignment explanation
Indices: 3099882--3099936 Score: 67
Period size: 2 Copynumber: 26.5 Consensus size: 2
3099872 TGTTTGTAAC
*
3099882 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AGT TT AGT AT CAT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT A-T AT -AT
3099927 AT -T AT AT AT A
1 AT AT AT AT AT A
3099937 GATTAACTTC
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
1 1 0.02
2 41 0.87
3 5 0.11
ACGTcount: A:0.45, C:0.02, G:0.04, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3102705 original size:38 final size:38
Alignment explanation
Indices: 3102628--3102698 Score: 94
Period size: 38 Copynumber: 1.9 Consensus size: 38
3102618 GGTAGTACAT
*
3102628 ATAAAAAAATATAATTAATGTATATTTTTTAAAATTAA
1 ATAAAAAAATATAATTAATATATATTTTTTAAAATTAA
*
3102666 ATAAAAATAATAT-ATTAA-ATA-ATTTTTTTAAAT
1 ATAAAAA-AATATAATTAATATATATTTTTTAAAAT
3102699 GGTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 11 0.37
37 2 0.07
38 12 0.40
39 5 0.17
ACGTcount: A:0.55, C:0.00, G:0.01, T:0.44
Consensus pattern (38 bp):
ATAAAAAAATATAATTAATATATATTTTTTAAAATTAA
Found at i:3103421 original size:2 final size:2
Alignment explanation
Indices: 3103416--3103443 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3103406 CGTACATGTG
3103416 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
3103444 ACAAATGATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:3104051 original size:2 final size:2
Alignment explanation
Indices: 3104044--3104068 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3104034 TCCCATTATT
3104044 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
3104069 TCTTTTAGTT
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:3104485 original size:2 final size:2
Alignment explanation
Indices: 3104478--3104519 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
3104468 TAAATGAAAG
3104478 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3104520 CAAATTTAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3108915 original size:2 final size:2
Alignment explanation
Indices: 3108902--3108941 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
3108892 TTTAACAGTT
* *
3108902 TA TA TA TT TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3108942 AATTTCAAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (2 bp):
TA
Found at i:3111368 original size:2 final size:2
Alignment explanation
Indices: 3111361--3111397 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
3111351 TTGCCTCTTT
*
3111361 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3111398 GCATATTAGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3111403 original size:8 final size:8
Alignment explanation
Indices: 3111361--3111403 Score: 50
Period size: 8 Copynumber: 5.4 Consensus size: 8
3111351 TTGCCTCTTT
*
3111361 TATATATA
1 TATATACA
3111369 TATATACA
1 TATATACA
*
3111377 TATATATA
1 TATATACA
*
3111385 TATATATA
1 TATATACA
*
3111393 TATATGCA
1 TATATACA
3111401 TAT
1 TAT
3111404 TAGTTAGAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 31 1.00
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (8 bp):
TATATACA
Found at i:3113595 original size:23 final size:21
Alignment explanation
Indices: 3113555--3113597 Score: 59
Period size: 23 Copynumber: 2.0 Consensus size: 21
3113545 TAATTTTATG
*
3113555 TTCATAAATATTTTTTTAATA
1 TTCATAAATATTTATTTAATA
3113576 TTCATAAATAAATTTATTTAAT
1 TTCATAAAT--ATTTATTTAAT
3113598 TTAAATGAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 9 0.47
23 10 0.53
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (21 bp):
TTCATAAATATTTATTTAATA
Found at i:3113801 original size:2 final size:2
Alignment explanation
Indices: 3113794--3113838 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
3113784 ATTAGCCCTA
*
3113794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT TT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3113836 AT A
1 AT A
3113839 CATCAAAGAG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:3117288 original size:37 final size:36
Alignment explanation
Indices: 3117247--3117351 Score: 110
Period size: 37 Copynumber: 2.9 Consensus size: 36
3117237 AGAAGGAAAA
3117247 AAAATTTGTATTTATATTTATATTATTTTTTATATAT-
1 AAAATTTGTATTTAT-TTTATA-TATTTTTTATATATG
* *
3117284 AAAATAT-TATAT-TTTTATATATTTTTTATATATG
1 AAAATTTGTATTTATTTTATATATTTTTTATATATG
* *
3117318 AATAATTCGT-TTTATTTTATGTATATTTTTATAT
1 AA-AATTTGTATTTATTTTATATAT-TTTTTATAT
3117352 GTATGTATAT
Statistics
Matches: 57, Mismatches: 6, Indels: 10
0.78 0.08 0.14
Matches are distributed among these distances:
33 14 0.25
34 8 0.14
35 6 0.11
36 14 0.25
37 15 0.26
ACGTcount: A:0.34, C:0.01, G:0.04, T:0.61
Consensus pattern (36 bp):
AAAATTTGTATTTATTTTATATATTTTTTATATATG
Found at i:3117331 original size:31 final size:34
Alignment explanation
Indices: 3117263--3117337 Score: 84
Period size: 33 Copynumber: 2.3 Consensus size: 34
3117253 TGTATTTATA
* *
3117263 TTTATATTATTTTTTATATATAAAATATTATATT
1 TTTATATTATTTTTTATATATAAAATAATATAGT
* *
3117297 TTTATA-TATTTTTTATATAT-GAATAAT-TCGT
1 TTTATATTATTTTTTATATATAAAATAATATAGT
*
3117328 TTTATTTTAT
1 TTTATATTAT
3117338 GTATATTTTT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 7 0.20
32 8 0.23
33 14 0.40
34 6 0.17
ACGTcount: A:0.33, C:0.01, G:0.03, T:0.63
Consensus pattern (34 bp):
TTTATATTATTTTTTATATATAAAATAATATAGT
Found at i:3118419 original size:22 final size:22
Alignment explanation
Indices: 3118379--3118420 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
3118369 TGTGTATTCG
*
3118379 TATTATGTTTATATCATTTTCA
1 TATTATGTTTAAATCATTTTCA
3118401 TATTATGTTTTAAAT-ATTTT
1 TATTATG-TTTAAATCATTTT
3118421 TTATAAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.29, C:0.05, G:0.05, T:0.62
Consensus pattern (22 bp):
TATTATGTTTAAATCATTTTCA
Found at i:3119107 original size:8 final size:8
Alignment explanation
Indices: 3119096--3119151 Score: 51
Period size: 8 Copynumber: 7.0 Consensus size: 8
3119086 TTTTATATAA
3119096 ATATTTAT
1 ATATTTAT
3119104 ATATTTAT
1 ATATTTAT
*
3119112 A-ATTCATT
1 ATATTTA-T
* * *
3119120 TTATATAA
1 ATATTTAT
3119128 ATATTTAT
1 ATATTTAT
*
3119136 ATATCTAT
1 ATATTTAT
3119144 ATATTTAT
1 ATATTTAT
3119152 GTCATGTTTA
Statistics
Matches: 36, Mismatches: 10, Indels: 4
0.72 0.20 0.08
Matches are distributed among these distances:
7 4 0.11
8 29 0.81
9 3 0.08
ACGTcount: A:0.39, C:0.04, G:0.00, T:0.57
Consensus pattern (8 bp):
ATATTTAT
Found at i:3119290 original size:26 final size:26
Alignment explanation
Indices: 3119250--3119323 Score: 78
Period size: 27 Copynumber: 2.7 Consensus size: 26
3119240 TATATAAATT
**
3119250 TTTTATATAATTAAATTTTAATTTTAAA
1 TTTTAT-TAATTAAATTTTAA-AATAAA
*
3119278 -TTTATTTATTAAATATTTAAAATAAA
1 TTTTATTAATTAAAT-TTTAAAATAAA
3119304 TTTTATTAATTATAATTTTA
1 TTTTATTAATTA-AATTTTA
3119324 TTTAATTAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
26 12 0.31
27 24 0.62
28 3 0.08
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (26 bp):
TTTTATTAATTAAATTTTAAAATAAA
Found at i:3119318 original size:16 final size:16
Alignment explanation
Indices: 3119299--3119341 Score: 61
Period size: 16 Copynumber: 2.7 Consensus size: 16
3119289 AATATTTAAA
3119299 ATAAATTTTATTAATT
1 ATAAATTTTATTAATT
3119315 AT-AATTTTATTTAATT
1 ATAAATTTTA-TTAATT
*
3119331 AAAAATTTTAT
1 ATAAATTTTAT
3119342 AAATATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 7 0.29
16 10 0.42
17 7 0.29
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (16 bp):
ATAAATTTTATTAATT
Found at i:3119802 original size:28 final size:28
Alignment explanation
Indices: 3119740--3119809 Score: 74
Period size: 28 Copynumber: 2.5 Consensus size: 28
3119730 ACACAGCCAC
* *
3119740 AAAAAATAAATAATTTTTTATTTATTTG
1 AAAAAATATATAATTTTTAATTTATTTG
*
3119768 AATAAATATATATATTTTTAAATTTA-TT-
1 AAAAAATATATA-ATTTTT-AATTTATTTG
3119796 AAAAAAT-TATAATT
1 AAAAAATATATAATT
3119810 AACATAAATA
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
26 3 0.08
27 4 0.11
28 16 0.44
29 8 0.22
30 5 0.14
ACGTcount: A:0.50, C:0.00, G:0.01, T:0.49
Consensus pattern (28 bp):
AAAAAATATATAATTTTTAATTTATTTG
Found at i:3119912 original size:24 final size:25
Alignment explanation
Indices: 3119872--3119930 Score: 61
Period size: 25 Copynumber: 2.4 Consensus size: 25
3119862 AAATAATTAT
3119872 ATTTTATATT-TAAAA-T-TTTAATAA
1 ATTTTAT-TTATAAAATTATTTAA-AA
* *
3119896 ATTTTATTTATATAATTATTTAAAT
1 ATTTTATTTATAAAATTATTTAAAA
3119921 ATTTTATTTA
1 ATTTTATTTA
3119931 ATTAACTATT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
23 2 0.07
24 11 0.37
25 12 0.40
26 5 0.17
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTTTATTTATAAAATTATTTAAAA
Found at i:3121834 original size:34 final size:35
Alignment explanation
Indices: 3121778--3121843 Score: 84
Period size: 34 Copynumber: 1.9 Consensus size: 35
3121768 TTAATAAGTT
3121778 ATTTAAAATTTATTAAATAAAT-AATTATAATTAAA
1 ATTTAAAATTTATTAAATAAATAAATTA-AATTAAA
*
3121813 ATTTAAAA-TTATT-TATCAAATAAATTAAATT
1 ATTTAAAATTTATTAAAT-AAATAAATTAAATT
3121844 TTAAAAATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
33 2 0.07
34 13 0.46
35 13 0.46
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.44
Consensus pattern (35 bp):
ATTTAAAATTTATTAAATAAATAAATTAAATTAAA
Found at i:3121860 original size:42 final size:40
Alignment explanation
Indices: 3121716--3121867 Score: 104
Period size: 38 Copynumber: 3.9 Consensus size: 40
3121706 GTTTATGACT
* **
3121716 TAAATTAAATTTTAAAAATTATATTTAATTTATTTATATT
1 TAAATTAAATTTTAAAAATTATATTTAAATTATTTATAAA
* * * * *
3121756 TGTAACTAATTTTTAATAAGT-TATTTAAA--ATTTATTAAA
1 T-AAATTAAATTTTAAAAATTATATTTAAATTATTTA-TAAA
* *
3121795 TAAA-T-AATTATAATTAAA--AT-TTAAAATTATTTATCAAA
1 TAAATTAAATTTTAA--AAATTATATTTAAATTATTTAT-AAA
*
3121833 TAAATTAAATTTTAAAAATTATATTTAATTTATTT
1 TAAATTAAATTTTAAAAATTATATTTAAATTATTT
3121868 TACGAATAAA
Statistics
Matches: 83, Mismatches: 16, Indels: 25
0.67 0.13 0.20
Matches are distributed among these distances:
36 11 0.13
37 3 0.04
38 24 0.29
39 4 0.05
40 17 0.20
41 24 0.29
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (40 bp):
TAAATTAAATTTTAAAAATTATATTTAAATTATTTATAAA
Found at i:3121898 original size:21 final size:22
Alignment explanation
Indices: 3121874--3121927 Score: 56
Period size: 21 Copynumber: 2.5 Consensus size: 22
3121864 ATTTTACGAA
3121874 TAAATTTATTT-ATAAATCATT
1 TAAATTTATTTAATAAATCATT
** * *
3121895 TAAAACTATTTAATACATCTTT
1 TAAATTTATTTAATAAATCATT
3121917 TAAAATTTATT
1 T-AAATTTATT
3121928 ATTTACTTAA
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
21 9 0.36
22 9 0.36
23 7 0.28
ACGTcount: A:0.43, C:0.07, G:0.00, T:0.50
Consensus pattern (22 bp):
TAAATTTATTTAATAAATCATT
Found at i:3121906 original size:117 final size:118
Alignment explanation
Indices: 3121671--3121899 Score: 308
Period size: 117 Copynumber: 2.0 Consensus size: 118
3121661 GCTTATGTAG
* * * **
3121671 TTAAATAAATAATTATAATTAAAATTTTAAATTTCGTTTATGACTTAAATTAAATTTTAAAAATT
1 TTAAATAAATAATTATAATTAAAATTTTAAAATTCATTTATCAAATAAATTAAATTTTAAAAATT
* * *
3121736 ATATTTAATTTATTTATATTTGTAACTAATTTTTAATAAGTTATTTAAAATTTA
66 ATATTTAATTTATTTATA-TCGTAACTAATTTTTAATAAATCATTTAAAATTTA
3121790 TTAAATAAATAATTATAATTAAAA-TTTAAAATT-ATTTATCAAATAAATTAAATTTTAAAAATT
1 TTAAATAAATAATTATAATTAAAATTTTAAAATTCATTTATCAAATAAATTAAATTTTAAAAATT
*
3121853 ATATTTAATTTATTT-TA-CG-AA-TAAATTTATTTATAAATCATTTAAAA
66 ATATTTAATTTATTTATATCGTAACT-AATTT-TTAATAAATCATTTAAAA
3121900 CTATTTAATA
Statistics
Matches: 99, Mismatches: 9, Indels: 9
0.85 0.08 0.08
Matches are distributed among these distances:
112 1 0.01
113 7 0.07
114 16 0.16
116 2 0.02
117 41 0.41
118 8 0.08
119 24 0.24
ACGTcount: A:0.47, C:0.03, G:0.02, T:0.48
Consensus pattern (118 bp):
TTAAATAAATAATTATAATTAAAATTTTAAAATTCATTTATCAAATAAATTAAATTTTAAAAATT
ATATTTAATTTATTTATATCGTAACTAATTTTTAATAAATCATTTAAAATTTA
Found at i:3121920 original size:22 final size:21
Alignment explanation
Indices: 3121880--3121921 Score: 57
Period size: 22 Copynumber: 2.0 Consensus size: 21
3121870 CGAATAAATT
3121880 TATTTATAAATCATTTAAAAC
1 TATTTATAAATCATTTAAAAC
* *
3121901 TATTTAATACATCTTTTAAAA
1 TATTT-ATAAATCATTTAAAA
3121922 TTTATTATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.45, C:0.10, G:0.00, T:0.45
Consensus pattern (21 bp):
TATTTATAAATCATTTAAAAC
Found at i:3121964 original size:15 final size:15
Alignment explanation
Indices: 3121943--3121984 Score: 50
Period size: 15 Copynumber: 2.8 Consensus size: 15
3121933 CTTAATTATA
3121943 ATAATATTATTATTT
1 ATAATATTATTATTT
*
3121958 GTAATA-TATTTATTT
1 ATAATATTA-TTATTT
*
3121973 ATAATATGATTA
1 ATAATATTATTA
3121985 ATAATACTTG
Statistics
Matches: 22, Mismatches: 3, Indels: 4
0.76 0.10 0.14
Matches are distributed among these distances:
14 2 0.09
15 19 0.86
16 1 0.05
ACGTcount: A:0.40, C:0.00, G:0.05, T:0.55
Consensus pattern (15 bp):
ATAATATTATTATTT
Found at i:3122072 original size:41 final size:39
Alignment explanation
Indices: 3121997--3122089 Score: 100
Period size: 41 Copynumber: 2.3 Consensus size: 39
3121987 AATACTTGTG
*
3121997 TTTTACTATTTCATAATTAATAATAACTTAATTTTAATAATATT
1 TTTTA-TATTT-ATAATTAAAAATAACTTAATTTT-AT--TATT
*
3122041 TTTT-TATTTATAATTAAAAAT-ATTTACATTTTATTATT
1 TTTTATATTTATAATTAAAAATAACTTA-ATTTTATTATT
3122079 TTTTATATTTA
1 TTTTATATTTA
3122090 ATATTAATTC
Statistics
Matches: 45, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
38 8 0.18
39 6 0.13
40 6 0.13
41 16 0.36
42 5 0.11
44 4 0.09
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (39 bp):
TTTTATATTTATAATTAAAAATAACTTAATTTTATTATT
Found at i:3122131 original size:16 final size:19
Alignment explanation
Indices: 3122091--3122135 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
3122081 TTATATTTAA
3122091 TATTAATTCAACTTAAATT
1 TATTAATTCAACTTAAATT
3122110 TAATTAATT-AA-TT-AATT
1 T-ATTAATTCAACTTAAATT
3122127 TATT-ATTCA
1 TATTAATTCA
3122136 TAAATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
15 3 0.12
16 4 0.17
17 5 0.21
18 2 0.08
19 3 0.12
20 7 0.29
ACGTcount: A:0.42, C:0.07, G:0.00, T:0.51
Consensus pattern (19 bp):
TATTAATTCAACTTAAATT
Found at i:3122246 original size:16 final size:16
Alignment explanation
Indices: 3122227--3122257 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3122217 ATTAATTTTA
3122227 AATTAAATTCAAACAC
1 AATTAAATTCAAACAC
*
3122243 AATTAAATTTAAACA
1 AATTAAATTCAAACA
3122258 ATCTGCACAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.58, C:0.13, G:0.00, T:0.29
Consensus pattern (16 bp):
AATTAAATTCAAACAC
Found at i:3123362 original size:32 final size:32
Alignment explanation
Indices: 3123326--3123454 Score: 149
Period size: 32 Copynumber: 4.1 Consensus size: 32
3123316 AATGAGTGTC
*
3123326 AAATTTATAAATAATTATATTTAATATTTATT
1 AAATTTATAAGTAATTATATTTAATATTTATT
* *
3123358 AAATTGATAAGTAATTTTATTTAATATTTATT
1 AAATTTATAAGTAATTATATTTAATATTTATT
* * *
3123390 AAATTTATGAGCAATTATATTT-A-ATTTATC
1 AAATTTATAAGTAATTATATTTAATATTTATT
*
3123420 AAATTTATAATTAA-TATTAGTTTAAT-TTTATT
1 AAATTTATAAGTAATTA-TA-TTTAATATTTATT
3123452 AAA
1 AAA
3123455 AATTTATATT
Statistics
Matches: 81, Mismatches: 12, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
29 2 0.02
30 19 0.23
31 4 0.05
32 56 0.69
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (32 bp):
AAATTTATAAGTAATTATATTTAATATTTATT
Found at i:3123705 original size:31 final size:31
Alignment explanation
Indices: 3123670--3123732 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
3123660 TTTCTAATTG
3123670 TTTATATATAGTATTAATTTCGTGGTCAAAT
1 TTTATATATAGTATTAATTTCGTGGTCAAAT
3123701 TTTATATATAGTATTAATTTCGTGGTCAAAT
1 TTTATATATAGTATTAATTTCGTGGTCAAAT
3123732 T
1 T
3123733 AAGCAACTTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.13, T:0.49
Consensus pattern (31 bp):
TTTATATATAGTATTAATTTCGTGGTCAAAT
Found at i:3130848 original size:29 final size:27
Alignment explanation
Indices: 3130786--3130848 Score: 65
Period size: 29 Copynumber: 2.2 Consensus size: 27
3130776 GAGTTAAGTC
3130786 ATAATTTTAAAAAAATTATTAATTTTAAA
1 ATAA-TTTAAAAAAATTATTAA-TTTAAA
*
3130815 TTAATTTAAAAGTAAATTTATTAA-TTAAA
1 ATAATTTAAAA--AAA-TTATTAATTTAAA
3130844 ATAAT
1 ATAAT
3130849 ATTATTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
28 7 0.24
29 12 0.41
30 3 0.10
31 7 0.24
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (27 bp):
ATAATTTAAAAAAATTATTAATTTAAA
Found at i:3130857 original size:19 final size:20
Alignment explanation
Indices: 3130835--3130887 Score: 56
Period size: 19 Copynumber: 2.7 Consensus size: 20
3130825 AGTAAATTTA
*
3130835 TTAATTAAAATAATA-TTAT
1 TTAATTAAAATAATAGTAAT
*
3130854 TTAATTATAA-AATAGTAAT
1 TTAATTAAAATAATAGTAAT
*
3130873 TTAGATTAAAGTAAT
1 TTA-ATTAAAATAAT
3130888 TAAAATTATG
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
18 4 0.15
19 15 0.56
20 5 0.19
21 3 0.11
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (20 bp):
TTAATTAAAATAATAGTAAT
Found at i:3131405 original size:2 final size:2
Alignment explanation
Indices: 3131398--3131427 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
3131388 TTAAATATTG
*
3131398 AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3131428 GATCTACGTC
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:3137221 original size:26 final size:24
Alignment explanation
Indices: 3137190--3137255 Score: 78
Period size: 26 Copynumber: 2.7 Consensus size: 24
3137180 AAAATCACTT
3137190 TTTTTGTTTGTTAAAAATGACGGTTC
1 TTTTTGTTTGTTAAAAATGACGG--C
* **
3137216 TTTTTGTTTGTAAAAAATGGTGGC
1 TTTTTGTTTGTTAAAAATGACGGC
*
3137240 TTGTTGTTTGTTAAAA
1 TTTTTGTTTGTTAAAA
3137256 TTGGTGGCTA
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 15 0.43
26 20 0.57
ACGTcount: A:0.24, C:0.05, G:0.21, T:0.50
Consensus pattern (24 bp):
TTTTTGTTTGTTAAAAATGACGGC
Found at i:3137246 original size:24 final size:24
Alignment explanation
Indices: 3137219--3137264 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
3137209 ACGGTTCTTT
3137219 TTGTTTGTAAAAAATGGTGGCTTG
1 TTGTTTGTAAAAAATGGTGGCTTG
* *
3137243 TTGTTTGTTAAAATTGGTGGCT
1 TTGTTTGTAAAAAATGGTGGCT
3137265 AATTTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.22, C:0.04, G:0.28, T:0.46
Consensus pattern (24 bp):
TTGTTTGTAAAAAATGGTGGCTTG
Found at i:3141891 original size:41 final size:41
Alignment explanation
Indices: 3141834--3141916 Score: 166
Period size: 41 Copynumber: 2.0 Consensus size: 41
3141824 GTATATTTTT
3141834 TTAATTTATTCTCATAATAGAATTGGTGGTGTTTGAGGACG
1 TTAATTTATTCTCATAATAGAATTGGTGGTGTTTGAGGACG
3141875 TTAATTTATTCTCATAATAGAATTGGTGGTGTTTGAGGACG
1 TTAATTTATTCTCATAATAGAATTGGTGGTGTTTGAGGACG
3141916 T
1 T
3141917 AGGCATAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.07, G:0.24, T:0.42
Consensus pattern (41 bp):
TTAATTTATTCTCATAATAGAATTGGTGGTGTTTGAGGACG
Found at i:3142544 original size:17 final size:17
Alignment explanation
Indices: 3142514--3142547 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3142504 TAAATTTTAC
*
3142514 ATTTTATTTCATTAATT
1 ATTTTATTTAATTAATT
*
3142531 ATTTTTTTTAATTAATT
1 ATTTTATTTAATTAATT
3142548 TTCATAATCT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (17 bp):
ATTTTATTTAATTAATT
Found at i:3145722 original size:9 final size:9
Alignment explanation
Indices: 3145708--3145732 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3145698 AATCTTCCTA
3145708 ATTTTCATC
1 ATTTTCATC
3145717 ATTTTCATC
1 ATTTTCATC
3145726 ATTTTCA
1 ATTTTCA
3145733 ATTTCAATAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.24, C:0.20, G:0.00, T:0.56
Consensus pattern (9 bp):
ATTTTCATC
Found at i:3150613 original size:13 final size:14
Alignment explanation
Indices: 3150583--3150620 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
3150573 AATAATAAAA
3150583 ATTTAAAATTTAAT
1 ATTTAAAATTTAAT
*
3150597 ATTTAATATTT-AT
1 ATTTAAAATTTAAT
*
3150610 ATTTATAATTT
1 ATTTAAAATTT
3150621 TATTAAATTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
13 11 0.52
14 10 0.48
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (14 bp):
ATTTAAAATTTAAT
Found at i:3151294 original size:33 final size:35
Alignment explanation
Indices: 3151243--3151311 Score: 99
Period size: 33 Copynumber: 2.0 Consensus size: 35
3151233 TAATAACTAA
3151243 ATATCAATTTATTATTAAA-TAATTAAATAATCATT
1 ATATCAATTTATTATTAAAGTAA-TAAATAATCATT
*
3151278 ATATCAA-TTATT-TTAAAGTAATAACTAATCATT
1 ATATCAATTTATTATTAAAGTAATAAATAATCATT
3151311 A
1 A
3151312 ACTATAATTA
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 17 0.53
34 8 0.25
35 7 0.22
ACGTcount: A:0.48, C:0.07, G:0.01, T:0.43
Consensus pattern (35 bp):
ATATCAATTTATTATTAAAGTAATAAATAATCATT
Found at i:3155225 original size:2 final size:2
Alignment explanation
Indices: 3155218--3155245 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
3155208 TGACTTTTCA
3155218 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
3155246 CTTAAACAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3157677 original size:18 final size:18
Alignment explanation
Indices: 3157654--3157705 Score: 51
Period size: 18 Copynumber: 3.1 Consensus size: 18
3157644 TGTAAGGTAA
3157654 TTTATATTTATATAAATT
1 TTTATATTTATATAAATT
3157672 TTTATATGTTA-AT-AA--
1 TTTATAT-TTATATAAATT
*
3157687 TTTATA-TCATATAAATT
1 TTTATATTTATATAAATT
3157704 TT
1 TT
3157706 AAAATTTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 11
0.70 0.03 0.28
Matches are distributed among these distances:
13 2 0.07
14 2 0.07
15 8 0.29
17 4 0.14
18 9 0.32
19 3 0.11
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (18 bp):
TTTATATTTATATAAATT
Found at i:3157704 original size:32 final size:33
Alignment explanation
Indices: 3157638--3157705 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 33
3157628 TTGTGTTATA
*
3157638 TTTATATGTAAGGTAATTTATATTTATATAAATT
1 TTTATATGTAA-GTAATTTATATTCATATAAATT
3157672 TTTATATGTTAA-TAATTTATA-TCATATAAATT
1 TTTATATG-TAAGTAATTTATATTCATATAAATT
3157704 TT
1 TT
3157706 AAAATTTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
32 12 0.38
33 9 0.28
34 8 0.25
35 3 0.09
ACGTcount: A:0.38, C:0.01, G:0.06, T:0.54
Consensus pattern (33 bp):
TTTATATGTAAGTAATTTATATTCATATAAATT
Found at i:3157720 original size:28 final size:29
Alignment explanation
Indices: 3157686--3157759 Score: 87
Period size: 28 Copynumber: 2.5 Consensus size: 29
3157676 TATGTTAATA
3157686 ATTTATATCATATAAATTTTAA-AATTTT
1 ATTTATATCATATAAATTTTAATAATTTT
* *
3157714 ATTTATATCATATTTAATTTTAATTATTTT
1 ATTTATATCATA-TAAATTTTAATAATTTT
**
3157744 ATACATATTCATATAA
1 ATTTATA-TCATATAA
3157760 TCATATAAAA
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
28 12 0.32
29 9 0.24
30 12 0.32
31 5 0.13
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.54
Consensus pattern (29 bp):
ATTTATATCATATAAATTTTAATAATTTT
Found at i:3161534 original size:15 final size:14
Alignment explanation
Indices: 3161516--3161567 Score: 52
Period size: 14 Copynumber: 3.7 Consensus size: 14
3161506 TTTATATTTG
*
3161516 ATATATATATTATAT
1 ATATAAATATTAT-T
3161531 ATATAAATATTATT
1 ATATAAATATTATT
* *
3161545 ATAAAAATATAATT
1 ATATAAATATTATT
*
3161559 -TTTAAATAT
1 ATATAAATAT
3161568 ATAAAGATAA
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
13 7 0.22
14 13 0.41
15 12 0.38
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATAAATATTATT
Done.